PARADIGM pathway analysis of mRNASeq expression data
Colorectal Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1JW8D8K
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1JW8D8K
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 36 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 234
Syndecan-1-mediated signaling events 205
Reelin signaling pathway 171
Osteopontin-mediated events 107
Lissencephaly gene (LIS1) in neuronal migration and development 101
FOXA2 and FOXA3 transcription factor networks 85
IL4-mediated signaling events 82
Glypican 1 network 81
Syndecan-4-mediated signaling events 71
Ephrin A reverse signaling 66
Results
Summary Table

The following list describes the columns found in Table 2.

  • Pathway.Name = Full pathway name of curated PARADIGM pathway

  • Significance.Ratio = (Ave.Num.Perturbations)/ (Cohort Size) where Cohort Size is 623 . Pathway is significant if Significance.Ratio > 0.05 .

  • Avg.Num.Perturbations = Average number of samples with perturbations across the pathway concepts determined by a background permutation model (>2 standard deviations away from the permuted distribution)

  • Total.Perturbations = Total number of perturbed concepts across all samples (>2 standard deviations away from the permuted distribution)

  • Num.Entities = Number of concepts that belong to the pathway

  • Min.Mean.Truth = Minimum IPL for concepts in the pathway among real samples

  • Max.Mean.Truth = Maximum IPL for concepts in the pathway among real samples

  • Min.Mean.Within = Minimum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Max.Mean.Within = Maximum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Min.Mean.Any = Minimum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes)

  • Max.Mean.Any = Maximum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes).

Table 2.  Get Full Table This summary table provides a report of cancer type specific pathway perturbations. Click on the links in the first column to display more detailed results for each pathway. A pathway is defined as significant (red number in Significance.Ratio column) if the Ave.Num.Perturbationsis > 5% of the cohort size ( 623 ).

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
TCGA08_retinoblastoma 0.3756 234 1875 8 -0.14 0.097 1000 -1000 -0.015 -1000
Syndecan-1-mediated signaling events 0.3291 205 6992 34 -0.72 0.013 1000 -1000 -0.062 -1000
Reelin signaling pathway 0.2745 171 9592 56 -0.58 0.036 1000 -1000 -0.075 -1000
Osteopontin-mediated events 0.1717 107 4091 38 -0.31 0.02 1000 -1000 -0.089 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1621 101 5457 54 -0.52 0.024 1000 -1000 -0.094 -1000
FOXA2 and FOXA3 transcription factor networks 0.1364 85 3945 46 -0.7 0.022 1000 -1000 -0.14 -1000
IL4-mediated signaling events 0.1316 82 7473 91 -0.81 0.59 1000 -1000 -0.19 -1000
Glypican 1 network 0.1300 81 3912 48 -0.34 0.025 1000 -1000 -0.052 -1000
Syndecan-4-mediated signaling events 0.1140 71 4786 67 -0.4 0.047 1000 -1000 -0.068 -1000
Ephrin A reverse signaling 0.1059 66 467 7 -0.084 0 1000 -1000 -0.022 -1000
BCR signaling pathway 0.1011 63 6317 99 -0.2 0.013 1000 -1000 -0.087 -1000
IL23-mediated signaling events 0.1011 63 3795 60 -0.47 0.013 1000 -1000 -0.22 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0995 62 4862 78 -0.16 0.069 1000 -1000 -0.075 -1000
HIF-1-alpha transcription factor network 0.0867 54 4179 76 -0.77 0.019 1000 -1000 -0.18 -1000
Caspase cascade in apoptosis 0.0851 53 3975 74 -0.13 0.066 1000 -1000 -0.046 -1000
Endothelins 0.0835 52 5068 96 -0.38 0.088 1000 -1000 -0.093 -1000
Glucocorticoid receptor regulatory network 0.0770 48 5525 114 -0.64 0.29 1000 -1000 -0.081 -1000
Presenilin action in Notch and Wnt signaling 0.0754 47 2910 61 -0.5 0.21 1000 -1000 -0.061 -1000
Fc-epsilon receptor I signaling in mast cells 0.0738 46 4525 97 -0.14 0.032 1000 -1000 -0.084 -1000
Visual signal transduction: Rods 0.0738 46 2404 52 -0.22 0.013 1000 -1000 -0.09 -1000
Signaling events mediated by the Hedgehog family 0.0722 45 2386 52 -0.12 0.11 1000 -1000 -0.055 -1000
Calcium signaling in the CD4+ TCR pathway 0.0722 45 1402 31 -0.47 0.013 1000 -1000 -0.065 -1000
BMP receptor signaling 0.0706 44 3587 81 -0.27 0.044 1000 -1000 -0.093 -1000
Ephrin B reverse signaling 0.0690 43 2091 48 -0.15 0.067 1000 -1000 -0.058 -1000
Syndecan-2-mediated signaling events 0.0642 40 2824 69 -0.41 0.036 1000 -1000 -0.044 -1000
IL1-mediated signaling events 0.0626 39 2446 62 -0.21 0.018 1000 -1000 -0.1 -1000
Canonical Wnt signaling pathway 0.0626 39 2021 51 -0.5 0.22 1000 -1000 -0.069 -1000
Effects of Botulinum toxin 0.0626 39 1023 26 -0.094 0.019 1000 -1000 -0.061 -1000
Ras signaling in the CD4+ TCR pathway 0.0610 38 654 17 -0.083 0.024 1000 -1000 -0.037 -1000
JNK signaling in the CD4+ TCR pathway 0.0594 37 634 17 -0.11 0.017 1000 -1000 -0.045 -1000
p75(NTR)-mediated signaling 0.0578 36 4567 125 -0.88 0.037 1000 -1000 -0.1 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0578 36 2456 68 -0.5 0.046 1000 -1000 -0.12 -1000
TCGA08_p53 0.0546 34 243 7 -0.1 0.052 1000 -1000 -0.014 -1000
Syndecan-3-mediated signaling events 0.0546 34 1204 35 -0.41 0.037 1000 -1000 -0.05 -1000
Wnt signaling 0.0546 34 238 7 -0.14 0.013 1000 -1000 -0.039 -1000
amb2 Integrin signaling 0.0530 33 2765 82 -0.16 0.017 1000 -1000 -0.075 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0498 31 2731 88 -0.26 0.072 1000 -1000 -0.1 -1000
Signaling events mediated by PRL 0.0433 27 943 34 -0.11 0.052 1000 -1000 -0.042 -1000
EPHB forward signaling 0.0417 26 2238 85 -0.15 0.075 1000 -1000 -0.092 -1000
Plasma membrane estrogen receptor signaling 0.0417 26 2247 86 -0.22 0.066 1000 -1000 -0.091 -1000
TCR signaling in naïve CD8+ T cells 0.0401 25 2370 93 -0.065 0.037 1000 -1000 -0.089 -1000
LPA receptor mediated events 0.0385 24 2480 102 -0.2 0.024 1000 -1000 -0.09 -1000
IL12-mediated signaling events 0.0369 23 2032 87 -0.18 0.034 1000 -1000 -0.15 -1000
Visual signal transduction: Cones 0.0369 23 907 38 -0.12 0.013 1000 -1000 -0.034 -1000
Nectin adhesion pathway 0.0369 23 1503 63 -0.68 0.041 1000 -1000 -0.065 -1000
S1P5 pathway 0.0369 23 398 17 -0.14 0.054 1000 -1000 -0.036 -1000
HIF-2-alpha transcription factor network 0.0369 23 995 43 -0.34 0.16 1000 -1000 -0.07 -1000
Signaling events regulated by Ret tyrosine kinase 0.0353 22 1812 82 -0.15 0.013 1000 -1000 -0.088 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0353 22 1195 52 -0.19 0.028 1000 -1000 -0.04 -1000
ErbB4 signaling events 0.0321 20 1426 69 -0.29 0.066 1000 -1000 -0.11 -1000
Retinoic acid receptors-mediated signaling 0.0321 20 1176 58 -0.25 0.026 1000 -1000 -0.069 -1000
S1P4 pathway 0.0321 20 503 25 -0.14 0.023 1000 -1000 -0.041 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0305 19 532 28 -0.14 0.023 1000 -1000 -0.043 -1000
Noncanonical Wnt signaling pathway 0.0305 19 502 26 -0.14 0.013 1000 -1000 -0.065 -1000
EGFR-dependent Endothelin signaling events 0.0305 19 409 21 -0.086 0.019 1000 -1000 -0.068 -1000
Thromboxane A2 receptor signaling 0.0289 18 1902 105 -0.22 0.074 1000 -1000 -0.07 -1000
Signaling events mediated by HDAC Class III 0.0289 18 726 40 -0.14 0.023 1000 -1000 -0.03 -1000
S1P1 pathway 0.0289 18 678 36 -0.14 0.015 1000 -1000 -0.059 -1000
Signaling mediated by p38-alpha and p38-beta 0.0289 18 803 44 -0.038 0.013 1000 -1000 -0.047 -1000
Glypican 2 network 0.0289 18 75 4 -0.011 -0.005 1000 -1000 -0.02 -1000
IL27-mediated signaling events 0.0289 18 929 51 -0.18 0.023 1000 -1000 -0.075 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0273 17 2043 120 -0.13 0.11 1000 -1000 -0.071 -1000
Arf6 signaling events 0.0241 15 961 62 -0.13 0.031 1000 -1000 -0.05 -1000
Signaling events mediated by PTP1B 0.0241 15 1203 76 -0.34 0.052 1000 -1000 -0.087 -1000
IL6-mediated signaling events 0.0241 15 1164 75 -0.11 0.05 1000 -1000 -0.075 -1000
S1P3 pathway 0.0241 15 666 42 -0.14 0.025 1000 -1000 -0.041 -1000
Regulation of nuclear SMAD2/3 signaling 0.0225 14 1976 136 -0.42 0.092 1000 -1000 -0.062 -1000
Aurora A signaling 0.0225 14 864 60 -0.24 0.035 1000 -1000 -0.037 -1000
Integrins in angiogenesis 0.0225 14 1243 84 -0.31 0.031 1000 -1000 -0.085 -1000
Nongenotropic Androgen signaling 0.0225 14 773 52 -0.14 0.025 1000 -1000 -0.058 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0209 13 463 34 -0.01 0.017 1000 -1000 -0.041 -1000
Regulation of Telomerase 0.0209 13 1332 102 -0.37 0.042 1000 -1000 -0.11 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0193 12 457 37 -0.18 0.033 1000 -1000 -0.056 -1000
Signaling mediated by p38-gamma and p38-delta 0.0193 12 188 15 -0.042 0.023 1000 -1000 -0.037 -1000
Regulation of Androgen receptor activity 0.0193 12 843 70 -0.2 0.025 1000 -1000 -0.075 -1000
FAS signaling pathway (CD95) 0.0177 11 562 47 -0.055 0.027 1000 -1000 -0.056 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0177 11 375 33 -0.14 0.036 1000 -1000 -0.041 -1000
Coregulation of Androgen receptor activity 0.0161 10 796 76 -0.19 0.047 1000 -1000 -0.034 -1000
a4b1 and a4b7 Integrin signaling 0.0161 10 50 5 -0.003 0.009 1000 -1000 -0.024 -1000
Cellular roles of Anthrax toxin 0.0161 10 410 39 -0.053 0.013 1000 -1000 -0.022 -1000
IFN-gamma pathway 0.0161 10 744 68 -0.065 0.031 1000 -1000 -0.097 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0144 9 763 83 -0.25 0.061 1000 -1000 -0.076 -1000
Class I PI3K signaling events 0.0144 9 679 73 -0.14 0.031 1000 -1000 -0.072 -1000
Aurora B signaling 0.0144 9 668 67 -0.36 0.075 1000 -1000 -0.058 -1000
ErbB2/ErbB3 signaling events 0.0128 8 568 65 -0.049 0.032 1000 -1000 -0.072 -1000
PDGFR-beta signaling pathway 0.0128 8 861 97 -0.18 0.043 1000 -1000 -0.083 -1000
Rapid glucocorticoid signaling 0.0112 7 143 20 -0.01 0.013 1000 -1000 -0.029 -1000
Hedgehog signaling events mediated by Gli proteins 0.0096 6 430 65 -0.14 0.051 1000 -1000 -0.069 -1000
Ceramide signaling pathway 0.0096 6 524 76 -0.086 0.044 1000 -1000 -0.053 -1000
FoxO family signaling 0.0096 6 432 64 -0.099 0.091 1000 -1000 -0.085 -1000
Regulation of p38-alpha and p38-beta 0.0096 6 373 54 -0.14 0.032 1000 -1000 -0.066 -1000
TCGA08_rtk_signaling 0.0096 6 178 26 -0.053 0.039 1000 -1000 -0.024 -1000
EPO signaling pathway 0.0080 5 320 55 -0.019 0.045 1000 -1000 -0.091 -1000
IGF1 pathway 0.0080 5 297 57 -0.082 0.026 1000 -1000 -0.1 -1000
VEGFR1 specific signals 0.0080 5 295 56 -0.026 0.042 1000 -1000 -0.066 -1000
Class IB PI3K non-lipid kinase events 0.0080 5 15 3 -0.009 0.009 1000 -1000 -0.018 -1000
FOXM1 transcription factor network 0.0080 5 298 51 -0.14 0.13 1000 -1000 -0.23 -1000
Signaling events mediated by HDAC Class II 0.0064 4 332 75 -0.046 0.03 1000 -1000 -0.041 -1000
IL2 signaling events mediated by PI3K 0.0064 4 239 58 -0.056 0.055 1000 -1000 -0.084 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0064 4 368 74 -0.086 0.063 1000 -1000 -0.092 -1000
E-cadherin signaling in keratinocytes 0.0064 4 210 43 -0.1 0.045 1000 -1000 -0.05 -1000
PLK2 and PLK4 events 0.0048 3 10 3 0.006 0.014 1000 -1000 -0.028 -1000
PLK1 signaling events 0.0048 3 333 85 -0.04 0.03 1000 -1000 -0.043 -1000
PDGFR-alpha signaling pathway 0.0048 3 151 44 -0.005 0.028 1000 -1000 -0.048 -1000
TRAIL signaling pathway 0.0048 3 167 48 -0.038 0.04 1000 -1000 -0.06 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0048 3 151 45 -0.013 0.056 1000 -1000 -0.094 -1000
IL2 signaling events mediated by STAT5 0.0048 3 81 22 0.002 0.058 1000 -1000 -0.064 -1000
Insulin Pathway 0.0048 3 242 74 -0.032 0.033 1000 -1000 -0.1 -1000
LPA4-mediated signaling events 0.0032 2 26 12 -0.094 0.016 1000 -1000 -0.032 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0032 2 226 85 -0.015 0.049 1000 -1000 -0.067 -1000
Arf6 downstream pathway 0.0032 2 94 43 -0.027 0.03 1000 -1000 -0.035 -1000
ceramide signaling pathway 0.0032 2 118 49 -0.008 0.045 1000 -1000 -0.056 -1000
Paxillin-dependent events mediated by a4b1 0.0032 2 81 36 -0.028 0.029 1000 -1000 -0.063 -1000
E-cadherin signaling in the nascent adherens junction 0.0032 2 153 76 -0.028 0.051 1000 -1000 -0.085 -1000
Arf6 trafficking events 0.0032 2 211 71 -0.037 0.035 1000 -1000 -0.073 -1000
p38 MAPK signaling pathway 0.0032 2 98 44 -0.028 0.034 1000 -1000 -0.066 -1000
Canonical NF-kappaB pathway 0.0016 1 52 39 -0.008 0.067 1000 -1000 -0.086 -1000
Circadian rhythm pathway 0.0016 1 28 22 -0.012 0.043 1000 -1000 -0.057 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0016 1 220 125 -0.002 0.073 1000 -1000 -0.091 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 8 23 0.011 0.039 1000 -1000 -0.049 -1000
BARD1 signaling events 0.0000 0 31 57 -0.031 0.059 1000 -1000 -0.058 -1000
Aurora C signaling 0.0000 0 4 7 0 0.023 1000 -1000 -0.028 -1000
Insulin-mediated glucose transport 0.0000 0 25 32 -0.002 0.038 1000 -1000 -0.047 -1000
mTOR signaling pathway 0.0000 0 29 53 -0.001 0.033 1000 -1000 -0.064 -1000
Class I PI3K signaling events mediated by Akt 0.0000 0 18 68 -0.037 0.049 1000 -1000 -0.055 -1000
Signaling events mediated by HDAC Class I 0.0000 0 84 104 -0.025 0.047 1000 -1000 -0.061 -1000
Atypical NF-kappaB pathway 0.0000 0 11 31 0 0.041 1000 -1000 -0.047 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 17 27 0 0.031 1000 -1000 -0.048 -1000
E-cadherin signaling events 0.0000 0 1 5 0.012 0.025 1000 -1000 -0.024 -1000
Arf1 pathway 0.0000 0 37 54 -0.002 0.025 1000 -1000 -0.037 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.037 1000 -1000 -0.046 -1000
Total NA 3314 182016 7203 -23 6.3 131000 -131000 -8.9 -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 -0.12 0.18 -10000 0 -0.36 219 219
CDKN2C 0.022 0.031 -10000 0 -10000 0 0
CDKN2A -0.14 0.31 -10000 0 -0.77 120 120
CCND2 0.093 0.1 0.19 306 -10000 0 306
RB1 -0.091 0.11 -10000 0 -0.2 308 308
CDK4 0.095 0.12 0.2 308 -10000 0 308
CDK6 0.097 0.12 0.21 308 -10000 0 308
G1/S progression 0.091 0.11 0.2 306 -10000 0 306
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 0.031 -9999 0 -0.75 1 1
CCL5 -0.004 0.08 -9999 0 -0.4 25 25
SDCBP 0.011 0.023 -9999 0 -0.4 2 2
FGFR/FGF2/Syndecan-1 -0.34 0.14 -9999 0 -0.44 408 408
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 -0.41 411 411
Syndecan-1/Syntenin -0.32 0.14 -9999 0 -0.41 408 408
MAPK3 -0.28 0.13 -9999 0 -0.51 46 46
HGF/MET 0.006 0.077 -9999 0 -0.38 20 20
TGFB1/TGF beta receptor Type II 0.011 0.031 -9999 0 -0.75 1 1
BSG 0.012 0.016 -9999 0 -0.4 1 1
keratinocyte migration -0.32 0.14 -9999 0 -0.41 411 411
Syndecan-1/RANTES -0.33 0.14 -9999 0 -0.41 420 420
Syndecan-1/CD147 -0.3 0.13 -9999 0 -0.39 406 406
Syndecan-1/Syntenin/PIP2 -0.31 0.13 -9999 0 -0.4 408 408
LAMA5 0.007 0.063 -9999 0 -0.68 5 5
positive regulation of cell-cell adhesion -0.3 0.13 -9999 0 -0.39 408 408
MMP7 -0.72 0.16 -9999 0 -0.75 595 595
HGF 0.002 0.067 -9999 0 -0.42 15 15
Syndecan-1/CASK -0.32 0.14 -9999 0 -0.42 408 408
Syndecan-1/HGF/MET -0.31 0.14 -9999 0 -0.4 412 412
regulation of cell adhesion -0.27 0.12 -9999 0 -0.51 41 41
HPSE 0.008 0.043 -9999 0 -0.4 7 7
positive regulation of cell migration -0.34 0.14 -9999 0 -0.44 408 408
SDC1 -0.34 0.14 -9999 0 -0.44 408 408
Syndecan-1/Collagen -0.34 0.14 -9999 0 -0.44 408 408
PPIB 0.013 0 -9999 0 -10000 0 0
MET 0.005 0.075 -9999 0 -0.75 6 6
PRKACA 0.013 0 -9999 0 -10000 0 0
MMP9 -0.045 0.2 -9999 0 -0.72 49 49
MAPK1 -0.28 0.13 -9999 0 -0.53 41 41
homophilic cell adhesion -0.34 0.14 -9999 0 -0.43 408 408
MMP1 -0.48 0.36 -9999 0 -0.75 405 405
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 0.018 0.024 -9999 0 -0.57 1 1
VLDLR -0.021 0.11 -9999 0 -0.4 52 52
CRKL 0.013 0 -9999 0 -10000 0 0
LRPAP1 0.013 0 -9999 0 -10000 0 0
FYN 0.013 0 -9999 0 -10000 0 0
ITGA3 0.012 0.016 -9999 0 -0.4 1 1
RELN/VLDLR/Fyn -0.11 0.14 -9999 0 -0.43 38 38
MAPK8IP1/MKK7/MAP3K11/JNK1 0.036 0.03 -9999 0 -0.48 2 2
AKT1 -0.12 0.15 -9999 0 -0.41 72 72
MAP2K7 0.012 0.016 -9999 0 -0.4 1 1
RAPGEF1 0.012 0.016 -9999 0 -0.4 1 1
DAB1 -0.079 0.24 -9999 0 -0.75 73 73
RELN/LRP8/DAB1 -0.45 0.27 -9999 0 -0.59 459 459
LRPAP1/LRP8 -0.39 0.27 -9999 0 -0.57 431 431
RELN/LRP8/DAB1/Fyn -0.43 0.26 -9999 0 -0.55 459 459
DAB1/alpha3/beta1 Integrin -0.4 0.24 -9999 0 -0.52 459 459
long-term memory -0.58 0.33 -9999 0 -0.7 500 500
DAB1/LIS1 -0.41 0.26 -9999 0 -0.54 459 459
DAB1/CRLK/C3G -0.4 0.24 -9999 0 -0.52 459 459
PIK3CA 0.012 0.016 -9999 0 -0.4 1 1
DAB1/NCK2 -0.42 0.26 -9999 0 -0.54 459 459
ARHGEF2 0.013 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.099 0.18 -9999 0 -0.4 164 164
CDK5R1 0.011 0.031 -9999 0 -0.75 1 1
RELN -0.18 0.2 -9999 0 -0.4 300 300
PIK3R1 0.013 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.43 0.26 -9999 0 -0.59 431 431
GRIN2A/RELN/LRP8/DAB1/Fyn -0.47 0.28 -9999 0 -0.59 481 481
MAPK8 0.013 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.15 0.2 -9999 0 -0.5 108 108
ITGB1 0.013 0 -9999 0 -10000 0 0
MAP1B -0.42 0.26 -9999 0 -0.53 471 471
RELN/LRP8 -0.43 0.26 -9999 0 -0.59 431 431
GRIN2B/RELN/LRP8/DAB1/Fyn -0.56 0.33 -9999 0 -0.68 500 500
PI3K 0.018 0.011 -9999 0 -10000 0 0
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin 0.018 0.011 -9999 0 -0.27 1 1
RAP1A -0.37 0.23 -9999 0 -0.58 260 260
PAFAH1B1 0.013 0 -9999 0 -10000 0 0
MAPK8IP1 0.011 0.035 -9999 0 -0.57 2 2
CRLK/C3G 0.018 0.011 -9999 0 -0.27 1 1
GRIN2B -0.24 0.36 -9999 0 -0.75 207 207
NCK2 0.013 0 -9999 0 -10000 0 0
neuron differentiation -0.21 0.14 -9999 0 -0.35 252 252
neuron adhesion -0.35 0.22 -9999 0 -0.55 260 260
LRP8 -0.52 0.35 -9999 0 -0.75 431 431
GSK3B -0.1 0.14 -9999 0 -0.38 72 72
RELN/VLDLR/DAB1/Fyn -0.14 0.19 -9999 0 -0.47 108 108
MAP3K11 0.012 0.016 -9999 0 -0.4 1 1
RELN/VLDLR/DAB1/P13K -0.13 0.16 -9999 0 -0.44 72 72
CDK5 0.013 0 -9999 0 -10000 0 0
MAPT -0.063 0.16 -9999 0 -0.34 146 146
neuron migration -0.32 0.2 -9999 0 -0.51 271 271
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.21 0.14 -9999 0 -0.36 252 252
RELN/VLDLR -0.41 0.25 -9999 0 -0.55 442 442
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 -0.15 0.22 -9999 0 -0.41 263 263
NF kappa B1 p50/RelA/I kappa B alpha -0.12 0.2 -9999 0 -0.5 33 33
alphaV/beta3 Integrin/Osteopontin/Src -0.23 0.29 -9999 0 -0.56 263 263
AP1 -0.12 0.22 -9999 0 -0.68 9 9
ILK -0.16 0.23 -9999 0 -0.43 263 263
bone resorption -0.12 0.2 -9999 0 -0.47 6 6
PTK2B 0.011 0.023 -9999 0 -0.4 2 2
PYK2/p130Cas -0.14 0.22 -9999 0 -0.39 263 263
ITGAV 0.015 0.004 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.018 0.016 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.19 0.26 -9999 0 -0.48 263 263
MAP3K1 -0.17 0.23 -9999 0 -0.44 263 263
JUN 0.013 0.001 -9999 0 -10000 0 0
MAPK3 -0.15 0.23 -9999 0 -0.41 263 263
MAPK1 -0.15 0.23 -9999 0 -0.41 263 263
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
NFKB1 0.013 0 -9999 0 -10000 0 0
MAPK8 -0.15 0.22 -9999 0 -0.4 263 263
ITGB3 0.01 0.043 -9999 0 -0.39 7 7
NFKBIA -0.14 0.22 -9999 0 -0.38 263 263
FOS 0.006 0.051 -9999 0 -0.39 10 10
CD44 0.013 0 -9999 0 -10000 0 0
CHUK 0.013 0 -9999 0 -10000 0 0
PLAU -0.14 0.25 -9999 0 -0.83 32 32
NF kappa B1 p50/RelA -0.15 0.18 -9999 0 -0.55 33 33
BCAR1 0.012 0.016 -9999 0 -0.4 1 1
RELA 0.013 0 -9999 0 -10000 0 0
alphaV beta3 Integrin 0.02 0.031 -9999 0 -0.28 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.17 0.23 -9999 0 -0.44 263 263
VAV3 -0.17 0.23 -9999 0 -0.43 263 263
MAP3K14 -0.17 0.24 -9999 0 -0.44 263 263
ROCK2 0.011 0.023 -9999 0 -0.4 2 2
SPP1 -0.31 0.38 -9999 0 -0.74 267 267
RAC1 0.013 0 -9999 0 -10000 0 0
Rac1/GTP -0.15 0.22 -9999 0 -0.39 263 263
MMP2 -0.096 0.19 -9999 0 -0.82 6 6
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 0.013 0 -9999 0 -10000 0 0
VLDLR -0.021 0.11 -9999 0 -0.4 52 52
LRPAP1 0.013 0 -9999 0 -10000 0 0
NUDC 0.013 0 -9999 0 -10000 0 0
RELN/LRP8 -0.43 0.26 -9999 0 -0.59 431 431
CaM/Ca2+ 0.009 0 -9999 0 -10000 0 0
KATNA1 0.013 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.39 0.24 -9999 0 -0.54 431 431
IQGAP1/CaM 0.019 0 -9999 0 -10000 0 0
DAB1 -0.079 0.24 -9999 0 -0.75 73 73
IQGAP1 0.013 0 -9999 0 -10000 0 0
PLA2G7 0.009 0.04 -9999 0 -0.4 6 6
CALM1 0.013 0 -9999 0 -10000 0 0
DYNLT1 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.39 0.27 -9999 0 -0.57 431 431
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.012 0.016 -9999 0 -0.4 1 1
CDK5R1 0.011 0.031 -9999 0 -0.75 1 1
LIS1/Poliovirus Protein 3A 0.014 0 -9999 0 -10000 0 0
CDK5R2 -0.034 0.14 -9999 0 -0.43 63 63
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.17 0.21 -9999 0 -0.55 108 108
YWHAE 0.013 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.31 0.2 -9999 0 -0.5 236 236
MAP1B -0.006 0.039 -9999 0 -0.25 16 16
RAC1 0.019 0 -9999 0 -10000 0 0
p35/CDK5 -0.34 0.22 -9999 0 -0.47 431 431
RELN -0.18 0.2 -9999 0 -0.4 300 300
PAFAH/LIS1 0.021 0.023 -9999 0 -10000 0 0
LIS1/CLIP170 0.023 0.01 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.25 0.15 -9999 0 -0.4 236 236
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.13 0.17 -9999 0 -0.48 76 76
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.34 0.21 -9999 0 -0.54 236 236
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 -0.001 0.1 -9999 0 -0.75 11 11
PAFAH1B2 0.013 0.001 -9999 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.018 0.026 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.3 0.19 -9999 0 -0.48 236 236
LRP8 -0.52 0.35 -9999 0 -0.75 431 431
NDEL1/Katanin 60 -0.31 0.2 -9999 0 -0.5 236 236
P39/CDK5 -0.36 0.22 -9999 0 -0.49 432 432
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.024 0 -9999 0 -10000 0 0
CDK5 -0.36 0.22 -9999 0 -0.5 431 431
PPP2R5D 0.013 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.02 0.008 -9999 0 -10000 0 0
CSNK2A1 0.013 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.13 0.19 -9999 0 -0.47 108 108
RELN/VLDLR -0.41 0.25 -9999 0 -0.55 442 442
CDC42 0.017 0.021 -9999 0 -0.35 2 2
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.42 0.33 -9999 0 -0.99 100 100
PCK1 -0.7 0.6 -9999 0 -1.4 276 276
HNF4A -0.49 0.39 -9999 0 -1.1 122 122
KCNJ11 -0.42 0.34 -9999 0 -1 100 100
AKT1 -0.22 0.13 -9999 0 -10000 0 0
response to starvation -0.016 0.026 -9999 0 -10000 0 0
DLK1 -0.44 0.35 -9999 0 -1 105 105
NKX2-1 -0.25 0.24 -9999 0 -0.77 75 75
ACADM -0.43 0.34 -9999 0 -1 100 100
TAT -0.66 0.58 -9999 0 -1.3 272 272
CEBPB -0.005 0.083 -9999 0 -0.75 7 7
CEBPA 0.004 0.035 -9999 0 -0.4 3 3
TTR -0.45 0.46 -9999 0 -1.1 190 190
PKLR -0.49 0.4 -9999 0 -1.1 155 155
APOA1 -0.52 0.41 -9999 0 -1.2 114 114
CPT1C -0.42 0.33 -9999 0 -0.97 111 111
ALAS1 -0.2 0.13 -9999 0 -10000 0 0
TFRC -0.36 0.23 -9999 0 -0.73 79 79
FOXF1 0.022 0.067 -9999 0 -0.39 10 10
NF1 0.018 0 -9999 0 -10000 0 0
HNF1A (dimer) -0.088 0.054 -9999 0 -0.46 2 2
CPT1A -0.42 0.33 -9999 0 -0.96 113 113
HMGCS1 -0.42 0.33 -9999 0 -0.99 102 102
NR3C1 -0.079 0.12 -9999 0 -0.43 46 46
CPT1B -0.42 0.33 -9999 0 -1 98 98
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 -0.081 0.042 -9999 0 -10000 0 0
GCK -0.43 0.34 -9999 0 -1 104 104
CREB1 -0.046 0.073 -9999 0 -10000 0 0
IGFBP1 -0.33 0.28 -9999 0 -0.8 130 130
PDX1 -0.63 0.24 -9999 0 -0.78 364 364
UCP2 -0.42 0.33 -9999 0 -0.98 103 103
ALDOB -0.48 0.39 -9999 0 -1.1 140 140
AFP -0.12 0.2 -9999 0 -0.69 55 55
BDH1 -0.42 0.33 -9999 0 -1 91 91
HADH -0.42 0.33 -9999 0 -1 93 93
F2 -0.58 0.44 -9999 0 -1.2 156 156
HNF1A -0.088 0.054 -9999 0 -0.46 2 2
G6PC -0.2 0.31 -9999 0 -1.3 45 45
SLC2A2 -0.33 0.2 -9999 0 -0.98 20 20
INS 0.009 0.041 -9999 0 -10000 0 0
FOXA1 -0.044 0.15 -9999 0 -0.39 63 63
FOXA3 -0.13 0.13 -9999 0 -0.38 67 67
FOXA2 -0.49 0.37 -9999 0 -1.1 107 107
ABCC8 -0.47 0.39 -9999 0 -1.1 146 146
ALB -0.13 0.22 -9999 0 -0.64 79 79
IL4-mediated signaling events

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
BCL2L1 -0.53 0.5 -10000 0 -1.2 150 150
STAT6 (cleaved dimer) -0.6 0.5 -10000 0 -1.2 217 217
IGHG1 -0.18 0.17 -10000 0 -0.5 6 6
IGHG3 -0.52 0.48 -10000 0 -1.1 181 181
AKT1 -0.27 0.27 -10000 0 -0.68 74 74
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.2 0.21 -10000 0 -1.1 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.26 0.25 -10000 0 -0.76 15 15
THY1 -0.54 0.52 -10000 0 -1.2 157 157
MYB 0.011 0.023 -10000 0 -0.4 2 2
HMGA1 0.01 0.043 -10000 0 -0.75 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.37 0.34 -10000 0 -0.82 151 151
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.26 0.25 -10000 0 -0.72 22 22
SP1 0.018 0.008 -10000 0 -10000 0 0
INPP5D 0.012 0.016 -10000 0 -0.4 1 1
SOCS5 0.033 0.018 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.56 0.53 -10000 0 -1.2 197 197
SOCS1 -0.37 0.33 -10000 0 -0.78 134 134
SOCS3 -0.3 0.29 -10000 0 -0.76 85 85
FCER2 -0.81 0.66 -10000 0 -1.4 320 320
PARP14 0.004 0.016 -10000 0 -10000 0 0
CCL17 -0.54 0.51 -10000 0 -1.2 154 154
GRB2 0.013 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.2 0.2 -10000 0 -0.81 4 4
T cell proliferation -0.54 0.52 -10000 0 -1.3 154 154
IL4R/JAK1 -0.54 0.51 -10000 0 -1.2 154 154
EGR2 -0.61 0.54 -10000 0 -1.3 176 176
JAK2 -0.019 0.041 -10000 0 -0.43 3 3
JAK3 0.009 0.032 -10000 0 -0.75 1 1
PIK3R1 0.013 0 -10000 0 -10000 0 0
JAK1 0.004 0.019 -10000 0 -0.39 1 1
COL1A2 -0.18 0.22 -10000 0 -0.8 39 39
CCL26 -0.57 0.53 -10000 0 -1.3 170 170
IL4R -0.57 0.54 -10000 0 -1.3 153 153
PTPN6 0.025 0.011 -10000 0 -10000 0 0
IL13RA2 -0.56 0.52 -10000 0 -1.2 170 170
IL13RA1 -0.017 0.03 -10000 0 -10000 0 0
IRF4 -0.45 0.63 -10000 0 -1.4 170 170
ARG1 -0.13 0.15 -10000 0 -0.67 9 9
CBL -0.34 0.32 -10000 0 -0.8 136 136
GTF3A -0.019 0.15 -10000 0 -0.77 24 24
PIK3CA 0.012 0.016 -10000 0 -0.4 1 1
IL13RA1/JAK2 -0.022 0.048 -10000 0 -10000 0 0
IRF4/BCL6 -0.39 0.58 -10000 0 -1.3 170 170
CD40LG -0.027 0.11 -10000 0 -0.41 44 44
MAPK14 -0.34 0.32 -10000 0 -0.8 132 132
mitosis -0.26 0.26 -10000 0 -0.65 73 73
STAT6 -0.61 0.6 -10000 0 -1.4 179 179
SPI1 0.009 0.049 -10000 0 -0.39 9 9
RPS6KB1 -0.24 0.25 -10000 0 -0.66 37 37
STAT6 (dimer) -0.6 0.6 -10000 0 -1.4 179 179
STAT6 (dimer)/PARP14 -0.62 0.56 -10000 0 -1.3 195 195
mast cell activation 0.013 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.26 0.26 -10000 0 -0.67 63 63
FRAP1 -0.27 0.27 -10000 0 -0.69 74 74
LTA -0.53 0.52 -10000 0 -1.3 138 138
FES 0.011 0.028 -10000 0 -0.4 3 3
T-helper 1 cell differentiation 0.59 0.58 1.3 179 -10000 0 179
CCL11 -0.57 0.56 -10000 0 -1.3 179 179
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.26 0.25 -10000 0 -0.66 53 53
IL2RG 0.008 0.03 -10000 0 -0.39 3 3
IL10 -0.56 0.55 -10000 0 -1.3 160 160
IRS1 0.013 0 -10000 0 -10000 0 0
IRS2 0.013 0 -10000 0 -10000 0 0
IL4 -0.12 0.12 -10000 0 -10000 0 0
IL5 -0.54 0.51 -10000 0 -1.2 156 156
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.42 0.38 -10000 0 -0.92 143 143
COL1A1 -0.28 0.31 -10000 0 -0.8 120 120
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.54 0.52 -10000 0 -1.3 136 136
IL2R gamma/JAK3 0.01 0.034 -10000 0 -0.57 1 1
TFF3 -0.55 0.53 -10000 0 -1.3 163 163
ALOX15 -0.56 0.53 -10000 0 -1.3 166 166
MYBL1 0.01 0.043 -10000 0 -0.75 2 2
T-helper 2 cell differentiation -0.45 0.4 -10000 0 -0.97 156 156
SHC1 0.013 0 -10000 0 -10000 0 0
CEBPB 0.007 0.081 -10000 0 -0.75 7 7
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.24 0.24 -10000 0 -0.86 9 9
mol:PI-3-4-5-P3 -0.27 0.27 -10000 0 -0.69 74 74
PI3K -0.28 0.28 -10000 0 -0.73 74 74
DOK2 0.003 0.06 -10000 0 -0.4 14 14
ETS1 0.025 0.021 -10000 0 -0.36 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.18 0.19 -10000 0 -0.76 4 4
ITGB3 -0.53 0.51 -10000 0 -1.2 154 154
PIGR -0.71 0.67 -10000 0 -1.5 239 239
IGHE 0.042 0.046 0.26 1 -0.25 3 4
MAPKKK cascade -0.18 0.18 -10000 0 -0.74 4 4
BCL6 0.018 0.01 -10000 0 -10000 0 0
OPRM1 -0.53 0.5 -10000 0 -1.2 154 154
RETNLB -0.76 0.68 -10000 0 -1.5 272 272
SELP -0.59 0.59 -10000 0 -1.4 167 167
AICDA -0.51 0.49 -10000 0 -1.2 147 147
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 0.005 0.07 -10000 0 -0.46 2 2
fibroblast growth factor receptor signaling pathway 0.005 0.07 -10000 0 -0.46 2 2
LAMA1 -0.11 0.18 -10000 0 -0.4 181 181
PRNP 0.011 0.023 -10000 0 -0.4 2 2
GPC1/SLIT2 -0.069 0.13 -10000 0 -0.57 1 1
SMAD2 0.025 0.026 -10000 0 -0.44 1 1
GPC1/PrPc/Cu2+ 0.015 0.026 -10000 0 -0.5 1 1
GPC1/Laminin alpha1 -0.066 0.13 -10000 0 -0.57 1 1
TDGF1 -0.34 0.38 -10000 0 -0.74 295 295
CRIPTO/GPC1 -0.26 0.29 -10000 0 -0.57 288 288
APP/GPC1 0.017 0.029 -10000 0 -0.37 3 3
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.22 0.26 -10000 0 -0.49 288 288
FLT1 0.013 0 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.024 0.025 -10000 0 -0.49 1 1
SERPINC1 -0.004 0.096 -10000 0 -0.75 10 10
FYN -0.22 0.25 -10000 0 -0.49 288 288
FGR -0.22 0.26 -10000 0 -0.49 289 289
positive regulation of MAPKKK cascade -0.19 0.2 -10000 0 -0.39 291 291
SLIT2 -0.11 0.19 -10000 0 -0.4 187 187
GPC1/NRG -0.017 0.095 -10000 0 -0.57 1 1
NRG1 -0.035 0.13 -10000 0 -0.4 73 73
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.023 0.037 -10000 0 -0.49 3 3
LYN -0.22 0.25 -10000 0 -0.49 288 288
mol:Spermine 0.008 0.026 -10000 0 -0.43 2 2
cell growth 0.005 0.07 -10000 0 -0.46 2 2
BMP signaling pathway -0.011 0.035 0.57 2 -10000 0 2
SRC -0.22 0.25 -10000 0 -0.49 288 288
TGFBR1 0.012 0.016 -10000 0 -0.4 1 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.1 0.19 -10000 0 -0.41 167 167
GPC1 0.011 0.035 -10000 0 -0.57 2 2
TGFBR1 (dimer) 0.012 0.016 -10000 0 -0.39 1 1
VEGFA 0.01 0.043 -10000 0 -0.75 2 2
BLK -0.3 0.28 -10000 0 -0.57 290 290
HCK -0.22 0.26 -10000 0 -0.5 288 288
FGF2 -0.017 0.1 -10000 0 -0.4 45 45
FGFR1 0.009 0.036 -10000 0 -0.4 5 5
VEGFR1 homodimer 0.013 0 -10000 0 -10000 0 0
TGFBR2 0.013 0 -10000 0 -10000 0 0
cell death 0.017 0.029 -10000 0 -0.37 3 3
ATIII/GPC1 0.004 0.078 -10000 0 -0.57 11 11
PLA2G2A/GPC1 -0.062 0.14 -10000 0 -0.57 7 7
LCK -0.22 0.26 -10000 0 -0.49 296 296
neuron differentiation -0.017 0.095 -10000 0 -0.57 1 1
PrPc/Cu2+ 0.008 0.016 -10000 0 -0.28 2 2
APP 0.012 0.016 -10000 0 -0.4 1 1
TGFBR2 (dimer) 0.013 0 -10000 0 -10000 0 0
Syndecan-4-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
PTK2 -0.025 0.098 -9999 0 -0.39 37 37
Syndecan-4/Syndesmos -0.16 0.22 -9999 0 -0.53 103 103
positive regulation of JNK cascade -0.17 0.2 -9999 0 -0.48 132 132
Syndecan-4/ADAM12 -0.37 0.28 -9999 0 -0.61 278 278
CCL5 -0.004 0.08 -9999 0 -0.4 25 25
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
DNM2 0.013 0 -9999 0 -10000 0 0
ITGA5 0.01 0.043 -9999 0 -0.75 2 2
SDCBP 0.011 0.023 -9999 0 -0.4 2 2
PLG -0.16 0.31 -9999 0 -0.76 133 133
ADAM12 -0.4 0.38 -9999 0 -0.75 334 334
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.069 0.07 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.21 0.22 -9999 0 -0.53 158 158
Syndecan-4/CXCL12/CXCR4 -0.18 0.22 -9999 0 -0.51 132 132
Syndecan-4/Laminin alpha3 -0.16 0.22 -9999 0 -0.53 107 107
MDK 0.005 0.075 -9999 0 -0.75 6 6
Syndecan-4/FZD7 -0.16 0.22 -9999 0 -0.53 105 105
Syndecan-4/Midkine -0.16 0.22 -9999 0 -0.53 111 111
FZD7 0.013 0 -9999 0 -10000 0 0
Syndecan-4/FGFR1/FGF -0.16 0.21 -9999 0 -0.51 105 105
THBS1 0.011 0.035 -9999 0 -0.57 2 2
integrin-mediated signaling pathway -0.16 0.21 -9999 0 -0.52 107 107
positive regulation of MAPKKK cascade -0.17 0.2 -9999 0 -0.48 132 132
Syndecan-4/TACI -0.24 0.23 -9999 0 -0.52 201 201
CXCR4 0.013 0 -9999 0 -10000 0 0
cell adhesion 0.013 0.071 -9999 0 -0.28 29 29
Syndecan-4/Dynamin -0.16 0.22 -9999 0 -0.53 105 105
Syndecan-4/TSP1 -0.16 0.22 -9999 0 -0.54 104 104
Syndecan-4/GIPC -0.16 0.22 -9999 0 -0.53 105 105
Syndecan-4/RANTES -0.17 0.22 -9999 0 -0.53 115 115
ITGB1 0.013 0 -9999 0 -10000 0 0
LAMA1 -0.11 0.18 -9999 0 -0.4 181 181
LAMA3 0.008 0.047 -9999 0 -0.45 6 6
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA 0.047 0.049 -9999 0 -10000 0 0
Syndecan-4/alpha-Actinin -0.16 0.22 -9999 0 -0.53 105 105
TFPI 0.009 0.036 -9999 0 -0.4 5 5
F2 -0.25 0.36 -9999 0 -0.75 214 214
alpha5/beta1 Integrin 0.017 0.033 -9999 0 -0.57 2 2
positive regulation of cell adhesion -0.2 0.22 -9999 0 -0.52 149 149
ACTN1 0.013 0 -9999 0 -10000 0 0
TNC -0.001 0.092 -9999 0 -0.56 15 15
Syndecan-4/CXCL12 -0.19 0.22 -9999 0 -0.52 145 145
FGF6 -0.002 0.043 -9999 0 -0.75 2 2
RHOA 0.013 0 -9999 0 -10000 0 0
CXCL12 -0.065 0.16 -9999 0 -0.4 119 119
TNFRSF13B -0.17 0.2 -9999 0 -0.4 270 270
FGF2 -0.017 0.1 -9999 0 -0.4 45 45
FGFR1 0.009 0.036 -9999 0 -0.4 5 5
Syndecan-4/PI-4-5-P2 -0.16 0.21 -9999 0 -0.53 105 105
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.025 0.17 -9999 0 -0.67 37 37
cell migration -0.025 0.025 -9999 0 -10000 0 0
PRKCD 0.016 0.011 -9999 0 -10000 0 0
vasculogenesis -0.15 0.21 -9999 0 -0.52 104 104
SDC4 -0.17 0.23 -9999 0 -0.56 105 105
Syndecan-4/Tenascin C -0.16 0.22 -9999 0 -0.54 107 107
Syndecan-4/PI-4-5-P2/PKC alpha -0.054 0.055 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.16 0.22 -9999 0 -0.53 106 106
MMP9 -0.048 0.2 -9999 0 -0.73 49 49
Rac1/GTP 0.013 0.072 -9999 0 -0.28 29 29
cytoskeleton organization -0.15 0.21 -9999 0 -0.51 103 103
GIPC1 0.012 0.016 -9999 0 -0.4 1 1
Syndecan-4/TFPI -0.16 0.22 -9999 0 -0.53 107 107
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.055 0.12 -9999 0 -0.26 92 92
EFNA5 -0.084 0.17 -9999 0 -0.4 147 147
FYN -0.043 0.11 -9999 0 -0.39 13 13
neuron projection morphogenesis -0.055 0.12 -9999 0 -0.26 92 92
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.055 0.12 -9999 0 -0.26 92 92
EPHA5 -0.014 0.087 -9999 0 -0.4 31 31
BCR signaling pathway

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
JUN -0.087 0.18 -9999 0 -0.45 100 100
IKBKB -0.037 0.093 -9999 0 -0.25 47 47
AKT1 -0.064 0.12 -9999 0 -0.27 91 91
IKBKG -0.039 0.1 -9999 0 -0.27 49 49
CALM1 -0.11 0.21 -9999 0 -0.52 105 105
PIK3CA 0.012 0.016 -9999 0 -0.4 1 1
MAP3K1 -0.14 0.27 -9999 0 -0.64 113 113
MAP3K7 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ -0.12 0.22 -9999 0 -0.55 107 107
DOK1 0.013 0 -9999 0 -10000 0 0
AP-1 -0.043 0.11 -9999 0 -0.26 87 87
LYN 0.013 0 -9999 0 -10000 0 0
BLNK 0.007 0.049 -9999 0 -0.39 9 9
SHC1 0.013 0 -9999 0 -10000 0 0
BCR complex -0.12 0.19 -9999 0 -0.51 78 78
CD22 -0.19 0.32 -9999 0 -0.67 161 161
CAMK2G -0.094 0.19 -9999 0 -0.5 93 93
CSNK2A1 0.013 0 -9999 0 -10000 0 0
INPP5D 0.012 0.016 -9999 0 -0.4 1 1
SHC/GRB2/SOS1 -0.075 0.11 -9999 0 -0.48 4 4
GO:0007205 -0.12 0.23 -9999 0 -0.56 107 107
SYK 0.013 0 -9999 0 -10000 0 0
ELK1 -0.11 0.21 -9999 0 -0.53 105 105
NFATC1 -0.13 0.23 -9999 0 -0.47 163 163
B-cell antigen/BCR complex -0.12 0.19 -9999 0 -0.51 78 78
PAG1/CSK 0.013 0.039 -9999 0 -10000 0 0
NFKBIB -0.003 0.032 -9999 0 -10000 0 0
HRAS -0.091 0.18 -9999 0 -0.48 92 92
NFKBIA -0.003 0.032 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.003 0.026 -9999 0 -10000 0 0
RasGAP/Csk -0.087 0.18 -9999 0 -0.44 97 97
mol:GDP -0.12 0.21 -9999 0 -0.54 105 105
PTEN 0.011 0.023 -9999 0 -0.4 2 2
CD79B -0.041 0.14 -9999 0 -0.39 82 82
NF-kappa-B/RelA/I kappa B alpha 0.004 0.026 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
PI3K/BCAP/CD19 -0.16 0.26 -9999 0 -0.54 173 173
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:IP3 -0.12 0.23 -9999 0 -0.57 107 107
CSK 0.013 0 -9999 0 -10000 0 0
FOS -0.098 0.2 -9999 0 -0.51 98 98
CHUK -0.039 0.099 -9999 0 -0.26 54 54
IBTK 0.012 0.016 -9999 0 -0.4 1 1
CARD11/BCL10/MALT1/TAK1 -0.11 0.19 -9999 0 -0.52 86 86
PTPN6 -0.18 0.3 -9999 0 -0.63 160 160
RELA 0.013 0 -9999 0 -10000 0 0
BCL2A1 0.004 0.026 -9999 0 -0.12 10 10
VAV2 -0.19 0.32 -9999 0 -0.64 168 168
ubiquitin-dependent protein catabolic process 0 0.031 -9999 0 -10000 0 0
BTK -0.13 0.35 -9999 0 -1.1 73 73
CD19 -0.19 0.32 -9999 0 -0.65 165 165
MAP4K1 -0.023 0.12 -9999 0 -0.4 54 54
CD72 0.012 0.016 -9999 0 -0.4 1 1
PAG1 0.005 0.056 -9999 0 -0.4 12 12
MAPK14 -0.11 0.22 -9999 0 -0.54 107 107
SH3BP5 0.009 0.036 -9999 0 -0.4 5 5
PIK3AP1 -0.11 0.22 -9999 0 -0.59 94 94
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.14 0.26 -9999 0 -0.65 102 102
RAF1 -0.081 0.17 -9999 0 -0.46 86 86
RasGAP/p62DOK/SHIP -0.081 0.17 -9999 0 -0.52 42 42
CD79A -0.14 0.2 -9999 0 -0.39 228 228
re-entry into mitotic cell cycle -0.044 0.11 -9999 0 -0.27 87 87
RASA1 0.013 0.001 -9999 0 -10000 0 0
MAPK3 -0.058 0.14 -9999 0 -0.42 58 58
MAPK1 -0.058 0.14 -9999 0 -0.42 58 58
CD72/SHP1 -0.16 0.28 -9999 0 -0.58 160 160
NFKB1 0.013 0 -9999 0 -10000 0 0
MAPK8 -0.11 0.22 -9999 0 -0.54 105 105
actin cytoskeleton organization -0.15 0.26 -9999 0 -0.53 165 165
NF-kappa-B/RelA 0.011 0.052 -9999 0 -0.26 1 1
Calcineurin -0.076 0.18 -9999 0 -0.47 86 86
PI3K -0.17 0.22 -9999 0 -0.53 136 136
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.12 0.24 -9999 0 -0.58 107 107
SOS1 0.013 0 -9999 0 -10000 0 0
Bam32/HPK1 -0.17 0.33 -9999 0 -0.82 112 112
DAPP1 -0.2 0.36 -9999 0 -0.95 102 102
cytokine secretion -0.12 0.22 -9999 0 -0.44 163 163
mol:DAG -0.12 0.23 -9999 0 -0.57 107 107
PLCG2 -0.019 0.11 -9999 0 -0.39 49 49
MAP2K1 -0.069 0.16 -9999 0 -0.42 83 83
B-cell antigen/BCR complex/FcgammaRIIB -0.12 0.2 -9999 0 -0.52 97 97
mol:PI-3-4-5-P3 -0.12 0.15 -9999 0 -0.36 136 136
ETS1 -0.08 0.18 -9999 0 -0.47 85 85
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.067 0.15 -9999 0 -0.55 4 4
B-cell antigen/BCR complex/LYN -0.17 0.28 -9999 0 -0.72 109 109
MALT1 0.012 0.016 -9999 0 -0.39 1 1
TRAF6 0.013 0 -9999 0 -10000 0 0
RAC1 -0.16 0.28 -9999 0 -0.58 165 165
B-cell antigen/BCR complex/LYN/SYK -0.18 0.27 -9999 0 -0.72 104 104
CARD11 -0.13 0.23 -9999 0 -0.55 123 123
FCGR2B -0.037 0.13 -9999 0 -0.4 75 75
PPP3CA 0.013 0 -9999 0 -10000 0 0
BCL10 0.012 0.016 -9999 0 -0.4 1 1
IKK complex -0.008 0.041 -9999 0 -10000 0 0
PTPRC -0.02 0.11 -9999 0 -0.4 50 50
PDPK1 -0.062 0.11 -9999 0 -0.26 84 84
PPP3CB 0.013 0 -9999 0 -10000 0 0
PPP3CC 0.012 0.016 -9999 0 -0.4 1 1
POU2F2 0.005 0.024 -9999 0 -10000 0 0
IL23-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
CCL2 -0.38 0.44 -10000 0 -1.1 103 103
IL23A -0.46 0.5 -10000 0 -1.2 114 114
NF kappa B1 p50/RelA/I kappa B alpha -0.44 0.42 -10000 0 -1.1 113 113
positive regulation of T cell mediated cytotoxicity -0.41 0.49 -10000 0 -1.2 106 106
ITGA3 -0.38 0.44 -10000 0 -1.1 98 98
IL17F -0.3 0.34 -10000 0 -0.79 123 123
IL12B -0.012 0.069 -10000 0 -0.79 4 4
STAT1 (dimer) -0.39 0.47 -10000 0 -1.2 105 105
CD4 -0.37 0.44 -10000 0 -1.2 91 91
IL23 -0.44 0.47 -10000 0 -1.2 108 108
IL23R -0.077 0.22 -10000 0 -1.4 15 15
IL1B -0.43 0.49 -10000 0 -1.3 100 100
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.47 0.49 -10000 0 -1.1 164 164
TYK2 -0.003 0.02 -10000 0 -10000 0 0
STAT4 -0.006 0.084 -10000 0 -0.4 28 28
STAT3 0.012 0.002 -10000 0 -10000 0 0
IL18RAP -0.008 0.089 -10000 0 -0.4 29 29
IL12RB1 -0.018 0.084 -10000 0 -0.44 22 22
PIK3CA 0.011 0.017 -10000 0 -0.4 1 1
IL12Rbeta1/TYK2 -0.013 0.064 -10000 0 -0.33 16 16
IL23R/JAK2 -0.083 0.22 -10000 0 -1.3 15 15
positive regulation of chronic inflammatory response -0.41 0.49 -10000 0 -1.2 106 106
natural killer cell activation 0.006 0.013 0.077 15 -10000 0 15
JAK2 -0.003 0.04 -10000 0 -0.42 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 -0.42 0.45 -10000 0 -1.1 108 108
ALOX12B -0.36 0.43 -10000 0 -1.1 82 82
CXCL1 -0.47 0.49 -10000 0 -1.1 151 151
T cell proliferation -0.41 0.49 -10000 0 -1.2 106 106
NFKBIA 0.009 0.003 -10000 0 -10000 0 0
IL17A -0.29 0.3 -10000 0 -0.67 153 153
PI3K -0.42 0.42 -10000 0 -1.1 113 113
IFNG -0.016 0.038 0.15 10 -0.099 59 69
STAT3 (dimer) -0.43 0.42 -10000 0 -1.1 122 122
IL18R1 0.006 0.051 -10000 0 -0.39 10 10
IL23/IL23R/JAK2/TYK2/SOCS3 -0.21 0.26 -10000 0 -0.75 33 33
IL18/IL18R 0.011 0.067 -10000 0 -0.45 2 2
macrophage activation -0.026 0.017 -10000 0 -0.046 9 9
TNF -0.42 0.47 -10000 0 -1.2 99 99
STAT3/STAT4 -0.42 0.42 -10000 0 -1.2 107 107
STAT4 (dimer) -0.4 0.47 -10000 0 -1.2 107 107
IL18 0.01 0.033 -10000 0 -0.39 4 4
IL19 -0.37 0.43 -10000 0 -1.1 94 94
STAT5A (dimer) -0.39 0.47 -10000 0 -1.2 105 105
STAT1 0.011 0.031 -10000 0 -0.75 1 1
SOCS3 0.01 0.043 -10000 0 -0.75 2 2
CXCL9 -0.4 0.46 -10000 0 -1.2 103 103
MPO -0.37 0.43 -10000 0 -1.1 85 85
positive regulation of humoral immune response -0.41 0.49 -10000 0 -1.2 106 106
IL23/IL23R/JAK2/TYK2 -0.43 0.52 -10000 0 -1.3 106 106
IL6 -0.42 0.48 -10000 0 -1.2 115 115
STAT5A 0.013 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 15 -10000 0 15
CD3E -0.38 0.45 -10000 0 -1.2 97 97
keratinocyte proliferation -0.41 0.49 -10000 0 -1.2 106 106
NOS2 -0.39 0.46 -10000 0 -1.2 106 106
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.047 0.18 -10000 0 -0.42 103 103
CRKL -0.04 0.17 -10000 0 -0.42 99 99
HRAS -0.029 0.17 -10000 0 -0.48 33 33
mol:PIP3 -0.047 0.16 -10000 0 -0.4 99 99
SPRED1 0.013 0 -10000 0 -10000 0 0
SPRED2 0.013 0 -10000 0 -10000 0 0
GAB1 -0.047 0.18 -10000 0 -0.44 99 99
FOXO3 -0.03 0.16 -10000 0 -0.38 99 99
AKT1 -0.039 0.17 -10000 0 -0.41 99 99
BAD -0.03 0.16 -10000 0 -0.38 99 99
megakaryocyte differentiation -0.08 0.21 -10000 0 -0.45 136 136
GSK3B -0.03 0.16 -10000 0 -0.38 99 99
RAF1 -0.015 0.14 -10000 0 -0.38 33 33
SHC1 0.013 0 -10000 0 -10000 0 0
STAT3 -0.047 0.18 -10000 0 -0.44 99 99
STAT1 -0.13 0.4 -10000 0 -1 99 99
HRAS/SPRED1 -0.016 0.14 -10000 0 -0.38 33 33
cell proliferation -0.046 0.17 -10000 0 -0.43 99 99
PIK3CA 0.012 0.016 -10000 0 -0.4 1 1
TEC 0.011 0.031 -10000 0 -0.75 1 1
RPS6KB1 -0.047 0.18 -10000 0 -0.44 99 99
HRAS/SPRED2 -0.016 0.14 -10000 0 -0.38 33 33
LYN/TEC/p62DOK -0.033 0.17 -10000 0 -0.41 100 100
MAPK3 0 0.1 -10000 0 -0.28 22 22
STAP1 -0.093 0.2 -10000 0 -0.5 103 103
GRAP2 -0.003 0.077 -10000 0 -0.4 23 23
JAK2 -0.1 0.34 -10000 0 -0.86 99 99
STAT1 (dimer) -0.12 0.4 -10000 0 -1 99 99
mol:Gleevec 0.001 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.053 0.2 -10000 0 -0.45 113 113
actin filament polymerization -0.053 0.18 -10000 0 -0.44 106 106
LYN 0.013 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.11 0.26 -10000 0 -0.66 103 103
PIK3R1 0.012 0 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.023 0.16 -10000 0 -0.37 99 99
PI3K -0.033 0.17 -10000 0 -0.42 99 99
PTEN 0.011 0.023 -10000 0 -0.4 2 2
SCF/KIT/EPO/EPOR -0.15 0.47 -10000 0 -1.2 99 99
MAPK8 -0.047 0.18 -10000 0 -0.44 99 99
STAT3 (dimer) -0.046 0.17 -10000 0 -0.43 99 99
positive regulation of transcription 0.004 0.088 -10000 0 -0.23 18 18
mol:GDP -0.036 0.18 -10000 0 -0.49 42 42
PIK3C2B -0.047 0.18 -10000 0 -0.44 99 99
CBL/CRKL -0.03 0.16 -10000 0 -0.39 99 99
FER -0.049 0.18 -10000 0 -0.44 100 100
SH2B3 -0.047 0.18 -10000 0 -0.44 99 99
PDPK1 -0.038 0.15 -10000 0 -0.36 99 99
SNAI2 -0.048 0.18 -10000 0 -0.44 99 99
positive regulation of cell proliferation -0.086 0.3 -10000 0 -0.75 99 99
KITLG 0.002 0.067 -10000 0 -0.42 15 15
cell motility -0.086 0.3 -10000 0 -0.75 99 99
PTPN6 0.014 0.009 -10000 0 -10000 0 0
EPOR -0.011 0.13 -10000 0 -0.81 1 1
STAT5A (dimer) -0.067 0.25 -10000 0 -0.62 99 99
SOCS1 -0.014 0.14 -10000 0 -0.75 22 22
cell migration 0.069 0.19 0.47 100 -10000 0 100
SOS1 0.013 0 -10000 0 -10000 0 0
EPO -0.002 0.081 -10000 0 -0.76 7 7
VAV1 -0.004 0.081 -10000 0 -0.4 26 26
GRB10 -0.048 0.18 -10000 0 -0.44 99 99
PTPN11 0.014 0.007 -10000 0 -10000 0 0
SCF/KIT -0.056 0.19 -10000 0 -0.47 99 99
GO:0007205 0.002 0.009 -10000 0 -10000 0 0
MAP2K1 -0.003 0.11 -10000 0 -0.31 20 20
CBL 0.013 0 -10000 0 -10000 0 0
KIT -0.16 0.47 -10000 0 -1.2 98 98
MAP2K2 -0.004 0.11 -10000 0 -0.3 25 25
SHC/Grb2/SOS1 -0.032 0.17 -10000 0 -0.41 99 99
STAT5A -0.07 0.26 -10000 0 -0.64 99 99
GRB2 0.013 0 -10000 0 -10000 0 0
response to radiation -0.047 0.18 -10000 0 -0.43 99 99
SHC/GRAP2 0.008 0.054 -10000 0 -10000 0 0
PTPRO -0.082 0.21 -10000 0 -0.46 136 136
SH2B2 -0.054 0.19 -10000 0 -0.45 106 106
DOK1 0.013 0 -10000 0 -10000 0 0
MATK -0.07 0.19 -10000 0 -0.48 100 100
CREBBP 0.012 0.048 -10000 0 -10000 0 0
BCL2 -0.061 0.31 -10000 0 -1.3 32 32
HIF-1-alpha transcription factor network

