PARADIGM pathway analysis of mRNASeq expression data
Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1WW7GMM
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1WW7GMM
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 54 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 183
Aurora B signaling 160
HIF-1-alpha transcription factor network 125
Signaling events regulated by Ret tyrosine kinase 120
Endothelins 107
Angiopoietin receptor Tie2-mediated signaling 105
p75(NTR)-mediated signaling 91
PDGFR-alpha signaling pathway 91
Signaling events mediated by the Hedgehog family 89
Integrins in angiogenesis 80
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 538 . 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 ( 538 ).

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 0.3401 183 9338 51 -0.97 0.011 1000 -1000 -0.14 -1000
Aurora B signaling 0.2974 160 10732 67 -0.52 0.011 1000 -1000 -0.038 -1000
HIF-1-alpha transcription factor network 0.2323 125 9515 76 -0.49 0.017 1000 -1000 -0.065 -1000
Signaling events regulated by Ret tyrosine kinase 0.2230 120 9865 82 -0.19 0.011 1000 -1000 -0.047 -1000
Endothelins 0.1989 107 10300 96 -0.34 0.011 1000 -1000 -0.046 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1952 105 9284 88 -0.32 0.043 1000 -1000 -0.074 -1000
p75(NTR)-mediated signaling 0.1691 91 11418 125 -0.2 0.03 1000 -1000 -0.055 -1000
PDGFR-alpha signaling pathway 0.1691 91 4047 44 -0.29 0.025 1000 -1000 -0.033 -1000
Signaling events mediated by the Hedgehog family 0.1654 89 4633 52 -0.26 0.14 1000 -1000 -0.018 -1000
Integrins in angiogenesis 0.1487 80 6795 84 -0.29 0.024 1000 -1000 -0.05 -1000
Cellular roles of Anthrax toxin 0.1301 70 2747 39 -0.13 0.019 1000 -1000 -0.013 -1000
S1P3 pathway 0.1283 69 2909 42 -0.41 0.016 1000 -1000 -0.025 -1000
Aurora C signaling 0.1264 68 478 7 -0.29 0.009 1000 -1000 -0.017 -1000
Nongenotropic Androgen signaling 0.1264 68 3581 52 -0.22 0.11 1000 -1000 -0.032 -1000
Wnt signaling 0.1134 61 427 7 -0.089 -0.002 1000 -1000 -0.014 -1000
PLK1 signaling events 0.1059 57 4868 85 -0.3 0.044 1000 -1000 -0.031 -1000
Signaling mediated by p38-alpha and p38-beta 0.1059 57 2548 44 -0.08 0.011 1000 -1000 -0.031 -1000
Reelin signaling pathway 0.1041 56 3165 56 -0.15 0.03 1000 -1000 -0.043 -1000
Effects of Botulinum toxin 0.1022 55 1450 26 -0.11 0.018 1000 -1000 -0.034 -1000
LPA4-mediated signaling events 0.1004 54 653 12 -0.12 0.015 1000 -1000 -0.007 -1000
Glypican 1 network 0.1004 54 2626 48 -0.22 0.022 1000 -1000 -0.012 -1000
IGF1 pathway 0.0929 50 2852 57 -0.076 0.022 1000 -1000 -0.048 -1000
Aurora A signaling 0.0911 49 2974 60 -0.25 0.022 1000 -1000 -0.017 -1000
Fc-epsilon receptor I signaling in mast cells 0.0911 49 4802 97 -0.12 0.028 1000 -1000 -0.046 -1000
S1P4 pathway 0.0911 49 1237 25 -0.1 0.024 1000 -1000 -0.013 -1000
S1P5 pathway 0.0874 47 801 17 -0.1 0.032 1000 -1000 -0.013 -1000
Noncanonical Wnt signaling pathway 0.0855 46 1197 26 -0.14 0.011 1000 -1000 -0.025 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0855 46 3159 68 -0.2 0.08 1000 -1000 -0.082 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0855 46 5574 120 -0.19 0.14 1000 -1000 -0.043 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0855 46 3646 78 -0.099 0.043 1000 -1000 -0.035 -1000
TCGA08_retinoblastoma 0.0836 45 365 8 -0.14 0.024 1000 -1000 -0.009 -1000
Thromboxane A2 receptor signaling 0.0818 44 4702 105 -0.18 0.031 1000 -1000 -0.039 -1000
BMP receptor signaling 0.0781 42 3417 81 -0.28 0.038 1000 -1000 -0.041 -1000
Plasma membrane estrogen receptor signaling 0.0781 42 3679 86 -0.15 0.066 1000 -1000 -0.042 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0762 41 1420 34 -0.039 0.011 1000 -1000 -0.014 -1000
Syndecan-1-mediated signaling events 0.0762 41 1411 34 -0.17 0.011 1000 -1000 -0.02 -1000
amb2 Integrin signaling 0.0762 41 3427 82 -0.15 0.022 1000 -1000 -0.045 -1000
Ephrin A reverse signaling 0.0706 38 267 7 -0.023 0 1000 -1000 -0.01 -1000
FOXA2 and FOXA3 transcription factor networks 0.0706 38 1764 46 -0.22 0.016 1000 -1000 -0.062 -1000
S1P1 pathway 0.0706 38 1375 36 -0.12 0.011 1000 -1000 -0.031 -1000
Ras signaling in the CD4+ TCR pathway 0.0706 38 658 17 -0.077 0.015 1000 -1000 -0.019 -1000
Osteopontin-mediated events 0.0632 34 1314 38 -0.12 0.014 1000 -1000 -0.053 -1000
Ephrin B reverse signaling 0.0613 33 1600 48 -0.095 0.015 1000 -1000 -0.04 -1000
TCGA08_p53 0.0595 32 228 7 -0.089 0.047 1000 -1000 -0.007 -1000
LPA receptor mediated events 0.0576 31 3235 102 -0.14 0.029 1000 -1000 -0.055 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0558 30 2611 85 -0.21 0.012 1000 -1000 -0.034 -1000
Glypican 2 network 0.0558 30 120 4 -0.014 -0.001 1000 -1000 -0.006 -1000
IL4-mediated signaling events 0.0539 29 2727 91 -0.52 0.26 1000 -1000 -0.13 -1000
FAS signaling pathway (CD95) 0.0539 29 1406 47 -0.075 0.037 1000 -1000 -0.025 -1000
EGFR-dependent Endothelin signaling events 0.0539 29 616 21 -0.11 0.02 1000 -1000 -0.042 -1000
Arf6 signaling events 0.0520 28 1747 62 -0.087 0.027 1000 -1000 -0.028 -1000
Visual signal transduction: Rods 0.0520 28 1504 52 -0.11 0.011 1000 -1000 -0.046 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0502 27 1490 54 -0.14 0.022 1000 -1000 -0.05 -1000
Syndecan-4-mediated signaling events 0.0502 27 1826 67 -0.26 0.016 1000 -1000 -0.051 -1000
Visual signal transduction: Cones 0.0483 26 994 38 -0.081 0.011 1000 -1000 -0.03 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0483 26 1379 52 -0.079 0.023 1000 -1000 -0.034 -1000
Coregulation of Androgen receptor activity 0.0465 25 1964 76 -0.13 0.022 1000 -1000 -0.021 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0446 24 3019 125 -0.067 0.029 1000 -1000 -0.054 -1000
Hedgehog signaling events mediated by Gli proteins 0.0428 23 1539 65 -0.1 0.038 1000 -1000 -0.037 -1000
Syndecan-2-mediated signaling events 0.0409 22 1532 69 -0.1 0.028 1000 -1000 -0.011 -1000
Presenilin action in Notch and Wnt signaling 0.0409 22 1346 61 -0.12 0.031 1000 -1000 -0.043 -1000
Glucocorticoid receptor regulatory network 0.0409 22 2513 114 -0.24 0.046 1000 -1000 -0.046 -1000
Calcium signaling in the CD4+ TCR pathway 0.0409 22 708 31 -0.12 0.015 1000 -1000 -0.047 -1000
TCGA08_rtk_signaling 0.0409 22 594 26 -0.15 0.023 1000 -1000 -0.011 -1000
IL2 signaling events mediated by STAT5 0.0409 22 488 22 -0.1 0.056 1000 -1000 -0.028 -1000
BCR signaling pathway 0.0409 22 2205 99 -0.06 0.047 1000 -1000 -0.047 -1000
Insulin Pathway 0.0390 21 1557 74 -0.13 0.03 1000 -1000 -0.049 -1000
Regulation of Androgen receptor activity 0.0390 21 1536 70 -0.22 0.023 1000 -1000 -0.048 -1000
IL6-mediated signaling events 0.0372 20 1553 75 -0.12 0.062 1000 -1000 -0.043 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0372 20 665 33 -0.16 0.034 1000 -1000 -0.025 -1000
Retinoic acid receptors-mediated signaling 0.0353 19 1105 58 -0.052 0.022 1000 -1000 -0.043 -1000
Regulation of nuclear SMAD2/3 signaling 0.0335 18 2472 136 -0.16 0.054 1000 -1000 -0.034 -1000
Signaling events mediated by PTP1B 0.0335 18 1390 76 -0.12 0.024 1000 -1000 -0.045 -1000
Nectin adhesion pathway 0.0335 18 1180 63 -0.067 0.021 1000 -1000 -0.04 -1000
Canonical Wnt signaling pathway 0.0335 18 932 51 -0.097 0.05 1000 -1000 -0.031 -1000
Regulation of p38-alpha and p38-beta 0.0335 18 993 54 -0.18 0.043 1000 -1000 -0.036 -1000
Rapid glucocorticoid signaling 0.0335 18 374 20 -0.051 0.011 1000 -1000 -0.007 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0316 17 501 28 -0.1 0.032 1000 -1000 -0.017 -1000
BARD1 signaling events 0.0297 16 967 57 -0.13 0.028 1000 -1000 -0.033 -1000
Class I PI3K signaling events mediated by Akt 0.0297 16 1138 68 -0.24 0.04 1000 -1000 -0.021 -1000
Signaling mediated by p38-gamma and p38-delta 0.0297 16 240 15 -0.017 0.021 1000 -1000 -0.014 -1000
Regulation of Telomerase 0.0297 16 1664 102 -0.3 0.038 1000 -1000 -0.052 -1000
IL12-mediated signaling events 0.0279 15 1314 87 -0.3 0.045 1000 -1000 -0.094 -1000
IL1-mediated signaling events 0.0260 14 900 62 -0.038 0.04 1000 -1000 -0.05 -1000
TCR signaling in naïve CD8+ T cells 0.0260 14 1338 93 -0.044 0.04 1000 -1000 -0.046 -1000
EPHB forward signaling 0.0260 14 1264 85 -0.034 0.03 1000 -1000 -0.051 -1000
Signaling events mediated by PRL 0.0260 14 479 34 -0.13 0.018 1000 -1000 -0.015 -1000
IFN-gamma pathway 0.0242 13 923 68 -0.23 0.048 1000 -1000 -0.051 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0242 13 1127 83 -0.24 0.044 1000 -1000 -0.043 -1000
FoxO family signaling 0.0242 13 884 64 -0.24 0.042 1000 -1000 -0.045 -1000
ErbB4 signaling events 0.0223 12 838 69 -0.072 0.03 1000 -1000 -0.056 -1000
Insulin-mediated glucose transport 0.0223 12 407 32 -0.24 0.025 1000 -1000 -0.03 -1000
Syndecan-3-mediated signaling events 0.0223 12 427 35 -0.089 0.03 1000 -1000 -0.023 -1000
PDGFR-beta signaling pathway 0.0223 12 1256 97 -0.021 0.039 1000 -1000 -0.043 -1000
EPO signaling pathway 0.0204 11 612 55 -0.025 0.035 1000 -1000 -0.045 -1000
mTOR signaling pathway 0.0204 11 627 53 -0.026 0.018 1000 -1000 -0.036 -1000
HIF-2-alpha transcription factor network 0.0204 11 498 43 -0.14 0.022 1000 -1000 -0.049 -1000
IL2 signaling events mediated by PI3K 0.0204 11 681 58 -0.11 0.043 1000 -1000 -0.053 -1000
Class IB PI3K non-lipid kinase events 0.0204 11 33 3 -0.003 0.003 1000 -1000 -0.007 -1000
ErbB2/ErbB3 signaling events 0.0186 10 672 65 -0.12 0.022 1000 -1000 -0.039 -1000
Signaling events mediated by HDAC Class III 0.0186 10 407 40 -0.078 0.016 1000 -1000 -0.021 -1000
JNK signaling in the CD4+ TCR pathway 0.0167 9 166 17 -0.014 0.034 1000 -1000 -0.019 -1000
Ceramide signaling pathway 0.0149 8 615 76 -0.068 0.036 1000 -1000 -0.023 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0149 8 328 37 -0.02 0.027 1000 -1000 -0.026 -1000
ceramide signaling pathway 0.0149 8 403 49 -0.031 0.038 1000 -1000 -0.016 -1000
IL27-mediated signaling events 0.0149 8 409 51 -0.053 0.014 1000 -1000 -0.059 -1000
Caspase cascade in apoptosis 0.0130 7 543 74 -0.032 0.035 1000 -1000 -0.018 -1000
Signaling events mediated by HDAC Class II 0.0130 7 533 75 -0.051 0.029 1000 -1000 -0.025 -1000
IL23-mediated signaling events 0.0130 7 444 60 -0.047 0.043 1000 -1000 -0.12 -1000
p38 MAPK signaling pathway 0.0130 7 324 44 -0.046 0.028 1000 -1000 -0.036 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0112 6 270 45 -0.032 0.057 1000 -1000 -0.048 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0093 5 373 74 -0.075 0.062 1000 -1000 -0.05 -1000
Canonical NF-kappaB pathway 0.0074 4 176 39 -0.032 0.058 1000 -1000 -0.048 -1000
PLK2 and PLK4 events 0.0074 4 12 3 0.008 0.015 1000 -1000 -0.008 -1000
TRAIL signaling pathway 0.0074 4 198 48 -0.001 0.037 1000 -1000 -0.041 -1000
Class I PI3K signaling events 0.0074 4 316 73 -0.015 0.053 1000 -1000 -0.034 -1000
Arf6 trafficking events 0.0074 4 351 71 -0.19 0.035 1000 -1000 -0.041 -1000
Signaling events mediated by HDAC Class I 0.0056 3 377 104 -0.032 0.044 1000 -1000 -0.034 -1000
Paxillin-dependent events mediated by a4b1 0.0056 3 143 36 -0.031 0.032 1000 -1000 -0.039 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0037 2 46 23 -0.004 0.036 1000 -1000 -0.018 -1000
a4b1 and a4b7 Integrin signaling 0.0037 2 11 5 0.009 0.015 1000 -1000 -0.008 -1000
VEGFR1 specific signals 0.0037 2 138 56 -0.062 0.052 1000 -1000 -0.025 -1000
Arf6 downstream pathway 0.0019 1 50 43 -0.023 0.023 1000 -1000 -0.021 -1000
Atypical NF-kappaB pathway 0.0019 1 36 31 0 0.04 1000 -1000 -0.017 -1000
E-cadherin signaling in the nascent adherens junction 0.0019 1 95 76 -0.003 0.048 1000 -1000 -0.047 -1000
E-cadherin signaling in keratinocytes 0.0019 1 80 43 -0.034 0.037 1000 -1000 -0.036 -1000
E-cadherin signaling events 0.0019 1 7 5 0.009 0.021 1000 -1000 -0.011 -1000
Circadian rhythm pathway 0.0000 0 15 22 -0.011 0.04 1000 -1000 -0.025 -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 -0.018 -1000
Alternative NF-kappaB pathway 0.0000 0 2 13 0 0.033 1000 -1000 -0.013 -1000
Total NA 4001 238234 7203 -17 4.3 131000 -131000 -4.7 -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 -0.99 208 208
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 -0.98 212 212
MAP2K1 -0.021 0.016 -9999 0 -10000 0 0
BRCA2 -0.63 0.36 -9999 0 -0.99 208 208
FOXM1 -0.76 0.48 -9999 0 -1.1 286 286
XRCC1 -0.63 0.36 -9999 0 -0.96 229 229
FOXM1B/p19 -0.68 0.4 -9999 0 -0.95 307 307
Cyclin D1/CDK4 -0.58 0.32 -9999 0 -0.87 244 244
CDC2 -0.67 0.38 -9999 0 -0.96 285 285
TGFA -0.57 0.31 -9999 0 -0.86 229 229
SKP2 -0.63 0.36 -9999 0 -0.95 242 242
CCNE1 -0.14 0.17 -9999 0 -0.34 217 217
CKS1B -0.63 0.36 -9999 0 -0.95 238 238
RB1 -0.24 0.12 -9999 0 -0.53 11 11
FOXM1C/SP1 -0.7 0.42 -9999 0 -1 282 282
AURKB -0.18 0.068 -9999 0 -10000 0 0
CENPF -0.67 0.38 -9999 0 -0.97 275 275
CDK4 -0.001 0.005 -9999 0 -10000 0 0
MYC -0.56 0.32 -9999 0 -0.84 244 244
CHEK2 -0.022 0.022 -9999 0 -0.35 1 1
ONECUT1 -0.62 0.35 -9999 0 -0.9 268 268
CDKN2A -0.13 0.17 -9999 0 -0.32 225 225
LAMA4 -0.66 0.4 -9999 0 -1 244 244
FOXM1B/HNF6 -0.7 0.42 -9999 0 -1 270 270
FOS -0.77 0.48 -9999 0 -1.1 286 286
SP1 0.011 0.001 -9999 0 -10000 0 0
CDC25B -0.63 0.36 -9999 0 -0.95 242 242
response to radiation -0.03 0.014 -9999 0 -10000 0 0
CENPB -0.63 0.36 -9999 0 -0.95 243 243
CENPA -0.69 0.38 -9999 0 -0.98 282 282
NEK2 -0.69 0.37 -9999 0 -0.98 281 281
HIST1H2BA -0.64 0.36 -9999 0 -0.95 249 249
CCNA2 -0.07 0.14 -9999 0 -0.34 114 114
EP300 0.011 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.72 0.43 -9999 0 -1.1 260 260
CCNB2 -0.69 0.38 -9999 0 -0.99 273 273
CCNB1 -0.67 0.39 -9999 0 -1 254 254
ETV5 -0.63 0.36 -9999 0 -0.97 228 228
ESR1 -0.68 0.41 -9999 0 -1 247 247
CCND1 -0.59 0.33 -9999 0 -0.88 248 248
GSK3A -0.014 0.013 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.12 0.14 -9999 0 -0.25 261 261
CDK2 0.003 0.004 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.038 0.017 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.67 0.39 -9999 0 -0.95 303 303
GAS1 -0.97 0.48 -9999 0 -1.3 375 375
MMP2 -0.64 0.38 -9999 0 -1 206 206
RB1/FOXM1C -0.62 0.36 -9999 0 -0.93 259 259
CREBBP 0.009 0.026 -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 -0.21 472 472
Aurora B/RasGAP/Survivin -0.27 0.12 -9999 0 -0.34 403 403
Chromosomal passenger complex/Cul3 protein complex -0.12 0.092 -9999 0 -0.29 91 91
BIRC5 -0.26 0.14 -9999 0 -0.33 416 416
DES -0.52 0.25 -9999 0 -0.63 448 448
Aurora C/Aurora B/INCENP -0.13 0.062 -9999 0 -0.31 3 3
Aurora B/TACC1 -0.19 0.11 -9999 0 -0.22 481 481
Aurora B/PP2A -0.18 0.077 -9999 0 -0.21 472 472
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 0.097 -9999 0 -0.23 473 473
Cul3 protein complex -0.026 0.099 -9999 0 -0.23 103 103
KIF2C -0.067 0.035 -9999 0 -10000 0 0
PEBP1 0.002 0.004 -9999 0 -10000 0 0
KIF20A -0.3 0.1 -9999 0 -0.33 485 485
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.18 0.082 -9999 0 -0.21 472 472
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 -0.01 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 0.002 -9999 0 -10000 0 0
H3F3B -0.074 0.034 -9999 0 -10000 0 0
AURKB -0.28 0.12 -9999 0 -0.33 472 472
AURKC 0.009 0.025 -9999 0 -0.33 3 3
CDCA8 -0.19 0.17 -9999 0 -0.34 312 312
cytokinesis -0.15 0.069 -9999 0 -0.25 19 19
Aurora B/Septin1 -0.13 0.079 -9999 0 -0.24 18 18
AURKA -0.091 0.16 -9999 0 -0.33 159 159
INCENP 0.004 0.004 -9999 0 -10000 0 0
KLHL13 -0.07 0.16 -9999 0 -0.41 103 103
BUB1 -0.26 0.14 -9999 0 -0.33 422 422
hSgo1/Aurora B/Survivin -0.37 0.15 -9999 0 -0.43 459 459
EVI5 0.011 0.001 -9999 0 -10000 0 0
RhoA/GTP -0.11 0.065 -9999 0 -0.28 23 23
SGOL1 -0.25 0.14 -9999 0 -0.33 418 418
CENPA -0.1 0.051 -9999 0 -0.15 152 152
NCAPG -0.22 0.16 -9999 0 -0.33 358 358
Aurora B/HC8 Proteasome -0.18 0.077 -9999 0 -0.21 472 472
NCAPD2 0.011 0 -9999 0 -10000 0 0
Aurora B/PP1-gamma -0.18 0.077 -9999 0 -0.21 472 472
RHOA 0.011 0 -9999 0 -10000 0 0
NCAPH -0.25 0.14 -9999 0 -0.33 416 416
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 0.077 -9999 0 -0.21 472 472
PPP1CC 0.011 0 -9999 0 -10000 0 0
Centraspindlin -0.12 0.072 -9999 0 -0.25 44 44
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 -0.37 308 308
KIF23 -0.006 0.069 -9999 0 -0.33 23 23
VIM -0.18 0.084 -9999 0 -0.21 472 472
RACGAP1 0.007 0.021 -9999 0 -0.34 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 0.067 -9999 0 -0.19 291 291
Chromosomal passenger complex/EVI5 -0.26 0.19 -9999 0 -0.36 417 417
TACC1 -0.066 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
HIF-1-alpha transcription factor network

Figure S3.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S3.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.36 0.4 -9999 0 -0.83 172 172
HDAC7 0.012 0.001 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.3 0.36 -9999 0 -0.75 145 145
SMAD4 0.011 0.018 -9999 0 -0.41 1 1
ID2 -0.36 0.41 -9999 0 -0.83 172 172
AP1 -0.076 0.14 -9999 0 -0.29 166 166
ABCG2 -0.46 0.47 -9999 0 -0.9 243 243
HIF1A -0.047 0.062 -9999 0 -10000 0 0
TFF3 -0.42 0.44 -9999 0 -0.87 205 205
GATA2 -0.028 0.12 -9999 0 -0.41 51 51
AKT1 -0.061 0.084 -9999 0 -0.22 18 18
response to hypoxia -0.078 0.086 -9999 0 -0.19 111 111
MCL1 -0.36 0.4 -9999 0 -0.83 171 171
NDRG1 -0.36 0.4 -9999 0 -0.83 172 172
SERPINE1 -0.36 0.41 -9999 0 -0.83 172 172
FECH -0.36 0.4 -9999 0 -0.83 171 171
FURIN -0.36 0.4 -9999 0 -0.83 172 172
NCOA2 -0.003 0.078 -9999 0 -0.41 19 19
EP300 -0.073 0.13 -9999 0 -0.34 74 74
HMOX1 -0.36 0.4 -9999 0 -0.83 174 174
BHLHE40 -0.36 0.4 -9999 0 -0.82 174 174
BHLHE41 -0.38 0.43 -9999 0 -0.87 179 179
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.041 0.083 -9999 0 -0.3 5 5
ENG -0.025 0.084 -9999 0 -0.27 5 5
JUN 0.006 0.048 -9999 0 -0.41 7 7
RORA -0.37 0.42 -9999 0 -0.84 178 178
ABCB1 -0.34 0.49 -9999 0 -1.2 137 137
TFRC -0.36 0.41 -9999 0 -0.83 174 174
CXCR4 -0.36 0.4 -9999 0 -0.82 174 174
TF -0.37 0.41 -9999 0 -0.84 176 176
CITED2 -0.37 0.41 -9999 0 -0.84 172 172
HIF1A/ARNT -0.39 0.47 -9999 0 -0.9 188 188
LDHA -0.053 0.048 -9999 0 -10000 0 0
ETS1 -0.36 0.4 -9999 0 -0.83 171 171
PGK1 -0.36 0.4 -9999 0 -0.82 174 174
NOS2 -0.37 0.41 -9999 0 -0.83 176 176
ITGB2 -0.36 0.4 -9999 0 -0.83 174 174
ALDOA -0.36 0.4 -9999 0 -0.83 172 172
Cbp/p300/CITED2 -0.39 0.45 -9999 0 -0.95 156 156
FOS -0.12 0.19 -9999 0 -0.41 165 165
HK2 -0.37 0.41 -9999 0 -0.83 177 177
SP1 0.01 0.023 -9999 0 -10000 0 0
GCK -0.23 0.46 -9999 0 -1.3 75 75
HK1 -0.36 0.4 -9999 0 -0.82 174 174
NPM1 -0.36 0.4 -9999 0 -0.82 174 174
EGLN1 -0.36 0.4 -9999 0 -0.82 174 174
CREB1 0.017 0 -9999 0 -10000 0 0
PGM1 -0.36 0.4 -9999 0 -0.83 172 172
SMAD3 0.009 0.036 -9999 0 -0.41 4 4
EDN1 -0.14 0.24 -9999 0 -0.66 56 56
IGFBP1 -0.39 0.43 -9999 0 -0.86 183 183
VEGFA -0.25 0.32 -9999 0 -0.69 109 109
HIF1A/JAB1 -0.023 0.036 -9999 0 -10000 0 0
CP -0.4 0.43 -9999 0 -0.87 189 189
CXCL12 -0.49 0.46 -9999 0 -0.92 235 235
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 0.4 -9999 0 -0.83 172 172
EGLN3 -0.36 0.41 -9999 0 -0.83 172 172
CA9 -0.43 0.44 -9999 0 -0.86 221 221
TERT -0.41 0.43 -9999 0 -0.87 197 197
ENO1 -0.36 0.4 -9999 0 -0.83 172 172
PFKL -0.36 0.4 -9999 0 -0.83 172 172
NCOA1 0.01 0.018 -9999 0 -0.41 1 1
ADM -0.37 0.41 -9999 0 -0.83 183 183
ARNT -0.048 0.062 -9999 0 -10000 0 0
HNF4A -0.049 0.12 -9999 0 -0.34 78 78
ADFP -0.37 0.4 -9999 0 -0.81 188 188
SLC2A1 -0.25 0.32 -9999 0 -0.69 113 113
LEP -0.36 0.4 -9999 0 -0.83 174 174
HIF1A/ARNT/Cbp/p300 -0.32 0.37 -9999 0 -0.77 155 155
EPO -0.22 0.29 -9999 0 -0.78 49 49
CREBBP -0.074 0.13 -9999 0 -0.34 75 75
HIF1A/ARNT/Cbp/p300/HDAC7 -0.29 0.36 -9999 0 -0.75 143 143
PFKFB3 -0.36 0.4 -9999 0 -0.82 174 174
NT5E -0.39 0.43 -9999 0 -0.88 183 183
Signaling events regulated by Ret tyrosine kinase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.032 0.034 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.13 0.13 -9999 0 -0.33 101 101
JUN -0.077 0.13 -9999 0 -0.39 37 37
HRAS 0.011 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.1 0.13 -9999 0 -0.23 259 259
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 -0.23 258 258
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 -0.089 0.11 -9999 0 -0.21 253 253
RHOA 0.011 0 -9999 0 -10000 0 0
RAP1A/GTP -0.098 0.11 -9999 0 -0.2 258 258
GRB7 -0.01 0.083 -9999 0 -0.34 33 33
RET51/GFRalpha1/GDNF -0.1 0.13 -9999 0 -0.23 258 258
MAPKKK cascade -0.098 0.11 -9999 0 -0.37 33 33
BCAR1 0.011 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.11 0.14 -9999 0 -0.24 268 268
lamellipodium assembly -0.12 0.13 -9999 0 -0.24 261 261
RET51/GFRalpha1/GDNF/SHC -0.1 0.13 -9999 0 -0.23 258 258
PIK3CA 0.01 0.018 -9999 0 -0.41 1 1
RET9/GFRalpha1/GDNF/SHC -0.089 0.11 -9999 0 -0.21 253 253
RET9/GFRalpha1/GDNF/Shank3 -0.089 0.11 -9999 0 -0.21 253 253
MAPK3 -0.075 0.11 -9999 0 -0.34 31 31
DOK1 0.011 0 -9999 0 -10000 0 0
DOK6 -0.072 0.17 -9999 0 -0.41 106 106
PXN 0.011 0 -9999 0 -10000 0 0
neurite development -0.082 0.12 -9999 0 -0.27 95 95
DOK5 -0.03 0.12 -9999 0 -0.41 52 52
GFRA1 -0.19 0.21 -9999 0 -0.41 253 253
MAPK8 -0.084 0.13 -9999 0 -0.37 38 38
HRAS/GTP -0.11 0.12 -9999 0 -0.23 258 258
tube development -0.078 0.11 -9999 0 -0.19 252 252
MAPK1 -0.075 0.11 -9999 0 -0.34 31 31
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.081 0.11 -9999 0 -0.2 251 251
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 -0.25 292 292
SHC1 0.011 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.1 0.13 -9999 0 -0.23 258 258
RET51/GFRalpha1/GDNF/Dok5 -0.12 0.16 -9999 0 -0.26 270 270
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 -0.25 251 251
PIK3R1 0.007 0.04 -9999 0 -0.41 5 5
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.083 0.12 -9999 0 -0.2 251 251
RET51/GFRalpha1/GDNF/Grb7 -0.11 0.14 -9999 0 -0.24 261 261
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.025 0.11 -9999 0 -0.37 50 50
DOK4 0.011 0 -9999 0 -10000 0 0
JNK cascade -0.076 0.13 -9999 0 -0.38 37 37
RET9/GFRalpha1/GDNF/FRS2 -0.089 0.11 -9999 0 -0.21 252 252
SHANK3 0.011 0 -9999 0 -10000 0 0
RASA1 0.007 0.04 -9999 0 -0.41 5 5
NCK1 0.009 0.026 -9999 0 -0.41 2 2
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.082 0.11 -9999 0 -0.2 251 251
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.09 0.13 -9999 0 -0.21 258 258
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.094 0.14 -9999 0 -0.22 259 259
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.094 0.14 -9999 0 -0.22 257 257
PI3K -0.16 0.21 -9999 0 -0.36 261 261
SOS1 0.011 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.077 0.11 -9999 0 -0.19 252 252
GRB10 0.01 0.018 -9999 0 -0.41 1 1
activation of MAPKK activity -0.082 0.11 -9999 0 -0.2 252 252
RET51/GFRalpha1/GDNF/FRS2 -0.1 0.13 -9999 0 -0.23 258 258
GAB1 0.008 0.036 -9999 0 -0.41 4 4
IRS1 -0.03 0.12 -9999 0 -0.41 53 53
IRS2 -0.043 0.14 -9999 0 -0.41 69 69
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.097 0.14 -9999 0 -0.23 258 258
RET51/GFRalpha1/GDNF/PKC alpha -0.12 0.15 -9999 0 -0.24 269 269
GRB2 0.011 0 -9999 0 -10000 0 0
PRKACA 0.011 0 -9999 0 -10000 0 0
GDNF 0.003 0.026 -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 -0.26 272 272
Rac1/GTP -0.15 0.15 -9999 0 -0.28 261 261
RET9/GFRalpha1/GDNF -0.11 0.13 -9999 0 -0.24 253 253
GFRalpha1/GDNF -0.13 0.15 -9999 0 -0.29 253 253
Endothelins

Figure S5.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S5.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.088 0.2 -10000 0 -0.39 115 115
PTK2B 0.011 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.12 0.31 -10000 0 -0.79 81 81
EDN1 -0.001 0.089 -10000 0 -0.39 11 11
EDN3 -0.1 0.17 -10000 0 -0.36 159 159
EDN2 -0.042 0.12 -10000 0 -0.33 84 84
HRAS/GDP -0.12 0.21 -10000 0 -0.42 136 136
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.084 0.18 -10000 0 -0.36 125 125
ADCY4 -0.11 0.19 -10000 0 -0.38 140 140
ADCY5 -0.14 0.2 -10000 0 -0.4 161 161
ADCY6 -0.1 0.18 -10000 0 -0.37 136 136
ADCY7 -0.1 0.18 -10000 0 -0.37 133 133
ADCY1 -0.11 0.2 -10000 0 -0.38 147 147
ADCY2 -0.21 0.23 -10000 0 -0.46 205 205
ADCY3 -0.1 0.19 -10000 0 -0.37 133 133
ADCY8 -0.11 0.18 -10000 0 -0.37 136 136
ADCY9 -0.13 0.22 -10000 0 -0.42 154 154
arachidonic acid secretion -0.17 0.28 -10000 0 -0.46 217 217
ETB receptor/Endothelin-1/Gq/GTP -0.067 0.15 -10000 0 -0.33 103 103
GNAO1 -0.1 0.18 -10000 0 -0.41 142 142
HRAS 0.009 0.004 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.057 0.21 0.17 4 -0.36 116 120
ETA receptor/Endothelin-1/Gs/GTP -0.087 0.22 0.16 100 -0.39 136 236
mol:GTP -0.002 0.005 -10000 0 -10000 0 0
COL3A1 -0.096 0.22 -10000 0 -0.42 117 117
EDNRB -0.084 0.18 -10000 0 -0.41 123 123
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.13 0.25 -10000 0 -0.52 127 127
CYSLTR1 -0.093 0.21 -10000 0 -0.47 83 83
SLC9A1 -0.057 0.11 -10000 0 -0.24 91 91
mol:GDP -0.13 0.22 -10000 0 -0.45 137 137
SLC9A3 -0.14 0.3 -10000 0 -0.62 132 132
RAF1 -0.16 0.24 -10000 0 -0.42 204 204
JUN -0.1 0.26 -10000 0 -0.67 75 75
JAK2 -0.092 0.2 -10000 0 -0.38 127 127
mol:IP3 -0.09 0.18 -10000 0 -0.4 95 95
ETA receptor/Endothelin-1 -0.084 0.26 -10000 0 -0.42 148 148
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 -0.32 281 281
FOS -0.29 0.43 -10000 0 -0.84 186 186
Gai/GDP -0.19 0.34 -10000 0 -0.73 143 143
CRK 0.011 0.001 -10000 0 -10000 0 0
mol:Ca ++ -0.14 0.25 -10000 0 -0.47 153 153
BCAR1 0.011 0 -10000 0 -10000 0 0
PRKCB1 -0.091 0.17 -10000 0 -0.38 101 101
GNAQ 0.007 0.026 -10000 0 -0.41 2 2
GNAZ -0.001 0.069 -10000 0 -0.41 15 15
GNAL -0.051 0.15 -10000 0 -0.41 79 79
Gs family/GDP -0.16 0.2 -10000 0 -0.42 166 166
ETA receptor/Endothelin-1/Gq/GTP -0.097 0.21 -10000 0 -0.41 127 127
MAPK14 -0.051 0.13 -10000 0 -0.33 64 64
TRPC6 -0.14 0.34 -10000 0 -0.85 81 81
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 -0.06 0.14 -10000 0 -0.33 80 80
ETB receptor/Endothelin-2 -0.085 0.15 -10000 0 -0.28 182 182
ETB receptor/Endothelin-3 -0.12 0.16 -10000 0 -0.28 251 251
ETB receptor/Endothelin-1 -0.056 0.15 -10000 0 -0.3 130 130
MAPK3 -0.26 0.38 -10000 0 -0.73 194 194
MAPK1 -0.26 0.38 -10000 0 -0.73 194 194
Rac1/GDP -0.12 0.21 -10000 0 -0.42 135 135
cAMP biosynthetic process -0.19 0.24 -10000 0 -0.43 217 217
MAPK8 -0.13 0.3 -10000 0 -0.73 85 85
SRC 0.011 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.087 0.16 -10000 0 -0.33 125 125
p130Cas/CRK/Src/PYK2 -0.11 0.23 -10000 0 -0.53 99 99
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 -0.52 121 121
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.12 0.18 -10000 0 -0.32 220 220
mol:DAG -0.09 0.18 -10000 0 -0.4 95 95
MAP2K2 -0.2 0.3 -10000 0 -0.55 199 199
MAP2K1 -0.2 0.3 -10000 0 -0.55 199 199
EDNRA -0.13 0.24 -10000 0 -0.47 163 163
positive regulation of muscle contraction -0.07 0.17 -10000 0 -0.33 115 115
Gq family/GDP -0.14 0.19 -10000 0 -0.44 110 110
HRAS/GTP -0.13 0.21 -10000 0 -0.41 139 139
PRKCH -0.086 0.18 -10000 0 -0.41 85 85
RAC1 0.011 0 -10000 0 -10000 0 0
PRKCA -0.098 0.19 -10000 0 -0.44 91 91
PRKCB -0.097 0.19 -10000 0 -0.42 102 102
PRKCE -0.084 0.17 -10000 0 -0.41 80 80
PRKCD -0.086 0.17 -10000 0 -0.42 78 78
PRKCG -0.11 0.18 -10000 0 -0.39 116 116
regulation of vascular smooth muscle contraction -0.34 0.5 -10000 0 -0.99 186 186
PRKCQ -0.1 0.18 -10000 0 -0.4 110 110
PLA2G4A -0.19 0.31 -10000 0 -0.51 217 217
GNA14 -0.034 0.13 -10000 0 -0.41 55 55
GNA15 0.004 0.039 -10000 0 -0.34 7 7
GNA12 0.011 0 -10000 0 -10000 0 0
GNA11 -0.001 0.063 -10000 0 -0.41 12 12
Rac1/GTP -0.057 0.21 0.17 107 -0.36 116 223
MMP1 -0.052 0.15 0.27 8 -10000 0 8
Angiopoietin receptor Tie2-mediated signaling

