PARADIGM pathway analysis of mRNASeq expression data
Breast Invasive Carcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1QJ7G4B
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1QJ7G4B
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 55 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
Class IB PI3K non-lipid kinase events 307
Signaling events mediated by Stem cell factor receptor (c-Kit) 292
EGFR-dependent Endothelin signaling events 250
Signaling mediated by p38-alpha and p38-beta 225
HIF-1-alpha transcription factor network 214
Reelin signaling pathway 205
FOXA2 and FOXA3 transcription factor networks 169
p75(NTR)-mediated signaling 168
Angiopoietin receptor Tie2-mediated signaling 165
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 161
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 1091 . 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 ( 1091 ).

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
Class IB PI3K non-lipid kinase events 0.2814 307 921 3 -0.22 -1000 1000 -1000 -0.023 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.2676 292 22821 78 -0.62 0.19 1000 -1000 -0.064 -1000
EGFR-dependent Endothelin signaling events 0.2291 250 5258 21 -0.34 0 1000 -1000 -0.067 -1000
Signaling mediated by p38-alpha and p38-beta 0.2062 225 9907 44 -0.4 0 1000 -1000 -0.047 -1000
HIF-1-alpha transcription factor network 0.1962 214 16273 76 -0.74 0.019 1000 -1000 -0.067 -1000
Reelin signaling pathway 0.1879 205 11522 56 -0.47 0 1000 -1000 -0.098 -1000
FOXA2 and FOXA3 transcription factor networks 0.1549 169 7786 46 -1.2 0.023 1000 -1000 -0.034 -1000
p75(NTR)-mediated signaling 0.1540 168 21003 125 -0.37 0 1000 -1000 -0.098 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1512 165 14528 88 -0.38 0.04 1000 -1000 -0.099 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1476 161 11012 68 -0.51 0.16 1000 -1000 -0.099 -1000
Glucocorticoid receptor regulatory network 0.1430 156 17830 114 -0.92 0.34 1000 -1000 -0.074 -1000
IL4-mediated signaling events 0.1320 144 13191 91 -0.99 0.52 1000 -1000 -0.13 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1292 141 7649 54 -0.47 0.022 1000 -1000 -0.092 -1000
Arf6 signaling events 0.1292 141 8787 62 -0.34 0.017 1000 -1000 -0.058 -1000
Wnt signaling 0.1265 138 967 7 -0.16 -0.007 1000 -1000 -0.048 -1000
FOXM1 transcription factor network 0.1228 134 6846 51 -0.44 0.014 1000 -1000 -0.14 -1000
Aurora B signaling 0.1228 134 8982 67 -0.32 0.009 1000 -1000 -0.06 -1000
Endothelins 0.1219 133 12850 96 -0.37 0.041 1000 -1000 -0.068 -1000
Ephrin B reverse signaling 0.1137 124 5957 48 -0.31 0.17 1000 -1000 -0.071 -1000
ErbB2/ErbB3 signaling events 0.1118 122 7950 65 -0.38 0.018 1000 -1000 -0.063 -1000
EPHB forward signaling 0.1091 119 10197 85 -0.31 0.17 1000 -1000 -0.085 -1000
IGF1 pathway 0.1072 117 6690 57 -0.18 0.08 1000 -1000 -0.089 -1000
Signaling events regulated by Ret tyrosine kinase 0.1027 112 9184 82 -0.17 0 1000 -1000 -0.076 -1000
BMP receptor signaling 0.0972 106 8599 81 -0.54 0.026 1000 -1000 -0.084 -1000
Calcium signaling in the CD4+ TCR pathway 0.0972 106 3315 31 -0.32 0.012 1000 -1000 -0.092 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0944 103 8816 85 -0.24 0.011 1000 -1000 -0.063 -1000
Nongenotropic Androgen signaling 0.0944 103 5356 52 -0.23 0.11 1000 -1000 -0.062 -1000
ErbB4 signaling events 0.0935 102 7099 69 -0.41 0.057 1000 -1000 -0.086 -1000
Syndecan-1-mediated signaling events 0.0898 98 3339 34 -0.22 0 1000 -1000 -0.062 -1000
Noncanonical Wnt signaling pathway 0.0898 98 2567 26 -0.16 0 1000 -1000 -0.074 -1000
Plasma membrane estrogen receptor signaling 0.0898 98 8491 86 -0.19 0.095 1000 -1000 -0.077 -1000
Glypican 1 network 0.0889 97 4660 48 -0.32 0.03 1000 -1000 -0.053 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0871 95 11458 120 -0.58 0.24 1000 -1000 -0.074 -1000
Signaling events mediated by PTP1B 0.0843 92 7007 76 -0.62 0.071 1000 -1000 -0.072 -1000
Aurora C signaling 0.0843 92 644 7 -0.17 0 1000 -1000 -0.04 -1000
Integrins in angiogenesis 0.0816 89 7534 84 -0.34 0 1000 -1000 -0.084 -1000
IL6-mediated signaling events 0.0816 89 6695 75 -0.28 0.051 1000 -1000 -0.073 -1000
IL23-mediated signaling events 0.0779 85 5149 60 -0.46 0.018 1000 -1000 -0.13 -1000
Visual signal transduction: Rods 0.0742 81 4250 52 -0.48 0 1000 -1000 -0.082 -1000
amb2 Integrin signaling 0.0733 80 6622 82 -0.48 0 1000 -1000 -0.072 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0724 79 2717 34 -0.096 0 1000 -1000 -0.049 -1000
Ephrin A reverse signaling 0.0687 75 527 7 -0.076 0 1000 -1000 -0.028 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0678 74 3867 52 -0.19 0.029 1000 -1000 -0.058 -1000
S1P1 pathway 0.0669 73 2631 36 -0.33 0.008 1000 -1000 -0.064 -1000
Signaling events mediated by PRL 0.0669 73 2491 34 -0.17 0.02 1000 -1000 -0.053 -1000
Syndecan-3-mediated signaling events 0.0651 71 2514 35 -0.35 0 1000 -1000 -0.063 -1000
LPA receptor mediated events 0.0651 71 7302 102 -0.3 0.028 1000 -1000 -0.081 -1000
Signaling events mediated by the Hedgehog family 0.0632 69 3606 52 -0.22 0.031 1000 -1000 -0.065 -1000
Fc-epsilon receptor I signaling in mast cells 0.0632 69 6778 97 -0.24 0.028 1000 -1000 -0.079 -1000
PDGFR-alpha signaling pathway 0.0623 68 3019 44 -0.36 0.019 1000 -1000 -0.065 -1000
Ras signaling in the CD4+ TCR pathway 0.0550 60 1024 17 -0.12 -0.001 1000 -1000 -0.059 -1000
PLK1 signaling events 0.0522 57 4917 85 -0.22 0.029 1000 -1000 -0.053 -1000
Nectin adhesion pathway 0.0522 57 3598 63 -0.088 0.001 1000 -1000 -0.061 -1000
Presenilin action in Notch and Wnt signaling 0.0504 55 3414 61 -0.42 0.014 1000 -1000 -0.069 -1000
Rapid glucocorticoid signaling 0.0504 55 1103 20 -0.19 0.027 1000 -1000 -0.036 -1000
Visual signal transduction: Cones 0.0495 54 2067 38 -0.17 0.011 1000 -1000 -0.064 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0495 54 1809 33 -0.54 0 1000 -1000 -0.054 -1000
FAS signaling pathway (CD95) 0.0477 52 2473 47 -0.47 0.013 1000 -1000 -0.045 -1000
Glypican 2 network 0.0477 52 211 4 -0.038 -0.031 1000 -1000 -0.034 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0477 52 3877 74 -0.3 0.072 1000 -1000 -0.091 -1000
Signaling events mediated by HDAC Class III 0.0467 51 2076 40 -0.56 0.022 1000 -1000 -0.038 -1000
TCGA08_rtk_signaling 0.0458 50 1316 26 -0.3 0.026 1000 -1000 -0.028 -1000
E-cadherin signaling in keratinocytes 0.0449 49 2112 43 -0.3 0.04 1000 -1000 -0.074 -1000
LPA4-mediated signaling events 0.0440 48 584 12 -0.16 0.02 1000 -1000 -0.018 -1000
Effects of Botulinum toxin 0.0431 47 1236 26 -0.1 0.001 1000 -1000 -0.058 -1000
IL27-mediated signaling events 0.0431 47 2414 51 -0.29 0.035 1000 -1000 -0.068 -1000
TCR signaling in naïve CD8+ T cells 0.0412 45 4210 93 -0.16 0.078 1000 -1000 -0.065 -1000
Canonical Wnt signaling pathway 0.0412 45 2333 51 -0.42 0.14 1000 -1000 -0.048 -1000
Syndecan-4-mediated signaling events 0.0412 45 3058 67 -0.32 0.005 1000 -1000 -0.08 -1000
IL12-mediated signaling events 0.0394 43 3786 87 -0.35 0.046 1000 -1000 -0.1 -1000
Coregulation of Androgen receptor activity 0.0367 40 3091 76 -0.18 0.034 1000 -1000 -0.051 -1000
Insulin Pathway 0.0367 40 3015 74 -0.21 0.033 1000 -1000 -0.084 -1000
Regulation of Androgen receptor activity 0.0367 40 2850 70 -0.25 0.021 1000 -1000 -0.065 -1000
Regulation of Telomerase 0.0357 39 4004 102 -0.34 0.025 1000 -1000 -0.076 -1000
Osteopontin-mediated events 0.0330 36 1384 38 -0.24 0.022 1000 -1000 -0.092 -1000
Regulation of p38-alpha and p38-beta 0.0312 34 1872 54 -0.35 0.029 1000 -1000 -0.067 -1000
TCGA08_retinoblastoma 0.0312 34 277 8 -0.054 0.01 1000 -1000 -0.024 -1000
Syndecan-2-mediated signaling events 0.0302 33 2324 69 -0.2 0.034 1000 -1000 -0.055 -1000
IL2 signaling events mediated by STAT5 0.0302 33 726 22 -0.11 0.063 1000 -1000 -0.045 -1000
BCR signaling pathway 0.0293 32 3207 99 -0.13 0.042 1000 -1000 -0.082 -1000
Regulation of nuclear SMAD2/3 signaling 0.0284 31 4273 136 -0.3 0.052 1000 -1000 -0.073 -1000
Thromboxane A2 receptor signaling 0.0275 30 3245 105 -0.3 0.066 1000 -1000 -0.068 -1000
Aurora A signaling 0.0266 29 1752 60 -0.21 0.006 1000 -1000 -0.056 -1000
Arf6 trafficking events 0.0257 28 2008 71 -0.44 0.032 1000 -1000 -0.071 -1000
Hedgehog signaling events mediated by Gli proteins 0.0174 19 1267 65 -0.066 0.044 1000 -1000 -0.078 -1000
Class I PI3K signaling events mediated by Akt 0.0174 19 1330 68 -0.25 0.054 1000 -1000 -0.057 -1000
Ceramide signaling pathway 0.0174 19 1498 76 -0.18 0.049 1000 -1000 -0.054 -1000
TRAIL signaling pathway 0.0174 19 947 48 -0.076 0.045 1000 -1000 -0.063 -1000
Retinoic acid receptors-mediated signaling 0.0174 19 1157 58 -0.1 0.037 1000 -1000 -0.067 -1000
Caspase cascade in apoptosis 0.0165 18 1353 74 -0.048 0.045 1000 -1000 -0.057 -1000
BARD1 signaling events 0.0165 18 1053 57 -0.11 0.024 1000 -1000 -0.065 -1000
JNK signaling in the CD4+ TCR pathway 0.0165 18 313 17 -0.02 0.043 1000 -1000 -0.059 -1000
Cellular roles of Anthrax toxin 0.0165 18 703 39 -0.14 0.02 1000 -1000 -0.028 -1000
Signaling mediated by p38-gamma and p38-delta 0.0165 18 274 15 -0.019 0.022 1000 -1000 -0.044 -1000
E-cadherin signaling events 0.0165 18 93 5 -0.022 0 1000 -1000 -0.04 -1000
IL2 signaling events mediated by PI3K 0.0156 17 1005 58 -0.043 0.06 1000 -1000 -0.072 -1000
PLK2 and PLK4 events 0.0137 15 47 3 -0.012 0.013 1000 -1000 -0.025 -1000
IL1-mediated signaling events 0.0137 15 952 62 -0.037 0.031 1000 -1000 -0.093 -1000
S1P5 pathway 0.0128 14 250 17 -0.045 0.024 1000 -1000 -0.057 -1000
S1P4 pathway 0.0128 14 364 25 -0.045 0.008 1000 -1000 -0.054 -1000
S1P3 pathway 0.0119 13 577 42 -0.033 0.021 1000 -1000 -0.059 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0110 12 343 28 -0.045 0.02 1000 -1000 -0.047 -1000
mTOR signaling pathway 0.0101 11 620 53 -0.021 0.025 1000 -1000 -0.059 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0101 11 954 83 -0.037 0.054 1000 -1000 -0.071 -1000
E-cadherin signaling in the nascent adherens junction 0.0101 11 895 76 -0.022 0.05 1000 -1000 -0.08 -1000
p38 MAPK signaling pathway 0.0101 11 527 44 -0.068 0.025 1000 -1000 -0.061 -1000
Signaling events mediated by HDAC Class II 0.0082 9 736 75 -0.15 0 1000 -1000 -0.06 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0082 9 364 37 -0.048 0.034 1000 -1000 -0.073 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0082 9 1234 125 -0.17 0.082 1000 -1000 -0.09 -1000
IFN-gamma pathway 0.0073 8 591 68 -0.068 0.075 1000 -1000 -0.082 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0073 8 371 45 -0.025 0.073 1000 -1000 -0.079 -1000
VEGFR1 specific signals 0.0073 8 479 56 -0.17 0.065 1000 -1000 -0.071 -1000
EPO signaling pathway 0.0064 7 430 55 -0.036 0.058 1000 -1000 -0.077 -1000
HIF-2-alpha transcription factor network 0.0064 7 337 43 -0.17 0.18 1000 -1000 -0.066 -1000
Class I PI3K signaling events 0.0064 7 522 73 -0.044 0.059 1000 -1000 -0.068 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0055 6 150 23 -0.029 0.042 1000 -1000 -0.062 -1000
PDGFR-beta signaling pathway 0.0055 6 625 97 -0.026 0.05 1000 -1000 -0.079 -1000
FoxO family signaling 0.0046 5 377 64 -0.038 0.09 1000 -1000 -0.074 -1000
Atypical NF-kappaB pathway 0.0046 5 176 31 -0.02 0.03 1000 -1000 -0.063 -1000
Circadian rhythm pathway 0.0037 4 89 22 -0.014 0.042 1000 -1000 -0.066 -1000
ceramide signaling pathway 0.0037 4 239 49 -0.027 0.054 1000 -1000 -0.05 -1000
Signaling events mediated by HDAC Class I 0.0037 4 509 104 -0.094 0.046 1000 -1000 -0.066 -1000
Canonical NF-kappaB pathway 0.0027 3 130 39 -0.021 0.077 1000 -1000 -0.078 -1000
a4b1 and a4b7 Integrin signaling 0.0027 3 18 5 -0.01 -0.002 1000 -1000 -0.039 -1000
Arf6 downstream pathway 0.0027 3 142 43 -0.023 0.023 1000 -1000 -0.043 -1000
Insulin-mediated glucose transport 0.0027 3 104 32 -0.13 0.032 1000 -1000 -0.057 -1000
Paxillin-dependent events mediated by a4b1 0.0027 3 110 36 -0.011 0.022 1000 -1000 -0.073 -1000
TCGA08_p53 0.0000 0 0 7 -0.026 0.017 1000 -1000 -0.022 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 8 27 -0.001 0.029 1000 -1000 -0.055 -1000
Arf1 pathway 0.0000 0 26 54 -0.001 0.025 1000 -1000 -0.042 -1000
Alternative NF-kappaB pathway 0.0000 0 11 13 -0.003 0 1000 -1000 -0.051 -1000
Total NA 8172 481110 7203 -31 -990 131000 -131000 -8.6 -131000
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process 0.22 0.35 0.79 307 -10000 0 307
PI3K Class IB/PDE3B -0.22 0.35 -10000 0 -0.79 307 307
PDE3B -0.22 0.36 -10000 0 -0.79 307 307
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.16 0.22 -10000 0 -0.39 501 501
CRKL -0.17 0.23 -10000 0 -0.41 502 502
HRAS -0.16 0.17 -10000 0 -0.5 47 47
mol:PIP3 -0.17 0.21 -10000 0 -0.4 503 503
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 0 0 -10000 0 -10000 0 0
GAB1 -0.18 0.24 -10000 0 -0.44 502 502
FOXO3 -0.15 0.21 -10000 0 -0.37 500 500
AKT1 -0.17 0.22 -10000 0 -0.41 501 501
BAD -0.15 0.21 -10000 0 -0.37 500 500
megakaryocyte differentiation -0.18 0.24 -10000 0 -0.43 503 503
GSK3B -0.15 0.21 -10000 0 -0.37 500 500
RAF1 -0.093 0.17 -10000 0 -0.44 28 28
SHC1 0 0 -10000 0 -10000 0 0
STAT3 -0.18 0.24 -10000 0 -0.44 502 502
STAT1 -0.46 0.56 -10000 0 -1 512 512
HRAS/SPRED1 -0.13 0.14 -10000 0 -0.4 43 43
cell proliferation -0.18 0.24 -10000 0 -0.44 503 503
PIK3CA 0 0.009 -10000 0 -0.29 1 1
TEC -0.002 0.041 -10000 0 -0.79 3 3
RPS6KB1 -0.18 0.24 -10000 0 -0.44 504 504
HRAS/SPRED2 -0.13 0.14 -10000 0 -0.39 44 44
LYN/TEC/p62DOK -0.19 0.2 -10000 0 -0.4 502 502
MAPK3 -0.055 0.13 -10000 0 -0.32 22 22
STAP1 -0.2 0.24 -10000 0 -0.45 504 504
GRAP2 -0.015 0.1 -10000 0 -0.72 22 22
JAK2 -0.4 0.44 -10000 0 -0.87 512 512
STAT1 (dimer) -0.44 0.54 -10000 0 -1 512 512
mol:Gleevec 0.006 0.009 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.19 0.2 -10000 0 -0.41 502 502
actin filament polymerization -0.19 0.24 -10000 0 -0.44 502 502
LYN 0 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.27 0.33 -10000 0 -0.62 505 505
PIK3R1 -0.009 0.086 -10000 0 -0.79 13 13
CBL/CRKL/GRB2 -0.17 0.18 -10000 0 -0.36 500 500
PI3K -0.19 0.21 -10000 0 -0.41 507 507
PTEN -0.001 0.034 -10000 0 -0.79 2 2
SCF/KIT/EPO/EPOR -0.57 0.7 -10000 0 -1.3 500 500
MAPK8 -0.19 0.24 -10000 0 -0.45 503 503
STAT3 (dimer) -0.18 0.23 -10000 0 -0.43 502 502
positive regulation of transcription -0.042 0.11 -10000 0 -0.25 22 22
mol:GDP -0.17 0.18 -10000 0 -0.49 59 59
PIK3C2B -0.18 0.24 -10000 0 -0.44 502 502
CBL/CRKL -0.15 0.22 -10000 0 -0.38 500 500
FER -0.19 0.24 -10000 0 -0.44 507 507
SH2B3 -0.18 0.24 -10000 0 -0.44 502 502
PDPK1 -0.15 0.2 -10000 0 -0.36 502 502
SNAI2 -0.19 0.25 -10000 0 -0.45 504 504
positive regulation of cell proliferation -0.32 0.4 -10000 0 -0.75 512 512
KITLG 0.002 0.067 -10000 0 -0.49 16 16
cell motility -0.32 0.4 -10000 0 -0.75 512 512
PTPN6 0.015 0.021 -10000 0 -0.29 2 2
EPOR -0.097 0.16 -10000 0 -10000 0 0
STAT5A (dimer) -0.26 0.34 -10000 0 -0.62 514 514
SOCS1 -0.005 0.043 -10000 0 -0.32 18 18
cell migration 0.19 0.24 0.44 510 -10000 0 510
SOS1 0 0 -10000 0 -10000 0 0
EPO -0.044 0.11 -10000 0 -0.3 177 177
VAV1 -0.003 0.043 -10000 0 -0.59 5 5
GRB10 -0.18 0.24 -10000 0 -0.44 502 502
PTPN11 0.013 0.013 -10000 0 -10000 0 0
SCF/KIT -0.22 0.23 -10000 0 -0.46 514 514
GO:0007205 0.009 0.013 -10000 0 -10000 0 0
MAP2K1 -0.064 0.14 -10000 0 -0.35 22 22
CBL 0 0 -10000 0 -10000 0 0
KIT -0.62 0.73 -10000 0 -1.4 498 498
MAP2K2 -0.064 0.14 -10000 0 -0.35 22 22
SHC/Grb2/SOS1 -0.19 0.2 -10000 0 -0.4 500 500
STAT5A -0.27 0.35 -10000 0 -0.64 514 514
GRB2 0 0.009 -10000 0 -0.29 1 1
response to radiation -0.18 0.24 -10000 0 -0.44 504 504
SHC/GRAP2 -0.011 0.079 -10000 0 -0.6 19 19
PTPRO -0.18 0.24 -10000 0 -0.44 503 503
SH2B2 -0.19 0.24 -10000 0 -0.44 502 502
DOK1 -0.001 0.018 -10000 0 -10000 0 0
MATK -0.2 0.25 -10000 0 -0.45 510 510
CREBBP 0.019 0.018 -10000 0 -10000 0 0
BCL2 -0.13 0.3 -10000 0 -1.5 37 37
EGFR-dependent Endothelin 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
HRAS -0.002 0.027 -9999 0 -0.29 9 9
EGFR -0.3 0.38 -9999 0 -0.78 414 414
EGF/EGFR -0.28 0.3 -9999 0 -0.54 565 565
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.25 0.27 -9999 0 -0.49 555 555
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.001 0.025 -9999 0 -0.54 2 2
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.16 0.31 -9999 0 -0.78 216 216
EGF/EGFR dimer/SHC -0.29 0.31 -9999 0 -0.58 555 555
mol:GDP -0.25 0.26 -9999 0 -0.49 555 555
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.06 0.21 -9999 0 -0.78 83 83
GRB2/SOS1 0 0.006 -9999 0 -10000 0 0
HRAS/GTP -0.23 0.24 -9999 0 -0.45 555 555
SHC1 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.23 0.25 -9999 0 -0.46 555 555
FRAP1 -0.24 0.25 -9999 0 -0.47 555 555
EGF/EGFR dimer -0.34 0.35 -9999 0 -0.66 555 555
SOS1 0 0 -9999 0 -10000 0 0
GRB2 0 0.009 -9999 0 -0.29 1 1
ETA receptor/Endothelin-1 -0.046 0.16 -9999 0 -0.6 83 83
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.4 0.62 -9999 0 -1.3 370 370
MKNK1 0 0 -9999 0 -10000 0 0
MAPK14 -0.081 0.15 -9999 0 -0.4 13 13
ATF2/c-Jun -0.052 0.15 -9999 0 -0.78 14 14
MAPK11 -0.084 0.16 -9999 0 -0.3 373 373
MITF -0.093 0.2 -9999 0 -0.36 377 377
MAPKAPK5 -0.089 0.19 -9999 0 -0.35 373 373
KRT8 -0.095 0.2 -9999 0 -0.36 374 374
MAPKAPK3 0 0 -9999 0 -10000 0 0
MAPKAPK2 0 0.009 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.12 0.23 -9999 0 -0.44 373 373
CEBPB -0.089 0.19 -9999 0 -0.35 373 373
SLC9A1 -0.089 0.19 -9999 0 -0.35 373 373
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.082 0.19 -9999 0 -0.34 374 374
p38alpha-beta/MNK1 -0.12 0.17 -9999 0 -0.56 16 16
JUN -0.051 0.15 -9999 0 -0.77 14 14
PPARGC1A -0.21 0.36 -9999 0 -0.58 452 452
USF1 -0.089 0.19 -9999 0 -0.35 373 373
RAB5/GDP/GDI1 -0.085 0.12 -9999 0 -0.38 16 16
NOS2 -0.092 0.21 -9999 0 -0.87 16 16
DDIT3 -0.089 0.19 -9999 0 -0.35 373 373
RAB5A 0 0 -9999 0 -10000 0 0
HSPB1 -0.075 0.17 -9999 0 -0.43 54 54
p38alpha-beta/HBP1 -0.12 0.17 -9999 0 -0.56 16 16
CREB1 -0.094 0.2 -9999 0 -0.37 373 373
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.07 0.17 -9999 0 -0.5 15 15
RPS6KA4 -0.089 0.19 -9999 0 -0.35 373 373
PLA2G4A -0.13 0.27 -9999 0 -0.72 142 142
GDI1 -0.089 0.19 -9999 0 -0.35 373 373
TP53 -0.12 0.23 -9999 0 -0.44 373 373
RPS6KA5 -0.095 0.2 -9999 0 -0.36 381 381
ESR1 -0.18 0.26 -9999 0 -0.42 508 508
HBP1 0 0 -9999 0 -10000 0 0
MEF2C -0.09 0.19 -9999 0 -0.35 373 373
MEF2A -0.09 0.19 -9999 0 -0.35 373 373
EIF4EBP1 -0.094 0.2 -9999 0 -0.37 373 373
KRT19 -0.1 0.21 -9999 0 -0.37 378 378
ELK4 -0.089 0.19 -9999 0 -0.35 373 373
ATF6 -0.089 0.19 -9999 0 -0.35 373 373
ATF1 -0.094 0.2 -9999 0 -0.37 373 373
p38alpha-beta/MAPKAPK2 -0.12 0.17 -9999 0 -0.55 17 17
p38alpha-beta/MAPKAPK3 -0.12 0.17 -9999 0 -0.52 19 19
HIF-1-alpha transcription factor network

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
PKM2 -0.4 0.46 -9999 0 -0.99 304 304
HDAC7 0 0.002 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.32 0.31 -9999 0 -0.77 236 236
SMAD4 -0.001 0.024 -9999 0 -0.79 1 1
ID2 -0.4 0.46 -9999 0 -0.99 303 303
AP1 -0.18 0.28 -9999 0 -0.61 326 326
ABCG2 -0.43 0.5 -9999 0 -1.1 315 315
HIF1A -0.05 0.065 -9999 0 -10000 0 0
TFF3 -0.47 0.52 -9999 0 -1.1 375 375
GATA2 -0.013 0.13 -9999 0 -0.62 42 42
AKT1 -0.05 0.081 -9999 0 -10000 0 0
response to hypoxia -0.072 0.087 -9999 0 -0.24 35 35
MCL1 -0.4 0.46 -9999 0 -0.99 303 303
NDRG1 -0.4 0.47 -9999 0 -1 289 289
SERPINE1 -0.4 0.46 -9999 0 -0.99 304 304
FECH -0.4 0.46 -9999 0 -0.99 302 302
FURIN -0.4 0.46 -9999 0 -0.99 303 303
NCOA2 -0.03 0.17 -9999 0 -0.79 53 53
EP300 -0.048 0.12 -9999 0 -0.35 55 55
HMOX1 -0.4 0.46 -9999 0 -0.99 300 300
BHLHE40 -0.4 0.46 -9999 0 -0.99 302 302
BHLHE41 -0.41 0.48 -9999 0 -1 304 304
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.049 0.055 -9999 0 -0.6 1 1
ENG -0.025 0.079 -9999 0 -0.54 1 1
JUN 0.003 0.064 -9999 0 -0.79 7 7
RORA -0.4 0.46 -9999 0 -0.99 303 303
ABCB1 -0.34 0.55 -9999 0 -1.4 214 214
TFRC -0.4 0.46 -9999 0 -0.99 305 305
CXCR4 -0.4 0.46 -9999 0 -0.99 301 301
TF -0.63 0.58 -9999 0 -1.1 562 562
CITED2 -0.4 0.46 -9999 0 -0.99 303 303
HIF1A/ARNT -0.48 0.53 -9999 0 -1.1 308 308
LDHA -0.048 0.047 -9999 0 -10000 0 0
ETS1 -0.4 0.47 -9999 0 -0.99 301 301
PGK1 -0.4 0.46 -9999 0 -0.98 305 305
NOS2 -0.4 0.47 -9999 0 -1 303 303
ITGB2 -0.4 0.46 -9999 0 -0.99 303 303
ALDOA -0.4 0.46 -9999 0 -0.99 304 304
Cbp/p300/CITED2 -0.42 0.45 -9999 0 -1 282 282
FOS -0.23 0.37 -9999 0 -0.79 325 325
HK2 -0.4 0.46 -9999 0 -0.99 300 300
SP1 0.012 0.023 -9999 0 -10000 0 0
GCK -0.13 0.36 -9999 0 -1.6 56 56
HK1 -0.4 0.46 -9999 0 -0.99 303 303
NPM1 -0.4 0.46 -9999 0 -0.99 303 303
EGLN1 -0.4 0.46 -9999 0 -0.99 302 302
CREB1 0.019 0 -9999 0 -10000 0 0
PGM1 -0.4 0.46 -9999 0 -0.99 303 303
SMAD3 0 0 -9999 0 -10000 0 0
EDN1 -0.18 0.4 -9999 0 -1.2 120 120
IGFBP1 -0.49 0.53 -9999 0 -1.1 377 377
VEGFA -0.24 0.32 -9999 0 -0.74 128 128
HIF1A/JAB1 -0.028 0.026 -9999 0 -10000 0 0
CP -0.51 0.55 -9999 0 -1.1 412 412
CXCL12 -0.43 0.5 -9999 0 -1.1 315 315
COPS5 0.009 0.006 -9999 0 -10000 0 0
SMAD3/SMAD4 -0.001 0.018 -9999 0 -0.6 1 1
BNIP3 -0.4 0.46 -9999 0 -0.99 302 302
EGLN3 -0.41 0.47 -9999 0 -1 311 311
CA9 -0.44 0.49 -9999 0 -1 322 322
TERT -0.42 0.48 -9999 0 -1 314 314
ENO1 -0.4 0.46 -9999 0 -0.99 303 303
PFKL -0.4 0.46 -9999 0 -0.99 302 302
NCOA1 0 0.024 -9999 0 -0.79 1 1
ADM -0.43 0.49 -9999 0 -1 325 325
ARNT -0.049 0.065 -9999 0 -10000 0 0
HNF4A -0.002 0.046 -9999 0 -0.29 22 22
ADFP -0.41 0.46 -9999 0 -0.99 306 306
SLC2A1 -0.24 0.32 -9999 0 -0.74 142 142
LEP -0.74 0.53 -9999 0 -1.1 652 652
HIF1A/ARNT/Cbp/p300 -0.32 0.34 -9999 0 -0.8 241 241
EPO -0.23 0.28 -9999 0 -0.86 49 49
CREBBP -0.048 0.12 -9999 0 -0.36 53 53
HIF1A/ARNT/Cbp/p300/HDAC7 -0.31 0.31 -9999 0 -0.78 221 221
PFKFB3 -0.4 0.47 -9999 0 -1 304 304
NT5E -0.4 0.47 -9999 0 -1 303 303
Reelin signaling pathway

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
CDK5R1/CDK5 -0.006 0.034 -9999 0 -10000 0 0
VLDLR -0.024 0.14 -9999 0 -0.79 33 33
CRKL 0 0 -9999 0 -10000 0 0
LRPAP1 0 0 -9999 0 -10000 0 0
FYN -0.001 0.034 -9999 0 -0.79 2 2
ITGA3 -0.004 0.05 -9999 0 -0.58 7 7
RELN/VLDLR/Fyn -0.32 0.27 -9999 0 -0.54 660 660
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.005 0.044 -9999 0 -0.44 11 11
AKT1 -0.2 0.17 -9999 0 -0.46 76 76
MAP2K7 0 0 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
DAB1 -0.017 0.069 -9999 0 -10000 0 0
RELN/LRP8/DAB1 -0.31 0.24 -9999 0 -0.5 652 652
LRPAP1/LRP8 -0.019 0.057 -9999 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.29 0.23 -9999 0 -0.47 652 652
DAB1/alpha3/beta1 Integrin -0.27 0.22 -9999 0 -0.58 145 145
long-term memory -0.35 0.29 -9999 0 -0.53 706 706
DAB1/LIS1 -0.28 0.23 -9999 0 -0.51 277 277
DAB1/CRLK/C3G -0.27 0.22 -9999 0 -0.57 142 142
PIK3CA 0 0.009 -9999 0 -0.29 1 1
DAB1/NCK2 -0.28 0.23 -9999 0 -0.46 657 657
ARHGEF2 0 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.092 0.25 -9999 0 -0.74 135 135
CDK5R1 -0.008 0.049 -9999 0 -0.29 31 31
RELN -0.47 0.39 -9999 0 -0.79 654 654
PIK3R1 -0.009 0.086 -9999 0 -0.79 13 13
RELN/LRP8/Fyn -0.32 0.26 -9999 0 -0.54 651 651
GRIN2A/RELN/LRP8/DAB1/Fyn -0.34 0.29 -9999 0 -0.53 671 671
MAPK8 -0.006 0.067 -9999 0 -0.79 8 8
RELN/VLDLR/DAB1 -0.31 0.25 -9999 0 -0.5 660 660
ITGB1 0 0 -9999 0 -10000 0 0
MAP1B -0.3 0.25 -9999 0 -0.49 666 666
RELN/LRP8 -0.32 0.26 -9999 0 -0.54 651 651
GRIN2B/RELN/LRP8/DAB1/Fyn -0.32 0.25 -9999 0 -0.49 689 689
PI3K -0.007 0.066 -9999 0 -0.6 13 13
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.003 0.038 -9999 0 -0.6 4 4
RAP1A -0.25 0.2 -9999 0 -0.53 142 142
PAFAH1B1 0 0 -9999 0 -10000 0 0
MAPK8IP1 -0.004 0.046 -9999 0 -0.48 8 8
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B -0.053 0.2 -9999 0 -0.78 75 75
NCK2 0 0 -9999 0 -10000 0 0
neuron differentiation -0.12 0.13 -9999 0 -0.47 12 12
neuron adhesion -0.23 0.19 -9999 0 -0.6 47 47
LRP8 -0.031 0.09 -9999 0 -10000 0 0
GSK3B -0.17 0.17 -9999 0 -0.45 69 69
RELN/VLDLR/DAB1/Fyn -0.29 0.24 -9999 0 -0.47 660 660
MAP3K11 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.21 0.18 -9999 0 -0.35 667 667
CDK5 -0.002 0.023 -9999 0 -0.29 7 7
MAPT -0.047 0.24 -9999 0 -0.69 129 129
neuron migration -0.23 0.23 -9999 0 -0.49 167 167
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.13 0.11 -9999 0 -0.48 12 12
RELN/VLDLR -0.31 0.25 -9999 0 -0.5 660 660
FOXA2 and FOXA3 transcription factor networks

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ACADVL -0.24 0.28 -9999 0 -0.77 128 128
PCK1 -1 0.7 -9999 0 -1.6 676 676
HNF4A -0.25 0.28 -9999 0 -0.85 86 86
KCNJ11 -0.28 0.31 -9999 0 -0.88 126 126
AKT1 -0.15 0.14 -9999 0 -0.39 42 42
response to starvation -0.001 0.008 -9999 0 -10000 0 0
DLK1 -0.5 0.56 -9999 0 -1.2 365 365
NKX2-1 -0.055 0.15 -9999 0 -10000 0 0
ACADM -0.25 0.28 -9999 0 -0.78 130 130
TAT -1.2 0.68 -9999 0 -1.6 776 776
CEBPB 0.006 0.007 -9999 0 -10000 0 0
CEBPA -0.001 0.072 -9999 0 -0.79 9 9
TTR -0.46 0.28 -9999 0 -0.8 300 300
PKLR -0.25 0.28 -9999 0 -0.77 134 134
APOA1 -0.3 0.3 -9999 0 -0.89 105 105
CPT1C -0.24 0.28 -9999 0 -0.79 116 116
ALAS1 -0.14 0.15 -9999 0 -10000 0 0
TFRC -0.45 0.26 -9999 0 -0.69 437 437
FOXF1 -0.003 0.054 -9999 0 -0.5 10 10
NF1 0.017 0.024 -9999 0 -0.78 1 1
HNF1A (dimer) 0.003 0.027 -9999 0 -0.3 8 8
CPT1A -0.24 0.28 -9999 0 -0.77 127 127
HMGCS1 -0.24 0.28 -9999 0 -0.8 107 107
NR3C1 -0.11 0.13 -9999 0 -0.48 50 50
CPT1B -0.24 0.28 -9999 0 -0.75 149 149
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.002 0.007 -9999 0 -10000 0 0
GCK -0.28 0.35 -9999 0 -0.94 158 158
CREB1 -0.059 0.067 -9999 0 -10000 0 0
IGFBP1 -0.44 0.59 -9999 0 -1.5 244 244
PDX1 -0.13 0.15 -9999 0 -10000 0 0
UCP2 -0.24 0.28 -9999 0 -0.74 153 153
ALDOB -0.27 0.3 -9999 0 -0.83 131 131
AFP -0.68 0.6 -9999 0 -1.1 604 604
BDH1 -0.24 0.28 -9999 0 -0.76 142 142
HADH -0.26 0.3 -9999 0 -0.8 143 143
F2 -0.3 0.3 -9999 0 -0.89 98 98
HNF1A 0.003 0.027 -9999 0 -0.3 8 8
G6PC -0.2 0.12 -9999 0 -0.64 8 8
SLC2A2 -0.16 0.17 -9999 0 -10000 0 0
INS 0.023 0.066 -9999 0 -10000 0 0
FOXA1 -0.24 0.28 -9999 0 -0.57 318 318
FOXA3 -0.42 0.23 -9999 0 -0.53 784 784
FOXA2 -0.32 0.34 -9999 0 -0.84 206 206
ABCC8 -0.34 0.43 -9999 0 -1.1 201 201
ALB -0.93 0.64 -9999 0 -1.4 706 706
p75(NTR)-mediated 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
Sortilin/TRAF6 -0.001 0.018 -9999 0 -0.6 1 1
Necdin/E2F1 -0.082 0.15 -9999 0 -0.68 43 43
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.14 0.21 -9999 0 -0.45 346 346
NGF (dimer)/p75(NTR)/BEX1 -0.26 0.31 -9999 0 -0.62 425 425
NT-4/5 (dimer)/p75(NTR) -0.37 0.41 -9999 0 -0.75 542 542
IKBKB -0.001 0.013 -9999 0 -0.29 2 2
AKT1 -0.15 0.22 -9999 0 -0.45 350 350
IKBKG 0 0 -9999 0 -10000 0 0
BDNF -0.065 0.21 -9999 0 -0.67 106 106
MGDIs/NGR/p75(NTR)/LINGO1 -0.2 0.25 -9999 0 -0.56 336 336
FURIN 0 0.009 -9999 0 -0.29 1 1
proBDNF (dimer)/p75(NTR)/Sortilin -0.2 0.28 -9999 0 -0.57 380 380
LINGO1 -0.07 0.12 -9999 0 -0.29 262 262
Sortilin/TRAF6/NRIF -0.001 0.024 -9999 0 -0.78 1 1
proBDNF (dimer) -0.065 0.21 -9999 0 -0.67 106 106
NTRK1 -0.011 0.07 -9999 0 -0.37 33 33
RTN4R -0.012 0.058 -9999 0 -0.29 44 44
neuron apoptosis -0.14 0.26 -9999 0 -0.48 380 380
IRAK1 -0.001 0.018 -9999 0 -10000 0 0
SHC1 -0.15 0.26 -9999 0 -0.53 344 344
ARHGDIA 0 0 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase 0 0.014 -9999 0 -0.44 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.15 0.23 -9999 0 -0.48 344 344
MAGEH1 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.17 0.26 -9999 0 -0.52 358 358
Mammalian IAPs/DIABLO -0.005 0.044 -9999 0 -0.47 9 9
proNGF (dimer) -0.014 0.098 -9999 0 -0.62 24 24
MAGED1 -0.001 0.018 -9999 0 -0.29 4 4
APP 0 0 -9999 0 -10000 0 0
NT-4/5 (dimer) -0.27 0.37 -9999 0 -0.79 372 372
ZNF274 0 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.14 0.21 -9999 0 -0.45 344 344
NGF -0.014 0.098 -9999 0 -0.62 24 24
cell cycle arrest -0.12 0.23 -9999 0 -0.44 344 344
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.1 0.16 -9999 0 -0.33 344 344
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.33 0.36 -9999 0 -0.66 542 542
NCSTN 0 0 -9999 0 -10000 0 0
mol:GTP -0.18 0.26 -9999 0 -0.54 344 344
PSENEN 0 0.009 -9999 0 -0.29 1 1
mol:ceramide -0.13 0.24 -9999 0 -0.48 344 344
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.082 0.12 -9999 0 -0.48 13 13
p75(NTR)/beta APP -0.18 0.28 -9999 0 -0.6 336 336
BEX1 -0.15 0.27 -9999 0 -0.52 319 319
mol:GDP -0.16 0.26 -9999 0 -0.54 344 344
NGF (dimer) -0.082 0.18 -9999 0 -0.48 173 173
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.18 0.22 -9999 0 -0.5 336 336
PIK3R1 -0.009 0.086 -9999 0 -0.79 13 13
RAC1/GTP -0.15 0.22 -9999 0 -0.46 344 344
MYD88 0 0 -9999 0 -10000 0 0
CHUK 0 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.18 0.26 -9999 0 -0.54 344 344
RHOB 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.06 0.087 -9999 0 -10000 0 0
NT3 (dimer) -0.13 0.28 -9999 0 -0.75 182 182
TP53 -0.16 0.23 -9999 0 -0.45 380 380
PRDM4 -0.13 0.24 -9999 0 -0.48 344 344
BDNF (dimer) -0.17 0.23 -9999 0 -0.57 226 226
PIK3CA 0 0.009 -9999 0 -0.29 1 1
SORT1 -0.001 0.024 -9999 0 -0.79 1 1
activation of caspase activity -0.14 0.21 -9999 0 -0.44 346 346
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.15 0.23 -9999 0 -0.48 344 344
RHOC 0 0 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
MAPK10 -0.15 0.27 -9999 0 -0.49 351 351
DIABLO 0 0 -9999 0 -10000 0 0
SMPD2 -0.13 0.24 -9999 0 -0.48 344 344
APH1B -0.001 0.024 -9999 0 -0.79 1 1
APH1A 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.17 0.25 -9999 0 -0.53 344 344
PSEN1 0 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.27 0.35 -9999 0 -0.68 434 434
MAPK8 -0.11 0.24 -9999 0 -0.43 336 336
MAPK9 -0.1 0.24 -9999 0 -0.43 336 336
APAF1 0 0 -9999 0 -10000 0 0
NTF3 -0.13 0.29 -9999 0 -0.75 182 182
NTF4 -0.27 0.37 -9999 0 -0.79 372 372
NDN -0.031 0.15 -9999 0 -0.79 43 43
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.14 0.2 -9999 0 -0.42 344 344
p75 CTF/Sortilin/TRAF6/NRIF 0 0.014 -9999 0 -0.47 1 1
RhoA-B-C/GTP -0.17 0.25 -9999 0 -0.54 344 344
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.17 0.24 -9999 0 -0.48 380 380
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.18 0.26 -9999 0 -0.52 380 380
PRKACB -0.016 0.077 -9999 0 -0.33 53 53
proBDNF (dimer)/p75 ECD -0.049 0.16 -9999 0 -0.6 80 80
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.01 0.077 -9999 0 -0.51 21 21
BIRC2 0 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.12 0.25 -9999 0 -0.46 344 344
BAD -0.12 0.24 -9999 0 -0.44 339 339
RIPK2 -0.001 0.02 -9999 0 -0.29 5 5
NGFR -0.24 0.36 -9999 0 -0.79 336 336
CYCS -0.14 0.21 -9999 0 -0.45 344 344
ADAM17 0 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.15 0.23 -9999 0 -0.48 344 344
BCL2L11 -0.12 0.24 -9999 0 -0.44 339 339
BDNF (dimer)/p75(NTR) -0.23 0.32 -9999 0 -0.65 380 380
PI3K -0.16 0.23 -9999 0 -0.49 350 350
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.15 0.23 -9999 0 -0.48 344 344
NDNL2 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
PRKCI 0 0.009 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.2 0.29 -9999 0 -0.61 344 344
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.15 0.23 -9999 0 -0.48 344 344
TRAF6 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
PRKCZ -0.001 0.024 -9999 0 -0.79 1 1
PLG -0.002 0.025 -9999 0 -0.29 8 8
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.19 0.26 -9999 0 -0.52 388 388
SQSTM1 0 0.009 -9999 0 -0.29 1 1
NGFRAP1 -0.001 0.034 -9999 0 -0.79 2 2
CASP3 -0.1 0.22 -9999 0 -0.41 339 339
E2F1 -0.094 0.14 -9999 0 -0.29 348 348
CASP9 0 0 -9999 0 -10000 0 0
IKK complex -0.065 0.11 -9999 0 -0.56 22 22
NGF (dimer)/TRKA -0.018 0.088 -9999 0 -0.6 21 21
MMP7 -0.12 0.28 -9999 0 -0.71 191 191
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.14 0.21 -9999 0 -0.45 344 344
MMP3 -0.12 0.16 -9999 0 -0.79 17 17
APAF-1/Caspase 9 -0.11 0.16 -9999 0 -0.64 15 15
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.13 0.42 -10000 0 -0.9 246 246
NCK1/PAK1/Dok-R -0.095 0.18 -10000 0 -0.42 246 246
NCK1/Dok-R -0.26 0.48 -10000 0 -1.1 246 246
PIK3CA 0.003 0.011 -10000 0 -0.29 1 1
mol:beta2-estradiol 0.039 0.1 0.24 209 -10000 0 209
RELA 0 0 -10000 0 -10000 0 0
SHC1 0.008 0.006 -10000 0 -10000 0 0
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 0.04 0.11 0.26 144 -0.32 11 155
TNIP2 0 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.24 0.44 -10000 0 -1 246 246
FN1 -0.12 0.14 -10000 0 -0.29 432 432
PLD2 -0.21 0.53 -10000 0 -1.2 246 246
PTPN11 0 0 -10000 0 -10000 0 0
GRB14 -0.1 0.22 -10000 0 -0.47 230 230
ELK1 -0.17 0.47 -10000 0 -1 246 246
GRB7 -0.023 0.085 -10000 0 -0.31 79 79
PAK1 -0.007 0.044 -10000 0 -0.29 25 25
Tie2/Ang1/alpha5/beta1 Integrin -0.22 0.5 -10000 0 -1.1 246 246
CDKN1A -0.07 0.28 -10000 0 -0.6 198 198
ITGA5 0 0.009 -10000 0 -0.29 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.26 0.48 -10000 0 -1.1 246 246
CRK 0 0 -10000 0 -10000 0 0
mol:NO -0.076 0.32 -10000 0 -0.66 246 246
PLG -0.22 0.53 -10000 0 -1.2 246 246
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.19 0.38 -10000 0 -0.88 246 246
GRB2 0 0.009 -10000 0 -0.29 1 1
PIK3R1 -0.002 0.087 -10000 0 -0.79 13 13
ANGPT2 -0.11 0.27 -10000 0 -0.7 135 135
BMX -0.38 0.6 -10000 0 -1.4 247 247
ANGPT1 -0.25 0.58 -10000 0 -1.4 217 217
tube development -0.088 0.31 -10000 0 -0.64 246 246
ANGPT4 -0.24 0.37 -10000 0 -0.79 330 330
response to hypoxia -0.011 0.031 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.3 0.55 -10000 0 -1.3 246 246
alpha5/beta1 Integrin 0 0.006 -10000 0 -10000 0 0
FGF2 -0.32 0.39 -10000 0 -0.79 444 444
STAT5A (dimer) -0.11 0.36 -10000 0 -0.75 225 225
mol:L-citrulline -0.076 0.32 -10000 0 -0.66 246 246
AGTR1 -0.2 0.34 -10000 0 -0.69 327 327
MAPK14 -0.2 0.51 -10000 0 -1.1 246 246
Tie2/SHP2 -0.1 0.29 -10000 0 -1.3 56 56
TEK -0.11 0.34 -10000 0 -1.5 56 56
RPS6KB1 -0.13 0.4 -10000 0 -0.87 246 246
Angiotensin II/AT1 -0.15 0.26 -10000 0 -0.53 327 327
Tie2/Ang1/GRB2 -0.28 0.52 -10000 0 -1.2 246 246
MAPK3 -0.18 0.49 -10000 0 -1.1 246 246
MAPK1 -0.18 0.49 -10000 0 -1.1 246 246
Tie2/Ang1/GRB7 -0.27 0.53 -10000 0 -1.2 246 246
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 -0.21 0.54 -10000 0 -1.2 246 246
PI3K -0.17 0.48 -10000 0 -1.1 246 246
FES -0.2 0.51 -10000 0 -1.1 246 246
Crk/Dok-R -0.26 0.48 -10000 0 -1.1 246 246
Tie2/Ang1/ABIN2 -0.28 0.52 -10000 0 -1.2 246 246
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.11 0.38 -10000 0 -0.8 246 246
STAT5A -0.005 0.068 -10000 0 -0.79 8 8
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.13 0.4 -10000 0 -0.87 246 246
Tie2/Ang2 -0.14 0.42 -10000 0 -0.88 245 245
Tie2/Ang1 -0.24 0.59 -10000 0 -1.3 246 246
FOXO1 -0.11 0.38 -10000 0 -0.81 247 247
ELF1 0.013 0.023 -10000 0 -10000 0 0
ELF2 -0.21 0.53 -10000 0 -1.2 246 246
mol:Choline -0.19 0.5 -10000 0 -1.1 246 246
cell migration -0.044 0.11 -10000 0 -0.24 246 246
FYN -0.11 0.35 -10000 0 -0.73 245 245
DOK2 -0.003 0.045 -10000 0 -0.51 7 7
negative regulation of cell cycle -0.06 0.26 -10000 0 -0.54 205 205
ETS1 -0.03 0.11 -10000 0 -0.96 5 5
PXN -0.088 0.34 -10000 0 -0.71 246 246
ITGB1 0 0 -10000 0 -10000 0 0
NOS3 -0.096 0.36 -10000 0 -0.75 246 246
RAC1 0 0 -10000 0 -10000 0 0
TNF -0.042 0.14 -10000 0 -0.76 18 18
MAPKKK cascade -0.19 0.5 -10000 0 -1.1 246 246
RASA1 0 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.23 0.55 -10000 0 -1.2 246 246
NCK1 0 0 -10000 0 -10000 0 0
vasculogenesis -0.062 0.29 -10000 0 -0.58 246 246
mol:Phosphatidic acid -0.19 0.5 -10000 0 -1.1 246 246
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.076 0.32 -10000 0 -0.66 246 246
Rac1/GTP -0.18 0.34 -10000 0 -0.81 246 246
MMP2 -0.21 0.54 -10000 0 -1.2 246 246
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.077 0.16 -10000 0 -0.39 144 144
NFATC2 -0.056 0.28 -10000 0 -0.76 126 126
NFATC3 -0.051 0.12 -10000 0 -0.31 49 49
CD40LG -0.36 0.57 -10000 0 -1.1 335 335
ITCH 0.015 0.096 -10000 0 -10000 0 0
CBLB 0.015 0.096 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.25 0.36 -10000 0 -1.1 118 118
JUNB -0.001 0.013 -10000 0 -0.29 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.034 0.1 -10000 0 -0.33 111 111
T cell anergy -0.026 0.16 -10000 0 -0.48 111 111
TLE4 -0.031 0.26 -10000 0 -0.74 98 98
Jun/NFAT1-c-4/p21SNFT -0.3 0.44 -10000 0 -0.93 306 306
AP-1/NFAT1-c-4 -0.51 0.66 -10000 0 -1.4 343 343
IKZF1 -0.02 0.21 -10000 0 -0.59 109 109
T-helper 2 cell differentiation -0.12 0.3 -10000 0 -0.84 118 118
AP-1/NFAT1 -0.23 0.32 -10000 0 -0.64 371 371
CALM1 -0.018 0.053 -10000 0 -10000 0 0
EGR2 -0.29 0.64 -10000 0 -1.6 179 179
EGR3 -0.37 0.72 -10000 0 -1.5 290 290
NFAT1/FOXP3 -0.12 0.22 -10000 0 -0.57 146 146
EGR1 -0.24 0.37 -10000 0 -0.79 345 345
JUN -0.001 0.066 -10000 0 -0.8 7 7
EGR4 -0.014 0.077 -10000 0 -0.31 3 3
mol:Ca2+ -0.021 0.061 -10000 0 -10000 0 0
GBP3 -0.024 0.22 -10000 0 -0.65 99 99
FOSL1 -0.009 0.06 -10000 0 -0.35 28 28
NFAT1-c-4/MAF/IRF4 -0.31 0.47 -10000 0 -0.95 325 325
DGKA -0.019 0.21 -10000 0 -0.61 93 93
CREM 0 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.39 0.52 -10000 0 -1.1 353 353
CTLA4 -0.089 0.24 -10000 0 -0.59 118 118
NFAT1-c-4 (dimer)/EGR1 -0.42 0.57 -10000 0 -1.2 350 350
NFAT1-c-4 (dimer)/EGR4 -0.29 0.45 -10000 0 -0.91 340 340
FOS -0.23 0.37 -10000 0 -0.8 325 325
IFNG -0.15 0.27 -10000 0 -0.82 117 117
T cell activation -0.17 0.35 -10000 0 -0.8 195 195
MAF -0.001 0.024 -10000 0 -0.79 1 1
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.16 0.36 0.69 285 -10000 0 285
TNF -0.31 0.52 -10000 0 -1 334 334
FASLG -0.36 0.68 -10000 0 -1.3 339 339
TBX21 -0.022 0.16 -10000 0 -0.66 55 55
BATF3 -0.002 0.03 -10000 0 -0.39 5 5
PRKCQ -0.025 0.16 -10000 0 -0.69 59 59
PTPN1 -0.02 0.21 -10000 0 -0.59 107 107
NFAT1-c-4/ICER1 -0.29 0.44 -10000 0 -0.91 339 339
GATA3 -0.035 0.16 -10000 0 -0.58 69 69
T-helper 1 cell differentiation -0.15 0.26 -10000 0 -0.8 117 117
IL2RA -0.24 0.34 -10000 0 -0.98 127 127
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.018 0.21 -10000 0 -0.57 113 113
E2F1 -0.079 0.14 -10000 0 -0.28 348 348
PPARG -0.19 0.34 -10000 0 -0.79 263 263
SLC3A2 -0.018 0.21 -10000 0 -0.58 112 112
IRF4 -0.072 0.22 -10000 0 -0.73 107 107
PTGS2 -0.47 0.65 -10000 0 -1.2 403 403
CSF2 -0.36 0.55 -10000 0 -1.1 330 330
JunB/Fra1/NFAT1-c-4 -0.28 0.43 -10000 0 -0.88 322 322
IL4 -0.12 0.32 -10000 0 -0.9 113 113
IL5 -0.36 0.55 -10000 0 -1.1 328 328
IL2 -0.17 0.36 -10000 0 -0.81 193 193
IL3 -0.063 0.065 -10000 0 -10000 0 0
RNF128 -0.047 0.27 -10000 0 -0.85 111 111
NFATC1 -0.16 0.36 -10000 0 -0.7 279 279
CDK4 0.084 0.23 0.56 80 -10000 0 80
PTPRK -0.023 0.23 -10000 0 -0.68 86 86
IL8 -0.36 0.56 -10000 0 -1.1 332 332
POU2F1 0.001 0.01 -10000 0 -0.29 1 1
Glucocorticoid receptor regulatory 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
PCK2 0.024 0.079 0.37 1 -10000 0 1
SMARCC2 0.012 0.009 -10000 0 -10000 0 0
SMARCC1 0.012 0.009 -10000 0 -10000 0 0
TBX21 -0.13 0.25 -10000 0 -0.69 113 113
SUMO2 0 0.01 -10000 0 -0.29 1 1
STAT1 (dimer) 0.014 0.04 -10000 0 -0.29 19 19
FKBP4 -0.002 0.027 -10000 0 -0.29 9 9
FKBP5 -0.014 0.1 -10000 0 -0.68 23 23
GR alpha/HSP90/FKBP51/HSP90 0.11 0.14 0.31 125 -0.4 21 146
PRL -0.087 0.12 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.26 0.3 0.54 451 -0.55 30 481
RELA -0.039 0.083 -10000 0 -0.3 1 1
FGG 0.23 0.22 0.48 348 -0.48 3 351
GR beta/TIF2 0.1 0.2 0.35 107 -0.56 55 162
IFNG -0.42 0.35 -10000 0 -0.74 515 515
apoptosis -0.27 0.3 0.59 3 -0.65 308 311
CREB1 -0.009 0.032 -10000 0 -10000 0 0
histone acetylation 0.022 0.14 0.39 45 -0.37 39 84
BGLAP -0.1 0.15 -10000 0 -0.53 17 17
GR/PKAc 0.11 0.12 0.32 71 -0.46 4 75
NF kappa B1 p50/RelA -0.066 0.15 -10000 0 -0.42 38 38
SMARCD1 0.012 0.009 -10000 0 -10000 0 0
MDM2 0.12 0.1 0.26 247 -10000 0 247
GATA3 -0.026 0.16 -10000 0 -0.58 69 69
AKT1 0 0.004 -10000 0 -10000 0 0
CSF2 -0.04 0.11 -10000 0 -0.6 7 7
GSK3B 0 0.004 -10000 0 -10000 0 0
NR1I3 -0.21 0.26 0.56 3 -0.62 170 173
CSN2 0.19 0.18 0.41 249 -0.53 1 250
BRG1/BAF155/BAF170/BAF60A -0.002 0.031 -10000 0 -0.46 5 5
NFATC1 0.001 0.042 -10000 0 -0.79 3 3
POU2F1 0.007 0.013 -10000 0 -0.29 1 1
CDKN1A 0.046 0.072 -10000 0 -1.5 2 2
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.007 0.008 -10000 0 -10000 0 0
SFN -0.016 0.099 -10000 0 -0.51 35 35
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.1 0.14 0.33 64 -0.4 19 83
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.37 0.43 0.54 3 -0.88 399 402
JUN -0.32 0.29 -10000 0 -0.6 448 448
IL4 -0.13 0.16 -10000 0 -0.56 23 23
CDK5R1 -0.008 0.05 -10000 0 -0.3 31 31
PRKACA 0 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.41 0.4 -10000 0 -0.74 581 581
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.11 0.13 0.32 84 -0.37 17 101
cortisol/GR alpha (monomer) 0.34 0.32 0.63 503 -0.51 3 506
NCOA2 -0.038 0.17 -10000 0 -0.79 53 53
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.28 0.38 -10000 0 -0.86 325 325
AP-1/NFAT1-c-4 -0.65 0.52 -10000 0 -1 650 650
AFP -0.61 0.7 -10000 0 -1.5 376 376
SUV420H1 0 0 -10000 0 -10000 0 0
IRF1 0.19 0.16 0.51 63 -10000 0 63
TP53 0.032 0.023 -10000 0 -0.5 2 2
PPP5C 0 0 -10000 0 -10000 0 0
KRT17 -0.82 0.8 -10000 0 -1.6 500 500
KRT14 -0.81 0.77 -10000 0 -1.5 567 567
TBP 0.019 0.006 -10000 0 -10000 0 0
CREBBP 0.14 0.14 0.29 352 -10000 0 352
HDAC1 0 0.004 -10000 0 -10000 0 0
HDAC2 0.001 0.004 -10000 0 -10000 0 0
AP-1 -0.66 0.52 -10000 0 -1 651 651
MAPK14 0 0.003 -10000 0 -10000 0 0
MAPK10 -0.12 0.29 -10000 0 -0.8 170 170
MAPK11 -0.002 0.042 -10000 0 -0.8 3 3
KRT5 -0.92 0.81 -10000 0 -1.7 575 575
interleukin-1 receptor activity -0.001 0.003 -10000 0 -10000 0 0
NCOA1 0.014 0.024 -10000 0 -0.78 1 1
STAT1 0.014 0.04 -10000 0 -0.29 19 19
CGA -0.16 0.18 -10000 0 -0.52 93 93
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.2 0.18 0.37 514 -10000 0 514
MAPK3 0 0.003 -10000 0 -10000 0 0
MAPK1 0 0.003 -10000 0 -10000 0 0
ICAM1 -0.18 0.25 -10000 0 -0.63 150 150
NFKB1 -0.039 0.083 -10000 0 -0.3 1 1
MAPK8 -0.23 0.22 -10000 0 -0.44 448 448
MAPK9 0 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.29 0.32 0.59 3 -0.69 309 312
BAX 0.048 0.032 -10000 0 -10000 0 0
POMC -0.19 0.31 -10000 0 -0.92 94 94
EP300 0.14 0.14 0.28 533 -0.25 1 534
cortisol/GR alpha (dimer)/p53 0.31 0.26 0.56 460 -0.56 1 461
proteasomal ubiquitin-dependent protein catabolic process 0.086 0.079 0.24 60 -10000 0 60
SGK1 0.22 0.2 -10000 0 -1.2 6 6
IL13 -0.31 0.28 -10000 0 -0.65 306 306
IL6 -0.49 0.62 -10000 0 -1.3 405 405
PRKACG 0 0 -10000 0 -10000 0 0
IL5 -0.27 0.23 -10000 0 -0.77 52 52
IL2 -0.41 0.35 -10000 0 -0.76 457 457
CDK5 -0.002 0.024 -10000 0 -0.3 7 7
PRKACB -0.016 0.077 -10000 0 -0.33 53 53
HSP90AA1 0 0.009 -10000 0 -0.29 1 1
IL8 -0.2 0.3 -10000 0 -0.83 115 115
CDK5R1/CDK5 -0.007 0.036 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.055 0.1 -10000 0 -0.52 8 8
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.28 0.24 0.52 445 -0.5 2 447
SMARCA4 0.012 0.013 -10000 0 -0.29 1 1
chromatin remodeling 0.2 0.16 0.38 346 -0.34 2 348
NF kappa B1 p50/RelA/Cbp 0.06 0.17 0.34 103 -0.45 2 105
JUN (dimer) -0.32 0.29 -10000 0 -0.6 449 449
YWHAH 0 0 -10000 0 -10000 0 0
VIPR1 -0.13 0.25 -10000 0 -0.81 84 84
NR3C1 0.2 0.2 0.44 314 -0.49 9 323
NR4A1 -0.056 0.23 -10000 0 -0.72 108 108
TIF2/SUV420H1 -0.029 0.13 -10000 0 -0.6 53 53
MAPKKK cascade -0.27 0.3 0.59 3 -0.65 308 311
cortisol/GR alpha (dimer)/Src-1 0.3 0.26 0.55 468 -0.57 1 469
PBX1 0.005 0.037 -10000 0 -0.78 2 2
POU1F1 0.003 0.015 -10000 0 -0.29 1 1
SELE -0.22 0.36 -10000 0 -1 120 120
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.2 0.16 0.38 343 -0.34 2 345
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.28 0.24 0.52 445 -0.5 2 447
mol:cortisol 0.2 0.2 0.37 518 -0.2 1 519
MMP1 -0.22 0.11 -10000 0 -10000 0 0
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.46 0.46 -10000 0 -1.1 270 270
STAT6 (cleaved dimer) -0.5 0.45 -10000 0 -0.97 423 423
IGHG1 -0.16 0.16 -10000 0 -0.36 92 92
IGHG3 -0.45 0.44 -10000 0 -0.94 389 389
AKT1 -0.21 0.24 -10000 0 -0.65 96 96
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.15 0.2 -10000 0 -0.58 65 65
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.22 0.24 -10000 0 -0.63 117 117
THY1 -0.46 0.46 -10000 0 -1.1 234 234
MYB -0.017 0.11 -10000 0 -0.73 26 26
HMGA1 -0.014 0.063 -10000 0 -0.29 53 53
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.28 0.29 -10000 0 -0.65 265 265
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.21 0.23 -10000 0 -0.58 115 115
SP1 0.018 0.006 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.024 0.029 -10000 0 -0.76 1 1
STAT6 (dimer)/ETS1 -0.48 0.44 -10000 0 -1 348 348
SOCS1 -0.3 0.31 -10000 0 -0.74 207 207
SOCS3 -0.23 0.26 -10000 0 -0.81 71 71
FCER2 -0.59 0.64 -10000 0 -1.4 377 377
PARP14 0.004 0.018 -10000 0 -0.3 3 3
CCL17 -0.47 0.46 -10000 0 -1.1 255 255
GRB2 0 0.009 -10000 0 -0.29 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.17 0.19 -10000 0 -0.59 29 29
T cell proliferation -0.46 0.48 -10000 0 -1.1 278 278
IL4R/JAK1 -0.46 0.46 -10000 0 -1.1 259 259
EGR2 -0.6 0.63 -10000 0 -1.4 355 355
JAK2 -0.008 0.035 -10000 0 -0.81 1 1
JAK3 0.01 0.035 -10000 0 -0.29 14 14
PIK3R1 -0.009 0.086 -10000 0 -0.79 13 13
JAK1 0.004 0.026 -10000 0 -0.79 1 1
COL1A2 -0.14 0.16 -10000 0 -1.6 3 3
CCL26 -0.46 0.46 -10000 0 -1.1 276 276
IL4R -0.49 0.49 -10000 0 -1.2 278 278
PTPN6 0.022 0.018 -10000 0 -0.28 2 2
IL13RA2 -0.46 0.46 -10000 0 -1.1 253 253
IL13RA1 -0.007 0.025 -10000 0 -10000 0 0
IRF4 -0.22 0.48 -10000 0 -1.5 115 115
ARG1 -0.11 0.12 -10000 0 -10000 0 0
CBL -0.26 0.28 -10000 0 -0.64 221 221
GTF3A 0.013 0.016 -10000 0 -0.29 2 2
PIK3CA 0 0.009 -10000 0 -0.29 1 1
IL13RA1/JAK2 -0.014 0.041 -10000 0 -0.62 1 1
IRF4/BCL6 -0.2 0.43 -10000 0 -1.4 119 119
CD40LG -0.031 0.18 -10000 0 -0.72 66 66
MAPK14 -0.26 0.28 -10000 0 -0.66 204 204
mitosis -0.2 0.23 -10000 0 -0.61 96 96
STAT6 -0.53 0.55 -10000 0 -1.2 347 347
SPI1 0.007 0.022 -10000 0 -0.29 5 5
RPS6KB1 -0.19 0.22 -10000 0 -0.6 84 84
STAT6 (dimer) -0.53 0.55 -10000 0 -1.2 347 347
STAT6 (dimer)/PARP14 -0.51 0.51 -10000 0 -1.1 370 370
mast cell activation 0.012 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.2 0.23 -10000 0 -0.58 117 117
FRAP1 -0.21 0.24 -10000 0 -0.65 96 96
LTA -0.47 0.46 -10000 0 -1.1 285 285
FES -0.002 0.041 -10000 0 -0.79 3 3
T-helper 1 cell differentiation 0.52 0.52 1.1 365 -10000 0 365
CCL11 -0.49 0.44 -10000 0 -1.1 283 283
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.2 0.23 -10000 0 -0.6 106 106
IL2RG -0.004 0.088 -10000 0 -0.36 53 53
IL10 -0.46 0.46 -10000 0 -1.1 246 246
IRS1 -0.033 0.16 -10000 0 -0.79 45 45
IRS2 -0.033 0.16 -10000 0 -0.79 45 45
IL4 -0.11 0.11 -10000 0 -10000 0 0
IL5 -0.47 0.46 -10000 0 -1.2 230 230
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.38 0.36 -10000 0 -0.82 310 310
COL1A1 -0.18 0.17 -10000 0 -1.7 1 1
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.46 0.48 -10000 0 -1.2 212 212
IL2R gamma/JAK3 -0.011 0.071 -10000 0 -0.45 20 20
TFF3 -0.56 0.58 -10000 0 -1.3 324 324
ALOX15 -0.54 0.57 -10000 0 -1.3 304 304
MYBL1 -0.041 0.1 -10000 0 -0.29 154 154
T-helper 2 cell differentiation -0.39 0.38 -10000 0 -0.84 345 345
SHC1 0 0 -10000 0 -10000 0 0
CEBPB 0.009 0.009 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.21 0.24 -10000 0 -0.57 139 139
mol:PI-3-4-5-P3 -0.21 0.24 -10000 0 -0.65 96 96
PI3K -0.22 0.26 -10000 0 -0.69 96 96
DOK2 -0.003 0.045 -10000 0 -0.51 7 7
ETS1 0.019 0.054 -10000 0 -0.75 5 5
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.15 0.18 -10000 0 -0.68 15 15
ITGB3 -0.48 0.5 -10000 0 -1.1 296 296
PIGR -0.99 0.75 -10000 0 -1.5 691 691
IGHE 0.046 0.04 -10000 0 -10000 0 0
MAPKKK cascade -0.15 0.18 -10000 0 -0.66 15 15
BCL6 0.001 0.06 -10000 0 -0.79 6 6
OPRM1 -0.47 0.46 -10000 0 -1.2 226 226
RETNLB -0.47 0.46 -10000 0 -1.1 305 305
SELP -0.63 0.68 -10000 0 -1.5 335 335
AICDA -0.45 0.44 -10000 0 -1.1 267 267
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0 0 -9999 0 -10000 0 0
VLDLR -0.024 0.14 -9999 0 -0.79 33 33
LRPAP1 0 0 -9999 0 -10000 0 0
NUDC 0 0 -9999 0 -10000 0 0
RELN/LRP8 -0.32 0.26 -9999 0 -0.54 651 651
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0 0.009 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.28 0.25 -9999 0 -0.48 651 651
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 -0.017 0.069 -9999 0 -10000 0 0
IQGAP1 0 0 -9999 0 -10000 0 0
PLA2G7 -0.015 0.091 -9999 0 -0.43 39 39
CALM1 0 0 -9999 0 -10000 0 0
DYNLT1 0 0.009 -9999 0 -0.29 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.019 0.057 -9999 0 -10000 0 0
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0 0 -9999 0 -10000 0 0
CDK5R1 -0.008 0.049 -9999 0 -0.29 31 31
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 -0.044 0.1 -9999 0 -0.29 165 165
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.33 0.27 -9999 0 -0.55 660 660
YWHAE 0 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.23 0.19 -9999 0 -0.45 185 185
MAP1B -0.008 0.053 -9999 0 -0.37 22 22
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.26 0.21 -9999 0 -0.42 651 651
RELN -0.47 0.39 -9999 0 -0.79 654 654
PAFAH/LIS1 -0.009 0.056 -9999 0 -0.52 11 11
LIS1/CLIP170 0 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.18 0.15 -9999 0 -0.43 4 4
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.2 0.17 -9999 0 -0.33 663 663
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.25 0.2 -9999 0 -0.48 185 185
LIS1/IQGAP1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.022 0 -9999 0 -10000 0 0
PAFAH1B3 -0.035 0.095 -9999 0 -0.29 130 130
PAFAH1B2 -0.004 0.058 -9999 0 -0.79 6 6
MAP1B/LIS1/Dynein heavy chain -0.005 0.033 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.22 0.18 -9999 0 -0.46 99 99
LRP8 -0.031 0.09 -9999 0 -10000 0 0
NDEL1/Katanin 60 -0.23 0.19 -9999 0 -0.45 186 186
P39/CDK5 -0.27 0.22 -9999 0 -0.45 651 651
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0 0 -9999 0 -10000 0 0
CDK5 -0.26 0.24 -9999 0 -0.45 651 651
PPP2R5D 0 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.28 0.24 -9999 0 -0.46 660 660
RELN/VLDLR -0.31 0.25 -9999 0 -0.5 660 660
CDC42 0 0 -9999 0 -10000 0 0
Arf6 signaling events

