PARADIGM pathway analysis of mRNASeq expression data
Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C15M651M
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C15M651M
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
FOXM1 transcription factor network 177
Aurora B signaling 164
Aurora C signaling 137
HIF-1-alpha transcription factor network 129
Signaling events regulated by Ret tyrosine kinase 113
Endothelins 108
Angiopoietin receptor Tie2-mediated signaling 108
p75(NTR)-mediated signaling 98
PDGFR-alpha signaling pathway 93
Integrins in angiogenesis 82
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 545 . 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 ( 545 ).

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
FOXM1 transcription factor network 0.3248 177 9053 51 -0.97 0.011 1000 -1000 -0.14 -1000
Aurora B signaling 0.3009 164 11039 67 -0.52 0.011 1000 -1000 -0.04 -1000
Aurora C signaling 0.2514 137 961 7 -0.29 0.009 1000 -1000 -0.017 -1000
HIF-1-alpha transcription factor network 0.2367 129 9837 76 -0.49 0.017 1000 -1000 -0.067 -1000
Signaling events regulated by Ret tyrosine kinase 0.2073 113 9278 82 -0.19 0.011 1000 -1000 -0.051 -1000
Endothelins 0.1982 108 10420 96 -0.34 0.011 1000 -1000 -0.044 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1982 108 9525 88 -0.32 0.043 1000 -1000 -0.068 -1000
p75(NTR)-mediated signaling 0.1798 98 12374 125 -0.2 0.03 1000 -1000 -0.052 -1000
PDGFR-alpha signaling pathway 0.1706 93 4097 44 -0.29 0.025 1000 -1000 -0.034 -1000
Integrins in angiogenesis 0.1505 82 6965 84 -0.29 0.024 1000 -1000 -0.049 -1000
Signaling events mediated by the Hedgehog family 0.1450 79 4128 52 -0.26 0.14 1000 -1000 -0.024 -1000
Cellular roles of Anthrax toxin 0.1284 70 2764 39 -0.13 0.019 1000 -1000 -0.016 -1000
S1P3 pathway 0.1284 70 2946 42 -0.41 0.016 1000 -1000 -0.015 -1000
Nongenotropic Androgen signaling 0.1248 68 3554 52 -0.22 0.11 1000 -1000 -0.031 -1000
Wnt signaling 0.1119 61 430 7 -0.088 -0.003 1000 -1000 -0.013 -1000
PLK1 signaling events 0.1064 58 4941 85 -0.3 0.044 1000 -1000 -0.025 -1000
Signaling mediated by p38-alpha and p38-beta 0.1046 57 2546 44 -0.084 0.011 1000 -1000 -0.034 -1000
Effects of Botulinum toxin 0.1028 56 1473 26 -0.11 0.018 1000 -1000 -0.034 -1000
LPA4-mediated signaling events 0.1009 55 668 12 -0.12 0.015 1000 -1000 -0.01 -1000
Glypican 1 network 0.1009 55 2653 48 -0.22 0.022 1000 -1000 -0.014 -1000
Fc-epsilon receptor I signaling in mast cells 0.1009 55 5381 97 -0.13 0.028 1000 -1000 -0.05 -1000
IGF1 pathway 0.0917 50 2871 57 -0.075 0.022 1000 -1000 -0.051 -1000
Aurora A signaling 0.0899 49 2998 60 -0.25 0.022 1000 -1000 -0.016 -1000
Reelin signaling pathway 0.0899 49 2797 56 -0.15 0.03 1000 -1000 -0.047 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0899 49 3385 68 -0.2 0.079 1000 -1000 -0.067 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0899 49 5963 120 -0.19 0.14 1000 -1000 -0.045 -1000
S1P4 pathway 0.0899 49 1248 25 -0.1 0.024 1000 -1000 -0.015 -1000
TCGA08_retinoblastoma 0.0844 46 368 8 -0.13 0.024 1000 -1000 -0.01 -1000
Noncanonical Wnt signaling pathway 0.0826 45 1184 26 -0.14 0.011 1000 -1000 -0.025 -1000
Plasma membrane estrogen receptor signaling 0.0789 43 3701 86 -0.15 0.066 1000 -1000 -0.045 -1000
Syndecan-1-mediated signaling events 0.0771 42 1438 34 -0.17 0.011 1000 -1000 -0.019 -1000
Thromboxane A2 receptor signaling 0.0771 42 4492 105 -0.18 0.031 1000 -1000 -0.043 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0734 40 1391 34 -0.039 0.011 1000 -1000 -0.02 -1000
Ephrin B reverse signaling 0.0734 40 1953 48 -0.098 0.016 1000 -1000 -0.033 -1000
FOXA2 and FOXA3 transcription factor networks 0.0716 39 1838 46 -0.22 0.016 1000 -1000 -0.059 -1000
BMP receptor signaling 0.0716 39 3208 81 -0.28 0.038 1000 -1000 -0.057 -1000
amb2 Integrin signaling 0.0716 39 3266 82 -0.15 0.022 1000 -1000 -0.049 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0716 39 3049 78 -0.1 0.043 1000 -1000 -0.049 -1000
Ephrin A reverse signaling 0.0697 38 272 7 -0.023 0 1000 -1000 -0.01 -1000
Ras signaling in the CD4+ TCR pathway 0.0679 37 642 17 -0.077 0.015 1000 -1000 -0.017 -1000
Osteopontin-mediated events 0.0624 34 1303 38 -0.12 0.014 1000 -1000 -0.055 -1000
IL4-mediated signaling events 0.0624 34 3153 91 -0.52 0.26 1000 -1000 -0.13 -1000
TCGA08_p53 0.0606 33 231 7 -0.089 0.047 1000 -1000 -0.009 -1000
S1P5 pathway 0.0587 32 552 17 -0.1 0.033 1000 -1000 -0.015 -1000
LPA receptor mediated events 0.0587 32 3299 102 -0.14 0.029 1000 -1000 -0.053 -1000
S1P1 pathway 0.0569 31 1122 36 -0.13 0.011 1000 -1000 -0.034 -1000
FAS signaling pathway (CD95) 0.0569 31 1478 47 -0.076 0.038 1000 -1000 -0.025 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0550 30 2555 85 -0.21 0.012 1000 -1000 -0.045 -1000
Glypican 2 network 0.0550 30 123 4 -0.014 -0.001 1000 -1000 -0.01 -1000
EGFR-dependent Endothelin signaling events 0.0550 30 632 21 -0.12 0.019 1000 -1000 -0.042 -1000
Arf6 signaling events 0.0532 29 1828 62 -0.086 0.027 1000 -1000 -0.036 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0532 29 1517 52 -0.078 0.022 1000 -1000 -0.024 -1000
Syndecan-4-mediated signaling events 0.0495 27 1855 67 -0.26 0.016 1000 -1000 -0.056 -1000
Coregulation of Androgen receptor activity 0.0477 26 2011 76 -0.13 0.022 1000 -1000 -0.028 -1000
Visual signal transduction: Cones 0.0477 26 1003 38 -0.08 0.011 1000 -1000 -0.033 -1000
TCGA08_rtk_signaling 0.0477 26 692 26 -0.15 0.023 1000 -1000 -0.01 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0459 25 1403 54 -0.14 0.022 1000 -1000 -0.053 -1000
Calcium signaling in the CD4+ TCR pathway 0.0459 25 785 31 -0.12 0.015 1000 -1000 -0.04 -1000
Visual signal transduction: Rods 0.0459 25 1334 52 -0.11 0.011 1000 -1000 -0.048 -1000
EPHB forward signaling 0.0440 24 2062 85 -0.034 0.029 1000 -1000 -0.045 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0440 24 3051 125 -0.068 0.029 1000 -1000 -0.059 -1000
BCR signaling pathway 0.0422 23 2292 99 -0.059 0.047 1000 -1000 -0.054 -1000
Regulation of Androgen receptor activity 0.0422 23 1610 70 -0.22 0.023 1000 -1000 -0.039 -1000
Syndecan-2-mediated signaling events 0.0404 22 1560 69 -0.1 0.028 1000 -1000 -0.019 -1000
Hedgehog signaling events mediated by Gli proteins 0.0404 22 1494 65 -0.1 0.039 1000 -1000 -0.045 -1000
Glucocorticoid receptor regulatory network 0.0404 22 2537 114 -0.24 0.046 1000 -1000 -0.043 -1000
IL6-mediated signaling events 0.0404 22 1651 75 -0.12 0.061 1000 -1000 -0.043 -1000
IL2 signaling events mediated by STAT5 0.0404 22 498 22 -0.1 0.056 1000 -1000 -0.033 -1000
Presenilin action in Notch and Wnt signaling 0.0385 21 1333 61 -0.12 0.031 1000 -1000 -0.047 -1000
Insulin Pathway 0.0385 21 1580 74 -0.13 0.03 1000 -1000 -0.05 -1000
Signaling events mediated by PTP1B 0.0367 20 1579 76 -0.11 0.023 1000 -1000 -0.047 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0367 20 671 33 -0.16 0.034 1000 -1000 -0.021 -1000
Regulation of nuclear SMAD2/3 signaling 0.0330 18 2527 136 -0.16 0.054 1000 -1000 -0.036 -1000
Retinoic acid receptors-mediated signaling 0.0330 18 1044 58 -0.053 0.022 1000 -1000 -0.042 -1000
Canonical Wnt signaling pathway 0.0330 18 940 51 -0.097 0.05 1000 -1000 -0.035 -1000
Rapid glucocorticoid signaling 0.0330 18 377 20 -0.051 0.011 1000 -1000 -0.01 -1000
BARD1 signaling events 0.0312 17 982 57 -0.13 0.028 1000 -1000 -0.031 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0312 17 495 28 -0.1 0.032 1000 -1000 -0.017 -1000
Class I PI3K signaling events mediated by Akt 0.0312 17 1157 68 -0.24 0.04 1000 -1000 -0.025 -1000
Nectin adhesion pathway 0.0312 17 1129 63 -0.068 0.021 1000 -1000 -0.046 -1000
Regulation of p38-alpha and p38-beta 0.0312 17 953 54 -0.18 0.043 1000 -1000 -0.038 -1000
Regulation of Telomerase 0.0294 16 1670 102 -0.3 0.038 1000 -1000 -0.067 -1000
IL12-mediated signaling events 0.0275 15 1358 87 -0.3 0.044 1000 -1000 -0.091 -1000
Signaling mediated by p38-gamma and p38-delta 0.0275 15 238 15 -0.017 0.021 1000 -1000 -0.014 -1000
Signaling events mediated by PRL 0.0275 15 518 34 -0.13 0.018 1000 -1000 -0.021 -1000
IL1-mediated signaling events 0.0257 14 915 62 -0.038 0.04 1000 -1000 -0.051 -1000
TCR signaling in naïve CD8+ T cells 0.0257 14 1350 93 -0.045 0.041 1000 -1000 -0.045 -1000
IFN-gamma pathway 0.0239 13 948 68 -0.22 0.048 1000 -1000 -0.051 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0239 13 1139 83 -0.24 0.044 1000 -1000 -0.042 -1000
FoxO family signaling 0.0239 13 889 64 -0.24 0.042 1000 -1000 -0.037 -1000
PDGFR-beta signaling pathway 0.0239 13 1335 97 -0.02 0.039 1000 -1000 -0.045 -1000
ErbB4 signaling events 0.0220 12 890 69 -0.075 0.03 1000 -1000 -0.054 -1000
Insulin-mediated glucose transport 0.0220 12 413 32 -0.24 0.025 1000 -1000 -0.031 -1000
Signaling events mediated by HDAC Class III 0.0220 12 519 40 -0.079 0.016 1000 -1000 -0.02 -1000
Syndecan-3-mediated signaling events 0.0220 12 429 35 -0.09 0.03 1000 -1000 -0.024 -1000
ErbB2/ErbB3 signaling events 0.0202 11 744 65 -0.12 0.022 1000 -1000 -0.039 -1000
JNK signaling in the CD4+ TCR pathway 0.0202 11 198 17 -0.014 0.034 1000 -1000 -0.019 -1000
mTOR signaling pathway 0.0202 11 635 53 -0.026 0.018 1000 -1000 -0.037 -1000
HIF-2-alpha transcription factor network 0.0202 11 508 43 -0.14 0.022 1000 -1000 -0.044 -1000
IL2 signaling events mediated by PI3K 0.0202 11 684 58 -0.11 0.043 1000 -1000 -0.053 -1000
Class IB PI3K non-lipid kinase events 0.0202 11 33 3 -0.003 0.003 1000 -1000 -0.005 -1000
EPO signaling pathway 0.0183 10 579 55 -0.024 0.035 1000 -1000 -0.05 -1000
IL27-mediated signaling events 0.0147 8 429 51 -0.056 0.014 1000 -1000 -0.048 -1000
IL23-mediated signaling events 0.0147 8 481 60 -0.046 0.043 1000 -1000 -0.11 -1000
Signaling events mediated by HDAC Class II 0.0128 7 545 75 -0.05 0.029 1000 -1000 -0.026 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0128 7 286 37 -0.02 0.027 1000 -1000 -0.029 -1000
p38 MAPK signaling pathway 0.0128 7 324 44 -0.045 0.028 1000 -1000 -0.041 -1000
Ceramide signaling pathway 0.0110 6 477 76 -0.067 0.037 1000 -1000 -0.028 -1000
Caspase cascade in apoptosis 0.0092 5 430 74 -0.032 0.035 1000 -1000 -0.022 -1000
ceramide signaling pathway 0.0092 5 257 49 -0.031 0.038 1000 -1000 -0.031 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0092 5 379 74 -0.076 0.062 1000 -1000 -0.052 -1000
Arf6 trafficking events 0.0092 5 356 71 -0.2 0.035 1000 -1000 -0.046 -1000
Canonical NF-kappaB pathway 0.0073 4 178 39 -0.032 0.058 1000 -1000 -0.044 -1000
PLK2 and PLK4 events 0.0073 4 14 3 0.007 0.015 1000 -1000 -0.007 -1000
TRAIL signaling pathway 0.0073 4 192 48 -0.001 0.037 1000 -1000 -0.037 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0073 4 197 45 -0.032 0.057 1000 -1000 -0.051 -1000
Class I PI3K signaling events 0.0073 4 317 73 -0.015 0.053 1000 -1000 -0.036 -1000
Signaling events mediated by HDAC Class I 0.0055 3 382 104 -0.032 0.044 1000 -1000 -0.039 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0037 2 47 23 -0.005 0.036 1000 -1000 -0.028 -1000
a4b1 and a4b7 Integrin signaling 0.0037 2 11 5 0.009 0.015 1000 -1000 -0.011 -1000
Paxillin-dependent events mediated by a4b1 0.0037 2 95 36 -0.031 0.032 1000 -1000 -0.04 -1000
VEGFR1 specific signals 0.0037 2 138 56 -0.062 0.052 1000 -1000 -0.027 -1000
Arf6 downstream pathway 0.0018 1 49 43 -0.023 0.023 1000 -1000 -0.032 -1000
Atypical NF-kappaB pathway 0.0018 1 36 31 0 0.04 1000 -1000 -0.019 -1000
E-cadherin signaling in the nascent adherens junction 0.0018 1 102 76 -0.003 0.048 1000 -1000 -0.049 -1000
E-cadherin signaling in keratinocytes 0.0018 1 66 43 -0.034 0.037 1000 -1000 -0.038 -1000
E-cadherin signaling events 0.0018 1 7 5 0.009 0.021 1000 -1000 -0.01 -1000
Circadian rhythm pathway 0.0000 0 16 22 -0.011 0.04 1000 -1000 -0.026 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 0 27 0 0.028 1000 -1000 -0.032 -1000
Arf1 pathway 0.0000 0 8 54 0 0.028 1000 -1000 -0.017 -1000
Alternative NF-kappaB pathway 0.0000 0 2 13 0 0.033 1000 -1000 -0.011 -1000
Total NA 4079 241308 7203 -17 4.3 131000 -131000 -4.9 -131000
FOXM1 transcription factor network

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
NFATC3 -0.63 0.36 -9999 0 -0.99 207 207
PLK1 -0.15 0.088 -9999 0 -10000 0 0
BIRC5 -0.16 0.082 -9999 0 -10000 0 0
HSPA1B -0.63 0.36 -9999 0 -0.97 221 221
MAP2K1 -0.021 0.017 -9999 0 -10000 0 0
BRCA2 -0.63 0.36 -9999 0 -0.99 207 207
FOXM1 -0.76 0.48 -9999 0 -1.1 286 286
XRCC1 -0.63 0.36 -9999 0 -0.99 207 207
FOXM1B/p19 -0.67 0.4 -9999 0 -0.98 287 287
Cyclin D1/CDK4 -0.58 0.33 -9999 0 -0.89 224 224
CDC2 -0.66 0.38 -9999 0 -0.96 284 284
TGFA -0.56 0.31 -9999 0 -0.86 221 221
SKP2 -0.63 0.36 -9999 0 -0.95 243 243
CCNE1 -0.14 0.17 -9999 0 -0.34 220 220
CKS1B -0.63 0.36 -9999 0 -0.97 219 219
RB1 -0.24 0.12 -9999 0 -0.51 13 13
FOXM1C/SP1 -0.69 0.42 -9999 0 -1 283 283
AURKB -0.17 0.067 -9999 0 -10000 0 0
CENPF -0.66 0.38 -9999 0 -0.97 275 275
CDK4 -0.001 0.006 -9999 0 -10000 0 0
MYC -0.56 0.32 -9999 0 -0.84 246 246
CHEK2 -0.022 0.022 -9999 0 -0.35 1 1
ONECUT1 -0.61 0.35 -9999 0 -0.91 252 252
CDKN2A -0.13 0.17 -9999 0 -0.32 228 228
LAMA4 -0.66 0.4 -9999 0 -1.1 211 211
FOXM1B/HNF6 -0.69 0.42 -9999 0 -1 262 262
FOS -0.77 0.48 -9999 0 -1.2 273 273
SP1 0.011 0.001 -9999 0 -10000 0 0
CDC25B -0.63 0.36 -9999 0 -0.98 209 209
response to radiation -0.03 0.014 -9999 0 -10000 0 0
CENPB -0.63 0.36 -9999 0 -0.98 209 209
CENPA -0.68 0.38 -9999 0 -1 264 264
NEK2 -0.68 0.37 -9999 0 -0.98 277 277
HIST1H2BA -0.63 0.36 -9999 0 -0.98 216 216
CCNA2 -0.071 0.14 -9999 0 -0.34 117 117
EP300 0.011 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.72 0.43 -9999 0 -1.1 257 257
CCNB2 -0.68 0.38 -9999 0 -0.98 283 283
CCNB1 -0.67 0.39 -9999 0 -1 256 256
ETV5 -0.63 0.36 -9999 0 -0.99 207 207
ESR1 -0.67 0.41 -9999 0 -1 238 238
CCND1 -0.59 0.33 -9999 0 -0.89 236 236
GSK3A -0.014 0.014 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.12 0.14 -9999 0 -0.25 265 265
CDK2 0.003 0.004 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.037 0.017 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.67 0.38 -9999 0 -0.95 305 305
GAS1 -0.97 0.48 -9999 0 -1.3 378 378
MMP2 -0.64 0.38 -9999 0 -1 205 205
RB1/FOXM1C -0.62 0.36 -9999 0 -0.93 259 259
CREBBP 0.009 0.025 -9999 0 -0.41 2 2
Aurora B signaling

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
Condensin I complex -0.12 0.064 -9999 0 -10000 0 0
STMN1 -0.18 0.076 -9999 0 -0.21 479 479
Aurora B/RasGAP/Survivin -0.27 0.12 -9999 0 -0.33 409 409
Chromosomal passenger complex/Cul3 protein complex -0.12 0.092 -9999 0 -0.28 97 97
BIRC5 -0.26 0.14 -9999 0 -0.33 423 423
DES -0.52 0.25 -9999 0 -0.63 453 453
Aurora C/Aurora B/INCENP -0.13 0.061 -9999 0 -0.15 330 330
Aurora B/TACC1 -0.19 0.11 -9999 0 -0.21 488 488
Aurora B/PP2A -0.18 0.076 -9999 0 -0.21 479 479
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.024 0.014 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition -0.004 0.003 -9999 0 -10000 0 0
NDC80 -0.2 0.096 -9999 0 -0.23 480 480
Cul3 protein complex -0.027 0.1 -9999 0 -0.23 106 106
KIF2C -0.067 0.034 -9999 0 -10000 0 0
PEBP1 0.002 0.004 -9999 0 -10000 0 0
KIF20A -0.3 0.1 -9999 0 -0.33 491 491
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.18 0.081 -9999 0 -0.21 479 479
SEPT1 0.01 0.018 -9999 0 -0.41 1 1
SMC2 0.01 0.015 -9999 0 -0.33 1 1
SMC4 0.011 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.009 0.015 -9999 0 -10000 0 0
PSMA3 0.011 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.004 0.001 -9999 0 -10000 0 0
H3F3B -0.073 0.034 -9999 0 -10000 0 0
AURKB -0.28 0.11 -9999 0 -0.33 479 479
AURKC 0.009 0.025 -9999 0 -0.33 3 3
CDCA8 -0.19 0.17 -9999 0 -0.33 318 318
cytokinesis -0.15 0.068 -9999 0 -0.25 19 19
Aurora B/Septin1 -0.13 0.078 -9999 0 -0.28 3 3
AURKA -0.092 0.16 -9999 0 -0.33 162 162
INCENP 0.004 0.004 -9999 0 -10000 0 0
KLHL13 -0.071 0.17 -9999 0 -0.41 106 106
BUB1 -0.26 0.14 -9999 0 -0.33 427 427
hSgo1/Aurora B/Survivin -0.37 0.15 -9999 0 -0.43 455 455
EVI5 0.011 0.001 -9999 0 -10000 0 0
RhoA/GTP -0.11 0.064 -9999 0 -0.28 23 23
SGOL1 -0.25 0.14 -9999 0 -0.33 423 423
CENPA -0.1 0.05 -9999 0 -10000 0 0
NCAPG -0.22 0.16 -9999 0 -0.33 364 364
Aurora B/HC8 Proteasome -0.18 0.076 -9999 0 -0.21 479 479
NCAPD2 0.011 0 -9999 0 -10000 0 0
Aurora B/PP1-gamma -0.18 0.076 -9999 0 -0.21 479 479
RHOA 0.011 0 -9999 0 -10000 0 0
NCAPH -0.25 0.14 -9999 0 -0.33 421 421
NPM1 -0.041 0.018 -9999 0 -10000 0 0
RASA1 0.007 0.04 -9999 0 -0.41 5 5
KLHL9 0.01 0.018 -9999 0 -0.41 1 1
mitotic prometaphase -0.009 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.18 0.076 -9999 0 -0.21 479 479
PPP1CC 0.011 0 -9999 0 -10000 0 0
Centraspindlin -0.12 0.072 -9999 0 -0.25 45 45
RhoA/GDP 0.008 0 -9999 0 -10000 0 0
NSUN2 -0.041 0.018 -9999 0 -10000 0 0
MYLK -0.24 0.15 -9999 0 -0.37 311 311
KIF23 -0.006 0.069 -9999 0 -0.33 23 23
VIM -0.18 0.083 -9999 0 -0.21 479 479
RACGAP1 0.007 0.021 -9999 0 -0.33 2 2
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.041 0.018 -9999 0 -10000 0 0
Chromosomal passenger complex -0.14 0.066 -9999 0 -0.18 295 295
Chromosomal passenger complex/EVI5 -0.26 0.19 -9999 0 -0.36 424 424
TACC1 -0.065 0.16 -9999 0 -0.41 98 98
PPP2R5D 0.011 0 -9999 0 -10000 0 0
CUL3 0.011 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Aurora C signaling

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
INCENP 0.011 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.13 0.059 -9999 0 -0.16 479 479
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.038 0.014 -9999 0 -10000 0 0
AURKB -0.29 0.11 -9999 0 -0.33 479 479
AURKC 0.009 0.025 -9999 0 -0.33 3 3
HIF-1-alpha transcription factor network

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
PKM2 -0.36 0.41 -9999 0 -0.83 177 177
HDAC7 0.012 0.001 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.3 0.36 -9999 0 -0.74 156 156
SMAD4 0.011 0.018 -9999 0 -0.41 1 1
ID2 -0.36 0.41 -9999 0 -0.83 177 177
AP1 -0.077 0.14 -9999 0 -0.29 168 168
ABCG2 -0.47 0.47 -9999 0 -0.89 256 256
HIF1A -0.047 0.062 -9999 0 -10000 0 0
TFF3 -0.42 0.44 -9999 0 -0.87 213 213
GATA2 -0.029 0.12 -9999 0 -0.41 53 53
AKT1 -0.061 0.084 -9999 0 -0.22 40 40
response to hypoxia -0.078 0.087 -9999 0 -0.21 86 86
MCL1 -0.36 0.41 -9999 0 -0.83 177 177
NDRG1 -0.36 0.41 -9999 0 -0.83 177 177
SERPINE1 -0.36 0.41 -9999 0 -0.83 177 177
FECH -0.36 0.41 -9999 0 -0.82 179 179
FURIN -0.36 0.41 -9999 0 -0.83 177 177
NCOA2 -0.003 0.077 -9999 0 -0.41 19 19
EP300 -0.073 0.13 -9999 0 -0.34 75 75
HMOX1 -0.36 0.41 -9999 0 -0.83 177 177
BHLHE40 -0.36 0.41 -9999 0 -0.83 177 177
BHLHE41 -0.38 0.43 -9999 0 -0.86 187 187
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.04 0.083 -9999 0 -0.3 5 5
ENG -0.025 0.085 -9999 0 -0.32 1 1
JUN 0.006 0.048 -9999 0 -0.41 7 7
RORA -0.37 0.42 -9999 0 -0.84 181 181
ABCB1 -0.35 0.49 -9999 0 -1.2 139 139
TFRC -0.36 0.41 -9999 0 -0.83 177 177
CXCR4 -0.36 0.41 -9999 0 -0.82 180 180
TF -0.37 0.42 -9999 0 -0.84 179 179
CITED2 -0.37 0.41 -9999 0 -0.83 182 182
HIF1A/ARNT -0.39 0.48 -9999 0 -0.89 199 199
LDHA -0.053 0.048 -9999 0 -10000 0 0
ETS1 -0.36 0.41 -9999 0 -0.83 177 177
PGK1 -0.36 0.41 -9999 0 -0.82 180 180
NOS2 -0.37 0.41 -9999 0 -0.83 181 181
ITGB2 -0.36 0.41 -9999 0 -0.83 177 177
ALDOA -0.36 0.41 -9999 0 -0.83 177 177
Cbp/p300/CITED2 -0.39 0.46 -9999 0 -0.94 165 165
FOS -0.12 0.19 -9999 0 -0.41 167 167
HK2 -0.37 0.41 -9999 0 -0.84 180 180
SP1 0.01 0.022 -9999 0 -10000 0 0
GCK -0.23 0.46 -9999 0 -1.3 76 76
HK1 -0.36 0.41 -9999 0 -0.83 177 177
NPM1 -0.36 0.41 -9999 0 -0.83 177 177
EGLN1 -0.36 0.41 -9999 0 -0.82 179 179
CREB1 0.017 0 -9999 0 -10000 0 0
PGM1 -0.36 0.41 -9999 0 -0.83 177 177
SMAD3 0.009 0.036 -9999 0 -0.41 4 4
EDN1 -0.14 0.24 -9999 0 -0.6 75 75
IGFBP1 -0.39 0.43 -9999 0 -0.86 195 195
VEGFA -0.25 0.32 -9999 0 -0.69 114 114
HIF1A/JAB1 -0.022 0.037 -9999 0 -10000 0 0
CP -0.4 0.43 -9999 0 -0.87 194 194
CXCL12 -0.49 0.47 -9999 0 -0.9 257 257
COPS5 0.011 0.003 -9999 0 -10000 0 0
SMAD3/SMAD4 0.016 0.028 -9999 0 -0.28 5 5
BNIP3 -0.36 0.41 -9999 0 -0.83 177 177
EGLN3 -0.36 0.41 -9999 0 -0.83 180 180
CA9 -0.43 0.44 -9999 0 -0.86 224 224
TERT -0.41 0.43 -9999 0 -0.87 199 199
ENO1 -0.36 0.41 -9999 0 -0.83 177 177
PFKL -0.36 0.41 -9999 0 -0.83 177 177
NCOA1 0.01 0.018 -9999 0 -0.41 1 1
ADM -0.37 0.41 -9999 0 -0.83 188 188
ARNT -0.047 0.062 -9999 0 -10000 0 0
HNF4A -0.048 0.12 -9999 0 -0.34 78 78
ADFP -0.37 0.4 -9999 0 -0.8 199 199
SLC2A1 -0.25 0.32 -9999 0 -0.69 112 112
LEP -0.36 0.41 -9999 0 -0.83 175 175
HIF1A/ARNT/Cbp/p300 -0.32 0.37 -9999 0 -0.76 164 164
EPO -0.22 0.29 -9999 0 -0.73 61 61
CREBBP -0.074 0.14 -9999 0 -0.34 76 76
HIF1A/ARNT/Cbp/p300/HDAC7 -0.29 0.36 -9999 0 -0.75 148 148
PFKFB3 -0.36 0.41 -9999 0 -0.82 180 180
NT5E -0.39 0.43 -9999 0 -0.88 188 188
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.032 0.034 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.13 0.13 -9999 0 -0.34 100 100
JUN -0.077 0.13 -9999 0 -0.39 36 36
HRAS 0.011 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.1 0.13 -9999 0 -0.23 263 263
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 -0.23 262 262
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 0.11 -9999 0 -0.21 257 257
RHOA 0.011 0 -9999 0 -10000 0 0
RAP1A/GTP -0.098 0.11 -9999 0 -0.2 262 262
GRB7 -0.011 0.084 -9999 0 -0.33 34 34
RET51/GFRalpha1/GDNF -0.1 0.13 -9999 0 -0.23 262 262
MAPKKK cascade -0.098 0.11 -9999 0 -0.37 32 32
BCAR1 0.011 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.11 0.14 -9999 0 -0.24 272 272
lamellipodium assembly -0.12 0.13 -9999 0 -0.24 264 264
RET51/GFRalpha1/GDNF/SHC -0.1 0.13 -9999 0 -0.23 262 262
PIK3CA 0.01 0.018 -9999 0 -0.41 1 1
RET9/GFRalpha1/GDNF/SHC -0.09 0.11 -9999 0 -0.21 256 256
RET9/GFRalpha1/GDNF/Shank3 -0.09 0.11 -9999 0 -0.21 256 256
MAPK3 -0.075 0.11 -9999 0 -0.34 30 30
DOK1 0.011 0 -9999 0 -10000 0 0
DOK6 -0.073 0.17 -9999 0 -0.41 108 108
PXN 0.011 0 -9999 0 -10000 0 0
neurite development -0.082 0.12 -9999 0 -0.27 95 95
DOK5 -0.028 0.12 -9999 0 -0.41 51 51
GFRA1 -0.19 0.21 -9999 0 -0.41 257 257
MAPK8 -0.084 0.13 -9999 0 -0.4 33 33
HRAS/GTP -0.11 0.12 -9999 0 -0.23 262 262
tube development -0.078 0.11 -9999 0 -0.19 256 256
MAPK1 -0.075 0.11 -9999 0 -0.34 30 30
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.081 0.11 -9999 0 -0.2 255 255
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 -0.28 222 222
SHC1 0.011 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.1 0.13 -9999 0 -0.23 262 262
RET51/GFRalpha1/GDNF/Dok5 -0.12 0.16 -9999 0 -0.26 273 273
PRKCA -0.017 0.1 -9999 0 -0.41 36 36
HRAS/GDP 0.008 0 -9999 0 -10000 0 0
CREB1 -0.1 0.14 -9999 0 -0.25 255 255
PIK3R1 0.007 0.04 -9999 0 -0.41 5 5
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.084 0.12 -9999 0 -0.2 255 255
RET51/GFRalpha1/GDNF/Grb7 -0.11 0.14 -9999 0 -0.23 265 265
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.024 0.11 -9999 0 -0.37 49 49
DOK4 0.011 0 -9999 0 -10000 0 0
JNK cascade -0.075 0.13 -9999 0 -0.38 36 36
RET9/GFRalpha1/GDNF/FRS2 -0.09 0.11 -9999 0 -0.21 257 257
SHANK3 0.011 0 -9999 0 -10000 0 0
RASA1 0.007 0.04 -9999 0 -0.41 5 5
NCK1 0.009 0.025 -9999 0 -0.41 2 2
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.082 0.11 -9999 0 -0.2 255 255
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.09 0.12 -9999 0 -0.22 172 172
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.094 0.13 -9999 0 -0.22 262 262
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.094 0.14 -9999 0 -0.44 30 30
PI3K -0.16 0.21 -9999 0 -0.36 264 264
SOS1 0.011 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.078 0.11 -9999 0 -0.19 256 256
GRB10 0.01 0.018 -9999 0 -0.41 1 1
activation of MAPKK activity -0.082 0.11 -9999 0 -0.31 29 29
RET51/GFRalpha1/GDNF/FRS2 -0.1 0.13 -9999 0 -0.23 262 262
GAB1 0.008 0.036 -9999 0 -0.41 4 4
IRS1 -0.031 0.13 -9999 0 -0.41 54 54
IRS2 -0.042 0.14 -9999 0 -0.41 69 69
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.096 0.14 -9999 0 -0.24 172 172
RET51/GFRalpha1/GDNF/PKC alpha -0.12 0.15 -9999 0 -0.24 273 273
GRB2 0.011 0 -9999 0 -10000 0 0
PRKACA 0.011 0 -9999 0 -10000 0 0
GDNF 0.003 0.025 -9999 0 -0.33 3 3
RAC1 0.011 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.12 0.16 -9999 0 -0.26 276 276
Rac1/GTP -0.15 0.15 -9999 0 -0.28 264 264
RET9/GFRalpha1/GDNF -0.11 0.13 -9999 0 -0.24 257 257
GFRalpha1/GDNF -0.13 0.15 -9999 0 -0.29 257 257
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 -0.089 0.2 -10000 0 -0.38 123 123
PTK2B 0.011 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.13 0.32 -10000 0 -0.8 83 83
EDN1 -0.002 0.089 -10000 0 -0.39 11 11
EDN3 -0.099 0.17 -10000 0 -0.36 160 160
EDN2 -0.042 0.12 -10000 0 -0.33 85 85
HRAS/GDP -0.12 0.21 -10000 0 -0.42 137 137
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.084 0.18 -10000 0 -0.36 128 128
ADCY4 -0.11 0.19 -10000 0 -0.39 138 138
ADCY5 -0.14 0.2 -10000 0 -0.4 164 164
ADCY6 -0.1 0.18 -10000 0 -0.37 134 134
ADCY7 -0.1 0.18 -10000 0 -0.37 134 134
ADCY1 -0.12 0.2 -10000 0 -0.38 144 144
ADCY2 -0.22 0.23 -10000 0 -0.46 210 210
ADCY3 -0.11 0.19 -10000 0 -0.38 134 134
ADCY8 -0.11 0.18 -10000 0 -0.38 134 134
ADCY9 -0.13 0.22 -10000 0 -0.42 156 156
arachidonic acid secretion -0.17 0.28 -10000 0 -0.46 221 221
ETB receptor/Endothelin-1/Gq/GTP -0.067 0.15 -10000 0 -0.32 106 106
GNAO1 -0.1 0.18 -10000 0 -0.41 143 143
HRAS 0.009 0.004 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.059 0.21 -10000 0 -0.36 116 116
ETA receptor/Endothelin-1/Gs/GTP -0.089 0.22 -10000 0 -0.4 134 134
mol:GTP -0.002 0.005 -10000 0 -10000 0 0
COL3A1 -0.097 0.22 -10000 0 -0.43 118 118
EDNRB -0.083 0.18 -10000 0 -0.41 124 124
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.13 0.26 -10000 0 -0.54 123 123
CYSLTR1 -0.094 0.21 -10000 0 -0.42 117 117
SLC9A1 -0.058 0.11 -10000 0 -0.23 116 116
mol:GDP -0.13 0.22 -10000 0 -0.44 141 141
SLC9A3 -0.14 0.3 -10000 0 -0.64 124 124
RAF1 -0.16 0.24 -10000 0 -0.42 208 208
JUN -0.1 0.26 -10000 0 -0.66 78 78
JAK2 -0.093 0.2 -10000 0 -0.38 135 135
mol:IP3 -0.09 0.18 -10000 0 -0.4 97 97
ETA receptor/Endothelin-1 -0.086 0.26 -10000 0 -0.43 145 145
PLCB1 0.006 0.032 -10000 0 -0.41 3 3
PLCB2 0.008 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.16 0.19 -10000 0 -0.33 284 284
FOS -0.29 0.43 -10000 0 -0.85 185 185
Gai/GDP -0.19 0.34 -10000 0 -0.73 144 144
CRK 0.011 0.001 -10000 0 -10000 0 0
mol:Ca ++ -0.14 0.25 -10000 0 -0.47 159 159
BCAR1 0.011 0 -10000 0 -10000 0 0
PRKCB1 -0.091 0.17 -10000 0 -0.38 102 102
GNAQ 0.007 0.026 -10000 0 -0.41 2 2
GNAZ -0.002 0.073 -10000 0 -0.41 17 17
GNAL -0.051 0.15 -10000 0 -0.41 80 80
Gs family/GDP -0.16 0.2 -10000 0 -0.42 168 168
ETA receptor/Endothelin-1/Gq/GTP -0.098 0.21 -10000 0 -0.4 130 130
MAPK14 -0.05 0.13 -10000 0 -0.31 73 73
TRPC6 -0.14 0.34 -10000 0 -0.86 83 83
GNAI2 0.011 0 -10000 0 -10000 0 0
GNAI3 0.011 0 -10000 0 -10000 0 0
GNAI1 0.005 0.051 -10000 0 -0.41 8 8
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.059 0.14 -10000 0 -0.32 88 88
ETB receptor/Endothelin-2 -0.085 0.15 -10000 0 -0.28 184 184
ETB receptor/Endothelin-3 -0.12 0.16 -10000 0 -0.28 253 253
ETB receptor/Endothelin-1 -0.056 0.15 -10000 0 -0.3 131 131
MAPK3 -0.26 0.38 -10000 0 -0.74 192 192
MAPK1 -0.26 0.38 -10000 0 -0.73 194 194
Rac1/GDP -0.12 0.21 -10000 0 -0.41 137 137
cAMP biosynthetic process -0.19 0.24 -10000 0 -0.44 215 215
MAPK8 -0.13 0.3 -10000 0 -0.74 86 86
SRC 0.011 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.087 0.16 -10000 0 -0.34 124 124
p130Cas/CRK/Src/PYK2 -0.11 0.23 -10000 0 -0.52 104 104
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.12 0.21 -10000 0 -0.42 135 135
COL1A2 -0.13 0.25 -10000 0 -0.52 122 122
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.12 0.18 -10000 0 -0.32 224 224
mol:DAG -0.09 0.18 -10000 0 -0.4 97 97
MAP2K2 -0.2 0.3 -10000 0 -0.55 200 200
MAP2K1 -0.2 0.3 -10000 0 -0.55 202 202
EDNRA -0.13 0.24 -10000 0 -0.47 166 166
positive regulation of muscle contraction -0.071 0.17 -10000 0 -0.34 116 116
Gq family/GDP -0.13 0.19 -10000 0 -0.44 115 115
HRAS/GTP -0.12 0.21 -10000 0 -0.4 144 144
PRKCH -0.086 0.18 -10000 0 -0.4 91 91
RAC1 0.011 0 -10000 0 -10000 0 0
PRKCA -0.098 0.19 -10000 0 -0.41 105 105
PRKCB -0.097 0.19 -10000 0 -0.41 106 106
PRKCE -0.084 0.17 -10000 0 -0.39 92 92
PRKCD -0.086 0.17 -10000 0 -0.4 89 89
PRKCG -0.11 0.18 -10000 0 -0.39 119 119
regulation of vascular smooth muscle contraction -0.34 0.5 -10000 0 -1 185 185
PRKCQ -0.1 0.18 -10000 0 -0.39 119 119
PLA2G4A -0.19 0.31 -10000 0 -0.5 221 221
GNA14 -0.033 0.13 -10000 0 -0.41 54 54
GNA15 0.004 0.039 -10000 0 -0.34 7 7
GNA12 0.011 0 -10000 0 -10000 0 0
GNA11 -0.001 0.062 -10000 0 -0.41 12 12
Rac1/GTP -0.059 0.21 0.17 106 -0.36 117 223
MMP1 -0.048 0.15 0.27 9 -10000 0 9
Angiopoietin receptor Tie2-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
AKT1 -0.19 0.44 -10000 0 -0.84 168 168
NCK1/PAK1/Dok-R -0.12 0.18 -10000 0 -0.4 168 168
NCK1/Dok-R -0.26 0.51 -10000 0 -1 168 168
PIK3CA 0.011 0.018 -10000 0 -0.41 1 1
mol:beta2-estradiol 0.043 0.095 0.23 110 -10000 0 110
RELA 0.011 0 -10000 0 -10000 0 0
SHC1 0.011 0.002 -10000 0 -10000 0 0
Rac/GDP 0.008 0 -10000 0 -10000 0 0
F2 0.026 0.14 0.25 110 -0.34 40 150
TNIP2 0.011 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.28 0.45 -10000 0 -0.93 168 168
FN1 0.007 0.04 -10000 0 -0.41 5 5
PLD2 -0.28 0.53 -10000 0 -1 168 168
PTPN11 0.011 0 -10000 0 -10000 0 0
GRB14 -0.11 0.16 -10000 0 -0.33 196 196
ELK1 -0.24 0.47 -10000 0 -0.93 168 168
GRB7 -0.011 0.084 -10000 0 -0.33 34 34
PAK1 0.011 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.3 0.47 -10000 0 -0.97 168 168
CDKN1A -0.11 0.3 -10000 0 -0.59 129 129
ITGA5 0.011 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.26 0.51 -10000 0 -1 168 168
CRK 0.011 0 -10000 0 -10000 0 0
mol:NO -0.13 0.33 -10000 0 -0.62 168 168
PLG -0.3 0.53 -10000 0 -1 168 168
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.22 0.4 -10000 0 -0.8 168 168
GRB2 0.011 0 -10000 0 -10000 0 0
PIK3R1 0.007 0.041 -10000 0 -0.41 5 5
ANGPT2 -0.06 0.2 -10000 0 -0.49 59 59
BMX -0.3 0.54 -10000 0 -1.1 168 168
ANGPT1 -0.23 0.48 -10000 0 -1.2 110 110
tube development -0.13 0.34 -10000 0 -0.61 166 166
ANGPT4 0 0.045 -10000 0 -0.39 7 7
response to hypoxia -0.017 0.032 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.32 0.56 -10000 0 -1.1 168 168
alpha5/beta1 Integrin 0.016 0 -10000 0 -10000 0 0
FGF2 -0.22 0.21 -10000 0 -0.41 295 295
STAT5A (dimer) -0.15 0.38 -10000 0 -0.69 166 166
mol:L-citrulline -0.13 0.33 -10000 0 -0.62 168 168
AGTR1 -0.085 0.17 -10000 0 -0.41 122 122
MAPK14 -0.28 0.54 -10000 0 -1.1 168 168
Tie2/SHP2 -0.21 0.4 -10000 0 -1.1 92 92
TEK -0.2 0.46 -10000 0 -1.2 92 92
RPS6KB1 -0.19 0.42 -10000 0 -0.8 168 168
Angiotensin II/AT1 -0.057 0.12 -10000 0 -0.28 122 122
Tie2/Ang1/GRB2 -0.29 0.55 -10000 0 -1.1 168 168
MAPK3 -0.25 0.48 -10000 0 -0.95 168 168
MAPK1 -0.25 0.48 -10000 0 -0.95 168 168
Tie2/Ang1/GRB7 -0.29 0.55 -10000 0 -1.1 168 168
NFKB1 0.01 0.018 -10000 0 -0.41 1 1
MAPK8 -0.28 0.53 -10000 0 -1 168 168
PI3K -0.24 0.5 -10000 0 -0.96 168 168
FES -0.27 0.54 -10000 0 -1 168 168
Crk/Dok-R -0.26 0.51 -10000 0 -1 168 168
Tie2/Ang1/ABIN2 -0.29 0.55 -10000 0 -1.1 168 168
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.17 0.39 -10000 0 -0.74 168 168
STAT5A 0.01 0.018 -10000 0 -0.41 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.19 0.42 -10000 0 -0.8 168 168
Tie2/Ang2 -0.19 0.45 -10000 0 -0.83 166 166
Tie2/Ang1 -0.31 0.58 -10000 0 -1.1 168 168
FOXO1 -0.16 0.4 -10000 0 -0.75 168 168
ELF1 -0.006 0.054 -10000 0 -0.44 4 4
ELF2 -0.28 0.53 -10000 0 -1 168 168
mol:Choline -0.26 0.5 -10000 0 -0.99 168 168
cell migration -0.07 0.1 -10000 0 -0.22 168 168
FYN -0.15 0.38 -10000 0 -0.7 166 166
DOK2 0.008 0.031 -10000 0 -0.35 4 4
negative regulation of cell cycle -0.094 0.28 -10000 0 -0.51 149 149
ETS1 -0.031 0.095 -10000 0 -0.22 110 110
PXN -0.14 0.35 -10000 0 -0.66 168 168
ITGB1 0.011 0 -10000 0 -10000 0 0
NOS3 -0.15 0.37 -10000 0 -0.7 168 168
RAC1 0.011 0 -10000 0 -10000 0 0
TNF -0.074 0.15 -10000 0 -0.28 168 168
MAPKKK cascade -0.26 0.5 -10000 0 -0.99 168 168
RASA1 0.007 0.04 -10000 0 -0.41 5 5
Tie2/Ang1/Shc -0.29 0.55 -10000 0 -1.1 168 168
NCK1 0.009 0.025 -10000 0 -0.41 2 2
vasculogenesis -0.11 0.3 -10000 0 -0.55 168 168
mol:Phosphatidic acid -0.26 0.5 -10000 0 -0.99 168 168
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.13 0.33 -10000 0 -0.62 168 168
Rac1/GTP -0.23 0.35 -10000 0 -0.75 168 168
MMP2 -0.29 0.54 -10000 0 -1.1 168 168
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.016 0 -10000 0 -10000 0 0
Necdin/E2F1 -0.17 0.18 -10000 0 -0.31 303 303
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.085 0.15 -10000 0 -0.24 239 239
NGF (dimer)/p75(NTR)/BEX1 -0.16 0.2 -10000 0 -0.33 281 281
NT-4/5 (dimer)/p75(NTR) -0.096 0.14 -10000 0 -0.28 205 205
IKBKB 0.011 0 -10000 0 -10000 0 0
AKT1 -0.085 0.14 -10000 0 -0.38 66 66
IKBKG 0.011 0 -10000 0 -10000 0 0
BDNF -0.044 0.12 -10000 0 -0.33 88 88
MGDIs/NGR/p75(NTR)/LINGO1 -0.065 0.12 -10000 0 -0.23 192 192
FURIN 0.011 0 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.093 0.13 -10000 0 -0.22 260 260
LINGO1 0.006 0.04 -10000 0 -0.34 7 7
Sortilin/TRAF6/NRIF -0.002 0.016 -10000 0 -10000 0 0
proBDNF (dimer) -0.044 0.12 -10000 0 -0.33 88 88
NTRK1 0.001 0.058 -10000 0 -0.37 13 13
RTN4R 0.01 0.018 -10000 0 -0.41 1 1
neuron apoptosis -0.093 0.14 -10000 0 -0.35 72 72
IRAK1 0.011 0 -10000 0 -10000 0 0
SHC1 -0.11 0.17 -10000 0 -0.29 236 236
ARHGDIA 0.011 0 -10000 0 -10000 0 0
RhoA/GTP 0.008 0 -10000 0 -10000 0 0
Gamma Secretase 0.03 0.024 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.15 0.19 -10000 0 -0.29 296 296
MAGEH1 -0.09 0.18 -10000 0 -0.41 130 130
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.2 0.2 -10000 0 -0.32 359 359
Mammalian IAPs/DIABLO 0.024 0.029 -10000 0 -0.2 8 8
proNGF (dimer) -0.078 0.17 -10000 0 -0.41 115 115
MAGED1 0.009 0.025 -10000 0 -0.41 2 2
APP 0.011 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.006 0.07 -10000 0 -0.33 24 24
ZNF274 0.011 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.089 0.14 -10000 0 -0.24 235 235
NGF -0.078 0.17 -10000 0 -0.41 115 115
cell cycle arrest -0.08 0.13 0.14 41 -0.33 73 114
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.09 0.15 -10000 0 -0.25 235 235
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.072 0.12 -10000 0 -0.23 205 205
NCSTN 0.011 0 -10000 0 -10000 0 0
mol:GTP -0.12 0.17 -10000 0 -0.29 240 240
PSENEN 0.011 0 -10000 0 -10000 0 0
mol:ceramide -0.095 0.15 -10000 0 -0.25 235 235
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.071 0.13 -10000 0 -0.34 64 64
p75(NTR)/beta APP -0.084 0.14 -10000 0 -0.28 185 185
BEX1 -0.074 0.17 -10000 0 -0.41 110 110
mol:GDP -0.12 0.17 -10000 0 -0.29 236 236
NGF (dimer) -0.078 0.14 -10000 0 -0.25 179 179
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.051 0.11 -10000 0 -0.2 185 185
PIK3R1 0.007 0.04 -10000 0 -0.41 5 5
RAC1/GTP -0.095 0.14 -10000 0 -0.24 236 236
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 -0.29 240 240
RHOB 0.009 0.025 -10000 0 -0.41 2 2
RHOA 0.011 0 -10000 0 -10000 0 0
MAGE-G1/E2F1 -0.027 0.091 -10000 0 -0.22 102 102
NT3 (dimer) -0.018 0.1 -10000 0 -0.4 38 38
TP53 -0.058 0.1 -10000 0 -0.31 13 13
PRDM4 -0.095 0.15 -10000 0 -0.26 235 235
BDNF (dimer) -0.089 0.14 -10000 0 -0.29 117 117
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
SORT1 0.011 0 -10000 0 -10000 0 0
activation of caspase activity -0.1 0.13 -10000 0 -0.23 239 239
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.095 0.15 -10000 0 -0.26 235 235
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 -0.4 132 132
DIABLO 0.011 0 -10000 0 -10000 0 0
SMPD2 -0.095 0.15 -10000 0 -0.26 235 235
APH1B 0.006 0.047 -10000 0 -0.41 7 7
APH1A 0.011 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.11 0.17 -10000 0 -0.29 236 236
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 -0.3 208 208
MAPK8 -0.095 0.15 -10000 0 -0.36 80 80
MAPK9 -0.093 0.15 -10000 0 -0.36 78 78
APAF1 0.011 0 -10000 0 -10000 0 0
NTF3 -0.018 0.1 -10000 0 -0.4 38 38
NTF4 -0.006 0.07 -10000 0 -0.33 24 24
NDN -0.19 0.21 -10000 0 -0.41 265 265
RAC1/GDP 0.008 0 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.094 0.12 -10000 0 -0.35 66 66
p75 CTF/Sortilin/TRAF6/NRIF 0.028 0 -10000 0 -10000 0 0
RhoA-B-C/GTP -0.11 0.17 -10000 0 -0.29 240 240
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.066 0.11 -10000 0 -0.32 14 14
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.077 0.11 -10000 0 -0.21 184 184
PRKACB 0.006 0.044 -10000 0 -0.41 6 6
proBDNF (dimer)/p75 ECD -0.021 0.086 -10000 0 -0.22 88 88
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.004 0.055 -10000 0 -0.39 10 10
BIRC2 0.011 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.19 0.2 0.15 17 -0.36 262 279
BAD -0.11 0.16 -10000 0 -0.34 130 130
RIPK2 0.011 0 -10000 0 -10000 0 0
NGFR -0.13 0.2 -10000 0 -0.41 185 185
CYCS -0.084 0.14 -10000 0 -0.23 237 237
ADAM17 0.011 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.095 0.15 -10000 0 -0.26 235 235
BCL2L11 -0.11 0.16 -10000 0 -0.34 130 130
BDNF (dimer)/p75(NTR) -0.12 0.15 -10000 0 -0.27 260 260
PI3K -0.097 0.15 -10000 0 -0.26 239 239
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.095 0.15 -10000 0 -0.26 235 235
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 0.19 -10000 0 -0.35 236 236
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.096 0.15 -10000 0 -0.26 237 237
TRAF6 0.011 0 -10000 0 -10000 0 0
RAC1 0.011 0 -10000 0 -10000 0 0
PRKCZ 0.01 0.023 -10000 0 -0.37 2 2
PLG -0.032 0.12 -10000 0 -0.4 55 55
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.12 0.16 -10000 0 -0.28 235 235
SQSTM1 0.011 0 -10000 0 -10000 0 0
NGFRAP1 0.006 0.044 -10000 0 -0.41 6 6
CASP3 -0.1 0.16 -10000 0 -0.32 130 130
E2F1 -0.053 0.13 -10000 0 -0.33 102 102
CASP9 0.011 0 -10000 0 -10000 0 0
IKK complex -0.093 0.13 -10000 0 -0.31 121 121
NGF (dimer)/TRKA -0.053 0.13 -10000 0 -0.28 126 126
MMP7 -0.058 0.14 -10000 0 -0.36 101 101
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.083 0.14 -10000 0 -0.24 235 235
MMP3 -0.05 0.13 -10000 0 -0.33 96 96
APAF-1/Caspase 9 -0.072 0.094 -10000 0 -0.28 65 65
PDGFR-alpha signaling pathway

