PARADIGM pathway analysis of mRNASeq expression data
Stomach Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1G16092
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/C1G16092
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 90
IL23-mediated signaling events 89
Syndecan-1-mediated signaling events 88
Reelin signaling pathway 86
FOXA2 and FOXA3 transcription factor networks 83
Osteopontin-mediated events 79
Ephrin B reverse signaling 67
EPHB forward signaling 66
Lissencephaly gene (LIS1) in neuronal migration and development 57
IL4-mediated signaling events 53
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 415 . 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 ( 415 ).

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 0.2169 90 726 8 -0.25 0.068 1000 -1000 -0.024 -1000
IL23-mediated signaling events 0.2145 89 5392 60 -0.76 0.012 1000 -1000 -0.2 -1000
Syndecan-1-mediated signaling events 0.2120 88 2993 34 -0.4 0.012 1000 -1000 -0.074 -1000
Reelin signaling pathway 0.2072 86 4836 56 -0.47 0.019 1000 -1000 -0.1 -1000
FOXA2 and FOXA3 transcription factor networks 0.2000 83 3858 46 -0.93 0.032 1000 -1000 -0.14 -1000
Osteopontin-mediated events 0.1904 79 3017 38 -0.39 0.015 1000 -1000 -0.11 -1000
Ephrin B reverse signaling 0.1614 67 3222 48 -0.43 0.33 1000 -1000 -0.08 -1000
EPHB forward signaling 0.1590 66 5637 85 -0.43 0.28 1000 -1000 -0.11 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1373 57 3125 54 -0.37 0.025 1000 -1000 -0.11 -1000
IL4-mediated signaling events 0.1277 53 4876 91 -0.81 0.7 1000 -1000 -0.21 -1000
HIF-1-alpha transcription factor network 0.1181 49 3732 76 -0.6 0.02 1000 -1000 -0.23 -1000
Effects of Botulinum toxin 0.1157 48 1249 26 -0.38 0.012 1000 -1000 -0.083 -1000
Wnt signaling 0.1108 46 322 7 -0.18 -0.058 1000 -1000 -0.034 -1000
Glypican 2 network 0.1012 42 171 4 -0.076 -1000 1000 -1000 -0.036 -1000
TCGA08_p53 0.0988 41 291 7 -0.19 0.075 1000 -1000 -0.026 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0892 37 2938 78 -0.2 0.064 1000 -1000 -0.094 -1000
Syndecan-4-mediated signaling events 0.0867 36 2420 67 -0.49 0.045 1000 -1000 -0.11 -1000
Glucocorticoid receptor regulatory network 0.0843 35 4001 114 -0.69 0.32 1000 -1000 -0.096 -1000
Syndecan-2-mediated signaling events 0.0795 33 2308 69 -0.43 0.039 1000 -1000 -0.061 -1000
Noncanonical Wnt signaling pathway 0.0747 31 823 26 -0.18 0.012 1000 -1000 -0.076 -1000
Visual signal transduction: Cones 0.0699 29 1118 38 -0.23 0.021 1000 -1000 -0.083 -1000
Signaling events mediated by the Hedgehog family 0.0699 29 1556 52 -0.11 0.07 1000 -1000 -0.081 -1000
amb2 Integrin signaling 0.0699 29 2412 82 -0.24 0.012 1000 -1000 -0.11 -1000
p75(NTR)-mediated signaling 0.0675 28 3502 125 -0.51 0.03 1000 -1000 -0.11 -1000
Glypican 1 network 0.0675 28 1355 48 -0.29 0.025 1000 -1000 -0.061 -1000
Signaling events regulated by Ret tyrosine kinase 0.0675 28 2335 82 -0.18 0.012 1000 -1000 -0.11 -1000
Endothelins 0.0627 26 2549 96 -0.27 0.048 1000 -1000 -0.11 -1000
BCR signaling pathway 0.0578 24 2389 99 -0.18 0.017 1000 -1000 -0.11 -1000
EGFR-dependent Endothelin signaling events 0.0578 24 506 21 -0.086 0.019 1000 -1000 -0.082 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0554 23 796 34 -0.08 0.012 1000 -1000 -0.076 -1000
Syndecan-3-mediated signaling events 0.0554 23 807 35 -0.41 0.019 1000 -1000 -0.083 -1000
Canonical Wnt signaling pathway 0.0554 23 1182 51 -0.36 0.057 1000 -1000 -0.084 -1000
BMP receptor signaling 0.0530 22 1847 81 -0.23 0.042 1000 -1000 -0.12 -1000
Fc-epsilon receptor I signaling in mast cells 0.0530 22 2173 97 -0.17 0.034 1000 -1000 -0.1 -1000
FOXM1 transcription factor network 0.0530 22 1139 51 -0.28 0.033 1000 -1000 -0.23 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0506 21 1473 68 -0.46 0.039 1000 -1000 -0.15 -1000
IL12-mediated signaling events 0.0482 20 1768 87 -0.3 0.018 1000 -1000 -0.15 -1000
ErbB4 signaling events 0.0482 20 1402 69 -0.25 0.097 1000 -1000 -0.11 -1000
IFN-gamma pathway 0.0458 19 1298 68 -0.2 0.023 1000 -1000 -0.12 -1000
Visual signal transduction: Rods 0.0458 19 991 52 -0.12 0.012 1000 -1000 -0.099 -1000
Presenilin action in Notch and Wnt signaling 0.0434 18 1154 61 -0.36 0.04 1000 -1000 -0.091 -1000
Calcium signaling in the CD4+ TCR pathway 0.0434 18 571 31 -0.24 0.012 1000 -1000 -0.11 -1000
Integrins in angiogenesis 0.0410 17 1475 84 -0.4 0.03 1000 -1000 -0.11 -1000
Regulation of Telomerase 0.0410 17 1759 102 -0.22 0.033 1000 -1000 -0.13 -1000
Retinoic acid receptors-mediated signaling 0.0386 16 949 58 -0.36 0.016 1000 -1000 -0.098 -1000
TCR signaling in naïve CD8+ T cells 0.0386 16 1531 93 -0.22 0.094 1000 -1000 -0.11 -1000
Aurora B signaling 0.0386 16 1102 67 -0.32 0.02 1000 -1000 -0.088 -1000
Nectin adhesion pathway 0.0361 15 986 63 -0.63 0.033 1000 -1000 -0.091 -1000
IL1-mediated signaling events 0.0361 15 930 62 -0.15 0.047 1000 -1000 -0.12 -1000
S1P1 pathway 0.0361 15 552 36 -0.095 0.012 1000 -1000 -0.075 -1000
Signaling mediated by p38-alpha and p38-beta 0.0361 15 697 44 -0.28 0.012 1000 -1000 -0.056 -1000
IL27-mediated signaling events 0.0361 15 784 51 -0.28 0.025 1000 -1000 -0.1 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0361 15 1829 120 -0.18 0.1 1000 -1000 -0.092 -1000
PDGFR-beta signaling pathway 0.0361 15 1476 97 -0.12 0.034 1000 -1000 -0.11 -1000
ErbB2/ErbB3 signaling events 0.0337 14 943 65 -0.2 0.02 1000 -1000 -0.089 -1000
S1P5 pathway 0.0337 14 238 17 -0.094 0.061 1000 -1000 -0.053 -1000
Nongenotropic Androgen signaling 0.0337 14 748 52 -0.094 0.012 1000 -1000 -0.069 -1000
PLK1 signaling events 0.0313 13 1186 85 -0.17 0.025 1000 -1000 -0.05 -1000
Arf6 signaling events 0.0289 12 798 62 -0.13 0.02 1000 -1000 -0.084 -1000
Signaling events mediated by PTP1B 0.0289 12 955 76 -0.36 0.057 1000 -1000 -0.1 -1000
Aurora A signaling 0.0289 12 764 60 -0.12 0.017 1000 -1000 -0.071 -1000
LPA receptor mediated events 0.0289 12 1286 102 -0.24 0.042 1000 -1000 -0.11 -1000
IL6-mediated signaling events 0.0289 12 954 75 -0.36 0.05 1000 -1000 -0.13 -1000
Cellular roles of Anthrax toxin 0.0265 11 435 39 -0.036 0.013 1000 -1000 -0.036 -1000
Plasma membrane estrogen receptor signaling 0.0265 11 983 86 -0.16 0.03 1000 -1000 -0.1 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0265 11 381 33 -0.24 0.037 1000 -1000 -0.077 -1000
S1P4 pathway 0.0265 11 299 25 -0.094 0.024 1000 -1000 -0.067 -1000
E-cadherin signaling events 0.0265 11 57 5 -0.03 0.01 1000 -1000 -0.049 -1000
Regulation of Androgen receptor activity 0.0265 11 805 70 -0.55 0.037 1000 -1000 -0.084 -1000
LPA4-mediated signaling events 0.0241 10 130 12 -0.05 0.019 1000 -1000 -0.026 -1000
Caspase cascade in apoptosis 0.0241 10 777 74 -0.1 0.039 1000 -1000 -0.051 -1000
Ephrin A reverse signaling 0.0241 10 71 7 -0.03 0 1000 -1000 -0.039 -1000
S1P3 pathway 0.0241 10 436 42 -0.092 0.023 1000 -1000 -0.054 -1000
Ras signaling in the CD4+ TCR pathway 0.0241 10 182 17 -0.023 0.019 1000 -1000 -0.052 -1000
Regulation of nuclear SMAD2/3 signaling 0.0217 9 1317 136 -0.19 0.12 1000 -1000 -0.095 -1000
Coregulation of Androgen receptor activity 0.0217 9 691 76 -0.24 0.025 1000 -1000 -0.059 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0217 9 268 28 -0.094 0.026 1000 -1000 -0.045 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0217 9 514 52 -0.18 0.035 1000 -1000 -0.081 -1000
IL2 signaling events mediated by PI3K 0.0217 9 562 58 -0.27 0.047 1000 -1000 -0.11 -1000
IGF1 pathway 0.0217 9 547 57 -0.071 0.021 1000 -1000 -0.13 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0217 9 840 88 -0.14 0.074 1000 -1000 -0.13 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0193 8 705 85 -0.061 0.035 1000 -1000 -0.1 -1000
Signaling events mediated by PRL 0.0193 8 281 34 -0.11 0.032 1000 -1000 -0.044 -1000
JNK signaling in the CD4+ TCR pathway 0.0169 7 134 17 -0.02 0.035 1000 -1000 -0.083 -1000
Thromboxane A2 receptor signaling 0.0169 7 777 105 -0.16 0.031 1000 -1000 -0.073 -1000
FAS signaling pathway (CD95) 0.0169 7 335 47 -0.1 0.023 1000 -1000 -0.06 -1000
Class I PI3K signaling events 0.0169 7 583 73 -0.11 0.029 1000 -1000 -0.077 -1000
BARD1 signaling events 0.0145 6 353 57 -0.11 0.035 1000 -1000 -0.09 -1000
PLK2 and PLK4 events 0.0145 6 20 3 0 0.005 1000 -1000 -0.015 -1000
Hedgehog signaling events mediated by Gli proteins 0.0120 5 360 65 -0.094 0.056 1000 -1000 -0.08 -1000
Aurora C signaling 0.0120 5 38 7 -0.012 0 1000 -1000 -0.036 -1000
EPO signaling pathway 0.0120 5 295 55 -0.019 0.05 1000 -1000 -0.11 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0120 5 221 37 -0.13 0.041 1000 -1000 -0.071 -1000
FoxO family signaling 0.0120 5 322 64 -0.088 0.11 1000 -1000 -0.1 -1000
TCGA08_rtk_signaling 0.0120 5 147 26 -0.055 0.039 1000 -1000 -0.03 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0120 5 406 74 -0.14 0.062 1000 -1000 -0.12 -1000
IL2 signaling events mediated by STAT5 0.0120 5 117 22 -0.032 0.047 1000 -1000 -0.082 -1000
Rapid glucocorticoid signaling 0.0120 5 109 20 -0.02 0.012 1000 -1000 -0.048 -1000
PDGFR-alpha signaling pathway 0.0096 4 217 44 -0.049 0.033 1000 -1000 -0.071 -1000
Signaling events mediated by HDAC Class III 0.0096 4 160 40 -0.035 0.021 1000 -1000 -0.053 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0096 4 391 83 -0.37 0.067 1000 -1000 -0.086 -1000
Insulin Pathway 0.0096 4 299 74 -0.11 0.037 1000 -1000 -0.12 -1000
VEGFR1 specific signals 0.0096 4 261 56 -0.017 0.045 1000 -1000 -0.091 -1000
E-cadherin signaling in keratinocytes 0.0096 4 197 43 -0.054 0.033 1000 -1000 -0.079 -1000
Ceramide signaling pathway 0.0072 3 297 76 -0.078 0.042 1000 -1000 -0.066 -1000
Signaling mediated by p38-gamma and p38-delta 0.0072 3 58 15 -0.043 0.027 1000 -1000 -0.058 -1000
Regulation of p38-alpha and p38-beta 0.0072 3 202 54 -0.11 0.032 1000 -1000 -0.075 -1000
E-cadherin signaling in the nascent adherens junction 0.0072 3 276 76 -0.028 0.048 1000 -1000 -0.099 -1000
Class IB PI3K non-lipid kinase events 0.0072 3 9 3 -0.007 0.007 1000 -1000 -0.019 -1000
a4b1 and a4b7 Integrin signaling 0.0048 2 12 5 0.006 0.013 1000 -1000 -0.03 -1000
TRAIL signaling pathway 0.0048 2 99 48 -0.008 0.048 1000 -1000 -0.077 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0048 2 96 45 -0.024 0.068 1000 -1000 -0.1 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0048 2 254 125 -0.015 0.078 1000 -1000 -0.11 -1000
Arf6 trafficking events 0.0048 2 157 71 -0.14 0.041 1000 -1000 -0.099 -1000
p38 MAPK signaling pathway 0.0048 2 92 44 -0.08 0.033 1000 -1000 -0.086 -1000
Canonical NF-kappaB pathway 0.0024 1 60 39 -0.022 0.077 1000 -1000 -0.1 -1000
Signaling events mediated by HDAC Class II 0.0024 1 85 75 -0.028 0.032 1000 -1000 -0.088 -1000
Circadian rhythm pathway 0.0024 1 22 22 -0.013 0.044 1000 -1000 -0.064 -1000
Arf6 downstream pathway 0.0024 1 70 43 -0.026 0.026 1000 -1000 -0.053 -1000
Insulin-mediated glucose transport 0.0024 1 61 32 -0.049 0.033 1000 -1000 -0.083 -1000
Class I PI3K signaling events mediated by Akt 0.0024 1 88 68 -0.069 0.051 1000 -1000 -0.071 -1000
ceramide signaling pathway 0.0024 1 69 49 -0.023 0.045 1000 -1000 -0.056 -1000
HIF-2-alpha transcription factor network 0.0024 1 82 43 -0.074 0.075 1000 -1000 -0.12 -1000
Signaling events mediated by HDAC Class I 0.0024 1 119 104 -0.022 0.053 1000 -1000 -0.078 -1000
Paxillin-dependent events mediated by a4b1 0.0024 1 53 36 -0.032 0.033 1000 -1000 -0.099 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0024 1 36 27 -0.01 0.031 1000 -1000 -0.055 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 6 23 -0.001 0.043 1000 -1000 -0.077 -1000
mTOR signaling pathway 0.0000 0 18 53 -0.002 0.036 1000 -1000 -0.073 -1000
Atypical NF-kappaB pathway 0.0000 0 15 31 -0.01 0.042 1000 -1000 -0.047 -1000
Arf1 pathway 0.0000 0 4 54 -0.003 0.033 1000 -1000 -0.058 -1000
Alternative NF-kappaB pathway 0.0000 0 5 13 -0.001 0.017 1000 -1000 -0.076 -1000
Total NA 2315 130570 7203 -25 -990 131000 -131000 -11 -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 -0.001 0.067 -10000 0 -0.45 9 9
CDKN2C 0.027 0.05 -10000 0 -0.78 1 1
CDKN2A -0.25 0.4 -10000 0 -0.84 127 127
CCND2 0.053 0.087 0.19 109 -0.15 2 111
RB1 -0.05 0.1 -10000 0 -0.21 114 114
CDK4 0.068 0.1 0.22 126 -10000 0 126
CDK6 0.059 0.099 0.21 117 -0.14 7 124
G1/S progression 0.05 0.1 0.21 114 -10000 0 114
IL23-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
CCL2 -0.62 0.44 -10000 0 -1.1 140 140
IL23A -0.68 0.49 -10000 0 -1.2 143 143
NF kappa B1 p50/RelA/I kappa B alpha -0.66 0.45 -10000 0 -1.1 176 176
positive regulation of T cell mediated cytotoxicity -0.71 0.52 -10000 0 -1.2 168 168
ITGA3 -0.62 0.44 -10000 0 -1.1 132 132
IL17F -0.45 0.28 -10000 0 -0.77 121 121
IL12B -0.015 0.1 -10000 0 -0.9 5 5
STAT1 (dimer) -0.68 0.51 -10000 0 -1.2 167 167
CD4 -0.61 0.43 -10000 0 -1.1 129 129
IL23 -0.65 0.46 -10000 0 -1.2 139 139
IL23R -0.12 0.22 -10000 0 -1.3 13 13
IL1B -0.68 0.5 -10000 0 -1.2 152 152
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.72 0.5 -10000 0 -1.2 176 176
TYK2 -0.009 0.015 -10000 0 -10000 0 0
STAT4 0.004 0.084 -10000 0 -0.85 4 4
STAT3 0.012 0.002 -10000 0 -10000 0 0
IL18RAP -0.006 0.1 -10000 0 -0.56 12 12
IL12RB1 -0.014 0.05 -10000 0 -0.5 4 4
PIK3CA 0.01 0.042 -10000 0 -0.85 1 1
IL12Rbeta1/TYK2 -0.016 0.038 -10000 0 -0.37 3 3
IL23R/JAK2 -0.14 0.22 -10000 0 -1.1 16 16
positive regulation of chronic inflammatory response -0.71 0.52 -10000 0 -1.2 168 168
natural killer cell activation 0.01 0.013 0.076 13 -10000 0 13
JAK2 -0.006 0.078 -10000 0 -0.9 3 3
PIK3R1 0.012 0.002 -10000 0 -10000 0 0
NFKB1 0.008 0.003 -10000 0 -10000 0 0
RELA 0.008 0.003 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.62 0.43 -10000 0 -1.1 140 140
ALOX12B -0.7 0.48 -10000 0 -1.2 171 171
CXCL1 -0.76 0.51 -10000 0 -1.2 200 200
T cell proliferation -0.71 0.52 -10000 0 -1.2 168 168
NFKBIA 0.008 0.003 -10000 0 -10000 0 0
IL17A -0.39 0.23 -10000 0 -0.64 108 108
PI3K -0.67 0.45 -10000 0 -1.1 172 172
IFNG -0.034 0.052 0.15 11 -0.11 103 114
STAT3 (dimer) -0.65 0.44 -10000 0 -1.1 172 172
IL18R1 0.008 0.048 -10000 0 -0.66 2 2
IL23/IL23R/JAK2/TYK2/SOCS3 -0.34 0.23 -10000 0 -0.76 23 23
IL18/IL18R 0.004 0.095 -10000 0 -0.61 7 7
macrophage activation -0.031 0.015 -10000 0 -0.045 110 110
TNF -0.67 0.48 -10000 0 -1.2 148 148
STAT3/STAT4 -0.66 0.45 -10000 0 -1.1 171 171
STAT4 (dimer) -0.68 0.5 -10000 0 -1.2 164 164
IL18 0.003 0.077 -10000 0 -0.76 4 4
IL19 -0.68 0.5 -10000 0 -1.2 151 151
STAT5A (dimer) -0.68 0.5 -10000 0 -1.2 163 163
STAT1 -0.008 0.13 -10000 0 -0.85 10 10
SOCS3 0.012 0 -10000 0 -10000 0 0
CXCL9 -0.73 0.48 -10000 0 -1.2 183 183
MPO -0.62 0.43 -10000 0 -1.1 136 136
positive regulation of humoral immune response -0.71 0.52 -10000 0 -1.2 168 168
IL23/IL23R/JAK2/TYK2 -0.74 0.58 -10000 0 -1.3 168 168
IL6 -0.68 0.48 -10000 0 -1.2 153 153
STAT5A 0.012 0 -10000 0 -10000 0 0
IL2 0.005 0.061 -10000 0 -0.85 2 2
positive regulation of tyrosine phosphorylation of STAT protein 0.01 0.013 0.076 13 -10000 0 13
CD3E -0.61 0.44 -10000 0 -1.1 132 132
keratinocyte proliferation -0.71 0.52 -10000 0 -1.2 168 168
NOS2 -0.74 0.49 -10000 0 -1.2 186 186
Syndecan-1-mediated signaling events

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
TGFB1 0.012 0 -9999 0 -10000 0 0
CCL5 0 0.086 -9999 0 -0.55 9 9
SDCBP 0.012 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.29 0.24 -9999 0 -0.56 145 145
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 -0.28 0.23 -9999 0 -0.54 148 148
Syndecan-1/Syntenin -0.27 0.23 -9999 0 -0.54 144 144
MAPK3 -0.24 0.21 -9999 0 -0.48 140 140
HGF/MET -0.05 0.2 -9999 0 -0.67 38 38
TGFB1/TGF beta receptor Type II 0.012 0 -9999 0 -10000 0 0
BSG 0.012 0 -9999 0 -10000 0 0
keratinocyte migration -0.27 0.23 -9999 0 -0.53 148 148
Syndecan-1/RANTES -0.28 0.23 -9999 0 -0.54 147 147
Syndecan-1/CD147 -0.26 0.22 -9999 0 -0.51 144 144
Syndecan-1/Syntenin/PIP2 -0.26 0.22 -9999 0 -0.52 144 144
LAMA5 0.004 0.084 -9999 0 -0.85 4 4
positive regulation of cell-cell adhesion -0.26 0.2 -9999 0 -0.51 144 144
MMP7 -0.4 0.43 -9999 0 -0.84 200 200
HGF -0.008 0.12 -9999 0 -0.64 13 13
Syndecan-1/CASK -0.28 0.23 -9999 0 -0.54 145 145
Syndecan-1/HGF/MET -0.3 0.26 -9999 0 -0.56 173 173
regulation of cell adhesion -0.22 0.2 -9999 0 -0.55 58 58
HPSE -0.014 0.15 -9999 0 -0.82 13 13
positive regulation of cell migration -0.29 0.24 -9999 0 -0.56 145 145
SDC1 -0.29 0.24 -9999 0 -0.57 145 145
Syndecan-1/Collagen -0.29 0.24 -9999 0 -0.56 145 145
PPIB 0.012 0 -9999 0 -10000 0 0
MET -0.055 0.23 -9999 0 -0.84 33 33
PRKACA 0.012 0 -9999 0 -10000 0 0
MMP9 -0.23 0.39 -9999 0 -0.85 115 115
MAPK1 -0.24 0.21 -9999 0 -0.48 140 140
homophilic cell adhesion -0.29 0.24 -9999 0 -0.56 145 145
MMP1 -0.33 0.42 -9999 0 -0.84 168 168
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.009 0.081 -9999 0 -0.66 6 6
VLDLR -0.05 0.16 -9999 0 -0.47 54 54
CRKL 0.012 0 -9999 0 -10000 0 0
LRPAP1 0.012 0 -9999 0 -10000 0 0
FYN 0.012 0 -9999 0 -10000 0 0
ITGA3 0.008 0.06 -9999 0 -0.85 2 2
RELN/VLDLR/Fyn -0.12 0.17 -9999 0 -0.53 35 35
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.012 0.057 -9999 0 -0.49 3 3
AKT1 -0.19 0.2 -9999 0 -0.46 111 111
MAP2K7 0.012 0 -9999 0 -10000 0 0
RAPGEF1 0.012 0 -9999 0 -10000 0 0
DAB1 -0.25 0.24 -9999 0 -0.47 223 223
RELN/LRP8/DAB1 -0.4 0.34 -9999 0 -0.71 204 204
LRPAP1/LRP8 -0.25 0.33 -9999 0 -0.66 166 166
RELN/LRP8/DAB1/Fyn -0.39 0.32 -9999 0 -0.68 204 204
DAB1/alpha3/beta1 Integrin -0.38 0.31 -9999 0 -0.76 140 140
long-term memory -0.47 0.38 -9999 0 -0.79 206 206
DAB1/LIS1 -0.39 0.32 -9999 0 -0.71 177 177
DAB1/CRLK/C3G -0.38 0.31 -9999 0 -0.75 139 139
PIK3CA 0.01 0.042 -9999 0 -0.85 1 1
DAB1/NCK2 -0.39 0.32 -9999 0 -0.72 177 177
ARHGEF2 0.012 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.11 0.22 -9999 0 -0.49 99 99
CDK5R1 0 0.1 -9999 0 -0.85 6 6
RELN -0.13 0.22 -9999 0 -0.47 125 125
PIK3R1 0.012 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.31 0.32 -9999 0 -0.67 168 168
GRIN2A/RELN/LRP8/DAB1/Fyn -0.44 0.36 -9999 0 -0.72 223 223
MAPK8 0.012 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.23 0.21 -9999 0 -0.52 111 111
ITGB1 0.01 0.042 -9999 0 -0.85 1 1
MAP1B -0.4 0.33 -9999 0 -0.66 226 226
RELN/LRP8 -0.31 0.32 -9999 0 -0.67 168 168
GRIN2B/RELN/LRP8/DAB1/Fyn -0.44 0.36 -9999 0 -0.72 222 222
PI3K 0.017 0.033 -9999 0 -0.66 1 1
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin 0.014 0.057 -9999 0 -0.66 3 3
RAP1A -0.33 0.3 -9999 0 -0.69 139 139
PAFAH1B1 0.012 0 -9999 0 -10000 0 0
MAPK8IP1 -0.012 0.12 -9999 0 -0.53 19 19
CRLK/C3G 0.019 0 -9999 0 -10000 0 0
GRIN2B -0.09 0.28 -9999 0 -0.85 48 48
NCK2 0.012 0 -9999 0 -10000 0 0
neuron differentiation -0.25 0.24 -9999 0 -0.5 167 167
neuron adhesion -0.31 0.29 -9999 0 -0.66 140 140
LRP8 -0.33 0.42 -9999 0 -0.85 166 166
GSK3B -0.17 0.19 -9999 0 -0.44 111 111
RELN/VLDLR/DAB1/Fyn -0.22 0.19 -9999 0 -0.49 111 111
MAP3K11 0.012 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.21 0.21 -9999 0 -0.49 112 112
CDK5 0.012 0 -9999 0 -10000 0 0
MAPT -0.069 0.2 -9999 0 -0.43 92 92
neuron migration -0.3 0.26 -9999 0 -0.56 177 177
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.25 0.24 -9999 0 -0.51 167 167
RELN/VLDLR -0.3 0.33 -9999 0 -0.63 186 186
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.59 0.43 -9999 0 -1.1 122 122
PCK1 -0.49 0.42 -9999 0 -1 128 128
HNF4A -0.76 0.56 -9999 0 -1.3 177 177
KCNJ11 -0.57 0.45 -9999 0 -1.2 113 113
AKT1 -0.24 0.14 -9999 0 -10000 0 0
response to starvation -0.022 0.033 -9999 0 -10000 0 0
DLK1 -0.62 0.48 -9999 0 -1.2 127 127
NKX2-1 -0.29 0.28 -9999 0 -0.92 50 50
ACADM -0.59 0.44 -9999 0 -1.1 132 132
TAT -0.39 0.36 -9999 0 -1.1 63 63
CEBPB 0.002 0.024 -9999 0 -10000 0 0
CEBPA -0.019 0.14 -9999 0 -0.78 12 12
TTR -0.56 0.52 -9999 0 -1.2 151 151
PKLR -0.63 0.48 -9999 0 -1.2 137 137
APOA1 -0.93 0.64 -9999 0 -1.5 211 211
CPT1C -0.61 0.46 -9999 0 -1.1 136 136
ALAS1 -0.25 0.15 -9999 0 -10000 0 0
TFRC -0.4 0.3 -9999 0 -1 52 52
FOXF1 0.006 0.1 -9999 0 -0.46 16 16
NF1 0.019 0 -9999 0 -10000 0 0
HNF1A (dimer) -0.067 0.14 -9999 0 -0.7 12 12
CPT1A -0.59 0.43 -9999 0 -1.1 124 124
HMGCS1 -0.59 0.43 -9999 0 -1.1 133 133
NR3C1 -0.032 0.079 -9999 0 -0.48 5 5
CPT1B -0.59 0.44 -9999 0 -1.1 132 132
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.014 0.024 -9999 0 -10000 0 0
GCK -0.61 0.46 -9999 0 -1.1 143 143
CREB1 -0.019 0.059 -9999 0 -10000 0 0
IGFBP1 -0.46 0.36 -9999 0 -0.9 146 146
PDX1 -0.33 0.3 -9999 0 -1.2 27 27
UCP2 -0.59 0.43 -9999 0 -1.1 137 137
ALDOB -0.71 0.52 -9999 0 -1.2 183 183
AFP -0.14 0.28 -9999 0 -0.8 51 51
BDH1 -0.59 0.44 -9999 0 -1.1 129 129
HADH -0.57 0.44 -9999 0 -1.1 112 112
F2 -0.78 0.55 -9999 0 -1.4 153 153
HNF1A -0.066 0.14 -9999 0 -0.7 12 12
G6PC -0.2 0.37 -9999 0 -1.1 53 53
SLC2A2 -0.78 0.58 -9999 0 -1.3 207 207
INS 0.032 0.059 -9999 0 -10000 0 0
FOXA1 -0.055 0.16 -9999 0 -0.5 25 25
FOXA3 -0.1 0.17 -9999 0 -0.48 45 45
FOXA2 -0.66 0.5 -9999 0 -1.2 128 128
ABCC8 -0.72 0.51 -9999 0 -1.2 193 193
ALB -0.17 0.31 -9999 0 -0.76 81 81
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.2 0.27 -9999 0 -0.48 197 197
NF kappa B1 p50/RelA/I kappa B alpha -0.16 0.25 -9999 0 -0.6 30 30
alphaV/beta3 Integrin/Osteopontin/Src -0.31 0.33 -9999 0 -0.65 195 195
AP1 -0.17 0.26 -9999 0 -0.58 40 40
ILK -0.22 0.28 -9999 0 -0.51 197 197
bone resorption -0.17 0.25 -9999 0 -0.73 5 5
PTK2B 0.012 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.22 0.24 -9999 0 -0.55 31 31
ITGAV 0.015 0.004 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.009 0.081 -9999 0 -0.66 6 6
alphaV/beta3 Integrin/Osteopontin -0.27 0.29 -9999 0 -0.57 197 197
MAP3K1 -0.22 0.28 -9999 0 -0.52 197 197
JUN 0.013 0.001 -9999 0 -10000 0 0
MAPK3 -0.21 0.28 -9999 0 -0.49 197 197
MAPK1 -0.21 0.28 -9999 0 -0.49 197 197
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
NFKB1 0.012 0 -9999 0 -10000 0 0
MAPK8 -0.2 0.27 -9999 0 -0.48 197 197
ITGB3 0.005 0.087 -9999 0 -0.77 5 5
NFKBIA -0.19 0.27 -9999 0 -0.46 197 197
FOS -0.014 0.11 -9999 0 -0.47 23 23
CD44 0 0.1 -9999 0 -0.85 6 6
CHUK 0.012 0 -9999 0 -10000 0 0
PLAU -0.2 0.31 -9999 0 -0.88 39 39
NF kappa B1 p50/RelA -0.2 0.22 -9999 0 -0.64 30 30
BCAR1 0.012 0 -9999 0 -10000 0 0
RELA 0.012 0 -9999 0 -10000 0 0
alphaV beta3 Integrin 0.001 0.067 -9999 0 -0.58 5 5
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.22 0.28 -9999 0 -0.52 198 198
VAV3 -0.24 0.29 -9999 0 -0.51 215 215
MAP3K14 -0.22 0.29 -9999 0 -0.52 197 197
ROCK2 0.012 0 -9999 0 -10000 0 0
SPP1 -0.39 0.43 -9999 0 -0.85 196 196
RAC1 0.012 0 -9999 0 -10000 0 0
Rac1/GTP -0.22 0.27 -9999 0 -0.46 215 215
MMP2 -0.14 0.22 -9999 0 -0.69 5 5
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.012 0 -10000 0 -10000 0 0
EPHB2 -0.43 0.43 -10000 0 -0.85 211 211
EFNB1 -0.007 0.13 -10000 0 -0.66 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.34 0.34 -10000 0 -0.6 232 232
Ephrin B2/EPHB1-2 -0.35 0.37 -10000 0 -0.66 229 229
neuron projection morphogenesis -0.32 0.32 -10000 0 -0.57 233 233
Ephrin B1/EPHB1-2/Tiam1 -0.35 0.39 -10000 0 -0.65 233 233
DNM1 -0.022 0.17 -10000 0 -0.86 16 16
cell-cell signaling 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.012 0.12 -10000 0 -0.64 13 13
YES1 -0.03 0.15 -10000 0 -0.74 17 17
Ephrin B1/EPHB1-2/NCK2 -0.34 0.38 -10000 0 -0.64 230 230
PI3K -0.013 0.12 -10000 0 -0.63 14 14
mol:GDP -0.34 0.38 -10000 0 -0.64 233 233
ITGA2B -0.017 0.15 -10000 0 -0.82 14 14
endothelial cell proliferation 0 0.029 -10000 0 -0.58 1 1
FYN -0.03 0.15 -10000 0 -0.74 17 17
MAP3K7 -0.028 0.12 -10000 0 -0.6 17 17
FGR -0.031 0.15 -10000 0 -0.74 17 17
TIAM1 -0.003 0.1 -10000 0 -0.62 10 10
PIK3R1 0.012 0 -10000 0 -10000 0 0
RGS3 0.012 0 -10000 0 -10000 0 0
cell adhesion -0.019 0.15 -10000 0 -0.52 31 31
LYN -0.03 0.15 -10000 0 -0.74 17 17
Ephrin B1/EPHB1-2/Src Family Kinases -0.032 0.14 -10000 0 -0.69 17 17
Ephrin B1/EPHB1-2 -0.036 0.13 -10000 0 -0.65 17 17
SRC -0.031 0.15 -10000 0 -0.74 17 17
ITGB3 0.003 0.088 -10000 0 -0.78 5 5
EPHB1 -0.15 0.34 -10000 0 -0.85 79 79
EPHB4 0.01 0.042 -10000 0 -0.85 1 1
RAC1 0.012 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0 0.029 -10000 0 -0.58 1 1
alphaIIb/beta3 Integrin -0.011 0.14 -10000 0 -0.62 19 19
BLK -0.059 0.17 -10000 0 -0.78 17 17
HCK -0.029 0.15 -10000 0 -0.73 17 17
regulation of stress fiber formation 0.33 0.38 0.63 230 -10000 0 230
MAPK8 -0.005 0.11 -10000 0 -0.6 13 13
Ephrin B1/EPHB1-2/RGS3 -0.34 0.38 -10000 0 -0.64 230 230
endothelial cell migration -0.02 0.11 -10000 0 -0.56 14 14
NCK2 0.012 0 -10000 0 -10000 0 0
PTPN13 -0.011 0.13 -10000 0 -0.64 17 17
regulation of focal adhesion formation 0.33 0.38 0.63 230 -10000 0 230
chemotaxis 0.33 0.38 0.63 230 -10000 0 230
PIK3CA 0.01 0.042 -10000 0 -0.85 1 1
Rac1/GTP -0.33 0.34 -10000 0 -0.59 232 232
angiogenesis -0.036 0.13 -10000 0 -0.64 17 17
LCK -0.033 0.15 -10000 0 -0.74 17 17
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.31 0.31 -10000 0 -0.6 213 213
cell-cell adhesion 0.28 0.27 0.74 69 -10000 0 69
Ephrin B/EPHB2/RasGAP -0.26 0.26 -10000 0 -0.51 212 212
ITSN1 0.012 0 -10000 0 -10000 0 0
PIK3CA 0.01 0.042 -10000 0 -0.85 1 1
SHC1 0.012 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.009 0.056 -10000 0 -0.58 2 2
Ephrin B1/EPHB1 -0.11 0.23 -10000 0 -0.58 78 78
HRAS/GDP -0.14 0.2 -10000 0 -0.52 80 80
Ephrin B/EPHB1/GRB7 -0.16 0.25 -10000 0 -0.54 115 115
Endophilin/SYNJ1 -0.23 0.26 -10000 0 -0.47 212 212
KRAS -0.023 0.17 -10000 0 -0.85 17 17
Ephrin B/EPHB1/Src -0.11 0.2 -10000 0 -0.51 80 80
endothelial cell migration -0.002 0.034 -10000 0 -0.49 2 2
GRB2 0.012 0 -10000 0 -10000 0 0
GRB7 -0.079 0.26 -10000 0 -0.84 45 45
PAK1 -0.23 0.26 -10000 0 -0.71 14 14
HRAS 0.012 0 -10000 0 -10000 0 0
RRAS -0.23 0.26 -10000 0 -0.48 212 212
DNM1 -0.021 0.17 -10000 0 -0.85 16 16
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.073 0.21 -10000 0 -0.49 80 80
lamellipodium assembly -0.28 0.27 -10000 0 -0.74 69 69
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.031 0.13 -10000 0 -0.48 5 5
PIK3R1 0.012 0 -10000 0 -10000 0 0
EPHB2 -0.43 0.43 -10000 0 -0.85 211 211
EPHB3 -0.002 0.091 -10000 0 -0.54 11 11
EPHB1 -0.15 0.34 -10000 0 -0.85 79 79
EPHB4 0.01 0.042 -10000 0 -0.85 1 1
mol:GDP -0.12 0.2 -10000 0 -0.5 62 62
Ephrin B/EPHB2 -0.27 0.26 -10000 0 -0.51 212 212
Ephrin B/EPHB3 -0.02 0.077 -10000 0 -0.5 6 6
JNK cascade -0.32 0.35 -10000 0 -0.6 229 229
Ephrin B/EPHB1 -0.11 0.21 -10000 0 -0.52 80 80
RAP1/GDP -0.12 0.16 -10000 0 -0.59 8 8
EFNB2 0.012 0 -10000 0 -10000 0 0
EFNB3 -0.014 0.12 -10000 0 -0.54 20 20
EFNB1 0.012 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.35 0.38 -10000 0 -0.66 229 229
RAP1B 0.006 0.073 -10000 0 -0.85 3 3
RAP1A 0.012 0 -10000 0 -10000 0 0
CDC42/GTP -0.28 0.29 -10000 0 -0.79 69 69
Rap1/GTP -0.28 0.28 -10000 0 -0.77 70 70
axon guidance -0.31 0.3 -10000 0 -0.6 213 213
MAPK3 -0.013 0.12 -10000 0 -0.42 5 5
MAPK1 -0.013 0.12 -10000 0 -0.42 5 5
Rac1/GDP -0.1 0.18 -10000 0 -0.46 61 61
actin cytoskeleton reorganization -0.23 0.21 -10000 0 -0.58 74 74
CDC42/GDP -0.1 0.18 -10000 0 -0.46 61 61
PI3K -0.002 0.034 -10000 0 -0.5 2 2
EFNA5 -0.018 0.13 -10000 0 -0.51 24 24
Ephrin B2/EPHB4 -0.001 0.028 -10000 0 -0.58 1 1
Ephrin B/EPHB2/Intersectin/N-WASP -0.13 0.17 -10000 0 -0.51 12 12
CDC42 0.012 0 -10000 0 -10000 0 0
RAS family/GTP -0.29 0.28 -10000 0 -0.75 74 74
PTK2 0.061 0.056 -10000 0 -10000 0 0
MAP4K4 -0.32 0.36 -10000 0 -0.62 229 229
SRC 0.012 0 -10000 0 -10000 0 0
KALRN 0.007 0.052 -10000 0 -0.47 5 5
Intersectin/N-WASP 0.019 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.18 0.23 -10000 0 -0.54 69 69
MAP2K1 -0.021 0.12 -10000 0 -0.45 5 5
WASL 0.012 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.35 0.38 -10000 0 -0.65 229 229
cell migration -0.022 0.13 -10000 0 -0.5 5 5
NRAS 0.012 0 -10000 0 -10000 0 0
SYNJ1 -0.23 0.26 -10000 0 -0.48 212 212
PXN 0.012 0 -10000 0 -10000 0 0
TF -0.32 0.29 -10000 0 -0.55 228 228
HRAS/GTP -0.3 0.3 -10000 0 -0.82 69 69
Ephrin B1/EPHB1-2 -0.35 0.38 -10000 0 -0.66 229 229
cell adhesion mediated by integrin 0.006 0.076 0.47 5 -10000 0 5
RAC1 0.012 0 -10000 0 -10000 0 0
mol:GTP -0.33 0.33 -10000 0 -0.59 229 229
RAC1-CDC42/GTP -0.28 0.28 -10000 0 -0.75 74 74
RASA1 0.012 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.11 0.16 -10000 0 -0.44 61 61
ruffle organization -0.26 0.31 -10000 0 -0.77 69 69
NCK1 0.012 0 -10000 0 -10000 0 0
receptor internalization -0.23 0.28 -10000 0 -0.48 213 213
Ephrin B/EPHB2/KALRN -0.26 0.26 -10000 0 -0.51 212 212
ROCK1 0.016 0.054 -10000 0 -0.53 2 2
RAS family/GDP -0.22 0.21 -10000 0 -0.55 74 74
Rac1/GTP -0.3 0.3 -10000 0 -0.82 69 69
Ephrin B/EPHB1/Src/Paxillin -0.035 0.14 -10000 0 -0.52 5 5
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.012 0 -9999 0 -10000 0 0
VLDLR -0.05 0.16 -9999 0 -0.47 54 54
LRPAP1 0.012 0 -9999 0 -10000 0 0
NUDC 0.012 0 -9999 0 -10000 0 0
RELN/LRP8 -0.31 0.32 -9999 0 -0.67 168 168
CaM/Ca2+ 0.009 0 -9999 0 -10000 0 0
KATNA1 0.012 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.26 0.31 -9999 0 -0.61 168 168
IQGAP1/CaM 0.017 0.033 -9999 0 -0.66 1 1
DAB1 -0.25 0.24 -9999 0 -0.47 223 223
IQGAP1 0.01 0.042 -9999 0 -0.85 1 1
PLA2G7 -0.37 0.43 -9999 0 -0.85 184 184
CALM1 0.012 0 -9999 0 -10000 0 0
DYNLT1 0.012 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.25 0.33 -9999 0 -0.66 166 166
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.01 0.042 -9999 0 -0.85 1 1
CDK5R1 0 0.1 -9999 0 -0.85 6 6
LIS1/Poliovirus Protein 3A 0.016 0 -9999 0 -10000 0 0
CDK5R2 -0.1 0.22 -9999 0 -0.51 93 93
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.26 0.22 -9999 0 -0.56 111 111
YWHAE 0.012 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.23 0.27 -9999 0 -0.6 107 107
MAP1B -0.007 0.045 -9999 0 -0.31 9 9
RAC1 -0.001 0.01 -9999 0 -10000 0 0
p35/CDK5 -0.23 0.28 -9999 0 -0.55 172 172
RELN -0.13 0.22 -9999 0 -0.47 125 125
PAFAH/LIS1 -0.24 0.3 -9999 0 -0.57 184 184
LIS1/CLIP170 0.024 0.029 -9999 0 -0.57 1 1
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.19 0.19 -9999 0 -0.47 105 105
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.21 0.23 -9999 0 -0.54 110 110
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.26 0.29 -9999 0 -0.65 110 110
LIS1/IQGAP1 0.024 0.029 -9999 0 -0.57 1 1
RHOA -0.001 0.01 -9999 0 -10000 0 0
PAFAH1B1 0.022 0 -9999 0 -10000 0 0
PAFAH1B3 0.012 0 -9999 0 -10000 0 0
PAFAH1B2 0.012 0 -9999 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.019 0.033 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.22 0.26 -9999 0 -0.58 106 106
LRP8 -0.33 0.42 -9999 0 -0.85 166 166
NDEL1/Katanin 60 -0.23 0.27 -9999 0 -0.61 106 106
P39/CDK5 -0.28 0.31 -9999 0 -0.6 181 181
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.025 0 -9999 0 -10000 0 0
CDK5 -0.24 0.29 -9999 0 -0.57 168 168
PPP2R5D 0.012 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.001 0.025 -9999 0 -0.5 1 1
CSNK2A1 0.012 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.2 0.2 -9999 0 -0.48 111 111
RELN/VLDLR -0.3 0.33 -9999 0 -0.63 186 186
CDC42 -0.001 0.01 -9999 0 -10000 0 0
IL4-mediated signaling events

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
BCL2L1 -0.62 0.52 -10000 0 -1.3 106 106
STAT6 (cleaved dimer) -0.66 0.51 -10000 0 -1.3 138 138
IGHG1 -0.2 0.16 -10000 0 -0.45 6 6
IGHG3 -0.61 0.5 -10000 0 -1.2 123 123
AKT1 -0.28 0.25 -10000 0 -0.78 28 28
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.21 0.22 -10000 0 -0.78 21 21
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.28 0.25 -10000 0 -0.92 15 15
THY1 -0.65 0.55 -10000 0 -1.4 113 113
MYB -0.15 0.34 -10000 0 -0.85 77 77
HMGA1 0.01 0.042 -10000 0 -0.85 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.36 0.3 -10000 0 -0.91 32 32
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.29 0.25 -10000 0 -0.91 16 16
SP1 0.016 0.012 -10000 0 -10000 0 0
INPP5D 0.007 0.064 -10000 0 -0.72 3 3
SOCS5 0.028 0.013 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.64 0.5 -10000 0 -1.3 127 127
SOCS1 -0.4 0.33 -10000 0 -0.81 78 78
SOCS3 -0.29 0.25 -10000 0 -0.87 13 13
FCER2 -0.66 0.59 -10000 0 -1.4 125 125
PARP14 -0.001 0.094 -10000 0 -0.85 5 5
CCL17 -0.66 0.55 -10000 0 -1.4 113 113
GRB2 0.012 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.23 0.2 -10000 0 -0.71 14 14
T cell proliferation -0.63 0.54 -10000 0 -1.3 115 115
IL4R/JAK1 -0.62 0.52 -10000 0 -1.3 113 113
EGR2 -0.67 0.56 -10000 0 -1.4 112 112
JAK2 -0.025 0.076 -10000 0 -0.84 3 3
JAK3 -0.02 0.18 -10000 0 -0.85 18 18
PIK3R1 0.012 0 -10000 0 -10000 0 0
JAK1 0.004 0.011 -10000 0 -10000 0 0
COL1A2 -0.27 0.3 -10000 0 -0.9 63 63
CCL26 -0.68 0.56 -10000 0 -1.4 118 118
IL4R -0.67 0.56 -10000 0 -1.4 113 113
PTPN6 0.026 0.043 -10000 0 -0.83 1 1
IL13RA2 -0.72 0.56 -10000 0 -1.4 137 137
IL13RA1 -0.02 0.053 -10000 0 -0.92 1 1
IRF4 -0.17 0.29 -10000 0 -1.1 27 27
ARG1 -0.15 0.16 -10000 0 -0.86 9 9
CBL -0.33 0.28 -10000 0 -0.89 29 29
GTF3A 0.005 0.05 -10000 0 -0.85 1 1
PIK3CA 0.01 0.042 -10000 0 -0.85 1 1
IL13RA1/JAK2 -0.032 0.076 -10000 0 -0.68 4 4
IRF4/BCL6 -0.13 0.26 -10000 0 -1.1 24 24
CD40LG -0.007 0.12 -10000 0 -0.58 15 15
MAPK14 -0.32 0.28 -10000 0 -0.89 27 27
mitosis -0.26 0.24 -10000 0 -0.73 28 28
STAT6 -0.73 0.64 -10000 0 -1.5 121 121
SPI1 0.01 0.074 -10000 0 -0.85 3 3
RPS6KB1 -0.25 0.23 -10000 0 -0.78 14 14
STAT6 (dimer) -0.73 0.64 -10000 0 -1.5 121 121
STAT6 (dimer)/PARP14 -0.7 0.59 -10000 0 -1.4 126 126
mast cell activation 0.015 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.28 0.26 -10000 0 -0.84 26 26
FRAP1 -0.28 0.25 -10000 0 -0.78 28 28
LTA -0.64 0.54 -10000 0 -1.3 114 114
FES 0.007 0.059 -10000 0 -0.56 4 4
T-helper 1 cell differentiation 0.7 0.6 1.5 122 -10000 0 122
CCL11 -0.65 0.55 -10000 0 -1.3 130 130
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.28 0.25 -10000 0 -0.82 27 27
IL2RG 0.004 0.096 -10000 0 -0.58 10 10
IL10 -0.63 0.53 -10000 0 -1.3 105 105
IRS1 0.011 0.023 -10000 0 -0.47 1 1
IRS2 -0.013 0.12 -10000 0 -0.55 19 19
IL4 -0.15 0.15 -10000 0 -0.88 7 7
IL5 -0.63 0.52 -10000 0 -1.3 107 107
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.5 0.38 -10000 0 -0.96 102 102
COL1A1 -0.41 0.4 -10000 0 -0.92 142 142
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.64 0.54 -10000 0 -1.4 104 104
IL2R gamma/JAK3 -0.023 0.15 -10000 0 -0.66 21 21
TFF3 -0.77 0.59 -10000 0 -1.4 157 157
ALOX15 -0.68 0.56 -10000 0 -1.4 127 127
MYBL1 -0.017 0.16 -10000 0 -0.85 14 14
T-helper 2 cell differentiation -0.52 0.41 -10000 0 -1 117 117
SHC1 0.012 0 -10000 0 -10000 0 0
CEBPB 0.016 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.28 0.25 -10000 0 -0.84 21 21
mol:PI-3-4-5-P3 -0.28 0.25 -10000 0 -0.78 28 28
PI3K -0.29 0.27 -10000 0 -0.84 28 28
DOK2 0.01 0.033 -10000 0 -0.47 2 2
ETS1 0.028 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.21 0.19 -10000 0 -0.68 13 13
ITGB3 -0.63 0.52 -10000 0 -1.3 108 108
PIGR -0.81 0.65 -10000 0 -1.5 170 170
IGHE 0.041 0.064 0.27 12 -10000 0 12
MAPKKK cascade -0.21 0.19 -10000 0 -0.67 13 13
BCL6 0.015 0.007 -10000 0 -10000 0 0
OPRM1 -0.64 0.53 -10000 0 -1.3 118 118
RETNLB -0.72 0.58 -10000 0 -1.4 133 133
SELP -0.7 0.59 -10000 0 -1.4 128 128
AICDA -0.63 0.52 -10000 0 -1.3 120 120
HIF-1-alpha transcription factor network

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
PKM2 -0.44 0.48 -9999 0 -1.2 62 62
HDAC7 0.012 0.006 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.34 0.34 -9999 0 -0.99 39 39
SMAD4 0.011 0.033 -9999 0 -0.46 2 2
ID2 -0.44 0.48 -9999 0 -1.2 74 74
AP1 0.001 0.079 -9999 0 -0.36 1 1
ABCG2 -0.45 0.48 -9999 0 -1.2 77 77
HIF1A -0.054 0.067 -9999 0 -10000 0 0
TFF3 -0.6 0.58 -9999 0 -1.3 122 122
GATA2 0.007 0.057 -9999 0 -0.46 6 6
AKT1 -0.056 0.081 -9999 0 -10000 0 0
response to hypoxia -0.076 0.085 -9999 0 -10000 0 0
MCL1 -0.44 0.48 -9999 0 -1.2 62 62
NDRG1 -0.44 0.48 -9999 0 -1.2 67 67
SERPINE1 -0.52 0.52 -9999 0 -1.3 87 87
FECH -0.44 0.48 -9999 0 -1.2 69 69
FURIN -0.44 0.48 -9999 0 -1.2 70 70
NCOA2 0.012 0.024 -9999 0 -0.47 1 1
EP300 -0.056 0.12 -9999 0 -0.36 22 22
HMOX1 -0.44 0.48 -9999 0 -1.2 74 74
BHLHE40 -0.44 0.48 -9999 0 -1.2 75 75
BHLHE41 -0.45 0.49 -9999 0 -1.2 76 76
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.042 0.063 -9999 0 -10000 0 0
ENG -0.014 0.087 -9999 0 -10000 0 0
JUN 0.013 0.002 -9999 0 -10000 0 0
RORA -0.44 0.48 -9999 0 -1.2 74 74
ABCB1 -0.13 0.2 -9999 0 -0.97 17 17
TFRC -0.45 0.49 -9999 0 -1.2 66 66
CXCR4 -0.46 0.49 -9999 0 -1.2 81 81
TF -0.53 0.53 -9999 0 -1.2 103 103
CITED2 -0.44 0.48 -9999 0 -1.2 74 74
HIF1A/ARNT -0.52 0.53 -9999 0 -1.4 77 77
LDHA -0.05 0.05 -9999 0 -10000 0 0
ETS1 -0.44 0.48 -9999 0 -1.2 74 74
PGK1 -0.44 0.48 -9999 0 -1.2 74 74
NOS2 -0.6 0.57 -9999 0 -1.3 121 121
ITGB2 -0.44 0.48 -9999 0 -1.2 73 73
ALDOA -0.44 0.48 -9999 0 -1.2 67 67
Cbp/p300/CITED2 -0.43 0.5 -9999 0 -1.2 64 64
FOS -0.013 0.11 -9999 0 -0.47 23 23
HK2 -0.45 0.49 -9999 0 -1.2 77 77
SP1 0.018 0.018 -9999 0 -10000 0 0
GCK -0.14 0.34 -9999 0 -1.3 29 29
HK1 -0.44 0.48 -9999 0 -1.2 74 74
NPM1 -0.44 0.48 -9999 0 -1.2 74 74
EGLN1 -0.44 0.48 -9999 0 -1.2 69 69
CREB1 0.02 0 -9999 0 -10000 0 0
PGM1 -0.44 0.48 -9999 0 -1.2 67 67
SMAD3 0.014 0 -9999 0 -10000 0 0
EDN1 -0.052 0.18 -9999 0 -0.72 11 11
IGFBP1 -0.59 0.58 -9999 0 -1.3 114 114
VEGFA -0.28 0.34 -9999 0 -0.93 32 32
HIF1A/JAB1 -0.029 0.032 -9999 0 -10000 0 0
CP -0.5 0.53 -9999 0 -1.3 86 86
CXCL12 -0.45 0.49 -9999 0 -1.2 76 76
COPS5 0.013 0.002 -9999 0 -10000 0 0
SMAD3/SMAD4 -0.002 0.022 -9999 0 -10000 0 0
BNIP3 -0.44 0.48 -9999 0 -1.2 70 70
EGLN3 -0.44 0.48 -9999 0 -1.2 74 74
CA9 -0.5 0.5 -9999 0 -1.2 94 94
TERT -0.57 0.57 -9999 0 -1.3 115 115
ENO1 -0.44 0.48 -9999 0 -1.2 67 67
PFKL -0.44 0.48 -9999 0 -1.2 69 69
NCOA1 0.013 0.001 -9999 0 -10000 0 0
ADM -0.44 0.48 -9999 0 -1.2 74 74
ARNT -0.054 0.067 -9999 0 -10000 0 0
HNF4A -0.028 0.17 -9999 0 -0.73 22 22
ADFP -0.44 0.48 -9999 0 -1.2 74 74
SLC2A1 -0.31 0.38 -9999 0 -1 43 43
LEP -0.46 0.49 -9999 0 -1.2 77 77
HIF1A/ARNT/Cbp/p300 -0.35 0.36 -9999 0 -1 45 45
EPO -0.22 0.29 -9999 0 -0.98 14 14
CREBBP -0.056 0.12 -9999 0 -0.36 22 22
HIF1A/ARNT/Cbp/p300/HDAC7 -0.35 0.36 -9999 0 -1.1 40 40
PFKFB3 -0.44 0.48 -9999 0 -1.2 74 74
NT5E -0.44 0.48 -9999 0 -1.2 75 75
Effects of Botulinum toxin

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
STX1A -0.001 0.087 -9999 0 -0.67 7 7
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.092 0.16 -9999 0 -0.33 131 131
STXBP1 -0.002 0.11 -9999 0 -0.85 7 7
ACh/CHRNA1 -0.29 0.31 -9999 0 -0.62 188 188
RAB3GAP2/RIMS1/UNC13B -0.085 0.13 -9999 0 -0.57 2 2
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 -0.14 0.23 -9999 0 -0.47 131 131
mol:ACh -0.022 0.056 -9999 0 -0.12 101 101
RAB3GAP2 0.012 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.1 0.14 -9999 0 -0.57 15 15
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.29 0.31 -9999 0 -0.62 188 188
UNC13B 0.012 0 -9999 0 -10000 0 0
CHRNA1 -0.38 0.43 -9999 0 -0.85 188 188
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.11 0.22 -9999 0 -0.54 82 82
SNAP25 -0.06 0.12 -9999 0 -0.28 99 99
VAMP2 0.006 0 -9999 0 -10000 0 0
SYT1 -0.13 0.31 -9999 0 -0.73 82 82
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.003 0.11 -9999 0 -0.62 13 13
STX1A/SNAP25 fragment 1/VAMP2 -0.1 0.14 -9999 0 -0.57 15 15
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.14 0.21 -9999 0 -0.55 53 53
FZD6 0.006 0.068 -9999 0 -0.66 4 4
WNT6 -0.064 0.19 -9999 0 -0.5 62 62
WNT4 -0.059 0.17 -9999 0 -0.47 62 62
FZD3 0.01 0.033 -9999 0 -0.47 2 2
WNT5A -0.058 0.24 -9999 0 -0.85 34 34
WNT11 -0.18 0.34 -9999 0 -0.73 105 105
Glypican 2 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
MDK -0.023 0.17 -9999 0 -0.81 18 18
GPC2 -0.073 0.26 -9999 0 -0.85 41 41
GPC2/Midkine -0.076 0.24 -9999 0 -0.67 56 56
neuron projection morphogenesis -0.076 0.24 -9999 0 -0.67 56 56
TCGA08_p53

