PARADIGM pathway analysis of mRNASeq expression and copy number data
Lung Adenocarcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C17D2SXR
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C17D2SXR
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 44 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 217
Glypican 2 network 171
Angiopoietin receptor Tie2-mediated signaling 141
HIF-1-alpha transcription factor network 133
Aurora B signaling 119
Signaling events mediated by the Hedgehog family 103
Endothelins 76
PLK1 signaling events 71
Aurora C signaling 67
Signaling mediated by p38-alpha and p38-beta 66
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 488 . 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 ( 488 ).

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 0.4447 217 11090 51 -0.03 0.76 1000 -1000 -0.075 -1000
Glypican 2 network 0.3504 171 687 4 0.094 0.14 1000 -1000 0.017 -1000
Angiopoietin receptor Tie2-mediated signaling 0.2889 141 12495 88 -0.57 0.11 1000 -1000 -0.047 -1000
HIF-1-alpha transcription factor network 0.2725 133 10112 76 -0.066 0.43 1000 -1000 -0.033 -1000
Aurora B signaling 0.2439 119 7990 67 -0.16 0.28 1000 -1000 -0.029 -1000
Signaling events mediated by the Hedgehog family 0.2111 103 5375 52 -0.22 0.1 1000 -1000 -0.022 -1000
Endothelins 0.1557 76 7357 96 -0.31 0.19 1000 -1000 -0.039 -1000
PLK1 signaling events 0.1455 71 6093 85 -0.048 0.19 1000 -1000 -0.027 -1000
Aurora C signaling 0.1373 67 474 7 0 0.16 1000 -1000 -0.006 -1000
Signaling mediated by p38-alpha and p38-beta 0.1352 66 2920 44 -0.1 0.021 1000 -1000 -0.017 -1000
Visual signal transduction: Cones 0.1250 61 2349 38 -0.08 0.12 1000 -1000 -0.015 -1000
FOXA2 and FOXA3 transcription factor networks 0.1209 59 2718 46 -0.2 0.15 1000 -1000 -0.068 -1000
Osteopontin-mediated events 0.1127 55 2094 38 -0.001 0.23 1000 -1000 -0.027 -1000
Fc-epsilon receptor I signaling in mast cells 0.1127 55 5337 97 -0.093 0.021 1000 -1000 -0.043 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.1045 51 2667 52 -0.14 0.045 1000 -1000 -0.032 -1000
BMP receptor signaling 0.1025 50 4128 81 -0.18 0.22 1000 -1000 -0.019 -1000
Signaling events regulated by Ret tyrosine kinase 0.1025 50 4114 82 -0.074 0.061 1000 -1000 -0.044 -1000
amb2 Integrin signaling 0.1004 49 4074 82 -0.29 0.079 1000 -1000 -0.016 -1000
IL4-mediated signaling events 0.0984 48 4433 91 -0.63 0.34 1000 -1000 -0.12 -1000
Visual signal transduction: Rods 0.0943 46 2432 52 -0.08 0.098 1000 -1000 -0.035 -1000
Ephrin B reverse signaling 0.0902 44 2146 48 -0.074 0.076 1000 -1000 -0.023 -1000
Syndecan-1-mediated signaling events 0.0799 39 1355 34 0 0.21 1000 -1000 -0.023 -1000
p75(NTR)-mediated signaling 0.0799 39 4908 125 -0.15 0.13 1000 -1000 -0.045 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0779 38 2584 68 -0.15 0.064 1000 -1000 -0.053 -1000
Thromboxane A2 receptor signaling 0.0758 37 3936 105 -0.12 0.07 1000 -1000 -0.032 -1000
IL23-mediated signaling events 0.0738 36 2194 60 -0.2 0.027 1000 -1000 -0.097 -1000
TCGA08_retinoblastoma 0.0697 34 279 8 -0.022 0.098 1000 -1000 -0.002 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0697 34 4133 120 -0.16 0.14 1000 -1000 -0.036 -1000
LPA4-mediated signaling events 0.0676 33 397 12 -0.072 0 1000 -1000 -0.016 -1000
Integrins in angiogenesis 0.0676 33 2805 84 -0.071 0.23 1000 -1000 -0.038 -1000
Arf6 signaling events 0.0656 32 2010 62 -0.1 0.07 1000 -1000 -0.026 -1000
HIF-2-alpha transcription factor network 0.0656 32 1391 43 -0.13 0.14 1000 -1000 -0.048 -1000
Canonical Wnt signaling pathway 0.0656 32 1680 51 -0.2 0.097 1000 -1000 -0.033 -1000
Presenilin action in Notch and Wnt signaling 0.0635 31 1921 61 -0.21 0.097 1000 -1000 -0.034 -1000
Glucocorticoid receptor regulatory network 0.0635 31 3596 114 -0.26 0.16 1000 -1000 -0.042 -1000
Reelin signaling pathway 0.0615 30 1734 56 -0.038 0.049 1000 -1000 -0.022 -1000
EGFR-dependent Endothelin signaling events 0.0615 30 637 21 -0.027 0.07 1000 -1000 -0.032 -1000
IL6-mediated signaling events 0.0594 29 2184 75 -0.15 0.051 1000 -1000 -0.047 -1000
Aurora A signaling 0.0574 28 1731 60 -0.028 0.18 1000 -1000 -0.02 -1000
Glypican 1 network 0.0574 28 1344 48 -0.06 0.037 1000 -1000 -0.021 -1000
TCGA08_p53 0.0553 27 191 7 -0.023 0.019 1000 -1000 -0.009 -1000
Wnt signaling 0.0553 27 191 7 -0.021 0.038 1000 -1000 -0.007 -1000
Effects of Botulinum toxin 0.0533 26 700 26 0 0.044 1000 -1000 -0.008 -1000
Noncanonical Wnt signaling pathway 0.0512 25 651 26 -0.043 0.038 1000 -1000 -0.026 -1000
Nongenotropic Androgen signaling 0.0492 24 1276 52 -0.062 0.044 1000 -1000 -0.021 -1000
ErbB2/ErbB3 signaling events 0.0471 23 1526 65 -0.049 0.03 1000 -1000 -0.054 -1000
ErbB4 signaling events 0.0471 23 1640 69 -0.11 0.15 1000 -1000 -0.019 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0451 22 769 34 -0.036 0.061 1000 -1000 -0.024 -1000
IL1-mediated signaling events 0.0451 22 1407 62 -0.082 0.043 1000 -1000 -0.039 -1000
FoxO family signaling 0.0451 22 1417 64 0 0.19 1000 -1000 -0.044 -1000
PDGFR-alpha signaling pathway 0.0430 21 964 44 -0.19 0.039 1000 -1000 -0.022 -1000
LPA receptor mediated events 0.0430 21 2157 102 -0.058 0.079 1000 -1000 -0.068 -1000
Syndecan-4-mediated signaling events 0.0430 21 1455 67 -0.043 0.12 1000 -1000 -0.031 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0430 21 701 33 -0.07 0.096 1000 -1000 -0.029 -1000
Regulation of Androgen receptor activity 0.0430 21 1523 70 -0.14 0.13 1000 -1000 -0.036 -1000
Syndecan-2-mediated signaling events 0.0410 20 1391 69 -0.047 0.053 1000 -1000 -0.037 -1000
EPHB forward signaling 0.0389 19 1687 85 -0.032 0.084 1000 -1000 -0.043 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0369 18 1018 54 -0.034 0.1 1000 -1000 -0.03 -1000
Ceramide signaling pathway 0.0369 18 1437 76 -0.019 0.07 1000 -1000 -0.021 -1000
FAS signaling pathway (CD95) 0.0369 18 892 47 -0.24 0.034 1000 -1000 -0.022 -1000
Class IB PI3K non-lipid kinase events 0.0369 18 54 3 -0.008 0.008 1000 -1000 -0.02 -1000
IL12-mediated signaling events 0.0348 17 1487 87 -0.13 0.057 1000 -1000 -0.059 -1000
Nectin adhesion pathway 0.0348 17 1113 63 -0.046 0.051 1000 -1000 -0.046 -1000
S1P5 pathway 0.0348 17 291 17 -0.016 0.021 1000 -1000 -0.002 -1000
Calcium signaling in the CD4+ TCR pathway 0.0348 17 537 31 -0.039 0.03 1000 -1000 -0.03 -1000
Coregulation of Androgen receptor activity 0.0328 16 1263 76 -0.057 0.096 1000 -1000 -0.023 -1000
PLK2 and PLK4 events 0.0328 16 50 3 -0.007 0.036 1000 -1000 -0.016 -1000
Signaling events mediated by PTP1B 0.0328 16 1254 76 -0.056 0.071 1000 -1000 -0.03 -1000
TCR signaling in naïve CD8+ T cells 0.0328 16 1535 93 -0.041 0.034 1000 -1000 -0.038 -1000
Plasma membrane estrogen receptor signaling 0.0328 16 1458 86 -0.061 0.057 1000 -1000 -0.038 -1000
Caspase cascade in apoptosis 0.0307 15 1134 74 -0.03 0.086 1000 -1000 -0.034 -1000
BARD1 signaling events 0.0307 15 867 57 -0.046 0.11 1000 -1000 -0.032 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0307 15 1331 85 -0.058 0.035 1000 -1000 -0.036 -1000
S1P1 pathway 0.0307 15 550 36 -0.09 0.021 1000 -1000 -0.022 -1000
BCR signaling pathway 0.0307 15 1570 99 -0.049 0.08 1000 -1000 -0.043 -1000
S1P4 pathway 0.0287 14 364 25 -0.019 0.027 1000 -1000 -0.018 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0287 14 1109 78 -0.038 0.023 1000 -1000 -0.034 -1000
Signaling events mediated by HDAC Class III 0.0266 13 536 40 -0.06 0.061 1000 -1000 -0.031 -1000
Syndecan-3-mediated signaling events 0.0266 13 468 35 -0.12 0.046 1000 -1000 -0.02 -1000
Regulation of p38-alpha and p38-beta 0.0266 13 744 54 -0.036 0.06 1000 -1000 -0.039 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0246 12 1601 125 -0.19 0.042 1000 -1000 -0.046 -1000
Signaling events mediated by PRL 0.0225 11 385 34 -0.021 0.082 1000 -1000 -0.033 -1000
IL27-mediated signaling events 0.0205 10 547 51 -0.044 0.03 1000 -1000 -0.054 -1000
Class I PI3K signaling events 0.0205 10 768 73 -0.033 0.06 1000 -1000 -0.03 -1000
Ephrin A reverse signaling 0.0184 9 63 7 -0.012 0.029 1000 -1000 -0.009 -1000
IL2 signaling events mediated by STAT5 0.0184 9 219 22 -0.024 0.091 1000 -1000 -0.024 -1000
PDGFR-beta signaling pathway 0.0184 9 937 97 -0.032 0.052 1000 -1000 -0.039 -1000
Regulation of nuclear SMAD2/3 signaling 0.0164 8 1190 136 -0.17 0.072 1000 -1000 -0.026 -1000
JNK signaling in the CD4+ TCR pathway 0.0164 8 146 17 -0.012 0.047 1000 -1000 -0.025 -1000
Cellular roles of Anthrax toxin 0.0164 8 321 39 -0.031 0.027 1000 -1000 -0.016 -1000
Hedgehog signaling events mediated by Gli proteins 0.0164 8 548 65 -0.14 0.048 1000 -1000 -0.038 -1000
EPO signaling pathway 0.0164 8 469 55 -0.025 0.046 1000 -1000 -0.029 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0164 8 604 74 -0.086 0.07 1000 -1000 -0.041 -1000
Regulation of Telomerase 0.0164 8 852 102 -0.02 0.099 1000 -1000 -0.029 -1000
Insulin Pathway 0.0164 8 642 74 -0.096 0.051 1000 -1000 -0.038 -1000
VEGFR1 specific signals 0.0164 8 497 56 -0.19 0.047 1000 -1000 -0.03 -1000
Ras signaling in the CD4+ TCR pathway 0.0164 8 148 17 -0.004 0.031 1000 -1000 -0.013 -1000
mTOR signaling pathway 0.0143 7 406 53 -0.057 0.025 1000 -1000 -0.031 -1000
IFN-gamma pathway 0.0143 7 491 68 -0.028 0.063 1000 -1000 -0.034 -1000
ceramide signaling pathway 0.0143 7 379 49 -0.007 0.029 1000 -1000 -0.025 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0143 7 604 83 -0.056 0.046 1000 -1000 -0.017 -1000
Retinoic acid receptors-mediated signaling 0.0143 7 449 58 -0.094 0.046 1000 -1000 -0.032 -1000
E-cadherin signaling in the nascent adherens junction 0.0143 7 546 76 -0.03 0.051 1000 -1000 -0.038 -1000
Arf6 trafficking events 0.0143 7 509 71 -0.037 0.039 1000 -1000 -0.031 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0123 6 178 28 -0.015 0.034 1000 -1000 -0.018 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0123 6 302 45 -0.015 0.051 1000 -1000 -0.041 -1000
IGF1 pathway 0.0123 6 345 57 -0.031 0.048 1000 -1000 -0.031 -1000
p38 MAPK signaling pathway 0.0123 6 298 44 -0.005 0.063 1000 -1000 -0.012 -1000
Signaling events mediated by HDAC Class I 0.0102 5 573 104 -0.035 0.048 1000 -1000 -0.029 -1000
Signaling mediated by p38-gamma and p38-delta 0.0102 5 89 15 -0.017 0.022 1000 -1000 -0.02 -1000
IL2 signaling events mediated by PI3K 0.0102 5 338 58 -0.014 0.077 1000 -1000 -0.031 -1000
TCGA08_rtk_signaling 0.0102 5 143 26 -0.013 0.047 1000 -1000 -0.008 -1000
E-cadherin signaling in keratinocytes 0.0102 5 241 43 -0.015 0.039 1000 -1000 -0.021 -1000
Signaling events mediated by HDAC Class II 0.0082 4 354 75 -0.021 0.057 1000 -1000 -0.023 -1000
Circadian rhythm pathway 0.0082 4 92 22 -0.004 0.046 1000 -1000 -0.025 -1000
Arf6 downstream pathway 0.0082 4 188 43 -0.048 0.049 1000 -1000 -0.022 -1000
Class I PI3K signaling events mediated by Akt 0.0082 4 273 68 -0.029 0.044 1000 -1000 -0.021 -1000
S1P3 pathway 0.0082 4 193 42 -0.022 0.035 1000 -1000 -0.026 -1000
Canonical NF-kappaB pathway 0.0041 2 101 39 -0.016 0.042 1000 -1000 -0.018 -1000
Insulin-mediated glucose transport 0.0041 2 78 32 -0.015 0.038 1000 -1000 -0.016 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0041 2 100 37 -0.023 0.05 1000 -1000 -0.016 -1000
TRAIL signaling pathway 0.0041 2 112 48 -0.017 0.046 1000 -1000 -0.018 -1000
Rapid glucocorticoid signaling 0.0041 2 46 20 -0.008 0.026 1000 -1000 -0.008 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0020 1 28 23 0 0.036 1000 -1000 -0.012 -1000
a4b1 and a4b7 Integrin signaling 0.0020 1 7 5 0.02 0.03 1000 -1000 0.019 -1000
Paxillin-dependent events mediated by a4b1 0.0020 1 64 36 -0.037 0.039 1000 -1000 -0.023 -1000
Atypical NF-kappaB pathway 0.0020 1 37 31 -0.017 0.029 1000 -1000 -0.018 -1000
E-cadherin signaling events 0.0020 1 6 5 0.019 0.039 1000 -1000 0.018 -1000
Arf1 pathway 0.0020 1 102 54 -0.008 0.034 1000 -1000 -0.015 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 23 27 -0.018 0.045 1000 -1000 -0.026 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.056 1000 -1000 0 -1000
Total NA 3389 200244 7203 -9.5 11 131000 -131000 -3.8 -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 0.62 0.47 1 261 -10000 0 261
PLK1 0.36 0.32 0.67 220 -0.68 2 222
BIRC5 0.39 0.32 0.69 220 -0.72 2 222
HSPA1B 0.63 0.48 1 260 -10000 0 260
MAP2K1 0.18 0.15 0.32 244 -10000 0 244
BRCA2 0.62 0.48 1 259 -10000 0 259
FOXM1 0.76 0.62 1.3 270 -0.82 1 271
XRCC1 0.62 0.48 1 261 -10000 0 261
FOXM1B/p19 0.21 0.35 0.83 100 -0.78 2 102
Cyclin D1/CDK4 0.51 0.42 0.9 246 -0.69 1 247
CDC2 0.69 0.55 1.1 271 -0.74 1 272
TGFA 0.55 0.44 0.93 260 -0.68 2 262
SKP2 0.68 0.53 1.1 268 -10000 0 268
CCNE1 0.15 0.16 0.37 155 -10000 0 155
CKS1B 0.67 0.52 1.1 264 -10000 0 264
RB1 0.36 0.35 0.72 218 -0.62 3 221
FOXM1C/SP1 0.55 0.42 0.91 250 -0.78 1 251
AURKB 0.33 0.36 0.67 219 -0.7 16 235
CENPF 0.7 0.55 1.1 271 -10000 0 271
CDK4 0.084 0.065 0.18 78 -10000 0 78
MYC 0.42 0.42 0.86 206 -0.67 2 208
CHEK2 0.19 0.15 0.32 241 -10000 0 241
ONECUT1 0.59 0.47 0.99 258 -0.72 1 259
CDKN2A -0.03 0.15 0.25 52 -0.21 140 192
LAMA4 0.61 0.49 1 260 -1.1 5 265
FOXM1B/HNF6 0.6 0.48 1 249 -0.78 1 250
FOS 0.56 0.52 1 240 -0.88 3 243
SP1 0.022 0.005 -10000 0 -10000 0 0
CDC25B 0.62 0.48 1 261 -10000 0 261
response to radiation 0.13 0.11 0.23 245 -10000 0 245
CENPB 0.62 0.48 1 260 -10000 0 260
CENPA 0.7 0.55 1.2 271 -10000 0 271
NEK2 0.72 0.55 1.2 275 -10000 0 275
HIST1H2BA 0.62 0.48 1 259 -10000 0 259
CCNA2 0.13 0.15 0.39 116 -10000 0 116
EP300 0.02 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.67 0.53 1.1 257 -10000 0 257
CCNB2 0.69 0.55 1.1 266 -10000 0 266
CCNB1 0.71 0.57 1.2 265 -10000 0 265
ETV5 0.61 0.5 1 254 -1.1 2 256
ESR1 0.6 0.5 1 253 -1.1 4 257
CCND1 0.59 0.47 0.98 262 -0.7 1 263
GSK3A 0.14 0.11 0.26 212 -10000 0 212
Cyclin A-E1/CDK1-2 0.26 0.21 0.43 254 -10000 0 254
CDK2 0.059 0.038 0.16 1 -10000 0 1
G2/M transition of mitotic cell cycle 0.17 0.14 0.28 267 -10000 0 267
FOXM1B/Cbp/p300 0.16 0.26 0.68 61 -0.74 2 63
GAS1 0.59 0.5 1 255 -1 5 260
MMP2 0.62 0.48 1 261 -10000 0 261
RB1/FOXM1C 0.49 0.43 0.9 236 -0.73 1 237
CREBBP 0.021 0.004 -10000 0 -10000 0 0
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK 0.11 0.14 0.32 145 -9999 0 145
GPC2 0.094 0.13 0.32 120 -9999 0 120
GPC2/Midkine 0.14 0.14 0.28 211 -9999 0 211
neuron projection morphogenesis 0.14 0.14 0.28 211 -9999 0 211
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.45 0.48 -10000 0 -0.94 227 227
NCK1/PAK1/Dok-R -0.21 0.2 -10000 0 -0.42 230 230
NCK1/Dok-R -0.49 0.57 -10000 0 -1.1 226 226
PIK3CA 0.021 0.005 -10000 0 -10000 0 0
mol:beta2-estradiol 0.059 0.094 0.23 112 -10000 0 112
RELA 0.021 0.004 -10000 0 -10000 0 0
SHC1 0.017 0.007 -10000 0 -10000 0 0
Rac/GDP 0.014 0.005 -10000 0 -10000 0 0
F2 0.11 0.16 0.32 159 -10000 0 159
TNIP2 0.021 0.003 -10000 0 -10000 0 0
NF kappa B/RelA -0.44 0.53 -10000 0 -0.97 226 226
FN1 0.019 0.034 0.32 1 -0.32 4 5
PLD2 -0.51 0.59 -10000 0 -1.1 225 225
PTPN11 0.021 0.004 -10000 0 -10000 0 0
GRB14 0.033 0.076 0.32 26 -0.32 5 31
ELK1 -0.46 0.51 -10000 0 -0.98 226 226
GRB7 0.019 0.022 -10000 0 -0.32 2 2
PAK1 0.02 0.004 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.46 0.56 -10000 0 -1 226 226
CDKN1A -0.32 0.32 -10000 0 -0.65 227 227
ITGA5 0.021 0.021 0.32 1 -0.32 1 2
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.49 0.57 -10000 0 -1.1 226 226
CRK 0.019 0.006 -10000 0 -10000 0 0
mol:NO -0.32 0.34 -10000 0 -0.67 225 225
PLG -0.51 0.59 -10000 0 -1.1 225 225
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.42 0.44 -10000 0 -0.87 227 227
GRB2 0.02 0.004 -10000 0 -10000 0 0
PIK3R1 0.016 0.018 -10000 0 -0.32 1 1
ANGPT2 -0.29 0.32 0.35 1 -0.66 170 171
BMX -0.55 0.61 -10000 0 -1.2 225 225
ANGPT1 -0.3 0.47 -10000 0 -1.1 116 116
tube development -0.36 0.36 -10000 0 -0.73 227 227
ANGPT4 -0.15 0.16 -10000 0 -0.32 233 233
response to hypoxia -0.031 0.032 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.52 0.62 -10000 0 -1.1 226 226
alpha5/beta1 Integrin 0.03 0.016 0.23 1 -0.23 1 2
FGF2 -0.023 0.11 -10000 0 -0.32 62 62
STAT5A (dimer) -0.42 0.42 -10000 0 -0.84 228 228
mol:L-citrulline -0.32 0.34 -10000 0 -0.67 225 225
AGTR1 -0.082 0.16 0.32 1 -0.32 147 148
MAPK14 -0.57 0.63 -10000 0 -1.2 228 228
Tie2/SHP2 -0.45 0.52 -10000 0 -1 208 208
TEK -0.49 0.57 -10000 0 -1.1 209 209
RPS6KB1 -0.42 0.46 -10000 0 -0.89 228 228
Angiotensin II/AT1 -0.054 0.11 0.22 1 -0.22 147 148
Tie2/Ang1/GRB2 -0.52 0.62 -10000 0 -1.1 226 226
MAPK3 -0.47 0.52 -10000 0 -1 225 225
MAPK1 -0.46 0.52 -10000 0 -1 223 223
Tie2/Ang1/GRB7 -0.52 0.62 -10000 0 -1.1 226 226
NFKB1 0.021 0.003 -10000 0 -10000 0 0
MAPK8 -0.51 0.59 -10000 0 -1.1 225 225
PI3K -0.52 0.57 -10000 0 -1.1 228 228
FES -0.57 0.63 -10000 0 -1.2 228 228
Crk/Dok-R -0.49 0.57 -10000 0 -1.1 226 226
Tie2/Ang1/ABIN2 -0.52 0.62 -10000 0 -1.1 226 226
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.39 0.41 -10000 0 -0.82 227 227
STAT5A 0.02 0.016 -10000 0 -0.32 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.41 0.46 -10000 0 -0.88 228 228
Tie2/Ang2 -0.51 0.53 -10000 0 -1 228 228
Tie2/Ang1 -0.55 0.66 -10000 0 -1.2 225 225
FOXO1 -0.4 0.42 -10000 0 -0.83 227 227
ELF1 -0.033 0.067 -10000 0 -10000 0 0
ELF2 -0.51 0.59 -10000 0 -1.1 224 224
mol:Choline -0.48 0.55 -10000 0 -1 225 225
cell migration -0.12 0.11 -10000 0 -0.23 231 231
FYN -0.42 0.42 -10000 0 -0.85 227 227
DOK2 -0.003 0.081 -10000 0 -0.32 29 29
negative regulation of cell cycle -0.29 0.29 -10000 0 -0.58 227 227
ETS1 -0.052 0.11 -10000 0 -0.25 104 104
PXN -0.34 0.37 -10000 0 -0.72 228 228
ITGB1 0.021 0.004 -10000 0 -10000 0 0
NOS3 -0.37 0.39 -10000 0 -0.78 225 225
RAC1 0.019 0.007 -10000 0 -10000 0 0
TNF -0.06 0.12 -10000 0 -0.26 116 116
MAPKKK cascade -0.48 0.55 -10000 0 -1 225 225
RASA1 0.02 0.005 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.51 0.61 -10000 0 -1.1 226 226
NCK1 0.021 0.003 -10000 0 -10000 0 0
vasculogenesis -0.29 0.3 -10000 0 -0.6 225 225
mol:Phosphatidic acid -0.48 0.55 -10000 0 -1 225 225
mol:Angiotensin II 0 0.002 -10000 0 -10000 0 0
mol:NADP -0.32 0.34 -10000 0 -0.67 225 225
Rac1/GTP -0.39 0.42 -10000 0 -0.82 227 227
MMP2 -0.51 0.59 -10000 0 -1.1 225 225
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 0.28 0.23 0.52 153 -0.66 4 157
HDAC7 0.031 0.014 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.31 0.31 0.63 177 -0.83 3 180
SMAD4 0.019 0.01 -10000 0 -10000 0 0
ID2 0.28 0.23 0.5 181 -0.67 4 185
AP1 -0.001 0.075 -10000 0 -0.23 37 37
ABCG2 0.26 0.24 0.51 162 -0.62 6 168
HIF1A 0.099 0.089 0.25 68 -0.25 1 69
TFF3 0.31 0.27 0.57 196 -0.7 4 200
GATA2 -0.018 0.098 -10000 0 -0.33 39 39
AKT1 0.095 0.098 0.26 63 -0.24 4 67
response to hypoxia 0.076 0.094 0.19 141 -0.22 8 149
MCL1 0.23 0.23 0.5 150 -0.74 2 152
NDRG1 0.24 0.23 0.51 145 -0.63 4 149
SERPINE1 0.27 0.23 0.51 165 -0.67 4 169
FECH 0.26 0.24 0.5 167 -0.67 4 171
FURIN 0.28 0.24 0.51 181 -0.66 4 185
NCOA2 0.017 0.032 -10000 0 -0.32 4 4
EP300 0.11 0.13 0.28 120 -0.3 13 133
HMOX1 0.27 0.23 0.5 179 -0.63 4 183
BHLHE40 0.28 0.23 0.5 179 -0.67 4 183
BHLHE41 0.25 0.24 0.5 163 -0.65 6 169
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.14 0.14 0.36 74 -0.32 1 75
ENG 0.11 0.097 0.28 41 -0.31 3 44
JUN 0.008 0.04 -10000 0 -0.33 4 4
RORA 0.27 0.23 0.5 173 -0.7 4 177
ABCB1 0.01 0.18 0.36 24 -0.73 19 43
TFRC 0.26 0.23 0.5 161 -0.67 4 165
CXCR4 0.28 0.23 0.5 178 -0.67 4 182
TF 0.32 0.28 0.58 196 -0.63 5 201
CITED2 0.26 0.24 0.5 170 -0.66 4 174
HIF1A/ARNT 0.43 0.39 0.83 193 -0.8 3 196
LDHA 0.053 0.1 0.41 11 -0.55 2 13
ETS1 0.27 0.23 0.5 176 -0.59 4 180
PGK1 0.28 0.23 0.51 169 -0.67 4 173
NOS2 0.26 0.25 0.51 178 -0.73 4 182
ITGB2 0.28 0.23 0.5 177 -0.77 4 181
ALDOA 0.28 0.23 0.5 181 -0.67 4 185
Cbp/p300/CITED2 0.27 0.28 0.57 160 -0.87 4 164
FOS -0.011 0.087 -10000 0 -0.33 31 31
HK2 0.28 0.23 0.5 178 -0.69 5 183
SP1 0.015 0.036 -10000 0 -0.16 17 17
GCK 0.15 0.26 0.5 52 -1 13 65
HK1 0.28 0.23 0.5 177 -0.67 4 181
NPM1 0.27 0.23 0.5 172 -0.67 4 176
EGLN1 0.26 0.23 0.5 173 -0.81 2 175
CREB1 0.023 0.009 -10000 0 -10000 0 0
PGM1 0.28 0.23 0.5 176 -0.66 4 180
SMAD3 0.02 0.008 -10000 0 -10000 0 0
EDN1 -0.066 0.41 0.39 5 -0.97 76 81
IGFBP1 0.28 0.26 0.55 179 -0.67 4 183
VEGFA 0.25 0.23 0.49 165 -0.68 3 168
HIF1A/JAB1 0.079 0.065 0.22 29 -0.17 1 30
CP 0.37 0.28 0.59 256 -0.66 4 260
CXCL12 0.27 0.24 0.52 152 -0.77 4 156
COPS5 0.02 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4 0.027 0.014 -10000 0 -10000 0 0
BNIP3 0.27 0.23 0.5 175 -0.67 4 179
EGLN3 0.31 0.28 0.58 192 -0.59 4 196
CA9 0.4 0.29 0.6 280 -0.66 4 284
TERT 0.29 0.28 0.58 190 -0.67 3 193
ENO1 0.28 0.23 0.52 151 -0.67 4 155
PFKL 0.28 0.23 0.5 178 -0.66 4 182
NCOA1 0.021 0.002 -10000 0 -10000 0 0
ADM 0.27 0.24 0.5 177 -0.7 4 181
ARNT 0.089 0.085 0.23 85 -10000 0 85
HNF4A 0.069 0.13 0.32 93 -0.24 17 110
ADFP 0.25 0.24 0.48 186 -0.66 4 190
SLC2A1 0.32 0.27 0.58 207 -0.65 3 210
LEP 0.29 0.25 0.53 185 -0.67 4 189
HIF1A/ARNT/Cbp/p300 0.32 0.32 0.66 177 -0.85 3 180
EPO 0.22 0.22 0.5 123 -0.71 3 126
CREBBP 0.11 0.13 0.28 119 -0.27 11 130
HIF1A/ARNT/Cbp/p300/HDAC7 0.34 0.33 0.68 184 -0.79 3 187
PFKFB3 0.27 0.23 0.5 174 -0.62 5 179
NT5E 0.27 0.24 0.52 178 -0.66 4 182
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.11 0.12 0.23 209 -0.18 6 215
STMN1 0.069 0.085 0.16 234 -10000 0 234
Aurora B/RasGAP/Survivin 0.21 0.17 0.36 267 -10000 0 267
Chromosomal passenger complex/Cul3 protein complex 0.088 0.1 0.2 162 -0.37 1 163
BIRC5 0.19 0.15 0.33 263 -10000 0 263
DES -0.16 0.28 -10000 0 -0.56 98 98
Aurora C/Aurora B/INCENP 0.12 0.094 0.22 229 -0.15 3 232
Aurora B/TACC1 0.089 0.099 0.2 193 -0.15 14 207
Aurora B/PP2A 0.12 0.1 0.23 223 -10000 0 223
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.035 0.035 0.14 15 -10000 0 15
mitotic metaphase/anaphase transition -0.004 0.006 -10000 0 -10000 0 0
NDC80 0.14 0.15 0.27 260 -10000 0 260
Cul3 protein complex 0.03 0.045 0.22 3 -0.19 15 18
KIF2C 0.16 0.12 0.25 297 -0.32 1 298
PEBP1 0.023 0.005 -10000 0 -10000 0 0
KIF20A 0.18 0.15 0.32 258 -10000 0 258
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.12 0.1 0.23 230 -10000 0 230
SEPT1 0.02 0.016 -10000 0 -0.32 1 1
SMC2 0.021 0.004 -10000 0 -10000 0 0
SMC4 0.02 0.004 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.1 0.19 0.29 117 -0.43 32 149
PSMA3 0.021 0.004 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.005 0.006 -10000 0 -10000 0 0
H3F3B 0.074 0.069 0.14 238 -10000 0 238
AURKB 0.17 0.15 0.32 237 -10000 0 237
AURKC 0.019 0.033 0.32 2 -0.32 3 5
CDCA8 0.12 0.14 0.33 159 -10000 0 159
cytokinesis 0.14 0.15 0.29 207 -0.36 2 209
Aurora B/Septin1 0.18 0.18 0.36 213 -0.26 4 217
AURKA 0.054 0.12 0.31 84 -10000 0 84
INCENP 0.028 0.009 -10000 0 -10000 0 0
KLHL13 0.012 0.064 0.32 3 -0.32 15 18
BUB1 0.087 0.14 0.32 126 -10000 0 126
hSgo1/Aurora B/Survivin 0.28 0.23 0.46 276 -10000 0 276
EVI5 0.026 0.007 -10000 0 -10000 0 0
RhoA/GTP 0.16 0.15 0.33 174 -0.32 1 175
SGOL1 0.15 0.15 0.32 217 -10000 0 217
CENPA 0.16 0.16 0.3 240 -0.27 4 244
NCAPG 0.15 0.15 0.32 211 -10000 0 211
Aurora B/HC8 Proteasome 0.12 0.1 0.23 229 -10000 0 229
NCAPD2 0.02 0.005 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.12 0.1 0.23 232 -10000 0 232
RHOA 0.021 0.004 -10000 0 -10000 0 0
NCAPH 0.15 0.15 0.32 205 -10000 0 205
NPM1 0.07 0.13 0.22 19 -0.35 22 41
RASA1 0.02 0.005 -10000 0 -10000 0 0
KLHL9 0.018 0.008 -10000 0 -10000 0 0
mitotic prometaphase 0.002 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.12 0.1 0.23 229 -10000 0 229
PPP1CC 0.021 0.003 -10000 0 -10000 0 0
Centraspindlin 0.18 0.17 0.36 186 -0.33 1 187
RhoA/GDP 0.015 0.003 -10000 0 -10000 0 0
NSUN2 0.088 0.13 0.24 103 -0.3 18 121
MYLK 0.066 0.075 0.14 228 -0.15 12 240
KIF23 0.087 0.12 0.33 99 -10000 0 99
VIM 0.07 0.089 0.16 231 -10000 0 231
RACGAP1 0.03 0.03 0.33 4 -10000 0 4
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.074 0.12 0.2 86 -0.3 25 111
Chromosomal passenger complex 0.16 0.15 0.29 248 -0.28 2 250
Chromosomal passenger complex/EVI5 0.27 0.22 0.47 250 -10000 0 250
TACC1 0.009 0.057 -10000 0 -0.32 14 14
PPP2R5D 0.02 0.004 -10000 0 -10000 0 0
CUL3 0.021 0.003 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.089 0.18 0.3 6 -0.49 43 49
IHH -0.013 0.12 0.27 7 -0.38 41 48
SHH Np/Cholesterol/GAS1 -0.011 0.066 -10000 0 -0.18 62 62
LRPAP1 0.021 0.003 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.035 0.056 0.18 62 -0.11 1 63
SMO/beta Arrestin2 -0.14 0.18 0.29 3 -0.32 187 190
SMO -0.14 0.18 0.34 1 -0.33 196 197
AKT1 -0.078 0.14 0.26 1 -0.48 30 31
ARRB2 0.02 0.006 -10000 0 -10000 0 0
BOC 0.02 0.016 -10000 0 -0.32 1 1
ADRBK1 0.021 0.003 -10000 0 -10000 0 0
heart looping -0.14 0.18 0.34 1 -0.33 196 197
STIL -0.083 0.14 0.26 11 -0.31 64 75
DHH N/PTCH2 0.011 0.069 -10000 0 -0.22 38 38
DHH N/PTCH1 -0.11 0.15 -10000 0 -0.35 62 62
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
DHH -0.006 0.092 -10000 0 -0.32 38 38
PTHLH -0.12 0.22 0.37 6 -0.55 41 47
determination of left/right symmetry -0.14 0.18 0.34 1 -0.33 196 197
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
skeletal system development -0.12 0.22 0.37 6 -0.54 41 47
IHH N/Hhip -0.22 0.18 0.21 3 -0.31 355 358
DHH N/Hhip -0.12 0.14 -10000 0 -0.24 268 268
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.14 0.18 0.34 1 -0.33 196 197
pancreas development -0.16 0.17 -10000 0 -0.32 261 261
HHAT 0.018 0.023 -10000 0 -0.32 2 2
PI3K 0.029 0.014 -10000 0 -0.23 1 1
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.012 0.053 -10000 0 -0.32 12 12
somite specification -0.14 0.18 0.34 1 -0.33 196 197
SHH Np/Cholesterol/PTCH1 -0.094 0.14 -10000 0 -0.33 68 68
SHH Np/Cholesterol/PTCH2 -0.009 0.061 0.11 1 -0.17 57 58
SHH Np/Cholesterol/Megalin -0.048 0.097 0.11 1 -0.19 146 147
SHH -0.039 0.069 0.15 1 -0.23 57 58
catabolic process -0.1 0.16 0.23 2 -0.25 231 233
SMO/Vitamin D3 -0.12 0.17 0.37 3 -0.4 64 67
SHH Np/Cholesterol/Hhip -0.09 0.11 0.11 1 -0.2 238 239
LRP2 -0.067 0.15 0.32 1 -0.32 126 127
receptor-mediated endocytosis -0.16 0.18 0.3 2 -0.4 124 126
SHH Np/Cholesterol/BOC -0.008 0.06 0.11 1 -0.17 56 57
SHH Np/Cholesterol/CDO -0.01 0.064 0.11 1 -0.18 60 61
mesenchymal cell differentiation 0.1 0.099 0.2 238 -0.11 1 239
mol:Vitamin D3 -0.089 0.15 0.38 5 -0.33 65 70
IHH N/PTCH2 -0.093 0.13 0.21 4 -0.21 262 266
CDON 0.014 0.046 -10000 0 -0.32 9 9
IHH N/PTCH1 -0.097 0.17 0.26 2 -0.25 233 235
Megalin/LRPAP1 -0.034 0.11 0.23 1 -0.22 123 124
PTCH2 0.02 0.016 -10000 0 -0.32 1 1
SHH Np/Cholesterol -0.028 0.051 -10000 0 -0.17 57 57
PTCH1 -0.1 0.16 0.23 2 -0.25 231 233
HHIP -0.16 0.17 -10000 0 -0.32 261 261
Endothelins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.079 0.11 0.23 1 -0.32 47 48
PTK2B 0.018 0.008 -10000 0 -10000 0 0
mol:Ca2+ -0.12 0.27 -10000 0 -0.84 50 50
EDN1 -0.074 0.13 0.19 1 -0.34 79 80
EDN3 -0.069 0.15 0.32 1 -0.32 125 126
EDN2 0.1 0.14 0.32 132 -0.32 2 134
HRAS/GDP -0.15 0.19 -10000 0 -0.41 119 119
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.069 0.13 -10000 0 -0.34 62 62
ADCY4 -0.067 0.1 0.21 4 -0.27 57 61
ADCY5 -0.077 0.12 0.23 4 -0.3 74 78
ADCY6 -0.063 0.1 0.22 5 -0.27 47 52
ADCY7 -0.062 0.1 0.24 4 -0.27 48 52
ADCY1 -0.058 0.098 0.19 8 -0.27 45 53
ADCY2 -0.059 0.11 0.21 10 -0.29 51 61
ADCY3 -0.063 0.1 0.22 6 -0.27 48 54
ADCY8 -0.099 0.12 0.25 4 -0.26 114 118
ADCY9 -0.065 0.1 0.23 5 -0.27 55 60
arachidonic acid secretion -0.12 0.19 -10000 0 -0.48 81 81
ETB receptor/Endothelin-1/Gq/GTP -0.14 0.16 -10000 0 -0.27 255 255
GNAO1 0.021 0.032 0.32 3 -0.32 2 5
HRAS 0.021 0.004 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.048 0.12 0.31 1 -0.29 42 43
ETA receptor/Endothelin-1/Gs/GTP -0.05 0.12 0.29 1 -0.28 50 51
mol:GTP -0.001 0.004 -10000 0 -10000 0 0
COL3A1 -0.047 0.16 0.29 29 -0.32 47 76
EDNRB -0.16 0.17 -10000 0 -0.32 256 256
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.084 0.12 0.23 1 -0.36 50 51
CYSLTR1 -0.088 0.13 0.23 1 -0.38 50 51
SLC9A1 -0.049 0.081 0.16 1 -0.22 52 53
mol:GDP -0.16 0.2 -10000 0 -0.42 130 130
SLC9A3 -0.31 0.34 -10000 0 -0.66 179 179
RAF1 -0.15 0.2 -10000 0 -0.46 102 102
JUN -0.1 0.21 -10000 0 -0.66 43 43
JAK2 -0.077 0.11 0.23 1 -0.32 47 48
mol:IP3 -0.12 0.17 -10000 0 -0.37 108 108
ETA receptor/Endothelin-1 -0.079 0.15 0.35 1 -0.35 59 60
PLCB1 0.018 0.017 0.32 1 -10000 0 1
PLCB2 0.01 0.047 -10000 0 -0.32 9 9
ETA receptor/Endothelin-3 -0.072 0.11 0.23 1 -0.24 132 133
FOS -0.15 0.23 -10000 0 -0.68 60 60
Gai/GDP -0.051 0.2 -10000 0 -0.8 29 29
CRK 0.019 0.006 -10000 0 -10000 0 0
mol:Ca ++ -0.16 0.19 -10000 0 -0.43 122 122
BCAR1 0.02 0.016 -10000 0 -0.32 1 1
PRKCB1 -0.12 0.16 -10000 0 -0.37 103 103
GNAQ 0.015 0.022 -10000 0 -0.32 1 1
GNAZ -0.007 0.092 -10000 0 -0.32 38 38
GNAL 0.018 0.045 0.32 3 -0.32 6 9
Gs family/GDP -0.14 0.18 -10000 0 -0.4 120 120
ETA receptor/Endothelin-1/Gq/GTP -0.069 0.13 -10000 0 -0.31 73 73
MAPK14 -0.14 0.16 0.2 1 -0.34 138 139
TRPC6 -0.13 0.29 -10000 0 -0.9 50 50
GNAI2 0.021 0.004 -10000 0 -10000 0 0
GNAI3 0.02 0.004 -10000 0 -10000 0 0
GNAI1 0.02 0.016 -10000 0 -0.32 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.14 0.17 -10000 0 -0.36 140 140
ETB receptor/Endothelin-2 -0.077 0.15 0.24 45 -0.2 254 299
ETB receptor/Endothelin-3 -0.16 0.16 0.23 1 -0.27 296 297
ETB receptor/Endothelin-1 -0.16 0.16 0.2 7 -0.29 259 266
MAPK3 -0.16 0.24 -10000 0 -0.65 71 71
MAPK1 -0.17 0.24 -10000 0 -0.64 75 75
Rac1/GDP -0.14 0.18 -10000 0 -0.4 112 112
cAMP biosynthetic process -0.076 0.14 0.29 6 -0.33 61 67
MAPK8 -0.12 0.24 -10000 0 -0.67 59 59
SRC 0.02 0.004 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.13 0.14 -10000 0 -0.28 178 178
p130Cas/CRK/Src/PYK2 -0.16 0.22 -10000 0 -0.55 89 89
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.14 0.18 -10000 0 -0.41 109 109
COL1A2 -0.16 0.18 0.31 7 -0.36 159 166
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.045 0.12 0.24 72 -0.19 14 86
mol:DAG -0.12 0.17 -10000 0 -0.37 108 108
MAP2K2 -0.16 0.21 -10000 0 -0.53 86 86
MAP2K1 -0.16 0.21 -10000 0 -0.54 82 82
EDNRA -0.032 0.075 0.23 1 -0.24 16 17
positive regulation of muscle contraction -0.055 0.11 0.21 19 -0.28 42 61
Gq family/GDP -0.11 0.18 0.35 1 -0.4 90 91
HRAS/GTP -0.15 0.19 -10000 0 -0.43 109 109
PRKCH -0.12 0.16 -10000 0 -0.38 94 94
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCA -0.12 0.16 -10000 0 -0.38 92 92
PRKCB -0.13 0.17 -10000 0 -0.4 97 97
PRKCE -0.13 0.16 -10000 0 -0.39 97 97
PRKCD -0.12 0.16 -10000 0 -0.39 93 93
PRKCG -0.12 0.16 -10000 0 -0.38 92 92
regulation of vascular smooth muscle contraction -0.18 0.28 -10000 0 -0.82 59 59
PRKCQ -0.14 0.17 -10000 0 -0.4 103 103
PLA2G4A -0.13 0.21 -10000 0 -0.53 81 81
GNA14 0.008 0.053 -10000 0 -0.33 11 11
GNA15 0.015 0.015 -10000 0 -10000 0 0
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA11 0.014 0.021 -10000 0 -0.32 1 1
Rac1/GTP -0.048 0.12 0.31 1 -0.29 43 44
MMP1 0.19 0.17 0.33 234 -0.67 2 236
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.048 0.062 0.12 17 -0.11 217 234
BUB1B 0.07 0.074 0.14 211 -0.11 10 221
PLK1 0.029 0.038 0.093 86 -0.08 2 88
PLK1S1 0.013 0.038 0.11 3 -0.17 15 18
KIF2A 0.022 0.041 0.16 15 -10000 0 15
regulation of mitotic centrosome separation 0.029 0.038 0.092 86 -0.08 2 88
GOLGA2 0.021 0.004 -10000 0 -10000 0 0
Hec1/SPC24 0.17 0.17 0.34 225 -10000 0 225
WEE1 0.029 0.058 0.19 1 -0.29 8 9
cytokinesis 0.086 0.093 0.18 197 -0.17 5 202
PP2A-alpha B56 0.077 0.096 -10000 0 -0.49 6 6
AURKA 0.035 0.057 0.14 92 -0.19 6 98
PICH/PLK1 0.075 0.11 0.21 167 -10000 0 167
CENPE 0.033 0.052 0.13 75 -10000 0 75
RhoA/GTP 0.015 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.023 0.041 0.16 15 -10000 0 15
PPP2CA 0.02 0.005 -10000 0 -10000 0 0
FZR1 0.02 0.005 -10000 0 -10000 0 0
TPX2 0.072 0.067 0.13 264 -0.16 5 269
PAK1 0.02 0.005 -10000 0 -10000 0 0
SPC24 0.1 0.13 0.32 133 -10000 0 133
FBXW11 0.02 0.005 -10000 0 -10000 0 0
CLSPN 0.06 0.074 0.15 177 -0.22 6 183
GORASP1 0.021 0.004 -10000 0 -10000 0 0
metaphase 0 0.002 0.016 10 -0.011 1 11
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.014 0.018 0.051 37 -0.041 2 39
G2 phase of mitotic cell cycle 0 0.003 0.015 10 -10000 0 10
STAG2 0.021 0.003 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.002 0.095 -10000 0 -0.51 16 16
spindle elongation 0.029 0.038 0.092 86 -0.08 2 88
ODF2 0.021 0.006 -10000 0 -10000 0 0
BUB1 0.067 0.11 -10000 0 -0.53 6 6
TPT1 0.009 0.044 0.11 2 -0.16 26 28
CDC25C 0.1 0.093 0.16 305 -0.23 14 319
CDC25B 0.022 0.011 -10000 0 -10000 0 0
SGOL1 0.048 0.063 0.11 217 -0.12 17 234
RHOA 0.021 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.073 0.085 0.21 121 -10000 0 121
CDC14B -0.008 0.004 -10000 0 -10000 0 0
CDC20 0.19 0.15 0.32 279 -10000 0 279
PLK1/PBIP1 0.009 0.039 0.14 34 -10000 0 34
mitosis -0.003 0.006 0.022 7 -0.016 14 21
FBXO5 0.013 0.039 0.12 10 -0.1 2 12
CDC2 0.003 0.005 0.011 124 -0.01 5 129
NDC80 0.15 0.15 0.32 215 -10000 0 215
metaphase plate congression 0.02 0.044 -10000 0 -0.22 11 11
ERCC6L 0.077 0.1 0.22 142 -10000 0 142
NLP/gamma Tubulin 0.016 0.021 0.071 18 -0.085 3 21
microtubule cytoskeleton organization 0.009 0.044 0.11 2 -0.16 26 28
G2/M transition DNA damage checkpoint -0.001 0.002 0.012 2 -10000 0 2
PPP1R12A 0.022 0.003 -10000 0 -10000 0 0
interphase -0.001 0.002 0.012 2 -10000 0 2
PLK1/PRC1-2 0.16 0.15 0.29 255 -10000 0 255
GRASP65/GM130/RAB1/GTP/PLK1 0.051 0.03 -10000 0 -10000 0 0
RAB1A 0.021 0.001 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.023 0.034 0.081 92 -0.07 2 94
mitotic prometaphase 0.001 0.003 0.019 11 -10000 0 11
proteasomal ubiquitin-dependent protein catabolic process 0.045 0.056 0.18 1 -0.39 1 2
microtubule-based process 0.14 0.12 0.25 258 -10000 0 258
Golgi organization 0.029 0.038 0.092 86 -0.08 2 88
Cohesin/SA2 0.036 0.03 0.11 15 -10000 0 15
PPP1CB/MYPT1 0.032 0.006 -10000 0 -10000 0 0
KIF20A 0.18 0.15 0.32 258 -10000 0 258
APC/C/CDC20 0.15 0.12 0.25 280 -10000 0 280
PPP2R1A 0.021 0.004 -10000 0 -10000 0 0
chromosome segregation 0.009 0.038 0.14 34 -10000 0 34
PRC1 0.063 0.1 0.32 69 -10000 0 69
ECT2 0.031 0.059 0.18 44 -10000 0 44
C13orf34 0.023 0.032 0.078 83 -0.067 2 85
NUDC 0.02 0.044 -10000 0 -0.22 11 11
regulation of attachment of spindle microtubules to kinetochore 0.07 0.074 0.14 211 -0.11 10 221
spindle assembly 0.022 0.029 0.086 34 -0.068 3 37
spindle stabilization 0.013 0.038 0.11 3 -0.16 15 18
APC/C/HCDH1 0.016 0.006 -10000 0 -10000 0 0
MKLP2/PLK1 0.14 0.12 0.25 258 -10000 0 258
CCNB1 0.1 0.13 0.32 131 -10000 0 131
PPP1CB 0.022 0.003 -10000 0 -10000 0 0
BTRC 0.021 0.003 -10000 0 -10000 0 0
ROCK2 0.024 0.039 0.17 2 -0.22 3 5
TUBG1 0.018 0.026 0.13 2 -0.2 3 5
G2/M transition of mitotic cell cycle 0.029 0.056 0.13 68 -10000 0 68
MLF1IP 0.004 0.042 0.16 32 -10000 0 32
INCENP 0.021 0.004 -10000 0 -10000 0 0
Aurora C signaling

Figure S9.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S9.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.021 0.003 -10000 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.11 0.093 0.21 229 -0.15 3 232
metaphase 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
H3F3B 0.016 0.014 -10000 0 -10000 0 0
AURKB 0.16 0.15 0.32 237 -10000 0 237
AURKC 0.019 0.033 0.32 2 -0.32 3 5
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.086 0.26 0.3 4 -0.64 76 80
MKNK1 0.021 0.003 -10000 0 -10000 0 0
MAPK14 -0.025 0.12 -10000 0 -0.3 77 77
ATF2/c-Jun -0.036 0.11 -10000 0 -0.26 75 75
MAPK11 -0.023 0.12 -10000 0 -0.31 72 72
MITF -0.048 0.15 -10000 0 -0.36 81 81
MAPKAPK5 -0.04 0.14 -10000 0 -0.35 74 74
KRT8 -0.042 0.14 0.27 2 -0.35 78 80
MAPKAPK3 0.021 0.004 -10000 0 -10000 0 0
MAPKAPK2 0.019 0.006 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.039 0.18 -10000 0 -0.42 79 79
CEBPB -0.04 0.14 -10000 0 -0.36 71 71
SLC9A1 -0.043 0.14 -10000 0 -0.36 76 76
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.042 0.14 0.24 1 -0.35 76 77
p38alpha-beta/MNK1 -0.018 0.15 -10000 0 -0.34 77 77
JUN -0.035 0.11 -10000 0 -0.26 75 75
PPARGC1A -0.1 0.19 -10000 0 -0.34 161 161
USF1 -0.033 0.13 0.31 1 -0.35 64 65
RAB5/GDP/GDI1 -0.028 0.1 -10000 0 -0.26 76 76
NOS2 -0.086 0.27 0.37 3 -0.65 74 77
DDIT3 -0.041 0.14 0.23 1 -0.35 76 77
RAB5A 0.021 0.004 -10000 0 -10000 0 0
HSPB1 -0.04 0.12 0.26 9 -0.3 69 78
p38alpha-beta/HBP1 -0.019 0.15 -10000 0 -0.35 74 74
CREB1 -0.047 0.15 0.23 2 -0.38 78 80
RAB5/GDP 0.015 0.003 -10000 0 -10000 0 0
EIF4E -0.059 0.12 0.18 1 -0.32 69 70
RPS6KA4 -0.043 0.14 -10000 0 -0.35 77 77
PLA2G4A -0.036 0.13 0.18 48 -0.31 64 112
GDI1 -0.04 0.13 0.28 1 -0.35 74 75
TP53 -0.067 0.16 0.26 1 -0.43 72 73
RPS6KA5 -0.042 0.14 0.29 3 -0.35 76 79
ESR1 -0.046 0.15 0.28 1 -0.38 77 78
HBP1 0.02 0.005 -10000 0 -10000 0 0
MEF2C -0.042 0.14 -10000 0 -0.35 75 75
MEF2A -0.042 0.14 -10000 0 -0.35 76 76
EIF4EBP1 -0.049 0.16 0.24 2 -0.39 77 79
KRT19 -0.043 0.14 -10000 0 -0.36 77 77
ELK4 -0.037 0.13 -10000 0 -0.34 70 70
ATF6 -0.034 0.13 0.31 1 -0.35 65 66
ATF1 -0.047 0.15 0.24 3 -0.38 79 82
p38alpha-beta/MAPKAPK2 -0.017 0.14 -10000 0 -0.34 73 73
p38alpha-beta/MAPKAPK3 -0.019 0.15 -10000 0 -0.35 76 76
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.039 0.048 0.2 28 -0.16 9 37
RGS9BP -0.029 0.12 -10000 0 -0.32 70 70
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.035 0.07 0.32 28 -10000 0 28
mol:Na + 0.1 0.11 0.23 191 -10000 0 191
mol:ADP -0.006 0.043 0.16 30 -10000 0 30
GNAT2 0.02 0.014 0.32 1 -10000 0 1
RGS9-1/Gbeta5/R9AP -0.058 0.12 -10000 0 -0.21 186 186
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.025 0.014 0.21 2 -10000 0 2
GRK7 0.02 0.014 0.32 1 -10000 0 1
CNGB3 0.063 0.11 0.32 74 -10000 0 74
Cone Metarhodopsin II/X-Arrestin 0.014 0.013 0.21 2 -10000 0 2
mol:Ca2+ 0.055 0.089 0.21 98 -10000 0 98
Cone PDE6 -0.04 0.12 -10000 0 -0.19 177 177
Cone Metarhodopsin II 0.033 0.041 0.2 28 -10000 0 28
Na + (4 Units) 0.11 0.11 0.24 195 -10000 0 195
GNAT2/GDP -0.044 0.11 -10000 0 -0.18 185 185
GNB5 0.02 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.015 0.017 0.17 3 -10000 0 3
Cone Transducin 0.042 0.052 0.21 28 -0.17 9 37
SLC24A2 0.042 0.081 0.32 38 -10000 0 38
GNB3/GNGT2 0.036 0.06 0.23 28 -0.23 9 37
GNB3 0.037 0.073 0.32 29 -0.32 1 30
GNAT2/GTP 0.015 0.01 0.21 1 -10000 0 1
CNGA3 0.12 0.14 0.32 162 -10000 0 162
ARR3 0.019 0.019 0.32 2 -10000 0 2
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.1 0.11 0.23 191 -10000 0 191
mol:Pi -0.058 0.12 -10000 0 -0.21 186 186
Cone CNG Channel 0.093 0.09 0.21 167 -10000 0 167
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.041 0.081 0.32 38 -10000 0 38
RGS9 -0.08 0.16 -10000 0 -0.32 143 143
PDE6C 0.018 0.003 -10000 0 -10000 0 0
GNGT2 0.015 0.044 -10000 0 -0.32 8 8
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.018 0.014 0.32 1 -10000 0 1
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.026 0.29 0.52 39 -0.6 32 71
PCK1 0.061 0.24 0.56 49 -0.59 2 51
HNF4A -0.098 0.46 0.67 57 -0.77 110 167
KCNJ11 0.015 0.3 0.59 34 -0.74 15 49
AKT1 0.038 0.18 0.42 41 -0.52 2 43
response to starvation -0.026 0.072 0.14 4 -0.2 35 39
DLK1 0.035 0.3 0.57 54 -0.59 18 72
NKX2-1 -0.041 0.32 0.44 13 -1.1 33 46
ACADM -0.028 0.29 0.52 35 -0.61 30 65
TAT 0.053 0.23 0.54 46 -0.51 1 47
CEBPB 0.027 0.02 0.16 1 -10000 0 1
CEBPA 0.015 0.077 0.2 4 -0.32 21 25
TTR 0.069 0.28 0.64 50 -0.72 8 58
PKLR -0.002 0.3 0.55 46 -0.61 29 75
APOA1 -0.2 0.61 0.72 46 -1 140 186
CPT1C -0.026 0.29 0.52 39 -0.6 32 71
ALAS1 0.03 0.19 0.48 15 -0.56 1 16
TFRC 0.083 0.29 0.6 65 -0.8 10 75
FOXF1 -0.022 0.13 0.23 18 -0.32 69 87
NF1 0.022 0.004 -10000 0 -10000 0 0
HNF1A (dimer) 0.11 0.15 0.38 105 -0.32 1 106
CPT1A -0.025 0.29 0.52 37 -0.61 29 66
HMGCS1 0.001 0.29 0.56 43 -0.6 30 73
NR3C1 0.045 0.047 0.21 14 -10000 0 14
CPT1B -0.026 0.29 0.51 40 -0.6 33 73
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.042 0.04 -10000 0 -10000 0 0
GCK -0.022 0.31 0.55 39 -0.64 35 74
CREB1 0.037 0.038 0.18 6 -10000 0 6
IGFBP1 0.031 0.21 0.52 34 -0.52 1 35
PDX1 0.098 0.27 0.66 59 -0.54 2 61
UCP2 -0.025 0.29 0.52 37 -0.61 30 67
ALDOB 0.029 0.31 0.64 42 -0.7 14 56
AFP 0.082 0.11 0.35 38 -10000 0 38
BDH1 -0.027 0.29 0.52 38 -0.61 30 68
HADH 0.017 0.28 0.57 35 -0.6 16 51
F2 -0.021 0.42 0.78 48 -0.79 38 86
HNF1A 0.11 0.15 0.38 105 -0.32 1 106
G6PC 0.081 0.13 0.55 12 -10000 0 12
SLC2A2 0.082 0.28 0.66 55 -0.73 3 58
INS -0.032 0.035 -10000 0 -10000 0 0
FOXA1 0.068 0.1 0.3 54 -0.32 1 55
FOXA3 0.15 0.18 0.41 137 -0.28 3 140
FOXA2 0.055 0.38 0.8 55 -0.66 23 78
ABCC8 -0.018 0.36 0.61 39 -0.76 56 95
ALB 0.093 0.12 0.35 56 -10000 0 56
Osteopontin-mediated events