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
PDGFRA -0.12 0.19 -9999 0 -0.43 149 149
PDGF/PDGFRA/CRKL -0.069 0.13 -9999 0 -0.28 149 149
positive regulation of JUN kinase activity -0.036 0.098 -9999 0 -0.21 57 57
CRKL 0.011 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.076 0.13 -9999 0 -0.29 150 150
AP1 -0.29 0.39 -9999 0 -0.86 167 167
mol:IP3 -0.08 0.14 -9999 0 -0.3 149 149
PLCG1 -0.08 0.14 -9999 0 -0.3 149 149
PDGF/PDGFRA/alphaV Integrin -0.069 0.13 -9999 0 -0.28 149 149
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 -0.3 149 149
CAV3 0.002 0.015 -9999 0 -0.33 1 1
CAV1 -0.062 0.16 -9999 0 -0.41 94 94
SHC/Grb2/SOS1 -0.036 0.099 -9999 0 -0.21 57 57
PDGF/PDGFRA/Shf -0.073 0.14 -9999 0 -0.29 151 151
FOS -0.27 0.4 -9999 0 -0.85 167 167
JUN -0.026 0.045 -9999 0 -0.34 7 7
oligodendrocyte development -0.069 0.13 -9999 0 -0.28 149 149
GRB2 0.011 0 -9999 0 -10000 0 0
PIK3R1 0.007 0.04 -9999 0 -0.41 5 5
mol:DAG -0.08 0.14 -9999 0 -0.3 149 149
PDGF/PDGFRA -0.12 0.19 -9999 0 -0.43 149 149
actin cytoskeleton reorganization -0.069 0.13 -9999 0 -0.28 149 149
SRF 0.025 0.011 -9999 0 -10000 0 0
SHC1 0.011 0 -9999 0 -10000 0 0
PI3K -0.051 0.11 -9999 0 -0.23 152 152
PDGF/PDGFRA/Crk/C3G -0.049 0.11 -9999 0 -0.23 149 149
JAK1 -0.069 0.14 -9999 0 -0.29 149 149
ELK1/SRF -0.041 0.11 -9999 0 -0.22 149 149
SHB 0.011 0 -9999 0 -10000 0 0
SHF 0.006 0.047 -9999 0 -0.41 7 7
CSNK2A1 0.021 0.024 -9999 0 -10000 0 0
GO:0007205 -0.09 0.15 -9999 0 -0.34 149 149
SOS1 0.011 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.036 0.098 -9999 0 -0.21 57 57
PDGF/PDGFRA/SHB -0.069 0.13 -9999 0 -0.28 149 149
PDGF/PDGFRA/Caveolin-1 -0.12 0.19 -9999 0 -0.35 191 191
ITGAV 0.011 0 -9999 0 -10000 0 0
ELK1 -0.081 0.14 -9999 0 -0.29 149 149
PIK3CA 0.01 0.018 -9999 0 -0.41 1 1
PDGF/PDGFRA/Crk -0.069 0.13 -9999 0 -0.28 149 149
JAK-STAT cascade -0.069 0.13 -9999 0 -0.28 149 149
cell proliferation -0.073 0.14 -9999 0 -0.29 151 151
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.002 0.071 -9999 0 -0.28 33 33
alphaV beta3 Integrin -0.16 0.16 -9999 0 -0.28 322 322
PTK2 -0.13 0.19 -9999 0 -0.42 134 134
IGF1R -0.005 0.081 -9999 0 -0.41 21 21
PI4KB 0.011 0 -9999 0 -10000 0 0
MFGE8 0.009 0.025 -9999 0 -0.41 2 2
SRC 0.011 0 -9999 0 -10000 0 0
CDKN1B -0.14 0.22 -9999 0 -0.59 88 88
VEGFA 0.011 0 -9999 0 -10000 0 0
ILK -0.12 0.19 -9999 0 -0.56 71 71
ROCK1 0.011 0 -9999 0 -10000 0 0
AKT1 -0.1 0.18 -9999 0 -0.52 71 71
PTK2B -0.021 0.1 -9999 0 -0.21 118 118
alphaV/beta3 Integrin/JAM-A -0.15 0.16 -9999 0 -0.32 186 186
CBL 0.011 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.029 0.099 -9999 0 -0.23 103 103
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.044 0.14 -9999 0 -0.26 136 136
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.039 0.12 -9999 0 -0.35 31 31
alphaV/beta3 Integrin/Syndecan-1 -0.078 0.12 -9999 0 -0.21 240 240
PI4KA 0.011 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.18 0.18 -9999 0 -0.42 156 156
PI4 Kinase 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.018 -9999 0 -0.41 1 1
alphaV/beta3 Integrin/Osteopontin -0.079 0.12 -9999 0 -0.21 241 241
RPS6KB1 -0.15 0.18 -9999 0 -0.39 156 156
TLN1 0.011 0 -9999 0 -10000 0 0
MAPK3 -0.29 0.28 -9999 0 -0.5 321 321
GPR124 -0.089 0.18 -9999 0 -0.41 129 129
MAPK1 -0.29 0.28 -9999 0 -0.5 321 321
PXN 0.011 0 -9999 0 -10000 0 0
PIK3R1 0.007 0.04 -9999 0 -0.41 5 5
alphaV/beta3 Integrin/Tumstatin -0.053 0.12 -9999 0 -0.26 132 132
cell adhesion -0.034 0.095 -9999 0 -0.23 100 100
ANGPTL3 0.004 0.025 -9999 0 -0.33 3 3
VEGFR2 homodimer/VEGFA homodimer/Src 0.007 0.06 -9999 0 -0.23 33 33
IGF-1R heterotetramer -0.005 0.081 -9999 0 -0.41 21 21
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
TGFBR2 0.002 0.062 -9999 0 -0.41 12 12
ITGB3 -0.068 0.16 -9999 0 -0.41 102 102
IGF1 -0.067 0.16 -9999 0 -0.41 101 101
RAC1 0.011 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.081 0.15 -9999 0 -0.27 190 190
apoptosis 0.011 0 -9999 0 -10000 0 0
CD47 0.011 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.024 0.097 -9999 0 -0.23 102 102
VCL 0.011 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.072 0.15 -9999 0 -0.28 168 168
CSF1 0.003 0.057 -9999 0 -0.41 10 10
PIK3C2A -0.12 0.19 -9999 0 -0.56 71 71
PI4 Kinase/Pyk2 -0.14 0.14 -9999 0 -0.35 131 131
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.027 0.11 -9999 0 -0.23 118 118
FAK1/Vinculin -0.099 0.15 -9999 0 -0.34 122 122
alphaV beta3/Integrin/ppsTEM5 -0.081 0.15 -9999 0 -0.28 190 190
RHOA 0.011 0 -9999 0 -10000 0 0
VTN -0.047 0.14 -9999 0 -0.41 74 74
BCAR1 0.011 0 -9999 0 -10000 0 0
FGF2 -0.22 0.21 -9999 0 -0.41 295 295
F11R -0.14 0.15 -9999 0 -0.28 296 296
alphaV/beta3 Integrin/Lactadherin -0.025 0.1 -9999 0 -0.23 100 100
alphaV/beta3 Integrin/TGFBR2 -0.029 0.11 -9999 0 -0.25 105 105
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.024 0.03 -9999 0 -0.2 10 10
HSP90AA1 0.011 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.021 0.088 -9999 0 -0.2 100 100
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 0.007 0.04 -9999 0 -0.41 5 5
alphaV/beta3 Integrin/Pyk2 -0.02 0.1 -9999 0 -0.21 118 118
SDC1 -0.084 0.15 -9999 0 -0.33 153 153
VAV3 -0.011 0.073 -9999 0 -0.2 10 10
PTPN11 0.011 0 -9999 0 -10000 0 0
IRS1 -0.031 0.13 -9999 0 -0.41 54 54
FAK1/Paxillin -0.099 0.15 -9999 0 -0.34 122 122
cell migration -0.086 0.14 -9999 0 -0.31 121 121
ITGAV 0.011 0 -9999 0 -10000 0 0
PI3K -0.14 0.14 -9999 0 -0.36 121 121
SPP1 -0.086 0.15 -9999 0 -0.33 155 155
KDR -0.015 0.1 -9999 0 -0.41 33 33
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 -0.039 0.13 -9999 0 -0.39 66 66
angiogenesis -0.29 0.28 -9999 0 -0.5 322 322
Rac1/GTP -0.004 0.067 -9999 0 -0.3 1 1
EDIL3 -0.072 0.17 -9999 0 -0.41 107 107
cell proliferation -0.029 0.11 -9999 0 -0.24 105 105
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.053 0.17 -10000 0 -0.59 36 36
IHH -0.13 0.2 -10000 0 -0.39 189 189
SHH Np/Cholesterol/GAS1 -0.15 0.13 -10000 0 -0.23 348 348
LRPAP1 0.011 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.14 0.13 0.23 348 -10000 0 348
SMO/beta Arrestin2 -0.051 0.15 -10000 0 -0.42 26 26
SMO -0.059 0.16 -10000 0 -0.32 136 136
AKT1 -0.017 0.095 -10000 0 -0.52 5 5
ARRB2 0.011 0 -10000 0 -10000 0 0
BOC -0.003 0.075 -10000 0 -0.41 18 18
ADRBK1 0.011 0 -10000 0 -10000 0 0
heart looping -0.059 0.16 -10000 0 -0.31 136 136
STIL -0.048 0.12 -10000 0 -0.34 33 33
DHH N/PTCH2 -0.024 0.11 -10000 0 -0.3 70 70
DHH N/PTCH1 -0.059 0.14 -10000 0 -0.35 51 51
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
DHH -0.024 0.12 -10000 0 -0.41 44 44
PTHLH -0.068 0.21 -10000 0 -0.65 36 36
determination of left/right symmetry -0.059 0.16 -10000 0 -0.31 136 136
PIK3R1 0.007 0.04 -10000 0 -0.41 5 5
skeletal system development -0.067 0.21 -10000 0 -0.64 36 36
IHH N/Hhip -0.079 0.13 -10000 0 -0.26 157 157
DHH N/Hhip -0.024 0.099 -10000 0 -0.26 77 77
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.059 0.16 -10000 0 -0.31 136 136
pancreas development -0.012 0.087 -10000 0 -0.34 35 35
HHAT 0.008 0.036 -10000 0 -0.41 4 4
PI3K 0.013 0.031 -10000 0 -0.28 6 6
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.26 0.2 -10000 0 -0.41 346 346
somite specification -0.059 0.16 -10000 0 -0.31 136 136
SHH Np/Cholesterol/PTCH1 -0.051 0.12 -10000 0 -0.36 25 25
SHH Np/Cholesterol/PTCH2 -0.017 0.079 -10000 0 -0.18 99 99
SHH Np/Cholesterol/Megalin -0.067 0.1 -10000 0 -0.23 64 64
SHH -0.015 0.082 -10000 0 -0.22 73 73
catabolic process -0.053 0.14 -10000 0 -0.35 36 36
SMO/Vitamin D3 -0.048 0.14 -10000 0 -0.4 26 26
SHH Np/Cholesterol/Hhip -0.017 0.075 -10000 0 -0.17 104 104
LRP2 -0.11 0.16 -10000 0 -0.33 193 193
receptor-mediated endocytosis -0.074 0.14 -10000 0 -0.32 77 77
SHH Np/Cholesterol/BOC -0.012 0.073 -10000 0 -0.23 23 23
SHH Np/Cholesterol/CDO -0.029 0.096 -10000 0 -0.2 118 118
mesenchymal cell differentiation 0.017 0.074 0.17 104 -10000 0 104
mol:Vitamin D3 -0.04 0.12 -10000 0 -0.36 25 25
IHH N/PTCH2 -0.079 0.14 -10000 0 -0.28 148 148
CDON -0.035 0.13 -10000 0 -0.41 59 59
IHH N/PTCH1 -0.034 0.15 -10000 0 -0.36 36 36
Megalin/LRPAP1 -0.067 0.11 -10000 0 -0.22 193 193
PTCH2 -0.012 0.096 -10000 0 -0.41 30 30
SHH Np/Cholesterol -0.012 0.06 -10000 0 -0.16 73 73
PTCH1 -0.053 0.14 -10000 0 -0.36 36 36
HHIP -0.012 0.087 -10000 0 -0.34 35 35
Cellular roles of Anthrax toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 -0.004 0.077 -10000 0 -0.41 19 19
ANTXR2 -0.13 0.2 -10000 0 -0.41 179 179
negative regulation of myeloid dendritic cell antigen processing and presentation -0.019 0.028 -10000 0 -0.057 183 183
monocyte activation -0.028 0.11 -10000 0 -0.41 41 41
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 -10000 0 0
MAP2K6 -0.035 0.055 -10000 0 -0.16 69 69
CYAA -0.064 0.11 -10000 0 -0.21 183 183
MAP2K4 -0.016 0.025 -10000 0 -0.25 1 1
IL1B -0.011 0.042 -10000 0 -0.14 30 30
Channel -0.067 0.12 -10000 0 -0.23 183 183
NLRP1 -0.026 0.053 -10000 0 -0.24 26 26
CALM1 0.011 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.021 0.03 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.019 0.028 0.057 183 -10000 0 183
MAPK3 -0.016 0.023 -10000 0 -10000 0 0
MAPK1 -0.016 0.023 -10000 0 -10000 0 0
PGR -0.077 0.1 -10000 0 -0.22 169 169
PA/Cellular Receptors -0.075 0.13 -10000 0 -0.25 183 183
apoptosis -0.019 0.028 -10000 0 -0.057 183 183
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.064 0.11 -10000 0 -0.22 183 183
macrophage activation -0.003 0.026 -10000 0 -10000 0 0
TNF -0.032 0.11 -10000 0 -0.33 68 68
VCAM1 -0.028 0.11 -10000 0 -0.41 41 41
platelet activation -0.021 0.03 -10000 0 -10000 0 0
MAPKKK cascade 0.013 0.031 0.085 32 -10000 0 32
IL18 -0.012 0.043 -10000 0 -0.14 35 35
negative regulation of macrophage activation -0.019 0.028 -10000 0 -0.057 183 183
LEF -0.019 0.028 -10000 0 -0.058 183 183
CASP1 -0.021 0.036 -10000 0 -0.12 41 41
mol:cAMP -0.021 0.03 -10000 0 -10000 0 0
necrosis -0.019 0.028 -10000 0 -0.057 183 183
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.063 0.11 -10000 0 -0.21 183 183
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
S1P3 pathway

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
PDGFRB -0.007 0.085 -9999 0 -0.41 23 23
mol:S1P -0.009 0.014 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.073 0.12 -9999 0 -0.24 156 156
GNAO1 -0.11 0.19 -9999 0 -0.42 143 143
S1P/S1P3/G12/G13 0.003 0.045 -9999 0 -0.22 19 19
AKT1 -0.063 0.16 -9999 0 -0.66 26 26
AKT3 -0.41 0.55 -9999 0 -1.1 204 204
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.007 0.085 -9999 0 -0.41 23 23
GNAI2 0.002 0.014 -9999 0 -10000 0 0
GNAI3 0.004 0.011 -9999 0 -10000 0 0
GNAI1 -0.002 0.052 -9999 0 -0.42 8 8
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 -0.013 0.079 -9999 0 -0.42 19 19
S1PR2 0.011 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.13 0.2 -9999 0 -0.31 263 263
MAPK3 -0.12 0.19 -9999 0 -0.32 211 211
MAPK1 -0.12 0.19 -9999 0 -0.32 211 211
JAK2 -0.12 0.2 -9999 0 -0.33 211 211
CXCR4 -0.12 0.19 -9999 0 -0.32 211 211
FLT1 0.003 0.016 -9999 0 -10000 0 0
RhoA/GDP 0.008 0 -9999 0 -10000 0 0
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
SRC -0.12 0.19 -9999 0 -0.32 211 211
S1P/S1P3/Gi -0.13 0.2 -9999 0 -0.31 263 263
RAC1 0.011 0 -9999 0 -10000 0 0
RhoA/GTP -0.12 0.18 -9999 0 -0.31 211 211
VEGFA 0.003 0.016 -9999 0 -10000 0 0
S1P/S1P2/Gi -0.084 0.14 -9999 0 -0.27 156 156
VEGFR1 homodimer/VEGFA homodimer 0 0.031 -9999 0 -10000 0 0
RHOA 0.011 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.02 0.1 -9999 0 -0.25 74 74
GNAQ 0.009 0.025 -9999 0 -0.41 2 2
GNAZ -0.009 0.074 -9999 0 -0.41 17 17
G12/G13 0.016 0 -9999 0 -10000 0 0
GNA14 -0.031 0.13 -9999 0 -0.41 54 54
GNA15 0.007 0.038 -9999 0 -0.33 7 7
GNA12 0.011 0 -9999 0 -10000 0 0
GNA13 0.011 0 -9999 0 -10000 0 0
GNA11 0.002 0.062 -9999 0 -0.41 12 12
Rac1/GTP -0.12 0.18 -9999 0 -0.31 211 211
Nongenotropic Androgen signaling

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
PTK2 0.009 0.001 -10000 0 -10000 0 0
GNB1/GNG2 -0.023 0.09 -10000 0 -0.21 101 101
regulation of S phase of mitotic cell cycle -0.018 0.088 -10000 0 -0.2 96 96
GNAO1 -0.1 0.18 -10000 0 -0.41 143 143
HRAS 0.01 0.002 -10000 0 -10000 0 0
SHBG/T-DHT 0.005 0.024 -10000 0 -0.24 5 5
PELP1 0.01 0.002 -10000 0 -10000 0 0
AKT1 0.009 0.001 -10000 0 -10000 0 0
MAP2K1 -0.031 0.092 -10000 0 -0.27 33 33
T-DHT/AR -0.044 0.11 -10000 0 -0.29 93 93
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.003 -10000 0 -0.007 167 167
GNAI2 0.011 0 -10000 0 -10000 0 0
GNAI3 0.011 0 -10000 0 -10000 0 0
GNAI1 0.005 0.051 -10000 0 -0.41 8 8
mol:GDP -0.059 0.14 -10000 0 -0.35 94 94
cell proliferation -0.1 0.2 -10000 0 -0.38 167 167
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
FOS -0.22 0.37 -10000 0 -0.77 167 167
mol:Ca2+ -0.024 0.03 -10000 0 -0.061 175 175
MAPK3 -0.071 0.15 -10000 0 -0.26 167 167
MAPK1 -0.049 0.1 -10000 0 -0.22 74 74
PIK3R1 0.007 0.04 -10000 0 -0.41 5 5
mol:IP3 -0.001 0.002 -10000 0 -0.004 167 167
cAMP biosynthetic process 0.008 0.03 0.094 5 -0.2 5 10
GNG2 0.003 0.056 -10000 0 -0.4 10 10
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 167 167
HRAS/GTP -0.041 0.072 -10000 0 -0.2 93 93
actin cytoskeleton reorganization -0.002 0.018 -10000 0 -0.18 6 6
SRC 0.01 0.002 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 167 167
PI3K 0.012 0.026 -10000 0 -0.23 6 6
apoptosis 0.11 0.2 0.4 167 -10000 0 167
T-DHT/AR/PELP1 -0.031 0.095 -10000 0 -0.24 93 93
HRAS/GDP -0.056 0.13 -10000 0 -0.33 93 93
CREB1 -0.12 0.21 -10000 0 -0.43 167 167
RAC1-CDC42/GTP -0.002 0.019 -10000 0 -0.18 6 6
AR -0.062 0.16 -10000 0 -0.41 93 93
GNB1 0.011 0 -10000 0 -10000 0 0
RAF1 -0.028 0.085 -10000 0 -0.25 33 33
RAC1-CDC42/GDP -0.049 0.12 -10000 0 -0.31 93 93
T-DHT/AR/PELP1/Src -0.024 0.086 -10000 0 -0.21 93 93
MAP2K2 -0.031 0.092 -10000 0 -0.27 33 33
T-DHT/AR/PELP1/Src/PI3K -0.018 0.088 -10000 0 -0.21 96 96
GNAZ -0.002 0.073 -10000 0 -0.41 17 17
SHBG 0.007 0.04 -10000 0 -0.41 5 5
Gi family/GNB1/GNG2/GDP -0.072 0.16 -10000 0 -0.32 147 147
mol:T-DHT -0.001 0.001 -10000 0 -0.003 134 134
RAC1 0.011 0 -10000 0 -10000 0 0
GNRH1 0.005 0.031 -10000 0 -0.29 6 6
Gi family/GTP -0.059 0.12 -10000 0 -0.21 156 156
CDC42 0.011 0 -10000 0 -10000 0 0
Wnt signaling

Figure S15.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S15.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.062 0.15 -9999 0 -0.25 162 162
FZD6 0.01 0.018 -9999 0 -0.41 1 1
WNT6 -0.031 0.12 -9999 0 -0.38 58 58
WNT4 -0.088 0.18 -9999 0 -0.41 128 128
FZD3 0.011 0 -9999 0 -10000 0 0
WNT5A -0.003 0.075 -9999 0 -0.41 18 18
WNT11 -0.03 0.12 -9999 0 -0.35 63 63
PLK1 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
regulation of centriole-centriole cohesion 0.044 0.028 0.07 73 -10000 0 73
BUB1B -0.06 0.05 -10000 0 -0.11 170 170
PLK1 -0.013 0.023 -10000 0 -10000 0 0
PLK1S1 -0.003 0.017 -10000 0 -0.26 1 1
KIF2A -0.005 0.02 -10000 0 -10000 0 0
regulation of mitotic centrosome separation -0.013 0.023 -10000 0 -10000 0 0
GOLGA2 0.011 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.11 0.1 -10000 0 -0.18 342 342
WEE1 -0.008 0.022 -10000 0 -10000 0 0
cytokinesis -0.078 0.042 -10000 0 -0.21 14 14
PP2A-alpha B56 0.037 0.005 -10000 0 -10000 0 0
AURKA -0.004 0.014 -10000 0 -10000 0 0
PICH/PLK1 -0.079 0.11 -10000 0 -0.23 135 135
CENPE -0.055 0.089 -10000 0 -0.19 161 161
RhoA/GTP 0.008 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.005 0.02 -10000 0 -10000 0 0
PPP2CA 0.011 0 -10000 0 -10000 0 0
FZR1 0.011 0 -10000 0 -10000 0 0
TPX2 -0.015 0.015 -10000 0 -10000 0 0
PAK1 0.01 0.001 -10000 0 -10000 0 0
SPC24 -0.2 0.17 -10000 0 -0.33 332 332
FBXW11 0.011 0 -10000 0 -10000 0 0
CLSPN -0.013 0.018 -10000 0 -10000 0 0
GORASP1 0.011 0 -10000 0 -10000 0 0
metaphase 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.007 0.013 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle -0.001 0.002 -10000 0 -10000 0 0
STAG2 0.011 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.012 0.007 -10000 0 -10000 0 0
spindle elongation -0.013 0.023 -10000 0 -10000 0 0
ODF2 0.01 0.001 -10000 0 -10000 0 0
BUB1 0.023 0.013 -10000 0 -10000 0 0
TPT1 -0.003 0.013 -10000 0 -10000 0 0
CDC25C -0.017 0.014 -10000 0 -10000 0 0
CDC25B 0.01 0.001 -10000 0 -10000 0 0
SGOL1 -0.044 0.028 -10000 0 -0.07 73 73
RHOA 0.011 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.018 0.048 -10000 0 -10000 0 0
CDC14B 0.008 0.013 -10000 0 -0.3 1 1
CDC20 -0.29 0.11 -10000 0 -0.33 482 482
PLK1/PBIP1 -0.016 0.045 -10000 0 -0.18 34 34
mitosis -0.004 0.007 -10000 0 -0.015 157 157
FBXO5 -0.005 0.02 -10000 0 -10000 0 0
CDC2 -0.001 0.002 -10000 0 -10000 0 0
NDC80 -0.014 0.089 -10000 0 -0.33 40 40
metaphase plate congression -0.006 0.015 -10000 0 -10000 0 0
ERCC6L -0.07 0.1 -10000 0 -0.26 72 72
NLP/gamma Tubulin -0.005 0.012 -10000 0 -10000 0 0
microtubule cytoskeleton organization -0.003 0.013 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint -0.001 0.001 -10000 0 -10000 0 0
PPP1R12A 0.01 0.018 -10000 0 -0.41 1 1
interphase -0.001 0.001 -10000 0 -10000 0 0
PLK1/PRC1-2 -0.15 0.069 -10000 0 -0.17 491 491
GRASP65/GM130/RAB1/GTP/PLK1 0.008 0.018 -10000 0 -10000 0 0
RAB1A 0.011 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA -0.006 0.022 -10000 0 -10000 0 0
mitotic prometaphase -0.002 0.001 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.012 0.018 -10000 0 -0.19 1 1
microtubule-based process -0.16 0.06 -10000 0 -0.18 491 491
Golgi organization -0.013 0.023 -10000 0 -10000 0 0
Cohesin/SA2 -0.013 0.014 -10000 0 -10000 0 0
PPP1CB/MYPT1 0.015 0.013 -10000 0 -0.28 1 1
KIF20A -0.3 0.1 -10000 0 -0.33 491 491
APC/C/CDC20 -0.15 0.065 -10000 0 -0.18 482 482
PPP2R1A 0.011 0 -10000 0 -10000 0 0
chromosome segregation -0.019 0.043 -10000 0 -0.17 34 34
PRC1 -0.003 0.068 -10000 0 -0.33 23 23
ECT2 -0.016 0.05 -10000 0 -0.19 34 34
C13orf34 -0.005 0.02 -10000 0 -10000 0 0
NUDC -0.006 0.015 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.059 0.05 -10000 0 -0.11 170 170
spindle assembly -0.008 0.018 -10000 0 -10000 0 0
spindle stabilization -0.003 0.017 -10000 0 -0.26 1 1
APC/C/HCDH1 0.014 0.011 -10000 0 -0.24 1 1
MKLP2/PLK1 -0.16 0.06 -10000 0 -0.18 491 491
CCNB1 -0.047 0.13 -10000 0 -0.33 94 94
PPP1CB 0.011 0.001 -10000 0 -10000 0 0
BTRC 0.011 0 -10000 0 -10000 0 0
ROCK2 -0.009 0.065 -10000 0 -0.4 14 14
TUBG1 -0.003 0.013 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.026 0.043 -10000 0 -10000 0 0
MLF1IP -0.012 0.057 -10000 0 -0.23 34 34
INCENP 0.01 0.001 -10000 0 -10000 0 0
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 -0.084 0.32 -9999 0 -0.96 62 62
MKNK1 0.011 0 -9999 0 -10000 0 0
MAPK14 -0.015 0.099 -9999 0 -0.27 69 69
ATF2/c-Jun -0.004 0.11 -9999 0 -0.5 11 11
MAPK11 -0.017 0.1 -9999 0 -0.28 71 71
MITF -0.043 0.17 -9999 0 -0.34 113 113
MAPKAPK5 -0.011 0.12 -9999 0 -0.32 71 71
KRT8 -0.028 0.13 -9999 0 -0.34 72 72
MAPKAPK3 0.011 0 -9999 0 -10000 0 0
MAPKAPK2 0.011 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.023 0.15 -9999 0 -0.4 69 69
CEBPB -0.011 0.12 -9999 0 -0.32 71 71
SLC9A1 -0.011 0.12 -9999 0 -0.32 71 71
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.009 0.12 -9999 0 -0.31 74 74
p38alpha-beta/MNK1 -0.008 0.12 -9999 0 -0.31 69 69
JUN -0.004 0.1 -9999 0 -0.49 11 11
PPARGC1A -0.075 0.19 -9999 0 -0.4 88 88
USF1 -0.011 0.12 -9999 0 -0.32 71 71
RAB5/GDP/GDI1 -0.03 0.076 -9999 0 -0.23 69 69
NOS2 -0.021 0.16 -9999 0 -0.81 12 12
DDIT3 -0.011 0.12 -9999 0 -0.32 71 71
RAB5A 0.011 0 -9999 0 -10000 0 0
HSPB1 -0.002 0.099 -9999 0 -0.26 69 69
p38alpha-beta/HBP1 -0.008 0.12 -9999 0 -0.31 69 69
CREB1 -0.012 0.13 -9999 0 -0.34 71 71
RAB5/GDP 0.008 0 -9999 0 -10000 0 0
EIF4E -0.003 0.1 -9999 0 -0.26 69 69
RPS6KA4 -0.011 0.12 -9999 0 -0.32 71 71
PLA2G4A -0.015 0.12 -9999 0 -0.31 70 70
GDI1 -0.011 0.12 -9999 0 -0.32 71 71
TP53 -0.018 0.15 -9999 0 -0.39 71 71
RPS6KA5 -0.014 0.13 -9999 0 -0.32 76 76
ESR1 -0.047 0.18 -9999 0 -0.35 116 116
HBP1 0.011 0 -9999 0 -10000 0 0
MEF2C -0.041 0.16 -9999 0 -0.38 79 79
MEF2A -0.015 0.13 -9999 0 -0.33 75 75
EIF4EBP1 -0.012 0.13 -9999 0 -0.34 71 71
KRT19 -0.016 0.13 -9999 0 -0.33 72 72
ELK4 -0.011 0.12 -9999 0 -0.32 71 71
ATF6 -0.011 0.12 -9999 0 -0.32 71 71
ATF1 -0.012 0.13 -9999 0 -0.34 71 71
p38alpha-beta/MAPKAPK2 -0.008 0.12 -9999 0 -0.31 69 69
p38alpha-beta/MAPKAPK3 -0.008 0.12 -9999 0 -0.31 69 69
Effects of Botulinum toxin

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
STX1A 0.009 0.01 -9999 0 -0.22 1 1
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B 0.011 0.022 -9999 0 -0.22 5 5
STXBP1 -0.018 0.11 -9999 0 -0.41 38 38
ACh/CHRNA1 -0.098 0.1 -9999 0 -0.23 196 196
RAB3GAP2/RIMS1/UNC13B 0.018 0.019 -9999 0 -0.17 5 5
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 0.003 0.032 -9999 0 -0.33 5 5
mol:ACh -0.043 0.056 -9999 0 -0.1 247 247
RAB3GAP2 0.011 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.062 0.076 -9999 0 -0.28 30 30
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.098 0.1 -9999 0 -0.23 196 196
UNC13B 0.011 0 -9999 0 -10000 0 0
CHRNA1 -0.11 0.16 -9999 0 -0.33 196 196
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.081 0.12 -9999 0 -0.3 119 119
SNAP25 -0.11 0.13 -9999 0 -0.25 247 247
VAMP2 0.005 0 -9999 0 -10000 0 0
SYT1 -0.081 0.17 -9999 0 -0.41 119 119
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.003 0.064 -9999 0 -0.23 39 39
STX1A/SNAP25 fragment 1/VAMP2 -0.062 0.076 -9999 0 -0.28 30 30
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.005 0.049 -9999 0 -0.24 22 22
ADCY5 -0.032 0.098 -9999 0 -0.24 102 102
ADCY6 0.015 0 -9999 0 -10000 0 0
ADCY7 0.015 0 -9999 0 -10000 0 0
ADCY1 0.003 0.053 -9999 0 -0.22 30 30
ADCY2 -0.12 0.12 -9999 0 -0.24 303 303
ADCY3 0.014 0.015 -9999 0 -0.24 2 2
ADCY8 0.008 0.018 -9999 0 -0.18 5 5
PRKCE 0.009 0 -9999 0 -10000 0 0
ADCY9 -0.018 0.085 -9999 0 -0.24 73 73
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.061 0.079 -9999 0 -0.17 131 131
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.11 0.12 -9999 0 -0.23 295 295
fibroblast growth factor receptor signaling pathway -0.11 0.12 -9999 0 -0.23 295 295
LAMA1 -0.1 0.16 -9999 0 -0.33 183 183
PRNP -0.048 0.15 -9999 0 -0.41 76 76
GPC1/SLIT2 -0.021 0.099 -9999 0 -0.28 69 69
SMAD2 0.022 0.033 -9999 0 -0.2 12 12
GPC1/PrPc/Cu2+ -0.02 0.086 -9999 0 -0.23 76 76
GPC1/Laminin alpha1 -0.062 0.11 -9999 0 -0.22 183 183
TDGF1 -0.019 0.1 -9999 0 -0.38 42 42
CRIPTO/GPC1 -0.005 0.073 -9999 0 -0.26 42 42
APP/GPC1 0.016 0 -9999 0 -10000 0 0
mol:NO 0 0 -9999 0 -10000 0 0
YES1 0.004 0.061 -9999 0 -0.2 42 42
FLT1 0.011 0 -9999 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.017 0.037 -9999 0 -0.23 12 12
SERPINC1 0.004 0.041 -9999 0 -0.33 8 8
FYN 0.004 0.061 -9999 0 -0.2 42 42
FGR 0 0.071 -9999 0 -0.22 51 51
positive regulation of MAPKKK cascade 0.015 0.073 -9999 0 -0.27 26 26
SLIT2 -0.043 0.14 -9999 0 -0.41 69 69
GPC1/NRG 0.005 0.057 -9999 0 -0.28 21 21
NRG1 -0.006 0.08 -9999 0 -0.41 21 21
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.022 0 -9999 0 -10000 0 0
LYN 0.004 0.061 -9999 0 -0.2 42 42
mol:Spermine 0.009 0 -9999 0 -10000 0 0
cell growth -0.11 0.12 -9999 0 -0.23 295 295
BMP signaling pathway -0.011 0 -9999 0 -10000 0 0
SRC 0.004 0.061 -9999 0 -0.2 42 42
TGFBR1 0.011 0 -9999 0 -10000 0 0
mol:Cu2+ 0 0 -9999 0 -10000 0 0
PLA2G2A -0.032 0.12 -9999 0 -0.39 55 55
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 -0.011 0.077 -9999 0 -0.2 79 79
HCK 0.002 0.064 -9999 0 -0.2 49 49
FGF2 -0.22 0.21 -9999 0 -0.41 295 295
FGFR1 0.01 0.018 -9999 0 -0.41 1 1
VEGFR1 homodimer 0.011 0 -9999 0 -10000 0 0
TGFBR2 0.002 0.062 -9999 0 -0.41 12 12
cell death 0.016 0 -9999 0 -10000 0 0
ATIII/GPC1 0.011 0.028 -9999 0 -0.22 8 8
PLA2G2A/GPC1 -0.014 0.085 -9999 0 -0.27 55 55
LCK 0.003 0.065 -9999 0 -0.21 46 46
neuron differentiation 0.005 0.056 -9999 0 -0.28 21 21
PrPc/Cu2+ -0.033 0.1 -9999 0 -0.29 76 76
APP 0.011 0 -9999 0 -10000 0 0
TGFBR2 (dimer) 0.002 0.062 -9999 0 -0.41 12 12
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.009 0.031 -9999 0 -0.41 3 3
LAT2 -0.067 0.13 -9999 0 -0.23 169 169
AP1 -0.13 0.14 -9999 0 -0.35 108 108
mol:PIP3 -0.068 0.15 -9999 0 -0.4 40 40
IKBKB -0.036 0.098 -9999 0 -0.22 54 54
AKT1 -0.032 0.1 -9999 0 -0.28 42 42
IKBKG -0.036 0.098 -9999 0 -0.22 53 53
MS4A2 -0.12 0.19 -9999 0 -0.41 168 168
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.018 -9999 0 -0.41 1 1
MAP3K1 -0.043 0.12 -9999 0 -0.31 39 39
mol:Ca2+ -0.051 0.12 -9999 0 -0.31 40 40
LYN 0.01 0.003 -9999 0 -10000 0 0
CBLB -0.066 0.13 -9999 0 -0.23 169 169
SHC1 0.011 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.035 0.1 -9999 0 -0.21 131 131
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.01 0.018 -9999 0 -0.41 1 1
PLD2 -0.059 0.12 -9999 0 -0.34 40 40
PTPN13 -0.093 0.15 -9999 0 -0.38 69 69
PTPN11 0.009 0.005 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.03 0.11 -9999 0 -0.26 42 42
SYK 0.01 0.015 -9999 0 -0.33 1 1
GRB2 0.011 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.1 0.13 -9999 0 -0.41 40 40
LAT -0.066 0.13 -9999 0 -0.23 169 169
PAK2 -0.053 0.13 -9999 0 -0.34 39 39
NFATC2 -0.082 0.16 -9999 0 -0.54 55 55
HRAS -0.063 0.14 -9999 0 -0.33 51 51
GAB2 0.008 0.036 -9999 0 -0.41 4 4
PLA2G1B 0.028 0.015 -9999 0 -10000 0 0
Fc epsilon R1 -0.1 0.14 -9999 0 -0.25 225 225
Antigen/IgE/Fc epsilon R1 -0.092 0.12 -9999 0 -0.22 225 225
mol:GDP -0.071 0.14 -9999 0 -0.26 169 169
JUN 0.006 0.047 -9999 0 -0.41 7 7
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.007 0.04 -9999 0 -0.41 5 5
FOS -0.12 0.19 -9999 0 -0.41 167 167
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.076 0.13 -9999 0 -0.25 171 171
CHUK -0.036 0.098 -9999 0 -0.22 53 53
KLRG1 -0.057 0.11 -9999 0 -0.32 40 40
VAV1 -0.068 0.13 -9999 0 -0.23 169 169
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.066 0.13 -9999 0 -0.23 169 169
negative regulation of mast cell degranulation -0.048 0.11 -9999 0 -0.3 38 38
BTK -0.076 0.14 -9999 0 -0.26 169 169
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.078 0.15 -9999 0 -0.31 96 96
GAB2/PI3K/SHP2 -0.065 0.09 -9999 0 -0.31 42 42
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.066 0.13 -9999 0 -0.26 95 95
RAF1 0.019 0.018 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.083 0.11 -9999 0 -0.37 41 41
FCER1G 0.016 0.024 -9999 0 -0.33 2 2
FCER1A -0.064 0.16 -9999 0 -0.42 93 93
Antigen/IgE/Fc epsilon R1/Fyn -0.083 0.11 -9999 0 -0.26 93 93
MAPK3 0.027 0.015 -9999 0 -10000 0 0
MAPK1 0.027 0.015 -9999 0 -10000 0 0
NFKB1 0.01 0.018 -9999 0 -0.41 1 1
MAPK8 -0.011 0.077 -9999 0 -0.55 7 7
DUSP1 -0.09 0.18 -9999 0 -0.41 130 130
NF-kappa-B/RelA -0.037 0.046 -9999 0 -0.18 6 6
actin cytoskeleton reorganization -0.077 0.14 -9999 0 -0.4 37 37
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.081 0.11 -9999 0 -0.34 42 42
FER -0.066 0.13 -9999 0 -0.23 169 169
RELA 0.011 0 -9999 0 -10000 0 0
ITK -0.032 0.061 -9999 0 -0.36 14 14
SOS1 0.011 0 -9999 0 -10000 0 0
PLCG1 -0.068 0.14 -9999 0 -0.26 168 168
cytokine secretion -0.027 0.034 -9999 0 -10000 0 0
SPHK1 -0.067 0.13 -9999 0 -0.23 170 170
PTK2 -0.08 0.15 -9999 0 -0.41 37 37
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.1 0.14 -9999 0 -0.27 171 171
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.066 0.15 -9999 0 -0.4 40 40
MAP2K2 0.024 0.016 -9999 0 -10000 0 0
MAP2K1 0.024 0.016 -9999 0 -10000 0 0
MAP2K7 0.011 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.059 0.088 -9999 0 -0.29 38 38
MAP2K4 0.011 0.037 -9999 0 -0.84 1 1
Fc epsilon R1/FcgammaRIIB -0.091 0.12 -9999 0 -0.29 95 95
mol:Choline -0.058 0.12 -9999 0 -0.34 40 40
SHC/Grb2/SOS1 -0.07 0.11 -9999 0 -0.33 37 37
FYN 0.011 0 -9999 0 -10000 0 0
DOK1 0.011 0 -9999 0 -10000 0 0
PXN -0.07 0.14 -9999 0 -0.38 37 37
HCLS1 -0.066 0.13 -9999 0 -0.23 170 170
PRKCB -0.057 0.13 -9999 0 -0.31 55 55
FCGR2B 0.008 0.034 -9999 0 -0.39 4 4
IGHE -0.001 0.004 -9999 0 -10000 0 0
KLRG1/SHIP -0.049 0.11 -9999 0 -0.31 38 38
LCP2 0.01 0.015 -9999 0 -0.33 1 1
PLA2G4A -0.077 0.14 -9999 0 -0.25 176 176
RASA1 0.007 0.04 -9999 0 -0.41 5 5
mol:Phosphatidic acid -0.058 0.12 -9999 0 -0.34 40 40
IKK complex -0.017 0.078 -9999 0 -0.16 53 53
WIPF1 0.009 0.025 -9999 0 -0.41 2 2
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.011 0 -10000 0 -10000 0 0
PTK2 0.011 0 -10000 0 -10000 0 0
CRKL -0.041 0.12 -10000 0 -0.25 111 111
GRB2/SOS1/SHC 0.022 0 -10000 0 -10000 0 0
HRAS 0.011 0 -10000 0 -10000 0 0
IRS1/Crk -0.041 0.12 -10000 0 -0.25 111 111
IGF-1R heterotetramer/IGF1/PTP1B -0.034 0.11 -10000 0 -0.25 111 111
AKT1 -0.021 0.11 -10000 0 -0.32 38 38
BAD -0.014 0.1 -10000 0 -0.3 38 38
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.041 0.12 -10000 0 -0.25 111 111
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.041 0.12 -10000 0 -0.26 111 111
RAF1 -0.009 0.099 -10000 0 -0.28 38 38
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.031 0.12 -10000 0 -0.24 111 111
YWHAZ 0.011 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.051 0.13 -10000 0 -0.28 111 111
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
RPS6KB1 -0.021 0.11 -10000 0 -0.32 38 38
GNB2L1 0.011 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.009 0.087 -10000 0 -0.25 38 38
PXN 0.011 0 -10000 0 -10000 0 0
PIK3R1 0.007 0.04 -10000 0 -0.41 5 5
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.016 0 -10000 0 -10000 0 0
HRAS/GTP -0.045 0.091 -10000 0 -0.32 37 37
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.012 0.091 -10000 0 -0.24 37 37
IGF-1R heterotetramer -0.019 0.093 -10000 0 -0.46 21 21
IGF-1R heterotetramer/IGF1/IRS/Nck -0.04 0.12 -10000 0 -0.26 111 111
Crk/p130 Cas/Paxillin -0.025 0.11 -10000 0 -0.34 37 37
IGF1R -0.019 0.093 -10000 0 -0.47 21 21
IGF1 -0.075 0.17 -10000 0 -0.44 101 101
IRS2/Crk -0.058 0.14 -10000 0 -0.25 161 161
PI3K -0.034 0.12 -10000 0 -0.24 114 114
apoptosis 0.006 0.091 0.26 38 -10000 0 38
HRAS/GDP 0.008 0 -10000 0 -10000 0 0
PRKCD -0.046 0.15 -10000 0 -0.34 111 111
RAF1/14-3-3 E -0.001 0.089 -10000 0 -0.28 13 13
BAD/14-3-3 -0.007 0.096 -10000 0 -0.28 38 38
PRKCZ -0.021 0.11 -10000 0 -0.32 38 38
Crk/p130 Cas/Paxillin/FAK1 -0.038 0.077 -10000 0 -0.27 38 38
PTPN1 0.011 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.054 0.16 -10000 0 -0.36 111 111
BCAR1 0.011 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.022 0.099 -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 -0.04 0.12 -10000 0 -0.25 111 111
GRB10 0.01 0.018 -10000 0 -0.41 1 1
PTPN11 -0.041 0.12 -10000 0 -0.25 111 111
IRS1 -0.045 0.13 -10000 0 -0.28 111 111
IRS2 -0.068 0.14 -10000 0 -0.27 161 161
IGF-1R heterotetramer/IGF1 -0.059 0.15 -10000 0 -0.34 111 111
GRB2 0.011 0 -10000 0 -10000 0 0
PDPK1 -0.027 0.11 -10000 0 -0.34 38 38
YWHAE 0.011 0 -10000 0 -10000 0 0
PRKD1 -0.06 0.17 -10000 0 -0.36 115 115
SHC1 0.011 0 -10000 0 -10000 0 0
Aurora A 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
Aurora A/GADD45A -0.012 0.043 -9999 0 -10000 0 0
BIRC5 -0.25 0.14 -9999 0 -0.33 423 423
NFKBIA -0.013 0.042 -9999 0 -10000 0 0
CPEB1 -0.17 0.21 -9999 0 -0.41 236 236
AKT1 -0.013 0.042 -9999 0 -10000 0 0
NDEL1 0.011 0 -9999 0 -10000 0 0
Aurora A/BRCA1 -0.011 0.038 -9999 0 -10000 0 0
NDEL1/TACC3 -0.04 0.09 -9999 0 -0.22 86 86
GADD45A 0.011 0 -9999 0 -10000 0 0
GSK3B 0.007 0.001 -9999 0 -10000 0 0
PAK1/Aurora A -0.012 0.043 -9999 0 -10000 0 0
MDM2 0.011 0 -9999 0 -10000 0 0
JUB 0.011 0 -9999 0 -10000 0 0
TPX2 -0.17 0.092 -9999 0 -0.22 441 441
TP53 0 0.029 -9999 0 -0.28 1 1
DLG7 -0.021 0.042 -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 -0.043 0.096 -9999 0 -0.23 86 86
G2/M transition of mitotic cell cycle -0.011 0.038 -9999 0 -10000 0 0
AURKA -0.024 0.053 -9999 0 -10000 0 0
AURKB -0.014 0.013 -9999 0 -10000 0 0
CDC25B -0.005 0.032 -9999 0 -10000 0 0
G2/M transition checkpoint -0.011 0.038 -9999 0 -10000 0 0
mRNA polyadenylation -0.11 0.12 -9999 0 -0.23 236 236
Aurora A/CPEB -0.11 0.12 -9999 0 -0.24 236 236
Aurora A/TACC1/TRAP/chTOG -0.034 0.092 -9999 0 -0.22 81 81
BRCA1 0.011 0 -9999 0 -10000 0 0
centrosome duplication -0.012 0.042 -9999 0 -10000 0 0
regulation of centrosome cycle -0.04 0.089 -9999 0 -0.22 86 86
spindle assembly -0.034 0.09 -9999 0 -0.22 81 81
TDRD7 0.011 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.12 0.086 -9999 0 -0.21 167 167
CENPA -0.003 0.016 -9999 0 -10000 0 0
Aurora A/PP2A -0.012 0.043 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.002 0.028 -9999 0 -10000 0 0
negative regulation of DNA binding 0 0.029 -9999 0 -0.28 1 1
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0.016 0 -9999 0 -10000 0 0
RASA1 0.007 0.04 -9999 0 -0.41 5 5
Ajuba/Aurora A -0.011 0.038 -9999 0 -10000 0 0
mitotic prometaphase -0.02 0.007 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.024 0.053 -9999 0 -10000 0 0
TACC1 -0.065 0.16 -9999 0 -0.41 98 98
TACC3 -0.068 0.14 -9999 0 -0.33 126 126
Aurora A/Antizyme1 -0.003 0.038 -9999 0 -10000 0 0
Aurora A/RasGAP -0.015 0.048 -9999 0 -0.24 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 0.007 0.001 -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 -0.17 0.092 -9999 0 -0.22 441 441
PPP2R5D 0.011 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.14 0.088 -9999 0 -0.23 162 162
PAK1 0.011 0 -9999 0 -10000 0 0
CKAP5 0.011 0 -9999 0 -10000 0 0
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.016 0.01 -9999 0 -0.22 1 1
VLDLR 0.009 0.025 -9999 0 -0.41 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 0.018 -9999 0 -0.41 1 1
RELN/VLDLR/Fyn -0.07 0.12 -9999 0 -0.23 194 194
MAPK8IP1/MKK7/MAP3K11/JNK1 0.03 0.025 -9999 0 -10000 0 0
AKT1 -0.052 0.1 -9999 0 -0.25 3 3
MAP2K7 0.011 0 -9999 0 -10000 0 0
RAPGEF1 0.011 0 -9999 0 -10000 0 0
DAB1 -0.001 0.052 -9999 0 -0.33 13 13
RELN/LRP8/DAB1 -0.07 0.11 -9999 0 -0.21 197 197
LRPAP1/LRP8 0.014 0.022 -9999 0 -0.22 5 5
RELN/LRP8/DAB1/Fyn -0.059 0.1 -9999 0 -0.19 195 195
DAB1/alpha3/beta1 Integrin -0.062 0.08 -9999 0 -0.33 5 5
long-term memory -0.13 0.15 -9999 0 -0.36 107 107
DAB1/LIS1 -0.066 0.083 -9999 0 -0.31 5 5
DAB1/CRLK/C3G -0.062 0.078 -9999 0 -0.3 5 5
PIK3CA 0.01 0.018 -9999 0 -0.41 1 1
DAB1/NCK2 -0.066 0.084 -9999 0 -0.31 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 -0.15 0.2 -9999 0 -0.41 212 212
CDK5R1 0.01 0.015 -9999 0 -0.33 1 1
RELN -0.14 0.2 -9999 0 -0.41 200 200
PIK3R1 0.007 0.04 -9999 0 -0.41 5 5
RELN/LRP8/Fyn -0.071 0.12 -9999 0 -0.23 194 194
GRIN2A/RELN/LRP8/DAB1/Fyn -0.13 0.15 -9999 0 -0.35 124 124
MAPK8 0.006 0.044 -9999 0 -0.41 6 6
RELN/VLDLR/DAB1 -0.069 0.11 -9999 0 -0.21 197 197
ITGB1 0.011 0 -9999 0 -10000 0 0
MAP1B -0.068 0.11 -9999 0 -0.2 198 198
RELN/LRP8 -0.071 0.12 -9999 0 -0.23 202 202
GRIN2B/RELN/LRP8/DAB1/Fyn -0.062 0.11 -9999 0 -0.21 55 55
PI3K 0.013 0.031 -9999 0 -0.28 6 6
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin 0.016 0.013 -9999 0 -0.28 1 1
RAP1A -0.032 0.092 -9999 0 -0.28 5 5
PAFAH1B1 0.011 0 -9999 0 -10000 0 0
MAPK8IP1 0.01 0.023 -9999 0 -0.37 2 2
CRLK/C3G 0.016 0 -9999 0 -10000 0 0
GRIN2B -0.007 0.065 -9999 0 -0.33 21 21
NCK2 0.011 0 -9999 0 -10000 0 0
neuron differentiation -0.031 0.083 -9999 0 -0.25 3 3
neuron adhesion -0.021 0.091 -9999 0 -0.33 3 3
LRP8 0.008 0.032 -9999 0 -0.33 5 5
GSK3B -0.044 0.096 -9999 0 -0.36 1 1
RELN/VLDLR/DAB1/Fyn -0.058 0.1 -9999 0 -0.19 195 195
MAP3K11 0.011 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.062 0.11 -9999 0 -0.2 200 200
CDK5 0.011 0 -9999 0 -10000 0 0
MAPT 0.002 0.076 -9999 0 -0.37 20 20
neuron migration -0.051 0.13 -9999 0 -0.32 4 4
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.031 0.083 -9999 0 -0.25 3 3
RELN/VLDLR -0.057 0.11 -9999 0 -0.2 195 195
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.035 0.13 -10000 0 -0.37 64 64
NFATC2 -0.023 0.18 -10000 0 -0.51 46 46
NFATC3 -0.015 0.083 -10000 0 -0.24 47 47
CD40LG -0.17 0.33 -10000 0 -0.81 90 90
ITCH 0.026 0.038 -10000 0 -10000 0 0
CBLB 0.026 0.038 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.14 0.25 -10000 0 -0.66 69 69
JUNB 0.007 0.04 -10000 0 -0.41 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.01 0.037 -10000 0 -0.23 1 1
T cell anergy 0.015 0.059 -10000 0 -0.26 3 3
TLE4 -0.032 0.21 -10000 0 -0.61 58 58
Jun/NFAT1-c-4/p21SNFT -0.093 0.33 -10000 0 -0.8 85 85
AP-1/NFAT1-c-4 -0.17 0.38 -10000 0 -0.93 88 88
IKZF1 0.002 0.13 -10000 0 -0.41 27 27
T-helper 2 cell differentiation -0.082 0.23 -10000 0 -0.64 54 54
AP-1/NFAT1 -0.082 0.18 -10000 0 -0.38 95 95
CALM1 0.015 0.026 -10000 0 -10000 0 0
EGR2 -0.11 0.4 -10000 0 -0.93 85 85
EGR3 -0.14 0.46 -10000 0 -1.1 85 85
NFAT1/FOXP3 -0.044 0.16 -10000 0 -0.38 62 62
EGR1 -0.045 0.14 -10000 0 -0.41 71 71
JUN 0 0.049 -10000 0 -0.41 7 7
EGR4 -0.003 0.057 -10000 0 -0.34 15 15
mol:Ca2+ 0.003 0.028 -10000 0 -10000 0 0
GBP3 -0.001 0.14 -10000 0 -0.48 25 25
FOSL1 -0.015 0.091 -10000 0 -0.33 42 42
NFAT1-c-4/MAF/IRF4 -0.12 0.35 -10000 0 -0.85 86 86
DGKA 0.004 0.12 -10000 0 -0.41 23 23
CREM 0.011 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.1 0.34 -10000 0 -0.83 85 85
CTLA4 -0.042 0.16 -10000 0 -0.41 50 50
NFAT1-c-4 (dimer)/EGR1 -0.12 0.36 -10000 0 -0.85 90 90
NFAT1-c-4 (dimer)/EGR4 -0.099 0.34 -10000 0 -0.81 86 86
FOS -0.12 0.19 -10000 0 -0.41 167 167
IFNG -0.076 0.19 -10000 0 -0.63 33 33
T cell activation -0.083 0.21 -10000 0 -0.61 49 49
MAF -0.066 0.16 -10000 0 -0.41 100 100
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.079 0.3 0.72 85 -10000 0 85
TNF -0.13 0.33 -10000 0 -0.77 93 93
FASLG -0.16 0.47 -10000 0 -1.2 85 85
TBX21 0.002 0.061 -10000 0 -0.4 12 12
BATF3 0.01 0.015 -10000 0 -0.33 1 1
PRKCQ -0.024 0.12 -10000 0 -0.41 48 48
PTPN1 0.004 0.12 -10000 0 -0.41 22 22
NFAT1-c-4/ICER1 -0.094 0.33 -10000 0 -0.81 85 85
GATA3 -0.002 0.069 -10000 0 -0.35 20 20
T-helper 1 cell differentiation -0.064 0.2 -10000 0 -0.62 33 33
IL2RA -0.13 0.25 -10000 0 -0.63 75 75
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.004 0.12 -10000 0 -0.41 22 22
E2F1 -0.047 0.13 -10000 0 -0.32 102 102
PPARG -0.012 0.096 -10000 0 -0.41 30 30
SLC3A2 0.004 0.12 -10000 0 -0.38 31 31
IRF4 -0.002 0.071 -10000 0 -0.37 19 19
PTGS2 -0.19 0.35 -10000 0 -0.8 104 104
CSF2 -0.17 0.33 -10000 0 -0.81 88 88
JunB/Fra1/NFAT1-c-4 -0.094 0.32 -10000 0 -0.78 85 85
IL4 -0.086 0.24 -10000 0 -0.68 51 51
IL5 -0.17 0.32 -10000 0 -0.81 87 87
IL2 -0.084 0.21 -10000 0 -0.62 48 48
IL3 -0.037 0.048 -10000 0 -10000 0 0
RNF128 0.012 0.08 -10000 0 -0.26 43 43
NFATC1 -0.079 0.3 -10000 0 -0.72 85 85
CDK4 0.041 0.18 0.56 22 -10000 0 22
PTPRK 0.003 0.13 -10000 0 -0.42 24 24
IL8 -0.2 0.34 -10000 0 -0.82 92 92
POU2F1 0.011 0 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.011 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.054 0.089 -10000 0 -0.24 38 38
NT3 (dimer)/TRKC -0.14 0.17 -10000 0 -0.3 269 269
NT3 (dimer)/TRKB -0.11 0.16 -10000 0 -0.28 228 228
SHC/Grb2/SOS1/GAB1/PI3K 0.026 0.03 -10000 0 -10000 0 0
RAPGEF1 0.011 0 -10000 0 -10000 0 0
BDNF -0.044 0.12 -10000 0 -0.33 88 88
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
DYNLT1 0.011 0 -10000 0 -10000 0 0
NTRK1 0.001 0.058 -10000 0 -0.37 13 13
NTRK2 -0.041 0.14 -10000 0 -0.4 69 69
NTRK3 -0.19 0.21 -10000 0 -0.41 257 257
NT-4/5 (dimer)/TRKB -0.1 0.15 -10000 0 -0.26 238 238
neuron apoptosis 0.14 0.19 0.4 149 -10000 0 149
SHC 2-3/Grb2 -0.15 0.21 -10000 0 -0.43 149 149
SHC1 0.011 0 -10000 0 -10000 0 0
SHC2 -0.18 0.24 0.17 1 -0.51 153 154
SHC3 -0.12 0.16 -10000 0 -0.4 97 97
STAT3 (dimer) 0.017 0.01 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.084 0.14 -10000 0 -0.25 205 205
RIN/GDP -0.044 0.08 -10000 0 -0.2 26 26
GIPC1 0.011 0 -10000 0 -10000 0 0
KRAS 0.01 0.015 -10000 0 -0.33 1 1
DNAJA3 -0.13 0.16 0.2 2 -0.32 186 188
RIN/GTP 0.002 0.003 -10000 0 -10000 0 0
CCND1 0.023 0.018 -10000 0 -10000 0 0
MAGED1 0.009 0.025 -10000 0 -0.41 2 2
PTPN11 0.011 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.006 0.07 -10000 0 -0.33 24 24
SHC/GRB2/SOS1 0.022 0 -10000 0 -10000 0 0
GRB2 0.011 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.042 0.11 -10000 0 -0.24 136 136
TRKA/NEDD4-2 0.009 0.042 -10000 0 -0.25 14 14
ELMO1 0.008 0.036 -10000 0 -0.41 4 4
RhoG/GTP/ELMO1/DOCK1 0.01 0.038 -10000 0 -0.26 10 10
NGF -0.078 0.17 -10000 0 -0.41 115 115
HRAS 0.011 0 -10000 0 -10000 0 0
DOCK1 0.006 0.047 -10000 0 -0.41 7 7
GAB2 0.008 0.036 -10000 0 -0.41 4 4
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 0.006 0.044 -10000 0 -0.41 6 6
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 -0.31 193 195
mol:GDP -0.064 0.11 -10000 0 -0.26 47 47
NGF (dimer) -0.078 0.17 -10000 0 -0.41 115 115
RhoG/GDP 0.006 0.025 -10000 0 -0.29 4 4
RIT1/GDP -0.04 0.08 -10000 0 -0.19 26 26
TIAM1 0 0.067 -10000 0 -0.41 14 14
PIK3R1 0.007 0.04 -10000 0 -0.41 5 5
BDNF (dimer)/TRKB -0.04 0.1 -10000 0 -0.2 153 153
KIDINS220/CRKL/C3G 0.016 0 -10000 0 -10000 0 0
SHC/RasGAP 0.014 0.028 -10000 0 -0.28 5 5
FRS2 family/SHP2 0.022 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.027 0.019 -10000 0 -0.2 4 4
RIT1/GTP 0.008 0 -10000 0 -10000 0 0
NT3 (dimer) -0.018 0.1 -10000 0 -0.4 38 38
RAP1/GDP -0.048 0.053 -10000 0 -0.17 22 22
KIDINS220/CRKL 0.011 0 -10000 0 -10000 0 0
BDNF (dimer) -0.044 0.12 -10000 0 -0.33 88 88
ubiquitin-dependent protein catabolic process -0.037 0.11 -10000 0 -0.23 126 126
Schwann cell development -0.037 0.03 -10000 0 -10000 0 0
EHD4 0.011 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.028 0 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.031 0.017 -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 0.12 -10000 0 -0.34 105 105
ABL1 0.009 0.025 -10000 0 -0.41 2 2
SH2B family/GRB2/SOS1 0.016 0 -10000 0 -10000 0 0
Rap1/GTP 0.014 0.046 -10000 0 -10000 0 0
STAT3 0.017 0.01 -10000 0 -10000 0 0
axon guidance -0.12 0.12 -10000 0 -0.32 105 105
MAPK3 -0.032 0.1 -10000 0 -0.21 130 130
MAPK1 -0.032 0.1 -10000 0 -0.21 130 130
CDC42/GDP -0.04 0.08 -10000 0 -0.2 22 22
NTF3 -0.018 0.1 -10000 0 -0.4 38 38
NTF4 -0.006 0.07 -10000 0 -0.33 24 24
NGF (dimer)/TRKA/FAIM -0.037 0.11 -10000 0 -0.23 127 127
PI3K 0.013 0.031 -10000 0 -0.28 6 6
FRS3 0.011 0 -10000 0 -10000 0 0
FAIM 0.01 0.018 -10000 0 -0.41 1 1
GAB1 0.008 0.036 -10000 0 -0.41 4 4
RASGRF1 -0.15 0.17 0.2 2 -0.34 200 202
SOS1 0.011 0 -10000 0 -10000 0 0
MCF2L -0.11 0.14 -10000 0 -0.25 266 266
RGS19 0.011 0 -10000 0 -10000 0 0
CDC42 0.011 0 -10000 0 -10000 0 0
RAS family/GTP -0.017 0.07 -10000 0 -10000 0 0
Rac1/GDP -0.04 0.08 -10000 0 -0.19 27 27
NGF (dimer)/TRKA/GRIT -0.043 0.11 -10000 0 -0.24 126 126
neuron projection morphogenesis -0.11 0.17 -10000 0 -0.43 69 69
NGF (dimer)/TRKA/NEDD4-2 -0.036 0.11 -10000 0 -0.23 126 126
MAP2K1 0.029 0.018 -10000 0 -10000 0 0
NGFR -0.13 0.2 -10000 0 -0.41 185 185
NGF (dimer)/TRKA/GIPC/GAIP -0.023 0.096 -10000 0 -0.2 125 125
RAS family/GTP/PI3K 0.023 0.023 -10000 0 -0.2 6 6
FRS2 family/SHP2/GRB2/SOS1 0.033 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 0.01 0.023 -10000 0 -0.37 2 2
MAPKKK cascade -0.15 0.25 -10000 0 -0.6 122 122
RASA1 0.007 0.04 -10000 0 -0.41 5 5
TRKA/c-Abl 0.009 0.044 -10000 0 -0.25 15 15
SQSTM1 0.011 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.028 0.093 -10000 0 -0.21 61 61
NGF (dimer)/TRKA/p62/Atypical PKCs -0.018 0.091 -10000 0 -0.18 122 122
MATK 0 0.066 -10000 0 -0.4 14 14
NEDD4L 0.01 0.018 -10000 0 -0.41 1 1
RAS family/GDP -0.045 0.05 -10000 0 -0.17 16 16
NGF (dimer)/TRKA -0.14 0.17 0.21 2 -0.31 238 240
Rac1/GTP -0.11 0.11 -10000 0 -0.24 205 205
FRS2 family/SHP2/CRK family 0.033 0 -10000 0 -10000 0 0
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.1 0.18 -9999 0 -0.41 143 143
CDC42/GTP -0.03 0.1 -9999 0 -0.19 145 145
PLCG1 -0.031 0.1 -9999 0 -0.19 145 145
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 -0.03 0.099 -9999 0 -0.18 145 145
S1PR5 0 0.063 -9999 0 -0.35 17 17
S1PR4 0.009 0.029 -9999 0 -0.38 3 3
MAPK3 -0.031 0.1 -9999 0 -0.19 145 145
MAPK1 -0.031 0.1 -9999 0 -0.19 145 145
S1P/S1P5/Gi -0.042 0.11 -9999 0 -0.21 158 158
GNAI1 0.005 0.051 -9999 0 -0.41 8 8
CDC42/GDP 0.008 0 -9999 0 -10000 0 0
S1P/S1P5/G12 0.008 0.036 -9999 0 -0.19 17 17
RHOA 0.024 0.014 -9999 0 -0.18 2 2
S1P/S1P4/Gi -0.039 0.11 -9999 0 -0.21 156 156
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.002 0.073 -9999 0 -0.41 17 17
S1P/S1P4/G12/G13 0.02 0.016 -9999 0 -0.2 2 2
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
TCGA08_retinoblastoma