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 -0.19 0.44 -10000 0 -0.84 166 166
NCK1/PAK1/Dok-R -0.12 0.18 -10000 0 -0.4 166 166
NCK1/Dok-R -0.26 0.51 -10000 0 -0.99 166 166
PIK3CA 0.011 0.018 -10000 0 -0.41 1 1
mol:beta2-estradiol 0.043 0.095 0.23 108 -10000 0 108
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 0.25 108 -0.34 39 147
TNIP2 0.011 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.28 0.44 -10000 0 -0.92 166 166
FN1 0.007 0.04 -10000 0 -0.41 5 5
PLD2 -0.28 0.53 -10000 0 -1 166 166
PTPN11 0.011 0 -10000 0 -10000 0 0
GRB14 -0.11 0.16 -10000 0 -0.33 195 195
ELK1 -0.24 0.47 -10000 0 -0.93 166 166
GRB7 -0.01 0.083 -10000 0 -0.34 33 33
PAK1 0.011 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.3 0.47 -10000 0 -0.97 166 166
CDKN1A -0.11 0.3 -10000 0 -0.61 109 109
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 -1 166 166
CRK 0.011 0 -10000 0 -10000 0 0
mol:NO -0.13 0.33 -10000 0 -0.62 166 166
PLG -0.3 0.53 -10000 0 -1 166 166
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.22 0.4 -10000 0 -0.8 166 166
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 -0.55 37 37
BMX -0.3 0.54 -10000 0 -1.1 166 166
ANGPT1 -0.22 0.48 -10000 0 -1.2 108 108
tube development -0.13 0.33 -10000 0 -0.61 164 164
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 -1.1 166 166
alpha5/beta1 Integrin 0.016 0 -10000 0 -10000 0 0
FGF2 -0.22 0.21 -10000 0 -0.41 291 291
STAT5A (dimer) -0.15 0.38 -10000 0 -0.75 128 128
mol:L-citrulline -0.13 0.33 -10000 0 -0.62 166 166
AGTR1 -0.085 0.17 -10000 0 -0.41 121 121
MAPK14 -0.28 0.54 -10000 0 -1.1 166 166
Tie2/SHP2 -0.21 0.4 -10000 0 -1.1 91 91
TEK -0.2 0.46 -10000 0 -1.2 91 91
RPS6KB1 -0.19 0.42 -10000 0 -0.8 166 166
Angiotensin II/AT1 -0.057 0.12 -10000 0 -0.28 121 121
Tie2/Ang1/GRB2 -0.29 0.55 -10000 0 -1.1 166 166
MAPK3 -0.25 0.48 -10000 0 -0.95 166 166
MAPK1 -0.25 0.48 -10000 0 -0.95 166 166
Tie2/Ang1/GRB7 -0.29 0.55 -10000 0 -1.1 166 166
NFKB1 0.01 0.018 -10000 0 -0.41 1 1
MAPK8 -0.28 0.53 -10000 0 -1 166 166
PI3K -0.24 0.5 -10000 0 -0.96 166 166
FES -0.27 0.54 -10000 0 -1 166 166
Crk/Dok-R -0.26 0.51 -10000 0 -0.99 166 166
Tie2/Ang1/ABIN2 -0.29 0.55 -10000 0 -1.1 166 166
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.17 0.39 -10000 0 -0.74 166 166
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 -0.8 166 166
Tie2/Ang2 -0.19 0.45 -10000 0 -0.85 150 150
Tie2/Ang1 -0.31 0.58 -10000 0 -1.1 166 166
FOXO1 -0.16 0.4 -10000 0 -0.75 166 166
ELF1 -0.006 0.054 -10000 0 -0.44 4 4
ELF2 -0.28 0.53 -10000 0 -1 166 166
mol:Choline -0.26 0.5 -10000 0 -0.98 166 166
cell migration -0.07 0.1 -10000 0 -0.22 166 166
FYN -0.15 0.38 -10000 0 -0.7 162 162
DOK2 0.008 0.031 -10000 0 -0.35 4 4
negative regulation of cell cycle -0.094 0.28 -10000 0 -0.54 124 124
ETS1 -0.031 0.095 -10000 0 -0.22 98 98
PXN -0.14 0.35 -10000 0 -0.66 166 166
ITGB1 0.011 0 -10000 0 -10000 0 0
NOS3 -0.15 0.37 -10000 0 -0.7 166 166
RAC1 0.011 0 -10000 0 -10000 0 0
TNF -0.074 0.15 -10000 0 -0.28 165 165
MAPKKK cascade -0.26 0.5 -10000 0 -0.98 166 166
RASA1 0.007 0.04 -10000 0 -0.41 5 5
Tie2/Ang1/Shc -0.29 0.55 -10000 0 -1.1 166 166
NCK1 0.009 0.026 -10000 0 -0.41 2 2
vasculogenesis -0.11 0.3 -10000 0 -0.55 166 166
mol:Phosphatidic acid -0.26 0.5 -10000 0 -0.98 166 166
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.13 0.33 -10000 0 -0.62 166 166
Rac1/GTP -0.23 0.35 -10000 0 -0.75 166 166
MMP2 -0.28 0.54 -10000 0 -1 166 166
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.016 0 -10000 0 -10000 0 0
Necdin/E2F1 -0.17 0.18 -10000 0 -0.31 300 300
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.085 0.14 -10000 0 -0.38 65 65
NGF (dimer)/p75(NTR)/BEX1 -0.16 0.2 -10000 0 -0.33 278 278
NT-4/5 (dimer)/p75(NTR) -0.096 0.14 -10000 0 -0.28 202 202
IKBKB 0.011 0 -10000 0 -10000 0 0
AKT1 -0.085 0.14 -10000 0 -0.38 65 65
IKBKG 0.011 0 -10000 0 -10000 0 0
BDNF -0.042 0.12 -10000 0 -0.33 84 84
MGDIs/NGR/p75(NTR)/LINGO1 -0.065 0.12 -10000 0 -0.23 189 189
FURIN 0.011 0 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.092 0.12 -10000 0 -0.22 254 254
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) -0.042 0.12 -10000 0 -0.33 84 84
NTRK1 0.001 0.058 -10000 0 -0.37 13 13
RTN4R 0.01 0.018 -10000 0 -0.41 1 1
neuron apoptosis -0.092 0.14 -10000 0 -0.35 70 70
IRAK1 0.011 0 -10000 0 -10000 0 0
SHC1 -0.11 0.17 -10000 0 -0.29 232 232
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 -0.18 7 7
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.15 0.19 -10000 0 -0.29 293 293
MAGEH1 -0.09 0.18 -10000 0 -0.41 129 129
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.2 0.2 -10000 0 -0.32 355 355
Mammalian IAPs/DIABLO 0.024 0.029 -10000 0 -0.2 8 8
proNGF (dimer) -0.078 0.17 -10000 0 -0.41 114 114
MAGED1 0.009 0.026 -10000 0 -0.41 2 2
APP 0.011 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.007 0.071 -10000 0 -0.33 24 24
ZNF274 0.011 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.088 0.14 -10000 0 -0.24 232 232
NGF -0.078 0.17 -10000 0 -0.41 114 114
cell cycle arrest -0.079 0.13 0.14 40 -0.36 63 103
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.09 0.15 -10000 0 -0.25 232 232
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.072 0.12 -10000 0 -0.23 182 182
NCSTN 0.011 0 -10000 0 -10000 0 0
mol:GTP -0.11 0.17 -10000 0 -0.29 236 236
PSENEN 0.011 0 -10000 0 -10000 0 0
mol:ceramide -0.094 0.15 -10000 0 -0.25 232 232
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.071 0.13 -10000 0 -0.34 63 63
p75(NTR)/beta APP -0.084 0.14 -10000 0 -0.28 182 182
BEX1 -0.074 0.17 -10000 0 -0.41 109 109
mol:GDP -0.12 0.16 -10000 0 -0.29 233 233
NGF (dimer) -0.078 0.14 -10000 0 -0.25 177 177
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.051 0.11 -10000 0 -0.2 182 182
PIK3R1 0.007 0.04 -10000 0 -0.41 5 5
RAC1/GTP -0.095 0.14 -10000 0 -0.24 232 232
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 -0.29 236 236
RHOB 0.009 0.026 -10000 0 -0.41 2 2
RHOA 0.011 0 -10000 0 -10000 0 0
MAGE-G1/E2F1 -0.028 0.091 -10000 0 -0.22 101 101
NT3 (dimer) -0.018 0.1 -10000 0 -0.4 37 37
TP53 -0.057 0.1 -10000 0 -0.31 12 12
PRDM4 -0.095 0.15 -10000 0 -0.25 232 232
BDNF (dimer) -0.089 0.14 -10000 0 -0.29 114 114
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 -0.38 65 65
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.094 0.15 -10000 0 -0.26 232 232
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 -0.4 128 128
DIABLO 0.011 0 -10000 0 -10000 0 0
SMPD2 -0.095 0.15 -10000 0 -0.25 232 232
APH1B 0.006 0.048 -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 -0.29 232 232
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 -0.3 204 204
MAPK8 -0.094 0.15 -10000 0 -0.36 77 77
MAPK9 -0.092 0.15 -10000 0 -0.36 75 75
APAF1 0.011 0 -10000 0 -10000 0 0
NTF3 -0.018 0.1 -10000 0 -0.4 37 37
NTF4 -0.007 0.071 -10000 0 -0.33 24 24
NDN -0.19 0.21 -10000 0 -0.41 262 262
RAC1/GDP 0.008 0 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.094 0.12 -10000 0 -0.35 65 65
p75 CTF/Sortilin/TRAF6/NRIF 0.028 0 -10000 0 -10000 0 0
RhoA-B-C/GTP -0.11 0.17 -10000 0 -0.29 236 236
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.065 0.11 -10000 0 -0.32 13 13
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.076 0.11 -10000 0 -0.21 181 181
PRKACB 0.006 0.044 -10000 0 -0.41 6 6
proBDNF (dimer)/p75 ECD -0.02 0.085 -10000 0 -0.22 84 84
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.003 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 -0.36 260 277
BAD -0.11 0.16 -10000 0 -0.35 121 121
RIPK2 0.011 0 -10000 0 -10000 0 0
NGFR -0.13 0.2 -10000 0 -0.41 182 182
CYCS -0.084 0.14 -10000 0 -0.37 64 64
ADAM17 0.011 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.094 0.15 -10000 0 -0.26 232 232
BCL2L11 -0.11 0.16 -10000 0 -0.35 121 121
BDNF (dimer)/p75(NTR) -0.12 0.15 -10000 0 -0.27 254 254
PI3K -0.096 0.15 -10000 0 -0.26 236 236
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.094 0.15 -10000 0 -0.26 232 232
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 -0.35 233 233
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.095 0.15 -10000 0 -0.26 234 234
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 -0.033 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 -0.3 186 186
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 -0.33 121 121
E2F1 -0.053 0.13 -10000 0 -0.33 101 101
CASP9 0.011 0 -10000 0 -10000 0 0
IKK complex -0.093 0.13 -10000 0 -0.31 120 120
NGF (dimer)/TRKA -0.053 0.13 -10000 0 -0.28 125 125
MMP7 -0.057 0.14 -10000 0 -0.36 98 98
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.083 0.14 -10000 0 -0.38 63 63
MMP3 -0.051 0.13 -10000 0 -0.33 96 96
APAF-1/Caspase 9 -0.072 0.093 -10000 0 -0.28 64 64
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.12 0.19 -9999 0 -0.43 147 147
PDGF/PDGFRA/CRKL -0.069 0.13 -9999 0 -0.28 147 147
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 -0.29 148 148
AP1 -0.29 0.39 -9999 0 -0.86 165 165
mol:IP3 -0.08 0.14 -9999 0 -0.3 147 147
PLCG1 -0.08 0.14 -9999 0 -0.3 147 147
PDGF/PDGFRA/alphaV Integrin -0.069 0.13 -9999 0 -0.28 147 147
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 -0.3 147 147
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 -0.072 0.14 -9999 0 -0.29 149 149
FOS -0.27 0.4 -9999 0 -0.85 165 165
JUN -0.026 0.045 -9999 0 -0.34 7 7
oligodendrocyte development -0.069 0.13 -9999 0 -0.28 147 147
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 -0.3 147 147
PDGF/PDGFRA -0.12 0.19 -9999 0 -0.42 147 147
actin cytoskeleton reorganization -0.069 0.13 -9999 0 -0.28 147 147
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 -0.23 150 150
PDGF/PDGFRA/Crk/C3G -0.049 0.11 -9999 0 -0.23 147 147
JAK1 -0.069 0.13 -9999 0 -0.28 147 147
ELK1/SRF -0.041 0.11 -9999 0 -0.22 147 147
SHB 0.011 0 -9999 0 -10000 0 0
SHF 0.006 0.048 -9999 0 -0.41 7 7
CSNK2A1 0.021 0.024 -9999 0 -10000 0 0
GO:0007205 -0.09 0.15 -9999 0 -0.34 147 147
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 -0.28 147 147
PDGF/PDGFRA/Caveolin-1 -0.12 0.19 -9999 0 -0.35 189 189
ITGAV 0.011 0 -9999 0 -10000 0 0
ELK1 -0.081 0.14 -9999 0 -0.29 147 147
PIK3CA 0.01 0.018 -9999 0 -0.41 1 1
PDGF/PDGFRA/Crk -0.069 0.13 -9999 0 -0.28 147 147
JAK-STAT cascade -0.069 0.13 -9999 0 -0.28 147 147
cell proliferation -0.072 0.14 -9999 0 -0.29 149 149
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.055 0.18 -10000 0 -0.59 37 37
IHH -0.13 0.2 -10000 0 -0.39 187 187
SHH Np/Cholesterol/GAS1 -0.15 0.13 -10000 0 -0.23 345 345
LRPAP1 0.011 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.14 0.13 0.23 345 -10000 0 345
SMO/beta Arrestin2 -0.052 0.16 -10000 0 -0.3 135 135
SMO -0.06 0.16 -10000 0 -0.32 136 136
AKT1 -0.018 0.096 -10000 0 -0.47 6 6
ARRB2 0.011 0 -10000 0 -10000 0 0
BOC -0.003 0.076 -10000 0 -0.41 18 18
ADRBK1 0.011 0 -10000 0 -10000 0 0
heart looping -0.06 0.16 -10000 0 -0.31 136 136
STIL -0.048 0.12 -10000 0 -0.34 33 33
DHH N/PTCH2 -0.023 0.1 -10000 0 -0.3 68 68
DHH N/PTCH1 -0.059 0.14 -10000 0 -0.35 52 52
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
DHH -0.023 0.11 -10000 0 -0.41 42 42
PTHLH -0.07 0.21 -10000 0 -0.65 37 37
determination of left/right symmetry -0.06 0.16 -10000 0 -0.31 136 136
PIK3R1 0.007 0.04 -10000 0 -0.41 5 5
skeletal system development -0.069 0.21 -10000 0 -0.64 37 37
IHH N/Hhip -0.079 0.13 -10000 0 -0.26 157 157
DHH N/Hhip -0.023 0.098 -10000 0 -0.26 75 75
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.06 0.16 -10000 0 -0.31 136 136
pancreas development -0.013 0.088 -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 -0.41 343 343
somite specification -0.06 0.16 -10000 0 -0.31 136 136
SHH Np/Cholesterol/PTCH1 -0.052 0.12 -10000 0 -0.36 27 27
SHH Np/Cholesterol/PTCH2 -0.017 0.08 -10000 0 -0.18 98 98
SHH Np/Cholesterol/Megalin -0.067 0.1 -10000 0 -0.24 64 64
SHH -0.015 0.082 -10000 0 -0.22 72 72
catabolic process -0.054 0.14 -10000 0 -0.26 151 151
SMO/Vitamin D3 -0.049 0.14 -10000 0 -0.4 27 27
SHH Np/Cholesterol/Hhip -0.017 0.075 -10000 0 -0.17 103 103
LRP2 -0.11 0.16 -10000 0 -0.33 192 192
receptor-mediated endocytosis -0.076 0.14 -10000 0 -0.32 79 79
SHH Np/Cholesterol/BOC -0.012 0.073 -10000 0 -0.17 87 87
SHH Np/Cholesterol/CDO -0.029 0.097 -10000 0 -0.2 117 117
mesenchymal cell differentiation 0.017 0.074 0.17 103 -10000 0 103
mol:Vitamin D3 -0.041 0.12 -10000 0 -0.35 28 28
IHH N/PTCH2 -0.079 0.14 -10000 0 -0.28 147 147
CDON -0.035 0.13 -10000 0 -0.41 59 59
IHH N/PTCH1 -0.035 0.15 -10000 0 -0.26 151 151
Megalin/LRPAP1 -0.068 0.11 -10000 0 -0.22 192 192
PTCH2 -0.012 0.096 -10000 0 -0.41 30 30
SHH Np/Cholesterol -0.012 0.061 -10000 0 -0.16 72 72
PTCH1 -0.054 0.14 -10000 0 -0.26 151 151
HHIP -0.013 0.088 -10000 0 -0.34 35 35
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 -0.001 0.07 -9999 0 -0.28 32 32
alphaV beta3 Integrin -0.16 0.16 -9999 0 -0.28 316 316
PTK2 -0.13 0.19 -9999 0 -0.41 131 131
IGF1R -0.005 0.081 -9999 0 -0.41 21 21
PI4KB 0.011 0 -9999 0 -10000 0 0
MFGE8 0.009 0.026 -9999 0 -0.41 2 2
SRC 0.011 0 -9999 0 -10000 0 0
CDKN1B -0.14 0.21 -9999 0 -0.58 86 86
VEGFA 0.011 0 -9999 0 -10000 0 0
ILK -0.12 0.18 -9999 0 -0.55 69 69
ROCK1 0.011 0 -9999 0 -10000 0 0
AKT1 -0.1 0.17 -9999 0 -0.52 69 69
PTK2B -0.02 0.1 -9999 0 -0.21 115 115
alphaV/beta3 Integrin/JAM-A -0.15 0.16 -9999 0 -0.4 116 116
CBL 0.011 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.028 0.098 -9999 0 -0.23 101 101
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.044 0.14 -9999 0 -0.26 135 135
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.038 0.12 -9999 0 -0.35 30 30
alphaV/beta3 Integrin/Syndecan-1 -0.078 0.12 -9999 0 -0.21 237 237
PI4KA 0.011 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.18 0.18 -9999 0 -0.42 154 154
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 -0.21 237 237
RPS6KB1 -0.15 0.18 -9999 0 -0.39 154 154
TLN1 0.011 0 -9999 0 -10000 0 0
MAPK3 -0.29 0.28 -9999 0 -0.5 316 316
GPR124 -0.089 0.18 -9999 0 -0.41 128 128
MAPK1 -0.29 0.28 -9999 0 -0.5 316 316
PXN 0.011 0 -9999 0 -10000 0 0
PIK3R1 0.007 0.04 -9999 0 -0.41 5 5
alphaV/beta3 Integrin/Tumstatin -0.052 0.12 -9999 0 -0.24 149 149
cell adhesion -0.033 0.094 -9999 0 -0.23 98 98
ANGPTL3 0.004 0.021 -9999 0 -0.33 2 2
VEGFR2 homodimer/VEGFA homodimer/Src 0.008 0.059 -9999 0 -0.23 32 32
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 -0.067 0.16 -9999 0 -0.41 100 100
IGF1 -0.068 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 -0.27 187 187
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 -0.23 100 100
VCL 0.011 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.07 0.15 -9999 0 -0.28 165 165
CSF1 0.003 0.057 -9999 0 -0.41 10 10
PIK3C2A -0.12 0.18 -9999 0 -0.55 69 69
PI4 Kinase/Pyk2 -0.14 0.14 -9999 0 -0.35 128 128
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.026 0.11 -9999 0 -0.23 115 115
FAK1/Vinculin -0.098 0.15 -9999 0 -0.34 121 121
alphaV beta3/Integrin/ppsTEM5 -0.081 0.15 -9999 0 -0.28 187 187
RHOA 0.011 0 -9999 0 -10000 0 0
VTN -0.046 0.14 -9999 0 -0.41 72 72
BCAR1 0.011 0 -9999 0 -10000 0 0
FGF2 -0.22 0.21 -9999 0 -0.41 291 291
F11R -0.14 0.15 -9999 0 -0.28 292 292
alphaV/beta3 Integrin/Lactadherin -0.025 0.099 -9999 0 -0.23 100 100
alphaV/beta3 Integrin/TGFBR2 -0.029 0.11 -9999 0 -0.25 103 103
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.024 0.031 -9999 0 -0.2 10 10
HSP90AA1 0.011 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.02 0.087 -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 -0.019 0.1 -9999 0 -0.21 115 115
SDC1 -0.085 0.15 -9999 0 -0.33 152 152
VAV3 -0.012 0.074 -9999 0 -0.33 1 1
PTPN11 0.011 0 -9999 0 -10000 0 0
IRS1 -0.03 0.12 -9999 0 -0.41 53 53
FAK1/Paxillin -0.098 0.15 -9999 0 -0.34 121 121
cell migration -0.084 0.14 -9999 0 -0.31 118 118
ITGAV 0.011 0 -9999 0 -10000 0 0
PI3K -0.14 0.14 -9999 0 -0.36 119 119
SPP1 -0.086 0.15 -9999 0 -0.33 153 153
KDR -0.014 0.099 -9999 0 -0.41 32 32
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 -0.038 0.13 -9999 0 -0.39 65 65
angiogenesis -0.29 0.28 -9999 0 -0.5 317 317
Rac1/GTP -0.005 0.068 -9999 0 -0.3 1 1
EDIL3 -0.071 0.17 -9999 0 -0.41 104 104
cell proliferation -0.029 0.11 -9999 0 -0.24 103 103
Cellular roles of Anthrax toxin

Figure S11.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S11.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 -0.004 0.078 -10000 0 -0.41 19 19
ANTXR2 -0.13 0.2 -10000 0 -0.41 177 177
negative regulation of myeloid dendritic cell antigen processing and presentation -0.019 0.028 -10000 0 -0.057 181 181
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 -0.078 15 15
MAP2K6 -0.036 0.055 -10000 0 -0.17 69 69
CYAA -0.064 0.11 -10000 0 -0.21 181 181
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 -0.23 181 181
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 0.057 181 -10000 0 181
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 -0.23 162 162
PA/Cellular Receptors -0.075 0.13 -10000 0 -0.25 181 181
apoptosis -0.019 0.028 -10000 0 -0.057 181 181
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.064 0.11 -10000 0 -0.22 181 181
macrophage activation -0.003 0.026 -10000 0 -10000 0 0
TNF -0.032 0.11 -10000 0 -0.33 67 67
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 -0.057 181 181
LEF -0.019 0.028 -10000 0 -0.058 181 181
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 -0.057 181 181
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 -0.21 181 181
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.006 0.083 -9999 0 -0.41 22 22
mol:S1P -0.009 0.014 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.072 0.12 -9999 0 -0.24 154 154
GNAO1 -0.11 0.19 -9999 0 -0.42 142 142
S1P/S1P3/G12/G13 0.003 0.046 -9999 0 -0.22 19 19
AKT1 -0.062 0.16 -9999 0 -0.66 25 25
AKT3 -0.41 0.55 -9999 0 -1.1 202 202
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.006 0.083 -9999 0 -0.41 22 22
GNAI2 0.002 0.014 -9999 0 -10000 0 0
GNAI3 0.004 0.011 -9999 0 -10000 0 0
GNAI1 -0.002 0.053 -9999 0 -0.42 8 8
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 -0.013 0.08 -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 -0.31 260 260
MAPK3 -0.12 0.19 -9999 0 -0.32 208 208
MAPK1 -0.12 0.19 -9999 0 -0.32 208 208
JAK2 -0.12 0.2 -9999 0 -0.33 208 208
CXCR4 -0.12 0.19 -9999 0 -0.32 208 208
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 -0.32 208 208
S1P/S1P3/Gi -0.13 0.2 -9999 0 -0.31 260 260
RAC1 0.011 0 -9999 0 -10000 0 0
RhoA/GTP -0.12 0.18 -9999 0 -0.31 208 208
VEGFA 0.003 0.016 -9999 0 -10000 0 0
S1P/S1P2/Gi -0.084 0.14 -9999 0 -0.26 154 154
VEGFR1 homodimer/VEGFA homodimer 0 0.031 -9999 0 -10000 0 0
RHOA 0.011 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.021 0.1 -9999 0 -0.25 75 75
GNAQ 0.009 0.026 -9999 0 -0.41 2 2
GNAZ -0.007 0.069 -9999 0 -0.41 15 15
G12/G13 0.016 0 -9999 0 -10000 0 0
GNA14 -0.032 0.13 -9999 0 -0.41 55 55
GNA15 0.007 0.039 -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 -0.31 208 208
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.011 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.13 0.059 -9999 0 -0.32 3 3
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 -0.33 472 472
AURKC 0.009 0.025 -9999 0 -0.33 3 3
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 -0.022 0.09 -10000 0 -0.21 98 98
regulation of S phase of mitotic cell cycle -0.017 0.087 -10000 0 -0.2 93 93
GNAO1 -0.1 0.18 -10000 0 -0.41 142 142
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 32 32
T-DHT/AR -0.043 0.11 -10000 0 -0.29 90 90
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.003 -10000 0 -0.007 165 165
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 -0.058 0.13 -10000 0 -0.35 90 90
cell proliferation -0.1 0.2 -10000 0 -0.38 165 165
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
FOS -0.22 0.37 -10000 0 -0.77 165 165
mol:Ca2+ -0.024 0.029 -10000 0 -0.061 173 173
MAPK3 -0.07 0.15 -10000 0 -0.26 165 165
MAPK1 -0.049 0.1 -10000 0 -0.2 165 165
PIK3R1 0.007 0.04 -10000 0 -0.41 5 5
mol:IP3 -0.001 0.002 -10000 0 -0.004 165 165
cAMP biosynthetic process 0.008 0.03 0.092 6 -0.2 5 11
GNG2 0.003 0.056 -10000 0 -0.4 10 10
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 165 165
HRAS/GTP -0.041 0.071 -10000 0 -0.19 90 90
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 -0.004 165 165
PI3K 0.012 0.026 -10000 0 -0.23 6 6
apoptosis 0.11 0.2 0.4 165 -10000 0 165
T-DHT/AR/PELP1 -0.03 0.094 -10000 0 -0.24 90 90
HRAS/GDP -0.055 0.13 -10000 0 -0.33 90 90
CREB1 -0.12 0.21 -10000 0 -0.43 165 165
RAC1-CDC42/GTP -0.002 0.019 -10000 0 -0.18 6 6
AR -0.061 0.16 -10000 0 -0.41 90 90
GNB1 0.011 0 -10000 0 -10000 0 0
RAF1 -0.027 0.085 -10000 0 -0.25 32 32
RAC1-CDC42/GDP -0.048 0.12 -10000 0 -0.31 90 90
T-DHT/AR/PELP1/Src -0.023 0.085 -10000 0 -0.21 90 90
MAP2K2 -0.031 0.092 -10000 0 -0.27 32 32
T-DHT/AR/PELP1/Src/PI3K -0.017 0.088 -10000 0 -0.21 93 93
GNAZ -0.001 0.069 -10000 0 -0.41 15 15
SHBG 0.007 0.04 -10000 0 -0.41 5 5
Gi family/GNB1/GNG2/GDP -0.072 0.16 -10000 0 -0.32 145 145
mol:T-DHT -0.001 0.001 -10000 0 -0.003 133 133
RAC1 0.011 0 -10000 0 -10000 0 0
GNRH1 0.005 0.031 -10000 0 -0.29 6 6
Gi family/GTP -0.058 0.12 -10000 0 -0.21 154 154
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 -0.063 0.15 -9999 0 -0.25 161 161
FZD6 0.01 0.018 -9999 0 -0.41 1 1
WNT6 -0.03 0.12 -9999 0 -0.38 57 57
WNT4 -0.089 0.18 -9999 0 -0.41 128 128
FZD3 0.011 0 -9999 0 -10000 0 0
WNT5A -0.002 0.074 -9999 0 -0.41 17 17
WNT11 -0.031 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 -9999 0 -10000 0 0
BUB1B -0.06 0.051 -9999 0 -0.11 167 167
PLK1 -0.013 0.023 -9999 0 -10000 0 0
PLK1S1 -0.003 0.017 -9999 0 -0.26 1 1
KIF2A -0.005 0.02 -9999 0 -10000 0 0
regulation of mitotic centrosome separation -0.013 0.023 -9999 0 -10000 0 0
GOLGA2 0.011 0 -9999 0 -10000 0 0
Hec1/SPC24 -0.11 0.1 -9999 0 -0.18 339 339
WEE1 -0.008 0.023 -9999 0 -10000 0 0
cytokinesis -0.079 0.043 -9999 0 -0.21 14 14
PP2A-alpha B56 0.037 0.005 -9999 0 -10000 0 0
AURKA -0.005 0.014 -9999 0 -10000 0 0
PICH/PLK1 -0.08 0.11 -9999 0 -0.2 210 210
CENPE -0.055 0.089 -9999 0 -0.19 159 159
RhoA/GTP 0.008 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization -0.005 0.02 -9999 0 -10000 0 0
PPP2CA 0.011 0 -9999 0 -10000 0 0
FZR1 0.011 0 -9999 0 -10000 0 0
TPX2 -0.016 0.015 -9999 0 -10000 0 0
PAK1 0.01 0.001 -9999 0 -10000 0 0
SPC24 -0.2 0.17 -9999 0 -0.33 329 329
FBXW11 0.011 0 -9999 0 -10000 0 0
CLSPN -0.014 0.019 -9999 0 -10000 0 0
GORASP1 0.011 0 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NLP -0.008 0.013 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle -0.001 0.002 -9999 0 -10000 0 0
STAG2 0.011 0 -9999 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.012 0.007 -9999 0 -10000 0 0
spindle elongation -0.013 0.023 -9999 0 -10000 0 0
ODF2 0.01 0.001 -9999 0 -10000 0 0
BUB1 0.023 0.011 -9999 0 -10000 0 0
TPT1 -0.003 0.013 -9999 0 -10000 0 0
CDC25C -0.018 0.014 -9999 0 -10000 0 0
CDC25B 0.01 0.001 -9999 0 -10000 0 0
SGOL1 -0.044 0.028 -9999 0 -10000 0 0
RHOA 0.011 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.018 0.048 -9999 0 -10000 0 0
CDC14B 0.008 0.013 -9999 0 -0.3 1 1
CDC20 -0.29 0.11 -9999 0 -0.33 476 476
PLK1/PBIP1 -0.016 0.044 -9999 0 -0.18 32 32
mitosis -0.004 0.007 -9999 0 -0.015 154 154
FBXO5 -0.005 0.02 -9999 0 -10000 0 0
CDC2 -0.001 0.002 -9999 0 -10000 0 0
NDC80 -0.014 0.088 -9999 0 -0.33 39 39
metaphase plate congression -0.006 0.015 -9999 0 -10000 0 0
ERCC6L -0.07 0.1 -9999 0 -0.21 131 131
NLP/gamma Tubulin -0.005 0.013 -9999 0 -10000 0 0
microtubule cytoskeleton organization -0.003 0.013 -9999 0 -10000 0 0
G2/M transition DNA damage checkpoint -0.001 0.001 -9999 0 -10000 0 0
PPP1R12A 0.01 0.018 -9999 0 -0.41 1 1
interphase -0.001 0.001 -9999 0 -10000 0 0
PLK1/PRC1-2 -0.15 0.069 -9999 0 -0.17 485 485
GRASP65/GM130/RAB1/GTP/PLK1 0.008 0.018 -9999 0 -10000 0 0
RAB1A 0.011 0 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
Aurora A/BORA -0.006 0.022 -9999 0 -10000 0 0
mitotic prometaphase -0.002 0.001 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.013 0.018 -9999 0 -0.19 1 1
microtubule-based process -0.16 0.06 -9999 0 -0.18 485 485
Golgi organization -0.013 0.023 -9999 0 -10000 0 0
Cohesin/SA2 -0.013 0.014 -9999 0 -10000 0 0
PPP1CB/MYPT1 0.015 0.013 -9999 0 -0.28 1 1
KIF20A -0.3 0.1 -9999 0 -0.33 485 485
APC/C/CDC20 -0.16 0.065 -9999 0 -0.18 476 476
PPP2R1A 0.011 0 -9999 0 -10000 0 0
chromosome segregation -0.019 0.042 -9999 0 -0.18 32 32
PRC1 -0.004 0.069 -9999 0 -0.33 23 23
ECT2 -0.016 0.05 -9999 0 -0.19 34 34
C13orf34 -0.005 0.02 -9999 0 -10000 0 0
NUDC -0.006 0.015 -9999 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.06 0.05 -9999 0 -0.11 167 167
spindle assembly -0.008 0.018 -9999 0 -10000 0 0
spindle stabilization -0.003 0.017 -9999 0 -0.26 1 1
APC/C/HCDH1 0.014 0.011 -9999 0 -0.24 1 1
MKLP2/PLK1 -0.16 0.06 -9999 0 -0.18 485 485
CCNB1 -0.048 0.13 -9999 0 -0.33 93 93
PPP1CB 0.011 0.001 -9999 0 -10000 0 0
BTRC 0.011 0 -9999 0 -10000 0 0
ROCK2 -0.009 0.065 -9999 0 -0.4 14 14
TUBG1 -0.003 0.013 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.026 0.043 -9999 0 -10000 0 0
MLF1IP -0.011 0.056 -9999 0 -0.23 32 32
INCENP 0.01 0.001 -9999 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 -0.08 0.31 -9999 0 -0.95 59 59
MKNK1 0.011 0 -9999 0 -10000 0 0
MAPK14 -0.013 0.097 -9999 0 -0.27 66 66
ATF2/c-Jun -0.003 0.1 -9999 0 -0.61 7 7
MAPK11 -0.015 0.1 -9999 0 -0.27 68 68
MITF -0.041 0.16 -9999 0 -0.34 110 110
MAPKAPK5 -0.009 0.12 -9999 0 -0.32 68 68
KRT8 -0.026 0.13 -9999 0 -0.34 70 70
MAPKAPK3 0.011 0 -9999 0 -10000 0 0
MAPKAPK2 0.011 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.021 0.14 -9999 0 -0.39 68 68
CEBPB -0.009 0.12 -9999 0 -0.32 68 68
SLC9A1 -0.009 0.12 -9999 0 -0.32 68 68
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.007 0.12 -9999 0 -0.31 71 71
p38alpha-beta/MNK1 -0.006 0.11 -9999 0 -0.3 66 66
JUN -0.003 0.1 -9999 0 -0.61 7 7
PPARGC1A -0.073 0.18 -9999 0 -0.32 161 161
USF1 -0.009 0.12 -9999 0 -0.32 68 68
RAB5/GDP/GDI1 -0.029 0.074 -9999 0 -0.22 66 66
NOS2 -0.019 0.16 -9999 0 -0.78 11 11
DDIT3 -0.009 0.12 -9999 0 -0.32 68 68
RAB5A 0.011 0 -9999 0 -10000 0 0
HSPB1 -0.001 0.096 -9999 0 -0.25 66 66
p38alpha-beta/HBP1 -0.006 0.11 -9999 0 -0.3 66 66
CREB1 -0.011 0.13 -9999 0 -0.34 68 68
RAB5/GDP 0.008 0 -9999 0 -10000 0 0
EIF4E -0.001 0.099 -9999 0 -0.26 66 66
RPS6KA4 -0.009 0.12 -9999 0 -0.32 68 68
PLA2G4A -0.014 0.12 -9999 0 -0.31 67 67
GDI1 -0.009 0.12 -9999 0 -0.32 68 68
TP53 -0.016 0.14 -9999 0 -0.39 68 68
RPS6KA5 -0.013 0.12 -9999 0 -0.32 73 73
ESR1 -0.045 0.17 -9999 0 -0.35 113 113
HBP1 0.011 0 -9999 0 -10000 0 0
MEF2C -0.04 0.16 -9999 0 -0.34 107 107
MEF2A -0.013 0.13 -9999 0 -0.33 72 72
EIF4EBP1 -0.011 0.13 -9999 0 -0.34 68 68
KRT19 -0.014 0.12 -9999 0 -0.32 72 72
ELK4 -0.009 0.12 -9999 0 -0.32 68 68
ATF6 -0.009 0.12 -9999 0 -0.32 68 68
ATF1 -0.011 0.13 -9999 0 -0.34 68 68
p38alpha-beta/MAPKAPK2 -0.006 0.11 -9999 0 -0.3 66 66
p38alpha-beta/MAPKAPK3 -0.006 0.11 -9999 0 -0.3 66 66
Reelin signaling pathway