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
CENTA1/KIF3B -0.004 0.043 -9999 0 -0.64 4 4
ARNO/beta Arrestin1-2 -0.12 0.19 -9999 0 -0.43 251 251
EGFR -0.3 0.38 -9999 0 -0.78 414 414
EPHA2 -0.004 0.058 -9999 0 -0.79 6 6
USP6 0 0 -9999 0 -10000 0 0
IQSEC1 0 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.34 0.35 -9999 0 -0.66 555 555
ARRB2 -0.051 0.15 -9999 0 -0.44 148 148
mol:GTP 0.017 0.018 -9999 0 -0.15 5 5
ARRB1 -0.002 0.035 -9999 0 -0.62 3 3
FBXO8 0 0 -9999 0 -10000 0 0
TSHR -0.037 0.16 -9999 0 -0.74 54 54
EGF -0.16 0.31 -9999 0 -0.78 216 216
somatostatin receptor activity 0 0 -9999 0 -0.001 383 383
ARAP2 -0.004 0.058 -9999 0 -0.79 6 6
mol:GDP -0.14 0.18 -9999 0 -0.34 352 352
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 339 339
ITGA2B -0.019 0.079 -9999 0 -0.32 64 64
ARF6 0 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.003 0.036 -9999 0 -0.47 6 6
ADAP1 -0.005 0.05 -9999 0 -0.41 13 13
KIF13B -0.001 0.034 -9999 0 -0.79 2 2
HGF/MET -0.14 0.28 -9999 0 -0.64 240 240
PXN 0 0 -9999 0 -10000 0 0
ARF6/GTP -0.13 0.15 -9999 0 -0.31 379 379
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.29 0.31 -9999 0 -0.58 555 555
ADRB2 -0.18 0.33 -9999 0 -0.79 250 250
receptor agonist activity 0 0 -9999 0 0 382 382
actin filament binding 0 0 -9999 0 -0.001 372 372
SRC 0 0.009 -9999 0 -0.29 1 1
ITGB3 -0.029 0.15 -9999 0 -0.74 42 42
GNAQ -0.002 0.041 -9999 0 -0.79 3 3
EFA6/PI-4-5-P2 0 0.001 -9999 0 -0.001 349 349
ARF6/GDP -0.014 0.083 -9999 0 -0.42 18 18
ARF6/GDP/GULP/ACAP1 -0.15 0.2 -9999 0 -0.51 187 187
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.025 0.095 -9999 0 -0.48 41 41
ACAP1 -0.02 0.095 -9999 0 -0.38 57 57
ACAP2 0 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.088 0.22 -9999 0 -0.65 148 148
EFNA1 0 0.009 -9999 0 -0.29 1 1
HGF -0.053 0.2 -9999 0 -0.78 75 75
CYTH3 0.01 0.019 -9999 0 -0.61 1 1
CYTH2 0.006 0.002 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 300 300
endosomal lumen acidification 0 0 -9999 0 -0.001 303 303
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.053 0.2 -9999 0 -0.79 73 73
GNAQ/ARNO 0.004 0.025 -9999 0 -0.45 3 3
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 378 378
MET -0.14 0.3 -9999 0 -0.79 188 188
GNA14 -0.013 0.085 -9999 0 -0.45 32 32
GNA15 -0.003 0.033 -9999 0 -0.36 8 8
GIT1 -0.001 0.02 -9999 0 -0.29 5 5
mol:PI-4-5-P2 0 0 -9999 0 -0.001 353 353
GNA11 -0.002 0.041 -9999 0 -0.79 3 3
LHCGR -0.11 0.27 -9999 0 -0.79 148 148
AGTR1 -0.21 0.34 -9999 0 -0.69 327 327
desensitization of G-protein coupled receptor protein signaling pathway -0.088 0.22 -9999 0 -0.65 148 148
IPCEF1/ARNO -0.24 0.25 -9999 0 -0.46 555 555
alphaIIb/beta3 Integrin -0.034 0.12 -9999 0 -0.62 41 41
Wnt signaling

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
Noncanonical Wnts/FZD -0.16 0.24 -9999 0 -0.44 381 381
FZD6 -0.007 0.075 -9999 0 -0.79 10 10
WNT6 -0.16 0.31 -9999 0 -0.69 255 255
WNT4 -0.022 0.12 -9999 0 -0.55 43 43
FZD3 -0.011 0.092 -9999 0 -0.79 15 15
WNT5A -0.016 0.1 -9999 0 -0.61 28 28
WNT11 -0.16 0.32 -9999 0 -0.76 235 235
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.24 0.44 -9999 0 -0.95 158 158
PLK1 -0.087 0.11 -9999 0 -10000 0 0
BIRC5 -0.1 0.1 -9999 0 -10000 0 0
HSPA1B -0.24 0.44 -9999 0 -0.98 141 141
MAP2K1 0.008 0.03 -9999 0 -10000 0 0
BRCA2 -0.24 0.44 -9999 0 -0.98 145 145
FOXM1 -0.29 0.52 -9999 0 -1.1 212 212
XRCC1 -0.24 0.44 -9999 0 -0.98 141 141
FOXM1B/p19 -0.29 0.42 -9999 0 -0.94 233 233
Cyclin D1/CDK4 -0.23 0.41 -9999 0 -0.91 144 144
CDC2 -0.26 0.46 -9999 0 -0.94 215 215
TGFA -0.22 0.42 -9999 0 -0.92 154 154
SKP2 -0.24 0.44 -9999 0 -1 121 121
CCNE1 -0.056 0.13 -9999 0 -0.3 223 223
CKS1B -0.24 0.44 -9999 0 -0.98 141 141
RB1 -0.12 0.13 -9999 0 -1.1 2 2
FOXM1C/SP1 -0.3 0.45 -9999 0 -0.99 219 219
AURKB -0.08 0.11 -9999 0 -10000 0 0
CENPF -0.27 0.46 -9999 0 -0.97 193 193
CDK4 0.007 0.022 -9999 0 -0.3 4 4
MYC -0.22 0.41 -9999 0 -0.88 172 172
CHEK2 0.007 0.033 -9999 0 -0.32 2 2
ONECUT1 -0.24 0.43 -9999 0 -0.94 164 164
CDKN2A -0.039 0.12 -9999 0 -0.29 177 177
LAMA4 -0.24 0.44 -9999 0 -1 140 140
FOXM1B/HNF6 -0.27 0.49 -9999 0 -1.1 147 147
FOS -0.44 0.67 -9999 0 -1.3 346 346
SP1 0 0 -9999 0 -10000 0 0
CDC25B -0.24 0.44 -9999 0 -0.98 143 143
response to radiation -0.007 0.03 -9999 0 -10000 0 0
CENPB -0.24 0.44 -9999 0 -0.98 138 138
CENPA -0.27 0.46 -9999 0 -0.98 185 185
NEK2 -0.29 0.45 -9999 0 -0.98 188 188
HIST1H2BA -0.25 0.44 -9999 0 -0.98 141 141
CCNA2 -0.11 0.15 -9999 0 -0.3 426 426
EP300 0 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.28 0.49 -9999 0 -1.1 184 184
CCNB2 -0.27 0.46 -9999 0 -0.98 192 192
CCNB1 -0.26 0.46 -9999 0 -0.99 189 189
ETV5 -0.24 0.44 -9999 0 -0.98 140 140
ESR1 -0.34 0.58 -9999 0 -1.3 238 238
CCND1 -0.23 0.42 -9999 0 -0.93 144 144
GSK3A 0.014 0.021 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.081 0.14 -9999 0 -0.33 189 189
CDK2 0.006 0.009 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.01 0.036 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.33 0.38 -9999 0 -0.92 240 240
GAS1 -0.28 0.5 -9999 0 -1.1 194 194
MMP2 -0.24 0.44 -9999 0 -1 141 141
RB1/FOXM1C -0.24 0.44 -9999 0 -0.94 180 180
CREBBP 0 0 -9999 0 -10000 0 0
Aurora B signaling

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
Condensin I complex -0.053 0.067 -9999 0 -10000 0 0
STMN1 -0.11 0.12 -9999 0 -0.37 81 81
Aurora B/RasGAP/Survivin -0.18 0.13 -9999 0 -10000 0 0
Chromosomal passenger complex/Cul3 protein complex -0.16 0.15 -9999 0 -0.33 438 438
BIRC5 -0.21 0.14 -9999 0 -0.3 779 779
DES -0.29 0.34 -9999 0 -0.66 496 496
Aurora C/Aurora B/INCENP -0.069 0.076 -9999 0 -0.62 1 1
Aurora B/TACC1 -0.1 0.13 -9999 0 -0.61 41 41
Aurora B/PP2A -0.099 0.097 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.008 0.017 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition -0.003 0.003 -9999 0 -10000 0 0
NDC80 -0.21 0.18 -9999 0 -0.37 549 549
Cul3 protein complex -0.21 0.26 -9999 0 -0.52 438 438
KIF2C -0.046 0.034 -9999 0 -10000 0 0
PEBP1 0.002 0.005 -9999 0 -10000 0 0
KIF20A -0.22 0.13 -9999 0 -0.3 819 819
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.099 0.097 -9999 0 -10000 0 0
SEPT1 -0.01 0.053 -9999 0 -0.29 37 37
SMC2 0 0 -9999 0 -10000 0 0
SMC4 -0.004 0.034 -9999 0 -0.29 15 15
NSUN2/NPM1/Nucleolin 0.005 0.02 -9999 0 -10000 0 0
PSMA3 0 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.003 0.002 -9999 0 -10000 0 0
H3F3B -0.034 0.046 -9999 0 -10000 0 0
AURKB -0.16 0.15 -9999 0 -0.3 625 625
AURKC -0.005 0.043 -9999 0 -0.32 18 18
CDCA8 -0.099 0.14 -9999 0 -0.3 370 370
cytokinesis -0.11 0.08 -9999 0 -10000 0 0
Aurora B/Septin1 -0.099 0.089 -9999 0 -10000 0 0
AURKA -0.14 0.15 -9999 0 -0.3 505 505
INCENP 0.003 0.005 -9999 0 -10000 0 0
KLHL13 -0.32 0.39 -9999 0 -0.79 437 437
BUB1 -0.2 0.14 -9999 0 -0.3 731 731
hSgo1/Aurora B/Survivin -0.26 0.18 -9999 0 -0.41 538 538
EVI5 0.009 0.004 -9999 0 -10000 0 0
RhoA/GTP -0.1 0.1 -9999 0 -0.34 35 35
SGOL1 -0.18 0.14 -9999 0 -0.29 681 681
CENPA -0.06 0.065 -9999 0 -10000 0 0
NCAPG -0.14 0.15 -9999 0 -0.29 529 529
Aurora B/HC8 Proteasome -0.099 0.097 -9999 0 -10000 0 0
NCAPD2 -0.002 0.025 -9999 0 -0.29 8 8
Aurora B/PP1-gamma -0.099 0.097 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
NCAPH -0.11 0.14 -9999 0 -10000 0 0
NPM1 -0.019 0.025 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
KLHL9 -0.001 0.034 -9999 0 -0.79 2 2
mitotic prometaphase -0.006 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.099 0.097 -9999 0 -10000 0 0
PPP1CC 0 0 -9999 0 -10000 0 0
Centraspindlin -0.12 0.11 -9999 0 -0.37 38 38
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.019 0.025 -9999 0 -10000 0 0
MYLK -0.088 0.15 -9999 0 -0.47 139 139
KIF23 -0.088 0.14 -9999 0 -0.3 336 336
VIM -0.095 0.1 -9999 0 -0.68 2 2
RACGAP1 -0.007 0.059 -9999 0 -0.3 42 42
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.019 0.025 -9999 0 -10000 0 0
Chromosomal passenger complex -0.085 0.079 -9999 0 -10000 0 0
Chromosomal passenger complex/EVI5 -0.16 0.18 -9999 0 -0.37 211 211
TACC1 -0.03 0.15 -9999 0 -0.79 41 41
PPP2R5D 0 0 -9999 0 -10000 0 0
CUL3 0 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Endothelins

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
AKT1 -0.008 0.19 -9999 0 -0.59 88 88
PTK2B 0.005 0.006 -9999 0 -10000 0 0
mol:Ca2+ 0.022 0.2 -9999 0 -0.95 33 33
EDN1 -0.034 0.24 -9999 0 -0.81 85 85
EDN3 -0.37 0.39 -9999 0 -0.79 512 512
EDN2 -0.076 0.14 -9999 0 -0.31 268 268
HRAS/GDP -0.029 0.21 -9999 0 -0.54 101 101
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.002 0.14 -9999 0 -0.42 63 63
ADCY4 -0.14 0.29 -9999 0 -0.55 313 313
ADCY5 -0.27 0.36 -9999 0 -0.6 513 513
ADCY6 -0.13 0.26 -9999 0 -0.52 295 295
ADCY7 -0.13 0.26 -9999 0 -0.52 295 295
ADCY1 -0.15 0.29 -9999 0 -0.56 310 310
ADCY2 -0.17 0.32 -9999 0 -0.59 327 327
ADCY3 -0.13 0.26 -9999 0 -0.52 295 295
ADCY8 -0.14 0.27 -9999 0 -0.53 295 295
ADCY9 -0.13 0.26 -9999 0 -0.52 295 295
arachidonic acid secretion -0.1 0.3 -9999 0 -0.59 210 210
ETB receptor/Endothelin-1/Gq/GTP -0.034 0.18 -9999 0 -0.39 164 164
GNAO1 -0.03 0.13 -9999 0 -0.49 67 67
HRAS -0.002 0.027 -9999 0 -0.29 9 9
ETA receptor/Endothelin-1/G12/GTP 0.04 0.21 -9999 0 -0.55 88 88
ETA receptor/Endothelin-1/Gs/GTP -0.087 0.32 -9999 0 -0.56 295 295
mol:GTP -0.001 0.006 -9999 0 -10000 0 0
COL3A1 -0.017 0.2 -9999 0 -0.59 88 88
EDNRB -0.073 0.24 -9999 0 -0.79 113 113
response to oxidative stress 0 0 -9999 0 -10000 0 0
CYSLTR2 -0.022 0.24 -9999 0 -0.68 104 104
CYSLTR1 -0.019 0.23 -9999 0 -0.66 101 101
SLC9A1 0.003 0.1 -9999 0 -0.31 72 72
mol:GDP -0.037 0.22 -9999 0 -0.56 108 108
SLC9A3 -0.051 0.28 -9999 0 -0.63 183 183
RAF1 -0.084 0.25 -9999 0 -0.56 155 155
JUN 0.029 0.18 -9999 0 -0.84 29 29
JAK2 -0.008 0.2 -9999 0 -0.59 88 88
mol:IP3 -0.029 0.18 -9999 0 -0.52 75 75
ETA receptor/Endothelin-1 0.038 0.25 -9999 0 -0.68 88 88
PLCB1 -0.052 0.21 -9999 0 -0.79 82 82
PLCB2 0.007 0.027 -9999 0 -0.54 2 2
ETA receptor/Endothelin-3 -0.27 0.31 -9999 0 -0.6 510 510
FOS -0.25 0.49 -9999 0 -0.99 331 331
Gai/GDP -0.016 0.16 -9999 0 -0.79 28 28
CRK 0.005 0.006 -9999 0 -10000 0 0
mol:Ca ++ -0.049 0.25 -9999 0 -0.67 114 114
BCAR1 0.005 0.006 -9999 0 -10000 0 0
PRKCB1 -0.031 0.17 -9999 0 -0.47 91 91
GNAQ 0.008 0.043 -9999 0 -0.8 3 3
GNAZ -0.007 0.071 -9999 0 -0.79 9 9
GNAL -0.19 0.34 -9999 0 -0.79 259 259
Gs family/GDP -0.17 0.26 -9999 0 -0.57 261 261
ETA receptor/Endothelin-1/Gq/GTP 0.018 0.13 -9999 0 -0.4 57 57
MAPK14 -0.032 0.17 -9999 0 -0.49 89 89
TRPC6 0.02 0.22 -9999 0 -1.1 32 32
GNAI2 0 0 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
GNAI1 -0.045 0.18 -9999 0 -0.79 62 62
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.041 0.18 -9999 0 -0.43 138 138
ETB receptor/Endothelin-2 -0.11 0.21 -9999 0 -0.65 120 120
ETB receptor/Endothelin-3 -0.34 0.34 -9999 0 -0.65 568 568
ETB receptor/Endothelin-1 -0.081 0.27 -9999 0 -0.66 183 183
MAPK3 -0.19 0.41 -9999 0 -0.79 335 335
MAPK1 -0.19 0.41 -9999 0 -0.79 335 335
Rac1/GDP -0.027 0.2 -9999 0 -0.53 102 102
cAMP biosynthetic process -0.17 0.3 -9999 0 -0.6 304 304
MAPK8 0.02 0.19 -9999 0 -0.75 40 40
SRC 0 0.009 -9999 0 -0.29 1 1
ETB receptor/Endothelin-1/Gi/GTP -0.049 0.19 -9999 0 -0.53 91 91
p130Cas/CRK/Src/PYK2 -0.014 0.22 -9999 0 -0.62 76 76
mol:K + 0 0 -9999 0 -10000 0 0
G12/GDP -0.027 0.2 -9999 0 -0.53 102 102
COL1A2 -0.054 0.25 -9999 0 -0.69 103 103
EntrezGene:2778 0 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-2 -0.029 0.12 -9999 0 -0.44 20 20
mol:DAG -0.029 0.18 -9999 0 -0.5 83 83
MAP2K2 -0.13 0.32 -9999 0 -0.57 341 341
MAP2K1 -0.13 0.32 -9999 0 -0.57 339 339
EDNRA 0.027 0.07 -9999 0 -0.43 5 5
positive regulation of muscle contraction -0.009 0.17 -9999 0 -0.51 88 88
Gq family/GDP -0.073 0.16 -9999 0 -0.6 62 62
HRAS/GTP -0.052 0.21 -9999 0 -0.49 136 136
PRKCH -0.023 0.17 -9999 0 -0.53 66 66
RAC1 0 0 -9999 0 -10000 0 0
PRKCA -0.035 0.2 -9999 0 -0.58 84 84
PRKCB -0.035 0.2 -9999 0 -0.57 79 79
PRKCE -0.023 0.17 -9999 0 -0.52 67 67
PRKCD -0.024 0.17 -9999 0 -0.51 71 71
PRKCG -0.033 0.18 -9999 0 -0.52 76 76
regulation of vascular smooth muscle contraction -0.29 0.57 -9999 0 -1.1 331 331
PRKCQ -0.045 0.21 -9999 0 -0.57 108 108
PLA2G4A -0.12 0.33 -9999 0 -0.66 210 210
GNA14 -0.004 0.088 -9999 0 -0.45 32 32
GNA15 0.007 0.035 -9999 0 -0.36 8 8
GNA12 0 0 -9999 0 -10000 0 0
GNA11 0.007 0.042 -9999 0 -0.79 3 3
Rac1/GTP 0.041 0.2 -9999 0 -0.55 88 88
MMP1 -0.13 0.13 -9999 0 -10000 0 0
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0 0 -10000 0 -10000 0 0
EPHB2 -0.003 0.039 -10000 0 -0.29 19 19
EFNB1 0.017 0.05 -10000 0 -0.6 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.16 0.2 -10000 0 -0.41 427 427
Ephrin B2/EPHB1-2 -0.19 0.23 -10000 0 -0.48 426 426
neuron projection morphogenesis -0.15 0.19 -10000 0 -0.39 427 427
Ephrin B1/EPHB1-2/Tiam1 -0.18 0.22 -10000 0 -0.44 427 427
DNM1 -0.005 0.064 -10000 0 -0.73 8 8
cell-cell signaling -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.003 0.13 -10000 0 -0.74 33 33
YES1 -0.025 0.17 -10000 0 -0.98 32 32
Ephrin B1/EPHB1-2/NCK2 -0.17 0.22 -10000 0 -0.44 427 427
PI3K -0.028 0.14 -10000 0 -0.68 44 44
mol:GDP -0.17 0.22 -10000 0 -0.44 427 427
ITGA2B -0.019 0.079 -10000 0 -0.32 64 64
endothelial cell proliferation 0 0.005 -10000 0 -10000 0 0
FYN -0.025 0.16 -10000 0 -0.97 32 32
MAP3K7 -0.022 0.14 -10000 0 -0.79 32 32
FGR -0.027 0.17 -10000 0 -0.98 32 32
TIAM1 -0.001 0.018 -10000 0 -0.29 4 4
PIK3R1 -0.009 0.086 -10000 0 -0.79 13 13
RGS3 0 0 -10000 0 -10000 0 0
cell adhesion -0.046 0.16 -10000 0 -0.62 73 73
LYN -0.025 0.16 -10000 0 -0.97 32 32
Ephrin B1/EPHB1-2/Src Family Kinases -0.026 0.16 -10000 0 -0.92 32 32
Ephrin B1/EPHB1-2 -0.029 0.14 -10000 0 -0.86 32 32
SRC -0.027 0.17 -10000 0 -0.98 32 32
ITGB3 -0.029 0.15 -10000 0 -0.74 42 42
EPHB1 -0.31 0.38 -10000 0 -0.79 426 426
EPHB4 0 0.009 -10000 0 -0.29 1 1
RAC1 0 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0 0.005 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.034 0.12 -10000 0 -0.62 41 41
BLK -0.027 0.17 -10000 0 -0.98 32 32
HCK -0.027 0.17 -10000 0 -0.98 32 32
regulation of stress fiber formation 0.17 0.22 0.44 427 -10000 0 427
MAPK8 0.002 0.14 -10000 0 -0.71 37 37
Ephrin B1/EPHB1-2/RGS3 -0.17 0.22 -10000 0 -0.44 427 427
endothelial cell migration -0.016 0.12 -10000 0 -0.69 32 32
NCK2 0 0 -10000 0 -10000 0 0
PTPN13 -0.017 0.15 -10000 0 -0.9 32 32
regulation of focal adhesion formation 0.17 0.22 0.44 427 -10000 0 427
chemotaxis 0.17 0.22 0.44 427 -10000 0 427
PIK3CA 0 0.009 -10000 0 -0.29 1 1
Rac1/GTP -0.16 0.2 -10000 0 -0.4 427 427
angiogenesis -0.028 0.14 -10000 0 -0.85 32 32
LCK -0.029 0.17 -10000 0 -0.98 32 32
ErbB2/ErbB3 signaling events