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
CDKN2B 0.001 0.048 -10000 0 -0.35 9 9
CDKN2C 0.021 0.055 -10000 0 -0.38 9 9
CDKN2A -0.13 0.17 -10000 0 -0.34 228 228
CCND2 0.005 0.049 0.16 10 -0.1 43 53
RB1 -0.006 0.048 0.13 5 -0.16 12 17
CDK4 0.024 0.037 0.17 12 -10000 0 12
CDK6 0.016 0.045 0.17 12 -0.18 11 23
G1/S progression 0.006 0.048 0.16 12 -0.13 5 17
Noncanonical Wnt signaling pathway

Figure S29.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S29.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.032 0.13 -9999 0 -0.41 55 55
GNB1/GNG2 -0.048 0.14 -9999 0 -0.4 41 41
mol:DAG -0.039 0.13 -9999 0 -0.37 41 41
PLCG1 -0.04 0.13 -9999 0 -0.38 41 41
YES1 -0.053 0.14 -9999 0 -0.43 38 38
FZD3 0.011 0 -9999 0 -10000 0 0
FZD6 0.01 0.018 -9999 0 -0.41 1 1
G protein -0.04 0.13 -9999 0 -0.38 41 41
MAP3K7 -0.12 0.14 -9999 0 -0.33 122 122
mol:Ca2+ -0.038 0.12 -9999 0 -0.36 41 41
mol:IP3 -0.039 0.13 -9999 0 -0.37 41 41
NLK -0.005 0.009 -9999 0 -10000 0 0
GNB1 0.011 0 -9999 0 -10000 0 0
CAMK2A -0.14 0.15 -9999 0 -0.36 122 122
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.062 0.15 -9999 0 -0.25 162 162
CSNK1A1 0.011 0 -9999 0 -10000 0 0
GNAS -0.053 0.14 -9999 0 -0.43 38 38
GO:0007205 -0.039 0.13 -9999 0 -0.36 41 41
WNT6 -0.031 0.12 -9999 0 -0.38 58 58
WNT4 -0.088 0.18 -9999 0 -0.41 128 128
NFAT1/CK1 alpha -0.051 0.14 -9999 0 -0.41 44 44
GNG2 0.003 0.056 -9999 0 -0.4 10 10
WNT5A -0.003 0.075 -9999 0 -0.41 18 18
WNT11 -0.03 0.12 -9999 0 -0.35 63 63
CDC42 -0.044 0.13 -9999 0 -0.4 38 38
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 -0.002 0.073 -10000 0 -0.19 71 71
ER alpha/Gai/GDP/Gbeta gamma -0.087 0.19 -10000 0 -0.32 185 185
AKT1 -0.07 0.25 -10000 0 -0.74 63 63
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.075 0.25 -10000 0 -0.76 63 63
mol:Ca2+ -0.015 0.12 -10000 0 -0.34 57 57
IGF1R -0.005 0.081 -10000 0 -0.41 21 21
E2/ER alpha (dimer)/Striatin -0.014 0.08 -10000 0 -0.23 64 64
SHC1 0.011 0 -10000 0 -10000 0 0
apoptosis 0.066 0.24 0.71 63 -10000 0 63
RhoA/GTP -0.018 0.05 -10000 0 -0.3 1 1
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.087 0.14 -10000 0 -0.39 75 75
regulation of stress fiber formation -0.017 0.058 0.26 3 -10000 0 3
E2/ERA-ERB (dimer) -0.014 0.079 -10000 0 -0.23 63 63
KRAS 0.01 0.015 -10000 0 -0.33 1 1
G13/GTP -0.011 0.071 -10000 0 -0.21 62 62
pseudopodium formation 0.017 0.058 -10000 0 -0.26 3 3
E2/ER alpha (dimer)/PELP1 -0.013 0.079 -10000 0 -0.23 62 62
GRB2 0.011 0 -10000 0 -10000 0 0
GNG2 0.003 0.056 -10000 0 -0.4 10 10
GNAO1 -0.1 0.18 -10000 0 -0.41 143 143
HRAS 0.011 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.056 0.18 -10000 0 -0.49 64 64
E2/ER beta (dimer) 0.008 0.01 -10000 0 -0.22 1 1
mol:GDP -0.035 0.098 -10000 0 -0.31 62 62
mol:NADP -0.056 0.18 -10000 0 -0.49 64 64
PIK3R1 0.007 0.04 -10000 0 -0.41 5 5
mol:IP3 -0.016 0.12 -10000 0 -0.36 57 57
IGF-1R heterotetramer -0.005 0.081 -10000 0 -0.41 21 21
PLCB1 -0.022 0.13 -10000 0 -0.37 57 57
PLCB2 -0.021 0.13 -10000 0 -0.37 56 56
IGF1 -0.067 0.16 -10000 0 -0.41 101 101
mol:L-citrulline -0.056 0.18 -10000 0 -0.49 64 64
RHOA 0.011 0 -10000 0 -10000 0 0
Gai/GDP -0.15 0.29 -10000 0 -0.63 144 144
JNK cascade 0.008 0.01 -10000 0 -0.22 1 1
BCAR1 0.011 0 -10000 0 -10000 0 0
ESR2 0.01 0.015 -10000 0 -0.33 1 1
GNAQ 0.009 0.025 -10000 0 -0.41 2 2
ESR1 -0.037 0.13 -10000 0 -0.41 62 62
Gq family/GDP/Gbeta gamma -0.002 0.094 -10000 0 -0.39 16 16
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.009 0.082 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.087 0.14 -10000 0 -0.39 75 75
GNAZ -0.002 0.073 -10000 0 -0.41 17 17
E2/ER alpha (dimer) -0.026 0.094 -10000 0 -0.29 62 62
STRN 0.009 0.025 -10000 0 -0.41 2 2
GNAL -0.051 0.15 -10000 0 -0.41 80 80
PELP1 0.011 0 -10000 0 -10000 0 0
MAPK11 0.014 0.017 -10000 0 -0.22 3 3
GNAI2 0.011 0 -10000 0 -10000 0 0
GNAI3 0.011 0 -10000 0 -10000 0 0
GNAI1 0.005 0.051 -10000 0 -0.41 8 8
HBEGF -0.1 0.18 -10000 0 -0.36 121 121
cAMP biosynthetic process -0.048 0.089 -10000 0 -0.2 130 130
SRC -0.077 0.18 -10000 0 -0.3 185 185
PI3K 0.013 0.031 -10000 0 -0.28 6 6
GNB1 0.011 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.032 0.085 -10000 0 -0.26 62 62
SOS1 0.011 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.099 0.15 -10000 0 -0.36 112 112
Gs family/GTP -0.048 0.091 -10000 0 -0.2 130 130
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.021 0.008 -10000 0 -0.15 1 1
vasodilation -0.053 0.17 -10000 0 -0.47 64 64
mol:DAG -0.016 0.12 -10000 0 -0.36 57 57
Gs family/GDP/Gbeta gamma -0.051 0.1 -10000 0 -0.29 66 66
MSN 0.017 0.062 -10000 0 -0.28 3 3
Gq family/GTP -0.028 0.13 -10000 0 -0.39 56 56
mol:PI-3-4-5-P3 -0.071 0.24 -10000 0 -0.73 63 63
NRAS 0.011 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.053 0.17 0.47 64 -10000 0 64
GRB2/SOS1 0.016 0 -10000 0 -10000 0 0
RhoA/GDP -0.033 0.091 -10000 0 -0.29 62 62
NOS3 -0.059 0.19 -10000 0 -0.52 64 64
GNA11 0.002 0.062 -10000 0 -0.41 12 12
MAPKKK cascade -0.05 0.19 -10000 0 -0.54 64 64
E2/ER alpha (dimer)/PELP1/Src -0.092 0.15 -10000 0 -0.41 75 75
ruffle organization 0.017 0.058 -10000 0 -0.26 3 3
ROCK2 0.012 0.065 -10000 0 -0.31 3 3
GNA14 -0.031 0.13 -10000 0 -0.41 54 54
GNA15 0.007 0.038 -10000 0 -0.33 7 7
GNA13 0.011 0 -10000 0 -10000 0 0
MMP9 -0.13 0.18 -10000 0 -0.4 119 119
MMP2 -0.076 0.18 -10000 0 -0.4 82 82
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.01 0.018 -9999 0 -0.41 1 1
CCL5 0.003 0.053 -9999 0 -0.37 11 11
SDCBP 0.011 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.07 0.07 -9999 0 -0.26 29 29
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 -0.061 0.066 -9999 0 -0.24 30 30
Syndecan-1/Syntenin -0.06 0.066 -9999 0 -0.24 29 29
MAPK3 -0.045 0.062 -9999 0 -0.25 15 15
HGF/MET -0.049 0.12 -9999 0 -0.28 118 118
TGFB1/TGF beta receptor Type II 0.01 0.018 -9999 0 -0.41 1 1
BSG 0.011 0 -9999 0 -10000 0 0
keratinocyte migration -0.06 0.066 -9999 0 -0.24 30 30
Syndecan-1/RANTES -0.064 0.073 -9999 0 -0.26 37 37
Syndecan-1/CD147 -0.052 0.065 -9999 0 -0.24 29 29
Syndecan-1/Syntenin/PIP2 -0.058 0.063 -9999 0 -0.24 29 29
LAMA5 0.01 0.015 -9999 0 -0.33 1 1
positive regulation of cell-cell adhesion -0.057 0.062 -9999 0 -0.23 29 29
MMP7 -0.058 0.14 -9999 0 -0.36 101 101
HGF -0.076 0.17 -9999 0 -0.41 112 112
Syndecan-1/CASK -0.067 0.066 -9999 0 -0.25 29 29
Syndecan-1/HGF/MET -0.095 0.11 -9999 0 -0.27 125 125
regulation of cell adhesion -0.038 0.06 -9999 0 -0.24 15 15
HPSE 0.002 0.06 -9999 0 -0.4 12 12
positive regulation of cell migration -0.07 0.07 -9999 0 -0.26 29 29
SDC1 -0.071 0.07 -9999 0 -0.26 29 29
Syndecan-1/Collagen -0.07 0.07 -9999 0 -0.26 29 29
PPIB 0.01 0.015 -9999 0 -0.33 1 1
MET 0.005 0.049 -9999 0 -0.37 9 9
PRKACA 0.011 0 -9999 0 -10000 0 0
MMP9 -0.13 0.17 -9999 0 -0.33 222 222
MAPK1 -0.045 0.062 -9999 0 -0.25 15 15
homophilic cell adhesion -0.07 0.069 -9999 0 -0.26 29 29
MMP1 -0.17 0.17 -9999 0 -0.33 292 292
Thromboxane A2 receptor 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
TGM2 -0.033 0.13 -10000 0 -0.41 56 56
GNB1/GNG2 -0.04 0.072 -10000 0 -0.19 95 95
AKT1 -0.016 0.097 -10000 0 -0.2 93 93
EGF -0.006 0.073 -10000 0 -0.34 25 25
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.018 0.053 -10000 0 -0.3 1 1
mol:Ca2+ -0.046 0.14 -10000 0 -0.3 110 110
LYN 0.021 0.047 -10000 0 -10000 0 0
RhoA/GTP -0.028 0.049 -10000 0 -0.13 93 93
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.045 0.16 -10000 0 -0.34 98 98
GNG2 0.003 0.056 -10000 0 -0.4 10 10
ARRB2 0.011 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.005 0.071 -10000 0 -0.33 15 15
G beta5/gamma2 -0.053 0.096 -10000 0 -0.25 95 95
PRKCH -0.053 0.16 -10000 0 -0.36 97 97
DNM1 0.006 0.044 -10000 0 -0.41 6 6
TXA2/TP beta/beta Arrestin3 -0.004 0.021 -10000 0 -0.21 1 1
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.026 0.12 -10000 0 -0.41 47 47
G12 family/GTP -0.07 0.12 -10000 0 -0.31 99 99
ADRBK1 0.011 0 -10000 0 -10000 0 0
ADRBK2 0.01 0.018 -10000 0 -0.41 1 1
RhoA/GTP/ROCK1 0.012 0.006 -10000 0 -10000 0 0
mol:GDP 0.022 0.093 0.24 35 -10000 0 35
mol:NADP 0.009 0.023 -10000 0 -0.37 2 2
RAB11A 0.011 0 -10000 0 -10000 0 0
PRKG1 -0.18 0.21 -10000 0 -0.41 241 241
mol:IP3 -0.061 0.18 -10000 0 -0.38 110 110
cell morphogenesis 0.012 0.006 -10000 0 -10000 0 0
PLCB2 -0.09 0.23 -10000 0 -0.53 108 108
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.007 0.056 -10000 0 -0.25 2 2
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.019 0.049 -10000 0 -0.26 1 1
RHOA 0.011 0 -10000 0 -10000 0 0
PTGIR 0.01 0.018 -10000 0 -0.41 1 1
PRKCB1 -0.058 0.17 -10000 0 -0.38 105 105
GNAQ 0.009 0.025 -10000 0 -0.41 2 2
mol:L-citrulline 0.009 0.023 -10000 0 -0.37 2 2
TXA2/TXA2-R family -0.084 0.23 -10000 0 -0.54 98 98
LCK 0.02 0.048 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.014 0.045 -10000 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma 0.018 0.028 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.014 0.044 -10000 0 -10000 0 0
MAPK14 -0.022 0.11 -10000 0 -0.23 96 96
TGM2/GTP -0.078 0.21 -10000 0 -0.45 122 122
MAPK11 -0.023 0.11 -10000 0 -0.23 97 97
ARHGEF1 -0.018 0.085 -10000 0 -0.18 96 96
GNAI2 0.011 0 -10000 0 -10000 0 0
JNK cascade -0.056 0.17 -10000 0 -0.39 98 98
RAB11/GDP 0.011 0.001 -10000 0 -10000 0 0
ICAM1 -0.034 0.13 -10000 0 -0.28 93 93
cAMP biosynthetic process -0.062 0.17 -10000 0 -0.36 122 122
Gq family/GTP/EBP50 -0.001 0.068 -10000 0 -0.26 13 13
actin cytoskeleton reorganization 0.012 0.006 -10000 0 -10000 0 0
SRC 0.021 0.047 -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 0.031 0.047 -10000 0 -0.21 3 3
VCAM1 -0.043 0.15 -10000 0 -0.33 93 93
TP beta/Gq family/GDP/G beta5/gamma2 0.005 0.071 -10000 0 -0.33 15 15
platelet activation -0.031 0.14 -10000 0 -0.3 101 101
PGI2/IP 0.008 0.013 -10000 0 -0.29 1 1
PRKACA -0.003 0.063 -10000 0 -0.21 48 48
Gq family/GDP/G beta5/gamma2 0.003 0.07 -10000 0 -0.31 15 15
TXA2/TP beta/beta Arrestin2 -0.006 0.046 -10000 0 -0.44 6 6
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.003 0.059 -10000 0 -0.19 48 48
mol:DAG -0.068 0.19 -10000 0 -0.43 102 102
EGFR 0 0.066 -10000 0 -0.4 14 14
TXA2/TP alpha -0.088 0.23 -10000 0 -0.49 120 120
Gq family/GTP -0.023 0.07 -10000 0 -0.2 64 64
YES1 0.021 0.047 -10000 0 -10000 0 0
GNAI2/GTP -0.013 0.041 -10000 0 -10000 0 0
PGD2/DP -0.018 0.083 -10000 0 -0.29 47 47
SLC9A3R1 0.008 0.029 -10000 0 -0.33 4 4
FYN 0.021 0.047 -10000 0 -10000 0 0
mol:NO 0.009 0.023 -10000 0 -0.37 2 2
GNA15 0.007 0.038 -10000 0 -0.33 7 7
PGK/cGMP -0.097 0.12 -10000 0 -0.24 242 242
RhoA/GDP 0.011 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.002 0.09 -10000 0 -0.34 17 17
NOS3 0.009 0.023 -10000 0 -0.37 2 2
RAC1 0.011 0 -10000 0 -10000 0 0
PRKCA -0.059 0.17 -10000 0 -0.38 100 100
PRKCB -0.058 0.17 -10000 0 -0.38 98 98
PRKCE -0.051 0.16 -10000 0 -0.36 95 95
PRKCD -0.056 0.17 -10000 0 -0.39 95 95
PRKCG -0.066 0.18 -10000 0 -0.4 102 102
muscle contraction -0.076 0.22 -10000 0 -0.5 99 99
PRKCZ -0.045 0.16 -10000 0 -0.35 98 98
ARR3 0.003 0.015 -10000 0 -0.33 1 1
TXA2/TP beta 0.01 0.055 -10000 0 -10000 0 0
PRKCQ -0.062 0.17 -10000 0 -0.38 100 100
MAPKKK cascade -0.077 0.21 -10000 0 -0.47 109 109
SELE -0.048 0.16 -10000 0 -0.36 95 95
TP beta/GNAI2/GDP/G beta/gamma 0.017 0.06 -10000 0 -0.33 2 2
ROCK1 0.011 0 -10000 0 -10000 0 0
GNA14 -0.031 0.13 -10000 0 -0.41 54 54
chemotaxis -0.092 0.26 -10000 0 -0.61 95 95
GNA12 0.011 0 -10000 0 -10000 0 0
GNA13 0.011 0 -10000 0 -10000 0 0
GNA11 0.002 0.062 -10000 0 -0.41 12 12
Rac1/GTP 0.006 0.004 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.028 0.1 0.28 78 -10000 0 78
KIRREL -0.039 0.14 -10000 0 -0.41 64 64
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.028 0.1 -10000 0 -0.28 78 78
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 -0.011 0.076 -10000 0 -0.2 65 65
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.005 0.077 -10000 0 -0.21 64 64
FYN -0.013 0.072 -10000 0 -0.2 65 65
mol:Ca2+ -0.015 0.074 -10000 0 -0.2 65 65
mol:DAG -0.011 0.075 -10000 0 -0.2 65 65
NPHS2 -0.004 0.028 -10000 0 -0.33 3 3
mol:IP3 -0.011 0.075 -10000 0 -0.2 65 65
regulation of endocytosis -0.006 0.068 -10000 0 -0.18 65 65
Nephrin/NEPH1/podocin/Cholesterol -0.018 0.076 -10000 0 -0.21 65 65
establishment of cell polarity -0.028 0.1 -10000 0 -0.28 78 78
Nephrin/NEPH1/podocin/NCK1-2 -0.003 0.072 -10000 0 -0.33 4 4
Nephrin/NEPH1/beta Arrestin2 -0.005 0.069 -10000 0 -0.18 65 65
NPHS1 -0.006 0.056 -10000 0 -0.33 15 15
Nephrin/NEPH1/podocin -0.013 0.072 -10000 0 -0.2 65 65
TJP1 0.01 0.018 -10000 0 -0.41 1 1
NCK1 0.009 0.025 -10000 0 -0.41 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 -0.011 0.076 -10000 0 -0.2 65 65
CD2AP 0.011 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.011 0.076 -10000 0 -0.2 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 95 95
cytoskeleton organization -0.001 0.08 -10000 0 -0.21 64 64
Nephrin/NEPH1 -0.017 0.071 -10000 0 -0.2 65 65
Nephrin/NEPH1/ZO-1 -0.014 0.083 -10000 0 -0.22 65 65
Ephrin B reverse 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
EFNB2 0.009 0.031 -10000 0 -0.41 3 3
EPHB2 0.01 0.025 -10000 0 -0.33 3 3
EFNB1 0.016 0.037 -10000 0 -0.32 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.01 0.07 -10000 0 -0.35 4 4
Ephrin B2/EPHB1-2 0 0.067 -10000 0 -0.2 58 58
neuron projection morphogenesis -0.021 0.056 -10000 0 -0.33 4 4
Ephrin B1/EPHB1-2/Tiam1 0.006 0.075 -10000 0 -0.2 48 48
DNM1 0.007 0.044 -10000 0 -0.41 6 6
cell-cell signaling 0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.049 0.18 -10000 0 -0.52 70 70
YES1 -0.096 0.25 -10000 0 -0.75 70 70
Ephrin B1/EPHB1-2/NCK2 0.012 0.066 -10000 0 -0.18 41 41
PI3K -0.05 0.19 -10000 0 -0.52 71 71
mol:GDP 0.005 0.075 -10000 0 -0.19 48 48
ITGA2B 0.005 0.05 -10000 0 -0.4 8 8
endothelial cell proliferation 0.014 0.021 -10000 0 -0.23 4 4
FYN -0.096 0.25 -10000 0 -0.75 70 70
MAP3K7 -0.058 0.19 -10000 0 -0.55 70 70
FGR -0.098 0.25 -10000 0 -0.75 70 70
TIAM1 0 0.067 -10000 0 -0.41 14 14
PIK3R1 0.007 0.04 -10000 0 -0.41 5 5
RGS3 0.011 0 -10000 0 -10000 0 0
cell adhesion -0.074 0.2 -10000 0 -0.56 70 70
LYN -0.096 0.25 -10000 0 -0.75 70 70
Ephrin B1/EPHB1-2/Src Family Kinases -0.089 0.23 -10000 0 -0.7 70 70
Ephrin B1/EPHB1-2 -0.077 0.2 -10000 0 -0.6 70 70
SRC -0.095 0.25 -10000 0 -0.75 70 70
ITGB3 -0.068 0.16 -10000 0 -0.41 102 102
EPHB1 -0.028 0.12 -10000 0 -0.4 52 52
EPHB4 0.01 0.018 -10000 0 -0.41 1 1
RAC1 0.011 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.014 0.021 -10000 0 -0.23 4 4
alphaIIb/beta3 Integrin -0.043 0.12 -10000 0 -0.28 110 110
BLK -0.095 0.25 -10000 0 -0.75 70 70
HCK -0.095 0.25 -10000 0 -0.75 70 70
regulation of stress fiber formation -0.011 0.066 0.18 41 -10000 0 41
MAPK8 -0.043 0.18 -10000 0 -0.5 70 70
Ephrin B1/EPHB1-2/RGS3 0.012 0.066 -10000 0 -0.18 41 41
endothelial cell migration -0.056 0.16 -10000 0 -0.45 72 72
NCK2 0.011 0 -10000 0 -10000 0 0
PTPN13 -0.059 0.18 -10000 0 -0.52 70 70
regulation of focal adhesion formation -0.011 0.066 0.18 41 -10000 0 41
chemotaxis -0.011 0.066 0.18 41 -10000 0 41
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
Rac1/GTP -0.021 0.057 -10000 0 -0.34 4 4
angiogenesis -0.077 0.2 -10000 0 -0.6 70 70
LCK -0.095 0.25 -10000 0 -0.75 70 70
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.1 0.25 -10000 0 -0.68 37 37
PCK1 -0.12 0.33 -10000 0 -1.2 37 37
HNF4A -0.16 0.33 -10000 0 -0.84 69 69
KCNJ11 -0.09 0.26 -10000 0 -0.69 37 37
AKT1 -0.049 0.14 -10000 0 -0.36 20 20
response to starvation -0.01 0.032 -10000 0 -0.15 2 2
DLK1 -0.15 0.34 -10000 0 -0.8 85 85
NKX2-1 -0.021 0.15 -10000 0 -0.5 1 1
ACADM -0.1 0.26 -10000 0 -0.7 40 40
TAT -0.098 0.2 -10000 0 -0.58 28 28
CEBPB 0.013 0.002 -10000 0 -10000 0 0
CEBPA 0.01 0.037 -10000 0 -0.38 5 5
TTR -0.038 0.13 -10000 0 -0.6 8 8
PKLR -0.11 0.25 -10000 0 -0.67 41 41
APOA1 -0.21 0.44 -10000 0 -1.2 71 71
CPT1C -0.11 0.26 -10000 0 -0.73 41 41
ALAS1 -0.044 0.16 -10000 0 -10000 0 0
TFRC -0.058 0.19 -10000 0 -0.64 7 7
FOXF1 0.008 0.046 -10000 0 -0.4 6 6
NF1 0.015 0.026 -10000 0 -0.41 2 2
HNF1A (dimer) 0.004 0.046 -10000 0 -0.35 8 8
CPT1A -0.1 0.25 -10000 0 -0.66 42 42
HMGCS1 -0.1 0.25 -10000 0 -0.66 43 43
NR3C1 -0.067 0.16 -10000 0 -0.38 98 98
CPT1B -0.1 0.25 -10000 0 -0.68 38 38
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.007 0.016 -10000 0 -10000 0 0
GCK -0.17 0.34 -10000 0 -0.78 99 99
CREB1 0.003 0.041 -10000 0 -0.2 7 7
IGFBP1 -0.22 0.44 -10000 0 -1.1 90 90
PDX1 -0.054 0.15 -10000 0 -10000 0 0
UCP2 -0.1 0.25 -10000 0 -0.67 40 40
ALDOB -0.092 0.26 -10000 0 -0.69 35 35
AFP -0.056 0.072 -10000 0 -0.41 9 9
BDH1 -0.1 0.25 -10000 0 -0.66 43 43
HADH -0.089 0.26 -10000 0 -0.7 33 33
F2 -0.15 0.31 -10000 0 -0.87 40 40
HNF1A 0.004 0.046 -10000 0 -0.35 8 8
G6PC 0.007 0.066 -10000 0 -10000 0 0
SLC2A2 -0.057 0.17 -10000 0 -10000 0 0
INS 0.016 0.06 0.2 28 -10000 0 28
FOXA1 -0.21 0.16 -10000 0 -0.32 361 361
FOXA3 -0.057 0.16 -10000 0 -0.33 119 119
FOXA2 -0.11 0.3 -10000 0 -0.75 44 44
ABCC8 -0.18 0.38 -10000 0 -0.85 107 107
ALB -0.063 0.14 -10000 0 -1 9 9
BMP 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
BMP7/BMPR2/BMPR1A-1B/FS -0.029 0.11 -9999 0 -0.34 26 26
SMAD6-7/SMURF1 0.021 0.019 -9999 0 -0.23 3 3
NOG -0.019 0.096 -9999 0 -0.33 47 47
SMAD9 -0.059 0.17 -9999 0 -0.51 60 60
SMAD4 0.01 0.018 -9999 0 -0.41 1 1
SMAD5 -0.018 0.094 -9999 0 -0.3 30 30
BMP7/USAG1 -0.048 0.12 -9999 0 -0.26 124 124
SMAD5/SKI -0.012 0.09 -9999 0 -0.3 24 24
SMAD1 0.034 0.014 -9999 0 -10000 0 0
BMP2 -0.025 0.12 -9999 0 -0.41 47 47
SMAD1/SMAD1/SMAD4 -0.001 0.012 -9999 0 -10000 0 0
BMPR1A 0.011 0 -9999 0 -10000 0 0
BMPR1B -0.015 0.1 -9999 0 -0.41 34 34
BMPR1A-1B/BAMBI -0.004 0.08 -9999 0 -0.24 55 55
AHSG 0 0.05 -9999 0 -0.33 12 12
CER1 0.004 0.005 -9999 0 -10000 0 0
BMP2-4/CER1 -0.018 0.092 -9999 0 -0.25 68 68
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.037 0.12 -9999 0 -0.34 39 39
BMP2-4 (homodimer) -0.026 0.11 -9999 0 -0.29 75 75
RGMB 0.01 0.018 -9999 0 -0.41 1 1
BMP6/BMPR2/BMPR1A-1B 0.01 0.064 -9999 0 -0.2 43 43
RGMA -0.082 0.18 -9999 0 -0.41 120 120
SMURF1 0.011 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.042 0.12 -9999 0 -0.34 41 41
BMP2-4/USAG1 -0.042 0.12 -9999 0 -0.27 92 92
SMAD6/SMURF1/SMAD5 -0.012 0.09 -9999 0 -0.3 23 23
SOSTDC1 -0.04 0.13 -9999 0 -0.36 72 72
BMP7/BMPR2/BMPR1A-1B -0.008 0.088 -9999 0 -0.22 60 60
SKI 0.011 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.002 0.059 -9999 0 -0.41 11 11
HFE2 0.003 0.021 -9999 0 -0.33 2 2
ZFYVE16 0.011 0 -9999 0 -10000 0 0
MAP3K7 0.011 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.056 0.14 -9999 0 -0.27 141 141
SMAD5/SMAD5/SMAD4 -0.012 0.092 -9999 0 -0.31 24 24
MAPK1 0.011 0 -9999 0 -10000 0 0
TAK1/TAB family -0.051 0.087 -9999 0 -0.31 35 35
BMP7 (homodimer) -0.032 0.12 -9999 0 -0.37 62 62
NUP214 0.011 0 -9999 0 -10000 0 0
BMP6/FETUA 0.003 0.053 -9999 0 -0.25 23 23
SMAD1/SKI 0.038 0.014 -9999 0 -10000 0 0
SMAD6 0.01 0.018 -9999 0 -0.41 1 1
CTDSP2 0.011 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.02 0.097 -9999 0 -0.25 66 66
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.093 0.18 -9999 0 -0.41 135 135
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 0.071 -9999 0 -0.28 34 34
CHRDL1 -0.28 0.2 -9999 0 -0.41 371 371
ENDOFIN/SMAD1 0.038 0.014 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 0 0.012 -9999 0 -10000 0 0
SMAD6/SMURF1 0.011 0 -9999 0 -10000 0 0
BAMBI -0.007 0.083 -9999 0 -0.38 25 25
SMURF2 0.011 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.18 0.15 -9999 0 -0.26 388 388
BMP2-4/GREM1 -0.074 0.14 -9999 0 -0.27 176 176
SMAD7 0.009 0.025 -9999 0 -0.41 2 2
SMAD8A/SMAD8A/SMAD4 -0.05 0.16 -9999 0 -0.47 61 61
SMAD1/SMAD6 0.038 0.014 -9999 0 -10000 0 0
TAK1/SMAD6 0.016 0 -9999 0 -10000 0 0
BMP7 -0.032 0.12 -9999 0 -0.37 62 62
BMP6 0.002 0.059 -9999 0 -0.41 11 11
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.038 0.11 -9999 0 -0.34 38 38
PPM1A 0.011 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.038 0.014 -9999 0 -10000 0 0
SMAD7/SMURF1 0.015 0.018 -9999 0 -0.28 2 2
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 -0.076 0.16 -9999 0 -0.42 69 69
CHRD -0.063 0.16 -9999 0 -0.41 96 96
BMPR2 0.011 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.05 0.13 -9999 0 -0.37 41 41
BMP4 -0.014 0.097 -9999 0 -0.39 34 34
FST -0.043 0.14 -9999 0 -0.4 70 70
BMP2-4/NOG -0.03 0.11 -9999 0 -0.26 71 71
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.002 0.082 -9999 0 -0.2 60 60
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.005 0.067 -9999 0 -0.25 30 30
alphaM/beta2 Integrin/GPIbA 0.014 0.041 -9999 0 -0.27 7 7
alphaM/beta2 Integrin/proMMP-9 -0.062 0.1 -9999 0 -0.22 57 57
PLAUR 0.009 0.025 -9999 0 -0.33 3 3
HMGB1 0.009 0.011 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.018 0.033 -9999 0 -0.24 5 5
AGER 0.008 0.021 -9999 0 -0.4 1 1
RAP1A 0.011 0 -9999 0 -10000 0 0
SELPLG 0.01 0.021 -9999 0 -0.33 2 2
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.019 0.056 -9999 0 -0.27 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.13 0.17 -9999 0 -0.33 222 222
CYR61 -0.027 0.12 -9999 0 -0.41 49 49
TLN1 0.011 0 -9999 0 -10000 0 0
Rap1/GTP -0.029 0.061 -9999 0 -0.26 15 15
RHOA 0.011 0 -9999 0 -10000 0 0
P-selectin oligomer -0.15 0.2 -9999 0 -0.41 207 207
MYH2 -0.031 0.11 -9999 0 -0.29 45 45
MST1R -0.021 0.1 -9999 0 -0.33 51 51
leukocyte activation during inflammatory response -0.015 0.05 -9999 0 -0.21 17 17
APOB -0.001 0.053 -9999 0 -0.39 10 10
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.01 0.091 -9999 0 -0.41 27 27
JAM3 -0.1 0.19 -9999 0 -0.41 145 145
GP1BA 0.008 0.029 -9999 0 -0.38 3 3
alphaM/beta2 Integrin/CTGF 0.011 0.052 -9999 0 -0.24 19 19
alphaM/beta2 Integrin -0.023 0.084 -9999 0 -0.23 40 40
JAM3 homodimer -0.1 0.19 -9999 0 -0.41 145 145
ICAM2 0.011 0 -9999 0 -10000 0 0
ICAM1 0.008 0.029 -9999 0 -0.33 4 4
phagocytosis triggered by activation of immune response cell surface activating receptor -0.022 0.084 -9999 0 -0.23 40 40
cell adhesion 0.014 0.04 -9999 0 -0.27 7 7
NFKB1 0.018 0.086 -9999 0 -0.3 19 19
THY1 0.011 0 -9999 0 -10000 0 0
RhoA/GDP 0.008 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.006 0.055 -9999 0 -0.2 41 41
alphaM/beta2 Integrin/LRP/tPA -0.001 0.08 -9999 0 -0.21 62 62
IL6 0.012 0.13 -9999 0 -0.53 23 23
ITGB2 0.006 0.034 -9999 0 -0.33 5 5
elevation of cytosolic calcium ion concentration 0.021 0.036 -9999 0 -0.22 4 4
alphaM/beta2 Integrin/JAM2/JAM3 -0.11 0.17 -9999 0 -0.28 247 247
JAM2 -0.14 0.2 -9999 0 -0.41 193 193
alphaM/beta2 Integrin/ICAM1 0.01 0.062 -9999 0 -0.36 3 3
alphaM/beta2 Integrin/uPA/Plg 0 0.076 -9999 0 -0.21 51 51
RhoA/GTP -0.034 0.11 -9999 0 -0.26 72 72
positive regulation of phagocytosis -0.02 0.055 -9999 0 -0.24 10 10
Ron/MSP -0.009 0.072 -9999 0 -0.22 58 58
alphaM/beta2 Integrin/uPAR/uPA 0.022 0.036 -9999 0 -0.22 4 4
alphaM/beta2 Integrin/uPAR 0.016 0.036 -9999 0 -0.23 7 7
PLAU 0.009 0.025 -9999 0 -0.33 3 3
PLAT -0.035 0.13 -9999 0 -0.41 59 59
actin filament polymerization -0.029 0.1 -9999 0 -0.28 45 45
MST1 0.007 0.038 -9999 0 -0.33 7 7
alphaM/beta2 Integrin/lipoprotein(a) 0.003 0.057 -9999 0 -0.21 17 17
TNF 0.011 0.11 -9999 0 -0.39 10 10
RAP1B 0.011 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.016 0.037 -9999 0 -0.2 12 12
fibrinolysis -0.001 0.075 -9999 0 -0.21 51 51
HCK 0.007 0.038 -9999 0 -0.33 7 7
dendritic cell antigen processing and presentation -0.022 0.084 -9999 0 -0.23 40 40
VTN -0.047 0.14 -9999 0 -0.41 74 74
alphaM/beta2 Integrin/CYR61 -0.005 0.08 -9999 0 -0.24 52 52
LPA -0.012 0.079 -9999 0 -0.33 32 32
LRP1 0.009 0.025 -9999 0 -0.41 2 2
cell migration -0.059 0.1 -9999 0 -0.25 41 41
FN1 0.007 0.04 -9999 0 -0.41 5 5
alphaM/beta2 Integrin/Thy1 0.018 0.033 -9999 0 -0.24 5 5
MPO 0.005 0.041 -9999 0 -0.33 8 8
KNG1 -0.01 0.07 -9999 0 -0.33 25 25
RAP1/GDP 0.015 0 -9999 0 -10000 0 0
ROCK1 -0.026 0.11 -9999 0 -0.3 37 37
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.032 0.12 -9999 0 -0.4 55 55
CTGF 0 0.067 -9999 0 -0.41 14 14
alphaM/beta2 Integrin/Hck 0.015 0.044 -9999 0 -0.22 14 14
ITGAM 0.006 0.038 -9999 0 -0.37 5 5
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.063 0.12 -9999 0 -0.2 211 211
HP -0.1 0.17 -9999 0 -0.35 170 170
leukocyte adhesion -0.11 0.13 -9999 0 -0.34 105 105
SELP -0.15 0.2 -9999 0 -0.41 207 207
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.029 0.14 -10000 0 -0.41 52 52
CRKL -0.033 0.15 -10000 0 -0.44 49 49
HRAS -0.012 0.13 -10000 0 -0.38 46 46
mol:PIP3 -0.039 0.14 -10000 0 -0.41 51 51
SPRED1 0.011 0 -10000 0 -10000 0 0
SPRED2 0.01 0.018 -10000 0 -0.41 1 1
GAB1 -0.041 0.16 -10000 0 -0.47 49 49
FOXO3 -0.024 0.14 -10000 0 -0.4 48 48
AKT1 -0.033 0.15 -10000 0 -0.43 49 49
BAD -0.024 0.14 -10000 0 -0.4 48 48
megakaryocyte differentiation -0.042 0.16 -10000 0 -0.43 56 56
GSK3B -0.024 0.14 -10000 0 -0.4 48 48
RAF1 -0.002 0.11 -10000 0 -0.3 46 46
SHC1 0.011 0 -10000 0 -10000 0 0
STAT3 -0.039 0.16 -10000 0 -0.46 49 49
STAT1 -0.099 0.34 -10000 0 -0.84 81 81
HRAS/SPRED1 -0.004 0.11 -10000 0 -0.3 46 46
cell proliferation -0.04 0.16 -10000 0 -0.46 49 49
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
TEC 0.01 0.015 -10000 0 -0.33 1 1
RPS6KB1 -0.04 0.16 -10000 0 -0.47 49 49
HRAS/SPRED2 -0.004 0.11 -10000 0 -0.31 46 46
LYN/TEC/p62DOK -0.027 0.15 -10000 0 -0.42 50 50
MAPK3 0.01 0.086 -10000 0 -0.24 24 24
STAP1 -0.042 0.16 -10000 0 -0.45 52 52
GRAP2 -0.002 0.073 -10000 0 -0.41 17 17
JAK2 -0.086 0.3 -10000 0 -0.72 82 82
STAT1 (dimer) -0.096 0.33 -10000 0 -0.82 81 81
mol:Gleevec 0 0.006 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.028 0.15 -10000 0 -0.42 52 52
actin filament polymerization -0.038 0.15 -10000 0 -0.45 49 49
LYN 0.011 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.053 0.21 -10000 0 -0.51 82 82
PIK3R1 0.007 0.04 -10000 0 -0.41 5 5
CBL/CRKL/GRB2 -0.019 0.14 -10000 0 -0.41 44 44
PI3K -0.03 0.16 -10000 0 -0.45 51 51
PTEN 0.006 0.044 -10000 0 -0.41 6 6
SCF/KIT/EPO/EPOR -0.1 0.37 -10000 0 -1.2 48 48
MAPK8 -0.041 0.16 -10000 0 -0.47 49 49
STAT3 (dimer) -0.038 0.15 -10000 0 -0.45 49 49
positive regulation of transcription 0.012 0.073 -10000 0 -0.2 24 24
mol:GDP -0.017 0.14 -10000 0 -0.39 46 46
PIK3C2B -0.039 0.16 -10000 0 -0.45 52 52
CBL/CRKL -0.025 0.14 -10000 0 -0.41 49 49
FER -0.039 0.16 -10000 0 -0.45 52 52
SH2B3 -0.04 0.16 -10000 0 -0.46 49 49
PDPK1 -0.031 0.13 -10000 0 -0.38 51 51
SNAI2 -0.064 0.18 -10000 0 -0.49 65 65
positive regulation of cell proliferation -0.069 0.26 -10000 0 -0.62 82 82
KITLG -0.029 0.13 -10000 0 -0.43 50 50
cell motility -0.069 0.26 -10000 0 -0.62 82 82
PTPN6 0.011 0.017 -10000 0 -0.33 1 1
EPOR -0.01 0.12 -10000 0 -0.71 2 2
STAT5A (dimer) -0.055 0.22 -10000 0 -0.52 82 82
SOCS1 0.01 0.018 -10000 0 -0.41 1 1
cell migration 0.043 0.16 0.46 50 -10000 0 50
SOS1 0.011 0 -10000 0 -10000 0 0
EPO -0.005 0.074 -10000 0 -0.41 17 17
VAV1 0.007 0.037 -10000 0 -0.34 6 6
GRB10 -0.04 0.16 -10000 0 -0.46 49 49
PTPN11 0.012 0.006 -10000 0 -10000 0 0
SCF/KIT -0.047 0.16 -10000 0 -0.39 80 80
GO:0007205 0.001 0.008 -10000 0 -10000 0 0
MAP2K1 0.007 0.093 -10000 0 -0.24 46 46
CBL 0.011 0 -10000 0 -10000 0 0
KIT -0.079 0.34 -10000 0 -1.3 40 40
MAP2K2 0.007 0.093 -10000 0 -0.24 46 46
SHC/Grb2/SOS1 -0.026 0.15 -10000 0 -0.42 49 49
STAT5A -0.058 0.22 -10000 0 -0.53 82 82
GRB2 0.011 0 -10000 0 -10000 0 0
response to radiation -0.063 0.18 -10000 0 -0.48 65 65
SHC/GRAP2 0.007 0.052 -10000 0 -0.28 17 17
PTPRO -0.043 0.16 -10000 0 -0.44 56 56
SH2B2 -0.039 0.16 -10000 0 -0.46 49 49
DOK1 0.011 0 -10000 0 -10000 0 0
MATK -0.044 0.16 -10000 0 -0.47 50 50
CREBBP 0.016 0.045 -10000 0 -0.43 2 2
BCL2 -0.098 0.38 -10000 0 -1.2 51 51
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.014 0.076 -9999 0 -0.24 54 54
EFNA5 -0.003 0.076 -9999 0 -0.4 19 19
FYN -0.006 0.069 -9999 0 -0.21 54 54
neuron projection morphogenesis -0.014 0.076 -9999 0 -0.24 54 54
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.014 0.077 -9999 0 -0.24 54 54
EPHA5 -0.023 0.1 -9999 0 -0.41 37 37
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.077 0.17 -9999 0 -0.31 169 169
MAP3K8 0.006 0.032 -9999 0 -0.41 3 3
FOS -0.044 0.12 -9999 0 -0.38 26 26
PRKCA -0.02 0.1 -9999 0 -0.41 36 36
PTPN7 0.005 0.037 -9999 0 -0.34 6 6
HRAS 0.01 0.001 -9999 0 -10000 0 0
PRKCB -0.016 0.099 -9999 0 -0.41 32 32
NRAS 0.01 0.001 -9999 0 -10000 0 0
RAS family/GTP 0.015 0.013 -9999 0 -0.15 1 1
MAPK3 -0.017 0.069 -9999 0 -0.25 5 5
MAP2K1 -0.038 0.14 -9999 0 -0.4 65 65
ELK1 0.005 0.01 -9999 0 -10000 0 0
BRAF -0.034 0.14 -9999 0 -0.38 64 64
mol:GTP -0.001 0.002 -9999 0 -0.005 167 167
MAPK1 -0.017 0.069 -9999 0 -0.27 3 3
RAF1 -0.034 0.14 -9999 0 -0.38 64 64
KRAS 0.01 0.015 -9999 0 -0.33 1 1
Osteopontin-mediated events

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
IKK alpha homodimer -0.04 0.1 -9999 0 -0.32 16 16
NF kappa B1 p50/RelA/I kappa B alpha -0.013 0.092 -9999 0 -0.27 15 15
alphaV/beta3 Integrin/Osteopontin/Src -0.043 0.1 -9999 0 -0.21 155 155
AP1 -0.081 0.15 -9999 0 -0.37 67 67
ILK -0.051 0.11 -9999 0 -0.34 16 16
bone resorption -0.029 0.1 -9999 0 -0.29 31 31
PTK2B 0.011 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.034 0.098 -9999 0 -0.3 17 17
ITGAV 0.014 0.001 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.004 0.058 -9999 0 -0.28 22 22
alphaV/beta3 Integrin/Osteopontin -0.066 0.12 -9999 0 -0.24 101 101
MAP3K1 -0.052 0.11 -9999 0 -0.32 20 20
JUN 0.006 0.047 -9999 0 -0.41 7 7
MAPK3 -0.037 0.1 -9999 0 -0.32 16 16
MAPK1 -0.037 0.1 -9999 0 -0.32 16 16
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
NFKB1 0.01 0.018 -9999 0 -0.41 1 1
MAPK8 -0.043 0.1 -9999 0 -0.32 22 22
ITGB3 -0.064 0.16 -9999 0 -0.4 102 102
NFKBIA -0.026 0.099 -9999 0 -0.3 16 16
FOS -0.12 0.19 -9999 0 -0.41 167 167
CD44 0.005 0.05 -9999 0 -0.4 8 8
CHUK 0.011 0 -9999 0 -10000 0 0
PLAU -0.021 0.095 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.046 0.06 -9999 0 -0.26 7 7
BCAR1 0.011 0 -9999 0 -10000 0 0
RELA 0.011 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.032 0.11 -9999 0 -0.27 102 102
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.052 0.11 -9999 0 -0.32 20 20
VAV3 -0.079 0.12 -9999 0 -0.3 68 68
MAP3K14 -0.049 0.11 -9999 0 -0.33 18 18
ROCK2 0 0.067 -9999 0 -0.41 14 14
SPP1 -0.082 0.15 -9999 0 -0.32 155 155
RAC1 0.011 0 -9999 0 -10000 0 0
Rac1/GTP -0.068 0.11 -9999 0 -0.27 68 68
MMP2 -0.073 0.15 -9999 0 -0.48 36 36
IL4-mediated signaling 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
BCL2L1 -0.24 0.37 -10000 0 -1 58 58
STAT6 (cleaved dimer) -0.27 0.34 -10000 0 -0.92 85 85
IGHG1 -0.085 0.14 -10000 0 -0.34 36 36
IGHG3 -0.24 0.36 -10000 0 -0.9 82 82
AKT1 -0.1 0.2 -10000 0 -0.59 22 22
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.064 0.16 -10000 0 -0.58 10 10
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.12 0.23 -10000 0 -0.62 43 43
THY1 -0.24 0.37 -10000 0 -1 58 58
MYB -0.022 0.1 -10000 0 -0.33 53 53
HMGA1 -0.038 0.12 -10000 0 -0.33 78 78
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.14 0.23 -10000 0 -0.59 47 47
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.1 0.2 -10000 0 -0.6 20 20
SP1 0.017 0.002 -10000 0 -10000 0 0
INPP5D 0.01 0.018 -10000 0 -0.41 1 1
SOCS5 0.017 0.013 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.22 0.37 -10000 0 -0.98 65 65
SOCS1 -0.14 0.26 -10000 0 -0.69 47 47
SOCS3 -0.1 0.21 -10000 0 -0.94 6 6
FCER2 -0.18 0.3 -10000 0 -0.79 54 54
PARP14 0.012 0.002 -10000 0 -10000 0 0
CCL17 -0.24 0.37 -10000 0 -1 58 58
GRB2 0.011 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.08 0.16 -10000 0 -0.52 11 11
T cell proliferation -0.24 0.38 -10000 0 -1 62 62
IL4R/JAK1 -0.24 0.38 -10000 0 -1 61 61
EGR2 -0.27 0.46 -10000 0 -1.2 68 68
JAK2 -0.009 0.06 -10000 0 -0.43 9 9
JAK3 0.012 0.03 -10000 0 -0.33 4 4
PIK3R1 0.007 0.04 -10000 0 -0.41 5 5
JAK1 0.007 0.027 -10000 0 -0.4 2 2
COL1A2 -0.078 0.18 -10000 0 -1.4 5 5
CCL26 -0.24 0.37 -10000 0 -1 57 57
IL4R -0.25 0.4 -10000 0 -1.1 60 60
PTPN6 0.017 0.018 -10000 0 -0.31 1 1
IL13RA2 -0.24 0.38 -10000 0 -1 60 60
IL13RA1 -0.002 0.027 -10000 0 -10000 0 0
IRF4 -0.061 0.22 -10000 0 -1.1 18 18
ARG1 -0.054 0.11 -10000 0 -10000 0 0
CBL -0.12 0.22 -10000 0 -0.56 41 41
GTF3A 0.018 0.001 -10000 0 -10000 0 0
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
IL13RA1/JAK2 -0.008 0.051 -10000 0 -0.28 9 9
IRF4/BCL6 -0.054 0.2 -10000 0 -1 18 18
CD40LG 0.007 0.064 -10000 0 -0.42 12 12
MAPK14 -0.12 0.22 -10000 0 -0.59 34 34
mitosis -0.097 0.2 -10000 0 -0.56 22 22
STAT6 -0.27 0.42 -10000 0 -1.1 77 77
SPI1 0.011 0.025 -10000 0 -0.32 3 3
RPS6KB1 -0.089 0.19 -10000 0 -0.57 17 17
STAT6 (dimer) -0.27 0.42 -10000 0 -1.1 77 77
STAT6 (dimer)/PARP14 -0.25 0.39 -10000 0 -1 74 74
mast cell activation 0.006 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.096 0.19 -10000 0 -0.53 25 25
FRAP1 -0.1 0.2 -10000 0 -0.59 22 22
LTA -0.24 0.37 -10000 0 -1.1 47 47
FES 0.01 0.018 -10000 0 -0.41 1 1
T-helper 1 cell differentiation 0.26 0.41 1 79 -10000 0 79
CCL11 -0.25 0.39 -10000 0 -1.1 64 64
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.095 0.19 -10000 0 -0.55 21 21
IL2RG 0.009 0.048 -10000 0 -0.36 9 9
IL10 -0.24 0.37 -10000 0 -1 54 54
IRS1 -0.031 0.13 -10000 0 -0.41 54 54
IRS2 -0.042 0.14 -10000 0 -0.41 69 69
IL4 -0.059 0.1 -10000 0 -10000 0 0
IL5 -0.24 0.37 -10000 0 -1 58 58
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.21 0.32 -10000 0 -0.83 62 62
COL1A1 -0.075 0.16 -10000 0 -1.5 1 1
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.24 0.38 -10000 0 -1.1 52 52
IL2R gamma/JAK3 0.015 0.045 -10000 0 -0.3 10 10
TFF3 -0.3 0.43 -10000 0 -1.1 79 79
ALOX15 -0.25 0.38 -10000 0 -1 64 64
MYBL1 0.011 0 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.21 0.32 -10000 0 -0.82 66 66
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 -0.12 0.21 -10000 0 -0.59 30 30
mol:PI-3-4-5-P3 -0.1 0.2 -10000 0 -0.59 22 22
PI3K -0.11 0.21 -10000 0 -0.63 22 22
DOK2 0.008 0.031 -10000 0 -0.35 4 4
ETS1 0.017 0.02 -10000 0 -0.38 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.072 0.16 -10000 0 -0.58 6 6
ITGB3 -0.37 0.57 -10000 0 -1.3 117 117
PIGR -0.33 0.47 -10000 0 -1.2 86 86
IGHE 0.019 0.033 -10000 0 -10000 0 0
MAPKKK cascade -0.071 0.16 -10000 0 -0.57 6 6
BCL6 0.01 0.018 -10000 0 -0.41 1 1
OPRM1 -0.24 0.37 -10000 0 -0.99 67 67
RETNLB -0.24 0.37 -10000 0 -1 60 60
SELP -0.52 0.66 -10000 0 -1.3 215 215
AICDA -0.23 0.36 -10000 0 -1 48 48
TCGA08_p53