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
CDK5R1/CDK5 0.016 0.01 -9999 0 -0.22 1 1
VLDLR 0.009 0.026 -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 -0.23 199 199
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 -0.2 212 212
LRPAP1/LRP8 0.014 0.022 -9999 0 -0.22 5 5
RELN/LRP8/DAB1/Fyn -0.059 0.1 -9999 0 -0.19 193 193
DAB1/alpha3/beta1 Integrin -0.062 0.08 -9999 0 -0.33 5 5
long-term memory -0.13 0.15 -9999 0 -0.36 106 106
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 -0.41 210 210
CDK5R1 0.01 0.015 -9999 0 -0.33 1 1
RELN -0.14 0.2 -9999 0 -0.41 198 198
PIK3R1 0.007 0.04 -9999 0 -0.41 5 5
RELN/LRP8/Fyn -0.071 0.12 -9999 0 -0.23 200 200
GRIN2A/RELN/LRP8/DAB1/Fyn -0.13 0.15 -9999 0 -0.25 311 311
MAPK8 0.006 0.044 -9999 0 -0.41 6 6
RELN/VLDLR/DAB1 -0.069 0.11 -9999 0 -0.21 195 195
ITGB1 0.011 0 -9999 0 -10000 0 0
MAP1B -0.069 0.11 -9999 0 -0.2 212 212
RELN/LRP8 -0.071 0.12 -9999 0 -0.23 200 200
GRIN2B/RELN/LRP8/DAB1/Fyn -0.062 0.11 -9999 0 -0.2 135 135
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 0.09 -9999 0 -0.29 5 5
LRP8 0.008 0.033 -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 -0.19 193 193
MAP3K11 0.011 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.062 0.11 -9999 0 -0.2 198 198
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 -0.23 80 80
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 -0.2 193 193
Effects of Botulinum toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
STX1A 0.009 0.01 -9999 0 -0.23 1 1
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B 0.011 0.022 -9999 0 -0.22 5 5
STXBP1 -0.017 0.1 -9999 0 -0.41 36 36
ACh/CHRNA1 -0.098 0.1 -9999 0 -0.23 193 193
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 0.033 -9999 0 -0.33 5 5
mol:ACh -0.043 0.056 -9999 0 -0.1 244 244
RAB3GAP2 0.011 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.062 0.075 -9999 0 -0.28 28 28
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.098 0.1 -9999 0 -0.23 193 193
UNC13B 0.011 0 -9999 0 -10000 0 0
CHRNA1 -0.11 0.16 -9999 0 -0.33 193 193
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.082 0.12 -9999 0 -0.3 119 119
SNAP25 -0.11 0.13 -9999 0 -0.25 244 244
VAMP2 0.005 0 -9999 0 -10000 0 0
SYT1 -0.082 0.17 -9999 0 -0.41 119 119
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.002 0.063 -9999 0 -0.23 37 37
STX1A/SNAP25 fragment 1/VAMP2 -0.062 0.075 -9999 0 -0.28 28 28
LPA4-mediated signaling events

Figure S20.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S20.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.005 0.049 -9999 0 -0.23 22 22
ADCY5 -0.03 0.096 -9999 0 -0.23 98 98
ADCY6 0.015 0 -9999 0 -10000 0 0
ADCY7 0.015 0 -9999 0 -10000 0 0
ADCY1 0.002 0.053 -9999 0 -0.22 30 30
ADCY2 -0.12 0.12 -9999 0 -0.23 297 297
ADCY3 0.014 0.015 -9999 0 -0.23 2 2
ADCY8 0.008 0.019 -9999 0 -0.18 5 5
PRKCE 0.009 0 -9999 0 -10000 0 0
ADCY9 -0.018 0.085 -9999 0 -0.23 72 72
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.06 0.078 -9999 0 -0.17 127 127
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.11 0.12 -9999 0 -0.23 291 291
fibroblast growth factor receptor signaling pathway -0.11 0.12 -9999 0 -0.23 291 291
LAMA1 -0.1 0.16 -9999 0 -0.33 182 182
PRNP -0.047 0.14 -9999 0 -0.41 74 74
GPC1/SLIT2 -0.021 0.098 -9999 0 -0.28 68 68
SMAD2 0.022 0.033 -9999 0 -0.2 12 12
GPC1/PrPc/Cu2+ -0.019 0.086 -9999 0 -0.23 74 74
GPC1/Laminin alpha1 -0.063 0.11 -9999 0 -0.22 182 182
TDGF1 -0.02 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 0.039 -9999 0 -0.33 7 7
FYN 0.004 0.061 -9999 0 -0.2 42 42
FGR -0.001 0.072 -9999 0 -0.22 52 52
positive regulation of MAPKKK cascade 0.014 0.073 -9999 0 -0.27 27 27
SLIT2 -0.042 0.14 -9999 0 -0.41 68 68
GPC1/NRG 0.005 0.057 -9999 0 -0.28 21 21
NRG1 -0.006 0.081 -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 -0.23 291 291
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 -0.033 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 78 78
HCK 0.002 0.064 -9999 0 -0.2 49 49
FGF2 -0.22 0.21 -9999 0 -0.41 291 291
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 0.012 0.027 -9999 0 -0.22 7 7
PLA2G2A/GPC1 -0.014 0.086 -9999 0 -0.27 55 55
LCK 0.002 0.065 -9999 0 -0.21 46 46
neuron differentiation 0.005 0.057 -9999 0 -0.28 21 21
PrPc/Cu2+ -0.032 0.1 -9999 0 -0.29 74 74
APP 0.011 0 -9999 0 -10000 0 0
TGFBR2 (dimer) 0.002 0.062 -9999 0 -0.41 12 12
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 -0.035 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 -0.25 111 111
RAF1 -0.009 0.099 -10000 0 -0.41 5 5
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.032 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 -0.26 135 135
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 -0.01 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 -0.046 0.091 -10000 0 -0.32 37 37
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.012 0.092 -10000 0 -0.24 37 37
IGF-1R heterotetramer -0.02 0.093 -10000 0 -0.46 21 21
IGF-1R heterotetramer/IGF1/IRS/Nck -0.04 0.12 -10000 0 -0.25 111 111
Crk/p130 Cas/Paxillin -0.025 0.11 -10000 0 -0.34 37 37
IGF1R -0.02 0.093 -10000 0 -0.46 21 21
IGF1 -0.076 0.18 -10000 0 -0.44 101 101
IRS2/Crk -0.059 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 -0.047 0.16 -10000 0 -0.34 106 106
RAF1/14-3-3 E -0.002 0.089 -10000 0 -0.35 5 5
BAD/14-3-3 -0.007 0.096 -10000 0 -0.28 38 38
PRKCZ -0.022 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 -0.055 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 0.1 -10000 0 -0.21 112 112
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.011 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.041 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 -0.046 0.13 -10000 0 -0.28 111 111
IRS2 -0.068 0.14 -10000 0 -0.27 161 161
IGF-1R heterotetramer/IGF1 -0.06 0.15 -10000 0 -0.34 111 111
GRB2 0.011 0 -10000 0 -10000 0 0
PDPK1 -0.028 0.11 -10000 0 -0.33 41 41
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 -0.33 416 416
NFKBIA -0.013 0.042 -9999 0 -10000 0 0
CPEB1 -0.17 0.21 -9999 0 -0.41 233 233
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 83 83
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 0.093 -9999 0 -0.22 436 436
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 83 83
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 0.033 -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 -0.23 233 233
Aurora A/CPEB -0.11 0.12 -9999 0 -0.23 233 233
Aurora A/TACC1/TRAP/chTOG -0.034 0.092 -9999 0 -0.22 91 91
BRCA1 0.011 0 -9999 0 -10000 0 0
centrosome duplication -0.012 0.043 -9999 0 -10000 0 0
regulation of centrosome cycle -0.04 0.089 -9999 0 -0.22 83 83
spindle assembly -0.035 0.091 -9999 0 -0.21 91 91
TDRD7 0.011 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.12 0.087 -9999 0 -0.21 164 164
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 0.008 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.024 0.053 -9999 0 -10000 0 0
TACC1 -0.066 0.16 -9999 0 -0.41 98 98
TACC3 -0.067 0.14 -9999 0 -0.33 123 123
Aurora A/Antizyme1 -0.003 0.038 -9999 0 -10000 0 0
Aurora A/RasGAP -0.014 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 -0.22 436 436
PPP2R5D 0.011 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.15 0.088 -9999 0 -0.23 159 159
PAK1 0.011 0 -9999 0 -10000 0 0
CKAP5 0.011 0 -9999 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.009 0.031 -9999 0 -0.41 3 3
LAT2 -0.066 0.13 -9999 0 -0.23 167 167
AP1 -0.12 0.14 -9999 0 -0.35 104 104
mol:PIP3 -0.067 0.15 -9999 0 -0.4 38 38
IKBKB -0.035 0.097 -9999 0 -0.22 51 51
AKT1 -0.03 0.1 -9999 0 -0.28 40 40
IKBKG -0.035 0.097 -9999 0 -0.22 51 51
MS4A2 -0.12 0.19 -9999 0 -0.4 166 166
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.018 -9999 0 -0.41 1 1
MAP3K1 -0.042 0.12 -9999 0 -0.31 37 37
mol:Ca2+ -0.05 0.12 -9999 0 -0.31 38 38
LYN 0.01 0.003 -9999 0 -10000 0 0
CBLB -0.065 0.13 -9999 0 -0.23 167 167
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 -0.057 0.12 -9999 0 -0.34 38 38
PTPN13 -0.091 0.15 -9999 0 -0.38 65 65
PTPN11 0.01 0.005 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.029 0.11 -9999 0 -0.26 40 40
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 -0.098 0.13 -9999 0 -0.41 38 38
LAT -0.065 0.13 -9999 0 -0.23 167 167
PAK2 -0.052 0.13 -9999 0 -0.34 37 37
NFATC2 -0.08 0.16 -9999 0 -0.53 53 53
HRAS -0.062 0.14 -9999 0 -0.37 37 37
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 -0.25 220 220
Antigen/IgE/Fc epsilon R1 -0.09 0.12 -9999 0 -0.22 220 220
mol:GDP -0.07 0.14 -9999 0 -0.39 38 38
JUN 0.006 0.048 -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 -0.41 165 165
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.075 0.13 -9999 0 -0.25 169 169
CHUK -0.035 0.097 -9999 0 -0.22 51 51
KLRG1 -0.056 0.11 -9999 0 -0.32 38 38
VAV1 -0.067 0.13 -9999 0 -0.23 167 167
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.065 0.13 -9999 0 -0.23 167 167
negative regulation of mast cell degranulation -0.047 0.1 -9999 0 -0.3 36 36
BTK -0.075 0.14 -9999 0 -0.4 38 38
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.076 0.15 -9999 0 -0.31 91 91
GAB2/PI3K/SHP2 -0.063 0.089 -9999 0 -0.31 40 40
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.064 0.13 -9999 0 -0.4 38 38
RAF1 0.019 0.018 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.081 0.11 -9999 0 -0.36 41 41
FCER1G 0.016 0.024 -9999 0 -0.33 2 2
FCER1A -0.061 0.16 -9999 0 -0.42 88 88
Antigen/IgE/Fc epsilon R1/Fyn -0.081 0.11 -9999 0 -0.26 88 88
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 -0.091 0.18 -9999 0 -0.41 130 130
NF-kappa-B/RelA -0.036 0.046 -9999 0 -0.18 6 6
actin cytoskeleton reorganization -0.076 0.14 -9999 0 -0.39 37 37
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.08 0.11 -9999 0 -0.34 40 40
FER -0.065 0.13 -9999 0 -0.23 167 167
RELA 0.011 0 -9999 0 -10000 0 0
ITK -0.032 0.062 -9999 0 -0.36 14 14
SOS1 0.011 0 -9999 0 -10000 0 0
PLCG1 -0.067 0.14 -9999 0 -0.4 37 37
cytokine secretion -0.027 0.034 -9999 0 -10000 0 0
SPHK1 -0.065 0.13 -9999 0 -0.23 167 167
PTK2 -0.079 0.15 -9999 0 -0.4 37 37
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.1 0.13 -9999 0 -0.27 169 169
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.064 0.15 -9999 0 -0.4 39 39
MAP2K2 0.023 0.015 -9999 0 -10000 0 0
MAP2K1 0.023 0.015 -9999 0 -10000 0 0
MAP2K7 0.011 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.057 0.087 -9999 0 -0.29 36 36
MAP2K4 0.012 0.038 -9999 0 -0.84 1 1
Fc epsilon R1/FcgammaRIIB -0.09 0.12 -9999 0 -0.29 90 90
mol:Choline -0.056 0.11 -9999 0 -0.33 38 38
SHC/Grb2/SOS1 -0.069 0.11 -9999 0 -0.33 35 35
FYN 0.011 0 -9999 0 -10000 0 0
DOK1 0.011 0 -9999 0 -10000 0 0
PXN -0.069 0.14 -9999 0 -0.38 35 35
HCLS1 -0.065 0.13 -9999 0 -0.23 168 168
PRKCB -0.056 0.13 -9999 0 -0.31 53 53
FCGR2B 0.008 0.035 -9999 0 -0.39 4 4
IGHE -0.001 0.004 -9999 0 -10000 0 0
KLRG1/SHIP -0.048 0.11 -9999 0 -0.3 36 36
LCP2 0.01 0.015 -9999 0 -0.33 1 1
PLA2G4A -0.076 0.14 -9999 0 -0.24 174 174
RASA1 0.007 0.04 -9999 0 -0.41 5 5
mol:Phosphatidic acid -0.056 0.11 -9999 0 -0.33 38 38
IKK complex -0.016 0.078 -9999 0 -0.16 51 51
WIPF1 0.009 0.026 -9999 0 -0.41 2 2
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.1 0.18 -9999 0 -0.41 142 142
CDC42/GTP -0.03 0.1 -9999 0 -0.18 144 144
PLCG1 -0.031 0.1 -9999 0 -0.19 144 144
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 0.098 -9999 0 -0.18 144 144
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 -0.19 144 144
MAPK1 -0.031 0.1 -9999 0 -0.19 144 144
S1P/S1P5/Gi -0.042 0.11 -9999 0 -0.21 156 156
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 0.037 -9999 0 -0.19 17 17
RHOA 0.024 0.015 -9999 0 -0.18 2 2
S1P/S1P4/Gi -0.039 0.11 -9999 0 -0.21 154 154
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.001 0.069 -9999 0 -0.41 15 15
S1P/S1P4/G12/G13 0.02 0.016 -9999 0 -0.19 3 3
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
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.032 0.1 0.18 145 -10000 0 145
GNAI2 0.011 0 -10000 0 -10000 0 0
S1P/S1P5/G12 0.008 0.037 -10000 0 -0.19 17 17
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.1 0.18 -10000 0 -0.41 142 142
RhoA/GTP -0.033 0.1 -10000 0 -0.19 145 145
negative regulation of cAMP metabolic process -0.042 0.11 -10000 0 -0.21 156 156
GNAZ -0.001 0.069 -10000 0 -0.41 15 15
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 -0.21 156 156
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
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.031 0.12 -9999 0 -0.41 53 53
GNB1/GNG2 -0.049 0.14 -9999 0 -0.4 41 41
mol:DAG -0.04 0.13 -9999 0 -0.37 41 41
PLCG1 -0.041 0.13 -9999 0 -0.38 41 41
YES1 -0.053 0.14 -9999 0 -0.42 38 38
FZD3 0.011 0 -9999 0 -10000 0 0
FZD6 0.01 0.018 -9999 0 -0.41 1 1
G protein -0.041 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 -0.04 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 -0.34 141 141
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.063 0.15 -9999 0 -0.25 161 161
CSNK1A1 0.011 0 -9999 0 -10000 0 0
GNAS -0.053 0.14 -9999 0 -0.42 38 38
GO:0007205 -0.039 0.13 -9999 0 -0.36 41 41
WNT6 -0.03 0.12 -9999 0 -0.38 57 57
WNT4 -0.089 0.18 -9999 0 -0.41 128 128
NFAT1/CK1 alpha -0.051 0.14 -9999 0 -0.41 43 43
GNG2 0.003 0.056 -9999 0 -0.4 10 10
WNT5A -0.002 0.074 -9999 0 -0.41 17 17
WNT11 -0.031 0.12 -9999 0 -0.35 63 63
CDC42 -0.045 0.13 -9999 0 -0.4 38 38
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.036 0.13 -10000 0 -0.38 64 64
NFATC2 -0.022 0.18 -10000 0 -0.51 45 45
NFATC3 -0.015 0.083 -10000 0 -0.26 27 27
CD40LG -0.17 0.33 -10000 0 -0.86 78 78
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 -0.72 53 53
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 0.06 -10000 0 -0.27 3 3
TLE4 -0.031 0.21 -10000 0 -0.59 60 60
Jun/NFAT1-c-4/p21SNFT -0.093 0.33 -10000 0 -0.8 85 85
AP-1/NFAT1-c-4 -0.17 0.39 -10000 0 -0.97 80 80
IKZF1 0.003 0.13 -10000 0 -0.42 26 26
T-helper 2 cell differentiation -0.081 0.23 -10000 0 -0.77 33 33
AP-1/NFAT1 -0.082 0.18 -10000 0 -0.37 97 97
CALM1 0.015 0.026 -10000 0 -10000 0 0
EGR2 -0.11 0.4 -10000 0 -1.1 58 58
EGR3 -0.14 0.46 -10000 0 -1.2 81 81
NFAT1/FOXP3 -0.044 0.16 -10000 0 -0.38 61 61
EGR1 -0.045 0.14 -10000 0 -0.41 70 70
JUN 0 0.05 -10000 0 -0.41 7 7
EGR4 -0.003 0.058 -10000 0 -0.34 15 15
mol:Ca2+ 0.003 0.028 -10000 0 -0.15 1 1
GBP3 0 0.14 -10000 0 -0.48 26 26
FOSL1 -0.014 0.089 -10000 0 -0.33 40 40
NFAT1-c-4/MAF/IRF4 -0.12 0.35 -10000 0 -0.85 86 86
DGKA 0.005 0.12 -10000 0 -0.42 22 22
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 -0.42 47 47
NFAT1-c-4 (dimer)/EGR1 -0.12 0.36 -10000 0 -0.88 85 85
NFAT1-c-4 (dimer)/EGR4 -0.1 0.34 -10000 0 -0.82 85 85
FOS -0.12 0.19 -10000 0 -0.41 165 165
IFNG -0.076 0.19 -10000 0 -0.65 30 30
T cell activation -0.083 0.21 -10000 0 -0.63 42 42
MAF -0.067 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 0.08 0.3 0.72 85 -10000 0 85
TNF -0.13 0.33 -10000 0 -0.79 88 88
FASLG -0.16 0.47 -10000 0 -1.2 83 83
TBX21 0.002 0.062 -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 0.005 0.12 -10000 0 -0.38 31 31
NFAT1-c-4/ICER1 -0.095 0.33 -10000 0 -0.81 85 85
GATA3 -0.002 0.069 -10000 0 -0.35 20 20
T-helper 1 cell differentiation -0.063 0.2 -10000 0 -0.64 30 30
IL2RA -0.13 0.25 -10000 0 -0.68 62 62
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.005 0.12 -10000 0 -0.41 24 24
E2F1 -0.048 0.13 -10000 0 -0.32 101 101
PPARG -0.012 0.096 -10000 0 -0.41 30 30
SLC3A2 0.005 0.12 -10000 0 -0.42 22 22
IRF4 -0.002 0.071 -10000 0 -0.37 19 19
PTGS2 -0.18 0.35 -10000 0 -0.85 89 89
CSF2 -0.17 0.33 -10000 0 -0.85 78 78
JunB/Fra1/NFAT1-c-4 -0.094 0.32 -10000 0 -0.79 85 85
IL4 -0.085 0.24 -10000 0 -0.84 30 30
IL5 -0.17 0.32 -10000 0 -0.85 77 77
IL2 -0.084 0.21 -10000 0 -0.65 39 39
IL3 -0.037 0.048 -10000 0 -10000 0 0
RNF128 0.012 0.08 -10000 0 -0.26 43 43
NFATC1 -0.08 0.3 -10000 0 -0.72 85 85
CDK4 0.041 0.18 0.55 24 -10000 0 24
PTPRK 0.004 0.13 -10000 0 -0.43 22 22
IL8 -0.2 0.34 -10000 0 -0.85 83 83
POU2F1 0.011 0 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.011 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.054 0.089 -10000 0 -0.25 35 35
NT3 (dimer)/TRKC -0.14 0.17 -10000 0 -0.3 264 264
NT3 (dimer)/TRKB -0.11 0.16 -10000 0 -0.28 233 233
SHC/Grb2/SOS1/GAB1/PI3K 0.026 0.03 -10000 0 -0.19 10 10
RAPGEF1 0.011 0 -10000 0 -10000 0 0
BDNF -0.042 0.12 -10000 0 -0.33 84 84
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 -0.042 0.14 -10000 0 -0.4 69 69
NTRK3 -0.19 0.21 -10000 0 -0.41 252 252
NT-4/5 (dimer)/TRKB -0.1 0.15 -10000 0 -0.27 212 212
neuron apoptosis 0.14 0.19 0.39 156 -10000 0 156
SHC 2-3/Grb2 -0.15 0.21 -10000 0 -0.42 156 156
SHC1 0.011 0 -10000 0 -10000 0 0
SHC2 -0.18 0.24 0.17 1 -0.51 151 152
SHC3 -0.12 0.16 0.17 1 -0.4 99 100
STAT3 (dimer) 0.017 0.011 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.084 0.14 -10000 0 -0.25 201 201
RIN/GDP -0.043 0.08 -10000 0 -0.2 22 22
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 -0.32 183 185
RIN/GTP 0.002 0.003 -10000 0 -10000 0 0
CCND1 0.023 0.018 -10000 0 -0.22 3 3
MAGED1 0.009 0.026 -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) -0.007 0.071 -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 -0.24 129 129
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 -0.41 114 114
HRAS 0.011 0 -10000 0 -10000 0 0
DOCK1 0.006 0.048 -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 -0.31 183 185
mol:GDP -0.063 0.11 -10000 0 -0.28 28 28
NGF (dimer) -0.078 0.17 -10000 0 -0.41 114 114
RhoG/GDP 0.006 0.025 -10000 0 -0.29 4 4
RIT1/GDP -0.04 0.08 -10000 0 -0.2 22 22
TIAM1 0 0.067 -10000 0 -0.41 14 14
PIK3R1 0.007 0.04 -10000 0 -0.41 5 5
BDNF (dimer)/TRKB -0.039 0.1 -10000 0 -0.2 149 149
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 37 37
RAP1/GDP -0.048 0.053 -10000 0 -0.17 22 22
KIDINS220/CRKL 0.011 0 -10000 0 -10000 0 0
BDNF (dimer) -0.042 0.12 -10000 0 -0.33 84 84
ubiquitin-dependent protein catabolic process -0.037 0.11 -10000 0 -0.23 120 120
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 -0.34 102 102
ABL1 0.009 0.026 -10000 0 -0.41 2 2
SH2B family/GRB2/SOS1 0.016 0 -10000 0 -10000 0 0
Rap1/GTP 0.015 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 -0.32 102 102
MAPK3 -0.032 0.1 -10000 0 -0.27 17 17
MAPK1 -0.032 0.1 -10000 0 -0.21 129 129
CDC42/GDP -0.04 0.08 -10000 0 -0.2 19 19
NTF3 -0.018 0.1 -10000 0 -0.4 37 37
NTF4 -0.007 0.071 -10000 0 -0.33 24 24
NGF (dimer)/TRKA/FAIM -0.037 0.11 -10000 0 -0.23 121 121
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 -0.35 188 190
SOS1 0.011 0 -10000 0 -10000 0 0
MCF2L -0.11 0.14 -10000 0 -0.25 265 265
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 -0.2 22 22
NGF (dimer)/TRKA/GRIT -0.044 0.11 -10000 0 -0.24 125 125
neuron projection morphogenesis -0.11 0.17 -10000 0 -0.43 68 68
NGF (dimer)/TRKA/NEDD4-2 -0.037 0.11 -10000 0 -0.23 120 120
MAP2K1 0.029 0.018 -10000 0 -10000 0 0
NGFR -0.13 0.2 -10000 0 -0.41 182 182
NGF (dimer)/TRKA/GIPC/GAIP -0.023 0.096 -10000 0 -0.2 124 124
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 -0.6 121 121
RASA1 0.007 0.04 -10000 0 -0.41 5 5
TRKA/c-Abl 0.008 0.044 -10000 0 -0.25 15 15
SQSTM1 0.011 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.027 0.093 -10000 0 -0.21 61 61
NGF (dimer)/TRKA/p62/Atypical PKCs -0.018 0.091 -10000 0 -0.21 12 12
MATK 0 0.066 -10000 0 -0.4 14 14
NEDD4L 0.01 0.018 -10000 0 -0.41 1 1
RAS family/GDP -0.044 0.05 -10000 0 -0.17 16 16
NGF (dimer)/TRKA -0.14 0.17 0.21 2 -0.31 235 237
Rac1/GTP -0.11 0.11 -10000 0 -0.26 168 168
FRS2 family/SHP2/CRK family 0.033 0 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.029 0.15 -10000 0 -0.41 51 51
CRKL -0.033 0.15 -10000 0 -0.43 51 51
HRAS -0.012 0.13 -10000 0 -0.38 45 45
mol:PIP3 -0.039 0.14 0.19 2 -0.4 53 55
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 -0.37 81 81
FOXO3 -0.024 0.14 -10000 0 -0.39 48 48
AKT1 -0.033 0.15 -10000 0 -0.43 48 48
BAD -0.024 0.14 -10000 0 -0.39 48 48
megakaryocyte differentiation -0.042 0.16 -10000 0 -0.36 80 80
GSK3B -0.024 0.14 -10000 0 -0.39 48 48
RAF1 -0.002 0.11 -10000 0 -0.3 45 45
SHC1 0.011 0 -10000 0 -10000 0 0
STAT3 -0.039 0.16 -10000 0 -0.37 79 79
STAT1 -0.099 0.34 -10000 0 -0.84 81 81
HRAS/SPRED1 -0.004 0.11 -10000 0 -0.3 45 45
cell proliferation -0.04 0.16 -10000 0 -0.36 81 81
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 -0.37 79 79
HRAS/SPRED2 -0.004 0.11 -10000 0 -0.31 45 45
LYN/TEC/p62DOK -0.026 0.15 -10000 0 -0.42 49 49
MAPK3 0.01 0.086 -10000 0 -0.23 30 30
STAP1 -0.042 0.16 -10000 0 -0.36 81 81
GRAP2 -0.002 0.074 -10000 0 -0.41 17 17
JAK2 -0.086 0.3 -10000 0 -0.72 81 81
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 51 51
actin filament polymerization -0.038 0.15 -10000 0 -0.36 81 81
LYN 0.011 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.052 0.21 -10000 0 -0.51 81 81
PIK3R1 0.007 0.04 -10000 0 -0.41 5 5
CBL/CRKL/GRB2 -0.019 0.14 -10000 0 -0.39 48 48
PI3K -0.03 0.16 -10000 0 -0.45 50 50
PTEN 0.006 0.044 -10000 0 -0.41 6 6
SCF/KIT/EPO/EPOR -0.099 0.37 -10000 0 -1.2 47 47
MAPK8 -0.041 0.16 -10000 0 -0.37 81 81
STAT3 (dimer) -0.038 0.15 -10000 0 -0.36 79 79
positive regulation of transcription 0.012 0.073 -10000 0 -0.19 26 26
mol:GDP -0.017 0.14 -10000 0 -0.39 46 46
PIK3C2B -0.039 0.16 -10000 0 -0.37 79 79
CBL/CRKL -0.025 0.14 -10000 0 -0.41 48 48
FER -0.039 0.16 -10000 0 -0.37 79 79
SH2B3 -0.04 0.16 -10000 0 -0.36 81 81
PDPK1 -0.031 0.13 0.18 2 -0.38 50 52
SNAI2 -0.064 0.18 -10000 0 -0.41 91 91
positive regulation of cell proliferation -0.069 0.26 -10000 0 -0.62 81 81
KITLG -0.029 0.13 -10000 0 -0.43 50 50
cell motility -0.069 0.26 -10000 0 -0.62 81 81
PTPN6 0.011 0.017 -10000 0 -0.33 1 1
EPOR -0.01 0.12 -10000 0 -0.46 14 14
STAT5A (dimer) -0.055 0.21 -10000 0 -0.52 81 81
SOCS1 0.01 0.018 -10000 0 -0.41 1 1
cell migration 0.043 0.16 0.36 80 -10000 0 80
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 -0.36 82 82
PTPN11 0.012 0.006 -10000 0 -10000 0 0
SCF/KIT -0.047 0.16 -10000 0 -0.34 107 107
GO:0007205 0.001 0.008 -10000 0 -10000 0 0
MAP2K1 0.007 0.093 -10000 0 -0.24 45 45
CBL 0.011 0 -10000 0 -10000 0 0
KIT -0.078 0.34 -10000 0 -1.2 40 40
MAP2K2 0.007 0.093 -10000 0 -0.24 45 45
SHC/Grb2/SOS1 -0.026 0.15 -10000 0 -0.43 48 48
STAT5A -0.058 0.22 -10000 0 -0.53 81 81
GRB2 0.011 0 -10000 0 -10000 0 0
response to radiation -0.063 0.18 -10000 0 -0.4 92 92
SHC/GRAP2 0.007 0.052 -10000 0 -0.28 17 17
PTPRO -0.043 0.16 -10000 0 -0.37 80 80
SH2B2 -0.039 0.16 -10000 0 -0.36 81 81
DOK1 0.011 0 -10000 0 -10000 0 0
MATK -0.044 0.16 -10000 0 -0.37 80 80
CREBBP 0.016 0.045 -10000 0 -0.42 2 2
BCL2 -0.099 0.38 -10000 0 -1.2 51 51
TCGA08_retinoblastoma

