PARADIGM pathway analysis of mRNASeq expression data
Colon Adenocarcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1G73C9J
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1G73C9J
Overview
Introduction

PAthway Representation and Analysis by Direct Inference on Graphical Models (PARADIGM) predicts the activity of a diverse set of molecular concepts such as genes, complexes, and processes. The predicted activities are called Inferred Pathway Levels (IPLs) and are derived from a probabilistic belief propagation strategy that incorporates multimodal data such as copy number and gene expression estimates with a concept's pathway context.

Summary

There were 39 significant pathways identified in this analysis.

Table 1.  Get Full Table Top 10 out of 131 pathways in order of significance.

Pathway.Name Avg.Num.Perturbations
TCGA08_retinoblastoma 181
Syndecan-1-mediated signaling events 146
Reelin signaling pathway 108
Osteopontin-mediated events 76
Lissencephaly gene (LIS1) in neuronal migration and development 64
IL23-mediated signaling events 60
FOXA2 and FOXA3 transcription factor networks 57
Glypican 1 network 56
IL4-mediated signaling events 50
BCR signaling pathway 48
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 432 . 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 ( 432 ).

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
TCGA08_retinoblastoma 0.4190 181 1452 8 -0.16 0.12 1000 -1000 -0.018 -1000
Syndecan-1-mediated signaling events 0.3380 146 4987 34 -0.71 0.012 1000 -1000 -0.064 -1000
Reelin signaling pathway 0.2500 108 6090 56 -0.54 0.035 1000 -1000 -0.086 -1000
Osteopontin-mediated events 0.1759 76 2899 38 -0.35 0.02 1000 -1000 -0.1 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1481 64 3486 54 -0.53 0.024 1000 -1000 -0.1 -1000
IL23-mediated signaling events 0.1389 60 3639 60 -0.5 0.012 1000 -1000 -0.18 -1000
FOXA2 and FOXA3 transcription factor networks 0.1319 57 2642 46 -0.72 0.02 1000 -1000 -0.15 -1000
Glypican 1 network 0.1296 56 2689 48 -0.29 0.025 1000 -1000 -0.049 -1000
IL4-mediated signaling events 0.1157 50 4592 91 -0.84 0.61 1000 -1000 -0.22 -1000
BCR signaling pathway 0.1111 48 4811 99 -0.23 0.012 1000 -1000 -0.1 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.1088 47 3708 78 -0.19 0.079 1000 -1000 -0.082 -1000
Syndecan-4-mediated signaling events 0.1065 46 3095 67 -0.44 0.045 1000 -1000 -0.082 -1000
Ephrin A reverse signaling 0.0926 40 283 7 -0.082 0 1000 -1000 -0.032 -1000
Endothelins 0.0903 39 3771 96 -0.38 0.096 1000 -1000 -0.091 -1000
Fc-epsilon receptor I signaling in mast cells 0.0833 36 3522 97 -0.15 0.032 1000 -1000 -0.098 -1000
Glucocorticoid receptor regulatory network 0.0833 36 4149 114 -0.65 0.3 1000 -1000 -0.078 -1000
IL1-mediated signaling events 0.0764 33 2055 62 -0.24 0.018 1000 -1000 -0.098 -1000
Visual signal transduction: Rods 0.0764 33 1736 52 -0.26 0.012 1000 -1000 -0.082 -1000
Presenilin action in Notch and Wnt signaling 0.0741 32 1974 61 -0.46 0.2 1000 -1000 -0.068 -1000
BMP receptor signaling 0.0741 32 2632 81 -0.28 0.045 1000 -1000 -0.091 -1000
HIF-1-alpha transcription factor network 0.0718 31 2431 76 -0.72 0.019 1000 -1000 -0.2 -1000
Caspase cascade in apoptosis 0.0694 30 2233 74 -0.14 0.06 1000 -1000 -0.053 -1000
p75(NTR)-mediated signaling 0.0671 29 3679 125 -0.85 0.036 1000 -1000 -0.11 -1000
Calcium signaling in the CD4+ TCR pathway 0.0671 29 926 31 -0.47 0.012 1000 -1000 -0.067 -1000
Signaling events mediated by the Hedgehog family 0.0648 28 1476 52 -0.11 0.11 1000 -1000 -0.068 -1000
Syndecan-2-mediated signaling events 0.0648 28 1982 69 -0.44 0.037 1000 -1000 -0.039 -1000
JNK signaling in the CD4+ TCR pathway 0.0625 27 459 17 -0.11 0.013 1000 -1000 -0.045 -1000
Ephrin B reverse signaling 0.0625 27 1301 48 -0.18 0.081 1000 -1000 -0.074 -1000
TCGA08_p53 0.0625 27 189 7 -0.12 0.058 1000 -1000 -0.012 -1000
Effects of Botulinum toxin 0.0625 27 726 26 -0.096 0.016 1000 -1000 -0.066 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0602 26 1792 68 -0.54 0.059 1000 -1000 -0.14 -1000
Syndecan-3-mediated signaling events 0.0579 25 907 35 -0.44 0.036 1000 -1000 -0.05 -1000
Canonical Wnt signaling pathway 0.0579 25 1315 51 -0.46 0.21 1000 -1000 -0.067 -1000
Ras signaling in the CD4+ TCR pathway 0.0579 25 434 17 -0.088 0.023 1000 -1000 -0.042 -1000
amb2 Integrin signaling 0.0556 24 2042 82 -0.14 0.017 1000 -1000 -0.08 -1000
Visual signal transduction: Cones 0.0509 22 844 38 -0.13 0.012 1000 -1000 -0.051 -1000
Signaling events regulated by Ret tyrosine kinase 0.0509 22 1838 82 -0.16 0.012 1000 -1000 -0.092 -1000
Wnt signaling 0.0509 22 159 7 -0.13 0.012 1000 -1000 -0.029 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0509 22 1941 88 -0.24 0.066 1000 -1000 -0.099 -1000
LPA4-mediated signaling events 0.0463 20 240 12 -0.1 0.016 1000 -1000 -0.032 -1000
TCR signaling in naïve CD8+ T cells 0.0463 20 1870 93 -0.089 0.049 1000 -1000 -0.091 -1000
EPHB forward signaling 0.0463 20 1744 85 -0.18 0.086 1000 -1000 -0.097 -1000
Signaling events mediated by PRL 0.0440 19 671 34 -0.11 0.053 1000 -1000 -0.038 -1000
IL12-mediated signaling events 0.0417 18 1641 87 -0.2 0.03 1000 -1000 -0.15 -1000
LPA receptor mediated events 0.0417 18 1862 102 -0.21 0.022 1000 -1000 -0.096 -1000
Plasma membrane estrogen receptor signaling 0.0394 17 1534 86 -0.17 0.055 1000 -1000 -0.089 -1000
Nectin adhesion pathway 0.0370 16 1062 63 -0.67 0.039 1000 -1000 -0.073 -1000
HIF-2-alpha transcription factor network 0.0370 16 695 43 -0.38 0.17 1000 -1000 -0.085 -1000
EGFR-dependent Endothelin signaling events 0.0370 16 346 21 -0.087 0.018 1000 -1000 -0.069 -1000
Noncanonical Wnt signaling pathway 0.0347 15 406 26 -0.13 0.012 1000 -1000 -0.06 -1000
Thromboxane A2 receptor signaling 0.0347 15 1634 105 -0.24 0.072 1000 -1000 -0.066 -1000
a4b1 and a4b7 Integrin signaling 0.0347 15 77 5 -0.005 0.006 1000 -1000 -0.022 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0347 15 830 52 -0.24 0.027 1000 -1000 -0.045 -1000
Retinoic acid receptors-mediated signaling 0.0347 15 926 58 -0.24 0.024 1000 -1000 -0.075 -1000
Signaling mediated by p38-alpha and p38-beta 0.0324 14 616 44 -0.044 0.012 1000 -1000 -0.043 -1000
ErbB4 signaling events 0.0301 13 958 69 -0.29 0.061 1000 -1000 -0.086 -1000
IL27-mediated signaling events 0.0301 13 679 51 -0.16 0.021 1000 -1000 -0.077 -1000
Arf6 signaling events 0.0278 12 754 62 -0.14 0.03 1000 -1000 -0.055 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0278 12 1475 120 -0.16 0.12 1000 -1000 -0.081 -1000
Regulation of nuclear SMAD2/3 signaling 0.0255 11 1558 136 -0.48 0.089 1000 -1000 -0.072 -1000
Signaling events mediated by PTP1B 0.0255 11 856 76 -0.37 0.058 1000 -1000 -0.093 -1000
Signaling events mediated by HDAC Class III 0.0255 11 463 40 -0.16 0.023 1000 -1000 -0.034 -1000
S1P5 pathway 0.0255 11 202 17 -0.11 0.035 1000 -1000 -0.043 -1000
Integrins in angiogenesis 0.0255 11 943 84 -0.35 0.031 1000 -1000 -0.089 -1000
Glypican 2 network 0.0255 11 45 4 -0.007 -0.002 1000 -1000 -0.025 -1000
IL6-mediated signaling events 0.0255 11 871 75 -0.14 0.051 1000 -1000 -0.085 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0231 10 289 28 -0.11 0.021 1000 -1000 -0.04 -1000
IFN-gamma pathway 0.0231 10 699 68 -0.067 0.032 1000 -1000 -0.1 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0231 10 384 37 -0.2 0.032 1000 -1000 -0.058 -1000
S1P1 pathway 0.0231 10 390 36 -0.11 0.014 1000 -1000 -0.059 -1000
FAS signaling pathway (CD95) 0.0231 10 485 47 -0.067 0.029 1000 -1000 -0.05 -1000
S1P4 pathway 0.0231 10 272 25 -0.11 0.021 1000 -1000 -0.042 -1000
Aurora A signaling 0.0208 9 559 60 -0.23 0.036 1000 -1000 -0.042 -1000
IGF1 pathway 0.0208 9 539 57 -0.1 0.025 1000 -1000 -0.1 -1000
Regulation of Androgen receptor activity 0.0208 9 686 70 -0.26 0.027 1000 -1000 -0.068 -1000
Nongenotropic Androgen signaling 0.0185 8 446 52 -0.11 0.029 1000 -1000 -0.054 -1000
Regulation of Telomerase 0.0185 8 860 102 -0.36 0.042 1000 -1000 -0.12 -1000
S1P3 pathway 0.0185 8 366 42 -0.11 0.025 1000 -1000 -0.049 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0185 8 285 33 -0.15 0.036 1000 -1000 -0.047 -1000
Coregulation of Androgen receptor activity 0.0162 7 593 76 -0.2 0.048 1000 -1000 -0.034 -1000
PDGFR-alpha signaling pathway 0.0162 7 315 44 -0.019 0.025 1000 -1000 -0.062 -1000
Signaling mediated by p38-gamma and p38-delta 0.0162 7 113 15 -0.04 0.023 1000 -1000 -0.033 -1000
Class I PI3K signaling events 0.0162 7 532 73 -0.16 0.032 1000 -1000 -0.067 -1000
ErbB2/ErbB3 signaling events 0.0139 6 423 65 -0.051 0.032 1000 -1000 -0.069 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0139 6 229 34 -0.003 0.022 1000 -1000 -0.047 -1000
Cellular roles of Anthrax toxin 0.0139 6 244 39 -0.044 0.014 1000 -1000 -0.02 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0139 6 578 83 -0.24 0.061 1000 -1000 -0.071 -1000
FoxO family signaling 0.0139 6 433 64 -0.13 0.078 1000 -1000 -0.088 -1000
Aurora B signaling 0.0139 6 433 67 -0.33 0.059 1000 -1000 -0.066 -1000
Regulation of p38-alpha and p38-beta 0.0116 5 277 54 -0.16 0.031 1000 -1000 -0.079 -1000
Rapid glucocorticoid signaling 0.0116 5 110 20 -0.016 0.012 1000 -1000 -0.023 -1000
PDGFR-beta signaling pathway 0.0116 5 552 97 -0.18 0.046 1000 -1000 -0.088 -1000
Hedgehog signaling events mediated by Gli proteins 0.0093 4 269 65 -0.11 0.052 1000 -1000 -0.067 -1000
Ceramide signaling pathway 0.0093 4 366 76 -0.1 0.044 1000 -1000 -0.053 -1000
TCGA08_rtk_signaling 0.0093 4 122 26 -0.057 0.039 1000 -1000 -0.021 -1000
Class IB PI3K non-lipid kinase events 0.0093 4 12 3 -0.008 0.008 1000 -1000 -0.015 -1000
Signaling events mediated by HDAC Class II 0.0069 3 278 75 -0.058 0.029 1000 -1000 -0.043 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0069 3 237 74 -0.1 0.065 1000 -1000 -0.099 -1000
VEGFR1 specific signals 0.0069 3 174 56 -0.026 0.044 1000 -1000 -0.064 -1000
E-cadherin signaling in keratinocytes 0.0069 3 143 43 -0.097 0.046 1000 -1000 -0.065 -1000
FOXM1 transcription factor network 0.0069 3 194 51 -0.16 0.16 1000 -1000 -0.24 -1000
PLK2 and PLK4 events 0.0046 2 8 3 0.005 0.014 1000 -1000 -0.023 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0046 2 175 85 -0.015 0.052 1000 -1000 -0.072 -1000
EPO signaling pathway 0.0046 2 153 55 -0.032 0.046 1000 -1000 -0.1 -1000
PLK1 signaling events 0.0046 2 188 85 -0.025 0.031 1000 -1000 -0.042 -1000
TRAIL signaling pathway 0.0046 2 116 48 -0.031 0.042 1000 -1000 -0.07 -1000
Paxillin-dependent events mediated by a4b1 0.0046 2 82 36 -0.026 0.028 1000 -1000 -0.075 -1000
IL2 signaling events mediated by PI3K 0.0046 2 131 58 -0.054 0.056 1000 -1000 -0.096 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0046 2 99 45 -0.019 0.057 1000 -1000 -0.097 -1000
IL2 signaling events mediated by STAT5 0.0046 2 58 22 -0.001 0.058 1000 -1000 -0.064 -1000
Arf6 trafficking events 0.0046 2 210 71 -0.039 0.035 1000 -1000 -0.083 -1000
Insulin Pathway 0.0046 2 189 74 -0.044 0.033 1000 -1000 -0.098 -1000
p38 MAPK signaling pathway 0.0046 2 89 44 -0.027 0.035 1000 -1000 -0.077 -1000
Arf6 downstream pathway 0.0023 1 73 43 -0.03 0.03 1000 -1000 -0.049 -1000
ceramide signaling pathway 0.0023 1 92 49 -0.013 0.045 1000 -1000 -0.061 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0023 1 156 125 -0.002 0.075 1000 -1000 -0.087 -1000
E-cadherin signaling in the nascent adherens junction 0.0023 1 120 76 -0.032 0.051 1000 -1000 -0.09 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 6 23 0.011 0.039 1000 -1000 -0.054 -1000
Canonical NF-kappaB pathway 0.0000 0 32 39 -0.005 0.068 1000 -1000 -0.087 -1000
BARD1 signaling events 0.0000 0 17 57 -0.031 0.061 1000 -1000 -0.074 -1000
Circadian rhythm pathway 0.0000 0 17 22 -0.012 0.043 1000 -1000 -0.05 -1000
Aurora C signaling 0.0000 0 2 7 0 0.022 1000 -1000 -0.026 -1000
Insulin-mediated glucose transport 0.0000 0 24 32 -0.002 0.039 1000 -1000 -0.049 -1000
mTOR signaling pathway 0.0000 0 26 53 -0.001 0.034 1000 -1000 -0.065 -1000
Class I PI3K signaling events mediated by Akt 0.0000 0 12 68 -0.037 0.05 1000 -1000 -0.05 -1000
Signaling events mediated by HDAC Class I 0.0000 0 56 104 -0.025 0.048 1000 -1000 -0.067 -1000
Atypical NF-kappaB pathway 0.0000 0 9 31 -0.002 0.041 1000 -1000 -0.05 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 12 27 0 0.03 1000 -1000 -0.052 -1000
E-cadherin signaling events 0.0000 0 1 5 0.011 0.024 1000 -1000 -0.035 -1000
Arf1 pathway 0.0000 0 35 54 -0.005 0.022 1000 -1000 -0.031 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.037 1000 -1000 -0.041 -1000
Total NA 2369 130919 7203 -24 6.4 131000 -131000 -9.3 -131000
TCGA08_retinoblastoma

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2B -0.15 0.21 -10000 0 -0.41 169 169
CDKN2C 0.023 0.033 -10000 0 -10000 0 0
CDKN2A -0.16 0.31 -10000 0 -0.75 95 95
CCND2 0.11 0.11 0.2 236 -10000 0 236
RB1 -0.11 0.12 -10000 0 -0.21 238 238
CDK4 0.12 0.12 0.21 238 -10000 0 238
CDK6 0.12 0.12 0.22 238 -10000 0 238
G1/S progression 0.11 0.12 0.21 238 -10000 0 238
Syndecan-1-mediated signaling events

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
TGFB1 0.011 0.036 -9999 0 -0.74 1 1
CCL5 -0.007 0.091 -9999 0 -0.44 18 18
SDCBP 0.01 0.031 -9999 0 -0.44 2 2
FGFR/FGF2/Syndecan-1 -0.34 0.14 -9999 0 -0.43 291 291
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.32 0.14 -9999 0 -0.4 293 293
Syndecan-1/Syntenin -0.32 0.14 -9999 0 -0.4 291 291
MAPK3 -0.28 0.12 -9999 0 -0.51 33 33
HGF/MET 0.006 0.077 -9999 0 -0.43 12 12
TGFB1/TGF beta receptor Type II 0.011 0.036 -9999 0 -0.74 1 1
BSG 0.011 0.022 -9999 0 -0.44 1 1
keratinocyte migration -0.32 0.13 -9999 0 -0.4 293 293
Syndecan-1/RANTES -0.33 0.14 -9999 0 -0.4 302 302
Syndecan-1/CD147 -0.3 0.13 -9999 0 -0.38 289 289
Syndecan-1/Syntenin/PIP2 -0.31 0.13 -9999 0 -0.39 291 291
LAMA5 0.006 0.066 -9999 0 -0.66 4 4
positive regulation of cell-cell adhesion -0.3 0.13 -9999 0 -0.38 291 291
MMP7 -0.71 0.14 -9999 0 -0.74 416 416
HGF 0.004 0.064 -9999 0 -0.48 7 7
Syndecan-1/CASK -0.32 0.13 -9999 0 -0.41 291 291
Syndecan-1/HGF/MET -0.31 0.13 -9999 0 -0.39 298 298
regulation of cell adhesion -0.27 0.12 -9999 0 -0.5 32 32
HPSE 0.006 0.053 -9999 0 -0.44 6 6
positive regulation of cell migration -0.34 0.14 -9999 0 -0.43 291 291
SDC1 -0.34 0.14 -9999 0 -0.43 291 291
Syndecan-1/Collagen -0.34 0.14 -9999 0 -0.43 291 291
PPIB 0.012 0 -9999 0 -10000 0 0
MET 0.004 0.08 -9999 0 -0.74 5 5
PRKACA 0.012 0 -9999 0 -10000 0 0
MMP9 -0.052 0.21 -9999 0 -0.71 38 38
MAPK1 -0.28 0.12 -9999 0 -0.52 32 32
homophilic cell adhesion -0.34 0.14 -9999 0 -0.42 291 291
MMP1 -0.48 0.36 -9999 0 -0.74 285 285
Reelin signaling pathway

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
CDK5R1/CDK5 0.017 0.028 -9999 0 -0.56 1 1
VLDLR -0.031 0.13 -9999 0 -0.44 41 41
CRKL 0.012 0 -9999 0 -10000 0 0
LRPAP1 0.012 0 -9999 0 -10000 0 0
FYN 0.012 0 -9999 0 -10000 0 0
ITGA3 0.011 0.022 -9999 0 -0.44 1 1
RELN/VLDLR/Fyn -0.12 0.17 -9999 0 -0.49 31 31
MAPK8IP1/MKK7/MAP3K11/JNK1 0.035 0.032 -9999 0 -0.63 1 1
AKT1 -0.11 0.15 -9999 0 -0.42 46 46
MAP2K7 0.011 0.022 -9999 0 -0.44 1 1
RAPGEF1 0.011 0.022 -9999 0 -0.44 1 1
DAB1 -0.061 0.22 -9999 0 -0.74 41 41
RELN/LRP8/DAB1 -0.45 0.26 -9999 0 -0.57 326 326
LRPAP1/LRP8 -0.4 0.26 -9999 0 -0.56 311 311
RELN/LRP8/DAB1/Fyn -0.42 0.25 -9999 0 -0.54 326 326
DAB1/alpha3/beta1 Integrin -0.4 0.24 -9999 0 -0.64 169 169
long-term memory -0.54 0.31 -9999 0 -0.74 265 265
DAB1/LIS1 -0.42 0.24 -9999 0 -0.63 183 183
DAB1/CRLK/C3G -0.4 0.24 -9999 0 -0.64 169 169
PIK3CA 0.012 0.001 -9999 0 -10000 0 0
DAB1/NCK2 -0.41 0.25 -9999 0 -0.52 333 333
ARHGEF2 0.012 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.11 0.2 -9999 0 -0.45 111 111
CDK5R1 0.011 0.036 -9999 0 -0.74 1 1
RELN -0.18 0.22 -9999 0 -0.44 184 184
PIK3R1 0.012 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.44 0.26 -9999 0 -0.58 311 311
GRIN2A/RELN/LRP8/DAB1/Fyn -0.47 0.27 -9999 0 -0.58 337 337
MAPK8 0.012 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.15 0.2 -9999 0 -0.5 70 70
ITGB1 0.012 0 -9999 0 -10000 0 0
MAP1B -0.41 0.26 -9999 0 -0.52 335 335
RELN/LRP8 -0.44 0.26 -9999 0 -0.58 311 311
GRIN2B/RELN/LRP8/DAB1/Fyn -0.51 0.3 -9999 0 -0.62 348 348
PI3K 0.018 0 -9999 0 -10000 0 0
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin 0.018 0.016 -9999 0 -0.3 1 1
RAP1A -0.37 0.23 -9999 0 -0.59 169 169
PAFAH1B1 0.012 0 -9999 0 -10000 0 0
MAPK8IP1 0.011 0.022 -9999 0 -0.44 1 1
CRLK/C3G 0.018 0.016 -9999 0 -0.3 1 1
GRIN2B -0.17 0.32 -9999 0 -0.74 106 106
NCK2 0.012 0 -9999 0 -10000 0 0
neuron differentiation -0.2 0.14 -9999 0 -0.35 162 162
neuron adhesion -0.34 0.22 -9999 0 -0.56 169 169
LRP8 -0.53 0.34 -9999 0 -0.74 311 311
GSK3B -0.096 0.15 -9999 0 -0.4 46 46
RELN/VLDLR/DAB1/Fyn -0.13 0.19 -9999 0 -0.47 70 70
MAP3K11 0.011 0.022 -9999 0 -0.44 1 1
RELN/VLDLR/DAB1/P13K -0.12 0.16 -9999 0 -0.45 46 46
CDK5 0.012 0 -9999 0 -10000 0 0
MAPT -0.07 0.17 -9999 0 -0.39 95 95
neuron migration -0.31 0.2 -9999 0 -0.52 177 177
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.2 0.14 -9999 0 -0.36 162 162
RELN/VLDLR -0.42 0.25 -9999 0 -0.55 319 319
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.17 0.22 -9999 0 -0.4 207 207
NF kappa B1 p50/RelA/I kappa B alpha -0.13 0.2 -9999 0 -0.49 28 28
alphaV/beta3 Integrin/Osteopontin/Src -0.25 0.29 -9999 0 -0.55 210 210
AP1 -0.13 0.21 -9999 0 -0.63 5 5
ILK -0.18 0.23 -9999 0 -0.42 207 207
bone resorption -0.14 0.2 -9999 0 -0.51 3 3
PTK2B 0.011 0.022 -9999 0 -0.44 1 1
PYK2/p130Cas -0.16 0.22 -9999 0 -0.38 207 207
ITGAV 0.014 0.003 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.017 0.022 -9999 0 -0.3 2 2
alphaV/beta3 Integrin/Osteopontin -0.21 0.25 -9999 0 -0.47 207 207
MAP3K1 -0.19 0.23 -9999 0 -0.42 207 207
JUN 0.013 0.001 -9999 0 -10000 0 0
MAPK3 -0.17 0.23 -9999 0 -0.4 207 207
MAPK1 -0.17 0.23 -9999 0 -0.4 207 207
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
NFKB1 0.012 0 -9999 0 -10000 0 0
MAPK8 -0.17 0.22 -9999 0 -0.39 207 207
ITGB3 0.01 0.043 -9999 0 -0.43 4 4
NFKBIA -0.15 0.22 -9999 0 -0.54 28 28
FOS 0.005 0.057 -9999 0 -0.44 7 7
CD44 0.012 0 -9999 0 -10000 0 0
CHUK 0.012 0 -9999 0 -10000 0 0
PLAU -0.15 0.25 -9999 0 -0.81 27 27
NF kappa B1 p50/RelA -0.17 0.18 -9999 0 -0.53 28 28
BCAR1 0.011 0.022 -9999 0 -0.44 1 1
RELA 0.012 0 -9999 0 -10000 0 0
alphaV beta3 Integrin 0.02 0.031 -9999 0 -0.29 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.19 0.23 -9999 0 -0.42 207 207
VAV3 -0.19 0.24 -9999 0 -0.43 207 207
MAP3K14 -0.19 0.23 -9999 0 -0.43 207 207
ROCK2 0.01 0.031 -9999 0 -0.44 2 2
SPP1 -0.35 0.37 -9999 0 -0.73 210 210
RAC1 0.012 0 -9999 0 -10000 0 0
Rac1/GTP -0.17 0.22 -9999 0 -0.5 57 57
MMP2 -0.11 0.18 -9999 0 -0.6 5 5
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.012 0 -9999 0 -10000 0 0
VLDLR -0.031 0.13 -9999 0 -0.44 41 41
LRPAP1 0.012 0 -9999 0 -10000 0 0
NUDC 0.012 0 -9999 0 -10000 0 0
RELN/LRP8 -0.44 0.26 -9999 0 -0.58 311 311
CaM/Ca2+ 0.009 0 -9999 0 -10000 0 0
KATNA1 0.012 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.4 0.24 -9999 0 -0.53 311 311
IQGAP1/CaM 0.018 0 -9999 0 -10000 0 0
DAB1 -0.061 0.22 -9999 0 -0.74 41 41
IQGAP1 0.012 0 -9999 0 -10000 0 0
PLA2G7 0.008 0.043 -9999 0 -0.44 4 4
CALM1 0.012 0 -9999 0 -10000 0 0
DYNLT1 0.012 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.4 0.26 -9999 0 -0.56 311 311
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.011 0.022 -9999 0 -0.44 1 1
CDK5R1 0.011 0.036 -9999 0 -0.74 1 1
LIS1/Poliovirus Protein 3A 0.014 0 -9999 0 -10000 0 0
CDK5R2 -0.038 0.15 -9999 0 -0.47 43 43
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.16 0.21 -9999 0 -0.55 70 70
YWHAE 0.012 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.32 0.2 -9999 0 -0.51 154 154
MAP1B -0.006 0.039 -9999 0 -0.26 10 10
RAC1 0.019 0 -9999 0 -10000 0 0
p35/CDK5 -0.35 0.21 -9999 0 -0.57 140 140
RELN -0.18 0.22 -9999 0 -0.44 184 184
PAFAH/LIS1 0.021 0.026 -9999 0 -10000 0 0
LIS1/CLIP170 0.023 0.013 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.25 0.14 -9999 0 -0.5 13 13
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.12 0.17 -9999 0 -0.48 50 50
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.34 0.21 -9999 0 -0.55 154 154
LIS1/IQGAP1 0.024 0 -9999 0 -10000 0 0
RHOA 0.019 0 -9999 0 -10000 0 0
PAFAH1B1 0.019 0 -9999 0 -10000 0 0
PAFAH1B3 0 0.094 -9999 0 -0.74 7 7
PAFAH1B2 0.012 0.001 -9999 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.018 0.027 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.3 0.19 -9999 0 -0.49 154 154
LRP8 -0.53 0.34 -9999 0 -0.74 311 311
NDEL1/Katanin 60 -0.32 0.2 -9999 0 -0.51 154 154
P39/CDK5 -0.37 0.22 -9999 0 -0.48 320 320
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.024 0 -9999 0 -10000 0 0
CDK5 -0.37 0.22 -9999 0 -0.49 311 311
PPP2R5D 0.012 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.02 0.011 -9999 0 -10000 0 0
CSNK2A1 0.012 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.13 0.19 -9999 0 -0.47 70 70
RELN/VLDLR -0.42 0.25 -9999 0 -0.55 319 319
CDC42 0.018 0.019 -9999 0 -0.37 1 1
IL23-mediated signaling events

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
CCL2 -0.4 0.44 -10000 0 -1.1 87 87
IL23A -0.49 0.5 -10000 0 -1.2 118 118
NF kappa B1 p50/RelA/I kappa B alpha -0.46 0.43 -10000 0 -1.1 110 110
positive regulation of T cell mediated cytotoxicity -0.44 0.5 -10000 0 -1.2 103 103
ITGA3 -0.41 0.44 -10000 0 -1.1 83 83
IL17F -0.32 0.33 -10000 0 -0.76 103 103
IL12B -0.015 0.079 -10000 0 -0.77 4 4
STAT1 (dimer) -0.43 0.48 -10000 0 -1.1 94 94
CD4 -0.41 0.46 -10000 0 -1.1 89 89
IL23 -0.47 0.48 -10000 0 -1.1 111 111
IL23R -0.084 0.23 -10000 0 -1.4 11 11
IL1B -0.47 0.5 -10000 0 -1.2 103 103
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.5 0.49 -10000 0 -1.1 129 129
TYK2 -0.004 0.019 -10000 0 -10000 0 0
STAT4 -0.013 0.1 -10000 0 -0.44 24 24
STAT3 0.012 0.002 -10000 0 -10000 0 0
IL18RAP -0.011 0.099 -10000 0 -0.44 22 22
IL12RB1 -0.024 0.099 -10000 0 -0.48 18 18
PIK3CA 0.012 0.002 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.018 0.074 -10000 0 -0.35 17 17
IL23R/JAK2 -0.092 0.22 -10000 0 -1.3 11 11
positive regulation of chronic inflammatory response -0.44 0.5 -10000 0 -1.2 103 103
natural killer cell activation 0.006 0.013 0.077 11 -10000 0 11
JAK2 -0.005 0.047 -10000 0 -0.46 3 3
PIK3R1 0.012 0.002 -10000 0 -10000 0 0
NFKB1 0.009 0.003 -10000 0 -10000 0 0
RELA 0.009 0.003 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.45 0.45 -10000 0 -1 113 113
ALOX12B -0.4 0.44 -10000 0 -1.1 89 89
CXCL1 -0.5 0.49 -10000 0 -1.1 132 132
T cell proliferation -0.44 0.5 -10000 0 -1.2 103 103
NFKBIA 0.009 0.003 -10000 0 -10000 0 0
IL17A -0.29 0.29 -10000 0 -0.64 117 117
PI3K -0.45 0.43 -10000 0 -1.1 109 109
IFNG -0.017 0.038 0.15 7 -0.098 41 48
STAT3 (dimer) -0.45 0.42 -10000 0 -1.1 110 110
IL18R1 0.003 0.065 -10000 0 -0.44 9 9
IL23/IL23R/JAK2/TYK2/SOCS3 -0.23 0.26 -10000 0 -0.68 42 42
IL18/IL18R 0.007 0.075 -10000 0 -10000 0 0
macrophage activation -0.026 0.017 -10000 0 -0.044 117 117
TNF -0.45 0.47 -10000 0 -1.1 98 98
STAT3/STAT4 -0.45 0.43 -10000 0 -1.1 113 113
STAT4 (dimer) -0.44 0.48 -10000 0 -1.2 97 97
IL18 0.01 0.031 -10000 0 -0.44 2 2
IL19 -0.4 0.44 -10000 0 -1.1 83 83
STAT5A (dimer) -0.43 0.48 -10000 0 -1.1 97 97
STAT1 0.011 0.036 -10000 0 -0.74 1 1
SOCS3 0.012 0 -10000 0 -10000 0 0
CXCL9 -0.44 0.47 -10000 0 -1.1 102 102
MPO -0.4 0.44 -10000 0 -1.1 89 89
positive regulation of humoral immune response -0.44 0.5 -10000 0 -1.2 103 103
IL23/IL23R/JAK2/TYK2 -0.46 0.54 -10000 0 -1.2 101 101
IL6 -0.45 0.49 -10000 0 -1.1 106 106
STAT5A 0.012 0 -10000 0 -10000 0 0
IL2 0.007 0.01 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.006 0.013 0.077 11 -10000 0 11
CD3E -0.41 0.45 -10000 0 -1.1 90 90
keratinocyte proliferation -0.44 0.5 -10000 0 -1.2 103 103
NOS2 -0.42 0.47 -10000 0 -1.1 100 100
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.41 0.33 -9999 0 -0.99 66 66
PCK1 -0.72 0.62 -9999 0 -1.4 196 196
HNF4A -0.47 0.39 -9999 0 -1.1 73 73
KCNJ11 -0.41 0.34 -9999 0 -1.1 52 52
AKT1 -0.21 0.13 -9999 0 -0.46 2 2
response to starvation -0.015 0.025 -9999 0 -10000 0 0
DLK1 -0.43 0.36 -9999 0 -1.1 58 58
NKX2-1 -0.25 0.24 -9999 0 -0.76 47 47
ACADM -0.41 0.34 -9999 0 -1 65 65
TAT -0.68 0.59 -9999 0 -1.3 189 189
CEBPB 0 0.027 -9999 0 -10000 0 0
CEBPA -0.001 0.045 -9999 0 -0.44 3 3
TTR -0.42 0.44 -9999 0 -1.1 116 116
PKLR -0.48 0.4 -9999 0 -1.1 105 105
APOA1 -0.5 0.41 -9999 0 -1.2 72 72
CPT1C -0.41 0.34 -9999 0 -1 63 63
ALAS1 -0.19 0.13 -9999 0 -10000 0 0
TFRC -0.36 0.23 -9999 0 -0.78 37 37
FOXF1 0.02 0.077 -9999 0 -0.44 8 8
NF1 0.018 0 -9999 0 -10000 0 0
HNF1A (dimer) -0.091 0.06 -9999 0 -0.35 5 5
CPT1A -0.41 0.33 -9999 0 -0.99 66 66
HMGCS1 -0.41 0.33 -9999 0 -1 63 63
NR3C1 -0.081 0.13 -9999 0 -0.48 31 31
CPT1B -0.41 0.33 -9999 0 -1 66 66
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 -0.079 0.041 -9999 0 -10000 0 0
GCK -0.42 0.35 -9999 0 -1 68 68
CREB1 -0.053 0.074 -9999 0 -10000 0 0
IGFBP1 -0.32 0.27 -9999 0 -0.79 80 80
PDX1 -0.61 0.24 -9999 0 -0.73 309 309
UCP2 -0.41 0.33 -9999 0 -0.99 67 67
ALDOB -0.46 0.38 -9999 0 -1.1 77 77
AFP -0.14 0.22 -9999 0 -0.68 46 46
BDH1 -0.41 0.33 -9999 0 -1 66 66
HADH -0.41 0.33 -9999 0 -1 58 58
F2 -0.56 0.44 -9999 0 -1.2 88 88
HNF1A -0.091 0.06 -9999 0 -0.35 5 5
G6PC -0.26 0.4 -9999 0 -1.3 57 57
SLC2A2 -0.32 0.2 -9999 0 -0.86 18 18
INS 0.008 0.04 -9999 0 -10000 0 0
FOXA1 -0.05 0.16 -9999 0 -0.4 60 60
FOXA3 -0.14 0.14 -9999 0 -0.42 39 39
FOXA2 -0.48 0.37 -9999 0 -1.1 70 70
ABCC8 -0.46 0.39 -9999 0 -1.1 91 91
ALB -0.15 0.23 -9999 0 -0.65 60 60
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer 0.002 0.08 -10000 0 -0.48 2 2
fibroblast growth factor receptor signaling pathway 0.002 0.08 -10000 0 -0.48 2 2
LAMA1 -0.11 0.2 -10000 0 -0.44 115 115
PRNP 0.011 0.022 -10000 0 -0.44 1 1
GPC1/SLIT2 -0.072 0.15 -10000 0 -0.56 1 1
SMAD2 0.025 0.032 -10000 0 -0.43 1 1
GPC1/PrPc/Cu2+ 0.014 0.03 -10000 0 -0.33 3 3
GPC1/Laminin alpha1 -0.07 0.14 -10000 0 -0.31 117 117
TDGF1 -0.29 0.36 -10000 0 -0.72 176 176
CRIPTO/GPC1 -0.21 0.28 -10000 0 -0.55 177 177
APP/GPC1 0.015 0.035 -10000 0 -0.39 3 3
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.18 0.24 -10000 0 -0.48 170 170
FLT1 0.012 0 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.023 0.03 -10000 0 -0.48 1 1
SERPINC1 0.001 0.071 -10000 0 -0.74 4 4
FYN -0.18 0.24 -10000 0 -0.48 170 170
FGR -0.18 0.25 -10000 0 -0.48 171 171
positive regulation of MAPKKK cascade -0.17 0.2 -10000 0 -0.39 176 176
SLIT2 -0.11 0.2 -10000 0 -0.44 117 117
GPC1/NRG -0.024 0.11 -10000 0 -0.31 56 56
NRG1 -0.045 0.15 -10000 0 -0.44 54 54
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.022 0.037 -10000 0 -0.48 2 2
LYN -0.18 0.24 -10000 0 -0.48 170 170
mol:Spermine 0.008 0.032 -10000 0 -0.44 2 2
cell growth 0.002 0.08 -10000 0 -0.48 2 2
BMP signaling pathway -0.009 0.042 0.59 2 -10000 0 2
SRC -0.18 0.24 -10000 0 -0.48 170 170
TGFBR1 0.011 0.022 -10000 0 -0.44 1 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.096 0.2 -10000 0 -0.46 99 99
GPC1 0.009 0.042 -10000 0 -0.59 2 2
TGFBR1 (dimer) 0.011 0.022 -10000 0 -0.44 1 1
VEGFA 0.011 0.036 -10000 0 -0.74 1 1
BLK -0.27 0.27 -10000 0 -0.57 171 171
HCK -0.18 0.25 -10000 0 -0.49 170 170
FGF2 -0.019 0.12 -10000 0 -0.44 30 30
FGFR1 0.008 0.043 -10000 0 -0.44 4 4
VEGFR1 homodimer 0.012 0 -10000 0 -10000 0 0
TGFBR2 0.012 0 -10000 0 -10000 0 0
cell death 0.015 0.035 -10000 0 -0.39 3 3
ATIII/GPC1 0.007 0.063 -10000 0 -0.51 6 6
PLA2G2A/GPC1 -0.062 0.15 -10000 0 -0.32 101 101
LCK -0.19 0.25 -10000 0 -0.48 177 177
neuron differentiation -0.024 0.11 -10000 0 -0.31 56 56
PrPc/Cu2+ 0.008 0.015 -10000 0 -0.31 1 1
APP 0.011 0.022 -10000 0 -0.44 1 1
TGFBR2 (dimer) 0.012 0 -10000 0 -10000 0 0
IL4-mediated signaling events

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
BCL2L1 -0.54 0.51 -10000 0 -1.3 85 85
STAT6 (cleaved dimer) -0.62 0.51 -10000 0 -1.2 138 138
IGHG1 -0.18 0.16 -10000 0 -10000 0 0
IGHG3 -0.53 0.49 -10000 0 -1.2 116 116
AKT1 -0.29 0.27 -10000 0 -0.7 39 39
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.22 0.22 -10000 0 -1 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.27 0.25 -10000 0 -1.1 3 3
THY1 -0.55 0.52 -10000 0 -1.3 83 83
MYB 0.012 0 -10000 0 -10000 0 0
HMGA1 0.011 0.036 -10000 0 -0.74 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.4 0.35 -10000 0 -0.84 110 110
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.27 0.25 -10000 0 -0.95 4 4
SP1 0.017 0.009 -10000 0 -10000 0 0
INPP5D 0.012 0 -10000 0 -10000 0 0
SOCS5 0.035 0.019 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.58 0.53 -10000 0 -1.3 113 113
SOCS1 -0.38 0.32 -10000 0 -0.8 64 64
SOCS3 -0.32 0.29 -10000 0 -0.82 21 21
FCER2 -0.84 0.67 -10000 0 -1.4 226 226
PARP14 0.004 0.015 -10000 0 -10000 0 0
CCL17 -0.55 0.51 -10000 0 -1.3 85 85
GRB2 0.012 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.21 0.2 -10000 0 -0.83 2 2
T cell proliferation -0.56 0.53 -10000 0 -1.3 103 103
IL4R/JAK1 -0.55 0.51 -10000 0 -1.3 100 100
EGR2 -0.62 0.54 -10000 0 -1.3 114 114
JAK2 -0.02 0.048 -10000 0 -0.47 3 3
JAK3 0.007 0.038 -10000 0 -0.74 1 1
PIK3R1 0.012 0 -10000 0 -10000 0 0
JAK1 0.004 0.024 -10000 0 -0.44 1 1
COL1A2 -0.19 0.21 -10000 0 -0.78 28 28
CCL26 -0.6 0.53 -10000 0 -1.4 93 93
IL4R -0.58 0.54 -10000 0 -1.4 94 94
PTPN6 0.025 0.011 -10000 0 -10000 0 0
IL13RA2 -0.58 0.51 -10000 0 -1.3 86 86
IL13RA1 -0.017 0.029 -10000 0 -10000 0 0
IRF4 -0.55 0.68 -10000 0 -1.5 145 145
ARG1 -0.13 0.14 -10000 0 -0.68 6 6
CBL -0.37 0.33 -10000 0 -0.81 102 102
GTF3A -0.016 0.14 -10000 0 -0.76 15 15
PIK3CA 0.012 0.001 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.023 0.05 -10000 0 -0.33 3 3
IRF4/BCL6 -0.48 0.63 -10000 0 -1.4 145 145
CD40LG -0.035 0.13 -10000 0 -0.46 35 35
MAPK14 -0.36 0.33 -10000 0 -0.82 92 92
mitosis -0.27 0.26 -10000 0 -0.67 35 35
STAT6 -0.63 0.6 -10000 0 -1.4 113 113
SPI1 0.009 0.054 -10000 0 -0.44 6 6
RPS6KB1 -0.26 0.25 -10000 0 -0.67 21 21
STAT6 (dimer) -0.62 0.6 -10000 0 -1.4 113 113
STAT6 (dimer)/PARP14 -0.63 0.57 -10000 0 -1.4 124 124
mast cell activation 0.014 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.28 0.26 -10000 0 -0.69 32 32
FRAP1 -0.29 0.27 -10000 0 -0.7 39 39
LTA -0.55 0.52 -10000 0 -1.3 84 84
FES 0.01 0.031 -10000 0 -0.44 2 2
T-helper 1 cell differentiation 0.61 0.58 1.4 114 -10000 0 114
CCL11 -0.59 0.57 -10000 0 -1.4 108 108
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.28 0.25 -10000 0 -0.68 24 24
IL2RG 0.007 0.032 -10000 0 -0.44 2 2
IL10 -0.57 0.54 -10000 0 -1.4 97 97
IRS1 0.012 0 -10000 0 -10000 0 0
IRS2 0.012 0 -10000 0 -10000 0 0
IL4 -0.13 0.12 -10000 0 -10000 0 0
IL5 -0.55 0.51 -10000 0 -1.3 84 84
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.43 0.38 -10000 0 -0.95 83 83
COL1A1 -0.28 0.3 -10000 0 -0.82 69 69
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.56 0.52 -10000 0 -1.4 83 83
IL2R gamma/JAK3 0.006 0.039 -10000 0 -0.44 2 2
TFF3 -0.56 0.53 -10000 0 -1.3 91 91
ALOX15 -0.58 0.53 -10000 0 -1.3 102 102
MYBL1 0.009 0.051 -10000 0 -0.74 2 2
T-helper 2 cell differentiation -0.46 0.4 -10000 0 -0.98 104 104
SHC1 0.012 0 -10000 0 -10000 0 0
CEBPB 0.015 0.007 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.26 0.24 -10000 0 -1.1 3 3
mol:PI-3-4-5-P3 -0.29 0.27 -10000 0 -0.7 39 39
PI3K -0.3 0.28 -10000 0 -0.75 39 39
DOK2 0.001 0.071 -10000 0 -0.44 11 11
ETS1 0.026 0.013 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.19 0.19 -10000 0 -0.8 2 2
ITGB3 -0.55 0.51 -10000 0 -1.3 94 94
PIGR -0.72 0.67 -10000 0 -1.5 151 151
IGHE 0.046 0.037 0.25 1 -10000 0 1
MAPKKK cascade -0.19 0.18 -10000 0 -0.78 2 2
BCL6 0.017 0.01 -10000 0 -10000 0 0
OPRM1 -0.55 0.51 -10000 0 -1.3 84 84
RETNLB -0.78 0.69 -10000 0 -1.5 179 179
SELP -0.62 0.6 -10000 0 -1.5 109 109
AICDA -0.53 0.49 -10000 0 -1.3 86 86
BCR signaling pathway

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
JUN -0.097 0.2 -9999 0 -0.48 69 69
IKBKB -0.042 0.098 -9999 0 -0.27 26 26
AKT1 -0.071 0.12 -9999 0 -0.27 71 71
IKBKG -0.044 0.1 -9999 0 -0.29 35 35
CALM1 -0.12 0.23 -9999 0 -0.53 82 82
PIK3CA 0.012 0.001 -9999 0 -10000 0 0
MAP3K1 -0.16 0.28 -9999 0 -0.7 76 76
MAP3K7 0.012 0 -9999 0 -10000 0 0
mol:Ca2+ -0.13 0.24 -9999 0 -0.57 84 84
DOK1 0.012 0 -9999 0 -10000 0 0
AP-1 -0.049 0.11 -9999 0 -0.27 63 63
LYN 0.012 0 -9999 0 -10000 0 0
BLNK 0.006 0.053 -9999 0 -0.44 6 6
SHC1 0.012 0 -9999 0 -10000 0 0
BCR complex -0.14 0.22 -9999 0 -0.4 165 165
CD22 -0.23 0.35 -9999 0 -0.75 111 111
CAMK2G -0.11 0.21 -9999 0 -0.52 71 71
CSNK2A1 0.012 0 -9999 0 -10000 0 0
INPP5D 0.012 0 -9999 0 -10000 0 0
SHC/GRB2/SOS1 -0.091 0.13 -9999 0 -0.55 3 3
GO:0007205 -0.14 0.25 -9999 0 -0.58 84 84
SYK 0.012 0 -9999 0 -10000 0 0
ELK1 -0.12 0.23 -9999 0 -0.58 72 72
NFATC1 -0.15 0.25 -9999 0 -0.61 77 77
B-cell antigen/BCR complex -0.14 0.22 -9999 0 -0.4 165 165
PAG1/CSK 0.012 0.046 -9999 0 -0.3 9 9
NFKBIB -0.005 0.033 -9999 0 -10000 0 0
HRAS -0.11 0.2 -9999 0 -0.51 71 71
NFKBIA -0.005 0.033 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.002 0.027 -9999 0 -10000 0 0
RasGAP/Csk -0.11 0.2 -9999 0 -0.5 70 70
mol:GDP -0.13 0.23 -9999 0 -0.56 82 82
PTEN 0.01 0.031 -9999 0 -0.44 2 2
CD79B -0.052 0.16 -9999 0 -0.44 61 61
NF-kappa-B/RelA/I kappa B alpha 0.002 0.027 -9999 0 -10000 0 0
GRB2 0.012 0 -9999 0 -10000 0 0
PI3K/BCAP/CD19 -0.18 0.28 -9999 0 -0.57 120 120
PIK3R1 0.012 0 -9999 0 -10000 0 0
mol:IP3 -0.14 0.25 -9999 0 -0.59 84 84
CSK 0.012 0 -9999 0 -10000 0 0
FOS -0.11 0.22 -9999 0 -0.53 74 74
CHUK -0.044 0.1 -9999 0 -0.28 40 40
IBTK 0.011 0.022 -9999 0 -0.44 1 1
CARD11/BCL10/MALT1/TAK1 -0.12 0.2 -9999 0 -0.58 54 54
PTPN6 -0.2 0.33 -9999 0 -0.69 111 111
RELA 0.012 0 -9999 0 -10000 0 0
BCL2A1 0.003 0.027 -9999 0 -0.12 9 9
VAV2 -0.21 0.34 -9999 0 -0.71 115 115
ubiquitin-dependent protein catabolic process -0.001 0.033 -9999 0 -10000 0 0
BTK -0.14 0.36 -9999 0 -1.1 54 54
CD19 -0.23 0.34 -9999 0 -0.73 112 112
MAP4K1 -0.033 0.14 -9999 0 -0.44 43 43
CD72 0.011 0.022 -9999 0 -0.44 1 1
PAG1 0.003 0.065 -9999 0 -0.44 9 9
MAPK14 -0.12 0.24 -9999 0 -0.58 73 73
SH3BP5 0.009 0.038 -9999 0 -0.44 3 3
PIK3AP1 -0.13 0.24 -9999 0 -0.62 71 71
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.17 0.29 -9999 0 -0.69 81 81
RAF1 -0.094 0.19 -9999 0 -0.49 65 65
RasGAP/p62DOK/SHIP -0.099 0.2 -9999 0 -0.48 70 70
CD79A -0.16 0.22 -9999 0 -0.44 163 163
re-entry into mitotic cell cycle -0.05 0.12 -9999 0 -0.27 63 63
RASA1 0.012 0.001 -9999 0 -10000 0 0
MAPK3 -0.068 0.16 -9999 0 -0.45 43 43
MAPK1 -0.068 0.16 -9999 0 -0.45 43 43
CD72/SHP1 -0.18 0.31 -9999 0 -0.64 110 110
NFKB1 0.012 0 -9999 0 -10000 0 0
MAPK8 -0.12 0.24 -9999 0 -0.57 74 74
actin cytoskeleton organization -0.17 0.28 -9999 0 -0.58 115 115
NF-kappa-B/RelA 0.008 0.054 -9999 0 -0.27 1 1
Calcineurin -0.088 0.19 -9999 0 -0.56 46 46
PI3K -0.18 0.24 -9999 0 -0.58 94 94
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.14 0.26 -9999 0 -0.6 84 84
SOS1 0.012 0 -9999 0 -10000 0 0
Bam32/HPK1 -0.18 0.35 -9999 0 -0.88 77 77
DAPP1 -0.22 0.38 -9999 0 -1 72 72
cytokine secretion -0.13 0.23 -9999 0 -0.56 77 77
mol:DAG -0.14 0.25 -9999 0 -0.59 84 84
PLCG2 -0.032 0.13 -9999 0 -0.44 42 42
MAP2K1 -0.081 0.17 -9999 0 -0.49 47 47
B-cell antigen/BCR complex/FcgammaRIIB -0.14 0.23 -9999 0 -0.59 70 70
mol:PI-3-4-5-P3 -0.13 0.16 -9999 0 -0.38 94 94
ETS1 -0.091 0.19 -9999 0 -0.49 64 64
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.086 0.17 -9999 0 -0.43 61 61
B-cell antigen/BCR complex/LYN -0.19 0.31 -9999 0 -0.81 73 73
MALT1 0.011 0.022 -9999 0 -0.44 1 1
TRAF6 0.012 0 -9999 0 -10000 0 0
RAC1 -0.18 0.31 -9999 0 -0.63 115 115
B-cell antigen/BCR complex/LYN/SYK -0.21 0.3 -9999 0 -0.67 109 109
CARD11 -0.14 0.26 -9999 0 -0.57 92 92
FCGR2B -0.037 0.14 -9999 0 -0.44 47 47
PPP3CA 0.012 0 -9999 0 -10000 0 0
BCL10 0.011 0.022 -9999 0 -0.44 1 1
IKK complex -0.011 0.042 -9999 0 -10000 0 0
PTPRC -0.022 0.12 -9999 0 -0.44 33 33
PDPK1 -0.068 0.12 -9999 0 -0.27 63 63
PPP3CB 0.012 0 -9999 0 -10000 0 0
PPP3CC 0.012 0 -9999 0 -10000 0 0
POU2F2 0.003 0.026 -9999 0 -0.096 8 8
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.06 0.19 -10000 0 -0.43 81 81
CRKL -0.049 0.18 -10000 0 -0.42 77 77
HRAS -0.037 0.18 -10000 0 -0.47 28 28
mol:PIP3 -0.056 0.17 -10000 0 -0.4 77 77
SPRED1 0.012 0 -10000 0 -10000 0 0
SPRED2 0.012 0 -10000 0 -10000 0 0
GAB1 -0.057 0.19 -10000 0 -0.45 77 77
FOXO3 -0.038 0.16 -10000 0 -0.38 77 77
AKT1 -0.048 0.18 -10000 0 -0.41 77 77
BAD -0.039 0.16 -10000 0 -0.38 77 77
megakaryocyte differentiation -0.092 0.22 -10000 0 -0.46 103 103
GSK3B -0.038 0.16 -10000 0 -0.38 77 77
RAF1 -0.021 0.15 -10000 0 -0.38 25 25
SHC1 0.012 0 -10000 0 -10000 0 0
STAT3 -0.057 0.19 -10000 0 -0.45 77 77
STAT1 -0.15 0.43 -10000 0 -0.99 86 86
HRAS/SPRED1 -0.023 0.14 -10000 0 -0.38 25 25
cell proliferation -0.056 0.18 -10000 0 -0.44 77 77
PIK3CA 0.012 0.001 -10000 0 -10000 0 0
TEC 0.011 0.036 -10000 0 -0.74 1 1
RPS6KB1 -0.057 0.19 -10000 0 -0.45 77 77
HRAS/SPRED2 -0.023 0.14 -10000 0 -0.38 25 25
LYN/TEC/p62DOK -0.043 0.18 -10000 0 -0.41 77 77
MAPK3 -0.004 0.11 -10000 0 -0.29 12 12
STAP1 -0.11 0.22 -10000 0 -0.52 79 79
GRAP2 -0.006 0.088 -10000 0 -0.44 17 17
JAK2 -0.13 0.37 -10000 0 -0.86 81 81
STAT1 (dimer) -0.15 0.42 -10000 0 -0.96 86 86
mol:Gleevec 0.001 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.06 0.21 -10000 0 -0.46 82 82
actin filament polymerization -0.059 0.19 -10000 0 -0.44 80 80
LYN 0.012 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.12 0.28 -10000 0 -0.68 79 79
PIK3R1 0.012 0 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.032 0.16 -10000 0 -0.44 21 21
PI3K -0.043 0.18 -10000 0 -0.42 77 77
PTEN 0.01 0.031 -10000 0 -0.44 2 2
SCF/KIT/EPO/EPOR -0.18 0.5 -10000 0 -1.2 77 77
MAPK8 -0.057 0.19 -10000 0 -0.45 77 77
STAT3 (dimer) -0.056 0.18 -10000 0 -0.44 77 77
positive regulation of transcription 0.001 0.093 -10000 0 -0.26 3 3
mol:GDP -0.044 0.18 -10000 0 -0.51 28 28
PIK3C2B -0.057 0.19 -10000 0 -0.45 77 77
CBL/CRKL -0.039 0.17 -10000 0 -0.39 77 77
FER -0.058 0.19 -10000 0 -0.45 77 77
SH2B3 -0.057 0.19 -10000 0 -0.45 77 77
PDPK1 -0.046 0.16 -10000 0 -0.37 77 77
SNAI2 -0.058 0.19 -10000 0 -0.45 77 77
positive regulation of cell proliferation -0.1 0.32 -10000 0 -0.76 77 77
KITLG -0.001 0.076 -10000 0 -0.47 11 11
cell motility -0.1 0.32 -10000 0 -0.76 77 77
PTPN6 0.014 0.01 -10000 0 -10000 0 0
EPOR -0.019 0.14 -10000 0 -0.8 1 1
STAT5A (dimer) -0.081 0.26 -10000 0 -0.62 77 77
SOCS1 -0.007 0.12 -10000 0 -0.74 11 11
cell migration 0.079 0.21 0.49 78 -10000 0 78
SOS1 0.012 0 -10000 0 -10000 0 0
EPO -0.001 0.072 -10000 0 -0.74 4 4
VAV1 -0.008 0.093 -10000 0 -0.44 19 19
GRB10 -0.057 0.19 -10000 0 -0.45 77 77
PTPN11 0.014 0.007 -10000 0 -10000 0 0
SCF/KIT -0.066 0.2 -10000 0 -0.47 77 77
GO:0007205 0.002 0.01 -10000 0 -10000 0 0
MAP2K1 -0.008 0.12 -10000 0 -0.32 10 10
CBL 0.012 0 -10000 0 -10000 0 0
KIT -0.19 0.5 -10000 0 -1.3 77 77
MAP2K2 -0.008 0.12 -10000 0 -0.31 18 18
SHC/Grb2/SOS1 -0.042 0.18 -10000 0 -0.41 77 77
STAT5A -0.085 0.27 -10000 0 -0.64 77 77
GRB2 0.012 0 -10000 0 -10000 0 0
response to radiation -0.057 0.18 -10000 0 -0.44 77 77
SHC/GRAP2 0.006 0.063 -10000 0 -0.3 17 17
PTPRO -0.095 0.22 -10000 0 -0.47 103 103
SH2B2 -0.061 0.19 -10000 0 -0.45 80 80
DOK1 0.012 0 -10000 0 -10000 0 0
MATK -0.081 0.21 -10000 0 -0.5 78 78
CREBBP 0.011 0.049 -10000 0 -10000 0 0
BCL2 -0.073 0.33 -10000 0 -1.4 24 24
Syndecan-4-mediated signaling events