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
CDKN2A -0.089 0.12 -9999 0 -0.22 228 228
TP53 -0.023 0.03 -9999 0 -0.34 1 1
Senescence -0.023 0.03 -9999 0 -0.34 1 1
Apoptosis -0.023 0.03 -9999 0 -0.34 1 1
Activated_Oncogenes 0 0 -9999 0 -10000 0 0
MDM2 0.047 0.055 -9999 0 -10000 0 0
MDM4 0.011 0 -9999 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.033 0.1 0.34 17 -10000 0 17
GNAI2 0.011 0 -10000 0 -10000 0 0
S1P/S1P5/G12 0.008 0.036 -10000 0 -0.19 17 17
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.1 0.18 -10000 0 -0.41 143 143
RhoA/GTP -0.033 0.1 -10000 0 -0.34 17 17
negative regulation of cAMP metabolic process -0.042 0.11 -10000 0 -0.21 158 158
GNAZ -0.002 0.073 -10000 0 -0.41 17 17
GNAI3 0.011 0 -10000 0 -10000 0 0
GNA12 0.011 0 -10000 0 -10000 0 0
S1PR5 0 0.063 -10000 0 -0.35 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.042 0.11 -10000 0 -0.21 158 158
RhoA/GDP 0.008 0 -10000 0 -10000 0 0
RHOA 0.011 0 -10000 0 -10000 0 0
GNAI1 0.005 0.051 -10000 0 -0.41 8 8
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.006 0.074 -9999 0 -0.23 43 43
NF kappa B1 p50/RelA/I kappa B alpha 0.007 0.068 -9999 0 -0.26 4 4
AP1 -0.08 0.11 -9999 0 -0.36 50 50
mol:PIP3 -0.03 0.069 -9999 0 -0.32 16 16
AKT1 0.029 0.056 -9999 0 -0.27 8 8
PTK2B 0.006 0.059 -9999 0 -0.21 27 27
RHOA 0.019 0.03 -9999 0 -10000 0 0
PIK3CB 0.011 0 -9999 0 -10000 0 0
mol:Ca2+ 0.005 0.063 -9999 0 -0.23 6 6
MAGI3 0.011 0 -9999 0 -10000 0 0
RELA 0.011 0 -9999 0 -10000 0 0
apoptosis -0.011 0.086 -9999 0 -0.23 63 63
HRAS/GDP 0.008 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.01 0.065 -9999 0 -0.22 18 18
NF kappa B1 p50/RelA -0.025 0.068 -9999 0 -0.33 10 10
endothelial cell migration -0.01 0.12 -9999 0 -0.53 27 27
ADCY4 -0.044 0.14 -9999 0 -0.37 56 56
ADCY5 -0.072 0.16 -9999 0 -0.38 78 78
ADCY6 -0.035 0.13 -9999 0 -0.34 48 48
ADCY7 -0.035 0.13 -9999 0 -0.34 48 48
ADCY1 -0.044 0.14 -9999 0 -0.37 57 57
ADCY2 -0.14 0.19 -9999 0 -0.4 143 143
ADCY3 -0.036 0.13 -9999 0 -0.34 50 50
ADCY8 -0.039 0.13 -9999 0 -0.35 47 47
ADCY9 -0.064 0.16 -9999 0 -0.41 73 73
GSK3B 0.011 0.056 -9999 0 -0.2 26 26
arachidonic acid secretion -0.04 0.13 -9999 0 -0.39 38 38
GNG2 0.003 0.056 -9999 0 -0.4 10 10
TRIP6 0.014 0.037 -9999 0 -0.35 5 5
GNAO1 -0.061 0.14 -9999 0 -0.26 164 164
HRAS 0.011 0 -9999 0 -10000 0 0
NFKBIA 0.009 0.076 -9999 0 -0.26 10 10
GAB1 0.008 0.036 -9999 0 -0.41 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.001 0.14 -9999 0 -0.86 14 14
JUN 0.006 0.047 -9999 0 -0.41 7 7
LPA/LPA2/NHERF2 0.012 0.022 -9999 0 -0.18 3 3
TIAM1 -0.024 0.16 -9999 0 -1 14 14
PIK3R1 0.007 0.04 -9999 0 -0.41 5 5
mol:IP3 0.005 0.064 -9999 0 -0.24 6 6
PLCB3 0.018 0.02 -9999 0 -0.15 3 3
FOS -0.12 0.19 -9999 0 -0.41 167 167
positive regulation of mitosis -0.04 0.13 -9999 0 -0.39 38 38
LPA/LPA1-2-3 -0.013 0.089 -9999 0 -0.22 63 63
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 0.007 0.068 -9999 0 -0.28 12 12
GNAZ -0.004 0.085 -9999 0 -0.25 54 54
EGFR/PI3K-beta/Gab1 -0.031 0.071 -9999 0 -0.33 16 16
positive regulation of dendritic cell cytokine production -0.017 0.087 -9999 0 -0.22 61 61
LPA/LPA2/MAGI-3 0.012 0.022 -9999 0 -0.18 3 3
ARHGEF1 0.015 0.061 -9999 0 -0.37 5 5
GNAI2 0.003 0.072 -9999 0 -0.25 39 39
GNAI3 0.003 0.072 -9999 0 -0.25 39 39
GNAI1 0 0.078 -9999 0 -0.25 46 46
LPA/LPA3 -0.019 0.081 -9999 0 -0.26 52 52
LPA/LPA2 0.005 0.027 -9999 0 -0.22 3 3
LPA/LPA1 -0.007 0.084 -9999 0 -0.3 39 39
HB-EGF/EGFR -0.064 0.1 -9999 0 -0.18 228 228
HBEGF -0.078 0.12 -9999 0 -0.22 222 222
mol:DAG 0.005 0.064 -9999 0 -0.24 6 6
cAMP biosynthetic process -0.067 0.15 -9999 0 -0.3 111 111
NFKB1 0.01 0.018 -9999 0 -0.41 1 1
SRC 0.011 0 -9999 0 -10000 0 0
GNB1 0.011 0 -9999 0 -10000 0 0
LYN 0.009 0.076 -9999 0 -0.25 14 14
GNAQ -0.002 0.06 -9999 0 -0.22 30 30
LPAR2 0.009 0.025 -9999 0 -0.33 3 3
LPAR3 -0.026 0.11 -9999 0 -0.37 52 52
LPAR1 -0.006 0.086 -9999 0 -0.45 17 17
IL8 -0.071 0.11 -9999 0 -0.37 27 27
PTK2 -0.004 0.084 -9999 0 -0.38 9 9
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
CASP3 -0.011 0.086 -9999 0 -0.23 63 63
EGFR 0 0.066 -9999 0 -0.4 14 14
PLCG1 -0.009 0.075 -9999 0 -0.22 46 46
PLD2 -0.004 0.084 -9999 0 -0.38 9 9
G12/G13 0.01 0.066 -9999 0 -0.26 17 17
PI3K-beta -0.014 0.049 -9999 0 -0.3 9 9
cell migration -0.014 0.049 -9999 0 -0.25 16 16
SLC9A3R2 0.011 0 -9999 0 -10000 0 0
PXN 0.007 0.069 -9999 0 -0.3 10 10
HRAS/GTP -0.042 0.14 -9999 0 -0.4 38 38
RAC1 0.011 0 -9999 0 -10000 0 0
MMP9 -0.13 0.17 -9999 0 -0.33 222 222
PRKCE 0.011 0.001 -9999 0 -10000 0 0
PRKCD 0.01 0.061 -9999 0 -0.23 5 5
Gi(beta/gamma) -0.034 0.12 -9999 0 -0.38 38 38
mol:LPA -0.004 0.034 -9999 0 -0.16 22 22
TRIP6/p130 Cas/FAK1/Paxillin -0.023 0.072 -9999 0 -0.38 10 10
MAPKKK cascade -0.04 0.13 -9999 0 -0.39 38 38
contractile ring contraction involved in cytokinesis 0.019 0.03 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.025 0.095 -9999 0 -0.24 79 79
GNA15 -0.003 0.06 -9999 0 -0.22 27 27
GNA12 0.011 0 -9999 0 -10000 0 0
GNA13 0.011 0 -9999 0 -10000 0 0
MAPT 0.009 0.067 -9999 0 -0.23 18 18
GNA11 -0.007 0.066 -9999 0 -0.22 39 39
Rac1/GTP -0.002 0.15 -9999 0 -0.91 14 14
MMP2 -0.01 0.13 -9999 0 -0.54 27 27
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.002 0.071 -9999 0 -0.28 33 33
PDGFRB -0.008 0.086 -9999 0 -0.42 23 23
SPHK1 -0.013 0.024 -9999 0 -10000 0 0
mol:S1P -0.016 0.03 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.081 0.19 -9999 0 -0.42 93 93
GNAO1 -0.1 0.19 -9999 0 -0.41 143 143
PDGFB-D/PDGFRB/PLCgamma1 -0.066 0.18 -9999 0 -0.39 94 94
PLCG1 -0.07 0.18 -9999 0 -0.4 91 91
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.008 0.086 -9999 0 -0.42 23 23
GNAI2 0.011 0.004 -9999 0 -10000 0 0
GNAI3 0.01 0.004 -9999 0 -10000 0 0
GNAI1 0.004 0.052 -9999 0 -0.42 8 8
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.001 0.06 -9999 0 -0.24 33 33
S1P1/S1P -0.023 0.065 -9999 0 -0.27 15 15
negative regulation of cAMP metabolic process -0.078 0.18 -9999 0 -0.41 93 93
MAPK3 -0.091 0.23 -9999 0 -0.53 89 89
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 -0.015 0.1 -9999 0 -0.41 33 33
PLCB2 0.004 0.069 -9999 0 -0.24 15 15
RAC1 0.011 0 -9999 0 -10000 0 0
RhoA/GTP -0.02 0.055 -9999 0 -0.23 14 14
receptor internalization -0.022 0.062 -9999 0 -0.25 15 15
PTGS2 -0.13 0.33 -9999 0 -0.97 66 66
Rac1/GTP -0.02 0.055 -9999 0 -0.23 15 15
RHOA 0.011 0 -9999 0 -10000 0 0
VEGFA 0.011 0.002 -9999 0 -10000 0 0
negative regulation of T cell proliferation -0.078 0.18 -9999 0 -0.41 93 93
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.003 0.074 -9999 0 -0.42 17 17
MAPK1 -0.091 0.23 -9999 0 -0.53 89 89
S1P1/S1P/PDGFB-D/PDGFRB -0.006 0.099 -9999 0 -0.32 27 27
ABCC1 0.01 0.002 -9999 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.019 0.058 0.2 52 -10000 0 52
RFC1 0.019 0.058 0.2 52 -10000 0 52
PRKDC 0.019 0.058 0.2 52 -10000 0 52
RIPK1 0.011 0.002 -10000 0 -10000 0 0
CASP7 -0.002 0.016 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1 0.019 0.065 0.19 62 -0.21 5 67
MAP2K4 0.037 0.056 -10000 0 -0.24 12 12
mol:ceramide 0.028 0.045 -10000 0 -0.24 4 4
GSN 0.017 0.062 0.2 51 -0.22 5 56
FASLG/FAS/FADD/FAF1/Caspase 8 0.038 0.056 0.17 57 -0.25 2 59
FAS 0.007 0.04 -10000 0 -0.41 5 5
BID 0.001 0.016 0.27 2 -10000 0 2
MAP3K1 0.034 0.038 -10000 0 -10000 0 0
MAP3K7 0.011 0.002 -10000 0 -10000 0 0
RB1 0.018 0.06 0.2 51 -0.22 2 53
CFLAR 0.011 0.002 -10000 0 -10000 0 0
HGF/MET -0.064 0.14 -10000 0 -0.26 169 169
ARHGDIB 0.019 0.058 0.2 52 -10000 0 52
FADD 0.011 0.003 -10000 0 -10000 0 0
actin filament polymerization -0.017 0.062 0.22 5 -0.2 51 56
NFKB1 -0.009 0.044 -10000 0 -0.65 1 1
MAPK8 0.036 0.086 -10000 0 -0.41 16 16
DFFA 0.019 0.058 0.2 52 -10000 0 52
DNA fragmentation during apoptosis 0.019 0.058 0.2 52 -10000 0 52
FAS/FADD/MET 0.017 0.038 -10000 0 -0.21 14 14
CFLAR/RIP1 0.015 0.003 -10000 0 -10000 0 0
FAIM3 0.009 0.029 -10000 0 -0.38 3 3
FAF1 0.011 0.004 -10000 0 -10000 0 0
PARP1 0.019 0.058 0.2 52 -10000 0 52
DFFB 0.019 0.058 0.2 52 -10000 0 52
CHUK -0.008 0.039 -10000 0 -0.6 1 1
FASLG 0.003 0.054 -10000 0 -0.36 12 12
FAS/FADD 0.014 0.029 -10000 0 -0.28 5 5
HGF -0.076 0.17 -10000 0 -0.41 112 112
LMNA 0.018 0.054 0.18 52 -10000 0 52
CASP6 0.019 0.058 0.2 52 -10000 0 52
CASP10 0.01 0.026 -10000 0 -0.41 2 2
CASP3 0.022 0.068 0.23 52 -10000 0 52
PTPN13 -0.043 0.14 -10000 0 -0.41 70 70
CASP8 0.001 0.02 0.33 2 -10000 0 2
IL6 -0.005 0.2 -10000 0 -1.2 16 16
MET 0.005 0.049 -10000 0 -0.37 9 9
ICAD/CAD 0.018 0.054 0.18 52 -10000 0 52
FASLG/FAS/FADD/FAF1/Caspase 10 0.028 0.046 -10000 0 -0.24 4 4
activation of caspase activity by cytochrome c 0.001 0.016 0.27 2 -10000 0 2
PAK2 0.019 0.058 0.2 52 -10000 0 52
BCL2 -0.028 0.12 -10000 0 -0.41 50 50
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.012 0.034 -10000 0 -0.25 9 9
CRKL -0.014 0.096 -10000 0 -0.43 9 9
mol:PIP3 -0.009 0.042 0.38 6 -10000 0 6
AKT1 0.005 0.03 0.28 6 -10000 0 6
PTK2B 0.011 0 -10000 0 -10000 0 0
RAPGEF1 -0.008 0.092 -10000 0 -0.46 7 7
RANBP10 0.011 0 -10000 0 -10000 0 0
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
HGF/MET/SHIP2 -0.033 0.11 -10000 0 -0.23 118 118
MAP3K5 0 0.09 -10000 0 -0.39 10 10
HGF/MET/CIN85/CBL/ENDOPHILINS -0.022 0.096 -10000 0 -0.2 114 114
AP1 -0.068 0.12 -10000 0 -0.25 168 168
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.011 0 -10000 0 -10000 0 0
apoptosis -0.21 0.34 -10000 0 -0.72 168 168
STAT3 (dimer) -0.016 0.097 -10000 0 -0.2 117 117
GAB1/CRKL/SHP2/PI3K -0.034 0.076 -10000 0 -0.4 11 11
INPP5D 0.01 0.018 -10000 0 -0.41 1 1
CBL/CRK -0.007 0.092 -10000 0 -0.46 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 0.044 -10000 0 -0.41 6 6
ELK1 -0.003 0.019 -10000 0 -0.14 9 9
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.026 0.052 -10000 0 -0.26 5 5
PAK1 0.01 0.028 0.27 6 -10000 0 6
HGF/MET/RANBP10 -0.033 0.11 -10000 0 -0.23 118 118
HRAS -0.026 0.12 -10000 0 -0.55 7 7
DOCK1 -0.01 0.097 -10000 0 -0.43 11 11
GAB1 -0.021 0.1 -10000 0 -0.42 11 11
CRK -0.014 0.096 -10000 0 -0.43 9 9
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.088 0.17 -10000 0 -0.42 114 114
JUN 0.006 0.047 -10000 0 -0.41 7 7
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.026 0.075 -10000 0 -0.17 114 114
PIK3R1 0.007 0.04 -10000 0 -0.41 5 5
cell morphogenesis -0.001 0.11 -10000 0 -0.4 10 10
GRB2/SHC -0.01 0.067 -10000 0 -0.27 5 5
FOS -0.12 0.19 -10000 0 -0.41 167 167
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.003 0.019 -10000 0 -0.14 9 9
HGF/MET/MUC20 -0.04 0.11 -10000 0 -0.24 118 118
cell migration -0.01 0.067 -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 0.034 -10000 0 -0.25 9 9
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.02 0.096 -10000 0 -0.2 117 117
MET/MUC20 0.004 0.034 -10000 0 -0.26 9 9
RAP1B -0.002 0.087 -10000 0 -0.43 7 7
RAP1A -0.002 0.087 -10000 0 -0.43 7 7
HGF/MET/RANBP9 -0.033 0.11 -10000 0 -0.23 118 118
RAF1 -0.019 0.11 -10000 0 -0.51 7 7
STAT3 -0.016 0.098 -10000 0 -0.2 117 117
cell proliferation -0.025 0.13 -10000 0 -0.28 114 114
RPS6KB1 -0.003 0.029 -10000 0 -0.14 3 3
MAPK3 -0.007 0.018 -10000 0 -10000 0 0
MAPK1 -0.007 0.018 -10000 0 -10000 0 0
RANBP9 0.011 0 -10000 0 -10000 0 0
MAPK8 0.01 0.096 -10000 0 -0.44 11 11
SRC -0.012 0.091 -10000 0 -0.37 5 5
PI3K -0.012 0.073 -10000 0 -0.29 10 10
MET/Glomulin 0.006 0.03 -10000 0 -0.22 9 9
SOS1 0.011 0 -10000 0 -10000 0 0
MAP2K1 -0.012 0.11 -10000 0 -0.55 5 5
MET 0.005 0.049 -10000 0 -0.37 9 9
MAP4K1 -0.006 0.092 -10000 0 -0.46 7 7
PTK2 0.011 0 -10000 0 -10000 0 0
MAP2K2 -0.012 0.11 -10000 0 -0.55 5 5
BAD 0.01 0.028 0.27 6 -10000 0 6
MAP2K4 0.006 0.084 -10000 0 -0.36 10 10
SHP2/GRB2/SOS1/GAB1 -0.034 0.076 -10000 0 -0.42 9 9
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 -0.018 0.07 -10000 0 -0.15 114 114
PLCgamma1/PKC 0.008 0 -10000 0 -10000 0 0
HGF -0.076 0.17 -10000 0 -0.41 112 112
RASA1 0.007 0.04 -10000 0 -0.41 5 5
NCK1 0.009 0.025 -10000 0 -0.41 2 2
PTPRJ 0.011 0 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.013 0.076 -10000 0 -0.16 115 115
PDPK1 -0.002 0.034 0.31 6 -10000 0 6
HGF/MET/SHIP -0.033 0.11 -10000 0 -0.23 119 119
Glypican 2 network

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
MDK 0.01 0.015 -9999 0 -0.33 1 1
GPC2 -0.014 0.089 -9999 0 -0.33 40 40
GPC2/Midkine -0.001 0.062 -9999 0 -0.22 41 41
neuron projection morphogenesis -0.001 0.061 -9999 0 -0.22 41 41
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 0.066 -9999 0 -0.4 14 14
EGF/EGFR -0.067 0.099 -9999 0 -0.2 175 175
EGF/EGFR dimer/SHC/GRB2/SOS1 0.019 0.049 -9999 0 -0.34 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.12 0.19 -9999 0 -0.41 163 163
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.006 0.073 -9999 0 -0.34 25 25
EGF/EGFR dimer/SHC 0.006 0.058 -9999 0 -0.2 38 38
mol:GDP -0.011 0.041 -9999 0 -0.33 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.006 0.047 -9999 0 -0.41 7 7
GRB2/SOS1 0.016 0 -9999 0 -10000 0 0
HRAS/GTP -0.01 0.036 -9999 0 -0.3 1 1
SHC1 0.011 0 -9999 0 -10000 0 0
HRAS/GDP -0.01 0.037 -9999 0 -0.31 1 1
FRAP1 0.015 0.046 -9999 0 -0.32 1 1
EGF/EGFR dimer -0.003 0.069 -9999 0 -0.25 38 38
SOS1 0.011 0 -9999 0 -10000 0 0
GRB2 0.011 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.076 0.14 -9999 0 -0.28 167 167
Arf6 signaling events

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
CENTA1/KIF3B 0.015 0 -9999 0 -10000 0 0
ARNO/beta Arrestin1-2 -0.02 0.068 -9999 0 -0.34 1 1
EGFR 0 0.066 -9999 0 -0.4 14 14
EPHA2 0.011 0 -9999 0 -10000 0 0
USP6 0.011 0 -9999 0 -10000 0 0
IQSEC1 0.01 0.018 -9999 0 -0.41 1 1
EGFR/EGFR/EGF/EGF -0.003 0.069 -9999 0 -0.25 38 38
ARRB2 0.008 0.002 -9999 0 -10000 0 0
mol:GTP 0.015 0.011 -9999 0 -0.14 1 1
ARRB1 0.009 0.025 -9999 0 -0.41 2 2
FBXO8 0.011 0 -9999 0 -10000 0 0
TSHR -0.006 0.071 -9999 0 -0.34 23 23
EGF -0.006 0.073 -9999 0 -0.34 25 25
somatostatin receptor activity 0 0 -9999 0 -0.001 75 75
ARAP2 0.009 0.031 -9999 0 -0.41 3 3
mol:GDP -0.046 0.091 -9999 0 -0.22 81 81
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 50 50
ITGA2B 0.005 0.05 -9999 0 -0.4 8 8
ARF6 0.011 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.027 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 -0.049 0.12 -9999 0 -0.28 118 118
PXN 0.011 0 -9999 0 -10000 0 0
ARF6/GTP -0.041 0.095 -9999 0 -0.22 71 71
EGFR/EGFR/EGF/EGF/ARFGEP100 0.006 0.059 -9999 0 -0.2 39 39
ADRB2 -0.063 0.16 -9999 0 -0.41 95 95
receptor agonist activity 0 0 -9999 0 0 78 78
actin filament binding 0 0 -9999 0 0 76 76
SRC 0.011 0 -9999 0 -10000 0 0
ITGB3 -0.068 0.16 -9999 0 -0.41 102 102
GNAQ 0.009 0.026 -9999 0 -0.41 2 2
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 63 63
ARF6/GDP 0.017 0.048 -9999 0 -0.28 5 5
ARF6/GDP/GULP/ACAP1 -0.047 0.11 -9999 0 -0.31 57 57
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.017 0.091 -9999 0 -0.2 107 107
ACAP1 0.008 0.036 -9999 0 -0.36 5 5
ACAP2 0.01 0.018 -9999 0 -0.41 1 1
LHCGR/beta Arrestin2 0.001 0.004 -9999 0 -10000 0 0
EFNA1 0.01 0.021 -9999 0 -0.33 2 2
HGF -0.076 0.17 -9999 0 -0.41 112 112
CYTH3 0.009 0 -9999 0 -10000 0 0
CYTH2 0.007 0.002 -9999 0 -10000 0 0
NCK1 0.009 0.025 -9999 0 -0.41 2 2
fibronectin binding 0 0 -9999 0 0 64 64
endosomal lumen acidification 0 0 0 1 0 46 47
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.036 0.13 -9999 0 -0.41 61 61
GNAQ/ARNO 0.012 0.013 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 0 2 2
PIP3-E 0 0 -9999 0 0 14 14
MET 0.005 0.049 -9999 0 -0.37 9 9
GNA14 -0.031 0.13 -9999 0 -0.41 54 54
GNA15 0.007 0.038 -9999 0 -0.33 7 7
GIT1 0.011 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 66 66
GNA11 0.002 0.062 -9999 0 -0.41 12 12
LHCGR 0.001 0.003 -9999 0 -10000 0 0
AGTR1 -0.086 0.17 -9999 0 -0.41 122 122
desensitization of G-protein coupled receptor protein signaling pathway 0.001 0.004 -9999 0 -10000 0 0
IPCEF1/ARNO 0.006 0.044 -9999 0 -0.31 1 1
alphaIIb/beta3 Integrin -0.043 0.12 -9999 0 -0.28 110 110
RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.007 0.049 -10000 0 -1.1 1 1
VDR 0.003 0.052 -10000 0 -0.33 13 13
FAM120B 0.011 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.01 0.086 -10000 0 -0.26 22 22
RXRs/LXRs/DNA/Oxysterols 0.016 0.087 -10000 0 -0.27 22 22
MED1 0.011 0 -10000 0 -10000 0 0
mol:9cRA 0.003 0.007 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.026 0.11 -10000 0 -0.21 129 129
RXRs/NUR77 -0.011 0.1 -10000 0 -0.22 97 97
RXRs/PPAR -0.007 0.091 -10000 0 -0.23 31 31
NCOR2 0.011 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.003 0.036 -10000 0 -0.22 13 13
RARs/VDR/DNA/Vit D3 0.018 0.039 -10000 0 -0.19 11 11
RARA 0.011 0 -10000 0 -10000 0 0
NCOA1 0.01 0.018 -10000 0 -0.41 1 1
VDR/VDR/DNA 0.003 0.052 -10000 0 -0.33 13 13
RARs/RARs/DNA/9cRA 0.018 0.03 -10000 0 -0.19 11 11
RARG 0.011 0 -10000 0 -10000 0 0
RPS6KB1 0.012 0.03 -10000 0 -0.4 1 1
RARs/THRs/DNA/SMRT -0.026 0.1 -10000 0 -0.2 129 129
THRA 0.002 0.059 -10000 0 -0.41 11 11
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.003 0.036 -10000 0 -0.22 13 13
RXRs/PPAR/9cRA/PGJ2/DNA 0 0.085 0.28 1 -0.21 71 72
NR1H4 -0.009 0.061 -10000 0 -0.33 19 19
RXRs/LXRs/DNA 0.017 0.084 -10000 0 -0.23 21 21
NR1H2 0.014 0.006 -10000 0 -10000 0 0
NR1H3 0.014 0.015 -10000 0 -0.32 1 1
RXRs/VDR/DNA/Vit D3 -0.001 0.082 -10000 0 -0.2 70 70
NR4A1 -0.016 0.1 -10000 0 -0.41 35 35
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.003 0.072 -10000 0 -0.18 70 70
RXRG -0.046 0.15 -10000 0 -0.4 79 79
RXR alpha/CCPG 0.018 0.007 -10000 0 -10000 0 0
RXRA 0.014 0.006 -10000 0 -10000 0 0
RXRB 0.015 0.005 -10000 0 -10000 0 0
THRB -0.078 0.17 -10000 0 -0.41 115 115
PPARG -0.012 0.096 -10000 0 -0.41 30 30
PPARD 0.011 0 -10000 0 -10000 0 0
TNF 0.011 0.11 -10000 0 -0.99 2 2
mol:Oxysterols 0.003 0.006 -10000 0 -10000 0 0
cholesterol transport 0.016 0.086 -10000 0 -0.27 22 22
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 -0.41 11 11
RXRs/NUR77/BCL2 -0.039 0.13 -10000 0 -0.25 128 128
SREBF1 0.022 0.08 -10000 0 -0.5 1 1
RXRs/RXRs/DNA/9cRA 0 0.085 0.27 1 -0.21 71 72
ABCA1 0.022 0.08 -10000 0 -0.5 1 1
RARs/THRs -0.021 0.099 -10000 0 -0.19 129 129
RXRs/FXR -0.007 0.091 -10000 0 -0.22 71 71
BCL2 -0.028 0.12 -10000 0 -0.41 50 50
Syndecan-4-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
PTK2 0.014 0.043 -9999 0 -0.41 5 5
Syndecan-4/Syndesmos -0.012 0.069 -9999 0 -10000 0 0
positive regulation of JNK cascade -0.12 0.11 -9999 0 -0.35 37 37
Syndecan-4/ADAM12 -0.015 0.072 -9999 0 -10000 0 0
CCL5 0.003 0.053 -9999 0 -0.37 11 11
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
DNM2 0.011 0 -9999 0 -10000 0 0
ITGA5 0.011 0 -9999 0 -10000 0 0
SDCBP 0.011 0 -9999 0 -10000 0 0
PLG -0.028 0.12 -9999 0 -0.38 55 55
ADAM12 0.003 0.05 -9999 0 -0.33 12 12
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 -0.039 0.042 -9999 0 -0.12 36 36
Syndecan-4/Laminin alpha1 -0.062 0.096 -9999 0 -0.34 18 18
Syndecan-4/CXCL12/CXCR4 -0.12 0.11 -9999 0 -0.37 37 37
Syndecan-4/Laminin alpha3 -0.017 0.075 -9999 0 -10000 0 0
MDK 0.01 0.015 -9999 0 -0.33 1 1
Syndecan-4/FZD7 -0.042 0.099 -9999 0 -0.4 7 7
Syndecan-4/Midkine -0.012 0.07 -9999 0 -10000 0 0
FZD7 -0.055 0.15 -9999 0 -0.41 85 85
Syndecan-4/FGFR1/FGF -0.11 0.1 -9999 0 -0.36 33 33
THBS1 -0.046 0.14 -9999 0 -0.41 74 74
integrin-mediated signaling pathway -0.016 0.074 -9999 0 -0.37 2 2
positive regulation of MAPKKK cascade -0.12 0.11 -9999 0 -0.35 37 37
Syndecan-4/TACI -0.018 0.076 -9999 0 -0.37 1 1
CXCR4 0.011 0 -9999 0 -10000 0 0
cell adhesion 0.013 0.051 -9999 0 -0.16 40 40
Syndecan-4/Dynamin -0.012 0.069 -9999 0 -10000 0 0
Syndecan-4/TSP1 -0.038 0.095 -9999 0 -0.38 8 8
Syndecan-4/GIPC -0.012 0.069 -9999 0 -10000 0 0
Syndecan-4/RANTES -0.015 0.074 -9999 0 -0.36 2 2
ITGB1 0.011 0 -9999 0 -10000 0 0
LAMA1 -0.1 0.16 -9999 0 -0.33 183 183
LAMA3 -0.001 0.069 -9999 0 -0.41 15 15
RAC1 0.011 0 -9999 0 -10000 0 0
PRKCA -0.007 0.1 -9999 0 -0.37 36 36
Syndecan-4/alpha-Actinin -0.012 0.069 -9999 0 -10000 0 0
TFPI -0.039 0.14 -9999 0 -0.41 64 64
F2 -0.024 0.095 -9999 0 -0.33 48 48
alpha5/beta1 Integrin 0.016 0 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.06 0.097 -9999 0 -0.35 10 10
ACTN1 0.011 0 -9999 0 -10000 0 0
TNC 0 0.066 -9999 0 -0.4 14 14
Syndecan-4/CXCL12 -0.13 0.12 -9999 0 -0.38 37 37
FGF6 0 0 -9999 0 -10000 0 0
RHOA 0.011 0 -9999 0 -10000 0 0
CXCL12 -0.26 0.2 -9999 0 -0.41 345 345
TNFRSF13B -0.002 0.059 -9999 0 -0.33 17 17
FGF2 -0.22 0.21 -9999 0 -0.41 295 295
FGFR1 0.01 0.018 -9999 0 -0.41 1 1
Syndecan-4/PI-4-5-P2 -0.018 0.069 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 0.011 0.039 -9999 0 -0.39 5 5
cell migration -0.017 0.019 -9999 0 -10000 0 0
PRKCD 0.015 0.008 -9999 0 -10000 0 0
vasculogenesis -0.037 0.092 -9999 0 -0.37 8 8
SDC4 -0.019 0.072 -9999 0 -10000 0 0
Syndecan-4/Tenascin C -0.017 0.076 -9999 0 -0.38 2 2
Syndecan-4/PI-4-5-P2/PKC alpha -0.031 0.034 -9999 0 -0.11 1 1
Syndecan-4/Syntenin -0.012 0.069 -9999 0 -10000 0 0
MMP9 -0.13 0.17 -9999 0 -0.33 222 222
Rac1/GTP 0.013 0.052 -9999 0 -0.16 40 40
cytoskeleton organization -0.011 0.068 -9999 0 -10000 0 0
GIPC1 0.011 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.034 0.097 -9999 0 -0.38 11 11
Coregulation of Androgen receptor activity

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
NRIP1 0.009 0.031 -9999 0 -0.41 3 3
SVIL -0.036 0.13 -9999 0 -0.41 61 61
ZNF318 0.01 0.005 -9999 0 -10000 0 0
JMJD2C -0.004 0.031 -9999 0 -0.11 38 38
T-DHT/AR/Ubc9 -0.026 0.1 -9999 0 -0.24 93 93
CARM1 0.011 0 -9999 0 -10000 0 0
PRDX1 0.011 0 -9999 0 -10000 0 0
PELP1 0.011 0.001 -9999 0 -10000 0 0
CTNNB1 0.011 0.002 -9999 0 -10000 0 0
AKT1 0.011 0.001 -9999 0 -10000 0 0
PTK2B 0.011 0.002 -9999 0 -10000 0 0
MED1 0.011 0.002 -9999 0 -10000 0 0
MAK -0.014 0.087 -9999 0 -0.33 38 38
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.007 0.04 -9999 0 -0.41 5 5
GSN 0.007 0.044 -9999 0 -0.41 6 6
NCOA2 -0.004 0.077 -9999 0 -0.41 19 19
NCOA6 0.011 0.002 -9999 0 -10000 0 0
DNA-PK 0.022 0.005 -9999 0 -10000 0 0
NCOA4 0.011 0 -9999 0 -10000 0 0
PIAS3 0.011 0.002 -9999 0 -10000 0 0
cell proliferation -0.013 0.024 -9999 0 -10000 0 0
XRCC5 0.011 0.001 -9999 0 -10000 0 0
UBE3A 0.012 0.002 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.047 0.12 -9999 0 -0.25 131 131
FHL2 0.001 0.11 -9999 0 -0.98 5 5
RANBP9 0.011 0.002 -9999 0 -10000 0 0
JMJD1A 0.005 0.03 -9999 0 -0.13 23 23
CDK6 0.001 0.064 -9999 0 -0.41 13 13
TGFB1I1 -0.12 0.2 -9999 0 -0.41 176 176
T-DHT/AR/CyclinD1 -0.026 0.11 -9999 0 -0.24 95 95
XRCC6 0.011 0.001 -9999 0 -10000 0 0
T-DHT/AR -0.021 0.12 -9999 0 -0.26 100 100
CTDSP1 0.011 0.001 -9999 0 -10000 0 0
CTDSP2 0.01 0.003 -9999 0 -10000 0 0
BRCA1 0.011 0.002 -9999 0 -10000 0 0
TCF4 -0.005 0.079 -9999 0 -0.41 20 20
CDKN2A -0.13 0.17 -9999 0 -0.33 228 228
SRF 0.016 0.011 -9999 0 -10000 0 0
NKX3-1 -0.023 0.17 -9999 0 -0.9 17 17
KLK3 -0.006 0.044 -9999 0 -10000 0 0
TMF1 0.011 0.001 -9999 0 -10000 0 0
HNRNPA1 0.011 0.002 -9999 0 -10000 0 0
AOF2 0 0.002 -9999 0 -10000 0 0
APPL1 0.018 0.003 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.026 0.1 -9999 0 -0.24 93 93
AR -0.062 0.16 -9999 0 -0.42 93 93
UBA3 0.011 0.001 -9999 0 -10000 0 0
PATZ1 0.011 0.002 -9999 0 -10000 0 0
PAWR 0.011 0.001 -9999 0 -10000 0 0
PRKDC 0.011 0.001 -9999 0 -10000 0 0
PA2G4 0.011 0.002 -9999 0 -10000 0 0
UBE2I 0.011 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.022 0.094 -9999 0 -0.22 93 93
RPS6KA3 0.011 0.018 -9999 0 -0.41 1 1
T-DHT/AR/ARA70 -0.026 0.1 -9999 0 -0.24 93 93
LATS2 0.01 0.018 -9999 0 -0.41 1 1
T-DHT/AR/PRX1 -0.022 0.094 -9999 0 -0.22 93 93
Cyclin D3/CDK11 p58 0.008 0 -9999 0 -10000 0 0
VAV3 -0.068 0.14 -9999 0 -0.33 127 127
KLK2 -0.067 0.2 -9999 0 -0.87 29 29
CASP8 0.011 0.001 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.023 0.11 -9999 0 -0.23 106 106
TMPRSS2 -0.018 0.14 -9999 0 -0.64 17 17
CCND1 0.009 0.025 -9999 0 -0.33 3 3
PIAS1 0.012 0.002 -9999 0 -10000 0 0
mol:T-DHT -0.001 0.02 -9999 0 -0.066 36 36
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.012 0.004 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.032 0.11 -9999 0 -0.25 107 107
CMTM2 0.009 0.025 -9999 0 -0.33 3 3
SNURF -0.024 0.11 -9999 0 -0.41 42 42
ZMIZ1 0.008 0.037 -9999 0 -0.42 3 3
CCND3 0.011 0 -9999 0 -10000 0 0
TGIF1 0.011 0.002 -9999 0 -10000 0 0
FKBP4 0.011 0.002 -9999 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.004 0.056 -9999 0 -0.2 37 37
RGS9BP -0.005 0.07 -9999 0 -0.33 24 24
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0.002 0.015 -9999 0 -0.33 1 1
mol:Na + -0.005 0.054 -9999 0 -0.23 30 30
mol:ADP 0.007 0.015 -9999 0 -0.22 2 2
GNAT2 0.007 0.025 -9999 0 -0.33 3 3
RGS9-1/Gbeta5/R9AP -0.041 0.11 -9999 0 -0.22 139 139
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.007 0.015 -9999 0 -0.19 3 3
GRK7 0.006 0.015 -9999 0 -0.33 1 1
CNGB3 -0.014 0.089 -9999 0 -0.41 26 26
Cone Metarhodopsin II/X-Arrestin 0.002 0.01 -9999 0 -0.22 1 1
mol:Ca2+ -0.002 0.05 -9999 0 -0.2 31 31
Cone PDE6 -0.031 0.092 -9999 0 -0.19 118 118
Cone Metarhodopsin II 0.006 0.011 -9999 0 -0.16 2 2
Na + (4 Units) -0.002 0.05 -9999 0 -0.2 31 31
GNAT2/GDP -0.03 0.093 -9999 0 -0.19 118 118
GNB5 0.011 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.008 0.016 -9999 0 -0.16 4 4
Cone Transducin 0.004 0.06 -9999 0 -0.21 37 37
SLC24A2 0.004 0.015 -9999 0 -0.33 1 1
GNB3/GNGT2 -0.003 0.075 -9999 0 -0.29 35 35
GNB3 -0.015 0.1 -9999 0 -0.41 33 33
GNAT2/GTP 0.006 0.017 -9999 0 -0.22 3 3
CNGA3 0.004 0.029 -9999 0 -0.33 4 4
ARR3 0.003 0.015 -9999 0 -0.33 1 1
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.005 0.055 -9999 0 -0.23 30 30
mol:Pi -0.041 0.11 -9999 0 -0.22 139 139
Cone CNG Channel -0.011 0.042 -9999 0 -0.18 26 26
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + 0.004 0.015 -9999 0 -0.33 1 1
RGS9 -0.08 0.17 -9999 0 -0.41 118 118
PDE6C 0.003 0.015 -9999 0 -0.33 1 1
GNGT2 0.009 0.031 -9999 0 -0.41 3 3
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.002 0.004 -9999 0 -10000 0 0
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.1 0.19 -10000 0 -0.41 149 149
HRAS 0.011 0 -10000 0 -10000 0 0
EGFR 0 0.066 -10000 0 -0.4 14 14
AKT -0.068 0.13 -10000 0 -0.23 201 201
FOXO3 0.011 0 -10000 0 -10000 0 0
AKT1 0.011 0 -10000 0 -10000 0 0
FOXO1 0.009 0.031 -10000 0 -0.41 3 3
AKT3 -0.15 0.2 -10000 0 -0.41 204 204
FOXO4 0.009 0.025 -10000 0 -0.41 2 2
MET 0.005 0.049 -10000 0 -0.37 9 9
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
PIK3CB 0.011 0 -10000 0 -10000 0 0
NRAS 0.011 0 -10000 0 -10000 0 0
PIK3CG -0.001 0.07 -10000 0 -0.4 16 16
PIK3R3 0.01 0.015 -10000 0 -0.33 1 1
PIK3R2 0.011 0 -10000 0 -10000 0 0
NF1 0.009 0.025 -10000 0 -0.41 2 2
RAS -0.022 0.073 0.18 1 -0.26 14 15
ERBB2 0.002 0.054 -10000 0 -0.33 14 14
proliferation/survival/translation 0.011 0.066 0.22 20 -10000 0 20
PI3K -0.013 0.074 0.15 2 -0.21 27 29
PIK3R1 0.007 0.04 -10000 0 -0.41 5 5
KRAS 0.01 0.015 -10000 0 -0.33 1 1
FOXO 0.023 0.022 -10000 0 -10000 0 0
AKT2 0.011 0 -10000 0 -10000 0 0
PTEN 0.006 0.044 -10000 0 -0.41 6 6
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.011 0 -9999 0 -10000 0 0
VLDLR 0.009 0.025 -9999 0 -0.41 2 2
LRPAP1 0.011 0 -9999 0 -10000 0 0
NUDC 0.011 0 -9999 0 -10000 0 0
RELN/LRP8 -0.071 0.12 -9999 0 -0.23 202 202
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 -0.058 0.11 -9999 0 -0.2 196 196
IQGAP1/CaM 0.016 0 -9999 0 -10000 0 0
DAB1 -0.001 0.052 -9999 0 -0.33 13 13
IQGAP1 0.011 0 -9999 0 -10000 0 0
PLA2G7 0.006 0.043 -9999 0 -0.4 6 6
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 0.022 -9999 0 -0.22 5 5
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.011 0 -9999 0 -10000 0 0
CDK5R1 0.01 0.015 -9999 0 -0.33 1 1
LIS1/Poliovirus Protein 3A 0.013 0 -9999 0 -10000 0 0
CDK5R2 -0.028 0.1 -9999 0 -0.33 57 57
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.077 0.12 -9999 0 -0.23 197 197
YWHAE 0.011 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.032 0.091 -9999 0 -0.22 18 18
MAP1B -0.012 0.055 -9999 0 -0.25 27 27
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.039 0.097 -9999 0 -0.3 3 3
RELN -0.14 0.2 -9999 0 -0.41 200 200
PAFAH/LIS1 0.019 0.025 -9999 0 -0.22 6 6
LIS1/CLIP170 0.022 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.039 0.054 -9999 0 -0.21 2 2
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.05 0.1 -9999 0 -0.19 195 195
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.04 0.095 -9999 0 -0.24 18 18
LIS1/IQGAP1 0.022 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.018 0 -9999 0 -10000 0 0
PAFAH1B3 0.005 0.043 -9999 0 -0.33 9 9
PAFAH1B2 0.01 0.018 -9999 0 -0.41 1 1
MAP1B/LIS1/Dynein heavy chain 0.012 0.037 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.027 0.088 -9999 0 -0.26 2 2
LRP8 0.008 0.032 -9999 0 -0.33 5 5
NDEL1/Katanin 60 -0.032 0.091 -9999 0 -0.22 18 18
P39/CDK5 -0.057 0.1 -9999 0 -0.31 19 19
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.022 0 -9999 0 -10000 0 0
CDK5 -0.048 0.1 -9999 0 -0.28 4 4
PPP2R5D 0.011 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.019 0 -9999 0 -10000 0 0
CSNK2A1 0.011 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.052 0.1 -9999 0 -0.34 2 2
RELN/VLDLR -0.057 0.11 -9999 0 -0.2 195 195
CDC42 0 0 -9999 0 -10000 0 0
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 0.008 0.045 -9999 0 -0.24 15 15
NFATC2 -0.011 0.079 -9999 0 -0.24 55 55
NFATC3 0.015 0.018 -9999 0 -10000 0 0
CD40LG -0.056 0.18 -9999 0 -0.47 50 50
PTGS2 -0.076 0.21 -9999 0 -0.49 79 79
JUNB 0.007 0.04 -9999 0 -0.41 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.007 -9999 0 -10000 0 0
CaM/Ca2+ -0.001 0.007 -9999 0 -10000 0 0
CALM1 0.011 0.005 -9999 0 -10000 0 0
JUN 0.006 0.048 -9999 0 -0.41 7 7
mol:Ca2+ -0.002 0.007 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.004 0.004 -9999 0 -10000 0 0
FOSL1 -0.015 0.091 -9999 0 -0.33 42 42
CREM 0.011 0.001 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.036 0.082 -9999 0 -0.32 23 23
FOS -0.12 0.2 -9999 0 -0.41 167 167
IFNG -0.067 0.19 -9999 0 -0.48 61 61
AP-1/NFAT1-c-4 -0.064 0.2 -9999 0 -0.49 57 57
FASLG -0.055 0.18 -9999 0 -0.5 40 40
NFAT1-c-4/ICER1 -0.011 0.082 -9999 0 -0.27 24 24
IL2RA -0.056 0.18 -9999 0 -0.5 43 43
FKBP12/FK506 0.008 0 -9999 0 -10000 0 0
CSF2 -0.056 0.18 -9999 0 -0.46 45 45
JunB/Fra1/NFAT1-c-4 -0.022 0.085 -9999 0 -0.27 25 25
IL4 -0.056 0.17 -9999 0 -0.45 46 46
IL2 -0.009 0.03 -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 0.015 -9999 0 -0.33 1 1
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.011 0 -9999 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.011 0 -9999 0 -10000 0 0
GNAT1/GTP 0.002 0.024 -9999 0 -0.22 6 6
Metarhodopsin II/Arrestin 0.006 0.015 -9999 0 -0.18 3 3
PDE6G/GNAT1/GTP -0.008 0.059 -9999 0 -0.18 53 53
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.002 0.035 -9999 0 -0.33 6 6
GRK1 0.002 0.015 -9999 0 -0.33 1 1
CNG Channel -0.03 0.064 -9999 0 -0.28 14 14
mol:Na + -0.019 0.054 -9999 0 -0.34 6 6
mol:ADP 0.002 0.015 -9999 0 -0.33 1 1
RGS9-1/Gbeta5/R9AP -0.041 0.11 -9999 0 -0.22 139 139
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.019 0.055 -9999 0 -0.34 6 6
CNGB1 -0.008 0.076 -9999 0 -0.33 29 29
RDH5 0.009 0.025 -9999 0 -0.33 3 3
SAG 0.005 0.005 -9999 0 -10000 0 0
mol:Ca2+ 0.01 0.061 -9999 0 -0.32 6 6
Na + (4 Units) -0.017 0.049 -9999 0 -0.31 6 6
RGS9 -0.08 0.17 -9999 0 -0.41 118 118
GNB1/GNGT1 -0.067 0.11 -9999 0 -0.22 193 193
GNAT1/GDP -0.032 0.093 -9999 0 -0.2 119 119
GUCY2D 0 0.052 -9999 0 -0.33 13 13
GNGT1 -0.11 0.16 -9999 0 -0.33 193 193
GUCY2F 0.005 0.005 -9999 0 -10000 0 0
GNB5 0.011 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.003 0.066 -9999 0 -0.21 23 23
mol:11-cis-retinal 0.009 0.025 -9999 0 -0.33 3 3
mol:cGMP 0.007 0.046 -9999 0 -0.25 4 4
GNB1 0.011 0 -9999 0 -10000 0 0
Rhodopsin 0.009 0.024 -9999 0 -0.22 6 6
SLC24A1 0.011 0 -9999 0 -10000 0 0
CNGA1 0.001 0.056 -9999 0 -0.33 15 15
Metarhodopsin II 0.004 0.015 -9999 0 -0.16 4 4
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family 0.004 0.049 -9999 0 -0.23 10 10
RGS9BP -0.005 0.07 -9999 0 -0.33 24 24
Metarhodopsin II/Transducin -0.014 0.038 -9999 0 -10000 0 0
GCAP Family/Ca ++ 0.003 0.04 -9999 0 -0.18 25 25
PDE6A/B 0.002 0.062 -9999 0 -0.26 28 28
mol:Pi -0.041 0.11 -9999 0 -0.22 139 139
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.046 0.087 -9999 0 -0.32 5 5
PDE6B -0.007 0.085 -9999 0 -0.4 24 24
PDE6A 0.008 0.029 -9999 0 -0.33 4 4
PDE6G -0.019 0.097 -9999 0 -0.33 48 48
RHO 0.003 0.025 -9999 0 -0.33 3 3
PDE6 -0.061 0.089 -9999 0 -0.33 21 21
GUCA1A -0.003 0.059 -9999 0 -0.33 17 17
GC2/GCAP Family 0.006 0.04 -9999 0 -0.21 8 8
GUCA1C 0 0 -9999 0 -10000 0 0
GUCA1B 0.005 0.051 -9999 0 -0.41 8 8
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.005 0.047 -10000 0 -0.22 22 22
cell-cell adhesion 0.029 0.062 0.3 8 -10000 0 8
Ephrin B/EPHB2/RasGAP 0.008 0.069 -10000 0 -0.18 60 60
ITSN1 0.011 0 -10000 0 -10000 0 0
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
SHC1 0.011 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.006 0.045 -10000 0 -0.2 22 22
Ephrin B1/EPHB1 -0.009 0.073 -10000 0 -0.23 53 53
HRAS/GDP -0.029 0.066 -10000 0 -0.2 45 45
Ephrin B/EPHB1/GRB7 -0.02 0.097 -10000 0 -0.2 101 101
Endophilin/SYNJ1 0.008 0.062 -10000 0 -0.17 55 55
KRAS 0.01 0.015 -10000 0 -0.33 1 1
Ephrin B/EPHB1/Src -0.009 0.09 -10000 0 -0.19 99 99
endothelial cell migration -0.003 0.025 -10000 0 -0.18 10 10
GRB2 0.011 0 -10000 0 -10000 0 0
GRB7 -0.011 0.084 -10000 0 -0.33 34 34
PAK1 0.012 0.067 -10000 0 -0.36 3 3
HRAS 0.011 0 -10000 0 -10000 0 0
RRAS 0.008 0.063 -10000 0 -0.17 55 55
DNM1 0.006 0.044 -10000 0 -0.41 6 6
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.01 0.085 -10000 0 -0.18 99 99
lamellipodium assembly -0.029 0.062 -10000 0 -0.3 8 8
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.008 0.088 -10000 0 -0.21 53 53
PIK3R1 0.007 0.04 -10000 0 -0.41 5 5
EPHB2 0.009 0.025 -10000 0 -0.33 3 3
EPHB3 -0.004 0.072 -10000 0 -0.35 22 22
EPHB1 -0.029 0.12 -10000 0 -0.41 52 52
EPHB4 0.01 0.018 -10000 0 -0.41 1 1
mol:GDP -0.001 0.083 -10000 0 -0.22 45 45
Ephrin B/EPHB2 0.004 0.066 -10000 0 -0.19 55 55
Ephrin B/EPHB3 -0.003 0.083 -10000 0 -0.22 58 58
JNK cascade 0.009 0.064 -10000 0 -0.18 52 52
Ephrin B/EPHB1 -0.016 0.09 -10000 0 -0.2 99 99
RAP1/GDP 0.01 0.075 -10000 0 -0.27 9 9
EFNB2 0.009 0.031 -10000 0 -0.41 3 3
EFNB3 -0.029 0.12 -10000 0 -0.41 52 52
EFNB1 0.01 0.018 -10000 0 -0.41 1 1
Ephrin B2/EPHB1-2 -0.002 0.069 -10000 0 -0.2 58 58
RAP1B 0.011 0 -10000 0 -10000 0 0
RAP1A 0.011 0 -10000 0 -10000 0 0
CDC42/GTP -0.034 0.072 -10000 0 -0.35 8 8
Rap1/GTP -0.029 0.061 -10000 0 -0.31 8 8
axon guidance 0.005 0.047 -10000 0 -0.22 22 22
MAPK3 0.004 0.079 -10000 0 -0.32 7 7
MAPK1 0.004 0.079 -10000 0 -0.32 7 7
Rac1/GDP 0.006 0.078 -10000 0 -0.2 45 45
actin cytoskeleton reorganization -0.023 0.05 -10000 0 -0.25 8 8
CDC42/GDP 0.006 0.078 -10000 0 -0.2 45 45
PI3K 0.022 0.028 -10000 0 -0.19 10 10
EFNA5 -0.003 0.076 -10000 0 -0.4 19 19
Ephrin B2/EPHB4 0.013 0.021 -10000 0 -0.23 4 4
Ephrin B/EPHB2/Intersectin/N-WASP 0.007 0.068 -10000 0 -0.19 55 55
CDC42 0.011 0 -10000 0 -10000 0 0
RAS family/GTP -0.028 0.06 -10000 0 -0.3 8 8
PTK2 0.006 0.018 -10000 0 -10000 0 0
MAP4K4 0.009 0.065 -10000 0 -0.18 52 52
SRC 0.011 0 -10000 0 -10000 0 0
KALRN 0.007 0.04 -10000 0 -0.41 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 -0.002 0.083 -10000 0 -0.35 7 7
WASL 0.011 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.005 0.07 -10000 0 -0.2 52 52
cell migration -0.003 0.097 -10000 0 -0.34 10 10
NRAS 0.011 0 -10000 0 -10000 0 0
SYNJ1 0.008 0.063 -10000 0 -0.17 55 55
PXN 0.011 0 -10000 0 -10000 0 0
TF 0.005 0.072 -10000 0 -0.32 5 5
HRAS/GTP -0.032 0.067 -10000 0 -0.33 8 8
Ephrin B1/EPHB1-2 -0.002 0.067 -10000 0 -0.2 56 56
cell adhesion mediated by integrin 0.018 0.067 0.21 55 -10000 0 55
RAC1 0.011 0 -10000 0 -10000 0 0
mol:GTP -0.006 0.086 -10000 0 -0.35 8 8
RAC1-CDC42/GTP -0.033 0.071 -10000 0 -0.3 19 19
RASA1 0.007 0.04 -10000 0 -0.41 5 5
RAC1-CDC42/GDP 0.01 0.075 -10000 0 -0.27 9 9
ruffle organization 0.01 0.08 -10000 0 -0.31 8 8
NCK1 0.009 0.025 -10000 0 -0.41 2 2
receptor internalization 0.012 0.067 -10000 0 -0.35 5 5
Ephrin B/EPHB2/KALRN 0.008 0.071 -10000 0 -0.19 58 58
ROCK1 0.012 0.04 -10000 0 -0.18 22 22
RAS family/GDP -0.022 0.05 -10000 0 -0.24 8 8
Rac1/GTP -0.031 0.065 -10000 0 -0.32 8 8
Ephrin B/EPHB1/Src/Paxillin -0.013 0.094 -10000 0 -0.2 99 99
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 -0.039 0.12 -9999 0 -0.28 102 102
AKT1 0.02 0.15 -9999 0 -0.51 35 35
PTK2B -0.022 0.15 -9999 0 -0.54 33 33
VEGFR2 homodimer/Frs2 -0.006 0.14 -9999 0 -0.56 33 33
CAV1 -0.062 0.16 -9999 0 -0.41 94 94
CALM1 0.011 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.004 0.13 -9999 0 -0.52 33 33
endothelial cell proliferation 0.017 0.15 -9999 0 -0.49 34 34
mol:Ca2+ -0.002 0.15 -9999 0 -0.55 33 33
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.011 0.13 -9999 0 -0.49 33 33
RP11-342D11.1 -0.009 0.15 -9999 0 -0.56 33 33
CDH5 0.006 0.047 -9999 0 -0.41 7 7
VEGFA homodimer 0.029 0.01 -9999 0 -0.2 1 1
SHC1 0.011 0 -9999 0 -10000 0 0
SHC2 -0.049 0.15 -9999 0 -0.41 77 77
HRAS/GDP -0.035 0.12 -9999 0 -0.47 33 33
SH2D2A -0.002 0.065 -9999 0 -0.33 21 21
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.035 0.12 -9999 0 -0.47 33 33
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.003 0.14 -9999 0 -0.53 33 33
VEGFR1 homodimer 0.011 0 -9999 0 -10000 0 0
SHC/GRB2/SOS1 -0.039 0.13 -9999 0 -0.52 33 33
GRB10 -0.002 0.15 -9999 0 -0.56 33 33
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 -0.5 33 33
HRAS 0.011 0 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.014 0.12 -9999 0 -0.38 33 33
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 0.009 0.12 -9999 0 -0.48 33 33
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 -0.005 0.081 -9999 0 -0.41 21 21
Nck/Pak 0.015 0.018 -9999 0 -0.28 2 2
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.004 0.13 -9999 0 -0.52 33 33
mol:GDP -0.038 0.12 -9999 0 -0.5 33 33
mol:NADP 0.023 0.12 -9999 0 -0.4 33 33
eNOS/Hsp90 0.028 0.11 -9999 0 -0.38 33 33
PIK3R1 0.007 0.04 -9999 0 -0.41 5 5
mol:IP3 -0.002 0.15 -9999 0 -0.56 33 33
HIF1A/ARNT 0.016 0 -9999 0 -10000 0 0
SHB 0.011 0 -9999 0 -10000 0 0
VEGFA 0.013 0.001 -9999 0 -10000 0 0
VEGFC 0.004 0.054 -9999 0 -0.41 9 9
FAK1/Vinculin -0.01 0.16 -9999 0 -0.59 33 33
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 -0.028 0.16 -9999 0 -0.58 33 33
PTPN6 0.01 0.015 -9999 0 -0.33 1 1
EPAS1 -0.001 0.084 -9999 0 -0.32 33 33
mol:L-citrulline 0.023 0.12 -9999 0 -0.4 33 33
ITGAV 0.011 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.018 -9999 0 -0.41 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.011 0.13 -9999 0 -0.49 33 33
VEGFR2 homodimer/VEGFA homodimer -0.009 0.16 -9999 0 -0.6 33 33
VEGFR2/3 heterodimer -0.016 0.15 -9999 0 -0.58 33 33
VEGFB 0.011 0 -9999 0 -10000 0 0
MAPK11 -0.004 0.16 -9999 0 -0.57 34 34
VEGFR2 homodimer -0.012 0.16 -9999 0 -0.65 33 33
FLT1 0.011 0 -9999 0 -10000 0 0
NEDD4 -0.021 0.12 -9999 0 -0.41 44 44
MAPK3 -0.007 0.14 -9999 0 -0.52 34 34
MAPK1 -0.007 0.14 -9999 0 -0.52 34 34
VEGFA145/NRP2 0.004 0.062 -9999 0 -0.28 25 25
VEGFR1/2 heterodimer -0.006 0.14 -9999 0 -0.56 33 33
KDR -0.012 0.16 -9999 0 -0.65 33 33
VEGFA165/NRP1/VEGFR2 homodimer -0.011 0.16 -9999 0 -0.56 35 35
SRC 0.011 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process -0.006 0.15 -9999 0 -0.53 34 34
PI3K 0.01 0.16 -9999 0 -0.57 35 35
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.003 0.13 -9999 0 -0.52 33 33
FES -0.003 0.15 -9999 0 -0.56 34 34
GAB1 -0.04 0.14 -9999 0 -0.6 33 33
VEGFR2 homodimer/VEGFA homodimer/Src 0.004 0.13 -9999 0 -0.52 33 33
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 0.012 0.13 -9999 0 -0.42 42 42
VEGFR2 homodimer/VEGFA homodimer/Yes 0.004 0.13 -9999 0 -0.52 33 33
PI3K/GAB1 0.021 0.16 -9999 0 -0.54 34 34
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.014 0.12 -9999 0 -0.47 33 33
PRKACA 0.011 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.011 0.15 -9999 0 -0.56 33 33
HSP90AA1 0.011 0 -9999 0 -10000 0 0
CDC42 -0.003 0.15 -9999 0 -0.56 33 33
actin cytoskeleton reorganization -0.003 0.14 -9999 0 -0.53 33 33
PTK2 -0.018 0.18 -9999 0 -0.64 33 33
EDG1 -0.009 0.15 -9999 0 -0.56 33 33
mol:DAG -0.002 0.15 -9999 0 -0.56 33 33
CaM/Ca2+ 0.003 0.14 -9999 0 -0.51 33 33
MAP2K3 0.002 0.15 -9999 0 -0.53 33 33
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.002 0.16 -9999 0 -0.58 33 33
PLCG1 -0.003 0.15 -9999 0 -0.56 33 33
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.011 0.13 -9999 0 -0.49 33 33
IQGAP1 0.011 0 -9999 0 -10000 0 0
YES1 0.011 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.004 0.13 -9999 0 -0.52 33 33
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.003 0.13 -9999 0 -0.52 33 33
cell migration 0.012 0.15 -9999 0 -0.53 33 33
mol:PI-3-4-5-P3 0.012 0.15 -9999 0 -0.53 35 35
FYN 0.011 0 -9999 0 -10000 0 0
VEGFB/NRP1 -0.002 0.14 -9999 0 -0.52 33 33
mol:NO 0.023 0.12 -9999 0 -0.4 33 33
PXN 0.011 0 -9999 0 -10000 0 0
HRAS/GTP -0.035 0.12 -9999 0 -0.47 33 33
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.002 0.16 -9999 0 -0.58 33 33
VHL 0.01 0.018 -9999 0 -0.41 1 1
ITGB3 -0.068 0.16 -9999 0 -0.41 102 102
NOS3 0.022 0.13 -9999 0 -0.46 33 33
VEGFR2 homodimer/VEGFA homodimer/Sck -0.028 0.15 -9999 0 -0.55 33 33
RAC1 0.011 0 -9999 0 -10000 0 0
PRKCA -0.009 0.16 -9999 0 -0.51 39 39
PRKCB -0.008 0.15 -9999 0 -0.52 36 36
VCL 0.011 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.008 0.15 -9999 0 -0.56 33 33
VEGFR1/2 heterodimer/VEGFA homodimer 0.004 0.13 -9999 0 -0.52 33 33
VEGFA165/NRP2 0.004 0.062 -9999 0 -0.28 25 25
MAPKKK cascade 0.019 0.13 -9999 0 -0.47 33 33
NRP2 -0.008 0.088 -9999 0 -0.41 25 25
VEGFC homodimer 0.004 0.054 -9999 0 -0.41 9 9
NCK1 0.009 0.025 -9999 0 -0.41 2 2
ROCK1 0.011 0 -9999 0 -10000 0 0
FAK1/Paxillin -0.01 0.16 -9999 0 -0.59 33 33
MAP3K13 -0.004 0.15 -9999 0 -0.57 33 33
PDPK1 0.019 0.14 -9999 0 -0.47 35 35
BCR signaling pathway