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
CDKN2B 0.001 0.049 -10000 0 -0.35 9 9
CDKN2C 0.021 0.056 -10000 0 -0.38 9 9
CDKN2A -0.14 0.17 -10000 0 -0.34 225 225
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
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 -0.032 0.13 -10000 0 -0.41 54 54
GNB1/GNG2 -0.04 0.072 -10000 0 -0.19 94 94
AKT1 -0.016 0.097 -10000 0 -0.2 94 94
EGF -0.005 0.07 -10000 0 -0.34 23 23
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.017 0.054 -10000 0 -0.3 1 1
mol:Ca2+ -0.045 0.14 -10000 0 -0.3 116 116
LYN 0.021 0.047 -10000 0 -10000 0 0
RhoA/GTP -0.028 0.049 -10000 0 -0.13 95 95
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.044 0.16 -10000 0 -0.34 107 107
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 0.004 0.071 -10000 0 -0.33 15 15
G beta5/gamma2 -0.053 0.097 -10000 0 -0.25 94 94
PRKCH -0.052 0.16 -10000 0 -0.35 107 107
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 -0.069 0.12 -10000 0 -0.3 108 108
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 0.021 0.093 0.22 49 -10000 0 49
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 -0.41 238 238
mol:IP3 -0.061 0.18 -10000 0 -0.38 116 116
cell morphogenesis 0.012 0.006 -10000 0 -10000 0 0
PLCB2 -0.089 0.23 -10000 0 -0.51 116 116
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 0.05 -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 -0.057 0.17 -10000 0 -0.37 109 109
GNAQ 0.009 0.026 -10000 0 -0.41 2 2
mol:L-citrulline 0.009 0.023 -10000 0 -0.37 2 2
TXA2/TXA2-R family -0.083 0.23 -10000 0 -0.52 107 107
LCK 0.02 0.049 -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 97 97
TGM2/GTP -0.078 0.21 -10000 0 -0.45 119 119
MAPK11 -0.022 0.11 -10000 0 -0.23 98 98
ARHGEF1 -0.017 0.085 -10000 0 -0.18 101 101
GNAI2 0.011 0 -10000 0 -10000 0 0
JNK cascade -0.056 0.17 -10000 0 -0.38 108 108
RAB11/GDP 0.011 0.001 -10000 0 -10000 0 0
ICAM1 -0.034 0.13 -10000 0 -0.28 96 96
cAMP biosynthetic process -0.062 0.17 -10000 0 -0.36 119 119
Gq family/GTP/EBP50 -0.002 0.069 -10000 0 -0.18 65 65
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 96 96
TP beta/Gq family/GDP/G beta5/gamma2 0.004 0.071 -10000 0 -0.33 15 15
platelet activation -0.031 0.14 -10000 0 -0.3 107 107
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 0.002 0.071 -10000 0 -0.31 15 15
TXA2/TP beta/beta Arrestin2 -0.006 0.047 -10000 0 -0.44 6 6
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.003 0.06 -10000 0 -0.19 48 48
mol:DAG -0.067 0.19 -10000 0 -0.42 107 107
EGFR 0 0.066 -10000 0 -0.4 14 14
TXA2/TP alpha -0.088 0.23 -10000 0 -0.49 119 119
Gq family/GTP -0.024 0.071 -10000 0 -0.2 65 65
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 0.039 -10000 0 -0.33 7 7
PGK/cGMP -0.096 0.12 -10000 0 -0.24 239 239
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 -0.37 107 107
PRKCB -0.058 0.17 -10000 0 -0.37 106 106
PRKCE -0.049 0.16 -10000 0 -0.35 102 102
PRKCD -0.055 0.17 -10000 0 -0.38 101 101
PRKCG -0.065 0.18 -10000 0 -0.4 108 108
muscle contraction -0.076 0.22 -10000 0 -0.48 108 108
PRKCZ -0.045 0.16 -10000 0 -0.34 107 107
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 -0.37 109 109
MAPKKK cascade -0.076 0.21 -10000 0 -0.46 109 109
SELE -0.048 0.16 -10000 0 -0.36 96 96
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 -0.032 0.13 -10000 0 -0.41 55 55
chemotaxis -0.091 0.26 -10000 0 -0.6 96 96
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
BMP receptor signaling

Figure S33.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S33.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.029 0.11 -9999 0 -0.22 117 117
SMAD6-7/SMURF1 0.021 0.019 -9999 0 -0.23 3 3
NOG -0.019 0.096 -9999 0 -0.33 46 46
SMAD9 -0.058 0.17 -9999 0 -0.5 59 59
SMAD4 0.01 0.018 -9999 0 -0.41 1 1
SMAD5 -0.018 0.095 -9999 0 -0.3 30 30
BMP7/USAG1 -0.048 0.12 -9999 0 -0.26 123 123
SMAD5/SKI -0.011 0.091 -9999 0 -0.29 28 28
SMAD1 0.034 0.014 -9999 0 -10000 0 0
BMP2 -0.025 0.12 -9999 0 -0.41 46 46
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 -0.003 0.08 -9999 0 -0.24 54 54
AHSG 0 0.048 -9999 0 -0.33 11 11
CER1 0.004 0.005 -9999 0 -10000 0 0
BMP2-4/CER1 -0.018 0.092 -9999 0 -0.24 74 74
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.036 0.12 -9999 0 -0.34 39 39
BMP2-4 (homodimer) -0.026 0.11 -9999 0 -0.29 74 74
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 -0.08 0.17 -9999 0 -0.41 116 116
SMURF1 0.011 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.041 0.12 -9999 0 -0.34 41 41
BMP2-4/USAG1 -0.043 0.12 -9999 0 -0.24 135 135
SMAD6/SMURF1/SMAD5 -0.011 0.091 -9999 0 -0.28 30 30
SOSTDC1 -0.04 0.13 -9999 0 -0.36 72 72
BMP7/BMPR2/BMPR1A-1B -0.008 0.088 -9999 0 -0.22 59 59
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 -0.26 148 148
SMAD5/SMAD5/SMAD4 -0.011 0.092 -9999 0 -0.29 30 30
MAPK1 0.011 0 -9999 0 -10000 0 0
TAK1/TAB family -0.051 0.087 -9999 0 -0.3 37 37
BMP7 (homodimer) -0.032 0.12 -9999 0 -0.37 61 61
NUP214 0.011 0 -9999 0 -10000 0 0
BMP6/FETUA 0.003 0.053 -9999 0 -0.25 22 22
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 -0.24 83 83
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.092 0.18 -9999 0 -0.41 132 132
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 0.072 -9999 0 -0.28 34 34
CHRDL1 -0.28 0.19 -9999 0 -0.41 368 368
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 0.082 -9999 0 -0.38 24 24
SMURF2 0.011 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.18 0.15 -9999 0 -0.26 386 386
BMP2-4/GREM1 -0.073 0.14 -9999 0 -0.26 182 182
SMAD7 0.009 0.026 -9999 0 -0.41 2 2
SMAD8A/SMAD8A/SMAD4 -0.049 0.16 -9999 0 -0.47 59 59
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 61 61
BMP6 0.002 0.06 -9999 0 -0.41 11 11
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.037 0.11 -9999 0 -0.32 43 43
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 -0.41 71 71
CHRD -0.062 0.16 -9999 0 -0.41 94 94
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 -0.23 113 113
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.002 0.082 -9999 0 -0.2 59 59
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.002 0.072 -10000 0 -0.19 70 70
ER alpha/Gai/GDP/Gbeta gamma -0.087 0.19 -10000 0 -0.31 183 183
AKT1 -0.07 0.25 -10000 0 -0.74 62 62
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.074 0.25 -10000 0 -0.76 62 62
mol:Ca2+ -0.016 0.12 -10000 0 -0.34 58 58
IGF1R -0.005 0.081 -10000 0 -0.41 21 21
E2/ER alpha (dimer)/Striatin -0.014 0.08 -10000 0 -0.23 63 63
SHC1 0.011 0 -10000 0 -10000 0 0
apoptosis 0.066 0.24 0.71 62 -10000 0 62
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 73 73
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 62 62
KRAS 0.01 0.015 -10000 0 -0.33 1 1
G13/GTP -0.011 0.071 -10000 0 -0.21 61 61
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 61 61
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 -0.41 142 142
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 63 63
E2/ER beta (dimer) 0.008 0.01 -10000 0 -0.23 1 1
mol:GDP -0.035 0.098 -10000 0 -0.31 61 61
mol:NADP -0.056 0.18 -10000 0 -0.49 63 63
PIK3R1 0.007 0.04 -10000 0 -0.41 5 5
mol:IP3 -0.017 0.13 -10000 0 -0.35 58 58
IGF-1R heterotetramer -0.005 0.081 -10000 0 -0.41 21 21
PLCB1 -0.023 0.13 -10000 0 -0.37 58 58
PLCB2 -0.022 0.13 -10000 0 -0.37 57 57
IGF1 -0.068 0.16 -10000 0 -0.41 101 101
mol:L-citrulline -0.056 0.18 -10000 0 -0.49 63 63
RHOA 0.011 0 -10000 0 -10000 0 0
Gai/GDP -0.15 0.29 -10000 0 -0.63 143 143
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 0.026 -10000 0 -0.41 2 2
ESR1 -0.037 0.13 -10000 0 -0.41 61 61
Gq family/GDP/Gbeta gamma -0.003 0.094 -10000 0 -0.39 16 16
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.009 0.082 -10000 0 -0.26 21 21
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.087 0.14 -10000 0 -0.39 73 73
GNAZ -0.001 0.069 -10000 0 -0.41 15 15
E2/ER alpha (dimer) -0.025 0.094 -10000 0 -0.29 61 61
STRN 0.009 0.026 -10000 0 -0.41 2 2
GNAL -0.051 0.15 -10000 0 -0.41 79 79
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 -0.36 119 119
cAMP biosynthetic process -0.047 0.089 -10000 0 -0.2 128 128
SRC -0.077 0.18 -10000 0 -0.29 183 183
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 61 61
SOS1 0.011 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.099 0.15 -10000 0 -0.36 110 110
Gs family/GTP -0.048 0.091 -10000 0 -0.2 128 128
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.021 0.008 -10000 0 -10000 0 0
vasodilation -0.053 0.17 -10000 0 -0.47 63 63
mol:DAG -0.017 0.13 -10000 0 -0.35 58 58
Gs family/GDP/Gbeta gamma -0.051 0.1 -10000 0 -0.29 65 65
MSN 0.017 0.062 -10000 0 -0.28 3 3
Gq family/GTP -0.029 0.13 -10000 0 -0.39 57 57
mol:PI-3-4-5-P3 -0.071 0.24 -10000 0 -0.73 62 62
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 63 -10000 0 63
GRB2/SOS1 0.016 0 -10000 0 -10000 0 0
RhoA/GDP -0.033 0.091 -10000 0 -0.29 61 61
NOS3 -0.059 0.19 -10000 0 -0.52 63 63
GNA11 0.002 0.062 -10000 0 -0.41 12 12
MAPKKK cascade -0.05 0.19 -10000 0 -0.54 63 63
E2/ER alpha (dimer)/PELP1/Src -0.092 0.15 -10000 0 -0.41 73 73
ruffle organization 0.017 0.058 -10000 0 -0.26 3 3
ROCK2 0.012 0.065 -10000 0 -0.31 3 3
GNA14 -0.032 0.13 -10000 0 -0.41 55 55
GNA15 0.007 0.039 -10000 0 -0.33 7 7
GNA13 0.011 0 -10000 0 -10000 0 0
MMP9 -0.13 0.18 -10000 0 -0.4 117 117
MMP2 -0.076 0.18 -10000 0 -0.4 80 80
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.028 0.1 0.28 76 -10000 0 76
KIRREL -0.039 0.14 -10000 0 -0.41 63 63
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.028 0.1 -10000 0 -0.28 76 76
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 -0.01 0.075 -10000 0 -0.2 64 64
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.004 0.077 -10000 0 -0.21 63 63
FYN -0.013 0.071 -10000 0 -0.2 64 64
mol:Ca2+ -0.014 0.074 -10000 0 -0.2 64 64
mol:DAG -0.011 0.075 -10000 0 -0.2 64 64
NPHS2 -0.004 0.028 -10000 0 -0.33 3 3
mol:IP3 -0.011 0.075 -10000 0 -0.2 64 64
regulation of endocytosis -0.005 0.067 -10000 0 -0.18 64 64
Nephrin/NEPH1/podocin/Cholesterol -0.017 0.075 -10000 0 -0.2 78 78
establishment of cell polarity -0.028 0.1 -10000 0 -0.28 76 76
Nephrin/NEPH1/podocin/NCK1-2 -0.003 0.072 -10000 0 -0.2 32 32
Nephrin/NEPH1/beta Arrestin2 -0.005 0.068 -10000 0 -0.18 64 64
NPHS1 -0.005 0.055 -10000 0 -0.33 14 14
Nephrin/NEPH1/podocin -0.013 0.072 -10000 0 -0.2 64 64
TJP1 0.01 0.018 -10000 0 -0.41 1 1
NCK1 0.009 0.026 -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 -0.01 0.075 -10000 0 -0.2 64 64
CD2AP 0.011 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.01 0.075 -10000 0 -0.2 64 64
GRB2 0.011 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.026 0.096 -10000 0 -0.22 93 93
cytoskeleton organization -0.001 0.08 -10000 0 -0.21 63 63
Nephrin/NEPH1 -0.017 0.07 -10000 0 -0.19 76 76
Nephrin/NEPH1/ZO-1 -0.013 0.082 -10000 0 -0.22 64 64
Syndecan-1-mediated signaling events

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
TGFB1 0.01 0.018 -9999 0 -0.41 1 1
CCL5 0.003 0.054 -9999 0 -0.37 11 11
SDCBP 0.011 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.071 0.069 -9999 0 -0.26 28 28
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 29 29
Syndecan-1/Syntenin -0.061 0.066 -9999 0 -0.25 28 28
MAPK3 -0.045 0.062 -9999 0 -0.25 15 15
HGF/MET -0.048 0.12 -9999 0 -0.28 115 115
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 -0.061 0.065 -9999 0 -0.24 29 29
Syndecan-1/RANTES -0.064 0.073 -9999 0 -0.26 36 36
Syndecan-1/CD147 -0.053 0.064 -9999 0 -0.24 28 28
Syndecan-1/Syntenin/PIP2 -0.059 0.063 -9999 0 -0.24 28 28
LAMA5 0.01 0.015 -9999 0 -0.33 1 1
positive regulation of cell-cell adhesion -0.058 0.062 -9999 0 -0.23 28 28
MMP7 -0.057 0.14 -9999 0 -0.36 98 98
HGF -0.075 0.17 -9999 0 -0.41 110 110
Syndecan-1/CASK -0.067 0.065 -9999 0 -0.25 28 28
Syndecan-1/HGF/MET -0.095 0.11 -9999 0 -0.27 123 123
regulation of cell adhesion -0.038 0.06 -9999 0 -0.24 15 15
HPSE 0.003 0.058 -9999 0 -0.4 11 11
positive regulation of cell migration -0.071 0.069 -9999 0 -0.26 28 28
SDC1 -0.071 0.07 -9999 0 -0.27 28 28
Syndecan-1/Collagen -0.071 0.069 -9999 0 -0.26 28 28
PPIB 0.01 0.015 -9999 0 -0.33 1 1
MET 0.005 0.046 -9999 0 -0.37 8 8
PRKACA 0.011 0 -9999 0 -10000 0 0
MMP9 -0.13 0.17 -9999 0 -0.33 220 220
MAPK1 -0.045 0.062 -9999 0 -0.25 15 15
homophilic cell adhesion -0.07 0.069 -9999 0 -0.26 28 28
MMP1 -0.17 0.17 -9999 0 -0.33 292 292
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 -0.23 11 11
alphaM/beta2 Integrin/proMMP-9 -0.062 0.1 -9999 0 -0.18 223 223
PLAUR 0.01 0.021 -9999 0 -0.33 2 2
HMGB1 0.009 0.011 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.017 0.033 -9999 0 -0.21 9 9
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 0.018 0.057 -9999 0 -0.27 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.13 0.17 -9999 0 -0.33 220 220
CYR61 -0.027 0.12 -9999 0 -0.41 48 48
TLN1 0.011 0 -9999 0 -10000 0 0
Rap1/GTP -0.028 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 -0.41 204 204
MYH2 -0.03 0.11 -9999 0 -0.31 35 35
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 0.052 -9999 0 -0.39 9 9
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.01 0.092 -9999 0 -0.41 27 27
JAM3 -0.1 0.19 -9999 0 -0.41 144 144
GP1BA 0.008 0.03 -9999 0 -0.38 3 3
alphaM/beta2 Integrin/CTGF 0.011 0.053 -9999 0 -0.24 19 19
alphaM/beta2 Integrin -0.022 0.085 -9999 0 -0.23 39 39
JAM3 homodimer -0.1 0.19 -9999 0 -0.41 144 144
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 39 39
cell adhesion 0.014 0.041 -9999 0 -0.23 11 11
NFKB1 0.018 0.086 -9999 0 -0.28 26 26
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 40 40
alphaM/beta2 Integrin/LRP/tPA -0.002 0.081 -9999 0 -0.21 63 63
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 0.035 -9999 0 -0.19 9 9
alphaM/beta2 Integrin/JAM2/JAM3 -0.11 0.17 -9999 0 -0.28 243 243
JAM2 -0.14 0.2 -9999 0 -0.41 189 189
alphaM/beta2 Integrin/ICAM1 0.01 0.063 -9999 0 -0.36 3 3
alphaM/beta2 Integrin/uPA/Plg -0.001 0.076 -9999 0 -0.21 53 53
RhoA/GTP -0.033 0.11 -9999 0 -0.26 70 70
positive regulation of phagocytosis -0.02 0.055 -9999 0 -0.24 11 11
Ron/MSP -0.009 0.073 -9999 0 -0.22 58 58
alphaM/beta2 Integrin/uPAR/uPA 0.022 0.035 -9999 0 -0.19 9 9
alphaM/beta2 Integrin/uPAR 0.017 0.036 -9999 0 -0.2 11 11
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 -0.3 35 35
MST1 0.007 0.039 -9999 0 -0.33 7 7
alphaM/beta2 Integrin/lipoprotein(a) 0.005 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 -0.21 12 12
fibrinolysis -0.001 0.075 -9999 0 -0.21 53 53
HCK 0.007 0.039 -9999 0 -0.33 7 7
dendritic cell antigen processing and presentation -0.022 0.084 -9999 0 -0.23 39 39
VTN -0.046 0.14 -9999 0 -0.41 72 72
alphaM/beta2 Integrin/CYR61 -0.005 0.08 -9999 0 -0.23 55 55
LPA -0.012 0.08 -9999 0 -0.33 32 32
LRP1 0.009 0.026 -9999 0 -0.41 2 2
cell migration -0.06 0.1 -9999 0 -0.25 41 41
FN1 0.007 0.04 -9999 0 -0.41 5 5
alphaM/beta2 Integrin/Thy1 0.017 0.033 -9999 0 -0.24 5 5
MPO 0.005 0.041 -9999 0 -0.33 8 8
KNG1 -0.01 0.069 -9999 0 -0.33 24 24
RAP1/GDP 0.015 0 -9999 0 -10000 0 0
ROCK1 -0.026 0.11 -9999 0 -0.31 34 34
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.033 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 -0.062 0.12 -9999 0 -0.2 208 208
HP -0.1 0.17 -9999 0 -0.35 166 166
leukocyte adhesion -0.11 0.13 -9999 0 -0.32 118 118
SELP -0.15 0.2 -9999 0 -0.41 204 204
Ephrin A reverse signaling

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
MAPKKK cascade -0.014 0.076 -9999 0 -0.24 53 53
EFNA5 -0.004 0.076 -9999 0 -0.4 19 19
FYN -0.006 0.069 -9999 0 -0.21 53 53
neuron projection morphogenesis -0.014 0.076 -9999 0 -0.24 53 53
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.014 0.076 -9999 0 -0.24 53 53
EPHA5 -0.023 0.1 -9999 0 -0.41 36 36
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.1 0.25 -10000 0 -0.68 36 36
PCK1 -0.12 0.32 -10000 0 -1.2 35 35
HNF4A -0.16 0.33 -10000 0 -0.84 69 69
KCNJ11 -0.089 0.26 -10000 0 -0.7 33 33
AKT1 -0.049 0.14 -10000 0 -0.37 11 11
response to starvation -0.01 0.032 -10000 0 -10000 0 0
DLK1 -0.15 0.34 -10000 0 -0.82 73 73
NKX2-1 -0.02 0.15 -10000 0 -0.5 1 1
ACADM -0.1 0.26 -10000 0 -0.71 37 37
TAT -0.098 0.2 -10000 0 -0.59 27 27
CEBPB 0.013 0.002 -10000 0 -10000 0 0
CEBPA 0.01 0.038 -10000 0 -0.38 5 5
TTR -0.038 0.13 -10000 0 -0.6 8 8
PKLR -0.11 0.25 -10000 0 -0.68 40 40
APOA1 -0.21 0.44 -10000 0 -1.2 70 70
CPT1C -0.1 0.26 -10000 0 -0.74 38 38
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 -0.4 2 2
HNF1A (dimer) 0.004 0.047 -10000 0 -0.35 8 8
CPT1A -0.1 0.25 -10000 0 -0.68 37 37
HMGCS1 -0.1 0.25 -10000 0 -0.68 35 35
NR3C1 -0.067 0.16 -10000 0 -0.39 94 94
CPT1B -0.1 0.25 -10000 0 -0.68 36 36
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 -0.79 95 95
CREB1 0.004 0.041 -10000 0 -0.19 9 9
IGFBP1 -0.22 0.44 -10000 0 -1.2 88 88
PDX1 -0.053 0.15 -10000 0 -0.47 7 7
UCP2 -0.1 0.25 -10000 0 -0.68 37 37
ALDOB -0.091 0.26 -10000 0 -0.7 33 33
AFP -0.056 0.072 -10000 0 -0.4 10 10
BDH1 -0.1 0.25 -10000 0 -0.68 36 36
HADH -0.088 0.26 -10000 0 -0.71 30 30
F2 -0.15 0.31 -10000 0 -0.85 44 44
HNF1A 0.004 0.047 -10000 0 -0.35 8 8
G6PC 0.007 0.066 -10000 0 -10000 0 0
SLC2A2 -0.057 0.17 -10000 0 -0.48 3 3
INS 0.016 0.06 0.21 21 -10000 0 21
FOXA1 -0.21 0.16 -10000 0 -0.32 359 359
FOXA3 -0.057 0.15 -10000 0 -0.33 117 117
FOXA2 -0.11 0.3 -10000 0 -0.75 42 42
ABCC8 -0.18 0.38 -10000 0 -0.85 105 105
ALB -0.063 0.14 -10000 0 -0.85 12 12
S1P1 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
VEGFR2 homodimer/VEGFA homodimer -0.002 0.071 -9999 0 -0.28 32 32
PDGFRB -0.007 0.084 -9999 0 -0.42 22 22
SPHK1 -0.013 0.023 -9999 0 -10000 0 0
mol:S1P -0.016 0.03 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.079 0.19 -9999 0 -0.31 181 181
GNAO1 -0.1 0.19 -9999 0 -0.41 142 142
PDGFB-D/PDGFRB/PLCgamma1 -0.064 0.17 -9999 0 -0.38 91 91
PLCG1 -0.068 0.18 -9999 0 -0.4 87 87
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.007 0.084 -9999 0 -0.41 22 22
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 32 32
S1P1/S1P -0.023 0.064 -9999 0 -0.27 15 15
negative regulation of cAMP metabolic process -0.076 0.18 -9999 0 -0.3 181 181
MAPK3 -0.088 0.22 -9999 0 -0.53 86 86
calcium-dependent phospholipase C activity -0.001 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 -0.014 0.1 -9999 0 -0.41 32 32
PLCB2 0.004 0.068 -9999 0 -0.24 15 15
RAC1 0.011 0 -9999 0 -10000 0 0
RhoA/GTP -0.019 0.055 -9999 0 -0.23 15 15
receptor internalization -0.022 0.061 -9999 0 -0.25 15 15
PTGS2 -0.12 0.33 -9999 0 -0.89 72 72
Rac1/GTP -0.019 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 -0.076 0.18 -9999 0 -0.3 181 181
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.002 0.07 -9999 0 -0.42 15 15
MAPK1 -0.088 0.22 -9999 0 -0.53 86 86
S1P1/S1P/PDGFB-D/PDGFRB -0.004 0.098 -9999 0 -0.3 30 30
ABCC1 0.01 0.002 -9999 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.077 0.17 -9999 0 -0.31 167 167
MAP3K8 0.006 0.032 -9999 0 -0.41 3 3
FOS -0.045 0.12 -9999 0 -0.38 26 26
PRKCA -0.02 0.1 -9999 0 -0.41 36 36
PTPN7 0.005 0.038 -9999 0 -0.34 6 6
HRAS 0.01 0.001 -9999 0 -10000 0 0
PRKCB -0.017 0.1 -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 -10000 0 0
MAPK3 -0.017 0.069 -9999 0 -0.25 5 5
MAP2K1 -0.039 0.15 -9999 0 -0.4 64 64
ELK1 0.005 0.01 -9999 0 -10000 0 0
BRAF -0.035 0.14 -9999 0 -0.38 64 64
mol:GTP -0.001 0.002 -9999 0 -0.005 165 165
MAPK1 -0.017 0.069 -9999 0 -0.21 25 25
RAF1 -0.035 0.14 -9999 0 -0.38 64 64
KRAS 0.01 0.015 -9999 0 -0.33 1 1
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.039 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 -0.21 153 153
AP1 -0.081 0.15 -9999 0 -0.37 66 66
ILK -0.051 0.11 -9999 0 -0.33 18 18
bone resorption -0.028 0.1 -9999 0 -0.3 30 30
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 0.005 0.057 -9999 0 -0.28 21 21
alphaV/beta3 Integrin/Osteopontin -0.065 0.12 -9999 0 -0.24 107 107
MAP3K1 -0.051 0.11 -9999 0 -0.29 25 25
JUN 0.006 0.048 -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 23 23
ITGB3 -0.063 0.16 -9999 0 -0.4 100 100
NFKBIA -0.025 0.099 -9999 0 -0.3 16 16
FOS -0.12 0.19 -9999 0 -0.41 165 165
CD44 0.006 0.048 -9999 0 -0.41 7 7
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 15 15
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 -0.27 100 100
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.052 0.11 -9999 0 -0.32 21 21
VAV3 -0.08 0.12 -9999 0 -0.3 68 68
MAP3K14 -0.049 0.11 -9999 0 -0.32 20 20
ROCK2 0 0.067 -9999 0 -0.41 14 14
SPP1 -0.082 0.15 -9999 0 -0.32 153 153
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
Ephrin B reverse signaling

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
EFNB2 0.009 0.031 -10000 0 -0.41 3 3
EPHB2 0.01 0.025 -10000 0 -0.33 3 3
EFNB1 0.015 0.037 -10000 0 -0.32 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.009 0.071 -10000 0 -0.35 4 4
Ephrin B2/EPHB1-2 -0.001 0.068 -10000 0 -0.2 54 54
neuron projection morphogenesis -0.021 0.056 -10000 0 -0.33 4 4
Ephrin B1/EPHB1-2/Tiam1 0.006 0.076 -10000 0 -0.38 4 4
DNM1 0.007 0.044 -10000 0 -0.41 6 6
cell-cell signaling 0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.048 0.18 -10000 0 -0.52 67 67
YES1 -0.093 0.25 -10000 0 -0.76 67 67
Ephrin B1/EPHB1-2/NCK2 0.011 0.067 -10000 0 -0.38 1 1
PI3K -0.048 0.18 -10000 0 -0.53 68 68
mol:GDP 0.005 0.075 -10000 0 -0.37 4 4
ITGA2B 0.006 0.046 -10000 0 -0.4 7 7
endothelial cell proliferation 0.014 0.021 -10000 0 -0.23 4 4
FYN -0.093 0.25 -10000 0 -0.76 67 67
MAP3K7 -0.056 0.19 -10000 0 -0.56 67 67
FGR -0.095 0.25 -10000 0 -0.76 67 67
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 -0.071 0.2 -10000 0 -0.56 67 67
LYN -0.093 0.25 -10000 0 -0.76 67 67
Ephrin B1/EPHB1-2/Src Family Kinases -0.087 0.23 -10000 0 -0.7 67 67
Ephrin B1/EPHB1-2 -0.075 0.2 -10000 0 -0.6 67 67
SRC -0.092 0.25 -10000 0 -0.75 67 67
ITGB3 -0.067 0.16 -10000 0 -0.41 100 100
EPHB1 -0.03 0.12 -10000 0 -0.4 53 53
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 -0.042 0.12 -10000 0 -0.28 107 107
BLK -0.092 0.25 -10000 0 -0.75 67 67
HCK -0.092 0.25 -10000 0 -0.75 67 67
regulation of stress fiber formation -0.01 0.066 0.37 1 -10000 0 1
MAPK8 -0.042 0.17 -10000 0 -0.5 67 67
Ephrin B1/EPHB1-2/RGS3 0.011 0.067 -10000 0 -0.38 1 1
endothelial cell migration -0.054 0.16 -10000 0 -0.46 67 67
NCK2 0.011 0 -10000 0 -10000 0 0
PTPN13 -0.057 0.18 -10000 0 -0.52 67 67
regulation of focal adhesion formation -0.01 0.066 0.37 1 -10000 0 1
chemotaxis -0.01 0.066 0.37 1 -10000 0 1
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
Rac1/GTP -0.022 0.057 -10000 0 -0.34 4 4
angiogenesis -0.075 0.2 -10000 0 -0.6 67 67
LCK -0.092 0.25 -10000 0 -0.75 67 67
TCGA08_p53