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
IKK alpha homodimer 0.073 0.076 0.2 79 -10000 0 79
NF kappa B1 p50/RelA/I kappa B alpha 0.081 0.088 0.29 22 -10000 0 22
alphaV/beta3 Integrin/Osteopontin/Src 0.18 0.097 0.24 334 -10000 0 334
AP1 0.087 0.096 0.32 16 -10000 0 16
ILK 0.065 0.068 0.23 20 -10000 0 20
bone resorption 0.043 0.072 0.23 17 -0.29 1 18
PTK2B 0.018 0.008 -10000 0 -10000 0 0
PYK2/p130Cas 0.14 0.11 0.23 264 -0.17 4 268
ITGAV 0.026 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.027 0.031 -10000 0 -0.23 7 7
alphaV/beta3 Integrin/Osteopontin 0.18 0.11 0.25 329 -0.19 4 333
MAP3K1 0.063 0.067 0.2 30 -0.18 4 34
JUN 0.019 0.031 -10000 0 -0.32 4 4
MAPK3 0.06 0.082 0.21 81 -10000 0 81
MAPK1 0.059 0.079 0.21 77 -10000 0 77
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
MAPK8 0.043 0.058 0.21 19 -10000 0 19
ITGB3 0.035 0.074 0.33 22 -0.32 5 27
NFKBIA 0.056 0.083 0.22 77 -10000 0 77
FOS -0.001 0.083 -10000 0 -0.32 31 31
CD44 0.015 0.044 -10000 0 -0.32 8 8
CHUK 0.021 0.003 -10000 0 -10000 0 0
PLAU 0.086 0.13 0.43 15 -10000 0 15
NF kappa B1 p50/RelA 0.086 0.1 0.26 83 -10000 0 83
BCAR1 0.02 0.016 -10000 0 -0.32 1 1
RELA 0.021 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.046 0.055 0.25 22 -0.22 5 27
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.063 0.067 0.2 31 -0.18 5 36
VAV3 0.041 0.059 0.2 21 -0.28 2 23
MAP3K14 0.073 0.077 0.2 89 -10000 0 89
ROCK2 0.02 0.016 -10000 0 -0.32 1 1
SPP1 0.23 0.14 0.32 337 -10000 0 337
RAC1 0.019 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.037 0.058 0.18 18 -0.26 2 20
MMP2 0.031 0.074 0.3 7 -10000 0 7
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.02 0.015 0.32 1 -10000 0 1
LAT2 -0.07 0.12 -10000 0 -0.31 79 79
AP1 -0.077 0.2 -10000 0 -0.44 81 81
mol:PIP3 -0.077 0.17 0.28 21 -0.35 95 116
IKBKB -0.03 0.12 0.24 31 -0.22 60 91
AKT1 -0.035 0.14 0.31 49 -0.27 41 90
IKBKG -0.039 0.11 0.23 22 -0.22 66 88
MS4A2 -0.055 0.14 -10000 0 -0.32 100 100
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.02 0.006 -10000 0 -10000 0 0
MAP3K1 -0.063 0.14 0.22 8 -0.35 66 74
mol:Ca2+ -0.057 0.14 0.23 33 -0.27 92 125
LYN 0.014 0.017 -10000 0 -10000 0 0
CBLB -0.07 0.12 -10000 0 -0.31 81 81
SHC1 0.018 0.008 -10000 0 -10000 0 0
RasGAP/p62DOK 0.018 0.062 -10000 0 -0.17 45 45
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.019 0.027 -10000 0 -0.32 3 3
PLD2 -0.041 0.15 0.29 53 -0.23 103 156
PTPN13 -0.084 0.16 -10000 0 -0.43 58 58
PTPN11 0.011 0.024 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.046 0.12 0.29 10 -0.28 39 49
SYK 0.015 0.027 -10000 0 -0.32 2 2
GRB2 0.02 0.004 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.083 0.16 0.17 2 -0.35 99 101
LAT -0.07 0.12 -10000 0 -0.31 80 80
PAK2 -0.069 0.16 0.24 7 -0.38 69 76
NFATC2 -0.034 0.096 -10000 0 -0.49 16 16
HRAS -0.071 0.17 0.25 7 -0.41 70 77
GAB2 0.017 0.031 -10000 0 -0.32 4 4
PLA2G1B -0.05 0.17 -10000 0 -0.92 16 16
Fc epsilon R1 -0.051 0.14 0.22 1 -0.25 146 147
Antigen/IgE/Fc epsilon R1 -0.044 0.13 0.2 1 -0.22 146 147
mol:GDP -0.086 0.17 -10000 0 -0.44 72 72
JUN 0.018 0.031 -10000 0 -0.32 4 4
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
FOS -0.001 0.083 -10000 0 -0.32 31 31
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.066 0.13 -10000 0 -0.32 84 84
CHUK -0.044 0.11 0.21 23 -0.22 69 92
KLRG1 -0.062 0.11 0.14 1 -0.23 121 122
VAV1 -0.066 0.12 -10000 0 -0.31 74 74
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.068 0.12 -10000 0 -0.31 79 79
negative regulation of mast cell degranulation -0.054 0.12 -10000 0 -0.31 55 55
BTK -0.093 0.2 -10000 0 -0.48 75 75
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.077 0.15 -10000 0 -0.29 135 135
GAB2/PI3K/SHP2 -0.076 0.084 -10000 0 -0.22 99 99
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.063 0.13 -10000 0 -0.25 131 131
RAF1 -0.014 0.18 -10000 0 -0.97 16 16
Fc epsilon R1/FcgammaRIIB/SHIP -0.03 0.13 0.22 1 -0.22 141 142
FCER1G 0.011 0.045 -10000 0 -0.32 7 7
FCER1A -0.065 0.15 0.32 1 -0.33 112 113
Antigen/IgE/Fc epsilon R1/Fyn -0.037 0.12 0.2 1 -0.22 143 144
MAPK3 -0.016 0.16 -10000 0 -0.88 16 16
MAPK1 -0.02 0.17 -10000 0 -0.91 16 16
NFKB1 0.021 0.003 -10000 0 -10000 0 0
MAPK8 -0.063 0.22 -10000 0 -0.66 45 45
DUSP1 -0.012 0.099 -10000 0 -0.32 45 45
NF-kappa-B/RelA -0.031 0.061 0.13 6 -0.15 48 54
actin cytoskeleton reorganization -0.07 0.16 -10000 0 -0.41 54 54
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.063 0.15 -10000 0 -0.37 63 63
FER -0.068 0.12 -10000 0 -0.31 78 78
RELA 0.021 0.004 -10000 0 -10000 0 0
ITK -0.023 0.066 -10000 0 -0.32 17 17
SOS1 0.021 0.003 -10000 0 -10000 0 0
PLCG1 -0.085 0.18 0.26 3 -0.4 91 94
cytokine secretion -0.027 0.038 -10000 0 -0.14 6 6
SPHK1 -0.069 0.12 -10000 0 -0.3 80 80
PTK2 -0.073 0.16 -10000 0 -0.43 51 51
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.083 0.16 0.22 1 -0.35 100 101
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.074 0.17 0.27 22 -0.34 96 118
MAP2K2 -0.02 0.16 -10000 0 -0.9 16 16
MAP2K1 -0.019 0.17 -10000 0 -0.9 16 16
MAP2K7 0.02 0.005 -10000 0 -10000 0 0
KLRG1/SHP2 -0.048 0.11 0.17 1 -0.28 57 58
MAP2K4 -0.091 0.32 -10000 0 -0.92 60 60
Fc epsilon R1/FcgammaRIIB -0.038 0.13 0.22 1 -0.23 146 147
mol:Choline -0.04 0.15 0.29 53 -0.23 103 156
SHC/Grb2/SOS1 -0.04 0.13 -10000 0 -0.3 68 68
FYN 0.019 0.017 -10000 0 -0.32 1 1
DOK1 0.021 0.002 -10000 0 -10000 0 0
PXN -0.071 0.15 -10000 0 -0.4 53 53
HCLS1 -0.07 0.13 -10000 0 -0.31 79 79
PRKCB -0.058 0.14 0.25 23 -0.29 79 102
FCGR2B 0.019 0.007 -10000 0 -10000 0 0
IGHE -0.001 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.055 0.12 -10000 0 -0.31 55 55
LCP2 0.018 0.027 -10000 0 -0.32 3 3
PLA2G4A -0.064 0.12 0.13 4 -0.31 74 78
RASA1 0.02 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.04 0.15 0.29 53 -0.23 103 156
IKK complex -0.021 0.098 0.23 29 -0.18 43 72
WIPF1 0.021 0.003 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.012 0.093 0.47 14 -10000 0 14
VDR 0.021 0.021 0.32 1 -0.32 1 2
FAM120B 0.019 0.006 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.088 0.11 -10000 0 -0.33 29 29
RXRs/LXRs/DNA/Oxysterols -0.089 0.13 -10000 0 -0.49 22 22
MED1 0.021 0.004 -10000 0 -10000 0 0
mol:9cRA -0.001 0.009 -10000 0 -0.093 1 1
RARs/THRs/DNA/Src-1 -0.009 0.067 -10000 0 -0.19 44 44
RXRs/NUR77 -0.095 0.13 -10000 0 -0.2 264 264
RXRs/PPAR -0.11 0.13 -10000 0 -0.22 245 245
NCOR2 0.021 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.015 0.014 0.21 1 -0.22 1 2
RARs/VDR/DNA/Vit D3 0.045 0.024 0.21 1 -0.17 3 4
RARA 0.021 0.004 -10000 0 -10000 0 0
NCOA1 0.021 0.002 -10000 0 -10000 0 0
VDR/VDR/DNA 0.021 0.021 0.32 1 -0.32 1 2
RARs/RARs/DNA/9cRA 0.032 0.021 -10000 0 -0.17 2 2
RARG 0.021 0.003 -10000 0 -10000 0 0
RPS6KB1 0.031 0.11 0.63 15 -10000 0 15
RARs/THRs/DNA/SMRT -0.009 0.067 -10000 0 -0.19 46 46
THRA 0.021 0.004 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.015 0.014 0.21 1 -0.22 1 2
RXRs/PPAR/9cRA/PGJ2/DNA -0.067 0.1 -10000 0 -0.17 229 229
NR1H4 0.041 0.078 0.32 35 -10000 0 35
RXRs/LXRs/DNA -0.057 0.12 -10000 0 -0.26 13 13
NR1H2 0.019 0.015 -10000 0 -10000 0 0
NR1H3 0.019 0.016 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.059 0.1 -10000 0 -0.17 225 225
NR4A1 -0.046 0.14 -10000 0 -0.32 95 95
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.072 0.095 0.17 1 -0.17 211 212
RXRG -0.14 0.17 -10000 0 -0.32 231 231
RXR alpha/CCPG 0.026 0.016 -10000 0 -10000 0 0
RXRA 0.019 0.016 -10000 0 -10000 0 0
RXRB 0.019 0.015 -10000 0 -10000 0 0
THRB -0.01 0.098 -10000 0 -0.32 44 44
PPARG -0.02 0.11 -10000 0 -0.32 57 57
PPARD 0.021 0.004 -10000 0 -10000 0 0
TNF -0.097 0.18 -10000 0 -0.83 20 20
mol:Oxysterols 0 0.009 -10000 0 -10000 0 0
cholesterol transport -0.088 0.12 -10000 0 -0.48 22 22
PPARA 0.02 0.005 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.019 0.022 -10000 0 -0.32 2 2
RXRs/NUR77/BCL2 -0.12 0.13 -10000 0 -0.23 261 261
SREBF1 -0.077 0.12 -10000 0 -0.51 13 13
RXRs/RXRs/DNA/9cRA -0.067 0.1 -10000 0 -0.17 229 229
ABCA1 -0.082 0.13 -10000 0 -0.56 15 15
RARs/THRs 0.037 0.069 -10000 0 -0.18 43 43
RXRs/FXR -0.057 0.12 0.23 13 -0.18 212 225
BCL2 0.019 0.022 0.32 1 -0.32 1 2
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS 0.022 0.11 0.23 29 -0.18 81 110
SMAD6-7/SMURF1 0.007 0.078 -10000 0 -0.19 62 62
NOG 0.01 0.088 0.32 11 -0.32 24 35
SMAD9 -0.11 0.21 -10000 0 -0.45 131 131
SMAD4 0.019 0.006 -10000 0 -10000 0 0
SMAD5 -0.037 0.1 -10000 0 -0.33 31 31
BMP7/USAG1 -0.12 0.14 0.23 7 -0.24 275 282
SMAD5/SKI -0.031 0.12 0.26 3 -0.36 27 30
SMAD1 -0.003 0.053 -10000 0 -0.28 8 8
BMP2 -0.025 0.12 -10000 0 -0.32 64 64
SMAD1/SMAD1/SMAD4 -0.01 0.074 -10000 0 -0.32 7 7
BMPR1A 0.021 0.003 -10000 0 -10000 0 0
BMPR1B -0.012 0.11 0.32 3 -0.32 49 52
BMPR1A-1B/BAMBI 0.022 0.08 0.22 14 -0.2 49 63
AHSG 0.038 0.075 0.32 32 -10000 0 32
CER1 0.02 0.031 0.32 5 -10000 0 5
BMP2-4/CER1 0.003 0.084 0.22 3 -0.2 69 72
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.029 0.1 -10000 0 -0.32 32 32
BMP2-4 (homodimer) -0.009 0.093 -10000 0 -0.23 70 70
RGMB 0.02 0.004 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0 0.11 0.22 3 -0.2 100 103
RGMA 0.022 0.043 0.32 6 -0.32 3 9
SMURF1 0.02 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.024 0.082 -10000 0 -0.28 22 22
BMP2-4/USAG1 -0.12 0.13 -10000 0 -0.22 282 282
SMAD6/SMURF1/SMAD5 -0.028 0.11 0.26 3 -0.36 27 30
SOSTDC1 -0.18 0.17 -10000 0 -0.32 283 283
BMP7/BMPR2/BMPR1A-1B 0.015 0.095 0.22 13 -0.19 76 89
SKI 0.02 0.004 -10000 0 -10000 0 0
BMP6 (homodimer) -0.027 0.12 0.32 2 -0.32 70 72
HFE2 0.022 0.042 0.32 9 -10000 0 9
ZFYVE16 0.02 0.005 -10000 0 -10000 0 0
MAP3K7 0.019 0.006 -10000 0 -10000 0 0
BMP2-4/CHRD 0.012 0.089 0.22 16 -0.19 66 82
SMAD5/SMAD5/SMAD4 -0.029 0.11 0.26 3 -0.36 26 29
MAPK1 0.02 0.005 -10000 0 -10000 0 0
TAK1/TAB family -0.011 0.088 -10000 0 -0.27 22 22
BMP7 (homodimer) 0.002 0.11 0.32 16 -0.32 39 55
NUP214 0.021 0.004 -10000 0 -10000 0 0
BMP6/FETUA 0.007 0.1 0.23 32 -0.22 65 97
SMAD1/SKI 0.008 0.065 -10000 0 -0.32 7 7
SMAD6 -0.027 0.12 -10000 0 -0.32 68 68
CTDSP2 0.02 0.005 -10000 0 -10000 0 0
BMP2-4/FETUA 0.015 0.095 0.22 28 -0.19 66 94
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.22 0.14 0.32 319 -10000 0 319
BMPR2 (homodimer) 0.021 0.002 -10000 0 -10000 0 0
GADD34/PP1CA 0.038 0.019 -10000 0 -0.19 2 2
BMPR1A-1B (homodimer) 0.006 0.078 0.23 3 -0.22 48 51
CHRDL1 -0.098 0.16 -10000 0 -0.32 169 169
ENDOFIN/SMAD1 0.008 0.063 0.22 1 -0.3 8 9
SMAD6-7/SMURF1/SMAD1 -0.001 0.085 -10000 0 -0.33 8 8
SMAD6/SMURF1 0.02 0.005 -10000 0 -10000 0 0
BAMBI 0.026 0.061 0.32 14 -0.32 5 19
SMURF2 0.021 0.004 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.066 0.14 -10000 0 -0.23 188 188
BMP2-4/GREM1 0.1 0.14 0.22 249 -0.16 68 317
SMAD7 0.019 0.017 -10000 0 -0.32 1 1
SMAD8A/SMAD8A/SMAD4 -0.1 0.21 -10000 0 -0.43 136 136
SMAD1/SMAD6 0.007 0.066 0.22 1 -0.3 9 10
TAK1/SMAD6 0.027 0.011 -10000 0 -10000 0 0
BMP7 0.002 0.11 0.32 16 -0.32 39 55
BMP6 -0.027 0.12 0.32 2 -0.32 70 72
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.028 0.09 -10000 0 -0.32 26 26
PPM1A 0.021 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.007 0.065 0.22 1 -0.31 8 9
SMAD7/SMURF1 0.027 0.016 -10000 0 -0.23 1 1
CTDSPL 0.021 0.004 -10000 0 -10000 0 0
PPP1CA 0.021 0.003 -10000 0 -10000 0 0
XIAP 0.021 0.003 -10000 0 -10000 0 0
CTDSP1 0.021 0.002 -10000 0 -10000 0 0
PPP1R15A 0.019 0.022 -10000 0 -0.32 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.026 0.1 -10000 0 -0.31 30 30
CHRD 0.032 0.063 0.32 21 -0.32 1 22
BMPR2 0.021 0.002 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.03 0.088 -10000 0 -0.3 23 23
BMP4 0.014 0.056 0.32 3 -0.32 11 14
FST 0.025 0.089 0.32 25 -0.32 14 39
BMP2-4/NOG -0.001 0.1 0.22 7 -0.22 79 86
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.024 0.092 0.22 13 -0.18 68 81
Signaling events regulated by Ret tyrosine kinase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.005 0.054 -10000 0 -0.35 9 9
Crk/p130 Cas/Paxillin -0.055 0.086 -10000 0 -0.23 79 79
JUN -0.038 0.082 0.16 8 -0.28 8 16
HRAS 0.021 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 0.012 0.11 0.23 41 -0.18 81 122
RAP1A 0.02 0.004 -10000 0 -10000 0 0
FRS2 0.02 0.005 -10000 0 -10000 0 0
RAP1A/GDP 0.015 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.01 0.11 0.23 43 -0.18 90 133
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.021 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.012 0.086 0.21 5 -0.17 104 109
RHOA 0.021 0.004 -10000 0 -10000 0 0
RAP1A/GTP 0.008 0.098 0.33 2 -0.16 86 88
GRB7 0.019 0.022 -10000 0 -0.32 2 2
RET51/GFRalpha1/GDNF 0.009 0.11 0.23 42 -0.18 90 132
MAPKKK cascade -0.031 0.092 0.18 6 -0.2 75 81
BCAR1 0.02 0.016 -10000 0 -0.32 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.011 0.087 0.21 6 -0.17 104 110
lamellipodium assembly -0.034 0.088 -10000 0 -0.22 67 67
RET51/GFRalpha1/GDNF/SHC 0.012 0.1 0.23 39 -0.18 74 113
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.008 0.079 0.21 4 -0.17 84 88
RET9/GFRalpha1/GDNF/Shank3 -0.013 0.089 0.21 6 -0.17 105 111
MAPK3 -0.017 0.1 0.18 60 -0.29 1 61
DOK1 0.021 0.002 -10000 0 -10000 0 0
DOK6 -0.008 0.091 -10000 0 -0.32 38 38
PXN 0.021 0.003 -10000 0 -10000 0 0
neurite development -0.025 0.091 0.24 6 -0.23 16 22
DOK5 0.061 0.1 0.32 67 -10000 0 67
GFRA1 -0.074 0.15 0.32 1 -0.32 135 136
MAPK8 -0.03 0.085 0.16 6 -0.27 8 14
HRAS/GTP -0.003 0.12 0.34 2 -0.21 88 90
tube development -0.011 0.086 0.2 13 -0.17 98 111
MAPK1 -0.017 0.095 0.25 11 -0.29 1 12
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.028 0.081 -10000 0 -0.19 92 92
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
SRC 0.02 0.004 -10000 0 -10000 0 0
PDLIM7 0.02 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 0 0.12 0.23 38 -0.2 98 136
SHC1 0.018 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.011 0.11 0.23 42 -0.18 88 130
RET51/GFRalpha1/GDNF/Dok5 0.023 0.12 0.24 70 -0.18 79 149
PRKCA 0.019 0.022 -10000 0 -0.32 2 2
HRAS/GDP 0.015 0.003 -10000 0 -10000 0 0
CREB1 -0.023 0.089 0.2 2 -0.22 68 70
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.024 0.079 0.16 3 -0.2 80 83
RET51/GFRalpha1/GDNF/Grb7 0.009 0.11 0.23 42 -0.18 90 132
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.057 0.1 0.32 63 -0.32 3 66
DOK4 0.02 0.004 -10000 0 -10000 0 0
JNK cascade -0.03 0.087 0.23 2 -0.28 8 10
RET9/GFRalpha1/GDNF/FRS2 -0.011 0.085 0.21 6 -0.17 99 105
SHANK3 0.017 0.031 -10000 0 -0.32 4 4
RASA1 0.02 0.005 -10000 0 -10000 0 0
NCK1 0.021 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.023 0.074 0.16 2 -0.19 78 80
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.019 0.092 0.18 9 -0.19 85 94
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.022 0.095 0.18 7 -0.19 94 101
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.011 0.086 0.18 11 -0.19 69 80
PI3K -0.043 0.13 0.23 5 -0.3 80 85
SOS1 0.021 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.005 0.088 0.21 6 -0.17 98 104
GRB10 0.019 0.006 -10000 0 -10000 0 0
activation of MAPKK activity -0.021 0.082 0.17 1 -0.25 5 6
RET51/GFRalpha1/GDNF/FRS2 0.009 0.11 0.23 42 -0.18 88 130
GAB1 0.019 0.027 -10000 0 -0.32 3 3
IRS1 0.02 0.016 -10000 0 -0.32 1 1
IRS2 0.019 0.016 -10000 0 -0.32 1 1
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.013 0.09 0.18 11 -0.2 73 84
RET51/GFRalpha1/GDNF/PKC alpha 0.01 0.11 0.23 42 -0.18 88 130
GRB2 0.02 0.004 -10000 0 -10000 0 0
PRKACA 0.02 0.005 -10000 0 -10000 0 0
GDNF 0.02 0.037 0.32 7 -10000 0 7
RAC1 0.019 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.01 0.11 0.23 43 -0.18 89 132
Rac1/GTP -0.031 0.11 0.22 1 -0.26 63 64
RET9/GFRalpha1/GDNF -0.021 0.089 0.21 6 -0.18 104 110
GFRalpha1/GDNF -0.028 0.11 0.23 6 -0.22 104 110
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.007 0.076 0.22 1 -0.29 19 20
alphaM/beta2 Integrin/GPIbA 0.005 0.081 0.22 2 -0.27 25 27
alphaM/beta2 Integrin/proMMP-9 0.045 0.11 0.22 90 -0.25 18 108
PLAUR 0.02 0.004 -10000 0 -10000 0 0
HMGB1 0.005 0.029 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.007 0.077 -10000 0 -0.29 20 20
AGER -0.29 0.11 -10000 0 -0.33 424 424
RAP1A 0.02 0.004 -10000 0 -10000 0 0
SELPLG 0.009 0.063 -10000 0 -0.32 17 17
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.19 0.12 -10000 0 -0.22 419 419
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.079 0.12 0.32 96 -10000 0 96
CYR61 0.005 0.071 -10000 0 -0.32 22 22
TLN1 0.019 0.016 -10000 0 -0.32 1 1
Rap1/GTP -0.048 0.13 -10000 0 -0.34 51 51
RHOA 0.021 0.004 -10000 0 -10000 0 0
P-selectin oligomer -0.048 0.14 -10000 0 -0.32 95 95
MYH2 -0.1 0.16 0.21 2 -0.38 80 82
MST1R 0.02 0.016 -10000 0 -0.32 1 1
leukocyte activation during inflammatory response 0.01 0.085 0.19 21 -0.21 38 59
APOB 0.022 0.099 0.32 26 -0.32 21 47
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.021 0.014 0.32 1 -10000 0 1
JAM3 0.019 0.022 -10000 0 -0.32 2 2
GP1BA 0.016 0.045 0.32 2 -0.32 7 9
alphaM/beta2 Integrin/CTGF -0.001 0.088 -10000 0 -0.26 37 37
alphaM/beta2 Integrin -0.064 0.14 0.21 2 -0.38 55 57
JAM3 homodimer 0.019 0.022 -10000 0 -0.32 2 2
ICAM2 0.018 0.027 -10000 0 -0.32 3 3
ICAM1 0.017 0.035 -10000 0 -0.32 5 5
phagocytosis triggered by activation of immune response cell surface activating receptor -0.065 0.14 0.21 2 -0.37 55 57
cell adhesion 0.004 0.08 0.22 2 -0.27 25 27
NFKB1 -0.22 0.16 -10000 0 -0.46 121 121
THY1 0.029 0.05 0.32 14 -10000 0 14
RhoA/GDP 0.015 0.003 -10000 0 -10000 0 0
Lipoprotein(a) 0.025 0.062 0.2 27 -0.18 22 49
alphaM/beta2 Integrin/LRP/tPA 0.033 0.095 0.22 31 -0.29 16 47
IL6 -0.24 0.24 -10000 0 -0.63 117 117
ITGB2 -0.001 0.055 -10000 0 -0.34 9 9
elevation of cytosolic calcium ion concentration 0.044 0.1 0.22 71 -0.28 16 87
alphaM/beta2 Integrin/JAM2/JAM3 -0.003 0.099 -10000 0 -0.24 54 54
JAM2 -0.012 0.1 -10000 0 -0.32 46 46
alphaM/beta2 Integrin/ICAM1 0.024 0.084 -10000 0 -0.25 22 22
alphaM/beta2 Integrin/uPA/Plg 0.047 0.11 0.23 76 -0.26 19 95
RhoA/GTP -0.077 0.16 0.23 2 -0.4 58 60
positive regulation of phagocytosis -0.051 0.13 -10000 0 -0.35 48 48
Ron/MSP 0.035 0.038 0.23 14 -0.23 2 16
alphaM/beta2 Integrin/uPAR/uPA 0.046 0.1 0.22 71 -0.28 16 87
alphaM/beta2 Integrin/uPAR 0.008 0.073 -10000 0 -0.29 17 17
PLAU 0.075 0.12 0.32 88 -10000 0 88
PLAT 0.047 0.092 0.32 48 -0.32 1 49
actin filament polymerization -0.099 0.15 0.21 2 -0.36 82 84
MST1 0.028 0.053 0.32 14 -0.32 1 15
alphaM/beta2 Integrin/lipoprotein(a) 0.013 0.088 0.21 21 -0.21 38 59
TNF -0.21 0.17 -10000 0 -0.47 116 116
RAP1B 0.02 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.04 0.11 0.22 73 -0.29 19 92
fibrinolysis 0.045 0.1 0.22 76 -0.25 19 95
HCK 0.007 0.066 -10000 0 -0.32 19 19
dendritic cell antigen processing and presentation -0.065 0.14 0.21 2 -0.37 55 57
VTN -0.032 0.13 0.32 7 -0.32 81 88
alphaM/beta2 Integrin/CYR61 -0.002 0.089 -10000 0 -0.26 38 38
LPA 0.017 0.025 0.32 2 -0.32 1 3
LRP1 0.018 0.031 -10000 0 -0.32 4 4
cell migration 0.021 0.077 0.24 2 -0.24 17 19
FN1 0.019 0.034 0.32 1 -0.32 4 5
alphaM/beta2 Integrin/Thy1 0.012 0.081 0.22 13 -0.27 20 33
MPO 0.014 0.051 0.32 1 -0.32 10 11
KNG1 0.038 0.075 0.32 32 -10000 0 32
RAP1/GDP 0.026 0.008 -10000 0 -10000 0 0
ROCK1 -0.071 0.15 0.24 5 -0.39 52 57
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.022 0.041 0.32 9 -10000 0 9
CTGF 0.003 0.072 -10000 0 -0.32 23 23
alphaM/beta2 Integrin/Hck 0.002 0.09 -10000 0 -0.32 25 25
ITGAM -0.008 0.072 -10000 0 -0.33 19 19
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.024 0.12 -10000 0 -0.23 96 96
HP -0.039 0.16 0.32 22 -0.32 103 125
leukocyte adhesion -0.18 0.12 -10000 0 -0.33 140 140
SELP -0.048 0.14 -10000 0 -0.32 95 95
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.3 0.55 0.76 2 -1.2 84 86
STAT6 (cleaved dimer) -0.32 0.55 -10000 0 -1.2 92 92
IGHG1 -0.087 0.23 0.41 14 -0.66 15 29
IGHG3 -0.3 0.52 0.58 3 -1.1 97 100
AKT1 -0.14 0.31 0.54 1 -0.88 37 38
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.11 0.29 0.53 1 -0.93 32 33
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.14 0.32 0.47 4 -0.87 33 37
THY1 -0.3 0.55 0.68 4 -1.2 85 89
MYB 0.02 0.029 0.32 3 -0.32 1 4
HMGA1 0.046 0.083 0.32 41 -10000 0 41
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.16 0.36 0.51 9 -0.78 62 71
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.14 0.32 0.46 5 -0.88 34 39
SP1 0.027 0.025 -10000 0 -10000 0 0
INPP5D 0.019 0.027 -10000 0 -0.32 3 3
SOCS5 0.011 0.036 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.31 0.54 0.61 1 -1.2 89 90
SOCS1 -0.19 0.36 0.52 2 -0.75 83 85
SOCS3 -0.14 0.3 0.51 1 -0.83 31 32
FCER2 -0.24 0.49 0.66 8 -1.1 80 88
PARP14 0.022 0.01 -10000 0 -10000 0 0
CCL17 -0.36 0.62 0.71 3 -1.4 102 105
GRB2 0.02 0.004 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.1 0.27 0.46 5 -0.72 32 37
T cell proliferation -0.32 0.55 0.62 1 -1.3 87 88
IL4R/JAK1 -0.31 0.55 0.62 1 -1.2 85 86
EGR2 -0.32 0.59 0.7 3 -1.3 87 90
JAK2 -0.008 0.064 -10000 0 -0.36 2 2
JAK3 0.02 0.016 -10000 0 -10000 0 0
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
JAK1 0.003 0.033 -10000 0 -10000 0 0
COL1A2 -0.064 0.22 0.49 2 -1.3 3 5
CCL26 -0.3 0.55 0.7 4 -1.3 79 83
IL4R -0.32 0.59 0.74 5 -1.3 85 90
PTPN6 0.016 0.03 -10000 0 -10000 0 0
IL13RA2 -0.34 0.6 0.66 3 -1.3 95 98
IL13RA1 -0.007 0.063 0.19 1 -10000 0 1
IRF4 -0.06 0.26 0.53 2 -1 23 25
ARG1 -0.096 0.25 0.5 3 -0.71 34 37
CBL -0.16 0.33 0.5 4 -0.74 61 65
GTF3A 0.062 0.058 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.001 0.087 0.23 10 -0.27 2 12
IRF4/BCL6 -0.062 0.24 -10000 0 -0.95 23 23
CD40LG 0.011 0.074 0.17 2 -0.32 21 23
MAPK14 -0.16 0.33 0.5 4 -0.78 52 56
mitosis -0.14 0.3 0.48 2 -0.82 37 39
STAT6 -0.36 0.67 0.78 6 -1.4 95 101
SPI1 0.006 0.075 -10000 0 -0.32 24 24
RPS6KB1 -0.13 0.29 0.51 1 -0.79 35 36
STAT6 (dimer) -0.35 0.67 0.78 6 -1.4 95 101
STAT6 (dimer)/PARP14 -0.34 0.6 0.65 2 -1.3 94 96
mast cell activation 0.005 0.017 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.17 0.36 0.48 3 -0.92 54 57
FRAP1 -0.14 0.31 0.54 1 -0.88 37 38
LTA -0.3 0.55 0.71 4 -1.2 83 87
FES 0.02 0.016 -10000 0 -0.32 1 1
T-helper 1 cell differentiation 0.34 0.64 1.4 95 -0.78 6 101
CCL11 -0.32 0.55 -10000 0 -1.2 96 96
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.14 0.33 0.46 4 -0.97 34 38
IL2RG 0.017 0.036 -10000 0 -0.3 5 5
IL10 -0.3 0.56 0.72 6 -1.3 83 89
IRS1 0.02 0.016 -10000 0 -0.32 1 1
IRS2 0.019 0.016 -10000 0 -0.32 1 1
IL4 -0.071 0.26 0.49 4 -1.1 20 24
IL5 -0.31 0.55 0.66 2 -1.2 85 87
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.26 0.49 0.63 11 -1 91 102
COL1A1 -0.016 0.28 0.56 13 -0.88 15 28
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.32 0.56 -10000 0 -1.3 85 85
IL2R gamma/JAK3 0.028 0.03 -10000 0 -0.19 5 5
TFF3 -0.31 0.59 0.72 6 -1.3 92 98
ALOX15 -0.63 0.72 0.68 1 -1.3 226 227
MYBL1 0.024 0.036 0.32 7 -10000 0 7
T-helper 2 cell differentiation -0.25 0.46 0.61 4 -0.99 90 94
SHC1 0.018 0.008 -10000 0 -10000 0 0
CEBPB 0.021 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.14 0.3 0.46 4 -0.81 33 37
mol:PI-3-4-5-P3 -0.14 0.31 0.54 1 -0.88 37 38
PI3K -0.15 0.34 0.55 1 -0.96 37 38
DOK2 -0.003 0.081 -10000 0 -0.32 29 29
ETS1 0.011 0.038 -10000 0 -0.28 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.093 0.24 0.43 6 -0.65 28 34
ITGB3 -0.31 0.56 0.66 5 -1.3 86 91
PIGR -0.43 0.69 0.71 6 -1.4 141 147
IGHE 0.009 0.072 0.2 20 -0.18 8 28
MAPKKK cascade -0.091 0.24 0.43 6 -0.64 28 34
BCL6 0.017 0.014 -10000 0 -10000 0 0
OPRM1 -0.31 0.55 0.65 3 -1.2 85 88
RETNLB -0.31 0.55 0.66 2 -1.2 85 87
SELP -0.41 0.68 0.69 5 -1.4 128 133
AICDA -0.33 0.56 0.69 2 -1.2 94 96
Visual signal transduction: Rods

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
mol:K + 0.021 0.003 -10000 0 -10000 0 0
GNAT1/GTP 0.017 0.027 0.21 9 -10000 0 9
Metarhodopsin II/Arrestin 0.025 0.009 0.2 1 -10000 0 1
PDE6G/GNAT1/GTP 0.028 0.033 0.23 9 -0.17 3 12
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.023 0.041 0.32 9 -10000 0 9
GRK1 0.035 0.07 0.32 28 -10000 0 28
CNG Channel 0.044 0.083 0.26 16 -0.17 28 44
mol:Na + 0.08 0.081 0.28 32 -0.16 3 35
mol:ADP 0.035 0.07 0.32 28 -10000 0 28
RGS9-1/Gbeta5/R9AP -0.058 0.12 -10000 0 -0.21 186 186
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.098 0.095 0.23 109 -0.17 3 112
CNGB1 0.071 0.11 0.32 83 -0.32 1 84
RDH5 0.026 0.04 0.32 9 -10000 0 9
SAG 0.019 0.014 0.32 1 -10000 0 1
mol:Ca2+ 0.015 0.089 0.3 31 -10000 0 31
Na + (4 Units) 0.022 0.08 0.13 158 -10000 0 158
RGS9 -0.08 0.16 -10000 0 -0.32 143 143
GNB1/GNGT1 0.062 0.077 0.23 83 -10000 0 83
GNAT1/GDP -0.042 0.11 0.21 5 -0.18 181 186
GUCY2D 0.02 0.041 0.32 5 -0.32 3 8
GNGT1 0.076 0.12 0.32 92 -10000 0 92
GUCY2F 0.019 0.014 0.32 1 -10000 0 1
GNB5 0.02 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.029 0.048 0.18 2 -0.17 37 39
mol:11-cis-retinal 0.026 0.04 0.32 9 -10000 0 9
mol:cGMP 0.059 0.072 0.22 75 -0.17 4 79
GNB1 0.02 0.004 -10000 0 -10000 0 0
Rhodopsin 0.033 0.028 0.23 9 -10000 0 9
SLC24A1 0.021 0.003 -10000 0 -10000 0 0
CNGA1 0.058 0.099 0.32 61 -10000 0 61
Metarhodopsin II 0.032 0.04 0.2 27 -10000 0 27
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.071 0.075 0.23 78 -0.17 5 83
RGS9BP -0.029 0.12 -10000 0 -0.32 70 70
Metarhodopsin II/Transducin 0.025 0.038 0.16 7 -10000 0 7
GCAP Family/Ca ++ 0.063 0.068 0.21 78 -0.14 2 80
PDE6A/B 0.009 0.071 0.23 1 -0.22 40 41
mol:Pi -0.058 0.12 -10000 0 -0.21 186 186
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.065 0.071 0.22 85 -10000 0 85
PDE6B 0.017 0.035 -10000 0 -0.32 5 5
PDE6A -0.005 0.092 0.32 1 -0.32 37 38
PDE6G 0.02 0.033 0.32 2 -0.32 3 5
RHO 0.019 0.003 -10000 0 -10000 0 0
PDE6 -0.047 0.13 -10000 0 -0.2 184 184
GUCA1A 0.068 0.11 0.32 78 -10000 0 78
GC2/GCAP Family 0.074 0.069 0.22 78 -0.15 2 80
GUCA1C 0.017 0.003 -10000 0 -10000 0 0
GUCA1B 0.021 0.035 0.32 4 -0.32 2 6
Ephrin B reverse signaling

Figure S21.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S21.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.014 0.044 -10000 0 -0.32 8 8
EPHB2 0.053 0.092 0.32 52 -10000 0 52
EFNB1 -0.012 0.028 0.18 6 -0.23 2 8
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.064 0.08 0.22 75 -0.24 5 80
Ephrin B2/EPHB1-2 0.067 0.082 0.22 88 -0.16 10 98
neuron projection morphogenesis 0.044 0.062 0.21 18 -0.23 5 23
Ephrin B1/EPHB1-2/Tiam1 0.07 0.087 0.23 85 -0.23 6 91
DNM1 0.024 0.031 0.32 5 -10000 0 5
cell-cell signaling 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.058 0.16 -10000 0 -0.5 54 54
YES1 -0.07 0.23 -10000 0 -0.72 54 54
Ephrin B1/EPHB1-2/NCK2 0.076 0.083 0.23 90 -0.2 4 94
PI3K -0.027 0.17 -10000 0 -0.49 55 55
mol:GDP 0.068 0.085 0.23 85 -0.23 6 91
ITGA2B -0.007 0.1 0.32 5 -0.32 44 49
endothelial cell proliferation 0.022 0.028 -10000 0 -0.18 8 8
FYN -0.074 0.23 -10000 0 -0.72 54 54
MAP3K7 -0.057 0.16 -10000 0 -0.53 53 53
FGR -0.074 0.23 -10000 0 -0.72 54 54
TIAM1 0.016 0.038 -10000 0 -0.32 6 6
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
RGS3 0.02 0.004 -10000 0 -10000 0 0
cell adhesion -0.047 0.17 0.23 1 -0.49 53 54
LYN -0.067 0.23 -10000 0 -0.72 53 53
Ephrin B1/EPHB1-2/Src Family Kinases -0.066 0.21 -10000 0 -0.65 55 55
Ephrin B1/EPHB1-2 -0.057 0.18 -10000 0 -0.56 53 53
SRC -0.067 0.23 -10000 0 -0.7 55 55
ITGB3 0.031 0.072 0.32 22 -0.32 5 27
EPHB1 0.052 0.096 0.32 52 -0.32 2 54
EPHB4 0.02 0.005 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.022 0.028 -10000 0 -0.18 8 8
alphaIIb/beta3 Integrin 0.016 0.094 0.23 27 -0.23 48 75
BLK -0.064 0.24 -10000 0 -0.72 54 54
HCK -0.073 0.24 -10000 0 -0.72 55 55
regulation of stress fiber formation -0.073 0.081 0.2 4 -0.23 90 94
MAPK8 -0.058 0.15 0.23 1 -0.48 53 54
Ephrin B1/EPHB1-2/RGS3 0.073 0.081 0.23 86 -0.2 4 90
endothelial cell migration -0.042 0.14 0.19 15 -0.43 49 64
NCK2 0.021 0.002 -10000 0 -10000 0 0
PTPN13 -0.022 0.14 -10000 0 -0.44 47 47
regulation of focal adhesion formation -0.073 0.081 0.2 4 -0.23 90 94
chemotaxis -0.071 0.079 0.2 4 -0.22 86 90
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.055 0.072 0.25 19 -0.24 5 24
angiogenesis -0.056 0.18 -10000 0 -0.56 53 53
LCK -0.067 0.23 -10000 0 -0.71 55 55
Syndecan-1-mediated signaling events

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
TGFB1 0.021 0.004 -10000 0 -10000 0 0
CCL5 0.017 0.035 -10000 0 -0.32 5 5
SDCBP 0.019 0.006 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.078 0.079 0.23 42 -0.26 2 44
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 0.071 0.085 0.22 32 -0.31 4 36
Syndecan-1/Syntenin 0.071 0.086 0.23 32 -0.31 4 36
MAPK3 0.055 0.084 0.21 36 -0.28 4 40
HGF/MET 0.015 0.074 0.23 10 -0.23 34 44
TGFB1/TGF beta receptor Type II 0.021 0.004 -10000 0 -10000 0 0
BSG 0.02 0.006 -10000 0 -10000 0 0
keratinocyte migration 0.071 0.084 0.22 32 -0.31 4 36
Syndecan-1/RANTES 0.075 0.089 0.23 36 -0.28 6 42
Syndecan-1/CD147 0.082 0.087 0.26 15 -0.29 4 19
Syndecan-1/Syntenin/PIP2 0.066 0.081 0.21 31 -0.3 4 35
LAMA5 0.017 0.031 -10000 0 -0.32 4 4
positive regulation of cell-cell adhesion 0.064 0.08 0.21 31 -0.3 4 35
MMP7 0.062 0.12 0.32 77 -0.32 8 85
HGF 0.008 0.075 0.32 4 -0.32 21 25
Syndecan-1/CASK 0.058 0.081 0.15 136 -0.25 7 143
Syndecan-1/HGF/MET 0.068 0.1 0.24 35 -0.31 7 42
regulation of cell adhesion 0.047 0.078 0.19 36 -0.29 3 39
HPSE 0.022 0.019 0.32 2 -10000 0 2
positive regulation of cell migration 0.078 0.079 0.23 42 -0.26 2 44
SDC1 0.077 0.078 0.22 41 -0.26 2 43
Syndecan-1/Collagen 0.078 0.079 0.23 42 -0.26 2 44
PPIB 0.021 0.014 0.32 1 -10000 0 1
MET 0.013 0.068 0.32 6 -0.32 15 21
PRKACA 0.02 0.005 -10000 0 -10000 0 0
MMP9 0.079 0.12 0.32 96 -10000 0 96
MAPK1 0.056 0.081 0.2 35 -0.27 4 39
homophilic cell adhesion 0.075 0.088 0.23 43 -0.24 3 46
MMP1 0.21 0.15 0.32 307 -0.32 2 309
p75(NTR)-mediated 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
Sortilin/TRAF6 0.029 0.018 -10000 0 -0.23 2 2
Necdin/E2F1 0.028 0.03 0.23 4 -0.22 4 8
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.048 0.07 0.22 25 -0.17 28 53
NGF (dimer)/p75(NTR)/BEX1 -0.011 0.13 0.24 33 -0.2 130 163
NT-4/5 (dimer)/p75(NTR) 0.016 0.072 0.26 7 -0.23 32 39
IKBKB 0.018 0.007 -10000 0 -10000 0 0
AKT1 -0.018 0.053 0.18 19 -10000 0 19
IKBKG 0.02 0.004 -10000 0 -10000 0 0
BDNF -0.15 0.17 -10000 0 -0.32 242 242
MGDIs/NGR/p75(NTR)/LINGO1 0.057 0.071 0.22 59 -0.18 9 68
FURIN 0.029 0.048 0.32 13 -10000 0 13
proBDNF (dimer)/p75(NTR)/Sortilin -0.074 0.12 0.22 5 -0.2 238 243
LINGO1 0.059 0.1 0.32 62 -10000 0 62
Sortilin/TRAF6/NRIF -0.028 0.019 -10000 0 -0.17 2 2
proBDNF (dimer) -0.15 0.17 -10000 0 -0.32 242 242
NTRK1 0.01 0.057 0.32 1 -0.32 13 14
RTN4R 0.02 0.005 -10000 0 -10000 0 0
neuron apoptosis -0.098 0.14 0.28 4 -0.42 30 34
IRAK1 0.02 0.004 -10000 0 -10000 0 0
SHC1 -0.015 0.041 -10000 0 -0.19 14 14
ARHGDIA 0.021 0.004 -10000 0 -10000 0 0
RhoA/GTP 0.015 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.046 0.031 -10000 0 -0.17 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.048 0.066 0.22 26 -0.18 24 50
MAGEH1 0.021 0.003 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.044 0.07 0.22 25 -0.18 26 51
Mammalian IAPs/DIABLO 0.051 0.026 0.22 4 -0.18 2 6
proNGF (dimer) 0.024 0.083 0.32 21 -0.32 13 34
MAGED1 0.021 0.014 0.32 1 -10000 0 1
APP 0.02 0.005 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.004 0.075 0.32 1 -0.32 24 25
ZNF274 0.02 0.004 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.02 0.045 0.19 1 -0.16 22 23
NGF 0.024 0.084 0.32 21 -0.32 13 34
cell cycle arrest 0.002 0.07 0.23 17 -10000 0 17
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.009 0.054 0.17 6 -0.19 24 30
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.028 0.066 0.25 7 -0.2 32 39
NCSTN 0.019 0.007 -10000 0 -10000 0 0
mol:GTP 0.039 0.065 0.22 27 -0.19 21 48
PSENEN 0.02 0.005 -10000 0 -10000 0 0
mol:ceramide -0.016 0.049 0.2 9 -0.18 18 27
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.003 0.052 0.16 8 -0.28 3 11
p75(NTR)/beta APP 0.027 0.043 0.23 7 -0.22 9 16
BEX1 -0.054 0.16 0.32 18 -0.32 122 140
mol:GDP -0.014 0.046 0.21 1 -0.18 22 23
NGF (dimer) 0.072 0.093 0.23 100 -0.18 18 118
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.065 0.069 0.23 58 -0.16 9 67
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
RAC1/GTP 0.03 0.055 0.2 22 -0.16 21 43
MYD88 0.021 0.004 -10000 0 -10000 0 0
CHUK 0.021 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.04 0.065 0.22 27 -0.19 21 48
RHOB 0.021 0.002 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.03 0.018 0.23 3 -10000 0 3
NT3 (dimer) 0.005 0.075 0.32 2 -0.32 23 25
TP53 -0.083 0.087 0.24 8 -0.29 6 14
PRDM4 -0.019 0.052 0.2 11 -0.18 21 32
BDNF (dimer) -0.009 0.16 0.26 99 -0.16 214 313
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
SORT1 0.019 0.022 -10000 0 -0.32 2 2
activation of caspase activity 0.043 0.067 -10000 0 -0.17 28 28
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.048 0.066 0.22 26 -0.18 24 50
RHOC 0.02 0.004 -10000 0 -10000 0 0
XIAP 0.021 0.003 -10000 0 -10000 0 0
MAPK10 -0.076 0.12 0.3 10 -0.32 47 57
DIABLO 0.021 0.003 -10000 0 -10000 0 0
SMPD2 -0.017 0.049 0.2 9 -0.18 18 27
APH1B 0.019 0.022 -10000 0 -0.32 2 2
APH1A 0.018 0.008 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.038 0.067 0.22 26 -0.19 24 50
PSEN1 0.02 0.004 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.03 0.007 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) 0.016 0.073 0.29 7 -0.23 31 38
MAPK8 -0.06 0.1 0.31 9 -0.29 25 34
MAPK9 -0.059 0.1 0.3 9 -0.29 23 32
APAF1 0.021 0.003 -10000 0 -10000 0 0
NTF3 0.005 0.075 0.32 2 -0.32 23 25
NTF4 0.004 0.075 0.32 1 -0.32 24 25
NDN 0.017 0.035 -10000 0 -0.32 5 5
RAC1/GDP 0.014 0.005 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.047 0.056 -10000 0 -0.16 20 20
p75 CTF/Sortilin/TRAF6/NRIF 0.049 0.022 -10000 0 -0.18 2 2
RhoA-B-C/GTP 0.039 0.065 0.22 27 -0.19 21 48
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.056 0.12 0.22 4 -0.17 234 238
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.062 0.12 0.22 5 -0.18 235 240
PRKACB 0.021 0.014 0.32 1 -10000 0 1
proBDNF (dimer)/p75 ECD -0.097 0.13 -10000 0 -0.23 240 240
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.021 0.035 0.32 4 -0.32 2 6
BIRC2 0.02 0.004 -10000 0 -10000 0 0
neuron projection morphogenesis 0.007 0.071 0.22 13 -0.19 14 27
BAD -0.07 0.11 0.31 11 -0.31 31 42
RIPK2 0.019 0.007 -10000 0 -10000 0 0
NGFR 0.019 0.059 0.32 7 -0.32 9 16
CYCS -0.021 0.049 0.19 10 -10000 0 10
ADAM17 0.021 0.002 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.043 0.064 0.22 23 -0.18 21 44
BCL2L11 -0.07 0.11 0.31 10 -0.31 31 41
BDNF (dimer)/p75(NTR) -0.095 0.13 0.23 5 -0.23 239 244
PI3K 0.046 0.065 0.22 25 -0.18 22 47
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.046 0.067 0.22 26 -0.18 23 49
NDNL2 0.02 0.005 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
PRKCI 0.02 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) 0.029 0.072 0.23 27 -0.22 22 49
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.048 0.066 0.22 26 -0.18 23 49
TRAF6 0.021 0.003 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCZ 0.018 0.027 -10000 0 -0.32 3 3
PLG 0.022 0.041 0.32 9 -10000 0 9
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.096 0.096 0.14 3 -0.19 231 234
SQSTM1 0.02 0.005 -10000 0 -10000 0 0
NGFRAP1 0.018 0.035 -10000 0 -0.32 5 5
CASP3 -0.067 0.11 0.3 10 -0.3 32 42
E2F1 0.023 0.027 0.32 4 -10000 0 4
CASP9 0.021 0.004 -10000 0 -10000 0 0
IKK complex 0.03 0.069 0.23 3 -0.26 9 12
NGF (dimer)/TRKA 0.023 0.067 0.23 19 -0.22 22 41
MMP7 0.062 0.12 0.32 77 -0.32 8 85
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.053 0.066 0.22 25 -0.17 22 47
MMP3 0.13 0.14 0.32 180 -10000 0 180
APAF-1/Caspase 9 -0.039 0.035 -10000 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.07 0.11 0.33 73 -0.22 2 75
NFATC2 0.005 0.14 -10000 0 -0.56 13 13
NFATC3 -0.006 0.083 -10000 0 -0.26 34 34
CD40LG -0.087 0.29 0.4 1 -0.76 62 63
ITCH -0.024 0.076 -10000 0 -0.2 79 79
CBLB -0.027 0.079 -10000 0 -0.2 87 87
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.028 0.25 0.43 19 -0.73 31 50
JUNB 0.018 0.027 -10000 0 -0.32 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.026 0.099 -10000 0 -0.23 91 91
T cell anergy -0.056 0.14 0.28 4 -0.33 87 91
TLE4 -0.009 0.11 -10000 0 -0.46 14 14
Jun/NFAT1-c-4/p21SNFT -0.034 0.29 0.5 1 -0.77 53 54
AP-1/NFAT1-c-4 -0.049 0.34 0.6 3 -0.85 58 61
IKZF1 -0.005 0.093 -10000 0 -0.43 11 11
T-helper 2 cell differentiation -0.028 0.19 -10000 0 -0.71 21 21
AP-1/NFAT1 0.012 0.13 0.32 4 -0.36 19 23
CALM1 -0.009 0.067 -10000 0 -0.15 90 90
EGR2 -0.087 0.32 -10000 0 -0.87 54 54
EGR3 -0.12 0.39 -10000 0 -1.2 55 55
NFAT1/FOXP3 0.056 0.14 0.41 21 -0.38 11 32
EGR1 0.001 0.079 -10000 0 -0.32 27 27
JUN 0.012 0.04 -10000 0 -0.32 4 4
EGR4 0.049 0.09 0.32 48 -10000 0 48
mol:Ca2+ -0.024 0.054 -10000 0 -0.14 92 92
GBP3 -0.017 0.13 -10000 0 -0.56 21 21
FOSL1 0.03 0.064 0.32 19 -0.32 3 22
NFAT1-c-4/MAF/IRF4 -0.032 0.28 -10000 0 -0.74 56 56
DGKA -0.006 0.095 0.5 1 -0.44 9 10
CREM 0.02 0.004 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.066 0.29 -10000 0 -0.8 57 57
CTLA4 0.015 0.1 0.37 8 -0.33 9 17
NFAT1-c-4 (dimer)/EGR1 -0.056 0.3 0.45 1 -0.81 58 59
NFAT1-c-4 (dimer)/EGR4 -0.031 0.3 0.45 2 -0.78 56 58
FOS -0.007 0.087 -10000 0 -0.33 31 31
IFNG -0.037 0.22 -10000 0 -0.9 19 19
T cell activation -0.037 0.17 -10000 0 -0.68 14 14
MAF 0.019 0.016 -10000 0 -0.32 1 1
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.064 0.23 0.66 57 -10000 0 57
TNF -0.077 0.27 0.46 1 -0.76 57 58
FASLG -0.15 0.43 -10000 0 -1.2 61 61
TBX21 0.014 0.078 0.32 2 -0.29 24 26
BATF3 0.02 0.015 0.32 1 -10000 0 1
PRKCQ -0.022 0.11 -10000 0 -0.32 61 61
PTPN1 -0.007 0.095 0.34 1 -0.41 11 12
NFAT1-c-4/ICER1 -0.046 0.28 -10000 0 -0.76 57 57
GATA3 0.02 0.021 0.32 1 -0.32 1 2
T-helper 1 cell differentiation -0.037 0.22 -10000 0 -0.88 19 19
IL2RA -0.016 0.26 0.47 23 -0.7 33 56
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.007 0.092 -10000 0 -0.39 13 13
E2F1 0.025 0.028 0.32 4 -10000 0 4
PPARG -0.02 0.11 -10000 0 -0.32 57 57
SLC3A2 -0.006 0.091 -10000 0 -0.42 10 10
IRF4 0.025 0.056 0.32 12 -0.32 4 16
PTGS2 -0.09 0.29 0.45 2 -0.78 56 58
CSF2 -0.088 0.29 0.45 4 -0.76 62 66
JunB/Fra1/NFAT1-c-4 -0.032 0.28 0.49 2 -0.74 57 59
IL4 -0.03 0.19 -10000 0 -0.74 21 21
IL5 -0.084 0.28 0.4 1 -0.74 60 61
IL2 -0.037 0.17 -10000 0 -0.7 14 14
IL3 -0.026 0.13 -10000 0 -0.75 10 10
RNF128 -0.07 0.17 -10000 0 -0.43 90 90
NFATC1 -0.064 0.23 -10000 0 -0.66 57 57
CDK4 0.047 0.16 0.56 25 -10000 0 25
PTPRK -0.005 0.09 -10000 0 -0.42 10 10
IL8 -0.078 0.28 0.45 6 -0.75 60 66
POU2F1 0.019 0.007 -10000 0 -10000 0 0
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.017 0.027 -10000 0 -0.32 3 3
GNB1/GNG2 -0.049 0.07 -10000 0 -0.18 95 95
AKT1 -0.038 0.1 0.28 1 -0.26 26 27
EGF 0.07 0.12 0.32 85 -0.32 4 89
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.029 0.058 -10000 0 -0.22 17 17
mol:Ca2+ -0.062 0.14 0.24 1 -0.3 104 105
LYN -0.021 0.039 -10000 0 -0.2 3 3
RhoA/GTP -0.025 0.057 -10000 0 -0.13 84 84
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.072 0.15 -10000 0 -0.34 96 96
GNG2 0.019 0.022 -10000 0 -0.32 2 2
ARRB2 0.02 0.006 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.031 0.15 -10000 0 -0.59 27 27
G beta5/gamma2 -0.062 0.092 -10000 0 -0.24 94 94
PRKCH -0.072 0.16 0.31 1 -0.35 100 101
DNM1 0.024 0.03 0.32 5 -10000 0 5
TXA2/TP beta/beta Arrestin3 0.008 0.046 -10000 0 -0.53 3 3
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR 0.013 0.049 -10000 0 -0.32 10 10
G12 family/GTP -0.061 0.13 -10000 0 -0.3 96 96
ADRBK1 0.021 0.003 -10000 0 -10000 0 0
ADRBK2 0.02 0.005 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.026 0.008 -10000 0 -10000 0 0
mol:GDP 0.042 0.11 0.36 28 -10000 0 28
mol:NADP 0.021 0.05 0.32 7 -0.32 5 12
RAB11A 0.021 0.003 -10000 0 -10000 0 0
PRKG1 -0.015 0.1 -10000 0 -0.32 51 51
mol:IP3 -0.08 0.17 -10000 0 -0.38 108 108
cell morphogenesis 0.026 0.008 -10000 0 -10000 0 0
PLCB2 -0.11 0.23 -10000 0 -0.51 108 108
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.005 0.071 0.22 4 -0.19 3 7
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.025 0.049 -10000 0 -0.22 10 10
RHOA 0.021 0.004 -10000 0 -10000 0 0
PTGIR 0.016 0.038 -10000 0 -0.32 6 6
PRKCB1 -0.077 0.16 -10000 0 -0.37 101 101
GNAQ 0.02 0.016 -10000 0 -0.32 1 1
mol:L-citrulline 0.021 0.05 0.32 7 -0.32 5 12
TXA2/TXA2-R family -0.11 0.22 -10000 0 -0.52 99 99
LCK -0.021 0.046 0.16 1 -0.21 5 6
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.011 0.047 0.18 2 -0.2 12 14
TXA2-R family/G12 family/GDP/G beta/gamma 0.01 0.06 -10000 0 -0.41 8 8
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.012 0.045 -10000 0 -0.19 12 12
MAPK14 -0.046 0.1 0.27 7 -0.23 92 99
TGM2/GTP -0.089 0.18 0.3 1 -0.42 99 100
MAPK11 -0.05 0.099 0.19 1 -0.23 94 95
ARHGEF1 -0.042 0.074 -10000 0 -0.18 84 84
GNAI2 0.021 0.004 -10000 0 -10000 0 0
JNK cascade -0.079 0.17 -10000 0 -0.38 96 96
RAB11/GDP 0.021 0.005 -10000 0 -10000 0 0
ICAM1 -0.057 0.12 0.23 1 -0.28 94 95
cAMP biosynthetic process -0.075 0.16 -10000 0 -0.35 104 104
Gq family/GTP/EBP50 -0.001 0.043 -10000 0 -0.19 20 20
actin cytoskeleton reorganization 0.026 0.008 -10000 0 -10000 0 0
SRC -0.021 0.041 -10000 0 -0.2 3 3
GNB5 0.02 0.004 -10000 0 -10000 0 0
GNB1 0.02 0.004 -10000 0 -10000 0 0
EGF/EGFR -0.007 0.076 0.2 10 -0.24 14 24
VCAM1 -0.058 0.13 0.22 1 -0.29 94 95
TP beta/Gq family/GDP/G beta5/gamma2 -0.031 0.15 -10000 0 -0.59 27 27
platelet activation -0.061 0.14 0.28 7 -0.3 95 102
PGI2/IP 0.012 0.026 -10000 0 -0.22 6 6
PRKACA 0.003 0.039 -10000 0 -0.22 14 14
Gq family/GDP/G beta5/gamma2 -0.017 0.11 -10000 0 -0.5 19 19
TXA2/TP beta/beta Arrestin2 -0.005 0.059 0.17 3 -0.36 8 11
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.013 0.034 -10000 0 -0.2 13 13
mol:DAG -0.088 0.19 -10000 0 -0.42 102 102
EGFR 0.015 0.041 0.32 1 -0.32 6 7
TXA2/TP alpha -0.1 0.21 -10000 0 -0.47 104 104
Gq family/GTP -0.014 0.065 0.22 1 -0.22 39 40
YES1 -0.02 0.043 -10000 0 -0.2 3 3
GNAI2/GTP -0.004 0.041 -10000 0 -0.18 10 10
PGD2/DP 0.01 0.033 -10000 0 -0.22 10 10
SLC9A3R1 0.021 0.014 0.32 1 -10000 0 1
FYN -0.019 0.041 0.16 1 -0.2 3 4
mol:NO 0.021 0.05 0.32 7 -0.32 5 12
GNA15 0.02 0.006 -10000 0 -10000 0 0
PGK/cGMP 0.006 0.072 0.21 7 -0.19 50 57
RhoA/GDP 0.021 0.005 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.02 0.05 -10000 0 -0.2 13 13
NOS3 0.021 0.05 0.32 7 -0.32 5 12
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCA -0.072 0.16 0.28 2 -0.35 98 100
PRKCB -0.075 0.16 -10000 0 -0.36 97 97
PRKCE -0.072 0.16 -10000 0 -0.36 96 96
PRKCD -0.078 0.16 -10000 0 -0.38 100 100
PRKCG -0.077 0.17 -10000 0 -0.38 100 100
muscle contraction -0.1 0.21 -10000 0 -0.48 101 101
PRKCZ -0.072 0.15 -10000 0 -0.34 96 96
ARR3 0.019 0.019 0.32 2 -10000 0 2
TXA2/TP beta 0.007 0.047 -10000 0 -0.19 11 11
PRKCQ -0.084 0.16 -10000 0 -0.37 101 101
MAPKKK cascade -0.097 0.2 -10000 0 -0.45 102 102
SELE -0.072 0.15 -10000 0 -0.36 94 94
TP beta/GNAI2/GDP/G beta/gamma 0.021 0.049 -10000 0 -0.22 6 6
ROCK1 0.02 0.005 -10000 0 -10000 0 0
GNA14 0.013 0.051 -10000 0 -0.32 11 11
chemotaxis -0.12 0.25 -10000 0 -0.59 96 96
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA13 0.021 0.004 -10000 0 -10000 0 0
GNA11 0.019 0.016 -10000 0 -0.32 1 1
Rac1/GTP 0.014 0.005 -10000 0 -10000 0 0
IL23-mediated signaling events