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
PKM2 -0.46 0.33 -9999 0 -1 81 81
HDAC7 0.013 0.003 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.34 0.25 -9999 0 -0.9 31 31
SMAD4 0.012 0.023 -9999 0 -0.39 2 2
ID2 -0.46 0.33 -9999 0 -1 68 68
AP1 0.016 0.036 -9999 0 -10000 0 0
ABCG2 -0.62 0.35 -9999 0 -1.1 157 157
HIF1A -0.072 0.047 -9999 0 -10000 0 0
TFF3 -0.46 0.33 -9999 0 -1 80 80
GATA2 0.007 0.054 -9999 0 -0.39 11 11
AKT1 -0.071 0.052 -9999 0 -10000 0 0
response to hypoxia -0.088 0.053 -9999 0 -10000 0 0
MCL1 -0.46 0.33 -9999 0 -1 69 69
NDRG1 -0.46 0.33 -9999 0 -1 69 69
SERPINE1 -0.54 0.4 -9999 0 -1.1 135 135
FECH -0.46 0.33 -9999 0 -1 75 75
FURIN -0.46 0.33 -9999 0 -1 78 78
NCOA2 0.011 0.028 -9999 0 -0.4 3 3
EP300 -0.069 0.069 -9999 0 -0.36 12 12
HMOX1 -0.46 0.33 -9999 0 -1 79 79
BHLHE40 -0.46 0.33 -9999 0 -1 81 81
BHLHE41 -0.47 0.34 -9999 0 -1.1 75 75
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.065 0.06 -9999 0 -10000 0 0
ENG -0.051 0.062 -9999 0 -10000 0 0
JUN 0.013 0.001 -9999 0 -10000 0 0
RORA -0.46 0.33 -9999 0 -1 83 83
ABCB1 -0.29 0.42 -9999 0 -1.1 119 119
TFRC -0.46 0.33 -9999 0 -1 78 78
CXCR4 -0.46 0.33 -9999 0 -1 75 75
TF -0.49 0.35 -9999 0 -1.1 100 100
CITED2 -0.46 0.33 -9999 0 -1 86 86
HIF1A/ARNT -0.51 0.38 -9999 0 -1.1 87 87
LDHA -0.056 0.041 -9999 0 -10000 0 0
ETS1 -0.46 0.33 -9999 0 -1 75 75
PGK1 -0.46 0.33 -9999 0 -1 80 80
NOS2 -0.48 0.34 -9999 0 -1 100 100
ITGB2 -0.46 0.33 -9999 0 -1.1 69 69
ALDOA -0.46 0.33 -9999 0 -1 68 68
Cbp/p300/CITED2 -0.44 0.34 -9999 0 -1.1 65 65
FOS 0.007 0.051 -9999 0 -0.39 10 10
HK2 -0.46 0.33 -9999 0 -1 78 78
SP1 0.01 0.027 -9999 0 -10000 0 0
GCK -0.12 0.2 -9999 0 -1.3 14 14
HK1 -0.46 0.33 -9999 0 -1 75 75
NPM1 -0.46 0.33 -9999 0 -1 75 75
EGLN1 -0.46 0.33 -9999 0 -1 78 78
CREB1 0.019 0 -9999 0 -10000 0 0
PGM1 -0.46 0.33 -9999 0 -1 77 77
SMAD3 0.012 0.023 -9999 0 -0.39 2 2
EDN1 -0.048 0.1 -9999 0 -0.94 2 2
IGFBP1 -0.53 0.4 -9999 0 -1.1 127 127
VEGFA -0.3 0.24 -9999 0 -0.87 23 23
HIF1A/JAB1 -0.036 0.028 -9999 0 -10000 0 0
CP -0.55 0.36 -9999 0 -1.1 124 124
CXCL12 -0.49 0.35 -9999 0 -1.1 92 92
COPS5 0.013 0.002 -9999 0 -10000 0 0
SMAD3/SMAD4 0.019 0.023 -9999 0 -10000 0 0
BNIP3 -0.46 0.33 -9999 0 -1 77 77
EGLN3 -0.46 0.33 -9999 0 -1 82 82
CA9 -0.77 0.39 -9999 0 -1.1 275 275
TERT -0.49 0.37 -9999 0 -1.1 98 98
ENO1 -0.46 0.33 -9999 0 -1 80 80
PFKL -0.46 0.33 -9999 0 -1 78 78
NCOA1 0.013 0.001 -9999 0 -10000 0 0
ADM -0.46 0.33 -9999 0 -1 75 75
ARNT -0.073 0.05 -9999 0 -0.46 1 1
HNF4A 0.013 0.02 -9999 0 -0.39 1 1
ADFP -0.47 0.33 -9999 0 -1 90 90
SLC2A1 -0.31 0.27 -9999 0 -0.94 40 40
LEP -0.48 0.34 -9999 0 -1.1 84 84
HIF1A/ARNT/Cbp/p300 -0.36 0.26 -9999 0 -0.91 35 35
EPO -0.25 0.19 -9999 0 -0.89 8 8
CREBBP -0.069 0.069 -9999 0 -0.36 12 12
HIF1A/ARNT/Cbp/p300/HDAC7 -0.34 0.26 -9999 0 -0.98 28 28
PFKFB3 -0.46 0.33 -9999 0 -1 69 69
NT5E -0.46 0.33 -9999 0 -1 78 78
Caspase cascade in apoptosis

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
TOP1 -0.049 0.14 -10000 0 -0.29 146 146
ACTA1 -0.075 0.17 -10000 0 -0.36 148 148
NUMA1 -0.049 0.14 -10000 0 -0.29 146 146
SPTAN1 -0.071 0.17 -10000 0 -0.36 146 146
LIMK1 -0.071 0.17 -10000 0 -0.36 146 146
BIRC3 0.005 0.057 -10000 0 -0.43 10 10
BIRC2 0.012 0.016 -10000 0 -0.4 1 1
BAX 0.013 0 -10000 0 -10000 0 0
CASP10 -0.1 0.23 -10000 0 -0.5 149 149
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.012 0 -10000 0 -10000 0 0
PTK2 -0.049 0.14 -10000 0 -0.29 146 146
DIABLO 0.013 0.001 -10000 0 -10000 0 0
apoptotic nuclear changes -0.07 0.16 -10000 0 -0.36 146 146
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.013 0 -10000 0 -10000 0 0
GSN -0.075 0.17 -10000 0 -0.37 147 147
MADD 0.013 0 -10000 0 -10000 0 0
TFAP2A -0.057 0.12 -10000 0 -0.63 7 7
BID -0.04 0.1 -10000 0 -0.22 149 149
MAP3K1 -0.021 0.064 -10000 0 -0.2 7 7
TRADD 0.013 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 -0.071 0.17 -10000 0 -0.36 146 146
CASP9 0.013 0.001 -10000 0 -10000 0 0
DNA repair 0.016 0.049 -10000 0 -0.16 7 7
neuron apoptosis 0.011 0.036 -10000 0 -0.72 1 1
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.061 0.16 -10000 0 -0.34 146 146
APAF1 0.013 0.001 -10000 0 -10000 0 0
CASP6 -0.012 0.082 -10000 0 -10000 0 0
TRAF2 0.012 0.016 -10000 0 -0.4 1 1
ICAD/CAD -0.063 0.16 -10000 0 -0.35 145 145
CASP7 0.002 0.039 0.24 10 -0.41 1 11
KRT18 0.005 0.025 -10000 0 -10000 0 0
apoptosis -0.055 0.15 -10000 0 -0.53 8 8
DFFA -0.071 0.17 -10000 0 -0.36 146 146
DFFB -0.071 0.17 -10000 0 -0.36 146 146
PARP1 -0.016 0.05 0.16 7 -10000 0 7
actin filament polymerization 0.066 0.16 0.34 145 -10000 0 145
TNF 0.009 0.036 -10000 0 -0.4 5 5
CYCS -0.029 0.084 -10000 0 -0.18 148 148
SATB1 -0.009 0.081 -10000 0 -10000 0 0
SLK -0.072 0.17 -10000 0 -0.36 146 146
p15 BID/BAX -0.029 0.094 -10000 0 -0.31 7 7
CASP2 0.037 0.03 -10000 0 -0.33 1 1
JNK cascade 0.021 0.064 0.2 7 -10000 0 7
CASP3 -0.081 0.18 -10000 0 -0.38 153 153
LMNB2 0.024 0.036 -10000 0 -10000 0 0
RIPK1 0.013 0 -10000 0 -10000 0 0
CASP4 0.013 0 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.028 0.034 -10000 0 -0.45 1 1
negative regulation of DNA binding -0.056 0.12 -10000 0 -0.62 7 7
stress fiber formation -0.071 0.17 -10000 0 -0.36 146 146
GZMB -0.13 0.26 -10000 0 -0.58 149 149
CASP1 0.013 0.02 -10000 0 -0.27 3 3
LMNB1 0.024 0.036 -10000 0 -10000 0 0
APP 0.011 0.036 -10000 0 -0.73 1 1
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.009 0 -10000 0 -10000 0 0
VIM -0.056 0.15 -10000 0 -0.32 145 145
LMNA 0.024 0.036 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.034 0.031 -10000 0 -0.36 1 1
LRDD 0.012 0.016 -10000 0 -0.4 1 1
SREBF1 -0.071 0.17 -10000 0 -0.36 146 146
APAF-1/Caspase 9 -0.013 0.032 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis -0.048 0.14 -10000 0 -0.28 146 146
CFL2 -0.068 0.16 -10000 0 -0.34 145 145
GAS2 -0.13 0.24 -10000 0 -0.44 201 201
positive regulation of apoptosis 0.028 0.035 -10000 0 -10000 0 0
PRF1 0.002 0.078 -10000 0 -0.5 13 13
Endothelins

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
AKT1 0.005 0.22 -10000 0 -0.5 58 58
PTK2B 0.012 0.023 -10000 0 -0.4 2 2
mol:Ca2+ 0.016 0.23 -10000 0 -0.96 27 27
EDN1 0.048 0.13 -10000 0 -0.4 1 1
EDN3 -0.18 0.2 -10000 0 -0.4 295 295
EDN2 -0.11 0.19 -10000 0 -0.4 187 187
HRAS/GDP 0.011 0.14 -10000 0 -0.5 10 10
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.039 0.11 -10000 0 -0.35 12 12
ADCY4 -0.025 0.17 -10000 0 -0.49 38 38
ADCY5 -0.09 0.2 -10000 0 -0.53 62 62
ADCY6 -0.025 0.17 -10000 0 -0.52 31 31
ADCY7 -0.025 0.17 -10000 0 -0.51 33 33
ADCY1 -0.035 0.18 -10000 0 -0.51 40 40
ADCY2 -0.05 0.2 -10000 0 -0.51 56 56
ADCY3 -0.025 0.17 -10000 0 -0.52 31 31
ADCY8 -0.037 0.18 -10000 0 -0.48 44 44
ADCY9 -0.025 0.17 -10000 0 -0.53 30 30
arachidonic acid secretion -0.007 0.16 -10000 0 -0.48 26 26
ETB receptor/Endothelin-1/Gq/GTP 0.028 0.081 -10000 0 -0.47 5 5
GNAO1 -0.14 0.2 -10000 0 -0.4 234 234
HRAS 0.012 0.016 -10000 0 -0.4 1 1
ETA receptor/Endothelin-1/G12/GTP 0.087 0.26 0.31 291 -0.47 54 345
ETA receptor/Endothelin-1/Gs/GTP 0.065 0.26 0.29 279 -0.46 60 339
mol:GTP 0.001 0.004 -10000 0 -10000 0 0
COL3A1 -0.003 0.25 -10000 0 -0.58 62 62
EDNRB -0.001 0.072 -10000 0 -0.39 18 18
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.021 0.26 -10000 0 -0.6 80 80
CYSLTR1 -0.043 0.29 -10000 0 -0.56 122 122
SLC9A1 0.023 0.12 -10000 0 -0.31 17 17
mol:GDP 0.004 0.15 -10000 0 -0.48 16 16
SLC9A3 -0.18 0.32 -10000 0 -0.58 174 174
RAF1 -0.002 0.13 -10000 0 -0.49 11 11
JUN 0.04 0.14 -10000 0 -0.72 4 4
JAK2 0.004 0.22 -10000 0 -0.49 63 63
mol:IP3 0.033 0.1 -10000 0 -0.54 5 5
ETA receptor/Endothelin-1 0.088 0.32 0.37 296 -0.55 76 372
PLCB1 0.009 0.053 -10000 0 -0.75 3 3
PLCB2 0.013 0.002 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.14 0.23 -10000 0 -0.46 123 123
FOS 0.008 0.15 -10000 0 -0.84 12 12
Gai/GDP -0.22 0.34 -10000 0 -0.64 234 234
CRK 0.013 0.001 -10000 0 -10000 0 0
mol:Ca ++ 0.011 0.2 -10000 0 -0.57 30 30
BCAR1 0.012 0.016 -10000 0 -0.39 1 1
PRKCB1 0.031 0.1 -10000 0 -0.52 5 5
GNAQ 0.012 0.029 -10000 0 -0.4 3 3
GNAZ 0.007 0.046 -10000 0 -0.4 8 8
GNAL -0.01 0.094 -10000 0 -0.4 35 35
Gs family/GDP -0.047 0.11 -10000 0 -0.5 15 15
ETA receptor/Endothelin-1/Gq/GTP 0.036 0.14 -10000 0 -0.4 17 17
MAPK14 0.036 0.07 -10000 0 -0.53 3 3
TRPC6 0.013 0.24 -10000 0 -1 27 27
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 -0.002 0.075 -10000 0 -0.4 22 22
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.033 0.075 -10000 0 -0.57 3 3
ETB receptor/Endothelin-2 -0.076 0.14 -10000 0 -0.27 201 201
ETB receptor/Endothelin-3 -0.12 0.15 -10000 0 -0.44 18 18
ETB receptor/Endothelin-1 0.037 0.12 -10000 0 -0.38 12 12
MAPK3 0.007 0.14 -10000 0 -0.71 13 13
MAPK1 0.007 0.14 -10000 0 -0.71 13 13
Rac1/GDP 0.011 0.14 -10000 0 -0.49 11 11
cAMP biosynthetic process -0.073 0.18 -10000 0 -0.48 55 55
MAPK8 0.032 0.16 -10000 0 -0.6 20 20
SRC 0.013 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.048 0.14 -10000 0 -0.4 39 39
p130Cas/CRK/Src/PYK2 -0.022 0.17 -10000 0 -0.58 24 24
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP 0.011 0.14 -10000 0 -0.5 10 10
COL1A2 0.004 0.25 -10000 0 -0.65 50 50
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.084 0.22 -10000 0 -0.42 124 124
mol:DAG 0.033 0.1 -10000 0 -0.54 5 5
MAP2K2 0.004 0.13 -10000 0 -0.55 13 13
MAP2K1 0.005 0.13 -10000 0 -0.55 13 13
EDNRA -0.001 0.24 -10000 0 -0.74 41 41
positive regulation of muscle contraction 0.011 0.19 -10000 0 -0.53 29 29
Gq family/GDP -0.047 0.1 -10000 0 -0.59 8 8
HRAS/GTP -0.01 0.13 -10000 0 -0.47 11 11
PRKCH 0.036 0.1 -10000 0 -0.51 5 5
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCA 0.036 0.1 -10000 0 -0.51 5 5
PRKCB -0.008 0.15 -10000 0 -0.44 16 16
PRKCE 0.037 0.099 -10000 0 -0.51 5 5
PRKCD 0.036 0.1 -10000 0 -0.51 5 5
PRKCG -0.11 0.23 -10000 0 -0.45 112 112
regulation of vascular smooth muscle contraction 0.006 0.17 -10000 0 -0.98 12 12
PRKCQ 0.034 0.1 -10000 0 -0.55 5 5
PLA2G4A -0.01 0.17 -10000 0 -0.52 26 26
GNA14 0.011 0.037 -10000 0 -0.4 5 5
GNA15 0.006 0.075 -10000 0 -0.75 6 6
GNA12 0.013 0 -10000 0 -10000 0 0
GNA11 0.011 0.033 -10000 0 -0.4 4 4
Rac1/GTP 0.087 0.26 0.31 293 -0.46 62 355
MMP1 -0.38 0.33 -10000 0 -0.61 405 405
Glucocorticoid receptor regulatory network

Figure S17.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S17.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.02 0.076 0.31 2 -10000 0 2
SMARCC2 0.012 0.012 -10000 0 -10000 0 0
SMARCC1 0.012 0.013 -10000 0 -10000 0 0
TBX21 -0.12 0.2 -10000 0 -0.56 70 70
SUMO2 0.013 0.006 -10000 0 -10000 0 0
STAT1 (dimer) 0.019 0.03 -10000 0 -0.74 1 1
FKBP4 0.011 0.031 -10000 0 -0.75 1 1
FKBP5 0.012 0.016 -10000 0 -0.4 1 1
GR alpha/HSP90/FKBP51/HSP90 0.1 0.11 0.33 15 -0.37 2 17
PRL -0.079 0.13 -10000 0 -0.69 13 13
cortisol/GR alpha (dimer)/TIF2 0.25 0.23 0.54 137 -0.5 4 141
RELA -0.055 0.083 -10000 0 -10000 0 0
FGG 0.13 0.27 0.49 58 -0.57 46 104
GR beta/TIF2 0.11 0.13 0.34 30 -0.41 8 38
IFNG -0.35 0.28 -10000 0 -0.77 136 136
apoptosis 0.014 0.16 0.48 16 -0.58 8 24
CREB1 0.013 0.025 -10000 0 -10000 0 0
histone acetylation -0.066 0.12 0.44 2 -0.39 19 21
BGLAP -0.08 0.12 -10000 0 -0.54 5 5
GR/PKAc 0.071 0.14 0.32 11 -0.39 11 22
NF kappa B1 p50/RelA -0.1 0.15 -10000 0 -0.39 51 51
SMARCD1 0.012 0.013 -10000 0 -10000 0 0
MDM2 0.096 0.078 0.27 36 -10000 0 36
GATA3 0.009 0.05 -10000 0 -0.46 5 5
AKT1 0.006 0.001 -10000 0 -10000 0 0
CSF2 -0.23 0.24 -10000 0 -0.52 224 224
GSK3B 0.013 0.006 -10000 0 -10000 0 0
NR1I3 0.023 0.16 0.47 14 -0.78 6 20
CSN2 0.14 0.15 0.42 31 -0.46 5 36
BRG1/BAF155/BAF170/BAF60A 0.031 0.041 -10000 0 -10000 0 0
NFATC1 0.01 0.037 -10000 0 -0.4 5 5
POU2F1 0.011 0.036 -10000 0 -0.74 1 1
CDKN1A 0.028 0.055 -10000 0 -1.3 1 1
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 0.023 -10000 0 -0.4 2 2
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.11 0.1 0.34 9 -10000 0 9
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.024 0.14 0.45 14 -0.64 5 19
JUN -0.28 0.17 -10000 0 -0.55 104 104
IL4 -0.095 0.12 -10000 0 -0.5 4 4
CDK5R1 0.012 0.03 -10000 0 -0.74 1 1
PRKACA 0.013 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.31 0.24 -10000 0 -0.6 171 171
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.11 0.1 0.33 12 -10000 0 12
cortisol/GR alpha (monomer) 0.29 0.27 0.63 149 -0.58 4 153
NCOA2 0.011 0.028 -10000 0 -0.4 3 3
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.097 0.064 -10000 0 -0.47 10 10
AP-1/NFAT1-c-4 -0.49 0.28 -10000 0 -0.79 200 200
AFP -0.22 0.19 -10000 0 -0.74 47 47
SUV420H1 0.013 0 -10000 0 -10000 0 0
IRF1 0.15 0.13 0.42 33 -10000 0 33
TP53 0.03 0.019 -10000 0 -0.45 1 1
PPP5C 0.013 0 -10000 0 -10000 0 0
KRT17 -0.64 0.31 -10000 0 -0.81 424 424
KRT14 -0.14 0.22 -10000 0 -0.94 28 28
TBP 0.02 0.014 -10000 0 -10000 0 0
CREBBP 0.033 0.07 0.31 7 -10000 0 7
HDAC1 0.012 0.008 -10000 0 -10000 0 0
HDAC2 0.032 0.025 -10000 0 -10000 0 0
AP-1 -0.49 0.28 -10000 0 -0.8 201 201
MAPK14 0.013 0.006 -10000 0 -10000 0 0
MAPK10 -0.038 0.13 -10000 0 -0.39 78 78
MAPK11 0.01 0.044 -10000 0 -0.77 2 2
KRT5 -0.39 0.32 -10000 0 -0.86 150 150
interleukin-1 receptor activity 0.019 0.025 -10000 0 -10000 0 0
NCOA1 0.015 0.001 -10000 0 -10000 0 0
STAT1 0.019 0.03 -10000 0 -0.74 1 1
CGA -0.095 0.14 -10000 0 -0.62 14 14
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.18 0.2 0.4 212 -0.4 10 222
MAPK3 0.012 0.018 -10000 0 -0.4 1 1
MAPK1 0.012 0.017 -10000 0 -0.4 1 1
ICAM1 -0.18 0.22 -10000 0 -0.6 71 71
NFKB1 -0.055 0.083 -10000 0 -10000 0 0
MAPK8 -0.21 0.15 -10000 0 -0.44 95 95
MAPK9 0.013 0.006 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.01 0.16 0.48 16 -0.61 8 24
BAX 0.029 0.02 -10000 0 -10000 0 0
POMC -0.15 0.27 -10000 0 -1.3 25 25
EP300 0.036 0.072 0.31 9 -10000 0 9
cortisol/GR alpha (dimer)/p53 0.27 0.22 0.54 150 -0.49 4 154
proteasomal ubiquitin-dependent protein catabolic process 0.068 0.06 0.24 5 -10000 0 5
SGK1 0.043 0.27 -10000 0 -1.2 25 25
IL13 -0.25 0.22 -10000 0 -0.79 52 52
IL6 -0.24 0.32 -10000 0 -0.87 101 101
PRKACG 0.001 0.043 -10000 0 -0.75 2 2
IL5 -0.21 0.16 -10000 0 -0.72 20 20
IL2 -0.31 0.21 -10000 0 -0.67 91 91
CDK5 0.013 0.003 -10000 0 -10000 0 0
PRKACB -0.037 0.13 -10000 0 -0.4 76 76
HSP90AA1 0.013 0 -10000 0 -10000 0 0
IL8 -0.41 0.38 -10000 0 -0.72 343 343
CDK5R1/CDK5 0.018 0.025 -10000 0 -0.56 1 1
NF kappa B1 p50/RelA/PKAc -0.079 0.13 -10000 0 -0.48 6 6
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.25 0.21 0.54 110 -0.48 3 113
SMARCA4 0.012 0.012 -10000 0 -10000 0 0
chromatin remodeling 0.14 0.17 0.39 61 -0.5 15 76
NF kappa B1 p50/RelA/Cbp -0.038 0.13 0.38 3 -0.45 2 5
JUN (dimer) -0.28 0.17 -10000 0 -0.54 104 104
YWHAH 0.013 0 -10000 0 -10000 0 0
VIPR1 -0.11 0.19 -10000 0 -0.61 53 53
NR3C1 0.15 0.19 0.45 67 -0.41 23 90
NR4A1 -0.011 0.14 -10000 0 -0.57 31 31
TIF2/SUV420H1 0.017 0.02 -10000 0 -10000 0 0
MAPKKK cascade 0.014 0.16 0.48 16 -0.58 8 24
cortisol/GR alpha (dimer)/Src-1 0.26 0.22 0.54 141 -0.5 4 145
PBX1 0.004 0.061 -10000 0 -0.39 13 13
POU1F1 0.001 0.042 -10000 0 -0.9 1 1
SELE -0.26 0.34 -10000 0 -0.82 133 133
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.14 0.17 0.39 60 -0.51 15 75
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.25 0.21 0.54 110 -0.48 3 113
mol:cortisol 0.16 0.15 0.35 169 -0.21 2 171
MMP1 -0.46 0.29 -10000 0 -0.67 405 405
Presenilin action in Notch and Wnt signaling

Figure S18.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S18.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.001 0.018 -10000 0 -10000 0 0
HDAC1 0.01 0.004 -10000 0 -10000 0 0
AES 0.012 0.001 -10000 0 -10000 0 0
FBXW11 0.013 0 -10000 0 -10000 0 0
DTX1 0.009 0.036 -10000 0 -0.4 5 5
LRP6/FZD1 0.018 0.016 -10000 0 -10000 0 0
TLE1 0.011 0.016 -10000 0 -0.4 1 1
AP1 -0.17 0.14 -10000 0 -0.26 413 413
NCSTN 0.013 0 -10000 0 -10000 0 0
ADAM10 0.012 0 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.058 0.04 -10000 0 -0.45 1 1
NICD/RBPSUH 0.03 0.012 -10000 0 -10000 0 0
WIF1 -0.15 0.31 -10000 0 -0.75 127 127
NOTCH1 0 0.012 -10000 0 -10000 0 0
PSENEN 0.012 0.016 -10000 0 -0.4 1 1
KREMEN2 -0.08 0.25 -10000 0 -0.75 76 76
DKK1 -0.15 0.31 -10000 0 -0.75 131 131
beta catenin/beta TrCP1 0.13 0.08 0.23 1 -10000 0 1
APH1B 0.013 0.001 -10000 0 -10000 0 0
APH1A 0.013 0 -10000 0 -10000 0 0
AXIN1 -0.043 0.038 -10000 0 -0.41 1 1
CtBP/CBP/TCF1/TLE1/AES 0.02 0.02 -10000 0 -10000 0 0
PSEN1 0.013 0 -10000 0 -10000 0 0
FOS 0.006 0.051 -10000 0 -0.4 10 10
JUN 0.013 0 -10000 0 -10000 0 0
MAP3K7 0.011 0.002 -10000 0 -10000 0 0
CTNNB1 0.13 0.086 0.2 294 -10000 0 294
MAPK3 0.012 0.016 -10000 0 -0.4 1 1
DKK2/LRP6/Kremen 2 -0.11 0.23 -10000 0 -0.51 154 154
HNF1A 0.011 0.023 -10000 0 -0.39 2 2
CTBP1 0.012 0.001 -10000 0 -10000 0 0
MYC 0.016 0.076 -10000 0 -0.55 11 11
NKD1 -0.5 0.36 -10000 0 -0.75 415 415
FZD1 0.011 0.023 -10000 0 -0.4 2 2
NOTCH1 precursor/Deltex homolog 1 0.028 0.021 -10000 0 -10000 0 0
apoptosis -0.17 0.14 -10000 0 -0.26 413 413
Delta 1/NOTCHprecursor 0.029 0.02 -10000 0 -10000 0 0
DLL1 0.01 0.033 -10000 0 -0.4 4 4
PPARD 0.023 0.053 -10000 0 -1.3 1 1
Gamma Secretase 0.038 0.009 -10000 0 -10000 0 0
APC -0.049 0.061 -10000 0 -0.44 10 10
DVL1 0.008 0.041 -10000 0 -0.35 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 -0.14 0.26 -10000 0 -0.53 191 191
LRP6 0.013 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 0.021 0.052 -10000 0 -0.55 5 5
WNT1 0.005 0.053 -10000 0 -0.75 3 3
Axin1/APC/beta catenin 0.071 0.049 -10000 0 -0.41 1 1
DKK2 -0.095 0.26 -10000 0 -0.73 90 90
NOTCH1 precursor/DVL1 -0.007 0.02 -10000 0 -10000 0 0
GSK3B 0.012 0.001 -10000 0 -10000 0 0
FRAT1 0.012 0.001 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.001 0.019 -10000 0 -10000 0 0
PPP2R5D 0.21 0.15 0.32 415 -10000 0 415
MAPK1 0.012 0.016 -10000 0 -0.4 1 1
WNT1/LRP6/FZD1 -0.072 0.2 -10000 0 -0.45 129 129
RBPJ 0.013 0 -10000 0 -10000 0 0
CREBBP 0.015 0.003 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.009 0.036 -9999 0 -0.4 5 5
LAT2 -0.085 0.16 -9999 0 -0.38 95 95
AP1 -0.1 0.22 -9999 0 -0.61 70 70
mol:PIP3 -0.1 0.2 -9999 0 -0.47 104 104
IKBKB -0.067 0.13 -9999 0 -0.31 84 84
AKT1 -0.045 0.12 -9999 0 -0.42 2 2
IKBKG -0.068 0.13 -9999 0 -0.31 84 84
MS4A2 -0.11 0.18 -9999 0 -0.4 184 184
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.011 0.016 -9999 0 -0.4 1 1
MAP3K1 -0.079 0.18 -9999 0 -0.49 53 53
mol:Ca2+ -0.076 0.15 -9999 0 -0.35 104 104
LYN 0.012 0.003 -9999 0 -10000 0 0
CBLB -0.084 0.15 -9999 0 -0.38 95 95
SHC1 0.013 0 -9999 0 -10000 0 0
RasGAP/p62DOK 0.023 0.015 -9999 0 -10000 0 0
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.012 0.016 -9999 0 -0.4 1 1
PLD2 -0.075 0.14 -9999 0 -0.41 13 13
PTPN13 -0.1 0.19 -9999 0 -0.42 114 114
PTPN11 0.009 0.008 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.043 0.13 -9999 0 -0.35 13 13
SYK 0.012 0.003 -9999 0 -10000 0 0
GRB2 0.012 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.14 0.18 -9999 0 -0.48 105 105
LAT -0.085 0.16 -9999 0 -0.38 96 96
PAK2 -0.094 0.2 -9999 0 -0.53 63 63
NFATC2 -0.055 0.11 -9999 0 -0.57 21 21
HRAS -0.11 0.21 -9999 0 -0.48 117 117
GAB2 0.013 0 -9999 0 -10000 0 0
PLA2G1B 0.032 0.021 -9999 0 -10000 0 0
Fc epsilon R1 -0.11 0.17 -9999 0 -0.44 93 93
Antigen/IgE/Fc epsilon R1 -0.098 0.16 -9999 0 -0.39 93 93
mol:GDP -0.12 0.24 -9999 0 -0.54 121 121
JUN 0.013 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 0.006 0.051 -9999 0 -0.4 10 10
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.094 0.16 -9999 0 -0.4 95 95
CHUK -0.067 0.13 -9999 0 -0.31 84 84
KLRG1 -0.077 0.14 -9999 0 -0.34 95 95
VAV1 -0.091 0.17 -9999 0 -0.4 104 104
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.083 0.15 -9999 0 -0.38 95 95
negative regulation of mast cell degranulation -0.066 0.13 -9999 0 -0.49 13 13
BTK -0.14 0.27 -9999 0 -0.59 128 128
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.13 0.22 -9999 0 -0.53 123 123
GAB2/PI3K/SHP2 -0.079 0.11 -9999 0 -0.45 5 5
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.09 0.16 -9999 0 -0.42 93 93
RAF1 0.025 0.024 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.1 0.18 -9999 0 -0.56 38 38
FCER1G 0.013 0.042 -9999 0 -0.41 6 6
FCER1A -0.11 0.19 -9999 0 -0.41 179 179
Antigen/IgE/Fc epsilon R1/Fyn -0.085 0.14 -9999 0 -0.36 93 93
MAPK3 0.032 0.021 -9999 0 -10000 0 0
MAPK1 0.032 0.021 -9999 0 -10000 0 0
NFKB1 0.013 0 -9999 0 -10000 0 0
MAPK8 -0.017 0.072 -9999 0 -0.47 4 4
DUSP1 0.011 0.028 -9999 0 -0.4 3 3
NF-kappa-B/RelA -0.054 0.066 -9999 0 -0.23 2 2
actin cytoskeleton reorganization -0.095 0.17 -9999 0 -0.42 95 95
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.11 0.16 -9999 0 -0.5 53 53
FER -0.085 0.16 -9999 0 -0.38 98 98
RELA 0.013 0 -9999 0 -10000 0 0
ITK -0.035 0.098 -9999 0 -0.44 29 29
SOS1 0.013 0 -9999 0 -10000 0 0
PLCG1 -0.12 0.23 -9999 0 -0.52 121 121
cytokine secretion -0.039 0.048 -9999 0 -10000 0 0
SPHK1 -0.11 0.18 -9999 0 -0.41 128 128
PTK2 -0.099 0.18 -9999 0 -0.44 95 95
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.14 0.19 -9999 0 -0.5 104 104
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.1 0.2 -9999 0 -0.46 107 107
MAP2K2 0.028 0.023 -9999 0 -10000 0 0
MAP2K1 0.029 0.021 -9999 0 -10000 0 0
MAP2K7 0.012 0.016 -9999 0 -0.4 1 1
KLRG1/SHP2 -0.064 0.13 -9999 0 -0.47 13 13
MAP2K4 0.007 0.075 -9999 0 -0.92 4 4
Fc epsilon R1/FcgammaRIIB -0.12 0.19 -9999 0 -0.44 123 123
mol:Choline -0.074 0.14 -9999 0 -0.4 13 13
SHC/Grb2/SOS1 -0.068 0.15 -9999 0 -0.5 13 13
FYN 0.013 0 -9999 0 -10000 0 0
DOK1 0.013 0 -9999 0 -10000 0 0
PXN -0.087 0.17 -9999 0 -0.4 95 95
HCLS1 -0.085 0.16 -9999 0 -0.38 95 95
PRKCB -0.1 0.18 -9999 0 -0.39 143 143
FCGR2B -0.037 0.13 -9999 0 -0.4 75 75
IGHE -0.002 0.005 -9999 0 -10000 0 0
KLRG1/SHIP -0.067 0.14 -9999 0 -0.5 13 13
LCP2 0.008 0.04 -9999 0 -0.4 6 6
PLA2G4A -0.11 0.18 -9999 0 -0.4 137 137
RASA1 0.013 0.001 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.074 0.14 -9999 0 -0.4 13 13
IKK complex -0.04 0.1 -9999 0 -0.24 47 47
WIPF1 0.011 0.028 -9999 0 -0.4 3 3
Visual signal transduction: Rods

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
mol:K + 0.013 0 -9999 0 -10000 0 0
GNAT1/GTP 0.001 0.023 -9999 0 -0.58 1 1
Metarhodopsin II/Arrestin 0 0.035 -9999 0 -0.5 3 3
PDE6G/GNAT1/GTP -0.004 0.059 -9999 0 -0.5 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.001 0.031 -9999 0 -0.75 1 1
GRK1 -0.002 0.052 -9999 0 -0.75 3 3
CNG Channel -0.15 0.14 -9999 0 -0.53 28 28
mol:Na + -0.076 0.15 -9999 0 -0.59 26 26
mol:ADP -0.002 0.052 -9999 0 -0.75 3 3
RGS9-1/Gbeta5/R9AP -0.019 0.098 -9999 0 -0.49 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.062 0.17 -9999 0 -0.64 23 23
CNGB1 -0.048 0.14 -9999 0 -0.4 83 83
RDH5 -0.017 0.1 -9999 0 -0.4 45 45
SAG 0.003 0.005 -9999 0 -10000 0 0
mol:Ca2+ -0.052 0.16 -9999 0 -0.61 22 22
Na + (4 Units) -0.07 0.14 -9999 0 -0.58 22 22
RGS9 -0.055 0.15 -9999 0 -0.4 103 103
GNB1/GNGT1 -0.16 0.27 -9999 0 -0.57 186 186
GNAT1/GDP -0.015 0.084 -9999 0 -0.42 5 5
GUCY2D -0.021 0.15 -9999 0 -0.75 24 24
GNGT1 -0.22 0.35 -9999 0 -0.75 186 186
GUCY2F -0.001 0.03 -9999 0 -0.75 1 1
GNB5 0.013 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.12 0.12 -9999 0 -0.39 43 43
mol:11-cis-retinal -0.017 0.1 -9999 0 -0.39 45 45
mol:cGMP -0.029 0.15 -9999 0 -0.47 60 60
GNB1 0.013 0 -9999 0 -10000 0 0
Rhodopsin -0.013 0.083 -9999 0 -0.3 43 43
SLC24A1 0.013 0 -9999 0 -10000 0 0
CNGA1 -0.024 0.12 -9999 0 -0.4 56 56
Metarhodopsin II -0.002 0.051 -9999 0 -0.55 5 5
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.029 0.16 -9999 0 -0.49 60 60
RGS9BP 0.006 0.061 -9999 0 -0.75 4 4
Metarhodopsin II/Transducin -0.068 0.12 -9999 0 -0.25 187 187
GCAP Family/Ca ++ -0.017 0.12 -9999 0 -0.46 41 41
PDE6A/B -0.16 0.15 -9999 0 -0.28 369 369
mol:Pi -0.019 0.097 -9999 0 -0.49 4 4
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.13 0.22 -9999 0 -0.46 186 186
PDE6B -0.008 0.091 -9999 0 -0.41 30 30
PDE6A -0.22 0.2 -9999 0 -0.4 359 359
PDE6G -0.011 0.094 -9999 0 -0.4 35 35
RHO -0.003 0.052 -9999 0 -0.75 3 3
PDE6 -0.13 0.15 -9999 0 -0.54 22 22
GUCA1A -0.036 0.18 -9999 0 -0.75 37 37
GC2/GCAP Family -0.017 0.12 -9999 0 -0.47 41 41
GUCA1C 0 0 -9999 0 -10000 0 0
GUCA1B 0.008 0.061 -9999 0 -0.75 4 4
Signaling events mediated by the Hedgehog family

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
TGFB2 0.019 0.14 -10000 0 -0.6 26 26
IHH 0.007 0.078 -10000 0 -0.45 16 16
SHH Np/Cholesterol/GAS1 -0.11 0.21 -10000 0 -0.49 125 125
LRPAP1 0.013 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.11 0.2 0.48 125 -10000 0 125
SMO/beta Arrestin2 0.013 0.094 -10000 0 -0.51 7 7
SMO 0.007 0.099 -10000 0 -0.49 10 10
AKT1 0.023 0.05 -10000 0 -0.31 1 1
ARRB2 0.013 0 -10000 0 -10000 0 0
BOC -0.004 0.081 -10000 0 -0.4 26 26
ADRBK1 0.013 0 -10000 0 -10000 0 0
heart looping 0.007 0.097 -10000 0 -0.49 10 10
STIL -0.05 0.18 -10000 0 -0.5 13 13
DHH N/PTCH2 0.004 0.07 -10000 0 -0.32 26 26
DHH N/PTCH1 0.018 0.09 -10000 0 -0.48 8 8
PIK3CA 0.012 0.016 -10000 0 -0.4 1 1
DHH -0.003 0.075 -10000 0 -0.4 22 22
PTHLH 0.015 0.16 -10000 0 -0.87 14 14
determination of left/right symmetry 0.007 0.097 -10000 0 -0.49 10 10
PIK3R1 0.013 0 -10000 0 -10000 0 0
skeletal system development 0.016 0.16 -10000 0 -0.86 14 14
IHH N/Hhip -0.044 0.14 -10000 0 -0.32 117 117
DHH N/Hhip -0.045 0.13 -10000 0 -0.51 11 11
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.007 0.097 -10000 0 -0.49 10 10
pancreas development -0.063 0.16 -10000 0 -0.39 116 116
HHAT 0.009 0.036 -10000 0 -0.4 5 5
PI3K 0.018 0.011 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.054 0.16 -10000 0 -0.41 99 99
somite specification 0.007 0.097 -10000 0 -0.49 10 10
SHH Np/Cholesterol/PTCH1 -0.057 0.18 -10000 0 -0.41 123 123
SHH Np/Cholesterol/PTCH2 -0.074 0.19 -10000 0 -0.45 124 124
SHH Np/Cholesterol/Megalin -0.12 0.23 -10000 0 -0.49 163 163
SHH -0.097 0.23 -10000 0 -0.56 125 125
catabolic process 0.022 0.088 -10000 0 -0.51 7 7
SMO/Vitamin D3 -0.046 0.18 -10000 0 -0.55 11 11
SHH Np/Cholesterol/Hhip -0.11 0.2 -10000 0 -0.47 123 123
LRP2 -0.062 0.22 -10000 0 -0.75 56 56
receptor-mediated endocytosis -0.062 0.19 -10000 0 -0.57 25 25
SHH Np/Cholesterol/BOC -0.08 0.19 -10000 0 -0.46 120 120
SHH Np/Cholesterol/CDO -0.072 0.19 -10000 0 -0.45 120 120
mesenchymal cell differentiation 0.11 0.19 0.46 123 -10000 0 123
mol:Vitamin D3 -0.054 0.19 -10000 0 -0.41 123 123
IHH N/PTCH2 0.012 0.069 -10000 0 -0.43 10 10
CDON 0.012 0.016 -10000 0 -0.4 1 1
IHH N/PTCH1 0.024 0.089 -10000 0 -0.52 7 7
Megalin/LRPAP1 -0.038 0.17 -10000 0 -0.57 56 56
PTCH2 0.008 0.061 -10000 0 -0.75 4 4
SHH Np/Cholesterol -0.079 0.19 -10000 0 -0.46 120 120
PTCH1 0.022 0.088 -10000 0 -0.51 7 7
HHIP -0.064 0.16 -10000 0 -0.4 116 116
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.009 0.04 -9999 0 -0.26 3 3
NFATC2 -0.015 0.055 -9999 0 -0.27 14 14
NFATC3 -0.007 0.033 -9999 0 -10000 0 0
CD40LG -0.13 0.24 -9999 0 -0.58 68 68
PTGS2 -0.14 0.25 -9999 0 -0.68 56 56
JUNB 0.011 0.023 -9999 0 -0.4 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.006 0.021 -9999 0 -10000 0 0
CaM/Ca2+ -0.006 0.021 -9999 0 -10000 0 0
CALM1 0.004 0.012 -9999 0 -10000 0 0
JUN 0.005 0.011 -9999 0 -10000 0 0
mol:Ca2+ -0.011 0.013 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.003 0.007 -9999 0 -10000 0 0
FOSL1 -0.47 0.37 -9999 0 -0.75 390 390
CREM 0.012 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.063 0.14 -9999 0 -0.59 9 9
FOS -0.002 0.051 -9999 0 -0.39 10 10
IFNG -0.15 0.28 -9999 0 -0.71 83 83
AP-1/NFAT1-c-4 -0.14 0.25 -9999 0 -0.65 63 63
FASLG -0.13 0.23 -9999 0 -0.59 53 53
NFAT1-c-4/ICER1 -0.03 0.088 -9999 0 -0.39 3 3
IL2RA -0.12 0.22 -9999 0 -0.56 68 68
FKBP12/FK506 0.009 0 -9999 0 -10000 0 0
CSF2 -0.26 0.36 -9999 0 -0.65 263 263
JunB/Fra1/NFAT1-c-4 -0.28 0.22 -9999 0 -0.49 259 259
IL4 -0.12 0.22 -9999 0 -0.56 50 50
IL2 -0.007 0.011 -9999 0 -10000 0 0
IL3 -0.018 0.021 -9999 0 -10000 0 0
FKBP1A 0.013 0 -9999 0 -10000 0 0
BATF3 0.004 0.076 -9999 0 -0.7 7 7
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.011 0.031 -9999 0 -0.75 1 1
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.17 0.24 -9999 0 -0.44 258 258
SMAD6-7/SMURF1 0.024 0.031 -9999 0 -0.49 2 2
NOG 0.007 0.043 -9999 0 -0.75 2 2
SMAD9 -0.047 0.16 -9999 0 -0.55 51 51
SMAD4 0.011 0.023 -9999 0 -0.4 2 2
SMAD5 -0.025 0.11 -9999 0 -0.34 30 30
BMP7/USAG1 -0.25 0.29 -9999 0 -0.6 231 231
SMAD5/SKI -0.017 0.1 -9999 0 -0.35 19 19
SMAD1 0.031 0.025 -9999 0 -10000 0 0
BMP2 -0.014 0.1 -9999 0 -0.4 41 41
SMAD1/SMAD1/SMAD4 -0.003 0.021 -9999 0 -10000 0 0
BMPR1A 0.013 0 -9999 0 -10000 0 0
BMPR1B -0.04 0.18 -9999 0 -0.66 47 47
BMPR1A-1B/BAMBI -0.039 0.17 -9999 0 -0.5 70 70
AHSG -0.087 0.25 -9999 0 -0.75 78 78
CER1 -0.015 0.12 -9999 0 -0.75 16 16
BMP2-4/CER1 -0.042 0.16 -9999 0 -0.53 55 55
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.039 0.12 -9999 0 -0.35 50 50
BMP2-4 (homodimer) -0.038 0.16 -9999 0 -0.6 39 39
RGMB 0.013 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.008 0.12 -9999 0 -0.44 36 36
RGMA -0.075 0.17 -9999 0 -0.4 134 134
SMURF1 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.044 0.12 -9999 0 -0.36 48 48
BMP2-4/USAG1 -0.067 0.17 -9999 0 -0.52 53 53
SMAD6/SMURF1/SMAD5 -0.017 0.1 -9999 0 -0.35 19 19
SOSTDC1 -0.062 0.16 -9999 0 -0.4 114 114
BMP7/BMPR2/BMPR1A-1B -0.18 0.25 -9999 0 -0.46 254 254
SKI 0.013 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.002 0.077 -9999 0 -0.39 23 23
HFE2 0.001 0.043 -9999 0 -0.75 2 2
ZFYVE16 0.011 0.023 -9999 0 -0.4 2 2
MAP3K7 0.013 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.024 0.14 -9999 0 -0.52 39 39
SMAD5/SMAD5/SMAD4 -0.018 0.1 -9999 0 -0.35 19 19
MAPK1 0.012 0.016 -9999 0 -0.4 1 1
TAK1/TAB family -0.054 0.089 -9999 0 -0.34 18 18
BMP7 (homodimer) -0.27 0.36 -9999 0 -0.73 237 237
NUP214 0.013 0 -9999 0 -10000 0 0
BMP6/FETUA -0.068 0.2 -9999 0 -0.58 78 78
SMAD1/SKI 0.037 0.025 -9999 0 -10000 0 0
SMAD6 0.01 0.043 -9999 0 -0.75 2 2
CTDSP2 0.013 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.089 0.22 -9999 0 -0.54 109 109
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.015 0.12 -9999 0 -0.5 34 34
BMPR2 (homodimer) 0.012 0.016 -9999 0 -0.39 1 1
GADD34/PP1CA 0.025 0.014 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.021 0.14 -9999 0 -0.49 47 47
CHRDL1 -0.21 0.2 -9999 0 -0.4 339 339
ENDOFIN/SMAD1 0.036 0.027 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 0.044 0.032 -9999 0 -10000 0 0
SMAD6/SMURF1 0.013 0 -9999 0 -10000 0 0
BAMBI -0.032 0.18 -9999 0 -0.74 37 37
SMURF2 0.011 0.035 -9999 0 -0.57 2 2
BMP2-4/CHRDL1 -0.15 0.18 -9999 0 -0.54 65 65
BMP2-4/GREM1 -0.041 0.16 -9999 0 -0.52 51 51
SMAD7 0.012 0.016 -9999 0 -0.4 1 1
SMAD8A/SMAD8A/SMAD4 -0.038 0.16 -9999 0 -0.52 50 50
SMAD1/SMAD6 0.037 0.025 -9999 0 -10000 0 0
TAK1/SMAD6 0.019 0 -9999 0 -10000 0 0
BMP7 -0.27 0.36 -9999 0 -0.73 237 237
BMP6 -0.003 0.077 -9999 0 -0.4 23 23
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.037 0.11 -9999 0 -0.33 49 49
PPM1A 0.013 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.036 0.031 -9999 0 -0.38 1 1
SMAD7/SMURF1 0.018 0.011 -9999 0 -0.27 1 1
CTDSPL 0.013 0 -9999 0 -10000 0 0
PPP1CA 0.013 0 -9999 0 -10000 0 0
XIAP 0.013 0 -9999 0 -10000 0 0
CTDSP1 0.013 0 -9999 0 -10000 0 0
PPP1R15A 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.06 0.15 -9999 0 -0.44 58 58
CHRD 0.012 0.016 -9999 0 -0.4 1 1
BMPR2 0.012 0.016 -9999 0 -0.4 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.052 0.13 -9999 0 -0.39 48 48
BMP4 -0.037 0.19 -9999 0 -0.73 42 42
FST -0.005 0.088 -9999 0 -0.42 25 25
BMP2-4/NOG -0.027 0.14 -9999 0 -0.52 41 41
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.16 0.23 -9999 0 -0.44 254 254
Ephrin B reverse signaling

