PARADIGM pathway analysis of mRNASeq expression data
Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C15719J9
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C15719J9
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 52 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
Aurora B signaling 140
FOXM1 transcription factor network 133
HIF-1-alpha transcription factor network 120
Signaling events regulated by Ret tyrosine kinase 111
Angiopoietin receptor Tie2-mediated signaling 107
Endothelins 103
p75(NTR)-mediated signaling 97
PDGFR-alpha signaling pathway 90
Integrins in angiogenesis 85
Nongenotropic Androgen signaling 68
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 513 . 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 ( 513 ).

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
Aurora B signaling 0.2729 140 9400 67 -0.49 0.025 1000 -1000 -0.032 -1000
FOXM1 transcription factor network 0.2593 133 6823 51 -0.9 0.011 1000 -1000 -0.12 -1000
HIF-1-alpha transcription factor network 0.2339 120 9193 76 -0.45 0.017 1000 -1000 -0.048 -1000
Signaling events regulated by Ret tyrosine kinase 0.2164 111 9171 82 -0.19 0.011 1000 -1000 -0.044 -1000
Angiopoietin receptor Tie2-mediated signaling 0.2086 107 9454 88 -0.33 0.043 1000 -1000 -0.064 -1000
Endothelins 0.2008 103 9917 96 -0.38 0.016 1000 -1000 -0.043 -1000
p75(NTR)-mediated signaling 0.1891 97 12159 125 -0.2 0.03 1000 -1000 -0.046 -1000
PDGFR-alpha signaling pathway 0.1754 90 3991 44 -0.32 0.025 1000 -1000 -0.039 -1000
Integrins in angiogenesis 0.1657 85 7141 84 -0.32 0.023 1000 -1000 -0.047 -1000
Nongenotropic Androgen signaling 0.1326 68 3575 52 -0.24 0.12 1000 -1000 -0.026 -1000
Cellular roles of Anthrax toxin 0.1306 67 2628 39 -0.13 0.02 1000 -1000 -0.016 -1000
S1P3 pathway 0.1306 67 2845 42 -0.46 0.016 1000 -1000 -0.02 -1000
Aurora C signaling 0.1248 64 451 7 -0.24 0.01 1000 -1000 -0.016 -1000
Signaling events mediated by the Hedgehog family 0.1228 63 3287 52 -0.26 0.14 1000 -1000 -0.023 -1000
Reelin signaling pathway 0.1209 62 3501 56 -0.18 0.029 1000 -1000 -0.038 -1000
LPA4-mediated signaling events 0.1150 59 714 12 -0.13 0.015 1000 -1000 -0.01 -1000
Signaling mediated by p38-alpha and p38-beta 0.1150 59 2603 44 -0.1 0.011 1000 -1000 -0.031 -1000
Glypican 1 network 0.1072 55 2685 48 -0.24 0.021 1000 -1000 -0.018 -1000
Effects of Botulinum toxin 0.1072 55 1449 26 -0.12 0.017 1000 -1000 -0.028 -1000
Fc-epsilon receptor I signaling in mast cells 0.1033 53 5212 97 -0.15 0.029 1000 -1000 -0.044 -1000
IGF1 pathway 0.1033 53 3033 57 -0.082 0.022 1000 -1000 -0.042 -1000
Thromboxane A2 receptor signaling 0.0955 49 5217 105 -0.19 0.029 1000 -1000 -0.032 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0936 48 5815 120 -0.19 0.14 1000 -1000 -0.037 -1000
Aurora A signaling 0.0897 46 2781 60 -0.22 0.024 1000 -1000 -0.011 -1000
Wnt signaling 0.0897 46 322 7 -0.058 -0.002 1000 -1000 -0.013 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0897 46 3151 68 -0.18 0.078 1000 -1000 -0.078 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0897 46 3615 78 -0.11 0.047 1000 -1000 -0.04 -1000
PLK1 signaling events 0.0858 44 3788 85 -0.25 0.055 1000 -1000 -0.024 -1000
Ephrin A reverse signaling 0.0799 41 290 7 -0.031 0 1000 -1000 -0.009 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0780 40 1374 34 -0.044 0.011 1000 -1000 -0.018 -1000
Osteopontin-mediated events 0.0780 40 1551 38 -0.13 0.014 1000 -1000 -0.044 -1000
amb2 Integrin signaling 0.0780 40 3310 82 -0.17 0.022 1000 -1000 -0.037 -1000
FOXA2 and FOXA3 transcription factor networks 0.0760 39 1799 46 -0.22 0.016 1000 -1000 -0.03 -1000
BMP receptor signaling 0.0760 39 3200 81 -0.29 0.036 1000 -1000 -0.051 -1000
TCGA08_retinoblastoma 0.0760 39 314 8 -0.12 0.02 1000 -1000 -0.01 -1000
Plasma membrane estrogen receptor signaling 0.0741 38 3315 86 -0.15 0.065 1000 -1000 -0.047 -1000
Ras signaling in the CD4+ TCR pathway 0.0721 37 642 17 -0.09 0.014 1000 -1000 -0.016 -1000
Syndecan-1-mediated signaling events 0.0663 34 1185 34 -0.11 0.011 1000 -1000 -0.019 -1000
Noncanonical Wnt signaling pathway 0.0663 34 904 26 -0.12 0.011 1000 -1000 -0.018 -1000
Ephrin B reverse signaling 0.0643 33 1594 48 -0.079 0.017 1000 -1000 -0.034 -1000
TCGA08_p53 0.0624 32 227 7 -0.075 0.038 1000 -1000 -0.005 -1000
LPA receptor mediated events 0.0624 32 3350 102 -0.15 0.026 1000 -1000 -0.042 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0604 31 1707 54 -0.15 0.021 1000 -1000 -0.044 -1000
IL4-mediated signaling events 0.0604 31 2906 91 -0.58 0.29 1000 -1000 -0.13 -1000
S1P1 pathway 0.0604 31 1127 36 -0.15 0.011 1000 -1000 -0.035 -1000
Syndecan-4-mediated signaling events 0.0585 30 2065 67 -0.26 0.015 1000 -1000 -0.029 -1000
S1P5 pathway 0.0565 29 501 17 -0.098 0.036 1000 -1000 -0.017 -1000
Arf6 signaling events 0.0546 28 1788 62 -0.1 0.026 1000 -1000 -0.037 -1000
FAS signaling pathway (CD95) 0.0546 28 1356 47 -0.069 0.033 1000 -1000 -0.023 -1000
EGFR-dependent Endothelin signaling events 0.0546 28 604 21 -0.12 0.02 1000 -1000 -0.037 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0526 27 1437 52 -0.082 0.032 1000 -1000 -0.033 -1000
TCGA08_rtk_signaling 0.0507 26 686 26 -0.17 0.021 1000 -1000 -0.012 -1000
IL6-mediated signaling events 0.0487 25 1880 75 -0.13 0.061 1000 -1000 -0.033 -1000
Insulin Pathway 0.0487 25 1897 74 -0.16 0.029 1000 -1000 -0.04 -1000
Coregulation of Androgen receptor activity 0.0468 24 1897 76 -0.12 0.021 1000 -1000 -0.028 -1000
Visual signal transduction: Cones 0.0468 24 918 38 -0.085 0.011 1000 -1000 -0.029 -1000
Glypican 2 network 0.0468 24 96 4 -0.006 0.004 1000 -1000 -0.005 -1000
Calcium signaling in the CD4+ TCR pathway 0.0468 24 752 31 -0.13 0.016 1000 -1000 -0.042 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0448 23 2004 85 -0.23 0.012 1000 -1000 -0.04 -1000
Glucocorticoid receptor regulatory network 0.0448 23 2709 114 -0.21 0.04 1000 -1000 -0.039 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0429 22 2757 125 -0.082 0.028 1000 -1000 -0.051 -1000
IL2 signaling events mediated by STAT5 0.0429 22 487 22 -0.098 0.055 1000 -1000 -0.025 -1000
BCR signaling pathway 0.0429 22 2235 99 -0.065 0.047 1000 -1000 -0.049 -1000
Regulation of Androgen receptor activity 0.0429 22 1541 70 -0.18 0.022 1000 -1000 -0.038 -1000
EPHB forward signaling 0.0409 21 1791 85 -0.033 0.029 1000 -1000 -0.046 -1000
S1P4 pathway 0.0409 21 548 25 -0.098 0.023 1000 -1000 -0.016 -1000
Syndecan-2-mediated signaling events 0.0390 20 1400 69 -0.11 0.027 1000 -1000 -0.011 -1000
Signaling events mediated by PTP1B 0.0390 20 1524 76 -0.12 0.02 1000 -1000 -0.037 -1000
Hedgehog signaling events mediated by Gli proteins 0.0390 20 1347 65 -0.098 0.037 1000 -1000 -0.035 -1000
Nectin adhesion pathway 0.0390 20 1276 63 -0.078 0.021 1000 -1000 -0.039 -1000
Rapid glucocorticoid signaling 0.0390 20 419 20 -0.063 0.011 1000 -1000 -0.009 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0370 19 645 33 -0.16 0.033 1000 -1000 -0.015 -1000
Presenilin action in Notch and Wnt signaling 0.0351 18 1131 61 -0.13 0.03 1000 -1000 -0.035 -1000
Regulation of p38-alpha and p38-beta 0.0351 18 996 54 -0.19 0.044 1000 -1000 -0.031 -1000
Class I PI3K signaling events mediated by Akt 0.0331 17 1161 68 -0.21 0.038 1000 -1000 -0.019 -1000
Visual signal transduction: Rods 0.0331 17 898 52 -0.085 0.016 1000 -1000 -0.044 -1000
Regulation of nuclear SMAD2/3 signaling 0.0312 16 2230 136 -0.13 0.043 1000 -1000 -0.035 -1000
BARD1 signaling events 0.0312 16 918 57 -0.11 0.027 1000 -1000 -0.029 -1000
IL1-mediated signaling events 0.0292 15 947 62 -0.027 0.039 1000 -1000 -0.045 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0292 15 1296 83 -0.21 0.037 1000 -1000 -0.029 -1000
Retinoic acid receptors-mediated signaling 0.0292 15 926 58 -0.039 0.022 1000 -1000 -0.035 -1000
Signaling events mediated by PRL 0.0273 14 508 34 -0.11 0.027 1000 -1000 -0.016 -1000
JNK signaling in the CD4+ TCR pathway 0.0253 13 225 17 -0.016 0.03 1000 -1000 -0.016 -1000
FoxO family signaling 0.0253 13 838 64 -0.21 0.044 1000 -1000 -0.035 -1000
TCR signaling in naïve CD8+ T cells 0.0253 13 1217 93 -0.047 0.043 1000 -1000 -0.036 -1000
Canonical Wnt signaling pathway 0.0253 13 673 51 -0.081 0.045 1000 -1000 -0.035 -1000
Regulation of Telomerase 0.0253 13 1389 102 -0.31 0.037 1000 -1000 -0.059 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0234 12 353 28 -0.098 0.031 1000 -1000 -0.014 -1000
Insulin-mediated glucose transport 0.0234 12 414 32 -0.21 0.024 1000 -1000 -0.021 -1000
mTOR signaling pathway 0.0234 12 653 53 -0.024 0.017 1000 -1000 -0.031 -1000
IFN-gamma pathway 0.0234 12 873 68 -0.22 0.051 1000 -1000 -0.045 -1000
IL2 signaling events mediated by PI3K 0.0234 12 696 58 -0.11 0.041 1000 -1000 -0.05 -1000
PDGFR-beta signaling pathway 0.0234 12 1190 97 -0.024 0.037 1000 -1000 -0.04 -1000
IL12-mediated signaling events 0.0214 11 980 87 -0.34 0.046 1000 -1000 -0.087 -1000
ErbB4 signaling events 0.0214 11 770 69 -0.073 0.03 1000 -1000 -0.046 -1000
Class IB PI3K non-lipid kinase events 0.0214 11 33 3 -0.003 0.003 1000 -1000 -0.007 -1000
ErbB2/ErbB3 signaling events 0.0195 10 708 65 -0.13 0.022 1000 -1000 -0.034 -1000
Signaling events mediated by HDAC Class III 0.0195 10 439 40 -0.081 0.016 1000 -1000 -0.018 -1000
Signaling mediated by p38-gamma and p38-delta 0.0195 10 159 15 -0.014 0.02 1000 -1000 -0.013 -1000
Syndecan-3-mediated signaling events 0.0175 9 344 35 -0.088 0.03 1000 -1000 -0.018 -1000
Signaling events mediated by HDAC Class II 0.0156 8 616 75 -0.068 0.027 1000 -1000 -0.023 -1000
Ceramide signaling pathway 0.0156 8 635 76 -0.074 0.037 1000 -1000 -0.017 -1000
HIF-2-alpha transcription factor network 0.0156 8 380 43 -0.14 0.021 1000 -1000 -0.043 -1000
IL27-mediated signaling events 0.0156 8 453 51 -0.073 0.019 1000 -1000 -0.032 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0156 8 611 74 -0.074 0.059 1000 -1000 -0.043 -1000
EPO signaling pathway 0.0136 7 388 55 -0.022 0.036 1000 -1000 -0.041 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0136 7 293 37 -0.024 0.026 1000 -1000 -0.023 -1000
IL23-mediated signaling events 0.0136 7 458 60 -0.033 0.063 1000 -1000 -0.12 -1000
Caspase cascade in apoptosis 0.0097 5 417 74 -0.018 0.05 1000 -1000 -0.019 -1000
ceramide signaling pathway 0.0097 5 275 49 -0.029 0.039 1000 -1000 -0.019 -1000
Arf6 trafficking events 0.0097 5 370 71 -0.21 0.033 1000 -1000 -0.032 -1000
p38 MAPK signaling pathway 0.0097 5 255 44 -0.045 0.029 1000 -1000 -0.032 -1000
PLK2 and PLK4 events 0.0078 4 12 3 0.008 0.015 1000 -1000 -0.008 -1000
Class I PI3K signaling events 0.0078 4 346 73 -0.014 0.052 1000 -1000 -0.032 -1000
Canonical NF-kappaB pathway 0.0058 3 137 39 -0.018 0.056 1000 -1000 -0.04 -1000
TRAIL signaling pathway 0.0058 3 173 48 -0.001 0.036 1000 -1000 -0.035 -1000
Signaling events mediated by HDAC Class I 0.0058 3 355 104 -0.029 0.042 1000 -1000 -0.023 -1000
Paxillin-dependent events mediated by a4b1 0.0058 3 138 36 -0.03 0.031 1000 -1000 -0.034 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0058 3 173 45 -0.018 0.053 1000 -1000 -0.048 -1000
VEGFR1 specific signals 0.0058 3 218 56 -0.082 0.05 1000 -1000 -0.017 -1000
E-cadherin signaling in keratinocytes 0.0058 3 129 43 -0.032 0.035 1000 -1000 -0.024 -1000
a4b1 and a4b7 Integrin signaling 0.0039 2 11 5 0.008 0.014 1000 -1000 -0.008 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0019 1 37 23 0.002 0.035 1000 -1000 -0.022 -1000
Arf6 downstream pathway 0.0019 1 53 43 -0.022 0.022 1000 -1000 -0.022 -1000
Atypical NF-kappaB pathway 0.0019 1 33 31 0 0.039 1000 -1000 -0.011 -1000
E-cadherin signaling in the nascent adherens junction 0.0019 1 101 76 -0.003 0.046 1000 -1000 -0.044 -1000
E-cadherin signaling events 0.0019 1 9 5 0.008 0.02 1000 -1000 -0.005 -1000
Circadian rhythm pathway 0.0000 0 13 22 -0.011 0.039 1000 -1000 -0.025 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 0 27 0 0.027 1000 -1000 -0.027 -1000
Arf1 pathway 0.0000 0 7 54 0 0.027 1000 -1000 -0.015 -1000
Alternative NF-kappaB pathway 0.0000 0 2 13 0 0.032 1000 -1000 -0.011 -1000
Total NA 3771 229339 7203 -17 4.4 131000 -131000 -4.3 -131000
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.069 0.046 -10000 0 -10000 0 0
STMN1 -0.14 0.063 -10000 0 -0.17 447 447
Aurora B/RasGAP/Survivin -0.22 0.095 -10000 0 -0.27 402 402
Chromosomal passenger complex/Cul3 protein complex -0.077 0.082 -10000 0 -0.24 96 96
BIRC5 -0.22 0.11 -10000 0 -0.27 423 423
DES -0.49 0.22 -10000 0 -0.58 443 443
Aurora C/Aurora B/INCENP -0.098 0.05 -10000 0 -0.25 2 2
Aurora B/TACC1 -0.16 0.11 -10000 0 -0.19 457 457
Aurora B/PP2A -0.14 0.064 -10000 0 -0.17 447 447
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 -0.011 0.009 -10000 0 -10000 0 0
mitotic metaphase/anaphase transition -0.005 0.002 -10000 0 -10000 0 0
NDC80 -0.15 0.076 -10000 0 -0.25 54 54
Cul3 protein complex -0.026 0.1 -10000 0 -0.24 96 96
KIF2C -0.027 0.017 -10000 0 -10000 0 0
PEBP1 0.003 0.004 -10000 0 -10000 0 0
KIF20A -0.25 0.08 -10000 0 -0.28 469 469
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP -0.14 0.07 -10000 0 -0.17 447 447
SEPT1 0.01 0.019 -10000 0 -0.42 1 1
SMC2 0.01 0.012 -10000 0 -0.27 1 1
SMC4 0.011 0 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.025 0.012 -10000 0 -10000 0 0
PSMA3 0.011 0 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.004 0.001 -10000 0 -10000 0 0
H3F3B -0.046 0.024 -10000 0 -10000 0 0
AURKB -0.23 0.097 -10000 0 -0.27 447 447
AURKC 0.01 0.018 -10000 0 -0.27 2 2
CDCA8 -0.15 0.14 -10000 0 -0.27 286 286
cytokinesis -0.093 0.043 -10000 0 -10000 0 0
Aurora B/Septin1 -0.069 0.062 -10000 0 -0.29 1 1
AURKA -0.082 0.13 -10000 0 -0.28 164 164
INCENP 0.006 0.003 -10000 0 -10000 0 0
KLHL13 -0.069 0.17 -10000 0 -0.42 96 96
BUB1 -0.21 0.12 -10000 0 -0.28 393 393
hSgo1/Aurora B/Survivin -0.3 0.12 -10000 0 -0.35 432 432
EVI5 0.012 0.001 -10000 0 -10000 0 0
RhoA/GTP -0.055 0.04 -10000 0 -0.18 16 16
SGOL1 -0.2 0.12 -10000 0 -0.27 391 391
CENPA -0.046 0.028 -10000 0 -10000 0 0
NCAPG -0.17 0.14 -10000 0 -0.27 325 325
Aurora B/HC8 Proteasome -0.14 0.064 -10000 0 -0.17 447 447
NCAPD2 0.011 0 -10000 0 -10000 0 0
Aurora B/PP1-gamma -0.14 0.064 -10000 0 -0.17 447 447
RHOA 0.011 0 -10000 0 -10000 0 0
NCAPH -0.2 0.12 -10000 0 -0.27 384 384
NPM1 -0.009 0.007 -10000 0 -10000 0 0
RASA1 0.006 0.042 -10000 0 -0.42 5 5
KLHL9 0.01 0.019 -10000 0 -0.42 1 1
mitotic prometaphase -0.007 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.14 0.064 -10000 0 -0.17 447 447
PPP1CC 0.011 0 -10000 0 -10000 0 0
Centraspindlin -0.064 0.045 -10000 0 -0.2 17 17
RhoA/GDP 0.008 0 -10000 0 -10000 0 0
NSUN2 -0.009 0.007 -10000 0 -10000 0 0
MYLK -0.21 0.15 -10000 0 -0.34 287 287
KIF23 0 0.051 -10000 0 -0.28 17 17
VIM -0.15 0.072 -10000 0 -0.17 447 447
RACGAP1 0.009 0.018 -10000 0 -0.27 2 2
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.009 0.007 -10000 0 -10000 0 0
Chromosomal passenger complex -0.072 0.041 -10000 0 -10000 0 0
Chromosomal passenger complex/EVI5 -0.1 0.23 0.19 166 -0.3 291 457
TACC1 -0.076 0.17 -10000 0 -0.42 104 104
PPP2R5D 0.011 0 -10000 0 -10000 0 0
CUL3 0.011 0 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
FOXM1 transcription factor network

Figure S2.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S2.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.53 0.35 -9999 0 -0.94 161 161
PLK1 -0.1 0.062 -9999 0 -10000 0 0
BIRC5 -0.12 0.054 -9999 0 -10000 0 0
HSPA1B -0.53 0.35 -9999 0 -0.94 161 161
MAP2K1 -0.019 0.017 -9999 0 -10000 0 0
BRCA2 -0.53 0.35 -9999 0 -0.94 164 164
FOXM1 -0.63 0.45 -9999 0 -1.1 200 200
XRCC1 -0.53 0.35 -9999 0 -0.94 160 160
FOXM1B/p19 -0.57 0.4 -9999 0 -0.93 225 225
Cyclin D1/CDK4 -0.49 0.32 -9999 0 -0.86 159 159
CDC2 -0.56 0.37 -9999 0 -0.93 201 201
TGFA -0.48 0.31 -9999 0 -0.83 162 162
SKP2 -0.53 0.35 -9999 0 -0.94 162 162
CCNE1 -0.12 0.14 -9999 0 -0.28 225 225
CKS1B -0.53 0.35 -9999 0 -0.92 173 173
RB1 -0.19 0.12 -9999 0 -0.64 6 6
FOXM1C/SP1 -0.58 0.4 -9999 0 -1 185 185
AURKB -0.12 0.05 -9999 0 -10000 0 0
CENPF -0.56 0.36 -9999 0 -0.97 163 163
CDK4 0 0.006 -9999 0 -10000 0 0
MYC -0.48 0.31 -9999 0 -0.84 166 166
CHEK2 -0.019 0.017 -9999 0 -10000 0 0
ONECUT1 -0.52 0.34 -9999 0 -0.9 169 169
CDKN2A -0.11 0.14 -9999 0 -0.27 224 224
LAMA4 -0.57 0.41 -9999 0 -1.1 168 168
FOXM1B/HNF6 -0.58 0.4 -9999 0 -1 169 169
FOS -0.7 0.51 -9999 0 -1.2 220 220
SP1 0.011 0.001 -9999 0 -10000 0 0
CDC25B -0.53 0.35 -9999 0 -0.94 161 161
response to radiation -0.028 0.015 -9999 0 -10000 0 0
CENPB -0.53 0.35 -9999 0 -0.94 160 160
CENPA -0.57 0.36 -9999 0 -0.93 199 199
NEK2 -0.57 0.36 -9999 0 -0.98 165 165
HIST1H2BA -0.53 0.35 -9999 0 -0.94 163 163
CCNA2 -0.077 0.13 -9999 0 -0.28 144 144
EP300 0.011 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.6 0.41 -9999 0 -1 182 182
CCNB2 -0.57 0.36 -9999 0 -0.94 190 190
CCNB1 -0.56 0.37 -9999 0 -0.95 191 191
ETV5 -0.53 0.35 -9999 0 -0.95 160 160
ESR1 -0.58 0.42 -9999 0 -1.1 173 173
CCND1 -0.5 0.33 -9999 0 -0.88 159 159
GSK3A -0.012 0.014 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.11 0.12 -9999 0 -0.21 270 270
CDK2 0.003 0.004 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.034 0.019 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.56 0.37 -9999 0 -0.92 211 211
GAS1 -0.9 0.51 -9999 0 -1.2 346 346
MMP2 -0.54 0.38 -9999 0 -0.99 161 161
RB1/FOXM1C -0.52 0.35 -9999 0 -0.93 164 164
CREBBP 0.01 0.019 -9999 0 -0.42 1 1
HIF-1-alpha transcription factor network

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
PKM2 -0.33 0.39 -9999 0 -0.77 168 168
HDAC7 0.012 0.001 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.27 0.35 -9999 0 -0.72 133 133
SMAD4 0.011 0.019 -9999 0 -0.42 1 1
ID2 -0.33 0.39 -9999 0 -0.77 168 168
AP1 -0.088 0.15 -9999 0 -0.29 174 174
ABCG2 -0.44 0.45 -9999 0 -0.84 246 246
HIF1A -0.044 0.062 -9999 0 -10000 0 0
TFF3 -0.37 0.42 -9999 0 -0.8 201 201
GATA2 -0.028 0.12 -9999 0 -0.42 48 48
AKT1 -0.056 0.082 -9999 0 -0.21 43 43
response to hypoxia -0.071 0.085 -9999 0 -0.21 72 72
MCL1 -0.33 0.39 -9999 0 -0.77 168 168
NDRG1 -0.33 0.39 -9999 0 -0.77 168 168
SERPINE1 -0.33 0.39 -9999 0 -0.77 169 169
FECH -0.33 0.39 -9999 0 -0.77 168 168
FURIN -0.33 0.39 -9999 0 -0.77 168 168
NCOA2 -0.003 0.079 -9999 0 -0.42 18 18
EP300 -0.065 0.13 -9999 0 -0.34 62 62
HMOX1 -0.33 0.39 -9999 0 -0.77 168 168
BHLHE40 -0.33 0.39 -9999 0 -0.77 168 168
BHLHE41 -0.33 0.4 -9999 0 -0.79 170 170
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.036 0.086 -9999 0 -0.3 5 5
ENG -0.023 0.083 -9999 0 -0.28 5 5
JUN 0.006 0.046 -9999 0 -0.42 6 6
RORA -0.34 0.4 -9999 0 -0.8 169 169
ABCB1 -0.33 0.48 -9999 0 -1.2 128 128
TFRC -0.33 0.39 -9999 0 -0.77 168 168
CXCR4 -0.33 0.39 -9999 0 -0.77 168 168
TF -0.33 0.4 -9999 0 -0.78 170 170
CITED2 -0.33 0.39 -9999 0 -0.78 170 170
HIF1A/ARNT -0.35 0.46 -9999 0 -0.86 168 168
LDHA -0.048 0.049 -9999 0 -10000 0 0
ETS1 -0.33 0.39 -9999 0 -0.77 168 168
PGK1 -0.33 0.39 -9999 0 -0.77 168 168
NOS2 -0.33 0.39 -9999 0 -0.77 169 169
ITGB2 -0.33 0.39 -9999 0 -0.77 168 168
ALDOA -0.33 0.39 -9999 0 -0.77 168 168
Cbp/p300/CITED2 -0.35 0.44 -9999 0 -0.89 150 150
FOS -0.13 0.2 -9999 0 -0.42 174 174
HK2 -0.33 0.39 -9999 0 -0.77 169 169
SP1 0.007 0.027 -9999 0 -10000 0 0
GCK -0.2 0.44 -9999 0 -1.3 62 62
HK1 -0.33 0.39 -9999 0 -0.77 168 168
NPM1 -0.33 0.39 -9999 0 -0.77 168 168
EGLN1 -0.33 0.39 -9999 0 -0.77 168 168
CREB1 0.017 0 -9999 0 -10000 0 0
PGM1 -0.33 0.39 -9999 0 -0.77 168 168
SMAD3 0.008 0.038 -9999 0 -0.42 4 4
EDN1 -0.14 0.24 -9999 0 -0.6 76 76
IGFBP1 -0.36 0.41 -9999 0 -0.8 180 180
VEGFA -0.22 0.31 -9999 0 -0.66 108 108
HIF1A/JAB1 -0.019 0.037 -9999 0 -10000 0 0
CP -0.35 0.41 -9999 0 -0.79 188 188
CXCL12 -0.45 0.45 -9999 0 -0.84 252 252
COPS5 0.011 0.001 -9999 0 -10000 0 0
SMAD3/SMAD4 0.015 0.03 -9999 0 -0.28 5 5
BNIP3 -0.33 0.39 -9999 0 -0.77 168 168
EGLN3 -0.33 0.39 -9999 0 -0.77 169 169
CA9 -0.38 0.42 -9999 0 -0.8 205 205
TERT -0.37 0.41 -9999 0 -0.8 195 195
ENO1 -0.33 0.39 -9999 0 -0.77 168 168
PFKL -0.33 0.39 -9999 0 -0.77 168 168
NCOA1 0.01 0.019 -9999 0 -0.42 1 1
ADM -0.33 0.39 -9999 0 -0.77 176 176
ARNT -0.044 0.061 -9999 0 -10000 0 0
HNF4A -0.029 0.092 -9999 0 -0.28 56 56
ADFP -0.34 0.38 -9999 0 -0.76 178 178
SLC2A1 -0.22 0.31 -9999 0 -0.65 113 113
LEP -0.33 0.39 -9999 0 -0.77 168 168
HIF1A/ARNT/Cbp/p300 -0.28 0.36 -9999 0 -0.73 145 145
EPO -0.18 0.26 -9999 0 -0.7 31 31
CREBBP -0.066 0.13 -9999 0 -0.34 62 62
HIF1A/ARNT/Cbp/p300/HDAC7 -0.26 0.35 -9999 0 -0.73 124 124
PFKFB3 -0.33 0.39 -9999 0 -0.77 168 168
NT5E -0.36 0.42 -9999 0 -0.82 179 179
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.032 0.034 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.12 0.13 -9999 0 -0.34 89 89
JUN -0.077 0.13 -9999 0 -0.39 33 33
HRAS 0.011 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.1 0.13 -9999 0 -0.23 244 244
RAP1A 0.011 0 -9999 0 -10000 0 0
FRS2 0.011 0 -9999 0 -10000 0 0
RAP1A/GDP 0.008 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.1 0.13 -9999 0 -0.23 243 243
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.011 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.011 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.09 0.12 -9999 0 -0.21 237 237
RHOA 0.011 0 -9999 0 -10000 0 0
RAP1A/GTP -0.097 0.11 -9999 0 -0.21 161 161
GRB7 -0.007 0.07 -9999 0 -0.28 31 31
RET51/GFRalpha1/GDNF -0.1 0.13 -9999 0 -0.23 243 243
MAPKKK cascade -0.098 0.11 -9999 0 -0.37 29 29
BCAR1 0.011 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.11 0.14 -9999 0 -0.24 252 252
lamellipodium assembly -0.12 0.13 -9999 0 -0.24 245 245
RET51/GFRalpha1/GDNF/SHC -0.1 0.13 -9999 0 -0.23 243 243
PIK3CA 0.01 0.019 -9999 0 -0.42 1 1
RET9/GFRalpha1/GDNF/SHC -0.09 0.12 -9999 0 -0.21 237 237
RET9/GFRalpha1/GDNF/Shank3 -0.09 0.12 -9999 0 -0.21 237 237
MAPK3 -0.075 0.11 -9999 0 -0.34 27 27
DOK1 0.011 0 -9999 0 -10000 0 0
DOK6 -0.071 0.17 -9999 0 -0.42 98 98
PXN 0.011 0 -9999 0 -10000 0 0
neurite development -0.082 0.12 -9999 0 -0.28 86 86
DOK5 -0.035 0.13 -9999 0 -0.41 55 55
GFRA1 -0.19 0.21 -9999 0 -0.42 238 238
MAPK8 -0.084 0.14 -9999 0 -0.41 30 30
HRAS/GTP -0.11 0.13 -9999 0 -0.23 243 243
tube development -0.079 0.11 -9999 0 -0.2 237 237
MAPK1 -0.075 0.11 -9999 0 -0.34 27 27
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.081 0.11 -9999 0 -0.2 236 236
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
SRC 0.011 0 -9999 0 -10000 0 0
PDLIM7 0.011 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.13 0.16 -9999 0 -0.26 274 274
SHC1 0.011 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.1 0.13 -9999 0 -0.23 243 243
RET51/GFRalpha1/GDNF/Dok5 -0.12 0.16 -9999 0 -0.26 256 256
PRKCA -0.017 0.1 -9999 0 -0.42 33 33
HRAS/GDP 0.008 0 -9999 0 -10000 0 0
CREB1 -0.1 0.14 -9999 0 -0.25 236 236
PIK3R1 0.007 0.038 -9999 0 -0.42 4 4
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.084 0.12 -9999 0 -0.21 236 236
RET51/GFRalpha1/GDNF/Grb7 -0.11 0.13 -9999 0 -0.24 246 246
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.022 0.11 -9999 0 -0.35 46 46
DOK4 0.011 0 -9999 0 -10000 0 0
JNK cascade -0.075 0.13 -9999 0 -0.38 33 33
RET9/GFRalpha1/GDNF/FRS2 -0.09 0.12 -9999 0 -0.21 237 237
SHANK3 0.011 0 -9999 0 -10000 0 0
RASA1 0.006 0.042 -9999 0 -0.42 5 5
NCK1 0.009 0.027 -9999 0 -0.42 2 2
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.082 0.11 -9999 0 -0.2 236 236
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.09 0.13 -9999 0 -0.22 242 242
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.093 0.14 -9999 0 -0.22 243 243
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.094 0.14 -9999 0 -0.22 242 242
PI3K -0.16 0.21 -9999 0 -0.36 245 245
SOS1 0.011 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.078 0.11 -9999 0 -0.2 237 237
GRB10 0.01 0.019 -9999 0 -0.42 1 1
activation of MAPKK activity -0.082 0.11 -9999 0 -0.2 236 236
RET51/GFRalpha1/GDNF/FRS2 -0.1 0.13 -9999 0 -0.23 243 243
GAB1 0.007 0.038 -9999 0 -0.42 4 4
IRS1 -0.029 0.12 -9999 0 -0.42 47 47
IRS2 -0.045 0.14 -9999 0 -0.42 67 67
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.096 0.14 -9999 0 -0.23 242 242
RET51/GFRalpha1/GDNF/PKC alpha -0.11 0.15 -9999 0 -0.25 253 253
GRB2 0.011 0 -9999 0 -10000 0 0
PRKACA 0.011 0 -9999 0 -10000 0 0
GDNF 0.004 0.018 -9999 0 -0.27 2 2
RAC1 0.011 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.12 0.16 -9999 0 -0.26 257 257
Rac1/GTP -0.15 0.15 -9999 0 -0.29 245 245
RET9/GFRalpha1/GDNF -0.11 0.13 -9999 0 -0.24 238 238
GFRalpha1/GDNF -0.13 0.15 -9999 0 -0.29 238 238
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.21 0.44 -10000 0 -0.84 168 168
NCK1/PAK1/Dok-R -0.13 0.19 -10000 0 -0.4 168 168
NCK1/Dok-R -0.28 0.51 -10000 0 -0.98 168 168
PIK3CA 0.01 0.019 -10000 0 -0.42 1 1
mol:beta2-estradiol 0.043 0.094 0.23 100 -10000 0 100
RELA 0.011 0 -10000 0 -10000 0 0
SHC1 0.01 0.002 -10000 0 -10000 0 0
Rac/GDP 0.008 0 -10000 0 -10000 0 0
F2 0.029 0.13 0.25 100 -0.28 38 138
TNIP2 0.011 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.3 0.45 -10000 0 -0.92 168 168
FN1 0.006 0.042 -10000 0 -0.42 5 5
PLD2 -0.3 0.54 -10000 0 -1 168 168
PTPN11 0.011 0 -10000 0 -10000 0 0
GRB14 -0.089 0.14 -10000 0 -0.27 179 179
ELK1 -0.26 0.48 -10000 0 -0.92 168 168
GRB7 -0.007 0.07 -10000 0 -0.28 31 31
PAK1 0.011 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.31 0.48 -10000 0 -0.96 168 168
CDKN1A -0.13 0.31 -10000 0 -0.6 131 131
ITGA5 0.01 0.019 -10000 0 -0.42 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.28 0.51 -10000 0 -0.99 168 168
CRK 0.011 0 -10000 0 -10000 0 0
mol:NO -0.14 0.34 -10000 0 -0.62 168 168
PLG -0.32 0.54 -10000 0 -1.1 168 168
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.23 0.41 -10000 0 -0.81 168 168
GRB2 0.011 0 -10000 0 -10000 0 0
PIK3R1 0.007 0.038 -10000 0 -0.42 4 4
ANGPT2 -0.071 0.21 -10000 0 -0.56 40 40
BMX -0.32 0.55 -10000 0 -1.1 168 168
ANGPT1 -0.22 0.48 -10000 0 -1.2 100 100
tube development -0.15 0.34 -10000 0 -0.62 167 167
ANGPT4 0.002 0.032 -10000 0 -0.34 4 4
response to hypoxia -0.019 0.032 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.3 0.58 -10000 0 -1.1 168 168
alpha5/beta1 Integrin 0.015 0.013 -10000 0 -0.29 1 1
FGF2 -0.24 0.21 -10000 0 -0.42 301 301
STAT5A (dimer) -0.17 0.39 -10000 0 -0.7 167 167
mol:L-citrulline -0.14 0.34 -10000 0 -0.62 168 168
AGTR1 -0.1 0.19 -10000 0 -0.41 136 136
MAPK14 -0.3 0.55 -10000 0 -1.1 168 168
Tie2/SHP2 -0.23 0.42 -10000 0 -1.1 99 99
TEK -0.23 0.48 -10000 0 -1.2 99 99
RPS6KB1 -0.21 0.43 -10000 0 -0.81 168 168
Angiotensin II/AT1 -0.071 0.13 -10000 0 -0.29 136 136
Tie2/Ang1/GRB2 -0.31 0.55 -10000 0 -1.1 168 168
MAPK3 -0.27 0.49 -10000 0 -0.94 168 168
MAPK1 -0.27 0.49 -10000 0 -0.94 168 168
Tie2/Ang1/GRB7 -0.31 0.56 -10000 0 -1.1 168 168
NFKB1 0.01 0.019 -10000 0 -0.42 1 1
MAPK8 -0.3 0.54 -10000 0 -1 168 168
PI3K -0.26 0.51 -10000 0 -0.97 168 168
FES -0.3 0.54 -10000 0 -1 168 168
Crk/Dok-R -0.28 0.51 -10000 0 -0.98 168 168
Tie2/Ang1/ABIN2 -0.31 0.55 -10000 0 -1.1 168 168
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.18 0.4 -10000 0 -0.75 168 168
STAT5A 0.011 0 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.21 0.43 -10000 0 -0.81 168 168
Tie2/Ang2 -0.22 0.46 -10000 0 -0.84 167 167
Tie2/Ang1 -0.33 0.59 -10000 0 -1.1 168 168
FOXO1 -0.18 0.4 -10000 0 -0.75 168 168
ELF1 -0.009 0.056 -10000 0 -0.44 4 4
ELF2 -0.3 0.54 -10000 0 -1 168 168
mol:Choline -0.28 0.5 -10000 0 -0.98 168 168
cell migration -0.074 0.11 -10000 0 -0.23 168 168
FYN -0.17 0.38 -10000 0 -0.7 167 167
DOK2 0.008 0.029 -10000 0 -0.31 4 4
negative regulation of cell cycle -0.11 0.28 -10000 0 -0.54 131 131
ETS1 -0.033 0.099 -10000 0 -0.22 101 101
PXN -0.16 0.36 -10000 0 -0.67 168 168
ITGB1 0.011 0 -10000 0 -10000 0 0
NOS3 -0.17 0.38 -10000 0 -0.7 168 168
RAC1 0.011 0 -10000 0 -10000 0 0
TNF -0.059 0.12 -10000 0 -0.25 144 144
MAPKKK cascade -0.28 0.5 -10000 0 -0.98 168 168
RASA1 0.006 0.042 -10000 0 -0.42 5 5
Tie2/Ang1/Shc -0.31 0.55 -10000 0 -1.1 168 168
NCK1 0.009 0.027 -10000 0 -0.42 2 2
vasculogenesis -0.12 0.3 -10000 0 -0.55 168 168
mol:Phosphatidic acid -0.28 0.5 -10000 0 -0.98 168 168
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.14 0.34 -10000 0 -0.62 168 168
Rac1/GTP -0.24 0.36 -10000 0 -0.75 168 168
MMP2 -0.3 0.54 -10000 0 -1 168 168
Endothelins

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
AKT1 -0.1 0.2 -10000 0 -0.4 115 115
PTK2B 0.01 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.13 0.31 -10000 0 -0.82 71 71
EDN1 -0.013 0.089 -10000 0 -0.37 13 13
EDN3 -0.081 0.14 -10000 0 -0.29 155 155
EDN2 -0.028 0.097 -10000 0 -0.27 69 69
HRAS/GDP -0.13 0.21 -10000 0 -0.42 132 132
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.095 0.18 -10000 0 -0.37 120 120
ADCY4 -0.13 0.21 -10000 0 -0.42 138 138
ADCY5 -0.16 0.21 -10000 0 -0.43 152 152
ADCY6 -0.12 0.19 -10000 0 -0.4 127 127
ADCY7 -0.12 0.19 -10000 0 -0.4 121 121
ADCY1 -0.12 0.2 -10000 0 -0.41 134 134
ADCY2 -0.23 0.24 -10000 0 -0.46 217 217
ADCY3 -0.12 0.2 -10000 0 -0.4 129 129
ADCY8 -0.15 0.2 -10000 0 -0.41 143 143
ADCY9 -0.14 0.22 -10000 0 -0.44 146 146
arachidonic acid secretion -0.19 0.28 -10000 0 -0.47 217 217
ETB receptor/Endothelin-1/Gq/GTP -0.076 0.16 -10000 0 -0.28 164 164
GNAO1 -0.098 0.19 -10000 0 -0.42 131 131
HRAS 0.008 0.004 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.081 0.2 -10000 0 -0.39 99 99
ETA receptor/Endothelin-1/Gs/GTP -0.12 0.22 -10000 0 -0.42 127 127
mol:GTP -0.002 0.005 -10000 0 -10000 0 0
COL3A1 -0.11 0.22 -10000 0 -0.49 90 90
EDNRB -0.093 0.18 -10000 0 -0.42 126 126
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.14 0.26 -10000 0 -0.53 131 131
CYSLTR1 -0.11 0.23 -10000 0 -0.45 118 118
SLC9A1 -0.067 0.11 -10000 0 -0.27 72 72
mol:GDP -0.14 0.23 -10000 0 -0.46 133 133
SLC9A3 -0.16 0.31 -10000 0 -0.62 135 135
RAF1 -0.17 0.25 -10000 0 -0.42 211 211
JUN -0.11 0.26 -10000 0 -0.68 70 70
JAK2 -0.1 0.2 -10000 0 -0.4 123 123
mol:IP3 -0.1 0.18 -10000 0 -0.4 98 98
ETA receptor/Endothelin-1 -0.11 0.25 -10000 0 -0.46 125 125
PLCB1 0.005 0.033 -10000 0 -0.42 3 3
PLCB2 0.007 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.15 0.18 -10000 0 -0.34 211 211
FOS -0.32 0.44 -10000 0 -0.89 182 182
Gai/GDP -0.19 0.34 -10000 0 -0.74 132 132
CRK 0.01 0.001 -10000 0 -10000 0 0
mol:Ca ++ -0.16 0.26 -10000 0 -0.49 151 151
BCAR1 0.011 0 -10000 0 -10000 0 0
PRKCB1 -0.1 0.17 -10000 0 -0.38 102 102
GNAQ 0.006 0.027 -10000 0 -0.42 2 2
GNAZ -0.011 0.094 -10000 0 -0.42 26 26
GNAL -0.063 0.16 -10000 0 -0.42 88 88
Gs family/GDP -0.18 0.2 -10000 0 -0.42 167 167
ETA receptor/Endothelin-1/Gq/GTP -0.11 0.21 -10000 0 -0.4 131 131
MAPK14 -0.06 0.13 -10000 0 -0.3 84 84
TRPC6 -0.14 0.34 -10000 0 -0.9 70 70
GNAI2 0.011 0 -10000 0 -10000 0 0
GNAI3 0.011 0 -10000 0 -10000 0 0
GNAI1 0.002 0.059 -10000 0 -0.42 10 10
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.069 0.14 -10000 0 -0.3 106 106
ETB receptor/Endothelin-2 -0.082 0.15 -10000 0 -0.28 172 172
ETB receptor/Endothelin-3 -0.12 0.14 -10000 0 -0.25 262 262
ETB receptor/Endothelin-1 -0.07 0.15 -10000 0 -0.31 133 133
MAPK3 -0.28 0.39 -10000 0 -0.76 193 193
MAPK1 -0.28 0.39 -10000 0 -0.76 193 193
Rac1/GDP -0.13 0.21 -10000 0 -0.42 132 132
cAMP biosynthetic process -0.22 0.25 -10000 0 -0.46 221 221
MAPK8 -0.14 0.3 -10000 0 -0.75 79 79
SRC 0.01 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.099 0.18 -10000 0 -0.37 109 109
p130Cas/CRK/Src/PYK2 -0.12 0.23 -10000 0 -0.54 93 93
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.13 0.21 -10000 0 -0.42 132 132
COL1A2 -0.15 0.25 -10000 0 -0.53 122 122
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.12 0.18 -10000 0 -0.33 179 179
mol:DAG -0.1 0.18 -10000 0 -0.4 98 98
MAP2K2 -0.22 0.3 -10000 0 -0.56 201 201
MAP2K1 -0.22 0.3 -10000 0 -0.56 202 202
EDNRA -0.14 0.24 -10000 0 -0.47 156 156
positive regulation of muscle contraction -0.082 0.18 -10000 0 -0.38 89 89
Gq family/GDP -0.14 0.19 -10000 0 -0.45 110 110
HRAS/GTP -0.14 0.21 -10000 0 -0.42 137 137
PRKCH -0.097 0.18 -10000 0 -0.41 90 90
RAC1 0.011 0 -10000 0 -10000 0 0
PRKCA -0.11 0.19 -10000 0 -0.41 106 106
PRKCB -0.11 0.19 -10000 0 -0.42 104 104
PRKCE -0.095 0.17 -10000 0 -0.4 89 89
PRKCD -0.097 0.17 -10000 0 -0.39 98 98
PRKCG -0.12 0.18 -10000 0 -0.4 112 112
regulation of vascular smooth muscle contraction -0.38 0.51 -10000 0 -1 181 181
PRKCQ -0.11 0.18 -10000 0 -0.4 111 111
PLA2G4A -0.21 0.31 -10000 0 -0.51 217 217
GNA14 -0.036 0.13 -10000 0 -0.42 53 53
GNA15 0.004 0.033 -10000 0 -0.28 7 7
GNA12 0.011 0 -10000 0 -10000 0 0
GNA11 -0.001 0.062 -10000 0 -0.42 11 11
Rac1/GTP -0.081 0.2 -10000 0 -0.4 95 95
MMP1 0.016 0.14 0.27 13 -10000 0 13
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.016 0 -10000 0 -10000 0 0
Necdin/E2F1 -0.16 0.17 -10000 0 -0.31 280 280
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.087 0.15 -10000 0 -0.24 223 223
NGF (dimer)/p75(NTR)/BEX1 -0.16 0.2 -10000 0 -0.33 262 262
NT-4/5 (dimer)/p75(NTR) -0.09 0.14 -10000 0 -0.28 180 180
IKBKB 0.011 0 -10000 0 -10000 0 0
AKT1 -0.087 0.14 -10000 0 -0.24 222 222
IKBKG 0.011 0 -10000 0 -10000 0 0
BDNF -0.028 0.096 -10000 0 -0.27 69 69
MGDIs/NGR/p75(NTR)/LINGO1 -0.065 0.12 -10000 0 -0.24 168 168
FURIN 0.011 0 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.083 0.12 -10000 0 -0.24 167 167
LINGO1 0.005 0.04 -10000 0 -0.29 9 9
Sortilin/TRAF6/NRIF -0.001 0.013 -10000 0 -10000 0 0
proBDNF (dimer) -0.028 0.096 -10000 0 -0.27 69 69
NTRK1 0 0.059 -10000 0 -0.34 14 14
RTN4R 0.01 0.019 -10000 0 -0.42 1 1
neuron apoptosis -0.084 0.14 -10000 0 -0.35 64 64
IRAK1 0.011 0 -10000 0 -10000 0 0
SHC1 -0.11 0.17 -10000 0 -0.29 219 219
ARHGDIA 0.011 0 -10000 0 -10000 0 0
RhoA/GTP 0.008 0 -10000 0 -10000 0 0
Gamma Secretase 0.03 0.019 -10000 0 -0.18 4 4
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.15 0.19 -10000 0 -0.3 273 273
MAGEH1 -0.086 0.18 -10000 0 -0.42 116 116
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.2 0.2 -10000 0 -0.32 333 333
Mammalian IAPs/DIABLO 0.023 0.031 -10000 0 -0.2 9 9
proNGF (dimer) -0.082 0.18 -10000 0 -0.42 111 111
MAGED1 0.009 0.027 -10000 0 -0.42 2 2
APP 0.011 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.001 0.053 -10000 0 -0.3 15 15
ZNF274 0.011 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.09 0.14 -10000 0 -0.24 219 219
NGF -0.082 0.18 -10000 0 -0.42 111 111
cell cycle arrest -0.081 0.14 0.14 41 -0.34 68 109
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.091 0.15 -10000 0 -0.25 219 219
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.068 0.12 -10000 0 -0.24 170 170
NCSTN 0.011 0 -10000 0 -10000 0 0
mol:GTP -0.12 0.17 -10000 0 -0.29 223 223
PSENEN 0.011 0 -10000 0 -10000 0 0
mol:ceramide -0.096 0.15 -10000 0 -0.26 219 219
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.072 0.13 -10000 0 -0.35 59 59
p75(NTR)/beta APP -0.083 0.14 -10000 0 -0.28 168 168
BEX1 -0.073 0.17 -10000 0 -0.42 100 100
mol:GDP -0.12 0.17 -10000 0 -0.3 220 220
NGF (dimer) -0.086 0.15 -10000 0 -0.26 185 185
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.051 0.11 -10000 0 -0.21 168 168
PIK3R1 0.007 0.038 -10000 0 -0.42 4 4
RAC1/GTP -0.096 0.14 -10000 0 -0.25 219 219
MYD88 0.011 0 -10000 0 -10000 0 0
CHUK 0.011 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.12 0.17 -10000 0 -0.3 223 223
RHOB 0.009 0.027 -10000 0 -0.42 2 2
RHOA 0.011 0 -10000 0 -10000 0 0
MAGE-G1/E2F1 -0.025 0.078 -10000 0 -0.18 109 109
NT3 (dimer) -0.023 0.11 -10000 0 -0.41 40 40
TP53 -0.05 0.098 -10000 0 -0.27 11 11
PRDM4 -0.097 0.15 -10000 0 -0.26 219 219
BDNF (dimer) -0.071 0.13 -10000 0 -0.27 123 123
PIK3CA 0.01 0.019 -10000 0 -0.42 1 1
SORT1 0.011 0 -10000 0 -10000 0 0
activation of caspase activity -0.1 0.13 -10000 0 -0.24 223 223
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.096 0.16 -10000 0 -0.26 219 219
RHOC 0.011 0 -10000 0 -10000 0 0
XIAP 0.011 0 -10000 0 -10000 0 0
MAPK10 -0.13 0.18 -10000 0 -0.33 196 196
DIABLO 0.011 0 -10000 0 -10000 0 0
SMPD2 -0.097 0.15 -10000 0 -0.26 219 219
APH1B 0.007 0.038 -10000 0 -0.42 4 4
APH1A 0.011 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.11 0.17 -10000 0 -0.29 219 219
PSEN1 0.011 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.016 0 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.1 0.16 -10000 0 -0.31 190 190
MAPK8 -0.09 0.15 -10000 0 -0.27 173 173
MAPK9 -0.088 0.15 -10000 0 -0.27 172 172
APAF1 0.011 0 -10000 0 -10000 0 0
NTF3 -0.023 0.11 -10000 0 -0.41 40 40
NTF4 -0.001 0.053 -10000 0 -0.3 15 15
NDN -0.19 0.21 -10000 0 -0.42 240 240
RAC1/GDP 0.008 0 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.096 0.12 -10000 0 -0.36 62 62
p75 CTF/Sortilin/TRAF6/NRIF 0.027 0 -10000 0 -10000 0 0
RhoA-B-C/GTP -0.12 0.17 -10000 0 -0.29 223 223
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.057 0.1 -10000 0 -0.19 167 167
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.067 0.11 -10000 0 -0.21 167 167
PRKACB 0.006 0.046 -10000 0 -0.42 6 6
proBDNF (dimer)/p75 ECD -0.01 0.065 -10000 0 -0.18 69 69
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.003 0.057 -10000 0 -0.4 10 10
BIRC2 0.011 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.19 0.2 0.15 17 -0.36 243 260
BAD -0.11 0.16 -10000 0 -0.3 188 188
RIPK2 0.011 0 -10000 0 -10000 0 0
NGFR -0.13 0.2 -10000 0 -0.42 168 168
CYCS -0.086 0.14 -10000 0 -0.24 221 221
ADAM17 0.011 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.096 0.16 -10000 0 -0.26 219 219
BCL2L11 -0.11 0.16 -10000 0 -0.3 188 188
BDNF (dimer)/p75(NTR) -0.11 0.14 -10000 0 -0.26 228 228
PI3K -0.098 0.16 -10000 0 -0.26 222 222
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.096 0.16 -10000 0 -0.26 219 219
NDNL2 0.011 0 -10000 0 -10000 0 0
YWHAE 0.011 0 -10000 0 -10000 0 0
PRKCI 0.011 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.14 0.2 -10000 0 -0.35 220 220
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.097 0.16 -10000 0 -0.26 221 221
TRAF6 0.011 0 -10000 0 -10000 0 0
RAC1 0.011 0 -10000 0 -10000 0 0
PRKCZ 0.009 0.023 -10000 0 -0.34 2 2
PLG -0.053 0.15 -10000 0 -0.41 76 76
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.11 0.16 -10000 0 -0.28 219 219
SQSTM1 0.011 0 -10000 0 -10000 0 0
NGFRAP1 0.006 0.042 -10000 0 -0.42 5 5
CASP3 -0.099 0.16 -10000 0 -0.28 188 188
E2F1 -0.05 0.12 -10000 0 -0.27 109 109
CASP9 0.011 0 -10000 0 -10000 0 0
IKK complex -0.095 0.13 -10000 0 -0.31 118 118
NGF (dimer)/TRKA -0.057 0.13 -10000 0 -0.28 123 123
MMP7 -0.048 0.13 -10000 0 -0.33 88 88
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.085 0.15 -10000 0 -0.24 219 219
MMP3 -0.02 0.09 -10000 0 -0.28 53 53
APAF-1/Caspase 9 -0.074 0.096 -10000 0 -0.29 60 60
PDGFR-alpha signaling pathway