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
CCL2 -0.11 0.44 0.64 3 -1.1 49 52
IL23A -0.094 0.46 0.7 6 -1.2 49 55
NF kappa B1 p50/RelA/I kappa B alpha -0.095 0.44 0.62 4 -1.1 52 56
positive regulation of T cell mediated cytotoxicity -0.12 0.51 0.68 5 -1.3 52 57
ITGA3 -0.11 0.44 0.65 3 -1.1 51 54
IL17F -0.069 0.3 0.47 14 -0.71 53 67
IL12B 0.018 0.059 0.26 5 -0.34 1 6
STAT1 (dimer) -0.12 0.48 0.62 2 -1.2 54 56
CD4 -0.11 0.45 0.68 4 -1.2 48 52
IL23 -0.086 0.44 0.67 5 -1.1 47 52
IL23R 0.004 0.17 -10000 0 -0.98 9 9
IL1B -0.12 0.49 0.72 3 -1.3 52 55
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.091 0.43 0.7 4 -1.1 47 51
TYK2 0.015 0.042 0.16 1 -10000 0 1
STAT4 0.021 0.002 -10000 0 -10000 0 0
STAT3 0.021 0.003 -10000 0 -10000 0 0
IL18RAP 0.009 0.065 -10000 0 -0.32 18 18
IL12RB1 0.007 0.071 0.16 1 -0.35 12 13
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.017 0.065 0.2 1 -0.26 11 12
IL23R/JAK2 0.014 0.18 -10000 0 -0.96 8 8
positive regulation of chronic inflammatory response -0.12 0.51 0.68 5 -1.3 52 57
natural killer cell activation 0 0.009 -10000 0 -0.041 3 3
JAK2 0.015 0.055 0.19 1 -0.34 2 3
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
NFKB1 0.013 0.021 -10000 0 -10000 0 0
RELA 0.013 0.021 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.078 0.42 0.67 5 -1.1 47 52
ALOX12B -0.094 0.44 0.65 6 -1.1 48 54
CXCL1 -0.12 0.46 0.71 3 -1.2 56 59
T cell proliferation -0.12 0.51 0.68 5 -1.3 52 57
NFKBIA 0.011 0.02 -10000 0 -10000 0 0
IL17A -0.023 0.26 0.45 29 -0.55 45 74
PI3K -0.11 0.46 0.59 2 -1.2 54 56
IFNG 0.006 0.046 0.14 24 -0.13 9 33
STAT3 (dimer) -0.1 0.44 0.59 4 -1.1 54 58
IL18R1 0.007 0.069 -10000 0 -0.32 20 20
IL23/IL23R/JAK2/TYK2/SOCS3 -0.063 0.34 0.47 15 -0.83 47 62
IL18/IL18R 0.027 0.084 0.19 1 -0.23 37 38
macrophage activation -0.003 0.024 0.05 29 -0.045 32 61
TNF -0.11 0.48 0.72 4 -1.2 52 56
STAT3/STAT4 -0.11 0.46 0.59 2 -1.2 56 58
STAT4 (dimer) -0.12 0.48 0.62 2 -1.2 54 56
IL18 0.014 0.047 -10000 0 -0.32 9 9
IL19 -0.089 0.43 0.66 5 -1.1 47 52
STAT5A (dimer) -0.12 0.48 0.62 2 -1.2 54 56
STAT1 0.021 0.002 -10000 0 -10000 0 0
SOCS3 0.018 0.031 -10000 0 -0.32 4 4
CXCL9 -0.1 0.46 0.64 10 -1.2 53 63
MPO -0.11 0.45 0.64 3 -1.1 54 57
positive regulation of humoral immune response -0.12 0.51 0.68 5 -1.3 52 57
IL23/IL23R/JAK2/TYK2 -0.14 0.55 0.7 4 -1.4 49 53
IL6 -0.2 0.58 0.65 3 -1.1 113 116
STAT5A 0.02 0.016 -10000 0 -0.32 1 1
IL2 0.013 0.027 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0.009 -10000 0 -0.041 3 3
CD3E -0.11 0.44 0.66 2 -1.1 51 53
keratinocyte proliferation -0.12 0.51 0.68 5 -1.3 52 57
NOS2 -0.15 0.5 0.65 6 -1.1 75 81
TCGA08_retinoblastoma

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
CDKN2B 0.012 0.038 -10000 0 -0.3 6 6
CDKN2C 0.001 0.031 0.32 1 -0.1 1 2
CDKN2A 0.098 0.14 0.32 130 -10000 0 130
CCND2 -0.02 0.042 0.16 4 -0.16 9 13
RB1 0.02 0.049 0.22 7 -0.17 5 12
CDK4 -0.022 0.046 0.17 5 -0.14 9 14
CDK6 -0.022 0.047 0.17 4 -0.17 10 14
G1/S progression 0.008 0.091 0.18 81 -0.25 7 88
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.02 0.005 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.023 0.07 -10000 0 -0.24 24 24
NT3 (dimer)/TRKC -0.026 0.11 0.23 2 -0.24 99 101
NT3 (dimer)/TRKB -0.045 0.13 0.3 7 -0.2 173 180
SHC/Grb2/SOS1/GAB1/PI3K 0.011 0.023 -10000 0 -0.18 6 6
RAPGEF1 0.021 0.004 -10000 0 -10000 0 0
BDNF -0.15 0.17 -10000 0 -0.32 242 242
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
DYNLT1 0.019 0.006 -10000 0 -10000 0 0
NTRK1 0.01 0.057 0.32 1 -0.32 13 14
NTRK2 -0.092 0.16 0.32 3 -0.32 163 166
NTRK3 -0.045 0.13 -10000 0 -0.32 93 93
NT-4/5 (dimer)/TRKB -0.046 0.13 0.28 6 -0.2 176 182
neuron apoptosis 0.14 0.16 0.39 109 -10000 0 109
SHC 2-3/Grb2 -0.15 0.18 -10000 0 -0.43 109 109
SHC1 0.018 0.008 -10000 0 -10000 0 0
SHC2 -0.11 0.15 -10000 0 -0.42 64 64
SHC3 -0.16 0.21 0.2 1 -0.51 108 109
STAT3 (dimer) 0.019 0.036 -10000 0 -0.3 6 6
NT3 (dimer)/TRKA 0.021 0.071 0.27 7 -0.2 34 41
RIN/GDP -0.02 0.073 0.22 3 -0.23 13 16
GIPC1 0.02 0.005 -10000 0 -10000 0 0
KRAS 0.02 0.006 -10000 0 -10000 0 0
DNAJA3 -0.015 0.057 0.19 4 -0.21 24 28
RIN/GTP 0.013 0.014 0.21 2 -10000 0 2
CCND1 -0.021 0.063 -10000 0 -0.59 6 6
MAGED1 0.021 0.014 0.32 1 -10000 0 1
PTPN11 0.021 0.004 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.004 0.075 0.32 1 -0.32 24 25
SHC/GRB2/SOS1 0.035 0.017 -10000 0 -10000 0 0
GRB2 0.02 0.004 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.024 0.072 0.22 16 -0.2 34 50
TRKA/NEDD4-2 0.018 0.043 0.23 1 -0.23 13 14
ELMO1 0.018 0.023 -10000 0 -0.32 2 2
RhoG/GTP/ELMO1/DOCK1 0.025 0.016 -10000 0 -0.19 2 2
NGF 0.024 0.084 0.32 21 -0.32 13 34
HRAS 0.021 0.004 -10000 0 -10000 0 0
DOCK1 0.021 0.003 -10000 0 -10000 0 0
GAB2 0.017 0.031 -10000 0 -0.32 4 4
RIT2 0.017 0.02 0.32 2 -10000 0 2
RIT1 0.018 0.008 -10000 0 -10000 0 0
FRS2 0.02 0.005 -10000 0 -10000 0 0
DNM1 0.024 0.03 0.32 5 -10000 0 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.006 0.062 0.18 2 -0.25 13 15
mol:GDP -0.034 0.1 0.26 3 -0.31 20 23
NGF (dimer) 0.024 0.083 0.32 21 -0.32 13 34
RhoG/GDP 0.013 0.016 -10000 0 -0.22 2 2
RIT1/GDP -0.025 0.065 0.22 1 -0.23 12 13
TIAM1 0.016 0.038 -10000 0 -0.32 6 6
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
BDNF (dimer)/TRKB -0.14 0.15 0.22 1 -0.24 312 313
KIDINS220/CRKL/C3G 0.029 0.009 -10000 0 -10000 0 0
SHC/RasGAP 0.025 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2 0.039 0.014 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.043 0.026 -10000 0 -0.18 2 2
RIT1/GTP 0.013 0.006 -10000 0 -10000 0 0
NT3 (dimer) 0.005 0.075 0.32 2 -0.32 23 25
RAP1/GDP -0.023 0.061 -10000 0 -0.19 16 16
KIDINS220/CRKL 0.02 0.005 -10000 0 -10000 0 0
BDNF (dimer) -0.15 0.17 -10000 0 -0.32 242 242
ubiquitin-dependent protein catabolic process 0.028 0.061 0.22 17 -0.19 22 39
Schwann cell development -0.036 0.025 -10000 0 -10000 0 0
EHD4 0.02 0.005 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.048 0.019 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.005 0.046 -10000 0 -0.18 12 12
RAP1B 0.02 0.005 -10000 0 -10000 0 0
RAP1A 0.02 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.14 0.14 -10000 0 -0.24 303 303
ABL1 0.021 0.004 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.03 0.007 -10000 0 -10000 0 0
Rap1/GTP -0.073 0.1 -10000 0 -0.38 27 27
STAT3 0.019 0.036 -10000 0 -0.3 6 6
axon guidance -0.16 0.12 -10000 0 -0.23 289 289
MAPK3 -0.013 0.072 0.18 36 -0.19 26 62
MAPK1 -0.011 0.071 0.18 37 -0.19 23 60
CDC42/GDP -0.021 0.074 0.22 3 -0.23 11 14
NTF3 0.005 0.075 0.32 2 -0.32 23 25
NTF4 0.004 0.075 0.32 1 -0.32 24 25
NGF (dimer)/TRKA/FAIM 0.033 0.061 0.22 19 -0.19 21 40
PI3K 0.029 0.014 -10000 0 -0.23 1 1
FRS3 0.02 0.004 -10000 0 -10000 0 0
FAIM 0.021 0.003 -10000 0 -10000 0 0
GAB1 0.019 0.027 -10000 0 -0.32 3 3
RASGRF1 -0.059 0.088 0.15 1 -0.28 32 33
SOS1 0.021 0.003 -10000 0 -10000 0 0
MCF2L -0.052 0.081 0.16 3 -0.21 91 94
RGS19 0.019 0.006 -10000 0 -10000 0 0
CDC42 0.021 0.004 -10000 0 -10000 0 0
RAS family/GTP 0 0.077 0.31 2 -0.39 4 6
Rac1/GDP -0.021 0.07 0.22 1 -0.23 14 15
NGF (dimer)/TRKA/GRIT 0.022 0.058 0.21 19 -0.18 22 41
neuron projection morphogenesis 0.005 0.1 -10000 0 -0.88 3 3
NGF (dimer)/TRKA/NEDD4-2 0.029 0.061 0.22 17 -0.19 22 39
MAP2K1 0.012 0.091 0.2 84 -10000 0 84
NGFR 0.019 0.059 0.32 7 -0.32 9 16
NGF (dimer)/TRKA/GIPC/GAIP 0.005 0.057 0.17 4 -0.22 19 23
RAS family/GTP/PI3K 0.01 0.02 0.15 1 -0.17 5 6
FRS2 family/SHP2/GRB2/SOS1 0.054 0.025 -10000 0 -10000 0 0
NRAS 0.02 0.005 -10000 0 -10000 0 0
GRB2/SOS1 0.03 0.007 -10000 0 -10000 0 0
PRKCI 0.02 0.005 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCZ 0.018 0.027 -10000 0 -0.32 3 3
MAPKKK cascade -0.066 0.18 -10000 0 -0.56 54 54
RASA1 0.02 0.005 -10000 0 -10000 0 0
TRKA/c-Abl 0.02 0.043 0.23 1 -0.23 13 14
SQSTM1 0.02 0.005 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.12 0.14 0.22 2 -0.22 311 313
NGF (dimer)/TRKA/p62/Atypical PKCs 0.043 0.064 0.22 16 -0.18 21 37
MATK 0.009 0.061 -10000 0 -0.32 16 16
NEDD4L 0.019 0.006 -10000 0 -10000 0 0
RAS family/GDP -0.029 0.045 -10000 0 -0.17 17 17
NGF (dimer)/TRKA -0.001 0.061 0.18 4 -0.21 25 29
Rac1/GTP -0.06 0.07 -10000 0 -0.21 55 55
FRS2 family/SHP2/CRK family 0.049 0.029 -10000 0 -10000 0 0
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.021 0.039 -10000 0 -0.19 23 23
ADCY5 -0.032 0.061 0.089 7 -0.19 57 64
ADCY6 -0.014 0.016 -10000 0 -0.19 4 4
ADCY7 -0.014 0.016 -10000 0 -0.19 4 4
ADCY1 -0.012 0.029 0.16 6 -0.19 6 12
ADCY2 -0.018 0.048 0.12 11 -0.19 29 40
ADCY3 -0.014 0.016 -10000 0 -0.19 4 4
ADCY8 -0.072 0.085 0.089 1 -0.19 168 169
PRKCE -0.01 0.019 -10000 0 -0.22 4 4
ADCY9 -0.017 0.027 -10000 0 -0.19 12 12
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.004 0.1 0.2 49 -0.24 12 61
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.024 0.039 -10000 0 -0.23 11 11
alphaV beta3 Integrin 0.017 0.091 0.22 20 -0.2 64 84
PTK2 -0.04 0.12 0.33 10 -0.36 22 32
IGF1R 0.02 0.016 -10000 0 -0.32 1 1
PI4KB 0.018 0.008 -10000 0 -10000 0 0
MFGE8 0.021 0.003 -10000 0 -10000 0 0
SRC 0.02 0.004 -10000 0 -10000 0 0
CDKN1B -0.056 0.16 0.17 6 -0.4 76 82
VEGFA 0.021 0.004 -10000 0 -10000 0 0
ILK -0.059 0.16 0.17 6 -0.4 80 86
ROCK1 0.02 0.005 -10000 0 -10000 0 0
AKT1 -0.066 0.14 -10000 0 -0.38 79 79
PTK2B -0.013 0.052 0.17 25 -0.31 1 26
alphaV/beta3 Integrin/JAM-A -0.002 0.11 0.22 24 -0.2 91 115
CBL 0.02 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.054 0.058 0.22 44 -0.19 5 49
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.046 0.04 0.22 1 -0.19 11 12
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.023 0.083 0.16 2 -0.31 15 17
alphaV/beta3 Integrin/Syndecan-1 0.047 0.046 0.22 22 -0.19 5 27
PI4KA 0.02 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.017 0.091 -10000 0 -0.2 57 57
PI4 Kinase 0.025 0.013 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.17 0.1 0.23 329 -0.18 5 334
RPS6KB1 -0.045 0.069 0.31 2 -0.36 7 9
TLN1 0.019 0.016 -10000 0 -0.32 1 1
MAPK3 -0.056 0.14 0.28 1 -0.43 52 53
GPR124 0.017 0.023 -10000 0 -0.32 2 2
MAPK1 -0.054 0.14 0.28 2 -0.43 53 55
PXN 0.021 0.003 -10000 0 -10000 0 0
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
alphaV/beta3 Integrin/Tumstatin -0.015 0.11 0.22 18 -0.19 130 148
cell adhesion 0.039 0.052 0.22 22 -0.2 7 29
ANGPTL3 0.033 0.064 0.32 23 -10000 0 23
VEGFR2 homodimer/VEGFA homodimer/Src 0.035 0.035 -10000 0 -0.19 10 10
IGF-1R heterotetramer 0.02 0.016 -10000 0 -0.32 1 1
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
TGFBR2 0.016 0.041 -10000 0 -0.32 7 7
ITGB3 0.031 0.072 0.32 22 -0.32 5 27
IGF1 0.014 0.051 0.32 1 -0.32 10 11
RAC1 0.019 0.007 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.04 0.049 0.22 20 -0.22 6 26
apoptosis 0.021 0.002 -10000 0 -10000 0 0
CD47 0.019 0.022 -10000 0 -0.32 2 2
alphaV/beta3 Integrin/CD47 0.046 0.048 0.22 22 -0.19 7 29
VCL 0.021 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.028 0.08 0.23 19 -0.2 39 58
CSF1 0.018 0.027 -10000 0 -0.32 3 3
PIK3C2A -0.059 0.16 0.18 6 -0.4 80 86
PI4 Kinase/Pyk2 -0.051 0.072 0.17 1 -0.28 16 17
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.05 0.058 0.22 21 -0.19 15 36
FAK1/Vinculin -0.032 0.11 0.31 10 -0.3 19 29
alphaV beta3/Integrin/ppsTEM5 0.041 0.05 0.22 20 -0.22 6 26
RHOA 0.021 0.004 -10000 0 -10000 0 0
VTN -0.032 0.13 0.32 7 -0.32 81 88
BCAR1 0.02 0.016 -10000 0 -0.32 1 1
FGF2 -0.023 0.11 -10000 0 -0.32 62 62
F11R -0.033 0.061 -10000 0 -0.23 44 44
alphaV/beta3 Integrin/Lactadherin 0.047 0.046 0.22 22 -0.19 5 27
alphaV/beta3 Integrin/TGFBR2 0.043 0.054 0.22 22 -0.19 12 34
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.046 0.027 -10000 0 -0.18 4 4
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.043 0.045 0.21 21 -0.19 5 26
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.019 0.034 0.32 1 -0.32 4 5
alphaV/beta3 Integrin/Pyk2 0.032 0.058 0.2 19 -0.18 14 33
SDC1 0.021 0.002 -10000 0 -10000 0 0
VAV3 -0.019 0.045 0.17 21 -0.31 1 22
PTPN11 0.021 0.004 -10000 0 -10000 0 0
IRS1 0.02 0.016 -10000 0 -0.32 1 1
FAK1/Paxillin -0.033 0.11 0.3 9 -0.3 20 29
cell migration -0.034 0.1 0.27 11 -0.28 19 30
ITGAV 0.021 0.002 -10000 0 -10000 0 0
PI3K 0.005 0.1 0.28 2 -0.19 75 77
SPP1 0.23 0.14 0.32 337 -10000 0 337
KDR 0.013 0.051 -10000 0 -0.32 11 11
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.021 0.002 -10000 0 -10000 0 0
COL4A3 -0.071 0.15 -10000 0 -0.32 130 130
angiogenesis -0.053 0.16 0.28 2 -0.45 49 51
Rac1/GTP -0.018 0.042 0.16 19 -0.27 1 20
EDIL3 -0.005 0.092 0.32 1 -0.32 37 38
cell proliferation 0.042 0.054 0.22 22 -0.19 12 34
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.021 0.015 -10000 0 -0.16 1 1
ARNO/beta Arrestin1-2 -0.051 0.17 -10000 0 -0.82 18 18
EGFR 0.015 0.041 0.32 1 -0.32 6 7
EPHA2 0.013 0.049 -10000 0 -0.32 10 10
USP6 0.02 0.006 -10000 0 -10000 0 0
IQSEC1 0.02 0.016 -10000 0 -0.32 1 1
EGFR/EGFR/EGF/EGF 0.052 0.085 0.23 72 -0.24 9 81
ARRB2 0.017 0.037 0.14 40 -10000 0 40
mol:GTP 0.005 0.038 0.14 8 -0.15 8 16
ARRB1 0.018 0.031 -10000 0 -0.32 4 4
FBXO8 0.02 0.004 -10000 0 -10000 0 0
TSHR 0.049 0.089 0.32 48 -10000 0 48
EGF 0.07 0.12 0.32 85 -0.32 4 89
somatostatin receptor activity 0 0 0.001 13 -0.001 56 69
ARAP2 0.011 0.055 -10000 0 -0.32 13 13
mol:GDP -0.062 0.14 0.17 7 -0.28 95 102
mol:PI-3-4-5-P3 0 0 0.001 11 -0.001 26 37
ITGA2B -0.007 0.1 0.32 5 -0.32 44 49
ARF6 0.02 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.04 0.035 -10000 0 -0.18 7 7
ADAP1 0.018 0.017 -10000 0 -0.32 1 1
KIF13B 0.018 0.008 -10000 0 -10000 0 0
HGF/MET 0.015 0.074 0.23 10 -0.23 34 44
PXN 0.021 0.003 -10000 0 -10000 0 0
ARF6/GTP -0.046 0.11 0.22 12 -0.26 58 70
EGFR/EGFR/EGF/EGF/ARFGEP100 0.056 0.076 0.22 65 -0.19 10 75
ADRB2 -0.1 0.16 -10000 0 -0.32 178 178
receptor agonist activity 0 0 0 4 0 57 61
actin filament binding 0 0 0 9 0 69 78
SRC 0.02 0.004 -10000 0 -10000 0 0
ITGB3 0.031 0.072 0.32 22 -0.32 5 27
GNAQ 0.02 0.016 -10000 0 -0.32 1 1
EFA6/PI-4-5-P2 0 0 0.001 17 -0.001 37 54
ARF6/GDP -0.037 0.14 0.27 2 -0.39 46 48
ARF6/GDP/GULP/ACAP1 -0.045 0.14 -10000 0 -0.32 58 58
alphaIIb/beta3 Integrin/paxillin/GIT1 0.037 0.083 0.22 25 -0.18 48 73
ACAP1 0.019 0.016 -10000 0 -0.32 1 1
ACAP2 0.02 0.005 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.032 0.07 0.25 42 -10000 0 42
EFNA1 0.017 0.017 -10000 0 -0.32 1 1
HGF 0.008 0.075 0.32 4 -0.32 21 25
CYTH3 -0.007 0.015 0.21 2 -10000 0 2
CYTH2 -0.023 0.19 -10000 0 -0.99 18 18
NCK1 0.021 0.003 -10000 0 -10000 0 0
fibronectin binding 0 0 0 15 0 40 55
endosomal lumen acidification 0 0 0 34 0 22 56
microtubule-based process 0 0 -10000 0 0 1 1
GULP1 0.018 0.031 -10000 0 -0.32 4 4
GNAQ/ARNO -0.009 0.18 -10000 0 -0.92 18 18
mol:Phosphatidic acid 0 0 0 3 -10000 0 3
PIP3-E 0 0 0 7 0 9 16
MET 0.013 0.068 0.32 6 -0.32 15 21
GNA14 0.013 0.051 -10000 0 -0.32 11 11
GNA15 0.02 0.006 -10000 0 -10000 0 0
GIT1 0.021 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 10 -0.001 40 50
GNA11 0.019 0.016 -10000 0 -0.32 1 1
LHCGR 0.044 0.085 0.32 42 -10000 0 42
AGTR1 -0.082 0.16 0.32 1 -0.32 147 148
desensitization of G-protein coupled receptor protein signaling pathway 0.032 0.07 0.25 42 -10000 0 42
IPCEF1/ARNO 0.017 0.18 -10000 0 -0.83 18 18
alphaIIb/beta3 Integrin 0.016 0.094 0.23 27 -0.23 48 75
HIF-2-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 0.021 0.069 0.41 2 -0.54 5 7
oxygen homeostasis 0.009 0.014 -10000 0 -10000 0 0
TCEB2 0.021 0.003 -10000 0 -10000 0 0
TCEB1 0.02 0.015 0.32 1 -10000 0 1
VHL/Elongin B/Elongin C/HIF2A 0.069 0.097 0.24 33 -0.28 5 38
EPO 0.098 0.15 0.4 52 -10000 0 52
FIH (dimer) 0.025 0.021 -10000 0 -10000 0 0
APEX1 0.028 0.025 -10000 0 -10000 0 0
SERPINE1 0.1 0.16 0.4 62 -10000 0 62
FLT1 -0.007 0.13 -10000 0 -0.56 17 17
ADORA2A 0.095 0.15 0.36 73 -10000 0 73
germ cell development 0.11 0.17 0.4 67 -0.4 3 70
SLC11A2 0.1 0.15 0.39 62 -10000 0 62
BHLHE40 0.11 0.16 0.39 64 -10000 0 64
HIF1AN 0.025 0.021 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.08 0.12 0.33 34 -0.29 1 35
ETS1 0.02 0.025 -10000 0 -0.35 1 1
CITED2 -0.015 0.14 -10000 0 -0.52 30 30
KDR -0.007 0.16 -10000 0 -0.83 14 14
PGK1 0.11 0.16 0.39 64 -10000 0 64
SIRT1 0.021 0.003 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.13 0.19 0.53 45 -10000 0 45
EPAS1 0.049 0.096 0.24 54 -0.25 6 60
SP1 0.023 0.01 -10000 0 -10000 0 0
ABCG2 0.094 0.18 0.39 64 -0.42 11 75
EFNA1 0.089 0.15 0.39 49 -10000 0 49
FXN 0.096 0.15 0.36 74 -10000 0 74
POU5F1 0.11 0.17 0.41 66 -0.41 3 69
neuron apoptosis -0.13 0.18 -10000 0 -0.52 45 45
EP300 0.02 0.004 -10000 0 -10000 0 0
EGLN3 0.089 0.13 0.33 107 -0.32 1 108
EGLN2 0.026 0.022 -10000 0 -10000 0 0
EGLN1 0.024 0.021 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.037 0.018 0.22 1 -10000 0 1
VHL 0.02 0.004 -10000 0 -10000 0 0
ARNT 0.024 0.025 -10000 0 -10000 0 0
SLC2A1 0.14 0.18 0.41 106 -10000 0 106
TWIST1 0.11 0.17 0.43 74 -10000 0 74
ELK1 0.022 0.007 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.086 0.12 0.35 32 -0.3 1 33
VEGFA 0.1 0.15 0.39 62 -10000 0 62
CREBBP 0.021 0.004 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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
HDAC1 0.023 0.016 0.19 1 -10000 0 1
AES 0.021 0.014 0.16 1 -10000 0 1
FBXW11 0.02 0.005 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.029 0.01 -10000 0 -10000 0 0
SMAD4 0.019 0.006 -10000 0 -10000 0 0
DKK2 -0.047 0.14 -10000 0 -0.32 96 96
TLE1 0.022 0.014 -10000 0 -10000 0 0
MACF1 0.019 0.031 -10000 0 -0.32 4 4
CTNNB1 0.079 0.1 0.28 26 -0.31 8 34
WIF1 -0.2 0.16 -10000 0 -0.32 321 321
beta catenin/RanBP3 0.044 0.1 0.45 18 -0.32 3 21
KREMEN2 0.097 0.13 0.32 124 -10000 0 124
DKK1 0.036 0.16 0.32 78 -0.32 47 125
beta catenin/beta TrCP1 0.08 0.099 0.29 18 -0.3 7 25
FZD1 0.021 0.004 -10000 0 -10000 0 0
AXIN2 -0.028 0.24 0.58 16 -1.2 16 32
AXIN1 0.022 0.004 -10000 0 -10000 0 0
RAN 0.021 0.014 0.32 1 -10000 0 1
Axin1/APC/GSK3/beta catenin 0.026 0.098 -10000 0 -0.66 8 8
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.02 0.17 0.32 1 -0.58 26 27
Axin1/APC/GSK3 0.05 0.071 0.22 21 -0.32 5 26
Axin1/APC/GSK3/beta catenin/Macf1 0.034 0.083 0.25 13 -0.35 9 22
HNF1A 0.081 0.12 0.32 97 -0.32 1 98
CTBP1 0.022 0.015 0.18 1 -10000 0 1
MYC 0.072 0.23 0.56 77 -1.3 2 79
RANBP3 0.02 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.03 0.12 0.22 79 -0.17 88 167
NKD1 -0.015 0.11 0.32 4 -0.32 53 57
TCF4 0.019 0.026 0.17 1 -0.32 2 3
TCF3 0.022 0.015 0.18 1 -10000 0 1
WNT1/LRP6/FZD1/Axin1 0.051 0.029 0.23 6 -10000 0 6
Ran/GTP 0.016 0.01 0.21 1 -10000 0 1
CtBP/CBP/TCF/TLE1/AES 0.007 0.12 0.4 18 -0.48 9 27
LEF1 0.024 0.024 0.32 2 -10000 0 2
DVL1 0.038 0.053 0.18 1 -0.32 4 5
CSNK2A1 0.021 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.028 0.16 -10000 0 -0.59 20 20
DKK1/LRP6/Kremen 2 0.083 0.13 0.25 149 -0.17 45 194
LRP6 0.02 0.006 -10000 0 -10000 0 0
CSNK1A1 0.023 0.015 -10000 0 -10000 0 0
NLK 0.019 0.01 -10000 0 -10000 0 0
CCND1 -0.003 0.19 0.58 19 -1.3 6 25
WNT1 0.027 0.04 0.32 9 -10000 0 9
GSK3A 0.021 0.004 -10000 0 -10000 0 0
GSK3B 0.021 0.003 -10000 0 -10000 0 0
FRAT1 0.021 0.004 -10000 0 -10000 0 0
PPP2R5D 0.047 0.075 0.24 41 -0.25 3 44
APC -0.003 0.058 0.18 42 -10000 0 42
WNT1/LRP6/FZD1 0.095 0.087 0.22 27 -0.19 3 30
CREBBP 0.023 0.015 0.18 1 -10000 0 1
Presenilin action in Notch and Wnt 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
Delta 1/NOTCH/NOTCH(cleaved) 0.005 0.1 -10000 0 -0.41 23 23
HDAC1 0.021 0.006 -10000 0 -10000 0 0
AES 0.02 0.006 -10000 0 -10000 0 0
FBXW11 0.02 0.005 -10000 0 -10000 0 0
DTX1 0.022 0.019 0.32 2 -10000 0 2
LRP6/FZD1 0.028 0.01 -10000 0 -10000 0 0
TLE1 0.02 0.004 -10000 0 -10000 0 0
AP1 -0.023 0.085 -10000 0 -0.22 62 62
NCSTN 0.019 0.007 -10000 0 -10000 0 0
ADAM10 0.021 0.004 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.02 0.1 -10000 0 -0.71 7 7
NICD/RBPSUH 0.004 0.1 -10000 0 -0.41 23 23
WIF1 -0.21 0.16 -10000 0 -0.32 321 321
NOTCH1 -0.004 0.089 -10000 0 -0.43 20 20
PSENEN 0.02 0.005 -10000 0 -10000 0 0
KREMEN2 0.097 0.13 0.32 124 -10000 0 124
DKK1 0.036 0.16 0.32 78 -0.32 47 125
beta catenin/beta TrCP1 0.013 0.073 0.3 1 -0.29 4 5
APH1B 0.019 0.022 -10000 0 -0.32 2 2
APH1A 0.018 0.008 -10000 0 -10000 0 0
AXIN1 0 0.072 -10000 0 -0.42 7 7
CtBP/CBP/TCF1/TLE1/AES 0.022 0.054 0.25 2 -10000 0 2
PSEN1 0.021 0.004 -10000 0 -10000 0 0
FOS -0.001 0.083 -10000 0 -0.32 31 31
JUN 0.018 0.031 -10000 0 -0.32 4 4
MAP3K7 0.019 0.007 -10000 0 -10000 0 0
CTNNB1 0.009 0.073 0.25 3 -0.29 5 8
MAPK3 0.021 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.03 0.12 0.22 79 -0.17 88 167
HNF1A 0.079 0.12 0.32 96 -0.32 1 97
CTBP1 0.02 0.004 -10000 0 -10000 0 0
MYC 0.008 0.081 -10000 0 -1.2 2 2
NKD1 -0.015 0.11 0.32 4 -0.32 53 57
FZD1 0.02 0.004 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.006 0.1 -10000 0 -0.41 22 22
apoptosis -0.024 0.086 -10000 0 -0.23 63 63
Delta 1/NOTCHprecursor 0.003 0.1 -10000 0 -0.41 23 23
DLL1 0.015 0.038 -10000 0 -0.32 6 6
PPARD 0.016 0.042 -10000 0 -0.85 1 1
Gamma Secretase 0.046 0.031 -10000 0 -0.17 1 1
APC -0.009 0.093 -10000 0 -0.41 16 16
DVL1 -0.032 0.069 -10000 0 -0.28 28 28
CSNK2A1 0.02 0.006 -10000 0 -10000 0 0
MAP3K7IP1 0 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.082 0.13 0.25 149 -0.17 45 194
LRP6 0.02 0.005 -10000 0 -10000 0 0
CSNK1A1 0.02 0.006 -10000 0 -10000 0 0
NLK 0.007 0.005 -10000 0 -10000 0 0
CCND1 0 0.14 -10000 0 -1.1 8 8
WNT1 0.026 0.04 0.32 9 -10000 0 9
Axin1/APC/beta catenin 0.004 0.11 0.31 4 -0.43 12 16
DKK2 -0.047 0.14 -10000 0 -0.32 96 96
NOTCH1 precursor/DVL1 -0.031 0.11 -10000 0 -0.44 24 24
GSK3B 0.021 0.003 -10000 0 -10000 0 0
FRAT1 0.021 0.003 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.009 0.1 -10000 0 -0.42 22 22
PPP2R5D 0.01 0.071 0.22 1 -0.32 7 8
MAPK1 0.02 0.005 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.093 0.11 0.22 2 -0.18 293 295
RBPJ 0.021 0.004 -10000 0 -10000 0 0
CREBBP 0.021 0.005 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.028 0.082 0.28 2 -0.32 1 3
SMARCC2 0.02 0.011 -10000 0 -0.17 1 1
SMARCC1 0.02 0.009 -10000 0 -0.11 1 1
TBX21 -0.046 0.17 0.36 6 -0.46 46 52
SUMO2 0.019 0.013 -10000 0 -10000 0 0
STAT1 (dimer) 0.023 0.002 -10000 0 -10000 0 0
FKBP4 0.02 0.005 -10000 0 -10000 0 0
FKBP5 0.02 0.016 -10000 0 -0.32 1 1
GR alpha/HSP90/FKBP51/HSP90 0.048 0.11 0.28 33 -10000 0 33
PRL -0.02 0.11 0.42 3 -0.57 1 4
cortisol/GR alpha (dimer)/TIF2 0.064 0.21 0.5 51 -0.36 5 56
RELA -0.036 0.1 -10000 0 -0.2 108 108
FGG 0.032 0.28 0.5 74 -0.39 61 135
GR beta/TIF2 0.037 0.11 0.28 33 -0.24 2 35
IFNG -0.06 0.26 0.45 9 -0.68 40 49
apoptosis 0.011 0.14 0.46 12 -0.49 9 21
CREB1 0.039 0.045 -10000 0 -10000 0 0
histone acetylation -0.073 0.12 -10000 0 -0.33 45 45
BGLAP -0.019 0.1 0.3 1 -0.35 10 11
GR/PKAc 0.053 0.1 0.28 32 -10000 0 32
NF kappa B1 p50/RelA -0.065 0.18 0.29 1 -0.32 138 139
SMARCD1 0.021 0.009 -10000 0 -0.11 1 1
MDM2 0.038 0.087 0.21 60 -10000 0 60
GATA3 0.022 0.021 0.32 1 -0.32 1 2
AKT1 0.019 0.004 -10000 0 -10000 0 0
CSF2 -0.12 0.27 -10000 0 -0.92 41 41
GSK3B 0.019 0.012 -10000 0 -10000 0 0
NR1I3 0.023 0.13 0.48 8 -0.48 3 11
CSN2 0.058 0.18 0.37 62 -0.3 9 71
BRG1/BAF155/BAF170/BAF60A 0.048 0.033 -10000 0 -0.29 3 3
NFATC1 0.018 0.023 -10000 0 -0.32 2 2
POU2F1 0.022 0.017 -10000 0 -10000 0 0
CDKN1A -0.005 0.068 -10000 0 -1 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 0.025 0.041 0.32 8 -0.32 1 9
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.057 0.1 0.28 27 -10000 0 27
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.013 0.2 0.45 9 -0.69 28 37
JUN -0.019 0.18 0.32 29 -0.38 39 68
IL4 -0.036 0.12 -10000 0 -0.52 9 9
CDK5R1 0.027 0.05 0.32 13 -10000 0 13
PRKACA 0.02 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.041 0.063 0.16 2 -0.23 20 22
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.053 0.1 0.28 24 -10000 0 24
cortisol/GR alpha (monomer) 0.094 0.27 0.6 66 -0.4 8 74
NCOA2 0.016 0.031 -10000 0 -0.32 4 4
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS 0.007 0.11 0.22 12 -0.31 25 37
AP-1/NFAT1-c-4 -0.015 0.27 0.42 30 -0.51 45 75
AFP -0.019 0.16 0.44 7 -0.51 3 10
SUV420H1 0.021 0.004 -10000 0 -10000 0 0
IRF1 0.055 0.14 0.37 30 -0.32 1 31
TP53 0.021 0.043 -10000 0 -0.91 1 1
PPP5C 0.02 0.005 -10000 0 -10000 0 0
KRT17 -0.066 0.3 0.44 19 -0.79 43 62
KRT14 0.031 0.18 0.47 3 -0.46 1 4
TBP 0.021 0.007 -10000 0 -10000 0 0
CREBBP -0.018 0.069 -10000 0 -0.28 2 2
HDAC1 0.021 0.003 -10000 0 -10000 0 0
HDAC2 0.023 0.022 -10000 0 -10000 0 0
AP-1 -0.015 0.27 0.42 31 -0.5 49 80
MAPK14 0.019 0.013 -10000 0 -10000 0 0
MAPK10 -0.017 0.11 -10000 0 -0.32 53 53
MAPK11 0.017 0.025 -10000 0 -0.32 2 2
KRT5 -0.21 0.45 0.44 15 -0.92 128 143
interleukin-1 receptor activity 0.004 0.02 -10000 0 -10000 0 0
NCOA1 0.022 0.002 -10000 0 -10000 0 0
STAT1 0.023 0.002 -10000 0 -10000 0 0
CGA -0.004 0.13 0.34 13 -0.38 10 23
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.008 0.17 0.47 32 -0.34 6 38
MAPK3 0.019 0.013 -10000 0 -10000 0 0
MAPK1 0.018 0.013 -10000 0 -10000 0 0
ICAM1 -0.1 0.21 -10000 0 -0.51 69 69
NFKB1 -0.038 0.1 -10000 0 -0.2 111 111
MAPK8 -0.023 0.16 0.29 14 -0.36 47 61
MAPK9 0.019 0.012 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.008 0.14 0.46 12 -0.51 9 21
BAX -0.009 0.056 -10000 0 -10000 0 0
POMC -0.13 0.29 0.37 1 -0.84 43 44
EP300 -0.018 0.07 -10000 0 -0.28 2 2
cortisol/GR alpha (dimer)/p53 0.078 0.22 0.52 54 -0.37 2 56
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.074 0.2 41 -10000 0 41
SGK1 -0.027 0.12 -10000 0 -0.84 4 4
IL13 -0.055 0.2 -10000 0 -0.56 26 26
IL6 -0.21 0.36 -10000 0 -0.79 122 122
PRKACG 0.017 0.004 -10000 0 -10000 0 0
IL5 -0.052 0.17 -10000 0 -0.61 9 9
IL2 -0.065 0.23 0.38 4 -0.6 39 43
CDK5 0.019 0.01 -10000 0 -10000 0 0
PRKACB 0.021 0.014 0.32 1 -10000 0 1
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
IL8 -0.094 0.2 0.32 6 -0.49 61 67
CDK5R1/CDK5 0.033 0.035 0.23 12 -10000 0 12
NF kappa B1 p50/RelA/PKAc -0.027 0.15 0.26 1 -0.26 108 109
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.076 0.21 0.48 59 -0.33 5 64
SMARCA4 0.019 0.017 -10000 0 -0.32 1 1
chromatin remodeling 0.044 0.13 0.34 36 -10000 0 36
NF kappa B1 p50/RelA/Cbp -0.069 0.16 0.37 1 -0.34 76 77
JUN (dimer) -0.019 0.18 0.32 29 -0.38 39 68
YWHAH 0.02 0.004 -10000 0 -10000 0 0
VIPR1 -0.26 0.34 -10000 0 -0.68 193 193
NR3C1 0.06 0.17 0.39 59 -0.26 1 60
NR4A1 -0.058 0.16 -10000 0 -0.35 105 105
TIF2/SUV420H1 0.026 0.025 -10000 0 -0.23 4 4
MAPKKK cascade 0.011 0.14 0.46 12 -0.49 9 21
cortisol/GR alpha (dimer)/Src-1 0.086 0.23 0.52 62 -0.36 5 67
PBX1 0.014 0.056 -10000 0 -0.32 12 12
POU1F1 0.021 0.023 0.42 1 -10000 0 1
SELE -0.18 0.35 -10000 0 -0.81 101 101
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.044 0.13 0.34 36 -10000 0 36
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.076 0.21 0.48 59 -0.33 5 64
mol:cortisol 0.053 0.15 0.35 67 -0.22 7 74
MMP1 0.16 0.19 0.4 41 -0.7 7 48
Reelin signaling pathway

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
CDK5R1/CDK5 0.034 0.032 0.23 12 -10000 0 12
VLDLR 0.014 0.044 -10000 0 -0.32 8 8
CRKL 0.02 0.005 -10000 0 -10000 0 0
LRPAP1 0.021 0.003 -10000 0 -10000 0 0
FYN 0.019 0.017 -10000 0 -0.32 1 1
ITGA3 0.018 0.031 -10000 0 -0.32 4 4
RELN/VLDLR/Fyn 0.006 0.084 0.22 5 -0.2 63 68
MAPK8IP1/MKK7/MAP3K11/JNK1 0.049 0.029 -10000 0 -0.17 1 1
AKT1 -0.033 0.073 0.19 3 -0.2 60 63
MAP2K7 0.02 0.005 -10000 0 -10000 0 0
RAPGEF1 0.021 0.004 -10000 0 -10000 0 0
DAB1 0.023 0.036 0.32 7 -10000 0 7
RELN/LRP8/DAB1 0.019 0.079 0.22 18 -0.17 58 76
LRPAP1/LRP8 0.034 0.026 0.23 8 -10000 0 8
RELN/LRP8/DAB1/Fyn 0.023 0.078 0.22 16 -0.17 56 72
DAB1/alpha3/beta1 Integrin 0.015 0.076 0.26 1 -0.17 56 57
long-term memory 0.01 0.1 0.25 14 -0.18 81 95
DAB1/LIS1 0.023 0.083 0.34 1 -0.17 56 57
DAB1/CRLK/C3G 0.016 0.075 0.26 1 -0.17 52 53
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
DAB1/NCK2 0.027 0.084 0.35 1 -0.17 56 57
ARHGEF2 0.018 0.008 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.009 0.14 0.32 38 -0.32 49 87
CDK5R1 0.029 0.048 0.32 13 -10000 0 13
RELN -0.018 0.12 0.32 6 -0.32 59 65
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
RELN/LRP8/Fyn 0.014 0.084 0.22 13 -0.19 59 72
GRIN2A/RELN/LRP8/DAB1/Fyn 0.021 0.11 0.23 39 -0.18 85 124
MAPK8 0.021 0.003 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.011 0.079 0.23 10 -0.18 62 72
ITGB1 0.021 0.004 -10000 0 -10000 0 0
MAP1B -0.028 0.075 0.17 23 -0.19 55 78
RELN/LRP8 0.017 0.083 0.22 13 -0.19 58 71
GRIN2B/RELN/LRP8/DAB1/Fyn 0.031 0.088 0.25 20 -0.17 53 73
PI3K 0.029 0.014 -10000 0 -0.23 1 1
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.028 0.024 -10000 0 -0.23 4 4
RAP1A -0.03 0.076 0.23 9 -0.28 3 12
PAFAH1B1 0.019 0.006 -10000 0 -10000 0 0
MAPK8IP1 0.021 0.003 -10000 0 -10000 0 0
CRLK/C3G 0.029 0.009 -10000 0 -10000 0 0
GRIN2B 0.023 0.041 0.32 9 -10000 0 9
NCK2 0.021 0.002 -10000 0 -10000 0 0
neuron differentiation -0.007 0.072 0.21 3 -0.25 16 19
neuron adhesion -0.032 0.083 0.28 9 -0.27 3 12
LRP8 0.026 0.04 0.32 9 -10000 0 9
GSK3B -0.035 0.07 0.18 3 -0.2 57 60
RELN/VLDLR/DAB1/Fyn 0.016 0.079 0.23 8 -0.17 60 68
MAP3K11 0.02 0.016 -10000 0 -0.32 1 1
RELN/VLDLR/DAB1/P13K -0.017 0.08 0.2 1 -0.21 62 63
CDK5 0.02 0.004 -10000 0 -10000 0 0
MAPT -0.007 0.1 0.76 6 -0.29 21 27
neuron migration -0.038 0.098 0.23 11 -0.26 53 64
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.005 0.068 0.21 3 -0.24 13 16
RELN/VLDLR 0.02 0.086 0.22 12 -0.18 62 74
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.021 0.004 -10000 0 -10000 0 0
EGFR 0.015 0.041 0.32 1 -0.32 6 7
EGF/EGFR 0.025 0.087 0.18 54 -0.16 65 119
EGF/EGFR dimer/SHC/GRB2/SOS1 0.061 0.071 0.22 53 -0.19 6 59
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.02 0.016 -10000 0 -0.32 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.07 0.12 0.32 85 -0.32 4 89
EGF/EGFR dimer/SHC 0.049 0.071 0.22 54 -0.2 7 61
mol:GDP 0.056 0.066 0.21 53 -0.19 6 59
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.027 0.12 -10000 0 -0.32 68 68
GRB2/SOS1 0.03 0.007 -10000 0 -10000 0 0
HRAS/GTP 0.036 0.046 0.22 1 -0.19 5 6
SHC1 0.018 0.008 -10000 0 -10000 0 0
HRAS/GDP 0.049 0.058 0.28 1 -0.19 5 6
FRAP1 -0.012 0.034 0.16 6 -0.18 6 12
EGF/EGFR dimer 0.053 0.085 0.23 72 -0.24 9 81
SOS1 0.021 0.003 -10000 0 -10000 0 0
GRB2 0.02 0.004 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 -0.006 0.089 -10000 0 -0.22 69 69
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.01 0.28 0.56 21 -0.64 9 30
CRP 0.027 0.29 0.56 34 -0.7 7 41
cell cycle arrest 0 0.3 0.54 29 -0.62 28 57
TIMP1 0.016 0.26 0.52 24 -0.62 12 36
IL6ST 0.005 0.067 -10000 0 -0.31 17 17
Rac1/GDP -0.002 0.14 0.31 17 -0.31 33 50
AP1 0.051 0.13 0.38 7 -0.47 8 15
GAB2 0.02 0.032 -10000 0 -0.32 4 4
TNFSF11 0.034 0.3 0.58 33 -0.66 9 42
HSP90B1 0.02 0.15 -10000 0 -0.73 11 11
GAB1 0.02 0.027 -10000 0 -0.32 3 3
MAPK14 -0.027 0.1 0.26 3 -0.4 13 16
AKT1 0.011 0.088 0.26 3 -0.64 5 8
FOXO1 0.009 0.086 0.32 2 -0.61 5 7
MAP2K6 -0.016 0.11 0.26 13 -0.29 34 47
mol:GTP 0 0.004 -10000 0 -10000 0 0
MAP2K4 0 0.17 0.35 26 -0.37 30 56
MITF -0.01 0.12 0.28 19 -0.29 38 57
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.02 0.005 -10000 0 -10000 0 0
A2M -0.12 0.38 -10000 0 -1.2 54 54
CEBPB 0.024 0.01 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.017 0.089 0.28 4 -0.4 6 10
STAT3 -0.005 0.31 0.57 22 -0.66 28 50
STAT1 0.023 0.036 -10000 0 -10000 0 0
CEBPD 0.016 0.29 0.57 26 -0.73 10 36
PIK3CA 0.021 0.005 -10000 0 -10000 0 0
PI3K 0.029 0.015 -10000 0 -0.23 1 1
JUN 0.018 0.031 -10000 0 -0.32 4 4
PIAS3/MITF -0.005 0.12 0.27 13 -0.29 33 46
MAPK11 -0.026 0.1 0.26 3 -0.4 13 16
STAT3 (dimer)/FOXO1 -0.019 0.26 0.48 25 -0.63 16 41
GRB2/SOS1/GAB family 0.006 0.12 0.27 4 -0.31 17 21
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.018 0.11 0.24 4 -0.28 46 50
GRB2 0.022 0.006 -10000 0 -10000 0 0
JAK2 0.018 0.023 -10000 0 -0.32 2 2
LBP 0.047 0.27 0.53 51 -0.6 10 61
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
JAK1 0.013 0.025 -10000 0 -10000 0 0
MYC 0.029 0.29 0.59 27 -0.72 8 35
FGG -0.15 0.5 0.58 28 -0.89 141 169
macrophage differentiation 0 0.3 0.54 29 -0.62 28 57
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.003 0.096 0.25 1 -0.2 51 52
JUNB 0 0.27 0.52 20 -0.68 11 31
FOS -0.001 0.084 -10000 0 -0.32 31 31
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.004 0.13 0.28 24 -0.3 39 63
STAT1/PIAS1 0.013 0.16 0.32 30 -0.31 30 60
GRB2/SOS1/GAB family/SHP2/PI3K 0.014 0.088 -10000 0 -0.56 7 7
STAT3 (dimer) -0.004 0.31 0.57 22 -0.65 28 50
PRKCD 0.017 0.22 0.42 43 -0.44 27 70
IL6R 0.005 0.049 -10000 0 -0.32 9 9
SOCS3 -0.024 0.13 0.34 1 -0.92 5 6
gp130 (dimer)/JAK1/JAK1/LMO4 0.029 0.07 0.24 2 -0.19 12 14
Rac1/GTP -0.002 0.15 0.31 23 -0.33 33 56
HCK 0.008 0.066 -10000 0 -0.32 19 19
MAPKKK cascade 0.033 0.11 0.33 1 -0.51 8 9
bone resorption 0.036 0.29 0.56 35 -0.63 9 44
IRF1 0.004 0.27 0.54 20 -0.66 10 30
mol:GDP -0.001 0.13 0.26 27 -0.3 35 62
SOS1 0.023 0.006 -10000 0 -10000 0 0
VAV1 -0.006 0.13 0.27 27 -0.3 35 62
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.022 0.11 -10000 0 -0.43 19 19
PTPN11 0.01 0.1 -10000 0 -0.7 9 9
IL6/IL6RA -0.016 0.097 0.17 1 -0.23 74 75
gp130 (dimer)/TYK2/TYK2/LMO4 0.027 0.06 0.18 2 -0.18 18 20
gp130 (dimer)/JAK2/JAK2/LMO4 0.025 0.059 0.2 1 -0.18 17 18
IL6 -0.046 0.14 -10000 0 -0.32 93 93
PIAS3 0.018 0.008 -10000 0 -10000 0 0
PTPRE -0.001 0.043 -10000 0 -0.23 4 4
PIAS1 0.021 0.004 -10000 0 -10000 0 0
RAC1 0.019 0.009 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.019 0.1 0.24 3 -0.25 58 61
LMO4 0.016 0.034 0.14 1 -0.29 1 2
STAT3 (dimer)/PIAS3 -0.026 0.27 0.51 17 -0.61 29 46
MCL1 0.038 0.11 0.38 6 -0.54 5 11
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A -0.006 0.054 -10000 0 -10000 0 0
BIRC5 0.18 0.15 0.32 263 -10000 0 263
NFKBIA 0.001 0.074 0.28 26 -10000 0 26
CPEB1 -0.025 0.12 0.32 2 -0.32 66 68
AKT1 -0.013 0.046 0.28 4 -10000 0 4
NDEL1 0.019 0.006 -10000 0 -10000 0 0
Aurora A/BRCA1 -0.004 0.05 0.24 1 -10000 0 1
NDEL1/TACC3 0.001 0.053 -10000 0 -10000 0 0
GADD45A 0.021 0.003 -10000 0 -10000 0 0
GSK3B -0.015 0.031 -10000 0 -10000 0 0
PAK1/Aurora A -0.006 0.054 -10000 0 -10000 0 0
MDM2 0.02 0.005 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.08 0.093 0.16 262 -10000 0 262
TP53 -0.003 0.053 0.21 1 -0.22 18 19
DLG7 -0.01 0.037 0.15 2 -10000 0 2
AURKAIP1 0.02 0.016 -10000 0 -0.32 1 1
ARHGEF7 0.02 0.005 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.002 0.056 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.004 0.05 0.24 1 -10000 0 1
AURKA -0.005 0.053 0.19 2 -10000 0 2
AURKB 0.095 0.086 0.19 215 -10000 0 215
CDC25B -0.002 0.042 -10000 0 -0.22 4 4
G2/M transition checkpoint -0.012 0.038 -10000 0 -0.13 3 3
mRNA polyadenylation -0.028 0.076 0.35 1 -0.19 50 51
Aurora A/CPEB -0.028 0.077 0.35 1 -0.19 50 51
Aurora A/TACC1/TRAP/chTOG 0.002 0.065 -10000 0 -0.21 6 6
BRCA1 0.021 0.014 0.32 1 -10000 0 1
centrosome duplication -0.006 0.054 -10000 0 -10000 0 0
regulation of centrosome cycle 0.001 0.052 -10000 0 -10000 0 0
spindle assembly 0.001 0.064 -10000 0 -0.21 6 6
TDRD7 0.021 0.004 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.11 0.098 0.24 101 -10000 0 101
CENPA 0.11 0.089 0.19 249 -10000 0 249
Aurora A/PP2A -0.006 0.054 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process -0.005 0.045 0.17 5 -0.18 2 7
negative regulation of DNA binding -0.003 0.053 0.21 1 -0.22 18 19
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.029 0.009 -10000 0 -10000 0 0
RASA1 0.02 0.005 -10000 0 -10000 0 0
Ajuba/Aurora A -0.012 0.038 -10000 0 -0.13 3 3
mitotic prometaphase -0.014 0.03 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.005 0.053 0.19 2 -10000 0 2
TACC1 0.009 0.057 -10000 0 -0.32 14 14
TACC3 0.021 0.014 0.32 1 -10000 0 1
Aurora A/Antizyme1 0.002 0.056 -10000 0 -0.17 1 1
Aurora A/RasGAP -0.005 0.052 -10000 0 -10000 0 0
OAZ1 0.02 0.005 -10000 0 -10000 0 0
RAN 0.021 0.014 0.32 1 -10000 0 1
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.015 0.03 -10000 0 -10000 0 0
GIT1 0.021 0.003 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.038 0.014 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.08 0.093 0.16 262 -10000 0 262
PPP2R5D 0.02 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 0.049 0.08 0.18 85 -10000 0 85
PAK1 0.02 0.004 -10000 0 -10000 0 0
CKAP5 0.021 0.003 -10000 0 -10000 0 0
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.01 0.077 -10000 0 -0.19 58 58
fibroblast growth factor receptor signaling pathway 0.009 0.077 -10000 0 -0.19 58 58
LAMA1 0.025 0.065 0.32 15 -0.32 6 21
PRNP 0.019 0.022 -10000 0 -0.32 2 2
GPC1/SLIT2 -0.03 0.11 -10000 0 -0.23 114 114
SMAD2 -0.021 0.025 0.17 2 -0.18 7 9
GPC1/PrPc/Cu2+ 0.025 0.02 -10000 0 -0.18 4 4
GPC1/Laminin alpha1 0.03 0.049 0.23 14 -0.22 9 23
TDGF1 0.023 0.073 0.32 16 -0.32 10 26
CRIPTO/GPC1 0.03 0.056 0.23 16 -0.23 13 29
APP/GPC1 0.028 0.022 -10000 0 -0.23 3 3
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.018 0.034 -10000 0 -0.19 11 11
FLT1 0.02 0.005 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.036 0.035 0.22 1 -0.19 10 11
SERPINC1 0.022 0.031 0.32 5 -10000 0 5
FYN -0.018 0.037 0.1 15 -0.21 11 26
FGR -0.03 0.056 0.1 14 -0.2 39 53
positive regulation of MAPKKK cascade -0.018 0.096 0.2 8 -0.32 30 38
SLIT2 -0.06 0.14 -10000 0 -0.32 114 114
GPC1/NRG -0.015 0.095 -10000 0 -0.23 77 77
NRG1 -0.035 0.12 -10000 0 -0.32 76 76
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.037 0.023 -10000 0 -0.19 3 3
LYN -0.017 0.034 0.1 16 -0.19 10 26
mol:Spermine -0.01 0.017 -10000 0 -0.22 3 3
cell growth 0.009 0.077 -10000 0 -0.19 58 58
BMP signaling pathway -0.019 0.027 0.32 3 -10000 0 3
SRC -0.019 0.035 0.1 15 -0.19 12 27
TGFBR1 0.021 0.014 0.32 1 -10000 0 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.01 0.12 0.32 15 -0.32 57 72
GPC1 0.019 0.027 -10000 0 -0.32 3 3
TGFBR1 (dimer) 0.021 0.014 0.32 1 -10000 0 1
VEGFA 0.021 0.004 -10000 0 -10000 0 0
BLK 0.009 0.073 0.16 81 -0.19 11 92
HCK -0.025 0.046 -10000 0 -0.19 26 26
FGF2 -0.023 0.11 -10000 0 -0.32 62 62
FGFR1 0.018 0.017 -10000 0 -0.32 1 1
VEGFR1 homodimer 0.02 0.005 -10000 0 -10000 0 0
TGFBR2 0.016 0.041 -10000 0 -0.32 7 7
cell death 0.027 0.022 -10000 0 -0.22 3 3
ATIII/GPC1 0.028 0.03 0.23 5 -0.23 3 8
PLA2G2A/GPC1 0.005 0.093 0.23 15 -0.23 58 73
LCK -0.02 0.038 0.1 17 -0.19 14 31
neuron differentiation -0.015 0.095 -10000 0 -0.23 77 77
PrPc/Cu2+ 0.014 0.015 -10000 0 -0.22 2 2
APP 0.02 0.005 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.016 0.041 -10000 0 -0.32 7 7
TCGA08_p53