Figure S24.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S24.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.013 0 -10000 0 -10000 0 0
EPHB2 0.008 0.053 -10000 0 -0.75 3 3
EFNB1 0.011 0.062 -10000 0 -0.57 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.077 0.19 -10000 0 -0.41 138 138
Ephrin B2/EPHB1-2 -0.078 0.2 -10000 0 -0.46 132 132
neuron projection morphogenesis -0.099 0.17 -10000 0 -0.4 138 138
Ephrin B1/EPHB1-2/Tiam1 -0.087 0.2 -10000 0 -0.44 139 139
DNM1 0.003 0.081 -10000 0 -0.75 7 7
cell-cell signaling -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.001 0.077 -10000 0 -0.64 6 6
YES1 -0.015 0.096 -10000 0 -0.71 8 8
Ephrin B1/EPHB1-2/NCK2 -0.067 0.19 -10000 0 -0.42 138 138
PI3K 0.003 0.078 -10000 0 -0.64 6 6
mol:GDP -0.087 0.2 -10000 0 -0.44 139 139
ITGA2B -0.019 0.15 -10000 0 -0.75 25 25
endothelial cell proliferation 0.017 0.001 -10000 0 -10000 0 0
FYN -0.014 0.096 -10000 0 -0.62 10 10
MAP3K7 -0.007 0.08 -10000 0 -0.68 6 6
FGR -0.017 0.099 -10000 0 -0.8 7 7
TIAM1 -0.028 0.12 -10000 0 -0.4 62 62
PIK3R1 0.013 0 -10000 0 -10000 0 0
RGS3 0.013 0 -10000 0 -10000 0 0
cell adhesion -0.005 0.11 -10000 0 -0.45 30 30
LYN -0.014 0.096 -10000 0 -0.62 10 10
Ephrin B1/EPHB1-2/Src Family Kinases -0.015 0.088 -10000 0 -0.36 28 28
Ephrin B1/EPHB1-2 -0.02 0.085 -10000 0 -0.36 28 28
SRC -0.015 0.096 -10000 0 -0.39 28 28
ITGB3 0.008 0.043 -10000 0 -0.4 7 7
EPHB1 -0.15 0.31 -10000 0 -0.75 132 132
EPHB4 0.013 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.017 0.001 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.009 0.12 -10000 0 -0.5 32 32
BLK -0.077 0.13 -10000 0 -0.57 19 19
HCK -0.021 0.1 -10000 0 -0.4 28 28
regulation of stress fiber formation 0.067 0.19 0.42 138 -10000 0 138
MAPK8 0.005 0.073 -10000 0 -0.6 6 6
Ephrin B1/EPHB1-2/RGS3 -0.067 0.19 -10000 0 -0.42 138 138
endothelial cell migration -0.003 0.071 -10000 0 -0.57 6 6
NCK2 0.013 0 -10000 0 -10000 0 0
PTPN13 -0.015 0.14 -10000 0 -0.66 28 28
regulation of focal adhesion formation 0.067 0.19 0.42 138 -10000 0 138
chemotaxis 0.067 0.19 0.42 138 -10000 0 138
PIK3CA 0.012 0.016 -10000 0 -0.4 1 1
Rac1/GTP -0.079 0.18 -10000 0 -0.41 138 138
angiogenesis -0.02 0.085 -10000 0 -0.36 28 28
LCK -0.017 0.098 -10000 0 -0.45 19 19
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.007 0.11 -9999 0 -0.49 31 31
EPHB2 0.009 0.053 -9999 0 -0.75 3 3
Syndecan-2/TACI -0.085 0.12 -9999 0 -0.43 4 4
LAMA1 -0.11 0.18 -9999 0 -0.4 181 181
Syndecan-2/alpha2 ITGB1 0.032 0.03 -9999 0 -0.42 1 1
HRAS 0.012 0.016 -9999 0 -0.4 1 1
Syndecan-2/CASK 0.011 0.019 -9999 0 -0.22 4 4
ITGA5 0.01 0.043 -9999 0 -0.75 2 2
BAX 0.031 0.017 -9999 0 -10000 0 0
EPB41 0.013 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion 0.018 0.021 -9999 0 -10000 0 0
LAMA3 0.008 0.047 -9999 0 -0.45 6 6
EZR 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.008 0.058 -9999 0 -0.61 5 5
Syndecan-2/MMP2 0.015 0.053 -9999 0 -0.48 6 6
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 0.019 0 -9999 0 -10000 0 0
dendrite morphogenesis 0.018 0.04 -9999 0 -0.49 3 3
Syndecan-2/GM-CSF -0.19 0.25 -9999 0 -0.49 256 256
determination of left/right symmetry 0.015 0.023 -9999 0 -0.27 4 4
Syndecan-2/PKC delta 0.02 0.019 -9999 0 -10000 0 0
GNB2L1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.17 0.23 -9999 0 -0.44 256 256
MAPK1 -0.17 0.23 -9999 0 -0.44 256 256
Syndecan-2/RACK1 0.025 0.018 -9999 0 -10000 0 0
NF1 0.013 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.015 0.023 -9999 0 -0.27 4 4
ITGA2 0.013 0 -9999 0 -10000 0 0
MAPK8 0.026 0.019 -9999 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin -0.026 0.095 -9999 0 -0.36 1 1
Syndecan-2/Kininogen -0.032 0.1 -9999 0 -0.43 2 2
ITGB1 0.013 0 -9999 0 -10000 0 0
SRC 0.029 0.017 -9999 0 -10000 0 0
Syndecan-2/CASK/Protein 4.1 0.019 0.017 -9999 0 -10000 0 0
extracellular matrix organization 0.019 0.028 -9999 0 -0.49 1 1
actin cytoskeleton reorganization -0.007 0.11 -9999 0 -0.48 31 31
Syndecan-2/Caveolin-2/Ras 0.024 0.042 -9999 0 -0.43 4 4
Syndecan-2/Laminin alpha3 0.018 0.035 -9999 0 -0.49 1 1
Syndecan-2/RasGAP 0.031 0.017 -9999 0 -10000 0 0
alpha5/beta1 Integrin 0.017 0.033 -9999 0 -0.57 2 2
PRKCD 0.013 0 -9999 0 -10000 0 0
Syndecan-2 dimer 0.018 0.04 -9999 0 -0.49 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 0.036 0.017 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
SDCBP 0.011 0.023 -9999 0 -0.4 2 2
TNFRSF13B -0.17 0.2 -9999 0 -0.4 270 270
RASA1 0.013 0.001 -9999 0 -10000 0 0
alpha2/beta1 Integrin 0.019 0 -9999 0 -10000 0 0
Syndecan-2/Synbindin 0.02 0.019 -9999 0 -10000 0 0
TGFB1 0.011 0.031 -9999 0 -0.75 1 1
CASP3 0.025 0.017 -9999 0 -10000 0 0
FN1 -0.028 0.17 -9999 0 -0.67 37 37
Syndecan-2/IL8 -0.27 0.25 -9999 0 -0.49 347 347
SDC2 0.015 0.023 -9999 0 -0.27 4 4
KNG1 -0.076 0.16 -9999 0 -0.4 132 132
Syndecan-2/Neurofibromin 0.02 0.019 -9999 0 -10000 0 0
TRAPPC4 0.013 0 -9999 0 -10000 0 0
CSF2 -0.3 0.38 -9999 0 -0.75 256 256
Syndecan-2/TGFB1 0.02 0.028 -9999 0 -0.49 1 1
Syndecan-2/Syntenin/PI-4-5-P2 0.018 0.021 -9999 0 -10000 0 0
Syndecan-2/Ezrin 0.027 0.017 -9999 0 -10000 0 0
PRKACA 0.025 0.017 -9999 0 -10000 0 0
angiogenesis -0.26 0.25 -9999 0 -0.49 347 347
MMP2 0.004 0.074 -9999 0 -0.62 8 8
IL8 -0.41 0.38 -9999 0 -0.75 347 347
calcineurin-NFAT signaling pathway -0.084 0.12 -9999 0 -0.43 4 4
IL1-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
UBC13/UEV1A -0.059 0.19 -9999 0 -0.57 76 76
PRKCZ 0.013 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.006 0.064 -9999 0 -10000 0 0
IRAK/TOLLIP -0.033 0.16 -9999 0 -0.45 76 76
IKBKB 0.013 0 -9999 0 -10000 0 0
IKBKG 0.012 0.016 -9999 0 -0.4 1 1
IL1 alpha/IL1R2 -0.21 0.26 -9999 0 -0.6 173 173
IL1A -0.2 0.34 -9999 0 -0.75 173 173
IL1B -0.035 0.17 -9999 0 -0.57 54 54
IRAK/TRAF6/p62/Atypical PKCs -0.012 0.14 -9999 0 -0.39 76 76
IL1R2 -0.087 0.18 -9999 0 -0.4 152 152
IL1R1 0.008 0.043 -9999 0 -0.4 7 7
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.002 0.081 -9999 0 -0.31 12 12
TOLLIP 0.013 0 -9999 0 -10000 0 0
TICAM2 0.003 0.056 -9999 0 -0.4 12 12
MAP3K3 0.013 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0.009 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.012 0.11 -9999 0 -0.49 1 1
JUN -0.012 0.12 -9999 0 -0.48 1 1
MAP3K7 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.001 0.13 -9999 0 -0.4 54 54
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.1 0.22 -9999 0 -0.45 173 173
PIK3R1 0.013 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.091 0.2 -9999 0 -0.42 173 173
IL1 beta fragment/IL1R1/IL1RAP -0.016 0.14 -9999 0 -0.44 55 55
NFKB1 0.013 0 -9999 0 -10000 0 0
MAPK8 -0.018 0.13 -9999 0 -0.36 76 76
IRAK1 -0.045 0.17 -9999 0 -0.5 76 76
IL1RN/IL1R1 -0.043 0.18 -9999 0 -0.57 62 62
IRAK4 0.013 0 -9999 0 -10000 0 0
PRKCI 0.011 0.023 -9999 0 -0.4 2 2
TRAF6 0.013 0 -9999 0 -10000 0 0
PI3K 0.018 0.011 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.009 0.073 -9999 0 -0.32 1 1
CHUK 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.016 0.14 -9999 0 -0.44 55 55
IL1 beta/IL1R2 -0.082 0.17 -9999 0 -0.5 59 59
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.025 0.14 -9999 0 -0.39 76 76
NF kappa B1 p50/RelA -0.034 0.1 -9999 0 -10000 0 0
IRAK3 0.005 0.056 -9999 0 -0.4 12 12
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.006 0.13 -9999 0 -0.4 54 54
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.043 0.12 -9999 0 -0.43 2 2
IL1 alpha/IL1R1/IL1RAP -0.12 0.23 -9999 0 -0.49 173 173
RELA 0.013 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.013 0 -9999 0 -10000 0 0
MYD88 0.013 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 -0.024 0.15 -9999 0 -0.42 76 76
IL1RAP 0.013 0 -9999 0 -10000 0 0
UBE2N 0.013 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.076 0.15 -9999 0 -0.6 19 19
CASP1 0.011 0.028 -9999 0 -0.4 3 3
IL1RN/IL1R2 -0.11 0.2 -9999 0 -0.57 62 62
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.007 0.13 -9999 0 -0.42 55 55
TMEM189-UBE2V1 -0.089 0.25 -9999 0 -0.74 78 78
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.045 0.11 -9999 0 -0.38 21 21
PIK3CA 0.012 0.016 -9999 0 -0.4 1 1
IL1RN -0.063 0.23 -9999 0 -0.75 62 62
TRAF6/TAK1/TAB1/TAB2 -0.032 0.14 -9999 0 -0.41 76 76
MAP2K6 -0.025 0.14 -9999 0 -0.38 76 76
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.014 0.017 -10000 0 -10000 0 0
AES 0.014 0.014 -10000 0 -10000 0 0
FBXW11 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.019 0.016 -10000 0 -10000 0 0
SMAD4 0.011 0.023 -10000 0 -0.4 2 2
DKK2 -0.095 0.26 -10000 0 -0.73 90 90
TLE1 0.013 0.02 -10000 0 -0.38 1 1
MACF1 0.013 0 -10000 0 -10000 0 0
CTNNB1 0.071 0.091 0.25 16 -10000 0 16
WIF1 -0.15 0.31 -10000 0 -0.75 127 127
beta catenin/RanBP3 0.031 0.11 0.31 73 -10000 0 73
KREMEN2 -0.08 0.25 -10000 0 -0.75 76 76
DKK1 -0.15 0.31 -10000 0 -0.75 131 131
beta catenin/beta TrCP1 0.074 0.086 0.25 13 -10000 0 13
FZD1 0.012 0.023 -10000 0 -0.39 2 2
AXIN2 -0.051 0.19 -10000 0 -0.55 74 74
AXIN1 0.013 0.016 -10000 0 -0.4 1 1
RAN 0.013 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.024 0.041 -10000 0 -0.52 1 1
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.045 0.084 -10000 0 -0.42 2 2
Axin1/APC/GSK3 0.11 0.061 -10000 0 -0.33 1 1
Axin1/APC/GSK3/beta catenin/Macf1 0.058 0.054 -10000 0 -10000 0 0
HNF1A 0.013 0.027 -10000 0 -0.4 2 2
CTBP1 0.014 0.014 -10000 0 -10000 0 0
MYC -0.004 0.087 -10000 0 -0.57 11 11
RANBP3 0.013 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.11 0.23 -10000 0 -0.51 154 154
NKD1 -0.5 0.36 -10000 0 -0.75 415 415
TCF4 0.012 0.032 -10000 0 -0.39 3 3
TCF3 0.014 0.014 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.029 0.037 -10000 0 -0.44 3 3
Ran/GTP 0.01 0.002 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.02 0.11 0.57 1 -10000 0 1
LEF1 -0.079 0.25 -10000 0 -0.74 76 76
DVL1 0.044 0.035 -10000 0 -0.25 1 1
CSNK2A1 0.013 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.039 0.093 -10000 0 -0.49 2 2
DKK1/LRP6/Kremen 2 -0.14 0.26 -10000 0 -0.53 191 191
LRP6 0.013 0.001 -10000 0 -10000 0 0
CSNK1A1 0.015 0.016 -10000 0 -10000 0 0
NLK 0.012 0.003 -10000 0 -10000 0 0
CCND1 0 0.068 -10000 0 -0.56 5 5
WNT1 0.005 0.053 -10000 0 -0.75 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 -10000 0 -10000 0 0
PPP2R5D 0.22 0.15 0.33 415 -10000 0 415
APC 0.026 0.042 -10000 0 -0.41 3 3
WNT1/LRP6/FZD1 0.065 0.081 0.22 126 -10000 0 126
CREBBP 0.014 0.014 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A -0.023 0.13 -9999 0 -0.58 34 34
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B 0.012 0.047 -9999 0 -0.57 4 4
STXBP1 0.004 0.081 -9999 0 -0.75 7 7
ACh/CHRNA1 -0.046 0.083 -9999 0 -0.27 57 57
RAB3GAP2/RIMS1/UNC13B 0.019 0.042 -9999 0 -0.49 4 4
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 0.003 0.061 -9999 0 -0.75 4 4
mol:ACh -0.042 0.056 -9999 0 -0.1 274 274
RAB3GAP2 0.012 0.016 -9999 0 -0.4 1 1
STX1A/SNAP25/VAMP2 -0.068 0.1 -9999 0 -0.38 44 44
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.046 0.083 -9999 0 -0.27 57 57
UNC13B 0.013 0 -9999 0 -10000 0 0
CHRNA1 -0.025 0.12 -9999 0 -0.4 57 57
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.053 0.095 -9999 0 -0.28 76 76
SNAP25 -0.094 0.12 -9999 0 -0.25 244 244
VAMP2 0.006 0 -9999 0 -10000 0 0
SYT1 -0.037 0.13 -9999 0 -0.4 76 76
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.017 0.13 -9999 0 -0.51 40 40
STX1A/SNAP25 fragment 1/VAMP2 -0.068 0.1 -9999 0 -0.38 44 44
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.007 0.12 -9999 0 -0.51 12 12
MAP3K8 0.013 0.001 -9999 0 -10000 0 0
FOS -0.016 0.11 -9999 0 -0.48 12 12
PRKCA 0.013 0.002 -9999 0 -10000 0 0
PTPN7 0 0.098 -9999 0 -0.62 14 14
HRAS 0.012 0.016 -9999 0 -0.39 1 1
PRKCB -0.083 0.17 -9999 0 -0.4 147 147
NRAS 0.011 0.023 -9999 0 -0.39 2 2
RAS family/GTP 0.024 0.018 -9999 0 -10000 0 0
MAPK3 -0.009 0.089 -9999 0 -0.55 7 7
MAP2K1 -0.051 0.16 -9999 0 -0.34 147 147
ELK1 0.013 0.003 -9999 0 -10000 0 0
BRAF -0.057 0.15 -9999 0 -0.33 147 147
mol:GTP 0 0.001 -9999 0 -0.005 10 10
MAPK1 -0.01 0.091 -9999 0 -0.59 7 7
RAF1 -0.057 0.15 -9999 0 -0.33 147 147
KRAS 0.012 0.016 -9999 0 -0.39 1 1
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.001 0.094 -9999 0 -0.41 19 19
MAP4K1 -0.023 0.12 -9999 0 -0.4 54 54
MAP3K8 0.013 0 -9999 0 -10000 0 0
PRKCB -0.084 0.17 -9999 0 -0.4 147 147
DBNL 0.013 0 -9999 0 -10000 0 0
CRKL 0.013 0 -9999 0 -10000 0 0
MAP3K1 0.012 0.082 -9999 0 -0.36 17 17
JUN -0.1 0.25 -9999 0 -0.54 147 147
MAP3K7 0.012 0.081 -9999 0 -0.36 17 17
GRAP2 -0.003 0.077 -9999 0 -0.4 23 23
CRK 0.013 0 -9999 0 -10000 0 0
MAP2K4 0.017 0.082 -9999 0 -0.36 17 17
LAT 0.009 0.049 -9999 0 -0.57 4 4
LCP2 0.009 0.04 -9999 0 -0.4 6 6
MAPK8 -0.11 0.26 -9999 0 -0.57 147 147
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.006 0.086 -9999 0 -0.39 17 17
LAT/GRAP2/SLP76/HPK1/HIP-55 0.008 0.089 -9999 0 -0.38 19 19
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.019 0 -9999 0 -10000 0 0
Necdin/E2F1 -0.007 0.1 -9999 0 -0.59 13 13
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.023 0.1 -9999 0 -0.37 13 13
NGF (dimer)/p75(NTR)/BEX1 -0.11 0.16 -9999 0 -0.45 69 69
NT-4/5 (dimer)/p75(NTR) -0.08 0.16 -9999 0 -0.34 119 119
IKBKB 0.013 0 -9999 0 -10000 0 0
AKT1 -0.027 0.099 -9999 0 -0.37 11 11
IKBKG 0.012 0.016 -9999 0 -0.4 1 1
BDNF 0 0.096 -9999 0 -0.75 10 10
MGDIs/NGR/p75(NTR)/LINGO1 -0.071 0.17 -9999 0 -0.55 40 40
FURIN 0.012 0.016 -9999 0 -0.4 1 1
proBDNF (dimer)/p75(NTR)/Sortilin -0.043 0.12 -9999 0 -0.51 10 10
LINGO1 -0.017 0.15 -9999 0 -0.75 24 24
Sortilin/TRAF6/NRIF -0.002 0.018 -9999 0 -10000 0 0
proBDNF (dimer) 0 0.096 -9999 0 -0.75 10 10
NTRK1 0.001 0.087 -9999 0 -0.71 9 9
RTN4R -0.012 0.13 -9999 0 -0.72 21 21
neuron apoptosis -0.032 0.13 -9999 0 -0.51 9 9
IRAK1 0.011 0.031 -9999 0 -0.75 1 1
SHC1 -0.046 0.12 -9999 0 -0.44 11 11
ARHGDIA 0.012 0.016 -9999 0 -0.4 1 1
RhoA/GTP 0.009 0 -9999 0 -10000 0 0
Gamma Secretase 0.037 0.009 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.034 0.11 -9999 0 -0.42 12 12
MAGEH1 0.009 0.04 -9999 0 -0.4 6 6
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.041 0.12 -9999 0 -0.4 28 28
Mammalian IAPs/DIABLO 0.028 0.034 -9999 0 -0.45 1 1
proNGF (dimer) -0.003 0.082 -9999 0 -0.43 21 21
MAGED1 0.013 0 -9999 0 -10000 0 0
APP 0.012 0.016 -9999 0 -0.4 1 1
NT-4/5 (dimer) -0.023 0.14 -9999 0 -0.75 23 23
ZNF274 0.009 0.04 -9999 0 -0.4 6 6
RhoA/GDP/RHOGDI -0.031 0.1 -9999 0 -0.38 11 11
NGF -0.003 0.082 -9999 0 -0.43 21 21
cell cycle arrest -0.018 0.1 -9999 0 -0.43 2 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.03 0.1 -9999 0 -0.39 9 9
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.059 0.14 -9999 0 -0.53 23 23
NCSTN 0.013 0 -9999 0 -10000 0 0
mol:GTP -0.073 0.14 -9999 0 -0.44 34 34
PSENEN 0.012 0.016 -9999 0 -0.4 1 1
mol:ceramide -0.035 0.1 -9999 0 -0.4 11 11
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.019 0.092 -9999 0 -0.34 9 9
p75(NTR)/beta APP -0.054 0.12 -9999 0 -0.27 157 157
BEX1 -0.099 0.18 -9999 0 -0.4 167 167
mol:GDP -0.054 0.12 -9999 0 -0.31 30 30
NGF (dimer) -0.53 0.2 -9999 0 -0.55 599 599
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.057 0.16 -9999 0 -0.5 41 41
PIK3R1 0.013 0 -9999 0 -10000 0 0
RAC1/GTP -0.037 0.1 -9999 0 -0.38 11 11
MYD88 0.013 0 -9999 0 -10000 0 0
CHUK 0.013 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.073 0.14 -9999 0 -0.45 34 34
RHOB 0.013 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 0.006 0.084 -9999 0 -0.57 13 13
NT3 (dimer) 0.007 0.05 -9999 0 -0.44 7 7
TP53 -0.021 0.1 -9999 0 -0.41 10 10
PRDM4 -0.035 0.1 -9999 0 -0.4 11 11
BDNF (dimer) -0.88 0.26 -9999 0 -0.89 615 615
PIK3CA 0.012 0.016 -9999 0 -0.4 1 1
SORT1 0.013 0 -9999 0 -10000 0 0
activation of caspase activity -0.026 0.1 -9999 0 -0.37 13 13
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.032 0.11 -9999 0 -0.4 11 11
RHOC 0.013 0 -9999 0 -10000 0 0
XIAP 0.013 0 -9999 0 -10000 0 0
MAPK10 -0.049 0.15 -9999 0 -0.43 41 41
DIABLO 0.013 0.001 -9999 0 -10000 0 0
SMPD2 -0.035 0.1 -9999 0 -0.4 11 11
APH1B 0.013 0.001 -9999 0 -10000 0 0
APH1A 0.013 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.044 0.12 -9999 0 -0.44 11 11
PSEN1 0.013 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.019 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.057 0.13 -9999 0 -0.27 161 161
MAPK8 -0.025 0.12 -9999 0 -0.5 1 1
MAPK9 -0.025 0.12 -9999 0 -0.5 1 1
APAF1 0.013 0.001 -9999 0 -10000 0 0
NTF3 0.007 0.05 -9999 0 -0.45 7 7
NTF4 -0.023 0.14 -9999 0 -0.75 23 23
NDN -0.006 0.086 -9999 0 -0.4 29 29
RAC1/GDP 0.009 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.064 0.097 -9999 0 -0.35 34 34
p75 CTF/Sortilin/TRAF6/NRIF 0.03 0.022 -9999 0 -10000 0 0
RhoA-B-C/GTP -0.073 0.14 -9999 0 -0.44 34 34
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.024 0.11 -9999 0 -0.42 13 13
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.031 0.11 -9999 0 -0.46 10 10
PRKACB -0.037 0.13 -9999 0 -0.4 76 76
proBDNF (dimer)/p75 ECD 0.009 0.074 -9999 0 -0.57 10 10
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 0.005 0.057 -9999 0 -0.43 10 10
BIRC2 0.012 0.016 -9999 0 -0.4 1 1
neuron projection morphogenesis -0.048 0.13 -9999 0 -0.37 32 32
BAD -0.033 0.14 -9999 0 -0.45 7 7
RIPK2 0.013 0 -9999 0 -10000 0 0
NGFR -0.089 0.18 -9999 0 -0.4 156 156
CYCS -0.027 0.099 -9999 0 -0.37 11 11
ADAM17 0.013 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.032 0.11 -9999 0 -0.4 11 11
BCL2L11 -0.033 0.14 -9999 0 -0.45 7 7
BDNF (dimer)/p75(NTR) -0.063 0.14 -9999 0 -0.59 10 10
PI3K -0.032 0.11 -9999 0 -0.4 11 11
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.032 0.11 -9999 0 -0.4 11 11
NDNL2 0.013 0.001 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
PRKCI 0.011 0.023 -9999 0 -0.4 2 2
NGF (dimer)/p75(NTR) -0.064 0.14 -9999 0 -0.28 168 168
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.032 0.11 -9999 0 -0.4 11 11
TRAF6 0.013 0 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCZ 0.013 0 -9999 0 -10000 0 0
PLG -0.16 0.31 -9999 0 -0.75 133 133
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.043 0.12 -9999 0 -0.38 21 21
SQSTM1 0.013 0 -9999 0 -10000 0 0
NGFRAP1 0.011 0.023 -9999 0 -0.4 2 2
CASP3 -0.03 0.13 -9999 0 -0.42 7 7
E2F1 -0.003 0.11 -9999 0 -0.75 13 13
CASP9 0.013 0 -9999 0 -10000 0 0
IKK complex -0.041 0.08 -9999 0 -0.4 11 11
NGF (dimer)/TRKA -0.001 0.092 -9999 0 -0.38 29 29
MMP7 -0.72 0.16 -9999 0 -0.75 595 595
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.025 0.1 -9999 0 -0.37 14 14
MMP3 -0.62 0.28 -9999 0 -0.75 519 519
APAF-1/Caspase 9 -0.035 0.062 -9999 0 -0.46 1 1
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.021 0.17 -10000 0 -0.79 28 28
NFATC2 -0.012 0.16 -10000 0 -0.6 17 17
NFATC3 -0.019 0.056 -10000 0 -10000 0 0
CD40LG -0.3 0.35 -10000 0 -0.95 64 64
ITCH 0.038 0.024 -10000 0 -0.48 1 1
CBLB 0.038 0.024 -10000 0 -0.48 1 1
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.15 0.26 -10000 0 -0.88 41 41
JUNB 0.011 0.023 -10000 0 -0.4 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.034 0.019 -10000 0 -10000 0 0
T cell anergy 0.036 0.044 -10000 0 -10000 0 0
TLE4 0.005 0.12 -10000 0 -0.59 6 6
Jun/NFAT1-c-4/p21SNFT -0.14 0.24 -10000 0 -0.89 26 26
AP-1/NFAT1-c-4 -0.33 0.39 -10000 0 -0.97 86 86
IKZF1 -0.024 0.2 -10000 0 -0.64 49 49
T-helper 2 cell differentiation -0.081 0.17 -10000 0 -0.71 21 21
AP-1/NFAT1 -0.07 0.12 -10000 0 -0.53 5 5
CALM1 0.024 0.011 -10000 0 -10000 0 0
EGR2 -0.045 0.22 -10000 0 -1.1 15 15
EGR3 -0.051 0.24 -10000 0 -1 22 22
NFAT1/FOXP3 -0.023 0.19 -10000 0 -0.63 36 36
EGR1 0.012 0.023 -10000 0 -0.39 2 2
JUN -0.027 0.037 -10000 0 -10000 0 0
EGR4 -0.11 0.28 -10000 0 -0.75 102 102
mol:Ca2+ 0.012 0.011 -10000 0 -10000 0 0
GBP3 -0.033 0.2 -10000 0 -0.62 58 58
FOSL1 -0.47 0.37 -10000 0 -0.75 390 390
NFAT1-c-4/MAF/IRF4 -0.11 0.24 -10000 0 -0.95 25 25
DGKA 0.005 0.12 -10000 0 -0.58 7 7
CREM 0.012 0 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.065 0.21 -10000 0 -0.97 16 16
CTLA4 -0.026 0.2 -10000 0 -0.63 43 43
NFAT1-c-4 (dimer)/EGR1 -0.062 0.21 -10000 0 -0.97 16 16
NFAT1-c-4 (dimer)/EGR4 -0.14 0.27 -10000 0 -0.89 30 30
FOS -0.034 0.059 -10000 0 -0.4 10 10
IFNG -0.12 0.24 -10000 0 -0.63 82 82
T cell activation -0.095 0.15 -10000 0 -0.7 5 5
MAF 0.003 0.06 -10000 0 -0.4 14 14
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.046 0.18 0.92 14 -10000 0 14
TNF -0.11 0.23 -10000 0 -0.88 21 21
FASLG -0.12 0.36 -10000 0 -1.3 45 45
TBX21 -0.017 0.1 -10000 0 -0.41 36 36
BATF3 0.005 0.076 -10000 0 -0.7 7 7
PRKCQ 0.005 0.055 -10000 0 -0.4 10 10
PTPN1 0.006 0.11 -10000 0 -0.52 6 6
NFAT1-c-4/ICER1 -0.065 0.21 -10000 0 -0.97 16 16
GATA3 0.009 0.045 -10000 0 -0.47 5 5
T-helper 1 cell differentiation -0.11 0.24 -10000 0 -0.62 82 82
IL2RA -0.18 0.22 -10000 0 -0.8 44 44
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.006 0.11 -10000 0 -0.52 6 6
E2F1 0.002 0.11 -10000 0 -0.74 13 13
PPARG 0.011 0.023 -10000 0 -0.39 2 2
SLC3A2 0.006 0.11 -10000 0 -0.52 6 6
IRF4 -0.095 0.18 -10000 0 -0.4 164 164
PTGS2 -0.31 0.36 -10000 0 -1 64 64
CSF2 -0.44 0.47 -10000 0 -0.96 246 246
JunB/Fra1/NFAT1-c-4 -0.33 0.29 -10000 0 -0.81 73 73
IL4 -0.084 0.18 -10000 0 -0.78 18 18
IL5 -0.3 0.34 -10000 0 -0.95 59 59
IL2 -0.096 0.15 -10000 0 -0.71 5 5
IL3 -0.063 0.05 -10000 0 -10000 0 0
RNF128 0.038 0.024 -10000 0 -0.48 1 1
NFATC1 -0.046 0.18 -10000 0 -0.93 14 14
CDK4 0.03 0.12 0.64 5 -10000 0 5
PTPRK 0.006 0.11 -10000 0 -0.52 6 6
IL8 -0.5 0.47 -10000 0 -0.95 267 267
POU2F1 0.011 0.031 -10000 0 -0.75 1 1
TCGA08_p53

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
CDKN2A -0.1 0.23 -10000 0 -0.58 120 120
TP53 -0.027 0.059 0.28 1 -10000 0 1
Senescence -0.027 0.059 0.28 1 -10000 0 1
Apoptosis -0.027 0.059 0.28 1 -10000 0 1
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.052 0.11 0.27 119 -10000 0 119
MDM4 0.011 0.031 -10000 0 -0.75 1 1
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.013 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.005 0.069 -9999 0 -10000 0 0
Syndecan-3/Neurocan 0.009 0.027 -9999 0 -0.41 2 2
POMC -0.004 0.081 -9999 0 -0.41 23 23
EGFR 0.011 0.023 -9999 0 -0.4 2 2
Syndecan-3/EGFR 0.022 0.011 -9999 0 -10000 0 0
AGRP -0.003 0.074 -9999 0 -0.75 6 6
NCSTN 0.013 0 -9999 0 -10000 0 0
PSENEN 0.012 0.016 -9999 0 -0.4 1 1
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.013 0.001 -9999 0 -10000 0 0
APH1A 0.013 0 -9999 0 -10000 0 0
NCAN 0.003 0.043 -9999 0 -0.75 2 2
long-term memory 0.029 0.002 -9999 0 -10000 0 0
Syndecan-3/IL8 -0.22 0.22 -9999 0 -0.41 347 347
PSEN1 0.013 0 -9999 0 -10000 0 0
Src/Cortactin 0.019 0 -9999 0 -10000 0 0
FYN 0.013 0 -9999 0 -10000 0 0
limb bud formation 0 0.002 -9999 0 -10000 0 0
MC4R -0.002 0.06 -9999 0 -0.75 4 4
SRC 0.013 0 -9999 0 -10000 0 0
PTN -0.054 0.15 -9999 0 -0.4 101 101
FGFR/FGF/Syndecan-3 0 0.002 -9999 0 -10000 0 0
neuron projection morphogenesis -0.01 0.065 -9999 0 -0.37 2 2
Syndecan-3/AgRP 0.004 0.043 -9999 0 -0.41 6 6
Syndecan-3/AgRP/MC4R 0.005 0.058 -9999 0 -0.45 9 9
Fyn/Cortactin 0.019 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 -0.22 0.21 -9999 0 -0.41 347 347
IL8 -0.41 0.38 -9999 0 -0.75 347 347
Syndecan-3/Fyn/Cortactin 0.03 0.002 -9999 0 -10000 0 0
Syndecan-3/CASK 0 0.001 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.004 0.074 -9999 0 -0.57 5 5
Gamma Secretase 0.037 0.009 -9999 0 -10000 0 0
Wnt 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
Noncanonical Wnts/FZD -0.054 0.14 -9999 0 -0.47 22 22
FZD6 0.013 0 -9999 0 -10000 0 0
WNT6 -0.032 0.15 -9999 0 -0.5 53 53
WNT4 -0.003 0.088 -9999 0 -0.47 20 20
FZD3 0.006 0.065 -9999 0 -0.63 6 6
WNT5A 0.003 0.082 -9999 0 -0.71 8 8
WNT11 -0.14 0.3 -9999 0 -0.72 129 129
amb2 Integrin signaling

Figure S36.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S36.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.002 0.093 -9999 0 -0.48 15 15
alphaM/beta2 Integrin/GPIbA -0.001 0.083 -9999 0 -0.45 10 10
alphaM/beta2 Integrin/proMMP-9 -0.035 0.16 -9999 0 -0.51 54 54
PLAUR 0.013 0 -9999 0 -10000 0 0
HMGB1 0.009 0.016 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.003 0.077 -9999 0 -0.44 10 10
AGER 0.007 0.036 -9999 0 -0.8 1 1
RAP1A 0.013 0 -9999 0 -10000 0 0
SELPLG 0.011 0.023 -9999 0 -0.4 2 2
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.001 0.1 -9999 0 -0.45 13 13
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.045 0.2 -9999 0 -0.72 49 49
CYR61 0.005 0.075 -9999 0 -0.75 6 6
TLN1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP -0.053 0.091 -9999 0 -0.42 13 13
RHOA 0.013 0 -9999 0 -10000 0 0
P-selectin oligomer -0.037 0.13 -9999 0 -0.39 75 75
MYH2 -0.049 0.13 -9999 0 -0.42 35 35
MST1R 0.012 0.016 -9999 0 -0.4 1 1
leukocyte activation during inflammatory response -0.058 0.15 -9999 0 -0.44 67 67
APOB -0.069 0.2 -9999 0 -0.5 95 95
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 0.004 0.074 -9999 0 -0.62 8 8
JAM3 0.013 0 -9999 0 -10000 0 0
GP1BA 0.005 0.049 -9999 0 -0.4 9 9
alphaM/beta2 Integrin/CTGF 0.001 0.085 -9999 0 -0.46 13 13
alphaM/beta2 Integrin -0.047 0.12 -9999 0 -0.37 49 49
JAM3 homodimer 0.013 0 -9999 0 -10000 0 0
ICAM2 0.013 0 -9999 0 -10000 0 0
ICAM1 0.011 0.031 -9999 0 -0.75 1 1
phagocytosis triggered by activation of immune response cell surface activating receptor -0.047 0.12 -9999 0 -0.36 49 49
cell adhesion -0.001 0.082 -9999 0 -0.45 10 10
NFKB1 -0.007 0.14 -9999 0 -0.64 7 7
THY1 -0.014 0.14 -9999 0 -0.75 22 22
RhoA/GDP 0.009 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.062 0.16 -9999 0 -0.52 56 56
alphaM/beta2 Integrin/LRP/tPA 0.01 0.076 -9999 0 -0.42 10 10
IL6 -0.045 0.23 -9999 0 -0.59 88 88
ITGB2 0.001 0.056 -9999 0 -0.4 11 11
elevation of cytosolic calcium ion concentration -0.02 0.14 -9999 0 -0.45 51 51
alphaM/beta2 Integrin/JAM2/JAM3 -0.039 0.13 -9999 0 -0.44 33 33
JAM2 -0.084 0.17 -9999 0 -0.4 147 147
alphaM/beta2 Integrin/ICAM1 -0.054 0.18 -9999 0 -0.43 103 103
alphaM/beta2 Integrin/uPA/Plg -0.12 0.22 -9999 0 -0.46 182 182
RhoA/GTP -0.051 0.14 -9999 0 -0.44 36 36
positive regulation of phagocytosis -0.041 0.12 -9999 0 -0.53 16 16
Ron/MSP -0.075 0.22 -9999 0 -0.57 99 99
alphaM/beta2 Integrin/uPAR/uPA -0.02 0.14 -9999 0 -0.45 51 51
alphaM/beta2 Integrin/uPAR 0.003 0.077 -9999 0 -0.44 10 10
PLAU -0.039 0.19 -9999 0 -0.75 42 42
PLAT 0.009 0.042 -9999 0 -0.48 4 4
actin filament polymerization -0.047 0.13 -9999 0 -0.41 35 35
MST1 -0.11 0.28 -9999 0 -0.75 99 99
alphaM/beta2 Integrin/lipoprotein(a) -0.058 0.15 -9999 0 -0.44 67 67
TNF -0.002 0.14 -9999 0 -0.77 7 7
RAP1B 0.013 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.031 0.15 -9999 0 -0.5 51 51
fibrinolysis -0.12 0.22 -9999 0 -0.46 182 182
HCK 0.003 0.062 -9999 0 -0.4 15 15
dendritic cell antigen processing and presentation -0.047 0.12 -9999 0 -0.36 49 49
VTN -0.013 0.13 -9999 0 -0.75 19 19
alphaM/beta2 Integrin/CYR61 -0.001 0.092 -9999 0 -0.46 16 16
LPA -0.029 0.16 -9999 0 -0.75 29 29
LRP1 0.011 0.023 -9999 0 -0.4 2 2
cell migration -0.03 0.16 -9999 0 -0.49 57 57
FN1 -0.028 0.17 -9999 0 -0.67 37 37
alphaM/beta2 Integrin/Thy1 -0.015 0.12 -9999 0 -0.48 31 31
MPO -0.013 0.14 -9999 0 -0.75 20 20
KNG1 -0.076 0.16 -9999 0 -0.4 132 132
RAP1/GDP 0.017 0 -9999 0 -10000 0 0
ROCK1 -0.043 0.13 -9999 0 -0.42 32 32
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.16 0.31 -9999 0 -0.75 133 133
CTGF 0.009 0.053 -9999 0 -0.75 3 3
alphaM/beta2 Integrin/Hck -0.002 0.097 -9999 0 -0.54 13 13
ITGAM -0.014 0.094 -9999 0 -0.4 34 34
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.014 0.11 -9999 0 -0.45 21 21
HP -0.031 0.17 -9999 0 -0.75 34 34
leukocyte adhesion -0.045 0.15 -9999 0 -0.54 19 19
SELP -0.037 0.13 -9999 0 -0.4 75 75
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.061 0.25 -10000 0 -0.84 33 33
NCK1/PAK1/Dok-R -0.029 0.099 -10000 0 -0.41 32 32
NCK1/Dok-R 0.028 0.27 -10000 0 -0.93 43 43
PIK3CA 0.011 0.016 -10000 0 -0.39 1 1
mol:beta2-estradiol 0.002 0.055 0.26 27 -10000 0 27
RELA 0.013 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 -0.26 0.36 0.24 12 -0.75 214 226
TNIP2 0.013 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.016 0.24 -10000 0 -0.86 43 43
FN1 -0.028 0.17 -10000 0 -0.67 37 37
PLD2 0.028 0.28 -10000 0 -0.95 43 43
PTPN11 0.013 0 -10000 0 -10000 0 0
GRB14 -0.024 0.14 -10000 0 -0.5 42 42
ELK1 0.036 0.25 -10000 0 -0.86 43 43
GRB7 -0.006 0.12 -10000 0 -0.75 15 15
PAK1 0.013 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.038 0.26 -10000 0 -0.9 45 45
CDKN1A 0.071 0.2 -10000 0 -0.62 26 26
ITGA5 0.01 0.043 -10000 0 -0.75 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.028 0.27 -10000 0 -0.93 43 43
CRK 0.013 0 -10000 0 -10000 0 0
mol:NO 0.066 0.2 -10000 0 -0.63 34 34
PLG -0.069 0.32 -10000 0 -1 43 43
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.054 0.24 -10000 0 -0.77 40 40
GRB2 0.013 0 -10000 0 -10000 0 0
PIK3R1 0.014 0.002 -10000 0 -10000 0 0
ANGPT2 0.041 0.19 0.38 7 -0.52 17 24
BMX -0.05 0.3 -10000 0 -1 43 43
ANGPT1 0.036 0.26 -10000 0 -1.1 27 27
tube development 0.065 0.22 -10000 0 -0.66 30 30
ANGPT4 0.001 0.061 -10000 0 -0.75 4 4
response to hypoxia -0.001 0.017 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 0.007 0.3 -10000 0 -1 43 43
alpha5/beta1 Integrin 0.017 0.033 -10000 0 -0.57 2 2
FGF2 -0.018 0.1 -10000 0 -0.39 45 45
STAT5A (dimer) 0.066 0.24 -10000 0 -0.77 27 27
mol:L-citrulline 0.066 0.2 -10000 0 -0.63 34 34
AGTR1 -0.13 0.19 -10000 0 -0.39 220 220
MAPK14 0.033 0.29 -10000 0 -1 40 40
Tie2/SHP2 -0.014 0.2 -10000 0 -1 22 22
TEK -0.017 0.22 -10000 0 -1.1 22 22
RPS6KB1 0.06 0.24 -10000 0 -0.81 33 33
Angiotensin II/AT1 -0.091 0.14 -10000 0 -0.27 220 220
Tie2/Ang1/GRB2 0.024 0.29 -10000 0 -0.98 43 43
MAPK3 0.033 0.26 -10000 0 -0.87 43 43
MAPK1 0.033 0.26 -10000 0 -0.87 43 43
Tie2/Ang1/GRB7 0.015 0.3 -10000 0 -1 43 43
NFKB1 0.013 0 -10000 0 -10000 0 0
MAPK8 0.028 0.28 -10000 0 -0.95 43 43
PI3K 0.05 0.28 -10000 0 -0.91 40 40
FES 0.032 0.29 -10000 0 -1 40 40
Crk/Dok-R 0.028 0.27 -10000 0 -0.93 43 43
Tie2/Ang1/ABIN2 0.024 0.29 -10000 0 -0.98 43 43
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.065 0.23 -10000 0 -0.75 33 33
STAT5A 0.013 0 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.06 0.24 -10000 0 -0.8 35 35
Tie2/Ang2 0.053 0.27 -10000 0 -0.9 30 30
Tie2/Ang1 0.023 0.3 -10000 0 -1 43 43
FOXO1 0.069 0.23 -10000 0 -0.76 32 32
ELF1 0.018 0.02 -10000 0 -10000 0 0
ELF2 0.027 0.28 -10000 0 -0.95 43 43
mol:Choline 0.03 0.27 -10000 0 -0.91 43 43
cell migration -0.021 0.059 -10000 0 -0.24 12 12
FYN 0.062 0.23 -10000 0 -0.75 30 30
DOK2 0.003 0.06 -10000 0 -0.4 14 14
negative regulation of cell cycle 0.072 0.19 -10000 0 -0.56 26 26
ETS1 0.008 0.058 -10000 0 -0.37 3 3
PXN 0.068 0.21 -10000 0 -0.67 33 33
ITGB1 0.013 0 -10000 0 -10000 0 0
NOS3 0.063 0.22 -10000 0 -0.72 34 34
RAC1 0.013 0 -10000 0 -10000 0 0
TNF 0.007 0.067 -10000 0 -0.43 5 5
MAPKKK cascade 0.03 0.27 -10000 0 -0.91 43 43
RASA1 0.013 0.001 -10000 0 -10000 0 0
Tie2/Ang1/Shc 0.026 0.29 -10000 0 -0.98 43 43
NCK1 0.013 0 -10000 0 -10000 0 0
vasculogenesis 0.068 0.19 -10000 0 -0.56 34 34
mol:Phosphatidic acid 0.03 0.27 -10000 0 -0.91 43 43
mol:Angiotensin II 0.001 0.004 -10000 0 -10000 0 0
mol:NADP 0.066 0.2 -10000 0 -0.63 34 34
Rac1/GTP -0.043 0.18 -10000 0 -0.72 40 40
MMP2 0.024 0.29 -10000 0 -0.96 43 43
Signaling events mediated by PRL

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCNE1 0.006 0.068 -10000 0 -0.75 5 5
mol:Halofuginone 0.005 0 -10000 0 -10000 0 0
ITGA1 0.013 0 -10000 0 -10000 0 0
CDKN1A 0.028 0.016 -10000 0 -0.36 1 1
PRL-3/alpha Tubulin -0.074 0.21 -10000 0 -0.57 98 98
mol:Ca2+ -0.036 0.23 0.33 73 -0.55 85 158
AGT -0.092 0.26 -10000 0 -0.75 85 85
CCNA2 0.033 0.011 -10000 0 -10000 0 0
TUBA1B 0.013 0 -10000 0 -10000 0 0
EGR1 0.02 0.016 -10000 0 -0.26 2 2
CDK2/Cyclin E1 0.035 0.042 -10000 0 -0.4 5 5
MAPK3 -0.074 0.22 -10000 0 -0.57 98 98
PRL-2 /Rab GGTase beta 0.019 0 -10000 0 -10000 0 0
MAPK1 -0.074 0.22 -10000 0 -0.57 98 98
PTP4A1 0.029 0.012 -10000 0 -10000 0 0
PTP4A3 -0.11 0.28 -10000 0 -0.75 98 98
PTP4A2 0.013 0 -10000 0 -10000 0 0
ITGB1 -0.074 0.21 -10000 0 -0.57 98 98
SRC 0.013 0 -10000 0 -10000 0 0
RAC1 -0.005 0.078 -10000 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0.019 0 -10000 0 -10000 0 0
PRL-1/ATF-5 0.034 0.011 -10000 0 -10000 0 0
RABGGTA 0.013 0 -10000 0 -10000 0 0
BCAR1 0.052 0.12 0.33 98 -0.28 1 99
RHOC -0.005 0.078 -10000 0 -10000 0 0
RHOA -0.005 0.078 -10000 0 -10000 0 0
cell motility -0.002 0.08 -10000 0 -10000 0 0
PRL-1/alpha Tubulin 0.034 0.011 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin -0.074 0.21 -10000 0 -0.57 98 98
ROCK1 -0.002 0.08 -10000 0 -10000 0 0
RABGGTB 0.013 0 -10000 0 -10000 0 0
CDK2 0.013 0 -10000 0 -10000 0 0
mitosis 0.029 0.012 -10000 0 -10000 0 0
ATF5 0.013 0 -10000 0 -10000 0 0
EPHB forward 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
Ephrin A5/EPHB2 -0.042 0.11 -10000 0 -0.56 3 3
cell-cell adhesion 0.075 0.14 0.61 4 -10000 0 4
Ephrin B/EPHB2/RasGAP 0.031 0.047 -10000 0 -0.42 5 5
ITSN1 0.012 0.016 -10000 0 -0.4 1 1
PIK3CA 0.012 0.016 -10000 0 -0.4 1 1
SHC1 0.013 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.014 0.12 -10000 0 -0.5 38 38
Ephrin B1/EPHB1 -0.091 0.21 -10000 0 -0.5 131 131
HRAS/GDP -0.076 0.14 -10000 0 -0.36 120 120
Ephrin B/EPHB1/GRB7 -0.073 0.21 -10000 0 -0.44 140 140
Endophilin/SYNJ1 0.024 0.044 -10000 0 -0.39 5 5
KRAS 0.012 0.016 -10000 0 -0.4 1 1
Ephrin B/EPHB1/Src -0.063 0.19 -10000 0 -0.42 132 132
endothelial cell migration 0.027 0.008 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
GRB7 -0.006 0.12 -10000 0 -0.75 15 15
PAK1 0.03 0.045 -10000 0 -0.39 5 5
HRAS 0.012 0.016 -10000 0 -0.4 1 1
RRAS 0.024 0.044 -10000 0 -0.4 5 5
DNM1 0.004 0.081 -10000 0 -0.75 7 7
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.064 0.18 -10000 0 -0.4 132 132
lamellipodium assembly -0.075 0.14 -10000 0 -0.61 4 4
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.024 0.11 -10000 0 -0.41 2 2
PIK3R1 0.013 0 -10000 0 -10000 0 0
EPHB2 0.009 0.053 -10000 0 -0.75 3 3
EPHB3 -0.034 0.18 -10000 0 -0.75 38 38
EPHB1 -0.15 0.31 -10000 0 -0.75 132 132
EPHB4 0.013 0 -10000 0 -10000 0 0
mol:GDP -0.031 0.14 -10000 0 -0.47 4 4
Ephrin B/EPHB2 0.023 0.047 -10000 0 -0.42 5 5
Ephrin B/EPHB3 -0.002 0.11 -10000 0 -0.43 40 40
JNK cascade -0.063 0.18 -10000 0 -0.42 132 132
Ephrin B/EPHB1 -0.07 0.19 -10000 0 -0.43 132 132
RAP1/GDP -0.016 0.13 -10000 0 -0.44 3 3
EFNB2 0.013 0 -10000 0 -10000 0 0
EFNB3 0.004 0.065 -10000 0 -0.46 11 11
EFNB1 0.013 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.078 0.2 -10000 0 -0.46 132 132
RAP1B 0.013 0 -10000 0 -10000 0 0
RAP1A 0.013 0 -10000 0 -10000 0 0
CDC42/GTP -0.078 0.15 -10000 0 -0.61 6 6
Rap1/GTP -0.076 0.14 -10000 0 -0.63 4 4
axon guidance -0.042 0.11 -10000 0 -0.56 3 3
MAPK3 -0.011 0.098 -10000 0 -0.36 2 2
MAPK1 -0.011 0.098 -10000 0 -0.36 2 2
Rac1/GDP -0.022 0.14 -10000 0 -0.47 3 3
actin cytoskeleton reorganization -0.063 0.12 -10000 0 -0.45 6 6
CDC42/GDP -0.022 0.14 -10000 0 -0.5 4 4
PI3K 0.029 0.008 -10000 0 -10000 0 0
EFNA5 -0.084 0.17 -10000 0 -0.4 147 147
Ephrin B2/EPHB4 0.017 0 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.026 0.036 -10000 0 -10000 0 0
CDC42 0.011 0.023 -10000 0 -0.4 2 2
RAS family/GTP -0.075 0.14 -10000 0 -0.57 6 6
PTK2 0.019 0.037 -10000 0 -10000 0 0
MAP4K4 -0.064 0.19 -10000 0 -0.42 132 132
SRC 0.013 0 -10000 0 -10000 0 0
KALRN 0.012 0.016 -10000 0 -0.4 1 1
Intersectin/N-WASP 0.018 0.011 -10000 0 -10000 0 0
neuron projection morphogenesis -0.013 0.13 -10000 0 -0.44 6 6
MAP2K1 -0.017 0.1 -10000 0 -0.38 2 2
WASL 0.013 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.071 0.2 -10000 0 -0.45 132 132
cell migration -0.012 0.11 -10000 0 -0.43 2 2
NRAS 0.011 0.023 -10000 0 -0.4 2 2
SYNJ1 0.024 0.044 -10000 0 -0.4 5 5
PXN 0.013 0 -10000 0 -10000 0 0
TF -0.002 0.097 -10000 0 -0.4 21 21
HRAS/GTP -0.081 0.15 -10000 0 -0.67 4 4
Ephrin B1/EPHB1-2 -0.078 0.2 -10000 0 -0.46 132 132
cell adhesion mediated by integrin 0 0.061 0.34 6 -10000 0 6
RAC1 0.013 0 -10000 0 -10000 0 0
mol:GTP -0.057 0.18 -10000 0 -0.39 133 133
RAC1-CDC42/GTP -0.096 0.17 -10000 0 -0.66 17 17
RASA1 0.013 0.001 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.016 0.13 -10000 0 -0.48 4 4
ruffle organization -0.038 0.16 -10000 0 -0.63 4 4
NCK1 0.013 0 -10000 0 -10000 0 0
receptor internalization 0.024 0.063 -10000 0 -0.4 12 12
Ephrin B/EPHB2/KALRN 0.03 0.048 -10000 0 -0.42 5 5
ROCK1 -0.008 0.11 -10000 0 -0.45 38 38
RAS family/GDP -0.053 0.1 -10000 0 -0.42 5 5
Rac1/GTP -0.08 0.15 -10000 0 -0.67 4 4
Ephrin B/EPHB1/Src/Paxillin -0.027 0.11 -10000 0 -0.45 2 2
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0 0.079 -10000 0 -0.37 8 8
ER alpha/Gai/GDP/Gbeta gamma -0.12 0.23 -10000 0 -0.64 70 70
AKT1 -0.063 0.25 -10000 0 -0.81 60 60
PIK3CA 0.012 0.016 -10000 0 -0.4 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.068 0.25 -10000 0 -0.84 60 60
mol:Ca2+ 0.019 0.061 -10000 0 -0.41 6 6
IGF1R 0.013 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.006 0.07 -10000 0 -10000 0 0
SHC1 0.013 0 -10000 0 -10000 0 0
apoptosis 0.059 0.24 0.77 60 -10000 0 60
RhoA/GTP -0.015 0.044 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.1 0.17 -10000 0 -0.6 49 49
regulation of stress fiber formation -0.024 0.048 -10000 0 -10000 0 0
E2/ERA-ERB (dimer) -0.008 0.074 -10000 0 -0.44 1 1
KRAS 0.012 0.016 -10000 0 -0.4 1 1
G13/GTP -0.005 0.063 -10000 0 -10000 0 0
pseudopodium formation 0.024 0.048 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1 -0.006 0.07 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
GNG2 -0.004 0.081 -10000 0 -0.4 26 26
GNAO1 -0.14 0.2 -10000 0 -0.4 234 234
HRAS 0.012 0.016 -10000 0 -0.4 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.07 0.2 -10000 0 -0.59 65 65
E2/ER beta (dimer) 0.007 0.025 -10000 0 -0.28 5 5
mol:GDP -0.031 0.09 -10000 0 -0.48 1 1
mol:NADP -0.07 0.2 -10000 0 -0.59 65 65
PIK3R1 0.013 0 -10000 0 -10000 0 0
mol:IP3 0.019 0.063 -10000 0 -0.42 6 6
IGF-1R heterotetramer 0.013 0 -10000 0 -10000 0 0
PLCB1 0.014 0.064 -10000 0 -0.38 10 10
PLCB2 0.016 0.058 -10000 0 -0.45 4 4
IGF1 -0.08 0.17 -10000 0 -0.4 142 142
mol:L-citrulline -0.07 0.2 -10000 0 -0.59 65 65
RHOA 0.013 0 -10000 0 -10000 0 0
Gai/GDP -0.22 0.34 -10000 0 -0.65 234 234
JNK cascade 0.007 0.025 -10000 0 -0.28 5 5
BCAR1 0.012 0.016 -10000 0 -0.4 1 1
ESR2 0.009 0.036 -10000 0 -0.4 5 5
GNAQ 0.011 0.028 -10000 0 -0.4 3 3
ESR1 -0.027 0.12 -10000 0 -0.4 59 59
Gq family/GDP/Gbeta gamma 0.018 0.067 -10000 0 -0.43 5 5
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.008 0.08 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.1 0.17 -10000 0 -0.6 49 49
GNAZ 0.007 0.046 -10000 0 -0.4 8 8
E2/ER alpha (dimer) -0.018 0.083 -10000 0 -0.28 59 59
STRN 0.013 0.001 -10000 0 -10000 0 0
GNAL -0.01 0.094 -10000 0 -0.4 35 35
PELP1 0.013 0 -10000 0 -10000 0 0
MAPK11 0.012 0.036 -10000 0 -0.5 2 2
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 -0.002 0.075 -10000 0 -0.4 22 22
HBEGF -0.11 0.2 -10000 0 -0.54 77 77
cAMP biosynthetic process -0.028 0.073 -10000 0 -0.35 13 13
SRC -0.11 0.22 -10000 0 -0.6 70 70
PI3K 0.018 0.011 -10000 0 -10000 0 0
GNB1 0.013 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.032 0.085 -10000 0 -0.42 8 8
SOS1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.11 0.16 -10000 0 -0.49 68 68
Gs family/GTP -0.012 0.08 -10000 0 -0.36 13 13
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.023 0.018 -10000 0 -10000 0 0
vasodilation -0.066 0.19 -10000 0 -0.56 65 65
mol:DAG 0.019 0.063 -10000 0 -0.42 6 6
Gs family/GDP/Gbeta gamma -0.038 0.095 -10000 0 -0.41 18 18
MSN 0.024 0.051 -10000 0 -10000 0 0
Gq family/GTP 0.011 0.061 -10000 0 -0.41 7 7
mol:PI-3-4-5-P3 -0.064 0.24 -10000 0 -0.8 60 60
NRAS 0.011 0.023 -10000 0 -0.4 2 2
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.066 0.19 0.56 65 -10000 0 65
GRB2/SOS1 0.019 0 -10000 0 -10000 0 0
RhoA/GDP -0.028 0.084 -10000 0 -0.45 1 1
NOS3 -0.075 0.21 -10000 0 -0.63 65 65
GNA11 0.01 0.033 -10000 0 -0.4 4 4
MAPKKK cascade -0.053 0.2 -10000 0 -0.63 59 59
E2/ER alpha (dimer)/PELP1/Src -0.11 0.18 -10000 0 -0.63 49 49
ruffle organization 0.024 0.048 -10000 0 -10000 0 0
ROCK2 0.02 0.054 -10000 0 -10000 0 0
GNA14 0.009 0.036 -10000 0 -0.4 5 5
GNA15 0.005 0.075 -10000 0 -0.75 6 6
GNA13 0.013 0 -10000 0 -10000 0 0
MMP9 -0.12 0.22 -10000 0 -0.51 101 101
MMP2 -0.098 0.21 -10000 0 -0.61 58 58
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 0.009 0.14 -10000 0 -0.52 34 34
FYN -0.007 0.19 -10000 0 -0.62 43 43
LAT/GRAP2/SLP76 -0.043 0.15 -10000 0 -0.53 41 41
IKBKB 0.013 0 -10000 0 -10000 0 0
AKT1 0.01 0.14 -10000 0 -0.43 41 41
B2M 0.012 0.023 -10000 0 -0.4 2 2
IKBKG -0.015 0.038 -10000 0 -0.17 9 9
MAP3K8 0.013 0 -10000 0 -10000 0 0
mol:Ca2+ -0.016 0.042 -10000 0 -0.15 54 54
integrin-mediated signaling pathway 0.015 0.023 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.003 0.19 -10000 0 -0.61 45 45
TRPV6 -0.065 0.21 -10000 0 -0.75 54 54
CD28 -0.004 0.081 -10000 0 -0.4 25 25
SHC1 -0.005 0.18 -10000 0 -0.63 39 39
receptor internalization -0.016 0.2 -10000 0 -0.65 44 44
PRF1 -0.013 0.21 -10000 0 -0.88 26 26
KRAS 0.012 0.016 -10000 0 -0.4 1 1
GRB2 0.013 0 -10000 0 -10000 0 0
COT/AKT1 0.018 0.11 -10000 0 -0.35 34 34
LAT -0.006 0.18 -10000 0 -0.59 45 45
EntrezGene:6955 0.001 0.003 -10000 0 -10000 0 0
CD3D 0.001 0.072 -10000 0 -0.4 19 19
CD3E -0.004 0.084 -10000 0 -0.4 26 26
CD3G -0.021 0.11 -10000 0 -0.4 52 52
RASGRP2 -0.007 0.051 -10000 0 -0.17 52 52
RASGRP1 0.016 0.14 -10000 0 -0.45 38 38
HLA-A 0.013 0.017 -10000 0 -0.4 1 1
RASSF5 0.009 0.04 -10000 0 -0.4 6 6
RAP1A/GTP/RAPL 0.015 0.023 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.021 0.047 -10000 0 -0.13 29 29
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.027 0.066 -10000 0 -0.26 23 23
PRKCA -0.02 0.071 -10000 0 -0.27 30 30
GRAP2 -0.003 0.077 -10000 0 -0.4 23 23
mol:IP3 -0.017 0.14 0.26 52 -0.43 34 86
EntrezGene:6957 0.001 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.016 0.17 -10000 0 -0.57 45 45
ORAI1 0.037 0.1 0.36 53 -10000 0 53
CSK -0.006 0.18 -10000 0 -0.63 39 39
B7 family/CD28 -0.006 0.19 -10000 0 -0.66 38 38
CHUK 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.015 0.21 -10000 0 -0.69 43 43
PTPN6 -0.007 0.18 -10000 0 -0.62 41 41
VAV1 -0.011 0.19 -10000 0 -0.63 45 45
Monovalent TCR/CD3 -0.017 0.15 -10000 0 -0.6 32 32
CBL 0.013 0 -10000 0 -10000 0 0
LCK -0.01 0.19 -10000 0 -0.64 41 41
PAG1 -0.008 0.18 -10000 0 -0.62 41 41
RAP1A 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.016 0.21 -10000 0 -0.69 43 43
CD80 0.009 0.049 -10000 0 -0.57 4 4
CD86 0.004 0.059 -10000 0 -0.4 13 13
PDK1/CARD11/BCL10/MALT1 -0.032 0.08 -10000 0 -0.3 31 31
HRAS 0.012 0.016 -10000 0 -0.4 1 1
GO:0035030 -0.002 0.16 -10000 0 -0.54 38 38
CD8A -0.016 0.11 -10000 0 -0.4 45 45
CD8B 0.003 0.068 -10000 0 -0.42 15 15
PTPRC -0.02 0.11 -10000 0 -0.4 50 50
PDK1/PKC theta 0.012 0.16 -10000 0 -0.54 38 38
CSK/PAG1 -0.002 0.18 -10000 0 -0.63 36 36
SOS1 0.013 0 -10000 0 -10000 0 0
peptide-MHC class I 0.019 0.021 -10000 0 -10000 0 0
GRAP2/SLP76 -0.05 0.17 -10000 0 -0.62 42 42
STIM1 0.018 0.052 -10000 0 -10000 0 0
RAS family/GTP 0.03 0.059 -10000 0 -0.18 19 19
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.02 0.22 -10000 0 -0.7 44 44
mol:DAG -0.026 0.11 -10000 0 -0.38 36 36
RAP1A/GDP 0.011 0.021 -10000 0 -10000 0 0
PLCG1 0.013 0 -10000 0 -10000 0 0
CD247 0.003 0.066 -10000 0 -0.4 16 16
cytotoxic T cell degranulation -0.011 0.2 -10000 0 -0.79 29 29
RAP1A/GTP -0.006 0.017 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.005 0.16 -10000 0 -0.5 45 45
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.027 0.17 0.28 49 -0.57 34 83
NRAS 0.011 0.023 -10000 0 -0.4 2 2
ZAP70 0.002 0.071 -10000 0 -0.45 14 14
GRB2/SOS1 0.019 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.045 0.15 -10000 0 -0.55 38 38
MALT1 0.012 0.016 -10000 0 -0.4 1 1
TRAF6 0.013 0 -10000 0 -10000 0 0
CD8 heterodimer -0.007 0.098 -10000 0 -0.52 9 9
CARD11 -0.023 0.15 -10000 0 -0.62 35 35
PRKCB -0.036 0.099 -10000 0 -0.31 54 54
PRKCE -0.02 0.071 -10000 0 -0.27 30 30
PRKCQ 0.003 0.18 -10000 0 -0.58 45 45
LCP2 0.009 0.04 -10000 0 -0.4 6 6
BCL10 0.012 0.016 -10000 0 -0.4 1 1
regulation of survival gene product expression 0.014 0.12 -10000 0 -0.37 39 39
IKK complex 0.019 0.05 -10000 0 -0.12 26 26
RAS family/GDP -0.003 0.008 -10000 0 -10000 0 0
MAP3K14 0.022 0.085 -10000 0 -0.28 25 25
PDPK1 0.013 0.13 -10000 0 -0.42 36 36
TCR/CD3/MHC I/CD8/Fyn -0.018 0.21 -10000 0 -0.72 41 41
LPA receptor mediated events