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
USP8 0.013 0.01 -9999 0 -10000 0 0
RAS family/GTP -0.11 0.14 -9999 0 -0.35 69 69
NFATC4 -0.088 0.16 -9999 0 -0.38 31 31
ERBB2IP 0.008 0.008 -9999 0 -10000 0 0
HSP90 (dimer) 0 0.009 -9999 0 -0.29 1 1
mammary gland morphogenesis -0.15 0.19 -9999 0 -0.39 403 403
JUN -0.018 0.08 -9999 0 -0.37 6 6
HRAS -0.002 0.027 -9999 0 -0.29 9 9
DOCK7 -0.12 0.19 -9999 0 -0.38 242 242
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.18 0.22 -9999 0 -0.46 403 403
AKT1 0.008 0.005 -9999 0 -10000 0 0
BAD 0.018 0.006 -9999 0 -10000 0 0
MAPK10 -0.11 0.13 -9999 0 -0.35 173 173
mol:GTP -0.001 0.001 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.16 0.2 -9999 0 -0.42 403 403
RAF1 -0.081 0.16 -9999 0 -0.44 18 18
ErbB2/ErbB3/neuregulin 2 -0.25 0.25 -9999 0 -0.5 528 528
STAT3 0.001 0.003 -9999 0 -10000 0 0
cell migration -0.062 0.13 -9999 0 -0.31 93 93
mol:PI-3-4-5-P3 -0.002 0.003 -9999 0 -10000 0 0
cell proliferation -0.14 0.22 -9999 0 -0.51 174 174
FOS -0.16 0.26 -9999 0 -0.53 329 329
NRAS -0.001 0.013 -9999 0 -0.3 2 2
mol:Ca2+ -0.15 0.19 -9999 0 -0.39 403 403
MAPK3 -0.11 0.19 -9999 0 -0.47 65 65
MAPK1 -0.11 0.19 -9999 0 -0.47 65 65
JAK2 -0.12 0.19 -9999 0 -0.37 404 404
NF2 -0.006 0.009 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.13 0.18 -9999 0 -0.36 403 403
NRG1 -0.29 0.38 -9999 0 -0.78 406 406
GRB2/SOS1 0 0.006 -9999 0 -10000 0 0
MAPK8 -0.11 0.17 -9999 0 -0.33 407 407
MAPK9 -0.069 0.087 -9999 0 -0.3 3 3
ERBB2 -0.017 0.059 -9999 0 -0.63 1 1
ERBB3 0 0.054 -9999 0 -0.8 5 5
SHC1 0.002 0.004 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
apoptosis 0.014 0.017 -9999 0 -10000 0 0
STAT3 (dimer) 0.001 0.003 -9999 0 -10000 0 0
RNF41 0.018 0.014 -9999 0 -10000 0 0
FRAP1 0.008 0.004 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.098 0.12 -9999 0 -0.33 26 26
ErbB2/ErbB2/HSP90 (dimer) -0.013 0.046 -9999 0 -0.54 1 1
CHRNA1 -0.092 0.16 -9999 0 -0.41 58 58
myelination -0.082 0.16 -9999 0 -0.36 31 31
PPP3CB -0.12 0.18 -9999 0 -0.34 403 403
KRAS -0.001 0.013 -9999 0 -0.29 2 2
RAC1-CDC42/GDP -0.11 0.15 -9999 0 -0.41 23 23
NRG2 -0.38 0.39 -9999 0 -0.79 523 523
mol:GDP -0.12 0.18 -9999 0 -0.36 403 403
SOS1 0 0 -9999 0 -10000 0 0
MAP2K2 -0.072 0.15 -9999 0 -0.44 16 16
SRC 0 0.009 -9999 0 -0.29 1 1
mol:cAMP -0.002 0.002 -9999 0 -10000 0 0
PTPN11 -0.14 0.18 -9999 0 -0.36 403 403
MAP2K1 -0.13 0.21 -9999 0 -0.48 171 171
heart morphogenesis -0.15 0.19 -9999 0 -0.39 403 403
RAS family/GDP -0.11 0.14 -9999 0 -0.4 29 29
GRB2 0 0.009 -9999 0 -0.3 1 1
PRKACA -0.01 0.014 -9999 0 -10000 0 0
CHRNE 0.007 0.023 -9999 0 -0.18 6 6
HSP90AA1 0 0.009 -9999 0 -0.29 1 1
activation of caspase activity -0.008 0.005 -9999 0 -10000 0 0
nervous system development -0.15 0.19 -9999 0 -0.39 403 403
CDC42 0 0 -9999 0 -10000 0 0
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.053 0.16 -10000 0 -0.53 104 104
cell-cell adhesion 0.17 0.21 0.67 78 -10000 0 78
Ephrin B/EPHB2/RasGAP -0.04 0.12 -10000 0 -0.44 96 96
ITSN1 -0.001 0.024 -10000 0 -0.79 1 1
PIK3CA 0 0.009 -10000 0 -0.29 1 1
SHC1 0 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.002 0.018 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.21 0.26 -10000 0 -0.53 426 426
HRAS/GDP -0.17 0.22 -10000 0 -0.64 104 104
Ephrin B/EPHB1/GRB7 -0.22 0.28 -10000 0 -0.52 451 451
Endophilin/SYNJ1 -0.038 0.12 -10000 0 -0.41 96 96
KRAS -0.001 0.013 -10000 0 -0.29 2 2
Ephrin B/EPHB1/Src -0.21 0.27 -10000 0 -0.51 449 449
endothelial cell migration -0.005 0.048 -10000 0 -0.44 13 13
GRB2 0 0.009 -10000 0 -0.29 1 1
GRB7 -0.023 0.085 -10000 0 -0.31 79 79
PAK1 -0.048 0.14 -10000 0 -0.45 107 107
HRAS -0.002 0.027 -10000 0 -0.29 9 9
RRAS -0.038 0.12 -10000 0 -0.42 96 96
DNM1 -0.005 0.064 -10000 0 -0.73 8 8
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.2 0.26 -10000 0 -0.48 449 449
lamellipodium assembly -0.17 0.21 -10000 0 -0.67 78 78
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.15 0.19 -10000 0 -0.36 426 426
PIK3R1 -0.009 0.086 -10000 0 -0.79 13 13
EPHB2 -0.005 0.038 -10000 0 -0.29 19 19
EPHB3 -0.004 0.034 -10000 0 -0.29 15 15
EPHB1 -0.31 0.38 -10000 0 -0.79 426 426
EPHB4 0 0.009 -10000 0 -0.29 1 1
mol:GDP -0.15 0.21 -10000 0 -0.64 97 97
Ephrin B/EPHB2 -0.041 0.13 -10000 0 -0.45 96 96
Ephrin B/EPHB3 -0.041 0.13 -10000 0 -0.45 96 96
JNK cascade -0.17 0.21 -10000 0 -0.43 426 426
Ephrin B/EPHB1 -0.21 0.28 -10000 0 -0.52 449 449
RAP1/GDP -0.13 0.18 -10000 0 -0.6 73 73
EFNB2 0 0 -10000 0 -10000 0 0
EFNB3 -0.069 0.22 -10000 0 -0.79 96 96
EFNB1 0 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.19 0.23 -10000 0 -0.48 426 426
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
CDC42/GTP -0.18 0.23 -10000 0 -0.75 77 77
Rap1/GTP -0.17 0.22 -10000 0 -0.7 77 77
axon guidance -0.053 0.15 -10000 0 -0.52 104 104
MAPK3 -0.096 0.19 -10000 0 -0.52 73 73
MAPK1 -0.096 0.19 -10000 0 -0.52 73 73
Rac1/GDP -0.14 0.19 -10000 0 -0.57 96 96
actin cytoskeleton reorganization -0.13 0.16 -10000 0 -0.51 83 83
CDC42/GDP -0.14 0.19 -10000 0 -0.57 95 95
PI3K -0.006 0.049 -10000 0 -0.45 13 13
EFNA5 -0.076 0.23 -10000 0 -0.78 105 105
Ephrin B2/EPHB4 0 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.029 0.094 -10000 0 -0.33 96 96
CDC42 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.16 0.21 -10000 0 -0.66 82 82
PTK2 0.041 0.05 -10000 0 -10000 0 0
MAP4K4 -0.17 0.21 -10000 0 -0.44 426 426
SRC 0 0.009 -10000 0 -0.29 1 1
KALRN -0.015 0.11 -10000 0 -0.79 21 21
Intersectin/N-WASP -0.001 0.018 -10000 0 -0.6 1 1
neuron projection morphogenesis -0.13 0.17 -10000 0 -0.54 83 83
MAP2K1 -0.11 0.2 -10000 0 -0.55 74 74
WASL 0 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.19 0.23 -10000 0 -0.47 426 426
cell migration -0.12 0.22 -10000 0 -0.62 75 75
NRAS -0.001 0.013 -10000 0 -0.29 2 2
SYNJ1 -0.038 0.12 -10000 0 -0.42 96 96
PXN 0 0 -10000 0 -10000 0 0
TF -0.24 0.26 -10000 0 -0.45 624 624
HRAS/GTP -0.18 0.23 -10000 0 -0.73 81 81
Ephrin B1/EPHB1-2 -0.19 0.23 -10000 0 -0.48 426 426
cell adhesion mediated by integrin 0.009 0.13 0.41 96 -10000 0 96
RAC1 0 0 -10000 0 -10000 0 0
mol:GTP -0.2 0.25 -10000 0 -0.47 449 449
RAC1-CDC42/GTP -0.17 0.21 -10000 0 -0.68 78 78
RASA1 0 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.13 0.18 -10000 0 -0.6 73 73
ruffle organization -0.17 0.22 -10000 0 -0.69 78 78
NCK1 0 0 -10000 0 -10000 0 0
receptor internalization 0.002 0.14 -10000 0 -0.41 98 98
Ephrin B/EPHB2/KALRN -0.049 0.15 -10000 0 -0.48 107 107
ROCK1 0.022 0.023 -10000 0 -0.48 1 1
RAS family/GDP -0.12 0.15 -10000 0 -0.52 73 73
Rac1/GTP -0.18 0.23 -10000 0 -0.74 78 78
Ephrin B/EPHB1/Src/Paxillin -0.15 0.2 -10000 0 -0.37 449 449
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0 0 -10000 0 -10000 0 0
PTK2 0 0 -10000 0 -10000 0 0
CRKL -0.1 0.24 -10000 0 -0.48 270 270
GRB2/SOS1/SHC 0 0.004 -10000 0 -10000 0 0
HRAS -0.002 0.027 -10000 0 -0.29 9 9
IRS1/Crk -0.12 0.23 -10000 0 -0.48 270 270
IGF-1R heterotetramer/IGF1/PTP1B -0.13 0.23 -10000 0 -0.53 255 255
AKT1 -0.068 0.21 -10000 0 -0.71 53 53
BAD -0.055 0.2 -10000 0 -0.66 51 51
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.1 0.24 -10000 0 -0.48 270 270
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.12 0.23 -10000 0 -0.48 270 270
RAF1 -0.048 0.19 -10000 0 -0.63 48 48
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.11 0.22 -10000 0 -0.46 255 255
YWHAZ -0.001 0.015 -10000 0 -0.29 3 3
IGF-1R heterotetramer/IGF1/IRS1 -0.13 0.24 -10000 0 -0.52 270 270
PIK3CA 0 0.009 -10000 0 -0.29 1 1
RPS6KB1 -0.068 0.21 -10000 0 -0.71 53 53
GNB2L1 0 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.04 0.16 -10000 0 -0.51 48 48
PXN 0 0 -10000 0 -10000 0 0
PIK3R1 -0.009 0.086 -10000 0 -0.79 13 13
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
HRAS/GTP -0.1 0.19 -10000 0 -0.71 46 46
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.098 0.19 -10000 0 -0.42 255 255
IGF-1R heterotetramer -0.033 0.13 -10000 0 -0.82 25 25
IGF-1R heterotetramer/IGF1/IRS/Nck -0.12 0.23 -10000 0 -0.48 270 270
Crk/p130 Cas/Paxillin -0.11 0.2 -10000 0 -0.44 255 255
IGF1R -0.033 0.13 -10000 0 -0.82 25 25
IGF1 -0.18 0.34 -10000 0 -0.81 246 246
IRS2/Crk -0.13 0.25 -10000 0 -0.51 273 273
PI3K -0.12 0.22 -10000 0 -0.48 257 257
apoptosis 0.08 0.15 0.55 49 -10000 0 49
HRAS/GDP -0.002 0.018 -10000 0 -10000 0 0
PRKCD -0.094 0.25 -10000 0 -0.53 255 255
RAF1/14-3-3 E -0.033 0.16 -10000 0 -0.52 48 48
BAD/14-3-3 -0.044 0.18 -10000 0 -0.6 49 49
PRKCZ -0.068 0.21 -10000 0 -0.7 54 54
Crk/p130 Cas/Paxillin/FAK1 -0.085 0.16 -10000 0 -0.62 48 48
PTPN1 -0.003 0.029 -10000 0 -0.29 11 11
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.13 0.25 -10000 0 -0.56 255 255
BCAR1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.11 0.2 -10000 0 -0.46 255 255
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.12 0.22 -10000 0 -0.48 270 270
GRB10 0 0 -10000 0 -10000 0 0
PTPN11 -0.1 0.24 -10000 0 -0.48 270 270
IRS1 -0.12 0.25 -10000 0 -0.52 270 270
IRS2 -0.12 0.27 -10000 0 -0.53 284 284
IGF-1R heterotetramer/IGF1 -0.16 0.28 -10000 0 -0.66 255 255
GRB2 0 0.009 -10000 0 -0.29 1 1
PDPK1 -0.11 0.21 -10000 0 -0.45 257 257
YWHAE 0 0 -10000 0 -10000 0 0
PRKD1 -0.11 0.28 -10000 0 -0.56 268 268
SHC1 0 0 -10000 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.035 0.049 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.082 0.16 -9999 0 -0.47 97 97
JUN -0.05 0.14 -9999 0 -0.42 63 63
HRAS -0.002 0.027 -9999 0 -0.29 9 9
RET51/GFRalpha1/GDNF/GRB10 -0.15 0.2 -9999 0 -0.52 211 211
RAP1A 0 0 -9999 0 -10000 0 0
FRS2 -0.003 0.029 -9999 0 -0.29 11 11
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.15 0.2 -9999 0 -0.52 211 211
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.1 0.19 -9999 0 -0.48 207 207
RHOA 0 0 -9999 0 -10000 0 0
RAP1A/GTP -0.13 0.18 -9999 0 -0.46 211 211
GRB7 -0.023 0.085 -9999 0 -0.31 79 79
RET51/GFRalpha1/GDNF -0.15 0.2 -9999 0 -0.52 211 211
MAPKKK cascade -0.1 0.16 -9999 0 -0.42 208 208
BCAR1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.12 0.23 -9999 0 -0.55 219 219
lamellipodium assembly -0.084 0.15 -9999 0 -0.36 210 210
RET51/GFRalpha1/GDNF/SHC -0.15 0.2 -9999 0 -0.52 211 211
PIK3CA 0 0.009 -9999 0 -0.29 1 1
RET9/GFRalpha1/GDNF/SHC -0.1 0.19 -9999 0 -0.48 207 207
RET9/GFRalpha1/GDNF/Shank3 -0.1 0.19 -9999 0 -0.48 207 207
MAPK3 -0.12 0.17 -9999 0 -0.44 208 208
DOK1 -0.001 0.018 -9999 0 -10000 0 0
DOK6 -0.013 0.095 -9999 0 -0.63 22 22
PXN 0 0 -9999 0 -10000 0 0
neurite development -0.11 0.16 -9999 0 -0.53 57 57
DOK5 -0.019 0.12 -9999 0 -0.71 30 30
GFRA1 -0.16 0.31 -9999 0 -0.68 256 256
MAPK8 -0.077 0.13 -9999 0 -0.35 149 149
HRAS/GTP -0.12 0.18 -9999 0 -0.48 208 208
tube development -0.095 0.18 -9999 0 -0.46 202 202
MAPK1 -0.12 0.17 -9999 0 -0.44 208 208
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.066 0.13 -9999 0 -0.33 202 202
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0 0.009 -9999 0 -0.29 1 1
PDLIM7 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.15 0.2 -9999 0 -0.5 217 217
SHC1 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.15 0.2 -9999 0 -0.52 211 211
RET51/GFRalpha1/GDNF/Dok5 -0.16 0.22 -9999 0 -0.54 227 227
PRKCA -0.021 0.12 -9999 0 -0.76 30 30
HRAS/GDP -0.002 0.018 -9999 0 -10000 0 0
CREB1 -0.074 0.15 -9999 0 -0.38 202 202
PIK3R1 -0.009 0.086 -9999 0 -0.79 13 13
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.065 0.13 -9999 0 -0.33 202 202
RET51/GFRalpha1/GDNF/Grb7 -0.16 0.21 -9999 0 -0.54 213 213
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.11 0.16 -9999 0 -0.31 393 393
DOK4 0 0 -9999 0 -10000 0 0
JNK cascade -0.049 0.14 -9999 0 -0.41 63 63
RET9/GFRalpha1/GDNF/FRS2 -0.1 0.19 -9999 0 -0.49 202 202
SHANK3 0 0 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.066 0.13 -9999 0 -0.33 202 202
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.083 0.14 -9999 0 -0.35 208 208
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.083 0.14 -9999 0 -0.35 208 208
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.084 0.15 -9999 0 -0.36 208 208
PI3K -0.14 0.24 -9999 0 -0.58 215 215
SOS1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.095 0.18 -9999 0 -0.46 202 202
GRB10 0 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.078 0.13 -9999 0 -0.33 202 202
RET51/GFRalpha1/GDNF/FRS2 -0.15 0.2 -9999 0 -0.52 211 211
GAB1 0 0 -9999 0 -10000 0 0
IRS1 -0.033 0.16 -9999 0 -0.79 45 45
IRS2 -0.033 0.16 -9999 0 -0.79 45 45
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.084 0.15 -9999 0 -0.36 208 208
RET51/GFRalpha1/GDNF/PKC alpha -0.16 0.21 -9999 0 -0.53 237 237
GRB2 0 0.009 -9999 0 -0.29 1 1
PRKACA 0 0 -9999 0 -10000 0 0
GDNF -0.015 0.065 -9999 0 -0.29 57 57
RAC1 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.17 0.24 -9999 0 -0.59 222 222
Rac1/GTP -0.1 0.18 -9999 0 -0.44 210 210
RET9/GFRalpha1/GDNF -0.11 0.21 -9999 0 -0.53 207 207
GFRalpha1/GDNF -0.13 0.24 -9999 0 -0.61 207 207
BMP receptor 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
BMP7/BMPR2/BMPR1A-1B/FS -0.12 0.21 -9999 0 -0.6 144 144
SMAD6-7/SMURF1 0 0.016 -9999 0 -0.52 1 1
NOG -0.025 0.13 -9999 0 -0.58 47 47
SMAD9 -0.11 0.26 -9999 0 -0.77 127 127
SMAD4 -0.001 0.024 -9999 0 -0.79 1 1
SMAD5 -0.075 0.18 -9999 0 -0.48 140 140
BMP7/USAG1 -0.34 0.34 -9999 0 -0.66 563 563
SMAD5/SKI -0.087 0.16 -9999 0 -0.51 92 92
SMAD1 0.026 0.03 -9999 0 -10000 0 0
BMP2 -0.14 0.3 -9999 0 -0.78 193 193
SMAD1/SMAD1/SMAD4 -0.002 0.014 -9999 0 -10000 0 0
BMPR1A -0.002 0.041 -9999 0 -0.79 3 3
BMPR1B -0.14 0.18 -9999 0 -0.32 469 469
BMPR1A-1B/BAMBI -0.092 0.14 -9999 0 -0.6 60 60
AHSG -0.005 0.038 -9999 0 -0.29 19 19
CER1 -0.001 0.015 -9999 0 -0.29 3 3
BMP2-4/CER1 -0.12 0.24 -9999 0 -0.57 240 240
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.1 0.2 -9999 0 -0.51 151 151
BMP2-4 (homodimer) -0.14 0.28 -9999 0 -0.64 240 240
RGMB -0.001 0.024 -9999 0 -0.79 1 1
BMP6/BMPR2/BMPR1A-1B -0.097 0.16 -9999 0 -0.54 109 109
RGMA -0.11 0.27 -9999 0 -0.79 146 146
SMURF1 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.11 0.2 -9999 0 -0.61 109 109
BMP2-4/USAG1 -0.37 0.36 -9999 0 -0.65 620 620
SMAD6/SMURF1/SMAD5 -0.087 0.16 -9999 0 -0.51 92 92
SOSTDC1 -0.38 0.39 -9999 0 -0.79 532 532
BMP7/BMPR2/BMPR1A-1B -0.11 0.17 -9999 0 -0.57 115 115
SKI 0 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.06 0.21 -9999 0 -0.78 84 84
HFE2 -0.003 0.029 -9999 0 -0.29 11 11
ZFYVE16 0 0 -9999 0 -10000 0 0
MAP3K7 0 0.009 -9999 0 -0.29 1 1
BMP2-4/CHRD -0.14 0.26 -9999 0 -0.6 244 244
SMAD5/SMAD5/SMAD4 -0.087 0.16 -9999 0 -0.51 93 93
MAPK1 0 0 -9999 0 -10000 0 0
TAK1/TAB family -0.086 0.17 -9999 0 -0.52 106 106
BMP7 (homodimer) -0.078 0.22 -9999 0 -0.64 132 132
NUP214 0 0 -9999 0 -10000 0 0
BMP6/FETUA -0.049 0.16 -9999 0 -0.61 82 82
SMAD1/SKI 0.004 0.018 -9999 0 -10000 0 0
SMAD6 -0.001 0.024 -9999 0 -0.79 1 1
CTDSP2 0 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.13 0.24 -9999 0 -0.57 240 240
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.037 0.12 -9999 0 -0.36 113 113
BMPR2 (homodimer) 0 0 -9999 0 -10000 0 0
GADD34/PP1CA -0.001 0.01 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.092 0.13 -9999 0 -0.62 29 29
CHRDL1 -0.54 0.37 -9999 0 -0.79 750 750
ENDOFIN/SMAD1 0.004 0.018 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.003 0.013 -9999 0 -10000 0 0
SMAD6/SMURF1 0 0 -9999 0 -10000 0 0
BAMBI -0.034 0.14 -9999 0 -0.5 73 73
SMURF2 0 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.47 0.36 -9999 0 -0.67 768 768
BMP2-4/GREM1 -0.14 0.25 -9999 0 -0.58 246 246
SMAD7 0 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.1 0.24 -9999 0 -0.72 127 127
SMAD1/SMAD6 0.004 0.018 -9999 0 -10000 0 0
TAK1/SMAD6 0 0.006 -9999 0 -10000 0 0
BMP7 -0.078 0.22 -9999 0 -0.65 132 132
BMP6 -0.06 0.21 -9999 0 -0.78 84 84
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.099 0.19 -9999 0 -0.59 106 106
PPM1A 0 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.004 0.018 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL 0 0 -9999 0 -10000 0 0
PPP1CA -0.001 0.02 -9999 0 -0.29 5 5
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0 0 -9999 0 -10000 0 0
PPP1R15A 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.13 0.24 -9999 0 -0.59 174 174
CHRD -0.032 0.13 -9999 0 -0.42 83 83
BMPR2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.13 0.23 -9999 0 -0.54 200 200
BMP4 -0.051 0.19 -9999 0 -0.78 71 71
FST -0.039 0.17 -9999 0 -0.76 57 57
BMP2-4/NOG -0.14 0.26 -9999 0 -0.58 255 255
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.096 0.16 -9999 0 -0.53 115 115
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.01 0.038 -9999 0 -0.53 3 3
NFATC2 -0.042 0.17 -9999 0 -0.55 104 104
NFATC3 0.012 0.025 -9999 0 -10000 0 0
CD40LG -0.22 0.36 -9999 0 -0.71 307 307
PTGS2 -0.32 0.46 -9999 0 -0.85 425 425
JUNB -0.001 0.013 -9999 0 -0.29 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.004 0.009 -9999 0 -10000 0 0
CaM/Ca2+ -0.004 0.009 -9999 0 -10000 0 0
CALM1 0 0.003 -9999 0 -10000 0 0
JUN -0.005 0.064 -9999 0 -0.8 7 7
mol:Ca2+ -0.007 0.009 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.005 -9999 0 -10000 0 0
FOSL1 -0.009 0.06 -9999 0 -0.35 28 28
CREM 0 0.001 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.077 0.15 -9999 0 -0.53 79 79
FOS -0.24 0.37 -9999 0 -0.8 325 325
IFNG -0.22 0.35 -9999 0 -0.68 317 317
AP-1/NFAT1-c-4 -0.31 0.38 -9999 0 -0.82 316 316
FASLG -0.21 0.35 -9999 0 -0.68 302 302
NFAT1-c-4/ICER1 -0.06 0.14 -9999 0 -0.46 107 107
IL2RA -0.21 0.35 -9999 0 -0.69 304 304
FKBP12/FK506 0 0.006 -9999 0 -10000 0 0
CSF2 -0.2 0.34 -9999 0 -0.67 300 300
JunB/Fra1/NFAT1-c-4 -0.057 0.14 -9999 0 -0.48 85 85
IL4 -0.2 0.34 -9999 0 -0.67 298 298
IL2 -0.009 0.024 -9999 0 -10000 0 0
IL3 -0.023 0.026 -9999 0 -10000 0 0
FKBP1A 0 0.009 -9999 0 -10000 0 0
BATF3 -0.002 0.03 -9999 0 -0.39 5 5
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.001 0.01 -9999 0 -0.29 1 1
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.1 0.23 -10000 0 -0.6 188 188
CRKL -0.04 0.16 -10000 0 -0.34 188 188
mol:PIP3 -0.018 0.035 0.77 2 -10000 0 2
AKT1 0.003 0.021 0.49 2 -10000 0 2
PTK2B 0 0 -10000 0 -10000 0 0
RAPGEF1 -0.03 0.15 -10000 0 -0.54 21 21
RANBP10 0 0 -10000 0 -10000 0 0
PIK3CA 0 0.009 -10000 0 -0.29 1 1
HGF/MET/SHIP2 -0.12 0.24 -10000 0 -0.56 240 240
MAP3K5 -0.021 0.15 -10000 0 -0.53 25 25
HGF/MET/CIN85/CBL/ENDOPHILINS -0.11 0.22 -10000 0 -0.51 240 240
AP1 -0.19 0.26 -10000 0 -0.58 326 326
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
apoptosis -0.23 0.36 -10000 0 -0.78 326 326
STAT3 (dimer) -0.039 0.16 -10000 0 -0.33 240 240
GAB1/CRKL/SHP2/PI3K -0.065 0.13 -10000 0 -0.52 34 34
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK -0.032 0.15 -10000 0 -0.54 21 21
PTPN11 0 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0 0 -10000 0 -10000 0 0
PTEN -0.001 0.034 -10000 0 -0.79 2 2
ELK1 -0.044 0.1 -10000 0 -0.27 188 188
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.046 0.092 -10000 0 -0.41 21 21
PAK1 0.008 0.028 0.45 2 -10000 0 2
HGF/MET/RANBP10 -0.12 0.24 -10000 0 -0.56 240 240
HRAS -0.15 0.3 -10000 0 -0.76 191 191
DOCK1 -0.03 0.15 -10000 0 -0.32 188 188
GAB1 -0.051 0.16 -10000 0 -0.35 240 240
CRK -0.04 0.16 -10000 0 -0.34 188 188
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.15 0.3 -10000 0 -0.7 240 240
JUN -0.005 0.063 -10000 0 -0.79 7 7
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.078 0.15 -10000 0 -0.35 240 240
PIK3R1 -0.009 0.086 -10000 0 -0.79 13 13
cell morphogenesis -0.019 0.18 -10000 0 -0.59 30 30
GRB2/SHC -0.067 0.13 -10000 0 -0.33 188 188
FOS -0.24 0.36 -10000 0 -0.79 325 325
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.044 0.1 -10000 0 -0.27 188 188
HGF/MET/MUC20 -0.12 0.24 -10000 0 -0.57 240 240
cell migration -0.066 0.13 -10000 0 -0.32 188 188
GRB2 0 0.009 -10000 0 -0.29 1 1
CBL 0 0 -10000 0 -10000 0 0
MET/RANBP10 -0.1 0.23 -10000 0 -0.6 188 188
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.077 0.15 -10000 0 -0.35 240 240
MET/MUC20 -0.1 0.23 -10000 0 -0.61 188 188
RAP1B -0.021 0.14 -10000 0 -0.5 21 21
RAP1A -0.021 0.14 -10000 0 -0.5 21 21
HGF/MET/RANBP9 -0.12 0.24 -10000 0 -0.56 240 240
RAF1 -0.1 0.29 -10000 0 -0.71 188 188
STAT3 -0.073 0.14 -10000 0 -0.33 240 240
cell proliferation -0.061 0.23 -10000 0 -0.48 240 240
RPS6KB1 -0.027 0.052 -10000 0 -10000 0 0
MAPK3 -0.045 0.092 -10000 0 -0.25 188 188
MAPK1 -0.045 0.092 -10000 0 -0.25 188 188
RANBP9 0 0 -10000 0 -10000 0 0
MAPK8 -0.004 0.14 -10000 0 -0.47 32 32
SRC -0.071 0.14 -10000 0 -0.61 21 21
PI3K -0.072 0.14 -10000 0 -0.35 197 197
MET/Glomulin -0.095 0.21 -10000 0 -0.55 188 188
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 -0.087 0.27 -10000 0 -0.64 188 188
MET -0.14 0.3 -10000 0 -0.79 188 188
MAP4K1 -0.03 0.15 -10000 0 -0.32 189 189
PTK2 0 0 -10000 0 -10000 0 0
MAP2K2 -0.087 0.27 -10000 0 -0.64 188 188
BAD 0.011 0.02 0.45 2 -10000 0 2
MAP2K4 -0.011 0.14 -10000 0 -0.47 26 26
SHP2/GRB2/SOS1/GAB1 -0.096 0.19 -10000 0 -0.5 188 188
INPPL1 0 0 -10000 0 -10000 0 0
PXN 0 0 -10000 0 -10000 0 0
SH3KBP1 0 0 -10000 0 -10000 0 0
HGS -0.071 0.14 -10000 0 -0.35 188 188
PLCgamma1/PKC 0 0 -10000 0 -10000 0 0
HGF -0.053 0.2 -10000 0 -0.78 75 75
RASA1 0 0 -10000 0 -10000 0 0
NCK1 0 0 -10000 0 -10000 0 0
PTPRJ 0 0 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.067 0.13 -10000 0 -0.32 188 188
PDPK1 -0.006 0.025 0.56 2 -10000 0 2
HGF/MET/SHIP -0.12 0.24 -10000 0 -0.56 240 240
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.011 0.001 -10000 0 -10000 0 0
GNB1/GNG2 -0.07 0.17 -10000 0 -0.48 158 158
regulation of S phase of mitotic cell cycle -0.044 0.12 -10000 0 -0.34 151 151
GNAO1 -0.03 0.13 -10000 0 -0.49 67 67
HRAS -0.002 0.027 -10000 0 -0.3 9 9
SHBG/T-DHT 0 0 -10000 0 -10000 0 0
PELP1 0 0 -10000 0 -10000 0 0
AKT1 0.011 0.001 -10000 0 -10000 0 0
MAP2K1 -0.045 0.16 -10000 0 -0.42 146 146
T-DHT/AR -0.082 0.21 -10000 0 -0.61 146 146
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.004 -10000 0 -0.007 323 323
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.045 0.18 -10000 0 -0.79 62 62
mol:GDP -0.084 0.21 -10000 0 -0.62 146 146
cell proliferation -0.1 0.24 -10000 0 -0.56 110 110
PIK3CA 0 0.009 -10000 0 -0.29 1 1
FOS -0.23 0.42 -10000 0 -0.86 325 325
mol:Ca2+ -0.017 0.028 -10000 0 -0.076 149 149
MAPK3 -0.076 0.2 -10000 0 -0.6 65 65
MAPK1 -0.047 0.12 -10000 0 -0.3 62 62
PIK3R1 -0.009 0.086 -10000 0 -0.79 13 13
mol:IP3 -0.001 0.002 -10000 0 -0.005 325 325
cAMP biosynthetic process 0.013 0.025 -10000 0 -10000 0 0
GNG2 -0.009 0.086 -10000 0 -0.79 13 13
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.005 325 325
HRAS/GTP -0.068 0.15 -10000 0 -0.45 146 146
actin cytoskeleton reorganization -0.005 0.046 -10000 0 -0.42 13 13
SRC 0 0.009 -10000 0 -0.29 1 1
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.005 325 325
PI3K -0.006 0.057 -10000 0 -0.53 13 13
apoptosis 0.11 0.23 0.43 325 -10000 0 325
T-DHT/AR/PELP1 -0.071 0.18 -10000 0 -0.53 146 146
HRAS/GDP -0.08 0.2 -10000 0 -0.59 147 147
CREB1 -0.12 0.24 -10000 0 -0.46 325 325
RAC1-CDC42/GTP -0.005 0.047 -10000 0 -0.43 13 13
AR -0.11 0.27 -10000 0 -0.79 147 147
GNB1 0 0 -10000 0 -10000 0 0
RAF1 -0.045 0.16 -10000 0 -0.44 146 146
RAC1-CDC42/GDP -0.075 0.19 -10000 0 -0.56 146 146
T-DHT/AR/PELP1/Src -0.065 0.17 -10000 0 -0.49 146 146
MAP2K2 -0.045 0.16 -10000 0 -0.42 146 146
T-DHT/AR/PELP1/Src/PI3K -0.044 0.12 -10000 0 -0.35 151 151
GNAZ -0.007 0.071 -10000 0 -0.79 9 9
SHBG 0 0 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.039 0.11 -10000 0 -0.49 39 39
mol:T-DHT -0.001 0.001 0.002 9 -0.003 261 270
RAC1 0 0 -10000 0 -10000 0 0
GNRH1 0.006 0.056 -10000 0 -0.61 9 9
Gi family/GTP -0.051 0.1 -10000 0 -0.3 97 97
CDC42 0 0 -10000 0 -10000 0 0
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.027 0.062 -10000 0 -0.49 2 2
epithelial cell differentiation -0.021 0.065 -10000 0 -0.53 6 6
ITCH 0.01 0.022 -10000 0 -10000 0 0
WWP1 0.007 0.068 -10000 0 -10000 0 0
FYN -0.001 0.034 -10000 0 -0.79 2 2
EGFR -0.3 0.38 -10000 0 -0.78 414 414
PRL -0.004 0.033 -10000 0 -10000 0 0
neuron projection morphogenesis -0.1 0.21 -10000 0 -0.46 72 72
PTPRZ1 -0.41 0.39 -10000 0 -0.78 573 573
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.16 0.2 -10000 0 -0.52 76 76
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.19 0.23 -10000 0 -0.49 401 401
ADAM17 0.01 0.022 -10000 0 -10000 0 0
ErbB4/ErbB4 0 0.086 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.056 0.13 -10000 0 -0.53 59 59
NCOR1 -0.001 0.024 -10000 0 -0.79 1 1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.18 0.22 -10000 0 -0.46 401 401
GRIN2B -0.17 0.25 -10000 0 -0.46 451 451
ErbB4/ErbB2/betacellulin -0.05 0.11 -10000 0 -0.47 62 62
STAT1 -0.005 0.038 -10000 0 -0.29 19 19
HBEGF -0.001 0.034 -10000 0 -0.79 2 2
PRLR -0.008 0.071 -10000 0 -0.79 8 8
E4ICDs/ETO2 -0.035 0.09 -10000 0 -0.55 19 19
axon guidance 0.043 0.12 -10000 0 -0.43 3 3
NEDD4 0.01 0.022 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.008 0.058 -10000 0 -0.61 8 8
CBFA2T3 -0.015 0.1 -10000 0 -0.69 24 24
ErbB4/ErbB2/HBEGF -0.026 0.054 -10000 0 -0.48 3 3
MAPK3 -0.15 0.18 -10000 0 -0.48 76 76
STAT1 (dimer) -0.028 0.063 -10000 0 -10000 0 0
MAPK1 -0.15 0.18 -10000 0 -0.48 76 76
JAK2 -0.001 0.024 -10000 0 -0.79 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.19 0.22 -10000 0 -0.47 401 401
NRG1 -0.21 0.3 -10000 0 -0.61 401 401
NRG3 -0.05 0.18 -10000 0 -0.79 59 59
NRG2 -0.38 0.39 -10000 0 -0.79 523 523
NRG4 -0.005 0.038 -10000 0 -0.29 19 19
heart development 0.043 0.12 -10000 0 -0.43 3 3
neural crest cell migration -0.19 0.22 -10000 0 -0.46 401 401
ERBB2 0.009 0.062 -10000 0 -0.6 1 1
WWOX/E4ICDs -0.026 0.059 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.19 0.21 -10000 0 -0.46 409 409
apoptosis 0.057 0.14 0.54 59 -10000 0 59
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.26 0.24 -10000 0 -0.5 523 523
ErbB4/ErbB2/epiregulin -0.084 0.15 -10000 0 -0.46 129 129
ErbB4/ErbB4/betacellulin/betacellulin -0.054 0.12 -10000 0 -0.51 61 61
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.025 0.067 -10000 0 -0.56 8 8
MDM2 0.008 0.075 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.18 0.22 -10000 0 -0.47 401 401
STAT5A 0.043 0.12 -10000 0 -0.47 7 7
ErbB4/EGFR/neuregulin 1 beta -0.34 0.35 -10000 0 -0.65 560 560
DLG4 0 0 -10000 0 -10000 0 0
GRB2/SHC 0 0.006 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.024 0.055 -10000 0 -0.46 1 1
STAT5A (dimer) -0.022 0.07 -10000 0 -0.6 5 5
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.025 0.11 -10000 0 -0.43 5 5
LRIG1 -0.002 0.041 -10000 0 -0.79 3 3
EREG -0.11 0.26 -10000 0 -0.6 207 207
BTC -0.045 0.18 -10000 0 -0.77 64 64
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.043 0.12 -10000 0 -0.43 3 3
ERBB4 -0.032 0.072 -10000 0 -10000 0 0
STAT5B -0.002 0.041 -10000 0 -0.79 3 3
YAP1 -0.01 0.043 -10000 0 -0.64 4 4
GRB2 0 0.009 -10000 0 -0.29 1 1
ErbB4/ErbB2/neuregulin 4 -0.027 0.055 -10000 0 -0.57 1 1
glial cell differentiation 0.024 0.055 0.45 1 -10000 0 1
WWOX -0.001 0.013 -10000 0 -0.29 2 2
cell proliferation -0.12 0.24 -10000 0 -0.58 75 75
Syndecan-1-mediated 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
TGFB1 -0.001 0.015 -9999 0 -0.29 3 3
CCL5 -0.015 0.079 -9999 0 -0.36 44 44
SDCBP 0 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.08 0.11 -9999 0 -0.34 108 108
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 -0.075 0.097 -9999 0 -0.35 49 49
Syndecan-1/Syntenin -0.075 0.097 -9999 0 -0.35 48 48
MAPK3 -0.048 0.096 -9999 0 -0.48 5 5
HGF/MET -0.14 0.28 -9999 0 -0.64 240 240
TGFB1/TGF beta receptor Type II -0.001 0.015 -9999 0 -0.29 3 3
BSG 0 0.009 -9999 0 -10000 0 0
keratinocyte migration -0.074 0.095 -9999 0 -0.35 49 49
Syndecan-1/RANTES -0.082 0.11 -9999 0 -0.34 110 110
Syndecan-1/CD147 -0.066 0.094 -9999 0 -0.49 6 6
Syndecan-1/Syntenin/PIP2 -0.072 0.093 -9999 0 -0.34 48 48
LAMA5 0 0.009 -9999 0 -0.29 1 1
positive regulation of cell-cell adhesion -0.071 0.092 -9999 0 -0.33 48 48
MMP7 -0.12 0.28 -9999 0 -0.71 191 191
HGF -0.053 0.2 -9999 0 -0.78 75 75
Syndecan-1/CASK -0.077 0.1 -9999 0 -0.33 108 108
Syndecan-1/HGF/MET -0.17 0.25 -9999 0 -0.58 243 243
regulation of cell adhesion -0.039 0.094 -9999 0 -0.48 4 4
HPSE -0.006 0.05 -9999 0 -0.34 20 20
positive regulation of cell migration -0.08 0.11 -9999 0 -0.34 108 108
SDC1 -0.081 0.11 -9999 0 -0.35 108 108
Syndecan-1/Collagen -0.08 0.11 -9999 0 -0.34 108 108
PPIB -0.001 0.015 -9999 0 -0.29 3 3
MET -0.14 0.3 -9999 0 -0.79 188 188
PRKACA 0 0 -9999 0 -10000 0 0
MMP9 -0.13 0.15 -9999 0 -0.29 484 484
MAPK1 -0.048 0.096 -9999 0 -0.48 5 5
homophilic cell adhesion -0.08 0.11 -9999 0 -0.34 108 108
MMP1 -0.22 0.13 -9999 0 -0.29 824 824
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.075 0.23 -9999 0 -0.79 104 104
GNB1/GNG2 -0.14 0.23 -9999 0 -0.68 111 111
mol:DAG -0.094 0.22 -9999 0 -0.6 111 111
PLCG1 -0.13 0.21 -9999 0 -0.63 111 111
YES1 -0.14 0.23 -9999 0 -0.66 117 117
FZD3 -0.011 0.092 -9999 0 -0.79 15 15
FZD6 -0.007 0.075 -9999 0 -0.79 10 10
G protein -0.13 0.21 -9999 0 -0.64 113 113
MAP3K7 -0.067 0.18 -9999 0 -0.49 109 109
mol:Ca2+ -0.09 0.21 -9999 0 -0.58 111 111
mol:IP3 -0.094 0.22 -9999 0 -0.6 111 111
NLK -0.005 0.01 -9999 0 -10000 0 0
GNB1 0 0 -9999 0 -10000 0 0
CAMK2A -0.081 0.2 -9999 0 -0.53 115 115
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.16 0.24 -9999 0 -0.44 381 381
CSNK1A1 0 0 -9999 0 -10000 0 0
GNAS -0.14 0.23 -9999 0 -0.66 118 118
GO:0007205 -0.091 0.22 -9999 0 -0.59 111 111
WNT6 -0.16 0.31 -9999 0 -0.69 255 255
WNT4 -0.022 0.12 -9999 0 -0.55 43 43
NFAT1/CK1 alpha -0.16 0.23 -9999 0 -0.63 143 143
GNG2 -0.009 0.086 -9999 0 -0.79 13 13
WNT5A -0.016 0.1 -9999 0 -0.61 28 28
WNT11 -0.16 0.32 -9999 0 -0.76 235 235
CDC42 -0.1 0.23 -9999 0 -0.66 102 102
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.096 0.18 -10000 0 -0.46 197 197
ER alpha/Gai/GDP/Gbeta gamma -0.093 0.19 -10000 0 -0.47 191 191
AKT1 -0.1 0.32 -10000 0 -0.83 172 172
PIK3CA 0 0.009 -10000 0 -0.29 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.11 0.32 -10000 0 -0.85 169 169
mol:Ca2+ -0.029 0.15 -10000 0 -0.45 93 93
IGF1R -0.02 0.12 -10000 0 -0.79 22 22
E2/ER alpha (dimer)/Striatin -0.11 0.2 -10000 0 -0.53 184 184
SHC1 0 0 -10000 0 -10000 0 0
apoptosis 0.095 0.3 0.79 172 -10000 0 172
RhoA/GTP -0.07 0.14 -10000 0 -0.39 167 167
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.094 0.2 -10000 0 -0.53 177 177
regulation of stress fiber formation 0.024 0.14 0.45 11 -10000 0 11
E2/ERA-ERB (dimer) -0.11 0.2 -10000 0 -0.54 188 188
KRAS -0.001 0.013 -10000 0 -0.29 2 2
G13/GTP -0.09 0.17 -10000 0 -0.48 167 167
pseudopodium formation -0.024 0.14 -10000 0 -0.45 11 11
E2/ER alpha (dimer)/PELP1 -0.098 0.19 -10000 0 -0.53 167 167
GRB2 0 0.009 -10000 0 -0.29 1 1
GNG2 -0.009 0.086 -10000 0 -0.79 13 13
GNAO1 -0.03 0.13 -10000 0 -0.49 67 67
HRAS -0.002 0.027 -10000 0 -0.29 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.062 0.22 -10000 0 -0.54 180 180
E2/ER beta (dimer) -0.013 0.088 -10000 0 -0.61 23 23
mol:GDP -0.087 0.2 -10000 0 -0.53 188 188
mol:NADP -0.062 0.22 -10000 0 -0.54 180 180
PIK3R1 -0.009 0.086 -10000 0 -0.79 13 13
mol:IP3 -0.031 0.16 -10000 0 -0.47 93 93
IGF-1R heterotetramer -0.02 0.12 -10000 0 -0.79 22 22
PLCB1 -0.065 0.15 -10000 0 -0.49 92 92
PLCB2 -0.034 0.092 -10000 0 -0.65 15 15
IGF1 -0.18 0.33 -10000 0 -0.79 246 246
mol:L-citrulline -0.062 0.22 -10000 0 -0.54 180 180
RHOA 0 0 -10000 0 -10000 0 0
Gai/GDP -0.04 0.15 -10000 0 -0.85 26 26
JNK cascade -0.013 0.087 -10000 0 -0.61 23 23
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 -0.017 0.11 -10000 0 -0.79 23 23
GNAQ -0.002 0.041 -10000 0 -0.79 3 3
ESR1 -0.15 0.28 -10000 0 -0.58 291 291
Gq family/GDP/Gbeta gamma -0.008 0.074 -10000 0 -0.7 8 8
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.024 0.13 -10000 0 -0.35 17 17
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.094 0.2 -10000 0 -0.53 177 177
GNAZ -0.007 0.071 -10000 0 -0.79 9 9
E2/ER alpha (dimer) -0.12 0.22 -10000 0 -0.61 167 167
STRN -0.014 0.11 -10000 0 -0.79 20 20
GNAL -0.19 0.34 -10000 0 -0.79 259 259
PELP1 0 0 -10000 0 -10000 0 0
MAPK11 0.005 0.083 -10000 0 -0.52 26 26
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.045 0.18 -10000 0 -0.79 62 62
HBEGF -0.072 0.19 -10000 0 -0.45 188 188
cAMP biosynthetic process -0.19 0.26 -10000 0 -0.51 389 389
SRC -0.052 0.2 -10000 0 -0.44 179 179
PI3K -0.007 0.066 -10000 0 -0.6 13 13
GNB1 0 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.079 0.18 -10000 0 -0.46 197 197
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.15 0.23 -10000 0 -0.53 222 222
Gs family/GTP -0.19 0.26 -10000 0 -0.52 389 389
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.002 0.014 -10000 0 -10000 0 0
vasodilation -0.058 0.21 -10000 0 -0.51 180 180
mol:DAG -0.031 0.16 -10000 0 -0.47 93 93
Gs family/GDP/Gbeta gamma -0.16 0.23 -10000 0 -0.44 391 391
MSN -0.027 0.15 -10000 0 -0.5 11 11
Gq family/GTP -0.038 0.097 -10000 0 -0.69 14 14
mol:PI-3-4-5-P3 -0.1 0.31 -10000 0 -0.81 169 169
NRAS -0.001 0.013 -10000 0 -0.29 2 2
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.058 0.21 0.51 180 -10000 0 180
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
RhoA/GDP -0.08 0.19 -10000 0 -0.49 188 188
NOS3 -0.067 0.24 -10000 0 -0.57 180 180
GNA11 -0.002 0.041 -10000 0 -0.79 3 3
MAPKKK cascade -0.069 0.26 -10000 0 -0.63 184 184
E2/ER alpha (dimer)/PELP1/Src -0.098 0.22 -10000 0 -0.56 177 177
ruffle organization -0.024 0.14 -10000 0 -0.45 11 11
ROCK2 -0.075 0.14 -10000 0 -0.37 195 195
GNA14 -0.013 0.085 -10000 0 -0.45 32 32
GNA15 -0.003 0.033 -10000 0 -0.36 8 8
GNA13 0 0 -10000 0 -10000 0 0
MMP9 -0.098 0.2 -10000 0 -0.48 188 188
MMP2 -0.045 0.19 -10000 0 -0.43 184 184
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.22 0.26 -10000 0 -0.53 450 450
fibroblast growth factor receptor signaling pathway -0.22 0.26 -10000 0 -0.52 450 450
LAMA1 -0.09 0.25 -10000 0 -0.77 127 127
PRNP -0.012 0.098 -10000 0 -0.79 17 17
GPC1/SLIT2 -0.07 0.19 -10000 0 -0.6 126 126
SMAD2 0.01 0.1 -10000 0 -0.47 49 49
GPC1/PrPc/Cu2+ -0.01 0.068 -10000 0 -0.53 18 18
GPC1/Laminin alpha1 -0.07 0.19 -10000 0 -0.6 124 124
TDGF1 -0.008 0.076 -10000 0 -0.79 10 10
CRIPTO/GPC1 -0.007 0.062 -10000 0 -0.6 11 11
APP/GPC1 -0.002 0.023 -10000 0 -0.6 1 1
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.019 0.058 -10000 0 -0.52 12 12
FLT1 -0.001 0.024 -10000 0 -0.79 1 1
GPC1/TGFB/TGFBR1/TGFBR2 -0.024 0.11 -10000 0 -0.52 49 49
SERPINC1 -0.018 0.07 -10000 0 -10000 0 0
FYN 0.018 0.06 -10000 0 -0.52 13 13
FGR 0.019 0.058 -10000 0 -0.52 12 12
positive regulation of MAPKKK cascade 0.03 0.072 -10000 0 -0.52 13 13
SLIT2 -0.09 0.25 -10000 0 -0.79 125 125
GPC1/NRG -0.22 0.29 -10000 0 -0.6 402 402
NRG1 -0.29 0.38 -10000 0 -0.78 406 406
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.003 0.029 -10000 0 -0.52 2 2
LYN 0.019 0.056 -10000 0 -0.52 11 11
mol:Spermine 0.009 0.024 -10000 0 -0.61 1 1
cell growth -0.22 0.26 -10000 0 -0.52 450 450
BMP signaling pathway 0.002 0.032 0.79 1 -10000 0 1
SRC 0.019 0.056 -10000 0 -0.52 11 11
TGFBR1 0 0.009 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.26 0.37 -10000 0 -0.75 379 379
GPC1 -0.002 0.032 -10000 0 -0.79 1 1
TGFBR1 (dimer) 0 0.009 -10000 0 -10000 0 0
VEGFA -0.003 0.031 -10000 0 -0.29 12 12
BLK -0.008 0.086 -10000 0 -0.55 13 13
HCK 0.017 0.059 -10000 0 -0.52 11 11
FGF2 -0.32 0.39 -10000 0 -0.79 444 444
FGFR1 -0.009 0.08 -10000 0 -0.68 14 14
VEGFR1 homodimer -0.001 0.024 -10000 0 -0.79 1 1
TGFBR2 -0.035 0.16 -10000 0 -0.79 48 48
cell death -0.002 0.023 -10000 0 -0.6 1 1
ATIII/GPC1 -0.013 0.05 -10000 0 -0.61 1 1
PLA2G2A/GPC1 -0.2 0.28 -10000 0 -0.6 352 352
LCK 0.006 0.087 -10000 0 -0.53 24 24
neuron differentiation -0.22 0.29 -10000 0 -0.6 402 402
PrPc/Cu2+ -0.01 0.076 -10000 0 -0.61 17 17
APP 0 0 -10000 0 -10000 0 0
TGFBR2 (dimer) -0.035 0.16 -10000 0 -0.79 48 48
Neurotrophic factor-mediated Trk 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
CRKL 0 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.1 0.12 -10000 0 -0.33 84 84
NT3 (dimer)/TRKC -0.29 0.36 -10000 0 -0.68 462 462
NT3 (dimer)/TRKB -0.5 0.44 -10000 0 -0.78 696 696
SHC/Grb2/SOS1/GAB1/PI3K -0.004 0.035 -10000 0 -0.32 13 13
RAPGEF1 0 0 -10000 0 -10000 0 0
BDNF -0.065 0.21 -10000 0 -0.67 106 106
PIK3CA 0 0.009 -10000 0 -0.29 1 1
DYNLT1 0 0.009 -10000 0 -0.29 1 1
NTRK1 -0.011 0.07 -10000 0 -0.37 33 33
NTRK2 -0.42 0.39 -10000 0 -0.79 574 574
NTRK3 -0.27 0.37 -10000 0 -0.78 376 376
NT-4/5 (dimer)/TRKB -0.58 0.48 -10000 0 -0.85 746 746
neuron apoptosis 0.24 0.24 0.58 301 -10000 0 301
SHC 2-3/Grb2 -0.26 0.28 -10000 0 -0.66 301 301
SHC1 0 0 -10000 0 -10000 0 0
SHC2 -0.25 0.29 -10000 0 -0.6 353 353
SHC3 -0.24 0.28 -10000 0 -0.66 290 290
STAT3 (dimer) -0.005 0.03 -10000 0 -0.38 4 4
NT3 (dimer)/TRKA -0.24 0.32 -10000 0 -0.6 434 434
RIN/GDP -0.065 0.12 -10000 0 -0.28 66 66
GIPC1 -0.001 0.015 -10000 0 -0.29 3 3
KRAS -0.001 0.013 -10000 0 -0.29 2 2
DNAJA3 -0.14 0.2 -10000 0 -0.43 344 344
RIN/GTP -0.001 0.01 -10000 0 -10000 0 0
CCND1 0.017 0.075 -10000 0 -1 4 4
MAGED1 -0.001 0.018 -10000 0 -0.29 4 4
PTPN11 0 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.27 0.37 -10000 0 -0.79 372 372
SHC/GRB2/SOS1 0 0.004 -10000 0 -10000 0 0
GRB2 0 0.009 -10000 0 -0.29 1 1
NGF (dimer)/TRKA/MATK -0.028 0.11 -10000 0 -0.55 38 38
TRKA/NEDD4-2 -0.008 0.053 -10000 0 -0.6 6 6
ELMO1 0 0 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0 0 -10000 0 -10000 0 0
NGF -0.014 0.098 -10000 0 -0.62 24 24
HRAS -0.002 0.027 -10000 0 -0.29 9 9
DOCK1 0 0 -10000 0 -10000 0 0
GAB2 -0.004 0.043 -10000 0 -0.79 2 2
RIT2 -0.001 0.015 -10000 0 -0.29 3 3
RIT1 0 0 -10000 0 -10000 0 0
FRS2 -0.003 0.029 -10000 0 -0.29 11 11
DNM1 -0.005 0.064 -10000 0 -0.73 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.13 0.2 -10000 0 -0.42 336 336
mol:GDP -0.1 0.18 -10000 0 -0.36 234 234
NGF (dimer) -0.014 0.098 -10000 0 -0.62 24 24
RhoG/GDP 0 0 -10000 0 -10000 0 0
RIT1/GDP -0.061 0.12 -10000 0 -0.27 67 67
TIAM1 -0.001 0.018 -10000 0 -0.29 4 4
PIK3R1 -0.009 0.086 -10000 0 -0.79 13 13
BDNF (dimer)/TRKB -0.31 0.3 -10000 0 -0.56 599 599
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2 -0.001 0.014 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0 0.004 -10000 0 -10000 0 0
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.13 0.28 -10000 0 -0.75 182 182
RAP1/GDP -0.072 0.084 -10000 0 -0.24 39 39
KIDINS220/CRKL 0 0 -10000 0 -10000 0 0
BDNF (dimer) -0.065 0.21 -10000 0 -0.67 106 106
ubiquitin-dependent protein catabolic process -0.015 0.076 -10000 0 -0.52 22 22
Schwann cell development -0.059 0.044 -10000 0 -10000 0 0
EHD4 0 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 -0.001 0.012 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 -0.001 0.011 -10000 0 -10000 0 0
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
CDC42/GTP -0.42 0.38 -10000 0 -0.85 404 404
ABL1 0 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
Rap1/GTP -0.1 0.097 -10000 0 -10000 0 0
STAT3 -0.005 0.03 -10000 0 -0.38 4 4
axon guidance -0.4 0.34 -10000 0 -0.77 422 422
MAPK3 0.006 0.1 -10000 0 -0.5 38 38
MAPK1 0.006 0.1 -10000 0 -0.5 38 38
CDC42/GDP -0.061 0.12 -10000 0 -0.28 61 61
NTF3 -0.13 0.29 -10000 0 -0.75 182 182
NTF4 -0.27 0.37 -10000 0 -0.79 372 372
NGF (dimer)/TRKA/FAIM -0.015 0.075 -10000 0 -0.52 21 21
PI3K -0.007 0.066 -10000 0 -0.6 13 13
FRS3 0 0 -10000 0 -10000 0 0
FAIM 0 0 -10000 0 -10000 0 0
GAB1 0 0 -10000 0 -10000 0 0
RASGRF1 -0.15 0.21 -10000 0 -0.45 347 347
SOS1 0 0 -10000 0 -10000 0 0
MCF2L -0.24 0.33 -10000 0 -0.6 464 464
RGS19 -0.001 0.015 -10000 0 -0.29 3 3
CDC42 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.001 0.082 -10000 0 -10000 0 0
Rac1/GDP -0.061 0.12 -10000 0 -0.27 67 67
NGF (dimer)/TRKA/GRIT -0.015 0.077 -10000 0 -0.53 21 21
neuron projection morphogenesis -0.1 0.21 -10000 0 -0.63 27 27
NGF (dimer)/TRKA/NEDD4-2 -0.015 0.077 -10000 0 -0.52 22 22
MAP2K1 0 0.003 -10000 0 -10000 0 0
NGFR -0.24 0.36 -10000 0 -0.79 336 336
NGF (dimer)/TRKA/GIPC/GAIP -0.01 0.053 -10000 0 -0.33 27 27
RAS family/GTP/PI3K -0.004 0.036 -10000 0 -0.33 13 13
FRS2 family/SHP2/GRB2/SOS1 -0.001 0.011 -10000 0 -10000 0 0
NRAS -0.001 0.013 -10000 0 -0.29 2 2
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
PRKCI 0 0.009 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PRKCZ -0.001 0.024 -10000 0 -0.79 1 1
MAPKKK cascade -0.064 0.12 -10000 0 -0.82 21 21
RASA1 0 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.008 0.05 -10000 0 -0.6 5 5
SQSTM1 0 0.009 -10000 0 -0.29 1 1
BDNF (dimer)/TRKB/GIPC -0.28 0.27 -10000 0 -0.52 599 599
NGF (dimer)/TRKA/p62/Atypical PKCs -0.012 0.064 -10000 0 -0.44 22 22
MATK -0.022 0.11 -10000 0 -0.79 19 19
NEDD4L -0.001 0.024 -10000 0 -0.79 1 1
RAS family/GDP -0.065 0.078 -10000 0 -0.24 1 1
NGF (dimer)/TRKA -0.15 0.22 -10000 0 -0.46 344 344
Rac1/GTP -0.12 0.14 -10000 0 -0.34 262 262
FRS2 family/SHP2/CRK family -0.001 0.01 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB -0.003 0.048 -10000 0 -0.79 4 4
Jak2/Leptin Receptor -0.16 0.23 -10000 0 -0.52 302 302
PTP1B/AKT1 -0.07 0.11 -10000 0 -0.34 116 116
FYN -0.001 0.034 -10000 0 -0.79 2 2
p210 bcr-abl/PTP1B -0.071 0.13 -10000 0 -0.35 146 146
EGFR -0.3 0.39 -10000 0 -0.79 414 414
EGF/EGFR -0.29 0.3 -10000 0 -0.56 557 557
CSF1 -0.005 0.063 -10000 0 -0.79 7 7
AKT1 0.001 0.004 -10000 0 -10000 0 0
INSR 0.001 0.01 -10000 0 -0.3 1 1
PTP1B/N-cadherin -0.097 0.12 -10000 0 -0.35 139 139
Insulin Receptor/Insulin -0.049 0.08 -10000 0 -0.4 21 21
HCK -0.004 0.033 -10000 0 -10000 0 0
CRK 0 0 -10000 0 -10000 0 0
TYK2 -0.06 0.12 -10000 0 -0.36 116 116
EGF -0.15 0.32 -10000 0 -0.8 215 215
YES1 -0.001 0.024 -10000 0 -0.79 1 1
CAV1 -0.18 0.24 -10000 0 -0.5 302 302
TXN 0 0.018 -10000 0 -0.3 4 4
PTP1B/IRS1/GRB2 -0.087 0.14 -10000 0 -0.4 151 151
cell migration 0.071 0.13 0.35 146 -10000 0 146
STAT3 0 0.001 -10000 0 -10000 0 0
PRLR -0.006 0.072 -10000 0 -0.79 8 8
ITGA2B -0.018 0.079 -10000 0 -0.32 64 64
CSF1R -0.001 0.025 -10000 0 -0.54 2 2
Prolactin Receptor/Prolactin -0.007 0.058 -10000 0 -0.61 8 8
FGR -0.001 0.025 -10000 0 -0.54 2 2
PTP1B/p130 Cas -0.074 0.11 -10000 0 -0.36 116 116
Crk/p130 Cas -0.069 0.11 -10000 0 -0.35 112 112
DOK1 -0.046 0.11 -10000 0 -0.32 108 108
JAK2 -0.042 0.081 -10000 0 -0.33 30 30
Jak2/Leptin Receptor/Leptin -0.36 0.19 -10000 0 -0.49 558 558
PIK3R1 -0.009 0.086 -10000 0 -0.79 13 13
PTPN1 -0.072 0.13 -10000 0 -0.35 146 146
LYN 0 0 -10000 0 -10000 0 0
CDH2 -0.055 0.12 -10000 0 -0.3 200 200
SRC -0.013 0.047 -10000 0 -10000 0 0
ITGB3 -0.028 0.15 -10000 0 -0.74 42 42
CAT1/PTP1B -0.084 0.17 -10000 0 -0.38 185 185
CAPN1 0.001 0.01 -10000 0 -0.3 1 1
CSK 0 0 -10000 0 -10000 0 0
PI3K -0.044 0.093 -10000 0 -0.53 20 20
mol:H2O2 -0.005 0.005 -10000 0 -10000 0 0
STAT3 (dimer) -0.32 0.16 -10000 0 -0.43 543 543
negative regulation of transcription -0.041 0.08 -10000 0 -0.32 30 30
FCGR2A -0.001 0.013 -10000 0 -0.29 2 2
FER -0.007 0.08 -10000 0 -0.8 11 11
alphaIIb/beta3 Integrin -0.034 0.12 -10000 0 -0.62 41 41
BLK -0.044 0.11 -10000 0 -0.3 159 159
Insulin Receptor/Insulin/Shc 0 0.005 -10000 0 -10000 0 0
RHOA 0.002 0.004 -10000 0 -10000 0 0
LEPR -0.21 0.36 -10000 0 -0.79 294 294
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0 0.009 -10000 0 -0.29 1 1
mol:NADPH -0.005 0.005 -10000 0 -10000 0 0
TRPV6 -0.031 0.13 -10000 0 -0.44 22 22
PRL -0.004 0.034 -10000 0 -0.31 2 2
SOCS3 0.018 0.11 -10000 0 -1.5 6 6
SPRY2 -0.093 0.26 -10000 0 -0.8 127 127
Insulin Receptor/Insulin/IRS1 -0.022 0.11 -10000 0 -0.53 45 45
CSF1/CSF1R -0.072 0.12 -10000 0 -0.36 121 121
Ras protein signal transduction 0.037 0.036 -10000 0 -10000 0 0
IRS1 -0.033 0.16 -10000 0 -0.79 45 45
INS 0 0.001 -10000 0 -10000 0 0
LEP -0.62 0.32 -10000 0 -0.79 861 861
STAT5B -0.058 0.11 -10000 0 -0.31 123 123
STAT5A -0.059 0.11 -10000 0 -0.31 126 126
GRB2 0 0.009 -10000 0 -0.29 1 1
PDGFB-D/PDGFRB -0.076 0.12 -10000 0 -0.37 118 118
CSN2 0.018 0.035 -10000 0 -10000 0 0
PIK3CA 0 0.009 -10000 0 -0.29 1 1
LAT -0.014 0.053 -10000 0 -0.57 2 2
YBX1 -0.001 0.014 -10000 0 -10000 0 0
LCK -0.02 0.1 -10000 0 -0.41 54 54
SHC1 0 0 -10000 0 -10000 0 0
NOX4 -0.004 0.05 -10000 0 -0.41 13 13
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.076 0.068 -9999 0 -0.61 1 1
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.02 0.018 -9999 0 -10000 0 0
AURKB -0.17 0.14 -9999 0 -0.29 625 625
AURKC -0.005 0.043 -9999 0 -0.32 18 18
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.005 0.045 -9999 0 -0.6 5 5
alphaV beta3 Integrin -0.23 0.28 -9999 0 -0.54 458 458
PTK2 -0.089 0.19 -9999 0 -0.64 49 49
IGF1R -0.02 0.12 -9999 0 -0.79 22 22
PI4KB 0 0 -9999 0 -10000 0 0
MFGE8 -0.011 0.089 -9999 0 -0.62 20 20
SRC 0 0.009 -9999 0 -0.29 1 1
CDKN1B -0.088 0.12 -9999 0 -0.88 11 11
VEGFA -0.003 0.031 -9999 0 -0.29 12 12
ILK -0.086 0.12 -9999 0 -0.83 8 8
ROCK1 -0.001 0.024 -9999 0 -0.79 1 1
AKT1 -0.076 0.1 -9999 0 -0.77 8 8
PTK2B -0.019 0.093 -9999 0 -0.48 39 39
alphaV/beta3 Integrin/JAM-A -0.2 0.24 -9999 0 -0.48 462 462
CBL 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.019 0.096 -9999 0 -0.52 38 38
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.14 0.25 -9999 0 -0.54 270 270
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.013 0.062 -9999 0 -0.44 10 10
alphaV/beta3 Integrin/Syndecan-1 -0.029 0.1 -9999 0 -0.53 39 39
PI4KA 0 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.33 0.35 -9999 0 -0.76 353 353
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -0.29 1 1
alphaV/beta3 Integrin/Osteopontin -0.056 0.11 -9999 0 -0.52 41 41
RPS6KB1 -0.3 0.32 -9999 0 -0.69 354 354
TLN1 0 0 -9999 0 -10000 0 0
MAPK3 -0.34 0.39 -9999 0 -0.77 458 458
GPR124 -0.009 0.082 -9999 0 -0.79 12 12
MAPK1 -0.34 0.39 -9999 0 -0.77 458 458
PXN 0 0 -9999 0 -10000 0 0
PIK3R1 -0.009 0.086 -9999 0 -0.79 13 13
alphaV/beta3 Integrin/Tumstatin -0.1 0.21 -9999 0 -0.53 215 215
cell adhesion -0.023 0.11 -9999 0 -0.5 48 48
ANGPTL3 -0.001 0.018 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src -0.004 0.038 -9999 0 -0.52 5 5
IGF-1R heterotetramer -0.02 0.12 -9999 0 -0.79 22 22
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 -0.035 0.16 -9999 0 -0.79 48 48
ITGB3 -0.029 0.15 -9999 0 -0.74 42 42
IGF1 -0.18 0.33 -9999 0 -0.79 246 246
RAC1 0 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.024 0.12 -9999 0 -0.58 44 44
apoptosis 0 0 -9999 0 -10000 0 0
CD47 -0.001 0.024 -9999 0 -0.79 1 1
alphaV/beta3 Integrin/CD47 -0.019 0.096 -9999 0 -0.52 39 39
VCL 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.05 0.18 -9999 0 -0.65 80 80
CSF1 -0.005 0.063 -9999 0 -0.79 7 7
PIK3C2A -0.087 0.12 -9999 0 -0.85 9 9
PI4 Kinase/Pyk2 -0.17 0.21 -9999 0 -0.6 76 76
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.02 0.1 -9999 0 -0.52 39 39
FAK1/Vinculin -0.065 0.16 -9999 0 -0.49 46 46
alphaV beta3/Integrin/ppsTEM5 -0.024 0.12 -9999 0 -0.58 44 44
RHOA 0 0 -9999 0 -10000 0 0
VTN -0.028 0.1 -9999 0 -0.34 89 89
BCAR1 0 0 -9999 0 -10000 0 0
FGF2 -0.32 0.39 -9999 0 -0.79 444 444
F11R -0.23 0.31 -9999 0 -0.6 444 444
alphaV/beta3 Integrin/Lactadherin -0.025 0.12 -9999 0 -0.55 48 48
alphaV/beta3 Integrin/TGFBR2 -0.04 0.16 -9999 0 -0.65 67 67
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.003 0.037 -9999 0 -0.47 7 7
HSP90AA1 0 0.009 -9999 0 -0.29 1 1
alphaV/beta3 Integrin/Talin -0.017 0.088 -9999 0 -0.48 38 38
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.12 0.14 -9999 0 -0.29 432 432
alphaV/beta3 Integrin/Pyk2 -0.019 0.094 -9999 0 -0.49 39 39
SDC1 -0.02 0.076 -9999 0 -0.3 73 73
VAV3 -0.007 0.051 -9999 0 -0.44 14 14
PTPN11 0 0 -9999 0 -10000 0 0
IRS1 -0.033 0.16 -9999 0 -0.79 45 45
FAK1/Paxillin -0.065 0.16 -9999 0 -0.49 46 46
cell migration -0.051 0.14 -9999 0 -0.44 43 43
ITGAV 0 0 -9999 0 -10000 0 0
PI3K -0.19 0.23 -9999 0 -0.43 465 465
SPP1 -0.077 0.13 -9999 0 -0.29 288 288
KDR -0.004 0.053 -9999 0 -0.79 5 5
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0 0 -9999 0 -10000 0 0
COL4A3 -0.13 0.29 -9999 0 -0.78 186 186
angiogenesis -0.3 0.39 -9999 0 -0.74 460 460
Rac1/GTP -0.007 0.046 -9999 0 -0.4 14 14
EDIL3 -0.051 0.19 -9999 0 -0.79 65 65
cell proliferation -0.04 0.16 -9999 0 -0.65 67 67
IL6-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
BCL2L1 -0.065 0.22 -9999 0 -0.62 63 63
CRP -0.069 0.22 -9999 0 -0.63 63 63
cell cycle arrest -0.083 0.24 -9999 0 -0.7 73 73
TIMP1 -0.062 0.2 -9999 0 -0.57 56 56
IL6ST -0.086 0.26 -9999 0 -0.79 136 136
Rac1/GDP -0.12 0.23 -9999 0 -0.65 96 96
AP1 -0.13 0.23 -9999 0 -0.49 257 257
GAB2 0.005 0.044 -9999 0 -0.79 2 2
TNFSF11 -0.075 0.22 -9999 0 -0.63 62 62
HSP90B1 0.015 0.047 -9999 0 -10000 0 0
GAB1 0.008 0.006 -9999 0 -10000 0 0
MAPK14 -0.13 0.25 -9999 0 -0.73 93 93
AKT1 0.038 0.041 -9999 0 -10000 0 0
FOXO1 0.047 0.058 -9999 0 -0.4 11 11
MAP2K6 -0.15 0.26 -9999 0 -0.67 122 122
mol:GTP 0 0.001 -9999 0 -10000 0 0
MAP2K4 -0.086 0.23 -9999 0 -0.64 87 87
MITF -0.14 0.26 -9999 0 -0.53 187 187
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0 0 -9999 0 -10000 0 0
A2M 0.014 0.12 -9999 0 -1.5 7 7
CEBPB 0.016 0.007 -9999 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.044 0.094 -9999 0 -0.59 5 5
STAT3 -0.091 0.26 -9999 0 -0.76 73 73
STAT1 -0.013 0.021 -9999 0 -10000 0 0
CEBPD -0.066 0.22 -9999 0 -0.64 63 63
PIK3CA 0.012 0.009 -9999 0 -0.29 1 1
PI3K -0.007 0.065 -9999 0 -0.6 13 13
JUN -0.005 0.063 -9999 0 -0.79 7 7
PIAS3/MITF -0.16 0.22 -9999 0 -0.7 90 90
MAPK11 -0.13 0.25 -9999 0 -0.73 96 96
STAT3 (dimer)/FOXO1 -0.035 0.22 -9999 0 -0.56 77 77
GRB2/SOS1/GAB family -0.14 0.2 -9999 0 -0.73 67 67
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.16 0.25 -9999 0 -0.49 232 232
GRB2 0.008 0.011 -9999 0 -0.29 1 1
JAK2 -0.001 0.024 -9999 0 -0.79 1 1
LBP -0.24 0.45 -9999 0 -0.95 281 281
PIK3R1 0.003 0.087 -9999 0 -0.79 13 13
JAK1 0.009 0.025 -9999 0 -0.79 1 1
MYC -0.078 0.26 -9999 0 -0.8 69 69
FGG -0.075 0.22 -9999 0 -0.62 67 67
macrophage differentiation -0.083 0.24 -9999 0 -0.7 73 73
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.23 0.28 -9999 0 -0.5 503 503
JUNB -0.064 0.21 -9999 0 -0.6 62 62
FOS -0.24 0.36 -9999 0 -0.79 325 325
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.15 0.26 -9999 0 -0.47 282 282
STAT1/PIAS1 -0.13 0.23 -9999 0 -0.57 125 125
GRB2/SOS1/GAB family/SHP2/PI3K -0.002 0.033 -9999 0 -0.3 3 3
STAT3 (dimer) -0.086 0.25 -9999 0 -0.74 71 71
PRKCD -0.061 0.22 -9999 0 -0.6 79 79
IL6R -0.021 0.16 -9999 0 -0.79 43 43
SOCS3 -0.12 0.24 -9999 0 -0.74 85 85
gp130 (dimer)/JAK1/JAK1/LMO4 -0.057 0.18 -9999 0 -0.52 139 139
Rac1/GTP -0.15 0.2 -9999 0 -0.62 105 105
HCK -0.004 0.033 -9999 0 -10000 0 0
MAPKKK cascade -0.006 0.084 -9999 0 -1 2 2
bone resorption -0.071 0.21 -9999 0 -0.6 62 62
IRF1 -0.065 0.22 -9999 0 -0.63 61 61
mol:GDP -0.13 0.25 -9999 0 -0.48 217 217
SOS1 0 0.003 -9999 0 -10000 0 0
VAV1 -0.13 0.25 -9999 0 -0.49 217 217
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.16 0.25 -9999 0 -0.8 91 91
PTPN11 -0.013 0.019 -9999 0 -10000 0 0
IL6/IL6RA -0.24 0.31 -9999 0 -0.63 418 418
gp130 (dimer)/TYK2/TYK2/LMO4 -0.06 0.18 -9999 0 -0.52 139 139
gp130 (dimer)/JAK2/JAK2/LMO4 -0.06 0.18 -9999 0 -0.52 139 139
IL6 -0.28 0.39 -9999 0 -0.79 399 399
PIAS3 0 0 -9999 0 -10000 0 0
PTPRE 0.003 0.025 -9999 0 -0.79 1 1
PIAS1 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.18 0.24 -9999 0 -0.4 502 502
LMO4 0.009 0.049 -9999 0 -0.44 10 10
STAT3 (dimer)/PIAS3 -0.15 0.21 -9999 0 -0.77 70 70
MCL1 0.051 0.034 -9999 0 -10000 0 0
IL23-mediated 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
CCL2 -0.16 0.39 -9999 0 -1 90 90
IL23A -0.17 0.39 -9999 0 -1 90 90
NF kappa B1 p50/RelA/I kappa B alpha -0.23 0.32 -9999 0 -0.89 134 134
positive regulation of T cell mediated cytotoxicity -0.18 0.42 -9999 0 -0.92 172 172
ITGA3 -0.16 0.38 -9999 0 -0.94 109 109
IL17F -0.1 0.28 -9999 0 -0.64 100 100
IL12B -0.051 0.12 -9999 0 -0.28 230 230
STAT1 (dimer) -0.22 0.37 -9999 0 -0.94 141 141
CD4 -0.16 0.38 -9999 0 -0.96 89 89
IL23 -0.17 0.38 -9999 0 -1 89 89
IL23R -0.012 0.087 -9999 0 -10000 0 0
IL1B -0.18 0.41 -9999 0 -1 110 110
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 -0.17 0.38 -9999 0 -0.93 108 108
TYK2 0.011 0.017 -9999 0 -10000 0 0
STAT4 -0.032 0.16 -9999 0 -0.78 45 45
STAT3 0 0 -9999 0 -10000 0 0
IL18RAP -0.022 0.15 -9999 0 -0.73 43 43
IL12RB1 -0.002 0.07 -9999 0 -0.33 37 37
PIK3CA 0 0.009 -9999 0 -0.29 1 1
IL12Rbeta1/TYK2 -0.002 0.052 -9999 0 -0.6 2 2
IL23R/JAK2 -0.01 0.11 -9999 0 -0.64 1 1
positive regulation of chronic inflammatory response -0.18 0.42 -9999 0 -0.92 172 172
natural killer cell activation 0.002 0.008 -9999 0 -10000 0 0
JAK2 0.018 0.034 -9999 0 -0.83 1 1
PIK3R1 -0.009 0.086 -9999 0 -0.79 13 13
NFKB1 0.005 0.007 -9999 0 -10000 0 0
RELA 0.005 0.007 -9999 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.16 0.37 -9999 0 -0.94 94 94
ALOX12B -0.16 0.38 -9999 0 -0.89 130 130
CXCL1 -0.34 0.63 -9999 0 -1.4 279 279
T cell proliferation -0.18 0.42 -9999 0 -0.92 172 172
NFKBIA 0.005 0.007 -9999 0 -10000 0 0
IL17A -0.069 0.24 -9999 0 -0.53 61 61
PI3K -0.24 0.33 -9999 0 -0.9 145 145
IFNG -0.005 0.027 -9999 0 -0.088 26 26
STAT3 (dimer) -0.23 0.31 -9999 0 -0.87 137 137
IL18R1 -0.006 0.1 -9999 0 -0.79 19 19
IL23/IL23R/JAK2/TYK2/SOCS3 -0.083 0.24 -9999 0 -0.57 50 50
IL18/IL18R -0.03 0.12 -9999 0 -0.53 55 55
macrophage activation -0.013 0.016 -9999 0 -0.042 104 104
TNF -0.18 0.41 -9999 0 -1.1 96 96
STAT3/STAT4 -0.25 0.35 -9999 0 -0.92 161 161
STAT4 (dimer) -0.23 0.39 -9999 0 -0.98 156 156
IL18 0.001 0.045 -9999 0 -0.3 24 24
IL19 -0.17 0.38 -9999 0 -1 85 85
STAT5A (dimer) -0.22 0.37 -9999 0 -0.92 153 153
STAT1 -0.005 0.038 -9999 0 -0.29 19 19
SOCS3 -0.004 0.058 -9999 0 -0.79 6 6
CXCL9 -0.18 0.38 -9999 0 -0.98 99 99
MPO -0.21 0.47 -9999 0 -1.1 149 149
positive regulation of humoral immune response -0.18 0.42 -9999 0 -0.92 172 172
IL23/IL23R/JAK2/TYK2 -0.19 0.44 -9999 0 -1 146 146
IL6 -0.46 0.7 -9999 0 -1.3 407 407
STAT5A -0.006 0.067 -9999 0 -0.79 8 8
IL2 0.004 0.028 -9999 0 -0.3 8 8
positive regulation of tyrosine phosphorylation of STAT protein 0.002 0.008 -9999 0 -10000 0 0
CD3E -0.17 0.41 -9999 0 -0.98 130 130
keratinocyte proliferation -0.18 0.42 -9999 0 -0.92 172 172
NOS2 -0.16 0.39 -9999 0 -0.95 109 109
Visual signal transduction: Rods