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2A 0.039 0.073 0.16 133 -10000 0 133
TP53 0.01 0.037 -10000 0 -0.12 12 12
Senescence 0.01 0.037 -10000 0 -0.12 12 12
Apoptosis 0.01 0.037 -10000 0 -0.12 12 12
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.023 0.072 0.25 19 -0.19 3 22
MDM4 0.019 0.006 -10000 0 -10000 0 0
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.017 0.092 0.17 1 -0.23 65 66
FZD6 0.018 0.017 -10000 0 -0.32 1 1
WNT6 0.038 0.07 0.32 28 -10000 0 28
WNT4 0.008 0.08 0.32 6 -0.32 23 29
FZD3 0.018 0.016 0.32 1 -10000 0 1
WNT5A 0.017 0.035 -10000 0 -0.32 5 5
WNT11 -0.021 0.11 0.32 1 -0.32 60 61
Effects of Botulinum toxin

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
STX1A 0.036 0.076 0.16 125 -10000 0 125
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.016 0.071 0.23 12 -0.23 31 43
STXBP1 0.019 0.027 -10000 0 -0.32 3 3
ACh/CHRNA1 0.028 0.068 0.25 33 -0.19 7 40
RAB3GAP2/RIMS1/UNC13B 0.025 0.062 0.22 10 -0.19 28 38
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.006 0.099 0.32 14 -0.32 31 45
mol:ACh 0.004 0.03 0.079 28 -0.11 9 37
RAB3GAP2 0.019 0.006 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.026 0.066 0.22 2 -0.16 25 27
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.028 0.068 0.24 33 -0.19 7 40
UNC13B 0.02 0.005 -10000 0 -10000 0 0
CHRNA1 0.036 0.088 0.32 33 -0.32 8 41
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.03 0.069 0.25 36 -0.14 8 44
SNAP25 0.004 0.029 0.12 17 -0.22 4 21
VAMP2 0.002 0.001 -10000 0 -10000 0 0
SYT1 0.038 0.089 0.32 36 -0.32 7 43
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.044 0.054 0.13 123 -0.19 3 126
STX1A/SNAP25 fragment 1/VAMP2 0.026 0.066 0.22 2 -0.16 25 27
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.009 0.061 -10000 0 -0.32 16 16
GNB1/GNG2 -0.005 0.1 0.23 1 -0.3 23 24
mol:DAG -0.035 0.082 0.18 3 -0.28 22 25
PLCG1 -0.036 0.084 0.19 3 -0.28 22 25
YES1 -0.028 0.087 0.24 4 -0.22 62 66
FZD3 0.018 0.016 0.32 1 -10000 0 1
FZD6 0.018 0.017 -10000 0 -0.32 1 1
G protein -0.004 0.1 0.24 3 -0.29 22 25
MAP3K7 -0.04 0.086 0.19 5 -0.26 33 38
mol:Ca2+ -0.034 0.08 0.18 3 -0.27 22 25
mol:IP3 -0.035 0.082 0.18 3 -0.28 22 25
NLK -0.002 0.089 -10000 0 -0.8 6 6
GNB1 0.02 0.004 -10000 0 -10000 0 0
CAMK2A -0.043 0.093 0.19 5 -0.27 37 42
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.017 0.092 0.17 1 -0.23 65 66
CSNK1A1 0.02 0.004 -10000 0 -10000 0 0
GNAS -0.029 0.084 0.15 1 -0.22 61 62
GO:0007205 -0.033 0.082 0.18 3 -0.28 23 26
WNT6 0.038 0.07 0.32 28 -10000 0 28
WNT4 0.008 0.08 0.32 6 -0.32 23 29
NFAT1/CK1 alpha -0.013 0.1 0.29 4 -0.3 22 26
GNG2 0.019 0.022 -10000 0 -0.32 2 2
WNT5A 0.017 0.035 -10000 0 -0.32 5 5
WNT11 -0.021 0.11 0.32 1 -0.32 60 61
CDC42 -0.035 0.083 0.22 5 -0.3 22 27
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.007 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.012 0.071 0.21 1 -0.18 59 60
regulation of S phase of mitotic cell cycle -0.015 0.072 0.15 2 -0.2 59 61
GNAO1 0.021 0.032 0.32 3 -0.32 2 5
HRAS 0.019 0.01 -10000 0 -10000 0 0
SHBG/T-DHT 0.013 0.009 0.19 1 -10000 0 1
PELP1 0.018 0.01 -10000 0 -10000 0 0
AKT1 -0.008 0.002 -10000 0 -10000 0 0
MAP2K1 -0.039 0.063 0.16 14 -0.26 11 25
T-DHT/AR -0.015 0.078 0.21 1 -0.22 61 62
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -0.006 32 32
GNAI2 0.021 0.004 -10000 0 -10000 0 0
GNAI3 0.02 0.004 -10000 0 -10000 0 0
GNAI1 0.02 0.016 -10000 0 -0.32 1 1
mol:GDP -0.047 0.1 0.19 2 -0.31 64 66
cell proliferation -0.059 0.12 0.23 1 -0.42 40 41
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
FOS -0.062 0.19 0.25 1 -0.69 36 37
mol:Ca2+ -0.008 0.018 0.05 1 -0.056 46 47
MAPK3 -0.05 0.096 0.24 2 -0.32 36 38
MAPK1 -0.032 0.097 -10000 0 -0.3 42 42
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
mol:IP3 0 0.001 -10000 0 -0.004 31 31
cAMP biosynthetic process 0.001 0.018 0.23 1 -10000 0 1
GNG2 0.019 0.022 -10000 0 -0.32 2 2
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 31 31
HRAS/GTP 0.008 0.068 -10000 0 -0.16 58 58
actin cytoskeleton reorganization 0.026 0.016 -10000 0 -0.16 1 1
SRC 0.019 0.009 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 31 31
PI3K 0.026 0.013 -10000 0 -0.19 1 1
apoptosis 0.044 0.12 0.43 37 -10000 0 37
T-DHT/AR/PELP1 -0.002 0.071 0.2 1 -0.19 61 62
HRAS/GDP -0.049 0.099 0.18 2 -0.3 63 65
CREB1 -0.048 0.13 -10000 0 -0.47 37 37
RAC1-CDC42/GTP 0.033 0.019 -10000 0 -0.16 1 1
AR -0.023 0.11 0.32 1 -0.32 61 62
GNB1 0.02 0.004 -10000 0 -10000 0 0
RAF1 -0.033 0.062 0.16 15 -0.23 10 25
RAC1-CDC42/GDP -0.017 0.1 0.2 1 -0.29 57 58
T-DHT/AR/PELP1/Src 0.008 0.07 0.19 1 -0.17 59 60
MAP2K2 -0.039 0.061 0.15 12 -0.26 11 23
T-DHT/AR/PELP1/Src/PI3K -0.015 0.073 0.15 2 -0.2 59 61
GNAZ -0.007 0.092 -10000 0 -0.32 38 38
SHBG 0.02 0.015 0.32 1 -10000 0 1
Gi family/GNB1/GNG2/GDP -0.022 0.096 -10000 0 -0.43 15 15
mol:T-DHT 0 0 -10000 0 -0.003 6 6
RAC1 0.019 0.007 -10000 0 -10000 0 0
GNRH1 -0.008 0.017 -10000 0 -0.22 3 3
Gi family/GTP -0.024 0.067 0.15 1 -0.2 46 47
CDC42 0.021 0.004 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.013 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.003 0.084 -10000 0 -0.23 6 6
NFATC4 -0.04 0.065 0.22 9 -0.17 3 12
ERBB2IP 0.02 0.008 -10000 0 -10000 0 0
HSP90 (dimer) 0.02 0.004 -10000 0 -10000 0 0
mammary gland morphogenesis -0.047 0.065 0.15 2 -0.19 67 69
JUN -0.006 0.063 0.25 2 -10000 0 2
HRAS 0.02 0.005 -10000 0 -10000 0 0
DOCK7 -0.049 0.064 -10000 0 -0.19 62 62
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.001 0.07 0.19 2 -0.18 58 60
AKT1 -0.008 0.006 -10000 0 -10000 0 0
BAD -0.013 0.005 -10000 0 -10000 0 0
MAPK10 -0.032 0.066 0.17 11 -0.18 22 33
mol:GTP 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.049 0.07 0.16 2 -0.2 67 69
RAF1 -0.012 0.093 0.25 12 -0.25 6 18
ErbB2/ErbB3/neuregulin 2 -0.011 0.064 0.19 2 -0.18 49 51
STAT3 0.002 0.14 -10000 0 -0.87 11 11
cell migration -0.024 0.073 0.2 16 -0.2 14 30
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.03 0.18 0.41 2 -0.56 29 31
FOS -0.027 0.15 0.32 5 -0.41 49 54
NRAS 0.02 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.047 0.065 0.15 2 -0.19 67 69
MAPK3 -0.018 0.15 0.39 3 -0.5 18 21
MAPK1 -0.027 0.16 0.37 4 -0.55 24 28
JAK2 -0.048 0.066 -10000 0 -0.19 62 62
NF2 -0.026 0.13 -10000 0 -0.62 22 22
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.017 0.07 0.2 3 -0.2 56 59
NRG1 -0.036 0.12 -10000 0 -0.32 76 76
GRB2/SOS1 0.03 0.007 -10000 0 -10000 0 0
MAPK8 -0.047 0.087 0.19 1 -0.23 56 57
MAPK9 -0.022 0.057 0.17 13 -10000 0 13
ERBB2 -0.019 0.02 0.26 2 -10000 0 2
ERBB3 0.014 0.026 -10000 0 -0.32 2 2
SHC1 0.018 0.008 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
apoptosis 0.011 0.008 -10000 0 -10000 0 0
STAT3 (dimer) 0.003 0.13 -10000 0 -0.85 11 11
RNF41 -0.018 0.009 -10000 0 -10000 0 0
FRAP1 -0.007 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.042 0.044 -10000 0 -0.15 56 56
ErbB2/ErbB2/HSP90 (dimer) -0.02 0.017 0.2 2 -10000 0 2
CHRNA1 -0.007 0.14 0.37 4 -0.48 18 22
myelination -0.031 0.082 0.25 18 -10000 0 18
PPP3CB -0.048 0.06 -10000 0 -0.18 62 62
KRAS 0.019 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.001 0.078 0.22 1 -0.19 49 50
NRG2 -0.016 0.11 -10000 0 -0.32 52 52
mol:GDP -0.017 0.07 0.2 3 -0.2 56 59
SOS1 0.021 0.003 -10000 0 -10000 0 0
MAP2K2 -0.014 0.094 0.26 13 -0.28 6 19
SRC 0.02 0.004 -10000 0 -10000 0 0
mol:cAMP -0.001 0.002 -10000 0 -10000 0 0
PTPN11 -0.049 0.065 -10000 0 -0.19 61 61
MAP2K1 -0.035 0.17 0.39 1 -0.58 21 22
heart morphogenesis -0.047 0.065 0.15 2 -0.19 67 69
RAS family/GDP 0.004 0.085 0.23 1 -0.22 6 7
GRB2 0.021 0.004 -10000 0 -10000 0 0
PRKACA -0.025 0.14 -10000 0 -0.65 24 24
CHRNE 0.002 0.021 0.17 4 -10000 0 4
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
activation of caspase activity 0.008 0.006 -10000 0 -10000 0 0
nervous system development -0.047 0.065 0.15 2 -0.19 67 69
CDC42 0.021 0.004 -10000 0 -10000 0 0
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.049 0.1 -10000 0 -0.28 35 35
epithelial cell differentiation -0.028 0.09 -10000 0 -0.29 10 10
ITCH 0.031 0.018 -10000 0 -10000 0 0
WWP1 -0.018 0.07 -10000 0 -10000 0 0
FYN 0.019 0.017 -10000 0 -0.32 1 1
EGFR 0.015 0.041 0.32 1 -0.32 6 7
PRL 0.025 0.045 0.32 11 -10000 0 11
neuron projection morphogenesis -0.028 0.095 0.29 10 -10000 0 10
PTPRZ1 0.033 0.15 0.32 66 -0.32 39 105
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.019 0.081 -10000 0 -0.23 23 23
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.041 0.081 -10000 0 -0.25 31 31
ADAM17 0.033 0.019 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.033 0.066 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.087 0.12 -10000 0 -0.28 82 82
NCOR1 0.02 0.006 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.037 0.083 -10000 0 -0.24 31 31
GRIN2B -0.047 0.077 0.26 3 -0.24 27 30
ErbB4/ErbB2/betacellulin -0.012 0.065 -10000 0 -0.25 6 6
STAT1 0.021 0.002 -10000 0 -10000 0 0
HBEGF -0.034 0.12 -10000 0 -0.32 78 78
PRLR 0.022 0.091 0.32 25 -0.32 15 40
E4ICDs/ETO2 -0.029 0.085 -10000 0 -0.27 16 16
axon guidance -0.027 0.068 -10000 0 -0.33 6 6
NEDD4 0.03 0.023 -10000 0 -0.3 1 1
Prolactin receptor/Prolactin receptor/Prolactin 0.029 0.071 0.24 31 -0.22 15 46
CBFA2T3 0.002 0.077 -10000 0 -0.32 26 26
ErbB4/ErbB2/HBEGF -0.034 0.085 -10000 0 -0.24 24 24
MAPK3 -0.035 0.079 0.22 1 -10000 0 1
STAT1 (dimer) -0.024 0.077 -10000 0 -0.27 3 3
MAPK1 -0.034 0.079 0.23 2 -10000 0 2
JAK2 0.018 0.023 -10000 0 -0.32 2 2
ErbB4/ErbB2/neuregulin 1 beta -0.051 0.074 -10000 0 -0.24 29 29
NRG1 -0.038 0.081 -10000 0 -0.22 76 76
NRG3 -0.11 0.17 0.32 1 -0.32 187 188
NRG2 -0.016 0.11 -10000 0 -0.32 52 52
NRG4 0.035 0.088 0.32 33 -0.32 8 41
heart development -0.027 0.068 -10000 0 -0.33 6 6
neural crest cell migration -0.05 0.073 -10000 0 -0.24 29 29
ERBB2 0.001 0.031 0.29 3 -10000 0 3
WWOX/E4ICDs -0.021 0.074 -10000 0 -0.29 2 2
SHC1 0.018 0.008 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.004 0.09 0.29 1 -0.27 9 10
apoptosis 0.15 0.2 0.38 175 -10000 0 175
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.041 0.097 -10000 0 -0.28 29 29
ErbB4/ErbB2/epiregulin -0.003 0.11 0.31 4 -0.25 21 25
ErbB4/ErbB4/betacellulin/betacellulin -0.025 0.083 -10000 0 -0.29 10 10
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.016 0.11 0.3 2 -0.26 26 28
MDM2 -0.024 0.073 0.24 16 -10000 0 16
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.031 0.075 -10000 0 -0.22 33 33
STAT5A -0.029 0.072 -10000 0 -0.33 7 7
ErbB4/EGFR/neuregulin 1 beta -0.033 0.08 -10000 0 -0.25 25 25
DLG4 0.02 0.006 -10000 0 -10000 0 0
GRB2/SHC 0.026 0.012 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.022 0.069 -10000 0 -0.25 3 3
STAT5A (dimer) -0.025 0.099 0.28 1 -0.32 9 10
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.021 0.081 -10000 0 -0.33 8 8
LRIG1 0.019 0.022 -10000 0 -0.32 2 2
EREG 0.011 0.18 0.32 74 -0.32 78 152
BTC 0.014 0.051 0.32 1 -0.32 10 11
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.027 0.066 -10000 0 -0.33 5 5
ERBB4 -0.033 0.066 -10000 0 -10000 0 0
STAT5B 0.021 0.003 -10000 0 -10000 0 0
YAP1 -0.005 0.06 -10000 0 -0.44 8 8
GRB2 0.02 0.004 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.001 0.078 -10000 0 -0.24 7 7
glial cell differentiation 0.022 0.068 0.24 3 -10000 0 3
WWOX 0.02 0.006 -10000 0 -10000 0 0
cell proliferation -0.059 0.1 0.32 3 -0.36 17 20
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.036 0.059 0.24 6 -0.23 29 35
KIRREL 0.017 0.04 -10000 0 -0.33 6 6
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.037 0.059 0.23 29 -0.24 6 35
PLCG1 0.02 0.005 -10000 0 -10000 0 0
ARRB2 0.02 0.006 -10000 0 -10000 0 0
WASL 0.02 0.005 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.051 0.056 0.22 29 -0.18 6 35
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.015 0.039 0.16 2 -0.21 6 8
FYN 0.017 0.082 0.2 66 -0.17 6 72
mol:Ca2+ 0.048 0.054 0.21 28 -0.17 6 34
mol:DAG 0.049 0.054 0.21 28 -0.17 6 34
NPHS2 -0.004 0.023 -10000 0 -10000 0 0
mol:IP3 0.049 0.054 0.21 28 -0.17 6 34
regulation of endocytosis 0.037 0.048 0.2 25 -0.17 6 31
Nephrin/NEPH1/podocin/Cholesterol 0.041 0.052 0.2 29 -0.17 6 35
establishment of cell polarity 0.036 0.059 0.23 29 -0.24 6 35
Nephrin/NEPH1/podocin/NCK1-2 0.061 0.056 0.22 29 -0.16 6 35
Nephrin/NEPH1/beta Arrestin2 0.039 0.05 0.2 25 -0.17 6 31
NPHS1 0.041 0.083 0.33 35 -10000 0 35
Nephrin/NEPH1/podocin 0.039 0.05 0.2 29 -0.17 6 35
TJP1 0.02 0.005 -10000 0 -10000 0 0
NCK1 0.021 0.003 -10000 0 -10000 0 0
NCK2 0.021 0.002 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.051 0.055 0.22 28 -0.18 6 34
CD2AP 0.02 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.051 0.055 0.22 28 -0.18 6 34
GRB2 0.02 0.004 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.008 0.094 0.22 61 -0.18 27 88
cytoskeleton organization -0.003 0.051 0.21 11 -0.22 6 17
Nephrin/NEPH1 0.031 0.046 0.19 29 -0.16 6 35
Nephrin/NEPH1/ZO-1 0.041 0.051 0.21 25 -0.19 6 31
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.028 0.008 -10000 0 -10000 0 0
PRKCZ 0.018 0.027 -10000 0 -0.32 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.02 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.002 0.061 -10000 0 -0.27 15 15
IRAK/TOLLIP -0.02 0.016 0.19 2 -10000 0 2
IKBKB 0.018 0.007 -10000 0 -10000 0 0
IKBKG 0.02 0.004 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.04 0.13 0.23 18 -0.23 148 166
IL1A -0.082 0.16 0.32 2 -0.32 148 150
IL1B -0.03 0.052 -10000 0 -0.23 32 32
IRAK/TRAF6/p62/Atypical PKCs 0.043 0.037 -10000 0 -0.17 3 3
IL1R2 0.029 0.061 0.32 17 -0.32 3 20
IL1R1 0.019 0.027 -10000 0 -0.32 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.007 0.052 -10000 0 -0.26 9 9
TOLLIP 0.021 0.004 -10000 0 -10000 0 0
TICAM2 0.018 0.031 -10000 0 -0.32 4 4
MAP3K3 0.02 0.016 -10000 0 -0.32 1 1
TAK1/TAB1/TAB2 0.013 0.004 -10000 0 -10000 0 0
IKK complex/ELKS 0.003 0.065 0.27 2 -0.36 2 4
JUN -0.018 0.047 0.16 23 -10000 0 23
MAP3K7 0.019 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.032 0.058 -10000 0 -0.18 26 26
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.018 0.11 0.22 1 -0.18 147 148
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.011 0.11 0.22 1 -0.17 146 147
IL1 beta fragment/IL1R1/IL1RAP 0.015 0.055 -10000 0 -0.18 32 32
NFKB1 0.021 0.003 -10000 0 -10000 0 0
MAPK8 -0.012 0.05 0.18 25 -10000 0 25
IRAK1 -0.017 0.016 0.21 2 -10000 0 2
IL1RN/IL1R1 0.026 0.037 -10000 0 -0.23 10 10
IRAK4 0.021 0.003 -10000 0 -10000 0 0
PRKCI 0.02 0.005 -10000 0 -10000 0 0
TRAF6 0.021 0.003 -10000 0 -10000 0 0
PI3K 0.029 0.014 -10000 0 -0.23 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.005 0.062 -10000 0 -0.3 12 12
CHUK 0.021 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.015 0.055 -10000 0 -0.18 32 32
IL1 beta/IL1R2 0.015 0.067 0.21 15 -0.2 32 47
IRAK/TRAF6/TAK1/TAB1/TAB2 0.022 0.014 0.16 2 -10000 0 2
NF kappa B1 p50/RelA 0.023 0.054 -10000 0 -0.18 24 24
IRAK3 0.012 0.053 -10000 0 -0.32 12 12
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.03 0.06 -10000 0 -0.18 27 27
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.048 0.1 -10000 0 -0.2 141 141
IL1 alpha/IL1R1/IL1RAP -0.029 0.11 0.22 2 -0.19 147 149
RELA 0.021 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.02 0.005 -10000 0 -10000 0 0
MYD88 0.021 0.004 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.033 0.029 0.19 2 -10000 0 2
IL1RAP 0.02 0.005 -10000 0 -10000 0 0
UBE2N 0.021 0.003 -10000 0 -10000 0 0
IRAK/TRAF6 -0.045 0.033 -10000 0 -10000 0 0
CASP1 0.017 0.035 -10000 0 -0.32 5 5
IL1RN/IL1R2 0.033 0.054 0.23 17 -0.25 9 26
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.025 0.056 -10000 0 -0.18 30 30
TMEM189-UBE2V1 0.018 0.005 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.042 0.098 -10000 0 -0.33 23 23
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
IL1RN 0.016 0.041 -10000 0 -0.32 7 7
TRAF6/TAK1/TAB1/TAB2 0.034 0.015 -10000 0 -10000 0 0
MAP2K6 -0.005 0.06 0.18 41 -10000 0 41
FoxO family signaling

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
G6PC 0.013 0.062 -10000 0 -10000 0 0
PLK1 0.2 0.26 0.55 128 -10000 0 128
CDKN1B 0.13 0.17 0.36 121 -0.34 7 128
FOXO3 0.18 0.23 0.51 127 -10000 0 127
KAT2B 0.053 0.043 0.17 11 -10000 0 11
FOXO1/SIRT1 0.009 0.042 -10000 0 -0.25 2 2
CAT 0.14 0.24 0.55 55 -0.76 8 63
CTNNB1 0.02 0.004 -10000 0 -10000 0 0
AKT1 0.053 0.042 0.18 2 -10000 0 2
FOXO1 0.016 0.056 0.23 11 -0.26 2 13
MAPK10 0.016 0.061 0.2 36 -0.16 9 45
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.033 0.073 0.31 5 -10000 0 5
response to oxidative stress 0.035 0.041 0.13 42 -10000 0 42
FOXO3A/SIRT1 0.15 0.2 0.43 118 -0.44 2 120
XPO1 0.021 0.002 -10000 0 -10000 0 0
EP300 0.022 0.007 -10000 0 -10000 0 0
BCL2L11 0.061 0.06 -10000 0 -10000 0 0
FOXO1/SKP2 0.022 0.041 -10000 0 -10000 0 0
mol:GDP 0.035 0.041 0.13 42 -10000 0 42
RAN 0.022 0.014 0.32 1 -10000 0 1
GADD45A 0.11 0.17 0.42 31 -0.63 8 39
YWHAQ 0.021 0.002 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.001 0.12 -10000 0 -0.45 23 23
MST1 0.061 0.066 0.28 23 -10000 0 23
CSNK1D 0.021 0.004 -10000 0 -10000 0 0
CSNK1E 0.02 0.005 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.005 0.088 -10000 0 -0.37 14 14
YWHAB 0.02 0.005 -10000 0 -10000 0 0
MAPK8 0.026 0.061 0.2 45 -10000 0 45
MAPK9 0.026 0.062 0.2 44 -10000 0 44
YWHAG 0.021 0.004 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
YWHAZ 0.019 0.007 -10000 0 -10000 0 0
SIRT1 0.003 0.023 -10000 0 -10000 0 0
SOD2 0.12 0.18 0.42 56 -0.44 3 59
RBL2 0.13 0.21 0.5 37 -0.65 8 45
RAL/GDP 0.046 0.03 0.16 1 -10000 0 1
CHUK 0.053 0.042 0.17 11 -10000 0 11
Ran/GTP 0.016 0.009 0.22 1 -10000 0 1
CSNK1G2 0.02 0.006 -10000 0 -10000 0 0
RAL/GTP 0.045 0.029 0.19 1 -10000 0 1
CSNK1G1 0.021 0.004 -10000 0 -10000 0 0
FASLG 0.046 0.15 0.43 1 -1.1 6 7
SKP2 0.018 0.016 0.32 1 -10000 0 1
USP7 0.021 0.004 -10000 0 -10000 0 0
IKBKB 0.045 0.041 0.15 23 -10000 0 23
CCNB1 0.18 0.25 0.57 108 -10000 0 108
FOXO1-3a-4/beta catenin 0.12 0.15 0.38 66 -10000 0 66
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.041 -10000 0 -10000 0 0
CSNK1A1 0.02 0.004 -10000 0 -10000 0 0
SGK1 0.051 0.044 0.17 12 -10000 0 12
CSNK1G3 0.02 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.029 0.01 0.21 1 -10000 0 1
ZFAND5 0.028 0.067 0.44 1 -10000 0 1
SFN 0.025 0.041 0.32 8 -0.32 1 9
CDK2 0.013 0.019 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.046 0.11 0.26 17 -0.38 10 27
CREBBP 0.012 0.02 -10000 0 -10000 0 0
FBXO32 0.19 0.26 0.63 78 -0.54 1 79
BCL6 0.13 0.22 0.5 38 -0.75 10 48
RALB 0.021 0.003 -10000 0 -10000 0 0
RALA 0.02 0.006 -10000 0 -10000 0 0
YWHAH 0.02 0.004 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.014 0.032 -10000 0 -0.32 3 3
PDGF/PDGFRA/CRKL 0.024 0.027 -10000 0 -0.2 4 4
positive regulation of JUN kinase activity 0.037 0.029 -10000 0 -0.17 1 1
CRKL 0.02 0.005 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.032 0.11 -10000 0 -0.23 107 107
AP1 -0.063 0.18 0.27 1 -0.73 32 33
mol:IP3 -0.02 0.024 -10000 0 -0.22 3 3
PLCG1 -0.02 0.024 -10000 0 -0.22 3 3
PDGF/PDGFRA/alphaV Integrin 0.025 0.028 -10000 0 -0.21 4 4
RAPGEF1 0.021 0.004 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.02 0.024 -10000 0 -0.22 3 3
CAV3 -0.054 0.14 -10000 0 -0.32 104 104
CAV1 -0.19 0.16 -10000 0 -0.32 296 296
SHC/Grb2/SOS1 0.039 0.03 -10000 0 -0.17 1 1
PDGF/PDGFRA/Shf 0.025 0.03 0.23 2 -0.2 4 6
FOS -0.063 0.18 0.31 2 -0.73 31 33
JUN -0.025 0.026 -10000 0 -0.22 4 4
oligodendrocyte development 0.024 0.028 -10000 0 -0.21 4 4
GRB2 0.02 0.004 -10000 0 -10000 0 0
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
mol:DAG -0.02 0.024 -10000 0 -0.22 3 3
PDGF/PDGFRA 0.014 0.032 -10000 0 -0.32 3 3
actin cytoskeleton reorganization 0.023 0.027 -10000 0 -0.2 4 4
SRF -0.013 0.012 -10000 0 -10000 0 0
SHC1 0.018 0.008 -10000 0 -10000 0 0
PI3K 0.032 0.03 -10000 0 -0.17 5 5
PDGF/PDGFRA/Crk/C3G 0.032 0.029 -10000 0 -0.17 4 4
JAK1 -0.017 0.018 -10000 0 -0.21 3 3
ELK1/SRF -0.021 0.036 0.15 16 -0.19 2 18
SHB 0.02 0.006 -10000 0 -10000 0 0
SHF 0.021 0.02 0.32 2 -10000 0 2
CSNK2A1 0.022 0.016 -10000 0 -10000 0 0
GO:0007205 -0.015 0.025 -10000 0 -0.25 3 3
SOS1 0.021 0.003 -10000 0 -10000 0 0
Ras protein signal transduction 0.037 0.029 -10000 0 -0.17 1 1
PDGF/PDGFRA/SHB 0.023 0.027 -10000 0 -0.2 4 4
PDGF/PDGFRA/Caveolin-1 -0.13 0.13 -10000 0 -0.23 289 289
ITGAV 0.021 0.002 -10000 0 -10000 0 0
ELK1 -0.02 0.027 -10000 0 -0.22 2 2
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk 0.022 0.028 -10000 0 -0.2 4 4
JAK-STAT cascade -0.017 0.018 -10000 0 -0.2 3 3
cell proliferation 0.025 0.03 0.23 2 -0.2 4 6
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.037 0.022 -10000 0 -0.17 2 2
NF kappa B1 p50/RelA/I kappa B alpha -0.009 0.1 0.22 3 -0.27 44 47
AP1 0.005 0.072 -10000 0 -0.16 70 70
mol:PIP3 -0.035 0.043 -10000 0 -0.17 36 36
AKT1 -0.01 0.067 0.24 6 -0.31 5 11
PTK2B -0.039 0.11 0.24 2 -0.34 33 35
RHOA -0.005 0.072 0.18 8 -0.35 14 22
PIK3CB 0.02 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.026 0.082 0.2 11 -0.22 42 53
MAGI3 0.017 0.035 -10000 0 -0.32 5 5
RELA 0.021 0.004 -10000 0 -10000 0 0
apoptosis -0.009 0.058 0.17 1 -0.19 43 44
HRAS/GDP 0.015 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.045 0.1 0.2 10 -0.33 29 39
NF kappa B1 p50/RelA -0.042 0.083 -10000 0 -0.24 47 47
endothelial cell migration -0.009 0.015 0.3 1 -10000 0 1
ADCY4 -0.015 0.051 -10000 0 -0.25 8 8
ADCY5 -0.024 0.068 0.2 1 -0.25 20 21
ADCY6 -0.011 0.043 -10000 0 -0.24 5 5
ADCY7 -0.011 0.04 -10000 0 -0.2 5 5
ADCY1 -0.01 0.045 -10000 0 -0.22 8 8
ADCY2 -0.015 0.054 -10000 0 -0.25 10 10
ADCY3 -0.01 0.04 -10000 0 -0.2 5 5
ADCY8 -0.058 0.081 -10000 0 -0.24 23 23
ADCY9 -0.014 0.049 -10000 0 -0.24 9 9
GSK3B -0.04 0.11 0.22 6 -0.35 28 34
arachidonic acid secretion -0.014 0.047 -10000 0 -0.28 6 6
GNG2 0.018 0.023 -10000 0 -0.32 2 2
TRIP6 0.01 0.026 -10000 0 -0.3 3 3
GNAO1 -0.009 0.02 0.16 4 -0.19 2 6
HRAS 0.021 0.004 -10000 0 -10000 0 0
NFKBIA -0.026 0.11 0.24 6 -0.28 49 55
GAB1 0.019 0.027 -10000 0 -0.32 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.013 0.2 -10000 0 -0.84 25 25
JUN 0.018 0.031 -10000 0 -0.32 4 4
LPA/LPA2/NHERF2 0.025 0.025 -10000 0 -0.18 6 6
TIAM1 -0.027 0.23 -10000 0 -0.99 25 25
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
mol:IP3 -0.021 0.072 0.2 12 -0.21 35 47
PLCB3 -0.013 0.034 0.18 11 -0.17 6 17
FOS -0.001 0.083 -10000 0 -0.32 31 31
positive regulation of mitosis -0.014 0.047 -10000 0 -0.28 6 6
LPA/LPA1-2-3 0.023 0.063 0.21 4 -0.17 43 47
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.02 0.016 -10000 0 -0.32 1 1
stress fiber formation -0.021 0.09 0.24 3 -0.34 17 20
GNAZ -0.023 0.048 0.12 1 -0.18 38 39
EGFR/PI3K-beta/Gab1 -0.034 0.047 -10000 0 -0.17 33 33
positive regulation of dendritic cell cytokine production 0.022 0.062 0.21 4 -0.17 43 47
LPA/LPA2/MAGI-3 0.025 0.023 -10000 0 -0.18 5 5
ARHGEF1 0.007 0.072 0.19 57 -10000 0 57
GNAI2 -0.01 0.008 0.12 1 -10000 0 1
GNAI3 -0.009 0.008 0.12 1 -10000 0 1
GNAI1 -0.01 0.011 0.12 1 -0.18 1 2
LPA/LPA3 -0.003 0.069 0.22 4 -0.22 43 47
LPA/LPA2 0.016 0.005 -10000 0 -10000 0 0
LPA/LPA1 0.017 0.009 0.18 1 -10000 0 1
HB-EGF/EGFR -0.016 0.087 0.13 74 -0.2 57 131
HBEGF -0.014 0.1 0.15 84 -0.22 69 153
mol:DAG -0.021 0.072 0.2 12 -0.21 35 47
cAMP biosynthetic process -0.019 0.061 0.24 4 -0.26 5 9
NFKB1 0.021 0.003 -10000 0 -10000 0 0
SRC 0.02 0.004 -10000 0 -10000 0 0
GNB1 0.02 0.006 -10000 0 -10000 0 0
LYN -0.03 0.1 0.3 4 -0.28 47 51
GNAQ -0.009 0.06 0.17 2 -0.2 41 43
LPAR2 0.02 0.005 -10000 0 -10000 0 0
LPAR3 -0.007 0.1 0.32 4 -0.32 43 47
LPAR1 0.021 0.006 -10000 0 -10000 0 0
IL8 -0.023 0.12 0.29 14 -0.36 26 40
PTK2 -0.023 0.052 0.19 9 -0.16 7 16
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
CASP3 -0.009 0.059 0.17 1 -0.19 43 44
EGFR 0.015 0.041 0.32 1 -0.32 6 7
PLCG1 -0.015 0.07 0.15 6 -0.23 40 46
PLD2 -0.023 0.054 0.19 12 -0.17 2 14
G12/G13 0.037 0.018 -10000 0 -10000 0 0
PI3K-beta -0.024 0.047 -10000 0 -0.28 9 9
cell migration -0.009 0.065 0.19 1 -0.25 24 25
SLC9A3R2 0.017 0.038 -10000 0 -0.32 6 6
PXN -0.022 0.092 0.24 3 -0.35 17 20
HRAS/GTP -0.014 0.046 -10000 0 -0.3 5 5
RAC1 0.019 0.007 -10000 0 -10000 0 0
MMP9 0.079 0.12 0.32 96 -10000 0 96
PRKCE 0.018 0.031 -10000 0 -0.32 4 4
PRKCD -0.034 0.083 0.2 10 -0.32 16 26
Gi(beta/gamma) -0.005 0.043 -10000 0 -0.23 3 3
mol:LPA 0.001 0.004 -10000 0 -10000 0 0
TRIP6/p130 Cas/FAK1/Paxillin -0.008 0.083 0.3 1 -0.34 11 12
MAPKKK cascade -0.014 0.047 -10000 0 -0.28 6 6
contractile ring contraction involved in cytokinesis -0.004 0.073 0.18 7 -0.34 15 22
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.013 0.067 0.17 2 -0.2 49 51
GNA15 -0.008 0.057 0.17 2 -0.19 39 41
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA13 0.021 0.004 -10000 0 -10000 0 0
MAPT -0.046 0.11 0.2 10 -0.34 29 39
GNA11 -0.009 0.056 0.17 1 -0.19 39 40
Rac1/GTP -0.014 0.21 -10000 0 -0.9 25 25
MMP2 -0.009 0.015 0.3 1 -10000 0 1
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.018 0.096 -10000 0 -0.58 8 8
Syndecan-4/Syndesmos 0.033 0.16 0.32 1 -0.72 14 15
positive regulation of JNK cascade 0.032 0.15 0.31 1 -0.69 13 14
Syndecan-4/ADAM12 0.092 0.19 0.33 84 -0.72 14 98
CCL5 0.017 0.035 -10000 0 -0.32 5 5
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
DNM2 0.02 0.005 -10000 0 -10000 0 0
ITGA5 0.021 0.021 0.32 1 -0.32 1 2
SDCBP 0.019 0.006 -10000 0 -10000 0 0
PLG 0.011 0.046 0.31 9 -10000 0 9
ADAM12 0.12 0.14 0.32 164 -10000 0 164
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.021 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.034 0.018 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.037 0.16 0.32 7 -0.7 14 21
Syndecan-4/CXCL12/CXCR4 0.034 0.16 0.32 1 -0.74 13 14
Syndecan-4/Laminin alpha3 0.017 0.16 0.32 1 -0.69 16 17
MDK 0.11 0.14 0.32 145 -10000 0 145
Syndecan-4/FZD7 0.035 0.16 0.3 4 -0.75 13 17
Syndecan-4/Midkine 0.086 0.18 0.34 50 -0.74 13 63
FZD7 0.02 0.016 -10000 0 -0.32 1 1
Syndecan-4/FGFR1/FGF 0.02 0.16 0.3 1 -0.62 18 19
THBS1 0.019 0.022 -10000 0 -0.32 2 2
integrin-mediated signaling pathway 0.042 0.16 0.31 12 -0.67 15 27
positive regulation of MAPKKK cascade 0.032 0.15 0.31 1 -0.69 13 14
Syndecan-4/TACI 0.043 0.17 0.32 22 -0.74 13 35
CXCR4 0.021 0.002 -10000 0 -10000 0 0
cell adhesion 0.007 0.038 0.19 9 -0.27 4 13
Syndecan-4/Dynamin 0.034 0.15 0.3 3 -0.74 13 16
Syndecan-4/TSP1 0.032 0.16 0.3 4 -0.72 14 18
Syndecan-4/GIPC 0.035 0.16 0.3 4 -0.74 13 17
Syndecan-4/RANTES 0.034 0.16 0.3 4 -0.73 14 18
ITGB1 0.021 0.004 -10000 0 -10000 0 0
LAMA1 0.025 0.065 0.32 15 -0.32 6 21
LAMA3 -0.043 0.13 0.32 1 -0.32 89 90
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCA 0.004 0.15 0.78 16 -0.31 2 18
Syndecan-4/alpha-Actinin 0.033 0.16 0.3 3 -0.72 14 17
TFPI 0.006 0.07 -10000 0 -0.32 21 21
F2 0.062 0.11 0.32 69 -10000 0 69
alpha5/beta1 Integrin 0.03 0.016 0.23 1 -0.23 1 2
positive regulation of cell adhesion 0 0.16 0.29 2 -0.64 17 19
ACTN1 0.021 0.004 -10000 0 -10000 0 0
TNC 0.032 0.081 0.32 27 -0.32 7 34
Syndecan-4/CXCL12 0.03 0.16 0.3 4 -0.74 14 18
FGF6 0.017 0.004 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
CXCL12 0 0.082 -10000 0 -0.32 30 30
TNFRSF13B 0.037 0.085 0.32 34 -0.32 5 39
FGF2 -0.023 0.11 -10000 0 -0.32 62 62
FGFR1 0.018 0.017 -10000 0 -0.32 1 1
Syndecan-4/PI-4-5-P2 0.019 0.15 0.28 5 -0.72 14 19
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.014 0.038 0.32 1 -0.32 4 5
cell migration -0.021 0.013 -10000 0 -10000 0 0
PRKCD 0.016 0.018 -10000 0 -10000 0 0
vasculogenesis 0.033 0.15 0.3 4 -0.68 14 18
SDC4 0.029 0.15 0.31 5 -0.85 10 15
Syndecan-4/Tenascin C 0.042 0.16 0.31 12 -0.7 15 27
Syndecan-4/PI-4-5-P2/PKC alpha -0.028 0.015 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.031 0.15 0.32 1 -0.71 14 15
MMP9 0.08 0.12 0.32 96 -10000 0 96
Rac1/GTP 0.007 0.038 0.19 9 -0.27 4 13
cytoskeleton organization 0.034 0.15 0.3 4 -0.68 14 18
GIPC1 0.02 0.005 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.03 0.16 0.32 1 -0.71 15 16
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.07 0.15 -10000 0 -0.32 128 128
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.021 0.003 -10000 0 -10000 0 0
TCEB1 0.02 0.015 0.32 1 -10000 0 1
HIF1A/p53 0.028 0.052 0.24 2 -0.24 8 10
HIF1A 0.001 0.036 -10000 0 -0.25 8 8
COPS5 0.019 0.006 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.051 0.027 -10000 0 -10000 0 0
FIH (dimer) 0.021 0.003 -10000 0 -10000 0 0
CDKN2A 0.096 0.14 0.32 130 -10000 0 130
ARNT/IPAS -0.033 0.1 -10000 0 -0.23 110 110
HIF1AN 0.021 0.003 -10000 0 -10000 0 0
GNB2L1 0.02 0.004 -10000 0 -10000 0 0
HIF1A/ARNT 0.021 0.043 0.24 1 -0.23 5 6
CUL2 0.021 0.004 -10000 0 -10000 0 0
OS9 0.02 0.005 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.037 0.018 0.22 1 -10000 0 1
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.028 0.05 -10000 0 -0.25 8 8
PHD1-3/OS9 0.073 0.077 0.22 93 -10000 0 93
HIF1A/RACK1/Elongin B/Elongin C 0.04 0.051 0.24 3 -0.24 6 9
VHL 0.02 0.004 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
HIF1A/JAB1 0.025 0.052 0.24 2 -0.25 8 10
EGLN3 0.084 0.13 0.32 107 -0.32 1 108
EGLN2 0.02 0.004 -10000 0 -10000 0 0
EGLN1 0.02 0.006 -10000 0 -10000 0 0
TP53 0.02 0.006 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.009 0.1 -10000 0 -0.5 19 19
ARNT 0.018 0.008 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.02 0.004 -10000 0 -10000 0 0
HIF1A/p19ARF 0.068 0.097 0.24 54 -0.22 6 60
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 -0.016 0.005 -10000 0 -10000 0 0
SMARCC1 0.002 0.013 -10000 0 -10000 0 0
REL 0.02 0.007 -10000 0 -10000 0 0
HDAC7 -0.034 0.076 0.29 6 -0.27 18 24
JUN 0.018 0.031 -10000 0 -0.32 4 4
EP300 0.02 0.004 -10000 0 -10000 0 0
KAT2B 0.021 0.004 -10000 0 -10000 0 0
KAT5 0.021 0.004 -10000 0 -10000 0 0
MAPK14 -0.011 0.036 0.15 17 -0.24 2 19
FOXO1 0.02 0.005 -10000 0 -10000 0 0
T-DHT/AR -0.03 0.079 0.26 4 -0.28 17 21
MAP2K6 0.026 0.062 0.32 17 -0.33 2 19
BRM/BAF57 0.027 0.023 -10000 0 -0.23 3 3
MAP2K4 0.016 0.015 -10000 0 -10000 0 0
SMARCA2 0.017 0.027 -10000 0 -0.32 3 3
PDE9A -0.029 0.15 -10000 0 -0.86 13 13
NCOA2 0.017 0.032 -10000 0 -0.32 4 4
CEBPA 0.004 0.071 -10000 0 -0.32 22 22
EHMT2 0.021 0.004 -10000 0 -10000 0 0
cell proliferation -0.025 0.13 0.32 19 -0.36 26 45
NR0B1 0.076 0.12 0.32 94 -10000 0 94
EGR1 0.002 0.078 -10000 0 -0.32 27 27
RXRs/9cRA -0.065 0.1 -10000 0 -0.17 229 229
AR/RACK1/Src -0.012 0.078 0.26 16 -0.29 2 18
AR/GR -0.012 0.084 0.2 5 -0.22 50 55
GNB2L1 0.021 0.004 -10000 0 -10000 0 0
PKN1 0.02 0.005 -10000 0 -10000 0 0
RCHY1 0.021 0.003 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -10000 0 -10000 0 0
MAPK8 -0.014 0.014 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.016 0.068 0.27 4 -0.27 3 7
SRC -0.021 0.03 0.19 3 -0.2 2 5
NR3C1 0.021 0.004 -10000 0 -10000 0 0
KLK3 0.014 0.091 -10000 0 -10000 0 0
APPBP2 0.016 0.015 -10000 0 -10000 0 0
TRIM24 0.02 0.006 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.019 0.063 0.21 13 -0.3 2 15
TMPRSS2 -0.078 0.27 -10000 0 -0.89 44 44
RXRG -0.14 0.17 -10000 0 -0.32 231 231
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.021 0.004 -10000 0 -10000 0 0
RXRB 0.021 0.004 -10000 0 -10000 0 0
CARM1 0.021 0.005 -10000 0 -10000 0 0
NR2C2 0.021 0.004 -10000 0 -10000 0 0
KLK2 -0.003 0.084 0.29 25 -10000 0 25
AR -0.027 0.075 0.19 2 -0.23 53 55
SENP1 0.021 0.003 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
MDM2 0.019 0.009 -10000 0 -10000 0 0
SRY 0 0.003 -10000 0 -0.027 7 7
GATA2 -0.006 0.093 -10000 0 -0.32 39 39
MYST2 0 0.001 -10000 0 -10000 0 0
HOXB13 0.13 0.14 0.32 174 -10000 0 174
T-DHT/AR/RACK1/Src -0.017 0.072 0.29 10 -0.3 2 12
positive regulation of transcription -0.006 0.093 -10000 0 -0.32 39 39
DNAJA1 0.016 0.016 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.008 0.011 0.17 2 -10000 0 2
NCOA1 0.024 0.015 -10000 0 -10000 0 0
SPDEF 0.12 0.14 0.32 156 -0.32 3 159
T-DHT/AR/TIF2 -0.007 0.073 0.22 9 -0.35 7 16
T-DHT/AR/Hsp90 -0.02 0.061 0.23 8 -0.3 2 10
GSK3B 0.018 0.012 -10000 0 -10000 0 0
NR2C1 0.02 0.006 -10000 0 -10000 0 0
mol:T-DHT -0.021 0.026 -10000 0 -0.21 2 2
SIRT1 0.021 0.003 -10000 0 -10000 0 0
ZMIZ2 0.018 0.01 -10000 0 -10000 0 0
POU2F1 0.009 0.039 -10000 0 -0.17 4 4
T-DHT/AR/DAX-1 0.017 0.1 0.22 75 -0.3 2 77
CREBBP 0.021 0.004 -10000 0 -10000 0 0
SMARCE1 0.021 0.004 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.014 0.03 0.22 1 -0.21 7 8
EPHB2 0.053 0.092 0.32 52 -10000 0 52
Syndecan-2/TACI 0.026 0.06 0.22 34 -0.18 8 42
LAMA1 0.025 0.065 0.32 15 -0.32 6 21
Syndecan-2/alpha2 ITGB1 0.007 0.081 0.23 10 -0.17 69 79
HRAS 0.021 0.004 -10000 0 -10000 0 0
Syndecan-2/CASK -0.006 0.016 -10000 0 -0.18 4 4
ITGA5 0.021 0.021 0.32 1 -0.32 1 2
BAX -0.013 0.013 -10000 0 -10000 0 0
EPB41 0.021 0.003 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.013 0.017 -10000 0 -0.16 4 4
LAMA3 -0.043 0.13 0.32 1 -0.32 89 90
EZR 0.019 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.047 0.14 -10000 0 -0.32 95 95
Syndecan-2/MMP2 0.015 0.021 0.22 1 -0.18 4 5
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.033 0.037 0.23 12 -0.23 2 14
dendrite morphogenesis 0.037 0.069 0.23 52 -0.18 4 56
Syndecan-2/GM-CSF 0.009 0.055 0.23 8 -0.19 25 33
determination of left/right symmetry -0.008 0.019 -10000 0 -0.22 4 4
Syndecan-2/PKC delta 0.014 0.019 -10000 0 -0.18 4 4
GNB2L1 0.02 0.004 -10000 0 -10000 0 0
MAPK3 -0.003 0.07 0.18 43 -0.18 24 67
MAPK1 -0.001 0.069 0.18 44 -0.18 19 63
Syndecan-2/RACK1 0.024 0.018 -10000 0 -0.16 3 3
NF1 0.021 0.003 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 -0.008 0.019 -10000 0 -0.22 4 4
ITGA2 0.026 0.052 0.32 12 -0.32 2 14
MAPK8 -0.011 0.016 -10000 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin 0.042 0.059 0.25 23 -0.19 6 29
Syndecan-2/Kininogen 0.027 0.055 0.22 32 -0.18 4 36
ITGB1 0.021 0.004 -10000 0 -10000 0 0
SRC 0.003 0.062 0.17 55 -10000 0 55
Syndecan-2/CASK/Protein 4.1 0.013 0.017 -10000 0 -0.17 4 4
extracellular matrix organization 0.014 0.019 -10000 0 -0.18 4 4
actin cytoskeleton reorganization 0.014 0.03 0.22 1 -0.21 7 8
Syndecan-2/Caveolin-2/Ras -0.007 0.073 -10000 0 -0.17 78 78
Syndecan-2/Laminin alpha3 -0.017 0.074 0.22 1 -0.18 77 78
Syndecan-2/RasGAP 0.032 0.021 -10000 0 -0.15 3 3
alpha5/beta1 Integrin 0.03 0.016 0.23 1 -0.23 1 2
PRKCD 0.021 0.004 -10000 0 -10000 0 0
Syndecan-2 dimer 0.037 0.069 0.23 52 -0.18 4 56
GO:0007205 0.001 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.017 0.024 0.16 6 -10000 0 6
RHOA 0.021 0.004 -10000 0 -10000 0 0
SDCBP 0.019 0.006 -10000 0 -10000 0 0
TNFRSF13B 0.037 0.085 0.32 34 -0.32 5 39
RASA1 0.02 0.005 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.033 0.037 0.23 12 -0.23 2 14
Syndecan-2/Synbindin 0.015 0.017 -10000 0 -0.18 3 3
TGFB1 0.021 0.004 -10000 0 -10000 0 0
CASP3 0.003 0.061 0.18 48 -0.17 4 52
FN1 0.019 0.034 0.32 1 -0.32 4 5
Syndecan-2/IL8 0.021 0.046 0.22 17 -0.18 7 24
SDC2 -0.008 0.019 -10000 0 -0.22 4 4
KNG1 0.038 0.075 0.32 32 -10000 0 32
Syndecan-2/Neurofibromin 0.015 0.019 -10000 0 -0.18 4 4
TRAPPC4 0.02 0.004 -10000 0 -10000 0 0
CSF2 0.005 0.091 0.32 8 -0.32 29 37
Syndecan-2/TGFB1 0.015 0.019 -10000 0 -0.18 4 4
Syndecan-2/Syntenin/PI-4-5-P2 0.013 0.017 -10000 0 -0.17 4 4
Syndecan-2/Ezrin 0.023 0.022 -10000 0 -0.17 4 4
PRKACA 0.005 0.062 0.18 52 -0.17 2 54
angiogenesis 0.021 0.046 0.22 17 -0.18 7 24
MMP2 0.021 0.014 0.32 1 -10000 0 1
IL8 0.028 0.064 0.32 17 -0.32 4 21
calcineurin-NFAT signaling pathway 0.026 0.06 0.22 34 -0.18 8 42
EPHB forward signaling

Figure S57.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S57.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.045 0.061 0.21 50 -0.17 3 53
cell-cell adhesion 0.021 0.036 0.18 11 -10000 0 11
Ephrin B/EPHB2/RasGAP 0.062 0.069 0.22 46 -0.19 11 57
ITSN1 0.021 0.004 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
SHC1 0.018 0.008 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.029 0.03 0.21 9 -0.19 3 12
Ephrin B1/EPHB1 0.045 0.061 0.21 51 -0.23 4 55
HRAS/GDP 0.014 0.074 0.28 1 -0.24 17 18
Ephrin B/EPHB1/GRB7 0.061 0.07 0.22 41 -0.2 13 54
Endophilin/SYNJ1 -0.011 0.05 0.18 15 -0.29 2 17
KRAS 0.02 0.006 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.061 0.066 0.22 41 -0.19 10 51
endothelial cell migration 0.035 0.032 -10000 0 -0.16 9 9
GRB2 0.02 0.004 -10000 0 -10000 0 0
GRB7 0.019 0.022 -10000 0 -0.32 2 2
PAK1 -0.015 0.052 0.18 18 -0.29 2 20
HRAS 0.021 0.004 -10000 0 -10000 0 0
RRAS -0.013 0.051 0.18 14 -0.3 3 17
DNM1 0.024 0.03 0.32 5 -10000 0 5
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.013 0.049 0.18 14 -0.19 10 24
lamellipodium assembly -0.021 0.036 -10000 0 -0.18 11 11
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.013 0.056 0.19 9 -0.21 9 18
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
EPHB2 0.053 0.092 0.32 52 -10000 0 52
EPHB3 0.026 0.041 0.32 9 -10000 0 9
EPHB1 0.051 0.095 0.32 52 -0.32 2 54
EPHB4 0.02 0.005 -10000 0 -10000 0 0
mol:GDP -0.009 0.057 0.21 7 -0.3 9 16
Ephrin B/EPHB2 0.054 0.065 0.21 48 -0.19 11 59
Ephrin B/EPHB3 0.04 0.045 0.21 7 -0.19 11 18
JNK cascade -0.004 0.056 0.24 11 -0.2 4 15
Ephrin B/EPHB1 0.051 0.064 0.21 42 -0.19 12 54
RAP1/GDP -0.013 0.081 0.23 15 -0.26 15 30
EFNB2 0.014 0.044 -10000 0 -0.32 8 8
EFNB3 0.019 0.026 0.32 1 -0.32 2 3
EFNB1 0.019 0.027 -10000 0 -0.32 3 3
Ephrin B2/EPHB1-2 0.066 0.083 0.22 88 -0.16 10 98
RAP1B 0.02 0.005 -10000 0 -10000 0 0
RAP1A 0.02 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.039 0.068 0.2 5 -0.24 10 15
Rap1/GTP -0.02 0.045 0.097 5 -0.19 10 15
axon guidance 0.044 0.06 0.21 50 -0.16 3 53
MAPK3 -0.003 0.047 0.24 3 -0.28 2 5
MAPK1 -0.002 0.044 0.23 2 -0.25 1 3
Rac1/GDP -0.018 0.07 0.22 5 -0.26 16 21
actin cytoskeleton reorganization -0.027 0.046 0.09 4 -0.22 8 12
CDC42/GDP -0.014 0.079 0.24 13 -0.26 16 29
PI3K 0.039 0.034 -10000 0 -0.17 9 9
EFNA5 0.019 0.033 0.32 2 -0.32 3 5
Ephrin B2/EPHB4 0.022 0.028 -10000 0 -0.19 8 8
Ephrin B/EPHB2/Intersectin/N-WASP 0.014 0.058 0.17 4 -0.2 22 26
CDC42 0.021 0.004 -10000 0 -10000 0 0
RAS family/GTP -0.023 0.04 -10000 0 -0.19 9 9
PTK2 0.056 0.18 0.53 64 -10000 0 64
MAP4K4 -0.004 0.056 0.24 11 -0.2 4 15
SRC 0.02 0.004 -10000 0 -10000 0 0
KALRN 0.019 0.027 -10000 0 -0.32 3 3
Intersectin/N-WASP 0.029 0.008 -10000 0 -10000 0 0
neuron projection morphogenesis -0.001 0.083 0.25 25 -0.29 3 28
MAP2K1 0.005 0.05 0.18 9 -0.23 5 14
WASL 0.02 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.084 0.082 0.24 93 -0.22 4 97
cell migration 0.012 0.078 0.24 15 -0.26 5 20
NRAS 0.02 0.005 -10000 0 -10000 0 0
SYNJ1 -0.011 0.05 0.18 15 -0.3 2 17
PXN 0.021 0.003 -10000 0 -10000 0 0
TF 0.006 0.069 0.2 19 -0.26 2 21
HRAS/GTP 0.04 0.052 0.18 6 -0.19 10 16
Ephrin B1/EPHB1-2 0.072 0.08 0.22 93 -0.21 4 97
cell adhesion mediated by integrin 0.015 0.041 0.2 10 -0.2 8 18
RAC1 0.019 0.007 -10000 0 -10000 0 0
mol:GTP 0.047 0.059 0.22 7 -0.19 11 18
RAC1-CDC42/GTP -0.023 0.038 -10000 0 -0.19 10 10
RASA1 0.02 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.018 0.07 0.22 5 -0.26 15 20
ruffle organization 0.004 0.091 0.28 24 -0.26 3 27
NCK1 0.021 0.003 -10000 0 -10000 0 0
receptor internalization -0.015 0.048 0.18 15 -0.29 2 17
Ephrin B/EPHB2/KALRN 0.062 0.072 0.22 48 -0.2 13 61
ROCK1 -0.011 0.033 0.18 11 -0.17 2 13
RAS family/GDP -0.032 0.041 -10000 0 -0.22 9 9
Rac1/GTP -0.018 0.044 0.11 5 -0.2 10 15
Ephrin B/EPHB1/Src/Paxillin 0.012 0.056 -10000 0 -0.2 23 23
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.02 0.004 -10000 0 -10000 0 0
VLDLR 0.014 0.044 -10000 0 -0.32 8 8
LRPAP1 0.021 0.003 -10000 0 -10000 0 0
NUDC 0.021 0.004 -10000 0 -10000 0 0
RELN/LRP8 0.017 0.083 0.22 13 -0.19 58 71
CaM/Ca2+ 0.015 0.003 -10000 0 -10000 0 0
KATNA1 0.019 0.006 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.03 0.066 0.17 17 -0.18 56 73
IQGAP1/CaM 0.03 0.008 -10000 0 -10000 0 0
DAB1 0.023 0.036 0.32 7 -10000 0 7
IQGAP1 0.021 0.003 -10000 0 -10000 0 0
PLA2G7 0.024 0.044 0.32 8 -0.32 2 10
CALM1 0.02 0.005 -10000 0 -10000 0 0
DYNLT1 0.019 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.034 0.026 0.23 8 -10000 0 8
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.021 0.003 -10000 0 -10000 0 0
CDK5R1 0.029 0.048 0.32 13 -10000 0 13
LIS1/Poliovirus Protein 3A -0.012 0.004 -10000 0 -10000 0 0
CDK5R2 0.1 0.13 0.32 132 -10000 0 132
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.01 0.087 0.24 10 -0.2 62 72
YWHAE 0.019 0.006 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.002 0.088 0.26 23 -0.21 5 28
MAP1B 0.003 0.013 0.11 3 -0.22 1 4
RAC1 0.005 0.003 -10000 0 -10000 0 0
p35/CDK5 -0.029 0.07 0.18 25 -0.17 48 73
RELN -0.018 0.12 0.32 6 -0.32 59 65
PAFAH/LIS1 -0.013 0.035 0.23 8 -0.19 2 10
LIS1/CLIP170 -0.017 0.007 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.02 0.06 0.16 2 -10000 0 2
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.021 0.09 0.26 2 -0.3 18 20
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.002 0.075 0.21 22 -0.22 3 25
LIS1/IQGAP1 -0.017 0.007 -10000 0 -10000 0 0
RHOA 0.005 0.002 -10000 0 -10000 0 0
PAFAH1B1 -0.015 0.005 -10000 0 -10000 0 0
PAFAH1B3 0.031 0.057 0.32 18 -10000 0 18
PAFAH1B2 0.02 0.005 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.01 0.03 -10000 0 -0.16 5 5
NDEL1/Katanin 60/Dynein heavy chain -0.002 0.09 0.28 16 -0.22 2 18
LRP8 0.026 0.04 0.32 9 -10000 0 9
NDEL1/Katanin 60 0 0.09 0.27 20 -0.21 3 23
P39/CDK5 0.016 0.12 0.2 119 -10000 0 119
LIS1/NudC/Dynein intermediate chain/microtubule organizing center -0.017 0.007 -10000 0 -10000 0 0
CDK5 -0.034 0.057 0.17 10 -0.17 52 62
PPP2R5D 0.02 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.014 0.006 -10000 0 -10000 0 0
CSNK2A1 0.02 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.011 0.079 0.24 9 -0.17 60 69
RELN/VLDLR 0.02 0.086 0.22 12 -0.18 62 74
CDC42 0.005 0.002 -10000 0 -10000 0 0
Ceramide signaling pathway