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
GNB1/GNG2 -0.011 0.096 -9999 0 -0.42 11 11
NF kappa B1 p50/RelA/I kappa B alpha -0.003 0.07 -9999 0 -10000 0 0
AP1 -0.04 0.087 -9999 0 -0.42 9 9
mol:PIP3 -0.034 0.075 -9999 0 -0.51 1 1
AKT1 0.024 0.071 -9999 0 -0.39 1 1
PTK2B -0.005 0.072 -9999 0 -0.26 13 13
RHOA 0.019 0.032 -9999 0 -10000 0 0
PIK3CB 0.011 0.031 -9999 0 -0.75 1 1
mol:Ca2+ 0.013 0.062 -9999 0 -0.35 1 1
MAGI3 0.011 0.023 -9999 0 -0.39 2 2
RELA 0.012 0 -9999 0 -10000 0 0
apoptosis -0.028 0.11 -9999 0 -0.41 16 16
HRAS/GDP 0.009 0.011 -9999 0 -0.28 1 1
positive regulation of microtubule depolymerization -0.036 0.1 -9999 0 -0.37 5 5
NF kappa B1 p50/RelA -0.035 0.075 -9999 0 -0.45 2 2
endothelial cell migration -0.016 0.11 -9999 0 -0.64 8 8
ADCY4 -0.079 0.17 -9999 0 -0.46 84 84
ADCY5 -0.18 0.24 -9999 0 -0.46 217 217
ADCY6 -0.079 0.17 -9999 0 -0.46 84 84
ADCY7 -0.079 0.17 -9999 0 -0.46 84 84
ADCY1 -0.083 0.18 -9999 0 -0.45 88 88
ADCY2 -0.11 0.22 -9999 0 -0.48 137 137
ADCY3 -0.079 0.17 -9999 0 -0.46 84 84
ADCY8 -0.085 0.18 -9999 0 -0.46 86 86
ADCY9 -0.08 0.17 -9999 0 -0.45 86 86
GSK3B 0.001 0.068 -9999 0 -0.3 3 3
arachidonic acid secretion -0.088 0.18 -9999 0 -0.53 65 65
GNG2 -0.005 0.081 -9999 0 -0.39 26 26
TRIP6 0.019 0.023 -9999 0 -0.32 2 2
GNAO1 -0.1 0.16 -9999 0 -0.44 61 61
HRAS 0.012 0.016 -9999 0 -0.4 1 1
NFKBIA 0.004 0.08 -9999 0 -0.37 1 1
GAB1 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.065 0.27 -9999 0 -0.87 62 62
JUN 0.012 0 -9999 0 -10000 0 0
LPA/LPA2/NHERF2 0.016 0.025 -9999 0 -0.49 1 1
TIAM1 -0.099 0.31 -9999 0 -1 62 62
PIK3R1 0.012 0 -9999 0 -10000 0 0
mol:IP3 0.013 0.063 -9999 0 -0.35 1 1
PLCB3 0.02 0.023 -9999 0 -0.45 1 1
FOS 0.006 0.051 -9999 0 -0.4 10 10
positive regulation of mitosis -0.088 0.18 -9999 0 -0.53 65 65
LPA/LPA1-2-3 -0.026 0.11 -9999 0 -0.43 17 17
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade -0.001 0.001 -9999 0 -10000 0 0
BCAR1 0.012 0.016 -9999 0 -0.4 1 1
stress fiber formation -0.006 0.082 -9999 0 -0.3 11 11
GNAZ -0.015 0.092 -9999 0 -0.35 10 10
EGFR/PI3K-beta/Gab1 -0.035 0.077 -9999 0 -0.53 1 1
positive regulation of dendritic cell cytokine production -0.027 0.11 -9999 0 -0.42 17 17
LPA/LPA2/MAGI-3 0.016 0.027 -9999 0 -0.49 1 1
ARHGEF1 0.002 0.073 -9999 0 -0.35 2 2
GNAI2 -0.012 0.087 -9999 0 -0.42 2 2
GNAI3 -0.012 0.087 -9999 0 -0.42 2 2
GNAI1 -0.02 0.1 -9999 0 -0.44 13 13
LPA/LPA3 -0.015 0.09 -9999 0 -0.32 44 44
LPA/LPA2 0.009 0.026 -9999 0 -0.57 1 1
LPA/LPA1 -0.025 0.1 -9999 0 -0.27 89 89
HB-EGF/EGFR -0.028 0.14 -9999 0 -0.49 47 47
HBEGF -0.029 0.16 -9999 0 -0.57 47 47
mol:DAG 0.013 0.063 -9999 0 -0.35 1 1
cAMP biosynthetic process -0.11 0.19 -9999 0 -0.53 74 74
NFKB1 0.012 0 -9999 0 -10000 0 0
SRC 0.013 0 -9999 0 -10000 0 0
GNB1 0.012 0 -9999 0 -10000 0 0
LYN 0.004 0.08 -9999 0 -0.37 1 1
GNAQ -0.001 0.068 -9999 0 -0.33 9 9
LPAR2 0.011 0.031 -9999 0 -0.75 1 1
LPAR3 -0.023 0.12 -9999 0 -0.45 44 44
LPAR1 -0.04 0.14 -9999 0 -0.39 83 83
IL8 -0.2 0.19 -9999 0 -0.44 84 84
PTK2 -0.018 0.1 -9999 0 -0.4 17 17
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
CASP3 -0.028 0.11 -9999 0 -0.41 16 16
EGFR 0.01 0.023 -9999 0 -0.4 2 2
PLCG1 0.003 0.072 -9999 0 -0.31 9 9
PLD2 -0.018 0.1 -9999 0 -0.4 17 17
G12/G13 -0.002 0.079 -9999 0 -0.38 2 2
PI3K-beta -0.022 0.057 -9999 0 -0.45 1 1
cell migration -0.01 0.094 -9999 0 -0.26 62 62
SLC9A3R2 0.012 0.016 -9999 0 -0.4 1 1
PXN -0.006 0.083 -9999 0 -0.31 11 11
HRAS/GTP -0.091 0.19 -9999 0 -0.55 65 65
RAC1 0.013 0 -9999 0 -10000 0 0
MMP9 -0.046 0.2 -9999 0 -0.72 49 49
PRKCE 0.012 0.001 -9999 0 -10000 0 0
PRKCD 0.016 0.06 -9999 0 -10000 0 0
Gi(beta/gamma) -0.079 0.18 -9999 0 -0.5 65 65
mol:LPA 0.001 0.019 -9999 0 -0.19 5 5
TRIP6/p130 Cas/FAK1/Paxillin -0.001 0.1 -9999 0 -0.43 3 3
MAPKKK cascade -0.088 0.18 -9999 0 -0.53 65 65
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 -0.002 0.069 -9999 0 -0.33 9 9
GNA15 -0.004 0.075 -9999 0 -0.34 14 14
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
MAPT -0.037 0.1 -9999 0 -0.38 5 5
GNA11 -0.002 0.068 -9999 0 -0.34 8 8
Rac1/GTP -0.07 0.28 -9999 0 -0.92 62 62
MMP2 -0.016 0.11 -9999 0 -0.64 8 8
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.003 0.12 -10000 0 -0.36 26 26
TBX21 -0.094 0.4 -10000 0 -1.1 62 62
B2M 0.011 0.024 -10000 0 -0.39 2 2
TYK2 0.014 0.021 -10000 0 -10000 0 0
IL12RB1 -0.001 0.087 -10000 0 -0.44 22 22
GADD45B -0.03 0.28 -10000 0 -0.96 22 22
IL12RB2 0.003 0.082 -10000 0 -0.51 13 13
GADD45G -0.035 0.28 -10000 0 -0.91 27 27
natural killer cell activation 0.001 0.022 -10000 0 -10000 0 0
RELB 0.013 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
IL18 0.013 0.034 -10000 0 -0.4 4 4
IL2RA 0.004 0.058 -10000 0 -0.4 13 13
IFNG -0.067 0.23 -10000 0 -0.75 63 63
STAT3 (dimer) -0.032 0.28 -10000 0 -0.76 42 42
HLA-DRB5 -0.02 0.14 -10000 0 -0.53 38 38
FASLG -0.094 0.4 -10000 0 -1.1 58 58
NF kappa B2 p52/RelB -0.15 0.27 -10000 0 -0.88 55 55
CD4 0.002 0.066 -10000 0 -0.39 17 17
SOCS1 -0.014 0.14 -10000 0 -0.75 22 22
EntrezGene:6955 0 0.01 -10000 0 -10000 0 0
CD3D 0.001 0.071 -10000 0 -0.4 19 19
CD3E -0.004 0.082 -10000 0 -0.4 26 26
CD3G -0.021 0.12 -10000 0 -0.4 52 52
IL12Rbeta2/JAK2 0.014 0.073 -10000 0 -0.4 12 12
CCL3 -0.077 0.35 -10000 0 -0.99 50 50
CCL4 -0.067 0.34 -10000 0 -0.97 48 48
HLA-A 0.012 0.018 -10000 0 -0.39 1 1
IL18/IL18R 0.034 0.08 -10000 0 -0.46 2 2
NOS2 -0.084 0.39 -10000 0 -1.1 53 53
IL12/IL12R/TYK2/JAK2/SPHK2 0.012 0.1 -10000 0 -0.37 13 13
IL1R1 -0.069 0.34 -10000 0 -0.96 53 53
IL4 0.001 0.022 -10000 0 -10000 0 0
JAK2 0.012 0.037 -10000 0 -0.42 3 3
EntrezGene:6957 0 0.009 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.044 0.26 -10000 0 -0.86 49 49
RAB7A -0.007 0.25 -10000 0 -0.79 19 19
lysosomal transport -0.004 0.24 -10000 0 -0.74 19 19
FOS -0.035 0.27 -10000 0 -0.92 39 39
STAT4 (dimer) -0.032 0.31 -10000 0 -0.86 43 43
STAT5A (dimer) -0.18 0.3 -10000 0 -0.88 70 70
GZMA -0.11 0.43 -10000 0 -1.2 71 71
GZMB -0.13 0.39 -10000 0 -0.91 77 77
HLX 0.012 0.016 -10000 0 -0.4 1 1
LCK -0.078 0.36 -10000 0 -0.97 55 55
TCR/CD3/MHC II/CD4 -0.027 0.2 -10000 0 -0.58 51 51
IL2/IL2R 0.015 0.06 -10000 0 -0.42 7 7
MAPK14 -0.025 0.29 -10000 0 -0.91 27 27
CCR5 -0.042 0.31 -10000 0 -1.1 26 26
IL1B -0.055 0.22 -10000 0 -0.73 58 58
STAT6 0.001 0.11 0.2 5 -0.25 5 10
STAT4 -0.006 0.084 -10000 0 -0.4 28 28
STAT3 0.013 0 -10000 0 -10000 0 0
STAT1 0.011 0.031 -10000 0 -0.75 1 1
NFKB1 0.013 0 -10000 0 -10000 0 0
NFKB2 0.013 0 -10000 0 -10000 0 0
IL12B 0.005 0.065 -10000 0 -0.75 4 4
CD8A -0.017 0.11 -10000 0 -0.4 45 45
CD8B 0.002 0.068 -10000 0 -0.42 15 15
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.003 0.12 0.36 26 -10000 0 26
IL2RB 0.001 0.066 -10000 0 -0.4 17 17
proteasomal ubiquitin-dependent protein catabolic process -0.024 0.28 -10000 0 -0.78 42 42
IL2RG 0.011 0.028 -10000 0 -0.4 3 3
IL12 0.012 0.071 -10000 0 -0.44 10 10
STAT5A 0.013 0 -10000 0 -10000 0 0
CD247 0.002 0.066 -10000 0 -0.4 16 16
IL2 0.003 0.006 -10000 0 -10000 0 0
SPHK2 0.012 0.016 -10000 0 -0.4 1 1
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.007 0.058 -10000 0 -0.45 8 8
IL12/IL12R/TYK2/JAK2 -0.082 0.38 -10000 0 -0.98 62 62
MAP2K3 -0.029 0.29 -10000 0 -0.86 33 33
RIPK2 0.013 0 -10000 0 -10000 0 0
MAP2K6 -0.03 0.29 -10000 0 -0.86 34 34
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.002 0.067 -10000 0 -0.4 17 17
IL18RAP -0.004 0.092 -10000 0 -0.41 29 29
IL12Rbeta1/TYK2 0.01 0.07 -10000 0 -0.33 19 19
EOMES -0.043 0.26 -10000 0 -1.2 29 29
STAT1 (dimer) -0.052 0.29 -10000 0 -0.74 51 51
T cell proliferation -0.013 0.24 -10000 0 -0.64 39 39
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.009 0.053 -10000 0 -0.4 10 10
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.1 0.2 -10000 0 -0.71 31 31
ATF2 -0.016 0.27 -10000 0 -0.88 22 22
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.007 0.075 -9999 0 -0.43 16 16
RGS9BP 0.006 0.061 -9999 0 -0.75 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.002 0.052 -9999 0 -0.75 3 3
mol:Na + -0.094 0.16 -9999 0 -0.56 34 34
mol:ADP 0.001 0.067 -9999 0 -0.65 6 6
GNAT2 -0.005 0.11 -9999 0 -0.75 13 13
RGS9-1/Gbeta5/R9AP -0.019 0.098 -9999 0 -0.49 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.003 0.076 -9999 0 -0.5 14 14
GRK7 0.003 0.061 -9999 0 -0.75 4 4
CNGB3 -0.036 0.17 -9999 0 -0.75 33 33
Cone Metarhodopsin II/X-Arrestin 0 0.04 -9999 0 -0.58 3 3
mol:Ca2+ -0.12 0.2 -9999 0 -0.55 83 83
Cone PDE6 -0.014 0.084 -9999 0 -0.42 5 5
Cone Metarhodopsin II 0.001 0.055 -9999 0 -0.53 6 6
Na + (4 Units) -0.12 0.2 -9999 0 -0.55 83 83
GNAT2/GDP -0.018 0.1 -9999 0 -0.44 17 17
GNB5 0.013 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.002 0.069 -9999 0 -0.46 14 14
Cone Transducin 0.008 0.079 -9999 0 -0.45 16 16
SLC24A2 -0.065 0.22 -9999 0 -0.75 59 59
GNB3/GNGT2 0.012 0.053 -9999 0 -0.34 12 12
GNB3 0.008 0.055 -9999 0 -0.66 4 4
GNAT2/GTP -0.004 0.084 -9999 0 -0.58 13 13
CNGA3 -0.12 0.19 -9999 0 -0.4 201 201
ARR3 0 0.053 -9999 0 -0.75 3 3
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.095 0.16 -9999 0 -0.56 34 34
mol:Pi -0.019 0.097 -9999 0 -0.49 4 4
Cone CNG Channel -0.08 0.14 -9999 0 -0.47 48 48
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.064 0.22 -9999 0 -0.75 59 59
RGS9 -0.055 0.15 -9999 0 -0.4 103 103
PDE6C 0.003 0.006 -9999 0 -10000 0 0
GNGT2 0.007 0.046 -9999 0 -0.4 8 8
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0 0.03 -9999 0 -0.75 1 1
Nectin adhesion pathway

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
PDGFRB 0.004 0.081 -9999 0 -0.75 7 7
alphaV beta3 Integrin 0.015 0.03 -9999 0 -0.27 7 7
PTK2 0.03 0.059 -9999 0 -0.5 1 1
positive regulation of JNK cascade -0.008 0.043 -9999 0 -0.26 17 17
CDC42/GDP 0.04 0.068 -9999 0 -0.35 17 17
Rac1/GDP 0.041 0.067 -9999 0 -0.34 17 17
RAP1B 0.013 0 -9999 0 -10000 0 0
RAP1A 0.013 0 -9999 0 -10000 0 0
CTNNB1 0.013 0 -9999 0 -10000 0 0
CDC42/GTP -0.009 0.052 -9999 0 -0.32 17 17
nectin-3/I-afadin 0.011 0.047 -9999 0 -0.27 17 17
RAPGEF1 0.036 0.07 -9999 0 -0.38 17 17
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.032 0.078 -9999 0 -0.43 17 17
PDGFB-D/PDGFRB 0.004 0.08 -9999 0 -0.75 7 7
TLN1 0.022 0.027 -9999 0 -10000 0 0
Rap1/GTP -0.008 0.045 -9999 0 -0.34 1 1
IQGAP1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.024 0.009 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.011 0.047 -9999 0 -0.27 17 17
PVR 0.013 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.013 0 -9999 0 -10000 0 0
mol:GDP 0.037 0.08 -9999 0 -0.42 17 17
MLLT4 0.012 0.016 -9999 0 -0.4 1 1
PIK3CA 0.012 0.016 -9999 0 -0.4 1 1
PI3K 0.026 0.059 -9999 0 -0.42 7 7
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.018 0.011 -9999 0 -10000 0 0
positive regulation of lamellipodium assembly -0.011 0.052 -9999 0 -0.27 19 19
PVRL1 0.013 0 -9999 0 -10000 0 0
PVRL3 0.002 0.064 -9999 0 -0.4 16 16
PVRL2 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
CDH1 0.013 0 -9999 0 -10000 0 0
CLDN1 -0.68 0.22 -9999 0 -0.75 569 569
JAM-A/CLDN1 -0.41 0.14 -9999 0 -0.45 569 569
SRC 0.027 0.084 -9999 0 -0.47 17 17
ITGB3 0.008 0.043 -9999 0 -0.4 7 7
nectin-1(dimer)/I-afadin/I-afadin 0.018 0.011 -9999 0 -10000 0 0
FARP2 0.035 0.075 -9999 0 -0.41 17 17
RAC1 0.013 0 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.019 0.04 -9999 0 -10000 0 0
nectin-1/I-afadin 0.018 0.011 -9999 0 -10000 0 0
nectin-2/I-afadin 0.018 0.011 -9999 0 -0.27 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 0.019 0.04 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1/filamentous actin 0.016 0.014 -9999 0 -10000 0 0
F11R 0.013 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.008 0.043 -9999 0 -0.26 17 17
alphaV/beta3 Integrin/Talin 0.032 0.035 -9999 0 -0.4 1 1
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.018 0.011 -9999 0 -0.27 1 1
nectin-2(dimer)/I-afadin/I-afadin 0.018 0.011 -9999 0 -0.27 1 1
PIP5K1C 0.017 0.029 -9999 0 -0.28 1 1
VAV2 0.028 0.093 -9999 0 -0.42 26 26
RAP1/GDP -0.01 0.053 -9999 0 -0.32 17 17
ITGAV 0.013 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.019 0.04 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin 0.011 0.047 -9999 0 -0.27 17 17
Rac1/GTP -0.013 0.062 -9999 0 -0.33 19 19
PTPRM 0.012 0.031 -9999 0 -0.31 1 1
E-cadherin/beta catenin/alpha catenin 0.037 0.008 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.011 0.023 -9999 0 -0.4 2 2
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.054 0.11 0.33 26 -10000 0 26
GNAI2 0.013 0 -10000 0 -10000 0 0
S1P/S1P5/G12 0.005 0.079 -10000 0 -0.5 15 15
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.14 0.2 -10000 0 -0.4 234 234
RhoA/GTP -0.054 0.11 -10000 0 -0.34 26 26
negative regulation of cAMP metabolic process -0.066 0.12 -10000 0 -0.37 26 26
GNAZ 0.007 0.046 -10000 0 -0.4 8 8
GNAI3 0.013 0 -10000 0 -10000 0 0
GNA12 0.013 0 -10000 0 -10000 0 0
S1PR5 -0.006 0.12 -10000 0 -0.75 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.066 0.12 -10000 0 -0.38 26 26
RhoA/GDP 0.009 0 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
GNAI1 -0.002 0.075 -10000 0 -0.4 22 22
HIF-2-alpha transcription factor network

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
MMP14 -0.015 0.078 -10000 0 -0.63 9 9
oxygen homeostasis -0.011 0.013 -10000 0 -10000 0 0
TCEB2 0.01 0.043 -10000 0 -0.75 2 2
TCEB1 0.013 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.028 0.06 -10000 0 -0.41 2 2
EPO -0.13 0.2 -10000 0 -0.6 50 50
FIH (dimer) 0.003 0.011 -10000 0 -10000 0 0
APEX1 -0.002 0.015 -10000 0 -10000 0 0
SERPINE1 -0.21 0.34 -10000 0 -0.83 124 124
FLT1 -0.005 0.037 -10000 0 -0.68 1 1
ADORA2A -0.14 0.22 -10000 0 -0.68 46 46
germ cell development -0.14 0.22 -10000 0 -0.68 49 49
SLC11A2 -0.14 0.23 -10000 0 -0.7 46 46
BHLHE40 -0.14 0.23 -10000 0 -0.71 46 46
HIF1AN 0.003 0.011 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.065 0.12 -10000 0 -0.4 1 1
ETS1 0.025 0.017 -10000 0 -0.39 1 1
CITED2 -0.009 0.049 -10000 0 -1.1 1 1
KDR -0.006 0.057 -10000 0 -0.89 2 2
PGK1 -0.14 0.23 -10000 0 -0.7 46 46
SIRT1 0.013 0.001 -10000 0 -10000 0 0
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT -0.16 0.27 -10000 0 -0.84 47 47
EPAS1 -0.039 0.081 -10000 0 -0.32 2 2
SP1 0.019 0.002 -10000 0 -10000 0 0
ABCG2 -0.34 0.28 -10000 0 -0.71 153 153
EFNA1 -0.14 0.23 -10000 0 -0.7 46 46
FXN -0.14 0.22 -10000 0 -0.68 46 46
POU5F1 -0.14 0.23 -10000 0 -0.71 49 49
neuron apoptosis 0.16 0.26 0.8 47 -10000 0 47
EP300 0.013 0 -10000 0 -10000 0 0
EGLN3 0 0.041 -10000 0 -0.4 6 6
EGLN2 0.003 0.02 -10000 0 -0.4 1 1
EGLN1 0.003 0.011 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.024 0.029 -10000 0 -0.49 2 2
VHL 0.013 0 -10000 0 -10000 0 0
ARNT -0.003 0.022 -10000 0 -0.42 1 1
SLC2A1 -0.15 0.25 -10000 0 -0.74 64 64
TWIST1 -0.16 0.27 -10000 0 -0.86 58 58
ELK1 0.019 0.001 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.06 0.12 -10000 0 -10000 0 0
VEGFA -0.14 0.23 -10000 0 -0.71 47 47
CREBBP 0.013 0 -10000 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.016 0.048 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.093 0.11 -9999 0 -0.38 2 2
JUN -0.067 0.13 -9999 0 -0.4 2 2
HRAS 0.012 0.016 -9999 0 -0.4 1 1
RET51/GFRalpha1/GDNF/GRB10 -0.089 0.15 -9999 0 -0.4 63 63
RAP1A 0.013 0 -9999 0 -10000 0 0
FRS2 0.013 0.001 -9999 0 -10000 0 0
RAP1A/GDP 0.009 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.089 0.15 -9999 0 -0.4 63 63
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.064 0.11 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
RAP1A/GTP -0.077 0.13 -9999 0 -0.49 2 2
GRB7 -0.006 0.12 -9999 0 -0.75 15 15
RET51/GFRalpha1/GDNF -0.089 0.15 -9999 0 -0.4 63 63
MAPKKK cascade -0.096 0.12 -9999 0 -0.49 2 2
BCAR1 0.012 0.016 -9999 0 -0.4 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.064 0.11 -9999 0 -10000 0 0
lamellipodium assembly -0.092 0.11 -9999 0 -0.3 62 62
RET51/GFRalpha1/GDNF/SHC -0.089 0.15 -9999 0 -0.4 63 63
PIK3CA 0.012 0.016 -9999 0 -0.4 1 1
RET9/GFRalpha1/GDNF/SHC -0.064 0.11 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3 -0.064 0.11 -9999 0 -0.4 1 1
MAPK3 -0.068 0.12 -9999 0 -0.46 2 2
DOK1 0.013 0 -9999 0 -10000 0 0
DOK6 0.003 0.06 -9999 0 -0.4 14 14
PXN 0.013 0 -9999 0 -10000 0 0
neurite development -0.059 0.12 -9999 0 -0.46 2 2
DOK5 0.002 0.067 -9999 0 -0.42 15 15
GFRA1 -0.15 0.2 -9999 0 -0.4 245 245
MAPK8 -0.076 0.14 -9999 0 -0.37 62 62
HRAS/GTP -0.11 0.14 -9999 0 -0.42 63 63
tube development -0.054 0.1 -9999 0 -0.37 1 1
MAPK1 -0.068 0.12 -9999 0 -0.55 1 1
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.06 0.11 -9999 0 -10000 0 0
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
SRC 0.013 0 -9999 0 -10000 0 0
PDLIM7 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.082 0.15 -9999 0 -0.39 70 70
SHC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.09 0.15 -9999 0 -0.4 64 64
RET51/GFRalpha1/GDNF/Dok5 -0.095 0.15 -9999 0 -0.4 69 69
PRKCA 0.013 0 -9999 0 -10000 0 0
HRAS/GDP 0.009 0.011 -9999 0 -0.28 1 1
CREB1 -0.093 0.15 -9999 0 -0.4 62 62
PIK3R1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.06 0.11 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Grb7 -0.1 0.17 -9999 0 -0.44 75 75
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.051 0.15 -9999 0 -0.4 96 96
DOK4 0.012 0.016 -9999 0 -0.4 1 1
JNK cascade -0.066 0.13 -9999 0 -0.4 2 2
RET9/GFRalpha1/GDNF/FRS2 -0.064 0.11 -9999 0 -10000 0 0
SHANK3 0.012 0.016 -9999 0 -0.4 1 1
RASA1 0.013 0.001 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.061 0.11 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.087 0.14 -9999 0 -0.39 62 62
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.087 0.14 -9999 0 -0.39 62 62
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.096 0.16 -9999 0 -0.48 62 62
PI3K -0.1 0.18 -9999 0 -0.45 62 62
SOS1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.054 0.1 -9999 0 -0.37 1 1
GRB10 0.013 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.073 0.12 -9999 0 -0.32 62 62
RET51/GFRalpha1/GDNF/FRS2 -0.09 0.15 -9999 0 -0.4 63 63
GAB1 0.013 0 -9999 0 -10000 0 0
IRS1 0.013 0 -9999 0 -10000 0 0
IRS2 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.096 0.16 -9999 0 -0.48 62 62
RET51/GFRalpha1/GDNF/PKC alpha -0.089 0.15 -9999 0 -0.4 63 63
GRB2 0.013 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GDNF 0.009 0.017 -9999 0 -0.4 1 1
RAC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.089 0.15 -9999 0 -0.4 63 63
Rac1/GTP -0.11 0.13 -9999 0 -0.36 62 62
RET9/GFRalpha1/GDNF -0.08 0.12 -9999 0 -10000 0 0
GFRalpha1/GDNF -0.097 0.14 -9999 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.019 0.034 -9999 0 -0.56 1 1
VDR 0.013 0 -9999 0 -10000 0 0
FAM120B 0.013 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.045 0.11 -9999 0 -0.43 3 3
RXRs/LXRs/DNA/Oxysterols -0.029 0.11 -9999 0 -0.39 12 12
MED1 0.01 0.043 -9999 0 -0.75 2 2
mol:9cRA 0.004 0.007 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.034 0.1 -9999 0 -0.39 2 2
RXRs/NUR77 -0.06 0.12 -9999 0 -0.53 10 10
RXRs/PPAR -0.056 0.11 -9999 0 -0.41 3 3
NCOR2 0.012 0.016 -9999 0 -0.4 1 1
VDR/VDR/Vit D3 0.009 0 -9999 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.028 0.026 -9999 0 -0.42 1 1
RARA 0.011 0.035 -9999 0 -0.57 2 2
NCOA1 0.013 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.013 0 -9999 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.023 0.026 -9999 0 -0.43 1 1
RARG 0.013 0 -9999 0 -10000 0 0
RPS6KB1 0.028 0.039 -9999 0 -0.37 1 1
RARs/THRs/DNA/SMRT -0.034 0.1 -9999 0 -0.39 3 3
THRA 0.011 0.031 -9999 0 -0.75 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 -0.057 0.11 -9999 0 -0.3 2 2
NR1H4 -0.19 0.2 -9999 0 -0.4 312 312
RXRs/LXRs/DNA -0.033 0.11 -9999 0 -0.35 1 1
NR1H2 0.017 0.017 -9999 0 -0.39 1 1
NR1H3 0.017 0.006 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.05 0.1 -9999 0 -10000 0 0
NR4A1 0.001 0.093 -9999 0 -0.72 10 10
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.16 0.15 -9999 0 -0.36 150 150
RXRG -0.16 0.2 -9999 0 -0.39 262 262
RXR alpha/CCPG 0.022 0.012 -9999 0 -0.26 1 1
RXRA 0.016 0.017 -9999 0 -0.39 1 1
RXRB 0.017 0.006 -9999 0 -10000 0 0
THRB -0.11 0.18 -9999 0 -0.4 181 181
PPARG 0.011 0.023 -9999 0 -0.4 2 2
PPARD 0.012 0.016 -9999 0 -0.4 1 1
TNF -0.024 0.13 -9999 0 -0.88 6 6
mol:Oxysterols 0.005 0.006 -9999 0 -10000 0 0
cholesterol transport -0.029 0.11 -9999 0 -0.39 12 12
PPARA 0.013 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB 0.01 0.033 -9999 0 -0.4 4 4
RXRs/NUR77/BCL2 -0.079 0.12 -9999 0 -0.47 17 17
SREBF1 -0.02 0.099 -9999 0 -0.49 2 2
RXRs/RXRs/DNA/9cRA -0.057 0.11 -9999 0 -0.3 2 2
ABCA1 -0.025 0.13 -9999 0 -0.89 7 7
RARs/THRs -0.026 0.099 -9999 0 -0.42 2 2
RXRs/FXR -0.16 0.15 -9999 0 -0.38 144 144
BCL2 -0.008 0.09 -9999 0 -0.4 32 32
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.028 0.041 -10000 0 -0.53 3 3
epithelial cell differentiation -0.014 0.059 -10000 0 -0.54 2 2
ITCH 0.013 0.017 -10000 0 -0.39 1 1
WWP1 0.027 0.051 -10000 0 -1.2 1 1
FYN 0.013 0 -10000 0 -10000 0 0
EGFR 0.011 0.023 -10000 0 -0.4 2 2
PRL -0.009 0.1 -10000 0 -0.75 12 12
neuron projection morphogenesis 0.031 0.063 -10000 0 -0.47 1 1
PTPRZ1 -0.14 0.2 -10000 0 -0.4 233 233
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.024 0.067 -10000 0 -0.52 1 1
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.005 0.074 -10000 0 -0.6 1 1
ADAM17 0.013 0.005 -10000 0 -10000 0 0
ErbB4/ErbB4 0.028 0.033 -10000 0 -0.74 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.024 0.037 -10000 0 -0.57 2 2
NCOR1 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.012 0.069 -10000 0 -0.56 1 1
GRIN2B -0.13 0.21 -10000 0 -0.41 208 208
ErbB4/ErbB2/betacellulin 0.024 0.069 -10000 0 -0.42 12 12
STAT1 0.011 0.031 -10000 0 -0.75 1 1
HBEGF 0.01 0.043 -10000 0 -0.75 2 2
PRLR 0.002 0.064 -10000 0 -0.4 16 16
E4ICDs/ETO2 0 0.083 -10000 0 -0.56 2 2
axon guidance 0.063 0.081 -10000 0 -0.74 1 1
NEDD4 0.013 0.005 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.005 0.093 -10000 0 -0.59 12 12
CBFA2T3 -0.041 0.14 -10000 0 -0.4 81 81
ErbB4/ErbB2/HBEGF 0.026 0.069 -10000 0 -0.42 14 14
MAPK3 0.026 0.065 -10000 0 -0.49 1 1
STAT1 (dimer) 0.029 0.035 -10000 0 -0.56 2 2
MAPK1 0.027 0.064 -10000 0 -0.49 1 1
JAK2 0.011 0.028 -10000 0 -0.4 3 3
ErbB4/ErbB2/neuregulin 1 beta 0.003 0.092 -10000 0 -0.46 12 12
NRG1 -0.015 0.094 -10000 0 -0.27 73 73
NRG3 0.005 0.035 -10000 0 -0.57 2 2
NRG2 -0.049 0.14 -10000 0 -0.4 89 89
NRG4 -0.026 0.12 -10000 0 -0.4 55 55
heart development 0.063 0.081 -10000 0 -0.74 1 1
neural crest cell migration 0.003 0.091 -10000 0 -0.45 12 12
ERBB2 0.009 0.079 -10000 0 -0.58 11 11
WWOX/E4ICDs 0.029 0.03 -10000 0 -0.67 1 1
SHC1 0.013 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.014 0.066 -10000 0 -0.63 1 1
apoptosis 0.026 0.06 0.61 2 -10000 0 2
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.006 0.086 -10000 0 -0.63 2 2
ErbB4/ErbB2/epiregulin -0.15 0.23 -10000 0 -0.42 249 249
ErbB4/ErbB4/betacellulin/betacellulin 0.026 0.041 -10000 0 -0.67 1 1
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.026 0.077 -10000 0 -0.54 3 3
MDM2 0.03 0.032 -10000 0 -0.67 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.007 0.071 -10000 0 -0.53 1 1
STAT5A 0.066 0.074 -10000 0 -0.71 1 1
ErbB4/EGFR/neuregulin 1 beta 0.011 0.07 -10000 0 -0.56 1 1
DLG4 0.011 0.031 -10000 0 -0.75 1 1
GRB2/SHC 0.019 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.027 0.028 -10000 0 -0.63 1 1
STAT5A (dimer) -0.015 0.063 -10000 0 -0.59 2 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.064 0.071 -10000 0 -0.71 1 1
LRIG1 0.012 0.016 -10000 0 -0.4 1 1
EREG -0.29 0.37 -10000 0 -0.73 256 256
BTC 0.006 0.051 -10000 0 -0.4 10 10
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.063 0.081 -10000 0 -0.75 1 1
ERBB4 0.028 0.033 -10000 0 -0.74 1 1
STAT5B 0.013 0 -10000 0 -10000 0 0
YAP1 0.016 0.007 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.008 0.085 -10000 0 -0.44 12 12
glial cell differentiation -0.026 0.027 0.62 1 -10000 0 1
WWOX 0.013 0 -10000 0 -10000 0 0
cell proliferation 0.022 0.1 -10000 0 -0.52 4 4
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.013 0 -9999 0 -10000 0 0
HDAC3 0.013 0 -9999 0 -10000 0 0
VDR 0.013 0 -9999 0 -10000 0 0
Cbp/p300/PCAF 0.015 0.049 -9999 0 -10000 0 0
EP300 0.013 0 -9999 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.001 0.057 -9999 0 -0.35 1 1
KAT2B -0.005 0.083 -9999 0 -0.4 27 27
MAPK14 0.013 0 -9999 0 -10000 0 0
AKT1 -0.005 0.066 -9999 0 -0.29 1 1
RAR alpha/9cRA/Cyclin H -0.054 0.073 -9999 0 -10000 0 0
mol:9cRA 0 0 -9999 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.003 0.063 -9999 0 -0.28 12 12
CDC2 0 0.001 -9999 0 -10000 0 0
response to UV 0.001 0.002 -9999 0 -10000 0 0
RAR alpha/Jnk1 -0.044 0.091 -9999 0 -0.37 1 1
NCOR2 0.012 0.016 -9999 0 -0.4 1 1
VDR/VDR/Vit D3 0.009 0 -9999 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.074 0.13 -9999 0 -0.46 3 3
NCOA2 0.011 0.028 -9999 0 -0.4 3 3
NCOA3 0.013 0 -9999 0 -10000 0 0
NCOA1 0.013 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.013 0 -9999 0 -10000 0 0
RARG 0.013 0.001 -9999 0 -10000 0 0
RAR gamma1/9cRA 0.017 0.001 -9999 0 -10000 0 0
MAPK3 0.012 0.016 -9999 0 -0.39 1 1
MAPK1 0.012 0.016 -9999 0 -0.4 1 1
MAPK8 0.013 0.001 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.092 0.14 -9999 0 -10000 0 0
RARA -0.054 0.11 -9999 0 -0.42 1 1
negative regulation of phosphoinositide 3-kinase cascade 0 0 -9999 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.004 0.066 -9999 0 -0.29 12 12
PRKCA 0.015 0.003 -9999 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.09 0.14 -9999 0 -0.53 3 3
RXRG -0.22 0.23 -9999 0 -0.36 395 395
RXRA -0.044 0.1 -9999 0 -10000 0 0
RXRB -0.092 0.16 -9999 0 -0.31 217 217
VDR/Vit D3/DNA 0.009 0 -9999 0 -10000 0 0
RBP1 -0.038 0.19 -9999 0 -0.75 41 41
CRBP1/9-cic-RA -0.029 0.14 -9999 0 -0.58 41 41
RARB 0.012 0.033 -9999 0 -0.4 4 4
PRKCG -0.25 0.36 -9999 0 -0.75 217 217
MNAT1 0.013 0.001 -9999 0 -10000 0 0
RAR alpha/RXRs -0.071 0.14 -9999 0 -0.4 1 1
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.064 0.13 -9999 0 -0.41 1 1
proteasomal ubiquitin-dependent protein catabolic process -0.021 0.084 -9999 0 -0.28 14 14
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.09 0.14 -9999 0 -0.53 3 3
positive regulation of DNA binding -0.052 0.07 -9999 0 -10000 0 0
NRIP1 -0.086 0.14 -9999 0 -1.1 2 2
RXRs/RARs -0.098 0.14 -9999 0 -0.34 87 87
RXRs/RXRs/DNA/9cRA -0.1 0.14 -9999 0 -0.34 86 86
PRKACA 0.013 0 -9999 0 -10000 0 0
CDK7 0.013 0 -9999 0 -10000 0 0
TFIIH 0.026 0 -9999 0 -10000 0 0
RAR alpha/9cRA -0.038 0.057 -9999 0 -10000 0 0
CCNH 0.013 0 -9999 0 -10000 0 0
CREBBP 0.013 0 -9999 0 -10000 0 0
RAR gamma2/9cRA 0 0 -9999 0 -10000 0 0
S1P4 pathway

Figure S52.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S52.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.14 0.2 -9999 0 -0.4 234 234
CDC42/GTP -0.053 0.11 -9999 0 -0.36 28 28
PLCG1 -0.055 0.12 -9999 0 -0.37 28 28
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.013 0 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
G12/G13 0.019 0 -9999 0 -10000 0 0
cell migration -0.052 0.11 -9999 0 -0.35 28 28
S1PR5 -0.006 0.12 -9999 0 -0.75 15 15
S1PR4 0.006 0.051 -9999 0 -0.4 10 10
MAPK3 -0.055 0.12 -9999 0 -0.37 29 29
MAPK1 -0.055 0.12 -9999 0 -0.37 28 28
S1P/S1P5/Gi -0.066 0.12 -9999 0 -0.38 26 26
GNAI1 -0.002 0.075 -9999 0 -0.4 22 22
CDC42/GDP 0.008 0.016 -9999 0 -0.28 2 2
S1P/S1P5/G12 0.005 0.079 -9999 0 -0.5 15 15
RHOA 0.023 0.025 -9999 0 -10000 0 0
S1P/S1P4/Gi -0.064 0.12 -9999 0 -0.39 28 28
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.007 0.046 -9999 0 -0.4 8 8
S1P/S1P4/G12/G13 0.021 0.028 -9999 0 -10000 0 0
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
CDC42 0.011 0.023 -9999 0 -0.4 2 2
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.012 0.016 -9999 0 -0.4 1 1
SPHK1 -0.037 0.19 -9999 0 -0.75 40 40
GNAI2 0.013 0 -9999 0 -10000 0 0
mol:S1P 0.001 0.067 -9999 0 -0.25 41 41
GNAO1 -0.14 0.2 -9999 0 -0.4 234 234
mol:Sphinganine-1-P -0.019 0.14 -9999 0 -0.56 41 41
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.023 0.051 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
G12/G13 0.019 0 -9999 0 -10000 0 0
S1PR3 0.011 0.031 -9999 0 -0.75 1 1
S1PR2 0.013 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.002 0.057 -9999 0 -0.22 41 41
S1PR5 -0.006 0.12 -9999 0 -0.75 15 15
S1PR4 0.006 0.051 -9999 0 -0.4 10 10
GNAI1 -0.002 0.075 -9999 0 -0.4 22 22
S1P/S1P5/G12 0.004 0.096 -9999 0 -0.51 15 15
S1P/S1P3/Gq 0.018 0.061 -9999 0 -0.38 8 8
S1P/S1P4/Gi -0.062 0.12 -9999 0 -0.37 37 37
GNAQ 0.011 0.028 -9999 0 -0.4 3 3
GNAZ 0.007 0.046 -9999 0 -0.4 8 8
GNA14 0.009 0.036 -9999 0 -0.4 5 5
GNA15 0.005 0.075 -9999 0 -0.75 6 6
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
GNA11 0.01 0.033 -9999 0 -0.4 4 4
ABCC1 0.013 0 -9999 0 -10000 0 0
Noncanonical Wnt signaling pathway

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
NFATC2 -0.001 0.073 -9999 0 -0.4 21 21
GNB1/GNG2 -0.044 0.13 -9999 0 -0.41 29 29
mol:DAG -0.036 0.12 -9999 0 -0.41 12 12
PLCG1 -0.037 0.12 -9999 0 -0.42 12 12
YES1 -0.045 0.13 -9999 0 -0.44 22 22
FZD3 0.006 0.065 -9999 0 -0.63 6 6
FZD6 0.013 0 -9999 0 -10000 0 0
G protein -0.036 0.13 -9999 0 -0.39 29 29
MAP3K7 -0.035 0.12 -9999 0 -0.42 6 6
mol:Ca2+ -0.035 0.12 -9999 0 -0.4 12 12
mol:IP3 -0.036 0.12 -9999 0 -0.41 12 12
NLK 0.006 0.011 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
CAMK2A -0.043 0.12 -9999 0 -0.46 6 6
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.054 0.14 -9999 0 -0.47 22 22
CSNK1A1 0.013 0 -9999 0 -10000 0 0
GNAS -0.045 0.13 -9999 0 -0.44 22 22
GO:0007205 -0.036 0.12 -9999 0 -0.38 20 20
WNT6 -0.032 0.15 -9999 0 -0.5 53 53
WNT4 -0.003 0.088 -9999 0 -0.47 20 20
NFAT1/CK1 alpha -0.03 0.12 -9999 0 -0.44 12 12
GNG2 -0.004 0.081 -9999 0 -0.4 26 26
WNT5A 0.003 0.082 -9999 0 -0.71 8 8
WNT11 -0.14 0.3 -9999 0 -0.72 129 129
CDC42 -0.038 0.12 -9999 0 -0.41 23 23
EGFR-dependent Endothelin signaling events

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
HRAS 0.012 0.016 -9999 0 -0.4 1 1
EGFR 0.011 0.023 -9999 0 -0.4 2 2
EGF/EGFR -0.052 0.15 -9999 0 -0.47 55 55
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.016 0.11 -9999 0 -0.42 20 20
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.035 0.18 -9999 0 -0.75 39 39
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.086 0.2 -9999 0 -0.45 131 131
EGF/EGFR dimer/SHC -0.036 0.12 -9999 0 -0.49 20 20
mol:GDP -0.018 0.11 -9999 0 -0.41 20 20
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.012 0.016 -9999 0 -0.4 1 1
GRB2/SOS1 0.019 0 -9999 0 -10000 0 0
HRAS/GTP -0.04 0.085 -9999 0 -0.38 20 20
SHC1 0.013 0 -9999 0 -10000 0 0
HRAS/GDP -0.041 0.087 -9999 0 -0.39 20 20
FRAP1 -0.021 0.1 -9999 0 -0.4 20 20
EGF/EGFR dimer -0.053 0.14 -9999 0 -0.57 20 20
SOS1 0.013 0 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.019 0.14 -9999 0 -0.56 40 40
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.007 0.061 -10000 0 -0.75 4 4
GNB1/GNG2 -0.069 0.059 -10000 0 -0.21 17 17
AKT1 -0.036 0.08 -10000 0 -0.22 1 1
EGF -0.086 0.2 -10000 0 -0.45 131 131
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR -0.056 0.08 -10000 0 -0.34 1 1
mol:Ca2+ -0.065 0.11 -10000 0 -0.3 17 17
LYN -0.055 0.077 -10000 0 -10000 0 0
RhoA/GTP -0.031 0.044 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.072 0.12 -10000 0 -0.34 18 18
GNG2 -0.005 0.081 -10000 0 -0.4 26 26
ARRB2 0.013 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.006 0.06 -10000 0 -0.38 8 8
G beta5/gamma2 -0.086 0.075 -10000 0 -0.28 17 17
PRKCH -0.069 0.12 -10000 0 -0.36 11 11
DNM1 0.004 0.081 -10000 0 -0.75 7 7
TXA2/TP beta/beta Arrestin3 -0.024 0.032 -10000 0 -0.26 5 5
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.22 0.2 -10000 0 -0.4 358 358
G12 family/GTP -0.083 0.093 -10000 0 -0.31 18 18
ADRBK1 0.012 0 -10000 0 -10000 0 0
ADRBK2 0.012 0.016 -10000 0 -0.4 1 1
RhoA/GTP/ROCK1 0.016 0.01 -10000 0 -10000 0 0
mol:GDP 0.074 0.088 0.26 32 -10000 0 32
mol:NADP 0 0.096 -10000 0 -0.75 10 10
RAB11A 0.013 0 -10000 0 -10000 0 0
PRKG1 -0.003 0.078 -10000 0 -0.4 24 24
mol:IP3 -0.081 0.13 -10000 0 -0.38 19 19
cell morphogenesis 0.016 0.01 -10000 0 -10000 0 0
PLCB2 -0.11 0.17 -10000 0 -0.51 19 19
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.11 0.12 -10000 0 -0.34 2 2
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.058 0.083 -10000 0 -0.41 1 1
RHOA 0.013 0 -10000 0 -10000 0 0
PTGIR 0.01 0.043 -10000 0 -0.75 2 2
PRKCB1 -0.075 0.13 -10000 0 -0.37 17 17
GNAQ 0.011 0.028 -10000 0 -0.4 3 3
mol:L-citrulline 0 0.096 -10000 0 -0.75 10 10
TXA2/TXA2-R family -0.11 0.18 -10000 0 -0.5 37 37
LCK -0.06 0.087 -10000 0 -0.4 8 8
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.088 0.084 -10000 0 -0.37 3 3
TXA2-R family/G12 family/GDP/G beta/gamma -0.015 0.045 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.074 0.09 -10000 0 -10000 0 0
MAPK14 -0.044 0.088 -10000 0 -0.24 8 8
TGM2/GTP -0.096 0.16 -10000 0 -0.42 36 36
MAPK11 -0.045 0.09 -10000 0 -0.26 10 10
ARHGEF1 -0.035 0.071 -10000 0 -0.2 2 2
GNAI2 0.013 0 -10000 0 -10000 0 0
JNK cascade -0.084 0.14 -10000 0 -0.37 37 37
RAB11/GDP 0.013 0.001 -10000 0 -10000 0 0
ICAM1 -0.056 0.1 -10000 0 -0.29 14 14
cAMP biosynthetic process -0.087 0.13 -10000 0 -0.35 36 36
Gq family/GTP/EBP50 0.019 0.041 -10000 0 -0.44 2 2
actin cytoskeleton reorganization 0.016 0.01 -10000 0 -10000 0 0
SRC -0.055 0.077 -10000 0 -10000 0 0
GNB5 0.012 0 -10000 0 -10000 0 0
GNB1 0.013 0 -10000 0 -10000 0 0
EGF/EGFR -0.079 0.094 -10000 0 -0.3 10 10
VCAM1 -0.063 0.11 -10000 0 -0.38 15 15
TP beta/Gq family/GDP/G beta5/gamma2 -0.006 0.06 -10000 0 -0.38 8 8
platelet activation -0.06 0.12 -10000 0 -0.31 14 14
PGI2/IP 0.007 0.033 -10000 0 -0.58 2 2
PRKACA -0.11 0.11 -10000 0 -0.28 4 4
Gq family/GDP/G beta5/gamma2 -0.017 0.063 -10000 0 -0.38 8 8
TXA2/TP beta/beta Arrestin2 -0.015 0.032 -10000 0 -0.3 7 7
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.096 0.1 -10000 0 -10000 0 0
mol:DAG -0.084 0.14 -10000 0 -0.41 17 17
EGFR 0.011 0.023 -10000 0 -0.4 2 2
TXA2/TP alpha -0.11 0.17 -10000 0 -0.48 36 36
Gq family/GTP 0.009 0.043 -10000 0 -0.23 13 13
YES1 -0.055 0.077 -10000 0 -10000 0 0
GNAI2/GTP -0.08 0.069 -10000 0 -10000 0 0
PGD2/DP -0.16 0.14 -10000 0 -0.28 358 358
SLC9A3R1 0.013 0 -10000 0 -10000 0 0
FYN -0.055 0.077 -10000 0 -10000 0 0
mol:NO 0 0.096 -10000 0 -0.75 10 10
GNA15 0.005 0.075 -10000 0 -0.75 6 6
PGK/cGMP -0.001 0.08 -10000 0 -0.52 10 10
RhoA/GDP 0.013 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.077 0.1 -10000 0 -0.45 4 4
NOS3 0 0.096 -10000 0 -0.75 10 10
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCA -0.069 0.12 -10000 0 -0.34 15 15
PRKCB -0.094 0.13 -10000 0 -0.42 19 19
PRKCE -0.065 0.12 -10000 0 -0.35 12 12
PRKCD -0.071 0.13 -10000 0 -0.37 16 16
PRKCG -0.13 0.19 -10000 0 -0.47 68 68
muscle contraction -0.1 0.17 -10000 0 -0.46 37 37
PRKCZ -0.072 0.12 -10000 0 -0.34 18 18
ARR3 0 0.053 -10000 0 -0.75 3 3
TXA2/TP beta -0.076 0.092 -10000 0 -0.33 1 1
PRKCQ -0.068 0.12 -10000 0 -0.35 16 16
MAPKKK cascade -0.097 0.15 -10000 0 -0.46 19 19
SELE -0.079 0.14 -10000 0 -0.31 125 125
TP beta/GNAI2/GDP/G beta/gamma -0.075 0.1 -10000 0 -10000 0 0
ROCK1 0.012 0.016 -10000 0 -0.4 1 1
GNA14 0.009 0.036 -10000 0 -0.4 5 5
chemotaxis -0.12 0.19 -10000 0 -0.54 37 37
GNA12 0.013 0 -10000 0 -10000 0 0
GNA13 0.013 0 -10000 0 -10000 0 0
GNA11 0.01 0.033 -10000 0 -0.4 4 4
Rac1/GTP 0.009 0.001 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.013 0 -10000 0 -10000 0 0
HDAC4 0.013 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.008 0.07 0.57 9 -10000 0 9
CDKN1A -0.001 0.024 -10000 0 -0.6 1 1
KAT2B -0.005 0.083 -10000 0 -0.4 27 27
BAX 0.013 0 -10000 0 -10000 0 0
FOXO3 0 0 -10000 0 -10000 0 0
FOXO1 0.012 0.016 -10000 0 -0.4 1 1
FOXO4 0.019 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.013 0 -10000 0 -10000 0 0
TAT -0.14 0.19 -10000 0 -0.4 231 231
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.003 0.058 -10000 0 -10000 0 0
PPARGC1A -0.045 0.14 -10000 0 -0.4 88 88
FHL2 0.013 0 -10000 0 -10000 0 0
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.016 0.005 -10000 0 -10000 0 0
HIST2H4A 0.008 0.07 -10000 0 -0.57 9 9
SIRT1/FOXO3a 0 0.005 -10000 0 -10000 0 0
SIRT1 0.008 0.007 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.023 0.004 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.004 0.058 -10000 0 -10000 0 0
apoptosis -0.023 0.004 -10000 0 -10000 0 0
SIRT1/PGC1A -0.02 0.083 -10000 0 -0.22 87 87
p53/SIRT1 0.001 0.014 0.36 1 -10000 0 1
SIRT1/FOXO4 0.02 0.005 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 0.021 0.01 -10000 0 -10000 0 0
HIST1H1E 0 0.068 -10000 0 -0.25 42 42
SIRT1/p300 0.016 0.005 -10000 0 -10000 0 0
muscle cell differentiation -0.005 0.049 -10000 0 -10000 0 0
TP53 0.008 0.007 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.023 0.004 -10000 0 -10000 0 0
CREBBP 0.013 0 -10000 0 -10000 0 0
MEF2D 0.013 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.093 0.14 -10000 0 -0.27 230 230
ACSS2 0.016 0.012 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.005 0.049 -10000 0 -10000 0 0
S1P1 pathway

Figure S58.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S58.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.017 0.035 -9999 0 -0.47 3 3
PDGFRB 0.003 0.081 -9999 0 -0.75 7 7
SPHK1 -0.025 0.062 -9999 0 -0.28 20 20
mol:S1P -0.025 0.06 -9999 0 -0.28 20 20
S1P1/S1P/Gi -0.077 0.16 -9999 0 -0.44 50 50
GNAO1 -0.14 0.2 -9999 0 -0.4 234 234
PDGFB-D/PDGFRB/PLCgamma1 -0.059 0.15 -9999 0 -0.5 23 23
PLCG1 -0.066 0.15 -9999 0 -0.45 37 37
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.003 0.08 -9999 0 -0.75 7 7
GNAI2 0.013 0.003 -9999 0 -10000 0 0
GNAI3 0.012 0.003 -9999 0 -10000 0 0
GNAI1 -0.003 0.076 -9999 0 -0.4 22 22
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.015 0.031 -9999 0 -0.49 2 2
S1P1/S1P 0.007 0.071 -9999 0 -0.31 12 12
negative regulation of cAMP metabolic process -0.075 0.16 -9999 0 -0.43 50 50
MAPK3 -0.073 0.18 -9999 0 -0.6 29 29
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 0.012 0.016 -9999 0 -0.39 1 1
PLCB2 0.011 0.066 -9999 0 -0.3 4 4
RAC1 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.011 0.056 -9999 0 -0.29 4 4
receptor internalization -0.012 0.062 -9999 0 -0.29 12 12
PTGS2 -0.075 0.21 -9999 0 -0.74 36 36
Rac1/GTP -0.011 0.056 -9999 0 -0.29 4 4
RHOA 0.013 0 -9999 0 -10000 0 0
VEGFA 0.011 0.043 -9999 0 -0.75 2 2
negative regulation of T cell proliferation -0.075 0.16 -9999 0 -0.43 50 50
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.007 0.046 -9999 0 -0.4 8 8
MAPK1 -0.073 0.18 -9999 0 -0.6 28 28
S1P1/S1P/PDGFB-D/PDGFRB 0.009 0.089 -9999 0 -0.4 13 13
ABCC1 0.012 0.002 -9999 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.021 0.2 -9999 0 -0.72 37 37
MKNK1 0.013 0 -9999 0 -10000 0 0
MAPK14 -0.003 0.09 -9999 0 -0.41 4 4
ATF2/c-Jun 0.013 0.072 -9999 0 -0.38 1 1
MAPK11 -0.005 0.1 -9999 0 -0.55 6 6
MITF -0.006 0.12 -9999 0 -0.37 44 44
MAPKAPK5 0.003 0.11 -9999 0 -0.33 42 42
KRT8 0.003 0.11 -9999 0 -0.33 42 42
MAPKAPK3 0.013 0 -9999 0 -10000 0 0
MAPKAPK2 0.013 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.007 0.14 -9999 0 -0.42 43 43
CEBPB -0.001 0.11 -9999 0 -0.51 6 6
SLC9A1 0.002 0.11 -9999 0 -0.34 42 42
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 0.007 0.11 -9999 0 -0.49 5 5
p38alpha-beta/MNK1 0.007 0.11 -9999 0 -0.55 6 6
JUN 0.013 0.071 -9999 0 -0.37 1 1
PPARGC1A -0.038 0.16 -9999 0 -0.42 47 47
USF1 0.003 0.11 -9999 0 -0.5 5 5
RAB5/GDP/GDI1 0.004 0.078 -9999 0 -0.38 5 5
NOS2 -0.032 0.24 -9999 0 -0.83 44 44
DDIT3 0.003 0.11 -9999 0 -0.5 5 5
RAB5A 0.011 0.023 -9999 0 -0.4 2 2
HSPB1 0.008 0.091 -9999 0 -0.43 6 6
p38alpha-beta/HBP1 0.007 0.11 -9999 0 -0.55 6 6
CREB1 0.005 0.11 -9999 0 -0.36 42 42
RAB5/GDP 0.008 0.016 -9999 0 -0.28 2 2
EIF4E 0.007 0.096 -9999 0 -0.51 5 5
RPS6KA4 0.003 0.11 -9999 0 -0.33 42 42
PLA2G4A -0.022 0.12 -9999 0 -0.48 17 17
GDI1 0.003 0.11 -9999 0 -0.5 5 5
TP53 -0.002 0.13 -9999 0 -0.41 43 43
RPS6KA5 0.002 0.11 -9999 0 -0.34 42 42
ESR1 -0.025 0.15 -9999 0 -0.42 44 44
HBP1 0.013 0 -9999 0 -10000 0 0
MEF2C -0.007 0.12 -9999 0 -0.57 9 9
MEF2A 0.003 0.11 -9999 0 -0.5 5 5
EIF4EBP1 0.004 0.12 -9999 0 -0.36 42 42
KRT19 0.002 0.11 -9999 0 -0.33 42 42
ELK4 0.003 0.11 -9999 0 -0.5 5 5
ATF6 0.003 0.11 -9999 0 -0.5 5 5
ATF1 0.005 0.11 -9999 0 -0.36 42 42
p38alpha-beta/MAPKAPK2 0.007 0.11 -9999 0 -0.55 6 6
p38alpha-beta/MAPKAPK3 0.007 0.11 -9999 0 -0.55 6 6
Glypican 2 network

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
MDK 0.005 0.075 -9999 0 -0.75 6 6
GPC2 -0.011 0.13 -9999 0 -0.75 19 19
GPC2/Midkine -0.005 0.12 -9999 0 -0.57 25 25
neuron projection morphogenesis -0.005 0.12 -9999 0 -0.57 25 25
IL27-mediated signaling events

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
TGFB1 -0.048 0.11 -10000 0 -0.75 1 1
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0 0.1 0.48 5 -10000 0 5
IL27/IL27R/JAK1 0.022 0.13 -10000 0 -0.65 2 2
TBX21 0.019 0.16 -10000 0 -0.53 18 18
IL12B 0.003 0.062 -10000 0 -0.76 4 4
IL12A 0.004 0.038 -10000 0 -0.31 8 8
IL6ST 0.002 0.068 -10000 0 -0.4 17 17
IL27RA/JAK1 0.023 0.023 -10000 0 -10000 0 0
IL27 -0.019 0.15 -10000 0 -0.75 24 24
TYK2 0.013 0.005 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.17 0.27 -10000 0 -0.58 173 173
T-helper 2 cell differentiation 0 0.1 0.48 5 -10000 0 5
T cell proliferation during immune response 0 0.1 0.48 5 -10000 0 5
MAPKKK cascade 0 0.1 -10000 0 -0.48 5 5
STAT3 0.013 0 -10000 0 -10000 0 0
STAT2 0.013 0 -10000 0 -10000 0 0
STAT1 0.012 0.031 -10000 0 -0.76 1 1
IL12RB1 -0.003 0.079 -10000 0 -0.41 22 22
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.023 0.15 -10000 0 -0.58 13 13
IL27/IL27R/JAK2/TYK2 0.001 0.1 -10000 0 -0.48 5 5
positive regulation of T cell mediated cytotoxicity 0 0.1 -10000 0 -0.48 5 5
STAT1 (dimer) 0.012 0.18 -10000 0 -0.68 6 6
JAK2 0.012 0.029 -10000 0 -0.4 3 3
JAK1 0.013 0.016 -10000 0 -0.39 1 1
STAT2 (dimer) 0.006 0.098 -10000 0 -0.51 3 3
T cell proliferation -0.076 0.19 -10000 0 -0.6 38 38
IL12/IL12R/TYK2/JAK2 0.006 0.085 -10000 0 -10000 0 0
IL17A -0.18 0.27 -10000 0 -0.58 173 173
mast cell activation 0 0.1 0.48 5 -10000 0 5
IFNG -0.002 0.034 -10000 0 -0.09 64 64
T cell differentiation -0.002 0.005 -10000 0 -0.019 12 12
STAT3 (dimer) 0.006 0.098 -10000 0 -0.51 3 3
STAT5A (dimer) 0.006 0.098 -10000 0 -0.51 3 3
STAT4 (dimer) -0.003 0.11 -10000 0 -0.43 11 11
STAT4 -0.006 0.084 -10000 0 -0.4 28 28
T cell activation -0.007 0.003 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.022 0.055 -10000 0 -10000 0 0
GATA3 0.003 0.1 -10000 0 -1.1 5 5
IL18 0.007 0.023 -10000 0 -0.28 4 4
positive regulation of mast cell cytokine production 0.006 0.096 -10000 0 -0.5 3 3
IL27/EBI3 -0.023 0.13 -10000 0 -0.39 63 63
IL27RA 0.014 0.02 -10000 0 -10000 0 0
IL6 -0.15 0.28 -10000 0 -0.78 86 86
STAT5A 0.013 0 -10000 0 -10000 0 0
monocyte differentiation 0 0.002 -10000 0 -10000 0 0
IL2 -0.004 0.013 -10000 0 -10000 0 0
IL1B -0.043 0.17 -10000 0 -0.56 58 58
EBI3 -0.014 0.1 -10000 0 -0.4 42 42
TNF 0.007 0.025 -10000 0 -0.28 5 5
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.013 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.025 0.093 -10000 0 -0.32 26 26
NT3 (dimer)/TRKC -0.047 0.12 -10000 0 -0.28 135 135
NT3 (dimer)/TRKB -0.11 0.17 -10000 0 -0.45 81 81
SHC/Grb2/SOS1/GAB1/PI3K 0.032 0.009 -10000 0 -10000 0 0
RAPGEF1 0.012 0.016 -10000 0 -0.4 1 1
BDNF 0 0.096 -10000 0 -0.75 10 10
PIK3CA 0.012 0.016 -10000 0 -0.4 1 1
DYNLT1 0.013 0 -10000 0 -10000 0 0
NTRK1 0.001 0.087 -10000 0 -0.71 9 9
NTRK2 -0.11 0.2 -10000 0 -0.41 182 182
NTRK3 -0.075 0.16 -10000 0 -0.4 131 131
NT-4/5 (dimer)/TRKB -0.13 0.19 -10000 0 -0.47 100 100
neuron apoptosis 0.11 0.17 0.4 115 -10000 0 115
SHC 2-3/Grb2 -0.12 0.18 -10000 0 -0.43 115 115
SHC1 0.013 0 -10000 0 -10000 0 0
SHC2 -0.093 0.16 -10000 0 -0.41 88 88
SHC3 -0.12 0.18 -10000 0 -0.45 110 110
STAT3 (dimer) 0.017 0.028 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.046 0.12 -10000 0 -0.48 11 11
RIN/GDP -0.004 0.065 -10000 0 -0.3 1 1
GIPC1 0.012 0.016 -10000 0 -0.4 1 1
KRAS 0.012 0.016 -10000 0 -0.4 1 1
DNAJA3 -0.054 0.12 -10000 0 -0.42 10 10
RIN/GTP 0 0.023 -10000 0 -0.58 1 1
CCND1 0.021 0.059 -10000 0 -0.63 5 5
MAGED1 0.013 0 -10000 0 -10000 0 0
PTPN11 0.013 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.023 0.14 -10000 0 -0.75 23 23
SHC/GRB2/SOS1 0.026 0 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.021 0.11 -10000 0 -0.54 11 11
TRKA/NEDD4-2 0.009 0.068 -10000 0 -0.51 10 10
ELMO1 0.011 0.028 -10000 0 -0.4 3 3
RhoG/GTP/ELMO1/DOCK1 0.016 0.019 -10000 0 -10000 0 0
NGF -0.003 0.082 -10000 0 -0.43 21 21
HRAS 0.012 0.016 -10000 0 -0.4 1 1
DOCK1 0.012 0.016 -10000 0 -0.4 1 1
GAB2 0.013 0 -10000 0 -10000 0 0
RIT2 0 0.03 -10000 0 -0.75 1 1
RIT1 0.013 0 -10000 0 -10000 0 0
FRS2 0.013 0.001 -10000 0 -10000 0 0
DNM1 0.004 0.081 -10000 0 -0.75 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.013 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.053 0.12 -10000 0 -0.41 10 10
mol:GDP -0.007 0.088 -10000 0 -0.31 1 1
NGF (dimer) -0.003 0.082 -10000 0 -0.43 21 21
RhoG/GDP 0.008 0.02 -10000 0 -0.28 3 3
RIT1/GDP 0.001 0.065 -10000 0 -10000 0 0
TIAM1 -0.028 0.12 -10000 0 -0.4 62 62
PIK3R1 0.013 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.058 0.14 -10000 0 -0.52 19 19
KIDINS220/CRKL/C3G 0.018 0.011 -10000 0 -0.27 1 1
SHC/RasGAP 0.019 0 -10000 0 -10000 0 0
FRS2 family/SHP2 0.025 0.021 -10000 0 -0.5 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) 0.007 0.05 -10000 0 -0.44 7 7
RAP1/GDP -0.022 0.038 -10000 0 -10000 0 0
KIDINS220/CRKL 0.013 0 -10000 0 -10000 0 0
BDNF (dimer) 0 0.096 -10000 0 -0.75 10 10
ubiquitin-dependent protein catabolic process 0.008 0.081 -10000 0 -0.54 9 9
Schwann cell development -0.026 0.028 -10000 0 -10000 0 0
EHD4 0.013 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.032 0.019 -10000 0 -0.45 1 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.034 0.013 -10000 0 -10000 0 0
RAP1B 0.013 0 -10000 0 -10000 0 0
RAP1A 0.013 0 -10000 0 -10000 0 0
CDC42/GTP -0.087 0.12 -10000 0 -0.45 21 21
ABL1 0.013 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.019 0 -10000 0 -10000 0 0
Rap1/GTP 0.005 0.061 -10000 0 -10000 0 0
STAT3 0.017 0.028 -10000 0 -10000 0 0
axon guidance -0.084 0.11 -10000 0 -0.42 22 22
MAPK3 -0.015 0.1 -10000 0 -0.49 11 11
MAPK1 -0.015 0.1 -10000 0 -0.49 11 11
CDC42/GDP 0.001 0.065 -10000 0 -0.28 1 1
NTF3 0.007 0.05 -10000 0 -0.45 7 7
NTF4 -0.023 0.14 -10000 0 -0.75 23 23
NGF (dimer)/TRKA/FAIM 0.007 0.083 -10000 0 -0.54 10 10
PI3K 0.018 0.011 -10000 0 -10000 0 0
FRS3 0.011 0.031 -10000 0 -0.75 1 1
FAIM 0.011 0.031 -10000 0 -0.75 1 1
GAB1 0.013 0 -10000 0 -10000 0 0
RASGRF1 -0.08 0.16 -10000 0 -0.45 49 49
SOS1 0.013 0 -10000 0 -10000 0 0
MCF2L -0.032 0.1 -10000 0 -0.44 4 4
RGS19 0.012 0.016 -10000 0 -0.4 1 1
CDC42 0.011 0.023 -10000 0 -0.4 2 2
RAS family/GTP 0.01 0.066 -10000 0 -0.39 2 2
Rac1/GDP 0.001 0.065 -10000 0 -10000 0 0
NGF (dimer)/TRKA/GRIT 0 0.08 -10000 0 -0.55 9 9
neuron projection morphogenesis -0.045 0.13 -10000 0 -0.43 9 9
NGF (dimer)/TRKA/NEDD4-2 0.008 0.081 -10000 0 -0.54 9 9
MAP2K1 0.032 0 -10000 0 -10000 0 0
NGFR -0.089 0.18 -10000 0 -0.4 156 156
NGF (dimer)/TRKA/GIPC/GAIP 0.016 0.059 -10000 0 -0.47 1 1
RAS family/GTP/PI3K 0.025 0.025 -10000 0 -0.49 1 1
FRS2 family/SHP2/GRB2/SOS1 0.037 0.018 -10000 0 -0.42 1 1
NRAS 0.011 0.023 -10000 0 -0.4 2 2
GRB2/SOS1 0.019 0 -10000 0 -10000 0 0
PRKCI 0.011 0.023 -10000 0 -0.4 2 2
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
MAPKKK cascade -0.039 0.12 -10000 0 -0.58 21 21
RASA1 0.013 0.001 -10000 0 -10000 0 0
TRKA/c-Abl 0.01 0.067 -10000 0 -0.57 8 8
SQSTM1 0.013 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.044 0.13 -10000 0 -0.48 19 19
NGF (dimer)/TRKA/p62/Atypical PKCs 0.022 0.074 -10000 0 -0.48 9 9
MATK -0.037 0.13 -10000 0 -0.4 76 76
NEDD4L 0.012 0.016 -10000 0 -0.4 1 1
RAS family/GDP -0.019 0.035 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.075 0.12 -10000 0 -0.27 157 157
Rac1/GTP -0.072 0.098 -10000 0 -0.32 38 38
FRS2 family/SHP2/CRK family 0.037 0.018 -10000 0 -0.42 1 1
Arf6 signaling events

Figure S63.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S63.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.016 0.021 -9999 0 -0.44 1 1
ARNO/beta Arrestin1-2 -0.005 0.065 -9999 0 -10000 0 0
EGFR 0.011 0.023 -9999 0 -0.4 2 2
EPHA2 0.01 0.043 -9999 0 -0.75 2 2
USP6 0.011 0.035 -9999 0 -0.57 2 2
IQSEC1 0.012 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.053 0.14 -9999 0 -0.57 20 20
ARRB2 0.008 0.002 -9999 0 -10000 0 0
mol:GTP 0.012 0.024 -9999 0 -0.35 1 1
ARRB1 0.012 0.016 -9999 0 -0.4 1 1
FBXO8 0.011 0.023 -9999 0 -0.4 2 2
TSHR 0.006 0.043 -9999 0 -0.75 2 2
EGF -0.086 0.2 -9999 0 -0.45 131 131
somatostatin receptor activity 0 0 -9999 0 -0.001 24 24
ARAP2 0.011 0.023 -9999 0 -0.4 2 2
mol:GDP -0.045 0.087 -9999 0 -0.24 53 53
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 5 5
ITGA2B -0.019 0.15 -9999 0 -0.75 25 25
ARF6 0.012 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.031 0.028 -9999 0 -0.45 2 2
ADAP1 0.012 0.016 -9999 0 -0.4 1 1
KIF13B 0.011 0.023 -9999 0 -0.4 2 2
HGF/MET 0.006 0.077 -9999 0 -0.38 20 20
PXN 0.013 0 -9999 0 -10000 0 0
ARF6/GTP -0.036 0.085 -9999 0 -0.25 24 24
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.036 0.12 -9999 0 -0.49 20 20
ADRB2 -0.052 0.15 -9999 0 -0.4 98 98
receptor agonist activity 0 0 -9999 0 0 27 27
actin filament binding 0 0 -9999 0 0 24 24
SRC 0.013 0 -9999 0 -10000 0 0
ITGB3 0.008 0.043 -9999 0 -0.4 7 7
GNAQ 0.01 0.028 -9999 0 -0.4 3 3
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 9 9
ARF6/GDP 0.01 0.072 -9999 0 -0.32 14 14
ARF6/GDP/GULP/ACAP1 -0.039 0.1 -9999 0 -0.4 12 12
alphaIIb/beta3 Integrin/paxillin/GIT1 0.01 0.096 -9999 0 -0.45 25 25
ACAP1 -0.003 0.077 -9999 0 -0.4 23 23
ACAP2 0.012 0.016 -9999 0 -0.4 1 1
LHCGR/beta Arrestin2 0.001 0.004 -9999 0 -10000 0 0
EFNA1 0.013 0 -9999 0 -10000 0 0
HGF 0.002 0.068 -9999 0 -0.42 15 15
CYTH3 0.009 0 -9999 0 -10000 0 0
CYTH2 0.009 0.002 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 6 6
endosomal lumen acidification 0 0 -9999 0 -0.001 5 5
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.009 0.091 -9999 0 -0.4 33 33
GNAQ/ARNO 0.015 0.014 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 3 3
MET 0.005 0.075 -9999 0 -0.75 6 6
GNA14 0.009 0.036 -9999 0 -0.4 5 5
GNA15 0.005 0.075 -9999 0 -0.75 6 6
GIT1 0.012 0.016 -9999 0 -0.4 1 1
mol:PI-4-5-P2 0 0 -9999 0 -0.001 20 20
GNA11 0.01 0.033 -9999 0 -0.4 4 4
LHCGR 0.001 0.004 -9999 0 -10000 0 0
AGTR1 -0.13 0.19 -9999 0 -0.4 220 220
desensitization of G-protein coupled receptor protein signaling pathway 0.001 0.004 -9999 0 -10000 0 0
IPCEF1/ARNO -0.025 0.095 -9999 0 -0.38 20 20
alphaIIb/beta3 Integrin -0.009 0.12 -9999 0 -0.5 32 32
Signaling events mediated by PTP1B

Figure S64.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S64.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.004 0.081 -10000 0 -0.75 7 7
Jak2/Leptin Receptor -0.029 0.075 -10000 0 -0.38 9 9
PTP1B/AKT1 -0.04 0.075 -10000 0 -10000 0 0
FYN 0.013 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.052 0.084 -10000 0 -0.3 2 2
EGFR 0.008 0.024 -10000 0 -0.41 2 2
EGF/EGFR -0.083 0.13 -10000 0 -0.35 86 86
CSF1 0.011 0.028 -10000 0 -0.4 3 3
AKT1 0.013 0.001 -10000 0 -10000 0 0
INSR 0.013 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.056 0.091 -10000 0 -0.43 6 6
Insulin Receptor/Insulin -0.039 0.044 -10000 0 -10000 0 0
HCK 0.003 0.062 -10000 0 -0.4 15 15
CRK 0.013 0 -10000 0 -10000 0 0
TYK2 -0.044 0.08 -10000 0 -0.28 2 2
EGF -0.088 0.2 -10000 0 -0.46 131 131
YES1 0.012 0.016 -10000 0 -0.4 1 1
CAV1 -0.052 0.093 -10000 0 -0.33 3 3
TXN 0.011 0.003 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.036 0.078 -10000 0 -10000 0 0
cell migration 0.052 0.084 0.3 2 -10000 0 2
STAT3 0.012 0.001 -10000 0 -10000 0 0
PRLR 0.001 0.065 -10000 0 -0.4 16 16
ITGA2B -0.02 0.15 -10000 0 -0.75 25 25
CSF1R -0.011 0.095 -10000 0 -0.4 36 36
Prolactin Receptor/Prolactin -0.007 0.093 -10000 0 -0.58 12 12
FGR 0.009 0.045 -10000 0 -0.47 5 5
PTP1B/p130 Cas -0.044 0.081 -10000 0 -0.29 2 2
Crk/p130 Cas -0.036 0.079 -10000 0 -10000 0 0
DOK1 -0.033 0.077 -10000 0 -0.37 3 3
JAK2 -0.032 0.077 -10000 0 -0.38 13 13
Jak2/Leptin Receptor/Leptin -0.056 0.082 -10000 0 -0.46 9 9
PIK3R1 0.013 0 -10000 0 -10000 0 0
PTPN1 -0.053 0.084 -10000 0 -0.3 2 2
LYN 0.013 0 -10000 0 -10000 0 0
CDH2 -0.012 0.1 -10000 0 -0.43 34 34
SRC -0.007 0.035 -10000 0 -10000 0 0
ITGB3 0.007 0.043 -10000 0 -0.4 7 7
CAT1/PTP1B -0.083 0.11 -10000 0 -0.36 25 25
CAPN1 0.012 0.002 -10000 0 -10000 0 0
CSK 0.013 0 -10000 0 -10000 0 0
PI3K -0.03 0.038 -10000 0 -10000 0 0
mol:H2O2 0.001 0.005 -10000 0 -10000 0 0
STAT3 (dimer) -0.05 0.075 -10000 0 -0.45 7 7
negative regulation of transcription -0.032 0.076 -10000 0 -0.37 13 13
FCGR2A 0.007 0.063 -10000 0 -0.68 5 5
FER 0.008 0.038 -10000 0 -0.52 3 3
alphaIIb/beta3 Integrin -0.01 0.12 -10000 0 -0.5 32 32
BLK -0.14 0.2 -10000 0 -0.4 236 236
Insulin Receptor/Insulin/Shc 0.017 0.001 -10000 0 -10000 0 0
RHOA 0.012 0.002 -10000 0 -10000 0 0
LEPR 0.007 0.048 -10000 0 -0.39 9 9
BCAR1 0.012 0.016 -10000 0 -0.4 1 1
p210 bcr-abl/Grb2 0.013 0 -10000 0 -10000 0 0
mol:NADPH -0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.077 0.13 -10000 0 -0.4 37 37
PRL -0.01 0.1 -10000 0 -0.75 12 12
SOCS3 0.013 0.034 -10000 0 -0.56 2 2
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 -0.047 0.086 -10000 0 -0.37 5 5
Ras protein signal transduction 0.028 0.026 -10000 0 -10000 0 0
IRS1 0.013 0 -10000 0 -10000 0 0
INS 0 0.001 -10000 0 -10000 0 0
LEP -0.034 0.14 -10000 0 -0.45 55 55
STAT5B -0.041 0.076 -10000 0 -0.27 8 8
STAT5A -0.041 0.076 -10000 0 -0.27 8 8
GRB2 0.013 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.048 0.097 -10000 0 -0.53 8 8
CSN2 0.009 0.052 -10000 0 -0.53 3 3
PIK3CA 0.012 0.016 -10000 0 -0.4 1 1
LAT -0.011 0.054 -10000 0 -0.38 6 6
YBX1 0.019 0.002 -10000 0 -10000 0 0
LCK 0.001 0.089 -10000 0 -0.68 10 10
SHC1 0.013 0 -10000 0 -10000 0 0
NOX4 -0.34 0.38 -10000 0 -0.75 284 284
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.012 0.17 -9999 0 -0.65 6 6
CRP -0.021 0.18 -9999 0 -0.73 14 14
cell cycle arrest -0.025 0.18 -9999 0 -0.67 16 16
TIMP1 -0.024 0.2 -9999 0 -0.62 29 29
IL6ST 0.004 0.067 -9999 0 -0.39 17 17
Rac1/GDP -0.038 0.14 -9999 0 -0.44 20 20
AP1 0.023 0.065 -9999 0 -10000 0 0
GAB2 0.013 0.002 -9999 0 -10000 0 0
TNFSF11 -0.026 0.2 -9999 0 -0.75 16 16
HSP90B1 0.018 0.052 -9999 0 -0.51 1 1
GAB1 0.013 0.001 -9999 0 -10000 0 0
MAPK14 -0.032 0.12 -9999 0 -0.5 8 8
AKT1 0.045 0.015 -9999 0 -10000 0 0
FOXO1 0.049 0.016 -9999 0 -10000 0 0
MAP2K6 -0.041 0.13 -9999 0 -0.41 26 26
mol:GTP 0 0.002 -9999 0 -10000 0 0
MAP2K4 -0.027 0.15 -9999 0 -0.46 17 17
MITF -0.046 0.14 -9999 0 -0.39 43 43
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0.013 0 -9999 0 -10000 0 0
A2M 0.012 0.09 -9999 0 -1.3 3 3
CEBPB 0.009 0.082 -9999 0 -0.76 7 7
GRB2/SOS1/GAB family/SHP2 0.002 0.061 -9999 0 -10000 0 0
STAT3 -0.028 0.19 -9999 0 -0.7 16 16
STAT1 -0.004 0.016 -9999 0 -0.24 1 1
CEBPD -0.013 0.17 -9999 0 -0.7 7 7
PIK3CA 0.013 0.016 -9999 0 -0.39 1 1
PI3K 0.021 0.012 -9999 0 -10000 0 0
JUN 0.012 0.001 -9999 0 -10000 0 0
PIAS3/MITF -0.038 0.14 -9999 0 -0.43 22 22
MAPK11 -0.034 0.13 -9999 0 -0.5 10 10
STAT3 (dimer)/FOXO1 0.011 0.16 -9999 0 -0.54 5 5
GRB2/SOS1/GAB family -0.059 0.1 -9999 0 -0.44 15 15
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.053 0.15 -9999 0 -0.42 40 40
GRB2 0.013 0.001 -9999 0 -10000 0 0
JAK2 0.011 0.028 -9999 0 -0.4 3 3
LBP -0.071 0.25 -9999 0 -0.63 55 55
PIK3R1 0.014 0 -9999 0 -10000 0 0
JAK1 0.014 0.017 -9999 0 -0.39 1 1
MYC -0.017 0.18 -9999 0 -0.66 11 11
FGG -0.045 0.22 -9999 0 -0.72 24 24
macrophage differentiation -0.025 0.18 -9999 0 -0.67 16 16
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.065 0.18 -9999 0 -0.44 86 86
JUNB -0.013 0.17 -9999 0 -0.71 8 8
FOS 0.006 0.051 -9999 0 -0.4 10 10
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.049 0.14 -9999 0 -0.4 43 43
STAT1/PIAS1 -0.031 0.13 -9999 0 -0.39 28 28
GRB2/SOS1/GAB family/SHP2/PI3K 0.037 0.015 -9999 0 -10000 0 0
STAT3 (dimer) -0.026 0.19 -9999 0 -0.7 16 16
PRKCD -0.017 0.16 -9999 0 -0.54 9 9
IL6R -0.071 0.16 -9999 0 -0.39 131 131
SOCS3 -0.029 0.12 -9999 0 -0.64 4 4
gp130 (dimer)/JAK1/JAK1/LMO4 0.026 0.046 -9999 0 -10000 0 0
Rac1/GTP -0.036 0.14 -9999 0 -0.45 20 20
HCK 0.002 0.062 -9999 0 -0.4 15 15
MAPKKK cascade 0.018 0.048 -9999 0 -10000 0 0
bone resorption -0.024 0.19 -9999 0 -0.71 16 16
IRF1 -0.012 0.17 -9999 0 -0.63 8 8
mol:GDP -0.046 0.14 -9999 0 -0.41 34 34
SOS1 0.013 0.002 -9999 0 -10000 0 0
VAV1 -0.047 0.15 -9999 0 -0.41 35 35
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.068 0.17 -9999 0 -0.52 27 27
PTPN11 -0.003 0.013 -9999 0 -10000 0 0
IL6/IL6RA -0.11 0.22 -9999 0 -0.59 83 83
gp130 (dimer)/TYK2/TYK2/LMO4 0.022 0.042 -9999 0 -10000 0 0
gp130 (dimer)/JAK2/JAK2/LMO4 0.021 0.047 -9999 0 -0.44 1 1
IL6 -0.085 0.26 -9999 0 -0.72 86 86
PIAS3 0.013 0 -9999 0 -10000 0 0
PTPRE 0.008 0.01 -9999 0 -10000 0 0
PIAS1 0.013 0 -9999 0 -10000 0 0
RAC1 0.013 0.001 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.057 0.13 -9999 0 -0.37 39 39
LMO4 0.015 0.018 -9999 0 -0.4 1 1
STAT3 (dimer)/PIAS3 -0.024 0.18 -9999 0 -0.67 14 14
MCL1 0.05 0.014 -9999 0 -10000 0 0
S1P3 pathway

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
PDGFRB 0.004 0.081 -9999 0 -0.75 7 7
mol:S1P 0.001 0.002 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.055 0.11 -9999 0 -0.34 32 32
GNAO1 -0.14 0.2 -9999 0 -0.4 234 234
S1P/S1P3/G12/G13 0.025 0.019 -9999 0 -0.45 1 1
AKT1 -0.011 0.056 -9999 0 -10000 0 0
AKT3 -0.025 0.16 -9999 0 -1.2 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.004 0.08 -9999 0 -0.75 7 7
GNAI2 0.014 0.003 -9999 0 -10000 0 0
GNAI3 0.014 0.002 -9999 0 -10000 0 0
GNAI1 -0.001 0.075 -9999 0 -0.4 22 22
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.012 0.031 -9999 0 -0.75 1 1
S1PR2 0.013 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.054 0.13 -9999 0 -0.38 32 32
MAPK3 -0.046 0.12 -9999 0 -0.36 33 33
MAPK1 -0.046 0.12 -9999 0 -0.36 32 32
JAK2 -0.046 0.12 -9999 0 -0.37 32 32
CXCR4 -0.046 0.12 -9999 0 -0.36 32 32
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 -0.046 0.12 -9999 0 -0.36 32 32
S1P/S1P3/Gi -0.055 0.13 -9999 0 -0.38 32 32
RAC1 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.044 0.12 -9999 0 -0.34 32 32
VEGFA 0.012 0.043 -9999 0 -0.75 2 2
S1P/S1P2/Gi -0.056 0.12 -9999 0 -0.35 32 32
VEGFR1 homodimer/VEGFA homodimer 0.023 0.034 -9999 0 -0.57 2 2
RHOA 0.013 0 -9999 0 -10000 0 0
S1P/S1P3/Gq 0.02 0.045 -9999 0 -0.44 2 2
GNAQ 0.011 0.028 -9999 0 -0.4 3 3
GNAZ 0.008 0.046 -9999 0 -0.39 8 8
G12/G13 0.019 0 -9999 0 -10000 0 0
GNA14 0.009 0.036 -9999 0 -0.4 5 5
GNA15 0.005 0.075 -9999 0 -0.75 6 6
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
GNA11 0.01 0.033 -9999 0 -0.4 4 4
Rac1/GTP -0.044 0.12 -9999 0 -0.34 32 32
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.016 0.017 -10000 0 -10000 0 0
HSPA8 0.012 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.007 0.11 -10000 0 -0.38 13 13
AKT1 -0.013 0.038 -10000 0 -10000 0 0
GSC -0.05 0.18 -10000 0 -0.55 67 67
NKX2-5 -0.025 0.14 -10000 0 -0.75 22 22
muscle cell differentiation 0.033 0.072 0.44 3 -10000 0 3
SMAD2-3/SMAD4/SP1 -0.018 0.094 -10000 0 -0.39 1 1
SMAD4 -0.005 0.048 -10000 0 -0.47 2 2
CBFB 0.013 0 -10000 0 -10000 0 0
SAP18 0.012 0.002 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.083 0.22 -10000 0 -0.49 139 139
SMAD3/SMAD4/VDR 0.041 0.04 -10000 0 -10000 0 0
MYC 0.024 0.11 -10000 0 -0.72 11 11
CDKN2B -0.42 0.62 -10000 0 -1.3 219 219
AP1 0.031 0.052 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.032 0.036 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.097 0.18 -10000 0 -0.5 42 42
SP3 0.015 0 -10000 0 -10000 0 0
CREB1 0.013 0 -10000 0 -10000 0 0
FOXH1 -0.009 0.093 -10000 0 -0.49 19 19
SMAD3/SMAD4/GR -0.001 0.097 -10000 0 -0.39 10 10
GATA3 0.004 0.055 -10000 0 -0.48 5 5
SKI/SIN3/HDAC complex/NCoR1 0.037 0.013 -10000 0 -10000 0 0
MEF2C/TIF2 -0.021 0.13 -10000 0 -0.55 9 9
endothelial cell migration 0.092 0.24 0.54 139 -10000 0 139
MAX 0.019 0.016 -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 0.013 0 -10000 0 -10000 0 0
RUNX3 0.012 0.016 -10000 0 -0.4 1 1
RUNX1 0.013 0 -10000 0 -10000 0 0
CTBP1 0.013 0 -10000 0 -10000 0 0
NR3C1 -0.011 0.11 -10000 0 -0.4 46 46
VDR 0.013 0 -10000 0 -10000 0 0
CDKN1A 0.023 0.083 -10000 0 -1.2 1 1
KAT2B -0.004 0.081 -10000 0 -0.38 27 27
SMAD2/SMAD2/SMAD4/FOXH1 -0.022 0.089 -10000 0 -0.48 6 6
DCP1A 0.013 0 -10000 0 -10000 0 0
SKI 0.012 0.002 -10000 0 -10000 0 0
SERPINE1 -0.092 0.24 -10000 0 -0.54 139 139
SMAD3/SMAD4/ATF2 0.012 0.051 -10000 0 -0.36 2 2
SMAD3/SMAD4/ATF3 0.01 0.058 -10000 0 -0.44 4 4
SAP30 0.012 0.002 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.039 0.039 -10000 0 -10000 0 0
JUN 0.028 0.051 -10000 0 -10000 0 0
SMAD3/SMAD4/IRF7 0.012 0.051 -10000 0 -0.36 2 2
TFE3 0.009 0.017 -10000 0 -10000 0 0
COL1A2 -0.026 0.15 -10000 0 -0.6 40 40
mesenchymal cell differentiation -0.012 0.049 0.36 2 -10000 0 2
DLX1 -0.013 0.13 -10000 0 -0.71 19 19
TCF3 0.013 0 -10000 0 -10000 0 0
FOS 0.009 0.053 -10000 0 -0.4 10 10
SMAD3/SMAD4/Max 0.017 0.056 -10000 0 -0.36 2 2
Cbp/p300/SNIP1 0.027 0.015 -10000 0 -10000 0 0
ZBTB17 0.031 0.033 -10000 0 -0.4 1 1
LAMC1 0.017 0.043 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.007 0.072 -10000 0 -0.48 8 8
IRF7 0.012 0.016 -10000 0 -0.4 1 1
ESR1 -0.026 0.12 -10000 0 -0.4 59 59
HNF4A 0.012 0.016 -10000 0 -0.4 1 1
MEF2C -0.029 0.13 -10000 0 -0.52 15 15
SMAD2-3/SMAD4 -0.015 0.077 -10000 0 -0.4 3 3
Cbp/p300/Src-1 0.032 0.025 -10000 0 -10000 0 0
IGHV3OR16-13 0.002 0.008 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.005 0.074 -10000 0 -0.75 6 6
CREBBP 0.015 0.012 -10000 0 -10000 0 0
SKIL 0.012 0.016 -10000 0 -0.4 1 1
HDAC1 0.012 0.002 -10000 0 -10000 0 0
HDAC2 0.012 0.002 -10000 0 -10000 0 0
SNIP1 0.012 0.004 -10000 0 -10000 0 0
GCN5L2 0.003 0.014 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.015 0.053 -10000 0 -0.35 2 2
MSG1/HSC70 -0.12 0.24 -10000 0 -0.57 139 139
SMAD2 -0.019 0.049 -10000 0 -0.42 2 2
SMAD3 0.007 0.044 -10000 0 -0.44 2 2
SMAD3/E2F4-5/DP1/p107/SMAD4 0.02 0.052 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 -0.008 0.064 -10000 0 -0.28 29 29
NCOR1 0.012 0.002 -10000 0 -10000 0 0
NCOA2 0.011 0.028 -10000 0 -0.4 3 3
NCOA1 0.013 0 -10000 0 -10000 0 0
MYOD/E2A 0.009 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 -0.009 0.094 -10000 0 -10000 0 0
IFNB1 0.016 0.045 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C -0.03 0.13 -10000 0 -0.56 8 8
CITED1 -0.16 0.32 -10000 0 -0.75 139 139
SMAD2-3/SMAD4/ARC105 -0.005 0.069 -10000 0 -10000 0 0
RBL1 0.011 0.031 -10000 0 -0.75 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.13 0.26 -10000 0 -0.48 219 219
RUNX1-3/PEBPB2 0.025 0.01 -10000 0 -10000 0 0
SMAD7 0.012 0.078 -10000 0 -0.62 1 1
MYC/MIZ-1 0.052 0.1 -10000 0 -0.53 11 11
SMAD3/SMAD4 0.023 0.14 0.32 11 -10000 0 11
IL10 0.001 0.13 -10000 0 -0.48 26 26
PIASy/HDAC complex 0.011 0.012 -10000 0 -10000 0 0
PIAS3 0.014 0.006 -10000 0 -10000 0 0
CDK2 0.015 0.011 -10000 0 -10000 0 0
IL5 0.007 0.1 -10000 0 -0.63 8 8
CDK4 0.015 0.032 -10000 0 -0.73 1 1
PIAS4 0.011 0.012 -10000 0 -10000 0 0
ATF3 0.01 0.043 -10000 0 -0.75 2 2
SMAD3/SMAD4/SP1 0 0.07 -10000 0 -0.38 2 2
FOXG1 -0.099 0.26 -10000 0 -0.75 83 83
FOXO3 -0.013 0.049 -10000 0 -10000 0 0
FOXO1 -0.013 0.05 -10000 0 -0.35 1 1
FOXO4 -0.012 0.048 -10000 0 -10000 0 0
heart looping -0.028 0.13 -10000 0 -0.5 18 18
CEBPB -0.01 0.084 -10000 0 -0.77 7 7
SMAD3/SMAD4/DLX1 -0.005 0.098 -10000 0 -0.49 19 19
MYOD1 0 0 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.012 0.05 -10000 0 -0.36 2 2
SMAD3/SMAD4/GATA3 0.004 0.087 -10000 0 -0.48 4 4
SnoN/SIN3/HDAC complex/NCoR1 0.012 0.016 -10000 0 -0.39 1 1
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.022 0.045 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1-3 0.015 0.064 -10000 0 -10000 0 0
MED15 0.012 0.016 -10000 0 -0.4 1 1
SP1 0.003 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 0.13 -10000 0 -0.5 26 26
ITGB5 0.024 0.058 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.039 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.008 0.089 -10000 0 -0.41 8 8
AR -0.021 0.11 -10000 0 -0.4 47 47
negative regulation of cell growth 0.019 0.066 -10000 0 -0.38 2 2
SMAD3/SMAD4/MYOD 0.005 0.049 -10000 0 -0.36 2 2
E2F5 -0.002 0.1 -10000 0 -0.72 12 12
E2F4 0.013 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.003 0.073 -10000 0 -0.43 5 5
SMAD2-3/SMAD4/FOXO1-3a-4 -0.079 0.18 -10000 0 -0.39 26 26
TFDP1 0.013 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.023 0.055 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX2 0.012 0.05 -10000 0 -0.36 2 2
TGIF2 0.005 0.075 -10000 0 -0.75 6 6
TGIF1 0.013 0 -10000 0 -10000 0 0
ATF2 0.012 0.016 -10000 0 -0.4 1 1
Aurora A signaling

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
Aurora A/GADD45A 0.023 0.001 -9999 0 -10000 0 0
BIRC5 0.01 0.043 -9999 0 -0.75 2 2
NFKBIA 0.024 0.002 -9999 0 -10000 0 0
CPEB1 -0.1 0.18 -9999 0 -0.4 174 174
AKT1 0.024 0.002 -9999 0 -10000 0 0
NDEL1 0.013 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.021 0.001 -9999 0 -10000 0 0
NDEL1/TACC3 0.027 0.018 -9999 0 -0.42 1 1
GADD45A 0.013 0 -9999 0 -10000 0 0
GSK3B 0.011 0.001 -9999 0 -10000 0 0
PAK1/Aurora A 0.023 0.001 -9999 0 -10000 0 0
MDM2 0.012 0.016 -9999 0 -0.4 1 1
JUB -0.24 0.36 -9999 0 -0.75 204 204
TPX2 0.013 0.058 -9999 0 -0.57 6 6
TP53 0.024 0.012 -9999 0 -0.27 1 1
DLG7 0.016 0.002 -9999 0 -10000 0 0
AURKAIP1 0.011 0.031 -9999 0 -0.75 1 1
ARHGEF7 0.013 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 0.019 -9999 0 -0.44 1 1
G2/M transition of mitotic cell cycle 0.021 0.001 -9999 0 -10000 0 0
AURKA 0.02 0.002 -9999 0 -10000 0 0
AURKB 0.013 0.003 -9999 0 -10000 0 0
CDC25B -0.04 0.095 -9999 0 -0.29 44 44
G2/M transition checkpoint -0.13 0.22 -9999 0 -0.45 204 204
mRNA polyadenylation -0.043 0.094 -9999 0 -10000 0 0
Aurora A/CPEB -0.043 0.094 -9999 0 -10000 0 0
Aurora A/TACC1/TRAP/chTOG 0.035 0.012 -9999 0 -10000 0 0
BRCA1 0.013 0 -9999 0 -10000 0 0
centrosome duplication 0.023 0.001 -9999 0 -10000 0 0
regulation of centrosome cycle 0.026 0.018 -9999 0 -0.42 1 1
spindle assembly 0.034 0.012 -9999 0 -10000 0 0
TDRD7 0.013 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.032 0.025 -9999 0 -0.4 2 2
CENPA 0.016 0.005 -9999 0 -10000 0 0
Aurora A/PP2A 0.023 0.001 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.028 0.007 -9999 0 -10000 0 0
negative regulation of DNA binding 0.024 0.012 -9999 0 -0.27 1 1
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0.018 0.011 -9999 0 -10000 0 0
RASA1 0.013 0.001 -9999 0 -10000 0 0
Ajuba/Aurora A -0.13 0.22 -9999 0 -0.45 204 204
mitotic prometaphase 0 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.002 -9999 0 -10000 0 0
TACC1 0.011 0.023 -9999 0 -0.4 2 2
TACC3 0.011 0.031 -9999 0 -0.75 1 1
Aurora A/Antizyme1 0.029 0.019 -9999 0 -0.44 1 1
Aurora A/RasGAP 0.023 0.002 -9999 0 -10000 0 0
OAZ1 0.013 0 -9999 0 -10000 0 0
RAN 0.013 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 0.012 0.016 -9999 0 -0.4 1 1
GIT1/beta-PIX/PAK1 0.025 0.01 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.013 0.057 -9999 0 -0.57 6 6
PPP2R5D 0.013 0 -9999 0 -10000 0 0
Aurora A/TPX2 0.024 0.046 -9999 0 -0.44 6 6
PAK1 0.013 0 -9999 0 -10000 0 0
CKAP5 0.013 0 -9999 0 -10000 0 0
Integrins in angiogenesis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.016 0.035 -9999 0 -0.47 3 3
alphaV beta3 Integrin 0.005 0.07 -9999 0 -0.43 3 3
PTK2 0.012 0.092 -9999 0 -0.41 5 5
IGF1R 0.013 0 -9999 0 -10000 0 0
PI4KB 0.013 0 -9999 0 -10000 0 0
MFGE8 0.013 0 -9999 0 -10000 0 0
SRC 0.013 0 -9999 0 -10000 0 0
CDKN1B 0.004 0.068 -9999 0 -0.33 19 19
VEGFA 0.01 0.043 -9999 0 -0.75 2 2
ILK 0.004 0.068 -9999 0 -0.33 19 19
ROCK1 0.012 0.016 -9999 0 -0.4 1 1
AKT1 0.01 0.063 -9999 0 -10000 0 0
PTK2B 0.027 0.036 -9999 0 -0.41 2 2
alphaV/beta3 Integrin/JAM-A 0.004 0.096 -9999 0 -0.41 22 22
CBL 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.015 0.044 -9999 0 -0.49 3 3
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.018 0.093 -9999 0 -10000 0 0
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.026 0.046 -9999 0 -0.42 1 1
alphaV/beta3 Integrin/Syndecan-1 0.023 0.026 -9999 0 -10000 0 0
PI4KA 0.013 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.068 0.12 -9999 0 -0.54 7 7
PI4 Kinase 0.019 0 -9999 0 -10000 0 0
PIK3CA 0.012 0.016 -9999 0 -0.4 1 1
alphaV/beta3 Integrin/Osteopontin -0.2 0.25 -9999 0 -0.49 263 263
RPS6KB1 -0.032 0.13 -9999 0 -0.51 7 7
TLN1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.026 0.15 -9999 0 -0.49 49 49
GPR124 0.012 0.016 -9999 0 -0.4 1 1
MAPK1 -0.026 0.15 -9999 0 -0.53 38 38
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.002 0.088 -9999 0 -0.49 9 9
cell adhesion 0.024 0.036 -9999 0 -0.35 3 3
ANGPTL3 0.001 0.053 -9999 0 -0.75 3 3
VEGFR2 homodimer/VEGFA homodimer/Src 0.024 0.031 -9999 0 -0.49 2 2
IGF-1R heterotetramer 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
TGFBR2 0.013 0 -9999 0 -10000 0 0
ITGB3 0.008 0.043 -9999 0 -0.4 7 7
IGF1 -0.08 0.17 -9999 0 -0.4 142 142
RAC1 0.013 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion 0.022 0.027 -9999 0 -10000 0 0
apoptosis 0.012 0 -9999 0 -10000 0 0
CD47 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.023 0.026 -9999 0 -10000 0 0
VCL 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.021 0.1 -9999 0 -0.43 7 7
CSF1 0.011 0.028 -9999 0 -0.4 3 3
PIK3C2A 0.003 0.071 -9999 0 -0.34 21 21
PI4 Kinase/Pyk2 -0.023 0.073 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.028 0.037 -9999 0 -0.45 2 2
FAK1/Vinculin 0.018 0.079 -9999 0 -0.34 3 3
alphaV beta3/Integrin/ppsTEM5 0.022 0.027 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
VTN -0.013 0.13 -9999 0 -0.75 19 19
BCAR1 0.012 0.016 -9999 0 -0.4 1 1
FGF2 -0.017 0.1 -9999 0 -0.4 45 45
F11R -0.002 0.074 -9999 0 -10000 0 0
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 0.031 0.018 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.022 0.023 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.028 0.17 -9999 0 -0.67 37 37
alphaV/beta3 Integrin/Pyk2 0.031 0.036 -9999 0 -0.41 2 2
SDC1 0.013 0 -9999 0 -10000 0 0
VAV3 0.014 0.058 -9999 0 -10000 0 0
PTPN11 0.013 0 -9999 0 -10000 0 0
IRS1 0.013 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.018 0.079 -9999 0 -0.34 3 3
cell migration 0.024 0.075 -9999 0 -10000 0 0
ITGAV 0.013 0 -9999 0 -10000 0 0
PI3K 0.01 0.088 -9999 0 -0.38 19 19
SPP1 -0.31 0.38 -9999 0 -0.75 267 267
KDR 0.012 0.016 -9999 0 -0.4 1 1
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.013 0 -9999 0 -10000 0 0
COL4A3 -0.028 0.13 -9999 0 -0.46 51 51
angiogenesis -0.023 0.15 -9999 0 -0.53 37 37
Rac1/GTP 0.019 0.054 -9999 0 -10000 0 0
EDIL3 -0.061 0.16 -9999 0 -0.4 113 113
cell proliferation 0.023 0.025 -9999 0 -10000 0 0
Nongenotropic Androgen signaling

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
PTK2 0.01 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.003 0.075 -10000 0 -0.41 4 4
regulation of S phase of mitotic cell cycle 0.009 0.057 -10000 0 -10000 0 0
GNAO1 -0.14 0.2 -10000 0 -0.4 234 234
HRAS 0.012 0.016 -10000 0 -0.39 1 1
SHBG/T-DHT 0.001 0.054 -10000 0 -0.5 7 7
PELP1 0.013 0 -10000 0 -10000 0 0
AKT1 0.009 0 -10000 0 -10000 0 0
MAP2K1 0.023 0.052 -10000 0 -0.35 1 1
T-DHT/AR -0.014 0.078 -10000 0 -0.28 47 47
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -0.007 10 10
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 -0.002 0.075 -10000 0 -0.4 22 22
mol:GDP -0.025 0.088 -10000 0 -0.33 47 47
cell proliferation 0.024 0.074 -10000 0 -0.4 4 4
PIK3CA 0.012 0.016 -10000 0 -0.4 1 1
FOS 0.023 0.11 -10000 0 -0.77 10 10
mol:Ca2+ -0.021 0.027 -10000 0 -0.084 55 55
MAPK3 0.022 0.063 -10000 0 -0.39 1 1
MAPK1 0.018 0.041 -10000 0 -0.34 2 2
PIK3R1 0.013 0 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.005 10 10
cAMP biosynthetic process 0.002 0.054 -10000 0 -0.46 7 7
GNG2 -0.004 0.081 -10000 0 -0.4 26 26
potassium channel inhibitor activity 0 0.001 -10000 0 -0.005 10 10
HRAS/GTP 0.01 0.054 -10000 0 -0.4 1 1
actin cytoskeleton reorganization -0.001 0.015 -10000 0 -0.35 1 1
SRC 0.013 0 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.005 10 10
PI3K 0.017 0.01 -10000 0 -10000 0 0
apoptosis -0.025 0.065 0.39 10 -10000 0 10
T-DHT/AR/PELP1 -0.003 0.066 -10000 0 -0.5 1 1
HRAS/GDP -0.024 0.082 -10000 0 -0.31 47 47
CREB1 0.025 0.069 -10000 0 -0.41 10 10
RAC1-CDC42/GTP 0.024 0.017 -10000 0 -0.35 1 1
AR -0.021 0.11 -10000 0 -0.4 47 47
GNB1 0.013 0 -10000 0 -10000 0 0
RAF1 0.017 0.053 -10000 0 -0.38 1 1
RAC1-CDC42/GDP 0.006 0.087 -10000 0 -0.32 1 1
T-DHT/AR/PELP1/Src 0.007 0.06 -10000 0 -0.45 1 1
MAP2K2 0.022 0.053 -10000 0 -0.35 1 1
T-DHT/AR/PELP1/Src/PI3K 0.009 0.058 -10000 0 -10000 0 0
GNAZ 0.007 0.046 -10000 0 -0.4 8 8
SHBG 0.001 0.08 -10000 0 -0.75 7 7
Gi family/GNB1/GNG2/GDP -0.096 0.18 -10000 0 -0.45 63 63
mol:T-DHT 0 0 -10000 0 -0.003 9 9
RAC1 0.013 0 -10000 0 -10000 0 0
GNRH1 0.009 0.012 -10000 0 -0.28 1 1
Gi family/GTP -0.058 0.12 -10000 0 -0.34 52 52
CDC42 0.011 0.023 -10000 0 -0.4 2 2
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.004 0.1 0.56 19 -10000 0 19
KIRREL 0.005 0.055 -10000 0 -0.45 8 8
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.004 0.1 -10000 0 -0.56 19 19
PLCG1 0.013 0 -10000 0 -10000 0 0
ARRB2 0.013 0 -10000 0 -10000 0 0
WASL 0.013 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.001 0.1 -10000 0 -0.45 23 23
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.016 0.06 -10000 0 -0.52 2 2
FYN 0.001 0.083 -10000 0 -0.4 23 23
mol:Ca2+ 0.006 0.092 -10000 0 -0.44 23 23
mol:DAG 0.006 0.092 -10000 0 -0.44 23 23
NPHS2 -0.003 0.076 -10000 0 -0.76 6 6
mol:IP3 0.006 0.092 -10000 0 -0.44 23 23
regulation of endocytosis 0.011 0.079 -10000 0 -0.37 23 23
Nephrin/NEPH1/podocin/Cholesterol -0.002 0.092 -10000 0 -0.45 23 23
establishment of cell polarity -0.004 0.1 -10000 0 -0.56 19 19
Nephrin/NEPH1/podocin/NCK1-2 0.014 0.086 -10000 0 -0.41 23 23
Nephrin/NEPH1/beta Arrestin2 0.012 0.08 -10000 0 -0.38 23 23
NPHS1 -0.01 0.12 -10000 0 -0.75 17 17
Nephrin/NEPH1/podocin 0.003 0.084 -10000 0 -0.4 23 23
TJP1 0.013 0 -10000 0 -10000 0 0
NCK1 0.013 0 -10000 0 -10000 0 0
NCK2 0.013 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.007 0.093 -10000 0 -0.44 23 23
CD2AP 0 0.07 -10000 0 -0.4 19 19
Nephrin/NEPH1/podocin/GRB2 0.007 0.093 -10000 0 -0.44 23 23
GRB2 0.013 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.005 0.095 -10000 0 -0.4 26 26
cytoskeleton organization 0.017 0.075 -10000 0 -0.35 15 15
Nephrin/NEPH1 -0.001 0.076 -10000 0 -0.41 19 19
Nephrin/NEPH1/ZO-1 0.007 0.085 -10000 0 -0.46 18 18
Regulation of Telomerase

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
Telomerase catalytic core complex -0.064 0.18 -9999 0 -0.59 57 57
RAD9A 0.013 0 -9999 0 -10000 0 0
AP1 0.014 0.036 -9999 0 -10000 0 0
IFNAR2 0.013 0.004 -9999 0 -10000 0 0
AKT1 -0.002 0.052 -9999 0 -10000 0 0
ER alpha/Oestrogen -0.018 0.084 -9999 0 -0.28 59 59
NFX1/SIN3/HDAC complex 0.038 0.012 -9999 0 -10000 0 0
EGF -0.086 0.2 -9999 0 -0.45 131 131
SMG5 0.013 0 -9999 0 -10000 0 0
SMG6 0.013 0 -9999 0 -10000 0 0
SP3/HDAC2 0.02 0.008 -9999 0 -10000 0 0
TERT/c-Abl -0.054 0.17 -9999 0 -0.57 48 48
SAP18 0.013 0.001 -9999 0 -10000 0 0
MRN complex 0.025 0.01 -9999 0 -10000 0 0
WT1 -0.37 0.38 -9999 0 -0.75 309 309
WRN 0.012 0.016 -9999 0 -0.4 1 1
SP1 0.013 0.006 -9999 0 -10000 0 0
SP3 0.012 0.003 -9999 0 -10000 0 0
TERF2IP 0.013 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.063 0.15 -9999 0 -0.54 36 36
Mad/Max 0.018 0.017 -9999 0 -0.27 2 2
TERT -0.066 0.19 -9999 0 -0.62 51 51
CCND1 -0.054 0.17 -9999 0 -0.57 40 40
MAX 0.012 0.003 -9999 0 -10000 0 0
RBBP7 0.013 0.001 -9999 0 -10000 0 0
RBBP4 0.013 0.001 -9999 0 -10000 0 0
TERF2 0.012 0.003 -9999 0 -10000 0 0
PTGES3 0.013 0 -9999 0 -10000 0 0
SIN3A 0.013 0.001 -9999 0 -10000 0 0
Telomerase/911 0.024 0.027 -9999 0 -10000 0 0
CDKN1B -0.021 0.15 -9999 0 -0.48 63 63
RAD1 0.011 0.031 -9999 0 -0.75 1 1
XRCC5 0.013 0 -9999 0 -10000 0 0
XRCC6 0.013 0 -9999 0 -10000 0 0
SAP30 0.013 0.001 -9999 0 -10000 0 0
TRF2/PARP2 0.019 0.002 -9999 0 -10000 0 0
UBE3A 0.012 0.017 -9999 0 -0.39 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 0.012 -9999 0 -0.28 1 1
FOS 0.006 0.051 -9999 0 -0.39 10 10
IFN-gamma/IRF1 -0.034 0.18 -9999 0 -0.56 63 63
PARP2 0.013 0 -9999 0 -10000 0 0
BLM 0.011 0.031 -9999 0 -0.75 1 1
Telomerase 0 0.061 -9999 0 -0.35 6 6
IRF1 0.017 0.003 -9999 0 -10000 0 0
ESR1 -0.027 0.12 -9999 0 -0.4 59 59
KU/TER 0.019 0 -9999 0 -10000 0 0
ATM/TRF2 0.019 0.011 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.042 0.015 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.042 0.015 -9999 0 -10000 0 0
HDAC1 0.013 0.001 -9999 0 -10000 0 0
HDAC2 0.013 0.006 -9999 0 -10000 0 0
ATM -0.001 0.014 -9999 0 -0.34 1 1
SMAD3 0.017 0.029 -9999 0 -0.37 3 3
ABL1 0.013 0 -9999 0 -10000 0 0
MXD1 0.011 0.023 -9999 0 -0.39 2 2
MRE11A 0.013 0.001 -9999 0 -10000 0 0
HUS1 0.013 0 -9999 0 -10000 0 0
RPS6KB1 0.012 0.016 -9999 0 -0.4 1 1
TERT/NF kappa B1/14-3-3 -0.038 0.17 -9999 0 -0.57 38 38
NR2F2 0.013 0.006 -9999 0 -10000 0 0
MAPK3 0.012 0.013 -9999 0 -0.29 1 1
MAPK1 0.012 0.013 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.011 0.031 -9999 0 -0.75 1 1
NFKB1 0.013 0 -9999 0 -10000 0 0
HNRNPC 0.013 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.001 0.014 -9999 0 -0.34 1 1
NBN 0.012 0.016 -9999 0 -0.4 1 1
EGFR 0.011 0.023 -9999 0 -0.4 2 2
mol:Oestrogen 0 0.002 -9999 0 -10000 0 0
EGF/EGFR -0.053 0.14 -9999 0 -0.44 36 36
MYC -0.001 0.1 -9999 0 -0.75 11 11
IL2 0.004 0.01 -9999 0 -10000 0 0
KU 0.019 0 -9999 0 -10000 0 0
RAD50 0.013 0 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
TGFB1 0.011 0.031 -9999 0 -0.75 1 1
TRF2/BLM 0.018 0.022 -9999 0 -0.54 1 1
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.049 0.17 -9999 0 -0.58 44 44
SP1/HDAC2 0.021 0.011 -9999 0 -10000 0 0
PINX1 0.013 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.063 0.15 -9999 0 -0.54 36 36
Smad3/Myc 0.013 0.072 -9999 0 -0.49 12 12
911 complex 0.025 0.021 -9999 0 -0.49 1 1
IFNG -0.062 0.23 -9999 0 -0.75 63 63
Telomerase/PinX1 -0.063 0.15 -9999 0 -0.54 36 36
Telomerase/AKT1/mTOR/p70S6K 0.008 0.049 -9999 0 -10000 0 0
SIN3B 0.013 0.001 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.063 0.15 -9999 0 -0.54 36 36
response to DNA damage stimulus 0.003 0.005 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0.036 0.008 -9999 0 -10000 0 0
TRF2/WRN 0.018 0.011 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.063 0.15 -9999 0 -0.54 35 35
E2F1 -0.003 0.11 -9999 0 -0.76 13 13
ZNFX1 0.013 0.001 -9999 0 -10000 0 0
PIF1 -0.008 0.12 -9999 0 -0.75 17 17
NCL 0.013 0 -9999 0 -10000 0 0
DKC1 0.013 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.008 0.075 -9999 0 -0.47 5 5
CRKL 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
DOCK1 0.012 0.016 -9999 0 -0.4 1 1
ITGA4 -0.002 0.075 -9999 0 -0.4 22 22
alpha4/beta7 Integrin/MAdCAM1 -0.085 0.13 -9999 0 -0.42 31 31
EPO -0.002 0.08 -9999 0 -0.75 7 7
alpha4/beta7 Integrin -0.002 0.08 -9999 0 -0.51 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.009 0.053 -9999 0 -10000 0 0
EPO/EPOR (dimer) 0.007 0.066 -9999 0 -0.57 8 8
lamellipodium assembly 0.031 0.01 -9999 0 -10000 0 0
PIK3CA 0.012 0.016 -9999 0 -0.4 1 1
PI3K 0.018 0.011 -9999 0 -10000 0 0
ARF6 0.013 0 -9999 0 -10000 0 0
JAK2 0.014 0.06 -9999 0 -0.42 3 3
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
MADCAM1 -0.18 0.2 -9999 0 -0.4 287 287
cell adhesion -0.085 0.13 -9999 0 -0.42 31 31
CRKL/CBL 0.019 0 -9999 0 -10000 0 0
ITGB1 0.013 0 -9999 0 -10000 0 0
SRC 0.016 0.06 -9999 0 -0.39 9 9
ITGB7 -0.003 0.077 -9999 0 -0.4 23 23
RAC1 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.012 0.067 -9999 0 -0.43 9 9
p130Cas/Crk/Dock1 0.033 0.054 -9999 0 -10000 0 0
VCAM1 0.004 0.058 -9999 0 -0.4 13 13
RHOA 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.024 0.042 -9999 0 -10000 0 0
BCAR1 0.02 0.057 -9999 0 -10000 0 0
EPOR 0.011 0.031 -9999 0 -0.75 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.013 0 -9999 0 -10000 0 0
GIT1 0.012 0.016 -9999 0 -0.4 1 1
Rac1/GTP 0.031 0.01 -9999 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.023 0 -9999 0 -10000 0 0
SNTA1 0.012 0.016 -9999 0 -0.4 1 1
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.023 0.01 -9999 0 -10000 0 0
MAPK12 0.016 0.063 -9999 0 -0.48 9 9
CCND1 0.014 0.03 -9999 0 -0.18 14 14
p38 gamma/SNTA1 0.022 0.06 -9999 0 -0.45 9 9
MAP2K3 0.013 0 -9999 0 -10000 0 0
PKN1 0.013 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.016 0.062 -9999 0 -0.48 9 9
MAP2K6 0.018 0.019 -9999 0 -10000 0 0
MAPT -0.042 0.12 -9999 0 -0.26 146 146
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
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 0.004 0.008 -9999 0 -10000 0 0
REL 0.015 0.007 -9999 0 -10000 0 0
HDAC7 0.02 0.082 -9999 0 -10000 0 0
JUN 0.011 0.005 -9999 0 -10000 0 0
EP300 0.012 0.001 -9999 0 -10000 0 0
KAT2B -0.006 0.083 -9999 0 -0.4 27 27
KAT5 0.013 0.001 -9999 0 -10000 0 0
MAPK14 0.015 0.027 -9999 0 -0.29 3 3
FOXO1 0.012 0.016 -9999 0 -0.39 1 1
T-DHT/AR 0.019 0.088 -9999 0 -0.44 2 2
MAP2K6 0.008 0.034 -9999 0 -0.41 4 4
BRM/BAF57 0.014 0.017 -9999 0 -10000 0 0
MAP2K4 0.009 0.029 -9999 0 -0.4 3 3
SMARCA2 0.01 0.018 -9999 0 -0.42 1 1
PDE9A -0.14 0.37 -9999 0 -0.96 104 104
NCOA2 0.01 0.028 -9999 0 -0.39 3 3
CEBPA 0.011 0.028 -9999 0 -0.39 3 3
EHMT2 0.01 0.031 -9999 0 -0.75 1 1
cell proliferation 0.024 0.1 -9999 0 -0.42 1 1
NR0B1 -0.002 0.068 -9999 0 -0.75 5 5
EGR1 0.01 0.023 -9999 0 -0.39 2 2
RXRs/9cRA -0.074 0.11 -9999 0 -10000 0 0
AR/RACK1/Src 0.019 0.056 -9999 0 -10000 0 0
AR/GR -0.006 0.088 -9999 0 -0.39 9 9
GNB2L1 0.013 0.001 -9999 0 -10000 0 0
PKN1 0.012 0.001 -9999 0 -10000 0 0
RCHY1 0.013 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity -0.001 0.002 -9999 0 -10000 0 0
MAPK8 0.015 0.024 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.025 0.054 -9999 0 -10000 0 0
SRC 0.023 0.036 -9999 0 -10000 0 0
NR3C1 -0.018 0.11 -9999 0 -0.4 46 46
KLK3 -0.2 0.43 -9999 0 -1.1 105 105
APPBP2 0.011 0.017 -9999 0 -0.39 1 1
TRIM24 0.011 0.006 -9999 0 -10000 0 0
T-DHT/AR/TIP60 0.02 0.05 -9999 0 -10000 0 0
TMPRSS2 -0.007 0.11 -9999 0 -1.1 4 4
RXRG -0.16 0.2 -9999 0 -0.4 262 262
mol:9cRA -0.001 0.002 -9999 0 -10000 0 0
RXRA 0.011 0.016 -9999 0 -0.39 1 1
RXRB 0.012 0.001 -9999 0 -10000 0 0
CARM1 0.013 0.002 -9999 0 -10000 0 0
NR2C2 0.012 0.016 -9999 0 -0.39 1 1
KLK2 0.011 0.12 -9999 0 -0.5 29 29
AR 0.005 0.073 -9999 0 -0.33 9 9
SENP1 0.012 0.001 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
MDM2 0.016 0.02 -9999 0 -0.4 1 1
SRY 0.003 0.032 -9999 0 -0.75 1 1
GATA2 0.005 0.054 -9999 0 -0.4 11 11
MYST2 0.013 0.001 -9999 0 -10000 0 0
HOXB13 -0.02 0.11 -9999 0 -0.4 45 45
T-DHT/AR/RACK1/Src 0.024 0.051 -9999 0 -10000 0 0
positive regulation of transcription 0.005 0.054 -9999 0 -0.39 11 11
DNAJA1 0.011 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.013 -9999 0 -0.27 1 1
NCOA1 0.014 0.006 -9999 0 -10000 0 0
SPDEF -0.08 0.17 -9999 0 -0.4 140 140
T-DHT/AR/TIF2 0.021 0.057 -9999 0 -10000 0 0
T-DHT/AR/Hsp90 0.019 0.05 -9999 0 -10000 0 0
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 0.038 -9999 0 -10000 0 0
SIRT1 0.012 0.001 -9999 0 -10000 0 0
ZMIZ2 0.017 0.012 -9999 0 -10000 0 0
POU2F1 0.01 0.048 -9999 0 -0.74 1 1
T-DHT/AR/DAX-1 0.01 0.062 -9999 0 -0.41 5 5
CREBBP 0.012 0.001 -9999 0 -10000 0 0
SMARCE1 0.01 0.007 -9999 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.018 0.06 0.36 5 -10000 0 5
RFC1 0.018 0.06 0.36 5 -10000 0 5
PRKDC 0.017 0.063 0.36 5 -0.48 1 6
RIPK1 0.013 0.003 -10000 0 -10000 0 0
CASP7 0.016 0.052 0.22 17 -0.54 1 18
FASLG/FAS/FADD/FAF1 0.008 0.076 0.22 20 -0.29 7 27
MAP2K4 0.01 0.093 -10000 0 -0.36 6 6
mol:ceramide 0.006 0.082 -10000 0 -0.37 7 7
GSN 0.014 0.061 0.36 4 -10000 0 4
FASLG/FAS/FADD/FAF1/Caspase 8 0.013 0.077 0.28 1 -0.36 5 6
FAS 0.006 0.049 -10000 0 -0.4 9 9
BID 0.019 0.059 0.27 29 -0.5 1 30
MAP3K1 0.02 0.065 0.25 3 -0.32 1 4
MAP3K7 0.012 0.003 -10000 0 -10000 0 0
RB1 0.018 0.06 0.36 5 -10000 0 5
CFLAR 0.013 0.003 -10000 0 -10000 0 0
HGF/MET -0.006 0.12 -10000 0 -0.5 31 31
ARHGDIB 0.018 0.06 0.36 5 -10000 0 5
FADD 0.012 0.005 -10000 0 -10000 0 0
actin filament polymerization -0.014 0.061 -10000 0 -0.36 4 4
NFKB1 -0.023 0.051 -10000 0 -10000 0 0
MAPK8 0.003 0.12 -10000 0 -0.44 10 10
DFFA 0.018 0.06 0.36 5 -10000 0 5
DNA fragmentation during apoptosis 0.018 0.06 0.36 5 -10000 0 5
FAS/FADD/MET 0.015 0.059 -10000 0 -0.49 6 6
CFLAR/RIP1 0.016 0.006 -10000 0 -10000 0 0
FAIM3 -0.006 0.086 -10000 0 -0.39 29 29
FAF1 0.012 0.005 -10000 0 -10000 0 0
PARP1 0.018 0.06 0.36 5 -10000 0 5
DFFB 0.018 0.06 0.36 5 -10000 0 5
CHUK -0.017 0.045 -10000 0 -10000 0 0
FASLG -0.011 0.096 -10000 0 -0.41 34 34
FAS/FADD 0.013 0.035 -10000 0 -0.27 9 9
HGF 0.002 0.067 -10000 0 -0.42 15 15
LMNA 0.027 0.052 0.32 5 -10000 0 5
CASP6 0.018 0.06 0.36 5 -10000 0 5
CASP10 0.012 0.005 -10000 0 -10000 0 0
CASP3 0.021 0.071 0.26 32 -10000 0 32
PTPN13 -0.018 0.15 -10000 0 -0.68 28 28
CASP8 0.015 0.069 0.33 29 -10000 0 29
IL6 -0.055 0.23 -10000 0 -0.6 83 83
MET 0.005 0.075 -10000 0 -0.75 6 6
ICAD/CAD 0.017 0.055 0.33 5 -10000 0 5
FASLG/FAS/FADD/FAF1/Caspase 10 0.006 0.083 -10000 0 -0.37 7 7
activation of caspase activity by cytochrome c 0.019 0.059 0.27 29 -0.5 1 30
PAK2 0.018 0.06 0.36 5 -10000 0 5
BCL2 -0.008 0.09 -10000 0 -0.4 32 32
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.065 0.16 -9999 0 -0.4 118 118
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.01 0.043 -9999 0 -0.75 2 2
TCEB1 0.013 0 -9999 0 -10000 0 0
HIF1A/p53 0.027 0.007 -9999 0 -10000 0 0
HIF1A 0.02 0.007 -9999 0 -10000 0 0
COPS5 0.013 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.036 0.027 -9999 0 -0.42 2 2
FIH (dimer) 0.013 0 -9999 0 -10000 0 0
CDKN2A -0.14 0.3 -9999 0 -0.75 120 120
ARNT/IPAS -0.036 0.11 -9999 0 -10000 0 0
HIF1AN 0.013 0 -9999 0 -10000 0 0
GNB2L1 0.013 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.027 0.01 -9999 0 -10000 0 0
CUL2 0.013 0 -9999 0 -10000 0 0
OS9 0.013 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.024 0.029 -9999 0 -0.49 2 2
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.027 0.007 -9999 0 -10000 0 0
PHD1-3/OS9 0.03 0.023 -9999 0 -10000 0 0
HIF1A/RACK1/Elongin B/Elongin C 0.036 0.023 -9999 0 -0.36 2 2
VHL 0.013 0 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.027 0.007 -9999 0 -10000 0 0
EGLN3 0.009 0.04 -9999 0 -0.4 6 6
EGLN2 0.012 0.016 -9999 0 -0.4 1 1
EGLN1 0.013 0 -9999 0 -10000 0 0
TP53 0.013 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.033 0.015 -9999 0 -10000 0 0
ARNT 0.012 0.016 -9999 0 -0.4 1 1
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.012 0.016 -9999 0 -0.4 1 1
HIF1A/p19ARF -0.053 0.16 -9999 0 -0.39 120 120
Coregulation of Androgen receptor activity

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
NRIP1 0 0.036 -9999 0 -0.39 2 2
SVIL 0.002 0.029 -9999 0 -0.39 1 1
ZNF318 0.036 0.058 -9999 0 -10000 0 0
JMJD2C 0.002 0.028 -9999 0 -0.12 29 29
T-DHT/AR/Ubc9 0.006 0.07 -9999 0 -0.33 5 5
CARM1 0.011 0.003 -9999 0 -10000 0 0
PRDX1 0.014 0.004 -9999 0 -10000 0 0
PELP1 0.017 0.01 -9999 0 -10000 0 0
CTNNB1 0.004 0.02 -9999 0 -10000 0 0
AKT1 0.019 0.016 -9999 0 -10000 0 0
PTK2B 0.004 0.029 -9999 0 -0.39 2 2
MED1 0.018 0.046 -9999 0 -0.72 2 2
MAK 0.009 0.15 -9999 0 -0.74 22 22
response to oxidative stress 0.002 0.004 -9999 0 -10000 0 0
HIP1 0.002 0.029 -9999 0 -0.39 1 1
GSN -0.007 0.065 -9999 0 -0.41 13 13
NCOA2 0.009 0.028 -9999 0 -0.39 3 3
NCOA6 0.003 0.024 -9999 0 -10000 0 0
DNA-PK 0.047 0.059 -9999 0 -0.49 1 1
NCOA4 0.011 0.017 -9999 0 -0.4 1 1
PIAS3 0.004 0.02 -9999 0 -10000 0 0
cell proliferation 0.007 0.093 -9999 0 -0.38 21 21
XRCC5 0.018 0.013 -9999 0 -10000 0 0
UBE3A -0.004 0.041 -9999 0 -0.4 1 1
T-DHT/AR/SNURF -0.025 0.11 -9999 0 -0.41 22 22
FHL2 0.043 0.053 -9999 0 -10000 0 0
RANBP9 0.002 0.029 -9999 0 -0.4 1 1
JMJD1A 0.007 0.025 -9999 0 -0.13 18 18
CDK6 0.014 0.003 -9999 0 -10000 0 0
TGFB1I1 0.003 0.025 -9999 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.006 0.086 -9999 0 -0.42 10 10
XRCC6 0.018 0.013 -9999 0 -10000 0 0
T-DHT/AR 0.018 0.083 -9999 0 -0.38 5 5
CTDSP1 0.009 0.009 -9999 0 -10000 0 0
CTDSP2 0.029 0.039 -9999 0 -10000 0 0
BRCA1 0.003 0.025 -9999 0 -10000 0 0
TCF4 0.022 0.04 -9999 0 -0.37 3 3
CDKN2A -0.13 0.3 -9999 0 -0.74 120 120
SRF 0.027 0.018 -9999 0 -10000 0 0
NKX3-1 -0.001 0.12 -9999 0 -0.78 14 14
KLK3 -0.19 0.49 -9999 0 -1.3 104 104
TMF1 0.01 0.017 -9999 0 -0.4 1 1
HNRNPA1 0.021 0.021 -9999 0 -10000 0 0
AOF2 -0.01 0.025 -9999 0 -0.068 100 100
APPL1 0.032 0.042 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 0.014 0.075 -9999 0 -0.33 5 5
AR -0.018 0.11 -9999 0 -0.4 47 47
UBA3 0.009 0.009 -9999 0 -10000 0 0
PATZ1 0.021 0.021 -9999 0 -10000 0 0
PAWR 0.011 0.005 -9999 0 -10000 0 0
PRKDC 0.017 0.033 -9999 0 -0.75 1 1
PA2G4 0.023 0.026 -9999 0 -10000 0 0
UBE2I 0.013 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.013 0.067 -9999 0 -0.3 5 5
RPS6KA3 0.001 0.028 -9999 0 -10000 0 0
T-DHT/AR/ARA70 0 0.07 -9999 0 -0.33 5 5
LATS2 0.021 0.021 -9999 0 -10000 0 0
T-DHT/AR/PRX1 0.018 0.073 -9999 0 -0.3 5 5
Cyclin D3/CDK11 p58 0.011 0.005 -9999 0 -10000 0 0
VAV3 -0.029 0.11 -9999 0 -0.4 52 52
KLK2 -0.016 0.13 -9999 0 -0.58 29 29
CASP8 0.016 0.008 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.006 0.068 -9999 0 -0.44 1 1
TMPRSS2 0.008 0.081 -9999 0 -0.81 4 4
CCND1 0.001 0.069 -9999 0 -0.75 5 5
PIAS1 -0.003 0.038 -9999 0 -10000 0 0
mol:T-DHT 0.003 0.017 -9999 0 -0.059 38 38
CDC2L1 0.001 0.002 -9999 0 -10000 0 0
PIAS4 -0.011 0.057 -9999 0 -10000 0 0
T-DHT/AR/CDK6 0.009 0.072 -9999 0 -0.33 5 5
CMTM2 -0.014 0.14 -9999 0 -0.75 23 23
SNURF -0.038 0.14 -9999 0 -0.42 68 68
ZMIZ1 0.015 0.016 -9999 0 -10000 0 0
CCND3 0.013 0.002 -9999 0 -10000 0 0
TGIF1 0.021 0.021 -9999 0 -10000 0 0
FKBP4 0.002 0.038 -9999 0 -0.75 1 1
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.013 0 -9999 0 -10000 0 0
ITGB7 -0.003 0.077 -9999 0 -0.4 23 23
ITGA4 -0.002 0.075 -9999 0 -0.4 22 22
alpha4/beta7 Integrin -0.002 0.08 -9999 0 -0.51 5 5
alpha4/beta1 Integrin 0.009 0.053 -9999 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.002 0.087 -10000 0 -0.71 9 9
ANTXR2 0.011 0.023 -10000 0 -0.4 2 2
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0.011 -10000 0 -0.08 11 11
monocyte activation 0.003 0.065 -10000 0 -0.37 18 18
MAP2K2 0.009 0.029 -10000 0 -0.69 1 1
MAP2K1 -0.001 0.009 -10000 0 -10000 0 0
MAP2K7 -0.002 0.012 -10000 0 -10000 0 0
MAP2K6 -0.002 0.018 -10000 0 -0.19 4 4
CYAA 0.005 0.052 -10000 0 -0.43 8 8
MAP2K4 -0.002 0.016 -10000 0 -0.19 3 3
IL1B -0.028 0.12 -10000 0 -0.42 57 57
Channel 0.009 0.055 -10000 0 -0.46 8 8
NLRP1 -0.004 0.029 -10000 0 -0.29 5 5
CALM1 0.013 0 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.01 0.014 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0.011 0.08 11 -10000 0 11
MAPK3 -0.002 0.012 -10000 0 -0.19 1 1
MAPK1 -0.002 0.012 -10000 0 -0.19 1 1
PGR -0.053 0.085 -10000 0 -0.19 168 168
PA/Cellular Receptors 0.009 0.06 -10000 0 -0.5 8 8
apoptosis -0.001 0.011 -10000 0 -0.08 11 11
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.009 0.05 -10000 0 -0.41 8 8
macrophage activation 0.013 0.015 -10000 0 -10000 0 0
TNF 0.009 0.036 -10000 0 -0.4 5 5
VCAM1 0.003 0.065 -10000 0 -0.37 18 18
platelet activation 0.01 0.014 -10000 0 -10000 0 0
MAPKKK cascade -0.01 0.013 0.12 1 -10000 0 1
IL18 0.01 0.023 -10000 0 -0.18 6 6
negative regulation of macrophage activation -0.001 0.011 -10000 0 -0.08 11 11
LEF -0.001 0.011 -10000 0 -0.081 11 11
CASP1 -0.002 0.016 -10000 0 -0.14 5 5
mol:cAMP 0.01 0.014 -10000 0 -10000 0 0
necrosis -0.001 0.011 -10000 0 -0.08 11 11
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.009 0.052 -10000 0 -0.43 8 8
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.006 0.12 -9999 0 -0.37 63 63
positive regulation of NF-kappaB transcription factor activity 0 0.001 -9999 0 -10000 0 0
CRKL 0.013 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.019 0.11 -9999 0 -0.67 1 1
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.016 0.034 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.022 0.047 -9999 0 -0.27 1 1
CaM/Ca2+ -0.003 0.11 -9999 0 -0.34 57 57
RAP1A 0.013 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.001 0.12 -9999 0 -0.75 1 1
AKT1 0.007 0.1 -9999 0 -10000 0 0
MAP2K1 0.003 0.11 -9999 0 -10000 0 0
MAP3K11 -0.004 0.12 -9999 0 -0.35 57 57
IFNGR1 0.01 0.013 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.025 0.13 -9999 0 -0.45 20 20
Rap1/GTP -0.027 0.079 -9999 0 -10000 0 0
CRKL/C3G 0.018 0.011 -9999 0 -0.27 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.007 0.13 -9999 0 -0.4 63 63
CEBPB 0.017 0.13 -9999 0 -0.5 2 2
STAT3 0.013 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.016 0.16 -9999 0 -0.54 22 22
STAT1 -0.003 0.12 -9999 0 -0.75 1 1
CALM1 0.013 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.065 0.23 -9999 0 -0.74 63 63
PIK3CA 0.012 0.016 -9999 0 -0.4 1 1
STAT1 (dimer)/PIAS1 0.005 0.11 -9999 0 -0.7 1 1
CEBPB/PTGES2/Cbp/p300 -0.027 0.066 -9999 0 -10000 0 0
mol:Ca2+ -0.007 0.12 -9999 0 -0.36 63 63
MAPK3 0.013 0.11 -9999 0 -0.9 1 1
STAT1 (dimer) -0.029 0.061 -9999 0 -0.37 1 1
MAPK1 0.013 0.1 -9999 0 -0.7 1 1
JAK2 0.008 0.031 -9999 0 -0.4 3 3
PIK3R1 0.013 0 -9999 0 -10000 0 0
JAK1 0.009 0.021 -9999 0 -0.39 1 1
CAMK2D 0.011 0.023 -9999 0 -0.4 2 2
DAPK1 0.014 0.14 -9999 0 -0.57 26 26
SMAD7 0.026 0.045 -9999 0 -0.22 1 1
CBL/CRKL/C3G 0.009 0.11 -9999 0 -10000 0 0
PI3K -0.034 0.099 -9999 0 -10000 0 0
IFNG -0.065 0.23 -9999 0 -0.74 63 63
apoptosis 0.009 0.11 -9999 0 -0.42 26 26
CAMK2G 0.013 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.013 0 -9999 0 -10000 0 0
CAMK2A -0.021 0.11 -9999 0 -0.4 50 50
CAMK2B -0.028 0.13 -9999 0 -0.45 52 52
FRAP1 0.007 0.098 -9999 0 -10000 0 0
PRKCD 0.008 0.11 -9999 0 -10000 0 0
RAP1B 0.013 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.022 0.047 -9999 0 -0.27 1 1
PTPN2 0.013 0.001 -9999 0 -10000 0 0
EP300 0.013 0.001 -9999 0 -10000 0 0
IRF1 0.021 0.1 -9999 0 -0.46 7 7
STAT1 (dimer)/PIASy 0.004 0.11 -9999 0 -0.7 1 1
SOCS1 -0.016 0.1 -9999 0 -0.55 22 22
mol:GDP 0.005 0.1 -9999 0 -10000 0 0
CASP1 0.025 0.047 -9999 0 -0.23 3 3
PTGES2 0.013 0 -9999 0 -10000 0 0
IRF9 0.031 0.046 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.033 0.097 -9999 0 -10000 0 0
RAP1/GDP -0.027 0.079 -9999 0 -10000 0 0
CBL -0.004 0.12 -9999 0 -10000 0 0
MAP3K1 -0.003 0.12 -9999 0 -0.35 1 1
PIAS1 0.013 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 -0.022 0.047 -9999 0 -0.27 1 1
PTPN11 -0.01 0.12 -9999 0 -0.36 63 63
CREBBP 0.013 0.001 -9999 0 -10000 0 0
RAPGEF1 0.012 0.016 -9999 0 -0.4 1 1
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.013 0 -10000 0 -10000 0 0
NFATC1 0.045 0.027 -10000 0 -10000 0 0
NFATC2 0.03 0.025 -10000 0 -10000 0 0
NFATC3 0.021 0.003 -10000 0 -10000 0 0
YWHAE 0.013 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.071 0.12 -10000 0 -0.35 53 53
Exportin 1/Ran/NUP214 0.026 0.001 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.076 0.1 -10000 0 -0.46 11 11
BCL2/BAX 0.004 0.063 -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 0.013 0 -10000 0 -10000 0 0
MAPK14 0.013 0.001 -10000 0 -10000 0 0
BAD 0.012 0.016 -10000 0 -0.4 1 1
CABIN1/MEF2D -0.061 0.11 -10000 0 -0.33 53 53
Calcineurin A alpha-beta B1/BCL2 -0.008 0.09 -10000 0 -0.39 32 32
FKBP8 0.012 0.016 -10000 0 -0.4 1 1
activation-induced cell death of T cells 0.061 0.11 0.32 53 -10000 0 53
KPNB1 0.013 0 -10000 0 -10000 0 0
KPNA2 0.011 0.031 -10000 0 -0.75 1 1
XPO1 0.013 0 -10000 0 -10000 0 0
SFN 0.011 0.023 -10000 0 -0.4 2 2
MAP3K8 0.013 0.001 -10000 0 -10000 0 0
NFAT4/CK1 alpha 0.03 0.009 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 0.051 0.049 -10000 0 -0.4 1 1
CABIN1 -0.072 0.12 -10000 0 -0.35 53 53
CALM1 0.013 0.001 -10000 0 -10000 0 0
RAN 0.013 0 -10000 0 -10000 0 0
MAP3K1 0.012 0.016 -10000 0 -0.4 1 1
CAMK4 -0.011 0.095 -10000 0 -0.4 36 36
mol:Ca2+ 0.001 0.002 -10000 0 -10000 0 0
MAPK3 0.012 0.016 -10000 0 -0.4 1 1
YWHAH 0.013 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.004 0.063 -10000 0 -10000 0 0
YWHAB 0.013 0 -10000 0 -10000 0 0
MAPK8 0.013 0.002 -10000 0 -10000 0 0
MAPK9 0.013 0 -10000 0 -10000 0 0
YWHAG 0.013 0 -10000 0 -10000 0 0
FKBP1A 0.013 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.06 0.026 -10000 0 -10000 0 0
PRKCH 0.012 0.016 -10000 0 -0.4 1 1
CABIN1/Cbp/p300 0.019 0.004 -10000 0 -10000 0 0
CASP3 0.013 0.001 -10000 0 -10000 0 0
PIM1 0.013 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.009 0.001 -10000 0 -10000 0 0
apoptosis -0.004 0.017 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.036 0.017 -10000 0 -0.36 1 1
PRKCB -0.084 0.17 -10000 0 -0.4 147 147
PRKCE 0.013 0 -10000 0 -10000 0 0
JNK2/NFAT4 0.026 0.002 -10000 0 -10000 0 0
BAD/BCL-XL 0.018 0.011 -10000 0 -0.27 1 1
PRKCD 0.013 0 -10000 0 -10000 0 0
NUP214 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.013 0.002 -10000 0 -10000 0 0
PRKCA 0.013 0 -10000 0 -10000 0 0
PRKCG -0.25 0.36 -10000 0 -0.75 217 217
PRKCQ 0.006 0.051 -10000 0 -0.4 10 10
FKBP38/BCL2 0.003 0.064 -10000 0 -10000 0 0
EP300 0.013 0.002 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.013 0 -10000 0 -10000 0 0
NFATc/JNK1 0.051 0.026 -10000 0 -10000 0 0
CaM/Ca2+/FKBP38 0.018 0.01 -10000 0 -0.23 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 0.004 0.056 -10000 0 -10000 0 0
NFATc/ERK1 0.051 0.026 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.077 0.1 -10000 0 -0.46 11 11
NR4A1 0.045 0.085 -10000 0 -0.6 10 10
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 0.028 0.02 -10000 0 -10000 0 0
RCH1/ KPNB1 0.018 0.024 -10000 0 -0.57 1 1
YWHAQ 0.013 0 -10000 0 -10000 0 0
PRKACA 0.013 0.001 -10000 0 -10000 0 0
AKAP5 -0.008 0.09 -10000 0 -0.4 32 32
MEF2D 0.013 0.002 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.013 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.051 0.026 -10000 0 -10000 0 0
CREBBP 0.013 0.002 -10000 0 -10000 0 0
BCL2 -0.008 0.09 -10000 0 -0.4 32 32
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 0.031 0.017 -9999 0 -10000 0 0
DAPP1 -0.036 0.11 -9999 0 -0.39 23 23
Src family/SYK family/BLNK-LAT/BTK-ITK -0.049 0.14 -9999 0 -0.48 21 21
mol:DAG -0.007 0.079 -9999 0 -0.25 10 10
HRAS 0.013 0.016 -9999 0 -0.39 1 1
RAP1A 0.013 0.001 -9999 0 -10000 0 0
ARF5/GDP 0.007 0.094 -9999 0 -0.4 20 20
PLCG2 -0.019 0.11 -9999 0 -0.4 49 49
PLCG1 0.013 0 -9999 0 -10000 0 0
ARF5 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0.017 -9999 0 -10000 0 0
ARF1/GTP 0.031 0.018 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
YES1 0.012 0.016 -9999 0 -0.4 1 1
RAP1A/GTP 0.022 0.018 -9999 0 -10000 0 0
ADAP1 -0.001 0.02 -9999 0 -10000 0 0
ARAP3 0 0.017 -9999 0 -10000 0 0
INPPL1 0.013 0 -9999 0 -10000 0 0
PREX1 0.011 0.023 -9999 0 -0.4 2 2
ARHGEF6 0.004 0.058 -9999 0 -0.4 13 13
ARHGEF7 0.013 0 -9999 0 -10000 0 0
ARF1 0.013 0 -9999 0 -10000 0 0
NRAS 0.012 0.023 -9999 0 -0.39 2 2
FYN 0.013 0 -9999 0 -10000 0 0
ARF6 0.013 0 -9999 0 -10000 0 0
FGR 0.009 0.045 -9999 0 -0.47 5 5
mol:Ca2+ 0.002 0.045 -9999 0 -10000 0 0
mol:IP4 0 0 -9999 0 -10000 0 0
TIAM1 -0.028 0.12 -9999 0 -0.4 62 62
ZAP70 0.002 0.07 -9999 0 -0.45 14 14
mol:IP3 0 0.06 -9999 0 -10000 0 0
LYN 0.013 0 -9999 0 -10000 0 0
ARF1/GDP 0.007 0.094 -9999 0 -0.4 20 20
RhoA/GDP 0.028 0.045 -9999 0 -10000 0 0
PDK1/Src/Hsp90 0.026 0 -9999 0 -10000 0 0
BLNK 0.007 0.049 -9999 0 -0.4 9 9
actin cytoskeleton reorganization 0.031 0.066 -9999 0 -0.42 1 1
SRC 0.013 0 -9999 0 -10000 0 0
PLEKHA2 0.023 0.01 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
PTEN 0.008 0.022 -9999 0 -0.37 2 2
HSP90AA1 0.013 0 -9999 0 -10000 0 0
ARF6/GTP 0.031 0.017 -9999 0 -10000 0 0
RhoA/GTP 0.027 0.017 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.033 0.11 -9999 0 -0.44 9 9
BLK -0.14 0.2 -9999 0 -0.4 236 236
PDPK1 0.013 0 -9999 0 -10000 0 0
CYTH1 0 0.017 -9999 0 -10000 0 0
HCK 0.003 0.062 -9999 0 -0.4 15 15
CYTH3 0 0.017 -9999 0 -10000 0 0
CYTH2 0 0.017 -9999 0 -10000 0 0
KRAS 0.013 0.016 -9999 0 -0.39 1 1
GO:0030676 0 0 -9999 0 -10000 0 0
FOXO3 0.019 0.084 -9999 0 -0.39 25 25
SGK1 -0.017 0.083 -9999 0 -0.42 25 25
INPP5D 0.012 0.016 -9999 0 -0.4 1 1
mol:GDP -0.001 0.097 -9999 0 -0.42 20 20
SOS1 0.013 0 -9999 0 -10000 0 0
SYK 0.013 0 -9999 0 -10000 0 0
ARF6/GDP 0.027 0.045 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0.018 -9999 0 -10000 0 0
ARAP3/RAP1A/GTP 0.022 0.018 -9999 0 -10000 0 0
VAV1 -0.004 0.081 -9999 0 -0.4 26 26
mol:PI-3-4-P2 0.019 0.011 -9999 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.027 0.016 -9999 0 -10000 0 0
PLEKHA1 0.023 0.01 -9999 0 -10000 0 0
Rac1/GDP 0.007 0.094 -9999 0 -0.4 20 20
LAT 0.009 0.049 -9999 0 -0.57 4 4
Rac1/GTP -0.005 0.12 -9999 0 -0.5 21 21
ITK -0.008 0.036 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.015 0.1 -9999 0 -0.35 11 11
LCK 0.001 0.089 -9999 0 -0.68 10 10
BTK -0.019 0.053 -9999 0 -10000 0 0
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.031 0.018 -9999 0 -0.36 1 1
STMN1 0.023 0.012 -9999 0 -10000 0 0
Aurora B/RasGAP/Survivin 0.034 0.029 -9999 0 -0.47 2 2
Chromosomal passenger complex/Cul3 protein complex 0.007 0.068 -9999 0 -0.42 1 1
BIRC5 0.013 0.043 -9999 0 -0.74 2 2
DES -0.36 0.24 -9999 0 -0.52 427 427
Aurora C/Aurora B/INCENP 0.032 0.019 -9999 0 -10000 0 0
Aurora B/TACC1 0.022 0.014 -9999 0 -10000 0 0
Aurora B/PP2A 0.025 0.004 -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 -0.01 0.089 -9999 0 -0.49 3 3
KIF2C 0.026 0.006 -9999 0 -10000 0 0
PEBP1 0.014 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 0.025 0.004 -9999 0 -10000 0 0
SEPT1 0.008 0.043 -9999 0 -0.4 7 7
SMC2 0.012 0.016 -9999 0 -0.4 1 1
SMC4 0.011 0.023 -9999 0 -0.4 2 2
NSUN2/NPM1/Nucleolin 0.01 0.016 -9999 0 -10000 0 0
PSMA3 0.013 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0.001 -9999 0 -10000 0 0
H3F3B 0.018 0.002 -9999 0 -10000 0 0
AURKB 0.021 0.006 -9999 0 -10000 0 0
AURKC 0.009 0.033 -9999 0 -0.4 4 4
CDCA8 0.015 0.001 -9999 0 -10000 0 0
cytokinesis 0.012 0.026 -9999 0 -10000 0 0
Aurora B/Septin1 0.041 0.026 -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 -0.046 0.15 -9999 0 -0.41 87 87
BUB1 0.012 0 -9999 0 -10000 0 0
hSgo1/Aurora B/Survivin 0.032 0.039 -9999 0 -0.44 4 4
EVI5 0.014 0.001 -9999 0 -10000 0 0
RhoA/GTP 0.012 0.025 -9999 0 -0.33 1 1
SGOL1 0.01 0.043 -9999 0 -0.75 2 2
CENPA 0.03 0.009 -9999 0 -10000 0 0
NCAPG 0.012 0.001 -9999 0 -10000 0 0
Aurora B/HC8 Proteasome 0.025 0.004 -9999 0 -10000 0 0
NCAPD2 0.013 0 -9999 0 -10000 0 0
Aurora B/PP1-gamma 0.025 0.004 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
NCAPH 0.013 0 -9999 0 -10000 0 0
NPM1 0.006 0.009 -9999 0 -10000 0 0
RASA1 0.013 0.001 -9999 0 -10000 0 0
KLHL9 0.013 0 -9999 0 -10000 0 0
mitotic prometaphase 0.001 0.001 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.004 -9999 0 -10000 0 0
PPP1CC 0.013 0 -9999 0 -10000 0 0
Centraspindlin 0.048 0.02 -9999 0 -0.36 1 1
RhoA/GDP 0.009 0 -9999 0 -10000 0 0
NSUN2 0.006 0.009 -9999 0 -10000 0 0
MYLK -0.036 0.11 -9999 0 -0.26 118 118
KIF23 0.013 0.03 -9999 0 -0.74 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 0.006 0.009 -9999 0 -10000 0 0
Chromosomal passenger complex 0.038 0.011 -9999 0 -10000 0 0
Chromosomal passenger complex/EVI5 0.075 0.039 -9999 0 -0.39 2 2
TACC1 0.011 0.023 -9999 0 -0.4 2 2
PPP2R5D 0.013 0 -9999 0 -10000 0 0
CUL3 0.013 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.015 0.013 -10000 0 -10000 0 0
RAS family/GTP 0.016 0.074 -10000 0 -10000 0 0
NFATC4 0.015 0.068 -10000 0 -0.37 2 2
ERBB2IP 0.007 0.045 -10000 0 -0.39 8 8
HSP90 (dimer) 0.013 0 -10000 0 -10000 0 0
mammary gland morphogenesis 0.005 0.084 -10000 0 -0.5 2 2
JUN 0.032 0.07 -10000 0 -0.29 11 11
HRAS 0.012 0.016 -10000 0 -0.39 1 1
DOCK7 0.009 0.081 -10000 0 -0.48 2 2
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.006 0.091 -10000 0 -0.46 11 11
AKT1 0.01 0.002 -10000 0 -10000 0 0
BAD 0.015 0.01 -10000 0 -10000 0 0
MAPK10 0.007 0.063 -10000 0 -0.31 2 2
mol:GTP 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.006 0.09 -10000 0 -0.55 2 2
RAF1 0.024 0.08 -10000 0 -0.36 1 1
ErbB2/ErbB3/neuregulin 2 -0.025 0.098 -10000 0 -0.47 12 12
STAT3 0.019 0.005 -10000 0 -10000 0 0
cell migration 0.011 0.067 0.16 4 -0.27 2 6
mol:PI-3-4-5-P3 0 0.002 -10000 0 -10000 0 0
cell proliferation 0.009 0.21 -10000 0 -0.6 57 57
FOS 0.025 0.14 -10000 0 -0.4 28 28
NRAS 0.011 0.023 -10000 0 -0.39 2 2
mol:Ca2+ 0.005 0.084 -10000 0 -0.5 2 2
MAPK3 0.014 0.17 -10000 0 -0.47 56 56
MAPK1 0.015 0.16 -10000 0 -0.46 56 56
JAK2 0.008 0.082 -10000 0 -0.48 2 2
NF2 -0.001 0.003 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.002 0.078 -10000 0 -0.34 2 2
NRG1 -0.035 0.13 -10000 0 -0.4 73 73
GRB2/SOS1 0.019 0.001 -10000 0 -10000 0 0
MAPK8 0.009 0.087 -10000 0 -0.39 2 2
MAPK9 0.017 0.046 -10000 0 -10000 0 0
ERBB2 -0.006 0.086 0.33 8 -0.58 11 19
ERBB3 0.012 0.002 -10000 0 -10000 0 0
SHC1 0.013 0.001 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
apoptosis -0.011 0.014 -10000 0 -10000 0 0
STAT3 (dimer) 0.018 0.005 -10000 0 -10000 0 0
RNF41 0.019 0.012 -10000 0 -10000 0 0
FRAP1 0.008 0.002 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.018 0.049 -10000 0 -0.33 2 2
ErbB2/ErbB2/HSP90 (dimer) 0.003 0.072 0.23 4 -0.5 11 15
CHRNA1 0.001 0.2 -10000 0 -0.62 57 57
myelination 0.015 0.067 -10000 0 -0.36 2 2
PPP3CB 0.009 0.076 -10000 0 -0.44 2 2
KRAS 0.012 0.016 -10000 0 -0.39 1 1
RAC1-CDC42/GDP 0.011 0.07 -10000 0 -0.3 1 1
NRG2 -0.049 0.14 -10000 0 -0.4 89 89
mol:GDP -0.002 0.078 -10000 0 -0.34 2 2
SOS1 0.013 0.001 -10000 0 -10000 0 0
MAP2K2 0.026 0.088 -10000 0 -0.38 1 1
SRC 0.013 0 -10000 0 -10000 0 0
mol:cAMP 0 0.001 -10000 0 -10000 0 0
PTPN11 0.009 0.081 -10000 0 -0.48 2 2
MAP2K1 0.011 0.15 -10000 0 -0.55 18 18
heart morphogenesis 0.005 0.084 -10000 0 -0.5 2 2
RAS family/GDP 0.017 0.071 -10000 0 -10000 0 0
GRB2 0.013 0.001 -10000 0 -10000 0 0
PRKACA -0.002 0.005 -10000 0 -10000 0 0
CHRNE 0.014 0.033 -10000 0 -0.21 11 11
HSP90AA1 0.013 0 -10000 0 -10000 0 0
activation of caspase activity -0.01 0.002 -10000 0 -10000 0 0
nervous system development 0.005 0.084 -10000 0 -0.5 2 2
CDC42 0.011 0.023 -10000 0 -0.4 2 2
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.001 0.1 -9999 0 -0.37 40 40
PDGFB-D/PDGFRB/SLAP 0.009 0.068 -9999 0 -0.57 7 7
PDGFB-D/PDGFRB/APS/CBL 0.012 0.084 -9999 0 -0.49 17 17
AKT1 0.04 0.041 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.004 0.11 -9999 0 -0.39 40 40
PIK3CA 0.012 0.016 -9999 0 -0.4 1 1
FGR -0.006 0.059 -9999 0 -0.42 11 11
mol:Ca2+ 0.007 0.047 -9999 0 -0.33 5 5
MYC 0.012 0.081 -9999 0 -0.46 11 11
SHC1 0.013 0 -9999 0 -10000 0 0
HRAS/GDP 0.026 0.046 -9999 0 -0.4 7 7
LRP1/PDGFRB/PDGFB 0.019 0.056 -9999 0 -0.48 7 7
GRB10 0.013 0 -9999 0 -10000 0 0
PTPN11 0.013 0 -9999 0 -10000 0 0
GO:0007205 0.007 0.047 -9999 0 -0.34 5 5
PTEN 0.011 0.023 -9999 0 -0.4 2 2
GRB2 0.013 0 -9999 0 -10000 0 0
GRB7 -0.006 0.12 -9999 0 -0.75 15 15
PDGFB-D/PDGFRB/SHP2 0.012 0.062 -9999 0 -0.57 7 7
PDGFB-D/PDGFRB/GRB10 0.012 0.062 -9999 0 -0.57 7 7
cell cycle arrest 0.009 0.067 -9999 0 -0.56 7 7
HRAS 0.012 0.016 -9999 0 -0.4 1 1
HIF1A 0.043 0.037 -9999 0 -10000 0 0
GAB1 0 0.064 -9999 0 -0.4 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.004 0.066 -9999 0 -0.41 5 5
PDGFB-D/PDGFRB 0.02 0.056 -9999 0 -0.5 7 7
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.012 0.062 -9999 0 -0.57 7 7
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.017 0.097 -9999 0 -0.44 16 16
positive regulation of MAPKKK cascade 0.012 0.061 -9999 0 -0.56 7 7
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:IP3 0.007 0.047 -9999 0 -0.34 5 5
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 0.11 -9999 0 -0.57 22 22
SHB 0.009 0.053 -9999 0 -0.75 3 3
BLK -0.18 0.23 -9999 0 -0.47 241 241
PTPN2 0.013 0.002 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.012 0.062 -9999 0 -0.57 7 7
BCAR1 0.012 0.016 -9999 0 -0.4 1 1
VAV2 0.002 0.068 -9999 0 -0.39 5 5
CBL 0.013 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.012 0.062 -9999 0 -0.57 7 7
LCK -0.007 0.058 -9999 0 -0.41 9 9
PDGFRB 0.004 0.081 -9999 0 -0.75 7 7
ACP1 0.013 0 -9999 0 -10000 0 0
HCK -0.007 0.085 -9999 0 -0.44 22 22
ABL1 -0.006 0.063 -9999 0 -0.41 5 5
PDGFB-D/PDGFRB/CBL -0.003 0.063 -9999 0 -0.37 5 5
PTPN1 0.013 0.002 -9999 0 -10000 0 0
SNX15 0.013 0 -9999 0 -10000 0 0
STAT3 0.013 0 -9999 0 -10000 0 0
STAT1 0.011 0.031 -9999 0 -0.75 1 1
cell proliferation 0.013 0.076 -9999 0 -0.42 11 11
SLA 0.009 0.04 -9999 0 -0.4 6 6
actin cytoskeleton reorganization 0.034 0.054 -9999 0 -0.38 8 8
SRC -0.002 0.043 -9999 0 -0.39 7 7
PI3K -0.005 0.039 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC 0.007 0.095 -9999 0 -0.49 22 22
SH2B2 0 0.096 -9999 0 -0.75 10 10
PLCgamma1/SPHK1 -0.005 0.11 -9999 0 -0.4 40 40
LYN -0.001 0.043 -9999 0 -0.39 7 7
LRP1 0.011 0.023 -9999 0 -0.4 2 2
SOS1 0.013 0 -9999 0 -10000 0 0
STAT5B 0.013 0 -9999 0 -10000 0 0
STAT5A 0.013 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas 0.033 0.047 -9999 0 -0.39 7 7
SPHK1 -0.036 0.19 -9999 0 -0.75 40 40
EDG1 0 0.002 -9999 0 -10000 0 0
mol:DAG 0.007 0.047 -9999 0 -0.34 5 5
PLCG1 0.007 0.048 -9999 0 -0.35 5 5
NHERF/PDGFRB 0.02 0.055 -9999 0 -0.48 7 7
YES1 -0.003 0.047 -9999 0 -0.4 8 8
cell migration 0.019 0.054 -9999 0 -0.48 7 7
SHC/Grb2/SOS1 0.034 0.046 -9999 0 -0.39 7 7
SLC9A3R2 0.012 0.016 -9999 0 -0.4 1 1
SLC9A3R1 0.013 0 -9999 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.026 0.052 -9999 0 -0.44 7 7
FYN -0.001 0.043 -9999 0 -0.39 7 7
DOK1 0.022 0.049 -9999 0 -0.44 7 7
HRAS/GTP 0.009 0.011 -9999 0 -0.28 1 1
PDGFB 0.013 0 -9999 0 -10000 0 0
RAC1 0.012 0.072 -9999 0 -0.39 2 2
PRKCD 0.021 0.05 -9999 0 -0.45 7 7
FER 0.02 0.055 -9999 0 -0.45 8 8
MAPKKK cascade -0.004 0.041 -9999 0 -0.39 7 7
RASA1 0.021 0.05 -9999 0 -0.45 7 7
NCK1 0.013 0 -9999 0 -10000 0 0
NCK2 0.013 0 -9999 0 -10000 0 0
p62DOK/Csk 0.028 0.046 -9999 0 -0.4 7 7
PDGFB-D/PDGFRB/SHB 0.009 0.074 -9999 0 -0.57 10 10
chemotaxis -0.005 0.062 -9999 0 -0.36 7 7
STAT1-3-5/STAT1-3-5 -0.004 0.043 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.003 0.062 -9999 0 -0.58 7 7
PTPRJ 0.013 0 -9999 0 -10000 0 0
Rapid glucocorticoid signaling

Figure S87.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S87.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.002 0.066 -10000 0 -0.37 6 6
MAPK9 0.007 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.002 0.033 -10000 0 -0.58 2 2
GNB1/GNG2 0.007 0.048 -10000 0 -10000 0 0
GNB1 0.013 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 -0.004 0.05 -10000 0 -0.21 35 35
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.003 0.013 0.058 35 -10000 0 35
GNAL -0.01 0.094 -10000 0 -0.4 35 35
GNG2 -0.004 0.081 -10000 0 -0.4 26 26
CRH -0.002 0.043 -10000 0 -0.75 2 2
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.007 0 -10000 0 -10000 0 0
MAPK11 0.006 0.019 -10000 0 -0.33 2 2
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.012 0 -9999 0 -10000 0 0
HDAC2 0.012 0 -9999 0 -10000 0 0
GNB1/GNG2 0.016 0.049 -9999 0 -10000 0 0
forebrain development 0.012 0.072 -9999 0 -0.48 5 5
GNAO1 -0.14 0.2 -9999 0 -0.39 234 234
SMO/beta Arrestin2 0.021 0.004 -9999 0 -10000 0 0
SMO 0.014 0.002 -9999 0 -10000 0 0
ARRB2 0.013 0.002 -9999 0 -10000 0 0
GLI3/SPOP 0.018 0.072 -9999 0 -10000 0 0
mol:GTP 0.001 0.001 -9999 0 -10000 0 0
GSK3B 0.013 0 -9999 0 -10000 0 0
GNAI2 0.013 0.001 -9999 0 -10000 0 0
SIN3/HDAC complex 0.032 0.002 -9999 0 -10000 0 0
GNAI1 -0.001 0.075 -9999 0 -0.4 22 22
XPO1 0.015 0.003 -9999 0 -10000 0 0
GLI1/Su(fu) 0.023 0.06 -9999 0 -0.46 3 3
SAP30 0.012 0 -9999 0 -10000 0 0
mol:GDP 0.014 0.002 -9999 0 -10000 0 0
MIM/GLI2A 0.014 0.042 -9999 0 -0.39 6 6
IFT88 0.013 0.001 -9999 0 -10000 0 0
GNAI3 0.013 0.001 -9999 0 -10000 0 0
GLI2 0.037 0.016 -9999 0 -10000 0 0
GLI3 0.012 0.075 -9999 0 -10000 0 0
CSNK1D 0.013 0 -9999 0 -10000 0 0
CSNK1E 0.013 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 -0.004 0.081 -9999 0 -0.4 26 26
Gi family/GTP -0.056 0.12 -9999 0 -0.36 26 26
SIN3B 0.012 0 -9999 0 -10000 0 0
SIN3A 0.012 0 -9999 0 -10000 0 0
GLI3/Su(fu) 0.035 0.055 -9999 0 -10000 0 0
GLI2/Su(fu) 0.051 0.016 -9999 0 -10000 0 0
FOXA2 -0.016 0.12 -9999 0 -0.65 22 22
neural tube patterning 0.012 0.072 -9999 0 -0.48 5 5
SPOP 0.013 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.03 0.003 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
CSNK1G2 0.012 0.016 -9999 0 -0.4 1 1
CSNK1G3 0.013 0 -9999 0 -10000 0 0
MTSS1 0.014 0.042 -9999 0 -0.39 6 6
embryonic limb morphogenesis 0.012 0.072 -9999 0 -0.48 5 5
SUFU 0.026 0.005 -9999 0 -10000 0 0
LGALS3 0.012 0.016 -9999 0 -0.4 1 1
catabolic process 0.041 0.066 -9999 0 -10000 0 0
GLI3A/CBP 0.019 0.022 -9999 0 -0.3 1 1
KIF3A 0.013 0.001 -9999 0 -10000 0 0
GLI1 0.012 0.074 -9999 0 -0.5 5 5
RAB23 0.011 0.023 -9999 0 -0.4 2 2
CSNK1A1 0.013 0 -9999 0 -10000 0 0
IFT172 0.013 0 -9999 0 -10000 0 0
RBBP7 0.012 0 -9999 0 -10000 0 0
Su(fu)/Galectin3 0.03 0.009 -9999 0 -10000 0 0
GNAZ 0.008 0.046 -9999 0 -0.39 8 8
RBBP4 0.012 0 -9999 0 -10000 0 0
CSNK1G1 0.012 0.016 -9999 0 -0.4 1 1
PIAS1 0.013 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GLI2/SPOP 0.041 0.015 -9999 0 -10000 0 0
STK36 0.015 0.003 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.051 0.13 -9999 0 -0.39 37 37
PTCH1 0.017 0.088 -9999 0 -0.92 3 3
MIM/GLI1 0.019 0.098 -9999 0 -0.51 10 10
CREBBP 0.019 0.022 -9999 0 -0.3 1 1
Su(fu)/SIN3/HDAC complex 0.042 0.002 -9999 0 -10000 0 0
Ceramide signaling pathway

Figure S89.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S89.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.019 0.012 -10000 0 -10000 0 0
MAP4K4 0.036 0.029 -10000 0 -10000 0 0
BAG4 0.012 0.001 -10000 0 -10000 0 0
PKC zeta/ceramide -0.012 0.03 -10000 0 -10000 0 0
NFKBIA 0.013 0 -10000 0 -10000 0 0
BIRC3 0.005 0.057 -10000 0 -0.43 10 10
BAX -0.003 0.014 -10000 0 -10000 0 0
RIPK1 0.013 0 -10000 0 -10000 0 0
AKT1 0.017 0.006 -10000 0 -10000 0 0
BAD -0.015 0.028 -10000 0 -10000 0 0
SMPD1 0.021 0.028 -10000 0 -0.23 5 5
RB1 -0.014 0.029 -10000 0 -10000 0 0
FADD/Caspase 8 0.044 0.028 -10000 0 -10000 0 0
MAP2K4 -0.009 0.031 -10000 0 -10000 0 0
NSMAF 0.013 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.008 0.027 -10000 0 -10000 0 0
EGF -0.086 0.2 -10000 0 -0.45 131 131
mol:ceramide -0.022 0.031 -10000 0 -10000 0 0
MADD 0.013 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 0.013 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.014 0.028 -10000 0 -10000 0 0
cell proliferation -0.025 0.074 -10000 0 -10000 0 0
BID 0.024 0.028 -10000 0 -0.31 1 1
MAP3K1 -0.015 0.03 -10000 0 -0.2 1 1
EIF2A -0.003 0.028 -10000 0 -10000 0 0
TRADD 0.013 0 -10000 0 -10000 0 0
CRADD 0.013 0 -10000 0 -10000 0 0
MAPK3 0.001 0.026 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.001 0.026 -10000 0 -10000 0 0
Cathepsin D/ceramide -0.012 0.029 -10000 0 -10000 0 0
FADD 0.036 0.029 -10000 0 -10000 0 0
KSR1 -0.014 0.029 -10000 0 -10000 0 0
MAPK8 -0.004 0.028 -10000 0 -10000 0 0
PRKRA -0.014 0.029 -10000 0 -10000 0 0
PDGFA 0.013 0 -10000 0 -10000 0 0
TRAF2 0.012 0.016 -10000 0 -0.4 1 1
IGF1 -0.08 0.17 -10000 0 -0.4 142 142
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.022 0.031 -10000 0 -10000 0 0
CTSD 0.012 0.016 -10000 0 -0.4 1 1
regulation of nitric oxide biosynthetic process 0.019 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.026 0.079 -10000 0 -10000 0 0
PRKCD 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.013 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 0.019 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.013 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.032 0.03 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.024 0.022 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.019 0.011 -10000 0 -10000 0 0
MAP2K1 -0.002 0.026 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
CYCS -0.001 0.036 0.14 26 -10000 0 26
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
NFKB1 0.013 0 -10000 0 -10000 0 0
TNFR1A/BAG4 0.019 0.001 -10000 0 -10000 0 0
EIF2AK2 -0.009 0.029 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN 0.024 0.022 -10000 0 -10000 0 0
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.036 0.019 -10000 0 -10000 0 0
MAP2K2 -0.002 0.026 -10000 0 -10000 0 0
SMPD3 0.019 0.049 -10000 0 -0.28 14 14
TNF 0.009 0.036 -10000 0 -0.4 5 5
PKC zeta/PAR4 0.019 0 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.034 0.082 0.19 128 -10000 0 128
NF kappa B1/RelA/I kappa B alpha 0.037 0 -10000 0 -10000 0 0
AIFM1 0 0.037 0.14 27 -10000 0 27
BCL2 -0.008 0.09 -10000 0 -0.4 32 32
FoxO family signaling

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
G6PC -0.056 0.32 -9999 0 -1.2 44 44
PLK1 0.049 0.13 -9999 0 -0.77 4 4
CDKN1B 0.083 0.077 -9999 0 -10000 0 0
FOXO3 0.046 0.14 -9999 0 -0.57 8 8
KAT2B 0.004 0.084 -9999 0 -0.39 27 27
FOXO1/SIRT1 -0.013 0.1 -9999 0 -0.37 44 44
CAT 0.05 0.12 -9999 0 -0.7 1 1
CTNNB1 0.012 0 -9999 0 -10000 0 0
AKT1 0.02 0.016 -9999 0 -10000 0 0
FOXO1 0.003 0.11 -9999 0 -0.4 44 44
MAPK10 0.007 0.069 -9999 0 -10000 0 0
mol:GTP 0.002 0 -9999 0 -10000 0 0
FOXO4 0.069 0.05 -9999 0 -10000 0 0
response to oxidative stress 0.009 0.017 -9999 0 -10000 0 0
FOXO3A/SIRT1 0.035 0.11 -9999 0 -0.54 8 8
XPO1 0.013 0 -9999 0 -10000 0 0
EP300 0.01 0.015 -9999 0 -10000 0 0
BCL2L11 0.026 0.026 -9999 0 -10000 0 0
FOXO1/SKP2 0.008 0.1 -9999 0 -0.37 44 44
mol:GDP 0.008 0.017 -9999 0 -10000 0 0
RAN 0.014 0 -9999 0 -10000 0 0
GADD45A 0.079 0.058 -9999 0 -10000 0 0
YWHAQ 0.013 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.056 0.031 -9999 0 -10000 0 0
MST1 -0.099 0.28 -9999 0 -0.74 99 99
CSNK1D 0.013 0 -9999 0 -10000 0 0
CSNK1E 0.013 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.049 0.015 -9999 0 -10000 0 0
YWHAB 0.013 0 -9999 0 -10000 0 0
MAPK8 0.033 0.007 -9999 0 -10000 0 0
MAPK9 0.033 0.007 -9999 0 -10000 0 0
YWHAG 0.013 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
YWHAZ 0.013 0 -9999 0 -10000 0 0
SIRT1 0.013 0.014 -9999 0 -10000 0 0
SOD2 0.084 0.087 -9999 0 -10000 0 0
RBL2 0.064 0.095 -9999 0 -10000 0 0
RAL/GDP 0.028 0.011 -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 0.012 0.016 -9999 0 -0.4 1 1
RAL/GTP 0.034 0.01 -9999 0 -10000 0 0
CSNK1G1 0.012 0.016 -9999 0 -0.4 1 1
FASLG -0.041 0.3 -9999 0 -1.3 34 34
SKP2 0.013 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 0.05 0.12 -9999 0 -0.7 1 1
FOXO1-3a-4/beta catenin 0.091 0.093 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.008 0.1 -9999 0 -0.37 44 44
CSNK1A1 0.013 0 -9999 0 -10000 0 0
SGK1 0.006 0.081 -9999 0 -0.39 25 25
CSNK1G3 0.013 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.023 0 -9999 0 -10000 0 0
ZFAND5 0.071 0.045 -9999 0 -10000 0 0
SFN 0.011 0.023 -9999 0 -0.4 2 2
CDK2 0.007 0.023 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.053 0.029 -9999 0 -10000 0 0
CREBBP 0.007 0.023 -9999 0 -10000 0 0
FBXO32 0.049 0.13 -9999 0 -1.4 1 1
BCL6 0.064 0.095 -9999 0 -10000 0 0
RALB 0.014 0 -9999 0 -10000 0 0
RALA 0.014 0 -9999 0 -10000 0 0
YWHAH 0.013 0 -9999 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.017 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.013 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.01 0.033 -9999 0 -0.4 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.011 0.028 -9999 0 -0.4 3 3
RAC1-CDC42/GTP/PAK family 0.021 0.011 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.012 0.016 -9999 0 -0.4 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 0.013 0 -9999 0 -10000 0 0
FYN 0.013 0 -9999 0 -10000 0 0
MAP3K12 0.013 0 -9999 0 -10000 0 0
FGR 0.009 0.045 -9999 0 -0.47 5 5
p38 alpha/TAB1 -0.032 0.046 -9999 0 -0.3 2 2
PRKG1 -0.003 0.078 -9999 0 -0.4 24 24
DUSP8 0.011 0.023 -9999 0 -0.4 2 2
PGK/cGMP/p38 alpha -0.035 0.056 -9999 0 -0.31 7 7
apoptosis -0.031 0.044 -9999 0 -0.28 2 2
RAL/GTP 0.017 0 -9999 0 -10000 0 0
LYN 0.013 0 -9999 0 -10000 0 0
DUSP1 0.011 0.028 -9999 0 -0.4 3 3
PAK1 0.013 0 -9999 0 -10000 0 0
SRC 0.013 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.032 0.009 -9999 0 -10000 0 0
TRAF6 0.013 0 -9999 0 -10000 0 0
RAC1 0.013 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 0.012 0.016 -9999 0 -0.4 1 1
RAC1-CDC42/GTP 0.016 0.014 -9999 0 -10000 0 0
MAPK11 -0.017 0.092 -9999 0 -0.33 9 9
BLK -0.14 0.2 -9999 0 -0.4 236 236
HCK 0.003 0.062 -9999 0 -0.4 15 15
MAP2K3 0.013 0 -9999 0 -10000 0 0
DUSP16 0.013 0 -9999 0 -10000 0 0
DUSP10 0.008 0.061 -9999 0 -0.75 4 4
TRAF6/MEKK3 0.016 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 -0.004 0.072 -9999 0 -0.32 2 2
positive regulation of innate immune response -0.012 0.098 -9999 0 -0.35 9 9
LCK 0.001 0.089 -9999 0 -0.68 10 10
p38alpha-beta/MKP7 -0.006 0.096 -9999 0 -0.44 2 2
p38alpha-beta/MKP5 -0.009 0.1 -9999 0 -0.45 4 4
PGK/cGMP -0.002 0.055 -9999 0 -0.28 24 24
PAK2 0.013 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.007 0.097 -9999 0 -0.44 2 2
CDC42 0.011 0.023 -9999 0 -0.4 2 2
RALB 0.013 0 -9999 0 -10000 0 0
RALA 0.013 0 -9999 0 -10000 0 0
PAK3 0.008 0.006 -9999 0 -10000 0 0
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.003 0.062 -10000 0 -0.4 15 15
HRAS 0.012 0.016 -10000 0 -0.4 1 1
EGFR 0.011 0.023 -10000 0 -0.4 2 2
AKT 0.029 0.038 -10000 0 -0.34 2 2
FOXO3 0.013 0 -10000 0 -10000 0 0
AKT1 0.013 0 -10000 0 -10000 0 0
FOXO1 0.012 0.016 -10000 0 -0.4 1 1
AKT3 0.007 0.049 -10000 0 -0.4 9 9
FOXO4 0.013 0 -10000 0 -10000 0 0
MET 0.005 0.075 -10000 0 -0.75 6 6
PIK3CA 0.012 0.016 -10000 0 -0.4 1 1
PIK3CB 0.011 0.031 -10000 0 -0.75 1 1
NRAS 0.011 0.023 -10000 0 -0.4 2 2
PIK3CG -0.053 0.15 -10000 0 -0.4 100 100
PIK3R3 0.013 0 -10000 0 -10000 0 0
PIK3R2 0.013 0 -10000 0 -10000 0 0
NF1 0.013 0 -10000 0 -10000 0 0
RAS 0.015 0.036 -10000 0 -0.26 2 2
ERBB2 -0.001 0.1 -10000 0 -0.75 11 11
proliferation/survival/translation -0.018 0.041 0.2 9 -10000 0 9
PI3K 0.018 0.043 -10000 0 -0.21 13 13
PIK3R1 0.013 0 -10000 0 -10000 0 0
KRAS 0.012 0.016 -10000 0 -0.4 1 1
FOXO 0.039 0.019 -10000 0 -10000 0 0
AKT2 0.013 0 -10000 0 -10000 0 0
PTEN 0.011 0.023 -10000 0 -0.4 2 2
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.044 0.085 -9999 0 -0.53 1 1
CRKL 0.028 0.051 -9999 0 -0.36 8 8
mol:DAG 0.033 0.052 -9999 0 -0.44 1 1
HRAS 0.045 0.045 -9999 0 -10000 0 0
MAPK8 0.022 0.051 -9999 0 -0.42 8 8
RAP1A 0.028 0.051 -9999 0 -0.36 8 8
GAB1 0.028 0.051 -9999 0 -0.36 8 8
MAPK14 0.022 0.051 -9999 0 -0.42 8 8
EPO 0.001 0.08 -9999 0 -0.75 7 7
PLCG1 0.033 0.052 -9999 0 -0.45 1 1
EPOR/TRPC2/IP3 Receptors 0.013 0.031 -9999 0 -0.74 1 1
RAPGEF1 0.012 0.016 -9999 0 -0.4 1 1
EPO/EPOR (dimer)/SOCS3 0.017 0.064 -9999 0 -0.48 10 10
GAB1/SHC/GRB2/SOS1 0.012 0.046 -9999 0 -0.4 1 1
EPO/EPOR (dimer) 0.011 0.066 -9999 0 -0.57 8 8
IRS2 0.028 0.051 -9999 0 -0.36 8 8
STAT1 0.036 0.07 -9999 0 -0.54 1 1
STAT5B 0.035 0.061 -9999 0 -0.5 1 1
cell proliferation 0.027 0.048 -9999 0 -0.39 8 8
GAB1/SHIP/PIK3R1/SHP2/SHC -0.006 0.035 -9999 0 -10000 0 0
TEC 0.028 0.054 -9999 0 -0.36 9 9
SOCS3 0.01 0.043 -9999 0 -0.75 2 2
STAT1 (dimer) 0.036 0.069 -9999 0 -0.53 1 1
JAK2 0.011 0.029 -9999 0 -0.4 3 3
PIK3R1 0.013 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.038 0.057 -9999 0 -0.38 8 8
EPO/EPOR 0.011 0.066 -9999 0 -0.57 8 8
LYN 0.013 0.004 -9999 0 -10000 0 0
TEC/VAV2 0.033 0.058 -9999 0 -0.41 2 2
elevation of cytosolic calcium ion concentration 0.013 0.031 -9999 0 -0.74 1 1
SHC1 0.013 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.024 0.058 -9999 0 -0.47 8 8
mol:IP3 0.033 0.052 -9999 0 -0.44 1 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.039 0.049 -9999 0 -0.41 1 1
SH2B3 0.013 0.006 -9999 0 -10000 0 0
NFKB1 0.022 0.051 -9999 0 -0.42 8 8
EPO/EPOR (dimer)/JAK2/SOCS3 -0.004 0.033 -9999 0 -0.25 7 7
PTPN6 0.023 0.053 -9999 0 -0.38 8 8
TEC/VAV2/GRB2 0.038 0.056 -9999 0 -0.43 1 1
EPOR 0.013 0.031 -9999 0 -0.74 1 1
INPP5D 0.012 0.016 -9999 0 -0.4 1 1
mol:GDP -0.007 0.038 -9999 0 -0.4 1 1
SOS1 0.013 0 -9999 0 -10000 0 0
PLCG2 -0.019 0.11 -9999 0 -0.4 49 49
CRKL/CBL/C3G 0.041 0.05 -9999 0 -0.42 1 1
VAV2 0.026 0.056 -9999 0 -0.36 8 8
CBL 0.028 0.051 -9999 0 -0.36 8 8
SHC/Grb2/SOS1 -0.007 0.04 -9999 0 -0.42 1 1
STAT5A 0.035 0.061 -9999 0 -0.5 1 1
GRB2 0.013 0 -9999 0 -10000 0 0
STAT5 (dimer) 0.045 0.083 -9999 0 -0.62 1 1
LYN/PLCgamma2 -0.003 0.078 -9999 0 -0.27 49 49
PTPN11 0.013 0 -9999 0 -10000 0 0
BTK 0.006 0.083 -9999 0 -0.36 10 10
BCL2 0.019 0.19 -9999 0 -0.78 32 32
IGF1 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
NCK2 0.013 0 -9999 0 -10000 0 0
PTK2 0.013 0 -9999 0 -10000 0 0
CRKL -0.024 0.086 -9999 0 -10000 0 0
GRB2/SOS1/SHC 0.026 0 -9999 0 -10000 0 0
HRAS 0.012 0.016 -9999 0 -0.4 1 1
IRS1/Crk -0.024 0.087 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/PTP1B -0.028 0.096 -9999 0 -10000 0 0
AKT1 -0.005 0.075 -9999 0 -10000 0 0
BAD 0 0.072 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.024 0.086 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.024 0.087 -9999 0 -10000 0 0
RAF1 0.006 0.071 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.014 0.084 -9999 0 -10000 0 0
YWHAZ 0.013 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.033 0.095 -9999 0 -10000 0 0
PIK3CA 0.012 0.016 -9999 0 -0.4 1 1
RPS6KB1 -0.005 0.076 -9999 0 -10000 0 0
GNB2L1 0.013 0 -9999 0 -10000 0 0
positive regulation of MAPKKK cascade 0.003 0.064 -9999 0 -10000 0 0
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
cell adhesion 0 0 -9999 0 -10000 0 0
GRB2/SOS1 0.019 0 -9999 0 -10000 0 0
HRAS/GTP -0.033 0.06 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.005 0.077 -9999 0 -10000 0 0
IGF-1R heterotetramer 0 0.024 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.022 0.088 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.008 0.08 -9999 0 -10000 0 0
IGF1R 0 0.024 -9999 0 -10000 0 0
IGF1 -0.082 0.18 -9999 0 -0.41 142 142
IRS2/Crk -0.016 0.082 -9999 0 -10000 0 0
PI3K -0.014 0.085 -9999 0 -0.36 1 1
apoptosis -0.007 0.066 -9999 0 -10000 0 0
HRAS/GDP 0.009 0.011 -9999 0 -0.28 1 1
PRKCD -0.037 0.13 -9999 0 -10000 0 0
RAF1/14-3-3 E 0.012 0.065 -9999 0 -10000 0 0
BAD/14-3-3 0.007 0.069 -9999 0 -10000 0 0
PRKCZ -0.005 0.075 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin/FAK1 -0.026 0.047 -9999 0 -10000 0 0
PTPN1 0.013 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.045 0.14 -9999 0 -0.3 142 142
BCAR1 0.012 0.016 -9999 0 -0.4 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.014 0.084 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
SOS1 0.013 0 -9999 0 -10000 0 0
IRS1/NCK2 -0.023 0.087 -9999 0 -10000 0 0
GRB10 0.013 0 -9999 0 -10000 0 0
PTPN11 -0.024 0.086 -9999 0 -10000 0 0
IRS1 -0.034 0.094 -9999 0 -10000 0 0
IRS2 -0.024 0.086 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.051 0.13 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
PDPK1 -0.011 0.079 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
PRKD1 -0.04 0.14 -9999 0 -0.46 8 8
SHC1 0.013 0 -9999 0 -10000 0 0
VEGFR1 specific signals

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
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 0.018 0.083 -9999 0 -0.44 20 20
VEGFR1 homodimer/NRP1/VEGFR 121 0.025 0.027 -9999 0 -0.45 2 2
CaM/Ca2+ 0.024 0.079 -9999 0 -0.41 20 20
HIF1A 0.02 0 -9999 0 -10000 0 0
GAB1 0.013 0 -9999 0 -10000 0 0
AKT1 0.035 0.068 -9999 0 -10000 0 0
PLCG1 0.018 0.083 -9999 0 -0.44 20 20
NOS3 0.036 0.072 -9999 0 -10000 0 0
CBL 0.013 0 -9999 0 -10000 0 0
mol:NO 0.036 0.07 -9999 0 -10000 0 0
FLT1 0.026 0 -9999 0 -10000 0 0
PGF -0.012 0.14 -9999 0 -0.75 20 20
VEGFR1 homodimer/NRP2/VEGFR121 0.032 0.031 -9999 0 -0.44 2 2
CALM1 0.013 0 -9999 0 -10000 0 0
PIK3CA 0.012 0.016 -9999 0 -0.4 1 1
eNOS/Hsp90 0.042 0.069 -9999 0 -10000 0 0
endothelial cell proliferation -0.011 0.098 -9999 0 -0.5 1 1
mol:Ca2+ 0.018 0.082 -9999 0 -0.43 20 20
MAPK3 0.026 0.074 -9999 0 -10000 0 0
MAPK1 0.026 0.074 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
PLGF homodimer -0.012 0.13 -9999 0 -0.75 20 20
PRKACA 0.013 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 0.004 0.058 -9999 0 -0.4 13 13
VEGFA homodimer 0.01 0.043 -9999 0 -0.75 2 2
VEGFR1 homodimer/VEGFA homodimer 0.027 0.029 -9999 0 -0.49 2 2
platelet activating factor biosynthetic process 0.03 0.072 -9999 0 -10000 0 0
PI3K 0.026 0.08 -9999 0 -0.41 20 20
PRKCA 0.022 0.077 -9999 0 -0.4 20 20
PRKCB -0.026 0.11 -9999 0 -0.41 20 20
VEGFR1 homodimer/PLGF homodimer 0.012 0.091 -9999 0 -0.49 20 20
VEGFA 0.01 0.043 -9999 0 -0.75 2 2
VEGFB 0.013 0 -9999 0 -10000 0 0
mol:IP3 0.018 0.083 -9999 0 -0.44 20 20
RASA1 0.033 0 -9999 0 -10000 0 0
NRP2 0.011 0.028 -9999 0 -0.4 3 3
VEGFR1 homodimer 0.026 0 -9999 0 -10000 0 0
VEGFB homodimer 0.013 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.041 0.069 -9999 0 -10000 0 0
PTPN11 0.013 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.025 0.079 -9999 0 -0.41 20 20
mol:L-citrulline 0.036 0.07 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.034 0.044 -9999 0 -0.41 2 2
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.033 0.027 -9999 0 -0.44 2 2
CD2AP 0 0.07 -9999 0 -0.4 19 19
PI3K/GAB1 0.031 0.076 -9999 0 -10000 0 0
PDPK1 0.027 0.075 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.033 0.027 -9999 0 -0.44 2 2
mol:NADP 0.036 0.07 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.032 0.043 -9999 0 -0.41 2 2
VEGFR1 homodimer/NRP2 0.028 0.017 -9999 0 -10000 0 0
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 -0.009 0.036 0.39 5 -10000 0 5
PI3K Class IB/PDE3B 0.009 0.036 -10000 0 -0.39 5 5
PDE3B 0.009 0.036 -10000 0 -0.4 5 5
FOXM1 transcription factor network

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
NFATC3 0.13 0.26 -9999 0 -0.99 2 2
PLK1 0.052 0.06 -9999 0 -0.55 2 2
BIRC5 0.052 0.057 -9999 0 -0.56 2 2
HSPA1B 0.1 0.29 -9999 0 -0.98 5 5
MAP2K1 0.035 0.03 -9999 0 -10000 0 0
BRCA2 0.12 0.27 -9999 0 -1.1 1 1
FOXM1 0.12 0.28 -9999 0 -1.2 2 2
XRCC1 0.13 0.26 -9999 0 -1.1 1 1
FOXM1B/p19 -0.12 0.21 -9999 0 -1 9 9
Cyclin D1/CDK4 0.12 0.25 -9999 0 -0.92 3 3
CDC2 0.12 0.27 -9999 0 -1 2 2
TGFA 0.12 0.25 -9999 0 -1 2 2
SKP2 0.13 0.26 -9999 0 -0.99 2 2
CCNE1 0.011 0.069 -9999 0 -0.75 5 5
CKS1B 0.12 0.26 -9999 0 -0.99 2 2
RB1 -0.024 0.071 -9999 0 -10000 0 0
FOXM1C/SP1 0.12 0.26 -9999 0 -1.1 2 2
AURKB 0.054 0.045 -9999 0 -10000 0 0
CENPF 0.13 0.26 -9999 0 -0.99 2 2
CDK4 0.02 0.033 -9999 0 -0.75 1 1
MYC 0.12 0.25 -9999 0 -0.92 1 1
CHEK2 0.035 0.03 -9999 0 -10000 0 0
ONECUT1 0.12 0.26 -9999 0 -1 2 2
CDKN2A -0.14 0.3 -9999 0 -0.76 120 120
LAMA4 0.13 0.26 -9999 0 -0.99 2 2
FOXM1B/HNF6 0.12 0.27 -9999 0 -1.2 2 2
FOS 0.11 0.29 -9999 0 -1 9 9
SP1 0.013 0.005 -9999 0 -10000 0 0
CDC25B 0.11 0.29 -9999 0 -1.1 3 3
response to radiation 0.02 0.027 -9999 0 -10000 0 0
CENPB 0.13 0.26 -9999 0 -0.99 2 2
CENPA 0.13 0.26 -9999 0 -0.99 2 2
NEK2 0.13 0.26 -9999 0 -0.99 2 2
HIST1H2BA 0.12 0.26 -9999 0 -0.99 2 2
CCNA2 0.017 0.007 -9999 0 -10000 0 0
EP300 0.013 0 -9999 0 -10000 0 0
CCNB1/CDK1 0.12 0.27 -9999 0 -1.1 2 2
CCNB2 0.13 0.26 -9999 0 -0.99 2 2
CCNB1 0.13 0.27 -9999 0 -1 2 2
ETV5 0.12 0.26 -9999 0 -1.1 1 1
ESR1 0.058 0.41 -9999 0 -1.2 34 34
CCND1 0.12 0.26 -9999 0 -0.95 3 3
GSK3A 0.033 0.026 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.043 0.057 -9999 0 -0.48 5 5
CDK2 0.017 0.007 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.023 0.031 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.056 0.16 -9999 0 -1.1 2 2
GAS1 0.012 0.48 -9999 0 -1.1 50 50
MMP2 0.12 0.27 -9999 0 -1.2 3 3
RB1/FOXM1C 0.13 0.26 -9999 0 -1 2 2
CREBBP 0.013 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.023 0.045 -9999 0 -10000 0 0
HDAC3 0.013 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 0.015 0.012 -9999 0 -10000 0 0
GATA2/HDAC5 0.013 0.039 -9999 0 -10000 0 0
HDAC5/BCL6/BCoR 0.025 0.01 -9999 0 -10000 0 0
HDAC9 -0.046 0.14 -9999 0 -0.4 90 90
Glucocorticoid receptor/Hsp90/HDAC6 0.008 0.063 -9999 0 -10000 0 0
HDAC4/ANKRA2 0.019 0 -9999 0 -10000 0 0
HDAC5/YWHAB 0.018 0.011 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.017 0.014 -9999 0 -10000 0 0
GATA2 0.005 0.054 -9999 0 -0.4 11 11
HDAC4/RFXANK 0.018 0.024 -9999 0 -0.57 1 1
BCOR 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.012 0.016 -9999 0 -0.4 1 1
HDAC5 0.012 0.016 -9999 0 -0.4 1 1
GNB1/GNG2 0.007 0.057 -9999 0 -10000 0 0
Histones 0.006 0.069 -9999 0 -0.36 1 1
ADRBK1 0.013 0 -9999 0 -10000 0 0
HDAC4 0.013 0 -9999 0 -10000 0 0
XPO1 0.013 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.018 0.011 -9999 0 -10000 0 0
HDAC4/Ubc9 0.019 0 -9999 0 -10000 0 0
HDAC7 0.013 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.018 0.011 -9999 0 -0.27 1 1
TUBA1B 0.013 0 -9999 0 -10000 0 0
HDAC6 0.013 0 -9999 0 -10000 0 0
HDAC5/RFXANK 0.017 0.026 -9999 0 -0.57 1 1
CAMK4 -0.011 0.095 -9999 0 -0.4 36 36
Tubulin/HDAC6 0.02 0.054 -9999 0 -0.49 7 7
SUMO1 0.011 0.023 -9999 0 -0.4 2 2
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.013 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 0.013 0 -9999 0 -10000 0 0
NR3C1 -0.018 0.11 -9999 0 -0.4 46 46
SUMO1/HDAC4 0.026 0.018 -9999 0 -0.26 2 2
SRF 0.013 0 -9999 0 -10000 0 0
HDAC4/YWHAB 0.019 0 -9999 0 -10000 0 0
Tubulin 0.012 0.062 -9999 0 -0.57 7 7
HDAC4/14-3-3 E 0.019 0 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
RANGAP1 0.011 0.031 -9999 0 -0.75 1 1
BCL6/BCoR 0.019 0 -9999 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.025 0.01 -9999 0 -10000 0 0
HDAC4/SRF 0.011 0.057 -9999 0 -10000 0 0
HDAC4/ER alpha -0.009 0.084 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.006 0.069 -9999 0 -0.36 1 1
cell motility 0.02 0.054 -9999 0 -0.49 7 7
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.013 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0.019 0 -9999 0 -10000 0 0
BCL6 0.013 0 -9999 0 -10000 0 0
HDAC4/CaMK II delta B 0.013 0 -9999 0 -10000 0 0
Hsp90/HDAC6 0.019 0 -9999 0 -10000 0 0
ESR1 -0.027 0.12 -9999 0 -0.4 59 59
HDAC6/HDAC11 0.019 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 -0.002 0.075 -9999 0 -0.4 22 22
RAN 0.013 0 -9999 0 -10000 0 0
HDAC4/MEF2C 0.03 0.039 -9999 0 -10000 0 0
GNG2 -0.004 0.081 -9999 0 -0.4 26 26
NCOR2 0.012 0.016 -9999 0 -0.4 1 1
TUBB2A 0.004 0.081 -9999 0 -0.75 7 7
HDAC11 0.013 0 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
RANBP2 0.013 0 -9999 0 -10000 0 0
ANKRA2 0.013 0 -9999 0 -10000 0 0
RFXANK 0.011 0.031 -9999 0 -0.75 1 1
nuclear import -0.026 0.01 -9999 0 -10000 0 0
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.042 0.045 -10000 0 -10000 0 0
UGCG 0.02 0.043 -10000 0 -0.67 2 2
AKT1/mTOR/p70S6K/Hsp90/TERT 0.037 0.091 -10000 0 -0.36 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.02 0.043 -10000 0 -0.66 2 2
mol:DAG 0.001 0.017 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.025 0.082 -10000 0 -0.45 6 6
FRAP1 0.044 0.12 -10000 0 -0.39 32 32
FOXO3 0.055 0.08 -10000 0 -0.42 1 1
AKT1 0.051 0.084 -10000 0 -0.39 3 3
GAB2 0.013 0.002 -10000 0 -10000 0 0
SMPD1 0.017 0.06 -10000 0 -0.62 5 5
SGMS1 0.022 0.018 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.017 0.011 -10000 0 -10000 0 0
CALM1 0.013 0 -10000 0 -10000 0 0
cell proliferation 0.036 0.049 -10000 0 -0.38 2 2
EIF3A 0.013 0 -10000 0 -10000 0 0
PI3K 0.022 0.013 -10000 0 -10000 0 0
RPS6KB1 0.022 0.035 -10000 0 -0.73 1 1
mol:sphingomyelin 0.001 0.017 -10000 0 -10000 0 0
natural killer cell activation 0 0.002 -10000 0 -10000 0 0
JAK3 0.014 0.031 -10000 0 -0.75 1 1
PIK3R1 0.015 0.002 -10000 0 -10000 0 0
JAK1 0.014 0.016 -10000 0 -0.39 1 1
NFKB1 0.013 0 -10000 0 -10000 0 0
MYC 0.051 0.095 -10000 0 -0.45 11 11
MYB 0.022 0.073 -10000 0 -1.2 2 2
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.049 0.068 -10000 0 -0.39 3 3
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.034 0.037 -10000 0 -0.52 2 2
mol:PI-3-4-5-P3 0.049 0.067 -10000 0 -0.38 3 3
Rac1/GDP 0.023 0.011 -10000 0 -10000 0 0
T cell proliferation 0.052 0.063 -10000 0 -0.36 3 3
SHC1 0.013 0.002 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.004 0.004 -10000 0 -0.065 2 2
PRKCZ 0.053 0.065 -10000 0 -0.37 3 3
NF kappa B1 p50/RelA 0.051 0.1 -10000 0 -0.44 6 6
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.036 0.049 -10000 0 -0.37 2 2
HSP90AA1 0.013 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
IL2RA 0.004 0.058 -10000 0 -0.39 13 13
IL2RB 0.004 0.067 -10000 0 -0.39 17 17
TERT -0.056 0.22 -10000 0 -0.74 57 57
E2F1 0.021 0.043 -10000 0 -0.42 3 3
SOS1 0.013 0.002 -10000 0 -10000 0 0
RPS6 0.011 0.031 -10000 0 -0.75 1 1
mol:cAMP -0.002 0.002 0.031 2 -10000 0 2
PTPN11 0.013 0.003 -10000 0 -10000 0 0
IL2RG 0.013 0.028 -10000 0 -0.4 3 3
actin cytoskeleton organization 0.052 0.063 -10000 0 -0.36 3 3
GRB2 0.013 0.002 -10000 0 -10000 0 0
IL2 0.006 0.006 -10000 0 -10000 0 0
PIK3CA 0.014 0.016 -10000 0 -0.39 1 1
Rac1/GTP 0.032 0.012 -10000 0 -10000 0 0
LCK 0.004 0.089 -10000 0 -0.68 10 10
BCL2 0.024 0.2 -10000 0 -0.82 32 32
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.024 0.026 -9999 0 -10000 0 0
epithelial cell differentiation 0.027 0 -9999 0 -10000 0 0
CYFIP2 0.012 0.016 -9999 0 -0.4 1 1
ENAH 0.049 0.018 -9999 0 -10000 0 0
EGFR 0.011 0.023 -9999 0 -0.4 2 2
EPHA2 0.01 0.043 -9999 0 -0.75 2 2
MYO6 0.031 0 -9999 0 -10000 0 0
CTNNB1 0.013 0 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 0.025 0.01 -9999 0 -10000 0 0
AQP5 -0.015 0.11 -9999 0 -10000 0 0
CTNND1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.03 0.008 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.022 0.038 -9999 0 -10000 0 0
EGF -0.086 0.2 -9999 0 -0.45 131 131
NCKAP1 0.013 0 -9999 0 -10000 0 0
AQP3 0.028 0.062 -9999 0 -0.38 2 2
cortical microtubule organization 0.027 0 -9999 0 -10000 0 0
GO:0000145 0.028 0.007 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.03 0 -9999 0 -10000 0 0
MLLT4 0.012 0.016 -9999 0 -0.4 1 1
ARF6/GDP -0.001 0.02 -9999 0 -10000 0 0
ARF6 0.013 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.031 0.028 -9999 0 -0.45 2 2
mol:Ca2+ 0 0 -9999 0 -10000 0 0
VASP 0.039 0.002 -9999 0 -10000 0 0
PVRL2 0.013 0 -9999 0 -10000 0 0
ZYX 0.031 0 -9999 0 -10000 0 0
ARF6/GTP 0.034 0.027 -9999 0 -0.41 2 2
CDH1 0.013 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.04 0.086 -9999 0 -0.38 20 20
RhoA/GDP 0 0 -9999 0 -10000 0 0
actin cytoskeleton organization 0.034 0 -9999 0 -10000 0 0
IGF-1R heterotetramer 0.013 0 -9999 0 -10000 0 0
GIT1 0.012 0.016 -9999 0 -0.4 1 1
IGF1R 0.013 0 -9999 0 -10000 0 0
IGF1 -0.08 0.17 -9999 0 -0.4 142 142
DIAPH1 -0.001 0.021 -9999 0 -0.52 1 1
Wnt receptor signaling pathway -0.027 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.001 0.019 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
VCL 0.035 0 -9999 0 -10000 0 0
EFNA1 0.013 0 -9999 0 -10000 0 0
LPP 0.034 0.008 -9999 0 -10000 0 0
Ephrin A1/EPHA2 -0.001 0.022 -9999 0 -0.38 2 2
SEC6/SEC8 0 0.005 -9999 0 -10000 0 0
MGAT3 0.023 0.039 -9999 0 -10000 0 0
HGF/MET -0.008 0.049 -9999 0 -0.41 7 7
HGF 0.002 0.067 -9999 0 -0.42 15 15
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.024 0.026 -9999 0 -10000 0 0
actin cable formation 0.063 0.016 -9999 0 -10000 0 0
KIAA1543 0.034 0.011 -9999 0 -10000 0 0
KIFC3 0.018 0.073 -9999 0 -0.4 18 18
NCK1 0.013 0 -9999 0 -10000 0 0
EXOC3 0.013 0 -9999 0 -10000 0 0
ACTN1 0.031 0 -9999 0 -10000 0 0
NCK1/GIT1 0.018 0.011 -9999 0 -10000 0 0
mol:GDP 0.027 0 -9999 0 -10000 0 0
EXOC4 0.013 0 -9999 0 -10000 0 0
STX4 0.031 0 -9999 0 -10000 0 0
PIP5K1C 0.03 0.008 -9999 0 -10000 0 0
LIMA1 0.007 0.049 -9999 0 -0.4 9 9
ABI1 0.013 0 -9999 0 -10000 0 0
ROCK1 0.047 0.02 -9999 0 -10000 0 0
adherens junction assembly 0.038 0.054 -9999 0 -0.5 1 1
IGF-1R heterotetramer/IGF1 -0.035 0.064 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.018 0.011 -9999 0 -0.27 1 1
MET 0.005 0.075 -9999 0 -0.75 6 6
PLEKHA7 0.03 0.008 -9999 0 -10000 0 0
mol:GTP 0.029 0.028 -9999 0 -0.44 2 2
establishment of epithelial cell apical/basal polarity 0.048 0.007 -9999 0 -10000 0 0
cortical actin cytoskeleton stabilization 0.024 0.026 -9999 0 -10000 0 0
regulation of cell-cell adhesion 0.034 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.024 0.026 -9999 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.041 0.011 -9999 0 -10000 0 0
adherens junction organization -0.006 0.064 -9999 0 -0.32 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0.045 0.013 -9999 0 -10000 0 0
FMN1 0.036 0.012 -9999 0 -10000 0 0
mol:IP3 0.035 0.009 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.032 0.01 -9999 0 -10000 0 0
CTNNB1 0.012 0 -9999 0 -10000 0 0
AKT1 0.04 0.01 -9999 0 -10000 0 0
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.034 0.011 -9999 0 -10000 0 0
CTNND1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.036 0.009 -9999 0 -10000 0 0
VASP 0.036 0.01 -9999 0 -10000 0 0
ZYX 0.036 0.01 -9999 0 -10000 0 0
JUB -0.1 0.2 -9999 0 -0.39 204 204
EGFR(dimer) 0.037 0.014 -9999 0 -10000 0 0
E-cadherin/beta catenin-gamma catenin 0.024 0.009 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.036 0.01 -9999 0 -10000 0 0
PIK3CA 0.013 0.016 -9999 0 -0.4 1 1
PI3K 0.037 0.01 -9999 0 -10000 0 0
FYN 0.018 0.06 -9999 0 -10000 0 0
mol:Ca2+ 0.034 0.009 -9999 0 -10000 0 0
JUP 0.012 0.016 -9999 0 -0.39 1 1
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:DAG 0.035 0.009 -9999 0 -10000 0 0
CDH1 0.012 0 -9999 0 -10000 0 0
RhoA/GDP 0.045 0.013 -9999 0 -10000 0 0
establishment of polarity of embryonic epithelium 0.036 0.009 -9999 0 -10000 0 0
SRC 0.013 0 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
EGFR 0.011 0.023 -9999 0 -0.4 2 2
CASR 0.011 0.063 -9999 0 -0.37 1 1
RhoA/GTP 0.038 0.009 -9999 0 -10000 0 0
AKT2 0.04 0.01 -9999 0 -10000 0 0
actin cable formation 0.04 0.012 -9999 0 -10000 0 0
apoptosis -0.038 0.01 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
mol:GDP 0.04 0.014 -9999 0 -10000 0 0
PIP5K1A 0.036 0.01 -9999 0 -10000 0 0
PLCG1 0.035 0.009 -9999 0 -10000 0 0
Rac1/GTP 0.039 0.013 -9999 0 -10000 0 0
homophilic cell adhesion 0.001 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 0.006 0.068 -9999 0 -0.75 5 5
PLK4 0.012 0.001 -9999 0 -10000 0 0
regulation of centriole replication 0.014 0.053 -9999 0 -0.57 5 5
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.008 0.012 0.2 2 -10000 0 2
BUB1B 0.015 0.024 -10000 0 -0.25 1 1
PLK1 0.014 0.011 -10000 0 -10000 0 0
PLK1S1 0.012 0.007 -10000 0 -10000 0 0
KIF2A 0.018 0.01 -10000 0 -10000 0 0
regulation of mitotic centrosome separation 0.014 0.011 -10000 0 -10000 0 0
GOLGA2 0.013 0 -10000 0 -10000 0 0
Hec1/SPC24 0.019 0.06 -10000 0 -0.42 11 11
WEE1 0.015 0.025 -10000 0 -10000 0 0
cytokinesis 0.026 0.015 -10000 0 -0.22 1 1
PP2A-alpha B56 0.03 0.015 -10000 0 -10000 0 0
AURKA 0.012 0.007 -10000 0 -10000 0 0
PICH/PLK1 0.001 0.1 -10000 0 -0.35 50 50
CENPE 0.018 0.021 -10000 0 -0.44 1 1
RhoA/GTP 0.009 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.018 0.01 -10000 0 -10000 0 0
PPP2CA 0.013 0 -10000 0 -10000 0 0
FZR1 0.012 0.016 -10000 0 -0.4 1 1
TPX2 0.011 0.017 -10000 0 -0.15 6 6
PAK1 0.012 0.001 -10000 0 -10000 0 0
SPC24 -0.001 0.1 -10000 0 -0.75 11 11
FBXW11 0.013 0 -10000 0 -10000 0 0
CLSPN 0.013 0.01 -10000 0 -0.17 1 1
GORASP1 0.013 0 -10000 0 -10000 0 0
metaphase 0 0.001 -10000 0 -0.011 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.007 0.007 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0.001 -10000 0 -10000 0 0
STAG2 0.013 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.017 0.014 -10000 0 -10000 0 0
spindle elongation 0.014 0.011 -10000 0 -10000 0 0
ODF2 0.012 0.001 -10000 0 -10000 0 0
BUB1 -0.003 0.011 -10000 0 -10000 0 0
TPT1 0.012 0.007 -10000 0 -10000 0 0
CDC25C 0.014 0.006 -10000 0 -10000 0 0
CDC25B -0.04 0.19 -10000 0 -0.75 44 44
SGOL1 0.008 0.012 -10000 0 -0.2 2 2
RHOA 0.013 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.024 0.087 -10000 0 -0.34 44 44
CDC14B 0.009 0.012 -10000 0 -0.28 1 1
CDC20 0.011 0.031 -10000 0 -0.75 1 1
PLK1/PBIP1 0.015 0.012 -10000 0 -10000 0 0
mitosis 0 0.001 -10000 0 -10000 0 0
FBXO5 0.014 0.019 -10000 0 -10000 0 0
CDC2 0 0.004 -10000 0 -0.015 44 44
NDC80 0.013 0.001 -10000 0 -10000 0 0
metaphase plate congression 0.013 0.007 -10000 0 -10000 0 0
ERCC6L 0.001 0.098 -10000 0 -0.33 50 50
NLP/gamma Tubulin 0.01 0.007 -10000 0 -10000 0 0
microtubule cytoskeleton organization 0.012 0.006 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0.001 -10000 0 -10000 0 0
PPP1R12A 0.011 0.023 -10000 0 -0.4 2 2
interphase 0 0.001 -10000 0 -10000 0 0
PLK1/PRC1-2 0.027 0.009 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0.03 0.008 -10000 0 -10000 0 0
RAB1A 0.013 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.015 0.008 -10000 0 -10000 0 0
mitotic prometaphase 0 0.001 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.029 0.012 -10000 0 -10000 0 0
microtubule-based process 0.019 0.01 -10000 0 -10000 0 0
Golgi organization 0.014 0.011 -10000 0 -10000 0 0
Cohesin/SA2 0.017 0.009 -10000 0 -10000 0 0
PPP1CB/MYPT1 0.017 0.024 -10000 0 -0.51 1 1
KIF20A 0.013 0 -10000 0 -10000 0 0
APC/C/CDC20 0.019 0.021 -10000 0 -0.44 1 1
PPP2R1A 0.013 0 -10000 0 -10000 0 0
chromosome segregation 0.015 0.011 -10000 0 -10000 0 0
PRC1 0.013 0 -10000 0 -10000 0 0
ECT2 0.015 0.04 -10000 0 -0.4 5 5
C13orf34 0.016 0.009 -10000 0 -10000 0 0
NUDC 0.013 0.007 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore 0.015 0.024 -10000 0 -0.24 1 1
spindle assembly 0.013 0.009 -10000 0 -10000 0 0
spindle stabilization 0.012 0.006 -10000 0 -10000 0 0
APC/C/HCDH1 0.016 0.014 -10000 0 -0.23 1 1
MKLP2/PLK1 0.02 0.01 -10000 0 -10000 0 0
CCNB1 0.012 0.003 -10000 0 -10000 0 0
PPP1CB 0.012 0.017 -10000 0 -0.4 1 1
BTRC 0.013 0 -10000 0 -10000 0 0
ROCK2 0.019 0.025 -10000 0 -0.41 2 2
TUBG1 0.012 0.007 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.024 0.085 -10000 0 -0.33 44 44
MLF1IP 0.009 0.012 -10000 0 -0.28 1 1
INCENP 0.012 0.001 -10000 0 -10000 0 0
PDGFR-alpha 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
PDGFRA 0.004 0.063 -9999 0 -0.39 15 15
PDGF/PDGFRA/CRKL 0.013 0.043 -9999 0 -10000 0 0
positive regulation of JUN kinase activity 0.027 0.032 -9999 0 -10000 0 0
CRKL 0.013 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 0.002 0.059 -9999 0 -0.58 3 3
AP1 0.016 0.11 -9999 0 -0.8 10 10
mol:IP3 0.014 0.045 -9999 0 -10000 0 0
PLCG1 0.014 0.045 -9999 0 -10000 0 0
PDGF/PDGFRA/alphaV Integrin 0.013 0.043 -9999 0 -10000 0 0
RAPGEF1 0.012 0.016 -9999 0 -0.4 1 1
CRK 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0.014 0.045 -9999 0 -10000 0 0
CAV3 -0.002 0.052 -9999 0 -0.75 3 3
CAV1 0.004 0.058 -9999 0 -0.4 13 13
SHC/Grb2/SOS1 0.028 0.032 -9999 0 -10000 0 0
PDGF/PDGFRA/Shf -0.001 0.098 -9999 0 -0.58 14 14
FOS 0.018 0.11 -9999 0 -0.79 10 10
JUN -0.001 0.008 -9999 0 -10000 0 0
oligodendrocyte development 0.013 0.043 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:DAG 0.014 0.045 -9999 0 -10000 0 0
PDGF/PDGFRA 0.004 0.063 -9999 0 -0.39 15 15
actin cytoskeleton reorganization 0.01 0.059 -9999 0 -0.58 3 3
SRF 0.017 0.004 -9999 0 -10000 0 0
SHC1 0.013 0 -9999 0 -10000 0 0
PI3K 0.02 0.037 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk/C3G 0.02 0.037 -9999 0 -10000 0 0
JAK1 0.013 0.044 -9999 0 -10000 0 0
ELK1/SRF 0.027 0.034 -9999 0 -10000 0 0
SHB 0.009 0.053 -9999 0 -0.75 3 3
SHF -0.005 0.11 -9999 0 -0.73 15 15
CSNK2A1 0.009 0.007 -9999 0 -10000 0 0
GO:0007205 0.014 0.05 -9999 0 -0.3 15 15
SOS1 0.013 0 -9999 0 -10000 0 0
Ras protein signal transduction 0.027 0.032 -9999 0 -10000 0 0
PDGF/PDGFRA/SHB 0.01 0.059 -9999 0 -0.58 3 3
PDGF/PDGFRA/Caveolin-1 0.007 0.065 -9999 0 -0.34 13 13
ITGAV 0.013 0 -9999 0 -10000 0 0
ELK1 0.019 0.043 -9999 0 -10000 0 0
PIK3CA 0.012 0.016 -9999 0 -0.4 1 1
PDGF/PDGFRA/Crk 0.013 0.043 -9999 0 -10000 0 0
JAK-STAT cascade 0.013 0.044 -9999 0 -10000 0 0
cell proliferation -0.001 0.098 -9999 0 -0.58 14 14
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.009 0.036 -9999 0 -0.4 5 5
positive regulation of NF-kappaB transcription factor activity 0.016 0.026 -9999 0 -10000 0 0
MAP2K4 0.036 0.025 -9999 0 -10000 0 0
IKBKB 0.013 0 -9999 0 -10000 0 0
TNFRSF10B 0.013 0 -9999 0 -10000 0 0
TNFRSF10A 0.013 0 -9999 0 -10000 0 0
SMPD1 0.013 0.037 -9999 0 -0.36 5 5
IKBKG 0.012 0.016 -9999 0 -0.4 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.013 0 -9999 0 -10000 0 0
TRAIL/TRAILR2 0.016 0.026 -9999 0 -0.27 5 5
TRAIL/TRAILR3 -0.022 0.15 -9999 0 -0.57 41 41
TRAIL/TRAILR1 0.016 0.026 -9999 0 -0.27 5 5
TRAIL/TRAILR4 0.016 0.026 -9999 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP 0.023 0.02 -9999 0 -10000 0 0
IKK complex -0.001 0.014 -9999 0 -0.3 1 1
RIPK1 0.013 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 0.016 0.028 -9999 0 -0.27 6 6
MAP3K1 0.033 0.022 -9999 0 -10000 0 0
TRAILR4 (trimer) 0.013 0 -9999 0 -10000 0 0
TRADD 0.013 0 -9999 0 -10000 0 0
TRAILR1 (trimer) 0.013 0 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.03 0.021 -9999 0 -10000 0 0
CFLAR 0.013 0 -9999 0 -10000 0 0
MAPK1 0.016 0.028 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP 0.036 0.019 -9999 0 -10000 0 0
mol:ceramide 0.013 0.037 -9999 0 -0.36 5 5
FADD 0.013 0 -9999 0 -10000 0 0
MAPK8 0.04 0.024 -9999 0 -10000 0 0
TRAF2 0.012 0.016 -9999 0 -0.4 1 1
TRAILR3 (trimer) -0.038 0.19 -9999 0 -0.75 41 41
CHUK 0.013 0 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.024 0.022 -9999 0 -10000 0 0
DAP3 0.013 0 -9999 0 -10000 0 0
CASP10 -0.002 0.021 -9999 0 -10000 0 0
JNK cascade 0.016 0.026 -9999 0 -10000 0 0
TRAIL (trimer) 0.009 0.036 -9999 0 -0.39 5 5
TNFRSF10C -0.038 0.19 -9999 0 -0.75 41 41
TRAIL/TRAILR1/DAP3/GTP/FADD 0.028 0.018 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD 0.024 0.022 -9999 0 -10000 0 0
cell death 0.013 0.037 -9999 0 -0.36 5 5
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.03 0.021 -9999 0 -10000 0 0
TRAILR2 (trimer) 0.013 0 -9999 0 -10000 0 0
CASP8 0.001 0.011 -9999 0 -10000 0 0
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.036 0.019 -9999 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BAG4 0.012 0.001 -9999 0 -10000 0 0
Caspase 8 (4 units) 0.025 0.055 -9999 0 -0.35 2 2
NEF -0.004 0.034 -9999 0 -10000 0 0
NFKBIA 0.014 0.012 -9999 0 -10000 0 0
BIRC3 0.029 0.062 -9999 0 -0.45 10 10
CYCS 0.025 0.064 -9999 0 -0.37 3 3
RIPK1 0.013 0 -9999 0 -10000 0 0
CD247 -0.002 0.083 -9999 0 -0.47 16 16
MAP2K7 0.033 0.056 -9999 0 -0.64 1 1
protein ubiquitination 0.055 0.021 -9999 0 -10000 0 0
CRADD 0.013 0 -9999 0 -10000 0 0
DAXX 0.013 0 -9999 0 -10000 0 0
FAS 0.007 0.049 -9999 0 -0.4 9 9
BID 0.021 0.066 -9999 0 -0.4 3 3
NF-kappa-B/RelA/I kappa B alpha 0.031 0.033 -9999 0 -10000 0 0
TRADD 0.013 0 -9999 0 -10000 0 0
MAP3K5 0.013 0 -9999 0 -10000 0 0
CFLAR 0.013 0 -9999 0 -10000 0 0
FADD 0.013 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.031 0.034 -9999 0 -10000 0 0
MAPK8 0.037 0.053 -9999 0 -0.59 1 1
APAF1 0.013 0.001 -9999 0 -10000 0 0
TRAF1 0.013 0 -9999 0 -10000 0 0
TRAF2 0.012 0.016 -9999 0 -0.4 1 1
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.016 0.067 -9999 0 -0.37 3 3
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.05 0.024 -9999 0 -10000 0 0
CHUK 0.056 0.022 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.034 0.025 -9999 0 -10000 0 0
TCRz/NEF -0.004 0.086 -9999 0 -0.31 41 41
TNF 0.009 0.036 -9999 0 -0.4 5 5
FASLG -0.009 0.13 -9999 0 -0.54 34 34
NFKB1 0.014 0.012 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.024 0.022 -9999 0 -10000 0 0
CASP6 0.039 0.04 -9999 0 -10000 0 0
CASP7 0.052 0.075 -9999 0 -0.42 9 9
RELA 0.014 0.012 -9999 0 -10000 0 0
CASP2 0.013 0 -9999 0 -10000 0 0
CASP3 0.052 0.074 -9999 0 -0.42 9 9
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
TNFR1A/BAG4 0.019 0.001 -9999 0 -10000 0 0
CASP8 0.013 0 -9999 0 -10000 0 0
CASP9 0.013 0 -9999 0 -10000 0 0
MAP3K14 0.054 0.023 -9999 0 -10000 0 0
APAF-1/Caspase 9 -0.013 0.048 -9999 0 -0.44 2 2
BCL2 0.032 0.066 -9999 0 -0.46 2 2
IL2 signaling events mediated by STAT5

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
GAB2 0.013 0 -9999 0 -10000 0 0
ELF1 0.014 0.046 -9999 0 -0.3 13 13
CCNA2 0.013 0 -9999 0 -10000 0 0
PIK3CA 0.013 0.016 -9999 0 -0.39 1 1
JAK3 0.012 0.031 -9999 0 -0.75 1 1
PIK3R1 0.013 0 -9999 0 -10000 0 0
JAK1 0.013 0.016 -9999 0 -0.39 1 1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.054 0.057 -9999 0 -0.45 2 2
SHC1 0.013 0 -9999 0 -10000 0 0
SP1 0.016 0.034 -9999 0 -0.3 7 7
IL2RA 0.013 0.095 -9999 0 -0.64 13 13
IL2RB 0.002 0.066 -9999 0 -0.39 17 17
SOS1 0.013 0 -9999 0 -10000 0 0
IL2RG 0.011 0.028 -9999 0 -0.39 3 3
G1/S transition of mitotic cell cycle 0.033 0.064 -9999 0 -0.6 6 6
PTPN11 0.013 0 -9999 0 -10000 0 0
CCND2 0.019 0.07 -9999 0 -0.64 7 7
LCK 0.002 0.089 -9999 0 -0.68 10 10
GRB2 0.013 0 -9999 0 -10000 0 0
IL2 0.004 0.006 -9999 0 -10000 0 0
CDK6 0.013 0 -9999 0 -10000 0 0
CCND3 0.058 0.051 -9999 0 -10000 0 0
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.01 0.055 -9999 0 -0.39 10 10
TC10/GTP -0.01 0.053 -9999 0 -0.38 10 10
Insulin Receptor/Insulin/IRS1/Shp2 0.027 0 -9999 0 -10000 0 0
HRAS 0.012 0.016 -9999 0 -0.4 1 1
APS homodimer 0 0.096 -9999 0 -0.75 10 10
GRB14 -0.024 0.14 -9999 0 -0.5 42 42
FOXO3 -0.001 0.11 -9999 0 -0.52 25 25
AKT1 0.023 0.066 -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 0.013 0 -9999 0 -10000 0 0
SORBS1 0.002 0.064 -9999 0 -0.4 16 16
CRK 0.013 0 -9999 0 -10000 0 0
PTPN1 0.027 0 -9999 0 -10000 0 0
CAV1 0.018 0.03 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II/C3G 0.024 0.066 -9999 0 -0.42 10 10
Insulin Receptor/Insulin/IRS1/NCK2 0.027 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0.007 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.033 0 -9999 0 -10000 0 0
RPS6KB1 0.027 0.062 -9999 0 -10000 0 0
PARD6A 0.01 0.043 -9999 0 -0.75 2 2
CBL 0.013 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 0.013 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.012 0.05 -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 0.033 0 -9999 0 -10000 0 0
PRKCI -0.005 0.027 -9999 0 -0.42 2 2
Insulin Receptor/Insulin/GRB14/PDK1 -0.015 0.062 -9999 0 -10000 0 0
SHC1 0.013 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0.024 0.001 -9999 0 -10000 0 0
PI3K 0.027 0.008 -9999 0 -10000 0 0
NCK2 0.013 0 -9999 0 -10000 0 0
RHOQ 0.013 0 -9999 0 -10000 0 0
mol:H2O2 0 0 -9999 0 -10000 0 0
HRAS/GDP 0.009 0.011 -9999 0 -0.28 1 1
AKT2 0.023 0.066 -9999 0 -10000 0 0
PRKCZ -0.003 0.014 -9999 0 -10000 0 0
SH2B2 0 0.096 -9999 0 -0.75 10 10
SHC/SHIP 0.029 0.008 -9999 0 -10000 0 0
F2RL2 -0.027 0.17 -9999 0 -0.71 34 34
TRIP10 0.013 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.019 0 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.017 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.033 0 -9999 0 -10000 0 0
RAPGEF1 0.012 0.016 -9999 0 -0.4 1 1
RASA1 0.013 0.001 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.019 0.069 -9999 0 -0.45 10 10
TC10/GDP 0.009 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.027 0 -9999 0 -10000 0 0
INPP5D 0.022 0.008 -9999 0 -10000 0 0
SOS1 0.013 0 -9999 0 -10000 0 0
SGK1 -0.032 0.15 -9999 0 -0.78 25 25
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.013 0 -9999 0 -10000 0 0
IRS1 0.013 0 -9999 0 -10000 0 0
p62DOK/RasGAP 0.024 0.001 -9999 0 -10000 0 0
INS 0.002 0 -9999 0 -10000 0 0
mol:PI-3-4-P2 0.022 0.008 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
EIF4EBP1 0.025 0.069 -9999 0 -10000 0 0
PTPRA 0.014 0 -9999 0 -10000 0 0
PIK3CA 0.012 0.016 -9999 0 -0.4 1 1
TC10/GTP/CIP4 0.017 0 -9999 0 -10000 0 0
PDPK1 0.013 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 0.019 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS3 0.012 0 -9999 0 -10000 0 0
Par3/Par6 0.005 0.1 -9999 0 -0.42 32 32
LPA4-mediated signaling events

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
ADCY4 0.016 0 -9999 0 -10000 0 0
ADCY5 -0.094 0.12 -9999 0 -10000 0 0
ADCY6 0.016 0 -9999 0 -10000 0 0
ADCY7 0.016 0 -9999 0 -10000 0 0
ADCY1 0.004 0.075 -9999 0 -0.5 13 13
ADCY2 -0.02 0.086 -9999 0 -0.5 1 1
ADCY3 0.016 0 -9999 0 -10000 0 0
ADCY8 0.002 0.061 -9999 0 -0.5 9 9
PRKCE 0.01 0 -9999 0 -10000 0 0
ADCY9 0.015 0.014 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.019 0.059 -9999 0 -0.26 3 3
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.013 0.059 -10000 0 -0.53 7 7
CRKL 0.027 0.038 -10000 0 -0.36 1 1
mol:PIP3 -0.015 0.022 0.37 2 -10000 0 2
AKT1 0.001 0.016 0.27 2 -10000 0 2
PTK2B 0.011 0.023 -10000 0 -0.4 2 2
RAPGEF1 0.031 0.037 -10000 0 -0.34 1 1
RANBP10 0.013 0 -10000 0 -10000 0 0
PIK3CA 0.012 0.016 -10000 0 -0.4 1 1
HGF/MET/SHIP2 0.014 0.067 -10000 0 -0.52 7 7
MAP3K5 0.019 0.077 -10000 0 -0.35 6 6
HGF/MET/CIN85/CBL/ENDOPHILINS 0.022 0.062 -10000 0 -0.47 7 7
AP1 0.012 0.035 -10000 0 -10000 0 0
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.013 0 -10000 0 -10000 0 0
apoptosis 0.007 0.094 -10000 0 -0.72 10 10
STAT3 (dimer) 0.028 0.044 -10000 0 -0.4 1 1
GAB1/CRKL/SHP2/PI3K 0.041 0.036 -10000 0 -10000 0 0
INPP5D 0.012 0.016 -10000 0 -0.4 1 1
CBL/CRK 0.033 0.036 -10000 0 -0.34 1 1
PTPN11 0.013 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.013 0 -10000 0 -10000 0 0
PTEN 0.011 0.023 -10000 0 -0.4 2 2
ELK1 -0.002 0.029 0.23 2 -0.27 6 8
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.022 0.028 -10000 0 -0.27 1 1
PAK1 0.006 0.014 0.27 1 -10000 0 1
HGF/MET/RANBP10 0.014 0.067 -10000 0 -0.52 7 7
HRAS 0.024 0.054 -10000 0 -0.48 2 2
DOCK1 0.031 0.037 -10000 0 -0.34 1 1
GAB1 0.022 0.039 -10000 0 -0.39 1 1
CRK 0.027 0.038 -10000 0 -0.36 1 1
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.017 0.076 -10000 0 -0.42 15 15
JUN 0.013 0 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.007 0.039 -10000 0 -0.27 7 7
PIK3R1 0.013 0 -10000 0 -10000 0 0
cell morphogenesis 0.049 0.045 -10000 0 -0.38 1 1
GRB2/SHC 0.021 0.035 -10000 0 -0.36 1 1
FOS 0.006 0.051 -10000 0 -0.4 10 10
GLMN -0.001 0.012 -10000 0 -0.22 2 2
cell motility -0.002 0.029 0.23 2 -0.26 6 8
HGF/MET/MUC20 0.006 0.067 -10000 0 -0.52 7 7
cell migration 0.021 0.035 -10000 0 -0.36 1 1
GRB2 0.013 0 -10000 0 -10000 0 0
CBL 0.013 0 -10000 0 -10000 0 0
MET/RANBP10 0.013 0.057 -10000 0 -0.57 6 6
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.024 0.045 -10000 0 -0.43 1 1
MET/MUC20 0.004 0.057 -10000 0 -0.58 6 6
RAP1B 0.036 0.036 -10000 0 -0.32 1 1
RAP1A 0.036 0.036 -10000 0 -10000 0 0
HGF/MET/RANBP9 0.014 0.068 -10000 0 -0.52 7 7
RAF1 0.029 0.052 -10000 0 -0.45 2 2
STAT3 0.028 0.044 -10000 0 -0.41 1 1
cell proliferation 0.035 0.056 -10000 0 -0.52 1 1
RPS6KB1 0.009 0.019 -10000 0 -0.28 1 1
MAPK3 -0.006 0.036 0.65 1 -0.25 6 7
MAPK1 -0.006 0.036 0.65 1 -0.25 6 7
RANBP9 0.012 0.016 -10000 0 -0.4 1 1
MAPK8 0.034 0.061 -10000 0 -10000 0 0
SRC 0.028 0.043 -10000 0 -0.4 1 1
PI3K 0.021 0.036 -10000 0 -0.36 1 1
MET/Glomulin 0.006 0.052 -10000 0 -0.52 6 6
SOS1 0.013 0 -10000 0 -10000 0 0
MAP2K1 0.033 0.049 -10000 0 -0.42 2 2
MET 0.005 0.075 -10000 0 -0.75 6 6
MAP4K1 0.013 0.081 -10000 0 -0.38 6 6
PTK2 0.013 0 -10000 0 -10000 0 0
MAP2K2 0.033 0.05 -10000 0 -0.39 3 3
BAD 0.006 0.016 0.26 2 -10000 0 2
MAP2K4 0.023 0.073 -10000 0 -0.34 1 1
SHP2/GRB2/SOS1/GAB1 -0.006 0.036 -10000 0 -0.45 1 1
INPPL1 0.013 0 -10000 0 -10000 0 0
PXN 0.013 0 -10000 0 -10000 0 0
SH3KBP1 0.013 0 -10000 0 -10000 0 0
HGS 0.012 0.036 -10000 0 -0.26 6 6
PLCgamma1/PKC 0.009 0 -10000 0 -10000 0 0
HGF 0.002 0.067 -10000 0 -0.42 15 15
RASA1 0.013 0.001 -10000 0 -10000 0 0
NCK1 0.013 0 -10000 0 -10000 0 0
PTPRJ 0.013 0 -10000 0 -10000 0 0
NCK/PLCgamma1 0.023 0.037 -10000 0 -0.38 1 1
PDPK1 -0.007 0.018 0.3 2 -10000 0 2
HGF/MET/SHIP 0.014 0.068 -10000 0 -0.52 7 7
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.031 0.017 -10000 0 -10000 0 0
regulation of axonogenesis -0.024 0.009 -10000 0 -10000 0 0
myoblast fusion -0.022 0.016 -10000 0 -10000 0 0
mol:GTP 0.01 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.001 0.095 0.5 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 0.023 0.013 -10000 0 -10000 0 0
lamellipodium assembly 0.009 0.025 -10000 0 -10000 0 0
MAPK3 0.022 0.013 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.002 0.096 -10000 0 -0.5 10 10
ARF1 0.013 0 -10000 0 -10000 0 0
ARF6/GDP 0.022 0.016 -10000 0 -10000 0 0
ARF1/GDP 0.03 0.016 -10000 0 -10000 0 0
ARF6 0.013 0.001 -10000 0 -10000 0 0
RAB11A 0.013 0 -10000 0 -10000 0 0
TIAM1 -0.027 0.12 -10000 0 -0.39 62 62
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.022 0.013 -10000 0 -10000 0 0
actin filament bundle formation -0.021 0.009 -10000 0 -10000 0 0
KALRN 0.007 0.023 -10000 0 -10000 0 0
RAB11FIP3/RAB11A 0.019 0 -10000 0 -10000 0 0
RhoA/GDP 0.021 0.009 -10000 0 -10000 0 0
NME1 0.002 0.096 -10000 0 -0.75 10 10
Rac1/GDP 0.021 0.009 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.01 0.004 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0.009 0.025 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
liver development 0.01 0.004 -10000 0 -10000 0 0
ARF6/GTP 0.01 0.004 -10000 0 -10000 0 0
RhoA/GTP 0.016 0.006 -10000 0 -10000 0 0
mol:GDP 0.009 0.026 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0.023 0.008 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
PLD1 0.018 0.015 -10000 0 -0.24 2 2
RAB11FIP3 0.013 0 -10000 0 -10000 0 0
tube morphogenesis 0.009 0.025 -10000 0 -10000 0 0
ruffle organization 0.024 0.009 -10000 0 -10000 0 0
regulation of epithelial cell migration 0.01 0.004 -10000 0 -10000 0 0
PLD2 0.019 0.001 -10000 0 -10000 0 0
PIP5K1A 0.024 0.009 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.023 0.013 -10000 0 -10000 0 0
Rac1/GTP 0.009 0.025 -10000 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.039 0.037 -10000 0 -10000 0 0
BAG4 0.012 0.001 -10000 0 -10000 0 0
BAD 0.025 0.021 -10000 0 -0.35 1 1
NFKBIA 0.013 0 -10000 0 -10000 0 0
BIRC3 0.005 0.057 -10000 0 -0.43 10 10
BAX 0.025 0.017 -10000 0 -0.18 1 1
EnzymeConsortium:3.1.4.12 0.013 0.01 -10000 0 -10000 0 0
IKBKB 0.043 0.035 -10000 0 -10000 0 0
MAP2K2 0.034 0.019 -10000 0 -0.29 1 1
MAP2K1 0.034 0.015 -10000 0 -10000 0 0
SMPD1 0.016 0.021 -10000 0 -0.19 5 5
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.045 0.036 -10000 0 -10000 0 0
MAP2K4 0.029 0.022 -10000 0 -10000 0 0
protein ubiquitination 0.044 0.036 -10000 0 -10000 0 0
EnzymeConsortium:2.7.1.37 0.038 0.018 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.031 0.016 -10000 0 -10000 0 0
CRADD 0.013 0 -10000 0 -10000 0 0
mol:ceramide 0.02 0.018 -10000 0 -0.19 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 0.019 -10000 0 -0.23 1 1
TRADD 0.013 0 -10000 0 -10000 0 0
RELA/p50 0.013 0 -10000 0 -10000 0 0
MAPK3 0.036 0.017 -10000 0 -10000 0 0
MAPK1 0.036 0.017 -10000 0 -10000 0 0
p50/RELA/I-kappa-B-alpha 0.019 0 -10000 0 -10000 0 0
FADD 0.039 0.037 -10000 0 -10000 0 0
KSR1 0.026 0.017 -10000 0 -10000 0 0
MAPK8 0.033 0.021 -10000 0 -10000 0 0
TRAF2 0.012 0.016 -10000 0 -0.4 1 1
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.043 0.035 -10000 0 -10000 0 0
TNF R/SODD 0.019 0.001 -10000 0 -10000 0 0
TNF 0.009 0.036 -10000 0 -0.4 5 5
CYCS 0.03 0.027 0.12 28 -0.26 1 29
IKBKG 0.043 0.038 -10000 0 -0.4 1 1
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.035 0.038 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
RIPK1 0.012 0 -10000 0 -10000 0 0
AIFM1 0.03 0.027 0.12 29 -0.26 1 30
TNF/TNF R/SODD 0.024 0.022 -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 0.01 -10000 0 -10000 0 0
NSMAF 0.039 0.036 -10000 0 -10000 0 0
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
BCL2 -0.008 0.09 -10000 0 -0.4 32 32
Paxillin-dependent events mediated by a4b1

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
CRKL 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0.001 0.007 -9999 0 -10000 0 0
DOCK1 0.012 0.016 -9999 0 -0.4 1 1
ITGA4 -0.002 0.075 -9999 0 -0.4 22 22
RAC1 0.013 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin -0.002 0.08 -9999 0 -0.51 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.017 0.045 -9999 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.014 0.062 -9999 0 -0.39 5 5
lamellipodium assembly 0.001 0.019 -9999 0 -10000 0 0
PIK3CA 0.012 0.016 -9999 0 -0.4 1 1
PI3K 0.018 0.011 -9999 0 -10000 0 0
ARF6 0.013 0 -9999 0 -10000 0 0
TLN1 0.013 0 -9999 0 -10000 0 0
PXN 0.019 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
ARF6/GTP 0.027 0.035 -9999 0 -10000 0 0
cell adhesion 0.028 0.038 -9999 0 -10000 0 0
CRKL/CBL 0.019 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.022 0.04 -9999 0 -10000 0 0
ITGB1 0.013 0 -9999 0 -10000 0 0
ITGB7 -0.003 0.077 -9999 0 -0.4 23 23
ARF6/GDP 0.001 0.007 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.025 0.058 -9999 0 -0.36 9 9
p130Cas/Crk/Dock1 0.025 0.014 -9999 0 -10000 0 0
VCAM1 0.004 0.058 -9999 0 -0.4 13 13
alpha4/beta1 Integrin/Paxillin/Talin 0.029 0.038 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.029 0.039 -9999 0 -10000 0 0
BCAR1 0.012 0.016 -9999 0 -0.4 1 1
mol:GDP -0.028 0.039 -9999 0 -10000 0 0
CBL 0.013 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GIT1 0.012 0.016 -9999 0 -0.4 1 1
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.029 0.038 -9999 0 -10000 0 0
Rac1/GTP 0.001 0.02 -9999 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.035 0.003 -9999 0 -10000 0 0
KLHL20 0.03 0.05 -9999 0 -0.23 5 5
CYFIP2 0.012 0.016 -9999 0 -0.4 1 1
Rac1/GDP 0.051 0.018 -9999 0 -10000 0 0
ENAH 0.035 0.008 -9999 0 -10000 0 0
AP1M1 0.013 0 -9999 0 -10000 0 0
RAP1B 0.013 0 -9999 0 -10000 0 0
RAP1A 0.013 0 -9999 0 -10000 0 0
CTNNB1 0.013 0 -9999 0 -10000 0 0
CDC42/GTP -0.001 0.008 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.007 0.025 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.024 0.042 -9999 0 -10000 0 0
RAPGEF1 0.043 0.008 -9999 0 -10000 0 0
CTNND1 0.013 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.03 0.003 -9999 0 -10000 0 0
CRK 0.04 0.003 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin 0.025 0.01 -9999 0 -10000 0 0
alphaE/beta7 Integrin 0.008 0.054 -9999 0 -10000 0 0
IQGAP1 0.013 0 -9999 0 -10000 0 0
NCKAP1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.024 0.009 -9999 0 -10000 0 0
DLG1 0.035 0.008 -9999 0 -10000 0 0
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0.005 -9999 0 -10000 0 0
MLLT4 0.012 0.016 -9999 0 -0.4 1 1
ARF6/GTP/NME1/Tiam1 -0.005 0.09 -9999 0 -0.49 10 10
PI3K 0 0.006 -9999 0 -10000 0 0
ARF6 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin 0.018 0.011 -9999 0 -10000 0 0
TIAM1 -0.028 0.12 -9999 0 -0.4 62 62
E-cadherin(dimer)/Ca2+ 0.03 0.001 -9999 0 -10000 0 0
AKT1 0 0.004 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
CDH1 0.013 0 -9999 0 -10000 0 0
RhoA/GDP 0.05 0.018 -9999 0 -10000 0 0
actin cytoskeleton organization 0.025 0.038 -9999 0 -0.17 5 5
CDC42/GDP 0.05 0.021 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.021 0.009 -9999 0 -10000 0 0
ITGB7 -0.003 0.077 -9999 0 -0.4 23 23
RAC1 0.013 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.033 0.001 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0.023 0 -9999 0 -10000 0 0
mol:GDP 0.048 0.02 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1 0.016 0.014 -9999 0 -10000 0 0
JUP 0.012 0.016 -9999 0 -0.4 1 1
p120 catenin/RhoA/GDP 0.049 0.018 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 0.017 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0.018 0.011 -9999 0 -0.27 1 1
RHOA 0.013 0 -9999 0 -10000 0 0
CDC42 0.011 0.023 -9999 0 -0.4 2 2
CTNNA1 0.013 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.02 0.034 -9999 0 -0.24 5 5
NME1 0 0.096 -9999 0 -0.75 10 10
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.035 0.003 -9999 0 -10000 0 0
regulation of cell-cell adhesion -0.001 0.007 -9999 0 -10000 0 0
WASF2 -0.004 0.013 -9999 0 -10000 0 0
Rap1/GTP 0 0.005 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.029 0.04 -9999 0 -10000 0 0
CCND1 0.023 0.041 -9999 0 -0.31 5 5
VAV2 0.035 0.081 -9999 0 -0.63 9 9
RAP1/GDP 0.042 0.018 -9999 0 -10000 0 0
adherens junction assembly 0.035 0.003 -9999 0 -10000 0 0
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.013 0 -9999 0 -10000 0 0
PIP5K1C 0.012 0.016 -9999 0 -0.4 1 1
regulation of heterotypic cell-cell adhesion 0.033 0.038 -9999 0 -10000 0 0
E-cadherin/beta catenin 0 0.006 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.035 0.004 -9999 0 -10000 0 0
PIK3CA 0.012 0.016 -9999 0 -0.4 1 1
Rac1/GTP -0.017 0.059 -9999 0 -0.35 11 11
E-cadherin/beta catenin/alpha catenin 0.026 0 -9999 0 -10000 0 0
ITGAE 0.013 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.031 0.003 -9999 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 -0.037 0.13 -10000 0 -0.4 76 76
CLTC 0.023 0.034 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.022 0.008 -10000 0 -10000 0 0
Dynamin 2/GTP 0.014 0.059 -10000 0 -0.45 10 10
EXOC4 0.013 0 -10000 0 -10000 0 0
CD59 0.021 0.021 -10000 0 -10000 0 0
CPE -0.002 0.065 -10000 0 -0.5 1 1
CTNNB1 0.013 0 -10000 0 -10000 0 0
membrane fusion 0.022 0.008 -10000 0 -10000 0 0
CTNND1 0.019 0.056 -10000 0 -0.42 10 10
DNM2 0.013 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.025 0.017 -10000 0 -10000 0 0
TSHR 0.012 0.029 -10000 0 -0.5 2 2
INS 0.009 0.006 -10000 0 -10000 0 0
BIN1 0.012 0.016 -10000 0 -0.4 1 1
mol:Choline 0.022 0.008 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.008 0.064 -10000 0 -0.5 10 10
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.013 0 -10000 0 -10000 0 0
mol:Ca2+ 0.014 0.059 -10000 0 -0.45 10 10
JUP 0.021 0.022 -10000 0 -10000 0 0
ASAP2/amphiphysin II 0.024 0.009 -10000 0 -10000 0 0
ARF6/GTP 0.009 0 -10000 0 -10000 0 0
CDH1 0.021 0.021 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0.009 0 -10000 0 -10000 0 0
MAPK8IP3 0.011 0.035 -10000 0 -0.57 2 2
positive regulation of endocytosis 0.009 0 -10000 0 -10000 0 0
EXOC2 0.012 0.016 -10000 0 -0.4 1 1
substrate adhesion-dependent cell spreading 0.035 0.029 -10000 0 -0.61 1 1
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.013 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.005 0.043 0.34 10 -10000 0 10
positive regulation of phagocytosis 0.016 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.016 0.023 -10000 0 -0.5 1 1
ACAP1 0.017 0.025 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.026 0.079 -10000 0 -0.4 2 2
clathrin heavy chain/ACAP1 0.026 0.031 -10000 0 -10000 0 0
JIP4/KLC1 0.024 0 -10000 0 -10000 0 0
EXOC1 0.012 0.016 -10000 0 -0.4 1 1
exocyst 0.035 0.029 -10000 0 -0.62 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 0.019 0.056 -10000 0 -0.42 10 10
NME1 0.008 0.065 -10000 0 -0.5 10 10
clathrin coat assembly 0.023 0.034 -10000 0 -10000 0 0
IL2RA 0.018 0.032 -10000 0 -10000 0 0
VAMP3 0.016 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.021 0.056 -10000 0 -0.36 3 3
EXOC6 0.013 0 -10000 0 -10000 0 0
PLD1 0.018 0.014 -10000 0 -0.23 2 2
PLD2 0.019 0 -10000 0 -10000 0 0
EXOC5 0.01 0.033 -10000 0 -0.4 4 4
PIP5K1C 0.025 0.017 -10000 0 -10000 0 0
SDC1 0.021 0.021 -10000 0 -10000 0 0
ARF6/GDP 0.008 0.064 -10000 0 -0.5 10 10
EXOC7 0.013 0 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.028 0.049 -10000 0 -0.35 10 10
mol:Phosphatidic acid 0.022 0.008 -10000 0 -10000 0 0
endocytosis -0.023 0.009 -10000 0 -10000 0 0
SCAMP2 0.013 0 -10000 0 -10000 0 0
ADRB2 -0.002 0.079 -10000 0 -0.4 5 5
EXOC3 0.013 0 -10000 0 -10000 0 0
ASAP2 0.013 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.015 0.059 -10000 0 -0.45 10 10
KLC1 0.013 0 -10000 0 -10000 0 0
AVPR2 0.01 0.071 -10000 0 -0.39 8 8
RALA 0.013 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.005 0.041 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.013 0 -10000 0 -10000 0 0
TRAF2/ASK1 0.017 0.01 -10000 0 -0.22 1 1
ATM 0.012 0.016 -10000 0 -0.4 1 1
MAP2K3 0.028 0.028 -10000 0 -0.3 2 2
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.034 0.028 -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 0.005 0.076 -10000 0 -0.7 7 7
TXN 0.007 0 -10000 0 -10000 0 0
CALM1 0.013 0 -10000 0 -10000 0 0
GADD45A 0.013 0 -10000 0 -10000 0 0
GADD45B 0.013 0 -10000 0 -10000 0 0
MAP3K1 0.012 0.016 -10000 0 -0.4 1 1
MAP3K6 0.011 0.023 -10000 0 -0.4 2 2
MAP3K7 0.013 0 -10000 0 -10000 0 0
MAP3K4 0.013 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.018 0.016 -10000 0 -10000 0 0
TAK1/TAB family 0.001 0.01 0.18 2 -10000 0 2
RAC1/OSM/MEKK3 0.024 0.009 -10000 0 -10000 0 0
TRAF2 0.012 0.016 -10000 0 -0.4 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 0.013 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.028 0.13 -10000 0 -0.45 52 52
CCM2 0.012 0.016 -10000 0 -0.4 1 1
CaM/Ca2+/CAMKIIB -0.008 0.083 -10000 0 -0.5 8 8
MAPK11 0.01 0.043 -10000 0 -0.75 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.002 0.076 -10000 0 -0.45 8 8
OSM/MEKK3 0.018 0.011 -10000 0 -10000 0 0
TAOK1 0.014 0.011 -10000 0 -0.27 1 1
TAOK2 0.014 0.011 -10000 0 -0.27 1 1
TAOK3 0.014 0.011 -10000 0 -0.27 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.013 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.013 0 -10000 0 -10000 0 0
MAP3K10 0.011 0.031 -10000 0 -0.75 1 1
MAP3K3 0.013 0 -10000 0 -10000 0 0
TRX/ASK1 0.015 0 -10000 0 -10000 0 0
GADD45/MTK1/MTK1 0.025 0.045 -10000 0 -0.42 6 6
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.067 0.027 -9999 0 -10000 0 0
ERC1 0.013 0 -9999 0 -10000 0 0
RIP2/NOD2 0.003 0.094 -9999 0 -0.57 16 16
NFKBIA 0.037 0 -9999 0 -10000 0 0
BIRC2 0.012 0.016 -9999 0 -0.4 1 1
IKBKB 0.013 0 -9999 0 -10000 0 0
RIPK2 0.013 0 -9999 0 -10000 0 0
IKBKG 0.032 0.044 -9999 0 -0.39 3 3
IKK complex/A20 0.045 0.043 -9999 0 -0.4 1 1
NEMO/A20/RIP2 0.013 0 -9999 0 -10000 0 0
XPO1 0.013 0 -9999 0 -10000 0 0
NEMO/ATM 0.037 0.043 -9999 0 -0.4 2 2
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0.017 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.005 0.031 -9999 0 -0.39 1 1
BCL10/MALT1/TRAF6 0.025 0.014 -9999 0 -10000 0 0
NOD2 -0.008 0.12 -9999 0 -0.73 17 17
NFKB1 0.015 0 -9999 0 -10000 0 0
RELA 0.015 0 -9999 0 -10000 0 0
MALT1 0.012 0.016 -9999 0 -0.4 1 1
cIAP1/UbcH5C 0.018 0.011 -9999 0 -10000 0 0
ATM 0.012 0.016 -9999 0 -0.4 1 1
TNF/TNFR1A 0.016 0.026 -9999 0 -10000 0 0
TRAF6 0.013 0 -9999 0 -10000 0 0
PRKCA 0.013 0 -9999 0 -10000 0 0
CHUK 0.013 0 -9999 0 -10000 0 0
UBE2D3 0.013 0 -9999 0 -10000 0 0
TNF 0.009 0.036 -9999 0 -0.4 5 5
NF kappa B1 p50/RelA 0.035 0 -9999 0 -10000 0 0
BCL10 0.012 0.016 -9999 0 -0.4 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.036 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.015 0 -9999 0 -10000 0 0
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
IKK complex 0.043 0.041 -9999 0 -0.42 1 1
CYLD 0.012 0.016 -9999 0 -0.4 1 1
IKK complex/PKC alpha 0.047 0.04 -9999 0 -0.4 1 1
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.043 0.009 -10000 0 -10000 0 0
CLOCK 0.015 0.002 -10000 0 -10000 0 0
TIMELESS/CRY2 0.038 0.01 -10000 0 -10000 0 0
DEC1/BMAL1 0.004 0.077 -10000 0 -0.57 11 11
ATR 0.013 0 -10000 0 -10000 0 0
NR1D1 0.035 0.023 -10000 0 -0.54 1 1
ARNTL 0.015 0.002 -10000 0 -10000 0 0
TIMELESS 0.035 0.011 -10000 0 -10000 0 0
NPAS2 0.015 0.002 -10000 0 -10000 0 0
CRY2 0.013 0 -10000 0 -10000 0 0
mol:CO -0.012 0.004 0.097 1 -10000 0 1
CHEK1 0.013 0 -10000 0 -10000 0 0
mol:HEME 0.012 0.004 -10000 0 -0.097 1 1
PER1 0.011 0.023 -10000 0 -0.4 2 2
BMAL/CLOCK/NPAS2 0.04 0.005 -10000 0 -10000 0 0
BMAL1/CLOCK 0.04 0.035 -10000 0 -10000 0 0
S phase of mitotic cell cycle 0.043 0.009 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.043 0.009 -10000 0 -10000 0 0
mol:NADPH 0.012 0.004 -10000 0 -0.097 1 1
PER1/TIMELESS 0.037 0.015 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 -0.009 0.1 -10000 0 -0.75 11 11
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.015 0.03 -9999 0 -0.27 7 7
AKT1 0.068 0.034 -9999 0 -0.45 1 1
PTK2B 0.041 0.041 -9999 0 -0.44 1 1
VEGFR2 homodimer/Frs2 0.031 0.025 -9999 0 -0.55 1 1
CAV1 0.004 0.058 -9999 0 -0.4 13 13
CALM1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.038 0.035 -9999 0 -0.46 3 3
endothelial cell proliferation 0.045 0.066 -9999 0 -0.47 1 1
mol:Ca2+ 0.044 0.033 -9999 0 -0.41 3 3
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.044 0.034 -9999 0 -0.43 3 3
RP11-342D11.1 0.036 0.033 -9999 0 -0.42 3 3
CDH5 0.013 0 -9999 0 -10000 0 0
VEGFA homodimer 0.032 0.028 -9999 0 -0.44 2 2
SHC1 0.013 0 -9999 0 -10000 0 0
SHC2 0.001 0.087 -9999 0 -0.62 11 11
HRAS/GDP -0.002 0.025 -9999 0 -10000 0 0
SH2D2A 0.011 0.031 -9999 0 -0.75 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.063 0.041 -9999 0 -0.55 1 1
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.037 0.04 -9999 0 -0.45 4 4
VEGFR1 homodimer 0.013 0 -9999 0 -10000 0 0
SHC/GRB2/SOS1 -0.002 0.027 -9999 0 -0.42 1 1
GRB10 0.044 0.033 -9999 0 -0.45 1 1
PTPN11 0.013 0 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
PAK1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.048 0.033 -9999 0 -0.44 1 1
HRAS 0.012 0.016 -9999 0 -0.4 1 1
VEGF/Rho/ROCK1/Integrin Complex 0.04 0.041 -9999 0 -0.76 1 1
HIF1A 0.013 0 -9999 0 -10000 0 0
FRS2 0.013 0.001 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.043 0.033 -9999 0 -0.42 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.01 0.033 -9999 0 -0.4 4 4
Nck/Pak 0.019 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.038 0.035 -9999 0 -0.46 3 3
mol:GDP -0.002 0.026 -9999 0 -0.41 1 1
mol:NADP 0.058 0.039 -9999 0 -0.5 1 1
eNOS/Hsp90 0.062 0.037 -9999 0 -0.47 1 1
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:IP3 0.044 0.033 -9999 0 -0.42 3 3
HIF1A/ARNT 0.018 0.011 -9999 0 -10000 0 0
SHB 0.009 0.053 -9999 0 -0.75 3 3
VEGFA 0.012 0.043 -9999 0 -0.75 2 2
VEGFC 0.006 0.051 -9999 0 -0.4 10 10
FAK1/Vinculin 0.057 0.042 -9999 0 -0.62 1 1
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.042 0.041 -9999 0 -0.43 3 3
PTPN6 0.013 0 -9999 0 -10000 0 0
EPAS1 0.02 0.021 -9999 0 -0.34 2 2
mol:L-citrulline 0.058 0.039 -9999 0 -0.5 1 1
ITGAV 0.013 0 -9999 0 -10000 0 0
PIK3CA 0.012 0.016 -9999 0 -0.4 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.044 0.034 -9999 0 -0.43 3 3
VEGFR2 homodimer/VEGFA homodimer 0.043 0.036 -9999 0 -0.45 3 3
VEGFR2/3 heterodimer 0.029 0.031 -9999 0 -0.55 1 1
VEGFB 0.013 0 -9999 0 -10000 0 0
MAPK11 0.045 0.034 -9999 0 -0.48 1 1
VEGFR2 homodimer 0.029 0.029 -9999 0 -0.63 1 1
FLT1 0.013 0 -9999 0 -10000 0 0
NEDD4 0.014 0.001 -9999 0 -10000 0 0
MAPK3 0.024 0.049 -9999 0 -0.41 1 1
MAPK1 0.024 0.049 -9999 0 -0.41 1 1
VEGFA145/NRP2 0.017 0.039 -9999 0 -0.57 2 2
VEGFR1/2 heterodimer 0.031 0.025 -9999 0 -0.55 1 1
KDR 0.029 0.029 -9999 0 -0.63 1 1
VEGFA165/NRP1/VEGFR2 homodimer 0.045 0.035 -9999 0 -0.41 3 3
SRC 0.013 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process 0.027 0.048 -9999 0 -0.42 1 1
PI3K 0.061 0.038 -9999 0 -0.48 1 1
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.038 0.035 -9999 0 -0.46 3 3
FES 0.043 0.036 -9999 0 -0.46 1 1
GAB1 0.054 0.031 -9999 0 -0.5 1 1
VEGFR2 homodimer/VEGFA homodimer/Src 0.038 0.035 -9999 0 -0.46 3 3
CTNNB1 0.013 0 -9999 0 -10000 0 0
SOS1 0.013 0 -9999 0 -10000 0 0
ARNT 0.012 0.016 -9999 0 -0.4 1 1
eNOS/Caveolin-1 0.06 0.041 -9999 0 -0.47 1 1
VEGFR2 homodimer/VEGFA homodimer/Yes 0.038 0.04 -9999 0 -0.52 3 3
PI3K/GAB1 0.071 0.033 -9999 0 -0.46 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.048 0.033 -9999 0 -0.44 1 1
PRKACA 0.013 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.032 0.041 -9999 0 -0.44 2 2
HSP90AA1 0.013 0 -9999 0 -10000 0 0
CDC42 0.044 0.035 -9999 0 -0.42 3 3
actin cytoskeleton reorganization 0.037 0.04 -9999 0 -0.45 4 4
PTK2 0.052 0.044 -9999 0 -0.67 1 1
EDG1 0.036 0.033 -9999 0 -0.42 3 3
mol:DAG 0.044 0.033 -9999 0 -0.42 3 3
CaM/Ca2+ 0.046 0.031 -9999 0 -0.42 1 1
MAP2K3 0.047 0.033 -9999 0 -0.44 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.049 0.034 -9999 0 -0.47 1 1
PLCG1 0.044 0.033 -9999 0 -0.42 3 3
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.042 0.046 -9999 0 -0.42 6 6
IQGAP1 0.013 0 -9999 0 -10000 0 0
YES1 0.012 0.016 -9999 0 -0.4 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.038 0.035 -9999 0 -0.46 3 3
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.038 0.035 -9999 0 -0.46 3 3
cell migration 0.073 0.037 -9999 0 -0.53 1 1
mol:PI-3-4-5-P3 0.06 0.036 -9999 0 -0.45 1 1
FYN 0.013 0 -9999 0 -10000 0 0
VEGFB/NRP1 0.042 0.031 -9999 0 -0.43 1 1
mol:NO 0.058 0.039 -9999 0 -0.5 1 1
PXN 0.013 0 -9999 0 -10000 0 0
HRAS/GTP -0.002 0.025 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.047 0.034 -9999 0 -0.47 1 1
VHL 0.013 0 -9999 0 -10000 0 0
ITGB3 0.008 0.043 -9999 0 -0.4 7 7
NOS3 0.06 0.043 -9999 0 -0.58 1 1
VEGFR2 homodimer/VEGFA homodimer/Sck 0.031 0.064 -9999 0 -0.44 10 10
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA 0.047 0.031 -9999 0 -0.43 1 1
PRKCB 0.001 0.088 -9999 0 -0.43 1 1
VCL 0.013 0 -9999 0 -10000 0 0
VEGFA165/NRP1 0.038 0.033 -9999 0 -0.43 3 3
VEGFR1/2 heterodimer/VEGFA homodimer 0.038 0.035 -9999 0 -0.46 3 3
VEGFA165/NRP2 0.017 0.039 -9999 0 -0.57 2 2
MAPKKK cascade 0.061 0.03 -9999 0 -10000 0 0
NRP2 0.011 0.028 -9999 0 -0.4 3 3
VEGFC homodimer 0.006 0.051 -9999 0 -0.39 10 10
NCK1 0.013 0 -9999 0 -10000 0 0
ROCK1 0.012 0.016 -9999 0 -0.4 1 1
FAK1/Paxillin 0.057 0.042 -9999 0 -0.62 1 1
MAP3K13 0.044 0.034 -9999 0 -0.42 3 3
PDPK1 0.062 0.033 -9999 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.011 0.023 -9999 0 -0.4 2 2
SMAD2 0.012 0.012 -9999 0 -10000 0 0
SMAD3 0.033 0.016 -9999 0 -10000 0 0
SMAD3/SMAD4 0.039 0.016 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy 0.025 0.014 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.034 0.021 -9999 0 -0.38 1 1
PPM1A 0.013 0 -9999 0 -10000 0 0
CALM1 0.013 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.018 0.016 -9999 0 -10000 0 0
MAP3K1 0.012 0.016 -9999 0 -0.4 1 1
TRAP-1/SMAD4 0.017 0.02 -9999 0 -10000 0 0
MAPK3 0.012 0.016 -9999 0 -0.4 1 1
MAPK1 0.012 0.016 -9999 0 -0.4 1 1
NUP214 0.013 0 -9999 0 -10000 0 0
CTDSP1 0.013 0 -9999 0 -10000 0 0
CTDSP2 0.013 0 -9999 0 -10000 0 0
CTDSPL 0.013 0 -9999 0 -10000 0 0
KPNB1 0.013 0 -9999 0 -10000 0 0
TGFBRAP1 0.012 0.016 -9999 0 -0.4 1 1
UBE2I 0.013 0 -9999 0 -10000 0 0
NUP153 0.013 0.001 -9999 0 -10000 0 0
KPNA2 0.011 0.031 -9999 0 -0.75 1 1
PIAS4 0.013 0 -9999 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 0.019 0 -9999 0 -10000 0 0
ATM 0.012 0.016 -9999 0 -0.4 1 1
UBE2D3 0.013 0 -9999 0 -10000 0 0
PRKDC 0.011 0.031 -9999 0 -0.75 1 1
ATR 0.013 0 -9999 0 -10000 0 0
UBE2L3 0.013 0 -9999 0 -10000 0 0
FANCD2 0.021 0.016 -9999 0 -0.26 2 2
protein ubiquitination 0.03 0.041 -9999 0 -0.41 5 5
XRCC5 0.013 0 -9999 0 -10000 0 0
XRCC6 0.013 0 -9999 0 -10000 0 0
M/R/N Complex 0.025 0.01 -9999 0 -10000 0 0
MRE11A 0.013 0.001 -9999 0 -10000 0 0
DNA-PK 0.025 0.021 -9999 0 -0.49 1 1
FA complex/FANCD2/Ubiquitin 0.043 0.014 -9999 0 -10000 0 0
FANCF 0.013 0 -9999 0 -10000 0 0
BRCA1 0.013 0 -9999 0 -10000 0 0
CCNE1 0.006 0.068 -9999 0 -0.75 5 5
CDK2/Cyclin E1 0.014 0.053 -9999 0 -0.57 5 5
FANCG 0.011 0.031 -9999 0 -0.75 1 1
BRCA1/BACH1/BARD1 0.019 0 -9999 0 -10000 0 0
FANCE 0.013 0 -9999 0 -10000 0 0
FANCC 0.013 0 -9999 0 -10000 0 0
NBN 0.012 0.016 -9999 0 -0.4 1 1
FANCA 0.013 0 -9999 0 -10000 0 0
DNA repair 0.059 0.015 -9999 0 -10000 0 0
BRCA1/BARD1/ubiquitin 0.019 0 -9999 0 -10000 0 0
BARD1/DNA-PK 0.032 0.019 -9999 0 -0.45 1 1
FANCL 0.013 0 -9999 0 -10000 0 0
mRNA polyadenylation -0.019 0 -9999 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.032 0.02 -9999 0 -0.29 2 2
BRCA1/BACH1/BARD1/TopBP1 0.026 0 -9999 0 -10000 0 0
BRCA1/BARD1/P53 0.032 0 -9999 0 -10000 0 0
BARD1/CSTF1/BRCA1 0.026 0 -9999 0 -10000 0 0
BRCA1/BACH1 0.013 0 -9999 0 -10000 0 0
BARD1 0.013 0 -9999 0 -10000 0 0
PCNA 0.013 0 -9999 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.026 0 -9999 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.026 0 -9999 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.032 0 -9999 0 -10000 0 0
BARD1/DNA-PK/P53 0.037 0.018 -9999 0 -0.42 1 1
BRCA1/BARD1/Ubiquitin 0.019 0 -9999 0 -10000 0 0
BRCA1/BARD1/CTIP 0.029 0.017 -9999 0 -10000 0 0
FA complex 0.034 0.01 -9999 0 -10000 0 0
BARD1/EWS 0.019 0 -9999 0 -10000 0 0
RBBP8 0.017 0.023 -9999 0 -10000 0 0
TP53 0.013 0 -9999 0 -10000 0 0
TOPBP1 0.013 0 -9999 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.031 0 -9999 0 -10000 0 0
BRCA1/BARD1 0.033 0.041 -9999 0 -0.42 5 5
CSTF1 0.013 0 -9999 0 -10000 0 0
BARD1/EWS-Fli1 0.009 0 -9999 0 -10000 0 0
CDK2 0.013 0 -9999 0 -10000 0 0
UniProt:Q9BZD1 0 0 -9999 0 -10000 0 0
RAD51 0.013 0 -9999 0 -10000 0 0
RAD50 0.013 0 -9999 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.019 0 -9999 0 -10000 0 0
EWSR1 0.013 0 -9999 0 -10000 0 0
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 0.013 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.023 0.018 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0 0.006 -9999 0 -10000 0 0
AURKB 0.013 0 -9999 0 -10000 0 0
AURKC 0.009 0.033 -9999 0 -0.4 4 4
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 0.061 -10000 0 -10000 0 0
CaM/Ca2+ 0.009 0 -10000 0 -10000 0 0
AKT1 0.013 0 -10000 0 -10000 0 0
AKT2 0.013 0 -10000 0 -10000 0 0
STXBP4 0.012 0.016 -10000 0 -0.4 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.018 0.069 0.27 6 -10000 0 6
YWHAZ 0.013 0 -10000 0 -10000 0 0
CALM1 0.013 0 -10000 0 -10000 0 0
YWHAQ 0.013 0 -10000 0 -10000 0 0
TBC1D4 0.019 0.012 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.013 0 -10000 0 -10000 0 0
YWHAB 0.013 0 -10000 0 -10000 0 0
SNARE/Synip 0.025 0.01 -10000 0 -10000 0 0
YWHAG 0.013 0 -10000 0 -10000 0 0
ASIP -0.002 0.086 -10000 0 -0.75 8 8
PRKCI 0.011 0.023 -10000 0 -0.4 2 2
AS160/CaM/Ca2+ 0.009 0 -10000 0 -10000 0 0
RHOQ 0.013 0 -10000 0 -10000 0 0
GYS1 0.026 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
TRIP10 0.013 0 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.017 0 -10000 0 -10000 0 0
AS160/14-3-3 0.038 0.012 -10000 0 -10000 0 0
VAMP2 0.013 0 -10000 0 -10000 0 0
SLC2A4 0.018 0.074 0.28 6 -10000 0 6
STX4 0.013 0 -10000 0 -10000 0 0
GSK3B 0.022 0 -10000 0 -10000 0 0
SFN 0.011 0.023 -10000 0 -0.4 2 2
LNPEP 0.012 0.001 -10000 0 -10000 0 0
YWHAE 0.013 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 0.013 0 -10000 0 -10000 0 0
mol:PIP3 0 0.015 0.23 2 -10000 0 2
FRAP1 0.013 0.007 -10000 0 -10000 0 0
AKT1 0.023 0.014 0.2 2 -10000 0 2
INSR 0.013 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.008 0 -10000 0 -10000 0 0
mol:GTP 0.03 0.008 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.001 0.011 -10000 0 -0.25 1 1
TSC2 0.012 0 -10000 0 -10000 0 0
RHEB/GDP 0 0.006 -10000 0 -10000 0 0
TSC1 0.013 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.015 0 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.001 0.013 -10000 0 -0.29 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.013 0 -10000 0 -10000 0 0
RPS6KB1 0.023 0.016 -10000 0 -0.3 1 1
MAP3K5 0.009 0 -10000 0 -10000 0 0
PIK3R1 0.013 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 0.015 -10000 0 -0.26 1 1
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.03 0.019 -10000 0 -0.32 1 1
eIF4E/eIF4G1/eIF4A1 0 0.006 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.023 0.008 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.025 0.009 0.15 2 -10000 0 2
FKBP1A 0.013 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 0.019 0.013 -10000 0 -10000 0 0
EIF4E 0.011 0.023 -10000 0 -0.4 2 2
ASK1/PP5C 0.021 0.004 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.014 0.023 -10000 0 -0.4 2 2
TSC1/TSC2 0.033 0.009 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RPS6 0.011 0.031 -10000 0 -0.75 1 1
PPP5C 0.013 0 -10000 0 -10000 0 0
EIF4G1 0.013 0 -10000 0 -10000 0 0
IRS1 0.007 0.001 -10000 0 -10000 0 0
INS 0 0 -10000 0 -10000 0 0
PTEN 0.011 0.023 -10000 0 -0.39 2 2
PDK2 0.019 0.015 0.21 2 -10000 0 2
EIF4EBP1 0.01 0.023 -10000 0 -0.28 4 4
PIK3CA 0.012 0.016 -10000 0 -0.4 1 1
PPP2R5D 0.017 0.006 -10000 0 -10000 0 0
peptide biosynthetic process 0.014 0.019 -10000 0 -0.46 1 1
RHEB 0.013 0 -10000 0 -10000 0 0
EIF4A1 0.013 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 0.003 2 -10000 0 2
EEF2 0.014 0.019 -10000 0 -0.46 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 0.03 0.009 -9999 0 -10000 0 0
CDKN1B 0.03 0.011 -9999 0 -10000 0 0
CDKN1A 0.03 0.014 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
PRKDC 0.011 0.031 -9999 0 -0.75 1 1
FOXO3 0.03 0.011 -9999 0 -10000 0 0
AKT1 0.025 0.012 -9999 0 -10000 0 0
BAD 0.012 0.016 -9999 0 -0.4 1 1
AKT3 0.011 0.034 -9999 0 -0.27 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
FOXO4 0.03 0.011 -9999 0 -10000 0 0
AKT1/ASK1 0.03 0.011 -9999 0 -10000 0 0
BAD/YWHAZ 0.025 0.01 -9999 0 -10000 0 0
RICTOR 0.009 0.036 -9999 0 -0.4 5 5
RAF1 0.013 0 -9999 0 -10000 0 0
JNK cascade -0.029 0.011 -9999 0 -10000 0 0
TSC1 0.03 0.011 -9999 0 -10000 0 0
YWHAZ 0.013 0 -9999 0 -10000 0 0
AKT1/RAF1 0.031 0.012 -9999 0 -10000 0 0
EP300 0.013 0 -9999 0 -10000 0 0
mol:GDP 0.025 0.012 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
TSC2 0.03 0.011 -9999 0 -10000 0 0
YWHAQ 0.013 0 -9999 0 -10000 0 0
TBC1D4 0.019 0.009 -9999 0 -10000 0 0
MAP3K5 0.013 0 -9999 0 -10000 0 0
MAPKAP1 0.013 0 -9999 0 -10000 0 0
negative regulation of cell cycle -0.037 0.009 -9999 0 -10000 0 0
YWHAH 0.013 0 -9999 0 -10000 0 0
AKT1S1 0.03 0.011 -9999 0 -10000 0 0
CASP9 0.03 0.011 -9999 0 -10000 0 0
YWHAB 0.013 0 -9999 0 -10000 0 0
p27Kip1/KPNA1 0.036 0.011 -9999 0 -10000 0 0
GBL 0 0 -9999 0 -10000 0 0
PDK1/Src/Hsp90 0.026 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
SRC 0.013 0 -9999 0 -10000 0 0
AKT2/p21CIP1 0.033 0.013 -9999 0 -10000 0 0
KIAA1303 0 0 -9999 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.015 0.004 -9999 0 -10000 0 0
CHUK 0.03 0.011 -9999 0 -10000 0 0
BAD/BCL-XL 0.042 0.013 -9999 0 -10000 0 0
mTORC2 0.014 0.019 -9999 0 -10000 0 0
AKT2 0.015 0 -9999 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.049 0.012 -9999 0 -10000 0 0
PDPK1 0.013 0 -9999 0 -10000 0 0
MDM2 0.03 0.014 -9999 0 -10000 0 0
MAPKKK cascade -0.031 0.011 -9999 0 -10000 0 0
MDM2/Cbp/p300 0.042 0.013 -9999 0 -10000 0 0
TSC1/TSC2 0.034 0.011 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.04 0.013 -9999 0 -10000 0 0
glucose import -0.002 0.069 -9999 0 -10000 0 0
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.026 0.009 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
SLC2A4 -0.002 0.07 -9999 0 -10000 0 0
GSK3A 0.03 0.011 -9999 0 -10000 0 0
FOXO1 0.03 0.014 -9999 0 -10000 0 0
GSK3B 0.03 0.011 -9999 0 -10000 0 0
SFN 0.011 0.023 -9999 0 -0.4 2 2
G1/S transition of mitotic cell cycle 0.034 0.011 -9999 0 -10000 0 0
p27Kip1/14-3-3 family 0.041 0.01 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
KPNA1 0.013 0 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
YWHAG 0.013 0 -9999 0 -10000 0 0
RHEB 0.013 0 -9999 0 -10000 0 0
CREBBP 0.013 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 -0.002 0.02 -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 0.039 0.024 -9999 0 -10000 0 0
SUMO1 0.011 0.023 -9999 0 -0.4 2 2
ZFPM1 -0.002 0.1 -9999 0 -0.75 12 12
NPC/RanGAP1/SUMO1/Ubc9 0.017 0.014 -9999 0 -10000 0 0
FKBP3 0.011 0.023 -9999 0 -0.4 2 2
Histones 0.04 0.013 -9999 0 -10000 0 0
YY1/LSF 0.018 0.044 -9999 0 -10000 0 0
SMG5 0.013 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 0.028 0.019 -9999 0 -10000 0 0
I kappa B alpha/HDAC1 0.028 0.014 -9999 0 -10000 0 0
SAP18 0.013 0 -9999 0 -10000 0 0
RELA 0.031 0.019 -9999 0 -10000 0 0
HDAC1/Smad7 0.025 0.01 -9999 0 -10000 0 0
RANGAP1 0.011 0.031 -9999 0 -0.75 1 1
HDAC3/TR2 0.028 0.014 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.04 0.01 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.034 0.017 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.005 0.054 -9999 0 -0.4 11 11
GATA1 0.008 0.006 -9999 0 -10000 0 0
Mad/Max 0.018 0.016 -9999 0 -0.27 2 2
NuRD/MBD3 Complex/GATA1/Fog1 0.044 0.028 -9999 0 -10000 0 0
RBBP7 0.013 0 -9999 0 -10000 0 0
NPC 0.007 0 -9999 0 -10000 0 0
RBBP4 0.013 0 -9999 0 -10000 0 0
MAX 0.013 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.013 0 -9999 0 -10000 0 0
NFKBIA 0.023 0.015 -9999 0 -10000 0 0
KAT2B -0.005 0.083 -9999 0 -0.4 27 27
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 0.013 0 -9999 0 -10000 0 0
CHD3 0.013 0 -9999 0 -10000 0 0
SAP30 0.013 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.013 0 -9999 0 -10000 0 0
YY1/HDAC3 0.028 0.039 -9999 0 -10000 0 0
YY1/HDAC2 0.018 0.043 -9999 0 -10000 0 0
YY1/HDAC1 0.018 0.043 -9999 0 -10000 0 0
NuRD/MBD2 Complex (MeCP1) 0.04 0 -9999 0 -10000 0 0
PPARG 0.03 0.029 -9999 0 -10000 0 0
HDAC8/hEST1B 0.026 0 -9999 0 -10000 0 0
UBE2I 0.013 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.013 0 -9999 0 -10000 0 0
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.027 0.016 -9999 0 -10000 0 0
MBD3L2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.025 0.01 -9999 0 -10000 0 0
CREBBP 0.013 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.043 0.01 -9999 0 -10000 0 0
HDAC1 0.013 0 -9999 0 -10000 0 0
HDAC3 0.023 0.015 -9999 0 -10000 0 0
HDAC2 0.013 0 -9999 0 -10000 0 0
YY1 0.015 0.051 -9999 0 -10000 0 0
HDAC8 0.013 0 -9999 0 -10000 0 0
SMAD7 0.012 0.016 -9999 0 -0.4 1 1
NCOR2 0.012 0.016 -9999 0 -0.4 1 1
MXD1 0.011 0.023 -9999 0 -0.4 2 2
STAT3 0.022 0 -9999 0 -10000 0 0
NFKB1 0.013 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.013 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 0.025 0.041 -9999 0 -10000 0 0
YY1/SAP30/HDAC1 0.025 0.04 -9999 0 -10000 0 0
EP300 0.013 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.022 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.015 -9999 0 -10000 0 0
histone deacetylation 0.04 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.034 0.013 -9999 0 -10000 0 0
nuclear export -0.025 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GATAD2B 0.013 0 -9999 0 -10000 0 0
GATAD2A 0.013 0 -9999 0 -10000 0 0
GATA2/HDAC3 0.024 0.033 -9999 0 -0.33 1 1
GATA1/HDAC1 0.015 0.004 -9999 0 -10000 0 0
GATA1/HDAC3 0.025 0.014 -9999 0 -10000 0 0
CHD4 0.013 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A 0.016 0.026 -9999 0 -10000 0 0
SIN3/HDAC complex/Mad/Max 0.04 0.01 -9999 0 -10000 0 0
NuRD Complex 0.047 0.01 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.039 0.012 -9999 0 -10000 0 0
SIN3B 0.013 0 -9999 0 -10000 0 0
MTA2 0.013 0 -9999 0 -10000 0 0
SIN3A 0.013 0 -9999 0 -10000 0 0
XPO1 0.013 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.026 0.018 -9999 0 -0.26 2 2
HDAC complex 0.032 0 -9999 0 -10000 0 0
GATA1/Fog1 0.004 0.081 -9999 0 -0.57 12 12
FKBP25/HDAC1/HDAC2 0.025 0.014 -9999 0 -10000 0 0
TNF 0.009 0.036 -9999 0 -0.4 5 5
negative regulation of cell growth 0.04 0.01 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.04 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 0.034 0.025 -9999 0 -10000 0 0
SIN3/HDAC complex/NCoR1 0.039 0 -9999 0 -10000 0 0
TFCP2 0.012 0.016 -9999 0 -0.4 1 1
NR2C1 0.013 0 -9999 0 -10000 0 0
MBD3 0.011 0.035 -9999 0 -0.57 2 2
MBD2 0.013 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 0.019 0 -9999 0 -10000 0 0
FBXW11 0.013 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 0.023 -9999 0 -10000 0 0
NFKBIA 0.021 0.026 -9999 0 -10000 0 0
MAPK14 0.013 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 0.016 -9999 0 -0.4 1 1
NF kappa B1 p50 dimer 0.018 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
NFKB1 0.019 0 -9999 0 -10000 0 0
RELA 0.013 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.027 0.025 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.041 0.023 -9999 0 -10000 0 0
SRC 0.013 0 -9999 0 -10000 0 0
PI3K 0.018 0.011 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.027 0.025 -9999 0 -10000 0 0
IKBKB 0.013 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.013 0 -9999 0 -10000 0 0
SYK 0.013 0 -9999 0 -10000 0 0
I kappa B alpha/PIK3R1 0.027 0.025 -9999 0 -10000 0 0
cell death 0.039 0.022 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.023 0.001 -9999 0 -10000 0 0
LCK 0.001 0.089 -9999 0 -0.68 10 10
BCL3 0.013 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 0.013 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.005 -9999 0 -10000 0 0
MDM2/SUMO1 0.026 0.024 -9999 0 -0.35 2 2
HDAC4 0.013 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0 0.005 -9999 0 -10000 0 0
SUMO1 0.011 0.023 -9999 0 -0.4 2 2
NPC/RanGAP1/SUMO1 0.014 0.015 -9999 0 -0.2 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.022 0.013 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.013 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.026 0.018 -9999 0 -0.26 2 2
SUMO1/HDAC1 0.026 0.018 -9999 0 -0.26 2 2
RANGAP1 0.011 0.031 -9999 0 -0.75 1 1
MDM2/SUMO1/SUMO1 0.031 0.019 -9999 0 -0.4 1 1
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.017 0.014 -9999 0 -0.18 3 3
Ran/GTP 0.023 0.013 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.012 0.016 -9999 0 -0.4 1 1
UBE2I 0.013 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 0.013 0.001 -9999 0 -10000 0 0
PIAS1 0.013 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 0.025 0.01 -9999 0 -10000 0 0
E-cadherin/beta catenin 0.019 0 -9999 0 -10000 0 0
CTNNB1 0.013 0 -9999 0 -10000 0 0
JUP 0.012 0.016 -9999 0 -0.4 1 1
CDH1 0.013 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 0.024 -9999 0 -0.35 3 3
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 0.011 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.018 0 -9999 0 -10000 0 0
CLTB 0.013 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.022 0 -9999 0 -10000 0 0
CD4 0.001 0.066 -9999 0 -0.4 17 17
CLTA 0.013 0 -9999 0 -10000 0 0
mol:GTP 0.001 0 -9999 0 -10000 0 0
ARFGAP1 0.007 0.035 -9999 0 -0.48 3 3
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
ARF1/GTP 0.015 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.021 0.026 -9999 0 -0.39 2 2
mol:Choline 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.013 0 -9999 0 -10000 0 0
DDEF1 0 0 -9999 0 -10000 0 0
ARF1/GDP 0.005 0.026 -9999 0 -0.36 3 3
AP2M1 0.013 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0.014 0 -9999 0 -10000 0 0
Rac/GTP 0.01 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.021 0.027 -9999 0 -0.43 2 2
ARFIP2 0.011 0 -9999 0 -10000 0 0
COPA 0.013 0 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.022 0 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0.009 0 -9999 0 -10000 0 0
GGA3 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0.017 0 -9999 0 -10000 0 0
AP2A1 0.012 0.016 -9999 0 -0.4 1 1
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.022 0.015 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0.017 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0.016 0 -9999 0 -10000 0 0
CYTH2 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0.018 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 0.025 0.032 -9999 0 -10000 0 0
PLD2 0 0 -9999 0 -10000 0 0
ARF-GAP1/v-SNARE 0.007 0.035 -9999 0 -0.48 3 3
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 0.007 0.035 -9999 0 -0.48 3 3
GOSR2 0.013 0 -9999 0 -10000 0 0
USO1 0.013 0 -9999 0 -10000 0 0
GBF1 0.013 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 0.019 0.041 -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 0.019 0 -9999 0 -9999 0 0
FBXW11 0.013 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 0.013 0 -9999 0 -9999 0 0
CHUK 0.013 0 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.037 0 -9999 0 -9999 0 0
NFKB1 0.013 0 -9999 0 -9999 0 0
MAP3K14 0.013 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.019 0 -9999 0 -9999 0 0
RELB 0.013 0 -9999 0 -9999 0 0
NFKB2 0.013 0 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.017 0 -9999 0 -9999 0 0
regulation of B cell activation 0.017 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 623 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.WS.AB45 TCGA.T9.A92H TCGA.SS.A7HO TCGA.RU.A8FL
109_MAP3K5 0.045 0.045 -0.19 -0.19
47_PPARGC1A 0.013 0.013 0.013 0.013
105_BMP4 0.013 0.013 0.013 0.013
105_BMP6 0.013 0.013 0.013 0.013
105_BMP7 -0.39 0.013 0.013 -0.75
105_BMP2 0.013 0.013 -0.39 -0.39
131_RELN/VLDLR -0.44 -0.63 -0.45 -0.63
30_TGFB1/TGF beta receptor Type II 0.012 0.012 0.017 0.018
84_STAT5B -0.039 0.04 -0.033 -0.021
84_STAT5A -0.039 0.04 -0.033 -0.021
Methods & Data
Input

  • Expression Data Normalization = Normal controls were used to median center the expression data used in this analysis.

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/COADREAD-TP/22314768/COADREAD-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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