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
PTK2 -0.021 0.096 -9999 0 -0.4 24 24
Syndecan-4/Syndesmos -0.14 0.21 -9999 0 -0.52 67 67
positive regulation of JNK cascade -0.16 0.2 -9999 0 -0.47 86 86
Syndecan-4/ADAM12 -0.38 0.26 -9999 0 -0.67 151 151
CCL5 -0.007 0.091 -9999 0 -0.44 18 18
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
DNM2 0.012 0 -9999 0 -10000 0 0
ITGA5 0.009 0.051 -9999 0 -0.74 2 2
SDCBP 0.01 0.031 -9999 0 -0.44 2 2
PLG -0.14 0.29 -9999 0 -0.74 82 82
ADAM12 -0.44 0.36 -9999 0 -0.74 264 264
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.065 0.068 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.2 0.22 -9999 0 -0.53 102 102
Syndecan-4/CXCL12/CXCR4 -0.17 0.21 -9999 0 -0.5 86 86
Syndecan-4/Laminin alpha3 -0.15 0.21 -9999 0 -0.52 69 69
MDK 0.005 0.072 -9999 0 -0.74 4 4
Syndecan-4/FZD7 -0.14 0.21 -9999 0 -0.52 66 66
Syndecan-4/Midkine -0.15 0.21 -9999 0 -0.52 69 69
FZD7 0.012 0 -9999 0 -10000 0 0
Syndecan-4/FGFR1/FGF -0.16 0.19 -9999 0 -0.51 67 67
THBS1 0.011 0.036 -9999 0 -0.74 1 1
integrin-mediated signaling pathway -0.15 0.21 -9999 0 -0.51 71 71
positive regulation of MAPKKK cascade -0.16 0.2 -9999 0 -0.47 86 86
Syndecan-4/TACI -0.23 0.22 -9999 0 -0.51 132 132
CXCR4 0.012 0 -9999 0 -10000 0 0
cell adhesion 0.014 0.069 -9999 0 -0.3 7 7
Syndecan-4/Dynamin -0.14 0.21 -9999 0 -0.52 67 67
Syndecan-4/TSP1 -0.14 0.21 -9999 0 -0.52 66 66
Syndecan-4/GIPC -0.14 0.21 -9999 0 -0.52 67 67
Syndecan-4/RANTES -0.15 0.21 -9999 0 -0.52 72 72
ITGB1 0.012 0 -9999 0 -10000 0 0
LAMA1 -0.11 0.2 -9999 0 -0.44 115 115
LAMA3 0.006 0.056 -9999 0 -0.5 5 5
RAC1 0.012 0 -9999 0 -10000 0 0
PRKCA 0.045 0.048 -9999 0 -10000 0 0
Syndecan-4/alpha-Actinin -0.14 0.21 -9999 0 -0.52 66 66
TFPI 0.009 0.038 -9999 0 -0.44 3 3
F2 -0.23 0.35 -9999 0 -0.74 139 139
alpha5/beta1 Integrin 0.016 0.039 -9999 0 -0.56 2 2
positive regulation of cell adhesion -0.19 0.22 -9999 0 -0.52 98 98
ACTN1 0.012 0 -9999 0 -10000 0 0
TNC -0.003 0.1 -9999 0 -0.6 11 11
Syndecan-4/CXCL12 -0.18 0.22 -9999 0 -0.51 93 93
FGF6 -0.002 0.035 -9999 0 -0.74 1 1
RHOA 0.012 0 -9999 0 -10000 0 0
CXCL12 -0.068 0.17 -9999 0 -0.44 76 76
TNFRSF13B -0.18 0.22 -9999 0 -0.44 181 181
FGF2 -0.019 0.12 -9999 0 -0.44 30 30
FGFR1 0.008 0.043 -9999 0 -0.44 4 4
Syndecan-4/PI-4-5-P2 -0.15 0.21 -9999 0 -0.52 67 67
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.022 0.16 -9999 0 -0.66 24 24
cell migration -0.024 0.025 -9999 0 -10000 0 0
PRKCD 0.016 0.01 -9999 0 -10000 0 0
vasculogenesis -0.14 0.2 -9999 0 -0.5 66 66
SDC4 -0.16 0.22 -9999 0 -0.55 67 67
Syndecan-4/Tenascin C -0.15 0.22 -9999 0 -0.53 71 71
Syndecan-4/PI-4-5-P2/PKC alpha -0.051 0.054 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.14 0.21 -9999 0 -0.52 67 67
MMP9 -0.054 0.21 -9999 0 -0.72 38 38
Rac1/GTP 0.01 0.07 -9999 0 -0.31 7 7
cytoskeleton organization -0.14 0.2 -9999 0 -0.5 67 67
GIPC1 0.011 0.022 -9999 0 -0.44 1 1
Syndecan-4/TFPI -0.14 0.21 -9999 0 -0.52 68 68
Ephrin A reverse signaling

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
MAPKKK cascade -0.053 0.12 -9999 0 -0.29 57 57
EFNA5 -0.082 0.18 -9999 0 -0.44 90 90
FYN -0.041 0.11 -9999 0 -0.45 6 6
neuron projection morphogenesis -0.053 0.12 -9999 0 -0.29 57 57
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.053 0.12 -9999 0 -0.29 57 57
EPHA5 -0.01 0.085 -9999 0 -0.44 16 16
Endothelins

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
AKT1 0.012 0.21 -10000 0 -0.5 35 35
PTK2B 0.012 0.022 -10000 0 -0.44 1 1
mol:Ca2+ 0.015 0.24 -10000 0 -0.97 21 21
EDN1 0.046 0.14 -10000 0 -0.49 3 3
EDN3 -0.21 0.23 -10000 0 -0.44 208 208
EDN2 -0.12 0.21 -10000 0 -0.44 126 126
HRAS/GDP 0.013 0.15 -10000 0 -0.46 11 11
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.043 0.11 -10000 0 -0.52 2 2
ADCY4 -0.022 0.17 -10000 0 -0.43 39 39
ADCY5 -0.12 0.2 -10000 0 -0.46 72 72
ADCY6 -0.022 0.17 -10000 0 -0.43 39 39
ADCY7 -0.022 0.17 -10000 0 -0.43 39 39
ADCY1 -0.031 0.18 -10000 0 -0.43 45 45
ADCY2 -0.04 0.19 -10000 0 -0.46 48 48
ADCY3 -0.022 0.17 -10000 0 -0.43 39 39
ADCY8 -0.035 0.17 -10000 0 -0.41 51 51
ADCY9 -0.023 0.17 -10000 0 -0.44 35 35
arachidonic acid secretion -0.002 0.16 -10000 0 -0.5 19 19
ETB receptor/Endothelin-1/Gq/GTP 0.025 0.093 -10000 0 -0.45 6 6
GNAO1 -0.11 0.2 -10000 0 -0.44 118 118
HRAS 0.011 0.022 -10000 0 -0.44 1 1
ETA receptor/Endothelin-1/G12/GTP 0.096 0.25 0.31 211 -0.46 35 246
ETA receptor/Endothelin-1/Gs/GTP 0.068 0.25 0.29 203 -0.44 44 247
mol:GTP 0.001 0.004 -10000 0 -10000 0 0
COL3A1 0.005 0.23 -10000 0 -0.56 41 41
EDNRB -0.008 0.091 -10000 0 -0.44 17 17
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.012 0.26 -10000 0 -0.61 50 50
CYSLTR1 -0.04 0.3 -10000 0 -0.6 79 79
SLC9A1 0.02 0.12 -10000 0 -0.28 14 14
mol:GDP 0.007 0.16 -10000 0 -0.49 12 12
SLC9A3 -0.25 0.34 -10000 0 -0.63 134 134
RAF1 0 0.13 -10000 0 -0.52 7 7
JUN 0.042 0.15 -10000 0 -0.78 2 2
JAK2 0.01 0.21 -10000 0 -0.5 36 36
mol:IP3 0.034 0.11 -10000 0 -0.78 2 2
ETA receptor/Endothelin-1 0.091 0.31 0.36 215 -0.56 41 256
PLCB1 0.007 0.062 -10000 0 -0.74 3 3
PLCB2 0.013 0.002 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.14 0.24 -10000 0 -0.46 87 87
FOS 0.011 0.16 -10000 0 -0.88 8 8
Gai/GDP -0.16 0.32 -10000 0 -0.67 118 118
CRK 0.013 0.001 -10000 0 -10000 0 0
mol:Ca ++ 0.015 0.19 -10000 0 -0.54 21 21
BCAR1 0.011 0.022 -10000 0 -0.44 1 1
PRKCB1 0.032 0.1 -10000 0 -0.74 2 2
GNAQ 0.012 0.031 -10000 0 -0.44 2 2
GNAZ 0.007 0.049 -10000 0 -0.44 5 5
GNAL -0.016 0.11 -10000 0 -0.44 27 27
Gs family/GDP -0.05 0.12 -10000 0 -0.45 20 20
ETA receptor/Endothelin-1/Gq/GTP 0.041 0.13 -10000 0 -0.42 7 7
MAPK14 0.034 0.081 -10000 0 -0.66 2 2
TRPC6 0.011 0.26 -10000 0 -1 21 21
GNAI2 0.012 0 -10000 0 -10000 0 0
GNAI3 0.012 0 -10000 0 -10000 0 0
GNAI1 -0.003 0.083 -10000 0 -0.44 15 15
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.03 0.086 -10000 0 -0.58 3 3
ETB receptor/Endothelin-2 -0.089 0.16 -10000 0 -0.31 139 139
ETB receptor/Endothelin-3 -0.15 0.17 -10000 0 -0.32 214 214
ETB receptor/Endothelin-1 0.031 0.14 -10000 0 -0.43 14 14
MAPK3 0.009 0.15 -10000 0 -0.74 9 9
MAPK1 0.009 0.15 -10000 0 -0.74 9 9
Rac1/GDP 0.013 0.15 -10000 0 -0.48 9 9
cAMP biosynthetic process -0.066 0.18 -10000 0 -0.46 42 42
MAPK8 0.034 0.17 -10000 0 -0.59 15 15
SRC 0.012 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.036 0.15 -10000 0 -0.49 26 26
p130Cas/CRK/Src/PYK2 -0.02 0.18 -10000 0 -0.59 18 18
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP 0.013 0.15 -10000 0 -0.49 8 8
COL1A2 0.005 0.25 -10000 0 -0.62 38 38
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.083 0.22 -10000 0 -0.48 55 55
mol:DAG 0.034 0.11 -10000 0 -0.78 2 2
MAP2K2 0.007 0.14 -10000 0 -0.58 9 9
MAP2K1 0.007 0.14 -10000 0 -0.58 9 9
EDNRA 0.012 0.22 -10000 0 -0.74 21 21
positive regulation of muscle contraction 0.018 0.18 -10000 0 -0.55 11 11
Gq family/GDP -0.047 0.11 -10000 0 -0.53 6 6
HRAS/GTP -0.008 0.13 -10000 0 -0.5 7 7
PRKCH 0.037 0.11 -10000 0 -0.6 3 3
RAC1 0.012 0 -10000 0 -10000 0 0
PRKCA 0.038 0.1 -10000 0 -0.73 2 2
PRKCB -0.01 0.16 -10000 0 -0.42 19 19
PRKCE 0.039 0.1 -10000 0 -0.73 2 2
PRKCD 0.038 0.1 -10000 0 -0.73 2 2
PRKCG -0.1 0.22 -10000 0 -0.46 67 67
regulation of vascular smooth muscle contraction 0.008 0.18 -10000 0 -1 8 8
PRKCQ 0.035 0.11 -10000 0 -0.53 4 4
PLA2G4A -0.005 0.18 -10000 0 -0.54 20 20
GNA14 0.012 0.031 -10000 0 -0.44 2 2
GNA15 0.006 0.072 -10000 0 -0.73 4 4
GNA12 0.012 0 -10000 0 -10000 0 0
GNA11 0.011 0.031 -10000 0 -0.44 2 2
Rac1/GTP 0.096 0.25 0.31 212 -0.46 35 247
MMP1 -0.38 0.32 -10000 0 -0.6 285 285
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.007 0.049 -9999 0 -0.44 5 5
LAT2 -0.089 0.17 -9999 0 -0.41 65 65
AP1 -0.14 0.21 -9999 0 -0.63 48 48
mol:PIP3 -0.11 0.21 -9999 0 -0.49 72 72
IKBKB -0.07 0.14 -9999 0 -0.32 60 60
AKT1 -0.055 0.14 -9999 0 -0.48 4 4
IKBKG -0.07 0.14 -9999 0 -0.32 61 61
MS4A2 -0.12 0.2 -9999 0 -0.44 124 124
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.012 0.001 -9999 0 -10000 0 0
MAP3K1 -0.083 0.18 -9999 0 -0.5 37 37
mol:Ca2+ -0.081 0.16 -9999 0 -0.36 72 72
LYN 0.011 0.004 -9999 0 -10000 0 0
CBLB -0.088 0.16 -9999 0 -0.4 65 65
SHC1 0.012 0 -9999 0 -10000 0 0
RasGAP/p62DOK 0.022 0.021 -9999 0 -10000 0 0
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.012 0 -9999 0 -10000 0 0
PLD2 -0.088 0.16 -9999 0 -0.39 65 65
PTPN13 -0.1 0.19 -9999 0 -0.44 68 68
PTPN11 0.009 0.008 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.046 0.14 -9999 0 -0.38 7 7
SYK 0.011 0.004 -9999 0 -10000 0 0
GRB2 0.012 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.15 0.2 -9999 0 -0.5 79 79
LAT -0.089 0.17 -9999 0 -0.41 65 65
PAK2 -0.099 0.2 -9999 0 -0.45 82 82
NFATC2 -0.06 0.12 -9999 0 -0.64 14 14
HRAS -0.11 0.22 -9999 0 -0.49 86 86
GAB2 0.012 0 -9999 0 -10000 0 0
PLA2G1B 0.032 0.023 -9999 0 -10000 0 0
Fc epsilon R1 -0.13 0.19 -9999 0 -0.5 65 65
Antigen/IgE/Fc epsilon R1 -0.11 0.18 -9999 0 -0.45 65 65
mol:GDP -0.13 0.25 -9999 0 -0.55 87 87
JUN 0.012 0 -9999 0 -10000 0 0
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.012 0.001 -9999 0 -10000 0 0
FOS 0.005 0.057 -9999 0 -0.44 7 7
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.098 0.17 -9999 0 -0.43 65 65
CHUK -0.07 0.14 -9999 0 -0.32 60 60
KLRG1 -0.081 0.15 -9999 0 -0.37 65 65
VAV1 -0.096 0.18 -9999 0 -0.42 73 73
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.087 0.16 -9999 0 -0.4 65 65
negative regulation of mast cell degranulation -0.069 0.14 -9999 0 -0.34 65 65
BTK -0.15 0.28 -9999 0 -0.6 95 95
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.14 0.24 -9999 0 -0.58 84 84
GAB2/PI3K/SHP2 -0.092 0.13 -9999 0 -0.52 4 4
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.097 0.18 -9999 0 -0.46 65 65
RAF1 0.025 0.025 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.12 0.2 -9999 0 -0.47 84 84
FCER1G 0.012 0.046 -9999 0 -0.46 4 4
FCER1A -0.12 0.21 -9999 0 -0.45 124 124
Antigen/IgE/Fc epsilon R1/Fyn -0.099 0.17 -9999 0 -0.42 65 65
MAPK3 0.032 0.023 -9999 0 -10000 0 0
MAPK1 0.032 0.023 -9999 0 -10000 0 0
NFKB1 0.012 0 -9999 0 -10000 0 0
MAPK8 -0.019 0.076 -9999 0 -0.51 3 3
DUSP1 0.009 0.038 -9999 0 -0.44 3 3
NF-kappa-B/RelA -0.056 0.069 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.097 0.18 -9999 0 -0.44 65 65
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.12 0.17 -9999 0 -0.55 32 32
FER -0.088 0.16 -9999 0 -0.4 66 66
RELA 0.012 0 -9999 0 -10000 0 0
ITK -0.041 0.088 -9999 0 -0.44 16 16
SOS1 0.012 0 -9999 0 -10000 0 0
PLCG1 -0.13 0.24 -9999 0 -0.54 86 86
cytokine secretion -0.041 0.05 -9999 0 -10000 0 0
SPHK1 -0.12 0.19 -9999 0 -0.43 89 89
PTK2 -0.1 0.19 -9999 0 -0.46 65 65
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.15 0.2 -9999 0 -0.53 72 72
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.11 0.21 -9999 0 -0.48 76 76
MAP2K2 0.029 0.026 -9999 0 -10000 0 0
MAP2K1 0.029 0.022 -9999 0 -10000 0 0
MAP2K7 0.011 0.022 -9999 0 -0.44 1 1
KLRG1/SHP2 -0.069 0.14 -9999 0 -0.45 12 12
MAP2K4 0.006 0.081 -9999 0 -0.96 3 3
Fc epsilon R1/FcgammaRIIB -0.13 0.22 -9999 0 -0.51 84 84
mol:Choline -0.087 0.16 -9999 0 -0.39 65 65
SHC/Grb2/SOS1 -0.072 0.16 -9999 0 -0.49 12 12
FYN 0.012 0 -9999 0 -10000 0 0
DOK1 0.012 0 -9999 0 -10000 0 0
PXN -0.089 0.18 -9999 0 -0.42 65 65
HCLS1 -0.09 0.17 -9999 0 -0.42 65 65
PRKCB -0.11 0.19 -9999 0 -0.41 102 102
FCGR2B -0.037 0.14 -9999 0 -0.44 47 47
IGHE -0.002 0.005 -9999 0 -10000 0 0
KLRG1/SHIP -0.07 0.14 -9999 0 -0.35 65 65
LCP2 0.008 0.044 -9999 0 -0.44 4 4
PLA2G4A -0.11 0.19 -9999 0 -0.43 91 91
RASA1 0.012 0.001 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.087 0.16 -9999 0 -0.39 65 65
IKK complex -0.041 0.11 -9999 0 -0.24 44 44
WIPF1 0.009 0.038 -9999 0 -0.44 3 3
Glucocorticoid receptor regulatory network

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
PCK2 0.021 0.077 0.33 1 -10000 0 1
SMARCC2 0.011 0.014 -10000 0 -10000 0 0
SMARCC1 0.01 0.016 -10000 0 -10000 0 0
TBX21 -0.13 0.2 -10000 0 -0.64 43 43
SUMO2 0.012 0.007 -10000 0 -10000 0 0
STAT1 (dimer) 0.018 0.036 -10000 0 -0.72 1 1
FKBP4 0.011 0.036 -10000 0 -0.74 1 1
FKBP5 0.011 0.022 -10000 0 -0.44 1 1
GR alpha/HSP90/FKBP51/HSP90 0.11 0.12 0.32 20 -0.4 3 23
PRL -0.089 0.15 -10000 0 -0.67 14 14
cortisol/GR alpha (dimer)/TIF2 0.27 0.22 0.54 99 -0.58 2 101
RELA -0.062 0.081 -10000 0 -10000 0 0
FGG 0.15 0.26 0.51 36 -0.58 23 59
GR beta/TIF2 0.11 0.13 0.34 24 -0.39 8 32
IFNG -0.36 0.28 -10000 0 -0.79 92 92
apoptosis 0.009 0.16 0.48 14 -0.57 5 19
CREB1 0.009 0.037 -10000 0 -10000 0 0
histone acetylation -0.072 0.13 0.47 2 -0.37 28 30
BGLAP -0.081 0.12 -10000 0 -0.56 4 4
GR/PKAc 0.066 0.15 0.32 10 -0.42 11 21
NF kappa B1 p50/RelA -0.11 0.15 -10000 0 -0.39 30 30
SMARCD1 0.01 0.016 -10000 0 -10000 0 0
MDM2 0.1 0.077 0.27 30 -0.22 1 31
GATA3 0.008 0.06 -10000 0 -0.5 5 5
AKT1 0.005 0.002 -10000 0 -10000 0 0
CSF2 -0.23 0.23 -10000 0 -0.5 151 151
GSK3B 0.012 0.007 -10000 0 -10000 0 0
NR1I3 0.018 0.17 0.47 12 -0.8 5 17
CSN2 0.15 0.15 0.42 28 -0.52 3 31
BRG1/BAF155/BAF170/BAF60A 0.027 0.051 -10000 0 -0.37 1 1
NFATC1 0.009 0.044 -10000 0 -0.44 4 4
POU2F1 0.011 0.023 -10000 0 -10000 0 0
CDKN1A 0.025 0.093 -10000 0 -1.3 2 2
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.007 -10000 0 -10000 0 0
SFN 0.011 0.022 -10000 0 -0.44 1 1
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.11 0.11 0.32 13 -0.36 3 16
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.021 0.15 0.45 13 -0.72 2 15
JUN -0.29 0.17 -10000 0 -0.54 84 84
IL4 -0.1 0.12 -10000 0 -0.49 4 4
CDK5R1 0.011 0.036 -10000 0 -0.73 1 1
PRKACA 0.012 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.31 0.24 -10000 0 -0.6 123 123
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.11 0.11 0.32 16 -0.36 3 19
cortisol/GR alpha (monomer) 0.3 0.27 0.62 114 -0.67 2 116
NCOA2 0.011 0.022 -10000 0 -0.44 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.096 0.069 -10000 0 -0.52 7 7
AP-1/NFAT1-c-4 -0.49 0.27 -10000 0 -0.8 136 136
AFP -0.22 0.19 -10000 0 -0.71 41 41
SUV420H1 0.012 0 -10000 0 -10000 0 0
IRF1 0.16 0.13 0.44 23 -10000 0 23
TP53 0.029 0.033 -10000 0 -0.45 2 2
PPP5C 0.012 0 -10000 0 -10000 0 0
KRT17 -0.65 0.3 -10000 0 -0.79 318 318
KRT14 -0.15 0.24 -10000 0 -0.96 23 23
TBP 0.02 0.009 -10000 0 -10000 0 0
CREBBP 0.031 0.077 0.31 7 -10000 0 7
HDAC1 0.012 0.009 -10000 0 -10000 0 0
HDAC2 0.03 0.024 -10000 0 -10000 0 0
AP-1 -0.5 0.28 -10000 0 -0.8 137 137
MAPK14 0.012 0.007 -10000 0 -10000 0 0
MAPK10 -0.054 0.16 -10000 0 -0.44 63 63
MAPK11 0.009 0.052 -10000 0 -0.75 2 2
KRT5 -0.39 0.31 -10000 0 -0.83 113 113
interleukin-1 receptor activity 0.018 0.025 -10000 0 -10000 0 0
NCOA1 0.015 0.001 -10000 0 -10000 0 0
STAT1 0.018 0.036 -10000 0 -0.72 1 1
CGA -0.11 0.15 -10000 0 -0.58 19 19
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.17 0.2 0.39 147 -0.41 8 155
MAPK3 0.011 0.023 -10000 0 -0.44 1 1
MAPK1 0.012 0.007 -10000 0 -10000 0 0
ICAM1 -0.2 0.22 -10000 0 -0.58 59 59
NFKB1 -0.062 0.081 -10000 0 -10000 0 0
MAPK8 -0.21 0.15 -10000 0 -0.43 75 75
MAPK9 0.012 0.007 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.004 0.17 0.49 14 -0.6 5 19
BAX 0.029 0.029 -10000 0 -10000 0 0
POMC -0.15 0.27 -10000 0 -1.3 16 16
EP300 0.034 0.079 0.31 7 -10000 0 7
cortisol/GR alpha (dimer)/p53 0.28 0.22 0.54 115 -0.58 2 117
proteasomal ubiquitin-dependent protein catabolic process 0.071 0.06 0.24 5 -10000 0 5
SGK1 0.028 0.31 0.4 2 -1.3 23 25
IL13 -0.25 0.2 -10000 0 -0.76 31 31
IL6 -0.26 0.33 -10000 0 -0.81 93 93
PRKACG 0.002 0.036 -10000 0 -0.74 1 1
IL5 -0.22 0.16 -10000 0 -0.92 7 7
IL2 -0.32 0.2 -10000 0 -0.7 53 53
CDK5 0.013 0.004 -10000 0 -10000 0 0
PRKACB -0.05 0.16 -10000 0 -0.44 59 59
HSP90AA1 0.012 0 -10000 0 -10000 0 0
IL8 -0.43 0.37 -10000 0 -0.7 260 260
CDK5R1/CDK5 0.017 0.029 -10000 0 -0.55 1 1
NF kappa B1 p50/RelA/PKAc -0.092 0.13 -10000 0 -0.42 15 15
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.26 0.21 0.52 87 -0.54 2 89
SMARCA4 0.011 0.014 -10000 0 -10000 0 0
chromatin remodeling 0.14 0.18 0.38 47 -0.48 14 61
NF kappa B1 p50/RelA/Cbp -0.049 0.14 0.36 3 -0.43 6 9
JUN (dimer) -0.29 0.17 -10000 0 -0.54 84 84
YWHAH 0.012 0 -10000 0 -10000 0 0
VIPR1 -0.12 0.21 -10000 0 -0.71 33 33
NR3C1 0.15 0.19 0.45 53 -0.44 17 70
NR4A1 -0.009 0.14 -10000 0 -0.58 20 20
TIF2/SUV420H1 0.018 0.016 -10000 0 -0.3 1 1
MAPKKK cascade 0.009 0.16 0.48 14 -0.57 5 19
cortisol/GR alpha (dimer)/Src-1 0.27 0.22 0.54 106 -0.58 2 108
PBX1 -0.001 0.078 -10000 0 -0.44 12 12
POU1F1 -0.001 0.049 -10000 0 -0.88 1 1
SELE -0.26 0.33 -10000 0 -0.8 95 95
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.14 0.18 0.39 46 -0.49 14 60
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.26 0.21 0.52 87 -0.54 2 89
mol:cortisol 0.17 0.15 0.35 127 -0.2 1 128
MMP1 -0.46 0.28 -10000 0 -0.66 285 285
IL1-mediated 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
UBC13/UEV1A -0.053 0.18 -9999 0 -0.55 50 50
PRKCZ 0.012 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.012 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.002 0.068 -9999 0 -10000 0 0
IRAK/TOLLIP -0.027 0.14 -9999 0 -0.43 49 49
IKBKB 0.012 0 -9999 0 -10000 0 0
IKBKG 0.011 0.022 -9999 0 -0.44 1 1
IL1 alpha/IL1R2 -0.24 0.27 -9999 0 -0.48 225 225
IL1A -0.24 0.35 -9999 0 -0.74 146 146
IL1B -0.045 0.18 -9999 0 -0.54 50 50
IRAK/TRAF6/p62/Atypical PKCs -0.007 0.13 -9999 0 -0.56 2 2
IL1R2 -0.082 0.18 -9999 0 -0.44 90 90
IL1R1 0.006 0.053 -9999 0 -0.44 6 6
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.003 0.084 -9999 0 -0.32 9 9
TOLLIP 0.012 0 -9999 0 -10000 0 0
TICAM2 0.004 0.057 -9999 0 -0.44 7 7
MAP3K3 0.012 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0.008 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.016 0.1 -9999 0 -10000 0 0
JUN -0.007 0.12 -9999 0 -0.49 1 1
MAP3K7 0.012 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.01 0.13 -9999 0 -0.38 47 47
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.13 0.22 -9999 0 -0.44 146 146
PIK3R1 0.012 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.12 0.21 -9999 0 -0.41 146 146
IL1 beta fragment/IL1R1/IL1RAP -0.025 0.15 -9999 0 -0.43 47 47
NFKB1 0.012 0 -9999 0 -10000 0 0
MAPK8 -0.013 0.12 -9999 0 -0.35 49 49
IRAK1 -0.038 0.16 -9999 0 -0.48 49 49
IL1RN/IL1R1 -0.078 0.21 -9999 0 -0.54 75 75
IRAK4 0.012 0 -9999 0 -10000 0 0
PRKCI 0.01 0.031 -9999 0 -0.44 2 2
TRAF6 0.012 0 -9999 0 -10000 0 0
PI3K 0.018 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.005 0.079 -9999 0 -0.35 1 1
CHUK 0.012 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.025 0.15 -9999 0 -0.43 47 47
IL1 beta/IL1R2 -0.089 0.18 -9999 0 -0.48 49 49
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.02 0.13 -9999 0 -0.38 49 49
NF kappa B1 p50/RelA -0.041 0.11 -9999 0 -10000 0 0
IRAK3 0.001 0.071 -9999 0 -0.44 11 11
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.014 0.14 -9999 0 -0.38 47 47
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.057 0.12 -9999 0 -0.44 2 2
IL1 alpha/IL1R1/IL1RAP -0.15 0.24 -9999 0 -0.48 146 146
RELA 0.012 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.012 0 -9999 0 -10000 0 0
MYD88 0.012 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 -0.018 0.14 -9999 0 -0.4 49 49
IL1RAP 0.012 0 -9999 0 -10000 0 0
UBE2N 0.012 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.077 0.15 -9999 0 -0.58 13 13
CASP1 0.011 0.022 -9999 0 -0.44 1 1
IL1RN/IL1R2 -0.14 0.22 -9999 0 -0.41 159 159
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.016 0.14 -9999 0 -0.4 47 47
TMEM189-UBE2V1 -0.08 0.24 -9999 0 -0.73 50 50
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.053 0.12 -9999 0 -0.37 20 20
PIK3CA 0.012 0.001 -9999 0 -10000 0 0
IL1RN -0.11 0.27 -9999 0 -0.74 69 69
TRAF6/TAK1/TAB1/TAB2 -0.027 0.13 -9999 0 -0.39 49 49
MAP2K6 -0.02 0.13 -9999 0 -0.37 49 49
Visual signal transduction: Rods

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
mol:K + 0.012 0 -9999 0 -10000 0 0
GNAT1/GTP 0 0 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin -0.001 0.041 -9999 0 -0.49 3 3
PDE6G/GNAT1/GTP -0.008 0.064 -9999 0 -0.26 26 26
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0 0 -9999 0 -10000 0 0
GRK1 -0.002 0.05 -9999 0 -0.74 2 2
CNG Channel -0.17 0.16 -9999 0 -0.45 80 80
mol:Na + -0.068 0.15 -9999 0 -0.68 11 11
mol:ADP -0.002 0.05 -9999 0 -0.74 2 2
RGS9-1/Gbeta5/R9AP -0.022 0.1 -9999 0 -0.48 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.066 0.15 -9999 0 -0.7 11 11
CNGB1 -0.045 0.14 -9999 0 -0.44 49 49
RDH5 -0.033 0.14 -9999 0 -0.44 43 43
SAG 0.002 0.005 -9999 0 -10000 0 0
mol:Ca2+ -0.043 0.15 -9999 0 -0.65 11 11
Na + (4 Units) -0.063 0.14 -9999 0 -0.62 11 11
RGS9 -0.06 0.17 -9999 0 -0.44 69 69
GNB1/GNGT1 -0.14 0.26 -9999 0 -0.56 120 120
GNAT1/GDP -0.018 0.089 -9999 0 -0.41 2 2
GUCY2D -0.017 0.14 -9999 0 -0.74 15 15
GNGT1 -0.2 0.33 -9999 0 -0.74 120 120
GUCY2F -0.001 0.036 -9999 0 -0.74 1 1
GNB5 0.012 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.14 0.14 -9999 0 -0.44 31 31
mol:11-cis-retinal -0.033 0.14 -9999 0 -0.44 43 43
mol:cGMP -0.017 0.13 -9999 0 -0.47 31 31
GNB1 0.012 0 -9999 0 -10000 0 0
Rhodopsin -0.026 0.11 -9999 0 -0.33 46 46
SLC24A1 0.012 0 -9999 0 -10000 0 0
CNGA1 -0.031 0.13 -9999 0 -0.44 41 41
Metarhodopsin II -0.003 0.056 -9999 0 -0.55 4 4
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.017 0.13 -9999 0 -0.48 31 31
RGS9BP 0.007 0.051 -9999 0 -0.74 2 2
Metarhodopsin II/Transducin -0.062 0.12 -9999 0 -0.25 121 121
GCAP Family/Ca ++ -0.006 0.094 -9999 0 -0.45 19 19
PDE6A/B -0.19 0.17 -9999 0 -0.32 260 260
mol:Pi -0.022 0.1 -9999 0 -0.48 2 2
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.11 0.2 -9999 0 -0.44 120 120
PDE6B -0.008 0.093 -9999 0 -0.44 19 19
PDE6A -0.26 0.22 -9999 0 -0.44 256 256
PDE6G -0.015 0.11 -9999 0 -0.44 26 26
RHO -0.004 0.061 -9999 0 -0.74 3 3
PDE6 -0.15 0.16 -9999 0 -0.44 65 65
GUCA1A -0.02 0.14 -9999 0 -0.74 17 17
GC2/GCAP Family -0.007 0.1 -9999 0 -0.47 19 19
GUCA1C 0 0 -9999 0 -10000 0 0
GUCA1B 0.009 0.051 -9999 0 -0.74 2 2
Presenilin action in Notch and Wnt 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
Delta 1/NOTCH/NOTCH(cleaved) -0.002 0.02 -10000 0 -10000 0 0
HDAC1 0.009 0.004 -10000 0 -10000 0 0
AES 0.012 0.001 -10000 0 -10000 0 0
FBXW11 0.012 0 -10000 0 -10000 0 0
DTX1 0.008 0.043 -10000 0 -0.44 4 4
LRP6/FZD1 0.018 0.016 -10000 0 -0.3 1 1
TLE1 0.011 0.022 -10000 0 -0.44 1 1
AP1 -0.16 0.14 -10000 0 -0.26 275 275
NCSTN 0.012 0 -10000 0 -10000 0 0
ADAM10 0.012 0 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.057 0.042 -10000 0 -0.47 1 1
NICD/RBPSUH 0.029 0.014 -10000 0 -10000 0 0
WIF1 -0.14 0.29 -10000 0 -0.74 83 83
NOTCH1 -0.001 0.014 -10000 0 -10000 0 0
PSENEN 0.011 0.022 -10000 0 -0.44 1 1
KREMEN2 -0.073 0.24 -10000 0 -0.74 49 49
DKK1 -0.14 0.3 -10000 0 -0.74 86 86
beta catenin/beta TrCP1 0.12 0.081 0.22 1 -10000 0 1
APH1B 0.012 0.001 -10000 0 -10000 0 0
APH1A 0.012 0 -10000 0 -10000 0 0
AXIN1 -0.04 0.04 -10000 0 -0.42 1 1
CtBP/CBP/TCF1/TLE1/AES 0.019 0.022 -10000 0 -10000 0 0
PSEN1 0.012 0 -10000 0 -10000 0 0
FOS 0.005 0.057 -10000 0 -0.44 7 7
JUN 0.012 0 -10000 0 -10000 0 0
MAP3K7 0.011 0.002 -10000 0 -10000 0 0
CTNNB1 0.13 0.087 0.2 198 -10000 0 198
MAPK3 0.011 0.022 -10000 0 -0.44 1 1
DKK2/LRP6/Kremen 2 -0.12 0.24 -10000 0 -0.51 121 121
HNF1A 0.009 0.03 -10000 0 -0.44 2 2
CTBP1 0.012 0.001 -10000 0 -10000 0 0
MYC 0.018 0.066 -10000 0 -0.54 6 6
NKD1 -0.46 0.36 -10000 0 -0.74 275 275
FZD1 0.011 0.022 -10000 0 -0.44 1 1
NOTCH1 precursor/Deltex homolog 1 0.027 0.026 -10000 0 -10000 0 0
apoptosis -0.16 0.14 -10000 0 -0.26 275 275
Delta 1/NOTCHprecursor 0.028 0.023 -10000 0 -10000 0 0
DLL1 0.009 0.038 -10000 0 -0.44 3 3
PPARD 0.022 0.064 -10000 0 -1.3 1 1
Gamma Secretase 0.037 0.012 -10000 0 -10000 0 0
APC -0.047 0.065 -10000 0 -0.45 8 8
DVL1 0.01 0.041 -10000 0 -0.37 1 1
CSNK2A1 0.013 0.001 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.13 0.25 -10000 0 -0.51 125 125
LRP6 0.012 0 -10000 0 -10000 0 0
CSNK1A1 0.013 0.001 -10000 0 -10000 0 0
NLK 0.011 0.005 -10000 0 -10000 0 0
CCND1 0.022 0.048 -10000 0 -0.54 3 3
WNT1 0.003 0.062 -10000 0 -0.74 3 3
Axin1/APC/beta catenin 0.068 0.052 -10000 0 -0.43 1 1
DKK2 -0.13 0.29 -10000 0 -0.74 80 80
NOTCH1 precursor/DVL1 -0.007 0.021 -10000 0 -10000 0 0
GSK3B 0.012 0.001 -10000 0 -10000 0 0
FRAT1 0.011 0.001 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.002 0.022 -10000 0 -10000 0 0
PPP2R5D 0.2 0.15 0.31 275 -10000 0 275
MAPK1 0.012 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.065 0.19 -10000 0 -0.44 85 85
RBPJ 0.012 0 -10000 0 -10000 0 0
CREBBP 0.015 0.002 -10000 0 -10000 0 0
BMP receptor 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
BMP7/BMPR2/BMPR1A-1B/FS -0.17 0.23 -9999 0 -0.43 182 182
SMAD6-7/SMURF1 0.024 0.013 -9999 0 -10000 0 0
NOG 0.007 0.036 -9999 0 -0.74 1 1
SMAD9 -0.049 0.17 -9999 0 -0.56 38 38
SMAD4 0.011 0.022 -9999 0 -0.44 1 1
SMAD5 -0.026 0.11 -9999 0 -0.34 24 24
BMP7/USAG1 -0.26 0.29 -9999 0 -0.52 221 221
SMAD5/SKI -0.019 0.11 -9999 0 -0.39 4 4
SMAD1 0.031 0.023 -9999 0 -10000 0 0
BMP2 -0.018 0.11 -9999 0 -0.44 29 29
SMAD1/SMAD1/SMAD4 -0.001 0.009 -9999 0 -10000 0 0
BMPR1A 0.012 0 -9999 0 -10000 0 0
BMPR1B -0.03 0.16 -9999 0 -0.64 27 27
BMPR1A-1B/BAMBI -0.037 0.16 -9999 0 -0.48 48 48
AHSG -0.11 0.27 -9999 0 -0.74 67 67
CER1 -0.023 0.14 -9999 0 -0.74 16 16
BMP2-4/CER1 -0.045 0.16 -9999 0 -0.52 39 39
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.037 0.13 -9999 0 -0.37 34 34
BMP2-4 (homodimer) -0.035 0.16 -9999 0 -0.45 49 49
RGMB 0.012 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.014 0.12 -9999 0 -0.43 19 19
RGMA -0.083 0.18 -9999 0 -0.44 91 91
SMURF1 0.012 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.041 0.12 -9999 0 -0.37 34 34
BMP2-4/USAG1 -0.07 0.17 -9999 0 -0.55 31 31
SMAD6/SMURF1/SMAD5 -0.019 0.11 -9999 0 -0.35 11 11
SOSTDC1 -0.07 0.17 -9999 0 -0.44 78 78
BMP7/BMPR2/BMPR1A-1B -0.17 0.23 -9999 0 -0.44 178 178
SKI 0.012 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.023 0.12 -9999 0 -0.44 34 34
HFE2 0.001 0.036 -9999 0 -0.74 1 1
ZFYVE16 0.01 0.031 -9999 0 -0.44 2 2
MAP3K7 0.012 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.021 0.14 -9999 0 -0.53 23 23
SMAD5/SMAD5/SMAD4 -0.019 0.11 -9999 0 -0.39 4 4
MAPK1 0.012 0 -9999 0 -10000 0 0
TAK1/TAB family -0.053 0.092 -9999 0 -0.36 12 12
BMP7 (homodimer) -0.28 0.36 -9999 0 -0.72 171 171
NUP214 0.012 0 -9999 0 -10000 0 0
BMP6/FETUA -0.098 0.22 -9999 0 -0.51 93 93
SMAD1/SKI 0.036 0.022 -9999 0 -10000 0 0
SMAD6 0.012 0 -9999 0 -10000 0 0
CTDSP2 0.012 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.1 0.23 -9999 0 -0.53 83 83
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.021 0.14 -9999 0 -0.57 25 25
BMPR2 (homodimer) 0.011 0.022 -9999 0 -0.44 1 1
GADD34/PP1CA 0.024 0.019 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.013 0.12 -9999 0 -0.47 27 27
CHRDL1 -0.23 0.23 -9999 0 -0.44 229 229
ENDOFIN/SMAD1 0.035 0.027 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 0.045 0.021 -9999 0 -10000 0 0
SMAD6/SMURF1 0.012 0 -9999 0 -10000 0 0
BAMBI -0.04 0.19 -9999 0 -0.74 30 30
SMURF2 0.011 0.022 -9999 0 -0.44 1 1
BMP2-4/CHRDL1 -0.16 0.19 -9999 0 -0.57 40 40
BMP2-4/GREM1 -0.042 0.16 -9999 0 -0.52 34 34
SMAD7 0.011 0.022 -9999 0 -0.44 1 1
SMAD8A/SMAD8A/SMAD4 -0.04 0.16 -9999 0 -0.53 37 37
SMAD1/SMAD6 0.036 0.022 -9999 0 -10000 0 0
TAK1/SMAD6 0.018 0 -9999 0 -10000 0 0
BMP7 -0.28 0.36 -9999 0 -0.72 171 171
BMP6 -0.023 0.12 -9999 0 -0.44 34 34
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.035 0.12 -9999 0 -0.34 35 35
PPM1A 0.012 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.036 0.025 -9999 0 -10000 0 0
SMAD7/SMURF1 0.018 0.016 -9999 0 -0.3 1 1
CTDSPL 0.012 0 -9999 0 -10000 0 0
PPP1CA 0.012 0 -9999 0 -10000 0 0
XIAP 0.012 0 -9999 0 -10000 0 0
CTDSP1 0.012 0 -9999 0 -10000 0 0
PPP1R15A 0.012 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.06 0.16 -9999 0 -0.49 39 39
CHRD 0.011 0.022 -9999 0 -0.44 1 1
BMPR2 0.011 0.022 -9999 0 -0.44 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.05 0.14 -9999 0 -0.41 34 34
BMP4 -0.03 0.17 -9999 0 -0.71 25 25
FST -0.009 0.1 -9999 0 -0.47 19 19
BMP2-4/NOG -0.024 0.14 -9999 0 -0.53 24 24
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.16 0.22 -9999 0 -0.42 178 178
HIF-1-alpha transcription factor network

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
PKM2 -0.44 0.35 -9999 0 -1.1 42 42
HDAC7 0.013 0.004 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.33 0.26 -9999 0 -0.9 22 22
SMAD4 0.012 0.022 -9999 0 -0.44 1 1
ID2 -0.44 0.35 -9999 0 -1.1 41 41
AP1 0.015 0.041 -9999 0 -0.3 7 7
ABCG2 -0.62 0.38 -9999 0 -1.1 101 101
HIF1A -0.068 0.05 -9999 0 -10000 0 0
TFF3 -0.45 0.36 -9999 0 -1.1 44 44
GATA2 0.004 0.065 -9999 0 -0.44 9 9
AKT1 -0.067 0.056 -9999 0 -10000 0 0
response to hypoxia -0.084 0.058 -9999 0 -10000 0 0
MCL1 -0.44 0.35 -9999 0 -1.1 41 41
NDRG1 -0.44 0.35 -9999 0 -1.1 41 41
SERPINE1 -0.53 0.42 -9999 0 -1.2 89 89
FECH -0.44 0.35 -9999 0 -1.1 41 41
FURIN -0.44 0.35 -9999 0 -1.1 42 42
NCOA2 0.012 0.022 -9999 0 -0.44 1 1
EP300 -0.064 0.075 -9999 0 -0.36 9 9
HMOX1 -0.45 0.35 -9999 0 -1.1 44 44
BHLHE40 -0.45 0.35 -9999 0 -1.1 42 42
BHLHE41 -0.45 0.36 -9999 0 -1.1 43 43
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.062 0.064 -9999 0 -10000 0 0
ENG -0.046 0.068 -9999 0 -10000 0 0
JUN 0.013 0.002 -9999 0 -10000 0 0
RORA -0.45 0.35 -9999 0 -1.1 44 44
ABCB1 -0.32 0.46 -9999 0 -1.2 95 95
TFRC -0.44 0.35 -9999 0 -1.1 41 41
CXCR4 -0.44 0.35 -9999 0 -1.1 41 41
TF -0.47 0.38 -9999 0 -1.2 50 50
CITED2 -0.44 0.35 -9999 0 -1.1 41 41
HIF1A/ARNT -0.5 0.4 -9999 0 -1.2 55 55
LDHA -0.053 0.043 -9999 0 -10000 0 0
ETS1 -0.44 0.35 -9999 0 -1.1 41 41
PGK1 -0.44 0.35 -9999 0 -1.1 41 41
NOS2 -0.46 0.37 -9999 0 -1.1 50 50
ITGB2 -0.45 0.35 -9999 0 -1.1 43 43
ALDOA -0.44 0.35 -9999 0 -1.1 41 41
Cbp/p300/CITED2 -0.43 0.36 -9999 0 -1.2 33 33
FOS 0.006 0.057 -9999 0 -0.44 7 7
HK2 -0.44 0.35 -9999 0 -1.1 41 41
SP1 0.008 0.03 -9999 0 -10000 0 0
GCK -0.11 0.22 -9999 0 -1.3 11 11
HK1 -0.44 0.35 -9999 0 -1.1 41 41
NPM1 -0.44 0.35 -9999 0 -1.1 41 41
EGLN1 -0.44 0.35 -9999 0 -1.1 41 41
CREB1 0.019 0 -9999 0 -10000 0 0
PGM1 -0.45 0.35 -9999 0 -1.1 43 43
SMAD3 0.011 0.031 -9999 0 -0.44 2 2
EDN1 -0.05 0.14 -9999 0 -0.98 5 5
IGFBP1 -0.51 0.4 -9999 0 -1.2 73 73
VEGFA -0.28 0.25 -9999 0 -0.88 13 13
HIF1A/JAB1 -0.033 0.03 -9999 0 -10000 0 0
CP -0.54 0.39 -9999 0 -1.1 79 79
CXCL12 -0.48 0.38 -9999 0 -1.1 59 59
COPS5 0.013 0.001 -9999 0 -10000 0 0
SMAD3/SMAD4 0.018 0.027 -9999 0 -0.3 3 3
BNIP3 -0.44 0.35 -9999 0 -1.1 40 40
EGLN3 -0.44 0.35 -9999 0 -1.1 45 45
CA9 -0.72 0.42 -9999 0 -1.1 155 155
TERT -0.48 0.38 -9999 0 -1.2 59 59
ENO1 -0.44 0.35 -9999 0 -1.1 41 41
PFKL -0.44 0.35 -9999 0 -1.1 42 42
NCOA1 0.012 0 -9999 0 -10000 0 0
ADM -0.44 0.35 -9999 0 -1.1 41 41
ARNT -0.069 0.054 -9999 0 -0.5 1 1
HNF4A 0.014 0.013 -9999 0 -10000 0 0
ADFP -0.45 0.35 -9999 0 -1.1 55 55
SLC2A1 -0.29 0.27 -9999 0 -1 18 18
LEP -0.46 0.37 -9999 0 -1.1 53 53
HIF1A/ARNT/Cbp/p300 -0.34 0.28 -9999 0 -0.92 24 24
EPO -0.24 0.2 -9999 0 -0.88 3 3
CREBBP -0.064 0.075 -9999 0 -0.36 9 9
HIF1A/ARNT/Cbp/p300/HDAC7 -0.33 0.27 -9999 0 -0.92 25 25
PFKFB3 -0.44 0.35 -9999 0 -1.1 41 41
NT5E -0.45 0.35 -9999 0 -1.1 44 44
Caspase cascade in apoptosis

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
TOP1 -0.045 0.13 -10000 0 -0.46 3 3
ACTA1 -0.071 0.16 -10000 0 -0.35 106 106
NUMA1 -0.046 0.13 -10000 0 -0.28 98 98
SPTAN1 -0.067 0.16 -10000 0 -0.35 99 99
LIMK1 -0.067 0.16 -10000 0 -0.35 99 99
BIRC3 0.003 0.067 -10000 0 -0.48 8 8
BIRC2 0.012 0.001 -10000 0 -10000 0 0
BAX 0.012 0 -10000 0 -10000 0 0
CASP10 -0.1 0.22 -10000 0 -0.49 102 102
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.012 0 -10000 0 -10000 0 0
PTK2 -0.045 0.13 -10000 0 -0.28 96 96
DIABLO 0.012 0.001 -10000 0 -10000 0 0
apoptotic nuclear changes -0.066 0.16 -10000 0 -0.34 99 99
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.012 0 -10000 0 -10000 0 0
GSN -0.071 0.16 -10000 0 -0.35 100 100
MADD 0.012 0 -10000 0 -10000 0 0
TFAP2A -0.064 0.11 -10000 0 -0.57 3 3
BID -0.038 0.1 -10000 0 -0.22 102 102
MAP3K1 -0.02 0.063 -10000 0 -0.25 2 2
TRADD 0.012 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.019 0.001 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.067 0.16 -10000 0 -0.35 99 99
CASP9 0.013 0.001 -10000 0 -10000 0 0
DNA repair 0.015 0.049 -10000 0 -0.16 5 5
neuron apoptosis 0.011 0.036 -10000 0 -0.62 1 1
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.057 0.16 -10000 0 -0.33 98 98
APAF1 0.012 0.001 -10000 0 -10000 0 0
CASP6 -0.01 0.08 -10000 0 -10000 0 0
TRAF2 0.011 0.022 -10000 0 -0.44 1 1
ICAD/CAD -0.059 0.16 -10000 0 -0.33 98 98
CASP7 0.002 0.044 0.26 8 -0.43 1 9
KRT18 0.006 0.024 -10000 0 -10000 0 0
apoptosis -0.051 0.15 -10000 0 -0.53 3 3
DFFA -0.067 0.16 -10000 0 -0.35 99 99
DFFB -0.067 0.16 -10000 0 -0.35 99 99
PARP1 -0.015 0.049 0.16 5 -10000 0 5
actin filament polymerization 0.06 0.15 0.55 3 -10000 0 3
TNF 0.01 0.031 -10000 0 -0.44 2 2
CYCS -0.027 0.083 -10000 0 -0.23 7 7
SATB1 -0.008 0.08 -10000 0 -10000 0 0
SLK -0.068 0.16 -10000 0 -0.35 99 99
p15 BID/BAX -0.027 0.092 -10000 0 -0.32 4 4
CASP2 0.038 0.032 -10000 0 -0.36 1 1
JNK cascade 0.02 0.063 0.25 2 -10000 0 2
CASP3 -0.077 0.17 -10000 0 -0.37 105 105
LMNB2 0.025 0.036 -10000 0 -10000 0 0
RIPK1 0.012 0 -10000 0 -10000 0 0
CASP4 0.012 0 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.027 0.039 -10000 0 -0.43 1 1
negative regulation of DNA binding -0.064 0.1 -10000 0 -0.56 3 3
stress fiber formation -0.067 0.16 -10000 0 -0.34 99 99
GZMB -0.12 0.25 -10000 0 -0.55 108 108
CASP1 0.014 0.015 -10000 0 -0.29 1 1
LMNB1 0.025 0.036 -10000 0 -10000 0 0
APP 0.011 0.037 -10000 0 -0.63 1 1
TNFRSF1A 0.012 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.01 0 -10000 0 -10000 0 0
VIM -0.053 0.14 -10000 0 -0.51 3 3
LMNA 0.025 0.036 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.034 0.034 -10000 0 -0.38 1 1
LRDD 0.011 0.022 -10000 0 -0.44 1 1
SREBF1 -0.067 0.16 -10000 0 -0.35 99 99
APAF-1/Caspase 9 -0.013 0.032 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis -0.045 0.13 -10000 0 -0.27 98 98
CFL2 -0.062 0.15 -10000 0 -0.57 3 3
GAS2 -0.14 0.24 -10000 0 -0.44 150 150
positive regulation of apoptosis 0.029 0.035 -10000 0 -10000 0 0
PRF1 0.003 0.067 -10000 0 -0.48 8 8
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.018 0 -9999 0 -10000 0 0
Necdin/E2F1 -0.008 0.11 -9999 0 -0.41 27 27
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.041 0.12 -9999 0 -0.42 11 11
NGF (dimer)/p75(NTR)/BEX1 -0.14 0.19 -9999 0 -0.51 57 57
NT-4/5 (dimer)/p75(NTR) -0.1 0.18 -9999 0 -0.35 136 136
IKBKB 0.012 0 -9999 0 -10000 0 0
AKT1 -0.042 0.12 -9999 0 -0.41 10 10
IKBKG 0.011 0.022 -9999 0 -0.44 1 1
BDNF -0.005 0.11 -9999 0 -0.74 10 10
MGDIs/NGR/p75(NTR)/LINGO1 -0.095 0.19 -9999 0 -0.56 34 34
FURIN 0.011 0.022 -9999 0 -0.44 1 1
proBDNF (dimer)/p75(NTR)/Sortilin -0.064 0.14 -9999 0 -0.5 10 10
LINGO1 -0.024 0.16 -9999 0 -0.74 21 21
Sortilin/TRAF6/NRIF -0.002 0.017 -9999 0 -10000 0 0
proBDNF (dimer) -0.005 0.11 -9999 0 -0.74 10 10
NTRK1 0.004 0.072 -9999 0 -0.74 4 4
RTN4R -0.017 0.14 -9999 0 -0.72 17 17
neuron apoptosis -0.051 0.14 -9999 0 -0.62 3 3
IRAK1 0.012 0 -9999 0 -10000 0 0
SHC1 -0.065 0.14 -9999 0 -0.49 10 10
ARHGDIA 0.011 0.022 -9999 0 -0.44 1 1
RhoA/GTP 0.009 0 -9999 0 -10000 0 0
Gamma Secretase 0.036 0.012 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.053 0.13 -9999 0 -0.47 10 10
MAGEH1 0.007 0.049 -9999 0 -0.44 5 5
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.06 0.14 -9999 0 -0.46 21 21
Mammalian IAPs/DIABLO 0.027 0.039 -9999 0 -0.43 1 1
proNGF (dimer) -0.008 0.095 -9999 0 -0.46 18 18
MAGED1 0.012 0 -9999 0 -10000 0 0
APP 0.011 0.022 -9999 0 -0.44 1 1
NT-4/5 (dimer) -0.026 0.15 -9999 0 -0.74 18 18
ZNF274 0.008 0.043 -9999 0 -0.44 4 4
RhoA/GDP/RHOGDI -0.048 0.12 -9999 0 -0.42 10 10
NGF -0.008 0.095 -9999 0 -0.46 18 18
cell cycle arrest -0.034 0.12 -9999 0 -0.4 10 10
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.043 0.12 -9999 0 -0.42 9 9
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.078 0.15 -9999 0 -0.53 18 18
NCSTN 0.012 0 -9999 0 -10000 0 0
mol:GTP -0.1 0.17 -9999 0 -0.5 30 30
PSENEN 0.011 0.022 -9999 0 -0.44 1 1
mol:ceramide -0.052 0.12 -9999 0 -0.44 10 10
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.03 0.1 -9999 0 -0.36 9 9
p75(NTR)/beta APP -0.074 0.15 -9999 0 -0.3 123 123
BEX1 -0.12 0.2 -9999 0 -0.44 118 118
mol:GDP -0.073 0.14 -9999 0 -0.27 131 131
NGF (dimer) -0.51 0.18 -9999 0 -0.52 419 419
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.079 0.17 -9999 0 -0.52 34 34
PIK3R1 0.012 0 -9999 0 -10000 0 0
RAC1/GTP -0.054 0.12 -9999 0 -0.43 10 10
MYD88 0.012 0 -9999 0 -10000 0 0
CHUK 0.012 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.1 0.17 -9999 0 -0.51 30 30
RHOB 0.012 0 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 0.005 0.086 -9999 0 -0.56 10 10
NT3 (dimer) 0.002 0.065 -9999 0 -0.44 9 9
TP53 -0.037 0.12 -9999 0 -0.58 1 1
PRDM4 -0.052 0.12 -9999 0 -0.44 10 10
BDNF (dimer) -0.85 0.25 -9999 0 -0.86 429 429
PIK3CA 0.012 0.001 -9999 0 -10000 0 0
SORT1 0.012 0 -9999 0 -10000 0 0
activation of caspase activity -0.043 0.12 -9999 0 -0.41 11 11
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.05 0.13 -9999 0 -0.44 10 10
RHOC 0.012 0 -9999 0 -10000 0 0
XIAP 0.012 0 -9999 0 -10000 0 0
MAPK10 -0.072 0.17 -9999 0 -0.46 36 36
DIABLO 0.012 0.001 -9999 0 -10000 0 0
SMPD2 -0.052 0.12 -9999 0 -0.44 10 10
APH1B 0.012 0.001 -9999 0 -10000 0 0
APH1A 0.012 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.064 0.14 -9999 0 -0.49 10 10
PSEN1 0.012 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.018 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.08 0.15 -9999 0 -0.31 128 128
MAPK8 -0.041 0.14 -9999 0 -0.51 1 1
MAPK9 -0.041 0.14 -9999 0 -0.51 1 1
APAF1 0.012 0.001 -9999 0 -10000 0 0
NTF3 0.002 0.065 -9999 0 -0.44 9 9
NTF4 -0.026 0.15 -9999 0 -0.74 18 18
NDN -0.007 0.091 -9999 0 -0.44 18 18
RAC1/GDP 0.009 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.085 0.12 -9999 0 -0.4 30 30
p75 CTF/Sortilin/TRAF6/NRIF 0.029 0.024 -9999 0 -10000 0 0
RhoA-B-C/GTP -0.1 0.17 -9999 0 -0.5 30 30
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.042 0.12 -9999 0 -0.42 12 12
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.05 0.13 -9999 0 -0.46 10 10
PRKACB -0.05 0.16 -9999 0 -0.44 59 59
proBDNF (dimer)/p75 ECD 0.005 0.086 -9999 0 -0.56 10 10
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 0.003 0.067 -9999 0 -0.48 8 8
BIRC2 0.012 0.001 -9999 0 -10000 0 0
neuron projection morphogenesis -0.067 0.15 -9999 0 -0.41 27 27
BAD -0.052 0.15 -9999 0 -0.49 6 6
RIPK2 0.012 0 -9999 0 -10000 0 0
NGFR -0.12 0.2 -9999 0 -0.44 122 122
CYCS -0.043 0.12 -9999 0 -0.41 10 10
ADAM17 0.012 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.05 0.13 -9999 0 -0.44 10 10
BCL2L11 -0.052 0.15 -9999 0 -0.49 6 6
BDNF (dimer)/p75(NTR) -0.086 0.16 -9999 0 -0.33 131 131
PI3K -0.05 0.13 -9999 0 -0.44 10 10
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.05 0.13 -9999 0 -0.44 10 10
NDNL2 0.012 0.001 -9999 0 -10000 0 0
YWHAE 0.012 0 -9999 0 -10000 0 0
PRKCI 0.01 0.031 -9999 0 -0.44 2 2
NGF (dimer)/p75(NTR) -0.087 0.16 -9999 0 -0.33 131 131
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.05 0.13 -9999 0 -0.44 10 10
TRAF6 0.012 0 -9999 0 -10000 0 0
RAC1 0.012 0 -9999 0 -10000 0 0
PRKCZ 0.012 0 -9999 0 -10000 0 0
PLG -0.14 0.29 -9999 0 -0.74 82 82
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.063 0.14 -9999 0 -0.47 10 10
SQSTM1 0.012 0 -9999 0 -10000 0 0
NGFRAP1 0.011 0.022 -9999 0 -0.44 1 1
CASP3 -0.048 0.15 -9999 0 -0.45 6 6
E2F1 -0.005 0.11 -9999 0 -0.74 10 10
CASP9 0.012 0 -9999 0 -10000 0 0
IKK complex -0.049 0.086 -9999 0 -0.41 10 10
NGF (dimer)/TRKA -0.003 0.087 -9999 0 -0.52 6 6
MMP7 -0.71 0.14 -9999 0 -0.74 416 416
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.042 0.12 -9999 0 -0.42 12 12
MMP3 -0.61 0.28 -9999 0 -0.74 359 359
APAF-1/Caspase 9 -0.047 0.077 -9999 0 -0.47 1 1
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.01 0.043 -9999 0 -0.28 4 4
NFATC2 -0.017 0.059 -9999 0 -0.3 9 9
NFATC3 -0.008 0.034 -9999 0 -10000 0 0
CD40LG -0.15 0.25 -9999 0 -0.68 32 32
PTGS2 -0.15 0.28 -9999 0 -0.78 40 40
JUNB 0.01 0.031 -9999 0 -0.44 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.009 0.02 -9999 0 -10000 0 0
CaM/Ca2+ -0.009 0.02 -9999 0 -10000 0 0
CALM1 0.005 0.011 -9999 0 -10000 0 0
JUN 0.006 0.011 -9999 0 -10000 0 0
mol:Ca2+ -0.011 0.014 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.003 0.007 -9999 0 -10000 0 0
FOSL1 -0.47 0.36 -9999 0 -0.74 280 280
CREM 0.012 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.069 0.15 -9999 0 -0.55 7 7
FOS -0.002 0.058 -9999 0 -0.44 7 7
IFNG -0.17 0.28 -9999 0 -0.69 66 66
AP-1/NFAT1-c-4 -0.15 0.27 -9999 0 -0.64 56 56
FASLG -0.14 0.24 -9999 0 -0.7 25 25
NFAT1-c-4/ICER1 -0.042 0.086 -9999 0 -0.5 1 1
IL2RA -0.13 0.24 -9999 0 -0.67 21 21
FKBP12/FK506 0.009 0 -9999 0 -10000 0 0
CSF2 -0.27 0.36 -9999 0 -0.66 181 181
JunB/Fra1/NFAT1-c-4 -0.29 0.22 -9999 0 -0.49 173 173
IL4 -0.14 0.23 -9999 0 -0.65 17 17
IL2 -0.007 0.012 -9999 0 -10000 0 0
IL3 -0.018 0.019 -9999 0 -10000 0 0
FKBP1A 0.012 0 -9999 0 -10000 0 0
BATF3 0.004 0.075 -9999 0 -0.68 5 5
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.012 0.001 -9999 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 0.02 0.14 -10000 0 -0.61 17 17
IHH 0.005 0.088 -10000 0 -0.5 12 12
SHH Np/Cholesterol/GAS1 -0.092 0.2 -10000 0 -0.48 78 78
LRPAP1 0.012 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.091 0.2 0.48 78 -10000 0 78
SMO/beta Arrestin2 0.016 0.096 -10000 0 -0.54 5 5
SMO 0.01 0.1 -10000 0 -0.58 5 5
AKT1 0.025 0.049 -10000 0 -10000 0 0
ARRB2 0.012 0 -10000 0 -10000 0 0
BOC 0.003 0.065 -10000 0 -0.44 9 9
ADRBK1 0.012 0 -10000 0 -10000 0 0
heart looping 0.011 0.099 -10000 0 -0.57 5 5
STIL -0.038 0.17 -10000 0 -0.56 5 5
DHH N/PTCH2 0.003 0.07 -10000 0 -0.32 19 19
DHH N/PTCH1 0.014 0.1 -10000 0 -0.59 4 4
PIK3CA 0.012 0.001 -10000 0 -10000 0 0
DHH -0.007 0.091 -10000 0 -0.44 18 18
PTHLH 0.018 0.16 -10000 0 -0.95 7 7
determination of left/right symmetry 0.011 0.099 -10000 0 -0.57 5 5
PIK3R1 0.012 0 -10000 0 -10000 0 0
skeletal system development 0.018 0.16 -10000 0 -0.93 7 7
IHH N/Hhip -0.063 0.16 -10000 0 -0.35 95 95
DHH N/Hhip -0.064 0.15 -10000 0 -0.33 102 102
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.011 0.099 -10000 0 -0.57 5 5
pancreas development -0.086 0.19 -10000 0 -0.44 93 93
HHAT 0.008 0.043 -10000 0 -0.44 4 4
PI3K 0.018 0 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.05 0.16 -10000 0 -0.46 57 57
somite specification 0.011 0.099 -10000 0 -0.57 5 5
SHH Np/Cholesterol/PTCH1 -0.045 0.17 -10000 0 -0.56 6 6
SHH Np/Cholesterol/PTCH2 -0.06 0.17 -10000 0 -0.44 74 74
SHH Np/Cholesterol/Megalin -0.1 0.21 -10000 0 -0.47 102 102
SHH -0.081 0.22 -10000 0 -0.54 77 77
catabolic process 0.022 0.092 -10000 0 -0.55 5 5
SMO/Vitamin D3 -0.034 0.17 -10000 0 -0.57 6 6
SHH Np/Cholesterol/Hhip -0.11 0.19 -10000 0 -0.46 76 76
LRP2 -0.056 0.2 -10000 0 -0.74 36 36
receptor-mediated endocytosis -0.049 0.18 -10000 0 -0.59 13 13
SHH Np/Cholesterol/BOC -0.064 0.18 -10000 0 -0.44 73 73
SHH Np/Cholesterol/CDO -0.059 0.17 -10000 0 -0.44 73 73
mesenchymal cell differentiation 0.11 0.19 0.46 76 -10000 0 76
mol:Vitamin D3 -0.042 0.18 -10000 0 -0.56 6 6
IHH N/PTCH2 0.013 0.061 -10000 0 -0.4 5 5
CDON 0.012 0 -10000 0 -10000 0 0
IHH N/PTCH1 0.023 0.093 -10000 0 -0.56 5 5
Megalin/LRPAP1 -0.034 0.16 -10000 0 -0.56 36 36
PTCH2 0.01 0.036 -10000 0 -0.74 1 1
SHH Np/Cholesterol -0.066 0.17 -10000 0 -0.44 73 73
PTCH1 0.022 0.093 -10000 0 -0.55 5 5
HHIP -0.086 0.19 -10000 0 -0.44 93 93
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.003 0.1 -9999 0 -0.48 18 18
EPHB2 0.009 0.051 -9999 0 -0.74 2 2
Syndecan-2/TACI -0.094 0.13 -9999 0 -0.49 1 1
LAMA1 -0.11 0.2 -9999 0 -0.44 115 115
Syndecan-2/alpha2 ITGB1 0.031 0.033 -9999 0 -0.4 1 1
HRAS 0.011 0.022 -9999 0 -0.44 1 1
Syndecan-2/CASK 0.012 0.013 -9999 0 -0.26 1 1
ITGA5 0.009 0.051 -9999 0 -0.74 2 2
BAX 0.033 0.012 -9999 0 -10000 0 0
EPB41 0.012 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion 0.018 0.02 -9999 0 -10000 0 0
LAMA3 0.006 0.056 -9999 0 -0.5 5 5
EZR 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.003 0.078 -9999 0 -0.64 6 6
Syndecan-2/MMP2 0.018 0.041 -9999 0 -0.34 5 5
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 0.018 0 -9999 0 -10000 0 0
dendrite morphogenesis 0.019 0.036 -9999 0 -0.4 3 3
Syndecan-2/GM-CSF -0.18 0.24 -9999 0 -0.48 174 174
determination of left/right symmetry 0.016 0.015 -9999 0 -0.3 1 1
Syndecan-2/PKC delta 0.021 0.013 -9999 0 -10000 0 0
GNB2L1 0.012 0 -9999 0 -10000 0 0
MAPK3 -0.16 0.23 -9999 0 -0.43 174 174
MAPK1 -0.16 0.22 -9999 0 -0.43 174 174
Syndecan-2/RACK1 0.026 0.016 -9999 0 -10000 0 0
NF1 0.012 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.016 0.015 -9999 0 -0.3 1 1
ITGA2 0.012 0 -9999 0 -10000 0 0
MAPK8 0.028 0.013 -9999 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin -0.028 0.1 -9999 0 -10000 0 0
Syndecan-2/Kininogen -0.044 0.12 -9999 0 -0.49 1 1
ITGB1 0.012 0 -9999 0 -10000 0 0
SRC 0.03 0.015 -9999 0 -10000 0 0
Syndecan-2/CASK/Protein 4.1 0.019 0.012 -9999 0 -10000 0 0
extracellular matrix organization 0.02 0.027 -9999 0 -0.48 1 1
actin cytoskeleton reorganization -0.003 0.1 -9999 0 -0.48 18 18
Syndecan-2/Caveolin-2/Ras 0.022 0.052 -9999 0 -0.44 5 5
Syndecan-2/Laminin alpha3 0.018 0.038 -9999 0 -0.48 1 1
Syndecan-2/RasGAP 0.031 0.015 -9999 0 -10000 0 0
alpha5/beta1 Integrin 0.016 0.039 -9999 0 -0.56 2 2
PRKCD 0.012 0 -9999 0 -10000 0 0
Syndecan-2 dimer 0.019 0.036 -9999 0 -0.4 3 3
GO:0007205 0.003 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.037 0.015 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
SDCBP 0.01 0.031 -9999 0 -0.44 2 2
TNFRSF13B -0.18 0.22 -9999 0 -0.44 181 181
RASA1 0.012 0.001 -9999 0 -10000 0 0
alpha2/beta1 Integrin 0.018 0 -9999 0 -10000 0 0
Syndecan-2/Synbindin 0.021 0.013 -9999 0 -0.25 1 1
TGFB1 0.011 0.036 -9999 0 -0.74 1 1
CASP3 0.027 0.012 -9999 0 -10000 0 0
FN1 -0.025 0.16 -9999 0 -0.66 24 24
Syndecan-2/IL8 -0.28 0.24 -9999 0 -0.48 259 259
SDC2 0.016 0.015 -9999 0 -0.3 1 1
KNG1 -0.096 0.19 -9999 0 -0.44 100 100
Syndecan-2/Neurofibromin 0.021 0.013 -9999 0 -10000 0 0
TRAPPC4 0.012 0 -9999 0 -10000 0 0
CSF2 -0.29 0.37 -9999 0 -0.74 174 174
Syndecan-2/TGFB1 0.02 0.027 -9999 0 -0.48 1 1
Syndecan-2/Syntenin/PI-4-5-P2 0.018 0.02 -9999 0 -10000 0 0
Syndecan-2/Ezrin 0.028 0.012 -9999 0 -10000 0 0
PRKACA 0.027 0.012 -9999 0 -10000 0 0
angiogenesis -0.28 0.24 -9999 0 -0.48 259 259
MMP2 0.007 0.059 -9999 0 -0.59 4 4
IL8 -0.44 0.37 -9999 0 -0.74 259 259
calcineurin-NFAT signaling pathway -0.094 0.13 -9999 0 -0.49 1 1
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 -0.007 0.12 -9999 0 -0.46 18 18
MAP4K1 -0.033 0.14 -9999 0 -0.44 43 43
MAP3K8 0.012 0 -9999 0 -10000 0 0
PRKCB -0.089 0.19 -9999 0 -0.44 96 96
DBNL 0.012 0 -9999 0 -10000 0 0
CRKL 0.012 0 -9999 0 -10000 0 0
MAP3K1 0.007 0.097 -9999 0 -0.39 17 17
JUN -0.099 0.25 -9999 0 -0.56 96 96
MAP3K7 0.008 0.096 -9999 0 -0.39 17 17
GRAP2 -0.006 0.088 -9999 0 -0.44 17 17
CRK 0.012 0 -9999 0 -10000 0 0
MAP2K4 0.013 0.097 -9999 0 -0.38 17 17
LAT 0.008 0.047 -9999 0 -0.54 3 3
LCP2 0.008 0.043 -9999 0 -0.44 4 4
MAPK8 -0.11 0.26 -9999 0 -0.6 96 96
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.002 0.1 -9999 0 -0.42 17 17
LAT/GRAP2/SLP76/HPK1/HIP-55 0 0.11 -9999 0 -0.43 18 18
Ephrin B reverse signaling