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
SPHK2 -0.019 0.031 -10000 0 -0.23 10 10
MAP4K4 -0.007 0.041 0.14 1 -0.26 4 5
BAG4 0.019 0.007 -10000 0 -10000 0 0
PKC zeta/ceramide 0.003 0.062 -10000 0 -0.18 48 48
NFKBIA 0.018 0.008 -10000 0 -10000 0 0
BIRC3 0.021 0.035 0.32 4 -0.32 2 6
BAX -0.008 0.075 -10000 0 -0.35 19 19
RIPK1 0.021 0.004 -10000 0 -10000 0 0
AKT1 0.005 0.11 0.72 11 -10000 0 11
BAD -0.012 0.06 0.2 3 -0.18 49 52
SMPD1 0.007 0.052 0.16 15 -0.14 18 33
RB1 -0.013 0.057 -10000 0 -0.18 49 49
FADD/Caspase 8 0.002 0.055 0.18 7 -0.28 5 12
MAP2K4 -0.014 0.058 0.17 7 -0.17 47 54
NSMAF 0.019 0.006 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.014 0.062 0.2 9 -0.17 48 57
EGF 0.07 0.12 0.32 85 -0.32 4 89
mol:ceramide -0.008 0.062 0.12 5 -0.18 49 54
MADD 0.021 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.016 0.026 -10000 0 -0.23 7 7
ASAH1 0.018 0.008 -10000 0 -10000 0 0
negative regulation of cell cycle -0.013 0.057 -10000 0 -0.17 49 49
cell proliferation 0.002 0.066 0.2 4 -0.18 23 27
BID -0.005 0.12 -10000 0 -0.6 17 17
MAP3K1 -0.01 0.062 0.18 8 -0.18 48 56
EIF2A -0.014 0.067 0.21 16 -0.17 45 61
TRADD 0.021 0.004 -10000 0 -10000 0 0
CRADD 0.022 0.014 0.32 1 -10000 0 1
MAPK3 -0.013 0.059 0.19 9 -0.17 30 39
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.017 0.062 0.19 9 -0.18 33 42
Cathepsin D/ceramide 0.004 0.063 -10000 0 -0.18 49 49
FADD -0.006 0.04 0.14 2 -0.26 4 6
KSR1 -0.009 0.065 0.22 9 -0.18 49 58
MAPK8 -0.009 0.065 -10000 0 -0.19 25 25
PRKRA -0.01 0.062 0.23 5 -0.18 48 53
PDGFA 0.013 0.046 -10000 0 -0.32 9 9
TRAF2 0.021 0.004 -10000 0 -10000 0 0
IGF1 0.014 0.051 0.32 1 -0.32 10 11
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.008 0.061 0.12 5 -0.18 49 54
CTSD 0.021 0.003 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.03 0.007 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.003 0.07 0.22 4 -0.19 23 27
PRKCD 0.021 0.004 -10000 0 -10000 0 0
PRKCZ 0.018 0.027 -10000 0 -0.32 3 3
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.016 0.026 -10000 0 -0.23 7 7
RelA/NF kappa B1 0.03 0.007 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.021 0.003 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0 0.043 0.16 2 -0.28 3 5
TNFR1A/BAG4/TNF-alpha 0.029 0.042 0.22 1 -0.19 14 15
mol:Sphingosine-1-phosphate -0.019 0.031 -10000 0 -0.22 10 10
MAP2K1 -0.016 0.06 0.18 12 -0.17 46 58
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.021 0.004 -10000 0 -10000 0 0
CYCS 0.005 0.051 0.18 4 -0.18 13 17
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
TNFR1A/BAG4 0.026 0.012 -10000 0 -10000 0 0
EIF2AK2 -0.013 0.061 0.2 9 -0.17 46 55
TNF-alpha/TNFR1A/FAN 0.03 0.041 0.22 1 -0.19 13 14
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.013 0.046 -10000 0 -0.27 7 7
MAP2K2 -0.017 0.058 0.19 9 -0.17 42 51
SMPD3 0.008 0.056 0.19 5 -0.26 8 13
TNF 0.011 0.061 0.32 1 -0.32 15 16
PKC zeta/PAR4 0.028 0.021 -10000 0 -0.23 3 3
mol:PHOSPHOCHOLINE -0.018 0.061 0.19 6 -0.14 45 51
NF kappa B1/RelA/I kappa B alpha 0.049 0.03 -10000 0 -0.17 2 2
AIFM1 -0.002 0.06 0.16 5 -0.19 13 18
BCL2 0.019 0.022 0.32 1 -0.32 1 2
FAS signaling pathway (CD95)

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
SPTAN1 -0.013 0.036 0.21 2 -0.2 12 14
RFC1 -0.01 0.041 0.22 7 -0.2 10 17
PRKDC -0.001 0.056 0.22 24 -0.19 9 33
RIPK1 0.023 0.006 -10000 0 -10000 0 0
CASP7 -0.013 0.093 -10000 0 -0.63 9 9
FASLG/FAS/FADD/FAF1 0.004 0.053 0.16 24 -0.26 3 27
MAP2K4 -0.061 0.14 0.24 2 -0.31 93 95
mol:ceramide -0.019 0.077 -10000 0 -0.26 14 14
GSN -0.014 0.032 -10000 0 -0.2 12 12
FASLG/FAS/FADD/FAF1/Caspase 8 -0.003 0.06 0.2 1 -0.29 3 4
FAS 0.007 0.038 -10000 0 -0.33 4 4
BID -0.021 0.028 0.5 1 -0.18 3 4
MAP3K1 -0.031 0.1 0.24 2 -0.46 11 13
MAP3K7 0.011 0.018 -10000 0 -10000 0 0
RB1 -0.012 0.027 -10000 0 -0.19 10 10
CFLAR 0.023 0.005 -10000 0 -10000 0 0
HGF/MET 0.009 0.097 0.22 10 -0.22 63 73
ARHGDIB -0.01 0.038 0.22 5 -0.2 10 15
FADD 0.009 0.023 -10000 0 -10000 0 0
actin filament polymerization 0.014 0.034 0.2 14 -10000 0 14
NFKB1 -0.023 0.11 -10000 0 -0.62 7 7
MAPK8 -0.1 0.2 0.24 1 -0.46 109 110
DFFA -0.012 0.032 0.21 2 -0.19 11 13
DNA fragmentation during apoptosis -0.012 0.037 0.21 4 -0.18 14 18
FAS/FADD/MET 0.017 0.056 0.22 6 -0.2 16 22
CFLAR/RIP1 0.034 0.01 -10000 0 -10000 0 0
FAIM3 0.021 0.029 0.32 3 -0.32 1 4
FAF1 0.008 0.025 -10000 0 -10000 0 0
PARP1 -0.013 0.035 0.22 2 -0.2 12 14
DFFB -0.011 0.035 0.21 4 -0.19 11 15
CHUK -0.028 0.099 -10000 0 -0.59 7 7
FASLG 0.007 0.038 0.32 1 -0.32 3 4
FAS/FADD 0.013 0.038 -10000 0 -0.24 4 4
HGF 0.008 0.075 0.32 4 -0.32 21 25
LMNA -0.008 0.051 0.19 21 -0.19 13 34
CASP6 -0.012 0.034 0.21 2 -0.2 10 12
CASP10 0.007 0.032 -10000 0 -0.33 2 2
CASP3 -0.006 0.024 -10000 0 -0.26 3 3
PTPN13 -0.012 0.1 -10000 0 -0.32 47 47
CASP8 -0.021 0.025 0.29 1 -0.23 4 5
IL6 -0.24 0.47 -10000 0 -1.1 112 112
MET 0.013 0.068 0.32 6 -0.32 15 21
ICAD/CAD -0.014 0.041 0.3 4 -0.18 11 15
FASLG/FAS/FADD/FAF1/Caspase 10 -0.019 0.078 -10000 0 -0.26 14 14
activation of caspase activity by cytochrome c -0.021 0.028 0.49 1 -0.18 3 4
PAK2 -0.008 0.044 0.21 10 -0.2 10 20
BCL2 0.02 0.022 0.32 1 -0.32 1 2
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.008 0.064 0.32 18 -10000 0 18
PI3K Class IB/PDE3B 0.008 0.065 -10000 0 -0.32 18 18
PDE3B 0.008 0.065 -10000 0 -0.32 18 18
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.012 0.093 -10000 0 -0.3 28 28
TBX21 -0.1 0.32 -10000 0 -1.1 32 32
B2M 0.02 0.009 -10000 0 -10000 0 0
TYK2 0.011 0.027 -10000 0 -10000 0 0
IL12RB1 0.003 0.061 -10000 0 -0.34 12 12
GADD45B -0.091 0.28 -10000 0 -0.98 30 30
IL12RB2 0.033 0.091 0.32 38 -0.34 3 41
GADD45G -0.084 0.27 -10000 0 -0.98 26 26
natural killer cell activation -0.003 0.013 -10000 0 -10000 0 0
RELB 0.02 0.004 -10000 0 -10000 0 0
RELA 0.021 0.004 -10000 0 -10000 0 0
IL18 0.007 0.05 -10000 0 -0.33 9 9
IL2RA 0.04 0.078 0.32 34 -0.32 1 35
IFNG 0.034 0.085 0.32 31 -0.32 7 38
STAT3 (dimer) -0.072 0.23 -10000 0 -0.72 35 35
HLA-DRB5 -0.016 0.1 -10000 0 -0.32 48 48
FASLG -0.071 0.27 -10000 0 -0.93 27 27
NF kappa B2 p52/RelB -0.069 0.27 -10000 0 -0.84 32 32
CD4 0.011 0.048 -10000 0 -0.32 9 9
SOCS1 0.021 0.014 0.32 1 -10000 0 1
EntrezGene:6955 -0.002 0.008 -10000 0 -10000 0 0
CD3D 0.014 0.032 -10000 0 -0.33 3 3
CD3E 0.013 0.038 -10000 0 -0.32 5 5
CD3G 0.009 0.054 -10000 0 -0.33 11 11
IL12Rbeta2/JAK2 0.029 0.069 0.24 29 -0.24 5 34
CCL3 -0.084 0.26 -10000 0 -1 22 22
CCL4 -0.085 0.27 -10000 0 -1 23 23
HLA-A 0.02 0.009 -10000 0 -10000 0 0
IL18/IL18R 0.017 0.087 -10000 0 -0.24 35 35
NOS2 -0.13 0.38 -10000 0 -1.1 55 55
IL12/IL12R/TYK2/JAK2/SPHK2 -0.014 0.099 -10000 0 -0.31 31 31
IL1R1 -0.085 0.27 -10000 0 -1 22 22
IL4 0.004 0.027 -10000 0 -10000 0 0
JAK2 0.009 0.034 -10000 0 -0.32 2 2
EntrezGene:6957 -0.001 0.008 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.016 0.13 -10000 0 -0.87 8 8
RAB7A -0.073 0.23 -10000 0 -0.84 21 21
lysosomal transport -0.069 0.22 -10000 0 -0.79 21 21
FOS -0.11 0.33 -10000 0 -0.99 52 52
STAT4 (dimer) -0.07 0.25 -10000 0 -0.81 31 31
STAT5A (dimer) -0.064 0.27 -10000 0 -0.84 33 33
GZMA -0.082 0.27 -10000 0 -1.1 21 21
GZMB -0.092 0.3 -10000 0 -1.1 27 27
HLX 0.017 0.031 -10000 0 -0.32 4 4
LCK -0.086 0.28 -10000 0 -0.93 31 31
TCR/CD3/MHC II/CD4 -0.028 0.12 -10000 0 -0.32 46 46
IL2/IL2R 0.057 0.057 0.22 34 -0.25 4 38
MAPK14 -0.089 0.28 -10000 0 -0.94 31 31
CCR5 -0.08 0.26 -10000 0 -1.1 20 20
IL1B -0.009 0.085 -10000 0 -0.33 28 28
STAT6 -0.01 0.076 -10000 0 -0.32 2 2
STAT4 0.021 0.002 -10000 0 -10000 0 0
STAT3 0.021 0.003 -10000 0 -10000 0 0
STAT1 0.021 0.002 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
NFKB2 0.021 0.003 -10000 0 -10000 0 0
IL12B 0.013 0.04 0.3 4 -0.33 1 5
CD8A 0.018 0.039 0.32 1 -0.33 5 6
CD8B 0.019 0.043 0.32 3 -0.32 5 8
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.012 0.093 0.3 28 -10000 0 28
IL2RB 0.019 0.022 -10000 0 -0.32 2 2
proteasomal ubiquitin-dependent protein catabolic process -0.063 0.23 -10000 0 -0.73 31 31
IL2RG 0.018 0.035 -10000 0 -0.32 5 5
IL12 0.018 0.047 0.23 2 -0.25 4 6
STAT5A 0.02 0.016 -10000 0 -0.32 1 1
CD247 0.014 0.026 -10000 0 -0.32 2 2
IL2 0.019 0.003 -10000 0 -10000 0 0
SPHK2 0.02 0.016 -10000 0 -0.32 1 1
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.007 0.047 0.32 1 -0.34 5 6
IL12/IL12R/TYK2/JAK2 -0.084 0.31 -10000 0 -1 30 30
MAP2K3 -0.095 0.29 -10000 0 -0.9 37 37
RIPK2 0.019 0.007 -10000 0 -10000 0 0
MAP2K6 -0.085 0.28 -10000 0 -0.89 35 35
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.004 0.067 -10000 0 -0.32 19 19
IL18RAP 0.002 0.067 -10000 0 -0.33 18 18
IL12Rbeta1/TYK2 0.012 0.053 -10000 0 -0.25 11 11
EOMES -0.012 0.15 -10000 0 -0.71 17 17
STAT1 (dimer) -0.058 0.24 -10000 0 -0.77 27 27
T cell proliferation -0.059 0.19 -10000 0 -0.6 31 31
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.001 0.07 -10000 0 -0.33 20 20
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.063 0.22 -10000 0 -0.58 49 49
ATF2 -0.083 0.26 0.45 1 -0.85 31 32
Nectin adhesion 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
PDGFRB 0.02 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.037 0.05 0.23 22 -0.23 5 27
PTK2 -0.021 0.11 -10000 0 -0.35 27 27
positive regulation of JNK cascade -0.021 0.11 -10000 0 -0.29 37 37
CDC42/GDP -0.021 0.15 -10000 0 -0.39 38 38
Rac1/GDP -0.022 0.14 -10000 0 -0.39 34 34
RAP1B 0.02 0.005 -10000 0 -10000 0 0
RAP1A 0.02 0.004 -10000 0 -10000 0 0
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.021 0.13 -10000 0 -0.36 36 36
nectin-3/I-afadin 0.011 0.064 -10000 0 -0.22 33 33
RAPGEF1 -0.038 0.14 0.28 1 -0.4 35 36
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.044 0.15 -10000 0 -0.45 36 36
PDGFB-D/PDGFRB 0.02 0.004 -10000 0 -10000 0 0
TLN1 -0.026 0.06 -10000 0 -0.21 32 32
Rap1/GTP -0.026 0.11 -10000 0 -0.3 34 34
IQGAP1 0.021 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.034 0.016 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.011 0.064 -10000 0 -0.22 33 33
PVR 0.02 0.005 -10000 0 -10000 0 0
Necl-5(dimer) 0.02 0.005 -10000 0 -10000 0 0
mol:GDP -0.039 0.17 -10000 0 -0.48 38 38
MLLT4 0.019 0.006 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
PI3K 0.038 0.059 -10000 0 -0.18 26 26
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.031 0.031 0.23 10 -10000 0 10
positive regulation of lamellipodium assembly -0.023 0.12 -10000 0 -0.31 37 37
PVRL1 0.026 0.043 0.32 10 -10000 0 10
PVRL3 -0.002 0.087 0.32 1 -0.32 33 34
PVRL2 0.02 0.004 -10000 0 -10000 0 0
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
CDH1 0.019 0.022 -10000 0 -0.32 2 2
CLDN1 0.023 0.055 0.32 10 -0.32 5 15
JAM-A/CLDN1 0.032 0.065 0.22 10 -0.19 27 37
SRC -0.046 0.17 -10000 0 -0.48 39 39
ITGB3 0.031 0.072 0.32 22 -0.32 5 27
nectin-1(dimer)/I-afadin/I-afadin 0.031 0.031 0.23 10 -10000 0 10
FARP2 -0.034 0.17 -10000 0 -0.51 20 20
RAC1 0.019 0.007 -10000 0 -10000 0 0
CTNNA1 0.021 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.022 0.057 -10000 0 -0.19 31 31
nectin-1/I-afadin 0.031 0.031 0.23 10 -10000 0 10
nectin-2/I-afadin 0.028 0.011 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.025 0.01 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.026 0.062 0.22 8 -0.19 30 38
CDC42/GTP/IQGAP1/filamentous actin 0.027 0.006 -10000 0 -10000 0 0
F11R 0.018 0.017 -10000 0 -0.32 1 1
positive regulation of filopodium formation -0.021 0.11 -10000 0 -0.29 37 37
alphaV/beta3 Integrin/Talin -0.026 0.082 0.19 23 -0.32 15 38
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.028 0.011 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.028 0.011 -10000 0 -10000 0 0
PIP5K1C -0.021 0.063 -10000 0 -0.21 35 35
VAV2 -0.041 0.18 -10000 0 -0.51 38 38
RAP1/GDP -0.019 0.14 -10000 0 -0.36 35 35
ITGAV 0.021 0.002 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.022 0.058 -10000 0 -0.19 32 32
nectin-3(dimer)/I-afadin/I-afadin 0.011 0.064 -10000 0 -0.22 33 33
Rac1/GTP -0.025 0.14 -10000 0 -0.38 36 36
PTPRM -0.013 0.074 -10000 0 -0.23 39 39
E-cadherin/beta catenin/alpha catenin 0.051 0.037 -10000 0 -0.15 1 1
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.021 0.004 -10000 0 -10000 0 0
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.014 0.078 0.21 32 -10000 0 32
GNAI2 0.021 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.013 0.049 0.21 1 -0.19 26 27
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.021 0.032 0.32 3 -0.32 2 5
RhoA/GTP -0.014 0.079 -10000 0 -0.22 32 32
negative regulation of cAMP metabolic process -0.016 0.075 -10000 0 -0.19 63 63
GNAZ -0.007 0.092 -10000 0 -0.32 38 38
GNAI3 0.02 0.004 -10000 0 -10000 0 0
GNA12 0.019 0.007 -10000 0 -10000 0 0
S1PR5 0 0.082 0.32 1 -0.32 29 30
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.016 0.075 -10000 0 -0.19 63 63
RhoA/GDP 0.015 0.003 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
GNAI1 0.02 0.016 -10000 0 -0.32 1 1
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.009 0.026 0.11 1 -0.22 2 3
NFATC2 -0.015 0.041 0.11 1 -0.2 16 17
NFATC3 -0.01 0.023 0.11 1 -10000 0 1
CD40LG -0.036 0.14 0.35 7 -0.39 32 39
PTGS2 -0.039 0.15 0.34 10 -0.37 45 55
JUNB 0.018 0.027 -10000 0 -0.32 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 0.01 0.02 -10000 0 -10000 0 0
CaM/Ca2+ 0.01 0.02 -10000 0 -10000 0 0
CALM1 0.013 0.02 -10000 0 -10000 0 0
JUN 0.011 0.037 -10000 0 -0.33 4 4
mol:Ca2+ -0.001 0.008 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.01 0.011 -10000 0 -10000 0 0
FOSL1 0.03 0.064 0.32 19 -0.32 3 22
CREM 0.02 0.004 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.016 0.092 0.27 15 -0.27 11 26
FOS -0.007 0.085 -10000 0 -0.33 31 31
IFNG -0.022 0.14 0.34 29 -0.36 25 54
AP-1/NFAT1-c-4 0.012 0.16 0.46 15 -0.39 25 40
FASLG -0.029 0.13 0.35 7 -0.35 25 32
NFAT1-c-4/ICER1 0.007 0.062 0.26 1 -0.24 6 7
IL2RA -0.019 0.15 0.34 36 -0.35 23 59
FKBP12/FK506 0.015 0.004 -10000 0 -10000 0 0
CSF2 -0.038 0.15 0.36 12 -0.38 39 51
JunB/Fra1/NFAT1-c-4 0.018 0.08 0.25 15 -0.2 18 33
IL4 -0.033 0.12 0.35 6 -0.35 24 30
IL2 0 0.11 -10000 0 -0.84 8 8
IL3 -0.013 0.13 -10000 0 -0.62 21 21
FKBP1A 0.02 0.005 -10000 0 -10000 0 0
BATF3 0.02 0.015 0.32 1 -10000 0 1
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.019 0.007 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.02 0.006 -10000 0 -10000 0 0
SVIL 0.021 0.005 -10000 0 -10000 0 0
ZNF318 0.019 0.01 -10000 0 -10000 0 0
JMJD2C 0.007 0.027 0.13 24 -10000 0 24
T-DHT/AR/Ubc9 0.004 0.084 0.17 5 -0.19 62 67
CARM1 0.02 0.005 -10000 0 -10000 0 0
PRDX1 0.021 0.005 -10000 0 -10000 0 0
PELP1 0.019 0.008 -10000 0 -10000 0 0
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
AKT1 0.02 0.008 -10000 0 -10000 0 0
PTK2B 0.018 0.008 -10000 0 -10000 0 0
MED1 0.02 0.007 -10000 0 -10000 0 0
MAK 0.009 0.06 -10000 0 -0.32 15 15
response to oxidative stress 0 0.001 -10000 0 -10000 0 0
HIP1 0.019 0.027 -10000 0 -0.32 3 3
GSN 0.021 0.005 -10000 0 -10000 0 0
NCOA2 0.016 0.031 -10000 0 -0.32 4 4
NCOA6 0.021 0.005 -10000 0 -10000 0 0
DNA-PK 0.036 0.018 -10000 0 -10000 0 0
NCOA4 0.021 0.003 -10000 0 -10000 0 0
PIAS3 0.018 0.008 -10000 0 -10000 0 0
cell proliferation -0.013 0.11 -10000 0 -0.58 17 17
XRCC5 0.02 0.006 -10000 0 -10000 0 0
UBE3A 0.02 0.006 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.003 0.091 0.17 5 -0.19 77 82
FHL2 0.04 0.1 0.31 45 -10000 0 45
RANBP9 0.021 0.004 -10000 0 -10000 0 0
JMJD1A -0.008 0.037 -10000 0 -0.12 42 42
CDK6 0.019 0.022 -10000 0 -0.32 2 2
TGFB1I1 0.019 0.027 -10000 0 -0.32 3 3
T-DHT/AR/CyclinD1 0.004 0.085 0.17 5 -0.2 61 66
XRCC6 0.02 0.007 -10000 0 -10000 0 0
T-DHT/AR 0.016 0.11 0.26 8 -0.21 64 72
CTDSP1 0.021 0.002 -10000 0 -10000 0 0
CTDSP2 0.019 0.008 -10000 0 -10000 0 0
BRCA1 0.022 0.014 0.32 1 -10000 0 1
TCF4 0.017 0.024 -10000 0 -0.32 2 2
CDKN2A 0.096 0.14 0.32 130 -10000 0 130
SRF 0.038 0.044 -10000 0 -10000 0 0
NKX3-1 -0.028 0.12 -10000 0 -0.41 31 31
KLK3 -0.005 0.058 -10000 0 -10000 0 0
TMF1 0.021 0.004 -10000 0 -10000 0 0
HNRNPA1 0.02 0.007 -10000 0 -10000 0 0
AOF2 0 0.002 -10000 0 -10000 0 0
APPL1 -0.016 0.005 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 0.005 0.085 0.17 4 -0.19 63 67
AR -0.021 0.12 0.32 1 -0.33 60 61
UBA3 0.021 0.004 -10000 0 -10000 0 0
PATZ1 0.02 0.007 -10000 0 -10000 0 0
PAWR 0.021 0.003 -10000 0 -10000 0 0
PRKDC 0.019 0.008 -10000 0 -10000 0 0
PA2G4 0.02 0.007 -10000 0 -10000 0 0
UBE2I 0.021 0.004 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.006 0.076 0.16 5 -0.17 61 66
RPS6KA3 0.021 0.005 -10000 0 -10000 0 0
T-DHT/AR/ARA70 0.006 0.084 0.17 5 -0.19 61 66
LATS2 0.019 0.008 -10000 0 -10000 0 0
T-DHT/AR/PRX1 0.007 0.076 0.16 4 -0.17 62 66
Cyclin D3/CDK11 p58 0.015 0.004 -10000 0 -10000 0 0
VAV3 0.018 0.034 0.32 1 -0.32 4 5
KLK2 0.007 0.077 0.29 21 -0.34 3 24
CASP8 0.02 0.016 -10000 0 -0.32 1 1
T-DHT/AR/TIF2/CARM1 0.014 0.08 0.21 1 -0.18 55 56
TMPRSS2 -0.057 0.22 -10000 0 -0.75 41 41
CCND1 0.016 0.038 -10000 0 -0.32 6 6
PIAS1 0.021 0.005 -10000 0 -10000 0 0
mol:T-DHT 0.002 0.018 0.056 6 -0.058 19 25
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.021 0.007 -10000 0 -10000 0 0
T-DHT/AR/CDK6 0.006 0.083 0.17 5 -0.19 60 65
CMTM2 -0.044 0.13 -10000 0 -0.32 91 91
SNURF 0.008 0.063 -10000 0 -0.32 17 17
ZMIZ1 0.02 0.026 -10000 0 -10000 0 0
CCND3 0.02 0.004 -10000 0 -10000 0 0
TGIF1 0.019 0.008 -10000 0 -10000 0 0
FKBP4 0.02 0.006 -10000 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.02 0.005 -10000 0 -9999 0 0
PLK4 0.036 0.066 0.32 25 -9999 0 25
regulation of centriole replication -0.007 0.039 0.16 25 -9999 0 25
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.02 0.004 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.006 0.12 0.24 1 -0.36 33 34
PTP1B/AKT1 0.013 0.072 0.19 2 -0.32 9 11
FYN 0.019 0.017 -10000 0 -0.32 1 1
p210 bcr-abl/PTP1B 0.006 0.075 0.21 4 -0.32 10 14
EGFR 0.016 0.042 0.32 1 -0.33 6 7
EGF/EGFR 0.036 0.094 0.21 49 -0.36 6 55
CSF1 0.018 0.027 -10000 0 -0.32 3 3
AKT1 0.019 0.009 -10000 0 -10000 0 0
INSR 0.02 0.006 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.032 0.092 0.23 37 -0.3 10 47
Insulin Receptor/Insulin 0.023 0.071 -10000 0 -0.34 6 6
HCK 0.007 0.066 -10000 0 -0.32 19 19
CRK 0.019 0.006 -10000 0 -10000 0 0
TYK2 0.002 0.071 0.27 3 -0.38 6 9
EGF 0.071 0.12 0.32 85 -0.33 4 89
YES1 0.02 0.005 -10000 0 -10000 0 0
CAV1 -0.056 0.1 0.24 4 -0.34 23 27
TXN 0.022 0.015 0.32 1 -10000 0 1
PTP1B/IRS1/GRB2 0.023 0.074 0.25 1 -0.36 5 6
cell migration -0.006 0.075 0.32 10 -0.21 4 14
STAT3 0.021 0.003 -10000 0 -10000 0 0
PRLR 0.022 0.091 0.32 25 -0.32 15 40
ITGA2B -0.007 0.1 0.32 5 -0.32 44 49
CSF1R 0.016 0.041 -10000 0 -0.32 7 7
Prolactin Receptor/Prolactin 0.03 0.071 0.24 31 -0.22 15 46
FGR -0.002 0.086 -10000 0 -0.32 33 33
PTP1B/p130 Cas 0.014 0.073 0.21 3 -0.31 10 13
Crk/p130 Cas 0.021 0.074 0.25 1 -0.33 7 8
DOK1 0.002 0.08 0.22 3 -0.33 12 15
JAK2 -0.006 0.12 0.23 1 -0.36 32 33
Jak2/Leptin Receptor/Leptin 0.027 0.095 0.23 11 -0.34 8 19
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
PTPN1 0.006 0.076 0.21 4 -0.32 10 14
LYN 0.019 0.006 -10000 0 -10000 0 0
CDH2 0.044 0.096 0.32 46 -0.32 5 51
SRC 0.007 0.092 -10000 0 -0.44 16 16
ITGB3 0.028 0.073 0.32 22 -0.32 5 27
CAT1/PTP1B -0.023 0.14 0.28 5 -0.39 37 42
CAPN1 0.021 0.005 -10000 0 -10000 0 0
CSK 0.021 0.004 -10000 0 -10000 0 0
PI3K 0.027 0.068 -10000 0 -0.31 5 5
mol:H2O2 0 0.003 -10000 0 -10000 0 0
STAT3 (dimer) 0.025 0.088 0.22 8 -0.3 10 18
negative regulation of transcription -0.005 0.12 0.23 1 -0.36 32 33
FCGR2A 0.016 0.031 -10000 0 -0.32 4 4
FER 0.021 0.007 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.016 0.095 0.23 27 -0.23 48 75
BLK 0.06 0.11 0.32 70 -0.32 1 71
Insulin Receptor/Insulin/Shc 0.033 0.017 -10000 0 -10000 0 0
RHOA 0.021 0.005 -10000 0 -10000 0 0
LEPR -0.012 0.1 -10000 0 -0.32 48 48
BCAR1 0.02 0.016 -10000 0 -0.32 1 1
p210 bcr-abl/Grb2 0.02 0.004 -10000 0 -10000 0 0
mol:NADPH 0.001 0.002 -10000 0 -10000 0 0
TRPV6 -0.039 0.16 0.22 4 -0.37 59 63
PRL 0.024 0.046 0.32 11 -10000 0 11
SOCS3 0.001 0.13 -10000 0 -1.1 7 7
SPRY2 0.019 0.017 -10000 0 -0.32 1 1
Insulin Receptor/Insulin/IRS1 0.038 0.015 -10000 0 -0.18 1 1
CSF1/CSF1R 0.021 0.08 -10000 0 -0.34 10 10
Ras protein signal transduction 0.006 0.11 0.56 17 -10000 0 17
IRS1 0.02 0.016 -10000 0 -0.32 1 1
INS 0.012 0.014 -10000 0 -10000 0 0
LEP 0.049 0.091 0.32 49 -10000 0 49
STAT5B 0.007 0.087 0.2 5 -0.32 16 21
STAT5A 0.007 0.088 0.2 5 -0.31 18 23
GRB2 0.02 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.016 0.073 0.22 2 -0.32 9 11
CSN2 0.018 0.062 0.56 1 -10000 0 1
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
LAT 0.013 0.068 -10000 0 -0.4 9 9
YBX1 0.024 0.005 -10000 0 -10000 0 0
LCK 0.02 0.026 0.32 1 -0.32 2 3
SHC1 0.018 0.008 -10000 0 -10000 0 0
NOX4 0.03 0.05 0.32 14 -10000 0 14
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.034 0.1 0.25 32 -0.34 13 45
FYN 0 0.12 0.25 12 -0.38 22 34
LAT/GRAP2/SLP76 0.013 0.1 0.25 4 -0.37 18 22
IKBKB 0.018 0.007 -10000 0 -10000 0 0
AKT1 -0.004 0.097 0.24 11 -0.31 23 34
B2M 0.018 0.013 -10000 0 -10000 0 0
IKBKG -0.001 0.034 0.11 11 -0.1 7 18
MAP3K8 0.02 0.016 -10000 0 -0.32 1 1
mol:Ca2+ -0.016 0.014 0.038 9 -0.055 11 20
integrin-mediated signaling pathway 0.024 0.016 -10000 0 -0.19 2 2
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.009 0.12 0.24 7 -0.41 24 31
TRPV6 0.008 0.26 1.2 20 -10000 0 20
CD28 0.019 0.018 -10000 0 -0.33 1 1
SHC1 0.018 0.12 0.26 41 -0.39 16 57
receptor internalization -0.006 0.11 0.2 1 -0.41 23 24
PRF1 -0.041 0.24 -10000 0 -0.95 30 30
KRAS 0.02 0.006 -10000 0 -10000 0 0
GRB2 0.02 0.004 -10000 0 -10000 0 0
COT/AKT1 0.007 0.083 0.24 8 -0.29 15 23
LAT -0.002 0.11 0.27 8 -0.38 22 30
EntrezGene:6955 -0.001 0.005 -10000 0 -0.032 2 2
CD3D 0.016 0.03 -10000 0 -0.33 3 3
CD3E 0.015 0.038 -10000 0 -0.34 5 5
CD3G 0.011 0.053 -10000 0 -0.33 11 11
RASGRP2 -0.006 0.038 -10000 0 -0.15 28 28
RASGRP1 -0.014 0.1 0.24 7 -0.34 21 28
HLA-A 0.019 0.013 -10000 0 -10000 0 0
RASSF5 0.018 0.023 -10000 0 -0.32 2 2
RAP1A/GTP/RAPL 0.025 0.017 -10000 0 -0.19 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.012 0.049 0.13 34 -0.12 7 41
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.015 0.035 -10000 0 -0.15 16 16
PRKCA -0.008 0.054 0.16 6 -0.23 7 13
GRAP2 0.01 0.057 -10000 0 -0.32 14 14
mol:IP3 0.013 0.087 0.17 41 -0.29 17 58
EntrezGene:6957 -0.001 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.009 0.078 -10000 0 -0.36 14 14
ORAI1 -0.025 0.21 0.37 4 -0.98 20 24
CSK -0.002 0.11 0.27 3 -0.38 21 24
B7 family/CD28 0.015 0.12 0.24 1 -0.41 25 26
CHUK 0.021 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.006 0.12 -10000 0 -0.39 25 25
PTPN6 -0.007 0.1 0.21 5 -0.38 19 24
VAV1 -0.006 0.11 0.23 2 -0.37 24 26
Monovalent TCR/CD3 0.001 0.049 -10000 0 -0.26 12 12
CBL 0.02 0.005 -10000 0 -10000 0 0
LCK 0.002 0.11 0.26 9 -0.4 17 26
PAG1 0.004 0.11 0.24 12 -0.36 21 33
RAP1A 0.02 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.006 0.11 0.2 1 -0.39 23 24
CD80 0.013 0.049 -10000 0 -0.32 10 10
CD86 0.013 0.047 -10000 0 -0.32 9 9
PDK1/CARD11/BCL10/MALT1 0.003 0.05 0.13 5 -0.17 15 20
HRAS 0.021 0.004 -10000 0 -10000 0 0
GO:0035030 -0.017 0.099 0.19 5 -0.32 31 36
CD8A 0.016 0.039 0.32 1 -0.33 5 6
CD8B 0.018 0.044 0.32 3 -0.33 5 8
PTPRC 0.013 0.047 -10000 0 -0.32 9 9
PDK1/PKC theta -0.014 0.12 0.3 10 -0.36 25 35
CSK/PAG1 0.001 0.11 0.23 15 -0.38 16 31
SOS1 0.021 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.027 0.018 -10000 0 -10000 0 0
GRAP2/SLP76 0.015 0.12 0.23 1 -0.4 20 21
STIM1 -0.002 0.07 1.2 1 -10000 0 1
RAS family/GTP 0.012 0.056 0.17 10 -0.16 12 22
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.007 0.12 -10000 0 -0.43 23 23
mol:DAG -0.02 0.063 0.091 6 -0.24 22 28
RAP1A/GDP 0.008 0.023 0.073 11 -0.06 5 16
PLCG1 0.02 0.005 -10000 0 -10000 0 0
CD247 0.016 0.024 -10000 0 -0.32 2 2
cytotoxic T cell degranulation -0.038 0.23 -10000 0 -0.9 30 30
RAP1A/GTP -0.002 0.015 -10000 0 -0.059 28 28
mol:PI-3-4-5-P3 -0.006 0.11 0.23 8 -0.35 23 31
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.017 0.1 0.22 16 -0.35 18 34
NRAS 0.02 0.005 -10000 0 -10000 0 0
ZAP70 0.017 0.038 -10000 0 -0.32 6 6
GRB2/SOS1 0.03 0.007 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.003 0.097 0.26 2 -0.35 19 21
MALT1 0.019 0.006 -10000 0 -10000 0 0
TRAF6 0.021 0.003 -10000 0 -10000 0 0
CD8 heterodimer 0.026 0.051 0.3 3 -0.32 7 10
CARD11 0.034 0.065 0.32 24 -10000 0 24
PRKCB -0.012 0.06 0.14 2 -0.24 14 16
PRKCE -0.009 0.057 0.16 6 -0.26 7 13
PRKCQ -0.017 0.12 0.24 7 -0.37 30 37
LCP2 0.018 0.027 -10000 0 -0.32 3 3
BCL10 0.021 0.004 -10000 0 -10000 0 0
regulation of survival gene product expression -0.002 0.086 0.23 11 -0.27 21 32
IKK complex 0.007 0.051 0.19 16 -0.13 3 19
RAS family/GDP -0.001 0.009 -10000 0 -0.039 3 3
MAP3K14 -0.005 0.065 0.19 10 -0.23 14 24
PDPK1 -0.004 0.095 0.26 12 -0.3 21 33
TCR/CD3/MHC I/CD8/Fyn -0.014 0.12 -10000 0 -0.45 21 21
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.041 0.041 0.21 7 -0.18 9 16
ER alpha/Gai/GDP/Gbeta gamma -0.032 0.14 -10000 0 -0.46 29 29
AKT1 -0.061 0.23 -10000 0 -0.68 57 57
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.057 0.24 -10000 0 -0.69 57 57
mol:Ca2+ -0.019 0.066 -10000 0 -0.34 16 16
IGF1R 0.02 0.016 -10000 0 -0.32 1 1
E2/ER alpha (dimer)/Striatin 0.025 0.039 0.21 9 -0.19 9 18
SHC1 0.018 0.008 -10000 0 -10000 0 0
apoptosis 0.057 0.22 0.65 57 -10000 0 57
RhoA/GTP -0.023 0.022 -10000 0 -0.15 6 6
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.016 0.12 -10000 0 -0.38 29 29
regulation of stress fiber formation 0.014 0.053 0.24 1 -0.16 11 12
E2/ERA-ERB (dimer) 0.025 0.039 0.21 9 -0.19 9 18
KRAS 0.02 0.006 -10000 0 -10000 0 0
G13/GTP 0.024 0.034 0.2 9 -0.16 7 16
pseudopodium formation -0.014 0.053 0.16 11 -0.24 1 12
E2/ER alpha (dimer)/PELP1 0.024 0.038 0.21 9 -0.18 8 17
GRB2 0.02 0.004 -10000 0 -10000 0 0
GNG2 0.019 0.022 -10000 0 -0.32 2 2
GNAO1 0.021 0.032 0.32 3 -0.32 2 5
HRAS 0.021 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.039 0.16 0.24 3 -0.43 56 59
E2/ER beta (dimer) 0.015 0.011 -10000 0 -0.22 1 1
mol:GDP 0 0.061 0.18 11 -0.19 31 42
mol:NADP -0.039 0.16 0.24 3 -0.43 56 59
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
mol:IP3 -0.02 0.068 -10000 0 -0.35 16 16
IGF-1R heterotetramer 0.02 0.016 -10000 0 -0.32 1 1
PLCB1 -0.006 0.064 -10000 0 -0.35 14 14
PLCB2 -0.009 0.068 -10000 0 -0.36 14 14
IGF1 0.014 0.051 0.32 1 -0.32 10 11
mol:L-citrulline -0.039 0.16 0.24 3 -0.43 56 59
RHOA 0.021 0.004 -10000 0 -10000 0 0
Gai/GDP -0.022 0.15 -10000 0 -0.61 27 27
JNK cascade 0.015 0.011 -10000 0 -0.22 1 1
BCAR1 0.02 0.016 -10000 0 -0.32 1 1
ESR2 0.02 0.016 -10000 0 -0.32 1 1
GNAQ 0.02 0.016 -10000 0 -0.32 1 1
ESR1 0.019 0.06 0.32 9 -0.32 8 17
Gq family/GDP/Gbeta gamma -0.042 0.2 -10000 0 -0.72 36 36
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.012 0.061 -10000 0 -0.6 2 2
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.013 0.11 -10000 0 -0.39 21 21
GNAZ -0.007 0.092 -10000 0 -0.32 38 38
E2/ER alpha (dimer) 0.014 0.041 0.21 9 -0.22 8 17
STRN 0.02 0.016 -10000 0 -0.32 1 1
GNAL 0.018 0.045 0.32 3 -0.32 6 9
PELP1 0.02 0.006 -10000 0 -10000 0 0
MAPK11 -0.013 0.018 0.22 1 -0.19 3 4
GNAI2 0.021 0.004 -10000 0 -10000 0 0
GNAI3 0.02 0.004 -10000 0 -10000 0 0
GNAI1 0.02 0.016 -10000 0 -0.32 1 1
HBEGF -0.042 0.15 0.33 10 -0.44 35 45
cAMP biosynthetic process 0.018 0.038 0.14 11 -0.17 13 24
SRC -0.031 0.13 0.28 1 -0.45 26 27
PI3K 0.029 0.014 -10000 0 -0.23 1 1
GNB1 0.02 0.004 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.019 0.064 -10000 0 -0.29 5 5
SOS1 0.021 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.024 0.089 -10000 0 -0.34 21 21
Gs family/GTP 0.024 0.041 0.16 11 -0.17 13 24
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.035 0.014 -10000 0 -10000 0 0
vasodilation -0.036 0.15 0.23 3 -0.41 56 59
mol:DAG -0.02 0.068 -10000 0 -0.35 16 16
Gs family/GDP/Gbeta gamma 0.001 0.061 -10000 0 -0.27 9 9
MSN -0.015 0.054 0.16 11 -0.26 1 12
Gq family/GTP 0.002 0.069 -10000 0 -0.36 15 15
mol:PI-3-4-5-P3 -0.054 0.23 -10000 0 -0.67 57 57
NRAS 0.02 0.005 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.036 0.15 0.41 56 -0.23 3 59
GRB2/SOS1 0.03 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.008 0.067 0.19 9 -0.24 10 19
NOS3 -0.041 0.17 0.24 3 -0.45 56 59
GNA11 0.019 0.016 -10000 0 -0.32 1 1
MAPKKK cascade -0.031 0.16 0.32 2 -0.47 51 53
E2/ER alpha (dimer)/PELP1/Src -0.019 0.13 0.24 4 -0.4 28 32
ruffle organization -0.014 0.053 0.16 11 -0.24 1 12
ROCK2 -0.01 0.058 0.18 12 -10000 0 12
GNA14 0.013 0.051 -10000 0 -0.32 11 11
GNA15 0.02 0.006 -10000 0 -10000 0 0
GNA13 0.021 0.004 -10000 0 -10000 0 0
MMP9 -0.021 0.13 0.35 6 -0.42 25 31
MMP2 -0.032 0.13 0.26 8 -0.44 24 32
Caspase cascade in apoptosis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TOP1 -0.016 0.098 0.25 1 -0.34 24 25
ACTA1 -0.023 0.087 0.2 3 -0.29 30 33
NUMA1 -0.01 0.083 0.25 1 -0.33 18 19
SPTAN1 -0.026 0.088 0.2 2 -0.29 33 35
LIMK1 -0.022 0.092 0.22 10 -0.29 31 41
BIRC3 0.021 0.035 0.32 4 -0.32 2 6
BIRC2 0.02 0.004 -10000 0 -10000 0 0
BAX 0.02 0.004 -10000 0 -10000 0 0
CASP10 -0.03 0.049 -10000 0 -0.21 30 30
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.021 0.003 -10000 0 -10000 0 0
PTK2 -0.012 0.081 0.22 1 -0.35 15 16
DIABLO 0.021 0.003 -10000 0 -10000 0 0
apoptotic nuclear changes -0.026 0.086 0.2 2 -0.29 33 35
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.022 0.014 0.32 1 -10000 0 1
GSN -0.027 0.087 0.21 1 -0.29 33 34
MADD 0.021 0.003 -10000 0 -10000 0 0
TFAP2A 0.086 0.14 0.37 1 -0.48 20 21
BID -0.012 0.037 -10000 0 -0.15 28 28
MAP3K1 -0.014 0.086 -10000 0 -0.41 18 18
TRADD 0.021 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.03 0.007 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.025 0.088 0.21 6 -0.29 32 38
CASP9 0.021 0.004 -10000 0 -10000 0 0
DNA repair 0 0.037 0.17 4 -10000 0 4
neuron apoptosis -0.01 0.13 -10000 0 -0.64 18 18
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.018 0.091 0.27 2 -0.36 18 20
APAF1 0.021 0.003 -10000 0 -10000 0 0
CASP6 -0.007 0.12 -10000 0 -0.84 7 7
TRAF2 0.021 0.004 -10000 0 -10000 0 0
ICAD/CAD -0.028 0.091 0.33 5 -0.29 31 36
CASP7 -0.004 0.064 0.28 1 -0.32 5 6
KRT18 0.012 0.036 -10000 0 -0.49 1 1
apoptosis -0.023 0.092 0.35 1 -0.4 16 17
DFFA -0.026 0.089 0.23 4 -0.29 33 37
DFFB -0.025 0.089 0.22 5 -0.29 32 37
PARP1 0 0.037 -10000 0 -0.18 4 4
actin filament polymerization 0.004 0.11 0.27 27 -0.32 17 44
TNF 0.011 0.061 0.32 1 -0.32 15 16
CYCS 0.001 0.042 0.15 7 -0.19 4 11
SATB1 -0.013 0.11 -10000 0 -0.8 7 7
SLK -0.027 0.088 0.27 2 -0.29 33 35
p15 BID/BAX 0.004 0.051 0.18 1 -0.27 6 7
CASP2 -0.003 0.041 -10000 0 -0.22 5 5
JNK cascade 0.014 0.086 0.41 18 -10000 0 18
CASP3 -0.024 0.093 0.23 1 -0.3 33 34
LMNB2 -0.01 0.12 -10000 0 -0.41 30 30
RIPK1 0.021 0.004 -10000 0 -10000 0 0
CASP4 0.02 0.004 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.051 0.026 0.22 4 -0.18 2 6
negative regulation of DNA binding 0.086 0.14 0.37 1 -0.48 20 21
stress fiber formation -0.027 0.087 0.27 2 -0.29 33 35
GZMB -0.03 0.059 -10000 0 -0.25 30 30
CASP1 0.005 0.026 -10000 0 -0.25 5 5
LMNB1 0.001 0.11 0.26 3 -0.45 17 20
APP -0.01 0.13 -10000 0 -0.64 18 18
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.009 0.01 -10000 0 -0.22 1 1
VIM -0.019 0.092 -10000 0 -0.4 16 16
LMNA 0.006 0.067 0.24 1 -0.35 6 7
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.003 0.048 -10000 0 -0.22 10 10
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.025 0.089 0.19 5 -0.29 33 38
APAF-1/Caspase 9 0.002 0.097 -10000 0 -0.64 10 10
nuclear fragmentation during apoptosis -0.01 0.082 0.25 1 -0.32 18 19
CFL2 -0.004 0.11 0.31 18 -0.27 27 45
GAS2 -0.028 0.094 0.21 6 -0.3 34 40
positive regulation of apoptosis -0.001 0.11 0.2 1 -0.44 15 16
PRF1 0.005 0.073 -10000 0 -0.32 23 23
BARD1 signaling events

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
BARD1/CSTF1 0.028 0.021 0.23 1 -0.23 2 3
ATM 0.02 0.004 -10000 0 -10000 0 0
UBE2D3 0.021 0.003 -10000 0 -10000 0 0
PRKDC 0.019 0.006 -10000 0 -10000 0 0
ATR 0.021 0.003 -10000 0 -10000 0 0
UBE2L3 0.02 0.005 -10000 0 -10000 0 0
FANCD2 0.011 0.009 -10000 0 -10000 0 0
protein ubiquitination 0.099 0.077 0.21 141 -0.17 1 142
XRCC5 0.021 0.003 -10000 0 -10000 0 0
XRCC6 0.02 0.004 -10000 0 -10000 0 0
M/R/N Complex 0.036 0.017 -10000 0 -10000 0 0
MRE11A 0.02 0.004 -10000 0 -10000 0 0
DNA-PK 0.038 0.015 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0 0.086 -10000 0 -0.44 12 12
FANCF 0.021 0.003 -10000 0 -10000 0 0
BRCA1 0.021 0.014 0.32 1 -10000 0 1
CCNE1 0.11 0.14 0.32 152 -10000 0 152
CDK2/Cyclin E1 0.089 0.094 0.23 147 -10000 0 147
FANCG 0.02 0.004 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.03 0.022 0.23 2 -0.23 2 4
FANCE 0.021 0.004 -10000 0 -10000 0 0
FANCC 0.02 0.004 -10000 0 -10000 0 0
NBN 0.019 0.007 -10000 0 -10000 0 0
FANCA 0.03 0.055 0.32 17 -10000 0 17
DNA repair 0.004 0.068 0.23 5 -0.34 6 11
BRCA1/BARD1/ubiquitin 0.03 0.022 0.23 2 -0.23 2 4
BARD1/DNA-PK 0.047 0.024 -10000 0 -0.18 2 2
FANCL 0.021 0.002 -10000 0 -10000 0 0
mRNA polyadenylation -0.028 0.021 0.22 2 -0.23 1 3
BRCA1/BARD1/CTIP/M/R/N Complex 0.013 0.039 -10000 0 -0.21 7 7
BRCA1/BACH1/BARD1/TopBP1 0.041 0.021 0.22 2 -0.19 2 4
BRCA1/BARD1/P53 0.048 0.024 0.22 1 -0.18 2 3
BARD1/CSTF1/BRCA1 0.039 0.023 0.22 2 -0.19 2 4
BRCA1/BACH1 0.021 0.014 0.32 1 -10000 0 1
BARD1 0.02 0.026 0.32 1 -0.32 2 3
PCNA 0.021 0.014 0.32 1 -10000 0 1
BRCA1/BARD1/UbcH5C 0.041 0.021 0.22 2 -0.19 2 4
BRCA1/BARD1/UbcH7 0.039 0.019 -10000 0 -0.19 2 2
BRCA1/BARD1/RAD51/PCNA 0.076 0.073 0.23 78 -0.18 2 80
BARD1/DNA-PK/P53 0.05 0.03 -10000 0 -0.17 2 2
BRCA1/BARD1/Ubiquitin 0.03 0.022 0.23 2 -0.23 2 4
BRCA1/BARD1/CTIP 0.028 0.02 0.21 2 -0.17 2 4
FA complex 0.01 0.043 0.25 1 -0.19 12 13
BARD1/EWS 0.029 0.02 0.23 1 -0.23 2 3
RBBP8 -0.015 0.005 -10000 0 -10000 0 0
TP53 0.02 0.006 -10000 0 -10000 0 0
TOPBP1 0.021 0.003 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.046 0.024 0.18 2 -0.22 1 3
BRCA1/BARD1 0.11 0.083 0.22 141 -0.17 1 142
CSTF1 0.02 0.005 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.015 0.018 0.21 1 -0.22 2 3
CDK2 0.021 0.003 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.07 0.11 0.32 82 -10000 0 82
RAD50 0.02 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.03 0.022 0.23 2 -0.23 2 4
EWSR1 0.02 0.004 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.024 0.049 0.23 6 -0.23 14 20
CRKL -0.002 0.096 0.29 5 -0.43 12 17
mol:PIP3 0.007 0.039 -10000 0 -0.83 1 1
AKT1 0.003 0.052 -10000 0 -0.73 1 1
PTK2B 0.018 0.008 -10000 0 -10000 0 0
RAPGEF1 -0.005 0.09 0.27 5 -0.4 12 17
RANBP10 0.021 0.004 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.028 0.065 0.22 10 -0.2 30 40
MAP3K5 -0.003 0.096 0.27 6 -0.41 13 19
HGF/MET/CIN85/CBL/ENDOPHILINS 0.035 0.065 0.22 9 -0.18 31 40
AP1 -0.02 0.06 0.15 1 -0.2 30 31
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.018 0.008 -10000 0 -10000 0 0
apoptosis -0.058 0.23 -10000 0 -0.71 54 54
STAT3 (dimer) -0.01 0.075 0.22 1 -0.28 14 15
GAB1/CRKL/SHP2/PI3K 0.022 0.093 0.28 2 -0.38 13 15
INPP5D 0.019 0.027 -10000 0 -0.32 3 3
CBL/CRK 0.006 0.092 0.35 2 -0.39 12 14
PTPN11 0.021 0.004 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.02 0.005 -10000 0 -10000 0 0
PTEN 0.021 0.004 -10000 0 -10000 0 0
ELK1 0.005 0.092 0.29 37 -10000 0 37
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.004 0.046 0.14 1 -0.23 7 8
PAK1 0.005 0.063 0.39 2 -0.7 1 3
HGF/MET/RANBP10 0.026 0.067 0.22 10 -0.2 33 43
HRAS -0.008 0.11 0.28 1 -0.48 21 22
DOCK1 -0.005 0.094 0.28 7 -0.41 12 19
GAB1 -0.002 0.089 0.23 2 -0.42 11 13
CRK -0.006 0.093 0.37 2 -0.42 12 14
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.01 0.12 -10000 0 -0.42 36 36
JUN 0.018 0.031 -10000 0 -0.32 4 4
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.003 0.051 0.15 5 -0.18 32 37
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
cell morphogenesis -0.012 0.095 0.3 12 -0.32 12 24
GRB2/SHC 0.019 0.052 0.21 1 -0.17 23 24
FOS -0.001 0.083 -10000 0 -0.32 31 31
GLMN 0.002 0.001 -10000 0 -10000 0 0
cell motility 0.005 0.091 0.29 37 -10000 0 37
HGF/MET/MUC20 0.015 0.063 0.21 10 -0.19 34 44
cell migration 0.018 0.052 0.2 1 -0.17 23 24
GRB2 0.02 0.004 -10000 0 -10000 0 0
CBL 0.02 0.005 -10000 0 -10000 0 0
MET/RANBP10 0.023 0.051 0.23 6 -0.23 15 21
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.001 0.06 0.17 1 -0.21 29 30
MET/MUC20 0.01 0.047 0.21 6 -0.22 15 21
RAP1B 0 0.092 0.25 8 -0.38 12 20
RAP1A -0.008 0.086 0.26 6 -0.38 12 18
HGF/MET/RANBP9 0.027 0.067 0.22 10 -0.2 32 42
RAF1 -0.008 0.11 0.26 1 -0.46 22 23
STAT3 -0.011 0.075 0.22 1 -0.28 14 15
cell proliferation 0.002 0.11 0.29 18 -0.31 25 43
RPS6KB1 0.004 0.029 -10000 0 -0.25 2 2
MAPK3 -0.005 0.076 0.35 10 -10000 0 10
MAPK1 0.014 0.14 0.52 26 -10000 0 26
RANBP9 0.021 0.003 -10000 0 -10000 0 0
MAPK8 0.001 0.09 0.26 5 -0.36 13 18
SRC -0.015 0.058 0.15 1 -0.21 23 24
PI3K 0.019 0.058 0.21 1 -0.18 28 29
MET/Glomulin 0.01 0.048 0.23 6 -0.19 15 21
SOS1 0.021 0.003 -10000 0 -10000 0 0
MAP2K1 -0.01 0.11 0.25 1 -0.44 21 22
MET 0.013 0.068 0.32 6 -0.32 15 21
MAP4K1 -0.001 0.1 0.28 6 -0.44 13 19
PTK2 0.018 0.007 -10000 0 -10000 0 0
MAP2K2 -0.011 0.1 0.25 1 -0.44 21 22
BAD -0.001 0.053 0.4 1 -0.7 1 2
MAP2K4 -0.006 0.089 0.26 6 -0.38 13 19
SHP2/GRB2/SOS1/GAB1 0.012 0.089 -10000 0 -0.33 20 20
INPPL1 0.021 0.004 -10000 0 -10000 0 0
PXN 0.021 0.003 -10000 0 -10000 0 0
SH3KBP1 0.02 0.004 -10000 0 -10000 0 0
HGS -0.012 0.046 0.14 5 -0.17 31 36
PLCgamma1/PKC 0.015 0.004 -10000 0 -10000 0 0
HGF 0.008 0.075 0.32 4 -0.32 21 25
RASA1 0.02 0.005 -10000 0 -10000 0 0
NCK1 0.021 0.003 -10000 0 -10000 0 0
PTPRJ 0.021 0.003 -10000 0 -10000 0 0
NCK/PLCgamma1 0.019 0.059 0.21 1 -0.18 30 31
PDPK1 0.005 0.047 -10000 0 -0.77 1 1
HGF/MET/SHIP 0.026 0.071 0.22 9 -0.21 33 42
S1P1 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
VEGFR2 homodimer/VEGFA homodimer 0.019 0.042 -10000 0 -0.23 11 11
PDGFRB 0.015 0.015 -10000 0 -10000 0 0
SPHK1 0.001 0.05 -10000 0 -0.64 2 2
mol:S1P -0.006 0.049 -10000 0 -0.55 2 2
S1P1/S1P/Gi -0.038 0.13 -10000 0 -0.37 50 50
GNAO1 0.017 0.035 0.31 3 -0.33 2 5
PDGFB-D/PDGFRB/PLCgamma1 -0.031 0.13 0.26 5 -0.34 49 54
PLCG1 -0.045 0.12 0.28 1 -0.36 49 50
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.015 0.015 -10000 0 -10000 0 0
GNAI2 0.016 0.016 -10000 0 -10000 0 0
GNAI3 0.016 0.015 -10000 0 -10000 0 0
GNAI1 0.016 0.022 -10000 0 -0.32 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.018 0.028 -10000 0 -0.19 11 11
S1P1/S1P -0.019 0.058 0.21 1 -0.31 5 6
negative regulation of cAMP metabolic process -0.037 0.13 -10000 0 -0.36 50 50
MAPK3 -0.061 0.17 0.27 9 -0.54 48 57
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
RhoA/GDP 0.015 0.003 -10000 0 -10000 0 0
KDR 0.009 0.052 -10000 0 -0.32 11 11
PLCB2 -0.015 0.064 0.22 5 -0.27 7 12
RAC1 0.019 0.007 -10000 0 -10000 0 0
RhoA/GTP -0.011 0.05 -10000 0 -0.28 5 5
receptor internalization -0.02 0.052 0.15 1 -0.3 5 6
PTGS2 -0.09 0.28 0.29 8 -0.88 50 58
Rac1/GTP -0.011 0.049 -10000 0 -0.28 5 5
RHOA 0.021 0.004 -10000 0 -10000 0 0
VEGFA 0.017 0.014 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.037 0.13 -10000 0 -0.36 50 50
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ -0.011 0.092 -10000 0 -0.32 38 38
MAPK1 -0.059 0.17 0.23 6 -0.52 49 55
S1P1/S1P/PDGFB-D/PDGFRB -0.008 0.071 0.25 3 -0.27 8 11
ABCC1 0.016 0.014 -10000 0 -10000 0 0
BCR 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
JUN 0.032 0.1 0.24 26 -0.38 9 35
IKBKB 0.025 0.09 0.24 8 -0.28 16 24
AKT1 0.032 0.074 0.23 27 -0.22 1 28
IKBKG 0.03 0.067 0.23 6 -0.26 7 13
CALM1 0.018 0.08 0.25 7 -0.43 6 13
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
MAP3K1 0.04 0.12 0.26 29 -0.47 7 36
MAP3K7 0.019 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0.018 0.084 0.21 2 -0.42 8 10
DOK1 0.021 0.002 -10000 0 -10000 0 0
AP-1 0.019 0.073 0.22 10 -0.25 5 15
LYN 0.019 0.006 -10000 0 -10000 0 0
BLNK 0.019 0.022 -10000 0 -0.32 2 2
SHC1 0.018 0.008 -10000 0 -10000 0 0
BCR complex 0.068 0.093 0.25 90 -0.32 2 92
CD22 0.012 0.066 0.24 11 -0.4 3 14
CAMK2G 0.014 0.076 0.25 6 -0.4 6 12
CSNK2A1 0.02 0.005 -10000 0 -10000 0 0
INPP5D 0.019 0.027 -10000 0 -0.32 3 3
SHC/GRB2/SOS1 -0.006 0.047 0.15 7 -10000 0 7
GO:0007205 0.018 0.086 0.21 2 -0.43 8 10
SYK 0.019 0.022 -10000 0 -0.32 2 2
ELK1 0.015 0.081 0.23 3 -0.48 5 8
NFATC1 0.034 0.091 0.24 19 -0.36 6 25
B-cell antigen/BCR complex 0.068 0.093 0.25 90 -0.32 2 92
PAG1/CSK 0.027 0.016 -10000 0 -0.23 1 1
NFKBIB 0.022 0.04 0.14 5 -0.13 11 16
HRAS 0.022 0.072 0.23 8 -0.35 4 12
NFKBIA 0.022 0.039 0.14 5 -0.13 10 15
NF-kappa-B/RelA/I kappa B beta 0.025 0.035 0.14 5 -10000 0 5
RasGAP/Csk 0.078 0.079 0.23 85 -0.15 1 86
mol:GDP 0.017 0.087 0.21 2 -0.42 8 10
PTEN 0.021 0.004 -10000 0 -10000 0 0
CD79B 0.025 0.041 0.32 8 -0.32 1 9
NF-kappa-B/RelA/I kappa B alpha 0.025 0.035 0.14 5 -10000 0 5
GRB2 0.02 0.004 -10000 0 -10000 0 0
PI3K/BCAP/CD19 0.048 0.11 0.3 11 -0.48 6 17
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
mol:IP3 0.02 0.082 0.22 1 -0.43 7 8
CSK 0.021 0.004 -10000 0 -10000 0 0
FOS 0.004 0.085 0.25 5 -0.41 7 12
CHUK 0.026 0.075 0.22 7 -0.26 13 20
IBTK 0.019 0.006 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.037 0.074 -10000 0 -0.33 5 5
PTPN6 0.005 0.063 0.22 11 -0.37 4 15
RELA 0.021 0.004 -10000 0 -10000 0 0
BCL2A1 0.016 0.026 0.12 1 -10000 0 1
VAV2 0.046 0.086 0.25 16 -0.44 3 19
ubiquitin-dependent protein catabolic process 0.023 0.039 0.14 5 -0.12 12 17
BTK -0.049 0.26 -10000 0 -0.98 35 35
CD19 0.045 0.082 0.26 21 -0.38 2 23
MAP4K1 0.017 0.031 -10000 0 -0.32 4 4
CD72 0.019 0.016 -10000 0 -0.32 1 1
PAG1 0.018 0.017 -10000 0 -0.32 1 1
MAPK14 0.04 0.11 0.26 35 -0.41 6 41
SH3BP5 0.018 0.031 -10000 0 -0.32 4 4
PIK3AP1 0.02 0.085 0.23 1 -0.47 7 8
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.016 0.13 0.21 1 -0.61 11 12
RAF1 0.016 0.069 0.23 6 -0.33 4 10
RasGAP/p62DOK/SHIP 0.074 0.074 0.35 7 -0.21 3 10
CD79A 0.073 0.12 0.32 89 -0.32 3 92
re-entry into mitotic cell cycle 0.019 0.072 0.21 11 -0.25 5 16
RASA1 0.02 0.005 -10000 0 -10000 0 0
MAPK3 0.012 0.066 0.22 7 -0.31 3 10
MAPK1 0.013 0.063 0.23 9 -0.35 2 11
CD72/SHP1 0.021 0.084 0.23 22 -0.35 4 26
NFKB1 0.021 0.003 -10000 0 -10000 0 0
MAPK8 0.036 0.11 0.25 31 -0.41 6 37
actin cytoskeleton organization 0.059 0.097 0.26 41 -0.42 2 43
NF-kappa-B/RelA 0.049 0.069 0.25 5 -0.21 7 12
Calcineurin 0.032 0.072 0.22 2 -0.39 4 6
PI3K 0.004 0.063 0.18 7 -0.28 4 11
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.023 0.077 0.25 1 -0.52 5 6
SOS1 0.021 0.003 -10000 0 -10000 0 0
Bam32/HPK1 0.036 0.12 -10000 0 -0.6 12 12
DAPP1 0.024 0.13 -10000 0 -0.66 12 12
cytokine secretion 0.034 0.088 0.24 19 -0.33 6 25
mol:DAG 0.02 0.082 0.22 1 -0.43 7 8
PLCG2 0.018 0.027 -10000 0 -0.32 3 3
MAP2K1 0.012 0.066 0.23 6 -0.34 3 9
B-cell antigen/BCR complex/FcgammaRIIB 0.069 0.083 0.24 86 -0.17 2 88
mol:PI-3-4-5-P3 0.015 0.065 0.18 18 -0.24 2 20
ETS1 0.011 0.072 0.24 9 -0.34 6 15
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.08 0.08 0.24 85 -0.24 2 87
B-cell antigen/BCR complex/LYN 0.029 0.062 0.28 7 -0.39 3 10
MALT1 0.019 0.006 -10000 0 -10000 0 0
TRAF6 0.021 0.003 -10000 0 -10000 0 0
RAC1 0.056 0.097 0.28 34 -0.45 2 36
B-cell antigen/BCR complex/LYN/SYK 0.057 0.099 0.34 13 -0.31 4 17
CARD11 0.033 0.093 0.26 14 -0.45 5 19
FCGR2B 0.019 0.007 -10000 0 -10000 0 0
PPP3CA 0.021 0.003 -10000 0 -10000 0 0
BCL10 0.021 0.004 -10000 0 -10000 0 0
IKK complex 0.023 0.046 0.14 27 -0.12 5 32
PTPRC 0.013 0.046 -10000 0 -0.32 9 9
PDPK1 0.019 0.067 0.2 27 -0.2 1 28
PPP3CB 0.021 0.003 -10000 0 -10000 0 0
PPP3CC 0.018 0.008 -10000 0 -10000 0 0
POU2F2 0.019 0.026 0.12 6 -10000 0 6
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.021 0.032 0.32 3 -0.32 2 5
CDC42/GTP -0.011 0.075 -10000 0 -0.26 11 11
PLCG1 -0.019 0.065 0.27 1 -0.22 20 21
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.021 0.004 -10000 0 -10000 0 0
GNAI3 0.02 0.004 -10000 0 -10000 0 0
G12/G13 0.027 0.011 -10000 0 -10000 0 0
cell migration -0.011 0.074 -10000 0 -0.26 11 11
S1PR5 0 0.082 0.32 1 -0.32 29 30
S1PR4 0.008 0.063 -10000 0 -0.32 17 17
MAPK3 -0.019 0.064 -10000 0 -0.22 19 19
MAPK1 -0.016 0.058 -10000 0 -0.2 16 16
S1P/S1P5/Gi -0.016 0.075 -10000 0 -0.19 63 63
GNAI1 0.02 0.016 -10000 0 -0.32 1 1
CDC42/GDP 0.015 0.003 -10000 0 -10000 0 0
S1P/S1P5/G12 0.013 0.049 0.21 1 -0.19 26 27
RHOA -0.001 0.074 0.2 50 -0.17 14 64
S1P/S1P4/Gi -0.013 0.07 -10000 0 -0.21 26 26
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ -0.007 0.092 -10000 0 -0.32 38 38
S1P/S1P4/G12/G13 0.027 0.039 -10000 0 -0.17 15 15
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA13 0.021 0.004 -10000 0 -10000 0 0
CDC42 0.021 0.004 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.013 0.089 0.42 2 -0.38 17 19
CRKL -0.017 0.084 0.48 1 -0.39 20 21
HRAS -0.005 0.077 -10000 0 -0.37 12 12
mol:PIP3 0.005 0.1 0.37 2 -0.41 17 19
SPRED1 0.02 0.005 -10000 0 -10000 0 0
SPRED2 0.021 0.001 -10000 0 -10000 0 0
GAB1 -0.014 0.091 0.32 1 -0.41 20 21
FOXO3 -0.001 0.11 0.32 1 -0.4 23 24
AKT1 0.002 0.12 -10000 0 -0.42 23 23
BAD 0 0.11 -10000 0 -0.4 23 23
megakaryocyte differentiation -0.024 0.097 -10000 0 -0.39 25 25
GSK3B 0 0.11 -10000 0 -0.4 23 23
RAF1 -0.002 0.074 0.22 3 -0.31 12 15
SHC1 0.018 0.008 -10000 0 -10000 0 0
STAT3 -0.015 0.093 0.31 1 -0.41 21 22
STAT1 -0.038 0.2 0.44 1 -0.91 21 22
HRAS/SPRED1 0.009 0.074 -10000 0 -0.31 12 12
cell proliferation -0.014 0.089 -10000 0 -0.4 20 20
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
TEC 0.021 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.001 0.11 -10000 0 -0.42 21 21
HRAS/SPRED2 0.009 0.075 -10000 0 -0.31 12 12
LYN/TEC/p62DOK 0.021 0.093 0.31 1 -0.4 17 18
MAPK3 0 0.065 0.22 5 -0.24 5 10
STAP1 -0.017 0.096 0.31 1 -0.42 21 22
GRAP2 0.011 0.057 -10000 0 -0.32 14 14
JAK2 -0.033 0.18 0.41 1 -0.77 22 23
STAT1 (dimer) -0.036 0.2 0.44 1 -0.89 21 22
mol:Gleevec 0 0.004 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.019 0.094 -10000 0 -0.41 15 15
actin filament polymerization -0.012 0.082 0.31 1 -0.4 16 17
LYN 0.019 0.006 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.03 0.13 0.35 1 -0.55 23 24
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
CBL/CRKL/GRB2 0.009 0.085 0.41 2 -0.37 14 16
PI3K 0.018 0.1 -10000 0 -0.42 18 18
PTEN 0.021 0.004 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.018 0.22 -10000 0 -1.1 20 20
MAPK8 -0.015 0.09 -10000 0 -0.41 20 20
STAT3 (dimer) -0.014 0.091 0.31 1 -0.4 21 22
positive regulation of transcription 0.002 0.057 0.2 7 -0.2 4 11
mol:GDP 0.001 0.08 -10000 0 -0.39 12 12
PIK3C2B -0.013 0.093 0.43 2 -0.43 17 19
CBL/CRKL 0 0.089 0.42 2 -0.38 17 19
FER -0.014 0.091 0.31 1 -0.4 21 22
SH2B3 -0.014 0.091 0.31 1 -0.41 21 22
PDPK1 0.004 0.099 0.33 4 -0.39 16 20
SNAI2 -0.011 0.086 0.31 1 -0.42 17 18
positive regulation of cell proliferation -0.03 0.16 0.4 1 -0.68 22 23
KITLG 0.014 0.037 -10000 0 -0.34 4 4
cell motility -0.03 0.16 0.4 1 -0.68 22 23
PTPN6 0.019 0.011 -10000 0 -10000 0 0
EPOR -0.016 0.15 -10000 0 -0.63 20 20
STAT5A (dimer) -0.022 0.13 0.37 1 -0.55 23 24
SOCS1 0.021 0.014 0.32 1 -10000 0 1
cell migration 0.018 0.092 0.41 21 -10000 0 21
SOS1 0.021 0.003 -10000 0 -10000 0 0
EPO 0.02 0.029 0.32 4 -10000 0 4
VAV1 0.018 0.027 -10000 0 -0.32 3 3
GRB10 -0.013 0.088 0.32 1 -0.42 17 18
PTPN11 0.019 0.01 -10000 0 -10000 0 0
SCF/KIT -0.009 0.098 0.34 1 -0.42 22 23
GO:0007205 0.001 0.005 -10000 0 -10000 0 0
MAP2K1 -0.004 0.064 0.19 7 -0.24 11 18
CBL 0.02 0.005 -10000 0 -10000 0 0
KIT -0.03 0.24 0.46 1 -1.1 23 24
MAP2K2 -0.003 0.063 0.19 7 -0.24 12 19
SHC/Grb2/SOS1 0.017 0.087 -10000 0 -0.41 13 13
STAT5A -0.021 0.14 0.37 1 -0.57 23 24
GRB2 0.02 0.004 -10000 0 -10000 0 0
response to radiation -0.011 0.085 0.31 1 -0.41 17 18
SHC/GRAP2 0.023 0.028 -10000 0 -0.23 5 5
PTPRO -0.024 0.098 -10000 0 -0.4 24 24
SH2B2 -0.012 0.084 0.31 1 -0.4 16 17
DOK1 0.021 0.002 -10000 0 -10000 0 0
MATK -0.018 0.093 -10000 0 -0.42 21 21
CREBBP 0.021 0.032 0.29 1 -10000 0 1
BCL2 -0.037 0.19 0.46 1 -0.7 21 22
Signaling events mediated by HDAC Class III

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
EP300 0.02 0.004 -10000 0 -10000 0 0
HDAC4 0.021 0.003 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.002 0.053 -10000 0 -0.2 28 28
CDKN1A -0.011 0.004 -10000 0 -10000 0 0
KAT2B 0.021 0.004 -10000 0 -10000 0 0
BAX 0.02 0.004 -10000 0 -10000 0 0
FOXO3 -0.003 0.002 -10000 0 -10000 0 0
FOXO1 0.02 0.005 -10000 0 -10000 0 0
FOXO4 0.006 0.002 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.02 0.004 -10000 0 -10000 0 0
TAT 0.046 0.084 0.32 42 -10000 0 42
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.016 0.014 0.15 3 -10000 0 3
PPARGC1A -0.06 0.15 0.32 1 -0.32 115 116
FHL2 0.061 0.1 0.32 65 -10000 0 65
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.03 0.012 0.25 1 -10000 0 1
HIST2H4A -0.002 0.053 0.2 28 -10000 0 28
SIRT1/FOXO3a 0.013 0.029 0.24 1 -0.19 4 5
SIRT1 0.021 0.015 0.35 1 -10000 0 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.036 0.019 0.24 1 -10000 0 1
SIRT1/Histone H1b 0.025 0.04 0.32 1 -0.22 4 5
apoptosis -0.039 0.015 -10000 0 -0.23 1 1
SIRT1/PGC1A -0.022 0.092 0.21 2 -0.19 113 115
p53/SIRT1 0.027 0.025 0.55 1 -10000 0 1
SIRT1/FOXO4 0.017 0.033 0.24 1 -0.22 4 5
FOXO1/FHL2/SIRT1 0.059 0.059 0.21 63 -10000 0 63
HIST1H1E 0.016 0.032 0.23 1 -10000 0 1
SIRT1/p300 0.03 0.012 0.25 1 -10000 0 1
muscle cell differentiation -0.025 0.02 -10000 0 -0.21 5 5
TP53 0.019 0.016 0.35 1 -10000 0 1
KU70/SIRT1/BAX 0.04 0.015 0.24 1 -10000 0 1
CREBBP 0.021 0.004 -10000 0 -10000 0 0
MEF2D 0.018 0.008 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.045 0.056 0.23 40 -10000 0 40
ACSS2 -0.016 0.017 0.27 1 -0.23 1 2
SIRT1/PCAF/MYOD 0.025 0.02 0.21 5 -10000 0 5
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.02 0.004 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.03 0.071 0.29 1 -0.38 1 2
Syndecan-3/Neurocan 0.025 0.047 0.29 5 -0.28 3 8
POMC 0.013 0.072 0.32 6 -0.32 17 23
EGFR 0.015 0.041 0.32 1 -0.32 6 7
Syndecan-3/EGFR 0.016 0.035 0.29 1 -0.29 3 4
AGRP -0.12 0.17 -10000 0 -0.32 195 195
NCSTN 0.019 0.007 -10000 0 -10000 0 0
PSENEN 0.02 0.005 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.019 0.022 -10000 0 -0.32 2 2
APH1A 0.018 0.008 -10000 0 -10000 0 0
NCAN 0.028 0.052 0.32 15 -10000 0 15
long-term memory 0.038 0.038 -10000 0 -0.29 2 2
Syndecan-3/IL8 0.025 0.05 0.25 5 -0.29 3 8
PSEN1 0.02 0.004 -10000 0 -10000 0 0
Src/Cortactin 0.029 0.009 -10000 0 -10000 0 0
FYN 0.019 0.017 -10000 0 -0.32 1 1
limb bud formation 0.005 0.019 -10000 0 -0.4 1 1
MC4R 0.038 0.076 0.32 33 -10000 0 33
SRC 0.02 0.004 -10000 0 -10000 0 0
PTN -0.018 0.12 0.32 5 -0.32 58 63
FGFR/FGF/Syndecan-3 0.005 0.019 -10000 0 -0.4 1 1
neuron projection morphogenesis -0.01 0.071 0.36 5 -0.37 1 6
Syndecan-3/AgRP -0.034 0.08 -10000 0 -0.31 4 4
Syndecan-3/AgRP/MC4R -0.02 0.099 0.27 3 -0.33 3 6
Fyn/Cortactin 0.027 0.011 -10000 0 -10000 0 0
SDC3 0.005 0.019 -10000 0 -0.41 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.024 0.049 0.25 5 -0.29 3 8
IL8 0.028 0.064 0.32 17 -0.32 4 21
Syndecan-3/Fyn/Cortactin 0.039 0.039 -10000 0 -0.3 2 2
Syndecan-3/CASK 0.003 0.024 -10000 0 -0.29 3 3
alpha-MSH/MC4R 0.034 0.07 0.23 34 -0.21 17 51
Gamma Secretase 0.046 0.031 -10000 0 -0.17 1 1
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.026 0.012 -10000 0 -0.19 1 1
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.021 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.03 0.059 0.32 17 -0.32 2 19
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.02 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.015 0.029 0.15 7 -0.16 1 8
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.02 0.005 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.02 0.016 -10000 0 -0.32 1 1
FYN 0.019 0.017 -10000 0 -0.32 1 1
MAP3K12 0.021 0.003 -10000 0 -10000 0 0
FGR -0.002 0.086 -10000 0 -0.32 33 33
p38 alpha/TAB1 -0.036 0.082 -10000 0 -0.28 35 35
PRKG1 -0.015 0.1 -10000 0 -0.32 51 51
DUSP8 0.014 0.049 -10000 0 -0.32 10 10
PGK/cGMP/p38 alpha -0.015 0.11 -10000 0 -0.31 40 40
apoptosis -0.034 0.078 -10000 0 -0.27 35 35
RAL/GTP 0.026 0.009 -10000 0 -10000 0 0
LYN 0.019 0.006 -10000 0 -10000 0 0
DUSP1 -0.012 0.099 -10000 0 -0.32 45 45
PAK1 0.02 0.004 -10000 0 -10000 0 0
SRC 0.02 0.004 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.043 0.024 -10000 0 -0.16 1 1
TRAF6 0.021 0.003 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.019 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.025 0.01 -10000 0 -10000 0 0
MAPK11 -0.002 0.12 0.25 11 -0.3 34 45
BLK 0.06 0.11 0.32 70 -0.32 1 71
HCK 0.007 0.066 -10000 0 -0.32 19 19
MAP2K3 0.02 0.006 -10000 0 -10000 0 0
DUSP16 0.02 0.005 -10000 0 -10000 0 0
DUSP10 0.018 0.023 -10000 0 -0.32 2 2
TRAF6/MEKK3 0.025 0.011 -10000 0 -0.17 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.002 0.11 0.21 13 -0.31 31 44
positive regulation of innate immune response -0.004 0.14 0.27 12 -0.36 32 44
LCK 0.02 0.026 0.32 1 -0.32 2 3
p38alpha-beta/MKP7 0.005 0.13 0.28 10 -0.35 31 41
p38alpha-beta/MKP5 0.005 0.13 0.28 9 -0.35 29 38
PGK/cGMP -0.009 0.072 -10000 0 -0.22 51 51
PAK2 0.02 0.005 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.004 0.14 0.3 8 -0.35 36 44
CDC42 0.021 0.004 -10000 0 -10000 0 0
RALB 0.021 0.003 -10000 0 -10000 0 0
RALA 0.019 0.006 -10000 0 -10000 0 0
PAK3 0.053 0.1 0.32 57 -0.32 4 61
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.037 0.05 0.23 22 -0.23 5 27
AKT1 -0.025 0.1 0.34 4 -0.44 12 16
PTK2B -0.03 0.089 0.33 2 -0.43 12 14
VEGFR2 homodimer/Frs2 -0.012 0.093 -10000 0 -0.47 11 11
CAV1 -0.19 0.16 -10000 0 -0.32 296 296
CALM1 0.02 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.002 0.089 -10000 0 -0.44 11 11
endothelial cell proliferation -0.024 0.12 0.36 9 -0.42 16 25
mol:Ca2+ -0.038 0.077 -10000 0 -0.42 10 10
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.009 0.091 -10000 0 -0.45 11 11
RP11-342D11.1 -0.035 0.078 -10000 0 -0.43 11 11
CDH5 -0.021 0.11 -10000 0 -0.32 59 59
VEGFA homodimer 0.042 0.024 -10000 0 -10000 0 0
SHC1 0.018 0.008 -10000 0 -10000 0 0
SHC2 0.015 0.043 0.32 1 -0.32 7 8
HRAS/GDP 0.005 0.075 -10000 0 -0.37 10 10
SH2D2A 0.019 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.019 0.13 -10000 0 -0.43 30 30
VEGFR2 homodimer/VEGFA homodimer/TsAd 0 0.091 -10000 0 -0.47 11 11
VEGFR1 homodimer 0.02 0.005 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.018 0.085 -10000 0 -0.4 10 10
GRB10 -0.036 0.078 -10000 0 -0.43 11 11
PTPN11 0.021 0.004 -10000 0 -10000 0 0
GRB2 0.02 0.004 -10000 0 -10000 0 0
PAK1 0.02 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.001 0.12 -10000 0 -0.4 26 26
HRAS 0.021 0.004 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.011 0.076 0.19 1 -0.31 18 19
HIF1A 0.021 0.004 -10000 0 -10000 0 0
FRS2 0.02 0.005 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.008 0.09 -10000 0 -0.44 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.011 0.055 -10000 0 -0.32 13 13
Nck/Pak 0.03 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.001 0.092 -10000 0 -0.45 11 11
mol:GDP 0.01 0.08 -10000 0 -0.38 10 10
mol:NADP -0.025 0.13 0.36 6 -0.4 33 39
eNOS/Hsp90 -0.016 0.12 0.39 3 -0.38 30 33
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
mol:IP3 -0.038 0.078 -10000 0 -0.42 10 10
HIF1A/ARNT 0.025 0.013 -10000 0 -10000 0 0
SHB 0.02 0.006 -10000 0 -10000 0 0
VEGFA 0.021 0.004 -10000 0 -10000 0 0
VEGFC 0.02 0.026 0.32 1 -0.32 2 3
FAK1/Vinculin -0.014 0.12 0.31 5 -0.46 16 21
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.017 0.11 0.32 1 -0.45 12 13
PTPN6 0.02 0.005 -10000 0 -10000 0 0
EPAS1 -0.023 0.12 -10000 0 -0.33 63 63
mol:L-citrulline -0.025 0.13 0.36 6 -0.4 33 39
ITGAV 0.021 0.002 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.012 0.088 -10000 0 -0.4 11 11
VEGFR2 homodimer/VEGFA homodimer 0.002 0.093 -10000 0 -0.47 11 11
VEGFR2/3 heterodimer -0.017 0.11 -10000 0 -0.49 15 15
VEGFB 0.021 0.003 -10000 0 -10000 0 0
MAPK11 -0.028 0.091 0.36 3 -0.45 11 14
VEGFR2 homodimer -0.046 0.1 -10000 0 -0.57 11 11
FLT1 0.02 0.005 -10000 0 -10000 0 0
NEDD4 0.02 0.016 -10000 0 -0.32 1 1
MAPK3 -0.028 0.092 0.32 7 -0.42 10 17
MAPK1 -0.027 0.089 0.28 9 -0.4 10 19
VEGFA145/NRP2 0.029 0.021 -10000 0 -0.22 3 3
VEGFR1/2 heterodimer -0.013 0.097 -10000 0 -0.5 11 11
KDR -0.046 0.1 -10000 0 -0.57 11 11
VEGFA165/NRP1/VEGFR2 homodimer 0.003 0.088 -10000 0 -0.44 11 11
SRC 0.02 0.004 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.025 0.096 0.31 9 -0.42 10 19
PI3K -0.039 0.085 -10000 0 -0.47 11 11
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.002 0.093 -10000 0 -0.47 11 11
FES -0.04 0.081 -10000 0 -0.44 11 11
GAB1 -0.012 0.1 -10000 0 -0.47 12 12
VEGFR2 homodimer/VEGFA homodimer/Src 0.001 0.092 -10000 0 -0.45 11 11
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
SOS1 0.021 0.003 -10000 0 -10000 0 0
ARNT 0.018 0.008 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.088 0.13 -10000 0 -0.44 36 36
VEGFR2 homodimer/VEGFA homodimer/Yes 0.001 0.092 -10000 0 -0.47 11 11
PI3K/GAB1 -0.016 0.1 -10000 0 -0.46 11 11
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.019 0.09 -10000 0 -0.41 11 11
PRKACA 0.02 0.005 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.006 0.1 -10000 0 -0.46 15 15
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
CDC42 -0.039 0.081 -10000 0 -0.44 11 11
actin cytoskeleton reorganization -0.001 0.091 -10000 0 -0.47 11 11
PTK2 -0.024 0.11 0.32 2 -0.5 15 17
EDG1 -0.035 0.078 -10000 0 -0.43 11 11
mol:DAG -0.038 0.078 -10000 0 -0.42 10 10
CaM/Ca2+ -0.037 0.072 -10000 0 -0.4 10 10
MAP2K3 -0.033 0.078 -10000 0 -0.4 10 10
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.012 0.1 -10000 0 -0.45 11 11
PLCG1 -0.039 0.078 -10000 0 -0.43 10 10
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.01 0.091 -10000 0 -0.43 11 11
IQGAP1 0.021 0.003 -10000 0 -10000 0 0
YES1 0.02 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0 0.093 -10000 0 -0.47 11 11
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.001 0.091 -10000 0 -0.45 11 11
cell migration -0.019 0.12 0.31 5 -0.46 16 21
mol:PI-3-4-5-P3 -0.037 0.08 -10000 0 -0.44 11 11
FYN 0.019 0.017 -10000 0 -0.32 1 1
VEGFB/NRP1 -0.037 0.075 -10000 0 -0.41 11 11
mol:NO -0.025 0.13 0.36 6 -0.4 33 39
PXN 0.021 0.003 -10000 0 -10000 0 0
HRAS/GTP -0.042 0.061 -10000 0 -0.37 10 10
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.006 0.085 -10000 0 -0.45 11 11
VHL 0.02 0.004 -10000 0 -10000 0 0
ITGB3 0.031 0.072 0.32 22 -0.32 5 27
NOS3 -0.029 0.14 0.39 5 -0.44 33 38
VEGFR2 homodimer/VEGFA homodimer/Sck -0.002 0.098 -10000 0 -0.45 14 14
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCA -0.036 0.077 -10000 0 -0.4 10 10
PRKCB -0.039 0.085 0.33 1 -0.43 11 12
VCL 0.021 0.003 -10000 0 -10000 0 0
VEGFA165/NRP1 -0.035 0.079 -10000 0 -0.43 11 11
VEGFR1/2 heterodimer/VEGFA homodimer 0 0.093 -10000 0 -0.47 11 11
VEGFA165/NRP2 0.029 0.021 -10000 0 -0.22 3 3
MAPKKK cascade -0.026 0.087 0.32 2 -0.4 8 10
NRP2 0.019 0.027 -10000 0 -0.32 3 3
VEGFC homodimer 0.02 0.026 0.32 1 -0.32 2 3
NCK1 0.021 0.003 -10000 0 -10000 0 0
ROCK1 0.02 0.005 -10000 0 -10000 0 0
FAK1/Paxillin -0.014 0.12 0.29 4 -0.47 16 20
MAP3K13 -0.036 0.077 -10000 0 -0.41 11 11
PDPK1 -0.038 0.075 0.24 2 -0.39 11 13
Signaling events mediated by PRL

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCNE1 0.11 0.14 0.32 152 -10000 0 152
mol:Halofuginone 0.001 0 -10000 0 -10000 0 0
ITGA1 0.017 0.031 -10000 0 -0.32 4 4
CDKN1A 0.004 0.026 -10000 0 -0.32 2 2
PRL-3/alpha Tubulin 0.028 0.014 0.23 1 -10000 0 1
mol:Ca2+ 0.001 0.064 0.16 58 -0.23 6 64
AGT 0.059 0.11 0.32 70 -0.32 5 75
CCNA2 -0.006 0.054 0.31 6 -10000 0 6
TUBA1B 0.021 0.003 -10000 0 -10000 0 0
EGR1 -0.017 0.048 -10000 0 -0.22 27 27
CDK2/Cyclin E1 0.082 0.092 0.31 7 -0.3 3 10
MAPK3 -0.014 0.01 0.15 1 -10000 0 1
PRL-2 /Rab GGTase beta 0.03 0.007 -10000 0 -10000 0 0
MAPK1 -0.014 0.01 0.15 1 -10000 0 1
PTP4A1 -0.021 0.034 -10000 0 -10000 0 0
PTP4A3 0.019 0.015 0.32 1 -10000 0 1
PTP4A2 0.021 0.003 -10000 0 -10000 0 0
ITGB1 -0.014 0.01 0.15 1 -10000 0 1
SRC 0.02 0.004 -10000 0 -10000 0 0
RAC1 0.003 0.033 -10000 0 -0.45 2 2
Rab GGTase beta/Rab GGTase alpha 0.029 0.009 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.018 0.048 -10000 0 -10000 0 0
RABGGTA 0.02 0.005 -10000 0 -10000 0 0
BCAR1 -0.018 0.016 -10000 0 -0.23 2 2
RHOC 0.001 0.044 -10000 0 -0.36 6 6
RHOA -0.001 0.049 -10000 0 -0.33 9 9
cell motility 0.003 0.062 0.27 2 -0.31 8 10
PRL-1/alpha Tubulin -0.019 0.046 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.025 0.022 0.23 1 -0.23 2 3
ROCK1 0.002 0.052 0.27 2 -0.33 5 7
RABGGTB 0.021 0.004 -10000 0 -10000 0 0
CDK2 0.021 0.003 -10000 0 -10000 0 0
mitosis -0.021 0.033 -10000 0 -10000 0 0
ATF5 0.021 0.014 0.32 1 -10000 0 1
IL27-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
TGFB1 0.024 0.017 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.019 0.11 0.44 11 -10000 0 11
IL27/IL27R/JAK1 0.03 0.091 -10000 0 -0.88 1 1
TBX21 -0.024 0.11 0.9 1 -0.43 10 11
IL12B 0.023 0.032 0.31 4 -0.32 1 5
IL12A -0.009 0.023 0.15 1 -0.22 5 6
IL6ST 0.007 0.065 -10000 0 -0.33 17 17
IL27RA/JAK1 0.009 0.058 0.38 1 -1.1 1 2
IL27 0.01 0.058 -10000 0 -0.33 13 13
TYK2 0.021 0.015 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.015 0.12 0.42 3 -10000 0 3
T-helper 2 cell differentiation 0.019 0.11 0.44 11 -10000 0 11
T cell proliferation during immune response 0.019 0.11 0.44 11 -10000 0 11
MAPKKK cascade -0.019 0.11 -10000 0 -0.44 11 11
STAT3 0.021 0.003 -10000 0 -10000 0 0
STAT2 0.021 0.003 -10000 0 -10000 0 0
STAT1 0.02 0.009 -10000 0 -10000 0 0
IL12RB1 0.012 0.053 -10000 0 -0.32 12 12
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.013 0.11 0.38 9 -0.44 6 15
IL27/IL27R/JAK2/TYK2 -0.019 0.11 -10000 0 -0.44 11 11
positive regulation of T cell mediated cytotoxicity -0.019 0.11 -10000 0 -0.44 11 11
STAT1 (dimer) 0.026 0.12 -10000 0 -0.58 5 5
JAK2 0.019 0.025 -10000 0 -0.32 2 2
JAK1 0.02 0.009 -10000 0 -10000 0 0
STAT2 (dimer) -0.011 0.12 0.45 1 -0.41 15 16
T cell proliferation -0.042 0.12 0.34 2 -0.45 18 20
IL12/IL12R/TYK2/JAK2 -0.03 0.23 -10000 0 -0.81 36 36
IL17A -0.018 0.12 0.43 2 -10000 0 2
mast cell activation 0.019 0.11 0.44 11 -10000 0 11
IFNG 0.002 0.041 0.11 32 -0.11 16 48
T cell differentiation -0.001 0.005 0.013 6 -0.02 13 19
STAT3 (dimer) -0.012 0.12 0.45 1 -0.41 14 15
STAT5A (dimer) -0.012 0.12 0.45 1 -0.42 14 15
STAT4 (dimer) -0.012 0.12 0.45 1 -0.4 15 16
STAT4 0.021 0.002 -10000 0 -10000 0 0
T cell activation -0.003 0.006 0.11 1 -10000 0 1
IL27R/JAK2/TYK2 0.027 0.076 -10000 0 -0.61 2 2
GATA3 -0.003 0.09 0.61 6 -1.1 1 7
IL18 -0.011 0.029 -10000 0 -0.22 9 9
positive regulation of mast cell cytokine production -0.012 0.12 0.45 1 -0.4 14 15
IL27/EBI3 0.023 0.048 -10000 0 -0.23 14 14
IL27RA 0 0.057 -10000 0 -1.1 1 1
IL6 -0.044 0.14 -10000 0 -0.32 94 94
STAT5A 0.02 0.016 -10000 0 -0.32 1 1
monocyte differentiation 0 0.002 -10000 0 -10000 0 0
IL2 -0.008 0.033 0.4 2 -10000 0 2
IL1B -0.02 0.049 -10000 0 -0.22 28 28
EBI3 0.02 0.021 -10000 0 -0.32 1 1
TNF -0.013 0.038 0.15 1 -0.22 15 16
Class I PI3K 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
ARF5/GTP -0.011 0.061 0.24 3 -10000 0 3
DAPP1 -0.017 0.11 0.21 4 -0.33 35 39
Src family/SYK family/BLNK-LAT/BTK-ITK -0.033 0.16 -10000 0 -0.48 41 41
mol:DAG -0.013 0.07 0.17 13 -0.22 20 33
HRAS 0.021 0.007 -10000 0 -10000 0 0
RAP1A 0.021 0.007 -10000 0 -10000 0 0
ARF5/GDP -0.002 0.089 -10000 0 -0.33 19 19
PLCG2 0.018 0.027 -10000 0 -0.32 3 3
PLCG1 0.02 0.005 -10000 0 -10000 0 0
ARF5 0.02 0.004 -10000 0 -10000 0 0
mol:GTP -0.016 0.046 0.15 32 -10000 0 32
ARF1/GTP -0.009 0.044 0.21 6 -0.18 2 8
RHOA 0.021 0.004 -10000 0 -10000 0 0
YES1 0.02 0.005 -10000 0 -10000 0 0
RAP1A/GTP -0.016 0.046 0.15 30 -10000 0 30
ADAP1 -0.017 0.047 0.2 7 -0.27 1 8
ARAP3 -0.016 0.046 0.15 32 -10000 0 32
INPPL1 0.021 0.004 -10000 0 -10000 0 0
PREX1 0.017 0.031 -10000 0 -0.32 4 4
ARHGEF6 0.009 0.063 -10000 0 -0.32 17 17
ARHGEF7 0.02 0.005 -10000 0 -10000 0 0
ARF1 0.02 0.006 -10000 0 -10000 0 0
NRAS 0.02 0.007 -10000 0 -10000 0 0
FYN 0.019 0.017 -10000 0 -0.32 1 1
ARF6 0.02 0.004 -10000 0 -10000 0 0
FGR -0.002 0.086 -10000 0 -0.32 33 33
mol:Ca2+ -0.01 0.039 0.12 8 -0.13 8 16
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.016 0.038 -10000 0 -0.32 6 6
ZAP70 0.017 0.038 -10000 0 -0.32 6 6
mol:IP3 -0.015 0.052 0.15 8 -0.16 17 25
LYN 0.019 0.006 -10000 0 -10000 0 0
ARF1/GDP 0.001 0.083 -10000 0 -0.32 16 16
RhoA/GDP -0.01 0.063 0.21 5 -0.25 4 9
PDK1/Src/Hsp90 0.039 0.013 -10000 0 -10000 0 0
BLNK 0.019 0.022 -10000 0 -0.32 2 2
actin cytoskeleton reorganization -0.006 0.083 0.27 6 -0.3 14 20
SRC 0.02 0.004 -10000 0 -10000 0 0
PLEKHA2 -0.017 0.011 -10000 0 -0.19 1 1
RAC1 0.019 0.007 -10000 0 -10000 0 0
PTEN 0.019 0.014 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.022 0.045 0.28 1 -10000 0 1
RhoA/GTP -0.018 0.047 0.22 4 -10000 0 4
Src family/SYK family/BLNK-LAT -0.014 0.11 -10000 0 -0.34 27 27
BLK 0.06 0.11 0.32 70 -0.32 1 71
PDPK1 0.021 0.003 -10000 0 -10000 0 0
CYTH1 -0.018 0.046 0.2 7 -10000 0 7
HCK 0.007 0.066 -10000 0 -0.32 19 19
CYTH3 -0.016 0.047 0.19 9 -10000 0 9
CYTH2 -0.019 0.047 0.2 7 -10000 0 7
KRAS 0.02 0.007 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0 0.049 -10000 0 -0.34 6 6
SGK1 -0.015 0.099 -10000 0 -0.33 38 38
INPP5D 0.019 0.027 -10000 0 -0.32 3 3
mol:GDP -0.012 0.09 0.18 2 -0.33 21 23
SOS1 0.021 0.003 -10000 0 -10000 0 0
SYK 0.019 0.022 -10000 0 -0.32 2 2
ARF6/GDP -0.011 0.059 0.2 6 -0.24 3 9
mol:PI-3-4-5-P3 -0.017 0.042 0.18 4 -10000 0 4
ARAP3/RAP1A/GTP -0.016 0.046 0.16 30 -10000 0 30
VAV1 0.018 0.027 -10000 0 -0.32 3 3
mol:PI-3-4-P2 -0.017 0.017 -10000 0 -0.23 3 3
RAS family/GTP/PI3K Class I -0.021 0.034 0.18 10 -10000 0 10
PLEKHA1 -0.02 0.014 -10000 0 -0.19 3 3
Rac1/GDP -0.002 0.085 -10000 0 -0.34 17 17
LAT 0.021 0.014 0.32 1 -10000 0 1
Rac1/GTP -0.003 0.091 0.2 1 -0.36 22 23
ITK -0.023 0.045 0.17 4 -10000 0 4
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.023 0.09 0.22 6 -0.29 23 29
LCK 0.02 0.026 0.32 1 -0.32 2 3
BTK -0.027 0.055 0.18 6 -0.28 2 8
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0.028 0.031 0.2 10 -0.17 3 13
EFNA5 0.019 0.033 0.32 2 -0.32 3 5
FYN -0.012 0.029 0.18 8 -0.17 2 10
neuron projection morphogenesis 0.028 0.031 0.2 10 -0.17 3 13
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.029 0.031 0.21 10 -0.17 3 13
EPHA5 0.025 0.041 0.32 9 -10000 0 9
IL2 signaling events mediated by STAT5

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
GAB2 0.018 0.031 -10000 0 -0.32 4 4
ELF1 0.032 0.039 -10000 0 -10000 0 0
CCNA2 0.091 0.13 0.32 115 -10000 0 115
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
JAK3 0.02 0.005 -10000 0 -10000 0 0
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
JAK1 0.021 0.004 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.017 0.069 -10000 0 -0.4 4 4
SHC1 0.018 0.008 -10000 0 -10000 0 0
SP1 0.017 0.044 -10000 0 -0.3 9 9
IL2RA 0.009 0.079 0.3 34 -10000 0 34
IL2RB 0.019 0.022 -10000 0 -0.32 2 2
SOS1 0.021 0.003 -10000 0 -10000 0 0
IL2RG 0.018 0.035 -10000 0 -0.32 5 5
G1/S transition of mitotic cell cycle 0.027 0.11 0.3 14 -0.46 11 25
PTPN11 0.021 0.004 -10000 0 -10000 0 0
CCND2 -0.024 0.077 -10000 0 -0.59 9 9
LCK 0.02 0.026 0.32 1 -0.32 2 3
GRB2 0.021 0.004 -10000 0 -10000 0 0
IL2 0.019 0.003 -10000 0 -10000 0 0
CDK6 0.019 0.022 -10000 0 -0.32 2 2
CCND3 0.019 0.076 0.38 3 -0.38 3 6
PDGFR-beta signaling pathway

Figure S87.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S87.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.001 0.077 0.26 2 -0.31 18 20
PDGFB-D/PDGFRB/SLAP 0.022 0.034 -10000 0 -0.22 8 8
PDGFB-D/PDGFRB/APS/CBL 0.038 0.018 -10000 0 -0.2 1 1
AKT1 -0.012 0.078 0.34 12 -10000 0 12
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.005 0.093 0.28 5 -0.35 19 24
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
FGR -0.03 0.15 0.32 2 -0.48 41 43
mol:Ca2+ -0.003 0.1 0.27 6 -0.39 21 27
MYC 0.033 0.12 0.37 15 -0.52 5 20
SHC1 0.018 0.008 -10000 0 -10000 0 0
HRAS/GDP -0.013 0.039 0.16 24 -10000 0 24
LRP1/PDGFRB/PDGFB 0.036 0.03 -10000 0 -0.19 7 7
GRB10 0.019 0.006 -10000 0 -10000 0 0
PTPN11 0.021 0.004 -10000 0 -10000 0 0
GO:0007205 -0.004 0.1 0.27 6 -0.4 21 27
PTEN 0.021 0.004 -10000 0 -10000 0 0
GRB2 0.02 0.004 -10000 0 -10000 0 0
GRB7 0.019 0.022 -10000 0 -0.32 2 2
PDGFB-D/PDGFRB/SHP2 0.03 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0.028 0.011 -10000 0 -10000 0 0
cell cycle arrest 0.022 0.034 -10000 0 -0.22 8 8
HRAS 0.021 0.004 -10000 0 -10000 0 0
HIF1A -0.016 0.073 0.32 12 -10000 0 12
GAB1 -0.001 0.097 0.28 4 -0.35 19 23
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 -0.001 0.085 0.26 9 -0.32 12 21
PDGFB-D/PDGFRB 0.038 0.016 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.031 0.007 -10000 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.007 0.057 -10000 0 -0.28 7 7
positive regulation of MAPKKK cascade 0.03 0.009 -10000 0 -10000 0 0
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
mol:IP3 -0.003 0.1 0.27 6 -0.4 21 27
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.019 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.029 0.019 -10000 0 -0.23 2 2
SHB 0.02 0.006 -10000 0 -10000 0 0
BLK -0.027 0.17 0.32 3 -0.39 69 72
PTPN2 0.019 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.03 0.008 -10000 0 -10000 0 0
BCAR1 0.02 0.016 -10000 0 -0.32 1 1
VAV2 -0.003 0.11 0.29 5 -0.39 18 23
CBL 0.02 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.03 0.008 -10000 0 -10000 0 0
LCK 0.006 0.059 0.32 2 -0.42 4 6
PDGFRB 0.02 0.008 -10000 0 -10000 0 0
ACP1 0.021 0.002 -10000 0 -10000 0 0
HCK -0.016 0.13 0.33 2 -0.55 24 26
ABL1 -0.006 0.098 0.25 7 -0.34 22 29
PDGFB-D/PDGFRB/CBL -0.005 0.11 0.3 2 -0.4 22 24
PTPN1 0.019 0.009 -10000 0 -10000 0 0
SNX15 0.021 0.004 -10000 0 -10000 0 0
STAT3 0.021 0.003 -10000 0 -10000 0 0
STAT1 0.021 0.002 -10000 0 -10000 0 0
cell proliferation 0.034 0.12 0.36 16 -0.47 5 21
SLA 0.012 0.046 -10000 0 -0.32 9 9
actin cytoskeleton reorganization -0.014 0.059 0.32 5 -10000 0 5
SRC -0.001 0.092 0.32 2 -0.58 9 11
PI3K -0.032 0.021 -10000 0 -0.16 7 7
PDGFB-D/PDGFRB/GRB7/SHC 0.033 0.023 -10000 0 -0.19 2 2
SH2B2 0.02 0.016 -10000 0 -0.32 1 1
PLCgamma1/SPHK1 0.005 0.095 0.28 5 -0.36 19 24
LYN 0.006 0.045 0.27 2 -0.33 2 4
LRP1 0.018 0.031 -10000 0 -0.32 4 4
SOS1 0.021 0.003 -10000 0 -10000 0 0
STAT5B 0.021 0.003 -10000 0 -10000 0 0
STAT5A 0.02 0.016 -10000 0 -0.32 1 1
NCK1-2/p130 Cas 0.052 0.03 -10000 0 -0.17 1 1
SPHK1 0.022 0.028 0.32 4 -10000 0 4
EDG1 0 0.002 -10000 0 -10000 0 0
mol:DAG -0.003 0.1 0.27 6 -0.4 21 27
PLCG1 -0.004 0.1 0.27 6 -0.41 21 27
NHERF/PDGFRB 0.037 0.03 0.22 1 -0.19 6 7
YES1 -0.009 0.11 0.34 1 -0.57 15 16
cell migration 0.037 0.03 0.22 1 -0.19 6 7
SHC/Grb2/SOS1 0.047 0.032 -10000 0 -10000 0 0
SLC9A3R2 0.016 0.038 -10000 0 -0.32 6 6
SLC9A3R1 0.021 0.014 0.32 1 -10000 0 1
NHERF1-2/PDGFRB/PTEN 0.047 0.031 0.22 1 -0.18 6 7
FYN -0.028 0.13 0.32 2 -0.41 44 46
DOK1 -0.012 0.039 0.16 22 -10000 0 22
HRAS/GTP 0.015 0.003 -10000 0 -10000 0 0
PDGFB 0.017 0.031 -10000 0 -0.32 4 4
RAC1 0.011 0.12 0.32 9 -0.39 15 24
PRKCD -0.011 0.04 0.16 23 -10000 0 23
FER -0.012 0.039 0.17 22 -10000 0 22
MAPKKK cascade 0.015 0.1 0.29 31 -10000 0 31
RASA1 -0.012 0.039 0.17 21 -10000 0 21
NCK1 0.021 0.003 -10000 0 -10000 0 0
NCK2 0.021 0.002 -10000 0 -10000 0 0
p62DOK/Csk -0.015 0.041 0.16 25 -10000 0 25
PDGFB-D/PDGFRB/SHB 0.029 0.01 -10000 0 -10000 0 0
chemotaxis -0.005 0.096 0.24 7 -0.33 22 29
STAT1-3-5/STAT1-3-5 0.043 0.025 -10000 0 -0.18 1 1
Bovine Papilomavirus E5/PDGFRB 0.015 0.006 -10000 0 -10000 0 0
PTPRJ 0.021 0.003 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.016 0.017 -10000 0 -10000 0 0
HSPA8 0.02 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.024 0.06 0.23 7 -0.22 8 15
AKT1 0.014 0.027 -10000 0 -10000 0 0
GSC 0.04 0.12 0.46 9 -0.42 6 15
NKX2-5 0.036 0.073 0.32 30 -10000 0 30
muscle cell differentiation -0.011 0.074 0.28 3 -10000 0 3
SMAD2-3/SMAD4/SP1 0.047 0.064 -10000 0 -10000 0 0
SMAD4 0.016 0.031 -10000 0 -10000 0 0
CBFB 0.021 0.004 -10000 0 -10000 0 0
SAP18 0.02 0.005 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.024 0.061 0.22 7 -0.19 25 32
SMAD3/SMAD4/VDR 0.044 0.048 -10000 0 -0.23 1 1
MYC 0.018 0.026 -10000 0 -0.32 2 2
CDKN2B -0.17 0.39 -10000 0 -1.1 54 54
AP1 0.005 0.06 -10000 0 -0.24 12 12
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.02 0.093 -10000 0 -0.31 30 30
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.021 0.098 0.18 1 -0.32 34 35
SP3 0.021 0.003 -10000 0 -10000 0 0
CREB1 0.021 0.002 -10000 0 -10000 0 0
FOXH1 0.049 0.088 0.32 44 -10000 0 44
SMAD3/SMAD4/GR 0.03 0.042 -10000 0 -10000 0 0
GATA3 0.02 0.025 0.32 1 -0.32 1 2
SKI/SIN3/HDAC complex/NCoR1 -0.013 0.072 -10000 0 -0.36 12 12
MEF2C/TIF2 0.009 0.065 0.24 7 -0.23 1 8
endothelial cell migration -0.015 0.073 0.74 3 -10000 0 3
MAX 0.02 0.009 -10000 0 -10000 0 0
RBBP7 0.021 0.004 -10000 0 -10000 0 0
RBBP4 0.021 0.003 -10000 0 -10000 0 0
RUNX2 0.025 0.036 0.32 7 -10000 0 7
RUNX3 0.019 0.027 -10000 0 -0.32 3 3
RUNX1 0.02 0.004 -10000 0 -10000 0 0
CTBP1 0.021 0.004 -10000 0 -10000 0 0
NR3C1 0.02 0.009 -10000 0 -10000 0 0
VDR 0.021 0.021 0.32 1 -0.32 1 2
CDKN1A -0.001 0.052 -10000 0 -0.84 1 1
KAT2B 0.017 0.013 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.059 0.076 0.25 36 -10000 0 36
DCP1A 0.021 0.004 -10000 0 -10000 0 0
SKI 0.021 0.004 -10000 0 -10000 0 0
SERPINE1 0.014 0.073 -10000 0 -0.75 3 3
SMAD3/SMAD4/ATF2 0.031 0.041 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.019 0.061 -10000 0 -0.2 20 20
SAP30 0.021 0.004 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.029 0.03 -10000 0 -10000 0 0
JUN -0.006 0.058 0.22 1 -0.24 11 12
SMAD3/SMAD4/IRF7 0.033 0.045 0.28 3 -10000 0 3
TFE3 0.022 0.007 -10000 0 -10000 0 0
COL1A2 0.02 0.077 0.3 19 -0.51 4 23
mesenchymal cell differentiation -0.033 0.045 -10000 0 -0.23 5 5
DLX1 0.038 0.072 0.32 30 -10000 0 30
TCF3 0.02 0.006 -10000 0 -10000 0 0
FOS -0.005 0.085 -10000 0 -0.33 30 30
SMAD3/SMAD4/Max 0.029 0.041 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.034 0.024 -10000 0 -10000 0 0
ZBTB17 0.021 0.009 -10000 0 -10000 0 0
LAMC1 -0.012 0.031 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.031 0.04 -10000 0 -10000 0 0
IRF7 0.022 0.021 0.34 2 -10000 0 2
ESR1 0.015 0.062 0.31 9 -0.32 8 17
HNF4A 0.07 0.13 0.32 93 -0.32 9 102
MEF2C 0.021 0.078 0.26 16 -10000 0 16
SMAD2-3/SMAD4 0.034 0.052 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.034 0.026 -10000 0 -10000 0 0
IGHV3OR16-13 0.004 0.016 -10000 0 -0.32 1 1
TGIF2/HDAC complex 0.02 0.004 -10000 0 -10000 0 0
CREBBP 0.016 0.015 -10000 0 -10000 0 0
SKIL 0.02 0.005 -10000 0 -10000 0 0
HDAC1 0.021 0.003 -10000 0 -10000 0 0
HDAC2 0.019 0.006 -10000 0 -10000 0 0
SNIP1 0.02 0.006 -10000 0 -10000 0 0
GCN5L2 0 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.034 0.042 -10000 0 -10000 0 0
MSG1/HSC70 0.02 0.063 0.23 8 -0.22 25 33
SMAD2 0.019 0.027 -10000 0 -10000 0 0
SMAD3 0.009 0.032 -10000 0 -0.14 1 1
SMAD3/E2F4-5/DP1/p107/SMAD4 0.002 0.044 -10000 0 -0.2 5 5
SMAD2/SMAD2/SMAD4 -0.006 0.074 0.19 2 -0.27 19 21
NCOR1 0.02 0.006 -10000 0 -10000 0 0
NCOA2 0.016 0.031 -10000 0 -0.32 4 4
NCOA1 0.021 0.002 -10000 0 -10000 0 0
MYOD/E2A 0.027 0.012 0.23 1 -10000 0 1
SMAD2-3/SMAD4/SP1/MIZ-1 0.053 0.067 -10000 0 -0.2 2 2
IFNB1 -0.013 0.033 0.28 3 -10000 0 3
SMAD3/SMAD4/MEF2C 0.05 0.07 0.26 4 -10000 0 4
CITED1 0.008 0.086 0.32 8 -0.32 25 33
SMAD2-3/SMAD4/ARC105 0.043 0.052 -10000 0 -10000 0 0
RBL1 0.02 0.004 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.04 0.15 -10000 0 -0.52 36 36
RUNX1-3/PEBPB2 0.038 0.021 -10000 0 -0.18 3 3
SMAD7 -0.001 0.078 -10000 0 -0.43 5 5
MYC/MIZ-1 0.028 0.024 0.18 2 -0.23 1 3
SMAD3/SMAD4 -0.004 0.066 0.24 1 -0.31 4 5
IL10 -0.015 0.048 0.3 3 -0.33 5 8
PIASy/HDAC complex 0.018 0.013 -10000 0 -10000 0 0
PIAS3 0.014 0.014 -10000 0 -10000 0 0
CDK2 0.017 0.015 -10000 0 -10000 0 0
IL5 -0.016 0.033 -10000 0 -10000 0 0
CDK4 0.016 0.015 -10000 0 -10000 0 0
PIAS4 0.018 0.013 -10000 0 -10000 0 0
ATF3 0.005 0.068 -10000 0 -0.32 20 20
SMAD3/SMAD4/SP1 0.036 0.051 -10000 0 -10000 0 0
FOXG1 0.044 0.087 0.32 44 -10000 0 44
FOXO3 -0.019 0.023 -10000 0 -10000 0 0
FOXO1 -0.02 0.023 -10000 0 -0.14 1 1
FOXO4 -0.021 0.023 -10000 0 -0.14 1 1
heart looping 0.021 0.078 0.26 16 -10000 0 16
CEBPB 0.015 0.021 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.042 0.057 0.23 20 -10000 0 20
MYOD1 0.019 0.024 0.32 3 -10000 0 3
SMAD3/SMAD4/HNF4 0.058 0.09 0.23 75 -0.2 9 84
SMAD3/SMAD4/GATA3 0.031 0.048 -10000 0 -0.21 3 3
SnoN/SIN3/HDAC complex/NCoR1 0.02 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.044 0.049 -10000 0 -0.2 1 1
SMAD3/SMAD4/SP1-3 0.045 0.053 -10000 0 -10000 0 0
MED15 0.02 0.005 -10000 0 -10000 0 0
SP1 0.019 0.021 -10000 0 -0.13 2 2
SIN3B 0.02 0.004 -10000 0 -10000 0 0
SIN3A 0.021 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.072 0.087 0.34 15 -10000 0 15
ITGB5 -0.014 0.04 0.2 1 -10000 0 1
TGIF/SIN3/HDAC complex/CtBP -0.01 0.059 -10000 0 -0.31 9 9
SMAD3/SMAD4/AR 0.003 0.088 -10000 0 -0.21 58 58
AR -0.021 0.11 0.32 1 -0.32 61 62
negative regulation of cell growth -0.005 0.064 -10000 0 -0.26 16 16
SMAD3/SMAD4/MYOD 0.03 0.042 0.24 2 -10000 0 2
E2F5 0.019 0.007 -10000 0 -10000 0 0
E2F4 0.02 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.071 0.073 0.3 6 -10000 0 6
SMAD2-3/SMAD4/FOXO1-3a-4 -0.019 0.098 -10000 0 -0.37 32 32
TFDP1 0.02 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.022 0.067 -10000 0 -0.24 11 11
SMAD3/SMAD4/RUNX2 0.033 0.045 0.24 5 -10000 0 5
TGIF2 0.02 0.004 -10000 0 -10000 0 0
TGIF1 0.02 0.006 -10000 0 -10000 0 0
ATF2 0.021 0.003 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.041 0.048 0.22 1 -0.2 14 15
MAP4K1 0.017 0.031 -10000 0 -0.32 4 4
MAP3K8 0.02 0.016 -10000 0 -0.32 1 1
PRKCB 0.012 0.055 -10000 0 -0.32 13 13
DBNL 0.019 0.006 -10000 0 -10000 0 0
CRKL 0.02 0.005 -10000 0 -10000 0 0
MAP3K1 0 0.051 -10000 0 -0.26 10 10
JUN -0.012 0.13 -10000 0 -0.55 23 23
MAP3K7 0.002 0.045 -10000 0 -0.23 10 10
GRAP2 0.011 0.057 -10000 0 -0.32 14 14
CRK 0.019 0.006 -10000 0 -10000 0 0
MAP2K4 -0.001 0.063 0.2 2 -0.37 6 8
LAT 0.021 0.014 0.32 1 -10000 0 1
LCP2 0.018 0.027 -10000 0 -0.32 3 3
MAPK8 -0.007 0.13 -10000 0 -0.57 23 23
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.007 0.06 -10000 0 -0.28 13 13
LAT/GRAP2/SLP76/HPK1/HIP-55 0.047 0.043 0.22 1 -0.21 7 8
Cellular roles of Anthrax toxin

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
ANTXR1 0.02 0.022 -10000 0 -0.32 2 2
ANTXR2 0.021 0.003 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.003 -10000 0 -0.046 2 2
monocyte activation -0.011 0.099 -10000 0 -0.36 33 33
MAP2K2 -0.028 0.14 -10000 0 -0.57 33 33
MAP2K1 -0.008 0.003 -10000 0 -10000 0 0
MAP2K7 -0.007 0.003 -10000 0 -10000 0 0
MAP2K6 -0.006 0.017 0.06 17 -0.15 2 19
CYAA -0.011 0.009 -10000 0 -0.16 2 2
MAP2K4 -0.007 0.003 -10000 0 -10000 0 0
IL1B -0.013 0.035 0.14 4 -0.15 23 27
Channel 0.026 0.013 -10000 0 -0.17 2 2
NLRP1 -0.007 0.007 -10000 0 -0.15 1 1
CALM1 0.02 0.005 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.002 0.059 -10000 0 -0.39 11 11
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.003 0.046 2 -10000 0 2
MAPK3 -0.008 0.003 -10000 0 -10000 0 0
MAPK1 -0.007 0.003 -10000 0 -10000 0 0
PGR -0.031 0.055 -10000 0 -0.16 79 79
PA/Cellular Receptors 0.027 0.014 -10000 0 -0.19 2 2
apoptosis -0.003 0.003 -10000 0 -0.046 2 2
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.025 0.013 -10000 0 -0.16 2 2
macrophage activation -0.011 0.004 -10000 0 -10000 0 0
TNF 0.011 0.061 0.32 1 -0.32 15 16
VCAM1 -0.009 0.098 -10000 0 -0.38 30 30
platelet activation -0.002 0.059 -10000 0 -0.39 11 11
MAPKKK cascade 0.004 0.016 -10000 0 -0.072 15 15
IL18 -0.009 0.024 0.14 2 -0.2 5 7
negative regulation of macrophage activation -0.003 0.003 -10000 0 -0.046 2 2
LEF -0.003 0.003 -10000 0 -0.046 2 2
CASP1 -0.004 0.012 -10000 0 -0.11 4 4
mol:cAMP -0.002 0.059 -10000 0 -0.39 11 11
necrosis -0.003 0.003 -10000 0 -0.046 2 2
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.026 0.012 -10000 0 -0.16 2 2
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.021 0.003 -10000 0 -10000 0 0
HDAC2 0.019 0.006 -10000 0 -10000 0 0
GNB1/GNG2 0.036 0.025 0.22 1 -0.19 3 4
forebrain development -0.033 0.14 -10000 0 -0.51 21 21
GNAO1 0.015 0.036 0.32 3 -0.32 2 5
SMO/beta Arrestin2 0.021 0.029 0.22 3 -0.2 1 4
SMO 0.015 0.033 0.32 3 -0.32 1 4
ARRB2 0.014 0.015 -10000 0 -10000 0 0
GLI3/SPOP 0.004 0.081 -10000 0 -0.32 17 17
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
GSK3B 0.021 0.003 -10000 0 -10000 0 0
GNAI2 0.015 0.015 -10000 0 -10000 0 0
SIN3/HDAC complex 0.048 0.02 -10000 0 -10000 0 0
GNAI1 0.014 0.021 -10000 0 -0.32 1 1
XPO1 0.013 0.019 -10000 0 -10000 0 0
GLI1/Su(fu) -0.03 0.13 -10000 0 -0.52 18 18
SAP30 0.021 0.004 -10000 0 -10000 0 0
mol:GDP 0.015 0.033 0.32 3 -0.32 1 4
MIM/GLI2A 0.001 0.047 -10000 0 -0.32 1 1
IFT88 0.02 0.006 -10000 0 -10000 0 0
GNAI3 0.014 0.015 -10000 0 -10000 0 0
GLI2 -0.006 0.074 -10000 0 -0.37 12 12
GLI3 -0.008 0.081 0.2 1 -0.32 20 21
CSNK1D 0.021 0.004 -10000 0 -10000 0 0
CSNK1E 0.02 0.005 -10000 0 -10000 0 0
SAP18 0.02 0.006 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.02 0.006 -10000 0 -10000 0 0
GNG2 0.019 0.022 -10000 0 -0.32 2 2
Gi family/GTP -0.013 0.066 -10000 0 -0.19 45 45
SIN3B 0.021 0.005 -10000 0 -10000 0 0
SIN3A 0.021 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) -0.006 0.085 -10000 0 -0.34 18 18
GLI2/Su(fu) -0.005 0.085 -10000 0 -0.38 17 17
FOXA2 -0.14 0.34 -10000 0 -0.86 87 87
neural tube patterning -0.033 0.14 -10000 0 -0.51 21 21
SPOP 0.021 0.004 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.014 0.037 -10000 0 -10000 0 0
GNB1 0.02 0.004 -10000 0 -10000 0 0
CSNK1G2 0.02 0.006 -10000 0 -10000 0 0
CSNK1G3 0.02 0.005 -10000 0 -10000 0 0
MTSS1 0.001 0.047 -10000 0 -0.33 1 1
embryonic limb morphogenesis -0.033 0.14 -10000 0 -0.51 21 21
SUFU 0.008 0.014 -10000 0 -10000 0 0
LGALS3 0.02 0.005 -10000 0 -10000 0 0
catabolic process -0.002 0.12 -10000 0 -0.45 23 23
GLI3A/CBP 0.008 0.056 -10000 0 -0.33 11 11
KIF3A 0.02 0.005 -10000 0 -10000 0 0
GLI1 -0.034 0.14 -10000 0 -0.52 21 21
RAB23 0.02 0.005 -10000 0 -10000 0 0
CSNK1A1 0.02 0.004 -10000 0 -10000 0 0
IFT172 0.021 0.002 -10000 0 -10000 0 0
RBBP7 0.021 0.004 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.013 0.038 -10000 0 -10000 0 0
GNAZ -0.012 0.092 -10000 0 -0.32 38 38
RBBP4 0.021 0.003 -10000 0 -10000 0 0
CSNK1G1 0.021 0.004 -10000 0 -10000 0 0
PIAS1 0.021 0.004 -10000 0 -10000 0 0
PRKACA 0.02 0.005 -10000 0 -10000 0 0
GLI2/SPOP 0.001 0.085 -10000 0 -0.39 15 15
STK36 0.013 0.019 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.012 0.063 -10000 0 -0.31 7 7
PTCH1 -0.04 0.16 -10000 0 -0.8 13 13
MIM/GLI1 -0.048 0.18 -10000 0 -0.46 68 68
CREBBP 0.008 0.056 -10000 0 -0.33 11 11
Su(fu)/SIN3/HDAC complex 0 0.064 -10000 0 -0.28 17 17
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.018 0.057 0.34 2 -10000 0 2
CRKL -0.01 0.045 0.2 10 -10000 0 10
mol:DAG 0.011 0.032 0.23 1 -0.22 1 2
HRAS 0 0.072 0.24 12 -10000 0 12
MAPK8 0 0.059 0.17 49 -10000 0 49
RAP1A -0.009 0.047 0.2 10 -10000 0 10
GAB1 -0.011 0.048 0.21 8 -0.25 1 9
MAPK14 -0.001 0.057 0.17 47 -10000 0 47
EPO 0.011 0.034 0.32 4 -10000 0 4
PLCG1 0.011 0.033 0.24 1 -0.23 1 2
EPOR/TRPC2/IP3 Receptors 0.022 0.009 -10000 0 -10000 0 0
RAPGEF1 0.021 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.038 0.03 0.21 3 -0.19 4 7
GAB1/SHC/GRB2/SOS1 -0.016 0.046 0.24 4 -10000 0 4
EPO/EPOR (dimer) 0.031 0.022 0.22 4 -10000 0 4
IRS2 -0.01 0.046 0.2 10 -10000 0 10
STAT1 0.011 0.036 0.31 1 -0.23 1 2
STAT5B 0.011 0.034 0.28 1 -0.23 1 2
cell proliferation -0.004 0.061 0.18 48 -10000 0 48
GAB1/SHIP/PIK3R1/SHP2/SHC -0.025 0.035 -10000 0 -0.28 1 1
TEC -0.01 0.047 0.2 10 -10000 0 10
SOCS3 0.018 0.031 -10000 0 -0.32 4 4
STAT1 (dimer) 0.011 0.036 0.31 1 -0.22 1 2
JAK2 0.019 0.024 -10000 0 -0.32 2 2
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
EPO/EPOR (dimer)/JAK2 0.046 0.038 0.35 1 -0.16 2 3
EPO/EPOR 0.031 0.022 0.22 4 -10000 0 4
LYN 0.02 0.006 -10000 0 -10000 0 0
TEC/VAV2 -0.013 0.047 0.2 9 -10000 0 9
elevation of cytosolic calcium ion concentration 0.022 0.009 -10000 0 -10000 0 0
SHC1 0.018 0.008 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.038 0.024 0.22 3 -10000 0 3
mol:IP3 0.011 0.032 0.23 1 -0.22 1 2
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.015 0.052 0.19 9 -0.28 1 10
SH2B3 0.021 0.023 -10000 0 -0.32 2 2
NFKB1 0 0.059 0.17 50 -10000 0 50
EPO/EPOR (dimer)/JAK2/SOCS3 0.003 0.044 0.19 2 -0.23 12 14
PTPN6 -0.008 0.042 0.14 30 -0.16 2 32
TEC/VAV2/GRB2 -0.015 0.047 0.2 9 -10000 0 9
EPOR 0.022 0.009 -10000 0 -10000 0 0
INPP5D 0.019 0.027 -10000 0 -0.32 3 3
mol:GDP -0.016 0.046 0.24 4 -10000 0 4
SOS1 0.021 0.003 -10000 0 -10000 0 0
PLCG2 0.018 0.027 -10000 0 -0.32 3 3
CRKL/CBL/C3G -0.015 0.046 0.2 9 -10000 0 9
VAV2 -0.01 0.047 0.15 32 -10000 0 32
CBL -0.009 0.047 0.18 15 -10000 0 15
SHC/Grb2/SOS1 0.024 0.023 -10000 0 -10000 0 0
STAT5A 0.011 0.038 0.28 1 -0.3 2 3
GRB2 0.02 0.004 -10000 0 -10000 0 0
STAT5 (dimer) 0.023 0.039 0.37 1 -0.33 1 2
LYN/PLCgamma2 0.026 0.023 -10000 0 -0.22 3 3
PTPN11 0.021 0.004 -10000 0 -10000 0 0
BTK -0.017 0.057 0.22 7 -0.27 3 10
BCL2 0.009 0.074 0.39 2 -0.46 1 3
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.01 0.025 -10000 0 -0.19 7 7
epithelial cell differentiation 0.041 0.019 -10000 0 -0.16 2 2
CYFIP2 0.016 0.041 -10000 0 -0.32 7 7
ENAH -0.019 0.055 0.3 3 -0.22 1 4
EGFR 0.015 0.041 0.32 1 -0.32 6 7
EPHA2 0.013 0.049 -10000 0 -0.32 10 10
MYO6 -0.018 0.038 0.23 8 -10000 0 8
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.039 0.022 -10000 0 -0.19 3 3
AQP5 -0.061 0.16 0.54 2 -0.37 93 95
CTNND1 0.021 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.018 0.039 0.22 9 -10000 0 9
regulation of calcium-dependent cell-cell adhesion -0.085 0.074 0.16 3 -0.29 1 4
EGF 0.07 0.12 0.32 85 -0.32 4 89
NCKAP1 0.021 0.003 -10000 0 -10000 0 0
AQP3 -0.02 0.069 0.24 1 -0.32 22 23
cortical microtubule organization 0.041 0.019 -10000 0 -0.16 2 2
GO:0000145 -0.017 0.037 0.21 9 -10000 0 9
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.045 0.02 -10000 0 -0.16 2 2
MLLT4 0.019 0.006 -10000 0 -10000 0 0
ARF6/GDP -0.032 0.023 -10000 0 -0.16 5 5
ARF6 0.02 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.04 0.035 -10000 0 -0.18 7 7
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.01 0.038 0.42 2 -0.21 1 3
PVRL2 0.02 0.004 -10000 0 -10000 0 0
ZYX -0.019 0.04 0.43 2 -10000 0 2
ARF6/GTP 0.043 0.035 -10000 0 -0.17 6 6
CDH1 0.019 0.022 -10000 0 -0.32 2 2
EGFR/EGFR/EGF/EGF 0.041 0.053 0.24 1 -0.18 9 10
RhoA/GDP 0.042 0.019 -10000 0 -0.15 2 2
actin cytoskeleton organization -0.019 0.036 0.22 8 -10000 0 8
IGF-1R heterotetramer 0.02 0.016 -10000 0 -0.32 1 1
GIT1 0.021 0.003 -10000 0 -10000 0 0
IGF1R 0.02 0.016 -10000 0 -0.32 1 1
IGF1 0.014 0.051 0.32 1 -0.32 10 11
DIAPH1 0.017 0.12 -10000 0 -0.52 18 18
Wnt receptor signaling pathway -0.041 0.019 0.16 2 -10000 0 2
RHOA 0.021 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.033 0.025 -10000 0 -0.18 6 6
CTNNA1 0.021 0.004 -10000 0 -10000 0 0
VCL -0.02 0.037 0.42 2 -10000 0 2
EFNA1 0.017 0.017 -10000 0 -0.32 1 1
LPP -0.021 0.038 0.21 9 -10000 0 9
Ephrin A1/EPHA2 0.027 0.034 -10000 0 -0.17 9 9
SEC6/SEC8 -0.024 0.018 -10000 0 -10000 0 0
MGAT3 -0.086 0.075 0.16 3 -0.3 1 4
HGF/MET 0.022 0.055 -10000 0 -0.16 33 33
HGF 0.008 0.075 0.32 4 -0.32 21 25
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.01 0.025 -10000 0 -0.19 7 7
actin cable formation 0.01 0.084 0.29 18 -0.26 2 20
KIAA1543 -0.02 0.027 0.18 7 -10000 0 7
KIFC3 -0.022 0.02 0.16 3 -10000 0 3
NCK1 0.021 0.003 -10000 0 -10000 0 0
EXOC3 0.016 0.009 -10000 0 -10000 0 0
ACTN1 -0.018 0.038 0.43 2 -10000 0 2
NCK1/GIT1 0.03 0.007 -10000 0 -10000 0 0
mol:GDP 0.041 0.019 -10000 0 -0.16 2 2
EXOC4 0.02 0.005 -10000 0 -10000 0 0
STX4 -0.02 0.028 0.34 1 -10000 0 1
PIP5K1C -0.018 0.039 0.22 9 -10000 0 9
LIMA1 0.021 0.003 -10000 0 -10000 0 0
ABI1 0.021 0.004 -10000 0 -10000 0 0
ROCK1 -0.006 0.078 0.31 10 -0.26 1 11
adherens junction assembly -0.023 0.088 0.34 7 -0.43 9 16
IGF-1R heterotetramer/IGF1 0.031 0.035 -10000 0 -0.16 12 12
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.028 0.011 -10000 0 -10000 0 0
MET 0.013 0.068 0.32 6 -0.32 15 21
PLEKHA7 -0.02 0.029 0.34 1 -10000 0 1
mol:GTP 0.038 0.034 -10000 0 -0.18 7 7
establishment of epithelial cell apical/basal polarity 0.02 0.096 0.32 15 -10000 0 15
cortical actin cytoskeleton stabilization 0.01 0.025 -10000 0 -0.19 7 7
regulation of cell-cell adhesion -0.019 0.036 0.22 8 -10000 0 8
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.01 0.025 -10000 0 -0.19 7 7
Regulation of Telomerase

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
Telomerase catalytic core complex 0.096 0.16 0.36 67 -0.42 2 69
RAD9A 0.021 0.003 -10000 0 -10000 0 0
AP1 0.02 0.067 -10000 0 -0.22 34 34
IFNAR2 0.028 0.014 -10000 0 -10000 0 0
AKT1 0.022 0.034 0.2 1 -0.34 1 2
ER alpha/Oestrogen 0.018 0.041 0.22 9 -0.21 8 17
NFX1/SIN3/HDAC complex 0.011 0.051 -10000 0 -0.29 5 5
EGF 0.073 0.12 0.32 85 -0.31 4 89
SMG5 0.018 0.008 -10000 0 -10000 0 0
SMG6 0.019 0.006 -10000 0 -10000 0 0
SP3/HDAC2 0.039 0.024 -10000 0 -10000 0 0
TERT/c-Abl 0.089 0.14 0.35 33 -0.39 2 35
SAP18 0.021 0.006 -10000 0 -10000 0 0
MRN complex 0.036 0.017 -10000 0 -10000 0 0
WT1 0.016 0.092 0.34 11 -0.32 26 37
WRN 0.018 0.008 -10000 0 -10000 0 0
SP1 0.031 0.018 -10000 0 -10000 0 0
SP3 0.024 0.008 -10000 0 -10000 0 0
TERF2IP 0.02 0.005 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.054 0.1 -10000 0 -0.39 2 2
Mad/Max 0.038 0.016 -10000 0 -10000 0 0
TERT 0.096 0.16 0.36 62 -0.42 2 64
CCND1 0.086 0.18 0.42 16 -0.86 6 22
MAX 0.024 0.008 -10000 0 -10000 0 0
RBBP7 0.022 0.005 -10000 0 -10000 0 0
RBBP4 0.022 0.004 -10000 0 -10000 0 0
TERF2 -0.017 0.014 -10000 0 -10000 0 0
PTGES3 0.021 0.004 -10000 0 -10000 0 0
SIN3A 0.022 0.005 -10000 0 -10000 0 0
Telomerase/911 0.054 0.06 0.23 4 -0.31 1 5
CDKN1B 0.002 0.039 0.22 2 -0.19 3 5
RAD1 0.018 0.008 -10000 0 -10000 0 0
XRCC5 0.021 0.003 -10000 0 -10000 0 0
XRCC6 0.02 0.004 -10000 0 -10000 0 0
SAP30 0.022 0.005 -10000 0 -10000 0 0
TRF2/PARP2 0.028 0.01 -10000 0 -10000 0 0
UBE3A 0.023 0.008 -10000 0 -10000 0 0
JUN 0.021 0.032 -10000 0 -0.32 4 4
E6 0.003 0.005 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.022 0.013 -10000 0 -10000 0 0
FOS 0.002 0.083 -10000 0 -0.32 31 31
IFN-gamma/IRF1 0.047 0.062 0.24 31 -0.22 7 38
PARP2 0.02 0.005 -10000 0 -10000 0 0
BLM 0.049 0.087 0.32 46 -10000 0 46
Telomerase 0.035 0.085 0.27 4 -0.54 3 7
IRF1 0.024 0.008 -10000 0 -10000 0 0
ESR1 0.021 0.06 0.32 9 -0.32 8 17
KU/TER 0.03 0.007 -10000 0 -10000 0 0
ATM/TRF2 0.029 0.008 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.011 0.057 -10000 0 -0.27 8 8
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.011 0.056 -10000 0 -0.28 7 7
HDAC1 0.022 0.003 -10000 0 -10000 0 0
HDAC2 0.027 0.017 -10000 0 -10000 0 0
ATM 0.009 0.008 -10000 0 -10000 0 0
SMAD3 -0.02 0.008 -10000 0 -10000 0 0
ABL1 0.021 0.004 -10000 0 -10000 0 0
MXD1 0.024 0.007 -10000 0 -10000 0 0
MRE11A 0.02 0.004 -10000 0 -10000 0 0
HUS1 0.019 0.006 -10000 0 -10000 0 0
RPS6KB1 0.02 0.004 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.092 0.14 0.38 14 -0.44 1 15
NR2F2 0.004 0.026 -10000 0 -10000 0 0
MAPK3 -0.005 0.019 -10000 0 -10000 0 0
MAPK1 -0.005 0.019 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.008 0.02 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
HNRNPC 0.02 0.004 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.009 0.008 -10000 0 -10000 0 0
NBN 0.019 0.007 -10000 0 -10000 0 0
EGFR 0.018 0.04 0.33 1 -0.31 6 7
mol:Oestrogen 0.002 0.003 -10000 0 -10000 0 0
EGF/EGFR 0.058 0.085 0.24 72 -0.22 9 81
MYC 0.02 0.025 -10000 0 -0.32 2 2
IL2 0.029 0.018 -10000 0 -10000 0 0
KU 0.03 0.007 -10000 0 -10000 0 0
RAD50 0.02 0.005 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
TGFB1 0.008 0.02 -10000 0 -10000 0 0
TRF2/BLM 0.046 0.055 0.22 43 -10000 0 43
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.099 0.14 0.36 27 -0.4 2 29
SP1/HDAC2 0.047 0.035 -10000 0 -10000 0 0
PINX1 0.018 0.008 -10000 0 -10000 0 0
Telomerase/EST1A 0.05 0.1 -10000 0 -0.38 2 2
Smad3/Myc -0.019 0.015 -10000 0 -0.18 2 2
911 complex 0.032 0.019 -10000 0 -10000 0 0
IFNG 0.038 0.085 0.32 31 -0.32 7 38
Telomerase/PinX1 0.045 0.1 -10000 0 -0.38 2 2
Telomerase/AKT1/mTOR/p70S6K 0.049 0.089 0.26 10 -0.44 5 15
SIN3B 0.022 0.006 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
Telomerase/EST1B 0.047 0.099 -10000 0 -0.39 2 2
response to DNA damage stimulus 0.002 0.017 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.048 0.026 -10000 0 -10000 0 0
TRF2/WRN 0.025 0.012 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.053 0.1 -10000 0 -0.39 2 2
E2F1 0.03 0.03 0.32 4 -10000 0 4
ZNFX1 0.021 0.006 -10000 0 -10000 0 0
PIF1 0.06 0.1 0.32 64 -10000 0 64
NCL 0.021 0.003 -10000 0 -10000 0 0
DKC1 0.02 0.004 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Insulin 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
CBL/APS/CAP 0.027 0.046 -10000 0 -0.17 17 17
TC10/GTP 0.023 0.044 -10000 0 -0.16 20 20
Insulin Receptor/Insulin/IRS1/Shp2 0.049 0.02 -10000 0 -0.14 1 1
HRAS 0.021 0.004 -10000 0 -10000 0 0
APS homodimer 0.02 0.016 -10000 0 -0.32 1 1
GRB14 0.033 0.076 0.32 26 -0.32 5 31
FOXO3 -0.05 0.2 -10000 0 -0.62 51 51
AKT1 -0.019 0.052 0.31 3 -10000 0 3
INSR 0.022 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.041 0.03 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.019 0.006 -10000 0 -10000 0 0
SORBS1 0.002 0.077 -10000 0 -0.32 26 26
CRK 0.019 0.006 -10000 0 -10000 0 0
PTPN1 -0.012 0.019 -10000 0 -10000 0 0
CAV1 -0.096 0.079 -10000 0 -0.17 254 254
CBL/APS/CAP/Crk-II/C3G 0.041 0.053 -10000 0 -0.18 21 21
Insulin Receptor/Insulin/IRS1/NCK2 0.05 0.019 -10000 0 -0.14 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.037 0.02 -10000 0 -0.16 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.001 0.07 -10000 0 -0.32 16 16
RPS6KB1 -0.023 0.048 0.26 4 -10000 0 4
PARD6A 0.02 0.016 -10000 0 -0.32 1 1
CBL 0.02 0.005 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.011 0.038 -10000 0 -0.57 2 2
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.025 0.043 -10000 0 -10000 0 0
HRAS/GTP -0.027 0.019 -10000 0 -10000 0 0
Insulin Receptor 0.022 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.049 0.029 -10000 0 -10000 0 0
PRKCI 0.004 0.071 -10000 0 -0.3 20 20
Insulin Receptor/Insulin/GRB14/PDK1 -0.022 0.032 -10000 0 -0.17 3 3
SHC1 0.018 0.008 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.029 0.04 -10000 0 -0.48 2 2
PI3K 0.046 0.024 -10000 0 -0.17 1 1
NCK2 0.021 0.002 -10000 0 -10000 0 0
RHOQ 0.021 0.003 -10000 0 -10000 0 0
mol:H2O2 -0.002 0.003 -10000 0 -10000 0 0
HRAS/GDP 0.015 0.003 -10000 0 -10000 0 0
AKT2 -0.02 0.051 0.31 3 -10000 0 3
PRKCZ -0.001 0.084 -10000 0 -0.36 10 10
SH2B2 0.02 0.016 -10000 0 -0.32 1 1
SHC/SHIP -0.019 0.022 0.15 2 -10000 0 2
F2RL2 0.036 0.08 0.32 31 -0.32 4 35
TRIP10 0.02 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.032 0.018 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.027 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.049 0.029 -10000 0 -10000 0 0
RAPGEF1 0.021 0.004 -10000 0 -10000 0 0
RASA1 0.02 0.005 -10000 0 -10000 0 0
NCK1 0.021 0.003 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.035 0.051 -10000 0 -0.18 21 21
TC10/GDP 0.016 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.04 0.025 -10000 0 -10000 0 0
INPP5D -0.019 0.019 0.15 2 -0.17 2 4
SOS1 0.021 0.003 -10000 0 -10000 0 0
SGK1 -0.053 0.2 -10000 0 -0.66 46 46
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.021 0.004 -10000 0 -10000 0 0
IRS1 0.02 0.016 -10000 0 -0.32 1 1
p62DOK/RasGAP 0.029 0.04 -10000 0 -0.49 2 2
INS -0.014 0.014 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.019 0.019 0.15 2 -0.17 2 4
GRB2 0.02 0.004 -10000 0 -10000 0 0
EIF4EBP1 -0.018 0.052 0.24 5 -10000 0 5
PTPRA 0.021 0.006 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.027 0.008 -10000 0 -10000 0 0
PDPK1 0.021 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.009 0.023 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.037 0.015 -10000 0 -0.14 1 1
Insulin Receptor/Insulin/IRS3 0.029 0.012 -10000 0 -10000 0 0
Par3/Par6 0.051 0.045 0.21 26 -0.16 4 30
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.019 0.006 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 -0.011 0.003 -10000 0 -10000 0 0
mol:DAG -0.013 0.033 0.23 5 -10000 0 5
VEGFR1 homodimer/NRP1/VEGFR 121 0.017 0.006 -10000 0 -10000 0 0
CaM/Ca2+ -0.017 0.028 0.19 2 -10000 0 2
HIF1A 0.023 0.004 -10000 0 -10000 0 0
GAB1 0.019 0.027 -10000 0 -0.32 3 3
AKT1 -0.014 0.045 0.46 2 -10000 0 2
PLCG1 -0.013 0.033 0.23 5 -10000 0 5
NOS3 -0.007 0.086 0.44 6 -0.39 7 13
CBL 0.02 0.005 -10000 0 -10000 0 0
mol:NO -0.003 0.097 0.48 8 -0.45 5 13
FLT1 -0.014 0.004 -10000 0 -10000 0 0
PGF 0.03 0.052 0.32 15 -10000 0 15
VEGFR1 homodimer/NRP2/VEGFR121 0.029 0.017 -10000 0 -10000 0 0
CALM1 0.02 0.005 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
eNOS/Hsp90 -0.012 0.085 0.35 4 -0.43 8 12
endothelial cell proliferation -0.007 0.056 0.32 6 -10000 0 6
mol:Ca2+ -0.013 0.033 0.23 5 -10000 0 5
MAPK3 -0.019 0.041 0.26 8 -10000 0 8
MAPK1 -0.019 0.038 0.28 6 -10000 0 6
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
PLGF homodimer 0.03 0.052 0.32 15 -10000 0 15
PRKACA 0.02 0.005 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.19 0.16 -10000 0 -0.32 296 296
VEGFA homodimer 0.021 0.004 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.018 0.007 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.021 0.04 0.3 5 -10000 0 5
PI3K 0.042 0.035 -10000 0 -10000 0 0
PRKCA -0.018 0.028 0.24 3 -10000 0 3
PRKCB -0.019 0.037 0.22 6 -10000 0 6
VEGFR1 homodimer/PLGF homodimer 0.025 0.035 0.22 15 -10000 0 15
VEGFA 0.021 0.004 -10000 0 -10000 0 0
VEGFB 0.021 0.003 -10000 0 -10000 0 0
mol:IP3 -0.013 0.033 0.23 5 -10000 0 5
RASA1 -0.016 0.026 -10000 0 -10000 0 0
NRP2 0.019 0.027 -10000 0 -0.32 3 3
VEGFR1 homodimer -0.014 0.004 -10000 0 -10000 0 0
VEGFB homodimer 0.021 0.003 -10000 0 -10000 0 0
NCK1 0.021 0.003 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.09 0.11 0.44 2 -0.4 22 24
PTPN11 0.021 0.004 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.041 0.034 -10000 0 -10000 0 0
mol:L-citrulline -0.003 0.097 0.48 8 -0.45 5 13
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.038 0.017 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.029 0.011 -10000 0 -10000 0 0
CD2AP 0.02 0.004 -10000 0 -10000 0 0
PI3K/GAB1 0.047 0.041 -10000 0 -10000 0 0
PDPK1 -0.015 0.049 0.39 3 -10000 0 3
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.029 0.011 -10000 0 -10000 0 0
mol:NADP -0.003 0.097 0.48 8 -0.45 5 13
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.037 0.017 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.018 0.015 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

Figure S97.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S97.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.009 0.11 -9999 0 -0.33 34 34
MAP3K8 0.017 0.019 -9999 0 -0.32 1 1
FOS 0.006 0.084 -9999 0 -0.38 10 10
PRKCA 0.016 0.025 -9999 0 -0.32 2 2
PTPN7 0.016 0.015 -9999 0 -10000 0 0
HRAS 0.02 0.006 -9999 0 -10000 0 0
PRKCB 0.009 0.056 -9999 0 -0.32 13 13
NRAS 0.02 0.007 -9999 0 -10000 0 0
RAS family/GTP 0.031 0.021 -9999 0 -10000 0 0
MAPK3 0.013 0.042 -9999 0 -0.34 1 1
MAP2K1 -0.002 0.08 -9999 0 -0.37 16 16
ELK1 0.017 0.015 -9999 0 -10000 0 0
BRAF -0.002 0.057 -9999 0 -0.34 12 12
mol:GTP 0 0.001 -9999 0 -0.004 32 32
MAPK1 0.001 0.086 -9999 0 -0.44 13 13
RAF1 -0.004 0.065 -9999 0 -0.36 14 14
KRAS 0.019 0.007 -9999 0 -10000 0 0
mTOR signaling pathway

Figure S98.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S98.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.021 0.003 -10000 0 -10000 0 0
mol:PIP3 -0.013 0.025 -10000 0 -0.2 6 6
FRAP1 -0.007 0.084 -10000 0 -0.42 17 17
AKT1 -0.008 0.036 0.15 12 -0.24 4 16
INSR 0.02 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.024 0.007 -10000 0 -10000 0 0
mol:GTP -0.012 0.045 0.25 1 -0.22 2 3
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.015 0.027 -10000 0 -0.2 5 5
TSC2 0.021 0.004 -10000 0 -10000 0 0
RHEB/GDP -0.022 0.025 -10000 0 -0.19 2 2
TSC1 0.021 0.004 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.015 0.027 -10000 0 -0.21 6 6
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.012 0.037 -10000 0 -0.24 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.021 0.003 -10000 0 -10000 0 0
RPS6KB1 0.005 0.059 0.21 3 -0.36 5 8
MAP3K5 -0.011 0.054 0.18 4 -0.18 42 46
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
apoptosis -0.011 0.054 0.18 4 -0.18 42 46
mol:LY294002 0 0 -10000 0 -0.001 2 2
EIF4B 0.003 0.058 0.25 3 -0.32 5 8
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.021 0.051 0.2 1 -0.3 4 5
eIF4E/eIF4G1/eIF4A1 0.003 0.053 -10000 0 -0.27 16 16
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.025 0.03 -10000 0 -0.21 6 6
mTOR/RHEB/GTP/Raptor/GBL -0.004 0.034 0.14 12 -0.15 3 15
FKBP1A 0.02 0.005 -10000 0 -10000 0 0
RHEB/GTP -0.016 0.037 -10000 0 -0.19 2 2
mol:Amino Acids 0 0 -10000 0 -0.001 2 2
FKBP12/Rapamycin 0.015 0.004 -10000 0 -10000 0 0
PDPK1 -0.018 0.021 -10000 0 -0.2 4 4
EIF4E 0.021 0.003 -10000 0 -10000 0 0
ASK1/PP5C -0.031 0.18 -10000 0 -0.53 50 50
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.005 0.04 -10000 0 -0.23 11 11
TSC1/TSC2 -0.012 0.048 0.27 1 -0.23 2 3
tumor necrosis factor receptor activity 0 0 0.001 2 -10000 0 2
RPS6 0.019 0.006 -10000 0 -10000 0 0
PPP5C 0.02 0.005 -10000 0 -10000 0 0
EIF4G1 0.02 0.005 -10000 0 -10000 0 0
IRS1 0.002 0.027 -10000 0 -0.24 6 6
INS 0.017 0.003 -10000 0 -10000 0 0
PTEN 0.021 0.004 -10000 0 -10000 0 0
PDK2 -0.017 0.024 0.17 1 -0.2 5 6
EIF4EBP1 -0.057 0.29 -10000 0 -1 38 38
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
PPP2R5D -0.004 0.082 0.21 3 -0.39 16 19
peptide biosynthetic process -0.016 0.013 0.17 2 -10000 0 2
RHEB 0.02 0.005 -10000 0 -10000 0 0
EIF4A1 0.02 0.006 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.004 8 -0.002 1 9
EEF2 -0.016 0.013 0.17 2 -10000 0 2
eIF4E/4E-BP1 -0.045 0.27 -10000 0 -0.96 38 38
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.045 0.058 -10000 0 -0.16 6 6
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.02 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.009 0.055 0.27 2 -10000 0 2
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.036 0.027 -10000 0 -0.18 2 2
antigen processing and presentation of peptide antigen via MHC class I -0.018 0.038 -10000 0 -0.28 1 1
CaM/Ca2+ 0.043 0.053 -10000 0 -0.16 6 6
RAP1A 0.02 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.01 0.047 0.16 2 -10000 0 2
AKT1 -0.011 0.058 0.27 7 -10000 0 7
MAP2K1 -0.013 0.049 0.2 7 -10000 0 7
MAP3K11 -0.01 0.05 0.2 7 -0.16 1 8
IFNGR1 0.02 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.003 0.12 0.22 4 -0.32 42 46
Rap1/GTP -0.028 0.024 -10000 0 -10000 0 0
CRKL/C3G 0.029 0.009 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.055 0.059 -10000 0 -0.17 4 4
CEBPB -0.005 0.1 0.29 4 -0.42 14 18
STAT3 0.021 0.003 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.052 0.081 -10000 0 -0.67 3 3
STAT1 -0.009 0.05 0.22 5 -10000 0 5
CALM1 0.02 0.005 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.032 0.086 0.32 31 -0.32 7 38
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.01 0.054 0.26 3 -10000 0 3
CEBPB/PTGES2/Cbp/p300 0.006 0.065 -10000 0 -0.29 11 11
mol:Ca2+ 0.043 0.055 -10000 0 -0.16 7 7
MAPK3 0.002 0.068 -10000 0 -0.47 3 3
STAT1 (dimer) -0.019 0.053 -10000 0 -0.39 1 1
MAPK1 -0.017 0.13 -10000 0 -0.68 16 16
JAK2 0.018 0.024 -10000 0 -0.31 2 2
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
JAK1 0.021 0.011 -10000 0 -10000 0 0
CAMK2D 0.021 0.003 -10000 0 -10000 0 0
DAPK1 -0.007 0.096 0.28 2 -0.48 12 14
SMAD7 -0.002 0.037 0.19 6 -0.16 2 8
CBL/CRKL/C3G -0.012 0.053 0.26 2 -10000 0 2
PI3K 0.039 0.05 -10000 0 -10000 0 0
IFNG 0.032 0.087 0.32 31 -0.32 7 38
apoptosis -0.004 0.091 0.3 1 -0.42 16 17
CAMK2G 0.021 0.003 -10000 0 -10000 0 0
STAT3 (dimer) 0.021 0.003 -10000 0 -10000 0 0
CAMK2A -0.01 0.099 0.32 1 -0.32 44 45
CAMK2B 0.063 0.11 0.32 72 -10000 0 72
FRAP1 -0.012 0.054 0.26 7 -10000 0 7
PRKCD -0.011 0.059 0.28 7 -10000 0 7
RAP1B 0.02 0.005 -10000 0 -10000 0 0
negative regulation of cell growth -0.018 0.038 -10000 0 -0.28 1 1
PTPN2 0.02 0.005 -10000 0 -10000 0 0
EP300 0.021 0.004 -10000 0 -10000 0 0
IRF1 -0.01 0.048 0.24 4 -10000 0 4
STAT1 (dimer)/PIASy -0.01 0.054 0.26 3 -10000 0 3
SOCS1 0.013 0.082 -10000 0 -1 3 3
mol:GDP -0.012 0.05 0.25 2 -10000 0 2
CASP1 -0.004 0.041 0.18 7 -0.19 5 12
PTGES2 0.021 0.004 -10000 0 -10000 0 0
IRF9 -0.001 0.034 -10000 0 -0.16 1 1
mol:PI-3-4-5-P3 0.027 0.041 -10000 0 -0.16 6 6
RAP1/GDP -0.025 0.034 -10000 0 -10000 0 0
CBL -0.009 0.049 0.2 7 -10000 0 7
MAP3K1 -0.009 0.049 0.22 5 -10000 0 5
PIAS1 0.021 0.004 -10000 0 -10000 0 0
PIAS4 0.02 0.006 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.018 0.038 -10000 0 -0.28 1 1
PTPN11 -0.006 0.05 0.15 31 -0.16 6 37
CREBBP 0.021 0.004 -10000 0 -10000 0 0
RAPGEF1 0.021 0.004 -10000 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.003 0.07 0.24 3 -0.38 7 10
BAG4 0.019 0.007 -10000 0 -10000 0 0
BAD -0.001 0.035 0.25 3 -0.13 4 7
NFKBIA 0.018 0.008 -10000 0 -10000 0 0
BIRC3 0.021 0.035 0.32 4 -0.32 2 6
BAX -0.001 0.03 0.16 2 -0.13 4 6
EnzymeConsortium:3.1.4.12 0.001 0.02 0.068 3 -0.085 7 10
IKBKB 0.008 0.084 0.28 9 -0.36 7 16
MAP2K2 -0.005 0.035 0.16 9 -10000 0 9
MAP2K1 -0.005 0.039 0.16 12 -0.15 1 13
SMPD1 0 0.024 0.13 1 -0.11 7 8
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.005 0.074 0.25 4 -0.38 7 11
MAP2K4 -0.002 0.036 0.19 8 -0.15 1 9
protein ubiquitination 0.003 0.079 0.28 6 -0.36 7 13
EnzymeConsortium:2.7.1.37 -0.007 0.041 0.15 11 -0.17 1 12
response to UV 0 0 0.002 2 -0.002 1 3
RAF1 -0.003 0.037 0.17 9 -0.15 1 10
CRADD 0.022 0.014 0.32 1 -10000 0 1
mol:ceramide 0.002 0.031 0.1 4 -0.12 8 12
I-kappa-B-alpha/RELA/p50/ubiquitin 0.024 0.011 -10000 0 -10000 0 0
MADD 0.021 0.003 -10000 0 -10000 0 0
MAP3K1 0.001 0.038 0.18 9 -0.14 3 12
TRADD 0.021 0.004 -10000 0 -10000 0 0
RELA/p50 0.021 0.004 -10000 0 -10000 0 0
MAPK3 -0.004 0.038 0.16 9 -10000 0 9
MAPK1 -0.006 0.042 0.16 9 -0.19 3 12
p50/RELA/I-kappa-B-alpha 0.026 0.012 -10000 0 -10000 0 0
FADD 0.001 0.071 0.22 4 -0.38 7 11
KSR1 0 0.039 0.16 11 -0.13 5 16
MAPK8 -0.005 0.041 0.19 13 -0.15 1 14
TRAF2 0.02 0.004 -10000 0 -10000 0 0
response to radiation 0 0 0.002 2 -10000 0 2
CHUK -0.005 0.072 0.33 3 -0.37 7 10
TNF R/SODD 0.026 0.012 -10000 0 -10000 0 0
TNF 0.01 0.061 0.32 1 -0.32 15 16
CYCS 0.008 0.042 0.15 11 -0.13 3 14
IKBKG 0.001 0.076 0.28 5 -0.35 7 12
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.001 0.07 -10000 0 -0.34 11 11
RELA 0.021 0.004 -10000 0 -10000 0 0
RIPK1 0.021 0.004 -10000 0 -10000 0 0
AIFM1 0.003 0.037 0.15 6 -0.13 3 9
TNF/TNF R/SODD 0.029 0.042 0.22 1 -0.19 14 15
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
response to heat 0 0 0.002 2 -10000 0 2
CASP8 0.01 0.087 -10000 0 -0.57 10 10
NSMAF 0.009 0.081 0.2 34 -0.34 9 43
response to hydrogen peroxide 0 0 0.002 2 -0.002 1 3
BCL2 0.019 0.022 0.32 1 -0.32 1 2
Role of Calcineurin-dependent NFAT signaling in lymphocytes

Figure S101.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S101.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.02 0.005 -10000 0 -10000 0 0
NFATC1 -0.014 0.098 0.24 3 -0.39 16 19
NFATC2 -0.011 0.061 0.17 7 -0.24 14 21
NFATC3 0.006 0.021 -10000 0 -0.29 2 2
YWHAE 0.019 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.019 0.094 0.26 1 -0.35 19 20
Exportin 1/Ran/NUP214 0.04 0.013 0.22 1 -10000 0 1
mol:DAG -0.001 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.002 0.086 -10000 0 -0.32 18 18
BCL2/BAX 0.028 0.018 0.23 1 -0.23 1 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.008 0.015 -10000 0 -10000 0 0
CaM/Ca2+ 0.008 0.015 -10000 0 -10000 0 0
BAX 0.02 0.004 -10000 0 -10000 0 0
MAPK14 0.013 0.015 -10000 0 -10000 0 0
BAD 0.021 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D -0.006 0.085 0.24 1 -0.33 17 18
Calcineurin A alpha-beta B1/BCL2 0.019 0.021 0.32 1 -0.32 1 2
FKBP8 0.02 0.016 -10000 0 -0.32 1 1
activation-induced cell death of T cells 0.005 0.084 0.33 17 -0.23 1 18
KPNB1 0.021 0.003 -10000 0 -10000 0 0
KPNA2 0.024 0.03 0.32 5 -10000 0 5
XPO1 0.021 0.002 -10000 0 -10000 0 0
SFN 0.025 0.041 0.32 8 -0.32 1 9
MAP3K8 0.012 0.022 -10000 0 -0.32 1 1
NFAT4/CK1 alpha 0.007 0.026 -10000 0 -0.16 2 2
MEF2D/NFAT1/Cbp/p300 -0.017 0.1 -10000 0 -0.22 80 80
CABIN1 -0.02 0.094 0.26 1 -0.36 19 20
CALM1 0.012 0.017 -10000 0 -10000 0 0
RAN 0.021 0.014 0.32 1 -10000 0 1
MAP3K1 0.02 0.005 -10000 0 -10000 0 0
CAMK4 0.016 0.043 0.32 1 -0.32 7 8
mol:Ca2+ -0.002 0.005 -10000 0 -10000 0 0
MAPK3 0.021 0.003 -10000 0 -10000 0 0
YWHAH 0.02 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.027 0.022 -10000 0 -0.23 3 3
YWHAB 0.02 0.005 -10000 0 -10000 0 0
MAPK8 0.013 0.016 -10000 0 -10000 0 0
MAPK9 0.02 0.004 -10000 0 -10000 0 0
YWHAG 0.021 0.004 -10000 0 -10000 0 0
FKBP1A 0.02 0.005 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.015 0.1 0.26 2 -0.38 20 22
PRKCH 0.021 0.004 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.017 0.028 -10000 0 -10000 0 0
CASP3 0.013 0.016 -10000 0 -10000 0 0
PIM1 0.021 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.009 0.011 -10000 0 -10000 0 0
apoptosis 0.012 0.016 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0 0.038 -10000 0 -0.31 2 2
PRKCB 0.012 0.055 -10000 0 -0.32 13 13
PRKCE 0.018 0.031 -10000 0 -0.32 4 4
JNK2/NFAT4 0.015 0.038 -10000 0 -0.27 2 2
BAD/BCL-XL 0.029 0.008 -10000 0 -10000 0 0
PRKCD 0.021 0.004 -10000 0 -10000 0 0
NUP214 0.02 0.004 -10000 0 -10000 0 0
PRKCZ 0.011 0.031 -10000 0 -0.32 3 3
PRKCA 0.019 0.022 -10000 0 -0.32 2 2
PRKCG 0.046 0.084 0.32 42 -10000 0 42
PRKCQ -0.023 0.11 -10000 0 -0.32 61 61
FKBP38/BCL2 0.027 0.022 0.23 1 -0.23 2 3
EP300 0.011 0.02 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.02 0.005 -10000 0 -10000 0 0
NFATc/JNK1 -0.006 0.098 0.25 2 -0.38 16 18
CaM/Ca2+/FKBP38 0.017 0.023 -10000 0 -0.2 1 1
FKBP12/FK506 0.015 0.004 -10000 0 -10000 0 0
CSNK1A1 -0.015 0.008 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.015 0.033 0.21 1 -0.19 7 8
NFATc/ERK1 -0.003 0.097 0.25 2 -0.38 15 17
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0 0.094 -10000 0 -0.32 20 20
NR4A1 -0.056 0.15 0.22 8 -0.35 87 95
GSK3B 0.013 0.016 -10000 0 -10000 0 0
positive T cell selection 0.006 0.021 -10000 0 -0.29 2 2
NFAT1/CK1 alpha -0.01 0.042 0.13 2 -0.18 10 12
RCH1/ KPNB1 0.032 0.021 0.23 5 -10000 0 5
YWHAQ 0.021 0.002 -10000 0 -10000 0 0
PRKACA 0.013 0.016 -10000 0 -10000 0 0
AKAP5 0.018 0.027 -10000 0 -0.32 3 3
MEF2D 0.01 0.019 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.019 0.007 -10000 0 -10000 0 0
NFATc/p38 alpha -0.01 0.094 -10000 0 -0.38 16 16
CREBBP 0.011 0.02 -10000 0 -10000 0 0
BCL2 0.019 0.022 0.32 1 -0.32 1 2
Retinoic acid receptors-mediated signaling

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
HDAC1 0.021 0.003 -10000 0 -10000 0 0
HDAC3 0.021 0.004 -10000 0 -10000 0 0
VDR 0.021 0.021 0.32 1 -0.32 1 2
Cbp/p300/PCAF 0.04 0.012 -10000 0 -10000 0 0
EP300 0.02 0.004 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.013 0.04 0.16 1 -0.34 2 3
KAT2B 0.021 0.004 -10000 0 -10000 0 0
MAPK14 0.02 0.004 -10000 0 -10000 0 0
AKT1 0.006 0.043 0.23 2 -0.23 2 4
RAR alpha/9cRA/Cyclin H 0.034 0.047 -10000 0 -0.23 2 2
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.008 0.054 -10000 0 -0.3 7 7
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.02 0.034 -10000 0 -0.2 4 4
NCOR2 0.021 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.015 0.014 0.21 1 -0.22 1 2
RXRs/RARs/NRIP1/9cRA -0.013 0.097 0.34 3 -0.43 12 15
NCOA2 0.016 0.031 -10000 0 -0.32 4 4
NCOA3 0.02 0.005 -10000 0 -10000 0 0
NCOA1 0.021 0.002 -10000 0 -10000 0 0
VDR/VDR/DNA 0.021 0.021 0.32 1 -0.32 1 2
RARG 0.021 0.003 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.027 0.007 -10000 0 -10000 0 0
MAPK3 0.021 0.003 -10000 0 -10000 0 0
MAPK1 0.02 0.005 -10000 0 -10000 0 0
MAPK8 0.021 0.003 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.008 0.086 0.27 1 -0.36 13 14
RARA 0.016 0.033 0.19 3 -0.19 2 5
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.006 0.053 -10000 0 -0.3 7 7
PRKCA 0.02 0.022 -10000 0 -0.32 2 2
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.019 0.11 0.33 2 -0.46 13 15
RXRG -0.094 0.13 0.24 2 -0.25 192 194
RXRA 0.01 0.028 0.18 4 -0.18 2 6
RXRB 0.022 0.043 0.21 4 -0.25 2 6
VDR/Vit D3/DNA 0.015 0.014 0.21 1 -0.22 1 2
RBP1 0.023 0.034 0.32 5 -0.32 1 6
CRBP1/9-cic-RA 0.017 0.023 0.21 5 -0.22 1 6
RARB 0.02 0.022 -10000 0 -0.32 2 2
PRKCG 0.046 0.084 0.32 42 -10000 0 42
MNAT1 0.021 0.004 -10000 0 -10000 0 0
RAR alpha/RXRs -0.014 0.086 0.27 1 -0.39 13 14
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.008 0.082 0.25 4 -0.37 11 15
proteasomal ubiquitin-dependent protein catabolic process 0.009 0.077 0.24 3 -0.34 11 14
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.019 0.11 0.33 2 -0.46 13 15
positive regulation of DNA binding 0.024 0.039 -10000 0 -0.22 2 2
NRIP1 -0.018 0.11 0.46 1 -0.52 6 7
RXRs/RARs -0.021 0.11 0.28 1 -0.46 14 15
RXRs/RXRs/DNA/9cRA -0.019 0.08 0.27 1 -0.36 13 14
PRKACA 0.02 0.005 -10000 0 -10000 0 0
CDK7 0.02 0.005 -10000 0 -10000 0 0
TFIIH 0.04 0.012 -10000 0 -10000 0 0
RAR alpha/9cRA 0.043 0.04 -10000 0 -0.22 1 1
CCNH 0.02 0.005 -10000 0 -10000 0 0
CREBBP 0.021 0.004 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.035 0.017 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.006 0.07 -10000 0 -0.3 23 23
KLHL20 -0.002 0.053 0.16 2 -0.2 14 16
CYFIP2 0.016 0.041 -10000 0 -0.32 7 7
Rac1/GDP -0.011 0.061 0.3 4 -0.25 8 12
ENAH -0.006 0.071 -10000 0 -0.31 24 24
AP1M1 0.02 0.005 -10000 0 -10000 0 0
RAP1B 0.02 0.005 -10000 0 -10000 0 0
RAP1A 0.02 0.004 -10000 0 -10000 0 0
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.026 0.022 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.015 0.028 -10000 0 -0.14 18 18
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.046 0.026 -10000 0 -0.17 3 3
RAPGEF1 -0.01 0.059 0.21 2 -0.28 14 16
CTNND1 0.021 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.001 0.073 -10000 0 -0.31 24 24
CRK -0.01 0.053 -10000 0 -0.3 14 14
E-cadherin/gamma catenin/alpha catenin 0.039 0.019 -10000 0 -0.19 2 2
alphaE/beta7 Integrin 0.028 0.015 -10000 0 -0.23 1 1
IQGAP1 0.021 0.003 -10000 0 -10000 0 0
NCKAP1 0.021 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.034 0.016 -10000 0 -10000 0 0
DLG1 -0.004 0.067 -10000 0 -0.31 21 21
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.025 0.015 -10000 0 -0.13 2 2
MLLT4 0.019 0.006 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.049 0.054 0.21 40 -0.17 5 45
PI3K -0.03 0.019 -10000 0 -0.16 2 2
ARF6 0.02 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.029 0.018 -10000 0 -0.23 2 2
TIAM1 0.016 0.038 -10000 0 -0.32 6 6
E-cadherin(dimer)/Ca2+ 0.045 0.02 -10000 0 -0.16 2 2
AKT1 -0.017 0.025 -10000 0 -10000 0 0
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
CDH1 0.019 0.022 -10000 0 -0.32 2 2
RhoA/GDP -0.012 0.063 0.3 4 -0.25 8 12
actin cytoskeleton organization 0.002 0.046 0.16 10 -0.15 12 22
CDC42/GDP -0.012 0.063 0.3 4 -0.25 9 13
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.009 0.013 -10000 0 -0.19 2 2
ITGB7 0.02 0.016 -10000 0 -0.32 1 1
RAC1 0.019 0.007 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.049 0.021 -10000 0 -0.17 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin 0.034 0.016 -10000 0 -0.15 2 2
mol:GDP -0.012 0.069 0.32 4 -0.29 9 13
CDC42/GTP/IQGAP1 0.027 0.006 -10000 0 -10000 0 0
JUP 0.021 0.003 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.004 0.06 0.23 2 -0.25 6 8
RAC1/GTP/IQGAP1 0.025 0.01 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.029 0.008 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
CDC42 0.021 0.004 -10000 0 -10000 0 0
CTNNA1 0.021 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.006 0.037 0.13 12 -0.12 13 25
NME1 0.048 0.086 0.32 44 -10000 0 44
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0 0.057 -10000 0 -0.3 14 14
regulation of cell-cell adhesion -0.024 0.018 -10000 0 -0.15 2 2
WASF2 -0.004 0.023 -10000 0 -0.088 4 4
Rap1/GTP -0.023 0.029 -10000 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.051 0.031 -10000 0 -0.17 3 3
CCND1 0.007 0.043 0.14 11 -0.14 13 24
VAV2 -0.011 0.13 -10000 0 -0.57 20 20
RAP1/GDP -0.019 0.044 0.2 1 -0.23 4 5
adherens junction assembly 0 0.055 -10000 0 -0.3 14 14
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.021 0.004 -10000 0 -10000 0 0
PIP5K1C 0.02 0.005 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.036 0.026 -10000 0 -0.16 3 3
E-cadherin/beta catenin 0.004 0.02 -10000 0 -0.28 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.006 0.07 -10000 0 -0.31 23 23
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
Rac1/GTP -0.007 0.068 -10000 0 -0.31 19 19
E-cadherin/beta catenin/alpha catenin 0.039 0.019 -10000 0 -0.18 2 2
ITGAE 0.019 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.001 0.075 -10000 0 -0.32 24 24
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 0.017 0.034 0.32 1 -0.32 4 5
CLTC 0.015 0.057 0.23 1 -0.44 5 6
calcium ion-dependent exocytosis 0.01 0.031 0.19 3 -0.16 4 7
Dynamin 2/GTP 0.025 0.032 0.12 41 -10000 0 41
EXOC4 0.02 0.005 -10000 0 -10000 0 0
CD59 0.011 0.036 -10000 0 -0.31 4 4
CPE -0.005 0.04 0.19 17 -10000 0 17
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
membrane fusion 0.01 0.025 -10000 0 -10000 0 0
CTNND1 -0.003 0.05 0.19 24 -10000 0 24
DNM2 0.02 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.007 0.045 0.18 6 -0.25 4 10
TSHR 0.005 0.054 0.17 48 -10000 0 48
INS 0.002 0.071 -10000 0 -0.5 9 9
BIN1 0.021 0.001 -10000 0 -10000 0 0
mol:Choline 0.01 0.025 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.006 0.06 0.18 47 -10000 0 47
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.02 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.004 0.04 0.12 41 -10000 0 41
JUP 0.01 0.032 -10000 0 -0.3 3 3
ASAP2/amphiphysin II 0.039 0.01 -10000 0 -10000 0 0
ARF6/GTP 0.015 0.003 -10000 0 -10000 0 0
CDH1 0.01 0.037 -10000 0 -0.31 4 4
clathrin-independent pinocytosis 0.015 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.021 0.014 0.32 1 -10000 0 1
positive regulation of endocytosis 0.015 0.003 -10000 0 -10000 0 0
EXOC2 0.02 0.004 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.007 0.02 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.021 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.03 0.045 0.28 5 -10000 0 5
positive regulation of phagocytosis -0.012 0.003 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.027 0.011 0.21 1 -10000 0 1
ACAP1 0.013 0.028 -10000 0 -0.15 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.011 0.062 -10000 0 -0.31 4 4
clathrin heavy chain/ACAP1 0.014 0.049 0.2 5 -0.32 4 9
JIP4/KLC1 0.038 0.012 -10000 0 -10000 0 0
EXOC1 0.021 0.003 -10000 0 -10000 0 0
exocyst 0.007 0.02 -10000 0 -10000 0 0
RALA/GTP 0.014 0.004 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.027 0.007 -10000 0 -10000 0 0
receptor recycling 0.015 0.003 -10000 0 -10000 0 0
CTNNA1 -0.003 0.049 0.19 23 -10000 0 23
NME1 0.006 0.06 0.18 47 -10000 0 47
clathrin coat assembly 0.015 0.06 0.23 1 -0.4 6 7
IL2RA 0.014 0.041 -10000 0 -0.33 4 4
VAMP3 -0.012 0.003 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.017 0.049 0.22 1 -0.31 5 6
EXOC6 0.021 0.003 -10000 0 -10000 0 0
PLD1 0.005 0.005 -10000 0 -10000 0 0
PLD2 0.005 0.005 -10000 0 -10000 0 0
EXOC5 0.02 0.004 -10000 0 -10000 0 0
PIP5K1C 0.007 0.042 0.17 5 -0.26 4 9
SDC1 0.011 0.037 -10000 0 -0.31 4 4
ARF6/GDP 0.027 0.034 0.13 44 -10000 0 44
EXOC7 0.021 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.033 0.048 -10000 0 -0.28 5 5
mol:Phosphatidic acid 0.01 0.025 -10000 0 -10000 0 0
endocytosis -0.037 0.01 -10000 0 -10000 0 0
SCAMP2 0.021 0.004 -10000 0 -10000 0 0
ADRB2 -0.037 0.089 0.21 1 -0.45 6 7
EXOC3 0.016 0.009 -10000 0 -10000 0 0
ASAP2 0.021 0.002 -10000 0 -10000 0 0
Dynamin 2/GDP 0.032 0.045 0.17 43 -10000 0 43
KLC1 0.02 0.005 -10000 0 -10000 0 0
AVPR2 -0.013 0.088 0.27 8 -0.4 6 14
RALA 0.019 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.023 0.05 0.33 2 -0.29 4 6
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.02 0.016 -10000 0 -0.32 1 1
SPHK1 0.023 0.027 0.32 4 -10000 0 4
GNAI2 0.021 0.004 -10000 0 -10000 0 0
mol:S1P 0.007 0.014 -10000 0 -0.22 1 1
GNAO1 0.021 0.032 0.32 3 -0.32 2 5
mol:Sphinganine-1-P -0.015 0.018 0.15 4 -0.23 1 5
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.034 0.034 -10000 0 -0.2 2 2
GNAI3 0.02 0.004 -10000 0 -10000 0 0
G12/G13 0.027 0.011 -10000 0 -10000 0 0
S1PR3 0.021 0.014 0.32 1 -10000 0 1
S1PR2 0.02 0.005 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0 0.028 -10000 0 -0.23 3 3
S1PR5 0 0.082 0.32 1 -0.32 29 30
S1PR4 0.008 0.063 -10000 0 -0.32 17 17
GNAI1 0.02 0.016 -10000 0 -0.32 1 1
S1P/S1P5/G12 0.016 0.051 0.21 1 -0.17 22 23
S1P/S1P3/Gq 0.004 0.068 -10000 0 -0.29 21 21
S1P/S1P4/Gi -0.015 0.084 -10000 0 -0.34 13 13
GNAQ 0.02 0.016 -10000 0 -0.32 1 1
GNAZ -0.007 0.092 -10000 0 -0.32 38 38
GNA14 0.013 0.051 -10000 0 -0.32 11 11
GNA15 0.02 0.006 -10000 0 -10000 0 0
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA13 0.021 0.004 -10000 0 -10000 0 0
GNA11 0.019 0.016 -10000 0 -0.32 1 1
ABCC1 0.021 0.004 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.019 0.007 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.022 0.047 -10000 0 -0.27 3 3
NEF -0.001 0.019 -10000 0 -0.16 6 6
NFKBIA 0.019 0.009 -10000 0 -10000 0 0
BIRC3 0.006 0.067 0.29 4 -10000 0 4
CYCS 0.003 0.044 0.15 26 -0.29 2 28
RIPK1 0.021 0.004 -10000 0 -10000 0 0
CD247 0.018 0.027 -10000 0 -0.22 5 5
MAP2K7 -0.014 0.17 -10000 0 -0.64 28 28
protein ubiquitination 0.003 0.065 0.29 2 -0.29 5 7
CRADD 0.022 0.014 0.32 1 -10000 0 1
DAXX 0.021 0.004 -10000 0 -10000 0 0
FAS 0.018 0.031 -10000 0 -0.32 4 4
BID 0.008 0.049 0.16 28 -0.27 3 31
NF-kappa-B/RelA/I kappa B alpha 0.039 0.024 0.22 4 -10000 0 4
TRADD 0.021 0.004 -10000 0 -10000 0 0
MAP3K5 0.019 0.006 -10000 0 -10000 0 0
CFLAR 0.021 0.002 -10000 0 -10000 0 0
FADD 0.02 0.004 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.039 0.024 0.22 4 -10000 0 4
MAPK8 -0.015 0.16 0.38 1 -0.6 28 29
APAF1 0.021 0.003 -10000 0 -10000 0 0
TRAF1 0.021 0.004 -10000 0 -10000 0 0
TRAF2 0.021 0.004 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.009 0.032 -10000 0 -0.28 3 3
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.003 0.066 -10000 0 -0.31 9 9
CHUK 0.001 0.068 0.3 2 -0.31 5 7
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.051 0.029 -10000 0 -0.17 1 1
TCRz/NEF 0.014 0.026 0.18 1 -0.23 5 6
TNF 0.011 0.061 0.32 1 -0.32 15 16
FASLG -0.013 0.038 0.3 1 -0.33 5 6
NFKB1 0.021 0.011 -10000 0 -0.13 2 2
TNFR1A/BAG4/TNF-alpha 0.029 0.042 0.22 1 -0.19 14 15
CASP6 0.029 0.07 -10000 0 -0.48 4 4
CASP7 0.028 0.093 0.31 18 -0.31 1 19
RELA 0.021 0.011 -10000 0 -0.13 2 2
CASP2 0.02 0.005 -10000 0 -10000 0 0
CASP3 0.025 0.09 0.32 15 -0.29 1 16
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.026 0.012 -10000 0 -10000 0 0
CASP8 0.02 0.016 -10000 0 -0.32 1 1
CASP9 0.021 0.004 -10000 0 -10000 0 0
MAP3K14 0.004 0.067 0.2 1 -0.34 5 6
APAF-1/Caspase 9 -0.009 0.049 0.17 4 -0.28 1 5
BCL2 -0.014 0.14 0.31 2 -0.54 28 30
IGF1 pathway

Figure S107.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S107.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.021 0.002 -10000 0 -10000 0 0
PTK2 0.018 0.007 -10000 0 -10000 0 0
CRKL -0.018 0.026 0.15 1 -0.19 9 10
GRB2/SOS1/SHC 0.035 0.017 -10000 0 -10000 0 0
HRAS 0.021 0.004 -10000 0 -10000 0 0
IRS1/Crk 0.009 0.032 -10000 0 -0.18 11 11
IGF-1R heterotetramer/IGF1/PTP1B 0.034 0.035 0.21 1 -0.19 9 10
AKT1 -0.023 0.039 0.15 11 -0.23 1 12
BAD -0.026 0.037 0.14 11 -0.23 1 12
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.019 0.027 0.15 1 -0.19 10 11
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.018 0.036 0.19 4 -0.19 11 15
RAF1 -0.016 0.07 0.26 1 -0.41 11 12
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.041 0.039 0.2 1 -0.19 8 9
YWHAZ 0.019 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.021 0.035 0.19 1 -0.2 11 12
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.022 0.039 0.15 13 -0.23 1 14
GNB2L1 0.02 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.005 0.069 0.27 5 -0.36 3 8
PXN 0.021 0.003 -10000 0 -10000 0 0
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.03 0.007 -10000 0 -10000 0 0
HRAS/GTP -0.023 0.018 -10000 0 -0.17 3 3
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.048 0.033 -10000 0 -0.16 3 3
IGF-1R heterotetramer 0.019 0.022 -10000 0 -0.34 1 1
IGF-1R heterotetramer/IGF1/IRS/Nck 0.031 0.039 0.2 1 -0.19 11 12
Crk/p130 Cas/Paxillin 0.036 0.04 -10000 0 -0.17 11 11
IGF1R 0.019 0.022 -10000 0 -0.34 1 1
IGF1 0.014 0.054 0.32 1 -0.34 10 11
IRS2/Crk -0.021 0.027 0.14 1 -0.18 11 12
PI3K 0.038 0.041 0.2 1 -0.18 11 12
apoptosis 0.022 0.042 0.21 1 -0.28 1 2
HRAS/GDP 0.015 0.003 -10000 0 -10000 0 0
PRKCD -0.004 0.041 -10000 0 -0.24 10 10
RAF1/14-3-3 E -0.011 0.073 0.25 2 -0.34 12 14
BAD/14-3-3 -0.023 0.044 0.28 1 -0.22 1 2
PRKCZ -0.024 0.04 0.15 11 -0.23 1 12
Crk/p130 Cas/Paxillin/FAK1 -0.031 0.033 -10000 0 -0.21 1 1
PTPN1 0.02 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0 0.044 -10000 0 -0.25 9 9
BCAR1 0.02 0.016 -10000 0 -0.32 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.038 0.033 0.21 1 -0.16 5 6
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.021 0.003 -10000 0 -10000 0 0
IRS1/NCK2 0.016 0.036 -10000 0 -0.19 11 11
GRB10 0.019 0.006 -10000 0 -10000 0 0
PTPN11 -0.019 0.029 0.15 2 -0.19 11 13
IRS1 -0.015 0.033 0.12 7 -0.2 11 18
IRS2 -0.019 0.029 0.15 2 -0.19 11 13
IGF-1R heterotetramer/IGF1 0.024 0.044 0.23 1 -0.25 11 12
GRB2 0.02 0.004 -10000 0 -10000 0 0
PDPK1 -0.02 0.041 0.16 12 -0.24 1 13
YWHAE 0.019 0.006 -10000 0 -10000 0 0
PRKD1 -0.006 0.045 -10000 0 -0.31 5 5
SHC1 0.018 0.008 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.013 0.011 -10000 0 -10000 0 0
TRAF2/ASK1 0.025 0.01 -10000 0 -10000 0 0
ATM 0.02 0.004 -10000 0 -10000 0 0
MAP2K3 -0.005 0.09 0.29 2 -0.31 24 26
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.001 0.081 0.37 1 -0.36 11 12
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.019 0.037 0.32 2 -0.32 4 6
TXN 0.004 0.011 0.17 2 -10000 0 2
CALM1 0.02 0.005 -10000 0 -10000 0 0
GADD45A 0.021 0.003 -10000 0 -10000 0 0
GADD45B 0.018 0.022 -10000 0 -0.32 2 2
MAP3K1 0.02 0.005 -10000 0 -10000 0 0
MAP3K6 0.021 0.003 -10000 0 -10000 0 0
MAP3K7 0.019 0.006 -10000 0 -10000 0 0
MAP3K4 0.019 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.028 0.01 -10000 0 -10000 0 0
TAK1/TAB family 0.001 0.018 0.13 2 -0.13 1 3
RAC1/OSM/MEKK3 0.035 0.017 -10000 0 -0.15 1 1
TRAF2 0.021 0.004 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.005 0.073 -10000 0 -0.27 17 17
TRAF6 0.004 0.001 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.063 0.11 0.32 72 -10000 0 72
CCM2 0.019 0.006 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.05 0.064 0.21 69 -10000 0 69
MAPK11 0.018 0.022 -10000 0 -0.32 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.055 0.062 0.21 64 -10000 0 64
OSM/MEKK3 0.027 0.015 -10000 0 -0.23 1 1
TAOK1 0.007 0.012 -10000 0 -0.25 1 1
TAOK2 0.007 0.002 -10000 0 -10000 0 0
TAOK3 0.007 0.002 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.02 0.004 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.019 0.006 -10000 0 -10000 0 0
MAP3K10 0.018 0.027 -10000 0 -0.32 3 3
MAP3K3 0.02 0.016 -10000 0 -0.32 1 1
TRX/ASK1 0.015 0.018 0.15 1 -0.099 9 10
GADD45/MTK1/MTK1 0.041 0.031 0.21 2 -0.2 4 6
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.031 0.063 0.22 1 -0.25 14 15
Ran/GTP/Exportin 1/HDAC1 -0.017 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.009 0.063 -10000 0 -0.28 13 13
SUMO1 0.021 0.002 -10000 0 -10000 0 0
ZFPM1 0.02 0.015 0.32 1 -10000 0 1
NPC/RanGAP1/SUMO1/Ubc9 0.006 0.002 -10000 0 -10000 0 0
FKBP3 0.02 0.005 -10000 0 -10000 0 0
Histones 0.035 0.052 -10000 0 -0.29 2 2
YY1/LSF 0.014 0.045 -10000 0 -0.24 7 7
SMG5 0.018 0.008 -10000 0 -10000 0 0
RAN 0.021 0.014 0.32 1 -10000 0 1
I kappa B alpha/HDAC3 0.006 0.032 -10000 0 -0.19 11 11
I kappa B alpha/HDAC1 0.014 0.039 -10000 0 -0.32 1 1
SAP18 0.02 0.005 -10000 0 -10000 0 0
RELA 0.008 0.045 -10000 0 -0.32 3 3
HDAC1/Smad7 0.036 0.019 -10000 0 -0.19 1 1
RANGAP1 0.02 0.004 -10000 0 -10000 0 0
HDAC3/TR2 0.016 0.048 -10000 0 -0.2 8 8
NuRD/MBD3 Complex -0.005 0.053 -10000 0 -0.3 8 8
NF kappa B1 p50/RelA 0.013 0.068 -10000 0 -0.3 12 12
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 -0.006 0.093 -10000 0 -0.32 39 39
GATA1 -0.014 0.1 -10000 0 -0.32 49 49
Mad/Max 0.03 0.007 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.018 0.091 -10000 0 -0.31 24 24
RBBP7 0.021 0.004 -10000 0 -10000 0 0
NPC 0.012 0.001 -10000 0 -10000 0 0
RBBP4 0.021 0.003 -10000 0 -10000 0 0
MAX 0.02 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.02 0.005 -10000 0 -10000 0 0
NFKBIA 0.006 0.023 -10000 0 -10000 0 0
KAT2B 0.021 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex -0.009 0.052 -10000 0 -0.37 3 3
SIN3 complex 0.047 0.019 -10000 0 -10000 0 0
SMURF1 0.02 0.005 -10000 0 -10000 0 0
CHD3 0.019 0.006 -10000 0 -10000 0 0
SAP30 0.021 0.004 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.02 0.006 -10000 0 -10000 0 0
YY1/HDAC3 0.006 0.047 -10000 0 -0.32 5 5
YY1/HDAC2 0.014 0.042 -10000 0 -0.24 7 7
YY1/HDAC1 0.014 0.045 -10000 0 -0.24 7 7
NuRD/MBD2 Complex (MeCP1) -0.007 0.057 -10000 0 -0.32 9 9
PPARG -0.02 0.1 -10000 0 -0.28 54 54
HDAC8/hEST1B 0.035 0.017 -10000 0 -10000 0 0
UBE2I 0.021 0.004 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0.005 -10000 0 -10000 0 0
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.017 0.047 -10000 0 -0.2 8 8
MBD3L2 0.016 0.004 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.036 0.019 -10000 0 -0.19 1 1
CREBBP 0.021 0.004 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.001 0.076 -10000 0 -0.31 19 19
HDAC1 0.021 0.003 -10000 0 -10000 0 0
HDAC3 0.007 0.028 -10000 0 -0.34 1 1
HDAC2 0.019 0.006 -10000 0 -10000 0 0
YY1 0.008 0.003 -10000 0 -10000 0 0
HDAC8 0.021 0.002 -10000 0 -10000 0 0
SMAD7 0.019 0.017 -10000 0 -0.32 1 1
NCOR2 0.021 0.003 -10000 0 -10000 0 0
MXD1 0.021 0.002 -10000 0 -10000 0 0
STAT3 0.011 0.003 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.021 0.002 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.025 0.045 -10000 0 -0.22 7 7
YY1/SAP30/HDAC1 0.025 0.045 -10000 0 -0.22 7 7
EP300 0.02 0.004 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.011 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.023 -10000 0 -10000 0 0
histone deacetylation 0 0.062 -10000 0 -0.32 9 9
STAT3 (dimer non-phopshorylated)/HDAC3 0.007 0.037 -10000 0 -0.22 6 6
nuclear export -0.035 0.017 -10000 0 -10000 0 0
PRKACA 0.02 0.005 -10000 0 -10000 0 0
GATAD2B 0.018 0.008 -10000 0 -10000 0 0
GATAD2A 0.02 0.005 -10000 0 -10000 0 0
GATA2/HDAC3 0.004 0.066 -10000 0 -0.23 13 13
GATA1/HDAC1 0.004 0.077 -10000 0 -0.23 49 49
GATA1/HDAC3 -0.001 0.071 -10000 0 -0.29 8 8
CHD4 0.02 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.022 0.045 0.23 1 -0.23 14 15
SIN3/HDAC complex/Mad/Max -0.008 0.056 -10000 0 -0.3 8 8
NuRD Complex -0.003 0.075 -10000 0 -0.3 18 18
positive regulation of chromatin silencing 0.033 0.051 -10000 0 -0.29 2 2
SIN3B 0.02 0.004 -10000 0 -10000 0 0
MTA2 0.021 0.003 -10000 0 -10000 0 0
SIN3A 0.021 0.003 -10000 0 -10000 0 0
XPO1 0.021 0.002 -10000 0 -10000 0 0
SUMO1/HDAC1 0.028 0.03 -10000 0 -0.21 3 3
HDAC complex 0.048 0.019 -10000 0 -10000 0 0
GATA1/Fog1 0.003 0.076 -10000 0 -0.22 49 49
FKBP25/HDAC1/HDAC2 0.037 0.015 -10000 0 -10000 0 0
TNF 0.011 0.061 0.32 1 -0.32 15 16
negative regulation of cell growth -0.007 0.057 -10000 0 -0.3 8 8
NuRD/MBD2/PRMT5 Complex -0.007 0.057 -10000 0 -0.32 9 9
Ran/GTP/Exportin 1 0.028 0.03 -10000 0 -0.19 4 4
NF kappa B/RelA/I kappa B alpha -0.001 0.055 -10000 0 -0.28 13 13
SIN3/HDAC complex/NCoR1 -0.01 0.072 -10000 0 -0.31 17 17
TFCP2 0.021 0.003 -10000 0 -10000 0 0
NR2C1 0.021 0.003 -10000 0 -10000 0 0
MBD3 0.018 0.022 -10000 0 -0.32 2 2
MBD2 0.019 0.006 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.017 0.007 -10000 0 -10000 0 0
SNTA1 0.022 0.024 0.32 3 -10000 0 3
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.017 0.017 0.2 2 -10000 0 2
MAPK12 -0.008 0.017 0.16 1 -0.16 2 3
CCND1 0 0.052 -10000 0 -0.38 8 8
p38 gamma/SNTA1 -0.007 0.046 0.18 17 -0.28 1 18
MAP2K3 0.02 0.006 -10000 0 -10000 0 0
PKN1 0.02 0.005 -10000 0 -10000 0 0
G2/M transition checkpoint -0.003 0.037 0.2 14 -0.16 2 16
MAP2K6 -0.003 0.02 0.19 1 -0.18 2 3
MAPT -0.007 0.071 0.21 12 -0.24 24 36
MAPK13 -0.015 0.005 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.007 0.002 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.002 0.061 -10000 0 -0.5 1 1
UGCG -0.001 0.11 -10000 0 -0.61 14 14
AKT1/mTOR/p70S6K/Hsp90/TERT 0.052 0.083 0.27 7 -0.37 5 12
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.001 0.11 -10000 0 -0.6 14 14
mol:DAG 0.002 0.083 -10000 0 -0.79 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 0.024 0.077 0.28 2 -0.36 7 9
FRAP1 0.019 0.085 0.31 2 -0.41 7 9
FOXO3 0.015 0.079 0.31 1 -0.42 6 7
AKT1 0.018 0.085 0.32 1 -0.45 6 7
GAB2 0.017 0.031 -10000 0 -0.32 4 4
SMPD1 0.006 0.083 -10000 0 -0.62 8 8
SGMS1 0.011 0.061 -10000 0 -0.56 5 5
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP -0.012 0.009 -10000 0 -0.19 1 1
CALM1 0.02 0.005 -10000 0 -10000 0 0
cell proliferation 0.024 0.085 0.27 3 -0.36 11 14
EIF3A 0.021 0.003 -10000 0 -10000 0 0
PI3K 0.029 0.015 -10000 0 -0.22 1 1
RPS6KB1 0.014 0.06 -10000 0 -0.84 2 2
mol:sphingomyelin 0.002 0.083 -10000 0 -0.79 5 5
natural killer cell activation 0 0.001 -10000 0 -10000 0 0
JAK3 0.02 0.006 -10000 0 -10000 0 0
PIK3R1 0.02 0.017 -10000 0 -0.32 1 1
JAK1 0.021 0.005 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
MYC 0.04 0.12 0.41 4 -0.76 3 7
MYB 0.002 0.12 -10000 0 -1 5 5
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.017 0.067 -10000 0 -0.38 4 4
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.034 0.059 -10000 0 -0.77 2 2
mol:PI-3-4-5-P3 0.017 0.066 -10000 0 -0.37 4 4
Rac1/GDP -0.014 0.01 -10000 0 -0.17 1 1
T cell proliferation 0.012 0.064 -10000 0 -0.33 3 3
SHC1 0.018 0.008 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.001 0.009 0.085 3 -0.066 4 7
PRKCZ 0.012 0.063 -10000 0 -0.33 2 2
NF kappa B1 p50/RelA 0.034 0.081 0.3 2 -0.38 6 8
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0 0.055 -10000 0 -0.37 5 5
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
RELA 0.021 0.004 -10000 0 -10000 0 0
IL2RA 0.04 0.078 0.32 34 -0.32 1 35
IL2RB 0.019 0.023 -10000 0 -0.32 2 2
TERT 0.077 0.12 0.32 99 -10000 0 99
E2F1 0.01 0.08 -10000 0 -0.44 12 12
SOS1 0.021 0.004 -10000 0 -10000 0 0
RPS6 0.019 0.006 -10000 0 -10000 0 0
mol:cAMP -0.001 0.005 0.031 4 -0.046 3 7
PTPN11 0.021 0.005 -10000 0 -10000 0 0
IL2RG 0.018 0.035 -10000 0 -0.32 5 5
actin cytoskeleton organization 0.012 0.064 -10000 0 -0.33 3 3
GRB2 0.02 0.005 -10000 0 -10000 0 0
IL2 0.02 0.006 -10000 0 -10000 0 0
PIK3CA 0.021 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.032 0.019 -10000 0 -0.16 1 1
LCK 0.021 0.026 0.32 1 -0.32 2 3
BCL2 0.016 0.082 0.46 1 -0.52 3 4
TCGA08_rtk_signaling

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
PDGFRA 0.018 0.031 -10000 0 -0.32 4 4
HRAS 0.021 0.004 -10000 0 -10000 0 0
EGFR 0.015 0.041 0.32 1 -0.32 6 7
AKT 0.03 0.063 0.24 10 -0.21 3 13
FOXO3 0.019 0.006 -10000 0 -10000 0 0
AKT1 0.02 0.005 -10000 0 -10000 0 0
FOXO1 0.02 0.005 -10000 0 -10000 0 0
AKT3 0.018 0.023 -10000 0 -0.32 2 2
FOXO4 0.021 0.002 -10000 0 -10000 0 0
MET 0.013 0.068 0.32 6 -0.32 15 21
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
PIK3CB 0.021 0.003 -10000 0 -10000 0 0
NRAS 0.02 0.005 -10000 0 -10000 0 0
PIK3CG 0.01 0.057 -10000 0 -0.32 14 14
PIK3R3 0.02 0.016 -10000 0 -0.32 1 1
PIK3R2 0.02 0.005 -10000 0 -10000 0 0
NF1 0.021 0.003 -10000 0 -10000 0 0
RAS 0.018 0.04 0.19 6 -0.12 11 17
ERBB2 0.021 0.004 -10000 0 -10000 0 0
proliferation/survival/translation -0.013 0.067 0.26 13 -0.21 1 14
PI3K 0.021 0.06 0.21 23 -0.14 14 37
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
KRAS 0.02 0.006 -10000 0 -10000 0 0
FOXO 0.047 0.048 0.22 12 -10000 0 12
AKT2 0.02 0.005 -10000 0 -10000 0 0
PTEN 0.021 0.004 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.002 0.044 0.3 2 -0.24 6 8
adherens junction organization -0.005 0.055 -10000 0 -0.38 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.012 0.05 0.22 1 -0.2 2 3
FMN1 -0.008 0.054 -10000 0 -0.27 12 12
mol:IP3 -0.013 0.029 -10000 0 -0.21 4 4
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.001 0.058 -10000 0 -0.28 13 13
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
AKT1 -0.014 0.039 0.2 2 -0.24 5 7
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.004 0.11 -10000 0 -0.56 12 12
CTNND1 0.021 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.005 0.044 -10000 0 -0.27 9 9
VASP -0.002 0.044 -10000 0 -0.32 6 6
ZYX -0.006 0.053 -10000 0 -0.28 12 12
JUB -0.002 0.055 -10000 0 -0.27 13 13
EGFR(dimer) 0.006 0.06 0.2 1 -0.26 14 15
E-cadherin/beta catenin-gamma catenin 0.039 0.018 -10000 0 -0.16 2 2
mol:PI-3-4-5-P3 0.02 0.05 0.22 2 -0.24 6 8
PIK3CA 0.019 0.009 -10000 0 -10000 0 0
PI3K 0.021 0.051 0.23 2 -0.25 6 8
FYN -0.015 0.064 0.33 2 -0.27 8 10
mol:Ca2+ -0.013 0.029 -10000 0 -0.2 4 4
JUP 0.021 0.004 -10000 0 -10000 0 0
PIK3R1 0.019 0.017 -10000 0 -0.32 1 1
mol:DAG -0.013 0.029 -10000 0 -0.21 4 4
CDH1 0.019 0.022 -10000 0 -0.32 2 2
RhoA/GDP -0.004 0.063 0.22 1 -10000 0 1
establishment of polarity of embryonic epithelium -0.002 0.043 -10000 0 -0.31 6 6
SRC 0.02 0.004 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
EGFR 0.015 0.041 0.32 1 -0.32 6 7
CASR -0.006 0.045 0.3 2 -0.2 4 6
RhoA/GTP 0.01 0.038 -10000 0 -0.2 3 3
AKT2 -0.013 0.038 0.2 2 -0.24 5 7
actin cable formation -0.012 0.046 -10000 0 -0.32 6 6
apoptosis -0.002 0.052 0.25 8 -0.24 5 13
CTNNA1 0.021 0.005 -10000 0 -10000 0 0
mol:GDP -0.014 0.039 0.17 4 -0.2 4 8
PIP5K1A -0.005 0.045 -10000 0 -0.28 9 9
PLCG1 -0.013 0.03 -10000 0 -0.21 4 4
Rac1/GTP 0.014 0.057 -10000 0 -0.26 11 11
homophilic cell adhesion -0.001 0.002 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.048 0.021 -10000 0 -0.18 1 1
HDAC3 0.021 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.017 0.005 -10000 0 -10000 0 0
GATA1/HDAC4 0.005 0.076 -10000 0 -0.22 48 48
GATA1/HDAC5 0.004 0.076 -10000 0 -0.23 48 48
GATA2/HDAC5 0.01 0.07 -10000 0 -0.23 39 39
HDAC5/BCL6/BCoR 0.039 0.013 -10000 0 -10000 0 0
HDAC9 0.019 0.046 0.32 5 -0.32 5 10
Glucocorticoid receptor/Hsp90/HDAC6 0.039 0.013 -10000 0 -10000 0 0
HDAC4/ANKRA2 0.03 0.008 -10000 0 -10000 0 0
HDAC5/YWHAB 0.029 0.009 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.006 0.002 -10000 0 -10000 0 0
GATA2 -0.006 0.093 -10000 0 -0.32 39 39
HDAC4/RFXANK 0.03 0.008 -10000 0 -10000 0 0
BCOR 0.021 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.019 0.016 -10000 0 -0.32 1 1
HDAC5 0.021 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.028 0.018 -10000 0 -0.23 2 2
Histones 0.01 0.05 -10000 0 -0.26 5 5
ADRBK1 0.021 0.003 -10000 0 -10000 0 0
HDAC4 0.021 0.003 -10000 0 -10000 0 0
XPO1 0.021 0.002 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.03 0.008 -10000 0 -10000 0 0
HDAC4/Ubc9 0.03 0.007 -10000 0 -10000 0 0
HDAC7 0.021 0.003 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.028 0.01 -10000 0 -10000 0 0
TUBA1B 0.021 0.003 -10000 0 -10000 0 0
HDAC6 0.021 0.004 -10000 0 -10000 0 0
HDAC5/RFXANK 0.03 0.008 -10000 0 -10000 0 0
CAMK4 0.016 0.043 0.32 1 -0.32 7 8
Tubulin/HDAC6 0.045 0.03 0.22 12 -10000 0 12
SUMO1 0.021 0.002 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.02 0.005 -10000 0 -10000 0 0
GATA1 -0.014 0.1 -10000 0 -0.32 49 49
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
NR3C1 0.021 0.004 -10000 0 -10000 0 0
SUMO1/HDAC4 0.028 0.029 -10000 0 -0.2 3 3
SRF 0.02 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.029 0.009 -10000 0 -10000 0 0
Tubulin 0.035 0.032 0.23 12 -10000 0 12
HDAC4/14-3-3 E 0.028 0.01 -10000 0 -10000 0 0
GNB1 0.02 0.004 -10000 0 -10000 0 0
RANGAP1 0.02 0.004 -10000 0 -10000 0 0
BCL6/BCoR 0.029 0.008 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.04 0.011 -10000 0 -10000 0 0
HDAC4/SRF 0.036 0.032 0.22 1 -0.19 7 8
HDAC4/ER alpha 0.027 0.043 0.23 8 -0.23 8 16
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.01 0.05 -10000 0 -0.26 5 5
cell motility 0.044 0.03 0.22 12 -10000 0 12
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.021 0.004 -10000 0 -10000 0 0
HDAC7/HDAC3 0.03 0.007 -10000 0 -10000 0 0
BCL6 0.02 0.005 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.021 0.003 -10000 0 -10000 0 0
Hsp90/HDAC6 0.029 0.008 -10000 0 -10000 0 0
ESR1 0.019 0.06 0.32 9 -0.32 8 17
HDAC6/HDAC11 0.03 0.008 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.028 0.03 -10000 0 -0.19 4 4
NPC 0.012 0.001 -10000 0 -10000 0 0
MEF2C 0.02 0.005 -10000 0 -10000 0 0
RAN 0.021 0.014 0.32 1 -10000 0 1
HDAC4/MEF2C 0.057 0.021 -10000 0 -10000 0 0
GNG2 0.019 0.022 -10000 0 -0.32 2 2
NCOR2 0.021 0.003 -10000 0 -10000 0 0
TUBB2A 0.028 0.047 0.32 12 -10000 0 12
HDAC11 0.021 0.004 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
RANBP2 0.021 0.002 -10000 0 -10000 0 0
ANKRA2 0.02 0.004 -10000 0 -10000 0 0
RFXANK 0.02 0.005 -10000 0 -10000 0 0
nuclear import -0.021 0.011 -10000 0 -10000 0 0
Circadian rhythm 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
chromatin modification 0.045 0.055 0.4 5 -10000 0 5
CLOCK 0.022 0.004 -10000 0 -10000 0 0
TIMELESS/CRY2 0.026 0.031 -10000 0 -10000 0 0
DEC1/BMAL1 0.028 0.008 -10000 0 -10000 0 0
ATR 0.021 0.003 -10000 0 -10000 0 0
NR1D1 0.008 0.02 -10000 0 -10000 0 0
ARNTL 0.022 0.005 -10000 0 -10000 0 0
TIMELESS 0.01 0.037 0.37 2 -10000 0 2
NPAS2 0.024 0.024 0.32 3 -10000 0 3
CRY2 0.021 0.003 -10000 0 -10000 0 0
mol:CO -0.004 0.012 -10000 0 -0.1 7 7
CHEK1 0.038 0.071 0.32 29 -10000 0 29
mol:HEME 0.004 0.012 0.1 7 -10000 0 7
PER1 0.007 0.065 -10000 0 -0.32 18 18
BMAL/CLOCK/NPAS2 0.046 0.022 0.22 3 -10000 0 3
BMAL1/CLOCK 0.011 0.041 -10000 0 -0.37 1 1
S phase of mitotic cell cycle 0.045 0.055 0.4 5 -10000 0 5
TIMELESS/CHEK1/ATR 0.046 0.055 0.41 5 -10000 0 5
mol:NADPH 0.004 0.012 0.1 7 -10000 0 7
PER1/TIMELESS 0.018 0.042 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.018 0.004 -10000 0 -10000 0 0
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.01 0.014 -10000 0 -10000 0 0
regulation of axonogenesis -0.001 0.016 0.25 2 -10000 0 2
myoblast fusion -0.012 0.021 -10000 0 -10000 0 0
mol:GTP 0.015 0.015 -10000 0 -0.16 3 3
regulation of calcium-dependent cell-cell adhesion -0.048 0.057 0.18 5 -0.21 39 44
ARF1/GTP 0.024 0.018 -10000 0 -10000 0 0
mol:GM1 0.005 0.01 -10000 0 -10000 0 0
mol:Choline -0.01 0.009 -10000 0 -10000 0 0
lamellipodium assembly 0.005 0.028 -10000 0 -0.34 2 2
MAPK3 0.012 0.012 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.049 0.058 0.22 39 -0.19 4 43
ARF1 0.02 0.006 -10000 0 -10000 0 0
ARF6/GDP 0.012 0.021 -10000 0 -10000 0 0
ARF1/GDP 0.014 0.029 -10000 0 -0.21 3 3
ARF6 0.026 0.009 -10000 0 -10000 0 0
RAB11A 0.021 0.003 -10000 0 -10000 0 0
TIAM1 0.015 0.038 -10000 0 -0.31 6 6
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.012 0.01 -10000 0 -10000 0 0
actin filament bundle formation -0.018 0.029 0.21 3 -10000 0 3
KALRN 0.004 0.016 -10000 0 -0.17 2 2
RAB11FIP3/RAB11A 0.03 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.018 0.029 -10000 0 -0.21 3 3
NME1 0.047 0.086 0.32 44 -10000 0 44
Rac1/GDP 0.016 0.028 -10000 0 -0.21 3 3
substrate adhesion-dependent cell spreading 0.015 0.015 -10000 0 -0.16 3 3
cortical actin cytoskeleton organization 0.005 0.028 -10000 0 -0.34 2 2
RAC1 0.019 0.007 -10000 0 -10000 0 0
liver development 0.015 0.015 -10000 0 -0.16 3 3
ARF6/GTP 0.015 0.015 -10000 0 -0.16 3 3
RhoA/GTP 0.025 0.018 -10000 0 -0.12 3 3
mol:GDP 0.005 0.017 -10000 0 -0.21 2 2
ARF6/GTP/RAB11FIP3/RAB11A 0.037 0.019 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
PLD1 0.009 0.013 -10000 0 -0.12 3 3
RAB11FIP3 0.021 0.004 -10000 0 -10000 0 0
tube morphogenesis 0.005 0.028 -10000 0 -0.34 2 2
ruffle organization 0.001 0.016 -10000 0 -0.25 2 2
regulation of epithelial cell migration 0.015 0.015 -10000 0 -0.16 3 3
PLD2 0.01 0.012 -10000 0 -10000 0 0
PIP5K1A 0.001 0.016 -10000 0 -0.25 2 2
mol:Phosphatidic acid -0.01 0.009 -10000 0 -10000 0 0
Rac1/GTP 0.005 0.028 -10000 0 -0.34 2 2
Class I PI3K signaling events mediated by Akt

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
BCL2L1 -0.015 0.005 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.025 0.013 -10000 0 -10000 0 0
CDKN1B 0.008 0.045 -10000 0 -0.29 7 7
CDKN1A 0.007 0.046 -10000 0 -0.29 8 8
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.019 0.006 -10000 0 -10000 0 0
FOXO3 0.008 0.035 -10000 0 -0.29 4 4
AKT1 0.001 0.039 -10000 0 -0.3 8 8
BAD 0.021 0.003 -10000 0 -10000 0 0
AKT3 0.006 0.012 -10000 0 -0.25 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.007 0.045 -10000 0 -0.29 8 8
AKT1/ASK1 0.024 0.054 -10000 0 -0.28 7 7
BAD/YWHAZ 0.035 0.017 -10000 0 -10000 0 0
RICTOR 0.017 0.008 -10000 0 -10000 0 0
RAF1 0.021 0.004 -10000 0 -10000 0 0
JNK cascade -0.023 0.052 0.27 7 -10000 0 7
TSC1 0.008 0.037 -10000 0 -0.29 5 5
YWHAZ 0.019 0.007 -10000 0 -10000 0 0
AKT1/RAF1 0.029 0.059 -10000 0 -0.28 8 8
EP300 0.02 0.004 -10000 0 -10000 0 0
mol:GDP 0.003 0.04 -10000 0 -0.29 8 8
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.005 0.043 -10000 0 -0.29 8 8
YWHAQ 0.021 0.002 -10000 0 -10000 0 0
TBC1D4 -0.005 0.002 -10000 0 -10000 0 0
MAP3K5 0.019 0.006 -10000 0 -10000 0 0
MAPKAP1 0.021 0.004 -10000 0 -10000 0 0
negative regulation of cell cycle -0.017 0.066 0.29 7 -0.22 8 15
YWHAH 0.02 0.004 -10000 0 -10000 0 0
AKT1S1 0.007 0.043 -10000 0 -0.29 7 7
CASP9 0.009 0.042 -10000 0 -0.29 6 6
YWHAB 0.02 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.029 0.063 0.27 5 -0.28 8 13
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.039 0.013 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
SRC 0.02 0.004 -10000 0 -10000 0 0
AKT2/p21CIP1 0.01 0.049 0.23 6 -0.26 5 11
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.008 0.037 0.18 1 -0.32 4 5
CHUK 0.007 0.044 -10000 0 -0.29 8 8
BAD/BCL-XL 0.026 0.054 -10000 0 -0.29 6 6
mTORC2 0.022 0.011 -10000 0 -10000 0 0
AKT2 0.007 0.002 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.019 0.082 0.35 3 -0.37 7 10
PDPK1 0.021 0.003 -10000 0 -10000 0 0
MDM2 0.014 0.055 -10000 0 -0.29 7 7
MAPKKK cascade -0.029 0.058 0.28 8 -10000 0 8
MDM2/Cbp/p300 0.044 0.07 0.34 3 -0.28 6 9
TSC1/TSC2 0.004 0.051 0.25 8 -0.29 6 14
proteasomal ubiquitin-dependent protein catabolic process 0.042 0.067 0.3 4 -0.27 6 10
glucose import -0.009 0.024 0.2 4 -0.16 4 8
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.011 0.037 -10000 0 -0.21 6 6
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.011 0.015 -10000 0 -0.16 4 4
GSK3A 0.008 0.046 -10000 0 -0.29 8 8
FOXO1 0.007 0.038 -10000 0 -0.29 6 6
GSK3B 0.007 0.042 -10000 0 -0.29 7 7
SFN 0.025 0.041 0.32 8 -0.32 1 9
G1/S transition of mitotic cell cycle 0.006 0.053 0.23 4 -0.29 7 11
p27Kip1/14-3-3 family 0.012 0.052 -10000 0 -0.34 6 6
PRKACA 0.02 0.005 -10000 0 -10000 0 0
KPNA1 0.021 0.003 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
YWHAG 0.021 0.004 -10000 0 -10000 0 0
RHEB 0.02 0.005 -10000 0 -10000 0 0
CREBBP 0.021 0.004 -10000 0 -10000 0 0
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.02 0.004 -10000 0 -10000 0 0
mol:S1P 0 0.002 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.009 0.061 -10000 0 -0.19 47 47
GNAO1 0.021 0.033 0.32 3 -0.33 2 5
S1P/S1P3/G12/G13 0.035 0.016 -10000 0 -10000 0 0
AKT1 0.005 0.066 -10000 0 -0.4 11 11
AKT3 -0.004 0.095 -10000 0 -0.83 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.02 0.004 -10000 0 -10000 0 0
GNAI2 0.02 0.006 -10000 0 -10000 0 0
GNAI3 0.021 0.005 -10000 0 -10000 0 0
GNAI1 0.02 0.017 -10000 0 -0.32 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.021 0.015 0.32 1 -10000 0 1
S1PR2 0.02 0.005 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.006 0.064 -10000 0 -0.27 6 6
MAPK3 -0.012 0.057 -10000 0 -0.32 3 3
MAPK1 -0.01 0.054 -10000 0 -0.57 1 1
JAK2 -0.022 0.077 0.2 2 -0.34 10 12
CXCR4 -0.013 0.06 -10000 0 -0.28 5 5
FLT1 0.02 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.015 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
SRC -0.012 0.062 0.27 2 -0.28 5 7
S1P/S1P3/Gi -0.005 0.064 -10000 0 -0.28 6 6
RAC1 0.019 0.007 -10000 0 -10000 0 0
RhoA/GTP -0.001 0.069 -10000 0 -0.33 4 4
VEGFA 0.021 0.006 -10000 0 -10000 0 0
S1P/S1P2/Gi -0.006 0.064 -10000 0 -0.23 12 12
VEGFR1 homodimer/VEGFA homodimer 0.03 0.012 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.007 0.037 -10000 0 -0.22 12 12
GNAQ 0.02 0.016 -10000 0 -0.32 1 1
GNAZ -0.006 0.092 -10000 0 -0.32 38 38
G12/G13 0.027 0.011 -10000 0 -10000 0 0
GNA14 0.013 0.051 -10000 0 -0.32 11 11
GNA15 0.02 0.006 -10000 0 -10000 0 0
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA13 0.021 0.004 -10000 0 -10000 0 0
GNA11 0.019 0.016 -10000 0 -0.32 1 1
Rac1/GTP -0.002 0.066 -10000 0 -0.3 5 5
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.021 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.018 0.061 0.22 3 -0.31 6 9
ERC1 0.02 0.005 -10000 0 -10000 0 0
RIP2/NOD2 0.027 0.012 -10000 0 -10000 0 0
NFKBIA -0.016 0.019 0.2 3 -10000 0 3
BIRC2 0.02 0.004 -10000 0 -10000 0 0
IKBKB 0.018 0.007 -10000 0 -10000 0 0
RIPK2 0.019 0.007 -10000 0 -10000 0 0
IKBKG 0.003 0.051 -10000 0 -0.36 7 7
IKK complex/A20 0.028 0.076 -10000 0 -0.39 7 7
NEMO/A20/RIP2 0.019 0.007 -10000 0 -10000 0 0
XPO1 0.021 0.002 -10000 0 -10000 0 0
NEMO/ATM 0.023 0.074 -10000 0 -0.37 11 11
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.021 0.014 0.32 1 -10000 0 1
Exportin 1/RanGTP 0.028 0.01 0.21 1 -10000 0 1
IKK complex/ELKS 0.023 0.068 -10000 0 -0.36 9 9
BCL10/MALT1/TRAF6 0.037 0.015 -10000 0 -10000 0 0
NOD2 0.02 0.005 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
RELA 0.021 0.004 -10000 0 -10000 0 0
MALT1 0.019 0.006 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.03 0.007 -10000 0 -10000 0 0
ATM 0.02 0.004 -10000 0 -10000 0 0
TNF/TNFR1A 0.022 0.045 0.23 1 -0.23 14 15
TRAF6 0.021 0.003 -10000 0 -10000 0 0
PRKCA 0.019 0.022 -10000 0 -0.32 2 2
CHUK 0.021 0.003 -10000 0 -10000 0 0
UBE2D3 0.021 0.003 -10000 0 -10000 0 0
TNF 0.011 0.061 0.32 1 -0.32 15 16
NF kappa B1 p50/RelA 0.042 0.013 -10000 0 -10000 0 0
BCL10 0.021 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.015 0.019 0.2 3 -10000 0 3
beta TrCP1/SCF ubiquitin ligase complex 0.021 0.005 -10000 0 -10000 0 0
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
IKK complex 0.027 0.073 -10000 0 -0.38 9 9
CYLD 0.02 0.005 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.032 0.073 -10000 0 -0.38 8 8
Insulin-mediated glucose transport

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Insulin responsive Vesicles 0.009 0.1 -10000 0 -0.36 16 16
CaM/Ca2+ 0.015 0.003 -10000 0 -10000 0 0
AKT1 0.02 0.005 -10000 0 -10000 0 0
AKT2 0.02 0.005 -10000 0 -10000 0 0
STXBP4 0.021 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.008 0.1 0.24 1 -0.36 21 22
YWHAZ 0.019 0.007 -10000 0 -10000 0 0
CALM1 0.02 0.005 -10000 0 -10000 0 0
YWHAQ 0.021 0.002 -10000 0 -10000 0 0
TBC1D4 -0.015 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.02 0.004 -10000 0 -10000 0 0
YWHAB 0.02 0.005 -10000 0 -10000 0 0
SNARE/Synip 0.038 0.014 -10000 0 -10000 0 0
YWHAG 0.021 0.004 -10000 0 -10000 0 0
ASIP 0.019 0.014 0.32 1 -10000 0 1
PRKCI 0.02 0.005 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.015 0.003 -10000 0 -10000 0 0
RHOQ 0.021 0.003 -10000 0 -10000 0 0
GYS1 -0.005 0.002 -10000 0 -10000 0 0
PRKCZ 0.018 0.027 -10000 0 -0.32 3 3
TRIP10 0.02 0.005 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.027 0.008 -10000 0 -10000 0 0
AS160/14-3-3 0.005 0.048 -10000 0 -0.25 5 5
VAMP2 0.019 0.006 -10000 0 -10000 0 0
SLC2A4 -0.01 0.12 0.24 1 -0.4 21 22
STX4 0.021 0.003 -10000 0 -10000 0 0
GSK3B 0.01 0.004 -10000 0 -10000 0 0
SFN 0.025 0.041 0.32 8 -0.32 1 9
LNPEP 0.02 0.004 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.008 0.017 -10000 0 -0.23 2 2
CRKL 0.02 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
DOCK1 0.021 0.003 -10000 0 -10000 0 0
ITGA4 0.02 0.022 -10000 0 -0.32 2 2
alpha4/beta7 Integrin/MAdCAM1 0.049 0.03 0.22 5 -0.17 3 8
EPO 0.021 0.028 0.32 4 -10000 0 4
alpha4/beta7 Integrin 0.029 0.021 -10000 0 -0.23 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.03 0.013 -10000 0 -0.23 1 1
EPO/EPOR (dimer) 0.029 0.021 0.23 4 -10000 0 4
lamellipodium assembly 0.003 0.051 -10000 0 -0.43 4 4
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
PI3K 0.029 0.014 -10000 0 -0.23 1 1
ARF6 0.02 0.004 -10000 0 -10000 0 0
JAK2 0.012 0.017 0.18 1 -0.29 1 2
PXN 0.021 0.003 -10000 0 -10000 0 0
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
MADCAM1 0.023 0.034 0.32 6 -10000 0 6
cell adhesion 0.047 0.03 0.22 5 -0.17 3 8
CRKL/CBL 0.028 0.01 -10000 0 -10000 0 0
ITGB1 0.021 0.004 -10000 0 -10000 0 0
SRC -0.017 0.033 0.17 13 -0.18 2 15
ITGB7 0.02 0.016 -10000 0 -0.32 1 1
RAC1 0.019 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.039 0.023 0.22 1 -0.19 3 4
p130Cas/Crk/Dock1 -0.023 0.036 0.17 12 -10000 0 12
VCAM1 0.02 0.026 0.32 1 -0.32 2 3
RHOA 0.021 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.05 0.018 -10000 0 -0.18 1 1
BCAR1 -0.02 0.032 0.17 11 -0.17 3 14
EPOR 0.02 0.005 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.02 0.005 -10000 0 -10000 0 0
GIT1 0.021 0.003 -10000 0 -10000 0 0
Rac1/GTP 0.003 0.052 -10000 0 -0.44 4 4
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.017 0.031 -10000 0 -0.32 4 4
positive regulation of NF-kappaB transcription factor activity 0.023 0.025 -10000 0 -0.22 4 4
MAP2K4 0.006 0.023 -10000 0 -0.24 1 1
IKBKB 0.018 0.007 -10000 0 -10000 0 0
TNFRSF10B 0.018 0.008 -10000 0 -10000 0 0
TNFRSF10A 0.018 0.008 -10000 0 -10000 0 0
SMPD1 0.004 0.013 -10000 0 -0.14 4 4
IKBKG 0.02 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.017 0.017 -10000 0 -0.32 1 1
TRAIL/TRAILR2 0.023 0.025 -10000 0 -0.21 4 4
TRAIL/TRAILR3 0.021 0.034 -10000 0 -0.22 8 8
TRAIL/TRAILR1 0.023 0.025 -10000 0 -0.22 4 4
TRAIL/TRAILR4 0.023 0.025 -10000 0 -0.22 4 4
TRAIL/TRAILR1/DAP3/GTP 0.028 0.024 -10000 0 -0.17 3 3
IKK complex 0.001 0.045 -10000 0 -0.24 1 1
RIPK1 0.021 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.013 0.006 -10000 0 -10000 0 0
MAPK3 -0.017 0.023 0.27 1 -0.22 4 5
MAP3K1 0.013 0.019 -10000 0 -0.19 1 1
TRAILR4 (trimer) 0.017 0.017 -10000 0 -0.32 1 1
TRADD 0.021 0.004 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.018 0.008 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.01 0.024 -10000 0 -0.18 7 7
CFLAR 0.021 0.002 -10000 0 -10000 0 0
MAPK1 -0.015 0.019 0.27 1 -0.22 2 3
TRAIL/TRAILR1/FADD/TRADD/RIP 0.046 0.033 -10000 0 -0.17 2 2
mol:ceramide 0.004 0.013 -10000 0 -0.14 4 4
FADD 0.02 0.004 -10000 0 -10000 0 0
MAPK8 -0.005 0.042 -10000 0 -0.25 3 3
TRAF2 0.021 0.004 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.014 0.035 -10000 0 -0.32 5 5
CHUK 0.021 0.003 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.032 0.027 -10000 0 -0.18 4 4
DAP3 0.018 0.008 -10000 0 -10000 0 0
CASP10 -0.003 0.04 0.26 2 -0.22 2 4
JNK cascade 0.023 0.025 -10000 0 -0.22 4 4
TRAIL (trimer) 0.017 0.031 -10000 0 -0.32 4 4
TNFRSF10C 0.014 0.035 -10000 0 -0.32 5 5
TRAIL/TRAILR1/DAP3/GTP/FADD 0.034 0.028 -10000 0 -0.16 3 3
TRAIL/TRAILR2/FADD 0.032 0.027 -10000 0 -0.18 4 4
cell death 0.004 0.013 -10000 0 -0.14 4 4
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.01 0.024 -10000 0 -0.18 7 7
TRAILR2 (trimer) 0.018 0.008 -10000 0 -10000 0 0
CASP8 0.008 0.051 -10000 0 -0.66 2 2
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.046 0.033 -10000 0 -0.17 2 2
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.031 0.029 0.2 3 -0.16 7 10
MAPK9 0.004 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.008 0.013 0.15 3 -10000 0 3
GNB1/GNG2 0.026 0.016 -10000 0 -0.19 2 2
GNB1 0.02 0.004 -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 0.004 0.001 -10000 0 -10000 0 0
Gs family/GTP 0.012 0.024 0.18 3 -0.16 6 9
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 0.002 0.005 0.047 6 -10000 0 6
GNAL 0.018 0.045 0.32 3 -0.32 6 9
GNG2 0.019 0.022 -10000 0 -0.32 2 2
CRH 0.019 0.024 0.32 3 -10000 0 3
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.004 0.001 -10000 0 -10000 0 0
MAPK11 0.003 0.016 -10000 0 -0.24 2 2
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.019 0.006 -10000 0 -10000 0 0
SMAD2 0 0.043 0.24 2 -0.22 4 6
SMAD3 0.01 0.035 -10000 0 -10000 0 0
SMAD3/SMAD4 0.023 0.038 0.25 1 -0.4 2 3
SMAD4/Ubc9/PIASy 0.036 0.016 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.028 0.05 -10000 0 -0.21 3 3
PPM1A 0.021 0.004 -10000 0 -10000 0 0
CALM1 0.02 0.005 -10000 0 -10000 0 0
SMAD2/SMAD4 0.006 0.042 0.22 1 -0.22 6 7
MAP3K1 0.02 0.005 -10000 0 -10000 0 0
TRAP-1/SMAD4 0.027 0.019 -10000 0 -0.23 2 2
MAPK3 0.021 0.003 -10000 0 -10000 0 0
MAPK1 0.02 0.005 -10000 0 -10000 0 0
NUP214 0.021 0.004 -10000 0 -10000 0 0
CTDSP1 0.021 0.002 -10000 0 -10000 0 0
CTDSP2 0.02 0.005 -10000 0 -10000 0 0
CTDSPL 0.021 0.004 -10000 0 -10000 0 0
KPNB1 0.021 0.003 -10000 0 -10000 0 0
TGFBRAP1 0.02 0.022 -10000 0 -0.32 2 2
UBE2I 0.021 0.004 -10000 0 -10000 0 0
NUP153 0.021 0.003 -10000 0 -10000 0 0
KPNA2 0.024 0.03 0.32 5 -10000 0 5
PIAS4 0.02 0.005 -10000 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.021 0.004 -9999 0 -10000 0 0
ITGB7 0.02 0.016 -9999 0 -0.32 1 1
ITGA4 0.02 0.022 -9999 0 -0.32 2 2
alpha4/beta7 Integrin 0.029 0.021 -9999 0 -0.23 3 3
alpha4/beta1 Integrin 0.03 0.013 -9999 0 -0.23 1 1
Paxillin-dependent events mediated by a4b1

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
CRKL 0.02 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.021 0.01 -10000 0 -10000 0 0
DOCK1 0.021 0.003 -10000 0 -10000 0 0
ITGA4 0.02 0.022 -10000 0 -0.32 2 2
RAC1 0.019 0.007 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.029 0.021 -10000 0 -0.23 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.039 0.016 -10000 0 -0.19 1 1
alpha4/beta7 Integrin/Paxillin 0.028 0.019 -10000 0 -0.18 3 3
lamellipodium assembly -0.006 0.08 -10000 0 -0.37 16 16
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
PI3K 0.029 0.014 -10000 0 -0.23 1 1
ARF6 0.02 0.004 -10000 0 -10000 0 0
TLN1 0.019 0.016 -10000 0 -0.32 1 1
PXN -0.016 0.004 -10000 0 -10000 0 0
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
ARF6/GTP 0.036 0.019 -10000 0 -0.16 1 1
cell adhesion 0.036 0.02 -10000 0 -0.16 2 2
CRKL/CBL 0.028 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.028 0.014 -10000 0 -0.18 1 1
ITGB1 0.021 0.004 -10000 0 -10000 0 0
ITGB7 0.02 0.016 -10000 0 -0.32 1 1
ARF6/GDP 0.022 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.038 0.024 0.21 1 -0.17 3 4
p130Cas/Crk/Dock1 0.037 0.018 -10000 0 -0.19 1 1
VCAM1 0.02 0.026 0.32 1 -0.32 2 3
alpha4/beta1 Integrin/Paxillin/Talin 0.037 0.02 -10000 0 -0.16 2 2
alpha4/beta1 Integrin/Paxillin/GIT1 0.038 0.018 -10000 0 -0.17 1 1
BCAR1 0.02 0.016 -10000 0 -0.32 1 1
mol:GDP -0.037 0.017 0.17 1 -10000 0 1
CBL 0.02 0.005 -10000 0 -10000 0 0
PRKACA 0.02 0.005 -10000 0 -10000 0 0
GIT1 0.021 0.003 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.037 0.02 -10000 0 -0.16 2 2
Rac1/GTP -0.008 0.087 -10000 0 -0.41 16 16
Atypical NF-kappaB pathway

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
BCL3/RelA 0.029 0.014 -10000 0 -0.23 1 1
FBXW11 0.02 0.005 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.017 0.007 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.02 0.042 0.23 1 -10000 0 1
NFKBIA 0.002 0.011 -10000 0 -0.16 2 2
MAPK14 0.02 0.004 -10000 0 -10000 0 0
NF kappa B1 p105/p50 -0.016 0.008 -10000 0 -10000 0 0
ARRB2 0.007 0.002 -10000 0 -10000 0 0
REL 0.021 0.002 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 -0.016 0.008 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA -0.017 0.007 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
NF kappa B1 p50 dimer -0.014 0.014 0.24 1 -10000 0 1
PIK3R1 0.02 0.016 -10000 0 -0.32 1 1
NFKB1 -0.014 0.006 -10000 0 -10000 0 0
RELA 0.021 0.004 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.008 0.035 -10000 0 -0.2 4 4
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.018 0.04 -10000 0 -0.19 1 1
SRC 0.02 0.004 -10000 0 -10000 0 0
PI3K 0.029 0.014 -10000 0 -0.23 1 1
NF kappa B1 p50/RelA 0.009 0.034 -10000 0 -0.18 4 4
IKBKB 0.018 0.007 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0.005 -10000 0 -10000 0 0
SYK 0.019 0.022 -10000 0 -0.32 2 2
I kappa B alpha/PIK3R1 0.026 0.053 0.24 11 -0.18 3 14
cell death 0.017 0.039 -10000 0 -0.18 1 1
NF kappa B1 p105/c-Rel -0.017 0.007 -10000 0 -10000 0 0
LCK 0.02 0.026 0.32 1 -0.32 2 3
BCL3 0.02 0.016 -10000 0 -0.32 1 1
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.039 0.019 -9999 0 -0.18 2 2
E-cadherin/beta catenin 0.029 0.017 -9999 0 -0.21 2 2
CTNNB1 0.021 0.004 -9999 0 -10000 0 0
JUP 0.021 0.003 -9999 0 -10000 0 0
CDH1 0.019 0.022 -9999 0 -0.32 2 2
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.008 0.041 0.15 35 -0.19 1 36
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.015 0.037 -10000 0 -0.15 3 3
AP2 0.029 0.008 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.022 0.016 -10000 0 -10000 0 0
CLTB 0.02 0.005 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.009 0.006 -10000 0 -10000 0 0
CD4 0.014 0.046 -10000 0 -0.32 9 9
CLTA 0.02 0.005 -10000 0 -10000 0 0
mol:GTP -0.002 0.002 -10000 0 -10000 0 0
ARFGAP1 -0.008 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.002 0.007 -10000 0 -10000 0 0
ARF1/GTP 0.022 0.014 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.003 0.013 -10000 0 -10000 0 0
mol:Choline -0.002 0.007 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.021 0.009 -10000 0 -10000 0 0
DDEF1 -0.001 0.007 -10000 0 -10000 0 0
ARF1/GDP 0.001 0.016 -10000 0 -0.11 1 1
AP2M1 0.02 0.005 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.007 0.011 -10000 0 -10000 0 0
Rac/GTP 0.015 0.008 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.024 0.013 -10000 0 -10000 0 0
ARFIP2 0.01 0.02 -10000 0 -10000 0 0
COPA 0.019 0.007 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.001 0.032 -10000 0 -0.17 10 10
ARF1/GTP/ARHGAP10 0.012 0.007 -10000 0 -10000 0 0
GGA3 0.02 0.004 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.012 0.025 -10000 0 -0.27 3 3
AP2A1 0.02 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.001 0.025 -10000 0 -0.16 8 8
ARF1/GDP/Membrin 0.016 0.03 -10000 0 -0.3 3 3
Arfaptin 2/Rac/GDP 0.019 0.018 -10000 0 -10000 0 0
CYTH2 0.024 0.008 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.026 0.012 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.014 0.005 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.005 0.038 -10000 0 -0.21 8 8
PLD2 -0.002 0.007 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE -0.008 0.002 -10000 0 -10000 0 0
PIP5K1A -0.002 0.007 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.008 0.02 -10000 0 -0.13 3 3
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.002 0.007 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 -0.008 0.002 -10000 0 -10000 0 0
GOSR2 0.006 0.015 -10000 0 -0.31 1 1
USO1 0.004 0.029 -10000 0 -0.31 4 4
GBF1 0.004 0.029 -10000 0 -0.31 4 4
ARF1/GTP/Arfaptin 2 0.026 0.013 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.034 0.034 -10000 0 -0.19 9 9
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.021 0.003 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.018 0.008 -10000 0 -10000 0 0
MDM2/SUMO1 0.027 0.031 -10000 0 -0.21 3 3
HDAC4 0.021 0.003 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.018 0.009 -10000 0 -10000 0 0
SUMO1 0.021 0.002 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.006 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 -0.005 0.015 -10000 0 -0.16 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.021 0.014 0.32 1 -10000 0 1
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.021 0.002 -10000 0 -10000 0 0
SUMO1/HDAC4 0.028 0.029 -10000 0 -0.2 3 3
SUMO1/HDAC1 0.028 0.03 -10000 0 -0.21 3 3
RANGAP1 0.02 0.004 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.045 0.021 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.006 0.002 -10000 0 -10000 0 0
Ran/GTP 0.017 0.028 -10000 0 -0.19 4 4
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.02 0.005 -10000 0 -10000 0 0
UBE2I 0.021 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.014 0.032 0.19 4 -0.19 4 8
NPC 0.012 0.001 -10000 0 -10000 0 0
PIAS2 0.019 0.006 -10000 0 -10000 0 0
PIAS1 0.021 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.03 0.006 -9999 0 -9999 0 0
FBXW11 0.02 0.005 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0.005 -9999 0 -9999 0 0
CHUK 0.021 0.003 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.056 0.021 -9999 0 -9999 0 0
NFKB1 0.021 0.003 -9999 0 -9999 0 0
MAP3K14 0.021 0.003 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.03 0.007 -9999 0 -9999 0 0
RELB 0.02 0.004 -9999 0 -9999 0 0
NFKB2 0.021 0.003 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.027 0.007 -9999 0 -9999 0 0
regulation of B cell activation 0.027 0.007 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 486 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.O1.A52J TCGA.NJ.A55R TCGA.NJ.A55O TCGA.NJ.A55A
109_MAP3K5 -0.019 0.009 0.009 0.009
47_PPARGC1A 0.021 0.021 0.021 0.021
105_BMP4 0.021 0.021 0.021 0.021
105_BMP6 -0.32 0.021 0.021 0.021
105_BMP7 0 0.021 0.021 0.021
105_BMP2 0.021 0.021 0.021 0.021
131_RELN/VLDLR -0.18 0.055 0.055 0.055
30_TGFB1/TGF beta receptor Type II 0.021 -0.023 0.021 0.021
84_STAT5B 0.074 0.016 0.02 -0.067
84_STAT5A 0.074 0.016 0.02 -0.067
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/LUAD-TP/9830463/LUAD-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/LUAD-TP/10006008/GDAC_Gistic2Report_10008718/all_data_by_genes.txt

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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