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
JUN 0.015 0.085 -10000 0 -0.3 29 29
IKBKB 0.027 0.048 -10000 0 -10000 0 0
AKT1 0.005 0.065 0.19 4 -0.2 28 32
IKBKG 0.029 0.049 -10000 0 -10000 0 0
CALM1 0.02 0.079 0.17 67 -0.25 20 87
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
MAP3K1 0.005 0.11 -10000 0 -0.43 26 26
MAP3K7 0.011 0 -10000 0 -10000 0 0
mol:Ca2+ 0.015 0.082 0.18 67 -0.27 20 87
DOK1 0.011 0 -10000 0 -10000 0 0
AP-1 0 0.076 0.14 40 -0.19 30 70
LYN 0.011 0 -10000 0 -10000 0 0
BLNK 0.009 0.029 -10000 0 -0.38 3 3
SHC1 0.011 0 -10000 0 -10000 0 0
BCR complex -0.023 0.096 -10000 0 -0.24 83 83
CD22 -0.059 0.13 -10000 0 -0.52 31 31
CAMK2G 0.025 0.075 0.17 67 -0.23 20 87
CSNK2A1 0.011 0 -10000 0 -10000 0 0
INPP5D 0.01 0.018 -10000 0 -0.41 1 1
SHC/GRB2/SOS1 -0.019 0.047 -10000 0 -0.3 3 3
GO:0007205 0.015 0.083 0.18 67 -0.27 20 87
SYK 0.01 0.015 -10000 0 -0.33 1 1
ELK1 0.02 0.079 0.17 66 -0.25 20 86
NFATC1 0.004 0.1 0.18 3 -0.35 28 31
B-cell antigen/BCR complex -0.023 0.096 -10000 0 -0.24 83 83
PAG1/CSK 0.015 0.022 -10000 0 -0.28 3 3
NFKBIB 0.019 0.021 0.083 1 -0.12 1 2
HRAS 0.02 0.071 0.19 1 -0.23 20 21
NFKBIA 0.019 0.021 0.083 1 -0.12 1 2
NF-kappa-B/RelA/I kappa B beta 0.022 0.02 0.084 1 -0.14 1 2
RasGAP/Csk 0.001 0.073 -10000 0 -0.36 4 4
mol:GDP 0.014 0.079 0.17 66 -0.25 21 87
PTEN 0.006 0.044 -10000 0 -0.41 6 6
CD79B -0.008 0.088 -10000 0 -0.41 25 25
NF-kappa-B/RelA/I kappa B alpha 0.022 0.02 0.084 1 -0.14 1 2
GRB2 0.011 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 0.009 0.12 -10000 0 -0.44 28 28
PIK3R1 0.007 0.04 -10000 0 -0.41 5 5
mol:IP3 0.015 0.084 0.18 67 -0.27 20 87
CSK 0.011 0 -10000 0 -10000 0 0
FOS -0.031 0.12 0.21 1 -0.28 26 27
CHUK 0.029 0.049 0.16 1 -0.18 2 3
IBTK 0.011 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.013 0.047 -10000 0 -0.3 5 5
PTPN6 -0.032 0.13 -10000 0 -0.51 28 28
RELA 0.011 0 -10000 0 -10000 0 0
BCL2A1 0.019 0.016 -10000 0 -10000 0 0
VAV2 -0.008 0.11 -10000 0 -0.45 25 25
ubiquitin-dependent protein catabolic process 0.022 0.021 0.086 1 -0.12 1 2
BTK -0.005 0.065 -10000 0 -1.1 2 2
CD19 -0.04 0.11 -10000 0 -0.44 28 28
MAP4K1 0.003 0.052 -10000 0 -0.33 13 13
CD72 0.009 0.025 -10000 0 -0.33 3 3
PAG1 0.009 0.031 -10000 0 -0.41 3 3
MAPK14 0.012 0.096 -10000 0 -0.37 26 26
SH3BP5 -0.05 0.15 -10000 0 -0.41 79 79
PIK3AP1 0.022 0.092 0.2 64 -0.3 20 84
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.014 0.054 -10000 0 -0.34 5 5
RAF1 0.025 0.068 0.17 2 -0.22 19 21
RasGAP/p62DOK/SHIP -0.024 0.058 -10000 0 -0.34 4 4
CD79A -0.027 0.11 -10000 0 -0.34 60 60
re-entry into mitotic cell cycle 0 0.076 0.14 40 -0.19 30 70
RASA1 0.007 0.04 -10000 0 -0.41 5 5
MAPK3 0.034 0.061 0.18 1 -0.26 3 4
MAPK1 0.034 0.061 0.18 1 -0.26 3 4
CD72/SHP1 -0.025 0.13 -10000 0 -0.47 29 29
NFKB1 0.01 0.018 -10000 0 -0.41 1 1
MAPK8 0.01 0.099 -10000 0 -0.36 30 30
actin cytoskeleton organization 0 0.1 -10000 0 -0.39 25 25
NF-kappa-B/RelA 0.047 0.038 0.16 1 -0.18 1 2
Calcineurin -0.011 0.045 -10000 0 -0.31 5 5
PI3K -0.046 0.093 -10000 0 -0.36 32 32
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.019 0.094 0.2 66 -0.31 20 86
SOS1 0.011 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.023 0.17 -10000 0 -0.64 34 34
DAPP1 -0.049 0.18 -10000 0 -0.72 34 34
cytokine secretion 0.005 0.096 0.18 3 -0.33 28 31
mol:DAG 0.015 0.084 0.18 67 -0.27 20 87
PLCG2 0.01 0.023 -10000 0 -0.37 2 2
MAP2K1 0.03 0.065 0.19 1 -0.29 3 4
B-cell antigen/BCR complex/FcgammaRIIB -0.013 0.084 -10000 0 -0.25 30 30
mol:PI-3-4-5-P3 -0.033 0.073 0.21 5 -0.27 29 34
ETS1 0.029 0.072 0.17 64 -0.3 3 67
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.003 0.07 -10000 0 -0.35 3 3
B-cell antigen/BCR complex/LYN -0.033 0.1 -10000 0 -0.47 26 26
MALT1 0.011 0 -10000 0 -10000 0 0
TRAF6 0.011 0 -10000 0 -10000 0 0
RAC1 -0.001 0.11 -10000 0 -0.42 25 25
B-cell antigen/BCR complex/LYN/SYK -0.054 0.12 -10000 0 -0.49 27 27
CARD11 0.016 0.085 0.21 1 -0.26 21 22
FCGR2B 0.008 0.034 -10000 0 -0.39 4 4
PPP3CA 0.011 0 -10000 0 -10000 0 0
BCL10 0.011 0 -10000 0 -10000 0 0
IKK complex 0.02 0.024 0.11 1 -10000 0 1
PTPRC 0.003 0.058 -10000 0 -0.4 11 11
PDPK1 -0.001 0.062 0.17 4 -0.19 28 32
PPP3CB 0.011 0 -10000 0 -10000 0 0
PPP3CC 0.008 0.036 -10000 0 -0.41 4 4
POU2F2 0.02 0.015 -10000 0 -0.1 1 1
Regulation of Androgen receptor activity

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
HDAC1 0.018 0.001 -9999 0 -10000 0 0
SMARCC1 0.007 0.016 -9999 0 -10000 0 0
REL 0.011 0.001 -9999 0 -10000 0 0
HDAC7 0.02 0.066 -9999 0 -0.31 2 2
JUN 0.006 0.047 -9999 0 -0.41 7 7
EP300 0.011 0 -9999 0 -10000 0 0
KAT2B 0.004 0.054 -9999 0 -0.41 9 9
KAT5 0.011 0 -9999 0 -10000 0 0
MAPK14 -0.01 0.078 -9999 0 -0.21 69 69
FOXO1 0.009 0.031 -9999 0 -0.41 3 3
T-DHT/AR 0.019 0.071 -9999 0 -0.3 3 3
MAP2K6 -0.031 0.11 -9999 0 -0.33 69 69
BRM/BAF57 0.008 0.05 -9999 0 -0.28 16 16
MAP2K4 0.011 0.018 -9999 0 -0.41 1 1
SMARCA2 -0.001 0.071 -9999 0 -0.41 16 16
PDE9A -0.02 0.1 -9999 0 -0.96 4 4
NCOA2 -0.004 0.077 -9999 0 -0.41 19 19
CEBPA 0.007 0.037 -9999 0 -0.38 5 5
EHMT2 0.011 0.001 -9999 0 -10000 0 0
cell proliferation 0.011 0.12 -9999 0 -0.37 20 20
NR0B1 -0.014 0.076 -9999 0 -0.33 30 30
EGR1 -0.044 0.14 -9999 0 -0.41 71 71
RXRs/9cRA -0.011 0.078 -9999 0 -0.2 79 79
AR/RACK1/Src 0.008 0.069 -9999 0 -0.29 5 5
AR/GR -0.048 0.12 -9999 0 -0.22 154 154
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 0.002 -9999 0 -10000 0 0
MAPK8 0.016 0.034 -9999 0 -0.28 7 7
T-DHT/AR/TIF2/CARM1 0.004 0.083 -9999 0 -0.32 14 14
SRC 0.011 0.06 -9999 0 -0.28 2 2
NR3C1 -0.05 0.15 -9999 0 -0.41 79 79
KLK3 -0.048 0.092 -9999 0 -0.47 2 2
APPBP2 0.012 0.002 -9999 0 -10000 0 0
TRIM24 0.011 0.002 -9999 0 -10000 0 0
T-DHT/AR/TIP60 0.004 0.063 -9999 0 -0.36 2 2
TMPRSS2 -0.031 0.14 -9999 0 -1 8 8
RXRG -0.049 0.14 -9999 0 -0.4 79 79
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 0.003 0.059 -9999 0 -0.41 11 11
KLK2 -0.012 0.16 -9999 0 -0.56 34 34
AR -0.023 0.099 -9999 0 -0.22 93 93
SENP1 0.011 0 -9999 0 -10000 0 0
HSP90AA1 0.011 0 -9999 0 -10000 0 0
MDM2 0.011 0.002 -9999 0 -10000 0 0
SRY 0 0.002 -9999 0 -10000 0 0
GATA2 -0.03 0.12 -9999 0 -0.41 53 53
MYST2 0.011 0 -9999 0 -10000 0 0
HOXB13 -0.22 0.16 -9999 0 -0.33 363 363
T-DHT/AR/RACK1/Src 0.009 0.065 -9999 0 -0.31 3 3
positive regulation of transcription -0.03 0.12 -9999 0 -0.41 53 53
DNAJA1 0.012 0.002 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.001 -9999 0 -10000 0 0
NCOA1 0.013 0.02 -9999 0 -0.44 1 1
SPDEF -0.11 0.17 -9999 0 -0.34 190 190
T-DHT/AR/TIF2 0.01 0.073 -9999 0 -0.29 16 16
T-DHT/AR/Hsp90 0.004 0.063 -9999 0 -0.36 2 2
GSK3B 0.011 0.002 -9999 0 -10000 0 0
NR2C1 0.011 0 -9999 0 -10000 0 0
mol:T-DHT 0.006 0.064 -9999 0 -0.22 7 7
SIRT1 0.009 0.025 -9999 0 -0.41 2 2
ZMIZ2 0.011 0.002 -9999 0 -10000 0 0
POU2F1 0.021 0.011 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.009 0.071 -9999 0 -0.31 5 5
CREBBP 0.009 0.025 -9999 0 -0.41 2 2
SMARCE1 0.011 0.001 -9999 0 -10000 0 0
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.011 0.045 -9999 0 -0.23 19 19
EPHB2 0.009 0.025 -9999 0 -0.33 3 3
Syndecan-2/TACI 0.006 0.052 -9999 0 -0.2 30 30
LAMA1 -0.1 0.16 -9999 0 -0.33 183 183
Syndecan-2/alpha2 ITGB1 0.015 0.062 -9999 0 -0.21 26 26
HRAS 0.011 0 -9999 0 -10000 0 0
Syndecan-2/CASK 0.006 0.039 -9999 0 -0.23 14 14
ITGA5 0.011 0 -9999 0 -10000 0 0
BAX 0.023 0.042 -9999 0 -10000 0 0
EPB41 0.01 0.018 -9999 0 -0.41 1 1
positive regulation of cell-cell adhesion 0.012 0.035 -9999 0 -0.2 14 14
LAMA3 -0.001 0.069 -9999 0 -0.41 15 15
EZR 0.011 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.024 0.12 -9999 0 -0.41 45 45
Syndecan-2/MMP2 0.001 0.068 -9999 0 -0.24 39 39
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 0.009 0.045 -9999 0 -0.28 13 13
dendrite morphogenesis 0.013 0.041 -9999 0 -0.22 17 17
Syndecan-2/GM-CSF 0.008 0.046 -9999 0 -0.22 21 21
determination of left/right symmetry 0.008 0.047 -9999 0 -0.28 14 14
Syndecan-2/PKC delta 0.014 0.039 -9999 0 -0.23 14 14
GNB2L1 0.011 0 -9999 0 -10000 0 0
MAPK3 0.015 0.042 -9999 0 -0.21 14 14
MAPK1 0.015 0.042 -9999 0 -0.21 14 14
Syndecan-2/RACK1 0.019 0.033 -9999 0 -0.18 14 14
NF1 0.009 0.025 -9999 0 -0.41 2 2
FGFR/FGF/Syndecan-2 0.008 0.047 -9999 0 -0.28 14 14
ITGA2 0.001 0.064 -9999 0 -0.41 13 13
MAPK8 0.018 0.047 -9999 0 -0.22 20 20
Syndecan-2/alpha2/beta1 Integrin -0.034 0.089 -9999 0 -0.22 30 30
Syndecan-2/Kininogen 0.001 0.055 -9999 0 -0.19 39 39
ITGB1 0.011 0 -9999 0 -10000 0 0
SRC 0.024 0.031 -9999 0 -0.17 14 14
Syndecan-2/CASK/Protein 4.1 0.012 0.036 -9999 0 -0.2 15 15
extracellular matrix organization 0.013 0.04 -9999 0 -0.23 15 15
actin cytoskeleton reorganization 0.011 0.045 -9999 0 -0.23 19 19
Syndecan-2/Caveolin-2/Ras 0.002 0.072 -9999 0 -0.21 57 57
Syndecan-2/Laminin alpha3 0.007 0.057 -9999 0 -0.24 28 28
Syndecan-2/RasGAP 0.022 0.037 -9999 0 -0.17 19 19
alpha5/beta1 Integrin 0.016 0 -9999 0 -10000 0 0
PRKCD 0.011 0 -9999 0 -10000 0 0
Syndecan-2 dimer 0.013 0.041 -9999 0 -0.22 17 17
GO:0007205 0.003 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.028 0.036 -9999 0 -10000 0 0
RHOA 0.011 0 -9999 0 -10000 0 0
SDCBP 0.011 0 -9999 0 -10000 0 0
TNFRSF13B -0.002 0.059 -9999 0 -0.33 17 17
RASA1 0.007 0.04 -9999 0 -0.41 5 5
alpha2/beta1 Integrin 0.009 0.045 -9999 0 -0.28 13 13
Syndecan-2/Synbindin 0.014 0.039 -9999 0 -0.23 14 14
TGFB1 0.01 0.018 -9999 0 -0.41 1 1
CASP3 0.02 0.035 -9999 0 -0.2 14 14
FN1 0.007 0.04 -9999 0 -0.41 5 5
Syndecan-2/IL8 -0.042 0.093 -9999 0 -0.18 171 171
SDC2 0.008 0.047 -9999 0 -0.28 14 14
KNG1 -0.01 0.07 -9999 0 -0.33 25 25
Syndecan-2/Neurofibromin 0.013 0.042 -9999 0 -0.23 16 16
TRAPPC4 0.011 0 -9999 0 -10000 0 0
CSF2 0.001 0.041 -9999 0 -0.33 8 8
Syndecan-2/TGFB1 0.013 0.04 -9999 0 -0.23 15 15
Syndecan-2/Syntenin/PI-4-5-P2 0.013 0.035 -9999 0 -0.2 14 14
Syndecan-2/Ezrin 0.02 0.035 -9999 0 -0.2 14 14
PRKACA 0.019 0.038 -9999 0 -0.2 16 16
angiogenesis -0.042 0.093 -9999 0 -0.18 171 171
MMP2 -0.01 0.091 -9999 0 -0.41 27 27
IL8 -0.088 0.15 -9999 0 -0.33 158 158
calcineurin-NFAT signaling pathway 0.006 0.052 -9999 0 -0.2 30 30
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.011 0 -9999 0 -10000 0 0
HDAC2 0.011 0.001 -9999 0 -10000 0 0
GNB1/GNG2 0.015 0.041 -9999 0 -0.22 15 15
forebrain development -0.068 0.2 -9999 0 -0.44 105 105
GNAO1 -0.1 0.18 -9999 0 -0.41 143 143
SMO/beta Arrestin2 0.015 0.029 -9999 0 -0.28 5 5
SMO 0.007 0.04 -9999 0 -0.41 5 5
ARRB2 0.011 0.003 -9999 0 -10000 0 0
GLI3/SPOP -0.029 0.11 -9999 0 -0.46 4 4
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 0.028 0.002 -9999 0 -10000 0 0
GNAI1 0.005 0.051 -9999 0 -0.41 8 8
XPO1 0.012 0.004 -9999 0 -10000 0 0
GLI1/Su(fu) -0.066 0.13 -9999 0 -0.44 33 33
SAP30 0.011 0.001 -9999 0 -10000 0 0
mol:GDP 0.007 0.04 -9999 0 -0.41 5 5
MIM/GLI2A 0.013 0.018 -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 -0.012 0.078 -9999 0 -10000 0 0
GLI3 -0.036 0.12 -9999 0 -0.22 140 140
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 0.003 0.056 -9999 0 -0.4 10 10
Gi family/GTP -0.039 0.11 -9999 0 -0.21 159 159
SIN3B 0.011 0.001 -9999 0 -10000 0 0
SIN3A 0.011 0 -9999 0 -10000 0 0
GLI3/Su(fu) -0.004 0.086 -9999 0 -0.39 3 3
GLI2/Su(fu) 0.004 0.07 -9999 0 -0.23 3 3
FOXA2 -0.1 0.3 -9999 0 -1.1 49 49
neural tube patterning -0.068 0.2 -9999 0 -0.44 105 105
SPOP 0.011 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.025 0.016 -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 0.018 -9999 0 -10000 0 0
embryonic limb morphogenesis -0.068 0.2 -9999 0 -0.44 105 105
SUFU 0.021 0.018 -9999 0 -10000 0 0
LGALS3 0.009 0.025 -9999 0 -0.41 2 2
catabolic process -0.035 0.13 -9999 0 -0.28 76 76
GLI3A/CBP -0.044 0.13 -9999 0 -0.31 104 104
KIF3A 0.01 0.018 -9999 0 -0.41 1 1
GLI1 -0.07 0.2 -9999 0 -0.45 105 105
RAB23 0.007 0.04 -9999 0 -0.41 5 5
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 -0.19 2 2
GNAZ -0.002 0.073 -9999 0 -0.41 17 17
RBBP4 0.009 0.031 -9999 0 -0.41 3 3
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 -0.006 0.073 -9999 0 -10000 0 0
STK36 0.012 0.004 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.03 0.1 -9999 0 -0.36 18 18
PTCH1 -0.055 0.18 -9999 0 -0.53 33 33
MIM/GLI1 -0.075 0.24 -9999 0 -0.47 127 127
CREBBP -0.044 0.13 -9999 0 -0.31 104 104
Su(fu)/SIN3/HDAC complex 0.039 0.016 -9999 0 -10000 0 0
Glucocorticoid receptor regulatory network

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
PCK2 -0.01 0.039 -10000 0 -10000 0 0
SMARCC2 0.012 0.002 -10000 0 -10000 0 0
SMARCC1 0.012 0.003 -10000 0 -10000 0 0
TBX21 0.006 0.12 -10000 0 -0.6 12 12
SUMO2 0.01 0.005 -10000 0 -10000 0 0
STAT1 (dimer) 0.016 0.02 -10000 0 -0.32 2 2
FKBP4 0.011 0 -10000 0 -10000 0 0
FKBP5 0.005 0.051 -10000 0 -0.41 8 8
GR alpha/HSP90/FKBP51/HSP90 0.001 0.1 0.21 12 -0.25 54 66
PRL -0.029 0.25 -10000 0 -1.3 19 19
cortisol/GR alpha (dimer)/TIF2 0.027 0.16 0.44 20 -0.43 8 28
RELA -0.015 0.062 -10000 0 -0.24 7 7
FGG 0.005 0.14 0.37 13 -0.48 4 17
GR beta/TIF2 -0.015 0.13 0.23 11 -0.31 66 77
IFNG -0.094 0.14 -10000 0 -0.48 15 15
apoptosis -0.078 0.19 0.47 8 -0.51 45 53
CREB1 0.009 0.022 -10000 0 -10000 0 0
histone acetylation 0.038 0.074 0.25 5 -0.25 5 10
BGLAP 0.024 0.064 -10000 0 -10000 0 0
GR/PKAc 0.005 0.092 0.2 10 -0.23 41 51
NF kappa B1 p50/RelA -0.024 0.11 -10000 0 -0.34 26 26
SMARCD1 0.012 0.003 -10000 0 -10000 0 0
MDM2 0.022 0.041 0.18 14 -10000 0 14
GATA3 0.002 0.069 -10000 0 -0.35 20 20
AKT1 0.005 0.002 -10000 0 -10000 0 0
CSF2 0.018 0.066 -10000 0 -10000 0 0
GSK3B 0.01 0.005 -10000 0 -10000 0 0
NR1I3 -0.055 0.17 0.46 7 -0.54 23 30
CSN2 0.003 0.11 0.31 11 -0.37 4 15
BRG1/BAF155/BAF170/BAF60A 0.035 0.009 -10000 0 -10000 0 0
NFATC1 0.002 0.069 -10000 0 -0.41 15 15
POU2F1 0.007 0.044 -10000 0 -0.23 17 17
CDKN1A 0.032 0.06 -10000 0 -1.3 1 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.001 0.006 -10000 0 -10000 0 0
SFN -0.24 0.15 -10000 0 -0.33 401 401
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.1 0.14 0.22 15 -0.34 76 91
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.11 0.29 0.43 8 -0.81 71 79
JUN -0.041 0.1 -10000 0 -0.36 15 15
IL4 0.007 0.08 -10000 0 -0.46 2 2
CDK5R1 0.01 0.015 -10000 0 -0.33 1 1
PRKACA 0.011 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.18 0.17 -10000 0 -0.37 191 191
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.009 0.095 0.21 11 -0.23 45 56
cortisol/GR alpha (monomer) 0.029 0.18 0.5 21 -0.47 4 25
NCOA2 -0.004 0.077 -10000 0 -0.41 19 19
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.15 0.2 -10000 0 -0.44 167 167
AP-1/NFAT1-c-4 -0.16 0.18 -10000 0 -0.48 68 68
AFP -0.016 0.08 -10000 0 -10000 0 0
SUV420H1 0.011 0 -10000 0 -10000 0 0
IRF1 0.026 0.088 0.32 2 -10000 0 2
TP53 0.027 0.027 -10000 0 -0.42 2 2
PPP5C 0.011 0 -10000 0 -10000 0 0
KRT17 -0.12 0.18 -10000 0 -0.72 19 19
KRT14 -0.052 0.11 0.43 1 -10000 0 1
TBP 0.019 0 -10000 0 -10000 0 0
CREBBP 0.031 0.046 -10000 0 -0.32 4 4
HDAC1 0.01 0.002 -10000 0 -10000 0 0
HDAC2 0.01 0.002 -10000 0 -10000 0 0
AP-1 -0.16 0.18 -10000 0 -0.48 69 69
MAPK14 0.01 0.005 -10000 0 -10000 0 0
MAPK10 -0.08 0.17 -10000 0 -0.41 116 116
MAPK11 0.008 0.026 -10000 0 -0.41 2 2
KRT5 -0.14 0.22 -10000 0 -0.76 31 31
interleukin-1 receptor activity -0.001 0.002 -10000 0 -10000 0 0
NCOA1 0.012 0.018 -10000 0 -0.41 1 1
STAT1 0.016 0.021 -10000 0 -0.32 2 2
CGA 0.006 0.082 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.009 0.097 0.28 4 -0.48 2 6
MAPK3 0.01 0.006 -10000 0 -10000 0 0
MAPK1 0.01 0.005 -10000 0 -10000 0 0
ICAM1 -0.015 0.11 -10000 0 -0.42 6 6
NFKB1 -0.016 0.064 -10000 0 -0.25 8 8
MAPK8 -0.017 0.097 0.26 1 -0.33 14 15
MAPK9 0.01 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.085 0.2 0.47 8 -0.53 48 56
BAX 0.034 0.025 -10000 0 -10000 0 0
POMC -0.019 0.21 -10000 0 -1.3 10 10
EP300 0.032 0.037 -10000 0 -0.23 2 2
cortisol/GR alpha (dimer)/p53 0.046 0.15 0.45 21 -0.46 2 23
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.033 0.15 4 -10000 0 4
SGK1 0.045 0.092 -10000 0 -1.3 2 2
IL13 -0.058 0.11 -10000 0 -0.52 6 6
IL6 -0.037 0.19 -10000 0 -0.77 23 23
PRKACG 0.003 0.005 -10000 0 -10000 0 0
IL5 -0.056 0.097 -10000 0 -0.58 2 2
IL2 -0.089 0.13 -10000 0 -0.48 12 12
CDK5 0.01 0.003 -10000 0 -10000 0 0
PRKACB 0.006 0.044 -10000 0 -0.41 6 6
HSP90AA1 0.011 0 -10000 0 -10000 0 0
IL8 -0.05 0.13 -10000 0 -0.48 7 7
CDK5R1/CDK5 0.014 0.013 -10000 0 -0.22 1 1
NF kappa B1 p50/RelA/PKAc -0.001 0.085 -10000 0 -0.31 11 11
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.043 0.14 0.42 21 -0.42 2 23
SMARCA4 0.012 0.002 -10000 0 -10000 0 0
chromatin remodeling 0.026 0.11 0.29 15 -0.43 4 19
NF kappa B1 p50/RelA/Cbp 0.021 0.1 -10000 0 -0.35 8 8
JUN (dimer) -0.041 0.1 -10000 0 -0.36 15 15
YWHAH 0.011 0 -10000 0 -10000 0 0
VIPR1 0.012 0.088 -10000 0 -0.74 2 2
NR3C1 -0.015 0.16 0.32 14 -0.4 65 79
NR4A1 -0.022 0.12 -10000 0 -0.43 44 44
TIF2/SUV420H1 0.006 0.054 -10000 0 -0.28 19 19
MAPKKK cascade -0.078 0.19 0.47 8 -0.51 45 53
cortisol/GR alpha (dimer)/Src-1 0.04 0.15 0.44 21 -0.4 4 25
PBX1 -0.01 0.096 -10000 0 -0.34 38 38
POU1F1 -0.003 0.049 -10000 0 -0.25 19 19
SELE -0.098 0.32 -10000 0 -0.93 65 65
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.026 0.11 0.29 15 -0.43 4 19
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.043 0.14 0.42 21 -0.42 2 23
mol:cortisol 0.024 0.075 0.28 19 -10000 0 19
MMP1 -0.12 0.11 -10000 0 -10000 0 0
IL6-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
BCL2L1 0.032 0.13 -10000 0 -0.55 3 3
CRP 0.026 0.13 -10000 0 -0.52 6 6
cell cycle arrest 0.026 0.14 -10000 0 -0.53 10 10
TIMP1 0.028 0.12 -10000 0 -0.57 4 4
IL6ST -0.052 0.15 -10000 0 -0.41 86 86
Rac1/GDP -0.001 0.12 -10000 0 -0.35 37 37
AP1 -0.021 0.12 -10000 0 -0.52 10 10
GAB2 0.009 0.036 -10000 0 -0.41 4 4
TNFSF11 0.013 0.14 -10000 0 -0.56 4 4
HSP90B1 0.032 0.03 -10000 0 -10000 0 0
GAB1 0.008 0.036 -10000 0 -0.41 4 4
MAPK14 -0.026 0.13 -10000 0 -0.38 39 39
AKT1 0.042 0.039 -10000 0 -0.39 2 2
FOXO1 0.045 0.04 -10000 0 -0.37 2 2
MAP2K6 -0.032 0.14 -10000 0 -0.38 44 44
mol:GTP 0 0.001 -10000 0 -10000 0 0
MAP2K4 0.015 0.12 -10000 0 -0.38 20 20
MITF -0.031 0.15 -10000 0 -0.39 56 56
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.011 0 -10000 0 -10000 0 0
A2M 0.012 0.078 -10000 0 -1.3 2 2
CEBPB 0.017 0.002 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.012 0.085 -10000 0 -0.63 5 5
STAT3 0.028 0.14 -10000 0 -0.56 10 10
STAT1 0.002 0.014 -10000 0 -10000 0 0
CEBPD 0.031 0.13 -10000 0 -0.67 4 4
PIK3CA 0.012 0.018 -10000 0 -0.41 1 1
PI3K 0.015 0.031 -10000 0 -0.28 6 6
JUN 0.006 0.047 -10000 0 -0.41 7 7
PIAS3/MITF -0.025 0.14 -10000 0 -0.37 56 56
MAPK11 -0.027 0.13 -10000 0 -0.38 39 39
STAT3 (dimer)/FOXO1 0.061 0.13 -10000 0 -0.47 6 6
GRB2/SOS1/GAB family -0.043 0.1 0.14 1 -0.37 33 34
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.02 0.13 -10000 0 -0.31 64 64
GRB2 0.012 0.001 -10000 0 -10000 0 0
JAK2 0.004 0.054 -10000 0 -0.41 9 9
LBP 0.018 0.12 -10000 0 -0.52 2 2
PIK3R1 0.008 0.04 -10000 0 -0.41 5 5
JAK1 0.012 0.025 -10000 0 -0.4 2 2
MYC 0.021 0.18 -10000 0 -0.86 13 13
FGG 0.025 0.13 -10000 0 -0.57 3 3
macrophage differentiation 0.026 0.14 -10000 0 -0.53 10 10
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.041 0.12 -10000 0 -0.35 45 45
JUNB 0.025 0.15 -10000 0 -0.7 10 10
FOS -0.12 0.19 -10000 0 -0.41 167 167
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.018 0.13 -10000 0 -0.37 44 44
STAT1/PIAS1 0.001 0.12 -10000 0 -0.33 35 35
GRB2/SOS1/GAB family/SHP2/PI3K 0.033 0.041 -10000 0 -0.33 4 4
STAT3 (dimer) 0.029 0.14 -10000 0 -0.55 10 10
PRKCD 0.029 0.12 -10000 0 -0.44 11 11
IL6R -0.022 0.12 -10000 0 -0.41 46 46
SOCS3 -0.026 0.14 -10000 0 -0.65 9 9
gp130 (dimer)/JAK1/JAK1/LMO4 -0.008 0.094 -10000 0 -0.22 88 88
Rac1/GTP 0.002 0.12 -10000 0 -0.35 36 36
HCK 0.006 0.038 -10000 0 -0.33 7 7
MAPKKK cascade 0.026 0.081 -10000 0 -0.77 4 4
bone resorption 0.014 0.13 -10000 0 -0.54 4 4
IRF1 0.032 0.13 -10000 0 -0.55 3 3
mol:GDP -0.01 0.13 -10000 0 -0.37 37 37
SOS1 0.011 0.001 -10000 0 -10000 0 0
VAV1 -0.01 0.13 -10000 0 -0.38 37 37
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.039 0.16 -10000 0 -0.46 49 49
PTPN11 0.002 0.014 -10000 0 -10000 0 0
IL6/IL6RA -0.015 0.1 -10000 0 -0.29 65 65
gp130 (dimer)/TYK2/TYK2/LMO4 -0.011 0.092 -10000 0 -0.22 86 86
gp130 (dimer)/JAK2/JAK2/LMO4 -0.015 0.098 -10000 0 -0.23 93 93
IL6 -0.003 0.083 -10000 0 -0.38 25 25
PIAS3 0.011 0 -10000 0 -10000 0 0
PTPRE 0.003 0.024 -10000 0 -0.37 2 2
PIAS1 0.011 0 -10000 0 -10000 0 0
RAC1 0.011 0.001 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.03 0.13 -10000 0 -0.25 115 115
LMO4 0.015 0.005 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 0.018 0.13 -10000 0 -0.54 10 10
MCL1 0.046 0.036 -10000 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.009 0.036 -9999 0 -0.41 4 4
ELF1 0.009 0.046 -9999 0 -0.38 5 5
CCNA2 -0.062 0.14 -9999 0 -0.33 117 117
PIK3CA 0.011 0.018 -9999 0 -0.41 1 1
JAK3 0.009 0.029 -9999 0 -0.33 4 4
PIK3R1 0.008 0.04 -9999 0 -0.41 5 5
JAK1 0.01 0.025 -9999 0 -0.41 2 2
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.053 0.044 -9999 0 -0.51 1 1
SHC1 0.012 0 -9999 0 -10000 0 0
SP1 -0.043 0.12 -9999 0 -0.3 102 102
IL2RA 0.013 0.059 -9999 0 -0.34 5 5
IL2RB 0.011 0.018 -9999 0 -0.41 1 1
SOS1 0.012 0 -9999 0 -10000 0 0
IL2RG 0.006 0.047 -9999 0 -0.36 9 9
G1/S transition of mitotic cell cycle -0.1 0.27 -9999 0 -0.64 103 103
PTPN11 0.012 0 -9999 0 -10000 0 0
CCND2 -0.1 0.26 -9999 0 -0.65 102 102
LCK 0.008 0.034 -9999 0 -0.34 5 5
GRB2 0.012 0 -9999 0 -10000 0 0
IL2 -0.006 0.06 -9999 0 -0.33 18 18
CDK6 0.001 0.064 -9999 0 -0.41 13 13
CCND3 0.056 0.04 -9999 0 -0.43 1 1
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) -0.01 0.063 -10000 0 -0.65 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 0.044 -10000 0 -0.41 6 6
LRP6/FZD1 0.015 0.018 -10000 0 -0.28 2 2
TLE1 0.01 0.018 -10000 0 -0.41 1 1
AP1 -0.064 0.12 -10000 0 -0.24 172 172
NCSTN 0.011 0 -10000 0 -10000 0 0
ADAM10 0.008 0.036 -10000 0 -0.41 4 4
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.03 0.052 -10000 0 -0.56 2 2
NICD/RBPSUH 0.023 0.046 -10000 0 -0.5 4 4
WIF1 -0.097 0.16 -10000 0 -0.35 163 163
NOTCH1 -0.004 0.046 -10000 0 -0.53 4 4
PSENEN 0.011 0 -10000 0 -10000 0 0
KREMEN2 -0.021 0.099 -10000 0 -0.33 51 51
DKK1 -0.065 0.14 -10000 0 -0.33 119 119
beta catenin/beta TrCP1 0.026 0.027 -10000 0 -10000 0 0
APH1B 0.006 0.047 -10000 0 -0.41 7 7
APH1A 0.011 0 -10000 0 -10000 0 0
AXIN1 0.001 0.019 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.017 0.027 0.19 1 -0.21 3 4
PSEN1 0.011 0 -10000 0 -10000 0 0
FOS -0.12 0.19 -10000 0 -0.41 167 167
JUN 0.006 0.047 -10000 0 -0.41 7 7
MAP3K7 0.01 0.002 -10000 0 -10000 0 0
CTNNB1 0.02 0.029 0.16 5 -10000 0 5
MAPK3 0.011 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.011 0.083 -10000 0 -0.2 80 80
HNF1A 0.005 0.041 -10000 0 -0.33 8 8
CTBP1 0.01 0.001 -10000 0 -10000 0 0
MYC -0.003 0.17 -10000 0 -1.3 10 10
NKD1 -0.021 0.1 -10000 0 -0.34 48 48
FZD1 0.009 0.025 -10000 0 -0.41 2 2
NOTCH1 precursor/Deltex homolog 1 0.021 0.05 -10000 0 -0.5 4 4
apoptosis -0.064 0.12 -10000 0 -0.24 172 172
Delta 1/NOTCHprecursor 0.017 0.067 -10000 0 -0.64 4 4
DLL1 -0.003 0.075 -10000 0 -0.41 18 18
PPARD 0.018 0.013 -10000 0 -10000 0 0
Gamma Secretase 0.031 0.024 -10000 0 -10000 0 0
APC 0.001 0.019 -10000 0 -10000 0 0
DVL1 0 0.015 -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 -0.039 0.096 -10000 0 -0.18 163 163
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 0.019 -10000 0 -10000 0 0
WNT1 0.004 0.041 -10000 0 -0.33 8 8
Axin1/APC/beta catenin 0.029 0.025 -10000 0 -10000 0 0
DKK2 -0.015 0.1 -10000 0 -0.4 34 34
NOTCH1 precursor/DVL1 0 0.04 -10000 0 -0.46 4 4
GSK3B 0.011 0 -10000 0 -10000 0 0
FRAT1 0.01 0.001 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.006 0.047 -10000 0 -0.51 4 4
PPP2R5D 0.012 0.046 0.21 11 -10000 0 11
MAPK1 0.011 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.033 0.089 -10000 0 -0.21 39 39
RBPJ 0.011 0 -10000 0 -10000 0 0
CREBBP 0.012 0.026 -10000 0 -0.41 2 2
Insulin 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
CBL/APS/CAP -0.075 0.11 -9999 0 -0.36 37 37
TC10/GTP -0.055 0.076 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 0.001 0.069 -9999 0 -0.21 54 54
HRAS 0.011 0 -9999 0 -10000 0 0
APS homodimer 0.011 0 -9999 0 -10000 0 0
GRB14 -0.11 0.16 -9999 0 -0.33 196 196
FOXO3 -0.009 0.036 -9999 0 -0.57 2 2
AKT1 -0.031 0.091 -9999 0 -0.28 28 28
INSR 0.012 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0.03 0.002 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.01 0.018 -9999 0 -0.41 1 1
SORBS1 -0.13 0.2 -9999 0 -0.41 187 187
CRK 0.011 0 -9999 0 -10000 0 0
PTPN1 0.027 0.001 -9999 0 -10000 0 0
CAV1 -0.036 0.11 -9999 0 -0.23 126 126
CBL/APS/CAP/Crk-II/C3G -0.04 0.1 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/NCK2 0.001 0.069 -9999 0 -0.21 54 54
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.019 0.057 -9999 0 -0.18 51 51
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.013 0.055 -9999 0 -10000 0 0
RPS6KB1 -0.023 0.086 -9999 0 -0.25 28 28
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 0.04 -9999 0 -0.41 5 5
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.047 0.066 -9999 0 -0.26 28 28
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 0.065 -9999 0 -0.19 47 47
PRKCI -0.012 0.018 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.059 0.08 -9999 0 -0.3 28 28
SHC1 0.011 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade -0.002 0.028 -9999 0 -0.39 2 2
PI3K -0.02 0.058 -9999 0 -0.18 51 51
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 -0.031 0.091 -9999 0 -0.28 28 28
PRKCZ -0.013 0.028 -9999 0 -0.52 1 1
SH2B2 0.011 0 -9999 0 -10000 0 0
SHC/SHIP 0.007 0.061 -9999 0 -0.18 55 55
F2RL2 -0.016 0.1 -9999 0 -0.4 35 35
TRIP10 0.011 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.017 0.002 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.015 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.029 0.001 -9999 0 -10000 0 0
RAPGEF1 0.011 0 -9999 0 -10000 0 0
RASA1 0.007 0.04 -9999 0 -0.41 5 5
NCK1 0.009 0.025 -9999 0 -0.41 2 2
CBL/APS/CAP/Crk-II -0.05 0.11 -9999 0 -0.2 187 187
TC10/GDP 0.008 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.024 0.01 -9999 0 -0.21 1 1
INPP5D 0 0.064 -9999 0 -0.19 55 55
SOS1 0.011 0 -9999 0 -10000 0 0
SGK1 -0.006 0.05 -9999 0 -0.82 2 2
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.011 0 -9999 0 -10000 0 0
IRS1 -0.031 0.13 -9999 0 -0.41 54 54
p62DOK/RasGAP -0.002 0.028 -9999 0 -0.4 2 2
INS 0.003 0.002 -9999 0 -10000 0 0
mol:PI-3-4-P2 0 0.064 -9999 0 -0.19 55 55
GRB2 0.011 0 -9999 0 -10000 0 0
EIF4EBP1 -0.026 0.089 -9999 0 -0.26 32 32
PTPRA 0.012 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.018 -9999 0 -0.41 1 1
TC10/GTP/CIP4 0.015 0 -9999 0 -10000 0 0
PDPK1 0.011 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.006 0.065 -9999 0 -0.19 54 54
Insulin Receptor/Insulin/IRS1 -0.006 0.069 -9999 0 -0.22 54 54
Insulin Receptor/Insulin/IRS3 0.012 0.002 -9999 0 -10000 0 0
Par3/Par6 0.013 0.051 -9999 0 -0.19 32 32
Signaling events mediated by PTP1B