Figure S28.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S28.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.012 0 -10000 0 -10000 0 0
EPHB2 0.008 0.051 -10000 0 -0.74 2 2
EFNB1 0.013 0.055 -10000 0 -0.56 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.093 0.2 -10000 0 -0.57 16 16
Ephrin B2/EPHB1-2 -0.094 0.2 -10000 0 -0.44 109 109
neuron projection morphogenesis -0.11 0.17 -10000 0 -0.54 17 17
Ephrin B1/EPHB1-2/Tiam1 -0.1 0.21 -10000 0 -0.43 112 112
DNM1 0.005 0.072 -10000 0 -0.74 4 4
cell-cell signaling -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.001 0.083 -10000 0 -0.68 5 5
YES1 -0.014 0.1 -10000 0 -0.89 5 5
Ephrin B1/EPHB1-2/NCK2 -0.081 0.2 -10000 0 -0.41 112 112
PI3K 0.003 0.083 -10000 0 -0.68 5 5
mol:GDP -0.1 0.21 -10000 0 -0.43 112 112
ITGA2B -0.022 0.15 -10000 0 -0.74 19 19
endothelial cell proliferation 0.016 0.001 -10000 0 -10000 0 0
FYN -0.014 0.1 -10000 0 -0.89 5 5
MAP3K7 -0.006 0.086 -10000 0 -0.72 5 5
FGR -0.016 0.11 -10000 0 -0.83 6 6
TIAM1 -0.032 0.13 -10000 0 -0.44 42 42
PIK3R1 0.012 0 -10000 0 -10000 0 0
RGS3 0.012 0 -10000 0 -10000 0 0
cell adhesion -0.006 0.12 -10000 0 -0.44 24 24
LYN -0.014 0.1 -10000 0 -0.89 5 5
Ephrin B1/EPHB1-2/Src Family Kinases -0.015 0.095 -10000 0 -0.82 5 5
Ephrin B1/EPHB1-2 -0.02 0.091 -10000 0 -0.42 16 16
SRC -0.015 0.1 -10000 0 -0.89 5 5
ITGB3 0.008 0.043 -10000 0 -0.44 4 4
EPHB1 -0.18 0.32 -10000 0 -0.74 109 109
EPHB4 0.012 0 -10000 0 -10000 0 0
RAC1 0.012 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.016 0.001 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.011 0.12 -10000 0 -0.51 23 23
BLK -0.076 0.13 -10000 0 -0.61 13 13
HCK -0.02 0.11 -10000 0 -0.86 6 6
regulation of stress fiber formation 0.081 0.2 0.41 112 -10000 0 112
MAPK8 0.005 0.079 -10000 0 -0.64 5 5
Ephrin B1/EPHB1-2/RGS3 -0.081 0.2 -10000 0 -0.41 112 112
endothelial cell migration -0.001 0.076 -10000 0 -0.62 5 5
NCK2 0.012 0 -10000 0 -10000 0 0
PTPN13 -0.009 0.12 -10000 0 -0.65 16 16
regulation of focal adhesion formation 0.081 0.2 0.41 112 -10000 0 112
chemotaxis 0.081 0.2 0.41 112 -10000 0 112
PIK3CA 0.012 0.001 -10000 0 -10000 0 0
Rac1/GTP -0.11 0.18 -10000 0 -0.56 16 16
angiogenesis -0.02 0.091 -10000 0 -0.41 16 16
LCK -0.017 0.1 -10000 0 -0.89 5 5
TCGA08_p53

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
CDKN2A -0.12 0.24 -10000 0 -0.56 95 95
TP53 -0.031 0.06 -10000 0 -10000 0 0
Senescence -0.031 0.059 -10000 0 -10000 0 0
Apoptosis -0.031 0.059 -10000 0 -10000 0 0
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.058 0.11 0.27 94 -10000 0 94
MDM4 0.012 0 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A -0.022 0.13 -9999 0 -0.56 24 24
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B 0.008 0.061 -9999 0 -0.56 5 5
STXBP1 0.004 0.08 -9999 0 -0.74 5 5
ACh/CHRNA1 -0.05 0.095 -9999 0 -0.31 40 40
RAB3GAP2/RIMS1/UNC13B 0.016 0.055 -9999 0 -0.48 5 5
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 -0.001 0.08 -9999 0 -0.74 5 5
mol:ACh -0.042 0.061 -9999 0 -0.11 179 179
RAB3GAP2 0.011 0.022 -9999 0 -0.44 1 1
STX1A/SNAP25/VAMP2 -0.071 0.11 -9999 0 -0.39 34 34
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.05 0.095 -9999 0 -0.31 40 40
UNC13B 0.012 0 -9999 0 -10000 0 0
CHRNA1 -0.03 0.13 -9999 0 -0.44 40 40
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.063 0.11 -9999 0 -0.32 61 61
SNAP25 -0.096 0.13 -9999 0 -0.26 163 163
VAMP2 0.006 0 -9999 0 -10000 0 0
SYT1 -0.052 0.16 -9999 0 -0.44 61 61
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.017 0.12 -9999 0 -0.48 29 29
STX1A/SNAP25 fragment 1/VAMP2 -0.071 0.11 -9999 0 -0.39 34 34
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.018 0.16 -10000 0 -0.81 17 17
NFATC2 -0.027 0.18 -10000 0 -0.7 11 11
NFATC3 -0.021 0.056 -10000 0 -10000 0 0
CD40LG -0.34 0.36 -10000 0 -0.96 60 60
ITCH 0.038 0.033 -10000 0 -0.52 1 1
CBLB 0.038 0.033 -10000 0 -0.52 1 1
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.18 0.27 -10000 0 -0.94 31 31
JUNB 0.01 0.031 -10000 0 -0.44 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.032 0.027 -10000 0 -10000 0 0
T cell anergy 0.036 0.052 -10000 0 -10000 0 0
TLE4 -0.006 0.13 -10000 0 -0.61 8 8
Jun/NFAT1-c-4/p21SNFT -0.16 0.25 -10000 0 -1 13 13
AP-1/NFAT1-c-4 -0.36 0.4 -10000 0 -1.1 56 56
IKZF1 -0.042 0.22 -10000 0 -0.7 40 40
T-helper 2 cell differentiation -0.098 0.18 -10000 0 -0.77 15 15
AP-1/NFAT1 -0.081 0.13 -10000 0 -0.6 4 4
CALM1 0.023 0.016 -10000 0 -10000 0 0
EGR2 -0.061 0.24 -10000 0 -1.2 10 10
EGR3 -0.067 0.25 -10000 0 -1.2 13 13
NFAT1/FOXP3 -0.031 0.19 -10000 0 -0.66 25 25
EGR1 0.012 0.022 -10000 0 -0.44 1 1
JUN -0.029 0.036 -10000 0 -10000 0 0
EGR4 -0.12 0.28 -10000 0 -0.73 75 75
mol:Ca2+ 0.011 0.016 -10000 0 -10000 0 0
GBP3 -0.047 0.22 -10000 0 -0.67 42 42
FOSL1 -0.47 0.36 -10000 0 -0.74 280 280
NFAT1-c-4/MAF/IRF4 -0.15 0.28 -10000 0 -0.98 22 22
DGKA -0.006 0.14 -10000 0 -0.67 7 7
CREM 0.012 0 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.083 0.23 -10000 0 -1 12 12
CTLA4 -0.035 0.21 -10000 0 -0.8 20 20
NFAT1-c-4 (dimer)/EGR1 -0.079 0.23 -10000 0 -1 12 12
NFAT1-c-4 (dimer)/EGR4 -0.16 0.28 -10000 0 -0.99 19 19
FOS -0.036 0.065 -10000 0 -0.45 7 7
IFNG -0.13 0.25 -10000 0 -0.67 51 51
T cell activation -0.11 0.16 -10000 0 -0.77 4 4
MAF 0 0.075 -10000 0 -0.44 12 12
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.059 0.2 0.99 10 -10000 0 10
TNF -0.12 0.24 -10000 0 -1 11 11
FASLG -0.14 0.4 -10000 0 -1.3 37 37
TBX21 -0.02 0.11 -10000 0 -0.44 26 26
BATF3 0.004 0.075 -10000 0 -0.68 5 5
PRKCQ 0.002 0.066 -10000 0 -0.45 8 8
PTPN1 -0.004 0.12 -10000 0 -0.57 6 6
NFAT1-c-4/ICER1 -0.083 0.23 -10000 0 -1 12 12
GATA3 0.007 0.056 -10000 0 -0.5 5 5
T-helper 1 cell differentiation -0.12 0.25 -10000 0 -0.66 51 51
IL2RA -0.19 0.24 -10000 0 -0.9 28 28
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.004 0.12 -10000 0 -0.57 6 6
E2F1 0 0.11 -10000 0 -0.73 10 10
PPARG 0.01 0.031 -10000 0 -0.44 2 2
SLC3A2 -0.004 0.12 -10000 0 -0.57 6 6
IRF4 -0.14 0.21 -10000 0 -0.44 144 144
PTGS2 -0.35 0.39 -10000 0 -1.1 58 58
CSF2 -0.46 0.47 -10000 0 -0.96 174 174
JunB/Fra1/NFAT1-c-4 -0.35 0.29 -10000 0 -0.9 40 40
IL4 -0.1 0.19 -10000 0 -0.81 15 15
IL5 -0.33 0.35 -10000 0 -0.95 53 53
IL2 -0.11 0.16 -10000 0 -0.78 4 4
IL3 -0.067 0.05 -10000 0 -10000 0 0
RNF128 0.036 0.041 -10000 0 -0.52 2 2
NFATC1 -0.059 0.2 -10000 0 -1 10 10
CDK4 0.039 0.13 0.67 4 -10000 0 4
PTPRK -0.004 0.12 -10000 0 -0.57 6 6
IL8 -0.54 0.47 -10000 0 -0.98 188 188
POU2F1 0.012 0.001 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.012 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin 0 0.079 -9999 0 -10000 0 0
Syndecan-3/Neurocan 0.009 0.03 -9999 0 -0.4 2 2
POMC -0.005 0.088 -9999 0 -0.46 15 15
EGFR 0.011 0.022 -9999 0 -0.44 1 1
Syndecan-3/EGFR 0.022 0.011 -9999 0 -10000 0 0
AGRP -0.001 0.062 -9999 0 -0.74 3 3
NCSTN 0.012 0 -9999 0 -10000 0 0
PSENEN 0.011 0.022 -9999 0 -0.44 1 1
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.012 0.001 -9999 0 -10000 0 0
APH1A 0.012 0 -9999 0 -10000 0 0
NCAN 0.003 0.051 -9999 0 -0.74 2 2
long-term memory 0.029 0.003 -9999 0 -10000 0 0
Syndecan-3/IL8 -0.23 0.21 -9999 0 -0.4 259 259
PSEN1 0.012 0 -9999 0 -10000 0 0
Src/Cortactin 0.018 0 -9999 0 -10000 0 0
FYN 0.012 0 -9999 0 -10000 0 0
limb bud formation 0 0.002 -9999 0 -10000 0 0
MC4R -0.004 0.071 -9999 0 -0.74 4 4
SRC 0.012 0 -9999 0 -10000 0 0
PTN -0.063 0.17 -9999 0 -0.44 72 72
FGFR/FGF/Syndecan-3 0 0.002 -9999 0 -10000 0 0
neuron projection morphogenesis -0.014 0.076 -9999 0 -0.36 2 2
Syndecan-3/AgRP 0.005 0.036 -9999 0 -0.4 3 3
Syndecan-3/AgRP/MC4R 0.005 0.059 -9999 0 -0.46 6 6
Fyn/Cortactin 0.018 0 -9999 0 -10000 0 0
SDC3 0 0.002 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.23 0.2 -9999 0 -0.4 259 259
IL8 -0.44 0.37 -9999 0 -0.74 259 259
Syndecan-3/Fyn/Cortactin 0.029 0.003 -9999 0 -10000 0 0
Syndecan-3/CASK 0 0.002 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.006 0.083 -9999 0 -0.38 19 19
Gamma Secretase 0.036 0.012 -9999 0 -10000 0 0
Canonical Wnt 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
HDAC1 0.013 0.016 -10000 0 -10000 0 0
AES 0.013 0.013 -10000 0 -10000 0 0
FBXW11 0.012 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.019 0.016 -10000 0 -0.3 1 1
SMAD4 0.011 0.022 -10000 0 -0.44 1 1
DKK2 -0.13 0.29 -10000 0 -0.74 80 80
TLE1 0.012 0.024 -10000 0 -0.42 1 1
MACF1 0.013 0 -10000 0 -10000 0 0
CTNNB1 0.063 0.09 0.25 6 -10000 0 6
WIF1 -0.14 0.29 -10000 0 -0.74 83 83
beta catenin/RanBP3 0.021 0.1 0.36 12 -10000 0 12
KREMEN2 -0.073 0.24 -10000 0 -0.74 49 49
DKK1 -0.14 0.3 -10000 0 -0.74 86 86
beta catenin/beta TrCP1 0.067 0.085 0.24 4 -10000 0 4
FZD1 0.012 0.022 -10000 0 -0.44 1 1
AXIN2 -0.04 0.18 -10000 0 -0.58 33 33
AXIN1 0.012 0.022 -10000 0 -0.44 1 1
RAN 0.012 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.021 0.042 -10000 0 -0.54 1 1
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.045 0.081 -10000 0 -0.41 1 1
Axin1/APC/GSK3 0.099 0.064 -10000 0 -0.35 1 1
Axin1/APC/GSK3/beta catenin/Macf1 0.055 0.057 -10000 0 -10000 0 0
HNF1A 0.011 0.034 -10000 0 -0.44 2 2
CTBP1 0.013 0.013 -10000 0 -10000 0 0
MYC 0 0.079 -10000 0 -0.57 6 6
RANBP3 0.012 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.12 0.24 -10000 0 -0.51 121 121
NKD1 -0.46 0.36 -10000 0 -0.74 275 275
TCF4 0.012 0.026 -10000 0 -0.44 1 1
TCF3 0.013 0.013 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.028 0.042 -10000 0 -0.43 3 3
Ran/GTP 0.009 0.001 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.014 0.1 0.49 2 -10000 0 2
LEF1 -0.074 0.24 -10000 0 -0.73 50 50
DVL1 0.042 0.035 -10000 0 -0.27 1 1
CSNK2A1 0.013 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.042 0.089 -10000 0 -0.42 2 2
DKK1/LRP6/Kremen 2 -0.13 0.25 -10000 0 -0.51 125 125
LRP6 0.013 0.001 -10000 0 -10000 0 0
CSNK1A1 0.013 0.016 -10000 0 -10000 0 0
NLK 0.012 0.004 -10000 0 -10000 0 0
CCND1 0.003 0.063 -10000 0 -0.55 3 3
WNT1 0.004 0.062 -10000 0 -0.74 3 3
GSK3A 0.013 0.001 -10000 0 -10000 0 0
GSK3B 0.013 0.001 -10000 0 -10000 0 0
FRAT1 0.012 0.001 -10000 0 -10000 0 0
PPP2R5D 0.21 0.15 0.32 275 -10000 0 275
APC 0.025 0.05 -10000 0 -0.4 3 3
WNT1/LRP6/FZD1 0.061 0.078 0.22 82 -10000 0 82
CREBBP 0.013 0.013 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.006 0.12 -9999 0 -0.55 10 10
MAP3K8 0.013 0.001 -9999 0 -10000 0 0
FOS -0.015 0.12 -9999 0 -0.5 10 10
PRKCA 0.013 0.002 -9999 0 -10000 0 0
PTPN7 0.002 0.086 -9999 0 -0.57 9 9
HRAS 0.011 0.022 -9999 0 -0.44 1 1
PRKCB -0.088 0.19 -9999 0 -0.44 96 96
NRAS 0.01 0.031 -9999 0 -0.44 2 2
RAS family/GTP 0.023 0.021 -9999 0 -10000 0 0
MAPK3 -0.01 0.098 -9999 0 -0.6 6 6
MAP2K1 -0.049 0.16 -9999 0 -0.36 96 96
ELK1 0.013 0.002 -9999 0 -10000 0 0
BRAF -0.056 0.16 -9999 0 -0.35 96 96
mol:GTP 0 0.001 -9999 0 -0.004 7 7
MAPK1 -0.009 0.096 -9999 0 -0.64 5 5
RAF1 -0.056 0.16 -9999 0 -0.35 96 96
KRAS 0.012 0 -9999 0 -10000 0 0
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.005 0.097 -9999 0 -0.44 14 14
alphaM/beta2 Integrin/GPIbA -0.007 0.094 -9999 0 -0.43 12 12
alphaM/beta2 Integrin/proMMP-9 -0.043 0.16 -9999 0 -0.49 45 45
PLAUR 0.012 0 -9999 0 -10000 0 0
HMGB1 0.007 0.017 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.002 0.087 -9999 0 -0.44 10 10
AGER 0.005 0.041 -9999 0 -0.78 1 1
RAP1A 0.012 0 -9999 0 -10000 0 0
SELPLG 0.009 0.038 -9999 0 -0.44 3 3
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.007 0.11 -9999 0 -0.45 11 11
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.052 0.21 -9999 0 -0.71 38 38
CYR61 0.007 0.062 -9999 0 -0.74 3 3
TLN1 0.012 0 -9999 0 -10000 0 0
Rap1/GTP -0.06 0.096 -9999 0 -0.39 16 16
RHOA 0.012 0 -9999 0 -10000 0 0
P-selectin oligomer -0.048 0.15 -9999 0 -0.44 57 57
MYH2 -0.056 0.14 -9999 0 -0.43 27 27
MST1R 0.012 0 -9999 0 -10000 0 0
leukocyte activation during inflammatory response -0.067 0.14 -9999 0 -0.43 42 42
APOB -0.076 0.2 -9999 0 -0.53 68 68
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 0.007 0.059 -9999 0 -0.59 4 4
JAM3 0.012 0 -9999 0 -10000 0 0
GP1BA 0.003 0.057 -9999 0 -0.44 7 7
alphaM/beta2 Integrin/CTGF -0.006 0.1 -9999 0 -0.46 14 14
alphaM/beta2 Integrin -0.055 0.13 -9999 0 -0.38 36 36
JAM3 homodimer 0.012 0 -9999 0 -10000 0 0
ICAM2 0.012 0 -9999 0 -10000 0 0
ICAM1 0.011 0.036 -9999 0 -0.74 1 1
phagocytosis triggered by activation of immune response cell surface activating receptor -0.055 0.13 -9999 0 -0.38 36 36
cell adhesion -0.007 0.094 -9999 0 -0.43 12 12
NFKB1 -0.017 0.14 -9999 0 -0.64 4 4
THY1 -0.015 0.14 -9999 0 -0.74 16 16
RhoA/GDP 0.009 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.058 0.15 -9999 0 -0.36 80 80
alphaM/beta2 Integrin/LRP/tPA 0.004 0.084 -9999 0 -0.44 7 7
IL6 -0.062 0.24 -9999 0 -0.58 73 73
ITGB2 -0.001 0.062 -9999 0 -0.44 8 8
elevation of cytosolic calcium ion concentration -0.027 0.14 -9999 0 -0.45 39 39
alphaM/beta2 Integrin/JAM2/JAM3 -0.048 0.15 -9999 0 -0.51 23 23
JAM2 -0.092 0.19 -9999 0 -0.44 99 99
alphaM/beta2 Integrin/ICAM1 -0.054 0.18 -9999 0 -0.42 73 73
alphaM/beta2 Integrin/uPA/Plg -0.12 0.22 -9999 0 -0.46 119 119
RhoA/GTP -0.059 0.14 -9999 0 -0.45 27 27
positive regulation of phagocytosis -0.059 0.12 -9999 0 -0.5 17 17
Ron/MSP -0.069 0.21 -9999 0 -0.56 66 66
alphaM/beta2 Integrin/uPAR/uPA -0.027 0.14 -9999 0 -0.45 39 39
alphaM/beta2 Integrin/uPAR -0.002 0.087 -9999 0 -0.47 8 8
PLAU -0.043 0.2 -9999 0 -0.74 32 32
PLAT 0.009 0.038 -9999 0 -0.44 3 3
actin filament polymerization -0.054 0.13 -9999 0 -0.42 27 27
MST1 -0.1 0.27 -9999 0 -0.74 66 66
alphaM/beta2 Integrin/lipoprotein(a) -0.058 0.15 -9999 0 -0.44 42 42
TNF -0.01 0.14 -9999 0 -0.82 3 3
RAP1B 0.012 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.038 0.16 -9999 0 -0.48 42 42
fibrinolysis -0.12 0.21 -9999 0 -0.45 119 119
HCK 0.001 0.071 -9999 0 -0.44 11 11
dendritic cell antigen processing and presentation -0.055 0.13 -9999 0 -0.38 36 36
VTN -0.009 0.12 -9999 0 -0.74 11 11
alphaM/beta2 Integrin/CYR61 -0.005 0.096 -9999 0 -0.47 11 11
LPA -0.016 0.13 -9999 0 -0.74 13 13
LRP1 0.01 0.031 -9999 0 -0.44 2 2
cell migration -0.036 0.16 -9999 0 -0.47 44 44
FN1 -0.025 0.16 -9999 0 -0.66 24 24
alphaM/beta2 Integrin/Thy1 -0.02 0.13 -9999 0 -0.48 24 24
MPO -0.025 0.16 -9999 0 -0.74 21 21
KNG1 -0.096 0.19 -9999 0 -0.44 100 100
RAP1/GDP 0.017 0 -9999 0 -10000 0 0
ROCK1 -0.05 0.14 -9999 0 -0.44 23 23
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.14 0.29 -9999 0 -0.74 82 82
CTGF 0.005 0.072 -9999 0 -0.74 4 4
alphaM/beta2 Integrin/Hck -0.008 0.11 -9999 0 -0.56 12 12
ITGAM -0.019 0.11 -9999 0 -0.44 25 25
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.026 0.14 -9999 0 -0.56 15 15
HP -0.03 0.17 -9999 0 -0.74 23 23
leukocyte adhesion -0.086 0.14 -9999 0 -0.55 15 15
SELP -0.048 0.15 -9999 0 -0.44 57 57
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.007 0.072 -9999 0 -0.42 10 10
RGS9BP 0.007 0.051 -9999 0 -0.74 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.002 0.05 -9999 0 -0.74 2 2
mol:Na + -0.096 0.16 -9999 0 -0.3 144 144
mol:ADP 0.002 0.062 -9999 0 -0.71 3 3
GNAT2 -0.001 0.094 -9999 0 -0.74 7 7
RGS9-1/Gbeta5/R9AP -0.022 0.1 -9999 0 -0.48 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.001 0.067 -9999 0 -0.49 8 8
GRK7 0.004 0.051 -9999 0 -0.74 2 2
CNGB3 -0.032 0.16 -9999 0 -0.74 21 21
Cone Metarhodopsin II/X-Arrestin 0 0.039 -9999 0 -0.56 2 2
mol:Ca2+ -0.13 0.2 -9999 0 -0.53 59 59
Cone PDE6 -0.017 0.091 -9999 0 -0.41 3 3
Cone Metarhodopsin II 0.002 0.052 -9999 0 -0.59 3 3
Na + (4 Units) -0.13 0.2 -9999 0 -0.53 59 59
GNAT2/GDP -0.019 0.1 -9999 0 -0.41 9 9
GNB5 0.012 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0 0.062 -9999 0 -0.45 8 8
Cone Transducin 0.008 0.076 -9999 0 -0.44 10 10
SLC24A2 -0.067 0.22 -9999 0 -0.74 43 43
GNB3/GNGT2 0.009 0.062 -9999 0 -0.38 10 10
GNB3 0.006 0.066 -9999 0 -0.66 4 4
GNAT2/GTP -0.001 0.072 -9999 0 -0.56 7 7
CNGA3 -0.13 0.21 -9999 0 -0.45 129 129
ARR3 0 0.05 -9999 0 -0.74 2 2
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.096 0.16 -9999 0 -0.31 144 144
mol:Pi -0.022 0.1 -9999 0 -0.48 2 2
Cone CNG Channel -0.084 0.14 -9999 0 -0.45 30 30
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.067 0.22 -9999 0 -0.74 43 43
RGS9 -0.06 0.17 -9999 0 -0.44 69 69
PDE6C 0.003 0.005 -9999 0 -10000 0 0
GNGT2 0.006 0.053 -9999 0 -0.44 6 6
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H -0.001 0.036 -9999 0 -0.74 1 1
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.031 0.043 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.1 0.12 -9999 0 -0.34 42 42
JUN -0.072 0.14 -9999 0 -0.37 41 41
HRAS 0.011 0.022 -9999 0 -0.44 1 1
RET51/GFRalpha1/GDNF/GRB10 -0.1 0.16 -9999 0 -0.46 42 42
RAP1A 0.012 0 -9999 0 -10000 0 0
FRS2 0.012 0.001 -9999 0 -10000 0 0
RAP1A/GDP 0.009 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.1 0.16 -9999 0 -0.46 42 42
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.012 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.073 0.12 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
RAP1A/GTP -0.11 0.14 -9999 0 -0.41 43 43
GRB7 -0.002 0.1 -9999 0 -0.74 8 8
RET51/GFRalpha1/GDNF -0.1 0.16 -9999 0 -0.46 42 42
MAPKKK cascade -0.11 0.14 -9999 0 -0.42 42 42
BCAR1 0.011 0.022 -9999 0 -0.44 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.073 0.12 -9999 0 -10000 0 0
lamellipodium assembly -0.097 0.12 -9999 0 -0.33 41 41
RET51/GFRalpha1/GDNF/SHC -0.1 0.16 -9999 0 -0.46 42 42
PIK3CA 0.012 0.001 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.073 0.12 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3 -0.074 0.12 -9999 0 -0.46 1 1
MAPK3 -0.081 0.14 -9999 0 -0.39 43 43
DOK1 0.012 0 -9999 0 -10000 0 0
DOK6 -0.001 0.075 -9999 0 -0.44 12 12
PXN 0.012 0 -9999 0 -10000 0 0
neurite development -0.07 0.14 -9999 0 -0.47 8 8
DOK5 0 0.079 -9999 0 -0.5 10 10
GFRA1 -0.16 0.22 -9999 0 -0.44 165 165
MAPK8 -0.082 0.14 -9999 0 -0.4 41 41
HRAS/GTP -0.12 0.15 -9999 0 -0.47 42 42
tube development -0.063 0.12 -9999 0 -0.43 1 1
MAPK1 -0.08 0.14 -9999 0 -0.39 43 43
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.063 0.11 -9999 0 -10000 0 0
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
PDLIM7 0.012 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.098 0.17 -9999 0 -0.46 48 48
SHC1 0.012 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.1 0.17 -9999 0 -0.46 43 43
RET51/GFRalpha1/GDNF/Dok5 -0.11 0.17 -9999 0 -0.46 47 47
PRKCA 0.012 0 -9999 0 -10000 0 0
HRAS/GDP 0.008 0.015 -9999 0 -0.31 1 1
CREB1 -0.097 0.16 -9999 0 -0.43 41 41
PIK3R1 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.063 0.11 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Grb7 -0.11 0.18 -9999 0 -0.48 49 49
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.061 0.17 -9999 0 -0.45 68 68
DOK4 0.011 0.022 -9999 0 -0.44 1 1
JNK cascade -0.071 0.14 -9999 0 -0.36 41 41
RET9/GFRalpha1/GDNF/FRS2 -0.073 0.12 -9999 0 -10000 0 0
SHANK3 0.011 0.022 -9999 0 -0.44 1 1
RASA1 0.012 0.001 -9999 0 -10000 0 0
NCK1 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.064 0.11 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.094 0.15 -9999 0 -0.42 41 41
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.094 0.15 -9999 0 -0.42 41 41
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.1 0.18 -9999 0 -0.53 41 41
PI3K -0.11 0.2 -9999 0 -0.49 42 42
SOS1 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.062 0.12 -9999 0 -0.43 1 1
GRB10 0.012 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.079 0.13 -9999 0 -0.34 41 41
RET51/GFRalpha1/GDNF/FRS2 -0.1 0.16 -9999 0 -0.46 42 42
GAB1 0.012 0 -9999 0 -10000 0 0
IRS1 0.012 0 -9999 0 -10000 0 0
IRS2 0.012 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.1 0.18 -9999 0 -0.53 41 41
RET51/GFRalpha1/GDNF/PKC alpha -0.1 0.16 -9999 0 -0.46 42 42
GRB2 0.012 0 -9999 0 -10000 0 0
PRKACA 0.012 0 -9999 0 -10000 0 0
GDNF 0.009 0.006 -9999 0 -10000 0 0
RAC1 0.012 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.1 0.16 -9999 0 -0.46 42 42
Rac1/GTP -0.11 0.14 -9999 0 -0.39 41 41
RET9/GFRalpha1/GDNF -0.09 0.13 -9999 0 -0.26 165 165
GFRalpha1/GDNF -0.11 0.16 -9999 0 -0.31 165 165
Wnt signaling

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
Noncanonical Wnts/FZD -0.05 0.14 -9999 0 -0.48 17 17
FZD6 0.012 0 -9999 0 -10000 0 0
WNT6 -0.026 0.15 -9999 0 -0.62 25 25
WNT4 -0.012 0.11 -9999 0 -0.48 21 21
FZD3 0.007 0.062 -9999 0 -0.74 3 3
WNT5A 0.004 0.075 -9999 0 -0.68 5 5
WNT11 -0.13 0.29 -9999 0 -0.7 88 88
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.058 0.25 -10000 0 -0.8 29 29
NCK1/PAK1/Dok-R -0.029 0.1 -10000 0 -0.4 27 27
NCK1/Dok-R 0.025 0.28 -10000 0 -0.96 29 29
PIK3CA 0.012 0.001 -10000 0 -10000 0 0
mol:beta2-estradiol 0.001 0.051 0.26 16 -10000 0 16
RELA 0.012 0 -10000 0 -10000 0 0
SHC1 0.013 0.001 -10000 0 -10000 0 0
Rac/GDP 0.009 0 -10000 0 -10000 0 0
F2 -0.24 0.35 -10000 0 -0.74 139 139
TNIP2 0.012 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.014 0.24 -10000 0 -0.87 29 29
FN1 -0.025 0.16 -10000 0 -0.66 24 24
PLD2 0.026 0.28 -10000 0 -0.97 29 29
PTPN11 0.012 0 -10000 0 -10000 0 0
GRB14 -0.027 0.14 -10000 0 -0.53 30 30
ELK1 0.036 0.25 -10000 0 -0.88 29 29
GRB7 -0.002 0.1 -10000 0 -0.74 8 8
PAK1 0.012 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.034 0.26 -10000 0 -0.91 31 31
CDKN1A 0.065 0.21 -10000 0 -0.62 22 22
ITGA5 0.009 0.051 -10000 0 -0.74 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.025 0.28 -10000 0 -0.96 29 29
CRK 0.012 0 -10000 0 -10000 0 0
mol:NO 0.062 0.2 -10000 0 -0.61 29 29
PLG -0.058 0.31 -10000 0 -1 29 29
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.051 0.24 -10000 0 -0.77 29 29
GRB2 0.012 0 -10000 0 -10000 0 0
PIK3R1 0.013 0.001 -10000 0 -10000 0 0
ANGPT2 0.035 0.2 0.38 5 -0.54 13 18
BMX -0.059 0.3 -10000 0 -1.1 29 29
ANGPT1 0.039 0.24 -10000 0 -1.1 16 16
tube development 0.06 0.22 -10000 0 -0.66 23 23
ANGPT4 -0.001 0.071 -10000 0 -0.73 4 4
response to hypoxia -0.001 0.017 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 0.003 0.3 -10000 0 -1 29 29
alpha5/beta1 Integrin 0.016 0.039 -10000 0 -0.56 2 2
FGF2 -0.02 0.12 -10000 0 -0.44 30 30
STAT5A (dimer) 0.06 0.24 -10000 0 -0.74 24 24
mol:L-citrulline 0.062 0.2 -10000 0 -0.61 29 29
AGTR1 -0.14 0.21 -10000 0 -0.44 144 144
MAPK14 0.03 0.29 -10000 0 -1 29 29
Tie2/SHP2 -0.017 0.21 -10000 0 -1 17 17
TEK -0.021 0.23 -10000 0 -1.1 17 17
RPS6KB1 0.057 0.24 -10000 0 -0.77 29 29
Angiotensin II/AT1 -0.097 0.15 -10000 0 -0.31 144 144
Tie2/Ang1/GRB2 0.023 0.29 -10000 0 -1 29 29
MAPK3 0.033 0.26 -10000 0 -0.89 29 29
MAPK1 0.033 0.26 -10000 0 -0.89 29 29
Tie2/Ang1/GRB7 0.016 0.3 -10000 0 -1 29 29
NFKB1 0.012 0 -10000 0 -10000 0 0
MAPK8 0.026 0.28 -10000 0 -0.97 29 29
PI3K 0.046 0.28 -10000 0 -0.92 29 29
FES 0.029 0.3 -10000 0 -1 29 29
Crk/Dok-R 0.025 0.28 -10000 0 -0.96 29 29
Tie2/Ang1/ABIN2 0.023 0.29 -10000 0 -1 29 29
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.062 0.23 -10000 0 -0.72 29 29
STAT5A 0.013 0 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.057 0.24 -10000 0 -0.77 29 29
Tie2/Ang2 0.047 0.27 -10000 0 -0.9 23 23
Tie2/Ang1 0.021 0.3 -10000 0 -1 29 29
FOXO1 0.065 0.23 -10000 0 -0.74 26 26
ELF1 0.017 0.021 -10000 0 -10000 0 0
ELF2 0.025 0.28 -10000 0 -0.98 29 29
mol:Choline 0.029 0.27 -10000 0 -0.93 29 29
cell migration -0.021 0.06 -10000 0 -0.24 16 16
FYN 0.057 0.24 -10000 0 -0.75 23 23
DOK2 0.001 0.071 -10000 0 -0.44 11 11
negative regulation of cell cycle 0.066 0.2 -10000 0 -0.56 22 22
ETS1 0.01 0.05 -10000 0 -0.27 7 7
PXN 0.066 0.21 -10000 0 -0.64 29 29
ITGB1 0.012 0 -10000 0 -10000 0 0
NOS3 0.059 0.22 -10000 0 -0.7 29 29
RAC1 0.012 0 -10000 0 -10000 0 0
TNF 0.009 0.059 -10000 0 -0.44 2 2
MAPKKK cascade 0.029 0.27 -10000 0 -0.93 29 29
RASA1 0.012 0.001 -10000 0 -10000 0 0
Tie2/Ang1/Shc 0.024 0.29 -10000 0 -1 29 29
NCK1 0.012 0 -10000 0 -10000 0 0
vasculogenesis 0.064 0.19 -10000 0 -0.55 29 29
mol:Phosphatidic acid 0.029 0.27 -10000 0 -0.93 29 29
mol:Angiotensin II 0.001 0.003 -10000 0 -10000 0 0
mol:NADP 0.062 0.2 -10000 0 -0.61 29 29
Rac1/GTP -0.044 0.19 -10000 0 -0.72 29 29
MMP2 0.024 0.28 -10000 0 -0.98 29 29
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.016 0 -9999 0 -10000 0 0
ADCY5 -0.1 0.14 -9999 0 -0.26 184 184
ADCY6 0.016 0 -9999 0 -10000 0 0
ADCY7 0.016 0 -9999 0 -10000 0 0
ADCY1 0.005 0.07 -9999 0 -0.44 10 10
ADCY2 -0.007 0.077 -9999 0 -0.26 35 35
ADCY3 0.016 0 -9999 0 -10000 0 0
ADCY8 0.002 0.063 -9999 0 -0.48 7 7
PRKCE 0.01 0 -9999 0 -10000 0 0
ADCY9 0.015 0.018 -9999 0 -0.26 2 2
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.014 0.057 -9999 0 -0.28 2 2
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.046 0.14 -10000 0 -0.54 26 26
FYN -0.011 0.21 -10000 0 -0.68 30 30
LAT/GRAP2/SLP76 -0.045 0.16 -10000 0 -0.56 31 31
IKBKB 0.012 0 -10000 0 -10000 0 0
AKT1 0.009 0.14 -10000 0 -0.44 31 31
B2M 0.012 0.022 -10000 0 -0.44 1 1
IKBKG -0.015 0.04 -10000 0 -0.17 9 9
MAP3K8 0.012 0 -10000 0 -10000 0 0
mol:Ca2+ -0.02 0.048 -10000 0 -0.15 52 52
integrin-mediated signaling pathway 0.014 0.026 -10000 0 -0.26 4 4
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.006 0.21 -10000 0 -0.65 33 33
TRPV6 -0.089 0.24 -10000 0 -0.74 52 52
CD28 -0.007 0.091 -10000 0 -0.44 18 18
SHC1 -0.008 0.2 -10000 0 -0.65 31 31
receptor internalization -0.021 0.22 -10000 0 -0.72 31 31
PRF1 -0.016 0.22 -10000 0 -0.82 24 24
KRAS 0.012 0 -10000 0 -10000 0 0
GRB2 0.012 0 -10000 0 -10000 0 0
COT/AKT1 0.017 0.11 -10000 0 -0.36 26 26
LAT -0.01 0.2 -10000 0 -0.63 33 33
EntrezGene:6955 0.001 0.002 -10000 0 -10000 0 0
CD3D -0.002 0.082 -10000 0 -0.45 14 14
CD3E -0.003 0.085 -10000 0 -0.45 15 15
CD3G -0.025 0.13 -10000 0 -0.44 36 36
RASGRP2 -0.01 0.055 -10000 0 -0.17 41 41
RASGRP1 0.016 0.14 -10000 0 -0.44 30 30
HLA-A 0.012 0.022 -10000 0 -0.44 1 1
RASSF5 0.008 0.043 -10000 0 -0.44 4 4
RAP1A/GTP/RAPL 0.014 0.026 -10000 0 -0.26 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.022 0.049 -10000 0 -0.13 23 23
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.028 0.069 -10000 0 -0.26 21 21
PRKCA -0.02 0.077 -10000 0 -0.28 23 23
GRAP2 -0.006 0.088 -10000 0 -0.44 17 17
mol:IP3 -0.012 0.15 0.26 49 -0.45 25 74
EntrezGene:6957 0.001 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.02 0.19 -10000 0 -0.62 33 33
ORAI1 0.049 0.12 0.36 51 -10000 0 51
CSK -0.009 0.2 -10000 0 -0.67 29 29
B7 family/CD28 -0.011 0.21 -10000 0 -0.71 27 27
CHUK 0.012 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.021 0.23 -10000 0 -0.76 31 31
PTPN6 -0.011 0.2 -10000 0 -0.7 27 27
VAV1 -0.016 0.21 -10000 0 -0.71 29 29
Monovalent TCR/CD3 -0.022 0.17 -10000 0 -0.7 21 21
CBL 0.012 0 -10000 0 -10000 0 0
LCK -0.014 0.21 -10000 0 -0.68 31 31
PAG1 -0.012 0.2 -10000 0 -0.67 30 30
RAP1A 0.012 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.02 0.23 -10000 0 -0.75 31 31
CD80 0.009 0.042 -10000 0 -0.59 2 2
CD86 0.001 0.072 -10000 0 -0.44 11 11
PDK1/CARD11/BCL10/MALT1 -0.034 0.084 -10000 0 -0.3 28 28
HRAS 0.011 0.022 -10000 0 -0.44 1 1
GO:0035030 -0.005 0.17 -10000 0 -0.58 27 27
CD8A -0.018 0.12 -10000 0 -0.45 30 30
CD8B -0.001 0.084 -10000 0 -0.47 13 13
PTPRC -0.022 0.12 -10000 0 -0.44 33 33
PDK1/PKC theta 0.01 0.17 -10000 0 -0.54 32 32
CSK/PAG1 -0.006 0.19 -10000 0 -0.66 28 28
SOS1 0.012 0 -10000 0 -10000 0 0
peptide-MHC class I 0.018 0.023 -10000 0 -10000 0 0
GRAP2/SLP76 -0.053 0.19 -10000 0 -0.68 30 30
STIM1 0.024 0.059 -10000 0 -10000 0 0
RAS family/GTP 0.03 0.061 -10000 0 -0.18 16 16
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.026 0.24 -10000 0 -0.78 31 31
mol:DAG -0.026 0.12 -10000 0 -0.4 27 27
RAP1A/GDP 0.011 0.022 -10000 0 -10000 0 0
PLCG1 0.012 0 -10000 0 -10000 0 0
CD247 -0.003 0.084 -10000 0 -0.45 15 15
cytotoxic T cell degranulation -0.013 0.21 -10000 0 -0.77 24 24
RAP1A/GTP -0.007 0.018 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.003 0.17 -10000 0 -0.52 33 33
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.023 0.18 0.28 46 -0.59 26 72
NRAS 0.01 0.031 -10000 0 -0.44 2 2
ZAP70 -0.002 0.083 -10000 0 -0.46 13 13
GRB2/SOS1 0.018 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.047 0.16 -10000 0 -0.56 31 31
MALT1 0.011 0.022 -10000 0 -0.44 1 1
TRAF6 0.012 0 -10000 0 -10000 0 0
CD8 heterodimer -0.012 0.11 -10000 0 -0.37 36 36
CARD11 -0.024 0.15 -10000 0 -0.59 26 26
PRKCB -0.04 0.11 -10000 0 -0.32 44 44
PRKCE -0.02 0.077 -10000 0 -0.28 24 24
PRKCQ 0 0.2 -10000 0 -0.62 33 33
LCP2 0.008 0.043 -10000 0 -0.44 4 4
BCL10 0.011 0.022 -10000 0 -0.44 1 1
regulation of survival gene product expression 0.013 0.12 -10000 0 -0.38 30 30
IKK complex 0.021 0.052 -10000 0 -0.12 18 18
RAS family/GDP -0.003 0.009 -10000 0 -10000 0 0
MAP3K14 0.022 0.089 -10000 0 -0.28 21 21
PDPK1 0.012 0.14 -10000 0 -0.43 28 28
TCR/CD3/MHC I/CD8/Fyn -0.022 0.23 -10000 0 -0.78 30 30
EPHB forward signaling

Figure S42.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S42.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.042 0.12 -10000 0 -0.26 92 92
cell-cell adhesion 0.086 0.15 0.6 4 -10000 0 4
Ephrin B/EPHB2/RasGAP 0.03 0.048 -10000 0 -0.4 4 4
ITSN1 0.011 0.022 -10000 0 -0.44 1 1
PIK3CA 0.012 0.001 -10000 0 -10000 0 0
SHC1 0.012 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.008 0.11 -10000 0 -0.48 21 21
Ephrin B1/EPHB1 -0.11 0.22 -10000 0 -0.48 109 109
HRAS/GDP -0.088 0.15 -10000 0 -0.54 3 3
Ephrin B/EPHB1/GRB7 -0.087 0.21 -10000 0 -0.42 114 114
Endophilin/SYNJ1 0.025 0.044 -10000 0 -0.38 4 4
KRAS 0.012 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.079 0.2 -10000 0 -0.41 110 110
endothelial cell migration 0.026 0 -10000 0 -10000 0 0
GRB2 0.012 0 -10000 0 -10000 0 0
GRB7 -0.002 0.1 -10000 0 -0.74 8 8
PAK1 0.031 0.046 -10000 0 -0.38 4 4
HRAS 0.011 0.022 -10000 0 -0.44 1 1
RRAS 0.026 0.045 -10000 0 -0.38 4 4
DNM1 0.005 0.072 -10000 0 -0.74 4 4
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.078 0.18 -10000 0 -0.39 110 110
lamellipodium assembly -0.086 0.15 -10000 0 -0.6 4 4
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.032 0.11 -10000 0 -0.41 2 2
PIK3R1 0.012 0 -10000 0 -10000 0 0
EPHB2 0.009 0.051 -10000 0 -0.74 2 2
EPHB3 -0.024 0.16 -10000 0 -0.74 21 21
EPHB1 -0.18 0.32 -10000 0 -0.74 109 109
EPHB4 0.012 0 -10000 0 -10000 0 0
mol:GDP -0.044 0.15 -10000 0 -0.52 3 3
Ephrin B/EPHB2 0.023 0.048 -10000 0 -0.41 4 4
Ephrin B/EPHB3 0.004 0.1 -10000 0 -0.41 23 23
JNK cascade -0.078 0.19 -10000 0 -0.4 109 109
Ephrin B/EPHB1 -0.086 0.2 -10000 0 -0.42 110 110
RAP1/GDP -0.027 0.14 -10000 0 -0.44 3 3
EFNB2 0.012 0 -10000 0 -10000 0 0
EFNB3 0.005 0.067 -10000 0 -0.54 6 6
EFNB1 0.012 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.095 0.21 -10000 0 -0.45 109 109
RAP1B 0.012 0 -10000 0 -10000 0 0
RAP1A 0.012 0 -10000 0 -10000 0 0
CDC42/GTP -0.089 0.15 -10000 0 -0.63 5 5
Rap1/GTP -0.087 0.15 -10000 0 -0.62 4 4
axon guidance -0.042 0.11 -10000 0 -0.26 92 92
MAPK3 -0.017 0.1 -10000 0 -0.36 2 2
MAPK1 -0.017 0.1 -10000 0 -0.36 2 2
Rac1/GDP -0.034 0.14 -10000 0 -0.47 3 3
actin cytoskeleton reorganization -0.072 0.12 -10000 0 -0.46 5 5
CDC42/GDP -0.034 0.14 -10000 0 -0.53 3 3
PI3K 0.029 0 -10000 0 -10000 0 0
EFNA5 -0.082 0.18 -10000 0 -0.44 90 90
Ephrin B2/EPHB4 0.017 0 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.027 0.035 -10000 0 -10000 0 0
CDC42 0.011 0.022 -10000 0 -0.44 1 1
RAS family/GTP -0.085 0.15 -10000 0 -0.58 5 5
PTK2 0.023 0.039 -10000 0 -10000 0 0
MAP4K4 -0.079 0.19 -10000 0 -0.41 109 109
SRC 0.012 0 -10000 0 -10000 0 0
KALRN 0.011 0.022 -10000 0 -0.44 1 1
Intersectin/N-WASP 0.018 0.016 -10000 0 -0.3 1 1
neuron projection morphogenesis -0.022 0.14 -10000 0 -0.45 5 5
MAP2K1 -0.024 0.11 -10000 0 -0.38 2 2
WASL 0.012 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.088 0.21 -10000 0 -0.44 109 109
cell migration -0.019 0.11 -10000 0 -0.42 2 2
NRAS 0.01 0.031 -10000 0 -0.44 2 2
SYNJ1 0.025 0.045 -10000 0 -0.38 4 4
PXN 0.012 0 -10000 0 -10000 0 0
TF 0 0.1 -10000 0 -0.43 14 14
HRAS/GTP -0.093 0.16 -10000 0 -0.66 4 4
Ephrin B1/EPHB1-2 -0.095 0.21 -10000 0 -0.45 109 109
cell adhesion mediated by integrin -0.006 0.059 0.33 4 -10000 0 4
RAC1 0.012 0 -10000 0 -10000 0 0
mol:GTP -0.071 0.19 -10000 0 -0.6 6 6
RAC1-CDC42/GTP -0.1 0.17 -10000 0 -0.67 11 11
RASA1 0.012 0.001 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.028 0.14 -10000 0 -0.5 3 3
ruffle organization -0.05 0.17 -10000 0 -0.62 4 4
NCK1 0.012 0 -10000 0 -10000 0 0
receptor internalization 0.026 0.061 -10000 0 -0.39 8 8
Ephrin B/EPHB2/KALRN 0.03 0.049 -10000 0 -0.4 4 4
ROCK1 -0.001 0.099 -10000 0 -0.44 21 21
RAS family/GDP -0.061 0.1 -10000 0 -0.42 5 5
Rac1/GTP -0.091 0.16 -10000 0 -0.66 4 4
Ephrin B/EPHB1/Src/Paxillin -0.035 0.11 -10000 0 -0.45 2 2
Signaling events mediated by PRL

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
CCNE1 0.007 0.062 -10000 0 -0.74 3 3
mol:Halofuginone 0.005 0 -10000 0 -10000 0 0
ITGA1 0.012 0 -10000 0 -10000 0 0
CDKN1A 0.027 0.027 -10000 0 -0.37 2 2
PRL-3/alpha Tubulin -0.076 0.21 -10000 0 -0.56 71 71
mol:Ca2+ -0.02 0.22 0.32 58 -0.55 50 108
AGT -0.075 0.24 -10000 0 -0.73 51 51
CCNA2 0.034 0.011 -10000 0 -10000 0 0
TUBA1B 0.012 0 -10000 0 -10000 0 0
EGR1 0.02 0.015 -10000 0 -0.3 1 1
CDK2/Cyclin E1 0.034 0.043 -10000 0 -0.36 5 5
MAPK3 -0.076 0.21 -10000 0 -0.55 72 72
PRL-2 /Rab GGTase beta 0.018 0 -10000 0 -10000 0 0
MAPK1 -0.075 0.21 -10000 0 -0.56 71 71
PTP4A1 0.03 0.012 -10000 0 -10000 0 0
PTP4A3 -0.11 0.28 -10000 0 -0.74 71 71
PTP4A2 0.012 0 -10000 0 -10000 0 0
ITGB1 -0.075 0.21 -10000 0 -0.56 71 71
SRC 0.012 0 -10000 0 -10000 0 0
RAC1 -0.005 0.077 -10000 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0.018 0 -10000 0 -10000 0 0
PRL-1/ATF-5 0.034 0.011 -10000 0 -10000 0 0
RABGGTA 0.012 0 -10000 0 -10000 0 0
BCAR1 0.053 0.12 0.32 71 -0.32 1 72
RHOC -0.005 0.077 -10000 0 -10000 0 0
RHOA -0.005 0.077 -10000 0 -10000 0 0
cell motility -0.002 0.08 -10000 0 -0.38 1 1
PRL-1/alpha Tubulin 0.034 0.011 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin -0.076 0.21 -10000 0 -0.56 71 71
ROCK1 -0.002 0.08 -10000 0 -0.38 1 1
RABGGTB 0.012 0 -10000 0 -10000 0 0
CDK2 0.012 0 -10000 0 -10000 0 0
mitosis 0.03 0.012 -10000 0 -10000 0 0
ATF5 0.012 0 -10000 0 -10000 0 0
IL12-mediated signaling events

Figure S44.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S44.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.001 0.12 -10000 0 -0.38 17 17
TBX21 -0.11 0.43 -10000 0 -1.1 48 48
B2M 0.01 0.024 -10000 0 -0.44 1 1
TYK2 0.013 0.021 -10000 0 -10000 0 0
IL12RB1 -0.007 0.1 -10000 0 -0.49 18 18
GADD45B -0.047 0.3 -10000 0 -0.98 22 22
IL12RB2 0.005 0.077 -10000 0 -0.55 7 7
GADD45G -0.051 0.31 -10000 0 -0.94 26 26
natural killer cell activation 0 0.022 -10000 0 -10000 0 0
RELB 0.012 0 -10000 0 -10000 0 0
RELA 0.012 0 -10000 0 -10000 0 0
IL18 0.013 0.031 -10000 0 -0.44 2 2
IL2RA 0.002 0.068 -10000 0 -0.44 10 10
IFNG -0.069 0.23 -10000 0 -0.74 46 46
STAT3 (dimer) -0.047 0.3 -10000 0 -0.8 33 33
HLA-DRB5 -0.03 0.16 -10000 0 -0.62 29 29
FASLG -0.12 0.43 -10000 0 -1.1 49 49
NF kappa B2 p52/RelB -0.16 0.3 -10000 0 -0.92 43 43
CD4 -0.004 0.086 -10000 0 -0.44 16 16
SOCS1 -0.007 0.12 -10000 0 -0.74 11 11
EntrezGene:6955 0 0.011 -10000 0 -10000 0 0
CD3D -0.002 0.081 -10000 0 -0.44 14 14
CD3E -0.003 0.084 -10000 0 -0.44 15 15
CD3G -0.026 0.13 -10000 0 -0.45 36 36
IL12Rbeta2/JAK2 0.014 0.073 -10000 0 -0.4 10 10
CCL3 -0.099 0.38 -10000 0 -0.92 52 52
CCL4 -0.087 0.36 -10000 0 -0.94 46 46
HLA-A 0.011 0.024 -10000 0 -0.44 1 1
IL18/IL18R 0.03 0.088 -10000 0 -10000 0 0
NOS2 -0.11 0.42 -10000 0 -1.1 45 45
IL12/IL12R/TYK2/JAK2/SPHK2 0.007 0.11 -10000 0 -0.36 16 16
IL1R1 -0.09 0.37 -10000 0 -1 42 42
IL4 0.002 0.023 -10000 0 -10000 0 0
JAK2 0.01 0.046 -10000 0 -0.48 3 3
EntrezGene:6957 0 0.01 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.064 0.32 -10000 0 -0.97 40 40
RAB7A -0.02 0.26 -10000 0 -0.79 21 21
lysosomal transport -0.016 0.25 -10000 0 -0.73 22 22
FOS -0.046 0.29 -10000 0 -0.96 29 29
STAT4 (dimer) -0.051 0.34 -10000 0 -0.94 34 34
STAT5A (dimer) -0.2 0.32 -10000 0 -0.89 60 60
GZMA -0.14 0.47 -10000 0 -1.3 52 52
GZMB -0.15 0.4 -10000 0 -0.93 61 61
HLX 0.011 0.022 -10000 0 -0.44 1 1
LCK -0.1 0.39 -10000 0 -1 46 46
TCR/CD3/MHC II/CD4 -0.034 0.21 -10000 0 -0.63 34 34
IL2/IL2R 0.014 0.069 -10000 0 -0.5 5 5
MAPK14 -0.041 0.31 -10000 0 -0.95 25 25
CCR5 -0.059 0.33 -10000 0 -1.1 23 23
IL1B -0.07 0.24 -10000 0 -0.72 49 49
STAT6 -0.003 0.11 -10000 0 -10000 0 0
STAT4 -0.013 0.1 -10000 0 -0.44 24 24
STAT3 0.012 0 -10000 0 -10000 0 0
STAT1 0.011 0.036 -10000 0 -0.74 1 1
NFKB1 0.012 0 -10000 0 -10000 0 0
NFKB2 0.012 0 -10000 0 -10000 0 0
IL12B 0.002 0.075 -10000 0 -0.74 4 4
CD8A -0.02 0.12 -10000 0 -0.45 30 30
CD8B -0.003 0.084 -10000 0 -0.47 13 13
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.001 0.12 0.38 17 -10000 0 17
IL2RB 0.002 0.068 -10000 0 -0.44 10 10
proteasomal ubiquitin-dependent protein catabolic process -0.041 0.31 -10000 0 -0.84 33 33
IL2RG 0.01 0.031 -10000 0 -0.44 2 2
IL12 0.008 0.082 -10000 0 -0.44 11 11
STAT5A 0.012 0 -10000 0 -10000 0 0
CD247 -0.003 0.085 -10000 0 -0.45 15 15
IL2 0.003 0.005 -10000 0 -10000 0 0
SPHK2 0.011 0.022 -10000 0 -0.44 1 1
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.004 0.07 -10000 0 -0.5 7 7
IL12/IL12R/TYK2/JAK2 -0.1 0.41 -10000 0 -1.1 45 45
MAP2K3 -0.046 0.31 -10000 0 -0.93 28 28
RIPK2 0.012 0 -10000 0 -10000 0 0
MAP2K6 -0.047 0.31 -10000 0 -0.93 28 28
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.003 0.068 -10000 0 -0.44 10 10
IL18RAP -0.008 0.1 -10000 0 -0.45 22 22
IL12Rbeta1/TYK2 0.005 0.082 -10000 0 -0.36 18 18
EOMES -0.062 0.3 -10000 0 -1.2 26 26
STAT1 (dimer) -0.067 0.3 -10000 0 -0.75 43 43
T cell proliferation -0.028 0.26 -10000 0 -0.66 35 35
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.006 0.066 -10000 0 -0.45 9 9
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.12 0.21 -10000 0 -0.76 27 27
ATF2 -0.031 0.29 -10000 0 -0.9 22 22
LPA receptor 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
GNB1/GNG2 -0.018 0.11 -9999 0 -0.46 9 9
NF kappa B1 p50/RelA/I kappa B alpha -0.011 0.072 -9999 0 -10000 0 0
AP1 -0.048 0.095 -9999 0 -0.38 15 15
mol:PIP3 -0.039 0.08 -9999 0 -10000 0 0
AKT1 0.022 0.078 -9999 0 -0.44 1 1
PTK2B -0.008 0.076 -9999 0 -0.28 8 8
RHOA 0.019 0.031 -9999 0 -10000 0 0
PIK3CB 0.012 0.001 -9999 0 -10000 0 0
mol:Ca2+ 0.012 0.067 -9999 0 -10000 0 0
MAGI3 0.011 0.022 -9999 0 -0.44 1 1
RELA 0.012 0 -9999 0 -10000 0 0
apoptosis -0.036 0.12 -9999 0 -0.42 12 12
HRAS/GDP 0.008 0.015 -9999 0 -0.31 1 1
positive regulation of microtubule depolymerization -0.041 0.12 -9999 0 -0.35 25 25
NF kappa B1 p50/RelA -0.041 0.084 -9999 0 -0.47 1 1
endothelial cell migration -0.02 0.11 -9999 0 -0.64 4 4
ADCY4 -0.072 0.19 -9999 0 -0.49 62 62
ADCY5 -0.16 0.26 -9999 0 -0.54 118 118
ADCY6 -0.072 0.19 -9999 0 -0.49 62 62
ADCY7 -0.072 0.19 -9999 0 -0.49 62 62
ADCY1 -0.076 0.19 -9999 0 -0.48 64 64
ADCY2 -0.091 0.22 -9999 0 -0.52 76 76
ADCY3 -0.072 0.19 -9999 0 -0.49 62 62
ADCY8 -0.078 0.19 -9999 0 -0.5 62 62
ADCY9 -0.073 0.19 -9999 0 -0.48 64 64
GSK3B -0.001 0.072 -9999 0 -0.34 2 2
arachidonic acid secretion -0.078 0.2 -9999 0 -0.55 50 50
GNG2 -0.007 0.09 -9999 0 -0.44 18 18
TRIP6 0.02 0.018 -9999 0 -0.33 1 1
GNAO1 -0.089 0.18 -9999 0 -0.49 43 43
HRAS 0.011 0.022 -9999 0 -0.44 1 1
NFKBIA 0.001 0.086 -9999 0 -10000 0 0
GAB1 0.012 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.064 0.27 -9999 0 -0.88 42 42
JUN 0.012 0 -9999 0 -10000 0 0
LPA/LPA2/NHERF2 0.017 0.016 -9999 0 -10000 0 0
TIAM1 -0.098 0.31 -9999 0 -1 42 42
PIK3R1 0.012 0.001 -9999 0 -10000 0 0
mol:IP3 0.011 0.068 -9999 0 -10000 0 0
PLCB3 0.021 0.014 -9999 0 -10000 0 0
FOS 0.005 0.057 -9999 0 -0.44 7 7
positive regulation of mitosis -0.078 0.2 -9999 0 -0.55 50 50
LPA/LPA1-2-3 -0.043 0.11 -9999 0 -0.44 12 12
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade -0.001 0.001 -9999 0 -10000 0 0
BCAR1 0.011 0.022 -9999 0 -0.44 1 1
stress fiber formation -0.01 0.089 -9999 0 -0.33 7 7
GNAZ -0.021 0.1 -9999 0 -0.26 31 31
EGFR/PI3K-beta/Gab1 -0.04 0.083 -9999 0 -10000 0 0
positive regulation of dendritic cell cytokine production -0.044 0.11 -9999 0 -0.44 12 12
LPA/LPA2/MAGI-3 0.017 0.016 -9999 0 -0.25 1 1
ARHGEF1 -0.002 0.083 -9999 0 -0.4 1 1
GNAI2 -0.018 0.098 -9999 0 -0.48 1 1
GNAI3 -0.018 0.098 -9999 0 -0.48 1 1
GNAI1 -0.026 0.12 -9999 0 -0.51 11 11
LPA/LPA3 -0.02 0.099 -9999 0 -0.35 34 34
LPA/LPA2 0.01 0.01 -9999 0 -10000 0 0
LPA/LPA1 -0.032 0.12 -9999 0 -0.31 64 64
HB-EGF/EGFR -0.033 0.14 -9999 0 -0.48 37 37
HBEGF -0.034 0.16 -9999 0 -0.54 40 40
mol:DAG 0.011 0.068 -9999 0 -10000 0 0
cAMP biosynthetic process -0.096 0.21 -9999 0 -0.55 57 57
NFKB1 0.012 0 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
GNB1 0.012 0.001 -9999 0 -10000 0 0
LYN 0.001 0.086 -9999 0 -10000 0 0
GNAQ -0.004 0.074 -9999 0 -0.32 6 6
LPAR2 0.012 0.001 -9999 0 -10000 0 0
LPAR3 -0.03 0.14 -9999 0 -0.48 34 34
LPAR1 -0.049 0.16 -9999 0 -0.44 61 61
IL8 -0.21 0.18 -9999 0 -0.44 65 65
PTK2 -0.025 0.11 -9999 0 -0.41 12 12
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
CASP3 -0.036 0.12 -9999 0 -0.43 12 12
EGFR 0.01 0.022 -9999 0 -0.44 1 1
PLCG1 0.001 0.078 -9999 0 -0.25 35 35
PLD2 -0.025 0.11 -9999 0 -0.41 12 12
G12/G13 -0.007 0.089 -9999 0 -0.43 1 1
PI3K-beta -0.026 0.065 -9999 0 -0.51 1 1
cell migration -0.012 0.095 -9999 0 -0.26 42 42
SLC9A3R2 0.011 0.022 -9999 0 -0.44 1 1
PXN -0.01 0.09 -9999 0 -0.34 7 7
HRAS/GTP -0.081 0.21 -9999 0 -0.58 47 47
RAC1 0.012 0 -9999 0 -10000 0 0
MMP9 -0.052 0.21 -9999 0 -0.71 38 38
PRKCE 0.012 0.001 -9999 0 -10000 0 0
PRKCD 0.015 0.065 -9999 0 -10000 0 0
Gi(beta/gamma) -0.072 0.2 -9999 0 -0.55 47 47
mol:LPA 0.002 0.016 -9999 0 -0.19 2 2
TRIP6/p130 Cas/FAK1/Paxillin -0.008 0.11 -9999 0 -0.4 8 8
MAPKKK cascade -0.078 0.2 -9999 0 -0.55 50 50
contractile ring contraction involved in cytokinesis 0.019 0.031 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.004 0.074 -9999 0 -0.32 6 6
GNA15 -0.006 0.079 -9999 0 -0.29 17 17
GNA12 0.012 0 -9999 0 -10000 0 0
GNA13 0.012 0 -9999 0 -10000 0 0
MAPT -0.042 0.12 -9999 0 -0.36 25 25
GNA11 -0.004 0.073 -9999 0 -0.28 11 11
Rac1/GTP -0.069 0.28 -9999 0 -0.93 42 42
MMP2 -0.02 0.11 -9999 0 -0.64 4 4
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.005 0.089 -10000 0 -0.42 5 5
ER alpha/Gai/GDP/Gbeta gamma -0.096 0.24 -10000 0 -0.71 43 43
AKT1 -0.059 0.25 -10000 0 -0.83 41 41
PIK3CA 0.012 0.001 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.064 0.26 -10000 0 -0.86 41 41
mol:Ca2+ 0.02 0.064 -10000 0 -0.42 5 5
IGF1R 0.012 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.01 0.08 -10000 0 -10000 0 0
SHC1 0.012 0 -10000 0 -10000 0 0
apoptosis 0.055 0.24 0.79 41 -10000 0 41
RhoA/GTP -0.018 0.052 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.095 0.18 -10000 0 -0.63 34 34
regulation of stress fiber formation -0.023 0.056 -10000 0 -10000 0 0
E2/ERA-ERB (dimer) -0.012 0.084 -10000 0 -0.26 43 43
KRAS 0.012 0 -10000 0 -10000 0 0
G13/GTP -0.008 0.072 -10000 0 -10000 0 0
pseudopodium formation 0.023 0.056 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1 -0.01 0.08 -10000 0 -10000 0 0
GRB2 0.012 0 -10000 0 -10000 0 0
GNG2 -0.007 0.091 -10000 0 -0.44 18 18
GNAO1 -0.11 0.2 -10000 0 -0.44 118 118
HRAS 0.011 0.022 -10000 0 -0.44 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.059 0.21 -10000 0 -0.6 47 47
E2/ER beta (dimer) 0.007 0.027 -10000 0 -0.31 3 3
mol:GDP -0.033 0.098 -10000 0 -0.33 41 41
mol:NADP -0.059 0.21 -10000 0 -0.6 47 47
PIK3R1 0.012 0 -10000 0 -10000 0 0
mol:IP3 0.02 0.066 -10000 0 -0.44 5 5
IGF-1R heterotetramer 0.012 0 -10000 0 -10000 0 0
PLCB1 0.015 0.067 -10000 0 -0.44 6 6
PLCB2 0.018 0.058 -10000 0 -0.54 2 2
IGF1 -0.1 0.2 -10000 0 -0.44 107 107
mol:L-citrulline -0.059 0.21 -10000 0 -0.6 47 47
RHOA 0.012 0 -10000 0 -10000 0 0
Gai/GDP -0.17 0.32 -10000 0 -0.68 118 118
JNK cascade 0.007 0.027 -10000 0 -0.31 3 3
BCAR1 0.011 0.022 -10000 0 -0.44 1 1
ESR2 0.009 0.038 -10000 0 -0.44 3 3
GNAQ 0.01 0.031 -10000 0 -0.44 2 2
ESR1 -0.031 0.13 -10000 0 -0.44 41 41
Gq family/GDP/Gbeta gamma 0.019 0.069 -10000 0 -0.48 3 3
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.004 0.085 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.094 0.18 -10000 0 -0.63 34 34
GNAZ 0.007 0.049 -10000 0 -0.44 5 5
E2/ER alpha (dimer) -0.022 0.094 -10000 0 -0.31 41 41
STRN 0.012 0.001 -10000 0 -10000 0 0
GNAL -0.016 0.11 -10000 0 -0.44 27 27
PELP1 0.012 0 -10000 0 -10000 0 0
MAPK11 0.012 0.041 -10000 0 -0.35 5 5
GNAI2 0.012 0 -10000 0 -10000 0 0
GNAI3 0.012 0 -10000 0 -10000 0 0
GNAI1 -0.003 0.083 -10000 0 -0.44 15 15
HBEGF -0.088 0.21 -10000 0 -0.59 46 46
cAMP biosynthetic process -0.033 0.086 -10000 0 -0.4 10 10
SRC -0.085 0.23 -10000 0 -0.66 43 43
PI3K 0.018 0 -10000 0 -10000 0 0
GNB1 0.012 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.035 0.093 -10000 0 -0.46 5 5
SOS1 0.012 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.11 0.18 -10000 0 -0.54 45 45
Gs family/GTP -0.033 0.087 -10000 0 -0.41 10 10
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.022 0.021 -10000 0 -10000 0 0
vasodilation -0.055 0.2 -10000 0 -0.57 47 47
mol:DAG 0.02 0.066 -10000 0 -0.44 5 5
Gs family/GDP/Gbeta gamma -0.043 0.1 -10000 0 -0.43 15 15
MSN 0.023 0.059 -10000 0 -10000 0 0
Gq family/GTP 0.012 0.06 -10000 0 -0.5 3 3
mol:PI-3-4-5-P3 -0.06 0.25 -10000 0 -0.82 41 41
NRAS 0.01 0.031 -10000 0 -0.44 2 2
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.055 0.2 0.57 47 -10000 0 47
GRB2/SOS1 0.018 0 -10000 0 -10000 0 0
RhoA/GDP -0.031 0.091 -10000 0 -0.5 1 1
NOS3 -0.064 0.22 -10000 0 -0.64 47 47
GNA11 0.01 0.031 -10000 0 -0.44 2 2
MAPKKK cascade -0.044 0.21 -10000 0 -0.65 41 41
E2/ER alpha (dimer)/PELP1/Src -0.1 0.19 -10000 0 -0.66 35 35
ruffle organization 0.023 0.056 -10000 0 -10000 0 0
ROCK2 0.018 0.064 -10000 0 -10000 0 0
GNA14 0.01 0.031 -10000 0 -0.44 2 2
GNA15 0.005 0.072 -10000 0 -0.74 4 4
GNA13 0.012 0 -10000 0 -10000 0 0
MMP9 -0.11 0.23 -10000 0 -0.61 47 47
MMP2 -0.076 0.22 -10000 0 -0.62 43 43
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.005 0.072 -9999 0 -0.74 4 4
alphaV beta3 Integrin 0.015 0.031 -9999 0 -0.3 4 4
PTK2 0.029 0.063 -9999 0 -10000 0 0
positive regulation of JNK cascade -0.008 0.046 -9999 0 -0.27 13 13
CDC42/GDP 0.038 0.072 -9999 0 -0.35 13 13
Rac1/GDP 0.039 0.072 -9999 0 -0.35 13 13
RAP1B 0.012 0 -9999 0 -10000 0 0
RAP1A 0.012 0 -9999 0 -10000 0 0
CTNNB1 0.012 0 -9999 0 -10000 0 0
CDC42/GTP -0.01 0.055 -9999 0 -0.32 13 13
nectin-3/I-afadin 0.009 0.055 -9999 0 -0.3 13 13
RAPGEF1 0.035 0.075 -9999 0 -0.38 13 13
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.03 0.082 -9999 0 -0.44 13 13
PDGFB-D/PDGFRB 0.005 0.072 -9999 0 -0.74 4 4
TLN1 0.022 0.029 -9999 0 -10000 0 0
Rap1/GTP -0.009 0.048 -9999 0 -10000 0 0
IQGAP1 0.012 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.023 0.012 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.009 0.055 -9999 0 -0.3 13 13
PVR 0.012 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.012 0 -9999 0 -10000 0 0
mol:GDP 0.035 0.085 -9999 0 -0.42 13 13
MLLT4 0.011 0.022 -9999 0 -0.44 1 1
PIK3CA 0.012 0.001 -9999 0 -10000 0 0
PI3K 0.025 0.058 -9999 0 -0.4 4 4
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.018 0.016 -9999 0 -0.3 1 1
positive regulation of lamellipodium assembly -0.013 0.056 -9999 0 -0.28 15 15
PVRL1 0.012 0 -9999 0 -10000 0 0
PVRL3 0 0.075 -9999 0 -0.44 12 12
PVRL2 0.012 0 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
CDH1 0.012 0 -9999 0 -10000 0 0
CLDN1 -0.67 0.21 -9999 0 -0.74 394 394
JAM-A/CLDN1 -0.4 0.14 -9999 0 -0.44 394 394
SRC 0.025 0.089 -9999 0 -0.48 13 13
ITGB3 0.008 0.043 -9999 0 -0.44 4 4
nectin-1(dimer)/I-afadin/I-afadin 0.018 0.016 -9999 0 -0.3 1 1
FARP2 0.034 0.08 -9999 0 -0.42 13 13
RAC1 0.012 0 -9999 0 -10000 0 0
CTNNA1 0.012 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.017 0.047 -9999 0 -10000 0 0
nectin-1/I-afadin 0.018 0.016 -9999 0 -0.3 1 1
nectin-2/I-afadin 0.018 0.016 -9999 0 -0.3 1 1
RAC1/GTP/IQGAP1/filamentous actin 0.017 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.017 0.047 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1/filamentous actin 0.016 0.013 -9999 0 -0.26 1 1
F11R 0.012 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.008 0.046 -9999 0 -0.27 13 13
alphaV/beta3 Integrin/Talin 0.032 0.034 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.018 0.016 -9999 0 -0.3 1 1
nectin-2(dimer)/I-afadin/I-afadin 0.018 0.016 -9999 0 -0.3 1 1
PIP5K1C 0.017 0.031 -9999 0 -10000 0 0
VAV2 0.025 0.1 -9999 0 -0.43 21 21
RAP1/GDP -0.011 0.056 -9999 0 -0.32 13 13
ITGAV 0.012 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.017 0.047 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin 0.009 0.055 -9999 0 -0.3 13 13
Rac1/GTP -0.015 0.067 -9999 0 -0.33 15 15
PTPRM 0.011 0.032 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin 0.036 0.011 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.011 0.022 -9999 0 -0.44 1 1
HIF-2-alpha transcription factor network

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
MMP14 -0.016 0.075 -10000 0 -0.62 6 6
oxygen homeostasis -0.012 0.013 -10000 0 -10000 0 0
TCEB2 0.011 0.036 -10000 0 -0.74 1 1
TCEB1 0.012 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.033 0.057 -10000 0 -0.4 1 1
EPO -0.14 0.2 -10000 0 -0.7 9 9
FIH (dimer) 0.003 0.011 -10000 0 -10000 0 0
APEX1 -0.002 0.015 -10000 0 -10000 0 0
SERPINE1 -0.22 0.34 -10000 0 -0.82 88 88
FLT1 -0.005 0.026 -10000 0 -10000 0 0
ADORA2A -0.15 0.22 -10000 0 -0.66 34 34
germ cell development -0.15 0.22 -10000 0 -0.67 37 37
SLC11A2 -0.15 0.23 -10000 0 -0.69 34 34
BHLHE40 -0.15 0.23 -10000 0 -0.7 35 35
HIF1AN 0.003 0.011 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.072 0.12 -10000 0 -10000 0 0
ETS1 0.026 0.001 -10000 0 -10000 0 0
CITED2 -0.009 0.023 -10000 0 -10000 0 0
KDR -0.007 0.059 -10000 0 -1.1 1 1
PGK1 -0.15 0.23 -10000 0 -0.69 34 34
SIRT1 0.012 0.001 -10000 0 -10000 0 0
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT -0.18 0.26 -10000 0 -0.82 34 34
EPAS1 -0.044 0.081 -10000 0 -10000 0 0
SP1 0.019 0.002 -10000 0 -10000 0 0
ABCG2 -0.38 0.28 -10000 0 -0.73 110 110
EFNA1 -0.15 0.23 -10000 0 -0.69 34 34
FXN -0.15 0.22 -10000 0 -0.66 34 34
POU5F1 -0.16 0.23 -10000 0 -0.7 37 37
neuron apoptosis 0.17 0.26 0.79 34 -10000 0 34
EP300 0.012 0 -10000 0 -10000 0 0
EGLN3 -0.003 0.05 -10000 0 -0.45 5 5
EGLN2 0.002 0.024 -10000 0 -0.45 1 1
EGLN1 0.003 0.011 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.024 0.024 -10000 0 -0.48 1 1
VHL 0.012 0 -10000 0 -10000 0 0
ARNT -0.003 0.026 -10000 0 -0.46 1 1
SLC2A1 -0.16 0.24 -10000 0 -0.71 45 45
TWIST1 -0.17 0.28 -10000 0 -0.84 44 44
ELK1 0.019 0 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.067 0.12 -10000 0 -10000 0 0
VEGFA -0.15 0.23 -10000 0 -0.69 35 35
CREBBP 0.012 0 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.011 0.022 -9999 0 -0.44 1 1
EGFR 0.011 0.022 -9999 0 -0.44 1 1
EGF/EGFR -0.048 0.15 -9999 0 -0.46 33 33
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.017 0.11 -9999 0 -0.4 16 16
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.024 0.16 -9999 0 -0.74 21 21
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.087 0.21 -9999 0 -0.5 83 83
EGF/EGFR dimer/SHC -0.037 0.13 -9999 0 -0.48 16 16
mol:GDP -0.02 0.11 -9999 0 -0.4 16 16
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.009 0.038 -9999 0 -0.44 3 3
GRB2/SOS1 0.018 0 -9999 0 -10000 0 0
HRAS/GTP -0.042 0.091 -9999 0 -0.37 16 16
SHC1 0.012 0 -9999 0 -10000 0 0
HRAS/GDP -0.043 0.093 -9999 0 -0.38 16 16
FRAP1 -0.021 0.11 -9999 0 -0.38 16 16
EGF/EGFR dimer -0.055 0.15 -9999 0 -0.35 84 84
SOS1 0.012 0 -9999 0 -10000 0 0
GRB2 0.012 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.012 0.13 -9999 0 -0.52 24 24
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.002 0.08 -9999 0 -0.44 14 14
GNB1/GNG2 -0.041 0.13 -9999 0 -0.42 23 23
mol:DAG -0.033 0.12 -9999 0 -0.39 20 20
PLCG1 -0.034 0.13 -9999 0 -0.4 19 19
YES1 -0.041 0.13 -9999 0 -0.45 17 17
FZD3 0.007 0.062 -9999 0 -0.74 3 3
FZD6 0.012 0 -9999 0 -10000 0 0
G protein -0.034 0.13 -9999 0 -0.4 20 20
MAP3K7 -0.033 0.12 -9999 0 -0.42 5 5
mol:Ca2+ -0.032 0.12 -9999 0 -0.38 20 20
mol:IP3 -0.033 0.12 -9999 0 -0.39 20 20
NLK -0.001 0.008 -9999 0 -10000 0 0
GNB1 0.012 0 -9999 0 -10000 0 0
CAMK2A -0.041 0.13 -9999 0 -0.4 12 12
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.05 0.14 -9999 0 -0.48 17 17
CSNK1A1 0.012 0 -9999 0 -10000 0 0
GNAS -0.041 0.13 -9999 0 -0.45 17 17
GO:0007205 -0.033 0.12 -9999 0 -0.38 20 20
WNT6 -0.026 0.15 -9999 0 -0.62 25 25
WNT4 -0.012 0.11 -9999 0 -0.48 21 21
NFAT1/CK1 alpha -0.027 0.13 -9999 0 -0.59 4 4
GNG2 -0.007 0.091 -9999 0 -0.44 18 18
WNT5A 0.004 0.075 -9999 0 -0.68 5 5
WNT11 -0.13 0.29 -9999 0 -0.7 88 88
CDC42 -0.034 0.13 -9999 0 -0.42 18 18
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.006 0.062 -10000 0 -0.74 3 3
GNB1/GNG2 -0.068 0.058 -10000 0 -0.2 23 23
AKT1 -0.034 0.079 -10000 0 -0.22 1 1
EGF -0.087 0.21 -10000 0 -0.5 83 83
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR -0.058 0.087 -10000 0 -0.32 4 4
mol:Ca2+ -0.062 0.11 -10000 0 -0.29 23 23
LYN -0.056 0.084 -10000 0 -10000 0 0
RhoA/GTP -0.03 0.043 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.068 0.12 -10000 0 -0.32 23 23
GNG2 -0.007 0.091 -10000 0 -0.44 18 18
ARRB2 0.012 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.005 0.064 -10000 0 -0.41 5 5
G beta5/gamma2 -0.085 0.074 -10000 0 -0.26 23 23
PRKCH -0.066 0.12 -10000 0 -0.36 11 11
DNM1 0.005 0.072 -10000 0 -0.74 4 4
TXA2/TP beta/beta Arrestin3 -0.025 0.029 -10000 0 -0.26 2 2
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.24 0.23 -10000 0 -0.44 238 238
G12 family/GTP -0.08 0.091 -10000 0 -0.29 23 23
ADRBK1 0.012 0 -10000 0 -10000 0 0
ADRBK2 0.012 0 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.015 0.013 -10000 0 -10000 0 0
mol:GDP 0.072 0.088 0.27 19 -10000 0 19
mol:NADP -0.003 0.11 -10000 0 -0.74 9 9
RAB11A 0.012 0 -10000 0 -10000 0 0
PRKG1 -0.011 0.1 -10000 0 -0.44 22 22
mol:IP3 -0.077 0.13 -10000 0 -0.36 23 23
cell morphogenesis 0.015 0.013 -10000 0 -10000 0 0
PLCB2 -0.1 0.16 -10000 0 -0.48 23 23
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.12 0.13 -10000 0 -0.32 75 75
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.061 0.091 -10000 0 -0.32 4 4
RHOA 0.012 0 -10000 0 -10000 0 0
PTGIR 0.012 0.001 -10000 0 -10000 0 0
PRKCB1 -0.072 0.12 -10000 0 -0.34 23 23
GNAQ 0.01 0.031 -10000 0 -0.44 2 2
mol:L-citrulline -0.003 0.11 -10000 0 -0.74 9 9
TXA2/TXA2-R family -0.11 0.17 -10000 0 -0.46 41 41
LCK -0.063 0.096 -10000 0 -0.39 9 9
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.092 0.091 -10000 0 -0.36 2 2
TXA2-R family/G12 family/GDP/G beta/gamma -0.016 0.048 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.077 0.098 -10000 0 -10000 0 0
MAPK14 -0.041 0.087 -10000 0 -0.24 8 8
TGM2/GTP -0.092 0.15 -10000 0 -0.42 23 23
MAPK11 -0.042 0.089 -10000 0 -0.25 10 10
ARHGEF1 -0.033 0.07 -10000 0 -0.19 4 4
GNAI2 0.012 0 -10000 0 -10000 0 0
JNK cascade -0.08 0.14 -10000 0 -0.34 41 41
RAB11/GDP 0.013 0.001 -10000 0 -10000 0 0
ICAM1 -0.053 0.1 -10000 0 -0.29 11 11
cAMP biosynthetic process -0.084 0.13 -10000 0 -0.35 23 23
Gq family/GTP/EBP50 0.02 0.041 -10000 0 -0.58 1 1
actin cytoskeleton reorganization 0.015 0.013 -10000 0 -10000 0 0
SRC -0.056 0.084 -10000 0 -10000 0 0
GNB5 0.012 0 -10000 0 -10000 0 0
GNB1 0.012 0 -10000 0 -10000 0 0
EGF/EGFR -0.081 0.097 -10000 0 -0.32 8 8
VCAM1 -0.059 0.11 -10000 0 -0.37 12 12
TP beta/Gq family/GDP/G beta5/gamma2 -0.005 0.064 -10000 0 -0.41 5 5
platelet activation -0.057 0.12 -10000 0 -0.31 12 12
PGI2/IP 0.009 0.001 -10000 0 -10000 0 0
PRKACA -0.11 0.12 -10000 0 -0.28 1 1
Gq family/GDP/G beta5/gamma2 -0.016 0.068 -10000 0 -0.42 5 5
TXA2/TP beta/beta Arrestin2 -0.015 0.028 -10000 0 -0.29 3 3
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.099 0.11 -10000 0 -10000 0 0
mol:DAG -0.08 0.14 -10000 0 -0.38 23 23
EGFR 0.011 0.022 -10000 0 -0.44 1 1
TXA2/TP alpha -0.11 0.17 -10000 0 -0.48 23 23
Gq family/GTP 0.009 0.044 -10000 0 -0.36 3 3
YES1 -0.057 0.084 -10000 0 -10000 0 0
GNAI2/GTP -0.083 0.075 -10000 0 -10000 0 0
PGD2/DP -0.17 0.16 -10000 0 -0.31 238 238
SLC9A3R1 0.012 0 -10000 0 -10000 0 0
FYN -0.056 0.084 -10000 0 -10000 0 0
mol:NO -0.003 0.11 -10000 0 -0.74 9 9
GNA15 0.005 0.072 -10000 0 -0.74 4 4
PGK/cGMP -0.008 0.094 -10000 0 -0.33 30 30
RhoA/GDP 0.013 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.082 0.12 -10000 0 -0.38 16 16
NOS3 -0.003 0.11 -10000 0 -0.74 9 9
RAC1 0.012 0 -10000 0 -10000 0 0
PRKCA -0.065 0.12 -10000 0 -0.35 11 11
PRKCB -0.093 0.13 -10000 0 -0.41 15 15
PRKCE -0.062 0.12 -10000 0 -0.35 11 11
PRKCD -0.068 0.12 -10000 0 -0.38 11 11
PRKCG -0.12 0.18 -10000 0 -0.42 63 63
muscle contraction -0.099 0.16 -10000 0 -0.43 41 41
PRKCZ -0.068 0.12 -10000 0 -0.32 23 23
ARR3 0 0.05 -10000 0 -0.74 2 2
TXA2/TP beta -0.079 0.1 -10000 0 -10000 0 0
PRKCQ -0.065 0.12 -10000 0 -0.32 24 24
MAPKKK cascade -0.092 0.15 -10000 0 -0.43 23 23
SELE -0.075 0.13 -10000 0 -0.31 83 83
TP beta/GNAI2/GDP/G beta/gamma -0.079 0.11 -10000 0 -0.36 13 13
ROCK1 0.011 0.022 -10000 0 -0.44 1 1
GNA14 0.01 0.031 -10000 0 -0.44 2 2
chemotaxis -0.11 0.19 -10000 0 -0.51 41 41
GNA12 0.012 0 -10000 0 -10000 0 0
GNA13 0.012 0 -10000 0 -10000 0 0
GNA11 0.01 0.031 -10000 0 -0.44 2 2
Rac1/GTP 0.008 0.002 -10000 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.012 0 -9999 0 -10000 0 0
ITGB7 -0.005 0.086 -9999 0 -0.44 16 16
ITGA4 -0.005 0.086 -9999 0 -0.44 16 16
alpha4/beta7 Integrin -0.005 0.09 -9999 0 -0.33 29 29
alpha4/beta1 Integrin 0.006 0.061 -9999 0 -0.3 16 16
RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.017 0.039 -9999 0 -0.55 1 1
VDR 0.012 0 -9999 0 -10000 0 0
FAM120B 0.012 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.042 0.12 -9999 0 -0.48 2 2
RXRs/LXRs/DNA/Oxysterols -0.025 0.11 -9999 0 -0.4 8 8
MED1 0.011 0.036 -9999 0 -0.74 1 1
mol:9cRA 0.004 0.007 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.036 0.11 -9999 0 -0.42 2 2
RXRs/NUR77 -0.063 0.14 -9999 0 -0.52 7 7
RXRs/PPAR -0.054 0.12 -9999 0 -0.45 3 3
NCOR2 0.011 0.022 -9999 0 -0.44 1 1
VDR/VDR/Vit D3 0.009 0 -9999 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.026 0.033 -9999 0 -0.41 1 1
RARA 0.009 0.042 -9999 0 -0.59 2 2
NCOA1 0.012 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.012 0 -9999 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.021 0.033 -9999 0 -0.41 1 1
RARG 0.012 0 -9999 0 -10000 0 0
RPS6KB1 0.027 0.044 -9999 0 -0.42 1 1
RARs/THRs/DNA/SMRT -0.037 0.11 -9999 0 -0.42 3 3
THRA 0.011 0.036 -9999 0 -0.74 1 1
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA 0.009 0 -9999 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.059 0.12 -9999 0 -0.33 1 1
NR1H4 -0.24 0.22 -9999 0 -0.44 237 237
RXRs/LXRs/DNA -0.036 0.12 -9999 0 -0.4 1 1
NR1H2 0.016 0.023 -9999 0 -0.44 1 1
NR1H3 0.017 0.006 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.053 0.11 -9999 0 -10000 0 0
NR4A1 0.001 0.09 -9999 0 -0.69 7 7
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.17 0.15 -9999 0 -0.39 101 101
RXRG -0.16 0.22 -9999 0 -0.44 164 164
RXR alpha/CCPG 0.021 0.016 -9999 0 -0.3 1 1
RXRA 0.016 0.023 -9999 0 -0.44 1 1
RXRB 0.017 0.006 -9999 0 -10000 0 0
THRB -0.11 0.2 -9999 0 -0.44 120 120
PPARG 0.01 0.031 -9999 0 -0.44 2 2
PPARD 0.011 0.022 -9999 0 -0.44 1 1
TNF -0.019 0.12 -9999 0 -0.81 3 3
mol:Oxysterols 0.005 0.006 -9999 0 -10000 0 0
cholesterol transport -0.025 0.11 -9999 0 -0.39 8 8
PPARA 0.012 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB 0.008 0.043 -9999 0 -0.44 4 4
RXRs/NUR77/BCL2 -0.078 0.13 -9999 0 -0.5 11 11
SREBF1 -0.016 0.1 -9999 0 -0.51 1 1
RXRs/RXRs/DNA/9cRA -0.059 0.12 -9999 0 -0.33 1 1
ABCA1 -0.023 0.14 -9999 0 -0.99 5 5
RARs/THRs -0.034 0.11 -9999 0 -0.41 4 4
RXRs/FXR -0.19 0.17 -9999 0 -0.44 98 98
BCL2 -0.013 0.1 -9999 0 -0.44 24 24
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.012 0 -10000 0 -10000 0 0
HDAC3 0.012 0 -10000 0 -10000 0 0
VDR 0.012 0 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.014 0.055 -10000 0 -10000 0 0
EP300 0.012 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.002 0.058 -10000 0 -0.37 1 1
KAT2B -0.007 0.091 -10000 0 -0.44 18 18
MAPK14 0.012 0 -10000 0 -10000 0 0
AKT1 -0.006 0.065 0.17 7 -10000 0 7
RAR alpha/9cRA/Cyclin H -0.052 0.074 -10000 0 -0.52 1 1
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.002 0.065 -10000 0 -0.29 9 9
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.002 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.041 0.088 -10000 0 -0.36 1 1
NCOR2 0.011 0.022 -10000 0 -0.44 1 1
VDR/VDR/Vit D3 0.009 0 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.069 0.13 -10000 0 -0.49 2 2
NCOA2 0.011 0.022 -10000 0 -0.44 1 1
NCOA3 0.012 0 -10000 0 -10000 0 0
NCOA1 0.012 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.012 0 -10000 0 -10000 0 0
RARG 0.013 0.001 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.017 0.001 -10000 0 -10000 0 0
MAPK3 0.012 0.022 -10000 0 -0.44 1 1
MAPK1 0.012 0 -10000 0 -10000 0 0
MAPK8 0.013 0.002 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.086 0.14 -10000 0 -10000 0 0
RARA -0.05 0.11 -10000 0 -0.2 147 147
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.002 0.066 -10000 0 -0.29 9 9
PRKCA 0.015 0.004 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.084 0.14 -10000 0 -0.59 2 2
RXRG -0.21 0.22 -10000 0 -0.36 263 263
RXRA -0.04 0.098 -10000 0 -10000 0 0
RXRB -0.086 0.16 -10000 0 -0.3 146 146
VDR/Vit D3/DNA 0.009 0 -10000 0 -10000 0 0
RBP1 -0.031 0.18 -10000 0 -0.74 25 25
CRBP1/9-cic-RA -0.024 0.13 -10000 0 -0.56 25 25
RARB 0.01 0.044 -10000 0 -0.44 4 4
PRKCG -0.24 0.35 -10000 0 -0.73 146 146
MNAT1 0.011 0.036 -10000 0 -0.74 1 1
RAR alpha/RXRs -0.067 0.13 -10000 0 -0.34 1 1
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.059 0.12 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.018 0.084 -10000 0 -0.28 10 10
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.084 0.14 -10000 0 -0.59 2 2
positive regulation of DNA binding -0.05 0.07 -10000 0 -0.48 1 1
NRIP1 -0.082 0.14 -10000 0 -1.2 2 2
RXRs/RARs -0.092 0.14 -10000 0 -0.34 49 49
RXRs/RXRs/DNA/9cRA -0.095 0.14 -10000 0 -0.33 49 49
PRKACA 0.012 0 -10000 0 -10000 0 0
CDK7 0.012 0 -10000 0 -10000 0 0
TFIIH 0.024 0.024 -10000 0 -0.48 1 1
RAR alpha/9cRA -0.038 0.057 -10000 0 -0.5 1 1
CCNH 0.012 0 -10000 0 -10000 0 0
CREBBP 0.012 0 -10000 0 -10000 0 0
RAR gamma2/9cRA -0.001 0.018 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.032 0.2 -9999 0 -0.63 35 35
MKNK1 0.012 0 -9999 0 -10000 0 0
MAPK14 -0.008 0.094 -9999 0 -0.39 3 3
ATF2/c-Jun 0.009 0.076 -9999 0 -0.44 2 2
MAPK11 -0.012 0.11 -9999 0 -0.6 5 5
MITF -0.01 0.13 -9999 0 -0.56 6 6
MAPKAPK5 -0.003 0.12 -9999 0 -0.34 29 29
KRT8 -0.003 0.12 -9999 0 -0.34 29 29
MAPKAPK3 0.012 0 -9999 0 -10000 0 0
MAPKAPK2 0.012 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.015 0.15 -9999 0 -0.44 30 30
CEBPB -0.003 0.12 -9999 0 -0.52 4 4
SLC9A1 -0.005 0.12 -9999 0 -0.36 30 30
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 0.002 0.11 -9999 0 -0.52 4 4
p38alpha-beta/MNK1 -0.001 0.12 -9999 0 -0.59 5 5
JUN 0.009 0.076 -9999 0 -0.43 2 2
PPARGC1A -0.044 0.17 -9999 0 -0.64 13 13
USF1 -0.003 0.12 -9999 0 -0.34 29 29
RAB5/GDP/GDI1 -0.001 0.084 -9999 0 -0.4 4 4
NOS2 -0.043 0.25 -9999 0 -0.89 32 32
DDIT3 -0.003 0.12 -9999 0 -0.34 29 29
RAB5A 0.01 0.031 -9999 0 -0.44 2 2
HSPB1 0.004 0.096 -9999 0 -0.43 5 5
p38alpha-beta/HBP1 -0.001 0.12 -9999 0 -0.59 5 5
CREB1 -0.001 0.12 -9999 0 -0.37 29 29
RAB5/GDP 0.008 0.022 -9999 0 -0.31 2 2
EIF4E 0.001 0.11 -9999 0 -0.57 4 4
RPS6KA4 -0.003 0.12 -9999 0 -0.34 29 29
PLA2G4A -0.026 0.13 -9999 0 -0.55 9 9
GDI1 -0.003 0.12 -9999 0 -0.34 29 29
TP53 -0.01 0.14 -9999 0 -0.43 30 30
RPS6KA5 -0.005 0.12 -9999 0 -0.36 29 29
ESR1 -0.033 0.16 -9999 0 -0.71 10 10
HBP1 0.012 0 -9999 0 -10000 0 0
MEF2C -0.012 0.13 -9999 0 -0.58 7 7
MEF2A -0.003 0.12 -9999 0 -0.52 4 4
EIF4EBP1 -0.002 0.12 -9999 0 -0.37 29 29
KRT19 -0.004 0.12 -9999 0 -0.35 30 30
ELK4 -0.003 0.12 -9999 0 -0.34 29 29
ATF6 -0.003 0.12 -9999 0 -0.52 4 4
ATF1 -0.001 0.12 -9999 0 -0.37 29 29
p38alpha-beta/MAPKAPK2 -0.001 0.12 -9999 0 -0.59 5 5
p38alpha-beta/MAPKAPK3 -0.001 0.12 -9999 0 -0.59 5 5
ErbB4 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
ErbB4/ErbB4/HBEGF/HBEGF 0.027 0.048 -10000 0 -0.52 3 3
epithelial cell differentiation -0.018 0.069 -10000 0 -0.49 3 3
ITCH 0.012 0.022 -10000 0 -0.44 1 1
WWP1 0.027 0.063 -10000 0 -1.3 1 1
FYN 0.012 0 -10000 0 -10000 0 0
EGFR 0.011 0.022 -10000 0 -0.44 1 1
PRL -0.015 0.12 -10000 0 -0.74 12 12
neuron projection morphogenesis 0.027 0.075 -10000 0 -0.47 1 1
PTPRZ1 -0.14 0.21 -10000 0 -0.44 143 143
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.018 0.079 -10000 0 -0.52 1 1
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0 0.087 -10000 0 -0.6 1 1
ADAM17 0.013 0.005 -10000 0 -10000 0 0
ErbB4/ErbB4 0.028 0.039 -10000 0 -0.74 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.024 0.042 -10000 0 -0.56 2 2
NCOR1 0.012 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.006 0.082 -10000 0 -0.57 1 1
GRIN2B -0.091 0.19 -10000 0 -0.39 107 107
ErbB4/ErbB2/betacellulin 0.029 0.056 -10000 0 -0.44 5 5
STAT1 0.011 0.036 -10000 0 -0.74 1 1
HBEGF 0.009 0.051 -10000 0 -0.74 2 2
PRLR 0.002 0.068 -10000 0 -0.44 10 10
E4ICDs/ETO2 -0.006 0.094 -10000 0 -0.67 1 1
axon guidance 0.056 0.085 -10000 0 -0.75 1 1
NEDD4 0.013 0.006 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.01 0.11 -10000 0 -0.46 21 21
CBFA2T3 -0.049 0.16 -10000 0 -0.44 58 58
ErbB4/ErbB2/HBEGF 0.029 0.059 -10000 0 -0.42 7 7
MAPK3 0.022 0.076 -10000 0 -0.49 1 1
STAT1 (dimer) 0.028 0.042 -10000 0 -0.56 2 2
MAPK1 0.022 0.075 -10000 0 -0.49 1 1
JAK2 0.009 0.038 -10000 0 -0.44 3 3
ErbB4/ErbB2/neuregulin 1 beta 0.002 0.092 -10000 0 -0.48 5 5
NRG1 -0.021 0.11 -10000 0 -0.31 54 54
NRG3 0.005 0.036 -10000 0 -0.74 1 1
NRG2 -0.051 0.15 -10000 0 -0.45 56 56
NRG4 -0.042 0.14 -10000 0 -0.44 49 49
heart development 0.056 0.085 -10000 0 -0.75 1 1
neural crest cell migration 0.002 0.091 -10000 0 -0.47 5 5
ERBB2 0.015 0.056 -10000 0 -0.56 4 4
WWOX/E4ICDs 0.029 0.035 -10000 0 -0.67 1 1
SHC1 0.012 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.005 0.082 -10000 0 -0.64 1 1
apoptosis 0.024 0.056 0.63 1 -10000 0 1
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.007 0.095 -10000 0 -0.63 2 2
ErbB4/ErbB2/epiregulin -0.14 0.22 -10000 0 -0.4 169 169
ErbB4/ErbB4/betacellulin/betacellulin 0.027 0.043 -10000 0 -0.67 1 1
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.021 0.09 -10000 0 -0.4 15 15
MDM2 0.03 0.039 -10000 0 -0.52 2 2
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.001 0.083 -10000 0 -0.53 1 1
STAT5A 0.061 0.078 -10000 0 -0.72 1 1
ErbB4/EGFR/neuregulin 1 beta 0.006 0.082 -10000 0 -0.57 1 1
DLG4 0.011 0.036 -10000 0 -0.74 1 1
GRB2/SHC 0.018 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.026 0.033 -10000 0 -0.64 1 1
STAT5A (dimer) -0.019 0.074 -10000 0 -0.54 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.058 0.074 -10000 0 -0.72 1 1
LRIG1 0.012 0 -10000 0 -10000 0 0
EREG -0.29 0.36 -10000 0 -0.72 177 177
BTC 0.008 0.043 -10000 0 -0.44 4 4
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.056 0.085 -10000 0 -0.76 1 1
ERBB4 0.028 0.039 -10000 0 -0.75 1 1
STAT5B 0.012 0 -10000 0 -10000 0 0
YAP1 0.016 0.009 -10000 0 -10000 0 0
GRB2 0.012 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.003 0.09 -10000 0 -0.48 5 5
glial cell differentiation -0.026 0.033 0.63 1 -10000 0 1
WWOX 0.012 0 -10000 0 -10000 0 0
cell proliferation 0.018 0.1 -10000 0 -0.62 2 2
IL27-mediated signaling events

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
TGFB1 -0.035 0.1 -10000 0 -0.74 1 1
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.003 0.11 0.51 3 -10000 0 3
IL27/IL27R/JAK1 0.012 0.13 -10000 0 -0.78 1 1
TBX21 0.011 0.16 -10000 0 -0.57 15 15
IL12B 0 0.072 -10000 0 -0.74 4 4
IL12A 0.003 0.047 -10000 0 -0.35 7 7
IL6ST 0.003 0.067 -10000 0 -0.45 9 9
IL27RA/JAK1 0.021 0.024 -10000 0 -10000 0 0
IL27 -0.016 0.14 -10000 0 -0.74 15 15
TYK2 0.013 0.005 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.15 0.26 -10000 0 -0.58 97 97
T-helper 2 cell differentiation 0.003 0.11 0.51 3 -10000 0 3
T cell proliferation during immune response 0.003 0.11 0.51 3 -10000 0 3
MAPKKK cascade -0.003 0.11 -10000 0 -0.51 3 3
STAT3 0.012 0 -10000 0 -10000 0 0
STAT2 0.012 0 -10000 0 -10000 0 0
STAT1 0.011 0.037 -10000 0 -0.75 1 1
IL12RB1 -0.008 0.095 -10000 0 -0.46 18 18
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.017 0.15 -10000 0 -0.65 8 8
IL27/IL27R/JAK2/TYK2 -0.004 0.11 -10000 0 -0.52 3 3
positive regulation of T cell mediated cytotoxicity -0.003 0.11 -10000 0 -0.51 3 3
STAT1 (dimer) -0.006 0.18 -10000 0 -0.72 6 6
JAK2 0.011 0.039 -10000 0 -0.44 3 3
JAK1 0.012 0.022 -10000 0 -0.44 1 1
STAT2 (dimer) 0.002 0.1 -10000 0 -0.49 3 3
T cell proliferation -0.088 0.2 -10000 0 -0.51 57 57
IL12/IL12R/TYK2/JAK2 0.001 0.09 -10000 0 -0.45 1 1
IL17A -0.15 0.25 -10000 0 -0.58 97 97
mast cell activation 0.003 0.11 0.51 3 -10000 0 3
IFNG -0.003 0.035 -10000 0 -0.089 47 47
T cell differentiation -0.002 0.005 -10000 0 -0.019 10 10
STAT3 (dimer) 0.002 0.1 -10000 0 -0.54 2 2
STAT5A (dimer) 0.002 0.1 -10000 0 -0.49 3 3
STAT4 (dimer) -0.01 0.12 -10000 0 -0.45 11 11
STAT4 -0.013 0.1 -10000 0 -0.44 24 24
T cell activation -0.007 0.003 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.017 0.057 -10000 0 -10000 0 0
GATA3 0 0.12 -10000 0 -1.2 4 4
IL18 0.008 0.022 -10000 0 -0.31 2 2
positive regulation of mast cell cytokine production 0.002 0.1 -10000 0 -0.52 2 2
IL27/EBI3 -0.028 0.14 -10000 0 -0.39 50 50
IL27RA 0.011 0.02 -10000 0 -10000 0 0
IL6 -0.16 0.3 -10000 0 -0.78 72 72
STAT5A 0.012 0 -10000 0 -10000 0 0
monocyte differentiation 0 0.002 -10000 0 -10000 0 0
IL2 0.001 0.01 -10000 0 -10000 0 0
IL1B -0.054 0.18 -10000 0 -0.55 49 49
EBI3 -0.025 0.13 -10000 0 -0.44 36 36
TNF 0.008 0.022 -10000 0 -0.31 2 2
Arf6 signaling events

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
CENTA1/KIF3B 0.015 0.028 -9999 0 -0.38 2 2
ARNO/beta Arrestin1-2 -0.012 0.075 -9999 0 -10000 0 0
EGFR 0.011 0.022 -9999 0 -0.44 1 1
EPHA2 0.011 0.036 -9999 0 -0.74 1 1
USP6 0.011 0.036 -9999 0 -0.74 1 1
IQSEC1 0.012 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.055 0.15 -9999 0 -0.35 84 84
ARRB2 0.008 0.002 -9999 0 -10000 0 0
mol:GTP 0.012 0.028 -9999 0 -0.25 2 2
ARRB1 0.011 0.022 -9999 0 -0.44 1 1
FBXO8 0.01 0.031 -9999 0 -0.44 2 2
TSHR 0 0.061 -9999 0 -0.44 8 8
EGF -0.087 0.21 -9999 0 -0.5 83 83
somatostatin receptor activity 0 0 -9999 0 -0.001 15 15
ARAP2 0.011 0.022 -9999 0 -0.44 1 1
mol:GDP -0.047 0.092 -9999 0 -0.25 41 41
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 3 3
ITGA2B -0.022 0.15 -9999 0 -0.74 19 19
ARF6 0.012 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.03 0.025 -9999 0 -0.43 1 1
ADAP1 0.011 0.022 -9999 0 -0.44 1 1
KIF13B 0.01 0.031 -9999 0 -0.44 2 2
HGF/MET 0.006 0.077 -9999 0 -0.43 12 12
PXN 0.012 0 -9999 0 -10000 0 0
ARF6/GTP -0.038 0.09 -9999 0 -0.26 17 17
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.038 0.13 -9999 0 -0.48 16 16
ADRB2 -0.063 0.17 -9999 0 -0.44 71 71
receptor agonist activity 0 0 -9999 0 0 18 18
actin filament binding 0 0 -9999 0 -0.001 16 16
SRC 0.012 0 -9999 0 -10000 0 0
ITGB3 0.008 0.043 -9999 0 -0.44 4 4
GNAQ 0.01 0.031 -9999 0 -0.44 2 2
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 10 10
ARF6/GDP 0.007 0.08 -9999 0 -0.32 16 16
ARF6/GDP/GULP/ACAP1 -0.043 0.11 -9999 0 -0.39 13 13
alphaIIb/beta3 Integrin/paxillin/GIT1 0.008 0.098 -9999 0 -0.43 19 19
ACAP1 -0.008 0.093 -9999 0 -0.44 19 19
ACAP2 0.011 0.022 -9999 0 -0.44 1 1
LHCGR/beta Arrestin2 0.001 0.004 -9999 0 -10000 0 0
EFNA1 0.012 0 -9999 0 -10000 0 0
HGF 0.004 0.064 -9999 0 -0.48 7 7
CYTH3 0.01 0 -9999 0 -10000 0 0
CYTH2 0.008 0.002 -9999 0 -10000 0 0
NCK1 0.012 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 8 8
endosomal lumen acidification 0 0 -9999 0 -0.001 2 2
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.01 0.098 -9999 0 -0.44 21 21
GNAQ/ARNO 0.014 0.016 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 2 2
MET 0.004 0.08 -9999 0 -0.74 5 5
GNA14 0.01 0.031 -9999 0 -0.44 2 2
GNA15 0.005 0.072 -9999 0 -0.74 4 4
GIT1 0.011 0.022 -9999 0 -0.44 1 1
mol:PI-4-5-P2 0 0 -9999 0 -0.001 15 15
GNA11 0.01 0.031 -9999 0 -0.44 2 2
LHCGR 0.001 0.004 -9999 0 -10000 0 0
AGTR1 -0.14 0.21 -9999 0 -0.44 144 144
desensitization of G-protein coupled receptor protein signaling pathway 0.001 0.004 -9999 0 -10000 0 0
IPCEF1/ARNO -0.027 0.1 -9999 0 -0.37 16 16
alphaIIb/beta3 Integrin -0.011 0.12 -9999 0 -0.51 23 23
Neurotrophic factor-mediated Trk receptor 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
CRKL 0.012 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.026 0.1 -10000 0 -0.35 19 19
NT3 (dimer)/TRKC -0.05 0.14 -10000 0 -0.32 85 85
NT3 (dimer)/TRKB -0.14 0.2 -10000 0 -0.51 64 64
SHC/Grb2/SOS1/GAB1/PI3K 0.032 0 -10000 0 -10000 0 0
RAPGEF1 0.011 0.022 -10000 0 -0.44 1 1
BDNF -0.005 0.11 -10000 0 -0.74 10 10
PIK3CA 0.012 0.001 -10000 0 -10000 0 0
DYNLT1 0.012 0 -10000 0 -10000 0 0
NTRK1 0.004 0.072 -10000 0 -0.74 4 4
NTRK2 -0.13 0.22 -10000 0 -0.46 128 128
NTRK3 -0.075 0.18 -10000 0 -0.44 81 81
NT-4/5 (dimer)/TRKB -0.16 0.21 -10000 0 -0.51 78 78
neuron apoptosis 0.12 0.18 0.42 84 -10000 0 84
SHC 2-3/Grb2 -0.13 0.2 -10000 0 -0.46 84 84
SHC1 0.012 0 -10000 0 -10000 0 0
SHC2 -0.12 0.16 -10000 0 -0.44 69 69
SHC3 -0.15 0.19 -10000 0 -0.48 86 86
STAT3 (dimer) 0.017 0.026 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.063 0.14 -10000 0 -0.48 7 7
RIN/GDP -0.007 0.069 -10000 0 -0.28 1 1
GIPC1 0.011 0.022 -10000 0 -0.44 1 1
KRAS 0.012 0 -10000 0 -10000 0 0
DNAJA3 -0.068 0.14 -10000 0 -0.46 9 9
RIN/GTP -0.001 0.027 -10000 0 -0.56 1 1
CCND1 0.022 0.054 -10000 0 -0.62 3 3
MAGED1 0.012 0 -10000 0 -10000 0 0
PTPN11 0.012 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.026 0.15 -10000 0 -0.74 18 18
SHC/GRB2/SOS1 0.025 0 -10000 0 -10000 0 0
GRB2 0.012 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.023 0.11 -10000 0 -0.48 6 6
TRKA/NEDD4-2 0.011 0.057 -10000 0 -0.51 5 5
ELMO1 0.011 0.022 -10000 0 -0.44 1 1
RhoG/GTP/ELMO1/DOCK1 0.016 0.013 -10000 0 -0.26 1 1
NGF -0.008 0.095 -10000 0 -0.46 18 18
HRAS 0.011 0.022 -10000 0 -0.44 1 1
DOCK1 0.012 0 -10000 0 -10000 0 0
GAB2 0.012 0 -10000 0 -10000 0 0
RIT2 -0.001 0.036 -10000 0 -0.74 1 1
RIT1 0.012 0 -10000 0 -10000 0 0
FRS2 0.012 0.001 -10000 0 -10000 0 0
DNM1 0.005 0.072 -10000 0 -0.74 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.012 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.066 0.13 -10000 0 -0.45 9 9
mol:GDP -0.01 0.095 -10000 0 -0.34 1 1
NGF (dimer) -0.008 0.095 -10000 0 -0.46 18 18
RhoG/GDP 0.008 0.015 -10000 0 -0.31 1 1
RIT1/GDP -0.001 0.069 -10000 0 -10000 0 0
TIAM1 -0.032 0.13 -10000 0 -0.44 42 42
PIK3R1 0.012 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.071 0.15 -10000 0 -0.49 16 16
KIDINS220/CRKL/C3G 0.018 0.016 -10000 0 -0.3 1 1
SHC/RasGAP 0.018 0 -10000 0 -10000 0 0
FRS2 family/SHP2 0.024 0.024 -10000 0 -0.48 1 1
SHC/GRB2/SOS1/GAB1 0.032 0 -10000 0 -10000 0 0
RIT1/GTP 0.009 0 -10000 0 -10000 0 0
NT3 (dimer) 0.002 0.065 -10000 0 -0.44 9 9
RAP1/GDP -0.024 0.042 -10000 0 -10000 0 0
KIDINS220/CRKL 0.012 0 -10000 0 -10000 0 0
BDNF (dimer) -0.005 0.11 -10000 0 -0.74 10 10
ubiquitin-dependent protein catabolic process 0.006 0.075 -10000 0 -0.48 5 5
Schwann cell development -0.029 0.03 -10000 0 -10000 0 0
EHD4 0.012 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.031 0.023 -10000 0 -0.44 1 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.034 0.016 -10000 0 -10000 0 0
RAP1B 0.012 0 -10000 0 -10000 0 0
RAP1A 0.012 0 -10000 0 -10000 0 0
CDC42/GTP -0.1 0.13 -10000 0 -0.55 7 7
ABL1 0.012 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.018 0 -10000 0 -10000 0 0
Rap1/GTP 0 0.067 -10000 0 -10000 0 0
STAT3 0.017 0.026 -10000 0 -10000 0 0
axon guidance -0.096 0.13 -10000 0 -0.53 7 7
MAPK3 -0.016 0.1 -10000 0 -0.43 6 6
MAPK1 -0.015 0.1 -10000 0 -0.43 6 6
CDC42/GDP -0.002 0.07 -10000 0 -0.29 1 1
NTF3 0.002 0.065 -10000 0 -0.44 9 9
NTF4 -0.026 0.15 -10000 0 -0.74 18 18
NGF (dimer)/TRKA/FAIM 0.007 0.075 -10000 0 -0.48 5 5
PI3K 0.018 0 -10000 0 -10000 0 0
FRS3 0.011 0.036 -10000 0 -0.74 1 1
FAIM 0.012 0.001 -10000 0 -10000 0 0
GAB1 0.012 0 -10000 0 -10000 0 0
RASGRF1 -0.094 0.17 -10000 0 -0.46 38 38
SOS1 0.012 0 -10000 0 -10000 0 0
MCF2L -0.035 0.12 -10000 0 -0.49 5 5
RGS19 0.011 0.022 -10000 0 -0.44 1 1
CDC42 0.011 0.022 -10000 0 -0.44 1 1
RAS family/GTP 0.005 0.069 -10000 0 -0.43 1 1
Rac1/GDP -0.001 0.069 -10000 0 -10000 0 0
NGF (dimer)/TRKA/GRIT -0.001 0.074 -10000 0 -0.48 5 5
neuron projection morphogenesis -0.059 0.14 -10000 0 -0.46 9 9
NGF (dimer)/TRKA/NEDD4-2 0.006 0.076 -10000 0 -0.48 5 5
MAP2K1 0.033 0 -10000 0 -10000 0 0
NGFR -0.12 0.2 -10000 0 -0.44 122 122
NGF (dimer)/TRKA/GIPC/GAIP 0.016 0.059 -10000 0 -10000 0 0
RAS family/GTP/PI3K 0.025 0.019 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.036 0.021 -10000 0 -0.41 1 1
NRAS 0.01 0.031 -10000 0 -0.44 2 2
GRB2/SOS1 0.018 0 -10000 0 -10000 0 0
PRKCI 0.01 0.031 -10000 0 -0.44 2 2
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.012 0 -10000 0 -10000 0 0
PRKCZ 0.012 0 -10000 0 -10000 0 0
MAPKKK cascade -0.055 0.12 -10000 0 -0.62 17 17
RASA1 0.012 0.001 -10000 0 -10000 0 0
TRKA/c-Abl 0.012 0.055 -10000 0 -0.56 4 4
SQSTM1 0.012 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.057 0.14 -10000 0 -0.45 16 16
NGF (dimer)/TRKA/p62/Atypical PKCs 0.02 0.07 -10000 0 -0.45 5 5
MATK -0.038 0.14 -10000 0 -0.44 48 48
NEDD4L 0.011 0.022 -10000 0 -0.44 1 1
RAS family/GDP -0.02 0.04 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.089 0.14 -10000 0 -0.29 122 122
Rac1/GTP -0.08 0.1 -10000 0 -0.34 25 25
FRS2 family/SHP2/CRK family 0.036 0.021 -10000 0 -0.41 1 1
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.017 0.017 -10000 0 -10000 0 0
HSPA8 0.011 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.026 0.11 -10000 0 -0.43 8 8
AKT1 -0.016 0.039 -10000 0 -10000 0 0
GSC -0.045 0.16 -10000 0 -0.53 42 42
NKX2-5 -0.017 0.12 -10000 0 -0.73 11 11
muscle cell differentiation 0.032 0.07 0.46 3 -10000 0 3
SMAD2-3/SMAD4/SP1 -0.023 0.098 -10000 0 -0.44 2 2
SMAD4 -0.006 0.048 -10000 0 -0.54 1 1
CBFB 0.012 0 -10000 0 -10000 0 0
SAP18 0.012 0.002 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.12 0.24 -10000 0 -0.47 133 133
SMAD3/SMAD4/VDR 0.032 0.043 -10000 0 -10000 0 0
MYC 0.03 0.094 -10000 0 -0.69 6 6
CDKN2B -0.48 0.65 -10000 0 -1.3 169 169
AP1 0.028 0.057 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.03 0.038 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.11 0.18 -10000 0 -0.45 43 43
SP3 0.014 0 -10000 0 -10000 0 0
CREB1 0.012 0 -10000 0 -10000 0 0
FOXH1 -0.009 0.092 -10000 0 -0.48 14 14
SMAD3/SMAD4/GR -0.005 0.1 -10000 0 -0.4 9 9
GATA3 0.002 0.066 -10000 0 -0.52 5 5
SKI/SIN3/HDAC complex/NCoR1 0.037 0.013 -10000 0 -10000 0 0
MEF2C/TIF2 -0.015 0.12 -10000 0 -0.49 4 4
endothelial cell migration 0.089 0.24 0.52 98 -10000 0 98
MAX 0.019 0.015 -10000 0 -10000 0 0
RBBP7 0.012 0.002 -10000 0 -10000 0 0
RBBP4 0.012 0.002 -10000 0 -10000 0 0
RUNX2 0.012 0 -10000 0 -10000 0 0
RUNX3 0.011 0.022 -10000 0 -0.44 1 1
RUNX1 0.012 0 -10000 0 -10000 0 0
CTBP1 0.012 0 -10000 0 -10000 0 0
NR3C1 -0.014 0.12 -10000 0 -0.44 31 31
VDR 0.012 0 -10000 0 -10000 0 0
CDKN1A 0.016 0.12 -10000 0 -1.3 2 2
KAT2B -0.005 0.089 -10000 0 -0.43 18 18
SMAD2/SMAD2/SMAD4/FOXH1 -0.022 0.089 -10000 0 -0.57 2 2
DCP1A 0.012 0 -10000 0 -10000 0 0
SKI 0.012 0.002 -10000 0 -10000 0 0
SERPINE1 -0.089 0.24 -10000 0 -0.53 97 97
SMAD3/SMAD4/ATF2 0.011 0.053 -10000 0 -0.4 1 1
SMAD3/SMAD4/ATF3 0.007 0.068 -10000 0 -0.44 5 5
SAP30 0.012 0.002 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.04 0.039 -10000 0 -10000 0 0
JUN 0.027 0.056 -10000 0 -10000 0 0
SMAD3/SMAD4/IRF7 0.011 0.055 -10000 0 -0.4 1 1
TFE3 0.009 0.016 -10000 0 -10000 0 0
COL1A2 -0.027 0.15 -10000 0 -0.58 29 29
mesenchymal cell differentiation -0.011 0.053 0.4 1 -10000 0 1
DLX1 -0.017 0.14 -10000 0 -0.74 15 15
TCF3 0.012 0 -10000 0 -10000 0 0
FOS 0.007 0.059 -10000 0 -0.45 7 7
SMAD3/SMAD4/Max 0.015 0.059 -10000 0 -0.4 1 1
Cbp/p300/SNIP1 0.026 0.016 -10000 0 -10000 0 0
ZBTB17 0.032 0.037 -10000 0 -0.44 1 1
LAMC1 0.017 0.047 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.001 0.089 -10000 0 -0.49 10 10
IRF7 0.012 0.022 -10000 0 -0.44 1 1
ESR1 -0.031 0.13 -10000 0 -0.44 41 41
HNF4A 0.012 0 -10000 0 -10000 0 0
MEF2C -0.023 0.12 -10000 0 -0.5 9 9
SMAD2-3/SMAD4 -0.018 0.081 -10000 0 -0.42 3 3
Cbp/p300/Src-1 0.032 0.024 -10000 0 -10000 0 0
IGHV3OR16-13 0 0.009 -10000 0 -10000 0 0
TGIF2/HDAC complex -0.002 0.1 -10000 0 -0.74 8 8
CREBBP 0.016 0.011 -10000 0 -10000 0 0
SKIL 0.011 0.022 -10000 0 -0.44 1 1
HDAC1 0.012 0.002 -10000 0 -10000 0 0
HDAC2 0.012 0.002 -10000 0 -10000 0 0
SNIP1 0.011 0.004 -10000 0 -10000 0 0
GCN5L2 0.004 0.014 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.013 0.056 -10000 0 -0.39 1 1
MSG1/HSC70 -0.16 0.26 -10000 0 -0.56 133 133
SMAD2 -0.022 0.052 -10000 0 -0.47 2 2
SMAD3 0.003 0.051 -10000 0 -0.52 2 2
SMAD3/E2F4-5/DP1/p107/SMAD4 0.019 0.052 -10000 0 -0.29 1 1
SMAD2/SMAD2/SMAD4 -0.006 0.067 -10000 0 -0.3 19 19
NCOR1 0.012 0.002 -10000 0 -10000 0 0
NCOA2 0.011 0.022 -10000 0 -0.44 1 1
NCOA1 0.012 0 -10000 0 -10000 0 0
MYOD/E2A 0.009 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 -0.018 0.097 -10000 0 -0.44 1 1
IFNB1 0.015 0.049 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C -0.026 0.12 -10000 0 -0.5 8 8
CITED1 -0.22 0.34 -10000 0 -0.74 133 133
SMAD2-3/SMAD4/ARC105 -0.008 0.073 -10000 0 -0.38 1 1
RBL1 0.012 0.001 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.15 0.26 -10000 0 -0.48 169 169
RUNX1-3/PEBPB2 0.024 0.013 -10000 0 -10000 0 0
SMAD7 0.009 0.086 -10000 0 -0.66 1 1
MYC/MIZ-1 0.06 0.097 -10000 0 -0.47 7 7
SMAD3/SMAD4 0.027 0.14 0.33 8 -0.33 1 9
IL10 -0.002 0.14 -10000 0 -0.51 23 23
PIASy/HDAC complex 0.011 0.012 -10000 0 -10000 0 0
PIAS3 0.014 0.006 -10000 0 -10000 0 0
CDK2 0.016 0.011 -10000 0 -10000 0 0
IL5 0.003 0.11 -10000 0 -0.62 7 7
CDK4 0.015 0.038 -10000 0 -0.73 1 1
PIAS4 0.011 0.012 -10000 0 -10000 0 0
ATF3 0.007 0.062 -10000 0 -0.74 3 3
SMAD3/SMAD4/SP1 -0.002 0.074 -10000 0 -0.43 2 2
FOXG1 -0.098 0.25 -10000 0 -0.74 58 58
FOXO3 -0.016 0.05 -10000 0 -10000 0 0
FOXO1 -0.017 0.053 -10000 0 -0.39 1 1
FOXO4 -0.016 0.05 -10000 0 -10000 0 0
heart looping -0.022 0.12 -10000 0 -0.5 9 9
CEBPB -0.003 0.02 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.009 0.11 -10000 0 -0.48 17 17
MYOD1 0 0 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.011 0.053 -10000 0 -0.4 1 1
SMAD3/SMAD4/GATA3 0.001 0.094 -10000 0 -0.51 3 3
SnoN/SIN3/HDAC complex/NCoR1 0.011 0.022 -10000 0 -0.44 1 1
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.02 0.049 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1-3 0.011 0.067 -10000 0 -10000 0 0
MED15 0.011 0.022 -10000 0 -0.44 1 1
SP1 0.001 0.035 -10000 0 -10000 0 0
SIN3B 0.012 0.002 -10000 0 -10000 0 0
SIN3A 0.012 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.028 0.11 -10000 0 -0.44 13 13
ITGB5 0.022 0.062 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.039 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.007 0.091 -10000 0 -0.42 7 7
AR -0.016 0.11 -10000 0 -0.47 24 24
negative regulation of cell growth 0.021 0.061 -10000 0 -0.38 2 2
SMAD3/SMAD4/MYOD 0.004 0.053 -10000 0 -0.38 2 2
E2F5 0 0.094 -10000 0 -0.74 7 7
E2F4 0.012 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.003 0.072 -10000 0 -0.59 1 1
SMAD2-3/SMAD4/FOXO1-3a-4 -0.097 0.18 -10000 0 -0.37 45 45
TFDP1 0.012 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.021 0.059 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX2 0.011 0.053 -10000 0 -0.4 1 1
TGIF2 -0.002 0.1 -10000 0 -0.74 8 8
TGIF1 0.012 0 -10000 0 -10000 0 0
ATF2 0.012 0.001 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.005 0.072 -10000 0 -0.74 4 4
Jak2/Leptin Receptor -0.038 0.074 -10000 0 -0.38 6 6
PTP1B/AKT1 -0.045 0.073 -10000 0 -10000 0 0
FYN 0.012 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.058 0.081 -10000 0 -0.3 1 1
EGFR 0.008 0.023 -10000 0 -0.45 1 1
EGF/EGFR -0.088 0.13 -10000 0 -0.37 57 57
CSF1 0.01 0.031 -10000 0 -0.44 2 2
AKT1 0.012 0.001 -10000 0 -10000 0 0
INSR 0.012 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.062 0.092 -10000 0 -0.51 4 4
Insulin Receptor/Insulin -0.04 0.042 -10000 0 -10000 0 0
HCK 0.001 0.071 -10000 0 -0.44 11 11
CRK 0.012 0 -10000 0 -10000 0 0
TYK2 -0.049 0.077 -10000 0 -0.28 1 1
EGF -0.089 0.21 -10000 0 -0.5 83 83
YES1 0.011 0.022 -10000 0 -0.44 1 1
CAV1 -0.053 0.09 -10000 0 -0.31 1 1
TXN 0.011 0.003 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.041 0.075 -10000 0 -10000 0 0
cell migration 0.058 0.081 0.3 1 -10000 0 1
STAT3 0.012 0.001 -10000 0 -10000 0 0
PRLR 0.001 0.069 -10000 0 -0.44 10 10
ITGA2B -0.022 0.15 -10000 0 -0.74 19 19
CSF1R -0.017 0.11 -10000 0 -0.44 28 28
Prolactin Receptor/Prolactin -0.012 0.11 -10000 0 -0.46 21 21
FGR 0.007 0.052 -10000 0 -0.52 4 4
PTP1B/p130 Cas -0.049 0.078 -10000 0 -0.29 2 2
Crk/p130 Cas -0.041 0.076 -10000 0 -10000 0 0
DOK1 -0.037 0.074 -10000 0 -0.37 3 3
JAK2 -0.037 0.077 -10000 0 -0.36 10 10
Jak2/Leptin Receptor/Leptin -0.056 0.077 -10000 0 -0.45 5 5
PIK3R1 0.012 0 -10000 0 -10000 0 0
PTPN1 -0.058 0.082 -10000 0 -0.3 1 1
LYN 0.012 0 -10000 0 -10000 0 0
CDH2 -0.014 0.11 -10000 0 -0.48 23 23
SRC -0.009 0.034 -10000 0 -10000 0 0
ITGB3 0.007 0.044 -10000 0 -0.44 4 4
CAT1/PTP1B -0.096 0.12 -10000 0 -0.4 17 17
CAPN1 0.012 0.002 -10000 0 -10000 0 0
CSK 0.012 0 -10000 0 -10000 0 0
PI3K -0.031 0.036 -10000 0 -10000 0 0
mol:H2O2 0.001 0.005 -10000 0 -10000 0 0
STAT3 (dimer) -0.05 0.069 -10000 0 -0.43 2 2
negative regulation of transcription -0.037 0.076 -10000 0 -0.36 10 10
FCGR2A 0.009 0.051 -10000 0 -0.74 2 2
FER 0.009 0.022 -10000 0 -0.45 1 1
alphaIIb/beta3 Integrin -0.012 0.12 -10000 0 -0.51 23 23
BLK -0.16 0.22 -10000 0 -0.44 160 160
Insulin Receptor/Insulin/Shc 0.017 0.001 -10000 0 -10000 0 0
RHOA 0.012 0.002 -10000 0 -10000 0 0
LEPR 0.006 0.053 -10000 0 -0.44 6 6
BCAR1 0.011 0.022 -10000 0 -0.44 1 1
p210 bcr-abl/Grb2 0.012 0 -10000 0 -10000 0 0
mol:NADPH -0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.087 0.14 -10000 0 -0.41 33 33
PRL -0.016 0.12 -10000 0 -0.74 12 12
SOCS3 0.016 0.012 -10000 0 -10000 0 0
SPRY2 0.014 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.017 0.001 -10000 0 -10000 0 0
CSF1/CSF1R -0.056 0.087 -10000 0 -0.38 4 4
Ras protein signal transduction 0.03 0.026 -10000 0 -10000 0 0
IRS1 0.012 0 -10000 0 -10000 0 0
INS 0 0.001 -10000 0 -10000 0 0
LEP -0.032 0.14 -10000 0 -0.52 32 32
STAT5B -0.046 0.073 -10000 0 -0.26 5 5
STAT5A -0.046 0.073 -10000 0 -0.26 5 5
GRB2 0.012 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.052 0.092 -10000 0 -0.59 4 4
CSN2 0.009 0.052 -10000 0 -0.52 2 2
PIK3CA 0.012 0.001 -10000 0 -10000 0 0
LAT -0.013 0.053 -10000 0 -0.46 3 3
YBX1 0.019 0.002 -10000 0 -10000 0 0
LCK -0.002 0.099 -10000 0 -0.67 9 9
SHC1 0.012 0 -10000 0 -10000 0 0
NOX4 -0.37 0.37 -10000 0 -0.74 222 222
Signaling events mediated by HDAC Class III

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
EP300 0.012 0 -10000 0 -10000 0 0
HDAC4 0.012 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.011 0.062 0.56 5 -10000 0 5
CDKN1A -0.003 0.044 -10000 0 -0.64 2 2
KAT2B -0.007 0.091 -10000 0 -0.44 18 18
BAX 0.012 0 -10000 0 -10000 0 0
FOXO3 0 0 -10000 0 -10000 0 0
FOXO1 0.011 0.022 -10000 0 -0.44 1 1
FOXO4 0.019 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.012 0 -10000 0 -10000 0 0
TAT -0.16 0.22 -10000 0 -0.44 162 162
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.004 0.064 -10000 0 -0.31 18 18
PPARGC1A -0.047 0.15 -10000 0 -0.44 56 56
FHL2 0.011 0.022 -10000 0 -0.44 1 1
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.016 0.009 -10000 0 -10000 0 0
HIST2H4A 0.011 0.062 -10000 0 -0.56 5 5
SIRT1/FOXO3a 0.001 0.009 -10000 0 -10000 0 0
SIRT1 0.009 0.012 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.023 0.008 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.003 0.06 -10000 0 -10000 0 0
apoptosis -0.022 0.008 -10000 0 -10000 0 0
SIRT1/PGC1A -0.021 0.09 -10000 0 -10000 0 0
p53/SIRT1 0.002 0.025 0.37 2 -10000 0 2
SIRT1/FOXO4 0.02 0.009 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 0.02 0.018 -10000 0 -10000 0 0
HIST1H1E -0.001 0.07 -10000 0 -0.25 32 32
SIRT1/p300 0.016 0.009 -10000 0 -10000 0 0
muscle cell differentiation -0.004 0.055 -10000 0 -10000 0 0
TP53 0.009 0.012 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.023 0.008 -10000 0 -10000 0 0
CREBBP 0.012 0 -10000 0 -10000 0 0
MEF2D 0.012 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.11 0.15 -10000 0 -0.31 161 161
ACSS2 0.017 0.008 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.004 0.055 -10000 0 -10000 0 0
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.035 0.11 0.35 13 -10000 0 13
GNAI2 0.012 0 -10000 0 -10000 0 0
S1P/S1P5/G12 0.01 0.059 -10000 0 -0.48 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.11 0.2 -10000 0 -0.44 118 118
RhoA/GTP -0.036 0.11 -10000 0 -0.36 13 13
negative regulation of cAMP metabolic process -0.045 0.12 -10000 0 -0.39 13 13
GNAZ 0.007 0.049 -10000 0 -0.44 5 5
GNAI3 0.012 0 -10000 0 -10000 0 0
GNA12 0.012 0 -10000 0 -10000 0 0
S1PR5 0.002 0.088 -10000 0 -0.74 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.046 0.12 -10000 0 -0.39 13 13
RhoA/GDP 0.009 0 -10000 0 -10000 0 0
RHOA 0.012 0 -10000 0 -10000 0 0
GNAI1 -0.003 0.083 -10000 0 -0.44 15 15
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.016 0.032 -9999 0 -0.43 2 2
alphaV beta3 Integrin 0.004 0.076 -9999 0 -0.49 1 1
PTK2 0.01 0.098 -9999 0 -0.43 3 3
IGF1R 0.012 0 -9999 0 -10000 0 0
PI4KB 0.012 0 -9999 0 -10000 0 0
MFGE8 0.012 0 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
CDKN1B 0.003 0.067 -9999 0 -0.34 12 12
VEGFA 0.011 0.036 -9999 0 -0.74 1 1
ILK 0.004 0.064 -9999 0 -0.33 11 11
ROCK1 0.011 0.022 -9999 0 -0.44 1 1
AKT1 0.012 0.06 -9999 0 -0.3 11 11
PTK2B 0.028 0.034 -9999 0 -0.4 1 1
alphaV/beta3 Integrin/JAM-A 0.005 0.095 -9999 0 -0.42 12 12
CBL 0.012 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.016 0.036 -9999 0 -0.48 1 1
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.03 0.11 -9999 0 -10000 0 0
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.028 0.045 -9999 0 -0.46 1 1
alphaV/beta3 Integrin/Syndecan-1 0.023 0.026 -9999 0 -10000 0 0
PI4KA 0.012 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.076 0.13 -9999 0 -0.58 4 4
PI4 Kinase 0.018 0 -9999 0 -10000 0 0
PIK3CA 0.012 0.001 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.22 0.25 -9999 0 -0.48 207 207
RPS6KB1 -0.04 0.14 -9999 0 -0.54 4 4
TLN1 0.012 0 -9999 0 -10000 0 0
MAPK3 -0.029 0.16 -9999 0 -0.56 29 29
GPR124 0.011 0.022 -9999 0 -0.44 1 1
MAPK1 -0.029 0.16 -9999 0 -0.54 33 33
PXN 0.012 0 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.009 0.095 -9999 0 -0.48 5 5
cell adhesion 0.025 0.031 -9999 0 -0.34 1 1
ANGPTL3 0.003 0.036 -9999 0 -0.74 1 1
VEGFR2 homodimer/VEGFA homodimer/Src 0.023 0.027 -9999 0 -0.48 1 1
IGF-1R heterotetramer 0.012 0 -9999 0 -10000 0 0
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
TGFBR2 0.012 0 -9999 0 -10000 0 0
ITGB3 0.008 0.043 -9999 0 -0.44 4 4
IGF1 -0.1 0.2 -9999 0 -0.44 107 107
RAC1 0.012 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion 0.022 0.029 -9999 0 -10000 0 0
apoptosis 0.012 0 -9999 0 -10000 0 0
CD47 0.012 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.023 0.026 -9999 0 -10000 0 0
VCL 0.012 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.029 0.11 -9999 0 -0.49 4 4
CSF1 0.01 0.031 -9999 0 -0.44 2 2
PIK3C2A 0.003 0.067 -9999 0 -0.34 12 12
PI4 Kinase/Pyk2 -0.022 0.072 -9999 0 -0.52 1 1
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.028 0.035 -9999 0 -0.43 1 1
FAK1/Vinculin 0.016 0.084 -9999 0 -0.34 3 3
alphaV beta3/Integrin/ppsTEM5 0.022 0.029 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
VTN -0.009 0.12 -9999 0 -0.74 11 11
BCAR1 0.011 0.022 -9999 0 -0.44 1 1
FGF2 -0.019 0.12 -9999 0 -0.44 30 30
F11R -0.003 0.082 -9999 0 -0.3 30 30
alphaV/beta3 Integrin/Lactadherin 0.023 0.026 -9999 0 -10000 0 0
alphaV/beta3 Integrin/TGFBR2 0.023 0.026 -9999 0 -10000 0 0
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.03 0.021 -9999 0 -10000 0 0
HSP90AA1 0.012 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.022 0.024 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.025 0.16 -9999 0 -0.66 24 24
alphaV/beta3 Integrin/Pyk2 0.031 0.034 -9999 0 -0.4 1 1
SDC1 0.012 0 -9999 0 -10000 0 0
VAV3 0.005 0.075 -9999 0 -10000 0 0
PTPN11 0.012 0 -9999 0 -10000 0 0
IRS1 0.012 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.016 0.084 -9999 0 -0.34 3 3
cell migration 0.022 0.079 -9999 0 -0.34 1 1
ITGAV 0.012 0 -9999 0 -10000 0 0
PI3K -0.023 0.076 -9999 0 -0.56 1 1
SPP1 -0.35 0.37 -9999 0 -0.73 210 210
KDR 0.011 0.022 -9999 0 -0.44 1 1
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.012 0 -9999 0 -10000 0 0
COL4A3 -0.038 0.15 -9999 0 -0.48 43 43
angiogenesis -0.025 0.16 -9999 0 -0.56 28 28
Rac1/GTP 0.011 0.069 -9999 0 -10000 0 0
EDIL3 -0.074 0.18 -9999 0 -0.44 82 82
cell proliferation 0.022 0.026 -9999 0 -10000 0 0
Glypican 2 network

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
MDK 0.005 0.072 -9999 0 -0.74 4 4
GPC2 -0.007 0.12 -9999 0 -0.74 11 11
GPC2/Midkine -0.002 0.1 -9999 0 -0.56 15 15
neuron projection morphogenesis -0.002 0.1 -9999 0 -0.56 15 15
IL6-mediated signaling events

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
BCL2L1 -0.008 0.16 -9999 0 -0.67 3 3
CRP -0.014 0.17 -9999 0 -0.76 4 4
cell cycle arrest -0.019 0.18 -9999 0 -0.68 8 8
TIMP1 -0.028 0.2 -9999 0 -0.6 23 23
IL6ST 0.006 0.065 -9999 0 -0.44 9 9
Rac1/GDP -0.045 0.15 -9999 0 -0.5 13 13
AP1 0.026 0.064 -9999 0 -10000 0 0
GAB2 0.013 0.002 -9999 0 -10000 0 0
TNFSF11 -0.026 0.21 -9999 0 -0.8 13 13
HSP90B1 0.024 0.037 -9999 0 -10000 0 0
GAB1 0.013 0.001 -9999 0 -10000 0 0
MAPK14 -0.04 0.13 -9999 0 -0.55 4 4
AKT1 0.047 0.011 -9999 0 -10000 0 0
FOXO1 0.051 0.015 -9999 0 -10000 0 0
MAP2K6 -0.048 0.14 -9999 0 -0.44 17 17
mol:GTP 0 0.002 -9999 0 -10000 0 0
MAP2K4 -0.03 0.15 -9999 0 -0.5 12 12
MITF -0.052 0.15 -9999 0 -0.44 22 22
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0.012 0 -9999 0 -10000 0 0
A2M 0.007 0.13 -9999 0 -1.3 4 4
CEBPB 0.018 0.004 -9999 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0 0.063 -9999 0 -10000 0 0
STAT3 -0.022 0.18 -9999 0 -0.71 8 8
STAT1 -0.004 0.016 -9999 0 -10000 0 0
CEBPD -0.009 0.17 -9999 0 -0.81 3 3
PIK3CA 0.014 0.001 -9999 0 -10000 0 0
PI3K 0.021 0.001 -9999 0 -10000 0 0
JUN 0.012 0.001 -9999 0 -10000 0 0
PIAS3/MITF -0.044 0.14 -9999 0 -0.42 20 20
MAPK11 -0.042 0.13 -9999 0 -0.54 7 7
STAT3 (dimer)/FOXO1 0.016 0.16 -9999 0 -0.56 2 2
GRB2/SOS1/GAB family -0.067 0.11 -9999 0 -0.51 10 10
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.063 0.16 -9999 0 -0.46 27 27
GRB2 0.013 0.001 -9999 0 -10000 0 0
JAK2 0.009 0.038 -9999 0 -0.44 3 3
LBP -0.034 0.21 -9999 0 -0.67 9 9
PIK3R1 0.013 0 -9999 0 -10000 0 0
JAK1 0.014 0.022 -9999 0 -0.44 1 1
MYC -0.011 0.17 -9999 0 -0.66 4 4
FGG -0.037 0.21 -9999 0 -0.74 7 7
macrophage differentiation -0.019 0.18 -9999 0 -0.68 8 8
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.085 0.19 -9999 0 -0.43 80 80
JUNB -0.01 0.17 -9999 0 -0.83 4 4
FOS 0.005 0.057 -9999 0 -0.44 7 7
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.057 0.15 -9999 0 -0.42 27 27
STAT1/PIAS1 -0.036 0.14 -9999 0 -0.43 15 15
GRB2/SOS1/GAB family/SHP2/PI3K 0.038 0.012 -9999 0 -10000 0 0
STAT3 (dimer) -0.02 0.18 -9999 0 -0.7 8 8
PRKCD -0.017 0.16 -9999 0 -0.57 4 4
IL6R -0.086 0.19 -9999 0 -0.44 96 96
SOCS3 -0.037 0.12 -9999 0 -0.61 2 2
gp130 (dimer)/JAK1/JAK1/LMO4 0.028 0.047 -9999 0 -10000 0 0
Rac1/GTP -0.042 0.15 -9999 0 -0.5 13 13
HCK 0 0.071 -9999 0 -0.44 11 11
MAPKKK cascade 0.019 0.049 -9999 0 -10000 0 0
bone resorption -0.023 0.2 -9999 0 -0.75 13 13
IRF1 -0.008 0.16 -9999 0 -0.67 3 3
mol:GDP -0.055 0.15 -9999 0 -0.43 27 27
SOS1 0.013 0.002 -9999 0 -10000 0 0
VAV1 -0.056 0.15 -9999 0 -0.44 27 27
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.079 0.18 -9999 0 -0.55 18 18
PTPN11 -0.003 0.012 -9999 0 -10000 0 0
IL6/IL6RA -0.14 0.24 -9999 0 -0.43 157 157
gp130 (dimer)/TYK2/TYK2/LMO4 0.023 0.044 -9999 0 -10000 0 0
gp130 (dimer)/JAK2/JAK2/LMO4 0.021 0.052 -9999 0 -0.5 1 1
IL6 -0.11 0.28 -9999 0 -0.72 72 72
PIAS3 0.012 0 -9999 0 -10000 0 0
PTPRE 0.006 0.009 -9999 0 -10000 0 0
PIAS1 0.012 0 -9999 0 -10000 0 0
RAC1 0.013 0.001 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.067 0.14 -9999 0 -0.35 36 36
LMO4 0.015 0.023 -9999 0 -0.45 1 1
STAT3 (dimer)/PIAS3 -0.019 0.18 -9999 0 -0.67 8 8
MCL1 0.051 0.01 -9999 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.011 0.022 -9999 0 -0.44 1 1
SPHK1 -0.04 0.19 -9999 0 -0.74 30 30
GNAI2 0.012 0 -9999 0 -10000 0 0
mol:S1P 0 0.069 -9999 0 -0.25 31 31
GNAO1 -0.11 0.2 -9999 0 -0.44 118 118
mol:Sphinganine-1-P -0.021 0.15 -9999 0 -0.55 31 31
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.021 0.051 -9999 0 -10000 0 0
GNAI3 0.012 0 -9999 0 -10000 0 0
G12/G13 0.018 0 -9999 0 -10000 0 0
S1PR3 0.011 0.036 -9999 0 -0.74 1 1
S1PR2 0.012 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.002 0.058 -9999 0 -0.22 1 1
S1PR5 0.002 0.088 -9999 0 -0.74 6 6
S1PR4 0.002 0.068 -9999 0 -0.44 10 10
GNAI1 -0.003 0.083 -9999 0 -0.44 15 15
S1P/S1P5/G12 0.008 0.079 -9999 0 -0.49 6 6
S1P/S1P3/Gq 0.019 0.057 -9999 0 -0.42 3 3
S1P/S1P4/Gi -0.048 0.13 -9999 0 -0.41 21 21
GNAQ 0.01 0.031 -9999 0 -0.44 2 2
GNAZ 0.007 0.049 -9999 0 -0.44 5 5
GNA14 0.01 0.031 -9999 0 -0.44 2 2
GNA15 0.005 0.072 -9999 0 -0.74 4 4
GNA12 0.012 0 -9999 0 -10000 0 0
GNA13 0.012 0 -9999 0 -10000 0 0
GNA11 0.01 0.031 -9999 0 -0.44 2 2
ABCC1 0.012 0 -9999 0 -10000 0 0
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.008 0.12 -9999 0 -0.35 46 46
positive regulation of NF-kappaB transcription factor activity 0 0.001 -9999 0 -10000 0 0
CRKL 0.012 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.019 0.11 -9999 0 -0.65 1 1
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.015 0.038 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.023 0.048 -9999 0 -10000 0 0
CaM/Ca2+ -0.006 0.11 -9999 0 -0.33 40 40
RAP1A 0.012 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.003 0.12 -9999 0 -0.34 40 40
AKT1 0.007 0.1 -9999 0 -10000 0 0
MAP2K1 0.002 0.11 -9999 0 -10000 0 0
MAP3K11 -0.005 0.12 -9999 0 -0.33 40 40
IFNGR1 0.009 0.013 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.028 0.14 -9999 0 -0.39 37 37
Rap1/GTP -0.028 0.077 -9999 0 -10000 0 0
CRKL/C3G 0.018 0.016 -9999 0 -0.3 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.01 0.13 -9999 0 -0.38 46 46
CEBPB 0.017 0.13 -9999 0 -0.51 2 2
STAT3 0.012 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.014 0.15 -9999 0 -0.78 6 6
STAT1 -0.004 0.12 -9999 0 -0.34 40 40
CALM1 0.012 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.067 0.23 -9999 0 -0.73 46 46
PIK3CA 0.012 0.001 -9999 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.003 0.11 -9999 0 -0.68 1 1
CEBPB/PTGES2/Cbp/p300 -0.028 0.067 -9999 0 -10000 0 0
mol:Ca2+ -0.009 0.12 -9999 0 -0.35 46 46
MAPK3 0.011 0.11 -9999 0 -0.9 1 1
STAT1 (dimer) -0.03 0.064 -9999 0 -10000 0 0
MAPK1 0.013 0.1 -9999 0 -10000 0 0
JAK2 0.006 0.039 -9999 0 -0.44 3 3
PIK3R1 0.012 0 -9999 0 -10000 0 0
JAK1 0.008 0.025 -9999 0 -0.44 1 1
CAMK2D 0.011 0.022 -9999 0 -0.44 1 1
DAPK1 0.012 0.15 -9999 0 -0.59 20 20
SMAD7 0.026 0.047 -9999 0 -0.24 1 1
CBL/CRKL/C3G 0.008 0.11 -9999 0 -10000 0 0
PI3K -0.035 0.098 -9999 0 -10000 0 0
IFNG -0.067 0.23 -9999 0 -0.73 46 46
apoptosis 0.009 0.11 -9999 0 -0.43 20 20
CAMK2G 0.012 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.012 0 -9999 0 -10000 0 0
CAMK2A -0.024 0.12 -9999 0 -0.44 34 34
CAMK2B -0.027 0.14 -9999 0 -0.49 33 33
FRAP1 0.007 0.098 -9999 0 -10000 0 0
PRKCD 0.008 0.11 -9999 0 -10000 0 0
RAP1B 0.012 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.023 0.048 -9999 0 -10000 0 0
PTPN2 0.012 0.001 -9999 0 -10000 0 0
EP300 0.013 0 -9999 0 -10000 0 0
IRF1 0.024 0.1 -9999 0 -0.45 7 7
STAT1 (dimer)/PIASy 0.001 0.11 -9999 0 -0.68 1 1
SOCS1 -0.01 0.086 -9999 0 -0.54 11 11
mol:GDP 0.005 0.1 -9999 0 -10000 0 0
CASP1 0.026 0.047 -9999 0 -0.28 1 1
PTGES2 0.012 0 -9999 0 -10000 0 0
IRF9 0.032 0.047 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.034 0.096 -9999 0 -10000 0 0
RAP1/GDP -0.028 0.078 -9999 0 -10000 0 0
CBL -0.005 0.12 -9999 0 -0.33 40 40
MAP3K1 -0.005 0.12 -9999 0 -0.33 40 40
PIAS1 0.012 0 -9999 0 -10000 0 0
PIAS4 0.012 0.001 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.023 0.048 -9999 0 -10000 0 0
PTPN11 -0.012 0.12 -9999 0 -0.35 46 46
CREBBP 0.013 0 -9999 0 -10000 0 0
RAPGEF1 0.011 0.022 -9999 0 -0.44 1 1
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.005 0.083 -9999 0 -0.34 16 16
CRKL 0.012 0 -9999 0 -10000 0 0
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
DOCK1 0.012 0 -9999 0 -10000 0 0
ITGA4 -0.005 0.086 -9999 0 -0.44 16 16
alpha4/beta7 Integrin/MAdCAM1 -0.1 0.15 -9999 0 -0.48 22 22
EPO 0 0.071 -9999 0 -0.74 4 4
alpha4/beta7 Integrin -0.005 0.09 -9999 0 -0.33 29 29
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.012 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.006 0.061 -9999 0 -0.3 16 16
EPO/EPOR (dimer) 0.008 0.061 -9999 0 -0.56 5 5
lamellipodium assembly 0.032 0.002 -9999 0 -10000 0 0
PIK3CA 0.012 0.001 -9999 0 -10000 0 0
PI3K 0.018 0 -9999 0 -10000 0 0
ARF6 0.012 0 -9999 0 -10000 0 0
JAK2 0.013 0.066 -9999 0 -0.46 3 3
PXN 0.012 0 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
MADCAM1 -0.2 0.23 -9999 0 -0.44 203 203
cell adhesion -0.1 0.15 -9999 0 -0.47 22 22
CRKL/CBL 0.018 0 -9999 0 -10000 0 0
ITGB1 0.012 0 -9999 0 -10000 0 0
SRC 0.014 0.07 -9999 0 -0.44 7 7
ITGB7 -0.005 0.086 -9999 0 -0.44 16 16
RAC1 0.012 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.01 0.077 -9999 0 -0.49 7 7
p130Cas/Crk/Dock1 0.032 0.062 -9999 0 -10000 0 0
VCAM1 0.003 0.065 -9999 0 -0.44 9 9
RHOA 0.012 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.022 0.049 -9999 0 -10000 0 0
BCAR1 0.019 0.067 -9999 0 -0.41 7 7
EPOR 0.011 0.036 -9999 0 -0.74 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.012 0 -9999 0 -10000 0 0
GIT1 0.011 0.022 -9999 0 -0.44 1 1
Rac1/GTP 0.032 0.002 -9999 0 -10000 0 0
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.017 0.032 -9999 0 -0.43 2 2
PDGFRB 0.005 0.072 -9999 0 -0.74 4 4
SPHK1 -0.025 0.063 -9999 0 -0.3 4 4
mol:S1P -0.025 0.062 -9999 0 -0.31 2 2
S1P1/S1P/Gi -0.059 0.16 -9999 0 -0.48 27 27
GNAO1 -0.11 0.2 -9999 0 -0.44 118 118
PDGFB-D/PDGFRB/PLCgamma1 -0.044 0.15 -9999 0 -0.48 18 18
PLCG1 -0.05 0.15 -9999 0 -0.46 24 24
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.005 0.072 -9999 0 -0.74 4 4
GNAI2 0.012 0.004 -9999 0 -10000 0 0
GNAI3 0.012 0.004 -9999 0 -10000 0 0
GNAI1 -0.004 0.084 -9999 0 -0.44 15 15
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.014 0.028 -9999 0 -0.36 2 2
S1P1/S1P 0.006 0.073 -9999 0 -0.32 3 3
negative regulation of cAMP metabolic process -0.057 0.16 -9999 0 -0.47 27 27
MAPK3 -0.057 0.18 -9999 0 -0.51 31 31
calcium-dependent phospholipase C activity -0.001 0.002 -9999 0 -10000 0 0
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
RhoA/GDP 0.009 0 -9999 0 -10000 0 0
KDR 0.011 0.022 -9999 0 -0.44 1 1
PLCB2 0.011 0.068 -9999 0 -10000 0 0
RAC1 0.012 0 -9999 0 -10000 0 0
RhoA/GTP -0.015 0.056 -9999 0 -10000 0 0
receptor internalization -0.016 0.062 -9999 0 -0.31 3 3
PTGS2 -0.062 0.21 -9999 0 -0.61 36 36
Rac1/GTP -0.015 0.056 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
VEGFA 0.011 0.036 -9999 0 -0.74 1 1
negative regulation of T cell proliferation -0.057 0.16 -9999 0 -0.47 27 27
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.006 0.049 -9999 0 -0.45 5 5
MAPK1 -0.056 0.18 -9999 0 -0.51 30 30
S1P1/S1P/PDGFB-D/PDGFRB 0.008 0.09 -9999 0 -0.46 6 6
ABCC1 0.012 0.002 -9999 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.021 0.066 0.38 5 -10000 0 5
RFC1 0.021 0.066 0.38 5 -10000 0 5
PRKDC 0.021 0.066 0.38 5 -10000 0 5
RIPK1 0.013 0.003 -10000 0 -10000 0 0
CASP7 -0.002 0.055 0.22 13 -0.55 1 14
FASLG/FAS/FADD/FAF1 -0.004 0.076 0.36 2 -0.26 3 5
MAP2K4 0.004 0.099 -10000 0 -0.36 4 4
mol:ceramide 0 0.089 -10000 0 -0.38 5 5
GSN 0.016 0.065 0.38 4 -10000 0 4
FASLG/FAS/FADD/FAF1/Caspase 8 0.009 0.08 0.29 1 -0.32 3 4
FAS 0.008 0.038 -10000 0 -0.45 3 3
BID 0.02 0.064 0.28 22 -0.49 1 23
MAP3K1 0.017 0.07 0.26 3 -0.32 1 4
MAP3K7 0.011 0.003 -10000 0 -10000 0 0
RB1 0.021 0.066 0.38 5 -10000 0 5
CFLAR 0.013 0.003 -10000 0 -10000 0 0
HGF/MET -0.002 0.11 -10000 0 -0.49 17 17
ARHGDIB 0.021 0.066 0.38 5 -10000 0 5
FADD 0.011 0.005 -10000 0 -10000 0 0
actin filament polymerization -0.016 0.065 -10000 0 -0.38 4 4
NFKB1 -0.027 0.054 -10000 0 -0.25 2 2
MAPK8 -0.004 0.13 -10000 0 -0.45 6 6
DFFA 0.021 0.066 0.25 22 -10000 0 22
DNA fragmentation during apoptosis 0.021 0.066 0.25 22 -10000 0 22
FAS/FADD/MET 0.014 0.059 -10000 0 -0.45 6 6
CFLAR/RIP1 0.015 0.007 -10000 0 -10000 0 0
FAIM3 -0.01 0.1 -10000 0 -0.44 22 22
FAF1 0.011 0.005 -10000 0 -10000 0 0
PARP1 0.021 0.066 0.38 5 -10000 0 5
DFFB 0.021 0.066 0.25 22 -10000 0 22
CHUK -0.023 0.046 -10000 0 -10000 0 0
FASLG -0.019 0.12 -10000 0 -0.45 28 28
FAS/FADD 0.014 0.029 -10000 0 -0.31 3 3
HGF 0.004 0.064 -10000 0 -0.48 7 7
LMNA 0.029 0.058 0.34 5 -10000 0 5
CASP6 0.021 0.066 0.38 5 -10000 0 5
CASP10 0.011 0.005 -10000 0 -10000 0 0
CASP3 0.024 0.079 0.29 24 -10000 0 24
PTPN13 -0.012 0.13 -10000 0 -0.64 16 16
CASP8 0.018 0.076 0.34 22 -10000 0 22
IL6 -0.067 0.23 -10000 0 -0.55 72 72
MET 0.004 0.08 -10000 0 -0.74 5 5
ICAD/CAD 0.019 0.061 0.34 5 -10000 0 5
FASLG/FAS/FADD/FAF1/Caspase 10 0 0.09 -10000 0 -0.38 5 5
activation of caspase activity by cytochrome c 0.02 0.064 0.28 22 -0.49 1 23
PAK2 0.021 0.066 0.25 22 -10000 0 22
BCL2 -0.013 0.1 -10000 0 -0.44 24 24
S1P4 pathway

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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.11 0.2 -9999 0 -0.44 118 118
CDC42/GTP -0.039 0.12 -9999 0 -0.4 16 16
PLCG1 -0.04 0.12 -9999 0 -0.41 16 16
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.012 0 -9999 0 -10000 0 0
GNAI3 0.012 0 -9999 0 -10000 0 0
G12/G13 0.018 0 -9999 0 -10000 0 0
cell migration -0.038 0.12 -9999 0 -0.39 16 16
S1PR5 0.002 0.088 -9999 0 -0.74 6 6
S1PR4 0.002 0.068 -9999 0 -0.44 10 10
MAPK3 -0.04 0.12 -9999 0 -0.41 17 17
MAPK1 -0.04 0.12 -9999 0 -0.41 16 16
S1P/S1P5/Gi -0.046 0.12 -9999 0 -0.39 13 13
GNAI1 -0.003 0.083 -9999 0 -0.44 15 15
CDC42/GDP 0.008 0.015 -9999 0 -0.31 1 1
S1P/S1P5/G12 0.01 0.059 -9999 0 -0.48 6 6
RHOA 0.021 0.035 -9999 0 -10000 0 0
S1P/S1P4/Gi -0.048 0.13 -9999 0 -0.44 16 16
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.007 0.049 -9999 0 -0.44 5 5
S1P/S1P4/G12/G13 0.018 0.037 -9999 0 -10000 0 0
GNA12 0.012 0 -9999 0 -10000 0 0
GNA13 0.012 0 -9999 0 -10000 0 0
CDC42 0.011 0.022 -9999 0 -0.44 1 1
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.023 0.002 -9999 0 -10000 0 0
BIRC5 0.011 0.036 -9999 0 -0.74 1 1
NFKBIA 0.024 0.002 -9999 0 -10000 0 0
CPEB1 -0.096 0.19 -9999 0 -0.44 101 101
AKT1 0.024 0.002 -9999 0 -10000 0 0
NDEL1 0.012 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.021 0.002 -9999 0 -10000 0 0
NDEL1/TACC3 0.028 0.001 -9999 0 -10000 0 0
GADD45A 0.012 0 -9999 0 -10000 0 0
GSK3B 0.011 0.001 -9999 0 -10000 0 0
PAK1/Aurora A 0.023 0.002 -9999 0 -10000 0 0
MDM2 0.011 0.022 -9999 0 -0.44 1 1
JUB -0.23 0.35 -9999 0 -0.74 139 139
TPX2 0.014 0.055 -9999 0 -0.56 4 4
TP53 0.025 0.015 -9999 0 -0.28 1 1
DLG7 0.016 0.002 -9999 0 -10000 0 0
AURKAIP1 0.012 0 -9999 0 -10000 0 0
ARHGEF7 0.012 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.029 0.002 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.021 0.002 -9999 0 -10000 0 0
AURKA 0.02 0.003 -9999 0 -10000 0 0
AURKB 0.013 0.003 -9999 0 -10000 0 0
CDC25B -0.032 0.084 -9999 0 -0.28 22 22
G2/M transition checkpoint -0.13 0.21 -9999 0 -0.44 139 139
mRNA polyadenylation -0.04 0.1 -9999 0 -10000 0 0
Aurora A/CPEB -0.04 0.1 -9999 0 -10000 0 0
Aurora A/TACC1/TRAP/chTOG 0.036 0.001 -9999 0 -10000 0 0
BRCA1 0.012 0 -9999 0 -10000 0 0
centrosome duplication 0.023 0.002 -9999 0 -10000 0 0
regulation of centrosome cycle 0.027 0.001 -9999 0 -10000 0 0
spindle assembly 0.035 0.001 -9999 0 -10000 0 0
TDRD7 0.012 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.032 0.02 -9999 0 -0.39 1 1
CENPA 0.016 0.005 -9999 0 -10000 0 0
Aurora A/PP2A 0.023 0.002 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.029 0.006 -9999 0 -10000 0 0
negative regulation of DNA binding 0.024 0.015 -9999 0 -0.28 1 1
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0.018 0.016 -9999 0 -0.3 1 1
RASA1 0.012 0.001 -9999 0 -10000 0 0
Ajuba/Aurora A -0.13 0.22 -9999 0 -0.44 139 139
mitotic prometaphase 0 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.003 -9999 0 -10000 0 0
TACC1 0.012 0 -9999 0 -10000 0 0
TACC3 0.012 0 -9999 0 -10000 0 0
Aurora A/Antizyme1 0.029 0.002 -9999 0 -10000 0 0
Aurora A/RasGAP 0.023 0.002 -9999 0 -10000 0 0
OAZ1 0.012 0 -9999 0 -10000 0 0
RAN 0.012 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.011 0.001 -9999 0 -10000 0 0
GIT1 0.011 0.022 -9999 0 -0.44 1 1
GIT1/beta-PIX/PAK1 0.024 0.013 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.014 0.055 -9999 0 -0.56 4 4
PPP2R5D 0.012 0 -9999 0 -10000 0 0
Aurora A/TPX2 0.024 0.044 -9999 0 -0.43 4 4
PAK1 0.012 0 -9999 0 -10000 0 0
CKAP5 0.012 0 -9999 0 -10000 0 0
IGF1 pathway

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
NCK2 0.012 0 -9999 0 -10000 0 0
PTK2 0.012 0 -9999 0 -10000 0 0
CRKL -0.034 0.099 -9999 0 -10000 0 0
GRB2/SOS1/SHC 0.025 0 -9999 0 -10000 0 0
HRAS 0.011 0.022 -9999 0 -0.44 1 1
IRS1/Crk -0.034 0.1 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/PTP1B -0.04 0.11 -9999 0 -10000 0 0
AKT1 -0.012 0.086 -9999 0 -10000 0 0
BAD -0.007 0.082 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.034 0.099 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.034 0.1 -9999 0 -10000 0 0
RAF1 -0.001 0.08 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.024 0.096 -9999 0 -10000 0 0
YWHAZ 0.012 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.044 0.11 -9999 0 -10000 0 0
PIK3CA 0.012 0.001 -9999 0 -10000 0 0
RPS6KB1 -0.013 0.086 -9999 0 -10000 0 0
GNB2L1 0.012 0 -9999 0 -10000 0 0
positive regulation of MAPKKK cascade -0.003 0.072 -9999 0 -10000 0 0
PXN 0.012 0 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
cell adhesion 0 0 -9999 0 -10000 0 0
GRB2/SOS1 0.018 0 -9999 0 -10000 0 0
HRAS/GTP -0.041 0.071 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.015 0.09 -9999 0 -10000 0 0
IGF-1R heterotetramer -0.002 0.027 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.032 0.1 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.018 0.092 -9999 0 -10000 0 0
IGF1R -0.002 0.027 -9999 0 -10000 0 0
IGF1 -0.1 0.2 -9999 0 -0.45 107 107
IRS2/Crk -0.025 0.095 -9999 0 -10000 0 0
PI3K -0.023 0.096 -9999 0 -10000 0 0
apoptosis -0.001 0.075 -9999 0 -10000 0 0
HRAS/GDP 0.008 0.015 -9999 0 -0.31 1 1
PRKCD -0.048 0.14 -9999 0 -0.3 107 107
RAF1/14-3-3 E 0.006 0.074 -9999 0 -10000 0 0
BAD/14-3-3 0.001 0.078 -9999 0 -10000 0 0
PRKCZ -0.012 0.086 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin/FAK1 -0.032 0.055 -9999 0 -10000 0 0
PTPN1 0.012 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.057 0.15 -9999 0 -0.32 107 107
BCAR1 0.011 0.022 -9999 0 -0.44 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.025 0.097 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
SOS1 0.012 0 -9999 0 -10000 0 0
IRS1/NCK2 -0.033 0.099 -9999 0 -10000 0 0
GRB10 0.012 0 -9999 0 -10000 0 0
PTPN11 -0.034 0.099 -9999 0 -10000 0 0
IRS1 -0.045 0.11 -9999 0 -10000 0 0
IRS2 -0.034 0.099 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.067 0.15 -9999 0 -0.32 107 107
GRB2 0.012 0 -9999 0 -10000 0 0
PDPK1 -0.019 0.09 -9999 0 -10000 0 0
YWHAE 0.012 0 -9999 0 -10000 0 0
PRKD1 -0.05 0.15 -9999 0 -0.31 108 108
SHC1 0.012 0 -9999 0 -10000 0 0
Regulation of Androgen receptor activity

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
HDAC1 0.018 0.004 -9999 0 -10000 0 0
SMARCC1 0.003 0.008 -9999 0 -10000 0 0
REL 0.015 0.007 -9999 0 -10000 0 0
HDAC7 0.021 0.085 -9999 0 -0.45 1 1
JUN 0.01 0.005 -9999 0 -10000 0 0
EP300 0.012 0.001 -9999 0 -10000 0 0
KAT2B -0.007 0.091 -9999 0 -0.44 18 18
KAT5 0.013 0.001 -9999 0 -10000 0 0
MAPK14 0.015 0.032 -9999 0 -0.33 3 3
FOXO1 0.011 0.022 -9999 0 -0.44 1 1
T-DHT/AR 0.019 0.091 -9999 0 -0.48 1 1
MAP2K6 0.007 0.04 -9999 0 -0.46 3 3
BRM/BAF57 0.014 0.02 -9999 0 -0.34 1 1
MAP2K4 0.009 0.031 -9999 0 -0.44 2 2
SMARCA2 0.009 0.023 -9999 0 -0.46 1 1
PDE9A -0.17 0.38 -9999 0 -0.99 74 74
NCOA2 0.011 0.022 -9999 0 -0.44 1 1
CEBPA 0.01 0.038 -9999 0 -0.44 3 3
EHMT2 0.009 0.036 -9999 0 -0.74 1 1
cell proliferation 0.025 0.11 -9999 0 -0.43 1 1
NR0B1 -0.004 0.079 -9999 0 -0.74 5 5
EGR1 0.01 0.022 -9999 0 -0.44 1 1
RXRs/9cRA -0.077 0.12 -9999 0 -10000 0 0
AR/RACK1/Src 0.021 0.057 -9999 0 -10000 0 0
AR/GR -0.004 0.09 -9999 0 -0.43 5 5
GNB2L1 0.012 0.001 -9999 0 -10000 0 0
PKN1 0.012 0.001 -9999 0 -10000 0 0
RCHY1 0.012 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -9999 0 -10000 0 0
MAPK8 0.015 0.025 -9999 0 -0.3 2 2
T-DHT/AR/TIF2/CARM1 0.027 0.056 -9999 0 -10000 0 0
SRC 0.024 0.039 -9999 0 -10000 0 0
NR3C1 -0.02 0.12 -9999 0 -0.44 31 31
KLK3 -0.25 0.43 -9999 0 -1.2 75 75
APPBP2 0.01 0.022 -9999 0 -0.44 1 1
TRIM24 0.011 0.005 -9999 0 -10000 0 0
T-DHT/AR/TIP60 0.022 0.052 -9999 0 -0.39 1 1
TMPRSS2 -0.023 0.094 -9999 0 -1.1 2 2
RXRG -0.16 0.22 -9999 0 -0.44 164 164
mol:9cRA -0.001 0.002 -9999 0 -10000 0 0
RXRA 0.011 0.022 -9999 0 -0.44 1 1
RXRB 0.012 0.001 -9999 0 -10000 0 0
CARM1 0.012 0.002 -9999 0 -10000 0 0
NR2C2 0.012 0.001 -9999 0 -10000 0 0
KLK2 0.017 0.11 -9999 0 -0.5 17 17
AR 0.009 0.069 -9999 0 -0.37 4 4
SENP1 0.012 0.001 -9999 0 -10000 0 0
HSP90AA1 0.012 0 -9999 0 -10000 0 0
MDM2 0.015 0.025 -9999 0 -0.44 1 1
SRY 0.005 0.012 -9999 0 -10000 0 0
GATA2 0.003 0.065 -9999 0 -0.44 9 9
MYST2 0.013 0.001 -9999 0 -10000 0 0
HOXB13 -0.26 0.36 -9999 0 -0.74 157 157
T-DHT/AR/RACK1/Src 0.026 0.054 -9999 0 -10000 0 0
positive regulation of transcription 0.003 0.065 -9999 0 -0.44 9 9
DNAJA1 0.011 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.016 -9999 0 -0.29 1 1
NCOA1 0.013 0.006 -9999 0 -10000 0 0
SPDEF -0.074 0.18 -9999 0 -0.44 82 82
T-DHT/AR/TIF2 0.023 0.059 -9999 0 -10000 0 0
T-DHT/AR/Hsp90 0.02 0.052 -9999 0 -0.39 1 1
GSK3B 0.012 0.003 -9999 0 -10000 0 0
NR2C1 0.013 0.003 -9999 0 -10000 0 0
mol:T-DHT 0.019 0.041 -9999 0 -10000 0 0
SIRT1 0.012 0.001 -9999 0 -10000 0 0
ZMIZ2 0.016 0.012 -9999 0 -10000 0 0
POU2F1 0.011 0.037 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 0.01 0.067 -9999 0 -0.38 6 6
CREBBP 0.012 0.001 -9999 0 -10000 0 0
SMARCE1 0.01 0.006 -9999 0 -10000 0 0
Nongenotropic Androgen signaling

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
PTK2 0.01 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.002 0.081 -10000 0 -0.44 4 4
regulation of S phase of mitotic cell cycle 0.013 0.053 -10000 0 -10000 0 0
GNAO1 -0.11 0.2 -10000 0 -0.44 118 118
HRAS 0.011 0.022 -10000 0 -0.44 1 1
SHBG/T-DHT 0.002 0.048 -10000 0 -0.49 4 4
PELP1 0.012 0 -10000 0 -10000 0 0
AKT1 0.01 0 -10000 0 -10000 0 0
MAP2K1 0.025 0.054 -10000 0 -0.34 2 2
T-DHT/AR -0.011 0.08 -10000 0 -0.33 24 24
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -0.008 7 7
GNAI2 0.012 0 -10000 0 -10000 0 0
GNAI3 0.012 0 -10000 0 -10000 0 0
GNAI1 -0.003 0.083 -10000 0 -0.44 15 15
mol:GDP -0.02 0.082 -10000 0 -0.36 24 24
cell proliferation 0.029 0.075 -10000 0 -0.36 7 7
PIK3CA 0.012 0.001 -10000 0 -10000 0 0
FOS 0.026 0.11 -10000 0 -0.78 7 7
mol:Ca2+ -0.017 0.027 -10000 0 -0.089 26 26
MAPK3 0.027 0.065 -10000 0 -10000 0 0
MAPK1 0.021 0.037 -10000 0 -10000 0 0
PIK3R1 0.012 0 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.005 7 7
cAMP biosynthetic process 0.009 0.05 -10000 0 -0.45 4 4
GNG2 -0.007 0.091 -10000 0 -0.44 18 18
potassium channel inhibitor activity 0 0.001 -10000 0 -0.005 7 7
HRAS/GTP 0.011 0.056 -10000 0 -0.39 2 2
actin cytoskeleton reorganization 0 0.009 -10000 0 -10000 0 0
SRC 0.012 0 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.005 7 7
PI3K 0.017 0 -10000 0 -10000 0 0
apoptosis -0.029 0.065 0.38 7 -10000 0 7
T-DHT/AR/PELP1 -0.001 0.068 -10000 0 -0.27 24 24
HRAS/GDP -0.019 0.077 -10000 0 -0.33 24 24
CREB1 0.029 0.069 -10000 0 -0.41 7 7
RAC1-CDC42/GTP 0.001 0.011 -10000 0 -10000 0 0
AR -0.016 0.11 -10000 0 -0.47 24 24
GNB1 0.012 0 -10000 0 -10000 0 0
RAF1 0.019 0.055 -10000 0 -0.36 2 2
RAC1-CDC42/GDP -0.013 0.075 -10000 0 -10000 0 0
T-DHT/AR/PELP1/Src 0.008 0.062 -10000 0 -0.44 2 2
MAP2K2 0.025 0.056 -10000 0 -0.35 3 3
T-DHT/AR/PELP1/Src/PI3K 0.013 0.053 -10000 0 -10000 0 0
GNAZ 0.007 0.049 -10000 0 -0.44 5 5
SHBG 0.003 0.072 -10000 0 -0.74 4 4
Gi family/GNB1/GNG2/GDP -0.068 0.18 -10000 0 -0.52 29 29
mol:T-DHT 0 0 -10000 0 -0.003 7 7
RAC1 0.012 0 -10000 0 -10000 0 0
GNRH1 0.009 0.001 -10000 0 -10000 0 0
Gi family/GTP -0.042 0.11 -10000 0 -0.38 23 23
CDC42 0.011 0.022 -10000 0 -0.44 1 1
Regulation of Telomerase

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
Telomerase catalytic core complex -0.061 0.18 -9999 0 -0.61 33 33
RAD9A 0.012 0 -9999 0 -10000 0 0
AP1 0.013 0.041 -9999 0 -0.3 7 7
IFNAR2 0.013 0.004 -9999 0 -10000 0 0
AKT1 -0.003 0.056 -9999 0 -10000 0 0
ER alpha/Oestrogen -0.022 0.094 -9999 0 -0.31 41 41
NFX1/SIN3/HDAC complex 0.038 0.012 -9999 0 -10000 0 0
EGF -0.087 0.21 -9999 0 -0.5 83 83
SMG5 0.012 0 -9999 0 -10000 0 0
SMG6 0.012 0 -9999 0 -10000 0 0
SP3/HDAC2 0.019 0.007 -9999 0 -10000 0 0
TERT/c-Abl -0.051 0.17 -9999 0 -0.57 33 33
SAP18 0.012 0.001 -9999 0 -10000 0 0
MRN complex 0.024 0.013 -9999 0 -10000 0 0
WT1 -0.36 0.37 -9999 0 -0.74 213 213
WRN 0.011 0.022 -9999 0 -0.44 1 1
SP1 0.013 0.006 -9999 0 -10000 0 0
SP3 0.012 0.003 -9999 0 -10000 0 0
TERF2IP 0.012 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.059 0.15 -9999 0 -0.58 15 15
Mad/Max 0.017 0.023 -9999 0 -10000 0 0
TERT -0.063 0.19 -9999 0 -0.63 33 33
CCND1 -0.05 0.17 -9999 0 -0.81 5 5
MAX 0.012 0.003 -9999 0 -10000 0 0
RBBP7 0.012 0.001 -9999 0 -10000 0 0
RBBP4 0.012 0.001 -9999 0 -10000 0 0
TERF2 0.011 0 -9999 0 -10000 0 0
PTGES3 0.012 0 -9999 0 -10000 0 0
SIN3A 0.012 0.001 -9999 0 -10000 0 0
Telomerase/911 0.025 0.028 -9999 0 -10000 0 0
CDKN1B -0.023 0.16 -9999 0 -0.46 47 47
RAD1 0.011 0.036 -9999 0 -0.74 1 1
XRCC5 0.012 0 -9999 0 -10000 0 0
XRCC6 0.012 0 -9999 0 -10000 0 0
SAP30 0.012 0.001 -9999 0 -10000 0 0
TRF2/PARP2 0.018 0 -9999 0 -10000 0 0
UBE3A 0.011 0.022 -9999 0 -0.44 1 1
JUN 0.012 0.003 -9999 0 -10000 0 0
E6 0 0.003 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.009 0.016 -9999 0 -0.31 1 1
FOS 0.005 0.057 -9999 0 -0.44 7 7
IFN-gamma/IRF1 -0.036 0.18 -9999 0 -0.55 46 46
PARP2 0.012 0 -9999 0 -10000 0 0
BLM 0.012 0 -9999 0 -10000 0 0
Telomerase 0.003 0.054 -9999 0 -0.36 1 1
IRF1 0.016 0.009 -9999 0 -10000 0 0
ESR1 -0.031 0.13 -9999 0 -0.44 41 41
KU/TER 0.018 0 -9999 0 -10000 0 0
ATM/TRF2 0.019 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.042 0.016 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.042 0.016 -9999 0 -10000 0 0
HDAC1 0.012 0.001 -9999 0 -10000 0 0
HDAC2 0.013 0.006 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.017 0.036 -9999 0 -0.39 3 3
ABL1 0.012 0 -9999 0 -10000 0 0
MXD1 0.01 0.031 -9999 0 -0.44 2 2
MRE11A 0.012 0.001 -9999 0 -10000 0 0
HUS1 0.012 0 -9999 0 -10000 0 0
RPS6KB1 0.011 0.022 -9999 0 -0.44 1 1
TERT/NF kappa B1/14-3-3 -0.036 0.17 -9999 0 -0.66 11 11
NR2F2 0.012 0.006 -9999 0 -10000 0 0
MAPK3 0.012 0.017 -9999 0 -0.32 1 1
MAPK1 0.012 0.006 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.011 0.036 -9999 0 -0.74 1 1
NFKB1 0.012 0 -9999 0 -10000 0 0
HNRNPC 0.012 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0 -9999 0 -10000 0 0
NBN 0.011 0.022 -9999 0 -0.44 1 1
EGFR 0.011 0.022 -9999 0 -0.44 1 1
mol:Oestrogen 0 0.002 -9999 0 -10000 0 0
EGF/EGFR -0.055 0.15 -9999 0 -0.35 84 84
MYC 0.002 0.088 -9999 0 -0.74 6 6
IL2 0.004 0.009 -9999 0 -10000 0 0
KU 0.018 0 -9999 0 -10000 0 0
RAD50 0.012 0 -9999 0 -10000 0 0
HSP90AA1 0.012 0 -9999 0 -10000 0 0
TGFB1 0.011 0.036 -9999 0 -0.74 1 1
TRF2/BLM 0.018 0 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.045 0.17 -9999 0 -0.63 17 17
SP1/HDAC2 0.021 0.011 -9999 0 -10000 0 0
PINX1 0.012 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.059 0.15 -9999 0 -0.61 11 11
Smad3/Myc 0.014 0.066 -9999 0 -0.48 7 7
911 complex 0.024 0.024 -9999 0 -0.48 1 1
IFNG -0.065 0.23 -9999 0 -0.73 46 46
Telomerase/PinX1 -0.059 0.15 -9999 0 -0.61 11 11
Telomerase/AKT1/mTOR/p70S6K 0.009 0.049 -9999 0 -10000 0 0
SIN3B 0.012 0.001 -9999 0 -10000 0 0
YWHAE 0.012 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.059 0.15 -9999 0 -0.6 12 12
response to DNA damage stimulus 0.003 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0.035 0.011 -9999 0 -10000 0 0
TRF2/WRN 0.017 0.014 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.059 0.15 -9999 0 -0.58 15 15
E2F1 -0.004 0.11 -9999 0 -0.74 10 10
ZNFX1 0.012 0.001 -9999 0 -10000 0 0
PIF1 -0.003 0.11 -9999 0 -0.74 9 9
NCL 0.012 0 -9999 0 -10000 0 0
DKC1 0.012 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
S1P3 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
PDGFRB 0.005 0.072 -9999 0 -0.74 4 4
mol:S1P 0.001 0.002 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.038 0.11 -9999 0 -0.36 18 18
GNAO1 -0.11 0.2 -9999 0 -0.44 118 118
S1P/S1P3/G12/G13 0.025 0.022 -9999 0 -0.44 1 1
AKT1 -0.002 0.055 -9999 0 -10000 0 0
AKT3 -0.013 0.16 -9999 0 -1.2 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.005 0.072 -9999 0 -0.74 4 4
GNAI2 0.013 0.003 -9999 0 -10000 0 0
GNAI3 0.013 0.002 -9999 0 -10000 0 0
GNAI1 -0.002 0.083 -9999 0 -0.44 15 15
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.012 0.036 -9999 0 -0.73 1 1
S1PR2 0.012 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.037 0.13 -9999 0 -0.41 18 18
MAPK3 -0.03 0.12 -9999 0 -0.39 19 19
MAPK1 -0.029 0.12 -9999 0 -0.39 18 18
JAK2 -0.028 0.12 -9999 0 -0.41 18 18
CXCR4 -0.029 0.12 -9999 0 -0.39 18 18
FLT1 0.015 0.002 -9999 0 -10000 0 0
RhoA/GDP 0.009 0 -9999 0 -10000 0 0
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
SRC -0.029 0.12 -9999 0 -0.39 18 18
S1P/S1P3/Gi -0.037 0.13 -9999 0 -0.41 18 18
RAC1 0.012 0 -9999 0 -10000 0 0
RhoA/GTP -0.028 0.12 -9999 0 -0.37 18 18
VEGFA 0.013 0.036 -9999 0 -0.73 1 1
S1P/S1P2/Gi -0.038 0.12 -9999 0 -0.38 18 18
VEGFR1 homodimer/VEGFA homodimer 0.023 0.029 -9999 0 -0.55 1 1
RHOA 0.012 0 -9999 0 -10000 0 0
S1P/S1P3/Gq 0.021 0.044 -9999 0 -0.54 1 1
GNAQ 0.01 0.031 -9999 0 -0.44 2 2
GNAZ 0.008 0.049 -9999 0 -0.44 5 5
G12/G13 0.018 0 -9999 0 -10000 0 0
GNA14 0.01 0.031 -9999 0 -0.44 2 2
GNA15 0.005 0.072 -9999 0 -0.74 4 4
GNA12 0.012 0 -9999 0 -10000 0 0
GNA13 0.012 0 -9999 0 -10000 0 0
GNA11 0.01 0.031 -9999 0 -0.44 2 2
Rac1/GTP -0.028 0.12 -9999 0 -0.37 18 18
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.074 0.18 -9999 0 -0.44 82 82
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.011 0.036 -9999 0 -0.74 1 1
TCEB1 0.012 0 -9999 0 -10000 0 0
HIF1A/p53 0.027 0.009 -9999 0 -10000 0 0
HIF1A 0.02 0.009 -9999 0 -10000 0 0
COPS5 0.012 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.035 0.024 -9999 0 -0.4 1 1
FIH (dimer) 0.012 0 -9999 0 -10000 0 0
CDKN2A -0.15 0.31 -9999 0 -0.74 95 95
ARNT/IPAS -0.044 0.13 -9999 0 -0.31 1 1
HIF1AN 0.012 0 -9999 0 -10000 0 0
GNB2L1 0.012 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.026 0.014 -9999 0 -10000 0 0
CUL2 0.012 0 -9999 0 -10000 0 0
OS9 0.012 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.024 0.024 -9999 0 -0.48 1 1
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.027 0.009 -9999 0 -10000 0 0
PHD1-3/OS9 0.028 0.029 -9999 0 -10000 0 0
HIF1A/RACK1/Elongin B/Elongin C 0.036 0.02 -9999 0 -0.35 1 1
VHL 0.012 0 -9999 0 -10000 0 0
HSP90AA1 0.012 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.027 0.009 -9999 0 -10000 0 0
EGLN3 0.007 0.049 -9999 0 -0.44 5 5
EGLN2 0.011 0.022 -9999 0 -0.44 1 1
EGLN1 0.012 0 -9999 0 -10000 0 0
TP53 0.012 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.033 0.015 -9999 0 -10000 0 0
ARNT 0.011 0.022 -9999 0 -0.44 1 1
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.011 0.022 -9999 0 -0.44 1 1
HIF1A/p19ARF -0.062 0.17 -9999 0 -0.38 95 95
Coregulation of Androgen receptor activity

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
NRIP1 -0.001 0.041 -9999 0 -0.44 2 2
SVIL 0.002 0.024 -9999 0 -10000 0 0
ZNF318 0.036 0.058 -9999 0 -10000 0 0
JMJD2C 0.003 0.026 -9999 0 -0.11 17 17
T-DHT/AR/Ubc9 0.008 0.076 -9999 0 -0.42 5 5
CARM1 0.011 0.004 -9999 0 -10000 0 0
PRDX1 0.014 0.004 -9999 0 -10000 0 0
PELP1 0.016 0.01 -9999 0 -10000 0 0
CTNNB1 0.004 0.02 -9999 0 -10000 0 0
AKT1 0.019 0.017 -9999 0 -10000 0 0
PTK2B 0.004 0.028 -9999 0 -0.44 1 1
MED1 0.019 0.041 -9999 0 -0.74 1 1
MAK 0.008 0.16 -9999 0 -0.73 16 16
response to oxidative stress 0.002 0.005 -9999 0 -10000 0 0
HIP1 0.001 0.032 -9999 0 -0.44 1 1
GSN -0.009 0.072 -9999 0 -0.46 9 9
NCOA2 0.01 0.022 -9999 0 -0.44 1 1
NCOA6 0.003 0.024 -9999 0 -10000 0 0
DNA-PK 0.048 0.055 -9999 0 -10000 0 0
NCOA4 0.01 0.022 -9999 0 -0.44 1 1
PIAS3 0.004 0.02 -9999 0 -10000 0 0
cell proliferation 0.007 0.095 -9999 0 -0.37 16 16
XRCC5 0.018 0.013 -9999 0 -10000 0 0
UBE3A -0.005 0.044 -9999 0 -0.44 1 1
T-DHT/AR/SNURF -0.023 0.12 -9999 0 -0.46 15 15
FHL2 0.043 0.077 -9999 0 -1.1 1 1
RANBP9 0.001 0.032 -9999 0 -0.44 1 1
JMJD1A 0.006 0.026 -9999 0 -0.13 14 14
CDK6 0.013 0.003 -9999 0 -10000 0 0
TGFB1I1 0.002 0.024 -9999 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.003 0.086 -9999 0 -0.4 11 11
XRCC6 0.018 0.013 -9999 0 -10000 0 0
T-DHT/AR 0.021 0.09 -9999 0 -0.48 5 5
CTDSP1 0.009 0.008 -9999 0 -10000 0 0
CTDSP2 0.029 0.04 -9999 0 -10000 0 0
BRCA1 0.002 0.024 -9999 0 -10000 0 0
TCF4 0.023 0.037 -9999 0 -0.44 1 1
CDKN2A -0.14 0.31 -9999 0 -0.73 95 95
SRF 0.027 0.02 -9999 0 -10000 0 0
NKX3-1 -0.003 0.14 -9999 0 -0.8 12 12
KLK3 -0.2 0.51 -9999 0 -1.3 74 74
TMF1 0.009 0.022 -9999 0 -0.44 1 1
HNRNPA1 0.021 0.022 -9999 0 -10000 0 0
AOF2 -0.011 0.026 -9999 0 -0.068 72 72
APPL1 0.033 0.043 -9999 0 -0.31 2 2
T-DHT/AR/Caspase 8 0.017 0.082 -9999 0 -0.42 5 5
AR -0.013 0.11 -9999 0 -0.47 24 24
UBA3 0.009 0.008 -9999 0 -10000 0 0
PATZ1 0.021 0.022 -9999 0 -10000 0 0
PAWR 0.01 0.005 -9999 0 -10000 0 0
PRKDC 0.018 0.013 -9999 0 -10000 0 0
PA2G4 0.023 0.026 -9999 0 -10000 0 0
UBE2I 0.012 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.015 0.073 -9999 0 -0.39 5 5
RPS6KA3 0.001 0.028 -9999 0 -10000 0 0
T-DHT/AR/ARA70 0.001 0.076 -9999 0 -0.31 13 13
LATS2 0.021 0.022 -9999 0 -10000 0 0
T-DHT/AR/PRX1 0.021 0.079 -9999 0 -0.39 5 5
Cyclin D3/CDK11 p58 0.011 0.005 -9999 0 -10000 0 0
VAV3 -0.046 0.14 -9999 0 -0.45 48 48
KLK2 -0.01 0.12 -9999 0 -0.58 17 17
CASP8 0.016 0.009 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.008 0.071 -9999 0 -0.38 5 5
TMPRSS2 0.01 0.078 -9999 0 -0.85 2 2
CCND1 0.002 0.063 -9999 0 -0.74 3 3
PIAS1 -0.004 0.039 -9999 0 -10000 0 0
mol:T-DHT 0.003 0.017 -9999 0 -0.059 25 25
CDC2L1 0.001 0.002 -9999 0 -10000 0 0
PIAS4 -0.011 0.057 -9999 0 -10000 0 0
T-DHT/AR/CDK6 0.012 0.077 -9999 0 -0.42 5 5
CMTM2 -0.015 0.15 -9999 0 -0.74 17 17
SNURF -0.039 0.15 -9999 0 -0.47 43 43
ZMIZ1 0.015 0.015 -9999 0 -10000 0 0
CCND3 0.013 0.002 -9999 0 -10000 0 0
TGIF1 0.021 0.022 -9999 0 -10000 0 0
FKBP4 0.001 0.043 -9999 0 -0.74 1 1
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0 0.078 -9999 0 -0.44 13 13
PDGF/PDGFRA/CRKL 0.01 0.054 -9999 0 -0.29 13 13
positive regulation of JUN kinase activity 0.024 0.04 -9999 0 -10000 0 0
CRKL 0.012 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.001 0.066 -9999 0 -0.34 15 15
AP1 -0.019 0.11 -9999 0 -0.84 7 7
mol:IP3 0.012 0.056 -9999 0 -0.3 13 13
PLCG1 0.012 0.056 -9999 0 -0.3 13 13
PDGF/PDGFRA/alphaV Integrin 0.01 0.054 -9999 0 -0.29 13 13
RAPGEF1 0.011 0.022 -9999 0 -0.44 1 1
CRK 0.012 0 -9999 0 -10000 0 0
mol:Ca2+ 0.012 0.056 -9999 0 -0.3 13 13
CAV3 -0.002 0.05 -9999 0 -0.74 2 2
CAV1 0.009 0.038 -9999 0 -0.44 3 3
SHC/Grb2/SOS1 0.025 0.041 -9999 0 -10000 0 0
PDGF/PDGFRA/Shf -0.009 0.11 -9999 0 -0.42 27 27
FOS 0.016 0.12 -9999 0 -0.82 7 7
JUN -0.002 0.008 -9999 0 -10000 0 0
oligodendrocyte development 0.009 0.053 -9999 0 -0.29 13 13
GRB2 0.012 0 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
mol:DAG 0.012 0.056 -9999 0 -0.3 13 13
PDGF/PDGFRA 0 0.078 -9999 0 -0.44 13 13
actin cytoskeleton reorganization 0.009 0.053 -9999 0 -0.29 13 13
SRF 0.018 0.004 -9999 0 -10000 0 0
SHC1 0.012 0 -9999 0 -10000 0 0
PI3K 0.018 0.045 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk/C3G 0.017 0.047 -9999 0 -10000 0 0
JAK1 0.01 0.056 -9999 0 -0.3 14 14
ELK1/SRF 0.025 0.043 -9999 0 -10000 0 0
SHB 0.012 0 -9999 0 -10000 0 0
SHF -0.011 0.13 -9999 0 -0.72 14 14
CSNK2A1 0.009 0.007 -9999 0 -10000 0 0
GO:0007205 0.011 0.061 -9999 0 -0.33 13 13
SOS1 0.012 0 -9999 0 -10000 0 0
Ras protein signal transduction 0.024 0.04 -9999 0 -10000 0 0
PDGF/PDGFRA/SHB 0.01 0.054 -9999 0 -0.29 13 13
PDGF/PDGFRA/Caveolin-1 0.007 0.062 -9999 0 -0.31 15 15
ITGAV 0.012 0 -9999 0 -10000 0 0
ELK1 0.017 0.053 -9999 0 -10000 0 0
PIK3CA 0.012 0.001 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk 0.01 0.054 -9999 0 -0.29 13 13
JAK-STAT cascade 0.01 0.056 -9999 0 -0.29 14 14
cell proliferation -0.009 0.11 -9999 0 -0.42 27 27
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.024 0 -9999 0 -10000 0 0
SNTA1 0.011 0.022 -9999 0 -0.44 1 1
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.023 0.013 -9999 0 -10000 0 0
MAPK12 0.018 0.06 -9999 0 -0.52 5 5
CCND1 0.015 0.028 -9999 0 -0.22 2 2
p38 gamma/SNTA1 0.023 0.058 -9999 0 -0.48 5 5
MAP2K3 0.012 0 -9999 0 -10000 0 0
PKN1 0.012 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.018 0.06 -9999 0 -0.51 5 5
MAP2K6 0.018 0.022 -9999 0 -10000 0 0
MAPT -0.04 0.13 -9999 0 -0.28 95 95
MAPK13 0.019 0 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.015 0 -9999 0 -10000 0 0
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0 0.021 -10000 0 -10000 0 0
DAPP1 -0.04 0.12 -10000 0 -0.41 17 17
Src family/SYK family/BLNK-LAT/BTK-ITK -0.054 0.15 -10000 0 -0.55 15 15
mol:DAG -0.011 0.086 -10000 0 -0.25 16 16
HRAS 0.012 0.022 -10000 0 -0.44 1 1
RAP1A 0.013 0.001 -10000 0 -10000 0 0
ARF5/GDP 0.006 0.098 -10000 0 -0.41 15 15
PLCG2 -0.032 0.13 -10000 0 -0.44 42 42
PLCG1 0.012 0 -10000 0 -10000 0 0
ARF5 0.012 0 -10000 0 -10000 0 0
mol:GTP 0 0.021 -10000 0 -10000 0 0
ARF1/GTP 0.032 0.021 0.22 2 -10000 0 2
RHOA 0.012 0 -10000 0 -10000 0 0
YES1 0.011 0.022 -10000 0 -0.44 1 1
RAP1A/GTP 0.023 0.021 -10000 0 -10000 0 0
ADAP1 -0.001 0.026 -10000 0 -0.38 1 1
ARAP3 0 0.021 -10000 0 -10000 0 0
INPPL1 0.012 0 -10000 0 -10000 0 0
PREX1 0.01 0.031 -10000 0 -0.44 2 2
ARHGEF6 0.002 0.068 -10000 0 -0.44 10 10
ARHGEF7 0.012 0 -10000 0 -10000 0 0
ARF1 0.012 0 -10000 0 -10000 0 0
NRAS 0.011 0.031 -10000 0 -0.44 2 2
FYN 0.012 0 -10000 0 -10000 0 0
ARF6 0.012 0 -10000 0 -10000 0 0
FGR 0.007 0.052 -10000 0 -0.52 4 4
mol:Ca2+ 0.001 0.048 -10000 0 -10000 0 0
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.032 0.13 -10000 0 -0.44 42 42
ZAP70 -0.002 0.083 -10000 0 -0.46 13 13
mol:IP3 -0.002 0.065 -10000 0 -10000 0 0
LYN 0.012 0 -10000 0 -10000 0 0
ARF1/GDP 0.006 0.098 -10000 0 -0.41 15 15
RhoA/GDP 0.028 0.049 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.025 0 -10000 0 -10000 0 0
BLNK 0.006 0.053 -10000 0 -0.44 6 6
actin cytoskeleton reorganization 0.03 0.072 -10000 0 -0.39 4 4
SRC 0.012 0 -10000 0 -10000 0 0
PLEKHA2 0.024 0 -10000 0 -10000 0 0
RAC1 0.012 0 -10000 0 -10000 0 0
PTEN 0.007 0.029 -10000 0 -0.42 2 2
HSP90AA1 0.012 0 -10000 0 -10000 0 0
ARF6/GTP 0 0.021 -10000 0 -10000 0 0
RhoA/GTP 0.028 0.021 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.039 0.12 -10000 0 -0.49 9 9
BLK -0.16 0.22 -10000 0 -0.44 160 160
PDPK1 0.012 0 -10000 0 -10000 0 0
CYTH1 0 0.02 -10000 0 -10000 0 0
HCK 0.001 0.071 -10000 0 -0.44 11 11
CYTH3 0 0.02 -10000 0 -10000 0 0
CYTH2 0 0.02 -10000 0 -10000 0 0
KRAS 0.013 0.002 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.014 0.1 -10000 0 -0.4 23 23
SGK1 -0.023 0.1 -10000 0 -0.44 23 23
INPP5D 0.012 0 -10000 0 -10000 0 0
mol:GDP -0.001 0.1 -10000 0 -0.43 15 15
SOS1 0.012 0 -10000 0 -10000 0 0
SYK 0.012 0 -10000 0 -10000 0 0
ARF6/GDP 0.027 0.049 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0.023 0.24 2 -10000 0 2
ARAP3/RAP1A/GTP 0.023 0.021 -10000 0 -10000 0 0
VAV1 -0.008 0.093 -10000 0 -0.44 19 19
mol:PI-3-4-P2 0.019 0 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.026 0.018 -10000 0 -10000 0 0
PLEKHA1 0.024 0 -10000 0 -10000 0 0
Rac1/GDP 0.006 0.098 -10000 0 -0.41 15 15
LAT 0.008 0.047 -10000 0 -0.54 3 3
Rac1/GTP -0.007 0.13 -10000 0 -0.52 16 16
ITK -0.007 0.038 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.02 0.11 -10000 0 -0.35 17 17
LCK -0.002 0.099 -10000 0 -0.67 9 9
BTK -0.023 0.063 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.015 0.018 -10000 0 -0.24 2 2
RAS family/GTP 0.014 0.078 -10000 0 -10000 0 0
NFATC4 0.015 0.069 -10000 0 -0.37 1 1
ERBB2IP 0.006 0.053 -10000 0 -0.44 6 6
HSP90 (dimer) 0.012 0 -10000 0 -10000 0 0
mammary gland morphogenesis 0.003 0.084 -10000 0 -0.51 1 1
JUN 0.032 0.069 -10000 0 -0.28 7 7
HRAS 0.011 0.022 -10000 0 -0.44 1 1
DOCK7 0.009 0.082 -10000 0 -0.48 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.006 0.091 -10000 0 -0.46 4 4
AKT1 0.01 0.002 -10000 0 -10000 0 0
BAD 0.015 0.013 -10000 0 -0.26 1 1
MAPK10 -0.004 0.077 -10000 0 -0.24 8 8
mol:GTP 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.004 0.09 -10000 0 -0.56 1 1
RAF1 0.023 0.084 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 2 -0.021 0.094 -10000 0 -0.44 4 4
STAT3 0.003 0.006 -10000 0 -10000 0 0
cell migration 0.008 0.072 0.17 2 -10000 0 2
mol:PI-3-4-5-P3 0 0.002 -10000 0 -10000 0 0
cell proliferation 0.007 0.21 -10000 0 -0.6 40 40
FOS 0.025 0.14 -10000 0 -0.36 46 46
NRAS 0.01 0.031 -10000 0 -0.44 2 2
mol:Ca2+ 0.003 0.084 -10000 0 -0.51 1 1
MAPK3 0.012 0.17 -10000 0 -0.48 39 39
MAPK1 0.014 0.17 -10000 0 -0.46 39 39
JAK2 0.007 0.083 -10000 0 -0.48 1 1
NF2 -0.001 0.003 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.004 0.084 -10000 0 -0.24 12 12
NRG1 -0.044 0.15 -10000 0 -0.44 54 54
GRB2/SOS1 0.018 0.001 -10000 0 -10000 0 0
MAPK8 0.008 0.09 -10000 0 -0.38 1 1
MAPK9 0.018 0.048 -10000 0 -10000 0 0
ERBB2 -0.001 0.068 0.34 6 -0.57 4 10
ERBB3 0.012 0.002 -10000 0 -10000 0 0
SHC1 0.012 0.001 -10000 0 -10000 0 0
RAC1 0.012 0 -10000 0 -10000 0 0
apoptosis -0.003 0.015 0.22 1 -10000 0 1
STAT3 (dimer) 0.018 0.005 -10000 0 -10000 0 0
RNF41 0.019 0.016 -10000 0 -10000 0 0
FRAP1 0.008 0.002 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.019 0.049 -10000 0 -0.33 1 1
ErbB2/ErbB2/HSP90 (dimer) 0.008 0.055 -10000 0 -0.49 4 4
CHRNA1 -0.001 0.21 -10000 0 -0.63 40 40
myelination 0.015 0.068 -10000 0 -0.37 1 1
PPP3CB 0.008 0.077 -10000 0 -0.44 1 1
KRAS 0.012 0.001 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.008 0.074 -10000 0 -10000 0 0
NRG2 -0.051 0.15 -10000 0 -0.45 56 56
mol:GDP -0.004 0.084 -10000 0 -0.24 12 12
SOS1 0.012 0.001 -10000 0 -10000 0 0
MAP2K2 0.025 0.092 -10000 0 -10000 0 0
SRC 0.012 0 -10000 0 -10000 0 0
mol:cAMP 0 0.001 -10000 0 -10000 0 0
PTPN11 0.008 0.082 -10000 0 -0.48 1 1
MAP2K1 0.009 0.15 -10000 0 -0.56 12 12
heart morphogenesis 0.003 0.084 -10000 0 -0.51 1 1
RAS family/GDP 0.015 0.076 -10000 0 -10000 0 0
GRB2 0.012 0.001 -10000 0 -10000 0 0
PRKACA -0.002 0.005 -10000 0 -10000 0 0
CHRNE 0.014 0.032 -10000 0 -0.21 7 7
HSP90AA1 0.012 0 -10000 0 -10000 0 0
activation of caspase activity -0.01 0.002 -10000 0 -10000 0 0
nervous system development 0.003 0.084 -10000 0 -0.51 1 1
CDC42 0.011 0.022 -10000 0 -0.44 1 1
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.003 0.084 0.48 12 -10000 0 12
KIRREL 0.007 0.045 -10000 0 -0.44 4 4
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.003 0.084 -10000 0 -0.48 12 12
PLCG1 0.012 0 -10000 0 -10000 0 0
ARRB2 0.012 0 -10000 0 -10000 0 0
WASL 0.012 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.002 0.091 -10000 0 -0.44 11 11
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.019 0.051 -10000 0 -0.48 1 1
FYN 0.006 0.071 -10000 0 -0.4 11 11
mol:Ca2+ 0.01 0.078 -10000 0 -0.44 11 11
mol:DAG 0.011 0.079 -10000 0 -0.44 11 11
NPHS2 -0.002 0.073 -10000 0 -0.75 4 4
mol:IP3 0.011 0.079 -10000 0 -0.44 11 11
regulation of endocytosis 0.015 0.067 -10000 0 -0.37 11 11
Nephrin/NEPH1/podocin/Cholesterol 0.003 0.079 -10000 0 -0.45 11 11
establishment of cell polarity 0.003 0.084 -10000 0 -0.48 12 12
Nephrin/NEPH1/podocin/NCK1-2 0.018 0.074 -10000 0 -0.4 11 11
Nephrin/NEPH1/beta Arrestin2 0.016 0.068 -10000 0 -0.37 11 11
NPHS1 -0.003 0.1 -10000 0 -0.74 8 8
Nephrin/NEPH1/podocin 0.008 0.071 -10000 0 -0.4 11 11
TJP1 0.012 0 -10000 0 -10000 0 0
NCK1 0.012 0 -10000 0 -10000 0 0
NCK2 0.012 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.011 0.079 -10000 0 -0.44 11 11
CD2AP -0.002 0.08 -10000 0 -0.44 14 14
Nephrin/NEPH1/podocin/GRB2 0.011 0.079 -10000 0 -0.44 11 11
GRB2 0.012 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.003 0.09 -10000 0 -0.41 13 13
cytoskeleton organization 0.022 0.064 -10000 0 -0.64 1 1
Nephrin/NEPH1 0.004 0.062 -10000 0 -0.41 8 8
Nephrin/NEPH1/ZO-1 0.012 0.069 -10000 0 -0.46 8 8
Cellular roles of Anthrax toxin

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
ANTXR1 0.006 0.066 -10000 0 -0.66 4 4
ANTXR2 0.011 0.022 -10000 0 -0.44 1 1
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0.008 -10000 0 -0.077 5 5
monocyte activation 0.005 0.062 -10000 0 -0.38 11 11
MAP2K2 -0.002 0.034 -10000 0 -0.71 1 1
MAP2K1 -0.001 0.007 -10000 0 -10000 0 0
MAP2K7 -0.001 0.013 -10000 0 -0.22 1 1
MAP2K6 -0.002 0.02 -10000 0 -0.22 3 3
CYAA 0.008 0.039 -10000 0 -0.34 5 5
MAP2K4 -0.002 0.017 -10000 0 -0.22 2 2
IL1B -0.035 0.13 -10000 0 -0.39 51 51
Channel 0.012 0.042 -10000 0 -0.36 5 5
NLRP1 -0.004 0.035 -10000 0 -0.3 5 5
CALM1 0.012 0 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.011 0.011 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0.008 0.077 5 -10000 0 5
MAPK3 -0.001 0.013 -10000 0 -0.22 1 1
MAPK1 -0.001 0.007 -10000 0 -10000 0 0
PGR -0.044 0.088 -10000 0 -0.22 85 85
PA/Cellular Receptors 0.012 0.045 -10000 0 -0.39 5 5
apoptosis -0.001 0.008 -10000 0 -0.077 5 5
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.011 0.038 -10000 0 -0.33 5 5
macrophage activation 0.014 0.013 -10000 0 -0.2 1 1
TNF 0.01 0.031 -10000 0 -0.44 2 2
VCAM1 0.005 0.063 -10000 0 -0.38 11 11
platelet activation 0.011 0.011 -10000 0 -10000 0 0
MAPKKK cascade -0.011 0.013 0.13 1 -10000 0 1
IL18 0.011 0.024 -10000 0 -0.2 4 4
negative regulation of macrophage activation -0.001 0.008 -10000 0 -0.077 5 5
LEF -0.001 0.008 -10000 0 -0.077 5 5
CASP1 -0.003 0.018 -10000 0 -0.15 5 5
mol:cAMP -0.001 0.01 -10000 0 -10000 0 0
necrosis -0.001 0.008 -10000 0 -0.077 5 5
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.011 0.04 -10000 0 -0.34 5 5
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.012 0 -10000 0 -10000 0 0
NFATC1 0.046 0.03 -10000 0 -10000 0 0
NFATC2 0.031 0.025 -10000 0 -10000 0 0
NFATC3 0.021 0.003 -10000 0 -10000 0 0
YWHAE 0.012 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.068 0.12 -10000 0 -0.36 34 34
Exportin 1/Ran/NUP214 0.025 0.003 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.077 0.11 -10000 0 -0.42 16 16
BCL2/BAX 0 0.074 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.01 0.003 -10000 0 -10000 0 0
CaM/Ca2+ 0.01 0.003 -10000 0 -10000 0 0
BAX 0.012 0 -10000 0 -10000 0 0
MAPK14 0.012 0.002 -10000 0 -10000 0 0
BAD 0.011 0.022 -10000 0 -0.44 1 1
CABIN1/MEF2D -0.058 0.11 -10000 0 -0.34 34 34
Calcineurin A alpha-beta B1/BCL2 -0.013 0.1 -10000 0 -0.44 24 24
FKBP8 0.011 0.022 -10000 0 -0.44 1 1
activation-induced cell death of T cells 0.058 0.11 0.33 34 -10000 0 34
KPNB1 0.012 0 -10000 0 -10000 0 0
KPNA2 0.011 0.036 -10000 0 -0.74 1 1
XPO1 0.012 0 -10000 0 -10000 0 0
SFN 0.011 0.022 -10000 0 -0.44 1 1
MAP3K8 0.012 0.002 -10000 0 -10000 0 0
NFAT4/CK1 alpha 0.03 0.011 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 0.051 0.048 -10000 0 -10000 0 0
CABIN1 -0.069 0.12 -10000 0 -0.36 34 34
CALM1 0.013 0.001 -10000 0 -10000 0 0
RAN 0.012 0 -10000 0 -10000 0 0
MAP3K1 0.011 0.022 -10000 0 -0.44 1 1
CAMK4 -0.015 0.11 -10000 0 -0.44 26 26
mol:Ca2+ 0.001 0.002 -10000 0 -10000 0 0
MAPK3 0.011 0.022 -10000 0 -0.44 1 1
YWHAH 0.012 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0 0.074 -10000 0 -0.3 24 24
YWHAB 0.012 0 -10000 0 -10000 0 0
MAPK8 0.013 0.002 -10000 0 -10000 0 0
MAPK9 0.012 0 -10000 0 -10000 0 0
YWHAG 0.012 0 -10000 0 -10000 0 0
FKBP1A 0.012 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.061 0.029 -10000 0 -10000 0 0
PRKCH 0.011 0.022 -10000 0 -0.44 1 1
CABIN1/Cbp/p300 0.019 0.004 -10000 0 -10000 0 0
CASP3 0.012 0.002 -10000 0 -10000 0 0
PIM1 0.012 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.009 0.001 -10000 0 -10000 0 0
apoptosis -0.005 0.021 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.036 0.02 -10000 0 -0.39 1 1
PRKCB -0.089 0.19 -10000 0 -0.44 96 96
PRKCE 0.012 0 -10000 0 -10000 0 0
JNK2/NFAT4 0.026 0.002 -10000 0 -10000 0 0
BAD/BCL-XL 0.018 0.016 -10000 0 -0.3 1 1
PRKCD 0.012 0 -10000 0 -10000 0 0
NUP214 0.012 0 -10000 0 -10000 0 0
PRKCZ 0.013 0.002 -10000 0 -10000 0 0
PRKCA 0.012 0 -10000 0 -10000 0 0
PRKCG -0.24 0.35 -10000 0 -0.74 146 146
PRKCQ 0.004 0.061 -10000 0 -0.44 8 8
FKBP38/BCL2 0 0.075 -10000 0 -10000 0 0
EP300 0.013 0.002 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.012 0 -10000 0 -10000 0 0
NFATc/JNK1 0.051 0.029 -10000 0 -10000 0 0
CaM/Ca2+/FKBP38 0.017 0.014 -10000 0 -0.27 1 1
FKBP12/FK506 0.009 0 -10000 0 -10000 0 0
CSNK1A1 0.017 0.003 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.001 0.065 -10000 0 -0.26 26 26
NFATc/ERK1 0.05 0.03 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.077 0.11 -10000 0 -0.49 10 10
NR4A1 0.046 0.083 -10000 0 -0.59 7 7
GSK3B 0.013 0.002 -10000 0 -10000 0 0
positive T cell selection 0.021 0.003 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.003 0.014 -10000 0 -10000 0 0
RCH1/ KPNB1 0.017 0.028 -10000 0 -0.56 1 1
YWHAQ 0.012 0 -10000 0 -10000 0 0
PRKACA 0.012 0.002 -10000 0 -10000 0 0
AKAP5 -0.013 0.1 -10000 0 -0.44 24 24
MEF2D 0.013 0.002 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.012 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.051 0.029 -10000 0 -10000 0 0
CREBBP 0.013 0.002 -10000 0 -10000 0 0
BCL2 -0.013 0.1 -10000 0 -0.44 24 24
FoxO family signaling

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
G6PC -0.13 0.42 -9999 0 -1.2 55 55
PLK1 0.046 0.14 -9999 0 -0.88 2 2
CDKN1B 0.072 0.092 -9999 0 -0.48 1 1
FOXO3 0.043 0.15 -9999 0 -0.65 6 6
KAT2B 0.003 0.092 -9999 0 -0.44 18 18
FOXO1/SIRT1 -0.035 0.13 -9999 0 -0.37 55 55
CAT 0.047 0.13 -9999 0 -0.97 1 1
CTNNB1 0.012 0 -9999 0 -10000 0 0
AKT1 0.017 0.019 -9999 0 -10000 0 0
FOXO1 -0.023 0.15 -9999 0 -0.41 55 55
MAPK10 -0.002 0.083 -9999 0 -10000 0 0
mol:GTP 0.002 0 -9999 0 -10000 0 0
FOXO4 0.065 0.056 -9999 0 -10000 0 0
response to oxidative stress 0.005 0.021 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.009 0.1 -9999 0 -0.58 6 6
XPO1 0.013 0 -9999 0 -10000 0 0
EP300 0.006 0.019 -9999 0 -10000 0 0
BCL2L11 0.025 0.028 -9999 0 -10000 0 0
FOXO1/SKP2 -0.016 0.14 -9999 0 -0.37 55 55
mol:GDP 0.005 0.021 -9999 0 -10000 0 0
RAN 0.014 0 -9999 0 -10000 0 0
GADD45A 0.078 0.061 -9999 0 -10000 0 0
YWHAQ 0.012 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.051 0.04 -9999 0 -10000 0 0
MST1 -0.092 0.27 -9999 0 -0.72 66 66
CSNK1D 0.012 0 -9999 0 -10000 0 0
CSNK1E 0.012 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.049 0.014 -9999 0 -10000 0 0
YWHAB 0.012 0 -9999 0 -10000 0 0
MAPK8 0.032 0.008 -9999 0 -10000 0 0
MAPK9 0.032 0.008 -9999 0 -10000 0 0
YWHAG 0.012 0 -9999 0 -10000 0 0
YWHAE 0.012 0 -9999 0 -10000 0 0
YWHAZ 0.012 0 -9999 0 -10000 0 0
SIRT1 0.014 0.015 -9999 0 -10000 0 0
SOD2 0.071 0.1 -9999 0 -10000 0 0
RBL2 0.061 0.1 -9999 0 -0.62 1 1
RAL/GDP 0.025 0.013 -9999 0 -10000 0 0
CHUK 0.022 0.008 -9999 0 -10000 0 0
Ran/GTP 0.013 0 -9999 0 -10000 0 0
CSNK1G2 0.011 0.022 -9999 0 -0.44 1 1
RAL/GTP 0.031 0.013 -9999 0 -10000 0 0
CSNK1G1 0.011 0.022 -9999 0 -0.44 1 1
FASLG -0.055 0.32 -9999 0 -1.3 28 28
SKP2 0.012 0 -9999 0 -10000 0 0
USP7 0.014 0 -9999 0 -10000 0 0
IKBKB 0.022 0.008 -9999 0 -10000 0 0
CCNB1 0.047 0.13 -9999 0 -0.97 1 1
FOXO1-3a-4/beta catenin 0.076 0.11 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.016 0.14 -9999 0 -0.37 55 55
CSNK1A1 0.012 0 -9999 0 -10000 0 0
SGK1 -0.002 0.1 -9999 0 -0.44 23 23
CSNK1G3 0.012 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.023 0 -9999 0 -10000 0 0
ZFAND5 0.067 0.05 -9999 0 -10000 0 0
SFN 0.011 0.022 -9999 0 -0.44 1 1
CDK2 0.002 0.029 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.053 0.03 -9999 0 -10000 0 0
CREBBP 0.002 0.029 -9999 0 -10000 0 0
FBXO32 0.046 0.14 -9999 0 -1.5 1 1
BCL6 0.061 0.1 -9999 0 -0.62 1 1
RALB 0.013 0 -9999 0 -10000 0 0
RALA 0.013 0 -9999 0 -10000 0 0
YWHAH 0.012 0 -9999 0 -10000 0 0
Aurora B signaling

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
Condensin I complex 0.031 0.024 -9999 0 -0.4 1 1
STMN1 0.022 0.016 -9999 0 -0.31 1 1
Aurora B/RasGAP/Survivin 0.033 0.025 -9999 0 -0.45 1 1
Chromosomal passenger complex/Cul3 protein complex 0.008 0.068 -9999 0 -10000 0 0
BIRC5 0.013 0.036 -9999 0 -0.72 1 1
DES -0.33 0.25 -9999 0 -0.52 274 274
Aurora C/Aurora B/INCENP 0.031 0.019 -9999 0 -10000 0 0
Aurora B/TACC1 0.022 0.004 -9999 0 -10000 0 0
Aurora B/PP2A 0.024 0.005 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.015 0.001 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition 0 0 -9999 0 -10000 0 0
NDC80 0.023 0.003 -9999 0 -10000 0 0
Cul3 protein complex -0.011 0.095 -9999 0 -0.48 2 2
KIF2C 0.025 0.005 -9999 0 -10000 0 0
PEBP1 0.013 0 -9999 0 -10000 0 0
KIF20A 0.012 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP 0.024 0.005 -9999 0 -10000 0 0
SEPT1 0.006 0.053 -9999 0 -0.44 6 6
SMC2 0.011 0.022 -9999 0 -0.44 1 1
SMC4 0.01 0.031 -9999 0 -0.44 2 2
NSUN2/NPM1/Nucleolin 0.012 0.016 -9999 0 -10000 0 0
PSMA3 0.012 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0.001 -9999 0 -10000 0 0
H3F3B 0.018 0.003 -9999 0 -10000 0 0
AURKB 0.02 0.006 -9999 0 -10000 0 0
AURKC 0.01 0.031 -9999 0 -0.44 2 2
CDCA8 0.015 0.001 -9999 0 -10000 0 0
cytokinesis 0.014 0.028 -9999 0 -10000 0 0
Aurora B/Septin1 0.024 0.036 -9999 0 -10000 0 0
AURKA 0.012 0.001 -9999 0 -10000 0 0
INCENP 0.015 0.001 -9999 0 -10000 0 0
KLHL13 -0.047 0.16 -9999 0 -0.45 55 55
BUB1 0.012 0 -9999 0 -10000 0 0
hSgo1/Aurora B/Survivin 0.032 0.033 -9999 0 -0.43 2 2
EVI5 0.014 0.001 -9999 0 -10000 0 0
RhoA/GTP -0.001 0.016 -9999 0 -0.32 1 1
SGOL1 0.011 0.036 -9999 0 -0.74 1 1
CENPA 0.029 0.009 -9999 0 -10000 0 0
NCAPG 0.012 0.001 -9999 0 -10000 0 0
Aurora B/HC8 Proteasome 0.024 0.005 -9999 0 -10000 0 0
NCAPD2 0.012 0 -9999 0 -10000 0 0
Aurora B/PP1-gamma 0.024 0.005 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
NCAPH 0.012 0 -9999 0 -10000 0 0
NPM1 0.007 0.01 -9999 0 -10000 0 0
RASA1 0.012 0.001 -9999 0 -10000 0 0
KLHL9 0.012 0 -9999 0 -10000 0 0
mitotic prometaphase 0.001 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.005 -9999 0 -10000 0 0
PPP1CC 0.012 0 -9999 0 -10000 0 0
Centraspindlin 0.014 0.027 -9999 0 -0.35 1 1
RhoA/GDP 0.009 0 -9999 0 -10000 0 0
NSUN2 0.007 0.01 -9999 0 -10000 0 0
MYLK -0.038 0.12 -9999 0 -0.28 80 80
KIF23 0.012 0.036 -9999 0 -0.73 1 1
VIM 0.023 0.003 -9999 0 -10000 0 0
RACGAP1 0.014 0.001 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL 0.007 0.01 -9999 0 -10000 0 0
Chromosomal passenger complex 0.037 0.01 -9999 0 -10000 0 0
Chromosomal passenger complex/EVI5 0.059 0.05 -9999 0 -0.37 1 1
TACC1 0.012 0 -9999 0 -10000 0 0
PPP2R5D 0.012 0 -9999 0 -10000 0 0
CUL3 0.012 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.017 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.012 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.009 0.038 -9999 0 -0.44 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.01 0.031 -9999 0 -0.44 2 2
RAC1-CDC42/GTP/PAK family 0.021 0.01 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.011 0.022 -9999 0 -0.44 1 1
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.012 0 -9999 0 -10000 0 0
FYN 0.012 0 -9999 0 -10000 0 0
MAP3K12 0.012 0 -9999 0 -10000 0 0
FGR 0.007 0.052 -9999 0 -0.52 4 4
p38 alpha/TAB1 -0.034 0.051 -9999 0 -0.31 2 2
PRKG1 -0.011 0.1 -9999 0 -0.44 22 22
DUSP8 0.011 0.022 -9999 0 -0.44 1 1
PGK/cGMP/p38 alpha -0.04 0.067 -9999 0 -0.35 8 8
apoptosis -0.033 0.049 -9999 0 -0.3 2 2
RAL/GTP 0.017 0 -9999 0 -10000 0 0
LYN 0.012 0 -9999 0 -10000 0 0
DUSP1 0.009 0.038 -9999 0 -0.44 3 3
PAK1 0.012 0 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.031 0.012 -9999 0 -10000 0 0
TRAF6 0.012 0 -9999 0 -10000 0 0
RAC1 0.012 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.011 0.022 -9999 0 -0.44 1 1
RAC1-CDC42/GTP 0.016 0.013 -9999 0 -0.26 1 1
MAPK11 -0.019 0.099 -9999 0 -0.36 7 7
BLK -0.16 0.22 -9999 0 -0.44 160 160
HCK 0.001 0.071 -9999 0 -0.44 11 11
MAP2K3 0.012 0 -9999 0 -10000 0 0
DUSP16 0.012 0 -9999 0 -10000 0 0
DUSP10 0.005 0.072 -9999 0 -0.74 4 4
TRAF6/MEKK3 0.016 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 -0.006 0.077 -9999 0 -0.33 2 2
positive regulation of innate immune response -0.015 0.1 -9999 0 -0.44 3 3
LCK -0.002 0.099 -9999 0 -0.67 9 9
p38alpha-beta/MKP7 -0.009 0.1 -9999 0 -0.46 2 2
p38alpha-beta/MKP5 -0.012 0.11 -9999 0 -0.46 4 4
PGK/cGMP -0.007 0.071 -9999 0 -0.31 22 22
PAK2 0.012 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.01 0.1 -9999 0 -0.46 2 2
CDC42 0.011 0.022 -9999 0 -0.44 1 1
RALB 0.012 0 -9999 0 -10000 0 0
RALA 0.012 0 -9999 0 -10000 0 0
PAK3 0.007 0.006 -9999 0 -10000 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.002 0.078 -10000 0 -0.43 5 5
MAPK9 0.007 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.002 0.038 -10000 0 -0.56 2 2
GNB1/GNG2 0.005 0.054 -10000 0 -10000 0 0
GNB1 0.012 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.007 0 -10000 0 -10000 0 0
Gs family/GTP -0.007 0.059 -10000 0 -0.24 27 27
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 0.004 0.016 0.065 27 -10000 0 27
GNAL -0.016 0.11 -10000 0 -0.44 27 27
GNG2 -0.007 0.091 -10000 0 -0.44 18 18
CRH -0.003 0.05 -10000 0 -0.74 2 2
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.007 0 -10000 0 -10000 0 0
MAPK11 0.006 0.022 -10000 0 -0.32 2 2
PDGFR-beta 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
S1P1/Sphingosine-1-phosphate -0.002 0.1 -9999 0 -0.37 30 30
PDGFB-D/PDGFRB/SLAP 0.01 0.063 -9999 0 -0.43 8 8
PDGFB-D/PDGFRB/APS/CBL 0.016 0.068 -9999 0 -0.48 8 8
AKT1 0.042 0.038 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0.001 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.005 0.11 -9999 0 -0.38 30 30
PIK3CA 0.012 0.001 -9999 0 -10000 0 0
FGR -0.006 0.059 -9999 0 -0.44 7 7
mol:Ca2+ 0.008 0.046 -9999 0 -0.32 4 4
MYC 0.014 0.077 -9999 0 -0.46 6 6
SHC1 0.012 0 -9999 0 -10000 0 0
HRAS/GDP 0.027 0.042 -9999 0 -0.39 4 4
LRP1/PDGFRB/PDGFB 0.019 0.051 -9999 0 -0.47 4 4
GRB10 0.012 0 -9999 0 -10000 0 0
PTPN11 0.012 0 -9999 0 -10000 0 0
GO:0007205 0.008 0.046 -9999 0 -0.32 4 4
PTEN 0.01 0.031 -9999 0 -0.44 2 2
GRB2 0.012 0 -9999 0 -10000 0 0
GRB7 -0.002 0.1 -9999 0 -0.74 8 8
PDGFB-D/PDGFRB/SHP2 0.013 0.055 -9999 0 -0.55 4 4
PDGFB-D/PDGFRB/GRB10 0.013 0.055 -9999 0 -0.55 4 4
cell cycle arrest 0.01 0.063 -9999 0 -0.43 8 8
HRAS 0.011 0.022 -9999 0 -0.44 1 1
HIF1A 0.046 0.035 -9999 0 -10000 0 0
GAB1 0 0.065 -9999 0 -0.38 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.004 0.068 -9999 0 -0.39 4 4
PDGFB-D/PDGFRB 0.021 0.05 -9999 0 -0.49 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.013 0.055 -9999 0 -0.55 4 4
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.019 0.098 -9999 0 -0.48 9 9
positive regulation of MAPKKK cascade 0.013 0.055 -9999 0 -0.55 4 4
PIK3R1 0.012 0 -9999 0 -10000 0 0
mol:IP3 0.008 0.047 -9999 0 -0.32 4 4
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.012 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.002 0.095 -9999 0 -0.56 12 12
SHB 0.012 0 -9999 0 -10000 0 0
BLK -0.18 0.24 -9999 0 -0.49 163 163
PTPN2 0.012 0.002 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.013 0.055 -9999 0 -0.55 4 4
BCAR1 0.011 0.022 -9999 0 -0.44 1 1
VAV2 0.002 0.07 -9999 0 -0.37 4 4
CBL 0.012 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.013 0.055 -9999 0 -0.55 4 4
LCK -0.008 0.061 -9999 0 -0.42 6 6
PDGFRB 0.006 0.072 -9999 0 -0.74 4 4
ACP1 0.012 0 -9999 0 -10000 0 0
HCK -0.008 0.088 -9999 0 -0.46 15 15
ABL1 -0.006 0.064 -9999 0 -0.38 4 4
PDGFB-D/PDGFRB/CBL -0.004 0.065 -9999 0 -0.41 1 1
PTPN1 0.012 0.002 -9999 0 -10000 0 0
SNX15 0.012 0 -9999 0 -10000 0 0
STAT3 0.012 0 -9999 0 -10000 0 0
STAT1 0.011 0.036 -9999 0 -0.74 1 1
cell proliferation 0.015 0.072 -9999 0 -0.42 6 6
SLA 0.008 0.043 -9999 0 -0.44 4 4
actin cytoskeleton reorganization 0.038 0.041 -9999 0 -10000 0 0
SRC -0.001 0.04 -9999 0 -0.39 4 4
PI3K -0.004 0.036 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC 0.011 0.083 -9999 0 -0.48 12 12
SH2B2 0.005 0.072 -9999 0 -0.74 4 4
PLCgamma1/SPHK1 -0.006 0.11 -9999 0 -0.4 30 30
LYN 0 0.04 -9999 0 -0.39 4 4
LRP1 0.01 0.031 -9999 0 -0.44 2 2
SOS1 0.012 0 -9999 0 -10000 0 0
STAT5B 0.012 0 -9999 0 -10000 0 0
STAT5A 0.012 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas 0.033 0.043 -9999 0 -0.39 1 1
SPHK1 -0.039 0.19 -9999 0 -0.74 30 30
EDG1 0 0.002 -9999 0 -10000 0 0
mol:DAG 0.008 0.047 -9999 0 -0.32 4 4
PLCG1 0.008 0.047 -9999 0 -0.33 4 4
NHERF/PDGFRB 0.02 0.05 -9999 0 -0.47 4 4
YES1 -0.003 0.046 -9999 0 -0.41 5 5
cell migration 0.02 0.049 -9999 0 -0.47 4 4
SHC/Grb2/SOS1 0.033 0.041 -9999 0 -0.38 4 4
SLC9A3R2 0.011 0.022 -9999 0 -0.44 1 1
SLC9A3R1 0.012 0 -9999 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.026 0.049 -9999 0 -0.43 4 4
FYN -0.001 0.04 -9999 0 -0.39 4 4
DOK1 0.023 0.044 -9999 0 -0.43 4 4
HRAS/GTP 0.008 0.015 -9999 0 -0.31 1 1
PDGFB 0.012 0 -9999 0 -10000 0 0
RAC1 0.013 0.072 -9999 0 -10000 0 0
PRKCD 0.023 0.045 -9999 0 -0.44 4 4
FER 0.022 0.046 -9999 0 -0.44 4 4
MAPKKK cascade -0.003 0.037 -9999 0 -0.38 4 4
RASA1 0.023 0.045 -9999 0 -0.44 4 4
NCK1 0.012 0 -9999 0 -10000 0 0
NCK2 0.012 0 -9999 0 -10000 0 0
p62DOK/Csk 0.03 0.041 -9999 0 -0.4 4 4
PDGFB-D/PDGFRB/SHB 0.013 0.055 -9999 0 -0.55 4 4
chemotaxis -0.005 0.063 -9999 0 -0.38 4 4
STAT1-3-5/STAT1-3-5 -0.004 0.04 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.004 0.055 -9999 0 -0.56 4 4
PTPRJ 0.012 0 -9999 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.012 0 -9999 0 -10000 0 0
HDAC2 0.012 0 -9999 0 -10000 0 0
GNB1/GNG2 0.014 0.055 -9999 0 -10000 0 0
forebrain development 0.018 0.083 -9999 0 -0.48 6 6
GNAO1 -0.11 0.2 -9999 0 -0.44 118 118
SMO/beta Arrestin2 0.021 0.004 -9999 0 -10000 0 0
SMO 0.013 0.002 -9999 0 -10000 0 0
ARRB2 0.013 0.002 -9999 0 -10000 0 0
GLI3/SPOP 0.024 0.065 -9999 0 -10000 0 0
mol:GTP 0.001 0.001 -9999 0 -10000 0 0
GSK3B 0.012 0 -9999 0 -10000 0 0
GNAI2 0.013 0.001 -9999 0 -10000 0 0
SIN3/HDAC complex 0.031 0.002 -9999 0 -10000 0 0
GNAI1 -0.003 0.083 -9999 0 -0.44 15 15
XPO1 0.015 0.003 -9999 0 -10000 0 0
GLI1/Su(fu) 0.027 0.068 -9999 0 -0.47 3 3
SAP30 0.012 0 -9999 0 -10000 0 0
mol:GDP 0.013 0.002 -9999 0 -10000 0 0
MIM/GLI2A 0.01 0.059 -9999 0 -0.44 7 7
IFT88 0.012 0.001 -9999 0 -10000 0 0
GNAI3 0.013 0.001 -9999 0 -10000 0 0
GLI2 0.037 0.018 -9999 0 -10000 0 0
GLI3 0.018 0.067 -9999 0 -10000 0 0
CSNK1D 0.012 0 -9999 0 -10000 0 0
CSNK1E 0.012 0 -9999 0 -10000 0 0
SAP18 0.012 0 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.012 0.001 -9999 0 -10000 0 0
GNG2 -0.007 0.091 -9999 0 -0.44 18 18
Gi family/GTP -0.038 0.12 -9999 0 -0.38 15 15
SIN3B 0.012 0 -9999 0 -10000 0 0
SIN3A 0.012 0 -9999 0 -10000 0 0
GLI3/Su(fu) 0.04 0.05 -9999 0 -10000 0 0
GLI2/Su(fu) 0.052 0.018 -9999 0 -10000 0 0
FOXA2 -0.024 0.14 -9999 0 -0.68 18 18
neural tube patterning 0.018 0.083 -9999 0 -0.48 6 6
SPOP 0.012 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.03 0.003 -9999 0 -10000 0 0
GNB1 0.012 0 -9999 0 -10000 0 0
CSNK1G2 0.011 0.022 -9999 0 -0.44 1 1
CSNK1G3 0.012 0 -9999 0 -10000 0 0
MTSS1 0.01 0.059 -9999 0 -0.44 7 7
embryonic limb morphogenesis 0.018 0.083 -9999 0 -0.48 6 6
SUFU 0.026 0.005 -9999 0 -10000 0 0
LGALS3 0.011 0.022 -9999 0 -0.44 1 1
catabolic process 0.047 0.061 -9999 0 -10000 0 0
GLI3A/CBP 0.017 0.032 -9999 0 -0.31 4 4
KIF3A 0.012 0.001 -9999 0 -10000 0 0
GLI1 0.018 0.085 -9999 0 -0.5 6 6
RAB23 0.012 0.001 -9999 0 -10000 0 0
CSNK1A1 0.012 0 -9999 0 -10000 0 0
IFT172 0.012 0 -9999 0 -10000 0 0
RBBP7 0.012 0 -9999 0 -10000 0 0
Su(fu)/Galectin3 0.03 0.012 -9999 0 -10000 0 0
GNAZ 0.008 0.049 -9999 0 -0.44 5 5
RBBP4 0.012 0 -9999 0 -10000 0 0
CSNK1G1 0.011 0.022 -9999 0 -0.44 1 1
PIAS1 0.012 0 -9999 0 -10000 0 0
PRKACA 0.012 0 -9999 0 -10000 0 0
GLI2/SPOP 0.041 0.017 -9999 0 -10000 0 0
STK36 0.015 0.003 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.035 0.13 -9999 0 -0.46 20 20
PTCH1 0.021 0.1 -9999 0 -0.94 3 3
MIM/GLI1 0.023 0.11 -9999 0 -0.6 5 5
CREBBP 0.017 0.032 -9999 0 -0.31 4 4
Su(fu)/SIN3/HDAC complex 0.042 0.002 -9999 0 -10000 0 0
Ceramide signaling pathway

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
SPHK2 0.019 0.016 -10000 0 -0.31 1 1
MAP4K4 0.036 0.03 -10000 0 -10000 0 0
BAG4 0.012 0.001 -10000 0 -10000 0 0
PKC zeta/ceramide -0.012 0.031 -10000 0 -10000 0 0
NFKBIA 0.012 0 -10000 0 -10000 0 0
BIRC3 0.003 0.067 -10000 0 -0.48 8 8
BAX -0.003 0.015 -10000 0 -10000 0 0
RIPK1 0.012 0 -10000 0 -10000 0 0
AKT1 0.017 0.006 -10000 0 -10000 0 0
BAD -0.015 0.03 -10000 0 -10000 0 0
SMPD1 0.02 0.034 -10000 0 -0.24 6 6
RB1 -0.014 0.03 -10000 0 -10000 0 0
FADD/Caspase 8 0.044 0.029 -10000 0 -10000 0 0
MAP2K4 -0.009 0.033 -10000 0 -10000 0 0
NSMAF 0.012 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.008 0.029 -10000 0 -10000 0 0
EGF -0.087 0.21 -10000 0 -0.5 83 83
mol:ceramide -0.022 0.032 -10000 0 -10000 0 0
MADD 0.012 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.019 0 -10000 0 -10000 0 0
ASAH1 0.012 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.014 0.03 -10000 0 -10000 0 0
cell proliferation -0.034 0.087 -10000 0 -10000 0 0
BID 0.024 0.031 -10000 0 -0.31 1 1
MAP3K1 -0.014 0.032 -10000 0 -0.23 1 1
EIF2A -0.002 0.029 -10000 0 -10000 0 0
TRADD 0.012 0 -10000 0 -10000 0 0
CRADD 0.012 0 -10000 0 -10000 0 0
MAPK3 0.001 0.027 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.002 0.027 -10000 0 -10000 0 0
Cathepsin D/ceramide -0.013 0.03 -10000 0 -10000 0 0
FADD 0.036 0.03 -10000 0 -10000 0 0
KSR1 -0.014 0.03 -10000 0 -10000 0 0
MAPK8 -0.004 0.03 -10000 0 -10000 0 0
PRKRA -0.014 0.03 -10000 0 -10000 0 0
PDGFA 0.012 0 -10000 0 -10000 0 0
TRAF2 0.011 0.022 -10000 0 -0.44 1 1
IGF1 -0.1 0.2 -10000 0 -0.44 107 107
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.022 0.032 -10000 0 -10000 0 0
CTSD 0.011 0.022 -10000 0 -0.44 1 1
regulation of nitric oxide biosynthetic process 0.018 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.035 0.092 -10000 0 -10000 0 0
PRKCD 0.012 0 -10000 0 -10000 0 0
PRKCZ 0.012 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.019 0 -10000 0 -10000 0 0
RelA/NF kappa B1 0.018 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.012 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.032 0.032 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.024 0.019 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.019 0.016 -10000 0 -0.3 1 1
MAP2K1 -0.002 0.028 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.012 0 -10000 0 -10000 0 0
CYCS 0 0.038 0.14 19 -10000 0 19
TNFRSF1A 0.012 0 -10000 0 -10000 0 0
NFKB1 0.012 0 -10000 0 -10000 0 0
TNFR1A/BAG4 0.018 0.001 -10000 0 -10000 0 0
EIF2AK2 -0.008 0.03 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN 0.024 0.019 -10000 0 -10000 0 0
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.036 0.02 -10000 0 -10000 0 0
MAP2K2 -0.002 0.027 -10000 0 -10000 0 0
SMPD3 0.019 0.052 -10000 0 -0.3 10 10
TNF 0.01 0.031 -10000 0 -0.44 2 2
PKC zeta/PAR4 0.018 0 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.032 0.083 0.2 81 -10000 0 81
NF kappa B1/RelA/I kappa B alpha 0.037 0 -10000 0 -10000 0 0
AIFM1 0 0.039 0.14 20 -10000 0 20
BCL2 -0.013 0.1 -10000 0 -0.44 24 24
TCGA08_rtk_signaling

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
PDGFRA -0.001 0.077 -10000 0 -0.44 13 13
HRAS 0.011 0.022 -10000 0 -0.44 1 1
EGFR 0.011 0.022 -10000 0 -0.44 1 1
AKT 0.029 0.038 -10000 0 -0.28 5 5
FOXO3 0.012 0 -10000 0 -10000 0 0
AKT1 0.012 0 -10000 0 -10000 0 0
FOXO1 0.011 0.022 -10000 0 -0.44 1 1
AKT3 0.006 0.053 -10000 0 -0.44 6 6
FOXO4 0.012 0 -10000 0 -10000 0 0
MET 0.004 0.08 -10000 0 -0.74 5 5
PIK3CA 0.012 0.001 -10000 0 -10000 0 0
PIK3CB 0.012 0.001 -10000 0 -10000 0 0
NRAS 0.01 0.031 -10000 0 -0.44 2 2
PIK3CG -0.057 0.16 -10000 0 -0.44 66 66
PIK3R3 0.012 0 -10000 0 -10000 0 0
PIK3R2 0.012 0 -10000 0 -10000 0 0
NF1 0.012 0 -10000 0 -10000 0 0
RAS 0.015 0.038 -10000 0 -0.27 2 2
ERBB2 0.005 0.072 -10000 0 -0.74 4 4
proliferation/survival/translation -0.018 0.04 0.2 5 -10000 0 5
PI3K 0.01 0.053 -10000 0 -0.21 9 9
PIK3R1 0.012 0 -10000 0 -10000 0 0
KRAS 0.012 0 -10000 0 -10000 0 0
FOXO 0.039 0.019 -10000 0 -10000 0 0
AKT2 0.012 0 -10000 0 -10000 0 0
PTEN 0.01 0.031 -10000 0 -0.44 2 2
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.008 0.043 0.44 4 -10000 0 4
PI3K Class IB/PDE3B 0.008 0.043 -10000 0 -0.44 4 4
PDE3B 0.008 0.043 -10000 0 -0.44 4 4
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.021 0.051 -9999 0 -10000 0 0
HDAC3 0.012 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
GATA1/HDAC4 0.015 0.004 -9999 0 -10000 0 0
GATA1/HDAC5 0.014 0.016 -9999 0 -0.31 1 1
GATA2/HDAC5 0.011 0.049 -9999 0 -0.3 10 10
HDAC5/BCL6/BCoR 0.024 0.013 -9999 0 -10000 0 0
HDAC9 -0.058 0.16 -9999 0 -0.44 67 67
Glucocorticoid receptor/Hsp90/HDAC6 0.005 0.071 -9999 0 -10000 0 0
HDAC4/ANKRA2 0.018 0 -9999 0 -10000 0 0
HDAC5/YWHAB 0.018 0.016 -9999 0 -0.3 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.018 0.014 -9999 0 -10000 0 0
GATA2 0.003 0.065 -9999 0 -0.44 9 9
HDAC4/RFXANK 0.018 0 -9999 0 -10000 0 0
BCOR 0.012 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.011 0.022 -9999 0 -0.44 1 1
HDAC5 0.011 0.022 -9999 0 -0.44 1 1
GNB1/GNG2 0.005 0.065 -9999 0 -0.3 18 18
Histones 0.002 0.076 -9999 0 -0.39 1 1
ADRBK1 0.012 0 -9999 0 -10000 0 0
HDAC4 0.012 0 -9999 0 -10000 0 0
XPO1 0.012 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.018 0.016 -9999 0 -0.3 1 1
HDAC4/Ubc9 0.018 0 -9999 0 -10000 0 0
HDAC7 0.012 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.018 0.016 -9999 0 -0.3 1 1
TUBA1B 0.012 0 -9999 0 -10000 0 0
HDAC6 0.012 0 -9999 0 -10000 0 0
HDAC5/RFXANK 0.018 0.016 -9999 0 -0.3 1 1
CAMK4 -0.015 0.11 -9999 0 -0.44 26 26
Tubulin/HDAC6 0.016 0.068 -9999 0 -0.48 8 8
SUMO1 0.01 0.031 -9999 0 -0.44 2 2
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.012 0 -9999 0 -10000 0 0
GATA1 0.008 0.006 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.012 0 -9999 0 -10000 0 0
NR3C1 -0.02 0.12 -9999 0 -0.44 31 31
SUMO1/HDAC4 0.026 0.021 -9999 0 -0.29 2 2
SRF 0.012 0 -9999 0 -10000 0 0
HDAC4/YWHAB 0.018 0 -9999 0 -10000 0 0
Tubulin 0.008 0.077 -9999 0 -0.56 8 8
HDAC4/14-3-3 E 0.018 0 -9999 0 -10000 0 0
GNB1 0.012 0 -9999 0 -10000 0 0
RANGAP1 0.012 0 -9999 0 -10000 0 0
BCL6/BCoR 0.018 0 -9999 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.024 0.013 -9999 0 -10000 0 0
HDAC4/SRF 0.008 0.065 -9999 0 -10000 0 0
HDAC4/ER alpha -0.013 0.095 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.002 0.076 -9999 0 -0.39 1 1
cell motility 0.015 0.067 -9999 0 -0.48 8 8
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.012 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0.018 0 -9999 0 -10000 0 0
BCL6 0.012 0 -9999 0 -10000 0 0
HDAC4/CaMK II delta B 0.012 0 -9999 0 -10000 0 0
Hsp90/HDAC6 0.018 0 -9999 0 -10000 0 0
ESR1 -0.031 0.13 -9999 0 -0.44 41 41
HDAC6/HDAC11 0.018 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.029 0.012 -9999 0 -10000 0 0
NPC 0.007 0 -9999 0 -10000 0 0
MEF2C 0 0.075 -9999 0 -0.44 12 12
RAN 0.012 0 -9999 0 -10000 0 0
HDAC4/MEF2C 0.029 0.04 -9999 0 -10000 0 0
GNG2 -0.007 0.091 -9999 0 -0.44 18 18
NCOR2 0.011 0.022 -9999 0 -0.44 1 1
TUBB2A -0.002 0.1 -9999 0 -0.74 8 8
HDAC11 0.012 0 -9999 0 -10000 0 0
HSP90AA1 0.012 0 -9999 0 -10000 0 0
RANBP2 0.012 0 -9999 0 -10000 0 0
ANKRA2 0.012 0 -9999 0 -10000 0 0
RFXANK 0.012 0 -9999 0 -10000 0 0
nuclear import -0.025 0.013 -9999 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.024 0.027 -9999 0 -10000 0 0
epithelial cell differentiation 0.027 0 -9999 0 -10000 0 0
CYFIP2 0.011 0.022 -9999 0 -0.44 1 1
ENAH 0.051 0.018 -9999 0 -10000 0 0
EGFR 0.011 0.022 -9999 0 -0.44 1 1
EPHA2 0.011 0.036 -9999 0 -0.74 1 1
MYO6 0.031 0 -9999 0 -10000 0 0
CTNNB1 0.012 0 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 0.024 0.013 -9999 0 -10000 0 0
AQP5 -0.053 0.1 -9999 0 -10000 0 0
CTNND1 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.031 0.011 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.02 0.047 -9999 0 -10000 0 0
EGF -0.087 0.21 -9999 0 -0.5 83 83
NCKAP1 0.012 0 -9999 0 -10000 0 0
AQP3 -0.012 0.053 -9999 0 -0.4 1 1
cortical microtubule organization 0.027 0 -9999 0 -10000 0 0
GO:0000145 0.028 0.01 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.029 0 -9999 0 -10000 0 0
MLLT4 0.011 0.022 -9999 0 -0.44 1 1
ARF6/GDP -0.001 0.017 -9999 0 -10000 0 0
ARF6 0.012 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.03 0.025 -9999 0 -0.43 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
VASP 0.04 0.007 -9999 0 -10000 0 0
PVRL2 0.012 0 -9999 0 -10000 0 0
ZYX 0.031 0 -9999 0 -10000 0 0
ARF6/GTP 0.033 0.024 -9999 0 -0.4 1 1
CDH1 0.012 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.042 0.092 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
actin cytoskeleton organization 0.035 0 -9999 0 -10000 0 0
IGF-1R heterotetramer 0.012 0 -9999 0 -10000 0 0
GIT1 0.011 0.022 -9999 0 -0.44 1 1
IGF1R 0.012 0 -9999 0 -10000 0 0
IGF1 -0.1 0.2 -9999 0 -0.44 107 107
DIAPH1 -0.001 0.026 -9999 0 -0.54 1 1
Wnt receptor signaling pathway -0.027 0 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
RhoA/GTP -0.001 0.017 -9999 0 -10000 0 0
CTNNA1 0.012 0 -9999 0 -10000 0 0
VCL 0.036 0 -9999 0 -10000 0 0
EFNA1 0.012 0 -9999 0 -10000 0 0
LPP 0.035 0.01 -9999 0 -10000 0 0
Ephrin A1/EPHA2 -0.001 0.018 -9999 0 -10000 0 0
SEC6/SEC8 0 0.008 -9999 0 -10000 0 0
MGAT3 0.021 0.048 -9999 0 -10000 0 0
HGF/MET -0.008 0.048 -9999 0 -10000 0 0
HGF 0.004 0.064 -9999 0 -0.48 7 7
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.024 0.027 -9999 0 -10000 0 0
actin cable formation 0.065 0.016 -9999 0 -10000 0 0
KIAA1543 0.035 0.01 -9999 0 -10000 0 0
KIFC3 0.016 0.08 -9999 0 -0.39 16 16
NCK1 0.012 0 -9999 0 -10000 0 0
EXOC3 0.012 0 -9999 0 -10000 0 0
ACTN1 0.031 0 -9999 0 -10000 0 0
NCK1/GIT1 0.018 0.016 -9999 0 -0.3 1 1
mol:GDP 0.027 0 -9999 0 -10000 0 0
EXOC4 0.012 0 -9999 0 -10000 0 0
STX4 0.031 0 -9999 0 -10000 0 0
PIP5K1C 0.031 0.011 -9999 0 -10000 0 0
LIMA1 0.006 0.053 -9999 0 -0.44 6 6
ABI1 0.012 0 -9999 0 -10000 0 0
ROCK1 0.049 0.02 -9999 0 -10000 0 0
adherens junction assembly 0.038 0.06 -9999 0 -0.54 1 1
IGF-1R heterotetramer/IGF1 -0.044 0.077 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.018 0.016 -9999 0 -0.3 1 1
MET 0.004 0.08 -9999 0 -0.74 5 5
PLEKHA7 0.031 0 -9999 0 -10000 0 0
mol:GTP 0.029 0.025 -9999 0 -0.43 1 1
establishment of epithelial cell apical/basal polarity 0.05 0.009 -9999 0 -10000 0 0
cortical actin cytoskeleton stabilization 0.024 0.027 -9999 0 -10000 0 0
regulation of cell-cell adhesion 0.035 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.024 0.027 -9999 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.029 0 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1 0.02 0 -9999 0 -10000 0 0
mol:DAG 0.021 0.075 -9999 0 -0.42 12 12
VEGFR1 homodimer/NRP1/VEGFR 121 0.025 0.022 -9999 0 -0.44 1 1
CaM/Ca2+ 0.026 0.071 -9999 0 -0.4 12 12
HIF1A 0.02 0 -9999 0 -10000 0 0
GAB1 0.012 0 -9999 0 -10000 0 0
AKT1 0.038 0.061 -9999 0 -10000 0 0
PLCG1 0.021 0.076 -9999 0 -0.43 12 12
NOS3 0.038 0.068 -9999 0 -10000 0 0
CBL 0.012 0 -9999 0 -10000 0 0
mol:NO 0.038 0.066 -9999 0 -10000 0 0
FLT1 0.027 0 -9999 0 -10000 0 0
PGF -0.009 0.12 -9999 0 -0.74 12 12
VEGFR1 homodimer/NRP2/VEGFR121 0.032 0.03 -9999 0 -0.43 1 1
CALM1 0.012 0 -9999 0 -10000 0 0
PIK3CA 0.012 0.001 -9999 0 -10000 0 0
eNOS/Hsp90 0.044 0.064 -9999 0 -10000 0 0
endothelial cell proliferation -0.01 0.1 -9999 0 -0.5 1 1
mol:Ca2+ 0.021 0.075 -9999 0 -0.42 12 12
MAPK3 0.029 0.068 -9999 0 -10000 0 0
MAPK1 0.03 0.067 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
PLGF homodimer -0.009 0.12 -9999 0 -0.74 12 12
PRKACA 0.012 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 0.009 0.038 -9999 0 -0.44 3 3
VEGFA homodimer 0.011 0.036 -9999 0 -0.74 1 1
VEGFR1 homodimer/VEGFA homodimer 0.028 0.024 -9999 0 -0.47 1 1
platelet activating factor biosynthetic process 0.034 0.066 -9999 0 -10000 0 0
PI3K 0.029 0.072 -9999 0 -0.4 12 12
PRKCA 0.025 0.07 -9999 0 -0.39 12 12
PRKCB -0.026 0.12 -9999 0 -0.41 12 12
VEGFR1 homodimer/PLGF homodimer 0.015 0.082 -9999 0 -0.47 12 12
VEGFA 0.011 0.036 -9999 0 -0.74 1 1
VEGFB 0.012 0 -9999 0 -10000 0 0
mol:IP3 0.021 0.075 -9999 0 -0.42 12 12
RASA1 0.033 0 -9999 0 -10000 0 0
NRP2 0.009 0.038 -9999 0 -0.44 3 3
VEGFR1 homodimer 0.027 0 -9999 0 -10000 0 0
VEGFB homodimer 0.012 0 -9999 0 -10000 0 0
NCK1 0.012 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.042 0.066 -9999 0 -10000 0 0
PTPN11 0.012 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.027 0.071 -9999 0 -0.39 12 12
mol:L-citrulline 0.038 0.066 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.032 0.047 -9999 0 -0.4 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.034 0.022 -9999 0 -0.43 1 1
CD2AP -0.002 0.08 -9999 0 -0.44 14 14
PI3K/GAB1 0.033 0.069 -9999 0 -10000 0 0
PDPK1 0.03 0.068 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.034 0.022 -9999 0 -0.43 1 1
mol:NADP 0.038 0.066 -9999 0 -10000 0 0
HSP90AA1 0.012 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.031 0.046 -9999 0 -0.4 1 1
VEGFR1 homodimer/NRP2 0.027 0.023 -9999 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.042 0.007 -9999 0 -10000 0 0
adherens junction organization -0.004 0.064 -9999 0 -0.33 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0.046 0.012 -9999 0 -10000 0 0
FMN1 0.036 0.019 -9999 0 -10000 0 0
mol:IP3 0.035 0.007 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.032 0.012 -9999 0 -10000 0 0
CTNNB1 0.012 0 -9999 0 -10000 0 0
AKT1 0.041 0.008 -9999 0 -10000 0 0
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.034 0.012 -9999 0 -10000 0 0
CTNND1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.036 0.011 -9999 0 -10000 0 0
VASP 0.037 0.011 -9999 0 -10000 0 0
ZYX 0.037 0.011 -9999 0 -10000 0 0
JUB -0.097 0.2 -9999 0 -0.38 139 139
EGFR(dimer) 0.037 0.016 -9999 0 -10000 0 0
E-cadherin/beta catenin-gamma catenin 0.023 0.012 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.036 0.008 -9999 0 -10000 0 0
PIK3CA 0.013 0.001 -9999 0 -10000 0 0
PI3K 0.037 0.008 -9999 0 -10000 0 0
FYN 0.018 0.066 -9999 0 -10000 0 0
mol:Ca2+ 0.035 0.006 -9999 0 -10000 0 0
JUP 0.011 0.022 -9999 0 -0.44 1 1
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:DAG 0.035 0.007 -9999 0 -10000 0 0
CDH1 0.012 0 -9999 0 -10000 0 0
RhoA/GDP 0.046 0.012 -9999 0 -10000 0 0
establishment of polarity of embryonic epithelium 0.036 0.011 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
RAC1 0.012 0 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
EGFR 0.011 0.022 -9999 0 -0.44 1 1
CASR 0.01 0.07 -9999 0 -0.36 1 1
RhoA/GTP 0.038 0.006 -9999 0 -10000 0 0
AKT2 0.041 0.008 -9999 0 -10000 0 0
actin cable formation 0.04 0.018 -9999 0 -10000 0 0
apoptosis -0.039 0.008 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
mol:GDP 0.041 0.012 -9999 0 -10000 0 0
PIP5K1A 0.037 0.011 -9999 0 -10000 0 0
PLCG1 0.036 0.007 -9999 0 -10000 0 0
Rac1/GTP 0.039 0.014 -9999 0 -10000 0 0
homophilic cell adhesion 0.001 0 -9999 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 0.16 0.24 -9999 0 -1.1 1 1
PLK1 0.061 0.053 -9999 0 -0.54 1 1
BIRC5 0.06 0.053 -9999 0 -0.56 1 1
HSPA1B 0.14 0.27 -9999 0 -1 2 2
MAP2K1 0.039 0.029 -9999 0 -10000 0 0
BRCA2 0.16 0.25 -9999 0 -1.1 1 1
FOXM1 0.16 0.27 -9999 0 -1.3 1 1
XRCC1 0.16 0.24 -9999 0 -1.1 1 1
FOXM1B/p19 -0.11 0.19 -9999 0 -1.1 2 2
Cyclin D1/CDK4 0.15 0.24 -9999 0 -0.96 1 1
CDC2 0.16 0.25 -9999 0 -1.1 1 1
TGFA 0.15 0.24 -9999 0 -0.92 1 1
SKP2 0.16 0.24 -9999 0 -1.1 1 1
CCNE1 0.013 0.063 -9999 0 -0.73 3 3
CKS1B 0.16 0.25 -9999 0 -1.1 1 1
RB1 -0.021 0.064 -9999 0 -10000 0 0
FOXM1C/SP1 0.15 0.25 -9999 0 -1.2 1 1
AURKB 0.062 0.044 -9999 0 -10000 0 0
CENPF 0.16 0.24 -9999 0 -1.1 1 1
CDK4 0.021 0.038 -9999 0 -0.73 1 1
MYC 0.15 0.24 -9999 0 -0.92 1 1
CHEK2 0.039 0.029 -9999 0 -10000 0 0
ONECUT1 0.15 0.24 -9999 0 -1 1 1
CDKN2A -0.16 0.31 -9999 0 -0.74 95 95
LAMA4 0.16 0.24 -9999 0 -1.1 1 1
FOXM1B/HNF6 0.15 0.26 -9999 0 -1.2 1 1
FOS 0.15 0.28 -9999 0 -1 7 7
SP1 0.013 0.004 -9999 0 -10000 0 0
CDC25B 0.14 0.27 -9999 0 -1.3 1 1
response to radiation 0.024 0.026 -9999 0 -10000 0 0
CENPB 0.16 0.24 -9999 0 -1.1 1 1
CENPA 0.16 0.25 -9999 0 -1.1 1 1
NEK2 0.16 0.24 -9999 0 -1.1 1 1
HIST1H2BA 0.15 0.24 -9999 0 -1.1 1 1
CCNA2 0.018 0.007 -9999 0 -10000 0 0
EP300 0.012 0 -9999 0 -10000 0 0
CCNB1/CDK1 0.16 0.26 -9999 0 -1.2 1 1
CCNB2 0.16 0.24 -9999 0 -1.1 1 1
CCNB1 0.16 0.25 -9999 0 -1.1 1 1
ETV5 0.15 0.25 -9999 0 -1.1 1 1
ESR1 0.087 0.41 -9999 0 -1.2 20 20
CCND1 0.15 0.24 -9999 0 -0.98 1 1
GSK3A 0.036 0.025 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.047 0.053 -9999 0 -0.47 3 3
CDK2 0.018 0.007 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.027 0.03 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.044 0.14 -9999 0 -1.1 1 1
GAS1 0.063 0.45 -9999 0 -1.1 31 31
MMP2 0.15 0.26 -9999 0 -1.4 1 1
RB1/FOXM1C 0.16 0.24 -9999 0 -1 1 1
CREBBP 0.012 0 -9999 0 -10000 0 0
PLK2 and PLK4 events

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
PLK2 0.005 0.072 -9999 0 -0.74 4 4
PLK4 0.012 0.001 -9999 0 -10000 0 0
regulation of centriole replication 0.014 0.055 -9999 0 -0.56 4 4
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.011 0.063 -10000 0 -0.51 6 6
CRKL 0.028 0.034 -10000 0 -10000 0 0
mol:PIP3 -0.015 0.029 0.41 2 -10000 0 2
AKT1 0.002 0.02 0.3 2 -10000 0 2
PTK2B 0.011 0.022 -10000 0 -0.44 1 1
RAPGEF1 0.033 0.035 -10000 0 -10000 0 0
RANBP10 0.012 0 -10000 0 -10000 0 0
PIK3CA 0.012 0.001 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.014 0.067 -10000 0 -0.48 6 6
MAP3K5 0.017 0.083 -10000 0 -0.37 5 5
HGF/MET/CIN85/CBL/ENDOPHILINS 0.022 0.061 -10000 0 -0.43 6 6
AP1 0.011 0.039 -10000 0 -0.26 7 7
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.012 0 -10000 0 -10000 0 0
apoptosis 0.006 0.097 -10000 0 -0.74 7 7
STAT3 (dimer) 0.029 0.039 -10000 0 -10000 0 0
GAB1/CRKL/SHP2/PI3K 0.043 0.031 -10000 0 -10000 0 0
INPP5D 0.012 0 -10000 0 -10000 0 0
CBL/CRK 0.034 0.033 -10000 0 -10000 0 0
PTPN11 0.012 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.012 0 -10000 0 -10000 0 0
PTEN 0.01 0.031 -10000 0 -0.44 2 2
ELK1 -0.002 0.031 0.23 1 -0.26 5 6
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.023 0.025 -10000 0 -10000 0 0
PAK1 0.007 0.019 0.28 2 -10000 0 2
HGF/MET/RANBP10 0.014 0.067 -10000 0 -0.48 6 6
HRAS 0.025 0.052 -10000 0 -0.48 1 1
DOCK1 0.033 0.033 -10000 0 -10000 0 0
GAB1 0.024 0.036 -10000 0 -10000 0 0
CRK 0.028 0.034 -10000 0 -10000 0 0
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.02 0.066 -10000 0 -0.42 7 7
JUN 0.012 0 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.007 0.036 -10000 0 -0.2 12 12
PIK3R1 0.012 0 -10000 0 -10000 0 0
cell morphogenesis 0.052 0.039 -10000 0 -10000 0 0
GRB2/SHC 0.022 0.033 -10000 0 -10000 0 0
FOS 0.005 0.057 -10000 0 -0.44 7 7
GLMN -0.001 0.011 -10000 0 -0.23 1 1
cell motility -0.002 0.031 0.23 1 -0.26 5 6
HGF/MET/MUC20 0.006 0.066 -10000 0 -0.37 12 12
cell migration 0.021 0.032 -10000 0 -10000 0 0
GRB2 0.012 0 -10000 0 -10000 0 0
CBL 0.012 0 -10000 0 -10000 0 0
MET/RANBP10 0.012 0.061 -10000 0 -0.56 5 5
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.025 0.041 -10000 0 -10000 0 0
MET/MUC20 0.003 0.061 -10000 0 -0.56 5 5
RAP1B 0.037 0.033 -10000 0 -10000 0 0
RAP1A 0.037 0.033 -10000 0 -10000 0 0
HGF/MET/RANBP9 0.014 0.068 -10000 0 -0.48 6 6
RAF1 0.03 0.05 -10000 0 -0.45 1 1
STAT3 0.03 0.04 -10000 0 -10000 0 0
cell proliferation 0.038 0.049 -10000 0 -10000 0 0
RPS6KB1 0.009 0.02 -10000 0 -0.28 1 1
MAPK3 -0.006 0.041 0.66 1 -0.24 5 6
MAPK1 -0.007 0.026 -10000 0 -0.24 5 5
RANBP9 0.011 0.022 -10000 0 -0.44 1 1
MAPK8 0.033 0.065 -10000 0 -10000 0 0
SRC 0.03 0.039 -10000 0 -10000 0 0
PI3K 0.022 0.033 -10000 0 -10000 0 0
MET/Glomulin 0.005 0.056 -10000 0 -0.45 6 6
SOS1 0.012 0 -10000 0 -10000 0 0
MAP2K1 0.035 0.047 -10000 0 -0.42 1 1
MET 0.004 0.08 -10000 0 -0.74 5 5
MAP4K1 0.011 0.087 -10000 0 -0.4 5 5
PTK2 0.012 0 -10000 0 -10000 0 0
MAP2K2 0.034 0.05 -10000 0 -0.41 2 2
BAD 0.006 0.021 0.28 2 -10000 0 2
MAP2K4 0.021 0.079 -10000 0 -0.34 5 5
SHP2/GRB2/SOS1/GAB1 -0.005 0.034 -10000 0 -10000 0 0
INPPL1 0.012 0 -10000 0 -10000 0 0
PXN 0.012 0 -10000 0 -10000 0 0
SH3KBP1 0.012 0 -10000 0 -10000 0 0
HGS 0.013 0.034 -10000 0 -10000 0 0
PLCgamma1/PKC 0.009 0 -10000 0 -10000 0 0
HGF 0.004 0.064 -10000 0 -0.48 7 7
RASA1 0.012 0.001 -10000 0 -10000 0 0
NCK1 0.012 0 -10000 0 -10000 0 0
PTPRJ 0.012 0 -10000 0 -10000 0 0
NCK/PLCgamma1 0.023 0.034 -10000 0 -10000 0 0
PDPK1 -0.006 0.023 0.33 2 -10000 0 2
HGF/MET/SHIP 0.014 0.067 -10000 0 -0.48 6 6
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.043 0.089 -9999 0 -0.53 1 1
CRKL 0.029 0.051 -9999 0 -0.45 1 1
mol:DAG 0.033 0.052 -9999 0 -0.43 1 1
HRAS 0.046 0.046 -9999 0 -10000 0 0
MAPK8 0.023 0.048 -9999 0 -0.41 5 5
RAP1A 0.029 0.051 -9999 0 -0.45 1 1
GAB1 0.029 0.051 -9999 0 -0.45 1 1
MAPK14 0.023 0.048 -9999 0 -0.41 5 5
EPO 0.002 0.072 -9999 0 -0.74 4 4
PLCG1 0.033 0.053 -9999 0 -0.44 1 1
EPOR/TRPC2/IP3 Receptors 0.012 0.036 -9999 0 -0.73 1 1
RAPGEF1 0.011 0.022 -9999 0 -0.44 1 1
EPO/EPOR (dimer)/SOCS3 0.019 0.052 -9999 0 -0.46 5 5
GAB1/SHC/GRB2/SOS1 -0.007 0.036 -9999 0 -10000 0 0
EPO/EPOR (dimer) 0.012 0.062 -9999 0 -0.56 5 5
IRS2 0.029 0.051 -9999 0 -0.45 1 1
STAT1 0.036 0.073 -9999 0 -0.53 1 1
STAT5B 0.035 0.063 -9999 0 -0.49 1 1
cell proliferation 0.028 0.045 -9999 0 -0.41 1 1
GAB1/SHIP/PIK3R1/SHP2/SHC -0.006 0.034 -9999 0 -10000 0 0
TEC 0.028 0.055 -9999 0 -0.42 2 2
SOCS3 0.012 0 -9999 0 -10000 0 0
STAT1 (dimer) 0.035 0.072 -9999 0 -0.52 1 1
JAK2 0.01 0.038 -9999 0 -0.44 3 3
PIK3R1 0.012 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.037 0.057 -9999 0 -0.38 5 5
EPO/EPOR 0.012 0.062 -9999 0 -0.56 5 5
LYN 0.013 0.003 -9999 0 -10000 0 0
TEC/VAV2 0.031 0.061 -9999 0 -0.43 1 1
elevation of cytosolic calcium ion concentration 0.012 0.036 -9999 0 -0.73 1 1
SHC1 0.012 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.024 0.054 -9999 0 -0.46 5 5
mol:IP3 0.033 0.052 -9999 0 -0.43 1 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.039 0.048 -9999 0 -0.4 1 1
SH2B3 0.013 0.006 -9999 0 -10000 0 0
NFKB1 0.023 0.048 -9999 0 -0.41 5 5
EPO/EPOR (dimer)/JAK2/SOCS3 -0.004 0.032 -9999 0 -0.26 1 1
PTPN6 0.023 0.053 -9999 0 -0.37 5 5
TEC/VAV2/GRB2 0.036 0.06 -9999 0 -0.42 1 1
EPOR 0.012 0.036 -9999 0 -0.73 1 1
INPP5D 0.012 0 -9999 0 -10000 0 0
mol:GDP -0.007 0.037 -9999 0 -10000 0 0
SOS1 0.012 0 -9999 0 -10000 0 0
PLCG2 -0.032 0.13 -9999 0 -0.44 42 42
CRKL/CBL/C3G 0.041 0.05 -9999 0 -0.41 1 1
VAV2 0.025 0.059 -9999 0 -0.45 1 1
CBL 0.029 0.051 -9999 0 -0.45 1 1
SHC/Grb2/SOS1 -0.007 0.039 -9999 0 -0.41 1 1
STAT5A 0.035 0.063 -9999 0 -0.49 1 1
GRB2 0.012 0 -9999 0 -10000 0 0
STAT5 (dimer) 0.045 0.087 -9999 0 -0.61 1 1
LYN/PLCgamma2 -0.013 0.096 -9999 0 -10000 0 0
PTPN11 0.012 0 -9999 0 -10000 0 0
BTK 0.001 0.094 -9999 0 -0.37 7 7
BCL2 0.015 0.2 -9999 0 -0.81 24 24
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.009 0.01 0.19 1 -10000 0 1
BUB1B 0.017 0.019 -10000 0 -10000 0 0
PLK1 0.015 0.009 -10000 0 -10000 0 0
PLK1S1 0.013 0.009 -10000 0 -0.14 1 1
KIF2A 0.02 0.008 -10000 0 -10000 0 0
regulation of mitotic centrosome separation 0.015 0.009 -10000 0 -10000 0 0
GOLGA2 0.012 0 -10000 0 -10000 0 0
Hec1/SPC24 0.018 0.062 -10000 0 -0.41 9 9
WEE1 0.018 0.022 -10000 0 -10000 0 0
cytokinesis 0.027 0.017 -10000 0 -0.23 1 1
PP2A-alpha B56 0.031 0.013 -10000 0 -10000 0 0
AURKA 0.013 0.006 -10000 0 -10000 0 0
PICH/PLK1 0.011 0.088 -10000 0 -0.34 26 26
CENPE 0.019 0.023 -10000 0 -0.43 1 1
RhoA/GTP 0.009 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.02 0.008 -10000 0 -10000 0 0
PPP2CA 0.012 0 -10000 0 -10000 0 0
FZR1 0.011 0.022 -10000 0 -0.44 1 1
TPX2 0.011 0.016 -10000 0 -0.15 4 4
PAK1 0.012 0.001 -10000 0 -10000 0 0
SPC24 -0.003 0.11 -10000 0 -0.74 9 9
FBXW11 0.012 0 -10000 0 -10000 0 0
CLSPN 0.013 0.01 -10000 0 -0.16 1 1
GORASP1 0.012 0 -10000 0 -10000 0 0
metaphase 0 0.001 -10000 0 -0.011 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.008 0.006 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0.001 -10000 0 -10000 0 0
STAG2 0.012 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP -0.001 0.007 -10000 0 -10000 0 0
spindle elongation 0.015 0.009 -10000 0 -10000 0 0
ODF2 0.012 0.001 -10000 0 -10000 0 0
BUB1 -0.002 0.009 -10000 0 -10000 0 0
TPT1 0.013 0.006 -10000 0 -10000 0 0
CDC25C 0.015 0.005 -10000 0 -10000 0 0
CDC25B -0.025 0.16 -10000 0 -0.73 22 22
SGOL1 0.009 0.01 -10000 0 -0.19 1 1
RHOA 0.012 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.017 0.073 -10000 0 -0.33 22 22
CDC14B 0.009 0.016 -10000 0 -0.32 1 1
CDC20 0.012 0 -10000 0 -10000 0 0
PLK1/PBIP1 0.016 0.013 -10000 0 -0.2 1 1
mitosis 0 0.001 -10000 0 -10000 0 0
FBXO5 0.016 0.016 -10000 0 -10000 0 0
CDC2 0 0.003 -10000 0 -0.015 22 22
NDC80 0.012 0.001 -10000 0 -10000 0 0
metaphase plate congression 0.014 0.006 -10000 0 -10000 0 0
ERCC6L 0.01 0.084 -10000 0 -0.32 26 26
NLP/gamma Tubulin 0.011 0.006 -10000 0 -10000 0 0
microtubule cytoskeleton organization 0.013 0.006 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0.001 -10000 0 -10000 0 0
PPP1R12A 0.01 0.031 -10000 0 -0.45 2 2
interphase 0 0.001 -10000 0 -10000 0 0
PLK1/PRC1-2 0.027 0.007 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0.031 0.007 -10000 0 -10000 0 0
RAB1A 0.012 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.017 0.007 -10000 0 -10000 0 0
mitotic prometaphase 0 0.001 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.03 0.014 -10000 0 -10000 0 0
microtubule-based process 0.02 0.008 -10000 0 -10000 0 0
Golgi organization 0.015 0.009 -10000 0 -10000 0 0
Cohesin/SA2 0.017 0.008 -10000 0 -10000 0 0
PPP1CB/MYPT1 0.016 0.033 -10000 0 -0.44 2 2
KIF20A 0.012 0 -10000 0 -10000 0 0
APC/C/CDC20 0.02 0.008 -10000 0 -10000 0 0
PPP2R1A 0.012 0 -10000 0 -10000 0 0
chromosome segregation 0.016 0.013 -10000 0 -0.2 1 1
PRC1 0.012 0 -10000 0 -10000 0 0
ECT2 0.016 0.04 -10000 0 -0.39 4 4
C13orf34 0.017 0.008 -10000 0 -10000 0 0
NUDC 0.014 0.006 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore 0.017 0.018 -10000 0 -10000 0 0
spindle assembly 0.014 0.008 -10000 0 -10000 0 0
spindle stabilization 0.013 0.009 -10000 0 -0.14 1 1
APC/C/HCDH1 0.015 0.019 -10000 0 -0.26 2 2
MKLP2/PLK1 0.02 0.008 -10000 0 -10000 0 0
CCNB1 0.012 0.003 -10000 0 -10000 0 0
PPP1CB 0.011 0.022 -10000 0 -0.45 1 1
BTRC 0.012 0 -10000 0 -10000 0 0
ROCK2 0.019 0.031 -10000 0 -0.43 2 2
TUBG1 0.013 0.006 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.016 0.071 -10000 0 -0.32 22 22
MLF1IP 0.009 0.016 -10000 0 -0.32 1 1
INCENP 0.012 0 -10000 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.01 0.031 -9999 0 -0.44 2 2
positive regulation of NF-kappaB transcription factor activity 0.017 0.022 -9999 0 -0.3 2 2
MAP2K4 0.037 0.025 -9999 0 -10000 0 0
IKBKB 0.012 0 -9999 0 -10000 0 0
TNFRSF10B 0.012 0 -9999 0 -10000 0 0
TNFRSF10A 0.012 0 -9999 0 -10000 0 0
SMPD1 0.011 0.049 -9999 0 -0.38 6 6
IKBKG 0.011 0.022 -9999 0 -0.44 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.012 0 -9999 0 -10000 0 0
TRAIL/TRAILR2 0.017 0.022 -9999 0 -0.3 2 2
TRAIL/TRAILR3 -0.016 0.14 -9999 0 -0.54 27 27
TRAIL/TRAILR1 0.017 0.022 -9999 0 -0.3 2 2
TRAIL/TRAILR4 0.017 0.022 -9999 0 -0.3 2 2
TRAIL/TRAILR1/DAP3/GTP 0.023 0.017 -9999 0 -10000 0 0
IKK complex -0.001 0.017 -9999 0 -10000 0 0
RIPK1 0.012 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0.009 0 -9999 0 -10000 0 0
MAPK3 0.017 0.027 -9999 0 -0.3 3 3
MAP3K1 0.034 0.021 -9999 0 -10000 0 0
TRAILR4 (trimer) 0.012 0 -9999 0 -10000 0 0
TRADD 0.012 0 -9999 0 -10000 0 0
TRAILR1 (trimer) 0.012 0 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.031 0.019 -9999 0 -10000 0 0
CFLAR 0.012 0 -9999 0 -10000 0 0
MAPK1 0.018 0.022 -9999 0 -0.3 2 2
TRAIL/TRAILR1/FADD/TRADD/RIP 0.036 0.016 -9999 0 -10000 0 0
mol:ceramide 0.011 0.048 -9999 0 -0.38 6 6
FADD 0.012 0 -9999 0 -10000 0 0
MAPK8 0.042 0.024 -9999 0 -10000 0 0
TRAF2 0.011 0.022 -9999 0 -0.44 1 1
TRAILR3 (trimer) -0.031 0.17 -9999 0 -0.74 25 25
CHUK 0.012 0 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.024 0.019 -9999 0 -10000 0 0
DAP3 0.012 0 -9999 0 -10000 0 0
CASP10 -0.001 0.018 -9999 0 -10000 0 0
JNK cascade 0.017 0.022 -9999 0 -0.3 2 2
TRAIL (trimer) 0.01 0.031 -9999 0 -0.44 2 2
TNFRSF10C -0.031 0.18 -9999 0 -0.74 25 25
TRAIL/TRAILR1/DAP3/GTP/FADD 0.028 0.016 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD 0.024 0.019 -9999 0 -10000 0 0
cell death 0.011 0.048 -9999 0 -0.38 6 6
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.031 0.019 -9999 0 -10000 0 0
TRAILR2 (trimer) 0.012 0 -9999 0 -10000 0 0
CASP8 0 0.007 -9999 0 -10000 0 0
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.036 0.016 -9999 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.012 0 -9999 0 -10000 0 0
Rac1/GDP 0.002 0.008 -9999 0 -10000 0 0
DOCK1 0.012 0 -9999 0 -10000 0 0
ITGA4 -0.005 0.086 -9999 0 -0.44 16 16
RAC1 0.012 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin -0.005 0.09 -9999 0 -0.33 29 29
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.012 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.015 0.052 -9999 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.012 0.07 -9999 0 -0.45 3 3
lamellipodium assembly 0.001 0.014 -9999 0 -10000 0 0
PIK3CA 0.012 0.001 -9999 0 -10000 0 0
PI3K 0.018 0 -9999 0 -10000 0 0
ARF6 0.012 0 -9999 0 -10000 0 0
TLN1 0.012 0 -9999 0 -10000 0 0
PXN 0.019 0 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
ARF6/GTP -0.007 0.034 -9999 0 -10000 0 0
cell adhesion 0.026 0.044 -9999 0 -10000 0 0
CRKL/CBL 0.018 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.021 0.047 -9999 0 -10000 0 0
ITGB1 0.012 0 -9999 0 -10000 0 0
ITGB7 -0.005 0.086 -9999 0 -0.44 16 16
ARF6/GDP 0.002 0.008 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.023 0.068 -9999 0 -0.42 7 7
p130Cas/Crk/Dock1 0.024 0.013 -9999 0 -10000 0 0
VCAM1 0.003 0.065 -9999 0 -0.44 9 9
alpha4/beta1 Integrin/Paxillin/Talin 0.028 0.044 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.027 0.046 -9999 0 -10000 0 0
BCAR1 0.011 0.022 -9999 0 -0.44 1 1
mol:GDP -0.026 0.045 -9999 0 -10000 0 0
CBL 0.012 0 -9999 0 -10000 0 0
PRKACA 0.012 0 -9999 0 -10000 0 0
GIT1 0.011 0.022 -9999 0 -0.44 1 1
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.028 0.044 -9999 0 -10000 0 0
Rac1/GTP 0.001 0.015 -9999 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.042 0.049 -9999 0 -10000 0 0
UGCG 0.022 0.018 -9999 0 -10000 0 0
AKT1/mTOR/p70S6K/Hsp90/TERT 0.038 0.09 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucosylceramide 0.022 0.018 -9999 0 -10000 0 0
mol:DAG 0.002 0.023 -9999 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.026 0.084 -9999 0 -0.44 4 4
FRAP1 0.044 0.12 -9999 0 -0.51 4 4
FOXO3 0.056 0.082 -9999 0 -10000 0 0
AKT1 0.052 0.086 -9999 0 -10000 0 0
GAB2 0.013 0.002 -9999 0 -10000 0 0
SMPD1 0.014 0.077 -9999 0 -0.62 6 6
SGMS1 0.022 0.018 -9999 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
mol:GDP 0.018 0.005 -9999 0 -10000 0 0
CALM1 0.012 0 -9999 0 -10000 0 0
cell proliferation 0.038 0.043 -9999 0 -10000 0 0
EIF3A 0.012 0 -9999 0 -10000 0 0
PI3K 0.022 0.006 -9999 0 -10000 0 0
RPS6KB1 0.022 0.039 -9999 0 -0.73 1 1
mol:sphingomyelin 0.002 0.023 -9999 0 -10000 0 0
natural killer cell activation 0 0.002 -9999 0 -10000 0 0
JAK3 0.013 0.036 -9999 0 -0.73 1 1
PIK3R1 0.015 0.002 -9999 0 -10000 0 0
JAK1 0.014 0.022 -9999 0 -0.44 1 1
NFKB1 0.012 0 -9999 0 -10000 0 0
MYC 0.053 0.092 -9999 0 -10000 0 0
MYB 0.026 0.032 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.049 0.071 -9999 0 -0.42 2 2
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.033 0.041 -9999 0 -0.52 2 2
mol:PI-3-4-5-P3 0.049 0.07 -9999 0 -0.42 2 2
Rac1/GDP 0.024 0.007 -9999 0 -10000 0 0
T cell proliferation 0.053 0.067 -9999 0 -0.38 2 2
SHC1 0.013 0.002 -9999 0 -10000 0 0
RAC1 0.012 0 -9999 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.005 0 -9999 0 -10000 0 0
PRKCZ 0.053 0.068 -9999 0 -0.4 2 2
NF kappa B1 p50/RelA 0.051 0.11 -9999 0 -0.44 4 4
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.036 0.053 -9999 0 -0.39 2 2
HSP90AA1 0.012 0 -9999 0 -10000 0 0
RELA 0.012 0 -9999 0 -10000 0 0
IL2RA 0.002 0.068 -9999 0 -0.44 10 10
IL2RB 0.004 0.069 -9999 0 -0.44 10 10
TERT -0.054 0.21 -9999 0 -0.72 39 39
E2F1 0.022 0.037 -9999 0 -0.39 1 1
SOS1 0.013 0.002 -9999 0 -10000 0 0
RPS6 0.011 0.036 -9999 0 -0.74 1 1
mol:cAMP -0.003 0 -9999 0 -10000 0 0
PTPN11 0.012 0.003 -9999 0 -10000 0 0
IL2RG 0.013 0.031 -9999 0 -0.44 2 2
actin cytoskeleton organization 0.053 0.067 -9999 0 -0.38 2 2
GRB2 0.013 0.002 -9999 0 -10000 0 0
IL2 0.006 0.006 -9999 0 -10000 0 0
PIK3CA 0.015 0.002 -9999 0 -10000 0 0
Rac1/GTP 0.032 0.009 -9999 0 -10000 0 0
LCK 0 0.099 -9999 0 -0.67 9 9
BCL2 0.021 0.21 -9999 0 -0.83 24 24
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.012 0.001 -9999 0 -10000 0 0
Caspase 8 (4 units) 0.024 0.057 -9999 0 -0.38 1 1
NEF -0.005 0.037 -9999 0 -10000 0 0
NFKBIA 0.013 0.014 -9999 0 -10000 0 0
BIRC3 0.027 0.072 -9999 0 -0.49 8 8
CYCS 0.024 0.069 -9999 0 -0.38 2 2
RIPK1 0.012 0 -9999 0 -10000 0 0
CD247 -0.01 0.11 -9999 0 -0.54 15 15
MAP2K7 0.031 0.061 -9999 0 -0.64 1 1
protein ubiquitination 0.056 0.022 -9999 0 -10000 0 0
CRADD 0.012 0 -9999 0 -10000 0 0
DAXX 0.012 0 -9999 0 -10000 0 0
FAS 0.009 0.038 -9999 0 -0.44 3 3
BID 0.019 0.071 -9999 0 -0.4 2 2
NF-kappa-B/RelA/I kappa B alpha 0.03 0.038 -9999 0 -10000 0 0
TRADD 0.012 0 -9999 0 -10000 0 0
MAP3K5 0.012 0 -9999 0 -10000 0 0
CFLAR 0.012 0 -9999 0 -10000 0 0
FADD 0.012 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.03 0.038 -9999 0 -10000 0 0
MAPK8 0.036 0.058 -9999 0 -0.6 1 1
APAF1 0.012 0.001 -9999 0 -10000 0 0
TRAF1 0.012 0 -9999 0 -10000 0 0
TRAF2 0.011 0.022 -9999 0 -0.44 1 1
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.015 0.072 -9999 0 -0.45 1 1
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.051 0.025 -9999 0 -10000 0 0
CHUK 0.057 0.023 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.035 0.02 -9999 0 -10000 0 0
TCRz/NEF -0.012 0.11 -9999 0 -0.46 16 16
TNF 0.01 0.031 -9999 0 -0.44 2 2
FASLG -0.019 0.16 -9999 0 -0.6 28 28
NFKB1 0.013 0.014 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.024 0.019 -9999 0 -10000 0 0
CASP6 0.039 0.041 -9999 0 -10000 0 0
CASP7 0.051 0.083 -9999 0 -0.46 7 7
RELA 0.013 0.014 -9999 0 -10000 0 0
CASP2 0.012 0 -9999 0 -10000 0 0
CASP3 0.051 0.082 -9999 0 -0.46 7 7
TNFRSF1A 0.012 0 -9999 0 -10000 0 0
TNFR1A/BAG4 0.018 0.001 -9999 0 -10000 0 0
CASP8 0.012 0 -9999 0 -10000 0 0
CASP9 0.012 0 -9999 0 -10000 0 0
MAP3K14 0.054 0.024 -9999 0 -10000 0 0
APAF-1/Caspase 9 -0.015 0.056 -9999 0 -0.43 3 3
BCL2 0.029 0.074 -9999 0 -0.54 1 1
IL2 signaling events mediated by STAT5

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
GAB2 0.013 0 -9999 0 -10000 0 0
ELF1 0.012 0.05 -9999 0 -0.31 10 10
CCNA2 0.012 0 -9999 0 -10000 0 0
PIK3CA 0.013 0.001 -9999 0 -10000 0 0
JAK3 0.011 0.036 -9999 0 -0.74 1 1
PIK3R1 0.013 0 -9999 0 -10000 0 0
JAK1 0.012 0.022 -9999 0 -0.44 1 1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.054 0.061 -9999 0 -0.48 2 2
SHC1 0.013 0 -9999 0 -10000 0 0
SP1 0.016 0.035 -9999 0 -0.31 4 4
IL2RA 0.011 0.11 -9999 0 -0.68 10 10
IL2RB 0.002 0.068 -9999 0 -0.44 10 10
SOS1 0.013 0 -9999 0 -10000 0 0
IL2RG 0.011 0.031 -9999 0 -0.44 2 2
G1/S transition of mitotic cell cycle 0.033 0.065 -9999 0 -0.61 4 4
PTPN11 0.013 0 -9999 0 -10000 0 0
CCND2 0.019 0.074 -9999 0 -0.67 5 5
LCK -0.001 0.099 -9999 0 -0.67 9 9
GRB2 0.013 0 -9999 0 -10000 0 0
IL2 0.004 0.005 -9999 0 -10000 0 0
CDK6 0.012 0 -9999 0 -10000 0 0
CCND3 0.058 0.055 -9999 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 -0.039 0.14 -10000 0 -0.44 49 49
CLTC 0.021 0.04 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.022 0.007 -10000 0 -10000 0 0
Dynamin 2/GTP 0.011 0.069 -10000 0 -0.44 10 10
EXOC4 0.012 0 -10000 0 -10000 0 0
CD59 0.021 0.025 -10000 0 -10000 0 0
CPE -0.005 0.074 -10000 0 -0.26 32 32
CTNNB1 0.012 0 -10000 0 -10000 0 0
membrane fusion 0.022 0.007 -10000 0 -10000 0 0
CTNND1 0.016 0.065 -10000 0 -0.41 10 10
DNM2 0.012 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.024 0.02 -10000 0 -10000 0 0
TSHR 0.009 0.037 -10000 0 -10000 0 0
INS 0.009 0.007 -10000 0 -10000 0 0
BIN1 0.011 0.022 -10000 0 -0.44 1 1
mol:Choline 0.022 0.007 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.005 0.075 -10000 0 -0.48 10 10
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.012 0 -10000 0 -10000 0 0
mol:Ca2+ 0.011 0.069 -10000 0 -0.44 10 10
JUP 0.02 0.026 -10000 0 -10000 0 0
ASAP2/amphiphysin II 0.023 0.012 -10000 0 -10000 0 0
ARF6/GTP 0.009 0 -10000 0 -10000 0 0
CDH1 0.021 0.025 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0.009 0 -10000 0 -10000 0 0
MAPK8IP3 0.009 0.042 -10000 0 -0.59 2 2
positive regulation of endocytosis 0.009 0 -10000 0 -10000 0 0
EXOC2 0.011 0.022 -10000 0 -0.44 1 1
substrate adhesion-dependent cell spreading 0.034 0.036 -10000 0 -0.66 1 1
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.012 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.008 0.05 0.33 10 -10000 0 10
positive regulation of phagocytosis 0.016 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.015 0.027 -10000 0 -0.37 2 2
ACAP1 0.016 0.027 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.024 0.083 -10000 0 -0.41 2 2
clathrin heavy chain/ACAP1 0.025 0.036 -10000 0 -10000 0 0
JIP4/KLC1 0.024 0 -10000 0 -10000 0 0
EXOC1 0.011 0.022 -10000 0 -0.44 1 1
exocyst 0.035 0.036 -10000 0 -0.67 1 1
RALA/GTP 0.009 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.017 0 -10000 0 -10000 0 0
receptor recycling 0.009 0 -10000 0 -10000 0 0
CTNNA1 0.016 0.065 -10000 0 -0.41 10 10
NME1 0.005 0.075 -10000 0 -0.48 10 10
clathrin coat assembly 0.021 0.04 -10000 0 -10000 0 0
IL2RA 0.016 0.037 -10000 0 -10000 0 0
VAMP3 0.016 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.024 0.063 -10000 0 -0.36 3 3
EXOC6 0.012 0 -10000 0 -10000 0 0
PLD1 0.019 0.013 -10000 0 -0.24 1 1
PLD2 0.019 0 -10000 0 -10000 0 0
EXOC5 0.009 0.038 -10000 0 -0.44 3 3
PIP5K1C 0.024 0.02 -10000 0 -10000 0 0
SDC1 0.021 0.025 -10000 0 -10000 0 0
ARF6/GDP 0.005 0.075 -10000 0 -0.48 10 10
EXOC7 0.012 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.008 0.052 -10000 0 -0.34 10 10
mol:Phosphatidic acid 0.022 0.007 -10000 0 -10000 0 0
endocytosis -0.022 0.012 -10000 0 -10000 0 0
SCAMP2 0.012 0 -10000 0 -10000 0 0
ADRB2 -0.009 0.092 -10000 0 -0.42 4 4
EXOC3 0.012 0 -10000 0 -10000 0 0
ASAP2 0.012 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.012 0.069 -10000 0 -0.44 10 10
KLC1 0.012 0 -10000 0 -10000 0 0
AVPR2 0.007 0.079 -10000 0 -0.39 7 7
RALA 0.012 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.007 0.047 -10000 0 -10000 0 0
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.009 0.047 -9999 0 -0.38 4 4
TC10/GTP -0.009 0.046 -9999 0 -0.37 4 4
Insulin Receptor/Insulin/IRS1/Shp2 0.026 0 -9999 0 -10000 0 0
HRAS 0.011 0.022 -9999 0 -0.44 1 1
APS homodimer 0.005 0.072 -9999 0 -0.74 4 4
GRB14 -0.027 0.14 -9999 0 -0.53 30 30
FOXO3 -0.008 0.13 -9999 0 -0.54 23 23
AKT1 0.023 0.068 -9999 0 -10000 0 0
INSR 0.014 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0.032 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.012 0 -9999 0 -10000 0 0
SORBS1 0 0.075 -9999 0 -0.44 12 12
CRK 0.012 0 -9999 0 -10000 0 0
PTPN1 0.028 0 -9999 0 -10000 0 0
CAV1 0.021 0.02 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II/C3G 0.025 0.058 -9999 0 -0.4 4 4
Insulin Receptor/Insulin/IRS1/NCK2 0.026 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.033 0 -9999 0 -10000 0 0
RPS6KB1 0.028 0.064 -9999 0 -10000 0 0
PARD6A 0.005 0.072 -9999 0 -0.74 4 4
CBL 0.012 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.013 0.052 -9999 0 -10000 0 0
HRAS/GTP 0 0.008 -9999 0 -10000 0 0
Insulin Receptor 0.014 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.032 0 -9999 0 -10000 0 0
PRKCI -0.007 0.038 -9999 0 -0.43 3 3
Insulin Receptor/Insulin/GRB14/PDK1 -0.016 0.063 -9999 0 -10000 0 0
SHC1 0.012 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0.024 0.001 -9999 0 -10000 0 0
PI3K 0.027 0 -9999 0 -10000 0 0
NCK2 0.012 0 -9999 0 -10000 0 0
RHOQ 0.012 0 -9999 0 -10000 0 0
mol:H2O2 0 0 -9999 0 -10000 0 0
HRAS/GDP 0.008 0.015 -9999 0 -0.31 1 1
AKT2 0.023 0.068 -9999 0 -10000 0 0
PRKCZ -0.005 0.024 -9999 0 -0.41 1 1
SH2B2 0.005 0.072 -9999 0 -0.74 4 4
SHC/SHIP 0.029 0 -9999 0 -10000 0 0
F2RL2 -0.039 0.19 -9999 0 -0.71 31 31
TRIP10 0.011 0.022 -9999 0 -0.44 1 1
Insulin Receptor/Insulin/Shc 0.018 0 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.016 0.013 -9999 0 -0.26 1 1
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.032 0 -9999 0 -10000 0 0
RAPGEF1 0.011 0.022 -9999 0 -0.44 1 1
RASA1 0.012 0.001 -9999 0 -10000 0 0
NCK1 0.012 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.02 0.06 -9999 0 -0.43 4 4
TC10/GDP 0.009 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.026 0 -9999 0 -10000 0 0
INPP5D 0.023 0 -9999 0 -10000 0 0
SOS1 0.012 0 -9999 0 -10000 0 0
SGK1 -0.044 0.18 -9999 0 -0.8 23 23
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.012 0 -9999 0 -10000 0 0
IRS1 0.012 0 -9999 0 -10000 0 0
p62DOK/RasGAP 0.024 0.001 -9999 0 -10000 0 0
INS 0.003 0 -9999 0 -10000 0 0
mol:PI-3-4-P2 0.023 0 -9999 0 -10000 0 0
GRB2 0.012 0 -9999 0 -10000 0 0
EIF4EBP1 0.026 0.068 -9999 0 -10000 0 0
PTPRA 0.014 0 -9999 0 -10000 0 0
PIK3CA 0.012 0.001 -9999 0 -10000 0 0
TC10/GTP/CIP4 0.016 0.013 -9999 0 -0.26 1 1
PDPK1 0.012 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.029 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.018 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS3 0.012 0 -9999 0 -10000 0 0
Par3/Par6 -0.006 0.12 -9999 0 -0.41 32 32
p38 MAPK signaling pathway

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
TRAF6/ASK1 0.013 0 -10000 0 -10000 0 0
TRAF2/ASK1 0.016 0.013 -10000 0 -0.26 1 1
ATM 0.012 0 -10000 0 -10000 0 0
MAP2K3 0.029 0.027 -10000 0 -0.32 1 1
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.035 0.029 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.008 0.055 -10000 0 -0.64 3 3
TXN 0.007 0 -10000 0 -10000 0 0
CALM1 0.012 0 -10000 0 -10000 0 0
GADD45A 0.012 0 -10000 0 -10000 0 0
GADD45B 0.012 0 -10000 0 -10000 0 0
MAP3K1 0.011 0.022 -10000 0 -0.44 1 1
MAP3K6 0.01 0.031 -10000 0 -0.44 2 2
MAP3K7 0.012 0 -10000 0 -10000 0 0
MAP3K4 0.012 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.017 0.022 -10000 0 -0.3 2 2
TAK1/TAB family 0.001 0.012 0.17 2 -10000 0 2
RAC1/OSM/MEKK3 0.023 0.012 -10000 0 -10000 0 0
TRAF2 0.011 0.022 -10000 0 -0.44 1 1
RAC1/OSM/MEKK3/MKK3 -0.002 0.016 -10000 0 -10000 0 0
TRAF6 0.007 0 -10000 0 -10000 0 0
RAC1 0.012 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.027 0.14 -10000 0 -0.49 33 33
CCM2 0.011 0.022 -10000 0 -0.44 1 1
CaM/Ca2+/CAMKIIB -0.008 0.084 -10000 0 -0.29 33 33
MAPK11 0.009 0.051 -10000 0 -0.74 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.001 0.077 -10000 0 -0.44 5 5
OSM/MEKK3 0.018 0.016 -10000 0 -10000 0 0
TAOK1 0.015 0 -10000 0 -10000 0 0
TAOK2 0.015 0 -10000 0 -10000 0 0
TAOK3 0.015 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.012 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.012 0 -10000 0 -10000 0 0
MAP3K10 0.012 0 -10000 0 -10000 0 0
MAP3K3 0.012 0 -10000 0 -10000 0 0
TRX/ASK1 0.015 0 -10000 0 -10000 0 0
GADD45/MTK1/MTK1 0.027 0.032 -10000 0 -0.41 2 2
Arf6 downstream 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
PLAUR 0.032 0.017 -10000 0 -10000 0 0
regulation of axonogenesis -0.024 0.008 -10000 0 -10000 0 0
myoblast fusion -0.022 0.016 -10000 0 -10000 0 0
mol:GTP 0.009 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.004 0.12 0.56 10 -10000 0 10
ARF1/GTP 0.016 0.006 -10000 0 -10000 0 0
mol:GM1 0.009 0.003 -10000 0 -10000 0 0
mol:Choline 0.024 0.013 -10000 0 -10000 0 0
lamellipodium assembly 0.009 0.028 -10000 0 -10000 0 0
MAPK3 0.022 0.016 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.004 0.12 -10000 0 -0.56 10 10
ARF1 0.012 0 -10000 0 -10000 0 0
ARF6/GDP 0.022 0.016 -10000 0 -10000 0 0
ARF1/GDP 0.03 0.018 -10000 0 -10000 0 0
ARF6 0.012 0.001 -10000 0 -10000 0 0
RAB11A 0.012 0 -10000 0 -10000 0 0
TIAM1 -0.03 0.14 -10000 0 -0.44 42 42
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.023 0.008 -10000 0 -10000 0 0
actin filament bundle formation -0.021 0.009 -10000 0 -10000 0 0
KALRN 0.007 0.026 -10000 0 -10000 0 0
RAB11FIP3/RAB11A 0.018 0 -10000 0 -10000 0 0
RhoA/GDP 0.021 0.009 -10000 0 -10000 0 0
NME1 -0.004 0.11 -10000 0 -0.73 10 10
Rac1/GDP 0.021 0.009 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.009 0.004 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0.009 0.028 -10000 0 -10000 0 0
RAC1 0.012 0 -10000 0 -10000 0 0
liver development 0.009 0.004 -10000 0 -10000 0 0
ARF6/GTP 0.009 0.004 -10000 0 -10000 0 0
RhoA/GTP 0.016 0.006 -10000 0 -10000 0 0
mol:GDP 0.01 0.028 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0.022 0.008 -10000 0 -10000 0 0
RHOA 0.012 0 -10000 0 -10000 0 0
PLD1 0.018 0.014 -10000 0 -0.28 1 1
RAB11FIP3 0.012 0 -10000 0 -10000 0 0
tube morphogenesis 0.009 0.028 -10000 0 -10000 0 0
ruffle organization 0.024 0.008 -10000 0 -10000 0 0
regulation of epithelial cell migration 0.009 0.004 -10000 0 -10000 0 0
PLD2 0.019 0.002 -10000 0 -10000 0 0
PIP5K1A 0.025 0.009 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.024 0.013 -10000 0 -10000 0 0
Rac1/GTP 0.009 0.028 -10000 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.039 0.04 -10000 0 -10000 0 0
BAG4 0.012 0.001 -10000 0 -10000 0 0
BAD 0.025 0.026 -10000 0 -0.39 1 1
NFKBIA 0.012 0 -10000 0 -10000 0 0
BIRC3 0.003 0.067 -10000 0 -0.48 8 8
BAX 0.025 0.02 -10000 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.013 0.011 -10000 0 -10000 0 0
IKBKB 0.044 0.038 -10000 0 -10000 0 0
MAP2K2 0.034 0.023 -10000 0 -0.32 1 1
MAP2K1 0.035 0.018 -10000 0 -10000 0 0
SMPD1 0.015 0.028 -10000 0 -0.2 6 6
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.045 0.039 -10000 0 -10000 0 0
MAP2K4 0.029 0.026 -10000 0 -10000 0 0
protein ubiquitination 0.045 0.04 -10000 0 -10000 0 0
EnzymeConsortium:2.7.1.37 0.039 0.021 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.031 0.019 -10000 0 -10000 0 0
CRADD 0.013 0 -10000 0 -10000 0 0
mol:ceramide 0.02 0.021 -10000 0 -0.2 1 1
I-kappa-B-alpha/RELA/p50/ubiquitin 0.017 0 -10000 0 -10000 0 0
MADD 0.013 0 -10000 0 -10000 0 0
MAP3K1 0.025 0.024 -10000 0 -0.26 1 1
TRADD 0.013 0 -10000 0 -10000 0 0
RELA/p50 0.012 0 -10000 0 -10000 0 0
MAPK3 0.037 0.021 -10000 0 -10000 0 0
MAPK1 0.037 0.02 -10000 0 -10000 0 0
p50/RELA/I-kappa-B-alpha 0.018 0 -10000 0 -10000 0 0
FADD 0.039 0.04 -10000 0 -10000 0 0
KSR1 0.026 0.02 -10000 0 -0.19 1 1
MAPK8 0.033 0.025 -10000 0 -10000 0 0
TRAF2 0.011 0.022 -10000 0 -0.44 1 1
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.044 0.038 -10000 0 -10000 0 0
TNF R/SODD 0.018 0.001 -10000 0 -10000 0 0
TNF 0.01 0.031 -10000 0 -0.44 2 2
CYCS 0.031 0.031 0.13 21 -0.29 1 22
IKBKG 0.043 0.043 -10000 0 -0.44 1 1
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.035 0.042 -10000 0 -10000 0 0
RELA 0.012 0 -10000 0 -10000 0 0
RIPK1 0.012 0 -10000 0 -10000 0 0
AIFM1 0.031 0.031 0.13 22 -0.29 1 23
TNF/TNF R/SODD 0.024 0.019 -10000 0 -10000 0 0
TNFRSF1A 0.012 0 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.027 0.011 -10000 0 -10000 0 0
NSMAF 0.039 0.039 -10000 0 -10000 0 0
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
BCL2 -0.013 0.1 -10000 0 -0.44 24 24
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.015 0.031 -9999 0 -0.3 4 4
AKT1 0.071 0.031 -9999 0 -0.47 1 1
PTK2B 0.043 0.04 -9999 0 -0.42 2 2
VEGFR2 homodimer/Frs2 0.031 0.03 -9999 0 -0.59 1 1
CAV1 0.009 0.038 -9999 0 -0.44 3 3
CALM1 0.012 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.038 0.035 -9999 0 -0.48 2 2
endothelial cell proliferation 0.046 0.07 -9999 0 -0.49 1 1
mol:Ca2+ 0.045 0.033 -9999 0 -0.49 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.044 0.034 -9999 0 -0.45 2 2
RP11-342D11.1 0.037 0.033 -9999 0 -0.44 2 2
CDH5 0.012 0 -9999 0 -10000 0 0
VEGFA homodimer 0.031 0.025 -9999 0 -0.43 1 1
SHC1 0.012 0 -9999 0 -10000 0 0
SHC2 -0.001 0.091 -9999 0 -0.6 9 9
HRAS/GDP -0.002 0.026 -9999 0 -0.42 1 1
SH2D2A 0.012 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.063 0.044 -9999 0 -0.57 1 1
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.038 0.035 -9999 0 -0.48 2 2
VEGFR1 homodimer 0.012 0 -9999 0 -10000 0 0
SHC/GRB2/SOS1 -0.002 0.028 -9999 0 -0.46 1 1
GRB10 0.046 0.033 -9999 0 -0.49 1 1
PTPN11 0.012 0 -9999 0 -10000 0 0
GRB2 0.012 0 -9999 0 -10000 0 0
PAK1 0.012 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.048 0.033 -9999 0 -0.48 1 1
HRAS 0.011 0.022 -9999 0 -0.44 1 1
VEGF/Rho/ROCK1/Integrin Complex 0.04 0.046 -9999 0 -0.8 1 1
HIF1A 0.012 0 -9999 0 -10000 0 0
FRS2 0.012 0.001 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.043 0.033 -9999 0 -0.44 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.008 0.043 -9999 0 -0.44 4 4
Nck/Pak 0.018 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.038 0.035 -9999 0 -0.48 2 2
mol:GDP -0.002 0.027 -9999 0 -0.45 1 1
mol:NADP 0.059 0.042 -9999 0 -0.52 1 1
eNOS/Hsp90 0.063 0.04 -9999 0 -0.48 1 1
PIK3R1 0.012 0 -9999 0 -10000 0 0
mol:IP3 0.045 0.033 -9999 0 -0.5 1 1
HIF1A/ARNT 0.018 0.016 -9999 0 -0.3 1 1
SHB 0.012 0 -9999 0 -10000 0 0
VEGFA 0.012 0.036 -9999 0 -0.73 1 1
VEGFC 0.008 0.043 -9999 0 -0.44 4 4
FAK1/Vinculin 0.058 0.043 -9999 0 -0.65 1 1
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.042 0.04 -9999 0 -0.45 2 2
PTPN6 0.012 0 -9999 0 -10000 0 0
EPAS1 0.021 0.016 -9999 0 -0.31 1 1
mol:L-citrulline 0.059 0.042 -9999 0 -0.52 1 1
ITGAV 0.012 0 -9999 0 -10000 0 0
PIK3CA 0.012 0.001 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.044 0.034 -9999 0 -0.45 2 2
VEGFR2 homodimer/VEGFA homodimer 0.043 0.036 -9999 0 -0.48 2 2
VEGFR2/3 heterodimer 0.028 0.039 -9999 0 -0.59 1 1
VEGFB 0.012 0 -9999 0 -10000 0 0
MAPK11 0.046 0.035 -9999 0 -0.51 1 1
VEGFR2 homodimer 0.029 0.034 -9999 0 -0.67 1 1
FLT1 0.012 0 -9999 0 -10000 0 0
NEDD4 0.014 0.001 -9999 0 -10000 0 0
MAPK3 0.026 0.051 -9999 0 -0.45 1 1
MAPK1 0.026 0.051 -9999 0 -0.45 1 1
VEGFA145/NRP2 0.016 0.038 -9999 0 -0.37 4 4
VEGFR1/2 heterodimer 0.031 0.03 -9999 0 -0.59 1 1
KDR 0.029 0.034 -9999 0 -0.68 1 1
VEGFA165/NRP1/VEGFR2 homodimer 0.045 0.038 -9999 0 -0.43 2 2
SRC 0.012 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process 0.029 0.049 -9999 0 -0.46 1 1
PI3K 0.064 0.034 -9999 0 -0.51 1 1
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.038 0.035 -9999 0 -0.48 2 2
FES 0.045 0.037 -9999 0 -0.44 2 2
GAB1 0.055 0.032 -9999 0 -0.53 1 1
VEGFR2 homodimer/VEGFA homodimer/Src 0.038 0.035 -9999 0 -0.48 2 2
CTNNB1 0.012 0 -9999 0 -10000 0 0
SOS1 0.012 0 -9999 0 -10000 0 0
ARNT 0.011 0.022 -9999 0 -0.44 1 1
eNOS/Caveolin-1 0.061 0.043 -9999 0 -0.48 1 1
VEGFR2 homodimer/VEGFA homodimer/Yes 0.038 0.044 -9999 0 -0.58 2 2
PI3K/GAB1 0.074 0.031 -9999 0 -0.48 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.048 0.033 -9999 0 -0.43 2 2
PRKACA 0.012 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.032 0.046 -9999 0 -0.49 2 2
HSP90AA1 0.012 0 -9999 0 -10000 0 0
CDC42 0.045 0.035 -9999 0 -0.44 2 2
actin cytoskeleton reorganization 0.038 0.035 -9999 0 -0.48 2 2
PTK2 0.054 0.046 -9999 0 -0.71 1 1
EDG1 0.037 0.033 -9999 0 -0.44 2 2
mol:DAG 0.045 0.033 -9999 0 -0.5 1 1
CaM/Ca2+ 0.048 0.031 -9999 0 -0.45 1 1
MAP2K3 0.05 0.032 -9999 0 -0.48 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.049 0.034 -9999 0 -0.5 1 1
PLCG1 0.046 0.034 -9999 0 -0.5 1 1
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.044 0.034 -9999 0 -0.45 2 2
IQGAP1 0.012 0 -9999 0 -10000 0 0
YES1 0.011 0.022 -9999 0 -0.44 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.038 0.035 -9999 0 -0.48 2 2
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.038 0.035 -9999 0 -0.48 2 2
cell migration 0.075 0.038 -9999 0 -0.56 1 1
mol:PI-3-4-5-P3 0.062 0.032 -9999 0 -0.48 1 1
FYN 0.012 0 -9999 0 -10000 0 0
VEGFB/NRP1 0.043 0.031 -9999 0 -0.41 2 2
mol:NO 0.059 0.042 -9999 0 -0.52 1 1
PXN 0.012 0 -9999 0 -10000 0 0
HRAS/GTP -0.002 0.026 -9999 0 -0.42 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.048 0.034 -9999 0 -0.5 1 1
VHL 0.012 0 -9999 0 -10000 0 0
ITGB3 0.008 0.043 -9999 0 -0.44 4 4
NOS3 0.061 0.046 -9999 0 -0.59 1 1
VEGFR2 homodimer/VEGFA homodimer/Sck 0.031 0.065 -9999 0 -0.44 7 7
RAC1 0.012 0 -9999 0 -10000 0 0
PRKCA 0.049 0.031 -9999 0 -0.46 1 1
PRKCB -0.001 0.097 -9999 0 -0.46 1 1
VCL 0.012 0 -9999 0 -10000 0 0
VEGFA165/NRP1 0.039 0.033 -9999 0 -0.45 2 2
VEGFR1/2 heterodimer/VEGFA homodimer 0.038 0.035 -9999 0 -0.48 2 2
VEGFA165/NRP2 0.016 0.038 -9999 0 -0.37 4 4
MAPKKK cascade 0.063 0.031 -9999 0 -10000 0 0
NRP2 0.009 0.038 -9999 0 -0.44 3 3
VEGFC homodimer 0.008 0.043 -9999 0 -0.44 4 4
NCK1 0.012 0 -9999 0 -10000 0 0
ROCK1 0.011 0.022 -9999 0 -0.44 1 1
FAK1/Paxillin 0.058 0.043 -9999 0 -0.65 1 1
MAP3K13 0.046 0.034 -9999 0 -0.45 2 2
PDPK1 0.065 0.029 -9999 0 -0.43 1 1
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.036 0.004 -9999 0 -10000 0 0
KLHL20 -0.013 0.042 -9999 0 -0.24 2 2
CYFIP2 0.011 0.022 -9999 0 -0.44 1 1
Rac1/GDP 0.051 0.022 -9999 0 -10000 0 0
ENAH 0.036 0.004 -9999 0 -10000 0 0
AP1M1 0.012 0 -9999 0 -10000 0 0
RAP1B 0.012 0 -9999 0 -10000 0 0
RAP1A 0.012 0 -9999 0 -10000 0 0
CTNNB1 0.012 0 -9999 0 -10000 0 0
CDC42/GTP -0.001 0.009 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.009 0.029 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.023 0.047 -9999 0 -10000 0 0
RAPGEF1 0.044 0.01 -9999 0 -10000 0 0
CTNND1 0.012 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.03 0.004 -9999 0 -10000 0 0
CRK 0.04 0.004 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin 0.025 0.013 -9999 0 -10000 0 0
alphaE/beta7 Integrin 0.006 0.061 -9999 0 -0.3 16 16
IQGAP1 0.012 0 -9999 0 -10000 0 0
NCKAP1 0.012 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.023 0.012 -9999 0 -10000 0 0
DLG1 0.035 0.011 -9999 0 -10000 0 0
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0.006 -9999 0 -10000 0 0
MLLT4 0.011 0.022 -9999 0 -0.44 1 1
ARF6/GTP/NME1/Tiam1 -0.011 0.11 -9999 0 -0.55 10 10
PI3K -0.001 0.007 -9999 0 -10000 0 0
ARF6 0.012 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin 0.018 0.016 -9999 0 -10000 0 0
TIAM1 -0.032 0.13 -9999 0 -0.44 42 42
E-cadherin(dimer)/Ca2+ 0.03 0.001 -9999 0 -10000 0 0
AKT1 0 0.004 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
CDH1 0.012 0 -9999 0 -10000 0 0
RhoA/GDP 0.051 0.022 -9999 0 -10000 0 0
actin cytoskeleton organization 0.024 0.043 -9999 0 -10000 0 0
CDC42/GDP 0.05 0.024 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.021 0.011 -9999 0 -10000 0 0
ITGB7 -0.005 0.086 -9999 0 -0.44 16 16
RAC1 0.012 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.032 0.001 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0.022 0 -9999 0 -10000 0 0
mol:GDP 0.048 0.025 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1 0.016 0.013 -9999 0 -0.26 1 1
JUP 0.011 0.022 -9999 0 -0.44 1 1
p120 catenin/RhoA/GDP 0.042 0.025 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 0.017 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0.018 0.016 -9999 0 -0.3 1 1
RHOA 0.012 0 -9999 0 -10000 0 0
CDC42 0.011 0.022 -9999 0 -0.44 1 1
CTNNA1 0.012 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.019 0.035 -9999 0 -0.24 3 3
NME1 -0.005 0.11 -9999 0 -0.74 10 10
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.036 0.004 -9999 0 -10000 0 0
regulation of cell-cell adhesion -0.001 0.008 -9999 0 -10000 0 0
WASF2 -0.005 0.015 -9999 0 -10000 0 0
Rap1/GTP 0 0.008 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.027 0.046 -9999 0 -10000 0 0
CCND1 0.022 0.043 -9999 0 -0.3 3 3
VAV2 0.032 0.094 -9999 0 -0.65 8 8
RAP1/GDP 0.042 0.02 -9999 0 -10000 0 0
adherens junction assembly 0.035 0.004 -9999 0 -10000 0 0
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.012 0 -9999 0 -10000 0 0
PIP5K1C 0.011 0.022 -9999 0 -0.44 1 1
regulation of heterotypic cell-cell adhesion 0.032 0.044 -9999 0 -10000 0 0
E-cadherin/beta catenin 0 0.008 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.036 0.005 -9999 0 -10000 0 0
PIK3CA 0.012 0.001 -9999 0 -10000 0 0
Rac1/GTP -0.021 0.068 -9999 0 -0.39 3 3
E-cadherin/beta catenin/alpha catenin 0.025 0 -9999 0 -10000 0 0
ITGAE 0.012 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.031 0.004 -9999 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.011 0.022 -9999 0 -0.44 1 1
SMAD2 0.013 0.011 -9999 0 -10000 0 0
SMAD3 0.034 0.017 -9999 0 -10000 0 0
SMAD3/SMAD4 0.039 0.017 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy 0.024 0.013 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.034 0.022 -9999 0 -0.37 1 1
PPM1A 0.012 0 -9999 0 -10000 0 0
CALM1 0.012 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.019 0.014 -9999 0 -10000 0 0
MAP3K1 0.011 0.022 -9999 0 -0.44 1 1
TRAP-1/SMAD4 0.018 0.016 -9999 0 -0.3 1 1
MAPK3 0.011 0.022 -9999 0 -0.44 1 1
MAPK1 0.012 0 -9999 0 -10000 0 0
NUP214 0.012 0 -9999 0 -10000 0 0
CTDSP1 0.012 0 -9999 0 -10000 0 0
CTDSP2 0.012 0 -9999 0 -10000 0 0
CTDSPL 0.012 0 -9999 0 -10000 0 0
KPNB1 0.012 0 -9999 0 -10000 0 0
TGFBRAP1 0.012 0 -9999 0 -10000 0 0
UBE2I 0.012 0 -9999 0 -10000 0 0
NUP153 0.012 0.001 -9999 0 -10000 0 0
KPNA2 0.011 0.036 -9999 0 -0.74 1 1
PIAS4 0.012 0 -9999 0 -10000 0 0
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.015 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.068 0.027 -9999 0 -10000 0 0
ERC1 0.012 0 -9999 0 -10000 0 0
RIP2/NOD2 0.006 0.083 -9999 0 -0.53 10 10
NFKBIA 0.038 0 -9999 0 -10000 0 0
BIRC2 0.012 0.001 -9999 0 -10000 0 0
IKBKB 0.012 0 -9999 0 -10000 0 0
RIPK2 0.012 0 -9999 0 -10000 0 0
IKBKG 0.033 0.043 -9999 0 -0.41 2 2
IKK complex/A20 0.046 0.042 -9999 0 -0.43 1 1
NEMO/A20/RIP2 0.012 0 -9999 0 -10000 0 0
XPO1 0.012 0 -9999 0 -10000 0 0
NEMO/ATM 0.038 0.042 -9999 0 -0.46 1 1
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.012 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0.017 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.005 0.03 -9999 0 -0.41 1 1
BCL10/MALT1/TRAF6 0.024 0.019 -9999 0 -10000 0 0
NOD2 -0.004 0.11 -9999 0 -0.71 10 10
NFKB1 0.015 0 -9999 0 -10000 0 0
RELA 0.015 0 -9999 0 -10000 0 0
MALT1 0.011 0.022 -9999 0 -0.44 1 1
cIAP1/UbcH5C 0.018 0 -9999 0 -10000 0 0
ATM 0.012 0 -9999 0 -10000 0 0
TNF/TNFR1A 0.017 0.022 -9999 0 -10000 0 0
TRAF6 0.012 0 -9999 0 -10000 0 0
PRKCA 0.012 0 -9999 0 -10000 0 0
CHUK 0.012 0 -9999 0 -10000 0 0
UBE2D3 0.012 0 -9999 0 -10000 0 0
TNF 0.01 0.031 -9999 0 -0.44 2 2
NF kappa B1 p50/RelA 0.035 0 -9999 0 -10000 0 0
BCL10 0.011 0.022 -9999 0 -0.44 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.038 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.015 0 -9999 0 -10000 0 0
TNFRSF1A 0.012 0 -9999 0 -10000 0 0
IKK complex 0.044 0.041 -9999 0 -0.44 1 1
CYLD 0.011 0.022 -9999 0 -0.44 1 1
IKK complex/PKC alpha 0.047 0.039 -9999 0 -0.43 1 1
BARD1 signaling events

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
BARD1/CSTF1 0.018 0 -9999 0 -10000 0 0
ATM 0.012 0 -9999 0 -10000 0 0
UBE2D3 0.012 0 -9999 0 -10000 0 0
PRKDC 0.012 0 -9999 0 -10000 0 0
ATR 0.012 0 -9999 0 -10000 0 0
UBE2L3 0.012 0 -9999 0 -10000 0 0
FANCD2 0.022 0.015 -9999 0 -0.28 1 1
protein ubiquitination 0.03 0.036 -9999 0 -0.4 3 3
XRCC5 0.012 0 -9999 0 -10000 0 0
XRCC6 0.012 0 -9999 0 -10000 0 0
M/R/N Complex 0.024 0.013 -9999 0 -10000 0 0
MRE11A 0.012 0.001 -9999 0 -10000 0 0
DNA-PK 0.025 0 -9999 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.045 0.008 -9999 0 -10000 0 0
FANCF 0.012 0 -9999 0 -10000 0 0
BRCA1 0.012 0 -9999 0 -10000 0 0
CCNE1 0.007 0.062 -9999 0 -0.74 3 3
CDK2/Cyclin E1 0.014 0.048 -9999 0 -0.56 3 3
FANCG 0.012 0 -9999 0 -10000 0 0
BRCA1/BACH1/BARD1 0.018 0 -9999 0 -10000 0 0
FANCE 0.012 0 -9999 0 -10000 0 0
FANCC 0.012 0 -9999 0 -10000 0 0
NBN 0.011 0.022 -9999 0 -0.44 1 1
FANCA 0.012 0 -9999 0 -10000 0 0
DNA repair 0.061 0.01 -9999 0 -10000 0 0
BRCA1/BARD1/ubiquitin 0.018 0 -9999 0 -10000 0 0
BARD1/DNA-PK 0.032 0 -9999 0 -10000 0 0
FANCL 0.012 0 -9999 0 -10000 0 0
mRNA polyadenylation -0.018 0 -9999 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.033 0.018 -9999 0 -0.31 1 1
BRCA1/BACH1/BARD1/TopBP1 0.025 0 -9999 0 -10000 0 0
BRCA1/BARD1/P53 0.032 0 -9999 0 -10000 0 0
BARD1/CSTF1/BRCA1 0.025 0 -9999 0 -10000 0 0
BRCA1/BACH1 0.012 0 -9999 0 -10000 0 0
BARD1 0.012 0 -9999 0 -10000 0 0
PCNA 0.012 0 -9999 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.025 0 -9999 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.025 0 -9999 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.032 0 -9999 0 -10000 0 0
BARD1/DNA-PK/P53 0.037 0 -9999 0 -10000 0 0
BRCA1/BARD1/Ubiquitin 0.018 0 -9999 0 -10000 0 0
BRCA1/BARD1/CTIP 0.029 0.017 -9999 0 -10000 0 0
FA complex 0.035 0 -9999 0 -10000 0 0
BARD1/EWS 0.018 0 -9999 0 -10000 0 0
RBBP8 0.018 0.022 -9999 0 -0.31 2 2
TP53 0.012 0 -9999 0 -10000 0 0
TOPBP1 0.012 0 -9999 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.031 0 -9999 0 -10000 0 0
BRCA1/BARD1 0.034 0.037 -9999 0 -0.4 3 3
CSTF1 0.012 0 -9999 0 -10000 0 0
BARD1/EWS-Fli1 0.009 0 -9999 0 -10000 0 0
CDK2 0.012 0 -9999 0 -10000 0 0
UniProt:Q9BZD1 0 0 -9999 0 -10000 0 0
RAD51 0.012 0 -9999 0 -10000 0 0
RAD50 0.012 0 -9999 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.018 0 -9999 0 -10000 0 0
EWSR1 0.012 0 -9999 0 -10000 0 0
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.043 0.011 -10000 0 -10000 0 0
CLOCK 0.015 0.002 -10000 0 -10000 0 0
TIMELESS/CRY2 0.038 0.011 -10000 0 -10000 0 0
DEC1/BMAL1 0.006 0.067 -10000 0 -0.55 6 6
ATR 0.012 0 -10000 0 -10000 0 0
NR1D1 0.035 0.027 -10000 0 -0.53 1 1
ARNTL 0.015 0.002 -10000 0 -10000 0 0
TIMELESS 0.036 0.012 -10000 0 -10000 0 0
NPAS2 0.015 0.002 -10000 0 -10000 0 0
CRY2 0.012 0 -10000 0 -10000 0 0
mol:CO -0.012 0.005 0.096 1 -10000 0 1
CHEK1 0.012 0 -10000 0 -10000 0 0
mol:HEME 0.012 0.005 -10000 0 -0.096 1 1
PER1 0.011 0.022 -10000 0 -0.44 1 1
BMAL/CLOCK/NPAS2 0.039 0.005 -10000 0 -10000 0 0
BMAL1/CLOCK 0.042 0.033 -10000 0 -10000 0 0
S phase of mitotic cell cycle 0.043 0.011 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.043 0.011 -10000 0 -10000 0 0
mol:NADPH 0.012 0.005 -10000 0 -0.096 1 1
PER1/TIMELESS 0.037 0.016 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 -0.006 0.087 -10000 0 -0.74 6 6
Aurora C signaling

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
INCENP 0.012 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.022 0.017 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0 0.005 -9999 0 -10000 0 0
AURKB 0.012 0 -9999 0 -10000 0 0
AURKC 0.01 0.031 -9999 0 -0.44 2 2
Insulin-mediated glucose transport

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Insulin responsive Vesicles 0.02 0.064 -10000 0 -0.31 1 1
CaM/Ca2+ 0.009 0 -10000 0 -10000 0 0
AKT1 0.012 0 -10000 0 -10000 0 0
AKT2 0.012 0 -10000 0 -10000 0 0
STXBP4 0.011 0.022 -10000 0 -0.44 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.018 0.074 0.27 5 -0.35 1 6
YWHAZ 0.012 0 -10000 0 -10000 0 0
CALM1 0.012 0 -10000 0 -10000 0 0
YWHAQ 0.012 0 -10000 0 -10000 0 0
TBC1D4 0.019 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.012 0 -10000 0 -10000 0 0
YWHAB 0.012 0 -10000 0 -10000 0 0
SNARE/Synip 0.024 0.013 -10000 0 -10000 0 0
YWHAG 0.012 0 -10000 0 -10000 0 0
ASIP -0.002 0.08 -10000 0 -0.74 5 5
PRKCI 0.01 0.031 -10000 0 -0.44 2 2
AS160/CaM/Ca2+ 0.009 0 -10000 0 -10000 0 0
RHOQ 0.012 0 -10000 0 -10000 0 0
GYS1 0.026 0 -10000 0 -10000 0 0
PRKCZ 0.012 0 -10000 0 -10000 0 0
TRIP10 0.011 0.022 -10000 0 -0.44 1 1
TC10/GTP/CIP4/Exocyst 0.016 0.013 -10000 0 -0.26 1 1
AS160/14-3-3 0.039 0.01 -10000 0 -10000 0 0
VAMP2 0.012 0 -10000 0 -10000 0 0
SLC2A4 0.017 0.079 0.28 5 -0.39 1 6
STX4 0.012 0 -10000 0 -10000 0 0
GSK3B 0.022 0 -10000 0 -10000 0 0
SFN 0.011 0.022 -10000 0 -0.44 1 1
LNPEP 0.012 0.001 -10000 0 -10000 0 0
YWHAE 0.012 0 -10000 0 -10000 0 0
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.012 0 -10000 0 -10000 0 0
mol:PIP3 0.001 0.016 0.24 2 -10000 0 2
FRAP1 0.013 0.008 -10000 0 -10000 0 0
AKT1 0.024 0.016 0.21 2 -10000 0 2
INSR 0.012 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.008 0 -10000 0 -10000 0 0
mol:GTP 0.03 0.009 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.001 0.014 -10000 0 -0.26 1 1
TSC2 0.012 0 -10000 0 -10000 0 0
RHEB/GDP 0 0.006 -10000 0 -10000 0 0
TSC1 0.012 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.015 0.001 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.001 0.016 -10000 0 -0.31 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.012 0 -10000 0 -10000 0 0
RPS6KB1 0.023 0.02 -10000 0 -0.3 1 1
MAP3K5 0.009 0 -10000 0 -10000 0 0
PIK3R1 0.012 0 -10000 0 -10000 0 0
apoptosis 0.009 0 -10000 0 -10000 0 0
mol:LY294002 0 0 -10000 0 -10000 0 0
EIF4B 0.027 0.018 -10000 0 -0.26 1 1
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.03 0.022 -10000 0 -0.31 1 1
eIF4E/eIF4G1/eIF4A1 -0.001 0.008 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.023 0.001 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.026 0.01 0.15 2 -10000 0 2
FKBP1A 0.012 0 -10000 0 -10000 0 0
RHEB/GTP 0 0.006 -10000 0 -10000 0 0
mol:Amino Acids 0 0 -10000 0 -10000 0 0
FKBP12/Rapamycin 0.01 0.001 -10000 0 -10000 0 0
PDPK1 0.001 0.014 0.21 2 -10000 0 2
EIF4E 0.01 0.031 -10000 0 -0.44 2 2
ASK1/PP5C 0.021 0.005 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.013 0.029 -10000 0 -0.42 2 2
TSC1/TSC2 0.034 0.009 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RPS6 0.011 0.036 -10000 0 -0.74 1 1
PPP5C 0.012 0 -10000 0 -10000 0 0
EIF4G1 0.012 0 -10000 0 -10000 0 0
IRS1 0.008 0.001 -10000 0 -10000 0 0
INS 0 0 -10000 0 -10000 0 0
PTEN 0.01 0.031 -10000 0 -0.44 2 2
PDK2 0 0.02 0.21 2 -10000 0 2
EIF4EBP1 0.01 0.019 -10000 0 -10000 0 0
PIK3CA 0.012 0.001 -10000 0 -10000 0 0
PPP2R5D 0.018 0.007 -10000 0 -10000 0 0
peptide biosynthetic process 0.014 0.022 -10000 0 -0.44 1 1
RHEB 0.012 0 -10000 0 -10000 0 0
EIF4A1 0.012 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 0.003 2 -10000 0 2
EEF2 0.014 0.022 -10000 0 -0.45 1 1
eIF4E/4E-BP1 0.016 0.024 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.019 0 -9999 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.029 0.012 -9999 0 -10000 0 0
CDKN1B 0.03 0.012 -9999 0 -10000 0 0
CDKN1A 0.03 0.016 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
PRKDC 0.012 0 -9999 0 -10000 0 0
FOXO3 0.031 0.006 -9999 0 -10000 0 0
AKT1 0.026 0.006 -9999 0 -10000 0 0
BAD 0.011 0.022 -9999 0 -0.44 1 1
AKT3 0.011 0.036 -9999 0 -0.29 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
FOXO4 0.031 0.006 -9999 0 -10000 0 0
AKT1/ASK1 0.03 0.006 -9999 0 -10000 0 0
BAD/YWHAZ 0.024 0.013 -9999 0 -10000 0 0
RICTOR 0.008 0.043 -9999 0 -0.44 4 4
RAF1 0.012 0 -9999 0 -10000 0 0
JNK cascade -0.029 0.006 -9999 0 -10000 0 0
TSC1 0.031 0.006 -9999 0 -10000 0 0
YWHAZ 0.012 0 -9999 0 -10000 0 0
AKT1/RAF1 0.032 0.006 -9999 0 -10000 0 0
EP300 0.012 0 -9999 0 -10000 0 0
mol:GDP 0.026 0.006 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
TSC2 0.031 0.006 -9999 0 -10000 0 0
YWHAQ 0.012 0 -9999 0 -10000 0 0
TBC1D4 0.02 0 -9999 0 -10000 0 0
MAP3K5 0.012 0 -9999 0 -10000 0 0
MAPKAP1 0.012 0 -9999 0 -10000 0 0
negative regulation of cell cycle -0.037 0.007 -9999 0 -10000 0 0
YWHAH 0.012 0 -9999 0 -10000 0 0
AKT1S1 0.031 0.006 -9999 0 -10000 0 0
CASP9 0.031 0.006 -9999 0 -10000 0 0
YWHAB 0.012 0 -9999 0 -10000 0 0
p27Kip1/KPNA1 0.036 0.012 -9999 0 -10000 0 0
GBL 0 0 -9999 0 -10000 0 0
PDK1/Src/Hsp90 0.025 0 -9999 0 -10000 0 0
YWHAE 0.012 0 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
AKT2/p21CIP1 0.034 0.015 -9999 0 -10000 0 0
KIAA1303 0 0 -9999 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.016 0.003 -9999 0 -10000 0 0
CHUK 0.031 0.006 -9999 0 -10000 0 0
BAD/BCL-XL 0.042 0.012 -9999 0 -10000 0 0
mTORC2 0.014 0.024 -9999 0 -10000 0 0
AKT2 0.015 0 -9999 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.05 0.009 -9999 0 -10000 0 0
PDPK1 0.012 0 -9999 0 -10000 0 0
MDM2 0.03 0.012 -9999 0 -10000 0 0
MAPKKK cascade -0.031 0.006 -9999 0 -10000 0 0
MDM2/Cbp/p300 0.042 0.011 -9999 0 -10000 0 0
TSC1/TSC2 0.036 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.04 0.011 -9999 0 -10000 0 0
glucose import -0.003 0.076 -9999 0 -10000 0 0
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.026 0.006 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
SLC2A4 -0.003 0.077 -9999 0 -10000 0 0
GSK3A 0.031 0.006 -9999 0 -10000 0 0
FOXO1 0.03 0.012 -9999 0 -10000 0 0
GSK3B 0.031 0.006 -9999 0 -10000 0 0
SFN 0.011 0.022 -9999 0 -0.44 1 1
G1/S transition of mitotic cell cycle 0.036 0.006 -9999 0 -10000 0 0
p27Kip1/14-3-3 family 0.041 0.009 -9999 0 -10000 0 0
PRKACA 0.012 0 -9999 0 -10000 0 0
KPNA1 0.012 0 -9999 0 -10000 0 0
HSP90AA1 0.012 0 -9999 0 -10000 0 0
YWHAG 0.012 0 -9999 0 -10000 0 0
RHEB 0.012 0 -9999 0 -10000 0 0
CREBBP 0.012 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.001 0.017 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.04 0.02 -9999 0 -10000 0 0
SUMO1 0.01 0.031 -9999 0 -0.44 2 2
ZFPM1 -0.002 0.1 -9999 0 -0.74 8 8
NPC/RanGAP1/SUMO1/Ubc9 0.018 0.014 -9999 0 -10000 0 0
FKBP3 0.011 0.022 -9999 0 -0.44 1 1
Histones 0.041 0.01 -9999 0 -10000 0 0
YY1/LSF 0.017 0.047 -9999 0 -10000 0 0
SMG5 0.012 0 -9999 0 -10000 0 0
RAN 0.012 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 0.029 0.016 -9999 0 -10000 0 0
I kappa B alpha/HDAC1 0.028 0.011 -9999 0 -10000 0 0
SAP18 0.012 0 -9999 0 -10000 0 0
RELA 0.032 0.016 -9999 0 -10000 0 0
HDAC1/Smad7 0.024 0.013 -9999 0 -10000 0 0
RANGAP1 0.012 0 -9999 0 -10000 0 0
HDAC3/TR2 0.028 0.011 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.04 0.009 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.035 0.014 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.003 0.065 -9999 0 -0.44 9 9
GATA1 0.008 0.006 -9999 0 -10000 0 0
Mad/Max 0.017 0.022 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.045 0.027 -9999 0 -10000 0 0
RBBP7 0.012 0 -9999 0 -10000 0 0
NPC 0.007 0 -9999 0 -10000 0 0
RBBP4 0.012 0 -9999 0 -10000 0 0
MAX 0.012 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.012 0 -9999 0 -10000 0 0
NFKBIA 0.024 0.013 -9999 0 -10000 0 0
KAT2B -0.007 0.091 -9999 0 -0.44 18 18
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.037 0 -9999 0 -10000 0 0
SIN3 complex 0.032 0 -9999 0 -10000 0 0
SMURF1 0.012 0 -9999 0 -10000 0 0
CHD3 0.012 0 -9999 0 -10000 0 0
SAP30 0.012 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.012 0 -9999 0 -10000 0 0
YY1/HDAC3 0.029 0.04 -9999 0 -10000 0 0
YY1/HDAC2 0.018 0.045 -9999 0 -10000 0 0
YY1/HDAC1 0.018 0.045 -9999 0 -10000 0 0
NuRD/MBD2 Complex (MeCP1) 0.041 0 -9999 0 -10000 0 0
PPARG 0.031 0.029 -9999 0 -10000 0 0
HDAC8/hEST1B 0.025 0 -9999 0 -10000 0 0
UBE2I 0.012 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.012 0 -9999 0 -10000 0 0
TNFRSF1A 0.012 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.028 0.016 -9999 0 -10000 0 0
MBD3L2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.024 0.013 -9999 0 -10000 0 0
CREBBP 0.012 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.043 0.009 -9999 0 -10000 0 0
HDAC1 0.012 0 -9999 0 -10000 0 0
HDAC3 0.024 0.013 -9999 0 -10000 0 0
HDAC2 0.012 0 -9999 0 -10000 0 0
YY1 0.015 0.053 -9999 0 -10000 0 0
HDAC8 0.012 0 -9999 0 -10000 0 0
SMAD7 0.011 0.022 -9999 0 -0.44 1 1
NCOR2 0.011 0.022 -9999 0 -0.44 1 1
MXD1 0.01 0.031 -9999 0 -0.44 2 2
STAT3 0.022 0 -9999 0 -10000 0 0
NFKB1 0.012 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.012 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 0.024 0.043 -9999 0 -10000 0 0
YY1/SAP30/HDAC1 0.025 0.042 -9999 0 -10000 0 0
EP300 0.012 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.022 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.013 -9999 0 -10000 0 0
histone deacetylation 0.041 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.035 0.011 -9999 0 -10000 0 0
nuclear export -0.025 0 -9999 0 -10000 0 0
PRKACA 0.012 0 -9999 0 -10000 0 0
GATAD2B 0.012 0 -9999 0 -10000 0 0
GATAD2A 0.012 0 -9999 0 -10000 0 0
GATA2/HDAC3 0.023 0.037 -9999 0 -10000 0 0
GATA1/HDAC1 0.015 0.004 -9999 0 -10000 0 0
GATA1/HDAC3 0.025 0.012 -9999 0 -10000 0 0
CHD4 0.012 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A 0.017 0.022 -9999 0 -10000 0 0
SIN3/HDAC complex/Mad/Max 0.04 0.012 -9999 0 -10000 0 0
NuRD Complex 0.048 0.009 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.039 0.01 -9999 0 -10000 0 0
SIN3B 0.012 0 -9999 0 -10000 0 0
MTA2 0.012 0 -9999 0 -10000 0 0
SIN3A 0.012 0 -9999 0 -10000 0 0
XPO1 0.012 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.026 0.021 -9999 0 -0.29 2 2
HDAC complex 0.032 0 -9999 0 -10000 0 0
GATA1/Fog1 0.004 0.078 -9999 0 -0.56 8 8
FKBP25/HDAC1/HDAC2 0.024 0.013 -9999 0 -10000 0 0
TNF 0.01 0.031 -9999 0 -0.44 2 2
negative regulation of cell growth 0.04 0.012 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.041 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.029 0.012 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.035 0.02 -9999 0 -10000 0 0
SIN3/HDAC complex/NCoR1 0.039 0 -9999 0 -10000 0 0
TFCP2 0.011 0.022 -9999 0 -0.44 1 1
NR2C1 0.012 0 -9999 0 -10000 0 0
MBD3 0.011 0.022 -9999 0 -0.44 1 1
MBD2 0.012 0 -9999 0 -10000 0 0
Atypical NF-kappaB 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
BCL3/RelA 0.018 0 -9999 0 -10000 0 0
FBXW11 0.012 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.023 0.001 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.038 0.026 -9999 0 -10000 0 0
NFKBIA 0.021 0.029 -9999 0 -10000 0 0
MAPK14 0.012 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.024 0 -9999 0 -10000 0 0
ARRB2 0.015 0 -9999 0 -10000 0 0
REL 0.012 0.001 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.024 0 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.024 0 -9999 0 -10000 0 0
PIK3CA 0.012 0.001 -9999 0 -10000 0 0
NF kappa B1 p50 dimer 0.018 0 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
NFKB1 0.019 0 -9999 0 -10000 0 0
RELA 0.012 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.026 0.028 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.041 0.026 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
PI3K 0.018 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.026 0.029 -9999 0 -10000 0 0
IKBKB 0.012 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.012 0 -9999 0 -10000 0 0
SYK 0.012 0 -9999 0 -10000 0 0
I kappa B alpha/PIK3R1 0.026 0.028 -9999 0 -10000 0 0
cell death 0.039 0.025 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.023 0.001 -9999 0 -10000 0 0
LCK -0.002 0.099 -9999 0 -0.67 9 9
BCL3 0.012 0 -9999 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.012 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.003 -9999 0 -10000 0 0
MDM2/SUMO1 0.025 0.029 -9999 0 -0.39 2 2
HDAC4 0.012 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0 0.003 -9999 0 -10000 0 0
SUMO1 0.01 0.031 -9999 0 -0.44 2 2
NPC/RanGAP1/SUMO1 0.014 0.014 -9999 0 -0.19 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.023 0.013 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.012 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.012 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.026 0.021 -9999 0 -0.29 2 2
SUMO1/HDAC1 0.026 0.021 -9999 0 -0.29 2 2
RANGAP1 0.012 0 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.03 0.026 -9999 0 -0.45 1 1
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.018 0.014 -9999 0 -10000 0 0
Ran/GTP 0.023 0.013 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.011 0.022 -9999 0 -0.44 1 1
UBE2I 0.012 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.028 0.012 -9999 0 -10000 0 0
NPC 0.007 0 -9999 0 -10000 0 0
PIAS2 0.012 0.001 -9999 0 -10000 0 0
PIAS1 0.012 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.024 0.013 -9999 0 -10000 0 0
E-cadherin/beta catenin 0.018 0 -9999 0 -10000 0 0
CTNNB1 0.012 0 -9999 0 -10000 0 0
JUP 0.011 0.022 -9999 0 -0.44 1 1
CDH1 0.012 0 -9999 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex -0.002 0.029 -9999 0 -0.42 2 2
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.018 0 -9999 0 -10000 0 0
AP2 0.018 0.016 -9999 0 -0.3 1 1
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.017 0 -9999 0 -10000 0 0
CLTB 0.011 0.022 -9999 0 -0.44 1 1
coatomer protein complex/ARF1/GTP/ER cargo protein 0.022 0.011 -9999 0 -10000 0 0
CD4 -0.005 0.086 -9999 0 -0.44 16 16
CLTA 0.012 0 -9999 0 -10000 0 0
mol:GTP 0.001 0 -9999 0 -10000 0 0
ARFGAP1 0.008 0.032 -9999 0 -0.44 2 2
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
ARF1/GTP 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.021 0.027 -9999 0 -0.37 2 2
mol:Choline 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.012 0 -9999 0 -10000 0 0
DDEF1 0 0 -9999 0 -10000 0 0
ARF1/GDP 0.006 0.024 -9999 0 -0.33 2 2
AP2M1 0.012 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0.015 0 -9999 0 -10000 0 0
Rac/GTP 0.01 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.021 0.024 -9999 0 -0.42 1 1
ARFIP2 0.011 0 -9999 0 -10000 0 0
COPA 0.012 0 -9999 0 -10000 0 0
RAC1 0.012 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.022 0.007 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0.009 0 -9999 0 -10000 0 0
GGA3 0.012 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0.017 0 -9999 0 -10000 0 0
AP2A1 0.011 0.022 -9999 0 -0.44 1 1
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.022 0.027 -9999 0 -0.35 2 2
ARF1/GDP/Membrin 0.017 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0.016 0 -9999 0 -10000 0 0
CYTH2 0.012 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0.017 0 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0.009 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.022 0.043 -9999 0 -0.34 1 1
PLD2 0 0 -9999 0 -10000 0 0
ARF-GAP1/v-SNARE 0.008 0.032 -9999 0 -0.44 2 2
PIP5K1A 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.019 0 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.008 0.032 -9999 0 -0.44 2 2
GOSR2 0 0 -9999 0 -10000 0 0
USO1 0 0 -9999 0 -10000 0 0
GBF1 0 0 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0.018 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.014 0.053 -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 0.018 0 -9999 0 -9999 0 0
FBXW11 0.012 0 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.012 0 -9999 0 -9999 0 0
CHUK 0.012 0 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.037 0 -9999 0 -9999 0 0
NFKB1 0.012 0 -9999 0 -9999 0 0
MAP3K14 0.012 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.018 0 -9999 0 -9999 0 0
RELB 0.012 0 -9999 0 -9999 0 0
NFKB2 0.012 0 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.017 0 -9999 0 -9999 0 0
regulation of B cell activation 0.016 0 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 432 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.QG.A5Z2 TCGA.QG.A5Z1 TCGA.QG.A5YX TCGA.QG.A5YW
109_MAP3K5 0.046 0.046 0.046 0.046
47_PPARGC1A 0.012 0.012 0.012 0.012
105_BMP4 0.012 0.012 0.012 0.012
105_BMP6 0.012 -0.44 -0.44 0.012
105_BMP7 0.012 -0.74 0.012 0.012
105_BMP2 0.012 0.012 0.012 0.012
131_RELN/VLDLR -0.65 -0.43 -0.65 -0.43
30_TGFB1/TGF beta receptor Type II 0.012 0.012 0.012 0.012
84_STAT5B 0.017 -0.079 -0.034 0.024
84_STAT5A 0.017 -0.079 -0.034 0.024
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/COAD-TP/8100371/COAD-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

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

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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