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
PDGFRA -0.11 0.19 -9999 0 -0.44 133 133
PDGF/PDGFRA/CRKL -0.068 0.13 -9999 0 -0.29 133 133
positive regulation of JUN kinase activity -0.036 0.099 -9999 0 -0.2 133 133
CRKL 0.011 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.075 0.13 -9999 0 -0.3 134 134
AP1 -0.32 0.4 -9999 0 -0.87 174 174
mol:IP3 -0.08 0.14 -9999 0 -0.31 133 133
PLCG1 -0.08 0.14 -9999 0 -0.31 133 133
PDGF/PDGFRA/alphaV Integrin -0.068 0.13 -9999 0 -0.29 133 133
RAPGEF1 0.011 0 -9999 0 -10000 0 0
CRK 0.011 0 -9999 0 -10000 0 0
mol:Ca2+ -0.08 0.14 -9999 0 -0.31 133 133
CAV3 0.002 0.013 -9999 0 -0.27 1 1
CAV1 -0.082 0.18 -9999 0 -0.42 111 111
SHC/Grb2/SOS1 -0.036 0.1 -9999 0 -0.2 133 133
PDGF/PDGFRA/Shf -0.07 0.14 -9999 0 -0.3 133 133
FOS -0.3 0.41 -9999 0 -0.86 174 174
JUN -0.027 0.045 -9999 0 -0.36 6 6
oligodendrocyte development -0.068 0.13 -9999 0 -0.29 133 133
GRB2 0.011 0 -9999 0 -10000 0 0
PIK3R1 0.007 0.038 -9999 0 -0.42 4 4
mol:DAG -0.08 0.14 -9999 0 -0.31 133 133
PDGF/PDGFRA -0.11 0.19 -9999 0 -0.44 133 133
actin cytoskeleton reorganization -0.068 0.13 -9999 0 -0.29 133 133
SRF 0.025 0.012 -9999 0 -10000 0 0
SHC1 0.011 0 -9999 0 -10000 0 0
PI3K -0.05 0.11 -9999 0 -0.24 135 135
PDGF/PDGFRA/Crk/C3G -0.048 0.11 -9999 0 -0.23 133 133
JAK1 -0.068 0.14 -9999 0 -0.3 133 133
ELK1/SRF -0.046 0.11 -9999 0 -0.23 133 133
SHB 0.011 0 -9999 0 -10000 0 0
SHF 0.007 0.038 -9999 0 -0.42 4 4
CSNK2A1 0.022 0.025 -9999 0 -10000 0 0
GO:0007205 -0.089 0.15 -9999 0 -0.34 133 133
SOS1 0.011 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.036 0.099 -9999 0 -0.2 133 133
PDGF/PDGFRA/SHB -0.068 0.13 -9999 0 -0.29 133 133
PDGF/PDGFRA/Caveolin-1 -0.13 0.2 -9999 0 -0.37 188 188
ITGAV 0.011 0 -9999 0 -10000 0 0
ELK1 -0.082 0.14 -9999 0 -0.3 133 133
PIK3CA 0.01 0.019 -9999 0 -0.42 1 1
PDGF/PDGFRA/Crk -0.068 0.13 -9999 0 -0.29 133 133
JAK-STAT cascade -0.068 0.14 -9999 0 -0.3 133 133
cell proliferation -0.07 0.14 -9999 0 -0.3 133 133
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.001 0.068 -9999 0 -0.29 28 28
alphaV beta3 Integrin -0.18 0.17 -9999 0 -0.29 322 322
PTK2 -0.16 0.2 -9999 0 -0.43 148 148
IGF1R -0.006 0.083 -9999 0 -0.42 20 20
PI4KB 0.011 0 -9999 0 -10000 0 0
MFGE8 0.009 0.027 -9999 0 -0.42 2 2
SRC 0.011 0 -9999 0 -10000 0 0
CDKN1B -0.15 0.22 -9999 0 -0.56 97 97
VEGFA 0.011 0 -9999 0 -10000 0 0
ILK -0.13 0.19 -9999 0 -0.56 73 73
ROCK1 0.011 0 -9999 0 -10000 0 0
AKT1 -0.12 0.18 -9999 0 -0.52 73 73
PTK2B -0.026 0.1 -9999 0 -0.21 119 119
alphaV/beta3 Integrin/JAM-A -0.17 0.17 -9999 0 -0.27 341 341
CBL 0.011 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.035 0.1 -9999 0 -0.24 105 105
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.047 0.14 -9999 0 -0.27 130 130
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.046 0.12 -9999 0 -0.36 30 30
alphaV/beta3 Integrin/Syndecan-1 -0.085 0.12 -9999 0 -0.26 106 106
PI4KA 0.011 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.2 0.18 -9999 0 -0.43 162 162
PI4 Kinase 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.019 -9999 0 -0.42 1 1
alphaV/beta3 Integrin/Osteopontin -0.072 0.11 -9999 0 -0.25 106 106
RPS6KB1 -0.17 0.19 -9999 0 -0.4 162 162
TLN1 0.011 0 -9999 0 -10000 0 0
MAPK3 -0.32 0.28 -9999 0 -0.51 322 322
GPR124 -0.08 0.18 -9999 0 -0.42 109 109
MAPK1 -0.32 0.28 -9999 0 -0.51 322 322
PXN 0.011 0 -9999 0 -10000 0 0
PIK3R1 0.007 0.038 -9999 0 -0.42 4 4
alphaV/beta3 Integrin/Tumstatin -0.068 0.14 -9999 0 -0.26 153 153
cell adhesion -0.028 0.1 -9999 0 -0.23 105 105
ANGPTL3 0.004 0.018 -9999 0 -0.27 2 2
VEGFR2 homodimer/VEGFA homodimer/Src 0.008 0.058 -9999 0 -0.23 28 28
IGF-1R heterotetramer -0.006 0.083 -9999 0 -0.42 20 20
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
TGFBR2 0 0.067 -9999 0 -0.42 13 13
ITGB3 -0.078 0.17 -9999 0 -0.41 107 107
IGF1 -0.074 0.17 -9999 0 -0.42 102 102
RAC1 0.011 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.083 0.15 -9999 0 -0.28 176 176
apoptosis 0.011 0 -9999 0 -10000 0 0
CD47 0.011 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.031 0.1 -9999 0 -0.23 105 105
VCL 0.011 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.11 0.17 -9999 0 -0.3 209 209
CSF1 0.002 0.059 -9999 0 -0.42 10 10
PIK3C2A -0.13 0.19 -9999 0 -0.37 144 144
PI4 Kinase/Pyk2 -0.15 0.14 -9999 0 -0.36 138 138
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.032 0.11 -9999 0 -0.23 119 119
FAK1/Vinculin -0.12 0.16 -9999 0 -0.34 140 140
alphaV beta3/Integrin/ppsTEM5 -0.083 0.15 -9999 0 -0.28 176 176
RHOA 0.011 0 -9999 0 -10000 0 0
VTN -0.053 0.15 -9999 0 -0.41 76 76
BCAR1 0.011 0 -9999 0 -10000 0 0
FGF2 -0.24 0.21 -9999 0 -0.42 301 301
F11R -0.16 0.15 -9999 0 -0.29 302 302
alphaV/beta3 Integrin/Lactadherin -0.032 0.1 -9999 0 -0.24 105 105
alphaV/beta3 Integrin/TGFBR2 -0.037 0.12 -9999 0 -0.25 108 108
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.023 0.032 -9999 0 -0.2 10 10
HSP90AA1 0.011 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.027 0.093 -9999 0 -0.21 105 105
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 0.006 0.042 -9999 0 -0.42 5 5
alphaV/beta3 Integrin/Pyk2 -0.025 0.11 -9999 0 -0.21 119 119
SDC1 -0.088 0.14 -9999 0 -0.27 179 179
VAV3 -0.008 0.064 -9999 0 -0.21 10 10
PTPN11 0.011 0 -9999 0 -10000 0 0
IRS1 -0.029 0.12 -9999 0 -0.42 47 47
FAK1/Paxillin -0.12 0.16 -9999 0 -0.34 140 140
cell migration -0.11 0.14 -9999 0 -0.31 140 140
ITGAV 0.011 0 -9999 0 -10000 0 0
PI3K -0.16 0.14 -9999 0 -0.37 130 130
SPP1 -0.063 0.12 -9999 0 -0.27 134 134
KDR -0.013 0.097 -9999 0 -0.42 28 28
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.011 0 -9999 0 -10000 0 0
COL4A3 -0.054 0.15 -9999 0 -0.4 79 79
angiogenesis -0.32 0.28 -9999 0 -0.51 323 323
Rac1/GTP -0.001 0.058 -9999 0 -0.28 2 2
EDIL3 -0.12 0.2 -9999 0 -0.42 161 161
cell proliferation -0.037 0.12 -9999 0 -0.25 108 108
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.008 0.001 -10000 0 -10000 0 0
GNB1/GNG2 -0.028 0.095 -10000 0 -0.22 102 102
regulation of S phase of mitotic cell cycle -0.02 0.088 -10000 0 -0.21 93 93
GNAO1 -0.099 0.19 -10000 0 -0.42 131 131
HRAS 0.01 0.002 -10000 0 -10000 0 0
SHBG/T-DHT 0.005 0.019 -10000 0 -0.25 3 3
PELP1 0.01 0.002 -10000 0 -10000 0 0
AKT1 0.009 0.001 -10000 0 -10000 0 0
MAP2K1 -0.038 0.094 -10000 0 -0.27 35 35
T-DHT/AR -0.047 0.12 -10000 0 -0.3 90 90
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.003 -10000 0 -0.007 174 174
GNAI2 0.01 0 -10000 0 -10000 0 0
GNAI3 0.01 0 -10000 0 -10000 0 0
GNAI1 0.002 0.059 -10000 0 -0.42 10 10
mol:GDP -0.061 0.14 -10000 0 -0.35 91 91
cell proliferation -0.12 0.2 -10000 0 -0.39 174 174
PIK3CA 0.01 0.019 -10000 0 -0.42 1 1
FOS -0.24 0.38 -10000 0 -0.77 174 174
mol:Ca2+ -0.025 0.031 -10000 0 -0.063 171 171
MAPK3 -0.083 0.15 -10000 0 -0.27 174 174
MAPK1 -0.058 0.1 -10000 0 -0.22 76 76
PIK3R1 0.007 0.038 -10000 0 -0.42 4 4
mol:IP3 -0.001 0.002 -10000 0 -0.004 174 174
cAMP biosynthetic process 0.013 0.03 0.094 9 -0.2 3 12
GNG2 -0.002 0.071 -10000 0 -0.41 15 15
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 174 174
HRAS/GTP -0.044 0.074 -10000 0 -0.2 90 90
actin cytoskeleton reorganization -0.002 0.018 -10000 0 -0.18 5 5
SRC 0.01 0.002 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 174 174
PI3K 0.012 0.025 -10000 0 -0.24 5 5
apoptosis 0.12 0.21 0.4 174 -10000 0 174
T-DHT/AR/PELP1 -0.034 0.097 -10000 0 -0.24 90 90
HRAS/GDP -0.058 0.13 -10000 0 -0.34 90 90
CREB1 -0.13 0.22 -10000 0 -0.43 174 174
RAC1-CDC42/GTP 0.002 0.02 -10000 0 -0.18 5 5
AR -0.066 0.16 -10000 0 -0.42 90 90
GNB1 0.011 0 -10000 0 -10000 0 0
RAF1 -0.034 0.088 -10000 0 -0.2 90 90
RAC1-CDC42/GDP -0.051 0.12 -10000 0 -0.32 90 90
T-DHT/AR/PELP1/Src -0.027 0.089 -10000 0 -0.22 90 90
MAP2K2 -0.038 0.094 -10000 0 -0.27 35 35
T-DHT/AR/PELP1/Src/PI3K -0.021 0.089 -10000 0 -0.21 93 93
GNAZ -0.011 0.094 -10000 0 -0.42 26 26
SHBG 0.008 0.033 -10000 0 -0.42 3 3
Gi family/GNB1/GNG2/GDP -0.079 0.17 -10000 0 -0.33 135 135
mol:T-DHT -0.001 0.001 -10000 0 -0.003 139 139
RAC1 0.011 0 -10000 0 -10000 0 0
GNRH1 0.005 0.032 -10000 0 -0.29 6 6
Gi family/GTP -0.065 0.12 -10000 0 -0.27 93 93
CDC42 0.011 0 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 -0.005 0.081 -10000 0 -0.42 19 19
ANTXR2 -0.13 0.2 -10000 0 -0.42 167 167
negative regulation of myeloid dendritic cell antigen processing and presentation -0.02 0.028 -10000 0 -0.059 171 171
monocyte activation -0.028 0.12 -10000 0 -0.41 42 42
MAP2K2 -0.007 0.011 -10000 0 -10000 0 0
MAP2K1 -0.016 0.023 -10000 0 -10000 0 0
MAP2K7 -0.016 0.023 -10000 0 -0.079 15 15
MAP2K6 -0.032 0.046 -10000 0 -0.12 80 80
CYAA -0.065 0.11 -10000 0 -0.22 171 171
MAP2K4 -0.017 0.026 -10000 0 -0.09 16 16
IL1B -0.012 0.044 -10000 0 -0.15 30 30
Channel -0.069 0.12 -10000 0 -0.23 171 171
NLRP1 -0.026 0.054 -10000 0 -0.24 24 24
CALM1 0.011 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.021 0.031 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.02 0.028 0.059 171 -10000 0 171
MAPK3 -0.016 0.023 -10000 0 -10000 0 0
MAPK1 -0.016 0.023 -10000 0 -10000 0 0
PGR -0.079 0.1 -10000 0 -0.23 154 154
PA/Cellular Receptors -0.077 0.13 -10000 0 -0.26 171 171
apoptosis -0.02 0.028 -10000 0 -0.059 171 171
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.065 0.12 -10000 0 -0.22 171 171
macrophage activation -0.004 0.026 -10000 0 -10000 0 0
TNF -0.018 0.086 -10000 0 -0.28 50 50
VCAM1 -0.029 0.12 -10000 0 -0.41 42 42
platelet activation -0.021 0.031 -10000 0 -10000 0 0
MAPKKK cascade 0.013 0.031 0.082 32 -10000 0 32
IL18 -0.012 0.042 -10000 0 -0.14 34 34
negative regulation of macrophage activation -0.02 0.028 -10000 0 -0.059 171 171
LEF -0.02 0.028 -10000 0 -0.059 171 171
CASP1 -0.022 0.038 -10000 0 -0.12 42 42
mol:cAMP -0.021 0.031 -10000 0 -10000 0 0
necrosis -0.02 0.028 -10000 0 -0.059 171 171
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.064 0.12 -10000 0 -0.22 171 171
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
S1P3 pathway

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
PDGFRB -0.007 0.085 -9999 0 -0.42 21 21
mol:S1P -0.01 0.014 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.083 0.13 -9999 0 -0.28 112 112
GNAO1 -0.11 0.19 -9999 0 -0.43 131 131
S1P/S1P3/G12/G13 0.002 0.045 -9999 0 -0.22 17 17
AKT1 -0.068 0.16 -9999 0 -0.59 29 29
AKT3 -0.46 0.56 -9999 0 -1.1 212 212
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.007 0.085 -9999 0 -0.42 21 21
GNAI2 0 0.015 -9999 0 -10000 0 0
GNAI3 0.003 0.011 -9999 0 -10000 0 0
GNAI1 -0.005 0.061 -9999 0 -0.43 10 10
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 -0.014 0.078 -9999 0 -0.43 17 17
S1PR2 0.011 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.15 0.2 -9999 0 -0.34 218 218
MAPK3 -0.14 0.19 -9999 0 -0.32 218 218
MAPK1 -0.14 0.19 -9999 0 -0.32 218 218
JAK2 -0.14 0.2 -9999 0 -0.33 218 218
CXCR4 -0.14 0.19 -9999 0 -0.32 218 218
FLT1 0 0.025 -9999 0 -0.43 1 1
RhoA/GDP 0.008 0 -9999 0 -10000 0 0
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
SRC -0.14 0.19 -9999 0 -0.32 218 218
S1P/S1P3/Gi -0.15 0.2 -9999 0 -0.34 218 218
RAC1 0.011 0 -9999 0 -10000 0 0
RhoA/GTP -0.13 0.19 -9999 0 -0.31 218 218
VEGFA 0.001 0.017 -9999 0 -10000 0 0
S1P/S1P2/Gi -0.095 0.14 -9999 0 -0.29 139 139
VEGFR1 homodimer/VEGFA homodimer -0.004 0.035 -9999 0 -0.31 1 1
RHOA 0.011 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.022 0.099 -9999 0 -0.25 73 73
GNAQ 0.009 0.027 -9999 0 -0.42 2 2
GNAZ -0.019 0.094 -9999 0 -0.42 26 26
G12/G13 0.016 0 -9999 0 -10000 0 0
GNA14 -0.034 0.13 -9999 0 -0.42 53 53
GNA15 0.007 0.033 -9999 0 -0.27 7 7
GNA12 0.011 0 -9999 0 -10000 0 0
GNA13 0.011 0 -9999 0 -10000 0 0
GNA11 0.001 0.062 -9999 0 -0.42 11 11
Rac1/GTP -0.13 0.19 -9999 0 -0.31 218 218
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.011 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.1 0.048 -9999 0 -0.26 2 2
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.028 0.011 -9999 0 -10000 0 0
AURKB -0.24 0.095 -9999 0 -0.27 447 447
AURKC 0.01 0.018 -9999 0 -0.27 2 2
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.055 0.19 -10000 0 -0.6 45 45
IHH -0.13 0.19 -10000 0 -0.34 205 205
SHH Np/Cholesterol/GAS1 -0.14 0.12 -10000 0 -0.23 327 327
LRPAP1 0.011 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.14 0.12 0.23 327 -10000 0 327
SMO/beta Arrestin2 -0.044 0.15 -10000 0 -0.43 21 21
SMO -0.052 0.16 -10000 0 -0.37 45 45
AKT1 -0.013 0.091 -10000 0 -0.48 4 4
ARRB2 0.011 0 -10000 0 -10000 0 0
BOC -0.015 0.1 -10000 0 -0.42 31 31
ADRBK1 0.011 0 -10000 0 -10000 0 0
heart looping -0.051 0.16 -10000 0 -0.36 45 45
STIL -0.047 0.11 -10000 0 -0.32 33 33
DHH N/PTCH2 -0.023 0.11 -10000 0 -0.3 62 62
DHH N/PTCH1 -0.062 0.14 -10000 0 -0.36 42 42
PIK3CA 0.01 0.019 -10000 0 -0.42 1 1
DHH -0.023 0.11 -10000 0 -0.42 40 40
PTHLH -0.069 0.22 -10000 0 -0.6 46 46
determination of left/right symmetry -0.051 0.16 -10000 0 -0.36 45 45
PIK3R1 0.007 0.038 -10000 0 -0.42 4 4
skeletal system development -0.068 0.21 -10000 0 -0.6 46 46
IHH N/Hhip -0.042 0.14 -10000 0 -0.26 141 141
DHH N/Hhip -0.024 0.095 -10000 0 -0.24 78 78
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.051 0.16 -10000 0 -0.36 45 45
pancreas development -0.013 0.08 -10000 0 -0.29 40 40
HHAT 0.008 0.033 -10000 0 -0.42 3 3
PI3K 0.013 0.03 -10000 0 -0.29 5 5
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.26 0.21 -10000 0 -0.42 325 325
somite specification -0.051 0.16 -10000 0 -0.36 45 45
SHH Np/Cholesterol/PTCH1 -0.043 0.11 -10000 0 -0.34 26 26
SHH Np/Cholesterol/PTCH2 -0.011 0.071 -10000 0 -0.23 29 29
SHH Np/Cholesterol/Megalin -0.052 0.084 -10000 0 -0.26 28 28
SHH -0.009 0.067 -10000 0 -0.18 64 64
catabolic process -0.057 0.14 -10000 0 -0.34 46 46
SMO/Vitamin D3 -0.037 0.14 -10000 0 -0.37 28 28
SHH Np/Cholesterol/Hhip -0.012 0.064 -10000 0 -0.24 13 13
LRP2 -0.094 0.14 -10000 0 -0.27 189 189
receptor-mediated endocytosis -0.063 0.13 -10000 0 -0.38 26 26
SHH Np/Cholesterol/BOC -0.014 0.074 -10000 0 -0.23 34 34
SHH Np/Cholesterol/CDO -0.038 0.1 -10000 0 -0.23 90 90
mesenchymal cell differentiation 0.012 0.063 0.23 13 -10000 0 13
mol:Vitamin D3 -0.031 0.12 -10000 0 -0.34 26 26
IHH N/PTCH2 -0.036 0.15 -10000 0 -0.28 126 126
CDON -0.062 0.16 -10000 0 -0.42 87 87
IHH N/PTCH1 -0.023 0.16 -10000 0 -0.34 46 46
Megalin/LRPAP1 -0.055 0.091 -10000 0 -0.18 189 189
PTCH2 -0.011 0.094 -10000 0 -0.42 26 26
SHH Np/Cholesterol -0.007 0.049 -10000 0 -0.13 64 64
PTCH1 -0.057 0.14 -10000 0 -0.34 46 46
HHIP -0.013 0.081 -10000 0 -0.29 40 40
Reelin signaling pathway

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
CDK5R1/CDK5 0.015 0.008 -9999 0 -0.18 1 1
VLDLR 0.009 0.027 -9999 0 -0.42 2 2
CRKL 0.011 0 -9999 0 -10000 0 0
LRPAP1 0.011 0 -9999 0 -10000 0 0
FYN 0.011 0 -9999 0 -10000 0 0
ITGA3 0.01 0.019 -9999 0 -0.42 1 1
RELN/VLDLR/Fyn -0.074 0.12 -9999 0 -0.23 187 187
MAPK8IP1/MKK7/MAP3K11/JNK1 0.029 0.024 -9999 0 -0.18 6 6
AKT1 -0.054 0.1 -9999 0 -0.18 192 192
MAP2K7 0.011 0 -9999 0 -10000 0 0
RAPGEF1 0.011 0 -9999 0 -10000 0 0
DAB1 0.001 0.043 -9999 0 -0.27 12 12
RELN/LRP8/DAB1 -0.071 0.11 -9999 0 -0.21 188 188
LRPAP1/LRP8 0.014 0.017 -9999 0 -0.18 4 4
RELN/LRP8/DAB1/Fyn -0.061 0.1 -9999 0 -0.19 188 188
DAB1/alpha3/beta1 Integrin -0.064 0.081 -9999 0 -0.3 5 5
long-term memory -0.14 0.15 -9999 0 -0.37 111 111
DAB1/LIS1 -0.067 0.085 -9999 0 -0.28 5 5
DAB1/CRLK/C3G -0.063 0.08 -9999 0 -0.26 5 5
PIK3CA 0.01 0.019 -9999 0 -0.42 1 1
DAB1/NCK2 -0.068 0.085 -9999 0 -0.28 5 5
ARHGEF2 0.011 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.18 0.21 -9999 0 -0.42 224 224
CDK5R1 0.01 0.012 -9999 0 -0.27 1 1
RELN -0.15 0.2 -9999 0 -0.41 191 191
PIK3R1 0.007 0.038 -9999 0 -0.42 4 4
RELN/LRP8/Fyn -0.074 0.12 -9999 0 -0.23 187 187
GRIN2A/RELN/LRP8/DAB1/Fyn -0.15 0.15 -9999 0 -0.25 315 315
MAPK8 0.006 0.042 -9999 0 -0.42 5 5
RELN/VLDLR/DAB1 -0.071 0.11 -9999 0 -0.21 188 188
ITGB1 0.011 0 -9999 0 -10000 0 0
MAP1B -0.071 0.12 -9999 0 -0.21 207 207
RELN/LRP8 -0.074 0.12 -9999 0 -0.23 187 187
GRIN2B/RELN/LRP8/DAB1/Fyn -0.062 0.1 -9999 0 -0.19 189 189
PI3K 0.013 0.03 -9999 0 -0.29 5 5
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin 0.015 0.013 -9999 0 -0.29 1 1
RAP1A -0.034 0.093 -9999 0 -0.29 3 3
PAFAH1B1 0.011 0 -9999 0 -10000 0 0
MAPK8IP1 0.009 0.023 -9999 0 -0.34 2 2
CRLK/C3G 0.016 0 -9999 0 -10000 0 0
GRIN2B -0.005 0.053 -9999 0 -0.27 19 19
NCK2 0.011 0 -9999 0 -10000 0 0
neuron differentiation -0.033 0.084 -9999 0 -0.37 1 1
neuron adhesion -0.023 0.091 -9999 0 -0.32 3 3
LRP8 0.008 0.025 -9999 0 -0.27 4 4
GSK3B -0.046 0.097 -9999 0 -0.18 77 77
RELN/VLDLR/DAB1/Fyn -0.061 0.1 -9999 0 -0.19 188 188
MAP3K11 0.011 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.064 0.11 -9999 0 -0.2 192 192
CDK5 0.011 0 -9999 0 -10000 0 0
MAPT 0.001 0.079 -9999 0 -0.38 20 20
neuron migration -0.054 0.13 -9999 0 -0.23 186 186
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.033 0.084 -9999 0 -0.37 1 1
RELN/VLDLR -0.06 0.11 -9999 0 -0.21 188 188
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.002 0.063 -9999 0 -0.24 34 34
ADCY5 -0.034 0.1 -9999 0 -0.24 99 99
ADCY6 0.015 0 -9999 0 -10000 0 0
ADCY7 0.015 0 -9999 0 -10000 0 0
ADCY1 0.004 0.049 -9999 0 -0.21 25 25
ADCY2 -0.13 0.13 -9999 0 -0.24 286 286
ADCY3 0.014 0.016 -9999 0 -0.24 2 2
ADCY8 -0.02 0.079 -9999 0 -0.24 59 59
PRKCE 0.009 0 -9999 0 -10000 0 0
ADCY9 -0.018 0.085 -9999 0 -0.24 65 65
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.079 0.089 -9999 0 -0.19 144 144
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.1 0.34 -9999 0 -0.96 68 68
MKNK1 0.011 0 -9999 0 -10000 0 0
MAPK14 -0.018 0.1 -9999 0 -0.27 72 72
ATF2/c-Jun -0.007 0.11 -9999 0 -0.5 9 9
MAPK11 -0.02 0.11 -9999 0 -0.27 74 74
MITF -0.051 0.17 -9999 0 -0.38 82 82
MAPKAPK5 -0.016 0.12 -9999 0 -0.32 74 74
KRT8 -0.029 0.13 -9999 0 -0.33 76 76
MAPKAPK3 0.011 0 -9999 0 -10000 0 0
MAPKAPK2 0.011 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.028 0.15 -9999 0 -0.39 72 72
CEBPB -0.016 0.12 -9999 0 -0.32 74 74
SLC9A1 -0.016 0.12 -9999 0 -0.32 74 74
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.014 0.13 -9999 0 -0.31 77 77
p38alpha-beta/MNK1 -0.012 0.12 -9999 0 -0.3 72 72
JUN -0.007 0.11 -9999 0 -0.63 6 6
PPARGC1A -0.081 0.19 -9999 0 -0.4 90 90
USF1 -0.016 0.12 -9999 0 -0.32 74 74
RAB5/GDP/GDI1 -0.033 0.079 -9999 0 -0.22 72 72
NOS2 -0.021 0.15 -9999 0 -0.7 8 8
DDIT3 -0.016 0.12 -9999 0 -0.32 74 74
RAB5A 0.011 0 -9999 0 -10000 0 0
HSPB1 -0.006 0.1 -9999 0 -0.25 72 72
p38alpha-beta/HBP1 -0.012 0.12 -9999 0 -0.3 72 72
CREB1 -0.018 0.14 -9999 0 -0.34 74 74
RAB5/GDP 0.008 0 -9999 0 -10000 0 0
EIF4E -0.007 0.1 -9999 0 -0.26 72 72
RPS6KA4 -0.016 0.12 -9999 0 -0.32 74 74
PLA2G4A -0.018 0.13 -9999 0 -0.3 73 73
GDI1 -0.016 0.12 -9999 0 -0.32 74 74
TP53 -0.024 0.15 -9999 0 -0.39 74 74
RPS6KA5 -0.019 0.13 -9999 0 -0.32 79 79
ESR1 -0.051 0.18 -9999 0 -0.36 112 112
HBP1 0.011 0 -9999 0 -10000 0 0
MEF2C -0.052 0.17 -9999 0 -0.38 83 83
MEF2A -0.02 0.13 -9999 0 -0.33 78 78
EIF4EBP1 -0.017 0.14 -9999 0 -0.34 74 74
KRT19 -0.02 0.13 -9999 0 -0.32 78 78
ELK4 -0.016 0.12 -9999 0 -0.32 74 74
ATF6 -0.016 0.12 -9999 0 -0.32 74 74
ATF1 -0.018 0.14 -9999 0 -0.34 74 74
p38alpha-beta/MAPKAPK2 -0.012 0.12 -9999 0 -0.3 72 72
p38alpha-beta/MAPKAPK3 -0.012 0.12 -9999 0 -0.3 72 72
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.13 0.13 -9999 0 -0.23 301 301
fibroblast growth factor receptor signaling pathway -0.13 0.12 -9999 0 -0.23 301 301
LAMA1 -0.11 0.14 -9999 0 -0.27 223 223
PRNP -0.052 0.15 -9999 0 -0.42 75 75
GPC1/SLIT2 -0.03 0.11 -9999 0 -0.29 77 77
SMAD2 0.02 0.036 -9999 0 -0.2 13 13
GPC1/PrPc/Cu2+ -0.023 0.09 -9999 0 -0.24 75 75
GPC1/Laminin alpha1 -0.067 0.095 -9999 0 -0.18 223 223
TDGF1 -0.019 0.1 -9999 0 -0.36 41 41
CRIPTO/GPC1 -0.005 0.072 -9999 0 -0.24 41 41
APP/GPC1 0.016 0 -9999 0 -10000 0 0
mol:NO 0 0 -9999 0 -10000 0 0
YES1 0.004 0.06 -9999 0 -0.23 25 25
FLT1 0.01 0.019 -9999 0 -0.42 1 1
GPC1/TGFB/TGFBR1/TGFBR2 0.015 0.04 -9999 0 -0.23 13 13
SERPINC1 0.007 0.022 -9999 0 -0.27 3 3
FYN 0.004 0.06 -9999 0 -0.23 25 25
FGR -0.003 0.072 -9999 0 -0.24 37 37
positive regulation of MAPKKK cascade 0.014 0.073 -9999 0 -0.28 26 26
SLIT2 -0.054 0.15 -9999 0 -0.42 77 77
GPC1/NRG 0.006 0.051 -9999 0 -0.28 16 16
NRG1 -0.003 0.073 -9999 0 -0.41 16 16
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.021 0.011 -9999 0 -0.23 1 1
LYN 0.004 0.06 -9999 0 -0.23 25 25
mol:Spermine 0.009 0 -9999 0 -10000 0 0
cell growth -0.13 0.12 -9999 0 -0.23 301 301
BMP signaling pathway -0.011 0 -9999 0 -10000 0 0
SRC 0.004 0.06 -9999 0 -0.23 25 25
TGFBR1 0.011 0 -9999 0 -10000 0 0
mol:Cu2+ 0 0 -9999 0 -10000 0 0
PLA2G2A -0.083 0.17 -9999 0 -0.41 112 112
GPC1 0.011 0 -9999 0 -10000 0 0
TGFBR1 (dimer) 0.011 0 -9999 0 -10000 0 0
VEGFA 0.011 0 -9999 0 -10000 0 0
BLK -0.01 0.072 -9999 0 -0.24 26 26
HCK 0.004 0.06 -9999 0 -0.23 25 25
FGF2 -0.24 0.21 -9999 0 -0.42 301 301
FGFR1 0.01 0.019 -9999 0 -0.42 1 1
VEGFR1 homodimer 0.01 0.019 -9999 0 -0.42 1 1
TGFBR2 0 0.067 -9999 0 -0.42 13 13
cell death 0.016 0 -9999 0 -10000 0 0
ATIII/GPC1 0.013 0.015 -9999 0 -0.18 3 3
PLA2G2A/GPC1 -0.05 0.12 -9999 0 -0.28 112 112
LCK 0.002 0.063 -9999 0 -0.24 26 26
neuron differentiation 0.006 0.051 -9999 0 -0.28 16 16
PrPc/Cu2+ -0.036 0.11 -9999 0 -0.29 75 75
APP 0.011 0 -9999 0 -10000 0 0
TGFBR2 (dimer) 0 0.067 -9999 0 -0.42 13 13
Effects of Botulinum toxin

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
STX1A 0.008 0.008 -9999 0 -0.18 1 1
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B 0.01 0.022 -9999 0 -0.18 7 7
STXBP1 -0.017 0.1 -9999 0 -0.42 33 33
ACh/CHRNA1 -0.092 0.09 -9999 0 -0.19 200 200
RAB3GAP2/RIMS1/UNC13B 0.017 0.018 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 0.003 0.033 -9999 0 -0.27 7 7
mol:ACh -0.047 0.057 -9999 0 -0.11 244 244
RAB3GAP2 0.011 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.066 0.076 -9999 0 -0.26 34 34
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.092 0.09 -9999 0 -0.19 200 200
UNC13B 0.011 0 -9999 0 -10000 0 0
CHRNA1 -0.099 0.14 -9999 0 -0.27 199 199
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.081 0.12 -9999 0 -0.31 106 106
SNAP25 -0.12 0.13 -9999 0 -0.25 244 244
VAMP2 0.005 0.01 -9999 0 -0.23 1 1
SYT1 -0.077 0.17 -9999 0 -0.42 105 105
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.002 0.062 -9999 0 -0.24 34 34
STX1A/SNAP25 fragment 1/VAMP2 -0.066 0.076 -9999 0 -0.26 34 34
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.008 0.033 -9999 0 -0.42 3 3
LAT2 -0.085 0.13 -9999 0 -0.24 196 196
AP1 -0.15 0.15 -9999 0 -0.36 122 122
mol:PIP3 -0.09 0.16 -9999 0 -0.41 44 44
IKBKB -0.049 0.1 -9999 0 -0.23 59 59
AKT1 -0.045 0.11 -9999 0 -0.29 46 46
IKBKG -0.049 0.1 -9999 0 -0.23 59 59
MS4A2 -0.15 0.2 -9999 0 -0.41 196 196
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.009 0.019 -9999 0 -0.42 1 1
MAP3K1 -0.061 0.12 -9999 0 -0.31 44 44
mol:Ca2+ -0.068 0.13 -9999 0 -0.31 44 44
LYN 0.009 0.003 -9999 0 -10000 0 0
CBLB -0.084 0.13 -9999 0 -0.32 57 57
SHC1 0.011 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.047 0.11 -9999 0 -0.22 146 146
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.01 0.019 -9999 0 -0.42 1 1
PLD2 -0.073 0.12 -9999 0 -0.27 84 84
PTPN13 -0.11 0.16 -9999 0 -0.39 67 67
PTPN11 0.009 0.005 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.046 0.11 -9999 0 -0.27 46 46
SYK 0.009 0.013 -9999 0 -0.27 1 1
GRB2 0.01 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.12 0.14 -9999 0 -0.37 58 58
LAT -0.084 0.13 -9999 0 -0.23 196 196
PAK2 -0.072 0.14 -9999 0 -0.35 44 44
NFATC2 -0.086 0.16 -9999 0 -0.54 51 51
HRAS -0.083 0.14 -9999 0 -0.38 44 44
GAB2 0.006 0.042 -9999 0 -0.42 5 5
PLA2G1B 0.029 0.015 -9999 0 -10000 0 0
Fc epsilon R1 -0.12 0.14 -9999 0 -0.26 239 239
Antigen/IgE/Fc epsilon R1 -0.11 0.13 -9999 0 -0.23 239 239
mol:GDP -0.092 0.15 -9999 0 -0.36 59 59
JUN 0.006 0.046 -9999 0 -0.42 6 6
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.007 0.038 -9999 0 -0.42 4 4
FOS -0.13 0.2 -9999 0 -0.42 174 174
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.094 0.14 -9999 0 -0.25 197 197
CHUK -0.049 0.1 -9999 0 -0.23 59 59
KLRG1 -0.072 0.12 -9999 0 -0.33 42 42
VAV1 -0.086 0.14 -9999 0 -0.24 196 196
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.084 0.13 -9999 0 -0.23 196 196
negative regulation of mast cell degranulation -0.062 0.11 -9999 0 -0.31 41 41
BTK -0.097 0.15 -9999 0 -0.41 45 45
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.095 0.15 -9999 0 -0.32 102 102
GAB2/PI3K/SHP2 -0.075 0.095 -9999 0 -0.31 46 46
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.081 0.13 -9999 0 -0.41 42 42
RAF1 0.021 0.018 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.085 0.13 -9999 0 -0.28 88 88
FCER1G 0.017 0.021 -9999 0 -0.28 2 2
FCER1A -0.063 0.16 -9999 0 -0.43 84 84
Antigen/IgE/Fc epsilon R1/Fyn -0.095 0.12 -9999 0 -0.29 84 84
MAPK3 0.028 0.015 -9999 0 -10000 0 0
MAPK1 0.028 0.015 -9999 0 -10000 0 0
NFKB1 0.01 0.019 -9999 0 -0.42 1 1
MAPK8 -0.018 0.076 -9999 0 -0.55 6 6
DUSP1 -0.11 0.19 -9999 0 -0.42 145 145
NF-kappa-B/RelA -0.043 0.049 -9999 0 -0.17 8 8
actin cytoskeleton reorganization -0.098 0.15 -9999 0 -0.4 41 41
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.096 0.11 -9999 0 -0.35 47 47
FER -0.084 0.13 -9999 0 -0.23 196 196
RELA 0.011 0 -9999 0 -10000 0 0
ITK -0.037 0.064 -9999 0 -0.38 13 13
SOS1 0.011 0 -9999 0 -10000 0 0
PLCG1 -0.089 0.15 -9999 0 -0.4 44 44
cytokine secretion -0.032 0.036 -9999 0 -10000 0 0
SPHK1 -0.084 0.13 -9999 0 -0.36 44 44
PTK2 -0.1 0.15 -9999 0 -0.41 41 41
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.12 0.14 -9999 0 -0.39 58 58
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.087 0.16 -9999 0 -0.41 45 45
MAP2K2 0.025 0.016 -9999 0 -10000 0 0
MAP2K1 0.025 0.016 -9999 0 -10000 0 0
MAP2K7 0.011 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.068 0.092 -9999 0 -0.29 41 41
MAP2K4 0.009 0.039 -9999 0 -0.84 1 1
Fc epsilon R1/FcgammaRIIB -0.096 0.14 -9999 0 -0.22 240 240
mol:Choline -0.072 0.12 -9999 0 -0.26 84 84
SHC/Grb2/SOS1 -0.084 0.11 -9999 0 -0.34 41 41
FYN 0.011 0 -9999 0 -10000 0 0
DOK1 0.011 0 -9999 0 -10000 0 0
PXN -0.09 0.14 -9999 0 -0.38 41 41
HCLS1 -0.084 0.13 -9999 0 -0.32 58 58
PRKCB -0.075 0.13 -9999 0 -0.32 61 61
FCGR2B 0.008 0.035 -9999 0 -0.38 4 4
IGHE -0.002 0.004 -9999 0 -10000 0 0
KLRG1/SHIP -0.063 0.11 -9999 0 -0.31 41 41
LCP2 0.01 0.013 -9999 0 -0.28 1 1
PLA2G4A -0.094 0.14 -9999 0 -0.25 201 201
RASA1 0.006 0.042 -9999 0 -0.42 5 5
mol:Phosphatidic acid -0.072 0.12 -9999 0 -0.26 84 84
IKK complex -0.028 0.081 -9999 0 -0.17 59 59
WIPF1 0.009 0.027 -9999 0 -0.42 2 2
IGF1 pathway

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
NCK2 0.011 0 -10000 0 -10000 0 0
PTK2 0.011 0 -10000 0 -10000 0 0
CRKL -0.044 0.12 -10000 0 -0.26 111 111
GRB2/SOS1/SHC 0.022 0 -10000 0 -10000 0 0
HRAS 0.011 0 -10000 0 -10000 0 0
IRS1/Crk -0.044 0.12 -10000 0 -0.26 111 111
IGF-1R heterotetramer/IGF1/PTP1B -0.041 0.12 -10000 0 -0.26 111 111
AKT1 -0.024 0.11 -10000 0 -0.34 36 36
BAD -0.018 0.1 -10000 0 -0.31 36 36
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.044 0.12 -10000 0 -0.26 111 111
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.045 0.12 -10000 0 -0.26 111 111
RAF1 -0.013 0.1 -10000 0 -0.3 36 36
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.035 0.12 -10000 0 -0.24 111 111
YWHAZ 0.011 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.055 0.13 -10000 0 -0.26 130 130
PIK3CA 0.01 0.019 -10000 0 -0.42 1 1
RPS6KB1 -0.024 0.11 -10000 0 -0.34 36 36
GNB2L1 0.011 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.013 0.09 -10000 0 -0.26 36 36
PXN 0.011 0 -10000 0 -10000 0 0
PIK3R1 0.007 0.038 -10000 0 -0.42 4 4
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.016 0 -10000 0 -10000 0 0
HRAS/GTP -0.048 0.095 -10000 0 -0.33 35 35
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.017 0.095 -10000 0 -0.26 35 35
IGF-1R heterotetramer -0.021 0.095 -10000 0 -0.47 20 20
IGF-1R heterotetramer/IGF1/IRS/Nck -0.044 0.12 -10000 0 -0.26 111 111
Crk/p130 Cas/Paxillin -0.029 0.11 -10000 0 -0.22 111 111
IGF1R -0.021 0.095 -10000 0 -0.47 20 20
IGF1 -0.082 0.18 -10000 0 -0.44 102 102
IRS2/Crk -0.063 0.14 -10000 0 -0.25 159 159
PI3K -0.037 0.12 -10000 0 -0.24 113 113
apoptosis 0.01 0.094 0.27 36 -10000 0 36
HRAS/GDP 0.008 0 -10000 0 -10000 0 0
PRKCD -0.052 0.16 -10000 0 -0.34 111 111
RAF1/14-3-3 E -0.005 0.092 -10000 0 -0.26 36 36
BAD/14-3-3 -0.01 0.099 -10000 0 -0.29 36 36
PRKCZ -0.025 0.11 -10000 0 -0.34 36 36
Crk/p130 Cas/Paxillin/FAK1 -0.04 0.081 -10000 0 -0.28 36 36
PTPN1 0.011 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.06 0.17 -10000 0 -0.36 111 111
BCAR1 0.011 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.026 0.1 -10000 0 -0.21 112 112
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.011 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.044 0.12 -10000 0 -0.26 111 111
GRB10 0.01 0.019 -10000 0 -0.42 1 1
PTPN11 -0.044 0.12 -10000 0 -0.26 111 111
IRS1 -0.05 0.13 -10000 0 -0.28 111 111
IRS2 -0.073 0.15 -10000 0 -0.27 159 159
IGF-1R heterotetramer/IGF1 -0.065 0.15 -10000 0 -0.34 111 111
GRB2 0.011 0 -10000 0 -10000 0 0
PDPK1 -0.031 0.12 -10000 0 -0.23 113 113
YWHAE 0.011 0 -10000 0 -10000 0 0
PRKD1 -0.064 0.17 -10000 0 -0.36 115 115
SHC1 0.011 0 -10000 0 -10000 0 0
Thromboxane A2 receptor signaling

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
TGM2 -0.032 0.13 -10000 0 -0.42 51 51
GNB1/GNG2 -0.046 0.077 -10000 0 -0.19 104 104
AKT1 -0.024 0.1 -10000 0 -0.2 104 104
EGF -0.002 0.058 -10000 0 -0.29 20 20
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.013 0.059 -10000 0 -0.22 8 8
mol:Ca2+ -0.056 0.15 -10000 0 -0.3 127 127
LYN 0.017 0.05 -10000 0 -10000 0 0
RhoA/GTP -0.031 0.052 -10000 0 -0.12 111 111
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.056 0.16 -10000 0 -0.34 116 116
GNG2 -0.002 0.071 -10000 0 -0.41 15 15
ARRB2 0.011 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.001 0.074 -10000 0 -0.33 15 15
G beta5/gamma2 -0.06 0.1 -10000 0 -0.26 104 104
PRKCH -0.064 0.17 -10000 0 -0.35 124 124
DNM1 0.008 0.033 -10000 0 -0.42 3 3
TXA2/TP beta/beta Arrestin3 -0.004 0.017 -10000 0 -0.2 2 2
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.032 0.13 -10000 0 -0.42 50 50
G12 family/GTP -0.077 0.13 -10000 0 -0.29 124 124
ADRBK1 0.011 0 -10000 0 -10000 0 0
ADRBK2 0.01 0.019 -10000 0 -0.42 1 1
RhoA/GTP/ROCK1 0.011 0.006 -10000 0 -10000 0 0
mol:GDP 0.029 0.098 0.21 70 -10000 0 70
mol:NADP 0.009 0.023 -10000 0 -0.34 2 2
RAB11A 0.011 0 -10000 0 -10000 0 0
PRKG1 -0.19 0.21 -10000 0 -0.42 242 242
mol:IP3 -0.074 0.18 -10000 0 -0.38 127 127
cell morphogenesis 0.011 0.006 -10000 0 -10000 0 0
PLCB2 -0.11 0.24 -10000 0 -0.52 127 127
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.015 0.055 -10000 0 -0.23 2 2
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.017 0.05 -10000 0 -10000 0 0
RHOA 0.011 0 -10000 0 -10000 0 0
PTGIR 0.01 0.019 -10000 0 -0.42 1 1
PRKCB1 -0.072 0.18 -10000 0 -0.37 127 127
GNAQ 0.009 0.027 -10000 0 -0.42 2 2
mol:L-citrulline 0.009 0.023 -10000 0 -0.34 2 2
TXA2/TXA2-R family -0.1 0.24 -10000 0 -0.53 116 116
LCK 0.017 0.051 -10000 0 -0.16 1 1
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.016 0.049 -10000 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma 0.015 0.033 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.015 0.048 -10000 0 -10000 0 0
MAPK14 -0.03 0.11 -10000 0 -0.22 114 114
TGM2/GTP -0.092 0.22 -10000 0 -0.45 127 127
MAPK11 -0.03 0.11 -10000 0 -0.22 114 114
ARHGEF1 -0.024 0.087 -10000 0 -0.17 117 117
GNAI2 0.011 0 -10000 0 -10000 0 0
JNK cascade -0.069 0.18 -10000 0 -0.38 117 117
RAB11/GDP 0.011 0.001 -10000 0 -10000 0 0
ICAM1 -0.044 0.13 -10000 0 -0.28 112 112
cAMP biosynthetic process -0.074 0.17 -10000 0 -0.36 127 127
Gq family/GTP/EBP50 -0.002 0.065 -10000 0 -0.17 63 63
actin cytoskeleton reorganization 0.011 0.006 -10000 0 -10000 0 0
SRC 0.017 0.05 -10000 0 -10000 0 0
GNB5 0.011 0 -10000 0 -10000 0 0
GNB1 0.011 0 -10000 0 -10000 0 0
EGF/EGFR 0.028 0.049 -10000 0 -0.2 5 5
VCAM1 -0.053 0.15 -10000 0 -0.32 110 110
TP beta/Gq family/GDP/G beta5/gamma2 0.001 0.074 -10000 0 -0.33 15 15
platelet activation -0.042 0.15 -10000 0 -0.3 117 117
PGI2/IP 0.007 0.013 -10000 0 -0.29 1 1
PRKACA -0.006 0.067 -10000 0 -0.21 51 51
Gq family/GDP/G beta5/gamma2 -0.001 0.074 -10000 0 -0.32 15 15
TXA2/TP beta/beta Arrestin2 -0.004 0.034 -10000 0 -0.44 3 3
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0 0.064 -10000 0 -0.19 51 51
mol:DAG -0.082 0.2 -10000 0 -0.42 124 124
EGFR -0.001 0.068 -10000 0 -0.41 14 14
TXA2/TP alpha -0.1 0.24 -10000 0 -0.5 127 127
Gq family/GTP -0.023 0.068 -10000 0 -0.2 63 63
YES1 0.017 0.05 -10000 0 -10000 0 0
GNAI2/GTP -0.015 0.045 -10000 0 -10000 0 0
PGD2/DP -0.022 0.089 -10000 0 -0.29 50 50
SLC9A3R1 0.008 0.028 -10000 0 -0.27 5 5
FYN 0.017 0.05 -10000 0 -10000 0 0
mol:NO 0.009 0.023 -10000 0 -0.34 2 2
GNA15 0.007 0.033 -10000 0 -0.27 7 7
PGK/cGMP -0.11 0.13 -10000 0 -0.24 243 243
RhoA/GDP 0.011 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.008 0.095 -10000 0 -0.34 19 19
NOS3 0.009 0.023 -10000 0 -0.34 2 2
RAC1 0.011 0 -10000 0 -10000 0 0
PRKCA -0.071 0.17 -10000 0 -0.36 124 124
PRKCB -0.071 0.18 -10000 0 -0.36 124 124
PRKCE -0.063 0.17 -10000 0 -0.35 116 116
PRKCD -0.068 0.18 -10000 0 -0.37 117 117
PRKCG -0.079 0.19 -10000 0 -0.39 124 124
muscle contraction -0.091 0.23 -10000 0 -0.49 117 117
PRKCZ -0.056 0.16 -10000 0 -0.34 116 116
ARR3 0.003 0.013 -10000 0 -0.27 1 1
TXA2/TP beta 0.006 0.058 -10000 0 -0.17 26 26
PRKCQ -0.071 0.18 -10000 0 -0.36 124 124
MAPKKK cascade -0.091 0.22 -10000 0 -0.46 124 124
SELE -0.061 0.16 -10000 0 -0.36 112 112
TP beta/GNAI2/GDP/G beta/gamma 0.012 0.067 -10000 0 -0.34 4 4
ROCK1 0.011 0 -10000 0 -10000 0 0
GNA14 -0.034 0.13 -10000 0 -0.42 53 53
chemotaxis -0.11 0.27 -10000 0 -0.6 111 111
GNA12 0.011 0 -10000 0 -10000 0 0
GNA13 0.011 0 -10000 0 -10000 0 0
GNA11 0.001 0.062 -10000 0 -0.42 11 11
Rac1/GTP 0.006 0.004 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.011 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.051 0.094 -10000 0 -0.25 43 43
NT3 (dimer)/TRKC -0.13 0.18 -10000 0 -0.32 229 229
NT3 (dimer)/TRKB -0.12 0.17 -10000 0 -0.3 223 223
SHC/Grb2/SOS1/GAB1/PI3K 0.025 0.029 -10000 0 -0.19 9 9
RAPGEF1 0.011 0 -10000 0 -10000 0 0
BDNF -0.028 0.096 -10000 0 -0.27 69 69
PIK3CA 0.01 0.019 -10000 0 -0.42 1 1
DYNLT1 0.011 0 -10000 0 -10000 0 0
NTRK1 0 0.059 -10000 0 -0.34 14 14
NTRK2 -0.058 0.16 -10000 0 -0.41 84 84
NTRK3 -0.17 0.21 -10000 0 -0.42 220 220
NT-4/5 (dimer)/TRKB -0.11 0.16 -10000 0 -0.28 213 213
neuron apoptosis 0.14 0.2 0.41 143 -10000 0 143
SHC 2-3/Grb2 -0.15 0.22 -10000 0 -0.44 143 143
SHC1 0.011 0 -10000 0 -10000 0 0
SHC2 -0.19 0.25 -10000 0 -0.54 138 138
SHC3 -0.13 0.17 -10000 0 -0.41 100 100
STAT3 (dimer) 0.017 0 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.086 0.14 -10000 0 -0.26 190 190
RIN/GDP -0.041 0.082 -10000 0 -0.18 52 52
GIPC1 0.011 0 -10000 0 -10000 0 0
KRAS 0.01 0.012 -10000 0 -0.27 1 1
DNAJA3 -0.12 0.17 0.2 2 -0.29 222 224
RIN/GTP 0.002 0.003 -10000 0 -10000 0 0
CCND1 0.024 0 -10000 0 -10000 0 0
MAGED1 0.009 0.027 -10000 0 -0.42 2 2
PTPN11 0.011 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.001 0.053 -10000 0 -0.3 15 15
SHC/GRB2/SOS1 0.022 0 -10000 0 -10000 0 0
GRB2 0.011 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.044 0.11 -10000 0 -0.24 124 124
TRKA/NEDD4-2 0.008 0.043 -10000 0 -0.23 15 15
ELMO1 0.007 0.038 -10000 0 -0.42 4 4
RhoG/GTP/ELMO1/DOCK1 0.01 0.038 -10000 0 -0.26 9 9
NGF -0.082 0.18 -10000 0 -0.42 111 111
HRAS 0.011 0 -10000 0 -10000 0 0
DOCK1 0.006 0.046 -10000 0 -0.42 6 6
GAB2 0.006 0.042 -10000 0 -0.42 5 5
RIT2 0.002 0.004 -10000 0 -10000 0 0
RIT1 0.011 0 -10000 0 -10000 0 0
FRS2 0.011 0 -10000 0 -10000 0 0
DNM1 0.008 0.033 -10000 0 -0.42 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.011 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.12 0.16 0.19 2 -0.28 224 226
mol:GDP -0.061 0.12 -10000 0 -0.26 58 58
NGF (dimer) -0.082 0.18 -10000 0 -0.42 111 111
RhoG/GDP 0.006 0.026 -10000 0 -0.29 4 4
RIT1/GDP -0.038 0.083 -10000 0 -0.18 49 49
TIAM1 -0.002 0.072 -10000 0 -0.42 15 15
PIK3R1 0.007 0.038 -10000 0 -0.42 4 4
BDNF (dimer)/TRKB -0.04 0.1 -10000 0 -0.24 79 79
KIDINS220/CRKL/C3G 0.016 0 -10000 0 -10000 0 0
SHC/RasGAP 0.013 0.03 -10000 0 -0.29 5 5
FRS2 family/SHP2 0.022 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.026 0.02 -10000 0 -0.2 4 4
RIT1/GTP 0.008 0 -10000 0 -10000 0 0
NT3 (dimer) -0.023 0.11 -10000 0 -0.41 40 40
RAP1/GDP -0.047 0.055 -10000 0 -0.16 39 39
KIDINS220/CRKL 0.011 0 -10000 0 -10000 0 0
BDNF (dimer) -0.028 0.096 -10000 0 -0.27 69 69
ubiquitin-dependent protein catabolic process -0.04 0.11 -10000 0 -0.24 118 118
Schwann cell development -0.036 0.031 -10000 0 -10000 0 0
EHD4 0.011 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.027 0 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.029 0.019 -10000 0 -10000 0 0
RAP1B 0.011 0 -10000 0 -10000 0 0
RAP1A 0.011 0 -10000 0 -10000 0 0
CDC42/GTP -0.12 0.13 -10000 0 -0.34 105 105
ABL1 0.009 0.027 -10000 0 -0.42 2 2
SH2B family/GRB2/SOS1 0.016 0 -10000 0 -10000 0 0
Rap1/GTP 0.012 0.047 -10000 0 -10000 0 0
STAT3 0.017 0 -10000 0 -10000 0 0
axon guidance -0.12 0.13 -10000 0 -0.33 105 105
MAPK3 -0.034 0.1 -10000 0 -0.21 124 124
MAPK1 -0.034 0.1 -10000 0 -0.21 124 124
CDC42/GDP -0.038 0.083 -10000 0 -0.18 52 52
NTF3 -0.023 0.11 -10000 0 -0.41 40 40
NTF4 -0.001 0.053 -10000 0 -0.3 15 15
NGF (dimer)/TRKA/FAIM -0.04 0.11 -10000 0 -0.24 119 119
PI3K 0.013 0.03 -10000 0 -0.29 5 5
FRS3 0.011 0 -10000 0 -10000 0 0
FAIM 0.01 0.019 -10000 0 -0.42 1 1
GAB1 0.007 0.038 -10000 0 -0.42 4 4
RASGRF1 -0.14 0.18 0.2 2 -0.31 244 246
SOS1 0.011 0 -10000 0 -10000 0 0
MCF2L -0.11 0.15 -10000 0 -0.26 229 229
RGS19 0.011 0 -10000 0 -10000 0 0
CDC42 0.011 0 -10000 0 -10000 0 0
RAS family/GTP -0.017 0.071 -10000 0 -10000 0 0
Rac1/GDP -0.038 0.083 -10000 0 -0.18 49 49
NGF (dimer)/TRKA/GRIT -0.046 0.11 -10000 0 -0.24 123 123
neuron projection morphogenesis -0.11 0.17 -10000 0 -0.44 65 65
NGF (dimer)/TRKA/NEDD4-2 -0.04 0.11 -10000 0 -0.24 118 118
MAP2K1 0.028 0.019 -10000 0 -0.18 4 4
NGFR -0.13 0.2 -10000 0 -0.42 168 168
NGF (dimer)/TRKA/GIPC/GAIP -0.025 0.096 -10000 0 -0.2 120 120
RAS family/GTP/PI3K 0.022 0.022 -10000 0 -0.2 5 5
FRS2 family/SHP2/GRB2/SOS1 0.032 0 -10000 0 -10000 0 0
NRAS 0.011 0 -10000 0 -10000 0 0
GRB2/SOS1 0.016 0 -10000 0 -10000 0 0
PRKCI 0.011 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.011 0 -10000 0 -10000 0 0
PRKCZ 0.009 0.023 -10000 0 -0.34 2 2
MAPKKK cascade -0.16 0.25 -10000 0 -0.6 119 119
RASA1 0.006 0.042 -10000 0 -0.42 5 5
TRKA/c-Abl 0.007 0.045 -10000 0 -0.24 16 16
SQSTM1 0.011 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.029 0.092 -10000 0 -0.21 79 79
NGF (dimer)/TRKA/p62/Atypical PKCs -0.021 0.093 -10000 0 -0.19 119 119
MATK 0.003 0.057 -10000 0 -0.4 10 10
NEDD4L 0.01 0.019 -10000 0 -0.42 1 1
RAS family/GDP -0.043 0.052 -10000 0 -0.16 27 27
NGF (dimer)/TRKA -0.13 0.17 0.21 2 -0.31 222 224
Rac1/GTP -0.11 0.12 -10000 0 -0.25 179 179
FRS2 family/SHP2/CRK family 0.032 0 -10000 0 -10000 0 0
Aurora A 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
Aurora A/GADD45A -0.011 0.033 -9999 0 -10000 0 0
BIRC5 -0.22 0.11 -9999 0 -0.27 423 423
NFKBIA -0.012 0.033 -9999 0 -10000 0 0
CPEB1 -0.19 0.21 -9999 0 -0.42 234 234
AKT1 -0.012 0.033 -9999 0 -10000 0 0
NDEL1 0.011 0 -9999 0 -10000 0 0
Aurora A/BRCA1 -0.01 0.029 -9999 0 -10000 0 0
NDEL1/TACC3 -0.029 0.07 -9999 0 -0.17 79 79
GADD45A 0.011 0 -9999 0 -10000 0 0
GSK3B 0.004 0.002 -9999 0 -10000 0 0
PAK1/Aurora A -0.011 0.033 -9999 0 -10000 0 0
MDM2 0.011 0 -9999 0 -10000 0 0
JUB 0.011 0 -9999 0 -10000 0 0
TPX2 -0.14 0.077 -9999 0 -0.18 410 410
TP53 0 0.024 -9999 0 -0.33 1 1
DLG7 -0.02 0.032 -9999 0 -10000 0 0
AURKAIP1 0.011 0 -9999 0 -10000 0 0
ARHGEF7 0.011 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.032 0.075 -9999 0 -0.18 79 79
G2/M transition of mitotic cell cycle -0.01 0.029 -9999 0 -10000 0 0
AURKA -0.025 0.04 -9999 0 -10000 0 0
AURKB 0.014 0.006 -9999 0 -10000 0 0
CDC25B -0.005 0.024 -9999 0 -10000 0 0
G2/M transition checkpoint -0.01 0.029 -9999 0 -10000 0 0
mRNA polyadenylation -0.12 0.11 -9999 0 -0.24 234 234
Aurora A/CPEB -0.12 0.12 -9999 0 -0.24 234 234
Aurora A/TACC1/TRAP/chTOG -0.039 0.093 -9999 0 -0.22 104 104
BRCA1 0.011 0 -9999 0 -10000 0 0
centrosome duplication -0.011 0.033 -9999 0 -10000 0 0
regulation of centrosome cycle -0.029 0.069 -9999 0 -0.17 79 79
spindle assembly -0.039 0.092 -9999 0 -0.22 104 104
TDRD7 0.011 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.1 0.066 -9999 0 -0.31 5 5
CENPA 0.024 0.011 -9999 0 -10000 0 0
Aurora A/PP2A -0.011 0.033 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.003 0.02 -9999 0 -10000 0 0
negative regulation of DNA binding 0 0.024 -9999 0 -0.33 1 1
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0.016 0 -9999 0 -10000 0 0
RASA1 0.006 0.042 -9999 0 -0.42 5 5
Ajuba/Aurora A -0.01 0.029 -9999 0 -10000 0 0
mitotic prometaphase -0.023 0.009 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.025 0.04 -9999 0 -10000 0 0
TACC1 -0.076 0.17 -9999 0 -0.42 104 104
TACC3 -0.048 0.12 -9999 0 -0.27 106 106
Aurora A/Antizyme1 -0.003 0.03 -9999 0 -10000 0 0
Aurora A/RasGAP -0.014 0.04 -9999 0 -0.25 5 5
OAZ1 0.011 0 -9999 0 -10000 0 0
RAN 0.011 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.004 0.002 -9999 0 -10000 0 0
GIT1 0.011 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.022 0 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.14 0.077 -9999 0 -0.18 410 410
PPP2R5D 0.011 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.12 0.073 -9999 0 -0.18 164 164
PAK1 0.011 0 -9999 0 -10000 0 0
CKAP5 0.011 0 -9999 0 -10000 0 0
Wnt signaling

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
Noncanonical Wnts/FZD -0.041 0.13 -9999 0 -0.26 113 113
FZD6 0.01 0.019 -9999 0 -0.42 1 1
WNT6 -0.027 0.11 -9999 0 -0.35 53 53
WNT4 -0.058 0.16 -9999 0 -0.42 82 82
FZD3 0.011 0 -9999 0 -10000 0 0
WNT5A -0.002 0.072 -9999 0 -0.42 15 15
WNT11 -0.024 0.1 -9999 0 -0.3 58 58
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.022 0.1 -10000 0 -0.32 50 50
NFATC2 -0.026 0.18 -10000 0 -0.51 42 42
NFATC3 -0.016 0.087 -10000 0 -0.24 53 53
CD40LG -0.16 0.34 -10000 0 -0.82 84 84
ITCH 0.027 0.031 -10000 0 -10000 0 0
CBLB 0.027 0.031 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.12 0.25 -10000 0 -0.75 44 44
JUNB 0.006 0.042 -10000 0 -0.42 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.008 0.029 -10000 0 -0.24 1 1
T cell anergy 0.015 0.052 -10000 0 -0.32 1 1
TLE4 -0.027 0.21 -10000 0 -0.59 54 54
Jun/NFAT1-c-4/p21SNFT -0.084 0.34 -10000 0 -0.77 88 88
AP-1/NFAT1-c-4 -0.16 0.39 -10000 0 -0.92 87 87
IKZF1 0.005 0.13 -10000 0 -0.41 28 28
T-helper 2 cell differentiation -0.077 0.22 -10000 0 -0.76 31 31
AP-1/NFAT1 -0.084 0.18 -10000 0 -0.38 97 97
CALM1 0.015 0.021 -10000 0 -10000 0 0
EGR2 -0.11 0.42 -10000 0 -0.91 88 88
EGR3 -0.15 0.48 -10000 0 -1.2 83 83
NFAT1/FOXP3 -0.019 0.15 -10000 0 -0.36 42 42
EGR1 -0.062 0.16 -10000 0 -0.42 86 86
JUN 0.003 0.047 -10000 0 -0.42 6 6
EGR4 0.001 0.045 -10000 0 -0.28 12 12
mol:Ca2+ 0.005 0.023 -10000 0 -0.15 1 1
GBP3 0.002 0.14 -10000 0 -0.46 28 28
FOSL1 -0.008 0.07 -10000 0 -0.27 34 34
NFAT1-c-4/MAF/IRF4 -0.12 0.36 -10000 0 -0.83 89 89
DGKA 0.006 0.12 -10000 0 -0.4 25 25
CREM 0.01 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.1 0.35 -10000 0 -0.81 88 88
CTLA4 -0.029 0.14 -10000 0 -0.37 36 36
NFAT1-c-4 (dimer)/EGR1 -0.13 0.37 -10000 0 -0.86 88 88
NFAT1-c-4 (dimer)/EGR4 -0.094 0.34 -10000 0 -0.8 88 88
FOS -0.14 0.2 -10000 0 -0.42 174 174
IFNG -0.058 0.18 -10000 0 -0.63 24 24
T cell activation -0.084 0.22 -10000 0 -0.66 41 41
MAF -0.065 0.16 -10000 0 -0.42 91 91
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.078 0.3 0.69 88 -10000 0 88
TNF -0.12 0.33 -10000 0 -0.77 90 90
FASLG -0.16 0.48 -10000 0 -1.1 87 87
TBX21 0.009 0.041 -10000 0 -0.36 6 6
BATF3 0.01 0.012 -10000 0 -0.27 1 1
PRKCQ -0.012 0.1 -10000 0 -0.41 31 31
PTPN1 0.006 0.12 -10000 0 -0.41 21 21
NFAT1-c-4/ICER1 -0.091 0.34 -10000 0 -0.79 88 88
GATA3 -0.002 0.064 -10000 0 -0.3 22 22
T-helper 1 cell differentiation -0.047 0.18 -10000 0 -0.62 24 24
IL2RA -0.12 0.24 -10000 0 -0.69 53 53
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.006 0.12 -10000 0 -0.41 21 21
E2F1 -0.044 0.12 -10000 0 -0.27 109 109
PPARG -0.014 0.099 -10000 0 -0.42 29 29
SLC3A2 0.006 0.12 -10000 0 -0.4 23 23
IRF4 -0.002 0.067 -10000 0 -0.34 18 18
PTGS2 -0.18 0.36 -10000 0 -0.85 91 91
CSF2 -0.16 0.33 -10000 0 -0.81 83 83
JunB/Fra1/NFAT1-c-4 -0.087 0.33 -10000 0 -0.76 88 88
IL4 -0.08 0.24 -10000 0 -0.82 29 29
IL5 -0.16 0.33 -10000 0 -0.82 83 83
IL2 -0.085 0.22 -10000 0 -0.67 41 41
IL3 -0.036 0.049 -10000 0 -10000 0 0
RNF128 0.016 0.064 -10000 0 -0.5 1 1
NFATC1 -0.079 0.3 -10000 0 -0.69 88 88
CDK4 0.043 0.18 0.51 36 -10000 0 36
PTPRK 0.004 0.13 -10000 0 -0.41 27 27
IL8 -0.18 0.33 -10000 0 -0.82 84 84
POU2F1 0.011 0 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.033 0.15 -10000 0 -0.41 51 51
CRKL -0.038 0.15 -10000 0 -0.44 49 49
HRAS -0.019 0.14 -10000 0 -0.38 46 46
mol:PIP3 -0.043 0.14 0.19 2 -0.34 77 79
SPRED1 0.011 0 -10000 0 -10000 0 0
SPRED2 0.01 0.019 -10000 0 -0.42 1 1
GAB1 -0.046 0.16 -10000 0 -0.38 77 77
FOXO3 -0.029 0.14 -10000 0 -0.4 48 48
AKT1 -0.037 0.15 -10000 0 -0.43 48 48
BAD -0.029 0.14 -10000 0 -0.4 48 48
megakaryocyte differentiation -0.048 0.16 -10000 0 -0.37 79 79
GSK3B -0.029 0.14 -10000 0 -0.4 48 48
RAF1 -0.008 0.12 -10000 0 -0.31 46 46
SHC1 0.011 0 -10000 0 -10000 0 0
STAT3 -0.044 0.16 -10000 0 -0.37 77 77
STAT1 -0.11 0.35 -10000 0 -0.84 80 80
HRAS/SPRED1 -0.01 0.12 -10000 0 -0.31 46 46
cell proliferation -0.045 0.16 -10000 0 -0.37 77 77
PIK3CA 0.01 0.019 -10000 0 -0.42 1 1
TEC 0.01 0.012 -10000 0 -0.27 1 1
RPS6KB1 -0.045 0.16 -10000 0 -0.36 86 86
HRAS/SPRED2 -0.01 0.12 -10000 0 -0.31 46 46
LYN/TEC/p62DOK -0.031 0.15 -10000 0 -0.43 49 49
MAPK3 0.005 0.088 -10000 0 -0.22 46 46
STAP1 -0.047 0.16 -10000 0 -0.37 77 77
GRAP2 -0.006 0.083 -10000 0 -0.42 20 20
JAK2 -0.092 0.3 -10000 0 -0.73 80 80
STAT1 (dimer) -0.1 0.34 -10000 0 -0.82 80 80
mol:Gleevec 0.001 0.006 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.033 0.15 -10000 0 -0.42 51 51
actin filament polymerization -0.043 0.16 -10000 0 -0.36 78 78
LYN 0.011 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.058 0.22 -10000 0 -0.51 80 80
PIK3R1 0.007 0.038 -10000 0 -0.42 4 4
CBL/CRKL/GRB2 -0.024 0.14 -10000 0 -0.4 48 48
PI3K -0.035 0.16 -10000 0 -0.45 49 49
PTEN 0.006 0.046 -10000 0 -0.42 6 6
SCF/KIT/EPO/EPOR -0.1 0.37 -10000 0 -1.2 45 45
MAPK8 -0.046 0.16 -10000 0 -0.38 77 77
STAT3 (dimer) -0.043 0.16 -10000 0 -0.36 77 77
positive regulation of transcription 0.007 0.075 -10000 0 -0.18 46 46
mol:GDP -0.023 0.14 -10000 0 -0.4 46 46
PIK3C2B -0.044 0.16 -10000 0 -0.37 78 78
CBL/CRKL -0.03 0.15 -10000 0 -0.41 48 48
FER -0.044 0.16 -10000 0 -0.37 78 78
SH2B3 -0.045 0.16 -10000 0 -0.38 77 77
PDPK1 -0.034 0.13 -10000 0 -0.38 49 49
SNAI2 -0.07 0.19 -10000 0 -0.42 86 86
positive regulation of cell proliferation -0.075 0.26 -10000 0 -0.63 80 80
KITLG -0.035 0.14 -10000 0 -0.43 54 54
cell motility -0.075 0.26 -10000 0 -0.63 80 80
PTPN6 0.011 0.015 -10000 0 -0.28 1 1
EPOR -0.012 0.12 -10000 0 -0.45 11 11
STAT5A (dimer) -0.061 0.22 -10000 0 -0.52 80 80
SOCS1 0.009 0.023 -10000 0 -0.34 2 2
cell migration 0.047 0.16 0.37 79 -10000 0 79
SOS1 0.011 0 -10000 0 -10000 0 0
EPO 0.005 0.036 -10000 0 -0.38 4 4
VAV1 0.007 0.034 -10000 0 -0.3 6 6
GRB10 -0.045 0.16 -10000 0 -0.37 78 78
PTPN11 0.011 0.006 -10000 0 -10000 0 0
SCF/KIT -0.052 0.17 -10000 0 -0.39 81 81
GO:0007205 0.001 0.008 -10000 0 -10000 0 0
MAP2K1 0.001 0.096 -10000 0 -0.24 46 46
CBL 0.011 0 -10000 0 -10000 0 0
KIT -0.084 0.35 -10000 0 -1.3 39 39
MAP2K2 0.001 0.096 -10000 0 -0.24 46 46
SHC/Grb2/SOS1 -0.031 0.15 -10000 0 -0.43 48 48
STAT5A -0.063 0.23 -10000 0 -0.54 80 80
GRB2 0.011 0 -10000 0 -10000 0 0
response to radiation -0.068 0.18 -10000 0 -0.41 86 86
SHC/GRAP2 0.004 0.058 -10000 0 -0.29 20 20
PTPRO -0.05 0.16 -10000 0 -0.38 79 79
SH2B2 -0.044 0.16 -10000 0 -0.37 78 78
DOK1 0.011 0 -10000 0 -10000 0 0
MATK -0.048 0.16 -10000 0 -0.38 79 79
CREBBP 0.016 0.041 -10000 0 -0.45 1 1
BCL2 -0.1 0.38 -10000 0 -1.3 48 48
PLK1 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
regulation of centriole-centriole cohesion 0.025 0.018 -9999 0 -10000 0 0
BUB1B -0.036 0.034 -9999 0 -10000 0 0
PLK1 -0.004 0.016 -9999 0 -10000 0 0
PLK1S1 0.001 0.015 -9999 0 -0.25 1 1
KIF2A 0.003 0.014 -9999 0 -10000 0 0
regulation of mitotic centrosome separation -0.004 0.016 -9999 0 -10000 0 0
GOLGA2 0.011 0 -9999 0 -10000 0 0
Hec1/SPC24 -0.072 0.079 -9999 0 -0.15 152 152
WEE1 0 0.016 -9999 0 -10000 0 0
cytokinesis -0.044 0.033 -9999 0 -0.19 13 13
PP2A-alpha B56 0.055 0.015 -9999 0 -10000 0 0
AURKA 0.005 0.006 -9999 0 -10000 0 0
PICH/PLK1 -0.064 0.088 -9999 0 -0.22 76 76
CENPE -0.033 0.068 -9999 0 -0.14 137 137
RhoA/GTP 0.008 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.003 0.014 -9999 0 -10000 0 0
PPP2CA 0.011 0 -9999 0 -10000 0 0
FZR1 0.011 0 -9999 0 -10000 0 0
TPX2 0.004 0.007 -9999 0 -10000 0 0
PAK1 0.01 0.001 -9999 0 -10000 0 0
SPC24 -0.15 0.14 -9999 0 -0.27 298 298
FBXW11 0.011 0 -9999 0 -10000 0 0
CLSPN 0.004 0.008 -9999 0 -10000 0 0
GORASP1 0.011 0 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NLP -0.003 0.01 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle -0.001 0.001 -9999 0 -10000 0 0
STAG2 0.011 0 -9999 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.012 0.006 -9999 0 -10000 0 0
spindle elongation -0.004 0.016 -9999 0 -10000 0 0
ODF2 0.01 0.001 -9999 0 -10000 0 0
BUB1 0.045 0.025 -9999 0 -10000 0 0
TPT1 0.002 0.01 -9999 0 -10000 0 0
CDC25C 0.009 0.008 -9999 0 -10000 0 0
CDC25B 0.011 0 -9999 0 -10000 0 0
SGOL1 -0.025 0.018 -9999 0 -10000 0 0
RHOA 0.011 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.011 0.035 -9999 0 -10000 0 0
CDC14B 0.008 0.014 -9999 0 -0.3 1 1
CDC20 -0.25 0.082 -9999 0 -0.27 465 465
PLK1/PBIP1 -0.016 0.044 -9999 0 -0.13 60 60
mitosis -0.005 0.007 -9999 0 -0.015 164 164
FBXO5 0.001 0.015 -9999 0 -10000 0 0
CDC2 -0.001 0.002 -9999 0 -10000 0 0
NDC80 -0.004 0.062 -9999 0 -0.27 26 26
metaphase plate congression 0 0.011 -9999 0 -10000 0 0
ERCC6L -0.056 0.081 -9999 0 -0.19 76 76
NLP/gamma Tubulin 0 0.009 -9999 0 -10000 0 0
microtubule cytoskeleton organization 0.002 0.01 -9999 0 -10000 0 0
G2/M transition DNA damage checkpoint -0.001 0.001 -9999 0 -10000 0 0
PPP1R12A 0.009 0.027 -9999 0 -0.42 2 2
interphase -0.001 0.001 -9999 0 -10000 0 0
PLK1/PRC1-2 -0.11 0.052 -9999 0 -0.15 163 163
GRASP65/GM130/RAB1/GTP/PLK1 0.015 0.012 -9999 0 -10000 0 0
RAB1A 0.011 0 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
Aurora A/BORA 0.001 0.016 -9999 0 -10000 0 0
mitotic prometaphase -0.002 0.001 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.004 0.013 -9999 0 -10000 0 0
microtubule-based process -0.12 0.044 -9999 0 -0.13 469 469
Golgi organization -0.004 0.016 -9999 0 -10000 0 0
Cohesin/SA2 -0.005 0.008 -9999 0 -10000 0 0
PPP1CB/MYPT1 0.014 0.019 -9999 0 -0.29 2 2
KIF20A -0.25 0.079 -9999 0 -0.27 469 469
APC/C/CDC20 -0.12 0.047 -9999 0 -0.14 465 465
PPP2R1A 0.011 0 -9999 0 -10000 0 0
chromosome segregation -0.019 0.042 -9999 0 -0.13 60 60
PRC1 -0.001 0.056 -9999 0 -0.27 21 21
ECT2 -0.005 0.037 -9999 0 -0.14 28 28
C13orf34 0.002 0.014 -9999 0 -10000 0 0
NUDC 0 0.011 -9999 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.035 0.034 -9999 0 -10000 0 0
spindle assembly -0.001 0.014 -9999 0 -10000 0 0
spindle stabilization 0.001 0.015 -9999 0 -0.25 1 1
APC/C/HCDH1 0.014 0.011 -9999 0 -0.24 1 1
MKLP2/PLK1 -0.12 0.044 -9999 0 -0.14 469 469
CCNB1 -0.042 0.11 -9999 0 -0.27 96 96
PPP1CB 0.01 0.001 -9999 0 -10000 0 0
BTRC 0.011 0 -9999 0 -10000 0 0
ROCK2 -0.003 0.064 -9999 0 -0.4 13 13
TUBG1 0.002 0.01 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.017 0.031 -9999 0 -10000 0 0
MLF1IP -0.019 0.061 -9999 0 -0.19 60 60
INCENP 0.01 0.001 -9999 0 -10000 0 0
Ephrin A reverse signaling

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
MAPKKK cascade -0.018 0.08 -9999 0 -0.24 58 58
EFNA5 -0.002 0.072 -9999 0 -0.4 16 16
FYN -0.01 0.072 -9999 0 -0.21 57 57
neuron projection morphogenesis -0.018 0.08 -9999 0 -0.24 58 58
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.018 0.08 -9999 0 -0.24 58 58
EPHA5 -0.031 0.12 -9999 0 -0.42 43 43
Nephrin/Neph1 signaling in the kidney podocyte

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
positive regulation of NF-kappaB transcription factor activity 0.03 0.1 0.28 75 -10000 0 75
KIRREL -0.044 0.14 -10000 0 -0.42 65 65
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.03 0.1 -10000 0 -0.28 75 75
PLCG1 0.011 0 -10000 0 -10000 0 0
ARRB2 0.011 0 -10000 0 -10000 0 0
WASL 0.011 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.009 0.077 -10000 0 -0.21 65 65
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.006 0.079 -10000 0 -0.21 65 65
FYN -0.014 0.073 -10000 0 -0.2 65 65
mol:Ca2+ -0.015 0.075 -10000 0 -0.2 65 65
mol:DAG -0.01 0.076 -10000 0 -0.2 65 65
NPHS2 -0.002 0.015 -10000 0 -10000 0 0
mol:IP3 -0.01 0.076 -10000 0 -0.2 65 65
regulation of endocytosis -0.003 0.07 -10000 0 -0.18 65 65
Nephrin/NEPH1/podocin/Cholesterol -0.018 0.076 -10000 0 -0.21 65 65
establishment of cell polarity -0.03 0.1 -10000 0 -0.28 75 75
Nephrin/NEPH1/podocin/NCK1-2 0 0.073 -10000 0 -0.36 3 3
Nephrin/NEPH1/beta Arrestin2 -0.002 0.07 -10000 0 -0.18 65 65
NPHS1 -0.003 0.042 -10000 0 -0.27 11 11
Nephrin/NEPH1/podocin -0.01 0.074 -10000 0 -0.2 65 65
TJP1 0.01 0.019 -10000 0 -0.42 1 1
NCK1 0.009 0.027 -10000 0 -0.42 2 2
NCK2 0.011 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.009 0.077 -10000 0 -0.21 65 65
CD2AP 0.011 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.009 0.077 -10000 0 -0.21 65 65
GRB2 0.011 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.027 0.097 -10000 0 -0.22 92 92
cytoskeleton organization -0.003 0.083 -10000 0 -0.22 65 65
Nephrin/NEPH1 -0.018 0.072 -10000 0 -0.2 65 65
Nephrin/NEPH1/ZO-1 -0.015 0.084 -10000 0 -0.23 65 65
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.035 0.094 -9999 0 -0.28 14 14
NF kappa B1 p50/RelA/I kappa B alpha -0.01 0.087 -9999 0 -0.25 11 11
alphaV/beta3 Integrin/Osteopontin/Src -0.027 0.082 -9999 0 -0.16 134 134
AP1 -0.085 0.15 -9999 0 -0.38 68 68
ILK -0.045 0.1 -9999 0 -0.29 16 16
bone resorption -0.026 0.099 -9999 0 -0.3 26 26
PTK2B 0.011 0 -9999 0 -10000 0 0
PYK2/p130Cas 0.011 0.1 -9999 0 -0.28 13 13
ITGAV 0.014 0.001 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.002 0.064 -9999 0 -0.29 24 24
alphaV/beta3 Integrin/Osteopontin -0.059 0.11 -9999 0 -0.23 106 106
MAP3K1 -0.046 0.1 -9999 0 -0.2 106 106
JUN 0.006 0.046 -9999 0 -0.42 6 6
MAPK3 -0.032 0.095 -9999 0 -0.29 12 12
MAPK1 -0.032 0.095 -9999 0 -0.29 12 12
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
NFKB1 0.01 0.019 -9999 0 -0.42 1 1
MAPK8 -0.038 0.099 -9999 0 -0.29 20 20
ITGB3 -0.074 0.17 -9999 0 -0.41 107 107
NFKBIA -0.022 0.093 -9999 0 -0.28 11 11
FOS -0.13 0.2 -9999 0 -0.42 174 174
CD44 0.001 0.062 -9999 0 -0.42 11 11
CHUK 0.011 0 -9999 0 -10000 0 0
PLAU -0.019 0.09 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.041 0.056 -9999 0 -0.25 3 3
BCAR1 0.011 0 -9999 0 -10000 0 0
RELA 0.011 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.04 0.12 -9999 0 -0.28 106 106
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.047 0.1 -9999 0 -0.2 106 106
VAV3 -0.07 0.11 -9999 0 -0.26 70 70
MAP3K14 -0.044 0.1 -9999 0 -0.2 106 106
ROCK2 0 0.067 -9999 0 -0.42 13 13
SPP1 -0.059 0.12 -9999 0 -0.27 134 134
RAC1 0.011 0 -9999 0 -10000 0 0
Rac1/GTP -0.059 0.099 -9999 0 -0.23 69 69
MMP2 -0.077 0.15 -9999 0 -0.37 72 72
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.005 0.067 -10000 0 -0.25 29 29
alphaM/beta2 Integrin/GPIbA 0.016 0.038 -10000 0 -0.25 7 7
alphaM/beta2 Integrin/proMMP-9 -0.051 0.084 -10000 0 -0.18 47 47
PLAUR 0.008 0.025 -10000 0 -0.27 4 4
HMGB1 0.01 0.01 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.018 0.03 -10000 0 -0.22 5 5
AGER 0.009 0.021 -10000 0 -0.41 1 1
RAP1A 0.011 0 -10000 0 -10000 0 0
SELPLG 0.011 0 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.02 0.054 -10000 0 -0.21 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.11 0.14 -10000 0 -0.27 222 222
CYR61 -0.033 0.13 -10000 0 -0.42 52 52
TLN1 0.011 0 -10000 0 -10000 0 0
Rap1/GTP -0.027 0.063 -10000 0 -0.26 13 13
RHOA 0.011 0 -10000 0 -10000 0 0
P-selectin oligomer -0.17 0.21 -10000 0 -0.42 222 222
MYH2 -0.027 0.11 -10000 0 -0.27 45 45
MST1R -0.03 0.1 -10000 0 -0.27 73 73
leukocyte activation during inflammatory response -0.008 0.036 -10000 0 -0.22 7 7
APOB 0.005 0.022 -10000 0 -0.27 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 -0.011 0.094 -10000 0 -0.42 26 26
JAM3 -0.1 0.19 -10000 0 -0.42 134 134
GP1BA 0.007 0.029 -10000 0 -0.37 3 3
alphaM/beta2 Integrin/CTGF 0.009 0.055 -10000 0 -0.23 23 23
alphaM/beta2 Integrin -0.02 0.085 -10000 0 -0.21 49 49
JAM3 homodimer -0.1 0.19 -10000 0 -0.42 134 134
ICAM2 0.011 0 -10000 0 -10000 0 0
ICAM1 0.009 0.022 -10000 0 -0.27 3 3
phagocytosis triggered by activation of immune response cell surface activating receptor -0.02 0.085 -10000 0 -0.21 49 49
cell adhesion 0.014 0.038 -10000 0 -0.25 7 7
NFKB1 0.021 0.083 -10000 0 -0.3 21 21
THY1 0.011 0 -10000 0 -10000 0 0
RhoA/GDP 0.008 0 -10000 0 -10000 0 0
Lipoprotein(a) 0.002 0.034 -10000 0 -0.15 23 23
alphaM/beta2 Integrin/LRP/tPA -0.002 0.081 -10000 0 -0.22 58 58
IL6 0.011 0.14 -10000 0 -0.63 20 20
ITGB2 0.007 0.027 -10000 0 -0.27 4 4
elevation of cytosolic calcium ion concentration 0.021 0.031 -10000 0 -0.21 4 4
alphaM/beta2 Integrin/JAM2/JAM3 -0.11 0.17 -10000 0 -0.29 228 228
JAM2 -0.14 0.2 -10000 0 -0.42 176 176
alphaM/beta2 Integrin/ICAM1 0.006 0.059 -10000 0 -0.24 8 8
alphaM/beta2 Integrin/uPA/Plg -0.011 0.086 -10000 0 -0.21 74 74
RhoA/GTP -0.03 0.11 -10000 0 -0.25 74 74
positive regulation of phagocytosis -0.017 0.052 -10000 0 -0.21 17 17
Ron/MSP -0.015 0.072 -10000 0 -0.18 82 82
alphaM/beta2 Integrin/uPAR/uPA 0.022 0.032 -10000 0 -0.21 4 4
alphaM/beta2 Integrin/uPAR 0.016 0.033 -10000 0 -0.21 6 6
PLAU 0.01 0.018 -10000 0 -0.27 2 2
PLAT -0.035 0.13 -10000 0 -0.42 55 55
actin filament polymerization -0.026 0.1 -10000 0 -0.26 45 45
MST1 0.005 0.039 -10000 0 -0.27 10 10
alphaM/beta2 Integrin/lipoprotein(a) 0.012 0.042 -10000 0 -0.22 7 7
TNF 0.018 0.096 -10000 0 -0.73 2 2
RAP1B 0.011 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.017 0.032 -10000 0 -0.21 6 6
fibrinolysis -0.012 0.086 -10000 0 -0.21 74 74
HCK 0.01 0.012 -10000 0 -0.27 1 1
dendritic cell antigen processing and presentation -0.02 0.085 -10000 0 -0.21 49 49
VTN -0.053 0.15 -10000 0 -0.41 76 76
alphaM/beta2 Integrin/CYR61 -0.008 0.084 -10000 0 -0.24 55 55
LPA -0.004 0.056 -10000 0 -0.27 21 21
LRP1 0.009 0.027 -10000 0 -0.42 2 2
cell migration -0.05 0.088 -10000 0 -0.24 37 37
FN1 0.006 0.042 -10000 0 -0.42 5 5
alphaM/beta2 Integrin/Thy1 0.018 0.03 -10000 0 -0.22 5 5
MPO 0.006 0.033 -10000 0 -0.27 7 7
KNG1 -0.008 0.06 -10000 0 -0.27 25 25
RAP1/GDP 0.014 0 -10000 0 -10000 0 0
ROCK1 -0.023 0.11 -10000 0 -0.26 51 51
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.053 0.15 -10000 0 -0.41 76 76
CTGF -0.004 0.079 -10000 0 -0.42 18 18
alphaM/beta2 Integrin/Hck 0.017 0.033 -10000 0 -0.25 5 5
ITGAM 0.006 0.038 -10000 0 -0.35 5 5
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.076 0.12 -10000 0 -0.21 224 224
HP -0.087 0.15 -10000 0 -0.31 155 155
leukocyte adhesion -0.11 0.13 0.16 1 -0.33 106 107
SELP -0.17 0.21 -10000 0 -0.42 222 222
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.072 0.24 -10000 0 -0.63 38 38
PCK1 -0.1 0.33 -10000 0 -1.2 36 36
HNF4A -0.12 0.32 -10000 0 -0.79 70 70
KCNJ11 -0.06 0.25 -10000 0 -0.68 27 27
AKT1 -0.033 0.14 -10000 0 -0.34 20 20
response to starvation -0.009 0.032 -10000 0 -0.15 1 1
DLK1 -0.12 0.33 -10000 0 -0.77 75 75
NKX2-1 -0.018 0.14 -10000 0 -0.43 2 2
ACADM -0.076 0.25 -10000 0 -0.64 43 43
TAT -0.086 0.19 -10000 0 -0.59 25 25
CEBPB 0.012 0.002 -10000 0 -10000 0 0
CEBPA 0.01 0.035 -10000 0 -0.38 4 4
TTR -0.004 0.12 -10000 0 -0.64 3 3
PKLR -0.078 0.24 -10000 0 -0.63 39 39
APOA1 -0.17 0.44 -10000 0 -1.1 71 71
CPT1C -0.077 0.26 -10000 0 -0.68 40 40
ALAS1 -0.029 0.16 -10000 0 -10000 0 0
TFRC -0.029 0.18 -10000 0 -0.54 5 5
FOXF1 0.006 0.047 -10000 0 -0.41 6 6
NF1 0.014 0.033 -10000 0 -0.41 3 3
HNF1A (dimer) -0.005 0.068 -10000 0 -0.28 29 29
CPT1A -0.072 0.24 -10000 0 -0.62 40 40
HMGCS1 -0.072 0.24 -10000 0 -0.62 41 41
NR3C1 -0.084 0.17 -10000 0 -0.39 114 114
CPT1B -0.074 0.24 -10000 0 -0.62 41 41
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.009 0.01 -10000 0 -10000 0 0
GCK -0.13 0.33 -10000 0 -0.76 86 86
CREB1 0.003 0.045 -10000 0 -0.19 12 12
IGFBP1 -0.22 0.45 -10000 0 -1.1 88 88
PDX1 -0.03 0.14 -10000 0 -10000 0 0
UCP2 -0.073 0.24 -10000 0 -0.62 41 41
ALDOB -0.061 0.25 -10000 0 -0.66 29 29
AFP -0.028 0.046 -10000 0 -0.33 2 2
BDH1 -0.072 0.24 -10000 0 -0.62 40 40
HADH -0.06 0.25 -10000 0 -0.65 31 31
F2 -0.11 0.3 -10000 0 -0.78 46 46
HNF1A -0.005 0.068 -10000 0 -0.28 29 29
G6PC 0.012 0.062 -10000 0 -10000 0 0
SLC2A2 -0.036 0.17 -10000 0 -10000 0 0
INS 0.016 0.06 0.18 41 -10000 0 41
FOXA1 -0.16 0.14 -10000 0 -0.26 328 328
FOXA3 -0.042 0.13 -10000 0 -0.27 112 112
FOXA2 -0.074 0.29 -10000 0 -0.69 44 44
ABCC8 -0.14 0.37 -10000 0 -0.81 96 96
ALB -0.027 0.064 -10000 0 -1.1 1 1
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.037 0.11 -9999 0 -0.22 112 112
SMAD6-7/SMURF1 0.021 0.016 -9999 0 -0.23 2 2
NOG -0.021 0.089 -9999 0 -0.27 57 57
SMAD9 -0.056 0.17 -9999 0 -0.51 54 54
SMAD4 0.01 0.019 -9999 0 -0.42 1 1
SMAD5 -0.016 0.091 -9999 0 -0.3 24 24
BMP7/USAG1 -0.048 0.11 -9999 0 -0.22 138 138
SMAD5/SKI -0.01 0.087 -9999 0 -0.29 23 23
SMAD1 0.032 0.015 -9999 0 -10000 0 0
BMP2 -0.022 0.11 -9999 0 -0.42 39 39
SMAD1/SMAD1/SMAD4 -0.001 0.011 -9999 0 -10000 0 0
BMPR1A 0.011 0 -9999 0 -10000 0 0
BMPR1B -0.014 0.099 -9999 0 -0.41 30 30
BMPR1A-1B/BAMBI -0.003 0.079 -9999 0 -0.26 41 41
AHSG 0.003 0.033 -9999 0 -0.27 7 7
CER1 0.004 0.005 -9999 0 -10000 0 0
BMP2-4/CER1 -0.015 0.087 -9999 0 -0.25 56 56
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.033 0.12 -9999 0 -0.34 32 32
BMP2-4 (homodimer) -0.022 0.1 -9999 0 -0.28 65 65
RGMB 0.01 0.019 -9999 0 -0.42 1 1
BMP6/BMPR2/BMPR1A-1B 0.007 0.066 -9999 0 -0.21 43 43
RGMA -0.078 0.17 -9999 0 -0.42 106 106
SMURF1 0.011 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.037 0.11 -9999 0 -0.29 47 47
BMP2-4/USAG1 -0.035 0.11 -9999 0 -0.27 71 71
SMAD6/SMURF1/SMAD5 -0.01 0.087 -9999 0 -0.29 23 23
SOSTDC1 -0.032 0.11 -9999 0 -0.32 66 66
BMP7/BMPR2/BMPR1A-1B -0.013 0.085 -9999 0 -0.24 46 46
SKI 0.011 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.002 0.072 -9999 0 -0.42 15 15
HFE2 0.004 0.013 -9999 0 -0.27 1 1
ZFYVE16 0.011 0 -9999 0 -10000 0 0
MAP3K7 0.011 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.053 0.14 -9999 0 -0.27 126 126
SMAD5/SMAD5/SMAD4 -0.01 0.089 -9999 0 -0.3 23 23
MAPK1 0.011 0 -9999 0 -10000 0 0
TAK1/TAB family -0.047 0.082 -9999 0 -0.3 30 30
BMP7 (homodimer) -0.042 0.12 -9999 0 -0.3 85 85
NUP214 0.011 0 -9999 0 -10000 0 0
BMP6/FETUA 0.002 0.055 -9999 0 -0.25 22 22
SMAD1/SKI 0.036 0.014 -9999 0 -10000 0 0
SMAD6 0.01 0.019 -9999 0 -0.42 1 1
CTDSP2 0.011 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.015 0.088 -9999 0 -0.25 56 56
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.1 0.19 -9999 0 -0.42 133 133
BMPR2 (homodimer) 0.011 0 -9999 0 -10000 0 0
GADD34/PP1CA 0.022 0 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.002 0.07 -9999 0 -0.28 30 30
CHRDL1 -0.29 0.19 -9999 0 -0.42 360 360
ENDOFIN/SMAD1 0.036 0.014 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 0 0.011 -9999 0 -10000 0 0
SMAD6/SMURF1 0.011 0 -9999 0 -10000 0 0
BAMBI -0.007 0.081 -9999 0 -0.37 24 24
SMURF2 0.011 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.19 0.14 -9999 0 -0.26 373 373
BMP2-4/GREM1 -0.075 0.14 -9999 0 -0.27 168 168
SMAD7 0.01 0.019 -9999 0 -0.42 1 1
SMAD8A/SMAD8A/SMAD4 -0.047 0.16 -9999 0 -0.47 55 55
SMAD1/SMAD6 0.036 0.014 -9999 0 -10000 0 0
TAK1/SMAD6 0.016 0 -9999 0 -10000 0 0
BMP7 -0.042 0.12 -9999 0 -0.3 85 85
BMP6 -0.002 0.072 -9999 0 -0.42 15 15
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.033 0.11 -9999 0 -0.31 35 35
PPM1A 0.011 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.036 0.014 -9999 0 -10000 0 0
SMAD7/SMURF1 0.015 0.013 -9999 0 -0.29 1 1
CTDSPL 0.011 0 -9999 0 -10000 0 0
PPP1CA 0.011 0 -9999 0 -10000 0 0
XIAP 0.011 0 -9999 0 -10000 0 0
CTDSP1 0.011 0 -9999 0 -10000 0 0
PPP1R15A 0.011 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.074 0.16 -9999 0 -0.39 65 65
CHRD -0.064 0.16 -9999 0 -0.42 89 89
BMPR2 0.011 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.045 0.12 -9999 0 -0.23 114 114
BMP4 -0.012 0.09 -9999 0 -0.37 30 30
FST -0.051 0.15 -9999 0 -0.41 74 74
BMP2-4/NOG -0.028 0.099 -9999 0 -0.26 59 59
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.006 0.08 -9999 0 -0.22 46 46
TCGA08_retinoblastoma

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
CDKN2B 0.006 0.024 -10000 0 -0.28 2 2
CDKN2C 0.02 0.054 -10000 0 -0.38 8 8
CDKN2A -0.12 0.15 -10000 0 -0.28 224 224
CCND2 -0.003 0.045 0.17 4 -0.11 40 44
RB1 0.002 0.04 0.13 2 -0.18 6 8
CDK4 0.015 0.029 0.19 6 -10000 0 6
CDK6 0.008 0.036 0.17 6 -0.18 8 14
G1/S progression -0.001 0.04 0.18 6 -0.13 2 8
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.004 0.076 -10000 0 -0.2 69 69
ER alpha/Gai/GDP/Gbeta gamma -0.092 0.2 -10000 0 -0.45 74 74
AKT1 -0.069 0.24 -10000 0 -0.75 57 57
PIK3CA 0.01 0.019 -10000 0 -0.42 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.073 0.25 -10000 0 -0.77 57 57
mol:Ca2+ -0.017 0.12 -10000 0 -0.34 56 56
IGF1R -0.006 0.083 -10000 0 -0.42 20 20
E2/ER alpha (dimer)/Striatin -0.014 0.08 -10000 0 -0.24 58 58
SHC1 0.011 0 -10000 0 -10000 0 0
apoptosis 0.065 0.23 0.71 57 -10000 0 57
RhoA/GTP -0.018 0.051 -10000 0 -0.27 1 1
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.091 0.15 -10000 0 -0.4 74 74
regulation of stress fiber formation -0.016 0.059 0.26 3 -10000 0 3
E2/ERA-ERB (dimer) -0.013 0.079 -10000 0 -0.24 56 56
KRAS 0.01 0.012 -10000 0 -0.27 1 1
G13/GTP -0.011 0.071 -10000 0 -0.22 56 56
pseudopodium formation 0.016 0.059 -10000 0 -0.26 3 3
E2/ER alpha (dimer)/PELP1 -0.013 0.079 -10000 0 -0.24 56 56
GRB2 0.011 0 -10000 0 -10000 0 0
GNG2 -0.002 0.071 -10000 0 -0.41 15 15
GNAO1 -0.098 0.19 -10000 0 -0.42 131 131
HRAS 0.011 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.059 0.18 -10000 0 -0.5 58 58
E2/ER beta (dimer) 0.008 0 -10000 0 -10000 0 0
mol:GDP -0.034 0.097 -10000 0 -0.31 56 56
mol:NADP -0.059 0.18 -10000 0 -0.5 58 58
PIK3R1 0.007 0.038 -10000 0 -0.42 4 4
mol:IP3 -0.019 0.13 -10000 0 -0.36 56 56
IGF-1R heterotetramer -0.006 0.083 -10000 0 -0.42 20 20
PLCB1 -0.025 0.13 -10000 0 -0.37 57 57
PLCB2 -0.023 0.13 -10000 0 -0.37 56 56
IGF1 -0.074 0.17 -10000 0 -0.42 102 102
mol:L-citrulline -0.059 0.18 -10000 0 -0.5 58 58
RHOA 0.011 0 -10000 0 -10000 0 0
Gai/GDP -0.15 0.3 -10000 0 -0.64 132 132
JNK cascade 0.008 0 -10000 0 -10000 0 0
BCAR1 0.011 0 -10000 0 -10000 0 0
ESR2 0.011 0.001 -10000 0 -10000 0 0
GNAQ 0.009 0.027 -10000 0 -0.42 2 2
ESR1 -0.036 0.13 -10000 0 -0.42 56 56
Gq family/GDP/Gbeta gamma -0.006 0.098 -10000 0 -0.4 16 16
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.01 0.081 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.091 0.15 -10000 0 -0.4 74 74
GNAZ -0.011 0.094 -10000 0 -0.42 26 26
E2/ER alpha (dimer) -0.025 0.094 -10000 0 -0.29 56 56
STRN 0.009 0.027 -10000 0 -0.42 2 2
GNAL -0.063 0.16 -10000 0 -0.42 88 88
PELP1 0.011 0 -10000 0 -10000 0 0
MAPK11 0.013 0.016 -10000 0 -0.24 2 2
GNAI2 0.011 0 -10000 0 -10000 0 0
GNAI3 0.011 0 -10000 0 -10000 0 0
GNAI1 0.002 0.059 -10000 0 -0.42 10 10
HBEGF -0.1 0.18 -10000 0 -0.37 114 114
cAMP biosynthetic process -0.052 0.094 -10000 0 -0.2 131 131
SRC -0.082 0.19 -10000 0 -0.43 74 74
PI3K 0.013 0.03 -10000 0 -0.29 5 5
GNB1 0.011 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.033 0.087 -10000 0 -0.27 56 56
SOS1 0.011 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.1 0.16 -10000 0 -0.37 108 108
Gs family/GTP -0.053 0.095 -10000 0 -0.21 131 131
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.02 0.006 -10000 0 -10000 0 0
vasodilation -0.055 0.17 -10000 0 -0.48 58 58
mol:DAG -0.019 0.13 -10000 0 -0.36 56 56
Gs family/GDP/Gbeta gamma -0.056 0.1 -10000 0 -0.3 61 61
MSN 0.016 0.062 -10000 0 -0.28 3 3
Gq family/GTP -0.031 0.13 -10000 0 -0.39 56 56
mol:PI-3-4-5-P3 -0.07 0.24 -10000 0 -0.74 57 57
NRAS 0.011 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.055 0.17 0.48 58 -10000 0 58
GRB2/SOS1 0.016 0 -10000 0 -10000 0 0
RhoA/GDP -0.032 0.091 -10000 0 -0.29 56 56
NOS3 -0.062 0.19 -10000 0 -0.53 58 58
GNA11 0.001 0.062 -10000 0 -0.42 11 11
MAPKKK cascade -0.053 0.19 -10000 0 -0.55 58 58
E2/ER alpha (dimer)/PELP1/Src -0.096 0.16 -10000 0 -0.42 74 74
ruffle organization 0.016 0.059 -10000 0 -0.26 3 3
ROCK2 0.011 0.065 -10000 0 -0.3 3 3
GNA14 -0.034 0.13 -10000 0 -0.42 53 53
GNA15 0.007 0.033 -10000 0 -0.27 7 7
GNA13 0.011 0 -10000 0 -10000 0 0
MMP9 -0.12 0.18 -10000 0 -0.4 109 109
MMP2 -0.081 0.19 -10000 0 -0.42 81 81
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.09 0.18 -9999 0 -0.32 176 176
MAP3K8 0.003 0.042 -9999 0 -0.42 5 5
FOS -0.053 0.12 -9999 0 -0.38 28 28
PRKCA -0.02 0.1 -9999 0 -0.42 33 33
PTPN7 0.005 0.032 -9999 0 -0.29 6 6
HRAS 0.01 0.001 -9999 0 -10000 0 0
PRKCB -0.018 0.1 -9999 0 -0.42 31 31
NRAS 0.01 0.001 -9999 0 -10000 0 0
RAS family/GTP 0.014 0.012 -9999 0 -10000 0 0
MAPK3 -0.021 0.07 -9999 0 -0.28 4 4
MAP2K1 -0.044 0.15 -9999 0 -0.41 62 62
ELK1 0.004 0.011 -9999 0 -10000 0 0
BRAF -0.037 0.14 -9999 0 -0.4 59 59
mol:GTP -0.002 0.003 -9999 0 -0.005 174 174
MAPK1 -0.021 0.07 -9999 0 -0.28 4 4
RAF1 -0.037 0.14 -9999 0 -0.4 59 59
KRAS 0.009 0.013 -9999 0 -0.27 1 1
Syndecan-1-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
TGFB1 0.01 0.019 -9999 0 -0.42 1 1
CCL5 0.006 0.038 -9999 0 -0.31 7 7
SDCBP 0.011 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.043 0.062 -9999 0 -0.24 27 27
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 -0.035 0.059 -9999 0 -0.22 27 27
Syndecan-1/Syntenin -0.035 0.059 -9999 0 -0.22 27 27
MAPK3 -0.021 0.055 -9999 0 -0.3 3 3
HGF/MET -0.044 0.12 -9999 0 -0.29 101 101
TGFB1/TGF beta receptor Type II 0.01 0.019 -9999 0 -0.42 1 1
BSG 0.011 0 -9999 0 -10000 0 0
keratinocyte migration -0.035 0.058 -9999 0 -0.22 27 27
Syndecan-1/RANTES -0.037 0.064 -9999 0 -0.23 28 28
Syndecan-1/CD147 -0.028 0.058 -9999 0 -0.24 12 12
Syndecan-1/Syntenin/PIP2 -0.033 0.056 -9999 0 -0.21 27 27
LAMA5 0.01 0.012 -9999 0 -0.27 1 1
positive regulation of cell-cell adhesion -0.033 0.056 -9999 0 -0.21 27 27
MMP7 -0.048 0.13 -9999 0 -0.33 88 88
HGF -0.069 0.17 -9999 0 -0.42 96 96
Syndecan-1/CASK -0.041 0.058 -9999 0 -0.22 27 27
Syndecan-1/HGF/MET -0.067 0.11 -9999 0 -0.26 91 91
regulation of cell adhesion -0.015 0.054 -9999 0 -0.28 3 3
HPSE 0.002 0.057 -9999 0 -0.4 10 10
positive regulation of cell migration -0.043 0.062 -9999 0 -0.24 27 27
SDC1 -0.043 0.062 -9999 0 -0.24 27 27
Syndecan-1/Collagen -0.043 0.062 -9999 0 -0.24 27 27
PPIB 0.01 0.012 -9999 0 -0.27 1 1
MET 0.005 0.045 -9999 0 -0.34 8 8
PRKACA 0.011 0 -9999 0 -10000 0 0
MMP9 -0.11 0.14 -9999 0 -0.27 222 222
MAPK1 -0.021 0.055 -9999 0 -0.3 3 3
homophilic cell adhesion -0.042 0.062 -9999 0 -0.23 27 27
MMP1 -0.11 0.14 -9999 0 -0.27 212 212
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.031 0.13 -9999 0 -0.42 50 50
GNB1/GNG2 -0.029 0.13 -9999 0 -0.39 33 33
mol:DAG -0.024 0.12 -9999 0 -0.4 26 26
PLCG1 -0.025 0.12 -9999 0 -0.41 26 26
YES1 -0.033 0.13 -9999 0 -0.41 29 29
FZD3 0.011 0 -9999 0 -10000 0 0
FZD6 0.01 0.019 -9999 0 -0.42 1 1
G protein -0.023 0.12 -9999 0 -0.37 33 33
MAP3K7 -0.11 0.14 -9999 0 -0.33 92 92
mol:Ca2+ -0.023 0.11 -9999 0 -0.38 26 26
mol:IP3 -0.024 0.12 -9999 0 -0.4 26 26
NLK -0.004 0.009 -9999 0 -10000 0 0
GNB1 0.011 0 -9999 0 -10000 0 0
CAMK2A -0.12 0.14 -9999 0 -0.33 110 110
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.041 0.13 -9999 0 -0.26 113 113
CSNK1A1 0.011 0 -9999 0 -10000 0 0
GNAS -0.033 0.13 -9999 0 -0.41 29 29
GO:0007205 -0.024 0.12 -9999 0 -0.39 26 26
WNT6 -0.027 0.11 -9999 0 -0.35 53 53
WNT4 -0.058 0.16 -9999 0 -0.42 82 82
NFAT1/CK1 alpha -0.031 0.13 -9999 0 -0.41 32 32
GNG2 -0.002 0.071 -9999 0 -0.41 15 15
WNT5A -0.002 0.072 -9999 0 -0.42 15 15
WNT11 -0.024 0.1 -9999 0 -0.3 58 58
CDC42 -0.026 0.12 -9999 0 -0.39 29 29
Ephrin B reverse 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
EFNB2 0.008 0.033 -10000 0 -0.42 3 3
EPHB2 0.01 0.018 -10000 0 -0.27 2 2
EFNB1 0.017 0.023 -10000 0 -0.28 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.01 0.069 -10000 0 -0.36 3 3
Ephrin B2/EPHB1-2 0 0.067 -10000 0 -0.2 49 49
neuron projection morphogenesis -0.02 0.055 -10000 0 -0.34 3 3
Ephrin B1/EPHB1-2/Tiam1 0.006 0.074 -10000 0 -0.2 47 47
DNM1 0.008 0.033 -10000 0 -0.42 3 3
cell-cell signaling 0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.036 0.16 -10000 0 -0.52 53 53
YES1 -0.076 0.23 -10000 0 -0.76 52 52
Ephrin B1/EPHB1-2/NCK2 0.012 0.063 -10000 0 -0.18 37 37
PI3K -0.037 0.17 -10000 0 -0.53 53 53
mol:GDP 0.005 0.073 -10000 0 -0.19 47 47
ITGA2B 0.005 0.047 -10000 0 -0.36 8 8
endothelial cell proliferation 0.013 0.022 -10000 0 -0.24 4 4
FYN -0.076 0.23 -10000 0 -0.76 52 52
MAP3K7 -0.044 0.17 -10000 0 -0.56 52 52
FGR -0.079 0.23 -10000 0 -0.76 52 52
TIAM1 -0.002 0.072 -10000 0 -0.42 15 15
PIK3R1 0.007 0.038 -10000 0 -0.42 4 4
RGS3 0.011 0 -10000 0 -10000 0 0
cell adhesion -0.066 0.19 -10000 0 -0.57 53 53
LYN -0.076 0.23 -10000 0 -0.76 52 52
Ephrin B1/EPHB1-2/Src Family Kinases -0.071 0.21 -10000 0 -0.7 52 52
Ephrin B1/EPHB1-2 -0.062 0.18 -10000 0 -0.61 52 52
SRC -0.075 0.23 -10000 0 -0.75 52 52
ITGB3 -0.078 0.17 -10000 0 -0.41 107 107
EPHB1 -0.028 0.12 -10000 0 -0.41 47 47
EPHB4 0.01 0.019 -10000 0 -0.42 1 1
RAC1 0.011 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.013 0.022 -10000 0 -0.24 4 4
alphaIIb/beta3 Integrin -0.051 0.12 -10000 0 -0.28 114 114
BLK -0.074 0.23 -10000 0 -0.76 52 52
HCK -0.075 0.23 -10000 0 -0.75 52 52
regulation of stress fiber formation -0.011 0.062 0.18 37 -10000 0 37
MAPK8 -0.031 0.16 -10000 0 -0.5 52 52
Ephrin B1/EPHB1-2/RGS3 0.012 0.063 -10000 0 -0.18 37 37
endothelial cell migration -0.044 0.14 -10000 0 -0.46 54 54
NCK2 0.011 0 -10000 0 -10000 0 0
PTPN13 -0.046 0.16 -10000 0 -0.53 52 52
regulation of focal adhesion formation -0.011 0.062 0.18 37 -10000 0 37
chemotaxis -0.011 0.062 0.18 37 -10000 0 37
PIK3CA 0.01 0.019 -10000 0 -0.42 1 1
Rac1/GTP -0.02 0.056 -10000 0 -0.35 3 3
angiogenesis -0.061 0.18 -10000 0 -0.6 52 52
LCK -0.075 0.23 -10000 0 -0.75 52 52
TCGA08_p53

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
CDKN2A -0.075 0.095 -9999 0 -0.18 224 224
TP53 -0.018 0.024 -9999 0 -0.33 1 1
Senescence -0.018 0.024 -9999 0 -0.33 1 1
Apoptosis -0.018 0.024 -9999 0 -0.33 1 1
Activated_Oncogenes 0 0 -9999 0 -10000 0 0
MDM2 0.038 0.043 -9999 0 -10000 0 0
MDM4 0.011 0 -9999 0 -10000 0 0
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.002 0.078 -9999 0 -0.23 47 47
NF kappa B1 p50/RelA/I kappa B alpha 0.017 0.066 -9999 0 -0.26 5 5
AP1 -0.09 0.12 -9999 0 -0.3 76 76
mol:PIP3 -0.032 0.068 -9999 0 -0.31 16 16
AKT1 0.026 0.059 -9999 0 -0.27 9 9
PTK2B 0.005 0.058 -9999 0 -0.2 30 30
RHOA 0.018 0.03 -9999 0 -10000 0 0
PIK3CB 0.01 0 -9999 0 -10000 0 0
mol:Ca2+ 0.002 0.061 -9999 0 -0.2 20 20
MAGI3 0.011 0 -9999 0 -10000 0 0
RELA 0.011 0 -9999 0 -10000 0 0
apoptosis -0.014 0.082 -9999 0 -0.23 52 52
HRAS/GDP 0.008 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.007 0.065 -9999 0 -0.22 16 16
NF kappa B1 p50/RelA -0.016 0.07 -9999 0 -0.32 10 10
endothelial cell migration -0.012 0.13 -9999 0 -0.44 37 37
ADCY4 -0.053 0.15 -9999 0 -0.38 65 65
ADCY5 -0.077 0.16 -9999 0 -0.39 79 79
ADCY6 -0.039 0.13 -9999 0 -0.34 49 49
ADCY7 -0.039 0.13 -9999 0 -0.34 49 49
ADCY1 -0.047 0.14 -9999 0 -0.38 56 56
ADCY2 -0.15 0.19 -9999 0 -0.41 137 137
ADCY3 -0.04 0.13 -9999 0 -0.35 50 50
ADCY8 -0.063 0.14 -9999 0 -0.38 55 55
ADCY9 -0.066 0.16 -9999 0 -0.38 83 83
GSK3B 0.01 0.056 -9999 0 -0.2 25 25
arachidonic acid secretion -0.045 0.14 -9999 0 -0.38 42 42
GNG2 -0.002 0.071 -9999 0 -0.41 15 15
TRIP6 0.014 0.036 -9999 0 -0.36 4 4
GNAO1 -0.061 0.14 -9999 0 -0.26 151 151
HRAS 0.011 0 -9999 0 -10000 0 0
NFKBIA 0.009 0.071 -9999 0 -0.25 12 12
GAB1 0.007 0.038 -9999 0 -0.42 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.005 0.15 -9999 0 -0.85 15 15
JUN 0.006 0.046 -9999 0 -0.42 6 6
LPA/LPA2/NHERF2 0.012 0.022 -9999 0 -0.14 3 3
TIAM1 -0.028 0.17 -9999 0 -1 15 15
PIK3R1 0.007 0.038 -9999 0 -0.42 4 4
mol:IP3 0.002 0.061 -9999 0 -0.2 20 20
PLCB3 0.017 0.019 -9999 0 -10000 0 0
FOS -0.13 0.2 -9999 0 -0.42 174 174
positive regulation of mitosis -0.045 0.14 -9999 0 -0.38 42 42
LPA/LPA1-2-3 -0.016 0.088 -9999 0 -0.23 52 52
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.011 0 -9999 0 -10000 0 0
stress fiber formation 0.004 0.067 -9999 0 -0.26 14 14
GNAZ -0.01 0.091 -9999 0 -0.25 61 61
EGFR/PI3K-beta/Gab1 -0.033 0.071 -9999 0 -0.33 16 16
positive regulation of dendritic cell cytokine production -0.02 0.086 -9999 0 -0.23 52 52
LPA/LPA2/MAGI-3 0.012 0.021 -9999 0 -0.14 3 3
ARHGEF1 0.014 0.061 -9999 0 -0.19 37 37
GNAI2 0.002 0.072 -9999 0 -0.24 37 37
GNAI3 0.002 0.072 -9999 0 -0.24 37 37
GNAI1 -0.002 0.081 -9999 0 -0.25 45 45
LPA/LPA3 -0.028 0.081 -9999 0 -0.21 79 79
LPA/LPA2 0.004 0.026 -9999 0 -0.18 3 3
LPA/LPA1 -0.007 0.084 -9999 0 -0.3 37 37
HB-EGF/EGFR -0.054 0.09 -9999 0 -0.32 14 14
HBEGF -0.066 0.096 -9999 0 -0.18 223 223
mol:DAG 0.002 0.061 -9999 0 -0.2 20 20
cAMP biosynthetic process -0.075 0.15 -9999 0 -0.29 135 135
NFKB1 0.01 0.019 -9999 0 -0.42 1 1
SRC 0.011 0 -9999 0 -10000 0 0
GNB1 0.01 0 -9999 0 -10000 0 0
LYN 0.009 0.071 -9999 0 -0.24 22 22
GNAQ -0.005 0.056 -9999 0 -0.22 21 21
LPAR2 0.009 0.022 -9999 0 -0.27 3 3
LPAR3 -0.038 0.12 -9999 0 -0.3 79 79
LPAR1 -0.006 0.084 -9999 0 -0.45 15 15
IL8 -0.054 0.11 -9999 0 -0.33 34 34
PTK2 -0.01 0.082 -9999 0 -0.23 34 34
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
CASP3 -0.014 0.082 -9999 0 -0.23 52 52
EGFR -0.001 0.068 -9999 0 -0.41 14 14
PLCG1 -0.011 0.071 -9999 0 -0.21 40 40
PLD2 -0.01 0.083 -9999 0 -0.21 48 48
G12/G13 0.009 0.065 -9999 0 -0.22 37 37
PI3K-beta -0.016 0.053 -9999 0 -0.31 9 9
cell migration -0.015 0.05 -9999 0 -0.24 17 17
SLC9A3R2 0.011 0 -9999 0 -10000 0 0
PXN 0.004 0.068 -9999 0 -0.26 14 14
HRAS/GTP -0.046 0.14 -9999 0 -0.39 42 42
RAC1 0.011 0 -9999 0 -10000 0 0
MMP9 -0.11 0.14 -9999 0 -0.27 222 222
PRKCE 0.01 0.002 -9999 0 -10000 0 0
PRKCD 0.007 0.059 -9999 0 -0.22 7 7
Gi(beta/gamma) -0.04 0.13 -9999 0 -0.37 42 42
mol:LPA -0.004 0.035 -9999 0 -0.16 22 22
TRIP6/p130 Cas/FAK1/Paxillin -0.024 0.07 -9999 0 -0.38 9 9
MAPKKK cascade -0.045 0.14 -9999 0 -0.38 42 42
contractile ring contraction involved in cytokinesis 0.018 0.03 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.029 0.096 -9999 0 -0.26 69 69
GNA15 -0.006 0.055 -9999 0 -0.22 19 19
GNA12 0.011 0 -9999 0 -10000 0 0
GNA13 0.011 0 -9999 0 -10000 0 0
MAPT 0.007 0.067 -9999 0 -0.23 16 16
GNA11 -0.01 0.063 -9999 0 -0.22 30 30
Rac1/GTP -0.006 0.16 -9999 0 -0.91 15 15
MMP2 -0.012 0.13 -9999 0 -0.44 37 37
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.011 0 -9999 0 -10000 0 0
VLDLR 0.009 0.027 -9999 0 -0.42 2 2
LRPAP1 0.011 0 -9999 0 -10000 0 0
NUDC 0.011 0 -9999 0 -10000 0 0
RELN/LRP8 -0.074 0.12 -9999 0 -0.23 187 187
CaM/Ca2+ 0.008 0 -9999 0 -10000 0 0
KATNA1 0.011 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.061 0.11 -9999 0 -0.2 189 189
IQGAP1/CaM 0.016 0 -9999 0 -10000 0 0
DAB1 0.001 0.043 -9999 0 -0.27 12 12
IQGAP1 0.011 0 -9999 0 -10000 0 0
PLA2G7 0.009 0.026 -9999 0 -0.32 3 3
CALM1 0.011 0 -9999 0 -10000 0 0
DYNLT1 0.011 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 0.014 0.017 -9999 0 -0.18 4 4
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.011 0 -9999 0 -10000 0 0
CDK5R1 0.01 0.012 -9999 0 -0.27 1 1
LIS1/Poliovirus Protein 3A 0.013 0 -9999 0 -10000 0 0
CDK5R2 -0.022 0.085 -9999 0 -0.27 53 53
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.08 0.12 -9999 0 -0.24 188 188
YWHAE 0.011 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.032 0.092 -9999 0 -0.2 15 15
MAP1B -0.013 0.057 -9999 0 -0.25 27 27
RAC1 0.017 0 -9999 0 -10000 0 0
p35/CDK5 -0.042 0.098 -9999 0 -0.26 3 3
RELN -0.15 0.2 -9999 0 -0.41 191 191
PAFAH/LIS1 0.02 0.015 -9999 0 -0.23 1 1
LIS1/CLIP170 0.021 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.04 0.056 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.053 0.1 -9999 0 -0.19 188 188
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.041 0.095 -9999 0 -0.22 15 15
LIS1/IQGAP1 0.021 0 -9999 0 -10000 0 0
RHOA 0.017 0 -9999 0 -10000 0 0
PAFAH1B1 0.017 0 -9999 0 -10000 0 0
PAFAH1B3 0.006 0.037 -9999 0 -0.27 9 9
PAFAH1B2 0.01 0.019 -9999 0 -0.42 1 1
MAP1B/LIS1/Dynein heavy chain 0.011 0.038 -9999 0 -0.15 27 27
NDEL1/Katanin 60/Dynein heavy chain -0.026 0.089 -9999 0 -0.24 2 2
LRP8 0.008 0.025 -9999 0 -0.27 4 4
NDEL1/Katanin 60 -0.032 0.092 -9999 0 -0.25 2 2
P39/CDK5 -0.045 0.11 -9999 0 -0.27 18 18
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.021 0 -9999 0 -10000 0 0
CDK5 -0.051 0.1 -9999 0 -0.18 189 189
PPP2R5D 0.011 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.018 0 -9999 0 -10000 0 0
CSNK2A1 0.011 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.055 0.1 -9999 0 -0.19 188 188
RELN/VLDLR -0.06 0.11 -9999 0 -0.21 188 188
CDC42 0.017 0 -9999 0 -10000 0 0
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.26 0.39 -10000 0 -1.1 47 47
STAT6 (cleaved dimer) -0.29 0.36 -10000 0 -0.91 94 94
IGHG1 -0.091 0.15 -10000 0 -0.36 16 16
IGHG3 -0.25 0.38 -10000 0 -0.92 80 80
AKT1 -0.11 0.22 -10000 0 -0.7 15 15
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.071 0.16 -10000 0 -0.59 11 11
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.13 0.24 -10000 0 -0.66 34 34
THY1 -0.26 0.39 -10000 0 -1.1 47 47
MYB -0.027 0.096 -10000 0 -0.27 68 68
HMGA1 -0.033 0.1 -10000 0 -0.27 79 79
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.15 0.24 -10000 0 -0.64 40 40
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.12 0.22 -10000 0 -0.73 13 13
SP1 0.017 0.002 -10000 0 -10000 0 0
INPP5D 0.01 0.019 -10000 0 -0.42 1 1
SOCS5 0.017 0.014 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.24 0.39 -10000 0 -0.99 69 69
SOCS1 -0.16 0.28 -10000 0 -0.72 42 42
SOCS3 -0.12 0.24 -10000 0 -1.1 10 10
FCER2 -0.2 0.31 -10000 0 -0.84 47 47
PARP14 0.011 0.001 -10000 0 -10000 0 0
CCL17 -0.26 0.39 -10000 0 -1.1 47 47
GRB2 0.011 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.088 0.18 -10000 0 -0.73 5 5
T cell proliferation -0.26 0.4 -10000 0 -1.1 60 60
IL4R/JAK1 -0.26 0.4 -10000 0 -1 59 59
EGR2 -0.29 0.48 -10000 0 -1.3 62 62
JAK2 -0.01 0.063 -10000 0 -0.43 9 9
JAK3 0.013 0.022 -10000 0 -0.27 3 3
PIK3R1 0.007 0.038 -10000 0 -0.42 4 4
JAK1 0.006 0.034 -10000 0 -0.41 3 3
COL1A2 -0.085 0.19 -10000 0 -1.4 5 5
CCL26 -0.26 0.39 -10000 0 -1.1 48 48
IL4R -0.27 0.42 -10000 0 -1.1 58 58
PTPN6 0.017 0.017 -10000 0 -0.25 1 1
IL13RA2 -0.26 0.4 -10000 0 -1 58 58
IL13RA1 -0.002 0.028 -10000 0 -10000 0 0
IRF4 -0.062 0.22 -10000 0 -1.1 17 17
ARG1 -0.058 0.12 -10000 0 -10000 0 0
CBL -0.13 0.23 -10000 0 -0.6 39 39
GTF3A 0.017 0 -10000 0 -10000 0 0
PIK3CA 0.01 0.019 -10000 0 -0.42 1 1
IL13RA1/JAK2 -0.009 0.054 -10000 0 -0.28 9 9
IRF4/BCL6 -0.056 0.2 -10000 0 -0.98 17 17
CD40LG 0.007 0.061 -10000 0 -0.42 10 10
MAPK14 -0.13 0.24 -10000 0 -0.68 28 28
mitosis -0.11 0.21 -10000 0 -0.66 15 15
STAT6 -0.29 0.44 -10000 0 -1.1 74 74
SPI1 0.011 0.022 -10000 0 -0.27 3 3
RPS6KB1 -0.098 0.2 -10000 0 -0.63 15 15
STAT6 (dimer) -0.29 0.44 -10000 0 -1.1 74 74
STAT6 (dimer)/PARP14 -0.27 0.41 -10000 0 -1 74 74
mast cell activation 0.006 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.1 0.2 -10000 0 -0.68 11 11
FRAP1 -0.11 0.22 -10000 0 -0.7 15 15
LTA -0.26 0.39 -10000 0 -1.1 47 47
FES 0.01 0.019 -10000 0 -0.42 1 1
T-helper 1 cell differentiation 0.29 0.44 1.1 74 -10000 0 74
CCL11 -0.32 0.48 -10000 0 -1.2 84 84
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.1 0.2 -10000 0 -0.7 10 10
IL2RG 0.01 0.039 -10000 0 -0.32 7 7
IL10 -0.26 0.39 -10000 0 -1.1 46 46
IRS1 -0.029 0.12 -10000 0 -0.42 47 47
IRS2 -0.045 0.14 -10000 0 -0.42 67 67
IL4 -0.062 0.11 -10000 0 -10000 0 0
IL5 -0.26 0.39 -10000 0 -1.1 51 51
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.22 0.34 -10000 0 -0.85 59 59
COL1A1 -0.079 0.15 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.26 0.4 -10000 0 -1.2 46 46
IL2R gamma/JAK3 0.016 0.035 -10000 0 -0.25 8 8
TFF3 -0.31 0.45 -10000 0 -1.2 73 73
ALOX15 -0.27 0.4 -10000 0 -1.1 53 53
MYBL1 0.011 0 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.22 0.33 -10000 0 -0.85 62 62
SHC1 0.011 0 -10000 0 -10000 0 0
CEBPB 0.013 0.003 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.13 0.23 -10000 0 -0.67 23 23
mol:PI-3-4-5-P3 -0.11 0.22 -10000 0 -0.7 15 15
PI3K -0.12 0.23 -10000 0 -0.75 15 15
DOK2 0.008 0.029 -10000 0 -0.31 4 4
ETS1 0.015 0.033 -10000 0 -0.38 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.079 0.17 -10000 0 -0.7 5 5
ITGB3 -0.4 0.59 -10000 0 -1.3 123 123
PIGR -0.32 0.46 -10000 0 -1.2 70 70
IGHE 0.02 0.034 -10000 0 -10000 0 0
MAPKKK cascade -0.078 0.16 -10000 0 -0.68 5 5
BCL6 0.009 0.019 -10000 0 -0.42 1 1
OPRM1 -0.26 0.39 -10000 0 -1.1 48 48
RETNLB -0.26 0.39 -10000 0 -1.1 51 51
SELP -0.58 0.68 -10000 0 -1.3 225 225
AICDA -0.25 0.38 -10000 0 -1.1 46 46
S1P1 pathway

Figure S45.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S45.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.002 0.069 -9999 0 -0.29 28 28
PDGFRB -0.008 0.086 -9999 0 -0.42 21 21
SPHK1 -0.015 0.025 -9999 0 -10000 0 0
mol:S1P -0.018 0.032 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.091 0.2 -9999 0 -0.44 96 96
GNAO1 -0.1 0.19 -9999 0 -0.42 131 131
PDGFB-D/PDGFRB/PLCgamma1 -0.076 0.19 -9999 0 -0.4 96 96
PLCG1 -0.08 0.19 -9999 0 -0.41 97 97
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.008 0.086 -9999 0 -0.42 21 21
GNAI2 0.01 0.004 -9999 0 -10000 0 0
GNAI3 0.009 0.004 -9999 0 -10000 0 0
GNAI1 0.001 0.06 -9999 0 -0.42 10 10
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.001 0.059 -9999 0 -0.24 28 28
S1P1/S1P -0.006 0.077 -9999 0 -0.27 16 16
negative regulation of cAMP metabolic process -0.088 0.2 -9999 0 -0.43 96 96
MAPK3 -0.1 0.24 -9999 0 -0.57 88 88
calcium-dependent phospholipase C activity -0.002 0.003 -9999 0 -10000 0 0
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
RhoA/GDP 0.008 0 -9999 0 -10000 0 0
KDR -0.013 0.097 -9999 0 -0.42 28 28
PLCB2 0 0.071 -9999 0 -0.25 14 14
RAC1 0.011 0 -9999 0 -10000 0 0
RhoA/GTP -0.023 0.057 -9999 0 -0.24 14 14
receptor internalization -0.025 0.064 -9999 0 -0.26 16 16
PTGS2 -0.15 0.36 -9999 0 -0.98 72 72
Rac1/GTP -0.023 0.057 -9999 0 -0.24 14 14
RHOA 0.011 0 -9999 0 -10000 0 0
VEGFA 0.01 0.003 -9999 0 -10000 0 0
negative regulation of T cell proliferation -0.088 0.2 -9999 0 -0.43 96 96
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.012 0.095 -9999 0 -0.42 26 26
MAPK1 -0.1 0.24 -9999 0 -0.56 92 92
S1P1/S1P/PDGFB-D/PDGFRB -0.011 0.1 -9999 0 -0.32 27 27
ABCC1 0.01 0.002 -9999 0 -10000 0 0
Syndecan-4-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
PTK2 0.014 0.044 -9999 0 -0.41 5 5
Syndecan-4/Syndesmos -0.009 0.078 -9999 0 -0.24 3 3
positive regulation of JNK cascade -0.12 0.12 -9999 0 -0.35 54 54
Syndecan-4/ADAM12 -0.011 0.08 -9999 0 -0.24 3 3
CCL5 0.006 0.038 -9999 0 -0.31 7 7
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
DNM2 0.011 0 -9999 0 -10000 0 0
ITGA5 0.01 0.019 -9999 0 -0.42 1 1
SDCBP 0.011 0 -9999 0 -10000 0 0
PLG -0.049 0.14 -9999 0 -0.39 76 76
ADAM12 0.003 0.046 -9999 0 -0.27 14 14
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.011 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.038 0.04 -9999 0 -0.12 7 7
Syndecan-4/Laminin alpha1 -0.029 0.11 -9999 0 -0.3 28 28
Syndecan-4/CXCL12/CXCR4 -0.12 0.12 -9999 0 -0.36 54 54
Syndecan-4/Laminin alpha3 -0.014 0.084 -9999 0 -0.29 5 5
MDK 0.01 0.012 -9999 0 -0.27 1 1
Syndecan-4/FZD7 -0.051 0.11 -9999 0 -0.39 15 15
Syndecan-4/Midkine -0.01 0.079 -9999 0 -0.26 4 4
FZD7 -0.08 0.18 -9999 0 -0.42 109 109
Syndecan-4/FGFR1/FGF -0.12 0.11 -9999 0 -0.36 51 51
THBS1 -0.056 0.16 -9999 0 -0.42 80 80
integrin-mediated signaling pathway -0.014 0.084 -9999 0 -0.31 7 7
positive regulation of MAPKKK cascade -0.12 0.12 -9999 0 -0.35 54 54
Syndecan-4/TACI -0.014 0.081 -9999 0 -0.27 5 5
CXCR4 0.011 0 -9999 0 -10000 0 0
cell adhesion 0.013 0.052 -9999 0 -0.17 33 33
Syndecan-4/Dynamin -0.009 0.078 -9999 0 -0.24 3 3
Syndecan-4/TSP1 -0.04 0.11 -9999 0 -0.36 16 16
Syndecan-4/GIPC -0.009 0.078 -9999 0 -10000 0 0
Syndecan-4/RANTES -0.011 0.081 -9999 0 -0.29 5 5
ITGB1 0.011 0 -9999 0 -10000 0 0
LAMA1 -0.11 0.14 -9999 0 -0.27 223 223
LAMA3 0 0.067 -9999 0 -0.42 13 13
RAC1 0.011 0 -9999 0 -10000 0 0
PRKCA -0.006 0.1 -9999 0 -0.38 33 33
Syndecan-4/alpha-Actinin -0.009 0.078 -9999 0 -0.24 3 3
TFPI -0.039 0.14 -9999 0 -0.42 60 60
F2 -0.018 0.078 -9999 0 -0.27 44 44
alpha5/beta1 Integrin 0.015 0.013 -9999 0 -0.29 1 1
positive regulation of cell adhesion -0.06 0.096 -9999 0 -0.3 32 32
ACTN1 0.011 0 -9999 0 -10000 0 0
TNC -0.001 0.068 -9999 0 -0.41 14 14
Syndecan-4/CXCL12 -0.13 0.13 -9999 0 -0.38 56 56
FGF6 0 0 -9999 0 -10000 0 0
RHOA 0.011 0 -9999 0 -10000 0 0
CXCL12 -0.26 0.21 -9999 0 -0.42 319 319
TNFRSF13B 0 0.047 -9999 0 -0.27 15 15
FGF2 -0.24 0.21 -9999 0 -0.42 301 301
FGFR1 0.01 0.019 -9999 0 -0.42 1 1
Syndecan-4/PI-4-5-P2 -0.016 0.077 -9999 0 -0.24 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 0.011 0.041 -9999 0 -0.4 5 5
cell migration -0.017 0.018 -9999 0 -10000 0 0
PRKCD 0.015 0.008 -9999 0 -10000 0 0
vasculogenesis -0.039 0.1 -9999 0 -0.35 16 16
SDC4 -0.017 0.081 -9999 0 -0.26 3 3
Syndecan-4/Tenascin C -0.014 0.086 -9999 0 -0.32 7 7
Syndecan-4/PI-4-5-P2/PKC alpha -0.03 0.032 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.009 0.078 -9999 0 -0.24 3 3
MMP9 -0.11 0.14 -9999 0 -0.27 222 222
Rac1/GTP 0.013 0.053 -9999 0 -0.18 30 30
cytoskeleton organization -0.009 0.076 -9999 0 -0.23 3 3
GIPC1 0.011 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.032 0.1 -9999 0 -0.36 18 18
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.036 0.1 0.34 19 -10000 0 19
GNAI2 0.011 0 -10000 0 -10000 0 0
S1P/S1P5/G12 0.01 0.028 -10000 0 -0.15 15 15
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.098 0.19 -10000 0 -0.42 131 131
RhoA/GTP -0.036 0.11 -10000 0 -0.35 19 19
negative regulation of cAMP metabolic process -0.045 0.12 -10000 0 -0.22 133 133
GNAZ -0.011 0.094 -10000 0 -0.42 26 26
GNAI3 0.011 0 -10000 0 -10000 0 0
GNA12 0.011 0 -10000 0 -10000 0 0
S1PR5 0.002 0.05 -10000 0 -0.28 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.046 0.12 -10000 0 -0.22 133 133
RhoA/GDP 0.008 0 -10000 0 -10000 0 0
RHOA 0.011 0 -10000 0 -10000 0 0
GNAI1 0.002 0.059 -10000 0 -0.42 10 10
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.014 0 -9999 0 -10000 0 0
ARNO/beta Arrestin1-2 -0.018 0.067 -9999 0 -10000 0 0
EGFR -0.001 0.068 -9999 0 -0.41 14 14
EPHA2 0.011 0 -9999 0 -10000 0 0
USP6 0.011 0 -9999 0 -10000 0 0
IQSEC1 0.01 0.019 -9999 0 -0.42 1 1
EGFR/EGFR/EGF/EGF -0.001 0.063 -9999 0 -0.23 33 33
ARRB2 0.007 0.002 -9999 0 -10000 0 0
mol:GTP 0.015 0.01 -9999 0 -0.14 1 1
ARRB1 0.01 0.019 -9999 0 -0.42 1 1
FBXO8 0.011 0 -9999 0 -10000 0 0
TSHR -0.004 0.06 -9999 0 -0.29 20 20
EGF -0.002 0.058 -9999 0 -0.29 20 20
somatostatin receptor activity 0 0 -9999 0 -0.001 80 80
ARAP2 0.009 0.027 -9999 0 -0.42 2 2
mol:GDP -0.05 0.093 -9999 0 -0.22 81 81
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 46 46
ITGA2B 0.005 0.047 -9999 0 -0.36 8 8
ARF6 0.011 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.026 0.017 -9999 0 -0.2 2 2
ADAP1 0.011 0 -9999 0 -10000 0 0
KIF13B 0.011 0 -9999 0 -10000 0 0
HGF/MET -0.044 0.12 -9999 0 -0.29 101 101
PXN 0.011 0 -9999 0 -10000 0 0
ARF6/GTP -0.046 0.096 -9999 0 -0.22 72 72
EGFR/EGFR/EGF/EGF/ARFGEP100 0.007 0.054 -9999 0 -0.24 16 16
ADRB2 -0.06 0.16 -9999 0 -0.42 85 85
receptor agonist activity 0 0 -9999 0 0 79 79
actin filament binding 0 0 -9999 0 0 77 77
SRC 0.011 0 -9999 0 -10000 0 0
ITGB3 -0.078 0.17 -9999 0 -0.41 107 107
GNAQ 0.009 0.027 -9999 0 -0.42 2 2
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 71 71
ARF6/GDP 0.015 0.046 -9999 0 -0.29 3 3
ARF6/GDP/GULP/ACAP1 -0.049 0.12 -9999 0 -0.29 65 65
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.023 0.096 -9999 0 -0.2 110 110
ACAP1 0.008 0.029 -9999 0 -0.31 4 4
ACAP2 0.01 0.019 -9999 0 -0.42 1 1
LHCGR/beta Arrestin2 0.001 0.004 -9999 0 -10000 0 0
EFNA1 0.01 0.018 -9999 0 -0.27 2 2
HGF -0.07 0.17 -9999 0 -0.42 96 96
CYTH3 0.009 0 -9999 0 -10000 0 0
CYTH2 0.007 0.002 -9999 0 -10000 0 0
NCK1 0.009 0.027 -9999 0 -0.42 2 2
fibronectin binding 0 0 -9999 0 0 60 60
endosomal lumen acidification 0 0 -9999 0 0 56 56
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.033 0.13 -9999 0 -0.42 52 52
GNAQ/ARNO 0.011 0.014 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 0 1 1
PIP3-E 0 0 -9999 0 0 17 17
MET 0.005 0.045 -9999 0 -0.34 8 8
GNA14 -0.034 0.13 -9999 0 -0.42 53 53
GNA15 0.007 0.033 -9999 0 -0.27 7 7
GIT1 0.011 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 71 71
GNA11 0.001 0.062 -9999 0 -0.42 11 11
LHCGR 0.001 0.003 -9999 0 -10000 0 0
AGTR1 -0.1 0.19 -9999 0 -0.42 136 136
desensitization of G-protein coupled receptor protein signaling pathway 0.001 0.004 -9999 0 -10000 0 0
IPCEF1/ARNO 0.007 0.04 -9999 0 -10000 0 0
alphaIIb/beta3 Integrin -0.051 0.12 -9999 0 -0.28 114 114
FAS signaling pathway (CD95)

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
SPTAN1 0.019 0.059 0.2 50 -10000 0 50
RFC1 0.019 0.059 0.2 50 -10000 0 50
PRKDC 0.019 0.059 0.2 50 -10000 0 50
RIPK1 0.011 0.002 -10000 0 -10000 0 0
CASP7 -0.002 0.017 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1 0.014 0.06 0.19 46 -0.21 5 51
MAP2K4 0.033 0.061 -10000 0 -0.24 16 16
mol:ceramide 0.026 0.046 -10000 0 -0.24 3 3
GSN 0.016 0.065 0.2 49 -0.23 7 56
FASLG/FAS/FADD/FAF1/Caspase 8 0.032 0.053 0.17 45 -0.23 3 48
FAS 0.007 0.042 -10000 0 -0.42 5 5
BID 0.001 0.017 0.27 2 -10000 0 2
MAP3K1 0.032 0.04 -10000 0 -10000 0 0
MAP3K7 0.01 0.002 -10000 0 -10000 0 0
RB1 0.018 0.061 0.2 49 -0.23 2 51
CFLAR 0.011 0.002 -10000 0 -10000 0 0
HGF/MET -0.054 0.13 -10000 0 -0.26 137 137
ARHGDIB 0.019 0.059 0.2 50 -10000 0 50
FADD 0.011 0.003 -10000 0 -10000 0 0
actin filament polymerization -0.016 0.065 0.23 7 -0.2 49 56
NFKB1 -0.01 0.048 -10000 0 -0.65 1 1
MAPK8 0.031 0.095 -10000 0 -0.41 20 20
DFFA 0.019 0.059 0.2 50 -10000 0 50
DNA fragmentation during apoptosis 0.019 0.059 0.2 50 -10000 0 50
FAS/FADD/MET 0.016 0.037 -10000 0 -0.23 9 9
CFLAR/RIP1 0.015 0.003 -10000 0 -10000 0 0
FAIM3 0.009 0.027 -10000 0 -0.42 2 2
FAF1 0.011 0.005 -10000 0 -10000 0 0
PARP1 0.019 0.059 0.2 50 -10000 0 50
DFFB 0.019 0.059 0.2 50 -10000 0 50
CHUK -0.009 0.043 -10000 0 -0.6 1 1
FASLG 0.003 0.048 -10000 0 -0.31 11 11
FAS/FADD 0.013 0.03 -10000 0 -0.28 5 5
HGF -0.069 0.17 -10000 0 -0.42 96 96
LMNA 0.018 0.055 0.18 50 -10000 0 50
CASP6 0.019 0.059 0.2 50 -10000 0 50
CASP10 0.01 0.019 -10000 0 -0.42 1 1
CASP3 0.023 0.069 0.23 50 -10000 0 50
PTPN13 -0.033 0.13 -10000 0 -0.42 52 52
CASP8 0.001 0.021 0.33 2 -10000 0 2
IL6 -0.017 0.23 -10000 0 -1.2 20 20
MET 0.005 0.045 -10000 0 -0.34 8 8
ICAD/CAD 0.018 0.055 0.18 50 -10000 0 50
FASLG/FAS/FADD/FAF1/Caspase 10 0.026 0.046 -10000 0 -0.25 3 3
activation of caspase activity by cytochrome c 0.001 0.017 0.27 2 -10000 0 2
PAK2 0.019 0.059 0.2 50 -10000 0 50
BCL2 -0.029 0.12 -10000 0 -0.42 48 48
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.011 0 -9999 0 -10000 0 0
EGFR -0.001 0.068 -9999 0 -0.41 14 14
EGF/EGFR -0.066 0.1 -9999 0 -0.2 162 162
EGF/EGFR dimer/SHC/GRB2/SOS1 0.02 0.045 -9999 0 -0.2 15 15
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.12 0.2 -9999 0 -0.42 151 151
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.002 0.058 -9999 0 -0.29 20 20
EGF/EGFR dimer/SHC 0.008 0.053 -9999 0 -0.24 15 15
mol:GDP -0.009 0.037 -9999 0 -0.19 15 15
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.005 0.05 -9999 0 -0.42 7 7
GRB2/SOS1 0.016 0 -9999 0 -10000 0 0
HRAS/GTP -0.008 0.033 -9999 0 -0.28 1 1
SHC1 0.011 0 -9999 0 -10000 0 0
HRAS/GDP -0.008 0.034 -9999 0 -0.29 1 1
FRAP1 0.016 0.042 -9999 0 -0.18 15 15
EGF/EGFR dimer 0 0.063 -9999 0 -0.23 33 33
SOS1 0.011 0 -9999 0 -10000 0 0
GRB2 0.011 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.077 0.14 -9999 0 -0.29 155 155
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.005 0.05 -10000 0 -1.1 1 1
VDR 0.005 0.039 -10000 0 -0.27 10 10
FAM120B 0.011 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.021 0.073 -10000 0 -0.25 12 12
RXRs/LXRs/DNA/Oxysterols 0.027 0.072 -10000 0 -0.46 2 2
MED1 0.011 0 -10000 0 -10000 0 0
mol:9cRA 0.004 0.005 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.026 0.11 -10000 0 -0.21 117 117
RXRs/NUR77 -0.039 0.12 -10000 0 -0.22 148 148
RXRs/PPAR 0 0.083 -10000 0 -0.2 75 75
NCOR2 0.011 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.004 0.026 -10000 0 -0.18 10 10
RARs/VDR/DNA/Vit D3 0.019 0.035 -10000 0 -0.19 10 10
RARA 0.011 0 -10000 0 -10000 0 0
NCOA1 0.01 0.019 -10000 0 -0.42 1 1
VDR/VDR/DNA 0.005 0.039 -10000 0 -0.27 10 10
RARs/RARs/DNA/9cRA 0.017 0.03 -10000 0 -0.19 10 10
RARG 0.011 0 -10000 0 -10000 0 0
RPS6KB1 0.008 0.028 -10000 0 -0.4 1 1
RARs/THRs/DNA/SMRT -0.025 0.1 -10000 0 -0.21 117 117
THRA 0.003 0.056 -10000 0 -0.42 9 9
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.004 0.026 -10000 0 -0.18 10 10
RXRs/PPAR/9cRA/PGJ2/DNA 0.009 0.074 0.28 1 -0.21 48 49
NR1H4 -0.007 0.051 -10000 0 -0.27 18 18
RXRs/LXRs/DNA 0.03 0.071 -10000 0 -0.22 11 11
NR1H2 0.015 0.004 -10000 0 -10000 0 0
NR1H3 0.015 0.013 -10000 0 -0.26 1 1
RXRs/VDR/DNA/Vit D3 0.008 0.07 -10000 0 -0.19 48 48
NR4A1 -0.082 0.18 -10000 0 -0.42 111 111
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.005 0.062 -10000 0 -0.21 14 14
RXRG -0.031 0.13 -10000 0 -0.39 57 57
RXR alpha/CCPG 0.019 0.003 -10000 0 -10000 0 0
RXRA 0.014 0.004 -10000 0 -10000 0 0
RXRB 0.015 0.004 -10000 0 -10000 0 0
THRB -0.077 0.17 -10000 0 -0.42 105 105
PPARG -0.014 0.099 -10000 0 -0.42 29 29
PPARD 0.011 0 -10000 0 -10000 0 0
TNF 0.025 0.094 -10000 0 -1 2 2
mol:Oxysterols 0.004 0.005 -10000 0 -10000 0 0
cholesterol transport 0.027 0.071 -10000 0 -0.45 2 2
PPARA 0.011 0 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.002 0.059 -10000 0 -0.42 10 10
RXRs/NUR77/BCL2 -0.066 0.14 -10000 0 -0.25 172 172
SREBF1 0.032 0.066 -10000 0 -0.42 2 2
RXRs/RXRs/DNA/9cRA 0.009 0.074 0.27 1 -0.21 48 49
ABCA1 0.032 0.066 -10000 0 -0.5 1 1
RARs/THRs -0.02 0.099 -10000 0 -0.2 117 117
RXRs/FXR 0.002 0.079 -10000 0 -0.22 48 48
BCL2 -0.029 0.12 -10000 0 -0.42 48 48
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.1 0.19 -10000 0 -0.42 133 133
HRAS 0.011 0 -10000 0 -10000 0 0
EGFR -0.001 0.068 -10000 0 -0.41 14 14
AKT -0.078 0.14 -10000 0 -0.23 210 210
FOXO3 0.011 0 -10000 0 -10000 0 0
AKT1 0.011 0 -10000 0 -10000 0 0
FOXO1 0.008 0.033 -10000 0 -0.42 3 3
AKT3 -0.17 0.21 -10000 0 -0.42 212 212
FOXO4 0.009 0.027 -10000 0 -0.42 2 2
MET 0.005 0.045 -10000 0 -0.34 8 8
PIK3CA 0.01 0.019 -10000 0 -0.42 1 1
PIK3CB 0.011 0 -10000 0 -10000 0 0
NRAS 0.011 0 -10000 0 -10000 0 0
PIK3CG -0.001 0.069 -10000 0 -0.4 15 15
PIK3R3 0.01 0.012 -10000 0 -0.27 1 1
PIK3R2 0.011 0 -10000 0 -10000 0 0
NF1 0.008 0.033 -10000 0 -0.42 3 3
RAS -0.021 0.073 0.18 1 -0.25 13 14
ERBB2 0.003 0.044 -10000 0 -0.27 13 13
proliferation/survival/translation 0.016 0.069 0.23 20 -10000 0 20
PI3K -0.012 0.073 0.15 2 -0.21 24 26
PIK3R1 0.007 0.038 -10000 0 -0.42 4 4
KRAS 0.01 0.012 -10000 0 -0.27 1 1
FOXO 0.021 0.021 -10000 0 -10000 0 0
AKT2 0.011 0 -10000 0 -10000 0 0
PTEN 0.006 0.046 -10000 0 -0.42 6 6
IL6-mediated signaling events

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
BCL2L1 0.032 0.13 -9999 0 -0.56 4 4
CRP 0.028 0.13 -9999 0 -0.57 4 4
cell cycle arrest 0.027 0.14 -9999 0 -0.53 12 12
TIMP1 0.027 0.13 -9999 0 -0.52 7 7
IL6ST -0.068 0.17 -9999 0 -0.41 100 100
Rac1/GDP -0.009 0.14 -9999 0 -0.37 42 42
AP1 -0.032 0.13 -9999 0 -0.47 14 14
GAB2 0.007 0.042 -9999 0 -0.42 5 5
TNFSF11 0.021 0.14 -9999 0 -0.54 6 6
HSP90B1 0.032 0.03 -9999 0 -10000 0 0
GAB1 0.008 0.038 -9999 0 -0.42 4 4
MAPK14 -0.037 0.15 -9999 0 -0.42 45 45
AKT1 0.04 0.041 -9999 0 -0.39 2 2
FOXO1 0.043 0.042 -9999 0 -0.37 2 2
MAP2K6 -0.041 0.15 -9999 0 -0.4 50 50
mol:GTP 0.001 0.001 -9999 0 -10000 0 0
MAP2K4 0.01 0.13 -9999 0 -0.36 38 38
MITF -0.043 0.17 -9999 0 -0.42 62 62
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0.011 0 -9999 0 -10000 0 0
A2M 0.011 0.08 -9999 0 -1.3 2 2
CEBPB 0.017 0.001 -9999 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.008 0.092 -9999 0 -0.55 7 7
STAT3 0.028 0.14 -9999 0 -0.56 12 12
STAT1 0.002 0.014 -9999 0 -10000 0 0
CEBPD 0.031 0.14 -9999 0 -0.59 7 7
PIK3CA 0.011 0.019 -9999 0 -0.42 1 1
PI3K 0.015 0.03 -9999 0 -0.28 5 5
JUN 0.006 0.046 -9999 0 -0.42 6 6
PIAS3/MITF -0.036 0.16 -9999 0 -0.39 61 61
MAPK11 -0.038 0.15 -9999 0 -0.42 45 45
STAT3 (dimer)/FOXO1 0.061 0.13 -9999 0 -0.48 7 7
GRB2/SOS1/GAB family -0.051 0.11 -9999 0 -0.38 38 38
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.031 0.15 -9999 0 -0.31 75 75
GRB2 0.011 0.001 -9999 0 -10000 0 0
JAK2 0.003 0.056 -9999 0 -0.42 9 9
LBP 0.024 0.12 -9999 0 -0.56 2 2
PIK3R1 0.008 0.038 -9999 0 -0.42 4 4
JAK1 0.01 0.033 -9999 0 -0.42 3 3
MYC 0.021 0.18 -9999 0 -0.94 11 11
FGG 0.027 0.13 -9999 0 -0.52 7 7
macrophage differentiation 0.027 0.14 -9999 0 -0.53 12 12
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.048 0.13 -9999 0 -0.31 66 66
JUNB 0.025 0.15 -9999 0 -0.69 11 11
FOS -0.13 0.2 -9999 0 -0.42 174 174
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.027 0.15 -9999 0 -0.4 47 47
STAT1/PIAS1 -0.005 0.13 -9999 0 -0.35 38 38
GRB2/SOS1/GAB family/SHP2/PI3K 0.031 0.043 -9999 0 -0.29 6 6
STAT3 (dimer) 0.029 0.14 -9999 0 -0.55 12 12
PRKCD 0.027 0.13 -9999 0 -0.45 15 15
IL6R -0.023 0.12 -9999 0 -0.41 43 43
SOCS3 -0.043 0.17 -9999 0 -0.71 19 19
gp130 (dimer)/JAK1/JAK1/LMO4 -0.019 0.1 -9999 0 -0.23 102 102
Rac1/GTP -0.005 0.14 -9999 0 -0.37 42 42
HCK 0.01 0.012 -9999 0 -0.27 1 1
MAPKKK cascade 0.021 0.088 -9999 0 -0.72 5 5
bone resorption 0.022 0.13 -9999 0 -0.52 6 6
IRF1 0.032 0.13 -9999 0 -0.52 6 6
mol:GDP -0.019 0.14 -9999 0 -0.39 43 43
SOS1 0.011 0.001 -9999 0 -10000 0 0
VAV1 -0.019 0.14 -9999 0 -0.4 43 43
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.054 0.19 -9999 0 -0.53 50 50
PTPN11 0.002 0.014 -9999 0 -10000 0 0
IL6/IL6RA -0.018 0.11 -9999 0 -0.29 65 65
gp130 (dimer)/TYK2/TYK2/LMO4 -0.021 0.1 -9999 0 -0.23 100 100
gp130 (dimer)/JAK2/JAK2/LMO4 -0.026 0.11 -9999 0 -0.23 106 106
IL6 -0.007 0.09 -9999 0 -0.37 29 29
PIAS3 0.011 0 -9999 0 -10000 0 0
PTPRE 0.002 0.023 -9999 0 -0.35 2 2
PIAS1 0.011 0 -9999 0 -10000 0 0
RAC1 0.011 0.001 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.04 0.14 -9999 0 -0.26 125 125
LMO4 0.015 0.005 -9999 0 -10000 0 0
STAT3 (dimer)/PIAS3 0.025 0.14 -9999 0 -0.55 12 12
MCL1 0.044 0.038 -9999 0 -0.36 1 1
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.086 0.11 -9999 0 -0.2 219 219
TC10/GTP -0.066 0.081 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 0.002 0.068 -9999 0 -0.21 47 47
HRAS 0.011 0 -9999 0 -10000 0 0
APS homodimer 0.011 0 -9999 0 -10000 0 0
GRB14 -0.089 0.14 -9999 0 -0.27 179 179
FOXO3 0.004 0.047 -9999 0 -0.55 3 3
AKT1 -0.02 0.079 -9999 0 -0.26 22 22
INSR 0.012 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0.029 0.001 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.01 0.019 -9999 0 -0.42 1 1
SORBS1 -0.16 0.21 -9999 0 -0.42 206 206
CRK 0.011 0 -9999 0 -10000 0 0
PTPN1 0.026 0.001 -9999 0 -10000 0 0
CAV1 -0.046 0.12 -9999 0 -0.23 135 135
CBL/APS/CAP/Crk-II/C3G -0.055 0.11 -9999 0 -0.18 206 206
Insulin Receptor/Insulin/IRS1/NCK2 0.002 0.068 -9999 0 -0.21 47 47
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.018 0.057 -9999 0 -0.19 50 50
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.013 0.053 -9999 0 -10000 0 0
RPS6KB1 -0.013 0.075 -9999 0 -0.24 22 22
PARD6A 0.011 0 -9999 0 -10000 0 0
CBL 0.011 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0.003 -9999 0 -10000 0 0
PIK3R1 0.007 0.038 -9999 0 -0.42 4 4
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.036 0.057 -9999 0 -0.24 22 22
HRAS/GTP -0.014 0.043 -9999 0 -10000 0 0
Insulin Receptor 0.012 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.008 0.063 -9999 0 -0.19 47 47
PRKCI -0.009 0.016 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.047 0.069 -9999 0 -0.28 22 22
SHC1 0.011 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade -0.003 0.029 -9999 0 -0.4 2 2
PI3K -0.018 0.057 -9999 0 -0.19 50 50
NCK2 0.011 0 -9999 0 -10000 0 0
RHOQ 0.011 0 -9999 0 -10000 0 0
mol:H2O2 0 0 -9999 0 -10000 0 0
HRAS/GDP 0.008 0 -9999 0 -10000 0 0
AKT2 -0.02 0.079 -9999 0 -0.26 22 22
PRKCZ -0.009 0.027 -9999 0 -0.5 1 1
SH2B2 0.011 0 -9999 0 -10000 0 0
SHC/SHIP 0.007 0.06 -9999 0 -0.18 48 48
F2RL2 -0.015 0.1 -9999 0 -0.4 32 32
TRIP10 0.011 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.016 0.001 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.014 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.028 0.001 -9999 0 -10000 0 0
RAPGEF1 0.011 0 -9999 0 -10000 0 0
RASA1 0.006 0.042 -9999 0 -0.42 5 5
NCK1 0.009 0.027 -9999 0 -0.42 2 2
CBL/APS/CAP/Crk-II -0.065 0.11 -9999 0 -0.2 206 206
TC10/GDP 0.008 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.023 0.011 -9999 0 -0.21 1 1
INPP5D 0.001 0.063 -9999 0 -0.2 48 48
SOS1 0.011 0 -9999 0 -10000 0 0
SGK1 -0.007 0.061 -9999 0 -0.8 3 3
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.011 0 -9999 0 -10000 0 0
IRS1 -0.029 0.12 -9999 0 -0.42 47 47
p62DOK/RasGAP 0.017 0.031 -9999 0 -0.4 2 2
INS 0.003 0.002 -9999 0 -10000 0 0
mol:PI-3-4-P2 0.001 0.063 -9999 0 -0.2 48 48
GRB2 0.011 0 -9999 0 -10000 0 0
EIF4EBP1 -0.016 0.078 -9999 0 -0.25 24 24
PTPRA 0.012 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.019 -9999 0 -0.42 1 1
TC10/GTP/CIP4 0.014 0 -9999 0 -10000 0 0
PDPK1 0.011 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.006 0.063 -9999 0 -0.19 47 47
Insulin Receptor/Insulin/IRS1 -0.005 0.068 -9999 0 -0.22 47 47
Insulin Receptor/Insulin/IRS3 0.011 0.002 -9999 0 -10000 0 0
Par3/Par6 0.012 0.051 -9999 0 -0.19 29 29
Coregulation of Androgen receptor activity

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
NRIP1 0.009 0.033 -9999 0 -0.42 3 3
SVIL -0.042 0.14 -9999 0 -0.42 64 64
ZNF318 0.01 0.004 -9999 0 -10000 0 0
JMJD2C 0 0.022 -9999 0 -0.13 14 14
T-DHT/AR/Ubc9 -0.027 0.1 -9999 0 -0.24 92 92
CARM1 0.011 0 -9999 0 -10000 0 0
PRDX1 0.011 0 -9999 0 -10000 0 0
PELP1 0.01 0.001 -9999 0 -10000 0 0
CTNNB1 0.011 0.001 -9999 0 -10000 0 0
AKT1 0.01 0.001 -9999 0 -10000 0 0
PTK2B 0.011 0.001 -9999 0 -10000 0 0
MED1 0.01 0.001 -9999 0 -10000 0 0
MAK -0.01 0.073 -9999 0 -0.27 36 36
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.007 0.042 -9999 0 -0.42 5 5
GSN 0.004 0.053 -9999 0 -0.42 8 8
NCOA2 -0.004 0.079 -9999 0 -0.42 18 18
NCOA6 0.011 0.002 -9999 0 -10000 0 0
DNA-PK 0.021 0.004 -9999 0 -10000 0 0
NCOA4 0.011 0 -9999 0 -10000 0 0
PIAS3 0.011 0.001 -9999 0 -10000 0 0
cell proliferation -0.008 0.024 -9999 0 -10000 0 0
XRCC5 0.01 0.001 -9999 0 -10000 0 0
UBE3A 0.011 0.002 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.047 0.12 -9999 0 -0.25 124 124
FHL2 -0.009 0.14 -9999 0 -0.92 10 10
RANBP9 0.011 0.002 -9999 0 -10000 0 0
JMJD1A 0.004 0.03 -9999 0 -0.13 22 22
CDK6 0.003 0.056 -9999 0 -0.42 9 9
TGFB1I1 -0.12 0.2 -9999 0 -0.42 151 151
T-DHT/AR/CyclinD1 -0.027 0.11 -9999 0 -0.25 90 90
XRCC6 0.01 0.001 -9999 0 -10000 0 0
T-DHT/AR -0.022 0.12 -9999 0 -0.26 97 97
CTDSP1 0.011 0 -9999 0 -10000 0 0
CTDSP2 0.01 0.002 -9999 0 -10000 0 0
BRCA1 0.011 0.002 -9999 0 -10000 0 0
TCF4 -0.006 0.081 -9999 0 -0.42 19 19
CDKN2A -0.11 0.14 -9999 0 -0.27 224 224
SRF 0.014 0.018 -9999 0 -10000 0 0
NKX3-1 -0.025 0.18 -9999 0 -0.79 21 21
KLK3 -0.005 0.036 -9999 0 -10000 0 0
TMF1 0.011 0 -9999 0 -10000 0 0
HNRNPA1 0.01 0.001 -9999 0 -10000 0 0
AOF2 0.001 0.002 -9999 0 -10000 0 0
APPL1 0.017 0.002 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.028 0.1 -9999 0 -0.24 92 92
AR -0.064 0.17 -9999 0 -0.42 90 90
UBA3 0.011 0 -9999 0 -10000 0 0
PATZ1 0.01 0.001 -9999 0 -10000 0 0
PAWR 0.011 0 -9999 0 -10000 0 0
PRKDC 0.01 0.001 -9999 0 -10000 0 0
PA2G4 0.01 0.001 -9999 0 -10000 0 0
UBE2I 0.011 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.024 0.096 -9999 0 -0.22 92 92
RPS6KA3 0.01 0.019 -9999 0 -0.42 1 1
T-DHT/AR/ARA70 -0.027 0.11 -9999 0 -0.24 92 92
LATS2 0.008 0.033 -9999 0 -0.42 3 3
T-DHT/AR/PRX1 -0.024 0.095 -9999 0 -0.22 90 90
Cyclin D3/CDK11 p58 0.008 0 -9999 0 -10000 0 0
VAV3 -0.06 0.12 -9999 0 -0.27 129 129
KLK2 -0.045 0.15 -9999 0 -0.89 14 14
CASP8 0.01 0 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.024 0.11 -9999 0 -0.23 102 102
TMPRSS2 -0.019 0.14 -9999 0 -0.68 15 15
CCND1 0.011 0 -9999 0 -10000 0 0
PIAS1 0.011 0.002 -9999 0 -10000 0 0
mol:T-DHT 0 0.019 -9999 0 -0.068 29 29
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.012 0.003 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.032 0.11 -9999 0 -0.25 99 99
CMTM2 0.008 0.022 -9999 0 -0.27 3 3
SNURF -0.022 0.11 -9999 0 -0.41 36 36
ZMIZ1 0.009 0.038 -9999 0 -0.43 3 3
CCND3 0.011 0 -9999 0 -10000 0 0
TGIF1 0.01 0.001 -9999 0 -10000 0 0
FKBP4 0.011 0.002 -9999 0 -10000 0 0
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 0.004 0.055 -9999 0 -0.21 31 31
RGS9BP -0.004 0.06 -9999 0 -0.27 24 24
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0.002 0.013 -9999 0 -0.27 1 1
mol:Na + -0.007 0.058 -9999 0 -0.24 30 30
mol:ADP 0.007 0.013 -9999 0 -0.18 2 2
GNAT2 0.007 0.022 -9999 0 -0.27 3 3
RGS9-1/Gbeta5/R9AP -0.043 0.11 -9999 0 -0.24 115 115
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.007 0.013 -9999 0 -0.15 3 3
GRK7 0.006 0.013 -9999 0 -0.27 1 1
CNGB3 -0.019 0.098 -9999 0 -0.42 29 29
Cone Metarhodopsin II/X-Arrestin 0.002 0.009 -9999 0 -0.18 1 1
mol:Ca2+ -0.004 0.052 -9999 0 -0.22 29 29
Cone PDE6 -0.033 0.093 -9999 0 -0.2 115 115
Cone Metarhodopsin II 0.006 0.01 -9999 0 -0.13 2 2
Na + (4 Units) -0.003 0.052 -9999 0 -0.22 29 29
GNAT2/GDP -0.032 0.093 -9999 0 -0.2 115 115
GNB5 0.011 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.008 0.012 -9999 0 -10000 0 0
Cone Transducin 0.004 0.059 -9999 0 -0.22 31 31
SLC24A2 0.004 0.005 -9999 0 -10000 0 0
GNB3/GNGT2 -0.003 0.075 -9999 0 -0.29 31 31
GNB3 -0.014 0.099 -9999 0 -0.42 29 29
GNAT2/GTP 0.006 0.015 -9999 0 -0.18 3 3
CNGA3 0.006 0.013 -9999 0 -0.27 1 1
ARR3 0.003 0.013 -9999 0 -0.27 1 1
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.007 0.058 -9999 0 -0.24 30 30
mol:Pi -0.043 0.11 -9999 0 -0.24 115 115
Cone CNG Channel -0.011 0.044 -9999 0 -0.19 29 29
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + 0.004 0.005 -9999 0 -10000 0 0
RGS9 -0.085 0.18 -9999 0 -0.42 115 115
PDE6C 0.004 0.005 -9999 0 -10000 0 0
GNGT2 0.008 0.033 -9999 0 -0.42 3 3
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.002 0.004 -9999 0 -10000 0 0
Glypican 2 network

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
MDK 0.01 0.012 -9999 0 -0.27 1 1
GPC2 -0.006 0.067 -9999 0 -0.27 31 31
GPC2/Midkine 0.004 0.046 -9999 0 -0.18 32 32
neuron projection morphogenesis 0.004 0.046 -9999 0 -0.17 32 32
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.01 0.042 -9999 0 -0.24 12 12
NFATC2 -0.009 0.078 -9999 0 -0.24 50 50
NFATC3 0.016 0.016 -9999 0 -10000 0 0
CD40LG -0.053 0.17 -9999 0 -0.45 48 48
PTGS2 -0.076 0.21 -9999 0 -0.48 80 80
JUNB 0.006 0.042 -9999 0 -0.42 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 0 0.008 -9999 0 -10000 0 0
CaM/Ca2+ 0 0.008 -9999 0 -10000 0 0
CALM1 0.011 0.004 -9999 0 -10000 0 0
JUN 0.006 0.046 -9999 0 -0.42 6 6
mol:Ca2+ -0.002 0.006 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.005 0.004 -9999 0 -10000 0 0
FOSL1 -0.008 0.07 -9999 0 -0.27 34 34
CREM 0.01 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.026 0.08 -9999 0 -0.28 23 23
FOS -0.13 0.2 -9999 0 -0.42 174 174
IFNG -0.057 0.18 -9999 0 -0.47 44 44
AP-1/NFAT1-c-4 -0.06 0.19 -9999 0 -0.47 57 57
FASLG -0.052 0.17 -9999 0 -0.47 39 39
NFAT1-c-4/ICER1 -0.007 0.078 -9999 0 -0.26 19 19
IL2RA -0.053 0.17 -9999 0 -0.44 49 49
FKBP12/FK506 0.008 0 -9999 0 -10000 0 0
CSF2 -0.053 0.17 -9999 0 -0.43 46 46
JunB/Fra1/NFAT1-c-4 -0.011 0.081 -9999 0 -0.25 24 24
IL4 -0.053 0.16 -9999 0 -0.45 41 41
IL2 -0.008 0.021 -9999 0 -10000 0 0
IL3 -0.011 0.015 -9999 0 -10000 0 0
FKBP1A 0.011 0 -9999 0 -10000 0 0
BATF3 0.01 0.012 -9999 0 -0.27 1 1
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.011 0 -9999 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.012 0.031 -10000 0 -0.23 8 8
CRKL -0.012 0.095 -10000 0 -0.42 10 10
mol:PIP3 -0.009 0.044 0.39 6 -10000 0 6
AKT1 0.005 0.031 0.28 6 -10000 0 6
PTK2B 0.011 0 -10000 0 -10000 0 0
RAPGEF1 -0.006 0.091 -10000 0 -0.41 9 9
RANBP10 0.011 0 -10000 0 -10000 0 0
PIK3CA 0.01 0.019 -10000 0 -0.42 1 1
HGF/MET/SHIP2 -0.029 0.1 -10000 0 -0.24 97 97
MAP3K5 0.001 0.089 -10000 0 -0.4 10 10
HGF/MET/CIN85/CBL/ENDOPHILINS -0.019 0.095 -10000 0 -0.21 97 97
AP1 -0.077 0.13 -10000 0 -0.26 174 174
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.011 0 -10000 0 -10000 0 0
apoptosis -0.23 0.35 -10000 0 -0.71 174 174
STAT3 (dimer) -0.013 0.095 -10000 0 -0.4 5 5
GAB1/CRKL/SHP2/PI3K -0.032 0.077 -10000 0 -0.41 11 11
INPP5D 0.01 0.019 -10000 0 -0.42 1 1
CBL/CRK -0.005 0.091 -10000 0 -0.47 7 7
PTPN11 0.011 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.011 0 -10000 0 -10000 0 0
PTEN 0.006 0.046 -10000 0 -0.42 6 6
ELK1 -0.003 0.018 -10000 0 -0.16 4 4
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.024 0.052 -10000 0 -0.27 5 5
PAK1 0.01 0.029 0.27 6 -10000 0 6
HGF/MET/RANBP10 -0.029 0.1 -10000 0 -0.24 97 97
HRAS -0.022 0.12 -10000 0 -0.68 4 4
DOCK1 -0.008 0.097 -10000 0 -0.44 11 11
GAB1 -0.018 0.1 -10000 0 -0.44 10 10
CRK -0.012 0.095 -10000 0 -0.44 9 9
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.08 0.17 -10000 0 -0.42 97 97
JUN 0.006 0.046 -10000 0 -0.42 6 6
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.023 0.074 -10000 0 -0.17 97 97
PIK3R1 0.007 0.038 -10000 0 -0.42 4 4
cell morphogenesis 0.001 0.11 -10000 0 -0.41 10 10
GRB2/SHC -0.008 0.066 -10000 0 -0.27 5 5
FOS -0.13 0.2 -10000 0 -0.42 174 174
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.003 0.018 -10000 0 -0.16 4 4
HGF/MET/MUC20 -0.036 0.1 -10000 0 -0.24 101 101
cell migration -0.008 0.065 -10000 0 -0.27 5 5
GRB2 0.011 0 -10000 0 -10000 0 0
CBL 0.011 0 -10000 0 -10000 0 0
MET/RANBP10 0.012 0.031 -10000 0 -0.23 8 8
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.017 0.094 -10000 0 -0.2 100 100
MET/MUC20 0.004 0.031 -10000 0 -0.24 8 8
RAP1B 0 0.086 -10000 0 -0.43 7 7
RAP1A 0 0.086 -10000 0 -0.43 7 7
HGF/MET/RANBP9 -0.029 0.1 -10000 0 -0.24 97 97
RAF1 -0.015 0.11 -10000 0 -0.64 4 4
STAT3 -0.014 0.096 -10000 0 -0.2 100 100
cell proliferation -0.021 0.13 -10000 0 -0.28 97 97
RPS6KB1 -0.002 0.028 -10000 0 -0.14 3 3
MAPK3 -0.007 0.016 -10000 0 -10000 0 0
MAPK1 -0.007 0.016 -10000 0 -10000 0 0
RANBP9 0.011 0 -10000 0 -10000 0 0
MAPK8 0.012 0.095 -10000 0 -0.42 12 12
SRC -0.01 0.089 -10000 0 -0.38 5 5
PI3K -0.01 0.072 -10000 0 -0.3 9 9
MET/Glomulin 0.007 0.027 -10000 0 -0.2 8 8
SOS1 0.011 0 -10000 0 -10000 0 0
MAP2K1 -0.009 0.1 -10000 0 -0.58 4 4
MET 0.005 0.045 -10000 0 -0.34 8 8
MAP4K1 -0.003 0.091 -10000 0 -0.46 7 7
PTK2 0.011 0 -10000 0 -10000 0 0
MAP2K2 -0.009 0.1 -10000 0 -0.58 4 4
BAD 0.01 0.029 0.27 6 -10000 0 6
MAP2K4 0.007 0.083 -10000 0 -0.36 10 10
SHP2/GRB2/SOS1/GAB1 -0.031 0.076 -10000 0 -0.44 8 8
INPPL1 0.011 0 -10000 0 -10000 0 0
PXN 0.011 0 -10000 0 -10000 0 0
SH3KBP1 0.011 0 -10000 0 -10000 0 0
HGS -0.015 0.068 -10000 0 -0.29 5 5
PLCgamma1/PKC 0.008 0 -10000 0 -10000 0 0
HGF -0.069 0.17 -10000 0 -0.42 96 96
RASA1 0.006 0.042 -10000 0 -0.42 5 5
NCK1 0.009 0.027 -10000 0 -0.42 2 2
PTPRJ 0.01 0.018 -10000 0 -0.27 2 2
NCK/PLCgamma1 -0.01 0.075 -10000 0 -0.28 7 7
PDPK1 -0.001 0.035 0.32 6 -10000 0 6
HGF/MET/SHIP -0.03 0.1 -10000 0 -0.24 98 98
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 -0.015 0.041 0.22 1 -10000 0 1
SMARCC2 0.012 0.003 -10000 0 -10000 0 0
SMARCC1 0.012 0.004 -10000 0 -10000 0 0
TBX21 0.028 0.088 -10000 0 -0.49 6 6
SUMO2 0.009 0.005 -10000 0 -10000 0 0
STAT1 (dimer) 0.016 0.012 -10000 0 -0.26 1 1
FKBP4 0.011 0 -10000 0 -10000 0 0
FKBP5 0.001 0.062 -10000 0 -0.42 11 11
GR alpha/HSP90/FKBP51/HSP90 -0.019 0.11 0.22 6 -0.26 65 71
PRL -0.03 0.28 -10000 0 -1.2 24 24
cortisol/GR alpha (dimer)/TIF2 -0.008 0.15 0.42 16 -0.38 8 24
RELA -0.015 0.069 -10000 0 -0.23 11 11
FGG -0.02 0.13 0.35 12 -0.31 17 29
GR beta/TIF2 -0.036 0.13 0.23 6 -0.3 81 87
IFNG -0.06 0.12 -10000 0 -0.56 3 3
apoptosis -0.1 0.2 0.46 10 -0.5 60 70
CREB1 0.01 0.015 -10000 0 -10000 0 0
histone acetylation 0.04 0.073 0.35 3 -0.25 5 8
BGLAP 0.038 0.062 -10000 0 -10000 0 0
GR/PKAc -0.012 0.096 0.22 4 -0.23 61 65
NF kappa B1 p50/RelA -0.025 0.12 -10000 0 -0.28 81 81
SMARCD1 0.012 0.004 -10000 0 -10000 0 0
MDM2 0.015 0.038 0.17 10 -10000 0 10
GATA3 0.001 0.064 -10000 0 -0.3 22 22
AKT1 0.005 0.001 -10000 0 -10000 0 0
CSF2 0.025 0.062 -10000 0 -10000 0 0
GSK3B 0.009 0.005 -10000 0 -10000 0 0
NR1I3 -0.075 0.19 0.46 8 -0.52 29 37
CSN2 -0.019 0.11 0.32 6 -0.29 9 15
BRG1/BAF155/BAF170/BAF60A 0.033 0.011 -10000 0 -10000 0 0
NFATC1 0.003 0.065 -10000 0 -0.41 12 12
POU2F1 0.004 0.052 -10000 0 -0.23 23 23
CDKN1A 0.027 0.1 -10000 0 -1.3 3 3
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.001 0.007 -10000 0 -10000 0 0
SFN -0.21 0.12 -10000 0 -0.27 400 400
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.096 0.15 0.22 16 -0.32 91 107
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.14 0.32 0.44 9 -0.8 88 97
JUN -0.011 0.083 -10000 0 -0.37 8 8
IL4 0.022 0.075 -10000 0 -10000 0 0
CDK5R1 0.009 0.013 -10000 0 -0.27 1 1
PRKACA 0.011 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.18 0.16 -10000 0 -0.36 174 174
GR alpha/HSP90/FKBP51/HSP90/PP5C -0.01 0.1 0.22 5 -0.23 62 67
cortisol/GR alpha (monomer) -0.01 0.17 0.48 15 -0.36 21 36
NCOA2 -0.004 0.079 -10000 0 -0.42 18 18
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.16 0.2 -10000 0 -0.44 174 174
AP-1/NFAT1-c-4 -0.12 0.16 -10000 0 -0.47 29 29
AFP 0.006 0.067 -10000 0 -0.48 2 2
SUV420H1 0.011 0 -10000 0 -10000 0 0
IRF1 0.007 0.087 0.37 2 -10000 0 2
TP53 0.024 0.042 -10000 0 -0.45 4 4
PPP5C 0.011 0 -10000 0 -10000 0 0
KRT17 -0.081 0.15 -10000 0 -0.65 10 10
KRT14 -0.015 0.11 0.42 1 -1.2 2 3
TBP 0.018 0 -10000 0 -10000 0 0
CREBBP 0.019 0.039 0.3 2 -0.28 4 6
HDAC1 0.01 0.002 -10000 0 -10000 0 0
HDAC2 0.01 0.001 -10000 0 -10000 0 0
AP-1 -0.12 0.16 -10000 0 -0.47 29 29
MAPK14 0.009 0.006 -10000 0 -10000 0 0
MAPK10 -0.086 0.18 -10000 0 -0.42 115 115
MAPK11 0.008 0.027 -10000 0 -0.42 2 2
KRT5 -0.097 0.14 -10000 0 -0.68 6 6
interleukin-1 receptor activity -0.001 0.001 -10000 0 -10000 0 0
NCOA1 0.011 0.019 -10000 0 -0.41 1 1
STAT1 0.016 0.012 -10000 0 -0.27 1 1
CGA 0.023 0.07 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.016 0.098 0.29 4 -0.44 4 8
MAPK3 0.009 0.006 -10000 0 -10000 0 0
MAPK1 0.009 0.006 -10000 0 -10000 0 0
ICAM1 0 0.12 -10000 0 -0.39 10 10
NFKB1 -0.016 0.071 -10000 0 -0.2 29 29
MAPK8 0.01 0.086 0.25 1 -0.32 8 9
MAPK9 0.009 0.006 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.11 0.21 0.46 10 -0.52 63 73
BAX 0.033 0.034 -10000 0 -10000 0 0
POMC -0.04 0.23 -10000 0 -1.3 11 11
EP300 0.02 0.033 0.3 2 -0.23 3 5
cortisol/GR alpha (dimer)/p53 0.009 0.15 0.44 15 -0.37 2 17
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.03 0.16 3 -10000 0 3
SGK1 0.027 0.11 -10000 0 -1.3 3 3
IL13 -0.036 0.1 -10000 0 -0.62 1 1
IL6 -0.029 0.22 -10000 0 -0.89 23 23
PRKACG 0.003 0.005 -10000 0 -10000 0 0
IL5 -0.036 0.089 -10000 0 -0.54 1 1
IL2 -0.062 0.12 -10000 0 -0.5 4 4
CDK5 0.01 0.004 -10000 0 -10000 0 0
PRKACB 0.006 0.046 -10000 0 -0.42 6 6
HSP90AA1 0.011 0 -10000 0 -10000 0 0
IL8 -0.017 0.12 -10000 0 -0.39 13 13
CDK5R1/CDK5 0.013 0.012 -10000 0 -0.18 1 1
NF kappa B1 p50/RelA/PKAc 0.001 0.096 -10000 0 -0.31 16 16
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.01 0.13 0.39 18 -0.34 2 20
SMARCA4 0.012 0.003 -10000 0 -10000 0 0
chromatin remodeling 0.004 0.11 0.3 8 -0.48 4 12
NF kappa B1 p50/RelA/Cbp 0.011 0.11 0.39 1 -0.34 15 16
JUN (dimer) -0.011 0.083 -10000 0 -0.36 8 8
YWHAH 0.011 0 -10000 0 -10000 0 0
VIPR1 0.03 0.084 -10000 0 -0.61 3 3
NR3C1 -0.044 0.17 0.3 10 -0.4 80 90
NR4A1 -0.089 0.19 -10000 0 -0.42 121 121
TIF2/SUV420H1 0.005 0.055 -10000 0 -0.29 18 18
MAPKKK cascade -0.1 0.2 0.46 10 -0.5 60 70
cortisol/GR alpha (dimer)/Src-1 0.005 0.15 0.41 18 -0.35 3 21
PBX1 -0.014 0.1 -10000 0 -0.34 42 42
POU1F1 -0.006 0.055 -10000 0 -0.25 24 24
SELE -0.11 0.35 -10000 0 -0.93 78 78
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.004 0.11 0.3 8 -0.49 4 12
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.01 0.13 0.39 18 -0.34 2 20
mol:cortisol 0.009 0.069 0.26 15 -10000 0 15
MMP1 -0.069 0.083 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.047 0.12 -9999 0 -0.28 107 107
AKT1 0.018 0.15 -9999 0 -0.52 30 30
PTK2B -0.027 0.15 -9999 0 -0.56 28 28
VEGFR2 homodimer/Frs2 -0.005 0.14 -9999 0 -0.57 28 28
CAV1 -0.082 0.18 -9999 0 -0.42 111 111
CALM1 0.011 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.005 0.13 -9999 0 -0.52 28 28
endothelial cell proliferation 0.014 0.15 -9999 0 -0.46 37 37
mol:Ca2+ -0.003 0.14 -9999 0 -0.56 28 28
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.011 0.12 -9999 0 -0.49 28 28
RP11-342D11.1 -0.01 0.14 -9999 0 -0.57 28 28
CDH5 0.005 0.05 -9999 0 -0.42 7 7
VEGFA homodimer 0.028 0.01 -9999 0 -0.2 1 1
SHC1 0.011 0 -9999 0 -10000 0 0
SHC2 -0.048 0.15 -9999 0 -0.42 70 70
HRAS/GDP -0.034 0.11 -9999 0 -0.48 28 28
SH2D2A 0.001 0.052 -9999 0 -0.27 18 18
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.034 0.11 -9999 0 -0.48 28 28
VEGFR2 homodimer/VEGFA homodimer/TsAd 0 0.13 -9999 0 -0.53 28 28
VEGFR1 homodimer 0.01 0.019 -9999 0 -0.42 1 1
SHC/GRB2/SOS1 -0.038 0.13 -9999 0 -0.53 28 28
GRB10 -0.003 0.15 -9999 0 -0.57 28 28
PTPN11 0.011 0 -9999 0 -10000 0 0
GRB2 0.011 0 -9999 0 -10000 0 0
PAK1 0.011 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.013 0.13 -9999 0 -0.52 28 28
HRAS 0.011 0 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.018 0.12 -9999 0 -0.39 28 28
HIF1A 0.011 0 -9999 0 -10000 0 0
FRS2 0.011 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.01 0.12 -9999 0 -0.49 28 28
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 -0.007 0.085 -9999 0 -0.42 21 21
Nck/Pak 0.015 0.019 -9999 0 -0.29 2 2
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.005 0.13 -9999 0 -0.52 28 28
mol:GDP -0.037 0.12 -9999 0 -0.52 28 28
mol:NADP 0.022 0.12 -9999 0 -0.41 28 28
eNOS/Hsp90 0.026 0.11 -9999 0 -0.39 28 28
PIK3R1 0.007 0.038 -9999 0 -0.42 4 4
mol:IP3 -0.003 0.15 -9999 0 -0.57 28 28
HIF1A/ARNT 0.016 0 -9999 0 -10000 0 0
SHB 0.011 0 -9999 0 -10000 0 0
VEGFA 0.012 0.001 -9999 0 -10000 0 0
VEGFC 0.004 0.053 -9999 0 -0.42 8 8
FAK1/Vinculin -0.014 0.16 -9999 0 -0.61 28 28
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.011 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.032 0.16 -9999 0 -0.6 28 28
PTPN6 0.01 0.012 -9999 0 -0.27 1 1
EPAS1 -0.001 0.084 -9999 0 -0.33 29 29
mol:L-citrulline 0.022 0.12 -9999 0 -0.41 28 28
ITGAV 0.011 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.019 -9999 0 -0.42 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.011 0.12 -9999 0 -0.49 28 28
VEGFR2 homodimer/VEGFA homodimer -0.01 0.16 -9999 0 -0.62 28 28
VEGFR2/3 heterodimer -0.015 0.15 -9999 0 -0.45 46 46
VEGFB 0.011 0 -9999 0 -10000 0 0
MAPK11 -0.005 0.16 -9999 0 -0.58 29 29
VEGFR2 homodimer -0.01 0.16 -9999 0 -0.64 29 29
FLT1 0.01 0.019 -9999 0 -0.42 1 1
NEDD4 -0.024 0.12 -9999 0 -0.41 44 44
MAPK3 -0.008 0.14 -9999 0 -0.47 36 36
MAPK1 -0.008 0.14 -9999 0 -0.47 36 36
VEGFA145/NRP2 0.002 0.066 -9999 0 -0.28 26 26
VEGFR1/2 heterodimer -0.005 0.14 -9999 0 -0.58 28 28
KDR -0.01 0.16 -9999 0 -0.65 29 29
VEGFA165/NRP1/VEGFR2 homodimer -0.013 0.16 -9999 0 -0.57 31 31
SRC 0.011 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process -0.008 0.15 -9999 0 -0.48 36 36
PI3K 0.008 0.16 -9999 0 -0.59 30 30
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.004 0.13 -9999 0 -0.53 28 28
FES -0.004 0.15 -9999 0 -0.57 29 29
GAB1 -0.039 0.14 -9999 0 -0.62 28 28
VEGFR2 homodimer/VEGFA homodimer/Src 0.005 0.13 -9999 0 -0.52 28 28
CTNNB1 0.011 0 -9999 0 -10000 0 0
SOS1 0.011 0 -9999 0 -10000 0 0
ARNT 0.011 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.007 0.14 -9999 0 -0.42 41 41
VEGFR2 homodimer/VEGFA homodimer/Yes 0.005 0.13 -9999 0 -0.52 28 28
PI3K/GAB1 0.019 0.15 -9999 0 -0.54 30 30
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.015 0.12 -9999 0 -0.48 28 28
PRKACA 0.011 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.01 0.14 -9999 0 -0.57 28 28
HSP90AA1 0.011 0 -9999 0 -10000 0 0
CDC42 -0.004 0.15 -9999 0 -0.58 28 28
actin cytoskeleton reorganization 0 0.13 -9999 0 -0.52 28 28
PTK2 -0.021 0.17 -9999 0 -0.66 28 28
EDG1 -0.01 0.14 -9999 0 -0.57 28 28
mol:DAG -0.003 0.15 -9999 0 -0.57 28 28
CaM/Ca2+ 0.002 0.14 -9999 0 -0.52 28 28
MAP2K3 0 0.14 -9999 0 -0.55 28 28
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.003 0.15 -9999 0 -0.59 28 28
PLCG1 -0.004 0.15 -9999 0 -0.58 28 28
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.011 0.12 -9999 0 -0.49 28 28
IQGAP1 0.011 0 -9999 0 -10000 0 0
YES1 0.011 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.005 0.13 -9999 0 -0.52 28 28
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.005 0.13 -9999 0 -0.52 28 28
cell migration 0.008 0.15 -9999 0 -0.54 28 28
mol:PI-3-4-5-P3 0.01 0.15 -9999 0 -0.54 30 30
FYN 0.011 0 -9999 0 -10000 0 0
VEGFB/NRP1 -0.003 0.14 -9999 0 -0.53 28 28
mol:NO 0.022 0.12 -9999 0 -0.41 28 28
PXN 0.011 0 -9999 0 -10000 0 0
HRAS/GTP -0.034 0.11 -9999 0 -0.48 28 28
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.003 0.15 -9999 0 -0.59 28 28
VHL 0.01 0.019 -9999 0 -0.42 1 1
ITGB3 -0.078 0.17 -9999 0 -0.41 107 107
NOS3 0.02 0.13 -9999 0 -0.47 28 28
VEGFR2 homodimer/VEGFA homodimer/Sck -0.026 0.15 -9999 0 -0.55 28 28
RAC1 0.011 0 -9999 0 -10000 0 0
PRKCA -0.01 0.15 -9999 0 -0.52 33 33
PRKCB -0.009 0.15 -9999 0 -0.52 33 33
VCL 0.011 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.009 0.14 -9999 0 -0.57 28 28
VEGFR1/2 heterodimer/VEGFA homodimer 0.004 0.13 -9999 0 -0.53 28 28
VEGFA165/NRP2 0.002 0.066 -9999 0 -0.28 26 26
MAPKKK cascade 0.018 0.13 -9999 0 -0.48 28 28
NRP2 -0.011 0.094 -9999 0 -0.42 26 26
VEGFC homodimer 0.004 0.053 -9999 0 -0.42 8 8
NCK1 0.009 0.027 -9999 0 -0.42 2 2
ROCK1 0.011 0 -9999 0 -10000 0 0
FAK1/Paxillin -0.014 0.16 -9999 0 -0.61 28 28
MAP3K13 -0.006 0.15 -9999 0 -0.58 28 28
PDPK1 0.017 0.14 -9999 0 -0.48 30 30
IL2 signaling events mediated by STAT5

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
GAB2 0.007 0.042 -9999 0 -0.42 5 5
ELF1 0.01 0.044 -9999 0 -0.39 5 5
CCNA2 -0.069 0.13 -9999 0 -0.27 144 144
PIK3CA 0.01 0.019 -9999 0 -0.42 1 1
JAK3 0.01 0.022 -9999 0 -0.27 3 3
PIK3R1 0.008 0.038 -9999 0 -0.42 4 4
JAK1 0.009 0.033 -9999 0 -0.42 3 3
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.052 0.044 -9999 0 -0.51 1 1
SHC1 0.011 0 -9999 0 -10000 0 0
SP1 -0.041 0.12 -9999 0 -0.31 92 92
IL2RA 0.015 0.051 -9999 0 -0.35 5 5
IL2RB 0.01 0.019 -9999 0 -0.42 1 1
SOS1 0.011 0 -9999 0 -10000 0 0
IL2RG 0.007 0.038 -9999 0 -0.31 7 7
G1/S transition of mitotic cell cycle -0.094 0.26 -9999 0 -0.64 92 92
PTPN11 0.011 0 -9999 0 -10000 0 0
CCND2 -0.098 0.26 -9999 0 -0.66 92 92
LCK 0.008 0.031 -9999 0 -0.3 5 5
GRB2 0.011 0 -9999 0 -10000 0 0
IL2 -0.004 0.05 -9999 0 -0.27 17 17
CDK6 0.003 0.056 -9999 0 -0.42 9 9
CCND3 0.055 0.04 -9999 0 -0.44 1 1
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.015 0.08 -10000 0 -0.3 24 24
IKBKB 0.028 0.045 0.16 1 -0.18 1 2
AKT1 0.007 0.061 0.18 5 -0.19 22 27
IKBKG 0.03 0.046 0.16 1 -0.18 1 2
CALM1 0.023 0.075 0.17 62 -0.25 16 78
PIK3CA 0.01 0.019 -10000 0 -0.42 1 1
MAP3K1 0.005 0.1 -10000 0 -0.41 24 24
MAP3K7 0.011 0 -10000 0 -10000 0 0
mol:Ca2+ 0.018 0.079 0.18 62 -0.26 16 78
DOK1 0.011 0 -10000 0 -10000 0 0
AP-1 -0.004 0.075 0.14 35 -0.19 24 59
LYN 0.011 0 -10000 0 -10000 0 0
BLNK 0.009 0.023 -10000 0 -0.34 2 2
SHC1 0.011 0 -10000 0 -10000 0 0
BCR complex -0.018 0.084 -10000 0 -0.21 75 75
CD22 -0.054 0.12 -10000 0 -0.47 29 29
CAMK2G 0.028 0.072 0.17 62 -0.23 16 78
CSNK2A1 0.011 0 -10000 0 -10000 0 0
INPP5D 0.01 0.019 -10000 0 -0.42 1 1
SHC/GRB2/SOS1 -0.015 0.04 -10000 0 -0.33 1 1
GO:0007205 0.018 0.079 0.18 62 -0.27 16 78
SYK 0.01 0.012 -10000 0 -0.27 1 1
ELK1 0.023 0.076 0.17 62 -0.25 16 78
NFATC1 0.012 0.088 0.18 4 -0.31 25 29
B-cell antigen/BCR complex -0.018 0.084 -10000 0 -0.21 75 75
PAG1/CSK 0.015 0.019 -10000 0 -0.29 2 2
NFKBIB 0.019 0.02 0.082 1 -0.12 1 2
HRAS 0.023 0.067 0.16 6 -0.23 16 22
NFKBIA 0.019 0.02 0.082 1 -0.12 1 2
NF-kappa-B/RelA/I kappa B beta 0.022 0.019 0.084 1 -0.14 1 2
RasGAP/Csk 0.004 0.065 -10000 0 -0.19 32 32
mol:GDP 0.017 0.075 0.17 62 -0.25 16 78
PTEN 0.006 0.046 -10000 0 -0.42 6 6
CD79B -0.006 0.083 -10000 0 -0.42 20 20
NF-kappa-B/RelA/I kappa B alpha 0.022 0.019 0.084 1 -0.14 1 2
GRB2 0.011 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 0.016 0.11 -10000 0 -0.45 21 21
PIK3R1 0.007 0.038 -10000 0 -0.42 4 4
mol:IP3 0.018 0.08 0.18 62 -0.27 16 78
CSK 0.011 0 -10000 0 -10000 0 0
FOS -0.036 0.12 0.17 39 -0.29 20 59
CHUK 0.03 0.046 0.16 1 -0.18 1 2
IBTK 0.011 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.009 0.041 -10000 0 -0.3 2 2
PTPN6 -0.028 0.13 -10000 0 -0.46 27 27
RELA 0.011 0 -10000 0 -10000 0 0
BCL2A1 0.019 0.015 -10000 0 -10000 0 0
VAV2 -0.002 0.099 -10000 0 -0.43 20 20
ubiquitin-dependent protein catabolic process 0.022 0.02 0.085 1 -0.12 1 2
BTK -0.009 0.093 -10000 0 -1 4 4
CD19 -0.033 0.093 -10000 0 -0.41 23 23
MAP4K1 0.004 0.043 -10000 0 -0.27 12 12
CD72 0.009 0.022 -10000 0 -0.27 3 3
PAG1 0.009 0.027 -10000 0 -0.42 2 2
MAPK14 0.011 0.092 -10000 0 -0.36 23 23
SH3BP5 -0.052 0.15 -10000 0 -0.42 75 75
PIK3AP1 0.026 0.087 0.2 60 -0.3 16 76
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.016 0.05 -10000 0 -0.31 5 5
RAF1 0.027 0.064 0.17 2 -0.21 16 18
RasGAP/p62DOK/SHIP -0.021 0.05 -10000 0 -0.29 2 2
CD79A -0.022 0.092 -10000 0 -0.28 56 56
re-entry into mitotic cell cycle -0.003 0.074 0.14 35 -0.19 24 59
RASA1 0.006 0.042 -10000 0 -0.42 5 5
MAPK3 0.035 0.058 0.18 1 -0.25 2 3
MAPK1 0.035 0.058 0.18 1 -0.25 2 3
CD72/SHP1 -0.021 0.12 -10000 0 -0.45 25 25
NFKB1 0.01 0.019 -10000 0 -0.42 1 1
MAPK8 0.01 0.095 -10000 0 -0.35 25 25
actin cytoskeleton organization 0.005 0.089 -10000 0 -0.38 20 20
NF-kappa-B/RelA 0.047 0.036 0.16 1 -0.18 1 2
Calcineurin -0.008 0.04 -10000 0 -0.21 17 17
PI3K -0.036 0.087 -10000 0 -0.36 24 24
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.023 0.09 0.2 66 -0.31 16 82
SOS1 0.011 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.037 0.2 -10000 0 -0.69 41 41
DAPP1 -0.065 0.22 -10000 0 -0.78 41 41
cytokine secretion 0.013 0.084 0.18 4 -0.29 25 29
mol:DAG 0.018 0.08 0.18 62 -0.27 16 78
PLCG2 0.01 0.019 -10000 0 -0.42 1 1
MAP2K1 0.031 0.061 0.19 1 -0.28 2 3
B-cell antigen/BCR complex/FcgammaRIIB -0.008 0.073 -10000 0 -0.24 27 27
mol:PI-3-4-5-P3 -0.029 0.068 0.21 5 -0.26 24 29
ETS1 0.031 0.07 0.17 62 -0.21 16 78
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.007 0.061 -10000 0 -0.19 25 25
B-cell antigen/BCR complex/LYN -0.028 0.094 -10000 0 -0.42 25 25
MALT1 0.011 0 -10000 0 -10000 0 0
TRAF6 0.01 0 -10000 0 -10000 0 0
RAC1 0.005 0.093 -10000 0 -0.4 20 20
B-cell antigen/BCR complex/LYN/SYK -0.035 0.11 -10000 0 -0.45 24 24
CARD11 0.019 0.078 0.17 60 -0.25 16 76
FCGR2B 0.008 0.035 -10000 0 -0.38 4 4
PPP3CA 0.011 0 -10000 0 -10000 0 0
BCL10 0.011 0 -10000 0 -10000 0 0
IKK complex 0.02 0.023 0.11 1 -10000 0 1
PTPRC 0.001 0.063 -10000 0 -0.4 12 12
PDPK1 0.002 0.057 0.16 5 -0.18 22 27
PPP3CB 0.011 0 -10000 0 -10000 0 0
PPP3CC 0.008 0.033 -10000 0 -0.42 3 3
POU2F2 0.02 0.014 -10000 0 -0.095 1 1
Regulation of Androgen receptor activity

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
HDAC1 0.018 0 -9999 0 -10000 0 0
SMARCC1 0.006 0.016 -9999 0 -10000 0 0
REL 0.01 0.001 -9999 0 -10000 0 0
HDAC7 0.022 0.06 -9999 0 -0.27 3 3
JUN 0.006 0.046 -9999 0 -0.42 6 6
EP300 0.011 0 -9999 0 -10000 0 0
KAT2B 0.002 0.059 -9999 0 -0.42 10 10
KAT5 0.011 0 -9999 0 -10000 0 0
MAPK14 -0.005 0.063 -9999 0 -0.17 65 65
FOXO1 0.008 0.033 -9999 0 -0.42 3 3
T-DHT/AR 0.021 0.065 -9999 0 -0.25 8 8
MAP2K6 -0.024 0.093 -9999 0 -0.27 65 65
BRM/BAF57 0.007 0.051 -9999 0 -0.28 15 15
MAP2K4 0.011 0.019 -9999 0 -0.41 1 1
SMARCA2 -0.002 0.072 -9999 0 -0.42 15 15
PDE9A -0.02 0.1 -9999 0 -0.99 4 4
NCOA2 -0.004 0.079 -9999 0 -0.42 18 18
CEBPA 0.007 0.035 -9999 0 -0.38 4 4
EHMT2 0.011 0 -9999 0 -10000 0 0
cell proliferation 0.015 0.11 -9999 0 -0.35 17 17
NR0B1 -0.005 0.05 -9999 0 -0.27 17 17
EGR1 -0.061 0.16 -9999 0 -0.42 86 86
RXRs/9cRA -0.004 0.069 -9999 0 -0.21 48 48
AR/RACK1/Src 0.014 0.058 -9999 0 -0.27 3 3
AR/GR -0.056 0.12 -9999 0 -0.22 166 166
GNB2L1 0.011 0.002 -9999 0 -10000 0 0
PKN1 0.011 0 -9999 0 -10000 0 0
RCHY1 0.011 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -9999 0 -10000 0 0
MAPK8 0.016 0.033 -9999 0 -0.28 6 6
T-DHT/AR/TIF2/CARM1 0.008 0.076 -9999 0 -0.31 13 13
SRC 0.015 0.05 -9999 0 -0.2 5 5
NR3C1 -0.068 0.16 -9999 0 -0.42 94 94
KLK3 -0.034 0.088 -9999 0 -0.46 1 1
APPBP2 0.011 0.002 -9999 0 -10000 0 0
TRIM24 0.011 0.001 -9999 0 -10000 0 0
T-DHT/AR/TIP60 0.007 0.055 -9999 0 -0.25 5 5
TMPRSS2 -0.03 0.14 -9999 0 -1 8 8
RXRG -0.035 0.13 -9999 0 -0.39 57 57
mol:9cRA 0 0 -9999 0 -10000 0 0
RXRA 0.011 0 -9999 0 -10000 0 0
RXRB 0.011 0 -9999 0 -10000 0 0
CARM1 0.011 0.002 -9999 0 -10000 0 0
NR2C2 0.002 0.059 -9999 0 -0.42 10 10
KLK2 0.005 0.12 -9999 0 -0.54 19 19
AR -0.022 0.099 -9999 0 -0.22 90 90
SENP1 0.011 0 -9999 0 -10000 0 0
HSP90AA1 0.011 0 -9999 0 -10000 0 0
MDM2 0.01 0.001 -9999 0 -10000 0 0
SRY 0 0.001 -9999 0 -10000 0 0
GATA2 -0.029 0.12 -9999 0 -0.42 48 48
MYST2 0.011 0 -9999 0 -10000 0 0
HOXB13 -0.18 0.13 -9999 0 -0.27 345 345
T-DHT/AR/RACK1/Src 0.013 0.056 -9999 0 -0.32 2 2
positive regulation of transcription -0.029 0.12 -9999 0 -0.42 48 48
DNAJA1 0.011 0.002 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.022 0 -9999 0 -10000 0 0
NCOA1 0.013 0.02 -9999 0 -0.45 1 1
SPDEF -0.1 0.15 -9999 0 -0.29 200 200
T-DHT/AR/TIF2 0.011 0.071 -9999 0 -0.29 15 15
T-DHT/AR/Hsp90 0.008 0.056 -9999 0 -0.25 5 5
GSK3B 0.011 0.001 -9999 0 -10000 0 0
NR2C1 0.01 0 -9999 0 -10000 0 0
mol:T-DHT 0.01 0.054 -9999 0 -0.22 6 6
SIRT1 0.009 0.027 -9999 0 -0.42 2 2
ZMIZ2 0.01 0.001 -9999 0 -10000 0 0
POU2F1 0.02 0.012 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 0.003 0.061 -9999 0 -0.26 6 6
CREBBP 0.01 0.019 -9999 0 -0.42 1 1
SMARCE1 0.011 0.001 -9999 0 -10000 0 0
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.006 0.043 -10000 0 -0.22 18 18
cell-cell adhesion 0.029 0.064 0.31 8 -10000 0 8
Ephrin B/EPHB2/RasGAP 0.008 0.068 -10000 0 -0.19 53 53
ITSN1 0.011 0 -10000 0 -10000 0 0
PIK3CA 0.01 0.019 -10000 0 -0.42 1 1
SHC1 0.011 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.007 0.036 -10000 0 -0.17 20 20
Ephrin B1/EPHB1 -0.009 0.073 -10000 0 -0.24 47 47
HRAS/GDP -0.029 0.067 -10000 0 -0.31 9 9
Ephrin B/EPHB1/GRB7 -0.017 0.095 -10000 0 -0.21 89 89
Endophilin/SYNJ1 0.009 0.061 -10000 0 -0.18 48 48
KRAS 0.01 0.012 -10000 0 -0.27 1 1
Ephrin B/EPHB1/Src -0.009 0.091 -10000 0 -0.2 88 88
endothelial cell migration -0.003 0.025 -10000 0 -0.19 9 9
GRB2 0.011 0 -10000 0 -10000 0 0
GRB7 -0.007 0.07 -10000 0 -0.28 31 31
PAK1 0.012 0.066 -10000 0 -0.36 3 3
HRAS 0.011 0 -10000 0 -10000 0 0
RRAS 0.008 0.062 -10000 0 -0.18 49 49
DNM1 0.008 0.033 -10000 0 -0.42 3 3
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.009 0.086 -10000 0 -0.19 88 88
lamellipodium assembly -0.029 0.064 -10000 0 -0.31 8 8
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.008 0.088 -10000 0 -0.22 49 49
PIK3R1 0.007 0.038 -10000 0 -0.42 4 4
EPHB2 0.01 0.018 -10000 0 -0.27 2 2
EPHB3 -0.002 0.063 -10000 0 -0.31 20 20
EPHB1 -0.028 0.12 -10000 0 -0.41 47 47
EPHB4 0.01 0.019 -10000 0 -0.42 1 1
mol:GDP -0.001 0.083 -10000 0 -0.23 40 40
Ephrin B/EPHB2 0.004 0.065 -10000 0 -0.2 48 48
Ephrin B/EPHB3 -0.001 0.078 -10000 0 -0.22 51 51
JNK cascade 0.009 0.063 -10000 0 -0.19 47 47
Ephrin B/EPHB1 -0.015 0.09 -10000 0 -0.21 88 88
RAP1/GDP 0.01 0.076 -10000 0 -0.28 9 9
EFNB2 0.008 0.033 -10000 0 -0.42 3 3
EFNB3 -0.028 0.12 -10000 0 -0.42 46 46
EFNB1 0.011 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.002 0.068 -10000 0 -0.21 49 49
RAP1B 0.011 0 -10000 0 -10000 0 0
RAP1A 0.011 0 -10000 0 -10000 0 0
CDC42/GTP -0.033 0.073 -10000 0 -0.36 8 8
Rap1/GTP -0.028 0.062 -10000 0 -0.31 8 8
axon guidance 0.006 0.043 -10000 0 -0.22 18 18
MAPK3 0.004 0.079 -10000 0 -0.33 7 7
MAPK1 0.004 0.079 -10000 0 -0.33 7 7
Rac1/GDP 0.006 0.078 -10000 0 -0.21 40 40
actin cytoskeleton reorganization -0.023 0.051 -10000 0 -0.25 8 8
CDC42/GDP 0.006 0.078 -10000 0 -0.21 40 40
PI3K 0.021 0.028 -10000 0 -0.19 9 9
EFNA5 -0.002 0.072 -10000 0 -0.4 16 16
Ephrin B2/EPHB4 0.012 0.022 -10000 0 -0.24 4 4
Ephrin B/EPHB2/Intersectin/N-WASP 0.008 0.067 -10000 0 -0.2 48 48
CDC42 0.011 0 -10000 0 -10000 0 0
RAS family/GTP -0.027 0.061 -10000 0 -0.31 8 8
PTK2 0.006 0.018 -10000 0 -10000 0 0
MAP4K4 0.009 0.064 -10000 0 -0.19 47 47
SRC 0.011 0 -10000 0 -10000 0 0
KALRN 0.006 0.042 -10000 0 -0.42 5 5
Intersectin/N-WASP 0.016 0 -10000 0 -10000 0 0
neuron projection morphogenesis 0.018 0.08 -10000 0 -0.28 10 10
MAP2K1 -0.001 0.083 -10000 0 -0.35 7 7
WASL 0.011 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.005 0.069 -10000 0 -0.21 47 47
cell migration -0.003 0.097 -10000 0 -0.38 8 8
NRAS 0.011 0 -10000 0 -10000 0 0
SYNJ1 0.009 0.061 -10000 0 -0.18 48 48
PXN 0.011 0 -10000 0 -10000 0 0
TF 0.005 0.069 -10000 0 -0.27 6 6
HRAS/GTP -0.031 0.068 -10000 0 -0.34 8 8
Ephrin B1/EPHB1-2 -0.001 0.066 -10000 0 -0.21 46 46
cell adhesion mediated by integrin 0.016 0.065 0.21 48 -10000 0 48
RAC1 0.011 0 -10000 0 -10000 0 0
mol:GTP -0.006 0.086 -10000 0 -0.36 8 8
RAC1-CDC42/GTP -0.032 0.07 -10000 0 -0.3 17 17
RASA1 0.006 0.042 -10000 0 -0.42 5 5
RAC1-CDC42/GDP 0.01 0.076 -10000 0 -0.28 9 9
ruffle organization 0.009 0.08 -10000 0 -0.31 8 8
NCK1 0.009 0.027 -10000 0 -0.42 2 2
receptor internalization 0.013 0.062 -10000 0 -0.26 4 4
Ephrin B/EPHB2/KALRN 0.008 0.07 -10000 0 -0.2 51 51
ROCK1 0.013 0.032 -10000 0 -0.21 5 5
RAS family/GDP -0.022 0.051 -10000 0 -0.25 8 8
Rac1/GTP -0.03 0.066 -10000 0 -0.33 8 8
Ephrin B/EPHB1/Src/Paxillin -0.012 0.093 -10000 0 -0.21 88 88
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.098 0.19 -9999 0 -0.42 131 131
CDC42/GTP -0.035 0.11 -9999 0 -0.36 17 17
PLCG1 -0.036 0.11 -9999 0 -0.38 16 16
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.011 0 -9999 0 -10000 0 0
GNAI3 0.011 0 -9999 0 -10000 0 0
G12/G13 0.016 0 -9999 0 -10000 0 0
cell migration -0.034 0.1 -9999 0 -0.35 17 17
S1PR5 0.002 0.05 -9999 0 -0.28 15 15
S1PR4 0.009 0.023 -9999 0 -0.34 2 2
MAPK3 -0.036 0.11 -9999 0 -0.38 16 16
MAPK1 -0.036 0.11 -9999 0 -0.38 16 16
S1P/S1P5/Gi -0.046 0.12 -9999 0 -0.22 133 133
GNAI1 0.002 0.059 -9999 0 -0.42 10 10
CDC42/GDP 0.008 0 -9999 0 -10000 0 0
S1P/S1P5/G12 0.01 0.028 -9999 0 -0.15 15 15
RHOA 0.023 0.011 -9999 0 -0.19 1 1
S1P/S1P4/Gi -0.044 0.12 -9999 0 -0.22 132 132
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.011 0.094 -9999 0 -0.42 26 26
S1P/S1P4/G12/G13 0.02 0.012 -9999 0 -0.21 1 1
GNA12 0.011 0 -9999 0 -10000 0 0
GNA13 0.011 0 -9999 0 -10000 0 0
CDC42 0.011 0 -9999 0 -10000 0 0
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.011 0.046 -9999 0 -0.23 18 18
EPHB2 0.01 0.018 -9999 0 -0.27 2 2
Syndecan-2/TACI 0.006 0.048 -9999 0 -0.19 27 27
LAMA1 -0.11 0.14 -9999 0 -0.27 223 223
Syndecan-2/alpha2 ITGB1 0.015 0.062 -9999 0 -0.21 34 34
HRAS 0.011 0 -9999 0 -10000 0 0
Syndecan-2/CASK 0.005 0.039 -9999 0 -0.24 13 13
ITGA5 0.01 0.019 -9999 0 -0.42 1 1
BAX 0.022 0.041 -9999 0 -10000 0 0
EPB41 0.011 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion 0.012 0.035 -9999 0 -0.21 13 13
LAMA3 0 0.067 -9999 0 -0.42 13 13
EZR 0.011 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.029 0.12 -9999 0 -0.42 48 48
Syndecan-2/MMP2 0 0.07 -9999 0 -0.24 37 37
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 0.009 0.046 -9999 0 -0.29 12 12
dendrite morphogenesis 0.012 0.04 -9999 0 -0.22 15 15
Syndecan-2/GM-CSF 0.008 0.042 -9999 0 -0.21 17 17
determination of left/right symmetry 0.008 0.047 -9999 0 -0.28 13 13
Syndecan-2/PKC delta 0.013 0.039 -9999 0 -0.23 13 13
GNB2L1 0.011 0 -9999 0 -10000 0 0
MAPK3 0.015 0.037 -9999 0 -0.2 13 13
MAPK1 0.015 0.037 -9999 0 -0.2 13 13
Syndecan-2/RACK1 0.018 0.034 -9999 0 -0.19 13 13
NF1 0.008 0.033 -9999 0 -0.42 3 3
FGFR/FGF/Syndecan-2 0.008 0.047 -9999 0 -0.28 13 13
ITGA2 0.001 0.065 -9999 0 -0.42 12 12
MAPK8 0.017 0.047 -9999 0 -0.23 18 18
Syndecan-2/alpha2/beta1 Integrin -0.038 0.08 -9999 0 -0.24 26 26
Syndecan-2/Kininogen 0.001 0.051 -9999 0 -0.17 38 38
ITGB1 0.011 0 -9999 0 -10000 0 0
SRC 0.023 0.032 -9999 0 -0.18 13 13
Syndecan-2/CASK/Protein 4.1 0.012 0.036 -9999 0 -0.21 13 13
extracellular matrix organization 0.012 0.041 -9999 0 -0.23 14 14
actin cytoskeleton reorganization 0.01 0.046 -9999 0 -0.23 18 18
Syndecan-2/Caveolin-2/Ras -0.002 0.076 -9999 0 -0.21 59 59
Syndecan-2/Laminin alpha3 0.007 0.057 -9999 0 -0.24 25 25
Syndecan-2/RasGAP 0.021 0.038 -9999 0 -0.18 18 18
alpha5/beta1 Integrin 0.015 0.013 -9999 0 -0.29 1 1
PRKCD 0.011 0 -9999 0 -10000 0 0
Syndecan-2 dimer 0.012 0.041 -9999 0 -0.22 15 15
GO:0007205 0.003 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.027 0.037 -9999 0 -0.17 18 18
RHOA 0.011 0 -9999 0 -10000 0 0
SDCBP 0.011 0 -9999 0 -10000 0 0
TNFRSF13B 0 0.047 -9999 0 -0.27 15 15
RASA1 0.006 0.042 -9999 0 -0.42 5 5
alpha2/beta1 Integrin 0.009 0.046 -9999 0 -0.29 12 12
Syndecan-2/Synbindin 0.013 0.039 -9999 0 -0.23 13 13
TGFB1 0.01 0.019 -9999 0 -0.42 1 1
CASP3 0.019 0.036 -9999 0 -0.2 13 13
FN1 0.006 0.042 -9999 0 -0.42 5 5
Syndecan-2/IL8 -0.018 0.072 -9999 0 -0.15 113 113
SDC2 0.008 0.047 -9999 0 -0.29 13 13
KNG1 -0.008 0.06 -9999 0 -0.27 25 25
Syndecan-2/Neurofibromin 0.011 0.044 -9999 0 -0.23 16 16
TRAPPC4 0.011 0 -9999 0 -10000 0 0
CSF2 0.004 0.025 -9999 0 -0.27 4 4
Syndecan-2/TGFB1 0.012 0.041 -9999 0 -0.23 14 14
Syndecan-2/Syntenin/PI-4-5-P2 0.012 0.036 -9999 0 -0.21 13 13
Syndecan-2/Ezrin 0.019 0.036 -9999 0 -0.2 13 13
PRKACA 0.018 0.039 -9999 0 -0.2 16 16
angiogenesis -0.018 0.072 -9999 0 -0.15 113 113
MMP2 -0.011 0.094 -9999 0 -0.42 26 26
IL8 -0.045 0.11 -9999 0 -0.27 101 101
calcineurin-NFAT signaling pathway 0.006 0.048 -9999 0 -0.19 27 27
Signaling events mediated by PTP1B

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
PDGFRB -0.007 0.085 -10000 0 -0.42 21 21
Jak2/Leptin Receptor -0.1 0.15 -10000 0 -0.36 86 86
PTP1B/AKT1 0.013 0.044 -10000 0 -0.22 7 7
FYN 0.011 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.009 0.048 -10000 0 -0.25 7 7
EGFR 0 0.069 -10000 0 -0.41 14 14
EGF/EGFR -0.012 0.054 0.13 1 -0.25 19 20
CSF1 0.002 0.059 -10000 0 -0.42 10 10
AKT1 0.011 0.001 -10000 0 -10000 0 0
INSR 0.011 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.006 0.084 -10000 0 -0.26 33 33
Insulin Receptor/Insulin -0.01 0.026 -10000 0 -0.23 1 1
HCK 0.01 0.012 -10000 0 -0.27 1 1
CRK 0.011 0 -10000 0 -10000 0 0
TYK2 0.014 0.046 -10000 0 -0.23 7 7
EGF -0.001 0.058 -10000 0 -0.28 20 20
YES1 0.011 0 -10000 0 -10000 0 0
CAV1 -0.011 0.084 -10000 0 -0.3 15 15
TXN 0.011 0.002 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.002 0.08 -10000 0 -0.24 32 32
cell migration -0.009 0.048 0.25 7 -10000 0 7
STAT3 0.011 0.001 -10000 0 -10000 0 0
PRLR -0.074 0.17 -10000 0 -0.42 101 101
ITGA2B 0.004 0.047 -10000 0 -0.36 8 8
CSF1R 0.008 0.033 -10000 0 -0.42 3 3
Prolactin Receptor/Prolactin -0.06 0.14 -10000 0 -0.3 118 118
FGR 0 0.067 -10000 0 -0.42 13 13
PTP1B/p130 Cas 0.014 0.046 -10000 0 -0.23 7 7
Crk/p130 Cas 0.02 0.045 -10000 0 -0.22 7 7
DOK1 0.011 0.061 -10000 0 -0.23 19 19
JAK2 -0.042 0.13 -10000 0 -0.26 108 108
Jak2/Leptin Receptor/Leptin -0.019 0.06 -10000 0 -0.32 14 14
PIK3R1 0.007 0.038 -10000 0 -0.42 4 4
PTPN1 0.009 0.049 -10000 0 -0.25 7 7
LYN 0.011 0 -10000 0 -10000 0 0
CDH2 -0.032 0.13 -10000 0 -0.41 52 52
SRC 0.017 0.02 -10000 0 -10000 0 0
ITGB3 -0.078 0.17 -10000 0 -0.42 107 107
CAT1/PTP1B 0.017 0.07 -10000 0 -0.33 7 7
CAPN1 0.011 0.001 -10000 0 -10000 0 0
CSK 0.011 0 -10000 0 -10000 0 0
PI3K -0.009 0.028 -10000 0 -0.23 3 3
mol:H2O2 0 0.001 -10000 0 -10000 0 0
STAT3 (dimer) -0.017 0.057 -10000 0 -0.32 13 13
negative regulation of transcription -0.042 0.13 -10000 0 -0.26 108 108
FCGR2A 0.01 0.012 -10000 0 -0.27 1 1
FER 0.011 0.002 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.051 0.13 -10000 0 -0.28 114 114
BLK -0.014 0.077 -10000 0 -0.27 42 42
Insulin Receptor/Insulin/Shc 0.015 0.002 -10000 0 -10000 0 0
RHOA 0.011 0.001 -10000 0 -10000 0 0
LEPR -0.12 0.19 -10000 0 -0.41 152 152
BCAR1 0.011 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.011 0 -10000 0 -10000 0 0
mol:NADPH 0.001 0.001 -10000 0 -10000 0 0
TRPV6 0.015 0.06 -10000 0 -0.41 3 3
PRL -0.012 0.089 -10000 0 -0.41 24 24
SOCS3 -0.003 0.13 -10000 0 -1.2 6 6
SPRY2 0.006 0.046 -10000 0 -0.42 6 6
Insulin Receptor/Insulin/IRS1 -0.008 0.074 -10000 0 -0.24 47 47
CSF1/CSF1R 0.015 0.06 -10000 0 -0.26 15 15
Ras protein signal transduction 0.008 0.015 -10000 0 -10000 0 0
IRS1 -0.029 0.12 -10000 0 -0.42 47 47
INS 0.001 0.003 -10000 0 -10000 0 0
LEP 0.005 0.022 -10000 0 -0.27 3 3
STAT5B -0.007 0.069 -10000 0 -0.24 21 21
STAT5A -0.007 0.068 -10000 0 -0.24 20 20
GRB2 0.011 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.006 0.066 -10000 0 -0.23 28 28
CSN2 -0.03 0.062 -10000 0 -10000 0 0
PIK3CA 0.01 0.019 -10000 0 -0.42 1 1
LAT 0.017 0.02 -10000 0 -10000 0 0
YBX1 0.016 0.019 -10000 0 -0.41 1 1
LCK 0.008 0.031 -10000 0 -0.3 5 5
SHC1 0.011 0 -10000 0 -10000 0 0
NOX4 0.004 0.052 -10000 0 -0.4 8 8
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.011 0 -9999 0 -10000 0 0
HDAC2 0.011 0.001 -9999 0 -10000 0 0
GNB1/GNG2 0.012 0.047 -9999 0 -0.23 18 18
forebrain development -0.054 0.18 -9999 0 -0.45 79 79
GNAO1 -0.098 0.19 -9999 0 -0.42 131 131
SMO/beta Arrestin2 0.015 0.027 -9999 0 -0.28 4 4
SMO 0.008 0.038 -9999 0 -0.42 4 4
ARRB2 0.011 0.003 -9999 0 -10000 0 0
GLI3/SPOP -0.038 0.12 -9999 0 -0.21 148 148
mol:GTP 0 0.001 -9999 0 -10000 0 0
GSK3B 0.011 0 -9999 0 -10000 0 0
GNAI2 0.011 0.002 -9999 0 -10000 0 0
SIN3/HDAC complex 0.027 0.002 -9999 0 -10000 0 0
GNAI1 0.002 0.059 -9999 0 -0.42 10 10
XPO1 0.012 0.004 -9999 0 -10000 0 0
GLI1/Su(fu) -0.056 0.12 -9999 0 -0.45 27 27
SAP30 0.011 0.001 -9999 0 -10000 0 0
mol:GDP 0.008 0.038 -9999 0 -0.42 4 4
MIM/GLI2A 0.013 0.016 -9999 0 -10000 0 0
IFT88 0.011 0 -9999 0 -10000 0 0
GNAI3 0.011 0.002 -9999 0 -10000 0 0
GLI2 -0.009 0.076 -9999 0 -10000 0 0
GLI3 -0.046 0.12 -9999 0 -0.22 158 158
CSNK1D 0.011 0 -9999 0 -10000 0 0
CSNK1E 0.011 0 -9999 0 -10000 0 0
SAP18 0.011 0 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.011 0 -9999 0 -10000 0 0
GNG2 -0.002 0.071 -9999 0 -0.41 15 15
Gi family/GTP -0.044 0.12 -9999 0 -0.27 55 55
SIN3B 0.011 0.001 -9999 0 -10000 0 0
SIN3A 0.011 0 -9999 0 -10000 0 0
GLI3/Su(fu) -0.012 0.09 -9999 0 -0.39 3 3
GLI2/Su(fu) 0.007 0.069 -9999 0 -0.24 3 3
FOXA2 -0.084 0.28 -9999 0 -1.1 39 39
neural tube patterning -0.054 0.18 -9999 0 -0.45 79 79
SPOP 0.011 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.025 0.015 -9999 0 -10000 0 0
GNB1 0.011 0 -9999 0 -10000 0 0
CSNK1G2 0.011 0 -9999 0 -10000 0 0
CSNK1G3 0.011 0 -9999 0 -10000 0 0
MTSS1 0.013 0.016 -9999 0 -10000 0 0
embryonic limb morphogenesis -0.054 0.18 -9999 0 -0.45 79 79
SUFU 0.021 0.017 -9999 0 -10000 0 0
LGALS3 0.009 0.027 -9999 0 -0.42 2 2
catabolic process -0.041 0.13 -9999 0 -0.28 72 72
GLI3A/CBP -0.032 0.12 -9999 0 -0.31 77 77
KIF3A 0.01 0.019 -9999 0 -0.42 1 1
GLI1 -0.055 0.19 -9999 0 -0.46 79 79
RAB23 0.005 0.05 -9999 0 -0.42 7 7
CSNK1A1 0.011 0 -9999 0 -10000 0 0
IFT172 0.011 0 -9999 0 -10000 0 0
RBBP7 0.011 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 0.024 0.021 -9999 0 -0.2 2 2
GNAZ -0.011 0.094 -9999 0 -0.42 26 26
RBBP4 0.009 0.027 -9999 0 -0.42 2 2
CSNK1G1 0.011 0 -9999 0 -10000 0 0
PIAS1 0.011 0 -9999 0 -10000 0 0
PRKACA 0.011 0 -9999 0 -10000 0 0
GLI2/SPOP -0.003 0.071 -9999 0 -10000 0 0
STK36 0.012 0.004 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.037 0.11 -9999 0 -0.37 24 24
PTCH1 -0.042 0.17 -9999 0 -0.54 26 26
MIM/GLI1 -0.058 0.22 -9999 0 -0.48 96 96
CREBBP -0.032 0.12 -9999 0 -0.31 77 77
Su(fu)/SIN3/HDAC complex 0.037 0.014 -9999 0 -10000 0 0
Nectin adhesion pathway

Figure S70.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S70.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.007 0.085 -9999 0 -0.42 21 21
alphaV beta3 Integrin -0.047 0.12 -9999 0 -0.28 107 107
PTK2 -0.041 0.09 -9999 0 -0.38 24 24
positive regulation of JNK cascade -0.016 0.06 -9999 0 -0.28 24 24
CDC42/GDP 0.014 0.091 -9999 0 -0.38 24 24
Rac1/GDP 0.015 0.09 -9999 0 -0.37 24 24
RAP1B 0.011 0 -9999 0 -10000 0 0
RAP1A 0.011 0 -9999 0 -10000 0 0
CTNNB1 0.011 0 -9999 0 -10000 0 0
CDC42/GTP -0.02 0.073 -9999 0 -0.34 24 24
nectin-3/I-afadin 0.002 0.064 -9999 0 -0.29 24 24
RAPGEF1 0.008 0.098 -9999 0 -0.41 24 24
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.001 0.11 -9999 0 -0.47 24 24
PDGFB-D/PDGFRB -0.007 0.085 -9999 0 -0.42 21 21
TLN1 0 0.077 -9999 0 -0.27 32 32
Rap1/GTP -0.016 0.063 -9999 0 -0.3 24 24
IQGAP1 0.011 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.021 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.002 0.064 -9999 0 -0.29 24 24
PVR 0.011 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.011 0 -9999 0 -10000 0 0
mol:GDP 0.009 0.11 -9999 0 -0.46 24 24
MLLT4 0.011 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.019 -9999 0 -0.42 1 1
PI3K 0.011 0.071 -9999 0 -0.21 44 44
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.015 0.008 -9999 0 -0.18 1 1
positive regulation of lamellipodium assembly -0.017 0.063 -9999 0 -0.3 24 24
PVRL1 0.01 0.012 -9999 0 -0.27 1 1
PVRL3 -0.009 0.09 -9999 0 -0.42 24 24
PVRL2 0.011 0 -9999 0 -10000 0 0
PIK3R1 0.007 0.038 -9999 0 -0.42 4 4
CDH1 0.008 0.029 -9999 0 -0.37 3 3
CLDN1 -0.078 0.17 -9999 0 -0.42 106 106
JAM-A/CLDN1 -0.031 0.11 -9999 0 -0.22 123 123
SRC -0.006 0.12 -9999 0 -0.52 24 24
ITGB3 -0.078 0.17 -9999 0 -0.41 107 107
nectin-1(dimer)/I-afadin/I-afadin 0.015 0.008 -9999 0 -0.18 1 1
FARP2 0.005 0.11 -9999 0 -0.45 24 24
RAC1 0.011 0 -9999 0 -10000 0 0
CTNNA1 0.011 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.01 0.054 -9999 0 -0.23 24 24
nectin-1/I-afadin 0.015 0.008 -9999 0 -0.18 1 1
nectin-2/I-afadin 0.016 0 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.014 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.009 0.055 -9999 0 -0.24 24 24
CDC42/GTP/IQGAP1/filamentous actin 0.014 0 -9999 0 -10000 0 0
F11R 0.01 0.019 -9999 0 -0.42 1 1
positive regulation of filopodium formation -0.016 0.06 -9999 0 -0.28 24 24
alphaV/beta3 Integrin/Talin -0.029 0.12 -9999 0 -0.34 38 38
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.016 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.016 0 -9999 0 -10000 0 0
PIP5K1C -0.006 0.082 -9999 0 -0.23 55 55
VAV2 0.004 0.11 -9999 0 -0.46 24 24
RAP1/GDP -0.019 0.074 -9999 0 -0.35 24 24
ITGAV 0.011 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.01 0.054 -9999 0 -0.23 24 24
nectin-3(dimer)/I-afadin/I-afadin 0.002 0.064 -9999 0 -0.29 24 24
Rac1/GTP -0.021 0.076 -9999 0 -0.36 24 24
PTPRM -0.014 0.09 -9999 0 -0.26 55 55
E-cadherin/beta catenin/alpha catenin -0.001 0.012 -9999 0 -0.17 2 2
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.011 0 -9999 0 -10000 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.024 0.091 -10000 0 -0.21 96 96
MAPK9 0.007 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.003 0.027 -10000 0 -0.18 11 11
GNB1/GNG2 0.007 0.042 -10000 0 -0.23 15 15
GNB1 0.011 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.007 0 -10000 0 -10000 0 0
Gs family/GTP -0.032 0.086 -10000 0 -0.22 88 88
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 0.011 0.023 0.062 88 -10000 0 88
GNAL -0.063 0.16 -10000 0 -0.42 88 88
GNG2 -0.002 0.071 -10000 0 -0.41 15 15
CRH -0.004 0.04 -10000 0 -0.27 11 11
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.004 0.029 -10000 0 -0.29 5 5
MAPK11 0.006 0.018 -10000 0 -0.29 2 2
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.16 0.21 -9999 0 -0.42 205 205
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.011 0 -9999 0 -10000 0 0
TCEB1 0.011 0 -9999 0 -10000 0 0
HIF1A/p53 0.024 0.01 -9999 0 -0.17 1 1
HIF1A 0.019 0.005 -9999 0 -10000 0 0
COPS5 0.011 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.031 0.01 -9999 0 -0.18 1 1
FIH (dimer) 0.011 0 -9999 0 -10000 0 0
CDKN2A -0.11 0.14 -9999 0 -0.27 224 224
ARNT/IPAS -0.1 0.15 -9999 0 -0.28 205 205
HIF1AN 0.011 0 -9999 0 -10000 0 0
GNB2L1 0.011 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.025 0.004 -9999 0 -10000 0 0
CUL2 0.011 0 -9999 0 -10000 0 0
OS9 0.011 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.022 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.025 0.004 -9999 0 -10000 0 0
PHD1-3/OS9 0.026 0.015 -9999 0 -0.2 1 1
HIF1A/RACK1/Elongin B/Elongin C 0.033 0.004 -9999 0 -10000 0 0
VHL 0.01 0.019 -9999 0 -0.42 1 1
HSP90AA1 0.011 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.025 0.004 -9999 0 -10000 0 0
EGLN3 0.008 0.029 -9999 0 -0.31 4 4
EGLN2 0.011 0 -9999 0 -10000 0 0
EGLN1 0.011 0 -9999 0 -10000 0 0
TP53 0.01 0.019 -9999 0 -0.42 1 1
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.029 0.023 -9999 0 -0.5 1 1
ARNT 0.011 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.011 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.028 0.06 -9999 0 -0.16 1 1
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.01 0.064 -10000 0 -0.66 4 4
HDAC1 0.008 0.005 -10000 0 -10000 0 0
AES 0.01 0.001 -10000 0 -10000 0 0
FBXW11 0.011 0 -10000 0 -10000 0 0
DTX1 0.006 0.042 -10000 0 -0.42 5 5
LRP6/FZD1 0.015 0.013 -10000 0 -0.29 1 1
TLE1 0.009 0.019 -10000 0 -0.42 1 1
AP1 -0.072 0.13 -10000 0 -0.24 175 175
NCSTN 0.011 0 -10000 0 -10000 0 0
ADAM10 0.007 0.038 -10000 0 -0.42 4 4
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.029 0.047 -10000 0 -0.6 1 1
NICD/RBPSUH 0.022 0.047 -10000 0 -0.51 4 4
WIF1 -0.081 0.14 -10000 0 -0.29 155 155
NOTCH1 -0.004 0.047 -10000 0 -0.54 4 4
PSENEN 0.011 0 -10000 0 -10000 0 0
KREMEN2 -0.017 0.084 -10000 0 -0.27 50 50
DKK1 -0.051 0.12 -10000 0 -0.28 108 108
beta catenin/beta TrCP1 0.025 0.024 -10000 0 -10000 0 0
APH1B 0.007 0.038 -10000 0 -0.42 4 4
APH1A 0.011 0 -10000 0 -10000 0 0
AXIN1 0.002 0.018 -10000 0 -0.18 4 4
CtBP/CBP/TCF1/TLE1/AES 0.015 0.028 -10000 0 -0.24 2 2
PSEN1 0.011 0 -10000 0 -10000 0 0
FOS -0.13 0.2 -10000 0 -0.42 174 174
JUN 0.006 0.046 -10000 0 -0.42 6 6
MAP3K7 0.009 0.002 -10000 0 -10000 0 0
CTNNB1 0.019 0.026 0.16 5 -10000 0 5
MAPK3 0.011 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.013 0.082 -10000 0 -0.25 38 38
HNF1A -0.006 0.065 -10000 0 -0.27 29 29
CTBP1 0.01 0.001 -10000 0 -10000 0 0
MYC -0.005 0.18 -10000 0 -1.3 10 10
NKD1 -0.016 0.088 -10000 0 -0.3 44 44
FZD1 0.01 0.019 -10000 0 -0.42 1 1
NOTCH1 precursor/Deltex homolog 1 0.02 0.051 -10000 0 -0.51 4 4
apoptosis -0.072 0.13 -10000 0 -0.24 175 175
Delta 1/NOTCHprecursor 0.016 0.067 -10000 0 -0.65 4 4
DLL1 -0.002 0.072 -10000 0 -0.42 15 15
PPARD 0.018 0.013 -10000 0 -10000 0 0
Gamma Secretase 0.03 0.019 -10000 0 -0.19 4 4
APC 0.002 0.018 -10000 0 -0.18 4 4
DVL1 0.002 0.013 -10000 0 -10000 0 0
CSNK2A1 0.011 0.001 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.028 0.078 -10000 0 -0.26 10 10
LRP6 0.011 0 -10000 0 -10000 0 0
CSNK1A1 0.011 0.001 -10000 0 -10000 0 0
NLK 0.011 0.006 -10000 0 -10000 0 0
CCND1 0.018 0.013 -10000 0 -10000 0 0
WNT1 0.004 0.035 -10000 0 -0.27 8 8
Axin1/APC/beta catenin 0.029 0.024 -10000 0 -10000 0 0
DKK2 -0.021 0.11 -10000 0 -0.4 39 39
NOTCH1 precursor/DVL1 0.001 0.042 -10000 0 -0.46 4 4
GSK3B 0.01 0 -10000 0 -10000 0 0
FRAT1 0.01 0.001 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.006 0.049 -10000 0 -0.52 4 4
PPP2R5D 0.011 0.041 0.23 8 -10000 0 8
MAPK1 0.011 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.023 0.074 -10000 0 -0.21 22 22
RBPJ 0.011 0 -10000 0 -10000 0 0
CREBBP 0.012 0.019 -10000 0 -0.42 1 1
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.014 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.011 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.025 0.094 -9999 0 -0.27 65 65
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.01 0.019 -9999 0 -0.42 1 1
RAC1-CDC42/GTP/PAK family -0.01 0.07 -9999 0 -0.18 76 76
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.011 0 -9999 0 -10000 0 0
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.011 0 -9999 0 -10000 0 0
FYN 0.011 0 -9999 0 -10000 0 0
MAP3K12 0.007 0.038 -9999 0 -0.42 4 4
FGR 0 0.067 -9999 0 -0.42 13 13
p38 alpha/TAB1 -0.003 0.016 -9999 0 -0.18 2 2
PRKG1 -0.19 0.21 -9999 0 -0.42 242 242
DUSP8 0.006 0.042 -9999 0 -0.42 5 5
PGK/cGMP/p38 alpha -0.073 0.078 -9999 0 -0.19 55 55
apoptosis -0.003 0.016 -9999 0 -0.18 2 2
RAL/GTP 0.014 0 -9999 0 -10000 0 0
LYN 0.011 0 -9999 0 -10000 0 0
DUSP1 -0.11 0.19 -9999 0 -0.42 145 145
PAK1 0.011 0 -9999 0 -10000 0 0
SRC 0.011 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.027 0 -9999 0 -10000 0 0
TRAF6 0.011 0 -9999 0 -10000 0 0
RAC1 0.011 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.011 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0.014 0 -9999 0 -10000 0 0
MAPK11 0.032 0.035 -9999 0 -0.2 1 1
BLK -0.014 0.077 -9999 0 -0.27 42 42
HCK 0.01 0.012 -9999 0 -0.27 1 1
MAP2K3 0.011 0 -9999 0 -10000 0 0
DUSP16 0.011 0 -9999 0 -10000 0 0
DUSP10 0.011 0 -9999 0 -10000 0 0
TRAF6/MEKK3 0.014 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.035 0.027 -9999 0 -0.2 2 2
positive regulation of innate immune response 0.04 0.038 -9999 0 -0.22 1 1
LCK 0.008 0.031 -9999 0 -0.3 5 5
p38alpha-beta/MKP7 0.044 0.037 -9999 0 -0.21 1 1
p38alpha-beta/MKP5 0.044 0.037 -9999 0 -0.21 1 1
PGK/cGMP -0.13 0.15 -9999 0 -0.29 242 242
PAK2 0.011 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 0.012 0.079 -9999 0 -0.26 14 14
CDC42 0.011 0 -9999 0 -10000 0 0
RALB 0.011 0 -9999 0 -10000 0 0
RALA 0.011 0 -9999 0 -10000 0 0
PAK3 -0.056 0.15 -9999 0 -0.42 76 76
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.017 0.008 -9999 0 -0.18 1 1
BAD/BCL-XL/YWHAZ 0.026 0.006 -9999 0 -10000 0 0
CDKN1B 0.02 0.04 -9999 0 -0.23 1 1
CDKN1A 0.027 0.016 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
PRKDC 0.011 0 -9999 0 -10000 0 0
FOXO3 0.028 0.004 -9999 0 -10000 0 0
AKT1 0 0.002 -9999 0 -10000 0 0
BAD 0.011 0 -9999 0 -10000 0 0
AKT3 -0.11 0.14 -9999 0 -0.28 212 212
mol:GTP 0 0 -9999 0 -10000 0 0
FOXO4 0.027 0.013 -9999 0 -10000 0 0
AKT1/ASK1 0.026 0.015 -9999 0 -10000 0 0
BAD/YWHAZ 0.022 0 -9999 0 -10000 0 0
RICTOR 0.009 0.027 -9999 0 -0.42 2 2
RAF1 0.011 0 -9999 0 -10000 0 0
JNK cascade -0.025 0.015 -9999 0 -10000 0 0
TSC1 0.028 0.01 -9999 0 -10000 0 0
YWHAZ 0.011 0 -9999 0 -10000 0 0
AKT1/RAF1 0.029 0.004 -9999 0 -10000 0 0
EP300 0.011 0 -9999 0 -10000 0 0
mol:GDP 0.024 0.004 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
TSC2 0.028 0.004 -9999 0 -10000 0 0
YWHAQ 0.011 0 -9999 0 -10000 0 0
TBC1D4 0.016 0.022 -9999 0 -0.23 4 4
MAP3K5 0.008 0.033 -9999 0 -0.42 3 3
MAPKAP1 0.011 0 -9999 0 -10000 0 0
negative regulation of cell cycle -0.017 0.009 -9999 0 -10000 0 0
YWHAH 0.011 0 -9999 0 -10000 0 0
AKT1S1 0.028 0.004 -9999 0 -10000 0 0
CASP9 0.028 0.004 -9999 0 -10000 0 0
YWHAB 0.011 0 -9999 0 -10000 0 0
p27Kip1/KPNA1 0.026 0.038 -9999 0 -0.22 1 1
GBL 0 0 -9999 0 -10000 0 0
PDK1/Src/Hsp90 0.022 0 -9999 0 -10000 0 0
YWHAE 0.011 0 -9999 0 -10000 0 0
SRC 0.011 0 -9999 0 -10000 0 0
AKT2/p21CIP1 0.03 0.015 -9999 0 -10000 0 0
KIAA1303 0 0 -9999 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.014 0.002 -9999 0 -10000 0 0
CHUK 0.028 0.004 -9999 0 -10000 0 0
BAD/BCL-XL 0.038 0.006 -9999 0 -10000 0 0
mTORC2 0.013 0.014 -9999 0 -0.22 2 2
AKT2 0.013 0 -9999 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.029 0.013 -9999 0 -10000 0 0
PDPK1 0.011 0 -9999 0 -10000 0 0
MDM2 0.028 0.004 -9999 0 -10000 0 0
MAPKKK cascade -0.028 0.004 -9999 0 -10000 0 0
MDM2/Cbp/p300 0.038 0.009 -9999 0 -10000 0 0
TSC1/TSC2 0.032 0.009 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.036 0.009 -9999 0 -10000 0 0
glucose import -0.095 0.11 -9999 0 -0.2 267 267
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.024 0.004 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
SLC2A4 -0.096 0.11 -9999 0 -0.2 267 267
GSK3A 0.028 0.004 -9999 0 -10000 0 0
FOXO1 0.027 0.016 -9999 0 -10000 0 0
GSK3B 0.028 0.004 -9999 0 -10000 0 0
SFN -0.21 0.12 -9999 0 -0.27 400 400
G1/S transition of mitotic cell cycle 0.033 0.004 -9999 0 -10000 0 0
p27Kip1/14-3-3 family 0.014 0.014 -9999 0 -10000 0 0
PRKACA 0.011 0 -9999 0 -10000 0 0
KPNA1 0.011 0 -9999 0 -10000 0 0
HSP90AA1 0.011 0 -9999 0 -10000 0 0
YWHAG 0.011 0 -9999 0 -10000 0 0
RHEB 0.011 0 -9999 0 -10000 0 0
CREBBP 0.01 0.019 -9999 0 -0.42 1 1
Visual signal transduction: Rods

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
mol:K + 0.011 0 -9999 0 -10000 0 0
GNAT1/GTP 0.003 0.019 -9999 0 -0.18 5 5
Metarhodopsin II/Arrestin 0.006 0.014 -9999 0 -0.14 4 4
PDE6G/GNAT1/GTP -0.003 0.046 -9999 0 -0.15 44 44
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.003 0.028 -9999 0 -0.27 5 5
GRK1 0.002 0.013 -9999 0 -0.27 1 1
CNG Channel -0.02 0.048 -9999 0 -0.24 7 7
mol:Na + -0.013 0.037 -9999 0 -0.2 6 6
mol:ADP 0.002 0.013 -9999 0 -0.27 1 1
RGS9-1/Gbeta5/R9AP -0.043 0.11 -9999 0 -0.24 115 115
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.013 0.038 -9999 0 -0.21 6 6
CNGB1 -0.001 0.053 -9999 0 -0.27 19 19
RDH5 0.009 0.027 -9999 0 -0.42 2 2
SAG 0.004 0.013 -9999 0 -0.27 1 1
mol:Ca2+ 0.016 0.044 -9999 0 -10000 0 0
Na + (4 Units) -0.011 0.034 -9999 0 -0.2 1 1
RGS9 -0.085 0.18 -9999 0 -0.42 115 115
GNB1/GNGT1 -0.005 0.059 -9999 0 -0.18 56 56
GNAT1/GDP -0.034 0.093 -9999 0 -0.2 116 116
GUCY2D 0.003 0.037 -9999 0 -0.27 9 9
GNGT1 -0.021 0.088 -9999 0 -0.27 56 56
GUCY2F 0.004 0.005 -9999 0 -10000 0 0
GNB5 0.011 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.003 0.054 -9999 0 -0.2 18 18
mol:11-cis-retinal 0.009 0.027 -9999 0 -0.42 2 2
mol:cGMP 0.01 0.037 -9999 0 -0.21 7 7
GNB1 0.011 0 -9999 0 -10000 0 0
Rhodopsin 0.009 0.024 -9999 0 -0.22 5 5
SLC24A1 0.011 0 -9999 0 -10000 0 0
CNGA1 0.002 0.048 -9999 0 -0.27 15 15
Metarhodopsin II 0.004 0.013 -9999 0 -0.13 4 4
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family 0.008 0.039 -9999 0 -0.22 7 7
RGS9BP -0.004 0.06 -9999 0 -0.27 24 24
Metarhodopsin II/Transducin 0.008 0.018 -9999 0 -10000 0 0
GCAP Family/Ca ++ 0.005 0.033 -9999 0 -0.22 5 5
PDE6A/B 0.005 0.055 -9999 0 -0.26 20 20
mol:Pi -0.043 0.11 -9999 0 -0.24 115 115
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin 0 0.047 -9999 0 -0.26 2 2
PDE6B -0.004 0.075 -9999 0 -0.39 18 18
PDE6A 0.009 0.023 -9999 0 -0.34 2 2
PDE6G -0.012 0.077 -9999 0 -0.28 40 40
RHO 0.003 0.022 -9999 0 -0.27 3 3
PDE6 -0.057 0.084 -9999 0 -0.29 16 16
GUCA1A -0.002 0.049 -9999 0 -0.27 16 16
GC2/GCAP Family 0.008 0.033 -9999 0 -0.21 5 5
GUCA1C 0 0 -9999 0 -10000 0 0
GUCA1B 0.006 0.042 -9999 0 -0.42 5 5
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.012 0.004 -10000 0 -10000 0 0
HSPA8 0.01 0.001 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.03 0.088 -10000 0 -0.26 60 60
AKT1 0.013 0.001 -10000 0 -10000 0 0
GSC -0.021 0.056 -10000 0 -10000 0 0
NKX2-5 -0.034 0.096 -10000 0 -0.28 64 64
muscle cell differentiation 0.03 0.1 0.37 19 -10000 0 19
SMAD2-3/SMAD4/SP1 0.034 0.055 -10000 0 -0.3 4 4
SMAD4 0.006 0.036 -10000 0 -0.43 1 1
CBFB 0.011 0 -10000 0 -10000 0 0
SAP18 0.011 0 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.017 0.038 -10000 0 -0.27 4 4
SMAD3/SMAD4/VDR 0.008 0.038 -10000 0 -0.23 4 4
MYC 0 0.059 -10000 0 -0.42 10 10
CDKN2B 0.026 0.024 -10000 0 -10000 0 0
AP1 -0.033 0.13 -10000 0 -0.45 14 14
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.043 0.019 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.018 0.041 -10000 0 -0.39 2 2
SP3 0.013 0 -10000 0 -10000 0 0
CREB1 0.011 0 -10000 0 -10000 0 0
FOXH1 -0.063 0.12 -10000 0 -0.28 119 119
SMAD3/SMAD4/GR -0.045 0.11 -10000 0 -0.26 96 96
GATA3 -0.002 0.065 -10000 0 -0.3 22 22
SKI/SIN3/HDAC complex/NCoR1 0.036 0.011 -10000 0 -10000 0 0
MEF2C/TIF2 -0.062 0.17 -10000 0 -0.45 68 68
endothelial cell migration -0.015 0.13 1.2 5 -10000 0 5
MAX 0.009 0.005 -10000 0 -10000 0 0
RBBP7 0.011 0 -10000 0 -10000 0 0
RBBP4 0.009 0.027 -10000 0 -0.42 2 2
RUNX2 0.003 0.048 -10000 0 -0.28 14 14
RUNX3 0.002 0.048 -10000 0 -0.27 15 15
RUNX1 0.011 0 -10000 0 -10000 0 0
CTBP1 0.011 0 -10000 0 -10000 0 0
NR3C1 -0.069 0.17 -10000 0 -0.42 94 94
VDR 0.005 0.039 -10000 0 -0.27 10 10
CDKN1A 0.043 0.1 -10000 0 -1.2 3 3
KAT2B 0.002 0.059 -10000 0 -0.42 10 10
SMAD2/SMAD2/SMAD4/FOXH1 -0.028 0.089 -10000 0 -0.28 16 16
DCP1A 0.011 0 -10000 0 -10000 0 0
SKI 0.011 0 -10000 0 -10000 0 0
SERPINE1 0.014 0.13 -10000 0 -1.2 5 5
SMAD3/SMAD4/ATF2 0.013 0.05 -10000 0 -0.31 7 7
SMAD3/SMAD4/ATF3 -0.02 0.1 -10000 0 -0.27 70 70
SAP30 0.011 0 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.024 0.015 -10000 0 -0.23 1 1
JUN -0.033 0.12 -10000 0 -0.44 14 14
SMAD3/SMAD4/IRF7 0.008 0.052 -10000 0 -0.28 8 8
TFE3 0.015 0.006 -10000 0 -10000 0 0
COL1A2 0.006 0.091 -10000 0 -0.82 5 5
mesenchymal cell differentiation -0.008 0.054 0.25 12 -10000 0 12
DLX1 -0.027 0.091 -10000 0 -0.27 62 62
TCF3 0.011 0 -10000 0 -10000 0 0
FOS -0.13 0.2 -10000 0 -0.42 174 174
SMAD3/SMAD4/Max 0.004 0.038 -10000 0 -0.27 5 5
Cbp/p300/SNIP1 0.022 0.012 -10000 0 -0.23 1 1
ZBTB17 0.009 0.001 -10000 0 -10000 0 0
LAMC1 0.031 0.037 -10000 0 -0.26 2 2
TGIF2/HDAC complex/SMAD3/SMAD4 0.014 0.041 -10000 0 -0.27 5 5
IRF7 0.005 0.043 -10000 0 -0.29 10 10
ESR1 -0.037 0.13 -10000 0 -0.42 56 56
HNF4A -0.022 0.089 -10000 0 -0.28 56 56
MEF2C -0.064 0.17 -10000 0 -0.47 64 64
SMAD2-3/SMAD4 0.016 0.049 -10000 0 -0.27 6 6
Cbp/p300/Src-1 0.022 0.017 -10000 0 -0.23 2 2
IGHV3OR16-13 -0.001 0.008 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.011 0 -10000 0 -10000 0 0
CREBBP 0.01 0.019 -10000 0 -0.42 1 1
SKIL 0.011 0 -10000 0 -10000 0 0
HDAC1 0.011 0 -10000 0 -10000 0 0
HDAC2 0.011 0 -10000 0 -10000 0 0
SNIP1 0.01 0.001 -10000 0 -10000 0 0
GCN5L2 0.001 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.029 0.044 -10000 0 -0.26 5 5
MSG1/HSC70 0.008 0.04 -10000 0 -0.19 19 19
SMAD2 0.007 0.019 -10000 0 -10000 0 0
SMAD3 0.009 0.048 -10000 0 -0.46 4 4
SMAD3/E2F4-5/DP1/p107/SMAD4 0.024 0.034 -10000 0 -0.22 5 5
SMAD2/SMAD2/SMAD4 0 0.046 -10000 0 -0.29 11 11
NCOR1 0.011 0 -10000 0 -10000 0 0
NCOA2 -0.004 0.079 -10000 0 -0.42 18 18
NCOA1 0.01 0.019 -10000 0 -0.42 1 1
MYOD/E2A -0.006 0.054 -10000 0 -0.18 47 47
SMAD2-3/SMAD4/SP1/MIZ-1 0.04 0.052 -10000 0 -0.3 3 3
IFNB1 0.013 0.057 -10000 0 -0.29 9 9
SMAD3/SMAD4/MEF2C -0.058 0.17 -10000 0 -0.46 63 63
CITED1 -0.001 0.059 -10000 0 -0.3 19 19
SMAD2-3/SMAD4/ARC105 0.022 0.045 -10000 0 -0.3 2 2
RBL1 0.011 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.039 0.037 -10000 0 -0.35 2 2
RUNX1-3/PEBPB2 0.017 0.027 -10000 0 -10000 0 0
SMAD7 -0.009 0.13 -10000 0 -0.47 13 13
MYC/MIZ-1 0.005 0.042 -10000 0 -0.29 10 10
SMAD3/SMAD4 0.009 0.06 -10000 0 -0.45 5 5
IL10 0.013 0.076 -10000 0 -0.4 4 4
PIASy/HDAC complex 0.01 0.003 -10000 0 -10000 0 0
PIAS3 0.011 0.001 -10000 0 -10000 0 0
CDK2 0.011 0.003 -10000 0 -10000 0 0
IL5 0.012 0.059 -10000 0 -0.31 6 6
CDK4 0.011 0.003 -10000 0 -10000 0 0
PIAS4 0.01 0.003 -10000 0 -10000 0 0
ATF3 -0.044 0.14 -10000 0 -0.42 66 66
SMAD3/SMAD4/SP1 0.03 0.052 -10000 0 -0.29 6 6
FOXG1 -0.12 0.14 -10000 0 -0.27 240 240
FOXO3 0.021 0.002 -10000 0 -10000 0 0
FOXO1 0.019 0.023 -10000 0 -0.28 3 3
FOXO4 0.02 0.019 -10000 0 -0.28 2 2
heart looping -0.064 0.17 -10000 0 -0.46 64 64
CEBPB 0.012 0.001 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.007 0.072 -10000 0 -0.28 13 13
MYOD1 -0.021 0.08 -10000 0 -0.27 47 47
SMAD3/SMAD4/HNF4 -0.005 0.066 -10000 0 -0.31 7 7
SMAD3/SMAD4/GATA3 0.006 0.066 -10000 0 -0.34 7 7
SnoN/SIN3/HDAC complex/NCoR1 0.011 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.028 0.043 -10000 0 -0.24 3 3
SMAD3/SMAD4/SP1-3 0.038 0.049 -10000 0 -0.3 3 3
MED15 0.011 0 -10000 0 -10000 0 0
SP1 0.017 0.015 -10000 0 -0.17 1 1
SIN3B 0.011 0 -10000 0 -10000 0 0
SIN3A 0.011 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.028 0.13 -10000 0 -0.32 56 56
ITGB5 0.04 0.039 -10000 0 -0.28 2 2
TGIF/SIN3/HDAC complex/CtBP 0.036 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.033 0.11 -10000 0 -0.26 93 93
AR -0.064 0.16 -10000 0 -0.42 90 90
negative regulation of cell growth 0.011 0.068 -10000 0 -0.3 6 6
SMAD3/SMAD4/MYOD -0.004 0.061 -10000 0 -0.27 7 7
E2F5 0.011 0 -10000 0 -10000 0 0
E2F4 0.011 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.004 0.076 -10000 0 -0.23 15 15
SMAD2-3/SMAD4/FOXO1-3a-4 0.036 0.039 -10000 0 -0.36 2 2
TFDP1 0.011 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.028 0.13 -10000 0 -0.45 14 14
SMAD3/SMAD4/RUNX2 0.01 0.055 -10000 0 -0.26 12 12
TGIF2 0.011 0 -10000 0 -10000 0 0
TGIF1 0.011 0 -10000 0 -10000 0 0
ATF2 0.008 0.033 -10000 0 -0.42 3 3
BARD1 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
BARD1/CSTF1 0.01 0.042 -10000 0 -0.29 10 10
ATM 0.011 0 -10000 0 -10000 0 0
UBE2D3 0.011 0 -10000 0 -10000 0 0
PRKDC 0.011 0 -10000 0 -10000 0 0
ATR 0.011 0 -10000 0 -10000 0 0
UBE2L3 0.011 0 -10000 0 -10000 0 0
FANCD2 0.02 0.005 -10000 0 -10000 0 0
protein ubiquitination -0.048 0.057 -10000 0 -0.24 10 10
XRCC5 0.011 0 -10000 0 -10000 0 0
XRCC6 0.011 0 -10000 0 -10000 0 0
M/R/N Complex 0.022 0 -10000 0 -10000 0 0
MRE11A 0.011 0 -10000 0 -10000 0 0
DNA-PK 0.022 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.024 0.022 -10000 0 -10000 0 0
FANCF 0.009 0.027 -10000 0 -0.42 2 2
BRCA1 0.011 0 -10000 0 -10000 0 0
CCNE1 -0.11 0.14 -10000 0 -0.27 225 225
CDK2/Cyclin E1 -0.068 0.094 -10000 0 -0.18 225 225
FANCG 0.011 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.01 0.042 -10000 0 -0.29 10 10
FANCE 0.011 0 -10000 0 -10000 0 0
FANCC 0.011 0 -10000 0 -10000 0 0
NBN 0.011 0 -10000 0 -10000 0 0
FANCA -0.048 0.12 -10000 0 -0.27 106 106
DNA repair 0.003 0.069 -10000 0 -0.28 7 7
BRCA1/BARD1/ubiquitin 0.01 0.042 -10000 0 -0.29 10 10
BARD1/DNA-PK 0.023 0.032 -10000 0 -0.2 10 10
FANCL 0.011 0 -10000 0 -10000 0 0
mRNA polyadenylation -0.01 0.042 0.28 10 -10000 0 10
BRCA1/BARD1/CTIP/M/R/N Complex 0.027 0.03 -10000 0 -0.19 10 10
BRCA1/BACH1/BARD1/TopBP1 0.017 0.035 -10000 0 -0.23 10 10
BRCA1/BARD1/P53 0.022 0.034 -10000 0 -0.2 11 11
BARD1/CSTF1/BRCA1 0.017 0.035 -10000 0 -0.23 10 10
BRCA1/BACH1 0.011 0 -10000 0 -10000 0 0
BARD1 0.002 0.059 -10000 0 -0.42 10 10
PCNA 0.011 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.017 0.035 -10000 0 -0.23 10 10
BRCA1/BARD1/UbcH7 0.017 0.035 -10000 0 -0.23 10 10
BRCA1/BARD1/RAD51/PCNA -0.013 0.072 -10000 0 -0.28 10 10
BARD1/DNA-PK/P53 0.027 0.031 -10000 0 -0.18 11 11
BRCA1/BARD1/Ubiquitin 0.01 0.042 -10000 0 -0.29 10 10
BRCA1/BARD1/CTIP 0.022 0.032 -10000 0 -0.2 10 10
FA complex 0.019 0.026 -10000 0 -0.22 1 1
BARD1/EWS 0.01 0.042 -10000 0 -0.29 10 10
RBBP8 0.017 0 -10000 0 -10000 0 0
TP53 0.01 0.019 -10000 0 -0.42 1 1
TOPBP1 0.011 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.021 0.033 0.2 11 -10000 0 11
BRCA1/BARD1 -0.031 0.073 -10000 0 -0.25 10 10
CSTF1 0.011 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.002 0.042 -10000 0 -0.29 10 10
CDK2 0.011 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.06 0.12 -10000 0 -0.27 128 128
RAD50 0.011 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.01 0.042 -10000 0 -0.29 10 10
EWSR1 0.011 0 -10000 0 -10000 0 0
IL1-mediated signaling events

Figure S79.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S79.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A -0.006 0.069 -10000 0 -0.29 29 29
PRKCZ 0.009 0.023 -10000 0 -0.34 2 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.011 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.003 0.025 -10000 0 -0.24 4 4
IRAK/TOLLIP 0.009 0.052 -10000 0 -0.2 29 29
IKBKB 0.011 0 -10000 0 -10000 0 0
IKBKG 0.011 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.011 0.072 -10000 0 -0.2 64 64
IL1A -0.007 0.066 -10000 0 -0.27 30 30
IL1B 0.012 0.043 -10000 0 -0.32 8 8
IRAK/TRAF6/p62/Atypical PKCs 0.023 0.047 -10000 0 -0.35 1 1
IL1R2 -0.012 0.08 -10000 0 -0.29 39 39
IL1R1 0.004 0.053 -10000 0 -0.42 8 8
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.025 0.057 0.18 21 -0.26 10 31
TOLLIP 0.011 0 -10000 0 -10000 0 0
TICAM2 0.003 0.053 -10000 0 -0.42 8 8
MAP3K3 0.011 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.007 0 -10000 0 -10000 0 0
IKK complex/ELKS 0.039 0.041 -10000 0 -10000 0 0
JUN 0.005 0.063 -10000 0 -0.22 16 16
MAP3K7 0.011 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.026 0.052 -10000 0 -0.21 21 21
IL1 alpha/IL1R1/IL1RAP/MYD88 0.014 0.05 -10000 0 -0.24 10 10
PIK3R1 0.007 0.038 -10000 0 -0.42 4 4
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.019 0.046 -10000 0 -0.22 10 10
IL1 beta fragment/IL1R1/IL1RAP 0.017 0.048 -10000 0 -0.23 18 18
NFKB1 0.01 0.019 -10000 0 -0.42 1 1
MAPK8 0.002 0.062 -10000 0 -0.18 34 34
IRAK1 0.003 0.058 -10000 0 -0.23 29 29
IL1RN/IL1R1 -0.014 0.075 -10000 0 -0.19 74 74
IRAK4 0.011 0 -10000 0 -10000 0 0
PRKCI 0.011 0 -10000 0 -10000 0 0
TRAF6 0.011 0 -10000 0 -10000 0 0
PI3K 0.013 0.03 -10000 0 -0.29 5 5
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.024 0.042 -10000 0 -0.22 11 11
CHUK 0.011 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.017 0.048 -10000 0 -0.23 18 18
IL1 beta/IL1R2 0.004 0.059 -10000 0 -0.27 11 11
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.01 0.039 -10000 0 -0.17 29 29
NF kappa B1 p50/RelA -0.008 0.041 -10000 0 -0.39 3 3
IRAK3 -0.009 0.088 -10000 0 -0.42 23 23
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.024 0.052 -10000 0 -0.37 3 3
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.021 0.037 -10000 0 -0.22 10 10
IL1 alpha/IL1R1/IL1RAP 0.007 0.054 -10000 0 -0.17 39 39
RELA 0.011 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.011 0 -10000 0 -10000 0 0
MYD88 0.011 0 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.016 0.049 -10000 0 -0.18 29 29
IL1RAP 0.008 0.033 -10000 0 -0.42 3 3
UBE2N 0.011 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.015 0.05 -10000 0 -0.31 7 7
CASP1 0.006 0.042 -10000 0 -0.42 5 5
IL1RN/IL1R2 -0.024 0.085 -10000 0 -0.19 99 99
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.023 0.046 -10000 0 -0.21 18 18
TMEM189-UBE2V1 -0.02 0.097 -10000 0 -0.42 29 29
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.019 0.056 -10000 0 -0.35 8 8
PIK3CA 0.01 0.019 -10000 0 -0.42 1 1
IL1RN -0.027 0.096 -10000 0 -0.27 68 68
TRAF6/TAK1/TAB1/TAB2 -0.01 0.042 -10000 0 -0.18 29 29
MAP2K6 -0.002 0.062 -10000 0 -0.19 29 29
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.01 0.012 -10000 0 -0.27 1 1
NFATC1 0.032 0.047 -10000 0 -0.26 12 12
NFATC2 0.004 0.055 -10000 0 -0.18 20 20
NFATC3 0.014 0.017 -10000 0 -0.32 1 1
YWHAE 0.011 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.01 0.093 -10000 0 -0.24 47 47
Exportin 1/Ran/NUP214 0.017 0.009 -10000 0 -10000 0 0
mol:DAG -0.001 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.026 0.072 -10000 0 -0.34 16 16
BCL2/BAX -0.012 0.088 -10000 0 -0.29 48 48
CaM/Ca2+/Calcineurin A alpha-beta B1 0.005 0.007 -10000 0 -10000 0 0
CaM/Ca2+ 0.005 0.007 -10000 0 -10000 0 0
BAX 0.011 0 -10000 0 -10000 0 0
MAPK14 0.009 0.004 -10000 0 -10000 0 0
BAD 0.011 0 -10000 0 -10000 0 0
CABIN1/MEF2D -0.005 0.089 -10000 0 -0.35 17 17
Calcineurin A alpha-beta B1/BCL2 -0.029 0.12 -10000 0 -0.42 48 48
FKBP8 0.011 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.005 0.088 0.35 17 -10000 0 17
KPNB1 0.011 0 -10000 0 -10000 0 0
KPNA2 0.002 0.048 -10000 0 -0.27 15 15
XPO1 0.01 0.001 -10000 0 -10000 0 0
SFN -0.21 0.12 -10000 0 -0.27 400 400
MAP3K8 0.004 0.042 -10000 0 -0.42 5 5
NFAT4/CK1 alpha 0.021 0.014 -10000 0 -0.16 1 1
MEF2D/NFAT1/Cbp/p300 -0.017 0.12 -10000 0 -0.23 112 112
CABIN1 -0.01 0.094 -10000 0 -0.24 47 47
CALM1 0.009 0.003 -10000 0 -10000 0 0
RAN 0.01 0.001 -10000 0 -10000 0 0
MAP3K1 0.011 0 -10000 0 -10000 0 0
CAMK4 0.006 0.038 -10000 0 -0.31 7 7
mol:Ca2+ -0.002 0.006 -10000 0 -10000 0 0
MAPK3 0.011 0 -10000 0 -10000 0 0
YWHAH 0.011 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.011 0.024 -10000 0 -0.29 3 3
YWHAB 0.011 0 -10000 0 -10000 0 0
MAPK8 0.004 0.042 -10000 0 -0.42 5 5
MAPK9 0.011 0 -10000 0 -10000 0 0
YWHAG 0.011 0 -10000 0 -10000 0 0
FKBP1A 0.011 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.036 0.049 -10000 0 -0.23 8 8
PRKCH 0.008 0.033 -10000 0 -0.42 3 3
CABIN1/Cbp/p300 0.011 0.017 -10000 0 -0.28 1 1
CASP3 0.009 0.004 -10000 0 -10000 0 0
PIM1 0.011 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.006 0.003 -10000 0 -10000 0 0
apoptosis -0.008 0.024 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.011 0.011 -10000 0 -10000 0 0
PRKCB -0.015 0.1 -10000 0 -0.42 31 31
PRKCE 0.011 0 -10000 0 -10000 0 0
JNK2/NFAT4 0.02 0.015 -10000 0 -0.28 1 1
BAD/BCL-XL 0.015 0.008 -10000 0 -0.18 1 1
PRKCD 0.011 0 -10000 0 -10000 0 0
NUP214 0.01 0.001 -10000 0 -10000 0 0
PRKCZ 0.007 0.023 -10000 0 -0.34 2 2
PRKCA -0.017 0.1 -10000 0 -0.42 33 33
PRKCG -0.031 0.1 -10000 0 -0.28 72 72
PRKCQ -0.015 0.1 -10000 0 -0.41 31 31
FKBP38/BCL2 -0.012 0.088 -10000 0 -0.29 48 48
EP300 0.008 0.005 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.011 0 -10000 0 -10000 0 0
NFATc/JNK1 0.029 0.051 -10000 0 -0.24 12 12
CaM/Ca2+/FKBP38 0.012 0.006 -10000 0 -10000 0 0
FKBP12/FK506 0.008 0 -10000 0 -10000 0 0
CSNK1A1 0.011 0.009 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.009 0.023 -10000 0 -0.17 7 7
NFATc/ERK1 0.037 0.045 -10000 0 -0.24 12 12
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.025 0.072 -10000 0 -0.32 17 17
NR4A1 -0.056 0.19 -10000 0 -0.41 112 112
GSK3B 0.009 0.005 -10000 0 -10000 0 0
positive T cell selection 0.014 0.017 -10000 0 -0.32 1 1
NFAT1/CK1 alpha -0.016 0.034 -10000 0 -0.24 3 3
RCH1/ KPNB1 0.01 0.032 -10000 0 -0.18 15 15
YWHAQ 0.011 0 -10000 0 -10000 0 0
PRKACA 0.009 0.004 -10000 0 -10000 0 0
AKAP5 0.008 0.033 -10000 0 -0.42 3 3
MEF2D 0.008 0.005 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.011 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.031 0.047 -10000 0 -0.24 12 12
CREBBP 0.007 0.019 -10000 0 -0.42 1 1
BCL2 -0.029 0.12 -10000 0 -0.42 48 48
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.011 0 -10000 0 -10000 0 0
HDAC3 0.011 0 -10000 0 -10000 0 0
VDR 0.005 0.039 -10000 0 -0.27 10 10
Cbp/p300/PCAF 0.016 0.037 -10000 0 -0.23 11 11
EP300 0.011 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.02 0.051 -10000 0 -0.28 7 7
KAT2B 0.002 0.059 -10000 0 -0.42 10 10
MAPK14 0.011 0 -10000 0 -10000 0 0
AKT1 0.012 0.058 0.19 19 -0.24 11 30
RAR alpha/9cRA/Cyclin H -0.017 0.066 -10000 0 -0.24 33 33
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.016 0.056 -10000 0 -0.26 13 13
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.002 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.002 0.065 -10000 0 -0.24 20 20
NCOR2 0.011 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.004 0.026 -10000 0 -0.18 10 10
RXRs/RARs/NRIP1/9cRA 0.003 0.13 -10000 0 -0.41 39 39
NCOA2 -0.004 0.079 -10000 0 -0.42 18 18
NCOA3 0.01 0.012 -10000 0 -0.27 1 1
NCOA1 0.01 0.019 -10000 0 -0.42 1 1
VDR/VDR/DNA 0.005 0.039 -10000 0 -0.27 10 10
RARG 0.011 0.001 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.015 0.001 -10000 0 -10000 0 0
MAPK3 0.011 0.001 -10000 0 -10000 0 0
MAPK1 0.011 0 -10000 0 -10000 0 0
MAPK8 0.007 0.042 -10000 0 -0.42 5 5
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.002 0.12 -10000 0 -0.39 39 39
RARA -0.002 0.07 -10000 0 -0.23 41 41
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.01 0.069 -10000 0 -0.28 18 18
PRKCA -0.015 0.1 -10000 0 -0.42 33 33
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.006 0.14 -10000 0 -0.43 39 39
RXRG -0.039 0.12 -10000 0 -0.3 80 80
RXRA 0.004 0.065 -10000 0 -0.21 41 41
RXRB -0.009 0.083 -10000 0 -0.29 37 37
VDR/Vit D3/DNA 0.004 0.026 -10000 0 -0.18 10 10
RBP1 -0.007 0.085 -10000 0 -0.42 21 21
CRBP1/9-cic-RA -0.004 0.06 -10000 0 -0.29 21 21
RARB 0.004 0.059 -10000 0 -0.42 10 10
PRKCG -0.029 0.1 -10000 0 -0.28 72 72
MNAT1 0.011 0 -10000 0 -10000 0 0
RAR alpha/RXRs 0.003 0.13 -10000 0 -0.43 38 38
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.008 0.11 -10000 0 -0.34 37 37
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.068 -10000 0 -0.35 8 8
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.006 0.14 -10000 0 -0.43 39 39
positive regulation of DNA binding -0.016 0.062 -10000 0 -0.23 33 33
NRIP1 -0.006 0.15 -10000 0 -0.82 9 9
RXRs/RARs -0.01 0.13 -10000 0 -0.42 40 40
RXRs/RXRs/DNA/9cRA -0.009 0.12 -10000 0 -0.4 39 39
PRKACA 0.011 0 -10000 0 -10000 0 0
CDK7 0.011 0 -10000 0 -10000 0 0
TFIIH 0.022 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.009 0.039 -10000 0 -0.33 2 2
CCNH 0.011 0 -10000 0 -10000 0 0
CREBBP 0.01 0.019 -10000 0 -0.42 1 1
RAR gamma2/9cRA 0 0 -10000 0 -10000 0 0
Signaling events mediated by PRL

Figure S82.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S82.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCNE1 -0.11 0.14 -9999 0 -0.27 225 225
mol:Halofuginone 0.004 0.001 -9999 0 -10000 0 0
ITGA1 0.008 0.033 -9999 0 -0.42 3 3
CDKN1A 0.005 0.053 -9999 0 -0.43 3 3
PRL-3/alpha Tubulin 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ -0.043 0.1 -9999 0 -0.29 77 77
AGT -0.052 0.15 -9999 0 -0.4 77 77
CCNA2 -0.04 0.098 -9999 0 -0.3 26 26
TUBA1B 0.011 0 -9999 0 -10000 0 0
EGR1 -0.032 0.11 -9999 0 -0.28 86 86
CDK2/Cyclin E1 0.027 0.087 -9999 0 -0.49 3 3
MAPK3 0.017 0 -9999 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.016 0 -9999 0 -10000 0 0
MAPK1 0.017 0 -9999 0 -10000 0 0
PTP4A1 -0.01 0.084 -9999 0 -10000 0 0
PTP4A3 0.011 0 -9999 0 -10000 0 0
PTP4A2 0.011 0 -9999 0 -10000 0 0
ITGB1 0.017 0 -9999 0 -10000 0 0
SRC 0.011 0 -9999 0 -10000 0 0
RAC1 0.008 0.041 -9999 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0.016 0 -9999 0 -10000 0 0
PRL-1/ATF-5 -0.005 0.08 -9999 0 -0.3 1 1
RABGGTA 0.011 0 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
RHOC 0.008 0.041 -9999 0 -10000 0 0
RHOA 0.008 0.041 -9999 0 -10000 0 0
cell motility 0.01 0.044 -9999 0 -10000 0 0
PRL-1/alpha Tubulin -0.004 0.078 -9999 0 -10000 0 0
PRL-3/alpha1 Integrin 0.014 0.023 -9999 0 -0.29 3 3
ROCK1 0.01 0.044 -9999 0 -10000 0 0
RABGGTB 0.011 0 -9999 0 -10000 0 0
CDK2 0.011 0 -9999 0 -10000 0 0
mitosis -0.01 0.084 -9999 0 -10000 0 0
ATF5 0.008 0.025 -9999 0 -0.27 4 4
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.015 0.051 -9999 0 -0.21 21 21
MAP4K1 0.004 0.043 -9999 0 -0.27 12 12
MAP3K8 0.006 0.042 -9999 0 -0.42 5 5
PRKCB -0.015 0.1 -9999 0 -0.42 31 31
DBNL 0.011 0 -9999 0 -10000 0 0
CRKL 0.011 0 -9999 0 -10000 0 0
MAP3K1 0.026 0.041 -9999 0 -0.21 1 1
JUN -0.012 0.14 -9999 0 -0.53 36 36
MAP3K7 0.026 0.041 -9999 0 -0.18 20 20
GRAP2 -0.006 0.083 -9999 0 -0.42 20 20
CRK 0.011 0 -9999 0 -10000 0 0
MAP2K4 0.03 0.043 -9999 0 -0.2 1 1
LAT 0.011 0 -9999 0 -10000 0 0
LCP2 0.01 0.012 -9999 0 -0.27 1 1
MAPK8 -0.016 0.15 -9999 0 -0.55 36 36
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.022 0.044 -9999 0 -0.19 20 20
LAT/GRAP2/SLP76/HPK1/HIP-55 0.02 0.048 -9999 0 -0.19 21 21
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.027 0.023 -9999 0 -10000 0 0
PLK1 -0.049 0.17 -9999 0 -0.52 23 23
CDKN1B 0.016 0.13 -9999 0 -0.44 24 24
FOXO3 -0.025 0.17 -9999 0 -0.46 55 55
KAT2B -0.002 0.061 -9999 0 -0.42 10 10
FOXO1/SIRT1 0.021 0.028 -9999 0 -10000 0 0
CAT -0.016 0.16 -9999 0 -0.68 4 4
CTNNB1 0.011 0 -9999 0 -10000 0 0
AKT1 0.009 0.016 -9999 0 -10000 0 0
FOXO1 0.027 0.024 -9999 0 -0.23 4 4
MAPK10 -0.022 0.093 -9999 0 -0.19 115 115
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
FOXO4 0.035 0.078 -9999 0 -0.32 5 5
response to oxidative stress -0.001 0.017 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.06 0.14 -9999 0 -0.41 67 67
XPO1 0.011 0 -9999 0 -10000 0 0
EP300 0.012 0.001 -9999 0 -10000 0 0
BCL2L11 0.015 0.024 -9999 0 -10000 0 0
FOXO1/SKP2 0.029 0.022 -9999 0 -10000 0 0
mol:GDP -0.001 0.017 -9999 0 -10000 0 0
RAN 0.012 0 -9999 0 -10000 0 0
GADD45A 0.021 0.093 -9999 0 -0.46 2 2
YWHAQ 0.011 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.04 0.011 -9999 0 -10000 0 0
MST1 0.001 0.043 -9999 0 -0.28 10 10
CSNK1D 0.011 0 -9999 0 -10000 0 0
CSNK1E 0.011 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.029 0.01 -9999 0 -10000 0 0
YWHAB 0.011 0 -9999 0 -10000 0 0
MAPK8 0.024 0.023 -9999 0 -0.2 5 5
MAPK9 0.026 0.008 -9999 0 -10000 0 0
YWHAG 0.011 0 -9999 0 -10000 0 0
YWHAE 0.011 0 -9999 0 -10000 0 0
YWHAZ 0.011 0 -9999 0 -10000 0 0
SIRT1 0.008 0.027 -9999 0 -0.41 2 2
SOD2 0.033 0.11 -9999 0 -0.43 3 3
RBL2 0.002 0.14 -9999 0 -0.77 5 5
RAL/GDP 0.018 0.01 -9999 0 -10000 0 0
CHUK 0.007 0.015 -9999 0 -10000 0 0
Ran/GTP 0.011 0.001 -9999 0 -10000 0 0
CSNK1G2 0.011 0 -9999 0 -10000 0 0
RAL/GTP 0.023 0.011 -9999 0 -10000 0 0
CSNK1G1 0.011 0 -9999 0 -10000 0 0
FASLG 0.005 0.1 -9999 0 -1.3 3 3
SKP2 0.011 0 -9999 0 -10000 0 0
USP7 0.012 0 -9999 0 -10000 0 0
IKBKB 0.007 0.015 -9999 0 -10000 0 0
CCNB1 -0.025 0.16 -9999 0 -0.52 22 22
FOXO1-3a-4/beta catenin 0.044 0.11 -9999 0 -0.36 7 7
proteasomal ubiquitin-dependent protein catabolic process 0.029 0.022 -9999 0 -10000 0 0
CSNK1A1 0.011 0 -9999 0 -10000 0 0
SGK1 0.004 0.037 -9999 0 -0.44 3 3
CSNK1G3 0.011 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.02 0.002 -9999 0 -10000 0 0
ZFAND5 0.04 0.068 -9999 0 -10000 0 0
SFN -0.21 0.12 -9999 0 -0.27 400 400
CDK2 0.012 0.002 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.02 0.031 -9999 0 -10000 0 0
CREBBP 0.011 0.019 -9999 0 -0.42 1 1
FBXO32 -0.11 0.4 -9999 0 -1.2 64 64
BCL6 0.004 0.13 -9999 0 -0.68 4 4
RALB 0.012 0 -9999 0 -10000 0 0
RALA 0.012 0 -9999 0 -10000 0 0
YWHAH 0.011 0 -9999 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.008 0.061 -10000 0 -0.42 8 8
FYN 0.036 0.092 -10000 0 -0.48 10 10
LAT/GRAP2/SLP76 -0.008 0.076 -10000 0 -0.37 15 15
IKBKB 0.011 0 -10000 0 -10000 0 0
AKT1 0.039 0.07 -10000 0 -0.3 15 15
B2M 0.012 0.002 -10000 0 -10000 0 0
IKBKG -0.003 0.016 -10000 0 -0.12 5 5
MAP3K8 0.006 0.042 -10000 0 -0.42 5 5
mol:Ca2+ -0.009 0.022 -10000 0 -0.073 47 47
integrin-mediated signaling pathway 0.014 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.039 0.096 -10000 0 -0.4 16 16
TRPV6 -0.047 0.12 -10000 0 -0.34 72 72
CD28 0.01 0.018 -10000 0 -0.27 2 2
SHC1 0.036 0.087 -10000 0 -0.49 9 9
receptor internalization 0.03 0.079 -10000 0 -0.42 10 10
PRF1 0.023 0.13 -10000 0 -1.1 6 6
KRAS 0.01 0.012 -10000 0 -0.27 1 1
GRB2 0.011 0 -10000 0 -10000 0 0
COT/AKT1 0.038 0.061 -10000 0 -0.25 14 14
LAT 0.036 0.087 -10000 0 -0.49 9 9
EntrezGene:6955 0.001 0.002 -10000 0 -10000 0 0
CD3D -0.002 0.068 -10000 0 -0.32 21 21
CD3E 0.004 0.057 -10000 0 -0.37 11 11
CD3G 0.007 0.039 -10000 0 -0.35 6 6
RASGRP2 -0.014 0.06 -10000 0 -0.16 74 74
RASGRP1 0.042 0.076 -10000 0 -0.32 14 14
HLA-A 0.011 0.013 -10000 0 -0.27 1 1
RASSF5 0.011 0 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.014 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.023 0.033 -10000 0 -0.11 11 11
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.006 0.029 -10000 0 -0.17 10 10
PRKCA -0.004 0.044 -10000 0 -0.19 16 16
GRAP2 -0.006 0.083 -10000 0 -0.42 20 20
mol:IP3 0.008 0.077 0.16 58 -0.3 12 70
EntrezGene:6957 0.001 0.002 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.021 0.075 -10000 0 -0.5 7 7
ORAI1 0.03 0.073 0.21 72 -10000 0 72
CSK 0.034 0.089 -10000 0 -0.5 9 9
B7 family/CD28 0.038 0.087 -10000 0 -0.42 12 12
CHUK 0.011 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.031 0.1 -10000 0 -0.46 13 13
PTPN6 0.033 0.089 -10000 0 -0.5 9 9
VAV1 0.034 0.091 -10000 0 -0.49 10 10
Monovalent TCR/CD3 0.013 0.055 -10000 0 -0.27 15 15
CBL 0.011 0 -10000 0 -10000 0 0
LCK 0.033 0.096 -10000 0 -0.48 11 11
PAG1 0.034 0.092 -10000 0 -0.49 10 10
RAP1A 0.011 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.03 0.098 -10000 0 -0.56 9 9
CD80 0 0.053 -10000 0 -0.27 19 19
CD86 0.01 0.018 -10000 0 -0.28 2 2
PDK1/CARD11/BCL10/MALT1 -0.007 0.035 -10000 0 -0.2 11 11
HRAS 0.011 0 -10000 0 -10000 0 0
GO:0035030 0.034 0.075 -10000 0 -0.36 12 12
CD8A 0.003 0.059 -10000 0 -0.37 12 12
CD8B -0.007 0.076 -10000 0 -0.3 31 31
PTPRC 0.001 0.063 -10000 0 -0.41 12 12
PDK1/PKC theta 0.043 0.087 -10000 0 -0.37 14 14
CSK/PAG1 0.036 0.089 -10000 0 -0.48 10 10
SOS1 0.011 0 -10000 0 -10000 0 0
peptide-MHC class I 0.018 0.009 -10000 0 -0.17 1 1
GRAP2/SLP76 -0.01 0.088 -10000 0 -0.43 15 15
STIM1 0.014 0.035 -10000 0 -10000 0 0
RAS family/GTP 0.04 0.033 -10000 0 -0.16 5 5
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.03 0.083 -10000 0 -0.47 9 9
mol:DAG -0.003 0.054 -10000 0 -0.27 13 13
RAP1A/GDP 0.011 0.015 -10000 0 -0.053 7 7
PLCG1 0.011 0 -10000 0 -10000 0 0
CD247 0.01 0.023 -10000 0 -0.35 2 2
cytotoxic T cell degranulation 0.024 0.12 -10000 0 -1 6 6
RAP1A/GTP -0.009 0.02 -10000 0 -0.058 74 74
mol:PI-3-4-5-P3 0.039 0.082 -10000 0 -0.34 16 16
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.006 0.091 0.18 56 -0.38 12 68
NRAS 0.011 0 -10000 0 -10000 0 0
ZAP70 0 0.056 -10000 0 -0.29 18 18
GRB2/SOS1 0.016 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.009 0.073 -10000 0 -0.35 16 16
MALT1 0.011 0 -10000 0 -10000 0 0
TRAF6 0.011 0 -10000 0 -10000 0 0
CD8 heterodimer 0 0.07 -10000 0 -0.23 39 39
CARD11 0.003 0.049 -10000 0 -0.29 13 13
PRKCB -0.007 0.056 -10000 0 -0.23 23 23
PRKCE -0.002 0.039 -10000 0 -0.2 12 12
PRKCQ 0.038 0.096 -10000 0 -0.42 14 14
LCP2 0.01 0.012 -10000 0 -0.27 1 1
BCL10 0.011 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.038 0.062 -10000 0 -0.25 15 15
IKK complex 0.029 0.035 -10000 0 -0.093 15 15
RAS family/GDP -0.001 0.004 -10000 0 -10000 0 0
MAP3K14 0.038 0.049 -10000 0 -0.2 11 11
PDPK1 0.04 0.068 -10000 0 -0.29 14 14
TCR/CD3/MHC I/CD8/Fyn 0.025 0.11 -10000 0 -0.58 12 12
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.011 0.02 0.18 1 -10000 0 1
AES 0.011 0.017 0.16 1 -10000 0 1
FBXW11 0.011 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.015 0.014 -10000 0 -0.29 1 1
SMAD4 0.01 0.019 -10000 0 -0.42 1 1
DKK2 -0.021 0.11 -10000 0 -0.4 39 39
TLE1 0.01 0.025 0.16 1 -0.42 1 2
MACF1 0.011 0 -10000 0 -10000 0 0
CTNNB1 0.035 0.04 0.21 4 -10000 0 4
WIF1 -0.081 0.14 -10000 0 -0.29 155 155
beta catenin/RanBP3 0.02 0.09 0.36 33 -10000 0 33
KREMEN2 -0.017 0.084 -10000 0 -0.27 50 50
DKK1 -0.051 0.12 -10000 0 -0.28 108 108
beta catenin/beta TrCP1 0.04 0.038 0.2 4 -10000 0 4
FZD1 0.01 0.019 -10000 0 -0.42 1 1
AXIN2 -0.051 0.28 -10000 0 -1.3 25 25
AXIN1 0.011 0 -10000 0 -10000 0 0
RAN 0.011 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.013 0.021 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.045 0.053 0.22 1 -0.33 5 6
Axin1/APC/GSK3 0.017 0.027 0.18 2 -10000 0 2
Axin1/APC/GSK3/beta catenin/Macf1 0.041 0.021 -10000 0 -10000 0 0
HNF1A -0.005 0.068 0.16 1 -0.27 29 30
CTBP1 0.011 0.017 0.17 1 -10000 0 1
MYC -0.018 0.19 -10000 0 -1.3 10 10
RANBP3 0.011 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.013 0.082 -10000 0 -0.25 38 38
NKD1 -0.016 0.088 -10000 0 -0.3 44 44
TCF4 -0.005 0.081 0.16 1 -0.41 19 20
TCF3 0.011 0.017 0.16 1 -10000 0 1
WNT1/LRP6/FZD1/Axin1 0.024 0.021 -10000 0 -0.21 1 1
Ran/GTP 0.008 0.002 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.019 0.11 0.44 27 -0.4 2 29
LEF1 0.006 0.045 0.16 1 -0.37 6 7
DVL1 0.03 0.016 -10000 0 -10000 0 0
CSNK2A1 0.011 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.041 0.076 -10000 0 -0.34 10 10
DKK1/LRP6/Kremen 2 -0.028 0.078 -10000 0 -0.26 10 10
LRP6 0.011 0 -10000 0 -10000 0 0
CSNK1A1 0.012 0.02 0.18 1 -10000 0 1
NLK 0.011 0.003 -10000 0 -10000 0 0
CCND1 0.003 0.055 -10000 0 -10000 0 0
WNT1 0.004 0.035 -10000 0 -0.27 8 8
GSK3A 0.011 0 -10000 0 -10000 0 0
GSK3B 0.011 0 -10000 0 -10000 0 0
FRAT1 0.011 0 -10000 0 -10000 0 0
PPP2R5D 0.027 0.041 0.25 8 -10000 0 8
APC 0.027 0.019 -10000 0 -0.18 1 1
WNT1/LRP6/FZD1 0.031 0.046 0.2 18 -0.19 1 19
CREBBP 0.01 0.024 0.16 1 -0.38 1 2
Regulation of Telomerase

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
Telomerase catalytic core complex -0.12 0.1 -9999 0 -0.46 2 2
RAD9A 0.011 0 -9999 0 -10000 0 0
AP1 -0.093 0.15 -9999 0 -0.3 174 174
IFNAR2 0.009 0.019 -9999 0 -0.42 1 1
AKT1 -0.012 0.056 -9999 0 -10000 0 0
ER alpha/Oestrogen -0.027 0.093 -9999 0 -0.29 56 56
NFX1/SIN3/HDAC complex 0.033 0.012 -9999 0 -10000 0 0
EGF -0.002 0.058 -9999 0 -0.29 20 20
SMG5 0.011 0 -9999 0 -10000 0 0
SMG6 0.011 0 -9999 0 -10000 0 0
SP3/HDAC2 0.01 0.009 -9999 0 -10000 0 0
TERT/c-Abl -0.11 0.097 -9999 0 -0.44 4 4
SAP18 0.01 0.001 -9999 0 -10000 0 0
MRN complex 0.022 0 -9999 0 -10000 0 0
WT1 -0.31 0.18 -9999 0 -0.42 386 386
WRN 0.011 0 -9999 0 -10000 0 0
SP1 0.007 0.006 -9999 0 -10000 0 0
SP3 0.01 0.001 -9999 0 -10000 0 0
TERF2IP 0.011 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.096 0.076 -9999 0 -0.44 1 1
Mad/Max 0.01 0.009 -9999 0 -10000 0 0
TERT -0.12 0.1 -9999 0 -0.46 2 2
CCND1 -0.1 0.095 -9999 0 -10000 0 0
MAX 0.01 0.001 -9999 0 -10000 0 0
RBBP7 0.01 0.001 -9999 0 -10000 0 0
RBBP4 0.009 0.027 -9999 0 -0.42 2 2
TERF2 0.01 0 -9999 0 -10000 0 0
PTGES3 0.011 0 -9999 0 -10000 0 0
SIN3A 0.01 0.001 -9999 0 -10000 0 0
Telomerase/911 0.008 0.018 -9999 0 -10000 0 0
CDKN1B -0.003 0.11 -9999 0 -0.51 20 20
RAD1 0.011 0 -9999 0 -10000 0 0
XRCC5 0.011 0 -9999 0 -10000 0 0
XRCC6 0.011 0 -9999 0 -10000 0 0
SAP30 0.01 0.001 -9999 0 -10000 0 0
TRF2/PARP2 0.016 0 -9999 0 -10000 0 0
UBE3A 0.01 0.001 -9999 0 -10000 0 0
JUN 0.005 0.046 -9999 0 -0.42 6 6
E6 -0.001 0.001 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.005 0.005 -9999 0 -10000 0 0
FOS -0.14 0.2 -9999 0 -0.42 174 174
IFN-gamma/IRF1 -0.008 0.067 -9999 0 -0.26 20 20
PARP2 0.011 0 -9999 0 -10000 0 0
BLM -0.013 0.078 -9999 0 -0.27 43 43
Telomerase -0.008 0.027 -9999 0 -10000 0 0
IRF1 0.008 0.032 -9999 0 -10000 0 0
ESR1 -0.036 0.13 -9999 0 -0.42 56 56
KU/TER 0.016 0 -9999 0 -10000 0 0
ATM/TRF2 0.017 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.037 0.012 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.037 0.012 -9999 0 -10000 0 0
HDAC1 0.01 0.001 -9999 0 -10000 0 0
HDAC2 0.009 0.004 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.015 0.03 -9999 0 -0.29 5 5
ABL1 0.009 0.027 -9999 0 -0.42 2 2
MXD1 0.01 0.001 -9999 0 -10000 0 0
MRE11A 0.011 0 -9999 0 -10000 0 0
HUS1 0.011 0 -9999 0 -10000 0 0
RPS6KB1 0.011 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.087 0.08 -9999 0 -0.41 1 1
NR2F2 -0.005 0.083 -9999 0 -0.42 20 20
MAPK3 0.005 0.034 -9999 0 -0.18 17 17
MAPK1 0.005 0.034 -9999 0 -0.18 17 17
TGFB1/TGF beta receptor Type II 0.01 0.019 -9999 0 -0.42 1 1
NFKB1 0.01 0.019 -9999 0 -0.42 1 1
HNRNPC 0.011 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0 -9999 0 -10000 0 0
NBN 0.011 0 -9999 0 -10000 0 0
EGFR -0.001 0.068 -9999 0 -0.41 14 14
mol:Oestrogen 0 0.001 -9999 0 -10000 0 0
EGF/EGFR -0.001 0.063 -9999 0 -0.23 33 33
MYC 0.002 0.059 -9999 0 -0.42 10 10
IL2 -0.007 0.05 -9999 0 -0.27 17 17
KU 0.016 0 -9999 0 -10000 0 0
RAD50 0.011 0 -9999 0 -10000 0 0
HSP90AA1 0.011 0 -9999 0 -10000 0 0
TGFB1 0.01 0.019 -9999 0 -0.42 1 1
TRF2/BLM 0.001 0.048 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.1 0.096 -9999 0 -0.48 1 1
SP1/HDAC2 0.012 0.01 -9999 0 -10000 0 0
PINX1 0.011 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.096 0.076 -9999 0 -0.44 1 1
Smad3/Myc 0.014 0.045 -9999 0 -0.25 14 14
911 complex 0.022 0 -9999 0 -10000 0 0
IFNG -0.012 0.072 -9999 0 -0.26 31 31
Telomerase/PinX1 -0.096 0.076 -9999 0 -0.44 1 1
Telomerase/AKT1/mTOR/p70S6K -0.013 0.036 -9999 0 -10000 0 0
SIN3B 0.01 0.001 -9999 0 -10000 0 0
YWHAE 0.011 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.096 0.076 -9999 0 -0.44 1 1
response to DNA damage stimulus 0.003 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0.031 0 -9999 0 -10000 0 0
TRF2/WRN 0.016 0 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.096 0.076 -9999 0 -0.44 1 1
E2F1 -0.051 0.12 -9999 0 -0.27 109 109
ZNFX1 0.01 0.001 -9999 0 -10000 0 0
PIF1 -0.058 0.12 -9999 0 -0.27 124 124
NCL 0.011 0 -9999 0 -10000 0 0
DKC1 0.011 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.011 0 -9999 0 -10000 0 0
SPHK1 0.01 0.018 -9999 0 -0.27 2 2
GNAI2 0.011 0 -9999 0 -10000 0 0
mol:S1P 0.017 0.003 -9999 0 -10000 0 0
GNAO1 -0.098 0.19 -9999 0 -0.42 131 131
mol:Sphinganine-1-P 0.017 0.012 -9999 0 -0.18 2 2
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.031 0.002 -9999 0 -10000 0 0
GNAI3 0.011 0 -9999 0 -10000 0 0
G12/G13 0.016 0 -9999 0 -10000 0 0
S1PR3 -0.004 0.076 -9999 0 -0.42 17 17
S1PR2 0.011 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P 0 0.002 -9999 0 -10000 0 0
S1PR5 0.002 0.05 -9999 0 -0.28 15 15
S1PR4 0.009 0.023 -9999 0 -0.34 2 2
GNAI1 0.002 0.059 -9999 0 -0.42 10 10
S1P/S1P5/G12 0.021 0.025 -9999 0 -0.2 1 1
S1P/S1P3/Gq -0.009 0.1 -9999 0 -0.26 57 57
S1P/S1P4/Gi -0.037 0.12 -9999 0 -0.39 17 17
GNAQ 0.009 0.027 -9999 0 -0.42 2 2
GNAZ -0.011 0.094 -9999 0 -0.42 26 26
GNA14 -0.034 0.13 -9999 0 -0.42 53 53
GNA15 0.007 0.033 -9999 0 -0.27 7 7
GNA12 0.011 0 -9999 0 -10000 0 0
GNA13 0.011 0 -9999 0 -10000 0 0
GNA11 0.001 0.062 -9999 0 -0.42 11 11
ABCC1 0.011 0 -9999 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.072 0.089 -9999 0 -0.28 1 1
CaM/Ca2+ 0.008 0 -9999 0 -10000 0 0
AKT1 0.011 0 -9999 0 -10000 0 0
AKT2 0.011 0 -9999 0 -10000 0 0
STXBP4 0.01 0.019 -9999 0 -0.42 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucose -0.078 0.1 -9999 0 -0.31 1 1
YWHAZ 0.011 0 -9999 0 -10000 0 0
CALM1 0.011 0 -9999 0 -10000 0 0
YWHAQ 0.011 0 -9999 0 -10000 0 0
TBC1D4 0.015 0.027 -9999 0 -0.29 4 4
mol:Ca2+ 0 0 -9999 0 -10000 0 0
YWHAH 0.011 0 -9999 0 -10000 0 0
YWHAB 0.011 0 -9999 0 -10000 0 0
SNARE/Synip 0.021 0.016 -9999 0 -0.23 2 2
YWHAG 0.011 0 -9999 0 -10000 0 0
ASIP 0.007 0.013 -9999 0 -0.27 1 1
PRKCI 0.011 0 -9999 0 -10000 0 0
AS160/CaM/Ca2+ 0.008 0 -9999 0 -10000 0 0
RHOQ 0.011 0 -9999 0 -10000 0 0
GYS1 0.024 0 -9999 0 -10000 0 0
PRKCZ 0.009 0.023 -9999 0 -0.34 2 2
TRIP10 0.011 0 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.014 0 -9999 0 -10000 0 0
AS160/14-3-3 0.012 0.018 -9999 0 -10000 0 0
VAMP2 0.01 0.019 -9999 0 -0.42 1 1
SLC2A4 -0.085 0.11 -9999 0 -0.34 1 1
STX4 0.011 0 -9999 0 -10000 0 0
GSK3B 0.02 0 -9999 0 -10000 0 0
SFN -0.21 0.12 -9999 0 -0.27 400 400
LNPEP 0.011 0 -9999 0 -10000 0 0
YWHAE 0.011 0 -9999 0 -10000 0 0
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.011 0 -10000 0 -10000 0 0
mol:PIP3 -0.022 0.079 0.23 5 -0.25 49 54
FRAP1 0.008 0.018 -10000 0 -10000 0 0
AKT1 0.001 0.071 0.2 5 -0.21 49 54
INSR 0.011 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.008 0.002 -10000 0 -10000 0 0
mol:GTP -0.015 0.048 -10000 0 -0.16 46 46
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.004 0.014 -10000 0 -10000 0 0
TSC2 0.011 0 -10000 0 -10000 0 0
RHEB/GDP -0.013 0.04 -10000 0 -0.28 2 2
TSC1 0.01 0.019 -10000 0 -0.42 1 1
Insulin Receptor/IRS1 -0.016 0.091 -10000 0 -0.3 47 47
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.005 0.017 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.011 0 -10000 0 -10000 0 0
RPS6KB1 0.011 0.04 0.16 5 -0.22 2 7
MAP3K5 0.006 0.026 -10000 0 -0.33 3 3
PIK3R1 0.007 0.038 -10000 0 -0.42 4 4
apoptosis 0.006 0.025 -10000 0 -0.33 3 3
mol:LY294002 0 0 -10000 0 -0.001 47 47
EIF4B 0.016 0.037 0.16 5 -0.19 2 7
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.017 0.032 -10000 0 -0.18 2 2
eIF4E/eIF4G1/eIF4A1 -0.001 0.004 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.008 0.088 -10000 0 -0.27 50 50
mTOR/RHEB/GTP/Raptor/GBL 0.017 0.028 0.15 5 -0.14 3 8
FKBP1A 0.011 0 -10000 0 -10000 0 0
RHEB/GTP -0.013 0.04 -10000 0 -0.27 2 2
mol:Amino Acids 0 0 -10000 0 -0.001 47 47
FKBP12/Rapamycin 0.008 0.001 -10000 0 -10000 0 0
PDPK1 -0.02 0.071 0.21 5 -0.23 49 54
EIF4E 0.011 0 -10000 0 -10000 0 0
ASK1/PP5C 0.012 0.047 -10000 0 -0.58 3 3
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.013 0.002 -10000 0 -10000 0 0
TSC1/TSC2 0.011 0.06 -10000 0 -0.17 46 46
tumor necrosis factor receptor activity 0 0 0.001 47 -10000 0 47
RPS6 0.011 0 -10000 0 -10000 0 0
PPP5C 0.011 0 -10000 0 -10000 0 0
EIF4G1 0.011 0 -10000 0 -10000 0 0
IRS1 -0.024 0.096 -10000 0 -0.33 47 47
INS 0.001 0.002 -10000 0 -10000 0 0
PTEN 0.005 0.046 -10000 0 -0.42 6 6
PDK2 -0.02 0.071 0.21 5 -0.23 49 54
EIF4EBP1 0.012 0.013 -10000 0 -10000 0 0
PIK3CA 0.01 0.019 -10000 0 -0.42 1 1
PPP2R5D 0.013 0.017 -10000 0 -10000 0 0
peptide biosynthetic process 0.014 0.001 -10000 0 -10000 0 0
RHEB 0.011 0 -10000 0 -10000 0 0
EIF4A1 0.011 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 0.003 6 -0.002 5 11
EEF2 0.014 0.001 -10000 0 -10000 0 0
eIF4E/4E-BP1 0.017 0.009 -10000 0 -10000 0 0
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.031 0.036 -10000 0 -0.17 12 12
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.011 0 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.043 0.037 -10000 0 -10000 0 0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.016 0.039 -10000 0 -0.23 12 12
antigen processing and presentation of peptide antigen via MHC class I -0.033 0.04 -10000 0 -0.22 7 7
CaM/Ca2+ 0.002 0.033 -10000 0 -0.16 4 4
RAP1A 0.011 0 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.025 0.039 -10000 0 -0.19 1 1
AKT1 0.029 0.041 -10000 0 -0.28 2 2
MAP2K1 0.03 0.036 -10000 0 -10000 0 0
MAP3K11 0.023 0.038 -10000 0 -10000 0 0
IFNGR1 0.011 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.18 0.17 -10000 0 -0.32 281 281
Rap1/GTP -0.005 0.019 -10000 0 -10000 0 0
CRKL/C3G 0.016 0 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.032 0.037 -10000 0 -0.18 12 12
CEBPB 0.051 0.043 -10000 0 -0.38 2 2
STAT3 0.011 0 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.034 0.059 -10000 0 -1 1 1
STAT1 0.024 0.038 -10000 0 -0.19 1 1
CALM1 0.011 0 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.007 0.066 -10000 0 -0.27 31 31
PIK3CA 0.01 0.019 -10000 0 -0.42 1 1
STAT1 (dimer)/PIAS1 0.029 0.037 -10000 0 -0.18 1 1
CEBPB/PTGES2/Cbp/p300 -0.002 0.019 -10000 0 -0.24 2 2
mol:Ca2+ 0.029 0.035 -10000 0 -0.17 12 12
MAPK3 0.037 0.035 -10000 0 -10000 0 0
STAT1 (dimer) -0.038 0.058 -10000 0 -0.3 7 7
MAPK1 0.037 0.035 -10000 0 -10000 0 0
JAK2 0.004 0.056 -10000 0 -0.42 9 9
PIK3R1 0.007 0.038 -10000 0 -0.42 4 4
JAK1 0.009 0.033 -10000 0 -0.41 3 3
CAMK2D 0.009 0.027 -10000 0 -0.42 2 2
DAPK1 0.048 0.047 -10000 0 -0.58 2 2
SMAD7 0.002 0.04 -10000 0 -0.3 1 1
CBL/CRKL/C3G 0.032 0.035 -10000 0 -10000 0 0
PI3K -0.001 0.037 -10000 0 -0.3 2 2
IFNG -0.007 0.066 -10000 0 -0.27 31 31
apoptosis 0.029 0.038 -10000 0 -0.43 2 2
CAMK2G 0.011 0 -10000 0 -10000 0 0
STAT3 (dimer) 0.011 0 -10000 0 -10000 0 0
CAMK2A -0.22 0.21 -10000 0 -0.42 281 281
CAMK2B -0.045 0.11 -10000 0 -0.27 100 100
FRAP1 0.028 0.039 -10000 0 -0.26 2 2
PRKCD 0.031 0.041 -10000 0 -0.28 2 2
RAP1B 0.011 0 -10000 0 -10000 0 0
negative regulation of cell growth -0.033 0.04 -10000 0 -0.22 7 7
PTPN2 0.011 0 -10000 0 -10000 0 0
EP300 0.011 0 -10000 0 -10000 0 0
IRF1 0.048 0.034 -10000 0 -0.26 1 1
STAT1 (dimer)/PIASy 0.026 0.037 0.17 1 -10000 0 1
SOCS1 -0.001 0.056 -10000 0 -1.3 1 1
mol:GDP -0.006 0.024 -10000 0 -10000 0 0
CASP1 0 0.044 -10000 0 -0.23 6 6
PTGES2 0.01 0.019 -10000 0 -0.42 1 1
IRF9 0.041 0.017 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.009 0.033 -10000 0 -0.29 2 2
RAP1/GDP -0.005 0.019 -10000 0 -10000 0 0
CBL 0.023 0.037 -10000 0 -0.16 4 4
MAP3K1 0.024 0.038 -10000 0 -10000 0 0
PIAS1 0.011 0 -10000 0 -10000 0 0
PIAS4 0.01 0 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.033 0.04 -10000 0 -0.22 7 7
PTPN11 0.017 0.039 -10000 0 -0.17 12 12
CREBBP 0.01 0.019 -10000 0 -0.42 1 1
RAPGEF1 0.011 0 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.038 0.04 -9999 0 -0.55 1 1
UGCG 0.005 0.093 -9999 0 -0.64 10 10
AKT1/mTOR/p70S6K/Hsp90/TERT 0.025 0.097 -9999 0 -0.24 46 46
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucosylceramide 0.005 0.092 -9999 0 -0.63 10 10
mol:DAG 0 0.001 -9999 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.039 0.11 -9999 0 -0.34 58 58
FRAP1 0.016 0.15 -9999 0 -0.39 58 58
FOXO3 0.037 0.098 -9999 0 -0.36 16 16
AKT1 0.032 0.1 -9999 0 -0.39 16 16
GAB2 0.006 0.042 -9999 0 -0.42 5 5
SMPD1 0.017 0.019 -9999 0 -10000 0 0
SGMS1 0.017 0.019 -9999 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
mol:GDP 0.013 0.026 -9999 0 -0.24 5 5
CALM1 0.011 0 -9999 0 -10000 0 0
cell proliferation 0.019 0.074 -9999 0 -0.29 20 20
EIF3A 0.011 0 -9999 0 -10000 0 0
PI3K 0.016 0.031 -9999 0 -0.29 5 5
RPS6KB1 0.013 0.02 -9999 0 -10000 0 0
mol:sphingomyelin 0 0.001 -9999 0 -10000 0 0
natural killer cell activation 0 0.003 -9999 0 -0.012 10 10
JAK3 0.01 0.022 -9999 0 -0.27 3 3
PIK3R1 0.008 0.038 -9999 0 -0.42 4 4
JAK1 0.01 0.033 -9999 0 -0.42 3 3
NFKB1 0.01 0.019 -9999 0 -0.42 1 1
MYC 0.027 0.15 -9999 0 -0.87 11 11
MYB 0.017 0.038 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.038 0.07 -9999 0 -0.3 7 7
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.024 0.019 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.038 0.069 -9999 0 -0.29 7 7
Rac1/GDP 0.018 0.024 -9999 0 -0.21 5 5
T cell proliferation 0.041 0.067 -9999 0 -0.34 3 3
SHC1 0.01 0.004 -9999 0 -10000 0 0
RAC1 0.011 0 -9999 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.002 0.006 -9999 0 -10000 0 0
PRKCZ 0.041 0.068 -9999 0 -0.35 3 3
NF kappa B1 p50/RelA -0.03 0.11 -9999 0 -0.34 58 58
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.034 0.043 -9999 0 -0.42 2 2
HSP90AA1 0.011 0 -9999 0 -10000 0 0
RELA 0.011 0 -9999 0 -10000 0 0
IL2RA 0 0.053 -9999 0 -0.28 17 17
IL2RB 0.011 0.019 -9999 0 -0.42 1 1
TERT -0.11 0.14 -9999 0 -0.27 225 225
E2F1 0.019 0.028 -9999 0 -10000 0 0
SOS1 0.01 0.004 -9999 0 -10000 0 0
RPS6 0.011 0 -9999 0 -10000 0 0
mol:cAMP -0.001 0.003 -9999 0 -10000 0 0
PTPN11 0.01 0.004 -9999 0 -10000 0 0
IL2RG 0.007 0.039 -9999 0 -0.31 7 7
actin cytoskeleton organization 0.041 0.067 -9999 0 -0.34 3 3
GRB2 0.01 0.004 -9999 0 -10000 0 0
IL2 -0.004 0.05 -9999 0 -0.27 17 17
PIK3CA 0.011 0.019 -9999 0 -0.42 1 1
Rac1/GTP 0.024 0.024 -9999 0 -0.2 5 5
LCK 0.009 0.031 -9999 0 -0.3 5 5
BCL2 -0.021 0.26 -9999 0 -0.82 48 48
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.015 0.084 -9999 0 -0.38 21 21
PDGFB-D/PDGFRB/SLAP 0.004 0.06 -9999 0 -0.28 21 21
PDGFB-D/PDGFRB/APS/CBL 0.012 0.05 -9999 0 -0.23 21 21
AKT1 0.033 0.047 -9999 0 -0.3 2 2
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.015 0.09 -9999 0 -0.41 21 21
PIK3CA 0.01 0.019 -9999 0 -0.42 1 1
FGR -0.024 0.1 -9999 0 -0.39 31 31
mol:Ca2+ 0.01 0.095 -9999 0 -0.44 21 21
MYC 0.019 0.13 -9999 0 -0.67 13 13
SHC1 0.011 0 -9999 0 -10000 0 0
HRAS/GDP 0.019 0.046 -9999 0 -0.18 26 26
LRP1/PDGFRB/PDGFB 0.011 0.054 -9999 0 -0.24 22 22
GRB10 0.01 0.019 -9999 0 -0.42 1 1
PTPN11 0.011 0 -9999 0 -10000 0 0
GO:0007205 0.01 0.096 -9999 0 -0.45 21 21
PTEN 0.006 0.046 -9999 0 -0.42 6 6
GRB2 0.011 0 -9999 0 -10000 0 0
GRB7 -0.007 0.07 -9999 0 -0.28 31 31
PDGFB-D/PDGFRB/SHP2 0.004 0.06 -9999 0 -0.28 21 21
PDGFB-D/PDGFRB/GRB10 0.003 0.061 -9999 0 -0.28 22 22
cell cycle arrest 0.004 0.06 -9999 0 -0.28 21 21
HRAS 0.011 0 -9999 0 -10000 0 0
HIF1A 0.037 0.043 -9999 0 -0.27 2 2
GAB1 0.013 0.093 -9999 0 -0.41 21 21
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.017 0.085 -9999 0 -0.37 21 21
PDGFB-D/PDGFRB 0.012 0.052 -9999 0 -0.24 21 21
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.004 0.06 -9999 0 -0.28 21 21
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.015 0.071 -9999 0 -0.34 21 21
positive regulation of MAPKKK cascade 0.004 0.06 -9999 0 -0.28 21 21
PIK3R1 0.007 0.038 -9999 0 -0.42 4 4
mol:IP3 0.01 0.097 -9999 0 -0.45 21 21
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.01 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.008 0.078 -9999 0 -0.24 49 49
SHB 0.011 0 -9999 0 -10000 0 0
BLK -0.009 0.054 -9999 0 -0.26 21 21
PTPN2 0.011 0.002 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.004 0.06 -9999 0 -0.28 21 21
BCAR1 0.011 0 -9999 0 -10000 0 0
VAV2 0.016 0.096 -9999 0 -0.4 21 21
CBL 0.011 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.003 0.061 -9999 0 -0.28 23 23
LCK -0.012 0.066 -9999 0 -0.29 21 21
PDGFRB -0.006 0.086 -9999 0 -0.42 21 21
ACP1 0.011 0 -9999 0 -10000 0 0
HCK -0.011 0.053 -9999 0 -0.26 21 21
ABL1 0.014 0.079 -9999 0 -0.35 21 21
PDGFB-D/PDGFRB/CBL 0.011 0.1 -9999 0 -0.47 21 21
PTPN1 0.011 0.002 -9999 0 -10000 0 0
SNX15 0.011 0 -9999 0 -10000 0 0
STAT3 0.011 0 -9999 0 -10000 0 0
STAT1 0.01 0.012 -9999 0 -0.27 1 1
cell proliferation 0.021 0.12 -9999 0 -0.6 13 13
SLA 0.011 0 -9999 0 -10000 0 0
actin cytoskeleton reorganization 0.03 0.042 -9999 0 -10000 0 0
SRC -0.011 0.053 -9999 0 -0.26 21 21
PI3K -0.01 0.04 -9999 0 -0.34 2 2
PDGFB-D/PDGFRB/GRB7/SHC 0.002 0.065 -9999 0 -0.25 23 23
SH2B2 0.011 0 -9999 0 -10000 0 0
PLCgamma1/SPHK1 0.015 0.092 -9999 0 -0.42 21 21
LYN -0.011 0.052 -9999 0 -0.26 21 21
LRP1 0.009 0.027 -9999 0 -0.42 2 2
SOS1 0.011 0 -9999 0 -10000 0 0
STAT5B 0.01 0.019 -9999 0 -0.42 1 1
STAT5A 0.011 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas -0.004 0.038 -9999 0 -10000 0 0
SPHK1 0.01 0.018 -9999 0 -0.27 2 2
EDG1 0.001 0.002 -9999 0 -10000 0 0
mol:DAG 0.01 0.097 -9999 0 -0.45 21 21
PLCG1 0.009 0.099 -9999 0 -0.46 21 21
NHERF/PDGFRB 0.01 0.052 -9999 0 -0.23 21 21
YES1 -0.011 0.052 -9999 0 -0.26 21 21
cell migration 0.01 0.052 -9999 0 -0.23 21 21
SHC/Grb2/SOS1 -0.003 0.037 -9999 0 -0.18 1 1
SLC9A3R2 0.011 0 -9999 0 -10000 0 0
SLC9A3R1 0.008 0.028 -9999 0 -0.27 5 5
NHERF1-2/PDGFRB/PTEN 0.014 0.055 -9999 0 -0.21 26 26
FYN -0.011 0.052 -9999 0 -0.26 21 21
DOK1 0.016 0.046 -9999 0 -0.21 21 21
HRAS/GTP 0.008 0 -9999 0 -10000 0 0
PDGFB 0.011 0 -9999 0 -10000 0 0
RAC1 0.021 0.1 -9999 0 -0.37 31 31
PRKCD 0.017 0.046 -9999 0 -0.21 21 21
FER 0.017 0.046 -9999 0 -0.21 21 21
MAPKKK cascade -0.006 0.035 -9999 0 -0.18 1 1
RASA1 0.014 0.051 -9999 0 -0.21 26 26
NCK1 0.009 0.027 -9999 0 -0.42 2 2
NCK2 0.011 0 -9999 0 -10000 0 0
p62DOK/Csk 0.021 0.042 -9999 0 -0.18 21 21
PDGFB-D/PDGFRB/SHB 0.004 0.06 -9999 0 -0.28 21 21
chemotaxis 0.015 0.077 -9999 0 -0.34 21 21
STAT1-3-5/STAT1-3-5 -0.007 0.033 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB -0.004 0.06 -9999 0 -0.3 21 21
PTPRJ 0.01 0.018 -9999 0 -0.27 2 2
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.024 0.07 -10000 0 -0.32 8 8
TBX21 0.016 0.2 -10000 0 -0.88 11 11
B2M 0.011 0.005 -10000 0 -10000 0 0
TYK2 0.014 0.015 -10000 0 -10000 0 0
IL12RB1 0.005 0.06 -10000 0 -0.35 13 13
GADD45B 0.041 0.16 -10000 0 -0.73 8 8
IL12RB2 0.001 0.062 -10000 0 -0.28 23 23
GADD45G 0.02 0.24 -10000 0 -1 19 19
natural killer cell activation 0.003 0.015 -10000 0 -10000 0 0
RELB 0.011 0 -10000 0 -10000 0 0
RELA 0.011 0 -10000 0 -10000 0 0
IL18 0.011 0.033 -10000 0 -0.27 7 7
IL2RA 0.001 0.053 -10000 0 -0.28 17 17
IFNG -0.009 0.067 -10000 0 -0.27 31 31
STAT3 (dimer) 0.032 0.17 -10000 0 -0.6 14 14
HLA-DRB5 -0.005 0.063 -10000 0 -0.37 14 14
FASLG 0.015 0.2 -10000 0 -0.99 9 9
NF kappa B2 p52/RelB -0.058 0.14 -10000 0 -0.63 20 20
CD4 0.005 0.016 -10000 0 -0.29 1 1
SOCS1 0.009 0.023 -10000 0 -0.34 2 2
EntrezGene:6955 -0.007 0.014 -10000 0 -10000 0 0
CD3D -0.008 0.069 -10000 0 -0.33 21 21
CD3E 0 0.056 -10000 0 -0.37 11 11
CD3G 0.001 0.042 -10000 0 -0.36 6 6
IL12Rbeta2/JAK2 0.009 0.063 -10000 0 -0.22 26 26
CCL3 0.018 0.19 -10000 0 -0.94 7 7
CCL4 0.016 0.2 -10000 0 -0.91 11 11
HLA-A 0.011 0.013 -10000 0 -0.27 1 1
IL18/IL18R 0.043 0.048 -10000 0 -0.25 8 8
NOS2 0.022 0.2 -10000 0 -1 9 9
IL12/IL12R/TYK2/JAK2/SPHK2 0.025 0.067 -10000 0 -0.28 9 9
IL1R1 0.009 0.23 -10000 0 -1.1 14 14
IL4 0.001 0.016 -10000 0 -10000 0 0
JAK2 0.006 0.059 -10000 0 -0.42 9 9
EntrezGene:6957 -0.006 0.012 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.001 0.12 -10000 0 -0.64 12 12
RAB7A 0.046 0.17 -10000 0 -0.63 13 13
lysosomal transport 0.046 0.16 -10000 0 -0.6 13 13
FOS -0.34 0.58 -10000 0 -1.1 175 175
STAT4 (dimer) 0.042 0.18 -10000 0 -0.62 16 16
STAT5A (dimer) -0.06 0.15 -10000 0 -0.62 22 22
GZMA 0.002 0.24 -10000 0 -0.98 19 19
GZMB 0.009 0.2 -10000 0 -1.1 8 8
HLX 0.011 0 -10000 0 -10000 0 0
LCK 0.026 0.2 -10000 0 -0.67 22 22
TCR/CD3/MHC II/CD4 -0.049 0.13 -10000 0 -0.35 27 27
IL2/IL2R 0.011 0.049 -10000 0 -0.26 10 10
MAPK14 0.038 0.19 -10000 0 -0.69 19 19
CCR5 0.034 0.18 -10000 0 -0.92 9 9
IL1B 0.01 0.043 -10000 0 -0.44 4 4
STAT6 0.025 0.071 -10000 0 -0.3 5 5
STAT4 0.01 0.019 -10000 0 -0.42 1 1
STAT3 0.011 0 -10000 0 -10000 0 0
STAT1 0.01 0.012 -10000 0 -0.27 1 1
NFKB1 0.01 0.019 -10000 0 -0.42 1 1
NFKB2 0.011 0 -10000 0 -10000 0 0
IL12B 0.01 0.019 -10000 0 -0.26 1 1
CD8A 0.003 0.059 -10000 0 -0.37 12 12
CD8B -0.007 0.075 -10000 0 -0.3 31 31
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.024 0.07 0.32 8 -10000 0 8
IL2RB 0.01 0.019 -10000 0 -0.42 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.044 0.17 -10000 0 -0.58 16 16
IL2RG 0.006 0.038 -10000 0 -0.31 7 7
IL12 0.013 0.046 -10000 0 -0.26 7 7
STAT5A 0.011 0 -10000 0 -10000 0 0
CD247 0.006 0.024 -10000 0 -0.35 2 2
IL2 -0.005 0.05 -10000 0 -0.27 17 17
SPHK2 0.011 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.004 0.057 -10000 0 -0.31 15 15
IL12/IL12R/TYK2/JAK2 0.028 0.21 -10000 0 -0.72 21 21
MAP2K3 0.033 0.19 -10000 0 -0.67 20 20
RIPK2 0.011 0 -10000 0 -10000 0 0
MAP2K6 0.036 0.19 -10000 0 -0.68 19 19
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.002 0.034 -10000 0 -0.43 3 3
IL18RAP 0.01 0.04 -10000 0 -0.35 6 6
IL12Rbeta1/TYK2 0.014 0.047 -10000 0 -0.24 13 13
EOMES -0.008 0.13 -10000 0 -1.2 6 6
STAT1 (dimer) 0.036 0.16 -10000 0 -0.64 11 11
T cell proliferation 0.04 0.15 -10000 0 -0.5 17 17
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.011 0.039 -10000 0 -0.42 4 4
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.032 0.12 0.26 1 -0.55 17 18
ATF2 0.042 0.18 -10000 0 -0.64 19 19
ErbB4 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
ErbB4/ErbB4/HBEGF/HBEGF 0.009 0.045 -9999 0 -10000 0 0
epithelial cell differentiation -0.042 0.078 -9999 0 -0.32 14 14
ITCH 0.016 0.01 -9999 0 -10000 0 0
WWP1 0.008 0.04 -9999 0 -10000 0 0
FYN 0.011 0 -9999 0 -10000 0 0
EGFR -0.001 0.068 -9999 0 -0.41 14 14
PRL -0.012 0.089 -9999 0 -0.41 24 24
neuron projection morphogenesis 0.03 0.046 -9999 0 -10000 0 0
PTPRZ1 -0.01 0.064 -9999 0 -0.27 29 29
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.023 0.049 -9999 0 -0.27 1 1
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.007 0.055 -9999 0 -0.3 5 5
ADAM17 0.016 0.01 -9999 0 -10000 0 0
ErbB4/ErbB4 0.005 0.051 -9999 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.003 0.051 -9999 0 -0.28 1 1
NCOR1 0.011 0 -9999 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.012 0.051 -9999 0 -0.28 5 5
GRIN2B 0.01 0.056 -9999 0 -0.29 6 6
ErbB4/ErbB2/betacellulin 0.008 0.055 -9999 0 -0.29 3 3
STAT1 0.01 0.012 -9999 0 -0.27 1 1
HBEGF 0.01 0.019 -9999 0 -0.42 1 1
PRLR -0.073 0.17 -9999 0 -0.42 101 101
E4ICDs/ETO2 -0.02 0.092 -9999 0 -0.35 10 10
axon guidance 0.013 0.034 -9999 0 -10000 0 0
NEDD4 -0.023 0.12 -9999 0 -0.42 44 44
Prolactin receptor/Prolactin receptor/Prolactin -0.059 0.14 -9999 0 -0.3 118 118
CBFA2T3 -0.041 0.14 -9999 0 -0.42 62 62
ErbB4/ErbB2/HBEGF 0.015 0.039 -9999 0 -10000 0 0
MAPK3 0.026 0.047 -9999 0 -10000 0 0
STAT1 (dimer) 0.009 0.044 -9999 0 -10000 0 0
MAPK1 0.026 0.047 -9999 0 -10000 0 0
JAK2 0.003 0.056 -9999 0 -0.42 9 9
ErbB4/ErbB2/neuregulin 1 beta 0.009 0.056 -9999 0 -0.28 6 6
NRG1 0.011 0.053 -9999 0 -0.28 16 16
NRG3 -0.004 0.053 -9999 0 -0.27 19 19
NRG2 -0.036 0.13 -9999 0 -0.41 56 56
NRG4 -0.013 0.078 -9999 0 -0.27 43 43
heart development 0.013 0.034 -9999 0 -10000 0 0
neural crest cell migration 0.009 0.056 -9999 0 -0.28 6 6
ERBB2 0.015 0.032 -9999 0 -0.18 13 13
WWOX/E4ICDs 0.009 0.043 -9999 0 -10000 0 0
SHC1 0.011 0 -9999 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.002 0.07 -9999 0 -0.34 7 7
apoptosis 0 0.038 -9999 0 -10000 0 0
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.017 0.088 -9999 0 -0.35 9 9
ErbB4/ErbB2/epiregulin 0.009 0.056 -9999 0 -10000 0 0
ErbB4/ErbB4/betacellulin/betacellulin 0 0.062 -9999 0 -0.36 3 3
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.028 0.11 -9999 0 -0.33 33 33
MDM2 0.01 0.044 -9999 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.012 0.047 -9999 0 -0.26 5 5
STAT5A 0.018 0.032 -9999 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta 0.007 0.066 -9999 0 -0.33 9 9
DLG4 0.009 0.027 -9999 0 -0.42 2 2
GRB2/SHC 0.016 0 -9999 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.008 0.039 -9999 0 -10000 0 0
STAT5A (dimer) -0.044 0.083 -9999 0 -0.35 10 10
MAP3K7IP2 0 0 -9999 0 -10000 0 0
STAT5B (dimer) 0.017 0.035 -9999 0 -0.33 1 1
LRIG1 0.008 0.033 -9999 0 -0.42 3 3
EREG -0.024 0.091 -9999 0 -0.27 61 61
BTC -0.005 0.079 -9999 0 -0.42 18 18
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.015 0.032 -9999 0 -10000 0 0
ERBB4 0.005 0.051 -9999 0 -10000 0 0
STAT5B 0.01 0.019 -9999 0 -0.42 1 1
YAP1 0 0.025 -9999 0 -0.52 1 1
GRB2 0.011 0 -9999 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.008 0.055 -9999 0 -10000 0 0
glial cell differentiation 0.006 0.034 -9999 0 -10000 0 0
WWOX 0.011 0 -9999 0 -10000 0 0
cell proliferation 0.01 0.066 -9999 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.003 0.049 0.32 11 -10000 0 11
PI3K Class IB/PDE3B 0.003 0.05 -10000 0 -0.32 11 11
PDE3B 0.003 0.05 -10000 0 -0.32 11 11
ErbB2/ErbB3 signaling 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
USP8 0.015 0.002 -9999 0 -10000 0 0
RAS family/GTP 0.008 0.048 -9999 0 -0.23 12 12
NFATC4 0.015 0.042 -9999 0 -0.25 2 2
ERBB2IP 0.011 0.001 -9999 0 -10000 0 0
HSP90 (dimer) 0.011 0 -9999 0 -10000 0 0
mammary gland morphogenesis 0.004 0.045 -9999 0 -0.21 17 17
JUN -0.005 0.07 -9999 0 -0.35 4 4
HRAS 0.01 0.001 -9999 0 -10000 0 0
DOCK7 0.014 0.045 -9999 0 -0.31 2 2
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.004 0.048 -9999 0 -0.22 17 17
AKT1 0.009 0.001 -9999 0 -10000 0 0
BAD 0.015 0.001 -9999 0 -10000 0 0
MAPK10 -0.012 0.067 -9999 0 -0.15 47 47
mol:GTP -0.001 0.001 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.004 0.048 -9999 0 -0.22 17 17
RAF1 0.01 0.054 -9999 0 -0.23 12 12
ErbB2/ErbB3/neuregulin 2 -0.019 0.076 -9999 0 -0.22 57 57
STAT3 0.001 0.003 -9999 0 -10000 0 0
cell migration -0.001 0.061 -9999 0 -0.2 14 14
mol:PI-3-4-5-P3 0 0.001 -9999 0 -10000 0 0
cell proliferation -0.079 0.19 -9999 0 -0.52 17 17
FOS -0.13 0.25 -9999 0 -0.47 174 174
NRAS 0.01 0.001 -9999 0 -10000 0 0
mol:Ca2+ 0.004 0.045 -9999 0 -0.21 17 17
MAPK3 -0.041 0.13 -9999 0 -0.41 16 16
MAPK1 -0.041 0.13 -9999 0 -0.41 16 16
JAK2 0.011 0.05 -9999 0 -0.2 12 12
NF2 0 0.002 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.011 0.049 -9999 0 -0.24 17 17
NRG1 -0.003 0.073 -9999 0 -0.41 16 16
GRB2/SOS1 0.015 0.001 -9999 0 -10000 0 0
MAPK8 0.013 0.056 -9999 0 -0.23 22 22
MAPK9 0.021 0.027 -9999 0 -0.16 2 2
ERBB2 -0.005 0.03 -9999 0 -0.19 13 13
ERBB3 0.007 0.033 -9999 0 -0.42 3 3
SHC1 0.01 0.001 -9999 0 -10000 0 0
RAC1 0.011 0 -9999 0 -10000 0 0
apoptosis 0.001 0.006 -9999 0 -10000 0 0
STAT3 (dimer) 0.016 0.003 -9999 0 -10000 0 0
RNF41 0.019 0.003 -9999 0 -10000 0 0
FRAP1 0.007 0.001 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.006 0.027 -9999 0 -0.23 2 2
ErbB2/ErbB2/HSP90 (dimer) -0.004 0.023 -9999 0 -0.15 1 1
CHRNA1 -0.048 0.12 -9999 0 -0.38 8 8
myelination 0.02 0.04 -9999 0 -0.24 2 2
PPP3CB 0.014 0.043 -9999 0 -0.19 12 12
KRAS 0.01 0.012 -9999 0 -0.27 1 1
RAC1-CDC42/GDP 0.022 0.043 -9999 0 -0.2 17 17
NRG2 -0.036 0.13 -9999 0 -0.41 56 56
mol:GDP 0.011 0.049 -9999 0 -0.24 17 17
SOS1 0.01 0.001 -9999 0 -10000 0 0
MAP2K2 0.003 0.062 -9999 0 -0.3 5 5
SRC 0.011 0 -9999 0 -10000 0 0
mol:cAMP 0 0.001 -9999 0 -10000 0 0
PTPN11 0.014 0.045 -9999 0 -0.31 2 2
MAP2K1 -0.049 0.13 -9999 0 -0.43 16 16
heart morphogenesis 0.004 0.045 -9999 0 -0.21 17 17
RAS family/GDP 0.017 0.046 -9999 0 -0.26 5 5
GRB2 0.01 0.001 -9999 0 -10000 0 0
PRKACA -0.001 0.003 -9999 0 -10000 0 0
CHRNE 0.006 0.023 -9999 0 -0.19 4 4
HSP90AA1 0.011 0 -9999 0 -10000 0 0
activation of caspase activity -0.009 0.001 -9999 0 -10000 0 0
nervous system development 0.004 0.045 -9999 0 -0.21 17 17
CDC42 0.011 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.011 0 -10000 0 -10000 0 0
HDAC4 0.011 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.012 0.03 0.2 9 -10000 0 9
CDKN1A -0.003 0.048 -10000 0 -0.62 3 3
KAT2B 0.002 0.059 -10000 0 -0.42 10 10
BAX 0.011 0 -10000 0 -10000 0 0
FOXO3 0 0.006 -10000 0 -10000 0 0
FOXO1 0.008 0.033 -10000 0 -0.42 3 3
FOXO4 0.016 0.02 -10000 0 -0.24 3 3
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.011 0 -10000 0 -10000 0 0
TAT 0.006 0.018 -10000 0 -0.27 2 2
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.011 0.068 -10000 0 -0.2 56 56
PPARGC1A -0.081 0.18 -10000 0 -0.42 110 110
FHL2 0.002 0.059 -10000 0 -0.42 10 10
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0 0.021 0.14 3 -0.29 2 5
HIST2H4A 0.012 0.03 -10000 0 -0.2 9 9
SIRT1/FOXO3a 0 0.018 0.13 3 -0.23 2 5
SIRT1 0.006 0.03 0.18 3 -0.42 2 5
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0 0.018 0.13 3 -0.23 2 5
SIRT1/Histone H1b 0.014 0.023 0.14 2 -0.23 3 5
apoptosis 0 0.018 0.23 2 -0.13 3 5
SIRT1/PGC1A -0.051 0.1 0.12 3 -0.24 111 114
p53/SIRT1 0 0.035 0.36 3 -0.29 3 6
SIRT1/FOXO4 0.016 0.024 0.14 3 -0.21 5 8
FOXO1/FHL2/SIRT1 0.012 0.039 -10000 0 -0.21 15 15
HIST1H1E 0.014 0.017 -10000 0 -0.24 1 1
SIRT1/p300 0 0.021 0.14 3 -0.29 2 5
muscle cell differentiation 0.011 0.058 0.27 11 -0.13 2 13
TP53 0.007 0.023 0.18 3 -0.42 1 4
KU70/SIRT1/BAX 0 0.018 0.13 3 -0.23 2 5
CREBBP 0.01 0.019 -10000 0 -0.42 1 1
MEF2D 0.011 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.001 0.024 0.14 3 -0.23 4 7
ACSS2 0.015 0.021 -10000 0 -0.29 2 2
SIRT1/PCAF/MYOD -0.011 0.058 0.14 2 -0.27 11 13
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.02 0.017 -9999 0 -10000 0 0
SNTA1 0.011 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.02 0.017 -9999 0 -10000 0 0
MAPK12 -0.007 0.066 -9999 0 -0.21 27 27
CCND1 0.004 0.03 -9999 0 -10000 0 0
p38 gamma/SNTA1 -0.001 0.062 -9999 0 -0.19 27 27
MAP2K3 0.011 0 -9999 0 -10000 0 0
PKN1 0.011 0 -9999 0 -10000 0 0
G2/M transition checkpoint -0.007 0.066 -9999 0 -0.21 27 27
MAP2K6 -0.014 0.073 -9999 0 -0.24 26 26
MAPT 0.001 0.062 -9999 0 -0.28 20 20
MAPK13 0.015 0.021 -9999 0 -0.18 6 6
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK -0.002 0.064 -9999 0 -0.28 26 26
Syndecan-3-mediated signaling events

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
CTTN 0.011 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.015 0.083 -9999 0 -0.22 1 1
Syndecan-3/Neurocan 0.007 0.022 -9999 0 -10000 0 0
POMC -0.008 0.078 -9999 0 -0.33 27 27
EGFR -0.001 0.068 -9999 0 -0.41 14 14
Syndecan-3/EGFR 0.014 0.033 -9999 0 -0.19 13 13
AGRP 0.006 0.013 -9999 0 -0.27 1 1
NCSTN 0.011 0 -9999 0 -10000 0 0
PSENEN 0.011 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.007 0.038 -9999 0 -0.42 4 4
APH1A 0.011 0 -9999 0 -10000 0 0
NCAN -0.002 0.047 -9999 0 -0.27 15 15
long-term memory 0.025 0.005 -9999 0 -10000 0 0
Syndecan-3/IL8 -0.005 0.05 -9999 0 -10000 0 0
PSEN1 0.011 0 -9999 0 -10000 0 0
Src/Cortactin 0.016 0 -9999 0 -10000 0 0
FYN 0.011 0 -9999 0 -10000 0 0
limb bud formation 0 0.004 -9999 0 -10000 0 0
MC4R 0.001 0.035 -9999 0 -0.27 8 8
SRC 0.011 0 -9999 0 -10000 0 0
PTN -0.088 0.18 -9999 0 -0.42 119 119
FGFR/FGF/Syndecan-3 0 0.004 -9999 0 -10000 0 0
neuron projection morphogenesis -0.025 0.077 -9999 0 -0.27 2 2
Syndecan-3/AgRP 0.011 0.012 -9999 0 -10000 0 0
Syndecan-3/AgRP/MC4R 0.006 0.02 -9999 0 -10000 0 0
Fyn/Cortactin 0.016 0 -9999 0 -10000 0 0
SDC3 0 0.004 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.005 0.05 -9999 0 -10000 0 0
IL8 -0.045 0.11 -9999 0 -0.27 101 101
Syndecan-3/Fyn/Cortactin 0.026 0.005 -9999 0 -10000 0 0
Syndecan-3/CASK 0 0.004 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.003 0.058 -9999 0 -0.21 35 35
Gamma Secretase 0.03 0.019 -9999 0 -0.18 4 4
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.021 0.038 -9999 0 -0.2 14 14
HDAC3 0.011 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
GATA1/HDAC4 0.012 0.004 -9999 0 -10000 0 0
GATA1/HDAC5 0.012 0.004 -9999 0 -10000 0 0
GATA2/HDAC5 -0.012 0.088 -9999 0 -0.29 48 48
HDAC5/BCL6/BCoR 0.021 0.011 -9999 0 -0.23 1 1
HDAC9 0.001 0.062 -9999 0 -0.42 11 11
Glucocorticoid receptor/Hsp90/HDAC6 -0.025 0.098 -9999 0 -0.23 94 94
HDAC4/ANKRA2 0.015 0.013 -9999 0 -0.29 1 1
HDAC5/YWHAB 0.016 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.017 0 -9999 0 -10000 0 0
GATA2 -0.029 0.12 -9999 0 -0.42 48 48
HDAC4/RFXANK 0.015 0.015 -9999 0 -0.18 3 3
BCOR 0.011 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.011 0 -9999 0 -10000 0 0
HDAC5 0.011 0 -9999 0 -10000 0 0
GNB1/GNG2 0.007 0.05 -9999 0 -0.28 15 15
Histones 0.027 0.029 -9999 0 -10000 0 0
ADRBK1 0.011 0 -9999 0 -10000 0 0
HDAC4 0.011 0 -9999 0 -10000 0 0
XPO1 0.011 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.015 0.013 -9999 0 -0.29 1 1
HDAC4/Ubc9 0.016 0 -9999 0 -10000 0 0
HDAC7 0.011 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.016 0 -9999 0 -10000 0 0
TUBA1B 0.011 0 -9999 0 -10000 0 0
HDAC6 0.011 0 -9999 0 -10000 0 0
HDAC5/RFXANK 0.015 0.015 -9999 0 -0.18 3 3
CAMK4 0.006 0.038 -9999 0 -0.31 7 7
Tubulin/HDAC6 0.019 0.024 -9999 0 -0.23 3 3
SUMO1 0.011 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.011 0 -9999 0 -10000 0 0
GATA1 0.006 0.005 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.011 0 -9999 0 -10000 0 0
NR3C1 -0.068 0.16 -9999 0 -0.42 94 94
SUMO1/HDAC4 0.024 0 -9999 0 -10000 0 0
SRF 0.011 0 -9999 0 -10000 0 0
HDAC4/YWHAB 0.016 0 -9999 0 -10000 0 0
Tubulin 0.013 0.028 -9999 0 -0.22 7 7
HDAC4/14-3-3 E 0.016 0 -9999 0 -10000 0 0
GNB1 0.011 0 -9999 0 -10000 0 0
RANGAP1 0.011 0 -9999 0 -10000 0 0
BCL6/BCoR 0.015 0.013 -9999 0 -0.29 1 1
HDAC4/HDAC3/SMRT (N-CoR2) 0.022 0 -9999 0 -10000 0 0
HDAC4/SRF 0.019 0.022 -9999 0 -0.23 2 2
HDAC4/ER alpha -0.017 0.094 -9999 0 -0.29 56 56
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.027 0.028 -9999 0 -10000 0 0
cell motility 0.019 0.024 -9999 0 -0.23 3 3
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.011 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0.016 0 -9999 0 -10000 0 0
BCL6 0.01 0.019 -9999 0 -0.42 1 1
HDAC4/CaMK II delta B 0.011 0 -9999 0 -10000 0 0
Hsp90/HDAC6 0.016 0 -9999 0 -10000 0 0
ESR1 -0.036 0.13 -9999 0 -0.42 56 56
HDAC6/HDAC11 0.015 0.008 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.026 0 -9999 0 -10000 0 0
NPC 0.006 0 -9999 0 -10000 0 0
MEF2C -0.039 0.14 -9999 0 -0.42 60 60
RAN 0.011 0 -9999 0 -10000 0 0
HDAC4/MEF2C 0.006 0.07 -9999 0 -0.18 60 60
GNG2 -0.002 0.071 -9999 0 -0.41 15 15
NCOR2 0.011 0 -9999 0 -10000 0 0
TUBB2A 0.006 0.041 -9999 0 -0.33 7 7
HDAC11 0.01 0.012 -9999 0 -0.27 1 1
HSP90AA1 0.011 0 -9999 0 -10000 0 0
RANBP2 0.011 0 -9999 0 -10000 0 0
ANKRA2 0.01 0.019 -9999 0 -0.42 1 1
RFXANK 0.009 0.022 -9999 0 -0.27 3 3
nuclear import -0.023 0 -9999 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.016 0.019 -10000 0 -0.29 2 2
MAP4K4 0.03 0.032 -10000 0 -0.4 1 1
BAG4 0.008 0.033 -10000 0 -0.42 3 3
PKC zeta/ceramide -0.001 0.015 0.12 2 -0.17 2 4
NFKBIA 0.011 0 -10000 0 -10000 0 0
BIRC3 0.003 0.057 -10000 0 -0.4 10 10
BAX 0.002 0.006 -10000 0 -10000 0 0
RIPK1 0.011 0 -10000 0 -10000 0 0
AKT1 0.014 0.002 -10000 0 -10000 0 0
BAD -0.001 0.011 0.13 2 -10000 0 2
SMPD1 0.017 0.02 -10000 0 -0.17 2 2
RB1 -0.002 0.02 0.13 2 -0.22 3 5
FADD/Caspase 8 0.037 0.031 -10000 0 -0.39 1 1
MAP2K4 0.004 0.014 0.13 2 -0.2 1 3
NSMAF 0.011 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.004 0.014 0.13 2 -0.2 1 3
EGF -0.002 0.058 -10000 0 -0.29 20 20
mol:ceramide -0.008 0.012 0.14 2 -10000 0 2
MADD 0.011 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.016 0.019 -10000 0 -0.29 2 2
ASAH1 0.011 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.003 0.02 0.13 2 -0.22 3 5
cell proliferation -0.014 0.072 -10000 0 -0.16 101 101
BID 0.025 0.024 -10000 0 -0.29 1 1
MAP3K1 -0.001 0.011 0.13 2 -10000 0 2
EIF2A 0.009 0.01 0.14 1 -10000 0 1
TRADD 0.011 0 -10000 0 -10000 0 0
CRADD 0.011 0 -10000 0 -10000 0 0
MAPK3 0.012 0.013 0.13 2 -0.18 1 3
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.012 0.013 0.13 2 -0.18 1 3
Cathepsin D/ceramide 0 0.012 0.12 2 -0.13 1 3
FADD 0.03 0.032 -10000 0 -0.4 1 1
KSR1 -0.002 0.014 0.13 2 -0.21 1 3
MAPK8 0.005 0.026 0.14 1 -0.21 6 7
PRKRA -0.001 0.011 0.13 2 -10000 0 2
PDGFA 0.009 0.027 -10000 0 -0.42 2 2
TRAF2 0.011 0 -10000 0 -10000 0 0
IGF1 -0.074 0.17 -10000 0 -0.42 102 102
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.008 0.012 0.14 2 -10000 0 2
CTSD 0.01 0.012 -10000 0 -0.27 1 1
regulation of nitric oxide biosynthetic process 0.015 0.013 -10000 0 -0.28 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.014 0.076 -10000 0 -0.17 101 101
PRKCD 0.011 0 -10000 0 -10000 0 0
PRKCZ 0.009 0.023 -10000 0 -0.34 2 2
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.016 0.019 -10000 0 -0.29 2 2
RelA/NF kappa B1 0.015 0.013 -10000 0 -0.29 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.011 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.025 0.034 -10000 0 -0.43 1 1
TNFR1A/BAG4/TNF-alpha 0.004 0.052 -10000 0 -0.23 5 5
mol:Sphingosine-1-phosphate 0.016 0.019 -10000 0 -0.28 2 2
MAP2K1 0.009 0.013 0.13 2 -0.18 1 3
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.011 0 -10000 0 -10000 0 0
CYCS 0.014 0.04 0.14 49 -10000 0 49
TNFRSF1A 0.011 0 -10000 0 -10000 0 0
NFKB1 0.01 0.019 -10000 0 -0.42 1 1
TNFR1A/BAG4 0.014 0.023 -10000 0 -0.29 3 3
EIF2AK2 0.004 0.01 0.13 2 -10000 0 2
TNF-alpha/TNFR1A/FAN 0.006 0.048 -10000 0 -0.23 2 2
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.03 0.022 -10000 0 -0.23 1 1
MAP2K2 0.009 0.013 0.14 1 -0.18 1 2
SMPD3 0.019 0.029 -10000 0 -0.25 4 4
TNF -0.018 0.086 -10000 0 -0.28 50 50
PKC zeta/PAR4 0.015 0.016 -10000 0 -0.23 2 2
mol:PHOSPHOCHOLINE -0.004 0.018 0.16 3 -10000 0 3
NF kappa B1/RelA/I kappa B alpha 0.031 0.015 -10000 0 -0.18 2 2
AIFM1 0.014 0.04 0.14 49 -10000 0 49
BCL2 -0.029 0.12 -10000 0 -0.42 48 48
HIF-2-alpha transcription factor network

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
MMP14 -0.006 0.049 -10000 0 -1.1 1 1
oxygen homeostasis -0.002 0.014 -10000 0 -10000 0 0
TCEB2 0.011 0 -10000 0 -10000 0 0
TCEB1 0.011 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.017 0.04 -10000 0 -0.29 5 5
EPO -0.006 0.18 -10000 0 -0.51 12 12
FIH (dimer) 0.009 0.013 -10000 0 -10000 0 0
APEX1 0.008 0.014 -10000 0 -10000 0 0
SERPINE1 -0.007 0.19 -10000 0 -0.59 12 12
FLT1 -0.016 0.095 -10000 0 -0.99 4 4
ADORA2A -0.005 0.18 -10000 0 -0.52 10 10
germ cell development -0.013 0.2 -10000 0 -0.53 23 23
SLC11A2 -0.005 0.19 -10000 0 -0.52 12 12
BHLHE40 -0.005 0.19 -10000 0 -0.52 12 12
HIF1AN 0.009 0.013 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.001 0.11 -10000 0 -0.4 5 5
ETS1 0.019 0.035 -10000 0 -0.43 3 3
CITED2 -0.035 0.18 -10000 0 -1 16 16
KDR -0.062 0.26 -10000 0 -1.1 29 29
PGK1 -0.005 0.19 -10000 0 -0.52 12 12
SIRT1 0.009 0.027 -10000 0 -0.42 2 2
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT -0.008 0.21 -10000 0 -0.58 13 13
EPAS1 0.013 0.086 -10000 0 -0.36 4 4
SP1 0.017 0.001 -10000 0 -10000 0 0
ABCG2 -0.14 0.29 -10000 0 -0.55 75 75
EFNA1 -0.005 0.19 -10000 0 -0.5 14 14
FXN -0.005 0.18 -10000 0 -0.51 11 11
POU5F1 -0.014 0.2 -10000 0 -0.55 23 23
neuron apoptosis 0.008 0.21 0.57 13 -10000 0 13
EP300 0.011 0 -10000 0 -10000 0 0
EGLN3 0.007 0.031 -10000 0 -0.31 4 4
EGLN2 0.009 0.013 -10000 0 -10000 0 0
EGLN1 0.009 0.013 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.021 0.011 -10000 0 -0.23 1 1
VHL 0.01 0.019 -10000 0 -0.42 1 1
ARNT 0.008 0.014 -10000 0 -10000 0 0
SLC2A1 -0.005 0.18 -10000 0 -0.52 11 11
TWIST1 -0.018 0.21 -10000 0 -0.55 35 35
ELK1 0.015 0.01 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.003 0.11 -10000 0 -0.36 6 6
VEGFA -0.005 0.19 -10000 0 -0.54 10 10
CREBBP 0.01 0.019 -10000 0 -0.42 1 1
IL27-mediated signaling events

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
TGFB1 0.004 0.057 -10000 0 -0.4 10 10
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.016 0.1 0.44 6 -10000 0 6
IL27/IL27R/JAK1 -0.016 0.12 -10000 0 -0.72 4 4
TBX21 0.002 0.11 -10000 0 -0.5 7 7
IL12B 0.006 0.013 -10000 0 -0.27 1 1
IL12A 0.002 0.038 -10000 0 -0.21 15 15
IL6ST -0.073 0.17 -10000 0 -0.42 100 100
IL27RA/JAK1 0.011 0.074 -10000 0 -1.1 2 2
IL27 0.004 0.039 -10000 0 -0.27 10 10
TYK2 0.012 0.004 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.025 0.17 -10000 0 -1.3 9 9
T-helper 2 cell differentiation 0.016 0.1 0.44 6 -10000 0 6
T cell proliferation during immune response 0.016 0.1 0.44 6 -10000 0 6
MAPKKK cascade -0.016 0.1 -10000 0 -0.44 6 6
STAT3 0.011 0 -10000 0 -10000 0 0
STAT2 0.011 0 -10000 0 -10000 0 0
STAT1 0.01 0.013 -10000 0 -0.28 1 1
IL12RB1 0.002 0.055 -10000 0 -0.33 13 13
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.001 0.11 -10000 0 -0.47 8 8
IL27/IL27R/JAK2/TYK2 -0.016 0.1 -10000 0 -0.45 6 6
positive regulation of T cell mediated cytotoxicity -0.016 0.1 -10000 0 -0.44 6 6
STAT1 (dimer) -0.037 0.12 0.39 8 -0.7 5 13
JAK2 0.003 0.056 -10000 0 -0.42 9 9
JAK1 0.008 0.033 -10000 0 -0.42 3 3
STAT2 (dimer) -0.009 0.097 -10000 0 -0.42 6 6
T cell proliferation -0.021 0.11 -10000 0 -0.41 15 15
IL12/IL12R/TYK2/JAK2 0.019 0.049 -10000 0 -0.53 1 1
IL17A -0.027 0.18 -10000 0 -1.3 9 9
mast cell activation 0.016 0.1 0.44 6 -10000 0 6
IFNG 0.001 0.02 -10000 0 -0.076 3 3
T cell differentiation -0.002 0.004 -10000 0 -0.021 3 3
STAT3 (dimer) -0.009 0.097 -10000 0 -0.42 6 6
STAT5A (dimer) -0.009 0.097 -10000 0 -0.42 6 6
STAT4 (dimer) -0.01 0.097 -10000 0 -0.42 6 6
STAT4 0.01 0.019 -10000 0 -0.42 1 1
T cell activation -0.007 0.009 0.12 2 -10000 0 2
IL27R/JAK2/TYK2 -0.021 0.12 -10000 0 -0.65 5 5
GATA3 -0.008 0.11 -10000 0 -1.2 4 4
IL18 0.006 0.022 -10000 0 -0.18 7 7
positive regulation of mast cell cytokine production -0.009 0.096 -10000 0 -0.42 6 6
IL27/EBI3 0.008 0.042 -10000 0 -0.2 19 19
IL27RA 0.003 0.076 -10000 0 -1.2 2 2
IL6 -0.017 0.1 -10000 0 -0.38 38 38
STAT5A 0.011 0 -10000 0 -10000 0 0
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 0 0.033 0.46 2 -10000 0 2
IL1B 0.006 0.027 -10000 0 -0.29 4 4
EBI3 0.005 0.042 -10000 0 -0.28 11 11
TNF -0.01 0.058 -10000 0 -0.19 50 50
Stabilization and expansion of the E-cadherin 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
adherens junction organization 0.023 0.014 -10000 0 -0.2 2 2
epithelial cell differentiation -0.001 0.013 -10000 0 -0.19 2 2
CYFIP2 0.008 0.033 -10000 0 -0.42 3 3
ENAH 0.046 0.017 -10000 0 -10000 0 0
EGFR -0.001 0.068 -10000 0 -0.41 14 14
EPHA2 0.011 0 -10000 0 -10000 0 0
MYO6 0.028 0.014 -10000 0 -0.18 2 2
CTNNB1 0.011 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.02 0.019 -10000 0 -0.23 3 3
AQP5 0.036 0.042 -10000 0 -0.38 3 3
CTNND1 0.011 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.027 0.014 -10000 0 -0.17 2 2
regulation of calcium-dependent cell-cell adhesion 0.022 0.039 -10000 0 -0.2 15 15
EGF -0.002 0.058 -10000 0 -0.29 20 20
NCKAP1 0.011 0 -10000 0 -10000 0 0
AQP3 -0.004 0.046 -10000 0 -0.45 5 5
cortical microtubule organization -0.001 0.013 -10000 0 -0.19 2 2
GO:0000145 0.026 0.013 -10000 0 -0.16 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.024 0.015 -10000 0 -0.19 2 2
MLLT4 0.011 0 -10000 0 -10000 0 0
ARF6/GDP -0.001 0.013 -10000 0 -10000 0 0
ARF6 0.011 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.026 0.017 -10000 0 -0.2 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.036 0.013 -10000 0 -10000 0 0
PVRL2 0.011 0 -10000 0 -10000 0 0
ZYX 0.028 0.014 -10000 0 -0.18 2 2
ARF6/GTP 0.029 0.016 -10000 0 -0.18 2 2
CDH1 0.008 0.029 -10000 0 -0.37 3 3
EGFR/EGFR/EGF/EGF -0.009 0.038 -10000 0 -0.23 7 7
RhoA/GDP -0.001 0.012 -10000 0 -0.17 2 2
actin cytoskeleton organization 0.031 0.014 -10000 0 -0.17 2 2
IGF-1R heterotetramer -0.006 0.083 -10000 0 -0.42 20 20
GIT1 0.011 0 -10000 0 -10000 0 0
IGF1R -0.006 0.083 -10000 0 -0.42 20 20
IGF1 -0.074 0.17 -10000 0 -0.42 102 102
DIAPH1 -0.003 0.04 -10000 0 -0.53 3 3
Wnt receptor signaling pathway 0.001 0.013 0.19 2 -10000 0 2
RHOA 0.011 0 -10000 0 -10000 0 0
RhoA/GTP -0.001 0.013 -10000 0 -10000 0 0
CTNNA1 0.011 0 -10000 0 -10000 0 0
VCL 0.032 0.014 -10000 0 -0.17 2 2
EFNA1 0.01 0.018 -10000 0 -0.27 2 2
LPP 0.032 0.013 -10000 0 -0.16 2 2
Ephrin A1/EPHA2 -0.001 0.012 -10000 0 -0.16 2 2
SEC6/SEC8 -0.001 0.01 -10000 0 -10000 0 0
MGAT3 0.022 0.039 -10000 0 -0.2 15 15
HGF/MET -0.034 0.073 -10000 0 -0.18 97 97
HGF -0.069 0.17 -10000 0 -0.42 96 96
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.023 0.014 -10000 0 -0.2 2 2
actin cable formation 0.059 0.017 -10000 0 -10000 0 0
KIAA1543 0.031 0.026 -10000 0 -0.36 2 2
KIFC3 0.028 0.014 -10000 0 -0.18 2 2
NCK1 0.009 0.027 -10000 0 -0.42 2 2
EXOC3 0.011 0 -10000 0 -10000 0 0
ACTN1 0.028 0.014 -10000 0 -0.18 2 2
NCK1/GIT1 0.015 0.019 -10000 0 -0.29 2 2
mol:GDP -0.001 0.013 -10000 0 -0.19 2 2
EXOC4 0.011 0 -10000 0 -10000 0 0
STX4 0.028 0.014 -10000 0 -0.18 2 2
PIP5K1C 0.028 0.014 -10000 0 -0.18 2 2
LIMA1 0.011 0 -10000 0 -10000 0 0
ABI1 0.011 0 -10000 0 -10000 0 0
ROCK1 0.045 0.017 -10000 0 -10000 0 0
adherens junction assembly 0.043 0.028 -10000 0 -0.37 2 2
IGF-1R heterotetramer/IGF1 -0.041 0.082 -10000 0 -0.19 112 112
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.016 0 -10000 0 -10000 0 0
MET 0.005 0.045 -10000 0 -0.34 8 8
PLEKHA7 0.027 0.017 -10000 0 -0.18 3 3
mol:GTP 0.025 0.017 -10000 0 -0.2 2 2
establishment of epithelial cell apical/basal polarity 0.045 0.012 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization 0.023 0.014 -10000 0 -0.2 2 2
regulation of cell-cell adhesion 0.031 0.014 -10000 0 -0.17 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.023 0.014 -10000 0 -0.2 2 2
EPO 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
BCL2L1 0.024 0.11 -10000 0 -0.42 4 4
CRKL 0.021 0.046 -10000 0 -0.24 4 4
mol:DAG 0.024 0.053 -10000 0 -0.25 6 6
HRAS 0.036 0.044 -10000 0 -0.21 2 2
MAPK8 0.019 0.036 -10000 0 -0.21 8 8
RAP1A 0.021 0.046 -10000 0 -0.24 4 4
GAB1 0.019 0.05 -10000 0 -0.24 7 7
MAPK14 0.021 0.027 -10000 0 -0.19 3 3
EPO 0.006 0.035 -10000 0 -0.38 4 4
PLCG1 0.024 0.054 -10000 0 -0.25 6 6
EPOR/TRPC2/IP3 Receptors 0.006 0.039 -10000 0 -0.26 10 10
RAPGEF1 0.011 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.014 0.041 -10000 0 -0.24 9 9
GAB1/SHC/GRB2/SOS1 -0.01 0.031 -10000 0 -0.21 6 6
EPO/EPOR (dimer) 0.011 0.036 -10000 0 -0.19 14 14
IRS2 -0.006 0.084 -10000 0 -0.22 32 32
STAT1 0.023 0.078 -10000 0 -0.35 4 4
STAT5B 0.023 0.068 -10000 0 -0.32 4 4
cell proliferation 0.023 0.033 -10000 0 -0.2 6 6
GAB1/SHIP/PIK3R1/SHP2/SHC -0.01 0.036 -10000 0 -0.22 10 10
TEC 0.021 0.046 -10000 0 -0.24 4 4
SOCS3 0.006 0.046 -10000 0 -0.42 6 6
STAT1 (dimer) 0.023 0.078 -10000 0 -0.35 4 4
JAK2 0.004 0.057 -10000 0 -0.42 9 9
PIK3R1 0.007 0.038 -10000 0 -0.42 4 4
EPO/EPOR (dimer)/JAK2 0.03 0.051 -10000 0 -0.2 13 13
EPO/EPOR 0.011 0.036 -10000 0 -0.19 14 14
LYN 0.011 0.005 -10000 0 -10000 0 0
TEC/VAV2 0.027 0.045 -10000 0 -0.23 4 4
elevation of cytosolic calcium ion concentration 0.006 0.039 -10000 0 -0.26 10 10
SHC1 0.011 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.021 0.032 -10000 0 -0.23 3 3
mol:IP3 0.024 0.053 -10000 0 -0.25 6 6
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.004 0.084 -10000 0 -0.26 19 19
SH2B3 0.01 0.019 -10000 0 -0.41 1 1
NFKB1 0.021 0.029 -10000 0 -0.2 4 4
EPO/EPOR (dimer)/JAK2/SOCS3 -0.007 0.041 0.23 1 -0.21 18 19
PTPN6 0.016 0.048 -10000 0 -0.2 13 13
TEC/VAV2/GRB2 0.032 0.044 -10000 0 -0.22 4 4
EPOR 0.006 0.039 -10000 0 -0.27 10 10
INPP5D 0.01 0.019 -10000 0 -0.42 1 1
mol:GDP -0.01 0.032 -10000 0 -0.22 6 6
SOS1 0.011 0 -10000 0 -10000 0 0
PLCG2 0.01 0.019 -10000 0 -0.42 1 1
CRKL/CBL/C3G 0.032 0.044 -10000 0 -0.22 4 4
VAV2 0.021 0.046 -10000 0 -0.24 4 4
CBL 0.021 0.046 -10000 0 -0.24 4 4
SHC/Grb2/SOS1 -0.007 0.03 -10000 0 -0.22 4 4
STAT5A 0.023 0.067 -10000 0 -0.28 6 6
GRB2 0.011 0 -10000 0 -10000 0 0
STAT5 (dimer) 0.027 0.099 -10000 0 -0.31 12 12
LYN/PLCgamma2 0.015 0.014 -10000 0 -0.28 1 1
PTPN11 0.011 0 -10000 0 -10000 0 0
BTK 0.019 0.052 -10000 0 -0.25 7 7
BCL2 -0.022 0.25 -10000 0 -0.79 48 48
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.022 0.02 -9999 0 -0.29 2 2
CRKL 0.011 0 -9999 0 -10000 0 0
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
DOCK1 0.006 0.046 -9999 0 -0.42 6 6
ITGA4 0.008 0.029 -9999 0 -0.37 3 3
alpha4/beta7 Integrin/MAdCAM1 0.013 0.042 -9999 0 -0.21 2 2
EPO 0.005 0.035 -9999 0 -0.38 4 4
alpha4/beta7 Integrin 0.014 0.022 -9999 0 -0.23 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.011 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.014 0.021 -9999 0 -0.25 3 3
EPO/EPOR (dimer) 0.008 0.036 -9999 0 -0.2 14 14
lamellipodium assembly 0.024 0.027 -9999 0 -0.25 4 4
PIK3CA 0.01 0.019 -9999 0 -0.42 1 1
PI3K 0.013 0.03 -9999 0 -0.29 5 5
ARF6 0.011 0 -9999 0 -10000 0 0
JAK2 0.016 0.047 -9999 0 -0.25 14 14
PXN 0.011 0 -9999 0 -10000 0 0
PIK3R1 0.007 0.038 -9999 0 -0.42 4 4
MADCAM1 -0.014 0.077 -9999 0 -0.27 42 42
cell adhesion 0.013 0.042 -9999 0 -0.21 2 2
CRKL/CBL 0.016 0 -9999 0 -10000 0 0
ITGB1 0.011 0 -9999 0 -10000 0 0
SRC 0.006 0.066 -9999 0 -0.21 41 41
ITGB7 0.01 0.012 -9999 0 -0.27 1 1
RAC1 0.011 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0 0.074 -9999 0 -0.24 41 41
p130Cas/Crk/Dock1 0.021 0.063 -9999 0 -0.44 2 2
VCAM1 -0.024 0.12 -9999 0 -0.42 41 41
RHOA 0.011 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.026 0.016 -9999 0 -0.2 2 2
BCAR1 0.012 0.062 -9999 0 -0.19 41 41
EPOR 0.005 0.039 -9999 0 -0.27 10 10
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.011 0 -9999 0 -10000 0 0
GIT1 0.011 0 -9999 0 -10000 0 0
Rac1/GTP -0.001 0.025 -9999 0 -0.26 4 4
IL23-mediated signaling events

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
CCL2 0.055 0.22 -9999 0 -1.1 12 12
IL23A 0.059 0.2 -9999 0 -1 9 9
NF kappa B1 p50/RelA/I kappa B alpha -0.027 0.16 -9999 0 -0.88 11 11
positive regulation of T cell mediated cytotoxicity 0.06 0.21 -9999 0 -0.95 12 12
ITGA3 0.061 0.2 -9999 0 -1.1 6 6
IL17F 0.062 0.15 -9999 0 -0.64 9 9
IL12B 0.021 0.022 -9999 0 -0.26 1 1
STAT1 (dimer) 0.056 0.2 -9999 0 -0.91 12 12
CD4 0.062 0.19 -9999 0 -0.91 9 9
IL23 0.055 0.2 -9999 0 -0.98 9 9
IL23R 0.034 0.049 -9999 0 -10000 0 0
IL1B 0.057 0.22 -9999 0 -1.1 9 9
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 0.059 0.19 -9999 0 -0.94 8 8
TYK2 0.019 0.012 -9999 0 -10000 0 0
STAT4 0.01 0.019 -9999 0 -0.42 1 1
STAT3 0.011 0.001 -9999 0 -10000 0 0
IL18RAP 0.006 0.039 -9999 0 -0.35 6 6
IL12RB1 0.01 0.058 -9999 0 -0.34 13 13
PIK3CA 0.01 0.019 -9999 0 -0.42 1 1
IL12Rbeta1/TYK2 0.018 0.044 -9999 0 -0.23 13 13
IL23R/JAK2 0.045 0.073 -9999 0 -10000 0 0
positive regulation of chronic inflammatory response 0.06 0.21 -9999 0 -0.95 12 12
natural killer cell activation -0.003 0.004 -9999 0 -10000 0 0
JAK2 0.018 0.062 -9999 0 -0.43 9 9
PIK3R1 0.007 0.038 -9999 0 -0.42 4 4
NFKB1 0.011 0.019 -9999 0 -0.41 1 1
RELA 0.012 0.002 -9999 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation 0.056 0.19 -9999 0 -0.93 9 9
ALOX12B 0.058 0.19 -9999 0 -0.92 9 9
CXCL1 0.037 0.25 -9999 0 -1.1 18 18
T cell proliferation 0.06 0.21 -9999 0 -0.95 12 12
NFKBIA 0.012 0.002 -9999 0 -10000 0 0
IL17A 0.063 0.14 -9999 0 -0.51 8 8
PI3K -0.015 0.17 -9999 0 -0.89 12 12
IFNG 0.008 0.014 -9999 0 -10000 0 0
STAT3 (dimer) -0.033 0.16 -9999 0 -0.85 12 12
IL18R1 0.007 0.037 -9999 0 -0.41 4 4
IL23/IL23R/JAK2/TYK2/SOCS3 0.057 0.15 -9999 0 -0.73 7 7
IL18/IL18R 0.015 0.039 -9999 0 -0.24 8 8
macrophage activation 0 0.01 -9999 0 -0.042 9 9
TNF 0.056 0.21 -9999 0 -1.1 7 7
STAT3/STAT4 -0.019 0.17 -9999 0 -0.88 12 12
STAT4 (dimer) 0.056 0.2 -9999 0 -0.91 12 12
IL18 0.007 0.033 -9999 0 -0.28 7 7
IL19 0.05 0.19 -9999 0 -0.94 8 8
STAT5A (dimer) 0.056 0.2 -9999 0 -0.91 12 12
STAT1 0.01 0.012 -9999 0 -0.27 1 1
SOCS3 0.006 0.046 -9999 0 -0.42 6 6
CXCL9 0.048 0.22 -9999 0 -1.1 11 11
MPO 0.062 0.19 -9999 0 -0.94 8 8
positive regulation of humoral immune response 0.06 0.21 -9999 0 -0.95 12 12
IL23/IL23R/JAK2/TYK2 0.059 0.22 -9999 0 -0.98 12 12
IL6 0.033 0.28 -9999 0 -1.1 24 24
STAT5A 0.011 0 -9999 0 -10000 0 0
IL2 -0.006 0.05 -9999 0 -0.27 17 17
positive regulation of tyrosine phosphorylation of STAT protein -0.003 0.004 -9999 0 -10000 0 0
CD3E 0.054 0.23 -9999 0 -1.1 12 12
keratinocyte proliferation 0.06 0.21 -9999 0 -0.95 12 12
NOS2 0.055 0.21 -9999 0 -1 10 10
Caspase cascade in apoptosis

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
TOP1 0.015 0.042 -10000 0 -0.27 5 5
ACTA1 0.006 0.051 0.16 4 -0.34 5 9
NUMA1 0.015 0.042 -10000 0 -0.27 5 5
SPTAN1 0.009 0.051 0.17 1 -0.34 5 6
LIMK1 0.009 0.051 0.16 6 -0.34 5 11
BIRC3 0.003 0.057 -10000 0 -0.4 10 10
BIRC2 0.011 0 -10000 0 -10000 0 0
BAX 0.011 0 -10000 0 -10000 0 0
CASP10 -0.001 0.066 -10000 0 -0.29 11 11
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.011 0 -10000 0 -10000 0 0
PTK2 0.015 0.042 -10000 0 -0.27 5 5
DIABLO 0.011 0 -10000 0 -10000 0 0
apoptotic nuclear changes 0.009 0.05 0.17 1 -0.33 5 6
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.011 0 -10000 0 -10000 0 0
GSN 0.005 0.055 -10000 0 -0.34 5 5
MADD 0.011 0 -10000 0 -10000 0 0
TFAP2A 0.05 0.043 -10000 0 -0.55 2 2
BID 0.008 0.032 -10000 0 -0.17 7 7
MAP3K1 0.008 0.021 -10000 0 -0.2 1 1
TRADD 0.011 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.016 0 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.009 0.051 0.16 6 -0.34 5 11
CASP9 0.011 0 -10000 0 -10000 0 0
DNA repair -0.005 0.022 0.14 1 -0.16 6 7
neuron apoptosis 0.019 0.007 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.015 0.049 -10000 0 -0.32 5 5
APAF1 0.011 0 -10000 0 -10000 0 0
CASP6 0.023 0.027 -10000 0 -10000 0 0
TRAF2 0.011 0 -10000 0 -10000 0 0
ICAD/CAD 0.014 0.049 -10000 0 -0.32 5 5
CASP7 -0.004 0.034 0.24 9 -10000 0 9
KRT18 0.015 0.033 -10000 0 -0.69 1 1
apoptosis 0.016 0.048 0.18 6 -0.29 4 10
DFFA 0.009 0.051 0.17 1 -0.34 5 6
DFFB 0.009 0.051 0.17 1 -0.34 5 6
PARP1 0.005 0.022 0.16 6 -0.14 1 7
actin filament polymerization -0.01 0.052 0.3 6 -0.17 1 7
TNF -0.018 0.086 -10000 0 -0.28 50 50
CYCS 0.009 0.028 -10000 0 -0.16 4 4
SATB1 -0.004 0.079 -10000 0 -0.34 5 5
SLK 0.009 0.051 0.16 6 -0.34 5 11
p15 BID/BAX 0.013 0.028 -10000 0 -0.15 7 7
CASP2 0.032 0.028 -10000 0 -0.3 1 1
JNK cascade -0.008 0.021 0.2 1 -10000 0 1
CASP3 0.003 0.054 0.17 6 -0.36 5 11
LMNB2 0.033 0.02 -10000 0 -10000 0 0
RIPK1 0.011 0 -10000 0 -10000 0 0
CASP4 0.01 0.019 -10000 0 -0.42 1 1
Mammalian IAPs/DIABLO 0.023 0.031 -10000 0 -0.2 9 9
negative regulation of DNA binding 0.05 0.043 -10000 0 -0.54 2 2
stress fiber formation 0.009 0.05 0.16 6 -0.33 5 11
GZMB -0.01 0.076 -10000 0 -0.2 64 64
CASP1 0.01 0.031 -10000 0 -0.28 6 6
LMNB1 0.034 0.021 -10000 0 -10000 0 0
APP 0.019 0.007 -10000 0 -10000 0 0
TNFRSF1A 0.011 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.009 0 -10000 0 -10000 0 0
VIM 0.011 0.048 0.18 6 -0.29 4 10
LMNA 0.033 0.02 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.028 0.03 -10000 0 -0.32 1 1
LRDD 0.011 0 -10000 0 -10000 0 0
SREBF1 0.009 0.051 0.17 1 -0.34 5 6
APAF-1/Caspase 9 0 0.017 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.015 0.041 -10000 0 -0.27 5 5
CFL2 0.01 0.053 0.17 1 -0.31 6 7
GAS2 -0.006 0.075 0.16 5 -0.23 34 39
positive regulation of apoptosis 0.036 0.021 -10000 0 -10000 0 0
PRF1 0.004 0.049 -10000 0 -0.35 9 9
ceramide signaling 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
MAP4K4 0.033 0.039 -10000 0 -0.24 9 9
BAG4 0.008 0.033 -10000 0 -0.42 3 3
BAD 0.023 0.013 -10000 0 -0.12 1 1
NFKBIA 0.011 0 -10000 0 -10000 0 0
BIRC3 0.002 0.057 -10000 0 -0.4 10 10
BAX 0.023 0.013 -10000 0 -0.12 1 1
EnzymeConsortium:3.1.4.12 0.011 0.01 -10000 0 -0.093 1 1
IKBKB 0.037 0.037 -10000 0 -0.36 1 1
MAP2K2 0.031 0.015 -10000 0 -0.16 1 1
MAP2K1 0.031 0.015 -10000 0 -0.16 1 1
SMPD1 0.015 0.01 -10000 0 -0.088 1 1
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.039 0.038 -10000 0 -0.37 1 1
MAP2K4 0.027 0.015 -10000 0 -0.16 1 1
protein ubiquitination 0.038 0.038 -10000 0 -0.36 1 1
EnzymeConsortium:2.7.1.37 0.035 0.015 -10000 0 -0.16 1 1
response to UV 0 0 -10000 0 -0.001 2 2
RAF1 0.028 0.015 -10000 0 -0.17 1 1
CRADD 0.011 0 -10000 0 -10000 0 0
mol:ceramide 0.018 0.014 -10000 0 -0.13 1 1
I-kappa-B-alpha/RELA/p50/ubiquitin 0.014 0 -10000 0 -10000 0 0
MADD 0.011 0 -10000 0 -10000 0 0
MAP3K1 0.023 0.013 -10000 0 -0.12 1 1
TRADD 0.011 0 -10000 0 -10000 0 0
RELA/p50 0.011 0 -10000 0 -10000 0 0
MAPK3 0.033 0.015 -10000 0 -0.15 1 1
MAPK1 0.033 0.015 -10000 0 -0.15 1 1
p50/RELA/I-kappa-B-alpha 0.016 0 -10000 0 -10000 0 0
FADD 0.033 0.039 -10000 0 -0.24 9 9
KSR1 0.023 0.016 -10000 0 -0.15 2 2
MAPK8 0.029 0.023 -10000 0 -0.15 6 6
TRAF2 0.011 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.037 0.037 -10000 0 -0.36 1 1
TNF R/SODD 0.014 0.023 -10000 0 -0.29 3 3
TNF -0.017 0.086 -10000 0 -0.28 50 50
CYCS 0.033 0.029 0.12 44 -0.11 1 45
IKBKG 0.037 0.037 -10000 0 -0.36 1 1
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.029 0.04 -10000 0 -0.25 9 9
RELA 0.011 0 -10000 0 -10000 0 0
RIPK1 0.011 0 -10000 0 -10000 0 0
AIFM1 0.033 0.029 0.12 44 -0.11 1 45
TNF/TNF R/SODD 0.005 0.051 -10000 0 -0.23 5 5
TNFRSF1A 0.011 0 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.023 0.011 -10000 0 -10000 0 0
NSMAF 0.033 0.038 -10000 0 -0.23 9 9
response to hydrogen peroxide 0 0 -10000 0 -0.001 2 2
BCL2 -0.029 0.12 -10000 0 -0.42 48 48
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.21 0.21 -10000 0 -0.42 265 265
CLTC 0.025 0.002 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.02 0.006 -10000 0 -10000 0 0
Dynamin 2/GTP 0.019 0 -10000 0 -10000 0 0
EXOC4 0.011 0 -10000 0 -10000 0 0
CD59 0.022 0.001 -10000 0 -10000 0 0
CPE -0.021 0.088 -10000 0 -0.24 71 71
CTNNB1 0.011 0 -10000 0 -10000 0 0
membrane fusion 0.02 0.006 -10000 0 -10000 0 0
CTNND1 0.024 0 -10000 0 -10000 0 0
DNM2 0.011 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.025 0.003 -10000 0 -10000 0 0
TSHR 0.006 0.034 -10000 0 -0.16 20 20
INS 0.009 0.002 -10000 0 -10000 0 0
BIN1 0.007 0.038 -10000 0 -0.42 4 4
mol:Choline 0.02 0.006 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.014 0 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.011 0 -10000 0 -10000 0 0
mol:Ca2+ 0.019 0 -10000 0 -10000 0 0
JUP 0.022 0.008 -10000 0 -10000 0 0
ASAP2/amphiphysin II 0.019 0.02 -10000 0 -0.21 4 4
ARF6/GTP 0.008 0 -10000 0 -10000 0 0
CDH1 0.021 0.012 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0.008 0 -10000 0 -10000 0 0
MAPK8IP3 0.011 0 -10000 0 -10000 0 0
positive regulation of endocytosis 0.008 0 -10000 0 -10000 0 0
EXOC2 0.011 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.033 0 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.011 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0 0.006 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.014 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.014 0 -10000 0 -10000 0 0
ACAP1 0.02 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.018 0.008 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.029 0.004 -10000 0 -10000 0 0
JIP4/KLC1 0.021 0 -10000 0 -10000 0 0
EXOC1 0.011 0 -10000 0 -10000 0 0
exocyst 0.033 0 -10000 0 -10000 0 0
RALA/GTP 0.008 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.014 0 -10000 0 -10000 0 0
receptor recycling 0.008 0 -10000 0 -10000 0 0
CTNNA1 0.024 0 -10000 0 -10000 0 0
NME1 0.015 0 -10000 0 -10000 0 0
clathrin coat assembly 0.025 0.002 -10000 0 -10000 0 0
IL2RA 0.02 0.012 -10000 0 -10000 0 0
VAMP3 0.015 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.081 0.079 -10000 0 -10000 0 0
EXOC6 0.011 0 -10000 0 -10000 0 0
PLD1 0.017 0 -10000 0 -10000 0 0
PLD2 0.017 0.011 -10000 0 -0.24 1 1
EXOC5 0.011 0 -10000 0 -10000 0 0
PIP5K1C 0.025 0.003 -10000 0 -10000 0 0
SDC1 0.004 0.025 -10000 0 -10000 0 0
ARF6/GDP 0.014 0 -10000 0 -10000 0 0
EXOC7 0.011 0 -10000 0 -10000 0 0
E-cadherin/beta catenin 0 0.006 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.02 0.006 -10000 0 -10000 0 0
endocytosis -0.018 0.02 0.21 4 -10000 0 4
SCAMP2 0.011 0 -10000 0 -10000 0 0
ADRB2 -0.004 0.075 -10000 0 -10000 0 0
EXOC3 0.011 0 -10000 0 -10000 0 0
ASAP2 0.011 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.02 0 -10000 0 -10000 0 0
KLC1 0.011 0 -10000 0 -10000 0 0
AVPR2 -0.032 0.092 -10000 0 -0.21 1 1
RALA 0.011 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0.005 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.01 0.016 -10000 0 -0.2 3 3
TRAF2/ASK1 0.013 0.019 -10000 0 -0.24 3 3
ATM 0.011 0 -10000 0 -10000 0 0
MAP2K3 0.025 0.018 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.029 0.023 -10000 0 -0.22 3 3
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.001 0.07 -10000 0 -0.42 14 14
TXN 0.007 0 -10000 0 -10000 0 0
CALM1 0.011 0 -10000 0 -10000 0 0
GADD45A 0.011 0 -10000 0 -10000 0 0
GADD45B 0.011 0 -10000 0 -10000 0 0
MAP3K1 0.011 0 -10000 0 -10000 0 0
MAP3K6 0.011 0 -10000 0 -10000 0 0
MAP3K7 0.011 0 -10000 0 -10000 0 0
MAP3K4 0.011 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.014 0.023 -10000 0 -0.29 3 3
TAK1/TAB family 0.001 0.009 0.15 2 -10000 0 2
RAC1/OSM/MEKK3 0.021 0 -10000 0 -10000 0 0
TRAF2 0.011 0 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.001 0.008 -10000 0 -10000 0 0
TRAF6 0.007 0 -10000 0 -10000 0 0
RAC1 0.011 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.045 0.11 -10000 0 -0.27 100 100
CCM2 0.011 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.016 0.062 -10000 0 -0.14 100 100
MAPK11 0.009 0.027 -10000 0 -0.42 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.009 0.058 -10000 0 -0.21 3 3
OSM/MEKK3 0.016 0 -10000 0 -10000 0 0
TAOK1 0.012 0.018 -10000 0 -0.28 2 2
TAOK2 0.013 0 -10000 0 -10000 0 0
TAOK3 0.013 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.011 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.008 0.033 -10000 0 -0.42 3 3
MAP3K10 0.011 0 -10000 0 -10000 0 0
MAP3K3 0.011 0 -10000 0 -10000 0 0
TRX/ASK1 0.011 0.019 -10000 0 -0.23 3 3
GADD45/MTK1/MTK1 0.019 0.035 -10000 0 -0.19 14 14
PLK2 and PLK4 events

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
PLK2 0.01 0.019 -9999 0 -0.42 1 1
PLK4 0.008 0.028 -9999 0 -0.27 5 5
regulation of centriole replication 0.015 0.023 -9999 0 -0.19 6 6
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0.002 0.024 0.21 6 -10000 0 6
DAPP1 0.022 0.054 -10000 0 -0.31 5 5
Src family/SYK family/BLNK-LAT/BTK-ITK 0.044 0.047 -10000 0 -0.49 1 1
mol:DAG 0.045 0.031 0.16 5 -0.18 1 6
HRAS 0.011 0.001 -10000 0 -10000 0 0
RAP1A 0.011 0.001 -10000 0 -10000 0 0
ARF5/GDP 0.025 0.048 -10000 0 -0.32 3 3
PLCG2 0.01 0.019 -10000 0 -0.42 1 1
PLCG1 0.011 0 -10000 0 -10000 0 0
ARF5 0.011 0 -10000 0 -10000 0 0
mol:GTP 0.002 0.023 0.2 6 -10000 0 6
ARF1/GTP 0.002 0.024 0.21 6 -10000 0 6
RHOA 0.011 0 -10000 0 -10000 0 0
YES1 0.011 0 -10000 0 -10000 0 0
RAP1A/GTP 0.023 0.021 0.2 6 -10000 0 6
ADAP1 0.002 0.023 0.2 6 -10000 0 6
ARAP3 0.002 0.023 0.2 6 -10000 0 6
INPPL1 0.011 0 -10000 0 -10000 0 0
PREX1 0.011 0 -10000 0 -10000 0 0
ARHGEF6 -0.001 0.07 -10000 0 -0.42 14 14
ARHGEF7 0.011 0 -10000 0 -10000 0 0
ARF1 0.011 0 -10000 0 -10000 0 0
NRAS 0.011 0.001 -10000 0 -10000 0 0
FYN 0.011 0 -10000 0 -10000 0 0
ARF6 0.011 0 -10000 0 -10000 0 0
FGR 0 0.067 -10000 0 -0.42 13 13
mol:Ca2+ 0.031 0.018 -10000 0 -10000 0 0
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.002 0.072 -10000 0 -0.42 15 15
ZAP70 0 0.056 -10000 0 -0.29 18 18
mol:IP3 0.038 0.023 -10000 0 -10000 0 0
LYN 0.011 0 -10000 0 -10000 0 0
ARF1/GDP 0.025 0.048 -10000 0 -0.2 14 14
RhoA/GDP -0.001 0.026 0.2 5 -0.21 1 6
PDK1/Src/Hsp90 0.022 0 -10000 0 -10000 0 0
BLNK 0.009 0.023 -10000 0 -0.34 2 2
actin cytoskeleton reorganization 0.043 0.037 0.2 5 -0.24 3 8
SRC 0.011 0 -10000 0 -10000 0 0
PLEKHA2 0.022 0.011 -10000 0 -0.23 1 1
RAC1 0.011 0 -10000 0 -10000 0 0
PTEN 0.003 0.043 -10000 0 -0.39 6 6
HSP90AA1 0.011 0 -10000 0 -10000 0 0
ARF6/GTP 0.002 0.024 0.21 6 -10000 0 6
RhoA/GTP 0.027 0.02 0.2 6 -10000 0 6
Src family/SYK family/BLNK-LAT 0.035 0.036 -10000 0 -0.31 1 1
BLK -0.014 0.077 -10000 0 -0.27 42 42
PDPK1 0.011 0 -10000 0 -10000 0 0
CYTH1 0.002 0.023 0.2 6 -10000 0 6
HCK 0.01 0.012 -10000 0 -0.27 1 1
CYTH3 0.002 0.023 0.2 6 -10000 0 6
CYTH2 0.002 0.023 0.2 6 -10000 0 6
KRAS 0.011 0.012 -10000 0 -0.27 1 1
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.032 0.035 -10000 0 -0.39 3 3
SGK1 -0.001 0.037 0.16 6 -0.42 3 9
INPP5D 0.01 0.019 -10000 0 -0.42 1 1
mol:GDP 0.019 0.05 -10000 0 -0.22 14 14
SOS1 0.011 0 -10000 0 -10000 0 0
SYK 0.01 0.012 -10000 0 -0.27 1 1
ARF6/GDP -0.001 0.026 0.2 6 -0.21 1 7
mol:PI-3-4-5-P3 0.002 0.026 0.23 6 -10000 0 6
ARAP3/RAP1A/GTP 0.023 0.021 0.2 6 -10000 0 6
VAV1 0.007 0.034 -10000 0 -0.3 6 6
mol:PI-3-4-P2 0.017 0.013 -10000 0 -0.29 1 1
RAS family/GTP/PI3K Class I 0.024 0.009 -10000 0 -10000 0 0
PLEKHA1 0.022 0.011 -10000 0 -0.23 1 1
Rac1/GDP 0.025 0.048 -10000 0 -0.2 14 14
LAT 0.011 0 -10000 0 -10000 0 0
Rac1/GTP 0.017 0.07 -10000 0 -0.27 26 26
ITK -0.002 0.036 0.2 6 -10000 0 6
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.052 0.038 0.18 5 -0.24 1 6
LCK 0.008 0.031 -10000 0 -0.3 5 5
BTK 0 0.028 0.2 6 -0.17 4 10
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.056 0.034 -9999 0 -10000 0 0
ERC1 0.011 0 -9999 0 -10000 0 0
RIP2/NOD2 0.015 0.008 -9999 0 -0.18 1 1
NFKBIA 0.034 0.01 -9999 0 -10000 0 0
BIRC2 0.011 0 -9999 0 -10000 0 0
IKBKB 0.011 0 -9999 0 -10000 0 0
RIPK2 0.011 0 -9999 0 -10000 0 0
IKBKG 0.036 0.002 -9999 0 -10000 0 0
IKK complex/A20 0.052 0.02 -9999 0 -10000 0 0
NEMO/A20/RIP2 0.011 0 -9999 0 -10000 0 0
XPO1 0.011 0 -9999 0 -10000 0 0
NEMO/ATM 0.04 0.001 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.011 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0.014 0 -9999 0 -10000 0 0
IKK complex/ELKS 0 0.001 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0.022 0 -9999 0 -10000 0 0
NOD2 0.01 0.012 -9999 0 -0.27 1 1
NFKB1 0.012 0.019 -9999 0 -0.41 1 1
RELA 0.013 0 -9999 0 -10000 0 0
MALT1 0.011 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0.016 0 -9999 0 -10000 0 0
ATM 0.011 0 -9999 0 -10000 0 0
TNF/TNFR1A -0.003 0.058 -9999 0 -0.18 50 50
TRAF6 0.011 0 -9999 0 -10000 0 0
PRKCA -0.017 0.1 -9999 0 -0.42 33 33
CHUK 0.011 0 -9999 0 -10000 0 0
UBE2D3 0.011 0 -9999 0 -10000 0 0
TNF -0.018 0.086 -9999 0 -0.28 50 50
NF kappa B1 p50/RelA 0.03 0.011 -9999 0 -0.22 1 1
BCL10 0.011 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.034 0.01 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.013 0 -9999 0 -10000 0 0
TNFRSF1A 0.011 0 -9999 0 -10000 0 0
IKK complex 0.045 0.001 -9999 0 -10000 0 0
CYLD 0.011 0 -9999 0 -10000 0 0
IKK complex/PKC alpha 0.035 0.047 -9999 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.007 0.034 -10000 0 -0.33 5 5
positive regulation of NF-kappaB transcription factor activity 0.006 0.051 -10000 0 -0.27 17 17
MAP2K4 0.034 0.018 -10000 0 -10000 0 0
IKBKB 0.011 0 -10000 0 -10000 0 0
TNFRSF10B 0.011 0 -10000 0 -10000 0 0
TNFRSF10A 0.009 0.027 -10000 0 -0.42 2 2
SMPD1 0.014 0.012 -10000 0 -0.16 2 2
IKBKG 0.011 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.001 0.065 -10000 0 -0.42 12 12
TRAIL/TRAILR2 0.014 0.024 -10000 0 -0.22 5 5
TRAIL/TRAILR3 0.012 0.033 -10000 0 -0.24 8 8
TRAIL/TRAILR1 0.012 0.03 -10000 0 -0.24 7 7
TRAIL/TRAILR4 0.006 0.051 -10000 0 -0.27 17 17
TRAIL/TRAILR1/DAP3/GTP 0.018 0.023 -10000 0 -0.21 4 4
IKK complex -0.001 0.006 -10000 0 -10000 0 0
RIPK1 0.011 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.008 0 -10000 0 -10000 0 0
MAPK3 0.015 0.024 -10000 0 -0.22 5 5
MAP3K1 0.031 0.017 -10000 0 -0.2 2 2
TRAILR4 (trimer) 0.001 0.064 -10000 0 -0.42 12 12
TRADD 0.011 0 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.009 0.027 -10000 0 -0.42 2 2
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.027 0.02 -10000 0 -0.19 4 4
CFLAR 0.011 0 -10000 0 -10000 0 0
MAPK1 0.015 0.024 -10000 0 -0.22 5 5
TRAIL/TRAILR1/FADD/TRADD/RIP 0.029 0.022 -10000 0 -0.18 4 4
mol:ceramide 0.014 0.012 -10000 0 -0.16 2 2
FADD 0.011 0 -10000 0 -10000 0 0
MAPK8 0.036 0.026 -10000 0 -10000 0 0
TRAF2 0.011 0 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.008 0.033 -10000 0 -0.42 3 3
CHUK 0.011 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.019 0.025 -10000 0 -0.23 4 4
DAP3 0.011 0 -10000 0 -10000 0 0
CASP10 0.003 0.044 0.22 12 -0.39 2 14
JNK cascade 0.006 0.051 -10000 0 -0.27 17 17
TRAIL (trimer) 0.007 0.034 -10000 0 -0.33 5 5
TNFRSF10C 0.008 0.033 -10000 0 -0.42 3 3
TRAIL/TRAILR1/DAP3/GTP/FADD 0.023 0.021 -10000 0 -0.19 4 4
TRAIL/TRAILR2/FADD 0.02 0.02 -10000 0 -0.23 2 2
cell death 0.014 0.012 -10000 0 -0.16 2 2
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.028 0.014 -10000 0 -0.19 2 2
TRAILR2 (trimer) 0.011 0 -10000 0 -10000 0 0
CASP8 0.001 0.007 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.03 0.017 -10000 0 -0.18 2 2
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.007 0.031 -9999 0 -0.22 3 3
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.031 0.025 -9999 0 -0.24 2 2
SUMO1 0.011 0 -9999 0 -10000 0 0
ZFPM1 0.009 0.027 -9999 0 -0.42 2 2
NPC/RanGAP1/SUMO1/Ubc9 0.017 0 -9999 0 -10000 0 0
FKBP3 0.011 0 -9999 0 -10000 0 0
Histones 0.03 0.019 -9999 0 -10000 0 0
YY1/LSF 0.017 0.041 -9999 0 -0.2 17 17
SMG5 0.011 0 -9999 0 -10000 0 0
RAN 0.011 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 0.019 0.025 -9999 0 -0.2 2 2
I kappa B alpha/HDAC1 0.019 0.02 -9999 0 -10000 0 0
SAP18 0.011 0 -9999 0 -10000 0 0
RELA 0.023 0.023 -9999 0 -0.19 3 3
HDAC1/Smad7 0.021 0.011 -9999 0 -0.23 1 1
RANGAP1 0.011 0 -9999 0 -10000 0 0
HDAC3/TR2 0.019 0.02 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.036 0.011 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.026 0.023 -9999 0 -0.17 4 4
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 -0.029 0.12 -9999 0 -0.42 48 48
GATA1 0.006 0.005 -9999 0 -10000 0 0
Mad/Max 0.016 0 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.042 0.016 -9999 0 -10000 0 0
RBBP7 0.011 0 -9999 0 -10000 0 0
NPC 0.006 0 -9999 0 -10000 0 0
RBBP4 0.009 0.027 -9999 0 -0.42 2 2
MAX 0.011 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.011 0 -9999 0 -10000 0 0
NFKBIA 0.015 0.023 -9999 0 -10000 0 0
KAT2B 0.002 0.059 -9999 0 -0.42 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.033 0.012 -9999 0 -10000 0 0
SIN3 complex 0.027 0 -9999 0 -10000 0 0
SMURF1 0.011 0 -9999 0 -10000 0 0
CHD3 0.011 0 -9999 0 -10000 0 0
SAP30 0.011 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.011 0 -9999 0 -10000 0 0
YY1/HDAC3 0.024 0.032 -9999 0 -10000 0 0
YY1/HDAC2 0.02 0.032 -9999 0 -0.19 11 11
YY1/HDAC1 0.02 0.032 -9999 0 -0.19 11 11
NuRD/MBD2 Complex (MeCP1) 0.036 0.011 -9999 0 -10000 0 0
PPARG 0.008 0.069 -9999 0 -0.25 31 31
HDAC8/hEST1B 0.022 0 -9999 0 -10000 0 0
UBE2I 0.011 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.011 0 -9999 0 -10000 0 0
TNFRSF1A 0.011 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.019 0.02 -9999 0 -10000 0 0
MBD3L2 0.002 0.004 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.021 0.011 -9999 0 -0.23 1 1
CREBBP 0.01 0.019 -9999 0 -0.42 1 1
NuRD/MBD3/MBD3L2 Complex 0.039 0.011 -9999 0 -10000 0 0
HDAC1 0.011 0 -9999 0 -10000 0 0
HDAC3 0.015 0.023 -9999 0 -0.16 2 2
HDAC2 0.011 0 -9999 0 -10000 0 0
YY1 0.018 0.037 -9999 0 -0.23 11 11
HDAC8 0.011 0 -9999 0 -10000 0 0
SMAD7 0.01 0.019 -9999 0 -0.42 1 1
NCOR2 0.011 0 -9999 0 -10000 0 0
MXD1 0.011 0 -9999 0 -10000 0 0
STAT3 0.019 0.013 -9999 0 -0.27 1 1
NFKB1 0.01 0.019 -9999 0 -0.42 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.011 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 0.022 0.037 -9999 0 -0.18 17 17
YY1/SAP30/HDAC1 0.025 0.029 -9999 0 -0.17 11 11
EP300 0.011 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.019 0.013 -9999 0 -0.27 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.023 -9999 0 -10000 0 0
histone deacetylation 0.036 0.011 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.026 0.021 -9999 0 -0.18 1 1
nuclear export -0.021 0 -9999 0 -10000 0 0
PRKACA 0.011 0 -9999 0 -10000 0 0
GATAD2B 0.011 0 -9999 0 -10000 0 0
GATAD2A 0.011 0 -9999 0 -10000 0 0
GATA2/HDAC3 -0.002 0.07 -9999 0 -0.21 48 48
GATA1/HDAC1 0.012 0.004 -9999 0 -10000 0 0
GATA1/HDAC3 0.008 0.021 -9999 0 -10000 0 0
CHD4 0.011 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.003 0.058 -9999 0 -0.18 50 50
SIN3/HDAC complex/Mad/Max 0.036 0.011 -9999 0 -10000 0 0
NuRD Complex 0.042 0.011 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.029 0.018 -9999 0 -10000 0 0
SIN3B 0.011 0 -9999 0 -10000 0 0
MTA2 0.011 0 -9999 0 -10000 0 0
SIN3A 0.011 0 -9999 0 -10000 0 0
XPO1 0.011 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.024 0 -9999 0 -10000 0 0
HDAC complex 0.027 0.014 -9999 0 -0.2 2 2
GATA1/Fog1 0.011 0.019 -9999 0 -0.29 2 2
FKBP25/HDAC1/HDAC2 0.022 0 -9999 0 -10000 0 0
TNF -0.018 0.086 -9999 0 -0.28 50 50
negative regulation of cell growth 0.036 0.011 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.036 0.011 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.026 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.026 0.024 -9999 0 -0.26 2 2
SIN3/HDAC complex/NCoR1 0.034 0.012 -9999 0 -10000 0 0
TFCP2 0.006 0.046 -9999 0 -0.42 6 6
NR2C1 0.011 0 -9999 0 -10000 0 0
MBD3 0.011 0 -9999 0 -10000 0 0
MBD2 0.011 0 -9999 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.011 0 -10000 0 -10000 0 0
Rac1/GDP 0 0.003 -10000 0 -10000 0 0
DOCK1 0.006 0.046 -10000 0 -0.42 6 6
ITGA4 0.008 0.029 -10000 0 -0.37 3 3
RAC1 0.011 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.014 0.022 -10000 0 -0.23 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.011 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.02 0.017 -10000 0 -0.23 2 2
alpha4/beta7 Integrin/Paxillin 0.025 0.017 -10000 0 -0.2 2 2
lamellipodium assembly -0.005 0.046 -10000 0 -0.42 5 5
PIK3CA 0.01 0.019 -10000 0 -0.42 1 1
PI3K 0.013 0.03 -10000 0 -0.29 5 5
ARF6 0.011 0 -10000 0 -10000 0 0
TLN1 0.011 0 -10000 0 -10000 0 0
PXN 0.017 0 -10000 0 -10000 0 0
PIK3R1 0.007 0.038 -10000 0 -0.42 4 4
ARF6/GTP -0.001 0.011 -10000 0 -10000 0 0
cell adhesion 0.03 0.015 -10000 0 -0.18 2 2
CRKL/CBL 0.016 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.025 0.016 -10000 0 -0.2 2 2
ITGB1 0.011 0 -10000 0 -10000 0 0
ITGB7 0.01 0.012 -10000 0 -0.27 1 1
ARF6/GDP 0 0.003 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.013 0.063 -10000 0 -0.2 41 41
p130Cas/Crk/Dock1 0.019 0.027 -10000 0 -0.23 6 6
VCAM1 -0.024 0.12 -10000 0 -0.42 41 41
alpha4/beta1 Integrin/Paxillin/Talin 0.031 0.015 -10000 0 -0.18 2 2
alpha4/beta1 Integrin/Paxillin/GIT1 0.031 0.015 -10000 0 -0.18 2 2
BCAR1 0.011 0 -10000 0 -10000 0 0
mol:GDP -0.03 0.015 0.18 2 -10000 0 2
CBL 0.011 0 -10000 0 -10000 0 0
PRKACA 0.011 0 -10000 0 -10000 0 0
GIT1 0.011 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.031 0.015 -10000 0 -0.18 2 2
Rac1/GTP -0.006 0.052 -10000 0 -0.47 5 5
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.008 0.033 -9999 0 -0.42 3 3
Caspase 8 (4 units) 0.03 0.031 -9999 0 -10000 0 0
NEF 0.002 0.017 -9999 0 -0.16 3 3
NFKBIA 0.011 0.013 -9999 0 -10000 0 0
BIRC3 0.025 0.064 -9999 0 -0.44 9 9
CYCS 0.034 0.032 -9999 0 -0.2 3 3
RIPK1 0.011 0 -9999 0 -10000 0 0
CD247 0.011 0.029 -9999 0 -0.38 2 2
MAP2K7 0.036 0.031 -9999 0 -10000 0 0
protein ubiquitination 0.049 0.024 -9999 0 -10000 0 0
CRADD 0.011 0 -9999 0 -10000 0 0
DAXX 0.011 0 -9999 0 -10000 0 0
FAS 0.006 0.042 -9999 0 -0.42 5 5
BID 0.03 0.034 -9999 0 -0.22 3 3
NF-kappa-B/RelA/I kappa B alpha 0.025 0.036 -9999 0 -0.23 10 10
TRADD 0.011 0 -9999 0 -10000 0 0
MAP3K5 0.008 0.033 -9999 0 -0.42 3 3
CFLAR 0.011 0 -9999 0 -10000 0 0
FADD 0.011 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.025 0.036 -9999 0 -0.23 10 10
MAPK8 0.039 0.036 -9999 0 -10000 0 0
APAF1 0.011 0 -9999 0 -10000 0 0
TRAF1 0.011 0 -9999 0 -10000 0 0
TRAF2 0.011 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.025 0.035 -9999 0 -0.22 4 4
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.044 0.028 -9999 0 -0.24 2 2
CHUK 0.05 0.026 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.028 0.027 -9999 0 -0.18 8 8
TCRz/NEF 0.011 0.033 -9999 0 -0.28 5 5
TNF -0.018 0.086 -9999 0 -0.28 50 50
FASLG 0.014 0.053 -9999 0 -0.3 12 12
NFKB1 0.011 0.023 -9999 0 -0.41 1 1
TNFR1A/BAG4/TNF-alpha 0.004 0.052 -9999 0 -0.23 5 5
CASP6 -0.003 0.021 -9999 0 -10000 0 0
CASP7 0.053 0.073 -9999 0 -0.46 9 9
RELA 0.011 0.013 -9999 0 -10000 0 0
CASP2 0.011 0 -9999 0 -10000 0 0
CASP3 0.053 0.073 -9999 0 -0.46 9 9
TNFRSF1A 0.011 0 -9999 0 -10000 0 0
TNFR1A/BAG4 0.014 0.023 -9999 0 -0.29 3 3
CASP8 0.011 0 -9999 0 -10000 0 0
CASP9 0.011 0 -9999 0 -10000 0 0
MAP3K14 0.047 0.027 -9999 0 -10000 0 0
APAF-1/Caspase 9 -0.007 0.042 -9999 0 -0.3 9 9
BCL2 0.025 0.068 -9999 0 -0.3 5 5
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.024 0.026 -9999 0 -0.57 1 1
VEGFR1 homodimer/NRP1 0.017 0.026 -9999 0 -0.57 1 1
mol:DAG 0.029 0.025 -9999 0 -0.51 1 1
VEGFR1 homodimer/NRP1/VEGFR 121 0.022 0.024 -9999 0 -0.53 1 1
CaM/Ca2+ 0.033 0.024 -9999 0 -0.48 1 1
HIF1A 0.016 0.014 -9999 0 -0.31 1 1
GAB1 0.007 0.038 -9999 0 -0.42 4 4
AKT1 0.04 0.033 -9999 0 -0.46 1 1
PLCG1 0.029 0.025 -9999 0 -0.52 1 1
NOS3 0.045 0.037 -9999 0 -0.75 1 1
CBL 0.011 0 -9999 0 -10000 0 0
mol:NO 0.045 0.035 -9999 0 -0.71 1 1
FLT1 0.023 0.03 -9999 0 -0.66 1 1
PGF 0.01 0.012 -9999 0 -0.27 1 1
VEGFR1 homodimer/NRP2/VEGFR121 0.018 0.056 -9999 0 -0.52 1 1
CALM1 0.011 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.019 -9999 0 -0.42 1 1
eNOS/Hsp90 0.05 0.034 -9999 0 -0.68 1 1
endothelial cell proliferation 0.016 0.074 -9999 0 -0.38 6 6
mol:Ca2+ 0.029 0.025 -9999 0 -0.51 1 1
MAPK3 0.024 0.055 -9999 0 -0.45 1 1
MAPK1 0.024 0.055 -9999 0 -0.45 1 1
PIK3R1 0.007 0.038 -9999 0 -0.42 4 4
PLGF homodimer 0.01 0.012 -9999 0 -0.27 1 1
PRKACA 0.011 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.082 0.18 -9999 0 -0.42 111 111
VEGFA homodimer 0.011 0 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.024 0.026 -9999 0 -0.57 1 1
platelet activating factor biosynthetic process 0.028 0.053 -9999 0 -0.43 1 1
PI3K 0.032 0.032 -9999 0 -0.49 1 1
PRKCA 0.019 0.058 -9999 0 -0.48 1 1
PRKCB 0.02 0.059 -9999 0 -0.67 1 1
VEGFR1 homodimer/PLGF homodimer 0.024 0.027 -9999 0 -0.57 1 1
VEGFA 0.011 0 -9999 0 -10000 0 0
VEGFB 0.011 0 -9999 0 -10000 0 0
mol:IP3 0.029 0.025 -9999 0 -0.51 1 1
RASA1 0.027 0.033 -9999 0 -0.52 1 1
NRP2 -0.011 0.094 -9999 0 -0.42 26 26
VEGFR1 homodimer 0.022 0.03 -9999 0 -0.65 1 1
VEGFB homodimer 0.011 0 -9999 0 -10000 0 0
NCK1 0.009 0.027 -9999 0 -0.42 2 2
eNOS/Caveolin-1 0.008 0.088 -9999 0 -0.84 1 1
PTPN11 0.011 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.031 0.031 -9999 0 -0.48 1 1
mol:L-citrulline 0.045 0.035 -9999 0 -0.71 1 1
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.035 0.023 -9999 0 -0.49 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.029 0.028 -9999 0 -0.52 1 1
CD2AP 0.011 0 -9999 0 -10000 0 0
PI3K/GAB1 0.035 0.035 -9999 0 -0.46 1 1
PDPK1 0.035 0.03 -9999 0 -0.45 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.03 0.024 -9999 0 -0.52 1 1
mol:NADP 0.045 0.035 -9999 0 -0.71 1 1
HSP90AA1 0.011 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.034 0.023 -9999 0 -0.48 1 1
VEGFR1 homodimer/NRP2 0.012 0.061 -9999 0 -0.24 27 27
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.035 0.029 -10000 0 -0.22 6 6
adherens junction organization 0.032 0.028 -10000 0 -0.35 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.035 0.042 -10000 0 -0.39 2 2
FMN1 0.028 0.034 -10000 0 -0.34 2 2
mol:IP3 0.029 0.025 -10000 0 -0.19 6 6
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.027 0.027 -10000 0 -0.36 2 2
CTNNB1 0.01 0.001 -10000 0 -10000 0 0
AKT1 0.034 0.026 -10000 0 -0.33 1 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.032 0.029 -10000 0 -0.42 2 2
CTNND1 0.011 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.031 0.026 -10000 0 -0.33 2 2
VASP 0.031 0.026 -10000 0 -0.34 2 2
ZYX 0.031 0.026 -10000 0 -0.34 2 2
JUB 0.031 0.026 -10000 0 -0.34 2 2
EGFR(dimer) 0.027 0.046 -10000 0 -0.21 14 14
E-cadherin/beta catenin-gamma catenin 0.019 0.023 -10000 0 -0.26 3 3
mol:PI-3-4-5-P3 0.029 0.028 -10000 0 -0.2 6 6
PIK3CA 0.01 0.019 -10000 0 -0.42 1 1
PI3K 0.03 0.028 -10000 0 -0.21 6 6
FYN 0.033 0.03 -10000 0 -0.25 1 1
mol:Ca2+ 0.029 0.025 -10000 0 -0.19 6 6
JUP 0.01 0.019 -10000 0 -0.41 1 1
PIK3R1 0.008 0.038 -10000 0 -0.42 4 4
mol:DAG 0.029 0.025 -10000 0 -0.19 6 6
CDH1 0.008 0.029 -10000 0 -0.37 3 3
RhoA/GDP 0.035 0.042 -10000 0 -0.39 2 2
establishment of polarity of embryonic epithelium 0.031 0.026 -10000 0 -0.33 2 2
SRC 0.011 0 -10000 0 -10000 0 0
RAC1 0.011 0 -10000 0 -10000 0 0
RHOA 0.011 0 -10000 0 -10000 0 0
EGFR -0.001 0.068 -10000 0 -0.41 14 14
CASR 0.026 0.034 -10000 0 -0.28 1 1
RhoA/GTP -0.002 0.019 -10000 0 -0.27 1 1
AKT2 0.034 0.026 -10000 0 -0.19 6 6
actin cable formation 0.032 0.033 -10000 0 -0.33 2 2
apoptosis -0.032 0.028 0.21 6 -10000 0 6
CTNNA1 0.011 0.001 -10000 0 -10000 0 0
mol:GDP 0.03 0.044 -10000 0 -0.42 2 2
PIP5K1A 0.031 0.026 -10000 0 -0.34 2 2
PLCG1 0.03 0.026 -10000 0 -0.2 6 6
Rac1/GTP -0.005 0.037 -10000 0 -0.34 3 3
homophilic cell adhesion 0.001 0.001 -10000 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.011 0 -9999 0 -10000 0 0
ITGB7 0.01 0.012 -9999 0 -0.27 1 1
ITGA4 0.008 0.029 -9999 0 -0.37 3 3
alpha4/beta7 Integrin 0.014 0.022 -9999 0 -0.23 4 4
alpha4/beta1 Integrin 0.014 0.021 -9999 0 -0.25 3 3
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.01 0.019 -9999 0 -0.42 1 1
SMAD2 0.011 0 -9999 0 -10000 0 0
SMAD3 0.03 0.017 -9999 0 -10000 0 0
SMAD3/SMAD4 0.035 0.02 -9999 0 -0.34 1 1
SMAD4/Ubc9/PIASy 0.021 0.011 -9999 0 -0.23 1 1
SMAD2/SMAD2/SMAD4 0.027 0.024 -9999 0 -10000 0 0
PPM1A 0.011 0 -9999 0 -10000 0 0
CALM1 0.011 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.016 0.01 -9999 0 -0.2 1 1
MAP3K1 0.011 0 -9999 0 -10000 0 0
TRAP-1/SMAD4 0.01 0.04 -9999 0 -0.29 9 9
MAPK3 0.011 0 -9999 0 -10000 0 0
MAPK1 0.011 0 -9999 0 -10000 0 0
NUP214 0.011 0 -9999 0 -10000 0 0
CTDSP1 0.011 0 -9999 0 -10000 0 0
CTDSP2 0.011 0 -9999 0 -10000 0 0
CTDSPL 0.011 0 -9999 0 -10000 0 0
KPNB1 0.011 0 -9999 0 -10000 0 0
TGFBRAP1 0.004 0.053 -9999 0 -0.42 8 8
UBE2I 0.011 0 -9999 0 -10000 0 0
NUP153 0.01 0.019 -9999 0 -0.42 1 1
KPNA2 0.002 0.048 -9999 0 -0.27 15 15
PIAS4 0.011 0 -9999 0 -10000 0 0
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.031 0.013 -10000 0 -10000 0 0
regulation of axonogenesis -0.022 0.008 -10000 0 -10000 0 0
myoblast fusion -0.016 0.013 -10000 0 -10000 0 0
mol:GTP 0.008 0.006 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.02 0.042 0.22 15 -10000 0 15
ARF1/GTP 0 0.002 -10000 0 -10000 0 0
mol:GM1 0.008 0.005 -10000 0 -10000 0 0
mol:Choline 0.021 0.011 -10000 0 -0.22 1 1
lamellipodium assembly 0.002 0.012 -10000 0 -10000 0 0
MAPK3 0.022 0.008 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.021 0.042 -10000 0 -0.22 15 15
ARF1 0.011 0 -10000 0 -10000 0 0
ARF6/GDP 0.016 0.013 -10000 0 -10000 0 0
ARF1/GDP 0.022 0.012 -10000 0 -10000 0 0
ARF6 0.01 0.003 -10000 0 -10000 0 0
RAB11A 0.011 0 -10000 0 -10000 0 0
TIAM1 0 0.072 -10000 0 -0.42 15 15
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.022 0.008 -10000 0 -10000 0 0
actin filament bundle formation -0.02 0.01 -10000 0 -10000 0 0
KALRN -0.001 0.024 -10000 0 -0.21 5 5
RAB11FIP3/RAB11A 0.016 0 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.01 -10000 0 -10000 0 0
NME1 0.012 0.001 -10000 0 -10000 0 0
Rac1/GDP 0.02 0.01 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.008 0.006 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0.002 0.012 -10000 0 -10000 0 0
RAC1 0.011 0 -10000 0 -10000 0 0
liver development 0.008 0.006 -10000 0 -10000 0 0
ARF6/GTP 0.008 0.006 -10000 0 -10000 0 0
RhoA/GTP 0 0.002 -10000 0 -10000 0 0
mol:GDP 0.002 0.013 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0.021 0.005 -10000 0 -10000 0 0
RHOA 0.011 0 -10000 0 -10000 0 0
PLD1 0.016 0.004 -10000 0 -10000 0 0
RAB11FIP3 0.011 0 -10000 0 -10000 0 0
tube morphogenesis 0.002 0.012 -10000 0 -10000 0 0
ruffle organization 0.022 0.008 -10000 0 -10000 0 0
regulation of epithelial cell migration 0.008 0.006 -10000 0 -10000 0 0
PLD2 0.016 0.013 -10000 0 -0.26 1 1
PIP5K1A 0.022 0.008 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.021 0.011 -10000 0 -0.22 1 1
Rac1/GTP 0.002 0.012 -10000 0 -10000 0 0
Atypical NF-kappaB 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
BCL3/RelA 0.015 0.008 -9999 0 -0.18 1 1
FBXW11 0.011 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.02 0.011 -9999 0 -0.24 1 1
NF kappa B1 p50/RelA/I kappa B alpha 0.036 0.012 -9999 0 -10000 0 0
NFKBIA 0.022 0.01 -9999 0 -0.18 1 1
MAPK14 0.011 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.02 0.011 -9999 0 -0.23 1 1
ARRB2 0.013 0 -9999 0 -10000 0 0
REL 0.011 0.001 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.02 0.013 -9999 0 -0.23 1 1
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.02 0.011 -9999 0 -0.23 1 1
PIK3CA 0.01 0.019 -9999 0 -0.42 1 1
NF kappa B1 p50 dimer 0.015 0.013 -9999 0 -0.29 1 1
PIK3R1 0.007 0.038 -9999 0 -0.42 4 4
NFKB1 0.017 0.013 -9999 0 -0.29 1 1
RELA 0.011 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.027 0.011 -9999 0 -0.18 1 1
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.039 0.012 -9999 0 -10000 0 0
SRC 0.011 0 -9999 0 -10000 0 0
PI3K 0.013 0.03 -9999 0 -0.29 5 5
NF kappa B1 p50/RelA 0.027 0.011 -9999 0 -0.18 1 1
IKBKB 0.011 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.011 0 -9999 0 -10000 0 0
SYK 0.01 0.012 -9999 0 -0.27 1 1
I kappa B alpha/PIK3R1 0.025 0.02 -9999 0 -0.18 5 5
cell death 0.037 0.011 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.02 0.011 -9999 0 -0.24 1 1
LCK 0.008 0.031 -9999 0 -0.3 5 5
BCL3 0.01 0.012 -9999 0 -0.27 1 1
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.031 0.026 -9999 0 -0.38 2 2
KLHL20 -0.002 0.012 -9999 0 -10000 0 0
CYFIP2 0.008 0.033 -9999 0 -0.42 3 3
Rac1/GDP 0.046 0.017 -9999 0 -0.21 2 2
ENAH 0.031 0.027 -9999 0 -0.38 2 2
AP1M1 0.011 0 -9999 0 -10000 0 0
RAP1B 0.011 0 -9999 0 -10000 0 0
RAP1A 0.011 0 -9999 0 -10000 0 0
CTNNB1 0.011 0 -9999 0 -10000 0 0
CDC42/GTP -0.001 0.008 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.002 0.01 -9999 0 -0.12 2 2
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.026 0.017 -9999 0 -0.2 2 2
RAPGEF1 0.039 0.023 -9999 0 -0.33 2 2
CTNND1 0.011 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.026 0.027 -9999 0 -0.4 2 2
CRK 0.035 0.025 -9999 0 -0.36 2 2
E-cadherin/gamma catenin/alpha catenin 0.02 0.025 -9999 0 -0.35 2 2
alphaE/beta7 Integrin 0.015 0.008 -9999 0 -0.18 1 1
IQGAP1 0.011 0 -9999 0 -10000 0 0
NCKAP1 0.011 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.021 0 -9999 0 -10000 0 0
DLG1 0.031 0.026 -9999 0 -0.38 2 2
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.001 0.01 -9999 0 -10000 0 0
MLLT4 0.011 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.014 0.039 -9999 0 -0.21 15 15
PI3K -0.001 0.012 -9999 0 -10000 0 0
ARF6 0.011 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin 0.014 0.029 -9999 0 -0.33 3 3
TIAM1 -0.002 0.072 -9999 0 -0.42 15 15
E-cadherin(dimer)/Ca2+ 0.025 0.015 -9999 0 -0.19 2 2
AKT1 -0.001 0.007 -9999 0 -10000 0 0
PIK3R1 0.007 0.038 -9999 0 -0.42 4 4
CDH1 0.008 0.029 -9999 0 -0.37 3 3
RhoA/GDP 0.046 0.017 -9999 0 -0.21 2 2
actin cytoskeleton organization 0.032 0.015 -9999 0 -10000 0 0
CDC42/GDP 0.046 0.017 -9999 0 -0.21 2 2
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.018 0.022 -9999 0 -0.31 2 2
ITGB7 0.01 0.012 -9999 0 -0.27 1 1
RAC1 0.011 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.027 0.016 -9999 0 -0.2 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin 0.018 0.015 -9999 0 -0.2 2 2
mol:GDP 0.044 0.019 -9999 0 -0.25 2 2
CDC42/GTP/IQGAP1 0.014 0 -9999 0 -10000 0 0
JUP 0.01 0.019 -9999 0 -0.42 1 1
p120 catenin/RhoA/GDP 0.043 0.018 -9999 0 -0.21 2 2
RAC1/GTP/IQGAP1 0.014 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0.016 0 -9999 0 -10000 0 0
RHOA 0.011 0 -9999 0 -10000 0 0
CDC42 0.011 0 -9999 0 -10000 0 0
CTNNA1 0.011 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.026 0.01 -9999 0 -10000 0 0
NME1 0.011 0 -9999 0 -10000 0 0
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.031 0.027 -9999 0 -0.38 2 2
regulation of cell-cell adhesion -0.001 0.008 -9999 0 -10000 0 0
WASF2 -0.001 0.005 -9999 0 -10000 0 0
Rap1/GTP -0.001 0.01 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.03 0.022 -9999 0 -0.29 2 2
CCND1 0.03 0.012 -9999 0 -10000 0 0
VAV2 0.039 0.025 -9999 0 -0.35 2 2
RAP1/GDP 0.041 0.016 -9999 0 -10000 0 0
adherens junction assembly 0.03 0.027 -9999 0 -0.37 2 2
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.011 0 -9999 0 -10000 0 0
PIP5K1C 0.011 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.034 0.022 -9999 0 -0.27 2 2
E-cadherin/beta catenin -0.001 0.019 -9999 0 -0.3 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.031 0.026 -9999 0 -0.38 2 2
PIK3CA 0.01 0.019 -9999 0 -0.42 1 1
Rac1/GTP -0.003 0.017 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin 0.021 0.017 -9999 0 -0.23 2 2
ITGAE 0.011 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.026 0.027 -9999 0 -0.41 2 2
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.02 0.025 -9999 0 -0.35 2 2
E-cadherin/beta catenin 0.014 0.021 -9999 0 -0.25 3 3
CTNNB1 0.011 0 -9999 0 -10000 0 0
JUP 0.01 0.019 -9999 0 -0.42 1 1
CDH1 0.008 0.029 -9999 0 -0.37 3 3
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.037 0.009 -9999 0 -10000 0 0
CLOCK 0.013 0.001 -9999 0 -10000 0 0
TIMELESS/CRY2 0.033 0.009 -9999 0 -10000 0 0
DEC1/BMAL1 0.01 0.014 -9999 0 -0.29 1 1
ATR 0.011 0 -9999 0 -10000 0 0
NR1D1 0.032 0.009 -9999 0 -10000 0 0
ARNTL 0.012 0.019 -9999 0 -0.41 1 1
TIMELESS 0.032 0.011 -9999 0 -10000 0 0
NPAS2 0.009 0.042 -9999 0 -0.41 5 5
CRY2 0.011 0 -9999 0 -10000 0 0
mol:CO -0.011 0.002 -9999 0 -10000 0 0
CHEK1 0.011 0 -9999 0 -10000 0 0
mol:HEME 0.011 0.002 -9999 0 -10000 0 0
PER1 0.011 0 -9999 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.032 0.028 -9999 0 -0.22 6 6
BMAL1/CLOCK 0.039 0.018 -9999 0 -10000 0 0
S phase of mitotic cell cycle 0.037 0.009 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.038 0.009 -9999 0 -10000 0 0
mol:NADPH 0.011 0.002 -9999 0 -10000 0 0
PER1/TIMELESS 0.033 0.009 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 0.001 0.004 -9999 0 -10000 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 0.011 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -9999 0 0
MDM2/SUMO1 0.024 0 -9999 0 -9999 0 0
HDAC4 0.011 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -9999 0 0
SUMO1 0.011 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1 0.013 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
XPO1 0.022 0 -9999 0 -9999 0 0
EntrezGene:23636 0 0 -9999 0 -9999 0 0
RAN 0.011 0 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.011 0 -9999 0 -9999 0 0
SUMO1/HDAC4 0.024 0 -9999 0 -9999 0 0
SUMO1/HDAC1 0.024 0 -9999 0 -9999 0 0
RANGAP1 0.011 0 -9999 0 -9999 0 0
MDM2/SUMO1/SUMO1 0.027 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.017 0 -9999 0 -9999 0 0
Ran/GTP 0.021 0 -9999 0 -9999 0 0
EntrezGene:23225 0 0 -9999 0 -9999 0 0
MDM2 0.011 0 -9999 0 -9999 0 0
UBE2I 0.011 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0.026 0 -9999 0 -9999 0 0
NPC 0.006 0 -9999 0 -9999 0 0
PIAS2 0.011 0 -9999 0 -9999 0 0
PIAS1 0.011 0 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0 0 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.016 0.004 -9999 0 -10000 0 0
AP2 0.016 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.015 0 -9999 0 -10000 0 0
CLTB 0.011 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.02 0 -9999 0 -10000 0 0
CD4 0.01 0.012 -9999 0 -0.27 1 1
CLTA 0.011 0 -9999 0 -10000 0 0
mol:GTP 0.001 0 -9999 0 -10000 0 0
ARFGAP1 0.009 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0.007 -9999 0 -0.15 1 1
ARF1/GTP 0 0.003 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.021 0 -9999 0 -10000 0 0
mol:Choline 0 0.007 -9999 0 -0.15 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.011 0 -9999 0 -10000 0 0
DDEF1 0 0.007 -9999 0 -0.16 1 1
ARF1/GDP 0 0.002 -9999 0 -10000 0 0
AP2M1 0.011 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0.013 0 -9999 0 -10000 0 0
Rac/GTP 0.009 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.02 0 -9999 0 -10000 0 0
ARFIP2 0.009 0 -9999 0 -10000 0 0
COPA 0.011 0 -9999 0 -10000 0 0
RAC1 0.011 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.02 0.002 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0.008 0 -9999 0 -10000 0 0
GGA3 0.011 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0.015 0.003 -9999 0 -10000 0 0
AP2A1 0.011 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.021 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0.014 0.003 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0.014 0 -9999 0 -10000 0 0
CYTH2 0.011 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0.015 0 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0.008 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 0.027 0.002 -9999 0 -10000 0 0
PLD2 0 0.007 -9999 0 -0.15 1 1
ARF-GAP1/v-SNARE 0.009 0 -9999 0 -10000 0 0
PIP5K1A 0 0.007 -9999 0 -0.15 1 1
ARF1/GTP/Membrin/GBF1/p115 0 0.003 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0.007 -9999 0 -0.15 1 1
KDEL Receptor/Ligand/ARF-GAP1 0.009 0 -9999 0 -10000 0 0
GOSR2 0 0 -9999 0 -10000 0 0
USO1 0 0 -9999 0 -10000 0 0
GBF1 0 0 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0.015 0.001 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.021 0.007 -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 0.016 0 -9999 0 -10000 0 0
FBXW11 0.011 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 0.011 0 -9999 0 -10000 0 0
CHUK 0.011 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB 0.032 0 -9999 0 -10000 0 0
NFKB1 0.01 0.019 -9999 0 -0.42 1 1
MAP3K14 0.011 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelB 0.015 0.013 -9999 0 -0.29 1 1
RELB 0.011 0 -9999 0 -10000 0 0
NFKB2 0.011 0 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0.014 0 -9999 0 -10000 0 0
regulation of B cell activation 0.014 0 -9999 0 -10000 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 513 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.SL.A6JA TCGA.SL.A6J9 TCGA.QS.A5YR TCGA.QS.A5YQ
109_MAP3K5 0.042 0.042 0.042 -0.13
47_PPARGC1A -0.42 -0.42 0.011 0.011
105_BMP4 0.011 -0.42 0.011 0.011
105_BMP6 0.011 0.011 0.011 0.011
105_BMP7 0.011 0.011 0.011 0.011
105_BMP2 0.011 -0.42 0.011 0.011
131_RELN/VLDLR -0.2 -0.2 0.027 0.027
30_TGFB1/TGF beta receptor Type II 0.012 0.01 0.012 0.01
84_STAT5B -0.025 -0.19 0.036 -0.022
84_STAT5A -0.025 -0.19 0.036 -0.022
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/UCEC-TP/6456935/UCEC-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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