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
CDKN2A -0.089 0.12 -9999 0 -0.23 225 225
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
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 44 44
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 48 48
mol:PIP3 -0.029 0.068 -9999 0 -0.32 15 15
AKT1 0.029 0.056 -9999 0 -0.27 8 8
PTK2B 0.006 0.059 -9999 0 -0.21 26 26
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 -0.24 5 5
MAGI3 0.011 0 -9999 0 -10000 0 0
RELA 0.011 0 -9999 0 -10000 0 0
apoptosis -0.01 0.084 -9999 0 -0.23 61 61
HRAS/GDP 0.008 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.01 0.065 -9999 0 -0.24 12 12
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 -0.043 0.14 -9999 0 -0.37 54 54
ADCY5 -0.07 0.16 -9999 0 -0.38 76 76
ADCY6 -0.035 0.13 -9999 0 -0.34 46 46
ADCY7 -0.035 0.13 -9999 0 -0.34 46 46
ADCY1 -0.044 0.14 -9999 0 -0.37 55 55
ADCY2 -0.14 0.19 -9999 0 -0.4 140 140
ADCY3 -0.036 0.13 -9999 0 -0.35 48 48
ADCY8 -0.038 0.13 -9999 0 -0.35 46 46
ADCY9 -0.063 0.16 -9999 0 -0.38 84 84
GSK3B 0.011 0.056 -9999 0 -0.22 14 14
arachidonic acid secretion -0.04 0.13 -9999 0 -0.4 36 36
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 -0.26 162 162
HRAS 0.011 0 -9999 0 -10000 0 0
NFKBIA 0.01 0.076 -9999 0 -0.27 8 8
GAB1 0.008 0.036 -9999 0 -0.41 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.002 0.14 -9999 0 -0.86 14 14
JUN 0.005 0.048 -9999 0 -0.41 7 7
LPA/LPA2/NHERF2 0.012 0.023 -9999 0 -0.18 3 3
TIAM1 -0.025 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 -0.25 5 5
PLCB3 0.018 0.02 -9999 0 -10000 0 0
FOS -0.12 0.19 -9999 0 -0.41 165 165
positive regulation of mitosis -0.04 0.13 -9999 0 -0.4 36 36
LPA/LPA1-2-3 -0.012 0.088 -9999 0 -0.23 47 47
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 0.008 0.068 -9999 0 -0.31 8 8
GNAZ -0.003 0.084 -9999 0 -0.25 51 51
EGFR/PI3K-beta/Gab1 -0.03 0.07 -9999 0 -0.33 15 15
positive regulation of dendritic cell cytokine production -0.017 0.086 -9999 0 -0.24 42 42
LPA/LPA2/MAGI-3 0.012 0.023 -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 38 38
GNAI3 0.003 0.072 -9999 0 -0.25 38 38
GNAI1 0 0.078 -9999 0 -0.25 45 45
LPA/LPA3 -0.019 0.08 -9999 0 -0.26 50 50
LPA/LPA2 0.005 0.027 -9999 0 -0.22 3 3
LPA/LPA1 -0.007 0.084 -9999 0 -0.3 38 38
HB-EGF/EGFR -0.064 0.1 -9999 0 -0.18 226 226
HBEGF -0.078 0.12 -9999 0 -0.22 220 220
mol:DAG 0.005 0.064 -9999 0 -0.25 5 5
cAMP biosynthetic process -0.066 0.15 -9999 0 -0.28 140 140
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 0.01 0.076 -9999 0 -0.27 8 8
GNAQ -0.002 0.059 -9999 0 -0.22 28 28
LPAR2 0.009 0.025 -9999 0 -0.33 3 3
LPAR3 -0.025 0.11 -9999 0 -0.37 50 50
LPAR1 -0.006 0.084 -9999 0 -0.45 16 16
IL8 -0.071 0.11 -9999 0 -0.34 36 36
PTK2 -0.003 0.082 -9999 0 -0.38 8 8
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
CASP3 -0.01 0.085 -9999 0 -0.23 61 61
EGFR 0 0.066 -9999 0 -0.4 14 14
PLCG1 -0.009 0.074 -9999 0 -0.22 45 45
PLD2 -0.004 0.083 -9999 0 -0.38 8 8
G12/G13 0.01 0.065 -9999 0 -0.22 38 38
PI3K-beta -0.014 0.049 -9999 0 -0.29 9 9
cell migration -0.013 0.049 -9999 0 -0.25 16 16
SLC9A3R2 0.011 0 -9999 0 -10000 0 0
PXN 0.008 0.068 -9999 0 -0.32 8 8
HRAS/GTP -0.041 0.14 -9999 0 -0.41 36 36
RAC1 0.011 0 -9999 0 -10000 0 0
MMP9 -0.13 0.17 -9999 0 -0.33 220 220
PRKCE 0.011 0.001 -9999 0 -10000 0 0
PRKCD 0.01 0.061 -9999 0 -0.24 4 4
Gi(beta/gamma) -0.034 0.12 -9999 0 -0.34 47 47
mol:LPA -0.004 0.034 -9999 0 -0.16 22 22
TRIP6/p130 Cas/FAK1/Paxillin -0.023 0.071 -9999 0 -0.39 9 9
MAPKKK cascade -0.04 0.13 -9999 0 -0.4 36 36
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 26 26
GNA12 0.011 0 -9999 0 -10000 0 0
GNA13 0.011 0 -9999 0 -10000 0 0
MAPT 0.009 0.066 -9999 0 -0.26 11 11
GNA11 -0.006 0.066 -9999 0 -0.22 38 38
Rac1/GTP -0.002 0.15 -9999 0 -0.91 14 14
MMP2 -0.01 0.13 -9999 0 -0.53 27 27
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.012 0.032 -10000 0 -0.25 8 8
CRKL -0.013 0.096 -10000 0 -0.41 10 10
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 -0.007 0.091 -10000 0 -0.38 10 10
RANBP10 0.011 0 -10000 0 -10000 0 0
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
HGF/MET/SHIP2 -0.032 0.1 -10000 0 -0.23 115 115
MAP3K5 0 0.089 -10000 0 -0.36 12 12
HGF/MET/CIN85/CBL/ENDOPHILINS -0.021 0.096 -10000 0 -0.2 111 111
AP1 -0.067 0.12 -10000 0 -0.25 166 166
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 -0.71 166 166
STAT3 (dimer) -0.016 0.097 -10000 0 -0.2 114 114
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 -0.38 10 10
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 0.018 -10000 0 -0.15 4 4
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.026 0.052 -10000 0 -0.22 8 8
PAK1 0.01 0.028 0.27 6 -10000 0 6
HGF/MET/RANBP10 -0.032 0.1 -10000 0 -0.23 115 115
HRAS -0.025 0.12 -10000 0 -0.55 6 6
DOCK1 -0.01 0.097 -10000 0 -0.41 12 12
GAB1 -0.02 0.1 -10000 0 -0.2 113 113
CRK -0.013 0.096 -10000 0 -0.41 10 10
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.087 0.17 -10000 0 -0.42 111 111
JUN 0.006 0.048 -10000 0 -0.41 7 7
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.025 0.075 -10000 0 -0.17 111 111
PIK3R1 0.007 0.04 -10000 0 -0.41 5 5
cell morphogenesis 0 0.11 -10000 0 -0.4 10 10
GRB2/SHC -0.009 0.067 -10000 0 -0.29 4 4
FOS -0.12 0.19 -10000 0 -0.41 165 165
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.003 0.018 -10000 0 -0.15 4 4
HGF/MET/MUC20 -0.039 0.1 -10000 0 -0.24 115 115
cell migration -0.009 0.066 -10000 0 -0.29 4 4
GRB2 0.011 0 -10000 0 -10000 0 0
CBL 0.011 0 -10000 0 -10000 0 0
MET/RANBP10 0.012 0.032 -10000 0 -0.25 8 8
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.019 0.096 -10000 0 -0.2 114 114
MET/MUC20 0.004 0.032 -10000 0 -0.26 8 8
RAP1B -0.001 0.087 -10000 0 -0.38 9 9
RAP1A -0.001 0.087 -10000 0 -0.38 9 9
HGF/MET/RANBP9 -0.032 0.1 -10000 0 -0.23 115 115
RAF1 -0.017 0.11 -10000 0 -0.51 6 6
STAT3 -0.016 0.098 -10000 0 -0.2 114 114
cell proliferation -0.024 0.13 -10000 0 -0.28 111 111
RPS6KB1 -0.003 0.029 -10000 0 -0.14 3 3
MAPK3 -0.007 0.017 -10000 0 -10000 0 0
MAPK1 -0.007 0.017 -10000 0 -10000 0 0
RANBP9 0.011 0 -10000 0 -10000 0 0
MAPK8 0.01 0.096 -10000 0 -0.39 15 15
SRC -0.012 0.09 -10000 0 -0.37 5 5
PI3K -0.011 0.072 -10000 0 -0.3 9 9
MET/Glomulin 0.007 0.028 -10000 0 -0.22 8 8
SOS1 0.011 0 -10000 0 -10000 0 0
MAP2K1 -0.011 0.1 -10000 0 -0.57 4 4
MET 0.005 0.046 -10000 0 -0.37 8 8
MAP4K1 -0.005 0.092 -10000 0 -0.38 10 10
PTK2 0.011 0 -10000 0 -10000 0 0
MAP2K2 -0.011 0.1 -10000 0 -0.57 4 4
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 -0.033 0.075 -10000 0 -0.39 10 10
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 -0.017 0.069 -10000 0 -0.15 111 111
PLCgamma1/PKC 0.008 0 -10000 0 -10000 0 0
HGF -0.075 0.17 -10000 0 -0.41 110 110
RASA1 0.007 0.04 -10000 0 -0.41 5 5
NCK1 0.009 0.026 -10000 0 -0.41 2 2
PTPRJ 0.011 0 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.012 0.076 -10000 0 -0.16 112 112
PDPK1 -0.002 0.034 0.31 6 -10000 0 6
HGF/MET/SHIP -0.032 0.11 -10000 0 -0.23 116 116
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK 0.01 0.015 -9999 0 -0.33 1 1
GPC2 -0.014 0.088 -9999 0 -0.33 39 39
GPC2/Midkine -0.001 0.061 -9999 0 -0.22 40 40
neuron projection morphogenesis -0.001 0.061 -9999 0 -0.22 40 40
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.24 0.37 -10000 0 -1 54 54
STAT6 (cleaved dimer) -0.27 0.34 -10000 0 -0.95 76 76
IGHG1 -0.085 0.14 -10000 0 -0.35 21 21
IGHG3 -0.23 0.36 -10000 0 -0.96 65 65
AKT1 -0.1 0.2 -10000 0 -0.71 10 10
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.064 0.16 -10000 0 -0.6 9 9
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.12 0.23 -10000 0 -0.64 36 36
THY1 -0.24 0.37 -10000 0 -1.1 48 48
MYB -0.021 0.1 -10000 0 -0.33 51 51
HMGA1 -0.037 0.12 -10000 0 -0.33 75 75
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.14 0.23 -10000 0 -0.61 39 39
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.1 0.2 -10000 0 -0.78 8 8
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 -1 60 60
SOCS1 -0.14 0.26 -10000 0 -0.7 42 42
SOCS3 -0.1 0.21 -10000 0 -0.94 6 6
FCER2 -0.18 0.3 -10000 0 -0.84 40 40
PARP14 0.012 0.002 -10000 0 -10000 0 0
CCL17 -0.24 0.37 -10000 0 -1.1 47 47
GRB2 0.011 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.08 0.16 -10000 0 -0.71 4 4
T cell proliferation -0.24 0.38 -10000 0 -1.1 53 53
IL4R/JAK1 -0.24 0.38 -10000 0 -1.1 52 52
EGR2 -0.27 0.46 -10000 0 -1.3 58 58
JAK2 -0.009 0.06 -10000 0 -0.42 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 56 56
IL4R -0.25 0.4 -10000 0 -1.1 51 51
PTPN6 0.017 0.018 -10000 0 -0.31 1 1
IL13RA2 -0.24 0.38 -10000 0 -1 59 59
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 -0.58 36 36
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 -0.63 24 24
mitosis -0.096 0.2 -10000 0 -0.67 10 10
STAT6 -0.27 0.42 -10000 0 -1.1 62 62
SPI1 0.011 0.025 -10000 0 -0.33 3 3
RPS6KB1 -0.088 0.19 -10000 0 -0.64 10 10
STAT6 (dimer) -0.27 0.42 -10000 0 -1.1 62 62
STAT6 (dimer)/PARP14 -0.25 0.39 -10000 0 -1.1 61 61
mast cell activation 0.006 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.095 0.19 -10000 0 -0.7 8 8
FRAP1 -0.1 0.2 -10000 0 -0.71 10 10
LTA -0.24 0.37 -10000 0 -1 56 56
FES 0.01 0.018 -10000 0 -0.41 1 1
T-helper 1 cell differentiation 0.26 0.41 1.1 63 -10000 0 63
CCL11 -0.25 0.39 -10000 0 -1.1 62 62
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.095 0.19 -10000 0 -0.73 7 7
IL2RG 0.009 0.048 -10000 0 -0.36 9 9
IL10 -0.24 0.37 -10000 0 -1 54 54
IRS1 -0.03 0.12 -10000 0 -0.41 53 53
IRS2 -0.043 0.14 -10000 0 -0.41 69 69
IL4 -0.058 0.1 -10000 0 -10000 0 0
IL5 -0.24 0.37 -10000 0 -1.1 49 49
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.21 0.32 -10000 0 -0.84 58 58
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 45 45
IL2R gamma/JAK3 0.015 0.046 -10000 0 -0.3 10 10
TFF3 -0.3 0.43 -10000 0 -1.2 74 74
ALOX15 -0.25 0.38 -10000 0 -1.1 51 51
MYBL1 0.011 0 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.21 0.32 -10000 0 -0.84 60 60
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 -0.64 22 22
mol:PI-3-4-5-P3 -0.1 0.2 -10000 0 -0.71 10 10
PI3K -0.11 0.21 -10000 0 -0.77 10 10
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 -0.62 5 5
ITGB3 -0.36 0.56 -10000 0 -1.3 115 115
PIGR -0.33 0.47 -10000 0 -1.2 84 84
IGHE 0.019 0.033 -10000 0 -10000 0 0
MAPKKK cascade -0.071 0.16 -10000 0 -0.61 5 5
BCL6 0.01 0.018 -10000 0 -0.41 1 1
OPRM1 -0.24 0.37 -10000 0 -1.1 48 48
RETNLB -0.24 0.37 -10000 0 -1.1 46 46
SELP -0.52 0.66 -10000 0 -1.3 208 208
AICDA -0.23 0.36 -10000 0 -1 55 55
FAS signaling pathway (CD95)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPTAN1 0.019 0.059 0.2 52 -10000 0 52
RFC1 0.019 0.059 0.2 52 -10000 0 52
PRKDC 0.019 0.059 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 0.018 0.065 0.19 59 -0.21 5 64
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 0.063 0.2 51 -0.22 5 56
FASLG/FAS/FADD/FAF1/Caspase 8 0.037 0.055 -10000 0 -0.25 2 2
FAS 0.007 0.04 -10000 0 -0.41 5 5
BID 0.001 0.017 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 -0.062 0.13 -10000 0 -0.25 164 164
ARHGDIB 0.019 0.059 0.2 52 -10000 0 52
FADD 0.011 0.003 -10000 0 -10000 0 0
actin filament polymerization -0.017 0.063 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 0.059 0.2 52 -10000 0 52
DNA fragmentation during apoptosis 0.019 0.059 0.2 52 -10000 0 52
FAS/FADD/MET 0.017 0.036 -10000 0 -0.21 13 13
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 0.059 0.2 52 -10000 0 52
DFFB 0.019 0.059 0.2 52 -10000 0 52
CHUK -0.008 0.039 -10000 0 -0.6 1 1
FASLG 0.003 0.055 -10000 0 -0.36 12 12
FAS/FADD 0.014 0.029 -10000 0 -0.28 5 5
HGF -0.075 0.17 -10000 0 -0.41 110 110
LMNA 0.018 0.054 0.18 52 -10000 0 52
CASP6 0.019 0.059 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 -0.041 0.14 -10000 0 -0.41 67 67
CASP8 0.001 0.02 0.33 2 -10000 0 2
IL6 -0.006 0.2 -10000 0 -1.2 16 16
MET 0.005 0.046 -10000 0 -0.37 8 8
ICAD/CAD 0.018 0.055 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 0.059 0.2 52 -10000 0 52
BCL2 -0.028 0.12 -10000 0 -0.41 50 50
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 -0.066 0.099 -9999 0 -0.2 171 171
EGF/EGFR dimer/SHC/GRB2/SOS1 0.02 0.048 -9999 0 -0.34 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.11 0.19 -9999 0 -0.41 160 160
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.005 0.07 -9999 0 -0.34 23 23
EGF/EGFR dimer/SHC 0.007 0.057 -9999 0 -0.2 36 36
mol:GDP -0.01 0.04 -9999 0 -0.33 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.006 0.048 -9999 0 -0.41 7 7
GRB2/SOS1 0.016 0 -9999 0 -10000 0 0
HRAS/GTP -0.009 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 0.016 0.045 -9999 0 -0.32 1 1
EGF/EGFR dimer -0.002 0.068 -9999 0 -0.25 36 36
SOS1 0.011 0 -9999 0 -10000 0 0
GRB2 0.011 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.075 0.14 -9999 0 -0.28 164 164
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 -0.33 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 -0.002 0.068 -9999 0 -0.25 36 36
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 0.026 -9999 0 -0.41 2 2
FBXO8 0.011 0 -9999 0 -10000 0 0
TSHR -0.007 0.072 -9999 0 -0.34 23 23
EGF -0.005 0.07 -9999 0 -0.34 23 23
somatostatin receptor activity 0 0 -9999 0 -0.001 64 64
ARAP2 0.009 0.031 -9999 0 -0.41 3 3
mol:GDP -0.046 0.091 -9999 0 -0.22 73 73
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 52 52
ITGA2B 0.006 0.046 -9999 0 -0.4 7 7
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 -0.048 0.12 -9999 0 -0.28 115 115
PXN 0.011 0 -9999 0 -10000 0 0
ARF6/GTP -0.041 0.095 -9999 0 -0.23 61 61
EGFR/EGFR/EGF/EGF/ARFGEP100 0.007 0.058 -9999 0 -0.2 37 37
ADRB2 -0.063 0.16 -9999 0 -0.41 94 94
receptor agonist activity 0 0 -9999 0 0 75 75
actin filament binding 0 0 -9999 0 0 65 65
SRC 0.011 0 -9999 0 -10000 0 0
ITGB3 -0.067 0.16 -9999 0 -0.41 100 100
GNAQ 0.009 0.026 -9999 0 -0.41 2 2
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 59 59
ARF6/GDP 0.017 0.048 -9999 0 -0.27 5 5
ARF6/GDP/GULP/ACAP1 -0.047 0.11 -9999 0 -0.3 61 61
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.016 0.09 -9999 0 -0.2 104 104
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 -0.075 0.17 -9999 0 -0.41 110 110
CYTH3 0.009 0 -9999 0 -10000 0 0
CYTH2 0.007 0.002 -9999 0 -10000 0 0
NCK1 0.009 0.026 -9999 0 -0.41 2 2
fibronectin binding 0 0 -9999 0 0 61 61
endosomal lumen acidification 0 0 -9999 0 0 46 46
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.036 0.13 -9999 0 -0.41 60 60
GNAQ/ARNO 0.012 0.013 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 0 1 1
PIP3-E 0 0 -9999 0 0 8 8
MET 0.005 0.046 -9999 0 -0.37 8 8
GNA14 -0.032 0.13 -9999 0 -0.41 55 55
GNA15 0.006 0.039 -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 60 60
GNA11 0.002 0.062 -9999 0 -0.41 12 12
LHCGR 0.001 0.003 -9999 0 -10000 0 0
AGTR1 -0.087 0.17 -9999 0 -0.41 121 121
desensitization of G-protein coupled receptor protein signaling pathway 0.001 0.004 -9999 0 -10000 0 0
IPCEF1/ARNO 0.006 0.043 -9999 0 -0.31 1 1
alphaIIb/beta3 Integrin -0.042 0.12 -9999 0 -0.28 107 107
Visual signal transduction: Rods

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:K + 0.011 0 -9999 0 -10000 0 0
GNAT1/GTP 0.002 0.024 -9999 0 -0.23 6 6
Metarhodopsin II/Arrestin 0.006 0.015 -9999 0 -0.18 3 3
PDE6G/GNAT1/GTP -0.008 0.059 -9999 0 -0.19 52 52
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.002 0.036 -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 + -0.018 0.053 -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 -0.22 138 138
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.019 0.054 -9999 0 -0.34 6 6
CNGB1 -0.007 0.074 -9999 0 -0.33 27 27
RDH5 0.009 0.025 -9999 0 -0.33 3 3
SAG 0.005 0.005 -9999 0 -10000 0 0
mol:Ca2+ 0.011 0.06 -9999 0 -0.32 6 6
Na + (4 Units) -0.017 0.049 -9999 0 -0.31 6 6
RGS9 -0.081 0.17 -9999 0 -0.41 117 117
GNB1/GNGT1 -0.067 0.11 -9999 0 -0.22 190 190
GNAT1/GDP -0.032 0.093 -9999 0 -0.2 118 118
GUCY2D 0.001 0.05 -9999 0 -0.33 12 12
GNGT1 -0.11 0.16 -9999 0 -0.33 190 190
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 0.025 -9999 0 -0.22 6 6
SLC24A1 0.011 0 -9999 0 -10000 0 0
CNGA1 0.002 0.054 -9999 0 -0.33 14 14
Metarhodopsin II 0.004 0.015 -9999 0 -0.16 4 4
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family 0.005 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 0.063 -9999 0 -0.26 28 28
mol:Pi -0.041 0.11 -9999 0 -0.22 138 138
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.046 0.087 -9999 0 -0.16 191 191
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 47 47
RHO 0.003 0.026 -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
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.011 0 -9999 0 -10000 0 0
VLDLR 0.009 0.026 -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 -0.23 200 200
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 -0.2 194 194
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 -0.23 211 211
YWHAE 0.011 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.033 0.091 -9999 0 -0.22 18 18
MAP1B -0.013 0.055 -9999 0 -0.25 27 27
RAC1 0.018 0 -9999 0 -10000 0 0
p35/CDK5 -0.04 0.097 -9999 0 -0.3 3 3
RELN -0.14 0.2 -9999 0 -0.41 198 198
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 -0.24 8 8
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.041 0.095 -9999 0 -0.24 18 18
LIS1/IQGAP1 0.022 0 -9999 0 -10000 0 0
RHOA 0.018 0 -9999 0 -10000 0 0
PAFAH1B1 0.018 0 -9999 0 -10000 0 0
PAFAH1B3 0.005 0.044 -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 0.033 -9999 0 -0.33 5 5
NDEL1/Katanin 60 -0.033 0.091 -9999 0 -0.22 18 18
P39/CDK5 -0.058 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 -0.18 194 194
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 -0.19 80 80
RELN/VLDLR -0.057 0.11 -9999 0 -0.2 193 193
CDC42 0.018 0 -9999 0 -10000 0 0
Syndecan-4-mediated signaling events

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
PTK2 0.014 0.043 -9999 0 -0.41 5 5
Syndecan-4/Syndesmos -0.012 0.07 -9999 0 -10000 0 0
positive regulation of JNK cascade -0.12 0.11 -9999 0 -0.35 37 37
Syndecan-4/ADAM12 -0.016 0.072 -9999 0 -10000 0 0
CCL5 0.003 0.054 -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 -0.029 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 6 6
Syndecan-4/Laminin alpha1 -0.063 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 -0.018 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 -0.013 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 -0.045 0.14 -9999 0 -0.41 72 72
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 -0.019 0.076 -9999 0 -0.34 2 2
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 0.07 -9999 0 -10000 0 0
Syndecan-4/TSP1 -0.038 0.095 -9999 0 -0.37 9 9
Syndecan-4/GIPC -0.012 0.07 -9999 0 -10000 0 0
Syndecan-4/RANTES -0.016 0.075 -9999 0 -0.36 2 2
ITGB1 0.011 0 -9999 0 -10000 0 0
LAMA1 -0.1 0.16 -9999 0 -0.33 182 182
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 0.07 -9999 0 -10000 0 0
TFPI -0.038 0.14 -9999 0 -0.41 63 63
F2 -0.024 0.095 -9999 0 -0.33 47 47
alpha5/beta1 Integrin 0.016 0 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.061 0.097 -9999 0 -0.32 22 22
ACTN1 0.011 0 -9999 0 -10000 0 0
TNC 0.002 0.061 -9999 0 -0.4 12 12
Syndecan-4/CXCL12 -0.13 0.12 -9999 0 -0.38 40 40
FGF6 0 0 -9999 0 -10000 0 0
RHOA 0.011 0 -9999 0 -10000 0 0
CXCL12 -0.26 0.2 -9999 0 -0.41 341 341
TNFRSF13B -0.003 0.059 -9999 0 -0.33 17 17
FGF2 -0.22 0.21 -9999 0 -0.41 291 291
FGFR1 0.01 0.018 -9999 0 -0.41 1 1
Syndecan-4/PI-4-5-P2 -0.019 0.069 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 0.011 0.04 -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 -0.36 9 9
SDC4 -0.019 0.072 -9999 0 -10000 0 0
Syndecan-4/Tenascin C -0.016 0.076 -9999 0 -0.38 2 2
Syndecan-4/PI-4-5-P2/PKC alpha -0.031 0.034 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.012 0.07 -9999 0 -10000 0 0
MMP9 -0.13 0.17 -9999 0 -0.33 220 220
Rac1/GTP 0.013 0.052 -9999 0 -0.16 40 40
cytoskeleton organization -0.012 0.068 -9999 0 -10000 0 0
GIPC1 0.011 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.035 0.097 -9999 0 -0.37 12 12
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 35 35
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 0.055 -9999 0 -0.23 30 30
mol:ADP 0.007 0.015 -9999 0 -0.22 2 2
GNAT2 0.007 0.026 -9999 0 -0.33 3 3
RGS9-1/Gbeta5/R9AP -0.041 0.11 -9999 0 -0.22 138 138
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 -0.015 0.089 -9999 0 -0.41 26 26
Cone Metarhodopsin II/X-Arrestin 0.002 0.011 -9999 0 -0.23 1 1
mol:Ca2+ -0.002 0.05 -9999 0 -0.2 31 31
Cone PDE6 -0.031 0.092 -9999 0 -0.19 117 117
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 -0.19 117 117
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 -0.22 35 35
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 0.018 -9999 0 -0.23 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 -0.22 138 138
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 -0.081 0.17 -9999 0 -0.41 117 117
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
RXR and RAR heterodimerization with other nuclear receptor

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
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 21 21
RXRs/LXRs/DNA/Oxysterols 0.017 0.086 -10000 0 -0.45 2 2
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 -0.21 128 128
RXRs/NUR77 -0.011 0.1 -10000 0 -0.21 95 95
RXRs/PPAR -0.007 0.091 -10000 0 -0.2 93 93
NCOR2 0.011 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.003 0.036 -10000 0 -0.23 13 13
RARs/VDR/DNA/Vit D3 0.018 0.039 -10000 0 -0.18 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 -0.2 128 128
THRA 0.003 0.057 -10000 0 -0.41 10 10
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.003 0.036 -10000 0 -0.23 13 13
RXRs/PPAR/9cRA/PGJ2/DNA 0 0.084 0.28 1 -0.2 69 70
NR1H4 -0.009 0.062 -10000 0 -0.33 19 19
RXRs/LXRs/DNA 0.018 0.083 -10000 0 -0.23 20 20
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 0.082 -10000 0 -0.2 68 68
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 0.071 -10000 0 -0.19 53 53
RXRG -0.045 0.14 -10000 0 -0.4 77 77
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 -0.079 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 0.017 0.086 -10000 0 -0.45 2 2
PPARA 0.011 0 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.002 0.06 -10000 0 -0.41 11 11
RXRs/NUR77/BCL2 -0.039 0.13 -10000 0 -0.25 125 125
SREBF1 0.023 0.08 -10000 0 -0.5 1 1
RXRs/RXRs/DNA/9cRA 0.001 0.084 0.27 1 -0.2 69 70
ABCA1 0.023 0.08 -10000 0 -0.5 1 1
RARs/THRs -0.021 0.099 -10000 0 -0.41 7 7
RXRs/FXR -0.007 0.091 -10000 0 -0.22 68 68
BCL2 -0.028 0.12 -10000 0 -0.41 50 50
Coregulation of Androgen receptor activity

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
NRIP1 0.009 0.031 -9999 0 -0.41 3 3
SVIL -0.035 0.13 -9999 0 -0.41 59 59
ZNF318 0.01 0.005 -9999 0 -10000 0 0
JMJD2C -0.003 0.031 -9999 0 -0.12 35 35
T-DHT/AR/Ubc9 -0.025 0.1 -9999 0 -0.24 90 90
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 0.001 -9999 0 -10000 0 0
MAK -0.013 0.087 -9999 0 -0.33 37 37
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.007 0.041 -9999 0 -0.41 5 5
GSN 0.007 0.044 -9999 0 -0.41 6 6
NCOA2 -0.004 0.078 -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 -0.045 0.12 -9999 0 -0.25 128 128
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 0.065 -9999 0 -0.41 13 13
TGFB1I1 -0.12 0.2 -9999 0 -0.41 175 175
T-DHT/AR/CyclinD1 -0.025 0.1 -9999 0 -0.24 92 92
XRCC6 0.011 0.001 -9999 0 -10000 0 0
T-DHT/AR -0.02 0.12 -9999 0 -0.26 97 97
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 -0.33 225 225
SRF 0.016 0.011 -9999 0 -10000 0 0
NKX3-1 -0.023 0.17 -9999 0 -0.94 16 16
KLK3 -0.006 0.043 -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 -0.025 0.1 -9999 0 -0.24 90 90
AR -0.06 0.16 -9999 0 -0.42 90 90
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 -0.021 0.093 -9999 0 -0.22 90 90
RPS6KA3 0.011 0.018 -9999 0 -0.41 1 1
T-DHT/AR/ARA70 -0.024 0.1 -9999 0 -0.24 90 90
LATS2 0.009 0.026 -9999 0 -0.41 2 2
T-DHT/AR/PRX1 -0.021 0.093 -9999 0 -0.22 90 90
Cyclin D3/CDK11 p58 0.008 0 -9999 0 -10000 0 0
VAV3 -0.069 0.14 -9999 0 -0.33 127 127
KLK2 -0.065 0.19 -9999 0 -0.87 28 28
CASP8 0.011 0.001 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.022 0.11 -9999 0 -0.22 103 103
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 -0.031 0.11 -9999 0 -0.25 102 102
CMTM2 0.008 0.025 -9999 0 -0.33 3 3
SNURF -0.024 0.11 -9999 0 -0.41 41 41
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
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.038 0.12 -9999 0 -0.28 100 100
AKT1 0.021 0.15 -9999 0 -0.51 34 34
PTK2B -0.021 0.15 -9999 0 -0.55 32 32
VEGFR2 homodimer/Frs2 -0.006 0.14 -9999 0 -0.56 32 32
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 32 32
endothelial cell proliferation 0.017 0.15 -9999 0 -0.45 41 41
mol:Ca2+ -0.001 0.15 -9999 0 -0.55 32 32
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.011 0.12 -9999 0 -0.48 32 32
RP11-342D11.1 -0.008 0.15 -9999 0 -0.55 32 32
CDH5 0.006 0.048 -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 -0.034 0.11 -9999 0 -0.47 32 32
SH2D2A -0.002 0.066 -9999 0 -0.33 21 21
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.034 0.11 -9999 0 -0.46 32 32
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.002 0.14 -9999 0 -0.53 32 32
VEGFR1 homodimer 0.011 0 -9999 0 -10000 0 0
SHC/GRB2/SOS1 -0.038 0.13 -9999 0 -0.52 32 32
GRB10 -0.001 0.15 -9999 0 -0.55 32 32
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 32 32
HRAS 0.011 0 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.013 0.12 -9999 0 -0.38 32 32
HIF1A 0.011 0 -9999 0 -10000 0 0
FRS2 0.011 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.01 0.12 -9999 0 -0.48 32 32
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 32 32
mol:GDP -0.037 0.12 -9999 0 -0.5 32 32
mol:NADP 0.024 0.12 -9999 0 -0.4 32 32
eNOS/Hsp90 0.028 0.11 -9999 0 -0.38 32 32
PIK3R1 0.007 0.04 -9999 0 -0.41 5 5
mol:IP3 -0.001 0.15 -9999 0 -0.55 32 32
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 -0.009 0.16 -9999 0 -0.6 32 32
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 -0.027 0.16 -9999 0 -0.58 32 32
PTPN6 0.01 0.015 -9999 0 -0.33 1 1
EPAS1 -0.001 0.084 -9999 0 -0.32 32 32
mol:L-citrulline 0.024 0.12 -9999 0 -0.4 32 32
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 0.12 -9999 0 -0.48 32 32
VEGFR2 homodimer/VEGFA homodimer -0.008 0.16 -9999 0 -0.6 32 32
VEGFR2/3 heterodimer -0.015 0.15 -9999 0 -0.45 50 50
VEGFB 0.011 0 -9999 0 -10000 0 0
MAPK11 -0.003 0.16 -9999 0 -0.57 33 33
VEGFR2 homodimer -0.011 0.16 -9999 0 -0.65 32 32
FLT1 0.011 0 -9999 0 -10000 0 0
NEDD4 -0.02 0.11 -9999 0 -0.41 42 42
MAPK3 -0.006 0.14 -9999 0 -0.47 40 40
MAPK1 -0.006 0.14 -9999 0 -0.47 40 40
VEGFA145/NRP2 0.004 0.062 -9999 0 -0.28 25 25
VEGFR1/2 heterodimer -0.006 0.14 -9999 0 -0.56 32 32
KDR -0.011 0.16 -9999 0 -0.65 32 32
VEGFA165/NRP1/VEGFR2 homodimer -0.01 0.16 -9999 0 -0.56 34 34
SRC 0.011 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process -0.005 0.15 -9999 0 -0.48 40 40
PI3K 0.011 0.16 -9999 0 -0.57 34 34
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.004 0.13 -9999 0 -0.52 32 32
FES -0.002 0.15 -9999 0 -0.56 33 33
GAB1 -0.039 0.14 -9999 0 -0.6 32 32
VEGFR2 homodimer/VEGFA homodimer/Src 0.004 0.13 -9999 0 -0.52 32 32
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 0.013 0.13 -9999 0 -0.41 41 41
VEGFR2 homodimer/VEGFA homodimer/Yes 0.004 0.13 -9999 0 -0.52 32 32
PI3K/GAB1 0.022 0.15 -9999 0 -0.53 34 34
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.015 0.12 -9999 0 -0.47 32 32
PRKACA 0.011 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.01 0.15 -9999 0 -0.56 32 32
HSP90AA1 0.011 0 -9999 0 -10000 0 0
CDC42 -0.002 0.15 -9999 0 -0.56 32 32
actin cytoskeleton reorganization -0.002 0.14 -9999 0 -0.53 32 32
PTK2 -0.017 0.17 -9999 0 -0.64 32 32
EDG1 -0.008 0.15 -9999 0 -0.55 32 32
mol:DAG -0.001 0.15 -9999 0 -0.55 32 32
CaM/Ca2+ 0.004 0.14 -9999 0 -0.51 32 32
MAP2K3 0.004 0.14 -9999 0 -0.53 32 32
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.001 0.15 -9999 0 -0.57 32 32
PLCG1 -0.002 0.15 -9999 0 -0.56 32 32
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.011 0.12 -9999 0 -0.48 32 32
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 32 32
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.004 0.13 -9999 0 -0.52 32 32
cell migration 0.013 0.15 -9999 0 -0.53 32 32
mol:PI-3-4-5-P3 0.013 0.15 -9999 0 -0.52 34 34
FYN 0.011 0 -9999 0 -10000 0 0
VEGFB/NRP1 -0.001 0.14 -9999 0 -0.52 32 32
mol:NO 0.024 0.12 -9999 0 -0.4 32 32
PXN 0.011 0 -9999 0 -10000 0 0
HRAS/GTP -0.034 0.11 -9999 0 -0.47 32 32
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.001 0.15 -9999 0 -0.57 32 32
VHL 0.01 0.018 -9999 0 -0.41 1 1
ITGB3 -0.067 0.16 -9999 0 -0.41 100 100
NOS3 0.023 0.13 -9999 0 -0.45 32 32
VEGFR2 homodimer/VEGFA homodimer/Sck -0.028 0.15 -9999 0 -0.55 32 32
RAC1 0.011 0 -9999 0 -10000 0 0
PRKCA -0.008 0.15 -9999 0 -0.51 38 38
PRKCB -0.007 0.15 -9999 0 -0.52 35 35
VCL 0.011 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.007 0.15 -9999 0 -0.55 32 32
VEGFR1/2 heterodimer/VEGFA homodimer 0.004 0.13 -9999 0 -0.52 32 32
VEGFA165/NRP2 0.004 0.062 -9999 0 -0.28 25 25
MAPKKK cascade 0.02 0.13 -9999 0 -0.47 32 32
NRP2 -0.009 0.089 -9999 0 -0.41 25 25
VEGFC homodimer 0.004 0.054 -9999 0 -0.41 9 9
NCK1 0.009 0.026 -9999 0 -0.41 2 2
ROCK1 0.011 0 -9999 0 -10000 0 0
FAK1/Paxillin -0.009 0.16 -9999 0 -0.6 32 32
MAP3K13 -0.003 0.15 -9999 0 -0.56 32 32
PDPK1 0.02 0.14 -9999 0 -0.46 34 34
Hedgehog signaling events mediated by Gli proteins