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
PDGFRB -0.007 0.085 -10000 0 -0.41 23 23
Jak2/Leptin Receptor -0.097 0.14 -10000 0 -0.35 89 89
PTP1B/AKT1 0.017 0.04 -10000 0 -0.2 5 5
FYN 0.011 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.013 0.044 -10000 0 -0.23 5 5
EGFR 0.001 0.067 -10000 0 -0.41 14 14
EGF/EGFR -0.016 0.05 -10000 0 -0.24 19 19
CSF1 0.003 0.057 -10000 0 -0.41 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 -0.012 0.089 -10000 0 -0.27 28 28
Insulin Receptor/Insulin -0.008 0.022 -10000 0 -10000 0 0
HCK 0.007 0.038 -10000 0 -0.33 7 7
CRK 0.011 0 -10000 0 -10000 0 0
TYK2 0.018 0.041 -10000 0 -0.22 5 5
EGF -0.005 0.073 -10000 0 -0.34 25 25
YES1 0.011 0 -10000 0 -10000 0 0
CAV1 -0.002 0.077 -10000 0 -0.3 13 13
TXN 0.011 0.002 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.004 0.078 -10000 0 -0.24 32 32
cell migration -0.013 0.044 0.23 5 -10000 0 5
STAT3 0.011 0.001 -10000 0 -10000 0 0
PRLR -0.075 0.17 -10000 0 -0.41 111 111
ITGA2B 0.004 0.05 -10000 0 -0.4 8 8
CSF1R 0.008 0.034 -10000 0 -0.39 4 4
Prolactin Receptor/Prolactin -0.059 0.13 -10000 0 -0.29 128 128
FGR 0.002 0.059 -10000 0 -0.41 11 11
PTP1B/p130 Cas 0.018 0.041 -10000 0 -0.22 5 5
Crk/p130 Cas 0.023 0.04 -10000 0 -0.2 5 5
DOK1 0.015 0.06 -10000 0 -0.24 16 16
JAK2 -0.039 0.13 -10000 0 -0.24 126 126
Jak2/Leptin Receptor/Leptin -0.014 0.051 -10000 0 -0.38 7 7
PIK3R1 0.007 0.04 -10000 0 -0.41 5 5
PTPN1 0.013 0.044 -10000 0 -0.23 5 5
LYN 0.011 0 -10000 0 -10000 0 0
CDH2 -0.052 0.15 -10000 0 -0.41 81 81
SRC 0.019 0.019 -10000 0 -10000 0 0
ITGB3 -0.068 0.16 -10000 0 -0.41 102 102
CAT1/PTP1B 0.017 0.072 -10000 0 -0.31 7 7
CAPN1 0.012 0.001 -10000 0 -10000 0 0
CSK 0.011 0 -10000 0 -10000 0 0
PI3K -0.007 0.025 -10000 0 -0.23 2 2
mol:H2O2 0 0.001 -10000 0 -10000 0 0
STAT3 (dimer) -0.012 0.047 -10000 0 -0.35 7 7
negative regulation of transcription -0.038 0.12 -10000 0 -0.24 126 126
FCGR2A 0.01 0.015 -10000 0 -0.33 1 1
FER 0.011 0.002 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.044 0.12 -10000 0 -0.28 110 110
BLK -0.015 0.087 -10000 0 -0.33 39 39
Insulin Receptor/Insulin/Shc 0.016 0.002 -10000 0 -10000 0 0
RHOA 0.012 0.001 -10000 0 -10000 0 0
LEPR -0.11 0.19 -10000 0 -0.41 161 161
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 0.012 0.068 -10000 0 -0.33 7 7
PRL -0.01 0.083 -10000 0 -0.39 24 24
SOCS3 0.005 0.075 -10000 0 -1.2 2 2
SPRY2 0.006 0.044 -10000 0 -0.42 6 6
Insulin Receptor/Insulin/IRS1 -0.009 0.075 -10000 0 -0.24 54 54
CSF1/CSF1R 0.018 0.056 -10000 0 -0.25 13 13
Ras protein signal transduction 0.008 0.014 -10000 0 -10000 0 0
IRS1 -0.031 0.13 -10000 0 -0.41 54 54
INS 0.001 0.003 -10000 0 -10000 0 0
LEP 0.005 0.025 -10000 0 -0.33 3 3
STAT5B -0.004 0.065 -10000 0 -0.23 20 20
STAT5A -0.004 0.064 -10000 0 -0.23 19 19
GRB2 0.011 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.009 0.064 -10000 0 -0.26 18 18
CSN2 -0.031 0.061 -10000 0 -10000 0 0
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
LAT 0.019 0.019 -10000 0 -10000 0 0
YBX1 0.017 0.018 -10000 0 -0.4 1 1
LCK 0.008 0.034 -10000 0 -0.34 5 5
SHC1 0.011 0 -10000 0 -10000 0 0
NOX4 0.007 0.039 -10000 0 -0.4 5 5
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 -0.41 216 216
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.01 0.015 -9999 0 -0.33 1 1
TCEB1 0.011 0 -9999 0 -10000 0 0
HIF1A/p53 0.025 0.01 -9999 0 -10000 0 0
HIF1A 0.02 0.005 -9999 0 -10000 0 0
COPS5 0.011 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.032 0.012 -9999 0 -10000 0 0
FIH (dimer) 0.011 0 -9999 0 -10000 0 0
CDKN2A -0.13 0.17 -9999 0 -0.33 228 228
ARNT/IPAS -0.1 0.14 -9999 0 -0.28 216 216
HIF1AN 0.011 0 -9999 0 -10000 0 0
GNB2L1 0.011 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.026 0.005 -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 0.008 -9999 0 -0.17 1 1
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.026 0.005 -9999 0 -10000 0 0
PHD1-3/OS9 0.027 0.016 -9999 0 -0.2 1 1
HIF1A/RACK1/Elongin B/Elongin C 0.034 0.008 -9999 0 -10000 0 0
VHL 0.01 0.018 -9999 0 -0.41 1 1
HSP90AA1 0.011 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.026 0.005 -9999 0 -10000 0 0
EGLN3 0.008 0.031 -9999 0 -0.35 4 4
EGLN2 0.011 0 -9999 0 -10000 0 0
EGLN1 0.011 0 -9999 0 -10000 0 0
TP53 0.01 0.018 -9999 0 -0.41 1 1
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.03 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 -0.037 0.074 -9999 0 -0.19 1 1
Regulation of nuclear SMAD2/3 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
EP300 0.012 0.004 -10000 0 -10000 0 0
HSPA8 0.011 0.001 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.029 0.088 0.15 3 -0.26 66 69
AKT1 0.013 0.002 -10000 0 -10000 0 0
GSC -0.029 0.077 -10000 0 -10000 0 0
NKX2-5 -0.05 0.12 -10000 0 -0.34 84 84
muscle cell differentiation 0.044 0.097 0.35 24 -10000 0 24
SMAD2-3/SMAD4/SP1 0.038 0.051 -10000 0 -0.26 3 3
SMAD4 0.007 0.035 -10000 0 -0.42 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 0.044 -10000 0 -0.2 19 19
SMAD3/SMAD4/VDR 0.005 0.041 -10000 0 -0.22 4 4
MYC 0.001 0.057 -10000 0 -0.41 10 10
CDKN2B 0.025 0.031 -10000 0 -10000 0 0
AP1 -0.025 0.12 -10000 0 -0.39 18 18
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.044 0.02 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.012 0.045 -10000 0 -0.34 3 3
SP3 0.013 0 -10000 0 -10000 0 0
CREB1 0.011 0 -10000 0 -10000 0 0
FOXH1 -0.08 0.15 -10000 0 -0.34 135 135
SMAD3/SMAD4/GR -0.036 0.096 -10000 0 -0.25 82 82
GATA3 -0.004 0.071 -10000 0 -0.35 20 20
SKI/SIN3/HDAC complex/NCoR1 0.036 0.013 -10000 0 -10000 0 0
MEF2C/TIF2 -0.07 0.18 -10000 0 -0.42 81 81
endothelial cell migration -0.015 0.11 1.2 4 -10000 0 4
MAX 0.01 0.004 -10000 0 -10000 0 0
RBBP7 0.011 0 -10000 0 -10000 0 0
RBBP4 0.009 0.031 -10000 0 -0.41 3 3
RUNX2 0.001 0.058 -10000 0 -0.33 16 16
RUNX3 0.002 0.054 -10000 0 -0.33 14 14
RUNX1 0.011 0 -10000 0 -10000 0 0
CTBP1 0.011 0 -10000 0 -10000 0 0
NR3C1 -0.052 0.15 -10000 0 -0.41 79 79
VDR 0.003 0.052 -10000 0 -0.33 13 13
CDKN1A 0.054 0.066 -10000 0 -1.2 1 1
KAT2B 0.004 0.054 -10000 0 -0.41 9 9
SMAD2/SMAD2/SMAD4/FOXH1 -0.036 0.1 -10000 0 -0.24 52 52
DCP1A 0.011 0 -10000 0 -10000 0 0
SKI 0.011 0 -10000 0 -10000 0 0
SERPINE1 0.015 0.11 -10000 0 -1.3 4 4
SMAD3/SMAD4/ATF2 0.011 0.048 -10000 0 -0.3 7 7
SMAD3/SMAD4/ATF3 -0.01 0.089 -10000 0 -0.27 51 51
SAP30 0.011 0 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.026 0.019 -10000 0 -0.22 2 2
JUN -0.025 0.12 -10000 0 -0.42 15 15
SMAD3/SMAD4/IRF7 0.006 0.055 -10000 0 -0.28 9 9
TFE3 0.016 0.005 -10000 0 -10000 0 0
COL1A2 0.008 0.086 -10000 0 -0.79 5 5
mesenchymal cell differentiation -0.006 0.059 0.27 17 -10000 0 17
DLX1 -0.031 0.11 -10000 0 -0.33 63 63
TCF3 0.011 0 -10000 0 -10000 0 0
FOS -0.12 0.2 -10000 0 -0.41 167 167
SMAD3/SMAD4/Max 0.001 0.036 -10000 0 -0.26 5 5
Cbp/p300/SNIP1 0.023 0.016 -10000 0 -0.23 2 2
ZBTB17 0.009 0.002 -10000 0 -10000 0 0
LAMC1 0.033 0.036 -10000 0 -0.26 2 2
TGIF2/HDAC complex/SMAD3/SMAD4 0.013 0.04 -10000 0 -0.25 5 5
IRF7 0.004 0.05 -10000 0 -0.35 10 10
ESR1 -0.038 0.13 -10000 0 -0.41 62 62
HNF4A -0.04 0.12 -10000 0 -0.33 78 78
MEF2C -0.073 0.17 -10000 0 -0.43 80 80
SMAD2-3/SMAD4 0.017 0.048 -10000 0 -0.28 4 4
Cbp/p300/Src-1 0.023 0.019 -10000 0 -0.22 3 3
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 0.026 -10000 0 -0.41 2 2
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 0.011 0.001 -10000 0 -10000 0 0
GCN5L2 0.001 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.03 0.044 -10000 0 -0.26 4 4
MSG1/HSC70 0.004 0.046 -10000 0 -0.23 20 20
SMAD2 0.008 0.018 -10000 0 -10000 0 0
SMAD3 0.009 0.046 -10000 0 -0.45 4 4
SMAD3/E2F4-5/DP1/p107/SMAD4 0.026 0.033 -10000 0 -0.22 4 4
SMAD2/SMAD2/SMAD4 0.002 0.042 -10000 0 -0.28 10 10
NCOR1 0.011 0 -10000 0 -10000 0 0
NCOA2 -0.004 0.077 -10000 0 -0.41 19 19
NCOA1 0.01 0.018 -10000 0 -0.41 1 1
MYOD/E2A -0.011 0.068 -10000 0 -0.22 53 53
SMAD2-3/SMAD4/SP1/MIZ-1 0.043 0.049 -10000 0 -0.24 3 3
IFNB1 0.014 0.063 -10000 0 -0.31 13 13
SMAD3/SMAD4/MEF2C -0.065 0.17 -10000 0 -0.44 69 69
CITED1 -0.002 0.066 -10000 0 -0.34 20 20
SMAD2-3/SMAD4/ARC105 0.023 0.044 -10000 0 -0.24 4 4
RBL1 0.011 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.041 0.037 -10000 0 -0.34 2 2
RUNX1-3/PEBPB2 0.017 0.031 -10000 0 -0.17 14 14
SMAD7 0 0.13 -10000 0 -0.48 12 12
MYC/MIZ-1 0.007 0.04 -10000 0 -0.28 10 10
SMAD3/SMAD4 0.012 0.055 -10000 0 -0.4 4 4
IL10 0.009 0.091 -10000 0 -0.29 34 34
PIASy/HDAC complex 0.01 0.003 -10000 0 -10000 0 0
PIAS3 0.011 0.002 -10000 0 -10000 0 0
CDK2 0.012 0.003 -10000 0 -10000 0 0
IL5 0.011 0.064 -10000 0 -0.31 5 5
CDK4 0.012 0.003 -10000 0 -10000 0 0
PIAS4 0.01 0.003 -10000 0 -10000 0 0
ATF3 -0.025 0.12 -10000 0 -0.41 47 47
SMAD3/SMAD4/SP1 0.033 0.048 -10000 0 -0.25 5 5
FOXG1 -0.16 0.17 -10000 0 -0.33 262 262
FOXO3 0.022 0.003 -10000 0 -10000 0 0
FOXO1 0.02 0.022 -10000 0 -0.28 3 3
FOXO4 0.021 0.018 -10000 0 -0.28 2 2
heart looping -0.072 0.17 -10000 0 -0.42 80 80
CEBPB 0.012 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.012 0.08 -10000 0 -0.24 38 38
MYOD1 -0.028 0.099 -10000 0 -0.33 53 53
SMAD3/SMAD4/HNF4 -0.016 0.079 -10000 0 -0.22 33 33
SMAD3/SMAD4/GATA3 -0.001 0.07 -10000 0 -0.28 12 12
SnoN/SIN3/HDAC complex/NCoR1 0.011 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.027 0.045 -10000 0 -0.22 4 4
SMAD3/SMAD4/SP1-3 0.041 0.046 -10000 0 -0.25 2 2
MED15 0.011 0 -10000 0 -10000 0 0
SP1 0.018 0.013 -10000 0 -10000 0 0
SIN3B 0.011 0 -10000 0 -10000 0 0
SIN3A 0.011 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.061 0.14 -10000 0 -0.33 70 70
ITGB5 0.043 0.036 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.037 0.013 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.032 0.11 -10000 0 -0.25 96 96
AR -0.061 0.16 -10000 0 -0.41 93 93
negative regulation of cell growth 0.019 0.061 -10000 0 -0.3 5 5
SMAD3/SMAD4/MYOD -0.009 0.07 -10000 0 -0.22 27 27
E2F5 0.011 0 -10000 0 -10000 0 0
E2F4 0.011 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.016 0.085 -10000 0 -0.25 13 13
SMAD2-3/SMAD4/FOXO1-3a-4 0.038 0.037 -10000 0 -0.35 2 2
TFDP1 0.011 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.019 0.12 -10000 0 -0.39 18 18
SMAD3/SMAD4/RUNX2 0.007 0.059 -10000 0 -0.27 17 17
TGIF2 0.011 0 -10000 0 -10000 0 0
TGIF1 0.011 0 -10000 0 -10000 0 0
ATF2 0.009 0.031 -10000 0 -0.41 3 3
Retinoic acid receptors-mediated signaling

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
HDAC1 0.011 0 -10000 0 -10000 0 0
HDAC3 0.011 0 -10000 0 -10000 0 0
VDR 0.003 0.052 -10000 0 -0.33 13 13
Cbp/p300/PCAF 0.017 0.035 -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 0.004 0.054 -10000 0 -0.41 9 9
MAPK14 0.011 0 -10000 0 -10000 0 0
AKT1 0.012 0.06 0.19 21 -0.24 12 33
RAR alpha/9cRA/Cyclin H -0.02 0.065 -10000 0 -0.24 39 39
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.017 0.055 -10000 0 -0.25 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 -0.005 0.068 -10000 0 -0.35 10 10
NCOR2 0.011 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.003 0.036 -10000 0 -0.22 13 13
RXRs/RARs/NRIP1/9cRA -0.003 0.13 -10000 0 -0.4 44 44
NCOA2 -0.004 0.077 -10000 0 -0.41 19 19
NCOA3 0.01 0.015 -10000 0 -0.33 1 1
NCOA1 0.01 0.018 -10000 0 -0.41 1 1
VDR/VDR/DNA 0.003 0.052 -10000 0 -0.33 13 13
RARG 0.012 0.001 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.015 0.001 -10000 0 -10000 0 0
MAPK3 0.012 0.001 -10000 0 -10000 0 0
MAPK1 0.011 0 -10000 0 -10000 0 0
MAPK8 0.007 0.044 -10000 0 -0.41 6 6
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.011 0.12 -10000 0 -0.38 44 44
RARA -0.004 0.073 -10000 0 -0.23 47 47
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.01 0.07 -10000 0 -0.3 17 17
PRKCA -0.014 0.1 -10000 0 -0.41 36 36
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.012 0.14 -10000 0 -0.42 45 45
RXRG -0.053 0.13 -10000 0 -0.3 106 106
RXRA 0.002 0.068 -10000 0 -0.2 47 47
RXRB -0.013 0.087 -10000 0 -0.28 42 42
VDR/Vit D3/DNA 0.003 0.036 -10000 0 -0.22 13 13
RBP1 -0.007 0.085 -10000 0 -0.41 23 23
CRBP1/9-cic-RA -0.004 0.06 -10000 0 -0.29 23 23
RARB 0.004 0.06 -10000 0 -0.41 11 11
PRKCG -0.035 0.12 -10000 0 -0.33 74 74
MNAT1 0.011 0 -10000 0 -10000 0 0
RAR alpha/RXRs -0.003 0.14 -10000 0 -0.42 44 44
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.003 0.11 -10000 0 -0.34 43 43
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.069 -10000 0 -0.35 8 8
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.012 0.14 -10000 0 -0.42 45 45
positive regulation of DNA binding -0.019 0.062 -10000 0 -0.22 39 39
NRIP1 -0.012 0.15 -10000 0 -0.78 10 10
RXRs/RARs -0.017 0.14 -10000 0 -0.41 47 47
RXRs/RXRs/DNA/9cRA -0.018 0.12 -10000 0 -0.4 44 44
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 -0.011 0.039 -10000 0 -0.33 2 2
CCNH 0.011 0 -10000 0 -10000 0 0
CREBBP 0.009 0.025 -10000 0 -0.41 2 2
RAR gamma2/9cRA 0 0 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.011 0.02 0.18 1 -10000 0 1
AES 0.011 0.017 -10000 0 -10000 0 0
FBXW11 0.011 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.015 0.018 -10000 0 -0.28 2 2
SMAD4 0.01 0.018 -10000 0 -0.41 1 1
DKK2 -0.015 0.1 -10000 0 -0.4 34 34
TLE1 0.011 0.024 -10000 0 -0.41 1 1
MACF1 0.011 0 -10000 0 -10000 0 0
CTNNB1 0.041 0.047 0.21 6 -10000 0 6
WIF1 -0.097 0.16 -10000 0 -0.35 163 163
beta catenin/RanBP3 0.02 0.092 0.36 35 -10000 0 35
KREMEN2 -0.021 0.099 -10000 0 -0.33 51 51
DKK1 -0.065 0.14 -10000 0 -0.33 119 119
beta catenin/beta TrCP1 0.045 0.044 0.2 6 -10000 0 6
FZD1 0.01 0.026 -10000 0 -0.41 2 2
AXIN2 -0.052 0.29 -10000 0 -1.3 27 27
AXIN1 0.011 0 -10000 0 -10000 0 0
RAN 0.011 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.014 0.023 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.05 0.055 0.22 1 -0.34 4 5
Axin1/APC/GSK3 0.018 0.031 0.16 5 -10000 0 5
Axin1/APC/GSK3/beta catenin/Macf1 0.044 0.026 -10000 0 -10000 0 0
HNF1A 0.006 0.045 0.16 1 -0.33 8 9
CTBP1 0.011 0.018 0.17 1 -10000 0 1
MYC -0.017 0.18 -10000 0 -1.3 10 10
RANBP3 0.011 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.011 0.083 -10000 0 -0.2 80 80
NKD1 -0.02 0.1 -10000 0 -0.34 48 48
TCF4 -0.004 0.08 0.16 1 -0.4 20 21
TCF3 0.011 0.017 0.16 1 -10000 0 1
WNT1/LRP6/FZD1/Axin1 0.024 0.026 -10000 0 -0.2 2 2
Ran/GTP 0.008 0.002 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.02 0.11 0.41 35 -0.4 2 37
LEF1 0.007 0.044 0.16 1 -0.38 6 7
DVL1 0.03 0.019 -10000 0 -10000 0 0
CSNK2A1 0.011 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.047 0.076 -10000 0 -0.34 9 9
DKK1/LRP6/Kremen 2 -0.039 0.096 -10000 0 -0.18 163 163
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 0.002 0.057 -10000 0 -0.51 1 1
WNT1 0.004 0.041 -10000 0 -0.33 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 0.031 0.047 0.17 45 -10000 0 45
APC 0.028 0.023 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.038 0.058 0.2 34 -0.2 2 36
CREBBP 0.01 0.03 0.16 1 -0.39 2 3
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.015 0.082 -10000 0 -0.2 85 85
MAPK9 0.007 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.004 0.033 -10000 0 -0.22 12 12
GNB1/GNG2 0.01 0.033 -10000 0 -0.23 10 10
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 -0.026 0.079 -10000 0 -0.22 80 80
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 0.009 0.021 0.061 80 -10000 0 80
GNAL -0.051 0.15 -10000 0 -0.41 80 80
GNG2 0.003 0.056 -10000 0 -0.4 10 10
CRH -0.006 0.049 -10000 0 -0.33 12 12
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.004 0.03 -10000 0 -0.28 6 6
MAPK11 0.006 0.018 -10000 0 -0.28 2 2
BARD1 signaling events

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
BARD1/CSTF1 0.01 0.042 -10000 0 -0.28 11 11
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 0.007 -10000 0 -10000 0 0
protein ubiquitination -0.057 0.07 -10000 0 -0.25 11 11
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 0.019 0.029 -10000 0 -10000 0 0
FANCF 0.009 0.025 -10000 0 -0.41 2 2
BRCA1 0.011 0 -10000 0 -10000 0 0
CCNE1 -0.13 0.17 -10000 0 -0.33 220 220
CDK2/Cyclin E1 -0.078 0.11 -10000 0 -0.22 220 220
FANCG 0.011 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.01 0.042 -10000 0 -0.28 11 11
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 -0.072 0.15 -10000 0 -0.33 133 133
DNA repair -0.015 0.087 -10000 0 -0.31 7 7
BRCA1/BARD1/ubiquitin 0.01 0.042 -10000 0 -0.28 11 11
BARD1/DNA-PK 0.024 0.032 -10000 0 -0.2 11 11
FANCL 0.011 0 -10000 0 -10000 0 0
mRNA polyadenylation -0.01 0.042 0.28 11 -10000 0 11
BRCA1/BARD1/CTIP/M/R/N Complex 0.028 0.031 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1/TopBP1 0.017 0.035 -10000 0 -0.23 11 11
BRCA1/BARD1/P53 0.023 0.033 -10000 0 -0.2 12 12
BARD1/CSTF1/BRCA1 0.017 0.035 -10000 0 -0.23 11 11
BRCA1/BACH1 0.011 0 -10000 0 -10000 0 0
BARD1 0.002 0.059 -10000 0 -0.41 11 11
PCNA 0.011 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.017 0.035 -10000 0 -0.23 11 11
BRCA1/BARD1/UbcH7 0.017 0.035 -10000 0 -0.23 11 11
BRCA1/BARD1/RAD51/PCNA -0.029 0.089 -10000 0 -0.29 11 11
BARD1/DNA-PK/P53 0.028 0.031 -10000 0 -0.18 12 12
BRCA1/BARD1/Ubiquitin 0.01 0.042 -10000 0 -0.28 11 11
BRCA1/BARD1/CTIP 0.023 0.032 -10000 0 -0.2 11 11
FA complex 0.013 0.036 -10000 0 -0.24 1 1
BARD1/EWS 0.01 0.042 -10000 0 -0.28 11 11
RBBP8 0.018 0 -10000 0 -10000 0 0
TP53 0.01 0.018 -10000 0 -0.41 1 1
TOPBP1 0.011 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.022 0.033 0.2 12 -10000 0 12
BRCA1/BARD1 -0.038 0.086 -10000 0 -0.25 11 11
CSTF1 0.011 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.002 0.042 -10000 0 -0.29 11 11
CDK2 0.011 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.091 0.16 -10000 0 -0.33 164 164
RAD50 0.011 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.01 0.042 -10000 0 -0.28 11 11
EWSR1 0.011 0 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

Figure S78.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S78.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.011 0 -9999 0 -10000 0 0
SPHK1 0.009 0.025 -9999 0 -0.33 3 3
GNAI2 0.011 0 -9999 0 -10000 0 0
mol:S1P 0.018 0.006 -9999 0 -10000 0 0
GNAO1 -0.1 0.18 -9999 0 -0.41 143 143
mol:Sphinganine-1-P 0.017 0.017 -9999 0 -0.22 3 3
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.032 0.004 -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 0.077 -9999 0 -0.41 19 19
S1PR2 0.011 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P 0 0.004 -9999 0 -10000 0 0
S1PR5 0 0.063 -9999 0 -0.35 17 17
S1PR4 0.009 0.029 -9999 0 -0.38 3 3
GNAI1 0.005 0.051 -9999 0 -0.41 8 8
S1P/S1P5/G12 0.021 0.032 -9999 0 -0.19 4 4
S1P/S1P3/Gq -0.007 0.1 -9999 0 -0.27 58 58
S1P/S1P4/Gi -0.032 0.11 -9999 0 -0.2 145 145
GNAQ 0.009 0.025 -9999 0 -0.41 2 2
GNAZ -0.002 0.073 -9999 0 -0.41 17 17
GNA14 -0.031 0.13 -9999 0 -0.41 54 54
GNA15 0.007 0.038 -9999 0 -0.33 7 7
GNA12 0.011 0 -9999 0 -10000 0 0
GNA13 0.011 0 -9999 0 -10000 0 0
GNA11 0.002 0.062 -9999 0 -0.41 12 12
ABCC1 0.011 0 -9999 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.018 0.01 -9999 0 -0.22 1 1
BAD/BCL-XL/YWHAZ 0.027 0.007 -9999 0 -10000 0 0
CDKN1B 0.021 0.041 -9999 0 -0.23 1 1
CDKN1A 0.029 0.009 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
PRKDC 0.011 0 -9999 0 -10000 0 0
FOXO3 0.029 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 -0.095 0.14 -9999 0 -0.28 204 204
mol:GTP 0 0 -9999 0 -10000 0 0
FOXO4 0.029 0.013 -9999 0 -10000 0 0
AKT1/ASK1 0.027 0.015 -9999 0 -10000 0 0
BAD/YWHAZ 0.022 0 -9999 0 -10000 0 0
RICTOR 0.009 0.025 -9999 0 -0.41 2 2
RAF1 0.011 0 -9999 0 -10000 0 0
JNK cascade -0.026 0.014 -9999 0 -10000 0 0
TSC1 0.029 0.009 -9999 0 -10000 0 0
YWHAZ 0.011 0 -9999 0 -10000 0 0
AKT1/RAF1 0.03 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 0.029 0.004 -9999 0 -10000 0 0
YWHAQ 0.011 0 -9999 0 -10000 0 0
TBC1D4 0.017 0.021 -9999 0 -0.22 4 4
MAP3K5 0.009 0.031 -9999 0 -0.41 3 3
MAPKAP1 0.011 0 -9999 0 -10000 0 0
negative regulation of cell cycle -0.011 0.015 -9999 0 -10000 0 0
YWHAH 0.011 0 -9999 0 -10000 0 0
AKT1S1 0.029 0.004 -9999 0 -10000 0 0
CASP9 0.029 0.004 -9999 0 -10000 0 0
YWHAB 0.011 0 -9999 0 -10000 0 0
p27Kip1/KPNA1 0.027 0.039 -9999 0 -0.21 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 0.033 0.009 -9999 0 -10000 0 0
KIAA1303 0 0 -9999 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.015 0.002 -9999 0 -10000 0 0
CHUK 0.029 0.004 -9999 0 -10000 0 0
BAD/BCL-XL 0.04 0.007 -9999 0 -10000 0 0
mTORC2 0.013 0.014 -9999 0 -0.21 2 2
AKT2 0.014 0 -9999 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.022 0.018 -9999 0 -10000 0 0
PDPK1 0.011 0 -9999 0 -10000 0 0
MDM2 0.029 0.004 -9999 0 -10000 0 0
MAPKKK cascade -0.029 0.004 -9999 0 -10000 0 0
MDM2/Cbp/p300 0.039 0.012 -9999 0 -10000 0 0
TSC1/TSC2 0.034 0.009 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.012 -9999 0 -10000 0 0
glucose import -0.086 0.11 -9999 0 -0.2 268 268
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.025 0.004 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
SLC2A4 -0.086 0.11 -9999 0 -0.2 268 268
GSK3A 0.029 0.004 -9999 0 -10000 0 0
FOXO1 0.028 0.015 -9999 0 -10000 0 0
GSK3B 0.029 0.004 -9999 0 -10000 0 0
SFN -0.24 0.15 -9999 0 -0.33 401 401
G1/S transition of mitotic cell cycle 0.034 0.003 -9999 0 -10000 0 0
p27Kip1/14-3-3 family -0.002 0.025 -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 0.009 0.025 -9999 0 -0.41 2 2
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.007 0.085 -9999 0 -0.41 23 23
alphaV beta3 Integrin -0.039 0.12 -9999 0 -0.28 102 102
PTK2 -0.037 0.086 -9999 0 -0.38 23 23
positive regulation of JNK cascade -0.014 0.057 -9999 0 -0.28 23 23
CDC42/GDP 0.019 0.088 -9999 0 -0.38 23 23
Rac1/GDP 0.02 0.087 -9999 0 -0.37 23 23
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 -0.017 0.07 -9999 0 -0.35 23 23
nectin-3/I-afadin 0.004 0.06 -9999 0 -0.28 23 23
RAPGEF1 0.012 0.094 -9999 0 -0.42 23 23
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.006 0.11 -9999 0 -0.47 23 23
PDGFB-D/PDGFRB -0.007 0.085 -9999 0 -0.41 23 23
TLN1 0.001 0.076 -9999 0 -0.26 35 35
Rap1/GTP -0.014 0.06 -9999 0 -0.3 23 23
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 0.004 0.06 -9999 0 -0.28 23 23
PVR 0.011 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.011 0 -9999 0 -10000 0 0
mol:GDP 0.014 0.1 -9999 0 -0.46 23 23
MLLT4 0.011 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.018 -9999 0 -0.41 1 1
PI3K 0.013 0.069 -9999 0 -0.38 6 6
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.016 0.014 -9999 0 -0.22 2 2
positive regulation of lamellipodium assembly -0.015 0.06 -9999 0 -0.3 23 23
PVRL1 0.01 0.021 -9999 0 -0.33 2 2
PVRL3 -0.007 0.085 -9999 0 -0.41 23 23
PVRL2 0.011 0 -9999 0 -10000 0 0
PIK3R1 0.007 0.04 -9999 0 -0.41 5 5
CDH1 0.009 0.025 -9999 0 -0.41 2 2
CLDN1 -0.043 0.14 -9999 0 -0.41 70 70
JAM-A/CLDN1 -0.011 0.09 -9999 0 -0.21 89 89
SRC -0.001 0.12 -9999 0 -0.52 23 23
ITGB3 -0.068 0.16 -9999 0 -0.41 102 102
nectin-1(dimer)/I-afadin/I-afadin 0.016 0.014 -9999 0 -0.22 2 2
FARP2 0.01 0.1 -9999 0 -0.45 23 23
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) 0.012 0.05 -9999 0 -0.23 23 23
nectin-1/I-afadin 0.016 0.014 -9999 0 -0.22 2 2
nectin-2/I-afadin 0.016 0 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.015 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.011 0.054 -9999 0 -0.24 23 23
CDC42/GTP/IQGAP1/filamentous actin 0.015 0 -9999 0 -10000 0 0
F11R 0.01 0.018 -9999 0 -0.41 1 1
positive regulation of filopodium formation -0.014 0.057 -9999 0 -0.28 23 23
alphaV/beta3 Integrin/Talin -0.023 0.11 -9999 0 -0.31 41 41
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 -0.005 0.081 -9999 0 -0.29 35 35
VAV2 0.009 0.1 -9999 0 -0.46 23 23
RAP1/GDP -0.016 0.07 -9999 0 -0.35 23 23
ITGAV 0.011 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.012 0.05 -9999 0 -0.23 23 23
nectin-3(dimer)/I-afadin/I-afadin 0.004 0.06 -9999 0 -0.28 23 23
Rac1/GTP -0.018 0.073 -9999 0 -0.36 23 23
PTPRM -0.013 0.089 -9999 0 -0.26 57 57
E-cadherin/beta catenin/alpha catenin -0.001 0.012 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.011 0 -9999 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.015 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 -0.032 0.11 -9999 0 -0.33 69 69
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.01 0.018 -9999 0 -0.41 1 1
RAC1-CDC42/GTP/PAK family -0.008 0.069 -9999 0 -0.18 80 80
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 0.008 0.036 -9999 0 -0.41 4 4
FGR 0.002 0.059 -9999 0 -0.41 11 11
p38 alpha/TAB1 -0.003 0.016 -9999 0 -0.21 1 1
PRKG1 -0.18 0.21 -9999 0 -0.41 241 241
DUSP8 0.007 0.04 -9999 0 -0.41 5 5
PGK/cGMP/p38 alpha -0.067 0.076 -9999 0 -0.22 24 24
apoptosis -0.003 0.015 -9999 0 -0.2 1 1
RAL/GTP 0.015 0 -9999 0 -10000 0 0
LYN 0.011 0 -9999 0 -10000 0 0
DUSP1 -0.09 0.18 -9999 0 -0.41 130 130
PAK1 0.011 0 -9999 0 -10000 0 0
SRC 0.011 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.028 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 0.015 0 -9999 0 -10000 0 0
MAPK11 0.032 0.036 -9999 0 -10000 0 0
BLK -0.015 0.087 -9999 0 -0.33 39 39
HCK 0.007 0.038 -9999 0 -0.33 7 7
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 0.028 -9999 0 -0.23 1 1
positive regulation of innate immune response 0.039 0.039 -9999 0 -0.22 1 1
LCK 0.008 0.034 -9999 0 -0.34 5 5
p38alpha-beta/MKP7 0.043 0.038 -9999 0 -10000 0 0
p38alpha-beta/MKP5 0.043 0.038 -9999 0 -10000 0 0
PGK/cGMP -0.12 0.15 -9999 0 -0.29 241 241
PAK2 0.011 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 0.018 0.074 -9999 0 -0.26 12 12
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 -0.054 0.15 -9999 0 -0.41 80 80
Regulation of Telomerase

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
Telomerase catalytic core complex -0.13 0.12 -9999 0 -0.46 3 3
RAD9A 0.011 0 -9999 0 -10000 0 0
AP1 -0.081 0.14 -9999 0 -0.29 168 168
IFNAR2 0.007 0.019 -9999 0 -0.41 1 1
AKT1 -0.012 0.058 -9999 0 -0.17 52 52
ER alpha/Oestrogen -0.028 0.094 -9999 0 -0.29 62 62
NFX1/SIN3/HDAC complex 0.032 0.016 -9999 0 -10000 0 0
EGF -0.006 0.073 -9999 0 -0.34 25 25
SMG5 0.011 0 -9999 0 -10000 0 0
SMG6 0.011 0 -9999 0 -10000 0 0
SP3/HDAC2 0.012 0.009 -9999 0 -10000 0 0
TERT/c-Abl -0.11 0.11 -9999 0 -0.45 5 5
SAP18 0.011 0.001 -9999 0 -10000 0 0
MRN complex 0.022 0 -9999 0 -10000 0 0
WT1 -0.3 0.18 -9999 0 -0.41 402 402
WRN 0.011 0 -9999 0 -10000 0 0
SP1 0.009 0.006 -9999 0 -10000 0 0
SP3 0.01 0.002 -9999 0 -10000 0 0
TERF2IP 0.011 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.1 0.09 -9999 0 -0.41 1 1
Mad/Max 0.012 0.009 -9999 0 -10000 0 0
TERT -0.13 0.12 -9999 0 -0.47 3 3
CCND1 -0.11 0.11 -9999 0 -0.48 1 1
MAX 0.01 0.002 -9999 0 -10000 0 0
RBBP7 0.011 0.001 -9999 0 -10000 0 0
RBBP4 0.008 0.031 -9999 0 -0.41 3 3
TERF2 0.01 0 -9999 0 -10000 0 0
PTGES3 0.011 0 -9999 0 -10000 0 0
SIN3A 0.011 0.001 -9999 0 -10000 0 0
Telomerase/911 0.009 0.021 -9999 0 -10000 0 0
CDKN1B -0.015 0.12 -9999 0 -0.5 23 23
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 0.011 0.001 -9999 0 -10000 0 0
TRF2/PARP2 0.016 0 -9999 0 -10000 0 0
UBE3A 0.01 0.002 -9999 0 -10000 0 0
JUN 0.005 0.048 -9999 0 -0.41 7 7
E6 -0.001 0.002 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.006 0.005 -9999 0 -10000 0 0
FOS -0.12 0.19 -9999 0 -0.41 167 167
IFN-gamma/IRF1 -0.02 0.086 -9999 0 -0.22 83 83
PARP2 0.011 0 -9999 0 -10000 0 0
BLM -0.026 0.11 -9999 0 -0.33 60 60
Telomerase -0.013 0.036 -9999 0 -10000 0 0
IRF1 0.008 0.033 -9999 0 -10000 0 0
ESR1 -0.037 0.13 -9999 0 -0.41 62 62
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 0.015 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.038 0.015 -9999 0 -10000 0 0
HDAC1 0.011 0.001 -9999 0 -10000 0 0
HDAC2 0.008 0.006 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.016 0.029 -9999 0 -0.28 5 5
ABL1 0.009 0.025 -9999 0 -0.41 2 2
MXD1 0.01 0.002 -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 -0.096 0.096 -9999 0 -10000 0 0
NR2F2 -0.008 0.09 -9999 0 -0.41 26 26
MAPK3 0.003 0.041 -9999 0 -0.22 18 18
MAPK1 0.003 0.041 -9999 0 -0.22 18 18
TGFB1/TGF beta receptor Type II 0.011 0.018 -9999 0 -0.41 1 1
NFKB1 0.01 0.018 -9999 0 -0.41 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 0.066 -9999 0 -0.41 14 14
mol:Oestrogen -0.001 0.001 -9999 0 -10000 0 0
EGF/EGFR -0.007 0.068 -9999 0 -0.25 38 38
MYC 0.002 0.057 -9999 0 -0.41 10 10
IL2 -0.009 0.06 -9999 0 -0.33 18 18
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 0.011 0.018 -9999 0 -0.41 1 1
TRF2/BLM -0.007 0.067 -9999 0 -0.2 60 60
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.11 0.11 -9999 0 -0.43 3 3
SP1/HDAC2 0.014 0.01 -9999 0 -10000 0 0
PINX1 0.011 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.1 0.09 -9999 0 -0.41 1 1
Smad3/Myc 0.016 0.043 -9999 0 -0.24 14 14
911 complex 0.022 0 -9999 0 -10000 0 0
IFNG -0.032 0.11 -9999 0 -0.3 69 69
Telomerase/PinX1 -0.1 0.09 -9999 0 -0.41 1 1
Telomerase/AKT1/mTOR/p70S6K -0.014 0.04 -9999 0 -10000 0 0
SIN3B 0.011 0.001 -9999 0 -10000 0 0
YWHAE 0.011 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.1 0.09 -9999 0 -0.41 1 1
response to DNA damage stimulus 0.003 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0.032 0 -9999 0 -10000 0 0
TRF2/WRN 0.016 0 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.1 0.09 -9999 0 -0.41 1 1
E2F1 -0.055 0.13 -9999 0 -0.33 102 102
ZNFX1 0.011 0.001 -9999 0 -10000 0 0
PIF1 -0.075 0.15 -9999 0 -0.33 138 138
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
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.023 0.076 -10000 0 -0.33 8 8
TBX21 0.004 0.25 -10000 0 -0.97 21 21
B2M 0.012 0.005 -10000 0 -10000 0 0
TYK2 0.014 0.016 -10000 0 -10000 0 0
IL12RB1 0.002 0.071 -10000 0 -0.37 18 18
GADD45B 0.037 0.17 -10000 0 -0.7 12 12
IL12RB2 -0.005 0.081 -10000 0 -0.33 30 30
GADD45G 0.015 0.25 -10000 0 -0.95 24 24
natural killer cell activation 0.003 0.016 -10000 0 -10000 0 0
RELB 0.011 0 -10000 0 -10000 0 0
RELA 0.011 0 -10000 0 -10000 0 0
IL18 0.009 0.044 -10000 0 -0.33 9 9
IL2RA -0.002 0.066 -10000 0 -0.33 21 21
IFNG -0.029 0.11 -10000 0 -0.33 60 60
STAT3 (dimer) 0.027 0.19 -10000 0 -0.64 20 20
HLA-DRB5 -0.005 0.067 -10000 0 -0.38 16 16
FASLG 0.008 0.23 -10000 0 -0.96 16 16
NF kappa B2 p52/RelB -0.064 0.17 -10000 0 -0.69 26 26
CD4 0.006 0.017 -10000 0 -0.34 1 1
SOCS1 0.01 0.018 -10000 0 -0.41 1 1
EntrezGene:6955 -0.006 0.014 -10000 0 -10000 0 0
CD3D -0.008 0.073 -10000 0 -0.37 21 21
CD3E -0.002 0.064 -10000 0 -0.39 14 14
CD3G 0 0.047 -10000 0 -0.35 9 9
IL12Rbeta2/JAK2 0.005 0.072 -10000 0 -0.24 39 39
CCL3 0.012 0.22 -10000 0 -0.88 15 15
CCL4 0.009 0.24 -10000 0 -0.98 16 16
HLA-A 0.011 0.015 -10000 0 -0.33 1 1
IL18/IL18R 0.043 0.054 -10000 0 -0.24 12 12
NOS2 0.017 0.23 -10000 0 -0.91 21 21
IL12/IL12R/TYK2/JAK2/SPHK2 0.023 0.073 -10000 0 -0.3 8 8
IL1R1 0.002 0.26 -10000 0 -1.1 20 20
IL4 0.001 0.017 -10000 0 -10000 0 0
JAK2 0.007 0.057 -10000 0 -0.42 9 9
EntrezGene:6957 -0.005 0.012 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.001 0.12 -10000 0 -0.56 18 18
RAB7A 0.043 0.18 -10000 0 -0.66 12 12
lysosomal transport 0.044 0.17 -10000 0 -0.62 13 13
FOS -0.3 0.56 -10000 0 -1.1 170 170
STAT4 (dimer) 0.04 0.2 -10000 0 -0.66 21 21
STAT5A (dimer) -0.073 0.18 -10000 0 -0.69 30 30
GZMA -0.004 0.26 -10000 0 -1 23 23
GZMB 0.002 0.23 -10000 0 -0.94 16 16
HLX 0.011 0 -10000 0 -10000 0 0
LCK 0.019 0.23 -10000 0 -0.76 26 26
TCR/CD3/MHC II/CD4 -0.042 0.12 -10000 0 -0.21 146 146
IL2/IL2R 0.008 0.062 -10000 0 -0.3 14 14
MAPK14 0.036 0.2 -10000 0 -0.68 24 24
CCR5 0.029 0.2 -10000 0 -0.83 15 15
IL1B 0.011 0.042 -10000 0 -0.44 4 4
STAT6 0.024 0.077 -10000 0 -0.26 10 10
STAT4 0.01 0.018 -10000 0 -0.41 1 1
STAT3 0.011 0 -10000 0 -10000 0 0
STAT1 0.01 0.021 -10000 0 -0.33 2 2
NFKB1 0.01 0.018 -10000 0 -0.41 1 1
NFKB2 0.011 0 -10000 0 -10000 0 0
IL12B 0.01 0.021 -10000 0 -0.31 1 1
CD8A 0.002 0.064 -10000 0 -0.39 14 14
CD8B -0.01 0.087 -10000 0 -0.35 33 33
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.023 0.075 0.33 8 -10000 0 8
IL2RB 0.01 0.018 -10000 0 -0.41 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.04 0.19 -10000 0 -0.61 21 21
IL2RG 0.005 0.047 -10000 0 -0.36 9 9
IL12 0.014 0.049 -10000 0 -0.23 16 16
STAT5A 0.01 0.018 -10000 0 -0.41 1 1
CD247 0.006 0.03 -10000 0 -0.38 3 3
IL2 -0.007 0.06 -10000 0 -0.33 18 18
SPHK2 0.011 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.003 0.061 -10000 0 -0.34 15 15
IL12/IL12R/TYK2/JAK2 0.019 0.24 -10000 0 -0.81 26 26
MAP2K3 0.03 0.2 -10000 0 -0.66 25 25
RIPK2 0.011 0 -10000 0 -10000 0 0
MAP2K6 0.032 0.2 -10000 0 -0.66 24 24
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.004 0.028 -10000 0 -0.42 2 2
IL18RAP 0.01 0.045 -10000 0 -0.38 7 7
IL12Rbeta1/TYK2 0.012 0.055 -10000 0 -0.26 18 18
EOMES -0.009 0.14 -10000 0 -1.2 7 7
STAT1 (dimer) 0.029 0.18 -10000 0 -0.63 20 20
T cell proliferation 0.038 0.16 -10000 0 -0.5 23 23
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.012 0.037 -10000 0 -0.41 4 4
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.039 0.13 -10000 0 -0.55 23 23
ATF2 0.039 0.19 -10000 0 -0.62 25 25
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.021 0.02 -9999 0 -0.17 6 6
SNTA1 0.011 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.021 0.02 -9999 0 -0.17 6 6
MAPK12 -0.009 0.073 -9999 0 -0.21 27 27
CCND1 0.003 0.033 -9999 0 -10000 0 0
p38 gamma/SNTA1 -0.003 0.068 -9999 0 -0.19 26 26
MAP2K3 0.011 0 -9999 0 -10000 0 0
PKN1 0.011 0 -9999 0 -10000 0 0
G2/M transition checkpoint -0.009 0.072 -9999 0 -0.21 27 27
MAP2K6 -0.017 0.08 -9999 0 -0.19 94 94
MAPT 0.002 0.061 -9999 0 -0.28 20 20
MAPK13 0.016 0.025 -9999 0 -0.22 6 6
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0 0.062 -9999 0 -0.28 26 26
Signaling events mediated by PRL

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
CCNE1 -0.13 0.17 -9999 0 -0.33 220 220
mol:Halofuginone 0.004 0 -9999 0 -10000 0 0
ITGA1 0.009 0.031 -9999 0 -0.41 3 3
CDKN1A 0.012 0.04 -9999 0 -0.36 1 1
PRL-3/alpha Tubulin 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ -0.042 0.1 -9999 0 -0.29 79 79
AGT -0.049 0.15 -9999 0 -0.4 79 79
CCNA2 -0.029 0.099 -9999 0 -0.33 20 20
TUBA1B 0.011 0 -9999 0 -10000 0 0
EGR1 -0.019 0.1 -9999 0 -0.28 71 71
CDK2/Cyclin E1 -0.041 0.087 -9999 0 -0.22 37 37
MAPK3 0.018 0 -9999 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.016 0 -9999 0 -10000 0 0
MAPK1 0.018 0 -9999 0 -10000 0 0
PTP4A1 0 0.075 -9999 0 -10000 0 0
PTP4A3 0.011 0 -9999 0 -10000 0 0
PTP4A2 0.011 0 -9999 0 -10000 0 0
ITGB1 0.018 0 -9999 0 -10000 0 0
SRC 0.011 0 -9999 0 -10000 0 0
RAC1 0.013 0.036 -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 0.071 -9999 0 -0.33 1 1
RABGGTA 0.011 0 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
RHOC 0.013 0.036 -9999 0 -10000 0 0
RHOA 0.013 0.036 -9999 0 -10000 0 0
cell motility 0.016 0.039 -9999 0 -10000 0 0
PRL-1/alpha Tubulin 0.006 0.07 -9999 0 -10000 0 0
PRL-3/alpha1 Integrin 0.015 0.022 -9999 0 -0.28 3 3
ROCK1 0.016 0.039 -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 0.074 -9999 0 -10000 0 0
ATF5 0.008 0.029 -9999 0 -0.33 4 4
IL1-mediated signaling events

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
UBC13/UEV1A -0.008 0.072 -10000 0 -0.28 35 35
PRKCZ 0.01 0.023 -10000 0 -0.37 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 0.022 -10000 0 -0.23 4 4
IRAK/TOLLIP 0.009 0.054 -10000 0 -0.2 35 35
IKBKB 0.011 0 -10000 0 -10000 0 0
IKBKG 0.011 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.016 0.086 -10000 0 -0.24 67 67
IL1A -0.012 0.083 -10000 0 -0.33 35 35
IL1B 0.015 0.035 -10000 0 -0.33 5 5
IRAK/TRAF6/p62/Atypical PKCs 0.01 0.048 -10000 0 -0.34 1 1
IL1R2 -0.013 0.089 -10000 0 -0.34 38 38
IL1R1 0.003 0.057 -10000 0 -0.41 10 10
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.025 0.057 0.18 22 -0.25 11 33
TOLLIP 0.011 0 -10000 0 -10000 0 0
TICAM2 0.004 0.051 -10000 0 -0.41 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 0.04 0.043 -10000 0 -10000 0 0
JUN 0.001 0.07 -10000 0 -0.28 10 10
MAP3K7 0.011 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.028 0.05 -10000 0 -0.42 3 3
IL1 alpha/IL1R1/IL1RAP/MYD88 0.011 0.057 -10000 0 -0.23 12 12
PIK3R1 0.007 0.04 -10000 0 -0.41 5 5
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.017 0.053 -10000 0 -0.26 5 5
IL1 beta fragment/IL1R1/IL1RAP 0.019 0.045 -10000 0 -0.22 17 17
NFKB1 0.01 0.018 -10000 0 -0.41 1 1
MAPK8 -0.002 0.07 -10000 0 -0.29 8 8
IRAK1 0.002 0.06 -10000 0 -0.23 35 35
IL1RN/IL1R1 -0.023 0.091 -10000 0 -0.23 87 87
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 0.031 -10000 0 -0.28 6 6
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.026 0.041 -10000 0 -0.28 4 4
CHUK 0.011 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.019 0.045 -10000 0 -0.22 17 17
IL1 beta/IL1R2 0.005 0.058 -10000 0 -0.19 43 43
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.011 0.041 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.007 0.039 -10000 0 -0.38 3 3
IRAK3 -0.007 0.085 -10000 0 -0.41 23 23
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.027 0.049 -10000 0 -0.36 3 3
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.019 0.041 -10000 0 -0.22 12 12
IL1 alpha/IL1R1/IL1RAP 0.003 0.063 -10000 0 -0.2 46 46
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 0.051 -10000 0 -10000 0 0
IL1RAP 0.009 0.031 -10000 0 -0.41 3 3
UBE2N 0.011 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.015 0.048 -10000 0 -0.3 6 6
CASP1 0.009 0.025 -10000 0 -0.41 2 2
IL1RN/IL1R2 -0.034 0.1 -10000 0 -0.24 107 107
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.026 0.043 -10000 0 -0.2 17 17
TMEM189-UBE2V1 -0.023 0.1 -10000 0 -0.41 35 35
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.017 0.059 -10000 0 -0.33 10 10
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
IL1RN -0.038 0.12 -10000 0 -0.33 79 79
TRAF6/TAK1/TAB1/TAB2 -0.011 0.043 -10000 0 -0.18 35 35
MAP2K6 -0.006 0.07 -10000 0 -0.31 7 7
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.012 0.066 -10000 0 -0.35 15 15
FYN 0.034 0.099 -10000 0 -0.44 16 16
LAT/GRAP2/SLP76 -0.012 0.081 -10000 0 -0.39 18 18
IKBKB 0.011 0 -10000 0 -10000 0 0
AKT1 0.039 0.076 -10000 0 -0.32 17 17
B2M 0.012 0.002 -10000 0 -10000 0 0
IKBKG -0.004 0.018 -10000 0 -0.12 7 7
MAP3K8 0.009 0.031 -10000 0 -0.41 3 3
mol:Ca2+ -0.006 0.017 -10000 0 -0.081 19 19
integrin-mediated signaling pathway 0.015 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.038 0.1 -10000 0 -0.44 18 18
TRPV6 -0.045 0.13 -10000 0 -0.4 61 61
CD28 0.01 0.021 -10000 0 -0.33 2 2
SHC1 0.033 0.095 -10000 0 -0.43 16 16
receptor internalization 0.028 0.088 -10000 0 -0.44 14 14
PRF1 0.022 0.13 -10000 0 -1.1 6 6
KRAS 0.01 0.015 -10000 0 -0.33 1 1
GRB2 0.011 0 -10000 0 -10000 0 0
COT/AKT1 0.04 0.063 -10000 0 -0.27 15 15
LAT 0.034 0.095 -10000 0 -0.43 16 16
EntrezGene:6955 0.001 0.002 -10000 0 -10000 0 0
CD3D -0.002 0.072 -10000 0 -0.36 21 21
CD3E 0.002 0.064 -10000 0 -0.39 14 14
CD3G 0.006 0.047 -10000 0 -0.35 9 9
RASGRP2 -0.01 0.058 -10000 0 -0.16 74 74
RASGRP1 0.041 0.084 -10000 0 -0.36 16 16
HLA-A 0.012 0.015 -10000 0 -0.33 1 1
RASSF5 0.011 0 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.015 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.025 0.035 -10000 0 -0.11 12 12
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.008 0.032 -10000 0 -0.2 10 10
PRKCA -0.006 0.046 -10000 0 -0.2 19 19
GRAP2 -0.002 0.073 -10000 0 -0.41 17 17
mol:IP3 0.004 0.081 0.18 53 -0.32 14 67
EntrezGene:6957 0.001 0.002 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.019 0.082 -10000 0 -0.41 14 14
ORAI1 0.027 0.075 0.24 61 -10000 0 61
CSK 0.032 0.097 -10000 0 -0.43 16 16
B7 family/CD28 0.032 0.097 -10000 0 -0.43 16 16
CHUK 0.011 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.028 0.11 -10000 0 -0.41 22 22
PTPN6 0.03 0.096 -10000 0 -0.43 16 16
VAV1 0.032 0.1 -10000 0 -0.46 15 15
Monovalent TCR/CD3 0.012 0.063 -10000 0 -0.29 19 19
CBL 0.011 0 -10000 0 -10000 0 0
LCK 0.031 0.1 -10000 0 -0.46 16 16
PAG1 0.031 0.099 -10000 0 -0.42 18 18
RAP1A 0.011 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.028 0.11 -10000 0 -0.46 17 17
CD80 -0.008 0.077 -10000 0 -0.33 30 30
CD86 0.01 0.021 -10000 0 -0.33 2 2
PDK1/CARD11/BCL10/MALT1 -0.01 0.039 -10000 0 -0.22 13 13
HRAS 0.011 0 -10000 0 -10000 0 0
GO:0035030 0.03 0.084 -10000 0 -0.37 16 16
CD8A 0.002 0.064 -10000 0 -0.39 14 14
CD8B -0.009 0.087 -10000 0 -0.35 33 33
PTPRC 0.003 0.059 -10000 0 -0.4 11 11
PDK1/PKC theta 0.041 0.095 -10000 0 -0.38 19 19
CSK/PAG1 0.034 0.097 -10000 0 -0.42 17 17
SOS1 0.011 0 -10000 0 -10000 0 0
peptide-MHC class I 0.018 0.011 -10000 0 -0.21 1 1
GRAP2/SLP76 -0.013 0.093 -10000 0 -0.45 18 18
STIM1 0.014 0.036 -10000 0 -10000 0 0
RAS family/GTP 0.04 0.036 -10000 0 -0.15 8 8
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.028 0.092 -10000 0 -0.46 14 14
mol:DAG -0.005 0.058 -10000 0 -0.29 15 15
RAP1A/GDP 0.012 0.015 -10000 0 -0.057 6 6
PLCG1 0.011 0 -10000 0 -10000 0 0
CD247 0.01 0.03 -10000 0 -0.39 3 3
cytotoxic T cell degranulation 0.023 0.12 -10000 0 -0.92 7 7
RAP1A/GTP -0.008 0.019 -10000 0 -0.057 74 74
mol:PI-3-4-5-P3 0.038 0.088 -10000 0 -0.37 18 18
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.002 0.095 0.19 51 -0.41 14 65
NRAS 0.011 0 -10000 0 -10000 0 0
ZAP70 0 0.063 -10000 0 -0.34 18 18
GRB2/SOS1 0.016 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.011 0.079 -10000 0 -0.39 17 17
MALT1 0.011 0 -10000 0 -10000 0 0
TRAF6 0.011 0 -10000 0 -10000 0 0
CD8 heterodimer -0.003 0.079 -10000 0 -0.26 43 43
CARD11 0.001 0.059 -10000 0 -0.34 15 15
PRKCB -0.007 0.057 -10000 0 -0.27 20 20
PRKCE -0.003 0.041 -10000 0 -0.21 14 14
PRKCQ 0.035 0.1 -10000 0 -0.42 20 20
LCP2 0.01 0.015 -10000 0 -0.33 1 1
BCL10 0.011 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.038 0.067 -10000 0 -0.28 17 17
IKK complex 0.03 0.036 -10000 0 -0.095 16 16
RAS family/GDP -0.001 0.005 -10000 0 -10000 0 0
MAP3K14 0.039 0.051 -10000 0 -0.21 13 13
PDPK1 0.04 0.073 -10000 0 -0.31 17 17
TCR/CD3/MHC I/CD8/Fyn 0.022 0.12 -10000 0 -0.48 21 21
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.014 0.051 -10000 0 -0.17 11 11
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 0.037 0.048 -10000 0 -10000 0 0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.015 0.037 -10000 0 -0.23 11 11
antigen processing and presentation of peptide antigen via MHC class I -0.031 0.042 -10000 0 -0.24 5 5
CaM/Ca2+ -0.013 0.036 -10000 0 -10000 0 0
RAP1A 0.011 0 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.018 0.05 -10000 0 -0.24 2 2
AKT1 0.024 0.049 -10000 0 -0.28 2 2
MAP2K1 0.024 0.046 -10000 0 -10000 0 0
MAP3K11 0.017 0.048 -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 0.16 -10000 0 -0.33 304 304
Rap1/GTP -0.009 0.023 -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 0.013 0.055 -10000 0 -0.18 11 11
CEBPB 0.048 0.048 -10000 0 -0.38 2 2
STAT3 0.011 0 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.018 0.067 -10000 0 -1 1 1
STAT1 0.017 0.05 -10000 0 -0.24 2 2
CALM1 0.011 0 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.027 0.1 -10000 0 -0.32 60 60
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
STAT1 (dimer)/PIAS1 0.023 0.048 -10000 0 -0.23 2 2
CEBPB/PTGES2/Cbp/p300 -0.003 0.018 -10000 0 -0.24 1 1
mol:Ca2+ 0.012 0.05 -10000 0 -0.17 11 11
MAPK3 0.033 0.042 -10000 0 -10000 0 0
STAT1 (dimer) -0.039 0.056 -10000 0 -0.36 4 4
MAPK1 0.033 0.042 -10000 0 -10000 0 0
JAK2 0.004 0.054 -10000 0 -0.41 9 9
PIK3R1 0.007 0.04 -10000 0 -0.41 5 5
JAK1 0.01 0.026 -10000 0 -0.41 2 2
CAMK2D 0.009 0.025 -10000 0 -0.41 2 2
DAPK1 0.046 0.049 -10000 0 -0.58 2 2
SMAD7 0.001 0.041 -10000 0 -0.29 2 2
CBL/CRKL/C3G 0.027 0.044 -10000 0 -10000 0 0
PI3K -0.014 0.039 -10000 0 -0.31 2 2
IFNG -0.027 0.1 -10000 0 -0.32 60 60
apoptosis 0.027 0.04 -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 -0.41 304 304
CAMK2B -0.045 0.13 -10000 0 -0.33 89 89
FRAP1 0.023 0.046 -10000 0 -0.27 2 2
PRKCD 0.026 0.049 -10000 0 -0.28 2 2
RAP1B 0.011 0 -10000 0 -10000 0 0
negative regulation of cell growth -0.031 0.042 -10000 0 -0.24 5 5
PTPN2 0.011 0 -10000 0 -10000 0 0
EP300 0.011 0 -10000 0 -10000 0 0
IRF1 0.044 0.043 -10000 0 -0.25 1 1
STAT1 (dimer)/PIASy 0.02 0.048 0.18 1 -0.23 2 3
SOCS1 0.001 0.055 -10000 0 -1.3 1 1
mol:GDP -0.011 0.029 -10000 0 -10000 0 0
CASP1 0.001 0.04 -10000 0 -0.19 4 4
PTGES2 0.01 0.018 -10000 0 -0.41 1 1
IRF9 0.04 0.019 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.014 0.038 -10000 0 -0.3 2 2
RAP1/GDP -0.009 0.023 -10000 0 -10000 0 0
CBL 0.017 0.047 -10000 0 -10000 0 0
MAP3K1 0.018 0.048 -10000 0 -10000 0 0
PIAS1 0.011 0 -10000 0 -10000 0 0
PIAS4 0.011 0 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.031 0.042 -10000 0 -0.24 5 5
PTPN11 0.011 0.05 -10000 0 -0.17 11 11
CREBBP 0.01 0.025 -10000 0 -0.41 2 2
RAPGEF1 0.011 0 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.01 0.015 -10000 0 -0.33 1 1
NFATC1 0.034 0.05 -10000 0 -0.25 15 15
NFATC2 0.015 0.049 -10000 0 -0.21 8 8
NFATC3 0.018 0.016 -10000 0 -0.31 1 1
YWHAE 0.011 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.016 0.1 -10000 0 -0.34 30 30
Exportin 1/Ran/NUP214 0.021 0.006 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.031 0.08 -10000 0 -0.35 22 22
BCL2/BAX -0.011 0.086 -10000 0 -0.28 50 50
CaM/Ca2+/Calcineurin A alpha-beta B1 0.008 0.004 -10000 0 -10000 0 0
CaM/Ca2+ 0.008 0.004 -10000 0 -10000 0 0
BAX 0.011 0 -10000 0 -10000 0 0
MAPK14 0.011 0.003 -10000 0 -10000 0 0
BAD 0.011 0 -10000 0 -10000 0 0
CABIN1/MEF2D -0.01 0.099 -10000 0 -0.38 21 21
Calcineurin A alpha-beta B1/BCL2 -0.028 0.12 -10000 0 -0.41 50 50
FKBP8 0.011 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.01 0.098 0.38 21 -10000 0 21
KPNB1 0.011 0 -10000 0 -10000 0 0
KPNA2 -0.005 0.071 -10000 0 -0.33 25 25
XPO1 0.011 0 -10000 0 -10000 0 0
SFN -0.24 0.15 -10000 0 -0.33 401 401
MAP3K8 0.008 0.031 -10000 0 -0.41 3 3
NFAT4/CK1 alpha 0.026 0.012 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 0.025 0.077 -10000 0 -0.23 36 36
CABIN1 -0.017 0.1 -10000 0 -0.34 30 30
CALM1 0.011 0.002 -10000 0 -10000 0 0
RAN 0.011 0 -10000 0 -10000 0 0
MAP3K1 0.011 0 -10000 0 -10000 0 0
CAMK4 0.004 0.05 -10000 0 -0.36 10 10
mol:Ca2+ 0 0.004 -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 0.014 0.022 -10000 0 -0.28 3 3
YWHAB 0.011 0 -10000 0 -10000 0 0
MAPK8 0.006 0.044 -10000 0 -0.41 6 6
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 0.044 0.048 -10000 0 -0.27 1 1
PRKCH 0.009 0.031 -10000 0 -0.41 3 3
CABIN1/Cbp/p300 0.015 0.019 -10000 0 -0.28 2 2
CASP3 0.011 0.003 -10000 0 -10000 0 0
PIM1 0.011 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.008 0.002 -10000 0 -10000 0 0
apoptosis -0.007 0.023 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.001 0.02 -10000 0 -10000 0 0
PRKCB -0.014 0.099 -10000 0 -0.41 32 32
PRKCE 0.011 0 -10000 0 -10000 0 0
JNK2/NFAT4 0.022 0.014 -10000 0 -0.28 1 1
BAD/BCL-XL 0.016 0.01 -10000 0 -0.22 1 1
PRKCD 0.011 0 -10000 0 -10000 0 0
NUP214 0.011 0 -10000 0 -10000 0 0
PRKCZ 0.009 0.023 -10000 0 -0.37 2 2
PRKCA -0.017 0.1 -10000 0 -0.41 36 36
PRKCG -0.037 0.12 -10000 0 -0.34 74 74
PRKCQ -0.026 0.12 -10000 0 -0.41 48 48
FKBP38/BCL2 -0.011 0.086 -10000 0 -0.28 50 50
EP300 0.011 0.003 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.011 0 -10000 0 -10000 0 0
NFATc/JNK1 0.036 0.053 -10000 0 -0.29 2 2
CaM/Ca2+/FKBP38 0.015 0.004 -10000 0 -10000 0 0
FKBP12/FK506 0.008 0 -10000 0 -10000 0 0
CSNK1A1 0.015 0.005 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.011 0.029 -10000 0 -0.2 10 10
NFATc/ERK1 0.039 0.048 -10000 0 -0.28 2 2
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.031 0.08 -10000 0 -0.35 22 22
NR4A1 0.015 0.12 -10000 0 -0.4 36 36
GSK3B 0.011 0.003 -10000 0 -10000 0 0
positive T cell selection 0.018 0.016 -10000 0 -0.31 1 1
NFAT1/CK1 alpha -0.01 0.028 -10000 0 -0.34 1 1
RCH1/ KPNB1 0.006 0.049 -10000 0 -0.22 25 25
YWHAQ 0.011 0 -10000 0 -10000 0 0
PRKACA 0.011 0.003 -10000 0 -10000 0 0
AKAP5 0.009 0.031 -10000 0 -0.41 3 3
MEF2D 0.011 0.003 -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 0.038 0.049 -10000 0 -0.29 2 2
CREBBP 0.009 0.026 -10000 0 -0.41 2 2
BCL2 -0.028 0.12 -10000 0 -0.41 50 50
FoxO family signaling