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
CDKN2A -0.19 0.31 -10000 0 -0.65 127 127
TP53 -0.044 0.094 0.27 11 -0.48 1 12
Senescence -0.044 0.094 0.27 11 -0.48 1 12
Apoptosis -0.044 0.094 0.27 11 -0.48 1 12
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.075 0.18 0.31 117 -0.63 11 128
MDM4 0.012 0 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.049 0.18 -10000 0 -0.54 12 12
CRKL -0.048 0.17 -10000 0 -0.44 6 6
HRAS -0.026 0.17 -10000 0 -0.53 10 10
mol:PIP3 -0.058 0.16 -10000 0 -0.38 80 80
SPRED1 0.012 0 -10000 0 -10000 0 0
SPRED2 0.012 0 -10000 0 -10000 0 0
GAB1 -0.058 0.18 -10000 0 -0.42 80 80
FOXO3 -0.038 0.16 -10000 0 -0.52 3 3
AKT1 -0.049 0.17 -10000 0 -0.39 80 80
BAD -0.038 0.16 -10000 0 -0.52 3 3
megakaryocyte differentiation -0.14 0.26 -10000 0 -0.48 133 133
GSK3B -0.038 0.16 -10000 0 -0.52 3 3
RAF1 -0.011 0.14 -10000 0 -0.42 10 10
SHC1 0.012 0 -10000 0 -10000 0 0
STAT3 -0.058 0.18 -10000 0 -0.42 80 80
STAT1 -0.15 0.4 -10000 0 -0.93 82 82
HRAS/SPRED1 -0.013 0.14 -10000 0 -0.42 10 10
cell proliferation -0.056 0.18 -10000 0 -0.41 80 80
PIK3CA 0.01 0.042 -10000 0 -0.85 1 1
TEC 0.012 0 -10000 0 -10000 0 0
RPS6KB1 -0.057 0.18 -10000 0 -0.42 80 80
HRAS/SPRED2 -0.013 0.14 -10000 0 -0.42 10 10
LYN/TEC/p62DOK -0.081 0.16 -10000 0 -0.57 4 4
MAPK3 0.006 0.11 -10000 0 -0.37 1 1
STAP1 -0.093 0.21 -10000 0 -0.47 92 92
GRAP2 -0.001 0.08 -10000 0 -0.47 12 12
JAK2 -0.15 0.33 -10000 0 -0.79 82 82
STAT1 (dimer) -0.15 0.39 -10000 0 -0.91 82 82
mol:Gleevec 0.001 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.09 0.17 -10000 0 -0.64 10 10
actin filament polymerization -0.06 0.18 -10000 0 -0.42 83 83
LYN 0.012 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.11 0.27 -10000 0 -0.61 81 81
PIK3R1 0.012 0 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.032 0.16 -10000 0 -0.61 2 2
PI3K -0.044 0.18 -10000 0 -0.39 80 80
PTEN 0.012 0 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.19 0.47 -10000 0 -1.1 81 81
MAPK8 -0.058 0.18 -10000 0 -0.42 80 80
STAT3 (dimer) -0.056 0.18 -10000 0 -0.41 80 80
positive regulation of transcription 0.009 0.09 -10000 0 -0.29 1 1
mol:GDP -0.079 0.15 -10000 0 -0.57 11 11
PIK3C2B -0.058 0.18 -10000 0 -0.42 80 80
CBL/CRKL -0.039 0.17 -10000 0 -0.64 2 2
FER -0.058 0.18 -10000 0 -0.42 80 80
SH2B3 -0.058 0.18 -10000 0 -0.42 80 80
PDPK1 -0.047 0.15 -10000 0 -0.43 3 3
SNAI2 -0.062 0.19 -10000 0 -0.43 83 83
positive regulation of cell proliferation -0.1 0.3 -10000 0 -0.69 81 81
KITLG 0.011 0.045 -10000 0 -0.88 1 1
cell motility -0.1 0.3 -10000 0 -0.69 81 81
PTPN6 0.012 0.043 -10000 0 -0.83 1 1
EPOR -0.016 0.13 -10000 0 -0.8 2 2
STAT5A (dimer) -0.082 0.25 -10000 0 -0.58 81 81
SOCS1 0.001 0.097 -10000 0 -0.79 6 6
cell migration 0.064 0.19 0.44 80 -10000 0 80
SOS1 0.012 0 -10000 0 -10000 0 0
EPO -0.023 0.16 -10000 0 -0.85 14 14
VAV1 0.003 0.088 -10000 0 -0.78 5 5
GRB10 -0.059 0.18 -10000 0 -0.42 80 80
PTPN11 0.014 0.007 -10000 0 -10000 0 0
SCF/KIT -0.068 0.19 -10000 0 -0.44 80 80
GO:0007205 0.002 0.01 -10000 0 -10000 0 0
MAP2K1 0.002 0.12 -10000 0 -0.42 1 1
CBL 0.01 0.042 -10000 0 -0.85 1 1
KIT -0.2 0.49 -10000 0 -1.2 81 81
MAP2K2 0.002 0.12 -10000 0 -0.42 1 1
SHC/Grb2/SOS1 -0.08 0.15 -10000 0 -0.52 2 2
STAT5A -0.086 0.26 -10000 0 -0.59 81 81
GRB2 0.012 0 -10000 0 -10000 0 0
response to radiation -0.061 0.18 -10000 0 -0.42 83 83
SHC/GRAP2 0.009 0.057 -10000 0 -10000 0 0
PTPRO -0.14 0.26 -10000 0 -0.5 133 133
SH2B2 -0.061 0.19 -10000 0 -0.42 83 83
DOK1 0.01 0.042 -10000 0 -0.85 1 1
MATK -0.066 0.2 -10000 0 -0.44 80 80
CREBBP 0.029 0.015 -10000 0 -10000 0 0
BCL2 -0.026 0.18 -10000 0 -1.2 6 6
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.045 0.15 -9999 0 -0.48 41 41
Syndecan-4/Syndesmos -0.17 0.25 -9999 0 -0.71 35 35
positive regulation of JNK cascade -0.19 0.26 -9999 0 -0.64 62 62
Syndecan-4/ADAM12 -0.44 0.36 -9999 0 -0.68 249 249
CCL5 0 0.086 -9999 0 -0.55 9 9
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
DNM2 0.012 0 -9999 0 -10000 0 0
ITGA5 -0.002 0.11 -9999 0 -0.85 7 7
SDCBP 0.012 0 -9999 0 -10000 0 0
PLG -0.005 0.092 -9999 0 -0.83 5 5
ADAM12 -0.49 0.43 -9999 0 -0.85 240 240
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.058 0.066 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.26 0.33 -9999 0 -0.72 96 96
Syndecan-4/CXCL12/CXCR4 -0.2 0.28 -9999 0 -0.69 62 62
Syndecan-4/Laminin alpha3 -0.19 0.26 -9999 0 -0.68 49 49
MDK -0.023 0.17 -9999 0 -0.81 18 18
Syndecan-4/FZD7 -0.17 0.26 -9999 0 -0.73 36 36
Syndecan-4/Midkine -0.19 0.27 -9999 0 -0.71 49 49
FZD7 0.007 0.064 -9999 0 -0.72 3 3
Syndecan-4/FGFR1/FGF -0.19 0.22 -9999 0 -0.66 39 39
THBS1 -0.007 0.13 -9999 0 -0.81 10 10
integrin-mediated signaling pathway -0.19 0.27 -9999 0 -0.68 57 57
positive regulation of MAPKKK cascade -0.19 0.26 -9999 0 -0.64 62 62
Syndecan-4/TACI -0.23 0.27 -9999 0 -0.68 73 73
CXCR4 -0.042 0.21 -9999 0 -0.85 26 26
cell adhesion -0.008 0.12 -9999 0 -0.36 40 40
Syndecan-4/Dynamin -0.17 0.25 -9999 0 -0.71 35 35
Syndecan-4/TSP1 -0.18 0.26 -9999 0 -0.71 42 42
Syndecan-4/GIPC -0.17 0.25 -9999 0 -0.71 35 35
Syndecan-4/RANTES -0.17 0.25 -9999 0 -0.69 39 39
ITGB1 0.01 0.042 -9999 0 -0.85 1 1
LAMA1 -0.16 0.34 -9999 0 -0.84 82 82
LAMA3 -0.02 0.16 -9999 0 -0.74 18 18
RAC1 0.012 0 -9999 0 -10000 0 0
PRKCA 0.045 0.051 -9999 0 -10000 0 0
Syndecan-4/alpha-Actinin -0.17 0.25 -9999 0 -0.7 38 38
TFPI 0.01 0.042 -9999 0 -0.85 1 1
F2 -0.13 0.31 -9999 0 -0.86 65 65
alpha5/beta1 Integrin 0.006 0.1 -9999 0 -0.74 7 7
positive regulation of cell adhesion -0.26 0.33 -9999 0 -0.79 79 79
ACTN1 0.006 0.073 -9999 0 -0.85 3 3
TNC -0.046 0.22 -9999 0 -0.82 29 29
Syndecan-4/CXCL12 -0.18 0.25 -9999 0 -0.69 41 41
FGF6 -0.003 0.059 -9999 0 -0.85 2 2
RHOA 0.012 0 -9999 0 -10000 0 0
CXCL12 -0.018 0.12 -9999 0 -0.48 26 26
TNFRSF13B -0.12 0.22 -9999 0 -0.47 113 113
FGF2 -0.01 0.11 -9999 0 -0.49 19 19
FGFR1 0.008 0.054 -9999 0 -0.6 3 3
Syndecan-4/PI-4-5-P2 -0.18 0.25 -9999 0 -0.71 36 36
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.067 0.26 -9999 0 -0.84 41 41
cell migration -0.02 0.023 -9999 0 -10000 0 0
PRKCD 0.018 0.011 -9999 0 -10000 0 0
vasculogenesis -0.17 0.25 -9999 0 -0.68 42 42
SDC4 -0.18 0.26 -9999 0 -0.76 36 36
Syndecan-4/Tenascin C -0.2 0.28 -9999 0 -0.72 57 57
Syndecan-4/PI-4-5-P2/PKC alpha -0.046 0.052 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.17 0.25 -9999 0 -0.71 35 35
MMP9 -0.23 0.39 -9999 0 -0.85 115 115
Rac1/GTP -0.009 0.12 -9999 0 -0.37 40 40
cytoskeleton organization -0.16 0.24 -9999 0 -0.68 35 35
GIPC1 0.012 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.17 0.25 -9999 0 -0.71 37 37
Glucocorticoid receptor regulatory network

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
PCK2 0.032 0.091 -10000 0 -10000 0 0
SMARCC2 0.014 0.006 -10000 0 -10000 0 0
SMARCC1 0.014 0.006 -10000 0 -10000 0 0
TBX21 -0.1 0.18 -10000 0 -0.56 26 26
SUMO2 0.012 0.007 -10000 0 -10000 0 0
STAT1 (dimer) 0 0.13 -10000 0 -0.84 10 10
FKBP4 0.008 0.06 -10000 0 -0.85 2 2
FKBP5 0.009 0.041 -10000 0 -0.47 3 3
GR alpha/HSP90/FKBP51/HSP90 0.11 0.12 0.35 10 -0.48 2 12
PRL -0.1 0.19 -10000 0 -0.77 18 18
cortisol/GR alpha (dimer)/TIF2 0.27 0.25 0.62 91 -10000 0 91
RELA -0.062 0.084 -10000 0 -10000 0 0
FGG 0.13 0.33 0.55 52 -0.62 31 83
GR beta/TIF2 0.12 0.12 0.37 17 -10000 0 17
IFNG -0.48 0.41 -10000 0 -0.93 153 153
apoptosis -0.008 0.17 0.48 15 -0.59 4 19
CREB1 -0.014 0.09 -10000 0 -0.34 11 11
histone acetylation -0.039 0.14 0.43 4 -0.37 20 24
BGLAP -0.084 0.15 -10000 0 -0.83 2 2
GR/PKAc 0.11 0.12 0.38 1 -0.5 4 5
NF kappa B1 p50/RelA -0.11 0.15 -10000 0 -0.42 23 23
SMARCD1 0.014 0.006 -10000 0 -10000 0 0
MDM2 0.098 0.12 0.28 48 -0.34 9 57
GATA3 -0.005 0.14 -10000 0 -0.84 11 11
AKT1 0 0.002 -10000 0 -10000 0 0
CSF2 -0.19 0.28 -10000 0 -0.66 97 97
GSK3B 0.012 0.007 -10000 0 -10000 0 0
NR1I3 0.019 0.17 0.49 6 -0.86 2 8
CSN2 0.17 0.19 0.46 25 -0.56 5 30
BRG1/BAF155/BAF170/BAF60A 0.039 0.019 -10000 0 -10000 0 0
NFATC1 0.006 0.066 -10000 0 -0.56 4 4
POU2F1 0.008 0.053 -10000 0 -0.85 1 1
CDKN1A 0.028 0.067 -10000 0 -1.2 1 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.007 -10000 0 -10000 0 0
SFN -0.008 0.12 -10000 0 -0.64 13 13
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.1 0.13 0.36 5 -0.46 2 7
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.006 0.2 0.47 7 -0.76 14 21
JUN -0.3 0.2 -10000 0 -0.6 73 73
IL4 -0.12 0.18 -10000 0 -0.79 11 11
CDK5R1 0 0.1 -10000 0 -0.85 6 6
PRKACA 0.012 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.32 0.28 -10000 0 -0.69 100 100
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.12 0.11 0.35 6 -0.47 1 7
cortisol/GR alpha (monomer) 0.32 0.3 0.73 102 -10000 0 102
NCOA2 0.011 0.023 -10000 0 -0.47 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.1 0.12 -10000 0 -0.54 23 23
AP-1/NFAT1-c-4 -0.52 0.34 -10000 0 -0.86 156 156
AFP -0.25 0.24 -10000 0 -0.84 45 45
SUV420H1 0.012 0 -10000 0 -10000 0 0
IRF1 0.17 0.16 0.47 21 -10000 0 21
TP53 0.031 0.034 -10000 0 -0.46 2 2
PPP5C 0.012 0 -10000 0 -10000 0 0
KRT17 -0.69 0.44 -10000 0 -0.95 285 285
KRT14 -0.26 0.38 -10000 0 -1 72 72
TBP 0.021 0.013 -10000 0 -10000 0 0
CREBBP 0.063 0.09 0.29 25 -10000 0 25
HDAC1 0.008 0.026 -10000 0 -0.47 1 1
HDAC2 0.026 0.027 -10000 0 -10000 0 0
AP-1 -0.52 0.35 -10000 0 -0.87 157 157
MAPK14 0.012 0.007 -10000 0 -10000 0 0
MAPK10 -0.05 0.16 -10000 0 -0.46 54 54
MAPK11 0.012 0.007 -10000 0 -10000 0 0
KRT5 -0.48 0.42 -10000 0 -0.99 139 139
interleukin-1 receptor activity 0.013 0.027 -10000 0 -10000 0 0
NCOA1 0.016 0.001 -10000 0 -10000 0 0
STAT1 0 0.13 -10000 0 -0.84 10 10
CGA -0.18 0.31 -10000 0 -0.97 47 47
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.18 0.21 0.5 96 -10000 0 96
MAPK3 0.012 0.007 -10000 0 -10000 0 0
MAPK1 0.012 0.007 -10000 0 -10000 0 0
ICAM1 -0.23 0.27 -10000 0 -0.66 75 75
NFKB1 -0.062 0.084 -10000 0 -10000 0 0
MAPK8 -0.22 0.17 -10000 0 -0.49 69 69
MAPK9 0.012 0.007 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.016 0.18 0.49 15 -0.62 4 19
BAX 0.031 0.028 -10000 0 -10000 0 0
POMC -0.2 0.35 -10000 0 -1.3 31 31
EP300 0.065 0.092 0.34 7 -10000 0 7
cortisol/GR alpha (dimer)/p53 0.29 0.25 0.62 99 -10000 0 99
proteasomal ubiquitin-dependent protein catabolic process 0.068 0.094 0.25 5 -0.31 8 13
SGK1 0.12 0.14 -10000 0 -1.2 2 2
IL13 -0.27 0.23 -10000 0 -0.79 28 28
IL6 -0.3 0.37 -10000 0 -0.82 107 107
PRKACG -0.003 0.094 -10000 0 -0.85 5 5
IL5 -0.24 0.2 -10000 0 -0.82 14 14
IL2 -0.36 0.27 -10000 0 -0.76 82 82
CDK5 0.012 0.004 -10000 0 -10000 0 0
PRKACB 0.01 0.033 -10000 0 -0.47 2 2
HSP90AA1 0.008 0.06 -10000 0 -0.85 2 2
IL8 -0.46 0.44 -10000 0 -0.87 207 207
CDK5R1/CDK5 0 0.081 -10000 0 -0.66 6 6
NF kappa B1 p50/RelA/PKAc -0.064 0.12 -10000 0 -0.55 5 5
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.26 0.24 0.59 86 -10000 0 86
SMARCA4 0.014 0.006 -10000 0 -10000 0 0
chromatin remodeling 0.19 0.15 0.41 72 -10000 0 72
NF kappa B1 p50/RelA/Cbp -0.026 0.14 0.42 2 -10000 0 2
JUN (dimer) -0.3 0.2 -10000 0 -0.6 73 73
YWHAH 0.012 0 -10000 0 -10000 0 0
VIPR1 -0.12 0.21 -10000 0 -0.57 52 52
NR3C1 0.18 0.19 0.51 59 -0.47 1 60
NR4A1 -0.021 0.13 -10000 0 -0.46 28 28
TIF2/SUV420H1 0.018 0.017 -10000 0 -10000 0 0
MAPKKK cascade -0.008 0.17 0.48 15 -0.59 4 19
cortisol/GR alpha (dimer)/Src-1 0.28 0.25 0.62 93 -10000 0 93
PBX1 0 0.076 -10000 0 -0.46 9 9
POU1F1 0.001 0.053 -10000 0 -0.84 1 1
SELE -0.31 0.38 -10000 0 -0.85 111 111
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.19 0.15 0.41 71 -10000 0 71
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.26 0.24 0.59 86 -10000 0 86
mol:cortisol 0.18 0.19 0.43 115 -10000 0 115
MMP1 -0.39 0.38 -10000 0 -0.83 168 168
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.037 0.18 -9999 0 -0.57 41 41
EPHB2 -0.43 0.43 -9999 0 -0.85 211 211
Syndecan-2/TACI -0.06 0.14 -9999 0 -0.65 3 3
LAMA1 -0.16 0.34 -9999 0 -0.84 82 82
Syndecan-2/alpha2 ITGB1 -0.012 0.16 -9999 0 -0.55 32 32
HRAS 0.012 0 -9999 0 -10000 0 0
Syndecan-2/CASK -0.002 0.031 -9999 0 -0.58 1 1
ITGA5 -0.002 0.11 -9999 0 -0.85 7 7
BAX 0.036 0.029 -9999 0 -10000 0 0
EPB41 0.012 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.002 0.028 -9999 0 -0.52 1 1
LAMA3 -0.02 0.16 -9999 0 -0.74 18 18
EZR 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.002 0.094 -9999 0 -0.85 5 5
Syndecan-2/MMP2 0.019 0.046 -9999 0 -0.57 2 2
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.017 0.15 -9999 0 -0.66 22 22
dendrite morphogenesis -0.28 0.3 -9999 0 -0.57 211 211
Syndecan-2/GM-CSF -0.12 0.26 -9999 0 -0.57 101 101
determination of left/right symmetry 0.017 0.037 -9999 0 -0.49 2 2
Syndecan-2/PKC delta 0.021 0.032 -9999 0 -0.57 1 1
GNB2L1 0.012 0 -9999 0 -10000 0 0
MAPK3 -0.1 0.24 -9999 0 -0.52 101 101
MAPK1 -0.1 0.24 -9999 0 -0.52 101 101
Syndecan-2/RACK1 0.027 0.028 -9999 0 -0.5 1 1
NF1 0.012 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.017 0.037 -9999 0 -0.49 2 2
ITGA2 -0.031 0.19 -9999 0 -0.85 21 21
MAPK8 0.03 0.033 -9999 0 -0.56 1 1
Syndecan-2/alpha2/beta1 Integrin -0.096 0.24 -9999 0 -0.51 99 99
Syndecan-2/Kininogen -0.032 0.16 -9999 0 -0.59 32 32
ITGB1 0.01 0.042 -9999 0 -0.85 1 1
SRC 0.033 0.027 -9999 0 -0.46 1 1
Syndecan-2/CASK/Protein 4.1 0.02 0.03 -9999 0 -0.53 1 1
extracellular matrix organization 0.021 0.032 -9999 0 -0.57 1 1
actin cytoskeleton reorganization -0.037 0.18 -9999 0 -0.57 41 41
Syndecan-2/Caveolin-2/Ras 0.021 0.067 -9999 0 -0.52 6 6
Syndecan-2/Laminin alpha3 -0.001 0.11 -9999 0 -0.57 14 14
Syndecan-2/RasGAP -0.002 0.025 -9999 0 -0.47 1 1
alpha5/beta1 Integrin 0.006 0.1 -9999 0 -0.74 7 7
PRKCD 0.012 0 -9999 0 -10000 0 0
Syndecan-2 dimer -0.28 0.3 -9999 0 -0.58 211 211
GO:0007205 0.003 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.039 0.027 -9999 0 -0.45 1 1
RHOA 0.012 0 -9999 0 -10000 0 0
SDCBP 0.012 0 -9999 0 -10000 0 0
TNFRSF13B -0.12 0.22 -9999 0 -0.47 113 113
RASA1 0.012 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.017 0.15 -9999 0 -0.66 22 22
Syndecan-2/Synbindin 0.021 0.032 -9999 0 -0.57 1 1
TGFB1 0.012 0 -9999 0 -10000 0 0
CASP3 0.029 0.03 -9999 0 -0.52 1 1
FN1 -0.072 0.26 -9999 0 -0.84 41 41
Syndecan-2/IL8 -0.27 0.3 -9999 0 -0.58 201 201
SDC2 0.017 0.037 -9999 0 -0.49 2 2
KNG1 -0.058 0.23 -9999 0 -0.85 32 32
Syndecan-2/Neurofibromin 0.021 0.032 -9999 0 -0.57 1 1
TRAPPC4 0.012 0 -9999 0 -10000 0 0
CSF2 -0.2 0.37 -9999 0 -0.85 100 100
Syndecan-2/TGFB1 0.021 0.032 -9999 0 -0.57 1 1
Syndecan-2/Syntenin/PI-4-5-P2 0.02 0.03 -9999 0 -0.53 1 1
Syndecan-2/Ezrin 0.028 0.03 -9999 0 -0.52 1 1
PRKACA 0.029 0.03 -9999 0 -0.52 1 1
angiogenesis -0.27 0.3 -9999 0 -0.57 201 201
MMP2 0.009 0.048 -9999 0 -0.66 2 2
IL8 -0.41 0.43 -9999 0 -0.85 201 201
calcineurin-NFAT signaling pathway -0.06 0.14 -9999 0 -0.65 3 3
Noncanonical Wnt signaling pathway

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
NFATC2 0.009 0.041 -9999 0 -0.47 3 3
GNB1/GNG2 -0.12 0.2 -9999 0 -0.54 40 40
mol:DAG -0.1 0.18 -9999 0 -0.48 39 39
PLCG1 -0.1 0.18 -9999 0 -0.5 39 39
YES1 -0.13 0.2 -9999 0 -0.51 53 53
FZD3 0.01 0.033 -9999 0 -0.47 2 2
FZD6 0.006 0.068 -9999 0 -0.66 4 4
G protein -0.1 0.19 -9999 0 -0.51 40 40
MAP3K7 -0.094 0.17 -9999 0 -0.54 15 15
mol:Ca2+ -0.097 0.17 -9999 0 -0.47 39 39
mol:IP3 -0.1 0.18 -9999 0 -0.48 39 39
NLK -0.006 0.008 -9999 0 -10000 0 0
GNB1 0.012 0 -9999 0 -10000 0 0
CAMK2A -0.11 0.18 -9999 0 -0.49 36 36
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.14 0.21 -9999 0 -0.55 53 53
CSNK1A1 0.012 0 -9999 0 -10000 0 0
GNAS -0.13 0.2 -9999 0 -0.51 54 54
GO:0007205 -0.098 0.18 -9999 0 -0.47 39 39
WNT6 -0.064 0.19 -9999 0 -0.5 62 62
WNT4 -0.059 0.17 -9999 0 -0.47 62 62
NFAT1/CK1 alpha -0.097 0.18 -9999 0 -0.66 11 11
GNG2 0.01 0.042 -9999 0 -0.85 1 1
WNT5A -0.058 0.24 -9999 0 -0.85 34 34
WNT11 -0.18 0.34 -9999 0 -0.73 105 105
CDC42 -0.11 0.19 -9999 0 -0.48 53 53
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.002 0.029 -9999 0 -0.51 1 1
RGS9BP -0.041 0.16 -9999 0 -0.5 43 43
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.009 0.1 -9999 0 -0.85 6 6
mol:Na + -0.2 0.27 -9999 0 -0.6 121 121
mol:ADP -0.009 0.11 -9999 0 -0.66 12 12
GNAT2 0.012 0.002 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.09 0.15 -9999 0 -0.54 19 19
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.004 0.049 -9999 0 -0.58 3 3
GRK7 -0.003 0.1 -9999 0 -0.85 6 6
CNGB3 -0.23 0.39 -9999 0 -0.85 116 116
Cone Metarhodopsin II/X-Arrestin 0 0.047 -9999 0 -0.67 2 2
mol:Ca2+ -0.2 0.29 -9999 0 -0.58 133 133
Cone PDE6 -0.08 0.14 -9999 0 -0.51 21 21
Cone Metarhodopsin II -0.008 0.092 -9999 0 -0.54 12 12
Na + (4 Units) -0.2 0.28 -9999 0 -0.58 133 133
GNAT2/GDP -0.075 0.13 -9999 0 -0.46 19 19
GNB5 0.012 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.009 0.063 -9999 0 -0.69 3 3
Cone Transducin 0.021 0.033 -9999 0 -0.54 1 1
SLC24A2 -0.036 0.19 -9999 0 -0.85 22 22
GNB3/GNGT2 0.015 0.041 -9999 0 -0.44 3 3
GNB3 0.008 0.054 -9999 0 -0.6 3 3
GNAT2/GTP 0.009 0.002 -9999 0 -10000 0 0
CNGA3 -0.058 0.18 -9999 0 -0.5 56 56
ARR3 0.001 0.06 -9999 0 -0.85 2 2
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.2 0.27 -9999 0 -0.6 121 121
mol:Pi -0.09 0.15 -9999 0 -0.54 19 19
Cone CNG Channel -0.17 0.23 -9999 0 -0.51 123 123
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.036 0.19 -9999 0 -0.85 22 22
RGS9 -0.095 0.2 -9999 0 -0.47 92 92
PDE6C 0.005 0.043 -9999 0 -0.85 1 1
GNGT2 0.012 0 -9999 0 -10000 0 0
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H -0.003 0.073 -9999 0 -0.85 3 3
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.056 0.28 -10000 0 -0.9 30 30
IHH -0.053 0.19 -10000 0 -0.55 49 49
SHH Np/Cholesterol/GAS1 -0.042 0.14 -10000 0 -0.54 15 15
LRPAP1 0.012 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.042 0.14 0.54 15 -10000 0 15
SMO/beta Arrestin2 -0.031 0.2 -10000 0 -0.7 17 17
SMO -0.04 0.21 -10000 0 -0.71 21 21
AKT1 0.004 0.088 -10000 0 -0.36 1 1
ARRB2 0.012 0 -10000 0 -10000 0 0
BOC -0.039 0.15 -10000 0 -0.48 44 44
ADRBK1 0.01 0.042 -10000 0 -0.85 1 1
heart looping -0.039 0.2 -10000 0 -0.69 21 21
STIL -0.1 0.25 -10000 0 -0.69 38 38
DHH N/PTCH2 -0.078 0.23 -10000 0 -0.65 53 53
DHH N/PTCH1 -0.03 0.18 -10000 0 -0.65 16 16
PIK3CA 0.01 0.042 -10000 0 -0.85 1 1
DHH 0 0.077 -10000 0 -0.47 11 11
PTHLH -0.075 0.32 -10000 0 -1 32 32
determination of left/right symmetry -0.039 0.2 -10000 0 -0.69 21 21
PIK3R1 0.012 0 -10000 0 -10000 0 0
skeletal system development -0.073 0.31 -10000 0 -0.99 32 32
IHH N/Hhip -0.11 0.21 -10000 0 -0.44 109 109
DHH N/Hhip -0.075 0.16 -10000 0 -0.34 108 108
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.039 0.2 -10000 0 -0.69 21 21
pancreas development -0.11 0.21 -10000 0 -0.47 102 102
HHAT 0.006 0.057 -10000 0 -0.47 6 6
PI3K 0.017 0.033 -10000 0 -0.66 1 1
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.053 0.17 -10000 0 -0.49 54 54
somite specification -0.039 0.2 -10000 0 -0.69 21 21
SHH Np/Cholesterol/PTCH1 -0.038 0.18 -10000 0 -0.63 18 18
SHH Np/Cholesterol/PTCH2 -0.077 0.2 -10000 0 -0.54 59 59
SHH Np/Cholesterol/Megalin -0.085 0.2 -10000 0 -0.54 62 62
SHH -0.016 0.12 -10000 0 -0.38 38 38
catabolic process -0.033 0.19 -10000 0 -0.68 16 16
SMO/Vitamin D3 -0.04 0.2 -10000 0 -0.71 16 16
SHH Np/Cholesterol/Hhip -0.07 0.16 -10000 0 -0.52 26 26
LRP2 -0.11 0.29 -10000 0 -0.85 56 56
receptor-mediated endocytosis -0.075 0.21 -10000 0 -0.63 27 27
SHH Np/Cholesterol/BOC -0.034 0.13 -10000 0 -0.52 12 12
SHH Np/Cholesterol/CDO -0.015 0.11 -10000 0 -0.52 12 12
mesenchymal cell differentiation 0.07 0.16 0.52 26 -10000 0 26
mol:Vitamin D3 -0.036 0.18 -10000 0 -0.64 18 18
IHH N/PTCH2 -0.11 0.26 -10000 0 -0.65 68 68
CDON -0.003 0.1 -10000 0 -0.62 10 10
IHH N/PTCH1 -0.033 0.19 -10000 0 -0.7 16 16
Megalin/LRPAP1 -0.075 0.23 -10000 0 -0.66 56 56
PTCH2 -0.099 0.29 -10000 0 -0.83 55 55
SHH Np/Cholesterol -0.027 0.092 -10000 0 -0.52 7 7
PTCH1 -0.033 0.19 -10000 0 -0.69 16 16
HHIP -0.11 0.21 -10000 0 -0.47 102 102
amb2 Integrin 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
alphaM/beta2 Integrin/proMMP-2 -0.026 0.11 -9999 0 -0.59 13 13
alphaM/beta2 Integrin/GPIbA -0.038 0.13 -9999 0 -0.62 15 15
alphaM/beta2 Integrin/proMMP-9 -0.18 0.29 -9999 0 -0.62 117 117
PLAUR 0.004 0.084 -9999 0 -0.85 4 4
HMGB1 0.008 0.018 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.024 0.1 -9999 0 -0.59 12 12
AGER 0.006 0.046 -9999 0 -0.85 1 1
RAP1A 0.012 0 -9999 0 -10000 0 0
SELPLG 0.012 0 -9999 0 -10000 0 0
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.046 0.12 -9999 0 -0.56 14 14
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.23 0.39 -9999 0 -0.85 115 115
CYR61 0.004 0.08 -9999 0 -0.7 5 5
TLN1 0.012 0 -9999 0 -10000 0 0
Rap1/GTP -0.09 0.14 -9999 0 -0.55 23 23
RHOA 0.012 0 -9999 0 -10000 0 0
P-selectin oligomer -0.05 0.16 -9999 0 -0.46 54 54
MYH2 -0.1 0.2 -9999 0 -0.57 46 46
MST1R 0.005 0.067 -9999 0 -0.53 6 6
leukocyte activation during inflammatory response -0.19 0.23 -9999 0 -0.57 90 90
APOB -0.24 0.32 -9999 0 -0.58 178 178
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 0.009 0.048 -9999 0 -0.66 2 2
JAM3 0.012 0 -9999 0 -10000 0 0
GP1BA -0.011 0.12 -9999 0 -0.56 17 17
alphaM/beta2 Integrin/CTGF -0.026 0.11 -9999 0 -0.59 13 13
alphaM/beta2 Integrin -0.086 0.18 -9999 0 -0.48 49 49
JAM3 homodimer 0.012 0 -9999 0 -10000 0 0
ICAM2 0.009 0.048 -9999 0 -0.66 2 2
ICAM1 -0.008 0.13 -9999 0 -0.85 10 10
phagocytosis triggered by activation of immune response cell surface activating receptor -0.085 0.18 -9999 0 -0.48 49 49
cell adhesion -0.038 0.13 -9999 0 -0.62 15 15
NFKB1 -0.017 0.18 -9999 0 -0.58 19 19
THY1 -0.056 0.23 -9999 0 -0.85 33 33
RhoA/GDP 0.009 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.2 0.26 -9999 0 -0.65 78 78
alphaM/beta2 Integrin/LRP/tPA -0.021 0.092 -9999 0 -0.54 12 12
IL6 -0.06 0.28 -9999 0 -0.7 59 59
ITGB2 -0.007 0.11 -9999 0 -0.86 7 7
elevation of cytosolic calcium ion concentration -0.072 0.19 -9999 0 -0.56 50 50
alphaM/beta2 Integrin/JAM2/JAM3 -0.043 0.12 -9999 0 -0.54 14 14
JAM2 -0.032 0.14 -9999 0 -0.47 39 39
alphaM/beta2 Integrin/ICAM1 -0.073 0.18 -9999 0 -0.52 54 54
alphaM/beta2 Integrin/uPA/Plg -0.076 0.18 -9999 0 -0.55 53 53
RhoA/GTP -0.11 0.22 -9999 0 -0.6 46 46
positive regulation of phagocytosis -0.079 0.14 -9999 0 -0.51 25 25
Ron/MSP -0.042 0.19 -9999 0 -0.62 39 39
alphaM/beta2 Integrin/uPAR/uPA -0.072 0.19 -9999 0 -0.57 50 50
alphaM/beta2 Integrin/uPAR -0.03 0.12 -9999 0 -0.59 16 16
PLAU -0.065 0.25 -9999 0 -0.85 37 37
PLAT 0.012 0 -9999 0 -10000 0 0
actin filament polymerization -0.096 0.2 -9999 0 -0.54 46 46
MST1 -0.057 0.24 -9999 0 -0.84 34 34
alphaM/beta2 Integrin/lipoprotein(a) -0.19 0.24 -9999 0 -0.58 90 90
TNF -0.024 0.22 -9999 0 -0.8 20 20
RAP1B 0.006 0.073 -9999 0 -0.85 3 3
alphaM/beta2 Integrin/uPA -0.075 0.19 -9999 0 -0.6 48 48
fibrinolysis -0.075 0.18 -9999 0 -0.55 53 53
HCK 0.012 0 -9999 0 -10000 0 0
dendritic cell antigen processing and presentation -0.085 0.18 -9999 0 -0.48 49 49
VTN -0.12 0.28 -9999 0 -0.66 82 82
alphaM/beta2 Integrin/CYR61 -0.03 0.12 -9999 0 -0.6 15 15
LPA -0.062 0.23 -9999 0 -0.85 33 33
LRP1 0.012 0 -9999 0 -10000 0 0
cell migration -0.14 0.28 -9999 0 -0.57 117 117
FN1 -0.072 0.26 -9999 0 -0.84 41 41
alphaM/beta2 Integrin/Thy1 -0.07 0.19 -9999 0 -0.61 43 43
MPO -0.001 0.1 -9999 0 -0.85 6 6
KNG1 -0.058 0.23 -9999 0 -0.85 32 32
RAP1/GDP -0.004 0.049 -9999 0 -0.58 3 3
ROCK1 -0.095 0.2 -9999 0 -0.56 46 46
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.009 0.093 -9999 0 -0.85 5 5
CTGF 0.009 0.048 -9999 0 -0.66 2 2
alphaM/beta2 Integrin/Hck -0.024 0.1 -9999 0 -0.59 12 12
ITGAM -0.005 0.1 -9999 0 -0.76 7 7
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.051 0.12 -9999 0 -0.54 13 13
HP -0.12 0.31 -9999 0 -0.85 62 62
leukocyte adhesion -0.085 0.16 -9999 0 -0.64 15 15
SELP -0.05 0.16 -9999 0 -0.47 54 54
p75(NTR)-mediated 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
Sortilin/TRAF6 0.019 0 -9999 0 -10000 0 0
Necdin/E2F1 -0.019 0.15 -9999 0 -0.57 27 27
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.096 0.16 -9999 0 -0.51 36 36
NGF (dimer)/p75(NTR)/BEX1 -0.24 0.24 -9999 0 -0.59 100 100
NT-4/5 (dimer)/p75(NTR) -0.15 0.23 -9999 0 -0.41 157 157
IKBKB 0.012 0 -9999 0 -10000 0 0
AKT1 -0.066 0.16 -9999 0 -0.47 33 33
IKBKG 0.012 0 -9999 0 -10000 0 0
BDNF -0.009 0.13 -9999 0 -0.82 11 11
MGDIs/NGR/p75(NTR)/LINGO1 -0.15 0.22 -9999 0 -0.64 55 55
FURIN 0.008 0.06 -9999 0 -0.85 2 2
proBDNF (dimer)/p75(NTR)/Sortilin -0.11 0.17 -9999 0 -0.58 24 24
LINGO1 -0.067 0.25 -9999 0 -0.85 38 38
Sortilin/TRAF6/NRIF -0.002 0.017 -9999 0 -10000 0 0
proBDNF (dimer) -0.009 0.13 -9999 0 -0.82 11 11
NTRK1 -0.009 0.097 -9999 0 -0.47 18 18
RTN4R 0 0.1 -9999 0 -0.85 6 6
neuron apoptosis -0.076 0.18 -9999 0 -0.65 10 10
IRAK1 0.012 0 -9999 0 -10000 0 0
SHC1 -0.093 0.18 -9999 0 -0.56 32 32
ARHGDIA 0.012 0 -9999 0 -10000 0 0
RhoA/GTP 0.009 0 -9999 0 -10000 0 0
Gamma Secretase 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.082 0.18 -9999 0 -0.53 35 35
MAGEH1 0.003 0.066 -9999 0 -0.47 8 8
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.084 0.18 -9999 0 -0.53 36 36
Mammalian IAPs/DIABLO 0.025 0.062 -9999 0 -0.52 5 5
proNGF (dimer) -0.019 0.12 -9999 0 -0.5 25 25
MAGED1 0.009 0.041 -9999 0 -0.47 3 3
APP 0.012 0 -9999 0 -10000 0 0
NT-4/5 (dimer) -0.046 0.21 -9999 0 -0.85 26 26
ZNF274 0.008 0.047 -9999 0 -0.47 4 4
RhoA/GDP/RHOGDI -0.072 0.16 -9999 0 -0.48 32 32
NGF -0.019 0.12 -9999 0 -0.5 25 25
cell cycle arrest -0.044 0.18 -9999 0 -0.48 32 32
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.06 0.14 -9999 0 -0.44 21 21
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.13 0.19 -9999 0 -0.58 39 39
NCSTN 0.012 0 -9999 0 -10000 0 0
mol:GTP -0.11 0.18 -9999 0 -0.56 32 32
PSENEN 0.012 0 -9999 0 -10000 0 0
mol:ceramide -0.077 0.17 -9999 0 -0.5 32 32
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.044 0.13 -9999 0 -0.39 22 22
p75(NTR)/beta APP -0.1 0.18 -9999 0 -0.66 13 13
BEX1 -0.2 0.27 -9999 0 -0.52 168 168
mol:GDP -0.1 0.18 -9999 0 -0.5 41 41
NGF (dimer) -0.26 0.29 -9999 0 -0.55 197 197
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.12 0.22 -9999 0 -0.58 55 55
PIK3R1 0.012 0 -9999 0 -10000 0 0
RAC1/GTP -0.095 0.15 -9999 0 -0.49 32 32
MYD88 0.012 0 -9999 0 -10000 0 0
CHUK 0.012 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.11 0.18 -9999 0 -0.57 32 32
RHOB 0.012 0 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.011 0.14 -9999 0 -0.66 18 18
NT3 (dimer) -0.033 0.14 -9999 0 -0.48 39 39
TP53 -0.056 0.15 -9999 0 -0.47 23 23
PRDM4 -0.077 0.17 -9999 0 -0.51 32 32
BDNF (dimer) -0.51 0.37 -9999 0 -0.69 309 309
PIK3CA 0.01 0.042 -9999 0 -0.85 1 1
SORT1 0.012 0 -9999 0 -10000 0 0
activation of caspase activity -0.095 0.16 -9999 0 -0.5 36 36
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.077 0.17 -9999 0 -0.51 32 32
RHOC 0.012 0 -9999 0 -10000 0 0
XIAP 0.012 0 -9999 0 -10000 0 0
MAPK10 -0.083 0.2 -9999 0 -0.61 14 14
DIABLO 0.012 0 -9999 0 -10000 0 0
SMPD2 -0.077 0.17 -9999 0 -0.51 32 32
APH1B 0.012 0 -9999 0 -10000 0 0
APH1A 0.012 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.11 0.18 -9999 0 -0.56 32 32
PSEN1 0.012 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.019 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.13 0.21 -9999 0 -0.39 152 152
MAPK8 -0.055 0.17 -9999 0 -0.61 3 3
MAPK9 -0.055 0.17 -9999 0 -0.61 3 3
APAF1 0.012 0 -9999 0 -10000 0 0
NTF3 -0.034 0.14 -9999 0 -0.48 39 39
NTF4 -0.046 0.21 -9999 0 -0.85 26 26
NDN 0 0.077 -9999 0 -0.47 11 11
RAC1/GDP 0.009 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.083 0.14 -9999 0 -0.5 15 15
p75 CTF/Sortilin/TRAF6/NRIF 0.03 0.026 -9999 0 -10000 0 0
RhoA-B-C/GTP -0.11 0.18 -9999 0 -0.56 32 32
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.09 0.14 -9999 0 -0.49 28 28
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.075 0.16 -9999 0 -0.53 24 24
PRKACB 0.01 0.033 -9999 0 -0.47 2 2
proBDNF (dimer)/p75 ECD 0.001 0.1 -9999 0 -0.66 10 10
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 0.001 0.097 -9999 0 -0.79 6 6
BIRC2 0.012 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.045 0.19 -9999 0 -0.48 34 34
BAD -0.063 0.18 -9999 0 -0.5 14 14
RIPK2 0.004 0.084 -9999 0 -0.85 4 4
NGFR -0.15 0.25 -9999 0 -0.5 132 132
CYCS -0.068 0.16 -9999 0 -0.48 35 35
ADAM17 0.012 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.083 0.18 -9999 0 -0.53 36 36
BCL2L11 -0.063 0.18 -9999 0 -0.5 14 14
BDNF (dimer)/p75(NTR) -0.12 0.2 -9999 0 -0.67 24 24
PI3K -0.078 0.17 -9999 0 -0.51 33 33
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.077 0.17 -9999 0 -0.51 32 32
NDNL2 0.012 0 -9999 0 -10000 0 0
YWHAE 0.012 0 -9999 0 -10000 0 0
PRKCI 0.004 0.084 -9999 0 -0.85 4 4
NGF (dimer)/p75(NTR) -0.12 0.21 -9999 0 -0.4 138 138
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.079 0.18 -9999 0 -0.52 34 34
TRAF6 0.012 0 -9999 0 -10000 0 0
RAC1 0.012 0 -9999 0 -10000 0 0
PRKCZ 0.012 0 -9999 0 -10000 0 0
PLG -0.009 0.093 -9999 0 -0.85 5 5
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.088 0.18 -9999 0 -0.48 43 43
SQSTM1 0.012 0 -9999 0 -10000 0 0
NGFRAP1 0.001 0.073 -9999 0 -0.47 10 10
CASP3 -0.057 0.17 -9999 0 -0.46 14 14
E2F1 -0.025 0.18 -9999 0 -0.85 18 18
CASP9 0.012 0 -9999 0 -10000 0 0
IKK complex -0.067 0.11 -9999 0 -0.6 4 4
NGF (dimer)/TRKA -0.019 0.12 -9999 0 -0.35 41 41
MMP7 -0.4 0.43 -9999 0 -0.84 200 200
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.093 0.15 -9999 0 -0.48 35 35
MMP3 -0.4 0.43 -9999 0 -0.83 202 202
APAF-1/Caspase 9 -0.068 0.11 -9999 0 -0.59 2 2
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.021 0.091 -10000 0 -0.56 8 8
fibroblast growth factor receptor signaling pathway -0.021 0.091 -10000 0 -0.56 8 8
LAMA1 -0.16 0.34 -10000 0 -0.84 82 82
PRNP 0.011 0.023 -10000 0 -0.47 1 1
GPC1/SLIT2 -0.053 0.16 -10000 0 -0.36 79 79
SMAD2 0.025 0.06 -10000 0 -0.52 5 5
GPC1/PrPc/Cu2+ -0.006 0.058 -10000 0 -0.58 4 4
GPC1/Laminin alpha1 -0.12 0.28 -10000 0 -0.66 84 84
TDGF1 -0.098 0.26 -10000 0 -0.67 67 67
CRIPTO/GPC1 -0.072 0.21 -10000 0 -0.67 39 39
APP/GPC1 0.012 0.066 -10000 0 -0.66 4 4
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.052 0.19 -10000 0 -0.58 39 39
FLT1 0.01 0.042 -10000 0 -0.85 1 1
GPC1/TGFB/TGFBR1/TGFBR2 -0.007 0.063 -10000 0 -0.57 5 5
SERPINC1 -0.009 0.13 -10000 0 -0.85 9 9
FYN -0.052 0.19 -10000 0 -0.58 39 39
FGR -0.052 0.19 -10000 0 -0.58 39 39
positive regulation of MAPKKK cascade -0.062 0.18 -10000 0 -0.48 51 51
SLIT2 -0.078 0.19 -10000 0 -0.48 76 76
GPC1/NRG -0.072 0.17 -10000 0 -0.68 10 10
NRG1 -0.1 0.22 -10000 0 -0.49 96 96
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.016 0.11 -10000 0 -0.68 10 10
LYN -0.052 0.19 -10000 0 -0.58 39 39
mol:Spermine 0.004 0.066 -10000 0 -0.67 4 4
cell growth -0.021 0.091 -10000 0 -0.56 8 8
BMP signaling pathway -0.004 0.084 0.85 4 -10000 0 4
SRC -0.052 0.19 -10000 0 -0.58 39 39
TGFBR1 0.01 0.042 -10000 0 -0.85 1 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.29 0.38 -10000 0 -0.74 165 165
GPC1 0.004 0.084 -10000 0 -0.85 4 4
TGFBR1 (dimer) 0.01 0.042 -10000 0 -0.85 1 1
VEGFA -0.002 0.11 -10000 0 -0.85 7 7
BLK -0.13 0.25 -10000 0 -0.64 68 68
HCK -0.052 0.19 -10000 0 -0.58 39 39
FGF2 -0.01 0.11 -10000 0 -0.49 19 19
FGFR1 0.008 0.054 -10000 0 -0.6 3 3
VEGFR1 homodimer 0.01 0.042 -10000 0 -0.85 1 1
TGFBR2 0.012 0 -10000 0 -10000 0 0
cell death 0.012 0.066 -10000 0 -0.66 4 4
ATIII/GPC1 -0.005 0.12 -10000 0 -0.66 13 13
PLA2G2A/GPC1 -0.22 0.31 -10000 0 -0.67 119 119
LCK -0.068 0.2 -10000 0 -0.58 50 50
neuron differentiation -0.072 0.17 -10000 0 -0.68 10 10
PrPc/Cu2+ 0.008 0.017 -10000 0 -0.33 1 1
APP 0.012 0 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.012 0 -10000 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.038 0.049 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.11 0.14 -9999 0 -0.47 15 15
JUN -0.077 0.16 -9999 0 -0.54 11 11
HRAS 0.012 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.13 0.22 -9999 0 -0.56 60 60
RAP1A 0.012 0 -9999 0 -10000 0 0
FRS2 0 0.1 -9999 0 -0.85 6 6
RAP1A/GDP 0.009 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.13 0.22 -9999 0 -0.57 59 59
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.012 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.095 0.16 -9999 0 -0.57 17 17
RHOA 0.012 0 -9999 0 -10000 0 0
RAP1A/GTP -0.13 0.19 -9999 0 -0.5 59 59
GRB7 -0.079 0.26 -9999 0 -0.84 45 45
RET51/GFRalpha1/GDNF -0.13 0.22 -9999 0 -0.56 59 59
MAPKKK cascade -0.12 0.17 -9999 0 -0.48 46 46
BCAR1 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.089 0.15 -9999 0 -0.58 13 13
lamellipodium assembly -0.11 0.13 -9999 0 -0.36 56 56
RET51/GFRalpha1/GDNF/SHC -0.13 0.22 -9999 0 -0.56 59 59
PIK3CA 0.01 0.042 -9999 0 -0.85 1 1
RET9/GFRalpha1/GDNF/SHC -0.088 0.15 -9999 0 -0.58 12 12
RET9/GFRalpha1/GDNF/Shank3 -0.088 0.15 -9999 0 -0.58 12 12
MAPK3 -0.098 0.19 -9999 0 -0.47 59 59
DOK1 0.01 0.042 -9999 0 -0.85 1 1
DOK6 -0.003 0.11 -9999 0 -0.8 8 8
PXN 0.012 0 -9999 0 -10000 0 0
neurite development -0.085 0.18 -9999 0 -0.68 11 11
DOK5 -0.026 0.17 -9999 0 -0.74 21 21
GFRA1 -0.16 0.23 -9999 0 -0.47 153 153
MAPK8 -0.088 0.17 -9999 0 -0.44 46 46
HRAS/GTP -0.14 0.2 -9999 0 -0.53 59 59
tube development -0.077 0.14 -9999 0 -0.55 12 12
MAPK1 -0.098 0.19 -9999 0 -0.47 59 59
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.074 0.13 -9999 0 -0.38 18 18
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
PDLIM7 0.002 0.094 -9999 0 -0.85 5 5
RET51/GFRalpha1/GDNF/Dok6 -0.14 0.2 -9999 0 -0.52 67 67
SHC1 0.012 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.13 0.22 -9999 0 -0.56 59 59
RET51/GFRalpha1/GDNF/Dok5 -0.15 0.23 -9999 0 -0.56 77 77
PRKCA 0.012 0 -9999 0 -10000 0 0
HRAS/GDP 0.009 0 -9999 0 -10000 0 0
CREB1 -0.1 0.18 -9999 0 -0.46 46 46
PIK3R1 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.07 0.13 -9999 0 -0.46 10 10
RET51/GFRalpha1/GDNF/Grb7 -0.18 0.28 -9999 0 -0.63 99 99
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.074 0.22 -9999 0 -0.6 59 59
DOK4 0.011 0.023 -9999 0 -0.47 1 1
JNK cascade -0.075 0.16 -9999 0 -0.53 11 11
RET9/GFRalpha1/GDNF/FRS2 -0.096 0.16 -9999 0 -0.56 18 18
SHANK3 0.012 0 -9999 0 -10000 0 0
RASA1 0.012 0 -9999 0 -10000 0 0
NCK1 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.07 0.13 -9999 0 -0.43 12 12
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.1 0.17 -9999 0 -0.46 46 46
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.1 0.18 -9999 0 -0.47 46 46
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.11 0.2 -9999 0 -0.56 46 46
PI3K -0.13 0.24 -9999 0 -0.57 56 56
SOS1 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.094 0.13 -9999 0 -0.55 12 12
GRB10 0.01 0.042 -9999 0 -0.85 1 1
activation of MAPKK activity -0.093 0.16 -9999 0 -0.41 47 47
RET51/GFRalpha1/GDNF/FRS2 -0.14 0.22 -9999 0 -0.56 65 65
GAB1 0.012 0 -9999 0 -10000 0 0
IRS1 0.011 0.023 -9999 0 -0.47 1 1
IRS2 -0.013 0.12 -9999 0 -0.55 19 19
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.11 0.2 -9999 0 -0.56 46 46
RET51/GFRalpha1/GDNF/PKC alpha -0.13 0.22 -9999 0 -0.56 59 59
GRB2 0.012 0 -9999 0 -10000 0 0
PRKACA 0.012 0 -9999 0 -10000 0 0
GDNF -0.014 0.12 -9999 0 -0.61 16 16
RAC1 0.012 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.13 0.22 -9999 0 -0.56 60 60
Rac1/GTP -0.13 0.16 -9999 0 -0.43 56 56
RET9/GFRalpha1/GDNF -0.12 0.16 -9999 0 -0.3 159 159
GFRalpha1/GDNF -0.13 0.19 -9999 0 -0.36 159 159
Endothelins

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
AKT1 -0.016 0.24 -10000 0 -0.55 39 39
PTK2B 0.013 0 -10000 0 -10000 0 0
mol:Ca2+ 0.045 0.11 -10000 0 -10000 0 0
EDN1 0.004 0.18 -10000 0 -0.74 8 8
EDN3 -0.12 0.21 -10000 0 -0.47 110 110
EDN2 -0.09 0.21 -10000 0 -0.51 81 81
HRAS/GDP -0.01 0.15 -10000 0 -0.44 3 3
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.028 0.12 -10000 0 -0.36 4 4
ADCY4 -0.037 0.2 -10000 0 -0.58 17 17
ADCY5 -0.086 0.23 -10000 0 -0.56 44 44
ADCY6 -0.037 0.2 -10000 0 -0.46 41 41
ADCY7 -0.037 0.2 -10000 0 -0.46 40 40
ADCY1 -0.056 0.21 -10000 0 -0.54 32 32
ADCY2 -0.08 0.22 -10000 0 -0.57 35 35
ADCY3 -0.037 0.2 -10000 0 -0.58 17 17
ADCY8 -0.048 0.2 -10000 0 -0.48 44 44
ADCY9 -0.038 0.2 -10000 0 -0.58 17 17
arachidonic acid secretion -0.004 0.16 -10000 0 -0.54 14 14
ETB receptor/Endothelin-1/Gq/GTP 0.022 0.084 -10000 0 -0.39 1 1
GNAO1 -0.094 0.2 -10000 0 -0.48 90 90
HRAS 0.012 0.003 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.012 0.27 0.35 114 -0.52 37 151
ETA receptor/Endothelin-1/Gs/GTP -0.008 0.26 0.32 107 -0.48 44 151
mol:GTP 0.002 0.002 -10000 0 -10000 0 0
COL3A1 -0.084 0.38 -10000 0 -0.86 69 69
EDNRB -0.002 0.061 -10000 0 -0.46 5 5
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.028 0.26 -10000 0 -0.57 50 50
CYSLTR1 -0.037 0.27 -10000 0 -0.62 39 39
SLC9A1 -0.006 0.13 -10000 0 -0.38 6 6
mol:GDP -0.018 0.16 -10000 0 -0.43 7 7
SLC9A3 -0.14 0.29 -10000 0 -0.63 71 71
RAF1 -0.022 0.15 -10000 0 -0.5 11 11
JUN 0.048 0.11 -10000 0 -10000 0 0
JAK2 -0.021 0.25 -10000 0 -0.55 42 42
mol:IP3 0.024 0.11 -10000 0 -0.39 3 3
ETA receptor/Endothelin-1 -0.001 0.33 0.41 114 -0.56 68 182
PLCB1 0 0.1 -10000 0 -0.85 6 6
PLCB2 0.004 0.085 -10000 0 -0.86 4 4
ETA receptor/Endothelin-3 -0.096 0.21 -10000 0 -0.5 47 47
FOS -0.028 0.24 -10000 0 -0.91 23 23
Gai/GDP -0.12 0.28 -10000 0 -0.65 87 87
CRK 0.013 0 -10000 0 -10000 0 0
mol:Ca ++ -0.011 0.23 -10000 0 -0.53 36 36
BCAR1 0.013 0 -10000 0 -10000 0 0
PRKCB1 0.022 0.11 -10000 0 -0.37 3 3
GNAQ 0.014 0.003 -10000 0 -10000 0 0
GNAZ -0.02 0.12 -10000 0 -0.47 28 28
GNAL -0.02 0.12 -10000 0 -0.47 28 28
Gs family/GDP -0.076 0.11 -10000 0 -0.44 9 9
ETA receptor/Endothelin-1/Gq/GTP 0.028 0.13 -10000 0 -0.42 6 6
MAPK14 0.029 0.077 -10000 0 -10000 0 0
TRPC6 0.045 0.11 -10000 0 -10000 0 0
GNAI2 0.012 0 -10000 0 -10000 0 0
GNAI3 0.012 0 -10000 0 -10000 0 0
GNAI1 0.003 0.066 -10000 0 -0.47 8 8
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.024 0.081 -10000 0 -0.35 1 1
ETB receptor/Endothelin-2 -0.065 0.16 -10000 0 -0.51 20 20
ETB receptor/Endothelin-3 -0.082 0.16 -10000 0 -0.49 7 7
ETB receptor/Endothelin-1 -0.006 0.16 -10000 0 -0.6 9 9
MAPK3 -0.026 0.22 -10000 0 -0.79 23 23
MAPK1 -0.026 0.22 -10000 0 -0.79 23 23
Rac1/GDP -0.01 0.15 -10000 0 -0.43 3 3
cAMP biosynthetic process -0.064 0.2 -10000 0 -0.53 30 30
MAPK8 0.041 0.12 -10000 0 -0.46 1 1
SRC 0.013 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.037 0.14 -10000 0 -0.44 24 24
p130Cas/CRK/Src/PYK2 -0.031 0.16 -10000 0 -0.46 2 2
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.01 0.15 -10000 0 -0.43 3 3
COL1A2 -0.073 0.37 -10000 0 -0.88 64 64
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.081 0.21 -10000 0 -0.57 39 39
mol:DAG 0.024 0.11 -10000 0 -0.38 3 3
MAP2K2 -0.021 0.18 -10000 0 -0.61 20 20
MAP2K1 -0.021 0.18 -10000 0 -0.61 20 20
EDNRA -0.003 0.2 -10000 0 -0.89 11 11
positive regulation of muscle contraction -0.006 0.21 -10000 0 -0.63 14 14
Gq family/GDP -0.064 0.1 -10000 0 -0.49 3 3
HRAS/GTP -0.027 0.14 -10000 0 -0.44 8 8
PRKCH 0.028 0.11 -10000 0 -10000 0 0
RAC1 0.012 0 -10000 0 -10000 0 0
PRKCA 0.029 0.11 -10000 0 -10000 0 0
PRKCB 0.014 0.13 -10000 0 -0.45 6 6
PRKCE 0.03 0.11 -10000 0 -10000 0 0
PRKCD 0.029 0.11 -10000 0 -0.37 2 2
PRKCG -0.19 0.27 -10000 0 -0.51 130 130
regulation of vascular smooth muscle contraction -0.036 0.27 -10000 0 -1.1 23 23
PRKCQ 0.018 0.13 -10000 0 -0.53 4 4
PLA2G4A -0.006 0.17 -10000 0 -0.59 14 14
GNA14 0.005 0.071 -10000 0 -0.52 7 7
GNA15 0.003 0.094 -10000 0 -0.85 5 5
GNA12 0.012 0 -10000 0 -10000 0 0
GNA11 0.014 0.003 -10000 0 -10000 0 0
Rac1/GTP 0.013 0.27 0.35 114 -0.51 39 153
MMP1 -0.27 0.39 -10000 0 -0.74 168 168
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.034 0.16 -9999 0 -0.47 32 32
IKBKB -0.042 0.096 -9999 0 -0.28 16 16
AKT1 -0.031 0.12 -9999 0 -0.28 36 36
IKBKG -0.044 0.1 -9999 0 -0.29 17 17
CALM1 -0.05 0.15 -9999 0 -0.46 39 39
PIK3CA 0.01 0.042 -9999 0 -0.85 1 1
MAP3K1 -0.069 0.23 -9999 0 -0.67 38 38
MAP3K7 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ -0.06 0.16 -9999 0 -0.48 40 40
DOK1 0.01 0.042 -9999 0 -0.85 1 1
AP-1 -0.012 0.094 -9999 0 -0.27 18 18
LYN 0.013 0 -9999 0 -10000 0 0
BLNK -0.009 0.1 -9999 0 -0.47 19 19
SHC1 0.012 0 -9999 0 -10000 0 0
BCR complex -0.086 0.23 -9999 0 -0.72 31 31
CD22 -0.15 0.28 -9999 0 -0.73 65 65
CAMK2G -0.04 0.14 -9999 0 -0.46 27 27
CSNK2A1 0.012 0 -9999 0 -10000 0 0
INPP5D 0.007 0.064 -9999 0 -0.72 3 3
SHC/GRB2/SOS1 -0.07 0.16 -9999 0 -0.78 11 11
GO:0007205 -0.061 0.16 -9999 0 -0.49 40 40
SYK 0.009 0.048 -9999 0 -0.66 2 2
ELK1 -0.051 0.15 -9999 0 -0.46 39 39
NFATC1 -0.065 0.2 -9999 0 -0.58 39 39
B-cell antigen/BCR complex -0.086 0.23 -9999 0 -0.72 31 31
PAG1/CSK 0.017 0.033 -9999 0 -0.66 1 1
NFKBIB -0.005 0.034 -9999 0 -10000 0 0
HRAS -0.045 0.15 -9999 0 -0.47 36 36
NFKBIA -0.004 0.033 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.003 0.027 -9999 0 -10000 0 0
RasGAP/Csk -0.079 0.18 -9999 0 -0.73 16 16
mol:GDP -0.058 0.15 -9999 0 -0.47 40 40
PTEN 0.012 0 -9999 0 -10000 0 0
CD79B -0.033 0.16 -9999 0 -0.57 32 32
NF-kappa-B/RelA/I kappa B alpha 0.003 0.027 -9999 0 -10000 0 0
GRB2 0.012 0 -9999 0 -10000 0 0
PI3K/BCAP/CD19 -0.094 0.23 -9999 0 -0.55 69 69
PIK3R1 0.012 0 -9999 0 -10000 0 0
mol:IP3 -0.061 0.16 -9999 0 -0.5 40 40
CSK 0.012 0 -9999 0 -10000 0 0
FOS -0.052 0.15 -9999 0 -0.57 19 19
CHUK -0.044 0.1 -9999 0 -0.29 17 17
IBTK 0.012 0 -9999 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.16 0.21 -9999 0 -0.61 37 37
PTPN6 -0.13 0.27 -9999 0 -0.68 65 65
RELA 0.012 0 -9999 0 -10000 0 0
BCL2A1 -0.003 0.041 -9999 0 -0.13 29 29
VAV2 -0.14 0.27 -9999 0 -0.72 59 59
ubiquitin-dependent protein catabolic process 0 0.033 -9999 0 -10000 0 0
BTK -0.023 0.13 -9999 0 -0.66 13 13
CD19 -0.14 0.28 -9999 0 -0.73 64 64
MAP4K1 -0.009 0.12 -9999 0 -0.6 15 15
CD72 -0.12 0.31 -9999 0 -0.85 61 61
PAG1 0.01 0.042 -9999 0 -0.85 1 1
MAPK14 -0.049 0.19 -9999 0 -0.56 35 35
SH3BP5 0.012 0 -9999 0 -10000 0 0
PIK3AP1 -0.065 0.19 -9999 0 -0.54 47 47
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.099 0.22 -9999 0 -0.63 41 41
RAF1 -0.036 0.14 -9999 0 -0.46 30 30
RasGAP/p62DOK/SHIP -0.079 0.19 -9999 0 -0.86 13 13
CD79A -0.092 0.21 -9999 0 -0.5 85 85
re-entry into mitotic cell cycle -0.013 0.094 -9999 0 -0.28 18 18
RASA1 0.012 0 -9999 0 -10000 0 0
MAPK3 -0.016 0.12 -9999 0 -0.45 14 14
MAPK1 -0.016 0.12 -9999 0 -0.45 14 14
CD72/SHP1 -0.16 0.33 -9999 0 -0.68 97 97
NFKB1 0.012 0 -9999 0 -10000 0 0
MAPK8 -0.049 0.19 -9999 0 -0.56 35 35
actin cytoskeleton organization -0.082 0.23 -9999 0 -0.59 58 58
NF-kappa-B/RelA 0.012 0.053 -9999 0 -10000 0 0
Calcineurin -0.054 0.12 -9999 0 -0.49 17 17
PI3K -0.12 0.21 -9999 0 -0.64 43 43
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.07 0.17 -9999 0 -0.54 41 41
SOS1 0.012 0 -9999 0 -10000 0 0
Bam32/HPK1 -0.1 0.29 -9999 0 -0.82 49 49
DAPP1 -0.14 0.3 -9999 0 -0.92 46 46
cytokine secretion -0.059 0.18 -9999 0 -0.53 39 39
mol:DAG -0.061 0.16 -9999 0 -0.5 40 40
PLCG2 0 0.096 -9999 0 -0.66 8 8
MAP2K1 -0.026 0.13 -9999 0 -0.5 15 15
B-cell antigen/BCR complex/FcgammaRIIB -0.094 0.21 -9999 0 -0.66 37 37
mol:PI-3-4-5-P3 -0.086 0.14 -9999 0 -0.42 40 40
ETS1 -0.029 0.13 -9999 0 -0.5 14 14
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.073 0.19 -9999 0 -0.79 15 15
B-cell antigen/BCR complex/LYN -0.1 0.22 -9999 0 -0.79 32 32
MALT1 0.013 0 -9999 0 -10000 0 0
TRAF6 0.013 0 -9999 0 -10000 0 0
RAC1 -0.091 0.26 -9999 0 -0.65 58 58
B-cell antigen/BCR complex/LYN/SYK -0.14 0.26 -9999 0 -0.81 41 41
CARD11 -0.18 0.27 -9999 0 -0.53 136 136
FCGR2B -0.007 0.095 -9999 0 -0.47 17 17
PPP3CA 0.008 0.06 -9999 0 -0.85 2 2
BCL10 0.013 0 -9999 0 -10000 0 0
IKK complex -0.007 0.041 -9999 0 -10000 0 0
PTPRC -0.026 0.18 -9999 0 -0.83 19 19
PDPK1 -0.031 0.11 -9999 0 -0.28 29 29
PPP3CB 0.012 0 -9999 0 -10000 0 0
PPP3CC 0.011 0.023 -9999 0 -0.47 1 1
POU2F2 0.006 0.025 -9999 0 -0.15 4 4
EGFR-dependent Endothelin signaling events

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
HRAS 0.012 0 -9999 0 -10000 0 0
EGFR -0.022 0.16 -9999 0 -0.7 20 20
EGF/EGFR -0.086 0.2 -9999 0 -0.52 64 64
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.068 0.17 -9999 0 -0.52 49 49
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.01 0.14 -9999 0 -0.85 11 11
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.078 0.26 -9999 0 -0.82 44 44
EGF/EGFR dimer/SHC -0.079 0.2 -9999 0 -0.6 49 49
mol:GDP -0.067 0.17 -9999 0 -0.51 49 49
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.001 0.11 -9999 0 -0.8 7 7
GRB2/SOS1 0.019 0 -9999 0 -10000 0 0
HRAS/GTP -0.062 0.16 -9999 0 -0.48 49 49
SHC1 0.012 0 -9999 0 -10000 0 0
HRAS/GDP -0.063 0.16 -9999 0 -0.48 49 49
FRAP1 -0.037 0.18 -9999 0 -0.5 49 49
EGF/EGFR dimer -0.077 0.24 -9999 0 -0.69 49 49
SOS1 0.012 0 -9999 0 -10000 0 0
GRB2 0.012 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.01 0.14 -9999 0 -0.66 17 17
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.058 0.2 0.54 56 -10000 0 56
KIRREL -0.001 0.07 -10000 0 -0.66 4 4
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.058 0.2 -10000 0 -0.54 56 56
PLCG1 0.012 0 -10000 0 -10000 0 0
ARRB2 0.012 0 -10000 0 -10000 0 0
WASL 0.012 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.058 0.15 -10000 0 -0.51 38 38
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.01 0.11 -10000 0 -0.6 1 1
FYN -0.034 0.15 -10000 0 -0.46 38 38
mol:Ca2+ -0.057 0.15 -10000 0 -0.5 38 38
mol:DAG -0.057 0.15 -10000 0 -0.51 38 38
NPHS2 -0.007 0.077 -10000 0 -0.87 3 3
mol:IP3 -0.057 0.15 -10000 0 -0.51 38 38
regulation of endocytosis -0.025 0.14 -10000 0 -0.43 38 38
Nephrin/NEPH1/podocin/Cholesterol -0.059 0.16 -10000 0 -0.52 38 38
establishment of cell polarity -0.058 0.2 -10000 0 -0.54 56 56
Nephrin/NEPH1/podocin/NCK1-2 -0.052 0.14 -10000 0 -0.47 38 38
Nephrin/NEPH1/beta Arrestin2 -0.024 0.14 -10000 0 -0.44 38 38
NPHS1 -0.08 0.25 -10000 0 -0.72 52 52
Nephrin/NEPH1/podocin -0.034 0.15 -10000 0 -0.46 38 38
TJP1 0.012 0 -10000 0 -10000 0 0
NCK1 0.012 0 -10000 0 -10000 0 0
NCK2 0.012 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.058 0.15 -10000 0 -0.51 38 38
CD2AP 0.012 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.058 0.15 -10000 0 -0.51 38 38
GRB2 0.012 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.031 0.15 -10000 0 -0.47 38 38
cytoskeleton organization -0.015 0.14 -10000 0 -0.82 1 1
Nephrin/NEPH1 -0.041 0.15 -10000 0 -0.49 37 37
Nephrin/NEPH1/ZO-1 -0.059 0.16 -10000 0 -0.54 36 36
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.012 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.028 0.066 -9999 0 -10000 0 0
Syndecan-3/Neurocan -0.018 0.091 -9999 0 -0.49 15 15
POMC -0.025 0.14 -9999 0 -0.52 29 29
EGFR -0.022 0.16 -9999 0 -0.7 20 20
Syndecan-3/EGFR -0.018 0.086 -9999 0 -0.49 12 12
AGRP -0.014 0.14 -9999 0 -0.85 11 11
NCSTN 0.012 0 -9999 0 -10000 0 0
PSENEN 0.012 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.012 0 -9999 0 -10000 0 0
APH1A 0.012 0 -9999 0 -10000 0 0
NCAN -0.022 0.16 -9999 0 -0.85 15 15
long-term memory 0 0 -9999 0 -10000 0 0
Syndecan-3/IL8 -0.24 0.24 -9999 0 -0.49 201 201
PSEN1 0.012 0 -9999 0 -10000 0 0
Src/Cortactin 0.019 0 -9999 0 -10000 0 0
FYN 0.012 0 -9999 0 -10000 0 0
limb bud formation 0 0 -9999 0 -10000 0 0
MC4R 0.006 0.006 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
PTN -0.058 0.17 -9999 0 -0.47 61 61
FGFR/FGF/Syndecan-3 0 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.042 0.1 -9999 0 -0.46 15 15
Syndecan-3/AgRP -0.013 0.079 -9999 0 -0.49 11 11
Syndecan-3/AgRP/MC4R -0.013 0.076 -9999 0 -0.47 11 11
Fyn/Cortactin 0.019 0 -9999 0 -10000 0 0
SDC3 0 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.23 0.24 -9999 0 -0.48 201 201
IL8 -0.41 0.43 -9999 0 -0.85 201 201
Syndecan-3/Fyn/Cortactin 0 0 -9999 0 -10000 0 0
Syndecan-3/CASK 0 0 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.013 0.1 -9999 0 -0.66 4 4
Gamma Secretase 0 0 -9999 0 -10000 0 0
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.005 0.031 -10000 0 -0.47 1 1
AES 0.012 0.015 -10000 0 -10000 0 0
FBXW11 0.012 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.015 0.008 -10000 0 -10000 0 0
SMAD4 0.01 0.033 -10000 0 -0.47 2 2
DKK2 -0.22 0.38 -10000 0 -0.84 111 111
TLE1 0.011 0.028 -10000 0 -0.47 1 1
MACF1 0.011 0.042 -10000 0 -0.85 1 1
CTNNB1 -0.006 0.11 0.3 2 -10000 0 2
WIF1 -0.11 0.23 -10000 0 -0.52 92 92
beta catenin/RanBP3 -0.014 0.11 0.36 22 -10000 0 22
KREMEN2 -0.16 0.35 -10000 0 -0.85 85 85
DKK1 -0.36 0.42 -10000 0 -0.81 188 188
beta catenin/beta TrCP1 0.001 0.1 0.28 2 -10000 0 2
FZD1 0.013 0.001 -10000 0 -10000 0 0
AXIN2 -0.04 0.22 -10000 0 -0.82 29 29
AXIN1 0.013 0.001 -10000 0 -10000 0 0
RAN 0.013 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.009 0.027 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.047 0.073 -10000 0 -10000 0 0
Axin1/APC/GSK3 0.02 0.058 0.24 1 -10000 0 1
Axin1/APC/GSK3/beta catenin/Macf1 0.032 0.071 -10000 0 -10000 0 0
HNF1A -0.008 0.12 -10000 0 -0.65 12 12
CTBP1 0.005 0.018 -10000 0 -10000 0 0
MYC 0.001 0.11 -10000 0 -1.1 3 3
RANBP3 0.013 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.26 0.33 -10000 0 -0.63 176 176
NKD1 -0.067 0.23 -10000 0 -0.66 49 49
TCF4 0.005 0.018 -10000 0 -10000 0 0
TCF3 0.011 0.016 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 -0.004 0.068 -10000 0 -0.52 3 3
Ran/GTP 0.009 0.002 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.018 0.11 0.51 7 -10000 0 7
LEF1 -0.019 0.14 -10000 0 -0.83 12 12
DVL1 0.045 0.039 -10000 0 -10000 0 0
CSNK2A1 0.013 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.049 0.087 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.36 0.34 -10000 0 -0.65 220 220
LRP6 0.013 0.001 -10000 0 -10000 0 0
CSNK1A1 0.007 0.02 -10000 0 -10000 0 0
NLK 0.012 0.004 -10000 0 -10000 0 0
CCND1 0.002 0.086 -10000 0 -0.72 4 4
WNT1 -0.015 0.12 -10000 0 -0.52 21 21
GSK3A 0.013 0.001 -10000 0 -10000 0 0
GSK3B 0.013 0.001 -10000 0 -10000 0 0
FRAT1 0.012 0.001 -10000 0 -10000 0 0
PPP2R5D 0.057 0.1 0.32 49 -10000 0 49
APC 0.023 0.066 -10000 0 -0.48 3 3
WNT1/LRP6/FZD1 0.053 0.096 0.22 86 -10000 0 86
CREBBP 0.011 0.016 -10000 0 -10000 0 0
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.12 0.19 -9999 0 -0.55 52 52
SMAD6-7/SMURF1 -0.005 0.05 -9999 0 -0.57 3 3
NOG -0.03 0.17 -9999 0 -0.64 27 27
SMAD9 -0.067 0.2 -9999 0 -0.6 43 43
SMAD4 0.01 0.033 -9999 0 -0.47 2 2
SMAD5 -0.035 0.13 -9999 0 -0.45 9 9
BMP7/USAG1 -0.22 0.25 -9999 0 -0.66 63 63
SMAD5/SKI -0.027 0.12 -9999 0 -0.48 4 4
SMAD1 0.036 0.022 -9999 0 -10000 0 0
BMP2 0.01 0.033 -9999 0 -0.47 2 2
SMAD1/SMAD1/SMAD4 -0.004 0.033 -9999 0 -10000 0 0
BMPR1A 0.011 0.023 -9999 0 -0.47 1 1
BMPR1B -0.057 0.18 -9999 0 -0.49 57 57
BMPR1A-1B/BAMBI -0.13 0.24 -9999 0 -0.61 74 74
AHSG -0.034 0.18 -9999 0 -0.85 20 20
CER1 -0.017 0.13 -9999 0 -0.85 10 10
BMP2-4/CER1 -0.024 0.11 -9999 0 -0.57 16 16
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.062 0.17 -9999 0 -0.56 15 15
BMP2-4 (homodimer) 0.006 0.085 -9999 0 -0.65 6 6
RGMB 0.011 0.023 -9999 0 -0.47 1 1
BMP6/BMPR2/BMPR1A-1B -0.009 0.11 -9999 0 -0.51 6 6
RGMA -0.14 0.22 -9999 0 -0.47 133 133
SMURF1 0.006 0.073 -9999 0 -0.85 3 3
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.06 0.15 -9999 0 -0.39 51 51
BMP2-4/USAG1 -0.14 0.15 -9999 0 -0.66 9 9
SMAD6/SMURF1/SMAD5 -0.03 0.13 -9999 0 -0.48 7 7
SOSTDC1 -0.23 0.24 -9999 0 -0.47 208 208
BMP7/BMPR2/BMPR1A-1B -0.066 0.17 -9999 0 -0.53 33 33
SKI 0.012 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.01 0.033 -9999 0 -0.46 2 2
HFE2 -0.019 0.14 -9999 0 -0.85 12 12
ZFYVE16 0.012 0 -9999 0 -10000 0 0
MAP3K7 0.012 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.016 0.089 -9999 0 -0.59 8 8
SMAD5/SMAD5/SMAD4 -0.028 0.12 -9999 0 -0.44 7 7
MAPK1 0.012 0 -9999 0 -10000 0 0
TAK1/TAB family -0.072 0.12 -9999 0 -0.52 9 9
BMP7 (homodimer) -0.088 0.23 -9999 0 -0.57 71 71
NUP214 0.012 0 -9999 0 -10000 0 0
BMP6/FETUA -0.019 0.15 -9999 0 -0.66 20 20
SMAD1/SKI 0.042 0.021 -9999 0 -10000 0 0
SMAD6 0.011 0.023 -9999 0 -0.47 1 1
CTDSP2 0.012 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.038 0.14 -9999 0 -0.57 26 26
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.14 0.32 -9999 0 -0.78 78 78
BMPR2 (homodimer) 0.012 0 -9999 0 -10000 0 0
GADD34/PP1CA 0 0 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.032 0.13 -9999 0 -0.35 57 57
CHRDL1 -0.17 0.23 -9999 0 -0.47 156 156
ENDOFIN/SMAD1 0.042 0.021 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.002 0.036 -9999 0 -10000 0 0
SMAD6/SMURF1 0.006 0.073 -9999 0 -0.85 3 3
BAMBI -0.13 0.32 -9999 0 -0.85 69 69
SMURF2 0.012 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.11 0.15 -9999 0 -0.7 8 8
BMP2-4/GREM1 -0.11 0.22 -9999 0 -0.57 70 70
SMAD7 0.012 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.058 0.18 -9999 0 -0.57 42 42
SMAD1/SMAD6 0.038 0.046 -9999 0 -0.44 3 3
TAK1/SMAD6 0.014 0.057 -9999 0 -0.66 3 3
BMP7 -0.088 0.23 -9999 0 -0.57 71 71
BMP6 0.01 0.033 -9999 0 -0.47 2 2
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.054 0.14 -9999 0 -0.36 43 43
PPM1A 0.012 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.042 0.021 -9999 0 -10000 0 0
SMAD7/SMURF1 0.014 0.057 -9999 0 -0.66 3 3
CTDSPL 0.012 0 -9999 0 -10000 0 0
PPP1CA 0.012 0 -9999 0 -10000 0 0
XIAP 0.012 0 -9999 0 -10000 0 0
CTDSP1 0.012 0 -9999 0 -10000 0 0
PPP1R15A 0.012 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.1 0.21 -9999 0 -0.51 67 67
CHRD 0.001 0.078 -9999 0 -0.51 9 9
BMPR2 0.012 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.071 0.16 -9999 0 -0.41 51 51
BMP4 -0.001 0.1 -9999 0 -0.71 8 8
FST -0.049 0.2 -9999 0 -0.64 39 39
BMP2-4/NOG -0.036 0.13 -9999 0 -0.57 18 18
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.086 0.16 -9999 0 -0.5 36 36
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.012 0 -9999 0 -10000 0 0
LAT2 -0.077 0.16 -9999 0 -0.41 53 53
AP1 -0.099 0.14 -9999 0 -0.53 15 15
mol:PIP3 -0.088 0.19 -9999 0 -0.46 53 53
IKBKB -0.042 0.12 -9999 0 -0.31 14 14
AKT1 -0.061 0.16 -9999 0 -0.62 6 6
IKBKG -0.042 0.12 -9999 0 -0.31 14 14
MS4A2 -0.066 0.18 -9999 0 -0.48 66 66
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.042 -9999 0 -0.85 1 1
MAP3K1 -0.048 0.14 -9999 0 -0.46 10 10
mol:Ca2+ -0.064 0.15 -9999 0 -0.34 53 53
LYN 0.012 0.004 -9999 0 -10000 0 0
CBLB -0.075 0.16 -9999 0 -0.4 52 52
SHC1 0.012 0 -9999 0 -10000 0 0
RasGAP/p62DOK 0.015 0.053 -9999 0 -0.53 1 1
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.007 0.064 -9999 0 -0.72 3 3
PLD2 -0.096 0.17 -9999 0 -0.55 12 12
PTPN13 -0.08 0.17 -9999 0 -0.42 56 56
PTPN11 0.009 0.008 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.038 0.14 -9999 0 -0.39 4 4
SYK 0.009 0.049 -9999 0 -0.66 2 2
GRB2 0.012 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.13 0.16 -9999 0 -0.47 53 53
LAT -0.077 0.16 -9999 0 -0.41 53 53
PAK2 -0.061 0.16 -9999 0 -0.51 11 11
NFATC2 -0.049 0.076 -9999 0 -0.64 3 3
HRAS -0.073 0.17 -9999 0 -0.42 56 56
GAB2 0.01 0.042 -9999 0 -0.85 1 1
PLA2G1B 0.021 0.032 -9999 0 -10000 0 0
Fc epsilon R1 -0.15 0.2 -9999 0 -0.55 57 57
Antigen/IgE/Fc epsilon R1 -0.14 0.18 -9999 0 -0.5 57 57
mol:GDP -0.083 0.18 -9999 0 -0.44 57 57
JUN 0.012 0 -9999 0 -10000 0 0
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.012 0.001 -9999 0 -10000 0 0
FOS -0.014 0.11 -9999 0 -0.47 23 23
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.087 0.16 -9999 0 -0.43 52 52
CHUK -0.042 0.12 -9999 0 -0.31 14 14
KLRG1 -0.076 0.15 -9999 0 -0.38 53 53
VAV1 -0.081 0.16 -9999 0 -0.41 56 56
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.076 0.16 -9999 0 -0.4 53 53
negative regulation of mast cell degranulation -0.067 0.14 -9999 0 -0.53 9 9
BTK -0.089 0.18 -9999 0 -0.45 57 57
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.12 0.21 -9999 0 -0.56 58 58
GAB2/PI3K/SHP2 -0.1 0.14 -9999 0 -0.69 6 6
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.093 0.17 -9999 0 -0.44 58 58
RAF1 0.025 0.025 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.14 0.18 -9999 0 -0.57 25 25
FCER1G -0.007 0.13 -9999 0 -0.86 10 10
FCER1A -0.17 0.24 -9999 0 -0.48 153 153
Antigen/IgE/Fc epsilon R1/Fyn -0.13 0.17 -9999 0 -0.46 57 57
MAPK3 0.034 0.021 -9999 0 -10000 0 0
MAPK1 0.034 0.021 -9999 0 -10000 0 0
NFKB1 0.012 0 -9999 0 -10000 0 0
MAPK8 -0.003 0.051 -9999 0 -10000 0 0
DUSP1 -0.002 0.083 -9999 0 -0.47 13 13
NF-kappa-B/RelA -0.043 0.054 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.078 0.16 -9999 0 -0.42 52 52
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.094 0.13 -9999 0 -0.52 12 12
FER -0.075 0.16 -9999 0 -0.4 52 52
RELA 0.012 0 -9999 0 -10000 0 0
ITK -0.039 0.077 -9999 0 -0.36 18 18
SOS1 0.012 0 -9999 0 -10000 0 0
PLCG1 -0.08 0.18 -9999 0 -0.44 56 56
cytokine secretion -0.031 0.039 -9999 0 -10000 0 0
SPHK1 -0.096 0.2 -9999 0 -0.49 62 62
PTK2 -0.081 0.16 -9999 0 -0.44 52 52
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.13 0.17 -9999 0 -0.49 52 52
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.082 0.18 -9999 0 -0.44 52 52
MAP2K2 0.03 0.021 -9999 0 -10000 0 0
MAP2K1 0.03 0.021 -9999 0 -10000 0 0
MAP2K7 0.012 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.089 0.12 -9999 0 -0.54 7 7
MAP2K4 0.015 0.01 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.14 0.19 -9999 0 -0.51 65 65
mol:Choline -0.094 0.17 -9999 0 -0.54 12 12
SHC/Grb2/SOS1 -0.087 0.13 -9999 0 -0.51 6 6
FYN 0.012 0 -9999 0 -10000 0 0
DOK1 0.01 0.042 -9999 0 -0.85 1 1
PXN -0.069 0.16 -9999 0 -0.54 4 4
HCLS1 -0.078 0.16 -9999 0 -0.4 55 55
PRKCB -0.069 0.16 -9999 0 -0.36 53 53
FCGR2B -0.007 0.095 -9999 0 -0.47 17 17
IGHE -0.002 0.006 -9999 0 -10000 0 0
KLRG1/SHIP -0.068 0.15 -9999 0 -0.54 9 9
LCP2 0.012 0.001 -9999 0 -10000 0 0
PLA2G4A -0.091 0.18 -9999 0 -0.46 60 60
RASA1 0.012 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.094 0.17 -9999 0 -0.54 12 12
IKK complex -0.019 0.093 -9999 0 -0.24 3 3
WIPF1 0.011 0.023 -9999 0 -0.47 1 1
FOXM1 transcription factor network

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
NFATC3 -0.009 0.43 -9999 0 -1.1 17 17
PLK1 0.025 0.16 -9999 0 -0.77 14 14
BIRC5 0.009 0.2 -9999 0 -0.79 22 22
HSPA1B -0.016 0.44 -9999 0 -1.1 20 20
MAP2K1 0.03 0.038 -9999 0 -10000 0 0
BRCA2 -0.03 0.46 -9999 0 -1.2 24 24
FOXM1 -0.038 0.52 -9999 0 -1.4 25 25
XRCC1 -0.009 0.43 -9999 0 -1.1 20 20
FOXM1B/p19 -0.28 0.4 -9999 0 -1.2 48 48
Cyclin D1/CDK4 -0.044 0.44 -9999 0 -1.1 19 19
CDC2 -0.016 0.45 -9999 0 -1.1 25 25
TGFA -0.032 0.43 -9999 0 -1 16 16
SKP2 -0.017 0.44 -9999 0 -1.1 26 26
CCNE1 -0.11 0.31 -9999 0 -0.86 60 60
CKS1B -0.01 0.43 -9999 0 -1.1 21 21
RB1 -0.11 0.18 -9999 0 -0.6 27 27
FOXM1C/SP1 -0.029 0.46 -9999 0 -1.2 26 26
AURKB 0.033 0.14 -9999 0 -0.78 9 9
CENPF -0.11 0.53 -9999 0 -1.2 43 43
CDK4 0.01 0.088 -9999 0 -0.87 4 4
MYC 0.004 0.39 -9999 0 -0.98 16 16
CHEK2 0.025 0.074 -9999 0 -0.89 2 2
ONECUT1 -0.055 0.47 -9999 0 -1.1 29 29
CDKN2A -0.25 0.39 -9999 0 -0.83 127 127
LAMA4 -0.01 0.43 -9999 0 -1.1 21 21
FOXM1B/HNF6 -0.077 0.53 -9999 0 -1.3 30 30
FOS -0.043 0.48 -9999 0 -1.2 33 33
SP1 0.013 0.001 -9999 0 -10000 0 0
CDC25B -0.016 0.44 -9999 0 -1.1 23 23
response to radiation 0.014 0.035 -9999 0 -10000 0 0
CENPB -0.009 0.43 -9999 0 -1.2 14 14
CENPA -0.018 0.45 -9999 0 -1.1 26 26
NEK2 -0.043 0.49 -9999 0 -1.2 34 34
HIST1H2BA -0.016 0.43 -9999 0 -1.2 14 14
CCNA2 0.015 0.009 -9999 0 -10000 0 0
EP300 0.012 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.029 0.48 -9999 0 -1.3 22 22
CCNB2 -0.009 0.43 -9999 0 -1.1 20 20
CCNB1 -0.015 0.45 -9999 0 -1.1 22 22
ETV5 -0.017 0.44 -9999 0 -1.2 18 18
ESR1 -0.029 0.47 -9999 0 -1.2 30 30
CCND1 -0.041 0.45 -9999 0 -1.1 19 19
GSK3A 0.029 0.032 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.049 0.22 -9999 0 -0.58 60 60
CDK2 0.015 0.009 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.015 0.041 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.18 0.34 -9999 0 -1.1 28 28
GAS1 -0.088 0.54 -9999 0 -1.2 45 45
MMP2 -0.011 0.43 -9999 0 -1.2 15 15
RB1/FOXM1C -0.052 0.46 -9999 0 -1.1 25 25
CREBBP 0.012 0 -9999 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.097 0.3 -10000 0 -0.98 42 42
NFATC2 0.012 0.12 -10000 0 -0.58 1 1
NFATC3 -0.015 0.061 -10000 0 -10000 0 0
CD40LG -0.26 0.39 -10000 0 -0.93 60 60
ITCH 0.039 0.039 -10000 0 -10000 0 0
CBLB 0.039 0.039 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.27 0.39 -10000 0 -1.1 63 63
JUNB 0.013 0 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.007 0.04 -10000 0 -10000 0 0
T cell anergy 0.035 0.076 -10000 0 -0.47 2 2
TLE4 0.021 0.12 -10000 0 -0.68 6 6
Jun/NFAT1-c-4/p21SNFT -0.12 0.22 -10000 0 -0.84 10 10
AP-1/NFAT1-c-4 -0.29 0.43 -10000 0 -1 59 59
IKZF1 0.008 0.16 -10000 0 -0.74 14 14
T-helper 2 cell differentiation -0.046 0.14 -10000 0 -0.68 7 7
AP-1/NFAT1 -0.072 0.12 -10000 0 -0.52 6 6
CALM1 0.022 0.026 -10000 0 -10000 0 0
EGR2 -0.017 0.2 -10000 0 -1 8 8
EGR3 -0.024 0.24 -10000 0 -1.3 10 10
NFAT1/FOXP3 -0.08 0.31 -10000 0 -0.9 44 44
EGR1 -0.002 0.084 -10000 0 -0.47 13 13
JUN -0.02 0.038 -10000 0 -10000 0 0
EGR4 -0.14 0.33 -10000 0 -0.83 74 74
mol:Ca2+ 0.01 0.028 -10000 0 -10000 0 0
GBP3 0.019 0.12 -10000 0 -0.68 7 7
FOSL1 -0.059 0.24 -10000 0 -0.83 35 35
NFAT1-c-4/MAF/IRF4 -0.058 0.2 -10000 0 -0.92 11 11
DGKA 0.027 0.085 -10000 0 -10000 0 0
CREM 0.012 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.071 0.18 -10000 0 -0.79 14 14
CTLA4 -0.12 0.4 -10000 0 -0.96 71 71
NFAT1-c-4 (dimer)/EGR1 -0.047 0.22 -10000 0 -0.91 13 13
NFAT1-c-4 (dimer)/EGR4 -0.14 0.28 -10000 0 -0.84 23 23
FOS -0.048 0.11 -10000 0 -0.49 23 23
IFNG -0.2 0.3 -10000 0 -0.68 108 108
T cell activation -0.048 0.16 -10000 0 -0.69 2 2
MAF 0.006 0.057 -10000 0 -0.47 6 6
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.023 0.17 0.81 9 -10000 0 9
TNF -0.12 0.29 -10000 0 -0.97 23 23
FASLG -0.07 0.32 -10000 0 -1.2 26 26
TBX21 -0.016 0.091 -10000 0 -0.63 6 6
BATF3 0.006 0.073 -10000 0 -0.85 3 3
PRKCQ -0.009 0.11 -10000 0 -0.51 18 18
PTPN1 0.027 0.085 -10000 0 -10000 0 0
NFAT1-c-4/ICER1 -0.067 0.18 -10000 0 -0.8 13 13
GATA3 -0.01 0.14 -10000 0 -0.85 11 11
T-helper 1 cell differentiation -0.16 0.32 -10000 0 -0.67 108 108
IL2RA -0.23 0.31 -10000 0 -0.94 52 52
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.027 0.085 -10000 0 -10000 0 0
E2F1 -0.02 0.18 -10000 0 -0.85 18 18
PPARG 0.005 0.067 -10000 0 -0.53 6 6
SLC3A2 0.027 0.085 -10000 0 -10000 0 0
IRF4 -0.009 0.11 -10000 0 -0.54 16 16
PTGS2 -0.3 0.44 -10000 0 -1.1 64 64
CSF2 -0.36 0.5 -10000 0 -1.1 111 111
JunB/Fra1/NFAT1-c-4 -0.076 0.24 -10000 0 -0.85 11 11
IL4 -0.047 0.15 -10000 0 -0.71 7 7
IL5 -0.26 0.38 -10000 0 -0.96 50 50
IL2 -0.049 0.16 -10000 0 -0.7 2 2
IL3 -0.064 0.096 -10000 0 -0.77 5 5
RNF128 0.029 0.094 -10000 0 -0.54 11 11
NFATC1 -0.023 0.17 -10000 0 -0.82 9 9
CDK4 -0.002 0.14 0.57 1 -0.81 4 5
PTPRK 0.027 0.085 -10000 0 -10000 0 0
IL8 -0.46 0.54 -10000 0 -1.1 156 156
POU2F1 0.011 0.043 -10000 0 -0.85 1 1
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.008 0.14 -10000 0 -0.49 14 14
TBX21 -0.13 0.37 -10000 0 -1 32 32
B2M 0.007 0.015 -10000 0 -10000 0 0
TYK2 0.012 0.023 -10000 0 -10000 0 0
IL12RB1 0.007 0.054 -10000 0 -0.49 4 4
GADD45B -0.09 0.29 -10000 0 -0.75 24 24
IL12RB2 -0.015 0.16 -10000 0 -0.85 14 14
GADD45G -0.091 0.29 -10000 0 -0.77 20 20
natural killer cell activation -0.001 0.025 -10000 0 -10000 0 0
RELB 0.01 0.042 -10000 0 -0.85 1 1
RELA 0.012 0 -10000 0 -10000 0 0
IL18 0.004 0.077 -10000 0 -0.75 4 4
IL2RA -0.056 0.23 -10000 0 -0.85 33 33
IFNG -0.21 0.38 -10000 0 -0.85 105 105
STAT3 (dimer) -0.1 0.3 -10000 0 -0.73 38 38
HLA-DRB5 -0.064 0.23 -10000 0 -0.72 43 43
FASLG -0.14 0.4 -10000 0 -1 44 44
NF kappa B2 p52/RelB -0.2 0.29 -10000 0 -0.84 49 49
CD4 0.009 0.06 -10000 0 -0.85 2 2
SOCS1 0.001 0.097 -10000 0 -0.79 6 6
EntrezGene:6955 -0.007 0.018 -10000 0 -10000 0 0
CD3D -0.004 0.08 -10000 0 -0.51 9 9
CD3E -0.001 0.076 -10000 0 -0.64 5 5
CD3G -0.007 0.081 -10000 0 -0.47 12 12
IL12Rbeta2/JAK2 -0.006 0.15 -10000 0 -0.75 15 15
CCL3 -0.21 0.45 -10000 0 -0.97 83 83
CCL4 -0.14 0.39 -10000 0 -1.1 35 35
HLA-A 0.007 0.014 -10000 0 -10000 0 0
IL18/IL18R 0.018 0.11 -10000 0 -0.62 7 7
NOS2 -0.25 0.45 -10000 0 -0.92 82 82
IL12/IL12R/TYK2/JAK2/SPHK2 -0.004 0.13 -10000 0 -0.48 12 12
IL1R1 -0.13 0.36 -10000 0 -0.87 45 45
IL4 -0.009 0.11 -10000 0 -0.85 7 7
JAK2 0.005 0.078 -10000 0 -0.87 3 3
EntrezGene:6957 -0.007 0.018 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.089 0.24 -10000 0 -0.54 69 69
RAB7A -0.063 0.26 -10000 0 -0.7 11 11
lysosomal transport -0.059 0.25 -10000 0 -0.66 11 11
FOS -0.094 0.33 -10000 0 -1.1 33 33
STAT4 (dimer) -0.082 0.31 -10000 0 -0.8 30 30
STAT5A (dimer) -0.3 0.36 -10000 0 -0.87 90 90
GZMA -0.14 0.4 -10000 0 -1.1 37 37
GZMB -0.14 0.39 -10000 0 -1 44 44
HLX 0.01 0.042 -10000 0 -0.85 1 1
LCK -0.15 0.39 -10000 0 -0.91 53 53
TCR/CD3/MHC II/CD4 -0.033 0.16 -10000 0 -0.51 24 24
IL2/IL2R -0.027 0.17 -10000 0 -0.55 36 36
MAPK14 -0.087 0.3 -10000 0 -0.77 22 22
CCR5 -0.1 0.31 -10000 0 -0.9 22 22
IL1B -0.063 0.24 -10000 0 -0.76 41 41
STAT6 -0.021 0.12 -10000 0 -10000 0 0
STAT4 0.004 0.084 -10000 0 -0.85 4 4
STAT3 0.012 0 -10000 0 -10000 0 0
STAT1 -0.008 0.13 -10000 0 -0.85 10 10
NFKB1 0.012 0 -10000 0 -10000 0 0
NFKB2 0.012 0 -10000 0 -10000 0 0
IL12B 0.001 0.097 -10000 0 -0.85 5 5
CD8A -0.009 0.096 -10000 0 -0.54 12 12
CD8B -0.035 0.16 -10000 0 -0.57 30 30
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.008 0.14 0.49 14 -10000 0 14
IL2RB 0.011 0.023 -10000 0 -0.47 1 1
proteasomal ubiquitin-dependent protein catabolic process -0.073 0.29 -10000 0 -0.73 30 30
IL2RG -0.002 0.095 -10000 0 -0.58 10 10
IL12 -0.009 0.12 -10000 0 -0.54 12 12
STAT5A 0.012 0 -10000 0 -10000 0 0
CD247 0 0.059 -10000 0 -0.47 6 6
IL2 0.002 0.06 -10000 0 -0.85 2 2
SPHK2 0.012 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.016 0.12 -10000 0 -0.51 22 22
IL12/IL12R/TYK2/JAK2 -0.15 0.41 -10000 0 -0.98 50 50
MAP2K3 -0.089 0.29 -10000 0 -0.74 25 25
RIPK2 0.004 0.084 -10000 0 -0.85 4 4
MAP2K6 -0.092 0.3 -10000 0 -0.78 22 22
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.003 0.07 -10000 0 -0.47 9 9
IL18RAP -0.005 0.1 -10000 0 -0.57 12 12
IL12Rbeta1/TYK2 0.013 0.049 -10000 0 -0.37 2 2
EOMES -0.11 0.28 -10000 0 -0.63 88 88
STAT1 (dimer) -0.17 0.34 -10000 0 -0.79 57 57
T cell proliferation -0.071 0.25 0.46 1 -0.59 27 28
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.008 0.051 -10000 0 -0.68 2 2
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.16 0.19 -10000 0 -0.66 19 19
ATF2 -0.074 0.28 -10000 0 -0.72 20 20
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.013 0.058 -10000 0 -0.44 1 1
epithelial cell differentiation -0.045 0.12 -10000 0 -0.69 5 5
ITCH 0.018 0.014 -10000 0 -10000 0 0
WWP1 0.014 0.06 -10000 0 -0.68 1 1
FYN 0.012 0 -10000 0 -10000 0 0
EGFR -0.022 0.16 -10000 0 -0.7 20 20
PRL -0.024 0.16 -10000 0 -0.85 15 15
neuron projection morphogenesis -0.003 0.11 -10000 0 -10000 0 0
PTPRZ1 -0.16 0.23 -10000 0 -0.47 143 143
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.055 0.098 -10000 0 -0.52 3 3
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.045 0.13 -10000 0 -0.56 6 6
ADAM17 0.018 0.014 -10000 0 -10000 0 0
ErbB4/ErbB4 0.01 0.067 -10000 0 -0.5 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.031 0.13 -10000 0 -0.52 14 14
NCOR1 0.012 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.035 0.13 -10000 0 -0.52 6 6
GRIN2B -0.086 0.2 -10000 0 -0.53 52 52
ErbB4/ErbB2/betacellulin -0.026 0.16 -10000 0 -0.54 28 28
STAT1 -0.008 0.13 -10000 0 -0.85 10 10
HBEGF 0.011 0.023 -10000 0 -0.47 1 1
PRLR -0.051 0.18 -10000 0 -0.55 47 47
E4ICDs/ETO2 -0.009 0.099 -10000 0 -0.48 4 4
axon guidance 0.038 0.085 -10000 0 -10000 0 0
NEDD4 0.018 0.014 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.055 0.19 -10000 0 -0.49 58 58
CBFA2T3 -0.025 0.14 -10000 0 -0.49 31 31
ErbB4/ErbB2/HBEGF -0.012 0.14 -10000 0 -0.51 28 28
MAPK3 -0.011 0.11 -10000 0 -0.5 2 2
STAT1 (dimer) -0.001 0.1 -10000 0 -0.53 11 11
MAPK1 -0.011 0.11 -10000 0 -0.5 2 2
JAK2 0.006 0.073 -10000 0 -0.85 3 3
ErbB4/ErbB2/neuregulin 1 beta -0.072 0.18 -10000 0 -0.54 34 34
NRG1 -0.061 0.16 -10000 0 -0.66 6 6
NRG3 -0.057 0.19 -10000 0 -0.56 49 49
NRG2 -0.14 0.22 -10000 0 -0.47 134 134
NRG4 -0.15 0.23 -10000 0 -0.47 138 138
heart development 0.038 0.085 -10000 0 -10000 0 0
neural crest cell migration -0.071 0.18 -10000 0 -0.53 34 34
ERBB2 -0.023 0.17 -10000 0 -0.67 27 27
WWOX/E4ICDs 0.013 0.057 -10000 0 -0.44 1 1
SHC1 0.012 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.087 0.17 -10000 0 -0.58 18 18
apoptosis 0.097 0.17 0.62 28 -10000 0 28
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.075 0.14 -10000 0 -0.39 27 27
ErbB4/ErbB2/epiregulin -0.17 0.28 -10000 0 -0.53 146 146
ErbB4/ErbB4/betacellulin/betacellulin -0.003 0.09 -10000 0 -0.68 1 1
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.061 0.15 -10000 0 -0.69 12 12
MDM2 0.001 0.11 -10000 0 -0.54 12 12
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.059 0.11 -10000 0 -0.53 6 6
STAT5A 0.046 0.078 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.055 0.16 -10000 0 -0.55 24 24
DLG4 0.011 0.023 -10000 0 -0.47 1 1
GRB2/SHC 0.019 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.016 0.041 -10000 0 -0.41 1 1
STAT5A (dimer) -0.048 0.12 -10000 0 -0.77 5 5
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.043 0.075 -10000 0 -10000 0 0
LRIG1 0.011 0.023 -10000 0 -0.47 1 1
EREG -0.25 0.4 -10000 0 -0.84 129 129
BTC -0.016 0.11 -10000 0 -0.47 25 25
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.034 0.085 -10000 0 -10000 0 0
ERBB4 0.01 0.068 -10000 0 -0.5 1 1
STAT5B 0.012 0 -10000 0 -10000 0 0
YAP1 -0.001 0.009 -10000 0 -10000 0 0
GRB2 0.012 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.095 0.19 -10000 0 -0.6 30 30
glial cell differentiation 0.016 0.041 0.4 1 -10000 0 1
WWOX 0.012 0 -10000 0 -10000 0 0
cell proliferation -0.074 0.19 -10000 0 -0.6 19 19
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.085 0.22 -9999 0 -0.45 105 105
positive regulation of NF-kappaB transcription factor activity 0 0.001 -9999 0 -10000 0 0
CRKL 0.012 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.054 0.22 -9999 0 -0.8 12 12
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.022 0.063 -9999 0 -0.67 3 3
antigen processing and presentation of peptide antigen via MHC class I -0.063 0.092 -9999 0 -0.37 11 11
CaM/Ca2+ -0.11 0.18 -9999 0 -0.48 17 17
RAP1A 0.012 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.085 0.24 -9999 0 -0.77 17 17
AKT1 -0.056 0.19 -9999 0 -0.72 3 3
MAP2K1 -0.062 0.2 -9999 0 -0.69 4 4
MAP3K11 -0.075 0.21 -9999 0 -0.42 102 102
IFNGR1 0.003 0.02 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.1 0.15 -9999 0 -0.52 26 26
Rap1/GTP -0.083 0.14 -9999 0 -0.59 3 3
CRKL/C3G 0.019 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.095 0.23 -9999 0 -0.48 106 106
CEBPB -0.021 0.18 -9999 0 -0.62 4 4
STAT3 0.012 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.086 0.24 -9999 0 -0.96 8 8
STAT1 -0.085 0.24 -9999 0 -0.76 17 17
CALM1 0.013 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.2 0.37 -9999 0 -0.85 105 105
PIK3CA 0.01 0.042 -9999 0 -0.85 1 1
STAT1 (dimer)/PIAS1 -0.073 0.22 -9999 0 -0.84 12 12
CEBPB/PTGES2/Cbp/p300 -0.051 0.087 -9999 0 -10000 0 0
mol:Ca2+ -0.086 0.21 -9999 0 -0.45 105 105
MAPK3 -0.037 0.17 -9999 0 -0.63 3 3
STAT1 (dimer) -0.084 0.13 -9999 0 -0.54 11 11
MAPK1 -0.037 0.17 -9999 0 -0.63 3 3
JAK2 -0.003 0.079 -9999 0 -0.9 3 3
PIK3R1 0.013 0 -9999 0 -10000 0 0
JAK1 0.003 0.02 -9999 0 -10000 0 0
CAMK2D 0.013 0 -9999 0 -10000 0 0
DAPK1 0.001 0.13 -9999 0 -0.55 5 5
SMAD7 0.003 0.071 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.059 0.19 -9999 0 -0.75 3 3
PI3K -0.1 0.18 -9999 0 -0.72 4 4
IFNG -0.2 0.37 -9999 0 -0.85 105 105
apoptosis -0.007 0.11 -9999 0 -0.42 4 4
CAMK2G 0.013 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.012 0 -9999 0 -10000 0 0
CAMK2A -0.032 0.18 -9999 0 -0.69 26 26
CAMK2B -0.08 0.2 -9999 0 -0.49 76 76
FRAP1 -0.051 0.18 -9999 0 -0.65 3 3
PRKCD -0.056 0.19 -9999 0 -0.74 3 3
RAP1B 0.006 0.073 -9999 0 -0.85 3 3
negative regulation of cell growth -0.063 0.092 -9999 0 -0.37 11 11
PTPN2 0.01 0.042 -9999 0 -0.85 1 1
EP300 0.013 0 -9999 0 -10000 0 0
IRF1 -0.027 0.18 -9999 0 -0.58 15 15
STAT1 (dimer)/PIASy -0.076 0.22 -9999 0 -0.84 12 12
SOCS1 -0.003 0.099 -9999 0 -0.78 6 6
mol:GDP -0.093 0.16 -9999 0 -0.7 3 3
CASP1 -0.001 0.086 -9999 0 -0.35 9 9
PTGES2 0.013 0 -9999 0 -10000 0 0
IRF9 0.023 0.061 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.1 0.18 -9999 0 -0.68 4 4
RAP1/GDP -0.084 0.14 -9999 0 -0.6 3 3
CBL -0.077 0.21 -9999 0 -0.43 103 103
MAP3K1 -0.074 0.21 -9999 0 -0.42 102 102
PIAS1 0.012 0 -9999 0 -10000 0 0
PIAS4 0.012 0.001 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.063 0.092 -9999 0 -0.37 11 11
PTPN11 -0.086 0.21 -9999 0 -0.45 105 105
CREBBP 0.013 0 -9999 0 -10000 0 0
RAPGEF1 0.012 0 -9999 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.012 0 -9999 0 -10000 0 0
GNAT1/GTP -0.012 0.1 -9999 0 -0.67 10 10
Metarhodopsin II/Arrestin -0.01 0.083 -9999 0 -0.67 6 6
PDE6G/GNAT1/GTP -0.032 0.13 -9999 0 -0.58 22 22
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.015 0.13 -9999 0 -0.85 10 10
GRK1 -0.009 0.1 -9999 0 -0.85 6 6
CNG Channel -0.089 0.21 -9999 0 -0.6 49 49
mol:Na + -0.08 0.18 -9999 0 -0.53 40 40
mol:ADP -0.009 0.1 -9999 0 -0.85 6 6
RGS9-1/Gbeta5/R9AP -0.09 0.15 -9999 0 -0.54 19 19
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.083 0.19 -9999 0 -0.58 30 30
CNGB1 -0.03 0.18 -9999 0 -0.83 20 20
RDH5 0.006 0.057 -9999 0 -0.47 6 6
SAG 0.002 0.042 -9999 0 -0.85 1 1
mol:Ca2+ -0.046 0.19 -9999 0 -0.82 8 8
Na + (4 Units) -0.075 0.17 -9999 0 -0.78 8 8
RGS9 -0.095 0.2 -9999 0 -0.47 92 92
GNB1/GNGT1 -0.063 0.22 -9999 0 -0.66 48 48
GNAT1/GDP -0.088 0.15 -9999 0 -0.52 27 27
GUCY2D -0.016 0.14 -9999 0 -0.85 12 12
GNGT1 -0.092 0.28 -9999 0 -0.85 48 48
GUCY2F 0.002 0.005 -9999 0 -10000 0 0
GNB5 0.012 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.038 0.19 -9999 0 -0.62 35 35
mol:11-cis-retinal 0.006 0.057 -9999 0 -0.46 6 6
mol:cGMP -0.034 0.17 -9999 0 -0.53 41 41
GNB1 0.012 0 -9999 0 -10000 0 0
Rhodopsin -0.002 0.089 -9999 0 -0.66 6 6
SLC24A1 0.012 0 -9999 0 -10000 0 0
CNGA1 -0.017 0.12 -9999 0 -0.48 25 25
Metarhodopsin II -0.011 0.1 -9999 0 -0.64 10 10
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.037 0.18 -9999 0 -0.55 41 41
RGS9BP -0.041 0.16 -9999 0 -0.5 43 43
Metarhodopsin II/Transducin -0.033 0.13 -9999 0 -0.34 55 55
GCAP Family/Ca ++ -0.027 0.15 -9999 0 -0.54 31 31
PDE6A/B -0.029 0.17 -9999 0 -0.71 20 20
mol:Pi -0.09 0.15 -9999 0 -0.54 19 19
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.06 0.2 -9999 0 -0.57 54 54
PDE6B -0.017 0.14 -9999 0 -0.66 18 18
PDE6A -0.022 0.16 -9999 0 -0.73 19 19
PDE6G -0.014 0.15 -9999 0 -0.82 13 13
RHO -0.008 0.1 -9999 0 -0.85 6 6
PDE6 -0.12 0.19 -9999 0 -0.78 15 15
GUCA1A -0.047 0.22 -9999 0 -0.85 28 28
GC2/GCAP Family -0.026 0.15 -9999 0 -0.53 31 31
GUCA1C -0.001 0.048 -9999 0 -0.66 2 2
GUCA1B 0.005 0.072 -9999 0 -0.62 5 5
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.007 0.061 -10000 0 -0.86 1 1
HDAC1 0.008 0.024 -10000 0 -0.47 1 1
AES 0.012 0.001 -10000 0 -10000 0 0
FBXW11 0.012 0 -10000 0 -10000 0 0
DTX1 0.004 0.08 -10000 0 -0.7 5 5
LRP6/FZD1 0.019 0 -10000 0 -10000 0 0
TLE1 0.011 0.023 -10000 0 -0.47 1 1
AP1 -0.025 0.12 -10000 0 -0.37 26 26
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 0.037 0.055 -10000 0 -0.46 2 2
NICD/RBPSUH -0.006 0.048 -10000 0 -0.37 7 7
WIF1 -0.11 0.23 -10000 0 -0.52 92 92
NOTCH1 -0.007 0.051 -10000 0 -0.4 7 7
PSENEN 0.013 0 -10000 0 -10000 0 0
KREMEN2 -0.16 0.35 -10000 0 -0.85 85 85
DKK1 -0.36 0.42 -10000 0 -0.81 188 188
beta catenin/beta TrCP1 0.04 0.059 0.26 1 -0.32 1 2
APH1B 0.013 0 -10000 0 -10000 0 0
APH1A 0.013 0 -10000 0 -10000 0 0
AXIN1 -0.004 0.032 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.013 0.048 -10000 0 -10000 0 0
PSEN1 0.013 0 -10000 0 -10000 0 0
FOS -0.014 0.11 -10000 0 -0.47 23 23
JUN 0.012 0 -10000 0 -10000 0 0
MAP3K7 0.011 0.002 -10000 0 -10000 0 0
CTNNB1 0.035 0.063 0.23 14 -0.34 1 15
MAPK3 0.012 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.27 0.32 -10000 0 -0.62 176 176
HNF1A -0.008 0.12 -10000 0 -0.66 12 12
CTBP1 0.012 0.001 -10000 0 -10000 0 0
MYC 0.017 0.095 -10000 0 -1.1 3 3
NKD1 -0.067 0.22 -10000 0 -0.66 49 49
FZD1 0.013 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.01 0.064 -10000 0 -0.48 3 3
apoptosis -0.025 0.12 -10000 0 -0.36 26 26
Delta 1/NOTCHprecursor -0.007 0.061 -10000 0 -0.86 1 1
DLL1 0.01 0.042 -10000 0 -0.85 1 1
PPARD 0.024 0.01 -10000 0 -10000 0 0
Gamma Secretase 0.033 0.014 -10000 0 -10000 0 0
APC -0.004 0.032 -10000 0 -10000 0 0
DVL1 -0.009 0.021 -10000 0 -10000 0 0
CSNK2A1 0.013 0.001 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.36 0.34 -10000 0 -0.65 220 220
LRP6 0.013 0 -10000 0 -10000 0 0
CSNK1A1 0.013 0.001 -10000 0 -10000 0 0
NLK 0.012 0.004 -10000 0 -10000 0 0
CCND1 0.018 0.07 -10000 0 -0.69 4 4
WNT1 -0.015 0.12 -10000 0 -0.52 21 21
Axin1/APC/beta catenin 0.039 0.039 -10000 0 -10000 0 0
DKK2 -0.22 0.38 -10000 0 -0.84 111 111
NOTCH1 precursor/DVL1 -0.008 0.048 -10000 0 -10000 0 0
GSK3B 0.012 0 -10000 0 -10000 0 0
FRAT1 0.012 0.001 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.011 0.064 -10000 0 -0.48 3 3
PPP2R5D 0.031 0.099 0.3 49 -10000 0 49
MAPK1 0.012 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.055 0.15 -10000 0 -0.54 20 20
RBPJ 0.012 0 -10000 0 -10000 0 0
CREBBP 0.016 0.002 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.009 0.052 -9999 0 -0.57 1 1
NFATC2 -0.007 0.044 -9999 0 -10000 0 0
NFATC3 -0.005 0.038 -9999 0 -10000 0 0
CD40LG -0.15 0.29 -9999 0 -0.78 34 34
PTGS2 -0.18 0.34 -9999 0 -0.83 61 61
JUNB 0.012 0 -9999 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.014 0.016 -9999 0 -10000 0 0
CaM/Ca2+ -0.014 0.016 -9999 0 -10000 0 0
CALM1 0.006 0.012 -9999 0 -10000 0 0
JUN 0.006 0.012 -9999 0 -10000 0 0
mol:Ca2+ -0.013 0.015 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 -0.001 0.004 -9999 0 -10000 0 0
FOSL1 -0.059 0.24 -9999 0 -0.83 35 35
CREM 0.012 0.001 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.1 0.12 -9999 0 -0.63 3 3
FOS -0.021 0.11 -9999 0 -0.48 23 23
IFNG -0.24 0.4 -9999 0 -0.82 113 113
AP-1/NFAT1-c-4 -0.18 0.34 -9999 0 -0.82 54 54
FASLG -0.15 0.3 -9999 0 -0.8 34 34
NFAT1-c-4/ICER1 -0.051 0.07 -9999 0 -0.45 1 1
IL2RA -0.17 0.33 -9999 0 -0.9 45 45
FKBP12/FK506 0.009 0 -9999 0 -10000 0 0
CSF2 -0.24 0.39 -9999 0 -0.82 104 104
JunB/Fra1/NFAT1-c-4 -0.087 0.14 -9999 0 -0.58 21 21
IL4 -0.15 0.29 -9999 0 -0.81 31 31
IL2 -0.007 0.05 -9999 0 -0.7 2 2
IL3 -0.027 0.081 -9999 0 -0.72 5 5
FKBP1A 0.012 0 -9999 0 -10000 0 0
BATF3 0.006 0.073 -9999 0 -0.85 3 3
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.011 0.042 -9999 0 -0.85 1 1
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.007 0.087 -9999 0 -0.66 7 7
alphaV beta3 Integrin -0.019 0.082 -9999 0 -0.57 5 5
PTK2 -0.017 0.14 -9999 0 -0.5 2 2
IGF1R 0.005 0.077 -9999 0 -0.76 4 4
PI4KB 0.012 0 -9999 0 -10000 0 0
MFGE8 0.012 0 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
CDKN1B -0.09 0.18 -9999 0 -0.44 82 82
VEGFA -0.002 0.11 -9999 0 -0.85 7 7
ILK -0.09 0.17 -9999 0 -0.43 82 82
ROCK1 0.012 0 -9999 0 -10000 0 0
AKT1 -0.056 0.17 -9999 0 -0.4 82 82
PTK2B 0.023 0.085 -9999 0 -0.49 11 11
alphaV/beta3 Integrin/JAM-A -0.056 0.19 -9999 0 -0.5 52 52
CBL 0.01 0.042 -9999 0 -0.85 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.032 0.12 -9999 0 -0.57 17 17
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.023 0.15 -9999 0 -0.53 28 28
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.012 0.1 -9999 0 -0.42 2 2
alphaV/beta3 Integrin/Syndecan-1 -0.009 0.067 -9999 0 -0.57 5 5
PI4KA 0.012 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.1 0.21 -9999 0 -0.83 14 14
PI4 Kinase 0.019 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.042 -9999 0 -0.85 1 1
alphaV/beta3 Integrin/Osteopontin -0.28 0.29 -9999 0 -0.58 197 197
RPS6KB1 -0.053 0.21 -9999 0 -0.76 14 14
TLN1 0.012 0 -9999 0 -10000 0 0
MAPK3 -0.046 0.16 -9999 0 -0.62 16 16
GPR124 0.012 0 -9999 0 -10000 0 0
MAPK1 -0.046 0.16 -9999 0 -0.62 16 16
PXN 0.012 0 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.068 0.17 -9999 0 -0.57 33 33
cell adhesion -0.025 0.092 -9999 0 -0.43 17 17
ANGPTL3 -0.031 0.17 -9999 0 -0.66 26 26
VEGFR2 homodimer/VEGFA homodimer/Src -0.01 0.074 -9999 0 -0.57 7 7
IGF-1R heterotetramer 0.005 0.077 -9999 0 -0.75 4 4
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
TGFBR2 0.012 0 -9999 0 -10000 0 0
ITGB3 0.003 0.088 -9999 0 -0.78 5 5
IGF1 -0.071 0.23 -9999 0 -0.64 53 53
RAC1 0.012 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.006 0.057 -9999 0 -0.57 4 4
apoptosis 0.012 0 -9999 0 -10000 0 0
CD47 0.012 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.006 0.057 -9999 0 -0.57 4 4
VCL 0.012 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.012 0.071 -9999 0 -0.56 5 5
CSF1 0.01 0.042 -9999 0 -0.85 1 1
PIK3C2A -0.09 0.17 -9999 0 -0.43 82 82
PI4 Kinase/Pyk2 -0.076 0.15 -9999 0 -0.68 3 3
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.017 0.09 -9999 0 -0.52 11 11
FAK1/Vinculin -0.006 0.11 -9999 0 -0.42 1 1
alphaV beta3/Integrin/ppsTEM5 -0.006 0.057 -9999 0 -0.57 4 4
RHOA 0.012 0 -9999 0 -10000 0 0
VTN -0.12 0.28 -9999 0 -0.66 82 82
BCAR1 0.012 0 -9999 0 -10000 0 0
FGF2 -0.01 0.11 -9999 0 -0.49 19 19
F11R 0.005 0.077 -9999 0 -0.66 1 1
alphaV/beta3 Integrin/Lactadherin -0.006 0.057 -9999 0 -0.57 4 4
alphaV/beta3 Integrin/TGFBR2 -0.006 0.057 -9999 0 -0.57 4 4
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.03 0.039 -9999 0 -0.52 2 2
HSP90AA1 0.008 0.06 -9999 0 -0.85 2 2
alphaV/beta3 Integrin/Talin 0.018 0.056 -9999 0 -0.53 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.072 0.26 -9999 0 -0.84 41 41
alphaV/beta3 Integrin/Pyk2 0.023 0.085 -9999 0 -0.49 11 11
SDC1 0.007 0.059 -9999 0 -0.56 4 4
VAV3 -0.001 0.14 -9999 0 -0.49 29 29
PTPN11 0.012 0 -9999 0 -10000 0 0
IRS1 0.011 0.023 -9999 0 -0.47 1 1
FAK1/Paxillin -0.006 0.11 -9999 0 -0.42 1 1
cell migration 0.003 0.11 -9999 0 -10000 0 0
ITGAV 0.012 0 -9999 0 -10000 0 0
PI3K -0.077 0.15 -9999 0 -0.46 46 46
SPP1 -0.4 0.43 -9999 0 -0.85 196 196
KDR 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.012 0 -9999 0 -10000 0 0
COL4A3 -0.089 0.25 -9999 0 -0.64 64 64
angiogenesis -0.054 0.18 -9999 0 -0.61 17 17
Rac1/GTP 0.005 0.13 -9999 0 -0.45 29 29
EDIL3 0.002 0.07 -9999 0 -0.47 9 9
cell proliferation -0.006 0.057 -9999 0 -0.57 4 4
Regulation of Telomerase

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
Telomerase catalytic core complex -0.22 0.33 -10000 0 -0.67 135 135
RAD9A 0.012 0 -10000 0 -10000 0 0
AP1 -0.005 0.079 -10000 0 -10000 0 0
IFNAR2 0.01 0.007 -10000 0 -10000 0 0
AKT1 -0.001 0.052 -10000 0 -0.41 2 2
ER alpha/Oestrogen -0.006 0.07 -10000 0 -0.36 15 15
NFX1/SIN3/HDAC complex 0.03 0.027 -10000 0 -10000 0 0
EGF -0.081 0.26 -10000 0 -0.82 44 44
SMG5 0.012 0 -10000 0 -10000 0 0
SMG6 0.012 0 -10000 0 -10000 0 0
SP3/HDAC2 0.014 0.012 -10000 0 -10000 0 0
TERT/c-Abl -0.22 0.29 -10000 0 -0.63 135 135
SAP18 0.009 0.042 -10000 0 -0.85 1 1
MRN complex -0.001 0.028 -10000 0 -0.57 1 1
WT1 -0.21 0.37 -10000 0 -0.86 103 103
WRN 0.012 0 -10000 0 -10000 0 0
SP1 0.009 0.01 -10000 0 -10000 0 0
SP3 0.009 0.006 -10000 0 -10000 0 0
TERF2IP 0.012 0 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.2 0.26 -10000 0 -0.61 81 81
Mad/Max 0.014 0.01 -10000 0 -10000 0 0
TERT -0.22 0.34 -10000 0 -0.69 135 135
CCND1 -0.19 0.3 -10000 0 -0.67 55 55
MAX 0.009 0.006 -10000 0 -10000 0 0
RBBP7 0.011 0.003 -10000 0 -10000 0 0
RBBP4 0.011 0.002 -10000 0 -10000 0 0
TERF2 -0.002 0.044 -10000 0 -0.88 1 1
PTGES3 0.012 0 -10000 0 -10000 0 0
SIN3A 0.011 0.002 -10000 0 -10000 0 0
Telomerase/911 0.009 0.047 -10000 0 -10000 0 0
CDKN1B -0.12 0.26 -10000 0 -0.56 106 106
RAD1 0.012 0 -10000 0 -10000 0 0
XRCC5 0.012 0 -10000 0 -10000 0 0
XRCC6 0.012 0 -10000 0 -10000 0 0
SAP30 0.011 0.003 -10000 0 -10000 0 0
TRF2/PARP2 -0.002 0.036 -10000 0 -0.74 1 1
UBE3A 0.009 0.006 -10000 0 -10000 0 0
JUN 0.009 0.006 -10000 0 -10000 0 0
E6 -0.003 0.006 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.007 0.007 -10000 0 -10000 0 0
FOS -0.017 0.11 -10000 0 -0.47 23 23
IFN-gamma/IRF1 -0.15 0.29 -10000 0 -0.65 105 105
PARP2 0.012 0 -10000 0 -10000 0 0
BLM -0.029 0.18 -10000 0 -0.85 20 20
Telomerase 0.005 0.1 -10000 0 -0.43 12 12
IRF1 0.012 0.011 -10000 0 -10000 0 0
ESR1 -0.007 0.096 -10000 0 -0.49 15 15
KU/TER 0.019 0 -10000 0 -10000 0 0
ATM/TRF2 0.016 0.046 -10000 0 -0.64 2 2
ubiquitin-dependent protein catabolic process 0.033 0.03 -10000 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.033 0.031 -10000 0 -10000 0 0
HDAC1 0.01 0.023 -10000 0 -0.46 1 1
HDAC2 0.009 0.01 -10000 0 -10000 0 0
ATM -0.001 0.028 0.24 1 -0.51 1 2
SMAD3 0.025 0.007 -10000 0 -10000 0 0
ABL1 0.012 0 -10000 0 -10000 0 0
MXD1 0.009 0.006 -10000 0 -10000 0 0
MRE11A 0.01 0.042 -10000 0 -0.85 1 1
HUS1 0.012 0 -10000 0 -10000 0 0
RPS6KB1 0.012 0 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.2 0.28 -10000 0 -0.63 87 87
NR2F2 0.018 0.011 -10000 0 -10000 0 0
MAPK3 0.009 0.047 -10000 0 -0.66 2 2
MAPK1 0.009 0.047 -10000 0 -0.66 2 2
TGFB1/TGF beta receptor Type II 0.014 0.003 -10000 0 -10000 0 0
NFKB1 0.012 0 -10000 0 -10000 0 0
HNRNPC 0.012 0 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.001 0.028 0.24 1 -0.51 1 2
NBN 0.012 0 -10000 0 -10000 0 0
EGFR -0.024 0.16 -10000 0 -0.7 20 20
mol:Oestrogen -0.002 0.004 -10000 0 -10000 0 0
EGF/EGFR -0.082 0.24 -10000 0 -0.67 53 53
MYC 0.005 0.054 -10000 0 -0.6 3 3
IL2 -0.003 0.061 -10000 0 -0.85 2 2
KU 0.019 0 -10000 0 -10000 0 0
RAD50 0.012 0 -10000 0 -10000 0 0
HSP90AA1 0.008 0.06 -10000 0 -0.85 2 2
TGFB1 0.014 0.003 -10000 0 -10000 0 0
TRF2/BLM -0.031 0.14 -10000 0 -0.65 20 20
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT -0.19 0.31 -10000 0 -0.67 87 87
SP1/HDAC2 0.012 0.019 -10000 0 -10000 0 0
PINX1 0 0.1 -10000 0 -0.85 6 6
Telomerase/EST1A -0.2 0.26 -10000 0 -0.61 84 84
Smad3/Myc 0.025 0.036 -10000 0 -0.57 1 1
911 complex 0 0 -10000 0 -10000 0 0
IFNG -0.21 0.37 -10000 0 -0.85 105 105
Telomerase/PinX1 -0.21 0.27 -10000 0 -0.62 88 88
Telomerase/AKT1/mTOR/p70S6K -0.022 0.085 -10000 0 -0.48 1 1
SIN3B 0.011 0.003 -10000 0 -10000 0 0
YWHAE 0.012 0 -10000 0 -10000 0 0
Telomerase/EST1B -0.2 0.26 -10000 0 -0.61 81 81
response to DNA damage stimulus 0.003 0.006 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 -0.002 0.037 -10000 0 -0.54 2 2
TRF2/WRN -0.002 0.036 -10000 0 -0.74 1 1
Telomerase/hnRNP C1/C2 -0.2 0.26 -10000 0 -0.61 85 85
E2F1 -0.028 0.18 -10000 0 -0.86 18 18
ZNFX1 0.009 0.042 -10000 0 -0.85 1 1
PIF1 -0.008 0.13 -10000 0 -0.85 10 10
NCL 0.012 0 -10000 0 -10000 0 0
DKC1 0.012 0 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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
HDAC1 0.011 0.023 -10000 0 -0.47 1 1
HDAC3 0.012 0 -10000 0 -10000 0 0
VDR 0.012 0 -10000 0 -10000 0 0
Cbp/p300/PCAF -0.003 0.026 -10000 0 -10000 0 0
EP300 0.012 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.005 0.059 -10000 0 -0.38 1 1
KAT2B 0.008 0.047 -10000 0 -0.47 4 4
MAPK14 0.012 0 -10000 0 -10000 0 0
AKT1 -0.024 0.077 0.2 15 -10000 0 15
RAR alpha/9cRA/Cyclin H -0.085 0.096 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.007 0.06 -10000 0 -0.34 2 2
CDC2 0.001 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.075 0.11 -10000 0 -0.45 2 2
NCOR2 0.012 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.009 0 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.13 0.18 -10000 0 -0.51 1 1
NCOA2 0.011 0.023 -10000 0 -0.47 1 1
NCOA3 0.012 0 -10000 0 -10000 0 0
NCOA1 0.012 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.012 0 -10000 0 -10000 0 0
RARG 0.011 0.042 -10000 0 -0.85 1 1
RAR gamma1/9cRA 0.016 0.029 -10000 0 -0.58 1 1
MAPK3 0.013 0 -10000 0 -10000 0 0
MAPK1 0.012 0 -10000 0 -10000 0 0
MAPK8 0.013 0 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.17 0.18 -10000 0 -0.42 79 79
RARA -0.091 0.14 -10000 0 -0.52 2 2
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.008 0.06 -10000 0 -0.34 2 2
PRKCA 0.015 0.001 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.15 0.19 -10000 0 -0.42 78 78
RXRG -0.3 0.28 -10000 0 -0.54 184 184
RXRA -0.077 0.13 -10000 0 -0.44 1 1
RXRB -0.15 0.2 -10000 0 -0.37 181 181
VDR/Vit D3/DNA 0.009 0 -10000 0 -10000 0 0
RBP1 -0.02 0.16 -10000 0 -0.74 18 18
CRBP1/9-cic-RA -0.016 0.12 -10000 0 -0.57 18 18
RARB 0.011 0.041 -10000 0 -0.47 3 3
PRKCG -0.36 0.43 -10000 0 -0.84 184 184
MNAT1 0.012 0 -10000 0 -10000 0 0
RAR alpha/RXRs -0.14 0.19 -10000 0 -0.5 2 2
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.12 0.17 -10000 0 -0.42 1 1
proteasomal ubiquitin-dependent protein catabolic process -0.04 0.099 -10000 0 -0.37 3 3
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.15 0.19 -10000 0 -0.53 1 1
positive regulation of DNA binding -0.081 0.091 -10000 0 -10000 0 0
NRIP1 -0.14 0.18 -10000 0 -10000 0 0
RXRs/RARs -0.16 0.19 -10000 0 -0.43 81 81
RXRs/RXRs/DNA/9cRA -0.18 0.19 -10000 0 -0.44 81 81
PRKACA 0.012 0 -10000 0 -10000 0 0
CDK7 0.012 0 -10000 0 -10000 0 0
TFIIH 0 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.062 0.071 -10000 0 -10000 0 0
CCNH 0.012 0 -10000 0 -10000 0 0
CREBBP 0.012 0 -10000 0 -10000 0 0
RAR gamma2/9cRA -0.001 0.022 -10000 0 -0.45 1 1
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.043 0.11 -10000 0 -0.53 15 15
FYN -0.014 0.17 -10000 0 -0.68 17 17
LAT/GRAP2/SLP76 -0.033 0.14 -10000 0 -0.57 18 18
IKBKB 0.012 0 -10000 0 -10000 0 0
AKT1 0.002 0.13 -10000 0 -0.46 17 17
B2M 0.013 0.003 -10000 0 -10000 0 0
IKBKG -0.039 0.059 -10000 0 -0.17 15 15
MAP3K8 0.008 0.06 -10000 0 -0.85 2 2
mol:Ca2+ -0.018 0.028 -10000 0 -0.13 5 5
integrin-mediated signaling pathway -0.001 0.013 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.012 0.18 -10000 0 -0.67 18 18
TRPV6 -0.16 0.23 -10000 0 -0.48 139 139
CD28 -0.025 0.17 -10000 0 -0.83 18 18
SHC1 -0.013 0.16 -10000 0 -0.65 17 17
receptor internalization -0.006 0.16 -10000 0 -0.65 19 19
PRF1 0.004 0.17 -10000 0 -0.86 12 12
KRAS -0.023 0.17 -10000 0 -0.85 17 17
GRB2 0.012 0 -10000 0 -10000 0 0
COT/AKT1 0.008 0.11 -10000 0 -0.37 17 17
LAT -0.015 0.17 -10000 0 -0.63 19 19
EntrezGene:6955 0 0.003 -10000 0 -10000 0 0
CD3D 0.002 0.079 -10000 0 -0.52 9 9
CD3E 0.006 0.073 -10000 0 -0.63 5 5
CD3G -0.001 0.081 -10000 0 -0.47 12 12
RASGRP2 -0.006 0.052 -10000 0 -0.16 42 42
RASGRP1 0.01 0.13 -10000 0 -0.45 19 19
HLA-A 0.013 0.003 -10000 0 -10000 0 0
RASSF5 0.011 0.023 -10000 0 -0.47 1 1
RAP1A/GTP/RAPL -0.001 0.013 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.021 0.048 -10000 0 -0.13 10 10
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.072 0.1 -10000 0 -0.27 49 49
PRKCA -0.006 0.073 -10000 0 -0.29 9 9
GRAP2 -0.001 0.08 -10000 0 -0.47 12 12
mol:IP3 0.026 0.15 0.21 81 -0.45 14 95
EntrezGene:6957 0 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.003 0.15 -10000 0 -0.62 17 17
ORAI1 0.094 0.13 0.39 2 -10000 0 2
CSK -0.016 0.17 -10000 0 -0.66 17 17
B7 family/CD28 -0.15 0.24 -10000 0 -0.71 40 40
CHUK 0.012 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.025 0.18 -10000 0 -0.68 21 21
PTPN6 -0.018 0.16 -10000 0 -0.68 17 17
VAV1 -0.017 0.18 -10000 0 -0.7 18 18
Monovalent TCR/CD3 0.004 0.11 -10000 0 -0.63 10 10
CBL 0.01 0.042 -10000 0 -0.85 1 1
LCK -0.022 0.18 -10000 0 -0.74 17 17
PAG1 -0.017 0.17 -10000 0 -0.69 17 17
RAP1A 0.012 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.024 0.18 -10000 0 -0.66 21 21
CD80 -0.22 0.38 -10000 0 -0.85 110 110
CD86 -0.005 0.12 -10000 0 -0.86 8 8
PDK1/CARD11/BCL10/MALT1 -0.089 0.13 -10000 0 -0.33 51 51
HRAS 0.012 0 -10000 0 -10000 0 0
GO:0035030 -0.089 0.23 -10000 0 -0.58 40 40
CD8A -0.003 0.095 -10000 0 -0.54 12 12
CD8B -0.028 0.16 -10000 0 -0.57 30 30
PTPRC -0.026 0.18 -10000 0 -0.83 19 19
PDK1/PKC theta 0.002 0.16 -10000 0 -0.56 18 18
CSK/PAG1 -0.012 0.16 -10000 0 -0.68 16 16
SOS1 0.012 0 -10000 0 -10000 0 0
peptide-MHC class I 0.019 0.007 -10000 0 -10000 0 0
GRAP2/SLP76 -0.041 0.16 -10000 0 -0.67 18 18
STIM1 0.047 0.063 -10000 0 -10000 0 0
RAS family/GTP 0.022 0.063 -10000 0 -0.18 3 3
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.008 0.18 -10000 0 -0.7 19 19
mol:DAG -0.009 0.1 -10000 0 -0.4 15 15
RAP1A/GDP 0.011 0.021 -10000 0 -10000 0 0
PLCG1 0.012 0 -10000 0 -10000 0 0
CD247 0.006 0.058 -10000 0 -0.47 6 6
cytotoxic T cell degranulation 0.006 0.16 -10000 0 -0.81 12 12
RAP1A/GTP -0.006 0.017 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.005 0.15 -10000 0 -0.54 18 18
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.016 0.18 0.3 2 -0.58 15 17
NRAS 0.012 0 -10000 0 -10000 0 0
ZAP70 -0.028 0.18 -10000 0 -0.8 21 21
GRB2/SOS1 0.019 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.03 0.14 -10000 0 -0.56 19 19
MALT1 0.012 0 -10000 0 -10000 0 0
TRAF6 0.012 0 -10000 0 -10000 0 0
CD8 heterodimer -0.022 0.15 -10000 0 -0.64 18 18
CARD11 -0.22 0.38 -10000 0 -0.84 113 113
PRKCB -0.015 0.09 -10000 0 -0.36 15 15
PRKCE -0.006 0.073 -10000 0 -0.28 11 11
PRKCQ -0.007 0.17 -10000 0 -0.66 18 18
LCP2 0.012 0 -10000 0 -10000 0 0
BCL10 0.012 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.005 0.11 -10000 0 -0.38 17 17
IKK complex 0.024 0.045 -10000 0 -0.12 2 2
RAS family/GDP -0.006 0.019 -10000 0 -0.094 17 17
MAP3K14 0.015 0.085 -10000 0 -0.29 9 9
PDPK1 0.005 0.12 -10000 0 -0.44 15 15
TCR/CD3/MHC I/CD8/Fyn -0.007 0.19 -10000 0 -0.75 18 18
Aurora B signaling

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
Condensin I complex 0.02 0.068 -9999 0 -0.52 2 2
STMN1 0.011 0.094 -9999 0 -0.65 8 8
Aurora B/RasGAP/Survivin -0.018 0.16 -9999 0 -0.62 26 26
Chromosomal passenger complex/Cul3 protein complex -0.012 0.12 -9999 0 -0.51 14 14
BIRC5 -0.031 0.19 -9999 0 -0.82 22 22
DES -0.32 0.31 -9999 0 -0.6 215 215
Aurora C/Aurora B/INCENP -0.005 0.12 -9999 0 -0.6 15 15
Aurora B/TACC1 0.003 0.083 -9999 0 -0.57 8 8
Aurora B/PP2A 0.003 0.094 -9999 0 -0.65 8 8
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.013 0.026 -9999 0 -0.16 8 8
mitotic metaphase/anaphase transition 0.001 0.005 -9999 0 -10000 0 0
NDC80 -0.023 0.19 -9999 0 -0.71 27 27
Cul3 protein complex -0.037 0.1 -9999 0 -0.56 4 4
KIF2C -0.01 0.091 -9999 0 -0.38 16 16
PEBP1 0.011 0.005 -9999 0 -10000 0 0
KIF20A -0.041 0.21 -9999 0 -0.85 26 26
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP 0.003 0.094 -9999 0 -0.65 8 8
SEPT1 0.005 0.077 -9999 0 -0.76 4 4
SMC2 0.012 0 -9999 0 -10000 0 0
SMC4 0.004 0.084 -9999 0 -0.85 4 4
NSUN2/NPM1/Nucleolin -0.004 0.076 -9999 0 -0.44 9 9
PSMA3 0.012 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0.004 -9999 0 -10000 0 0
H3F3B 0.011 0.057 -9999 0 -0.37 9 9
AURKB 0.002 0.12 -9999 0 -0.81 9 9
AURKC -0.012 0.14 -9999 0 -0.71 14 14
CDCA8 0.01 0.044 -9999 0 -0.87 1 1
cytokinesis -0.086 0.18 -9999 0 -0.52 44 44
Aurora B/Septin1 -0.062 0.18 -9999 0 -0.59 25 25
AURKA -0.06 0.24 -9999 0 -0.86 34 34
INCENP 0.012 0.005 -9999 0 -10000 0 0
KLHL13 -0.05 0.17 -9999 0 -0.49 52 52
BUB1 -0.11 0.3 -9999 0 -0.86 60 60
hSgo1/Aurora B/Survivin -0.041 0.21 -9999 0 -0.63 40 40
EVI5 0.013 0.002 -9999 0 -10000 0 0
RhoA/GTP -0.093 0.21 -9999 0 -0.57 59 59
SGOL1 -0.027 0.18 -9999 0 -0.85 19 19
CENPA -0.021 0.14 -9999 0 -0.44 32 32
NCAPG 0 0.1 -9999 0 -0.85 6 6
Aurora B/HC8 Proteasome 0.003 0.094 -9999 0 -0.65 8 8
NCAPD2 0.01 0.042 -9999 0 -0.85 1 1
Aurora B/PP1-gamma 0.003 0.094 -9999 0 -0.65 8 8
RHOA 0.012 0 -9999 0 -10000 0 0
NCAPH 0.006 0.073 -9999 0 -0.85 3 3
NPM1 -0.011 0.067 -9999 0 -0.45 9 9
RASA1 0.012 0 -9999 0 -10000 0 0
KLHL9 0.01 0.033 -9999 0 -0.47 2 2
mitotic prometaphase -0.001 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.003 0.094 -9999 0 -0.65 8 8
PPP1CC 0.012 0 -9999 0 -10000 0 0
Centraspindlin -0.1 0.23 -9999 0 -0.63 59 59
RhoA/GDP 0.009 0 -9999 0 -10000 0 0
NSUN2 -0.011 0.067 -9999 0 -0.45 9 9
MYLK -0.016 0.11 -9999 0 -0.34 40 40
KIF23 -0.1 0.3 -9999 0 -0.85 56 56
VIM 0.011 0.094 -9999 0 -0.65 8 8
RACGAP1 0.011 0.005 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.011 0.067 -9999 0 -0.45 9 9
Chromosomal passenger complex -0.023 0.14 -9999 0 -0.47 27 27
Chromosomal passenger complex/EVI5 0.017 0.16 -9999 0 -0.57 26 26
TACC1 0.011 0.023 -9999 0 -0.47 1 1
PPP2R5D 0.012 0 -9999 0 -10000 0 0
CUL3 0.012 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Nectin adhesion pathway

Figure S48.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S48.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.042 0.21 -9999 0 -0.85 26 26
alphaV beta3 Integrin 0.011 0.068 -9999 0 -0.59 5 5
PTK2 -0.029 0.092 -9999 0 -0.56 3 3
positive regulation of JNK cascade -0.016 0.057 -9999 0 -0.34 2 2
CDC42/GDP 0.031 0.091 -9999 0 -0.44 3 3
Rac1/GDP 0.033 0.09 -9999 0 -0.44 3 3
RAP1B 0.006 0.073 -9999 0 -0.85 3 3
RAP1A 0.012 0 -9999 0 -10000 0 0
CTNNB1 0.01 0.042 -9999 0 -0.85 1 1
CDC42/GTP -0.019 0.069 -9999 0 -0.42 2 2
nectin-3/I-afadin 0.004 0.07 -9999 0 -10000 0 0
RAPGEF1 0.026 0.097 -9999 0 -0.52 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.019 0.11 -9999 0 -0.45 18 18
PDGFB-D/PDGFRB -0.042 0.21 -9999 0 -0.85 26 26
TLN1 0.024 0.034 -9999 0 -10000 0 0
Rap1/GTP -0.018 0.064 -9999 0 -0.36 2 2
IQGAP1 0.01 0.042 -9999 0 -0.85 1 1
Rap1/GTP/I-afadin 0.02 0.047 -9999 0 -0.53 3 3
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.004 0.07 -9999 0 -10000 0 0
PVR 0.002 0.094 -9999 0 -0.85 5 5
Necl-5(dimer) 0.002 0.094 -9999 0 -0.85 5 5
mol:GDP 0.027 0.11 -9999 0 -0.44 18 18
MLLT4 0.012 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.042 -9999 0 -0.85 1 1
PI3K -0.041 0.13 -9999 0 -0.49 27 27
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.012 0.14 -9999 0 -0.66 19 19
positive regulation of lamellipodium assembly -0.018 0.063 -9999 0 -0.36 3 3
PVRL1 -0.027 0.18 -9999 0 -0.85 19 19
PVRL3 -0.008 0.097 -9999 0 -0.47 18 18
PVRL2 0.012 0 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
CDH1 -0.001 0.08 -9999 0 -0.47 12 12
CLDN1 -0.63 0.38 -9999 0 -0.85 310 310
JAM-A/CLDN1 -0.39 0.24 -9999 0 -0.53 310 310
SRC -0.029 0.1 -9999 0 -0.5 18 18
ITGB3 0.003 0.088 -9999 0 -0.78 5 5
nectin-1(dimer)/I-afadin/I-afadin -0.012 0.14 -9999 0 -0.66 19 19
FARP2 0.023 0.1 -9999 0 -0.56 2 2
RAC1 0.012 0 -9999 0 -10000 0 0
CTNNA1 0.012 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.018 0.082 -9999 0 -0.57 5 5
nectin-1/I-afadin -0.012 0.14 -9999 0 -0.66 19 19
nectin-2/I-afadin 0.019 0 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin -0.001 0.028 -9999 0 -0.58 1 1
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.038 0.13 -9999 0 -0.6 19 19
CDC42/GTP/IQGAP1/filamentous actin -0.001 0.028 -9999 0 -0.58 1 1
F11R 0.012 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.016 0.057 -9999 0 -0.34 2 2
alphaV/beta3 Integrin/Talin 0.031 0.058 -9999 0 -0.45 4 4
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.019 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.019 0 -9999 0 -10000 0 0
PIP5K1C 0.018 0.036 -9999 0 -10000 0 0
VAV2 0.02 0.11 -9999 0 -0.45 18 18
RAP1/GDP -0.021 0.074 -9999 0 -0.4 3 3
ITGAV 0.012 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.011 0.054 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin 0.004 0.07 -9999 0 -10000 0 0
Rac1/GTP -0.021 0.075 -9999 0 -0.45 3 3
PTPRM 0.01 0.04 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin -0.028 0.1 -9999 0 -0.47 20 20
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.012 0 -9999 0 -10000 0 0
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A -0.008 0.09 -9999 0 -10000 0 0
PRKCZ 0.012 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.01 0.042 -9999 0 -0.85 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.029 0.073 -9999 0 -0.35 1 1
IRAK/TOLLIP 0.011 0.068 -9999 0 -10000 0 0
IKBKB 0.012 0 -9999 0 -10000 0 0
IKBKG 0.012 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.15 0.27 -9999 0 -0.67 75 75
IL1A -0.14 0.33 -9999 0 -0.84 73 73
IL1B -0.049 0.2 -9999 0 -0.68 36 36
IRAK/TRAF6/p62/Atypical PKCs -0.018 0.064 -9999 0 -10000 0 0
IL1R2 -0.063 0.18 -9999 0 -0.49 62 62
IL1R1 0.01 0.042 -9999 0 -0.85 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.006 0.082 -9999 0 -10000 0 0
TOLLIP 0.012 0 -9999 0 -10000 0 0
TICAM2 0.007 0.052 -9999 0 -0.47 5 5
MAP3K3 0.012 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.047 0.057 -9999 0 -10000 0 0
JUN 0.026 0.062 -9999 0 -10000 0 0
MAP3K7 0.012 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.025 0.17 -9999 0 -0.48 48 48
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.078 0.23 -9999 0 -0.55 78 78
PIK3R1 0.012 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.098 0.21 -9999 0 -0.52 78 78
IL1 beta fragment/IL1R1/IL1RAP -0.04 0.18 -9999 0 -0.54 47 47
NFKB1 0.012 0 -9999 0 -10000 0 0
MAPK8 0.02 0.065 -9999 0 -0.43 1 1
IRAK1 0.004 0.076 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.022 0.13 -9999 0 -0.66 7 7
IRAK4 0.012 0 -9999 0 -10000 0 0
PRKCI 0.004 0.084 -9999 0 -0.85 4 4
TRAF6 0.012 0 -9999 0 -10000 0 0
PI3K 0.017 0.033 -9999 0 -0.66 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.002 0.092 -9999 0 -0.36 2 2
CHUK 0.012 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.04 0.18 -9999 0 -0.54 47 47
IL1 beta/IL1R2 -0.083 0.21 -9999 0 -0.6 44 44
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.014 0.051 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.055 0.14 -9999 0 -0.72 2 2
IRAK3 -0.001 0.092 -9999 0 -0.6 9 9
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.026 0.17 -9999 0 -0.48 47 47
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.027 0.13 -9999 0 -0.55 4 4
IL1 alpha/IL1R1/IL1RAP -0.11 0.24 -9999 0 -0.6 78 78
RELA 0.012 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.012 0 -9999 0 -10000 0 0
MYD88 0.012 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.019 0.065 -9999 0 -10000 0 0
IL1RAP -0.008 0.13 -9999 0 -0.85 10 10
UBE2N 0.012 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.062 0.14 -9999 0 -0.61 7 7
CASP1 -0.005 0.12 -9999 0 -0.81 9 9
IL1RN/IL1R2 -0.072 0.19 -9999 0 -0.62 28 28
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.031 0.18 -9999 0 -0.5 47 47
TMEM189-UBE2V1 -0.024 0.12 -9999 0 -0.47 31 31
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.014 0.11 -9999 0 -0.47 4 4
PIK3CA 0.01 0.042 -9999 0 -0.85 1 1
IL1RN -0.04 0.16 -9999 0 -0.52 41 41
TRAF6/TAK1/TAB1/TAB2 -0.015 0.054 -9999 0 -10000 0 0
MAP2K6 0.013 0.068 -9999 0 -0.46 1 1
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.006 0.088 -9999 0 -0.66 7 7
PDGFRB -0.043 0.21 -9999 0 -0.85 26 26
SPHK1 -0.028 0.074 -9999 0 -0.36 18 18
mol:S1P -0.029 0.071 -9999 0 -0.34 18 18
S1P1/S1P/Gi -0.066 0.18 -9999 0 -0.48 33 33
GNAO1 -0.095 0.21 -9999 0 -0.48 90 90
PDGFB-D/PDGFRB/PLCgamma1 -0.07 0.19 -9999 0 -0.56 20 20
PLCG1 -0.058 0.17 -9999 0 -0.52 15 15
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.042 0.21 -9999 0 -0.85 26 26
GNAI2 0.012 0.004 -9999 0 -10000 0 0
GNAI3 0.011 0.004 -9999 0 -10000 0 0
GNAI1 0.002 0.066 -9999 0 -0.47 8 8
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.007 0.077 -9999 0 -0.57 7 7
S1P1/S1P -0.031 0.09 -9999 0 -0.43 12 12
negative regulation of cAMP metabolic process -0.064 0.17 -9999 0 -0.47 33 33
MAPK3 -0.068 0.2 -9999 0 -0.61 19 19
calcium-dependent phospholipase C activity -0.002 0.003 -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 0.002 -9999 0 -10000 0 0
PLCB2 -0.003 0.1 -9999 0 -0.4 14 14
RAC1 0.012 0 -9999 0 -10000 0 0
RhoA/GTP -0.026 0.076 -9999 0 -0.38 9 9
receptor internalization -0.03 0.084 -9999 0 -0.4 12 12
PTGS2 -0.085 0.25 -9999 0 -0.69 47 47
Rac1/GTP -0.026 0.076 -9999 0 -0.38 10 10
RHOA 0.012 0 -9999 0 -10000 0 0
VEGFA -0.002 0.11 -9999 0 -0.85 7 7
negative regulation of T cell proliferation -0.064 0.17 -9999 0 -0.47 33 33
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.021 0.12 -9999 0 -0.47 28 28
MAPK1 -0.068 0.2 -9999 0 -0.57 25 25
S1P1/S1P/PDGFB-D/PDGFRB -0.023 0.15 -9999 0 -0.45 35 35
ABCC1 0.012 0.002 -9999 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.15 0.27 -9999 0 -0.79 46 46
MKNK1 0.012 0 -9999 0 -10000 0 0
MAPK14 -0.096 0.14 -9999 0 -0.41 13 13
ATF2/c-Jun -0.051 0.1 -9999 0 -10000 0 0
MAPK11 -0.096 0.14 -9999 0 -0.41 13 13
MITF -0.1 0.17 -9999 0 -0.54 19 19
MAPKAPK5 -0.098 0.16 -9999 0 -0.5 13 13
KRT8 -0.099 0.16 -9999 0 -0.51 14 14
MAPKAPK3 0.012 0 -9999 0 -10000 0 0
MAPKAPK2 0.012 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.14 0.2 -9999 0 -0.66 13 13
CEBPB -0.098 0.16 -9999 0 -0.5 13 13
SLC9A1 -0.098 0.16 -9999 0 -0.5 13 13
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.093 0.16 -9999 0 -0.49 13 13
p38alpha-beta/MNK1 -0.098 0.16 -9999 0 -0.55 13 13
JUN -0.05 0.1 -9999 0 -10000 0 0
PPARGC1A -0.13 0.19 -9999 0 -0.54 32 32
USF1 -0.098 0.16 -9999 0 -0.5 13 13
RAB5/GDP/GDI1 -0.084 0.096 -9999 0 -0.37 13 13
NOS2 -0.28 0.37 -9999 0 -0.72 164 164
DDIT3 -0.1 0.16 -9999 0 -0.49 16 16
RAB5A 0.012 0 -9999 0 -10000 0 0
HSPB1 -0.075 0.14 -9999 0 -0.43 19 19
p38alpha-beta/HBP1 -0.098 0.16 -9999 0 -0.55 13 13
CREB1 -0.094 0.16 -9999 0 -0.49 13 13
RAB5/GDP 0.009 0 -9999 0 -10000 0 0
EIF4E -0.079 0.14 -9999 0 -0.48 13 13
RPS6KA4 -0.098 0.16 -9999 0 -0.5 13 13
PLA2G4A -0.097 0.17 -9999 0 -0.57 24 24
GDI1 -0.098 0.16 -9999 0 -0.5 13 13
TP53 -0.12 0.19 -9999 0 -0.62 13 13
RPS6KA5 -0.098 0.16 -9999 0 -0.5 13 13
ESR1 -0.11 0.17 -9999 0 -0.54 18 18
HBP1 0.012 0 -9999 0 -10000 0 0
MEF2C -0.098 0.16 -9999 0 -0.5 13 13
MEF2A -0.098 0.16 -9999 0 -0.5 13 13
EIF4EBP1 -0.094 0.16 -9999 0 -0.49 13 13
KRT19 -0.11 0.17 -9999 0 -0.52 20 20
ELK4 -0.098 0.16 -9999 0 -0.5 13 13
ATF6 -0.098 0.16 -9999 0 -0.5 13 13
ATF1 -0.094 0.16 -9999 0 -0.49 13 13
p38alpha-beta/MAPKAPK2 -0.098 0.16 -9999 0 -0.55 13 13
p38alpha-beta/MAPKAPK3 -0.098 0.16 -9999 0 -0.55 13 13
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 -0.061 0.16 -10000 0 -0.39 65 65
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.006 0.12 0.66 3 -0.39 2 5
IL27/IL27R/JAK1 -0.001 0.16 -10000 0 -0.76 3 3
TBX21 0.025 0.18 -10000 0 -0.68 6 6
IL12B -0.002 0.095 -10000 0 -0.86 5 5
IL12A -0.012 0.087 -10000 0 -0.36 22 22
IL6ST 0.008 0.049 -10000 0 -0.48 4 4
IL27RA/JAK1 0.018 0.057 -10000 0 -0.63 2 2
IL27 -0.019 0.16 -10000 0 -0.86 14 14
TYK2 0.012 0.008 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.27 0.53 -10000 0 -1.3 85 85
T-helper 2 cell differentiation 0.006 0.12 0.66 3 -0.39 2 5
T cell proliferation during immune response 0.006 0.12 0.66 3 -0.39 2 5
MAPKKK cascade -0.006 0.12 0.39 2 -0.66 3 5
STAT3 0.012 0 -10000 0 -10000 0 0
STAT2 0.012 0 -10000 0 -10000 0 0
STAT1 -0.007 0.13 -10000 0 -0.85 10 10
IL12RB1 0.005 0.047 -10000 0 -0.47 4 4
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.01 0.21 -10000 0 -0.72 14 14
IL27/IL27R/JAK2/TYK2 -0.006 0.12 0.39 2 -0.67 3 5
positive regulation of T cell mediated cytotoxicity -0.006 0.12 0.39 2 -0.66 3 5
STAT1 (dimer) 0.004 0.24 -10000 0 -1 5 5
JAK2 0.005 0.076 -10000 0 -0.88 3 3
JAK1 0.014 0.003 -10000 0 -10000 0 0
STAT2 (dimer) -0.001 0.12 0.35 1 -0.63 3 4
T cell proliferation -0.072 0.18 0.36 2 -0.62 21 23
IL12/IL12R/TYK2/JAK2 -0.033 0.13 -10000 0 -0.48 7 7
IL17A -0.28 0.53 -10000 0 -1.3 85 85
mast cell activation 0.006 0.12 0.66 3 -0.39 2 5
IFNG -0.015 0.053 0.11 2 -0.1 105 107
T cell differentiation -0.004 0.008 0.025 2 -0.023 18 20
STAT3 (dimer) -0.001 0.12 0.34 2 -0.63 3 5
STAT5A (dimer) -0.001 0.12 0.35 1 -0.63 3 4
STAT4 (dimer) -0.006 0.13 0.35 1 -0.57 6 7
STAT4 0.004 0.084 -10000 0 -0.85 4 4
T cell activation -0.007 0.008 0.096 2 -10000 0 2
IL27R/JAK2/TYK2 -0.004 0.088 -10000 0 -0.63 4 4
GATA3 -0.001 0.11 -10000 0 -0.62 11 11
IL18 0.004 0.06 -10000 0 -0.58 4 4
positive regulation of mast cell cytokine production -0.001 0.12 0.34 2 -0.61 3 5
IL27/EBI3 -0.021 0.15 -10000 0 -0.64 20 20
IL27RA -0.002 0.057 -10000 0 -0.69 2 2
IL6 -0.14 0.28 -10000 0 -0.53 121 121
STAT5A 0.012 0 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.003 -10000 0 -10000 0 0
IL2 0.001 0.05 -10000 0 -0.6 2 2
IL1B -0.047 0.18 -10000 0 -0.57 41 41
EBI3 -0.003 0.1 -10000 0 -0.62 10 10
TNF -0.017 0.13 -10000 0 -0.58 19 19
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.012 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.04 0.12 -10000 0 -0.42 22 22
NT3 (dimer)/TRKC -0.093 0.19 -10000 0 -0.38 117 117
NT3 (dimer)/TRKB -0.17 0.23 -10000 0 -0.57 81 81
SHC/Grb2/SOS1/GAB1/PI3K 0.035 0.015 -10000 0 -10000 0 0
RAPGEF1 0.012 0 -10000 0 -10000 0 0
BDNF -0.009 0.13 -10000 0 -0.82 11 11
PIK3CA 0.01 0.042 -10000 0 -0.85 1 1
DYNLT1 0.012 0 -10000 0 -10000 0 0
NTRK1 -0.009 0.097 -10000 0 -0.47 18 18
NTRK2 -0.078 0.2 -10000 0 -0.5 73 73
NTRK3 -0.1 0.2 -10000 0 -0.47 97 97
NT-4/5 (dimer)/TRKB -0.18 0.23 -10000 0 -0.57 92 92
neuron apoptosis 0.1 0.19 0.47 63 -10000 0 63
SHC 2-3/Grb2 -0.12 0.21 -10000 0 -0.52 63 63
SHC1 0.012 0 -10000 0 -10000 0 0
SHC2 -0.12 0.19 -10000 0 -0.48 68 68
SHC3 -0.14 0.2 -10000 0 -0.47 93 93
STAT3 (dimer) 0.017 0.034 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.13 0.18 -10000 0 -0.55 43 43
RIN/GDP -0.017 0.09 -10000 0 -0.31 2 2
GIPC1 0.012 0 -10000 0 -10000 0 0
KRAS -0.023 0.17 -10000 0 -0.85 17 17
DNAJA3 -0.11 0.16 -10000 0 -0.45 38 38
RIN/GTP -0.003 0.057 -10000 0 -0.67 3 3
CCND1 0.022 0.076 -10000 0 -0.75 4 4
MAGED1 0.009 0.041 -10000 0 -0.47 3 3
PTPN11 0.012 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.046 0.21 -10000 0 -0.85 26 26
SHC/GRB2/SOS1 0 0 -10000 0 -10000 0 0
GRB2 0.012 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.039 0.11 -10000 0 -0.54 7 7
TRKA/NEDD4-2 0.002 0.071 -10000 0 -0.32 19 19
ELMO1 0.01 0.042 -10000 0 -0.85 1 1
RhoG/GTP/ELMO1/DOCK1 -0.001 0.028 -10000 0 -0.58 1 1
NGF -0.019 0.12 -10000 0 -0.5 25 25
HRAS 0.012 0 -10000 0 -10000 0 0
DOCK1 0.012 0 -10000 0 -10000 0 0
GAB2 0.01 0.042 -10000 0 -0.85 1 1
RIT2 -0.004 0.072 -10000 0 -0.85 3 3
RIT1 0.012 0 -10000 0 -10000 0 0
FRS2 0 0.1 -10000 0 -0.85 6 6
DNM1 -0.021 0.17 -10000 0 -0.85 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.012 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.1 0.16 -10000 0 -0.5 27 27
mol:GDP -0.025 0.12 -10000 0 -0.37 2 2
NGF (dimer) -0.019 0.12 -10000 0 -0.5 25 25
RhoG/GDP 0.008 0.033 -10000 0 -0.67 1 1
RIT1/GDP -0.01 0.087 -10000 0 -10000 0 0
TIAM1 -0.003 0.1 -10000 0 -0.62 10 10
PIK3R1 0.012 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.066 0.15 -10000 0 -0.6 17 17
KIDINS220/CRKL/C3G 0.019 0 -10000 0 -10000 0 0
SHC/RasGAP 0.019 0 -10000 0 -10000 0 0
FRS2 family/SHP2 -0.008 0.068 -10000 0 -0.57 6 6
SHC/GRB2/SOS1/GAB1 0.032 0 -10000 0 -10000 0 0
RIT1/GTP 0.009 0 -10000 0 -10000 0 0
NT3 (dimer) -0.033 0.14 -10000 0 -0.48 39 39
RAP1/GDP -0.036 0.058 -10000 0 -0.31 2 2
KIDINS220/CRKL 0.012 0 -10000 0 -10000 0 0
BDNF (dimer) -0.009 0.13 -10000 0 -0.82 11 11
ubiquitin-dependent protein catabolic process -0.029 0.092 -10000 0 -0.55 4 4
Schwann cell development -0.031 0.034 -10000 0 -10000 0 0
EHD4 0.012 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.024 0.066 -10000 0 -0.52 6 6
FRS2 family/SHP2/CRK family/C3G/GAB2 0.034 0.032 -10000 0 -10000 0 0
RAP1B 0.006 0.073 -10000 0 -0.85 3 3
RAP1A 0.012 0 -10000 0 -10000 0 0
CDC42/GTP -0.11 0.18 -10000 0 -0.67 16 16
ABL1 0.012 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.019 0 -10000 0 -10000 0 0
Rap1/GTP -0.025 0.058 -10000 0 -0.44 2 2
STAT3 0.017 0.034 -10000 0 -10000 0 0
axon guidance -0.11 0.17 -10000 0 -0.63 16 16
MAPK3 -0.007 0.1 -10000 0 -0.49 7 7
MAPK1 -0.007 0.1 -10000 0 -0.49 7 7
CDC42/GDP -0.01 0.087 -10000 0 -10000 0 0
NTF3 -0.034 0.14 -10000 0 -0.48 39 39
NTF4 -0.046 0.21 -10000 0 -0.85 26 26
NGF (dimer)/TRKA/FAIM -0.029 0.094 -10000 0 -0.54 5 5
PI3K 0.017 0.033 -10000 0 -0.66 1 1
FRS3 0.012 0 -10000 0 -10000 0 0
FAIM 0.011 0.023 -10000 0 -0.47 1 1
GAB1 0.012 0 -10000 0 -10000 0 0
RASGRF1 -0.13 0.19 -10000 0 -0.49 61 61
SOS1 0.012 0 -10000 0 -10000 0 0
MCF2L -0.072 0.16 -10000 0 -0.53 23 23
RGS19 0.01 0.042 -10000 0 -0.85 1 1
CDC42 0.012 0 -10000 0 -10000 0 0
RAS family/GTP -0.012 0.097 -10000 0 -0.4 3 3
Rac1/GDP -0.01 0.087 -10000 0 -10000 0 0
NGF (dimer)/TRKA/GRIT -0.03 0.093 -10000 0 -0.56 4 4
neuron projection morphogenesis -0.079 0.17 -10000 0 -0.52 10 10
NGF (dimer)/TRKA/NEDD4-2 -0.03 0.092 -10000 0 -0.55 4 4
MAP2K1 0.037 0 -10000 0 -10000 0 0
NGFR -0.15 0.25 -10000 0 -0.5 132 132
NGF (dimer)/TRKA/GIPC/GAIP -0.003 0.1 -10000 0 -0.52 4 4
RAS family/GTP/PI3K 0.016 0.063 -10000 0 -0.28 18 18
FRS2 family/SHP2/GRB2/SOS1 -0.007 0.059 -10000 0 -0.49 6 6
NRAS 0.012 0 -10000 0 -10000 0 0
GRB2/SOS1 0.019 0 -10000 0 -10000 0 0
PRKCI 0.004 0.084 -10000 0 -0.85 4 4
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.012 0 -10000 0 -10000 0 0
PRKCZ 0.012 0 -10000 0 -10000 0 0
MAPKKK cascade -0.079 0.19 -10000 0 -0.63 39 39
RASA1 0.012 0 -10000 0 -10000 0 0
TRKA/c-Abl 0.003 0.07 -10000 0 -0.32 18 18
SQSTM1 0.012 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.033 0.14 -10000 0 -0.55 17 17
NGF (dimer)/TRKA/p62/Atypical PKCs -0.028 0.09 -10000 0 -0.51 8 8
MATK -0.005 0.093 -10000 0 -0.49 14 14
NEDD4L 0.011 0.023 -10000 0 -0.47 1 1
RAS family/GDP -0.036 0.058 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.12 0.17 -10000 0 -0.34 131 131
Rac1/GTP -0.098 0.12 -10000 0 -0.35 38 38
FRS2 family/SHP2/CRK family -0.007 0.059 -10000 0 -0.49 6 6
PDGFR-beta 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
S1P1/Sphingosine-1-phosphate -0.036 0.12 -9999 0 -0.43 22 22
PDGFB-D/PDGFRB/SLAP -0.027 0.17 -9999 0 -0.65 28 28
PDGFB-D/PDGFRB/APS/CBL -0.036 0.15 -9999 0 -0.58 29 29
AKT1 0.027 0.11 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0.001 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.009 0.14 -9999 0 -0.44 23 23
PIK3CA 0.01 0.042 -9999 0 -0.85 1 1
FGR -0.027 0.11 -9999 0 -0.43 27 27
mol:Ca2+ 0 0.099 -9999 0 -0.36 27 27
MYC 0.018 0.1 -9999 0 -0.7 3 3
SHC1 0.012 0 -9999 0 -10000 0 0
HRAS/GDP 0.003 0.12 -9999 0 -0.46 27 27
LRP1/PDGFRB/PDGFB -0.034 0.15 -9999 0 -0.6 27 27
GRB10 0.01 0.042 -9999 0 -0.85 1 1
PTPN11 0.012 0 -9999 0 -10000 0 0
GO:0007205 0 0.1 -9999 0 -0.36 27 27
PTEN 0.012 0 -9999 0 -10000 0 0
GRB2 0.012 0 -9999 0 -10000 0 0
GRB7 -0.079 0.26 -9999 0 -0.84 45 45
PDGFB-D/PDGFRB/SHP2 -0.023 0.16 -9999 0 -0.65 26 26
PDGFB-D/PDGFRB/GRB10 -0.025 0.16 -9999 0 -0.65 27 27
cell cycle arrest -0.027 0.17 -9999 0 -0.65 28 28
HRAS 0.012 0 -9999 0 -10000 0 0
HIF1A 0.034 0.096 -9999 0 -10000 0 0
GAB1 -0.003 0.11 -9999 0 -0.44 7 7
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.001 0.11 -9999 0 -0.44 6 6
PDGFB-D/PDGFRB -0.031 0.14 -9999 0 -0.57 27 27
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.023 0.16 -9999 0 -0.65 26 26
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.037 0.12 -9999 0 -0.55 6 6
positive regulation of MAPKKK cascade -0.023 0.16 -9999 0 -0.65 26 26
PIK3R1 0.012 0 -9999 0 -10000 0 0
mol:IP3 0 0.1 -9999 0 -0.37 27 27
E5 0 0.002 -9999 0 -10000 0 0
CSK 0.012 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.096 0.25 -9999 0 -0.66 69 69
SHB 0.012 0 -9999 0 -10000 0 0
BLK -0.12 0.2 -9999 0 -0.48 89 89
PTPN2 0.01 0.042 -9999 0 -0.85 1 1
PDGFB-D/PDGFRB/SNX15 -0.023 0.16 -9999 0 -0.65 26 26
BCAR1 0.012 0 -9999 0 -10000 0 0
VAV2 0.001 0.11 -9999 0 -0.44 6 6
CBL 0.01 0.042 -9999 0 -0.85 1 1
PDGFB-D/PDGFRB/DEP1 -0.027 0.17 -9999 0 -0.65 28 28
LCK -0.035 0.12 -9999 0 -0.44 29 29
PDGFRB -0.041 0.21 -9999 0 -0.85 26 26
ACP1 0.012 0 -9999 0 -10000 0 0
HCK -0.023 0.11 -9999 0 -0.43 27 27
ABL1 -0.007 0.11 -9999 0 -0.4 27 27
PDGFB-D/PDGFRB/CBL -0.004 0.1 -9999 0 -0.43 7 7
PTPN1 0.012 0.002 -9999 0 -10000 0 0
SNX15 0.012 0 -9999 0 -10000 0 0
STAT3 0.012 0 -9999 0 -10000 0 0
STAT1 -0.008 0.13 -9999 0 -0.85 10 10
cell proliferation 0.019 0.095 -9999 0 -0.62 3 3
SLA 0.008 0.06 -9999 0 -0.85 2 2
actin cytoskeleton reorganization 0.016 0.12 -9999 0 -10000 0 0
SRC -0.026 0.11 -9999 0 -0.43 27 27
PI3K -0.028 0.1 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC -0.092 0.22 -9999 0 -0.57 69 69
SH2B2 0.006 0.073 -9999 0 -0.85 3 3
PLCgamma1/SPHK1 -0.01 0.14 -9999 0 -0.46 23 23
LYN -0.026 0.11 -9999 0 -0.43 27 27
LRP1 0.012 0 -9999 0 -10000 0 0
SOS1 0.012 0 -9999 0 -10000 0 0
STAT5B 0.012 0 -9999 0 -10000 0 0
STAT5A 0.012 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas -0.021 0.12 -9999 0 -10000 0 0
SPHK1 -0.025 0.18 -9999 0 -0.85 18 18
EDG1 0 0.003 -9999 0 -10000 0 0
mol:DAG 0 0.1 -9999 0 -0.37 27 27
PLCG1 -0.001 0.1 -9999 0 -0.37 27 27
NHERF/PDGFRB -0.03 0.14 -9999 0 -0.56 26 26
YES1 -0.026 0.11 -9999 0 -0.43 27 27
cell migration -0.03 0.14 -9999 0 -0.56 26 26
SHC/Grb2/SOS1 -0.021 0.12 -9999 0 -0.45 27 27
SLC9A3R2 0.012 0 -9999 0 -10000 0 0
SLC9A3R1 0.012 0 -9999 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN -0.003 0.13 -9999 0 -0.51 26 26
FYN -0.026 0.11 -9999 0 -0.43 27 27
DOK1 -0.005 0.14 -9999 0 -0.51 28 28
HRAS/GTP 0.009 0 -9999 0 -10000 0 0
PDGFB 0.006 0.073 -9999 0 -0.85 3 3
RAC1 0.013 0.11 -9999 0 -0.43 3 3
PRKCD -0.004 0.13 -9999 0 -0.51 27 27
FER -0.004 0.14 -9999 0 -0.51 27 27
MAPKKK cascade -0.029 0.11 -9999 0 -0.45 27 27
RASA1 -0.004 0.13 -9999 0 -0.51 27 27
NCK1 0.012 0 -9999 0 -10000 0 0
NCK2 0.012 0 -9999 0 -10000 0 0
p62DOK/Csk 0.002 0.13 -9999 0 -0.47 28 28
PDGFB-D/PDGFRB/SHB -0.023 0.16 -9999 0 -0.65 26 26
chemotaxis -0.007 0.11 -9999 0 -0.38 27 27
STAT1-3-5/STAT1-3-5 -0.039 0.13 -9999 0 -0.91 1 1
Bovine Papilomavirus E5/PDGFRB -0.032 0.16 -9999 0 -0.66 26 26
PTPRJ 0.008 0.06 -9999 0 -0.85 2 2
ErbB2/ErbB3 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
USP8 0.016 0.005 -9999 0 -10000 0 0
RAS family/GTP -0.061 0.14 -9999 0 -0.56 18 18
NFATC4 -0.031 0.12 -9999 0 -0.41 5 5
ERBB2IP 0.014 0.003 -9999 0 -10000 0 0
HSP90 (dimer) 0.008 0.06 -9999 0 -0.85 2 2
mammary gland morphogenesis -0.064 0.14 -9999 0 -0.57 5 5
JUN -0.021 0.085 -9999 0 -0.4 9 9
HRAS 0.012 0.001 -9999 0 -10000 0 0
DOCK7 -0.056 0.14 -9999 0 -0.54 5 5
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.084 0.17 -9999 0 -0.53 37 37
AKT1 0.009 0.003 -9999 0 -10000 0 0
BAD 0.017 0.003 -9999 0 -10000 0 0
MAPK10 -0.044 0.088 -9999 0 -0.32 7 7
mol:GTP -0.002 0.002 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.068 0.15 -9999 0 -0.63 5 5
RAF1 -0.062 0.14 -9999 0 -0.53 18 18
ErbB2/ErbB3/neuregulin 2 -0.12 0.18 -9999 0 -0.62 30 30
STAT3 0.002 0.003 -9999 0 -10000 0 0
cell migration -0.02 0.089 -9999 0 -0.32 1 1
mol:PI-3-4-5-P3 -0.001 0.002 -9999 0 -10000 0 0
cell proliferation -0.18 0.24 -9999 0 -0.55 55 55
FOS -0.11 0.18 -9999 0 -0.48 26 26
NRAS 0.012 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.064 0.14 -9999 0 -0.57 5 5
MAPK3 -0.15 0.21 -9999 0 -0.5 40 40
MAPK1 -0.15 0.21 -9999 0 -0.5 40 40
JAK2 -0.06 0.14 -9999 0 -0.54 5 5
NF2 -0.003 0.006 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.049 0.12 -9999 0 -0.38 10 10
NRG1 -0.1 0.22 -9999 0 -0.49 96 96
GRB2/SOS1 0.012 0.009 -9999 0 -10000 0 0
MAPK8 -0.051 0.12 -9999 0 -0.41 5 5
MAPK9 -0.026 0.07 -9999 0 -10000 0 0
ERBB2 -0.047 0.17 -9999 0 -0.63 31 31
ERBB3 0.006 0.054 -9999 0 -0.6 3 3
SHC1 0.012 0.001 -9999 0 -10000 0 0
RAC1 0.012 0 -9999 0 -10000 0 0
apoptosis 0.005 0.013 -9999 0 -10000 0 0
STAT3 (dimer) 0.016 0.007 -9999 0 -10000 0 0
RNF41 0.02 0.008 -9999 0 -10000 0 0
FRAP1 0.008 0.003 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.052 0.088 -9999 0 -0.36 5 5
ErbB2/ErbB2/HSP90 (dimer) -0.043 0.15 -9999 0 -0.58 29 29
CHRNA1 -0.2 0.26 -9999 0 -0.47 189 189
myelination -0.029 0.12 -9999 0 -0.4 5 5
PPP3CB -0.053 0.13 -9999 0 -0.49 5 5
KRAS -0.024 0.17 -9999 0 -0.85 17 17
RAC1-CDC42/GDP -0.028 0.1 -9999 0 -0.6 1 1
NRG2 -0.14 0.22 -9999 0 -0.47 134 134
mol:GDP -0.048 0.12 -9999 0 -0.37 10 10
SOS1 0.012 0.001 -9999 0 -10000 0 0
MAP2K2 -0.069 0.14 -9999 0 -0.55 13 13
SRC 0.012 0 -9999 0 -10000 0 0
mol:cAMP -0.001 0.002 -9999 0 -10000 0 0
PTPN11 -0.057 0.14 -9999 0 -0.54 5 5
MAP2K1 -0.14 0.19 -9999 0 -0.51 33 33
heart morphogenesis -0.064 0.14 -9999 0 -0.57 5 5
RAS family/GDP -0.054 0.14 -9999 0 -0.56 18 18
GRB2 0.012 0.001 -9999 0 -10000 0 0
PRKACA -0.005 0.009 -9999 0 -10000 0 0
CHRNE 0.002 0.038 -9999 0 -0.23 9 9
HSP90AA1 0.008 0.06 -9999 0 -0.85 2 2
activation of caspase activity -0.009 0.003 -9999 0 -10000 0 0
nervous system development -0.064 0.14 -9999 0 -0.57 5 5
CDC42 0.012 0 -9999 0 -10000 0 0
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.061 0.11 0.41 22 -10000 0 22
GNAI2 0.012 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.017 0.097 -10000 0 -0.58 12 12
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.094 0.2 -10000 0 -0.48 90 90
RhoA/GTP -0.036 0.13 -10000 0 -0.42 22 22
negative regulation of cAMP metabolic process -0.046 0.14 -10000 0 -0.46 22 22
GNAZ -0.02 0.12 -10000 0 -0.47 28 28
GNAI3 0.012 0 -10000 0 -10000 0 0
GNA12 0.012 0 -10000 0 -10000 0 0
S1PR5 -0.013 0.14 -10000 0 -0.85 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.046 0.14 -10000 0 -0.46 22 22
RhoA/GDP 0.009 0 -10000 0 -10000 0 0
RHOA 0.012 0 -10000 0 -10000 0 0
GNAI1 0.003 0.066 -10000 0 -0.47 8 8
Nongenotropic Androgen signaling

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
PTK2 0.011 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.012 0.095 -10000 0 -0.53 2 2
regulation of S phase of mitotic cell cycle -0.003 0.083 -10000 0 -0.28 3 3
GNAO1 -0.094 0.2 -10000 0 -0.48 90 90
HRAS 0.012 0.001 -10000 0 -10000 0 0
SHBG/T-DHT -0.024 0.12 -10000 0 -0.59 17 17
PELP1 0.01 0.042 -10000 0 -0.85 1 1
AKT1 0.011 0 -10000 0 -10000 0 0
MAP2K1 0.01 0.084 -10000 0 -0.41 2 2
T-DHT/AR -0.036 0.12 -10000 0 -0.34 54 54
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -0.007 23 23
GNAI2 0.012 0 -10000 0 -10000 0 0
GNAI3 0.012 0 -10000 0 -10000 0 0
GNAI1 0.003 0.066 -10000 0 -0.47 8 8
mol:GDP -0.049 0.12 -10000 0 -0.37 54 54
cell proliferation 0.008 0.12 -10000 0 -0.54 4 4
PIK3CA 0.01 0.042 -10000 0 -0.85 1 1
FOS -0.007 0.19 -10000 0 -0.77 23 23
mol:Ca2+ -0.019 0.032 -10000 0 -0.096 46 46
MAPK3 0.009 0.1 -10000 0 -0.44 4 4
MAPK1 0.01 0.062 -10000 0 -0.26 4 4
PIK3R1 0.012 0 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.005 23 23
cAMP biosynthetic process -0.007 0.12 -10000 0 -0.56 17 17
GNG2 0.01 0.042 -10000 0 -0.85 1 1
potassium channel inhibitor activity 0 0.001 -10000 0 -0.005 23 23
HRAS/GTP -0.03 0.076 -10000 0 -0.47 2 2
actin cytoskeleton reorganization -0.001 0.023 -10000 0 -0.47 1 1
SRC 0.012 0.001 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.005 23 23
PI3K 0 0.029 -10000 0 -0.58 1 1
apoptosis -0.009 0.11 0.4 23 -10000 0 23
T-DHT/AR/PELP1 -0.037 0.099 -10000 0 -0.38 6 6
HRAS/GDP -0.045 0.12 -10000 0 -0.34 54 54
CREB1 0.007 0.12 -10000 0 -0.42 23 23
RAC1-CDC42/GTP -0.001 0.023 -10000 0 -0.48 1 1
AR -0.051 0.16 -10000 0 -0.47 54 54
GNB1 0.012 0 -10000 0 -10000 0 0
RAF1 0.003 0.085 -10000 0 -0.44 2 2
RAC1-CDC42/GDP -0.042 0.11 -10000 0 -0.4 1 1
T-DHT/AR/PELP1/Src -0.012 0.095 -10000 0 -0.53 2 2
MAP2K2 0.01 0.084 -10000 0 -0.41 2 2
T-DHT/AR/PELP1/Src/PI3K -0.003 0.083 -10000 0 -0.28 3 3
GNAZ -0.02 0.12 -10000 0 -0.47 28 28
SHBG -0.026 0.17 -10000 0 -0.85 17 17
Gi family/GNB1/GNG2/GDP -0.056 0.18 -10000 0 -0.48 39 39
mol:T-DHT 0 0.001 -10000 0 -0.003 19 19
RAC1 0.012 0 -10000 0 -10000 0 0
GNRH1 0.009 0.024 -10000 0 -0.33 2 2
Gi family/GTP -0.054 0.14 -10000 0 -0.4 45 45
CDC42 0.012 0 -10000 0 -10000 0 0
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.004 0.056 0.25 19 -10000 0 19
BUB1B -0.045 0.14 -10000 0 -0.36 66 66
PLK1 0.001 0.044 -10000 0 -0.17 11 11
PLK1S1 0.007 0.023 -10000 0 -0.18 1 1
KIF2A 0.009 0.04 -10000 0 -10000 0 0
regulation of mitotic centrosome separation 0.001 0.044 -10000 0 -0.17 11 11
GOLGA2 0.012 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.016 0.15 -10000 0 -0.57 25 25
WEE1 0.007 0.049 -10000 0 -0.4 2 2
cytokinesis -0.015 0.13 -10000 0 -0.48 27 27
PP2A-alpha B56 -0.017 0.12 -10000 0 -10000 0 0
AURKA -0.006 0.063 -10000 0 -0.21 35 35
PICH/PLK1 -0.007 0.13 -10000 0 -0.53 22 22
CENPE -0.17 0.27 -10000 0 -0.55 140 140
RhoA/GTP 0.009 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.009 0.039 -10000 0 -10000 0 0
PPP2CA 0.012 0 -10000 0 -10000 0 0
FZR1 0.012 0 -10000 0 -10000 0 0
TPX2 -0.011 0.069 -10000 0 -0.21 42 42
PAK1 0.012 0.001 -10000 0 -10000 0 0
SPC24 0.002 0.094 -10000 0 -0.85 5 5
FBXW11 0.012 0 -10000 0 -10000 0 0
CLSPN -0.062 0.11 -10000 0 -0.23 122 122
GORASP1 0.012 0 -10000 0 -10000 0 0
metaphase 0 0.004 0.011 1 -0.017 14 15
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.002 0.021 -10000 0 -0.092 9 9
G2 phase of mitotic cell cycle -0.001 0.004 -10000 0 -0.013 34 34
STAG2 0.012 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.003 0.013 -10000 0 -10000 0 0
spindle elongation 0.001 0.044 -10000 0 -0.17 11 11
ODF2 0.011 0.004 -10000 0 -10000 0 0
BUB1 -0.052 0.13 -10000 0 -0.36 60 60
TPT1 0.007 0.021 -10000 0 -10000 0 0
CDC25C 0.002 0.055 -10000 0 -0.34 9 9
CDC25B -0.008 0.13 -10000 0 -0.85 10 10
SGOL1 -0.004 0.056 -10000 0 -0.25 19 19
RHOA 0.012 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.023 0.089 -10000 0 -0.5 13 13
CDC14B 0.01 0.003 -10000 0 -10000 0 0
CDC20 -0.003 0.11 -10000 0 -0.8 8 8
PLK1/PBIP1 -0.011 0.039 -10000 0 -0.36 2 2
mitosis 0.003 0.012 0.042 34 -0.028 4 38
FBXO5 0.01 0.032 -10000 0 -0.2 2 2
CDC2 0 0.004 -10000 0 -0.019 13 13
NDC80 -0.031 0.19 -10000 0 -0.85 21 21
metaphase plate congression 0.006 0.027 -10000 0 -10000 0 0
ERCC6L -0.033 0.12 -10000 0 -0.52 22 22
NLP/gamma Tubulin 0.006 0.021 -10000 0 -0.12 4 4
microtubule cytoskeleton organization 0.007 0.021 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0.002 -10000 0 -0.013 3 3
PPP1R12A 0.01 0.042 -10000 0 -0.85 1 1
interphase 0 0.002 -10000 0 -0.013 3 3
PLK1/PRC1-2 -0.032 0.17 -10000 0 -0.57 37 37
GRASP65/GM130/RAB1/GTP/PLK1 -0.007 0.025 -10000 0 -10000 0 0
RAB1A 0.012 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0 0.067 -10000 0 -0.52 4 4
mitotic prometaphase -0.001 0.002 -10000 0 -0.013 5 5
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.03 -10000 0 -10000 0 0
microtubule-based process -0.025 0.15 -10000 0 -0.57 26 26
Golgi organization 0.001 0.044 -10000 0 -0.17 11 11
Cohesin/SA2 -0.011 0.031 -10000 0 -10000 0 0
PPP1CB/MYPT1 0.015 0.034 -10000 0 -0.66 1 1
KIF20A -0.042 0.21 -10000 0 -0.85 26 26
APC/C/CDC20 -0.001 0.091 -10000 0 -0.59 8 8
PPP2R1A 0.012 0 -10000 0 -10000 0 0
chromosome segregation -0.011 0.038 -10000 0 -0.36 2 2
PRC1 -0.015 0.15 -10000 0 -0.85 13 13
ECT2 -0.13 0.25 -10000 0 -0.55 106 106
C13orf34 0.002 0.064 -10000 0 -0.53 4 4
NUDC 0.006 0.027 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.044 0.14 -10000 0 -0.36 66 66
spindle assembly 0.005 0.033 -10000 0 -0.15 8 8
spindle stabilization 0.007 0.023 -10000 0 -0.18 1 1
APC/C/HCDH1 0.017 0.002 -10000 0 -10000 0 0
MKLP2/PLK1 -0.025 0.15 -10000 0 -0.58 26 26
CCNB1 0.006 0.073 -10000 0 -0.85 3 3
PPP1CB 0.012 0.001 -10000 0 -10000 0 0
BTRC 0.012 0 -10000 0 -10000 0 0
ROCK2 0.012 0.03 -10000 0 -10000 0 0
TUBG1 0.007 0.021 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.022 0.086 -10000 0 -0.48 13 13
MLF1IP 0.009 0.034 -10000 0 -0.68 1 1
INCENP 0.011 0.004 -10000 0 -10000 0 0
Arf6 signaling events

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
CENTA1/KIF3B -0.006 0.057 -9999 0 -0.58 4 4
ARNO/beta Arrestin1-2 -0.059 0.088 -9999 0 -10000 0 0
EGFR -0.022 0.16 -9999 0 -0.7 20 20
EPHA2 -0.001 0.11 -9999 0 -0.8 7 7
USP6 0.006 0.068 -9999 0 -0.66 4 4
IQSEC1 0.012 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.077 0.24 -9999 0 -0.69 49 49
ARRB2 0.007 0.047 -9999 0 -0.38 6 6
mol:GTP 0.014 0.023 -9999 0 -0.23 1 1
ARRB1 0.011 0.023 -9999 0 -0.47 1 1
FBXO8 0.012 0 -9999 0 -10000 0 0
TSHR -0.006 0.092 -9999 0 -0.47 16 16
EGF -0.079 0.26 -9999 0 -0.82 44 44
somatostatin receptor activity 0 0 -9999 0 -0.001 9 9
ARAP2 0.011 0.023 -9999 0 -0.47 1 1
mol:GDP -0.056 0.099 -9999 0 -0.31 20 20
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 1 1
ITGA2B -0.017 0.15 -9999 0 -0.82 14 14
ARF6 0.012 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.02 0.082 -9999 0 -0.52 9 9
ADAP1 0.004 0.084 -9999 0 -0.85 4 4
KIF13B 0.012 0 -9999 0 -10000 0 0
HGF/MET -0.05 0.2 -9999 0 -0.67 38 38
PXN 0.013 0 -9999 0 -10000 0 0
ARF6/GTP -0.049 0.1 -9999 0 -0.28 15 15
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.079 0.2 -9999 0 -0.6 49 49
ADRB2 -0.13 0.22 -9999 0 -0.47 121 121
receptor agonist activity 0 0 -9999 0 0 13 13
actin filament binding 0 0 -9999 0 -0.001 13 13
SRC 0.012 0 -9999 0 -10000 0 0
ITGB3 0.003 0.088 -9999 0 -0.78 5 5
GNAQ 0.012 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 1 1
ARF6/GDP 0.009 0.067 -9999 0 -0.39 3 3
ARF6/GDP/GULP/ACAP1 -0.07 0.11 -9999 0 -0.43 16 16
alphaIIb/beta3 Integrin/paxillin/GIT1 0.008 0.11 -9999 0 -0.52 17 17
ACAP1 -0.008 0.12 -9999 0 -0.75 11 11
ACAP2 0.012 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 0 0.07 -9999 0 -0.58 6 6
EFNA1 0.006 0.073 -9999 0 -0.85 3 3
HGF -0.008 0.12 -9999 0 -0.64 13 13
CYTH3 0.011 0 -9999 0 -10000 0 0
CYTH2 0.008 0.002 -9999 0 -10000 0 0
NCK1 0.012 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 3 3
endosomal lumen acidification 0 0 -9999 0 0 7 7
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.005 0.089 -9999 0 -0.47 15 15
GNAQ/ARNO 0.014 0.006 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 2 2
MET -0.055 0.23 -9999 0 -0.84 33 33
GNA14 0.003 0.071 -9999 0 -0.52 7 7
GNA15 0.002 0.094 -9999 0 -0.85 5 5
GIT1 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 4 4
GNA11 0.012 0 -9999 0 -10000 0 0
LHCGR -0.006 0.1 -9999 0 -0.85 6 6
AGTR1 -0.12 0.24 -9999 0 -0.51 108 108
desensitization of G-protein coupled receptor protein signaling pathway 0 0.07 -9999 0 -0.58 6 6
IPCEF1/ARNO -0.05 0.16 -9999 0 -0.48 49 49
alphaIIb/beta3 Integrin -0.012 0.14 -9999 0 -0.62 19 19
Signaling events mediated by PTP1B

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
PDGFRB -0.042 0.21 -10000 0 -0.85 26 26
Jak2/Leptin Receptor -0.067 0.095 -10000 0 -0.4 11 11
PTP1B/AKT1 -0.044 0.095 0.23 3 -0.34 5 8
FYN 0.012 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.057 0.11 0.26 3 -0.36 7 10
EGFR -0.024 0.16 -10000 0 -0.7 20 20
EGF/EGFR -0.12 0.18 -10000 0 -0.54 52 52
CSF1 0.01 0.042 -10000 0 -0.85 1 1
AKT1 0.013 0.001 -10000 0 -10000 0 0
INSR 0.013 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.077 0.13 0.23 2 -0.48 17 19
Insulin Receptor/Insulin -0.044 0.055 -10000 0 -10000 0 0
HCK 0.012 0 -10000 0 -10000 0 0
CRK 0.012 0 -10000 0 -10000 0 0
TYK2 -0.047 0.1 0.25 3 -0.36 5 8
EGF -0.08 0.26 -10000 0 -0.82 44 44
YES1 0.012 0 -10000 0 -10000 0 0
CAV1 -0.049 0.11 0.25 3 -0.36 10 13
TXN 0.01 0.005 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.042 0.094 -10000 0 -10000 0 0
cell migration 0.057 0.11 0.36 7 -0.26 3 10
STAT3 0.012 0.001 -10000 0 -10000 0 0
PRLR -0.053 0.19 -10000 0 -0.55 47 47
ITGA2B -0.017 0.15 -10000 0 -0.82 14 14
CSF1R 0.008 0.047 -10000 0 -0.47 4 4
Prolactin Receptor/Prolactin -0.067 0.2 -10000 0 -0.76 22 22
FGR 0.012 0 -10000 0 -10000 0 0
PTP1B/p130 Cas -0.048 0.1 0.23 3 -0.36 5 8
Crk/p130 Cas -0.041 0.094 -10000 0 -0.35 2 2
DOK1 -0.048 0.11 0.24 3 -0.34 25 28
JAK2 -0.058 0.11 -10000 0 -0.37 25 25
Jak2/Leptin Receptor/Leptin -0.069 0.087 -10000 0 -0.45 3 3
PIK3R1 0.012 0 -10000 0 -10000 0 0
PTPN1 -0.058 0.11 0.26 3 -0.36 7 10
LYN 0.012 0 -10000 0 -10000 0 0
CDH2 -0.041 0.18 -10000 0 -0.6 36 36
SRC -0.007 0.044 -10000 0 -10000 0 0
ITGB3 0.002 0.087 -10000 0 -0.77 5 5
CAT1/PTP1B -0.11 0.14 0.25 1 -0.41 21 22
CAPN1 0.012 0.003 -10000 0 -10000 0 0
CSK 0.012 0 -10000 0 -10000 0 0
PI3K -0.037 0.053 -10000 0 -0.58 1 1
mol:H2O2 0.002 0.007 -10000 0 -10000 0 0
STAT3 (dimer) -0.061 0.078 -10000 0 -0.41 1 1
negative regulation of transcription -0.057 0.11 -10000 0 -0.36 25 25
FCGR2A 0 0.1 -10000 0 -0.85 6 6
FER 0.009 0.024 -10000 0 -0.47 1 1
alphaIIb/beta3 Integrin -0.023 0.13 -10000 0 -0.62 19 19
BLK -0.11 0.25 -10000 0 -0.56 86 86
Insulin Receptor/Insulin/Shc 0.007 0.009 -10000 0 -10000 0 0
RHOA 0.012 0.003 -10000 0 -10000 0 0
LEPR 0.008 0.054 -10000 0 -0.59 3 3
BCAR1 0.012 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.012 0 -10000 0 -10000 0 0
mol:NADPH -0.001 0.004 -10000 0 -10000 0 0
TRPV6 -0.082 0.14 -10000 0 -0.4 33 33
PRL -0.026 0.16 -10000 0 -0.86 15 15
SOCS3 0.019 0.015 -10000 0 -10000 0 0
SPRY2 0.013 0.025 -10000 0 -0.48 1 1
Insulin Receptor/Insulin/IRS1 0.006 0.017 -10000 0 -10000 0 0
CSF1/CSF1R -0.044 0.096 -10000 0 -0.34 5 5
Ras protein signal transduction 0.032 0.034 -10000 0 -10000 0 0
IRS1 0.011 0.023 -10000 0 -0.47 1 1
INS 0.001 0.003 -10000 0 -10000 0 0
LEP -0.04 0.16 -10000 0 -0.49 42 42
STAT5B -0.054 0.098 0.2 3 -0.33 12 15
STAT5A -0.054 0.098 0.2 3 -0.33 12 15
GRB2 0.012 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.079 0.17 0.23 2 -0.57 31 33
CSN2 -0.013 0.11 -10000 0 -0.73 6 6
PIK3CA 0.01 0.042 -10000 0 -0.85 1 1
LAT -0.013 0.063 -10000 0 -0.35 7 7
YBX1 0.019 0.002 -10000 0 -10000 0 0
LCK -0.01 0.14 -10000 0 -0.85 11 11
SHC1 0.012 0 -10000 0 -10000 0 0
NOX4 -0.36 0.43 -10000 0 -0.85 180 180
Aurora A signaling

Figure S61.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S61.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A -0.001 0.09 -9999 0 -0.32 2 2
BIRC5 -0.031 0.19 -9999 0 -0.82 22 22
NFKBIA 0.002 0.091 -9999 0 -0.31 26 26
CPEB1 -0.12 0.21 -9999 0 -0.47 113 113
AKT1 0.002 0.091 -9999 0 -10000 0 0
NDEL1 0.012 0 -9999 0 -10000 0 0
Aurora A/BRCA1 -0.027 0.09 -9999 0 -0.52 4 4
NDEL1/TACC3 -0.022 0.084 -9999 0 -0.72 2 2
GADD45A 0.012 0 -9999 0 -10000 0 0
GSK3B 0.012 0.005 -9999 0 -10000 0 0
PAK1/Aurora A -0.001 0.09 -9999 0 -0.32 2 2
MDM2 -0.01 0.14 -9999 0 -0.85 11 11
JUB -0.12 0.31 -9999 0 -0.85 65 65
TPX2 -0.047 0.21 -9999 0 -0.66 42 42
TP53 0.002 0.076 -9999 0 -0.47 1 1
DLG7 -0.008 0.09 -9999 0 -0.31 34 34
AURKAIP1 0.012 0 -9999 0 -10000 0 0
ARHGEF7 0.01 0.042 -9999 0 -0.85 1 1
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.004 0.096 -9999 0 -0.75 2 2
G2/M transition of mitotic cell cycle -0.026 0.089 -9999 0 -0.52 4 4
AURKA -0.009 0.11 -9999 0 -0.36 34 34
AURKB -0.014 0.055 -9999 0 -0.27 14 14
CDC25B -0.028 0.12 -9999 0 -0.39 19 19
G2/M transition checkpoint -0.1 0.21 -9999 0 -0.48 88 88
mRNA polyadenylation -0.086 0.13 -9999 0 -0.52 11 11
Aurora A/CPEB -0.087 0.13 -9999 0 -0.52 11 11
Aurora A/TACC1/TRAP/chTOG 0.014 0.078 -9999 0 -10000 0 0
BRCA1 0.004 0.084 -9999 0 -0.85 4 4
centrosome duplication -0.001 0.089 -9999 0 -0.32 2 2
regulation of centrosome cycle -0.022 0.083 -9999 0 -0.71 2 2
spindle assembly -0.019 0.067 -9999 0 -10000 0 0
TDRD7 0.012 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.047 0.14 -9999 0 -0.57 23 23
CENPA -0.002 0.07 -9999 0 -0.35 11 11
Aurora A/PP2A -0.001 0.09 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.007 0.079 -9999 0 -0.38 1 1
negative regulation of DNA binding 0.002 0.076 -9999 0 -0.47 1 1
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0.017 0.033 -9999 0 -0.66 1 1
RASA1 0.012 0 -9999 0 -10000 0 0
Ajuba/Aurora A -0.1 0.21 -9999 0 -0.48 88 88
mitotic prometaphase 0.001 0.011 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.009 0.11 -9999 0 -0.36 34 34
TACC1 0.011 0.023 -9999 0 -0.47 1 1
TACC3 0.007 0.064 -9999 0 -0.72 3 3
Aurora A/Antizyme1 0.007 0.082 -9999 0 -10000 0 0
Aurora A/RasGAP -0.001 0.09 -9999 0 -10000 0 0
OAZ1 0.012 0 -9999 0 -10000 0 0
RAN 0.012 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.012 0.005 -9999 0 -10000 0 0
GIT1 0.012 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 -0.001 0.028 -9999 0 -0.57 1 1
Importin alpha/Importin beta/TPX2 -0.047 0.2 -9999 0 -0.66 42 42
PPP2R5D 0.012 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.047 0.21 -9999 0 -0.64 42 42
PAK1 0.012 0 -9999 0 -10000 0 0
CKAP5 0.012 0 -9999 0 -10000 0 0
LPA receptor mediated events

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
GNB1/GNG2 -0.016 0.063 -9999 0 -0.49 2 2
NF kappa B1 p50/RelA/I kappa B alpha -0.027 0.078 -9999 0 -10000 0 0
AP1 -0.051 0.11 -9999 0 -0.47 9 9
mol:PIP3 -0.051 0.12 -9999 0 -0.59 3 3
AKT1 0.042 0.053 -9999 0 -0.43 1 1
PTK2B 0.011 0.057 -9999 0 -0.27 5 5
RHOA 0.025 0.023 -9999 0 -10000 0 0
PIK3CB 0.012 0 -9999 0 -10000 0 0
mol:Ca2+ 0.006 0.091 -9999 0 -0.45 4 4
MAGI3 0.011 0.023 -9999 0 -0.46 1 1
RELA 0.012 0 -9999 0 -10000 0 0
apoptosis -0.025 0.12 -9999 0 -0.44 13 13
HRAS/GDP 0.009 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization -0.029 0.12 -9999 0 -0.44 9 9
NF kappa B1 p50/RelA -0.038 0.092 -9999 0 -0.54 1 1
endothelial cell migration 0.007 0.085 -9999 0 -0.77 2 2
ADCY4 -0.034 0.15 -9999 0 -0.56 18 18
ADCY5 -0.086 0.22 -9999 0 -0.52 67 67
ADCY6 -0.034 0.15 -9999 0 -0.56 18 18
ADCY7 -0.034 0.15 -9999 0 -0.56 18 18
ADCY1 -0.041 0.15 -9999 0 -0.54 21 21
ADCY2 -0.071 0.2 -9999 0 -0.55 45 45
ADCY3 -0.034 0.15 -9999 0 -0.56 18 18
ADCY8 -0.038 0.15 -9999 0 -0.57 18 18
ADCY9 -0.035 0.16 -9999 0 -0.59 18 18
GSK3B 0.017 0.054 -9999 0 -10000 0 0
arachidonic acid secretion -0.035 0.15 -9999 0 -0.56 18 18
GNG2 0.01 0.042 -9999 0 -0.85 1 1
TRIP6 0.021 0.031 -9999 0 -0.34 3 3
GNAO1 -0.056 0.15 -9999 0 -0.53 19 19
HRAS 0.012 0 -9999 0 -10000 0 0
NFKBIA 0.005 0.1 -9999 0 -0.48 1 1
GAB1 0.012 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.014 0.1 -9999 0 -0.84 6 6
JUN 0.012 0 -9999 0 -10000 0 0
LPA/LPA2/NHERF2 0 0.005 -9999 0 -10000 0 0
TIAM1 -0.017 0.12 -9999 0 -0.98 6 6
PIK3R1 0.012 0 -9999 0 -10000 0 0
mol:IP3 0.005 0.092 -9999 0 -0.46 4 4
PLCB3 0.025 0.014 -9999 0 -10000 0 0
FOS -0.014 0.11 -9999 0 -0.47 23 23
positive regulation of mitosis -0.035 0.15 -9999 0 -0.56 18 18
LPA/LPA1-2-3 -0.048 0.12 -9999 0 -0.5 13 13
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade -0.001 0.001 -9999 0 -10000 0 0
BCAR1 0.012 0 -9999 0 -10000 0 0
stress fiber formation 0.006 0.08 -9999 0 -0.34 5 5
GNAZ -0.011 0.1 -9999 0 -0.51 2 2
EGFR/PI3K-beta/Gab1 -0.053 0.12 -9999 0 -0.62 3 3
positive regulation of dendritic cell cytokine production -0.048 0.11 -9999 0 -0.5 13 13
LPA/LPA2/MAGI-3 -0.001 0.014 -9999 0 -10000 0 0
ARHGEF1 0.021 0.061 -9999 0 -0.43 1 1
GNAI2 0.008 0.072 -9999 0 -0.51 1 1
GNAI3 0.008 0.072 -9999 0 -0.51 1 1
GNAI1 0.003 0.089 -9999 0 -0.52 5 5
LPA/LPA3 -0.046 0.13 -9999 0 -0.38 50 50
LPA/LPA2 0 0.006 -9999 0 -10000 0 0
LPA/LPA1 -0.02 0.08 -9999 0 -0.33 25 25
HB-EGF/EGFR -0.17 0.28 -9999 0 -0.59 125 125
HBEGF -0.17 0.3 -9999 0 -0.66 116 116
mol:DAG 0.005 0.092 -9999 0 -0.46 4 4
cAMP biosynthetic process -0.054 0.18 -9999 0 -0.52 33 33
NFKB1 0.012 0 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
GNB1 0.012 0 -9999 0 -10000 0 0
LYN 0.005 0.1 -9999 0 -0.42 4 4
GNAQ -0.013 0.095 -9999 0 -0.39 8 8
LPAR2 0.012 0.001 -9999 0 -10000 0 0
LPAR3 -0.055 0.18 -9999 0 -0.53 50 50
LPAR1 -0.012 0.11 -9999 0 -0.46 24 24
IL8 -0.24 0.23 -9999 0 -0.48 115 115
PTK2 -0.016 0.12 -9999 0 -0.47 13 13
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
CASP3 -0.025 0.12 -9999 0 -0.44 13 13
EGFR -0.023 0.16 -9999 0 -0.7 20 20
PLCG1 -0.01 0.1 -9999 0 -0.42 8 8
PLD2 -0.016 0.12 -9999 0 -0.47 13 13
G12/G13 -0.014 0.058 -9999 0 -0.46 1 1
PI3K-beta -0.011 0.046 -9999 0 -0.51 1 1
cell migration -0.019 0.05 -9999 0 -0.28 4 4
SLC9A3R2 0.012 0 -9999 0 -10000 0 0
PXN 0.006 0.081 -9999 0 -0.34 5 5
HRAS/GTP -0.036 0.16 -9999 0 -0.58 18 18
RAC1 0.012 0 -9999 0 -10000 0 0
MMP9 -0.23 0.39 -9999 0 -0.85 115 115
PRKCE 0.012 0.001 -9999 0 -10000 0 0
PRKCD 0.011 0.088 -9999 0 -0.43 4 4
Gi(beta/gamma) -0.03 0.14 -9999 0 -0.53 18 18
mol:LPA 0.002 0.011 -9999 0 -10000 0 0
TRIP6/p130 Cas/FAK1/Paxillin -0.038 0.095 -9999 0 -0.57 2 2
MAPKKK cascade -0.035 0.15 -9999 0 -0.56 18 18
contractile ring contraction involved in cytokinesis 0.025 0.023 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.018 0.1 -9999 0 -0.38 10 10
GNA15 -0.018 0.11 -9999 0 -0.5 10 10
GNA12 0.012 0 -9999 0 -10000 0 0
GNA13 0.012 0 -9999 0 -10000 0 0
MAPT -0.031 0.12 -9999 0 -0.45 9 9
GNA11 -0.013 0.095 -9999 0 -0.39 8 8
Rac1/GTP -0.004 0.11 -9999 0 -0.89 6 6
MMP2 0.007 0.085 -9999 0 -0.77 2 2
IL6-mediated 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
BCL2L1 -0.17 0.25 -10000 0 -0.77 12 12
CRP -0.2 0.28 -10000 0 -0.89 22 22
cell cycle arrest -0.2 0.28 -10000 0 -0.77 35 35
TIMP1 -0.15 0.24 -10000 0 -0.73 22 22
IL6ST 0.003 0.048 -10000 0 -0.47 4 4
Rac1/GDP -0.054 0.13 -10000 0 -0.5 7 7
AP1 0.006 0.078 -10000 0 -10000 0 0
GAB2 0.011 0.042 -10000 0 -0.85 1 1
TNFSF11 -0.36 0.37 -10000 0 -0.83 89 89
HSP90B1 -0.007 0.048 -10000 0 -10000 0 0
GAB1 0.013 0.001 -10000 0 -10000 0 0
MAPK14 -0.009 0.11 -10000 0 -0.58 3 3
AKT1 0.044 0.019 -10000 0 -10000 0 0
FOXO1 0.05 0.018 -10000 0 -10000 0 0
MAP2K6 -0.032 0.12 -10000 0 -0.56 5 5
mol:GTP -0.002 0.003 -10000 0 -10000 0 0
MAP2K4 -0.078 0.15 -10000 0 -0.52 5 5
MITF -0.049 0.12 -10000 0 -0.46 10 10
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.012 0 -10000 0 -10000 0 0
A2M 0.02 0.004 -10000 0 -10000 0 0
CEBPB 0.018 0.005 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.003 0.054 -10000 0 -10000 0 0
STAT3 -0.21 0.29 -10000 0 -0.81 35 35
STAT1 -0.014 0.063 -10000 0 -0.41 10 10
CEBPD -0.18 0.25 -10000 0 -0.79 13 13
PIK3CA 0.012 0.042 -10000 0 -0.85 1 1
PI3K 0.02 0.033 -10000 0 -0.66 1 1
JUN 0.012 0.001 -10000 0 -10000 0 0
PIAS3/MITF -0.039 0.12 -10000 0 -0.5 6 6
MAPK11 -0.009 0.11 -10000 0 -0.58 3 3
STAT3 (dimer)/FOXO1 -0.12 0.22 -10000 0 -0.64 6 6
GRB2/SOS1/GAB family -0.034 0.082 -10000 0 -0.47 3 3
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.028 0.11 -10000 0 -0.39 13 13
GRB2 0.013 0.001 -10000 0 -10000 0 0
JAK2 0.006 0.073 -10000 0 -0.85 3 3
LBP -0.22 0.32 -10000 0 -0.76 84 84
PIK3R1 0.014 0 -10000 0 -10000 0 0
JAK1 0.011 0.005 -10000 0 -10000 0 0
MYC -0.18 0.25 -10000 0 -0.79 14 14
FGG -0.26 0.37 -10000 0 -0.99 64 64
macrophage differentiation -0.2 0.28 -10000 0 -0.77 35 35
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.049 0.14 -10000 0 -0.54 23 23
JUNB -0.17 0.24 -10000 0 -0.74 12 12
FOS -0.014 0.11 -10000 0 -0.47 23 23
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.056 0.12 0.3 1 -0.39 23 24
STAT1/PIAS1 -0.075 0.13 -10000 0 -0.43 12 12
GRB2/SOS1/GAB family/SHP2/PI3K 0.027 0.025 -10000 0 -10000 0 0
STAT3 (dimer) -0.21 0.29 -10000 0 -0.81 35 35
PRKCD -0.1 0.19 -10000 0 -0.57 2 2
IL6R -0.004 0.083 -10000 0 -0.47 13 13
SOCS3 0.01 0.1 -10000 0 -0.63 1 1
gp130 (dimer)/JAK1/JAK1/LMO4 0.009 0.05 -10000 0 -0.56 1 1
Rac1/GTP -0.068 0.14 -10000 0 -0.52 6 6
HCK 0.012 0 -10000 0 -10000 0 0
MAPKKK cascade 0.011 0.047 -10000 0 -10000 0 0
bone resorption -0.34 0.35 -10000 0 -0.78 89 89
IRF1 -0.17 0.25 -10000 0 -0.77 12 12
mol:GDP -0.055 0.13 -10000 0 -0.49 9 9
SOS1 0.012 0.001 -10000 0 -10000 0 0
VAV1 -0.056 0.13 -10000 0 -0.5 9 9
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.004 0.12 -10000 0 -0.53 6 6
PTPN11 -0.004 0.013 -10000 0 -10000 0 0
IL6/IL6RA -0.061 0.17 -10000 0 -0.46 50 50
gp130 (dimer)/TYK2/TYK2/LMO4 0.007 0.047 -10000 0 -0.56 1 1
gp130 (dimer)/JAK2/JAK2/LMO4 0.002 0.069 -10000 0 -0.57 4 4
IL6 -0.074 0.22 -10000 0 -0.59 56 56
PIAS3 0.012 0 -10000 0 -10000 0 0
PTPRE 0.015 0.062 -10000 0 -0.85 2 2
PIAS1 0.012 0 -10000 0 -10000 0 0
RAC1 0.011 0.002 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.039 0.11 0.27 1 -0.36 18 19
LMO4 0.003 0.054 -10000 0 -0.59 3 3
STAT3 (dimer)/PIAS3 -0.23 0.23 0.37 1 -0.74 35 36
MCL1 0.049 0.018 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 -0.029 0.18 -10000 0 -0.85 20 20
ANTXR2 0.009 0.041 -10000 0 -0.47 3 3
negative regulation of myeloid dendritic cell antigen processing and presentation -0.005 0.022 -10000 0 -0.096 23 23
monocyte activation -0.002 0.069 -10000 0 -0.29 22 22
MAP2K2 -0.002 0.009 -10000 0 -10000 0 0
MAP2K1 -0.005 0.019 -10000 0 -10000 0 0
MAP2K7 -0.005 0.019 -10000 0 -10000 0 0
MAP2K6 -0.009 0.04 -10000 0 -0.28 6 6
CYAA -0.013 0.11 -10000 0 -0.51 20 20
MAP2K4 -0.005 0.019 -10000 0 -10000 0 0
IL1B -0.036 0.14 -10000 0 -0.4 47 47
Channel -0.012 0.12 -10000 0 -0.54 20 20
NLRP1 -0.013 0.065 -10000 0 -0.48 7 7
CALM1 0.012 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.006 0.027 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.005 0.022 0.096 23 -10000 0 23
MAPK3 -0.005 0.019 -10000 0 -10000 0 0
MAPK1 -0.005 0.019 -10000 0 -10000 0 0
PGR -0.031 0.087 -10000 0 -0.28 40 40
PA/Cellular Receptors -0.03 0.13 -10000 0 -0.58 20 20
apoptosis -0.005 0.022 -10000 0 -0.096 23 23
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.01 0.11 -10000 0 -0.48 20 20
macrophage activation 0.013 0.021 -10000 0 -10000 0 0
TNF -0.022 0.16 -10000 0 -0.75 19 19
VCAM1 -0.002 0.069 -10000 0 -0.29 22 22
platelet activation -0.006 0.027 -10000 0 -10000 0 0
MAPKKK cascade -0.009 0.024 -10000 0 -10000 0 0
IL18 0.003 0.056 -10000 0 -0.43 4 4
negative regulation of macrophage activation -0.005 0.022 -10000 0 -0.096 23 23
LEF -0.005 0.022 -10000 0 -0.097 23 23
CASP1 -0.009 0.034 -10000 0 -0.22 7 7
mol:cAMP -0.006 0.027 -10000 0 -10000 0 0
necrosis -0.005 0.022 -10000 0 -0.096 23 23
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.011 0.11 -10000 0 -0.51 20 20
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.02 0.092 -10000 0 -0.55 9 9
ER alpha/Gai/GDP/Gbeta gamma -0.049 0.17 -10000 0 -0.53 24 24
AKT1 -0.003 0.15 -10000 0 -0.76 14 14
PIK3CA 0.01 0.042 -10000 0 -0.85 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.007 0.15 -10000 0 -0.78 14 14
mol:Ca2+ 0.016 0.093 -10000 0 -0.43 11 11
IGF1R 0.005 0.077 -10000 0 -0.76 4 4
E2/ER alpha (dimer)/Striatin -0.011 0.057 -10000 0 -0.58 1 1
SHC1 0.012 0 -10000 0 -10000 0 0
apoptosis 0.002 0.14 0.72 14 -10000 0 14
RhoA/GTP -0.025 0.096 -10000 0 -0.45 18 18
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.06 0.12 -10000 0 -0.61 8 8
regulation of stress fiber formation -0.026 0.086 0.47 1 -10000 0 1
E2/ERA-ERB (dimer) -0.022 0.097 -10000 0 -0.58 9 9
KRAS -0.023 0.17 -10000 0 -0.85 17 17
G13/GTP 0.006 0.054 -10000 0 -0.54 1 1
pseudopodium formation 0.026 0.086 -10000 0 -0.47 1 1
E2/ER alpha (dimer)/PELP1 -0.012 0.063 -10000 0 -0.58 2 2
GRB2 0.012 0 -10000 0 -10000 0 0
GNG2 0.01 0.042 -10000 0 -0.85 1 1
GNAO1 -0.094 0.2 -10000 0 -0.48 90 90
HRAS 0.012 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.016 0.13 -10000 0 -0.53 15 15
E2/ER beta (dimer) -0.005 0.094 -10000 0 -0.63 9 9
mol:GDP -0.029 0.097 -10000 0 -0.38 23 23
mol:NADP -0.016 0.13 -10000 0 -0.53 15 15
PIK3R1 0.012 0 -10000 0 -10000 0 0
mol:IP3 0.016 0.096 -10000 0 -0.44 11 11
IGF-1R heterotetramer 0.005 0.077 -10000 0 -0.75 4 4
PLCB1 0.014 0.088 -10000 0 -0.47 7 7
PLCB2 0.016 0.081 -10000 0 -0.47 5 5
IGF1 -0.071 0.23 -10000 0 -0.64 53 53
mol:L-citrulline -0.016 0.13 -10000 0 -0.53 15 15
RHOA 0.012 0 -10000 0 -10000 0 0
Gai/GDP -0.15 0.27 -10000 0 -0.65 87 87
JNK cascade -0.005 0.094 -10000 0 -0.63 9 9
BCAR1 0.012 0 -10000 0 -10000 0 0
ESR2 -0.005 0.12 -10000 0 -0.81 9 9
GNAQ 0.012 0 -10000 0 -10000 0 0
ESR1 -0.006 0.096 -10000 0 -0.49 15 15
Gq family/GDP/Gbeta gamma 0.03 0.052 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.015 0.057 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.06 0.12 -10000 0 -0.61 8 8
GNAZ -0.02 0.12 -10000 0 -0.47 28 28
E2/ER alpha (dimer) -0.004 0.07 -10000 0 -0.36 15 15
STRN 0.012 0 -10000 0 -10000 0 0
GNAL -0.02 0.12 -10000 0 -0.47 28 28
PELP1 0.01 0.042 -10000 0 -0.85 1 1
MAPK11 0.006 0.083 -10000 0 -0.58 8 8
GNAI2 0.012 0 -10000 0 -10000 0 0
GNAI3 0.012 0 -10000 0 -10000 0 0
GNAI1 0.003 0.066 -10000 0 -0.47 8 8
HBEGF -0.091 0.17 -10000 0 -0.51 24 24
cAMP biosynthetic process -0.032 0.099 -10000 0 -0.48 13 13
SRC -0.039 0.16 -10000 0 -0.64 10 10
PI3K 0.017 0.033 -10000 0 -0.66 1 1
GNB1 0.012 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.026 0.09 -10000 0 -0.65 3 3
SOS1 0.012 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.081 0.14 -10000 0 -0.52 17 17
Gs family/GTP -0.033 0.1 -10000 0 -0.49 13 13
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.002 0.11 -10000 0 -0.53 17 17
vasodilation -0.014 0.13 -10000 0 -0.51 15 15
mol:DAG 0.016 0.096 -10000 0 -0.44 11 11
Gs family/GDP/Gbeta gamma -0.035 0.096 -10000 0 -0.52 7 7
MSN 0.026 0.092 -10000 0 -0.52 1 1
Gq family/GTP 0.014 0.069 -10000 0 -0.38 7 7
mol:PI-3-4-5-P3 -0.006 0.14 -10000 0 -0.75 14 14
NRAS 0.012 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.014 0.13 0.51 15 -10000 0 15
GRB2/SOS1 0.019 0 -10000 0 -10000 0 0
RhoA/GDP -0.027 0.09 -10000 0 -0.54 3 3
NOS3 -0.017 0.14 -10000 0 -0.56 15 15
GNA11 0.012 0 -10000 0 -10000 0 0
MAPKKK cascade 0.002 0.13 -10000 0 -0.58 14 14
E2/ER alpha (dimer)/PELP1/Src -0.063 0.13 -10000 0 -0.62 9 9
ruffle organization 0.026 0.086 -10000 0 -0.47 1 1
ROCK2 0.019 0.099 -10000 0 -0.41 18 18
GNA14 0.003 0.071 -10000 0 -0.52 7 7
GNA15 0.002 0.094 -10000 0 -0.85 5 5
GNA13 0.012 0 -10000 0 -10000 0 0
MMP9 -0.16 0.25 -10000 0 -0.49 122 122
MMP2 -0.032 0.15 -10000 0 -0.64 8 8
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.13 0.24 -9999 0 -0.5 117 117
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.012 0 -9999 0 -10000 0 0
TCEB1 0.012 0 -9999 0 -10000 0 0
HIF1A/p53 0.03 0.012 -9999 0 -10000 0 0
HIF1A 0.024 0.004 -9999 0 -10000 0 0
COPS5 0.012 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0 0 -9999 0 -10000 0 0
FIH (dimer) 0.012 0 -9999 0 -10000 0 0
CDKN2A -0.24 0.39 -9999 0 -0.83 127 127
ARNT/IPAS -0.088 0.18 -9999 0 -0.66 12 12
HIF1AN 0.012 0 -9999 0 -10000 0 0
GNB2L1 0.012 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.031 0.004 -9999 0 -10000 0 0
CUL2 0.012 0 -9999 0 -10000 0 0
OS9 0.012 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.028 0.034 -9999 0 -0.46 2 2
PHD1-3/OS9 0.032 0.013 -9999 0 -10000 0 0
HIF1A/RACK1/Elongin B/Elongin C 0 0.002 -9999 0 -10000 0 0
VHL 0.012 0 -9999 0 -10000 0 0
HSP90AA1 0.008 0.06 -9999 0 -0.85 2 2
HIF1A/JAB1 0.031 0.004 -9999 0 -10000 0 0
EGLN3 0.011 0.023 -9999 0 -0.47 1 1
EGLN2 0.012 0 -9999 0 -10000 0 0
EGLN1 0.012 0 -9999 0 -10000 0 0
TP53 0.011 0.023 -9999 0 -0.47 1 1
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.037 0.001 -9999 0 -10000 0 0
ARNT 0.012 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.012 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.11 0.22 -9999 0 -0.46 119 119
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.094 0.2 -9999 0 -0.48 90 90
CDC42/GTP -0.031 0.12 -9999 0 -0.39 19 19
PLCG1 -0.031 0.13 -9999 0 -0.41 19 19
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.012 0 -9999 0 -10000 0 0
GNAI3 0.012 0 -9999 0 -10000 0 0
G12/G13 0.019 0 -9999 0 -10000 0 0
cell migration -0.056 0.1 -9999 0 -0.38 19 19
S1PR5 -0.013 0.14 -9999 0 -0.85 12 12
S1PR4 0.003 0.088 -9999 0 -0.78 5 5
MAPK3 -0.031 0.13 -9999 0 -0.41 19 19
MAPK1 -0.031 0.13 -9999 0 -0.41 19 19
S1P/S1P5/Gi -0.046 0.14 -9999 0 -0.46 22 22
GNAI1 0.003 0.066 -9999 0 -0.47 8 8
CDC42/GDP 0.009 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.017 0.097 -9999 0 -0.58 12 12
RHOA 0.024 0.052 -9999 0 -0.49 4 4
S1P/S1P4/Gi -0.041 0.13 -9999 0 -0.44 19 19
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.02 0.12 -9999 0 -0.47 28 28
S1P/S1P4/G12/G13 0.018 0.056 -9999 0 -0.53 4 4
GNA12 0.012 0 -9999 0 -10000 0 0
GNA13 0.012 0 -9999 0 -10000 0 0
CDC42 0.012 0 -9999 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin -0.03 0.12 -9999 0 -0.57 16 16
E-cadherin/beta catenin 0.007 0.066 -9999 0 -0.35 13 13
CTNNB1 0.01 0.042 -9999 0 -0.85 1 1
JUP -0.019 0.16 -9999 0 -0.85 15 15
CDH1 -0.001 0.08 -9999 0 -0.47 12 12
Regulation of Androgen receptor activity

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
HDAC1 0.021 0.017 -9999 0 -10000 0 0
SMARCC1 0.006 0.01 -9999 0 -10000 0 0
REL 0.013 0.003 -9999 0 -10000 0 0
HDAC7 0.027 0.095 -9999 0 -0.57 1 1
JUN 0.012 0.003 -9999 0 -10000 0 0
EP300 0.012 0 -9999 0 -10000 0 0
KAT2B 0.008 0.047 -9999 0 -0.47 4 4
KAT5 0.013 0 -9999 0 -10000 0 0
MAPK14 0.015 0.053 -9999 0 -0.43 4 4
FOXO1 0.012 0.001 -9999 0 -10000 0 0
T-DHT/AR 0.024 0.1 -9999 0 -0.6 1 1
MAP2K6 0.004 0.068 -9999 0 -0.54 6 6
BRM/BAF57 0.004 0.092 -9999 0 -0.66 7 7
MAP2K4 0.012 0.006 -9999 0 -10000 0 0
SMARCA2 0.009 0.041 -9999 0 -0.47 3 3
PDE9A -0.12 0.32 -9999 0 -0.99 48 48
NCOA2 0.011 0.024 -9999 0 -0.47 1 1
CEBPA -0.01 0.13 -9999 0 -0.76 12 12
EHMT2 0.01 0.042 -9999 0 -0.85 1 1
cell proliferation 0.037 0.12 -9999 0 -0.48 2 2
NR0B1 -0.004 0.084 -9999 0 -0.85 4 4
EGR1 -0.003 0.083 -9999 0 -0.47 13 13
RXRs/9cRA -0.087 0.13 -9999 0 -10000 0 0
AR/RACK1/Src 0.007 0.071 -9999 0 -0.56 1 1
AR/GR -0.002 0.094 -9999 0 -0.44 3 3
GNB2L1 0.012 0.002 -9999 0 -10000 0 0
PKN1 0.012 0.001 -9999 0 -10000 0 0
RCHY1 0.01 0.042 -9999 0 -0.85 1 1
epidermal growth factor receptor activity 0 0.002 -9999 0 -10000 0 0
MAPK8 0.021 0.012 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.026 0.071 -9999 0 -0.53 1 1
SRC 0.03 0.049 -9999 0 -0.53 1 1
NR3C1 0.007 0.052 -9999 0 -0.47 5 5
KLK3 -0.19 0.21 -9999 0 -0.77 29 29
APPBP2 0.012 0.005 -9999 0 -10000 0 0
TRIM24 0.01 0.042 -9999 0 -0.85 1 1
T-DHT/AR/TIP60 0.021 0.065 -9999 0 -0.47 2 2
TMPRSS2 -0.054 0.21 -9999 0 -1 17 17
RXRG -0.19 0.23 -9999 0 -0.47 171 171
mol:9cRA 0 0.001 -9999 0 -10000 0 0
RXRA 0.011 0.024 -9999 0 -0.47 1 1
RXRB 0.012 0.001 -9999 0 -10000 0 0
CARM1 0.012 0.003 -9999 0 -10000 0 0
NR2C2 0.012 0.001 -9999 0 -10000 0 0
KLK2 0.004 0.17 -9999 0 -0.61 26 26
AR -0.004 0.099 -9999 0 -0.3 19 19
SENP1 0.012 0.001 -9999 0 -10000 0 0
HSP90AA1 0.008 0.06 -9999 0 -0.85 2 2
MDM2 -0.01 0.14 -9999 0 -0.85 11 11
SRY -0.001 0.059 -9999 0 -0.84 2 2
GATA2 0.006 0.057 -9999 0 -0.47 6 6
MYST2 0.013 0.001 -9999 0 -10000 0 0
HOXB13 -0.55 0.4 -9999 0 -0.83 276 276
T-DHT/AR/RACK1/Src 0.026 0.068 -9999 0 -0.52 1 1
positive regulation of transcription 0.006 0.057 -9999 0 -0.46 6 6
DNAJA1 0.012 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.054 -9999 0 -0.28 12 12
NCOA1 0.015 0.004 -9999 0 -10000 0 0
SPDEF -0.087 0.2 -9999 0 -0.48 85 85
T-DHT/AR/TIF2 0.034 0.053 -9999 0 -10000 0 0
T-DHT/AR/Hsp90 0.018 0.074 -9999 0 -0.47 4 4
GSK3B 0.012 0.003 -9999 0 -10000 0 0
NR2C1 0.013 0.001 -9999 0 -10000 0 0
mol:T-DHT 0.025 0.052 -9999 0 -0.55 1 1
SIRT1 0.012 0 -9999 0 -10000 0 0
ZMIZ2 0.013 0.005 -9999 0 -10000 0 0
POU2F1 0.021 0.044 -9999 0 -0.84 1 1
T-DHT/AR/DAX-1 -0.008 0.08 -9999 0 -0.51 6 6
CREBBP 0.012 0.001 -9999 0 -10000 0 0
SMARCE1 -0.003 0.11 -9999 0 -0.85 7 7
LPA4-mediated signaling events

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
ADCY4 0.019 0 -9999 0 -10000 0 0
ADCY5 -0.05 0.13 -9999 0 -0.28 94 94
ADCY6 0.019 0 -9999 0 -10000 0 0
ADCY7 0.019 0 -9999 0 -10000 0 0
ADCY1 -0.003 0.11 -9999 0 -0.58 15 15
ADCY2 -0.038 0.14 -9999 0 -0.58 11 11
ADCY3 0.019 0 -9999 0 -10000 0 0
ADCY8 0.006 0.058 -9999 0 -0.58 4 4
PRKCE 0.011 0 -9999 0 -10000 0 0
ADCY9 0.017 0.02 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.011 0.074 -9999 0 -0.27 6 6
Caspase cascade in apoptosis

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
TOP1 0.008 0.092 -10000 0 -0.34 22 22
ACTA1 -0.013 0.12 -10000 0 -0.43 23 23
NUMA1 0.008 0.092 -10000 0 -0.34 22 22
SPTAN1 -0.002 0.11 -10000 0 -0.43 22 22
LIMK1 -0.004 0.12 -10000 0 -0.43 24 24
BIRC3 0.001 0.097 -10000 0 -0.79 6 6
BIRC2 0.013 0 -10000 0 -10000 0 0
BAX 0.012 0 -10000 0 -10000 0 0
CASP10 -0.01 0.14 -10000 0 -0.57 22 22
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.012 0 -10000 0 -10000 0 0
PTK2 0.008 0.092 -10000 0 -0.34 22 22
DIABLO 0.012 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.002 0.11 -10000 0 -0.42 22 22
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.012 0 -10000 0 -10000 0 0
GSN -0.006 0.12 -10000 0 -0.44 23 23
MADD 0.012 0 -10000 0 -10000 0 0
TFAP2A -0.1 0.17 -10000 0 -0.43 34 34
BID 0.005 0.065 -10000 0 -0.25 22 22
MAP3K1 0.006 0.042 -10000 0 -10000 0 0
TRADD 0.012 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.018 0.002 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.003 0.12 -10000 0 -0.43 23 23
CASP9 0.013 0 -10000 0 -10000 0 0
DNA repair -0.003 0.04 0.24 1 -0.2 6 7
neuron apoptosis 0.022 0.014 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.006 0.11 -10000 0 -0.41 22 22
APAF1 0.012 0 -10000 0 -10000 0 0
CASP6 0.022 0.057 -10000 0 -10000 0 0
TRAF2 0.012 0 -10000 0 -10000 0 0
ICAD/CAD 0.005 0.11 -10000 0 -0.41 21 21
CASP7 -0.005 0.038 0.29 6 -10000 0 6
KRT18 0.012 0.044 -10000 0 -0.46 3 3
apoptosis 0.011 0.1 -10000 0 -0.38 21 21
DFFA -0.002 0.11 -10000 0 -0.43 22 22
DFFB -0.002 0.11 -10000 0 -0.43 22 22
PARP1 0.003 0.04 0.2 6 -0.25 1 7
actin filament polymerization 0.006 0.12 0.41 30 -10000 0 30
TNF -0.022 0.16 -10000 0 -0.75 19 19
CYCS 0.008 0.053 -10000 0 -0.2 22 22
SATB1 0.027 0.056 -10000 0 -10000 0 0
SLK -0.002 0.11 -10000 0 -0.43 22 22
p15 BID/BAX 0.011 0.058 -10000 0 -10000 0 0
CASP2 0.035 0.054 -10000 0 -0.37 1 1
JNK cascade -0.006 0.042 -10000 0 -10000 0 0
CASP3 -0.009 0.12 -10000 0 -0.42 29 29
LMNB2 0.036 0.041 -10000 0 -10000 0 0
RIPK1 0.012 0 -10000 0 -10000 0 0
CASP4 0.012 0 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.022 0.062 -10000 0 -0.52 5 5
negative regulation of DNA binding -0.1 0.17 -10000 0 -0.43 34 34
stress fiber formation -0.002 0.11 -10000 0 -0.42 22 22
GZMB -0.021 0.16 -10000 0 -0.57 30 30
CASP1 0.008 0.057 -10000 0 -0.37 9 9
LMNB1 0.036 0.041 -10000 0 -10000 0 0
APP 0.022 0.014 -10000 0 -10000 0 0
TNFRSF1A 0.012 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.011 0 -10000 0 -10000 0 0
VIM 0.006 0.1 -10000 0 -0.37 22 22
LMNA 0.036 0.041 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.029 0.057 -10000 0 -0.4 1 1
LRDD 0.011 0.023 -10000 0 -0.47 1 1
SREBF1 -0.004 0.12 -10000 0 -0.43 24 24
APAF-1/Caspase 9 -0.003 0.024 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.008 0.09 -10000 0 -0.33 22 22
CFL2 -0.007 0.13 -10000 0 -0.42 30 30
GAS2 -0.02 0.14 -10000 0 -0.47 32 32
positive regulation of apoptosis 0.039 0.042 -10000 0 -10000 0 0
PRF1 0.008 0.047 -10000 0 -0.47 4 4
Ephrin A reverse signaling

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
MAPKKK cascade -0.03 0.1 -9999 0 -0.58 9 9
EFNA5 -0.018 0.13 -9999 0 -0.51 24 24
FYN -0.005 0.1 -9999 0 -0.53 9 9
neuron projection morphogenesis -0.03 0.1 -9999 0 -0.58 9 9
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.03 0.11 -9999 0 -0.58 9 9
EPHA5 -0.008 0.12 -9999 0 -0.68 11 11
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.042 0.21 -9999 0 -0.85 26 26
mol:S1P 0.001 0.001 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.034 0.12 -9999 0 -0.42 19 19
GNAO1 -0.092 0.2 -9999 0 -0.48 90 90
S1P/S1P3/G12/G13 0.023 0.043 -9999 0 -0.53 2 2
AKT1 -0.014 0.082 -9999 0 -10000 0 0
AKT3 0.004 0.088 -9999 0 -0.65 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.042 0.21 -9999 0 -0.85 26 26
GNAI2 0.014 0.001 -9999 0 -10000 0 0
GNAI3 0.014 0.001 -9999 0 -10000 0 0
GNAI1 0.005 0.066 -9999 0 -0.46 8 8
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.008 0.068 -9999 0 -0.66 4 4
S1PR2 0.01 0.042 -9999 0 -0.85 1 1
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.03 0.13 -9999 0 -0.44 19 19
MAPK3 -0.021 0.13 -9999 0 -0.41 19 19
MAPK1 -0.021 0.13 -9999 0 -0.41 19 19
JAK2 -0.035 0.14 -9999 0 -0.42 22 22
CXCR4 -0.054 0.17 -9999 0 -0.46 45 45
FLT1 0.013 0.042 -9999 0 -0.85 1 1
RhoA/GDP 0.009 0 -9999 0 -10000 0 0
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
SRC -0.021 0.13 -9999 0 -0.41 19 19
S1P/S1P3/Gi -0.03 0.14 -9999 0 -0.44 19 19
RAC1 0.012 0 -9999 0 -10000 0 0
RhoA/GTP -0.022 0.12 -9999 0 -0.65 3 3
VEGFA 0.001 0.11 -9999 0 -0.85 7 7
S1P/S1P2/Gi -0.031 0.13 -9999 0 -0.41 19 19
VEGFR1 homodimer/VEGFA homodimer 0.014 0.1 -9999 0 -0.73 7 7
RHOA 0.012 0 -9999 0 -10000 0 0
S1P/S1P3/Gq 0.02 0.056 -9999 0 -0.44 1 1
GNAQ 0.012 0 -9999 0 -10000 0 0
GNAZ -0.018 0.12 -9999 0 -0.46 28 28
G12/G13 0.019 0 -9999 0 -10000 0 0
GNA14 0.003 0.071 -9999 0 -0.52 7 7
GNA15 0.002 0.094 -9999 0 -0.85 5 5
GNA12 0.012 0 -9999 0 -10000 0 0
GNA13 0.012 0 -9999 0 -10000 0 0
GNA11 0.012 0 -9999 0 -10000 0 0
Rac1/GTP -0.022 0.12 -9999 0 -0.4 19 19
Ras signaling in the CD4+ TCR pathway

Figure S74.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S74.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.019 0.11 -9999 0 -0.51 6 6
MAP3K8 0.008 0.06 -9999 0 -0.86 2 2
FOS 0.017 0.09 -9999 0 -0.43 5 5
PRKCA 0.013 0.003 -9999 0 -10000 0 0
PTPN7 -0.001 0.11 -9999 0 -0.86 7 7
HRAS 0.013 0.001 -9999 0 -10000 0 0
PRKCB -0.018 0.12 -9999 0 -0.48 26 26
NRAS 0.013 0.001 -9999 0 -10000 0 0
RAS family/GTP 0.002 0.11 -9999 0 -0.53 17 17
MAPK3 0.016 0.061 -9999 0 -0.37 2 2
MAP2K1 0.009 0.1 -9999 0 -0.38 25 25
ELK1 0.012 0.005 -9999 0 -10000 0 0
BRAF 0.001 0.099 -9999 0 -0.37 26 26
mol:GTP 0 0.001 -9999 0 -0.005 21 21
MAPK1 0.016 0.061 -9999 0 -0.37 2 2
RAF1 0.001 0.099 -9999 0 -0.37 26 26
KRAS -0.023 0.17 -9999 0 -0.85 17 17
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.012 0.014 -10000 0 -10000 0 0
HSPA8 0.013 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.018 0.1 -10000 0 -0.59 1 1
AKT1 0.014 0.011 -10000 0 -10000 0 0
GSC -0.1 0.32 -10000 0 -0.9 51 51
NKX2-5 -0.11 0.3 -10000 0 -0.85 60 60
muscle cell differentiation 0.071 0.11 0.54 4 -10000 0 4
SMAD2-3/SMAD4/SP1 0.026 0.081 -10000 0 -10000 0 0
SMAD4 0.013 0.047 -10000 0 -0.46 2 2
CBFB 0.012 0 -10000 0 -10000 0 0
SAP18 0.011 0.042 -10000 0 -0.85 1 1
Cbp/p300/MSG1 -0.043 0.17 -10000 0 -0.58 36 36
SMAD3/SMAD4/VDR 0.015 0.043 -10000 0 -10000 0 0
MYC 0.007 0.055 -10000 0 -0.6 3 3
CDKN2B 0.01 0.19 -10000 0 -1.3 9 9
AP1 0.036 0.066 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.054 0.036 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.033 0.063 -10000 0 -0.42 1 1
SP3 0.015 0 -10000 0 -10000 0 0
CREB1 0.012 0 -10000 0 -10000 0 0
FOXH1 -0.19 0.36 -10000 0 -0.86 94 94
SMAD3/SMAD4/GR 0.009 0.058 -10000 0 -10000 0 0
GATA3 -0.009 0.14 -10000 0 -0.84 11 11
SKI/SIN3/HDAC complex/NCoR1 0.043 0.023 -10000 0 -10000 0 0
MEF2C/TIF2 -0.14 0.27 -10000 0 -0.73 29 29
endothelial cell migration 0.12 0.28 0.69 78 -10000 0 78
MAX 0.019 0.017 -10000 0 -10000 0 0
RBBP7 0.013 0.002 -10000 0 -10000 0 0
RBBP4 0.013 0.002 -10000 0 -10000 0 0
RUNX2 -0.002 0.11 -10000 0 -0.85 7 7
RUNX3 0.008 0.06 -10000 0 -0.85 2 2
RUNX1 -0.004 0.12 -10000 0 -0.85 8 8
CTBP1 0.012 0 -10000 0 -10000 0 0
NR3C1 0.013 0.056 -10000 0 -0.47 5 5
VDR 0.012 0 -10000 0 -10000 0 0
CDKN1A 0.044 0.087 -10000 0 -1.2 1 1
KAT2B 0.007 0.046 -10000 0 -0.46 4 4
SMAD2/SMAD2/SMAD4/FOXH1 -0.12 0.27 -10000 0 -0.6 94 94
DCP1A 0.012 0 -10000 0 -10000 0 0
SKI 0.013 0.002 -10000 0 -10000 0 0
SERPINE1 -0.12 0.28 -10000 0 -0.7 78 78
SMAD3/SMAD4/ATF2 0.008 0.04 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.004 0.051 -10000 0 -10000 0 0
SAP30 0.013 0.002 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.011 0.035 -10000 0 -10000 0 0
JUN 0.042 0.065 -10000 0 -10000 0 0
SMAD3/SMAD4/IRF7 0.004 0.058 -10000 0 -0.58 1 1
TFE3 0.01 0.023 -10000 0 -10000 0 0
COL1A2 -0.1 0.26 -10000 0 -0.72 63 63
mesenchymal cell differentiation 0.003 0.09 0.62 7 -10000 0 7
DLX1 -0.064 0.2 -10000 0 -0.54 56 56
TCF3 0.012 0 -10000 0 -10000 0 0
FOS -0.008 0.11 -10000 0 -0.46 23 23
SMAD3/SMAD4/Max 0.013 0.049 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.006 0.016 -10000 0 -10000 0 0
ZBTB17 0.012 0.009 -10000 0 -10000 0 0
LAMC1 0.032 0.089 -10000 0 -0.77 4 4
TGIF2/HDAC complex/SMAD3/SMAD4 0.008 0.04 -10000 0 -10000 0 0
IRF7 0.009 0.046 -10000 0 -0.85 1 1
ESR1 -0.001 0.099 -10000 0 -0.49 15 15
HNF4A -0.027 0.17 -10000 0 -0.73 22 22
MEF2C -0.15 0.28 -10000 0 -0.78 28 28
SMAD2-3/SMAD4 0.004 0.045 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.01 0.023 -10000 0 -10000 0 0
IGHV3OR16-13 -0.003 0.018 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.012 0 -10000 0 -10000 0 0
CREBBP 0.012 0.009 -10000 0 -10000 0 0
SKIL 0.008 0.06 -10000 0 -0.85 2 2
HDAC1 0.012 0.024 -10000 0 -0.47 1 1
HDAC2 0.013 0.002 -10000 0 -10000 0 0
SNIP1 0.013 0.004 -10000 0 -10000 0 0
GCN5L2 -0.001 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.036 0.058 -10000 0 -10000 0 0
MSG1/HSC70 -0.043 0.19 -10000 0 -0.66 36 36
SMAD2 0.01 0.027 -10000 0 -10000 0 0
SMAD3 0.02 0.032 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.035 0.044 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.009 0.04 -10000 0 -0.29 4 4
NCOR1 0.013 0.002 -10000 0 -10000 0 0
NCOA2 0.011 0.023 -10000 0 -0.47 1 1
NCOA1 0.012 0 -10000 0 -10000 0 0
MYOD/E2A 0.001 0.08 -10000 0 -0.66 6 6
SMAD2-3/SMAD4/SP1/MIZ-1 0.034 0.077 -10000 0 -10000 0 0
IFNB1 0.03 0.085 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C -0.14 0.27 -10000 0 -0.76 24 24
CITED1 -0.066 0.25 -10000 0 -0.82 39 39
SMAD2-3/SMAD4/ARC105 0.035 0.058 -10000 0 -0.59 1 1
RBL1 0.012 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.042 0.083 -10000 0 -0.48 9 9
RUNX1-3/PEBPB2 -0.014 0.095 -10000 0 -0.63 9 9
SMAD7 0.047 0.078 -10000 0 -10000 0 0
MYC/MIZ-1 0 0.046 -10000 0 -0.67 1 1
SMAD3/SMAD4 -0.023 0.14 0.28 8 -0.51 1 9
IL10 0.025 0.13 -10000 0 -0.78 4 4
PIASy/HDAC complex 0.015 0.011 -10000 0 -10000 0 0
PIAS3 0.011 0.006 -10000 0 -10000 0 0
CDK2 0.012 0.009 -10000 0 -10000 0 0
IL5 0.022 0.13 -10000 0 -0.76 5 5
CDK4 0.004 0.086 -10000 0 -0.86 4 4
PIAS4 0.015 0.011 -10000 0 -10000 0 0
ATF3 0.007 0.052 -10000 0 -0.47 5 5
SMAD3/SMAD4/SP1 0.018 0.084 -10000 0 -10000 0 0
FOXG1 -0.019 0.14 -10000 0 -0.85 11 11
FOXO3 0.024 0.015 -10000 0 -10000 0 0
FOXO1 0.024 0.014 -10000 0 -10000 0 0
FOXO4 0.023 0.022 -10000 0 -10000 0 0
heart looping -0.15 0.28 -10000 0 -0.76 29 29
CEBPB 0.013 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.039 0.14 -10000 0 -0.62 11 11
MYOD1 -0.01 0.1 -10000 0 -0.85 6 6
SMAD3/SMAD4/HNF4 -0.019 0.13 -10000 0 -0.6 15 15
SMAD3/SMAD4/GATA3 -0.011 0.11 -10000 0 -0.57 11 11
SnoN/SIN3/HDAC complex/NCoR1 0.008 0.06 -10000 0 -0.85 2 2
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.013 0.1 -10000 0 -0.58 9 9
SMAD3/SMAD4/SP1-3 0.031 0.076 -10000 0 -10000 0 0
MED15 0.01 0.042 -10000 0 -0.85 1 1
SP1 0 0.055 -10000 0 -10000 0 0
SIN3B 0.013 0.002 -10000 0 -10000 0 0
SIN3A 0.013 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.18 0.3 -10000 0 -0.58 141 141
ITGB5 0.044 0.068 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.045 0.014 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.029 0.11 -10000 0 -0.54 3 3
AR -0.051 0.16 -10000 0 -0.47 54 54
negative regulation of cell growth 0.041 0.048 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD -0.003 0.081 -10000 0 -0.59 6 6
E2F5 0.006 0.073 -10000 0 -0.85 3 3
E2F4 0.012 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.094 0.23 -10000 0 -0.54 47 47
SMAD2-3/SMAD4/FOXO1-3a-4 0.041 0.063 -10000 0 -0.5 1 1
TFDP1 0.01 0.042 -10000 0 -0.85 1 1
SMAD3/SMAD4/AP1 0.041 0.069 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX2 -0.003 0.091 -10000 0 -0.62 7 7
TGIF2 0.012 0 -10000 0 -10000 0 0
TGIF1 0.012 0 -10000 0 -10000 0 0
ATF2 0.012 0 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.01 0.011 -9999 0 -10000 0 0
SVIL 0.005 0.065 -9999 0 -0.72 3 3
ZNF318 0.011 0.078 -9999 0 -0.86 3 3
JMJD2C -0.003 0.032 -9999 0 -0.12 26 26
T-DHT/AR/Ubc9 -0.018 0.11 -9999 0 -0.38 10 10
CARM1 0.012 0.002 -9999 0 -10000 0 0
PRDX1 0.013 0.002 -9999 0 -10000 0 0
PELP1 0.011 0.043 -9999 0 -0.85 1 1
CTNNB1 0.009 0.043 -9999 0 -0.85 1 1
AKT1 0.014 0.007 -9999 0 -10000 0 0
PTK2B 0.011 0.007 -9999 0 -10000 0 0
MED1 0.006 0.085 -9999 0 -0.85 4 4
MAK -0.012 0.16 -9999 0 -0.85 14 14
response to oxidative stress 0 0.002 -9999 0 -10000 0 0
HIP1 0.011 0.01 -9999 0 -10000 0 0
GSN 0.002 0.062 -9999 0 -0.46 7 7
NCOA2 0.011 0.023 -9999 0 -0.47 1 1
NCOA6 0.011 0.01 -9999 0 -10000 0 0
DNA-PK 0.008 0.031 -9999 0 -10000 0 0
NCOA4 0.012 0.001 -9999 0 -10000 0 0
PIAS3 0.011 0.007 -9999 0 -10000 0 0
cell proliferation -0.02 0.095 -9999 0 -0.5 14 14
XRCC5 0.014 0.006 -9999 0 -10000 0 0
UBE3A 0.009 0.016 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.074 0.16 -9999 0 -0.44 32 32
FHL2 0.001 0.11 -9999 0 -0.94 4 4
RANBP9 0.011 0.01 -9999 0 -10000 0 0
JMJD1A 0.006 0.035 -9999 0 -0.13 24 24
CDK6 -0.029 0.18 -9999 0 -0.85 20 20
TGFB1I1 0.003 0.077 -9999 0 -0.76 4 4
T-DHT/AR/CyclinD1 -0.025 0.12 -9999 0 -0.44 14 14
XRCC6 0.014 0.006 -9999 0 -10000 0 0
T-DHT/AR -0.01 0.12 -9999 0 -0.44 10 10
CTDSP1 0.012 0.003 -9999 0 -10000 0 0
CTDSP2 0.016 0.018 -9999 0 -10000 0 0
BRCA1 0.002 0.086 -9999 0 -0.86 4 4
TCF4 0.015 0.013 -9999 0 -10000 0 0
CDKN2A -0.24 0.39 -9999 0 -0.83 127 127
SRF 0.02 0.015 -9999 0 -10000 0 0
NKX3-1 -0.028 0.15 -9999 0 -0.94 9 9
KLK3 -0.016 0.18 -9999 0 -0.68 26 26
TMF1 0.012 0.003 -9999 0 -10000 0 0
HNRNPA1 0.014 0.01 -9999 0 -10000 0 0
AOF2 -0.002 0.012 -9999 0 -10000 0 0
APPL1 0.025 0.016 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.016 0.11 -9999 0 -0.38 10 10
AR -0.051 0.17 -9999 0 -0.47 54 54
UBA3 0.012 0.003 -9999 0 -10000 0 0
PATZ1 0.014 0.01 -9999 0 -10000 0 0
PAWR 0.012 0.003 -9999 0 -10000 0 0
PRKDC 0.014 0.006 -9999 0 -10000 0 0
PA2G4 0.015 0.011 -9999 0 -10000 0 0
UBE2I 0.012 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.014 0.099 -9999 0 -0.35 10 10
RPS6KA3 0.01 0.011 -9999 0 -10000 0 0
T-DHT/AR/ARA70 -0.019 0.11 -9999 0 -0.38 10 10
LATS2 0.014 0.009 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.013 0.1 -9999 0 -0.35 10 10
Cyclin D3/CDK11 p58 0.01 0.002 -9999 0 -10000 0 0
VAV3 -0.047 0.22 -9999 0 -0.83 29 29
KLK2 -0.059 0.17 -9999 0 -0.71 26 26
CASP8 0.013 0.004 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.009 0.1 -9999 0 -0.4 4 4
TMPRSS2 -0.042 0.19 -9999 0 -0.92 17 17
CCND1 0.003 0.084 -9999 0 -0.85 4 4
PIAS1 0.009 0.016 -9999 0 -10000 0 0
mol:T-DHT -0.001 0.023 -9999 0 -0.067 38 38
CDC2L1 0 0.001 -9999 0 -10000 0 0
PIAS4 0.008 0.024 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.045 0.17 -9999 0 -0.57 28 28
CMTM2 -0.01 0.13 -9999 0 -0.73 13 13
SNURF -0.082 0.18 -9999 0 -0.47 78 78
ZMIZ1 0.012 0.021 -9999 0 -10000 0 0
CCND3 0.013 0.001 -9999 0 -10000 0 0
TGIF1 0.014 0.01 -9999 0 -10000 0 0
FKBP4 0.007 0.06 -9999 0 -0.85 2 2
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.012 0 -9999 0 -10000 0 0
SPHK1 -0.025 0.18 -9999 0 -0.85 18 18
GNAI2 0.012 0 -9999 0 -10000 0 0
mol:S1P 0.008 0.066 -9999 0 -0.3 18 18
GNAO1 -0.094 0.2 -9999 0 -0.48 90 90
mol:Sphinganine-1-P -0.008 0.14 -9999 0 -0.66 18 18
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.026 0.055 -9999 0 -0.48 1 1
GNAI3 0.012 0 -9999 0 -10000 0 0
G12/G13 0.019 0 -9999 0 -10000 0 0
S1PR3 0.006 0.068 -9999 0 -0.66 4 4
S1PR2 0.01 0.042 -9999 0 -0.85 1 1
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.011 0.053 -9999 0 -0.26 18 18
S1PR5 -0.013 0.14 -9999 0 -0.85 12 12
S1PR4 0.003 0.088 -9999 0 -0.78 5 5
GNAI1 0.003 0.066 -9999 0 -0.47 8 8
S1P/S1P5/G12 0.004 0.11 -9999 0 -0.59 12 12
S1P/S1P3/Gq 0.021 0.064 -9999 0 -0.43 2 2
S1P/S1P4/Gi -0.037 0.14 -9999 0 -0.42 21 21
GNAQ 0.012 0 -9999 0 -10000 0 0
GNAZ -0.02 0.12 -9999 0 -0.47 28 28
GNA14 0.003 0.071 -9999 0 -0.52 7 7
GNA15 0.002 0.094 -9999 0 -0.85 5 5
GNA12 0.012 0 -9999 0 -10000 0 0
GNA13 0.012 0 -9999 0 -10000 0 0
GNA11 0.012 0 -9999 0 -10000 0 0
ABCC1 0.012 0 -9999 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.023 0.026 -9999 0 -10000 0 0
VDR 0.012 0 -9999 0 -10000 0 0
FAM120B 0.012 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.052 0.13 -9999 0 -0.4 9 9
RXRs/LXRs/DNA/Oxysterols -0.037 0.13 -9999 0 -0.49 9 9
MED1 0.004 0.084 -9999 0 -0.85 4 4
mol:9cRA 0.004 0.01 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.012 0.081 -9999 0 -0.6 2 2
RXRs/NUR77 -0.076 0.14 -9999 0 -0.48 6 6
RXRs/PPAR -0.063 0.12 -9999 0 -0.43 5 5
NCOR2 0.012 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 0.009 0 -9999 0 -10000 0 0
RARs/VDR/DNA/Vit D3 -0.005 0.046 -9999 0 -0.5 3 3
RARA 0.008 0.06 -9999 0 -0.85 2 2
NCOA1 0.012 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.012 0 -9999 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.019 0.049 -9999 0 -0.5 3 3
RARG 0.01 0.042 -9999 0 -0.85 1 1
RPS6KB1 0.035 0.04 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT 0.012 0.081 -9999 0 -0.6 2 2
THRA 0.006 0.073 -9999 0 -0.85 3 3
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 -0.074 0.13 -9999 0 -10000 0 0
NR1H4 -0.13 0.3 -9999 0 -0.69 85 85
RXRs/LXRs/DNA -0.049 0.13 -9999 0 -10000 0 0
NR1H2 0.017 0.008 -9999 0 -10000 0 0
NR1H3 0.017 0.008 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.065 0.12 -9999 0 -10000 0 0
NR4A1 0 0.077 -9999 0 -0.47 11 11
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.11 0.16 -9999 0 -0.43 47 47
RXRG -0.18 0.23 -9999 0 -0.46 171 171
RXR alpha/CCPG 0.021 0.017 -9999 0 -10000 0 0
RXRA 0.016 0.025 -9999 0 -0.46 1 1
RXRB 0.017 0.008 -9999 0 -10000 0 0
THRB -0.022 0.12 -9999 0 -0.47 30 30
PPARG 0.005 0.067 -9999 0 -0.53 6 6
PPARD 0.012 0 -9999 0 -10000 0 0
TNF -0.046 0.19 -9999 0 -0.8 19 19
mol:Oxysterols 0.004 0.009 -9999 0 -10000 0 0
cholesterol transport -0.037 0.13 -9999 0 -0.49 9 9
PPARA 0.012 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB 0.009 0.041 -9999 0 -0.47 3 3
RXRs/NUR77/BCL2 -0.078 0.13 -9999 0 -0.49 11 11
SREBF1 -0.027 0.13 -9999 0 -0.73 2 2
RXRs/RXRs/DNA/9cRA -0.074 0.13 -9999 0 -10000 0 0
ABCA1 -0.026 0.12 -9999 0 -10000 0 0
RARs/THRs -0.024 0.09 -9999 0 -0.63 5 5
RXRs/FXR -0.16 0.23 -9999 0 -0.61 59 59
BCL2 0.006 0.057 -9999 0 -0.47 6 6
IL2 signaling events mediated by PI3K

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
BCL2L1 0.036 0.076 -10000 0 -10000 0 0
UGCG 0.015 0.036 -10000 0 -0.55 1 1
AKT1/mTOR/p70S6K/Hsp90/TERT -0.025 0.13 -10000 0 -0.4 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.018 0.035 -10000 0 -0.55 1 1
mol:DAG -0.001 0.002 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.021 0.062 -10000 0 -0.41 2 2
FRAP1 0.038 0.1 -10000 0 -0.45 3 3
FOXO3 0.047 0.087 -10000 0 -10000 0 0
AKT1 0.041 0.091 -10000 0 -0.41 1 1
GAB2 0.011 0.043 -10000 0 -0.85 1 1
SMPD1 0.017 0.023 -10000 0 -10000 0 0
SGMS1 0.017 0.023 -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 0.019 0.029 -10000 0 -0.57 1 1
CALM1 0.012 0 -10000 0 -10000 0 0
cell proliferation 0.031 0.048 -10000 0 -10000 0 0
EIF3A 0.012 0 -10000 0 -10000 0 0
PI3K 0.022 0.033 -10000 0 -0.65 1 1
RPS6KB1 -0.006 0.067 -10000 0 -10000 0 0
mol:sphingomyelin -0.001 0.002 -10000 0 -10000 0 0
natural killer cell activation 0 0.002 -10000 0 -10000 0 0
JAK3 -0.023 0.18 -10000 0 -0.85 18 18
PIK3R1 0.015 0.002 -10000 0 -10000 0 0
JAK1 0.015 0.002 -10000 0 -10000 0 0
NFKB1 0.012 0 -10000 0 -10000 0 0
MYC 0.044 0.1 -10000 0 -0.78 3 3
MYB -0.1 0.27 -10000 0 -0.66 77 77
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.029 0.09 -10000 0 -0.46 1 1
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.009 0.062 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.029 0.089 -10000 0 -0.44 1 1
Rac1/GDP 0.025 0.027 -10000 0 -0.52 1 1
T cell proliferation 0.041 0.084 -10000 0 -0.41 1 1
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 -0.006 0.023 -10000 0 -0.053 77 77
PRKCZ 0.041 0.085 -10000 0 -0.43 1 1
NF kappa B1 p50/RelA -0.018 0.061 -10000 0 -0.43 1 1
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.03 0.082 -10000 0 -0.44 4 4
HSP90AA1 0.008 0.06 -10000 0 -0.85 2 2
RELA 0.012 0 -10000 0 -10000 0 0
IL2RA -0.056 0.23 -10000 0 -0.85 33 33
IL2RB 0.014 0.024 -10000 0 -0.47 1 1
TERT -0.27 0.4 -10000 0 -0.85 135 135
E2F1 -0.047 0.15 -10000 0 -0.33 79 79
SOS1 0.013 0.002 -10000 0 -10000 0 0
RPS6 0.012 0 -10000 0 -10000 0 0
mol:cAMP 0.002 0.011 0.025 77 -10000 0 77
PTPN11 0.013 0.002 -10000 0 -10000 0 0
IL2RG 0.001 0.095 -10000 0 -0.58 10 10
actin cytoskeleton organization 0.041 0.084 -10000 0 -0.41 1 1
GRB2 0.013 0.002 -10000 0 -10000 0 0
IL2 0.005 0.06 -10000 0 -0.85 2 2
PIK3CA 0.013 0.042 -10000 0 -0.85 1 1
Rac1/GTP 0.027 0.03 -10000 0 -0.5 1 1
LCK -0.008 0.14 -10000 0 -0.85 11 11
BCL2 0.037 0.13 -10000 0 -0.82 6 6
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.012 0 -10000 0 -10000 0 0
PTK2 0.012 0 -10000 0 -10000 0 0
CRKL -0.02 0.12 -10000 0 -0.42 28 28
GRB2/SOS1/SHC 0 0 -10000 0 -10000 0 0
HRAS 0.012 0 -10000 0 -10000 0 0
IRS1/Crk -0.02 0.12 -10000 0 -0.42 28 28
IGF-1R heterotetramer/IGF1/PTP1B -0.052 0.14 -10000 0 -0.53 28 28
AKT1 0.002 0.11 -10000 0 -0.57 1 1
BAD 0.009 0.1 -10000 0 -0.52 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.02 0.12 -10000 0 -0.42 28 28
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.021 0.12 -10000 0 -0.42 28 28
RAF1 0.014 0.099 -10000 0 -0.49 1 1
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.012 0.12 -10000 0 -0.53 2 2
YWHAZ 0.012 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.031 0.13 -10000 0 -0.46 28 28
PIK3CA 0.01 0.042 -10000 0 -0.85 1 1
RPS6KB1 0.002 0.11 -10000 0 -0.57 1 1
GNB2L1 0.012 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.011 0.087 -10000 0 -0.42 1 1
PXN 0.012 0 -10000 0 -10000 0 0
PIK3R1 0.012 0 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.019 0 -10000 0 -10000 0 0
HRAS/GTP -0.035 0.095 -10000 0 -0.58 1 1
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.008 0.12 -10000 0 -0.42 27 27
IGF-1R heterotetramer -0.004 0.083 -10000 0 -0.78 4 4
IGF-1R heterotetramer/IGF1/IRS/Nck -0.02 0.12 -10000 0 -0.42 28 28
Crk/p130 Cas/Paxillin -0.005 0.11 -10000 0 -0.62 1 1
IGF1R -0.004 0.083 -10000 0 -0.78 4 4
IGF1 -0.071 0.23 -10000 0 -0.64 53 53
IRS2/Crk -0.026 0.13 -10000 0 -0.53 6 6
PI3K -0.013 0.12 -10000 0 -0.51 3 3
apoptosis -0.016 0.093 0.44 1 -10000 0 1
HRAS/GDP 0.009 0 -10000 0 -10000 0 0
PRKCD -0.008 0.12 -10000 0 -0.58 2 2
RAF1/14-3-3 E 0.021 0.089 -10000 0 -0.42 1 1
BAD/14-3-3 0.016 0.098 -10000 0 -0.48 1 1
PRKCZ 0.002 0.11 -10000 0 -0.57 1 1
Crk/p130 Cas/Paxillin/FAK1 -0.029 0.079 -10000 0 -10000 0 0
PTPN1 0.012 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.016 0.13 -10000 0 -0.35 53 53
BCAR1 0.012 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.046 0.13 -10000 0 -0.46 29 29
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.012 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.02 0.12 -10000 0 -0.42 28 28
GRB10 0.01 0.042 -10000 0 -0.85 1 1
PTPN11 -0.02 0.12 -10000 0 -0.42 28 28
IRS1 -0.031 0.13 -10000 0 -0.46 28 28
IRS2 -0.035 0.14 -10000 0 -0.44 33 33
IGF-1R heterotetramer/IGF1 -0.051 0.19 -10000 0 -0.66 28 28
GRB2 0.012 0 -10000 0 -10000 0 0
PDPK1 -0.006 0.11 -10000 0 -0.53 2 2
YWHAE 0.012 0 -10000 0 -10000 0 0
PRKD1 -0.015 0.14 -10000 0 -0.6 8 8
SHC1 0.012 0 -10000 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 0.061 0.17 -10000 0 -0.78 6 6
NCK1/PAK1/Dok-R -0.019 0.061 -10000 0 -0.39 5 5
NCK1/Dok-R 0.039 0.12 -10000 0 -0.86 6 6
PIK3CA 0.01 0.042 -10000 0 -0.85 1 1
mol:beta2-estradiol -0.009 0.021 0.23 3 -10000 0 3
RELA 0.012 0 -10000 0 -10000 0 0
SHC1 0.013 0.002 -10000 0 -10000 0 0
Rac/GDP 0.009 0 -10000 0 -10000 0 0
F2 -0.14 0.32 -10000 0 -0.87 65 65
TNIP2 0.012 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.014 0.098 -10000 0 -0.81 6 6
FN1 -0.072 0.26 -10000 0 -0.84 41 41
PLD2 0.066 0.13 -10000 0 -0.89 6 6
PTPN11 0.012 0 -10000 0 -10000 0 0
GRB14 -0.11 0.29 -10000 0 -0.74 68 68
ELK1 0.074 0.12 -10000 0 -0.82 6 6
GRB7 -0.079 0.26 -10000 0 -0.84 45 45
PAK1 0.012 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.061 0.18 -10000 0 -0.88 13 13
CDKN1A 0.047 0.19 -10000 0 -0.64 5 5
ITGA5 -0.002 0.11 -10000 0 -0.85 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.039 0.12 -10000 0 -0.86 6 6
CRK 0.012 0 -10000 0 -10000 0 0
mol:NO 0.063 0.15 -10000 0 -0.58 7 7
PLG 0.053 0.14 -10000 0 -0.9 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.037 0.14 -10000 0 -0.76 6 6
GRB2 0.012 0 -10000 0 -10000 0 0
PIK3R1 0.013 0.002 -10000 0 -10000 0 0
ANGPT2 -0.021 0.24 0.42 1 -0.66 34 35
BMX 0.027 0.17 -10000 0 -0.99 6 6
ANGPT1 0.05 0.13 -10000 0 -1.1 3 3
tube development 0.041 0.2 -10000 0 -0.63 7 7
ANGPT4 -0.002 0.094 -10000 0 -0.85 5 5
response to hypoxia 0.002 0.009 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.007 0.21 -10000 0 -0.97 6 6
alpha5/beta1 Integrin 0.006 0.1 -10000 0 -0.74 7 7
FGF2 -0.011 0.11 -10000 0 -0.49 19 19
STAT5A (dimer) 0.042 0.22 -10000 0 -0.75 6 6
mol:L-citrulline 0.063 0.15 -10000 0 -0.58 7 7
AGTR1 -0.12 0.24 -10000 0 -0.51 108 108
MAPK14 0.06 0.15 -10000 0 -0.94 6 6
Tie2/SHP2 -0.009 0.083 -10000 0 -0.95 3 3
TEK 0.029 0.098 -10000 0 -1 3 3
RPS6KB1 0.065 0.16 -10000 0 -0.76 6 6
Angiotensin II/AT1 -0.09 0.18 -10000 0 -0.37 108 108
Tie2/Ang1/GRB2 0.063 0.13 -10000 0 -0.91 6 6
MAPK3 0.069 0.12 -10000 0 -0.83 6 6
MAPK1 0.069 0.12 -10000 0 -0.83 6 6
Tie2/Ang1/GRB7 0.009 0.2 -10000 0 -0.98 6 6
NFKB1 0.012 0 -10000 0 -10000 0 0
MAPK8 0.066 0.13 -10000 0 -0.89 6 6
PI3K 0.058 0.17 -10000 0 -0.88 6 6
FES 0.057 0.15 -10000 0 -0.97 6 6
Crk/Dok-R 0.039 0.12 -10000 0 -0.86 6 6
Tie2/Ang1/ABIN2 0.063 0.13 -10000 0 -0.91 6 6
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.062 0.16 -10000 0 -0.7 6 6
STAT5A 0.013 0 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.065 0.16 -10000 0 -0.76 6 6
Tie2/Ang2 0.028 0.24 -10000 0 -0.74 15 15
Tie2/Ang1 0.063 0.14 -10000 0 -0.95 6 6
FOXO1 0.061 0.18 -10000 0 -0.7 6 6
ELF1 0.021 0.009 -10000 0 -10000 0 0
ELF2 0.063 0.13 -10000 0 -0.89 6 6
mol:Choline 0.066 0.13 -10000 0 -0.86 6 6
cell migration -0.023 0.054 -10000 0 -0.24 1 1
FYN 0.037 0.21 -10000 0 -0.71 7 7
DOK2 0.01 0.033 -10000 0 -0.47 2 2
negative regulation of cell cycle 0.048 0.18 -10000 0 -0.58 5 5
ETS1 0.021 0.02 -10000 0 -10000 0 0
PXN 0.07 0.14 -10000 0 -0.63 6 6
ITGB1 0.01 0.042 -10000 0 -0.85 1 1
NOS3 0.062 0.16 -10000 0 -0.66 7 7
RAC1 0.012 0 -10000 0 -10000 0 0
TNF -0.013 0.16 -10000 0 -0.74 19 19
MAPKKK cascade 0.066 0.13 -10000 0 -0.86 6 6
RASA1 0.012 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc 0.062 0.13 -10000 0 -0.91 6 6
NCK1 0.012 0 -10000 0 -10000 0 0
vasculogenesis 0.063 0.14 -10000 0 -0.52 7 7
mol:Phosphatidic acid 0.066 0.13 -10000 0 -0.86 6 6
mol:Angiotensin II -0.001 0.009 -10000 0 -10000 0 0
mol:NADP 0.063 0.15 -10000 0 -0.58 7 7
Rac1/GTP -0.031 0.11 -10000 0 -0.71 6 6
MMP2 0.064 0.14 -10000 0 -0.89 6 6
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.034 0.18 -9999 0 -0.66 32 32
CRKL 0.009 0.083 -9999 0 -0.42 1 1
mol:PIP3 -0.019 0.004 -9999 0 -10000 0 0
AKT1 0.001 0.003 -9999 0 -10000 0 0
PTK2B 0.012 0 -9999 0 -10000 0 0
RAPGEF1 0.016 0.079 -9999 0 -10000 0 0
RANBP10 0.012 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.042 -9999 0 -0.85 1 1
HGF/MET/SHIP2 -0.059 0.17 -9999 0 -0.58 39 39
MAP3K5 0.017 0.088 -9999 0 -0.43 2 2
HGF/MET/CIN85/CBL/ENDOPHILINS -0.025 0.17 -9999 0 -0.53 39 39
AP1 -0.013 0.085 -9999 0 -0.44 3 3
mol:SU11274 0 0 -9999 0 -10000 0 0
SHC1 0.012 0 -9999 0 -10000 0 0
apoptosis -0.029 0.16 -9999 0 -0.69 23 23
STAT3 (dimer) 0.01 0.088 -9999 0 -0.47 1 1
GAB1/CRKL/SHP2/PI3K -0.022 0.063 -9999 0 -10000 0 0
INPP5D 0.007 0.064 -9999 0 -0.72 3 3
CBL/CRK 0.015 0.085 -9999 0 -0.49 2 2
PTPN11 0.012 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
PLCG1 0.012 0 -9999 0 -10000 0 0
PTEN 0.012 0 -9999 0 -10000 0 0
ELK1 -0.021 0.078 -9999 0 -0.29 32 32
mol:SU5416 0 0 -9999 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.018 0.051 -9999 0 -0.31 1 1
PAK1 0.007 0.003 -9999 0 -10000 0 0
HGF/MET/RANBP10 -0.058 0.17 -9999 0 -0.58 38 38
HRAS -0.004 0.12 -9999 0 -0.58 2 2
DOCK1 0.016 0.079 -9999 0 -0.4 1 1
GAB1 0.002 0.087 -9999 0 -0.45 1 1
CRK 0.009 0.083 -9999 0 -0.42 1 1
mol:PHA665752 0 0 -9999 0 -10000 0 0
mol:GDP -0.042 0.12 -9999 0 -0.48 8 8
JUN 0.012 0 -9999 0 -10000 0 0
EntrezGene:200958 0 0 -9999 0 -10000 0 0
HGF/MET -0.019 0.095 -9999 0 -0.31 35 35
PIK3R1 0.012 0 -9999 0 -10000 0 0
cell morphogenesis 0.035 0.089 -9999 0 -10000 0 0
GRB2/SHC -0.001 0.086 -9999 0 -0.42 1 1
FOS -0.014 0.11 -9999 0 -0.47 23 23
GLMN -0.001 0.013 -9999 0 -0.27 1 1
cell motility -0.021 0.078 -9999 0 -0.29 32 32
HGF/MET/MUC20 -0.058 0.17 -9999 0 -0.59 38 38
cell migration -0.002 0.085 -9999 0 -0.41 1 1
GRB2 0.012 0 -9999 0 -10000 0 0
CBL 0.01 0.042 -9999 0 -0.85 1 1
MET/RANBP10 -0.034 0.18 -9999 0 -0.65 33 33
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.003 0.096 -9999 0 -0.5 1 1
MET/MUC20 -0.044 0.18 -9999 0 -0.66 33 33
RAP1B 0.019 0.085 -9999 0 -10000 0 0
RAP1A 0.022 0.076 -9999 0 -10000 0 0
HGF/MET/RANBP9 -0.058 0.17 -9999 0 -0.58 38 38
RAF1 0.004 0.12 -9999 0 -0.54 2 2
STAT3 0.01 0.089 -9999 0 -0.47 1 1
cell proliferation 0.013 0.11 -9999 0 -0.6 1 1
RPS6KB1 0.001 0.036 -9999 0 -10000 0 0
MAPK3 -0.024 0.071 -9999 0 -0.27 32 32
MAPK1 -0.024 0.071 -9999 0 -0.27 32 32
RANBP9 0.012 0 -9999 0 -10000 0 0
MAPK8 0.034 0.074 -9999 0 -10000 0 0
SRC 0.01 0.091 -9999 0 -0.46 1 1
PI3K -0.003 0.089 -9999 0 -0.45 2 2
MET/Glomulin -0.037 0.16 -9999 0 -0.59 33 33
SOS1 0.012 0 -9999 0 -10000 0 0
MAP2K1 0.011 0.11 -9999 0 -0.5 2 2
MET -0.055 0.23 -9999 0 -0.84 33 33
MAP4K1 0.01 0.093 -9999 0 -0.44 3 3
PTK2 0.012 0 -9999 0 -10000 0 0
MAP2K2 0.011 0.11 -9999 0 -0.5 2 2
BAD 0.007 0.003 -9999 0 -10000 0 0
MAP2K4 0.023 0.083 -9999 0 -0.39 2 2
SHP2/GRB2/SOS1/GAB1 -0.034 0.1 -9999 0 -0.53 1 1
INPPL1 0.01 0.042 -9999 0 -0.85 1 1
PXN 0.012 0 -9999 0 -10000 0 0
SH3KBP1 0.012 0 -9999 0 -10000 0 0
HGS -0.01 0.089 -9999 0 -0.28 34 34
PLCgamma1/PKC 0.009 0 -9999 0 -10000 0 0
HGF -0.008 0.12 -9999 0 -0.64 13 13
RASA1 0.012 0 -9999 0 -10000 0 0
NCK1 0.012 0 -9999 0 -10000 0 0
PTPRJ 0.008 0.06 -9999 0 -0.85 2 2
NCK/PLCgamma1 0 0.087 -9999 0 -0.43 1 1
PDPK1 -0.008 0.003 -9999 0 -10000 0 0
HGF/MET/SHIP -0.061 0.17 -9999 0 -0.58 40 40
Signaling events mediated by PRL

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
CCNE1 -0.11 0.3 -10000 0 -0.85 60 60
mol:Halofuginone 0.005 0 -10000 0 -10000 0 0
ITGA1 -0.006 0.13 -10000 0 -0.85 9 9
CDKN1A 0.027 0.036 -10000 0 -0.58 1 1
PRL-3/alpha Tubulin 0.015 0.047 -10000 0 -0.66 2 2
mol:Ca2+ -0.082 0.22 0.39 1 -0.63 55 56
AGT -0.096 0.28 -10000 0 -0.8 55 55
CCNA2 0.032 0.042 -10000 0 -10000 0 0
TUBA1B 0.012 0 -10000 0 -10000 0 0
EGR1 0.012 0.06 -10000 0 -0.32 13 13
CDK2/Cyclin E1 -0.037 0.18 -10000 0 -0.47 61 61
MAPK3 0.018 0.047 -10000 0 -0.66 2 2
PRL-2 /Rab GGTase beta 0.019 0 -10000 0 -10000 0 0
MAPK1 0.018 0.047 -10000 0 -0.66 2 2
PTP4A1 0.027 0.045 -10000 0 -10000 0 0
PTP4A3 0.008 0.06 -10000 0 -0.85 2 2
PTP4A2 0.012 0 -10000 0 -10000 0 0
ITGB1 0.017 0.058 -10000 0 -0.66 3 3
SRC 0.012 0 -10000 0 -10000 0 0
RAC1 0.027 0.029 -10000 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0.019 0 -10000 0 -10000 0 0
PRL-1/ATF-5 0.03 0.049 -10000 0 -0.49 1 1
RABGGTA 0.012 0 -10000 0 -10000 0 0
BCAR1 0.002 0.027 0.39 2 -10000 0 2
RHOC 0.027 0.029 -10000 0 -10000 0 0
RHOA 0.027 0.029 -10000 0 -10000 0 0
cell motility 0.031 0.03 -10000 0 -10000 0 0
PRL-1/alpha Tubulin 0.031 0.042 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.001 0.11 -10000 0 -0.66 11 11
ROCK1 0.031 0.03 -10000 0 -10000 0 0
RABGGTB 0.012 0 -10000 0 -10000 0 0
CDK2 0.012 0 -10000 0 -10000 0 0
mitosis 0.027 0.045 -10000 0 -10000 0 0
ATF5 0.01 0.042 -10000 0 -0.85 1 1
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.009 0.1 -9999 0 -0.53 11 11
MAP4K1 -0.009 0.12 -9999 0 -0.6 15 15
MAP3K8 0.008 0.06 -9999 0 -0.85 2 2
PRKCB -0.018 0.12 -9999 0 -0.48 26 26
DBNL 0.012 0 -9999 0 -10000 0 0
CRKL 0.012 0 -9999 0 -10000 0 0
MAP3K1 0.029 0.064 -9999 0 -0.41 1 1
JUN 0 0.14 -9999 0 -0.54 25 25
MAP3K7 0.029 0.064 -9999 0 -0.41 1 1
GRAP2 -0.001 0.08 -9999 0 -0.47 12 12
CRK 0.012 0 -9999 0 -10000 0 0
MAP2K4 0.035 0.065 -9999 0 -0.39 1 1
LAT 0.008 0.06 -9999 0 -0.85 2 2
LCP2 0.012 0 -9999 0 -10000 0 0
MAPK8 -0.007 0.15 -9999 0 -0.57 26 26
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.022 0.068 -9999 0 -0.4 5 5
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.02 0.087 -9999 0 -0.52 7 7
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 -0.006 0.12 -10000 0 -0.81 9 9
GNB1/GNG2 -0.058 0.059 -10000 0 -0.21 6 6
AKT1 -0.031 0.095 -10000 0 -10000 0 0
EGF -0.078 0.26 -10000 0 -0.82 44 44
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.031 0.045 -10000 0 -10000 0 0
mol:Ca2+ -0.06 0.13 -10000 0 -0.32 8 8
LYN 0.031 0.045 -10000 0 -0.35 1 1
RhoA/GTP -0.039 0.04 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.069 0.14 -10000 0 -0.36 7 7
GNG2 0.01 0.042 -10000 0 -0.85 1 1
ARRB2 0.012 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.029 0.045 -10000 0 -0.37 1 1
G beta5/gamma2 -0.068 0.074 -10000 0 -0.29 6 6
PRKCH -0.065 0.14 -10000 0 -0.37 7 7
DNM1 -0.021 0.17 -10000 0 -0.85 16 16
TXA2/TP beta/beta Arrestin3 -0.013 0.053 -10000 0 -0.26 16 16
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.015 0.12 -10000 0 -0.48 23 23
G12 family/GTP -0.093 0.095 -10000 0 -0.32 7 7
ADRBK1 0.01 0.042 -10000 0 -0.85 1 1
ADRBK2 0.012 0 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.007 0.009 -10000 0 -10000 0 0
mol:GDP 0.029 0.083 0.31 1 -10000 0 1
mol:NADP 0.004 0.084 -10000 0 -0.85 4 4
RAB11A 0.012 0 -10000 0 -10000 0 0
PRKG1 0.005 0.072 -10000 0 -0.62 5 5
mol:IP3 -0.077 0.15 -10000 0 -0.4 8 8
cell morphogenesis 0.007 0.009 -10000 0 -10000 0 0
PLCB2 -0.1 0.19 -10000 0 -0.56 8 8
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.025 0.13 -10000 0 -0.4 23 23
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.031 0.045 -10000 0 -0.35 1 1
RHOA 0.012 0 -10000 0 -10000 0 0
PTGIR 0.012 0 -10000 0 -10000 0 0
PRKCB1 -0.073 0.15 -10000 0 -0.37 12 12
GNAQ 0.012 0 -10000 0 -10000 0 0
mol:L-citrulline 0.004 0.084 -10000 0 -0.85 4 4
TXA2/TXA2-R family -0.11 0.2 -10000 0 -0.48 44 44
LCK 0.019 0.081 -10000 0 -0.39 11 11
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.012 0.051 -10000 0 -0.44 2 2
TXA2-R family/G12 family/GDP/G beta/gamma 0.027 0.019 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.009 0.04 -10000 0 -10000 0 0
MAPK14 -0.039 0.1 -10000 0 -0.25 1 1
TGM2/GTP -0.096 0.18 -10000 0 -0.49 10 10
MAPK11 -0.039 0.1 -10000 0 -0.25 1 1
ARHGEF1 -0.032 0.082 -10000 0 -10000 0 0
GNAI2 0.012 0 -10000 0 -10000 0 0
JNK cascade -0.081 0.16 -10000 0 -0.36 44 44
RAB11/GDP 0.013 0.001 -10000 0 -10000 0 0
ICAM1 -0.057 0.13 -10000 0 -0.4 10 10
cAMP biosynthetic process -0.083 0.15 -10000 0 -0.38 9 9
Gq family/GTP/EBP50 0.021 0.039 -10000 0 -0.25 5 5
actin cytoskeleton reorganization 0.007 0.009 -10000 0 -10000 0 0
SRC 0.031 0.045 -10000 0 -0.35 1 1
GNB5 0.012 0 -10000 0 -10000 0 0
GNB1 0.012 0 -10000 0 -10000 0 0
EGF/EGFR 0.006 0.081 -10000 0 -0.3 1 1
VCAM1 -0.061 0.13 -10000 0 -0.33 9 9
TP beta/Gq family/GDP/G beta5/gamma2 0.029 0.045 -10000 0 -0.37 1 1
platelet activation -0.053 0.14 -10000 0 -0.32 6 6
PGI2/IP 0.007 0.004 -10000 0 -10000 0 0
PRKACA 0.006 0.057 -10000 0 -0.34 1 1
Gq family/GDP/G beta5/gamma2 0.027 0.045 -10000 0 -0.38 1 1
TXA2/TP beta/beta Arrestin2 -0.016 0.074 -10000 0 -0.38 16 16
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.013 0.054 -10000 0 -10000 0 0
mol:DAG -0.08 0.16 -10000 0 -0.43 10 10
EGFR -0.022 0.16 -10000 0 -0.7 20 20
TXA2/TP alpha -0.11 0.19 -10000 0 -0.51 12 12
Gq family/GTP -0.005 0.037 -10000 0 -0.23 3 3
YES1 0.031 0.045 -10000 0 -0.35 1 1
GNAI2/GTP -0.01 0.041 -10000 0 -0.4 1 1
PGD2/DP -0.013 0.083 -10000 0 -0.35 23 23
SLC9A3R1 0.012 0 -10000 0 -10000 0 0
FYN 0.031 0.045 -10000 0 -10000 0 0
mol:NO 0.004 0.084 -10000 0 -0.85 4 4
GNA15 0.002 0.094 -10000 0 -0.85 5 5
PGK/cGMP -0.002 0.074 -10000 0 -0.48 9 9
RhoA/GDP 0.013 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.021 0.085 -10000 0 -10000 0 0
NOS3 0.004 0.084 -10000 0 -0.85 4 4
RAC1 0.012 0 -10000 0 -10000 0 0
PRKCA -0.064 0.14 -10000 0 -0.37 7 7
PRKCB -0.072 0.14 -10000 0 -0.38 10 10
PRKCE -0.062 0.14 -10000 0 -0.37 8 8
PRKCD -0.067 0.14 -10000 0 -0.38 9 9
PRKCG -0.16 0.22 -10000 0 -0.51 55 55
muscle contraction -0.1 0.19 -10000 0 -0.45 44 44
PRKCZ -0.067 0.14 -10000 0 -0.36 7 7
ARR3 0.001 0.06 -10000 0 -0.85 2 2
TXA2/TP beta 0.004 0.053 -10000 0 -0.45 1 1
PRKCQ -0.069 0.14 -10000 0 -0.37 9 9
MAPKKK cascade -0.091 0.17 -10000 0 -0.47 9 9
SELE -0.082 0.16 -10000 0 -0.35 80 80
TP beta/GNAI2/GDP/G beta/gamma 0.03 0.054 -10000 0 -0.43 1 1
ROCK1 0.012 0 -10000 0 -10000 0 0
GNA14 0.003 0.071 -10000 0 -0.52 7 7
chemotaxis -0.12 0.22 -10000 0 -0.54 44 44
GNA12 0.012 0 -10000 0 -10000 0 0
GNA13 0.012 0 -10000 0 -10000 0 0
GNA11 0.012 0 -10000 0 -10000 0 0
Rac1/GTP 0.004 0.005 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.01 0.04 -10000 0 -10000 0 0
RFC1 0.01 0.04 -10000 0 -10000 0 0
PRKDC 0.01 0.04 -10000 0 -10000 0 0
RIPK1 0.013 0.003 -10000 0 -10000 0 0
CASP7 0 0.055 0.24 17 -10000 0 17
FASLG/FAS/FADD/FAF1 0.003 0.08 0.23 19 -0.31 6 25
MAP2K4 0.014 0.11 -10000 0 -0.42 5 5
mol:ceramide 0.012 0.089 -10000 0 -0.42 5 5
GSN 0.006 0.051 -10000 0 -0.27 1 1
FASLG/FAS/FADD/FAF1/Caspase 8 0.016 0.08 -10000 0 -0.35 9 9
FAS 0.012 0.005 -10000 0 -10000 0 0
BID 0.01 0.049 -10000 0 -10000 0 0
MAP3K1 0.023 0.074 -10000 0 -10000 0 0
MAP3K7 0.011 0.004 -10000 0 -10000 0 0
RB1 0.01 0.04 -10000 0 -10000 0 0
CFLAR 0.013 0.003 -10000 0 -10000 0 0
HGF/MET -0.071 0.18 -10000 0 -0.58 44 44
ARHGDIB 0.009 0.049 -10000 0 -0.56 1 1
FADD 0.012 0.005 -10000 0 -10000 0 0
actin filament polymerization -0.006 0.051 0.26 1 -10000 0 1
NFKB1 -0.027 0.065 -10000 0 -0.28 1 1
MAPK8 0.003 0.16 -10000 0 -0.54 4 4
DFFA 0.01 0.04 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.01 0.04 -10000 0 -10000 0 0
FAS/FADD/MET -0.024 0.16 -10000 0 -0.57 32 32
CFLAR/RIP1 0.015 0.006 -10000 0 -10000 0 0
FAIM3 -0.025 0.18 -10000 0 -0.85 18 18
FAF1 0.012 0.005 -10000 0 -10000 0 0
PARP1 0.009 0.049 -10000 0 -0.56 1 1
DFFB 0.01 0.04 -10000 0 -10000 0 0
CHUK -0.024 0.057 -10000 0 -10000 0 0
FASLG -0.012 0.13 -10000 0 -0.62 16 16
FAS/FADD 0.017 0.008 -10000 0 -10000 0 0
HGF -0.008 0.12 -10000 0 -0.64 13 13
LMNA 0.009 0.037 -10000 0 -10000 0 0
CASP6 0.01 0.04 -10000 0 -10000 0 0
CASP10 0.011 0.024 -10000 0 -0.46 1 1
CASP3 0.012 0.048 0.25 6 -10000 0 6
PTPN13 -0.011 0.12 -10000 0 -0.56 17 17
CASP8 0.017 0.079 0.39 18 -10000 0 18
IL6 -0.1 0.37 -10000 0 -1 56 56
MET -0.055 0.23 -10000 0 -0.84 33 33
ICAD/CAD 0.01 0.039 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 0.012 0.09 -10000 0 -0.43 5 5
activation of caspase activity by cytochrome c 0.01 0.049 -10000 0 -10000 0 0
PAK2 0.01 0.04 -10000 0 -10000 0 0
BCL2 0.006 0.057 -10000 0 -0.47 6 6
Class I PI3K signaling events

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
ARF5/GTP -0.019 0.085 -9999 0 -10000 0 0
DAPP1 -0.007 0.1 -9999 0 -0.36 15 15
Src family/SYK family/BLNK-LAT/BTK-ITK -0.015 0.15 -9999 0 -0.55 14 14
mol:DAG 0.011 0.092 -9999 0 -0.29 12 12
HRAS 0.012 0.006 -9999 0 -10000 0 0
RAP1A 0.012 0.006 -9999 0 -10000 0 0
ARF5/GDP 0.029 0.05 -9999 0 -0.36 2 2
PLCG2 0 0.096 -9999 0 -0.66 8 8
PLCG1 0.012 0 -9999 0 -10000 0 0
ARF5 0.012 0 -9999 0 -10000 0 0
mol:GTP -0.02 0.091 -9999 0 -0.44 19 19
ARF1/GTP -0.018 0.081 -9999 0 -0.39 19 19
RHOA 0.012 0 -9999 0 -10000 0 0
YES1 0.012 0 -9999 0 -10000 0 0
RAP1A/GTP -0.02 0.09 -9999 0 -0.43 19 19
ADAP1 -0.023 0.096 -9999 0 -0.42 23 23
ARAP3 -0.02 0.089 -9999 0 -0.43 19 19
INPPL1 0.01 0.042 -9999 0 -0.85 1 1
PREX1 0.012 0 -9999 0 -10000 0 0
ARHGEF6 0.008 0.047 -9999 0 -0.47 4 4
ARHGEF7 0.01 0.042 -9999 0 -0.85 1 1
ARF1 0.012 0 -9999 0 -10000 0 0
NRAS 0.012 0.006 -9999 0 -10000 0 0
FYN 0.012 0 -9999 0 -10000 0 0
ARF6 0.012 0 -9999 0 -10000 0 0
FGR 0.012 0 -9999 0 -10000 0 0
mol:Ca2+ 0.016 0.049 -9999 0 -10000 0 0
mol:IP4 0 0 -9999 0 -10000 0 0
TIAM1 -0.003 0.1 -9999 0 -0.62 10 10
ZAP70 -0.028 0.18 -9999 0 -0.8 21 21
mol:IP3 0.017 0.066 -9999 0 -10000 0 0
LYN 0.012 0 -9999 0 -10000 0 0
ARF1/GDP 0.029 0.05 -9999 0 -0.34 3 3
RhoA/GDP -0.019 0.079 -9999 0 -10000 0 0
PDK1/Src/Hsp90 -0.003 0.04 -9999 0 -0.57 2 2
BLNK -0.009 0.1 -9999 0 -0.47 19 19
actin cytoskeleton reorganization 0.037 0.086 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
PLEKHA2 0.023 0.053 -9999 0 -0.57 3 3
RAC1 0.012 0 -9999 0 -10000 0 0
PTEN 0.002 0.01 -9999 0 -10000 0 0
HSP90AA1 0.008 0.06 -9999 0 -0.85 2 2
ARF6/GTP -0.019 0.085 -9999 0 -10000 0 0
RhoA/GTP -0.019 0.086 -9999 0 -0.41 19 19
Src family/SYK family/BLNK-LAT -0.014 0.14 -9999 0 -0.51 12 12
BLK -0.11 0.25 -9999 0 -0.56 86 86
PDPK1 0.012 0 -9999 0 -10000 0 0
CYTH1 -0.019 0.086 -9999 0 -0.41 19 19
HCK 0.012 0 -9999 0 -10000 0 0
CYTH3 -0.019 0.086 -9999 0 -0.41 19 19
CYTH2 -0.019 0.086 -9999 0 -0.41 19 19
KRAS -0.022 0.17 -9999 0 -0.85 17 17
GO:0030676 0 0 -9999 0 -10000 0 0
FOXO3 0.028 0.059 -9999 0 -0.39 2 2
SGK1 -0.012 0.054 -9999 0 -0.43 2 2
INPP5D 0.007 0.064 -9999 0 -0.72 3 3
mol:GDP 0.023 0.052 -9999 0 -0.36 3 3
SOS1 0.012 0 -9999 0 -10000 0 0
SYK 0.009 0.048 -9999 0 -0.66 2 2
ARF6/GDP -0.019 0.077 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.02 0.091 -9999 0 -0.44 19 19
ARAP3/RAP1A/GTP -0.02 0.091 -9999 0 -0.44 19 19
VAV1 0.003 0.088 -9999 0 -0.78 5 5
mol:PI-3-4-P2 0.016 0.06 -9999 0 -0.57 4 4
RAS family/GTP/PI3K Class I 0.008 0.099 -9999 0 -0.44 19 19
PLEKHA1 0.022 0.055 -9999 0 -0.57 3 3
Rac1/GDP 0.029 0.05 -9999 0 -0.34 3 3
LAT 0.008 0.06 -9999 0 -0.85 2 2
Rac1/GTP 0.025 0.069 -9999 0 -0.56 3 3
ITK -0.038 0.12 -9999 0 -0.43 36 36
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.006 0.12 -9999 0 -0.42 12 12
LCK -0.01 0.14 -9999 0 -0.85 11 11
BTK -0.032 0.11 -9999 0 -0.43 28 28
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.019 0 -10000 0 -10000 0 0
ATM 0.01 0.042 -10000 0 -0.85 1 1
UBE2D3 0.012 0 -10000 0 -10000 0 0
PRKDC 0.012 0 -10000 0 -10000 0 0
ATR 0.012 0 -10000 0 -10000 0 0
UBE2L3 0.012 0 -10000 0 -10000 0 0
FANCD2 0.012 0.069 -10000 0 -0.37 13 13
protein ubiquitination -0.076 0.18 -10000 0 -0.5 63 63
XRCC5 0.012 0 -10000 0 -10000 0 0
XRCC6 0.012 0 -10000 0 -10000 0 0
M/R/N Complex -0.001 0.028 -10000 0 -0.57 1 1
MRE11A 0.01 0.042 -10000 0 -0.85 1 1
DNA-PK 0 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.027 0.064 -10000 0 -0.41 1 1
FANCF 0.01 0.042 -10000 0 -0.85 1 1
BRCA1 0.004 0.084 -10000 0 -0.85 4 4
CCNE1 -0.11 0.3 -10000 0 -0.85 60 60
CDK2/Cyclin E1 -0.079 0.24 -10000 0 -0.66 60 60
FANCG 0.008 0.06 -10000 0 -0.85 2 2
BRCA1/BACH1/BARD1 0.012 0.066 -10000 0 -0.66 4 4
FANCE 0.012 0 -10000 0 -10000 0 0
FANCC 0.012 0 -10000 0 -10000 0 0
NBN 0.012 0 -10000 0 -10000 0 0
FANCA -0.008 0.13 -10000 0 -0.85 10 10
DNA repair 0.035 0.092 -10000 0 -0.58 3 3
BRCA1/BARD1/ubiquitin 0.012 0.066 -10000 0 -0.66 4 4
BARD1/DNA-PK 0.032 0 -10000 0 -10000 0 0
FANCL 0.01 0.042 -10000 0 -0.85 1 1
mRNA polyadenylation -0.019 0 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.032 0.041 -10000 0 -0.45 1 1
BRCA1/BACH1/BARD1/TopBP1 -0.007 0.063 -10000 0 -0.57 5 5
BRCA1/BARD1/P53 0.026 0.056 -10000 0 -0.52 4 4
BARD1/CSTF1/BRCA1 -0.006 0.056 -10000 0 -0.57 4 4
BRCA1/BACH1 0.004 0.084 -10000 0 -0.85 4 4
BARD1 0.012 0 -10000 0 -10000 0 0
PCNA 0.008 0.06 -10000 0 -0.85 2 2
BRCA1/BARD1/UbcH5C -0.006 0.056 -10000 0 -0.57 4 4
BRCA1/BARD1/UbcH7 -0.006 0.056 -10000 0 -0.57 4 4
BRCA1/BARD1/RAD51/PCNA 0.024 0.075 -10000 0 -0.62 5 5
BARD1/DNA-PK/P53 -0.001 0.01 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin 0.012 0.066 -10000 0 -0.66 4 4
BRCA1/BARD1/CTIP 0.02 0.081 -10000 0 -0.52 9 9
FA complex 0.028 0.055 -10000 0 -10000 0 0
BARD1/EWS 0.019 0 -10000 0 -10000 0 0
RBBP8 0.013 0.074 -10000 0 -0.66 5 5
TP53 0.011 0.023 -10000 0 -0.47 1 1
TOPBP1 0.01 0.042 -10000 0 -0.85 1 1
G1/S transition of mitotic cell cycle 0.006 0.052 0.52 4 -10000 0 4
BRCA1/BARD1 -0.077 0.18 -10000 0 -0.5 63 63
CSTF1 0.012 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.009 0 -10000 0 -10000 0 0
CDK2 0.012 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.012 0 -10000 0 -10000 0 0
RAD50 0.012 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.012 0.066 -10000 0 -0.66 4 4
EWSR1 0.012 0 -10000 0 -10000 0 0
PLK2 and PLK4 events

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
PLK2 0 0.1 -9999 0 -0.85 6 6
PLK4 0.004 0.084 -9999 0 -0.85 4 4
regulation of centriole replication 0.005 0.1 -9999 0 -0.66 10 10
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.011 0.023 -9999 0 -0.47 1 1
HDAC2 0.012 0.001 -9999 0 -10000 0 0
GNB1/GNG2 0.016 0.055 -9999 0 -0.58 1 1
forebrain development -0.005 0.14 -9999 0 -0.6 11 11
GNAO1 -0.094 0.2 -9999 0 -0.48 90 90
SMO/beta Arrestin2 0.011 0.056 -9999 0 -10000 0 0
SMO 0.001 0.077 -9999 0 -0.47 11 11
ARRB2 0.013 0.004 -9999 0 -10000 0 0
GLI3/SPOP 0.035 0.059 -9999 0 -10000 0 0
mol:GTP 0 0.002 -9999 0 -10000 0 0
GSK3B 0.012 0 -9999 0 -10000 0 0
GNAI2 0.012 0.003 -9999 0 -10000 0 0
SIN3/HDAC complex 0.004 0.029 -9999 0 -0.52 1 1
GNAI1 0.003 0.066 -9999 0 -0.46 8 8
XPO1 0.015 0.004 -9999 0 -10000 0 0
GLI1/Su(fu) -0.037 0.11 -9999 0 -0.67 6 6
SAP30 0.012 0.001 -9999 0 -10000 0 0
mol:GDP 0.001 0.077 -9999 0 -0.47 11 11
MIM/GLI2A 0.015 0.051 -9999 0 -0.97 1 1
IFT88 0.012 0 -9999 0 -10000 0 0
GNAI3 0.012 0.003 -9999 0 -10000 0 0
GLI2 0.039 0.031 -9999 0 -10000 0 0
GLI3 0.029 0.062 -9999 0 -10000 0 0
CSNK1D 0.012 0 -9999 0 -10000 0 0
CSNK1E 0.012 0 -9999 0 -10000 0 0
SAP18 0.01 0.042 -9999 0 -0.85 1 1
embryonic digit morphogenesis 0.012 0 -9999 0 -10000 0 0
GNG2 0.01 0.042 -9999 0 -0.85 1 1
Gi family/GTP -0.042 0.15 -9999 0 -0.49 24 24
SIN3B 0.012 0.001 -9999 0 -10000 0 0
SIN3A 0.012 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.045 0.048 -9999 0 -10000 0 0
GLI2/Su(fu) 0.048 0.04 -9999 0 -10000 0 0
FOXA2 -0.064 0.24 -9999 0 -0.89 31 31
neural tube patterning -0.005 0.14 -9999 0 -0.6 11 11
SPOP 0.012 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.026 0.029 -9999 0 -10000 0 0
GNB1 0.012 0 -9999 0 -10000 0 0
CSNK1G2 0.012 0 -9999 0 -10000 0 0
CSNK1G3 0.012 0 -9999 0 -10000 0 0
MTSS1 0.015 0.051 -9999 0 -0.97 1 1
embryonic limb morphogenesis -0.005 0.14 -9999 0 -0.6 11 11
SUFU 0.022 0.032 -9999 0 -10000 0 0
LGALS3 0.008 0.054 -9999 0 -0.6 3 3
catabolic process 0.056 0.062 -9999 0 -10000 0 0
GLI3A/CBP 0.006 0.067 -9999 0 -0.32 17 17
KIF3A 0.01 0.042 -9999 0 -0.85 1 1
GLI1 -0.005 0.14 -9999 0 -0.62 11 11
RAB23 -0.019 0.16 -9999 0 -0.85 15 15
CSNK1A1 0.012 0 -9999 0 -10000 0 0
IFT172 0.012 0 -9999 0 -10000 0 0
RBBP7 0.012 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 0.024 0.043 -9999 0 -0.52 1 1
GNAZ -0.02 0.12 -9999 0 -0.47 28 28
RBBP4 0.012 0.001 -9999 0 -10000 0 0
CSNK1G1 0.012 0 -9999 0 -10000 0 0
PIAS1 0.012 0 -9999 0 -10000 0 0
PRKACA 0.012 0 -9999 0 -10000 0 0
GLI2/SPOP 0.043 0.029 -9999 0 -10000 0 0
STK36 0.015 0.004 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.029 0.14 -9999 0 -0.43 24 24
PTCH1 0.001 0.14 -9999 0 -0.78 7 7
MIM/GLI1 -0.01 0.18 -9999 0 -0.66 15 15
CREBBP 0.006 0.067 -9999 0 -0.32 17 17
Su(fu)/SIN3/HDAC complex 0.045 0.018 -9999 0 -10000 0 0
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.012 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.002 0.12 -9999 0 -0.6 15 15
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.006 0.029 -9999 0 -10000 0 0
AURKB -0.005 0.12 -9999 0 -0.81 9 9
AURKC -0.012 0.14 -9999 0 -0.71 14 14
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.048 0.092 -9999 0 -10000 0 0
CRKL 0.022 0.098 -9999 0 -10000 0 0
mol:DAG 0.03 0.086 -9999 0 -10000 0 0
HRAS 0.044 0.085 -9999 0 -10000 0 0
MAPK8 0.013 0.1 -9999 0 -0.48 16 16
RAP1A 0.022 0.098 -9999 0 -0.42 3 3
GAB1 0.022 0.098 -9999 0 -0.42 2 2
MAPK14 0.013 0.1 -9999 0 -0.48 16 16
EPO -0.019 0.15 -9999 0 -0.84 14 14
PLCG1 0.03 0.087 -9999 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.009 0.06 -9999 0 -0.84 2 2
RAPGEF1 0.012 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.004 0.11 -9999 0 -0.55 16 16
GAB1/SHC/GRB2/SOS1 -0.017 0.075 -9999 0 -10000 0 0
EPO/EPOR (dimer) -0.006 0.13 -9999 0 -0.65 16 16
IRS2 0.009 0.12 -9999 0 -0.48 7 7
STAT1 0.028 0.11 -9999 0 -0.66 1 1
STAT5B 0.034 0.089 -9999 0 -10000 0 0
cell proliferation 0.02 0.094 -9999 0 -0.45 16 16
GAB1/SHIP/PIK3R1/SHP2/SHC -0.019 0.08 -9999 0 -0.73 1 1
TEC 0.022 0.098 -9999 0 -0.42 2 2
SOCS3 0.012 0 -9999 0 -10000 0 0
STAT1 (dimer) 0.028 0.11 -9999 0 -0.64 1 1
JAK2 0.006 0.073 -9999 0 -0.85 3 3
PIK3R1 0.012 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.028 0.1 -9999 0 -0.44 20 20
EPO/EPOR -0.006 0.13 -9999 0 -0.65 16 16
LYN 0.014 0.002 -9999 0 -10000 0 0
TEC/VAV2 0.025 0.11 -9999 0 -0.44 4 4
elevation of cytosolic calcium ion concentration 0.009 0.06 -9999 0 -0.84 2 2
SHC1 0.012 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.011 0.11 -9999 0 -0.54 16 16
mol:IP3 0.03 0.086 -9999 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.018 0.12 -9999 0 -0.99 1 1
SH2B3 0.012 0.01 -9999 0 -10000 0 0
NFKB1 0.013 0.1 -9999 0 -0.48 16 16
EPO/EPOR (dimer)/JAK2/SOCS3 -0.013 0.062 -9999 0 -0.3 17 17
PTPN6 0.015 0.1 -9999 0 -0.43 20 20
TEC/VAV2/GRB2 0.03 0.1 -9999 0 -10000 0 0
EPOR 0.009 0.06 -9999 0 -0.84 2 2
INPP5D 0.007 0.064 -9999 0 -0.72 3 3
mol:GDP -0.018 0.077 -9999 0 -10000 0 0
SOS1 0.012 0 -9999 0 -10000 0 0
PLCG2 0 0.096 -9999 0 -0.66 8 8
CRKL/CBL/C3G 0.034 0.1 -9999 0 -0.83 1 1
VAV2 0.017 0.11 -9999 0 -0.42 24 24
CBL 0.021 0.1 -9999 0 -0.53 4 4
SHC/Grb2/SOS1 -0.019 0.08 -9999 0 -10000 0 0
STAT5A 0.034 0.089 -9999 0 -10000 0 0
GRB2 0.012 0 -9999 0 -10000 0 0
STAT5 (dimer) 0.05 0.095 -9999 0 -10000 0 0
LYN/PLCgamma2 0.01 0.074 -9999 0 -0.49 8 8
PTPN11 0.012 0 -9999 0 -10000 0 0
BTK 0.008 0.13 -9999 0 -0.49 11 11
BCL2 0.041 0.13 -9999 0 -0.79 6 6
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.024 0.052 -9999 0 -0.48 4 4
CRKL 0.012 0 -9999 0 -10000 0 0
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
DOCK1 0.012 0 -9999 0 -10000 0 0
ITGA4 0.006 0.073 -9999 0 -0.85 3 3
alpha4/beta7 Integrin/MAdCAM1 -0.054 0.13 -9999 0 -0.52 7 7
EPO -0.022 0.16 -9999 0 -0.85 14 14
alpha4/beta7 Integrin 0.013 0.06 -9999 0 -0.66 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.012 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.012 0.066 -9999 0 -0.66 4 4
EPO/EPOR (dimer) -0.012 0.13 -9999 0 -0.66 16 16
lamellipodium assembly -0.001 0.02 -9999 0 -10000 0 0
PIK3CA 0.01 0.042 -9999 0 -0.85 1 1
PI3K 0.017 0.033 -9999 0 -0.66 1 1
ARF6 0.012 0 -9999 0 -10000 0 0
JAK2 0.009 0.085 -9999 0 -0.42 3 3
PXN 0.012 0 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
MADCAM1 -0.13 0.23 -9999 0 -0.48 124 124
cell adhesion -0.076 0.12 -9999 0 -0.52 7 7
CRKL/CBL 0.017 0.033 -9999 0 -0.66 1 1
ITGB1 0.01 0.042 -9999 0 -0.85 1 1
SRC 0.022 0.071 -9999 0 -0.52 7 7
ITGB7 0.011 0.023 -9999 0 -0.47 1 1
RAC1 0.012 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.01 0.074 -9999 0 -0.57 7 7
p130Cas/Crk/Dock1 0.041 0.062 -9999 0 -10000 0 0
VCAM1 0.006 0.073 -9999 0 -0.85 3 3
RHOA 0.012 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.027 0.054 -9999 0 -0.52 4 4
BCAR1 0.029 0.067 -9999 0 -0.48 7 7
EPOR 0.008 0.06 -9999 0 -0.85 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.01 0.042 -9999 0 -0.85 1 1
GIT1 0.012 0 -9999 0 -10000 0 0
Rac1/GTP -0.001 0.02 -9999 0 -10000 0 0
FoxO family signaling

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
G6PC -0.088 0.37 -9999 0 -1.1 46 46
PLK1 0.066 0.17 -9999 0 -0.93 4 4
CDKN1B 0.093 0.094 -9999 0 -0.45 1 1
FOXO3 0.077 0.13 -9999 0 -0.58 3 3
KAT2B 0.019 0.048 -9999 0 -0.45 4 4
FOXO1/SIRT1 -0.031 0.12 -9999 0 -0.36 40 40
CAT 0.077 0.13 -9999 0 -1.2 1 1
CTNNB1 0.01 0.042 -9999 0 -0.85 1 1
AKT1 0.021 0.019 -9999 0 -10000 0 0
FOXO1 -0.006 0.14 -9999 0 -0.4 40 40
MAPK10 0.004 0.086 -9999 0 -10000 0 0
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
FOXO4 0.078 0.059 -9999 0 -10000 0 0
response to oxidative stress 0.008 0.022 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.008 0.088 -9999 0 -0.53 2 2
XPO1 0.013 0 -9999 0 -10000 0 0
EP300 0.009 0.017 -9999 0 -10000 0 0
BCL2L11 0.035 0.024 -9999 0 -10000 0 0
FOXO1/SKP2 -0.015 0.15 -9999 0 -0.4 50 50
mol:GDP 0.008 0.022 -9999 0 -10000 0 0
RAN 0.014 0 -9999 0 -10000 0 0
GADD45A 0.095 0.063 -9999 0 -10000 0 0
YWHAQ 0.012 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.057 0.042 -9999 0 -10000 0 0
MST1 -0.046 0.24 -9999 0 -0.83 34 34
CSNK1D 0.012 0 -9999 0 -10000 0 0
CSNK1E 0.012 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.047 0.047 -9999 0 -10000 0 0
YWHAB 0.012 0 -9999 0 -10000 0 0
MAPK8 0.037 0.009 -9999 0 -10000 0 0
MAPK9 0.036 0.009 -9999 0 -10000 0 0
YWHAG 0.012 0 -9999 0 -10000 0 0
YWHAE 0.012 0 -9999 0 -10000 0 0
YWHAZ 0.012 0 -9999 0 -10000 0 0
SIRT1 0.006 0.013 -9999 0 -10000 0 0
SOD2 0.097 0.12 -9999 0 -10000 0 0
RBL2 0.089 0.094 -9999 0 -10000 0 0
RAL/GDP 0.028 0.014 -9999 0 -10000 0 0
CHUK 0.023 0.01 -9999 0 -10000 0 0
Ran/GTP 0.013 0.001 -9999 0 -10000 0 0
CSNK1G2 0.012 0 -9999 0 -10000 0 0
RAL/GTP 0.035 0.014 -9999 0 -10000 0 0
CSNK1G1 0.012 0 -9999 0 -10000 0 0
FASLG -0.004 0.22 -9999 0 -1 16 16
SKP2 -0.01 0.14 -9999 0 -0.85 11 11
USP7 0.014 0 -9999 0 -10000 0 0
IKBKB 0.023 0.01 -9999 0 -10000 0 0
CCNB1 0.077 0.13 -9999 0 -0.86 1 1
FOXO1-3a-4/beta catenin 0.11 0.11 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.015 0.15 -9999 0 -0.4 50 50
CSNK1A1 0.012 0 -9999 0 -10000 0 0
SGK1 0.021 0.036 -9999 0 -0.47 2 2
CSNK1G3 0.012 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.024 0.002 -9999 0 -10000 0 0
ZFAND5 0.08 0.053 -9999 0 -10000 0 0
SFN -0.008 0.12 -9999 0 -0.64 13 13
CDK2 0.005 0.026 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.058 0.052 -9999 0 -10000 0 0
CREBBP 0.005 0.026 -9999 0 -10000 0 0
FBXO32 0.074 0.15 -9999 0 -1.1 3 3
BCL6 0.089 0.094 -9999 0 -10000 0 0
RALB 0.014 0 -9999 0 -10000 0 0
RALA 0.014 0 -9999 0 -10000 0 0
YWHAH 0.012 0 -9999 0 -10000 0 0
TCGA08_rtk_signaling

Figure S95.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S95.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.006 0.057 -9999 0 -0.47 6 6
HRAS 0.012 0 -9999 0 -10000 0 0
EGFR -0.022 0.16 -9999 0 -0.7 20 20
AKT 0.032 0.025 -9999 0 -0.3 1 1
FOXO3 0.012 0 -9999 0 -10000 0 0
AKT1 0.012 0 -9999 0 -10000 0 0
FOXO1 0.012 0 -9999 0 -10000 0 0
AKT3 0.01 0.042 -9999 0 -0.85 1 1
FOXO4 0.011 0.023 -9999 0 -0.47 1 1
MET -0.055 0.23 -9999 0 -0.84 33 33
PIK3CA 0.01 0.042 -9999 0 -0.85 1 1
PIK3CB 0.012 0 -9999 0 -10000 0 0
NRAS 0.012 0 -9999 0 -10000 0 0
PIK3CG -0.009 0.11 -9999 0 -0.57 15 15
PIK3R3 0.012 0 -9999 0 -10000 0 0
PIK3R2 0.012 0 -9999 0 -10000 0 0
NF1 0.012 0 -9999 0 -10000 0 0
RAS -0.017 0.08 -9999 0 -0.29 8 8
ERBB2 -0.048 0.22 -9999 0 -0.8 31 31
proliferation/survival/translation -0.029 0.034 -9999 0 -10000 0 0
PI3K -0.004 0.079 -9999 0 -0.27 13 13
PIK3R1 0.012 0 -9999 0 -10000 0 0
KRAS -0.023 0.17 -9999 0 -0.85 17 17
FOXO 0.039 0.023 -9999 0 -10000 0 0
AKT2 0.012 0 -9999 0 -10000 0 0
PTEN 0.012 0 -9999 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.022 0.042 -10000 0 -10000 0 0
epithelial cell differentiation -0.007 0.043 -10000 0 -0.49 1 1
CYFIP2 0.003 0.071 -10000 0 -0.52 7 7
ENAH 0.047 0.064 -10000 0 -10000 0 0
EGFR -0.022 0.16 -10000 0 -0.7 20 20
EPHA2 -0.001 0.11 -10000 0 -0.8 7 7
MYO6 0.028 0.046 -10000 0 -0.47 1 1
CTNNB1 0.01 0.042 -10000 0 -0.85 1 1
ABI1/Sra1/Nap1 -0.005 0.042 -10000 0 -0.57 1 1
AQP5 -0.14 0.19 -10000 0 -0.61 8 8
CTNND1 0.012 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.028 0.046 -10000 0 -0.46 1 1
regulation of calcium-dependent cell-cell adhesion 0.023 0.064 -10000 0 -0.53 3 3
EGF -0.078 0.26 -10000 0 -0.82 44 44
NCKAP1 0.012 0 -10000 0 -10000 0 0
AQP3 -0.03 0.097 -10000 0 -10000 0 0
cortical microtubule organization -0.007 0.043 -10000 0 -0.49 1 1
GO:0000145 0.026 0.044 -10000 0 -0.44 1 1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.007 0.044 -10000 0 -0.5 1 1
MLLT4 0.012 0 -10000 0 -10000 0 0
ARF6/GDP -0.014 0.066 -10000 0 -10000 0 0
ARF6 0.012 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.02 0.082 -10000 0 -0.52 9 9
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.036 0.056 -10000 0 -0.49 2 2
PVRL2 0.012 0 -10000 0 -10000 0 0
ZYX 0.028 0.046 -10000 0 -0.47 1 1
ARF6/GTP -0.011 0.071 -10000 0 -0.48 9 9
CDH1 -0.001 0.08 -10000 0 -0.47 12 12
EGFR/EGFR/EGF/EGF -0.069 0.16 -10000 0 -0.49 50 50
RhoA/GDP -0.007 0.04 -10000 0 -0.46 1 1
actin cytoskeleton organization 0.033 0.045 -10000 0 -0.43 1 1
IGF-1R heterotetramer 0.005 0.077 -10000 0 -0.75 4 4
GIT1 0.012 0 -10000 0 -10000 0 0
IGF1R 0.005 0.077 -10000 0 -0.76 4 4
IGF1 -0.071 0.23 -10000 0 -0.64 53 53
DIAPH1 -0.009 0.065 -10000 0 -0.53 6 6
Wnt receptor signaling pathway 0.007 0.043 0.49 1 -10000 0 1
RHOA 0.012 0 -10000 0 -10000 0 0
RhoA/GTP -0.014 0.066 -10000 0 -10000 0 0
CTNNA1 0.012 0 -10000 0 -10000 0 0
VCL 0.033 0.046 -10000 0 -0.44 1 1
EFNA1 0.006 0.073 -10000 0 -0.85 3 3
LPP 0.028 0.087 -10000 0 -0.72 4 4
Ephrin A1/EPHA2 -0.017 0.077 -10000 0 -0.45 10 10
SEC6/SEC8 -0.006 0.034 -10000 0 -10000 0 0
MGAT3 0.024 0.065 -10000 0 -0.55 3 3
HGF/MET -0.052 0.14 -10000 0 -0.46 39 39
HGF -0.008 0.12 -10000 0 -0.64 13 13
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.022 0.043 -10000 0 -10000 0 0
actin cable formation 0.062 0.058 -10000 0 -10000 0 0
KIAA1543 0.031 0.057 -10000 0 -0.45 2 2
KIFC3 0.028 0.046 -10000 0 -0.47 1 1
NCK1 0.012 0 -10000 0 -10000 0 0
EXOC3 0.012 0 -10000 0 -10000 0 0
ACTN1 0.024 0.067 -10000 0 -0.53 4 4
NCK1/GIT1 0.019 0 -10000 0 -10000 0 0
mol:GDP -0.007 0.043 -10000 0 -0.49 1 1
EXOC4 0.012 0 -10000 0 -10000 0 0
STX4 0.028 0.046 -10000 0 -0.47 1 1
PIP5K1C 0.028 0.046 -10000 0 -0.47 1 1
LIMA1 0.012 0 -10000 0 -10000 0 0
ABI1 0.012 0 -10000 0 -10000 0 0
ROCK1 0.043 0.07 -10000 0 -10000 0 0
adherens junction assembly 0.045 0.055 -10000 0 -0.45 1 1
IGF-1R heterotetramer/IGF1 -0.05 0.13 -10000 0 -0.48 28 28
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.019 0 -10000 0 -10000 0 0
MET -0.055 0.23 -10000 0 -0.84 33 33
PLEKHA7 0.027 0.048 -10000 0 -0.47 1 1
mol:GTP -0.012 0.076 -10000 0 -0.52 9 9
establishment of epithelial cell apical/basal polarity 0.051 0.041 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization 0.022 0.042 -10000 0 -10000 0 0
regulation of cell-cell adhesion 0.033 0.045 -10000 0 -0.43 1 1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.022 0.043 -10000 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.011 0.042 -9999 0 -0.85 1 1
ELF1 -0.007 0.095 -9999 0 -10000 0 0
CCNA2 0.012 0 -9999 0 -10000 0 0
PIK3CA 0.011 0.042 -9999 0 -0.85 1 1
JAK3 -0.024 0.18 -9999 0 -0.85 18 18
PIK3R1 0.013 0 -9999 0 -10000 0 0
JAK1 0.013 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.041 0.084 -9999 0 -10000 0 0
SHC1 0.013 0 -9999 0 -10000 0 0
SP1 0.013 0.049 -9999 0 -0.33 2 2
IL2RA -0.032 0.21 -9999 0 -0.75 33 33
IL2RB 0.012 0.023 -9999 0 -0.46 1 1
SOS1 0.013 0 -9999 0 -10000 0 0
IL2RG -0.001 0.095 -9999 0 -0.58 10 10
G1/S transition of mitotic cell cycle 0.01 0.13 -9999 0 -0.61 9 9
PTPN11 0.013 0 -9999 0 -10000 0 0
CCND2 0.013 0.11 -9999 0 -0.71 9 9
LCK -0.01 0.14 -9999 0 -0.85 11 11
GRB2 0.013 0 -9999 0 -10000 0 0
IL2 0.003 0.06 -9999 0 -0.85 2 2
CDK6 -0.029 0.18 -9999 0 -0.85 20 20
CCND3 0.047 0.077 -9999 0 -10000 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.016 0.065 -10000 0 -0.73 1 1
MAPK9 0.008 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.016 0.11 -10000 0 -0.67 11 11
GNB1/GNG2 -0.001 0.028 -10000 0 -0.58 1 1
GNB1 0.012 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.008 0 -10000 0 -10000 0 0
Gs family/GTP -0.01 0.066 -10000 0 -0.25 28 28
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 0.005 0.017 0.069 28 -10000 0 28
GNAL -0.02 0.12 -10000 0 -0.47 28 28
GNG2 0.01 0.042 -10000 0 -0.85 1 1
CRH -0.02 0.14 -10000 0 -0.85 11 11
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.008 0 -10000 0 -10000 0 0
MAPK11 0.008 0 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.005 0.059 -9999 0 -0.48 6 6
PDGF/PDGFRA/CRKL 0.014 0.041 -9999 0 -10000 0 0
positive regulation of JUN kinase activity -0.003 0.027 -9999 0 -10000 0 0
CRKL 0.012 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 0.007 0.053 -9999 0 -0.38 7 7
AP1 -0.049 0.2 -9999 0 -0.85 23 23
mol:IP3 0.017 0.046 -9999 0 -0.34 6 6
PLCG1 0.017 0.046 -9999 0 -0.34 6 6
PDGF/PDGFRA/alphaV Integrin 0.014 0.041 -9999 0 -0.32 6 6
RAPGEF1 0.012 0 -9999 0 -10000 0 0
CRK 0.012 0 -9999 0 -10000 0 0
mol:Ca2+ 0.017 0.046 -9999 0 -0.34 6 6
CAV3 0.003 0.042 -9999 0 -0.85 1 1
CAV1 0.004 0.084 -9999 0 -0.85 4 4
SHC/Grb2/SOS1 0.029 0.031 -9999 0 -10000 0 0
PDGF/PDGFRA/Shf -0.003 0.092 -9999 0 -0.37 23 23
FOS -0.008 0.2 -9999 0 -0.84 23 23
JUN -0.003 0.014 -9999 0 -10000 0 0
oligodendrocyte development 0.014 0.041 -9999 0 -0.32 6 6
GRB2 0.012 0 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
mol:DAG 0.017 0.046 -9999 0 -0.34 6 6
PDGF/PDGFRA 0.005 0.059 -9999 0 -0.48 6 6
actin cytoskeleton reorganization 0.014 0.041 -9999 0 -0.32 6 6
SRF 0.02 0.006 -9999 0 -10000 0 0
SHC1 0.012 0 -9999 0 -10000 0 0
PI3K -0.005 0.042 -9999 0 -0.58 1 1
PDGF/PDGFRA/Crk/C3G -0.003 0.031 -9999 0 -10000 0 0
JAK1 0.017 0.042 -9999 0 -0.32 6 6
ELK1/SRF 0.033 0.034 -9999 0 -10000 0 0
SHB 0.012 0 -9999 0 -10000 0 0
SHF -0.01 0.11 -9999 0 -0.49 19 19
CSNK2A1 0.003 0.013 -9999 0 -10000 0 0
GO:0007205 0.017 0.05 -9999 0 -0.37 6 6
SOS1 0.012 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.003 0.027 -9999 0 -10000 0 0
PDGF/PDGFRA/SHB 0.014 0.041 -9999 0 -0.32 6 6
PDGF/PDGFRA/Caveolin-1 0.007 0.079 -9999 0 -0.56 6 6
ITGAV 0.012 0 -9999 0 -10000 0 0
ELK1 0.022 0.048 -9999 0 -0.39 2 2
PIK3CA 0.01 0.042 -9999 0 -0.85 1 1
PDGF/PDGFRA/Crk 0.014 0.041 -9999 0 -0.32 6 6
JAK-STAT cascade 0.017 0.041 -9999 0 -0.32 6 6
cell proliferation -0.003 0.092 -9999 0 -0.37 23 23
Signaling events mediated by HDAC Class III

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
EP300 0.012 0 -10000 0 -10000 0 0
HDAC4 0.012 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.005 0.095 0.62 9 -10000 0 9
CDKN1A -0.001 0.032 -10000 0 -0.65 1 1
KAT2B 0.008 0.047 -10000 0 -0.47 4 4
BAX 0.012 0 -10000 0 -10000 0 0
FOXO3 0 0 -10000 0 -10000 0 0
FOXO1 0.012 0 -10000 0 -10000 0 0
FOXO4 0.021 0.013 -10000 0 -0.25 1 1
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.012 0 -10000 0 -10000 0 0
TAT -0.029 0.14 -10000 0 -0.52 30 30
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0 0.087 -10000 0 -0.66 6 6
PPARGC1A -0.035 0.16 -10000 0 -0.53 36 36
FHL2 0.008 0.047 -10000 0 -0.47 4 4
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0 0.007 -10000 0 -10000 0 0
HIST2H4A 0.005 0.095 -10000 0 -0.62 9 9
SIRT1/FOXO3a 0 0.006 -10000 0 -10000 0 0
SIRT1 0 0.009 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0 0.007 -10000 0 -10000 0 0
SIRT1/Histone H1b -0.005 0.036 -10000 0 -10000 0 0
apoptosis 0 0.007 -10000 0 -10000 0 0
SIRT1/PGC1A -0.028 0.097 -10000 0 -0.58 6 6
p53/SIRT1 0 0.024 0.37 1 -10000 0 1
SIRT1/FOXO4 0 0.013 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.002 0.022 -10000 0 -10000 0 0
HIST1H1E 0.015 0.045 -10000 0 -0.28 9 9
SIRT1/p300 0 0.007 -10000 0 -10000 0 0
muscle cell differentiation 0.011 0.073 0.57 6 -10000 0 6
TP53 -0.001 0.025 -10000 0 -0.47 1 1
KU70/SIRT1/BAX 0 0.007 -10000 0 -10000 0 0
CREBBP 0.012 0 -10000 0 -10000 0 0
MEF2D 0.012 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.026 0.1 -10000 0 -0.37 30 30
ACSS2 0.018 0.018 -10000 0 -0.32 1 1
SIRT1/PCAF/MYOD -0.011 0.074 -10000 0 -0.57 6 6
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.012 0 -10000 0 -10000 0 0
NFATC1 0.049 0.036 -10000 0 -10000 0 0
NFATC2 0.037 0.02 -10000 0 -10000 0 0
NFATC3 0.023 0.004 -10000 0 -10000 0 0
YWHAE 0.012 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.073 0.12 -10000 0 -0.4 17 17
Exportin 1/Ran/NUP214 0.025 0.005 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.077 0.097 -10000 0 -0.54 6 6
BCL2/BAX 0.014 0.041 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.011 0.003 -10000 0 -10000 0 0
CaM/Ca2+ 0.011 0.003 -10000 0 -10000 0 0
BAX 0.012 0 -10000 0 -10000 0 0
MAPK14 0.013 0.002 -10000 0 -10000 0 0
BAD 0.012 0 -10000 0 -10000 0 0
CABIN1/MEF2D -0.063 0.11 -10000 0 -0.38 17 17
Calcineurin A alpha-beta B1/BCL2 0.006 0.057 -10000 0 -0.46 6 6
FKBP8 0.012 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.062 0.11 0.38 17 -10000 0 17
KPNB1 0.012 0 -10000 0 -10000 0 0
KPNA2 0.008 0.06 -10000 0 -0.85 2 2
XPO1 0.013 0 -10000 0 -10000 0 0
SFN -0.008 0.12 -10000 0 -0.64 13 13
MAP3K8 0.008 0.06 -10000 0 -0.85 2 2
NFAT4/CK1 alpha 0 0 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 0.056 0.049 -10000 0 -10000 0 0
CABIN1 -0.074 0.12 -10000 0 -0.41 17 17
CALM1 0.013 0.001 -10000 0 -10000 0 0
RAN 0.013 0 -10000 0 -10000 0 0
MAP3K1 0.012 0 -10000 0 -10000 0 0
CAMK4 -0.005 0.093 -10000 0 -0.49 14 14
mol:Ca2+ 0.001 0.003 -10000 0 -10000 0 0
MAPK3 0.012 0 -10000 0 -10000 0 0
YWHAH 0.012 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.01 0.074 -10000 0 -0.66 5 5
YWHAB 0.012 0 -10000 0 -10000 0 0
MAPK8 0.013 0.002 -10000 0 -10000 0 0
MAPK9 0.012 0 -10000 0 -10000 0 0
YWHAG 0.012 0 -10000 0 -10000 0 0
FKBP1A 0.012 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.067 0.029 -10000 0 -10000 0 0
PRKCH 0.011 0.023 -10000 0 -0.47 1 1
CABIN1/Cbp/p300 0.019 0.004 -10000 0 -10000 0 0
CASP3 0.013 0.002 -10000 0 -10000 0 0
PIM1 0.01 0.033 -10000 0 -0.47 2 2
Calcineurin A alpha-beta B1/FKBP12/FK506 0.009 0.001 -10000 0 -10000 0 0
apoptosis -0.001 0.011 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.035 0.034 -10000 0 -10000 0 0
PRKCB -0.018 0.12 -10000 0 -0.48 26 26
PRKCE 0.012 0 -10000 0 -10000 0 0
JNK2/NFAT4 0.027 0.002 -10000 0 -10000 0 0
BAD/BCL-XL 0.019 0 -10000 0 -10000 0 0
PRKCD 0.012 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 0.012 0 -10000 0 -10000 0 0
PRKCG -0.37 0.43 -10000 0 -0.85 184 184
PRKCQ -0.01 0.11 -10000 0 -0.51 18 18
FKBP38/BCL2 0.014 0.041 -10000 0 -10000 0 0
EP300 0.013 0.002 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.012 0 -10000 0 -10000 0 0
NFATc/JNK1 0.054 0.035 -10000 0 -10000 0 0
CaM/Ca2+/FKBP38 0.018 0.003 -10000 0 -10000 0 0
FKBP12/FK506 0.009 0 -10000 0 -10000 0 0
CSNK1A1 0.019 0.003 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.007 0.058 -10000 0 -0.29 14 14
NFATc/ERK1 0.054 0.034 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.077 0.097 -10000 0 -0.53 6 6
NR4A1 0.053 0.082 -10000 0 -0.44 11 11
GSK3B 0.013 0.002 -10000 0 -10000 0 0
positive T cell selection 0.023 0.004 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.002 0.011 -10000 0 -10000 0 0
RCH1/ KPNB1 0.015 0.047 -10000 0 -0.66 2 2
YWHAQ 0.012 0 -10000 0 -10000 0 0
PRKACA 0.013 0.002 -10000 0 -10000 0 0
AKAP5 0.002 0.094 -10000 0 -0.85 5 5
MEF2D 0.013 0.002 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.012 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.054 0.035 -10000 0 -10000 0 0
CREBBP 0.013 0.002 -10000 0 -10000 0 0
BCL2 0.006 0.057 -10000 0 -0.47 6 6
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.031 0.094 -9999 0 -0.59 5 5
TC10/GTP -0.029 0.089 -9999 0 -0.57 5 5
Insulin Receptor/Insulin/IRS1/Shp2 -0.001 0.012 -9999 0 -10000 0 0
HRAS 0.012 0 -9999 0 -10000 0 0
APS homodimer 0.006 0.073 -9999 0 -0.85 3 3
GRB14 -0.11 0.29 -9999 0 -0.74 68 68
FOXO3 -0.011 0.041 -9999 0 -0.51 2 2
AKT1 -0.017 0.15 -9999 0 -0.79 1 1
INSR 0.014 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0.035 0.002 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.01 0.042 -9999 0 -0.85 1 1
SORBS1 -0.05 0.17 -9999 0 -0.48 53 53
CRK 0.012 0 -9999 0 -10000 0 0
PTPN1 0.033 0.002 -9999 0 -10000 0 0
CAV1 0.02 0.054 -9999 0 -0.51 4 4
CBL/APS/CAP/Crk-II/C3G -0.033 0.1 -9999 0 -0.63 5 5
Insulin Receptor/Insulin/IRS1/NCK2 -0.001 0.012 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.002 0.025 -9999 0 -0.47 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.037 0.01 -9999 0 -10000 0 0
RPS6KB1 -0.007 0.14 -9999 0 -0.69 1 1
PARD6A 0.012 0 -9999 0 -10000 0 0
CBL 0.01 0.042 -9999 0 -0.85 1 1
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 -0.001 0.024 -9999 0 -0.47 1 1
PIK3R1 0.012 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.05 0.12 -9999 0 -0.67 1 1
HRAS/GTP -0.003 0.03 -9999 0 -10000 0 0
Insulin Receptor 0.014 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.001 0.011 -9999 0 -10000 0 0
PRKCI -0.017 0.046 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.062 0.15 -9999 0 -0.88 1 1
SHC1 0.012 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade -0.001 0.019 -9999 0 -0.38 1 1
PI3K -0.002 0.025 -9999 0 -0.48 1 1
NCK2 0.012 0 -9999 0 -10000 0 0
RHOQ 0.012 0 -9999 0 -10000 0 0
mol:H2O2 0 0 -9999 0 -10000 0 0
HRAS/GDP 0.009 0 -9999 0 -10000 0 0
AKT2 -0.017 0.15 -9999 0 -0.79 1 1
PRKCZ -0.014 0.033 -9999 0 -10000 0 0
SH2B2 0.006 0.073 -9999 0 -0.85 3 3
SHC/SHIP 0.029 0.039 -9999 0 -0.48 2 2
F2RL2 -0.11 0.3 -9999 0 -0.85 61 61
TRIP10 0.012 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0 0 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0 0 -9999 0 -10000 0 0
RAPGEF1 0.012 0 -9999 0 -10000 0 0
RASA1 0.012 0 -9999 0 -10000 0 0
NCK1 0.012 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.008 0.12 -9999 0 -0.67 5 5
TC10/GDP 0.009 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 -0.001 0.026 -9999 0 -0.54 1 1
INPP5D 0.022 0.041 -9999 0 -0.51 2 2
SOS1 0.012 0 -9999 0 -10000 0 0
SGK1 -0.008 0.054 -9999 0 -0.77 2 2
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.012 0 -9999 0 -10000 0 0
IRS1 0.011 0.023 -9999 0 -0.47 1 1
p62DOK/RasGAP -0.001 0.02 -9999 0 -0.39 1 1
INS 0.004 0.003 -9999 0 -10000 0 0
mol:PI-3-4-P2 0.022 0.041 -9999 0 -0.51 2 2
GRB2 0.012 0 -9999 0 -10000 0 0
EIF4EBP1 -0.009 0.15 -9999 0 -0.73 2 2
PTPRA 0.014 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.042 -9999 0 -0.85 1 1
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0.012 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.032 0.012 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.001 0.012 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS3 0 0 -9999 0 -10000 0 0
Par3/Par6 -0.073 0.18 -9999 0 -0.5 60 60
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.029 0.034 -9999 0 -0.66 1 1
VEGFR1 homodimer/NRP1 0.02 0.034 -9999 0 -0.67 1 1
mol:DAG 0.019 0.1 -9999 0 -0.52 14 14
VEGFR1 homodimer/NRP1/VEGFR 121 0.018 0.086 -9999 0 -0.61 7 7
CaM/Ca2+ 0.025 0.095 -9999 0 -0.48 14 14
HIF1A 0.019 0.017 -9999 0 -10000 0 0
GAB1 0.012 0 -9999 0 -10000 0 0
AKT1 0.039 0.087 -9999 0 -10000 0 0
PLCG1 0.019 0.1 -9999 0 -0.52 14 14
NOS3 0.042 0.088 -9999 0 -0.48 1 1
CBL 0.01 0.042 -9999 0 -0.85 1 1
mol:NO 0.042 0.085 -9999 0 -0.46 1 1
FLT1 0.027 0.038 -9999 0 -0.75 1 1
PGF -0.015 0.15 -9999 0 -0.85 13 13
VEGFR1 homodimer/NRP2/VEGFR121 0.025 0.09 -9999 0 -0.59 8 8
CALM1 0.012 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.042 -9999 0 -0.85 1 1
eNOS/Hsp90 0.045 0.089 -9999 0 -10000 0 0
endothelial cell proliferation 0.022 0.099 -9999 0 -0.51 1 1
mol:Ca2+ 0.019 0.1 -9999 0 -0.51 14 14
MAPK3 0.031 0.09 -9999 0 -0.52 1 1
MAPK1 0.031 0.09 -9999 0 -0.52 1 1
PIK3R1 0.012 0 -9999 0 -10000 0 0
PLGF homodimer -0.015 0.15 -9999 0 -0.85 13 13
PRKACA 0.012 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 0.004 0.084 -9999 0 -0.85 4 4
VEGFA homodimer -0.002 0.11 -9999 0 -0.85 7 7
VEGFR1 homodimer/VEGFA homodimer 0.02 0.092 -9999 0 -0.65 7 7
platelet activating factor biosynthetic process 0.037 0.087 -9999 0 -0.5 1 1
PI3K 0.024 0.099 -9999 0 -0.49 15 15
PRKCA 0.025 0.094 -9999 0 -0.48 14 14
PRKCB 0.009 0.11 -9999 0 -0.48 15 15
VEGFR1 homodimer/PLGF homodimer 0.011 0.11 -9999 0 -0.57 14 14
VEGFA -0.002 0.11 -9999 0 -0.85 7 7
VEGFB 0.012 0 -9999 0 -10000 0 0
mol:IP3 0.019 0.1 -9999 0 -0.52 14 14
RASA1 0.036 0.031 -9999 0 -0.6 1 1
NRP2 0.01 0.042 -9999 0 -0.85 1 1
VEGFR1 homodimer 0.027 0.038 -9999 0 -0.75 1 1
VEGFB homodimer 0.012 0 -9999 0 -10000 0 0
NCK1 0.012 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.043 0.094 -9999 0 -10000 0 0
PTPN11 0.012 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.017 0.09 -9999 0 -0.48 15 15
mol:L-citrulline 0.042 0.085 -9999 0 -0.46 1 1
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.032 0.086 -9999 0 -0.56 8 8
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.026 0.086 -9999 0 -0.6 7 7
CD2AP 0.012 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.017 0.086 -9999 0 -0.54 1 1
PDPK1 0.029 0.094 -9999 0 -0.53 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.026 0.086 -9999 0 -0.6 7 7
mol:NADP 0.042 0.085 -9999 0 -0.46 1 1
HSP90AA1 0.008 0.06 -9999 0 -0.85 2 2
ubiquitin-dependent protein catabolic process -0.011 0.079 -9999 0 -0.55 8 8
VEGFR1 homodimer/NRP2 0.028 0.045 -9999 0 -0.61 2 2
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.036 0.045 -10000 0 -0.38 1 1
adherens junction organization 0.001 0.086 -10000 0 -0.36 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.024 0.091 -10000 0 -10000 0 0
FMN1 0.021 0.073 -10000 0 -0.43 2 2
mol:IP3 0.028 0.047 -10000 0 -0.41 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.018 0.067 -10000 0 -10000 0 0
CTNNB1 0.011 0.042 -10000 0 -0.85 1 1
AKT1 0.033 0.051 -10000 0 -0.4 1 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.016 0.082 -10000 0 -10000 0 0
CTNND1 0.013 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.025 0.063 -10000 0 -10000 0 0
VASP 0.025 0.064 -10000 0 -10000 0 0
ZYX 0.025 0.064 -10000 0 -10000 0 0
JUB -0.054 0.19 -10000 0 -0.47 65 65
EGFR(dimer) 0.005 0.11 -10000 0 -0.46 13 13
E-cadherin/beta catenin-gamma catenin -0.029 0.12 -10000 0 -0.58 16 16
mol:PI-3-4-5-P3 -0.011 0.044 -10000 0 -0.43 1 1
PIK3CA 0.011 0.042 -10000 0 -0.85 1 1
PI3K 0.026 0.054 -10000 0 -0.44 1 1
FYN 0.015 0.088 -10000 0 -0.47 1 1
mol:Ca2+ 0.028 0.046 -10000 0 -0.4 1 1
JUP -0.019 0.16 -10000 0 -0.85 15 15
PIK3R1 0.013 0.001 -10000 0 -10000 0 0
mol:DAG 0.028 0.047 -10000 0 -0.41 1 1
CDH1 -0.001 0.08 -10000 0 -0.46 12 12
RhoA/GDP 0.024 0.091 -10000 0 -10000 0 0
establishment of polarity of embryonic epithelium 0.025 0.063 -10000 0 -10000 0 0
SRC 0.012 0 -10000 0 -10000 0 0
RAC1 0.012 0 -10000 0 -10000 0 0
RHOA 0.012 0 -10000 0 -10000 0 0
EGFR -0.022 0.16 -10000 0 -0.7 20 20
CASR 0.004 0.1 -10000 0 -0.46 10 10
RhoA/GTP -0.008 0.032 -10000 0 -10000 0 0
AKT2 0.033 0.051 -10000 0 -0.4 1 1
actin cable formation 0.027 0.071 -10000 0 -0.42 2 2
apoptosis -0.031 0.049 0.38 1 -10000 0 1
CTNNA1 0.013 0.001 -10000 0 -10000 0 0
mol:GDP 0.017 0.097 -10000 0 -0.43 13 13
PIP5K1A 0.025 0.064 -10000 0 -10000 0 0
PLCG1 0.028 0.047 -10000 0 -0.42 1 1
Rac1/GTP -0.029 0.087 -10000 0 -0.42 13 13
homophilic cell adhesion 0.001 0.001 -10000 0 -10000 0 0
Ceramide 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
SPHK2 0.02 0.033 -10000 0 -0.66 1 1
MAP4K4 0.03 0.067 -10000 0 -0.47 3 3
BAG4 0.01 0.042 -10000 0 -0.85 1 1
PKC zeta/ceramide -0.01 0.035 0.19 1 -10000 0 1
NFKBIA 0.012 0 -10000 0 -10000 0 0
BIRC3 0.001 0.097 -10000 0 -0.79 6 6
BAX -0.002 0.017 -10000 0 -10000 0 0
RIPK1 0.012 0 -10000 0 -10000 0 0
AKT1 0.019 0.008 -10000 0 -10000 0 0
BAD -0.011 0.035 0.21 1 -10000 0 1
SMPD1 0.018 0.049 -10000 0 -0.27 1 1
RB1 -0.011 0.035 0.21 1 -10000 0 1
FADD/Caspase 8 0.042 0.054 -10000 0 -0.43 1 1
MAP2K4 -0.003 0.033 -10000 0 -10000 0 0
NSMAF 0.012 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.003 0.033 -10000 0 -10000 0 0
EGF -0.078 0.26 -10000 0 -0.82 44 44
mol:ceramide -0.02 0.037 0.22 1 -10000 0 1
MADD 0.012 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.02 0.033 -10000 0 -0.66 1 1
ASAH1 0.012 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.011 0.034 0.21 1 -10000 0 1
cell proliferation -0.022 0.11 -10000 0 -0.4 24 24
BID 0.024 0.041 -10000 0 -0.28 1 1
MAP3K1 -0.011 0.035 0.21 1 -10000 0 1
EIF2A 0.004 0.031 -10000 0 -10000 0 0
TRADD 0.012 0 -10000 0 -10000 0 0
CRADD 0.012 0 -10000 0 -10000 0 0
MAPK3 0.007 0.031 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.007 0.031 -10000 0 -10000 0 0
Cathepsin D/ceramide -0.01 0.035 0.19 1 -10000 0 1
FADD 0.033 0.057 -10000 0 -0.47 1 1
KSR1 -0.011 0.035 0.21 1 -10000 0 1
MAPK8 0.001 0.032 0.2 1 -10000 0 1
PRKRA -0.011 0.035 0.21 1 -10000 0 1
PDGFA 0.01 0.042 -10000 0 -0.85 1 1
TRAF2 0.012 0 -10000 0 -10000 0 0
IGF1 -0.071 0.23 -10000 0 -0.64 53 53
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.02 0.037 0.22 1 -10000 0 1
CTSD 0.012 0 -10000 0 -10000 0 0
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 -0.021 0.12 -10000 0 -0.43 24 24
PRKCD 0.012 0 -10000 0 -10000 0 0
PRKCZ 0.012 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.02 0.033 -10000 0 -0.66 1 1
RelA/NF kappa B1 0.019 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.012 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.027 0.06 -10000 0 -0.5 1 1
TNFR1A/BAG4/TNF-alpha -0.024 0.11 -10000 0 -0.57 15 15
mol:Sphingosine-1-phosphate 0.02 0.033 -10000 0 -0.66 1 1
MAP2K1 0.004 0.031 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.012 0 -10000 0 -10000 0 0
CYCS -0.003 0.032 -10000 0 -0.23 1 1
TNFRSF1A 0.012 0 -10000 0 -10000 0 0
NFKB1 0.012 0 -10000 0 -10000 0 0
TNFR1A/BAG4 0.017 0.033 -10000 0 -0.66 1 1
EIF2AK2 -0.003 0.033 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.023 0.11 -10000 0 -0.57 14 14
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.034 0.035 -10000 0 -10000 0 0
MAP2K2 0.004 0.031 -10000 0 -10000 0 0
SMPD3 0.006 0.083 -10000 0 -0.29 21 21
TNF -0.022 0.16 -10000 0 -0.75 19 19
PKC zeta/PAR4 0.019 0 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.015 0.079 0.24 44 -10000 0 44
NF kappa B1/RelA/I kappa B alpha 0 0 -10000 0 -10000 0 0
AIFM1 -0.003 0.03 -10000 0 -10000 0 0
BCL2 0.006 0.057 -10000 0 -0.47 6 6
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.027 0.014 -9999 0 -10000 0 0
SNTA1 -0.001 0.08 -9999 0 -0.47 12 12
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.027 0.014 -9999 0 -10000 0 0
MAPK12 0.013 0.08 -9999 0 -0.52 6 6
CCND1 0.012 0.042 -9999 0 -0.26 4 4
p38 gamma/SNTA1 0.012 0.086 -9999 0 -0.48 7 7
MAP2K3 0.012 0 -9999 0 -10000 0 0
PKN1 0.012 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.013 0.079 -9999 0 -0.52 6 6
MAP2K6 0.013 0.059 -9999 0 -0.36 7 7
MAPT -0.043 0.13 -9999 0 -0.42 10 10
MAPK13 0.021 0.017 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.011 0.047 -9999 0 -0.38 6 6
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.012 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.005 0.067 -9999 0 -0.53 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.012 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.007 0.077 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.012 0 -9999 0 -10000 0 0
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.012 0 -9999 0 -10000 0 0
FYN 0.012 0 -9999 0 -10000 0 0
MAP3K12 0.012 0 -9999 0 -10000 0 0
FGR 0.012 0 -9999 0 -10000 0 0
p38 alpha/TAB1 -0.02 0.039 -9999 0 -10000 0 0
PRKG1 0.005 0.072 -9999 0 -0.62 5 5
DUSP8 0.01 0.033 -9999 0 -0.47 2 2
PGK/cGMP/p38 alpha -0.021 0.047 -9999 0 -0.37 3 3
apoptosis -0.019 0.038 -9999 0 -10000 0 0
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.012 0 -9999 0 -10000 0 0
DUSP1 -0.002 0.083 -9999 0 -0.47 13 13
PAK1 0.012 0 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.032 0 -9999 0 -10000 0 0
TRAF6 0.012 0 -9999 0 -10000 0 0
RAC1 0.012 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.012 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 0.011 0.086 -9999 0 -10000 0 0
BLK -0.11 0.25 -9999 0 -0.56 86 86
HCK 0.012 0 -9999 0 -10000 0 0
MAP2K3 0.012 0 -9999 0 -10000 0 0
DUSP16 0.01 0.042 -9999 0 -0.85 1 1
DUSP10 0.008 0.06 -9999 0 -0.85 2 2
TRAF6/MEKK3 0.016 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.02 0.064 -9999 0 -10000 0 0
positive regulation of innate immune response 0.017 0.092 -9999 0 -10000 0 0
LCK -0.01 0.14 -9999 0 -0.85 11 11
p38alpha-beta/MKP7 0.022 0.092 -9999 0 -0.5 1 1
p38alpha-beta/MKP5 0.021 0.099 -9999 0 -0.69 2 2
PGK/cGMP 0.004 0.055 -9999 0 -0.47 5 5
PAK2 0.012 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 0.017 0.1 -9999 0 -0.41 1 1
CDC42 0.012 0 -9999 0 -10000 0 0
RALB 0.012 0 -9999 0 -10000 0 0
RALA 0.012 0 -9999 0 -10000 0 0
PAK3 -0.066 0.19 -9999 0 -0.5 64 64
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.026 0.076 -9999 0 -0.39 12 12
KLHL20 -0.009 0.034 -9999 0 -10000 0 0
CYFIP2 0.003 0.071 -9999 0 -0.52 7 7
Rac1/GDP 0.048 0.052 -9999 0 -10000 0 0
ENAH 0.025 0.079 -9999 0 -0.4 13 13
AP1M1 0.012 0 -9999 0 -10000 0 0
RAP1B 0.006 0.073 -9999 0 -0.85 3 3
RAP1A 0.013 0 -9999 0 -10000 0 0
CTNNB1 0.01 0.042 -9999 0 -0.85 1 1
CDC42/GTP -0.007 0.039 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.007 0.026 -9999 0 -0.23 1 1
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.023 0.053 -9999 0 -0.52 1 1
RAPGEF1 0.038 0.067 -9999 0 -10000 0 0
CTNND1 0.013 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.013 0.071 -9999 0 -0.41 13 13
CRK 0.032 0.072 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin -0.028 0.11 -9999 0 -0.57 15 15
alphaE/beta7 Integrin 0.018 0.017 -9999 0 -10000 0 0
IQGAP1 0.01 0.042 -9999 0 -0.85 1 1
NCKAP1 0.012 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.02 0.047 -9999 0 -0.53 3 3
DLG1 0.026 0.076 -9999 0 -0.39 12 12
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.006 0.028 -9999 0 -10000 0 0
MLLT4 0.013 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.014 0.068 -9999 0 -0.53 5 5
PI3K -0.007 0.036 -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 -0.016 0.14 -9999 0 -0.51 27 27
TIAM1 -0.003 0.1 -9999 0 -0.62 10 10
E-cadherin(dimer)/Ca2+ 0.02 0.049 -9999 0 -0.5 1 1
AKT1 -0.004 0.021 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
CDH1 -0.001 0.08 -9999 0 -0.47 12 12
RhoA/GDP 0.047 0.052 -9999 0 -10000 0 0
actin cytoskeleton organization 0.034 0.037 -9999 0 -10000 0 0
CDC42/GDP 0.047 0.052 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.006 0.07 -9999 0 -0.29 15 15
ITGB7 0.011 0.023 -9999 0 -0.47 1 1
RAC1 0.013 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.023 0.052 -9999 0 -0.52 1 1
E-cadherin/Ca2+/beta catenin/alpha catenin 0.014 0.049 -9999 0 -0.5 1 1
mol:GDP 0.044 0.059 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1 -0.001 0.028 -9999 0 -0.58 1 1
JUP -0.019 0.16 -9999 0 -0.85 15 15
p120 catenin/RhoA/GDP -0.008 0.041 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 -0.001 0.029 -9999 0 -0.58 1 1
PIP5K1C/AP1M1 0.019 0 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
CDC42 0.012 0 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.026 0.036 -9999 0 -0.26 4 4
NME1 0.01 0.042 -9999 0 -0.85 1 1
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.026 0.076 -9999 0 -0.39 12 12
regulation of cell-cell adhesion -0.006 0.034 -9999 0 -10000 0 0
WASF2 -0.004 0.013 -9999 0 -10000 0 0
Rap1/GTP -0.008 0.044 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.024 0.097 -9999 0 -0.49 15 15
CCND1 0.03 0.044 -9999 0 -0.33 4 4
VAV2 0.033 0.078 -9999 0 -10000 0 0
RAP1/GDP 0.042 0.056 -9999 0 -10000 0 0
adherens junction assembly 0.026 0.073 -9999 0 -0.38 12 12
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.012 0 -9999 0 -10000 0 0
PIP5K1C 0.012 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.016 0.1 -9999 0 -0.46 16 16
E-cadherin/beta catenin -0.009 0.055 -9999 0 -0.32 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.026 0.076 -9999 0 -0.39 12 12
PIK3CA 0.01 0.042 -9999 0 -0.85 1 1
Rac1/GTP -0.014 0.054 -9999 0 -0.39 1 1
E-cadherin/beta catenin/alpha catenin -0.009 0.052 -9999 0 -0.57 1 1
ITGAE 0.012 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.014 0.073 -9999 0 -0.42 13 13
Class IB PI3K non-lipid kinase 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
cAMP biosynthetic process -0.007 0.064 0.72 3 -10000 0 3
PI3K Class IB/PDE3B 0.007 0.064 -10000 0 -0.72 3 3
PDE3B 0.007 0.064 -10000 0 -0.72 3 3
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.01 0.042 -9999 0 -0.85 1 1
ITGB7 0.011 0.023 -9999 0 -0.47 1 1
ITGA4 0.006 0.073 -9999 0 -0.85 3 3
alpha4/beta7 Integrin 0.013 0.06 -9999 0 -0.66 3 3
alpha4/beta1 Integrin 0.012 0.066 -9999 0 -0.66 4 4
TRAIL signaling 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
TNFSF10 0.009 0.048 -10000 0 -0.66 2 2
positive regulation of NF-kappaB transcription factor activity 0.012 0.057 -10000 0 -0.43 6 6
MAP2K4 0.043 0.022 -10000 0 -10000 0 0
IKBKB 0.012 0 -10000 0 -10000 0 0
TNFRSF10B 0.008 0.06 -10000 0 -0.85 2 2
TNFRSF10A 0.01 0.042 -10000 0 -0.85 1 1
SMPD1 0.016 0.026 -10000 0 -0.27 3 3
IKBKG 0.012 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.007 0.059 -10000 0 -0.56 4 4
TRAIL/TRAILR2 0.013 0.06 -10000 0 -0.66 3 3
TRAIL/TRAILR3 0 0.11 -10000 0 -0.66 11 11
TRAIL/TRAILR1 0.015 0.05 -10000 0 -0.66 2 2
TRAIL/TRAILR4 0.012 0.057 -10000 0 -0.44 6 6
TRAIL/TRAILR1/DAP3/GTP 0.021 0.04 -10000 0 -0.53 2 2
IKK complex -0.002 0.015 -10000 0 -10000 0 0
RIPK1 0.012 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.009 0 -10000 0 -10000 0 0
MAPK3 0.019 0.037 -10000 0 -0.66 1 1
MAP3K1 0.037 0.023 -10000 0 -10000 0 0
TRAILR4 (trimer) 0.007 0.058 -10000 0 -0.56 4 4
TRADD 0.012 0 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.01 0.042 -10000 0 -0.85 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.034 0.024 -10000 0 -10000 0 0
CFLAR 0.012 0 -10000 0 -10000 0 0
MAPK1 0.019 0.037 -10000 0 -0.66 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP -0.003 0.035 -10000 0 -0.49 2 2
mol:ceramide 0.016 0.026 -10000 0 -0.27 3 3
FADD 0.012 0 -10000 0 -10000 0 0
MAPK8 0.048 0.021 -10000 0 -10000 0 0
TRAF2 0.012 0 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.008 0.13 -10000 0 -0.85 10 10
CHUK 0.012 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.003 0.042 -10000 0 -0.57 2 2
DAP3 0.012 0 -10000 0 -10000 0 0
CASP10 -0.002 0.044 0.28 1 -0.47 1 2
JNK cascade 0.012 0.057 -10000 0 -0.43 6 6
TRAIL (trimer) 0.009 0.048 -10000 0 -0.66 2 2
TNFRSF10C -0.008 0.13 -10000 0 -0.85 10 10
TRAIL/TRAILR1/DAP3/GTP/FADD -0.003 0.036 -10000 0 -0.5 2 2
TRAIL/TRAILR2/FADD -0.005 0.05 -10000 0 -0.57 3 3
cell death 0.016 0.026 -10000 0 -0.27 3 3
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.033 0.029 -10000 0 -10000 0 0
TRAILR2 (trimer) 0.008 0.06 -10000 0 -0.85 2 2
CASP8 0.001 0.01 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.004 0.043 -10000 0 -0.49 3 3
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.01 0.042 -9999 0 -0.85 1 1
Caspase 8 (4 units) -0.007 0.036 -9999 0 -10000 0 0
NEF -0.002 0.036 -9999 0 -10000 0 0
NFKBIA 0.014 0.015 -9999 0 -10000 0 0
BIRC3 0.031 0.094 -9999 0 -0.74 6 6
CYCS 0.038 0.057 -9999 0 -0.44 1 1
RIPK1 0.012 0 -9999 0 -10000 0 0
CD247 0.003 0.068 -9999 0 -0.48 6 6
MAP2K7 0.042 0.041 -9999 0 -10000 0 0
protein ubiquitination 0.057 0.043 -9999 0 -10000 0 0
CRADD 0.012 0 -9999 0 -10000 0 0
DAXX 0.012 0 -9999 0 -10000 0 0
FAS 0.012 0 -9999 0 -10000 0 0
BID 0.034 0.054 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha -0.005 0.038 -9999 0 -10000 0 0
TRADD 0.012 0 -9999 0 -10000 0 0
MAP3K5 0.012 0 -9999 0 -10000 0 0
CFLAR 0.012 0 -9999 0 -10000 0 0
FADD 0.012 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.005 0.039 -9999 0 -10000 0 0
MAPK8 0.047 0.039 -9999 0 -10000 0 0
APAF1 0.012 0 -9999 0 -10000 0 0
TRAF1 0.008 0.06 -9999 0 -0.85 2 2
TRAF2 0.012 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.027 0.057 -9999 0 -10000 0 0
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.049 0.05 -9999 0 -10000 0 0
CHUK 0.058 0.045 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0 0 -9999 0 -10000 0 0
TCRz/NEF -0.016 0.072 -9999 0 -0.36 12 12
TNF -0.022 0.16 -9999 0 -0.75 19 19
FASLG -0.002 0.14 -9999 0 -0.66 16 16
NFKB1 0.014 0.015 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.024 0.11 -9999 0 -0.57 15 15
CASP6 -0.004 0.019 -9999 0 -10000 0 0
CASP7 0.068 0.071 -9999 0 -0.43 6 6
RELA 0.014 0.015 -9999 0 -10000 0 0
CASP2 0.012 0 -9999 0 -10000 0 0
CASP3 0.068 0.071 -9999 0 -0.43 6 6
TNFRSF1A 0.012 0 -9999 0 -10000 0 0
TNFR1A/BAG4 0.017 0.033 -9999 0 -0.66 1 1
CASP8 0.012 0 -9999 0 -10000 0 0
CASP9 0.012 0 -9999 0 -10000 0 0
MAP3K14 0.054 0.048 -9999 0 -10000 0 0
APAF-1/Caspase 9 -0.012 0.057 -9999 0 -0.45 5 5
BCL2 0.049 0.047 -9999 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaV beta3 Integrin 0.011 0.068 -9999 0 -0.59 5 5
AKT1 0.074 0.057 -9999 0 -0.5 1 1
PTK2B 0.04 0.082 -9999 0 -0.45 4 4
VEGFR2 homodimer/Frs2 0.026 0.072 -9999 0 -0.56 6 6
CAV1 0.004 0.084 -9999 0 -0.85 4 4
CALM1 0.012 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.026 0.097 -9999 0 -0.51 13 13
endothelial cell proliferation 0.075 0.069 -9999 0 -10000 0 0
mol:Ca2+ 0.044 0.068 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.039 0.073 -9999 0 -0.48 8 8
RP11-342D11.1 0.036 0.068 -9999 0 -0.46 7 7
CDH5 0.012 0 -9999 0 -10000 0 0
VEGFA homodimer 0.024 0.071 -9999 0 -0.52 7 7
SHC1 0.012 0 -9999 0 -10000 0 0
SHC2 0.006 0.057 -9999 0 -0.47 6 6
HRAS/GDP -0.007 0.051 -9999 0 -10000 0 0
SH2D2A 0.01 0.042 -9999 0 -0.85 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.009 0.051 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.033 0.077 -9999 0 -0.51 8 8
VEGFR1 homodimer 0.01 0.042 -9999 0 -0.85 1 1
SHC/GRB2/SOS1 -0.008 0.056 -9999 0 -10000 0 0
GRB10 0.044 0.077 -9999 0 -0.76 1 1
PTPN11 0.012 0 -9999 0 -10000 0 0
GRB2 0.012 0 -9999 0 -10000 0 0
PAK1 0.012 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.01 0.066 -9999 0 -10000 0 0
HRAS 0.012 0 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.041 0.044 -9999 0 -10000 0 0
HIF1A 0.012 0 -9999 0 -10000 0 0
FRS2 0 0.1 -9999 0 -0.85 6 6
oxygen and reactive oxygen species metabolic process -0.009 0.065 -9999 0 -0.47 8 8
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.012 0 -9999 0 -10000 0 0
Nck/Pak 0.019 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.034 0.072 -9999 0 -0.51 7 7
mol:GDP -0.008 0.055 -9999 0 -10000 0 0
mol:NADP 0.064 0.056 -9999 0 -10000 0 0
eNOS/Hsp90 0.065 0.061 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
mol:IP3 0.045 0.069 -9999 0 -10000 0 0
HIF1A/ARNT 0.019 0 -9999 0 -10000 0 0
SHB 0.012 0 -9999 0 -10000 0 0
VEGFA 0 0.11 -9999 0 -0.85 7 7
VEGFC 0.011 0.023 -9999 0 -0.47 1 1
FAK1/Vinculin 0.059 0.064 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.035 0.086 -9999 0 -0.48 11 11
PTPN6 0.01 0.042 -9999 0 -0.85 1 1
EPAS1 0.022 0.004 -9999 0 -10000 0 0
mol:L-citrulline 0.064 0.056 -9999 0 -10000 0 0
ITGAV 0.012 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.042 -9999 0 -0.85 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.033 0.092 -9999 0 -0.48 6 6
VEGFR2 homodimer/VEGFA homodimer 0.039 0.074 -9999 0 -0.5 7 7
VEGFR2/3 heterodimer 0.035 0.005 -9999 0 -10000 0 0
VEGFB 0.012 0 -9999 0 -10000 0 0
MAPK11 0.047 0.067 -9999 0 -10000 0 0
VEGFR2 homodimer 0.034 0.006 -9999 0 -10000 0 0
FLT1 0.01 0.042 -9999 0 -0.85 1 1
NEDD4 0.015 0.004 -9999 0 -10000 0 0
MAPK3 0.044 0.069 -9999 0 -0.52 1 1
MAPK1 0.044 0.069 -9999 0 -0.52 1 1
VEGFA145/NRP2 0.007 0.093 -9999 0 -0.66 8 8
VEGFR1/2 heterodimer 0.033 0.03 -9999 0 -0.57 1 1
KDR 0.034 0.006 -9999 0 -10000 0 0
VEGFA165/NRP1/VEGFR2 homodimer 0.042 0.072 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process 0.046 0.069 -9999 0 -0.51 1 1
PI3K 0.063 0.071 -9999 0 -0.68 1 1
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.034 0.072 -9999 0 -0.51 7 7
FES 0.042 0.077 -9999 0 -10000 0 0
GAB1 -0.007 0.057 -9999 0 -0.73 1 1
VEGFR2 homodimer/VEGFA homodimer/Src 0.034 0.072 -9999 0 -0.51 7 7
CTNNB1 0.01 0.042 -9999 0 -0.85 1 1
SOS1 0.012 0 -9999 0 -10000 0 0
ARNT 0.012 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.063 0.067 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Yes 0.034 0.072 -9999 0 -0.51 7 7
PI3K/GAB1 0.076 0.057 -9999 0 -0.48 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.015 0.079 -9999 0 -10000 0 0
PRKACA 0.012 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.039 0.014 -9999 0 -10000 0 0
HSP90AA1 0.008 0.06 -9999 0 -0.85 2 2
CDC42 0.045 0.069 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.01 0.07 -9999 0 -0.51 8 8
PTK2 0.054 0.067 -9999 0 -10000 0 0
EDG1 0.036 0.068 -9999 0 -0.46 7 7
mol:DAG 0.045 0.069 -9999 0 -10000 0 0
CaM/Ca2+ -0.008 0.056 -9999 0 -10000 0 0
MAP2K3 0.044 0.086 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.044 0.079 -9999 0 -0.77 1 1
PLCG1 0.045 0.069 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.04 0.068 -9999 0 -0.48 7 7
IQGAP1 0.01 0.042 -9999 0 -0.85 1 1
YES1 0.012 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.034 0.072 -9999 0 -0.51 7 7
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.033 0.077 -9999 0 -0.51 8 8
cell migration 0.078 0.059 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.062 0.066 -9999 0 -0.62 1 1
FYN 0.012 0 -9999 0 -10000 0 0
VEGFB/NRP1 0.042 0.065 -9999 0 -0.44 7 7
mol:NO 0.064 0.056 -9999 0 -10000 0 0
PXN 0.012 0 -9999 0 -10000 0 0
HRAS/GTP -0.007 0.051 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.044 0.079 -9999 0 -0.76 1 1
VHL 0.012 0 -9999 0 -10000 0 0
ITGB3 0.003 0.088 -9999 0 -0.78 5 5
NOS3 0.066 0.06 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Sck 0.03 0.078 -9999 0 -0.51 7 7
RAC1 0.012 0 -9999 0 -10000 0 0
PRKCA 0.05 0.065 -9999 0 -10000 0 0
PRKCB 0.035 0.091 -9999 0 -0.65 1 1
VCL 0.012 0 -9999 0 -10000 0 0
VEGFA165/NRP1 0.036 0.07 -9999 0 -0.48 7 7
VEGFR1/2 heterodimer/VEGFA homodimer 0.033 0.084 -9999 0 -0.58 7 7
VEGFA165/NRP2 0.007 0.093 -9999 0 -0.66 8 8
MAPKKK cascade 0.064 0.068 -9999 0 -0.62 1 1
NRP2 0.01 0.042 -9999 0 -0.85 1 1
VEGFC homodimer 0.011 0.023 -9999 0 -0.46 1 1
NCK1 0.012 0 -9999 0 -10000 0 0
ROCK1 0.012 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.059 0.064 -9999 0 -10000 0 0
MAP3K13 0.038 0.091 -9999 0 -10000 0 0
PDPK1 0.067 0.061 -9999 0 -0.55 1 1
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.14 0.23 -10000 0 -0.47 134 134
CLTC 0.03 0.016 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.025 0.009 -10000 0 -10000 0 0
Dynamin 2/GTP 0.022 0.027 -10000 0 -0.53 1 1
EXOC4 0.012 0 -10000 0 -10000 0 0
CD59 0.027 0.01 -10000 0 -10000 0 0
CPE -0.017 0.1 -10000 0 -0.58 3 3
CTNNB1 0.01 0.042 -10000 0 -0.85 1 1
membrane fusion 0.025 0.01 -10000 0 -10000 0 0
CTNND1 0.029 0.026 -10000 0 -0.49 1 1
DNM2 0.012 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.03 0.008 -10000 0 -10000 0 0
TSHR 0.006 0.056 -10000 0 -10000 0 0
INS 0.012 0.003 -10000 0 -10000 0 0
BIN1 0.012 0 -10000 0 -10000 0 0
mol:Choline 0.025 0.01 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.016 0.029 -10000 0 -0.58 1 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.012 0 -10000 0 -10000 0 0
mol:Ca2+ 0.022 0.027 -10000 0 -0.53 1 1
JUP 0.017 0.05 -10000 0 -10000 0 0
ASAP2/amphiphysin II 0.024 0 -10000 0 -10000 0 0
ARF6/GTP 0.009 0 -10000 0 -10000 0 0
CDH1 0.021 0.034 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0.009 0 -10000 0 -10000 0 0
MAPK8IP3 0.011 0.023 -10000 0 -0.47 1 1
positive regulation of endocytosis 0.009 0 -10000 0 -10000 0 0
EXOC2 0.012 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.041 0 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.012 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.005 0.034 0.42 2 -10000 0 2
positive regulation of phagocytosis 0.018 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 -0.001 0.013 -10000 0 -10000 0 0
ACAP1 0.022 0.017 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.055 0.099 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.034 0.015 -10000 0 -10000 0 0
JIP4/KLC1 0.024 0 -10000 0 -10000 0 0
EXOC1 0.012 0 -10000 0 -10000 0 0
exocyst 0.041 0 -10000 0 -10000 0 0
RALA/GTP 0.009 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -10000 0 -10000 0 0
receptor recycling 0.009 0 -10000 0 -10000 0 0
CTNNA1 0.029 0.026 -10000 0 -0.49 1 1
NME1 0.016 0.029 -10000 0 -0.58 1 1
clathrin coat assembly 0.03 0.016 -10000 0 -10000 0 0
IL2RA 0.006 0.072 -10000 0 -10000 0 0
VAMP3 0.018 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.06 0.089 -10000 0 -0.43 3 3
EXOC6 0.012 0 -10000 0 -10000 0 0
PLD1 0.021 0.014 -10000 0 -0.26 1 1
PLD2 0.021 0 -10000 0 -10000 0 0
EXOC5 0.012 0 -10000 0 -10000 0 0
PIP5K1C 0.03 0.008 -10000 0 -10000 0 0
SDC1 0.025 0.023 -10000 0 -10000 0 0
ARF6/GDP 0.016 0.029 -10000 0 -0.58 1 1
EXOC7 0.012 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.005 0.035 -10000 0 -0.44 2 2
mol:Phosphatidic acid 0.025 0.01 -10000 0 -10000 0 0
endocytosis 0 0 -10000 0 -10000 0 0
SCAMP2 0.012 0 -10000 0 -10000 0 0
ADRB2 -0.032 0.11 -10000 0 -10000 0 0
EXOC3 0.012 0 -10000 0 -10000 0 0
ASAP2 0.012 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.023 0.027 -10000 0 -0.53 1 1
KLC1 0.012 0 -10000 0 -10000 0 0
AVPR2 0.018 0.067 -10000 0 -0.46 2 2
RALA 0.012 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.004 0.031 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.013 0 -9999 0 -10000 0 0
TRAF2/ASK1 0 0 -9999 0 -10000 0 0
ATM 0.01 0.042 -9999 0 -0.85 1 1
MAP2K3 0.025 0.032 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.033 0.036 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G 0.009 0.048 -9999 0 -0.66 2 2
TXN 0.008 0 -9999 0 -10000 0 0
CALM1 0.012 0 -9999 0 -10000 0 0
GADD45A 0.012 0 -9999 0 -10000 0 0
GADD45B 0.011 0.023 -9999 0 -0.47 1 1
MAP3K1 0.012 0 -9999 0 -10000 0 0
MAP3K6 0.012 0 -9999 0 -10000 0 0
MAP3K7 0.012 0 -9999 0 -10000 0 0
MAP3K4 0.012 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 0.019 0 -9999 0 -10000 0 0
TAK1/TAB family 0 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3 0.024 0 -9999 0 -10000 0 0
TRAF2 0.012 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.003 0.011 -9999 0 -10000 0 0
TRAF6 0.008 0 -9999 0 -10000 0 0
RAC1 0.012 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B -0.08 0.2 -9999 0 -0.49 76 76
CCM2 0.012 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.053 0.12 -9999 0 -0.58 4 4
MAPK11 0.012 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.027 0.11 -9999 0 -0.53 4 4
OSM/MEKK3 0.019 0 -9999 0 -10000 0 0
TAOK1 0.015 0.019 -9999 0 -0.38 1 1
TAOK2 0.015 0.019 -9999 0 -0.38 1 1
TAOK3 0.015 0.019 -9999 0 -0.38 1 1
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.012 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
MAP3K5 0.012 0 -9999 0 -10000 0 0
MAP3K10 0.012 0 -9999 0 -10000 0 0
MAP3K3 0.012 0 -9999 0 -10000 0 0
TRX/ASK1 0.015 0 -9999 0 -10000 0 0
GADD45/MTK1/MTK1 -0.002 0.029 -9999 0 -0.5 1 1
Canonical NF-kappaB 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
FBXW11 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.077 0.025 -9999 0 -10000 0 0
ERC1 0.01 0.042 -9999 0 -0.85 1 1
RIP2/NOD2 0.004 0.096 -9999 0 -0.59 10 10
NFKBIA 0.043 0 -9999 0 -10000 0 0
BIRC2 0.012 0 -9999 0 -10000 0 0
IKBKB 0.012 0 -9999 0 -10000 0 0
RIPK2 0.004 0.084 -9999 0 -0.85 4 4
IKBKG -0.005 0.03 -9999 0 -10000 0 0
IKK complex/A20 -0.02 0.081 -9999 0 -10000 0 0
NEMO/A20/RIP2 0.004 0.084 -9999 0 -0.85 4 4
XPO1 0.012 0 -9999 0 -10000 0 0
NEMO/ATM 0.042 0.043 -9999 0 -0.45 1 1
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.012 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.005 0.031 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0 0 -9999 0 -10000 0 0
NOD2 0.002 0.091 -9999 0 -0.72 6 6
NFKB1 0.016 0 -9999 0 -10000 0 0
RELA 0.016 0 -9999 0 -10000 0 0
MALT1 0.012 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0.019 0 -9999 0 -10000 0 0
ATM 0.01 0.042 -9999 0 -0.85 1 1
TNF/TNFR1A -0.008 0.13 -9999 0 -0.66 14 14
TRAF6 0.012 0 -9999 0 -10000 0 0
PRKCA 0.012 0 -9999 0 -10000 0 0
CHUK 0.012 0 -9999 0 -10000 0 0
UBE2D3 0.012 0 -9999 0 -10000 0 0
TNF -0.022 0.16 -9999 0 -0.75 19 19
NF kappa B1 p50/RelA 0 0 -9999 0 -10000 0 0
BCL10 0.012 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.043 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -10000 0 0
TNFRSF1A 0.012 0 -9999 0 -10000 0 0
IKK complex 0.049 0.034 -9999 0 -10000 0 0
CYLD 0.012 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.004 0.024 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.03 0.039 -9999 0 -0.52 2 2
HDAC3 0.012 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
GATA1/HDAC4 0.012 0.041 -9999 0 -0.32 6 6
GATA1/HDAC5 0.012 0.041 -9999 0 -10000 0 0
GATA2/HDAC5 0.014 0.041 -9999 0 -10000 0 0
HDAC5/BCL6/BCoR 0 0 -9999 0 -10000 0 0
HDAC9 -0.01 0.11 -9999 0 -0.49 19 19
Glucocorticoid receptor/Hsp90/HDAC6 -0.006 0.049 -9999 0 -0.57 2 2
HDAC4/ANKRA2 0.019 0 -9999 0 -10000 0 0
HDAC5/YWHAB 0.019 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.021 0 -9999 0 -10000 0 0
GATA2 0.006 0.057 -9999 0 -0.47 6 6
HDAC4/RFXANK 0.019 0 -9999 0 -10000 0 0
BCOR 0.012 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.012 0 -9999 0 -10000 0 0
HDAC5 0.012 0 -9999 0 -10000 0 0
GNB1/GNG2 0.017 0.033 -9999 0 -0.66 1 1
Histones 0.029 0.044 -9999 0 -10000 0 0
ADRBK1 0.01 0.042 -9999 0 -0.85 1 1
HDAC4 0.012 0 -9999 0 -10000 0 0
XPO1 0.012 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.019 0 -9999 0 -10000 0 0
HDAC4/Ubc9 0.019 0 -9999 0 -10000 0 0
HDAC7 0.012 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.019 0 -9999 0 -10000 0 0
TUBA1B 0.012 0 -9999 0 -10000 0 0
HDAC6 0.012 0 -9999 0 -10000 0 0
HDAC5/RFXANK 0.019 0 -9999 0 -10000 0 0
CAMK4 -0.005 0.093 -9999 0 -0.49 14 14
Tubulin/HDAC6 -0.001 0.013 -9999 0 -10000 0 0
SUMO1 0.012 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.012 0 -9999 0 -10000 0 0
GATA1 0.003 0.057 -9999 0 -0.47 6 6
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.012 0 -9999 0 -10000 0 0
NR3C1 0.007 0.052 -9999 0 -0.47 5 5
SUMO1/HDAC4 0.029 0 -9999 0 -10000 0 0
SRF 0.012 0 -9999 0 -10000 0 0
HDAC4/YWHAB 0.019 0 -9999 0 -10000 0 0
Tubulin 0.018 0.017 -9999 0 -10000 0 0
HDAC4/14-3-3 E 0.019 0 -9999 0 -10000 0 0
GNB1 0.012 0 -9999 0 -10000 0 0
RANGAP1 0.012 0 -9999 0 -10000 0 0
BCL6/BCoR 0.019 0 -9999 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0 0 -9999 0 -10000 0 0
HDAC4/SRF -0.01 0.054 -9999 0 -0.57 1 1
HDAC4/ER alpha 0.005 0.07 -9999 0 -0.66 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.029 0.044 -9999 0 -10000 0 0
cell motility -0.001 0.013 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.012 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0.019 0 -9999 0 -10000 0 0
BCL6 0.012 0 -9999 0 -10000 0 0
HDAC4/CaMK II delta B 0.012 0 -9999 0 -10000 0 0
Hsp90/HDAC6 0.015 0.047 -9999 0 -0.66 2 2
ESR1 -0.006 0.096 -9999 0 -0.49 15 15
HDAC6/HDAC11 0.019 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.032 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
MEF2C 0.012 0 -9999 0 -10000 0 0
RAN 0.012 0 -9999 0 -10000 0 0
HDAC4/MEF2C 0 0 -9999 0 -10000 0 0
GNG2 0.01 0.042 -9999 0 -0.85 1 1
NCOR2 0.012 0 -9999 0 -10000 0 0
TUBB2A 0.011 0.023 -9999 0 -0.47 1 1
HDAC11 0.012 0 -9999 0 -10000 0 0
HSP90AA1 0.008 0.06 -9999 0 -0.85 2 2
RANBP2 0.012 0 -9999 0 -10000 0 0
ANKRA2 0.012 0 -9999 0 -10000 0 0
RFXANK 0.012 0 -9999 0 -10000 0 0
nuclear import -0.028 0 -9999 0 -10000 0 0
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 0.044 0.038 -10000 0 -10000 0 0
CLOCK 0.016 0.002 -10000 0 -10000 0 0
TIMELESS/CRY2 0.041 0.014 -10000 0 -10000 0 0
DEC1/BMAL1 0.01 0.037 -10000 0 -0.49 2 2
ATR 0.012 0 -10000 0 -10000 0 0
NR1D1 0.039 0.035 -10000 0 -0.67 1 1
ARNTL 0.014 0.023 -10000 0 -0.46 1 1
TIMELESS 0.04 0.015 -10000 0 -10000 0 0
NPAS2 0.016 0.002 -10000 0 -10000 0 0
CRY2 0.012 0 -10000 0 -10000 0 0
mol:CO -0.013 0.006 0.11 1 -10000 0 1
CHEK1 0.008 0.06 -10000 0 -0.85 2 2
mol:HEME 0.013 0.006 -10000 0 -0.11 1 1
PER1 -0.001 0.08 -10000 0 -0.47 12 12
BMAL/CLOCK/NPAS2 0.041 0.016 -10000 0 -10000 0 0
BMAL1/CLOCK 0.044 0.038 -10000 0 -10000 0 0
S phase of mitotic cell cycle 0.044 0.038 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.044 0.038 -10000 0 -10000 0 0
mol:NADPH 0.013 0.006 -10000 0 -0.11 1 1
PER1/TIMELESS 0.034 0.045 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 -0.001 0.042 -10000 0 -0.85 1 1
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.033 0.072 -10000 0 -0.69 4 4
regulation of axonogenesis -0.026 0.023 0.33 1 -10000 0 1
myoblast fusion -0.015 0.039 0.36 4 -10000 0 4
mol:GTP -0.002 0.02 -10000 0 -0.25 1 1
regulation of calcium-dependent cell-cell adhesion -0.021 0.073 0.54 5 -10000 0 5
ARF1/GTP -0.001 0.014 -10000 0 -10000 0 0
mol:GM1 0.009 0.016 -10000 0 -10000 0 0
mol:Choline 0.025 0.032 -10000 0 -0.55 1 1
lamellipodium assembly -0.001 0.039 -10000 0 -0.35 4 4
MAPK3 0.025 0.03 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.021 0.074 -10000 0 -0.55 5 5
ARF1 0.012 0 -10000 0 -10000 0 0
ARF6/GDP 0.015 0.04 -10000 0 -0.36 4 4
ARF1/GDP 0.024 0.037 -10000 0 -0.47 1 1
ARF6 0.011 0.012 -10000 0 -10000 0 0
RAB11A 0.012 0 -10000 0 -10000 0 0
TIAM1 -0.001 0.1 -10000 0 -0.62 10 10
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.025 0.03 -10000 0 -0.31 1 1
actin filament bundle formation -0.021 0.036 0.46 1 -10000 0 1
KALRN -0.003 0.042 -10000 0 -0.52 1 1
RAB11FIP3/RAB11A 0.019 0 -10000 0 -10000 0 0
RhoA/GDP 0.021 0.036 -10000 0 -0.47 1 1
NME1 0.012 0.042 -10000 0 -0.85 1 1
Rac1/GDP 0.021 0.036 -10000 0 -0.47 1 1
substrate adhesion-dependent cell spreading -0.002 0.02 -10000 0 -0.25 1 1
cortical actin cytoskeleton organization -0.001 0.039 -10000 0 -0.35 4 4
RAC1 0.012 0 -10000 0 -10000 0 0
liver development -0.002 0.02 -10000 0 -0.25 1 1
ARF6/GTP -0.002 0.02 -10000 0 -0.25 1 1
RhoA/GTP -0.001 0.014 -10000 0 -10000 0 0
mol:GDP -0.001 0.04 -10000 0 -0.36 4 4
ARF6/GTP/RAB11FIP3/RAB11A -0.001 0.011 -10000 0 -10000 0 0
RHOA 0.012 0 -10000 0 -10000 0 0
PLD1 0.017 0.035 -10000 0 -0.62 1 1
RAB11FIP3 0.012 0 -10000 0 -10000 0 0
tube morphogenesis -0.001 0.039 -10000 0 -0.35 4 4
ruffle organization 0.026 0.023 -10000 0 -0.33 1 1
regulation of epithelial cell migration -0.002 0.02 -10000 0 -0.25 1 1
PLD2 0.019 0.016 -10000 0 -10000 0 0
PIP5K1A 0.026 0.023 -10000 0 -0.33 1 1
mol:Phosphatidic acid 0.025 0.032 -10000 0 -0.55 1 1
Rac1/GTP -0.001 0.039 -10000 0 -0.35 4 4
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.049 0.074 -10000 0 -10000 0 0
CaM/Ca2+ 0.009 0 -10000 0 -10000 0 0
AKT1 0.012 0 -10000 0 -10000 0 0
AKT2 0.012 0 -10000 0 -10000 0 0
STXBP4 0.01 0.042 -10000 0 -0.85 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.022 0.11 0.3 10 -10000 0 10
YWHAZ 0.012 0 -10000 0 -10000 0 0
CALM1 0.012 0 -10000 0 -10000 0 0
YWHAQ 0.012 0 -10000 0 -10000 0 0
TBC1D4 0.007 0.099 -10000 0 -0.66 9 9
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.012 0 -10000 0 -10000 0 0
YWHAB 0.012 0 -10000 0 -10000 0 0
SNARE/Synip -0.001 0.028 -10000 0 -0.57 1 1
YWHAG 0.012 0 -10000 0 -10000 0 0
ASIP -0.016 0.15 -10000 0 -0.85 13 13
PRKCI 0.004 0.084 -10000 0 -0.85 4 4
AS160/CaM/Ca2+ 0.009 0 -10000 0 -10000 0 0
RHOQ 0.012 0 -10000 0 -10000 0 0
GYS1 0.03 0 -10000 0 -10000 0 0
PRKCZ 0.012 0 -10000 0 -10000 0 0
TRIP10 0.012 0 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -10000 0 -10000 0 0
AS160/14-3-3 0.033 0.05 -10000 0 -10000 0 0
VAMP2 0.012 0 -10000 0 -10000 0 0
SLC2A4 -0.025 0.12 0.31 10 -10000 0 10
STX4 0.012 0 -10000 0 -10000 0 0
GSK3B 0.025 0 -10000 0 -10000 0 0
SFN -0.008 0.12 -10000 0 -0.64 13 13
LNPEP 0.012 0 -10000 0 -10000 0 0
YWHAE 0.012 0 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.022 0 -9999 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.032 0 -9999 0 -10000 0 0
CDKN1B 0.033 0.017 -9999 0 -10000 0 0
CDKN1A 0.033 0.017 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
PRKDC 0.012 0 -9999 0 -10000 0 0
FOXO3 0.034 0.013 -9999 0 -10000 0 0
AKT1 -0.001 0.011 -9999 0 -10000 0 0
BAD 0.012 0 -9999 0 -10000 0 0
AKT3 0.015 0.02 -9999 0 -0.38 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
FOXO4 0.033 0.017 -9999 0 -10000 0 0
AKT1/ASK1 0.032 0.013 -9999 0 -10000 0 0
BAD/YWHAZ 0 0 -9999 0 -10000 0 0
RICTOR 0.008 0.06 -9999 0 -0.85 2 2
RAF1 0.012 0 -9999 0 -10000 0 0
JNK cascade 0.001 0.009 -9999 0 -10000 0 0
TSC1 0.034 0.013 -9999 0 -10000 0 0
YWHAZ 0.012 0 -9999 0 -10000 0 0
AKT1/RAF1 0.034 0.013 -9999 0 -10000 0 0
EP300 0.012 0 -9999 0 -10000 0 0
mol:GDP 0.028 0.014 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
TSC2 0.034 0.013 -9999 0 -10000 0 0
YWHAQ 0.012 0 -9999 0 -10000 0 0
TBC1D4 0.01 0.086 -9999 0 -0.57 9 9
MAP3K5 0.012 0 -9999 0 -10000 0 0
MAPKAP1 0.012 0 -9999 0 -10000 0 0
negative regulation of cell cycle -0.037 0.025 -9999 0 -10000 0 0
YWHAH 0.012 0 -9999 0 -10000 0 0
AKT1S1 0.034 0.013 -9999 0 -10000 0 0
CASP9 0.034 0.013 -9999 0 -10000 0 0
YWHAB 0.012 0 -9999 0 -10000 0 0
p27Kip1/KPNA1 0.039 0.017 -9999 0 -10000 0 0
GBL 0 0 -9999 0 -10000 0 0
PDK1/Src/Hsp90 -0.003 0.04 -9999 0 -0.57 2 2
YWHAE 0.012 0 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
AKT2/p21CIP1 -0.001 0.013 -9999 0 -10000 0 0
KIAA1303 0 0 -9999 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.017 0.005 -9999 0 -10000 0 0
CHUK 0.034 0.013 -9999 0 -10000 0 0
BAD/BCL-XL 0.046 0.012 -9999 0 -10000 0 0
mTORC2 0.013 0.038 -9999 0 -0.54 2 2
AKT2 0.016 0 -9999 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.051 0.03 -9999 0 -10000 0 0
PDPK1 0.012 0 -9999 0 -10000 0 0
MDM2 0.021 0.085 -9999 0 -0.49 11 11
MAPKKK cascade -0.034 0.013 -9999 0 -10000 0 0
MDM2/Cbp/p300 0.033 0.079 -9999 0 -0.44 11 11
TSC1/TSC2 0.04 0.013 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.032 0.076 -9999 0 -0.42 11 11
glucose import -0.069 0.15 -9999 0 -0.59 12 12
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.029 0.01 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
SLC2A4 -0.069 0.15 -9999 0 -0.6 12 12
GSK3A 0.034 0.013 -9999 0 -10000 0 0
FOXO1 0.034 0.013 -9999 0 -10000 0 0
GSK3B 0.034 0.013 -9999 0 -10000 0 0
SFN -0.008 0.12 -9999 0 -0.64 13 13
G1/S transition of mitotic cell cycle 0.04 0.013 -9999 0 -10000 0 0
p27Kip1/14-3-3 family 0.039 0.037 -9999 0 -10000 0 0
PRKACA 0.012 0 -9999 0 -10000 0 0
KPNA1 0.012 0 -9999 0 -10000 0 0
HSP90AA1 0.008 0.06 -9999 0 -0.85 2 2
YWHAG 0.012 0 -9999 0 -10000 0 0
RHEB 0.012 0 -9999 0 -10000 0 0
CREBBP 0.012 0 -9999 0 -10000 0 0
ceramide signaling pathway

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
MAP4K4 0.036 0.065 -9999 0 -0.43 3 3
BAG4 0.01 0.042 -9999 0 -0.85 1 1
BAD 0.028 0.022 -9999 0 -10000 0 0
NFKBIA 0.012 0 -9999 0 -10000 0 0
BIRC3 0.001 0.097 -9999 0 -0.79 6 6
BAX 0.028 0.022 -9999 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.012 0.016 -9999 0 -0.099 1 1
IKBKB 0.041 0.062 -9999 0 -0.4 3 3
MAP2K2 0.038 0.025 -9999 0 -10000 0 0
MAP2K1 0.038 0.025 -9999 0 -10000 0 0
SMPD1 0.018 0.016 -9999 0 -10000 0 0
GO:0005551 0 0 -9999 0 -10000 0 0
FADD/Caspase 8 0.045 0.054 -9999 0 -0.39 1 1
MAP2K4 0.033 0.022 -9999 0 -10000 0 0
protein ubiquitination 0.043 0.062 -9999 0 -0.41 3 3
EnzymeConsortium:2.7.1.37 0.042 0.027 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
RAF1 0.034 0.024 -9999 0 -10000 0 0
CRADD 0.013 0 -9999 0 -10000 0 0
mol:ceramide 0.021 0.023 -9999 0 -0.14 1 1
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -9999 0 -10000 0 0
MADD 0.013 0 -9999 0 -10000 0 0
MAP3K1 0.028 0.023 -9999 0 -10000 0 0
TRADD 0.013 0 -9999 0 -10000 0 0
RELA/p50 0.012 0 -9999 0 -10000 0 0
MAPK3 0.04 0.024 -9999 0 -10000 0 0
MAPK1 0.04 0.024 -9999 0 -10000 0 0
p50/RELA/I-kappa-B-alpha 0.019 0 -9999 0 -10000 0 0
FADD 0.038 0.055 -9999 0 -0.41 1 1
KSR1 0.028 0.023 -9999 0 -10000 0 0
MAPK8 0.039 0.021 -9999 0 -10000 0 0
TRAF2 0.012 0 -9999 0 -10000 0 0
response to radiation 0 0 -9999 0 -10000 0 0
CHUK 0.041 0.062 -9999 0 -0.4 3 3
TNF R/SODD 0.017 0.033 -9999 0 -0.66 1 1
TNF -0.022 0.16 -9999 0 -0.75 19 19
CYCS 0.03 0.026 -9999 0 -10000 0 0
IKBKG 0.041 0.062 -9999 0 -0.4 3 3
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.032 0.058 -9999 0 -0.44 1 1
RELA 0.012 0 -9999 0 -10000 0 0
RIPK1 0.012 0 -9999 0 -10000 0 0
AIFM1 0.03 0.025 -9999 0 -10000 0 0
TNF/TNF R/SODD -0.023 0.11 -9999 0 -0.57 15 15
TNFRSF1A 0.012 0 -9999 0 -10000 0 0
response to heat 0 0 -9999 0 -10000 0 0
CASP8 0.027 0.015 -9999 0 -10000 0 0
NSMAF 0.038 0.055 -9999 0 -0.41 1 1
response to hydrogen peroxide 0 0 -9999 0 -10000 0 0
BCL2 0.006 0.057 -9999 0 -0.47 6 6
HIF-2-alpha transcription factor network

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
MMP14 -0.002 0.052 -10000 0 -0.72 2 2
oxygen homeostasis 0.005 0.016 -10000 0 -10000 0 0
TCEB2 0.012 0 -10000 0 -10000 0 0
TCEB1 0.012 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.01 0.027 -10000 0 -10000 0 0
EPO 0.063 0.22 -10000 0 -0.77 4 4
FIH (dimer) 0.017 0.016 -10000 0 -10000 0 0
APEX1 0.017 0.015 -10000 0 -10000 0 0
SERPINE1 -0.007 0.34 -10000 0 -0.84 20 20
FLT1 0.001 0.037 -10000 0 -0.7 1 1
ADORA2A 0.069 0.21 -10000 0 -0.74 2 2
germ cell development 0.048 0.25 -10000 0 -0.8 8 8
SLC11A2 0.073 0.21 -10000 0 -0.73 1 1
BHLHE40 0.072 0.21 -10000 0 -0.78 2 2
HIF1AN 0.017 0.016 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.035 0.06 -10000 0 -10000 0 0
ETS1 0.027 0.001 -10000 0 -10000 0 0
CITED2 -0.004 0.069 -10000 0 -0.97 2 2
KDR 0.003 0.015 -10000 0 -10000 0 0
PGK1 0.073 0.21 -10000 0 -0.73 1 1
SIRT1 0.012 0.002 -10000 0 -10000 0 0
response to hypoxia 0 0.003 -10000 0 -10000 0 0
HIF2A/ARNT 0.075 0.23 -10000 0 -0.79 2 2
EPAS1 0.057 0.095 -10000 0 -10000 0 0
SP1 0.02 0.001 -10000 0 -10000 0 0
ABCG2 0.06 0.23 -10000 0 -0.71 5 5
EFNA1 0.07 0.22 -10000 0 -0.8 3 3
FXN 0.071 0.2 -10000 0 -0.71 1 1
POU5F1 0.047 0.26 -10000 0 -0.85 8 8
neuron apoptosis -0.074 0.23 0.76 2 -10000 0 2
EP300 0.012 0 -10000 0 -10000 0 0
EGLN3 0.016 0.029 -10000 0 -0.47 1 1
EGLN2 0.018 0.016 -10000 0 -10000 0 0
EGLN1 0.017 0.016 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0 0 -10000 0 -10000 0 0
VHL 0.012 0 -10000 0 -10000 0 0
ARNT 0.017 0.015 -10000 0 -10000 0 0
SLC2A1 0.035 0.27 -10000 0 -0.82 11 11
TWIST1 0.057 0.22 -10000 0 -0.82 3 3
ELK1 0.02 0.005 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.03 0.055 -10000 0 -10000 0 0
VEGFA 0.066 0.22 -10000 0 -0.8 3 3
CREBBP 0.012 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.018 0.084 -9999 0 -0.44 14 14
Ran/GTP/Exportin 1/HDAC1 0 0.009 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.03 0.073 -9999 0 -10000 0 0
SUMO1 0.012 0 -9999 0 -10000 0 0
ZFPM1 0.011 0.023 -9999 0 -0.47 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.021 0 -9999 0 -10000 0 0
FKBP3 0.012 0 -9999 0 -10000 0 0
Histones 0.033 0.047 -9999 0 -10000 0 0
YY1/LSF 0.027 0.023 -9999 0 -10000 0 0
SMG5 0.012 0 -9999 0 -10000 0 0
RAN 0.012 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 0.018 0.07 -9999 0 -10000 0 0
I kappa B alpha/HDAC1 0.02 0.052 -9999 0 -10000 0 0
SAP18 0.01 0.042 -9999 0 -0.85 1 1
RELA 0.023 0.06 -9999 0 -10000 0 0
HDAC1/Smad7 -0.005 0.05 -9999 0 -0.57 3 3
RANGAP1 0.012 0 -9999 0 -10000 0 0
HDAC3/TR2 0.02 0.05 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.045 0.009 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.027 0.055 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.006 0.057 -9999 0 -0.47 6 6
GATA1 0.003 0.057 -9999 0 -0.47 6 6
Mad/Max 0.019 0 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.051 0.026 -9999 0 -10000 0 0
RBBP7 0.012 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
RBBP4 0.012 0 -9999 0 -10000 0 0
MAX 0.012 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.012 0 -9999 0 -10000 0 0
NFKBIA 0.015 0.056 -9999 0 -10000 0 0
KAT2B 0.008 0.047 -9999 0 -0.47 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.04 0.016 -9999 0 -10000 0 0
SIN3 complex 0.031 0.027 -9999 0 -0.52 1 1
SMURF1 0.006 0.073 -9999 0 -0.85 3 3
CHD3 0.012 0 -9999 0 -10000 0 0
SAP30 0.012 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.012 0 -9999 0 -10000 0 0
YY1/HDAC3 0.03 0.05 -9999 0 -10000 0 0
YY1/HDAC2 0.027 0.023 -9999 0 -10000 0 0
YY1/HDAC1 0.027 0.026 -9999 0 -10000 0 0
NuRD/MBD2 Complex (MeCP1) 0.045 0.009 -9999 0 -10000 0 0
PPARG 0.016 0.086 -9999 0 -0.36 14 14
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0.012 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.012 0 -9999 0 -10000 0 0
TNFRSF1A 0.012 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.02 0.05 -9999 0 -10000 0 0
MBD3L2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.005 0.05 -9999 0 -0.57 3 3
CREBBP 0.012 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.048 0.009 -9999 0 -10000 0 0
HDAC1 0.011 0.023 -9999 0 -0.47 1 1
HDAC3 0.015 0.056 -9999 0 -10000 0 0
HDAC2 0.012 0 -9999 0 -10000 0 0
YY1 0.026 0.027 -9999 0 -10000 0 0
HDAC8 0.012 0 -9999 0 -10000 0 0
SMAD7 0.012 0 -9999 0 -10000 0 0
NCOR2 0.012 0 -9999 0 -10000 0 0
MXD1 0.012 0 -9999 0 -10000 0 0
STAT3 0.025 0 -9999 0 -10000 0 0
NFKB1 0.012 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.012 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 0.033 0.024 -9999 0 -10000 0 0
YY1/SAP30/HDAC1 0.033 0.024 -9999 0 -10000 0 0
EP300 0.012 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.025 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.056 -9999 0 -10000 0 0
histone deacetylation 0.045 0.009 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.029 0.047 -9999 0 -10000 0 0
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0.012 0 -9999 0 -10000 0 0
GATAD2B 0.012 0 -9999 0 -10000 0 0
GATAD2A 0.012 0 -9999 0 -10000 0 0
GATA2/HDAC3 0.017 0.058 -9999 0 -10000 0 0
GATA1/HDAC1 0.011 0.044 -9999 0 -0.32 7 7
GATA1/HDAC3 0.011 0.061 -9999 0 -0.47 1 1
CHD4 0.012 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.008 0.13 -9999 0 -0.66 14 14
SIN3/HDAC complex/Mad/Max 0.044 0.013 -9999 0 -10000 0 0
NuRD Complex 0.053 0.009 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.008 0.037 -9999 0 -10000 0 0
SIN3B 0.012 0 -9999 0 -10000 0 0
MTA2 0.012 0 -9999 0 -10000 0 0
SIN3A 0.012 0 -9999 0 -10000 0 0
XPO1 0.012 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.028 0.012 -9999 0 -10000 0 0
HDAC complex 0.032 0.013 -9999 0 -10000 0 0
GATA1/Fog1 0.011 0.044 -9999 0 -0.32 7 7
FKBP25/HDAC1/HDAC2 -0.001 0.013 -9999 0 -10000 0 0
TNF -0.022 0.16 -9999 0 -0.75 19 19
negative regulation of cell growth 0.044 0.013 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.045 0.009 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.032 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.024 0.076 -9999 0 -0.34 14 14
SIN3/HDAC complex/NCoR1 0.042 0.015 -9999 0 -10000 0 0
TFCP2 0.012 0 -9999 0 -10000 0 0
NR2C1 0.012 0 -9999 0 -10000 0 0
MBD3 0.012 0 -9999 0 -10000 0 0
MBD2 0.012 0 -9999 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.012 0 -10000 0 -10000 0 0
Rac1/GDP 0.001 0.007 -10000 0 -10000 0 0
DOCK1 0.012 0 -10000 0 -10000 0 0
ITGA4 0.006 0.073 -10000 0 -0.85 3 3
RAC1 0.012 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.013 0.06 -10000 0 -0.66 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.012 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin -0.006 0.056 -10000 0 -0.57 4 4
alpha4/beta7 Integrin/Paxillin 0.027 0.049 -10000 0 -0.52 3 3
lamellipodium assembly 0 0.017 -10000 0 -10000 0 0
PIK3CA 0.01 0.042 -10000 0 -0.85 1 1
PI3K 0.017 0.033 -10000 0 -0.66 1 1
ARF6 0.012 0 -10000 0 -10000 0 0
TLN1 0.012 0 -10000 0 -10000 0 0
PXN 0.022 0 -10000 0 -10000 0 0
PIK3R1 0.012 0 -10000 0 -10000 0 0
ARF6/GTP -0.004 0.044 -10000 0 -10000 0 0
cell adhesion 0.032 0.051 -10000 0 -0.48 4 4
CRKL/CBL 0.017 0.033 -10000 0 -0.66 1 1
alpha4/beta1 Integrin/Paxillin 0.026 0.054 -10000 0 -0.52 4 4
ITGB1 0.01 0.042 -10000 0 -0.85 1 1
ITGB7 0.011 0.023 -10000 0 -0.47 1 1
ARF6/GDP 0.001 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.029 0.068 -10000 0 -0.49 7 7
p130Cas/Crk/Dock1 0 0 -10000 0 -10000 0 0
VCAM1 0.006 0.073 -10000 0 -0.85 3 3
alpha4/beta1 Integrin/Paxillin/Talin 0.033 0.052 -10000 0 -0.49 4 4
alpha4/beta1 Integrin/Paxillin/GIT1 0.033 0.052 -10000 0 -0.49 4 4
BCAR1 0.012 0 -10000 0 -10000 0 0
mol:GDP -0.032 0.051 0.48 4 -10000 0 4
CBL 0.01 0.042 -10000 0 -0.85 1 1
PRKACA 0.012 0 -10000 0 -10000 0 0
GIT1 0.012 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.033 0.052 -10000 0 -0.49 4 4
Rac1/GTP -0.001 0.018 -10000 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.011 0.023 -9999 0 -0.47 1 1
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
MDM2/SUMO1 0.015 0.082 -9999 0 -0.48 11 11
HDAC4 0.012 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0 0.008 -9999 0 -10000 0 0
SUMO1 0.012 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.027 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.012 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.012 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.029 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.028 0.012 -9999 0 -10000 0 0
RANGAP1 0.012 0 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.016 0.093 -9999 0 -0.52 12 12
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.021 0 -9999 0 -10000 0 0
Ran/GTP 0.026 0 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 -0.01 0.14 -9999 0 -0.85 11 11
UBE2I 0.012 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.031 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
PIAS2 0.01 0.042 -9999 0 -0.85 1 1
PIAS1 0.012 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

Figure S127.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S127.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.01 0.033 -9999 0 -0.47 2 2
SMAD2 0.013 0 -9999 0 -10000 0 0
SMAD3 0.039 0 -9999 0 -10000 0 0
SMAD3/SMAD4 0.043 0.023 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy -0.001 0.018 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.034 0.037 -9999 0 -0.45 2 2
PPM1A 0.012 0 -9999 0 -10000 0 0
CALM1 0.012 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.019 0.018 -9999 0 -10000 0 0
MAP3K1 0.012 0 -9999 0 -10000 0 0
TRAP-1/SMAD4 0.017 0.024 -9999 0 -10000 0 0
MAPK3 0.012 0 -9999 0 -10000 0 0
MAPK1 0.012 0 -9999 0 -10000 0 0
NUP214 0.012 0 -9999 0 -10000 0 0
CTDSP1 0.012 0 -9999 0 -10000 0 0
CTDSP2 0.012 0 -9999 0 -10000 0 0
CTDSPL 0.012 0 -9999 0 -10000 0 0
KPNB1 0.012 0 -9999 0 -10000 0 0
TGFBRAP1 0.012 0 -9999 0 -10000 0 0
UBE2I 0.012 0 -9999 0 -10000 0 0
NUP153 0.012 0 -9999 0 -10000 0 0
KPNA2 0.008 0.06 -9999 0 -0.85 2 2
PIAS4 0.012 0 -9999 0 -10000 0 0
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.012 0 -10000 0 -10000 0 0
mol:PIP3 -0.002 0.026 -10000 0 -0.47 1 1
FRAP1 0.014 0.009 -10000 0 -10000 0 0
AKT1 0.025 0.026 -10000 0 -0.42 1 1
INSR 0.012 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0 0.001 -10000 0 -10000 0 0
mol:GTP -0.001 0.019 -10000 0 -0.34 1 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0 0.007 -10000 0 -10000 0 0
TSC2 0.012 0 -10000 0 -10000 0 0
RHEB/GDP -0.001 0.017 -10000 0 -10000 0 0
TSC1 0.013 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.015 0.016 -10000 0 -0.31 1 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.001 0.008 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.012 0 -10000 0 -10000 0 0
RPS6KB1 0.026 0.016 -10000 0 -10000 0 0
MAP3K5 0.01 0 -10000 0 -10000 0 0
PIK3R1 0.013 0 -10000 0 -10000 0 0
apoptosis 0.01 0 -10000 0 -10000 0 0
mol:LY294002 0 0 -10000 0 -0.001 1 1
EIF4B 0.031 0.015 -10000 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.001 0.011 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1 0 0.004 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.022 0.029 -10000 0 -0.48 1 1
mTOR/RHEB/GTP/Raptor/GBL 0.029 0.012 -10000 0 -10000 0 0
FKBP1A 0.013 0 -10000 0 -10000 0 0
RHEB/GTP -0.001 0.017 -10000 0 -10000 0 0
mol:Amino Acids 0 0 -10000 0 -0.001 1 1
FKBP12/Rapamycin 0.01 0.001 -10000 0 -10000 0 0
PDPK1 -0.002 0.024 -10000 0 -0.44 1 1
EIF4E 0.012 0 -10000 0 -10000 0 0
ASK1/PP5C 0.021 0.006 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.016 0.001 -10000 0 -10000 0 0
TSC1/TSC2 0.036 0.023 -10000 0 -0.37 1 1
tumor necrosis factor receptor activity 0 0 0.001 1 -10000 0 1
RPS6 0.012 0 -10000 0 -10000 0 0
PPP5C 0.012 0 -10000 0 -10000 0 0
EIF4G1 0.012 0 -10000 0 -10000 0 0
IRS1 0.007 0.017 -10000 0 -0.34 1 1
INS 0.001 0.003 -10000 0 -10000 0 0
PTEN 0.012 0 -10000 0 -10000 0 0
PDK2 -0.002 0.026 -10000 0 -0.44 1 1
EIF4EBP1 0.01 0.029 -10000 0 -0.41 2 2
PIK3CA 0.011 0.042 -10000 0 -0.85 1 1
PPP2R5D 0.02 0.008 -10000 0 -10000 0 0
peptide biosynthetic process 0.017 0.002 -10000 0 -10000 0 0
RHEB 0.013 0 -10000 0 -10000 0 0
EIF4A1 0.012 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 -10000 0 -0.003 1 1
EEF2 0.017 0.002 -10000 0 -10000 0 0
eIF4E/4E-BP1 0.016 0.026 -10000 0 -0.36 2 2
Atypical NF-kappaB pathway

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
BCL3/RelA 0.019 0 -9999 0 -10000 0 0
FBXW11 0.012 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.025 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.039 0.038 -9999 0 -10000 0 0
NFKBIA 0.02 0.043 -9999 0 -10000 0 0
MAPK14 0.012 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.025 0 -9999 0 -10000 0 0
ARRB2 0.016 0 -9999 0 -10000 0 0
REL 0.012 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.025 0 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.025 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.042 -9999 0 -0.85 1 1
NF kappa B1 p50 dimer 0.019 0 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
NFKB1 0.022 0 -9999 0 -10000 0 0
RELA 0.012 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.027 0.042 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.042 0.037 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
PI3K 0.017 0.033 -9999 0 -0.66 1 1
NF kappa B1 p50/RelA 0.027 0.042 -9999 0 -10000 0 0
IKBKB 0.012 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.012 0 -9999 0 -10000 0 0
SYK 0.009 0.048 -9999 0 -0.66 2 2
I kappa B alpha/PIK3R1 0.026 0.041 -9999 0 -10000 0 0
cell death 0.04 0.036 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.025 0 -9999 0 -10000 0 0
LCK -0.01 0.14 -9999 0 -0.85 11 11
BCL3 0.012 0 -9999 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0 0 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.02 0 -9999 0 -10000 0 0
AP2 0.019 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0 -9999 0 -10000 0 0
CLTB 0.012 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.024 0 -9999 0 -10000 0 0
CD4 0.008 0.06 -9999 0 -0.85 2 2
CLTA 0.012 0 -9999 0 -10000 0 0
mol:GTP 0.002 0 -9999 0 -10000 0 0
ARFGAP1 0.011 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
ARF1/GTP 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.026 0 -9999 0 -10000 0 0
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 0 -9999 0 -10000 0 0
AP2M1 0.012 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0.016 0 -9999 0 -10000 0 0
Rac/GTP 0.01 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.024 0 -9999 0 -10000 0 0
ARFIP2 0.011 0 -9999 0 -10000 0 0
COPA 0.012 0 -9999 0 -10000 0 0
RAC1 0.012 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.024 0 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0 -9999 0 -10000 0 0
GGA3 0.012 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0 -9999 0 -10000 0 0
AP2A1 0.012 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.026 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0.018 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0 -9999 0 -10000 0 0
CYTH2 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 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 0.033 0.017 -9999 0 -10000 0 0
PLD2 0 0 -9999 0 -10000 0 0
ARF-GAP1/v-SNARE 0.011 0 -9999 0 -10000 0 0
PIP5K1A 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0 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 0.011 0 -9999 0 -10000 0 0
GOSR2 0 0 -9999 0 -10000 0 0
USO1 0 0 -9999 0 -10000 0 0
GBF1 0 0 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex -0.003 0.04 -9999 0 -0.57 2 2
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 -10000 0 0
FBXW11 0.012 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.012 0 -9999 0 -10000 0 0
CHUK 0.012 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB -0.001 0.024 -9999 0 -0.49 1 1
NFKB1 0.012 0 -9999 0 -10000 0 0
MAP3K14 0.012 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelB 0.017 0.033 -9999 0 -0.66 1 1
RELB 0.01 0.042 -9999 0 -0.85 1 1
NFKB2 0.012 0 -9999 0 -10000 0 0
NF kappa B2 p52/RelB -0.001 0.028 -9999 0 -0.58 1 1
regulation of B cell activation -0.001 0.028 -9999 0 -0.58 1 1
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 415 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.ZQ.A9CR TCGA.ZA.A8F6 TCGA.VQ.AA6K TCGA.VQ.AA6J
109_MAP3K5 0.052 0.052 0.052 0.052
47_PPARGC1A 0.012 0.012 0.012 0.012
105_BMP4 0.012 0.012 0.012 0.012
105_BMP6 0.012 0.012 0.012 0.012
105_BMP7 0.012 0.012 0.012 0.012
105_BMP2 0.012 0.012 0.012 0.012
131_RELN/VLDLR -0.75 0.032 0.032 -0.75
30_TGFB1/TGF beta receptor Type II 0.012 0.012 0.019 0.018
84_STAT5B -0.32 -0.042 -0.1 0.043
84_STAT5A -0.32 -0.042 -0.1 0.043
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/STAD-TP/22315237/STAD-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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