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
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 -0.44 104 104
GNAO1 -0.1 0.18 -9999 0 -0.41 142 142
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 34 34
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 -0.013 0.078 -9999 0 -10000 0 0
GLI3 -0.037 0.12 -9999 0 -0.22 149 149
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 -0.21 157 157
SIN3B 0.011 0.001 -9999 0 -10000 0 0
SIN3A 0.011 0 -9999 0 -10000 0 0
GLI3/Su(fu) -0.004 0.087 -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 48 48
neural tube patterning -0.068 0.2 -9999 0 -0.44 104 104
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 -0.44 104 104
SUFU 0.021 0.018 -9999 0 -10000 0 0
LGALS3 0.009 0.026 -9999 0 -0.41 2 2
catabolic process -0.036 0.13 -9999 0 -0.28 76 76
GLI3A/CBP -0.044 0.13 -9999 0 -0.31 103 103
KIF3A 0.01 0.018 -9999 0 -0.41 1 1
GLI1 -0.07 0.2 -9999 0 -0.45 104 104
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 -0.001 0.069 -9999 0 -0.41 15 15
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 -0.27 34 34
PTCH1 -0.055 0.18 -9999 0 -0.45 66 66
MIM/GLI1 -0.075 0.24 -9999 0 -0.47 125 125
CREBBP -0.044 0.13 -9999 0 -0.31 103 103
Su(fu)/SIN3/HDAC complex 0.038 0.016 -9999 0 -10000 0 0
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.012 0.044 -9999 0 -0.23 18 18
EPHB2 0.009 0.025 -9999 0 -0.33 3 3
Syndecan-2/TACI 0.006 0.051 -9999 0 -0.2 29 29
LAMA1 -0.1 0.16 -9999 0 -0.33 182 182
Syndecan-2/alpha2 ITGB1 0.016 0.061 -9999 0 -0.2 37 37
HRAS 0.011 0 -9999 0 -10000 0 0
Syndecan-2/CASK 0.006 0.038 -9999 0 -0.23 13 13
ITGA5 0.011 0 -9999 0 -10000 0 0
BAX 0.024 0.041 -9999 0 -10000 0 0
EPB41 0.01 0.018 -9999 0 -0.41 1 1
positive regulation of cell-cell adhesion 0.013 0.034 -9999 0 -0.2 13 13
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 0.002 0.068 -9999 0 -0.24 38 38
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 0.04 -9999 0 -0.22 16 16
Syndecan-2/GM-CSF 0.008 0.046 -9999 0 -0.22 20 20
determination of left/right symmetry 0.009 0.045 -9999 0 -0.28 13 13
Syndecan-2/PKC delta 0.014 0.038 -9999 0 -0.23 13 13
GNB2L1 0.011 0 -9999 0 -10000 0 0
MAPK3 0.015 0.041 -9999 0 -0.21 13 13
MAPK1 0.015 0.041 -9999 0 -0.21 13 13
Syndecan-2/RACK1 0.02 0.032 -9999 0 -0.18 13 13
NF1 0.009 0.026 -9999 0 -0.41 2 2
FGFR/FGF/Syndecan-2 0.009 0.045 -9999 0 -0.28 13 13
ITGA2 0.001 0.065 -9999 0 -0.41 13 13
MAPK8 0.018 0.046 -9999 0 -0.22 19 19
Syndecan-2/alpha2/beta1 Integrin -0.035 0.089 -9999 0 -0.22 29 29
Syndecan-2/Kininogen 0.001 0.054 -9999 0 -0.19 37 37
ITGB1 0.011 0 -9999 0 -10000 0 0
SRC 0.024 0.03 -9999 0 -0.17 13 13
Syndecan-2/CASK/Protein 4.1 0.013 0.035 -9999 0 -0.2 14 14
extracellular matrix organization 0.014 0.039 -9999 0 -0.23 14 14
actin cytoskeleton reorganization 0.012 0.044 -9999 0 -0.23 18 18
Syndecan-2/Caveolin-2/Ras 0.002 0.072 -9999 0 -0.21 56 56
Syndecan-2/Laminin alpha3 0.007 0.057 -9999 0 -0.24 27 27
Syndecan-2/RasGAP 0.022 0.036 -9999 0 -0.17 18 18
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 0.04 -9999 0 -0.22 16 16
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 0.035 -9999 0 -0.16 2 2
RHOA 0.011 0 -9999 0 -10000 0 0
SDCBP 0.011 0 -9999 0 -10000 0 0
TNFRSF13B -0.003 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 0.038 -9999 0 -0.23 13 13
TGFB1 0.01 0.018 -9999 0 -0.41 1 1
CASP3 0.02 0.034 -9999 0 -0.2 13 13
FN1 0.007 0.04 -9999 0 -0.41 5 5
Syndecan-2/IL8 -0.043 0.093 -9999 0 -0.18 169 169
SDC2 0.009 0.045 -9999 0 -0.28 13 13
KNG1 -0.01 0.069 -9999 0 -0.33 24 24
Syndecan-2/Neurofibromin 0.013 0.041 -9999 0 -0.23 15 15
TRAPPC4 0.011 0 -9999 0 -10000 0 0
CSF2 0.001 0.041 -9999 0 -0.33 8 8
Syndecan-2/TGFB1 0.014 0.039 -9999 0 -0.23 14 14
Syndecan-2/Syntenin/PI-4-5-P2 0.013 0.034 -9999 0 -0.2 13 13
Syndecan-2/Ezrin 0.02 0.034 -9999 0 -0.2 13 13
PRKACA 0.019 0.037 -9999 0 -0.2 15 15
angiogenesis -0.042 0.093 -9999 0 -0.18 169 169
MMP2 -0.01 0.092 -9999 0 -0.41 27 27
IL8 -0.089 0.16 -9999 0 -0.33 157 157
calcineurin-NFAT signaling pathway 0.006 0.051 -9999 0 -0.2 29 29
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.24 170 170
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 -0.096 0.16 -10000 0 -0.35 160 160
NOTCH1 -0.004 0.046 -10000 0 -0.53 4 4
PSENEN 0.011 0 -10000 0 -10000 0 0
KREMEN2 -0.021 0.1 -10000 0 -0.33 51 51
DKK1 -0.064 0.14 -10000 0 -0.34 115 115
beta catenin/beta TrCP1 0.026 0.027 -10000 0 -10000 0 0
APH1B 0.006 0.048 -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 -0.41 165 165
JUN 0.006 0.048 -10000 0 -0.41 7 7
MAP3K7 0.01 0.002 -10000 0 -10000 0 0
CTNNB1 0.02 0.028 -10000 0 -10000 0 0
MAPK3 0.011 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.012 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 -0.004 0.17 -10000 0 -1.3 10 10
NKD1 -0.02 0.1 -10000 0 -0.34 46 46
FZD1 0.009 0.026 -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 -0.24 170 170
Delta 1/NOTCHprecursor 0.017 0.066 -10000 0 -0.64 4 4
DLL1 -0.002 0.074 -10000 0 -0.41 17 17
PPARD 0.018 0.013 -10000 0 -10000 0 0
Gamma Secretase 0.031 0.024 -10000 0 -0.18 7 7
APC 0.001 0.019 -10000 0 -0.18 4 4
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 -0.18 159 159
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 -0.016 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 0.048 -10000 0 -0.51 4 4
PPP2R5D 0.011 0.046 0.16 39 -10000 0 39
MAPK1 0.011 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.032 0.089 -10000 0 -0.21 38 38
RBPJ 0.011 0 -10000 0 -10000 0 0
CREBBP 0.012 0.026 -10000 0 -0.41 2 2
Glucocorticoid receptor regulatory network

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
PCK2 -0.01 0.04 -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 -0.72 9 9
SUMO2 0.01 0.005 -10000 0 -10000 0 0
STAT1 (dimer) 0.017 0.015 -10000 0 -0.32 1 1
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 13 -0.25 54 67
PRL -0.029 0.25 -10000 0 -1.2 20 20
cortisol/GR alpha (dimer)/TIF2 0.027 0.16 0.43 23 -0.42 8 31
RELA -0.015 0.062 -10000 0 -0.23 9 9
FGG 0.005 0.14 0.37 14 -0.48 4 18
GR beta/TIF2 -0.015 0.13 0.22 13 -0.31 66 79
IFNG -0.094 0.14 -10000 0 -0.5 12 12
apoptosis -0.078 0.19 0.47 8 -0.57 31 39
CREB1 0.008 0.022 -10000 0 -10000 0 0
histone acetylation 0.038 0.075 0.24 9 -0.24 9 18
BGLAP 0.025 0.065 -10000 0 -10000 0 0
GR/PKAc 0.005 0.093 0.21 8 -0.24 36 44
NF kappa B1 p50/RelA -0.024 0.11 -10000 0 -0.33 29 29
SMARCD1 0.012 0.003 -10000 0 -10000 0 0
MDM2 0.022 0.041 0.18 15 -10000 0 15
GATA3 0.001 0.07 -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 -0.056 0.17 0.46 7 -0.54 23 30
CSN2 0.003 0.11 0.31 13 -0.36 4 17
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 16 16
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 -0.33 395 395
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.11 0.14 0.22 15 -0.33 80 95
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.11 0.29 0.44 7 -0.81 70 77
JUN -0.041 0.1 -10000 0 -0.36 15 15
IL4 0.006 0.08 -10000 0 -0.56 1 1
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 -0.37 187 187
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.009 0.095 0.21 12 -0.23 45 57
cortisol/GR alpha (monomer) 0.029 0.18 0.49 24 -0.47 4 28
NCOA2 -0.004 0.078 -10000 0 -0.41 19 19
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.15 0.2 -10000 0 -0.44 165 165
AP-1/NFAT1-c-4 -0.16 0.18 -10000 0 -0.5 57 57
AFP -0.016 0.08 -10000 0 -10000 0 0
SUV420H1 0.011 0 -10000 0 -10000 0 0
IRF1 0.026 0.089 0.31 6 -10000 0 6
TP53 0.027 0.028 -10000 0 -0.42 2 2
PPP5C 0.011 0 -10000 0 -10000 0 0
KRT17 -0.12 0.19 -10000 0 -0.75 17 17
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 -0.5 58 58
MAPK14 0.01 0.005 -10000 0 -10000 0 0
MAPK10 -0.08 0.17 -10000 0 -0.41 115 115
MAPK11 0.008 0.026 -10000 0 -0.41 2 2
KRT5 -0.14 0.21 -10000 0 -0.71 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 0.017 0.015 -10000 0 -0.32 1 1
CGA 0.005 0.082 -10000 0 -0.38 2 2
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.009 0.098 0.27 6 -0.41 3 9
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 -0.39 11 11
NFKB1 -0.016 0.064 -10000 0 -0.25 8 8
MAPK8 -0.017 0.098 0.26 1 -0.33 15 16
MAPK9 0.01 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.085 0.2 0.47 8 -0.6 31 39
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 0.16 0.44 24 -0.46 2 26
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.033 0.14 8 -10000 0 8
SGK1 0.045 0.093 -10000 0 -1.3 2 2
IL13 -0.059 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 -0.5 9 9
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 -0.051 0.13 -10000 0 -0.44 12 12
CDK5R1/CDK5 0.014 0.013 -10000 0 -0.22 1 1
NF kappa B1 p50/RelA/PKAc -0.001 0.085 -10000 0 -0.3 12 12
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.043 0.14 0.41 24 -0.42 2 26
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 -0.34 9 9
JUN (dimer) -0.041 0.1 -10000 0 -0.36 15 15
YWHAH 0.011 0 -10000 0 -10000 0 0
VIPR1 0.012 0.089 -10000 0 -0.32 15 15
NR3C1 -0.015 0.16 0.32 13 -0.4 64 77
NR4A1 -0.023 0.12 -10000 0 -0.43 44 44
TIF2/SUV420H1 0.006 0.055 -10000 0 -0.28 19 19
MAPKKK cascade -0.078 0.19 0.47 8 -0.57 31 39
cortisol/GR alpha (dimer)/Src-1 0.04 0.15 0.43 24 -0.42 3 27
PBX1 -0.009 0.095 -10000 0 -0.34 37 37
POU1F1 -0.003 0.049 -10000 0 -0.25 19 19
SELE -0.098 0.32 -10000 0 -0.93 64 64
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 0.41 24 -0.42 2 26
mol:cortisol 0.024 0.076 0.28 21 -10000 0 21
MMP1 -0.12 0.11 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.008 0.045 -9999 0 -0.24 15 15
NFATC2 -0.01 0.078 -9999 0 -0.24 53 53
NFATC3 0.015 0.018 -9999 0 -10000 0 0
CD40LG -0.055 0.18 -9999 0 -0.51 39 39
PTGS2 -0.074 0.21 -9999 0 -0.49 74 74
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 -0.014 0.089 -9999 0 -0.33 40 40
CREM 0.011 0.001 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.036 0.081 -9999 0 -0.33 19 19
FOS -0.12 0.19 -9999 0 -0.41 165 165
IFNG -0.066 0.19 -9999 0 -0.48 56 56
AP-1/NFAT1-c-4 -0.062 0.2 -9999 0 -0.53 43 43
FASLG -0.054 0.18 -9999 0 -0.52 36 36
NFAT1-c-4/ICER1 -0.01 0.081 -9999 0 -0.27 23 23
IL2RA -0.055 0.18 -9999 0 -0.51 40 40
FKBP12/FK506 0.008 0 -9999 0 -10000 0 0
CSF2 -0.055 0.17 -9999 0 -0.49 37 37
JunB/Fra1/NFAT1-c-4 -0.022 0.084 -9999 0 -0.28 23 23
IL4 -0.055 0.17 -9999 0 -0.5 32 32
IL2 -0.009 0.031 -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
TCGA08_rtk_signaling

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
PDGFRA -0.1 0.19 -10000 0 -0.41 147 147
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 -0.28 108 108
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 -0.41 202 202
FOXO4 0.009 0.026 -10000 0 -0.41 2 2
MET 0.005 0.046 -10000 0 -0.37 8 8
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 0.026 -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
IL2 signaling events mediated by STAT5

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
GAB2 0.009 0.036 -9999 0 -0.41 4 4
ELF1 0.009 0.046 -9999 0 -0.38 5 5
CCNA2 -0.061 0.14 -9999 0 -0.33 114 114
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 0.026 -9999 0 -0.41 2 2
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.053 0.045 -9999 0 -0.51 1 1
SHC1 0.012 0 -9999 0 -10000 0 0
SP1 -0.043 0.12 -9999 0 -0.3 101 101
IL2RA 0.013 0.06 -9999 0 -0.65 1 1
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 -0.64 102 102
PTPN11 0.012 0 -9999 0 -10000 0 0
CCND2 -0.1 0.26 -9999 0 -0.65 101 101
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 0.065 -9999 0 -0.41 13 13
CCND3 0.056 0.041 -9999 0 -0.43 1 1
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.015 0.085 -10000 0 -0.29 31 31
IKBKB 0.027 0.048 0.16 1 -0.17 2 3
AKT1 0.004 0.066 0.19 4 -0.2 28 32
IKBKG 0.029 0.049 -10000 0 -0.18 1 1
CALM1 0.02 0.079 0.18 4 -0.25 20 24
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 65 -0.27 20 85
DOK1 0.011 0 -10000 0 -10000 0 0
AP-1 -0.001 0.077 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 82 82
CD22 -0.06 0.13 -10000 0 -0.5 32 32
CAMK2G 0.025 0.075 0.18 3 -0.23 20 23
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 65 -0.27 20 85
SYK 0.01 0.015 -10000 0 -0.33 1 1
ELK1 0.02 0.079 0.18 4 -0.25 20 24
NFATC1 0.004 0.1 0.18 3 -0.32 35 38
B-cell antigen/BCR complex -0.023 0.096 -10000 0 -0.24 82 82
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 0.074 -10000 0 -0.2 35 35
mol:GDP 0.014 0.079 0.18 6 -0.25 21 27
PTEN 0.006 0.044 -10000 0 -0.41 6 6
CD79B -0.009 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 0.008 0.12 -10000 0 -0.43 30 30
PIK3R1 0.007 0.04 -10000 0 -0.41 5 5
mol:IP3 0.015 0.083 0.18 65 -0.27 20 85
CSK 0.011 0 -10000 0 -10000 0 0
FOS -0.031 0.12 0.21 1 -0.25 44 45
CHUK 0.029 0.049 0.16 1 -0.18 3 4
IBTK 0.011 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.013 0.047 -10000 0 -0.3 5 5
PTPN6 -0.033 0.14 -10000 0 -0.48 31 31
RELA 0.011 0 -10000 0 -10000 0 0
BCL2A1 0.019 0.016 -10000 0 -10000 0 0
VAV2 -0.009 0.12 -10000 0 -0.44 27 27
ubiquitin-dependent protein catabolic process 0.022 0.021 0.085 1 -0.12 1 2
BTK -0.005 0.065 -10000 0 -1.1 2 2
CD19 -0.04 0.11 -10000 0 -0.33 52 52
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 -0.049 0.15 -10000 0 -0.41 77 77
PIK3AP1 0.021 0.092 0.2 62 -0.3 20 82
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 0.19 1 -0.31 3 4
RasGAP/p62DOK/SHIP -0.024 0.058 -10000 0 -0.3 5 5
CD79A -0.027 0.11 -10000 0 -0.34 59 59
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 0.033 0.061 0.18 1 -0.26 3 4
MAPK1 0.033 0.061 0.18 1 -0.26 3 4
CD72/SHP1 -0.026 0.13 -10000 0 -0.45 31 31
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 -0.38 26 26
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 0.094 -10000 0 -0.36 32 32
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.019 0.094 0.2 64 -0.31 20 84
SOS1 0.011 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.024 0.17 -10000 0 -0.64 34 34
DAPP1 -0.049 0.18 -10000 0 -0.72 34 34
cytokine secretion 0.005 0.097 0.18 3 -0.3 35 38
mol:DAG 0.015 0.083 0.18 65 -0.27 20 85
PLCG2 0.01 0.023 -10000 0 -0.37 2 2
MAP2K1 0.029 0.065 0.19 1 -0.29 3 4
B-cell antigen/BCR complex/FcgammaRIIB -0.013 0.084 -10000 0 -0.2 84 84
mol:PI-3-4-5-P3 -0.034 0.073 0.21 5 -0.26 32 37
ETS1 0.029 0.072 0.2 1 -0.3 3 4
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.003 0.071 -10000 0 -0.2 30 30
B-cell antigen/BCR complex/LYN -0.033 0.1 -10000 0 -0.45 28 28
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 -0.41 26 26
B-cell antigen/BCR complex/LYN/SYK -0.054 0.12 -10000 0 -0.46 30 30
CARD11 0.016 0.084 0.17 63 -0.26 21 84
FCGR2B 0.008 0.035 -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 0.019 0.024 0.11 1 -10000 0 1
PTPRC 0.003 0.059 -10000 0 -0.4 11 11
PDPK1 -0.001 0.062 0.17 4 -0.18 29 33
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
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.074 0.11 -9999 0 -0.36 37 37
TC10/GTP -0.054 0.075 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 0.001 0.069 -9999 0 -0.21 53 53
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 -0.33 195 195
FOXO3 -0.01 0.037 -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 -0.41 183 183
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 -0.23 125 125
CBL/APS/CAP/Crk-II/C3G -0.039 0.1 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/NCK2 0.001 0.069 -9999 0 -0.21 53 53
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.019 0.057 -9999 0 -0.18 49 49
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.013 0.054 -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 0.064 -9999 0 -0.19 53 53
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 -0.019 0.058 -9999 0 -0.18 49 49
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 54 54
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 0.026 -9999 0 -0.41 2 2
CBL/APS/CAP/Crk-II -0.049 0.11 -9999 0 -0.2 183 183
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 54 54
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 -0.03 0.12 -9999 0 -0.41 53 53
p62DOK/RasGAP -0.002 0.028 -9999 0 -0.39 2 2
INS 0.003 0.002 -9999 0 -10000 0 0
mol:PI-3-4-P2 0 0.064 -9999 0 -0.19 54 54
GRB2 0.011 0 -9999 0 -10000 0 0
EIF4EBP1 -0.027 0.09 -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 0.064 -9999 0 -0.19 46 46
Insulin Receptor/Insulin/IRS1 -0.006 0.069 -9999 0 -0.21 53 53
Insulin Receptor/Insulin/IRS3 0.012 0.002 -9999 0 -10000 0 0
Par3/Par6 0.013 0.051 -9999 0 -0.18 32 32
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.018 0.001 -9999 0 -10000 0 0
SMARCC1 0.006 0.016 -9999 0 -10000 0 0
REL 0.011 0.001 -9999 0 -10000 0 0
HDAC7 0.02 0.066 -9999 0 -0.28 3 3
JUN 0.006 0.048 -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 0.079 -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 -0.032 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 0.078 -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 0.012 0.11 -9999 0 -0.37 19 19
NR0B1 -0.014 0.076 -9999 0 -0.33 29 29
EGR1 -0.044 0.14 -9999 0 -0.41 70 70
RXRs/9cRA -0.01 0.077 -9999 0 -0.2 69 69
AR/RACK1/Src 0.009 0.069 -9999 0 -0.29 5 5
AR/GR -0.047 0.12 -9999 0 -0.25 103 103
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 0.061 -9999 0 -0.28 2 2
NR3C1 -0.051 0.15 -9999 0 -0.41 79 79
KLK3 -0.048 0.091 -9999 0 -0.41 8 8
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 -0.048 0.14 -9999 0 -0.4 77 77
mol:9cRA 0 0 -9999 0 -10000 0 0
RXRA 0.011 0 -9999 0 -10000 0 0
RXRB 0.011 0 -9999 0 -10000 0 0
CARM1 0.011 0.002 -9999 0 -10000 0 0
NR2C2 0.002 0.059 -9999 0 -0.41 11 11
KLK2 -0.011 0.16 -9999 0 -0.56 33 33
AR -0.022 0.098 -9999 0 -0.22 90 90
SENP1 0.011 0 -9999 0 -10000 0 0
HSP90AA1 0.011 0 -9999 0 -10000 0 0
MDM2 0.011 0.002 -9999 0 -10000 0 0
SRY 0 0.002 -9999 0 -10000 0 0
GATA2 -0.029 0.12 -9999 0 -0.41 51 51
MYST2 0.011 0 -9999 0 -10000 0 0
HOXB13 -0.22 0.16 -9999 0 -0.33 360 360
T-DHT/AR/RACK1/Src 0.009 0.065 -9999 0 -0.31 3 3
positive regulation of transcription -0.029 0.12 -9999 0 -0.41 51 51
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 -0.34 186 186
T-DHT/AR/TIF2 0.011 0.073 -9999 0 -0.29 16 16
T-DHT/AR/Hsp90 0.004 0.063 -9999 0 -0.36 2 2
GSK3B 0.012 0.002 -9999 0 -10000 0 0
NR2C1 0.011 0 -9999 0 -10000 0 0
mol:T-DHT 0.006 0.065 -9999 0 -0.22 7 7
SIRT1 0.009 0.026 -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 -0.008 0.072 -9999 0 -0.31 5 5
CREBBP 0.009 0.026 -9999 0 -0.41 2 2
SMARCE1 0.011 0.001 -9999 0 -10000 0 0
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.033 0.13 -10000 0 -0.5 6 6
CRP 0.027 0.13 -10000 0 -0.51 7 7
cell cycle arrest 0.027 0.14 -10000 0 -0.53 10 10
TIMP1 0.029 0.12 -10000 0 -0.48 9 9
IL6ST -0.048 0.15 -10000 0 -0.41 81 81
Rac1/GDP 0 0.12 -10000 0 -0.35 36 36
AP1 -0.021 0.12 -10000 0 -0.52 10 10
GAB2 0.009 0.036 -10000 0 -0.41 4 4
TNFSF11 0.014 0.14 -10000 0 -0.53 6 6
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 -0.031 0.14 -10000 0 -0.38 44 44
mol:GTP 0 0.001 -10000 0 -10000 0 0
MAP2K4 0.016 0.12 -10000 0 -0.38 20 20
MITF -0.03 0.15 -10000 0 -0.39 55 55
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 0.013 0.085 -10000 0 -0.57 6 6
STAT3 0.029 0.14 -10000 0 -0.56 10 10
STAT1 0.002 0.014 -10000 0 -10000 0 0
CEBPD 0.032 0.13 -10000 0 -0.6 6 6
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 0.048 -10000 0 -0.41 7 7
PIAS3/MITF -0.023 0.14 -10000 0 -0.37 55 55
MAPK11 -0.026 0.13 -10000 0 -0.38 39 39
STAT3 (dimer)/FOXO1 0.062 0.13 -10000 0 -0.46 7 7
GRB2/SOS1/GAB family -0.042 0.1 0.14 1 -0.36 33 34
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.019 0.13 -10000 0 -0.37 41 41
GRB2 0.012 0.001 -10000 0 -10000 0 0
JAK2 0.004 0.054 -10000 0 -0.41 9 9
LBP 0.019 0.12 -10000 0 -0.52 2 2
PIK3R1 0.008 0.04 -10000 0 -0.41 5 5
JAK1 0.012 0.026 -10000 0 -0.4 2 2
MYC 0.022 0.18 -10000 0 -0.86 13 13
FGG 0.026 0.13 -10000 0 -0.55 4 4
macrophage differentiation 0.027 0.14 -10000 0 -0.53 10 10
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.04 0.12 -10000 0 -0.38 36 36
JUNB 0.026 0.15 -10000 0 -0.76 8 8
FOS -0.12 0.19 -10000 0 -0.41 165 165
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.017 0.13 -10000 0 -0.39 38 38
STAT1/PIAS1 0.002 0.12 -10000 0 -0.33 35 35
GRB2/SOS1/GAB family/SHP2/PI3K 0.033 0.041 -10000 0 -0.3 5 5
STAT3 (dimer) 0.029 0.14 -10000 0 -0.55 10 10
PRKCD 0.03 0.12 -10000 0 -0.44 11 11
IL6R -0.023 0.12 -10000 0 -0.41 46 46
SOCS3 -0.026 0.14 -10000 0 -0.61 11 11
gp130 (dimer)/JAK1/JAK1/LMO4 -0.006 0.092 -10000 0 -0.22 83 83
Rac1/GTP 0.003 0.12 -10000 0 -0.35 36 36
HCK 0.006 0.039 -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 -0.51 6 6
IRF1 0.033 0.12 -10000 0 -0.5 6 6
mol:GDP -0.009 0.13 -10000 0 -0.37 37 37
SOS1 0.011 0.001 -10000 0 -10000 0 0
VAV1 -0.009 0.13 -10000 0 -0.38 37 37
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.038 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 -0.009 0.09 -10000 0 -0.22 81 81
gp130 (dimer)/JAK2/JAK2/LMO4 -0.013 0.096 -10000 0 -0.23 88 88
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 -0.028 0.13 -10000 0 -0.32 58 58
LMO4 0.015 0.005 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 0.019 0.13 -10000 0 -0.54 10 10
MCL1 0.046 0.036 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.16 0.2 -9999 0 -0.41 214 214
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 -0.17 1 1
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 -0.33 225 225
ARNT/IPAS -0.1 0.14 -9999 0 -0.28 214 214
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
Retinoic acid receptors-mediated signaling

Figure S71.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S71.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.011 0.06 0.19 20 -0.24 12 32
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 0.016 0.056 -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 -0.2 47 47
NCOR2 0.011 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.003 0.036 -10000 0 -0.23 13 13
RXRs/RARs/NRIP1/9cRA -0.003 0.13 -10000 0 -0.4 45 45
NCOA2 -0.004 0.078 -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 -0.012 0.12 -10000 0 -0.38 44 44
RARA -0.005 0.073 -10000 0 -0.22 47 47
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.01 0.071 -10000 0 -0.22 36 36
PRKCA -0.015 0.11 -10000 0 -0.41 36 36
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.012 0.14 -10000 0 -0.42 45 45
RXRG -0.052 0.13 -10000 0 -0.3 104 104
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 -0.23 13 13
RBP1 -0.006 0.083 -10000 0 -0.41 22 22
CRBP1/9-cic-RA -0.004 0.059 -10000 0 -0.29 22 22
RARB 0.004 0.06 -10000 0 -0.41 11 11
PRKCG -0.035 0.12 -10000 0 -0.34 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 -0.33 45 45
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.069 -10000 0 -0.26 15 15
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.012 0.14 -10000 0 -0.42 45 45
positive regulation of DNA binding -0.02 0.062 -10000 0 -0.22 39 39
NRIP1 -0.013 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 0.026 -10000 0 -0.41 2 2
RAR gamma2/9cRA 0 0 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.25 65 68
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 83 83
muscle cell differentiation 0.044 0.098 0.35 25 -10000 0 25
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 0.016 0.044 -10000 0 -0.2 18 18
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 -0.47 12 12
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.045 0.02 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.011 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 -0.079 0.15 -10000 0 -0.34 132 132
SMAD3/SMAD4/GR -0.037 0.097 -10000 0 -0.25 82 82
GATA3 -0.004 0.072 -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 -0.41 85 85
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 0.057 -10000 0 -0.34 15 15
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 -0.25 46 46
DCP1A 0.011 0 -10000 0 -10000 0 0
SKI 0.011 0 -10000 0 -10000 0 0
SERPINE1 0.015 0.12 -10000 0 -1.3 4 4
SMAD3/SMAD4/ATF2 0.011 0.048 -10000 0 -0.3 7 7
SMAD3/SMAD4/ATF3 -0.01 0.09 -10000 0 -0.27 52 52
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 -0.48 11 11
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 16 -10000 0 16
DLX1 -0.031 0.11 -10000 0 -0.33 61 61
TCF3 0.011 0 -10000 0 -10000 0 0
FOS -0.11 0.2 -10000 0 -0.41 165 165
SMAD3/SMAD4/Max 0.001 0.036 -10000 0 -0.27 4 4
Cbp/p300/SNIP1 0.023 0.016 -10000 0 -0.22 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 -0.27 4 4
IRF7 0.004 0.051 -10000 0 -0.35 10 10
ESR1 -0.038 0.13 -10000 0 -0.41 61 61
HNF4A -0.04 0.12 -10000 0 -0.33 78 78
MEF2C -0.073 0.18 -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 0.02 -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 0.047 -10000 0 -0.44 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 0.078 -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 0.044 0.049 -10000 0 -0.25 2 2
IFNB1 0.013 0.063 -10000 0 -0.31 13 13
SMAD3/SMAD4/MEF2C -0.065 0.17 -10000 0 -0.44 69 69
CITED1 -0.002 0.067 -10000 0 -0.34 20 20
SMAD2-3/SMAD4/ARC105 0.024 0.044 -10000 0 -0.28 2 2
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 0.008 0.092 -10000 0 -0.28 37 37
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 -0.32 4 4
CDK4 0.012 0.003 -10000 0 -10000 0 0
PIAS4 0.01 0.003 -10000 0 -10000 0 0
ATF3 -0.027 0.12 -10000 0 -0.41 48 48
SMAD3/SMAD4/SP1 0.033 0.048 -10000 0 -0.25 5 5
FOXG1 -0.16 0.17 -10000 0 -0.33 259 259
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 -0.011 0.081 -10000 0 -0.24 37 37
MYOD1 -0.029 0.1 -10000 0 -0.33 53 53
SMAD3/SMAD4/HNF4 -0.017 0.08 -10000 0 -0.23 30 30
SMAD3/SMAD4/GATA3 0 0.071 -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 -0.24 2 2
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 -0.34 65 65
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 -0.031 0.11 -10000 0 -0.25 92 92
AR -0.059 0.16 -10000 0 -0.41 90 90
negative regulation of cell growth 0.018 0.061 -10000 0 -0.3 5 5
SMAD3/SMAD4/MYOD -0.01 0.07 -10000 0 -0.22 25 25
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 -0.47 12 12
SMAD3/SMAD4/RUNX2 0.007 0.059 -10000 0 -0.27 16 16
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
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.006 0.083 -10000 0 -0.41 22 22
Jak2/Leptin Receptor -0.097 0.14 -10000 0 -0.36 79 79
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 0.049 -10000 0 -0.24 18 18
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 27 27
Insulin Receptor/Insulin -0.008 0.022 -10000 0 -10000 0 0
HCK 0.007 0.039 -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 -0.004 0.07 -10000 0 -0.33 23 23
YES1 0.011 0 -10000 0 -10000 0 0
CAV1 -0.002 0.077 -10000 0 -0.29 14 14
TXN 0.011 0.002 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.005 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 -0.072 0.17 -10000 0 -0.41 106 106
ITGA2B 0.005 0.047 -10000 0 -0.4 7 7
CSF1R 0.008 0.035 -10000 0 -0.39 4 4
Prolactin Receptor/Prolactin -0.057 0.13 -10000 0 -0.29 123 123
FGR 0.002 0.062 -10000 0 -0.41 12 12
PTP1B/p130 Cas 0.018 0.041 -10000 0 -0.22 5 5
Crk/p130 Cas 0.024 0.04 -10000 0 -0.2 5 5
DOK1 0.015 0.06 -10000 0 -0.24 15 15
JAK2 -0.037 0.12 -10000 0 -0.32 50 50
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 80 80
SRC 0.019 0.019 -10000 0 -10000 0 0
ITGB3 -0.067 0.16 -10000 0 -0.41 100 100
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 -0.036 0.12 -10000 0 -0.32 50 50
FCGR2A 0.01 0.015 -10000 0 -0.33 1 1
FER 0.011 0.002 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.043 0.12 -10000 0 -0.28 107 107
BLK -0.015 0.087 -10000 0 -0.33 38 38
Insulin Receptor/Insulin/Shc 0.016 0.002 -10000 0 -10000 0 0
RHOA 0.012 0.001 -10000 0 -10000 0 0
LEPR -0.12 0.19 -10000 0 -0.41 162 162
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 0.045 -10000 0 -0.41 6 6
Insulin Receptor/Insulin/IRS1 -0.009 0.075 -10000 0 -0.24 53 53
CSF1/CSF1R 0.019 0.057 -10000 0 -0.26 12 12
Ras protein signal transduction 0.007 0.014 -10000 0 -10000 0 0
IRS1 -0.03 0.12 -10000 0 -0.41 53 53
INS 0.001 0.003 -10000 0 -10000 0 0
LEP 0.005 0.026 -10000 0 -0.33 3 3
STAT5B -0.003 0.065 -10000 0 -0.23 19 19
STAT5A -0.003 0.064 -10000 0 -0.23 18 18
GRB2 0.011 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.01 0.063 -10000 0 -0.26 17 17
CSN2 -0.03 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 -0.35 5 5
SHC1 0.011 0 -10000 0 -10000 0 0
NOX4 0.007 0.039 -10000 0 -0.4 5 5
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.006 0.083 -9999 0 -0.41 22 22
alphaV beta3 Integrin -0.038 0.12 -9999 0 -0.28 100 100
PTK2 -0.037 0.086 -9999 0 -0.38 23 23
positive regulation of JNK cascade -0.014 0.058 -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 -0.34 23 23
nectin-3/I-afadin 0.004 0.06 -9999 0 -0.28 23 23
RAPGEF1 0.012 0.095 -9999 0 -0.41 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 -0.006 0.083 -9999 0 -0.41 22 22
TLN1 0.002 0.076 -9999 0 -0.26 34 34
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 -0.21 45 45
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 0.026 -9999 0 -0.41 2 2
CLDN1 -0.044 0.14 -9999 0 -0.41 70 70
JAM-A/CLDN1 -0.011 0.091 -9999 0 -0.21 89 89
SRC -0.001 0.12 -9999 0 -0.52 23 23
ITGB3 -0.067 0.16 -9999 0 -0.41 100 100
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 0.058 -9999 0 -0.28 23 23
alphaV/beta3 Integrin/Talin -0.022 0.11 -9999 0 -0.31 40 40
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 -0.23 56 56
VAV2 0.009 0.1 -9999 0 -0.46 23 23
RAP1/GDP -0.016 0.071 -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 56 56
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
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 0.012 0.02 0.18 1 -10000 0 1
AES 0.012 0.017 0.16 1 -10000 0 1
FBXW11 0.011 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.015 0.018 -10000 0 -0.28 2 2
SMAD4 0.01 0.018 -10000 0 -0.41 1 1
DKK2 -0.016 0.1 -10000 0 -0.4 34 34
TLE1 0.011 0.025 0.16 1 -0.41 1 2
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 -0.35 160 160
beta catenin/RanBP3 0.02 0.093 0.36 35 -10000 0 35
KREMEN2 -0.021 0.1 -10000 0 -0.33 51 51
DKK1 -0.064 0.14 -10000 0 -0.34 115 115
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 -0.053 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 -0.32 5 6
Axin1/APC/GSK3 0.018 0.031 0.17 4 -10000 0 4
Axin1/APC/GSK3/beta catenin/Macf1 0.044 0.026 -10000 0 -10000 0 0
HNF1A 0.006 0.045 0.16 1 -0.34 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 -0.012 0.083 -10000 0 -0.2 80 80
NKD1 -0.02 0.1 -10000 0 -0.34 46 46
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 10 10
DKK1/LRP6/Kremen 2 -0.039 0.096 -10000 0 -0.18 159 159
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 0.058 -10000 0 -0.44 2 2
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 0.046 0.17 46 -10000 0 46
APC 0.028 0.024 -10000 0 -0.18 1 1
WNT1/LRP6/FZD1 0.038 0.058 0.2 33 -0.2 2 35
CREBBP 0.01 0.03 0.16 1 -0.39 2 3
Regulation of p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
RIP1/MEKK3 0.015 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 -0.033 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 -0.007 0.068 -9999 0 -0.17 76 76
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.011 0 -9999 0 -10000 0 0
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.011 0 -9999 0 -10000 0 0
FYN 0.011 0 -9999 0 -10000 0 0
MAP3K12 0.008 0.036 -9999 0 -0.41 4 4
FGR 0.002 0.062 -9999 0 -0.41 12 12
p38 alpha/TAB1 -0.003 0.016 -9999 0 -0.21 1 1
PRKG1 -0.18 0.21 -9999 0 -0.41 238 238
DUSP8 0.007 0.04 -9999 0 -0.41 5 5
PGK/cGMP/p38 alpha -0.067 0.076 -9999 0 -0.18 77 77
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 -0.091 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 -0.19 1 1
BLK -0.015 0.087 -9999 0 -0.33 38 38
HCK 0.007 0.039 -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 -0.35 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 -0.29 238 238
PAK2 0.011 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 0.018 0.074 -9999 0 -0.25 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 -0.052 0.14 -9999 0 -0.41 76 76
Rapid glucocorticoid signaling