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
mol:K + 0 0 -9999 0 -10000 0 0
GNAT1/GTP -0.003 0.023 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin -0.01 0.04 -9999 0 -0.31 2 2
PDE6G/GNAT1/GTP -0.009 0.036 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.004 0.034 -9999 0 -0.29 15 15
GRK1 -0.003 0.029 -9999 0 -0.29 11 11
CNG Channel -0.14 0.2 -9999 0 -0.43 316 316
mol:Na + -0.13 0.18 -9999 0 -0.42 309 309
mol:ADP -0.003 0.029 -9999 0 -0.29 11 11
RGS9-1/Gbeta5/R9AP -0.062 0.16 -9999 0 -0.53 107 107
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.13 0.19 -9999 0 -0.43 309 309
CNGB1 -0.015 0.064 -9999 0 -10000 0 0
RDH5 -0.48 0.39 -9999 0 -0.79 658 658
SAG -0.015 0.064 -9999 0 -0.29 55 55
mol:Ca2+ -0.12 0.18 -9999 0 -0.53 22 22
Na + (4 Units) -0.12 0.17 -9999 0 -0.51 22 22
RGS9 -0.081 0.24 -9999 0 -0.73 122 122
GNB1/GNGT1 -0.03 0.068 -9999 0 -10000 0 0
GNAT1/GDP -0.055 0.14 -9999 0 -0.46 107 107
GUCY2D -0.008 0.061 -9999 0 -0.38 23 23
GNGT1 -0.047 0.11 -9999 0 -0.29 175 175
GUCY2F -0.001 0.013 -9999 0 -10000 0 0
GNB5 0 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.019 0.071 -9999 0 -0.45 23 23
mol:11-cis-retinal -0.48 0.39 -9999 0 -0.79 658 658
mol:cGMP -0.011 0.05 -9999 0 -0.45 9 9
GNB1 0 0 -9999 0 -10000 0 0
Rhodopsin -0.37 0.3 -9999 0 -0.61 658 658
SLC24A1 0 0 -9999 0 -10000 0 0
CNGA1 -0.22 0.35 -9999 0 -0.78 310 310
Metarhodopsin II -0.003 0.022 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.012 0.053 -9999 0 -0.48 9 9
RGS9BP -0.019 0.073 -9999 0 -10000 0 0
Metarhodopsin II/Transducin -0.009 0.021 -9999 0 -10000 0 0
GCAP Family/Ca ++ -0.008 0.043 -9999 0 -0.49 5 5
PDE6A/B -0.017 0.091 -9999 0 -0.6 23 23
mol:Pi -0.062 0.16 -9999 0 -0.53 107 107
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.023 0.051 -9999 0 -0.28 2 2
PDE6B -0.017 0.11 -9999 0 -0.79 23 23
PDE6A -0.006 0.042 -9999 0 -0.29 23 23
PDE6G -0.012 0.058 -9999 0 -0.29 45 45
RHO -0.004 0.035 -9999 0 -0.29 16 16
PDE6 -0.063 0.14 -9999 0 -0.62 18 18
GUCA1A -0.012 0.059 -9999 0 -0.29 46 46
GC2/GCAP Family -0.008 0.043 -9999 0 -0.49 5 5
GUCA1C 0 0.009 -9999 0 -0.29 1 1
GUCA1B -0.004 0.053 -9999 0 -0.79 5 5
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.023 0.062 -9999 0 -0.56 11 11
alphaM/beta2 Integrin/GPIbA -0.024 0.058 -9999 0 -0.53 9 9
alphaM/beta2 Integrin/proMMP-9 -0.083 0.082 -9999 0 -0.39 8 8
PLAUR -0.022 0.078 -9999 0 -0.29 83 83
HMGB1 -0.013 0.017 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.017 0.029 -9999 0 -10000 0 0
AGER -0.015 0.041 -9999 0 -0.66 3 3
RAP1A 0 0 -9999 0 -10000 0 0
SELPLG 0 0 -9999 0 -10000 0 0
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.074 0.096 -9999 0 -0.39 13 13
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.13 0.15 -9999 0 -0.29 484 484
CYR61 -0.042 0.18 -9999 0 -0.79 58 58
TLN1 0 0 -9999 0 -10000 0 0
Rap1/GTP -0.057 0.11 -9999 0 -0.52 22 22
RHOA 0 0 -9999 0 -10000 0 0
P-selectin oligomer -0.18 0.33 -9999 0 -0.79 256 256
MYH2 -0.07 0.16 -9999 0 -0.5 47 47
MST1R -0.011 0.083 -9999 0 -0.55 21 21
leukocyte activation during inflammatory response -0.29 0.22 -9999 0 -0.47 664 664
APOB -0.48 0.38 -9999 0 -0.79 664 664
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.008 0.079 -9999 0 -0.75 12 12
JAM3 -0.005 0.063 -9999 0 -0.79 7 7
GP1BA -0.012 0.077 -9999 0 -0.4 33 33
alphaM/beta2 Integrin/CTGF -0.025 0.069 -9999 0 -0.58 14 14
alphaM/beta2 Integrin -0.072 0.13 -9999 0 -0.36 94 94
JAM3 homodimer -0.005 0.063 -9999 0 -0.79 7 7
ICAM2 -0.004 0.053 -9999 0 -0.79 5 5
ICAM1 -0.004 0.035 -9999 0 -0.29 16 16
phagocytosis triggered by activation of immune response cell surface activating receptor -0.061 0.14 -9999 0 -0.36 95 95
cell adhesion -0.024 0.057 -9999 0 -0.52 9 9
NFKB1 -0.096 0.21 -9999 0 -0.66 15 15
THY1 -0.002 0.025 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.32 0.26 -9999 0 -0.53 664 664
alphaM/beta2 Integrin/LRP/tPA -0.034 0.11 -9999 0 -0.54 46 46
IL6 -0.3 0.48 -9999 0 -0.93 399 399
ITGB2 -0.017 0.039 -9999 0 -0.3 16 16
elevation of cytosolic calcium ion concentration -0.025 0.05 -9999 0 -0.4 1 1
alphaM/beta2 Integrin/JAM2/JAM3 -0.044 0.13 -9999 0 -0.54 67 67
JAM2 -0.047 0.19 -9999 0 -0.79 65 65
alphaM/beta2 Integrin/ICAM1 -0.021 0.08 -9999 0 -0.53 21 21
alphaM/beta2 Integrin/uPA/Plg -0.019 0.033 -9999 0 -10000 0 0
RhoA/GTP -0.088 0.16 -9999 0 -0.43 119 119
positive regulation of phagocytosis -0.045 0.092 -9999 0 -0.46 19 19
Ron/MSP -0.016 0.098 -9999 0 -0.66 22 22
alphaM/beta2 Integrin/uPAR/uPA -0.025 0.05 -9999 0 -0.4 1 1
alphaM/beta2 Integrin/uPAR -0.028 0.048 -9999 0 -0.39 2 2
PLAU -0.008 0.047 -9999 0 -0.29 29 29
PLAT -0.029 0.15 -9999 0 -0.74 42 42
actin filament polymerization -0.067 0.15 -9999 0 -0.47 51 51
MST1 -0.012 0.089 -9999 0 -0.6 21 21
alphaM/beta2 Integrin/lipoprotein(a) -0.29 0.22 -9999 0 -0.47 664 664
TNF -0.087 0.22 -9999 0 -0.87 21 21
RAP1B 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.021 0.036 -9999 0 -10000 0 0
fibrinolysis -0.019 0.033 -9999 0 -10000 0 0
HCK -0.004 0.033 -9999 0 -10000 0 0
dendritic cell antigen processing and presentation -0.061 0.14 -9999 0 -0.36 95 95
VTN -0.028 0.1 -9999 0 -0.34 89 89
alphaM/beta2 Integrin/CYR61 -0.046 0.13 -9999 0 -0.57 58 58
LPA -0.001 0.02 -9999 0 -0.29 5 5
LRP1 -0.009 0.082 -9999 0 -0.79 12 12
cell migration -0.073 0.084 -9999 0 -0.47 16 16
FN1 -0.12 0.14 -9999 0 -0.29 432 432
alphaM/beta2 Integrin/Thy1 -0.018 0.031 -9999 0 -10000 0 0
MPO -0.053 0.2 -9999 0 -0.77 75 75
KNG1 -0.006 0.041 -9999 0 -0.29 22 22
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.066 0.16 -9999 0 -0.41 106 106
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.002 0.025 -9999 0 -0.29 8 8
CTGF -0.011 0.09 -9999 0 -0.7 17 17
alphaM/beta2 Integrin/Hck -0.019 0.035 -9999 0 -10000 0 0
ITGAM -0.015 0.028 -9999 0 -0.31 6 6
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.13 0.21 -9999 0 -0.5 256 256
HP -0.16 0.31 -9999 0 -0.79 204 204
leukocyte adhesion -0.076 0.13 -9999 0 -0.58 45 45
SELP -0.18 0.34 -9999 0 -0.79 256 256
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.096 0.2 0.63 120 -10000 0 120
KIRREL -0.081 0.25 -10000 0 -0.8 120 120
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.096 0.2 -10000 0 -0.63 120 120
PLCG1 0 0 -10000 0 -10000 0 0
ARRB2 0 0 -10000 0 -10000 0 0
WASL 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.07 0.15 -10000 0 -0.48 120 120
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.043 0.11 -10000 0 -0.36 120 120
FYN -0.065 0.14 -10000 0 -0.46 120 120
mol:Ca2+ -0.069 0.15 -10000 0 -0.48 120 120
mol:DAG -0.069 0.15 -10000 0 -0.48 120 120
NPHS2 -0.008 0.031 -10000 0 -0.29 5 5
mol:IP3 -0.069 0.15 -10000 0 -0.48 120 120
regulation of endocytosis -0.055 0.14 -10000 0 -0.43 120 120
Nephrin/NEPH1/podocin/Cholesterol -0.072 0.15 -10000 0 -0.49 121 121
establishment of cell polarity -0.096 0.2 -10000 0 -0.63 120 120
Nephrin/NEPH1/podocin/NCK1-2 -0.062 0.14 -10000 0 -0.44 120 120
Nephrin/NEPH1/beta Arrestin2 -0.056 0.14 -10000 0 -0.43 120 120
NPHS1 -0.047 0.11 -10000 0 -0.29 179 179
Nephrin/NEPH1/podocin -0.065 0.14 -10000 0 -0.46 120 120
TJP1 -0.001 0.024 -10000 0 -0.79 1 1
NCK1 0 0 -10000 0 -10000 0 0
NCK2 0 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.07 0.15 -10000 0 -0.48 120 120
CD2AP 0 0.009 -10000 0 -0.29 1 1
Nephrin/NEPH1/podocin/GRB2 -0.07 0.15 -10000 0 -0.48 120 120
GRB2 0 0.009 -10000 0 -0.29 1 1
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.057 0.17 -10000 0 -0.5 129 129
cytoskeleton organization -0.055 0.14 -10000 0 -0.45 120 120
Nephrin/NEPH1 -0.07 0.15 -10000 0 -0.47 120 120
Nephrin/NEPH1/ZO-1 -0.076 0.16 -10000 0 -0.52 120 120
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.051 0.16 -9999 0 -0.53 104 104
EFNA5 -0.076 0.23 -9999 0 -0.78 105 105
FYN -0.027 0.15 -9999 0 -0.48 105 105
neuron projection morphogenesis -0.051 0.16 -9999 0 -0.53 104 104
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.051 0.16 -9999 0 -0.53 104 104
EPHA5 -0.001 0.02 -9999 0 -0.29 5 5
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.017 0.031 -9999 0 -10000 0 0
VDR 0 0 -9999 0 -10000 0 0
FAM120B 0 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.033 0.16 -9999 0 -0.42 19 19
RXRs/LXRs/DNA/Oxysterols -0.013 0.14 -9999 0 -0.42 33 33
MED1 -0.006 0.043 -9999 0 -0.29 24 24
mol:9cRA 0.005 0.008 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.023 0.091 -9999 0 -0.35 71 71
RXRs/NUR77 -0.15 0.24 -9999 0 -0.5 327 327
RXRs/PPAR -0.13 0.23 -9999 0 -0.38 448 448
NCOR2 0 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 0 0 -9999 0 -10000 0 0
RARs/VDR/DNA/Vit D3 -0.007 0.052 -9999 0 -0.45 14 14
RARA -0.004 0.034 -9999 0 -0.29 15 15
NCOA1 -0.001 0.024 -9999 0 -0.79 1 1
VDR/VDR/DNA 0 0 -9999 0 -10000 0 0
RARs/RARs/DNA/9cRA -0.007 0.052 -9999 0 -0.45 14 14
RARG 0 0 -9999 0 -10000 0 0
RPS6KB1 0.029 0.052 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT -0.023 0.088 -9999 0 -0.34 71 71
THRA -0.001 0.024 -9999 0 -0.79 1 1
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA 0 0 -9999 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.12 0.2 -9999 0 -0.46 265 265
NR1H4 -0.003 0.032 -9999 0 -0.29 13 13
RXRs/LXRs/DNA -0.1 0.18 -9999 0 -0.42 265 265
NR1H2 0.016 0.006 -9999 0 -10000 0 0
NR1H3 0.016 0.007 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.11 0.19 -9999 0 -0.44 265 265
NR4A1 -0.065 0.22 -9999 0 -0.79 90 90
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.042 0.13 -9999 0 -0.27 265 265
RXRG -0.18 0.34 -9999 0 -0.78 268 268
RXR alpha/CCPG 0 0 -9999 0 -10000 0 0
RXRA 0.016 0.006 -9999 0 -10000 0 0
RXRB 0.016 0.007 -9999 0 -10000 0 0
THRB -0.044 0.18 -9999 0 -0.79 61 61
PPARG -0.19 0.34 -9999 0 -0.79 263 263
PPARD 0 0 -9999 0 -10000 0 0
TNF -0.014 0.19 -9999 0 -1.2 14 14
mol:Oxysterols 0.005 0.007 -9999 0 -10000 0 0
cholesterol transport -0.013 0.14 -9999 0 -0.42 33 33
PPARA -0.005 0.063 -9999 0 -0.79 7 7
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.01 0.089 -9999 0 -0.79 14 14
RXRs/NUR77/BCL2 -0.12 0.19 -9999 0 -0.37 349 349
SREBF1 -0.004 0.14 -9999 0 -0.63 7 7
RXRs/RXRs/DNA/9cRA -0.12 0.2 -9999 0 -0.46 265 265
ABCA1 -0.008 0.16 -9999 0 -0.96 12 12
RARs/THRs -0.032 0.12 -9999 0 -0.47 71 71
RXRs/FXR -0.11 0.2 -9999 0 -0.47 265 265
BCL2 -0.027 0.14 -9999 0 -0.79 37 37
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer -0.005 0.046 -9999 0 -0.62 5 5
PDGFRB 0.005 0.049 -9999 0 -0.8 4 4
SPHK1 -0.025 0.055 -9999 0 -1.1 2 2
mol:S1P -0.031 0.058 -9999 0 -0.97 2 2
S1P1/S1P/Gi -0.1 0.23 -9999 0 -0.39 381 381
GNAO1 -0.023 0.14 -9999 0 -0.5 67 67
PDGFB-D/PDGFRB/PLCgamma1 -0.12 0.18 -9999 0 -0.59 77 77
PLCG1 -0.091 0.22 -9999 0 -0.62 76 76
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.005 0.049 -9999 0 -0.79 4 4
GNAI2 0.008 0.006 -9999 0 -10000 0 0
GNAI3 0.008 0.006 -9999 0 -10000 0 0
GNAI1 -0.038 0.19 -9999 0 -0.8 62 62
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.006 0.043 -9999 0 -0.54 5 5
S1P1/S1P -0.044 0.074 -9999 0 -0.61 7 7
negative regulation of cAMP metabolic process -0.098 0.22 -9999 0 -0.38 381 381
MAPK3 -0.16 0.31 -9999 0 -0.58 371 371
calcium-dependent phospholipase C activity -0.003 0.004 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR -0.004 0.054 -9999 0 -0.8 5 5
PLCB2 -0.008 0.086 -9999 0 -0.53 8 8
RAC1 0 0 -9999 0 -10000 0 0
RhoA/GTP -0.038 0.061 -9999 0 -0.5 7 7
receptor internalization -0.043 0.069 -9999 0 -0.56 7 7
PTGS2 -0.33 0.55 -9999 0 -1.1 371 371
Rac1/GTP -0.038 0.061 -9999 0 -0.5 7 7
RHOA 0 0 -9999 0 -10000 0 0
VEGFA -0.003 0.031 -9999 0 -0.29 12 12
negative regulation of T cell proliferation -0.098 0.22 -9999 0 -0.38 381 381
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.001 0.073 -9999 0 -0.8 9 9
MAPK1 -0.16 0.31 -9999 0 -0.58 371 371
S1P1/S1P/PDGFB-D/PDGFRB -0.02 0.11 -9999 0 -0.67 9 9
ABCC1 0 0 -9999 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 -0.06 0.12 -9999 0 -0.29 223 223
mol:Halofuginone 0 0.003 -9999 0 -10000 0 0
ITGA1 -0.007 0.075 -9999 0 -0.79 10 10
CDKN1A -0.056 0.088 -9999 0 -0.84 2 2
PRL-3/alpha Tubulin -0.002 0.019 -9999 0 -10000 0 0
mol:Ca2+ -0.033 0.097 -9999 0 -0.62 15 15
AGT -0.048 0.13 -9999 0 -0.34 152 152
CCNA2 -0.16 0.24 -9999 0 -0.49 345 345
TUBA1B 0 0 -9999 0 -10000 0 0
EGR1 -0.17 0.29 -9999 0 -0.6 345 345
CDK2/Cyclin E1 -0.067 0.09 -9999 0 -0.82 2 2
MAPK3 0.02 0.021 -9999 0 -10000 0 0
PRL-2 /Rab GGTase beta 0 0.006 -9999 0 -10000 0 0
MAPK1 0.02 0.021 -9999 0 -10000 0 0
PTP4A1 -0.12 0.23 -9999 0 -0.46 345 345
PTP4A3 -0.003 0.029 -9999 0 -10000 0 0
PTP4A2 0 0.009 -9999 0 -10000 0 0
ITGB1 0.02 0.021 -9999 0 -10000 0 0
SRC 0 0.009 -9999 0 -0.29 1 1
RAC1 -0.055 0.081 -9999 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0 0 -9999 0 -10000 0 0
PRL-1/ATF-5 -0.14 0.2 -9999 0 -0.42 345 345
RABGGTA 0 0 -9999 0 -10000 0 0
BCAR1 0.001 0.009 -9999 0 -10000 0 0
RHOC -0.055 0.081 -9999 0 -10000 0 0
RHOA -0.055 0.081 -9999 0 -10000 0 0
cell motility -0.034 0.1 -9999 0 -0.24 1 1
PRL-1/alpha Tubulin -0.13 0.2 -9999 0 -0.42 345 345
PRL-3/alpha1 Integrin -0.007 0.06 -9999 0 -0.6 10 10
ROCK1 -0.034 0.1 -9999 0 -0.24 1 1
RABGGTB 0 0 -9999 0 -10000 0 0
CDK2 0 0 -9999 0 -10000 0 0
mitosis -0.12 0.23 -9999 0 -0.46 345 345
ATF5 -0.001 0.018 -9999 0 -0.29 4 4
Syndecan-3-mediated signaling events

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
CTTN -0.002 0.027 -9999 0 -0.29 9 9
Syndecan-3/Src/Cortactin -0.18 0.2 -9999 0 -0.4 477 477
Syndecan-3/Neurocan -0.007 0.028 -9999 0 -10000 0 0
POMC -0.024 0.12 -9999 0 -0.49 53 53
EGFR -0.3 0.38 -9999 0 -0.78 414 414
Syndecan-3/EGFR -0.17 0.21 -9999 0 -0.44 409 409
AGRP -0.003 0.028 -9999 0 -0.29 10 10
NCSTN 0 0 -9999 0 -10000 0 0
PSENEN 0 0.009 -9999 0 -0.29 1 1
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B -0.001 0.024 -9999 0 -0.79 1 1
APH1A 0 0 -9999 0 -10000 0 0
NCAN -0.019 0.073 -9999 0 -0.29 72 72
long-term memory -0.002 0.02 -9999 0 -0.41 2 2
Syndecan-3/IL8 -0.016 0.067 -9999 0 -0.44 22 22
PSEN1 0 0 -9999 0 -10000 0 0
Src/Cortactin -0.002 0.018 -9999 0 -10000 0 0
FYN -0.001 0.034 -9999 0 -0.79 2 2
limb bud formation 0 0.003 -9999 0 -10000 0 0
MC4R -0.003 0.032 -9999 0 -0.29 13 13
SRC 0 0.009 -9999 0 -0.29 1 1
PTN -0.35 0.39 -9999 0 -0.79 479 479
FGFR/FGF/Syndecan-3 0 0.003 -9999 0 -10000 0 0
neuron projection morphogenesis -0.18 0.19 -9999 0 -0.39 477 477
Syndecan-3/AgRP -0.001 0.011 -9999 0 -10000 0 0
Syndecan-3/AgRP/MC4R -0.002 0.015 -9999 0 -10000 0 0
Fyn/Cortactin -0.003 0.031 -9999 0 -0.6 2 2
SDC3 0 0.003 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.015 0.066 -9999 0 -0.43 22 22
IL8 -0.033 0.13 -9999 0 -0.79 22 22
Syndecan-3/Fyn/Cortactin -0.002 0.02 -9999 0 -0.42 2 2
Syndecan-3/CASK 0 0.003 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.019 0.093 -9999 0 -0.6 23 23
Gamma Secretase 0 0.014 -9999 0 -0.44 1 1
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.019 0.094 -9999 0 -0.5 36 36
NF kappa B1 p50/RelA/I kappa B alpha -0.043 0.11 -9999 0 -0.46 6 6
AP1 -0.18 0.25 -9999 0 -0.47 419 419
mol:PIP3 -0.2 0.24 -9999 0 -0.45 467 467
AKT1 -0.016 0.075 -9999 0 -0.59 8 8
PTK2B 0.014 0.062 -9999 0 -0.29 26 26
RHOA 0.028 0.028 -9999 0 -10000 0 0
PIK3CB 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.007 0.13 -9999 0 -0.35 128 128
MAGI3 -0.001 0.034 -9999 0 -0.79 2 2
RELA 0 0 -9999 0 -10000 0 0
apoptosis -0.062 0.15 -9999 0 -0.42 148 148
HRAS/GDP -0.002 0.018 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization -0.02 0.15 -9999 0 -0.4 126 126
NF kappa B1 p50/RelA -0.053 0.14 -9999 0 -0.55 16 16
endothelial cell migration 0.007 0.12 -9999 0 -0.63 34 34
ADCY4 -0.004 0.15 -9999 0 -0.63 41 41
ADCY5 -0.071 0.19 -9999 0 -0.59 81 81
ADCY6 0.006 0.13 -9999 0 -0.6 31 31
ADCY7 0.006 0.13 -9999 0 -0.6 31 31
ADCY1 -0.003 0.14 -9999 0 -0.64 37 37
ADCY2 -0.015 0.16 -9999 0 -0.62 49 49
ADCY3 0.006 0.13 -9999 0 -0.6 31 31
ADCY8 0.003 0.13 -9999 0 -0.61 31 31
ADCY9 0.006 0.13 -9999 0 -0.6 31 31
GSK3B 0.021 0.059 -9999 0 -0.36 10 10
arachidonic acid secretion 0.009 0.13 -9999 0 -0.56 34 34
GNG2 -0.009 0.086 -9999 0 -0.79 13 13
TRIP6 -0.001 0.016 -9999 0 -0.51 1 1
GNAO1 -0.006 0.13 -9999 0 -0.53 56 56
HRAS -0.002 0.027 -9999 0 -0.29 9 9
NFKBIA -0.003 0.15 -9999 0 -0.4 128 128
GAB1 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly 0.001 0.004 -9999 0 -10000 0 0
JUN -0.005 0.063 -9999 0 -0.79 7 7
LPA/LPA2/NHERF2 -0.002 0.016 -9999 0 -10000 0 0
TIAM1 0.001 0.004 -9999 0 -10000 0 0
PIK3R1 -0.009 0.086 -9999 0 -0.79 13 13
mol:IP3 -0.007 0.13 -9999 0 -0.36 128 128
PLCB3 0.026 0.016 -9999 0 -10000 0 0
FOS -0.24 0.36 -9999 0 -0.79 325 325
positive regulation of mitosis 0.009 0.13 -9999 0 -0.56 34 34
LPA/LPA1-2-3 -0.073 0.17 -9999 0 -0.49 147 147
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
stress fiber formation 0.002 0.1 -9999 0 -0.38 25 25
GNAZ 0.008 0.1 -9999 0 -0.48 42 42
EGFR/PI3K-beta/Gab1 -0.21 0.26 -9999 0 -0.48 464 464
positive regulation of dendritic cell cytokine production -0.072 0.17 -9999 0 -0.48 147 147
LPA/LPA2/MAGI-3 -0.002 0.025 -9999 0 -0.52 2 2
ARHGEF1 -0.011 0.069 -9999 0 -0.44 24 24
GNAI2 0.013 0.087 -9999 0 -0.46 34 34
GNAI3 0.013 0.087 -9999 0 -0.46 34 34
GNAI1 -0.018 0.16 -9999 0 -0.53 89 89
LPA/LPA3 -0.08 0.2 -9999 0 -0.61 128 128
LPA/LPA2 -0.002 0.016 -9999 0 -10000 0 0
LPA/LPA1 -0.017 0.096 -9999 0 -0.54 34 34
HB-EGF/EGFR -0.26 0.26 -9999 0 -0.57 414 414
HBEGF -0.072 0.11 -9999 0 -0.6 3 3
mol:DAG -0.007 0.13 -9999 0 -0.36 128 128
cAMP biosynthetic process -0.012 0.15 -9999 0 -0.56 55 55
NFKB1 0 0 -9999 0 -10000 0 0
SRC 0 0.009 -9999 0 -0.29 1 1
GNB1 0 0 -9999 0 -10000 0 0
LYN -0.003 0.15 -9999 0 -0.4 128 128
GNAQ -0.053 0.13 -9999 0 -0.41 131 131
LPAR2 -0.001 0.015 -9999 0 -0.29 2 2
LPAR3 -0.1 0.26 -9999 0 -0.79 128 128
LPAR1 -0.019 0.12 -9999 0 -0.79 24 24
IL8 -0.19 0.23 -9999 0 -0.46 354 354
PTK2 -0.067 0.16 -9999 0 -0.45 147 147
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.062 0.15 -9999 0 -0.42 148 148
EGFR -0.3 0.38 -9999 0 -0.78 414 414
PLCG1 -0.029 0.15 -9999 0 -0.42 128 128
PLD2 -0.067 0.16 -9999 0 -0.45 147 147
G12/G13 -0.013 0.075 -9999 0 -0.48 24 24
PI3K-beta -0.018 0.089 -9999 0 -0.72 8 8
cell migration -0.021 0.053 -9999 0 -0.24 6 6
SLC9A3R2 -0.001 0.02 -9999 0 -0.29 5 5
PXN 0.002 0.1 -9999 0 -0.39 25 25
HRAS/GTP -0.035 0.12 -9999 0 -0.58 34 34
RAC1 0 0 -9999 0 -10000 0 0
MMP9 -0.13 0.15 -9999 0 -0.29 484 484
PRKCE 0.01 0.002 -9999 0 -10000 0 0
PRKCD 0.001 0.12 -9999 0 -0.4 8 8
Gi(beta/gamma) -0.036 0.12 -9999 0 -0.57 39 39
mol:LPA -0.002 0.021 -9999 0 -0.22 10 10
TRIP6/p130 Cas/FAK1/Paxillin -0.055 0.14 -9999 0 -0.66 10 10
MAPKKK cascade 0.009 0.13 -9999 0 -0.56 34 34
contractile ring contraction involved in cytokinesis 0.028 0.028 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.058 0.14 -9999 0 -0.42 136 136
GNA15 -0.053 0.13 -9999 0 -0.41 129 129
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
MAPT -0.022 0.15 -9999 0 -0.41 126 126
GNA11 -0.053 0.13 -9999 0 -0.41 131 131
Rac1/GTP 0.001 0.005 -9999 0 -10000 0 0
MMP2 0.007 0.12 -9999 0 -0.64 34 34
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.053 0.3 -10000 0 -0.81 131 131
IHH -0.014 0.082 -10000 0 -0.42 9 9
SHH Np/Cholesterol/GAS1 -0.032 0.12 -10000 0 -0.49 65 65
LRPAP1 0 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.031 0.12 0.49 65 -10000 0 65
SMO/beta Arrestin2 -0.075 0.23 -10000 0 -0.84 81 81
SMO -0.036 0.26 -10000 0 -0.85 90 90
AKT1 0.007 0.12 -10000 0 -0.44 22 22
ARRB2 0 0 -10000 0 -10000 0 0
BOC -0.059 0.21 -10000 0 -0.79 82 82
ADRBK1 0 0 -10000 0 -10000 0 0
heart looping -0.034 0.25 -10000 0 -0.82 90 90
STIL -0.038 0.21 -10000 0 -0.68 88 88
DHH N/PTCH2 -0.063 0.19 -10000 0 -0.64 107 107
DHH N/PTCH1 -0.089 0.24 -10000 0 -0.74 115 115
PIK3CA 0 0.009 -10000 0 -0.29 1 1
DHH -0.022 0.13 -10000 0 -0.76 32 32
PTHLH -0.081 0.38 -10000 0 -1.1 131 131
determination of left/right symmetry -0.034 0.25 -10000 0 -0.82 90 90
PIK3R1 -0.009 0.086 -10000 0 -0.79 13 13
skeletal system development -0.079 0.37 -10000 0 -1 131 131
IHH N/Hhip -0.015 0.049 -10000 0 -0.41 6 6
DHH N/Hhip -0.019 0.1 -10000 0 -0.61 32 32
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.034 0.25 -10000 0 -0.82 90 90
pancreas development -0.004 0.042 -10000 0 -0.39 10 10
HHAT -0.001 0.024 -10000 0 -0.79 1 1
PI3K -0.007 0.066 -10000 0 -0.6 13 13
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.046 0.19 -10000 0 -0.79 64 64
somite specification -0.034 0.25 -10000 0 -0.82 90 90
SHH Np/Cholesterol/PTCH1 -0.071 0.2 -10000 0 -0.7 94 94
SHH Np/Cholesterol/PTCH2 -0.04 0.13 -10000 0 -0.49 85 85
SHH Np/Cholesterol/Megalin -0.14 0.21 -10000 0 -0.49 291 291
SHH 0.01 0.036 -10000 0 -0.61 1 1
catabolic process -0.047 0.26 -10000 0 -0.82 96 96
SMO/Vitamin D3 -0.074 0.22 -10000 0 -0.79 86 86
SHH Np/Cholesterol/Hhip -0.005 0.036 -10000 0 -0.37 7 7
LRP2 -0.22 0.35 -10000 0 -0.75 317 317
receptor-mediated endocytosis -0.15 0.25 -10000 0 -0.81 100 100
SHH Np/Cholesterol/BOC -0.04 0.13 -10000 0 -0.49 83 83
SHH Np/Cholesterol/CDO -0.01 0.061 -10000 0 -0.48 16 16
mesenchymal cell differentiation 0.005 0.035 0.36 7 -10000 0 7
mol:Vitamin D3 -0.029 0.22 -10000 0 -0.7 94 94
IHH N/PTCH2 -0.063 0.18 -10000 0 -0.66 88 88
CDON -0.011 0.092 -10000 0 -0.79 15 15
IHH N/PTCH1 -0.044 0.26 -10000 0 -0.82 96 96
Megalin/LRPAP1 -0.16 0.26 -10000 0 -0.6 290 290
PTCH2 -0.061 0.21 -10000 0 -0.79 84 84
SHH Np/Cholesterol -0.003 0.025 -10000 0 -0.49 1 1
PTCH1 -0.047 0.26 -10000 0 -0.82 96 96
HHIP -0.004 0.042 -10000 0 -0.39 10 10
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A -0.001 0.034 -9999 0 -0.79 2 2
LAT2 -0.063 0.14 -9999 0 -0.43 95 95
AP1 -0.15 0.21 -9999 0 -0.43 347 347
mol:PIP3 -0.027 0.2 -9999 0 -0.49 107 107
IKBKB 0.002 0.12 -9999 0 -0.32 54 54
AKT1 -0.082 0.17 -9999 0 -0.67 45 45
IKBKG 0.002 0.12 -9999 0 -0.32 54 54
MS4A2 -0.069 0.22 -9999 0 -0.76 99 99
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -0.3 1 1
MAP3K1 0.006 0.13 -9999 0 -0.44 45 45
mol:Ca2+ -0.013 0.15 -9999 0 -0.36 108 108
LYN 0.011 0.004 -9999 0 -10000 0 0
CBLB -0.062 0.14 -9999 0 -0.43 95 95
SHC1 0 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.062 0.16 -9999 0 -0.48 141 141
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0 0 -9999 0 -10000 0 0
PLD2 -0.096 0.21 -9999 0 -0.48 216 216
PTPN13 -0.031 0.17 -9999 0 -0.54 68 68
PTPN11 0.01 0.006 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation 0.006 0.15 -9999 0 -0.41 44 44
SYK 0.011 0.01 -9999 0 -0.3 1 1
GRB2 0 0.009 -9999 0 -0.29 1 1
LAT/PLCgamma1/GRB2/SLP76/GADs -0.086 0.18 -9999 0 -0.43 216 216
LAT -0.064 0.14 -9999 0 -0.43 96 96
PAK2 -0.004 0.14 -9999 0 -0.5 45 45
NFATC2 -0.1 0.24 -9999 0 -0.69 130 130
HRAS -0.013 0.15 -9999 0 -0.41 98 98
GAB2 -0.004 0.043 -9999 0 -0.79 2 2
PLA2G1B 0.028 0.018 -9999 0 -10000 0 0
Fc epsilon R1 -0.12 0.25 -9999 0 -0.6 216 216
Antigen/IgE/Fc epsilon R1 -0.11 0.23 -9999 0 -0.55 216 216
mol:GDP -0.02 0.16 -9999 0 -0.42 98 98
JUN -0.005 0.063 -9999 0 -0.79 7 7
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 -0.009 0.086 -9999 0 -0.79 13 13
FOS -0.24 0.36 -9999 0 -0.79 325 325
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.067 0.15 -9999 0 -0.45 98 98
CHUK 0.002 0.12 -9999 0 -0.32 55 55
KLRG1 -0.062 0.14 -9999 0 -0.4 99 99
VAV1 -0.064 0.14 -9999 0 -0.44 98 98
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.062 0.14 -9999 0 -0.43 95 95
negative regulation of mast cell degranulation -0.056 0.12 -9999 0 -0.51 43 43
BTK -0.061 0.14 -9999 0 -0.43 97 97
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.086 0.2 -9999 0 -0.43 218 218
GAB2/PI3K/SHP2 -0.091 0.19 -9999 0 -0.74 47 47
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.069 0.16 -9999 0 -0.6 53 53
RAF1 0.015 0.022 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.1 0.22 -9999 0 -0.51 218 218
FCER1G 0.003 0.013 -9999 0 -0.29 1 1
FCER1A -0.11 0.29 -9999 0 -0.8 160 160
Antigen/IgE/Fc epsilon R1/Fyn -0.1 0.22 -9999 0 -0.52 216 216
MAPK3 0.026 0.019 -9999 0 -10000 0 0
MAPK1 0.026 0.019 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAPK8 0.01 0.078 -9999 0 -0.67 9 9
DUSP1 -0.1 0.26 -9999 0 -0.79 141 141
NF-kappa-B/RelA -0.027 0.054 -9999 0 -0.23 6 6
actin cytoskeleton reorganization -0.027 0.15 -9999 0 -0.42 95 95
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.059 0.13 -9999 0 -0.52 54 54
FER -0.066 0.15 -9999 0 -0.45 102 102
RELA 0 0 -9999 0 -10000 0 0
ITK -0.035 0.11 -9999 0 -0.6 39 39
SOS1 0 0 -9999 0 -10000 0 0
PLCG1 -0.017 0.16 -9999 0 -0.44 98 98
cytokine secretion -0.019 0.04 -9999 0 -10000 0 0
SPHK1 -0.065 0.14 -9999 0 -0.44 98 98
PTK2 -0.029 0.16 -9999 0 -0.57 45 45
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.089 0.19 -9999 0 -0.45 216 216
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.022 0.2 -9999 0 -0.48 107 107
MAP2K2 0.023 0.019 -9999 0 -10000 0 0
MAP2K1 0.023 0.019 -9999 0 -10000 0 0
MAP2K7 0 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.058 0.13 -9999 0 -0.51 43 43
MAP2K4 0.017 0.033 -9999 0 -1 1 1
Fc epsilon R1/FcgammaRIIB -0.11 0.23 -9999 0 -0.55 218 218
mol:Choline -0.094 0.2 -9999 0 -0.47 216 216
SHC/Grb2/SOS1 -0.056 0.13 -9999 0 -0.54 41 41
FYN -0.001 0.034 -9999 0 -0.79 2 2
DOK1 -0.001 0.018 -9999 0 -10000 0 0
PXN -0.019 0.15 -9999 0 -0.54 41 41
HCLS1 -0.062 0.14 -9999 0 -0.43 95 95
PRKCB -0.015 0.16 -9999 0 -0.38 104 104
FCGR2B -0.004 0.054 -9999 0 -0.71 6 6
IGHE 0 0.006 -9999 0 -10000 0 0
KLRG1/SHIP -0.057 0.13 -9999 0 -0.52 43 43
LCP2 0 0.009 -9999 0 -0.29 1 1
PLA2G4A -0.12 0.21 -9999 0 -0.5 208 208
RASA1 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.094 0.2 -9999 0 -0.47 216 216
IKK complex 0.019 0.093 -9999 0 -0.23 50 50
WIPF1 0 0 -9999 0 -10000 0 0
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.052 0.2 -9999 0 -0.81 74 74
PDGF/PDGFRA/CRKL -0.041 0.15 -9999 0 -0.61 73 73
positive regulation of JUN kinase activity -0.031 0.12 -9999 0 -0.46 73 73
CRKL 0 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.044 0.15 -9999 0 -0.61 73 73
AP1 -0.36 0.53 -9999 0 -1.2 325 325
mol:IP3 -0.035 0.16 -9999 0 -0.63 73 73
PLCG1 -0.035 0.16 -9999 0 -0.63 73 73
PDGF/PDGFRA/alphaV Integrin -0.041 0.15 -9999 0 -0.61 73 73
RAPGEF1 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.035 0.16 -9999 0 -0.63 73 73
CAV3 -0.001 0.015 -9999 0 -0.29 3 3
CAV1 -0.17 0.33 -9999 0 -0.79 238 238
SHC/Grb2/SOS1 -0.031 0.12 -9999 0 -0.47 73 73
PDGF/PDGFRA/Shf -0.042 0.15 -9999 0 -0.61 73 73
FOS -0.32 0.54 -9999 0 -1.1 325 325
JUN -0.024 0.059 -9999 0 -0.67 7 7
oligodendrocyte development -0.041 0.15 -9999 0 -0.6 73 73
GRB2 0 0.009 -9999 0 -0.29 1 1
PIK3R1 -0.009 0.086 -9999 0 -0.79 13 13
mol:DAG -0.035 0.16 -9999 0 -0.63 73 73
PDGF/PDGFRA -0.052 0.2 -9999 0 -0.8 74 74
actin cytoskeleton reorganization -0.041 0.15 -9999 0 -0.6 74 74
SRF 0.015 0.022 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
PI3K -0.041 0.14 -9999 0 -0.54 83 83
PDGF/PDGFRA/Crk/C3G -0.035 0.13 -9999 0 -0.52 73 73
JAK1 -0.025 0.16 -9999 0 -0.6 74 74
ELK1/SRF -0.028 0.12 -9999 0 -0.48 73 73
SHB -0.001 0.025 -9999 0 -0.79 1 1
SHF -0.001 0.027 -9999 0 -0.79 1 1
CSNK2A1 0.019 0.027 -9999 0 -10000 0 0
GO:0007205 -0.037 0.17 -9999 0 -0.65 73 73
SOS1 0 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.031 0.12 -9999 0 -0.46 73 73
PDGF/PDGFRA/SHB -0.042 0.15 -9999 0 -0.61 74 74
PDGF/PDGFRA/Caveolin-1 -0.17 0.32 -9999 0 -0.71 263 263
ITGAV 0 0 -9999 0 -10000 0 0
ELK1 -0.035 0.16 -9999 0 -0.59 73 73
PIK3CA 0 0.009 -9999 0 -0.29 1 1
PDGF/PDGFRA/Crk -0.041 0.15 -9999 0 -0.61 73 73
JAK-STAT cascade -0.025 0.16 -9999 0 -0.6 74 74
cell proliferation -0.041 0.15 -9999 0 -0.61 73 73
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.12 0.18 -9999 0 -0.39 326 326
MAP3K8 0.001 0.073 -9999 0 -0.74 10 10
FOS -0.034 0.14 -9999 0 -0.46 39 39
PRKCA -0.012 0.13 -9999 0 -0.77 30 30
PTPN7 -0.009 0.074 -9999 0 -0.3 64 64
HRAS -0.002 0.027 -9999 0 -0.3 9 9
PRKCB -0.011 0.12 -9999 0 -0.56 39 39
NRAS -0.001 0.013 -9999 0 -0.3 2 2
RAS family/GTP -0.002 0.015 -9999 0 -10000 0 0
MAPK3 -0.007 0.073 -9999 0 -0.25 34 34
MAP2K1 -0.013 0.14 -9999 0 -0.6 47 47
ELK1 -0.003 0.01 -9999 0 -0.29 1 1
BRAF -0.032 0.12 -9999 0 -0.57 47 47
mol:GTP -0.002 0.003 -9999 0 -0.006 325 325
MAPK1 -0.007 0.073 -9999 0 -0.28 2 2
RAF1 -0.032 0.12 -9999 0 -0.57 47 47
KRAS -0.001 0.013 -9999 0 -0.29 2 2
PLK1 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
regulation of centriole-centriole cohesion 0.029 0.031 -9999 0 -10000 0 0
BUB1B -0.041 0.053 -9999 0 -10000 0 0
PLK1 -0.008 0.024 -9999 0 -10000 0 0
PLK1S1 0 0.014 -9999 0 -10000 0 0
KIF2A 0.001 0.022 -9999 0 -10000 0 0
regulation of mitotic centrosome separation -0.008 0.024 -9999 0 -10000 0 0
GOLGA2 0 0 -9999 0 -10000 0 0
Hec1/SPC24 -0.17 0.12 -9999 0 -0.28 529 529
WEE1 -0.002 0.024 -9999 0 -10000 0 0
cytokinesis -0.056 0.058 -9999 0 -0.27 12 12
PP2A-alpha B56 0.027 0.019 -9999 0 -10000 0 0
AURKA -0.001 0.015 -9999 0 -10000 0 0
PICH/PLK1 -0.073 0.098 -9999 0 -0.34 11 11
CENPE -0.05 0.086 -9999 0 -0.19 17 17
RhoA/GTP 0 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.001 0.022 -9999 0 -10000 0 0
PPP2CA 0 0 -9999 0 -10000 0 0
FZR1 0 0 -9999 0 -10000 0 0
TPX2 -0.006 0.017 -9999 0 -10000 0 0
PAK1 -0.006 0.043 -9999 0 -0.29 25 25
SPC24 -0.18 0.14 -9999 0 -0.29 680 680
FBXW11 0 0 -9999 0 -10000 0 0
CLSPN -0.006 0.019 -9999 0 -10000 0 0
GORASP1 0 0 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NLP -0.005 0.014 -9999 0 -0.052 2 2
G2 phase of mitotic cell cycle -0.001 0.002 -9999 0 -10000 0 0
STAG2 -0.001 0.024 -9999 0 -0.79 1 1
GRASP65/GM130/RAB1/GTP 0.008 0.009 -9999 0 -10000 0 0
spindle elongation -0.008 0.024 -9999 0 -10000 0 0
ODF2 0.002 0.004 -9999 0 -10000 0 0
BUB1 0.02 0.015 -9999 0 -10000 0 0
TPT1 0 0.014 -9999 0 -10000 0 0
CDC25C -0.009 0.017 -9999 0 -10000 0 0
CDC25B 0.005 0.041 -9999 0 -0.29 20 20
SGOL1 -0.03 0.031 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.021 0.044 -9999 0 -10000 0 0
CDC14B -0.01 0.11 -9999 0 -0.62 35 35
CDC20 -0.16 0.15 -9999 0 -0.29 588 588
PLK1/PBIP1 -0.029 0.053 -9999 0 -0.18 6 6
mitosis -0.006 0.007 -9999 0 -0.022 2 2
FBXO5 0 0.023 -9999 0 -10000 0 0
CDC2 -0.001 0.002 -9999 0 -10000 0 0
NDC80 -0.18 0.14 -9999 0 -0.29 660 660
metaphase plate congression -0.002 0.016 -9999 0 -10000 0 0
ERCC6L -0.064 0.09 -9999 0 -10000 0 0
NLP/gamma Tubulin -0.001 0.014 -9999 0 -10000 0 0
microtubule cytoskeleton organization 0 0.014 -9999 0 -10000 0 0
G2/M transition DNA damage checkpoint -0.001 0.001 -9999 0 -10000 0 0
PPP1R12A 0 0 -9999 0 -10000 0 0
interphase -0.001 0.001 -9999 0 -10000 0 0
PLK1/PRC1-2 -0.14 0.1 -9999 0 -0.29 275 275
GRASP65/GM130/RAB1/GTP/PLK1 -0.002 0.004 -9999 0 -10000 0 0
RAB1A 0 0 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
Aurora A/BORA -0.003 0.024 -9999 0 -0.17 2 2
mitotic prometaphase -0.002 0.001 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.014 0.05 -9999 0 -0.29 30 30
microtubule-based process -0.12 0.069 -9999 0 -0.19 23 23
Golgi organization -0.008 0.024 -9999 0 -10000 0 0
Cohesin/SA2 -0.01 0.018 -9999 0 -0.45 1 1
PPP1CB/MYPT1 0 0 -9999 0 -10000 0 0
KIF20A -0.22 0.13 -9999 0 -0.29 819 819
APC/C/CDC20 -0.088 0.081 -9999 0 -0.17 423 423
PPP2R1A 0 0 -9999 0 -10000 0 0
chromosome segregation -0.029 0.053 -9999 0 -0.18 6 6
PRC1 -0.074 0.13 -9999 0 -0.29 276 276
ECT2 -0.004 0.039 -9999 0 -0.2 4 4
C13orf34 -0.001 0.022 -9999 0 -0.17 2 2
NUDC -0.002 0.016 -9999 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.041 0.052 -9999 0 -10000 0 0
spindle assembly -0.004 0.02 -9999 0 -10000 0 0
spindle stabilization 0 0.014 -9999 0 -10000 0 0
APC/C/HCDH1 -0.017 0.093 -9999 0 -0.53 35 35
MKLP2/PLK1 -0.12 0.069 -9999 0 -0.19 23 23
CCNB1 -0.05 0.12 -9999 0 -0.29 221 221
PPP1CB 0 0 -9999 0 -10000 0 0
BTRC 0 0 -9999 0 -10000 0 0
ROCK2 -0.009 0.088 -9999 0 -0.51 31 31
TUBG1 0 0.014 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.024 0.041 -9999 0 -10000 0 0
MLF1IP -0.026 0.074 -9999 0 -0.2 158 158
INCENP 0.002 0.004 -9999 0 -10000 0 0
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.003 0.048 -9999 0 -0.79 4 4
alphaV beta3 Integrin -0.022 0.11 -9999 0 -0.6 38 38
PTK2 -0.067 0.19 -9999 0 -0.56 123 123
positive regulation of JNK cascade -0.039 0.11 -9999 0 -0.34 123 123
CDC42/GDP -0.002 0.16 -9999 0 -0.46 123 123
Rac1/GDP 0 0.16 -9999 0 -0.45 123 123
RAP1B 0 0 -9999 0 -10000 0 0
RAP1A 0 0 -9999 0 -10000 0 0
CTNNB1 0 0 -9999 0 -10000 0 0
CDC42/GTP -0.048 0.13 -9999 0 -0.42 123 123
nectin-3/I-afadin -0.07 0.2 -9999 0 -0.62 123 123
RAPGEF1 -0.01 0.18 -9999 0 -0.52 123 123
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.025 0.21 -9999 0 -0.61 123 123
PDGFB-D/PDGFRB -0.003 0.048 -9999 0 -0.79 4 4
TLN1 0.001 0.1 -9999 0 -0.54 13 13
Rap1/GTP -0.041 0.11 -9999 0 -0.36 123 123
IQGAP1 0 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.003 0.036 -9999 0 -0.48 6 6
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.07 0.2 -9999 0 -0.62 123 123
PVR 0 0.009 -9999 0 -0.29 1 1
Necl-5(dimer) 0 0.009 -9999 0 -0.29 1 1
mol:GDP -0.014 0.2 -9999 0 -0.57 123 123
MLLT4 -0.005 0.059 -9999 0 -0.72 7 7
PIK3CA 0 0.009 -9999 0 -0.29 1 1
PI3K -0.058 0.17 -9999 0 -0.49 129 129
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.003 0.045 -9999 0 -0.6 6 6
positive regulation of lamellipodium assembly -0.04 0.11 -9999 0 -0.35 123 123
PVRL1 0 0 -9999 0 -10000 0 0
PVRL3 -0.088 0.25 -9999 0 -0.79 122 122
PVRL2 -0.001 0.015 -9999 0 -0.29 3 3
PIK3R1 -0.009 0.086 -9999 0 -0.79 13 13
CDH1 -0.022 0.13 -9999 0 -0.79 30 30
CLDN1 -0.037 0.16 -9999 0 -0.59 69 69
JAM-A/CLDN1 -0.076 0.19 -9999 0 -0.52 154 154
SRC -0.079 0.22 -9999 0 -0.69 123 123
ITGB3 -0.029 0.15 -9999 0 -0.74 42 42
nectin-1(dimer)/I-afadin/I-afadin -0.003 0.045 -9999 0 -0.6 6 6
FARP2 -0.019 0.2 -9999 0 -0.56 123 123
RAC1 0 0 -9999 0 -10000 0 0
CTNNA1 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.061 0.17 -9999 0 -0.54 123 123
nectin-1/I-afadin -0.003 0.045 -9999 0 -0.6 6 6
nectin-2/I-afadin -0.004 0.046 -9999 0 -0.6 6 6
RAC1/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.061 0.17 -9999 0 -0.54 123 123
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.039 0.11 -9999 0 -0.34 123 123
alphaV/beta3 Integrin/Talin -0.041 0.13 -9999 0 -0.58 43 43
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.004 0.046 -9999 0 -0.6 6 6
nectin-2(dimer)/I-afadin/I-afadin -0.004 0.046 -9999 0 -0.6 6 6
PIP5K1C -0.033 0.1 -9999 0 -0.56 14 14
VAV2 -0.02 0.2 -9999 0 -0.58 123 123
RAP1/GDP -0.048 0.13 -9999 0 -0.42 123 123
ITGAV 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.061 0.17 -9999 0 -0.54 123 123
nectin-3(dimer)/I-afadin/I-afadin -0.07 0.2 -9999 0 -0.62 123 123
Rac1/GTP -0.05 0.14 -9999 0 -0.44 123 123
PTPRM -0.037 0.11 -9999 0 -0.32 127 127
E-cadherin/beta catenin/alpha catenin -0.014 0.076 -9999 0 -0.43 35 35
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.005 0.054 -10000 0 -0.55 10 10
HDAC1 0.002 0.008 -10000 0 -10000 0 0
AES 0.001 0.004 -10000 0 -10000 0 0
FBXW11 0 0 -10000 0 -10000 0 0
DTX1 -0.069 0.22 -10000 0 -0.79 96 96
LRP6/FZD1 0 0.006 -10000 0 -10000 0 0
TLE1 -0.005 0.068 -10000 0 -0.79 8 8
AP1 -0.11 0.17 -10000 0 -0.37 328 328
NCSTN 0 0 -10000 0 -10000 0 0
ADAM10 -0.003 0.048 -10000 0 -0.79 4 4
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.008 0.044 -10000 0 -0.34 1 1
NICD/RBPSUH -0.003 0.042 -10000 0 -0.7 4 4
WIF1 -0.42 0.39 -10000 0 -0.78 583 583
NOTCH1 -0.003 0.045 -10000 0 -0.75 4 4
PSENEN 0 0.009 -10000 0 -0.29 1 1
KREMEN2 -0.14 0.15 -10000 0 -0.29 525 525
DKK1 -0.081 0.19 -10000 0 -0.42 207 207
beta catenin/beta TrCP1 -0.008 0.024 -10000 0 -10000 0 0
APH1B -0.001 0.024 -10000 0 -0.79 1 1
APH1A 0 0 -10000 0 -10000 0 0
AXIN1 0.003 0.015 -10000 0 -0.21 4 4
CtBP/CBP/TCF1/TLE1/AES 0.003 0.039 -10000 0 -0.33 8 8
PSEN1 0 0 -10000 0 -10000 0 0
FOS -0.24 0.36 -10000 0 -0.79 325 325
JUN -0.005 0.063 -10000 0 -0.79 7 7
MAP3K7 0.001 0.01 -10000 0 -0.3 1 1
CTNNB1 -0.002 0.034 0.23 2 -10000 0 2
MAPK3 0 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.085 0.12 -10000 0 -0.61 32 32
HNF1A -0.001 0.025 -10000 0 -0.29 8 8
CTBP1 0.001 0.004 -10000 0 -10000 0 0
MYC -0.033 0.22 -10000 0 -1.5 24 24
NKD1 -0.009 0.069 -10000 0 -0.79 6 6
FZD1 0 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.041 0.13 -10000 0 -0.44 100 100
apoptosis -0.11 0.17 -10000 0 -0.36 328 328
Delta 1/NOTCHprecursor -0.005 0.053 -10000 0 -0.54 10 10
DLL1 -0.004 0.058 -10000 0 -0.79 6 6
PPARD -0.001 0.013 -10000 0 -10000 0 0
Gamma Secretase 0 0.014 -10000 0 -0.44 1 1
APC 0.003 0.015 -10000 0 -0.21 4 4
DVL1 -0.037 0.035 -10000 0 -10000 0 0
CSNK2A1 0.011 0.003 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.12 0.14 -10000 0 -0.57 56 56
LRP6 0 0.009 -10000 0 -0.29 1 1
CSNK1A1 0.011 0.003 -10000 0 -10000 0 0
NLK 0.002 0.01 -10000 0 -10000 0 0
CCND1 -0.012 0.094 -10000 0 -1.5 4 4
WNT1 -0.001 0.013 -10000 0 -0.29 2 2
Axin1/APC/beta catenin 0.011 0.037 -10000 0 -10000 0 0
DKK2 -0.024 0.13 -10000 0 -0.76 34 34
NOTCH1 precursor/DVL1 -0.019 0.041 -10000 0 -0.64 4 4
GSK3B 0.001 0.003 -10000 0 -10000 0 0
FRAT1 0.001 0.004 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.041 0.13 -10000 0 -0.44 100 100
PPP2R5D -0.015 0.037 0.35 6 -10000 0 6
MAPK1 0 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.25 0.23 -10000 0 -0.47 569 569
RBPJ 0 0 -10000 0 -10000 0 0
CREBBP 0.014 0.004 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.11 0.2 -10000 0 -0.47 263 263
MAPK9 0.008 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.001 0.022 -10000 0 -0.2 13 13
GNB1/GNG2 -0.006 0.057 -10000 0 -0.53 13 13
GNB1 0 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 -0.12 0.21 -10000 0 -0.49 259 259
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 0.027 0.048 0.11 259 -10000 0 259
GNAL -0.19 0.34 -10000 0 -0.79 259 259
GNG2 -0.009 0.086 -10000 0 -0.79 13 13
CRH -0.003 0.032 -10000 0 -0.29 13 13
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.005 0.039 -10000 0 -0.45 8 8
MAPK11 0.007 0.024 -10000 0 -0.45 3 3
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.007 0.054 -9999 0 -0.45 15 15
RGS9BP -0.019 0.073 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.003 0.029 -9999 0 -0.29 11 11
mol:Na + -0.02 0.053 -9999 0 -10000 0 0
mol:ADP 0.007 0.028 -9999 0 -10000 0 0
GNAT2 -0.001 0.018 -9999 0 -0.29 4 4
RGS9-1/Gbeta5/R9AP -0.062 0.16 -9999 0 -0.53 107 107
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.001 0.015 -9999 0 -10000 0 0
GRK7 -0.002 0.027 -9999 0 -0.29 9 9
CNGB3 -0.01 0.054 -9999 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin -0.001 0.017 -9999 0 -0.2 8 8
mol:Ca2+ -0.092 0.089 -9999 0 -10000 0 0
Cone PDE6 -0.054 0.14 -9999 0 -0.46 107 107
Cone Metarhodopsin II -0.003 0.019 -9999 0 -10000 0 0
Na + (4 Units) -0.098 0.082 -9999 0 -10000 0 0
GNAT2/GDP -0.053 0.14 -9999 0 -0.46 107 107
GNB5 0 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.011 0.016 -9999 0 -10000 0 0
Cone Transducin -0.008 0.057 -9999 0 -0.48 15 15
SLC24A2 -0.17 0.14 -9999 0 -0.29 649 649
GNB3/GNGT2 -0.009 0.071 -9999 0 -0.6 15 15
GNB3 -0.011 0.088 -9999 0 -0.63 19 19
GNAT2/GTP -0.001 0.012 -9999 0 -0.2 4 4
CNGA3 -0.028 0.086 -9999 0 -0.29 103 103
ARR3 -0.002 0.025 -9999 0 -0.29 8 8
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.021 0.053 -9999 0 -10000 0 0
mol:Pi -0.062 0.16 -9999 0 -0.53 107 107
Cone CNG Channel -0.016 0.04 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.17 0.14 -9999 0 -0.29 649 649
RGS9 -0.081 0.24 -9999 0 -0.73 122 122
PDE6C 0 0.009 -9999 0 -10000 0 0
GNGT2 -0.001 0.034 -9999 0 -0.79 2 2
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H -0.002 0.022 -9999 0 -0.29 6 6
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.54 0.37 -9999 0 -0.79 748 748
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 -0.007 0.045 -9999 0 -0.29 26 26
TCEB1 -0.001 0.013 -9999 0 -0.29 2 2
HIF1A/p53 -0.001 0.005 -9999 0 -10000 0 0
HIF1A -0.002 0.008 -9999 0 -10000 0 0
COPS5 0 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.003 0.016 -9999 0 -10000 0 0
FIH (dimer) 0 0 -9999 0 -10000 0 0
CDKN2A -0.052 0.11 -9999 0 -0.29 192 192
ARNT/IPAS -0.41 0.28 -9999 0 -0.6 748 748
HIF1AN 0 0 -9999 0 -10000 0 0
GNB2L1 0 0 -9999 0 -10000 0 0
HIF1A/ARNT -0.001 0.005 -9999 0 -10000 0 0
CUL2 0 0 -9999 0 -10000 0 0
OS9 -0.001 0.013 -9999 0 -0.29 2 2
RACK1/Elongin B/Elongin C -0.004 0.023 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.001 0.006 -9999 0 -10000 0 0
PHD1-3/OS9 -0.011 0.038 -9999 0 -0.47 2 2
HIF1A/RACK1/Elongin B/Elongin C -0.002 0.015 -9999 0 -10000 0 0
VHL 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0.009 -9999 0 -0.29 1 1
HIF1A/JAB1 -0.001 0.005 -9999 0 -10000 0 0
EGLN3 -0.022 0.08 -9999 0 -0.3 81 81
EGLN2 -0.002 0.022 -9999 0 -0.29 6 6
EGLN1 -0.001 0.024 -9999 0 -0.79 1 1
TP53 0 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A -0.001 0.005 -9999 0 -10000 0 0
ARNT 0 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.019 0.04 -9999 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.011 0.052 0.28 37 -10000 0 37
RFC1 0.011 0.052 0.28 39 -10000 0 39
PRKDC 0.01 0.053 0.28 37 -10000 0 37
RIPK1 0 0.001 -10000 0 -10000 0 0
CASP7 -0.023 0.037 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1 -0.017 0.067 0.25 14 -0.38 17 31
MAP2K4 -0.058 0.16 -10000 0 -0.47 24 24
mol:ceramide -0.032 0.12 -10000 0 -0.55 21 21
GSN 0.004 0.075 0.28 36 -0.49 13 49
FASLG/FAS/FADD/FAF1/Caspase 8 -0.03 0.072 0.23 14 -0.46 17 31
FAS 0.004 0.055 -10000 0 -0.8 5 5
BID 0.001 0.015 0.32 2 -10000 0 2
MAP3K1 -0.021 0.093 -10000 0 -0.3 11 11
MAP3K7 0.006 0.011 -10000 0 -0.29 1 1
RB1 0.01 0.055 0.28 36 -0.4 2 38
CFLAR 0 0.001 -10000 0 -10000 0 0
HGF/MET -0.14 0.26 -10000 0 -0.58 256 256
ARHGDIB 0.01 0.053 0.28 37 -10000 0 37
FADD 0.003 0.038 -10000 0 -0.31 16 16
actin filament polymerization -0.004 0.075 0.49 13 -0.28 36 49
NFKB1 -0.076 0.1 -10000 0 -0.3 13 13
MAPK8 -0.12 0.24 -10000 0 -0.43 402 402
DFFA 0.011 0.052 0.28 38 -10000 0 38
DNA fragmentation during apoptosis 0.011 0.052 0.28 37 -10000 0 37
FAS/FADD/MET -0.096 0.21 -10000 0 -0.54 190 190
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.002 0.056 -10000 0 -0.33 26 26
FAF1 0.008 0.006 -10000 0 -10000 0 0
PARP1 0.01 0.052 0.28 37 -10000 0 37
DFFB 0.011 0.052 0.28 37 -10000 0 37
CHUK -0.066 0.088 -10000 0 -10000 0 0
FASLG -0.015 0.11 -10000 0 -0.43 57 57
FAS/FADD -0.006 0.05 -10000 0 -0.65 5 5
HGF -0.053 0.2 -10000 0 -0.78 75 75
LMNA 0.01 0.048 0.26 37 -10000 0 37
CASP6 0.01 0.052 0.28 37 -10000 0 37
CASP10 0.005 0.049 -10000 0 -0.8 4 4
CASP3 0.013 0.063 0.34 39 -10000 0 39
PTPN13 -0.023 0.13 -10000 0 -0.79 32 32
CASP8 0.003 0.023 0.45 2 -10000 0 2
IL6 -0.47 0.67 -10000 0 -1.4 399 399
MET -0.14 0.3 -10000 0 -0.79 188 188
ICAD/CAD 0.01 0.048 0.26 37 -10000 0 37
FASLG/FAS/FADD/FAF1/Caspase 10 -0.032 0.12 -10000 0 -0.56 21 21
activation of caspase activity by cytochrome c 0.001 0.015 0.32 2 -10000 0 2
PAK2 0.01 0.052 0.28 37 -10000 0 37
BCL2 -0.022 0.14 -10000 0 -0.79 37 37
Glypican 2 network

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
MDK -0.011 0.056 -9999 0 -0.29 41 41
GPC2 -0.038 0.1 -9999 0 -0.3 136 136
GPC2/Midkine -0.031 0.08 -9999 0 -0.41 17 17
neuron projection morphogenesis -0.031 0.08 -9999 0 -0.41 17 17
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.009 0.054 -10000 0 -0.32 31 31
epithelial cell differentiation -0.012 0.072 -10000 0 -0.44 30 30
CYFIP2 -0.01 0.066 -10000 0 -0.36 31 31
ENAH 0.057 0.058 -10000 0 -10000 0 0
EGFR -0.3 0.38 -10000 0 -0.78 414 414
EPHA2 -0.004 0.058 -10000 0 -0.79 6 6
MYO6 -0.012 0.069 -10000 0 -0.42 31 31
CTNNB1 0 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.005 0.038 -10000 0 -0.52 4 4
AQP5 -0.23 0.29 -10000 0 -0.58 426 426
CTNND1 0 0.009 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.011 0.067 -10000 0 -0.41 30 30
regulation of calcium-dependent cell-cell adhesion -0.033 0.11 -10000 0 -0.42 86 86
EGF -0.16 0.31 -10000 0 -0.78 216 216
NCKAP1 0 0 -10000 0 -10000 0 0
AQP3 -0.038 0.14 -10000 0 -0.59 56 56
cortical microtubule organization -0.012 0.072 -10000 0 -0.44 30 30
GO:0000145 0.026 0.07 -10000 0 -0.39 30 30
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.012 0.073 -10000 0 -0.45 30 30
MLLT4 -0.005 0.059 -10000 0 -0.72 7 7
ARF6/GDP -0.012 0.061 -10000 0 -10000 0 0
ARF6 0 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.003 0.036 -10000 0 -0.47 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.036 0.074 -10000 0 -0.38 30 30
PVRL2 -0.001 0.015 -10000 0 -0.29 3 3
ZYX -0.012 0.068 -10000 0 -0.42 30 30
ARF6/GTP -0.003 0.033 -10000 0 -0.43 6 6
CDH1 -0.022 0.13 -10000 0 -0.79 30 30
EGFR/EGFR/EGF/EGF -0.24 0.26 -10000 0 -0.47 566 566
RhoA/GDP -0.011 0.067 -10000 0 -0.41 30 30
actin cytoskeleton organization 0.032 0.073 -10000 0 -0.39 31 31
IGF-1R heterotetramer -0.02 0.12 -10000 0 -0.79 22 22
GIT1 -0.001 0.02 -10000 0 -0.29 5 5
IGF1R -0.02 0.12 -10000 0 -0.79 22 22
IGF1 -0.18 0.33 -10000 0 -0.79 246 246
DIAPH1 -0.002 0.043 -10000 0 -0.69 4 4
Wnt receptor signaling pathway 0.012 0.072 0.44 30 -10000 0 30
RHOA 0 0 -10000 0 -10000 0 0
RhoA/GTP -0.012 0.061 -10000 0 -10000 0 0
CTNNA1 0 0 -10000 0 -10000 0 0
VCL 0.033 0.074 -10000 0 -0.4 30 30
EFNA1 0 0.009 -10000 0 -0.29 1 1
LPP 0.03 0.081 -10000 0 -0.39 38 38
Ephrin A1/EPHA2 -0.013 0.071 -10000 0 -0.4 36 36
SEC6/SEC8 -0.012 0.067 -10000 0 -0.75 1 1
MGAT3 -0.034 0.11 -10000 0 -0.42 86 86
HGF/MET -0.11 0.2 -10000 0 -0.45 264 264
HGF -0.053 0.2 -10000 0 -0.78 75 75
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.009 0.054 -10000 0 -0.33 31 31
actin cable formation 0.072 0.057 -10000 0 -0.32 1 1
KIAA1543 0.031 0.089 -10000 0 -0.46 31 31
KIFC3 -0.012 0.07 -10000 0 -0.42 32 32
NCK1 0 0 -10000 0 -10000 0 0
EXOC3 0 0 -10000 0 -10000 0 0
ACTN1 -0.012 0.069 -10000 0 -0.42 31 31
NCK1/GIT1 -0.001 0.013 -10000 0 -10000 0 0
mol:GDP -0.012 0.072 -10000 0 -0.44 30 30
EXOC4 0 0 -10000 0 -10000 0 0
STX4 -0.012 0.068 -10000 0 -0.42 30 30
PIP5K1C -0.012 0.068 -10000 0 -0.42 30 30
LIMA1 -0.001 0.024 -10000 0 -0.79 1 1
ABI1 0 0 -10000 0 -10000 0 0
ROCK1 -0.01 0.054 -10000 0 -10000 0 0
adherens junction assembly 0.047 0.085 -10000 0 -0.66 6 6
IGF-1R heterotetramer/IGF1 -0.11 0.2 -10000 0 -0.43 280 280
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.004 0.046 -10000 0 -0.6 6 6
MET -0.14 0.3 -10000 0 -0.79 188 188
PLEKHA7 -0.013 0.078 -10000 0 -0.46 30 30
mol:GTP -0.003 0.036 -10000 0 -0.47 6 6
establishment of epithelial cell apical/basal polarity -0.012 0.063 -10000 0 -0.7 1 1
cortical actin cytoskeleton stabilization -0.009 0.054 -10000 0 -0.32 31 31
regulation of cell-cell adhesion 0.032 0.073 -10000 0 -0.39 31 31
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.009 0.054 -10000 0 -0.33 31 31
Signaling events mediated by HDAC Class III

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
EP300 0 0 -10000 0 -10000 0 0
HDAC4 -0.001 0.024 -10000 0 -0.79 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.012 0.077 0.6 1 -10000 0 1
CDKN1A -0.002 0.04 -10000 0 -0.94 2 2
KAT2B -0.001 0.024 -10000 0 -0.79 1 1
BAX -0.001 0.02 -10000 0 -0.29 5 5
FOXO3 -0.001 0.017 -10000 0 -0.33 3 3
FOXO1 -0.008 0.079 -10000 0 -0.79 11 11
FOXO4 0.022 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0 0 -10000 0 -10000 0 0
TAT -0.56 0.36 -10000 0 -0.77 787 787
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.01 0.029 -10000 0 -0.6 1 1
PPARGC1A -0.17 0.32 -10000 0 -0.77 240 240
FHL2 -0.005 0.059 -10000 0 -0.72 7 7
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0 0.007 -10000 0 -10000 0 0
HIST2H4A -0.012 0.077 -10000 0 -0.6 1 1
SIRT1/FOXO3a 0 0.014 -10000 0 -0.25 3 3
SIRT1 0 0.009 0.21 2 -10000 0 2
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0 0.017 -10000 0 -0.52 1 1
SIRT1/Histone H1b -0.003 0.012 -10000 0 -10000 0 0
apoptosis 0 0.012 -10000 0 -10000 0 0
SIRT1/PGC1A -0.11 0.21 -10000 0 -0.53 229 229
p53/SIRT1 0.001 0.019 0.43 2 -10000 0 2
SIRT1/FOXO4 0 0.007 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.007 0.06 -10000 0 -0.48 17 17
HIST1H1E 0.014 0.022 -10000 0 -10000 0 0
SIRT1/p300 0 0.007 -10000 0 -10000 0 0
muscle cell differentiation 0.002 0.023 0.52 1 -10000 0 1
TP53 0 0.009 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0 0.012 -10000 0 -10000 0 0
CREBBP 0 0 -10000 0 -10000 0 0
MEF2D 0 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.42 0.27 -10000 0 -0.6 759 759
ACSS2 0.02 0.02 -10000 0 -0.6 1 1
SIRT1/PCAF/MYOD -0.002 0.024 -10000 0 -0.52 1 1
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.053 0.2 -10000 0 -0.78 74 74
HRAS -0.002 0.027 -10000 0 -0.29 9 9
EGFR -0.3 0.38 -10000 0 -0.78 414 414
AKT 0.013 0.081 -10000 0 -0.56 19 19
FOXO3 -0.002 0.041 -10000 0 -0.79 3 3
AKT1 0 0 -10000 0 -10000 0 0
FOXO1 -0.008 0.079 -10000 0 -0.79 11 11
AKT3 -0.014 0.1 -10000 0 -0.79 19 19
FOXO4 0 0 -10000 0 -10000 0 0
MET -0.14 0.3 -10000 0 -0.79 188 188
PIK3CA 0 0.009 -10000 0 -0.29 1 1
PIK3CB 0 0 -10000 0 -10000 0 0
NRAS -0.001 0.013 -10000 0 -0.29 2 2
PIK3CG -0.013 0.096 -10000 0 -0.69 20 20
PIK3R3 0 0.009 -10000 0 -0.29 1 1
PIK3R2 0 0 -10000 0 -10000 0 0
NF1 -0.001 0.024 -10000 0 -0.79 1 1
RAS -0.097 0.16 0.26 1 -0.37 213 214
ERBB2 -0.024 0.083 -10000 0 -0.3 89 89
proliferation/survival/translation -0.004 0.058 0.26 13 -10000 0 13
PI3K -0.088 0.16 -10000 0 -0.36 220 220
PIK3R1 -0.009 0.086 -10000 0 -0.79 13 13
KRAS -0.001 0.013 -10000 0 -0.29 2 2
FOXO 0.026 0.029 -10000 0 -0.49 1 1
AKT2 0 0 -10000 0 -10000 0 0
PTEN -0.001 0.034 -10000 0 -0.79 2 2
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.009 0.052 -10000 0 -0.42 13 13
adherens junction organization 0.031 0.064 -10000 0 -0.3 31 31
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.14 0.18 -10000 0 -0.58 24 24
FMN1 0.022 0.093 -10000 0 -0.45 26 26
mol:IP3 -0.009 0.049 -10000 0 -0.39 13 13
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.01 0.053 -10000 0 -0.31 31 31
CTNNB1 0.001 0.004 -10000 0 -10000 0 0
AKT1 -0.01 0.051 -10000 0 -0.38 13 13
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.014 0.082 -10000 0 -0.5 30 30
CTNND1 0.011 0.009 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.033 0.057 -10000 0 -10000 0 0
VASP 0.033 0.058 -10000 0 -10000 0 0
ZYX 0.033 0.058 -10000 0 -10000 0 0
JUB 0.031 0.064 -10000 0 -0.3 35 35
EGFR(dimer) -0.16 0.21 -10000 0 -0.43 410 410
E-cadherin/beta catenin-gamma catenin -0.014 0.084 -10000 0 -0.5 31 31
mol:PI-3-4-5-P3 -0.011 0.055 -10000 0 -0.4 13 13
PIK3CA 0.011 0.009 -10000 0 -0.29 1 1
PI3K -0.011 0.056 -10000 0 -0.41 13 13
FYN 0.04 0.055 -10000 0 -0.38 2 2
mol:Ca2+ -0.009 0.048 -10000 0 -0.38 13 13
JUP 0 0.026 -10000 0 -0.54 2 2
PIK3R1 0.002 0.087 -10000 0 -0.79 13 13
mol:DAG -0.009 0.049 -10000 0 -0.39 13 13
CDH1 -0.022 0.13 -10000 0 -0.79 30 30
RhoA/GDP -0.14 0.18 -10000 0 -0.58 24 24
establishment of polarity of embryonic epithelium 0.033 0.057 -10000 0 -10000 0 0
SRC 0 0.009 -10000 0 -0.29 1 1
RAC1 0 0 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
EGFR -0.3 0.38 -10000 0 -0.78 414 414
CASR 0.033 0.055 -10000 0 -0.36 13 13
RhoA/GTP -0.008 0.044 -10000 0 -0.34 13 13
AKT2 -0.01 0.051 -10000 0 -0.38 13 13
actin cable formation 0.03 0.09 -10000 0 -0.43 25 25
apoptosis 0.01 0.052 0.4 13 -10000 0 13
CTNNA1 0.012 0.002 -10000 0 -10000 0 0
mol:GDP -0.16 0.2 -10000 0 -0.4 416 416
PIP5K1A 0.033 0.058 -10000 0 -10000 0 0
PLCG1 -0.009 0.051 -10000 0 -0.4 13 13
Rac1/GTP -0.15 0.19 -10000 0 -0.39 410 410
homophilic cell adhesion 0.001 0.002 -10000 0 -10000 0 0
LPA4-mediated signaling events

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
ADCY4 0 0.1 -9999 0 -0.53 40 40
ADCY5 -0.16 0.26 -9999 0 -0.53 351 351
ADCY6 0.02 0 -9999 0 -10000 0 0
ADCY7 0.02 0 -9999 0 -10000 0 0
ADCY1 -0.008 0.098 -9999 0 -0.53 29 29
ADCY2 -0.032 0.15 -9999 0 -0.53 90 90
ADCY3 0.02 0.005 -9999 0 -10000 0 0
ADCY8 0.01 0.028 -9999 0 -10000 0 0
PRKCE 0.011 0 -9999 0 -10000 0 0
ADCY9 0.02 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.031 0.1 -9999 0 -0.31 74 74
Effects of Botulinum toxin

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
STX1A 0.003 0.041 -9999 0 -0.2 43 43
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.047 0.13 -9999 0 -0.6 47 47
STXBP1 -0.005 0.063 -9999 0 -0.79 7 7
ACh/CHRNA1 -0.063 0.082 -9999 0 -0.23 26 26
RAB3GAP2/RIMS1/UNC13B -0.038 0.11 -9999 0 -0.52 47 47
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 -0.067 0.18 -9999 0 -0.43 170 170
mol:ACh 0.001 0.031 -9999 0 -0.15 35 35
RAB3GAP2 0 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.038 0.093 -9999 0 -0.39 54 54
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.062 0.082 -9999 0 -0.23 26 26
UNC13B 0 0 -9999 0 -10000 0 0
CHRNA1 -0.1 0.14 -9999 0 -0.29 372 372
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.059 0.12 -9999 0 -0.48 60 60
SNAP25 -0.016 0.067 -9999 0 -0.37 35 35
VAMP2 0 0 -9999 0 -10000 0 0
SYT1 -0.088 0.18 -9999 0 -0.38 253 253
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.009 0.051 -9999 0 -0.53 7 7
STX1A/SNAP25 fragment 1/VAMP2 -0.038 0.093 -9999 0 -0.39 54 54
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.001 0.017 -10000 0 -0.29 3 3
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.035 0.13 0.44 34 -10000 0 34
IL27/IL27R/JAK1 -0.074 0.19 -10000 0 -0.62 61 61
TBX21 -0.043 0.21 -10000 0 -0.59 85 85
IL12B -0.056 0.12 -10000 0 -0.29 230 230
IL12A -0.028 0.14 -10000 0 -0.52 79 79
IL6ST -0.091 0.27 -10000 0 -0.8 136 136
IL27RA/JAK1 -0.008 0.073 -10000 0 -1.1 4 4
IL27 -0.025 0.095 -10000 0 -0.3 120 120
TYK2 0.01 0.006 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.12 0.18 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.035 0.13 0.44 34 -10000 0 34
T cell proliferation during immune response 0.035 0.13 0.44 34 -10000 0 34
MAPKKK cascade -0.035 0.13 -10000 0 -0.44 34 34
STAT3 0 0 -10000 0 -10000 0 0
STAT2 0 0 -10000 0 -10000 0 0
STAT1 -0.004 0.039 -10000 0 -0.3 19 19
IL12RB1 -0.005 0.067 -10000 0 -0.32 43 43
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.059 0.23 -10000 0 -0.62 100 100
IL27/IL27R/JAK2/TYK2 -0.035 0.13 -10000 0 -0.45 33 33
positive regulation of T cell mediated cytotoxicity -0.035 0.13 -10000 0 -0.44 34 34
STAT1 (dimer) -0.093 0.22 0.46 21 -0.72 62 83
JAK2 0.005 0.025 -10000 0 -0.79 1 1
JAK1 0 0.024 -10000 0 -0.79 1 1
STAT2 (dimer) -0.044 0.11 -10000 0 -0.45 23 23
T cell proliferation -0.18 0.25 -10000 0 -0.46 415 415
IL12/IL12R/TYK2/JAK2 0.011 0.07 -10000 0 -10000 0 0
IL17A -0.12 0.18 -10000 0 -10000 0 0
mast cell activation 0.035 0.13 0.44 34 -10000 0 34
IFNG -0.001 0.025 -10000 0 -0.077 11 11
T cell differentiation -0.004 0.006 -10000 0 -0.019 23 23
STAT3 (dimer) -0.044 0.11 -10000 0 -0.46 22 22
STAT5A (dimer) -0.048 0.12 -10000 0 -0.47 31 31
STAT4 (dimer) -0.062 0.14 -10000 0 -0.49 67 67
STAT4 -0.032 0.16 -10000 0 -0.78 45 45
T cell activation -0.009 0.009 0.13 3 -10000 0 3
IL27R/JAK2/TYK2 -0.062 0.17 -10000 0 -0.61 30 30
GATA3 -0.039 0.28 -10000 0 -1.4 40 40
IL18 0.007 0.031 -10000 0 -10000 0 0
positive regulation of mast cell cytokine production -0.044 0.11 -10000 0 -0.45 23 23
IL27/EBI3 -0.026 0.083 -10000 0 -0.53 13 13
IL27RA -0.001 0.079 -10000 0 -1.4 3 3
IL6 -0.29 0.38 -10000 0 -0.79 399 399
STAT5A -0.006 0.067 -10000 0 -0.79 8 8
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 0.004 0.03 0.48 3 -10000 0 3
IL1B 0.001 0.076 -10000 0 -0.53 20 20
EBI3 -0.004 0.075 -10000 0 -0.5 20 20
TNF -0.001 0.074 -10000 0 -0.61 13 13
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.035 0.12 -10000 0 -0.58 41 41
FYN 0.016 0.18 -10000 0 -0.7 48 48
LAT/GRAP2/SLP76 -0.029 0.14 -10000 0 -0.62 47 47
IKBKB -0.001 0.013 -10000 0 -0.29 2 2
AKT1 0.03 0.12 -10000 0 -0.45 48 48
B2M 0.011 0.004 -10000 0 -10000 0 0
IKBKG -0.008 0.026 -10000 0 -0.14 14 14
MAP3K8 -0.007 0.072 -10000 0 -0.74 10 10
mol:Ca2+ -0.024 0.047 -10000 0 -0.12 213 213
integrin-mediated signaling pathway -0.002 0.028 -10000 0 -0.52 3 3
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.021 0.17 -10000 0 -0.67 50 50
TRPV6 -0.16 0.32 -10000 0 -0.77 226 226
CD28 0.002 0.074 -10000 0 -0.53 17 17
SHC1 0.011 0.18 -10000 0 -0.72 48 48
receptor internalization -0.001 0.2 -10000 0 -0.62 75 75
PRF1 0 0.22 -10000 0 -1.1 36 36
KRAS -0.001 0.013 -10000 0 -0.29 2 2
GRB2 0 0.009 -10000 0 -0.29 1 1
COT/AKT1 0.031 0.1 -10000 0 -0.37 49 49
LAT 0.009 0.18 -10000 0 -0.71 51 51
EntrezGene:6955 0.001 0.003 -10000 0 -10000 0 0
CD3D -0.023 0.14 -10000 0 -0.48 77 77
CD3E -0.017 0.13 -10000 0 -0.5 62 62
CD3G -0.032 0.17 -10000 0 -0.56 83 83
RASGRP2 0.003 0.041 -10000 0 -0.18 45 45
RASGRP1 0.036 0.12 -10000 0 -0.46 47 47
HLA-A 0.009 0.031 -10000 0 -0.29 11 11
RASSF5 -0.002 0.042 -10000 0 -0.66 4 4
RAP1A/GTP/RAPL -0.002 0.028 -10000 0 -0.53 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.033 0.043 -10000 0 -0.12 40 40
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.014 0.047 -10000 0 -0.23 35 35
PRKCA -0.013 0.084 -10000 0 -0.31 59 59
GRAP2 -0.014 0.1 -10000 0 -0.72 22 22
mol:IP3 0.019 0.15 0.27 183 -0.44 44 227
EntrezGene:6957 0.001 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.006 0.2 -10000 0 -0.81 47 47
ORAI1 0.078 0.15 0.38 212 -10000 0 212
CSK 0.009 0.18 -10000 0 -0.65 59 59
B7 family/CD28 -0.027 0.18 -10000 0 -0.65 61 61
CHUK 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.002 0.22 -10000 0 -0.73 65 65
PTPN6 0.008 0.18 -10000 0 -0.65 59 59
VAV1 0.01 0.18 -10000 0 -0.63 64 64
Monovalent TCR/CD3 -0.024 0.2 -10000 0 -0.66 72 72
CBL 0 0 -10000 0 -10000 0 0
LCK 0.01 0.19 -10000 0 -0.67 60 60
PAG1 0.008 0.18 -10000 0 -0.66 59 59
RAP1A 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.001 0.21 -10000 0 -0.73 63 63
CD80 -0.069 0.13 -10000 0 -0.29 285 285
CD86 0.008 0.023 -10000 0 -0.3 6 6
PDK1/CARD11/BCL10/MALT1 -0.018 0.058 -10000 0 -0.27 37 37
HRAS -0.002 0.027 -10000 0 -0.29 9 9
GO:0035030 -0.001 0.15 -10000 0 -0.53 61 61
CD8A 0 0.074 -10000 0 -0.37 34 34
CD8B -0.021 0.15 -10000 0 -0.55 66 66
PTPRC -0.001 0.075 -10000 0 -0.5 19 19
PDK1/PKC theta 0.033 0.15 -10000 0 -0.57 51 51
CSK/PAG1 0.014 0.18 -10000 0 -0.73 45 45
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I -0.002 0.018 -10000 0 -10000 0 0
GRAP2/SLP76 -0.035 0.17 -10000 0 -0.7 51 51
STIM1 0.041 0.078 -10000 0 -10000 0 0
RAS family/GTP 0.041 0.054 -10000 0 -0.17 34 34
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.005 0.22 -10000 0 -0.68 75 75
mol:DAG -0.008 0.1 -10000 0 -0.4 44 44
RAP1A/GDP 0.015 0.018 -10000 0 -10000 0 0
PLCG1 0.001 0.003 -10000 0 -10000 0 0
CD247 -0.008 0.12 -10000 0 -0.58 37 37
cytotoxic T cell degranulation 0.002 0.21 -10000 0 -0.95 39 39
RAP1A/GTP -0.003 0.013 -10000 0 -0.067 33 33
mol:PI-3-4-5-P3 0.026 0.14 -10000 0 -0.53 50 50
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.012 0.18 0.29 171 -0.6 44 215
NRAS -0.001 0.013 -10000 0 -0.29 2 2
ZAP70 -0.031 0.12 -10000 0 -0.79 20 20
GRB2/SOS1 0 0.006 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.026 0.14 -10000 0 -0.6 47 47
MALT1 0 0 -10000 0 -10000 0 0
TRAF6 0 0 -10000 0 -10000 0 0
CD8 heterodimer -0.031 0.13 -10000 0 -0.57 53 53
CARD11 -0.007 0.051 -10000 0 -0.34 21 21
PRKCB -0.012 0.085 -10000 0 -0.32 54 54
PRKCE -0.006 0.069 -10000 0 -0.28 38 38
PRKCQ 0.024 0.18 -10000 0 -0.65 53 53
LCP2 0 0.009 -10000 0 -0.29 1 1
BCL10 0 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.032 0.1 -10000 0 -0.37 48 48
IKK complex 0.041 0.045 -10000 0 -0.12 29 29
RAS family/GDP -0.002 0.006 -10000 0 -10000 0 0
MAP3K14 0.036 0.081 -10000 0 -0.29 39 39
PDPK1 0.033 0.12 -10000 0 -0.43 45 45
TCR/CD3/MHC I/CD8/Fyn -0.005 0.23 -10000 0 -0.9 52 52
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.004 0.018 -10000 0 -10000 0 0
AES 0.004 0.015 -10000 0 -10000 0 0
FBXW11 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0 0.006 -10000 0 -10000 0 0
SMAD4 -0.001 0.024 -10000 0 -0.79 1 1
DKK2 -0.024 0.13 -10000 0 -0.76 34 34
TLE1 -0.002 0.069 -10000 0 -0.79 8 8
MACF1 0.007 0.006 -10000 0 -10000 0 0
CTNNB1 0.1 0.087 -10000 0 -10000 0 0
WIF1 -0.42 0.39 -10000 0 -0.78 583 583
beta catenin/RanBP3 0.014 0.078 0.38 43 -10000 0 43
KREMEN2 -0.14 0.15 -10000 0 -0.29 525 525
DKK1 -0.081 0.19 -10000 0 -0.42 207 207
beta catenin/beta TrCP1 0.1 0.083 -10000 0 -10000 0 0
FZD1 0 0.002 -10000 0 -10000 0 0
AXIN2 -0.014 0.21 -10000 0 -1.6 20 20
AXIN1 0.007 0.006 -10000 0 -10000 0 0
RAN 0.001 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.007 0.024 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.093 0.077 0.3 1 -0.49 6 7
Axin1/APC/GSK3 0.001 0.014 0.24 1 -10000 0 1
Axin1/APC/GSK3/beta catenin/Macf1 0.077 0.033 -10000 0 -10000 0 0
HNF1A 0.002 0.029 -10000 0 -0.29 7 7
CTBP1 0.004 0.016 -10000 0 -10000 0 0
MYC -0.019 0.23 -10000 0 -1.5 25 25
RANBP3 0.001 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.084 0.12 -10000 0 -0.61 32 32
NKD1 -0.009 0.069 -10000 0 -0.79 6 6
TCF4 -0.004 0.08 -10000 0 -0.78 11 11
TCF3 0.004 0.017 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0 0.006 -10000 0 -10000 0 0
Ran/GTP 0 0.001 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.014 0.099 0.45 45 -0.42 1 46
LEF1 -0.033 0.1 -10000 0 -0.3 132 132
DVL1 0.072 0.065 -10000 0 -10000 0 0
CSNK2A1 0 0.002 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.099 0.089 -10000 0 -0.58 5 5
DKK1/LRP6/Kremen 2 -0.12 0.14 -10000 0 -0.57 56 56
LRP6 0 0.009 -10000 0 -0.29 1 1
CSNK1A1 0.004 0.018 -10000 0 -10000 0 0
NLK 0.011 0.014 -10000 0 -0.3 2 2
CCND1 0.001 0.11 -10000 0 -1.6 4 4
WNT1 0.005 0.014 -10000 0 -0.29 2 2
GSK3A 0.009 0.006 -10000 0 -10000 0 0
GSK3B 0 0.001 -10000 0 -10000 0 0
FRAT1 0 0 -10000 0 -10000 0 0
PPP2R5D 0.044 0.045 0.36 6 -10000 0 6
APC 0.001 0.009 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.14 0.13 0.27 569 -10000 0 569
CREBBP 0.004 0.016 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.003 0.036 -9999 0 -10000 0 0
Syndecan-4/Syndesmos -0.025 0.037 -9999 0 -0.63 1 1
positive regulation of JNK cascade -0.051 0.1 -9999 0 -0.46 7 7
Syndecan-4/ADAM12 -0.033 0.055 -9999 0 -0.54 2 2
CCL5 -0.015 0.079 -9999 0 -0.36 44 44
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0 0 -9999 0 -10000 0 0
ITGA5 0 0.009 -9999 0 -0.29 1 1
SDCBP 0 0 -9999 0 -10000 0 0
PLG -0.001 0.026 -9999 0 -0.29 8 8
ADAM12 -0.019 0.077 -9999 0 -0.31 68 68
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 -0.001 0.02 -9999 0 -0.29 5 5
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.054 0.044 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.072 0.13 -9999 0 -0.46 62 62
Syndecan-4/CXCL12/CXCR4 -0.053 0.11 -9999 0 -0.48 7 7
Syndecan-4/Laminin alpha3 -0.13 0.19 -9999 0 -0.48 204 204
MDK -0.011 0.056 -9999 0 -0.29 41 41
Syndecan-4/FZD7 -0.033 0.068 -9999 0 -0.46 14 14
Syndecan-4/Midkine -0.028 0.042 -9999 0 -0.63 1 1
FZD7 -0.016 0.11 -9999 0 -0.79 22 22
Syndecan-4/FGFR1/FGF -0.19 0.21 -9999 0 -0.48 167 167
THBS1 -0.004 0.053 -9999 0 -0.79 5 5
integrin-mediated signaling pathway -0.035 0.072 -9999 0 -0.47 14 14
positive regulation of MAPKKK cascade -0.051 0.1 -9999 0 -0.46 7 7
Syndecan-4/TACI -0.036 0.067 -9999 0 -0.5 7 7
CXCR4 -0.007 0.045 -9999 0 -10000 0 0
cell adhesion -0.02 0.061 -9999 0 -0.34 28 28
Syndecan-4/Dynamin -0.024 0.036 -9999 0 -0.63 1 1
Syndecan-4/TSP1 -0.026 0.046 -9999 0 -0.48 5 5
Syndecan-4/GIPC -0.024 0.037 -9999 0 -0.63 1 1
Syndecan-4/RANTES -0.031 0.053 -9999 0 -0.5 5 5
ITGB1 0 0 -9999 0 -10000 0 0
LAMA1 -0.09 0.25 -9999 0 -0.77 127 127
LAMA3 -0.2 0.34 -9999 0 -0.79 276 276
RAC1 0 0 -9999 0 -10000 0 0
PRKCA 0.004 0.12 -9999 0 -0.73 29 29
Syndecan-4/alpha-Actinin -0.025 0.039 -9999 0 -0.54 2 2
TFPI -0.039 0.17 -9999 0 -0.79 54 54
F2 0 0.034 -9999 0 -0.29 14 14
alpha5/beta1 Integrin 0 0.006 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.16 0.23 -9999 0 -0.55 154 154
ACTN1 -0.001 0.024 -9999 0 -0.79 1 1
TNC -0.022 0.12 -9999 0 -0.79 26 26
Syndecan-4/CXCL12 -0.056 0.11 -9999 0 -0.46 40 40
FGF6 -0.001 0.034 -9999 0 -0.79 2 2
RHOA 0 0 -9999 0 -10000 0 0
CXCL12 -0.061 0.21 -9999 0 -0.79 84 84
TNFRSF13B -0.028 0.11 -9999 0 -0.39 77 77
FGF2 -0.32 0.39 -9999 0 -0.79 444 444
FGFR1 -0.009 0.08 -9999 0 -0.68 14 14
Syndecan-4/PI-4-5-P2 -0.018 0.048 -9999 0 -0.64 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.11 0.15 -9999 0 -0.3 432 432
cell migration -0.024 0.019 -9999 0 -10000 0 0
PRKCD 0.005 0.014 -9999 0 -0.29 1 1
vasculogenesis -0.026 0.044 -9999 0 -0.46 5 5
SDC4 -0.019 0.051 -9999 0 -0.68 1 1
Syndecan-4/Tenascin C -0.036 0.076 -9999 0 -0.52 8 8
Syndecan-4/PI-4-5-P2/PKC alpha -0.043 0.035 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.024 0.036 -9999 0 -0.63 1 1
MMP9 -0.12 0.15 -9999 0 -0.29 484 484
Rac1/GTP -0.028 0.057 -9999 0 -0.34 28 28
cytoskeleton organization -0.025 0.035 -9999 0 -0.6 1 1
GIPC1 -0.001 0.015 -9999 0 -0.29 3 3
Syndecan-4/TFPI -0.045 0.097 -9999 0 -0.48 22 22
IL12-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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.005 0.13 -10000 0 -0.4 55 55
TBX21 -0.014 0.34 -10000 0 -1.2 60 60
B2M 0.011 0.005 -10000 0 -10000 0 0
TYK2 0.017 0.015 -10000 0 -10000 0 0
IL12RB1 0.004 0.072 -10000 0 -0.33 38 38
GADD45B 0.031 0.22 -10000 0 -0.83 32 32
IL12RB2 -0.057 0.19 -10000 0 -0.43 185 185
GADD45G 0.02 0.22 -10000 0 -0.81 36 36
natural killer cell activation 0.007 0.018 -10000 0 -10000 0 0
RELB -0.003 0.028 -10000 0 -0.29 10 10
RELA 0 0 -10000 0 -10000 0 0
IL18 0.008 0.045 -10000 0 -0.29 24 24
IL2RA -0.031 0.12 -10000 0 -0.38 87 87
IFNG -0.04 0.1 -10000 0 -0.29 150 150
STAT3 (dimer) 0.023 0.22 -10000 0 -0.64 61 61
HLA-DRB5 -0.018 0.096 -10000 0 -0.33 85 85
FASLG 0.001 0.29 -10000 0 -1.1 49 49
NF kappa B2 p52/RelB -0.08 0.2 -10000 0 -0.73 69 69
CD4 0.009 0.006 -10000 0 -10000 0 0
SOCS1 -0.005 0.043 -10000 0 -0.32 18 18
EntrezGene:6955 -0.006 0.014 -10000 0 -10000 0 0
CD3D -0.026 0.14 -10000 0 -0.49 77 77
CD3E -0.02 0.13 -10000 0 -0.5 62 62
CD3G -0.035 0.17 -10000 0 -0.57 83 83
IL12Rbeta2/JAK2 -0.026 0.15 -10000 0 -0.59 55 55
CCL3 0.011 0.26 -10000 0 -0.98 40 40
CCL4 0.013 0.26 -10000 0 -0.92 42 42
HLA-A 0.008 0.032 -10000 0 -0.3 11 11
IL18/IL18R 0.021 0.14 -10000 0 -0.54 55 55
NOS2 0.017 0.25 -10000 0 -0.9 44 44
IL12/IL12R/TYK2/JAK2/SPHK2 -0.004 0.13 -10000 0 -0.39 60 60
IL1R1 -0.002 0.31 -10000 0 -1.2 50 50
IL4 -0.005 0.018 -10000 0 -10000 0 0
JAK2 0.016 0.03 -10000 0 -0.82 1 1
EntrezGene:6957 -0.005 0.013 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.032 0.25 -10000 0 -1 50 50
RAB7A 0.045 0.2 -10000 0 -0.74 25 25
lysosomal transport 0.046 0.19 -10000 0 -0.7 25 25
FOS -0.35 0.66 -10000 0 -1.3 336 336
STAT4 (dimer) 0.019 0.26 -10000 0 -0.86 57 57
STAT5A (dimer) -0.087 0.22 -10000 0 -0.7 83 83
GZMA 0.002 0.28 -10000 0 -0.99 49 49
GZMB -0.013 0.31 -10000 0 -1.1 55 55
HLX -0.001 0.015 -10000 0 -0.29 3 3
LCK 0.002 0.29 -10000 0 -0.82 76 76
TCR/CD3/MHC II/CD4 -0.065 0.19 -10000 0 -0.53 93 93
IL2/IL2R -0.031 0.1 -10000 0 -0.48 41 41
MAPK14 0.034 0.22 -10000 0 -0.78 43 43
CCR5 0.024 0.22 -10000 0 -0.87 32 32
IL1B 0.004 0.1 -10000 0 -0.7 20 20
STAT6 0.025 0.087 -10000 0 -0.25 13 13
STAT4 -0.032 0.16 -10000 0 -0.78 45 45
STAT3 0 0 -10000 0 -10000 0 0
STAT1 -0.005 0.038 -10000 0 -0.29 19 19
NFKB1 0 0 -10000 0 -10000 0 0
NFKB2 0 0.009 -10000 0 -0.29 1 1
IL12B -0.048 0.12 -10000 0 -0.29 230 230
CD8A 0 0.074 -10000 0 -0.37 34 34
CD8B -0.022 0.15 -10000 0 -0.55 66 66
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.005 0.13 0.39 55 -10000 0 55
IL2RB -0.012 0.064 -10000 0 -0.32 42 42
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.24 -10000 0 -0.77 57 57
IL2RG -0.017 0.086 -10000 0 -0.36 53 53
IL12 -0.054 0.16 -10000 0 -0.59 68 68
STAT5A -0.006 0.067 -10000 0 -0.79 8 8
CD247 -0.011 0.12 -10000 0 -0.58 37 37
IL2 -0.002 0.025 -10000 0 -0.29 8 8
SPHK2 0 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.034 0.19 -10000 0 -0.68 79 79
IL12/IL12R/TYK2/JAK2 0.006 0.29 -10000 0 -0.82 74 74
MAP2K3 0.03 0.22 -10000 0 -0.79 41 41
RIPK2 -0.001 0.02 -10000 0 -0.29 5 5
MAP2K6 0.025 0.23 -10000 0 -0.77 48 48
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.008 0.026 -10000 0 -0.54 2 2
IL18RAP -0.015 0.15 -10000 0 -0.73 43 43
IL12Rbeta1/TYK2 0.014 0.056 -10000 0 -0.64 2 2
EOMES -0.024 0.18 -10000 0 -1.5 17 17
STAT1 (dimer) 0.026 0.22 -10000 0 -0.66 51 51
T cell proliferation 0.031 0.2 -10000 0 -0.62 55 55
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0 0.11 -10000 0 -0.79 19 19
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.063 0.17 -10000 0 -0.75 45 45
ATF2 0.041 0.21 -10000 0 -0.72 42 42
Coregulation of Androgen receptor activity

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
NRIP1 -0.002 0.032 -10000 0 -0.79 1 1
SVIL -0.005 0.057 -10000 0 -0.79 5 5
ZNF318 0.022 0.057 -10000 0 -10000 0 0
JMJD2C -0.003 0.041 -10000 0 -0.12 106 106
T-DHT/AR/Ubc9 -0.082 0.18 -10000 0 -0.54 146 146
CARM1 0 0 -10000 0 -10000 0 0
PRDX1 0.003 0.012 -10000 0 -0.29 1 1
PELP1 0.005 0.012 -10000 0 -10000 0 0
CTNNB1 0.001 0.015 -10000 0 -10000 0 0
AKT1 0.007 0.018 -10000 0 -10000 0 0
PTK2B 0.001 0.013 -10000 0 -10000 0 0
MED1 0.002 0.047 -10000 0 -0.29 20 20
MAK 0.012 0.1 0.26 1 -0.55 20 21
response to oxidative stress 0.001 0.004 -10000 0 -10000 0 0
HIP1 -0.005 0.061 -10000 0 -0.79 6 6
GSN -0.011 0.088 -10000 0 -0.79 13 13
NCOA2 -0.038 0.17 -10000 0 -0.79 53 53
NCOA6 -0.001 0.02 -10000 0 -0.29 1 1
DNA-PK 0.022 0.058 -10000 0 -10000 0 0
NCOA4 0 0 -10000 0 -10000 0 0
PIAS3 0.001 0.015 -10000 0 -10000 0 0
cell proliferation -0.008 0.11 -10000 0 -0.88 11 11
XRCC5 0.006 0.015 -10000 0 -10000 0 0
UBE3A -0.005 0.031 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.095 0.21 -10000 0 -0.58 162 162
FHL2 -0.019 0.12 -10000 0 -1.2 6 6
RANBP9 0 0.018 -10000 0 -10000 0 0
JMJD1A -0.01 0.055 -10000 0 -0.14 151 151
CDK6 -0.008 0.09 -10000 0 -0.73 16 16
TGFB1I1 -0.003 0.046 -10000 0 -0.79 3 3
T-DHT/AR/CyclinD1 -0.094 0.19 -10000 0 -0.54 154 154
XRCC6 0.006 0.015 -10000 0 -10000 0 0
T-DHT/AR -0.067 0.21 -10000 0 -0.53 162 162
CTDSP1 0.004 0.005 -10000 0 -10000 0 0
CTDSP2 0.015 0.039 -10000 0 -10000 0 0
BRCA1 -0.002 0.034 -10000 0 -0.49 3 3
TCF4 0.004 0.085 -10000 0 -0.78 11 11
CDKN2A -0.043 0.11 -10000 0 -0.29 169 169
SRF 0.024 0.019 -10000 0 -10000 0 0
NKX3-1 -0.081 0.19 -10000 0 -1.2 21 21
KLK3 -0.18 0.5 -10000 0 -1.5 128 128
TMF1 0.004 0.005 -10000 0 -10000 0 0
HNRNPA1 0.009 0.021 -10000 0 -10000 0 0
AOF2 -0.008 0.023 -10000 0 -0.072 128 128
APPL1 0.034 0.032 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.074 0.19 -10000 0 -0.54 146 146
AR -0.1 0.28 -10000 0 -0.8 147 147
UBA3 0.004 0.005 -10000 0 -10000 0 0
PATZ1 0.009 0.021 -10000 0 -10000 0 0
PAWR 0.003 0.025 -10000 0 -0.79 1 1
PRKDC 0.005 0.024 -10000 0 -0.29 4 4
PA2G4 0.011 0.028 -10000 0 -10000 0 0
UBE2I 0 0 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.069 0.17 -10000 0 -0.5 146 146
RPS6KA3 -0.007 0.07 -10000 0 -0.79 8 8
T-DHT/AR/ARA70 -0.086 0.18 -10000 0 -0.54 147 147
LATS2 0.009 0.023 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.065 0.18 0.19 1 -0.5 146 147
Cyclin D3/CDK11 p58 0 0.006 -10000 0 -10000 0 0
VAV3 -0.01 0.076 -10000 0 -0.43 26 26
KLK2 -0.12 0.32 -10000 0 -1.2 79 79
CASP8 0.004 0.011 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.099 0.2 -10000 0 -0.54 180 180
TMPRSS2 -0.17 0.39 -10000 0 -1.2 135 135
CCND1 -0.016 0.074 -10000 0 -0.34 46 46
PIAS1 -0.005 0.031 -10000 0 -10000 0 0
mol:T-DHT -0.008 0.033 -10000 0 -0.078 181 181
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.011 0.049 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.085 0.2 -10000 0 -0.54 160 160
CMTM2 0.003 0.013 -10000 0 -0.29 1 1
SNURF -0.021 0.13 -10000 0 -0.79 29 29
ZMIZ1 0.004 0.03 -10000 0 -0.36 1 1
CCND3 0.002 0.01 -10000 0 -10000 0 0
TGIF1 0.009 0.021 -10000 0 -10000 0 0
FKBP4 -0.003 0.033 -10000 0 -0.3 9 9
Insulin Pathway

Figure S72.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S72.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.13 0.22 -9999 0 -0.46 300 300
TC10/GTP -0.11 0.18 -9999 0 -0.41 284 284
Insulin Receptor/Insulin/IRS1/Shp2 -0.02 0.097 -9999 0 -0.49 45 45
HRAS -0.002 0.027 -9999 0 -0.29 9 9
APS homodimer -0.014 0.062 -9999 0 -0.29 52 52
GRB14 -0.1 0.22 -9999 0 -0.47 230 230
FOXO3 -0.014 0.065 -9999 0 -0.68 9 9
AKT1 -0.057 0.12 -9999 0 -0.51 11 11
INSR 0.012 0.009 -9999 0 -0.29 1 1
Insulin Receptor/Insulin -0.003 0.026 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0 0 -9999 0 -10000 0 0
SORBS1 -0.21 0.35 -9999 0 -0.79 284 284
CRK 0 0 -9999 0 -10000 0 0
PTPN1 0.033 0.03 -9999 0 -10000 0 0
CAV1 -0.098 0.24 -9999 0 -0.51 256 256
CBL/APS/CAP/Crk-II/C3G -0.12 0.2 -9999 0 -0.45 284 284
Insulin Receptor/Insulin/IRS1/NCK2 -0.02 0.097 -9999 0 -0.49 45 45
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.023 0.096 -9999 0 -0.43 58 58
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.012 0.055 -9999 0 -10000 0 0
RPS6KB1 -0.008 0.13 -9999 0 -0.46 11 11
PARD6A -0.002 0.023 -9999 0 -0.29 7 7
CBL 0 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0.002 -9999 0 -10000 0 0
PIK3R1 -0.009 0.086 -9999 0 -0.79 13 13
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.05 0.11 -9999 0 -0.48 11 11
HRAS/GTP -0.016 0.073 -9999 0 -0.47 2 2
Insulin Receptor 0.012 0.009 -9999 0 -0.29 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.019 0.09 -9999 0 -0.45 45 45
PRKCI -0.013 0.032 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.062 0.14 -9999 0 -0.4 140 140
SHC1 0 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0 0.002 -9999 0 -10000 0 0
PI3K -0.023 0.097 -9999 0 -0.43 58 58
NCK2 0 0 -9999 0 -10000 0 0
RHOQ 0 0 -9999 0 -10000 0 0
mol:H2O2 0 0.003 -9999 0 -10000 0 0
HRAS/GDP -0.002 0.018 -9999 0 -10000 0 0
AKT2 -0.057 0.12 -9999 0 -0.51 11 11
PRKCZ -0.014 0.036 -9999 0 -0.6 1 1
SH2B2 -0.014 0.062 -9999 0 -0.29 52 52
SHC/SHIP -0.018 0.085 -9999 0 -0.43 45 45
F2RL2 -0.06 0.15 -9999 0 -0.36 185 185
TRIP10 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0 0.004 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0 0.004 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.13 0.21 -9999 0 -0.48 284 284
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0 0.003 -9999 0 -10000 0 0
INPP5D 0.007 0.096 -9999 0 -0.46 45 45
SOS1 0 0 -9999 0 -10000 0 0
SGK1 -0.009 0.073 -9999 0 -0.98 6 6
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
IRS1 -0.033 0.16 -9999 0 -0.79 45 45
p62DOK/RasGAP 0 0.002 -9999 0 -10000 0 0
INS 0.003 0.004 -9999 0 -10000 0 0
mol:PI-3-4-P2 0.007 0.095 -9999 0 -0.45 45 45
GRB2 0 0.009 -9999 0 -0.29 1 1
EIF4EBP1 -0.014 0.14 -9999 0 -0.46 25 25
PTPRA 0.012 0.003 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -0.29 1 1
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.013 0.064 -9999 0 -0.32 45 45
Insulin Receptor/Insulin/IRS1 -0.021 0.099 -9999 0 -0.5 45 45
Insulin Receptor/Insulin/IRS3 -0.001 0.007 -9999 0 -10000 0 0
Par3/Par6 -0.027 0.074 -9999 0 -0.45 23 23
Regulation of Androgen receptor activity

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
HDAC1 0.021 0.003 -9999 0 -10000 0 0
SMARCC1 0.005 0.019 -9999 0 -0.55 1 1
REL -0.005 0.087 -9999 0 -0.79 13 13
HDAC7 0.009 0.13 -9999 0 -0.58 18 18
JUN 0 0.064 -9999 0 -0.79 7 7
EP300 0 0 -9999 0 -10000 0 0
KAT2B -0.001 0.024 -9999 0 -0.79 1 1
KAT5 0.002 0.005 -9999 0 -10000 0 0
MAPK14 0.006 0.096 -9999 0 -0.61 25 25
FOXO1 -0.008 0.079 -9999 0 -0.79 11 11
T-DHT/AR -0.004 0.14 -9999 0 -0.52 34 34
MAP2K6 -0.01 0.12 -9999 0 -0.78 26 26
BRM/BAF57 -0.001 0.011 -9999 0 -10000 0 0
MAP2K4 0.008 0.025 -9999 0 -0.8 1 1
SMARCA2 0.004 0.006 -9999 0 -10000 0 0
PDE9A -0.087 0.29 -9999 0 -1.2 62 62
NCOA2 -0.032 0.17 -9999 0 -0.79 53 53
CEBPA -0.004 0.072 -9999 0 -0.79 9 9
EHMT2 0.005 0.006 -9999 0 -10000 0 0
cell proliferation 0.015 0.14 -9999 0 -0.47 32 32
NR0B1 -0.01 0.057 -9999 0 -0.31 36 36
EGR1 -0.25 0.37 -9999 0 -0.79 345 345
RXRs/9cRA -0.12 0.21 -9999 0 -0.48 265 265
AR/RACK1/Src -0.004 0.11 -9999 0 -0.48 33 33
AR/GR -0.054 0.13 -9999 0 -0.43 63 63
GNB2L1 0.001 0.004 -9999 0 -10000 0 0
PKN1 0 0.009 -9999 0 -0.29 1 1
RCHY1 0 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity -0.001 0.003 -9999 0 -10000 0 0
MAPK8 0.015 0.058 -9999 0 -0.61 9 9
T-DHT/AR/TIF2/CARM1 -0.018 0.16 -9999 0 -0.58 46 46
SRC 0.021 0.093 -9999 0 -0.46 33 33
NR3C1 -0.011 0.092 -9999 0 -0.79 15 15
KLK3 -0.2 0.41 -9999 0 -1.2 151 151
APPBP2 0.008 0.017 -9999 0 -0.29 3 3
TRIM24 0.005 0.006 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.027 0.098 -9999 0 -0.51 33 33
TMPRSS2 -0.16 0.41 -9999 0 -1.2 137 137
RXRG -0.19 0.34 -9999 0 -0.78 268 268
mol:9cRA -0.001 0.002 -9999 0 -10000 0 0
RXRA 0 0 -9999 0 -10000 0 0
RXRB 0 0 -9999 0 -10000 0 0
CARM1 0.007 0.006 -9999 0 -10000 0 0
NR2C2 -0.008 0.079 -9999 0 -0.79 11 11
KLK2 -0.043 0.24 -9999 0 -0.74 99 99
AR -0.028 0.14 -9999 0 -0.34 171 171
SENP1 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0.009 -9999 0 -0.29 1 1
MDM2 0.004 0.024 -9999 0 -0.29 5 5
SRY 0.003 0.01 -9999 0 -10000 0 0
GATA2 -0.024 0.13 -9999 0 -0.62 42 42
MYST2 0.002 0.01 -9999 0 -0.29 1 1
HOXB13 -0.14 0.15 -9999 0 -0.3 502 502
T-DHT/AR/RACK1/Src -0.014 0.1 -9999 0 -0.49 33 33
positive regulation of transcription -0.024 0.13 -9999 0 -0.62 42 42
DNAJA1 0.009 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.013 -9999 0 -10000 0 0
NCOA1 0.012 0.026 -9999 0 -0.82 1 1
SPDEF -0.058 0.2 -9999 0 -0.75 80 80
T-DHT/AR/TIF2 0.011 0.1 -9999 0 -0.44 27 27
T-DHT/AR/Hsp90 -0.034 0.094 -9999 0 -0.51 33 33
GSK3B 0.008 0.006 -9999 0 -10000 0 0
NR2C1 0.003 0.006 -9999 0 -10000 0 0
mol:T-DHT 0.014 0.098 -9999 0 -0.5 33 33
SIRT1 0 0 -9999 0 -10000 0 0
ZMIZ2 0.005 0.013 -9999 0 -10000 0 0
POU2F1 0.021 0.026 -9999 0 -0.43 1 1
T-DHT/AR/DAX-1 -0.036 0.099 -9999 0 -0.52 34 34
CREBBP 0 0 -9999 0 -10000 0 0
SMARCE1 0.003 0.017 -9999 0 -0.3 3 3
Regulation of Telomerase

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
Telomerase catalytic core complex -0.055 0.12 -9999 0 -0.57 6 6
RAD9A 0 0.009 -9999 0 -0.29 1 1
AP1 -0.18 0.28 -9999 0 -0.61 326 326
IFNAR2 0.011 0.005 -9999 0 -10000 0 0
AKT1 -0.037 0.11 -9999 0 -0.28 167 167
ER alpha/Oestrogen -0.12 0.22 -9999 0 -0.61 167 167
NFX1/SIN3/HDAC complex 0.025 0.025 -9999 0 -10000 0 0
EGF -0.15 0.32 -9999 0 -0.78 216 216
SMG5 0 0 -9999 0 -10000 0 0
SMG6 0 0 -9999 0 -10000 0 0
SP3/HDAC2 0 0 -9999 0 -10000 0 0
TERT/c-Abl -0.067 0.089 -9999 0 -0.53 6 6
SAP18 0.006 0.006 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.14 0.15 -9999 0 -0.29 553 553
WRN 0 0 -9999 0 -10000 0 0
SP1 0.012 0.005 -9999 0 -10000 0 0
SP3 0.009 0.005 -9999 0 -10000 0 0
TERF2IP 0 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.052 0.078 -9999 0 -0.52 4 4
Mad/Max 0 0.006 -9999 0 -10000 0 0
TERT -0.056 0.12 -9999 0 -0.58 6 6
CCND1 -0.048 0.13 -9999 0 -1.3 4 4
MAX 0.009 0.005 -9999 0 -10000 0 0
RBBP7 0.004 0.026 -9999 0 -0.29 8 8
RBBP4 0.005 0.025 -9999 0 -0.79 1 1
TERF2 0 0 -9999 0 -10000 0 0
PTGES3 0 0 -9999 0 -10000 0 0
SIN3A 0.006 0.006 -9999 0 -10000 0 0
Telomerase/911 0.012 0.024 -9999 0 -10000 0 0
CDKN1B 0.009 0.074 -9999 0 -0.87 3 3
RAD1 0 0 -9999 0 -10000 0 0
XRCC5 0 0 -9999 0 -10000 0 0
XRCC6 0 0 -9999 0 -10000 0 0
SAP30 0.005 0.019 -9999 0 -0.29 4 4
TRF2/PARP2 0 0 -9999 0 -10000 0 0
UBE3A 0.009 0.005 -9999 0 -10000 0 0
JUN 0.002 0.064 -9999 0 -0.79 7 7
E6 0 0.001 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0 0 -9999 0 -10000 0 0
FOS -0.23 0.36 -9999 0 -0.79 325 325
IFN-gamma/IRF1 -0.025 0.063 -9999 0 -0.36 5 5
PARP2 0 0 -9999 0 -10000 0 0
BLM -0.03 0.089 -9999 0 -0.29 113 113
Telomerase -0.006 0.028 -9999 0 -10000 0 0
IRF1 0.011 0.02 -9999 0 -0.28 3 3
ESR1 -0.15 0.29 -9999 0 -0.58 291 291
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0.007 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0 0.007 -9999 0 -10000 0 0
HDAC1 0.006 0.006 -9999 0 -10000 0 0
HDAC2 0.011 0.005 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.021 0.011 -9999 0 -10000 0 0
ABL1 0 0 -9999 0 -10000 0 0
MXD1 0.009 0.01 -9999 0 -0.29 1 1
MRE11A 0 0 -9999 0 -10000 0 0
HUS1 0 0 -9999 0 -10000 0 0
RPS6KB1 -0.001 0.015 -9999 0 -0.29 3 3
TERT/NF kappa B1/14-3-3 -0.066 0.1 -9999 0 -0.62 4 4
NR2F2 0.001 0.042 -9999 0 -0.79 3 3
MAPK3 0.014 0.019 -9999 0 -10000 0 0
MAPK1 0.014 0.019 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.001 0.016 -9999 0 -0.29 3 3
NFKB1 0 0 -9999 0 -10000 0 0
HNRNPC 0 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0 -9999 0 -10000 0 0
NBN 0 0 -9999 0 -10000 0 0
EGFR -0.29 0.38 -9999 0 -0.78 414 414
mol:Oestrogen 0 0.001 -9999 0 -10000 0 0
EGF/EGFR -0.34 0.35 -9999 0 -0.66 555 555
MYC -0.008 0.12 -9999 0 -0.79 24 24
IL2 0.004 0.026 -9999 0 -0.29 8 8
KU 0 0 -9999 0 -10000 0 0
RAD50 0 0 -9999 0 -10000 0 0
HSP90AA1 0 0.009 -9999 0 -0.29 1 1
TGFB1 0.001 0.016 -9999 0 -0.29 3 3
TRF2/BLM -0.017 0.051 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.063 0.087 -9999 0 -0.55 5 5
SP1/HDAC2 0 0 -9999 0 -10000 0 0
PINX1 0 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.052 0.078 -9999 0 -0.52 4 4
Smad3/Myc -0.012 0.076 -9999 0 -0.52 24 24
911 complex 0 0.004 -9999 0 -10000 0 0
IFNG -0.03 0.1 -9999 0 -0.28 150 150
Telomerase/PinX1 -0.052 0.078 -9999 0 -0.52 4 4
Telomerase/AKT1/mTOR/p70S6K 0.002 0.055 -9999 0 -10000 0 0
SIN3B 0.006 0.006 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.052 0.078 -9999 0 -0.52 4 4
response to DNA damage stimulus 0.003 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0 -9999 0 -10000 0 0
TRF2/WRN 0 0 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.052 0.078 -9999 0 -0.52 4 4
E2F1 -0.086 0.14 -9999 0 -0.29 348 348
ZNFX1 0.006 0.006 -9999 0 -10000 0 0
PIF1 -0.06 0.12 -9999 0 -0.29 224 224
NCL 0 0 -9999 0 -10000 0 0
DKC1 -0.001 0.013 -9999 0 -0.29 2 2
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Osteopontin-mediated events

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
IKK alpha homodimer -0.037 0.085 -9999 0 -0.44 38 38
NF kappa B1 p50/RelA/I kappa B alpha -0.024 0.07 -9999 0 -0.46 6 6
alphaV/beta3 Integrin/Osteopontin/Src -0.046 0.076 -9999 0 -10000 0 0
AP1 -0.14 0.21 -9999 0 -0.78 38 38
ILK -0.007 0.11 -9999 0 -0.47 38 38
bone resorption -0.038 0.11 -9999 0 -0.66 21 21
PTK2B 0 0 -9999 0 -10000 0 0
PYK2/p130Cas 0.003 0.09 -9999 0 -0.42 38 38
ITGAV 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.018 0.1 -9999 0 -0.6 31 31
alphaV/beta3 Integrin/Osteopontin -0.051 0.11 -9999 0 -0.52 38 38
MAP3K1 -0.008 0.11 -9999 0 -0.48 38 38
JUN -0.005 0.063 -9999 0 -0.79 7 7
MAPK3 0.008 0.11 -9999 0 -0.43 38 38
MAPK1 0.008 0.11 -9999 0 -0.43 38 38
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAPK8 0.002 0.13 -9999 0 -0.52 40 40
ITGB3 -0.028 0.14 -9999 0 -0.74 42 42
NFKBIA 0.022 0.1 -9999 0 -0.42 38 38
FOS -0.24 0.36 -9999 0 -0.79 325 325
CD44 -0.001 0.015 -9999 0 -0.29 3 3
CHUK 0 0 -9999 0 -10000 0 0
PLAU 0.02 0.1 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.023 0.066 -9999 0 -0.44 6 6
BCAR1 0 0 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.021 0.11 -9999 0 -0.59 38 38
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.008 0.11 -9999 0 -0.47 38 38
VAV3 -0.003 0.11 -9999 0 -0.44 45 45
MAP3K14 -0.005 0.11 -9999 0 -0.47 38 38
ROCK2 -0.022 0.13 -9999 0 -0.79 31 31
SPP1 -0.075 0.12 -9999 0 -0.28 288 288
RAC1 0 0 -9999 0 -10000 0 0
Rac1/GTP -0.036 0.084 -9999 0 -0.4 45 45
MMP2 -0.073 0.21 -9999 0 -0.68 38 38
Regulation of p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.018 0.12 -9999 0 -0.77 26 26
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 -0.001 0.024 -9999 0 -0.79 1 1
RAC1-CDC42/GTP/PAK family -0.12 0.14 -9999 0 -0.27 489 489
response to UV 0 0 -9999 0 -10000 0 0
YES1 -0.001 0.024 -9999 0 -0.79 1 1
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0 0 -9999 0 -10000 0 0
FYN -0.001 0.034 -9999 0 -0.79 2 2
MAP3K12 0 0 -9999 0 -10000 0 0
FGR -0.001 0.025 -9999 0 -0.54 2 2
p38 alpha/TAB1 -0.007 0.033 -9999 0 -0.32 4 4
PRKG1 -0.053 0.2 -9999 0 -0.79 73 73
DUSP8 -0.002 0.042 -9999 0 -0.66 4 4
PGK/cGMP/p38 alpha -0.032 0.1 -9999 0 -0.39 76 76
apoptosis -0.007 0.032 -9999 0 -0.33 3 3
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0 0 -9999 0 -10000 0 0
DUSP1 -0.1 0.26 -9999 0 -0.79 141 141
PAK1 -0.007 0.044 -9999 0 -0.29 25 25
SRC 0 0.009 -9999 0 -0.29 1 1
RAC1/OSM/MEKK3/MKK3 0 0.006 -9999 0 -10000 0 0
TRAF6 0 0 -9999 0 -10000 0 0
RAC1 0 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 -0.001 0.013 -9999 0 -0.29 2 2
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 0.018 0.069 -9999 0 -0.34 21 21
BLK -0.044 0.11 -9999 0 -0.3 159 159
HCK -0.004 0.033 -9999 0 -10000 0 0
MAP2K3 0 0.009 -9999 0 -0.29 1 1
DUSP16 0 0 -9999 0 -10000 0 0
DUSP10 -0.001 0.015 -9999 0 -0.29 3 3
TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.029 0.048 -9999 0 -0.34 4 4
positive regulation of innate immune response 0.024 0.074 -9999 0 -0.36 21 21
LCK -0.02 0.1 -9999 0 -0.41 54 54
p38alpha-beta/MKP7 -0.012 0.054 -9999 0 -0.34 20 20
p38alpha-beta/MKP5 -0.012 0.055 -9999 0 -0.34 20 20
PGK/cGMP -0.041 0.15 -9999 0 -0.61 73 73
PAK2 0 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.058 0.13 -9999 0 -0.37 157 157
CDC42 0 0 -9999 0 -10000 0 0
RALB 0 0 -9999 0 -10000 0 0
RALA 0 0 -9999 0 -10000 0 0
PAK3 -0.35 0.39 -9999 0 -0.79 489 489
TCGA08_retinoblastoma

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
CDKN2B -0.003 0.063 -10000 0 -0.66 9 9
CDKN2C 0.006 0.038 -10000 0 -0.78 2 2
CDKN2A -0.054 0.12 -10000 0 -0.31 192 192
CCND2 0.007 0.033 0.24 8 -0.16 12 20
RB1 -0.008 0.032 0.19 4 -0.25 8 12
CDK4 0.01 0.03 0.25 9 -10000 0 9
CDK6 0.007 0.038 0.27 8 -0.22 13 21
G1/S progression -0.006 0.036 0.25 8 -0.19 4 12
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.06 0.076 -9999 0 -0.41 6 6
EPHB2 -0.005 0.038 -9999 0 -0.29 19 19
Syndecan-2/TACI -0.018 0.074 -9999 0 -0.52 18 18
LAMA1 -0.09 0.25 -9999 0 -0.77 127 127
Syndecan-2/alpha2 ITGB1 -0.12 0.21 -9999 0 -0.46 292 292
HRAS -0.002 0.027 -9999 0 -0.29 9 9
Syndecan-2/CASK -0.002 0.029 -9999 0 -0.52 3 3
ITGA5 0 0.009 -9999 0 -0.29 1 1
BAX 0.034 0.056 -9999 0 -0.64 3 3
EPB41 0 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.002 0.026 -9999 0 -0.47 3 3
LAMA3 -0.2 0.34 -9999 0 -0.79 276 276
EZR -0.001 0.015 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.11 0.27 -9999 0 -0.79 147 147
Syndecan-2/MMP2 -0.007 0.069 -9999 0 -0.65 11 11
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.015 0.095 -9999 0 -0.6 28 28
dendrite morphogenesis -0.005 0.034 -9999 0 -0.51 3 3
Syndecan-2/GM-CSF -0.005 0.036 -9999 0 -0.52 3 3
determination of left/right symmetry 0.017 0.035 -9999 0 -0.36 7 7
Syndecan-2/PKC delta -0.002 0.029 -9999 0 -0.52 3 3
GNB2L1 0 0 -9999 0 -10000 0 0
MAPK3 0.022 0.036 -9999 0 -0.47 3 3
MAPK1 0.022 0.036 -9999 0 -0.47 3 3
Syndecan-2/RACK1 -0.003 0.027 -9999 0 -0.44 3 3
NF1 -0.001 0.024 -9999 0 -0.79 1 1
FGFR/FGF/Syndecan-2 0.017 0.035 -9999 0 -0.36 7 7
ITGA2 -0.02 0.12 -9999 0 -0.79 28 28
MAPK8 0.028 0.059 -9999 0 -0.54 11 11
Syndecan-2/alpha2/beta1 Integrin -0.063 0.17 -9999 0 -0.5 136 136
Syndecan-2/Kininogen -0.005 0.035 -9999 0 -0.52 3 3
ITGB1 0 0 -9999 0 -10000 0 0
SRC -0.002 0.025 -9999 0 -0.42 3 3
Syndecan-2/CASK/Protein 4.1 -0.002 0.026 -9999 0 -0.48 3 3
extracellular matrix organization -0.002 0.029 -9999 0 -0.51 3 3
actin cytoskeleton reorganization -0.06 0.076 -9999 0 -0.41 6 6
Syndecan-2/Caveolin-2/Ras -0.066 0.17 -9999 0 -0.48 147 147
Syndecan-2/Laminin alpha3 -0.13 0.23 -9999 0 -0.52 279 279
Syndecan-2/RasGAP -0.002 0.025 -9999 0 -0.42 3 3
alpha5/beta1 Integrin 0 0.006 -9999 0 -10000 0 0
PRKCD 0 0.009 -9999 0 -0.29 1 1
Syndecan-2 dimer -0.005 0.034 -9999 0 -0.52 3 3
GO:0007205 0 0.002 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.002 0.023 -9999 0 -0.4 3 3
RHOA 0 0 -9999 0 -10000 0 0
SDCBP 0 0 -9999 0 -10000 0 0
TNFRSF13B -0.028 0.11 -9999 0 -0.39 77 77
RASA1 0 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.015 0.095 -9999 0 -0.6 28 28
Syndecan-2/Synbindin -0.002 0.028 -9999 0 -0.52 3 3
TGFB1 -0.001 0.015 -9999 0 -0.29 3 3
CASP3 0.03 0.028 -9999 0 -0.46 3 3
FN1 -0.12 0.14 -9999 0 -0.29 432 432
Syndecan-2/IL8 -0.021 0.084 -9999 0 -0.52 25 25
SDC2 0.017 0.035 -9999 0 -0.36 7 7
KNG1 -0.006 0.041 -9999 0 -0.29 22 22
Syndecan-2/Neurofibromin -0.002 0.032 -9999 0 -0.52 4 4
TRAPPC4 0 0 -9999 0 -10000 0 0
CSF2 -0.007 0.044 -9999 0 -0.29 25 25
Syndecan-2/TGFB1 -0.002 0.029 -9999 0 -0.52 3 3
Syndecan-2/Syntenin/PI-4-5-P2 -0.002 0.026 -9999 0 -0.48 3 3
Syndecan-2/Ezrin -0.002 0.026 -9999 0 -0.47 3 3
PRKACA 0.03 0.032 -9999 0 -0.47 4 4
angiogenesis -0.021 0.084 -9999 0 -0.52 25 25
MMP2 -0.008 0.079 -9999 0 -0.75 12 12
IL8 -0.033 0.13 -9999 0 -0.79 22 22
calcineurin-NFAT signaling pathway -0.017 0.074 -9999 0 -0.52 18 18
IL2 signaling events mediated by STAT5

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
GAB2 0.008 0.044 -9999 0 -0.79 2 2
ELF1 -0.012 0.051 -9999 0 -0.38 16 16
CCNA2 -0.11 0.14 -9999 0 -0.29 426 426
PIK3CA 0.012 0.009 -9999 0 -0.29 1 1
JAK3 0.008 0.034 -9999 0 -0.29 14 14
PIK3R1 0.002 0.087 -9999 0 -0.79 13 13
JAK1 0.011 0.024 -9999 0 -0.79 1 1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.057 0.08 -9999 0 -0.58 9 9
SHC1 0.012 0.001 -9999 0 -10000 0 0
SP1 -0.005 0.041 -9999 0 -0.38 13 13
IL2RA 0.001 0.13 -9999 0 -1 16 16
IL2RB -0.001 0.066 -9999 0 -0.32 42 42
SOS1 0.012 0.001 -9999 0 -10000 0 0
IL2RG -0.006 0.088 -9999 0 -0.36 53 53
G1/S transition of mitotic cell cycle 0.004 0.13 -9999 0 -0.81 23 23
PTPN11 0.012 0.001 -9999 0 -10000 0 0
CCND2 0.017 0.11 -9999 0 -1 13 13
LCK -0.009 0.1 -9999 0 -0.41 54 54
GRB2 0.011 0.009 -9999 0 -0.29 1 1
IL2 0.004 0.026 -9999 0 -0.29 8 8
CDK6 -0.011 0.09 -9999 0 -0.73 16 16
CCND3 0.063 0.071 -9999 0 -0.58 5 5
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.004 0.11 -10000 0 -0.44 36 36
IKBKB 0.016 0.053 -10000 0 -0.26 3 3
AKT1 0.002 0.082 0.24 2 -0.27 25 27
IKBKG 0.018 0.055 -10000 0 -0.24 10 10
CALM1 -0.011 0.092 -10000 0 -0.45 30 30
PIK3CA 0 0.009 -10000 0 -0.29 1 1
MAP3K1 -0.01 0.15 -10000 0 -0.63 35 35
MAP3K7 0 0.009 -10000 0 -0.29 1 1
mol:Ca2+ -0.02 0.097 0.24 1 -0.48 30 31
DOK1 -0.001 0.018 -10000 0 -10000 0 0
AP-1 -0.04 0.11 -10000 0 -0.26 70 70
LYN 0 0.001 -10000 0 -10000 0 0
BLNK 0 0 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
BCR complex -0.079 0.21 -10000 0 -0.62 119 119
CD22 -0.061 0.18 -10000 0 -0.54 100 100
CAMK2G -0.002 0.086 -10000 0 -0.41 30 30
CSNK2A1 0 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.047 0.13 -10000 0 -0.76 16 16
GO:0007205 -0.02 0.098 0.24 1 -0.49 30 31
SYK 0 0.009 -10000 0 -0.29 1 1
ELK1 -0.011 0.093 -10000 0 -0.46 30 30
NFATC1 -0.018 0.13 -10000 0 -0.57 34 34
B-cell antigen/BCR complex -0.079 0.21 -10000 0 -0.62 119 119
PAG1/CSK -0.001 0.013 -10000 0 -10000 0 0
NFKBIB 0.015 0.02 0.085 1 -10000 0 1
HRAS -0.009 0.1 -10000 0 -0.47 31 31
NFKBIA 0.016 0.02 0.085 1 -10000 0 1
NF-kappa-B/RelA/I kappa B beta 0.019 0.016 -10000 0 -10000 0 0
RasGAP/Csk -0.058 0.16 -10000 0 -0.51 100 100
mol:GDP -0.02 0.091 0.22 1 -0.46 30 31
PTEN -0.001 0.034 -10000 0 -0.79 2 2
CD79B -0.028 0.14 -10000 0 -0.58 52 52
NF-kappa-B/RelA/I kappa B alpha 0.019 0.016 -10000 0 -10000 0 0
GRB2 0 0.009 -10000 0 -0.29 1 1
PI3K/BCAP/CD19 -0.028 0.16 -10000 0 -0.47 100 100
PIK3R1 -0.009 0.086 -10000 0 -0.79 13 13
mol:IP3 -0.029 0.097 0.24 1 -0.5 30 31
CSK 0 0 -10000 0 -10000 0 0
FOS -0.13 0.22 -10000 0 -0.44 345 345
CHUK 0.018 0.055 -10000 0 -0.24 18 18
IBTK 0 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.023 0.077 -10000 0 -0.48 18 18
PTPN6 -0.057 0.16 -10000 0 -0.72 41 41
RELA 0 0 -10000 0 -10000 0 0
BCL2A1 0.015 0.02 -10000 0 -0.12 1 1
VAV2 -0.071 0.16 -10000 0 -0.8 33 33
ubiquitin-dependent protein catabolic process 0.019 0.019 0.088 1 -10000 0 1
BTK -0.004 0.005 -10000 0 -10000 0 0
CD19 -0.082 0.17 -10000 0 -0.53 97 97
MAP4K1 -0.015 0.07 -10000 0 -0.31 53 53
CD72 -0.009 0.054 -10000 0 -0.79 1 1
PAG1 -0.001 0.02 -10000 0 -0.29 5 5
MAPK14 0.002 0.13 -10000 0 -0.54 31 31
SH3BP5 -0.001 0.024 -10000 0 -0.79 1 1
PIK3AP1 -0.01 0.11 0.27 1 -0.53 30 31
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.042 0.13 -10000 0 -0.47 85 85
RAF1 0 0.096 -10000 0 -0.44 29 29
RasGAP/p62DOK/SHIP -0.055 0.15 -10000 0 -0.49 100 100
CD79A -0.083 0.22 -10000 0 -0.54 170 170
re-entry into mitotic cell cycle -0.04 0.11 -10000 0 -0.26 68 68
RASA1 0 0 -10000 0 -10000 0 0
MAPK3 0.016 0.082 -10000 0 -0.42 17 17
MAPK1 0.016 0.082 -10000 0 -0.42 17 17
CD72/SHP1 -0.055 0.15 -10000 0 -0.68 41 41
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 -0.001 0.13 -10000 0 -0.52 39 39
actin cytoskeleton organization -0.027 0.15 -10000 0 -0.65 33 33
NF-kappa-B/RelA 0.042 0.033 0.17 1 -10000 0 1
Calcineurin -0.02 0.071 -10000 0 -0.44 17 17
PI3K -0.06 0.13 -10000 0 -0.53 44 44
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.031 0.11 0.27 1 -0.57 30 31
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.048 0.17 -10000 0 -0.82 36 36
DAPP1 -0.05 0.19 -10000 0 -0.96 35 35
cytokine secretion -0.016 0.12 -10000 0 -0.52 34 34
mol:DAG -0.029 0.097 0.24 1 -0.5 30 31
PLCG2 -0.002 0.035 -10000 0 -0.79 2 2
MAP2K1 0.008 0.09 -10000 0 -0.48 17 17
B-cell antigen/BCR complex/FcgammaRIIB -0.07 0.19 -10000 0 -0.55 122 122
mol:PI-3-4-5-P3 -0.044 0.093 0.34 2 -0.37 39 41
ETS1 0.004 0.088 -10000 0 -0.48 20 20
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.057 0.16 -10000 0 -0.51 97 97
B-cell antigen/BCR complex/LYN -0.057 0.18 -10000 0 -0.57 97 97
MALT1 0 0 -10000 0 -10000 0 0
TRAF6 0.001 0.003 -10000 0 -10000 0 0
RAC1 -0.03 0.16 -10000 0 -0.71 33 33
B-cell antigen/BCR complex/LYN/SYK -0.057 0.17 -10000 0 -0.55 98 98
CARD11 -0.014 0.1 0.24 1 -0.48 30 31
FCGR2B -0.004 0.054 -10000 0 -0.71 6 6
PPP3CA -0.001 0.013 -10000 0 -0.29 2 2
BCL10 0 0 -10000 0 -10000 0 0
IKK complex 0.017 0.027 0.091 2 -0.098 1 3
PTPRC -0.009 0.073 -10000 0 -0.5 19 19
PDPK1 -0.029 0.062 0.22 2 -0.26 25 27
PPP3CB 0 0 -10000 0 -10000 0 0
PPP3CC 0 0 -10000 0 -10000 0 0
POU2F2 0.019 0.014 -10000 0 -0.14 1 1
Regulation of nuclear SMAD2/3 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
EP300 0.002 0.01 -10000 0 -10000 0 0
HSPA8 0 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.1 0.2 0.24 2 -0.56 167 169
AKT1 0.014 0.006 -10000 0 -10000 0 0
GSC -0.035 0.29 -10000 0 -1.5 41 41
NKX2-5 -0.045 0.1 -10000 0 -0.29 171 171
muscle cell differentiation 0.007 0.049 0.76 1 -10000 0 1
SMAD2-3/SMAD4/SP1 0.006 0.04 -10000 0 -0.45 2 2
SMAD4 0.014 0.041 -10000 0 -0.83 1 1
CBFB 0 0 -10000 0 -10000 0 0
SAP18 0 0.002 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.2 0.25 -10000 0 -0.52 411 411
SMAD3/SMAD4/VDR 0.005 0.03 -10000 0 -0.43 2 2
MYC -0.017 0.12 -10000 0 -0.79 24 24
CDKN2B 0.03 0.13 -10000 0 -1.5 7 7
AP1 -0.12 0.2 -10000 0 -0.51 59 59
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.002 0.02 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0 0.041 -10000 0 -0.33 2 2
SP3 0 0 -10000 0 -10000 0 0
CREB1 0 0 -10000 0 -10000 0 0
FOXH1 -0.044 0.12 -10000 0 -0.29 203 203
SMAD3/SMAD4/GR -0.009 0.071 -10000 0 -0.56 16 16
GATA3 -0.037 0.15 -10000 0 -0.57 69 69
SKI/SIN3/HDAC complex/NCoR1 0.002 0.014 -10000 0 -10000 0 0
MEF2C/TIF2 -0.054 0.12 -10000 0 -0.58 40 40
endothelial cell migration -0.007 0.06 1.5 1 -10000 0 1
MAX 0.001 0.005 -10000 0 -10000 0 0
RBBP7 -0.002 0.025 -10000 0 -0.29 8 8
RBBP4 0 0.024 -10000 0 -0.79 1 1
RUNX2 -0.005 0.036 -10000 0 -0.29 17 17
RUNX3 -0.006 0.066 -10000 0 -0.58 12 12
RUNX1 -0.001 0.024 -10000 0 -0.79 1 1
CTBP1 0 0 -10000 0 -10000 0 0
NR3C1 -0.01 0.093 -10000 0 -0.79 15 15
VDR 0 0 -10000 0 -10000 0 0
CDKN1A 0.051 0.078 -10000 0 -1.5 2 2
KAT2B 0 0.024 -10000 0 -0.79 1 1
SMAD2/SMAD2/SMAD4/FOXH1 -0.029 0.071 -10000 0 -0.47 5 5
DCP1A 0 0 -10000 0 -10000 0 0
SKI 0 0.002 -10000 0 -10000 0 0
SERPINE1 0.007 0.061 -10000 0 -1.5 1 1
SMAD3/SMAD4/ATF2 -0.002 0.036 -10000 0 -0.55 3 3
SMAD3/SMAD4/ATF3 -0.081 0.2 -10000 0 -0.56 159 159
SAP30 -0.001 0.018 -10000 0 -0.29 4 4
Cbp/p300/PIAS3 0.005 0.023 -10000 0 -10000 0 0
JUN -0.073 0.22 -10000 0 -0.51 53 53
SMAD3/SMAD4/IRF7 -0.02 0.068 -10000 0 -0.36 12 12
TFE3 0.017 0.006 -10000 0 -10000 0 0
COL1A2 0.028 0.1 -10000 0 -1.2 3 3
mesenchymal cell differentiation 0.004 0.034 0.54 1 -10000 0 1
DLX1 -0.054 0.13 -10000 0 -0.32 185 185
TCF3 0 0.009 -10000 0 -0.29 1 1
FOS -0.22 0.37 -10000 0 -0.78 325 325
SMAD3/SMAD4/Max -0.002 0.029 -10000 0 -0.54 1 1
Cbp/p300/SNIP1 0 0.002 -10000 0 -10000 0 0
ZBTB17 0 0.006 -10000 0 -10000 0 0
LAMC1 0.042 0.047 -10000 0 -0.62 2 2
TGIF2/HDAC complex/SMAD3/SMAD4 -0.001 0.028 -10000 0 -0.54 1 1
IRF7 -0.031 0.092 -10000 0 -0.31 104 104
ESR1 -0.15 0.29 -10000 0 -0.58 290 290
HNF4A -0.006 0.041 -10000 0 -0.29 22 22
MEF2C 0.001 0.093 -10000 0 -0.66 3 3
SMAD2-3/SMAD4 -0.003 0.032 -10000 0 -0.53 1 1
Cbp/p300/Src-1 0.003 0.022 -10000 0 -0.52 1 1
IGHV3OR16-13 -0.001 0.01 -10000 0 -10000 0 0
TGIF2/HDAC complex 0 0 -10000 0 -10000 0 0
CREBBP 0.002 0.007 -10000 0 -10000 0 0
SKIL -0.003 0.029 -10000 0 -0.29 11 11
HDAC1 0 0.002 -10000 0 -10000 0 0
HDAC2 0 0.002 -10000 0 -10000 0 0
SNIP1 0.001 0.003 -10000 0 -10000 0 0
GCN5L2 0.001 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.001 0.029 -10000 0 -0.53 1 1
MSG1/HSC70 -0.23 0.29 -10000 0 -0.6 411 411
SMAD2 0.015 0.02 -10000 0 -10000 0 0
SMAD3 0.015 0.029 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.034 0.038 -10000 0 -0.33 3 3
SMAD2/SMAD2/SMAD4 0.027 0.039 -10000 0 -1.1 1 1
NCOR1 0 0.024 -10000 0 -0.79 1 1
NCOA2 -0.038 0.17 -10000 0 -0.79 53 53
NCOA1 -0.001 0.024 -10000 0 -0.79 1 1
MYOD/E2A -0.003 0.022 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.029 0.051 -10000 0 -0.42 2 2
IFNB1 0.011 0.094 -10000 0 -0.42 19 19
SMAD3/SMAD4/MEF2C -0.026 0.074 -10000 0 -0.76 2 2
CITED1 -0.3 0.38 -10000 0 -0.77 426 426
SMAD2-3/SMAD4/ARC105 0 0.028 -10000 0 -0.47 1 1
RBL1 -0.003 0.043 -10000 0 -0.59 5 5
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.048 0.062 -10000 0 -0.49 7 7
RUNX1-3/PEBPB2 -0.004 0.049 -10000 0 -0.58 7 7
SMAD7 -0.066 0.14 -10000 0 -0.58 8 8
MYC/MIZ-1 -0.012 0.09 -10000 0 -0.61 24 24
SMAD3/SMAD4 0.017 0.06 0.28 38 -0.43 2 40
IL10 0.019 0.12 -10000 0 -0.5 42 42
PIASy/HDAC complex 0.01 0.005 -10000 0 -10000 0 0
PIAS3 0.001 0.005 -10000 0 -10000 0 0
CDK2 0.002 0.008 -10000 0 -10000 0 0
IL5 0.014 0.11 -10000 0 -0.5 38 38
CDK4 0.001 0.02 -10000 0 -0.29 4 4
PIAS4 0.01 0.005 -10000 0 -10000 0 0
ATF3 -0.12 0.28 -10000 0 -0.79 158 158
SMAD3/SMAD4/SP1 0 0.032 -10000 0 -0.52 2 2
FOXG1 -0.023 0.077 -10000 0 -0.29 81 81
FOXO3 0.025 0.034 -10000 0 -0.6 3 3
FOXO1 0.02 0.063 -10000 0 -0.6 11 11
FOXO4 0.026 0.008 -10000 0 -10000 0 0
heart looping 0.001 0.093 -10000 0 -0.65 3 3
CEBPB 0.012 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.03 0.08 -10000 0 -0.55 11 11
MYOD1 -0.004 0.033 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 -0.006 0.037 -10000 0 -0.68 1 1
SMAD3/SMAD4/GATA3 -0.024 0.11 -10000 0 -0.56 40 40
SnoN/SIN3/HDAC complex/NCoR1 -0.003 0.029 -10000 0 -0.29 11 11
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.001 0.051 -10000 0 -0.52 8 8
SMAD3/SMAD4/SP1-3 0.003 0.029 -10000 0 -0.45 2 2
MED15 0 0 -10000 0 -10000 0 0
SP1 0.019 0.014 -10000 0 -10000 0 0
SIN3B 0 0.002 -10000 0 -10000 0 0
SIN3A 0 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.014 0.09 -10000 0 -0.47 6 6
ITGB5 0.052 0.046 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.002 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.075 0.19 -10000 0 -0.55 147 147
AR -0.11 0.27 -10000 0 -0.79 147 147
negative regulation of cell growth -0.026 0.073 -10000 0 -0.48 2 2
SMAD3/SMAD4/MYOD -0.006 0.034 -10000 0 -0.54 1 1
E2F5 -0.005 0.039 -10000 0 -0.29 20 20
E2F4 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.003 0.056 -10000 0 -0.44 2 2
SMAD2-3/SMAD4/FOXO1-3a-4 0.003 0.046 -10000 0 -0.34 6 6
TFDP1 -0.001 0.018 -10000 0 -0.29 4 4
SMAD3/SMAD4/AP1 -0.12 0.2 -10000 0 -0.55 44 44
SMAD3/SMAD4/RUNX2 -0.004 0.034 -10000 0 -0.54 1 1
TGIF2 0 0 -10000 0 -10000 0 0
TGIF1 0 0 -10000 0 -10000 0 0
ATF2 -0.001 0.034 -10000 0 -0.79 2 2
Thromboxane A2 receptor signaling

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
TGM2 0.005 0.037 -10000 0 -10000 0 0
GNB1/GNG2 -0.015 0.048 -10000 0 -0.2 41 41
AKT1 0.05 0.072 -10000 0 -0.21 30 30
EGF -0.16 0.31 -10000 0 -0.78 216 216
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR -0.01 0.052 -10000 0 -0.54 3 3
mol:Ca2+ 0.047 0.1 -10000 0 -0.3 64 64
LYN -0.01 0.05 -10000 0 -0.51 2 2
RhoA/GTP -0.008 0.03 -10000 0 -0.14 2 2
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.052 0.11 -10000 0 -0.35 64 64
GNG2 -0.009 0.086 -10000 0 -0.79 13 13
ARRB2 0 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.029 0.058 -10000 0 -0.53 8 8
G beta5/gamma2 -0.019 0.064 -10000 0 -0.28 40 40
PRKCH 0.048 0.11 -10000 0 -0.35 64 64
DNM1 -0.005 0.064 -10000 0 -0.73 8 8
TXA2/TP beta/beta Arrestin3 -0.004 0.027 -10000 0 -0.3 7 7
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
PTGDR -0.03 0.15 -10000 0 -0.71 46 46
G12 family/GTP -0.022 0.073 -10000 0 -0.31 64 64
ADRBK1 0 0 -10000 0 -10000 0 0
ADRBK2 -0.004 0.053 -10000 0 -0.79 5 5
RhoA/GTP/ROCK1 0 0.016 -10000 0 -0.53 1 1
mol:GDP -0.036 0.081 0.36 23 -10000 0 23
mol:NADP 0 0 -10000 0 -10000 0 0
RAB11A -0.001 0.013 -10000 0 -0.29 2 2
PRKG1 -0.053 0.2 -10000 0 -0.79 73 73
mol:IP3 0.047 0.12 -10000 0 -0.38 64 64
cell morphogenesis 0 0.016 -10000 0 -0.52 1 1
PLCB2 0.045 0.15 -10000 0 -0.52 64 64
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.008 0.062 -10000 0 -0.44 6 6
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.011 0.05 -10000 0 -0.51 2 2
RHOA 0 0 -10000 0 -10000 0 0
PTGIR -0.002 0.027 -10000 0 -0.29 9 9
PRKCB1 0.045 0.12 -10000 0 -0.38 64 64
GNAQ -0.002 0.041 -10000 0 -0.79 3 3
mol:L-citrulline 0 0 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.047 0.16 -10000 0 -0.55 64 64
LCK -0.015 0.071 -10000 0 -0.47 15 15
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.012 0.056 -10000 0 -0.35 1 1
TXA2-R family/G12 family/GDP/G beta/gamma 0.025 0.035 -10000 0 -0.29 8 8
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.011 0.054 -10000 0 -0.34 1 1
MAPK14 0.051 0.079 -10000 0 -0.24 38 38
TGM2/GTP 0.047 0.13 -10000 0 -0.43 64 64
MAPK11 0.051 0.082 -10000 0 -0.24 64 64
ARHGEF1 0.038 0.061 -10000 0 -0.18 38 38
GNAI2 0 0 -10000 0 -10000 0 0
JNK cascade 0.049 0.12 -10000 0 -0.4 64 64
RAB11/GDP -0.001 0.012 -10000 0 -0.29 2 2
ICAM1 0.046 0.093 -10000 0 -0.28 64 64
cAMP biosynthetic process 0.043 0.12 -10000 0 -0.36 64 64
Gq family/GTP/EBP50 0.017 0.038 -10000 0 -0.31 4 4
actin cytoskeleton reorganization 0 0.016 -10000 0 -0.52 1 1
SRC -0.01 0.05 -10000 0 -0.51 2 2
GNB5 0 0 -10000 0 -10000 0 0
GNB1 0 0 -10000 0 -10000 0 0
EGF/EGFR -0.029 0.1 -10000 0 -0.33 30 30
VCAM1 0.044 0.1 -10000 0 -0.32 64 64
TP beta/Gq family/GDP/G beta5/gamma2 0.029 0.058 -10000 0 -0.53 8 8
platelet activation 0.066 0.1 -10000 0 -0.31 64 64
PGI2/IP -0.002 0.018 -10000 0 -10000 0 0
PRKACA -0.014 0.069 -10000 0 -0.37 39 39
Gq family/GDP/G beta5/gamma2 0.027 0.06 -10000 0 -0.52 8 8
TXA2/TP beta/beta Arrestin2 -0.005 0.053 -10000 0 -0.65 7 7
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.01 0.07 -10000 0 -0.34 39 39
mol:DAG 0.046 0.13 -10000 0 -0.42 64 64
EGFR -0.3 0.38 -10000 0 -0.78 414 414
TXA2/TP alpha 0.048 0.15 -10000 0 -0.5 64 64
Gq family/GTP -0.004 0.035 -10000 0 -0.27 17 17
YES1 -0.01 0.051 -10000 0 -0.46 3 3
GNAI2/GTP -0.012 0.058 -10000 0 -0.46 5 5
PGD2/DP -0.023 0.11 -10000 0 -0.59 41 41
SLC9A3R1 -0.026 0.083 -10000 0 -10000 0 0
FYN -0.011 0.053 -10000 0 -0.5 4 4
mol:NO 0 0 -10000 0 -10000 0 0
GNA15 -0.003 0.033 -10000 0 -0.36 8 8
PGK/cGMP -0.035 0.13 -10000 0 -0.53 73 73
RhoA/GDP 0 0 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.017 0.079 -10000 0 -0.59 12 12
NOS3 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PRKCA 0.042 0.12 -10000 0 -0.38 71 71
PRKCB 0.043 0.12 -10000 0 -0.37 73 73
PRKCE 0.05 0.11 -10000 0 -0.35 64 64
PRKCD 0.048 0.12 -10000 0 -0.38 64 64
PRKCG 0.044 0.12 -10000 0 -0.39 64 64
muscle contraction 0.05 0.15 -10000 0 -0.5 64 64
PRKCZ 0.052 0.11 -10000 0 -0.35 64 64
ARR3 -0.002 0.025 -10000 0 -0.29 8 8
TXA2/TP beta -0.013 0.065 -10000 0 -0.5 6 6
PRKCQ 0.037 0.14 -10000 0 -0.39 79 79
MAPKKK cascade 0.044 0.14 -10000 0 -0.48 64 64
SELE 0.038 0.12 -10000 0 -0.42 64 64
TP beta/GNAI2/GDP/G beta/gamma -0.015 0.079 -10000 0 -0.57 13 13
ROCK1 -0.001 0.024 -10000 0 -0.79 1 1
GNA14 -0.013 0.085 -10000 0 -0.45 32 32
chemotaxis 0.046 0.18 -10000 0 -0.62 64 64
GNA12 0 0 -10000 0 -10000 0 0
GNA13 0 0 -10000 0 -10000 0 0
GNA11 -0.002 0.041 -10000 0 -0.79 3 3
Rac1/GTP 0 0 -10000 0 -10000 0 0
Aurora A signaling

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
Aurora A/GADD45A -0.026 0.032 -9999 0 -10000 0 0
BIRC5 -0.21 0.13 -9999 0 -0.29 779 779
NFKBIA -0.024 0.034 -9999 0 -10000 0 0
CPEB1 -0.15 0.31 -9999 0 -0.79 204 204
AKT1 -0.024 0.034 -9999 0 -10000 0 0
NDEL1 0 0 -9999 0 -10000 0 0
Aurora A/BRCA1 -0.024 0.033 -9999 0 -0.55 1 1
NDEL1/TACC3 -0.041 0.061 -9999 0 -10000 0 0
GADD45A 0 0 -9999 0 -10000 0 0
GSK3B 0.003 0.004 -9999 0 -10000 0 0
PAK1/Aurora A -0.03 0.04 -9999 0 -10000 0 0
MDM2 -0.001 0.02 -9999 0 -0.29 5 5
JUB -0.003 0.048 -9999 0 -0.79 4 4
TPX2 -0.11 0.1 -9999 0 -10000 0 0
TP53 -0.011 0.017 -9999 0 -10000 0 0
DLG7 -0.03 0.037 -9999 0 -10000 0 0
AURKAIP1 -0.003 0.031 -9999 0 -0.29 12 12
ARHGEF7 0 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.044 0.066 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.024 0.033 -9999 0 -0.54 1 1
AURKA -0.037 0.046 -9999 0 -10000 0 0
AURKB -0.01 0.011 -9999 0 -10000 0 0
CDC25B -0.018 0.026 -9999 0 -10000 0 0
G2/M transition checkpoint -0.025 0.04 -9999 0 -0.49 4 4
mRNA polyadenylation -0.11 0.2 -9999 0 -0.52 204 204
Aurora A/CPEB -0.12 0.2 -9999 0 -0.52 204 204
Aurora A/TACC1/TRAP/chTOG -0.032 0.088 -9999 0 -0.47 41 41
BRCA1 -0.001 0.027 -9999 0 -0.46 3 3
centrosome duplication -0.03 0.04 -9999 0 -10000 0 0
regulation of centrosome cycle -0.04 0.061 -9999 0 -10000 0 0
spindle assembly -0.032 0.087 -9999 0 -0.46 41 41
TDRD7 0 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.1 0.072 -9999 0 -0.61 1 1
CENPA -0.006 0.012 -9999 0 -10000 0 0
Aurora A/PP2A -0.026 0.032 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.006 0.029 -9999 0 -10000 0 0
negative regulation of DNA binding -0.009 0.02 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX -0.001 0.013 -9999 0 -10000 0 0
RASA1 0 0 -9999 0 -10000 0 0
Ajuba/Aurora A -0.025 0.04 -9999 0 -0.5 4 4
mitotic prometaphase -0.012 0.011 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.037 0.046 -9999 0 -10000 0 0
TACC1 -0.03 0.15 -9999 0 -0.79 41 41
TACC3 -0.046 0.11 -9999 0 -0.29 173 173
Aurora A/Antizyme1 -0.022 0.025 -9999 0 -10000 0 0
Aurora A/RasGAP -0.026 0.032 -9999 0 -10000 0 0
OAZ1 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.003 0.004 -9999 0 -10000 0 0
GIT1 -0.001 0.02 -9999 0 -0.29 5 5
GIT1/beta-PIX/PAK1 -0.004 0.023 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.11 0.1 -9999 0 -10000 0 0
PPP2R5D 0 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.11 0.09 -9999 0 -10000 0 0
PAK1 -0.007 0.044 -9999 0 -0.29 25 25
CKAP5 0 0 -9999 0 -10000 0 0
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.44 0.39 -10000 0 -0.79 610 610
CLTC 0.027 0.018 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.024 0.02 -10000 0 -10000 0 0
Dynamin 2/GTP -0.006 0.028 -10000 0 -10000 0 0
EXOC4 0 0 -10000 0 -10000 0 0
CD59 0.025 0.019 -10000 0 -10000 0 0
CPE 0.006 0.08 -10000 0 -0.53 24 24
CTNNB1 0 0 -10000 0 -10000 0 0
membrane fusion -0.002 0.019 -10000 0 -10000 0 0
CTNND1 0.025 0.031 -10000 0 -10000 0 0
DNM2 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.03 0.014 -10000 0 -10000 0 0
TSHR -0.007 0.11 -10000 0 -0.53 49 49
INS 0.011 0.005 -10000 0 -10000 0 0
BIN1 -0.007 0.072 -10000 0 -0.74 10 10
mol:Choline -0.002 0.019 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.01 0.037 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.006 0.028 -10000 0 -10000 0 0
JUP 0.025 0.017 -10000 0 -10000 0 0
ASAP2/amphiphysin II -0.004 0.046 -10000 0 -0.48 10 10
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 0.017 0.05 -10000 0 -0.37 1 1
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 0 0.009 -10000 0 -10000 0 0
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 -0.005 0.037 -10000 0 -0.29 18 18
substrate adhesion-dependent cell spreading 0 0.001 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.009 0.033 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.018 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0 0.005 -10000 0 -10000 0 0
ACAP1 -0.001 0.019 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.02 0.015 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.032 0.022 -10000 0 -10000 0 0
JIP4/KLC1 0 0 -10000 0 -10000 0 0
EXOC1 0 0 -10000 0 -10000 0 0
exocyst 0 0.001 -10000 0 -10000 0 0
RALA/GTP 0 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -10000 0 -10000 0 0
receptor recycling 0 0 -10000 0 -10000 0 0
CTNNA1 0.025 0.031 -10000 0 -10000 0 0
NME1 0.01 0.038 -10000 0 -10000 0 0
clathrin coat assembly 0.027 0.018 -10000 0 -10000 0 0
IL2RA 0.017 0.045 -10000 0 -0.37 7 7
VAMP3 0.018 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.22 0.2 -10000 0 -0.39 610 610
EXOC6 0 0 -10000 0 -10000 0 0
PLD1 -0.003 0.032 -10000 0 -0.34 10 10
PLD2 0 0 -10000 0 -10000 0 0
EXOC5 0 0 -10000 0 -10000 0 0
PIP5K1C 0.03 0.014 -10000 0 -10000 0 0
SDC1 0.021 0.024 -10000 0 -0.35 1 1
ARF6/GDP -0.008 0.033 -10000 0 -10000 0 0
EXOC7 0 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.009 0.033 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.002 0.019 -10000 0 -10000 0 0
endocytosis 0.004 0.045 0.47 10 -10000 0 10
SCAMP2 0 0 -10000 0 -10000 0 0
ADRB2 -0.07 0.19 -10000 0 -0.42 250 250
EXOC3 0 0 -10000 0 -10000 0 0
ASAP2 -0.001 0.024 -10000 0 -0.79 1 1
Dynamin 2/GDP -0.006 0.028 -10000 0 -10000 0 0
KLC1 0 0 -10000 0 -10000 0 0
AVPR2 -0.13 0.22 -10000 0 -0.42 397 397
RALA 0 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.007 0.028 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.001 0.004 -9999 0 -10000 0 0
HDAC2 0.001 0.004 -9999 0 -10000 0 0
GNB1/GNG2 -0.01 0.074 -9999 0 -0.54 20 20
forebrain development -0.024 0.2 -9999 0 -0.51 135 135
GNAO1 -0.021 0.13 -9999 0 -0.49 67 67
SMO/beta Arrestin2 -0.005 0.052 -9999 0 -0.6 8 8
SMO 0.005 0.069 -9999 0 -0.74 9 9
ARRB2 0.011 0.004 -9999 0 -10000 0 0
GLI3/SPOP 0.044 0.037 -9999 0 -10000 0 0
mol:GTP 0 0.003 -9999 0 -10000 0 0
GSK3B 0 0 -9999 0 -10000 0 0
GNAI2 0.01 0.004 -9999 0 -10000 0 0
SIN3/HDAC complex 0 0.007 -9999 0 -10000 0 0
GNAI1 -0.036 0.18 -9999 0 -0.79 62 62
XPO1 0.012 0.004 -9999 0 -10000 0 0
GLI1/Su(fu) -0.054 0.16 -9999 0 -0.53 71 71
SAP30 0 0.018 -9999 0 -0.29 4 4
mol:GDP 0.005 0.069 -9999 0 -0.74 9 9
MIM/GLI2A 0.002 0.028 -9999 0 -0.3 9 9
IFT88 0 0 -9999 0 -10000 0 0
GNAI3 0.01 0.004 -9999 0 -10000 0 0
GLI2 0.04 0.036 -9999 0 -10000 0 0
GLI3 0.04 0.039 -9999 0 -10000 0 0
CSNK1D 0 0 -9999 0 -10000 0 0
CSNK1E 0 0 -9999 0 -10000 0 0
SAP18 0.001 0.004 -9999 0 -10000 0 0
embryonic digit morphogenesis 0 0 -9999 0 -10000 0 0
GNG2 -0.009 0.086 -9999 0 -0.79 13 13
Gi family/GTP -0.001 0.1 -9999 0 -0.36 49 49
SIN3B 0.001 0.004 -9999 0 -10000 0 0
SIN3A 0.001 0.004 -9999 0 -10000 0 0
GLI3/Su(fu) -0.002 0.025 -9999 0 -0.44 1 1
GLI2/Su(fu) 0.008 0.046 -9999 0 -0.39 6 6
FOXA2 -0.012 0.032 -9999 0 -10000 0 0
neural tube patterning -0.024 0.2 -9999 0 -0.51 135 135
SPOP 0 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 -0.002 0.025 -9999 0 -0.45 1 1
GNB1 0 0 -9999 0 -10000 0 0
CSNK1G2 0 0 -9999 0 -10000 0 0
CSNK1G3 0 0 -9999 0 -10000 0 0
MTSS1 0.002 0.029 -9999 0 -0.3 9 9
embryonic limb morphogenesis -0.024 0.2 -9999 0 -0.51 135 135
SUFU 0.004 0.031 -9999 0 -0.34 4 4
LGALS3 -0.012 0.095 -9999 0 -0.79 16 16
catabolic process -0.004 0.027 -9999 0 -10000 0 0
GLI3A/CBP -0.008 0.098 -9999 0 -0.38 70 70
KIF3A 0 0 -9999 0 -10000 0 0
GLI1 -0.026 0.21 -9999 0 -0.52 135 135
RAB23 0 0 -9999 0 -10000 0 0
CSNK1A1 0 0 -9999 0 -10000 0 0
IFT172 -0.001 0.024 -9999 0 -0.79 1 1
RBBP7 -0.001 0.025 -9999 0 -0.29 8 8
Su(fu)/Galectin3 -0.009 0.067 -9999 0 -0.52 17 17
GNAZ 0.003 0.072 -9999 0 -0.79 9 9
RBBP4 0.001 0.024 -9999 0 -0.79 1 1
CSNK1G1 0 0 -9999 0 -10000 0 0
PIAS1 0 0 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GLI2/SPOP -0.004 0.026 -9999 0 -10000 0 0
STK36 0.011 0.025 -9999 0 -0.79 1 1
Gi family/GNB1/GNG2/GDP -0.03 0.1 -9999 0 -0.47 27 27
PTCH1 -0.066 0.34 -9999 0 -1.1 91 91
MIM/GLI1 -0.018 0.19 -9999 0 -0.57 74 74
CREBBP -0.008 0.097 -9999 0 -0.38 70 70
Su(fu)/SIN3/HDAC complex 0.007 0.022 -9999 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.022 0 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0 0.007 -10000 0 -10000 0 0
CDKN1B 0.036 0.024 -10000 0 -0.42 3 3
CDKN1A 0.036 0.02 -10000 0 -0.42 2 2
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC -0.001 0.018 -10000 0 -0.29 4 4
FOXO3 0.036 0.024 -10000 0 -0.42 3 3
AKT1 0 0.001 -10000 0 -10000 0 0
BAD 0 0.009 -10000 0 -0.29 1 1
AKT3 0.009 0.059 -10000 0 -0.44 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.037 0.003 -10000 0 -10000 0 0
AKT1/ASK1 -0.001 0.025 -10000 0 -0.41 4 4
BAD/YWHAZ -0.001 0.009 -10000 0 -10000 0 0
RICTOR 0 0 -10000 0 -10000 0 0
RAF1 0 0 -10000 0 -10000 0 0
JNK cascade 0.001 0.024 0.4 4 -10000 0 4
TSC1 0.037 0.003 -10000 0 -10000 0 0
YWHAZ -0.001 0.015 -10000 0 -0.29 3 3
AKT1/RAF1 0 0.001 -10000 0 -10000 0 0
EP300 0 0 -10000 0 -10000 0 0
mol:GDP 0 0.001 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.037 0.003 -10000 0 -10000 0 0
YWHAQ 0 0 -10000 0 -10000 0 0
TBC1D4 0.022 0.04 -10000 0 -0.51 6 6
MAP3K5 -0.003 0.048 -10000 0 -0.79 4 4
MAPKAP1 0 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.04 0.022 -10000 0 -10000 0 0
YWHAH 0 0 -10000 0 -10000 0 0
AKT1S1 0.037 0.003 -10000 0 -10000 0 0
CASP9 0.037 0.003 -10000 0 -10000 0 0
YWHAB 0 0 -10000 0 -10000 0 0
p27Kip1/KPNA1 -0.001 0.021 -10000 0 -0.39 3 3
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0 0.006 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
SRC 0 0.009 -10000 0 -0.29 1 1
AKT2/p21CIP1 -0.001 0.017 -10000 0 -0.4 2 2
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.018 0.001 -10000 0 -10000 0 0
CHUK 0.037 0.003 -10000 0 -10000 0 0
BAD/BCL-XL 0 0.003 -10000 0 -10000 0 0
mTORC2 0 0 -10000 0 -10000 0 0
AKT2 0.017 0 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.054 0.03 -10000 0 -10000 0 0
PDPK1 0 0 -10000 0 -10000 0 0
MDM2 0.037 0.01 -10000 0 -10000 0 0
MAPKKK cascade 0 0.001 -10000 0 -10000 0 0
MDM2/Cbp/p300 0 0.005 -10000 0 -10000 0 0
TSC1/TSC2 0.044 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0.005 -10000 0 -10000 0 0
glucose import -0.25 0.25 -10000 0 -0.47 612 612
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.031 0.002 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.25 0.25 -10000 0 -0.47 612 612
GSK3A 0.037 0.003 -10000 0 -10000 0 0
FOXO1 0.033 0.046 -10000 0 -0.42 11 11
GSK3B 0.037 0.003 -10000 0 -10000 0 0
SFN -0.016 0.099 -10000 0 -0.51 35 35
G1/S transition of mitotic cell cycle 0.044 0.003 -10000 0 -10000 0 0
p27Kip1/14-3-3 family 0.043 0.032 -10000 0 -10000 0 0
PRKACA 0 0 -10000 0 -10000 0 0
KPNA1 0 0 -10000 0 -10000 0 0
HSP90AA1 0 0.009 -10000 0 -0.29 1 1
YWHAG 0 0 -10000 0 -10000 0 0
RHEB 0 0 -10000 0 -10000 0 0
CREBBP 0 0 -10000 0 -10000 0 0
Ceramide signaling pathway

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
SPHK2 0.022 0.02 -10000 0 -0.6 1 1
MAP4K4 0.041 0.044 -10000 0 -0.68 1 1
BAG4 -0.006 0.055 -10000 0 -0.44 14 14
PKC zeta/ceramide -0.023 0.047 0.18 1 -0.57 1 2
NFKBIA 0 0 -10000 0 -10000 0 0
BIRC3 -0.01 0.077 -10000 0 -0.51 21 21
BAX -0.008 0.021 -10000 0 -10000 0 0
RIPK1 0 0 -10000 0 -10000 0 0
AKT1 0.024 0.009 -10000 0 -10000 0 0
BAD -0.022 0.045 0.2 1 -0.25 1 2
SMPD1 0.026 0.032 -10000 0 -0.24 13 13
RB1 -0.022 0.049 0.2 1 -0.47 2 3
FADD/Caspase 8 0.049 0.046 -10000 0 -0.64 1 1
MAP2K4 -0.014 0.046 -10000 0 -0.45 2 2
NSMAF 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.014 0.045 -10000 0 -0.45 1 1
EGF -0.16 0.31 -10000 0 -0.78 216 216
mol:ceramide -0.033 0.047 0.21 1 -10000 0 1
MADD 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.021 0.023 -10000 0 -0.6 1 1
ASAH1 -0.001 0.015 -10000 0 -0.29 3 3
negative regulation of cell cycle -0.022 0.048 0.2 1 -0.46 2 3
cell proliferation -0.094 0.16 -10000 0 -0.38 246 246
BID 0.024 0.033 -10000 0 -0.39 1 1
MAP3K1 -0.022 0.047 0.2 1 -0.47 1 2
EIF2A -0.005 0.041 -10000 0 -10000 0 0
TRADD 0 0 -10000 0 -10000 0 0
CRADD 0 0 -10000 0 -10000 0 0
MAPK3 -0.002 0.043 -10000 0 -0.41 1 1
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.002 0.043 -10000 0 -0.41 1 1
Cathepsin D/ceramide -0.027 0.05 0.18 1 -0.25 2 3
FADD 0.039 0.048 -10000 0 -0.47 3 3
KSR1 -0.022 0.048 0.2 1 -0.33 3 4
MAPK8 -0.012 0.054 0.2 1 -0.35 10 11
PRKRA -0.022 0.045 0.2 1 -10000 0 1
PDGFA -0.001 0.025 -10000 0 -0.79 1 1
TRAF2 -0.001 0.018 -10000 0 -0.29 4 4
IGF1 -0.18 0.33 -10000 0 -0.79 246 246
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.033 0.047 0.21 1 -10000 0 1
CTSD -0.01 0.053 -10000 0 -0.29 37 37
regulation of nitric oxide biosynthetic process 0 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.1 0.17 -10000 0 -0.41 246 246
PRKCD 0 0.009 -10000 0 -0.29 1 1
PRKCZ -0.001 0.024 -10000 0 -0.79 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.021 0.023 -10000 0 -0.6 1 1
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR -0.001 0.024 -10000 0 -0.79 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.006 0.04 -10000 0 -0.72 1 1
TNFR1A/BAG4/TNF-alpha -0.013 0.069 -10000 0 -0.53 17 17
mol:Sphingosine-1-phosphate 0.022 0.02 -10000 0 -0.6 1 1
MAP2K1 -0.005 0.043 -10000 0 -0.42 1 1
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0 0 -10000 0 -10000 0 0
CYCS -0.007 0.043 0.18 25 -10000 0 25
TNFRSF1A 0 0 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
TNFR1A/BAG4 -0.004 0.04 -10000 0 -0.6 4 4
EIF2AK2 -0.013 0.042 0.2 1 -10000 0 1
TNF-alpha/TNFR1A/FAN -0.009 0.06 -10000 0 -0.52 13 13
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.002 0.02 -10000 0 -0.32 1 1
MAP2K2 -0.005 0.043 -10000 0 -0.42 1 1
SMPD3 0.025 0.041 -10000 0 -0.28 17 17
TNF -0.016 0.096 -10000 0 -0.46 38 38
PKC zeta/PAR4 -0.001 0.026 -10000 0 -0.6 2 2
mol:PHOSPHOCHOLINE 0.045 0.11 0.27 215 -10000 0 215
NF kappa B1/RelA/I kappa B alpha -0.001 0.019 -10000 0 -0.44 2 2
AIFM1 -0.007 0.043 0.18 25 -10000 0 25
BCL2 -0.027 0.14 -10000 0 -0.79 37 37
TRAIL signaling pathway

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
TNFSF10 -0.007 0.072 -10000 0 -0.74 10 10
positive regulation of NF-kappaB transcription factor activity -0.062 0.18 -10000 0 -0.6 113 113
MAP2K4 0.042 0.038 -10000 0 -0.42 1 1
IKBKB -0.001 0.013 -10000 0 -0.29 2 2
TNFRSF10B 0 0 -10000 0 -10000 0 0
TNFRSF10A -0.005 0.063 -10000 0 -0.79 7 7
SMPD1 -0.002 0.026 -10000 0 -0.28 9 9
IKBKG 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.076 0.23 -10000 0 -0.78 105 105
TRAIL/TRAILR2 -0.005 0.055 -10000 0 -0.6 9 9
TRAIL/TRAILR3 -0.008 0.068 -10000 0 -0.65 11 11
TRAIL/TRAILR1 -0.009 0.073 -10000 0 -0.6 16 16
TRAIL/TRAILR4 -0.063 0.18 -10000 0 -0.6 113 113
TRAIL/TRAILR1/DAP3/GTP -0.007 0.058 -10000 0 -0.48 16 16
IKK complex -0.003 0.019 -10000 0 -10000 0 0
RIPK1 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0 0.006 -10000 0 -10000 0 0
MAPK3 0.017 0.057 -10000 0 -0.6 9 9
MAP3K1 -0.004 0.032 -10000 0 -0.32 10 10
TRAILR4 (trimer) -0.075 0.23 -10000 0 -0.78 105 105
TRADD 0 0 -10000 0 -10000 0 0
TRAILR1 (trimer) -0.005 0.063 -10000 0 -0.79 7 7
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.005 0.039 -10000 0 -0.32 16 16
CFLAR 0 0 -10000 0 -10000 0 0
MAPK1 0.017 0.057 -10000 0 -0.6 9 9
TRAIL/TRAILR1/FADD/TRADD/RIP -0.008 0.055 -10000 0 -0.45 16 16
mol:ceramide -0.002 0.025 -10000 0 -0.28 9 9
FADD -0.004 0.035 -10000 0 -0.29 16 16
MAPK8 0.045 0.055 -10000 0 -0.44 9 9
TRAF2 -0.001 0.018 -10000 0 -0.29 4 4
TRAILR3 (trimer) -0.004 0.048 -10000 0 -0.43 11 11
CHUK 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.01 0.065 -10000 0 -0.53 16 16
DAP3 0 0.009 -10000 0 -0.29 1 1
CASP10 0.021 0.11 0.31 98 -0.49 13 111
JNK cascade -0.062 0.18 -10000 0 -0.6 113 113
TRAIL (trimer) -0.007 0.072 -10000 0 -0.74 10 10
TNFRSF10C -0.004 0.048 -10000 0 -0.43 11 11
TRAIL/TRAILR1/DAP3/GTP/FADD -0.008 0.056 -10000 0 -0.45 16 16
TRAIL/TRAILR2/FADD -0.007 0.05 -10000 0 -0.52 9 9
cell death -0.002 0.025 -10000 0 -0.28 9 9
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.003 0.029 -10000 0 -0.32 9 9
TRAILR2 (trimer) 0 0 -10000 0 -10000 0 0
CASP8 0.001 0.014 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.005 0.041 -10000 0 -0.44 9 9
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0 0 -10000 0 -10000 0 0
HDAC3 0 0 -10000 0 -10000 0 0
VDR 0 0 -10000 0 -10000 0 0
Cbp/p300/PCAF 0 0.016 -10000 0 -0.52 1 1
EP300 0 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.037 0.04 -10000 0 -0.32 5 5
KAT2B -0.001 0.024 -10000 0 -0.79 1 1
MAPK14 0 0 -10000 0 -10000 0 0
AKT1 0.02 0.05 0.24 4 -0.34 13 17
RAR alpha/9cRA/Cyclin H -0.011 0.064 -10000 0 -0.38 28 28
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.034 0.049 -10000 0 -0.32 15 15
CDC2 0.001 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.012 0.068 -10000 0 -0.56 11 11
NCOR2 0 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0 0 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA 0.007 0.12 -10000 0 -0.56 34 34
NCOA2 -0.038 0.17 -10000 0 -0.79 53 53
NCOA3 0 0.009 -10000 0 -0.29 1 1
NCOA1 -0.001 0.024 -10000 0 -0.79 1 1
VDR/VDR/DNA 0 0 -10000 0 -10000 0 0
RARG 0.012 0.001 -10000 0 -10000 0 0
RAR gamma1/9cRA 0 0 -10000 0 -10000 0 0
MAPK3 0.011 0.002 -10000 0 -10000 0 0
MAPK1 0 0 -10000 0 -10000 0 0
MAPK8 0.006 0.068 -10000 0 -0.79 8 8
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.041 0.11 -10000 0 -0.62 28 28
RARA 0.014 0.062 -10000 0 -0.31 35 35
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.02 0.085 -10000 0 -0.29 65 65
PRKCA -0.007 0.13 -10000 0 -0.76 30 30
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.004 0.13 -10000 0 -0.58 35 35
RXRG -0.1 0.21 -10000 0 -0.44 287 287
RXRA 0.022 0.065 -10000 0 -0.32 35 35
RXRB 0.011 0.075 -10000 0 -0.43 28 28
VDR/Vit D3/DNA 0 0 -10000 0 -10000 0 0
RBP1 -0.026 0.097 -10000 0 -0.34 84 84
CRBP1/9-cic-RA -0.018 0.07 -10000 0 -0.23 84 84
RARB 0.003 0.09 -10000 0 -0.79 14 14
PRKCG -0.003 0.062 -10000 0 -0.29 49 49
MNAT1 0 0 -10000 0 -10000 0 0
RAR alpha/RXRs -0.007 0.12 -10000 0 -0.6 32 32
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.013 0.1 -10000 0 -0.49 33 33
proteasomal ubiquitin-dependent protein catabolic process 0.036 0.057 -10000 0 -0.44 6 6
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.004 0.13 -10000 0 -0.58 35 35
positive regulation of DNA binding -0.011 0.06 -10000 0 -0.36 28 28
NRIP1 -0.002 0.12 -10000 0 -0.84 9 9
RXRs/RARs -0.011 0.13 -10000 0 -0.57 35 35
RXRs/RXRs/DNA/9cRA -0.045 0.11 -10000 0 -0.63 29 29
PRKACA 0 0 -10000 0 -10000 0 0
CDK7 0 0 -10000 0 -10000 0 0
TFIIH 0 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.006 0.035 -10000 0 -0.52 1 1
CCNH 0 0 -10000 0 -10000 0 0
CREBBP 0 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0 0 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 0.005 0.094 0.23 1 -0.44 38 39
ACTA1 -0.018 0.13 0.27 1 -0.61 39 40
NUMA1 0.005 0.094 0.23 1 -0.44 38 39
SPTAN1 -0.005 0.12 0.27 1 -0.61 35 36
LIMK1 -0.005 0.13 -10000 0 -0.61 35 35
BIRC3 -0.01 0.077 -10000 0 -0.51 21 21
BIRC2 0 0 -10000 0 -10000 0 0
BAX -0.001 0.02 -10000 0 -0.29 5 5
CASP10 -0.016 0.14 -10000 0 -0.65 39 39
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 0.005 0.094 0.23 1 -0.44 38 39
DIABLO 0 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.004 0.12 0.27 1 -0.6 35 36
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0 0 -10000 0 -10000 0 0
GSN -0.01 0.14 0.27 1 -0.62 44 45
MADD 0 0 -10000 0 -10000 0 0
TFAP2A 0.014 0.083 -10000 0 -0.67 15 15
BID 0.005 0.063 -10000 0 -0.29 38 38
MAP3K1 0.004 0.042 -10000 0 -0.27 9 9
TRADD 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.005 0.12 0.27 1 -0.61 35 36
CASP9 0.002 0.004 -10000 0 -10000 0 0
DNA repair -0.002 0.031 0.18 2 -0.22 4 6
neuron apoptosis 0.022 0.013 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.003 0.12 -10000 0 -0.58 35 35
APAF1 0.001 0.003 -10000 0 -10000 0 0
CASP6 0.023 0.057 -10000 0 -0.39 5 5
TRAF2 -0.001 0.018 -10000 0 -0.29 4 4
ICAD/CAD 0.003 0.12 -10000 0 -0.58 35 35
CASP7 -0.007 0.037 0.36 9 -10000 0 9
KRT18 0.015 0.024 -10000 0 -0.59 1 1
apoptosis 0.009 0.11 0.3 1 -0.52 35 36
DFFA -0.005 0.12 0.27 1 -0.6 36 37
DFFB -0.005 0.12 -10000 0 -0.61 35 35
PARP1 0.002 0.031 0.22 4 -0.19 2 6
actin filament polymerization -0.002 0.12 0.55 39 -10000 0 39
TNF -0.016 0.096 -10000 0 -0.46 38 38
CYCS 0.007 0.05 -10000 0 -0.21 36 36
SATB1 0.017 0.098 -10000 0 -0.47 31 31
SLK -0.005 0.12 -10000 0 -0.61 35 35
p15 BID/BAX -0.014 0.049 -10000 0 -0.35 8 8
CASP2 0.044 0.039 -10000 0 -0.45 1 1
JNK cascade -0.004 0.042 0.27 9 -10000 0 9
CASP3 -0.014 0.13 0.28 1 -0.62 39 40
LMNB2 0.041 0.036 -10000 0 -0.38 2 2
RIPK1 0 0 -10000 0 -10000 0 0
CASP4 -0.001 0.024 -10000 0 -0.79 1 1
Mammalian IAPs/DIABLO -0.005 0.044 -10000 0 -0.47 9 9
negative regulation of DNA binding 0.014 0.082 -10000 0 -0.66 15 15
stress fiber formation -0.004 0.12 0.27 1 -0.6 35 36
GZMB -0.029 0.15 -10000 0 -0.64 47 47
CASP1 0.014 0.034 -10000 0 -0.44 6 6
LMNB1 0.044 0.037 -10000 0 -0.38 2 2
APP 0.022 0.013 -10000 0 -10000 0 0
TNFRSF1A 0 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 0.003 0.1 0.3 1 -0.5 35 36
LMNA 0.04 0.036 -10000 0 -0.38 2 2
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.005 0.035 -10000 0 -0.48 1 1
LRDD -0.001 0.02 -10000 0 -0.29 5 5
SREBF1 -0.008 0.13 -10000 0 -0.62 35 35
APAF-1/Caspase 9 -0.004 0.02 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.005 0.093 0.23 1 -0.43 38 39
CFL2 0.001 0.12 -10000 0 -0.57 39 39
GAS2 -0.048 0.19 -10000 0 -0.52 129 129
positive regulation of apoptosis 0.045 0.036 -10000 0 -0.37 2 2
PRF1 -0.017 0.11 -10000 0 -0.64 29 29
BARD1 signaling events

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
BARD1/CSTF1 -0.011 0.079 -10000 0 -0.6 19 19
ATM 0 0 -10000 0 -10000 0 0
UBE2D3 0 0 -10000 0 -10000 0 0
PRKDC -0.001 0.018 -10000 0 -0.29 4 4
ATR 0 0 -10000 0 -10000 0 0
UBE2L3 0 0 -10000 0 -10000 0 0
FANCD2 0.024 0.01 -10000 0 -10000 0 0
protein ubiquitination -0.029 0.074 -10000 0 -0.47 20 20
XRCC5 0 0 -10000 0 -10000 0 0
XRCC6 0 0 -10000 0 -10000 0 0
M/R/N Complex 0 0 -10000 0 -10000 0 0
MRE11A 0 0 -10000 0 -10000 0 0
DNA-PK -0.001 0.009 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0 0.011 -10000 0 -10000 0 0
FANCF 0 0.009 -10000 0 -10000 0 0
BRCA1 -0.001 0.027 -10000 0 -0.46 3 3
CCNE1 -0.06 0.12 -10000 0 -0.29 223 223
CDK2/Cyclin E1 -0.038 0.075 -10000 0 -10000 0 0
FANCG 0 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.012 0.081 -10000 0 -0.6 20 20
FANCE 0 0 -10000 0 -10000 0 0
FANCC 0 0 -10000 0 -10000 0 0
NBN 0 0 -10000 0 -10000 0 0
FANCA -0.052 0.11 -10000 0 -10000 0 0
DNA repair 0.008 0.094 -10000 0 -0.47 6 6
BRCA1/BARD1/ubiquitin -0.012 0.081 -10000 0 -0.6 20 20
BARD1/DNA-PK -0.009 0.062 -10000 0 -0.47 19 19
FANCL 0 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.011 0.079 0.6 19 -10000 0 19
BRCA1/BARD1/CTIP/M/R/N Complex -0.006 0.041 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1/TopBP1 -0.01 0.07 -10000 0 -0.52 20 20
BRCA1/BARD1/P53 -0.009 0.063 -10000 0 -0.47 20 20
BARD1/CSTF1/BRCA1 -0.01 0.07 -10000 0 -0.52 20 20
BRCA1/BACH1 -0.001 0.027 -10000 0 -0.46 3 3
BARD1 -0.014 0.1 -10000 0 -0.76 20 20
PCNA -0.001 0.015 -10000 0 -0.29 3 3
BRCA1/BARD1/UbcH5C -0.01 0.07 -10000 0 -0.52 20 20
BRCA1/BARD1/UbcH7 -0.01 0.07 -10000 0 -0.52 20 20
BRCA1/BARD1/RAD51/PCNA -0.053 0.086 -10000 0 -0.51 20 20
BARD1/DNA-PK/P53 -0.008 0.058 -10000 0 -0.44 19 19
BRCA1/BARD1/Ubiquitin -0.012 0.081 -10000 0 -0.6 20 20
BRCA1/BARD1/CTIP -0.009 0.063 -10000 0 -0.47 20 20
FA complex -0.005 0.011 -10000 0 -10000 0 0
BARD1/EWS -0.011 0.079 -10000 0 -0.6 19 19
RBBP8 0.022 0.006 -10000 0 -10000 0 0
TP53 0 0 -10000 0 -10000 0 0
TOPBP1 0 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.009 0.063 0.47 20 -10000 0 20
BRCA1/BARD1 -0.029 0.075 -10000 0 -0.48 20 20
CSTF1 0 0.009 -10000 0 -0.29 1 1
BARD1/EWS-Fli1 -0.011 0.08 -10000 0 -0.61 19 19
CDK2 0 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.11 0.14 -10000 0 -0.29 396 396
RAD50 0 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.012 0.081 -10000 0 -0.6 20 20
EWSR1 0 0 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 -0.018 0.084 -9999 0 -0.51 24 24
MAP4K1 -0.015 0.07 -9999 0 -0.31 53 53
MAP3K8 -0.007 0.072 -9999 0 -0.74 10 10
PRKCB -0.02 0.11 -9999 0 -0.55 39 39
DBNL 0 0 -9999 0 -10000 0 0
CRKL 0 0 -9999 0 -10000 0 0
MAP3K1 0.036 0.054 -9999 0 -0.47 4 4
JUN 0.017 0.11 -9999 0 -0.6 34 34
MAP3K7 0.036 0.053 -9999 0 -0.32 19 19
GRAP2 -0.015 0.1 -9999 0 -0.72 22 22
CRK 0 0 -9999 0 -10000 0 0
MAP2K4 0.043 0.057 -9999 0 -0.32 20 20
LAT -0.005 0.048 -9999 0 -0.35 17 17
LCP2 0 0.009 -9999 0 -0.29 1 1
MAPK8 0.013 0.12 -9999 0 -0.68 27 27
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.008 0.049 -9999 0 -0.35 19 19
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.016 0.078 -9999 0 -0.48 24 24
Cellular roles of Anthrax toxin

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
ANTXR1 -0.002 0.042 -10000 0 -0.66 4 4
ANTXR2 -0.008 0.079 -10000 0 -0.79 11 11
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0.011 -10000 0 -0.1 13 13
monocyte activation 0.004 0.073 -10000 0 -0.46 26 26
MAP2K2 -0.001 0.005 -10000 0 -10000 0 0
MAP2K1 -0.001 0.009 -10000 0 -10000 0 0
MAP2K7 -0.001 0.009 -10000 0 -10000 0 0
MAP2K6 -0.012 0.071 -10000 0 -0.47 25 25
CYAA 0.01 0.057 -10000 0 -0.49 13 13
MAP2K4 -0.001 0.017 -10000 0 -0.47 1 1
IL1B 0.007 0.065 -10000 0 -0.34 32 32
Channel -0.006 0.058 -10000 0 -0.52 13 13
NLRP1 -0.008 0.06 -10000 0 -0.49 16 16
CALM1 0 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.001 0.013 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0.011 0.1 13 -10000 0 13
MAPK3 -0.001 0.009 -10000 0 -10000 0 0
MAPK1 -0.001 0.009 -10000 0 -10000 0 0
PGR -0.14 0.21 -10000 0 -0.47 314 314
PA/Cellular Receptors -0.007 0.063 -10000 0 -0.56 13 13
apoptosis -0.001 0.011 -10000 0 -0.1 13 13
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.006 0.054 -10000 0 -0.49 13 13
macrophage activation 0.02 0.01 -10000 0 -10000 0 0
TNF -0.016 0.096 -10000 0 -0.46 38 38
VCAM1 -0.011 0.071 -10000 0 -0.46 26 26
platelet activation -0.001 0.013 -10000 0 -10000 0 0
MAPKKK cascade -0.013 0.022 0.1 26 -10000 0 26
IL18 0.011 0.036 -10000 0 -0.22 16 16
negative regulation of macrophage activation -0.001 0.011 -10000 0 -0.1 13 13
LEF -0.001 0.011 -10000 0 -0.1 13 13
CASP1 -0.005 0.031 -10000 0 -0.18 25 25
mol:cAMP -0.001 0.013 -10000 0 -10000 0 0
necrosis -0.001 0.011 -10000 0 -0.1 13 13
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.006 0.055 -10000 0 -0.5 13 13
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.03 0.007 -9999 0 -10000 0 0
SNTA1 0 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.017 0.046 -9999 0 -10000 0 0
MAPK12 0.017 0.083 -9999 0 -0.46 30 30
CCND1 0.015 0.043 -9999 0 -0.22 28 28
p38 gamma/SNTA1 -0.012 0.072 -9999 0 -0.43 30 30
MAP2K3 0 0.009 -9999 0 -0.29 1 1
PKN1 0 0.009 -9999 0 -0.29 1 1
G2/M transition checkpoint 0.017 0.082 -9999 0 -0.46 30 30
MAP2K6 0.01 0.085 -9999 0 -0.49 30 30
MAPT -0.019 0.14 -9999 0 -0.4 119 119
MAPK13 0.022 0.009 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.014 0.031 -9999 0 -0.44 5 5
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin -0.015 0.086 -9999 0 -0.52 31 31
E-cadherin/beta catenin -0.017 0.098 -9999 0 -0.6 30 30
CTNNB1 0 0 -9999 0 -10000 0 0
JUP -0.001 0.025 -9999 0 -0.54 2 2
CDH1 -0.022 0.13 -9999 0 -0.79 30 30
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.045 0.065 -10000 0 -0.51 5 5
UGCG -0.011 0.095 -10000 0 -0.79 15 15
AKT1/mTOR/p70S6K/Hsp90/TERT 0.054 0.091 -10000 0 -0.39 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.013 0.097 -10000 0 -0.78 15 15
mol:DAG 0 0.002 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.026 0.09 -10000 0 -0.38 43 43
FRAP1 0.052 0.13 -10000 0 -0.41 64 64
FOXO3 0.06 0.11 -10000 0 -0.42 32 32
AKT1 0.055 0.11 -10000 0 -0.45 34 34
GAB2 0.007 0.044 -10000 0 -0.79 2 2
SMPD1 -0.002 0.014 -10000 0 -10000 0 0
SGMS1 -0.002 0.014 -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 0.015 0.06 -10000 0 -0.52 13 13
CALM1 0 0 -10000 0 -10000 0 0
cell proliferation 0.032 0.089 -10000 0 -0.35 39 39
EIF3A 0 0 -10000 0 -10000 0 0
PI3K -0.007 0.065 -10000 0 -0.6 13 13
RPS6KB1 0.021 0.034 -10000 0 -10000 0 0
mol:sphingomyelin 0 0.002 -10000 0 -10000 0 0
natural killer cell activation 0 0.002 -10000 0 -0.012 22 22
JAK3 0.01 0.034 -10000 0 -0.29 14 14
PIK3R1 0.004 0.087 -10000 0 -0.79 13 13
JAK1 0.013 0.024 -10000 0 -0.79 1 1
NFKB1 0 0 -10000 0 -10000 0 0
MYC 0.046 0.18 -10000 0 -0.94 29 29
MYB 0.006 0.2 -10000 0 -1.3 23 23
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.052 0.094 -10000 0 -0.59 10 10
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.004 0.022 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.052 0.092 -10000 0 -0.57 10 10
Rac1/GDP -0.006 0.052 -10000 0 -0.47 13 13
T cell proliferation 0.058 0.087 -10000 0 -0.52 10 10
SHC1 0.011 0.003 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.004 0.01 -10000 0 -0.066 23 23
PRKCZ 0.058 0.09 -10000 0 -0.55 10 10
NF kappa B1 p50/RelA -0.025 0.088 -10000 0 -0.49 15 15
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.039 0.07 -10000 0 -0.53 6 6
HSP90AA1 0 0.009 -10000 0 -0.29 1 1
RELA 0 0 -10000 0 -10000 0 0
IL2RA -0.02 0.12 -10000 0 -0.38 87 87
IL2RB 0.001 0.066 -10000 0 -0.31 42 42
TERT -0.043 0.1 -10000 0 -0.29 160 160
E2F1 0.02 0.068 -10000 0 -0.44 23 23
SOS1 0.011 0.003 -10000 0 -10000 0 0
RPS6 0 0 -10000 0 -10000 0 0
mol:cAMP -0.002 0.005 0.03 23 -10000 0 23
PTPN11 0.011 0.003 -10000 0 -10000 0 0
IL2RG -0.004 0.088 -10000 0 -0.36 53 53
actin cytoskeleton organization 0.058 0.087 -10000 0 -0.52 10 10
GRB2 0.011 0.01 -10000 0 -0.29 1 1
IL2 0.006 0.026 -10000 0 -0.29 8 8
PIK3CA 0.013 0.01 -10000 0 -0.29 1 1
Rac1/GTP 0.026 0.053 -10000 0 -0.45 13 13
LCK -0.007 0.1 -10000 0 -0.41 54 54
BCL2 0.039 0.2 -10000 0 -0.86 43 43
PLK2 and PLK4 events

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
PLK2 0 0.009 -9999 0 -0.29 1 1
PLK4 -0.012 0.059 -9999 0 -0.29 46 46
regulation of centriole replication 0.013 0.042 -9999 0 -10000 0 0
IL1-mediated signaling events

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
UBC13/UEV1A 0 0.008 -10000 0 -10000 0 0
PRKCZ -0.001 0.024 -10000 0 -0.79 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.007 0.042 -10000 0 -0.48 4 4
IRAK/TOLLIP -0.001 0.01 -10000 0 -10000 0 0
IKBKB -0.001 0.013 -10000 0 -0.29 2 2
IKBKG 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.031 0.12 -10000 0 -0.59 43 43
IL1A -0.005 0.039 -10000 0 -0.29 20 20
IL1B 0.01 0.094 -10000 0 -0.68 18 18
IRAK/TRAF6/p62/Atypical PKCs -0.001 0.014 -10000 0 -10000 0 0
IL1R2 -0.037 0.16 -10000 0 -0.57 71 71
IL1R1 -0.017 0.12 -10000 0 -0.79 24 24
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.001 0.064 0.24 34 -0.32 19 53
TOLLIP 0 0.009 -10000 0 -0.29 1 1
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0 0.005 -10000 0 -10000 0 0
IKK complex/ELKS 0 0.004 -10000 0 -10000 0 0
JUN 0.031 0.079 -10000 0 -0.37 39 39
MAP3K7 0 0.009 -10000 0 -0.29 1 1
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.023 0.11 -10000 0 -0.48 51 51
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.013 0.074 -10000 0 -0.49 24 24
PIK3R1 -0.009 0.086 -10000 0 -0.79 13 13
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.012 0.069 -10000 0 -0.46 24 24
IL1 beta fragment/IL1R1/IL1RAP -0.02 0.11 -10000 0 -0.54 40 40
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 0.027 0.074 -10000 0 -0.39 33 33
IRAK1 0.021 0.013 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.021 0.097 -10000 0 -0.6 26 26
IRAK4 0 0 -10000 0 -10000 0 0
PRKCI 0 0.009 -10000 0 -10000 0 0
TRAF6 0 0 -10000 0 -10000 0 0
PI3K -0.007 0.066 -10000 0 -0.6 13 13
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.012 0.063 -10000 0 -0.36 25 25
CHUK 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.02 0.11 -10000 0 -0.54 40 40
IL1 beta/IL1R2 -0.033 0.13 -10000 0 -0.56 57 57
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.001 0.008 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.02 0.097 -10000 0 -0.86 6 6
IRAK3 -0.032 0.16 -10000 0 -0.79 44 44
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.018 0.097 -10000 0 -0.48 40 40
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.008 0.05 -10000 0 -0.33 24 24
IL1 alpha/IL1R1/IL1RAP -0.014 0.082 -10000 0 -0.54 24 24
RELA 0 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0 0.009 -10000 0 -0.29 1 1
MYD88 0 0 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 -0.001 0.008 -10000 0 -10000 0 0
IL1RAP -0.001 0.024 -10000 0 -0.79 1 1
UBE2N 0 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.015 0.078 -10000 0 -0.81 4 4
CASP1 -0.004 0.053 -10000 0 -0.79 5 5
IL1RN/IL1R2 -0.035 0.12 -10000 0 -0.58 47 47
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.019 0.1 -10000 0 -0.5 40 40
TMEM189-UBE2V1 -0.001 0.013 -10000 0 -0.29 2 2
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.008 0.057 -10000 0 -0.38 24 24
PIK3CA 0 0.009 -10000 0 -0.29 1 1
IL1RN -0.012 0.064 -10000 0 -0.32 41 41
TRAF6/TAK1/TAB1/TAB2 0 0.006 -10000 0 -10000 0 0
MAP2K6 -0.01 0.062 -10000 0 -0.41 25 25
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.024 0.077 0.5 6 -10000 0 6
GNAI2 0 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.005 0.035 -10000 0 -0.53 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.03 0.13 -10000 0 -0.49 67 67
RhoA/GTP -0.024 0.078 -10000 0 -0.51 6 6
negative regulation of cAMP metabolic process -0.028 0.087 -10000 0 -0.36 36 36
GNAZ -0.007 0.071 -10000 0 -0.79 9 9
GNAI3 0 0 -10000 0 -10000 0 0
GNA12 0 0 -10000 0 -10000 0 0
S1PR5 -0.008 0.058 -10000 0 -0.35 25 25
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.028 0.088 -10000 0 -0.36 36 36
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
GNAI1 -0.045 0.18 -10000 0 -0.79 62 62
S1P4 pathway

Figure S100.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S100.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.03 0.13 -9999 0 -0.49 67 67
CDC42/GTP -0.026 0.077 -9999 0 -0.49 4 4
PLCG1 0.008 0.092 -9999 0 -0.5 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0 0 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
cell migration -0.025 0.076 -9999 0 -0.48 4 4
S1PR5 -0.008 0.058 -9999 0 -0.35 25 25
S1PR4 -0.015 0.08 -9999 0 -0.36 46 46
MAPK3 0.008 0.092 -9999 0 -0.32 40 40
MAPK1 0.008 0.092 -9999 0 -0.37 12 12
S1P/S1P5/Gi -0.028 0.088 -9999 0 -0.36 36 36
GNAI1 -0.045 0.18 -9999 0 -0.79 62 62
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.005 0.035 -9999 0 -0.53 3 3
RHOA -0.006 0.038 -9999 0 -0.44 6 6
S1P/S1P4/Gi -0.029 0.087 -9999 0 -0.34 40 40
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.007 0.071 -9999 0 -0.79 9 9
S1P/S1P4/G12/G13 -0.007 0.042 -9999 0 -0.48 6 6
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
S1P3 pathway

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
PDGFRB -0.003 0.048 -9999 0 -0.79 4 4
mol:S1P 0.001 0.004 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.03 0.095 -9999 0 -0.33 94 94
GNAO1 -0.018 0.13 -9999 0 -0.48 67 67
S1P/S1P3/G12/G13 -0.001 0.013 -9999 0 -10000 0 0
AKT1 -0.011 0.051 -9999 0 -0.68 4 4
AKT3 0.013 0.19 -9999 0 -1.4 19 19
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.003 0.048 -9999 0 -0.79 4 4
GNAI2 0.013 0.003 -9999 0 -10000 0 0
GNAI3 0.012 0.002 -9999 0 -10000 0 0
GNAI1 -0.033 0.19 -9999 0 -0.79 62 62
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.01 0.03 -9999 0 -0.3 10 10
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.01 0.11 -9999 0 -0.39 40 40
MAPK3 0.018 0.1 -9999 0 -0.51 14 14
MAPK1 0.018 0.1 -9999 0 -0.51 14 14
JAK2 0.02 0.1 -9999 0 -0.47 18 18
CXCR4 0.014 0.1 -9999 0 -0.48 19 19
FLT1 0.013 0.025 -9999 0 -0.8 1 1
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.017 0.1 -9999 0 -0.51 14 14
S1P/S1P3/Gi 0.009 0.11 -9999 0 -0.39 40 40
RAC1 0 0 -9999 0 -10000 0 0
RhoA/GTP -0.026 0.084 -9999 0 -0.49 14 14
VEGFA 0.01 0.032 -9999 0 -0.3 12 12
S1P/S1P2/Gi 0.008 0.1 -9999 0 -0.37 39 39
VEGFR1 homodimer/VEGFA homodimer 0.021 0.03 -9999 0 -0.45 2 2
RHOA 0 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.007 0.042 -9999 0 -0.33 17 17
GNAQ -0.002 0.041 -9999 0 -0.79 3 3
GNAZ 0.006 0.073 -9999 0 -0.79 9 9
G12/G13 0 0 -9999 0 -10000 0 0
GNA14 -0.013 0.085 -9999 0 -0.45 32 32
GNA15 -0.003 0.033 -9999 0 -0.36 8 8
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
GNA11 -0.002 0.041 -9999 0 -0.79 3 3
Rac1/GTP -0.026 0.084 -9999 0 -0.49 14 14
Sphingosine 1-phosphate (S1P) 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
SPHK2 0 0 -9999 0 -10000 0 0
SPHK1 -0.007 0.052 -9999 0 -0.34 23 23
GNAI2 0 0 -9999 0 -10000 0 0
mol:S1P 0.02 0.019 -9999 0 -0.36 2 2
GNAO1 -0.03 0.13 -9999 0 -0.49 67 67
mol:Sphinganine-1-P 0.017 0.039 -9999 0 -0.6 2 2
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.001 0.011 -9999 0 -10000 0 0
GNAI3 0 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
S1PR3 -0.003 0.028 -9999 0 -0.29 10 10
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.001 0.014 -9999 0 -0.31 2 2
S1PR5 -0.008 0.058 -9999 0 -0.35 25 25
S1PR4 -0.015 0.08 -9999 0 -0.36 46 46
GNAI1 -0.045 0.18 -9999 0 -0.79 62 62
S1P/S1P5/G12 -0.005 0.032 -9999 0 -0.46 3 3
S1P/S1P3/Gq -0.005 0.037 -9999 0 -0.31 4 4
S1P/S1P4/Gi -0.028 0.084 -9999 0 -0.33 42 42
GNAQ -0.002 0.041 -9999 0 -0.79 3 3
GNAZ -0.007 0.071 -9999 0 -0.79 9 9
GNA14 -0.013 0.085 -9999 0 -0.45 32 32
GNA15 -0.003 0.033 -9999 0 -0.36 8 8
GNA12 0 0 -9999 0 -10000 0 0
GNA13 0 0 -9999 0 -10000 0 0
GNA11 -0.002 0.041 -9999 0 -0.79 3 3
ABCC1 0 0 -9999 0 -10000 0 0
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0 0 -10000 0 -10000 0 0
mol:PIP3 -0.019 0.081 0.33 1 -0.36 57 58
FRAP1 0.01 0.022 -10000 0 -10000 0 0
AKT1 -0.016 0.07 0.24 1 -0.3 57 58
INSR 0 0.009 -10000 0 -0.29 1 1
Insulin Receptor/Insulin 0 0.005 -10000 0 -10000 0 0
mol:GTP -0.013 0.055 -10000 0 -0.33 14 14
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.004 0.018 -10000 0 -10000 0 0
TSC2 0 0.002 -10000 0 -10000 0 0
RHEB/GDP -0.011 0.047 -10000 0 -0.3 14 14
TSC1 0 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.017 0.083 -10000 0 -0.42 45 45
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.005 0.021 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0 0 -10000 0 -10000 0 0
RPS6KB1 0.018 0.045 -10000 0 -0.25 14 14
MAP3K5 0.009 0.027 -10000 0 -0.44 4 4
PIK3R1 -0.009 0.086 -10000 0 -0.79 13 13
apoptosis 0.009 0.027 -10000 0 -0.44 4 4
mol:LY294002 0 0 -10000 0 -0.002 45 45
EIF4B 0.025 0.041 -10000 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.007 0.03 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1 -0.001 0.008 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.021 0.087 -10000 0 -0.38 58 58
mTOR/RHEB/GTP/Raptor/GBL 0.025 0.032 0.18 1 -10000 0 1
FKBP1A 0 0.009 -10000 0 -10000 0 0
RHEB/GTP -0.011 0.047 -10000 0 -0.34 1 1
mol:Amino Acids 0 0 -10000 0 -0.002 45 45
FKBP12/Rapamycin 0 0.006 -10000 0 -10000 0 0
PDPK1 -0.017 0.074 0.26 1 -0.33 57 58
EIF4E 0 0 -10000 0 -10000 0 0
ASK1/PP5C -0.004 0.039 -10000 0 -0.62 4 4
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.016 0.001 -10000 0 -10000 0 0
TSC1/TSC2 -0.014 0.058 -10000 0 -0.36 14 14
tumor necrosis factor receptor activity 0 0 0.002 45 -10000 0 45
RPS6 0 0 -10000 0 -10000 0 0
PPP5C 0 0 -10000 0 -10000 0 0
EIF4G1 0 0 -10000 0 -10000 0 0
IRS1 -0.011 0.09 -10000 0 -0.45 45 45
INS 0 0 -10000 0 -10000 0 0
PTEN -0.001 0.034 -10000 0 -0.79 2 2
PDK2 -0.018 0.079 0.26 1 -0.34 60 61
EIF4EBP1 0.013 0.01 -10000 0 -10000 0 0
PIK3CA 0 0.009 -10000 0 -0.29 1 1
PPP2R5D 0.017 0.021 -10000 0 -10000 0 0
peptide biosynthetic process 0.016 0.005 -10000 0 -10000 0 0
RHEB 0 0 -10000 0 -10000 0 0
EIF4A1 0 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 0.003 2 -0.003 13 15
EEF2 0.016 0.005 -10000 0 -10000 0 0
eIF4E/4E-BP1 0 0 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0 0 -10000 0 -10000 0 0
NFATC1 0.049 0.029 -10000 0 -0.36 3 3
NFATC2 0.016 0.064 -10000 0 -0.31 11 11
NFATC3 0 0.015 -10000 0 -0.51 1 1
YWHAE 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.012 0.095 -10000 0 -0.4 38 38
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG 0 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.019 0.077 -10000 0 -0.49 18 18
BCL2/BAX -0.021 0.11 -10000 0 -0.61 37 37
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.003 -10000 0 -10000 0 0
CaM/Ca2+ -0.001 0.003 -10000 0 -10000 0 0
BAX -0.001 0.02 -10000 0 -0.29 5 5
MAPK14 0.011 0.003 -10000 0 -10000 0 0
BAD 0 0.009 -10000 0 -0.29 1 1
CABIN1/MEF2D -0.02 0.081 -10000 0 -0.51 19 19
Calcineurin A alpha-beta B1/BCL2 -0.027 0.14 -10000 0 -0.79 37 37
FKBP8 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.02 0.08 0.5 19 -10000 0 19
KPNB1 0 0 -10000 0 -10000 0 0
KPNA2 -0.029 0.088 -10000 0 -0.29 108 108
XPO1 0 0 -10000 0 -10000 0 0
SFN -0.016 0.099 -10000 0 -0.51 35 35
MAP3K8 0.004 0.073 -10000 0 -0.74 10 10
NFAT4/CK1 alpha -0.001 0.016 -10000 0 -0.43 1 1
MEF2D/NFAT1/Cbp/p300 -0.036 0.09 -10000 0 -0.32 90 90
CABIN1 0.012 0.096 -10000 0 -0.4 38 38
CALM1 0.001 0.003 -10000 0 -10000 0 0
RAN 0 0 -10000 0 -10000 0 0
MAP3K1 -0.001 0.024 -10000 0 -0.79 1 1
CAMK4 -0.011 0.059 -10000 0 -0.31 39 39
mol:Ca2+ 0 0.006 -10000 0 -10000 0 0
MAPK3 0 0 -10000 0 -10000 0 0
YWHAH 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.01 0.044 -10000 0 -0.6 1 1
YWHAB 0 0 -10000 0 -10000 0 0
MAPK8 0.005 0.068 -10000 0 -0.79 8 8
MAPK9 0 0 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
FKBP1A 0 0.009 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.002 0.021 -10000 0 -0.4 1 1
PRKCH -0.001 0.024 -10000 0 -0.79 1 1
CABIN1/Cbp/p300 -0.001 0.003 -10000 0 -10000 0 0
CASP3 0.011 0.003 -10000 0 -10000 0 0
PIM1 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.005 -10000 0 -10000 0 0
apoptosis -0.007 0.035 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.003 0.024 -10000 0 -10000 0 0
PRKCB -0.02 0.11 -10000 0 -0.55 39 39
PRKCE 0 0 -10000 0 -10000 0 0
JNK2/NFAT4 0 0.014 -10000 0 -0.46 1 1
BAD/BCL-XL 0 0.006 -10000 0 -10000 0 0
PRKCD 0 0.009 -10000 0 -0.29 1 1
NUP214 0 0 -10000 0 -10000 0 0
PRKCZ 0.01 0.024 -10000 0 -0.79 1 1
PRKCA -0.021 0.12 -10000 0 -0.76 30 30
PRKCG -0.013 0.061 -10000 0 -0.29 49 49
PRKCQ -0.037 0.16 -10000 0 -0.69 59 59
FKBP38/BCL2 -0.02 0.11 -10000 0 -0.6 37 37
EP300 0 0.001 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0 0 -10000 0 -10000 0 0
NFATc/JNK1 0.048 0.047 -10000 0 -0.37 9 9
CaM/Ca2+/FKBP38 0 0 -10000 0 -10000 0 0
FKBP12/FK506 0 0.006 -10000 0 -10000 0 0
CSNK1A1 0.018 0.006 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.006 0.032 -10000 0 -0.53 1 1
NFATc/ERK1 0.054 0.027 -10000 0 -0.36 1 1
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.019 0.076 -10000 0 -0.48 18 18
NR4A1 -0.007 0.21 -10000 0 -0.7 90 90
GSK3B 0.011 0.003 -10000 0 -10000 0 0
positive T cell selection 0 0.015 -10000 0 -0.5 1 1
NFAT1/CK1 alpha -0.015 0.039 -10000 0 -10000 0 0
RCH1/ KPNB1 -0.018 0.056 -10000 0 -10000 0 0
YWHAQ 0 0 -10000 0 -10000 0 0
PRKACA 0.011 0.003 -10000 0 -10000 0 0
AKAP5 -0.015 0.067 -10000 0 -0.3 54 54
MEF2D 0 0.001 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ -0.001 0.015 -10000 0 -0.29 3 3
NFATc/p38 alpha 0.051 0.03 -10000 0 -0.36 1 1
CREBBP 0 0.001 -10000 0 -10000 0 0
BCL2 -0.027 0.14 -10000 0 -0.79 37 37
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.017 0.095 -9999 0 -0.58 30 30
KLHL20 -0.008 0.032 -9999 0 -0.24 3 3
CYFIP2 -0.01 0.066 -9999 0 -0.36 31 31
Rac1/GDP 0.05 0.067 -9999 0 -0.44 2 2
ENAH -0.016 0.094 -9999 0 -0.57 30 30
AP1M1 0 0 -9999 0 -10000 0 0
RAP1B 0 0 -9999 0 -10000 0 0
RAP1A 0 0 -9999 0 -10000 0 0
CTNNB1 0 0 -9999 0 -10000 0 0
CDC42/GTP -0.008 0.047 -9999 0 -0.49 1 1
ABI1/Sra1/Nap1 -0.006 0.024 -9999 0 -0.21 2 2
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.017 0.081 -9999 0 -0.47 32 32
RAPGEF1 0.039 0.088 -9999 0 -0.48 30 30
CTNND1 0 0.009 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.017 0.098 -9999 0 -0.6 30 30
CRK 0.031 0.095 -9999 0 -0.53 30 30
E-cadherin/gamma catenin/alpha catenin -0.015 0.086 -9999 0 -0.52 31 31
alphaE/beta7 Integrin -0.006 0.04 -9999 0 -0.6 2 2
IQGAP1 0 0 -9999 0 -10000 0 0
NCKAP1 0 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.003 0.036 -9999 0 -0.48 6 6
DLG1 -0.016 0.094 -9999 0 -0.57 30 30
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.008 0.04 -9999 0 -0.31 2 2
MLLT4 -0.005 0.059 -9999 0 -0.72 7 7
ARF6/GTP/NME1/Tiam1 -0.007 0.029 -9999 0 -10000 0 0
PI3K -0.011 0.051 -9999 0 -0.42 2 2
ARF6 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.017 0.1 -9999 0 -0.6 31 31
TIAM1 -0.001 0.018 -9999 0 -0.29 4 4
E-cadherin(dimer)/Ca2+ -0.012 0.073 -9999 0 -0.44 30 30
AKT1 -0.006 0.029 -9999 0 -0.24 1 1
PIK3R1 -0.009 0.086 -9999 0 -0.79 13 13
CDH1 -0.022 0.13 -9999 0 -0.79 30 30
RhoA/GDP 0.049 0.067 -9999 0 -0.52 1 1
actin cytoskeleton organization -0.006 0.024 -9999 0 -0.18 3 3
CDC42/GDP 0.049 0.067 -9999 0 -0.52 1 1
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.01 0.055 -9999 0 -0.33 31 31
ITGB7 -0.01 0.058 -9999 0 -0.79 2 2
RAC1 0 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.013 0.077 -9999 0 -0.47 30 30
E-cadherin/Ca2+/beta catenin/alpha catenin -0.012 0.074 -9999 0 -0.45 30 30
mol:GDP 0.046 0.078 -9999 0 -0.41 30 30
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP -0.001 0.025 -9999 0 -0.54 2 2
p120 catenin/RhoA/GDP -0.01 0.058 -9999 0 -0.54 1 1
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
CDC42 0 0 -9999 0 -10000 0 0
CTNNA1 0 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle -0.007 0.029 -9999 0 -0.22 7 7
NME1 -0.015 0.064 -9999 0 -0.29 55 55
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.017 0.095 -9999 0 -0.57 31 31
regulation of cell-cell adhesion -0.007 0.041 -9999 0 -0.42 1 1
WASF2 -0.003 0.012 -9999 0 -10000 0 0
Rap1/GTP -0.01 0.054 -9999 0 -0.58 1 1
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.016 0.076 -9999 0 -0.44 33 33
CCND1 -0.009 0.036 -9999 0 -0.27 7 7
VAV2 0.035 0.092 -9999 0 -0.51 30 30
RAP1/GDP -0.009 0.055 -9999 0 -0.56 1 1
adherens junction assembly -0.016 0.091 -9999 0 -0.55 31 31
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0 0 -9999 0 -10000 0 0
PIP5K1C 0 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.015 0.072 -9999 0 -0.41 33 33
E-cadherin/beta catenin -0.013 0.08 -9999 0 -0.49 30 30
mol:GTP 0 0 -9999 0 -10000 0 0
SRC -0.016 0.094 -9999 0 -0.57 30 30
PIK3CA 0 0.009 -9999 0 -0.29 1 1
Rac1/GTP -0.011 0.052 -9999 0 -0.4 3 3
E-cadherin/beta catenin/alpha catenin -0.014 0.085 -9999 0 -0.52 30 30
ITGAE 0 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.017 0.1 -9999 0 -0.61 30 30
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 -0.002 0.028 -10000 0 -0.46 4 4
TRAF2/ASK1 -0.002 0.033 -10000 0 -0.53 4 4
ATM 0 0 -10000 0 -10000 0 0
MAP2K3 0.024 0.046 -10000 0 -0.44 2 2
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.025 0.064 -10000 0 -0.38 9 9
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.038 0.099 -10000 0 -0.29 142 142
TXN 0.008 0.006 -10000 0 -10000 0 0
CALM1 0 0 -10000 0 -10000 0 0
GADD45A 0 0 -10000 0 -10000 0 0
GADD45B 0 0 -10000 0 -10000 0 0
MAP3K1 -0.001 0.024 -10000 0 -0.79 1 1
MAP3K6 -0.001 0.024 -10000 0 -0.79 1 1
MAP3K7 0 0.009 -10000 0 -0.29 1 1
MAP3K4 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 -0.003 0.041 -10000 0 -0.6 5 5
TAK1/TAB family 0.001 0.011 0.21 3 -10000 0 3
RAC1/OSM/MEKK3 0 0.005 -10000 0 -10000 0 0
TRAF2 -0.001 0.018 -10000 0 -0.29 4 4
RAC1/OSM/MEKK3/MKK3 -0.007 0.023 -10000 0 -0.4 1 1
TRAF6 0.008 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.068 0.21 -10000 0 -0.59 126 126
CCM2 -0.001 0.013 -10000 0 -0.29 2 2
CaM/Ca2+/CAMKIIB -0.044 0.14 -10000 0 -0.53 76 76
MAPK11 -0.002 0.041 -10000 0 -0.79 3 3
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.041 0.13 -10000 0 -0.48 79 79
OSM/MEKK3 0 0.008 -10000 0 -10000 0 0
TAOK1 -0.006 0.099 -10000 0 -0.44 55 55
TAOK2 0.017 0 -10000 0 -10000 0 0
TAOK3 0.017 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 -0.003 0.048 -10000 0 -0.79 4 4
MAP3K10 0 0.009 -10000 0 -0.29 1 1
MAP3K3 0 0 -10000 0 -10000 0 0
TRX/ASK1 -0.002 0.032 -10000 0 -0.52 4 4
GADD45/MTK1/MTK1 -0.014 0.037 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 -0.006 0.051 -10000 0 -0.47 13 13
HDAC3 0 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.012 -10000 0 -0.4 1 1
GATA1/HDAC4 -0.004 0.03 -10000 0 -0.6 1 1
GATA1/HDAC5 -0.003 0.024 -10000 0 -10000 0 0
GATA2/HDAC5 -0.018 0.097 -10000 0 -0.6 28 28
HDAC5/BCL6/BCoR -0.004 0.044 -10000 0 -0.52 8 8
HDAC9 -0.01 0.081 -10000 0 -0.52 22 22
Glucocorticoid receptor/Hsp90/HDAC6 -0.007 0.06 -10000 0 -0.52 15 15
HDAC4/ANKRA2 -0.001 0.018 -10000 0 -0.6 1 1
HDAC5/YWHAB 0 0 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0 0.001 -10000 0 -10000 0 0
GATA2 -0.024 0.13 -10000 0 -0.62 42 42
HDAC4/RFXANK -0.002 0.023 -10000 0 -0.6 1 1
BCOR -0.001 0.034 -10000 0 -0.79 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 -0.001 0.013 -10000 0 -0.29 2 2
HDAC5 0 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.007 0.065 -10000 0 -0.6 13 13
Histones -0.003 0.026 -10000 0 -10000 0 0
ADRBK1 0 0 -10000 0 -10000 0 0
HDAC4 -0.001 0.024 -10000 0 -0.79 1 1
XPO1 0 0 -10000 0 -10000 0 0
HDAC5/ANKRA2 0 0 -10000 0 -10000 0 0
HDAC4/Ubc9 -0.001 0.018 -10000 0 -0.6 1 1
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0 0 -10000 0 -10000 0 0
TUBA1B 0 0 -10000 0 -10000 0 0
HDAC6 0 0 -10000 0 -10000 0 0
HDAC5/RFXANK -0.001 0.014 -10000 0 -10000 0 0
CAMK4 -0.011 0.059 -10000 0 -0.31 39 39
Tubulin/HDAC6 -0.001 0.017 -10000 0 -0.52 1 1
SUMO1 0 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0 0 -10000 0 -10000 0 0
GATA1 -0.005 0.037 -10000 0 -0.29 18 18
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
NR3C1 -0.011 0.092 -10000 0 -0.79 15 15
SUMO1/HDAC4 0 0.013 -10000 0 -0.43 1 1
SRF 0 0 -10000 0 -10000 0 0
HDAC4/YWHAB -0.001 0.018 -10000 0 -0.6 1 1
Tubulin -0.001 0.02 -10000 0 -0.6 1 1
HDAC4/14-3-3 E -0.001 0.018 -10000 0 -0.6 1 1
GNB1 0 0 -10000 0 -10000 0 0
RANGAP1 0 0.009 -10000 0 -10000 0 0
BCL6/BCoR -0.004 0.051 -10000 0 -0.6 8 8
HDAC4/HDAC3/SMRT (N-CoR2) 0 0.016 -10000 0 -0.52 1 1
HDAC4/SRF -0.006 0.034 -10000 0 -0.52 2 2
HDAC4/ER alpha -0.11 0.22 -10000 0 -0.6 168 168
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing -0.003 0.025 -10000 0 -10000 0 0
cell motility -0.001 0.017 -10000 0 -0.52 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0 0 -10000 0 -10000 0 0
HDAC7/HDAC3 0 0 -10000 0 -10000 0 0
BCL6 -0.004 0.058 -10000 0 -0.79 6 6
HDAC4/CaMK II delta B -0.001 0.024 -10000 0 -0.79 1 1
Hsp90/HDAC6 0 0.006 -10000 0 -10000 0 0
ESR1 -0.15 0.28 -10000 0 -0.58 291 291
HDAC6/HDAC11 -0.001 0.01 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -10000 0 -10000 0 0
NPC 0 0 -10000 0 -10000 0 0
MEF2C -0.001 0.024 -10000 0 -0.79 1 1
RAN 0 0 -10000 0 -10000 0 0
HDAC4/MEF2C -0.001 0.019 -10000 0 -0.44 2 2
GNG2 -0.009 0.086 -10000 0 -0.79 13 13
NCOR2 0 0 -10000 0 -10000 0 0
TUBB2A -0.001 0.027 -10000 0 -0.46 3 3
HDAC11 -0.001 0.015 -10000 0 -0.29 3 3
HSP90AA1 0 0.009 -10000 0 -0.29 1 1
RANBP2 0 0 -10000 0 -10000 0 0
ANKRA2 0 0 -10000 0 -10000 0 0
RFXANK -0.002 0.022 -10000 0 -0.29 6 6
nuclear import 0 0.013 0.43 1 -10000 0 1
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.004 0.024 -9999 0 -0.4 2 2
CRKL 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0 0 -9999 0 -10000 0 0
ITGA4 -0.003 0.028 -9999 0 -0.29 10 10
alpha4/beta7 Integrin/MAdCAM1 -0.01 0.043 -9999 0 -0.45 3 3
EPO -0.048 0.11 -9999 0 -0.29 177 177
alpha4/beta7 Integrin -0.008 0.046 -9999 0 -0.45 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.002 0.018 -9999 0 -10000 0 0
EPO/EPOR (dimer) -0.03 0.069 -9999 0 -10000 0 0
lamellipodium assembly -0.004 0.044 -9999 0 -0.4 13 13
PIK3CA 0 0.009 -9999 0 -0.29 1 1
PI3K -0.007 0.066 -9999 0 -0.6 13 13
ARF6 0 0 -9999 0 -10000 0 0
JAK2 -0.01 0.025 -9999 0 -0.5 1 1
PXN 0 0 -9999 0 -10000 0 0
PIK3R1 -0.009 0.086 -9999 0 -0.79 13 13
MADCAM1 -0.012 0.057 -9999 0 -0.29 43 43
cell adhesion -0.01 0.043 -9999 0 -0.45 3 3
CRKL/CBL 0 0 -9999 0 -10000 0 0
ITGB1 0 0 -9999 0 -10000 0 0
SRC 0.025 0.057 -9999 0 -0.47 13 13
ITGB7 -0.01 0.058 -9999 0 -0.79 2 2
RAC1 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.008 0.059 -9999 0 -0.52 13 13
p130Cas/Crk/Dock1 -0.006 0.043 -9999 0 -10000 0 0
VCAM1 -0.011 0.088 -9999 0 -0.63 19 19
RHOA 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.002 0.014 -9999 0 -10000 0 0
BCAR1 0.034 0.054 -9999 0 -0.43 13 13
EPOR 0 0.009 -9999 0 -0.29 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0 0 -9999 0 -10000 0 0
GIT1 -0.001 0.02 -9999 0 -0.29 5 5
Rac1/GTP -0.004 0.046 -9999 0 -0.42 13 13
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.022 0.11 -9999 0 -0.6 38 38
AKT1 0.08 0.069 -9999 0 -0.68 6 6
PTK2B 0.035 0.12 -9999 0 -0.51 39 39
VEGFR2 homodimer/Frs2 -0.008 0.078 -9999 0 -0.8 9 9
CAV1 -0.17 0.33 -9999 0 -0.79 238 238
CALM1 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.008 0.073 -9999 0 -0.74 9 9
endothelial cell proliferation 0.082 0.084 -9999 0 -0.68 6 6
mol:Ca2+ 0.05 0.07 -9999 0 -0.87 5 5
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.007 0.069 -9999 0 -0.7 9 9
RP11-342D11.1 0.042 0.07 -9999 0 -0.66 9 9
CDH5 -0.007 0.071 -9999 0 -0.79 9 9
VEGFA homodimer -0.001 0.012 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
SHC2 -0.02 0.12 -9999 0 -0.77 28 28
HRAS/GDP -0.006 0.056 -9999 0 -0.76 5 5
SH2D2A -0.035 0.1 -9999 0 -0.3 126 126
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.003 0.052 -9999 0 -0.68 5 5
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.02 0.084 -9999 0 -0.69 12 12
VEGFR1 homodimer -0.001 0.024 -9999 0 -0.79 1 1
SHC/GRB2/SOS1 -0.004 0.062 -9999 0 -0.84 5 5
GRB10 0.05 0.07 -9999 0 -0.87 5 5
PTPN11 0 0 -9999 0 -10000 0 0
GRB2 0 0.009 -9999 0 -0.29 1 1
PAK1 -0.007 0.044 -9999 0 -0.29 25 25
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.008 0.089 -9999 0 -0.78 11 11
HRAS -0.002 0.027 -9999 0 -0.29 9 9
VEGF/Rho/ROCK1/Integrin Complex -0.011 0.063 -9999 0 -0.55 8 8
HIF1A 0 0 -9999 0 -10000 0 0
FRS2 -0.003 0.029 -9999 0 -0.29 11 11
oxygen and reactive oxygen species metabolic process -0.007 0.067 -9999 0 -0.68 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 -0.002 0.041 -9999 0 -0.79 3 3
Nck/Pak -0.004 0.028 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.008 0.08 -9999 0 -0.77 10 10
mol:GDP -0.004 0.059 -9999 0 -0.8 5 5
mol:NADP 0.073 0.05 -9999 0 -0.55 5 5
eNOS/Hsp90 0.075 0.047 -9999 0 -0.51 5 5
PIK3R1 -0.009 0.086 -9999 0 -0.79 13 13
mol:IP3 0.051 0.072 -9999 0 -0.89 5 5
HIF1A/ARNT 0 0 -9999 0 -10000 0 0
SHB -0.001 0.025 -9999 0 -0.79 1 1
VEGFA -0.003 0.03 -9999 0 -0.29 12 12
VEGFC 0 0 -9999 0 -10000 0 0
FAK1/Vinculin 0.056 0.099 -9999 0 -0.88 7 7
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.022 0.12 -9999 0 -0.54 42 42
PTPN6 -0.001 0.013 -9999 0 -0.29 2 2
EPAS1 -0.006 0.07 -9999 0 -0.72 9 9
mol:L-citrulline 0.073 0.05 -9999 0 -0.55 5 5
ITGAV 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -0.29 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.008 0.07 -9999 0 -0.7 9 9
VEGFR2 homodimer/VEGFA homodimer -0.007 0.072 -9999 0 -0.73 9 9
VEGFR2/3 heterodimer -0.008 0.088 -9999 0 -0.86 10 10
VEGFB 0 0 -9999 0 -10000 0 0
MAPK11 0.055 0.076 -9999 0 -0.7 9 9
VEGFR2 homodimer 0.028 0.089 -9999 0 -0.89 9 9
FLT1 -0.001 0.024 -9999 0 -0.79 1 1
NEDD4 0 0 -9999 0 -10000 0 0
MAPK3 0.051 0.08 -9999 0 -0.84 6 6
MAPK1 0.051 0.08 -9999 0 -0.84 6 6
VEGFA145/NRP2 -0.004 0.039 -9999 0 -0.65 3 3
VEGFR1/2 heterodimer -0.007 0.083 -9999 0 -0.85 9 9
KDR 0.028 0.09 -9999 0 -0.9 9 9
VEGFA165/NRP1/VEGFR2 homodimer -0.006 0.079 -9999 0 -0.73 10 10
SRC 0 0.009 -9999 0 -0.29 1 1
platelet activating factor biosynthetic process 0.053 0.081 -9999 0 -0.87 6 6
PI3K -0.008 0.073 -9999 0 -0.88 6 6
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.007 0.073 -9999 0 -0.74 9 9
FES 0.049 0.077 -9999 0 -0.62 12 12
GAB1 -0.005 0.068 -9999 0 -0.93 5 5
VEGFR2 homodimer/VEGFA homodimer/Src -0.007 0.073 -9999 0 -0.74 9 9
CTNNB1 0 0 -9999 0 -10000 0 0
SOS1 0 0 -9999 0 -10000 0 0
ARNT 0 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.009 0.17 -9999 0 -0.54 16 16
VEGFR2 homodimer/VEGFA homodimer/Yes -0.008 0.074 -9999 0 -0.71 10 10
PI3K/GAB1 0.079 0.077 -9999 0 -0.71 6 6
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.002 0.068 -9999 0 -0.89 5 5
PRKACA 0 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.007 0.083 -9999 0 -0.8 10 10
HSP90AA1 0 0.009 -9999 0 -0.29 1 1
CDC42 0.051 0.073 -9999 0 -0.68 9 9
actin cytoskeleton reorganization -0.02 0.083 -9999 0 -0.68 12 12
PTK2 0.052 0.11 -9999 0 -0.82 10 10
EDG1 0.042 0.07 -9999 0 -0.66 9 9
mol:DAG 0.051 0.072 -9999 0 -0.89 5 5
CaM/Ca2+ -0.006 0.06 -9999 0 -0.81 5 5
MAP2K3 0.056 0.076 -9999 0 -0.85 5 5
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.005 0.069 -9999 0 -0.93 5 5
PLCG1 0.051 0.073 -9999 0 -0.91 5 5
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.007 0.07 -9999 0 -0.67 10 10
IQGAP1 0 0 -9999 0 -10000 0 0
YES1 -0.001 0.024 -9999 0 -0.79 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.007 0.073 -9999 0 -0.74 9 9
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.007 0.073 -9999 0 -0.74 9 9
cell migration 0.078 0.088 -9999 0 -0.79 6 6
mol:PI-3-4-5-P3 -0.007 0.065 -9999 0 -0.78 6 6
FYN -0.001 0.034 -9999 0 -0.79 2 2
VEGFB/NRP1 -0.006 0.061 -9999 0 -0.62 9 9
mol:NO 0.073 0.05 -9999 0 -0.55 5 5
PXN 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.006 0.056 -9999 0 -0.76 5 5
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.005 0.069 -9999 0 -0.93 5 5
VHL 0 0 -9999 0 -10000 0 0
ITGB3 -0.029 0.15 -9999 0 -0.74 42 42
NOS3 0.075 0.056 -9999 0 -0.64 5 5
VEGFR2 homodimer/VEGFA homodimer/Sck -0.019 0.1 -9999 0 -0.53 36 36
RAC1 0 0 -9999 0 -10000 0 0
PRKCA 0.046 0.1 -9999 0 -0.97 5 5
PRKCB 0.047 0.1 -9999 0 -0.89 7 7
VCL 0 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.007 0.065 -9999 0 -0.67 9 9
VEGFR1/2 heterodimer/VEGFA homodimer -0.008 0.078 -9999 0 -0.79 9 9
VEGFA165/NRP2 -0.004 0.039 -9999 0 -0.65 3 3
MAPKKK cascade -0.004 0.056 -9999 0 -0.76 5 5
NRP2 -0.002 0.042 -9999 0 -0.66 4 4
VEGFC homodimer 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
ROCK1 -0.001 0.024 -9999 0 -0.79 1 1
FAK1/Paxillin 0.056 0.099 -9999 0 -0.88 7 7
MAP3K13 0.049 0.08 -9999 0 -0.59 14 14
PDPK1 0.073 0.066 -9999 0 -0.66 6 6
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.01 0.034 -9999 0 -0.41 2 2
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
CRKL 0 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.007 0.028 -9999 0 -10000 0 0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0 0.022 -9999 0 -0.52 2 2
antigen processing and presentation of peptide antigen via MHC class I -0.006 0.039 -9999 0 -0.33 2 2
CaM/Ca2+ 0.009 0.031 -9999 0 -0.38 2 2
RAP1A 0 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.011 0.036 -9999 0 -0.39 2 2
AKT1 -0.011 0.046 -9999 0 -0.45 2 2
MAP2K1 0.04 0.044 -9999 0 -0.38 2 2
MAP3K11 0.03 0.043 -9999 0 -0.38 2 2
IFNGR1 0.012 0.003 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.024 0.094 -9999 0 -0.41 24 24
Rap1/GTP -0.004 0.015 -9999 0 -10000 0 0
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.013 0.036 -9999 0 -0.43 2 2
CEBPB 0.075 0.039 -9999 0 -0.4 1 1
STAT3 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.007 0.055 -9999 0 -1.2 1 1
STAT1 -0.011 0.036 -9999 0 -0.38 2 2
CALM1 0 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.03 0.1 -9999 0 -0.28 150 150
PIK3CA 0 0.009 -9999 0 -0.29 1 1
STAT1 (dimer)/PIAS1 -0.01 0.032 -9999 0 -0.37 1 1
CEBPB/PTGES2/Cbp/p300 -0.001 0.012 -9999 0 -10000 0 0
mol:Ca2+ 0.005 0.034 -9999 0 -0.41 2 2
MAPK3 0.054 0.04 -9999 0 -0.43 1 1
STAT1 (dimer) -0.006 0.054 -9999 0 -0.48 2 2
MAPK1 0.054 0.04 -9999 0 -10000 0 0
JAK2 0.011 0.024 -9999 0 -0.79 1 1
PIK3R1 -0.009 0.086 -9999 0 -0.79 13 13
JAK1 0.011 0.024 -9999 0 -0.78 1 1
CAMK2D -0.002 0.041 -9999 0 -0.79 3 3
DAPK1 0.07 0.033 -9999 0 -10000 0 0
SMAD7 0.05 0.038 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.007 0.022 -9999 0 -10000 0 0
PI3K 0.003 0.053 -9999 0 -0.41 14 14
IFNG -0.03 0.1 -9999 0 -0.29 150 150
apoptosis 0.053 0.029 -9999 0 -10000 0 0
CAMK2G 0 0 -9999 0 -10000 0 0
STAT3 (dimer) 0 0 -9999 0 -10000 0 0
CAMK2A -0.01 0.053 -9999 0 -0.29 37 37
CAMK2B -0.068 0.21 -9999 0 -0.59 126 126
FRAP1 0.038 0.057 -9999 0 -0.42 2 2
PRKCD -0.011 0.046 -9999 0 -0.39 8 8
RAP1B 0 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.006 0.039 -9999 0 -0.33 2 2
PTPN2 0 0 -9999 0 -10000 0 0
EP300 0 0 -9999 0 -10000 0 0
IRF1 0.064 0.047 -9999 0 -10000 0 0
STAT1 (dimer)/PIASy -0.01 0.033 -9999 0 -0.37 1 1
SOCS1 0 0.049 -9999 0 -1.5 1 1
mol:GDP -0.007 0.021 -9999 0 -10000 0 0
CASP1 0.049 0.045 -9999 0 -0.35 5 5
PTGES2 0 0.009 -9999 0 -0.29 1 1
IRF9 0.058 0.019 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.012 0.049 -9999 0 -0.4 14 14
RAP1/GDP -0.004 0.016 -9999 0 -10000 0 0
CBL 0.027 0.043 -9999 0 -0.38 2 2
MAP3K1 0.031 0.045 -9999 0 -0.4 3 3
PIAS1 0 0 -9999 0 -10000 0 0
PIAS4 0 0.002 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.006 0.039 -9999 0 -0.33 2 2
PTPN11 0.02 0.045 -9999 0 -0.41 2 2
CREBBP 0 0 -9999 0 -10000 0 0
RAPGEF1 0 0 -9999 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 -0.006 0.055 -9999 0 -0.44 14 14
Caspase 8 (4 units) -0.009 0.047 -9999 0 -0.99 1 1
NEF -0.006 0.028 -9999 0 -0.22 11 11
NFKBIA -0.001 0.011 -9999 0 -10000 0 0
BIRC3 0.035 0.081 -9999 0 -0.79 9 9
CYCS 0.04 0.06 -9999 0 -0.94 1 1
RIPK1 0 0 -9999 0 -10000 0 0
CD247 -0.025 0.12 -9999 0 -0.69 30 30
MAP2K7 0.042 0.049 -9999 0 -0.81 1 1
protein ubiquitination 0.066 0.034 -9999 0 -10000 0 0
CRADD 0 0 -9999 0 -10000 0 0
DAXX 0 0 -9999 0 -10000 0 0
FAS -0.004 0.053 -9999 0 -0.79 5 5
BID 0.033 0.063 -9999 0 -1 1 1
NF-kappa-B/RelA/I kappa B alpha -0.004 0.033 -9999 0 -0.33 9 9
TRADD 0 0 -9999 0 -10000 0 0
MAP3K5 -0.003 0.048 -9999 0 -0.79 4 4
CFLAR 0 0 -9999 0 -10000 0 0
FADD -0.004 0.035 -9999 0 -0.29 16 16
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.004 0.033 -9999 0 -0.33 9 9
MAPK8 0.045 0.062 -9999 0 -0.47 9 9
APAF1 0 0 -9999 0 -10000 0 0
TRAF1 -0.001 0.015 -9999 0 -0.29 3 3
TRAF2 -0.001 0.018 -9999 0 -0.29 4 4
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.012 0.057 -9999 0 -0.33 23 23
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.002 0.031 -9999 0 -0.39 1 1
CHUK 0.068 0.035 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.005 0.048 -9999 0 -0.51 8 8
TCRz/NEF -0.025 0.11 -9999 0 -0.51 41 41
TNF -0.016 0.096 -9999 0 -0.46 38 38
FASLG -0.007 0.15 -9999 0 -0.66 41 41
NFKB1 -0.001 0.011 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.013 0.069 -9999 0 -0.53 17 17
CASP6 -0.004 0.032 -9999 0 -0.7 1 1
CASP7 0.073 0.076 -9999 0 -0.62 9 9
RELA -0.001 0.011 -9999 0 -10000 0 0
CASP2 0 0 -9999 0 -10000 0 0
CASP3 0.073 0.076 -9999 0 -0.62 9 9
TNFRSF1A 0 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.004 0.04 -9999 0 -0.6 4 4
CASP8 0 0 -9999 0 -10000 0 0
CASP9 0 0 -9999 0 -10000 0 0
MAP3K14 0.063 0.038 -9999 0 -10000 0 0
APAF-1/Caspase 9 -0.009 0.053 -9999 0 -0.5 9 9
BCL2 0.037 0.1 -9999 0 -0.42 43 43
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer -0.001 0.027 -9999 0 -0.9 1 1
VEGFR1 homodimer/NRP1 -0.001 0.027 -9999 0 -0.9 1 1
mol:DAG 0.038 0.032 -9999 0 -0.64 2 2
VEGFR1 homodimer/NRP1/VEGFR 121 -0.002 0.028 -9999 0 -0.84 1 1
CaM/Ca2+ -0.002 0.028 -9999 0 -0.6 2 2
HIF1A 0 0.011 -9999 0 -0.38 1 1
GAB1 0 0 -9999 0 -10000 0 0
AKT1 -0.006 0.051 -9999 0 -0.71 1 1
PLCG1 0.038 0.032 -9999 0 -0.64 2 2
NOS3 0.061 0.033 -9999 0 -0.55 2 2
CBL 0 0 -9999 0 -10000 0 0
mol:NO 0.061 0.032 -9999 0 -0.53 2 2
FLT1 0.029 0.031 -9999 0 -1 1 1
PGF -0.002 0.031 -9999 0 -0.79 1 1
VEGFR1 homodimer/NRP2/VEGFR121 -0.003 0.046 -9999 0 -0.78 3 3
CALM1 0 0 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -0.29 1 1
eNOS/Hsp90 0.065 0.03 -9999 0 -0.64 1 1
endothelial cell proliferation 0.036 0.088 -9999 0 -0.58 7 7
mol:Ca2+ 0.038 0.031 -9999 0 -0.63 2 2
MAPK3 0.039 0.081 -9999 0 -0.43 28 28
MAPK1 0.039 0.081 -9999 0 -1.1 1 1
PIK3R1 -0.009 0.086 -9999 0 -0.79 13 13
PLGF homodimer -0.002 0.031 -9999 0 -0.79 1 1
PRKACA 0 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.17 0.33 -9999 0 -0.79 238 238
VEGFA homodimer -0.003 0.031 -9999 0 -0.29 12 12
VEGFR1 homodimer/VEGFA homodimer -0.002 0.031 -9999 0 -0.9 1 1
platelet activating factor biosynthetic process 0.046 0.079 -9999 0 -1.1 1 1
PI3K -0.007 0.055 -9999 0 -0.46 15 15
PRKCA 0.033 0.085 -9999 0 -0.46 29 29
PRKCB 0.034 0.077 -9999 0 -0.47 21 21
VEGFR1 homodimer/PLGF homodimer -0.002 0.033 -9999 0 -0.7 2 2
VEGFA -0.003 0.031 -9999 0 -0.29 12 12
VEGFB 0 0 -9999 0 -10000 0 0
mol:IP3 0.038 0.032 -9999 0 -0.64 2 2
RASA1 0.039 0.026 -9999 0 -0.83 1 1
NRP2 -0.002 0.042 -9999 0 -0.66 4 4
VEGFR1 homodimer 0.029 0.031 -9999 0 -1 1 1
VEGFB homodimer 0 0 -9999 0 -10000 0 0
NCK1 0 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.029 0.18 -9999 0 -0.59 8 8
PTPN11 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.007 0.054 -9999 0 -0.45 15 15
mol:L-citrulline 0.061 0.032 -9999 0 -0.53 2 2
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.002 0.027 -9999 0 -0.79 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.002 0.028 -9999 0 -0.84 1 1
CD2AP 0 0.009 -9999 0 -0.29 1 1
PI3K/GAB1 -0.006 0.052 -9999 0 -0.43 15 15
PDPK1 -0.006 0.05 -9999 0 -0.42 15 15
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.002 0.028 -9999 0 -0.84 1 1
mol:NADP 0.061 0.032 -9999 0 -0.53 2 2
HSP90AA1 0 0.009 -9999 0 -0.29 1 1
ubiquitin-dependent protein catabolic process -0.002 0.026 -9999 0 -0.78 1 1
VEGFR1 homodimer/NRP2 -0.002 0.046 -9999 0 -0.79 3 3
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.058 0.076 -9999 0 -0.52 1 1
CRKL 0.028 0.05 -9999 0 -0.48 1 1
mol:DAG -0.007 0.026 -9999 0 -0.39 1 1
HRAS -0.006 0.022 -9999 0 -0.39 1 1
MAPK8 0.011 0.068 -9999 0 -0.51 8 8
RAP1A 0.028 0.05 -9999 0 -0.48 1 1
GAB1 0.028 0.05 -9999 0 -0.48 1 1
MAPK14 0.015 0.052 -9999 0 -10000 0 0
EPO -0.036 0.11 -9999 0 -0.29 177 177
PLCG1 -0.008 0.026 -9999 0 -0.4 1 1
EPOR/TRPC2/IP3 Receptors 0.012 0.01 -9999 0 -0.28 1 1
RAPGEF1 0 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.024 0.065 -9999 0 -0.62 6 6
GAB1/SHC/GRB2/SOS1 -0.008 0.022 -9999 0 -0.41 1 1
EPO/EPOR (dimer) -0.027 0.067 -9999 0 -10000 0 0
IRS2 0.009 0.11 -9999 0 -0.46 46 46
STAT1 0.048 0.057 -9999 0 -0.5 1 1
STAT5B -0.004 0.043 -9999 0 -0.43 4 4
cell proliferation 0.02 0.064 -9999 0 -0.47 8 8
GAB1/SHIP/PIK3R1/SHP2/SHC -0.01 0.043 -9999 0 -0.42 5 5
TEC 0.027 0.056 -9999 0 -0.48 4 4
SOCS3 -0.004 0.058 -9999 0 -0.79 6 6
STAT1 (dimer) 0.048 0.056 -9999 0 -0.49 1 1
JAK2 0.011 0.025 -9999 0 -0.8 1 1
PIK3R1 -0.009 0.086 -9999 0 -0.79 13 13
EPO/EPOR (dimer)/JAK2 0.054 0.04 -9999 0 -0.51 1 1
EPO/EPOR -0.027 0.067 -9999 0 -10000 0 0
LYN 0.013 0.002 -9999 0 -10000 0 0
TEC/VAV2 0.034 0.055 -9999 0 -0.46 4 4
elevation of cytosolic calcium ion concentration 0.012 0.01 -9999 0 -0.28 1 1
SHC1 0 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.017 0.05 -9999 0 -10000 0 0
mol:IP3 -0.007 0.026 -9999 0 -0.39 1 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.03 0.094 -9999 0 -0.41 59 59
SH2B3 0.012 0.004 -9999 0 -10000 0 0
NFKB1 0.015 0.052 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2/SOCS3 -0.01 0.031 -9999 0 -0.32 7 7
PTPN6 0.021 0.052 -9999 0 -0.51 1 1
TEC/VAV2/GRB2 -0.011 0.034 -9999 0 -0.44 4 4
EPOR 0.012 0.01 -9999 0 -0.28 1 1
INPP5D 0 0 -9999 0 -10000 0 0
mol:GDP -0.008 0.022 -9999 0 -0.42 1 1
SOS1 0 0 -9999 0 -10000 0 0
PLCG2 -0.002 0.035 -9999 0 -0.79 2 2
CRKL/CBL/C3G -0.009 0.025 -9999 0 -0.44 1 1
VAV2 0.028 0.05 -9999 0 -0.48 1 1
CBL 0.028 0.05 -9999 0 -0.48 1 1
SHC/Grb2/SOS1 0.004 0.028 -9999 0 -0.44 1 1
STAT5A -0.006 0.055 -9999 0 -0.47 9 9
GRB2 0 0.009 -9999 0 -0.29 1 1
STAT5 (dimer) 0.058 0.085 -9999 0 -0.56 5 5
LYN/PLCgamma2 -0.001 0.026 -9999 0 -0.6 2 2
PTPN11 0 0 -9999 0 -10000 0 0
BTK 0.028 0.051 -9999 0 -0.48 1 1
BCL2 0.036 0.19 -9999 0 -0.98 37 37
HIF-2-alpha transcription factor network

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
MMP14 0 0.017 -10000 0 -10000 0 0
oxygen homeostasis 0.012 0.012 -10000 0 -10000 0 0
TCEB2 -0.007 0.045 -10000 0 -0.29 26 26
TCEB1 -0.001 0.013 -10000 0 -0.29 2 2
VHL/Elongin B/Elongin C/HIF2A -0.006 0.038 -10000 0 -0.43 2 2
EPO 0.14 0.15 -10000 0 -0.65 3 3
FIH (dimer) 0.023 0.012 -10000 0 -10000 0 0
APEX1 0.022 0.014 -10000 0 -0.31 1 1
SERPINE1 0.16 0.16 -10000 0 -0.67 5 5
FLT1 -0.003 0.079 -10000 0 -1.1 5 5
ADORA2A 0.14 0.16 -10000 0 -0.64 5 5
germ cell development 0.16 0.15 -10000 0 -0.65 6 6
SLC11A2 0.16 0.15 -10000 0 -0.68 4 4
BHLHE40 0.16 0.16 -10000 0 -0.81 5 5
HIF1AN 0.023 0.012 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.012 0.07 -10000 0 -0.42 5 5
ETS1 0.023 0.056 -10000 0 -0.8 5 5
CITED2 0.001 0.01 -10000 0 -10000 0 0
KDR -0.006 0.11 -10000 0 -1.2 8 8
PGK1 0.16 0.15 -10000 0 -0.68 4 4
SIRT1 0 0 -10000 0 -10000 0 0
response to hypoxia -0.001 0.003 -10000 0 -10000 0 0
HIF2A/ARNT 0.18 0.16 -10000 0 -0.77 5 5
EPAS1 0.091 0.084 -10000 0 -0.41 5 5
SP1 0.019 0.002 -10000 0 -10000 0 0
ABCG2 0.12 0.25 -10000 0 -0.69 79 79
EFNA1 0.16 0.15 -10000 0 -0.68 4 4
FXN 0.15 0.15 -10000 0 -0.66 4 4
POU5F1 0.16 0.16 -10000 0 -0.68 6 6
neuron apoptosis -0.17 0.16 0.74 5 -10000 0 5
EP300 0 0 -10000 0 -10000 0 0
EGLN3 0 0.084 -10000 0 -0.29 81 81
EGLN2 0.021 0.026 -10000 0 -0.3 3 3
EGLN1 0.022 0.028 -10000 0 -0.8 1 1
VHL/Elongin B/Elongin C -0.004 0.023 -10000 0 -10000 0 0
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.023 0.01 -10000 0 -10000 0 0
SLC2A1 0.15 0.16 -10000 0 -0.64 6 6
TWIST1 0.13 0.21 -10000 0 -0.69 45 45
ELK1 0.019 0.009 -10000 0 -0.29 1 1
HIF2A/ARNT/Cbp/p300 0.008 0.063 -10000 0 -0.48 2 2
VEGFA 0.16 0.15 -10000 0 -0.71 4 4
CREBBP 0 0 -10000 0 -10000 0 0
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.001 0.024 0.3 2 -0.36 3 5
DAPP1 0.036 0.053 -10000 0 -0.58 4 4
Src family/SYK family/BLNK-LAT/BTK-ITK 0.046 0.078 -10000 0 -0.56 10 10
mol:DAG 0.052 0.05 0.21 1 -0.27 7 8
HRAS 0.009 0.027 -10000 0 -0.29 9 9
RAP1A 0 0 -10000 0 -10000 0 0
ARF5/GDP 0.038 0.032 -10000 0 -0.26 4 4
PLCG2 -0.002 0.035 -10000 0 -0.79 2 2
PLCG1 0 0 -10000 0 -10000 0 0
ARF5 0 0.009 -10000 0 -0.29 1 1
mol:GTP -0.001 0.022 0.26 2 -0.39 2 4
ARF1/GTP -0.001 0.022 0.28 2 -0.37 2 4
RHOA 0 0 -10000 0 -10000 0 0
YES1 -0.001 0.024 -10000 0 -0.79 1 1
RAP1A/GTP -0.001 0.022 0.25 2 -0.38 2 4
ADAP1 -0.003 0.032 0.26 2 -0.39 5 7
ARAP3 -0.001 0.022 0.26 2 -0.39 2 4
INPPL1 0 0 -10000 0 -10000 0 0
PREX1 -0.01 0.057 -10000 0 -0.31 36 36
ARHGEF6 -0.011 0.092 -10000 0 -0.79 15 15
ARHGEF7 0 0 -10000 0 -10000 0 0
ARF1 0 0 -10000 0 -10000 0 0
NRAS 0.011 0.013 -10000 0 -0.29 2 2
FYN -0.001 0.034 -10000 0 -0.79 2 2
ARF6 0 0 -10000 0 -10000 0 0
FGR -0.001 0.025 -10000 0 -0.54 2 2
mol:Ca2+ 0.039 0.029 -10000 0 -10000 0 0
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.001 0.018 -10000 0 -0.29 4 4
ZAP70 -0.031 0.12 -10000 0 -0.79 20 20
mol:IP3 0.047 0.038 -10000 0 -0.22 1 1
LYN 0 0 -10000 0 -10000 0 0
ARF1/GDP 0.038 0.032 -10000 0 -0.3 2 2
RhoA/GDP -0.002 0.022 0.27 2 -10000 0 2
PDK1/Src/Hsp90 0 0.006 -10000 0 -10000 0 0
BLNK 0 0 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.061 0.034 -10000 0 -10000 0 0
SRC 0 0.009 -10000 0 -0.29 1 1
PLEKHA2 0.03 0.007 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PTEN -0.001 0.033 -10000 0 -0.77 2 2
HSP90AA1 0 0.009 -10000 0 -0.29 1 1
ARF6/GTP -0.001 0.021 0.3 2 -10000 0 2
RhoA/GTP -0.001 0.021 0.25 2 -0.36 2 4
Src family/SYK family/BLNK-LAT -0.011 0.056 -10000 0 -0.53 6 6
BLK -0.044 0.11 -10000 0 -0.3 159 159
PDPK1 0 0 -10000 0 -10000 0 0
CYTH1 -0.001 0.021 0.26 2 -0.36 2 4
HCK -0.004 0.033 -10000 0 -10000 0 0
CYTH3 -0.001 0.024 0.26 2 -0.38 3 5
CYTH2 -0.001 0.021 0.26 2 -0.36 2 4
KRAS 0.011 0.013 -10000 0 -0.29 2 2
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.004 0.052 -10000 0 -0.55 9 9
SGK1 -0.004 0.054 0.23 2 -0.7 6 8
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.034 0.033 -10000 0 -0.28 4 4
SOS1 0 0 -10000 0 -10000 0 0
SYK 0 0.009 -10000 0 -0.29 1 1
ARF6/GDP -0.002 0.022 0.28 2 -10000 0 2
mol:PI-3-4-5-P3 -0.001 0.024 0.36 2 -0.38 2 4
ARAP3/RAP1A/GTP -0.001 0.022 0.25 2 -0.39 2 4
VAV1 -0.003 0.043 -10000 0 -0.59 5 5
mol:PI-3-4-P2 0.022 0 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I -0.002 0.019 -10000 0 -0.39 2 2
PLEKHA1 0.03 0.017 -10000 0 -0.52 1 1
Rac1/GDP 0.038 0.032 -10000 0 -0.3 2 2
LAT -0.005 0.048 -10000 0 -0.35 17 17
Rac1/GTP -0.006 0.045 -10000 0 -0.37 15 15
ITK -0.019 0.083 0.26 1 -0.44 38 39
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.059 0.065 0.24 1 -0.39 7 8
LCK -0.02 0.1 -10000 0 -0.41 54 54
BTK -0.001 0.021 0.26 2 -0.36 2 4
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 -0.001 0.024 -9999 0 -0.79 1 1
SMAD2 0.014 0.004 -9999 0 -10000 0 0
SMAD3 0.042 0 -9999 0 -10000 0 0
SMAD3/SMAD4 0.004 0.015 -9999 0 -0.29 1 1
SMAD4/Ubc9/PIASy 0 0.016 -9999 0 -0.52 1 1
SMAD2/SMAD2/SMAD4 -0.009 0.031 -9999 0 -0.52 1 1
PPM1A 0 0 -9999 0 -10000 0 0
CALM1 0 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0 0.015 -9999 0 -0.47 1 1
MAP3K1 -0.001 0.024 -9999 0 -0.79 1 1
TRAP-1/SMAD4 -0.01 0.077 -9999 0 -0.6 18 18
MAPK3 0 0 -9999 0 -10000 0 0
MAPK1 0 0 -9999 0 -10000 0 0
NUP214 0 0 -9999 0 -10000 0 0
CTDSP1 0 0 -9999 0 -10000 0 0
CTDSP2 0 0 -9999 0 -10000 0 0
CTDSPL 0 0 -9999 0 -10000 0 0
KPNB1 0 0 -9999 0 -10000 0 0
TGFBRAP1 -0.012 0.098 -9999 0 -0.79 17 17
UBE2I 0 0 -9999 0 -10000 0 0
NUP153 0 0.009 -9999 0 -0.29 1 1
KPNA2 -0.029 0.088 -9999 0 -0.29 108 108
PIAS4 0 0 -9999 0 -10000 0 0
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.004 0.045 -9999 0 -0.56 6 6
PDGFB-D/PDGFRB/SLAP -0.004 0.041 -9999 0 -0.6 4 4
PDGFB-D/PDGFRB/APS/CBL -0.009 0.043 -9999 0 -0.51 4 4
AKT1 -0.012 0.051 -9999 0 -0.52 3 3
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.035 0.052 -9999 0 -0.59 6 6
PIK3CA 0 0.009 -9999 0 -0.29 1 1
FGR -0.003 0.038 -9999 0 -0.53 5 5
mol:Ca2+ 0.033 0.048 -9999 0 -0.68 4 4
MYC 0.039 0.14 -9999 0 -0.8 28 28
SHC1 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.003 0.028 -9999 0 -0.42 4 4
LRP1/PDGFRB/PDGFB -0.008 0.068 -9999 0 -0.58 14 14
GRB10 0 0 -9999 0 -10000 0 0
PTPN11 0 0 -9999 0 -10000 0 0
GO:0007205 0.033 0.049 -9999 0 -0.69 4 4
PTEN -0.001 0.034 -9999 0 -0.79 2 2
GRB2 0 0.009 -9999 0 -0.29 1 1
GRB7 -0.023 0.085 -9999 0 -0.31 79 79
PDGFB-D/PDGFRB/SHP2 -0.002 0.036 -9999 0 -0.6 4 4
PDGFB-D/PDGFRB/GRB10 -0.002 0.036 -9999 0 -0.6 4 4
cell cycle arrest -0.004 0.041 -9999 0 -0.6 4 4
HRAS -0.002 0.027 -9999 0 -0.29 9 9
HIF1A 0.05 0.06 -9999 0 -0.44 3 3
GAB1 0.035 0.055 -9999 0 -0.67 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.04 0.053 -9999 0 -0.61 4 4
PDGFB-D/PDGFRB -0.003 0.035 -9999 0 -0.53 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.002 0.036 -9999 0 -0.6 4 4
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.005 0.049 -9999 0 -0.57 6 6
positive regulation of MAPKKK cascade -0.002 0.036 -9999 0 -0.6 4 4
PIK3R1 -0.009 0.086 -9999 0 -0.79 13 13
mol:IP3 0.033 0.049 -9999 0 -0.7 4 4
E5 0 0.001 -9999 0 -10000 0 0
CSK 0 0.002 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.017 0.067 -9999 0 -0.6 7 7
SHB -0.001 0.025 -9999 0 -0.79 1 1
BLK -0.002 0.049 -9999 0 -0.58 7 7
PTPN2 0.002 0.005 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.002 0.036 -9999 0 -0.6 4 4
BCAR1 0 0 -9999 0 -10000 0 0
VAV2 0.04 0.062 -9999 0 -0.61 5 5
CBL 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.002 0.036 -9999 0 -0.6 4 4
LCK -0.01 0.08 -9999 0 -0.64 16 16
PDGFRB 0.009 0.049 -9999 0 -0.8 4 4
ACP1 0 0 -9999 0 -10000 0 0
HCK -0.002 0.034 -9999 0 -0.51 4 4
ABL1 0.034 0.049 -9999 0 -0.63 4 4
PDGFB-D/PDGFRB/CBL 0.034 0.06 -9999 0 -0.79 4 4
PTPN1 -0.001 0.03 -9999 0 -0.29 11 11
SNX15 0 0 -9999 0 -10000 0 0
STAT3 0 0 -9999 0 -10000 0 0
STAT1 -0.005 0.038 -9999 0 -0.29 19 19
cell proliferation 0.041 0.12 -9999 0 -0.69 28 28
SLA -0.003 0.029 -9999 0 -0.29 11 11
actin cytoskeleton reorganization -0.002 0.028 -9999 0 -0.4 5 5
SRC -0.002 0.033 -9999 0 -0.5 4 4
PI3K -0.014 0.057 -9999 0 -0.58 3 3
PDGFB-D/PDGFRB/GRB7/SHC -0.013 0.055 -9999 0 -0.52 7 7
SH2B2 -0.014 0.062 -9999 0 -0.29 52 52
PLCgamma1/SPHK1 0.036 0.054 -9999 0 -0.61 6 6
LYN -0.002 0.033 -9999 0 -0.51 4 4
LRP1 -0.009 0.082 -9999 0 -0.79 12 12
SOS1 0 0 -9999 0 -10000 0 0
STAT5B -0.002 0.041 -9999 0 -0.79 3 3
STAT5A -0.006 0.067 -9999 0 -0.79 8 8
NCK1-2/p130 Cas -0.002 0.026 -9999 0 -0.41 4 4
SPHK1 0.004 0.054 -9999 0 -0.33 23 23
EDG1 0.001 0.001 -9999 0 -10000 0 0
mol:DAG 0.033 0.049 -9999 0 -0.7 4 4
PLCG1 0.033 0.051 -9999 0 -0.72 4 4
NHERF/PDGFRB -0.015 0.052 -9999 0 -0.44 6 6
YES1 -0.003 0.038 -9999 0 -0.52 5 5
cell migration -0.015 0.052 -9999 0 -0.44 6 6
SHC/Grb2/SOS1 -0.002 0.027 -9999 0 -0.41 4 4
SLC9A3R2 -0.001 0.02 -9999 0 -0.29 5 5
SLC9A3R1 -0.026 0.083 -9999 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN -0.014 0.049 -9999 0 -0.47 6 6
FYN -0.003 0.06 -9999 0 -0.89 4 4
DOK1 0.029 0.035 -9999 0 -0.47 4 4
HRAS/GTP -0.002 0.018 -9999 0 -10000 0 0
PDGFB 0 0 -9999 0 -10000 0 0
RAC1 0.046 0.083 -9999 0 -0.44 28 28
PRKCD 0.03 0.035 -9999 0 -0.47 4 4
FER 0.025 0.061 -9999 0 -0.48 15 15
MAPKKK cascade -0.002 0.027 -9999 0 -0.4 4 4
RASA1 0.03 0.035 -9999 0 -0.47 4 4
NCK1 0 0 -9999 0 -10000 0 0
NCK2 0 0 -9999 0 -10000 0 0
p62DOK/Csk -0.002 0.029 -9999 0 -0.43 4 4
PDGFB-D/PDGFRB/SHB -0.003 0.041 -9999 0 -0.6 5 5
chemotaxis 0.034 0.048 -9999 0 -0.61 4 4
STAT1-3-5/STAT1-3-5 -0.008 0.054 -9999 0 -0.46 13 13
Bovine Papilomavirus E5/PDGFRB -0.002 0.037 -9999 0 -0.61 4 4
PTPRJ 0 0 -9999 0 -10000 0 0
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.029 0.038 -9999 0 -10000 0 0
PLK1 0.005 0.12 -9999 0 -0.62 8 8
CDKN1B 0.08 0.072 -9999 0 -0.54 3 3
FOXO3 0.039 0.11 -9999 0 -0.55 13 13
KAT2B 0.008 0.028 -9999 0 -0.83 1 1
FOXO1/SIRT1 0.007 0.038 -9999 0 -0.32 11 11
CAT 0.041 0.13 -9999 0 -0.99 8 8
CTNNB1 0 0 -9999 0 -10000 0 0
AKT1 0.015 0.011 -9999 0 -10000 0 0
FOXO1 0.032 0.04 -9999 0 -0.36 11 11
MAPK10 -0.038 0.18 -9999 0 -0.45 170 170
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
FOXO4 0.064 0.088 -9999 0 -0.41 1 1
response to oxidative stress 0.005 0.013 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.016 0.069 -9999 0 -0.51 9 9
XPO1 0.012 0.001 -9999 0 -10000 0 0
EP300 0.01 0.005 -9999 0 -10000 0 0
BCL2L11 0.028 0.02 -9999 0 -10000 0 0
FOXO1/SKP2 -0.003 0.032 -9999 0 -0.32 10 10
mol:GDP 0.005 0.013 -9999 0 -10000 0 0
RAN 0.013 0.001 -9999 0 -10000 0 0
GADD45A 0.068 0.065 -9999 0 -10000 0 0
YWHAQ 0 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.069 0.027 -9999 0 -10000 0 0
MST1 -0.003 0.092 -9999 0 -0.6 21 21
CSNK1D 0 0 -9999 0 -10000 0 0
CSNK1E 0 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.049 0.045 -9999 0 -10000 0 0
YWHAB 0 0 -9999 0 -10000 0 0
MAPK8 0.033 0.042 -9999 0 -0.44 8 8
MAPK9 0.036 0.007 -9999 0 -10000 0 0
YWHAG 0 0 -9999 0 -10000 0 0
YWHAE 0 0 -9999 0 -10000 0 0
YWHAZ -0.001 0.015 -9999 0 -0.29 3 3
SIRT1 0.004 0.009 -9999 0 -10000 0 0
SOD2 0.09 0.078 -9999 0 -0.45 1 1
RBL2 0.06 0.083 -9999 0 -0.56 2 2
RAL/GDP 0.012 0.016 -9999 0 -10000 0 0
CHUK 0.009 0.013 -9999 0 -10000 0 0
Ran/GTP 0 0 -9999 0 -10000 0 0
CSNK1G2 0 0 -9999 0 -10000 0 0
RAL/GTP 0.031 0.01 -9999 0 -10000 0 0
CSNK1G1 0 0 -9999 0 -10000 0 0
FASLG 0.002 0.18 -9999 0 -1.5 15 15
SKP2 0 0 -9999 0 -10000 0 0
USP7 0.013 0.001 -9999 0 -10000 0 0
IKBKB 0.009 0.018 -9999 0 -0.28 2 2
CCNB1 0.031 0.12 -9999 0 -0.64 6 6
FOXO1-3a-4/beta catenin -0.009 0.043 -9999 0 -0.41 7 7
proteasomal ubiquitin-dependent protein catabolic process -0.003 0.032 -9999 0 -0.32 10 10
CSNK1A1 0 0 -9999 0 -10000 0 0
SGK1 0.005 0.061 -9999 0 -0.8 6 6
CSNK1G3 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
ZFAND5 0.068 0.078 -9999 0 -10000 0 0
SFN -0.016 0.099 -9999 0 -0.51 35 35
CDK2 0.004 0.006 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.045 0.048 -9999 0 -10000 0 0
CREBBP 0.004 0.006 -9999 0 -10000 0 0
FBXO32 0.041 0.13 -9999 0 -0.95 9 9
BCL6 0.055 0.13 -9999 0 -1.2 7 7
RALB 0 0 -9999 0 -10000 0 0
RALA 0 0 -9999 0 -10000 0 0
YWHAH 0 0 -9999 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA -0.001 0.01 -9999 0 -10000 0 0
FBXW11 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.006 0.057 -9999 0 -0.52 13 13
NF kappa B1 p50/RelA/I kappa B alpha -0.003 0.024 -9999 0 -10000 0 0
NFKBIA 0.024 0.034 -9999 0 -0.27 13 13
MAPK14 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0 0.006 -9999 0 -10000 0 0
ARRB2 0.017 0 -9999 0 -10000 0 0
REL -0.009 0.086 -9999 0 -0.79 13 13
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 -0.001 0.01 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0 0.006 -9999 0 -10000 0 0
PIK3CA 0 0.009 -9999 0 -0.29 1 1
NF kappa B1 p50 dimer 0 0.008 -9999 0 -10000 0 0
PIK3R1 -0.009 0.086 -9999 0 -0.79 13 13
NFKB1 0.022 0.009 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.03 0.034 -9999 0 -0.26 13 13
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.003 0.023 -9999 0 -10000 0 0
SRC 0 0.009 -9999 0 -0.29 1 1
PI3K -0.007 0.066 -9999 0 -0.6 13 13
NF kappa B1 p50/RelA -0.004 0.029 -9999 0 -0.27 13 13
IKBKB -0.001 0.013 -9999 0 -0.29 2 2
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
SYK 0 0.009 -9999 0 -0.29 1 1
I kappa B alpha/PIK3R1 -0.009 0.054 -9999 0 -0.44 13 13
cell death -0.003 0.022 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel -0.006 0.057 -9999 0 -0.52 13 13
LCK -0.02 0.1 -9999 0 -0.41 54 54
BCL3 -0.001 0.015 -9999 0 -10000 0 0
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification -0.003 0.019 -9999 0 -10000 0 0
CLOCK 0.005 0.083 -9999 0 -0.78 12 12
TIMELESS/CRY2 -0.001 0.01 -9999 0 -10000 0 0
DEC1/BMAL1 -0.001 0.014 -9999 0 -10000 0 0
ATR 0 0 -9999 0 -10000 0 0
NR1D1 0.041 0.016 -9999 0 -10000 0 0
ARNTL 0.014 0.002 -9999 0 -10000 0 0
TIMELESS 0.041 0.019 -9999 0 -10000 0 0
NPAS2 0.009 0.061 -9999 0 -0.62 9 9
CRY2 0 0 -9999 0 -10000 0 0
mol:CO -0.014 0.003 -9999 0 -10000 0 0
CHEK1 -0.006 0.043 -9999 0 -0.29 24 24
mol:HEME 0.014 0.003 -9999 0 -10000 0 0
PER1 -0.014 0.11 -9999 0 -0.79 20 20
BMAL/CLOCK/NPAS2 0.03 0.07 -9999 0 -0.51 18 18
BMAL1/CLOCK 0.042 0.053 -9999 0 -10000 0 0
S phase of mitotic cell cycle -0.003 0.019 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR -0.003 0.019 -9999 0 -10000 0 0
mol:NADPH 0.014 0.003 -9999 0 -10000 0 0
PER1/TIMELESS -0.01 0.061 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.002 0.022 -9999 0 -0.29 6 6
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.046 0.045 -10000 0 -0.55 1 1
BAG4 -0.006 0.055 -10000 0 -0.44 14 14
BAD 0.032 0.017 -10000 0 -10000 0 0
NFKBIA 0 0 -10000 0 -10000 0 0
BIRC3 -0.01 0.077 -10000 0 -0.51 21 21
BAX 0.032 0.019 -10000 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.015 0.012 -10000 0 -0.1 2 2
IKBKB 0.052 0.044 -10000 0 -0.51 1 1
MAP2K2 0.044 0.024 -10000 0 -0.46 1 1
MAP2K1 0.044 0.024 -10000 0 -0.46 1 1
SMPD1 0.021 0.012 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.051 0.048 -10000 0 -0.45 3 3
MAP2K4 0.038 0.025 -10000 0 -0.38 2 2
protein ubiquitination 0.054 0.044 -10000 0 -0.52 1 1
EnzymeConsortium:2.7.1.37 0.049 0.026 -10000 0 -0.48 1 1
response to UV 0 0 -10000 0 -0.003 1 1
RAF1 0.039 0.024 -10000 0 -0.49 1 1
CRADD 0.011 0.002 -10000 0 -10000 0 0
mol:ceramide 0.025 0.017 -10000 0 -0.14 2 2
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -10000 0 -10000 0 0
MADD 0.011 0.002 -10000 0 -10000 0 0
MAP3K1 0.032 0.022 -10000 0 -0.4 1 1
TRADD 0.011 0.002 -10000 0 -10000 0 0
RELA/p50 0 0 -10000 0 -10000 0 0
MAPK3 0.047 0.023 -10000 0 -0.45 1 1
MAPK1 0.047 0.023 -10000 0 -0.45 1 1
p50/RELA/I-kappa-B-alpha 0 0 -10000 0 -10000 0 0
FADD 0.044 0.049 -10000 0 -0.47 3 3
KSR1 0.032 0.025 -10000 0 -0.52 1 1
MAPK8 0.041 0.046 -10000 0 -0.42 9 9
TRAF2 -0.001 0.018 -10000 0 -0.29 4 4
response to radiation 0 0 -10000 0 -0.002 1 1
CHUK 0.052 0.043 -10000 0 -0.51 1 1
TNF R/SODD -0.004 0.04 -10000 0 -0.6 4 4
TNF -0.005 0.097 -10000 0 -0.46 38 38
CYCS 0.037 0.026 0.15 32 -10000 0 32
IKBKG 0.052 0.043 -10000 0 -0.51 1 1
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.039 0.047 -10000 0 -0.58 1 1
RELA 0 0 -10000 0 -10000 0 0
RIPK1 0 0.001 -10000 0 -10000 0 0
AIFM1 0.037 0.026 0.15 32 -10000 0 32
TNF/TNF R/SODD -0.013 0.069 -10000 0 -0.53 17 17
TNFRSF1A 0 0.001 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -0.002 1 1
CASP8 0.028 0.012 -10000 0 -10000 0 0
NSMAF 0.046 0.045 -10000 0 -0.54 1 1
response to hydrogen peroxide 0 0 -10000 0 -0.003 1 1
BCL2 -0.027 0.14 -10000 0 -0.79 37 37
Signaling events mediated by HDAC Class I

Figure S122.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S122.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA -0.004 0.053 -9999 0 -0.48 13 13
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.005 0.044 -9999 0 -0.4 13 13
SUMO1 0 0 -9999 0 -10000 0 0
ZFPM1 -0.002 0.025 -9999 0 -0.29 8 8
NPC/RanGAP1/SUMO1/Ubc9 0 0.001 -9999 0 -10000 0 0
FKBP3 0 0 -9999 0 -10000 0 0
Histones -0.003 0.022 -9999 0 -10000 0 0
YY1/LSF -0.001 0.018 -9999 0 -0.4 2 2
SMG5 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 -0.005 0.039 -9999 0 -0.36 13 13
I kappa B alpha/HDAC1 -0.004 0.026 -9999 0 -10000 0 0
SAP18 0 0 -9999 0 -10000 0 0
RELA -0.004 0.034 -9999 0 -0.31 13 13
HDAC1/Smad7 0 0 -9999 0 -10000 0 0
RANGAP1 0 0.009 -9999 0 -10000 0 0
HDAC3/TR2 -0.004 0.026 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0 0.006 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.004 0.03 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 -0.024 0.13 -9999 0 -0.62 42 42
GATA1 -0.005 0.037 -9999 0 -0.29 18 18
Mad/Max 0 0.006 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0 0.007 -9999 0 -10000 0 0
RBBP7 -0.002 0.025 -9999 0 -0.29 8 8
NPC 0 0 -9999 0 -10000 0 0
RBBP4 -0.001 0.024 -9999 0 -0.79 1 1
MAX 0 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0 0 -9999 0 -10000 0 0
NFKBIA -0.004 0.031 -9999 0 -10000 0 0
KAT2B -0.001 0.024 -9999 0 -0.79 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0 0.008 -9999 0 -10000 0 0
SIN3 complex 0 0.007 -9999 0 -10000 0 0
SMURF1 0 0 -9999 0 -10000 0 0
CHD3 0 0 -9999 0 -10000 0 0
SAP30 -0.001 0.018 -9999 0 -0.29 4 4
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 -0.001 0.024 -9999 0 -0.79 1 1
YY1/HDAC3 -0.003 0.024 -9999 0 -10000 0 0
YY1/HDAC2 0 0.009 -9999 0 -0.29 1 1
YY1/HDAC1 0 0.009 -9999 0 -0.29 1 1
NuRD/MBD2 Complex (MeCP1) 0 0.006 -9999 0 -10000 0 0
PPARG -0.094 0.17 -9999 0 -0.38 272 272
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
TNFRSF1A 0 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) -0.004 0.026 -9999 0 -10000 0 0
MBD3L2 -0.001 0.013 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
CREBBP 0 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0 0.007 -9999 0 -10000 0 0
HDAC1 0 0 -9999 0 -10000 0 0
HDAC3 -0.004 0.031 -9999 0 -10000 0 0
HDAC2 0 0 -9999 0 -10000 0 0
YY1 0.029 0.011 -9999 0 -0.35 1 1
HDAC8 0 0 -9999 0 -10000 0 0
SMAD7 0 0 -9999 0 -10000 0 0
NCOR2 0 0 -9999 0 -10000 0 0
MXD1 0 0.009 -9999 0 -0.29 1 1
STAT3 0.025 0 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 -0.001 0.016 -9999 0 -0.46 1 1
YY1/SAP30/HDAC1 -0.001 0.01 -9999 0 -10000 0 0
EP300 0 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.025 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.004 0.03 -9999 0 -10000 0 0
histone deacetylation 0.046 0.008 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 -0.003 0.023 -9999 0 -10000 0 0
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GATAD2B 0 0 -9999 0 -10000 0 0
GATAD2A 0 0 -9999 0 -10000 0 0
GATA2/HDAC3 -0.017 0.079 -9999 0 -0.47 28 28
GATA1/HDAC1 -0.003 0.024 -9999 0 -10000 0 0
GATA1/HDAC3 -0.006 0.031 -9999 0 -10000 0 0
CHD4 0 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.011 0.071 -9999 0 -0.6 13 13
SIN3/HDAC complex/Mad/Max 0 0.006 -9999 0 -10000 0 0
NuRD Complex 0 0.007 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.003 0.022 -9999 0 -10000 0 0
SIN3B 0 0 -9999 0 -10000 0 0
MTA2 0 0 -9999 0 -10000 0 0
SIN3A 0 0 -9999 0 -10000 0 0
XPO1 0 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0 0.001 -9999 0 -10000 0 0
HDAC complex -0.001 0.017 -9999 0 -0.47 1 1
GATA1/Fog1 -0.004 0.029 -9999 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF -0.016 0.096 -9999 0 -0.46 38 38
negative regulation of cell growth 0.046 0.009 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0 0.006 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.006 0.046 -9999 0 -0.42 13 13
SIN3/HDAC complex/NCoR1 0 0.01 -9999 0 -10000 0 0
TFCP2 -0.001 0.024 -9999 0 -0.79 1 1
NR2C1 0 0 -9999 0 -10000 0 0
MBD3 0 0.009 -9999 0 -0.29 1 1
MBD2 0 0 -9999 0 -10000 0 0
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0 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 0.036 -9999 0 -10000 0 0
ERC1 0 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.007 0.04 -9999 0 -0.48 2 2
NFKBIA 0.047 0 -9999 0 -10000 0 0
BIRC2 0 0 -9999 0 -10000 0 0
IKBKB -0.001 0.013 -9999 0 -0.29 2 2
RIPK2 -0.001 0.02 -9999 0 -0.29 5 5
IKBKG 0 0.008 -9999 0 -10000 0 0
IKK complex/A20 -0.003 0.043 -9999 0 -10000 0 0
NEMO/A20/RIP2 -0.001 0.02 -9999 0 -0.29 5 5
XPO1 0 0 -9999 0 -10000 0 0
NEMO/ATM 0 0.007 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0 0.007 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0 0 -9999 0 -10000 0 0
NOD2 -0.01 0.056 -9999 0 -0.31 35 35
NFKB1 0 0 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
MALT1 0 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
TNF/TNFR1A -0.011 0.071 -9999 0 -0.6 13 13
TRAF6 0 0 -9999 0 -10000 0 0
PRKCA -0.021 0.12 -9999 0 -0.76 30 30
CHUK 0 0 -9999 0 -10000 0 0
UBE2D3 0 0 -9999 0 -10000 0 0
TNF -0.016 0.096 -9999 0 -0.46 38 38
NF kappa B1 p50/RelA 0 0 -9999 0 -10000 0 0
BCL10 0 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.047 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
TNFRSF1A 0 0 -9999 0 -10000 0 0
IKK complex 0 0.008 -9999 0 -10000 0 0
CYLD 0 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.009 0.059 -9999 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0 0 -9999 0 -10000 0 0
ITGB7 -0.01 0.058 -9999 0 -0.79 2 2
ITGA4 -0.003 0.028 -9999 0 -0.29 10 10
alpha4/beta7 Integrin -0.008 0.046 -9999 0 -0.45 6 6
alpha4/beta1 Integrin -0.002 0.018 -9999 0 -10000 0 0
Arf6 downstream pathway

Figure S125.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S125.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.028 0.047 -10000 0 -10000 0 0
regulation of axonogenesis -0.023 0.034 0.31 10 -10000 0 10
myoblast fusion 0.008 0.026 -10000 0 -10000 0 0
mol:GTP -0.005 0.016 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.009 0.031 -10000 0 -10000 0 0
ARF1/GTP -0.003 0.008 -10000 0 -10000 0 0
mol:GM1 0.006 0.015 -10000 0 -10000 0 0
mol:Choline 0.02 0.053 -10000 0 -0.51 10 10
lamellipodium assembly -0.004 0.032 -10000 0 -10000 0 0
MAPK3 0.02 0.025 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.009 0.031 -10000 0 -10000 0 0
ARF1 0 0 -10000 0 -10000 0 0
ARF6/GDP -0.008 0.027 -10000 0 -10000 0 0
ARF1/GDP -0.004 0.025 -10000 0 -10000 0 0
ARF6 0.007 0.008 -10000 0 -10000 0 0
RAB11A -0.001 0.013 -10000 0 -0.29 2 2
TIAM1 0.011 0.019 -10000 0 -0.29 4 4
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.02 0.025 -10000 0 -10000 0 0
actin filament bundle formation 0.006 0.021 -10000 0 -10000 0 0
KALRN -0.011 0.067 -10000 0 -0.47 21 21
RAB11FIP3/RAB11A 0 0.008 -10000 0 -10000 0 0
RhoA/GDP -0.006 0.022 -10000 0 -10000 0 0
NME1 -0.003 0.066 -10000 0 -0.29 55 55
Rac1/GDP -0.006 0.022 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading -0.005 0.016 -10000 0 -10000 0 0
cortical actin cytoskeleton organization -0.005 0.032 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
liver development -0.005 0.016 -10000 0 -10000 0 0
ARF6/GTP -0.005 0.016 -10000 0 -10000 0 0
RhoA/GTP -0.003 0.008 -10000 0 -10000 0 0
mol:GDP -0.006 0.03 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A -0.001 0.007 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
PLD1 0.011 0.058 -10000 0 -0.58 10 10
RAB11FIP3 0 0 -10000 0 -10000 0 0
tube morphogenesis -0.004 0.032 -10000 0 -10000 0 0
ruffle organization 0.023 0.034 -10000 0 -0.31 10 10
regulation of epithelial cell migration -0.005 0.016 -10000 0 -10000 0 0
PLD2 0.016 0.014 -10000 0 -10000 0 0
PIP5K1A -0.004 0.03 -10000 0 -0.31 10 10
mol:Phosphatidic acid 0.02 0.053 -10000 0 -0.51 10 10
Rac1/GTP -0.005 0.032 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.13 0.12 -9999 0 -0.5 10 10
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
AKT1 0 0 -9999 0 -10000 0 0
AKT2 0 0 -9999 0 -10000 0 0
STXBP4 -0.001 0.013 -9999 0 -0.29 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucose -0.12 0.15 -9999 0 -0.34 13 13
YWHAZ -0.001 0.015 -9999 0 -0.29 3 3
CALM1 0 0 -9999 0 -10000 0 0
YWHAQ 0 0 -9999 0 -10000 0 0
TBC1D4 0.019 0.046 -9999 0 -0.6 6 6
mol:Ca2+ 0 0 -9999 0 -10000 0 0
YWHAH 0 0 -9999 0 -10000 0 0
YWHAB 0 0 -9999 0 -10000 0 0
SNARE/Synip 0 0.006 -9999 0 -10000 0 0
YWHAG 0 0 -9999 0 -10000 0 0
ASIP -0.003 0.031 -9999 0 -0.29 12 12
PRKCI 0 0.009 -9999 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -9999 0 -10000 0 0
RHOQ 0 0 -9999 0 -10000 0 0
GYS1 0.032 0 -9999 0 -10000 0 0
PRKCZ -0.001 0.024 -9999 0 -0.79 1 1
TRIP10 0 0 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
AS160/14-3-3 -0.004 0.031 -9999 0 -10000 0 0
VAMP2 0 0 -9999 0 -10000 0 0
SLC2A4 -0.13 0.16 -9999 0 -0.38 13 13
STX4 0 0 -9999 0 -10000 0 0
GSK3B 0.025 0 -9999 0 -10000 0 0
SFN -0.016 0.099 -9999 0 -0.51 35 35
LNPEP -0.007 0.071 -9999 0 -0.79 9 9
YWHAE 0 0 -9999 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0.003 -9999 0 -10000 0 0
DOCK1 0 0 -9999 0 -10000 0 0
ITGA4 -0.003 0.028 -9999 0 -0.29 10 10
RAC1 0 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin -0.008 0.046 -9999 0 -0.45 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.001 0.014 -9999 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin -0.005 0.032 -9999 0 -0.47 2 2
lamellipodium assembly -0.005 0.05 -9999 0 -0.46 13 13
PIK3CA 0 0.009 -9999 0 -0.29 1 1
PI3K -0.007 0.066 -9999 0 -0.6 13 13
ARF6 0 0 -9999 0 -10000 0 0
TLN1 0 0 -9999 0 -10000 0 0
PXN 0.022 0 -9999 0 -10000 0 0
PIK3R1 -0.009 0.086 -9999 0 -0.79 13 13
ARF6/GTP -0.001 0.01 -9999 0 -10000 0 0
cell adhesion -0.001 0.01 -9999 0 -10000 0 0
CRKL/CBL 0 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin -0.001 0.011 -9999 0 -10000 0 0
ITGB1 0 0 -9999 0 -10000 0 0
ITGB7 -0.01 0.058 -9999 0 -0.79 2 2
ARF6/GDP 0 0.003 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.007 0.049 -9999 0 -0.44 13 13
p130Cas/Crk/Dock1 0 0 -9999 0 -10000 0 0
VCAM1 -0.011 0.088 -9999 0 -0.63 19 19
alpha4/beta1 Integrin/Paxillin/Talin -0.001 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.001 0.012 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
mol:GDP 0.001 0.012 -9999 0 -10000 0 0
CBL 0 0 -9999 0 -10000 0 0
PRKACA 0 0 -9999 0 -10000 0 0
GIT1 -0.001 0.02 -9999 0 -0.29 5 5
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.001 0.01 -9999 0 -10000 0 0
Rac1/GTP -0.005 0.056 -9999 0 -0.51 13 13
TCGA08_p53

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
CDKN2A -0.026 0.08 -9999 0 -9999 0 0
TP53 -0.008 0.02 -9999 0 -9999 0 0
Senescence -0.008 0.02 -9999 0 -9999 0 0
Apoptosis -0.008 0.02 -9999 0 -9999 0 0
Activated_Oncogenes 0 0 -9999 0 -9999 0 0
MDM2 0.017 0.041 -9999 0 -9999 0 0
MDM4 0 0 -9999 0 -9999 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.011 -9999 0 -0.36 1 1
MDM2/SUMO1 -0.001 0.007 -9999 0 -10000 0 0
HDAC4 -0.001 0.024 -9999 0 -0.79 1 1
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
SUMO1 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0 0.002 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.029 0.001 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0 0.013 -9999 0 -0.43 1 1
SUMO1/HDAC1 0 0.001 -9999 0 -10000 0 0
RANGAP1 0 0.009 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 -0.001 0.008 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0 0.001 -9999 0 -10000 0 0
Ran/GTP 0 0.001 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 -0.001 0.02 -9999 0 -0.29 5 5
UBE2I 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
PIAS2 0 0 -9999 0 -10000 0 0
PIAS1 0 0 -9999 0 -10000 0 0
EntrezGene:9972 0 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 -0.001 0.009 -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 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 -0.001 0.02 -9999 0 -0.29 5 5
coatomer protein complex/ARF1/GTP/ER cargo protein 0 0.003 -9999 0 -10000 0 0
CD4 0 0 -9999 0 -10000 0 0
CLTA 0 0 -9999 0 -10000 0 0
mol:GTP 0.002 0 -9999 0 -10000 0 0
ARFGAP1 0.01 0.017 -9999 0 -0.2 7 7
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 -0.001 0.008 -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 0 -9999 0 -10000 0 0
DDEF1 0 0 -9999 0 -10000 0 0
ARF1/GDP -0.001 0.009 -9999 0 -10000 0 0
AP2M1 0 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0 0 -9999 0 -10000 0 0
Rac/GTP 0 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 -0.001 0.01 -9999 0 -10000 0 0
ARFIP2 0 0 -9999 0 -10000 0 0
COPA 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.025 0.003 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0 -9999 0 -10000 0 0
GGA3 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0 -9999 0 -10000 0 0
AP2A1 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0 0.004 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0 -9999 0 -10000 0 0
CYTH2 0 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 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 0.001 -9999 0 -10000 0 0
PLD2 0 0 -9999 0 -10000 0 0
ARF-GAP1/v-SNARE 0.01 0.017 -9999 0 -0.2 7 7
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 0.01 0.017 -9999 0 -0.2 7 7
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 0 -9999 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0 0 -9999 0 -10000 0 0
FBXW11 0 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 0 -9999 0 -10000 0 0
CHUK 0 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB -0.001 0.01 -9999 0 -10000 0 0
NFKB1 0 0 -9999 0 -10000 0 0
MAP3K14 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelB -0.002 0.018 -9999 0 -10000 0 0
RELB -0.003 0.028 -9999 0 -0.29 10 10
NFKB2 0 0.009 -9999 0 -0.29 1 1
NF kappa B2 p52/RelB -0.002 0.015 -9999 0 -10000 0 0
regulation of B cell activation -0.002 0.015 -9999 0 -10000 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 1091 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.Z7.A8R6 TCGA.Z7.A8R5 TCGA.XX.A89A TCGA.XX.A899
109_MAP3K5 -0.27 0.054 0.054 0.054
47_PPARGC1A -0.79 0 0 0
105_BMP4 0 0 0 0
105_BMP6 0 0 0 0
105_BMP7 0 0 0 0
105_BMP2 -0.79 0 0 0
131_RELN/VLDLR -0.47 -0.47 0 0
30_TGFB1/TGF beta receptor Type II 0.013 0 0.013 0.012
84_STAT5B -0.1 -0.073 0.032 0.046
84_STAT5A -0.1 -0.073 0.032 0.046
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/BRCA-TP/11493679/BRCA-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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