Figure S90.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S90.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.027 0.025 -9999 0 -10000 0 0
PLK1 -0.087 0.18 -9999 0 -0.6 23 23
CDKN1B 0.003 0.14 -9999 0 -0.44 28 28
FOXO3 -0.048 0.18 -9999 0 -0.5 58 58
KAT2B -0.002 0.057 -9999 0 -0.42 9 9
FOXO1/SIRT1 0.022 0.03 -9999 0 -0.2 5 5
CAT -0.038 0.17 -9999 0 -0.54 22 22
CTNNB1 0.011 0 -9999 0 -10000 0 0
AKT1 0.007 0.016 -9999 0 -10000 0 0
FOXO1 0.026 0.026 -9999 0 -0.22 5 5
MAPK10 -0.019 0.09 -9999 0 -0.19 116 116
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
FOXO4 0.038 0.076 -9999 0 -0.31 3 3
response to oxidative stress -0.005 0.018 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.072 0.15 -9999 0 -0.44 70 70
XPO1 0.012 0 -9999 0 -10000 0 0
EP300 0.012 0.001 -9999 0 -10000 0 0
BCL2L11 0.011 0.025 -9999 0 -10000 0 0
FOXO1/SKP2 0.029 0.023 -9999 0 -0.2 5 5
mol:GDP -0.005 0.018 -9999 0 -10000 0 0
RAN 0.012 0 -9999 0 -10000 0 0
GADD45A 0.012 0.096 -9999 0 -0.42 2 2
YWHAQ 0.011 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.033 0.017 -9999 0 -10000 0 0
MST1 0.001 0.042 -9999 0 -0.34 7 7
CSNK1D 0.011 0 -9999 0 -10000 0 0
CSNK1E 0.011 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.011 0.021 -9999 0 -10000 0 0
YWHAB 0.011 0 -9999 0 -10000 0 0
MAPK8 0.024 0.024 -9999 0 -0.19 6 6
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 0.009 0.026 -9999 0 -0.41 2 2
SOD2 0.02 0.12 -9999 0 -0.41 6 6
RBL2 -0.013 0.15 -9999 0 -0.8 5 5
RAL/GDP 0.016 0.012 -9999 0 -10000 0 0
CHUK 0.005 0.016 -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 0.022 0.012 -9999 0 -10000 0 0
CSNK1G1 0.011 0 -9999 0 -10000 0 0
FASLG 0 0.12 -9999 0 -1.3 4 4
SKP2 0.011 0 -9999 0 -10000 0 0
USP7 0.012 0 -9999 0 -10000 0 0
IKBKB 0.005 0.016 -9999 0 -10000 0 0
CCNB1 -0.049 0.18 -9999 0 -0.6 22 22
FOXO1-3a-4/beta catenin 0.035 0.11 -9999 0 -0.37 7 7
proteasomal ubiquitin-dependent protein catabolic process 0.029 0.023 -9999 0 -0.2 5 5
CSNK1A1 0.011 0 -9999 0 -10000 0 0
SGK1 0.004 0.031 -9999 0 -0.44 2 2
CSNK1G3 0.011 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.02 0.002 -9999 0 -10000 0 0
ZFAND5 0.042 0.067 -9999 0 -10000 0 0
SFN -0.24 0.15 -9999 0 -0.33 401 401
CDK2 0.013 0.002 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.004 0.035 -9999 0 -10000 0 0
CREBBP 0.011 0.026 -9999 0 -0.41 2 2
FBXO32 -0.13 0.4 -9999 0 -1.2 69 69
BCL6 -0.011 0.14 -9999 0 -0.67 5 5
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
PDGFR-beta signaling 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
S1P1/Sphingosine-1-phosphate 0.015 0.085 -9999 0 -0.38 23 23
PDGFB-D/PDGFRB/SLAP 0.004 0.06 -9999 0 -0.28 24 24
PDGFB-D/PDGFRB/APS/CBL 0.012 0.05 -9999 0 -0.23 23 23
AKT1 0.035 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 0.091 -9999 0 -0.41 23 23
PIK3CA 0.01 0.018 -9999 0 -0.41 1 1
FGR -0.02 0.1 -9999 0 -0.37 31 31
mol:Ca2+ 0.011 0.096 -9999 0 -0.44 23 23
MYC 0.022 0.13 -9999 0 -0.62 15 15
SHC1 0.011 0 -9999 0 -10000 0 0
HRAS/GDP 0.02 0.047 -9999 0 -0.18 27 27
LRP1/PDGFRB/PDGFB 0.011 0.054 -9999 0 -0.24 24 24
GRB10 0.01 0.018 -9999 0 -0.41 1 1
PTPN11 0.011 0 -9999 0 -10000 0 0
GO:0007205 0.01 0.097 -9999 0 -0.45 23 23
PTEN 0.006 0.044 -9999 0 -0.41 6 6
GRB2 0.011 0 -9999 0 -10000 0 0
GRB7 -0.011 0.084 -9999 0 -0.33 34 34
PDGFB-D/PDGFRB/SHP2 0.004 0.06 -9999 0 -0.28 23 23
PDGFB-D/PDGFRB/GRB10 0.004 0.061 -9999 0 -0.28 24 24
cell cycle arrest 0.004 0.06 -9999 0 -0.28 24 24
HRAS 0.011 0 -9999 0 -10000 0 0
HIF1A 0.039 0.043 -9999 0 -0.26 2 2
GAB1 0.014 0.093 -9999 0 -0.41 23 23
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.018 0.086 -9999 0 -0.37 23 23
PDGFB-D/PDGFRB 0.013 0.052 -9999 0 -0.23 23 23
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.004 0.06 -9999 0 -0.28 23 23
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.015 0.072 -9999 0 -0.34 23 23
positive regulation of MAPKKK cascade 0.004 0.059 -9999 0 -0.28 23 23
PIK3R1 0.007 0.04 -9999 0 -0.41 5 5
mol:IP3 0.01 0.098 -9999 0 -0.45 23 23
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.01 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.01 0.085 -9999 0 -0.26 53 53
SHB 0.011 0 -9999 0 -10000 0 0
BLK -0.011 0.053 -9999 0 -0.26 23 23
PTPN2 0.011 0.002 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.004 0.06 -9999 0 -0.28 23 23
BCAR1 0.011 0 -9999 0 -10000 0 0
VAV2 0.017 0.096 -9999 0 -0.39 24 24
CBL 0.011 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.004 0.06 -9999 0 -0.28 23 23
LCK -0.013 0.065 -9999 0 -0.29 23 23
PDGFRB -0.006 0.086 -9999 0 -0.41 23 23
ACP1 0.011 0 -9999 0 -10000 0 0
HCK -0.01 0.053 -9999 0 -0.26 23 23
ABL1 0.015 0.079 -9999 0 -0.34 23 23
PDGFB-D/PDGFRB/CBL 0.012 0.1 -9999 0 -0.47 23 23
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 0.021 -9999 0 -0.33 2 2
cell proliferation 0.023 0.11 -9999 0 -0.53 16 16
SLA 0.01 0.015 -9999 0 -0.33 1 1
actin cytoskeleton reorganization 0.032 0.043 -9999 0 -0.35 1 1
SRC -0.01 0.053 -9999 0 -0.26 23 23
PI3K -0.01 0.039 -9999 0 -0.33 2 2
PDGFB-D/PDGFRB/GRB7/SHC 0 0.072 -9999 0 -0.21 53 53
SH2B2 0.011 0 -9999 0 -10000 0 0
PLCgamma1/SPHK1 0.015 0.094 -9999 0 -0.42 23 23
LYN -0.01 0.053 -9999 0 -0.26 23 23
LRP1 0.009 0.025 -9999 0 -0.41 2 2
SOS1 0.011 0 -9999 0 -10000 0 0
STAT5B 0.009 0.025 -9999 0 -0.41 2 2
STAT5A 0.01 0.018 -9999 0 -0.41 1 1
NCK1-2/p130 Cas -0.004 0.039 -9999 0 -0.37 1 1
SPHK1 0.009 0.025 -9999 0 -0.33 3 3
EDG1 0.001 0.002 -9999 0 -10000 0 0
mol:DAG 0.01 0.098 -9999 0 -0.45 23 23
PLCG1 0.01 0.1 -9999 0 -0.46 23 23
NHERF/PDGFRB 0.011 0.052 -9999 0 -0.22 27 27
YES1 -0.011 0.052 -9999 0 -0.26 23 23
cell migration 0.011 0.052 -9999 0 -0.22 27 27
SHC/Grb2/SOS1 -0.004 0.036 -9999 0 -10000 0 0
SLC9A3R2 0.011 0 -9999 0 -10000 0 0
SLC9A3R1 0.008 0.029 -9999 0 -0.33 4 4
NHERF1-2/PDGFRB/PTEN 0.015 0.054 -9999 0 -0.2 28 28
FYN -0.01 0.053 -9999 0 -0.26 23 23
DOK1 0.017 0.046 -9999 0 -0.2 23 23
HRAS/GTP 0.008 0 -9999 0 -10000 0 0
PDGFB 0.011 0 -9999 0 -10000 0 0
RAC1 0.023 0.1 -9999 0 -0.37 33 33
PRKCD 0.018 0.046 -9999 0 -0.2 23 23
FER 0.018 0.046 -9999 0 -0.2 23 23
MAPKKK cascade -0.006 0.034 -9999 0 -10000 0 0
RASA1 0.016 0.052 -9999 0 -0.21 27 27
NCK1 0.009 0.025 -9999 0 -0.41 2 2
NCK2 0.011 0 -9999 0 -10000 0 0
p62DOK/Csk 0.022 0.042 -9999 0 -0.18 23 23
PDGFB-D/PDGFRB/SHB 0.004 0.06 -9999 0 -0.28 23 23
chemotaxis 0.016 0.077 -9999 0 -0.34 23 23
STAT1-3-5/STAT1-3-5 -0.008 0.036 -9999 0 -0.35 1 1
Bovine Papilomavirus E5/PDGFRB -0.003 0.06 -9999 0 -0.29 23 23
PTPRJ 0.011 0 -9999 0 -10000 0 0
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.007 0.045 -9999 0 -10000 0 0
epithelial cell differentiation -0.041 0.076 -9999 0 -0.33 13 13
ITCH 0.017 0.011 -9999 0 -10000 0 0
WWP1 0.007 0.042 -9999 0 -10000 0 0
FYN 0.011 0 -9999 0 -10000 0 0
EGFR 0 0.066 -9999 0 -0.4 14 14
PRL -0.01 0.083 -9999 0 -0.39 24 24
neuron projection morphogenesis 0.03 0.051 -9999 0 -10000 0 0
PTPRZ1 -0.015 0.081 -9999 0 -0.33 34 34
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.021 0.054 -9999 0 -0.27 3 3
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.005 0.059 -9999 0 -0.3 6 6
ADAM17 0.017 0.011 -9999 0 -10000 0 0
ErbB4/ErbB4 0.003 0.054 -9999 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.009 0.058 -9999 0 -0.28 2 2
NCOR1 0.011 0 -9999 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.011 0.055 -9999 0 -0.28 6 6
GRIN2B 0.007 0.062 -9999 0 -0.34 3 3
ErbB4/ErbB2/betacellulin 0.007 0.056 -9999 0 -0.29 3 3
STAT1 0.01 0.021 -9999 0 -0.33 2 2
HBEGF 0.011 0 -9999 0 -10000 0 0
PRLR -0.075 0.17 -9999 0 -0.41 111 111
E4ICDs/ETO2 -0.026 0.096 -9999 0 -0.35 11 11
axon guidance 0.014 0.037 -9999 0 -10000 0 0
NEDD4 -0.02 0.12 -9999 0 -0.41 44 44
Prolactin receptor/Prolactin receptor/Prolactin -0.058 0.13 -9999 0 -0.29 128 128
CBFA2T3 -0.049 0.15 -9999 0 -0.41 78 78
ErbB4/ErbB2/HBEGF 0.015 0.042 -9999 0 -10000 0 0
MAPK3 0.025 0.052 -9999 0 -10000 0 0
STAT1 (dimer) 0.007 0.047 -9999 0 -0.28 1 1
MAPK1 0.025 0.052 -9999 0 -10000 0 0
JAK2 0.004 0.054 -9999 0 -0.41 9 9
ErbB4/ErbB2/neuregulin 1 beta 0.007 0.061 -9999 0 -0.29 7 7
NRG1 0.01 0.058 -9999 0 -0.28 21 21
NRG3 -0.008 0.068 -9999 0 -0.33 23 23
NRG2 -0.052 0.15 -9999 0 -0.41 81 81
NRG4 -0.02 0.097 -9999 0 -0.33 49 49
heart development 0.014 0.037 -9999 0 -10000 0 0
neural crest cell migration 0.007 0.061 -9999 0 -0.29 7 7
ERBB2 0.015 0.039 -9999 0 -0.22 14 14
WWOX/E4ICDs 0.007 0.045 -9999 0 -10000 0 0
SHC1 0.011 0 -9999 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.007 0.077 -9999 0 -0.34 9 9
apoptosis 0.007 0.037 -9999 0 -10000 0 0
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.029 0.097 -9999 0 -0.34 13 13
ErbB4/ErbB2/epiregulin -0.009 0.068 -9999 0 -0.3 3 3
ErbB4/ErbB4/betacellulin/betacellulin -0.001 0.062 -9999 0 -0.36 3 3
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.032 0.11 -9999 0 -0.32 34 34
MDM2 0.009 0.046 -9999 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.008 0.046 -9999 0 -0.27 6 6
STAT5A 0.018 0.037 -9999 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta 0.006 0.067 -9999 0 -0.32 10 10
DLG4 0.008 0.036 -9999 0 -0.41 4 4
GRB2/SHC 0.016 0 -9999 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.011 0.033 -9999 0 -10000 0 0
STAT5A (dimer) -0.043 0.081 -9999 0 -0.35 13 13
MAP3K7IP2 0 0 -9999 0 -10000 0 0
STAT5B (dimer) 0.018 0.039 -9999 0 -0.32 1 1
LRIG1 0.009 0.031 -9999 0 -0.41 3 3
EREG -0.034 0.11 -9999 0 -0.33 70 70
BTC -0.003 0.075 -9999 0 -0.41 18 18
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.016 0.035 -9999 0 -10000 0 0
ERBB4 0.003 0.054 -9999 0 -10000 0 0
STAT5B 0.009 0.025 -9999 0 -0.41 2 2
YAP1 -0.001 0.023 -9999 0 -0.52 1 1
GRB2 0.011 0 -9999 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0 0.067 -9999 0 -0.3 5 5
glial cell differentiation 0.011 0.033 -9999 0 -10000 0 0
WWOX 0.011 0 -9999 0 -10000 0 0
cell proliferation 0.01 0.069 -9999 0 -0.3 1 1
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.069 0.088 -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 0.018 -9999 0 -0.41 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucose -0.074 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 0.016 0.026 -9999 0 -0.28 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 0.022 0.011 -9999 0 -0.23 1 1
YWHAG 0.011 0 -9999 0 -10000 0 0
ASIP 0.007 0.015 -9999 0 -0.33 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 0.025 0 -9999 0 -10000 0 0
PRKCZ 0.01 0.023 -9999 0 -0.37 2 2
TRIP10 0.011 0 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.015 0 -9999 0 -10000 0 0
AS160/14-3-3 -0.006 0.028 -9999 0 -10000 0 0
VAMP2 0.011 0 -9999 0 -10000 0 0
SLC2A4 -0.081 0.11 -9999 0 -0.34 1 1
STX4 0.011 0 -9999 0 -10000 0 0
GSK3B 0.021 0 -9999 0 -10000 0 0
SFN -0.24 0.15 -9999 0 -0.33 401 401
LNPEP 0.011 0 -9999 0 -10000 0 0
YWHAE 0.011 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
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 0.032 0.23 9 -10000 0 9
CDKN1A -0.001 0.027 -10000 0 -0.61 1 1
KAT2B 0.004 0.054 -10000 0 -0.41 9 9
BAX 0.011 0 -10000 0 -10000 0 0
FOXO3 0 0.006 -10000 0 -10000 0 0
FOXO1 0.009 0.031 -10000 0 -0.41 3 3
FOXO4 0.016 0.022 -10000 0 -0.24 4 4
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.011 0 -10000 0 -10000 0 0
TAT 0.007 0.015 -10000 0 -0.33 1 1
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.015 0.078 -10000 0 -0.23 61 61
PPARGC1A -0.079 0.17 -10000 0 -0.41 116 116
FHL2 0.007 0.04 -10000 0 -0.41 5 5
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 -0.001 0.018 0.14 1 -0.28 2 3
HIST2H4A 0.012 0.032 -10000 0 -0.23 9 9
SIRT1/FOXO3a -0.001 0.015 0.13 1 -0.23 2 3
SIRT1 0.006 0.026 0.18 1 -0.41 2 3
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 -0.001 0.015 -10000 0 -0.23 2 2
SIRT1/Histone H1b 0.012 0.026 -10000 0 -0.22 4 4
apoptosis 0.001 0.015 0.23 2 -0.13 1 3
SIRT1/PGC1A -0.051 0.098 0.12 1 -0.24 117 118
p53/SIRT1 -0.001 0.026 0.36 1 -0.28 3 4
SIRT1/FOXO4 0.016 0.024 0.14 1 -0.2 6 7
FOXO1/FHL2/SIRT1 0.015 0.03 -10000 0 -0.21 10 10
HIST1H1E 0.012 0.025 -10000 0 -0.24 2 2
SIRT1/p300 -0.001 0.018 0.14 1 -0.28 2 3
muscle cell differentiation 0.014 0.065 0.19 62 -0.14 1 63
TP53 0.006 0.019 0.18 1 -0.41 1 2
KU70/SIRT1/BAX -0.001 0.015 0.13 1 -0.23 2 3
CREBBP 0.009 0.025 -10000 0 -0.41 2 2
MEF2D 0.011 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.001 0.02 0.14 1 -0.26 3 4
ACSS2 0.015 0.019 -10000 0 -0.28 2 2
SIRT1/PCAF/MYOD -0.014 0.065 0.14 1 -0.19 62 63
Syndecan-3-mediated 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
CTTN 0.011 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.015 0.082 -9999 0 -10000 0 0
Syndecan-3/Neurocan 0.006 0.028 -9999 0 -10000 0 0
POMC -0.012 0.088 -9999 0 -0.35 34 34
EGFR 0 0.066 -9999 0 -0.4 14 14
Syndecan-3/EGFR 0.015 0.032 -9999 0 -10000 0 0
AGRP 0.005 0.021 -9999 0 -0.33 2 2
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 0.006 0.047 -9999 0 -0.41 7 7
APH1A 0.011 0 -9999 0 -10000 0 0
NCAN -0.004 0.058 -9999 0 -0.33 17 17
long-term memory 0.026 0.006 -9999 0 -10000 0 0
Syndecan-3/IL8 -0.025 0.071 -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 -0.001 0.005 -9999 0 -10000 0 0
MC4R -0.004 0.057 -9999 0 -0.33 16 16
SRC 0.011 0 -9999 0 -10000 0 0
PTN -0.09 0.18 -9999 0 -0.41 130 130
FGFR/FGF/Syndecan-3 -0.001 0.005 -9999 0 -10000 0 0
neuron projection morphogenesis -0.026 0.078 -9999 0 -0.29 3 3
Syndecan-3/AgRP 0.011 0.015 -9999 0 -10000 0 0
Syndecan-3/AgRP/MC4R 0.004 0.028 -9999 0 -10000 0 0
Fyn/Cortactin 0.016 0 -9999 0 -10000 0 0
SDC3 -0.001 0.005 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.025 0.07 -9999 0 -10000 0 0
IL8 -0.088 0.15 -9999 0 -0.33 158 158
Syndecan-3/Fyn/Cortactin 0.026 0.006 -9999 0 -10000 0 0
Syndecan-3/CASK 0 0.004 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.01 0.073 -9999 0 -0.24 48 48
Gamma Secretase 0.03 0.024 -9999 0 -10000 0 0
ErbB2/ErbB3 signaling 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
USP8 0.015 0.002 -9999 0 -10000 0 0
RAS family/GTP 0.009 0.05 -9999 0 -0.27 5 5
NFATC4 0.015 0.047 -9999 0 -0.33 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 0.003 0.048 -9999 0 -0.33 2 2
JUN -0.006 0.068 -9999 0 -0.34 4 4
HRAS 0.01 0.001 -9999 0 -10000 0 0
DOCK7 0.014 0.048 -9999 0 -0.32 2 2
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.003 0.052 -9999 0 -0.21 22 22
AKT1 0.009 0.001 -9999 0 -10000 0 0
BAD 0.015 0.001 -9999 0 -10000 0 0
MAPK10 -0.009 0.067 -9999 0 -0.22 12 12
mol:GTP -0.001 0.001 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.004 0.052 -9999 0 -0.36 2 2
RAF1 0.011 0.055 -9999 0 -0.28 5 5
ErbB2/ErbB3/neuregulin 2 -0.028 0.086 -9999 0 -0.21 94 94
STAT3 0.001 0.003 -9999 0 -10000 0 0
cell migration 0.001 0.062 -9999 0 -0.2 17 17
mol:PI-3-4-5-P3 0 0.001 -9999 0 -10000 0 0
cell proliferation -0.078 0.18 -9999 0 -0.41 65 65
FOS -0.12 0.24 -9999 0 -0.47 168 168
NRAS 0.01 0.001 -9999 0 -10000 0 0
mol:Ca2+ 0.003 0.048 -9999 0 -0.33 2 2
MAPK3 -0.043 0.13 -9999 0 -0.41 16 16
MAPK1 -0.043 0.13 -9999 0 -0.41 16 16
JAK2 0.011 0.052 -9999 0 -0.32 2 2
NF2 0 0.002 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.01 0.052 -9999 0 -0.23 22 22
NRG1 -0.006 0.081 -9999 0 -0.41 21 21
GRB2/SOS1 0.016 0.001 -9999 0 -10000 0 0
MAPK8 0.004 0.058 -9999 0 -0.22 28 28
MAPK9 0.021 0.029 -9999 0 -0.16 2 2
ERBB2 -0.006 0.036 -9999 0 -0.23 14 14
ERBB3 0.008 0.031 -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) 0.017 0.003 -9999 0 -10000 0 0
RNF41 0.02 0.003 -9999 0 -10000 0 0
FRAP1 0.008 0.001 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.007 0.029 -9999 0 -0.23 2 2
ErbB2/ErbB2/HSP90 (dimer) -0.005 0.029 -9999 0 -0.18 14 14
CHRNA1 -0.053 0.12 -9999 0 -0.3 58 58
myelination 0.02 0.044 -9999 0 -0.31 2 2
PPP3CB 0.005 0.045 -9999 0 -0.3 2 2
KRAS 0.01 0.015 -9999 0 -0.33 1 1
RAC1-CDC42/GDP 0.022 0.046 -9999 0 -0.34 2 2
NRG2 -0.052 0.15 -9999 0 -0.41 81 81
mol:GDP 0.01 0.052 -9999 0 -0.23 22 22
SOS1 0.011 0.001 -9999 0 -10000 0 0
MAP2K2 0.011 0.061 -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 0.048 -9999 0 -0.31 2 2
MAP2K1 -0.048 0.13 -9999 0 -0.43 15 15
heart morphogenesis 0.003 0.048 -9999 0 -0.33 2 2
RAS family/GDP 0.016 0.048 -9999 0 -0.28 4 4
GRB2 0.011 0.001 -9999 0 -10000 0 0
PRKACA -0.001 0.003 -9999 0 -10000 0 0
CHRNE 0.006 0.022 -9999 0 -0.18 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 0.003 0.048 -9999 0 -0.33 2 2
CDC42 0.011 0 -9999 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.017 0.05 -9999 0 -0.21 18 18
MAP4K1 0.003 0.052 -9999 0 -0.33 13 13
MAP3K8 0.009 0.031 -9999 0 -0.41 3 3
PRKCB -0.014 0.099 -9999 0 -0.41 32 32
DBNL 0.011 0 -9999 0 -10000 0 0
CRKL 0.011 0 -9999 0 -10000 0 0
MAP3K1 0.029 0.038 -9999 0 -0.22 1 1
JUN -0.01 0.14 -9999 0 -0.52 38 38
MAP3K7 0.029 0.038 -9999 0 -0.22 1 1
GRAP2 -0.002 0.073 -9999 0 -0.41 17 17
CRK 0.011 0 -9999 0 -10000 0 0
MAP2K4 0.034 0.039 -9999 0 -0.22 1 1
LAT 0.011 0 -9999 0 -10000 0 0
LCP2 0.01 0.015 -9999 0 -0.33 1 1
MAPK8 -0.014 0.15 -9999 0 -0.55 38 38
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.024 0.04 -9999 0 -0.19 17 17
LAT/GRAP2/SLP76/HPK1/HIP-55 0.022 0.047 -9999 0 -0.2 18 18
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.011 0 -10000 0 -10000 0 0
mol:PIP3 -0.024 0.081 0.23 5 -0.25 57 62
FRAP1 0.008 0.019 -10000 0 -10000 0 0
AKT1 0 0.073 0.2 5 -0.2 57 62
INSR 0.011 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.008 0.002 -10000 0 -10000 0 0
mol:GTP -0.016 0.049 -10000 0 -0.31 2 2
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.005 0.014 -10000 0 -10000 0 0
TSC2 0.011 0 -10000 0 -10000 0 0
RHEB/GDP -0.014 0.041 -10000 0 -0.27 2 2
TSC1 0.01 0.018 -10000 0 -0.41 1 1
Insulin Receptor/IRS1 -0.017 0.093 -10000 0 -0.3 54 54
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.006 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 0.041 0.16 5 -0.21 2 7
MAP3K5 0.007 0.025 -10000 0 -0.32 3 3
PIK3R1 0.007 0.04 -10000 0 -0.41 5 5
apoptosis 0.007 0.025 -10000 0 -0.32 3 3
mol:LY294002 0 0 -10000 0 -0.001 54 54
EIF4B 0.016 0.038 0.16 5 -0.19 2 7
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.018 0.033 -10000 0 -0.17 2 2
eIF4E/eIF4G1/eIF4A1 -0.001 0.004 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.01 0.09 -10000 0 -0.27 58 58
mTOR/RHEB/GTP/Raptor/GBL 0.017 0.029 0.15 5 -0.14 2 7
FKBP1A 0.011 0 -10000 0 -10000 0 0
RHEB/GTP -0.014 0.041 -10000 0 -0.27 2 2
mol:Amino Acids 0 0 -10000 0 -0.001 54 54
FKBP12/Rapamycin 0.008 0.001 -10000 0 -10000 0 0
PDPK1 -0.022 0.073 0.21 5 -0.22 57 62
EIF4E 0.011 0 -10000 0 -10000 0 0
ASK1/PP5C 0.012 0.046 -10000 0 -0.58 3 3
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.014 0.002 -10000 0 -10000 0 0
TSC1/TSC2 0.011 0.061 -10000 0 -0.33 2 2
tumor necrosis factor receptor activity 0 0 0.001 54 -10000 0 54
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 -0.026 0.099 -10000 0 -0.32 54 54
INS 0.001 0.003 -10000 0 -10000 0 0
PTEN 0.006 0.044 -10000 0 -0.41 6 6
PDK2 -0.022 0.073 0.21 5 -0.22 57 62
EIF4EBP1 0.012 0.007 -10000 0 -10000 0 0
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
PPP2R5D 0.013 0.018 -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 -10000 0 6
EEF2 0.014 0.001 -10000 0 -10000 0 0
eIF4E/4E-BP1 0.017 0.005 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 -0.007 0.048 -10000 0 -1.1 1 1
oxygen homeostasis -0.002 0.014 -10000 0 -10000 0 0
TCEB2 0.01 0.015 -10000 0 -0.33 1 1
TCEB1 0.011 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.017 0.04 -10000 0 -0.29 4 4
EPO -0.023 0.21 -10000 0 -0.52 28 28
FIH (dimer) 0.009 0.013 -10000 0 -10000 0 0
APEX1 0.007 0.015 -10000 0 -10000 0 0
SERPINE1 -0.015 0.2 -10000 0 -0.53 17 17
FLT1 -0.012 0.061 -10000 0 -1.1 1 1
ADORA2A -0.013 0.19 -10000 0 -0.48 17 17
germ cell development -0.022 0.21 -10000 0 -0.52 27 27
SLC11A2 -0.013 0.19 -10000 0 -0.49 16 16
BHLHE40 -0.013 0.19 -10000 0 -0.5 15 15
HIF1AN 0.009 0.013 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.005 0.12 -10000 0 -0.32 11 11
ETS1 0.021 0.02 -10000 0 -0.42 1 1
CITED2 -0.036 0.18 -10000 0 -1 17 17
KDR -0.066 0.26 -10000 0 -1.1 33 33
PGK1 -0.013 0.19 -10000 0 -0.49 16 16
SIRT1 0.009 0.025 -10000 0 -0.41 2 2
response to hypoxia 0 0.002 -10000 0 -10000 0 0
HIF2A/ARNT -0.017 0.22 -10000 0 -0.55 18 18
EPAS1 0.01 0.088 -10000 0 -0.37 3 3
SP1 0.017 0.001 -10000 0 -10000 0 0
ABCG2 -0.14 0.3 -10000 0 -0.53 103 103
EFNA1 -0.013 0.19 -10000 0 -0.5 16 16
FXN -0.013 0.19 -10000 0 -0.48 17 17
POU5F1 -0.024 0.21 -10000 0 -0.54 27 27
neuron apoptosis 0.017 0.21 0.54 18 -10000 0 18
EP300 0.011 0 -10000 0 -10000 0 0
EGLN3 0.006 0.033 -10000 0 -0.35 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 0.022 0.014 -10000 0 -0.2 2 2
VHL 0.01 0.018 -10000 0 -0.41 1 1
ARNT 0.007 0.015 -10000 0 -10000 0 0
SLC2A1 -0.013 0.19 -10000 0 -0.5 14 14
TWIST1 -0.039 0.23 -10000 0 -0.54 57 57
ELK1 0.016 0.01 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0 0.11 -10000 0 -0.43 3 3
VEGFA -0.013 0.19 -10000 0 -0.49 16 16
CREBBP 0.009 0.025 -10000 0 -0.41 2 2
IL2 signaling events mediated by PI3K

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
BCL2L1 0.039 0.042 -9999 0 -0.54 1 1
UGCG 0.004 0.094 -9999 0 -0.63 11 11
AKT1/mTOR/p70S6K/Hsp90/TERT 0.023 0.098 -9999 0 -0.26 31 31
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucosylceramide 0.006 0.093 -9999 0 -0.62 11 11
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 60 60
FRAP1 0.019 0.15 -9999 0 -0.39 60 60
FOXO3 0.039 0.098 -9999 0 -0.36 17 17
AKT1 0.034 0.1 -9999 0 -0.38 17 17
GAB2 0.007 0.036 -9999 0 -0.41 4 4
SMPD1 0.017 0.02 -9999 0 -10000 0 0
SGMS1 0.017 0.02 -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 0.027 -9999 0 -0.24 6 6
CALM1 0.011 0 -9999 0 -10000 0 0
cell proliferation 0.021 0.074 -9999 0 -0.29 21 21
EIF3A 0.011 0 -9999 0 -10000 0 0
PI3K 0.016 0.032 -9999 0 -0.28 6 6
RPS6KB1 0.014 0.023 -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 0.029 -9999 0 -0.33 4 4
PIK3R1 0.008 0.041 -9999 0 -0.41 5 5
JAK1 0.011 0.026 -9999 0 -0.41 2 2
NFKB1 0.01 0.018 -9999 0 -0.41 1 1
MYC 0.03 0.15 -9999 0 -0.82 12 12
MYB 0.012 0.047 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.039 0.071 -9999 0 -0.29 9 9
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.025 0.021 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.039 0.07 -9999 0 -0.28 9 9
Rac1/GDP 0.019 0.025 -9999 0 -0.21 6 6
T cell proliferation 0.043 0.068 -9999 0 -0.35 3 3
SHC1 0.011 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 0.007 -9999 0 -10000 0 0
PRKCZ 0.043 0.069 -9999 0 -0.36 3 3
NF kappa B1 p50/RelA -0.032 0.11 -9999 0 -0.34 60 60
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.034 0.045 -9999 0 -0.44 2 2
HSP90AA1 0.011 0 -9999 0 -10000 0 0
RELA 0.011 0 -9999 0 -10000 0 0
IL2RA -0.003 0.066 -9999 0 -0.33 21 21
IL2RB 0.012 0.018 -9999 0 -0.41 1 1
TERT -0.11 0.16 -9999 0 -0.33 198 198
E2F1 0.014 0.032 -9999 0 -10000 0 0
SOS1 0.011 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 0.011 0.004 -9999 0 -10000 0 0
IL2RG 0.006 0.047 -9999 0 -0.35 9 9
actin cytoskeleton organization 0.043 0.068 -9999 0 -0.35 3 3
GRB2 0.011 0.004 -9999 0 -10000 0 0
IL2 -0.005 0.06 -9999 0 -0.33 18 18
PIK3CA 0.011 0.018 -9999 0 -0.41 1 1
Rac1/GTP 0.024 0.025 -9999 0 -0.19 6 6
LCK 0.009 0.034 -9999 0 -0.34 5 5
BCL2 -0.018 0.26 -9999 0 -0.81 51 51
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.003 0.052 0.36 11 -10000 0 11
PI3K Class IB/PDE3B 0.003 0.052 -10000 0 -0.36 11 11
PDE3B 0.003 0.052 -10000 0 -0.36 11 11
EPO 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
BCL2L1 0.021 0.11 -10000 0 -0.44 6 6
CRKL 0.019 0.053 -10000 0 -0.24 6 6
mol:DAG 0.019 0.066 -10000 0 -0.24 19 19
HRAS 0.035 0.05 -10000 0 -10000 0 0
MAPK8 0.015 0.048 -10000 0 -0.21 9 9
RAP1A 0.019 0.053 -10000 0 -0.24 6 6
GAB1 0.017 0.057 -10000 0 -0.24 8 8
MAPK14 0.018 0.041 -10000 0 -0.18 16 16
EPO -0.003 0.073 -10000 0 -0.4 17 17
PLCG1 0.019 0.067 -10000 0 -0.24 19 19
EPOR/TRPC2/IP3 Receptors 0.007 0.038 -10000 0 -0.32 7 7
RAPGEF1 0.011 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.012 0.049 -10000 0 -0.22 18 18
GAB1/SHC/GRB2/SOS1 -0.012 0.036 -10000 0 -0.22 2 2
EPO/EPOR (dimer) 0.005 0.057 -10000 0 -0.26 24 24
IRS2 -0.007 0.085 -10000 0 -0.26 19 19
STAT1 0.019 0.088 -10000 0 -0.37 6 6
STAT5B 0.018 0.079 -10000 0 -0.25 20 20
cell proliferation 0.021 0.044 -10000 0 -0.21 2 2
GAB1/SHIP/PIK3R1/SHP2/SHC -0.013 0.04 -10000 0 -0.23 7 7
TEC 0.019 0.054 -10000 0 -0.24 6 6
SOCS3 0.009 0.025 -10000 0 -0.41 2 2
STAT1 (dimer) 0.019 0.087 -10000 0 -0.37 6 6
JAK2 0.004 0.054 -10000 0 -0.41 9 9
PIK3R1 0.007 0.04 -10000 0 -0.41 5 5
EPO/EPOR (dimer)/JAK2 0.024 0.06 -10000 0 -0.23 8 8
EPO/EPOR 0.005 0.057 -10000 0 -0.26 24 24
LYN 0.011 0.004 -10000 0 -10000 0 0
TEC/VAV2 0.025 0.053 -10000 0 -0.22 6 6
elevation of cytosolic calcium ion concentration 0.007 0.038 -10000 0 -0.32 7 7
SHC1 0.011 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.017 0.048 -10000 0 -0.22 16 16
mol:IP3 0.019 0.066 -10000 0 -0.24 19 19
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.003 0.085 -10000 0 -0.25 22 22
SH2B3 0.01 0.019 -10000 0 -0.41 1 1
NFKB1 0.018 0.042 -10000 0 -0.19 17 17
EPO/EPOR (dimer)/JAK2/SOCS3 -0.01 0.049 0.23 1 -0.22 27 28
PTPN6 0.013 0.056 -10000 0 -0.19 21 21
TEC/VAV2/GRB2 0.03 0.051 -10000 0 -0.21 6 6
EPOR 0.007 0.038 -10000 0 -0.32 7 7
INPP5D 0.01 0.018 -10000 0 -0.41 1 1
mol:GDP -0.012 0.036 -10000 0 -0.22 2 2
SOS1 0.011 0 -10000 0 -10000 0 0
PLCG2 0.01 0.023 -10000 0 -0.37 2 2
CRKL/CBL/C3G 0.03 0.051 -10000 0 -0.21 6 6
VAV2 0.019 0.053 -10000 0 -0.24 6 6
CBL 0.019 0.053 -10000 0 -0.24 6 6
SHC/Grb2/SOS1 -0.012 0.036 -10000 0 -0.21 6 6
STAT5A 0.018 0.079 -10000 0 -0.25 20 20
GRB2 0.011 0 -10000 0 -10000 0 0
STAT5 (dimer) 0.024 0.1 -10000 0 -0.27 51 51
LYN/PLCgamma2 0.015 0.017 -10000 0 -0.25 2 2
PTPN11 0.011 0 -10000 0 -10000 0 0
BTK 0.018 0.056 -10000 0 -0.27 6 6
BCL2 -0.024 0.25 -10000 0 -0.79 50 50
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.011 0.018 -10000 0 -0.4 1 1
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.011 0.097 0.46 5 -10000 0 5
IL27/IL27R/JAK1 -0.017 0.11 -10000 0 -0.84 3 3
TBX21 0.001 0.12 -10000 0 -0.52 7 7
IL12B 0.006 0.015 -10000 0 -0.33 1 1
IL12A 0.002 0.041 -10000 0 -0.24 15 15
IL6ST -0.056 0.16 -10000 0 -0.42 86 86
IL27RA/JAK1 0.012 0.071 -10000 0 -1.1 2 2
IL27 0.002 0.05 -10000 0 -0.33 12 12
TYK2 0.012 0.005 -10000 0 -10000 0 0
T-helper cell lineage commitment 0 0.047 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.011 0.097 0.46 5 -10000 0 5
T cell proliferation during immune response 0.011 0.097 0.46 5 -10000 0 5
MAPKKK cascade -0.011 0.097 -10000 0 -0.46 5 5
STAT3 0.011 0 -10000 0 -10000 0 0
STAT2 0.011 0 -10000 0 -10000 0 0
STAT1 0.01 0.021 -10000 0 -0.33 2 2
IL12RB1 -0.001 0.065 -10000 0 -0.35 18 18
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.003 0.12 -10000 0 -0.47 11 11
IL27/IL27R/JAK2/TYK2 -0.012 0.098 -10000 0 -0.47 5 5
positive regulation of T cell mediated cytotoxicity -0.011 0.097 -10000 0 -0.46 5 5
STAT1 (dimer) -0.041 0.12 0.47 4 -0.78 4 8
JAK2 0.004 0.054 -10000 0 -0.41 9 9
JAK1 0.01 0.025 -10000 0 -0.41 2 2
STAT2 (dimer) -0.005 0.093 -10000 0 -0.44 5 5
T cell proliferation -0.012 0.1 -10000 0 -0.41 12 12
IL12/IL12R/TYK2/JAK2 0.014 0.052 -10000 0 -0.52 1 1
IL17A -0.002 0.046 -10000 0 -10000 0 0
mast cell activation 0.011 0.097 0.46 5 -10000 0 5
IFNG 0 0.022 -10000 0 -0.073 5 5
T cell differentiation -0.002 0.004 -10000 0 -0.015 16 16
STAT3 (dimer) -0.005 0.093 -10000 0 -0.44 5 5
STAT5A (dimer) -0.005 0.093 -10000 0 -0.44 5 5
STAT4 (dimer) -0.005 0.093 -10000 0 -0.44 5 5
STAT4 0.01 0.018 -10000 0 -0.41 1 1
T cell activation -0.007 0.009 0.12 2 -10000 0 2
IL27R/JAK2/TYK2 -0.015 0.11 -10000 0 -0.71 4 4
GATA3 -0.012 0.13 -10000 0 -1.2 6 6
IL18 0.005 0.03 -10000 0 -0.23 9 9
positive regulation of mast cell cytokine production -0.005 0.092 -10000 0 -0.43 5 5
IL27/EBI3 0.005 0.055 -10000 0 -0.25 21 21
IL27RA 0.004 0.075 -10000 0 -1.2 2 2
IL6 -0.006 0.083 -10000 0 -0.38 25 25
STAT5A 0.01 0.018 -10000 0 -0.41 1 1
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 -0.002 0.036 0.46 2 -10000 0 2
IL1B 0.007 0.025 -10000 0 -0.29 4 4
EBI3 0.003 0.053 -10000 0 -0.34 13 13
TNF -0.02 0.078 -10000 0 -0.23 68 68
IL23-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
CCL2 0.018 0.23 -9999 0 -1.2 11 11
IL23A 0.019 0.21 -9999 0 -0.99 11 11
NF kappa B1 p50/RelA/I kappa B alpha -0.042 0.16 -9999 0 -0.95 10 10
positive regulation of T cell mediated cytotoxicity 0.019 0.22 -9999 0 -1 11 11
ITGA3 0.023 0.2 -9999 0 -1 8 8
IL17F 0.032 0.15 -9999 0 -0.63 10 10
IL12B 0.015 0.025 -9999 0 -0.32 1 1
STAT1 (dimer) 0.018 0.21 -9999 0 -0.97 11 11
CD4 0.025 0.2 -9999 0 -0.99 8 8
IL23 0.015 0.2 -9999 0 -0.95 11 11
IL23R 0.021 0.052 -9999 0 -10000 0 0
IL1B 0.017 0.22 -9999 0 -1.1 11 11
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 0.02 0.2 -9999 0 -0.96 9 9
TYK2 0.015 0.013 -9999 0 -10000 0 0
STAT4 0.01 0.018 -9999 0 -0.41 1 1
STAT3 0.011 0 -9999 0 -10000 0 0
IL18RAP 0.005 0.044 -9999 0 -0.38 7 7
IL12RB1 0.003 0.07 -9999 0 -0.36 18 18
PIK3CA 0.01 0.018 -9999 0 -0.41 1 1
IL12Rbeta1/TYK2 0.011 0.052 -9999 0 -0.25 18 18
IL23R/JAK2 0.028 0.075 -9999 0 -10000 0 0
positive regulation of chronic inflammatory response 0.019 0.22 -9999 0 -1 11 11
natural killer cell activation -0.001 0.005 -9999 0 -10000 0 0
JAK2 0.013 0.059 -9999 0 -0.42 9 9
PIK3R1 0.007 0.04 -9999 0 -0.41 5 5
NFKB1 0.011 0.018 -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 0.016 0.2 -9999 0 -0.9 11 11
ALOX12B 0.019 0.2 -9999 0 -0.96 9 9
CXCL1 -0.003 0.24 -9999 0 -1.1 15 15
T cell proliferation 0.019 0.22 -9999 0 -1 11 11
NFKBIA 0.012 0.002 -9999 0 -10000 0 0
IL17A 0.043 0.13 -9999 0 -0.52 7 7
PI3K -0.025 0.18 -9999 0 -0.93 11 11
IFNG 0.003 0.019 -9999 0 -10000 0 0
STAT3 (dimer) -0.046 0.16 -9999 0 -0.92 10 10
IL18R1 0.007 0.036 -9999 0 -0.41 4 4
IL23/IL23R/JAK2/TYK2/SOCS3 0.03 0.14 -9999 0 -0.6 9 9
IL18/IL18R 0.014 0.045 -9999 0 -0.22 15 15
macrophage activation -0.003 0.01 -9999 0 -0.041 12 12
TNF 0.015 0.22 -9999 0 -1.1 9 9
STAT3/STAT4 -0.024 0.18 -9999 0 -0.93 11 11
STAT4 (dimer) 0.019 0.21 -9999 0 -0.97 11 11
IL18 0.005 0.044 -9999 0 -0.33 9 9
IL19 0.006 0.2 -9999 0 -0.94 10 10
STAT5A (dimer) 0.019 0.21 -9999 0 -0.98 11 11
STAT1 0.01 0.021 -9999 0 -0.33 2 2
SOCS3 0.009 0.025 -9999 0 -0.41 2 2
CXCL9 0.004 0.23 -9999 0 -1.2 10 10
MPO 0.024 0.2 -9999 0 -0.99 8 8
positive regulation of humoral immune response 0.019 0.22 -9999 0 -1 11 11
IL23/IL23R/JAK2/TYK2 0.018 0.22 -9999 0 -1 11 11
IL6 0.002 0.27 -9999 0 -1.1 20 20
STAT5A 0.01 0.018 -9999 0 -0.41 1 1
IL2 -0.008 0.06 -9999 0 -0.33 18 18
positive regulation of tyrosine phosphorylation of STAT protein -0.001 0.005 -9999 0 -10000 0 0
CD3E 0.014 0.24 -9999 0 -1.1 14 14
keratinocyte proliferation 0.019 0.22 -9999 0 -1 11 11
NOS2 0.013 0.23 -9999 0 -1 15 15
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.024 0.03 -9999 0 -0.2 9 9
HDAC3 0.011 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
GATA1/HDAC4 0.013 0.004 -9999 0 -10000 0 0
GATA1/HDAC5 0.013 0.004 -9999 0 -10000 0 0
GATA2/HDAC5 -0.013 0.088 -9999 0 -0.28 53 53
HDAC5/BCL6/BCoR 0.022 0.011 -9999 0 -0.23 1 1
HDAC9 0.003 0.057 -9999 0 -0.41 10 10
Glucocorticoid receptor/Hsp90/HDAC6 -0.014 0.088 -9999 0 -0.23 79 79
HDAC4/ANKRA2 0.016 0.013 -9999 0 -0.28 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 -0.03 0.12 -9999 0 -0.41 53 53
HDAC4/RFXANK 0.015 0.017 -9999 0 -0.22 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 0.011 0.039 -9999 0 -0.27 10 10
Histones 0.029 0.026 -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 0.016 0.013 -9999 0 -0.28 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 0.017 -9999 0 -0.22 3 3
CAMK4 0.004 0.05 -9999 0 -0.36 10 10
Tubulin/HDAC6 0.02 0.024 -9999 0 -0.19 7 7
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 -0.05 0.15 -9999 0 -0.41 79 79
SUMO1/HDAC4 0.025 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 -0.24 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 0.016 0.013 -9999 0 -0.28 1 1
HDAC4/HDAC3/SMRT (N-CoR2) 0.022 0 -9999 0 -10000 0 0
HDAC4/SRF 0.018 0.029 -9999 0 -0.19 10 10
HDAC4/ER alpha -0.017 0.094 -9999 0 -0.28 62 62
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.029 0.026 -9999 0 -10000 0 0
cell motility 0.019 0.024 -9999 0 -0.19 7 7
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 0.018 -9999 0 -0.41 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 -0.037 0.13 -9999 0 -0.41 62 62
HDAC6/HDAC11 0.016 0.01 -9999 0 -0.22 1 1
Ran/GTP/Exportin 1 0.027 0 -9999 0 -10000 0 0
NPC 0.007 0 -9999 0 -10000 0 0
MEF2C -0.03 0.12 -9999 0 -0.41 53 53
RAN 0.011 0 -9999 0 -10000 0 0
HDAC4/MEF2C 0.012 0.063 -9999 0 -10000 0 0
GNG2 0.003 0.056 -9999 0 -0.4 10 10
NCOR2 0.011 0 -9999 0 -10000 0 0
TUBB2A 0.006 0.041 -9999 0 -0.35 7 7
HDAC11 0.01 0.015 -9999 0 -0.33 1 1
HSP90AA1 0.011 0 -9999 0 -10000 0 0
RANBP2 0.011 0 -9999 0 -10000 0 0
ANKRA2 0.01 0.018 -9999 0 -0.41 1 1
RFXANK 0.009 0.025 -9999 0 -0.33 3 3
nuclear import -0.024 0 -9999 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.023 0.02 -9999 0 -0.28 2 2
CRKL 0.011 0 -9999 0 -10000 0 0
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
DOCK1 0.006 0.047 -9999 0 -0.41 7 7
ITGA4 0.009 0.029 -9999 0 -0.38 3 3
alpha4/beta7 Integrin/MAdCAM1 0.013 0.049 -9999 0 -0.2 2 2
EPO -0.004 0.072 -9999 0 -0.41 17 17
alpha4/beta7 Integrin 0.014 0.023 -9999 0 -0.25 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.011 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.015 0.021 -9999 0 -0.26 3 3
EPO/EPOR (dimer) 0.002 0.057 -9999 0 -0.26 24 24
lamellipodium assembly 0.025 0.028 -9999 0 -0.25 4 4
PIK3CA 0.01 0.018 -9999 0 -0.41 1 1
PI3K 0.013 0.031 -9999 0 -0.28 6 6
ARF6 0.011 0 -9999 0 -10000 0 0
JAK2 0.013 0.056 -9999 0 -0.22 27 27
PXN 0.011 0 -9999 0 -10000 0 0
PIK3R1 0.007 0.04 -9999 0 -0.41 5 5
MADCAM1 -0.016 0.089 -9999 0 -0.33 41 41
cell adhesion 0.012 0.049 -9999 0 -0.2 2 2
CRKL/CBL 0.016 0 -9999 0 -10000 0 0
ITGB1 0.011 0 -9999 0 -10000 0 0
SRC 0.009 0.063 -9999 0 -0.21 40 40
ITGB7 0.01 0.015 -9999 0 -0.33 1 1
RAC1 0.011 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.003 0.07 -9999 0 -0.24 40 40
p130Cas/Crk/Dock1 0.024 0.06 -9999 0 -0.43 2 2
VCAM1 -0.02 0.11 -9999 0 -0.41 40 40
RHOA 0.011 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.027 0.016 -9999 0 -0.2 2 2
BCAR1 0.015 0.059 -9999 0 -0.38 2 2
EPOR 0.007 0.038 -9999 0 -0.33 7 7
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 -0.002 0.026 -9999 0 -0.26 4 4
p38 MAPK signaling pathway