Figure S77.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S77.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.034 -10000 0 -0.23 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 79 79
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 0.06 79 -10000 0 79
GNAL -0.051 0.15 -10000 0 -0.41 79 79
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 0.031 -10000 0 -0.28 6 6
MAPK11 0.006 0.018 -10000 0 -0.28 2 2
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 0.01 0.021 -9999 0 -0.33 2 2
GNAI2 0.011 0 -9999 0 -10000 0 0
mol:S1P 0.018 0.005 -9999 0 -10000 0 0
GNAO1 -0.1 0.18 -9999 0 -0.41 142 142
mol:Sphinganine-1-P 0.017 0.014 -9999 0 -0.22 2 2
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 0.078 -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 0.003 -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 -0.008 0.11 -9999 0 -0.27 59 59
S1P/S1P4/Gi -0.032 0.11 -9999 0 -0.2 154 154
GNAQ 0.009 0.026 -9999 0 -0.41 2 2
GNAZ -0.001 0.069 -9999 0 -0.41 15 15
GNA14 -0.032 0.13 -9999 0 -0.41 55 55
GNA15 0.007 0.039 -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
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.026 -10000 0 -0.41 2 2
BRCA1 0.011 0 -10000 0 -10000 0 0
CCNE1 -0.13 0.17 -10000 0 -0.33 217 217
CDK2/Cyclin E1 -0.078 0.12 -10000 0 -0.22 217 217
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 -0.071 0.15 -10000 0 -0.33 129 129
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 -0.18 11 11
BRCA1/BACH1/BARD1/TopBP1 0.017 0.035 -10000 0 -0.23 11 11
BRCA1/BARD1/P53 0.023 0.034 -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 -10000 0 0
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 -0.09 0.16 -10000 0 -0.33 160 160
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
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.018 0.01 -9999 0 -0.22 1 1
BAD/BCL-XL/YWHAZ 0.027 0.008 -9999 0 -10000 0 0
CDKN1B 0.021 0.041 -9999 0 -0.22 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 -0.28 202 202
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 0.026 -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 0.026 0.039 -9999 0 -10000 0 0
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 -0.085 0.11 -9999 0 -0.2 263 263
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 -0.085 0.11 -9999 0 -0.2 263 263
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 -0.33 395 395
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 0.026 -9999 0 -0.41 2 2
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.021 0.021 -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 0.021 -9999 0 -0.17 6 6
MAPK12 -0.01 0.073 -9999 0 -0.21 27 27
CCND1 0.003 0.033 -9999 0 -0.14 1 1
p38 gamma/SNTA1 -0.003 0.068 -9999 0 -0.19 27 27
MAP2K3 0.011 0 -9999 0 -10000 0 0
PKN1 0.011 0 -9999 0 -10000 0 0
G2/M transition checkpoint -0.01 0.073 -9999 0 -0.21 27 27
MAP2K6 -0.017 0.08 -9999 0 -0.19 94 94
MAPT 0.002 0.062 -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
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 -0.4 12 12
RAD9A 0.011 0 -9999 0 -10000 0 0
AP1 -0.081 0.14 -9999 0 -0.29 166 166
IFNAR2 0.007 0.019 -9999 0 -0.41 1 1
AKT1 -0.012 0.058 -9999 0 -0.18 24 24
ER alpha/Oestrogen -0.027 0.093 -9999 0 -0.29 61 61
NFX1/SIN3/HDAC complex 0.032 0.016 -9999 0 -10000 0 0
EGF -0.005 0.07 -9999 0 -0.34 23 23
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 -0.41 9 9
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 -0.41 397 397
WRN 0.011 0 -9999 0 -10000 0 0
SP1 0.009 0.007 -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 0.091 -9999 0 -0.37 5 5
Mad/Max 0.012 0.009 -9999 0 -10000 0 0
TERT -0.13 0.12 -9999 0 -0.43 8 8
CCND1 -0.11 0.11 -9999 0 -0.44 3 3
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 -0.016 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 -0.41 165 165
IFN-gamma/IRF1 -0.02 0.086 -9999 0 -0.22 82 82
PARP2 0.011 0 -9999 0 -10000 0 0
BLM -0.027 0.11 -9999 0 -0.33 60 60
Telomerase -0.012 0.036 -9999 0 -10000 0 0
IRF1 0.007 0.033 -9999 0 -10000 0 0
ESR1 -0.037 0.13 -9999 0 -0.41 61 61
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 0.026 -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 -0.38 5 5
NR2F2 -0.008 0.091 -9999 0 -0.41 26 26
MAPK3 0.003 0.042 -9999 0 -0.22 18 18
MAPK1 0.003 0.042 -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 -0.4 14 14
mol:Oestrogen -0.001 0.001 -9999 0 -10000 0 0
EGF/EGFR -0.006 0.067 -9999 0 -0.25 36 36
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 -0.008 0.067 -9999 0 -0.2 60 60
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.11 0.11 -9999 0 -0.39 7 7
SP1/HDAC2 0.014 0.01 -9999 0 -10000 0 0
PINX1 0.011 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.1 0.091 -9999 0 -0.37 5 5
Smad3/Myc 0.015 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 -0.32 59 59
Telomerase/PinX1 -0.1 0.091 -9999 0 -0.37 5 5
Telomerase/AKT1/mTOR/p70S6K -0.014 0.041 -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 0.091 -9999 0 -0.36 6 6
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 0.091 -9999 0 -0.36 6 6
E2F1 -0.056 0.13 -9999 0 -0.33 101 101
ZNFX1 0.011 0.001 -9999 0 -10000 0 0
PIF1 -0.075 0.15 -9999 0 -0.33 136 136
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 -1 18 18
B2M 0.012 0.005 -10000 0 -10000 0 0
TYK2 0.014 0.016 -10000 0 -10000 0 0
IL12RB1 0.002 0.072 -10000 0 -0.37 18 18
GADD45B 0.038 0.17 -10000 0 -0.71 11 11
IL12RB2 -0.005 0.081 -10000 0 -0.33 30 30
GADD45G 0.016 0.25 -10000 0 -0.97 23 23
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 0.045 -10000 0 -0.33 9 9
IL2RA -0.003 0.067 -10000 0 -0.33 21 21
IFNG -0.029 0.11 -10000 0 -0.33 59 59
STAT3 (dimer) 0.028 0.18 -10000 0 -0.65 19 19
HLA-DRB5 -0.005 0.067 -10000 0 -0.38 16 16
FASLG 0.009 0.23 -10000 0 -1 14 14
NF kappa B2 p52/RelB -0.063 0.17 -10000 0 -0.74 21 21
CD4 0.006 0.017 -10000 0 -0.35 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 0.073 -10000 0 -0.24 39 39
CCL3 0.013 0.22 -10000 0 -0.92 13 13
CCL4 0.01 0.24 -10000 0 -0.97 16 16
HLA-A 0.011 0.015 -10000 0 -0.33 1 1
IL18/IL18R 0.042 0.054 -10000 0 -0.22 16 16
NOS2 0.019 0.23 -10000 0 -0.98 16 16
IL12/IL12R/TYK2/JAK2/SPHK2 0.023 0.073 -10000 0 -0.3 8 8
IL1R1 0.004 0.25 -10000 0 -1.1 18 18
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 -0.002 0.12 -10000 0 -0.56 18 18
RAB7A 0.044 0.18 -10000 0 -0.64 14 14
lysosomal transport 0.045 0.17 -10000 0 -0.6 14 14
FOS -0.3 0.56 -10000 0 -1.1 168 168
STAT4 (dimer) 0.041 0.2 -10000 0 -0.67 19 19
STAT5A (dimer) -0.073 0.18 -10000 0 -0.73 25 25
GZMA -0.003 0.26 -10000 0 -1.1 20 20
GZMB 0.003 0.23 -10000 0 -0.99 14 14
HLX 0.011 0 -10000 0 -10000 0 0
LCK 0.02 0.23 -10000 0 -0.82 21 21
TCR/CD3/MHC II/CD4 -0.042 0.12 -10000 0 -0.2 164 164
IL2/IL2R 0.008 0.062 -10000 0 -0.3 14 14
MAPK14 0.036 0.2 -10000 0 -0.68 23 23
CCR5 0.03 0.2 -10000 0 -0.94 11 11
IL1B 0.011 0.042 -10000 0 -0.44 4 4
STAT6 0.024 0.077 -10000 0 -0.35 3 3
STAT4 0.01 0.018 -10000 0 -0.41 1 1
STAT3 0.011 0 -10000 0 -10000 0 0
STAT1 0.01 0.015 -10000 0 -0.33 1 1
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 0.001 0.067 -10000 0 -0.39 15 15
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 0.041 0.19 -10000 0 -0.62 19 19
IL2RG 0.005 0.047 -10000 0 -0.36 9 9
IL12 0.014 0.05 -10000 0 -0.23 16 16
STAT5A 0.01 0.018 -10000 0 -0.41 1 1
CD247 0.006 0.031 -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 0.062 -10000 0 -0.35 15 15
IL12/IL12R/TYK2/JAK2 0.02 0.24 -10000 0 -0.85 22 22
MAP2K3 0.032 0.2 -10000 0 -0.66 24 24
RIPK2 0.011 0 -10000 0 -10000 0 0
MAP2K6 0.033 0.2 -10000 0 -0.67 23 23
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 0.056 -10000 0 -0.26 18 18
EOMES -0.009 0.14 -10000 0 -1.2 7 7
STAT1 (dimer) 0.03 0.18 -10000 0 -0.66 17 17
T cell proliferation 0.038 0.16 -10000 0 -0.51 20 20
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 0.24 1 -0.55 22 23
ATF2 0.039 0.19 -10000 0 -0.63 24 24
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.023 -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 -0.015 0.086 -10000 0 -0.24 65 65
IL1A -0.011 0.083 -10000 0 -0.33 34 34
IL1B 0.015 0.035 -10000 0 -0.33 5 5
IRAK/TRAF6/p62/Atypical PKCs 0.023 0.049 -10000 0 -0.34 1 1
IL1R2 -0.013 0.089 -10000 0 -0.34 37 37
IL1R1 0.004 0.054 -10000 0 -0.41 9 9
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.026 0.057 0.18 23 -0.26 10 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 0.049 -10000 0 -0.42 3 3
IL1 alpha/IL1R1/IL1RAP/MYD88 0.012 0.056 -10000 0 -0.23 11 11
PIK3R1 0.007 0.04 -10000 0 -0.41 5 5
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.017 0.053 -10000 0 -0.21 11 11
IL1 beta fragment/IL1R1/IL1RAP 0.02 0.044 -10000 0 -0.22 16 16
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 -0.022 0.091 -10000 0 -0.23 85 85
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 0.04 -10000 0 -0.21 12 12
CHUK 0.011 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.02 0.044 -10000 0 -0.22 16 16
IL1 beta/IL1R2 0.005 0.058 -10000 0 -0.25 9 9
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 -0.008 0.087 -10000 0 -0.41 24 24
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.027 0.048 -10000 0 -0.36 3 3
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.02 0.04 -10000 0 -0.22 11 11
IL1 alpha/IL1R1/IL1RAP 0.004 0.062 -10000 0 -0.2 44 44
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 0.015 0.051 -10000 0 -0.18 35 35
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 0.026 -10000 0 -0.41 2 2
IL1RN/IL1R2 -0.034 0.1 -10000 0 -0.24 106 106
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.026 0.042 -10000 0 -0.38 2 2
TMEM189-UBE2V1 -0.023 0.1 -10000 0 -0.41 35 35
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.017 0.058 -10000 0 -0.34 9 9
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
IL1RN -0.038 0.12 -10000 0 -0.33 78 78
TRAF6/TAK1/TAB1/TAB2 -0.011 0.044 -10000 0 -0.18 35 35
MAP2K6 -0.006 0.071 -10000 0 -0.31 7 7
TCR signaling in naïve CD8+ T cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GRB2/SOS1/SHC -0.012 0.067 -10000 0 -0.35 15 15
FYN 0.033 0.1 -10000 0 -0.44 16 16
LAT/GRAP2/SLP76 -0.012 0.082 -10000 0 -0.39 18 18
IKBKB 0.011 0 -10000 0 -10000 0 0
AKT1 0.038 0.077 -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 8 8
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 0.037 0.1 -10000 0 -0.44 18 18
TRPV6 -0.044 0.13 -10000 0 -0.4 59 59
CD28 0.01 0.021 -10000 0 -0.33 2 2
SHC1 0.033 0.096 -10000 0 -0.43 16 16
receptor internalization 0.027 0.089 -10000 0 -0.43 15 15
PRF1 0.021 0.13 -10000 0 -0.99 7 7
KRAS 0.01 0.015 -10000 0 -0.33 1 1
GRB2 0.011 0 -10000 0 -10000 0 0
COT/AKT1 0.039 0.064 -10000 0 -0.27 15 15
LAT 0.033 0.096 -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 -0.011 0.058 -10000 0 -0.16 73 73
RASGRP1 0.04 0.085 -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 -0.18 13 13
PRKCA -0.006 0.046 -10000 0 -0.21 16 16
GRAP2 -0.002 0.073 -10000 0 -0.41 17 17
mol:IP3 0.003 0.081 0.18 51 -0.32 14 65
EntrezGene:6957 0.001 0.002 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.019 0.083 -10000 0 -0.41 14 14
ORAI1 0.027 0.074 0.24 59 -10000 0 59
CSK 0.031 0.098 -10000 0 -0.42 17 17
B7 family/CD28 0.036 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 0.027 0.11 -10000 0 -0.47 17 17
PTPN6 0.03 0.097 -10000 0 -0.43 16 16
VAV1 0.031 0.1 -10000 0 -0.45 16 16
Monovalent TCR/CD3 0.012 0.063 -10000 0 -0.29 19 19
CBL 0.011 0 -10000 0 -10000 0 0
LCK 0.03 0.1 -10000 0 -0.46 16 16
PAG1 0.031 0.1 -10000 0 -0.42 18 18
RAP1A 0.011 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.027 0.11 -10000 0 -0.48 16 16
CD80 -0.008 0.078 -10000 0 -0.33 30 30
CD86 0.01 0.021 -10000 0 -0.34 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 0.085 -10000 0 -0.37 16 16
CD8A 0.001 0.067 -10000 0 -0.39 15 15
CD8B -0.01 0.087 -10000 0 -0.35 33 33
PTPRC 0.003 0.059 -10000 0 -0.4 11 11
PDK1/PKC theta 0.04 0.096 -10000 0 -0.38 19 19
CSK/PAG1 0.033 0.098 -10000 0 -0.41 18 18
SOS1 0.011 0 -10000 0 -10000 0 0
peptide-MHC class I 0.018 0.011 -10000 0 -0.22 1 1
GRAP2/SLP76 -0.014 0.094 -10000 0 -0.44 19 19
STIM1 0.013 0.036 -10000 0 -10000 0 0
RAS family/GTP 0.039 0.036 -10000 0 -0.16 6 6
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.027 0.093 -10000 0 -0.45 15 15
mol:DAG -0.006 0.059 -10000 0 -0.29 15 15
RAP1A/GDP 0.012 0.015 -10000 0 -0.055 7 7
PLCG1 0.011 0 -10000 0 -10000 0 0
CD247 0.01 0.03 -10000 0 -0.39 3 3
cytotoxic T cell degranulation 0.022 0.13 -10000 0 -0.92 7 7
RAP1A/GTP -0.008 0.019 -10000 0 -0.057 73 73
mol:PI-3-4-5-P3 0.038 0.089 -10000 0 -0.37 18 18
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.001 0.096 0.19 49 -0.41 14 63
NRAS 0.011 0 -10000 0 -10000 0 0
ZAP70 -0.001 0.063 -10000 0 -0.34 18 18
GRB2/SOS1 0.016 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.012 0.08 -10000 0 -0.4 16 16
MALT1 0.011 0 -10000 0 -10000 0 0
TRAF6 0.011 0 -10000 0 -10000 0 0
CD8 heterodimer -0.004 0.08 -10000 0 -0.26 44 44
CARD11 0.002 0.057 -10000 0 -0.35 14 14
PRKCB -0.008 0.057 -10000 0 -0.27 20 20
PRKCE -0.003 0.042 -10000 0 -0.21 14 14
PRKCQ 0.034 0.11 -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 0.037 0.068 -10000 0 -0.28 16 16
IKK complex 0.03 0.037 -10000 0 -0.097 15 15
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 0.074 -10000 0 -0.31 16 16
TCR/CD3/MHC I/CD8/Fyn 0.021 0.12 -10000 0 -0.48 21 21
EPHB forward signaling

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
Ephrin A5/EPHB2 0.005 0.047 -10000 0 -0.22 22 22
cell-cell adhesion 0.03 0.063 0.3 9 -10000 0 9
Ephrin B/EPHB2/RasGAP 0.008 0.069 -10000 0 -0.38 1 1
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 0.044 -10000 0 -0.21 21 21
Ephrin B1/EPHB1 -0.01 0.074 -10000 0 -0.23 54 54
HRAS/GDP -0.03 0.067 -10000 0 -0.3 10 10
Ephrin B/EPHB1/GRB7 -0.02 0.098 -10000 0 -0.36 12 12
Endophilin/SYNJ1 0.008 0.062 -10000 0 -0.36 1 1
KRAS 0.01 0.015 -10000 0 -0.33 1 1
Ephrin B/EPHB1/Src -0.01 0.092 -10000 0 -0.38 8 8
endothelial cell migration -0.003 0.025 -10000 0 -0.18 10 10
GRB2 0.011 0 -10000 0 -10000 0 0
GRB7 -0.01 0.083 -10000 0 -0.34 33 33
PAK1 0.012 0.067 -10000 0 -0.36 3 3
HRAS 0.011 0 -10000 0 -10000 0 0
RRAS 0.009 0.062 -10000 0 -0.36 1 1
DNM1 0.006 0.044 -10000 0 -0.41 6 6
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.01 0.086 -10000 0 -0.36 8 8
lamellipodium assembly -0.03 0.063 -10000 0 -0.3 9 9
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.009 0.089 -10000 0 -0.21 54 54
PIK3R1 0.007 0.04 -10000 0 -0.41 5 5
EPHB2 0.009 0.025 -10000 0 -0.33 3 3
EPHB3 -0.003 0.071 -10000 0 -0.35 21 21
EPHB1 -0.03 0.12 -10000 0 -0.41 53 53
EPHB4 0.01 0.018 -10000 0 -0.41 1 1
mol:GDP -0.001 0.084 -10000 0 -0.32 10 10
Ephrin B/EPHB2 0.004 0.066 -10000 0 -0.19 54 54
Ephrin B/EPHB3 -0.002 0.082 -10000 0 -0.22 57 57
JNK cascade 0.008 0.065 -10000 0 -0.37 1 1
Ephrin B/EPHB1 -0.016 0.091 -10000 0 -0.2 98 98
RAP1/GDP 0.01 0.076 -10000 0 -0.27 10 10
EFNB2 0.009 0.031 -10000 0 -0.41 3 3
EFNB3 -0.029 0.12 -10000 0 -0.41 51 51
EFNB1 0.01 0.018 -10000 0 -0.41 1 1
Ephrin B2/EPHB1-2 -0.003 0.069 -10000 0 -0.2 54 54
RAP1B 0.011 0 -10000 0 -10000 0 0
RAP1A 0.011 0 -10000 0 -10000 0 0
CDC42/GTP -0.034 0.073 -10000 0 -0.35 9 9
Rap1/GTP -0.029 0.062 -10000 0 -0.3 9 9
axon guidance 0.005 0.047 -10000 0 -0.22 22 22
MAPK3 0.004 0.08 -10000 0 -0.32 8 8
MAPK1 0.004 0.08 -10000 0 -0.32 8 8
Rac1/GDP 0.006 0.079 -10000 0 -0.29 10 10
actin cytoskeleton reorganization -0.023 0.05 -10000 0 -0.25 9 9
CDC42/GDP 0.006 0.079 -10000 0 -0.29 10 10
PI3K 0.022 0.029 -10000 0 -0.18 10 10
EFNA5 -0.004 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 54 54
CDC42 0.011 0 -10000 0 -10000 0 0
RAS family/GTP -0.028 0.061 -10000 0 -0.3 9 9
PTK2 0.006 0.018 -10000 0 -10000 0 0
MAP4K4 0.008 0.065 -10000 0 -0.38 1 1
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 11 11
MAP2K1 -0.002 0.084 -10000 0 -0.34 8 8
WASL 0.011 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.004 0.071 -10000 0 -0.2 53 53
cell migration -0.004 0.099 -10000 0 -0.34 11 11
NRAS 0.011 0 -10000 0 -10000 0 0
SYNJ1 0.009 0.062 -10000 0 -0.36 1 1
PXN 0.011 0 -10000 0 -10000 0 0
TF 0.005 0.072 -10000 0 -0.32 5 5
HRAS/GTP -0.032 0.068 -10000 0 -0.33 9 9
Ephrin B1/EPHB1-2 -0.002 0.068 -10000 0 -0.2 57 57
cell adhesion mediated by integrin 0.017 0.066 0.2 54 -10000 0 54
RAC1 0.011 0 -10000 0 -10000 0 0
mol:GTP -0.007 0.087 -10000 0 -0.35 9 9
RAC1-CDC42/GTP -0.034 0.072 -10000 0 -0.3 19 19
RASA1 0.007 0.04 -10000 0 -0.41 5 5
RAC1-CDC42/GDP 0.01 0.076 -10000 0 -0.29 8 8
ruffle organization 0.009 0.081 -10000 0 -0.31 9 9
NCK1 0.009 0.026 -10000 0 -0.41 2 2
receptor internalization 0.012 0.067 -10000 0 -0.34 5 5
Ephrin B/EPHB2/KALRN 0.008 0.071 -10000 0 -0.38 3 3
ROCK1 0.012 0.04 -10000 0 -0.24 6 6
RAS family/GDP -0.023 0.05 -10000 0 -0.24 9 9
Rac1/GTP -0.031 0.066 -10000 0 -0.32 9 9
Ephrin B/EPHB1/Src/Paxillin -0.013 0.095 -10000 0 -0.21 98 98
Signaling events mediated by PRL

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
CCNE1 -0.13 0.17 -9999 0 -0.33 217 217
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+ -0.043 0.1 -9999 0 -0.29 80 80
AGT -0.05 0.15 -9999 0 -0.4 80 80
CCNA2 -0.028 0.098 -9999 0 -0.33 19 19
TUBA1B 0.011 0 -9999 0 -10000 0 0
EGR1 -0.019 0.099 -9999 0 -0.28 70 70
CDK2/Cyclin E1 -0.041 0.088 -9999 0 -0.46 1 1
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 0.069 -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
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 0.047 -10000 0 -0.21 1 1
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 -0.26 4 4
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 0.049 -10000 0 -0.24 1 1
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 -0.19 0.16 -10000 0 -0.33 301 301
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 -10000 0 0
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 0.017 0.067 -10000 0 -1 1 1
STAT1 0.018 0.049 -10000 0 -0.24 1 1
CALM1 0.011 0 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.027 0.1 -10000 0 -0.32 59 59
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
STAT1 (dimer)/PIAS1 0.023 0.047 -10000 0 -0.23 1 1
CEBPB/PTGES2/Cbp/p300 -0.003 0.018 -10000 0 -0.24 2 2
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 0.057 -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 0.026 -10000 0 -0.41 2 2
DAPK1 0.046 0.049 -10000 0 -0.57 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 -0.3 2 2
IFNG -0.027 0.1 -10000 0 -0.32 59 59
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 -0.23 0.21 -10000 0 -0.41 301 301
CAMK2B -0.046 0.13 -10000 0 -0.33 89 89
FRAP1 0.023 0.046 -10000 0 -0.27 2 2
PRKCD 0.025 0.05 -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 -0.26 4 4
PTPN2 0.011 0 -10000 0 -10000 0 0
EP300 0.011 0 -10000 0 -10000 0 0
IRF1 0.044 0.042 -10000 0 -0.25 1 1
STAT1 (dimer)/PIASy 0.02 0.047 0.18 1 -0.23 1 2
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 -0.21 3 3
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 0.024 -10000 0 -10000 0 0
CBL 0.017 0.048 -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 -0.26 4 4
PTPN11 0.011 0.05 -10000 0 -0.17 11 11
CREBBP 0.01 0.026 -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 0.048 -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 -0.017 0.1 -10000 0 -0.36 27 27
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 -0.032 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 -0.011 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 -0.004 0.07 -10000 0 -0.33 24 24
XPO1 0.011 0 -10000 0 -10000 0 0
SFN -0.24 0.15 -10000 0 -0.33 395 395
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 -0.36 27 27
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 0.003 0.051 -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 -0.038 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 0.03 -10000 0 -0.2 10 10
NFATc/ERK1 0.039 0.048 -10000 0 -0.28 2 2
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.032 0.081 -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 -0.22 3 3
RCH1/ KPNB1 0.006 0.048 -10000 0 -0.22 24 24
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 -0.088 0.18 -9999 0 -0.53 56 56
CDKN1B 0.002 0.14 -9999 0 -0.44 27 27
FOXO3 -0.05 0.18 -9999 0 -0.51 56 56
KAT2B -0.002 0.057 -9999 0 -0.42 9 9
FOXO1/SIRT1 0.022 0.03 -9999 0 -10000 0 0
CAT -0.039 0.17 -9999 0 -0.55 20 20
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 -0.19 115 115
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
FOXO4 0.037 0.076 -9999 0 -0.29 5 5
response to oxidative stress -0.005 0.018 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.073 0.15 -9999 0 -0.47 59 59
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 -10000 0 0
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 0.019 0.12 -9999 0 -0.45 3 3
RBL2 -0.014 0.15 -9999 0 -0.7 7 7
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 -0.001 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 -0.051 0.18 -9999 0 -0.61 21 21
FOXO1-3a-4/beta catenin 0.034 0.11 -9999 0 -0.37 7 7
proteasomal ubiquitin-dependent protein catabolic process 0.029 0.023 -9999 0 -10000 0 0
CSNK1A1 0.011 0 -9999 0 -10000 0 0
SGK1 0.003 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 -0.33 395 395
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 0.41 -9999 0 -1.2 69 69
BCL6 -0.013 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
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.007 0.045 -9999 0 -10000 0 0
epithelial cell differentiation -0.04 0.076 -9999 0 -0.35 9 9
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 0.049 -9999 0 -10000 0 0
PTPRZ1 -0.014 0.08 -9999 0 -0.33 32 32
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.022 0.053 -9999 0 -0.27 2 2
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 0.053 -9999 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.008 0.057 -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 0.015 -9999 0 -0.33 1 1
HBEGF 0.011 0 -9999 0 -10000 0 0
PRLR -0.072 0.17 -9999 0 -0.41 106 106
E4ICDs/ETO2 -0.026 0.095 -9999 0 -0.34 10 10
axon guidance 0.014 0.037 -9999 0 -10000 0 0
NEDD4 -0.018 0.11 -9999 0 -0.41 42 42
Prolactin receptor/Prolactin receptor/Prolactin -0.056 0.13 -9999 0 -0.29 123 123
CBFA2T3 -0.049 0.15 -9999 0 -0.41 77 77
ErbB4/ErbB2/HBEGF 0.015 0.042 -9999 0 -10000 0 0
MAPK3 0.025 0.05 -9999 0 -10000 0 0
STAT1 (dimer) 0.007 0.046 -9999 0 -0.28 1 1
MAPK1 0.025 0.05 -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 0.009 0.058 -9999 0 -0.28 21 21
NRG3 -0.008 0.068 -9999 0 -0.33 23 23
NRG2 -0.05 0.15 -9999 0 -0.41 78 78
NRG4 -0.02 0.097 -9999 0 -0.33 48 48
heart development 0.014 0.037 -9999 0 -10000 0 0
neural crest cell migration 0.007 0.061 -9999 0 -0.28 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 -0.006 0.077 -9999 0 -0.34 8 8
apoptosis 0.007 0.037 -9999 0 -10000 0 0
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.027 0.095 -9999 0 -0.34 12 12
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 -0.031 0.11 -9999 0 -0.37 16 16
MDM2 0.009 0.046 -9999 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.011 0.051 -9999 0 -0.26 6 6
STAT5A 0.018 0.036 -9999 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta 0.006 0.067 -9999 0 -0.32 10 10
DLG4 0.009 0.031 -9999 0 -0.41 3 3
GRB2/SHC 0.016 0 -9999 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.011 0.033 -9999 0 -10000 0 0
STAT5A (dimer) -0.042 0.08 -9999 0 -0.38 8 8
MAP3K7IP2 0 0 -9999 0 -10000 0 0
STAT5B (dimer) 0.018 0.038 -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 69 69
BTC -0.003 0.076 -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 0.053 -9999 0 -10000 0 0
STAT5B 0.009 0.026 -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 -0.29 6 6
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 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
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 0.029 -9999 0 -10000 0 0
VAMP2 0.011 0 -9999 0 -10000 0 0
SLC2A4 -0.08 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 -0.33 395 395
LNPEP 0.011 0 -9999 0 -10000 0 0
YWHAE 0.011 0 -9999 0 -10000 0 0
Syndecan-3-mediated signaling events

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
CTTN 0.011 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.014 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 33 33
EGFR 0 0.066 -9999 0 -0.4 14 14
Syndecan-3/EGFR 0.015 0.032 -9999 0 -10000 0 0
AGRP 0.006 0.015 -9999 0 -0.33 1 1
NCSTN 0.011 0 -9999 0 -10000 0 0
PSENEN 0.011 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.006 0.048 -9999 0 -0.41 7 7
APH1A 0.011 0 -9999 0 -10000 0 0
NCAN -0.005 0.059 -9999 0 -0.33 17 17
long-term memory 0.026 0.006 -9999 0 -10000 0 0
Syndecan-3/IL8 -0.026 0.072 -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 0.056 -9999 0 -0.33 15 15
SRC 0.011 0 -9999 0 -10000 0 0
PTN -0.088 0.18 -9999 0 -0.41 127 127
FGFR/FGF/Syndecan-3 -0.001 0.005 -9999 0 -10000 0 0
neuron projection morphogenesis -0.025 0.078 -9999 0 -0.29 3 3
Syndecan-3/AgRP 0.011 0.013 -9999 0 -10000 0 0
Syndecan-3/AgRP/MC4R 0.004 0.027 -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 0.071 -9999 0 -10000 0 0
IL8 -0.089 0.16 -9999 0 -0.33 157 157
Syndecan-3/Fyn/Cortactin 0.026 0.006 -9999 0 -10000 0 0
Syndecan-3/CASK -0.001 0.004 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.01 0.073 -9999 0 -0.24 46 46
Gamma Secretase 0.03 0.024 -9999 0 -0.18 7 7
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.016 0.084 -9999 0 -0.38 22 22
PDGFB-D/PDGFRB/SLAP 0.004 0.059 -9999 0 -0.28 23 23
PDGFB-D/PDGFRB/APS/CBL 0.013 0.049 -9999 0 -0.22 22 22
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 0.016 0.09 -9999 0 -0.41 22 22
PIK3CA 0.01 0.018 -9999 0 -0.41 1 1
FGR -0.021 0.1 -9999 0 -0.38 31 31
mol:Ca2+ 0.011 0.095 -9999 0 -0.44 22 22
MYC 0.022 0.13 -9999 0 -0.67 13 13
SHC1 0.011 0 -9999 0 -10000 0 0
HRAS/GDP 0.02 0.046 -9999 0 -0.24 3 3
LRP1/PDGFRB/PDGFB 0.012 0.053 -9999 0 -0.24 23 23
GRB10 0.01 0.018 -9999 0 -0.41 1 1
PTPN11 0.011 0 -9999 0 -10000 0 0
GO:0007205 0.011 0.096 -9999 0 -0.45 22 22
PTEN 0.006 0.044 -9999 0 -0.41 6 6
GRB2 0.011 0 -9999 0 -10000 0 0
GRB7 -0.01 0.083 -9999 0 -0.34 33 33
PDGFB-D/PDGFRB/SHP2 0.005 0.059 -9999 0 -0.28 22 22
PDGFB-D/PDGFRB/GRB10 0.004 0.06 -9999 0 -0.28 23 23
cell cycle arrest 0.004 0.059 -9999 0 -0.28 23 23
HRAS 0.011 0 -9999 0 -10000 0 0
HIF1A 0.039 0.043 -9999 0 -0.26 2 2
GAB1 0.015 0.092 -9999 0 -0.41 22 22
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.019 0.085 -9999 0 -0.37 22 22
PDGFB-D/PDGFRB 0.013 0.051 -9999 0 -0.23 22 22
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.005 0.059 -9999 0 -0.28 22 22
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.015 0.071 -9999 0 -0.34 22 22
positive regulation of MAPKKK cascade 0.005 0.058 -9999 0 -0.28 22 22
PIK3R1 0.007 0.04 -9999 0 -0.41 5 5
mol:IP3 0.011 0.097 -9999 0 -0.45 22 22
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 0.083 -9999 0 -0.26 52 52
SHB 0.011 0 -9999 0 -10000 0 0
BLK -0.011 0.052 -9999 0 -0.26 22 22
PTPN2 0.011 0.002 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.005 0.059 -9999 0 -0.28 22 22
BCAR1 0.011 0 -9999 0 -10000 0 0
VAV2 0.018 0.095 -9999 0 -0.39 23 23
CBL 0.011 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.005 0.059 -9999 0 -0.28 22 22
LCK -0.011 0.065 -9999 0 -0.29 22 22
PDGFRB -0.006 0.084 -9999 0 -0.41 22 22
ACP1 0.011 0 -9999 0 -10000 0 0
HCK -0.01 0.052 -9999 0 -0.26 22 22
ABL1 0.016 0.078 -9999 0 -0.34 22 22
PDGFB-D/PDGFRB/CBL 0.012 0.1 -9999 0 -0.47 22 22
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 0.015 -9999 0 -0.33 1 1
cell proliferation 0.023 0.11 -9999 0 -0.59 13 13
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 -0.009 0.052 -9999 0 -0.26 22 22
PI3K -0.01 0.039 -9999 0 -0.33 2 2
PDGFB-D/PDGFRB/GRB7/SHC 0 0.07 -9999 0 -0.21 52 52
SH2B2 0.011 0 -9999 0 -10000 0 0
PLCgamma1/SPHK1 0.016 0.092 -9999 0 -0.42 22 22
LYN -0.009 0.052 -9999 0 -0.26 22 22
LRP1 0.009 0.026 -9999 0 -0.41 2 2
SOS1 0.011 0 -9999 0 -10000 0 0
STAT5B 0.009 0.026 -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 -0.36 1 1
SPHK1 0.01 0.021 -9999 0 -0.33 2 2
EDG1 0.001 0.002 -9999 0 -10000 0 0
mol:DAG 0.011 0.097 -9999 0 -0.45 22 22
PLCG1 0.011 0.099 -9999 0 -0.46 22 22
NHERF/PDGFRB 0.011 0.052 -9999 0 -0.22 26 26
YES1 -0.011 0.051 -9999 0 -0.26 22 22
cell migration 0.011 0.051 -9999 0 -0.22 26 26
SHC/Grb2/SOS1 -0.003 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 0.016 0.054 -9999 0 -0.2 27 27
FYN -0.009 0.052 -9999 0 -0.26 22 22
DOK1 0.017 0.045 -9999 0 -0.2 22 22
HRAS/GTP 0.008 0 -9999 0 -10000 0 0
PDGFB 0.011 0 -9999 0 -10000 0 0
RAC1 0.024 0.1 -9999 0 -0.37 32 32
PRKCD 0.018 0.045 -9999 0 -0.2 22 22
FER 0.018 0.045 -9999 0 -0.2 22 22
MAPKKK cascade -0.006 0.033 -9999 0 -10000 0 0
RASA1 0.016 0.052 -9999 0 -0.21 26 26
NCK1 0.009 0.026 -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 22 22
PDGFB-D/PDGFRB/SHB 0.005 0.059 -9999 0 -0.28 22 22
chemotaxis 0.016 0.076 -9999 0 -0.34 22 22
STAT1-3-5/STAT1-3-5 -0.008 0.035 -9999 0 -0.35 1 1
Bovine Papilomavirus E5/PDGFRB -0.003 0.059 -9999 0 -0.29 22 22
PTPRJ 0.011 0 -9999 0 -10000 0 0
EPO signaling pathway

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
BCL2L1 0.02 0.11 -10000 0 -0.44 6 6
CRKL 0.019 0.054 -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 -0.19 22 22
RAP1A 0.019 0.054 -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 -0.21 5 5
EPO/EPOR (dimer) 0.005 0.058 -10000 0 -0.26 24 24
IRS2 -0.007 0.086 -10000 0 -0.26 19 19
STAT1 0.018 0.088 -10000 0 -0.37 6 6
STAT5B 0.017 0.08 -10000 0 -0.25 21 21
cell proliferation 0.02 0.045 -10000 0 -0.21 2 2
GAB1/SHIP/PIK3R1/SHP2/SHC -0.013 0.04 -10000 0 -0.22 10 10
TEC 0.018 0.054 -10000 0 -0.24 6 6
SOCS3 0.009 0.026 -10000 0 -0.41 2 2
STAT1 (dimer) 0.018 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 -0.18 26 26
EPO/EPOR 0.005 0.058 -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 0.049 -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 0.002 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 -0.21 4 4
EPO/EPOR (dimer)/JAK2/SOCS3 -0.01 0.05 0.23 1 -0.22 27 28
PTPN6 0.013 0.056 -10000 0 -0.18 26 26
TEC/VAV2/GRB2 0.029 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 -0.21 5 5
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 0.054 -10000 0 -0.24 6 6
CBL 0.019 0.054 -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) 0.023 0.11 -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 0.057 -10000 0 -0.27 6 6
BCL2 -0.025 0.25 -10000 0 -0.79 50 50
mTOR signaling pathway

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
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 56 61
FRAP1 0.008 0.019 -10000 0 -10000 0 0
AKT1 0 0.072 0.2 5 -0.2 56 61
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 53 53
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 53 53
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 57 57
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 0.04 -10000 0 -0.27 2 2
mol:Amino Acids 0 0 -10000 0 -0.001 53 53
FKBP12/Rapamycin 0.008 0.001 -10000 0 -10000 0 0
PDPK1 -0.021 0.073 0.21 5 -0.22 56 61
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 53 -10000 0 53
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 53 53
INS 0.001 0.003 -10000 0 -10000 0 0
PTEN 0.006 0.044 -10000 0 -0.41 6 6
PDK2 -0.021 0.073 0.21 5 -0.22 56 61
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 -0.002 2 8
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 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
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 -0.014 0.2 -10000 0 -0.54 16 16
FLT1 -0.012 0.061 -10000 0 -1.1 1 1
ADORA2A -0.013 0.19 -10000 0 -0.49 16 16
germ cell development -0.022 0.21 -10000 0 -0.52 27 27
SLC11A2 -0.013 0.19 -10000 0 -0.5 15 15
BHLHE40 -0.013 0.19 -10000 0 -0.49 16 16
HIF1AN 0.009 0.013 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.004 0.12 -10000 0 -0.34 8 8
ETS1 0.021 0.02 -10000 0 -0.42 1 1
CITED2 -0.036 0.18 -10000 0 -1 17 17
KDR -0.065 0.26 -10000 0 -1.1 32 32
PGK1 -0.013 0.19 -10000 0 -0.49 16 16
SIRT1 0.009 0.026 -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 0.011 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 -0.54 101 101
EFNA1 -0.013 0.2 -10000 0 -0.5 16 16
FXN -0.013 0.19 -10000 0 -0.49 16 16
POU5F1 -0.023 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 0.034 -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 -0.23 1 1
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 -0.49 15 15
TWIST1 -0.039 0.23 -10000 0 -0.54 56 56
ELK1 0.016 0.01 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0 0.11 -10000 0 -0.42 3 3
VEGFA -0.013 0.19 -10000 0 -0.49 16 16
CREBBP 0.009 0.026 -10000 0 -0.41 2 2
IL2 signaling events mediated by PI3K

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
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 0.022 0.099 -9999 0 -0.26 32 32
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucosylceramide 0.005 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 0.099 -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 0.02 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 9 9
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 0.029 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 0.072 -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 0.071 -9999 0 -0.28 9 9
Rac1/GDP 0.019 0.025 -9999 0 -0.2 6 6
T cell proliferation 0.042 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 0.07 -9999 0 -0.36 3 3
NF kappa B1 p50/RelA -0.033 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 0.067 -9999 0 -0.33 21 21
IL2RB 0.012 0.018 -9999 0 -0.41 1 1
TERT -0.11 0.16 -9999 0 -0.33 196 196
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 -0.36 9 9
actin cytoskeleton organization 0.042 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 0.019 -9999 0 -0.41 1 1
Rac1/GTP 0.024 0.025 -9999 0 -0.19 6 6
LCK 0.009 0.035 -9999 0 -0.34 5 5
BCL2 -0.019 0.26 -9999 0 -0.82 50 50
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.003 0.052 0.36 11 -10000 0 11
PI3K Class IB/PDE3B 0.003 0.053 -10000 0 -0.36 11 11
PDE3B 0.003 0.053 -10000 0 -0.36 11 11
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.049 -9999 0 -0.22 11 11
JUN -0.006 0.069 -9999 0 -0.34 4 4
HRAS 0.01 0.001 -9999 0 -10000 0 0
DOCK7 0.013 0.048 -9999 0 -0.32 2 2
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.002 0.053 -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 -0.23 11 11
RAF1 0.011 0.055 -9999 0 -0.3 4 4
ErbB2/ErbB3/neuregulin 2 -0.027 0.085 -9999 0 -0.21 91 91
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 -0.079 0.18 -9999 0 -0.54 17 17
FOS -0.12 0.24 -9999 0 -0.47 166 166
NRAS 0.01 0.001 -9999 0 -10000 0 0
mol:Ca2+ 0.003 0.049 -9999 0 -0.22 11 11
MAPK3 -0.043 0.13 -9999 0 -0.48 10 10
MAPK1 -0.043 0.13 -9999 0 -0.48 10 10
JAK2 0.011 0.053 -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 0.037 -9999 0 -0.23 14 14
ERBB3 0.008 0.032 -9999 0 -0.41 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 0.13 -9999 0 -0.37 10 10
myelination 0.019 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 -0.05 0.15 -9999 0 -0.41 78 78
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 0.049 -9999 0 -0.22 11 11
RAS family/GDP 0.016 0.048 -9999 0 -0.27 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 0.049 -9999 0 -0.22 11 11
CDC42 0.011 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
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 -0.011 0.033 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 -0.078 0.17 -10000 0 -0.41 114 114
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 -10000 0 -0.28 2 2
HIST2H4A 0.011 0.033 -10000 0 -0.23 9 9
SIRT1/FOXO3a -0.001 0.015 0.13 1 -0.23 2 3
SIRT1 0.006 0.027 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 -10000 0 2
SIRT1/PGC1A -0.05 0.097 0.12 1 -0.24 115 116
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 0.031 -10000 0 -0.2 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 0.015 0.066 0.27 10 -10000 0 10
TP53 0.006 0.019 0.18 1 -0.41 1 2
KU70/SIRT1/BAX -0.001 0.015 -10000 0 -0.23 2 2
CREBBP 0.009 0.026 -10000 0 -0.41 2 2
MEF2D 0.011 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.001 0.021 0.14 1 -0.26 3 4
ACSS2 0.015 0.019 -10000 0 -0.28 2 2
SIRT1/PCAF/MYOD -0.015 0.066 0.14 1 -0.27 10 11
JNK signaling in the CD4+ TCR 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
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 -0.011 0.14 -9999 0 -0.52 38 38
MAP3K7 0.029 0.038 -9999 0 -0.22 1 1
GRAP2 -0.002 0.074 -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 -0.24 1 1
LAT/GRAP2/SLP76/HPK1/HIP-55 0.022 0.047 -9999 0 -0.31 2 2
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.001 0.016 0.12 2 -0.18 2 4
NFKBIA 0.011 0 -10000 0 -10000 0 0
BIRC3 0.003 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 -0.17 2 2
RB1 -0.003 0.02 0.13 2 -0.22 3 5
FADD/Caspase 8 0.036 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 -0.005 0.07 -10000 0 -0.34 23 23
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 -0.003 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 0.012 0.015 0.13 2 -0.17 2 4
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.012 0.015 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 0.13 2 -0.22 7 9
PRKRA -0.002 0.012 0.13 2 -10000 0 2
PDGFA 0.009 0.026 -10000 0 -0.41 2 2
TRAF2 0.011 0 -10000 0 -10000 0 0
IGF1 -0.068 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 0.074 -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 -0.19 9 9
TNFR1A/BAG4/TNF-alpha -0.003 0.067 -10000 0 -0.18 70 70
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 0.014 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 0.004 0.011 0.13 2 -10000 0 2
TNF-alpha/TNFR1A/FAN -0.002 0.065 -10000 0 -0.18 67 67
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.03 0.023 -10000 0 -0.22 1 1
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 67 67
PKC zeta/PAR4 0.015 0.016 -10000 0 -0.25 2 2
mol:PHOSPHOCHOLINE -0.005 0.021 0.16 3 -10000 0 3
NF kappa B1/RelA/I kappa B alpha 0.032 0.015 -10000 0 -10000 0 0
AIFM1 0.014 0.04 0.14 51 -10000 0 51
BCL2 -0.028 0.12 -10000 0 -0.41 50 50
Paxillin-independent events mediated by a4b1 and a4b7

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
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 0.048 -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 -0.005 0.073 -9999 0 -0.4 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 -0.24 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
JAK2 0.012 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 40 40
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 41 41
p130Cas/Crk/Dock1 0.023 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 -0.19 40 40
EPOR 0.007 0.039 -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 -0.24 6 6
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.032 0.038 -10000 0 -0.24 8 8
BAG4 0.009 0.031 -10000 0 -0.41 3 3
BAD 0.023 0.014 -10000 0 -0.12 1 1
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 -0.12 1 1
EnzymeConsortium:3.1.4.12 0.01 0.01 -10000 0 -0.056 8 8
IKBKB 0.037 0.037 -10000 0 -0.22 8 8
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 -0.22 8 8
MAP2K4 0.027 0.016 -10000 0 -0.15 1 1
protein ubiquitination 0.038 0.037 -10000 0 -0.22 8 8
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 -0.24 8 8
KSR1 0.023 0.018 -10000 0 -0.16 3 3
MAPK8 0.03 0.024 -10000 0 -0.15 7 7
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 -0.22 8 8
TNF R/SODD 0.015 0.022 -10000 0 -0.28 3 3
TNF -0.031 0.11 -10000 0 -0.33 67 67
CYCS 0.032 0.03 0.12 47 -0.11 1 48
IKBKG 0.037 0.037 -10000 0 -0.22 8 8
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.028 0.04 -10000 0 -0.25 8 8
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 -0.11 1 48
TNF/TNF R/SODD -0.003 0.067 -10000 0 -0.18 70 70
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 -0.23 8 8
response to hydrogen peroxide 0 0 -10000 0 -0.002 1 1
BCL2 -0.028 0.12 -10000 0 -0.41 50 50
IL27-mediated signaling events

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
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 0.01 0.096 0.46 5 -10000 0 5
IL27/IL27R/JAK1 -0.015 0.11 -10000 0 -0.84 3 3
TBX21 0.002 0.11 -10000 0 -0.56 6 6
IL12B 0.006 0.016 -10000 0 -0.33 1 1
IL12A 0.001 0.042 -10000 0 -0.24 15 15
IL6ST -0.053 0.15 -10000 0 -0.42 81 81
IL27RA/JAK1 0.012 0.072 -10000 0 -1.1 2 2
IL27 0.001 0.051 -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 0.01 0.096 0.46 5 -10000 0 5
T cell proliferation during immune response 0.01 0.096 0.46 5 -10000 0 5
MAPKKK cascade -0.01 0.096 -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 0.011 0.015 -10000 0 -0.34 1 1
IL12RB1 -0.001 0.066 -10000 0 -0.35 18 18
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.002 0.12 -10000 0 -0.47 11 11
IL27/IL27R/JAK2/TYK2 -0.01 0.097 -10000 0 -0.47 5 5
positive regulation of T cell mediated cytotoxicity -0.01 0.096 -10000 0 -0.46 5 5
STAT1 (dimer) -0.04 0.12 0.47 4 -0.78 4 8
JAK2 0.004 0.054 -10000 0 -0.41 9 9
JAK1 0.01 0.026 -10000 0 -0.41 2 2
STAT2 (dimer) -0.004 0.092 -10000 0 -0.44 5 5
T cell proliferation -0.011 0.1 -10000 0 -0.42 11 11
IL12/IL12R/TYK2/JAK2 0.014 0.052 -10000 0 -0.52 1 1
IL17A -0.002 0.047 -10000 0 -10000 0 0
mast cell activation 0.01 0.096 0.46 5 -10000 0 5
IFNG 0 0.022 -10000 0 -0.075 4 4
T cell differentiation -0.002 0.004 -10000 0 -0.019 6 6
STAT3 (dimer) -0.004 0.092 -10000 0 -0.44 5 5
STAT5A (dimer) -0.004 0.092 -10000 0 -0.44 5 5
STAT4 (dimer) -0.004 0.092 -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 -0.014 0.11 -10000 0 -0.81 3 3
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 -0.004 0.091 -10000 0 -0.43 5 5
IL27/EBI3 0.005 0.056 -10000 0 -0.25 22 22
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 0.037 0.46 2 -10000 0 2
IL1B 0.007 0.025 -10000 0 -0.29 4 4
EBI3 0.003 0.054 -10000 0 -0.34 13 13
TNF -0.02 0.078 -10000 0 -0.23 67 67
Caspase cascade in apoptosis

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
TOP1 0.013 0.049 -10000 0 -0.29 6 6
ACTA1 0.004 0.058 0.16 3 -0.3 10 13
NUMA1 0.013 0.049 -10000 0 -0.29 6 6
SPTAN1 0.007 0.058 0.16 5 -0.3 10 15
LIMK1 0.007 0.058 0.17 1 -0.3 10 11
BIRC3 0.003 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 -0.2 59 59
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.011 0 -10000 0 -10000 0 0
PTK2 0.013 0.049 -10000 0 -0.29 6 6
DIABLO 0.011 0 -10000 0 -10000 0 0
apoptotic nuclear changes 0.007 0.057 0.16 5 -0.3 10 15
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.011 0 -10000 0 -10000 0 0
GSN 0.004 0.06 0.16 4 -0.3 10 14
MADD 0.011 0 -10000 0 -10000 0 0
TFAP2A 0.028 0.039 -10000 0 -0.59 2 2
BID 0.008 0.037 -10000 0 -0.18 11 11
MAP3K1 0.008 0.024 -10000 0 -0.17 2 2
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 0.16 5 -0.3 10 15
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 0.056 -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 0.033 0.25 8 -10000 0 8
KRT18 0.013 0.032 -10000 0 -0.7 1 1
apoptosis 0.014 0.054 0.18 5 -0.28 6 11
DFFA 0.007 0.058 0.16 5 -0.3 10 15
DFFB 0.007 0.058 0.16 5 -0.3 10 15
PARP1 0.005 0.022 0.16 5 -0.14 1 6
actin filament polymerization -0.009 0.058 0.28 11 -0.17 1 12
TNF -0.032 0.11 -10000 0 -0.33 67 67
CYCS 0.009 0.031 -10000 0 -0.15 8 8
SATB1 -0.005 0.081 -10000 0 -0.37 5 5
SLK 0.007 0.058 0.17 1 -0.3 10 11
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 0.17 2 -10000 0 2
CASP3 0.001 0.061 0.17 5 -0.32 10 15
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 0.039 -10000 0 -0.58 2 2
stress fiber formation 0.007 0.057 0.16 5 -0.3 10 15
GZMB -0.011 0.086 -10000 0 -0.25 58 58
CASP1 0.012 0.022 -10000 0 -0.28 3 3
LMNB1 0.032 0.024 -10000 0 -0.17 1 1
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 0.16 5 -0.3 10 15
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 0.17 1 -0.28 11 12
GAS2 -0.008 0.081 0.17 4 -0.34 14 18
positive regulation of apoptosis 0.035 0.024 -10000 0 -10000 0 0
PRF1 0.005 0.05 -10000 0 -0.37 9 9
Signaling events mediated by HDAC Class II

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
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 -0.012 0.087 -9999 0 -0.28 51 51
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 -0.029 0.12 -9999 0 -0.41 51 51
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 0.027 -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 0.003 0.051 -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 -0.051 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 0.029 -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 0.03 -9999 0 -0.23 4 4
HDAC4/ER alpha -0.017 0.094 -9999 0 -0.28 61 61
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 61 61
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
IL23-mediated signaling events

Figure S109.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S109.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 0.018 0.23 -9999 0 -1.2 11 11
IL23A 0.018 0.21 -9999 0 -0.99 11 11
NF kappa B1 p50/RelA/I kappa B alpha -0.042 0.16 -9999 0 -0.98 9 9
positive regulation of T cell mediated cytotoxicity 0.018 0.22 -9999 0 -1.1 9 9
ITGA3 0.023 0.2 -9999 0 -1 8 8
IL17F 0.032 0.15 -9999 0 -0.66 8 8
IL12B 0.015 0.025 -9999 0 -0.32 1 1
STAT1 (dimer) 0.018 0.21 -9999 0 -1 9 9
CD4 0.025 0.2 -9999 0 -0.99 8 8
IL23 0.014 0.2 -9999 0 -0.95 11 11
IL23R 0.021 0.053 -9999 0 -10000 0 0
IL1B 0.017 0.22 -9999 0 -1.1 10 10
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 0.02 0.2 -9999 0 -1 8 8
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 0.076 -9999 0 -10000 0 0
positive regulation of chronic inflammatory response 0.018 0.22 -9999 0 -1.1 9 9
natural killer cell activation -0.001 0.005 -9999 0 -10000 0 0
JAK2 0.013 0.06 -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 -0.91 11 11
ALOX12B 0.019 0.2 -9999 0 -1 7 7
CXCL1 -0.003 0.24 -9999 0 -1.1 14 14
T cell proliferation 0.018 0.22 -9999 0 -1.1 9 9
NFKBIA 0.012 0.002 -9999 0 -10000 0 0
IL17A 0.043 0.13 -9999 0 -0.54 6 6
PI3K -0.026 0.18 -9999 0 -1 9 9
IFNG 0.003 0.019 -9999 0 -10000 0 0
STAT3 (dimer) -0.047 0.16 -9999 0 -0.96 9 9
IL18R1 0.007 0.036 -9999 0 -0.41 4 4
IL23/IL23R/JAK2/TYK2/SOCS3 0.03 0.14 -9999 0 -0.64 7 7
IL18/IL18R 0.014 0.045 -9999 0 -0.21 18 18
macrophage activation -0.003 0.01 -9999 0 -0.041 12 12
TNF 0.015 0.22 -9999 0 -1.1 8 8
STAT3/STAT4 -0.024 0.18 -9999 0 -1 9 9
STAT4 (dimer) 0.018 0.21 -9999 0 -1 9 9
IL18 0.005 0.044 -9999 0 -0.33 9 9
IL19 0.006 0.2 -9999 0 -1 8 8
STAT5A (dimer) 0.018 0.21 -9999 0 -1.1 9 9
STAT1 0.01 0.015 -9999 0 -0.33 1 1
SOCS3 0.009 0.026 -9999 0 -0.41 2 2
CXCL9 0.004 0.23 -9999 0 -1.2 10 10
MPO 0.023 0.2 -9999 0 -0.99 8 8
positive regulation of humoral immune response 0.018 0.22 -9999 0 -1.1 9 9
IL23/IL23R/JAK2/TYK2 0.017 0.22 -9999 0 -1.1 9 9
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 0.061 -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 0.018 0.22 -9999 0 -1.1 9 9
NOS2 0.014 0.23 -9999 0 -1.1 13 13
p38 MAPK 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
TRAF6/ASK1 0.01 0.015 -10000 0 -0.2 3 3
TRAF2/ASK1 0.014 0.019 -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 -0.046 0.13 -10000 0 -0.33 89 89
CCM2 0.011 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.017 0.073 -10000 0 -0.18 89 89
MAPK11 0.009 0.026 -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 -0.18 15 15
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BAG4 0.009 0.031 -9999 0 -0.41 3 3
Caspase 8 (4 units) 0.03 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 0.061 -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 -0.18 2 2
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 0.035 -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 0.04 -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 -0.24 2 2
CHUK 0.05 0.028 -9999 0 -0.2 2 2
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 67 67
FASLG 0.013 0.061 -9999 0 -0.35 13 13
NFKB1 0.011 0.022 -9999 0 -0.4 1 1
TNFR1A/BAG4/TNF-alpha -0.003 0.067 -9999 0 -0.18 70 70
CASP6 -0.003 0.022 -9999 0 -10000 0 0
CASP7 0.057 0.068 -9999 0 -0.42 9 9
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 -0.42 9 9
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 -0.22 2 2
APAF-1/Caspase 9 -0.007 0.04 -9999 0 -0.28 9 9
BCL2 0.026 0.067 -9999 0 -0.29 6 6
Stabilization and expansion of the E-cadherin adherens junction

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
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 0.048 -10000 0 -0.38 7 7
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 -0.005 0.07 -10000 0 -0.34 23 23
NCKAP1 0.011 0 -10000 0 -10000 0 0
AQP3 -0.004 0.044 -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 -0.18 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 0.026 -10000 0 -0.41 2 2
EGFR/EGFR/EGF/EGF -0.01 0.04 -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 -0.068 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 0.013 -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 0.038 -10000 0 -0.36 1 1
HGF/MET -0.036 0.073 -10000 0 -0.47 3 3
HGF -0.075 0.17 -10000 0 -0.41 110 110
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 0.026 -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 0.027 -10000 0 -0.36 2 2
IGF-1R heterotetramer/IGF1 -0.038 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 0.046 -10000 0 -0.37 8 8
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
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 67 67
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 67 67
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 0.01 -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 0.008 0.033 -9999 0 -0.33 5 5
regulation of centriole replication 0.015 0.026 -9999 0 -0.23 6 6
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 0.026 -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 0.065 -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 -0.2 3 3
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 0.026 -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 -0.18 5 5
TRAIL/TRAILR2/FADD 0.02 0.024 -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 -0.19 3 3
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
Class I PI3K signaling events

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
ARF5/GTP 0.002 0.023 0.21 6 -10000 0 6
DAPP1 0.028 0.043 -10000 0 -0.3 3 3
Src family/SYK family/BLNK-LAT/BTK-ITK 0.044 0.047 -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 0.021 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 0.062 -10000 0 -0.41 12 12
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 0.024 -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 0.2 5 -0.2 1 6
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 -0.38 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 0.034 0.04 -10000 0 -0.3 1 1
BLK -0.015 0.087 -10000 0 -0.33 38 38
PDPK1 0.011 0 -10000 0 -10000 0 0
CYTH1 0.002 0.022 0.2 6 -10000 0 6
HCK 0.007 0.039 -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 0.021 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 0.026 0.2 6 -0.2 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 0.068 -10000 0 -0.26 25 25
ITK -0.002 0.035 0.2 6 -10000 0 6
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.053 0.039 0.18 5 -0.24 1 6
LCK 0.008 0.034 -10000 0 -0.35 5 5
BTK 0.001 0.025 0.2 6 -10000 0 6
Arf6 trafficking 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
SLC2A4 -0.19 0.21 -10000 0 -0.41 261 261
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 -0.009 0.074 -10000 0 -0.23 53 53
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 0.018 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 0.016 -10000 0 -10000 0 0
VAMP3 0.015 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.074 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 -0.21 1 1
RALA 0.011 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0.005 -10000 0 -10000 0 0
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 0.026 -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 0.041 -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 0.028 -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 0.028 -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 -0.18 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 -0.029 0.12 -9999 0 -0.41 51 51
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 0.036 -9999 0 -10000 0 0
YY1/HDAC2 0.021 0.031 -9999 0 -0.19 11 11
YY1/HDAC1 0.021 0.031 -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 0.028 -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 0.026 -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 0.026 -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 0.018 -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 0.018 -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 -0.004 0.073 -9999 0 -0.21 51 51
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 67 67
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 0.025 -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 67 67
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 0.015 -9999 0 -10000 0 0
TFCP2 0.006 0.048 -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
Paxillin-dependent events mediated by a4b1

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
CRKL 0.011 0 -10000 0 -10000 0 0
Rac1/GDP 0 0.003 -10000 0 -10000 0 0
DOCK1 0.006 0.048 -10000 0 -0.41 7 7
ITGA4 0.009 0.029 -10000 0 -0.38 3 3
RAC1 0.011 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.014 0.023 -10000 0 -0.25 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.011 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.021 0.017 -10000 0 -0.21 3 3
alpha4/beta7 Integrin/Paxillin 0.026 0.017 -10000 0 -0.2 2 2
lamellipodium assembly -0.006 0.047 -10000 0 -0.4 6 6
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
PI3K 0.013 0.031 -10000 0 -0.28 6 6
ARF6 0.011 0 -10000 0 -10000 0 0
TLN1 0.011 0 -10000 0 -10000 0 0
PXN 0.018 0 -10000 0 -10000 0 0
PIK3R1 0.007 0.04 -10000 0 -0.41 5 5
ARF6/GTP -0.001 0.011 -10000 0 -10000 0 0
cell adhesion 0.031 0.015 -10000 0 -0.18 2 2
CRKL/CBL 0.016 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.026 0.016 -10000 0 -0.2 2 2
ITGB1 0.011 0 -10000 0 -10000 0 0
ITGB7 0.01 0.015 -10000 0 -0.33 1 1
ARF6/GDP 0 0.003 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.016 0.06 -10000 0 -0.19 40 40
p130Cas/Crk/Dock1 0.019 0.028 -10000 0 -0.23 7 7
VCAM1 -0.02 0.11 -10000 0 -0.41 40 40
alpha4/beta1 Integrin/Paxillin/Talin 0.032 0.015 -10000 0 -0.18 2 2
alpha4/beta1 Integrin/Paxillin/GIT1 0.032 0.015 -10000 0 -0.18 2 2
BCAR1 0.011 0 -10000 0 -10000 0 0
mol:GDP -0.031 0.015 0.18 2 -10000 0 2
CBL 0.011 0 -10000 0 -10000 0 0
PRKACA 0.011 0 -10000 0 -10000 0 0
GIT1 0.011 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.032 0.015 -10000 0 -0.18 2 2
Rac1/GTP -0.007 0.053 -10000 0 -0.44 6 6
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.01 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 -0.004 0.07 -9999 0 -0.33 24 24
PIAS4 0.011 0 -9999 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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
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
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 0.008 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0.024 0 -9999 0 -10000 0 0
CaM/Ca2+ 0.036 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 0.008 -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 0.051 -9999 0 -10000 0 0
MAPK1 0.026 0.051 -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 0.03 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 0.051 -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 0.008 -9999 0 -10000 0 0
RASA1 0.03 0.022 -9999 0 -10000 0 0
NRP2 -0.009 0.089 -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 0.026 -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 0.013 -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 0.009 0.006 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.023 0.039 0.21 14 -10000 0 14
ARF1/GTP 0 0.002 -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 0.008 -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 0.023 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 0.008 -10000 0 -10000 0 0
actin filament bundle formation -0.021 0.01 -10000 0 -10000 0 0
KALRN -0.001 0.023 -10000 0 -0.21 5 5
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 0.009 0.006 -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 0.009 0.006 -10000 0 -10000 0 0
ARF6/GTP 0.009 0.006 -10000 0 -10000 0 0
RhoA/GTP 0 0.002 -10000 0 -10000 0 0
mol:GDP 0.002 0.013 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0.022 0.005 -10000 0 -10000 0 0
RHOA 0.011 0 -10000 0 -10000 0 0
PLD1 0.017 0.004 -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 0.009 0.006 -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 -0.35 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 -0.13 1 1
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 -0.18 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 0.026 -9999 0 -0.41 2 2
RhoA/GDP 0.048 0.016 -9999 0 -10000 0 0
actin cytoskeleton organization 0.034 0.016 -9999 0 -10000 0 0
CDC42/GDP 0.048 0.016 -9999 0 -10000 0 0
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 -10000 0 0
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 0.006 -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 0.019 -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 -0.22 7 7
adherens junction organization 0.033 0.028 -10000 0 -0.34 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 -0.34 2 2
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 -0.41 2 2
CTNND1 0.012 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.033 0.025 -10000 0 -0.47 1 1
VASP 0.033 0.025 -10000 0 -0.34 2 2
ZYX 0.033 0.025 -10000 0 -0.34 2 2
JUB 0.033 0.025 -10000 0 -0.34 2 2
EGFR(dimer) 0.028 0.045 -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 0.031 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 -0.33 2 2
SRC 0.011 0 -10000 0 -10000 0 0
RAC1 0.011 0 -10000 0 -10000 0 0
RHOA 0.011 0 -10000 0 -10000 0 0
EGFR 0 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 0.037 -10000 0 -0.46 1 1
apoptosis -0.034 0.028 0.2 7 -10000 0 7
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 -0.48 1 1
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 0.026 -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 0.026 -9999 0 -0.41 2 2
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 0.034 0.017 -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 0.023 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 0.016 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 0.007 -9999 0 -0.15 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.011 0 -9999 0 -10000 0 0
DDEF1 0 0.007 -9999 0 -0.16 1 1
ARF1/GDP 0 0.002 -9999 0 -10000 0 0
AP2M1 0.011 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0.014 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 0.021 0.002 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0.008 0 -9999 0 -10000 0 0
GGA3 0.011 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0.015 0.003 -9999 0 -10000 0 0
AP2A1 0.011 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.022 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 0.007 -9999 0 -0.15 1 1
KDEL Receptor/Ligand/ARF-GAP1 0.009 0 -9999 0 -10000 0 0
GOSR2 0 0 -9999 0 -10000 0 0
USO1 0 0 -9999 0 -10000 0 0
GBF1 0 0 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0.016 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 538 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/11493814/UCEC-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = Copy number data was not used in this analysis.

Data Sets and Pathway Interactions

Both copy number and expression data are incorporated into PARADIGM's inference. Whenever normal tissue controls are available for analysis in the expression data, each patient's gene-value is normalized by subtracting the gene's median level observed in the normal control. Copy number data is also normalized to reflect the difference in copy number between a gene's levels detected in tumor versus control (e.g. blood normal). The collection of pathways used by PARADIGM includes those from NCI-PID on September 15, 2009 containing 131 pathways, 11,563 interactions, and 7,204 entities. All gene identifiers were translated into HUGO standard identifiers wherever possible. We refer to molecular entities as "concepts," which include gene products such as proteins and miRNAs, small molecules, protein complexes, and abstract concepts. Each concept is represented as "node" in PARADIGM's graphical model. The abstract concepts correspond to general cellular processes (such as "apoptosis" or "DNA damage response") and families of genes that share functional activity such as the RAS family of signal transducers. Various types of concept-concept interactions are included in the pathways including protein-protein interactions, transcriptional regulatory interactions, and protein modifications such as phosphorylation and ubiquitinylation interactions.

Pathway Inference Method

The PARADIGM algorithm (described in PMID: 20529912) assigns an integrated pathway level (IPL) reflecting the activity of a concept determined through a belief propagation strategy. The belief propagation is given the copy number and gene expression measurements of all of the genes and iteratively updates hidden states reflecting the activities of all of the genes in a pathway so as to maximize the likelihood of the observed data given the interactions in the pathway. In the end, the inferred level of a concept reflects both the data observed for the concept and the neighborhood of activity surrounding the concept.

Determining significantly altered levels

The significance of the IPL obtained for each concept in each patient sample is assessed using a permutation analysis. Importantly, the permutation analysis preserves data tuples so as to preserve any implicit correlations between the different data modalities. For example, genes that are deleted have concomitantly lower expression levels. Preserving the copy number and expression pairs therefore retains this data property. The simulation therefore makes "null samples" by permuting data tuples across all of the genes in the genome so that each gene in a null sample is associated with a random tuple of another gene with equal probability. This approach has the added benefit of preserving the pathway structure so that every observed IPL can be compared to a distribution of random IPLs derived from exactly the same interaction context. PARADIGM inferences are then obtained for 1000 "null" patients and serve as a background distribution to contrast the observed IPLs against. Pathway concepts are excluded from further analysis if they did not obtain a minimum IPL of 0.5 in any patient sample both observed or simulated.

An IPL I(i,j) for concept i in sample j, is considered to be deviated if its absolute level is two standard deviations from the average level observed for concept i in the 1000 null samples. The degree to which a concept has significantly altered levels across a patient cohort is summarized in the proportion of deviated samples (PDS) score. For example, a protein with a PDS of 0.10 reflects that the protein's level of activity was inferred to be significantly higher or lower in tumors compared to normal in 10% of the patient samples. An average PDS for a pathway is also reported by computing the mean PDS over all concepts in the pathway.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[2] Charles J. Vaske, Stephen C. Benz, J. Zachary Sanborn, Dent Earl, Christopher Szeto, Jingchun Zhu, David Haussler, and Joshua M. Stuart, Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM, Bioinformatics 12(26):237-245 (2010)
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