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
TRAF6/ASK1 0.01 0.015 -10000 0 -0.2 3 3
TRAF2/ASK1 0.014 0.018 -10000 0 -0.23 3 3
ATM 0.011 0 -10000 0 -10000 0 0
MAP2K3 0.026 0.02 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.028 0.025 -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 0.069 -10000 0 -0.41 15 15
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 0.015 0.022 -10000 0 -0.28 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 0.009 -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 0.13 -10000 0 -0.33 89 89
CCM2 0.011 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.017 0.072 -10000 0 -0.18 89 89
MAPK11 0.009 0.025 -10000 0 -0.41 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.009 0.067 -10000 0 -0.16 92 92
OSM/MEKK3 0.016 0 -10000 0 -10000 0 0
TAOK1 0.013 0.018 -10000 0 -0.28 2 2
TAOK2 0.014 0 -10000 0 -10000 0 0
TAOK3 0.014 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 0.009 0.031 -10000 0 -0.41 3 3
MAP3K10 0.011 0 -10000 0 -10000 0 0
MAP3K3 0.011 0 -10000 0 -10000 0 0
TRX/ASK1 0.012 0.018 -10000 0 -0.23 3 3
GADD45/MTK1/MTK1 0.02 0.035 -10000 0 -0.19 15 15
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.017 0.018 -10000 0 -0.28 2 2
MAP4K4 0.028 0.034 -10000 0 -0.4 1 1
BAG4 0.009 0.031 -10000 0 -0.41 3 3
PKC zeta/ceramide -0.002 0.016 0.12 2 -0.18 2 4
NFKBIA 0.011 0 -10000 0 -10000 0 0
BIRC3 0.004 0.055 -10000 0 -0.39 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 -0.002 0.012 0.13 2 -10000 0 2
SMPD1 0.015 0.025 -10000 0 -0.2 1 1
RB1 -0.003 0.02 0.13 2 -0.22 3 5
FADD/Caspase 8 0.037 0.032 -10000 0 -0.39 1 1
MAP2K4 0.003 0.014 0.13 2 -0.19 1 3
NSMAF 0.011 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.003 0.016 0.13 2 -0.19 2 4
EGF -0.006 0.073 -10000 0 -0.34 25 25
mol:ceramide -0.009 0.013 0.13 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 0.017 0.018 -10000 0 -0.28 2 2
ASAH1 0.011 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.004 0.02 0.13 2 -0.22 3 5
cell proliferation -0.011 0.069 -10000 0 -0.2 8 8
BID 0.024 0.025 -10000 0 -0.29 1 1
MAP3K1 -0.002 0.012 0.13 2 -10000 0 2
EIF2A 0.009 0.011 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 0.011 0.016 0.14 1 -0.17 2 3
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.011 0.016 0.14 1 -0.17 2 3
Cathepsin D/ceramide -0.001 0.014 0.12 2 -0.16 1 3
FADD 0.028 0.034 -10000 0 -0.4 1 1
KSR1 -0.003 0.017 0.13 2 -0.21 2 4
MAPK8 0.005 0.028 0.14 1 -0.22 7 8
PRKRA -0.002 0.012 0.13 2 -10000 0 2
PDGFA 0.009 0.025 -10000 0 -0.41 2 2
TRAF2 0.011 0 -10000 0 -10000 0 0
IGF1 -0.067 0.16 -10000 0 -0.41 101 101
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.009 0.013 0.13 2 -10000 0 2
CTSD 0.01 0.015 -10000 0 -0.33 1 1
regulation of nitric oxide biosynthetic process 0.016 0.013 -10000 0 -0.28 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.011 0.073 -10000 0 -0.21 8 8
PRKCD 0.011 0 -10000 0 -10000 0 0
PRKCZ 0.01 0.023 -10000 0 -0.37 2 2
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.017 0.018 -10000 0 -0.28 2 2
RelA/NF kappa B1 0.016 0.013 -10000 0 -0.28 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 0.024 0.036 -10000 0 -0.43 1 1
TNFR1A/BAG4/TNF-alpha -0.003 0.067 -10000 0 -0.23 5 5
mol:Sphingosine-1-phosphate 0.017 0.018 -10000 0 -0.28 2 2
MAP2K1 0.008 0.016 0.14 1 -0.18 2 3
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.011 0 -10000 0 -10000 0 0
CYCS 0.013 0.04 0.14 51 -10000 0 51
TNFRSF1A 0.011 0 -10000 0 -10000 0 0
NFKB1 0.01 0.018 -10000 0 -0.41 1 1
TNFR1A/BAG4 0.015 0.022 -10000 0 -0.28 3 3
EIF2AK2 0.003 0.011 0.13 2 -10000 0 2
TNF-alpha/TNFR1A/FAN -0.002 0.065 -10000 0 -0.23 2 2
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.03 0.023 -10000 0 -10000 0 0
MAP2K2 0.008 0.016 0.14 1 -0.18 2 3
SMPD3 0.016 0.032 -10000 0 -0.28 3 3
TNF -0.032 0.11 -10000 0 -0.33 68 68
PKC zeta/PAR4 0.015 0.016 -10000 0 -0.25 2 2
mol:PHOSPHOCHOLINE -0.004 0.023 0.16 4 -10000 0 4
NF kappa B1/RelA/I kappa B alpha 0.032 0.015 -10000 0 -10000 0 0
AIFM1 0.013 0.04 0.14 51 -10000 0 51
BCL2 -0.028 0.12 -10000 0 -0.41 50 50
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 0.013 0.048 -10000 0 -0.29 6 6
ACTA1 0.004 0.058 -10000 0 -0.3 10 10
NUMA1 0.013 0.048 -10000 0 -0.29 6 6
SPTAN1 0.007 0.058 -10000 0 -0.3 10 10
LIMK1 0.007 0.058 -10000 0 -0.3 10 10
BIRC3 0.004 0.055 -10000 0 -0.39 10 10
BIRC2 0.011 0 -10000 0 -10000 0 0
BAX 0.011 0 -10000 0 -10000 0 0
CASP10 -0.002 0.075 -10000 0 -0.32 12 12
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.011 0 -10000 0 -10000 0 0
PTK2 0.013 0.048 -10000 0 -0.29 6 6
DIABLO 0.011 0 -10000 0 -10000 0 0
apoptotic nuclear changes 0.007 0.057 -10000 0 -0.3 10 10
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.011 0 -10000 0 -10000 0 0
GSN 0.004 0.06 -10000 0 -0.3 10 10
MADD 0.011 0 -10000 0 -10000 0 0
TFAP2A 0.028 0.039 -10000 0 -0.58 2 2
BID 0.008 0.037 -10000 0 -0.18 11 11
MAP3K1 0.008 0.023 -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 0.007 0.058 -10000 0 -0.3 10 10
CASP9 0.011 0 -10000 0 -10000 0 0
DNA repair -0.005 0.022 0.14 1 -0.16 5 6
neuron apoptosis 0.019 0.008 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.013 0.055 -10000 0 -0.34 6 6
APAF1 0.011 0 -10000 0 -10000 0 0
CASP6 0.022 0.032 -10000 0 -0.28 1 1
TRAF2 0.011 0 -10000 0 -10000 0 0
ICAD/CAD 0.012 0.056 -10000 0 -0.34 6 6
CASP7 -0.005 0.032 0.25 8 -10000 0 8
KRT18 0.013 0.032 -10000 0 -0.7 1 1
apoptosis 0.014 0.053 0.18 5 -0.41 2 7
DFFA 0.007 0.058 -10000 0 -0.3 10 10
DFFB 0.007 0.058 -10000 0 -0.3 10 10
PARP1 0.005 0.022 0.16 5 -0.14 1 6
actin filament polymerization -0.009 0.058 0.32 7 -10000 0 7
TNF -0.032 0.11 -10000 0 -0.33 68 68
CYCS 0.009 0.031 -10000 0 -0.15 7 7
SATB1 -0.005 0.081 -10000 0 -0.35 6 6
SLK 0.007 0.058 -10000 0 -0.3 10 10
p15 BID/BAX 0.013 0.033 -10000 0 -0.26 2 2
CASP2 0.03 0.03 -10000 0 -0.3 1 1
JNK cascade -0.008 0.023 0.19 1 -10000 0 1
CASP3 0.001 0.061 0.18 1 -0.32 10 11
LMNB2 0.032 0.024 -10000 0 -10000 0 0
RIPK1 0.011 0 -10000 0 -10000 0 0
CASP4 0.01 0.018 -10000 0 -0.41 1 1
Mammalian IAPs/DIABLO 0.024 0.029 -10000 0 -0.2 8 8
negative regulation of DNA binding 0.028 0.038 -10000 0 -0.58 2 2
stress fiber formation 0.007 0.057 -10000 0 -0.3 10 10
GZMB -0.011 0.086 -10000 0 -0.25 59 59
CASP1 0.012 0.021 -10000 0 -0.28 3 3
LMNB1 0.032 0.024 -10000 0 -10000 0 0
APP 0.02 0.008 -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 0.01 0.053 0.18 5 -0.27 6 11
LMNA 0.032 0.024 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.026 0.032 -10000 0 -0.32 1 1
LRDD 0.011 0 -10000 0 -10000 0 0
SREBF1 0.007 0.058 0.17 1 -0.3 10 11
APAF-1/Caspase 9 -0.001 0.017 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.013 0.048 -10000 0 -0.29 6 6
CFL2 0.009 0.059 -10000 0 -0.33 7 7
GAS2 -0.008 0.081 -10000 0 -0.34 14 14
positive regulation of apoptosis 0.035 0.024 -10000 0 -10000 0 0
PRF1 0.005 0.049 -10000 0 -0.37 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 0.032 0.038 -10000 0 -0.38 1 1
BAG4 0.009 0.031 -10000 0 -0.41 3 3
BAD 0.023 0.014 -10000 0 -10000 0 0
NFKBIA 0.011 0 -10000 0 -10000 0 0
BIRC3 0.003 0.055 -10000 0 -0.39 10 10
BAX 0.023 0.014 -10000 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.01 0.01 -10000 0 -0.092 1 1
IKBKB 0.037 0.037 -10000 0 -0.36 1 1
MAP2K2 0.031 0.017 -10000 0 -0.16 1 1
MAP2K1 0.031 0.017 -10000 0 -0.16 1 1
SMPD1 0.015 0.01 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.038 0.037 -10000 0 -0.37 1 1
MAP2K4 0.027 0.016 -10000 0 -0.16 1 1
protein ubiquitination 0.038 0.037 -10000 0 -0.36 1 1
EnzymeConsortium:2.7.1.37 0.035 0.018 -10000 0 -0.16 1 1
response to UV 0 0 -10000 0 -0.002 1 1
RAF1 0.027 0.018 -10000 0 -0.16 2 2
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 0.015 0 -10000 0 -10000 0 0
MADD 0.011 0 -10000 0 -10000 0 0
MAP3K1 0.023 0.014 -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 0.017 -10000 0 -0.16 1 1
MAPK1 0.033 0.017 -10000 0 -0.16 1 1
p50/RELA/I-kappa-B-alpha 0.016 0 -10000 0 -10000 0 0
FADD 0.032 0.038 -10000 0 -0.38 1 1
KSR1 0.023 0.018 -10000 0 -0.17 2 2
MAPK8 0.03 0.024 -10000 0 -10000 0 0
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 0.015 0.022 -10000 0 -0.28 3 3
TNF -0.031 0.11 -10000 0 -0.33 68 68
CYCS 0.032 0.03 0.12 47 -10000 0 47
IKBKG 0.037 0.037 -10000 0 -0.36 1 1
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.028 0.04 -10000 0 -0.4 1 1
RELA 0.011 0 -10000 0 -10000 0 0
RIPK1 0.011 0 -10000 0 -10000 0 0
AIFM1 0.032 0.03 0.12 47 -10000 0 47
TNF/TNF R/SODD -0.003 0.067 -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 0.032 0.038 -10000 0 -0.37 1 1
response to hydrogen peroxide 0 0 -10000 0 -0.002 1 1
BCL2 -0.028 0.12 -10000 0 -0.41 50 50
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.024 0.013 -10000 0 -0.19 2 2
epithelial cell differentiation -0.001 0.011 -10000 0 -0.18 2 2
CYFIP2 0.009 0.031 -10000 0 -0.41 3 3
ENAH 0.048 0.018 -10000 0 -10000 0 0
EGFR 0 0.066 -10000 0 -0.4 14 14
EPHA2 0.011 0 -10000 0 -10000 0 0
MYO6 0.029 0.012 -10000 0 -10000 0 0
CTNNB1 0.011 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.021 0.019 -10000 0 -0.23 3 3
AQP5 0.013 0.051 -10000 0 -0.38 8 8
CTNND1 0.011 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.029 0.012 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.023 0.038 -10000 0 -0.36 1 1
EGF -0.006 0.073 -10000 0 -0.34 25 25
NCKAP1 0.011 0 -10000 0 -10000 0 0
AQP3 -0.004 0.043 -10000 0 -0.45 5 5
cortical microtubule organization -0.001 0.011 -10000 0 -0.18 2 2
GO:0000145 0.027 0.011 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.025 0.013 -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 0.027 0.017 -10000 0 -0.2 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.037 0.012 -10000 0 -10000 0 0
PVRL2 0.011 0 -10000 0 -10000 0 0
ZYX 0.029 0.012 -10000 0 -10000 0 0
ARF6/GTP 0.03 0.016 -10000 0 -10000 0 0
CDH1 0.009 0.025 -10000 0 -0.41 2 2
EGFR/EGFR/EGF/EGF -0.01 0.041 -10000 0 -0.32 3 3
RhoA/GDP -0.001 0.01 -10000 0 -10000 0 0
actin cytoskeleton organization 0.033 0.012 -10000 0 -10000 0 0
IGF-1R heterotetramer -0.005 0.081 -10000 0 -0.41 21 21
GIT1 0.011 0 -10000 0 -10000 0 0
IGF1R -0.005 0.081 -10000 0 -0.41 21 21
IGF1 -0.067 0.16 -10000 0 -0.41 101 101
DIAPH1 -0.003 0.039 -10000 0 -0.52 3 3
Wnt receptor signaling pathway 0.001 0.011 0.18 2 -10000 0 2
RHOA 0.011 0 -10000 0 -10000 0 0
RhoA/GTP -0.001 0.012 -10000 0 -10000 0 0
CTNNA1 0.011 0 -10000 0 -10000 0 0
VCL 0.033 0.012 -10000 0 -10000 0 0
EFNA1 0.01 0.021 -10000 0 -0.33 2 2
LPP 0.034 0.012 -10000 0 -10000 0 0
Ephrin A1/EPHA2 -0.001 0.012 -10000 0 -10000 0 0
SEC6/SEC8 -0.001 0.009 -10000 0 -10000 0 0
MGAT3 0.023 0.039 -10000 0 -0.36 1 1
HGF/MET -0.036 0.073 -10000 0 -0.47 3 3
HGF -0.076 0.17 -10000 0 -0.41 112 112
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.024 0.013 -10000 0 -0.2 2 2
actin cable formation 0.062 0.017 -10000 0 -10000 0 0
KIAA1543 0.033 0.025 -10000 0 -0.35 2 2
KIFC3 0.029 0.012 -10000 0 -10000 0 0
NCK1 0.009 0.025 -10000 0 -0.41 2 2
EXOC3 0.011 0 -10000 0 -10000 0 0
ACTN1 0.029 0.012 -10000 0 -10000 0 0
NCK1/GIT1 0.015 0.018 -10000 0 -0.28 2 2
mol:GDP -0.001 0.011 -10000 0 -0.18 2 2
EXOC4 0.011 0 -10000 0 -10000 0 0
STX4 0.029 0.012 -10000 0 -10000 0 0
PIP5K1C 0.029 0.012 -10000 0 -10000 0 0
LIMA1 0.011 0 -10000 0 -10000 0 0
ABI1 0.011 0 -10000 0 -10000 0 0
ROCK1 0.047 0.016 -10000 0 -10000 0 0
adherens junction assembly 0.045 0.026 -10000 0 -0.36 2 2
IGF-1R heterotetramer/IGF1 -0.037 0.078 -10000 0 -0.35 12 12
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 0.049 -10000 0 -0.37 9 9
PLEKHA7 0.029 0.015 -10000 0 -10000 0 0
mol:GTP 0.026 0.017 -10000 0 -0.2 2 2
establishment of epithelial cell apical/basal polarity 0.047 0.011 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization 0.024 0.013 -10000 0 -0.19 2 2
regulation of cell-cell adhesion 0.033 0.012 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.024 0.013 -10000 0 -0.2 2 2
Arf6 trafficking events

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
SLC2A4 -0.2 0.21 -10000 0 -0.41 266 266
CLTC 0.026 0.001 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.021 0.006 -10000 0 -10000 0 0
Dynamin 2/GTP 0.02 0 -10000 0 -10000 0 0
EXOC4 0.011 0 -10000 0 -10000 0 0
CD59 0.023 0.001 -10000 0 -10000 0 0
CPE -0.01 0.075 -10000 0 -0.24 54 54
CTNNB1 0.011 0 -10000 0 -10000 0 0
membrane fusion 0.021 0.006 -10000 0 -10000 0 0
CTNND1 0.025 0 -10000 0 -10000 0 0
DNM2 0.011 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.026 0.003 -10000 0 -10000 0 0
TSHR 0.005 0.041 -10000 0 -0.19 23 23
INS 0.01 0.002 -10000 0 -10000 0 0
BIN1 0.008 0.036 -10000 0 -0.41 4 4
mol:Choline 0.021 0.006 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.015 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+ 0.02 0 -10000 0 -10000 0 0
JUP 0.023 0.008 -10000 0 -10000 0 0
ASAP2/amphiphysin II 0.02 0.019 -10000 0 -0.2 4 4
ARF6/GTP 0.008 0 -10000 0 -10000 0 0
CDH1 0.022 0.011 -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 0.035 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 0.015 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.015 0 -10000 0 -10000 0 0
ACAP1 0.02 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.019 0.012 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.03 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 0.035 0 -10000 0 -10000 0 0
RALA/GTP 0.008 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.015 0 -10000 0 -10000 0 0
receptor recycling 0.008 0 -10000 0 -10000 0 0
CTNNA1 0.025 0 -10000 0 -10000 0 0
NME1 0.015 0 -10000 0 -10000 0 0
clathrin coat assembly 0.026 0.002 -10000 0 -10000 0 0
IL2RA 0.02 0.015 -10000 0 -10000 0 0
VAMP3 0.015 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.075 0.076 -10000 0 -10000 0 0
EXOC6 0.011 0 -10000 0 -10000 0 0
PLD1 0.018 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 0.026 0.001 -10000 0 -10000 0 0
SDC1 0.003 0.032 -10000 0 -10000 0 0
ARF6/GDP 0.015 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 0.021 0.006 -10000 0 -10000 0 0
endocytosis -0.019 0.019 0.2 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 0.021 0 -10000 0 -10000 0 0
KLC1 0.011 0 -10000 0 -10000 0 0
AVPR2 -0.031 0.091 -10000 0 -10000 0 0
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
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.014 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.058 0.035 -9999 0 -10000 0 0
ERC1 0.011 0 -9999 0 -10000 0 0
RIP2/NOD2 0.015 0.016 -9999 0 -0.25 2 2
NFKBIA 0.036 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 0.037 0.009 -9999 0 -10000 0 0
IKK complex/A20 -0.012 0.032 -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 0.041 0.008 -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 0.015 0 -9999 0 -10000 0 0
IKK complex/ELKS 0 0.005 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0.022 0 -9999 0 -10000 0 0
NOD2 0.01 0.023 -9999 0 -0.37 2 2
NFKB1 0.013 0.018 -9999 0 -0.4 1 1
RELA 0.014 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 -0.013 0.078 -9999 0 -0.22 68 68
TRAF6 0.011 0 -9999 0 -10000 0 0
PRKCA -0.017 0.1 -9999 0 -0.41 36 36
CHUK 0.011 0 -9999 0 -10000 0 0
UBE2D3 0.011 0 -9999 0 -10000 0 0
TNF -0.032 0.11 -9999 0 -0.33 68 68
NF kappa B1 p50/RelA 0.031 0.011 -9999 0 -0.22 1 1
BCL10 0.011 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.035 0.009 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.014 0 -9999 0 -10000 0 0
TNFRSF1A 0.011 0 -9999 0 -10000 0 0
IKK complex 0.046 0.008 -9999 0 -10000 0 0
CYLD 0.011 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.009 0.035 -9999 0 -10000 0 0
PLK2 and PLK4 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
PLK2 0.01 0.018 -9999 0 -0.41 1 1
PLK4 0.007 0.035 -9999 0 -0.33 6 6
regulation of centriole replication 0.015 0.028 -9999 0 -0.23 7 7
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.007 0.04 -10000 0 -0.37 6 6
positive regulation of NF-kappaB transcription factor activity 0.006 0.053 -10000 0 -0.27 19 19
MAP2K4 0.035 0.02 -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 0.025 -10000 0 -0.41 2 2
SMPD1 0.014 0.015 -10000 0 -0.16 3 3
IKBKG 0.011 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.001 0.064 -10000 0 -0.41 13 13
TRAIL/TRAILR2 0.013 0.028 -10000 0 -0.25 6 6
TRAIL/TRAILR3 0.013 0.031 -10000 0 -0.25 7 7
TRAIL/TRAILR1 0.012 0.033 -10000 0 -0.26 8 8
TRAIL/TRAILR4 0.006 0.053 -10000 0 -0.27 19 19
TRAIL/TRAILR1/DAP3/GTP 0.018 0.025 -10000 0 -0.19 8 8
IKK complex -0.001 0.007 -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 0.028 -10000 0 -0.25 6 6
MAP3K1 0.031 0.019 -10000 0 -10000 0 0
TRAILR4 (trimer) 0.001 0.064 -10000 0 -0.41 13 13
TRADD 0.011 0 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.009 0.025 -10000 0 -0.41 2 2
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.028 0.022 -10000 0 -0.19 5 5
CFLAR 0.011 0 -10000 0 -10000 0 0
MAPK1 0.015 0.028 -10000 0 -0.25 6 6
TRAIL/TRAILR1/FADD/TRADD/RIP 0.03 0.024 -10000 0 -10000 0 0
mol:ceramide 0.014 0.015 -10000 0 -0.16 3 3
FADD 0.011 0 -10000 0 -10000 0 0
MAPK8 0.037 0.028 -10000 0 -10000 0 0
TRAF2 0.011 0 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.01 0.018 -10000 0 -0.41 1 1
CHUK 0.011 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.019 0.028 -10000 0 -0.21 8 8
DAP3 0.011 0 -10000 0 -10000 0 0
CASP10 0.002 0.046 0.22 13 -0.31 4 17
JNK cascade 0.006 0.053 -10000 0 -0.27 19 19
TRAIL (trimer) 0.007 0.04 -10000 0 -0.37 6 6
TNFRSF10C 0.01 0.018 -10000 0 -0.41 1 1
TRAIL/TRAILR1/DAP3/GTP/FADD 0.023 0.024 -10000 0 -0.19 5 5
TRAIL/TRAILR2/FADD 0.02 0.023 -10000 0 -0.2 6 6
cell death 0.014 0.015 -10000 0 -0.16 3 3
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.028 0.017 -10000 0 -10000 0 0
TRAILR2 (trimer) 0.011 0 -10000 0 -10000 0 0
CASP8 0.001 0.009 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.031 0.02 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.009 0.031 -9999 0 -0.41 3 3
Caspase 8 (4 units) 0.031 0.034 -9999 0 -0.36 1 1
NEF 0.001 0.019 -9999 0 -0.16 4 4
NFKBIA 0.012 0.012 -9999 0 -10000 0 0
BIRC3 0.027 0.06 -9999 0 -0.4 10 10
CYCS 0.035 0.036 -9999 0 -0.25 4 4
RIPK1 0.011 0 -9999 0 -10000 0 0
CD247 0.01 0.036 -9999 0 -0.41 3 3
MAP2K7 0.037 0.034 -9999 0 -0.36 1 1
protein ubiquitination 0.049 0.026 -9999 0 -10000 0 0
CRADD 0.011 0 -9999 0 -10000 0 0
DAXX 0.011 0 -9999 0 -10000 0 0
FAS 0.007 0.04 -9999 0 -0.41 5 5
BID 0.031 0.038 -9999 0 -0.26 4 4
NF-kappa-B/RelA/I kappa B alpha 0.027 0.034 -9999 0 -0.22 9 9
TRADD 0.011 0 -9999 0 -10000 0 0
MAP3K5 0.009 0.031 -9999 0 -0.41 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 0.027 0.035 -9999 0 -0.22 9 9
MAPK8 0.039 0.038 -9999 0 -0.34 1 1
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 0.026 0.039 -9999 0 -0.28 4 4
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.044 0.03 -9999 0 -10000 0 0
CHUK 0.05 0.028 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.03 0.026 -9999 0 -10000 0 0
TCRz/NEF 0.01 0.039 -9999 0 -0.22 14 14
TNF -0.032 0.11 -9999 0 -0.33 68 68
FASLG 0.013 0.061 -9999 0 -0.34 14 14
NFKB1 0.011 0.021 -9999 0 -0.4 1 1
TNFR1A/BAG4/TNF-alpha -0.003 0.067 -9999 0 -0.23 5 5
CASP6 -0.003 0.022 -9999 0 -10000 0 0
CASP7 0.057 0.068 -9999 0 -0.44 8 8
RELA 0.012 0.012 -9999 0 -10000 0 0
CASP2 0.011 0 -9999 0 -10000 0 0
CASP3 0.057 0.068 -9999 0 -0.44 8 8
TNFRSF1A 0.011 0 -9999 0 -10000 0 0
TNFR1A/BAG4 0.015 0.022 -9999 0 -0.28 3 3
CASP8 0.011 0 -9999 0 -10000 0 0
CASP9 0.011 0 -9999 0 -10000 0 0
MAP3K14 0.047 0.029 -9999 0 -10000 0 0
APAF-1/Caspase 9 -0.007 0.039 -9999 0 -0.28 9 9
BCL2 0.026 0.067 -9999 0 -0.29 6 6
Class I PI3K signaling events

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
ARF5/GTP 0.002 0.023 0.21 6 -10000 0 6
DAPP1 0.028 0.042 -10000 0 -0.3 3 3
Src family/SYK family/BLNK-LAT/BTK-ITK 0.045 0.046 -10000 0 -0.49 1 1
mol:DAG 0.046 0.031 0.16 5 -0.18 1 6
HRAS 0.012 0.001 -10000 0 -10000 0 0
RAP1A 0.012 0.001 -10000 0 -10000 0 0
ARF5/GDP 0.027 0.046 -10000 0 -0.32 3 3
PLCG2 0.01 0.023 -10000 0 -0.37 2 2
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 0.023 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 0.02 0.2 6 -10000 0 6
ADAP1 0.002 0.022 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 0.067 -10000 0 -0.41 14 14
ARHGEF7 0.011 0 -10000 0 -10000 0 0
ARF1 0.011 0 -10000 0 -10000 0 0
NRAS 0.012 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 0.002 0.059 -10000 0 -0.41 11 11
mol:Ca2+ 0.032 0.018 -10000 0 -10000 0 0
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0 0.067 -10000 0 -0.41 14 14
ZAP70 -0.001 0.063 -10000 0 -0.34 18 18
mol:IP3 0.039 0.023 -10000 0 -10000 0 0
LYN 0.011 0 -10000 0 -10000 0 0
ARF1/GDP 0.027 0.046 -10000 0 -0.32 3 3
RhoA/GDP 0 0.025 0.19 6 -0.2 1 7
PDK1/Src/Hsp90 0.022 0 -10000 0 -10000 0 0
BLNK 0.009 0.029 -10000 0 -0.38 3 3
actin cytoskeleton reorganization 0.046 0.036 0.2 5 -0.23 3 8
SRC 0.011 0 -10000 0 -10000 0 0
PLEKHA2 0.023 0.011 -10000 0 -0.23 1 1
RAC1 0.011 0 -10000 0 -10000 0 0
PTEN 0.003 0.041 -10000 0 -0.39 6 6
HSP90AA1 0.011 0 -10000 0 -10000 0 0
ARF6/GTP 0.002 0.023 0.21 6 -10000 0 6
RhoA/GTP 0.028 0.02 0.2 6 -10000 0 6
Src family/SYK family/BLNK-LAT 0.035 0.039 -10000 0 -0.3 1 1
BLK -0.015 0.087 -10000 0 -0.33 39 39
PDPK1 0.011 0 -10000 0 -10000 0 0
CYTH1 0.002 0.022 0.2 6 -10000 0 6
HCK 0.007 0.038 -10000 0 -0.33 7 7
CYTH3 0.002 0.022 0.2 6 -10000 0 6
CYTH2 0.002 0.022 0.2 6 -10000 0 6
KRAS 0.011 0.015 -10000 0 -0.33 1 1
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.035 0.029 -10000 0 -0.38 2 2
SGK1 0 0.031 0.16 6 -0.42 2 8
INPP5D 0.01 0.018 -10000 0 -0.41 1 1
mol:GDP 0.022 0.048 -10000 0 -0.22 13 13
SOS1 0.011 0 -10000 0 -10000 0 0
SYK 0.01 0.015 -10000 0 -0.33 1 1
ARF6/GDP 0 0.025 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 0.037 -10000 0 -0.34 6 6
mol:PI-3-4-P2 0.018 0.013 -10000 0 -0.28 1 1
RAS family/GTP/PI3K Class I 0.025 0.01 -10000 0 -10000 0 0
PLEKHA1 0.023 0.011 -10000 0 -0.23 1 1
Rac1/GDP 0.027 0.046 -10000 0 -0.32 3 3
LAT 0.011 0 -10000 0 -10000 0 0
Rac1/GTP 0.019 0.067 -10000 0 -0.26 25 25
ITK -0.002 0.034 0.2 6 -10000 0 6
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.053 0.038 0.18 5 -0.24 1 6
LCK 0.008 0.034 -10000 0 -0.34 5 5
BTK 0.001 0.025 0.2 6 -10000 0 6
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.012 0.032 -9999 0 -0.24 2 2
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.027 0.032 -9999 0 -0.24 2 2
SUMO1 0.011 0 -9999 0 -10000 0 0
ZFPM1 0.009 0.025 -9999 0 -0.41 2 2
NPC/RanGAP1/SUMO1/Ubc9 0.017 0 -9999 0 -10000 0 0
FKBP3 0.011 0 -9999 0 -10000 0 0
Histones 0.028 0.025 -9999 0 -10000 0 0
YY1/LSF 0.018 0.04 -9999 0 -0.2 18 18
SMG5 0.011 0 -9999 0 -10000 0 0
RAN 0.011 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 0.015 0.035 -9999 0 -0.19 2 2
I kappa B alpha/HDAC1 0.016 0.027 -9999 0 -10000 0 0
SAP18 0.011 0 -9999 0 -10000 0 0
RELA 0.02 0.031 -9999 0 -0.19 4 4
HDAC1/Smad7 0.022 0.015 -9999 0 -0.23 2 2
RANGAP1 0.011 0 -9999 0 -10000 0 0
HDAC3/TR2 0.016 0.027 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.037 0.013 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.023 0.03 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 -0.03 0.12 -9999 0 -0.41 53 53
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 0.044 0.017 -9999 0 -10000 0 0
RBBP7 0.011 0 -9999 0 -10000 0 0
NPC 0.007 0 -9999 0 -10000 0 0
RBBP4 0.009 0.031 -9999 0 -0.41 3 3
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 0.012 0.031 -9999 0 -10000 0 0
KAT2B 0.004 0.054 -9999 0 -0.41 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.034 0.014 -9999 0 -10000 0 0
SIN3 complex 0.028 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 0.022 0.035 -9999 0 -10000 0 0
YY1/HDAC2 0.021 0.03 -9999 0 -0.19 11 11
YY1/HDAC1 0.021 0.03 -9999 0 -0.19 11 11
NuRD/MBD2 Complex (MeCP1) 0.037 0.013 -9999 0 -10000 0 0
PPARG 0.005 0.071 -9999 0 -0.26 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) 0.016 0.027 -9999 0 -10000 0 0
MBD3L2 0.002 0.004 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.021 0.015 -9999 0 -0.23 2 2
CREBBP 0.009 0.025 -9999 0 -0.41 2 2
NuRD/MBD3/MBD3L2 Complex 0.041 0.013 -9999 0 -10000 0 0
HDAC1 0.011 0 -9999 0 -10000 0 0
HDAC3 0.012 0.031 -9999 0 -10000 0 0
HDAC2 0.011 0 -9999 0 -10000 0 0
YY1 0.019 0.036 -9999 0 -0.23 11 11
HDAC8 0.011 0 -9999 0 -10000 0 0
SMAD7 0.009 0.025 -9999 0 -0.41 2 2
NCOR2 0.011 0 -9999 0 -10000 0 0
MXD1 0.011 0 -9999 0 -10000 0 0
STAT3 0.02 0.017 -9999 0 -0.27 2 2
NFKB1 0.01 0.018 -9999 0 -0.41 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.011 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 0.024 0.037 -9999 0 -0.19 7 7
YY1/SAP30/HDAC1 0.026 0.028 -9999 0 -10000 0 0
EP300 0.011 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.02 0.017 -9999 0 -0.27 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.012 0.031 -9999 0 -10000 0 0
histone deacetylation 0.037 0.013 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.023 0.028 -9999 0 -10000 0 0
nuclear export -0.022 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 -0.005 0.074 -9999 0 -0.21 53 53
GATA1/HDAC1 0.013 0.004 -9999 0 -10000 0 0
GATA1/HDAC3 0.005 0.027 -9999 0 -10000 0 0
CHD4 0.011 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.013 0.078 -9999 0 -0.22 68 68
SIN3/HDAC complex/Mad/Max 0.037 0.013 -9999 0 -10000 0 0
NuRD Complex 0.044 0.013 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.027 0.024 -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 0.025 0 -9999 0 -10000 0 0
HDAC complex 0.027 0.017 -9999 0 -0.2 3 3
GATA1/Fog1 0.012 0.018 -9999 0 -0.28 2 2
FKBP25/HDAC1/HDAC2 0.022 0 -9999 0 -10000 0 0
TNF -0.032 0.11 -9999 0 -0.33 68 68
negative regulation of cell growth 0.037 0.013 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.037 0.013 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.027 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.023 0.032 -9999 0 -0.25 2 2
SIN3/HDAC complex/NCoR1 0.035 0.014 -9999 0 -10000 0 0
TFCP2 0.006 0.047 -9999 0 -0.41 7 7
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
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.01 0.018 -9999 0 -0.41 1 1
SMAD2 0.011 0 -9999 0 -10000 0 0
SMAD3 0.031 0.017 -9999 0 -10000 0 0
SMAD3/SMAD4 0.036 0.019 -9999 0 -0.33 1 1
SMAD4/Ubc9/PIASy 0.022 0.011 -9999 0 -0.23 1 1
SMAD2/SMAD2/SMAD4 0.025 0.033 -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 0.017 0.009 -9999 0 -0.2 1 1
MAP3K1 0.011 0 -9999 0 -10000 0 0
TRAP-1/SMAD4 0.011 0.038 -9999 0 -0.28 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 0.005 0.051 -9999 0 -0.41 8 8
UBE2I 0.011 0 -9999 0 -10000 0 0
NUP153 0.01 0.018 -9999 0 -0.41 1 1
KPNA2 -0.005 0.071 -9999 0 -0.33 25 25
PIAS4 0.011 0 -9999 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.011 0 -9999 0 -10000 0 0
ITGB7 0.01 0.015 -9999 0 -0.33 1 1
ITGA4 0.009 0.029 -9999 0 -0.38 3 3
alpha4/beta7 Integrin 0.014 0.023 -9999 0 -0.25 4 4
alpha4/beta1 Integrin 0.015 0.021 -9999 0 -0.26 3 3
Paxillin-dependent events mediated by a4b1

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
CRKL 0.011 0 -9999 0 -10000 0 0
Rac1/GDP 0 0.003 -9999 0 -10000 0 0
DOCK1 0.006 0.047 -9999 0 -0.41 7 7
ITGA4 0.009 0.029 -9999 0 -0.38 3 3
RAC1 0.011 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.014 0.023 -9999 0 -0.25 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.011 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.021 0.017 -9999 0 -0.21 3 3
alpha4/beta7 Integrin/Paxillin 0.026 0.017 -9999 0 -0.2 2 2
lamellipodium assembly -0.006 0.047 -9999 0 -0.4 6 6
PIK3CA 0.01 0.018 -9999 0 -0.41 1 1
PI3K 0.013 0.031 -9999 0 -0.28 6 6
ARF6 0.011 0 -9999 0 -10000 0 0
TLN1 0.011 0 -9999 0 -10000 0 0
PXN 0.018 0 -9999 0 -10000 0 0
PIK3R1 0.007 0.04 -9999 0 -0.41 5 5
ARF6/GTP -0.001 0.011 -9999 0 -10000 0 0
cell adhesion 0.031 0.014 -9999 0 -10000 0 0
CRKL/CBL 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.026 0.016 -9999 0 -0.2 2 2
ITGB1 0.011 0 -9999 0 -10000 0 0
ITGB7 0.01 0.015 -9999 0 -0.33 1 1
ARF6/GDP 0 0.003 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.016 0.06 -9999 0 -0.38 2 2
p130Cas/Crk/Dock1 0.019 0.028 -9999 0 -0.23 7 7
VCAM1 -0.02 0.11 -9999 0 -0.41 40 40
alpha4/beta1 Integrin/Paxillin/Talin 0.032 0.015 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.032 0.015 -9999 0 -10000 0 0
BCAR1 0.011 0 -9999 0 -10000 0 0
mol:GDP -0.031 0.014 -9999 0 -10000 0 0
CBL 0.011 0 -9999 0 -10000 0 0
PRKACA 0.011 0 -9999 0 -10000 0 0
GIT1 0.011 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.032 0.015 -9999 0 -10000 0 0
Rac1/GTP -0.007 0.053 -9999 0 -0.44 6 6
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.027 0 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1 0.018 0 -9999 0 -10000 0 0
mol:DAG 0.031 0.007 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0.024 0 -9999 0 -10000 0 0
CaM/Ca2+ 0.035 0.007 -9999 0 -10000 0 0
HIF1A 0.018 0 -9999 0 -10000 0 0
GAB1 0.008 0.036 -9999 0 -0.41 4 4
AKT1 0.043 0.026 -9999 0 -10000 0 0
PLCG1 0.031 0.007 -9999 0 -10000 0 0
NOS3 0.048 0.017 -9999 0 -10000 0 0
CBL 0.011 0 -9999 0 -10000 0 0
mol:NO 0.048 0.017 -9999 0 -10000 0 0
FLT1 0.025 0 -9999 0 -10000 0 0
PGF 0.01 0.015 -9999 0 -0.33 1 1
VEGFR1 homodimer/NRP2/VEGFR121 0.021 0.047 -9999 0 -10000 0 0
CALM1 0.011 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.018 -9999 0 -0.41 1 1
eNOS/Hsp90 0.052 0.016 -9999 0 -10000 0 0
endothelial cell proliferation 0.019 0.065 -9999 0 -0.31 4 4
mol:Ca2+ 0.031 0.007 -9999 0 -10000 0 0
MAPK3 0.026 0.05 -9999 0 -10000 0 0
MAPK1 0.026 0.05 -9999 0 -10000 0 0
PIK3R1 0.007 0.04 -9999 0 -0.41 5 5
PLGF homodimer 0.01 0.015 -9999 0 -0.33 1 1
PRKACA 0.011 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.062 0.16 -9999 0 -0.41 94 94
VEGFA homodimer 0.011 0 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.027 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process 0.031 0.049 -9999 0 -10000 0 0
PI3K 0.035 0.023 -9999 0 -10000 0 0
PRKCA 0.021 0.053 -9999 0 -10000 0 0
PRKCB 0.023 0.05 -9999 0 -10000 0 0
VEGFR1 homodimer/PLGF homodimer 0.026 0.008 -9999 0 -10000 0 0
VEGFA 0.011 0 -9999 0 -10000 0 0
VEGFB 0.011 0 -9999 0 -10000 0 0
mol:IP3 0.031 0.007 -9999 0 -10000 0 0
RASA1 0.03 0.022 -9999 0 -10000 0 0
NRP2 -0.008 0.088 -9999 0 -0.41 25 25
VEGFR1 homodimer 0.025 0 -9999 0 -10000 0 0
VEGFB homodimer 0.011 0 -9999 0 -10000 0 0
NCK1 0.009 0.025 -9999 0 -0.41 2 2
eNOS/Caveolin-1 0.02 0.074 -9999 0 -0.41 1 1
PTPN11 0.011 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.033 0.023 -9999 0 -10000 0 0
mol:L-citrulline 0.048 0.017 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.037 0 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.031 0.014 -9999 0 -10000 0 0
CD2AP 0.011 0 -9999 0 -10000 0 0
PI3K/GAB1 0.037 0.028 -9999 0 -10000 0 0
PDPK1 0.037 0.022 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.032 0 -9999 0 -10000 0 0
mol:NADP 0.048 0.017 -9999 0 -10000 0 0
HSP90AA1 0.011 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.036 0 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.015 0.052 -9999 0 -10000 0 0
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.033 0.015 -10000 0 -10000 0 0
regulation of axonogenesis -0.023 0.008 -10000 0 -10000 0 0
myoblast fusion -0.017 0.013 -10000 0 -10000 0 0
mol:GTP -0.001 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.023 0.039 0.22 14 -10000 0 14
ARF1/GTP 0 0.003 -10000 0 -10000 0 0
mol:GM1 0.008 0.005 -10000 0 -10000 0 0
mol:Choline 0.022 0.011 -10000 0 -0.22 1 1
lamellipodium assembly 0.001 0.012 -10000 0 -10000 0 0
MAPK3 0.023 0.009 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.023 0.039 -10000 0 -0.22 14 14
ARF1 0.011 0 -10000 0 -10000 0 0
ARF6/GDP 0.017 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 0.002 0.067 -10000 0 -0.41 14 14
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.023 0.009 -10000 0 -10000 0 0
actin filament bundle formation -0.02 0.01 -10000 0 -10000 0 0
KALRN -0.001 0.023 -10000 0 -0.21 4 4
RAB11FIP3/RAB11A 0.016 0 -10000 0 -10000 0 0
RhoA/GDP 0.021 0.01 -10000 0 -10000 0 0
NME1 0.012 0.001 -10000 0 -10000 0 0
Rac1/GDP 0.021 0.01 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading -0.001 0.005 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0.001 0.012 -10000 0 -10000 0 0
RAC1 0.011 0 -10000 0 -10000 0 0
liver development -0.001 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.001 0.005 -10000 0 -10000 0 0
RhoA/GTP 0 0.003 -10000 0 -10000 0 0
mol:GDP 0.001 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 0.017 0.005 -10000 0 -10000 0 0
RAB11FIP3 0.011 0 -10000 0 -10000 0 0
tube morphogenesis 0.001 0.012 -10000 0 -10000 0 0
ruffle organization 0.023 0.008 -10000 0 -10000 0 0
regulation of epithelial cell migration -0.001 0.005 -10000 0 -10000 0 0
PLD2 0.017 0.013 -10000 0 -0.26 1 1
PIP5K1A 0.023 0.008 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.022 0.011 -10000 0 -0.22 1 1
Rac1/GTP 0.001 0.012 -10000 0 -10000 0 0
Atypical NF-kappaB 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
BCL3/RelA 0.016 0.01 -9999 0 -0.22 1 1
FBXW11 0.011 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.021 0.011 -9999 0 -0.23 1 1
NF kappa B1 p50/RelA/I kappa B alpha 0.037 0.012 -9999 0 -10000 0 0
NFKBIA 0.023 0.01 -9999 0 -0.17 1 1
MAPK14 0.011 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.021 0.011 -9999 0 -0.23 1 1
ARRB2 0.014 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 0.021 0.014 -9999 0 -0.2 2 2
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.021 0.011 -9999 0 -0.23 1 1
PIK3CA 0.01 0.018 -9999 0 -0.41 1 1
NF kappa B1 p50 dimer 0.016 0.013 -9999 0 -0.28 1 1
PIK3R1 0.007 0.04 -9999 0 -0.41 5 5
NFKB1 0.018 0.013 -9999 0 -0.28 1 1
RELA 0.011 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.028 0.012 -9999 0 -0.18 1 1
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.04 0.012 -9999 0 -10000 0 0
SRC 0.011 0 -9999 0 -10000 0 0
PI3K 0.013 0.031 -9999 0 -0.28 6 6
NF kappa B1 p50/RelA 0.028 0.012 -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 0.015 -9999 0 -0.33 1 1
I kappa B alpha/PIK3R1 0.025 0.022 -9999 0 -0.18 5 5
cell death 0.039 0.012 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.021 0.011 -9999 0 -0.23 1 1
LCK 0.008 0.034 -9999 0 -0.34 5 5
BCL3 0.01 0.015 -9999 0 -0.33 1 1
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.032 0.025 -9999 0 -0.38 2 2
KLHL20 -0.002 0.013 -9999 0 -10000 0 0
CYFIP2 0.009 0.031 -9999 0 -0.41 3 3
Rac1/GDP 0.048 0.016 -9999 0 -0.21 2 2
ENAH 0.032 0.028 -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 0.008 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.002 0.011 -9999 0 -0.12 2 2
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.027 0.016 -9999 0 -0.2 2 2
RAPGEF1 0.041 0.022 -9999 0 -0.32 2 2
CTNND1 0.011 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.027 0.026 -9999 0 -0.4 2 2
CRK 0.037 0.024 -9999 0 -0.35 2 2
E-cadherin/gamma catenin/alpha catenin 0.021 0.023 -9999 0 -0.34 2 2
alphaE/beta7 Integrin 0.016 0.01 -9999 0 -0.22 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 0.032 0.025 -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 0.016 0.036 -9999 0 -0.2 14 14
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 0.015 0.027 -9999 0 -0.4 2 2
TIAM1 0 0.067 -9999 0 -0.41 14 14
E-cadherin(dimer)/Ca2+ 0.026 0.013 -9999 0 -0.19 2 2
AKT1 -0.001 0.007 -9999 0 -10000 0 0
PIK3R1 0.007 0.04 -9999 0 -0.41 5 5
CDH1 0.009 0.025 -9999 0 -0.41 2 2
RhoA/GDP 0.048 0.016 -9999 0 -0.21 2 2
actin cytoskeleton organization 0.034 0.016 -9999 0 -10000 0 0
CDC42/GDP 0.048 0.016 -9999 0 -0.21 2 2
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.019 0.021 -9999 0 -0.31 2 2
ITGB7 0.01 0.015 -9999 0 -0.33 1 1
RAC1 0.011 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.028 0.014 -9999 0 -0.2 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin 0.019 0.013 -9999 0 -0.19 2 2
mol:GDP 0.046 0.018 -9999 0 -0.24 2 2
CDC42/GTP/IQGAP1 0.015 0 -9999 0 -10000 0 0
JUP 0.01 0.018 -9999 0 -0.41 1 1
p120 catenin/RhoA/GDP 0.045 0.017 -9999 0 -0.21 2 2
RAC1/GTP/IQGAP1 0.015 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 0.015 -9999 0 -0.13 3 3
NME1 0.011 0 -9999 0 -10000 0 0
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.032 0.026 -9999 0 -0.38 2 2
regulation of cell-cell adhesion 0 0.007 -9999 0 -10000 0 0
WASF2 -0.001 0.005 -9999 0 -10000 0 0
Rap1/GTP -0.001 0.009 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.031 0.021 -9999 0 -0.38 1 1
CCND1 0.031 0.018 -9999 0 -0.15 3 3
VAV2 0.041 0.024 -9999 0 -0.35 2 2
RAP1/GDP 0.043 0.015 -9999 0 -10000 0 0
adherens junction assembly 0.032 0.026 -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 0.036 0.02 -9999 0 -0.36 1 1
E-cadherin/beta catenin -0.001 0.018 -9999 0 -0.3 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.032 0.025 -9999 0 -0.38 2 2
PIK3CA 0.01 0.018 -9999 0 -0.41 1 1
Rac1/GTP -0.003 0.018 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin 0.022 0.015 -9999 0 -0.23 2 2
ITGAE 0.011 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.027 0.026 -9999 0 -0.4 2 2
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.036 0.03 -10000 0 -0.29 1 1
adherens junction organization 0.033 0.028 -10000 0 -0.35 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.037 0.041 -10000 0 -0.38 2 2
FMN1 0.027 0.038 -10000 0 -0.48 1 1
mol:IP3 0.031 0.026 -10000 0 -0.29 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.028 0.027 -10000 0 -0.36 2 2
CTNNB1 0.011 0.001 -10000 0 -10000 0 0
AKT1 0.036 0.027 -10000 0 -0.33 1 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.033 0.028 -10000 0 -0.42 2 2
CTNND1 0.012 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.033 0.025 -10000 0 -0.33 2 2
VASP 0.033 0.025 -10000 0 -0.48 1 1
ZYX 0.033 0.025 -10000 0 -0.48 1 1
JUB 0.033 0.025 -10000 0 -0.34 2 2
EGFR(dimer) 0.028 0.044 -10000 0 -0.36 3 3
E-cadherin/beta catenin-gamma catenin -0.001 0.02 -10000 0 -0.31 2 2
mol:PI-3-4-5-P3 0.03 0.028 -10000 0 -0.35 1 1
PIK3CA 0.011 0.018 -10000 0 -0.41 1 1
PI3K 0.031 0.028 -10000 0 -0.36 1 1
FYN 0.032 0.036 -10000 0 -0.24 1 1
mol:Ca2+ 0.03 0.025 -10000 0 -0.29 1 1
JUP 0.01 0.018 -10000 0 -0.4 1 1
PIK3R1 0.008 0.04 -10000 0 -0.41 5 5
mol:DAG 0.031 0.026 -10000 0 -0.29 1 1
CDH1 0.009 0.025 -10000 0 -0.41 2 2
RhoA/GDP 0.037 0.041 -10000 0 -0.38 2 2
establishment of polarity of embryonic epithelium 0.033 0.025 -10000 0 -0.47 1 1
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 0.066 -10000 0 -0.4 14 14
CASR 0.024 0.043 -10000 0 -0.27 1 1
RhoA/GTP -0.002 0.019 -10000 0 -0.26 1 1
AKT2 0.036 0.027 -10000 0 -0.33 1 1
actin cable formation 0.032 0.036 -10000 0 -0.46 1 1
apoptosis -0.034 0.028 0.32 1 -10000 0 1
CTNNA1 0.012 0.001 -10000 0 -10000 0 0
mol:GDP 0.032 0.043 -10000 0 -0.41 2 2
PIP5K1A 0.033 0.025 -10000 0 -0.34 2 2
PLCG1 0.031 0.026 -10000 0 -0.3 1 1
Rac1/GTP -0.005 0.035 -10000 0 -0.41 2 2
homophilic cell adhesion 0.001 0.001 -10000 0 -10000 0 0
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 0.021 0.023 -9999 0 -0.34 2 2
E-cadherin/beta catenin 0.015 0.018 -9999 0 -0.28 2 2
CTNNB1 0.011 0 -9999 0 -10000 0 0
JUP 0.01 0.018 -9999 0 -0.41 1 1
CDH1 0.009 0.025 -9999 0 -0.41 2 2
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 0.039 0.011 -9999 0 -10000 0 0
CLOCK 0.014 0.001 -9999 0 -10000 0 0
TIMELESS/CRY2 0.034 0.011 -9999 0 -10000 0 0
DEC1/BMAL1 0.011 0.013 -9999 0 -0.28 1 1
ATR 0.011 0 -9999 0 -10000 0 0
NR1D1 0.033 0.009 -9999 0 -10000 0 0
ARNTL 0.013 0.018 -9999 0 -0.41 1 1
TIMELESS 0.033 0.013 -9999 0 -10000 0 0
NPAS2 0.01 0.04 -9999 0 -0.41 5 5
CRY2 0.011 0 -9999 0 -10000 0 0
mol:CO -0.011 0.003 -9999 0 -10000 0 0
CHEK1 0.011 0 -9999 0 -10000 0 0
mol:HEME 0.011 0.003 -9999 0 -10000 0 0
PER1 0.009 0.031 -9999 0 -0.41 3 3
BMAL/CLOCK/NPAS2 0.033 0.027 -9999 0 -0.22 6 6
BMAL1/CLOCK 0.04 0.019 -9999 0 -10000 0 0
S phase of mitotic cell cycle 0.039 0.011 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.039 0.011 -9999 0 -10000 0 0
mol:NADPH 0.011 0.003 -9999 0 -10000 0 0
PER1/TIMELESS 0.033 0.02 -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 0.025 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 0.014 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 0.025 0 -9999 0 -9999 0 0
SUMO1/HDAC1 0.025 0 -9999 0 -9999 0 0
RANGAP1 0.011 0 -9999 0 -9999 0 0
MDM2/SUMO1/SUMO1 0.028 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.017 0 -9999 0 -9999 0 0
Ran/GTP 0.022 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 0.027 0 -9999 0 -9999 0 0
NPC 0.007 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 0.021 0 -9999 0 -10000 0 0
CD4 0.01 0.015 -9999 0 -0.33 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 0.006 -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 0.022 0 -9999 0 -10000 0 0
mol:Choline 0 0.006 -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 0.014 0 -9999 0 -10000 0 0
Rac/GTP 0.009 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.021 0 -9999 0 -10000 0 0
ARFIP2 0.01 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 0.002 -9999 0 -10000 0 0
AP2A1 0.011 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.022 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0.015 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 0.016 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 0.028 0.003 -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 0.006 -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 0.006 -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 0.016 0.001 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.022 0.008 -9999 0 -0.17 1 1
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 0.033 0 -9999 0 -10000 0 0
NFKB1 0.01 0.018 -9999 0 -0.41 1 1
MAP3K14 0.011 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelB 0.016 0.013 -9999 0 -0.28 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 0.015 0 -9999 0 -10000 0 0
regulation of B cell activation 0.015 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 545 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.SL.A6JA TCGA.SL.A6J9 TCGA.SJ.A6ZJ TCGA.SJ.A6ZI
109_MAP3K5 -0.13 0.043 0.043 0.043
47_PPARGC1A -0.41 0.011 0.011 -0.41
105_BMP4 0.011 -0.41 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 -0.41 0.011 0.011
131_RELN/VLDLR -0.2 -0.2 0.028 -0.2
30_TGFB1/TGF beta receptor Type II 0.011 0.011 0.013 0.01
84_STAT5B -0.023 -0.091 -0.024 0.038
84_STAT5A -0.023 -0.091 -0.024 0.038
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/19439595/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)
Copyright © 2015 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle