PARADIGM pathway analysis of mRNASeq expression and copy number data
Liver Hepatocellular Carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1N015R8
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1N015R8
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 58 significant pathways identified in this analysis.

Table 1.  Get Full Table Top 10 out of 129 pathways in order of significance.

Pathway.Name Avg.Num.Perturbations
FOXM1 transcription factor network 167
Signaling mediated by p38-alpha and p38-beta 96
Plasma membrane estrogen receptor signaling 87
PDGFR-alpha signaling pathway 82
FOXA2 and FOXA3 transcription factor networks 79
Signaling events regulated by Ret tyrosine kinase 76
IL4-mediated signaling events 73
TCGA08_retinoblastoma 66
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 65
Signaling events mediated by the Hedgehog family 61
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 371 . 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 ( 371 ).

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 0.4501 167 8517 51 -0.055 1.2 1000 -1000 0.01 -1000
Signaling mediated by p38-alpha and p38-beta 0.2588 96 4264 44 -0.23 0.03 1000 -1000 -0.012 -1000
Plasma membrane estrogen receptor signaling 0.2345 87 7483 86 -0.47 0.44 1000 -1000 -0.039 -1000
PDGFR-alpha signaling pathway 0.2210 82 3649 44 -0.45 0.052 1000 -1000 -0.019 -1000
FOXA2 and FOXA3 transcription factor networks 0.2129 79 3676 46 -0.59 0.049 1000 -1000 -0.003 -1000
Signaling events regulated by Ret tyrosine kinase 0.2049 76 6239 82 -0.18 0.03 1000 -1000 -0.041 -1000
IL4-mediated signaling events 0.1968 73 6699 91 -0.8 0.42 1000 -1000 -0.11 -1000
TCGA08_retinoblastoma 0.1779 66 532 8 -0.096 0.083 1000 -1000 -0.007 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1752 65 4453 68 -0.47 0.22 1000 -1000 -0.059 -1000
Signaling events mediated by the Hedgehog family 0.1644 61 3207 52 -0.15 0.12 1000 -1000 -0.02 -1000
Nongenotropic Androgen signaling 0.1644 61 3191 52 -0.38 0.22 1000 -1000 -0.022 -1000
Ephrin B reverse signaling 0.1590 59 2848 48 -0.24 0.038 1000 -1000 -0.03 -1000
IGF1 pathway 0.1590 59 3387 57 -0.13 0.06 1000 -1000 -0.026 -1000
FoxO family signaling 0.1563 58 3756 64 -0.17 0.53 1000 -1000 -0.006 -1000
p75(NTR)-mediated signaling 0.1509 56 7118 125 -0.18 0.075 1000 -1000 -0.05 -1000
Reelin signaling pathway 0.1456 54 3070 56 -0.11 0.18 1000 -1000 -0.012 -1000
Endothelins 0.1456 54 5215 96 -0.51 0.059 1000 -1000 -0.015 -1000
IL6-mediated signaling events 0.1456 54 4124 75 -0.44 0.051 1000 -1000 -0.019 -1000
Noncanonical Wnt signaling pathway 0.1429 53 1397 26 -0.1 0.029 1000 -1000 -0.027 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.1348 50 4297 85 -0.4 0.038 1000 -1000 -0.021 -1000
Glypican 1 network 0.1321 49 2376 48 -0.12 0.038 1000 -1000 -0.023 -1000
IL23-mediated signaling events 0.1321 49 2998 60 -0.26 0.042 1000 -1000 -0.005 -1000
Syndecan-1-mediated signaling events 0.1213 45 1542 34 -0.18 0.029 1000 -1000 -0.021 -1000
Wnt signaling 0.1213 45 319 7 -0.1 0.027 1000 -1000 -0.006 -1000
HIF-1-alpha transcription factor network 0.1186 44 3369 76 -0.31 0.052 1000 -1000 -0.034 -1000
LPA receptor mediated events 0.1186 44 4574 102 -0.17 0.035 1000 -1000 -0.047 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1159 43 3836 88 -0.17 0.043 1000 -1000 -0.05 -1000
PLK1 signaling events 0.1105 41 3523 85 -0.063 0.18 1000 -1000 -0.026 -1000
TCGA08_p53 0.1105 41 288 7 -0.092 0.027 1000 -1000 -0.012 -1000
ErbB2/ErbB3 signaling events 0.0997 37 2467 65 -0.22 0.042 1000 -1000 -0.046 -1000
EPHB forward signaling 0.0997 37 3199 85 -0.094 0.11 1000 -1000 -0.049 -1000
EPO signaling pathway 0.0970 36 1983 55 -0.12 0.03 1000 -1000 -0.018 -1000
Glucocorticoid receptor regulatory network 0.0970 36 4185 114 -0.46 0.11 1000 -1000 -0.05 -1000
S1P1 pathway 0.0889 33 1210 36 -0.35 0.029 1000 -1000 -0.018 -1000
Calcium signaling in the CD4+ TCR pathway 0.0863 32 993 31 -0.18 0.029 1000 -1000 -0.024 -1000
amb2 Integrin signaling 0.0836 31 2546 82 -0.14 0.046 1000 -1000 -0.009 -1000
Signaling mediated by p38-gamma and p38-delta 0.0836 31 472 15 -0.006 0.077 1000 -1000 -0.017 -1000
IL12-mediated signaling events 0.0809 30 2684 87 -0.58 0.041 1000 -1000 -0.053 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0809 30 3615 120 -0.19 0.077 1000 -1000 -0.029 -1000
S1P5 pathway 0.0782 29 494 17 -0.14 0.036 1000 -1000 -0.002 -1000
S1P4 pathway 0.0755 28 721 25 -0.14 0.053 1000 -1000 -0.012 -1000
Aurora B signaling 0.0701 26 1790 67 -0.052 0.2 1000 -1000 -0.025 -1000
BCR signaling pathway 0.0674 25 2484 99 -0.11 0.031 1000 -1000 -0.056 -1000
Thromboxane A2 receptor signaling 0.0647 24 2521 105 -0.15 0.044 1000 -1000 -0.031 -1000
TCR signaling in naïve CD8+ T cells 0.0647 24 2324 93 -0.081 0.042 1000 -1000 -0.032 -1000
Ras signaling in the CD4+ TCR pathway 0.0647 24 416 17 -0.13 0.028 1000 -1000 -0.01 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0620 23 1287 54 -0.1 0.041 1000 -1000 -0.032 -1000
Nectin adhesion pathway 0.0620 23 1464 63 -0.078 0.053 1000 -1000 -0.024 -1000
Coregulation of Androgen receptor activity 0.0593 22 1675 76 -0.083 0.044 1000 -1000 -0.017 -1000
FAS signaling pathway (CD95) 0.0593 22 1079 47 -0.18 0.039 1000 -1000 -0.019 -1000
Regulation of Telomerase 0.0593 22 2305 102 -0.16 0.26 1000 -1000 -0.026 -1000
Syndecan-4-mediated signaling events 0.0593 22 1479 67 -0.13 0.043 1000 -1000 -0.024 -1000
p38 MAPK signaling pathway 0.0593 22 981 44 -0.16 0.054 1000 -1000 -0.007 -1000
Fc-epsilon receptor I signaling in mast cells 0.0566 21 2097 97 -0.15 0.039 1000 -1000 -0.044 -1000
IL1-mediated signaling events 0.0566 21 1335 62 -0.082 0.051 1000 -1000 -0.048 -1000
LPA4-mediated signaling events 0.0539 20 247 12 -0.088 0 1000 -1000 -0.015 -1000
PLK2 and PLK4 events 0.0539 20 60 3 0.018 -1000 1000 -1000 -0.015 -1000
Integrins in angiogenesis 0.0539 20 1695 84 -0.13 0.065 1000 -1000 -0.035 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0485 18 1396 74 -0.18 0.048 1000 -1000 -0.047 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0431 16 564 34 -0.013 0.05 1000 -1000 -0.025 -1000
BMP receptor signaling 0.0431 16 1331 81 -0.048 0.057 1000 -1000 -0.025 -1000
IL27-mediated signaling events 0.0431 16 859 51 -0.074 0.053 1000 -1000 -0.023 -1000
Osteopontin-mediated events 0.0404 15 607 38 -0.15 0.057 1000 -1000 -0.017 -1000
JNK signaling in the CD4+ TCR pathway 0.0404 15 267 17 -0.086 0.066 1000 -1000 -0.017 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0404 15 591 37 -0.12 0.067 1000 -1000 -0.014 -1000
E-cadherin signaling in the nascent adherens junction 0.0404 15 1195 76 -0.042 0.051 1000 -1000 -0.039 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0377 14 415 28 -0.14 0.065 1000 -1000 -0.02 -1000
Signaling events mediated by HDAC Class III 0.0377 14 586 40 -0.12 0.056 1000 -1000 -0.031 -1000
HIF-2-alpha transcription factor network 0.0377 14 641 43 -0.13 0.044 1000 -1000 -0.063 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0377 14 640 45 -0.021 0.055 1000 -1000 -0.024 -1000
S1P3 pathway 0.0377 14 623 42 -0.14 0.048 1000 -1000 -0.022 -1000
Signaling events mediated by PRL 0.0377 14 479 34 -0.12 0.042 1000 -1000 -0.02 -1000
Regulation of nuclear SMAD2/3 signaling 0.0350 13 1817 136 -0.32 0.32 1000 -1000 -0.028 -1000
E-cadherin signaling events 0.0350 13 66 5 0.003 0.037 1000 -1000 0.017 -1000
Regulation of Androgen receptor activity 0.0350 13 977 70 -0.1 0.039 1000 -1000 -0.019 -1000
Presenilin action in Notch and Wnt signaling 0.0323 12 773 61 -0.15 0.066 1000 -1000 -0.026 -1000
Canonical Wnt signaling pathway 0.0323 12 654 51 -0.043 0.062 1000 -1000 -0.017 -1000
Effects of Botulinum toxin 0.0323 12 335 26 -0.034 0.039 1000 -1000 -0.01 -1000
TCGA08_rtk_signaling 0.0323 12 335 26 -0.12 0.03 1000 -1000 -0.019 -1000
Visual signal transduction: Rods 0.0323 12 655 52 -0.067 0.065 1000 -1000 -0.013 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0323 12 995 78 -0.12 0.034 1000 -1000 -0.02 -1000
Syndecan-2-mediated signaling events 0.0296 11 802 69 -0.051 0.051 1000 -1000 -0.011 -1000
IL2 signaling events mediated by PI3K 0.0296 11 675 58 -0.043 0.13 1000 -1000 -0.025 -1000
Caspase cascade in apoptosis 0.0270 10 768 74 -0.072 0.075 1000 -1000 -0.022 -1000
Class I PI3K signaling events mediated by Akt 0.0270 10 696 68 -0.053 0.053 1000 -1000 -0.018 -1000
Ceramide signaling pathway 0.0270 10 786 76 -0.13 0.061 1000 -1000 -0.021 -1000
Class IB PI3K non-lipid kinase events 0.0270 10 30 3 -0.018 0.018 1000 -1000 -0.017 -1000
Syndecan-3-mediated signaling events 0.0243 9 324 35 -0.051 0.06 1000 -1000 -0.02 -1000
Regulation of p38-alpha and p38-beta 0.0243 9 495 54 -0.052 0.068 1000 -1000 -0.033 -1000
E-cadherin signaling in keratinocytes 0.0243 9 412 43 -0.043 0.038 1000 -1000 -0.009 -1000
Signaling events mediated by PTP1B 0.0216 8 659 76 -0.15 0.061 1000 -1000 -0.022 -1000
Arf6 downstream pathway 0.0216 8 352 43 -0.038 0.051 1000 -1000 -0.025 -1000
mTOR signaling pathway 0.0216 8 440 53 -0.14 0.04 1000 -1000 -0.035 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0216 8 422 52 -0.031 0.071 1000 -1000 -0.019 -1000
Hedgehog signaling events mediated by Gli proteins 0.0189 7 504 65 -0.14 0.066 1000 -1000 -0.033 -1000
IFN-gamma pathway 0.0189 7 494 68 -0.16 0.075 1000 -1000 -0.043 -1000
Signaling events mediated by HDAC Class II 0.0162 6 475 75 -0.17 0.079 1000 -1000 -0.027 -1000
a4b1 and a4b7 Integrin signaling 0.0162 6 31 5 0.022 0.037 1000 -1000 0.018 -1000
Insulin-mediated glucose transport 0.0162 6 206 32 -0.021 0.062 1000 -1000 -0.019 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0162 6 517 83 -0.049 0.057 1000 -1000 -0.017 -1000
Retinoic acid receptors-mediated signaling 0.0162 6 365 58 -0.049 0.057 1000 -1000 -0.01 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0162 6 787 125 -0.03 0.054 1000 -1000 -0.046 -1000
IL2 signaling events mediated by STAT5 0.0162 6 152 22 -0.008 0.043 1000 -1000 -0.023 -1000
Class I PI3K signaling events 0.0162 6 488 73 -0.063 0.053 1000 -1000 -0.017 -1000
EGFR-dependent Endothelin signaling events 0.0162 6 127 21 -0.001 0.063 1000 -1000 -0.024 -1000
PDGFR-beta signaling pathway 0.0162 6 637 97 -0.12 0.068 1000 -1000 -0.043 -1000
ErbB4 signaling events 0.0135 5 396 69 -0.091 0.062 1000 -1000 -0.015 -1000
Canonical NF-kappaB pathway 0.0108 4 174 39 -0.019 0.057 1000 -1000 -0.003 -1000
Visual signal transduction: Cones 0.0108 4 170 38 -0.017 0.067 1000 -1000 -0.019 -1000
ceramide signaling pathway 0.0108 4 203 49 -0.008 0.042 1000 -1000 -0.01 -1000
Paxillin-dependent events mediated by a4b1 0.0108 4 160 36 -0.055 0.057 1000 -1000 -0.035 -1000
Aurora A signaling 0.0081 3 235 60 -0.004 0.068 1000 -1000 -0.017 -1000
TRAIL signaling pathway 0.0081 3 153 48 -0.021 0.052 1000 -1000 -0.022 -1000
Atypical NF-kappaB pathway 0.0081 3 107 31 -0.015 0.041 1000 -1000 -0.018 -1000
Insulin Pathway 0.0081 3 249 74 -0.059 0.07 1000 -1000 -0.038 -1000
Signaling events mediated by HDAC Class I 0.0054 2 311 104 -0.044 0.067 1000 -1000 -0.027 -1000
Arf6 trafficking events 0.0054 2 208 71 -0.052 0.054 1000 -1000 -0.028 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0054 2 86 33 0 0.061 1000 -1000 -0.017 -1000
Arf1 pathway 0.0054 2 150 54 -0.009 0.043 1000 -1000 -0.013 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0027 1 44 23 -0.005 0.054 1000 -1000 -0.016 -1000
Arf6 signaling events 0.0027 1 68 62 -0.2 0.069 1000 -1000 -0.012 -1000
VEGFR1 specific signals 0.0027 1 78 56 -0.031 0.063 1000 -1000 -0.026 -1000
Rapid glucocorticoid signaling 0.0027 1 28 20 -0.007 0.034 1000 -1000 -0.01 -1000
BARD1 signaling events 0.0000 0 46 57 -0.063 0.097 1000 -1000 -0.039 -1000
Circadian rhythm pathway 0.0000 0 10 22 -0.004 0.061 1000 -1000 -0.011 -1000
Aurora C signaling 0.0000 0 0 7 0 0.029 1000 -1000 -0.009 -1000
Glypican 2 network 0.0000 0 0 4 0.013 0.025 1000 -1000 0.018 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 17 27 -0.021 0.072 1000 -1000 -0.03 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.08 1000 -1000 0 -1000
Total NA 3143 191093 7157 -17 -990 129000 -129000 -3 -129000
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 0.83 0.68 1.3 216 -0.9 6 222
PLK1 0.56 0.55 1.1 176 -10000 0 176
BIRC5 0.61 0.54 1.1 202 -10000 0 202
HSPA1B 0.88 0.72 1.4 217 -0.94 3 220
MAP2K1 0.32 0.22 0.47 236 -10000 0 236
BRCA2 0.84 0.72 1.4 212 -1.1 4 216
FOXM1 1.2 1.2 2.2 202 -1.1 7 209
XRCC1 0.84 0.69 1.3 214 -0.93 5 219
FOXM1B/p19 -0.016 0.24 0.98 3 -0.95 7 10
Cyclin D1/CDK4 0.58 0.59 1.1 169 -0.89 8 177
CDC2 1.1 0.84 1.6 229 -0.92 7 236
TGFA 0.52 0.66 1.1 167 -0.98 14 181
SKP2 0.86 0.71 1.4 215 -0.91 5 220
CCNE1 0.043 0.054 0.14 18 -10000 0 18
CKS1B 0.84 0.68 1.3 221 -0.88 7 228
RB1 0.11 0.3 0.77 50 -0.71 2 52
FOXM1C/SP1 0.6 0.62 1.1 185 -0.97 8 193
AURKB 0.48 0.57 1.1 157 -1.1 6 163
CENPF 1.2 0.93 1.8 229 -0.96 3 232
CDK4 0.11 0.086 0.2 151 -10000 0 151
MYC 0.55 0.63 1.1 176 -0.82 8 184
CHEK2 0.3 0.22 0.46 231 -10000 0 231
ONECUT1 0.56 0.66 1.2 172 -0.93 8 180
CDKN2A -0.055 0.16 -10000 0 -0.45 46 46
LAMA4 0.84 0.69 1.3 216 -1.1 2 218
FOXM1B/HNF6 0.56 0.68 1.2 164 -1.1 8 172
FOS 0.34 0.79 1.4 109 -1.1 36 145
SP1 0.007 0.085 -10000 0 -0.27 30 30
CDC25B 0.84 0.7 1.3 214 -0.93 5 219
response to radiation 0.19 0.13 0.28 241 -10000 0 241
CENPB 0.84 0.69 1.3 216 -0.93 5 221
CENPA 1.1 0.9 1.8 219 -0.93 5 224
NEK2 1.2 0.92 1.8 238 -0.96 3 241
HIST1H2BA 0.87 0.71 1.4 216 -0.89 5 221
CCNA2 0.02 0.039 0.14 3 -10000 0 3
EP300 0.029 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.94 0.84 1.6 208 -0.99 7 215
CCNB2 1.1 0.9 1.8 231 -0.93 5 236
CCNB1 1.2 0.97 1.9 228 -0.97 5 233
ETV5 0.84 0.68 1.3 215 -0.95 4 219
ESR1 0.21 0.66 1.3 72 -1.1 26 98
CCND1 0.64 0.65 1.2 179 -0.9 8 187
GSK3A 0.22 0.15 0.32 227 -10000 0 227
Cyclin A-E1/CDK1-2 0.13 0.17 0.37 110 -10000 0 110
CDK2 0.09 0.059 0.16 23 -10000 0 23
G2/M transition of mitotic cell cycle 0.29 0.2 0.42 246 -10000 0 246
FOXM1B/Cbp/p300 0.027 0.3 0.83 4 -0.92 8 12
GAS1 0.66 0.77 1.3 181 -1.2 17 198
MMP2 0.81 0.71 1.3 210 -1.2 4 214
RB1/FOXM1C 0.51 0.61 1.1 154 -0.91 8 162
CREBBP 0.028 0.006 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.23 0.42 0.47 1 -0.83 116 117
MKNK1 0.028 0.006 -10000 0 -10000 0 0
MAPK14 -0.058 0.18 0.23 22 -0.33 102 124
ATF2/c-Jun -0.064 0.17 -10000 0 -0.4 40 40
MAPK11 -0.062 0.19 0.23 23 -0.34 104 127
MITF -0.068 0.2 0.27 23 -0.39 96 119
MAPKAPK5 -0.068 0.2 0.27 23 -0.39 95 118
KRT8 -0.071 0.2 0.27 23 -0.38 99 122
MAPKAPK3 0.029 0.003 -10000 0 -10000 0 0
MAPKAPK2 0.023 0.012 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.095 0.28 0.32 23 -0.5 102 125
CEBPB -0.067 0.2 0.27 23 -0.38 95 118
SLC9A1 -0.075 0.21 0.26 22 -0.4 97 119
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.069 0.21 0.29 23 -0.38 100 123
p38alpha-beta/MNK1 -0.065 0.24 0.29 21 -0.41 102 123
JUN -0.064 0.17 -10000 0 -0.39 40 40
PPARGC1A -0.11 0.25 0.27 22 -0.42 117 139
USF1 -0.055 0.18 0.27 23 -0.36 88 111
RAB5/GDP/GDI1 -0.051 0.15 -10000 0 -0.29 98 98
NOS2 -0.049 0.24 0.55 23 -0.46 32 55
DDIT3 -0.068 0.2 0.27 23 -0.38 96 119
RAB5A 0.03 0.003 -10000 0 -10000 0 0
HSPB1 -0.058 0.16 0.24 6 -0.32 86 92
p38alpha-beta/HBP1 -0.061 0.24 0.29 23 -0.42 96 119
CREB1 -0.092 0.23 0.27 23 -0.43 102 125
RAB5/GDP 0.022 0.002 -10000 0 -10000 0 0
EIF4E -0.097 0.19 0.32 2 -0.39 94 96
RPS6KA4 -0.071 0.2 0.27 23 -0.39 98 121
PLA2G4A -0.092 0.17 0.24 1 -0.36 92 93
GDI1 -0.068 0.2 0.27 23 -0.38 97 120
TP53 -0.1 0.25 0.28 23 -0.51 92 115
RPS6KA5 -0.079 0.22 0.27 23 -0.42 98 121
ESR1 -0.22 0.29 0.27 14 -0.43 196 210
HBP1 0.029 0.005 -10000 0 -10000 0 0
MEF2C -0.068 0.2 0.27 23 -0.38 97 120
MEF2A -0.07 0.2 0.27 22 -0.39 96 118
EIF4EBP1 -0.1 0.25 0.27 22 -0.48 100 122
KRT19 -0.16 0.3 0.28 21 -0.46 150 171
ELK4 -0.058 0.19 0.27 23 -0.36 90 113
ATF6 -0.056 0.18 0.27 23 -0.36 89 112
ATF1 -0.091 0.23 0.27 23 -0.43 102 125
p38alpha-beta/MAPKAPK2 -0.05 0.2 0.29 21 -0.37 93 114
p38alpha-beta/MAPKAPK3 -0.062 0.24 0.29 23 -0.42 97 120
Plasma membrane estrogen receptor 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
GNB1/GNG2 -0.066 0.13 -10000 0 -0.19 176 176
ER alpha/Gai/GDP/Gbeta gamma -0.32 0.32 -10000 0 -0.61 172 172
AKT1 -0.46 0.42 -10000 0 -0.8 214 214
PIK3CA 0.028 0.021 -10000 0 -0.37 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.47 0.43 -10000 0 -0.82 214 214
mol:Ca2+ -0.1 0.16 -10000 0 -0.43 64 64
IGF1R 0.02 0.059 -10000 0 -0.37 8 8
E2/ER alpha (dimer)/Striatin -0.099 0.13 -10000 0 -0.22 187 187
SHC1 0.022 0.013 -10000 0 -10000 0 0
apoptosis 0.44 0.4 0.76 214 -10000 0 214
RhoA/GTP -0.1 0.079 -10000 0 -0.18 167 167
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.27 0.27 0.24 1 -0.48 204 205
regulation of stress fiber formation 0.092 0.076 0.29 4 -10000 0 4
E2/ERA-ERB (dimer) -0.09 0.12 -10000 0 -0.22 177 177
KRAS 0.029 0.005 -10000 0 -10000 0 0
G13/GTP -0.079 0.11 -10000 0 -0.2 172 172
pseudopodium formation -0.092 0.076 -10000 0 -0.29 4 4
E2/ER alpha (dimer)/PELP1 -0.092 0.12 -10000 0 -0.22 178 178
GRB2 0.028 0.006 -10000 0 -10000 0 0
GNG2 0.027 0.03 -10000 0 -0.37 2 2
GNAO1 -0.14 0.2 -10000 0 -0.37 153 153
HRAS 0.029 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.33 0.31 -10000 0 -0.57 211 211
E2/ER beta (dimer) 0.02 0.006 -10000 0 -10000 0 0
mol:GDP -0.16 0.17 -10000 0 -0.31 205 205
mol:NADP -0.33 0.31 -10000 0 -0.57 211 211
PIK3R1 0.027 0.03 -10000 0 -0.37 2 2
mol:IP3 -0.1 0.17 -10000 0 -0.44 64 64
IGF-1R heterotetramer 0.02 0.059 -10000 0 -0.37 8 8
PLCB1 -0.098 0.17 -10000 0 -0.44 64 64
PLCB2 -0.11 0.18 -10000 0 -0.46 65 65
IGF1 -0.13 0.2 -10000 0 -0.37 142 142
mol:L-citrulline -0.33 0.31 -10000 0 -0.57 211 211
RHOA 0.029 0.004 -10000 0 -10000 0 0
Gai/GDP -0.33 0.4 -10000 0 -0.72 181 181
JNK cascade 0.02 0.006 -10000 0 -10000 0 0
BCAR1 0.027 0.008 -10000 0 -10000 0 0
ESR2 0.027 0.008 -10000 0 -10000 0 0
GNAQ 0.029 0.004 -10000 0 -10000 0 0
ESR1 -0.17 0.2 -10000 0 -0.37 178 178
Gq family/GDP/Gbeta gamma -0.073 0.19 -10000 0 -0.52 36 36
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.1 0.13 -10000 0 -0.39 4 4
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.24 0.25 0.24 1 -0.45 190 191
GNAZ 0.014 0.025 -10000 0 -0.37 1 1
E2/ER alpha (dimer) -0.12 0.14 -10000 0 -0.26 178 178
STRN 0.017 0.071 -10000 0 -0.37 12 12
GNAL 0.024 0.011 -10000 0 -10000 0 0
PELP1 0.025 0.011 -10000 0 -10000 0 0
MAPK11 -0.012 0.015 0.17 2 -10000 0 2
GNAI2 0.029 0.003 -10000 0 -10000 0 0
GNAI3 0.029 0.006 -10000 0 -10000 0 0
GNAI1 0.027 0.03 -10000 0 -0.37 2 2
HBEGF -0.27 0.28 0.31 3 -0.53 167 170
cAMP biosynthetic process -0.063 0.096 -10000 0 -0.18 146 146
SRC -0.3 0.3 -10000 0 -0.58 172 172
PI3K 0.041 0.032 -10000 0 -0.37 2 2
GNB1 0.027 0.009 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.13 0.17 -10000 0 -0.29 179 179
SOS1 0.03 0.002 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.25 0.22 -10000 0 -0.42 206 206
Gs family/GTP -0.061 0.1 -10000 0 -0.18 146 146
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.054 0.015 -10000 0 -10000 0 0
vasodilation -0.31 0.29 -10000 0 -0.54 211 211
mol:DAG -0.1 0.17 -10000 0 -0.44 64 64
Gs family/GDP/Gbeta gamma -0.13 0.15 -10000 0 -0.28 171 171
MSN -0.098 0.081 -10000 0 -0.31 4 4
Gq family/GTP -0.098 0.18 -10000 0 -0.47 64 64
mol:PI-3-4-5-P3 -0.45 0.41 -10000 0 -0.78 214 214
NRAS 0.029 0.005 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.31 0.29 0.54 211 -10000 0 211
GRB2/SOS1 0.042 0.009 -10000 0 -10000 0 0
RhoA/GDP -0.15 0.17 -10000 0 -0.31 186 186
NOS3 -0.35 0.33 -10000 0 -0.6 211 211
GNA11 0.019 0.062 -10000 0 -0.37 9 9
MAPKKK cascade -0.34 0.31 -10000 0 -0.59 214 214
E2/ER alpha (dimer)/PELP1/Src -0.28 0.28 0.26 1 -0.49 205 206
ruffle organization -0.092 0.076 -10000 0 -0.29 4 4
ROCK2 -0.099 0.086 -10000 0 -0.33 3 3
GNA14 -0.035 0.15 -10000 0 -0.37 58 58
GNA15 0.028 0.021 -10000 0 -0.37 1 1
GNA13 0.029 0.005 -10000 0 -10000 0 0
MMP9 -0.26 0.28 0.26 9 -0.53 166 175
MMP2 -0.29 0.29 0.26 1 -0.55 175 176
PDGFR-alpha signaling pathway

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
PDGFRA -0.15 0.19 -9999 0 -0.4 133 133
PDGF/PDGFRA/CRKL -0.093 0.14 -9999 0 -0.27 133 133
positive regulation of JUN kinase activity -0.022 0.11 -9999 0 -0.22 85 85
CRKL 0.029 0.005 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.095 0.14 -9999 0 -0.28 132 132
AP1 -0.45 0.41 -9999 0 -0.86 177 177
mol:IP3 -0.13 0.13 -9999 0 -0.3 129 129
PLCG1 -0.13 0.13 -9999 0 -0.3 129 129
PDGF/PDGFRA/alphaV Integrin -0.093 0.14 -9999 0 -0.28 132 132
RAPGEF1 0.029 0.004 -9999 0 -10000 0 0
CRK 0.025 0.011 -9999 0 -10000 0 0
mol:Ca2+ -0.13 0.13 -9999 0 -0.3 129 129
CAV3 0.019 0.004 -9999 0 -10000 0 0
CAV1 0.029 0.006 -9999 0 -10000 0 0
SHC/Grb2/SOS1 -0.021 0.11 -9999 0 -0.22 85 85
PDGF/PDGFRA/Shf -0.11 0.15 -9999 0 -0.28 145 145
FOS -0.44 0.41 -9999 0 -0.85 176 176
JUN -0.06 0.045 -9999 0 -0.33 5 5
oligodendrocyte development -0.093 0.14 -9999 0 -0.28 132 132
GRB2 0.028 0.006 -9999 0 -10000 0 0
PIK3R1 0.027 0.03 -9999 0 -0.37 2 2
mol:DAG -0.13 0.13 -9999 0 -0.3 129 129
PDGF/PDGFRA -0.15 0.19 -9999 0 -0.4 133 133
actin cytoskeleton reorganization -0.094 0.14 -9999 0 -0.28 134 134
SRF 0.008 0.023 -9999 0 -10000 0 0
SHC1 0.022 0.013 -9999 0 -10000 0 0
PI3K -0.056 0.14 -9999 0 -0.24 132 132
PDGF/PDGFRA/Crk/C3G -0.054 0.13 -9999 0 -0.23 132 132
JAK1 -0.11 0.12 -9999 0 -0.28 128 128
ELK1/SRF -0.1 0.099 -9999 0 -0.25 109 109
SHB 0.028 0.021 -9999 0 -0.37 1 1
SHF 0.01 0.087 -9999 0 -0.37 18 18
CSNK2A1 0.052 0.021 -9999 0 -10000 0 0
GO:0007205 -0.14 0.15 -9999 0 -0.33 129 129
SOS1 0.03 0.002 -9999 0 -10000 0 0
Ras protein signal transduction -0.022 0.11 -9999 0 -0.22 85 85
PDGF/PDGFRA/SHB -0.094 0.14 -9999 0 -0.28 134 134
PDGF/PDGFRA/Caveolin-1 -0.089 0.14 -9999 0 -0.28 127 127
ITGAV 0.029 0.003 -9999 0 -10000 0 0
ELK1 -0.14 0.13 -9999 0 -0.31 128 128
PIK3CA 0.028 0.021 -9999 0 -0.37 1 1
PDGF/PDGFRA/Crk -0.09 0.14 -9999 0 -0.27 132 132
JAK-STAT cascade -0.11 0.12 -9999 0 -0.28 128 128
cell proliferation -0.1 0.15 -9999 0 -0.28 145 145
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.28 0.47 -10000 0 -0.94 94 94
PCK1 -0.58 0.68 -10000 0 -1.3 166 166
HNF4A -0.33 0.57 -10000 0 -1.1 92 92
KCNJ11 -0.26 0.5 0.76 5 -0.99 87 92
AKT1 -0.12 0.21 0.38 1 -0.41 81 82
response to starvation -0.008 0.028 -10000 0 -0.18 5 5
DLK1 -0.24 0.51 0.82 7 -1 84 91
NKX2-1 -0.093 0.22 0.52 4 -0.42 64 68
ACADM -0.28 0.48 -10000 0 -0.96 92 92
TAT -0.59 0.69 -10000 0 -1.3 159 159
CEBPB 0 0.048 -10000 0 -0.12 14 14
CEBPA -0.003 0.06 -10000 0 -0.16 20 20
TTR -0.36 0.59 -10000 0 -1.3 103 103
PKLR -0.26 0.49 0.65 2 -0.97 89 91
APOA1 -0.42 0.68 -10000 0 -1.3 103 103
CPT1C -0.27 0.47 0.72 1 -0.94 93 94
ALAS1 -0.13 0.28 -10000 0 -1.5 6 6
TFRC -0.24 0.43 -10000 0 -0.86 78 78
FOXF1 -0.005 0.11 -10000 0 -0.37 29 29
NF1 0.03 0.018 -10000 0 -10000 0 0
HNF1A (dimer) 0.019 0.12 0.26 37 -0.25 27 64
CPT1A -0.27 0.47 -10000 0 -0.96 89 89
HMGCS1 -0.28 0.47 -10000 0 -0.95 90 90
NR3C1 -0.086 0.13 -10000 0 -0.24 133 133
CPT1B -0.28 0.47 -10000 0 -0.94 95 95
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.049 0.099 0.25 53 -0.2 16 69
GCK -0.39 0.57 0.66 9 -0.98 146 155
CREB1 -0.062 0.12 -10000 0 -0.22 116 116
IGFBP1 -0.39 0.57 -10000 0 -1.3 95 95
PDX1 -0.13 0.44 0.74 13 -1 43 56
UCP2 -0.28 0.47 -10000 0 -0.95 92 92
ALDOB -0.34 0.56 -10000 0 -1.1 109 109
AFP -0.047 0.26 0.36 45 -0.58 42 87
BDH1 -0.29 0.5 -10000 0 -0.97 97 97
HADH -0.27 0.48 -10000 0 -0.98 86 86
F2 -0.36 0.62 -10000 0 -1.3 89 89
HNF1A 0.019 0.12 0.26 37 -0.25 27 64
G6PC -0.26 0.49 -10000 0 -1.3 61 61
SLC2A2 -0.22 0.5 0.64 1 -1.3 47 48
INS 0.032 0.091 0.25 33 -10000 0 33
FOXA1 0.031 0.15 0.26 57 -0.26 53 110
FOXA3 -0.11 0.21 -10000 0 -0.38 116 116
FOXA2 -0.31 0.55 0.9 1 -1.1 91 92
ABCC8 -0.25 0.5 0.8 9 -0.97 86 95
ALB -0.14 0.34 -10000 0 -0.89 56 56
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.023 0.046 -10000 0 -0.31 2 2
Crk/p130 Cas/Paxillin -0.14 0.13 -10000 0 -0.3 93 93
JUN -0.15 0.14 -10000 0 -0.37 74 74
HRAS 0.029 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.13 0.17 -10000 0 -0.26 216 216
RAP1A 0.029 0.006 -10000 0 -10000 0 0
FRS2 0.029 0.004 -10000 0 -10000 0 0
RAP1A/GDP 0.021 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.13 0.17 -10000 0 -0.25 221 221
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.029 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.025 0.011 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.019 0.11 -10000 0 -0.2 91 91
RHOA 0.029 0.004 -10000 0 -10000 0 0
RAP1A/GTP -0.12 0.15 -10000 0 -0.23 219 219
GRB7 0.024 0.042 -10000 0 -0.37 4 4
RET51/GFRalpha1/GDNF -0.13 0.17 -10000 0 -0.25 220 220
MAPKKK cascade -0.15 0.16 -10000 0 -0.27 206 206
BCAR1 0.027 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.02 0.11 -10000 0 -0.2 95 95
lamellipodium assembly -0.11 0.13 -10000 0 -0.28 95 95
RET51/GFRalpha1/GDNF/SHC -0.1 0.16 -10000 0 -0.26 171 171
PIK3CA 0.028 0.021 -10000 0 -0.37 1 1
RET9/GFRalpha1/GDNF/SHC -0.019 0.098 -10000 0 -0.2 76 76
RET9/GFRalpha1/GDNF/Shank3 -0.02 0.11 -10000 0 -0.2 94 94
MAPK3 -0.14 0.12 0.2 2 -0.34 56 58
DOK1 0.03 0.002 -10000 0 -10000 0 0
DOK6 -0.027 0.14 -10000 0 -0.37 50 50
PXN 0.029 0.003 -10000 0 -10000 0 0
neurite development -0.14 0.13 -10000 0 -0.31 84 84
DOK5 0.023 0.047 -10000 0 -0.37 5 5
GFRA1 -0.083 0.18 -10000 0 -0.37 102 102
MAPK8 -0.15 0.15 -10000 0 -0.29 140 140
HRAS/GTP -0.15 0.18 -10000 0 -0.29 217 217
tube development -0.013 0.11 0.21 7 -0.2 88 95
MAPK1 -0.14 0.12 0.2 2 -0.34 56 58
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.035 0.097 -10000 0 -0.2 87 87
Rac1/GDP 0.022 0.003 -10000 0 -10000 0 0
SRC 0.029 0.005 -10000 0 -10000 0 0
PDLIM7 0.028 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.14 0.18 -10000 0 -0.27 226 226
SHC1 0.022 0.013 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.13 0.17 -10000 0 -0.25 221 221
RET51/GFRalpha1/GDNF/Dok5 -0.12 0.17 -10000 0 -0.25 214 214
PRKCA 0.028 0.006 -10000 0 -10000 0 0
HRAS/GDP 0.022 0.003 -10000 0 -10000 0 0
CREB1 -0.09 0.15 -10000 0 -0.32 88 88
PIK3R1 0.027 0.03 -10000 0 -0.37 2 2
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.033 0.093 -10000 0 -0.21 71 71
RET51/GFRalpha1/GDNF/Grb7 -0.13 0.17 -10000 0 -0.25 217 217
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.18 0.2 -10000 0 -0.37 191 191
DOK4 0.028 0.008 -10000 0 -10000 0 0
JNK cascade -0.15 0.14 -10000 0 -0.36 74 74
RET9/GFRalpha1/GDNF/FRS2 -0.02 0.11 -10000 0 -0.2 94 94
SHANK3 0.028 0.006 -10000 0 -10000 0 0
RASA1 0.027 0.03 -10000 0 -0.37 2 2
NCK1 0.03 0.002 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.03 0.088 -10000 0 -0.2 71 71
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.14 0.15 -10000 0 -0.25 214 214
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.15 0.15 -10000 0 -0.25 222 222
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.14 0.17 -10000 0 -0.29 167 167
PI3K -0.16 0.19 -10000 0 -0.41 95 95
SOS1 0.03 0.002 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.004 0.11 -10000 0 -0.2 88 88
GRB10 0.029 0.004 -10000 0 -10000 0 0
activation of MAPKK activity -0.096 0.12 -10000 0 -0.26 96 96
RET51/GFRalpha1/GDNF/FRS2 -0.13 0.17 -10000 0 -0.25 219 219
GAB1 0.028 0.008 -10000 0 -10000 0 0
IRS1 0.03 0.003 -10000 0 -10000 0 0
IRS2 0.02 0.055 -10000 0 -0.37 7 7
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.14 0.17 -10000 0 -0.29 167 167
RET51/GFRalpha1/GDNF/PKC alpha -0.12 0.16 -10000 0 -0.25 214 214
GRB2 0.028 0.006 -10000 0 -10000 0 0
PRKACA 0.029 0.004 -10000 0 -10000 0 0
GDNF 0.022 0.009 -10000 0 -10000 0 0
RAC1 0.029 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.13 0.17 -10000 0 -0.25 221 221
Rac1/GTP -0.13 0.15 0.18 1 -0.34 93 94
RET9/GFRalpha1/GDNF -0.035 0.11 -10000 0 -0.22 95 95
GFRalpha1/GDNF -0.043 0.13 -10000 0 -0.26 95 95
IL4-mediated signaling events

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
BCL2L1 -0.38 0.75 0.99 8 -1.3 114 122
STAT6 (cleaved dimer) -0.52 0.66 -10000 0 -1.2 155 155
IGHG1 -0.071 0.34 0.66 25 -0.51 25 50
IGHG3 -0.38 0.7 0.82 8 -1.1 143 151
AKT1 -0.17 0.44 0.67 7 -0.76 76 83
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.13 0.37 0.63 8 -0.67 58 66
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.15 0.45 0.71 9 -0.78 59 68
THY1 -0.32 0.83 1.2 35 -1.3 112 147
MYB 0.024 0.011 -10000 0 -10000 0 0
HMGA1 0.026 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.24 0.58 0.88 19 -0.91 105 124
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.15 0.45 0.71 9 -0.78 60 69
SP1 0.042 0.053 0.27 17 -10000 0 17
INPP5D 0.029 0.003 -10000 0 -10000 0 0
SOCS5 0.018 0.064 -10000 0 -0.19 4 4
STAT6 (dimer)/ETS1 -0.43 0.75 0.77 8 -1.3 126 134
SOCS1 -0.23 0.48 0.7 6 -0.77 112 118
SOCS3 -0.26 0.57 0.76 3 -1.1 84 87
FCER2 -0.32 0.7 1.1 12 -1.1 112 124
PARP14 0.032 0.031 0.18 8 -0.37 1 9
CCL17 -0.37 0.77 1.2 12 -1.3 112 124
GRB2 0.028 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.084 0.35 0.64 14 -0.59 39 53
T cell proliferation -0.42 0.75 0.93 2 -1.3 121 123
IL4R/JAK1 -0.41 0.73 0.85 3 -1.2 121 124
EGR2 -0.52 0.89 1.1 9 -1.5 138 147
JAK2 0.007 0.1 0.26 18 -10000 0 18
JAK3 0.012 0.043 0.29 1 -0.35 1 2
PIK3R1 0.027 0.03 -10000 0 -0.37 2 2
JAK1 0.01 0.058 0.22 1 -10000 0 1
COL1A2 -0.044 0.34 0.75 17 -1.2 7 24
CCL26 -0.35 0.79 1.3 16 -1.3 111 127
IL4R -0.39 0.84 1.2 18 -1.4 115 133
PTPN6 0.015 0.046 -10000 0 -0.12 1 1
IL13RA2 -0.8 0.8 1 6 -1.4 192 198
IL13RA1 0.007 0.1 0.26 18 -10000 0 18
IRF4 -0.24 0.63 0.81 11 -1.4 76 87
ARG1 -0.24 0.55 0.67 3 -1.2 72 75
CBL -0.23 0.53 0.74 14 -0.84 108 122
GTF3A 0.052 0.081 0.28 37 -10000 0 37
PIK3CA 0.028 0.021 -10000 0 -0.37 1 1
IL13RA1/JAK2 0.02 0.14 0.34 30 -10000 0 30
IRF4/BCL6 -0.24 0.56 0.6 5 -1.3 77 82
CD40LG -0.001 0.11 0.31 9 -0.3 21 30
MAPK14 -0.24 0.57 0.76 12 -0.94 103 115
mitosis -0.16 0.42 0.65 9 -0.71 76 85
STAT6 -0.46 1 1.4 30 -1.6 115 145
SPI1 -0.009 0.097 -10000 0 -0.2 60 60
RPS6KB1 -0.15 0.4 0.63 7 -0.68 73 80
STAT6 (dimer) -0.45 1 1.4 30 -1.6 115 145
STAT6 (dimer)/PARP14 -0.44 0.8 0.92 6 -1.3 146 152
mast cell activation 0.001 0.03 -10000 0 -0.13 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.18 0.45 0.7 11 -0.74 83 94
FRAP1 -0.17 0.44 0.67 7 -0.76 76 83
LTA -0.36 0.77 1.2 12 -1.2 113 125
FES 0.023 0.047 -10000 0 -0.37 5 5
T-helper 1 cell differentiation 0.42 0.94 1.5 115 -1.4 27 142
CCL11 -0.36 0.73 0.97 18 -1.2 115 133
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.15 0.43 0.7 11 -0.71 73 84
IL2RG 0.008 0.058 0.22 2 -0.36 5 7
IL10 -0.39 0.81 1.2 12 -1.3 117 129
IRS1 0.03 0.003 -10000 0 -10000 0 0
IRS2 0.02 0.055 -10000 0 -0.37 7 7
IL4 0.003 0.32 0.89 16 -1.1 2 18
IL5 -0.38 0.75 0.99 7 -1.3 113 120
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.24 0.66 1.1 23 -0.97 98 121
COL1A1 -0.057 0.53 1 34 -1.2 29 63
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.42 0.75 -10000 0 -1.3 118 118
IL2R gamma/JAK3 0.019 0.063 0.18 5 -0.25 7 12
TFF3 -0.38 0.77 1 10 -1.3 114 124
ALOX15 -0.37 0.75 1 11 -1.2 115 126
MYBL1 0.024 0.012 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.29 0.64 0.89 13 -1 116 129
SHC1 0.022 0.013 -10000 0 -10000 0 0
CEBPB -0.006 0.09 -10000 0 -0.2 56 56
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.15 0.44 0.69 8 -0.78 59 67
mol:PI-3-4-5-P3 -0.17 0.44 0.67 7 -0.76 76 83
PI3K -0.18 0.46 0.71 4 -0.82 76 80
DOK2 0.021 0.032 -10000 0 -0.37 2 2
ETS1 0.007 0.063 -10000 0 -0.28 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.074 0.33 0.62 15 -0.56 33 48
ITGB3 -0.42 0.79 0.97 11 -1.3 123 134
PIGR -0.45 0.81 1.2 9 -1.4 121 130
IGHE -0.025 0.12 0.2 9 -0.33 24 33
MAPKKK cascade -0.07 0.33 0.61 15 -0.56 32 47
BCL6 0.027 0.018 -10000 0 -0.13 1 1
OPRM1 -0.38 0.75 0.98 8 -1.3 115 123
RETNLB -0.38 0.75 1 6 -1.3 108 114
SELP -0.49 0.87 1.2 11 -1.4 139 150
AICDA -0.38 0.7 1.1 3 -1.2 116 119
TCGA08_retinoblastoma

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
CDKN2B 0.024 0.02 -10000 0 -10000 0 0
CDKN2C -0.028 0.04 -10000 0 -0.086 2 2
CDKN2A 0.008 0.014 -10000 0 -10000 0 0
CCND2 -0.083 0.09 -10000 0 -0.15 203 203
RB1 0.083 0.1 0.32 32 -10000 0 32
CDK4 -0.096 0.1 -10000 0 -0.17 205 205
CDK6 -0.094 0.11 -10000 0 -0.33 38 38
G1/S progression -0.095 0.11 0.18 7 -0.3 45 52
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.039 0.09 0.22 39 -0.31 11 50
NFATC2 -0.081 0.26 0.54 7 -0.52 58 65
NFATC3 -0.045 0.13 0.33 3 -0.28 63 66
CD40LG -0.38 0.51 0.82 7 -1 128 135
ITCH 0.013 0.028 -10000 0 -10000 0 0
CBLB 0.014 0.028 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.21 0.46 0.96 14 -0.84 84 98
JUNB 0.011 0.084 -10000 0 -0.37 17 17
CaM/Ca2+/Calcineurin A alpha-beta B1 0.031 0.035 -10000 0 -0.26 5 5
T cell anergy -0.016 0.063 -10000 0 -0.36 5 5
TLE4 -0.063 0.18 -10000 0 -0.42 36 36
Jun/NFAT1-c-4/p21SNFT -0.26 0.49 0.74 6 -0.9 118 124
AP-1/NFAT1-c-4 -0.42 0.62 0.96 4 -1.2 129 133
IKZF1 -0.066 0.2 0.47 3 -0.45 39 42
T-helper 2 cell differentiation -0.2 0.34 0.58 3 -0.8 68 71
AP-1/NFAT1 -0.14 0.24 0.5 7 -0.39 130 137
CALM1 0.03 0.024 -10000 0 -0.16 5 5
EGR2 -0.42 0.68 0.92 5 -1.4 113 118
EGR3 -0.37 0.63 0.92 5 -1.2 106 111
NFAT1/FOXP3 -0.045 0.22 0.5 17 -0.41 50 67
EGR1 -0.1 0.19 -10000 0 -0.37 121 121
JUN 0.014 0.068 0.23 7 -0.38 6 13
EGR4 0.024 0.013 -10000 0 -10000 0 0
mol:Ca2+ 0.003 0.018 -10000 0 -0.15 5 5
GBP3 -0.079 0.22 0.37 2 -0.52 47 49
FOSL1 0.012 0.079 -10000 0 -0.37 15 15
NFAT1-c-4/MAF/IRF4 -0.27 0.49 0.64 4 -0.89 125 129
DGKA -0.061 0.18 0.46 4 -0.39 44 48
CREM 0.029 0.006 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.27 0.5 0.64 5 -0.92 122 127
CTLA4 -0.025 0.23 0.53 32 -0.38 44 76
NFAT1-c-4 (dimer)/EGR1 -0.33 0.53 0.63 3 -1 126 129
NFAT1-c-4 (dimer)/EGR4 -0.27 0.5 0.65 5 -0.92 123 128
FOS -0.15 0.2 0.24 6 -0.38 157 163
IFNG -0.12 0.28 0.67 12 -0.64 42 54
T cell activation -0.22 0.32 0.68 4 -0.69 90 94
MAF 0.026 0.022 -10000 0 -0.37 1 1
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.22 0.39 0.73 111 -0.84 5 116
TNF -0.31 0.46 0.58 4 -0.89 126 130
FASLG -0.47 0.74 1.1 4 -1.4 130 134
TBX21 0.031 0.08 0.26 16 -0.37 9 25
BATF3 0.021 0.032 -10000 0 -0.37 2 2
PRKCQ 0.015 0.075 0.14 2 -0.37 13 15
PTPN1 -0.062 0.18 0.37 2 -0.4 39 41
NFAT1-c-4/ICER1 -0.27 0.5 0.64 5 -0.91 123 128
GATA3 0.001 0.1 -10000 0 -0.37 25 25
T-helper 1 cell differentiation -0.11 0.28 0.69 13 -0.63 40 53
IL2RA -0.23 0.42 0.81 12 -0.78 97 109
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.055 0.17 0.37 2 -0.4 38 40
E2F1 0.012 0.016 -10000 0 -10000 0 0
PPARG 0.03 0.003 -10000 0 -10000 0 0
SLC3A2 -0.061 0.18 0.43 3 -0.39 44 47
IRF4 -0.041 0.15 -10000 0 -0.37 61 61
PTGS2 -0.39 0.53 0.8 8 -1 129 137
CSF2 -0.38 0.5 0.8 8 -0.98 128 136
JunB/Fra1/NFAT1-c-4 -0.26 0.51 0.64 5 -0.9 126 131
IL4 -0.21 0.36 0.58 3 -0.84 68 71
IL5 -0.38 0.5 0.79 8 -0.98 128 136
IL2 -0.23 0.33 0.68 4 -0.7 90 94
IL3 -0.051 0.085 -10000 0 -0.99 1 1
RNF128 0.01 0.058 -10000 0 -0.48 5 5
NFATC1 -0.22 0.4 0.85 5 -0.74 111 116
CDK4 0.22 0.3 0.65 81 -0.84 3 84
PTPRK -0.054 0.17 0.37 2 -0.4 36 38
IL8 -0.42 0.51 0.84 7 -1 134 141
POU2F1 0.023 0.013 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 0.093 0.26 0.57 67 -0.47 15 82
IHH 0.059 0.12 0.24 72 -0.24 23 95
SHH Np/Cholesterol/GAS1 -0.018 0.087 -10000 0 -0.22 54 54
LRPAP1 0.029 0.006 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.018 0.087 0.22 54 -10000 0 54
SMO/beta Arrestin2 0.068 0.2 0.36 66 -0.45 28 94
SMO 0.066 0.22 0.38 76 -0.48 26 102
AKT1 0.045 0.16 0.31 25 -0.44 17 42
ARRB2 0.025 0.011 -10000 0 -10000 0 0
BOC 0.029 0.005 -10000 0 -10000 0 0
ADRBK1 0.029 0.005 -10000 0 -10000 0 0
heart looping 0.067 0.21 0.38 76 -0.47 26 102
STIL 0.049 0.16 0.32 61 -0.37 14 75
DHH N/PTCH2 0.039 0.025 -10000 0 -0.26 2 2
DHH N/PTCH1 0.076 0.18 0.38 70 -0.36 27 97
PIK3CA 0.028 0.021 -10000 0 -0.37 1 1
DHH 0.028 0.005 -10000 0 -10000 0 0
PTHLH 0.12 0.31 0.66 75 -0.52 15 90
determination of left/right symmetry 0.067 0.21 0.38 76 -0.47 26 102
PIK3R1 0.027 0.03 -10000 0 -0.37 2 2
skeletal system development 0.12 0.31 0.66 75 -0.52 15 90
IHH N/Hhip -0.096 0.17 0.2 9 -0.27 164 173
DHH N/Hhip -0.098 0.15 -10000 0 -0.26 161 161
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.067 0.21 0.38 76 -0.47 26 102
pancreas development -0.15 0.19 -10000 0 -0.37 161 161
HHAT 0.022 0.024 -10000 0 -0.37 1 1
PI3K 0.041 0.032 -10000 0 -0.37 2 2
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.045 0.16 -10000 0 -0.37 67 67
somite specification 0.067 0.21 0.38 76 -0.47 26 102
SHH Np/Cholesterol/PTCH1 0.04 0.16 0.32 57 -0.33 22 79
SHH Np/Cholesterol/PTCH2 0.011 0.043 -10000 0 -0.22 11 11
SHH Np/Cholesterol/Megalin -0.02 0.076 -10000 0 -0.2 50 50
SHH -0.021 0.046 -10000 0 -0.28 10 10
catabolic process 0.089 0.23 0.47 76 -0.39 27 103
SMO/Vitamin D3 0.082 0.2 0.38 74 -0.41 25 99
SHH Np/Cholesterol/Hhip -0.072 0.1 -10000 0 -0.21 130 130
LRP2 -0.029 0.14 -10000 0 -0.37 49 49
receptor-mediated endocytosis 0.035 0.2 0.35 59 -0.47 23 82
SHH Np/Cholesterol/BOC 0.012 0.042 -10000 0 -0.22 10 10
SHH Np/Cholesterol/CDO 0.012 0.043 -10000 0 -0.22 11 11
mesenchymal cell differentiation 0.072 0.1 0.21 130 -10000 0 130
mol:Vitamin D3 0.09 0.19 0.37 74 -0.36 18 92
IHH N/PTCH2 0.051 0.082 0.17 65 -0.22 12 77
CDON 0.028 0.006 -10000 0 -10000 0 0
IHH N/PTCH1 0.087 0.22 0.48 68 -0.39 27 95
Megalin/LRPAP1 -0.003 0.1 -10000 0 -0.26 49 49
PTCH2 0.026 0.03 -10000 0 -0.37 2 2
SHH Np/Cholesterol 0.005 0.04 -10000 0 -0.21 11 11
PTCH1 0.089 0.23 0.47 76 -0.39 27 103
HHIP -0.15 0.19 -10000 0 -0.37 161 161
Nongenotropic Androgen signaling

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
PTK2 -0.007 0.004 -10000 0 -10000 0 0
GNB1/GNG2 -0.02 0.11 -10000 0 -0.2 99 99
regulation of S phase of mitotic cell cycle -0.053 0.1 -10000 0 -0.21 98 98
GNAO1 -0.14 0.2 -10000 0 -0.37 153 153
HRAS 0.028 0.006 -10000 0 -10000 0 0
SHBG/T-DHT -0.054 0.1 -10000 0 -0.21 110 110
PELP1 0.024 0.011 -10000 0 -10000 0 0
AKT1 -0.009 0.002 -10000 0 -10000 0 0
MAP2K1 -0.12 0.097 -10000 0 -0.29 53 53
T-DHT/AR -0.058 0.12 -10000 0 -0.26 98 98
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.003 0.003 -10000 0 -0.007 124 124
GNAI2 0.029 0.003 -10000 0 -10000 0 0
GNAI3 0.028 0.006 -10000 0 -10000 0 0
GNAI1 0.027 0.03 -10000 0 -0.37 2 2
mol:GDP -0.11 0.15 -10000 0 -0.35 100 100
cell proliferation -0.23 0.21 -10000 0 -0.44 174 174
PIK3CA 0.028 0.021 -10000 0 -0.37 1 1
FOS -0.38 0.38 -10000 0 -0.76 177 177
mol:Ca2+ -0.023 0.038 -10000 0 -0.07 130 130
MAPK3 -0.18 0.16 -10000 0 -0.33 165 165
MAPK1 -0.12 0.13 -10000 0 -0.32 42 42
PIK3R1 0.027 0.03 -10000 0 -0.37 2 2
mol:IP3 -0.002 0.002 -10000 0 -0.005 11 11
cAMP biosynthetic process -0.051 0.092 -10000 0 -0.18 110 110
GNG2 0.027 0.03 -10000 0 -0.37 2 2
potassium channel inhibitor activity -0.002 0.002 -10000 0 -0.005 11 11
HRAS/GTP -0.058 0.11 -10000 0 -0.21 95 95
actin cytoskeleton reorganization 0.039 0.028 -10000 0 -0.27 2 2
SRC 0.027 0.006 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.002 0.002 -10000 0 -0.005 11 11
PI3K 0.038 0.028 -10000 0 -0.31 2 2
apoptosis 0.22 0.22 0.44 176 -10000 0 176
T-DHT/AR/PELP1 -0.04 0.11 -10000 0 -0.22 98 98
HRAS/GDP -0.095 0.16 -10000 0 -0.35 99 99
CREB1 -0.24 0.24 -10000 0 -0.47 176 176
RAC1-CDC42/GTP 0.049 0.031 -10000 0 -0.27 2 2
AR -0.081 0.18 -10000 0 -0.37 98 98
GNB1 0.027 0.009 -10000 0 -10000 0 0
RAF1 -0.099 0.091 -10000 0 -0.26 53 53
RAC1-CDC42/GDP -0.077 0.16 -10000 0 -0.33 100 100
T-DHT/AR/PELP1/Src -0.046 0.11 -10000 0 -0.21 95 95
MAP2K2 -0.12 0.098 -10000 0 -0.29 52 52
T-DHT/AR/PELP1/Src/PI3K -0.053 0.1 -10000 0 -0.21 98 98
GNAZ 0.014 0.025 -10000 0 -0.37 1 1
SHBG -0.096 0.18 -10000 0 -0.37 110 110
Gi family/GNB1/GNG2/GDP -0.14 0.21 -10000 0 -0.37 132 132
mol:T-DHT -0.001 0.001 -10000 0 -0.005 6 6
RAC1 0.029 0.004 -10000 0 -10000 0 0
GNRH1 -0.006 0.016 0.2 2 -10000 0 2
Gi family/GTP -0.066 0.13 -10000 0 -0.23 121 121
CDC42 0.028 0.007 -10000 0 -10000 0 0
Ephrin B reverse signaling

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
EFNB2 0.028 0.006 -10000 0 -10000 0 0
EPHB2 0.022 0.025 -10000 0 -0.36 1 1
EFNB1 0 0.064 0.21 21 -0.26 7 28
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.12 -10000 0 -0.2 61 61
Ephrin B2/EPHB1-2 0.002 0.088 -10000 0 -0.19 57 57
neuron projection morphogenesis -0.001 0.1 -10000 0 -0.19 66 66
Ephrin B1/EPHB1-2/Tiam1 0.011 0.12 -10000 0 -0.21 71 71
DNM1 0.022 0.051 -10000 0 -0.37 6 6
cell-cell signaling 0.002 0.005 -10000 0 -10000 0 0
MAP2K4 -0.16 0.24 -10000 0 -0.52 111 111
YES1 -0.22 0.36 -10000 0 -0.76 111 111
Ephrin B1/EPHB1-2/NCK2 0.023 0.11 -10000 0 -0.2 62 62
PI3K -0.13 0.27 -10000 0 -0.54 110 110
mol:GDP 0.01 0.12 -10000 0 -0.2 71 71
ITGA2B 0.026 0.007 -10000 0 -10000 0 0
endothelial cell proliferation 0.038 0.011 -10000 0 -10000 0 0
FYN -0.22 0.36 -10000 0 -0.76 111 111
MAP3K7 -0.16 0.26 0.22 1 -0.56 110 111
FGR -0.21 0.36 -10000 0 -0.76 110 110
TIAM1 0.008 0.089 -10000 0 -0.37 19 19
PIK3R1 0.027 0.03 -10000 0 -0.37 2 2
RGS3 0.029 0.005 -10000 0 -10000 0 0
cell adhesion -0.14 0.26 -10000 0 -0.52 109 109
LYN -0.22 0.36 -10000 0 -0.75 111 111
Ephrin B1/EPHB1-2/Src Family Kinases -0.21 0.33 -10000 0 -0.7 111 111
Ephrin B1/EPHB1-2 -0.18 0.28 -10000 0 -0.6 109 109
SRC -0.21 0.36 -10000 0 -0.75 111 111
ITGB3 -0.002 0.11 -10000 0 -0.37 28 28
EPHB1 -0.055 0.16 -10000 0 -0.36 79 79
EPHB4 0.029 0.005 -10000 0 -10000 0 0
RAC1 0.029 0.004 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.038 0.012 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.017 0.082 -10000 0 -0.26 28 28
BLK -0.24 0.36 -10000 0 -0.78 111 111
HCK -0.22 0.36 -10000 0 -0.76 111 111
regulation of stress fiber formation -0.021 0.11 0.19 62 -10000 0 62
MAPK8 -0.16 0.24 -10000 0 -0.51 111 111
Ephrin B1/EPHB1-2/RGS3 0.024 0.11 -10000 0 -0.19 61 61
endothelial cell migration -0.13 0.22 -10000 0 -0.46 107 107
NCK2 0.028 0.021 -10000 0 -0.37 1 1
PTPN13 -0.083 0.21 -10000 0 -0.48 79 79
regulation of focal adhesion formation -0.021 0.11 0.19 62 -10000 0 62
chemotaxis -0.023 0.11 0.19 61 -10000 0 61
PIK3CA 0.028 0.021 -10000 0 -0.37 1 1
Rac1/GTP 0.011 0.11 -10000 0 -0.19 66 66
angiogenesis -0.18 0.28 -10000 0 -0.59 111 111
LCK -0.22 0.36 -10000 0 -0.76 110 110
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.028 0.021 -10000 0 -0.37 1 1
PTK2 0.022 0.013 -10000 0 -10000 0 0
CRKL -0.091 0.093 -10000 0 -0.2 142 142
GRB2/SOS1/SHC 0.043 0.027 -10000 0 -10000 0 0
HRAS 0.029 0.004 -10000 0 -10000 0 0
IRS1/Crk -0.067 0.11 -10000 0 -0.2 141 141
IGF-1R heterotetramer/IGF1/PTP1B -0.052 0.13 -10000 0 -0.22 138 138
AKT1 -0.089 0.086 -10000 0 -0.35 5 5
BAD -0.088 0.082 -10000 0 -0.34 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.079 0.092 -10000 0 -0.21 123 123
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.063 0.12 -10000 0 -0.21 142 142
RAF1 -0.062 0.09 0.27 1 -0.39 3 4
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.038 0.13 -10000 0 -0.2 137 137
YWHAZ 0.022 0.013 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.064 0.12 -10000 0 -0.22 142 142
PIK3CA 0.028 0.021 -10000 0 -0.37 1 1
RPS6KB1 -0.087 0.085 -10000 0 -0.38 3 3
GNB2L1 0.029 0.006 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.044 0.093 0.26 3 -0.3 2 5
PXN 0.029 0.003 -10000 0 -10000 0 0
PIK3R1 0.027 0.03 -10000 0 -0.37 2 2
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.042 0.009 -10000 0 -10000 0 0
HRAS/GTP -0.037 0.094 -10000 0 -0.19 96 96
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.011 0.11 -10000 0 -0.18 96 96
IGF-1R heterotetramer -0.018 0.077 -10000 0 -0.4 8 8
IGF-1R heterotetramer/IGF1/IRS/Nck -0.05 0.13 -10000 0 -0.21 142 142
Crk/p130 Cas/Paxillin -0.04 0.12 0.22 1 -0.19 141 142
IGF1R -0.018 0.077 -10000 0 -0.4 8 8
IGF1 -0.13 0.2 -10000 0 -0.39 142 142
IRS2/Crk -0.087 0.09 -10000 0 -0.2 138 138
PI3K -0.041 0.13 -10000 0 -0.2 141 141
apoptosis 0.06 0.072 0.27 3 -0.28 1 4
HRAS/GDP 0.022 0.003 -10000 0 -10000 0 0
PRKCD -0.089 0.15 0.19 1 -0.27 137 138
RAF1/14-3-3 E -0.048 0.09 0.27 1 -0.33 3 4
BAD/14-3-3 -0.062 0.076 0.29 1 -0.28 3 4
PRKCZ -0.092 0.093 -10000 0 -0.2 124 124
Crk/p130 Cas/Paxillin/FAK1 -0.07 0.073 -10000 0 -0.29 1 1
PTPN1 0.029 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.1 0.15 -10000 0 -0.28 140 140
BCAR1 0.027 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.022 0.11 -10000 0 -0.2 100 100
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.03 0.002 -10000 0 -10000 0 0
IRS1/NCK2 -0.063 0.12 -10000 0 -0.21 142 142
GRB10 0.029 0.004 -10000 0 -10000 0 0
PTPN11 -0.091 0.093 0.11 1 -0.2 142 143
IRS1 -0.077 0.11 0.12 4 -0.22 141 145
IRS2 -0.088 0.095 -10000 0 -0.21 134 134
IGF-1R heterotetramer/IGF1 -0.088 0.16 -10000 0 -0.29 142 142
GRB2 0.028 0.006 -10000 0 -10000 0 0
PDPK1 -0.09 0.091 -10000 0 -0.2 128 128
YWHAE 0.025 0.011 -10000 0 -10000 0 0
PRKD1 -0.088 0.15 -10000 0 -0.27 134 134
SHC1 0.022 0.013 -10000 0 -10000 0 0
FoxO family signaling

Figure S14.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S14.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC -0.17 0.45 -10000 0 -1.2 61 61
PLK1 0.56 0.49 0.95 202 -0.6 1 203
CDKN1B 0.26 0.25 0.59 94 -10000 0 94
FOXO3 0.45 0.49 0.9 178 -0.54 3 181
KAT2B 0.14 0.1 0.25 148 -0.32 2 150
FOXO1/SIRT1 -0.057 0.15 0.38 1 -0.37 61 62
CAT 0.38 0.43 0.81 149 -0.76 11 160
CTNNB1 0.029 0.003 -10000 0 -10000 0 0
AKT1 0.12 0.1 0.25 126 -10000 0 126
FOXO1 -0.038 0.16 -10000 0 -0.37 61 61
MAPK10 0.039 0.055 0.19 4 -0.19 8 12
mol:GTP 0 0.002 -10000 0 -10000 0 0
FOXO4 0.057 0.12 -10000 0 -0.56 4 4
response to oxidative stress 0.11 0.095 0.18 204 -0.071 1 205
FOXO3A/SIRT1 0.38 0.34 0.67 195 -0.63 1 196
XPO1 0.03 0.003 -10000 0 -10000 0 0
EP300 0.016 0.037 -10000 0 -10000 0 0
BCL2L11 0.15 0.14 -10000 0 -0.64 1 1
FOXO1/SKP2 -0.025 0.15 -10000 0 -0.35 57 57
mol:GDP 0.11 0.095 0.18 204 -0.071 1 205
RAN 0.029 0.009 -10000 0 -10000 0 0
GADD45A 0.26 0.3 0.56 117 -0.75 10 127
YWHAQ 0.03 0.003 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.056 0.098 -10000 0 -0.35 4 4
MST1 0.12 0.13 0.25 136 -0.32 11 147
CSNK1D 0.028 0.007 -10000 0 -10000 0 0
CSNK1E 0.029 0.005 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.064 0.13 -10000 0 -0.36 13 13
YWHAB 0.029 0.005 -10000 0 -10000 0 0
MAPK8 0.044 0.062 0.2 5 -0.2 12 17
MAPK9 0.051 0.043 0.2 5 -10000 0 5
YWHAG 0.029 0.004 -10000 0 -10000 0 0
YWHAE 0.025 0.011 -10000 0 -10000 0 0
YWHAZ 0.022 0.013 -10000 0 -10000 0 0
SIRT1 -0.001 0.065 0.32 7 -0.29 3 10
SOD2 0.25 0.27 0.62 73 -0.58 5 78
RBL2 0.28 0.39 0.68 124 -0.93 11 135
RAL/GDP 0.1 0.065 0.18 109 -10000 0 109
CHUK 0.14 0.1 0.25 148 -10000 0 148
Ran/GTP 0.021 0.009 -10000 0 -10000 0 0
CSNK1G2 0.029 0.005 -10000 0 -10000 0 0
RAL/GTP 0.1 0.062 0.2 16 -10000 0 16
CSNK1G1 0.029 0.004 -10000 0 -10000 0 0
FASLG 0.12 0.28 0.58 8 -1.1 14 22
SKP2 0.029 0.006 -10000 0 -10000 0 0
USP7 0.028 0.009 -10000 0 -10000 0 0
IKBKB 0.12 0.1 0.25 133 -10000 0 133
CCNB1 0.53 0.49 1 165 -0.6 1 166
FOXO1-3a-4/beta catenin 0.22 0.24 0.55 81 -0.42 3 84
proteasomal ubiquitin-dependent protein catabolic process -0.025 0.15 -10000 0 -0.35 57 57
CSNK1A1 0.029 0.005 -10000 0 -10000 0 0
SGK1 0.12 0.11 0.25 137 -0.32 5 142
CSNK1G3 0.029 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.039 0.015 -10000 0 -10000 0 0
ZFAND5 0.052 0.11 -10000 0 -0.68 2 2
SFN 0.011 0.014 -10000 0 -10000 0 0
CDK2 -0.012 0.055 -10000 0 -0.13 35 35
FOXO3A/14-3-3 0.2 0.16 0.35 160 -0.32 2 162
CREBBP -0.012 0.054 -10000 0 -0.12 60 60
FBXO32 0.5 0.45 0.91 169 -1.3 1 170
BCL6 0.36 0.3 0.68 136 -10000 0 136
RALB 0.029 0.009 -10000 0 -10000 0 0
RALA 0.029 0.009 -10000 0 -10000 0 0
YWHAH 0.029 0.005 -10000 0 -10000 0 0
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.04 0.02 -10000 0 -0.26 1 1
Necdin/E2F1 0.014 0.033 -10000 0 -0.26 3 3
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.036 0.16 -10000 0 -0.22 137 137
NGF (dimer)/p75(NTR)/BEX1 -0.13 0.18 -10000 0 -0.28 189 189
NT-4/5 (dimer)/p75(NTR) -0.075 0.14 -10000 0 -0.26 134 134
IKBKB 0.026 0.01 -10000 0 -10000 0 0
AKT1 -0.094 0.1 -10000 0 -0.38 14 14
IKBKG 0.029 0.005 -10000 0 -10000 0 0
BDNF 0.028 0.006 -10000 0 -10000 0 0
MGDIs/NGR/p75(NTR)/LINGO1 -0.052 0.13 -10000 0 -0.23 124 124
FURIN 0.022 0.051 -10000 0 -0.37 6 6
proBDNF (dimer)/p75(NTR)/Sortilin -0.047 0.13 -10000 0 -0.22 128 128
LINGO1 0.023 0.024 -10000 0 -0.37 1 1
Sortilin/TRAF6/NRIF 0.025 0.023 -10000 0 -10000 0 0
proBDNF (dimer) 0.028 0.006 -10000 0 -10000 0 0
NTRK1 0.02 0.012 -10000 0 -10000 0 0
RTN4R 0.025 0.042 -10000 0 -0.37 4 4
neuron apoptosis -0.06 0.18 0.37 2 -0.48 30 32
IRAK1 0.029 0.005 -10000 0 -10000 0 0
SHC1 -0.081 0.11 -10000 0 -0.24 107 107
ARHGDIA 0.028 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.022 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.06 0.042 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.039 0.15 -10000 0 -0.23 136 136
MAGEH1 0.024 0.047 -10000 0 -0.37 5 5
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.038 0.16 -10000 0 -0.23 130 130
Mammalian IAPs/DIABLO 0.075 0.029 -10000 0 -0.21 1 1
proNGF (dimer) 0.01 0.084 -10000 0 -0.37 17 17
MAGED1 0.026 0.036 -10000 0 -0.37 3 3
APP 0.024 0.042 -10000 0 -0.37 4 4
NT-4/5 (dimer) 0.019 0.006 -10000 0 -10000 0 0
ZNF274 0.029 0.005 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.052 0.12 -10000 0 -0.21 129 129
NGF 0.01 0.084 -10000 0 -0.37 17 17
cell cycle arrest -0.056 0.12 0.3 5 -0.33 14 19
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.063 0.11 -10000 0 -0.22 107 107
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.052 0.13 -10000 0 -0.23 135 135
NCSTN 0.023 0.013 -10000 0 -10000 0 0
mol:GTP -0.057 0.15 -10000 0 -0.24 137 137
PSENEN 0.029 0.004 -10000 0 -10000 0 0
mol:ceramide -0.087 0.11 0.18 1 -0.23 121 122
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.053 0.13 -10000 0 -0.33 34 34
p75(NTR)/beta APP -0.074 0.15 -10000 0 -0.26 138 138
BEX1 -0.097 0.18 -10000 0 -0.37 111 111
mol:GDP -0.098 0.11 -10000 0 -0.24 137 137
NGF (dimer) -0.036 0.14 -10000 0 -0.23 122 122
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.015 0.14 -10000 0 -0.21 117 117
PIK3R1 0.027 0.03 -10000 0 -0.37 2 2
RAC1/GTP -0.045 0.13 -10000 0 -0.21 133 133
MYD88 0.03 0.003 -10000 0 -10000 0 0
CHUK 0.029 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.057 0.15 -10000 0 -0.24 137 137
RHOB 0.01 0.087 -10000 0 -0.37 18 18
RHOA 0.029 0.004 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.017 0.021 -10000 0 -10000 0 0
NT3 (dimer) -0.16 0.2 -10000 0 -0.37 168 168
TP53 -0.074 0.099 0.39 2 -10000 0 2
PRDM4 -0.093 0.11 0.16 10 -0.23 128 138
BDNF (dimer) -0.019 0.13 -10000 0 -0.21 104 104
PIK3CA 0.028 0.021 -10000 0 -0.37 1 1
SORT1 0.028 0.008 -10000 0 -10000 0 0
activation of caspase activity -0.04 0.15 -10000 0 -0.22 137 137
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.037 0.15 -10000 0 -0.23 135 135
RHOC 0.029 0.006 -10000 0 -10000 0 0
XIAP 0.029 0.003 -10000 0 -10000 0 0
MAPK10 -0.11 0.16 0.36 2 -0.31 124 126
DIABLO 0.029 0.003 -10000 0 -10000 0 0
SMPD2 -0.087 0.11 0.18 1 -0.23 121 122
APH1B 0.029 0.004 -10000 0 -10000 0 0
APH1A 0.023 0.013 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.057 0.15 -10000 0 -0.24 135 135
PSEN1 0.028 0.007 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.041 0.012 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.18 0.21 -10000 0 -0.36 204 204
MAPK8 -0.11 0.14 0.32 2 -0.29 125 127
MAPK9 -0.1 0.14 0.32 2 -0.28 122 124
APAF1 0.029 0.004 -10000 0 -10000 0 0
NTF3 -0.16 0.2 -10000 0 -0.37 168 168
NTF4 0.019 0.006 -10000 0 -10000 0 0
NDN 0.02 0.059 -10000 0 -0.37 8 8
RAC1/GDP 0.022 0.003 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.039 0.15 -10000 0 -0.22 135 135
p75 CTF/Sortilin/TRAF6/NRIF 0.072 0.03 -10000 0 -0.21 1 1
RhoA-B-C/GTP -0.057 0.15 -10000 0 -0.24 137 137
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.017 0.14 -10000 0 -0.2 126 126
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.027 0.14 -10000 0 -0.21 129 129
PRKACB 0.029 0.006 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD 0.042 0.009 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.026 0.022 -10000 0 -0.37 1 1
BIRC2 0.029 0.006 -10000 0 -10000 0 0
neuron projection morphogenesis -0.073 0.14 0.26 4 -0.27 87 91
BAD -0.12 0.15 0.33 2 -0.31 122 124
RIPK2 0.023 0.013 -10000 0 -10000 0 0
NGFR -0.12 0.19 -10000 0 -0.37 136 136
CYCS -0.089 0.11 0.29 1 -0.22 127 128
ADAM17 0.03 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.032 0.13 -10000 0 -0.22 108 108
BCL2L11 -0.12 0.15 0.33 2 -0.31 122 124
BDNF (dimer)/p75(NTR) -0.07 0.15 -10000 0 -0.26 132 132
PI3K -0.041 0.15 -10000 0 -0.23 137 137
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.037 0.15 -10000 0 -0.23 135 135
NDNL2 0.029 0.003 -10000 0 -10000 0 0
YWHAE 0.025 0.011 -10000 0 -10000 0 0
PRKCI 0.03 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.081 0.16 -10000 0 -0.28 137 137
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.039 0.15 -10000 0 -0.23 137 137
TRAF6 0.029 0.021 -10000 0 -0.37 1 1
RAC1 0.029 0.004 -10000 0 -10000 0 0
PRKCZ 0.014 0.071 -10000 0 -0.37 12 12
PLG -0.029 0.14 -10000 0 -0.37 51 51
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.093 0.13 0.16 9 -0.25 128 137
SQSTM1 0.028 0.007 -10000 0 -10000 0 0
NGFRAP1 0.012 0.082 -10000 0 -0.37 16 16
CASP3 -0.12 0.15 0.32 2 -0.3 124 126
E2F1 0.011 0.014 -10000 0 -10000 0 0
CASP9 0.028 0.007 -10000 0 -10000 0 0
IKK complex -0.027 0.12 -10000 0 -0.31 27 27
NGF (dimer)/TRKA 0.021 0.056 -10000 0 -0.26 12 12
MMP7 -0.062 0.16 -10000 0 -0.37 79 79
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.027 0.15 -10000 0 -0.22 133 133
MMP3 0.02 0.009 -10000 0 -10000 0 0
APAF-1/Caspase 9 -0.098 0.08 -10000 0 -0.2 116 116
Reelin signaling pathway

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
CDK5R1/CDK5 0.041 0.011 -10000 0 -10000 0 0
VLDLR -0.004 0.1 -10000 0 -0.37 26 26
CRKL 0.029 0.005 -10000 0 -10000 0 0
LRPAP1 0.029 0.006 -10000 0 -10000 0 0
FYN 0.028 0.008 -10000 0 -10000 0 0
ITGA3 0.026 0.022 -10000 0 -0.37 1 1
RELN/VLDLR/Fyn -0.054 0.14 -10000 0 -0.25 118 118
MAPK8IP1/MKK7/MAP3K11/JNK1 0.051 0.07 -10000 0 -0.21 16 16
AKT1 -0.086 0.13 -10000 0 -0.24 136 136
MAP2K7 0.029 0.004 -10000 0 -10000 0 0
RAPGEF1 0.029 0.004 -10000 0 -10000 0 0
DAB1 -0.03 0.14 -10000 0 -0.37 52 52
RELN/LRP8/DAB1 -0.056 0.13 -10000 0 -0.21 135 135
LRPAP1/LRP8 0.037 0.017 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.044 0.13 -10000 0 -0.2 135 135
DAB1/alpha3/beta1 Integrin -0.046 0.14 -10000 0 -0.22 126 126
long-term memory -0.03 0.13 0.27 3 -0.21 115 118
DAB1/LIS1 -0.043 0.15 -10000 0 -0.22 128 128
DAB1/CRLK/C3G -0.052 0.14 -10000 0 -0.22 130 130
PIK3CA 0.028 0.021 -10000 0 -0.37 1 1
DAB1/NCK2 -0.042 0.15 -10000 0 -0.23 131 131
ARHGEF2 0.022 0.013 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.022 0.012 -10000 0 -10000 0 0
CDK5R1 0.029 0.006 -10000 0 -10000 0 0
RELN -0.1 0.19 -10000 0 -0.37 120 120
PIK3R1 0.027 0.03 -10000 0 -0.37 2 2
RELN/LRP8/Fyn -0.036 0.12 -10000 0 -0.22 106 106
GRIN2A/RELN/LRP8/DAB1/Fyn -0.027 0.14 -10000 0 -0.21 117 117
MAPK8 0.009 0.087 -10000 0 -0.37 18 18
RELN/VLDLR/DAB1 -0.075 0.14 -10000 0 -0.23 148 148
ITGB1 0.029 0.005 -10000 0 -10000 0 0
MAP1B -0.084 0.14 0.27 5 -0.24 127 132
RELN/LRP8 -0.034 0.12 -10000 0 -0.22 104 104
GRIN2B/RELN/LRP8/DAB1/Fyn -0.041 0.14 -10000 0 -0.21 135 135
PI3K 0.041 0.032 -10000 0 -0.37 2 2
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.039 0.021 -10000 0 -0.26 1 1
RAP1A -0.079 0.12 0.27 6 -0.34 23 29
PAFAH1B1 0.025 0.011 -10000 0 -10000 0 0
MAPK8IP1 0.025 0.042 -10000 0 -0.37 4 4
CRLK/C3G 0.042 0.009 -10000 0 -10000 0 0
GRIN2B 0.022 0.007 -10000 0 -10000 0 0
NCK2 0.028 0.021 -10000 0 -0.37 1 1
neuron differentiation -0.054 0.12 0.18 2 -0.3 44 46
neuron adhesion -0.071 0.13 0.34 6 -0.34 19 25
LRP8 0.026 0.01 -10000 0 -10000 0 0
GSK3B -0.093 0.13 0.2 1 -0.23 141 142
RELN/VLDLR/DAB1/Fyn -0.059 0.15 -10000 0 -0.22 148 148
MAP3K11 0.029 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.09 0.15 -10000 0 -0.25 148 148
CDK5 0.029 0.006 -10000 0 -10000 0 0
MAPT 0.18 0.26 0.54 120 -10000 0 120
neuron migration -0.11 0.16 0.3 2 -0.3 115 117
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.054 0.12 0.18 2 -0.3 43 45
RELN/VLDLR -0.019 0.15 -10000 0 -0.23 107 107
Endothelins

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
AKT1 -0.029 0.1 0.38 9 -0.35 9 18
PTK2B 0.024 0.013 -10000 0 -10000 0 0
mol:Ca2+ -0.034 0.3 0.65 34 -0.62 32 66
EDN1 0 0.097 0.29 9 -0.28 21 30
EDN3 0.021 0.007 -10000 0 -10000 0 0
EDN2 -0.005 0.11 -10000 0 -0.37 29 29
HRAS/GDP -0.11 0.24 0.4 8 -0.46 77 85
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.049 0.17 0.34 11 -0.34 63 74
ADCY4 0.016 0.12 0.33 11 -0.31 6 17
ADCY5 -0.014 0.14 0.33 11 -0.33 16 27
ADCY6 0.015 0.12 0.34 10 -0.32 7 17
ADCY7 0.014 0.12 0.34 10 -0.32 7 17
ADCY1 -0.045 0.15 0.36 6 -0.35 22 28
ADCY2 0.009 0.11 0.34 7 -0.32 7 14
ADCY3 0.015 0.12 0.34 10 -0.32 7 17
ADCY8 0.004 0.093 0.33 6 -0.33 3 9
ADCY9 0.014 0.12 0.34 10 -0.32 7 17
arachidonic acid secretion -0.21 0.34 0.45 19 -0.52 161 180
ETB receptor/Endothelin-1/Gq/GTP -0.037 0.18 0.28 25 -0.32 70 95
GNAO1 -0.14 0.2 -10000 0 -0.37 153 153
HRAS 0.028 0.004 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.021 0.11 0.4 9 -0.24 27 36
ETA receptor/Endothelin-1/Gs/GTP 0.025 0.11 0.36 10 -0.24 22 32
mol:GTP 0.001 0.015 -10000 0 -10000 0 0
COL3A1 -0.037 0.14 0.56 6 -0.48 16 22
EDNRB 0.01 0.11 0.2 17 -0.35 25 42
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.029 0.11 0.43 6 -0.41 11 17
CYSLTR1 -0.036 0.12 0.43 6 -0.46 14 20
SLC9A1 -0.012 0.083 0.3 6 -0.3 12 18
mol:GDP -0.12 0.24 0.41 8 -0.49 77 85
SLC9A3 -0.029 0.3 0.55 14 -0.7 44 58
RAF1 -0.19 0.28 0.4 6 -0.46 153 159
JUN -0.059 0.31 0.56 22 -0.74 34 56
JAK2 -0.029 0.1 0.38 9 -0.36 9 18
mol:IP3 -0.067 0.2 0.37 11 -0.4 69 80
ETA receptor/Endothelin-1 0.008 0.13 0.43 8 -0.32 28 36
PLCB1 0.018 0.021 -10000 0 -10000 0 0
PLCB2 0.001 0.059 -10000 0 -0.38 7 7
ETA receptor/Endothelin-3 0.013 0.069 0.23 5 -0.19 20 25
FOS -0.43 0.47 0.42 1 -0.9 178 179
Gai/GDP -0.3 0.39 -10000 0 -0.69 173 173
CRK 0.026 0.011 -10000 0 -10000 0 0
mol:Ca ++ -0.065 0.22 0.48 12 -0.46 49 61
BCAR1 0.028 0.009 -10000 0 -10000 0 0
PRKCB1 -0.07 0.2 0.36 12 -0.39 70 82
GNAQ 0.014 0.036 -10000 0 -10000 0 0
GNAZ 0.014 0.025 -10000 0 -0.37 1 1
GNAL 0.024 0.011 -10000 0 -10000 0 0
Gs family/GDP -0.1 0.22 0.38 7 -0.45 69 76
ETA receptor/Endothelin-1/Gq/GTP -0.035 0.18 0.36 22 -0.33 59 81
MAPK14 -0.045 0.17 0.29 14 -0.37 49 63
TRPC6 -0.038 0.31 0.65 34 -0.66 31 65
GNAI2 0.029 0.003 -10000 0 -10000 0 0
GNAI3 0.029 0.006 -10000 0 -10000 0 0
GNAI1 0.027 0.03 -10000 0 -0.37 2 2
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.046 0.18 0.3 12 -0.37 55 67
ETB receptor/Endothelin-2 0 0.11 0.16 13 -0.27 49 62
ETB receptor/Endothelin-3 0.021 0.078 0.16 13 -0.27 21 34
ETB receptor/Endothelin-1 0.003 0.12 0.38 9 -0.32 28 37
MAPK3 -0.38 0.43 0.42 3 -0.79 179 182
MAPK1 -0.37 0.43 0.42 3 -0.78 179 182
Rac1/GDP -0.11 0.23 0.39 9 -0.46 75 84
cAMP biosynthetic process -0.035 0.16 0.37 6 -0.36 33 39
MAPK8 -0.072 0.33 0.57 29 -0.69 50 79
SRC 0.029 0.005 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.044 0.14 0.28 8 -0.3 45 53
p130Cas/CRK/Src/PYK2 -0.1 0.28 0.49 26 -0.54 66 92
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.11 0.23 0.4 8 -0.46 75 83
COL1A2 -0.025 0.17 0.65 9 -0.44 22 31
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.008 0.1 0.23 5 -0.25 44 49
mol:DAG -0.067 0.2 0.37 11 -0.4 69 80
MAP2K2 -0.27 0.34 0.41 4 -0.6 168 172
MAP2K1 -0.28 0.34 0.41 4 -0.6 169 173
EDNRA 0.004 0.091 0.32 6 -0.24 25 31
positive regulation of muscle contraction -0.025 0.09 0.36 6 -0.33 6 12
Gq family/GDP -0.11 0.24 0.34 20 -0.45 84 104
HRAS/GTP -0.13 0.24 0.38 9 -0.47 80 89
PRKCH -0.072 0.2 0.36 12 -0.4 65 77
RAC1 0.029 0.004 -10000 0 -10000 0 0
PRKCA -0.067 0.2 0.36 12 -0.39 65 77
PRKCB -0.09 0.22 0.37 11 -0.41 80 91
PRKCE -0.075 0.2 0.34 12 -0.4 70 82
PRKCD -0.076 0.2 0.36 11 -0.4 69 80
PRKCG -0.072 0.2 0.35 12 -0.4 66 78
regulation of vascular smooth muscle contraction -0.51 0.55 -10000 0 -1.1 178 178
PRKCQ -0.078 0.21 0.36 11 -0.41 70 81
PLA2G4A -0.23 0.37 0.46 19 -0.57 162 181
GNA14 -0.047 0.15 -10000 0 -0.38 58 58
GNA15 0.027 0.03 -10000 0 -0.37 1 1
GNA12 0.029 0.005 -10000 0 -10000 0 0
GNA11 0.019 0.066 -10000 0 -0.38 9 9
Rac1/GTP 0.021 0.11 0.4 9 -0.24 27 36
MMP1 0.059 0.16 0.38 64 -10000 0 64
IL6-mediated signaling events

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
BCL2L1 -0.34 0.36 -10000 0 -0.82 102 102
CRP -0.44 0.5 -10000 0 -0.98 150 150
cell cycle arrest -0.4 0.45 -10000 0 -0.97 114 114
TIMP1 -0.29 0.33 -10000 0 -0.73 97 97
IL6ST -0.1 0.16 -10000 0 -0.38 90 90
Rac1/GDP -0.15 0.21 -10000 0 -0.45 88 88
AP1 -0.053 0.16 -10000 0 -0.53 12 12
GAB2 0.032 0.009 -10000 0 -10000 0 0
TNFSF11 -0.43 0.45 -10000 0 -0.94 137 137
HSP90B1 -0.022 0.11 -10000 0 -0.87 4 4
GAB1 0.03 0.009 -10000 0 -10000 0 0
MAPK14 -0.14 0.25 -10000 0 -0.66 57 57
AKT1 0.015 0.062 -10000 0 -0.49 3 3
FOXO1 0.009 0.064 -10000 0 -0.47 3 3
MAP2K6 -0.14 0.22 -10000 0 -0.53 70 70
mol:GTP -0.002 0.003 -10000 0 -10000 0 0
MAP2K4 -0.2 0.24 -10000 0 -0.56 79 79
MITF -0.14 0.2 -10000 0 -0.43 79 79
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.029 0.004 -10000 0 -10000 0 0
A2M -0.19 0.5 -10000 0 -1.3 59 59
CEBPB 0.03 0.009 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.01 0.13 -10000 0 -0.48 12 12
STAT3 -0.44 0.5 -10000 0 -1.1 114 114
STAT1 0.002 0.061 -10000 0 -1 1 1
CEBPD -0.32 0.38 -10000 0 -0.83 101 101
PIK3CA 0.029 0.021 -10000 0 -0.37 1 1
PI3K 0.042 0.032 -10000 0 -0.37 2 2
JUN 0.022 0.051 -10000 0 -0.37 6 6
PIAS3/MITF -0.11 0.18 -10000 0 -0.41 74 74
MAPK11 -0.15 0.28 -10000 0 -0.71 58 58
STAT3 (dimer)/FOXO1 -0.32 0.36 -10000 0 -0.75 118 118
GRB2/SOS1/GAB family -0.049 0.18 -10000 0 -0.36 51 51
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.1 0.17 -10000 0 -0.36 80 80
GRB2 0.03 0.008 -10000 0 -10000 0 0
JAK2 0.028 0.006 -10000 0 -10000 0 0
LBP -0.28 0.32 -10000 0 -0.76 77 77
PIK3R1 0.028 0.03 -10000 0 -0.37 2 2
JAK1 -0.003 0.036 -10000 0 -0.11 1 1
MYC -0.34 0.44 0.69 1 -0.9 110 111
FGG -0.37 0.41 -10000 0 -0.9 112 112
macrophage differentiation -0.4 0.45 -10000 0 -0.97 114 114
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.065 0.14 -10000 0 -0.25 103 103
JUNB -0.34 0.37 -10000 0 -0.83 104 104
FOS -0.15 0.2 -10000 0 -0.37 160 160
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.14 0.2 -10000 0 -0.45 82 82
STAT1/PIAS1 -0.14 0.2 -10000 0 -0.42 83 83
GRB2/SOS1/GAB family/SHP2/PI3K 0.02 0.069 -10000 0 -0.42 5 5
STAT3 (dimer) -0.43 0.49 -10000 0 -1 114 114
PRKCD -0.26 0.3 -10000 0 -0.65 99 99
IL6R -0.006 0.057 -10000 0 -0.38 6 6
SOCS3 -0.17 0.38 -10000 0 -1 52 52
gp130 (dimer)/JAK1/JAK1/LMO4 -0.07 0.13 -10000 0 -0.25 97 97
Rac1/GTP -0.17 0.22 -10000 0 -0.48 91 91
HCK 0.017 0.071 -10000 0 -0.37 12 12
MAPKKK cascade 0.008 0.12 -10000 0 -0.6 8 8
bone resorption -0.4 0.41 -10000 0 -0.87 137 137
IRF1 -0.33 0.37 -10000 0 -0.82 101 101
mol:GDP -0.15 0.2 -10000 0 -0.48 74 74
SOS1 0.033 0.008 -10000 0 -10000 0 0
VAV1 -0.15 0.21 -10000 0 -0.48 74 74
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.11 0.26 -10000 0 -0.6 62 62
PTPN11 -0.001 0.082 -10000 0 -0.85 3 3
IL6/IL6RA -0.033 0.1 -10000 0 -0.28 44 44
gp130 (dimer)/TYK2/TYK2/LMO4 -0.049 0.12 -10000 0 -0.24 92 92
gp130 (dimer)/JAK2/JAK2/LMO4 -0.048 0.12 -10000 0 -0.24 91 91
IL6 -0.059 0.14 -10000 0 -0.38 51 51
PIAS3 0.023 0.013 -10000 0 -10000 0 0
PTPRE 0.038 0.039 -10000 0 -0.36 2 2
PIAS1 0.029 0.004 -10000 0 -10000 0 0
RAC1 0.028 0.007 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.094 0.14 -10000 0 -0.33 69 69
LMO4 -0.009 0.044 -10000 0 -0.41 1 1
STAT3 (dimer)/PIAS3 -0.38 0.42 -10000 0 -0.88 127 127
MCL1 0.051 0.093 -10000 0 -0.53 1 1
Noncanonical Wnt signaling pathway

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
NFATC2 -0.042 0.15 -10000 0 -0.37 64 64
GNB1/GNG2 -0.072 0.18 -10000 0 -0.35 71 71
mol:DAG -0.075 0.16 0.22 11 -0.34 67 78
PLCG1 -0.078 0.17 0.22 11 -0.34 67 78
YES1 -0.091 0.16 -10000 0 -0.36 74 74
FZD3 0.017 0.047 -10000 0 -0.37 5 5
FZD6 0.021 0.024 -10000 0 -0.37 1 1
G protein -0.065 0.18 0.31 2 -0.34 66 68
MAP3K7 -0.068 0.14 0.23 9 -0.29 62 71
mol:Ca2+ -0.073 0.16 0.22 11 -0.33 67 78
mol:IP3 -0.075 0.16 0.22 11 -0.34 67 78
NLK 0.013 0.014 -10000 0 -10000 0 0
GNB1 0.027 0.009 -10000 0 -10000 0 0
CAMK2A -0.069 0.15 0.24 8 -0.31 63 71
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.1 0.17 -10000 0 -0.3 119 119
CSNK1A1 0.029 0.005 -10000 0 -10000 0 0
GNAS -0.086 0.16 -10000 0 -0.29 114 114
GO:0007205 -0.078 0.16 0.29 2 -0.33 67 69
WNT6 0.027 0.008 -10000 0 -10000 0 0
WNT4 -0.038 0.14 -10000 0 -0.37 57 57
NFAT1/CK1 alpha -0.096 0.18 0.32 2 -0.36 87 89
GNG2 0.027 0.03 -10000 0 -0.37 2 2
WNT5A -0.012 0.12 -10000 0 -0.37 37 37
WNT11 -0.081 0.18 -10000 0 -0.37 100 100
CDC42 -0.085 0.16 0.2 7 -0.35 66 73
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.038 0.022 -10000 0 -0.26 1 1
CRKL -0.1 0.17 -10000 0 -0.61 26 26
mol:PIP3 0.016 0.015 -10000 0 -10000 0 0
AKT1 0.003 0.023 -10000 0 -10000 0 0
PTK2B 0.023 0.012 -10000 0 -10000 0 0
RAPGEF1 -0.1 0.16 -10000 0 -0.58 26 26
RANBP10 0.027 0.008 -10000 0 -10000 0 0
PIK3CA 0.028 0.021 -10000 0 -0.37 1 1
HGF/MET/SHIP2 -0.092 0.14 -10000 0 -0.23 190 190
MAP3K5 -0.11 0.18 -10000 0 -0.49 43 43
HGF/MET/CIN85/CBL/ENDOPHILINS -0.077 0.14 -10000 0 -0.21 193 193
AP1 -0.097 0.12 -10000 0 -0.23 158 158
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.022 0.013 -10000 0 -10000 0 0
apoptosis -0.4 0.44 -10000 0 -0.82 184 184
STAT3 (dimer) -0.09 0.13 -10000 0 -0.24 139 139
GAB1/CRKL/SHP2/PI3K -0.081 0.18 -10000 0 -0.56 26 26
INPP5D 0.029 0.003 -10000 0 -10000 0 0
CBL/CRK -0.088 0.17 0.28 1 -0.57 26 27
PTPN11 0.029 0.003 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.029 0.004 -10000 0 -10000 0 0
PTEN 0.028 0.007 -10000 0 -10000 0 0
ELK1 0.007 0.1 0.33 24 -10000 0 24
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.06 0.082 -10000 0 -0.22 31 31
PAK1 0 0.03 -10000 0 -10000 0 0
HGF/MET/RANBP10 -0.093 0.14 -10000 0 -0.22 192 192
HRAS -0.099 0.13 -10000 0 -0.51 9 9
DOCK1 -0.1 0.16 -10000 0 -0.54 31 31
GAB1 -0.1 0.18 -10000 0 -0.62 27 27
CRK -0.1 0.17 -10000 0 -0.6 26 26
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.2 0.22 -10000 0 -0.42 177 177
JUN 0.022 0.051 -10000 0 -0.37 6 6
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.079 0.087 -10000 0 -0.16 192 192
PIK3R1 0.027 0.03 -10000 0 -0.37 2 2
cell morphogenesis -0.12 0.15 -10000 0 -0.37 59 59
GRB2/SHC -0.037 0.091 -10000 0 -0.15 130 130
FOS -0.15 0.2 -10000 0 -0.37 160 160
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility 0.007 0.1 0.33 24 -10000 0 24
HGF/MET/MUC20 -0.099 0.13 -10000 0 -0.22 192 192
cell migration -0.037 0.09 -10000 0 -0.15 130 130
GRB2 0.028 0.006 -10000 0 -10000 0 0
CBL 0.028 0.006 -10000 0 -10000 0 0
MET/RANBP10 0.038 0.021 -10000 0 -0.26 1 1
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.081 0.12 -10000 0 -0.24 134 134
MET/MUC20 0.02 0.015 -10000 0 -0.26 1 1
RAP1B -0.1 0.15 -10000 0 -0.54 26 26
RAP1A -0.1 0.15 -10000 0 -0.54 26 26
HGF/MET/RANBP9 -0.08 0.14 -10000 0 -0.23 169 169
RAF1 -0.094 0.13 -10000 0 -0.47 9 9
STAT3 -0.081 0.14 -10000 0 -0.24 139 139
cell proliferation -0.093 0.17 0.26 14 -0.32 99 113
RPS6KB1 -0.015 0.033 -10000 0 -10000 0 0
MAPK3 0.01 0.15 0.76 12 -10000 0 12
MAPK1 0.002 0.13 0.73 9 -10000 0 9
RANBP9 0.027 0.008 -10000 0 -10000 0 0
MAPK8 -0.1 0.18 -10000 0 -0.51 43 43
SRC -0.07 0.12 -10000 0 -0.23 127 127
PI3K -0.056 0.1 -10000 0 -0.15 187 187
MET/Glomulin 0.019 0.027 -10000 0 -0.1 12 12
SOS1 0.03 0.002 -10000 0 -10000 0 0
MAP2K1 -0.094 0.12 -10000 0 -0.46 8 8
MET 0.027 0.022 -10000 0 -0.37 1 1
MAP4K1 -0.097 0.18 -10000 0 -0.6 29 29
PTK2 0.022 0.013 -10000 0 -10000 0 0
MAP2K2 -0.092 0.13 -10000 0 -0.44 9 9
BAD -0.002 0.022 -10000 0 -10000 0 0
MAP2K4 -0.099 0.16 -10000 0 -0.47 37 37
SHP2/GRB2/SOS1/GAB1 -0.078 0.16 -10000 0 -0.52 27 27
INPPL1 0.029 0.005 -10000 0 -10000 0 0
PXN 0.029 0.003 -10000 0 -10000 0 0
SH3KBP1 0.028 0.021 -10000 0 -0.37 1 1
HGS -0.077 0.078 -10000 0 -0.16 177 177
PLCgamma1/PKC 0.022 0.003 -10000 0 -10000 0 0
HGF -0.18 0.2 -10000 0 -0.37 194 194
RASA1 0.027 0.03 -10000 0 -0.37 2 2
NCK1 0.03 0.002 -10000 0 -10000 0 0
PTPRJ 0.03 0.002 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.064 0.11 -10000 0 -0.17 186 186
PDPK1 0.007 0.016 -10000 0 -10000 0 0
HGF/MET/SHIP -0.094 0.14 -10000 0 -0.23 192 192
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer 0.012 0.099 -10000 0 -0.24 45 45
fibroblast growth factor receptor signaling pathway 0.011 0.099 -10000 0 -0.24 45 45
LAMA1 -0.022 0.13 -10000 0 -0.37 43 43
PRNP 0.004 0.097 -10000 0 -0.37 23 23
GPC1/SLIT2 -0.007 0.12 -10000 0 -0.28 53 53
SMAD2 -0.035 0.05 0.17 2 -0.21 25 27
GPC1/PrPc/Cu2+ 0.006 0.095 -10000 0 -0.25 41 41
GPC1/Laminin alpha1 -0.016 0.12 -10000 0 -0.28 62 62
TDGF1 -0.002 0.094 -10000 0 -0.37 22 22
CRIPTO/GPC1 0.001 0.093 -10000 0 -0.27 37 37
APP/GPC1 0.017 0.083 -10000 0 -0.26 29 29
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.002 0.11 0.17 74 -0.23 36 110
FLT1 0.027 0.008 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.038 0.073 -10000 0 -0.23 25 25
SERPINC1 -0.023 0.13 -10000 0 -0.37 42 42
FYN -0.003 0.1 0.17 67 -0.23 33 100
FGR -0.004 0.11 0.17 71 -0.23 38 109
positive regulation of MAPKKK cascade -0.031 0.15 0.24 10 -0.33 48 58
SLIT2 -0.008 0.11 -10000 0 -0.37 32 32
GPC1/NRG -0.083 0.15 -10000 0 -0.28 132 132
NRG1 -0.11 0.18 -10000 0 -0.37 117 117
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.032 0.067 -10000 0 -0.23 20 20
LYN -0.006 0.1 0.17 59 -0.23 35 94
mol:Spermine -0.026 0.064 0.2 1 -0.26 25 26
cell growth 0.011 0.099 -10000 0 -0.24 45 45
BMP signaling pathway -0.002 0.1 0.37 25 -10000 0 25
SRC -0.001 0.11 0.17 76 -0.23 36 112
TGFBR1 0.029 0.005 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.12 0.19 -10000 0 -0.37 134 134
GPC1 0.002 0.1 -10000 0 -0.37 25 25
TGFBR1 (dimer) 0.029 0.005 -10000 0 -10000 0 0
VEGFA 0.026 0.01 -10000 0 -10000 0 0
BLK -0.026 0.12 0.17 45 -0.26 53 98
HCK -0.007 0.11 0.17 71 -0.24 41 112
FGF2 0.005 0.091 -10000 0 -0.37 20 20
FGFR1 0.019 0.047 -10000 0 -0.37 5 5
VEGFR1 homodimer 0.027 0.008 -10000 0 -10000 0 0
TGFBR2 0.029 0.003 -10000 0 -10000 0 0
cell death 0.017 0.083 -10000 0 -0.26 29 29
ATIII/GPC1 -0.017 0.11 -10000 0 -0.26 60 60
PLA2G2A/GPC1 -0.093 0.16 -10000 0 -0.28 148 148
LCK -0.007 0.11 0.17 70 -0.24 42 112
neuron differentiation -0.083 0.15 -10000 0 -0.28 132 132
PrPc/Cu2+ 0.004 0.068 -10000 0 -0.26 23 23
APP 0.024 0.042 -10000 0 -0.37 4 4
TGFBR2 (dimer) 0.029 0.003 -10000 0 -10000 0 0
IL23-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
CCL2 -0.16 0.65 1.2 12 -1.2 69 81
IL23A -0.16 0.64 1.2 13 -1.3 56 69
NF kappa B1 p50/RelA/I kappa B alpha -0.17 0.55 0.75 2 -1.1 75 77
positive regulation of T cell mediated cytotoxicity -0.14 0.72 1.4 18 -1.3 58 76
ITGA3 -0.12 0.62 1.3 14 -1.2 55 69
IL17F -0.082 0.4 0.8 12 -0.73 54 66
IL12B 0.039 0.12 0.39 21 -10000 0 21
STAT1 (dimer) -0.16 0.64 0.98 12 -1.2 75 87
CD4 -0.15 0.64 1.1 12 -1.2 62 74
IL23 -0.16 0.6 1 12 -1.2 56 68
IL23R 0.036 0.3 0.89 16 -1 12 28
IL1B -0.2 0.71 1.2 13 -1.3 74 87
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.082 0.6 1.2 13 -1.1 51 64
TYK2 0.027 0.083 0.27 18 -10000 0 18
STAT4 0.013 0.079 -10000 0 -0.37 15 15
STAT3 0.029 0.005 -10000 0 -10000 0 0
IL18RAP 0.005 0.096 -10000 0 -0.37 22 22
IL12RB1 0.015 0.11 0.26 21 -0.4 12 33
PIK3CA 0.029 0.021 -10000 0 -0.37 1 1
IL12Rbeta1/TYK2 0.025 0.11 0.28 25 -0.3 12 37
IL23R/JAK2 0.042 0.3 0.75 18 -0.94 12 30
positive regulation of chronic inflammatory response -0.14 0.72 1.4 18 -1.3 58 76
natural killer cell activation -0.004 0.021 -10000 0 -0.069 23 23
JAK2 0.042 0.11 0.37 22 -10000 0 22
PIK3R1 0.027 0.03 -10000 0 -0.37 2 2
NFKB1 0.024 0.023 -10000 0 -10000 0 0
RELA 0.024 0.024 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.15 0.57 1 12 -1.1 55 67
ALOX12B -0.12 0.6 1.2 13 -1.1 55 68
CXCL1 -0.26 0.74 1.3 14 -1.2 103 117
T cell proliferation -0.14 0.72 1.4 18 -1.3 58 76
NFKBIA 0.024 0.024 -10000 0 -10000 0 0
IL17A -0.038 0.35 0.76 15 -0.58 38 53
PI3K -0.17 0.58 0.76 6 -1.1 75 81
IFNG 0.01 0.089 0.33 17 -0.19 2 19
STAT3 (dimer) -0.16 0.55 0.74 7 -1 75 82
IL18R1 -0.032 0.14 -10000 0 -0.37 56 56
IL23/IL23R/JAK2/TYK2/SOCS3 -0.061 0.47 0.95 18 -0.89 44 62
IL18/IL18R 0.003 0.14 0.29 14 -0.26 67 81
macrophage activation -0.012 0.023 0.064 9 -10000 0 9
TNF -0.14 0.65 1.2 13 -1.3 54 67
STAT3/STAT4 -0.18 0.58 0.76 6 -1.1 76 82
STAT4 (dimer) -0.16 0.64 0.97 13 -1.2 76 89
IL18 0.021 0.057 -10000 0 -0.37 7 7
IL19 -0.087 0.59 1.2 12 -1.1 50 62
STAT5A (dimer) -0.16 0.64 0.98 12 -1.2 73 85
STAT1 0.029 0.003 -10000 0 -10000 0 0
SOCS3 -0.02 0.13 -10000 0 -0.37 44 44
CXCL9 -0.11 0.62 1.2 20 -1.1 56 76
MPO -0.13 0.61 1.1 13 -1.1 60 73
positive regulation of humoral immune response -0.14 0.72 1.4 18 -1.3 58 76
IL23/IL23R/JAK2/TYK2 -0.17 0.78 1.4 18 -1.5 58 76
IL6 -0.2 0.68 1.1 12 -1.2 80 92
STAT5A 0.029 0.004 -10000 0 -10000 0 0
IL2 0.017 0.046 0.2 15 -10000 0 15
positive regulation of tyrosine phosphorylation of STAT protein -0.004 0.021 -10000 0 -0.069 23 23
CD3E -0.13 0.61 1.2 12 -1.2 56 68
keratinocyte proliferation -0.14 0.72 1.4 18 -1.3 58 76
NOS2 -0.1 0.6 1.2 15 -1.1 55 70
Syndecan-1-mediated signaling events

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
TGFB1 0.029 0.005 -10000 0 -10000 0 0
CCL5 0.02 0.059 -10000 0 -0.37 8 8
SDCBP 0.024 0.011 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.007 0.15 0.27 42 -0.37 17 59
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 0.005 0.15 0.25 38 -0.36 23 61
Syndecan-1/Syntenin 0.005 0.14 0.25 38 -0.34 22 60
MAPK3 -0.002 0.14 0.24 31 -0.34 22 53
HGF/MET -0.12 0.15 -10000 0 -0.26 192 192
TGFB1/TGF beta receptor Type II 0.029 0.005 -10000 0 -10000 0 0
BSG 0.029 0.005 -10000 0 -10000 0 0
keratinocyte migration 0.006 0.15 0.25 38 -0.35 23 61
Syndecan-1/RANTES 0.004 0.16 0.25 39 -0.35 28 67
Syndecan-1/CD147 0.017 0.16 0.27 31 -0.34 23 54
Syndecan-1/Syntenin/PIP2 0.003 0.14 0.24 37 -0.33 22 59
LAMA5 0.028 0.006 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.003 0.14 0.23 37 -0.33 22 59
MMP7 -0.062 0.16 -10000 0 -0.37 79 79
HGF -0.18 0.2 -10000 0 -0.37 194 194
Syndecan-1/CASK -0.011 0.14 0.22 36 -0.34 25 61
Syndecan-1/HGF/MET -0.087 0.19 0.26 23 -0.34 87 110
regulation of cell adhesion -0.017 0.14 0.26 14 -0.33 22 36
HPSE 0.008 0.084 -10000 0 -0.37 17 17
positive regulation of cell migration 0.007 0.15 0.27 42 -0.37 17 59
SDC1 0.007 0.15 0.26 41 -0.37 18 59
Syndecan-1/Collagen 0.007 0.15 0.27 42 -0.37 17 59
PPIB 0.029 0.004 -10000 0 -10000 0 0
MET 0.027 0.022 -10000 0 -0.37 1 1
PRKACA 0.029 0.004 -10000 0 -10000 0 0
MMP9 0.012 0.065 -10000 0 -0.37 10 10
MAPK1 -0.002 0.14 0.23 40 -0.33 23 63
homophilic cell adhesion 0.005 0.15 0.26 42 -0.37 19 61
MMP1 0.021 0.013 -10000 0 -10000 0 0
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.1 0.17 -9999 0 -0.3 119 119
FZD6 0.021 0.024 -9999 0 -0.37 1 1
WNT6 0.027 0.008 -9999 0 -10000 0 0
WNT4 -0.038 0.14 -9999 0 -0.37 57 57
FZD3 0.017 0.047 -9999 0 -0.37 5 5
WNT5A -0.012 0.12 -9999 0 -0.37 37 37
WNT11 -0.081 0.18 -9999 0 -0.37 100 100
HIF-1-alpha transcription factor network

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
PKM2 -0.11 0.36 0.81 8 -0.84 34 42
HDAC7 0.033 0.022 0.18 5 -10000 0 5
HIF1A/ARNT/Cbp/p300/Src-1 -0.22 0.42 0.84 10 -0.82 80 90
SMAD4 0.029 0.006 -10000 0 -10000 0 0
ID2 0.007 0.46 -10000 0 -0.85 34 34
AP1 -0.097 0.16 -10000 0 -0.27 161 161
ABCG2 -0.048 0.43 -10000 0 -0.84 37 37
HIF1A 0.014 0.13 0.34 13 -0.24 7 20
TFF3 -0.03 0.43 0.99 1 -0.83 35 36
GATA2 0.026 0.033 -10000 0 -0.38 2 2
AKT1 0 0.17 0.41 15 -0.25 34 49
response to hypoxia -0.016 0.15 0.34 22 -0.22 48 70
MCL1 -0.014 0.43 -10000 0 -0.84 30 30
NDRG1 -0.019 0.41 -10000 0 -0.83 31 31
SERPINE1 -0.043 0.48 -10000 0 -0.82 53 53
FECH 0.012 0.46 -10000 0 -0.83 36 36
FURIN 0.005 0.47 -10000 0 -0.85 35 35
NCOA2 -0.03 0.12 0.23 7 -0.34 36 43
EP300 -0.016 0.28 0.71 18 -0.37 64 82
HMOX1 0.003 0.46 -10000 0 -0.84 36 36
BHLHE40 0.011 0.47 -10000 0 -0.84 36 36
BHLHE41 -0.004 0.46 -10000 0 -0.84 36 36
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.031 0.14 0.42 9 -10000 0 9
ENG 0.052 0.15 -10000 0 -10000 0 0
JUN 0.021 0.052 -10000 0 -0.37 6 6
RORA 0.006 0.46 -10000 0 -0.83 35 35
ABCB1 -0.12 0.28 -10000 0 -0.89 37 37
TFRC 0.012 0.46 -10000 0 -0.83 35 35
CXCR4 0.007 0.46 -10000 0 -0.84 35 35
TF -0.012 0.46 -10000 0 -0.83 37 37
CITED2 -0.002 0.46 -10000 0 -0.83 35 35
HIF1A/ARNT -0.16 0.34 0.91 1 -0.9 38 39
LDHA -0.034 0.075 -10000 0 -0.65 2 2
ETS1 0.01 0.46 -10000 0 -0.84 34 34
PGK1 0.014 0.46 -10000 0 -0.83 36 36
NOS2 -0.013 0.45 -10000 0 -0.83 35 35
ITGB2 0.005 0.46 -10000 0 -0.81 39 39
ALDOA 0.005 0.46 -10000 0 -0.82 36 36
Cbp/p300/CITED2 -0.2 0.49 0.91 9 -0.95 71 80
FOS -0.15 0.2 -10000 0 -0.37 160 160
HK2 -0.03 0.43 -10000 0 -0.82 37 37
SP1 0.011 0.063 -10000 0 -0.21 18 18
GCK -0.31 0.73 1 15 -1.2 135 150
HK1 0.006 0.46 -10000 0 -0.83 35 35
NPM1 0.007 0.46 -10000 0 -0.83 35 35
EGLN1 -0.004 0.44 -10000 0 -0.83 30 30
CREB1 0.032 0.003 -10000 0 -10000 0 0
PGM1 0.007 0.46 -10000 0 -0.84 35 35
SMAD3 0.029 0.005 -10000 0 -10000 0 0
EDN1 -0.15 0.34 0.65 2 -0.62 81 83
IGFBP1 -0.056 0.46 -10000 0 -0.84 45 45
VEGFA -0.097 0.43 0.96 7 -0.72 63 70
HIF1A/JAB1 0.007 0.1 0.4 9 -0.18 6 15
CP -0.013 0.47 -10000 0 -0.84 42 42
CXCL12 -0.11 0.43 -10000 0 -0.85 49 49
COPS5 0.005 0.044 0.17 9 -0.11 4 13
SMAD3/SMAD4 0.042 0.011 -10000 0 -10000 0 0
BNIP3 0.01 0.46 -10000 0 -0.83 35 35
EGLN3 -0.044 0.42 0.98 4 -0.85 35 39
CA9 -0.12 0.41 0.98 3 -0.84 50 53
TERT -0.085 0.37 0.98 5 -0.83 35 40
ENO1 -0.001 0.45 -10000 0 -0.83 35 35
PFKL 0.008 0.46 -10000 0 -0.83 35 35
NCOA1 0.019 0.03 -10000 0 -0.11 1 1
ADM 0.012 0.46 -10000 0 -0.81 38 38
ARNT 0.024 0.11 0.32 7 -0.19 1 8
HNF4A -0.023 0.13 0.18 46 -0.18 108 154
ADFP -0.11 0.36 0.81 8 -0.84 34 42
SLC2A1 -0.12 0.41 0.84 2 -0.74 66 68
LEP -0.036 0.43 0.97 2 -0.82 35 37
HIF1A/ARNT/Cbp/p300 -0.21 0.41 0.81 9 -0.83 77 86
EPO -0.3 0.56 1.1 8 -0.92 133 141
CREBBP -0.018 0.29 0.69 19 -0.38 71 90
HIF1A/ARNT/Cbp/p300/HDAC7 -0.2 0.41 0.78 10 -0.82 75 85
PFKFB3 0.005 0.46 -10000 0 -0.84 36 36
NT5E -0.005 0.46 -10000 0 -0.84 35 35
LPA receptor mediated 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
GNB1/GNG2 -0.015 0.12 -10000 0 -0.22 93 93
NF kappa B1 p50/RelA/I kappa B alpha -0.015 0.1 0.26 6 -0.3 7 13
AP1 -0.11 0.16 0.26 6 -0.25 169 175
mol:PIP3 -0.068 0.081 -10000 0 -0.21 76 76
AKT1 -0.041 0.08 0.24 2 -0.28 7 9
PTK2B -0.077 0.15 0.25 5 -0.32 66 71
RHOA -0.004 0.055 0.21 2 -0.29 2 4
PIK3CB 0.03 0.002 -10000 0 -10000 0 0
mol:Ca2+ -0.008 0.072 0.24 6 -0.31 3 9
MAGI3 0.029 0.006 -10000 0 -10000 0 0
RELA 0.029 0.005 -10000 0 -10000 0 0
apoptosis -0.035 0.13 0.34 6 -0.24 84 90
HRAS/GDP 0.022 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.031 0.15 0.27 8 -0.32 37 45
NF kappa B1 p50/RelA -0.047 0.12 0.27 9 -0.26 42 51
endothelial cell migration -0.049 0.14 0.45 4 -0.49 17 21
ADCY4 -0.09 0.18 0.29 4 -0.36 87 91
ADCY5 -0.13 0.22 0.29 4 -0.42 112 116
ADCY6 -0.09 0.18 0.29 4 -0.36 88 92
ADCY7 -0.089 0.18 0.29 4 -0.37 86 90
ADCY1 -0.17 0.23 0.28 3 -0.41 139 142
ADCY2 -0.087 0.18 0.35 4 -0.36 85 89
ADCY3 -0.09 0.18 0.31 4 -0.37 87 91
ADCY8 -0.078 0.16 0.29 4 -0.34 84 88
ADCY9 -0.092 0.18 0.29 4 -0.37 89 93
GSK3B -0.079 0.14 0.23 5 -0.32 62 67
arachidonic acid secretion -0.12 0.18 0.27 4 -0.36 99 103
GNG2 0.027 0.03 -10000 0 -0.37 2 2
TRIP6 0.022 0.032 -10000 0 -0.31 1 1
GNAO1 -0.13 0.15 0.29 4 -0.26 192 196
HRAS 0.029 0.004 -10000 0 -10000 0 0
NFKBIA -0.031 0.097 0.26 6 -0.34 7 13
GAB1 0.028 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.033 0.27 -10000 0 -0.86 35 35
JUN 0.022 0.051 -10000 0 -0.37 6 6
LPA/LPA2/NHERF2 0.032 0.036 -10000 0 -0.22 3 3
TIAM1 -0.059 0.31 -10000 0 -1 35 35
PIK3R1 0.027 0.03 -10000 0 -0.37 2 2
mol:IP3 -0.007 0.072 0.24 6 -0.31 3 9
PLCB3 -0.006 0.052 0.17 22 -0.2 3 25
FOS -0.15 0.2 -10000 0 -0.37 160 160
positive regulation of mitosis -0.12 0.18 0.27 4 -0.36 99 103
LPA/LPA1-2-3 -0.018 0.12 0.18 1 -0.22 85 86
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0.001 -10000 0 -10000 0 0
BCAR1 0.027 0.008 -10000 0 -10000 0 0
stress fiber formation -0.042 0.14 0.29 7 -0.33 40 47
GNAZ -0.026 0.099 0.34 6 -0.24 48 54
EGFR/PI3K-beta/Gab1 -0.057 0.094 -10000 0 -0.22 74 74
positive regulation of dendritic cell cytokine production -0.02 0.12 0.18 1 -0.22 85 86
LPA/LPA2/MAGI-3 0.035 0.03 0.14 2 -0.22 1 3
ARHGEF1 -0.052 0.098 0.25 7 -0.32 11 18
GNAI2 -0.05 0.12 0.28 8 -0.24 91 99
GNAI3 -0.047 0.12 0.28 8 -0.24 85 93
GNAI1 -0.05 0.12 0.28 8 -0.24 90 98
LPA/LPA3 0.012 0.019 -10000 0 -0.1 5 5
LPA/LPA2 0.017 0.025 -10000 0 -0.12 7 7
LPA/LPA1 -0.051 0.14 -10000 0 -0.28 93 93
HB-EGF/EGFR 0.031 0.085 0.17 65 -0.23 18 83
HBEGF 0.017 0.1 0.21 69 -0.26 12 81
mol:DAG -0.007 0.072 0.24 6 -0.31 3 9
cAMP biosynthetic process -0.13 0.18 0.29 4 -0.36 105 109
NFKB1 0.027 0.009 -10000 0 -10000 0 0
SRC 0.029 0.005 -10000 0 -10000 0 0
GNB1 0.027 0.009 -10000 0 -10000 0 0
LYN -0.02 0.11 0.26 6 -0.36 7 13
GNAQ 0.022 0.054 0.16 40 -0.22 1 41
LPAR2 0.027 0.022 -10000 0 -0.37 1 1
LPAR3 0.017 0.013 -10000 0 -10000 0 0
LPAR1 -0.07 0.18 0.18 4 -0.37 92 96
IL8 -0.13 0.26 0.56 11 -0.48 100 111
PTK2 -0.029 0.11 0.33 8 -0.32 7 15
Rac1/GDP 0.022 0.003 -10000 0 -10000 0 0
CASP3 -0.035 0.13 0.34 6 -0.24 84 90
EGFR 0.019 0.062 -10000 0 -0.37 9 9
PLCG1 0.006 0.074 0.27 8 -0.19 8 16
PLD2 -0.039 0.12 0.33 8 -0.33 11 19
G12/G13 -0.006 0.12 -10000 0 -0.22 79 79
PI3K-beta -0.023 0.089 -10000 0 -0.28 12 12
cell migration -0.017 0.1 0.24 4 -0.26 34 38
SLC9A3R2 0.026 0.03 -10000 0 -0.37 2 2
PXN -0.043 0.14 0.3 7 -0.34 41 48
HRAS/GTP -0.12 0.18 0.27 4 -0.37 99 103
RAC1 0.029 0.004 -10000 0 -10000 0 0
MMP9 0.012 0.065 -10000 0 -0.37 10 10
PRKCE 0.028 0.021 -10000 0 -0.37 1 1
PRKCD -0.014 0.071 0.25 3 -0.3 3 6
Gi(beta/gamma) -0.099 0.18 0.29 4 -0.38 79 83
mol:LPA -0.003 0.023 -10000 0 -0.15 6 6
TRIP6/p130 Cas/FAK1/Paxillin -0.026 0.14 0.34 6 -0.31 34 40
MAPKKK cascade -0.12 0.18 0.27 4 -0.36 99 103
contractile ring contraction involved in cytokinesis -0.004 0.055 0.21 2 -0.29 2 4
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.01 0.098 0.16 32 -0.23 49 81
GNA15 0.022 0.053 0.16 39 -0.22 1 40
GNA12 0.029 0.005 -10000 0 -10000 0 0
GNA13 0.029 0.005 -10000 0 -10000 0 0
MAPT -0.033 0.15 0.28 8 -0.33 39 47
GNA11 0.017 0.064 0.15 41 -0.22 9 50
Rac1/GTP -0.037 0.29 -10000 0 -0.91 35 35
MMP2 -0.049 0.14 0.45 4 -0.49 17 21
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.11 0.38 0.56 3 -0.85 70 73
NCK1/PAK1/Dok-R -0.085 0.16 -10000 0 -0.41 72 72
NCK1/Dok-R -0.11 0.36 -10000 0 -0.82 71 71
PIK3CA 0.029 0.021 -10000 0 -0.37 1 1
mol:beta2-estradiol 0.002 0.031 0.26 3 -0.17 3 6
RELA 0.029 0.005 -10000 0 -10000 0 0
SHC1 0.022 0.013 -10000 0 -10000 0 0
Rac/GDP 0.022 0.003 -10000 0 -10000 0 0
F2 -0.015 0.11 0.3 3 -0.35 26 29
TNIP2 0.029 0.005 -10000 0 -10000 0 0
NF kappa B/RelA -0.092 0.35 -10000 0 -0.79 71 71
FN1 0.028 0.021 -10000 0 -0.37 1 1
PLD2 -0.13 0.36 -10000 0 -0.87 66 66
PTPN11 0.029 0.003 -10000 0 -10000 0 0
GRB14 0.023 0.051 -10000 0 -0.37 6 6
ELK1 -0.13 0.35 -10000 0 -0.82 71 71
GRB7 0.024 0.042 -10000 0 -0.37 4 4
PAK1 0.029 0.005 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.094 0.36 -10000 0 -0.81 71 71
CDKN1A -0.078 0.3 0.57 10 -0.64 69 79
ITGA5 0.03 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.11 0.36 -10000 0 -0.83 71 71
CRK 0.025 0.011 -10000 0 -10000 0 0
mol:NO -0.07 0.3 0.5 10 -0.64 70 80
PLG -0.16 0.37 -10000 0 -0.88 70 70
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.12 0.35 0.48 2 -0.8 70 72
GRB2 0.028 0.006 -10000 0 -10000 0 0
PIK3R1 0.027 0.03 -10000 0 -0.37 2 2
ANGPT2 -0.038 0.24 0.61 15 -0.76 8 23
BMX -0.15 0.38 -10000 0 -0.9 71 71
ANGPT1 -0.001 0.14 0.47 3 -1.1 3 6
tube development -0.093 0.31 0.56 11 -0.68 68 79
ANGPT4 0.017 0.019 -10000 0 -10000 0 0
response to hypoxia -0.009 0.026 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.12 0.38 -10000 0 -0.86 71 71
alpha5/beta1 Integrin 0.043 0.009 -10000 0 -10000 0 0
FGF2 0.001 0.091 -10000 0 -0.37 20 20
STAT5A (dimer) -0.098 0.36 0.59 10 -0.78 69 79
mol:L-citrulline -0.07 0.3 0.5 10 -0.64 70 80
AGTR1 -0.001 0.12 -10000 0 -0.37 32 32
MAPK14 -0.16 0.45 -10000 0 -1.1 72 72
Tie2/SHP2 -0.15 0.39 -10000 0 -0.92 72 72
TEK -0.17 0.42 -10000 0 -1 70 70
RPS6KB1 -0.1 0.37 0.55 4 -0.81 71 75
Angiotensin II/AT1 0.007 0.089 0.2 17 -0.25 32 49
Tie2/Ang1/GRB2 -0.12 0.37 -10000 0 -0.85 71 71
MAPK3 -0.13 0.34 -10000 0 -0.82 67 67
MAPK1 -0.12 0.34 -10000 0 -0.82 66 66
Tie2/Ang1/GRB7 -0.12 0.37 -10000 0 -0.86 71 71
NFKB1 0.027 0.009 -10000 0 -10000 0 0
MAPK8 -0.14 0.37 -10000 0 -0.87 70 70
PI3K -0.13 0.43 0.58 1 -0.97 70 71
FES -0.17 0.46 -10000 0 -1 74 74
Crk/Dok-R -0.11 0.36 -10000 0 -0.82 71 71
Tie2/Ang1/ABIN2 -0.12 0.38 -10000 0 -0.86 71 71
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.091 0.35 0.52 10 -0.76 70 80
STAT5A 0.029 0.004 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.069 0.38 0.71 2 -0.8 70 72
Tie2/Ang2 -0.13 0.41 0.61 10 -0.92 68 78
Tie2/Ang1 -0.14 0.39 -10000 0 -0.9 71 71
FOXO1 -0.092 0.35 0.54 11 -0.77 70 81
ELF1 0.007 0.063 -10000 0 -0.14 44 44
ELF2 -0.13 0.37 -10000 0 -0.86 71 71
mol:Choline -0.12 0.35 -10000 0 -0.84 66 66
cell migration -0.041 0.094 -10000 0 -0.23 72 72
FYN -0.11 0.35 0.58 10 -0.78 68 78
DOK2 0.021 0.032 -10000 0 -0.37 2 2
negative regulation of cell cycle -0.066 0.28 0.56 11 -0.58 67 78
ETS1 0.014 0.049 0.2 3 -0.31 4 7
PXN -0.051 0.33 0.6 3 -0.67 69 72
ITGB1 0.029 0.005 -10000 0 -10000 0 0
NOS3 -0.088 0.33 0.51 10 -0.73 70 80
RAC1 0.029 0.004 -10000 0 -10000 0 0
TNF 0.005 0.083 0.2 3 -0.36 15 18
MAPKKK cascade -0.12 0.35 -10000 0 -0.84 66 66
RASA1 0.027 0.03 -10000 0 -0.37 2 2
Tie2/Ang1/Shc -0.12 0.36 -10000 0 -0.82 71 71
NCK1 0.03 0.002 -10000 0 -10000 0 0
vasculogenesis -0.058 0.27 0.48 12 -0.57 70 82
mol:Phosphatidic acid -0.12 0.35 -10000 0 -0.84 66 66
mol:Angiotensin II 0.004 0.017 0.091 1 -10000 0 1
mol:NADP -0.07 0.3 0.5 10 -0.64 70 80
Rac1/GTP -0.089 0.35 0.46 10 -0.76 71 81
MMP2 -0.14 0.38 -10000 0 -0.88 70 70
PLK1 signaling events

Figure S28.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S28.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.063 0.07 0.16 1 -0.15 144 145
BUB1B 0.12 0.098 0.2 205 -0.12 1 206
PLK1 0.054 0.046 0.099 151 -10000 0 151
PLK1S1 0.034 0.032 0.14 6 -0.15 3 9
KIF2A 0.042 0.042 0.2 3 -10000 0 3
regulation of mitotic centrosome separation 0.054 0.046 0.099 151 -10000 0 151
GOLGA2 0.029 0.004 -10000 0 -10000 0 0
Hec1/SPC24 0.013 0.023 -10000 0 -10000 0 0
WEE1 0.069 0.058 0.19 4 -0.42 1 5
cytokinesis 0.18 0.13 0.27 214 -10000 0 214
PP2A-alpha B56 0.12 0.1 -10000 0 -0.46 4 4
AURKA 0.052 0.049 0.13 80 -0.17 1 81
PICH/PLK1 0.037 0.07 0.18 59 -10000 0 59
CENPE 0.12 0.12 0.24 167 -10000 0 167
RhoA/GTP 0.022 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.042 0.042 0.2 3 -10000 0 3
PPP2CA 0.029 0.005 -10000 0 -10000 0 0
FZR1 0.029 0.005 -10000 0 -10000 0 0
TPX2 0.046 0.046 0.15 48 -10000 0 48
PAK1 0.029 0.005 -10000 0 -10000 0 0
SPC24 0.015 0.015 -10000 0 -10000 0 0
FBXW11 0.029 0.005 -10000 0 -10000 0 0
CLSPN 0.055 0.086 0.15 109 -0.21 18 127
GORASP1 0.03 0.003 -10000 0 -10000 0 0
metaphase 0.005 0.005 0.018 22 -0.009 1 23
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.028 0.024 0.053 148 -10000 0 148
G2 phase of mitotic cell cycle 0 0.003 0.016 5 -10000 0 5
STAG2 0.029 0.004 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.025 0.031 -10000 0 -0.46 1 1
spindle elongation 0.054 0.046 0.099 151 -10000 0 151
ODF2 0.031 0.005 -10000 0 -10000 0 0
BUB1 0.04 0.077 -10000 0 -0.52 3 3
TPT1 0.017 0.057 -10000 0 -0.15 26 26
CDC25C 0.12 0.064 0.16 197 -0.16 1 198
CDC25B 0.034 0.008 -10000 0 -10000 0 0
SGOL1 0.063 0.07 0.15 144 -0.16 1 145
RHOA 0.029 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.03 0.034 -10000 0 -0.18 1 1
CDC14B -0.015 0.042 -10000 0 -0.26 10 10
CDC20 0.008 0.013 -10000 0 -10000 0 0
PLK1/PBIP1 0.03 0.034 0.091 48 -10000 0 48
mitosis -0.001 0.003 0.025 3 -10000 0 3
FBXO5 0.04 0.045 0.12 11 -0.11 1 12
CDC2 0.006 0.005 0.011 145 -10000 0 145
NDC80 0.009 0.014 -10000 0 -10000 0 0
metaphase plate congression 0.031 0.064 -10000 0 -0.21 17 17
ERCC6L 0.043 0.061 0.17 58 -0.18 1 59
NLP/gamma Tubulin 0.031 0.026 0.081 19 -10000 0 19
microtubule cytoskeleton organization 0.017 0.056 -10000 0 -0.15 26 26
G2/M transition DNA damage checkpoint -0.001 0.002 0.014 5 -10000 0 5
PPP1R12A 0.03 0.003 -10000 0 -10000 0 0
interphase -0.001 0.002 0.014 5 -10000 0 5
PLK1/PRC1-2 0.013 0.023 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0.083 0.034 0.16 1 -10000 0 1
RAB1A 0.03 0.003 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.041 0.04 0.1 93 -10000 0 93
mitotic prometaphase 0.003 0.005 0.022 22 -10000 0 22
proteasomal ubiquitin-dependent protein catabolic process 0.069 0.052 -10000 0 -10000 0 0
microtubule-based process 0.009 0.018 0.13 1 -10000 0 1
Golgi organization 0.054 0.046 0.099 151 -10000 0 151
Cohesin/SA2 0.062 0.037 0.11 82 -10000 0 82
PPP1CB/MYPT1 0.045 0.006 -10000 0 -10000 0 0
KIF20A 0.009 0.014 -10000 0 -10000 0 0
APC/C/CDC20 0.008 0.015 0.11 1 -10000 0 1
PPP2R1A 0.029 0.005 -10000 0 -10000 0 0
chromosome segregation 0.03 0.034 0.09 48 -10000 0 48
PRC1 0.014 0.015 -10000 0 -10000 0 0
ECT2 0.082 0.1 0.25 84 -10000 0 84
C13orf34 0.042 0.037 0.094 91 -10000 0 91
NUDC 0.031 0.064 -10000 0 -0.21 17 17
regulation of attachment of spindle microtubules to kinetochore 0.12 0.097 0.2 205 -0.11 1 206
spindle assembly 0.042 0.037 0.092 82 -10000 0 82
spindle stabilization 0.034 0.032 0.13 6 -0.15 3 9
APC/C/HCDH1 0.018 0.04 -10000 0 -0.22 10 10
MKLP2/PLK1 0.009 0.018 0.13 1 -10000 0 1
CCNB1 0.016 0.016 -10000 0 -10000 0 0
PPP1CB 0.03 0.003 -10000 0 -10000 0 0
BTRC 0.029 0.005 -10000 0 -10000 0 0
ROCK2 0.037 0.074 -10000 0 -0.33 11 11
TUBG1 0.034 0.028 0.12 2 -0.15 1 3
G2/M transition of mitotic cell cycle 0.086 0.083 0.18 150 -0.18 1 151
MLF1IP 0.019 0.064 0.21 36 -10000 0 36
INCENP 0.03 0.006 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A 0.13 0.098 0.2 238 -10000 0 238
TP53 0.039 0.04 -10000 0 -10000 0 0
Senescence 0.027 0.066 -10000 0 -0.17 25 25
Apoptosis 0.027 0.066 -10000 0 -0.17 25 25
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.092 0.062 -10000 0 -10000 0 0
MDM4 0.023 0.012 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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
USP8 -0.018 0.007 -10000 0 -10000 0 0
RAS family/GTP -0.056 0.11 0.28 3 -0.23 35 38
NFATC4 -0.088 0.082 0.26 3 -0.19 105 108
ERBB2IP 0.032 0.004 -10000 0 -10000 0 0
HSP90 (dimer) 0.028 0.007 -10000 0 -10000 0 0
mammary gland morphogenesis -0.11 0.089 -10000 0 -0.23 118 118
JUN -0.067 0.078 0.33 1 -0.39 7 8
HRAS 0.029 0.004 -10000 0 -10000 0 0
DOCK7 -0.11 0.088 -10000 0 -0.22 112 112
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.046 0.1 -10000 0 -0.21 95 95
AKT1 -0.011 0.006 -10000 0 -10000 0 0
BAD -0.016 0.005 -10000 0 -10000 0 0
MAPK10 -0.068 0.068 0.28 2 -0.2 16 18
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.12 0.095 -10000 0 -0.24 118 118
RAF1 -0.073 0.11 0.38 3 -0.25 28 31
ErbB2/ErbB3/neuregulin 2 -0.01 0.051 -10000 0 -0.22 6 6
STAT3 0.03 0.067 -10000 0 -0.84 2 2
cell migration -0.073 0.065 0.18 1 -0.19 22 23
mol:PI-3-4-5-P3 -0.002 0.002 -10000 0 -10000 0 0
cell proliferation -0.17 0.22 0.6 3 -0.55 26 29
FOS -0.22 0.25 0.53 3 -0.46 176 179
NRAS 0.029 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.11 0.089 -10000 0 -0.23 118 118
MAPK3 -0.12 0.19 0.55 3 -0.56 17 20
MAPK1 -0.12 0.18 0.55 3 -0.55 14 17
JAK2 -0.1 0.088 -10000 0 -0.22 117 117
NF2 -0.003 0.051 -10000 0 -0.67 2 2
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.053 0.099 -10000 0 -0.22 91 91
NRG1 -0.11 0.18 -10000 0 -0.37 117 117
GRB2/SOS1 0.042 0.009 -10000 0 -10000 0 0
MAPK8 -0.14 0.12 -10000 0 -0.26 130 130
MAPK9 -0.066 0.057 0.16 2 -0.19 3 5
ERBB2 -0.034 0.032 -10000 0 -0.28 6 6
ERBB3 0.023 0.036 -10000 0 -0.37 3 3
SHC1 0.022 0.013 -10000 0 -10000 0 0
RAC1 0.029 0.004 -10000 0 -10000 0 0
apoptosis 0.009 0.013 -10000 0 -0.2 1 1
STAT3 (dimer) 0.031 0.065 -10000 0 -0.82 2 2
RNF41 -0.024 0.01 -10000 0 -10000 0 0
FRAP1 -0.009 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.091 0.065 -10000 0 -0.18 114 114
ErbB2/ErbB2/HSP90 (dimer) -0.032 0.029 -10000 0 -0.24 6 6
CHRNA1 -0.088 0.15 0.5 9 -0.39 6 15
myelination -0.084 0.086 0.26 5 -0.2 35 40
PPP3CB -0.1 0.082 -10000 0 -0.21 114 114
KRAS 0.029 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.045 0.11 -10000 0 -0.2 87 87
NRG2 0.022 0.012 -10000 0 -10000 0 0
mol:GDP -0.053 0.099 -10000 0 -0.22 91 91
SOS1 0.029 0.002 -10000 0 -10000 0 0
MAP2K2 -0.08 0.12 0.41 3 -0.27 27 30
SRC 0.029 0.005 -10000 0 -10000 0 0
mol:cAMP -0.002 0.001 -10000 0 -10000 0 0
PTPN11 -0.11 0.086 -10000 0 -0.22 117 117
MAP2K1 -0.15 0.18 0.49 3 -0.56 10 13
heart morphogenesis -0.11 0.089 -10000 0 -0.23 118 118
RAS family/GDP -0.052 0.11 -10000 0 -0.21 81 81
GRB2 0.028 0.006 -10000 0 -10000 0 0
PRKACA 0.004 0.053 -10000 0 -0.7 2 2
CHRNE -0.013 0.027 -10000 0 -0.17 7 7
HSP90AA1 0.028 0.007 -10000 0 -10000 0 0
activation of caspase activity 0.011 0.006 -10000 0 -10000 0 0
nervous system development -0.11 0.089 -10000 0 -0.23 118 118
CDC42 0.028 0.007 -10000 0 -10000 0 0
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.018 0.094 -10000 0 -0.22 63 63
cell-cell adhesion 0.076 0.083 0.21 89 -10000 0 89
Ephrin B/EPHB2/RasGAP 0.026 0.11 -10000 0 -0.2 52 52
ITSN1 0.029 0.005 -10000 0 -10000 0 0
PIK3CA 0.028 0.021 -10000 0 -0.37 1 1
SHC1 0.022 0.013 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.012 0.079 -10000 0 -0.22 38 38
Ephrin B1/EPHB1 -0.017 0.11 -10000 0 -0.22 79 79
HRAS/GDP -0.06 0.13 -10000 0 -0.26 73 73
Ephrin B/EPHB1/GRB7 -0.034 0.15 -10000 0 -0.23 125 125
Endophilin/SYNJ1 -0.021 0.092 0.24 2 -10000 0 2
KRAS 0.029 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.032 0.15 -10000 0 -0.23 121 121
endothelial cell migration 0.057 0.026 -10000 0 -0.19 2 2
GRB2 0.028 0.006 -10000 0 -10000 0 0
GRB7 0.024 0.042 -10000 0 -0.37 4 4
PAK1 -0.026 0.094 0.28 1 -0.36 1 2
HRAS 0.029 0.004 -10000 0 -10000 0 0
RRAS -0.02 0.092 0.24 2 -10000 0 2
DNM1 0.021 0.051 -10000 0 -0.37 6 6
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.085 0.1 0.18 1 -0.35 25 26
lamellipodium assembly -0.076 0.083 -10000 0 -0.21 89 89
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.054 0.12 -10000 0 -0.27 60 60
PIK3R1 0.027 0.03 -10000 0 -0.37 2 2
EPHB2 0.021 0.024 -10000 0 -0.37 1 1
EPHB3 -0.012 0.12 -10000 0 -0.37 37 37
EPHB1 -0.057 0.16 -10000 0 -0.37 79 79
EPHB4 0.029 0.005 -10000 0 -10000 0 0
mol:GDP -0.064 0.11 0.2 3 -0.27 61 64
Ephrin B/EPHB2 0.02 0.1 -10000 0 -0.19 51 51
Ephrin B/EPHB3 -0.015 0.13 -10000 0 -0.22 93 93
JNK cascade -0.031 0.099 0.35 1 -0.36 1 2
Ephrin B/EPHB1 -0.041 0.14 -10000 0 -0.23 124 124
RAP1/GDP -0.056 0.12 -10000 0 -0.29 34 34
EFNB2 0.028 0.006 -10000 0 -10000 0 0
EFNB3 -0.057 0.16 -10000 0 -0.37 74 74
EFNB1 0.029 0.021 -10000 0 -0.37 1 1
Ephrin B2/EPHB1-2 -0.001 0.091 -10000 0 -0.2 57 57
RAP1B 0.029 0.004 -10000 0 -10000 0 0
RAP1A 0.029 0.006 -10000 0 -10000 0 0
CDC42/GTP -0.04 0.14 -10000 0 -0.27 72 72
Rap1/GTP -0.08 0.085 -10000 0 -0.22 86 86
axon guidance -0.018 0.093 -10000 0 -0.22 63 63
MAPK3 -0.053 0.11 -10000 0 -0.29 36 36
MAPK1 -0.052 0.11 -10000 0 -0.3 36 36
Rac1/GDP -0.076 0.11 -10000 0 -0.3 33 33
actin cytoskeleton reorganization -0.08 0.079 -10000 0 -0.22 63 63
CDC42/GDP -0.075 0.11 0.21 3 -0.29 35 38
PI3K 0.062 0.028 -10000 0 -0.19 2 2
EFNA5 -0.059 0.16 -10000 0 -0.37 78 78
Ephrin B2/EPHB4 0.037 0.011 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.024 0.1 0.22 1 -0.21 55 56
CDC42 0.028 0.007 -10000 0 -10000 0 0
RAS family/GTP -0.082 0.084 -10000 0 -0.22 90 90
PTK2 0.11 0.24 0.58 73 -10000 0 73
MAP4K4 -0.031 0.099 0.35 1 -0.36 1 2
SRC 0.029 0.005 -10000 0 -10000 0 0
KALRN 0.027 0.03 -10000 0 -0.37 2 2
Intersectin/N-WASP 0.041 0.011 -10000 0 -10000 0 0
neuron projection morphogenesis -0.071 0.11 0.29 3 -0.3 22 25
MAP2K1 -0.059 0.11 -10000 0 -0.31 35 35
WASL 0.029 0.006 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.032 0.12 -10000 0 -0.21 60 60
cell migration -0.073 0.14 -10000 0 -0.36 36 36
NRAS 0.029 0.005 -10000 0 -10000 0 0
SYNJ1 -0.022 0.093 0.24 2 -10000 0 2
PXN 0.029 0.003 -10000 0 -10000 0 0
TF -0.036 0.092 0.19 1 -0.34 3 4
HRAS/GTP -0.027 0.13 -10000 0 -0.22 96 96
Ephrin B1/EPHB1-2 -0.003 0.095 -10000 0 -0.2 60 60
cell adhesion mediated by integrin 0.046 0.081 0.2 63 -0.19 6 69
RAC1 0.029 0.004 -10000 0 -10000 0 0
mol:GTP -0.024 0.13 -10000 0 -0.22 97 97
RAC1-CDC42/GTP -0.094 0.098 -10000 0 -0.23 102 102
RASA1 0.027 0.03 -10000 0 -0.37 2 2
RAC1-CDC42/GDP -0.056 0.12 -10000 0 -0.29 33 33
ruffle organization -0.06 0.11 0.27 4 -0.33 17 21
NCK1 0.03 0.002 -10000 0 -10000 0 0
receptor internalization -0.021 0.099 0.26 9 -0.34 2 11
Ephrin B/EPHB2/KALRN 0.027 0.11 -10000 0 -0.2 52 52
ROCK1 -0.032 0.064 0.16 10 -0.2 36 46
RAS family/GDP -0.079 0.078 -10000 0 -0.22 61 61
Rac1/GTP -0.079 0.087 -10000 0 -0.22 83 83
Ephrin B/EPHB1/Src/Paxillin -0.08 0.14 -10000 0 -0.25 121 121
EPO signaling pathway

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
BCL2L1 -0.052 0.15 -10000 0 -10000 0 0
CRKL -0.07 0.091 0.26 2 -10000 0 2
mol:DAG -0.058 0.14 -10000 0 -0.26 109 109
HRAS -0.033 0.11 0.32 10 -10000 0 10
MAPK8 -0.052 0.13 0.19 37 -0.21 111 148
RAP1A -0.067 0.091 0.26 2 -10000 0 2
GAB1 -0.067 0.09 0.26 2 -10000 0 2
MAPK14 -0.047 0.12 0.2 31 -0.2 101 132
EPO -0.12 0.19 -10000 0 -0.37 130 130
PLCG1 -0.059 0.14 -10000 0 -0.26 109 109
EPOR/TRPC2/IP3 Receptors 0.007 0.035 -10000 0 -10000 0 0
RAPGEF1 0.029 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.071 0.15 -10000 0 -0.24 150 150
GAB1/SHC/GRB2/SOS1 -0.021 0.096 -10000 0 -10000 0 0
EPO/EPOR (dimer) -0.069 0.15 -10000 0 -0.27 129 129
IRS2 -0.069 0.092 0.26 2 -0.34 1 3
STAT1 -0.055 0.15 -10000 0 -0.28 1 1
STAT5B -0.055 0.14 -10000 0 -0.26 103 103
cell proliferation -0.054 0.12 0.19 27 -0.29 9 36
GAB1/SHIP/PIK3R1/SHP2/SHC -0.026 0.094 -10000 0 -10000 0 0
TEC -0.07 0.094 0.26 2 -0.34 2 4
SOCS3 -0.02 0.13 -10000 0 -0.37 44 44
STAT1 (dimer) -0.054 0.14 -10000 0 -0.28 1 1
JAK2 0.006 0.034 -10000 0 -10000 0 0
PIK3R1 0.027 0.03 -10000 0 -0.37 2 2
EPO/EPOR (dimer)/JAK2 -0.018 0.13 -10000 0 -10000 0 0
EPO/EPOR -0.069 0.15 -10000 0 -0.27 129 129
LYN 0.025 0.012 -10000 0 -10000 0 0
TEC/VAV2 -0.073 0.092 0.26 2 -0.33 2 4
elevation of cytosolic calcium ion concentration 0.006 0.035 -10000 0 -10000 0 0
SHC1 0.022 0.013 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.039 0.12 -10000 0 -0.22 113 113
mol:IP3 -0.058 0.14 -10000 0 -0.26 109 109
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.037 0.11 0.28 1 -0.27 2 3
SH2B3 0.006 0.035 -10000 0 -10000 0 0
NFKB1 -0.038 0.12 0.19 41 -0.2 96 137
EPO/EPOR (dimer)/JAK2/SOCS3 -0.088 0.13 0.18 1 -0.24 152 153
PTPN6 -0.067 0.094 0.27 1 -10000 0 1
TEC/VAV2/GRB2 -0.036 0.11 0.28 1 -0.33 2 3
EPOR 0.007 0.035 -10000 0 -10000 0 0
INPP5D 0.029 0.003 -10000 0 -10000 0 0
mol:GDP -0.022 0.096 -10000 0 -10000 0 0
SOS1 0.03 0.002 -10000 0 -10000 0 0
PLCG2 0.02 0.051 -10000 0 -0.37 6 6
CRKL/CBL/C3G -0.036 0.11 0.26 2 -10000 0 2
VAV2 -0.068 0.091 0.26 2 -10000 0 2
CBL -0.068 0.092 0.26 2 -10000 0 2
SHC/Grb2/SOS1 -0.023 0.095 -10000 0 -0.18 84 84
STAT5A -0.055 0.14 -10000 0 -0.26 105 105
GRB2 0.028 0.006 -10000 0 -10000 0 0
STAT5 (dimer) -0.035 0.14 -10000 0 -0.3 1 1
LYN/PLCgamma2 0.028 0.042 -10000 0 -0.26 6 6
PTPN11 0.029 0.003 -10000 0 -10000 0 0
BTK -0.073 0.095 0.26 2 -0.31 3 5
BCL2 -0.058 0.15 -10000 0 -0.81 1 1
Glucocorticoid receptor regulatory network

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
PCK2 -0.043 0.26 -10000 0 -0.81 33 33
SMARCC2 0.027 0.02 -10000 0 -0.1 2 2
SMARCC1 0.027 0.02 -10000 0 -0.12 2 2
TBX21 -0.038 0.16 -10000 0 -0.48 22 22
SUMO2 0.01 0.034 0.2 1 -10000 0 1
STAT1 (dimer) 0.033 0.004 -10000 0 -10000 0 0
FKBP4 0.029 0.006 -10000 0 -10000 0 0
FKBP5 0.027 0.009 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90 0.053 0.11 0.24 38 -10000 0 38
PRL -0.012 0.14 0.79 3 -0.62 1 4
cortisol/GR alpha (dimer)/TIF2 0.039 0.25 0.48 47 -0.49 15 62
RELA -0.059 0.13 0.27 2 -0.2 150 152
FGG 0.028 0.25 0.4 48 -0.51 23 71
GR beta/TIF2 0.016 0.14 0.25 44 -0.31 17 61
IFNG -0.025 0.27 0.66 26 -0.54 11 37
apoptosis -0.11 0.35 0.53 23 -0.72 50 73
CREB1 0.046 0.053 0.24 26 -10000 0 26
histone acetylation -0.059 0.13 -10000 0 -0.33 30 30
BGLAP -0.006 0.12 0.37 1 -0.38 3 4
GR/PKAc 0.064 0.12 0.27 23 -10000 0 23
NF kappa B1 p50/RelA -0.11 0.22 0.3 14 -0.35 150 164
SMARCD1 0.027 0.019 -10000 0 -0.12 1 1
MDM2 0.035 0.09 0.18 59 -10000 0 59
GATA3 0.012 0.1 0.27 6 -0.37 21 27
AKT1 0.037 0.04 0.19 15 -10000 0 15
CSF2 -0.051 0.1 -10000 0 -0.46 1 1
GSK3B 0.01 0.034 0.2 1 -10000 0 1
NR1I3 -0.13 0.4 0.59 21 -0.76 76 97
CSN2 0.035 0.2 0.35 31 -0.4 18 49
BRG1/BAF155/BAF170/BAF60A 0.068 0.052 -10000 0 -0.22 10 10
NFATC1 0.024 0.042 -10000 0 -0.37 4 4
POU2F1 0.024 0.018 0.2 2 -10000 0 2
CDKN1A -0.033 0.24 -10000 0 -1.4 10 10
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.002 0.016 0.12 1 -10000 0 1
SFN 0.011 0.014 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.094 0.12 0.28 61 -10000 0 61
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.24 0.42 0.6 9 -0.73 133 142
JUN 0.11 0.29 0.61 66 -0.41 8 74
IL4 -0.035 0.13 -10000 0 -0.48 5 5
CDK5R1 0.015 0.026 -10000 0 -10000 0 0
PRKACA 0.029 0.004 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.047 0.079 0.14 1 -0.25 26 27
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.061 0.12 0.27 19 -10000 0 19
cortisol/GR alpha (monomer) 0.085 0.3 0.55 62 -0.5 17 79
NCOA2 -0.013 0.11 -10000 0 -0.37 33 33
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.071 0.22 0.31 30 -0.37 117 147
AP-1/NFAT1-c-4 0.016 0.29 0.65 36 -0.49 9 45
AFP 0.089 0.4 0.67 67 -1.1 15 82
SUV420H1 0.029 0.006 -10000 0 -10000 0 0
IRF1 0.056 0.15 0.36 17 -10000 0 17
TP53 0.022 0.068 -10000 0 -0.46 7 7
PPP5C 0.029 0.005 -10000 0 -10000 0 0
KRT17 -0.009 0.37 0.73 45 -0.81 20 65
KRT14 0.022 0.22 0.64 34 -0.42 1 35
TBP 0.031 0.017 0.2 2 -10000 0 2
CREBBP -0.001 0.083 -10000 0 -0.22 45 45
HDAC1 0.028 0.007 -10000 0 -10000 0 0
HDAC2 0.027 0.008 -10000 0 -10000 0 0
AP-1 0.016 0.29 0.65 37 -0.49 10 47
MAPK14 0.009 0.031 0.14 1 -10000 0 1
MAPK10 -0.01 0.085 0.14 1 -0.37 17 18
MAPK11 0.011 0.033 0.2 1 -10000 0 1
KRT5 -0.008 0.31 0.69 41 -0.53 18 59
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
NCOA1 0.02 0.033 -10000 0 -0.1 17 17
STAT1 0.033 0.004 -10000 0 -10000 0 0
CGA -0.009 0.17 0.54 15 -0.4 5 20
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.03 0.16 0.31 1 -0.41 27 28
MAPK3 0.008 0.033 0.16 1 -10000 0 1
MAPK1 0.009 0.033 0.14 1 -10000 0 1
ICAM1 -0.12 0.22 0.42 1 -0.54 41 42
NFKB1 -0.055 0.12 0.28 1 -0.22 103 104
MAPK8 0.048 0.24 0.5 48 -0.33 27 75
MAPK9 0.008 0.033 0.14 1 -10000 0 1
cortisol/GR alpha (dimer) -0.13 0.37 0.52 25 -0.76 52 77
BAX -0.017 0.09 -10000 0 -0.46 3 3
POMC -0.081 0.22 0.55 3 -0.84 9 12
EP300 0.001 0.082 -10000 0 -0.22 44 44
cortisol/GR alpha (dimer)/p53 0.047 0.24 0.48 40 -0.49 8 48
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.085 0.21 25 -10000 0 25
SGK1 -0.047 0.25 -10000 0 -1.2 13 13
IL13 -0.038 0.24 0.62 7 -0.67 14 21
IL6 -0.2 0.38 0.67 4 -0.77 85 89
PRKACG 0.019 0.005 -10000 0 -10000 0 0
IL5 -0.032 0.21 0.57 2 -0.65 9 11
IL2 -0.051 0.26 0.58 20 -0.58 20 40
CDK5 0.015 0.026 -10000 0 -10000 0 0
PRKACB 0.029 0.006 -10000 0 -10000 0 0
HSP90AA1 0.028 0.007 -10000 0 -10000 0 0
IL8 -0.25 0.44 0.66 9 -0.91 94 103
CDK5R1/CDK5 0.021 0.04 0.16 2 -10000 0 2
NF kappa B1 p50/RelA/PKAc -0.057 0.19 0.41 1 -0.29 113 114
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.077 0.25 0.46 57 -0.46 8 65
SMARCA4 0.026 0.022 -10000 0 -0.14 1 1
chromatin remodeling 0.045 0.17 0.3 46 -0.4 6 52
NF kappa B1 p50/RelA/Cbp -0.1 0.21 0.43 1 -0.4 75 76
JUN (dimer) 0.11 0.29 0.61 66 -0.41 8 74
YWHAH 0.029 0.005 -10000 0 -10000 0 0
VIPR1 -0.46 0.37 -10000 0 -0.73 234 234
NR3C1 0.056 0.18 0.34 60 -0.31 5 65
NR4A1 -0.031 0.15 0.21 1 -0.37 58 59
TIF2/SUV420H1 0.005 0.087 -10000 0 -0.26 33 33
MAPKKK cascade -0.11 0.35 0.53 23 -0.72 50 73
cortisol/GR alpha (dimer)/Src-1 0.075 0.27 0.48 63 -0.46 18 81
PBX1 0 0.096 0.2 2 -0.37 22 24
POU1F1 0.021 0.014 0.19 2 -10000 0 2
SELE -0.24 0.42 0.47 5 -0.88 96 101
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.044 0.17 0.3 46 -0.41 6 52
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.077 0.25 0.46 57 -0.46 8 65
mol:cortisol 0.044 0.16 0.3 62 -0.26 13 75
MMP1 0.079 0.27 0.6 61 -0.73 8 69
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.02 0.049 -10000 0 -0.27 6 6
PDGFRB 0.02 0.019 -10000 0 -10000 0 0
SPHK1 -0.009 0.12 -10000 0 -0.85 6 6
mol:S1P -0.016 0.12 0.26 2 -0.77 6 8
S1P1/S1P/Gi -0.15 0.22 -10000 0 -0.42 117 117
GNAO1 -0.15 0.19 -10000 0 -0.38 153 153
PDGFB-D/PDGFRB/PLCgamma1 -0.13 0.2 -10000 0 -0.39 104 104
PLCG1 -0.14 0.21 -10000 0 -0.4 114 114
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.02 0.019 -10000 0 -10000 0 0
GNAI2 0.011 0.029 -10000 0 -10000 0 0
GNAI3 0.009 0.028 -10000 0 -10000 0 0
GNAI1 0.008 0.04 -10000 0 -0.38 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.018 0.032 -10000 0 -0.23 6 6
S1P1/S1P -0.023 0.11 0.22 7 -0.47 9 16
negative regulation of cAMP metabolic process -0.15 0.22 -10000 0 -0.42 116 116
MAPK3 -0.21 0.3 -10000 0 -0.59 125 125
calcium-dependent phospholipase C activity -0.003 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.022 0.003 -10000 0 -10000 0 0
RhoA/GDP 0.022 0.003 -10000 0 -10000 0 0
KDR 0.012 0.058 -10000 0 -0.38 7 7
PLCB2 -0.01 0.12 0.23 6 -0.41 11 17
RAC1 0.029 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.026 0.091 -10000 0 -0.38 10 10
receptor internalization -0.023 0.1 0.21 5 -0.43 9 14
PTGS2 -0.35 0.47 -10000 0 -0.98 125 125
Rac1/GTP -0.026 0.09 -10000 0 -0.37 10 10
RHOA 0.029 0.004 -10000 0 -10000 0 0
VEGFA 0.017 0.021 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.15 0.22 -10000 0 -0.42 116 116
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.002 0.029 -10000 0 -0.38 1 1
MAPK1 -0.21 0.29 -10000 0 -0.59 124 124
S1P1/S1P/PDGFB-D/PDGFRB -0.016 0.13 0.25 2 -0.4 11 13
ABCC1 0.012 0.026 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.01 0.085 0.5 7 -0.24 4 11
NFATC2 -0.04 0.12 0.5 7 -0.23 56 63
NFATC3 -0.006 0.081 0.5 7 -10000 0 7
CD40LG -0.17 0.24 0.68 12 -0.54 47 59
PTGS2 -0.17 0.28 0.74 14 -0.54 83 97
JUNB 0.011 0.084 -10000 0 -0.37 17 17
CaM/Ca2+/Calcineurin A alpha-beta B1 0.007 0.027 -10000 0 -10000 0 0
CaM/Ca2+ 0.007 0.027 -10000 0 -10000 0 0
CALM1 0.017 0.037 0.2 6 -10000 0 6
JUN 0.01 0.063 0.2 6 -0.38 6 12
mol:Ca2+ -0.004 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.018 0.012 0.093 3 -10000 0 3
FOSL1 0.012 0.079 -10000 0 -0.37 15 15
CREM 0.029 0.006 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.027 0.13 0.37 9 -0.29 28 37
FOS -0.15 0.2 0.2 6 -0.38 159 165
IFNG -0.18 0.19 0.55 5 -0.5 46 51
AP-1/NFAT1-c-4 -0.16 0.25 0.52 7 -0.47 109 116
FASLG -0.14 0.22 0.61 11 -0.53 36 47
NFAT1-c-4/ICER1 -0.035 0.12 0.32 8 -0.26 33 41
IL2RA -0.18 0.19 0.47 3 -0.5 50 53
FKBP12/FK506 0.022 0.003 -10000 0 -10000 0 0
CSF2 -0.16 0.25 1 7 -0.51 40 47
JunB/Fra1/NFAT1-c-4 -0.036 0.15 0.38 11 -0.28 49 60
IL4 -0.16 0.25 0.73 13 -0.51 43 56
IL2 -0.059 0.26 -10000 0 -1 25 25
IL3 -0.004 0.065 -10000 0 -0.66 3 3
FKBP1A 0.029 0.005 -10000 0 -10000 0 0
BATF3 0.021 0.032 -10000 0 -0.37 2 2
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.023 0.013 -10000 0 -10000 0 0
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.021 0.09 0.19 3 -0.25 22 25
alphaM/beta2 Integrin/GPIbA 0.025 0.074 0.18 9 -0.19 19 28
alphaM/beta2 Integrin/proMMP-9 0.015 0.083 0.18 8 -0.22 24 32
PLAUR 0.027 0.03 -10000 0 -0.37 2 2
HMGB1 0.018 0.035 -10000 0 -0.13 1 1
alphaM/beta2 Integrin/Talin 0.032 0.073 0.18 10 -0.19 17 27
AGER 0.017 0.035 -10000 0 -10000 0 0
RAP1A 0.029 0.006 -10000 0 -10000 0 0
SELPLG 0.027 0.03 -10000 0 -0.37 2 2
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.031 0.12 0.36 7 -0.22 50 57
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.012 0.065 -10000 0 -0.37 10 10
CYR61 -0.008 0.12 -10000 0 -0.37 33 33
TLN1 0.029 0.005 -10000 0 -10000 0 0
Rap1/GTP -0.042 0.13 -10000 0 -0.32 42 42
RHOA 0.029 0.004 -10000 0 -10000 0 0
P-selectin oligomer -0.064 0.16 -10000 0 -0.37 79 79
MYH2 -0.082 0.16 -10000 0 -0.4 51 51
MST1R 0.018 0.055 -10000 0 -0.37 7 7
leukocyte activation during inflammatory response -0.074 0.13 0.18 1 -0.21 157 158
APOB 0.012 0.082 -10000 0 -0.37 16 16
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.012 0.077 -10000 0 -0.37 14 14
JAM3 0.028 0.006 -10000 0 -10000 0 0
GP1BA 0.021 0.037 -10000 0 -0.37 3 3
alphaM/beta2 Integrin/CTGF 0.026 0.084 0.18 10 -0.22 21 31
alphaM/beta2 Integrin -0.064 0.13 -10000 0 -0.3 59 59
JAM3 homodimer 0.028 0.006 -10000 0 -10000 0 0
ICAM2 0.029 0.006 -10000 0 -10000 0 0
ICAM1 0.029 0.004 -10000 0 -10000 0 0
phagocytosis triggered by activation of immune response cell surface activating receptor -0.064 0.13 -10000 0 -0.3 58 58
cell adhesion 0.025 0.074 0.18 9 -0.19 19 28
NFKB1 -0.046 0.16 0.46 10 -0.37 46 56
THY1 0.021 0.014 -10000 0 -10000 0 0
RhoA/GDP 0.022 0.003 -10000 0 -10000 0 0
Lipoprotein(a) -0.081 0.13 -10000 0 -0.23 157 157
alphaM/beta2 Integrin/LRP/tPA 0.037 0.081 0.21 1 -0.24 12 13
IL6 -0.083 0.24 0.53 9 -0.6 49 58
ITGB2 0.013 0.056 0.12 2 -0.17 14 16
elevation of cytosolic calcium ion concentration 0.04 0.078 0.21 1 -0.23 12 13
alphaM/beta2 Integrin/JAM2/JAM3 0.038 0.088 0.21 2 -0.23 20 22
JAM2 0.017 0.068 -10000 0 -0.37 11 11
alphaM/beta2 Integrin/ICAM1 0.046 0.1 0.28 3 -0.21 26 29
alphaM/beta2 Integrin/uPA/Plg 0.008 0.11 0.21 1 -0.22 47 48
RhoA/GTP -0.086 0.17 -10000 0 -0.3 106 106
positive regulation of phagocytosis -0.045 0.13 -10000 0 -0.31 44 44
Ron/MSP 0.021 0.069 -10000 0 -0.26 19 19
alphaM/beta2 Integrin/uPAR/uPA 0.042 0.08 0.21 1 -0.23 12 13
alphaM/beta2 Integrin/uPAR 0.029 0.076 0.18 9 -0.2 19 28
PLAU 0.028 0.007 -10000 0 -10000 0 0
PLAT 0.021 0.043 -10000 0 -0.37 4 4
actin filament polymerization -0.078 0.16 0.23 1 -0.38 51 52
MST1 0.002 0.1 -10000 0 -0.37 25 25
alphaM/beta2 Integrin/lipoprotein(a) -0.072 0.14 0.2 1 -0.21 157 158
TNF -0.061 0.18 0.49 9 -0.66 15 24
RAP1B 0.029 0.004 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.03 0.073 0.18 10 -0.19 17 27
fibrinolysis 0.007 0.11 0.21 1 -0.22 47 48
HCK 0.016 0.071 -10000 0 -0.37 12 12
dendritic cell antigen processing and presentation -0.064 0.13 -10000 0 -0.3 58 58
VTN 0.015 0.074 -10000 0 -0.37 13 13
alphaM/beta2 Integrin/CYR61 0.008 0.11 0.18 9 -0.23 45 54
LPA -0.14 0.19 -10000 0 -0.37 151 151
LRP1 0.028 0.021 -10000 0 -0.37 1 1
cell migration 0.032 0.11 0.26 3 -0.24 28 31
FN1 0.028 0.021 -10000 0 -0.37 1 1
alphaM/beta2 Integrin/Thy1 0.02 0.071 0.18 7 -0.19 17 24
MPO 0.016 0.062 -10000 0 -0.37 9 9
KNG1 -0.003 0.11 -10000 0 -0.37 29 29
RAP1/GDP 0.038 0.009 -10000 0 -10000 0 0
ROCK1 -0.084 0.16 -10000 0 -0.38 53 53
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.029 0.14 -10000 0 -0.37 51 51
CTGF 0.02 0.055 -10000 0 -0.37 7 7
alphaM/beta2 Integrin/Hck 0.026 0.096 0.18 10 -0.28 20 30
ITGAM 0.012 0.061 0.13 1 -0.26 9 10
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.015 0.13 0.21 1 -0.24 76 77
HP -0.079 0.18 -10000 0 -0.37 97 97
leukocyte adhesion 0.039 0.12 0.29 11 -0.28 14 25
SELP -0.064 0.16 -10000 0 -0.37 79 79
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.008 0.072 0.18 52 -0.23 3 55
SNTA1 0.029 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 0.019 0.09 0.2 62 -0.23 3 65
MAPK12 0.014 0.072 0.17 54 -0.19 5 59
CCND1 0.006 0.084 0.22 3 -0.38 13 16
p38 gamma/SNTA1 0.018 0.079 0.17 68 -0.19 5 73
MAP2K3 0.028 0.008 -10000 0 -10000 0 0
PKN1 0.029 0.004 -10000 0 -10000 0 0
G2/M transition checkpoint 0.02 0.078 0.18 64 -0.19 5 69
MAP2K6 -0.006 0.037 0.19 6 -0.21 7 13
MAPT 0.077 0.094 0.23 63 -0.18 2 65
MAPK13 0.016 0.083 0.21 54 -0.26 3 57
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.006 0.001 -10000 0 -10000 0 0
IL12-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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.013 0.13 0.47 2 -0.39 14 16
TBX21 -0.17 0.41 1.1 1 -1.1 38 39
B2M 0.02 0.029 -10000 0 -10000 0 0
TYK2 0.002 0.051 0.28 1 -10000 0 1
IL12RB1 -0.01 0.089 0.28 1 -0.4 12 13
GADD45B -0.26 0.52 0.92 1 -1.1 77 78
IL12RB2 -0.01 0.08 0.3 1 -0.38 11 12
GADD45G -0.26 0.49 0.92 1 -1.1 74 75
natural killer cell activation -0.005 0.029 0.16 3 -10000 0 3
RELB 0.029 0.005 -10000 0 -10000 0 0
RELA 0.029 0.005 -10000 0 -10000 0 0
IL18 0.008 0.064 -10000 0 -0.38 7 7
IL2RA 0.02 0.055 -10000 0 -0.37 7 7
IFNG 0.026 0.008 -10000 0 -10000 0 0
STAT3 (dimer) -0.16 0.35 0.85 1 -0.78 53 54
HLA-DRB5 -0.009 0.011 -10000 0 -0.029 13 13
FASLG -0.14 0.42 1 3 -1.1 34 37
NF kappa B2 p52/RelB -0.17 0.39 0.53 1 -0.9 54 55
CD4 -0.029 0.11 -10000 0 -0.38 29 29
SOCS1 0.026 0.03 -10000 0 -0.37 2 2
EntrezGene:6955 -0.015 0.019 -10000 0 -0.042 74 74
CD3D -0.017 0.069 -10000 0 -0.38 9 9
CD3E -0.017 0.079 -10000 0 -0.4 12 12
CD3G -0.016 0.071 -10000 0 -0.39 9 9
IL12Rbeta2/JAK2 0.001 0.085 0.33 2 -0.27 11 13
CCL3 -0.21 0.48 1.1 1 -1.3 45 46
CCL4 -0.19 0.45 1.1 1 -1.3 37 38
HLA-A -0.004 0.014 -10000 0 -0.048 32 32
IL18/IL18R -0.006 0.17 0.34 23 -0.29 65 88
NOS2 -0.14 0.4 1.1 1 -1 30 31
IL12/IL12R/TYK2/JAK2/SPHK2 -0.014 0.13 0.47 2 -0.38 11 13
IL1R1 -0.17 0.4 1.1 1 -1.1 32 33
IL4 0.008 0.042 -10000 0 -0.28 1 1
JAK2 0.002 0.051 0.28 1 -10000 0 1
EntrezGene:6957 -0.013 0.018 -10000 0 -0.047 51 51
TCR/CD3/MHC I/CD8 -0.14 0.36 -10000 0 -0.93 52 52
RAB7A -0.2 0.38 0.82 1 -0.82 64 65
lysosomal transport -0.19 0.36 0.81 1 -0.77 62 63
FOS -0.58 0.66 0.8 1 -1.2 182 183
STAT4 (dimer) -0.17 0.39 0.83 1 -0.84 60 61
STAT5A (dimer) -0.17 0.38 -10000 0 -0.89 53 53
GZMA -0.17 0.42 1.3 1 -1.1 35 36
GZMB -0.18 0.42 1.3 1 -1.1 37 38
HLX 0.024 0.012 -10000 0 -10000 0 0
LCK -0.18 0.44 0.96 2 -1.1 40 42
TCR/CD3/MHC II/CD4 -0.11 0.18 -10000 0 -0.33 93 93
IL2/IL2R 0.041 0.092 -10000 0 -0.24 31 31
MAPK14 -0.25 0.48 0.89 1 -0.97 86 87
CCR5 -0.16 0.4 0.84 3 -1.1 33 36
IL1B -0.062 0.16 0.28 1 -0.39 62 63
STAT6 -0.027 0.16 0.78 1 -0.72 4 5
STAT4 0.013 0.079 -10000 0 -0.37 15 15
STAT3 0.029 0.004 -10000 0 -10000 0 0
STAT1 0.029 0.003 -10000 0 -10000 0 0
NFKB1 0.027 0.009 -10000 0 -10000 0 0
NFKB2 0.029 0.005 -10000 0 -10000 0 0
IL12B -0.001 0.048 0.28 2 -10000 0 2
CD8A -0.003 0.1 -10000 0 -0.38 22 22
CD8B 0.001 0.091 -10000 0 -0.38 18 18
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.012 0.13 0.39 14 -0.47 2 16
IL2RB 0 0.1 -10000 0 -0.37 26 26
proteasomal ubiquitin-dependent protein catabolic process -0.15 0.36 0.83 1 -0.78 55 56
IL2RG 0.024 0.047 -10000 0 -0.37 5 5
IL12 0.005 0.07 0.36 2 -10000 0 2
STAT5A 0.029 0.004 -10000 0 -10000 0 0
CD247 -0.005 0.043 -10000 0 -0.39 2 2
IL2 0.019 0.007 -10000 0 -10000 0 0
SPHK2 0.029 0.005 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.001 0.051 0.28 1 -10000 0 1
IL12/IL12R/TYK2/JAK2 -0.19 0.48 1.5 1 -1.3 38 39
MAP2K3 -0.26 0.49 0.9 1 -0.97 94 95
RIPK2 0.023 0.013 -10000 0 -10000 0 0
MAP2K6 -0.25 0.48 0.9 1 -0.96 85 86
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.01 0.012 -10000 0 -0.028 71 71
IL18RAP -0.006 0.1 -10000 0 -0.38 22 22
IL12Rbeta1/TYK2 -0.002 0.088 0.34 1 -0.31 12 13
EOMES -0.12 0.38 -10000 0 -1.2 42 42
STAT1 (dimer) -0.14 0.34 0.96 1 -0.77 50 51
T cell proliferation -0.13 0.31 0.74 1 -0.64 55 56
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.042 0.15 -10000 0 -0.38 56 56
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.19 0.32 0.35 1 -0.64 100 101
ATF2 -0.24 0.43 0.82 1 -0.88 86 87
Neurotrophic factor-mediated Trk receptor 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
CRKL 0.029 0.005 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.07 0.1 -10000 0 -0.26 40 40
NT3 (dimer)/TRKC -0.11 0.16 -10000 0 -0.27 177 177
NT3 (dimer)/TRKB -0.19 0.23 -10000 0 -0.37 212 212
SHC/Grb2/SOS1/GAB1/PI3K 0.013 0.031 -10000 0 -0.23 2 2
RAPGEF1 0.029 0.004 -10000 0 -10000 0 0
BDNF 0.028 0.006 -10000 0 -10000 0 0
PIK3CA 0.028 0.021 -10000 0 -0.37 1 1
DYNLT1 0.027 0.009 -10000 0 -10000 0 0
NTRK1 0.02 0.012 -10000 0 -10000 0 0
NTRK2 -0.06 0.16 -10000 0 -0.37 80 80
NTRK3 0.008 0.084 -10000 0 -0.37 17 17
NT-4/5 (dimer)/TRKB -0.097 0.18 -10000 0 -0.29 156 156
neuron apoptosis 0.073 0.18 0.37 71 -0.35 1 72
SHC 2-3/Grb2 -0.079 0.19 0.36 1 -0.4 71 72
SHC1 0.022 0.013 -10000 0 -10000 0 0
SHC2 -0.1 0.2 -10000 0 -0.43 79 79
SHC3 -0.086 0.18 -10000 0 -0.41 65 65
STAT3 (dimer) 0.022 0.065 -10000 0 -0.31 13 13
NT3 (dimer)/TRKA -0.13 0.18 -10000 0 -0.3 182 182
RIN/GDP -0.026 0.099 0.21 5 -0.22 13 18
GIPC1 0.029 0.004 -10000 0 -10000 0 0
KRAS 0.029 0.005 -10000 0 -10000 0 0
DNAJA3 -0.087 0.14 0.22 2 -0.28 108 110
RIN/GTP 0.014 0.004 -10000 0 -10000 0 0
CCND1 -0.034 0.11 -10000 0 -0.64 12 12
MAGED1 0.026 0.036 -10000 0 -0.37 3 3
PTPN11 0.029 0.003 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.019 0.006 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.043 0.027 -10000 0 -10000 0 0
GRB2 0.028 0.006 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.032 0.056 -10000 0 -0.22 13 13
TRKA/NEDD4-2 0.03 0.019 -10000 0 -10000 0 0
ELMO1 0.028 0.021 -10000 0 -0.37 1 1
RhoG/GTP/ELMO1/DOCK1 0.031 0.043 -10000 0 -0.24 8 8
NGF 0.01 0.084 -10000 0 -0.37 17 17
HRAS 0.029 0.004 -10000 0 -10000 0 0
DOCK1 0.019 0.059 -10000 0 -0.37 8 8
GAB2 0.029 0.005 -10000 0 -10000 0 0
RIT2 0.019 0.005 -10000 0 -10000 0 0
RIT1 0.022 0.013 -10000 0 -10000 0 0
FRS2 0.029 0.004 -10000 0 -10000 0 0
DNM1 0.021 0.051 -10000 0 -0.37 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.025 0.011 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.066 0.15 0.25 1 -0.28 109 110
mol:GDP -0.044 0.13 0.26 3 -0.3 22 25
NGF (dimer) 0.01 0.084 -10000 0 -0.37 17 17
RhoG/GDP 0.021 0.015 -10000 0 -0.26 1 1
RIT1/GDP -0.035 0.081 0.21 1 -0.22 13 14
TIAM1 0.008 0.089 -10000 0 -0.37 19 19
PIK3R1 0.027 0.03 -10000 0 -0.37 2 2
BDNF (dimer)/TRKB -0.008 0.12 -10000 0 -0.23 79 79
KIDINS220/CRKL/C3G 0.042 0.009 -10000 0 -10000 0 0
SHC/RasGAP 0.032 0.025 -10000 0 -0.26 1 1
FRS2 family/SHP2 0.054 0.019 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.052 0.036 -10000 0 -10000 0 0
RIT1/GTP 0.017 0.01 -10000 0 -10000 0 0
NT3 (dimer) -0.16 0.2 -10000 0 -0.37 168 168
RAP1/GDP -0.024 0.086 0.16 7 -0.18 20 27
KIDINS220/CRKL 0.029 0.005 -10000 0 -10000 0 0
BDNF (dimer) 0.028 0.006 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.032 0.054 -10000 0 -0.22 12 12
Schwann cell development -0.037 0.03 -10000 0 -10000 0 0
EHD4 0.029 0.003 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.066 0.026 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.005 0.054 -10000 0 -0.21 10 10
RAP1B 0.029 0.004 -10000 0 -10000 0 0
RAP1A 0.029 0.006 -10000 0 -10000 0 0
CDC42/GTP -0.1 0.15 -10000 0 -0.24 179 179
ABL1 0.029 0.004 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.042 0.009 -10000 0 -10000 0 0
Rap1/GTP -0.006 0.088 -10000 0 -0.32 10 10
STAT3 0.022 0.065 -10000 0 -0.31 13 13
axon guidance -0.11 0.14 -10000 0 -0.23 177 177
MAPK3 0.015 0.095 0.18 74 -0.21 12 86
MAPK1 0.015 0.094 0.18 78 -0.21 11 89
CDC42/GDP -0.024 0.1 0.21 6 -0.22 13 19
NTF3 -0.16 0.2 -10000 0 -0.37 168 168
NTF4 0.019 0.006 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.034 0.053 -10000 0 -0.23 11 11
PI3K 0.041 0.032 -10000 0 -0.37 2 2
FRS3 0.027 0.008 -10000 0 -10000 0 0
FAIM 0.03 0.002 -10000 0 -10000 0 0
GAB1 0.028 0.008 -10000 0 -10000 0 0
RASGRF1 -0.068 0.15 0.22 2 -0.28 95 97
SOS1 0.03 0.002 -10000 0 -10000 0 0
MCF2L -0.11 0.11 0.17 2 -0.23 163 165
RGS19 0.029 0.005 -10000 0 -10000 0 0
CDC42 0.028 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.026 0.092 0.3 1 -0.38 4 5
Rac1/GDP -0.024 0.1 0.21 7 -0.22 14 21
NGF (dimer)/TRKA/GRIT 0.02 0.047 -10000 0 -0.22 12 12
neuron projection morphogenesis -0.08 0.18 -10000 0 -0.62 13 13
NGF (dimer)/TRKA/NEDD4-2 0.033 0.054 -10000 0 -0.22 12 12
MAP2K1 0.032 0.099 0.18 102 -10000 0 102
NGFR -0.12 0.19 -10000 0 -0.37 136 136
NGF (dimer)/TRKA/GIPC/GAIP 0.004 0.063 0.23 1 -0.23 15 16
RAS family/GTP/PI3K 0.015 0.03 -10000 0 -0.21 3 3
FRS2 family/SHP2/GRB2/SOS1 0.077 0.031 -10000 0 -10000 0 0
NRAS 0.029 0.005 -10000 0 -10000 0 0
GRB2/SOS1 0.042 0.009 -10000 0 -10000 0 0
PRKCI 0.03 0.003 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.029 0.004 -10000 0 -10000 0 0
PRKCZ 0.014 0.071 -10000 0 -0.37 12 12
MAPKKK cascade -0.03 0.16 -10000 0 -0.57 25 25
RASA1 0.027 0.03 -10000 0 -0.37 2 2
TRKA/c-Abl 0.031 0.019 -10000 0 -10000 0 0
SQSTM1 0.028 0.007 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.01 0.12 -10000 0 -0.21 79 79
NGF (dimer)/TRKA/p62/Atypical PKCs 0.042 0.071 -10000 0 -0.2 18 18
MATK 0.027 0.03 -10000 0 -0.37 2 2
NEDD4L 0.029 0.006 -10000 0 -10000 0 0
RAS family/GDP -0.045 0.057 -10000 0 -0.15 35 35
NGF (dimer)/TRKA -0.092 0.14 0.19 1 -0.27 135 136
Rac1/GTP -0.088 0.11 -10000 0 -0.23 121 121
FRS2 family/SHP2/CRK family 0.067 0.039 -10000 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.036 0.11 0.19 81 -10000 0 81
GNAI2 0.029 0.003 -10000 0 -10000 0 0
S1P/S1P5/G12 0.035 0.031 -10000 0 -0.22 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.14 0.2 -10000 0 -0.37 153 153
RhoA/GTP -0.036 0.11 -10000 0 -0.19 81 81
negative regulation of cAMP metabolic process -0.04 0.12 0.19 1 -0.2 82 83
GNAZ 0.014 0.025 -10000 0 -0.37 1 1
GNAI3 0.029 0.006 -10000 0 -10000 0 0
GNA12 0.029 0.005 -10000 0 -10000 0 0
S1PR5 0.024 0.047 -10000 0 -0.37 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.041 0.12 0.19 1 -0.21 82 83
RhoA/GDP 0.022 0.003 -10000 0 -10000 0 0
RHOA 0.029 0.004 -10000 0 -10000 0 0
GNAI1 0.027 0.03 -10000 0 -0.37 2 2
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 -0.14 0.2 -10000 0 -0.37 153 153
CDC42/GTP -0.034 0.11 -10000 0 -0.19 72 72
PLCG1 -0.043 0.1 0.17 1 -0.2 77 78
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.029 0.003 -10000 0 -10000 0 0
GNAI3 0.029 0.006 -10000 0 -10000 0 0
G12/G13 0.042 0.01 -10000 0 -10000 0 0
cell migration -0.034 0.11 -10000 0 -0.19 72 72
S1PR5 0.024 0.047 -10000 0 -0.37 5 5
S1PR4 0.029 0.005 -10000 0 -10000 0 0
MAPK3 -0.041 0.1 0.17 1 -0.2 74 75
MAPK1 -0.041 0.1 0.17 1 -0.2 74 75
S1P/S1P5/Gi -0.041 0.12 0.19 1 -0.21 82 83
GNAI1 0.027 0.03 -10000 0 -0.37 2 2
CDC42/GDP 0.021 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 0.035 0.031 -10000 0 -0.22 5 5
RHOA -0.012 0.048 0.18 19 -10000 0 19
S1P/S1P4/Gi -0.038 0.11 0.19 1 -0.2 80 81
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.014 0.025 -10000 0 -0.37 1 1
S1P/S1P4/G12/G13 0.053 0.016 -10000 0 -10000 0 0
GNA12 0.029 0.005 -10000 0 -10000 0 0
GNA13 0.029 0.005 -10000 0 -10000 0 0
CDC42 0.028 0.007 -10000 0 -10000 0 0
Aurora B 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
Condensin I complex 0.13 0.13 0.27 159 -0.16 1 160
STMN1 0.083 0.12 0.22 149 -10000 0 149
Aurora B/RasGAP/Survivin 0.018 0.028 -10000 0 -10000 0 0
Chromosomal passenger complex/Cul3 protein complex 0.1 0.12 0.24 144 -0.23 1 145
BIRC5 0.011 0.016 -10000 0 -10000 0 0
DES -0.052 0.18 -10000 0 -0.55 38 38
Aurora C/Aurora B/INCENP 0.024 0.032 0.17 2 -10000 0 2
Aurora B/TACC1 0.013 0.019 -10000 0 -10000 0 0
Aurora B/PP2A 0.015 0.021 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.024 0.033 -10000 0 -10000 0 0
mitotic metaphase/anaphase transition -0.007 0.008 -10000 0 -10000 0 0
NDC80 0.2 0.21 0.38 198 -10000 0 198
Cul3 protein complex 0.05 0.044 -10000 0 -0.22 8 8
KIF2C 0.047 0.086 0.23 60 -10000 0 60
PEBP1 0.036 0.048 -10000 0 -0.36 5 5
KIF20A 0.008 0.014 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.016 0.021 -10000 0 -10000 0 0
SEPT1 0.029 0.005 -10000 0 -10000 0 0
SMC2 0.029 0.004 -10000 0 -10000 0 0
SMC4 0.029 0.003 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.059 0.16 0.28 69 -0.4 24 93
PSMA3 0.029 0.006 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.002 0.007 -10000 0 -10000 0 0
H3F3B 0.062 0.066 0.14 149 -10000 0 149
AURKB 0.009 0.016 -10000 0 -10000 0 0
AURKC 0.029 0.005 -10000 0 -10000 0 0
CDCA8 0.018 0.019 -10000 0 -10000 0 0
cytokinesis 0.026 0.061 0.24 18 -10000 0 18
Aurora B/Septin1 0.041 0.079 0.29 14 -10000 0 14
AURKA 0.018 0.017 -10000 0 -10000 0 0
INCENP 0.047 0.017 -10000 0 -10000 0 0
KLHL13 0.021 0.059 -10000 0 -0.37 8 8
BUB1 0.008 0.014 -10000 0 -10000 0 0
hSgo1/Aurora B/Survivin 0.017 0.028 -10000 0 -10000 0 0
EVI5 0.037 0.011 -10000 0 -10000 0 0
RhoA/GTP 0.064 0.087 0.26 39 -10000 0 39
SGOL1 0.018 0.015 -10000 0 -10000 0 0
CENPA 0.17 0.19 0.37 152 -10000 0 152
NCAPG 0.01 0.014 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.016 0.021 -10000 0 -10000 0 0
NCAPD2 0.028 0.007 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.017 0.022 -10000 0 -10000 0 0
RHOA 0.029 0.004 -10000 0 -10000 0 0
NCAPH 0.015 0.015 -10000 0 -10000 0 0
NPM1 0.01 0.069 -10000 0 -0.26 11 11
RASA1 0.027 0.03 -10000 0 -0.37 2 2
KLHL9 0.028 0.007 -10000 0 -10000 0 0
mitotic prometaphase 0.011 0.009 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.021 -10000 0 -10000 0 0
PPP1CC 0.029 0.004 -10000 0 -10000 0 0
Centraspindlin 0.068 0.097 0.28 47 -10000 0 47
RhoA/GDP 0.022 0.003 -10000 0 -10000 0 0
NSUN2 0.008 0.081 -10000 0 -0.3 12 12
MYLK 0.062 0.066 0.14 148 -10000 0 148
KIF23 0.018 0.018 -10000 0 -10000 0 0
VIM 0.076 0.1 0.19 155 -10000 0 155
RACGAP1 0.035 0.017 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.009 0.07 -10000 0 -0.26 11 11
Chromosomal passenger complex 0.2 0.2 0.41 166 -10000 0 166
Chromosomal passenger complex/EVI5 0.034 0.053 -10000 0 -10000 0 0
TACC1 0.024 0.011 -10000 0 -10000 0 0
PPP2R5D 0.027 0.009 -10000 0 -10000 0 0
CUL3 0.029 0.003 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
BCR signaling pathway

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
JUN -0.025 0.13 0.28 6 -0.33 25 31
IKBKB -0.029 0.11 0.3 4 -0.29 27 31
AKT1 -0.017 0.097 0.28 11 -0.21 12 23
IKBKG 0.002 0.073 0.26 4 -0.29 3 7
CALM1 -0.019 0.095 -10000 0 -0.32 12 12
PIK3CA 0.028 0.021 -10000 0 -0.37 1 1
MAP3K1 -0.033 0.17 0.31 8 -0.4 34 42
MAP3K7 0.028 0.008 -10000 0 -10000 0 0
mol:Ca2+ -0.018 0.1 -10000 0 -0.33 13 13
DOK1 0.03 0.002 -10000 0 -10000 0 0
AP-1 -0.052 0.089 0.26 1 -0.23 21 22
LYN 0.025 0.011 -10000 0 -10000 0 0
BLNK 0.019 0.062 -10000 0 -0.37 9 9
SHC1 0.022 0.013 -10000 0 -10000 0 0
BCR complex -0.025 0.12 -10000 0 -0.26 77 77
CD22 -0.062 0.14 0.38 3 -0.31 63 66
CAMK2G -0.021 0.091 -10000 0 -0.31 11 11
CSNK2A1 0.029 0.005 -10000 0 -10000 0 0
INPP5D 0.029 0.003 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.045 0.07 -10000 0 -0.2 52 52
GO:0007205 -0.019 0.1 -10000 0 -0.34 13 13
SYK 0.026 0.036 -10000 0 -0.37 3 3
ELK1 -0.024 0.098 -10000 0 -0.33 12 12
NFATC1 -0.011 0.13 0.26 11 -0.36 14 25
B-cell antigen/BCR complex -0.025 0.12 -10000 0 -0.26 77 77
PAG1/CSK 0.031 0.029 -10000 0 -0.26 2 2
NFKBIB 0.001 0.056 0.16 3 -0.12 35 38
HRAS -0.008 0.098 0.24 3 -0.29 14 17
NFKBIA 0.001 0.055 0.16 3 -0.12 36 39
NF-kappa-B/RelA/I kappa B beta 0.007 0.048 0.15 5 -0.095 1 6
RasGAP/Csk -0.063 0.15 -10000 0 -0.24 140 140
mol:GDP -0.015 0.1 -10000 0 -0.33 13 13
PTEN 0.028 0.007 -10000 0 -10000 0 0
CD79B 0.029 0.006 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha 0.007 0.047 0.15 5 -0.094 3 8
GRB2 0.028 0.006 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.035 0.17 0.37 4 -0.41 19 23
PIK3R1 0.027 0.03 -10000 0 -0.37 2 2
mol:IP3 -0.017 0.1 -10000 0 -0.34 13 13
CSK 0.029 0.005 -10000 0 -10000 0 0
FOS -0.092 0.13 -10000 0 -0.33 45 45
CHUK -0.005 0.088 0.26 4 -0.29 14 18
IBTK 0.028 0.007 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.001 0.12 0.3 3 -0.32 16 19
PTPN6 -0.053 0.14 0.36 3 -0.32 50 53
RELA 0.029 0.005 -10000 0 -10000 0 0
BCL2A1 0.002 0.038 0.12 2 -0.1 7 9
VAV2 -0.033 0.14 0.29 12 -0.41 16 28
ubiquitin-dependent protein catabolic process 0.003 0.056 0.16 3 -0.12 39 42
BTK 0.006 0.16 -10000 0 -1 8 8
CD19 -0.046 0.13 0.31 8 -0.28 55 63
MAP4K1 0.021 0.055 -10000 0 -0.37 7 7
CD72 0.024 0.042 -10000 0 -0.37 4 4
PAG1 0.02 0.032 -10000 0 -0.37 2 2
MAPK14 -0.019 0.15 0.3 14 -0.34 27 41
SH3BP5 0.027 0.03 -10000 0 -0.37 2 2
PIK3AP1 -0.012 0.099 0.25 1 -0.35 10 11
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.044 0.17 0.25 3 -0.47 25 28
RAF1 -0.011 0.094 0.25 2 -0.28 11 13
RasGAP/p62DOK/SHIP -0.061 0.15 -10000 0 -0.24 140 140
CD79A -0.062 0.17 -10000 0 -0.37 82 82
re-entry into mitotic cell cycle -0.051 0.088 0.26 1 -0.23 19 20
RASA1 0.027 0.03 -10000 0 -0.37 2 2
MAPK3 -0.016 0.083 0.22 1 -0.27 6 7
MAPK1 -0.016 0.083 -10000 0 -0.27 7 7
CD72/SHP1 -0.041 0.15 0.25 13 -0.33 45 58
NFKB1 0.027 0.009 -10000 0 -10000 0 0
MAPK8 -0.038 0.15 0.3 6 -0.35 34 40
actin cytoskeleton organization -0.018 0.15 0.31 12 -0.36 16 28
NF-kappa-B/RelA 0.015 0.094 0.29 3 -0.19 36 39
Calcineurin 0 0.097 -10000 0 -0.29 11 11
PI3K -0.061 0.11 -10000 0 -0.28 55 55
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.005 0.098 -10000 0 -0.34 10 10
SOS1 0.03 0.002 -10000 0 -10000 0 0
Bam32/HPK1 -0.086 0.26 -10000 0 -0.73 41 41
DAPP1 -0.1 0.28 -10000 0 -0.82 40 40
cytokine secretion -0.009 0.13 0.25 12 -0.33 14 26
mol:DAG -0.017 0.1 -10000 0 -0.34 13 13
PLCG2 0.02 0.051 -10000 0 -0.37 6 6
MAP2K1 -0.014 0.09 0.23 2 -0.27 10 12
B-cell antigen/BCR complex/FcgammaRIIB -0.084 0.16 -10000 0 -0.27 140 140
mol:PI-3-4-5-P3 -0.027 0.11 0.23 18 -0.25 19 37
ETS1 -0.025 0.085 -10000 0 -0.3 9 9
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.009 0.12 -10000 0 -0.2 74 74
B-cell antigen/BCR complex/LYN -0.053 0.12 0.24 1 -0.28 61 62
MALT1 0.029 0.006 -10000 0 -10000 0 0
TRAF6 0.029 0.021 -10000 0 -0.37 1 1
RAC1 -0.027 0.14 0.31 11 -0.38 16 27
B-cell antigen/BCR complex/LYN/SYK -0.053 0.13 0.27 1 -0.31 56 57
CARD11 -0.023 0.11 0.32 3 -0.35 17 20
FCGR2B -0.11 0.18 -10000 0 -0.37 124 124
PPP3CA 0.027 0.008 -10000 0 -10000 0 0
BCL10 0.029 0.006 -10000 0 -10000 0 0
IKK complex 0.001 0.048 0.19 6 -0.12 5 11
PTPRC 0.001 0.09 -10000 0 -0.37 20 20
PDPK1 -0.018 0.09 0.21 20 -0.19 14 34
PPP3CB 0.029 0.005 -10000 0 -10000 0 0
PPP3CC 0.023 0.013 -10000 0 -10000 0 0
POU2F2 0.004 0.038 0.16 3 -0.099 7 10
Thromboxane A2 receptor signaling

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
TGM2 0.023 0.046 -10000 0 -0.37 4 4
GNB1/GNG2 -0.058 0.086 -10000 0 -0.19 87 87
AKT1 -0.048 0.14 0.43 6 -0.37 10 16
EGF 0.017 0.012 -10000 0 -10000 0 0
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.038 0.076 -10000 0 -0.33 6 6
mol:Ca2+ -0.064 0.17 0.51 6 -0.38 12 18
LYN -0.033 0.071 -10000 0 -0.34 5 5
RhoA/GTP -0.026 0.077 0.27 5 -0.14 30 35
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.082 0.18 0.52 6 -0.36 35 41
GNG2 0.026 0.033 -10000 0 -0.37 2 2
ARRB2 0.025 0.011 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.034 0.12 -10000 0 -0.39 19 19
G beta5/gamma2 -0.073 0.12 -10000 0 -0.25 85 85
PRKCH -0.08 0.19 0.52 6 -0.38 34 40
DNM1 0.02 0.056 -10000 0 -0.37 6 6
TXA2/TP beta/beta Arrestin3 0.007 0.034 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR 0.01 0.084 -10000 0 -0.37 14 14
G12 family/GTP -0.072 0.15 -10000 0 -0.3 86 86
ADRBK1 0.029 0.005 -10000 0 -10000 0 0
ADRBK2 0.027 0.024 -10000 0 -0.37 1 1
RhoA/GTP/ROCK1 0.039 0.006 -10000 0 -10000 0 0
mol:GDP 0.044 0.14 0.38 17 -0.37 6 23
mol:NADP 0.026 0.033 -10000 0 -0.37 2 2
RAB11A 0.029 0.004 -10000 0 -10000 0 0
PRKG1 0.01 0.084 -10000 0 -0.37 14 14
mol:IP3 -0.085 0.2 0.54 6 -0.42 34 40
cell morphogenesis 0.039 0.006 -10000 0 -10000 0 0
PLCB2 -0.12 0.27 0.57 6 -0.52 76 82
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.051 0.091 0.18 1 -0.31 16 17
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.043 0.082 0.18 1 -0.33 8 9
RHOA 0.029 0.003 -10000 0 -10000 0 0
PTGIR -0.003 0.11 -10000 0 -0.37 24 24
PRKCB1 -0.085 0.2 0.53 6 -0.41 33 39
GNAQ 0.029 0.004 -10000 0 -10000 0 0
mol:L-citrulline 0.026 0.033 -10000 0 -0.37 2 2
TXA2/TXA2-R family -0.13 0.27 0.58 6 -0.52 85 91
LCK -0.041 0.081 -10000 0 -0.34 7 7
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.01 0.087 -10000 0 -0.21 31 31
TXA2-R family/G12 family/GDP/G beta/gamma -0.017 0.12 -10000 0 -0.42 25 25
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.006 0.086 -10000 0 -0.22 27 27
MAPK14 -0.045 0.13 0.46 6 -0.27 2 8
TGM2/GTP -0.096 0.22 0.57 6 -0.46 35 41
MAPK11 -0.049 0.13 0.46 6 -0.27 4 10
ARHGEF1 -0.037 0.1 0.36 6 -10000 0 6
GNAI2 0.03 0.002 -10000 0 -10000 0 0
JNK cascade -0.089 0.2 0.55 6 -0.39 72 78
RAB11/GDP 0.028 0.01 -10000 0 -10000 0 0
ICAM1 -0.061 0.16 0.49 6 -0.31 1 7
cAMP biosynthetic process -0.081 0.19 0.5 6 -0.4 23 29
Gq family/GTP/EBP50 -0.02 0.077 -10000 0 -0.17 55 55
actin cytoskeleton reorganization 0.039 0.006 -10000 0 -10000 0 0
SRC -0.037 0.074 0.18 1 -0.34 5 6
GNB5 0.029 0.005 -10000 0 -10000 0 0
GNB1 0.027 0.008 -10000 0 -10000 0 0
EGF/EGFR -0.032 0.1 -10000 0 -0.26 24 24
VCAM1 -0.067 0.17 0.54 6 -0.38 17 23
TP beta/Gq family/GDP/G beta5/gamma2 -0.034 0.12 -10000 0 -0.39 19 19
platelet activation -0.063 0.17 0.55 6 -0.34 12 18
PGI2/IP -0.001 0.075 -10000 0 -0.26 24 24
PRKACA -0.012 0.078 -10000 0 -0.22 34 34
Gq family/GDP/G beta5/gamma2 -0.032 0.11 -10000 0 -0.32 25 25
TXA2/TP beta/beta Arrestin2 -0.017 0.09 -10000 0 -0.38 12 12
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.039 0.081 -10000 0 -0.22 46 46
mol:DAG -0.097 0.22 0.56 6 -0.43 72 78
EGFR 0.02 0.06 -10000 0 -0.37 7 7
TXA2/TP alpha -0.11 0.25 0.57 6 -0.52 43 49
Gq family/GTP -0.033 0.087 -10000 0 -0.2 61 61
YES1 -0.038 0.074 -10000 0 -0.34 5 5
GNAI2/GTP -0.019 0.084 -10000 0 -0.2 40 40
PGD2/DP 0.008 0.058 -10000 0 -0.26 14 14
SLC9A3R1 0.027 0.024 -10000 0 -0.37 1 1
FYN -0.036 0.073 -10000 0 -0.34 5 5
mol:NO 0.026 0.033 -10000 0 -0.37 2 2
GNA15 0.028 0.023 -10000 0 -0.37 1 1
PGK/cGMP 0.024 0.056 -10000 0 -0.22 15 15
RhoA/GDP 0.029 0.009 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.005 0.1 -10000 0 -0.22 36 36
NOS3 0.026 0.033 -10000 0 -0.37 2 2
RAC1 0.029 0.004 -10000 0 -10000 0 0
PRKCA -0.076 0.19 0.52 6 -0.38 30 36
PRKCB -0.089 0.2 0.52 6 -0.41 46 52
PRKCE -0.08 0.19 0.52 6 -0.39 34 40
PRKCD -0.089 0.2 0.54 6 -0.39 80 86
PRKCG -0.088 0.21 0.54 6 -0.39 66 72
muscle contraction -0.12 0.25 0.57 6 -0.48 86 92
PRKCZ -0.084 0.18 0.52 6 -0.38 33 39
ARR3 0.02 0.005 -10000 0 -10000 0 0
TXA2/TP beta -0.005 0.094 -10000 0 -0.22 39 39
PRKCQ -0.083 0.2 0.52 6 -0.39 40 46
MAPKKK cascade -0.11 0.24 0.55 6 -0.46 77 83
SELE -0.085 0.19 0.52 6 -0.38 75 81
TP beta/GNAI2/GDP/G beta/gamma 0.008 0.099 -10000 0 -0.22 30 30
ROCK1 0.029 0.003 -10000 0 -10000 0 0
GNA14 -0.034 0.15 -10000 0 -0.37 48 48
chemotaxis -0.15 0.3 0.61 6 -0.6 84 90
GNA12 0.029 0.005 -10000 0 -10000 0 0
GNA13 0.029 0.005 -10000 0 -10000 0 0
GNA11 0.019 0.064 -10000 0 -0.37 8 8
Rac1/GTP 0.021 0.004 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.05 0.19 0.29 60 -0.43 31 91
FYN -0.004 0.22 0.37 8 -0.56 35 43
LAT/GRAP2/SLP76 0.009 0.18 0.36 4 -0.48 33 37
IKBKB 0.026 0.01 -10000 0 -10000 0 0
AKT1 -0.003 0.15 0.41 5 -0.42 30 35
B2M 0.029 0.011 -10000 0 -10000 0 0
IKBKG -0.003 0.049 0.13 9 -0.13 23 32
MAP3K8 0.027 0.03 -10000 0 -0.37 2 2
mol:Ca2+ -0.026 0.022 0.072 3 -0.06 67 70
integrin-mediated signaling pathway 0.028 0.028 -10000 0 -0.22 3 3
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.012 0.21 0.46 5 -0.58 32 37
TRPV6 -0.081 0.25 0.84 14 -10000 0 14
CD28 0.029 0.021 -10000 0 -0.37 1 1
SHC1 0.028 0.22 0.3 67 -0.53 32 99
receptor internalization -0.007 0.2 0.38 6 -0.51 37 43
PRF1 -0.022 0.25 0.49 1 -0.88 22 23
KRAS 0.029 0.005 -10000 0 -10000 0 0
GRB2 0.028 0.006 -10000 0 -10000 0 0
COT/AKT1 0.012 0.13 0.38 5 -0.33 30 35
LAT -0.01 0.2 0.46 5 -0.54 35 40
EntrezGene:6955 0 0.002 -10000 0 -10000 0 0
CD3D 0.017 0.064 -10000 0 -0.38 9 9
CD3E 0.016 0.074 -10000 0 -0.38 12 12
CD3G 0.016 0.063 -10000 0 -0.37 9 9
RASGRP2 0.008 0.037 0.15 4 -0.17 8 12
RASGRP1 -0.002 0.16 0.47 5 -0.44 28 33
HLA-A 0.001 0.004 -10000 0 -10000 0 0
RASSF5 0.02 0.038 -10000 0 -0.37 3 3
RAP1A/GTP/RAPL 0.029 0.028 -10000 0 -0.22 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.039 0.077 0.2 26 -0.13 11 37
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.015 0.066 -10000 0 -0.2 35 35
PRKCA 0 0.096 0.24 12 -0.24 28 40
GRAP2 0.02 0.059 -10000 0 -0.37 8 8
mol:IP3 0.028 0.16 0.2 84 -0.37 32 116
EntrezGene:6957 0 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.008 0.16 0.35 3 -0.49 28 31
ORAI1 0.028 0.18 -10000 0 -0.7 14 14
CSK -0.007 0.2 0.35 8 -0.54 35 43
B7 family/CD28 0.02 0.2 0.33 3 -0.54 31 34
CHUK 0.029 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.014 0.23 0.31 7 -0.59 37 44
PTPN6 -0.014 0.2 0.33 8 -0.53 36 44
VAV1 -0.017 0.21 0.41 5 -0.56 37 42
Monovalent TCR/CD3 -0.001 0.086 -10000 0 -0.34 18 18
CBL 0.028 0.006 -10000 0 -10000 0 0
LCK -0.009 0.23 0.36 8 -0.6 35 43
PAG1 0.012 0.22 0.3 27 -0.54 35 62
RAP1A 0.029 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.015 0.22 0.29 7 -0.58 37 44
CD80 0.014 0.077 -10000 0 -0.37 14 14
CD86 0.019 0.066 -10000 0 -0.37 10 10
PDK1/CARD11/BCL10/MALT1 -0.002 0.086 -10000 0 -0.23 35 35
HRAS 0.029 0.004 -10000 0 -10000 0 0
GO:0035030 -0.013 0.16 0.26 5 -0.45 31 36
CD8A 0.005 0.097 -10000 0 -0.38 22 22
CD8B 0.009 0.089 -10000 0 -0.38 18 18
PTPRC 0.001 0.091 -10000 0 -0.37 20 20
PDK1/PKC theta -0.011 0.18 0.5 4 -0.49 32 36
CSK/PAG1 0.013 0.21 0.3 25 -0.54 33 58
SOS1 0.03 0.002 -10000 0 -10000 0 0
peptide-MHC class I 0.021 0.013 -10000 0 -10000 0 0
GRAP2/SLP76 0.011 0.2 0.32 6 -0.54 34 40
STIM1 0.022 0.12 1.1 3 -10000 0 3
RAS family/GTP 0.035 0.089 0.24 15 -0.18 21 36
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.011 0.21 0.33 5 -0.55 37 42
mol:DAG -0.013 0.12 0.1 20 -0.32 35 55
RAP1A/GDP 0.021 0.038 0.11 16 -0.066 7 23
PLCG1 0.029 0.004 -10000 0 -10000 0 0
CD247 0.02 0.033 -10000 0 -0.38 2 2
cytotoxic T cell degranulation -0.019 0.24 0.49 1 -0.83 22 23
RAP1A/GTP 0.002 0.012 -10000 0 -0.064 8 8
mol:PI-3-4-5-P3 -0.003 0.17 0.44 5 -0.47 32 37
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.033 0.19 0.25 39 -0.47 33 72
NRAS 0.029 0.005 -10000 0 -10000 0 0
ZAP70 0.025 0.042 -10000 0 -0.37 4 4
GRB2/SOS1 0.042 0.009 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.004 0.17 0.34 3 -0.47 34 37
MALT1 0.029 0.006 -10000 0 -10000 0 0
TRAF6 0.029 0.021 -10000 0 -0.37 1 1
CD8 heterodimer 0.012 0.11 -10000 0 -0.33 32 32
CARD11 0.018 0.065 -10000 0 -0.37 10 10
PRKCB -0.009 0.11 0.24 12 -0.27 37 49
PRKCE -0.002 0.099 0.24 12 -0.25 29 41
PRKCQ -0.014 0.2 0.47 5 -0.55 33 38
LCP2 0.022 0.051 -10000 0 -0.37 6 6
BCL10 0.029 0.006 -10000 0 -10000 0 0
regulation of survival gene product expression 0.001 0.13 0.4 5 -0.35 30 35
IKK complex 0.005 0.061 0.23 7 -0.12 19 26
RAS family/GDP 0 0.011 -10000 0 -0.04 9 9
MAP3K14 0.005 0.1 0.33 5 -0.25 28 33
PDPK1 -0.001 0.14 0.38 6 -0.38 30 36
TCR/CD3/MHC I/CD8/Fyn -0.026 0.24 0.26 1 -0.67 35 36
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.13 0.21 -9999 0 -0.51 43 43
MAP3K8 0.007 0.038 -9999 0 -0.37 2 2
FOS -0.073 0.15 -9999 0 -0.42 36 36
PRKCA 0.002 0.029 -9999 0 -10000 0 0
PTPN7 -0.004 0.04 -9999 0 -0.37 2 2
HRAS 0.028 0.004 -9999 0 -10000 0 0
PRKCB -0.029 0.11 -9999 0 -0.38 30 30
NRAS 0.028 0.005 -9999 0 -10000 0 0
RAS family/GTP 0.018 0.044 -9999 0 -10000 0 0
MAPK3 -0.038 0.14 -9999 0 -0.61 15 15
MAP2K1 -0.054 0.12 -9999 0 -0.38 40 40
ELK1 -0.004 0.036 -9999 0 -10000 0 0
BRAF -0.033 0.1 -9999 0 -0.34 33 33
mol:GTP -0.002 0.002 -9999 0 -0.005 168 168
MAPK1 -0.032 0.11 -9999 0 -0.53 12 12
RAF1 -0.036 0.11 -9999 0 -0.34 35 35
KRAS 0.028 0.005 -9999 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.028 0.007 -10000 0 -10000 0 0
VLDLR -0.004 0.1 -10000 0 -0.37 26 26
LRPAP1 0.029 0.006 -10000 0 -10000 0 0
NUDC 0.028 0.007 -10000 0 -10000 0 0
RELN/LRP8 -0.034 0.12 -10000 0 -0.22 104 104
CaM/Ca2+ 0.021 0.005 -10000 0 -10000 0 0
KATNA1 0.027 0.009 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.062 0.1 0.16 29 -0.21 104 133
IQGAP1/CaM 0.041 0.012 -10000 0 -10000 0 0
DAB1 -0.03 0.14 -10000 0 -0.37 52 52
IQGAP1 0.029 0.005 -10000 0 -10000 0 0
PLA2G7 0.025 0.023 -10000 0 -0.37 1 1
CALM1 0.028 0.007 -10000 0 -10000 0 0
DYNLT1 0.027 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.037 0.017 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.029 0.004 -10000 0 -10000 0 0
CDK5R1 0.029 0.006 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A -0.012 0.005 -10000 0 -10000 0 0
CDK5R2 0.02 0.007 -10000 0 -10000 0 0
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.084 0.16 -10000 0 -0.26 148 148
YWHAE 0.025 0.011 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.049 0.1 0.3 6 -0.22 20 26
MAP1B 0.007 0.017 -10000 0 -10000 0 0
RAC1 0.009 0.004 -10000 0 -10000 0 0
p35/CDK5 -0.062 0.093 0.18 4 -10000 0 4
RELN -0.1 0.19 -10000 0 -0.37 120 120
PAFAH/LIS1 0.02 0.018 -10000 0 -0.23 1 1
LIS1/CLIP170 0.024 0.011 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.062 0.081 0.16 2 -0.21 11 13
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.091 0.16 0.22 1 -0.27 134 135
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.049 0.1 0.3 5 -0.24 22 27
LIS1/IQGAP1 0.024 0.011 -10000 0 -10000 0 0
RHOA 0.009 0.004 -10000 0 -10000 0 0
PAFAH1B1 -0.016 0.007 -10000 0 -10000 0 0
PAFAH1B3 0.025 0.023 -10000 0 -0.37 1 1
PAFAH1B2 0.027 0.022 -10000 0 -0.37 1 1
MAP1B/LIS1/Dynein heavy chain 0.016 0.032 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.049 0.11 0.3 6 -0.24 15 21
LRP8 0.026 0.01 -10000 0 -10000 0 0
NDEL1/Katanin 60 -0.054 0.1 0.3 5 -0.23 23 28
P39/CDK5 -0.064 0.091 0.17 4 -0.2 91 95
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.023 0.011 -10000 0 -10000 0 0
CDK5 -0.063 0.096 0.18 4 -0.2 92 96
PPP2R5D 0.027 0.009 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.021 0.009 -10000 0 -10000 0 0
CSNK2A1 0.029 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.061 0.15 -10000 0 -0.22 148 148
RELN/VLDLR -0.019 0.15 -10000 0 -0.23 107 107
CDC42 0.009 0.004 -10000 0 -10000 0 0
Nectin adhesion pathway

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
PDGFRB 0.028 0.006 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.019 0.082 -10000 0 -0.26 28 28
PTK2 -0.048 0.14 0.23 1 -0.39 37 38
positive regulation of JNK cascade -0.033 0.13 -10000 0 -0.29 48 48
CDC42/GDP -0.037 0.18 -10000 0 -0.39 47 47
Rac1/GDP -0.037 0.18 -10000 0 -0.39 48 48
RAP1B 0.029 0.004 -10000 0 -10000 0 0
RAP1A 0.029 0.006 -10000 0 -10000 0 0
CTNNB1 0.03 0.003 -10000 0 -10000 0 0
CDC42/GTP -0.038 0.16 -10000 0 -0.37 40 40
nectin-3/I-afadin 0 0.1 -10000 0 -0.26 46 46
RAPGEF1 -0.058 0.17 -10000 0 -0.39 68 68
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.062 0.19 -10000 0 -0.42 72 72
PDGFB-D/PDGFRB 0.028 0.006 -10000 0 -10000 0 0
TLN1 -0.031 0.052 -10000 0 -0.36 3 3
Rap1/GTP -0.038 0.13 -10000 0 -0.29 69 69
IQGAP1 0.029 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.049 0.02 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0 0.1 -10000 0 -0.26 46 46
PVR 0.029 0.004 -10000 0 -10000 0 0
Necl-5(dimer) 0.029 0.004 -10000 0 -10000 0 0
mol:GDP -0.061 0.2 -10000 0 -0.47 48 48
MLLT4 0.027 0.009 -10000 0 -10000 0 0
PIK3CA 0.028 0.021 -10000 0 -0.37 1 1
PI3K 0.039 0.1 -10000 0 -0.21 46 46
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.038 0.016 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly -0.033 0.14 -10000 0 -0.31 49 49
PVRL1 0.028 0.006 -10000 0 -10000 0 0
PVRL3 -0.021 0.13 -10000 0 -0.37 46 46
PVRL2 0.029 0.005 -10000 0 -10000 0 0
PIK3R1 0.027 0.03 -10000 0 -0.37 2 2
CDH1 0.003 0.095 -10000 0 -0.37 22 22
CLDN1 0.024 0.047 -10000 0 -0.37 5 5
JAM-A/CLDN1 0.02 0.089 -10000 0 -0.21 39 39
SRC -0.078 0.21 -10000 0 -0.46 73 73
ITGB3 -0.002 0.11 -10000 0 -0.37 28 28
nectin-1(dimer)/I-afadin/I-afadin 0.038 0.016 -10000 0 -10000 0 0
FARP2 -0.058 0.21 -10000 0 -0.49 41 41
RAC1 0.029 0.004 -10000 0 -10000 0 0
CTNNA1 0.029 0.005 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.016 0.094 -10000 0 -0.23 46 46
nectin-1/I-afadin 0.038 0.016 -10000 0 -10000 0 0
nectin-2/I-afadin 0.039 0.015 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.038 0.009 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.015 0.094 -10000 0 -0.23 46 46
CDC42/GTP/IQGAP1/filamentous actin 0.037 0.011 -10000 0 -10000 0 0
F11R 0.023 0.013 -10000 0 -10000 0 0
positive regulation of filopodium formation -0.033 0.13 -10000 0 -0.29 48 48
alphaV/beta3 Integrin/Talin -0.014 0.097 0.35 1 -0.27 28 29
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.039 0.015 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.039 0.015 -10000 0 -10000 0 0
PIP5K1C -0.024 0.056 -10000 0 -0.16 45 45
VAV2 -0.059 0.21 -10000 0 -0.5 38 38
RAP1/GDP -0.033 0.17 -10000 0 -0.36 52 52
ITGAV 0.029 0.003 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.016 0.094 -10000 0 -0.23 46 46
nectin-3(dimer)/I-afadin/I-afadin 0 0.1 -10000 0 -0.26 46 46
Rac1/GTP -0.039 0.17 -10000 0 -0.38 47 47
PTPRM -0.013 0.065 -10000 0 -0.17 46 46
E-cadherin/beta catenin/alpha catenin 0.053 0.074 -10000 0 -0.2 22 22
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.028 0.007 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.028 0.028 -10000 0 -0.13 7 7
SVIL 0.027 0.033 -10000 0 -0.16 7 7
ZNF318 0.024 0.033 0.2 6 -10000 0 6
JMJD2C 0.021 0.068 0.25 29 -10000 0 29
T-DHT/AR/Ubc9 -0.034 0.13 0.18 15 -0.23 97 112
CARM1 0.029 0.009 -10000 0 -10000 0 0
PRDX1 0.026 0.013 -10000 0 -10000 0 0
PELP1 0.023 0.016 -10000 0 -10000 0 0
CTNNB1 0.029 0.015 -10000 0 -10000 0 0
AKT1 0.024 0.019 -10000 0 -10000 0 0
PTK2B 0.023 0.015 -10000 0 -10000 0 0
MED1 0.027 0.017 -10000 0 -10000 0 0
MAK 0.023 0.033 0.19 6 -10000 0 6
response to oxidative stress 0 0.003 -10000 0 -10000 0 0
HIP1 0.022 0.053 -10000 0 -0.37 6 6
GSN 0.029 0.018 -10000 0 -10000 0 0
NCOA2 -0.014 0.11 -10000 0 -0.37 33 33
NCOA6 0.03 0.016 -10000 0 -10000 0 0
DNA-PK 0.044 0.041 0.21 5 -0.12 1 6
NCOA4 0.029 0.007 -10000 0 -10000 0 0
PIAS3 0.023 0.017 -10000 0 -10000 0 0
cell proliferation 0.001 0.033 0.21 1 -10000 0 1
XRCC5 0.026 0.017 -10000 0 -10000 0 0
UBE3A 0.029 0.022 -10000 0 -0.12 6 6
T-DHT/AR/SNURF -0.036 0.13 0.18 15 -0.24 97 112
FHL2 -0.083 0.26 -10000 0 -0.83 37 37
RANBP9 0.027 0.018 -10000 0 -0.085 5 5
JMJD1A -0.002 0.026 -10000 0 -0.12 17 17
CDK6 0.003 0.097 -10000 0 -0.37 23 23
TGFB1I1 0.029 0.018 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.038 0.13 0.2 16 -0.24 98 114
XRCC6 0.026 0.017 -10000 0 -10000 0 0
T-DHT/AR -0.03 0.16 0.32 18 -0.24 111 129
CTDSP1 0.029 0.01 -10000 0 -10000 0 0
CTDSP2 0.026 0.024 -10000 0 -10000 0 0
BRCA1 0.029 0.017 -10000 0 -10000 0 0
TCF4 0.025 0.021 -10000 0 -10000 0 0
CDKN2A 0.007 0.016 -10000 0 -10000 0 0
SRF 0.012 0.052 -10000 0 -0.15 32 32
NKX3-1 -0.039 0.072 -10000 0 -0.14 100 100
KLK3 -0.004 0.22 0.6 19 -1.3 6 25
TMF1 0.029 0.008 -10000 0 -10000 0 0
HNRNPA1 0.026 0.019 -10000 0 -10000 0 0
AOF2 0.001 0.012 0.064 1 -0.066 6 7
APPL1 -0.018 0.019 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.032 0.13 0.19 6 -0.23 96 102
AR -0.076 0.18 -10000 0 -0.38 93 93
UBA3 0.029 0.01 -10000 0 -10000 0 0
PATZ1 0.026 0.018 -10000 0 -10000 0 0
PAWR 0.029 0.008 -10000 0 -10000 0 0
PRKDC 0.022 0.019 -10000 0 -10000 0 0
PA2G4 0.026 0.02 -10000 0 -10000 0 0
UBE2I 0.028 0.007 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.027 0.11 0.18 7 -0.21 91 98
RPS6KA3 0.028 0.028 -10000 0 -0.37 1 1
T-DHT/AR/ARA70 -0.032 0.13 0.19 17 -0.23 97 114
LATS2 0.025 0.018 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.029 0.12 0.18 7 -0.21 96 103
Cyclin D3/CDK11 p58 0.019 0.009 -10000 0 -10000 0 0
VAV3 0.027 0.025 -10000 0 -0.37 1 1
KLK2 0.013 0.16 0.55 27 -0.38 1 28
CASP8 0.026 0.014 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.028 0.14 0.21 11 -0.25 85 96
TMPRSS2 -0.057 0.2 -10000 0 -0.84 20 20
CCND1 0.013 0.075 -10000 0 -0.37 13 13
PIAS1 0.029 0.022 -10000 0 -0.12 6 6
mol:T-DHT -0.001 0.029 0.081 20 -0.066 30 50
CDC2L1 0 0.002 -10000 0 -10000 0 0
PIAS4 0.029 0.032 -10000 0 -0.18 6 6
T-DHT/AR/CDK6 -0.046 0.14 0.18 7 -0.24 108 115
CMTM2 0.023 0.013 -10000 0 -10000 0 0
SNURF 0.019 0.055 -10000 0 -0.37 7 7
ZMIZ1 0.023 0.041 -10000 0 -0.12 2 2
CCND3 0.027 0.009 -10000 0 -10000 0 0
TGIF1 0.026 0.019 -10000 0 -10000 0 0
FKBP4 0.029 0.017 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 -0.017 0.04 -10000 0 -0.2 3 3
RFC1 -0.014 0.048 0.22 5 -0.2 4 9
PRKDC 0.007 0.083 0.22 39 -0.19 4 43
RIPK1 0.026 0.016 -10000 0 -10000 0 0
CASP7 -0.009 0.12 -10000 0 -0.67 11 11
FASLG/FAS/FADD/FAF1 0.02 0.074 0.18 34 -0.22 11 45
MAP2K4 -0.033 0.16 0.37 8 -0.38 48 56
mol:ceramide 0 0.1 0.34 8 -0.31 15 23
GSN -0.016 0.041 0.17 1 -0.2 4 5
FASLG/FAS/FADD/FAF1/Caspase 8 0.017 0.083 0.26 4 -0.27 11 15
FAS 0.01 0.071 -10000 0 -0.37 11 11
BID -0.02 0.027 0.24 3 -10000 0 3
MAP3K1 -0.025 0.13 0.27 7 -0.4 22 29
MAP3K7 0.023 0.017 -10000 0 -10000 0 0
RB1 -0.015 0.037 -10000 0 -0.2 3 3
CFLAR 0.029 0.013 -10000 0 -10000 0 0
HGF/MET -0.14 0.18 -10000 0 -0.28 204 204
ARHGDIB -0.016 0.039 -10000 0 -0.2 4 4
FADD 0.021 0.024 -10000 0 -10000 0 0
actin filament polymerization 0.016 0.041 0.2 4 -0.17 1 5
NFKB1 -0.048 0.21 0.39 6 -0.65 31 37
MAPK8 -0.065 0.21 0.44 8 -0.49 58 66
DFFA -0.016 0.042 0.22 1 -0.19 18 19
DNA fragmentation during apoptosis -0.016 0.042 0.22 1 -0.21 2 3
FAS/FADD/MET 0.038 0.058 -10000 0 -0.23 10 10
CFLAR/RIP1 0.039 0.023 -10000 0 -10000 0 0
FAIM3 0.019 0.038 -10000 0 -0.37 3 3
FAF1 0.022 0.026 -10000 0 -10000 0 0
PARP1 -0.018 0.043 -10000 0 -0.2 5 5
DFFB -0.016 0.042 0.22 1 -0.2 4 5
CHUK -0.052 0.19 0.32 6 -0.64 28 34
FASLG 0.008 0.063 -10000 0 -0.37 8 8
FAS/FADD 0.023 0.061 -10000 0 -0.27 11 11
HGF -0.18 0.2 -10000 0 -0.37 194 194
LMNA -0.007 0.049 0.2 2 -0.21 1 3
CASP6 -0.013 0.031 -10000 0 -0.21 2 2
CASP10 0.022 0.024 -10000 0 -10000 0 0
CASP3 -0.015 0.048 -10000 0 -0.21 21 21
PTPN13 -0.06 0.16 -10000 0 -0.37 79 79
CASP8 -0.018 0.033 0.31 3 -10000 0 3
IL6 -0.16 0.45 0.65 7 -1.1 62 69
MET 0.027 0.022 -10000 0 -0.37 1 1
ICAD/CAD -0.018 0.045 0.41 1 -0.21 1 2
FASLG/FAS/FADD/FAF1/Caspase 10 0 0.1 0.34 8 -0.32 15 23
activation of caspase activity by cytochrome c -0.02 0.027 0.24 3 -10000 0 3
PAK2 -0.017 0.048 0.22 3 -0.2 5 8
BCL2 0.028 0.022 -10000 0 -0.37 1 1
Regulation of Telomerase

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
Telomerase catalytic core complex 0.26 0.33 0.65 136 -0.53 3 139
RAD9A 0.029 0.005 -10000 0 -10000 0 0
AP1 -0.073 0.16 0.15 1 -0.25 161 162
IFNAR2 0.058 0.038 -10000 0 -10000 0 0
AKT1 -0.022 0.11 0.18 4 -0.32 14 18
ER alpha/Oestrogen -0.1 0.14 -10000 0 -0.24 178 178
NFX1/SIN3/HDAC complex 0.046 0.088 0.19 5 -0.3 10 15
EGF 0.024 0.02 -10000 0 -10000 0 0
SMG5 0.023 0.013 -10000 0 -10000 0 0
SMG6 0.025 0.011 -10000 0 -10000 0 0
SP3/HDAC2 0.085 0.06 0.16 89 -10000 0 89
TERT/c-Abl 0.16 0.25 0.53 99 -0.49 4 103
SAP18 0.033 0.01 -10000 0 -10000 0 0
MRN complex 0.042 0.028 -10000 0 -10000 0 0
WT1 0.057 0.047 0.23 11 -10000 0 11
WRN 0.023 0.012 -10000 0 -10000 0 0
SP1 0.071 0.051 0.15 4 -10000 0 4
SP3 0.043 0.018 -10000 0 -10000 0 0
TERF2IP 0.027 0.008 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.024 0.1 0.35 5 -0.46 4 9
Mad/Max 0.075 0.046 0.16 6 -10000 0 6
TERT 0.26 0.33 0.66 135 -0.54 3 138
CCND1 0.22 0.36 0.64 120 -0.77 14 134
MAX 0.042 0.021 -10000 0 -10000 0 0
RBBP7 0.035 0.008 -10000 0 -10000 0 0
RBBP4 0.033 0.01 -10000 0 -10000 0 0
TERF2 0.024 0.01 -10000 0 -10000 0 0
PTGES3 0.029 0.004 -10000 0 -10000 0 0
SIN3A 0.034 0.008 -10000 0 -10000 0 0
Telomerase/911 0.1 0.099 0.27 37 -10000 0 37
CDKN1B 0.026 0.06 0.22 15 -10000 0 15
RAD1 0.029 0.006 -10000 0 -10000 0 0
XRCC5 0.029 0.003 -10000 0 -10000 0 0
XRCC6 0.029 0.005 -10000 0 -10000 0 0
SAP30 0.032 0.012 -10000 0 -10000 0 0
TRF2/PARP2 0.038 0.014 -10000 0 -10000 0 0
UBE3A 0.042 0.017 -10000 0 -10000 0 0
JUN 0.032 0.053 -10000 0 -0.36 6 6
E6 0.013 0.016 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.052 0.037 0.1 77 -10000 0 77
FOS -0.14 0.2 -10000 0 -0.36 160 160
IFN-gamma/IRF1 0.08 0.051 0.23 9 -10000 0 9
PARP2 0.029 0.004 -10000 0 -10000 0 0
BLM 0.019 0.014 -10000 0 -10000 0 0
Telomerase 0.094 0.13 0.29 57 -0.39 3 60
IRF1 0.045 0.021 -10000 0 -10000 0 0
ESR1 -0.16 0.2 -10000 0 -0.36 178 178
KU/TER 0.043 0.008 -10000 0 -10000 0 0
ATM/TRF2 0.039 0.018 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.045 0.088 0.19 3 -0.26 12 15
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.045 0.089 0.19 3 -0.27 12 15
HDAC1 0.033 0.01 -10000 0 -10000 0 0
HDAC2 0.061 0.045 0.14 1 -10000 0 1
ATM 0.016 0.016 -10000 0 -10000 0 0
SMAD3 -0.031 0.033 0.21 4 -10000 0 4
ABL1 0.029 0.004 -10000 0 -10000 0 0
MXD1 0.044 0.019 -10000 0 -10000 0 0
MRE11A 0.029 0.006 -10000 0 -10000 0 0
HUS1 0.029 0.004 -10000 0 -10000 0 0
RPS6KB1 0.028 0.006 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.15 0.27 0.53 106 -0.55 4 110
NR2F2 -0.016 0.053 -10000 0 -0.094 4 4
MAPK3 0.017 0.042 -10000 0 -10000 0 0
MAPK1 0.016 0.042 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.001 0.035 -10000 0 -10000 0 0
NFKB1 0.027 0.009 -10000 0 -10000 0 0
HNRNPC 0.029 0.004 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.016 0.015 -10000 0 -10000 0 0
NBN 0.023 0.013 -10000 0 -10000 0 0
EGFR 0.03 0.063 -10000 0 -0.35 9 9
mol:Oestrogen 0.005 0.007 -10000 0 -10000 0 0
EGF/EGFR 0.038 0.053 -10000 0 -0.24 6 6
MYC -0.009 0.12 -10000 0 -0.36 38 38
IL2 0.059 0.052 0.16 3 -10000 0 3
KU 0.043 0.008 -10000 0 -10000 0 0
RAD50 0.029 0.006 -10000 0 -10000 0 0
HSP90AA1 0.028 0.007 -10000 0 -10000 0 0
TGFB1 0.001 0.035 -10000 0 -10000 0 0
TRF2/BLM 0.026 0.021 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.24 0.28 0.58 133 -0.5 3 136
SP1/HDAC2 0.11 0.092 0.23 135 -10000 0 135
PINX1 0.023 0.012 -10000 0 -10000 0 0
Telomerase/EST1A 0.018 0.091 0.32 1 -0.47 3 4
Smad3/Myc -0.024 0.076 0.17 3 -0.23 36 39
911 complex 0.056 0.017 -10000 0 -10000 0 0
IFNG 0.041 0.022 -10000 0 -10000 0 0
Telomerase/PinX1 0.018 0.093 0.35 3 -0.45 4 7
Telomerase/AKT1/mTOR/p70S6K 0.097 0.18 0.33 105 -0.33 12 117
SIN3B 0.035 0.008 -10000 0 -10000 0 0
YWHAE 0.025 0.011 -10000 0 -10000 0 0
Telomerase/EST1B 0.02 0.09 0.35 5 -0.5 2 7
response to DNA damage stimulus 0.004 0.018 -10000 0 -0.1 7 7
MRN complex/TRF2/Rap1 0.054 0.041 -10000 0 -10000 0 0
TRF2/WRN 0.031 0.019 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.024 0.1 0.35 5 -0.46 4 9
E2F1 0.076 0.094 0.23 91 -10000 0 91
ZNFX1 0.034 0.008 -10000 0 -10000 0 0
PIF1 0.021 0.013 -10000 0 -10000 0 0
NCL 0.03 0.003 -10000 0 -10000 0 0
DKC1 0.029 0.004 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.03 0.075 -10000 0 -0.46 3 3
Syndecan-4/Syndesmos -0.021 0.2 -10000 0 -0.52 37 37
positive regulation of JNK cascade -0.081 0.2 -10000 0 -0.47 49 49
Syndecan-4/ADAM12 -0.021 0.18 -10000 0 -0.5 35 35
CCL5 0.02 0.059 -10000 0 -0.37 8 8
Rac1/GDP 0.022 0.003 -10000 0 -10000 0 0
DNM2 0.029 0.003 -10000 0 -10000 0 0
ITGA5 0.03 0.003 -10000 0 -10000 0 0
SDCBP 0.024 0.011 -10000 0 -10000 0 0
PLG -0.032 0.13 -10000 0 -0.35 51 51
ADAM12 0.024 0.023 -10000 0 -0.37 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.028 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.026 0.025 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.039 0.19 -10000 0 -0.51 37 37
Syndecan-4/CXCL12/CXCR4 -0.085 0.21 -10000 0 -0.5 49 49
Syndecan-4/Laminin alpha3 -0.026 0.19 -10000 0 -0.53 34 34
MDK 0.013 0.015 -10000 0 -10000 0 0
Syndecan-4/FZD7 -0.023 0.2 -10000 0 -0.51 37 37
Syndecan-4/Midkine -0.037 0.16 -10000 0 -0.48 34 34
FZD7 0.022 0.055 -10000 0 -0.37 7 7
Syndecan-4/FGFR1/FGF -0.026 0.19 -10000 0 -0.48 40 40
THBS1 -0.027 0.14 -10000 0 -0.37 51 51
integrin-mediated signaling pathway -0.031 0.19 -10000 0 -0.5 39 39
positive regulation of MAPKKK cascade -0.081 0.2 -10000 0 -0.47 49 49
Syndecan-4/TACI -0.026 0.2 -10000 0 -0.52 37 37
CXCR4 0.026 0.036 -10000 0 -0.37 3 3
cell adhesion 0.018 0.037 0.19 13 -0.23 1 14
Syndecan-4/Dynamin -0.022 0.2 -10000 0 -0.53 37 37
Syndecan-4/TSP1 -0.045 0.21 -10000 0 -0.52 41 41
Syndecan-4/GIPC -0.021 0.2 -10000 0 -0.53 37 37
Syndecan-4/RANTES -0.026 0.2 -10000 0 -0.53 37 37
ITGB1 0.029 0.005 -10000 0 -10000 0 0
LAMA1 -0.022 0.13 -10000 0 -0.37 43 43
LAMA3 0.02 0.043 -10000 0 -0.37 4 4
RAC1 0.029 0.004 -10000 0 -10000 0 0
PRKCA 0.024 0.16 0.77 16 -10000 0 16
Syndecan-4/alpha-Actinin -0.022 0.2 -10000 0 -0.53 37 37
TFPI 0.013 0.079 -10000 0 -0.37 15 15
F2 0.004 0.098 -10000 0 -0.36 24 24
alpha5/beta1 Integrin 0.043 0.009 -10000 0 -10000 0 0
positive regulation of cell adhesion -0.026 0.19 0.3 1 -0.51 32 33
ACTN1 0.028 0.007 -10000 0 -10000 0 0
TNC -0.002 0.11 -10000 0 -0.37 28 28
Syndecan-4/CXCL12 -0.088 0.21 -10000 0 -0.51 48 48
FGF6 0.017 0.004 -10000 0 -10000 0 0
RHOA 0.029 0.004 -10000 0 -10000 0 0
CXCL12 -0.13 0.2 -10000 0 -0.37 146 146
TNFRSF13B 0.022 0.031 -10000 0 -0.37 2 2
FGF2 0.005 0.091 -10000 0 -0.37 20 20
FGFR1 0.019 0.047 -10000 0 -0.37 5 5
Syndecan-4/PI-4-5-P2 -0.039 0.19 -10000 0 -0.52 37 37
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.024 0.028 -10000 0 -0.33 1 1
cell migration -0.015 0.013 -10000 0 -10000 0 0
PRKCD 0.026 0.02 -10000 0 -10000 0 0
vasculogenesis -0.042 0.2 -10000 0 -0.5 42 42
SDC4 -0.039 0.2 -10000 0 -0.56 37 37
Syndecan-4/Tenascin C -0.033 0.2 -10000 0 -0.52 39 39
Syndecan-4/PI-4-5-P2/PKC alpha -0.022 0.019 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.029 0.19 -10000 0 -0.53 35 35
MMP9 0.009 0.066 -10000 0 -0.37 10 10
Rac1/GTP 0.018 0.037 0.2 13 -0.24 1 14
cytoskeleton organization -0.019 0.19 -10000 0 -0.5 37 37
GIPC1 0.029 0.004 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.028 0.21 -10000 0 -0.54 39 39
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.002 0.059 -10000 0 -0.18 34 34
TRAF2/ASK1 0.013 0.074 -10000 0 -0.22 33 33
ATM 0.029 0.006 -10000 0 -10000 0 0
MAP2K3 -0.045 0.081 0.22 1 -0.27 17 18
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.048 0.095 0.22 1 -0.27 39 40
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.017 0.13 -10000 0 -0.37 42 42
TXN 0.006 0.001 -10000 0 -10000 0 0
CALM1 0.028 0.007 -10000 0 -10000 0 0
GADD45A 0.025 0.037 -10000 0 -0.37 3 3
GADD45B -0.027 0.14 -10000 0 -0.37 51 51
MAP3K1 0.03 0.002 -10000 0 -10000 0 0
MAP3K6 0.028 0.007 -10000 0 -10000 0 0
MAP3K7 0.028 0.008 -10000 0 -10000 0 0
MAP3K4 0.027 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.012 0.087 -10000 0 -0.26 33 33
TAK1/TAB family -0.008 0.032 -10000 0 -0.15 16 16
RAC1/OSM/MEKK3 0.054 0.013 -10000 0 -10000 0 0
TRAF2 0.029 0.005 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.032 0.08 -10000 0 -0.23 16 16
TRAF6 0.005 0.014 -10000 0 -0.27 1 1
RAC1 0.029 0.004 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.16 0.2 -10000 0 -0.37 175 175
CCM2 0.029 0.004 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.087 0.13 -10000 0 -0.22 175 175
MAPK11 0.027 0.008 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.091 0.14 -10000 0 -0.22 191 191
OSM/MEKK3 0.042 0.01 -10000 0 -10000 0 0
TAOK1 0.01 0.021 -10000 0 -0.27 2 2
TAOK2 0.012 0.003 -10000 0 -10000 0 0
TAOK3 0.012 0.003 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.027 0.009 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 -0.009 0.11 -10000 0 -0.37 33 33
MAP3K10 0.029 0.005 -10000 0 -10000 0 0
MAP3K3 0.029 0.006 -10000 0 -10000 0 0
TRX/ASK1 0.001 0.07 -10000 0 -0.19 39 39
GADD45/MTK1/MTK1 -0.004 0.12 -10000 0 -0.22 79 79
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.029 0.003 -10000 0 -10000 0 0
LAT2 -0.002 0.065 0.18 1 -0.29 6 7
AP1 -0.047 0.17 -10000 0 -0.43 35 35
mol:PIP3 0.032 0.14 0.31 16 -0.38 8 24
IKBKB 0.021 0.11 0.25 21 -0.23 15 36
AKT1 0.022 0.15 0.28 74 -0.32 1 75
IKBKG 0.021 0.11 0.25 22 -0.24 15 37
MS4A2 0.019 0.021 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.029 0.021 -10000 0 -0.37 1 1
MAP3K1 0.024 0.11 0.23 7 -0.37 8 15
mol:Ca2+ 0.032 0.12 0.28 18 -0.29 8 26
LYN 0.026 0.015 -10000 0 -10000 0 0
CBLB -0.004 0.067 0.18 1 -0.27 8 9
SHC1 0.022 0.013 -10000 0 -10000 0 0
RasGAP/p62DOK 0.03 0.079 -10000 0 -0.21 35 35
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.029 0.003 -10000 0 -10000 0 0
PLD2 0.035 0.15 0.32 71 -0.2 16 87
PTPN13 -0.008 0.12 -10000 0 -0.54 7 7
PTPN11 0.027 0.021 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.021 0.11 0.31 3 -0.29 4 7
SYK 0.028 0.038 -10000 0 -0.38 3 3
GRB2 0.029 0.006 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.005 0.092 -10000 0 -0.26 28 28
LAT -0.003 0.067 0.18 1 -0.27 8 9
PAK2 0.029 0.11 0.23 13 -0.4 8 21
NFATC2 -0.06 0.15 -10000 0 -0.44 49 49
HRAS 0.032 0.12 0.24 14 -0.41 9 23
GAB2 0.029 0.005 -10000 0 -10000 0 0
PLA2G1B 0.016 0.071 -10000 0 -0.97 1 1
Fc epsilon R1 0.016 0.082 -10000 0 -0.24 31 31
Antigen/IgE/Fc epsilon R1 0.016 0.075 -10000 0 -0.21 31 31
mol:GDP 0.008 0.1 -10000 0 -0.42 10 10
JUN 0.022 0.051 -10000 0 -0.37 6 6
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.028 0.03 -10000 0 -0.37 2 2
FOS -0.15 0.2 -10000 0 -0.37 160 160
Antigen/IgE/Fc epsilon R1/LYN/SYK 0.002 0.07 -10000 0 -0.27 9 9
CHUK 0.018 0.1 0.24 18 -0.24 14 32
KLRG1 -0.004 0.066 -10000 0 -0.23 11 11
VAV1 -0.009 0.079 0.18 1 -0.34 9 10
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.003 0.064 0.18 1 -0.28 6 7
negative regulation of mast cell degranulation 0.037 0.092 0.22 11 -0.28 5 16
BTK -0.001 0.11 -10000 0 -0.48 11 11
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.074 0.14 -10000 0 -0.26 97 97
GAB2/PI3K/SHP2 -0.044 0.055 -10000 0 -0.21 31 31
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.006 0.063 -10000 0 -0.2 30 30
RAF1 0.019 0.07 -10000 0 -0.95 1 1
Fc epsilon R1/FcgammaRIIB/SHIP -0.049 0.15 -10000 0 -0.24 127 127
FCER1G 0.015 0.04 -10000 0 -0.37 3 3
FCER1A -0.011 0.11 -10000 0 -0.38 29 29
Antigen/IgE/Fc epsilon R1/Fyn 0.026 0.078 -10000 0 -0.2 31 31
MAPK3 0.012 0.073 -10000 0 -1 1 1
MAPK1 0.013 0.068 -10000 0 -0.88 1 1
NFKB1 0.027 0.009 -10000 0 -10000 0 0
MAPK8 -0.044 0.23 -10000 0 -0.58 43 43
DUSP1 -0.009 0.12 -10000 0 -0.37 34 34
NF-kappa-B/RelA 0.019 0.065 0.15 16 -0.15 12 28
actin cytoskeleton reorganization 0.031 0.11 -10000 0 -0.58 5 5
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.039 0.11 -10000 0 -0.37 9 9
FER -0.004 0.066 0.18 1 -0.27 8 9
RELA 0.029 0.005 -10000 0 -10000 0 0
ITK -0.01 0.077 0.13 1 -0.36 16 17
SOS1 0.03 0.002 -10000 0 -10000 0 0
PLCG1 0.023 0.12 0.25 4 -0.4 11 15
cytokine secretion 0.006 0.04 -10000 0 -0.12 6 6
SPHK1 0.012 0.084 0.17 32 -0.3 6 38
PTK2 0.031 0.11 -10000 0 -0.61 5 5
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.001 0.094 -10000 0 -0.33 13 13
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.037 0.14 0.31 18 -0.37 8 26
MAP2K2 0.012 0.068 -10000 0 -0.89 1 1
MAP2K1 0.01 0.065 -10000 0 -0.89 1 1
MAP2K7 0.029 0.004 -10000 0 -10000 0 0
KLRG1/SHP2 0.004 0.068 0.24 1 -0.19 25 26
MAP2K4 -0.084 0.32 -10000 0 -0.84 53 53
Fc epsilon R1/FcgammaRIIB -0.057 0.15 -10000 0 -0.25 127 127
mol:Choline 0.035 0.15 0.32 71 -0.2 16 87
SHC/Grb2/SOS1 0.032 0.085 -10000 0 -0.28 7 7
FYN 0.028 0.008 -10000 0 -10000 0 0
DOK1 0.03 0.002 -10000 0 -10000 0 0
PXN 0.026 0.1 -10000 0 -0.56 5 5
HCLS1 -0.005 0.067 0.18 1 -0.27 8 9
PRKCB 0.02 0.13 0.27 19 -0.32 16 35
FCGR2B -0.11 0.18 -10000 0 -0.37 124 124
IGHE 0.001 0.007 -10000 0 -10000 0 0
KLRG1/SHIP 0.038 0.093 0.22 11 -0.29 5 16
LCP2 0.023 0.051 -10000 0 -0.37 6 6
PLA2G4A -0.012 0.084 0.21 2 -0.33 12 14
RASA1 0.027 0.03 -10000 0 -0.37 2 2
mol:Phosphatidic acid 0.035 0.15 0.32 71 -0.2 16 87
IKK complex 0.021 0.093 0.26 17 -0.19 10 27
WIPF1 0.029 0.003 -10000 0 -10000 0 0
IL1-mediated signaling events

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
UBC13/UEV1A 0.022 0.003 -10000 0 -10000 0 0
PRKCZ 0.014 0.071 -10000 0 -0.37 12 12
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.029 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.03 0.11 -10000 0 -0.27 44 44
IRAK/TOLLIP 0.03 0.015 0.18 3 -10000 0 3
IKBKB 0.026 0.01 -10000 0 -10000 0 0
IKBKG 0.029 0.005 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.038 0.017 -10000 0 -0.26 1 1
IL1A 0.023 0.007 -10000 0 -10000 0 0
IL1B -0.056 0.091 -10000 0 -0.27 56 56
IRAK/TRAF6/p62/Atypical PKCs 0.051 0.056 -10000 0 -0.19 12 12
IL1R2 0.028 0.021 -10000 0 -0.37 1 1
IL1R1 0.026 0.036 -10000 0 -0.37 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.03 0.089 0.21 1 -0.36 9 10
TOLLIP 0.029 0.003 -10000 0 -10000 0 0
TICAM2 0.028 0.021 -10000 0 -0.37 1 1
MAP3K3 0.029 0.006 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.019 0.005 -10000 0 -10000 0 0
IKK complex/ELKS 0 0.079 0.32 1 -0.29 4 5
JUN -0.034 0.052 0.15 3 -0.19 26 29
MAP3K7 0.028 0.008 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.006 0.14 -10000 0 -0.22 96 96
IL1 alpha/IL1R1/IL1RAP/MYD88 0.037 0.097 -10000 0 -0.22 43 43
PIK3R1 0.027 0.03 -10000 0 -0.37 2 2
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.049 0.096 -10000 0 -0.21 43 43
IL1 beta fragment/IL1R1/IL1RAP -0.029 0.13 -10000 0 -0.23 98 98
NFKB1 0.027 0.009 -10000 0 -10000 0 0
MAPK8 -0.029 0.049 0.16 3 -0.19 22 25
IRAK1 -0.014 0.003 -10000 0 -10000 0 0
IL1RN/IL1R1 0.006 0.1 -10000 0 -0.26 45 45
IRAK4 0.03 0.003 -10000 0 -10000 0 0
PRKCI 0.03 0.003 -10000 0 -10000 0 0
TRAF6 0.029 0.021 -10000 0 -0.37 1 1
PI3K 0.041 0.032 -10000 0 -0.37 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.037 0.12 -10000 0 -0.29 45 45
CHUK 0.029 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.029 0.13 -10000 0 -0.23 98 98
IL1 beta/IL1R2 -0.01 0.1 -10000 0 -0.23 62 62
IRAK/TRAF6/TAK1/TAB1/TAB2 0.036 0.019 0.16 2 -0.18 1 3
NF kappa B1 p50/RelA -0.018 0.13 -10000 0 -0.22 92 92
IRAK3 0.019 0.062 -10000 0 -0.37 9 9
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.004 0.13 -10000 0 -0.22 94 94
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.004 0.08 -10000 0 -0.22 24 24
IL1 alpha/IL1R1/IL1RAP 0.02 0.098 -10000 0 -0.24 44 44
RELA 0.029 0.005 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.028 0.007 -10000 0 -10000 0 0
MYD88 0.03 0.003 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.045 0.021 0.18 2 -0.2 1 3
IL1RAP -0.019 0.13 -10000 0 -0.37 44 44
UBE2N 0.029 0.004 -10000 0 -10000 0 0
IRAK/TRAF6 -0.082 0.078 -10000 0 -0.21 85 85
CASP1 0.028 0.022 -10000 0 -0.37 1 1
IL1RN/IL1R2 0.008 0.1 -10000 0 -0.27 42 42
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.014 0.13 -10000 0 -0.22 97 97
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0 0.075 -10000 0 -0.35 6 6
PIK3CA 0.028 0.021 -10000 0 -0.37 1 1
IL1RN -0.017 0.13 -10000 0 -0.37 42 42
TRAF6/TAK1/TAB1/TAB2 0.04 0.017 -10000 0 -0.18 1 1
MAP2K6 -0.019 0.034 0.18 3 -0.2 7 10
LPA4-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
ADCY4 -0.015 0.015 0.18 1 -0.22 1 2
ADCY5 -0.05 0.081 0.18 2 -0.22 65 67
ADCY6 -0.014 0.01 0.18 1 -10000 0 1
ADCY7 -0.014 0.015 0.18 1 -0.22 1 2
ADCY1 -0.088 0.1 0.18 2 -0.22 133 135
ADCY2 -0.01 0.029 0.18 8 -10000 0 8
ADCY3 -0.014 0.021 0.18 3 -0.22 1 4
ADCY8 0 0.044 0.18 20 -10000 0 20
PRKCE -0.009 0.017 0.2 1 -0.26 1 2
ADCY9 -0.014 0.015 0.18 1 -0.22 1 2
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.003 0.064 0.19 3 -0.2 1 4
PLK2 and PLK4 events

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
PLK2 0.029 0.021 -10000 0 -0.37 1 1
PLK4 0.023 0.012 -10000 0 -10000 0 0
regulation of centriole replication 0.018 0.083 0.21 58 -0.26 1 59
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.032 0.042 -10000 0 -0.26 6 6
alphaV beta3 Integrin 0.02 0.1 -10000 0 -0.25 42 42
PTK2 0.036 0.14 0.3 15 -0.38 16 31
IGF1R 0.02 0.059 -10000 0 -0.37 8 8
PI4KB 0.023 0.013 -10000 0 -10000 0 0
MFGE8 0.029 0.006 -10000 0 -10000 0 0
SRC 0.029 0.005 -10000 0 -10000 0 0
CDKN1B -0.008 0.088 -10000 0 -0.4 14 14
VEGFA 0.026 0.01 -10000 0 -10000 0 0
ILK -0.007 0.087 -10000 0 -0.39 14 14
ROCK1 0.029 0.003 -10000 0 -10000 0 0
AKT1 -0.014 0.077 0.2 1 -0.37 13 14
PTK2B -0.018 0.082 0.18 31 -0.24 17 48
alphaV/beta3 Integrin/JAM-A 0.045 0.1 -10000 0 -0.22 37 37
CBL 0.028 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.007 0.11 -10000 0 -0.24 59 59
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.04 0.14 -10000 0 -0.21 142 142
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0 0.077 -10000 0 -0.29 7 7
alphaV/beta3 Integrin/Syndecan-1 0.033 0.081 -10000 0 -0.23 32 32
PI4KA 0.029 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.063 0.15 -10000 0 -0.23 151 151
PI4 Kinase 0.033 0.019 -10000 0 -10000 0 0
PIK3CA 0.028 0.021 -10000 0 -0.37 1 1
alphaV/beta3 Integrin/Osteopontin 0.006 0.083 -10000 0 -0.23 34 34
RPS6KB1 -0.11 0.1 -10000 0 -0.36 26 26
TLN1 0.029 0.005 -10000 0 -10000 0 0
MAPK3 -0.049 0.18 -10000 0 -0.45 49 49
GPR124 0.022 0.031 -10000 0 -0.37 2 2
MAPK1 -0.049 0.18 -10000 0 -0.45 50 50
PXN 0.029 0.003 -10000 0 -10000 0 0
PIK3R1 0.027 0.03 -10000 0 -0.37 2 2
alphaV/beta3 Integrin/Tumstatin 0.021 0.1 -10000 0 -0.26 39 39
cell adhesion 0.001 0.11 -10000 0 -0.24 56 56
ANGPTL3 -0.012 0.12 -10000 0 -0.37 37 37
VEGFR2 homodimer/VEGFA homodimer/Src 0.044 0.042 -10000 0 -0.23 6 6
IGF-1R heterotetramer 0.02 0.059 -10000 0 -0.37 8 8
Rac1/GDP 0.022 0.003 -10000 0 -10000 0 0
TGFBR2 0.029 0.003 -10000 0 -10000 0 0
ITGB3 -0.002 0.11 -10000 0 -0.37 28 28
IGF1 -0.13 0.2 -10000 0 -0.37 142 142
RAC1 0.029 0.004 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.028 0.076 -10000 0 -0.22 29 29
apoptosis 0.029 0.003 -10000 0 -10000 0 0
CD47 0.029 0.021 -10000 0 -0.37 1 1
alphaV/beta3 Integrin/CD47 0.036 0.078 -10000 0 -0.23 29 29
VCL 0.029 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.023 0.076 -10000 0 -0.23 28 28
CSF1 0.024 0.042 -10000 0 -0.37 4 4
PIK3C2A -0.007 0.087 -10000 0 -0.39 14 14
PI4 Kinase/Pyk2 -0.003 0.079 -10000 0 -0.23 29 29
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.041 0.085 -10000 0 -0.23 27 27
FAK1/Vinculin 0.048 0.13 0.29 18 -0.32 15 33
alphaV beta3/Integrin/ppsTEM5 0.028 0.076 -10000 0 -0.22 29 29
RHOA 0.029 0.004 -10000 0 -10000 0 0
VTN 0.015 0.074 -10000 0 -0.37 13 13
BCAR1 0.027 0.008 -10000 0 -10000 0 0
FGF2 0.005 0.091 -10000 0 -0.37 20 20
F11R -0.021 0.056 0.21 4 -0.26 15 19
alphaV/beta3 Integrin/Lactadherin 0.035 0.076 -10000 0 -0.23 27 27
alphaV/beta3 Integrin/TGFBR2 0.038 0.073 -10000 0 -0.23 25 25
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.065 0.036 -10000 0 -0.2 3 3
HSP90AA1 0.028 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.034 0.07 -10000 0 -0.2 28 28
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.028 0.021 -10000 0 -0.37 1 1
alphaV/beta3 Integrin/Pyk2 0.029 0.083 -10000 0 -0.22 26 26
SDC1 0.025 0.042 -10000 0 -0.37 4 4
VAV3 -0.026 0.025 -10000 0 -10000 0 0
PTPN11 0.029 0.003 -10000 0 -10000 0 0
IRS1 0.03 0.003 -10000 0 -10000 0 0
FAK1/Paxillin 0.048 0.12 0.29 17 -0.32 15 32
cell migration 0.039 0.12 0.28 17 -0.3 15 32
ITGAV 0.029 0.003 -10000 0 -10000 0 0
PI3K 0.049 0.11 -10000 0 -0.22 38 38
SPP1 -0.002 0.083 -10000 0 -0.37 17 17
KDR 0.021 0.055 -10000 0 -0.37 7 7
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.029 0.003 -10000 0 -10000 0 0
COL4A3 0.007 0.086 -10000 0 -0.37 18 18
angiogenesis -0.05 0.19 0.29 2 -0.46 50 52
Rac1/GTP -0.026 0.028 -10000 0 -10000 0 0
EDIL3 0.022 0.012 -10000 0 -10000 0 0
cell proliferation 0.038 0.073 -10000 0 -0.23 25 25
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.001 0.06 -10000 0 -0.19 26 26
epithelial cell differentiation 0.041 0.063 -10000 0 -0.2 22 22
CYFIP2 0.007 0.091 -10000 0 -0.37 20 20
ENAH -0.027 0.064 0.28 3 -0.26 3 6
EGFR 0.019 0.062 -10000 0 -0.37 9 9
EPHA2 0.009 0.084 -10000 0 -0.37 17 17
MYO6 -0.031 0.054 -10000 0 -0.35 2 2
CTNNB1 0.03 0.003 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.044 0.061 -10000 0 -0.23 17 17
AQP5 -0.014 0.062 -10000 0 -0.28 1 1
CTNND1 0.029 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.03 0.051 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.03 0.05 -10000 0 -0.19 2 2
EGF 0.017 0.012 -10000 0 -10000 0 0
NCKAP1 0.03 0.002 -10000 0 -10000 0 0
AQP3 -0.054 0.13 -10000 0 -0.43 31 31
cortical microtubule organization 0.041 0.063 -10000 0 -0.2 22 22
GO:0000145 -0.029 0.048 0.17 2 -10000 0 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.047 0.066 -10000 0 -0.2 22 22
MLLT4 0.027 0.009 -10000 0 -10000 0 0
ARF6/GDP -0.044 0.05 -10000 0 -0.2 26 26
ARF6 0.029 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.044 0.059 -10000 0 -0.21 12 12
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.02 0.047 -10000 0 -10000 0 0
PVRL2 0.029 0.005 -10000 0 -10000 0 0
ZYX -0.03 0.052 -10000 0 -0.19 22 22
ARF6/GTP 0.048 0.061 -10000 0 -0.2 12 12
CDH1 0.003 0.095 -10000 0 -0.37 22 22
EGFR/EGFR/EGF/EGF 0.04 0.072 -10000 0 -0.21 21 21
RhoA/GDP 0.042 0.063 -10000 0 -0.19 22 22
actin cytoskeleton organization -0.032 0.052 -10000 0 -0.34 2 2
IGF-1R heterotetramer 0.02 0.059 -10000 0 -0.37 8 8
GIT1 0.029 0.003 -10000 0 -10000 0 0
IGF1R 0.02 0.059 -10000 0 -0.37 8 8
IGF1 -0.13 0.2 -10000 0 -0.37 142 142
DIAPH1 0.019 0.16 -10000 0 -0.54 26 26
Wnt receptor signaling pathway -0.041 0.063 0.2 22 -10000 0 22
RHOA 0.029 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.043 0.049 -10000 0 -0.2 25 25
CTNNA1 0.029 0.005 -10000 0 -10000 0 0
VCL -0.033 0.053 -10000 0 -0.35 2 2
EFNA1 0.019 0.038 -10000 0 -0.37 3 3
LPP -0.035 0.047 -10000 0 -10000 0 0
Ephrin A1/EPHA2 0.02 0.071 -10000 0 -0.21 26 26
SEC6/SEC8 -0.042 0.04 -10000 0 -0.19 22 22
MGAT3 -0.03 0.051 -10000 0 -0.19 2 2
HGF/MET -0.083 0.13 -10000 0 -0.2 189 189
HGF -0.18 0.2 -10000 0 -0.37 194 194
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.001 0.06 -10000 0 -0.2 26 26
actin cable formation 0.02 0.097 0.31 8 -10000 0 8
KIAA1543 -0.031 0.049 0.17 1 -0.18 25 26
KIFC3 -0.031 0.051 -10000 0 -0.19 22 22
NCK1 0.03 0.002 -10000 0 -10000 0 0
EXOC3 0.028 0.007 -10000 0 -10000 0 0
ACTN1 -0.031 0.048 -10000 0 -0.19 22 22
NCK1/GIT1 0.044 0.006 -10000 0 -10000 0 0
mol:GDP 0.041 0.063 -10000 0 -0.2 22 22
EXOC4 0.028 0.006 -10000 0 -10000 0 0
STX4 -0.031 0.052 -10000 0 -10000 0 0
PIP5K1C -0.03 0.052 -10000 0 -10000 0 0
LIMA1 0.03 0.003 -10000 0 -10000 0 0
ABI1 0.029 0.005 -10000 0 -10000 0 0
ROCK1 -0.009 0.095 0.31 5 -0.3 3 8
adherens junction assembly -0.03 0.076 -10000 0 -0.63 2 2
IGF-1R heterotetramer/IGF1 -0.058 0.12 -10000 0 -0.2 155 155
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.039 0.015 -10000 0 -10000 0 0
MET 0.027 0.022 -10000 0 -0.37 1 1
PLEKHA7 -0.033 0.052 -10000 0 -0.19 25 25
mol:GTP 0.043 0.058 -10000 0 -0.21 12 12
establishment of epithelial cell apical/basal polarity -0.025 0.081 0.31 6 -10000 0 6
cortical actin cytoskeleton stabilization -0.001 0.06 -10000 0 -0.19 26 26
regulation of cell-cell adhesion -0.032 0.052 -10000 0 -0.34 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.001 0.06 -10000 0 -0.2 26 26
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.013 0.071 0.27 20 -10000 0 20
KIRREL -0.001 0.096 -10000 0 -0.37 22 22
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.013 0.072 -10000 0 -0.27 20 20
PLCG1 0.029 0.004 -10000 0 -10000 0 0
ARRB2 0.025 0.011 -10000 0 -10000 0 0
WASL 0.029 0.006 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.035 0.066 -10000 0 -0.21 17 17
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.007 0.06 -10000 0 -0.22 18 18
FYN 0.042 0.13 0.26 82 -0.2 19 101
mol:Ca2+ 0.037 0.068 -10000 0 -0.2 19 19
mol:DAG 0.038 0.069 -10000 0 -0.21 19 19
NPHS2 0.002 0.025 -10000 0 -10000 0 0
mol:IP3 0.038 0.069 -10000 0 -0.21 19 19
regulation of endocytosis 0.025 0.058 -10000 0 -0.18 19 19
Nephrin/NEPH1/podocin/Cholesterol 0.022 0.061 0.18 4 -0.2 19 23
establishment of cell polarity 0.013 0.071 -10000 0 -0.27 20 20
Nephrin/NEPH1/podocin/NCK1-2 0.05 0.075 -10000 0 -0.2 19 19
Nephrin/NEPH1/beta Arrestin2 0.027 0.06 -10000 0 -0.18 19 19
NPHS1 0.014 0.034 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin 0.023 0.058 -10000 0 -0.2 19 19
TJP1 0.029 0.003 -10000 0 -10000 0 0
NCK1 0.03 0.002 -10000 0 -10000 0 0
NCK2 0.028 0.021 -10000 0 -0.37 1 1
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.039 0.07 -10000 0 -0.21 19 19
CD2AP 0.027 0.008 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.039 0.067 -10000 0 -0.21 17 17
GRB2 0.028 0.006 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.035 0.12 0.26 72 -0.19 17 89
cytoskeleton organization -0.01 0.065 0.2 8 -0.24 16 24
Nephrin/NEPH1 0.013 0.05 -10000 0 -0.18 20 20
Nephrin/NEPH1/ZO-1 0.027 0.066 -10000 0 -0.22 20 20
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.013 0.12 -10000 0 -0.2 80 80
SMAD6-7/SMURF1 0.046 0.053 -10000 0 -0.23 12 12
NOG 0.022 0.007 -10000 0 -10000 0 0
SMAD9 -0.032 0.16 -10000 0 -0.45 40 40
SMAD4 0.029 0.006 -10000 0 -10000 0 0
SMAD5 -0.018 0.1 -10000 0 -0.3 13 13
BMP7/USAG1 0.027 0.018 -10000 0 -10000 0 0
SMAD5/SKI -0.012 0.12 0.29 2 -0.31 19 21
SMAD1 -0.008 0.076 -10000 0 -0.36 9 9
BMP2 0.026 0.036 -10000 0 -0.37 3 3
SMAD1/SMAD1/SMAD4 0.005 0.087 -10000 0 -0.35 8 8
BMPR1A 0.029 0.006 -10000 0 -10000 0 0
BMPR1B -0.048 0.15 -10000 0 -0.37 66 66
BMPR1A-1B/BAMBI -0.015 0.13 -10000 0 -0.24 81 81
AHSG -0.034 0.15 -10000 0 -0.37 58 58
CER1 0.018 0.005 -10000 0 -10000 0 0
BMP2-4/CER1 0.042 0.029 -10000 0 -0.23 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.024 0.098 -10000 0 -0.29 16 16
BMP2-4 (homodimer) 0.037 0.027 -10000 0 -0.26 2 2
RGMB 0.027 0.03 -10000 0 -0.37 2 2
BMP6/BMPR2/BMPR1A-1B 0.015 0.11 -10000 0 -0.21 61 61
RGMA 0.026 0.01 -10000 0 -10000 0 0
SMURF1 0.029 0.006 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.024 0.094 0.18 1 -0.3 13 14
BMP2-4/USAG1 0.04 0.034 -10000 0 -0.23 2 2
SMAD6/SMURF1/SMAD5 -0.012 0.12 0.29 2 -0.3 20 22
SOSTDC1 0.022 0.012 -10000 0 -10000 0 0
BMP7/BMPR2/BMPR1A-1B 0.024 0.11 -10000 0 -0.21 61 61
SKI 0.027 0.009 -10000 0 -10000 0 0
BMP6 (homodimer) 0.021 0.047 -10000 0 -0.37 5 5
HFE2 -0.015 0.12 -10000 0 -0.37 34 34
ZFYVE16 0.03 0.003 -10000 0 -10000 0 0
MAP3K7 0.028 0.008 -10000 0 -10000 0 0
BMP2-4/CHRD 0.046 0.046 -10000 0 -0.22 8 8
SMAD5/SMAD5/SMAD4 -0.011 0.12 0.29 2 -0.31 19 21
MAPK1 0.029 0.004 -10000 0 -10000 0 0
TAK1/TAB family -0.007 0.1 0.2 1 -0.27 16 17
BMP7 (homodimer) 0.02 0.01 -10000 0 -10000 0 0
NUP214 0.029 0.004 -10000 0 -10000 0 0
BMP6/FETUA -0.011 0.11 -10000 0 -0.26 60 60
SMAD1/SKI 0.005 0.079 -10000 0 -0.35 9 9
SMAD6 0.017 0.068 -10000 0 -0.37 11 11
CTDSP2 0.029 0.004 -10000 0 -10000 0 0
BMP2-4/FETUA 0.008 0.1 -10000 0 -0.23 55 55
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.011 0.12 -10000 0 -0.37 34 34
BMPR2 (homodimer) 0.029 0.003 -10000 0 -10000 0 0
GADD34/PP1CA 0.057 0.015 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) -0.018 0.12 -10000 0 -0.26 66 66
CHRDL1 -0.044 0.15 -10000 0 -0.37 64 64
ENDOFIN/SMAD1 0.004 0.082 -10000 0 -0.34 10 10
SMAD6-7/SMURF1/SMAD1 0.016 0.097 -10000 0 -0.38 8 8
SMAD6/SMURF1 0.029 0.006 -10000 0 -10000 0 0
BAMBI 0.002 0.1 -10000 0 -0.37 25 25
SMURF2 0.029 0.006 -10000 0 -10000 0 0
BMP2-4/CHRDL1 0.004 0.1 -10000 0 -0.23 57 57
BMP2-4/GREM1 0.021 0.081 -10000 0 -0.23 32 32
SMAD7 0.026 0.03 -10000 0 -0.37 2 2
SMAD8A/SMAD8A/SMAD4 -0.035 0.18 -10000 0 -0.45 47 47
SMAD1/SMAD6 0.004 0.08 -10000 0 -0.34 9 9
TAK1/SMAD6 0.04 0.014 -10000 0 -10000 0 0
BMP7 0.02 0.01 -10000 0 -10000 0 0
BMP6 0.021 0.047 -10000 0 -0.37 5 5
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.013 0.1 -10000 0 -0.3 16 16
PPM1A 0.028 0.006 -10000 0 -10000 0 0
SMAD1/SMURF2 0.003 0.082 -10000 0 -0.34 10 10
SMAD7/SMURF1 0.04 0.02 -10000 0 -0.26 1 1
CTDSPL 0.03 0.003 -10000 0 -10000 0 0
PPP1CA 0.029 0.005 -10000 0 -10000 0 0
XIAP 0.029 0.003 -10000 0 -10000 0 0
CTDSP1 0.029 0.003 -10000 0 -10000 0 0
PPP1R15A 0.029 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.024 0.12 0.18 11 -0.32 29 40
CHRD 0.022 0.055 -10000 0 -0.37 7 7
BMPR2 0.03 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.02 0.1 -10000 0 -0.31 13 13
BMP4 0.026 0.01 -10000 0 -10000 0 0
FST -0.005 0.11 -10000 0 -0.37 31 31
BMP2-4/NOG 0.046 0.026 -10000 0 -0.23 1 1
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.03 0.11 -10000 0 -0.2 60 60
IL27-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
TGFB1 0.03 0.013 0.2 1 -10000 0 1
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.053 0.16 0.5 18 -0.38 4 22
IL27/IL27R/JAK1 -0.02 0.17 0.7 2 -0.4 1 3
TBX21 -0.062 0.16 0.52 9 -0.49 5 14
IL12B 0.028 0.023 0.23 3 -10000 0 3
IL12A 0 0.039 0.2 12 -10000 0 12
IL6ST -0.066 0.17 -10000 0 -0.37 88 88
IL27RA/JAK1 0.018 0.055 -10000 0 -10000 0 0
IL27 -0.032 0.15 -10000 0 -0.37 57 57
TYK2 0.033 0.027 0.15 5 -10000 0 5
T-helper cell lineage commitment -0.001 0.11 0.7 2 -10000 0 2
T-helper 2 cell differentiation 0.053 0.16 0.5 18 -0.38 4 22
T cell proliferation during immune response 0.053 0.16 0.5 18 -0.38 4 22
MAPKKK cascade -0.053 0.16 0.38 4 -0.5 18 22
STAT3 0.029 0.004 -10000 0 -10000 0 0
STAT2 0.029 0.003 -10000 0 -10000 0 0
STAT1 0.031 0.008 -10000 0 -10000 0 0
IL12RB1 0.017 0.072 -10000 0 -0.37 12 12
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.058 0.18 0.64 10 -0.49 7 17
IL27/IL27R/JAK2/TYK2 -0.054 0.16 0.38 4 -0.51 18 22
positive regulation of T cell mediated cytotoxicity -0.053 0.16 0.38 4 -0.5 18 22
STAT1 (dimer) -0.025 0.22 0.57 17 -0.49 10 27
JAK2 0.032 0.017 -10000 0 -10000 0 0
JAK1 0.03 0.009 -10000 0 -10000 0 0
STAT2 (dimer) -0.046 0.16 -10000 0 -0.49 18 18
T cell proliferation -0.074 0.16 0.34 1 -0.48 23 24
IL12/IL12R/TYK2/JAK2 0.038 0.15 0.52 4 -0.83 6 10
IL17A -0.002 0.11 0.7 2 -10000 0 2
mast cell activation 0.053 0.16 0.5 18 -0.38 4 22
IFNG 0.004 0.053 0.22 15 -0.12 4 19
T cell differentiation -0.003 0.007 0.019 13 -0.02 12 25
STAT3 (dimer) -0.045 0.16 0.35 3 -0.49 18 21
STAT5A (dimer) -0.045 0.16 -10000 0 -0.49 18 18
STAT4 (dimer) -0.053 0.17 0.35 3 -0.49 20 23
STAT4 0.013 0.079 -10000 0 -0.37 15 15
T cell activation -0.008 0.013 -10000 0 -0.24 1 1
IL27R/JAK2/TYK2 0.013 0.14 0.42 5 -10000 0 5
GATA3 -0.063 0.33 0.73 6 -1.2 25 31
IL18 -0.011 0.04 0.2 3 -0.26 7 10
positive regulation of mast cell cytokine production -0.045 0.16 0.35 4 -0.48 18 22
IL27/EBI3 -0.014 0.12 0.18 2 -0.26 71 73
IL27RA 0.006 0.049 0.41 1 -10000 0 1
IL6 -0.025 0.14 0.2 2 -0.37 49 51
STAT5A 0.029 0.004 -10000 0 -10000 0 0
monocyte differentiation 0.001 0.003 0.019 4 -10000 0 4
IL2 -0.011 0.033 -10000 0 -0.48 1 1
IL1B -0.05 0.094 -10000 0 -0.26 62 62
EBI3 0.015 0.077 -10000 0 -0.36 14 14
TNF -0.015 0.048 0.2 2 -0.26 12 14
Osteopontin-mediated events

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
IKK alpha homodimer 0.049 0.12 0.36 9 -0.36 1 10
NF kappa B1 p50/RelA/I kappa B alpha 0.051 0.12 0.42 11 -0.34 1 12
alphaV/beta3 Integrin/Osteopontin/Src 0.013 0.067 0.21 2 -0.26 17 19
AP1 -0.048 0.19 0.69 5 -0.4 33 38
ILK 0.025 0.12 0.33 11 -0.38 1 12
bone resorption 0 0.11 0.26 8 -0.33 5 13
PTK2B 0.023 0.012 -10000 0 -10000 0 0
PYK2/p130Cas 0.054 0.11 0.3 6 -0.21 21 27
ITGAV 0.031 0.013 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.031 0.06 -10000 0 -0.26 14 14
alphaV/beta3 Integrin/Osteopontin 0.011 0.088 0.33 2 -0.23 34 36
MAP3K1 0.025 0.12 0.33 11 -0.28 3 14
JUN 0.022 0.052 -10000 0 -0.37 6 6
MAPK3 0.022 0.12 0.5 7 -0.36 1 8
MAPK1 0.021 0.12 0.5 7 -0.36 1 8
Rac1/GDP 0.022 0.003 -10000 0 -10000 0 0
NFKB1 0.027 0.009 -10000 0 -10000 0 0
MAPK8 0.011 0.13 0.36 9 -0.37 7 16
ITGB3 0 0.11 0.14 2 -0.37 28 30
NFKBIA 0.029 0.12 0.47 10 -0.35 1 11
FOS -0.15 0.2 -10000 0 -0.37 160 160
CD44 0.027 0.03 -10000 0 -0.37 2 2
CHUK 0.029 0.005 -10000 0 -10000 0 0
PLAU 0.02 0.14 0.78 6 -10000 0 6
NF kappa B1 p50/RelA 0.057 0.12 0.54 6 -0.34 1 7
BCAR1 0.027 0.008 -10000 0 -10000 0 0
RELA 0.029 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.024 0.086 0.19 6 -0.26 28 34
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.023 0.12 0.3 11 -0.38 2 13
VAV3 0.018 0.12 0.28 14 -0.32 3 17
MAP3K14 0.024 0.12 0.39 9 -0.38 1 10
ROCK2 0.016 0.071 -10000 0 -0.37 12 12
SPP1 -0.001 0.083 -10000 0 -0.37 17 17
RAC1 0.029 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.018 0.11 0.25 14 -0.3 3 17
MMP2 -0.073 0.16 0.63 4 -0.37 34 38
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 0.058 0.073 -10000 0 -0.25 16 16
MAP4K1 0.021 0.055 -10000 0 -0.37 7 7
MAP3K8 0.027 0.03 -10000 0 -0.37 2 2
PRKCB -0.004 0.11 -10000 0 -0.37 30 30
DBNL 0.029 0.004 -10000 0 -10000 0 0
CRKL 0.029 0.005 -10000 0 -10000 0 0
MAP3K1 -0.01 0.086 0.28 1 -0.38 11 12
JUN -0.086 0.24 -10000 0 -0.59 65 65
MAP3K7 -0.008 0.084 0.28 1 -0.38 11 12
GRAP2 0.02 0.059 -10000 0 -0.37 8 8
CRK 0.025 0.011 -10000 0 -10000 0 0
MAP2K4 -0.015 0.098 0.27 1 -0.41 13 14
LAT 0.029 0.006 -10000 0 -10000 0 0
LCP2 0.022 0.051 -10000 0 -0.37 6 6
MAPK8 -0.082 0.26 -10000 0 -0.61 65 65
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0 0.092 0.31 1 -0.37 13 14
LAT/GRAP2/SLP76/HPK1/HIP-55 0.066 0.075 -10000 0 -0.24 16 16
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.006 0.049 0.16 1 -0.26 11 12
CRKL 0.029 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.022 0.003 -10000 0 -10000 0 0
DOCK1 0.019 0.059 -10000 0 -0.37 8 8
ITGA4 0.022 0.055 -10000 0 -0.37 7 7
alpha4/beta7 Integrin/MAdCAM1 0.065 0.053 -10000 0 -0.2 12 12
EPO -0.12 0.19 -10000 0 -0.37 130 130
alpha4/beta7 Integrin 0.034 0.054 -10000 0 -0.26 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.025 0.011 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.037 0.042 -10000 0 -0.26 7 7
EPO/EPOR (dimer) -0.069 0.14 -10000 0 -0.26 129 129
lamellipodium assembly 0.01 0.051 -10000 0 -0.29 8 8
PIK3CA 0.028 0.021 -10000 0 -0.37 1 1
PI3K 0.041 0.032 -10000 0 -0.37 2 2
ARF6 0.029 0.005 -10000 0 -10000 0 0
JAK2 -0.059 0.12 -10000 0 -0.22 125 125
PXN 0.029 0.003 -10000 0 -10000 0 0
PIK3R1 0.027 0.03 -10000 0 -0.37 2 2
MADCAM1 0.027 0.007 -10000 0 -10000 0 0
cell adhesion 0.063 0.053 -10000 0 -0.2 12 12
CRKL/CBL 0.041 0.011 -10000 0 -10000 0 0
ITGB1 0.029 0.005 -10000 0 -10000 0 0
SRC -0.026 0.066 0.17 18 -0.22 21 39
ITGB7 0.024 0.047 -10000 0 -0.37 5 5
RAC1 0.029 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.035 0.075 -10000 0 -0.24 23 23
p130Cas/Crk/Dock1 -0.03 0.072 -10000 0 -0.33 5 5
VCAM1 0.006 0.091 -10000 0 -0.37 20 20
RHOA 0.029 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.067 0.042 -10000 0 -0.2 7 7
BCAR1 -0.027 0.063 -10000 0 -0.22 17 17
EPOR 0.029 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.028 0.006 -10000 0 -10000 0 0
GIT1 0.029 0.003 -10000 0 -10000 0 0
Rac1/GTP 0.01 0.053 -10000 0 -0.3 8 8
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.028 0.12 -10000 0 -0.33 49 49
KLHL20 -0.009 0.07 0.57 1 -0.23 7 8
CYFIP2 0.007 0.091 -10000 0 -0.37 20 20
Rac1/GDP -0.01 0.084 -10000 0 -0.25 21 21
ENAH -0.02 0.11 -10000 0 -0.31 40 40
AP1M1 0.029 0.004 -10000 0 -10000 0 0
RAP1B 0.029 0.004 -10000 0 -10000 0 0
RAP1A 0.029 0.006 -10000 0 -10000 0 0
CTNNB1 0.03 0.003 -10000 0 -10000 0 0
CDC42/GTP -0.03 0.05 0.12 7 -0.18 22 29
ABI1/Sra1/Nap1 -0.03 0.045 -10000 0 -0.15 30 30
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.043 0.077 -10000 0 -0.21 27 27
RAPGEF1 -0.037 0.11 -10000 0 -0.32 39 39
CTNND1 0.029 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.021 0.13 -10000 0 -0.33 52 52
CRK -0.023 0.11 -10000 0 -0.34 37 37
E-cadherin/gamma catenin/alpha catenin 0.036 0.069 -10000 0 -0.23 22 22
alphaE/beta7 Integrin 0.033 0.037 -10000 0 -0.25 5 5
IQGAP1 0.029 0.005 -10000 0 -10000 0 0
NCKAP1 0.03 0.002 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.049 0.02 -10000 0 -10000 0 0
DLG1 -0.03 0.12 -10000 0 -0.33 51 51
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.034 0.031 -10000 0 -0.14 22 22
MLLT4 0.027 0.009 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.04 0.057 -10000 0 -0.2 18 18
PI3K -0.042 0.04 0.13 1 -0.18 22 23
ARF6 0.029 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.021 0.074 -10000 0 -0.26 22 22
TIAM1 0.008 0.089 -10000 0 -0.37 19 19
E-cadherin(dimer)/Ca2+ 0.047 0.066 -10000 0 -0.2 22 22
AKT1 -0.024 0.034 -10000 0 -10000 0 0
PIK3R1 0.027 0.03 -10000 0 -0.37 2 2
CDH1 0.003 0.095 -10000 0 -0.37 22 22
RhoA/GDP -0.01 0.084 -10000 0 -0.25 22 22
actin cytoskeleton organization -0.006 0.054 0.5 1 -0.2 1 2
CDC42/GDP -0.009 0.083 -10000 0 -0.25 22 22
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.003 0.052 -10000 0 -0.2 22 22
ITGB7 0.024 0.047 -10000 0 -0.37 5 5
RAC1 0.029 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.051 0.07 -10000 0 -0.21 22 22
E-cadherin/Ca2+/beta catenin/alpha catenin 0.033 0.059 -10000 0 -0.19 22 22
mol:GDP -0.027 0.088 -10000 0 -0.28 22 22
CDC42/GTP/IQGAP1 0.037 0.011 -10000 0 -10000 0 0
JUP 0.029 0.003 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP -0.001 0.09 -10000 0 -0.26 22 22
RAC1/GTP/IQGAP1 0.038 0.009 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.043 0.008 -10000 0 -10000 0 0
RHOA 0.029 0.004 -10000 0 -10000 0 0
CDC42 0.028 0.007 -10000 0 -10000 0 0
CTNNA1 0.029 0.005 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle -0.008 0.047 0.16 1 -0.18 15 16
NME1 0.029 0.005 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.03 0.12 -10000 0 -0.33 51 51
regulation of cell-cell adhesion -0.031 0.038 0.073 1 -0.16 22 23
WASF2 -0.013 0.03 0.092 3 -0.093 9 12
Rap1/GTP -0.028 0.057 0.16 7 -0.2 22 29
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.05 0.08 -10000 0 -0.2 27 27
CCND1 -0.011 0.058 0.18 1 -0.21 16 17
VAV2 -0.029 0.16 -10000 0 -0.59 11 11
RAP1/GDP 0.003 0.072 -10000 0 -0.21 21 21
adherens junction assembly -0.029 0.12 -10000 0 -0.32 51 51
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.029 0.005 -10000 0 -10000 0 0
PIP5K1C 0.029 0.005 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.034 0.072 -10000 0 -0.2 27 27
E-cadherin/beta catenin -0.007 0.074 -10000 0 -0.3 22 22
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.029 0.13 -10000 0 -0.33 52 52
PIK3CA 0.028 0.021 -10000 0 -0.37 1 1
Rac1/GTP -0.03 0.1 -10000 0 -0.35 20 20
E-cadherin/beta catenin/alpha catenin 0.037 0.069 -10000 0 -0.23 22 22
ITGAE 0.025 0.011 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.022 0.13 -10000 0 -0.34 52 52
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.029 0.005 -10000 0 -10000 0 0
SPHK1 0.018 0.047 -10000 0 -0.37 5 5
GNAI2 0.029 0.003 -10000 0 -10000 0 0
mol:S1P 0.03 0.07 0.29 7 -0.29 5 12
GNAO1 -0.14 0.2 -10000 0 -0.37 153 153
mol:Sphinganine-1-P 0.018 0.089 0.21 61 -0.26 4 65
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.065 0.065 -10000 0 -0.24 7 7
GNAI3 0.029 0.006 -10000 0 -10000 0 0
G12/G13 0.042 0.01 -10000 0 -10000 0 0
S1PR3 0.019 0.062 -10000 0 -0.37 9 9
S1PR2 0.026 0.036 -10000 0 -0.37 3 3
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0 0.035 -10000 0 -0.25 5 5
S1PR5 0.024 0.047 -10000 0 -0.37 5 5
S1PR4 0.029 0.005 -10000 0 -10000 0 0
GNAI1 0.027 0.03 -10000 0 -0.37 2 2
S1P/S1P5/G12 0.052 0.066 0.2 9 -0.24 8 17
S1P/S1P3/Gq -0.017 0.12 0.18 1 -0.28 47 48
S1P/S1P4/Gi -0.008 0.11 0.24 2 -0.26 13 15
GNAQ 0.029 0.004 -10000 0 -10000 0 0
GNAZ 0.014 0.025 -10000 0 -0.37 1 1
GNA14 -0.035 0.15 -10000 0 -0.37 58 58
GNA15 0.028 0.021 -10000 0 -0.37 1 1
GNA12 0.029 0.005 -10000 0 -10000 0 0
GNA13 0.029 0.005 -10000 0 -10000 0 0
GNA11 0.019 0.062 -10000 0 -0.37 9 9
ABCC1 0.028 0.007 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.029 0.004 -10000 0 -10000 0 0
HDAC4 0.029 0.004 -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 0.052 -10000 0 -0.19 23 23
CDKN1A -0.025 0.089 -10000 0 -0.55 10 10
KAT2B 0.026 0.036 -10000 0 -0.37 3 3
BAX 0.029 0.005 -10000 0 -10000 0 0
FOXO3 -0.004 0.008 -10000 0 -10000 0 0
FOXO1 0.026 0.022 -10000 0 -0.37 1 1
FOXO4 0.011 0.003 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.029 0.005 -10000 0 -10000 0 0
TAT -0.12 0.19 -10000 0 -0.37 132 132
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.02 0.022 -10000 0 -0.26 3 3
PPARGC1A -0.021 0.13 -10000 0 -0.37 45 45
FHL2 -0.012 0.12 -10000 0 -0.37 38 38
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.042 0.027 0.16 6 -0.2 2 8
HIST2H4A -0.002 0.052 0.19 23 -10000 0 23
SIRT1/FOXO3a 0.019 0.028 -10000 0 -0.2 2 2
SIRT1 0.03 0.032 0.2 6 -0.37 1 7
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.044 0.031 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.034 0.043 -10000 0 -0.25 2 2
apoptosis -0.056 0.027 0.17 2 -0.16 5 7
SIRT1/PGC1A 0.006 0.086 0.15 3 -0.22 46 49
p53/SIRT1 0.039 0.049 0.38 6 -0.27 1 7
SIRT1/FOXO4 0.023 0.038 -10000 0 -0.2 3 3
FOXO1/FHL2/SIRT1 0.024 0.081 0.16 2 -0.2 40 42
HIST1H1E 0.016 0.027 0.14 15 -10000 0 15
SIRT1/p300 0.042 0.026 0.16 6 -0.2 2 8
muscle cell differentiation -0.034 0.035 0.29 3 -10000 0 3
TP53 0.026 0.025 0.2 6 -10000 0 6
KU70/SIRT1/BAX 0.056 0.027 0.17 5 -0.18 2 7
CREBBP 0.028 0.006 -10000 0 -10000 0 0
MEF2D 0.023 0.013 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.072 0.15 -10000 0 -0.26 132 132
ACSS2 -0.017 0.03 0.16 6 -0.27 1 7
SIRT1/PCAF/MYOD 0.034 0.035 -10000 0 -0.29 3 3
HIF-2-alpha transcription factor network

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
MMP14 0.008 0.082 0.64 2 -0.65 3 5
oxygen homeostasis 0.005 0.042 0.18 11 -0.092 1 12
TCEB2 0.028 0.006 -10000 0 -10000 0 0
TCEB1 0.023 0.012 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.034 0.15 0.48 16 -0.32 4 20
EPO -0.13 0.35 0.86 13 -0.58 87 100
FIH (dimer) 0.01 0.054 0.24 4 -10000 0 4
APEX1 0.005 0.052 0.22 6 -10000 0 6
SERPINE1 -0.041 0.33 0.85 13 -0.56 40 53
FLT1 -0.031 0.16 -10000 0 -0.64 22 22
ADORA2A -0.008 0.28 0.86 14 -0.6 5 19
germ cell development -0.002 0.26 0.79 16 -0.6 3 19
SLC11A2 0.006 0.28 0.85 13 -0.6 4 17
BHLHE40 0.004 0.28 0.85 13 -0.67 5 18
HIF1AN 0.01 0.054 0.24 4 -10000 0 4
HIF2A/ARNT/SIRT1 -0.022 0.19 0.62 12 -0.41 7 19
ETS1 0.029 0.035 -10000 0 -0.32 2 2
CITED2 -0.038 0.17 -10000 0 -0.64 25 25
KDR -0.038 0.2 -10000 0 -0.75 24 24
PGK1 0.006 0.28 0.85 13 -0.6 4 17
SIRT1 0.013 0.04 0.14 1 -0.37 2 3
response to hypoxia -0.002 0.012 -10000 0 -10000 0 0
HIF2A/ARNT -0.025 0.25 0.78 9 -0.57 10 19
EPAS1 0.033 0.2 0.7 18 -0.37 1 19
SP1 0.039 0.042 0.3 9 -10000 0 9
ABCG2 -0.021 0.27 0.86 9 -0.61 13 22
EFNA1 -0.017 0.25 0.88 9 -0.6 4 13
FXN -0.006 0.29 0.84 15 -0.59 5 20
POU5F1 -0.004 0.26 0.8 16 -0.62 3 19
neuron apoptosis 0.024 0.25 0.56 10 -0.77 9 19
EP300 0.029 0.004 -10000 0 -10000 0 0
EGLN3 0.002 0.091 0.27 12 -0.38 10 22
EGLN2 0.012 0.057 0.23 8 -10000 0 8
EGLN1 0.012 0.049 0.23 5 -10000 0 5
VHL/Elongin B/Elongin C 0.044 0.027 -10000 0 -10000 0 0
VHL 0.03 0.003 -10000 0 -10000 0 0
ARNT 0.006 0.046 0.22 5 -10000 0 5
SLC2A1 -0.007 0.3 0.85 18 -0.59 6 24
TWIST1 -0.006 0.29 0.83 18 -0.6 4 22
ELK1 0.032 0.01 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.005 0.17 0.58 8 -0.4 4 12
VEGFA 0.004 0.26 0.85 11 -0.62 3 14
CREBBP 0.028 0.006 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BAG4 0.019 0.047 -10000 0 -0.37 5 5
Caspase 8 (4 units) 0.026 0.11 0.24 2 -0.25 31 33
NEF -0.006 0.04 -10000 0 -0.21 13 13
NFKBIA 0.034 0.027 0.16 14 -0.1 1 15
BIRC3 -0.021 0.028 0.18 2 -0.44 1 3
CYCS -0.002 0.1 0.27 3 -0.34 11 14
RIPK1 0.027 0.009 -10000 0 -10000 0 0
CD247 0.019 0.045 0.18 2 -0.23 8 10
MAP2K7 0.008 0.16 0.3 2 -0.55 17 19
protein ubiquitination -0.008 0.097 0.26 5 -0.32 9 14
CRADD 0.028 0.021 -10000 0 -0.37 1 1
DAXX 0.027 0.008 -10000 0 -10000 0 0
FAS 0.017 0.068 -10000 0 -0.37 11 11
BID 0.008 0.1 0.18 48 -0.26 30 78
NF-kappa-B/RelA/I kappa B alpha 0.055 0.028 -10000 0 -0.25 1 1
TRADD 0.027 0.008 -10000 0 -10000 0 0
MAP3K5 -0.009 0.11 -10000 0 -0.37 33 33
CFLAR 0.03 0.003 -10000 0 -10000 0 0
FADD 0.028 0.006 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.055 0.028 -10000 0 -0.25 1 1
MAPK8 -0.003 0.15 0.28 1 -0.48 21 22
APAF1 0.029 0.004 -10000 0 -10000 0 0
TRAF1 0.029 0.005 -10000 0 -10000 0 0
TRAF2 0.029 0.005 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.015 0.11 0.19 48 -0.26 31 79
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.009 0.11 0.28 2 -0.34 16 18
CHUK -0.008 0.1 0.27 5 -0.32 13 18
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.042 0.093 -10000 0 -0.22 33 33
TCRz/NEF 0.014 0.047 -10000 0 -0.28 8 8
TNF 0.013 0.071 -10000 0 -0.37 12 12
FASLG 0.003 0.078 0.45 2 -0.46 8 10
NFKB1 0.032 0.027 0.16 13 -10000 0 13
TNFR1A/BAG4/TNF-alpha 0.032 0.062 -10000 0 -0.22 17 17
CASP6 0.001 0.16 -10000 0 -0.47 29 29
CASP7 0.017 0.14 0.44 14 -0.38 13 27
RELA 0.034 0.026 0.16 13 -0.1 1 14
CASP2 0.029 0.005 -10000 0 -10000 0 0
CASP3 0.008 0.14 0.43 14 -0.38 16 30
TNFRSF1A 0.028 0.006 -10000 0 -10000 0 0
TNFR1A/BAG4 0.031 0.039 -10000 0 -0.26 5 5
CASP8 0.029 0.003 -10000 0 -10000 0 0
CASP9 0.028 0.007 -10000 0 -10000 0 0
MAP3K14 -0.009 0.11 0.26 2 -0.32 17 19
APAF-1/Caspase 9 -0.018 0.082 0.18 4 -0.28 11 15
BCL2 -0.006 0.14 -10000 0 -0.46 20 20
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.028 0.006 -10000 0 -10000 0 0
mol:S1P 0 0.003 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.027 0.1 -10000 0 -0.18 80 80
GNAO1 -0.14 0.2 -10000 0 -0.37 153 153
S1P/S1P3/G12/G13 0.048 0.043 0.17 1 -0.21 8 9
AKT1 -0.009 0.11 -10000 0 -0.47 14 14
AKT3 -0.012 0.13 0.56 1 -0.88 4 5
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.028 0.006 -10000 0 -10000 0 0
GNAI2 0.03 0.008 -10000 0 -10000 0 0
GNAI3 0.029 0.009 -10000 0 -10000 0 0
GNAI1 0.027 0.03 -10000 0 -0.37 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.02 0.063 -10000 0 -0.37 9 9
S1PR2 0.026 0.036 -10000 0 -0.37 3 3
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.04 0.12 -10000 0 -0.36 13 13
MAPK3 -0.043 0.11 -10000 0 -0.35 12 12
MAPK1 -0.043 0.12 -10000 0 -0.36 12 12
JAK2 -0.048 0.12 -10000 0 -0.37 17 17
CXCR4 -0.045 0.12 -10000 0 -0.37 12 12
FLT1 0.028 0.013 0.17 1 -10000 0 1
RhoA/GDP 0.022 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.022 0.003 -10000 0 -10000 0 0
SRC -0.042 0.11 0.25 1 -0.34 12 13
S1P/S1P3/Gi -0.04 0.12 -10000 0 -0.36 13 13
RAC1 0.029 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.036 0.12 -10000 0 -0.33 15 15
VEGFA 0.026 0.015 0.17 1 -10000 0 1
S1P/S1P2/Gi -0.039 0.12 0.19 1 -0.21 80 81
VEGFR1 homodimer/VEGFA homodimer 0.038 0.027 0.35 1 -10000 0 1
RHOA 0.029 0.004 -10000 0 -10000 0 0
S1P/S1P3/Gq -0.024 0.1 -10000 0 -0.22 72 72
GNAQ 0.029 0.004 -10000 0 -10000 0 0
GNAZ 0.015 0.025 -10000 0 -0.37 1 1
G12/G13 0.042 0.01 -10000 0 -10000 0 0
GNA14 -0.035 0.15 -10000 0 -0.37 58 58
GNA15 0.028 0.021 -10000 0 -0.37 1 1
GNA12 0.029 0.005 -10000 0 -10000 0 0
GNA13 0.029 0.005 -10000 0 -10000 0 0
GNA11 0.019 0.062 -10000 0 -0.37 9 9
Rac1/GTP -0.038 0.12 -10000 0 -0.33 16 16
Signaling events mediated by PRL

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
CCNE1 0.019 0.014 -10000 0 -10000 0 0
mol:Halofuginone 0.002 0.006 -10000 0 -0.12 1 1
ITGA1 0.027 0.03 -10000 0 -0.37 2 2
CDKN1A -0.033 0.12 -10000 0 -0.42 26 26
PRL-3/alpha Tubulin 0.029 0.021 -10000 0 -10000 0 0
mol:Ca2+ -0.017 0.027 -10000 0 -0.27 3 3
AGT 0.019 0.043 -10000 0 -0.37 4 4
CCNA2 0.02 0.12 0.33 9 -0.62 1 10
TUBA1B 0.03 0.003 -10000 0 -10000 0 0
EGR1 -0.079 0.13 -10000 0 -0.26 121 121
CDK2/Cyclin E1 -0.012 0.11 -10000 0 -0.37 22 22
MAPK3 0.007 0.063 0.21 32 -10000 0 32
PRL-2 /Rab GGTase beta 0.041 0.011 -10000 0 -10000 0 0
MAPK1 0.006 0.063 0.21 32 -10000 0 32
PTP4A1 -0.068 0.096 -10000 0 -0.79 1 1
PTP4A3 0.019 0.014 -10000 0 -10000 0 0
PTP4A2 0.028 0.007 -10000 0 -10000 0 0
ITGB1 0.006 0.062 0.21 31 -10000 0 31
SRC 0.029 0.005 -10000 0 -10000 0 0
RAC1 0.002 0.055 -10000 0 -0.32 2 2
Rab GGTase beta/Rab GGTase alpha 0.042 0.01 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.12 0.13 -10000 0 -0.37 40 40
RABGGTA 0.029 0.003 -10000 0 -10000 0 0
BCAR1 -0.016 0.013 -10000 0 -10000 0 0
RHOC -0.006 0.077 -10000 0 -0.36 9 9
RHOA 0 0.063 -10000 0 -0.36 4 4
cell motility 0.003 0.08 0.27 1 -0.34 5 6
PRL-1/alpha Tubulin -0.062 0.1 0.35 1 -0.75 1 2
PRL-3/alpha1 Integrin 0.027 0.03 -10000 0 -0.26 2 2
ROCK1 0.007 0.074 0.27 1 -0.35 4 5
RABGGTB 0.029 0.006 -10000 0 -10000 0 0
CDK2 0.029 0.003 -10000 0 -10000 0 0
mitosis -0.068 0.096 -10000 0 -0.78 1 1
ATF5 -0.11 0.19 -10000 0 -0.37 123 123
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.002 0.038 -10000 0 -10000 0 0
HSPA8 0.03 0.022 -10000 0 -0.36 1 1
SMAD3/SMAD4/ER alpha -0.12 0.14 -10000 0 -0.26 166 166
AKT1 0.031 0.021 -10000 0 -10000 0 0
GSC 0.047 0.16 0.68 15 -0.42 1 16
NKX2-5 0 0 -10000 0 -10000 0 0
muscle cell differentiation -0.005 0.072 0.28 2 -10000 0 2
SMAD2-3/SMAD4/SP1 0.059 0.1 0.4 4 -0.3 2 6
SMAD4 0.002 0.06 -10000 0 -10000 0 0
CBFB 0.027 0.008 -10000 0 -10000 0 0
SAP18 0.029 0.007 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.017 0.056 -10000 0 -10000 0 0
SMAD3/SMAD4/VDR 0.024 0.093 0.33 1 -0.24 8 9
MYC -0.026 0.12 -10000 0 -0.34 46 46
CDKN2B -0.006 0.18 0.6 16 -0.48 6 22
AP1 -0.067 0.13 -10000 0 -0.3 31 31
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.004 0.1 -10000 0 -0.3 27 27
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.01 0.068 0.28 12 -0.32 3 15
SP3 0.03 0.003 -10000 0 -10000 0 0
CREB1 0.029 0.003 -10000 0 -10000 0 0
FOXH1 0.022 0.02 0.17 1 -10000 0 1
SMAD3/SMAD4/GR 0.039 0.086 0.26 1 -10000 0 1
GATA3 -0.014 0.12 0.18 1 -0.28 47 48
SKI/SIN3/HDAC complex/NCoR1 -0.009 0.099 -10000 0 -0.32 24 24
MEF2C/TIF2 0.01 0.078 0.26 2 -0.23 1 3
endothelial cell migration 0.32 0.55 1.2 101 -10000 0 101
MAX 0.04 0.023 -10000 0 -10000 0 0
RBBP7 0.03 0.004 -10000 0 -10000 0 0
RBBP4 0.029 0.007 -10000 0 -10000 0 0
RUNX2 0.02 0.051 -10000 0 -0.37 6 6
RUNX3 0.019 0.059 -10000 0 -0.37 8 8
RUNX1 0.028 0.021 -10000 0 -0.37 1 1
CTBP1 0.029 0.005 -10000 0 -10000 0 0
NR3C1 0.041 0.022 -10000 0 -10000 0 0
VDR 0.021 0.055 -10000 0 -0.37 7 7
CDKN1A -0.024 0.2 -10000 0 -1.2 10 10
KAT2B 0.005 0.046 -10000 0 -0.38 3 3
SMAD2/SMAD2/SMAD4/FOXH1 0.041 0.067 0.33 10 -10000 0 10
DCP1A 0.029 0.003 -10000 0 -10000 0 0
SKI 0.028 0.009 -10000 0 -10000 0 0
SERPINE1 -0.32 0.56 -10000 0 -1.2 101 101
SMAD3/SMAD4/ATF2 0.013 0.081 0.26 1 -0.23 5 6
SMAD3/SMAD4/ATF3 0.009 0.084 0.26 1 -0.28 12 13
SAP30 0.028 0.009 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.011 0.056 -10000 0 -10000 0 0
JUN -0.076 0.12 -10000 0 -0.31 29 29
SMAD3/SMAD4/IRF7 0.014 0.083 0.26 1 -0.27 5 6
TFE3 0.004 0.051 0.19 4 -10000 0 4
COL1A2 0.074 0.15 0.58 16 -0.71 5 21
mesenchymal cell differentiation -0.01 0.08 0.29 6 -10000 0 6
DLX1 0.023 0.009 -10000 0 -10000 0 0
TCF3 0.029 0.004 -10000 0 -10000 0 0
FOS -0.15 0.2 -10000 0 -0.38 160 160
SMAD3/SMAD4/Max 0.038 0.087 0.26 1 -10000 0 1
Cbp/p300/SNIP1 0.022 0.051 -10000 0 -10000 0 0
ZBTB17 0.02 0.035 -10000 0 -0.16 11 11
LAMC1 -0.027 0.046 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.017 0.075 0.26 1 -10000 0 1
IRF7 0.024 0.047 -10000 0 -0.37 5 5
ESR1 -0.17 0.2 -10000 0 -0.37 178 178
HNF4A 0.022 0.051 -10000 0 -0.37 6 6
MEF2C 0.047 0.098 0.27 14 -10000 0 14
SMAD2-3/SMAD4 0.025 0.084 0.31 1 -10000 0 1
Cbp/p300/Src-1 0.019 0.055 -10000 0 -10000 0 0
IGHV3OR16-13 0.003 0.03 -10000 0 -0.34 2 2
TGIF2/HDAC complex 0.029 0.003 -10000 0 -10000 0 0
CREBBP 0.005 0.034 -10000 0 -10000 0 0
SKIL 0.03 0.003 -10000 0 -10000 0 0
HDAC1 0.029 0.007 -10000 0 -10000 0 0
HDAC2 0.029 0.008 -10000 0 -10000 0 0
SNIP1 0.031 0.008 -10000 0 -10000 0 0
GCN5L2 -0.009 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.004 0.087 -10000 0 -0.23 1 1
MSG1/HSC70 0.044 0.015 -10000 0 -10000 0 0
SMAD2 0.036 0.022 0.17 1 -10000 0 1
SMAD3 -0.001 0.059 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.007 0.048 0.21 1 -0.21 2 3
SMAD2/SMAD2/SMAD4 0.002 0.048 0.22 1 -0.26 3 4
NCOR1 0.026 0.011 -10000 0 -10000 0 0
NCOA2 -0.013 0.11 -10000 0 -0.37 33 33
NCOA1 0.03 0.003 -10000 0 -10000 0 0
MYOD/E2A 0.034 0.006 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.077 0.11 0.44 4 -0.34 1 5
IFNB1 -0.023 0.055 -10000 0 -0.26 3 3
SMAD3/SMAD4/MEF2C 0.06 0.1 0.33 5 -10000 0 5
CITED1 0.028 0.007 -10000 0 -10000 0 0
SMAD2-3/SMAD4/ARC105 0.037 0.088 0.31 1 -10000 0 1
RBL1 0.028 0.007 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.015 0.078 0.35 13 -0.31 2 15
RUNX1-3/PEBPB2 0.046 0.049 -10000 0 -0.24 8 8
SMAD7 -0.085 0.16 0.39 1 -0.51 12 13
MYC/MIZ-1 -0.011 0.1 -10000 0 -0.26 47 47
SMAD3/SMAD4 -0.13 0.22 -10000 0 -0.45 104 104
IL10 -0.042 0.13 0.51 1 -0.44 26 27
PIASy/HDAC complex 0.037 0.014 -10000 0 -10000 0 0
PIAS3 0.007 0.025 -10000 0 -10000 0 0
CDK2 0.006 0.033 -10000 0 -10000 0 0
IL5 -0.043 0.1 0.36 1 -0.34 15 16
CDK4 0.005 0.033 -10000 0 -10000 0 0
PIAS4 0.037 0.014 -10000 0 -10000 0 0
ATF3 0.009 0.074 -10000 0 -0.37 13 13
SMAD3/SMAD4/SP1 0.025 0.1 0.36 3 -0.3 4 7
FOXG1 0.018 0.006 -10000 0 -10000 0 0
FOXO3 -0.009 0.029 0.14 6 -10000 0 6
FOXO1 -0.011 0.031 0.14 8 -0.26 1 9
FOXO4 -0.01 0.029 0.14 6 -10000 0 6
heart looping 0.047 0.097 0.27 14 -10000 0 14
CEBPB 0.031 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.014 0.071 -10000 0 -10000 0 0
MYOD1 0.018 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.013 0.079 -10000 0 -0.31 3 3
SMAD3/SMAD4/GATA3 -0.011 0.13 -10000 0 -0.3 44 44
SnoN/SIN3/HDAC complex/NCoR1 0.029 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.039 0.09 -10000 0 -0.26 8 8
SMAD3/SMAD4/SP1-3 0.045 0.1 0.38 2 -0.28 3 5
MED15 0.029 0.005 -10000 0 -10000 0 0
SP1 0.032 0.037 0.17 1 -0.18 2 3
SIN3B 0.03 0.004 -10000 0 -10000 0 0
SIN3A 0.03 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.044 0.065 0.32 10 -10000 0 10
ITGB5 -0.017 0.072 0.31 3 -0.33 1 4
TGIF/SIN3/HDAC complex/CtBP 0.004 0.07 -10000 0 -0.28 14 14
SMAD3/SMAD4/AR -0.052 0.13 -10000 0 -0.26 87 87
AR -0.078 0.18 -10000 0 -0.37 98 98
negative regulation of cell growth 0.017 0.068 0.24 1 -0.28 5 6
SMAD3/SMAD4/MYOD 0.012 0.073 0.25 1 -10000 0 1
E2F5 0.021 0.024 -10000 0 -0.37 1 1
E2F4 0.027 0.008 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.055 0.073 0.32 7 -10000 0 7
SMAD2-3/SMAD4/FOXO1-3a-4 0.014 0.065 0.29 12 -10000 0 12
TFDP1 0.028 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.054 0.14 -10000 0 -0.3 33 33
SMAD3/SMAD4/RUNX2 0.01 0.08 -10000 0 -0.29 6 6
TGIF2 0.029 0.003 -10000 0 -10000 0 0
TGIF1 0.029 0.004 -10000 0 -10000 0 0
ATF2 0.024 0.047 -10000 0 -0.37 5 5
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.037 0.069 -9999 0 -0.23 22 22
E-cadherin/beta catenin 0.022 0.074 -9999 0 -0.26 22 22
CTNNB1 0.03 0.003 -9999 0 -10000 0 0
JUP 0.029 0.003 -9999 0 -10000 0 0
CDH1 0.003 0.095 -9999 0 -0.37 22 22
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 -0.015 0.013 -10000 0 -10000 0 0
SMARCC1 0.009 0.018 -10000 0 -10000 0 0
REL 0.011 0.074 -10000 0 -0.37 12 12
HDAC7 -0.056 0.11 -10000 0 -0.31 28 28
JUN 0.023 0.052 -10000 0 -0.37 6 6
EP300 0.029 0.005 -10000 0 -10000 0 0
KAT2B 0.027 0.036 -10000 0 -0.37 3 3
KAT5 0.027 0.01 -10000 0 -10000 0 0
MAPK14 -0.015 0.051 0.2 5 -0.27 7 12
FOXO1 0.027 0.023 -10000 0 -0.37 1 1
T-DHT/AR -0.023 0.13 -10000 0 -0.31 31 31
MAP2K6 0.016 0.059 -10000 0 -0.37 7 7
BRM/BAF57 0.039 0.048 -10000 0 -0.27 6 6
MAP2K4 0.022 0.022 -10000 0 -10000 0 0
SMARCA2 0.023 0.053 -10000 0 -0.37 6 6
PDE9A -0.082 0.27 0.52 1 -0.86 36 37
NCOA2 -0.011 0.11 -10000 0 -0.37 33 33
CEBPA 0.022 0.039 -10000 0 -0.37 3 3
EHMT2 0.028 0.012 -10000 0 -10000 0 0
cell proliferation 0.015 0.15 0.42 17 -0.43 6 23
NR0B1 0.017 0.009 -10000 0 -10000 0 0
EGR1 -0.1 0.19 -10000 0 -0.37 121 121
RXRs/9cRA 0.035 0.045 0.2 3 -0.2 5 8
AR/RACK1/Src -0.005 0.15 0.42 27 -0.29 12 39
AR/GR -0.044 0.12 0.23 3 -0.23 89 92
GNB2L1 0.03 0.008 -10000 0 -10000 0 0
PKN1 0.03 0.005 -10000 0 -10000 0 0
RCHY1 0.027 0.008 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0.002 0.007 0.027 27 -10000 0 27
MAPK8 -0.022 0.055 -10000 0 -0.25 15 15
T-DHT/AR/TIF2/CARM1 -0.025 0.13 0.41 15 -0.31 19 34
SRC -0.008 0.086 0.32 5 -0.22 15 20
NR3C1 0.029 0.005 -10000 0 -10000 0 0
KLK3 0.015 0.21 0.62 20 -1.1 6 26
APPBP2 0.021 0.022 -10000 0 -10000 0 0
TRIM24 0.031 0.016 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.031 0.1 0.31 3 -0.28 20 23
TMPRSS2 -0.054 0.23 -10000 0 -0.92 22 22
RXRG 0.015 0.043 -10000 0 -0.37 4 4
mol:9cRA 0 0.002 -10000 0 -10000 0 0
RXRA 0.028 0.022 -10000 0 -0.37 1 1
RXRB 0.028 0.009 -10000 0 -10000 0 0
CARM1 0.031 0.008 -10000 0 -10000 0 0
NR2C2 0.025 0.046 -10000 0 -0.37 5 5
KLK2 -0.01 0.16 0.63 15 -0.36 7 22
AR -0.049 0.12 0.28 2 -0.25 83 85
SENP1 0.03 0.005 -10000 0 -10000 0 0
HSP90AA1 0.028 0.007 -10000 0 -10000 0 0
MDM2 0.023 0.028 -10000 0 -0.094 19 19
SRY -0.004 0.018 0.031 6 -0.076 20 26
GATA2 0.027 0.03 -10000 0 -0.37 2 2
MYST2 -0.001 0.004 -10000 0 -0.02 9 9
HOXB13 0.024 0.038 0.23 10 -10000 0 10
T-DHT/AR/RACK1/Src -0.019 0.12 0.33 16 -0.3 12 28
positive regulation of transcription 0.027 0.03 -10000 0 -0.37 2 2
DNAJA1 0.021 0.023 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.019 -10000 0 -0.22 2 2
NCOA1 0.035 0.02 -10000 0 -10000 0 0
SPDEF 0.029 0.042 0.26 9 -10000 0 9
T-DHT/AR/TIF2 -0.016 0.12 0.28 6 -0.32 27 33
T-DHT/AR/Hsp90 -0.028 0.1 0.33 3 -0.27 20 23
GSK3B 0.029 0.012 -10000 0 -10000 0 0
NR2C1 0.026 0.017 -10000 0 -10000 0 0
mol:T-DHT -0.02 0.071 0.24 7 -0.23 15 22
SIRT1 0.027 0.03 -10000 0 -0.37 2 2
ZMIZ2 0.022 0.031 -10000 0 -0.11 16 16
POU2F1 0.011 0.048 0.29 1 -0.18 1 2
T-DHT/AR/DAX-1 -0.025 0.096 0.35 2 -0.28 18 20
CREBBP 0.029 0.007 -10000 0 -10000 0 0
SMARCE1 0.03 0.013 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.022 0.085 -10000 0 -0.41 12 12
HDAC1 0.032 0.017 0.12 1 -10000 0 1
AES 0.03 0.009 -10000 0 -10000 0 0
FBXW11 0.029 0.005 -10000 0 -10000 0 0
DTX1 -0.077 0.18 -10000 0 -0.37 97 97
LRP6/FZD1 0.034 0.046 -10000 0 -0.26 8 8
TLE1 0.029 0.022 -10000 0 -0.37 1 1
AP1 -0.072 0.15 0.18 1 -0.26 123 124
NCSTN 0.023 0.013 -10000 0 -10000 0 0
ADAM10 0.028 0.021 -10000 0 -0.37 1 1
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.035 0.18 -10000 0 -0.64 21 21
NICD/RBPSUH 0.049 0.087 -10000 0 -0.39 11 11
WIF1 0.018 0.01 -10000 0 -10000 0 0
NOTCH1 0.009 0.071 -10000 0 -0.41 10 10
PSENEN 0.029 0.004 -10000 0 -10000 0 0
KREMEN2 0.023 0.011 -10000 0 -10000 0 0
DKK1 0.018 0.014 -10000 0 -10000 0 0
beta catenin/beta TrCP1 0.004 0.086 -10000 0 -0.26 5 5
APH1B 0.029 0.004 -10000 0 -10000 0 0
APH1A 0.023 0.013 -10000 0 -10000 0 0
AXIN1 0.006 0.1 -10000 0 -0.43 13 13
CtBP/CBP/TCF1/TLE1/AES 0.023 0.063 0.27 4 -0.27 3 7
PSEN1 0.028 0.007 -10000 0 -10000 0 0
FOS -0.15 0.2 -10000 0 -0.37 160 160
JUN 0.022 0.051 -10000 0 -0.37 6 6
MAP3K7 0.029 0.011 -10000 0 -10000 0 0
CTNNB1 -0.006 0.082 -10000 0 -0.26 5 5
MAPK3 0.029 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.038 0.028 -10000 0 -10000 0 0
HNF1A 0.026 0.042 -10000 0 -0.37 4 4
CTBP1 0.03 0.009 -10000 0 -10000 0 0
MYC -0.14 0.42 -10000 0 -1.3 43 43
NKD1 0.005 0.079 -10000 0 -0.37 15 15
FZD1 0.02 0.059 -10000 0 -0.37 8 8
NOTCH1 precursor/Deltex homolog 1 0.002 0.12 -10000 0 -0.45 12 12
apoptosis -0.072 0.15 0.18 1 -0.26 123 124
Delta 1/NOTCHprecursor 0.042 0.093 -10000 0 -0.4 12 12
DLL1 0.022 0.042 -10000 0 -0.37 4 4
PPARD 0.003 0.1 -10000 0 -1 3 3
Gamma Secretase 0.06 0.042 -10000 0 -10000 0 0
APC 0.022 0.056 0.24 1 -0.3 4 5
DVL1 0.013 0.035 -10000 0 -0.25 1 1
CSNK2A1 0.028 0.007 -10000 0 -10000 0 0
MAP3K7IP1 0.001 0.006 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.033 0.029 -10000 0 -10000 0 0
LRP6 0.028 0.006 -10000 0 -10000 0 0
CSNK1A1 0.028 0.007 -10000 0 -10000 0 0
NLK 0.015 0.015 -10000 0 -10000 0 0
CCND1 -0.04 0.27 0.6 1 -1.3 16 17
WNT1 0.025 0.009 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.023 0.099 0.32 2 -0.37 6 8
DKK2 0.023 0.012 -10000 0 -10000 0 0
NOTCH1 precursor/DVL1 0.012 0.087 -10000 0 -0.43 6 6
GSK3B 0.03 0.001 -10000 0 -10000 0 0
FRAT1 0.028 0.022 -10000 0 -0.37 1 1
NOTCH/Deltex homolog 1 -0.015 0.11 -10000 0 -0.45 12 12
PPP2R5D -0.021 0.11 -10000 0 -0.35 8 8
MAPK1 0.029 0.004 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.066 0.054 -10000 0 -0.2 8 8
RBPJ 0.029 0.006 -10000 0 -10000 0 0
CREBBP 0.025 0.015 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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
HDAC1 0.031 0.058 0.21 17 -10000 0 17
AES 0.031 0.051 0.2 15 -10000 0 15
FBXW11 0.029 0.005 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
LRP6/FZD1 0.034 0.046 -10000 0 -0.26 8 8
SMAD4 0.029 0.006 -10000 0 -10000 0 0
DKK2 0.023 0.012 -10000 0 -10000 0 0
TLE1 0.029 0.054 0.19 15 -0.37 1 16
MACF1 0.028 0.007 -10000 0 -10000 0 0
CTNNB1 0.024 0.079 0.27 5 -0.28 1 6
WIF1 0.018 0.011 -10000 0 -10000 0 0
beta catenin/RanBP3 0.05 0.19 0.44 49 -0.38 3 52
KREMEN2 0.023 0.011 -10000 0 -10000 0 0
DKK1 0.018 0.014 -10000 0 -10000 0 0
beta catenin/beta TrCP1 0.034 0.081 0.28 4 -0.26 1 5
FZD1 0.02 0.059 -10000 0 -0.37 8 8
AXIN2 -0.007 0.39 0.61 52 -1.2 22 74
AXIN1 0.028 0.007 -10000 0 -10000 0 0
RAN 0.03 0.004 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.016 0.11 -10000 0 -0.43 17 17
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.041 0.12 0.31 2 -0.47 10 12
Axin1/APC/GSK3 -0.002 0.064 0.24 2 -0.38 1 3
Axin1/APC/GSK3/beta catenin/Macf1 0.02 0.058 0.39 1 -0.42 1 2
HNF1A 0.025 0.064 0.19 13 -0.36 4 17
CTBP1 0.029 0.052 0.2 16 -10000 0 16
MYC -0.007 0.54 0.57 92 -1.3 41 133
RANBP3 0.03 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.039 0.028 -10000 0 -10000 0 0
NKD1 0.005 0.079 -10000 0 -0.37 15 15
TCF4 0.029 0.05 0.21 12 -10000 0 12
TCF3 0.03 0.051 0.2 13 -10000 0 13
WNT1/LRP6/FZD1/Axin1 0.062 0.048 -10000 0 -0.2 8 8
Ran/GTP 0.022 0.005 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.039 0.27 0.59 40 -0.46 17 57
LEF1 0.023 0.045 0.22 11 -10000 0 11
DVL1 0.006 0.061 0.27 1 -0.4 2 3
CSNK2A1 0.029 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.027 0.15 -10000 0 -0.42 16 16
DKK1/LRP6/Kremen 2 0.033 0.029 -10000 0 -10000 0 0
LRP6 0.029 0.006 -10000 0 -10000 0 0
CSNK1A1 0.032 0.058 0.23 16 -10000 0 16
NLK 0.022 0.022 -10000 0 -10000 0 0
CCND1 -0.043 0.33 0.67 15 -1.3 17 32
WNT1 0.024 0.011 -10000 0 -10000 0 0
GSK3A 0.029 0.004 -10000 0 -10000 0 0
GSK3B 0.03 0.001 -10000 0 -10000 0 0
FRAT1 0.028 0.022 -10000 0 -0.37 1 1
PPP2R5D -0.021 0.12 0.25 3 -0.28 21 24
APC -0.021 0.051 0.18 13 -0.2 6 19
WNT1/LRP6/FZD1 0.003 0.057 0.19 1 -0.2 10 11
CREBBP 0.029 0.051 0.19 15 -10000 0 15
Effects of Botulinum toxin

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
STX1A -0.002 0.039 0.2 13 -10000 0 13
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.035 0.013 -10000 0 -10000 0 0
STXBP1 0.027 0.03 -10000 0 -0.37 2 2
ACh/CHRNA1 0.007 0.041 -10000 0 -0.098 26 26
RAB3GAP2/RIMS1/UNC13B 0.039 0.026 -10000 0 -10000 0 0
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 0.021 0.008 -10000 0 -10000 0 0
mol:ACh -0.005 0.047 0.086 28 -0.12 26 54
RAB3GAP2 0.024 0.012 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.022 0.067 0.19 5 -0.17 15 20
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.007 0.041 -10000 0 -0.098 26 26
UNC13B 0.029 0.005 -10000 0 -10000 0 0
CHRNA1 0.024 0.008 -10000 0 -10000 0 0
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.026 0.1 0.1 4 -0.21 72 76
SNAP25 -0.015 0.063 -10000 0 -0.24 27 27
VAMP2 0.003 0.001 -10000 0 -10000 0 0
SYT1 -0.034 0.14 -10000 0 -0.37 56 56
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.028 0.032 0.16 13 -0.22 2 15
STX1A/SNAP25 fragment 1/VAMP2 0.022 0.067 0.19 5 -0.17 15 20
TCGA08_rtk_signaling

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
PDGFRA -0.12 0.19 -10000 0 -0.37 133 133
HRAS 0.029 0.004 -10000 0 -10000 0 0
EGFR 0.019 0.062 -10000 0 -0.37 9 9
AKT -0.007 0.08 0.24 1 -0.27 7 8
FOXO3 0.028 0.008 -10000 0 -10000 0 0
AKT1 0.028 0.008 -10000 0 -10000 0 0
FOXO1 0.026 0.022 -10000 0 -0.37 1 1
AKT3 0.022 0.031 -10000 0 -0.37 2 2
FOXO4 0.03 0.002 -10000 0 -10000 0 0
MET 0.027 0.022 -10000 0 -0.37 1 1
PIK3CA 0.028 0.021 -10000 0 -0.37 1 1
PIK3CB 0.03 0.002 -10000 0 -10000 0 0
NRAS 0.029 0.005 -10000 0 -10000 0 0
PIK3CG 0.015 0.074 -10000 0 -0.37 13 13
PIK3R3 0.028 0.007 -10000 0 -10000 0 0
PIK3R2 0.029 0.005 -10000 0 -10000 0 0
NF1 0.029 0.005 -10000 0 -10000 0 0
RAS -0.034 0.074 -10000 0 -0.14 116 116
ERBB2 0.023 0.051 -10000 0 -0.37 6 6
proliferation/survival/translation -0.02 0.075 0.24 17 -10000 0 17
PI3K -0.024 0.073 0.25 1 -0.18 23 24
PIK3R1 0.027 0.03 -10000 0 -0.37 2 2
KRAS 0.029 0.005 -10000 0 -10000 0 0
FOXO 0.026 0.057 0.25 1 -0.11 1 2
AKT2 0.029 0.005 -10000 0 -10000 0 0
PTEN 0.028 0.007 -10000 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.029 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0.021 0.004 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.028 0.009 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.029 0.047 -10000 0 -0.22 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.028 0.005 -10000 0 -10000 0 0
GRK1 0.017 0.004 -10000 0 -10000 0 0
CNG Channel -0.008 0.1 -10000 0 -0.2 71 71
mol:Na + -0.005 0.098 -10000 0 -0.2 65 65
mol:ADP 0.017 0.004 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.043 0.049 -10000 0 -0.23 10 10
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.002 0.11 -10000 0 -0.2 64 64
CNGB1 0.022 0.01 -10000 0 -10000 0 0
RDH5 -0.025 0.14 -10000 0 -0.37 50 50
SAG 0.019 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.02 0.13 0.32 22 -0.34 2 24
Na + (4 Units) -0.015 0.091 -10000 0 -0.19 64 64
RGS9 0.017 0.065 -10000 0 -0.37 10 10
GNB1/GNGT1 0.029 0.016 -10000 0 -10000 0 0
GNAT1/GDP 0.06 0.051 -10000 0 -0.2 10 10
GUCY2D 0.019 0.013 -10000 0 -10000 0 0
GNGT1 0.017 0.009 -10000 0 -10000 0 0
GUCY2F 0.02 0.005 -10000 0 -10000 0 0
GNB5 0.029 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) 0.009 0.053 0.15 1 -0.19 11 12
mol:11-cis-retinal -0.025 0.14 -10000 0 -0.37 50 50
mol:cGMP 0.043 0.058 -10000 0 -0.2 7 7
GNB1 0.027 0.009 -10000 0 -10000 0 0
Rhodopsin 0.001 0.1 -10000 0 -0.26 45 45
SLC24A1 0.029 0.004 -10000 0 -10000 0 0
CNGA1 -0.067 0.17 -10000 0 -0.37 87 87
Metarhodopsin II 0.025 0.009 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.052 0.056 -10000 0 -0.21 7 7
RGS9BP 0.026 0.007 -10000 0 -10000 0 0
Metarhodopsin II/Transducin 0.028 0.036 -10000 0 -10000 0 0
GCAP Family/Ca ++ 0.035 0.036 -10000 0 -0.2 7 7
PDE6A/B 0.034 0.027 -10000 0 -0.26 2 2
mol:Pi 0.043 0.049 -10000 0 -0.23 10 10
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.039 0.022 -10000 0 -10000 0 0
PDE6B 0.025 0.03 -10000 0 -0.37 2 2
PDE6A 0.025 0.008 -10000 0 -10000 0 0
PDE6G 0.015 0.071 -10000 0 -0.37 12 12
RHO 0.024 0.008 -10000 0 -10000 0 0
PDE6 0.065 0.078 -10000 0 -0.21 20 20
GUCA1A 0.019 0.008 -10000 0 -10000 0 0
GC2/GCAP Family 0.047 0.04 -10000 0 -0.21 7 7
GUCA1C 0.018 0 -10000 0 -10000 0 0
GUCA1B 0.019 0.055 -10000 0 -0.37 7 7
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.018 0.088 0.31 5 -0.38 11 16
CRKL -0.014 0.083 0.33 5 -0.4 10 15
HRAS -0.004 0.09 0.34 5 -0.35 9 14
mol:PIP3 0.024 0.1 0.32 5 -0.38 8 13
SPRED1 0.028 0.021 -10000 0 -0.37 1 1
SPRED2 0.029 0.003 -10000 0 -10000 0 0
GAB1 -0.009 0.087 0.36 5 -0.41 10 15
FOXO3 -0.011 0.12 0.34 3 -0.41 16 19
AKT1 -0.008 0.13 0.34 4 -0.42 19 23
BAD -0.012 0.12 0.34 3 -0.41 17 20
megakaryocyte differentiation -0.02 0.097 0.36 5 -0.4 12 17
GSK3B -0.012 0.12 0.34 3 -0.4 18 21
RAF1 0.015 0.092 0.31 6 -0.3 8 14
SHC1 0.022 0.013 -10000 0 -10000 0 0
STAT3 -0.013 0.091 0.36 5 -0.4 11 16
STAT1 -0.048 0.2 0.49 3 -1 11 14
HRAS/SPRED1 0.023 0.093 0.32 5 -0.29 9 14
cell proliferation -0.02 0.096 0.36 4 -0.42 12 16
PIK3CA 0.029 0.021 -10000 0 -0.37 1 1
TEC 0.022 0.051 -10000 0 -0.37 6 6
RPS6KB1 0.003 0.099 0.37 4 -0.42 11 15
HRAS/SPRED2 0.023 0.093 0.32 5 -0.3 9 14
LYN/TEC/p62DOK 0.029 0.097 0.36 4 -0.38 9 13
MAPK3 0.012 0.083 0.28 5 -0.26 4 9
STAP1 -0.008 0.089 0.36 5 -0.41 10 15
GRAP2 0.02 0.059 -10000 0 -0.37 8 8
JAK2 -0.042 0.18 0.48 3 -0.85 12 15
STAT1 (dimer) -0.047 0.2 0.49 3 -0.98 11 14
mol:Gleevec 0 0.005 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.031 0.11 0.36 5 -0.4 9 14
actin filament polymerization -0.012 0.089 0.36 5 -0.4 10 15
LYN 0.025 0.011 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.017 0.12 0.39 5 -0.56 12 17
PIK3R1 0.027 0.03 -10000 0 -0.37 2 2
CBL/CRKL/GRB2 0.003 0.09 0.33 5 -0.36 10 15
PI3K 0.029 0.11 0.37 4 -0.42 11 15
PTEN 0.028 0.007 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.082 0.25 -10000 0 -1.2 11 11
MAPK8 -0.021 0.098 0.36 4 -0.42 12 16
STAT3 (dimer) -0.013 0.09 0.36 5 -0.4 11 16
positive regulation of transcription 0.013 0.073 0.25 7 -0.22 3 10
mol:GDP -0.001 0.095 0.35 5 -0.37 10 15
PIK3C2B -0.01 0.085 0.36 5 -0.4 9 14
CBL/CRKL -0.004 0.088 0.33 5 -0.37 11 16
FER -0.014 0.089 0.36 4 -0.4 11 15
SH2B3 -0.012 0.089 0.36 5 -0.41 10 15
PDPK1 0.019 0.095 0.32 3 -0.35 8 11
SNAI2 -0.011 0.09 0.36 5 -0.4 9 14
positive regulation of cell proliferation -0.026 0.15 0.46 3 -0.7 12 15
KITLG 0.01 0.03 -10000 0 -10000 0 0
cell motility -0.026 0.15 0.46 3 -0.7 12 15
PTPN6 0.028 0.012 -10000 0 -10000 0 0
EPOR -0.014 0.17 -10000 0 -0.7 12 12
STAT5A (dimer) -0.017 0.13 0.42 4 -0.57 12 16
SOCS1 0.026 0.03 -10000 0 -0.37 2 2
cell migration 0.012 0.093 0.39 12 -0.36 5 17
SOS1 0.03 0.002 -10000 0 -10000 0 0
EPO -0.12 0.19 -10000 0 -0.38 130 130
VAV1 0.013 0.079 -10000 0 -0.37 15 15
GRB10 -0.013 0.091 0.36 5 -0.4 11 16
PTPN11 0.029 0.01 -10000 0 -10000 0 0
SCF/KIT -0.008 0.095 0.39 5 -0.42 11 16
GO:0007205 0.001 0.006 -10000 0 -10000 0 0
MAP2K1 0.01 0.079 0.29 4 -0.27 2 6
CBL 0.028 0.006 -10000 0 -10000 0 0
KIT -0.04 0.27 0.64 5 -1.1 17 22
MAP2K2 0.013 0.082 0.3 7 -0.27 2 9
SHC/Grb2/SOS1 0.028 0.093 0.36 5 -0.39 8 13
STAT5A -0.018 0.13 0.42 4 -0.59 12 16
GRB2 0.028 0.006 -10000 0 -10000 0 0
response to radiation -0.011 0.089 0.36 5 -0.39 9 14
SHC/GRAP2 0.027 0.04 -10000 0 -0.26 5 5
PTPRO -0.021 0.098 0.36 5 -0.41 12 17
SH2B2 -0.012 0.09 0.36 5 -0.4 10 15
DOK1 0.03 0.002 -10000 0 -10000 0 0
MATK -0.013 0.094 0.36 5 -0.4 12 17
CREBBP 0.034 0.044 0.34 5 -10000 0 5
BCL2 -0.021 0.19 -10000 0 -0.8 13 13
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.02 0.018 -10000 0 -0.22 1 1
EPHB2 0.021 0.024 -10000 0 -0.37 1 1
Syndecan-2/TACI 0.015 0.022 -10000 0 -0.22 2 2
LAMA1 -0.022 0.13 -10000 0 -0.37 43 43
Syndecan-2/alpha2 ITGB1 0.051 0.051 -10000 0 -0.2 2 2
HRAS 0.029 0.004 -10000 0 -10000 0 0
Syndecan-2/CASK 0.004 0.003 -10000 0 -10000 0 0
ITGA5 0.03 0.003 -10000 0 -10000 0 0
BAX -0.013 0.028 -10000 0 -10000 0 0
EPB41 0.028 0.007 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.019 0.011 -10000 0 -10000 0 0
LAMA3 0.02 0.043 -10000 0 -0.37 4 4
EZR 0.026 0.023 -10000 0 -0.37 1 1
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.018 0.065 -10000 0 -0.37 10 10
Syndecan-2/MMP2 0.013 0.037 -10000 0 -0.22 8 8
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.035 0.018 -10000 0 -10000 0 0
dendrite morphogenesis 0.015 0.018 -10000 0 -0.22 1 1
Syndecan-2/GM-CSF 0.017 0.011 -10000 0 -10000 0 0
determination of left/right symmetry 0.006 0.004 -10000 0 -10000 0 0
Syndecan-2/PKC delta 0.021 0.012 -10000 0 -10000 0 0
GNB2L1 0.029 0.006 -10000 0 -10000 0 0
MAPK3 0.032 0.086 0.18 87 -10000 0 87
MAPK1 0.032 0.086 0.18 87 -10000 0 87
Syndecan-2/RACK1 0.031 0.02 -10000 0 -10000 0 0
NF1 0.029 0.005 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.006 0.004 -10000 0 -10000 0 0
ITGA2 0.024 0.012 -10000 0 -10000 0 0
MAPK8 -0.013 0.033 -10000 0 -0.22 9 9
Syndecan-2/alpha2/beta1 Integrin 0.037 0.073 -10000 0 -0.19 20 20
Syndecan-2/Kininogen 0.005 0.059 -10000 0 -0.22 23 23
ITGB1 0.029 0.005 -10000 0 -10000 0 0
SRC 0.034 0.094 0.19 88 -10000 0 88
Syndecan-2/CASK/Protein 4.1 0.018 0.012 -10000 0 -10000 0 0
extracellular matrix organization 0.02 0.013 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.02 0.018 -10000 0 -0.22 1 1
Syndecan-2/Caveolin-2/Ras 0.029 0.034 -10000 0 -0.2 5 5
Syndecan-2/Laminin alpha3 0.016 0.022 -10000 0 -0.22 2 2
Syndecan-2/RasGAP 0.041 0.029 -10000 0 -0.19 1 1
alpha5/beta1 Integrin 0.043 0.009 -10000 0 -10000 0 0
PRKCD 0.029 0.004 -10000 0 -10000 0 0
Syndecan-2 dimer 0.015 0.019 -10000 0 -0.22 1 1
GO:0007205 0.002 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.025 0.026 -10000 0 -0.19 1 1
RHOA 0.029 0.004 -10000 0 -10000 0 0
SDCBP 0.024 0.011 -10000 0 -10000 0 0
TNFRSF13B 0.022 0.031 -10000 0 -0.37 2 2
RASA1 0.027 0.03 -10000 0 -0.37 2 2
alpha2/beta1 Integrin 0.035 0.018 -10000 0 -10000 0 0
Syndecan-2/Synbindin 0.02 0.013 -10000 0 -10000 0 0
TGFB1 0.029 0.005 -10000 0 -10000 0 0
CASP3 0.033 0.085 0.19 85 -10000 0 85
FN1 0.028 0.021 -10000 0 -0.37 1 1
Syndecan-2/IL8 -0.018 0.084 -10000 0 -0.22 54 54
SDC2 0.006 0.004 -10000 0 -10000 0 0
KNG1 -0.003 0.11 -10000 0 -0.37 29 29
Syndecan-2/Neurofibromin 0.02 0.013 -10000 0 -10000 0 0
TRAPPC4 0.028 0.006 -10000 0 -10000 0 0
CSF2 0.022 0.007 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.02 0.013 -10000 0 -10000 0 0
Syndecan-2/Syntenin/PI-4-5-P2 0.019 0.011 -10000 0 -10000 0 0
Syndecan-2/Ezrin 0.03 0.025 -10000 0 -0.2 1 1
PRKACA 0.033 0.087 0.19 89 -10000 0 89
angiogenesis -0.018 0.084 -10000 0 -0.22 54 54
MMP2 0.012 0.077 -10000 0 -0.37 14 14
IL8 -0.051 0.16 -10000 0 -0.37 71 71
calcineurin-NFAT signaling pathway 0.015 0.021 -10000 0 -0.22 2 2
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.014 0.11 -10000 0 -0.52 7 7
UGCG -0.043 0.21 -10000 0 -0.66 36 36
AKT1/mTOR/p70S6K/Hsp90/TERT 0.043 0.16 0.36 13 -0.48 13 26
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.043 0.21 -10000 0 -0.65 36 36
mol:DAG -0.007 0.12 -10000 0 -0.83 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 0.006 0.17 0.44 1 -0.42 32 33
FRAP1 -0.007 0.2 0.48 1 -0.59 18 19
FOXO3 -0.019 0.19 0.42 1 -0.48 35 36
AKT1 -0.016 0.2 0.45 1 -0.5 37 38
GAB2 0.025 0.017 -10000 0 -10000 0 0
SMPD1 0.02 0.056 -10000 0 -0.6 2 2
SGMS1 0.009 0.1 -10000 0 -0.63 8 8
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP -0.015 0.025 -10000 0 -0.31 2 2
CALM1 0.028 0.007 -10000 0 -10000 0 0
cell proliferation -0.017 0.21 -10000 0 -0.62 23 23
EIF3A 0.028 0.006 -10000 0 -10000 0 0
PI3K 0.037 0.039 -10000 0 -0.36 2 2
RPS6KB1 0.051 0.093 0.35 8 -10000 0 8
mol:sphingomyelin -0.007 0.12 -10000 0 -0.83 8 8
natural killer cell activation 0 0.004 -10000 0 -10000 0 0
JAK3 0.025 0.026 -10000 0 -0.37 1 1
PIK3R1 0.024 0.034 -10000 0 -0.37 2 2
JAK1 0.025 0.017 -10000 0 -10000 0 0
NFKB1 0.027 0.009 -10000 0 -10000 0 0
MYC -0.026 0.34 -10000 0 -0.88 44 44
MYB 0.12 0.18 0.64 36 -10000 0 36
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.01 0.14 0.43 1 -0.44 18 19
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.073 0.078 0.34 1 -10000 0 1
mol:PI-3-4-5-P3 0.01 0.14 0.43 1 -0.43 18 19
Rac1/GDP 0.014 0.03 -10000 0 -0.28 2 2
T cell proliferation 0.002 0.13 0.4 1 -0.42 16 17
SHC1 0.019 0.018 -10000 0 -10000 0 0
RAC1 0.029 0.004 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.025 0.071 0.24 36 -10000 0 36
PRKCZ 0.002 0.13 0.4 1 -0.45 15 16
NF kappa B1 p50/RelA 0.017 0.18 0.46 1 -0.5 18 19
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.009 0.12 0.33 1 -0.43 21 22
HSP90AA1 0.028 0.007 -10000 0 -10000 0 0
RELA 0.029 0.005 -10000 0 -10000 0 0
IL2RA 0.016 0.057 -10000 0 -0.37 7 7
IL2RB -0.002 0.1 -10000 0 -0.37 26 26
TERT 0.016 0.014 -10000 0 -10000 0 0
E2F1 0.13 0.16 0.6 36 -10000 0 36
SOS1 0.026 0.016 -10000 0 -10000 0 0
RPS6 0.029 0.006 -10000 0 -10000 0 0
mol:cAMP -0.014 0.039 -10000 0 -0.13 36 36
PTPN11 0.025 0.017 -10000 0 -10000 0 0
IL2RG 0.02 0.049 -10000 0 -0.37 5 5
actin cytoskeleton organization 0.002 0.13 0.4 1 -0.42 16 17
GRB2 0.025 0.016 -10000 0 -10000 0 0
IL2 0.017 0.015 -10000 0 -10000 0 0
PIK3CA 0.025 0.027 -10000 0 -0.37 1 1
Rac1/GTP 0.047 0.042 -10000 0 -0.27 2 2
LCK 0.013 0.067 -10000 0 -0.37 10 10
BCL2 0.001 0.16 0.45 1 -0.56 8 9
Caspase cascade in apoptosis

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
TOP1 -0.023 0.12 -10000 0 -0.41 22 22
ACTA1 -0.015 0.087 0.21 1 -0.31 14 15
NUMA1 -0.029 0.15 -10000 0 -0.47 24 24
SPTAN1 -0.032 0.082 -10000 0 -0.32 13 13
LIMK1 -0.027 0.088 -10000 0 -0.33 13 13
BIRC3 0.026 0.022 -10000 0 -0.37 1 1
BIRC2 0.029 0.006 -10000 0 -10000 0 0
BAX 0.029 0.005 -10000 0 -10000 0 0
CASP10 -0.027 0.047 0.18 4 -0.24 13 17
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.029 0.003 -10000 0 -10000 0 0
PTK2 -0.028 0.12 -10000 0 -0.38 23 23
DIABLO 0.029 0.003 -10000 0 -10000 0 0
apoptotic nuclear changes -0.031 0.081 -10000 0 -0.32 13 13
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.028 0.021 -10000 0 -0.37 1 1
GSN -0.032 0.083 -10000 0 -0.33 13 13
MADD 0.03 0.002 -10000 0 -10000 0 0
TFAP2A 0.009 0.16 -10000 0 -0.65 15 15
BID -0.005 0.032 -10000 0 -0.16 13 13
MAP3K1 0.003 0.032 -10000 0 -0.2 1 1
TRADD 0.027 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.041 0.012 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.032 0.082 -10000 0 -0.33 13 13
CASP9 0.028 0.007 -10000 0 -10000 0 0
DNA repair 0 0.056 0.27 7 -10000 0 7
neuron apoptosis -0.017 0.16 -10000 0 -0.69 17 17
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.035 0.14 -10000 0 -0.42 23 23
APAF1 0.029 0.004 -10000 0 -10000 0 0
CASP6 -0.055 0.25 -10000 0 -0.89 29 29
TRAF2 0.029 0.005 -10000 0 -10000 0 0
ICAD/CAD -0.033 0.082 0.36 1 -0.32 13 14
CASP7 -0.015 0.083 0.22 1 -0.29 16 17
KRT18 0.005 0.078 -10000 0 -0.84 2 2
apoptosis -0.045 0.13 -10000 0 -0.42 29 29
DFFA -0.03 0.082 -10000 0 -0.32 13 13
DFFB -0.031 0.082 -10000 0 -0.32 13 13
PARP1 0 0.057 -10000 0 -0.28 7 7
actin filament polymerization 0.03 0.084 0.31 14 -0.31 1 15
TNF 0.013 0.071 -10000 0 -0.37 12 12
CYCS 0.003 0.031 0.17 2 -0.16 1 3
SATB1 -0.072 0.24 -10000 0 -0.86 29 29
SLK -0.031 0.081 -10000 0 -0.32 13 13
p15 BID/BAX 0.011 0.045 -10000 0 -0.15 17 17
CASP2 0.001 0.055 0.2 3 -0.34 1 4
JNK cascade -0.003 0.032 0.2 1 -10000 0 1
CASP3 -0.028 0.087 -10000 0 -0.32 16 16
LMNB2 -0.005 0.13 -10000 0 -0.39 26 26
RIPK1 0.027 0.009 -10000 0 -10000 0 0
CASP4 0.028 0.022 -10000 0 -0.37 1 1
Mammalian IAPs/DIABLO 0.075 0.029 -10000 0 -0.21 1 1
negative regulation of DNA binding 0.013 0.16 -10000 0 -0.64 15 15
stress fiber formation -0.031 0.08 -10000 0 -0.32 13 13
GZMB -0.025 0.056 0.21 4 -0.28 13 17
CASP1 0.01 0.021 -10000 0 -0.27 2 2
LMNB1 -0.002 0.11 -10000 0 -0.35 24 24
APP -0.018 0.16 -10000 0 -0.7 17 17
TNFRSF1A 0.028 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.009 0.001 -10000 0 -10000 0 0
VIM -0.041 0.14 -10000 0 -0.44 29 29
LMNA -0.004 0.11 -10000 0 -0.36 22 22
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.006 0.057 -10000 0 -0.36 1 1
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.03 0.082 0.3 1 -0.3 15 16
APAF-1/Caspase 9 -0.008 0.14 -10000 0 -0.61 18 18
nuclear fragmentation during apoptosis -0.028 0.14 -10000 0 -0.46 24 24
CFL2 -0.031 0.086 0.31 1 -0.31 14 15
GAS2 -0.037 0.085 -10000 0 -0.32 14 14
positive regulation of apoptosis -0.001 0.12 0.22 1 -0.37 27 28
PRF1 0.021 0.055 -10000 0 -0.37 7 7
Class I PI3K signaling events mediated by Akt

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
BCL2L1 -0.018 0.003 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.032 0.021 -10000 0 -10000 0 0
CDKN1B -0.011 0.079 -10000 0 -0.32 14 14
CDKN1A -0.008 0.089 -10000 0 -0.3 17 17
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.025 0.011 -10000 0 -10000 0 0
FOXO3 -0.012 0.079 -10000 0 -0.29 25 25
AKT1 -0.009 0.087 -10000 0 -0.3 28 28
BAD 0.029 0.004 -10000 0 -10000 0 0
AKT3 0.009 0.017 0.15 1 -0.27 1 2
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 -0.014 0.083 -10000 0 -0.29 28 28
AKT1/ASK1 -0.005 0.1 -10000 0 -0.29 30 30
BAD/YWHAZ 0.042 0.028 -10000 0 -10000 0 0
RICTOR 0.029 0.005 -10000 0 -10000 0 0
RAF1 0.029 0.003 -10000 0 -10000 0 0
JNK cascade 0.005 0.1 0.29 30 -10000 0 30
TSC1 -0.014 0.083 -10000 0 -0.31 17 17
YWHAZ 0.022 0.013 -10000 0 -10000 0 0
AKT1/RAF1 0.015 0.097 -10000 0 -0.29 30 30
EP300 0.029 0.004 -10000 0 -10000 0 0
mol:GDP -0.01 0.088 -10000 0 -0.3 29 29
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 -0.01 0.08 0.26 1 -0.32 14 15
YWHAQ 0.03 0.003 -10000 0 -10000 0 0
TBC1D4 -0.004 0.028 0.23 3 -0.21 3 6
MAP3K5 -0.009 0.11 -10000 0 -0.37 33 33
MAPKAP1 0.029 0.004 -10000 0 -10000 0 0
negative regulation of cell cycle -0.053 0.089 0.29 9 -0.23 2 11
YWHAH 0.029 0.005 -10000 0 -10000 0 0
AKT1S1 -0.011 0.085 0.25 2 -0.3 21 23
CASP9 -0.009 0.077 -10000 0 -0.32 13 13
YWHAB 0.029 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.011 0.094 -10000 0 -0.3 18 18
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.053 0.02 -10000 0 -10000 0 0
YWHAE 0.025 0.011 -10000 0 -10000 0 0
SRC 0.029 0.005 -10000 0 -10000 0 0
AKT2/p21CIP1 0.007 0.1 0.25 10 -0.28 21 31
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.005 0.061 -10000 0 -0.39 6 6
CHUK -0.009 0.072 -10000 0 -0.3 15 15
BAD/BCL-XL 0.016 0.096 -10000 0 -0.3 18 18
mTORC2 0.036 0.008 -10000 0 -10000 0 0
AKT2 0.012 0.003 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.049 0.12 0.29 1 -0.37 13 14
PDPK1 0.028 0.006 -10000 0 -10000 0 0
MDM2 -0.012 0.089 0.26 1 -0.29 29 30
MAPKKK cascade -0.015 0.096 0.28 30 -10000 0 30
MDM2/Cbp/p300 0.027 0.099 0.26 1 -0.3 17 18
TSC1/TSC2 -0.016 0.08 0.24 1 -0.31 16 17
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.095 0.25 1 -0.29 17 18
glucose import -0.005 0.044 0.17 14 -0.19 8 22
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 -0.004 0.064 0.18 2 -0.39 3 5
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.005 0.044 0.17 14 -0.19 8 22
GSK3A -0.013 0.088 0.25 2 -0.29 29 31
FOXO1 -0.006 0.069 -10000 0 -0.32 11 11
GSK3B -0.015 0.084 -10000 0 -0.31 18 18
SFN 0.011 0.014 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.011 0.091 0.24 1 -0.31 18 19
p27Kip1/14-3-3 family 0.04 0.061 0.26 1 -0.44 1 2
PRKACA 0.029 0.004 -10000 0 -10000 0 0
KPNA1 0.03 0 -10000 0 -10000 0 0
HSP90AA1 0.028 0.007 -10000 0 -10000 0 0
YWHAG 0.029 0.004 -10000 0 -10000 0 0
RHEB 0.029 0.006 -10000 0 -10000 0 0
CREBBP 0.028 0.006 -10000 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.004 0.055 0.21 23 -10000 0 23
MAP4K4 0.001 0.052 0.2 1 -10000 0 1
BAG4 0.019 0.047 -10000 0 -0.37 5 5
PKC zeta/ceramide 0.016 0.064 -10000 0 -0.16 30 30
NFKBIA 0.029 0.004 -10000 0 -10000 0 0
BIRC3 0.026 0.022 -10000 0 -0.37 1 1
BAX 0.012 0.047 -10000 0 -0.32 5 5
RIPK1 0.027 0.009 -10000 0 -10000 0 0
AKT1 -0.011 0.055 0.72 2 -10000 0 2
BAD 0.002 0.051 -10000 0 -0.18 10 10
SMPD1 0.023 0.067 0.23 13 -0.25 2 15
RB1 0.001 0.05 -10000 0 -0.18 10 10
FADD/Caspase 8 0.006 0.065 0.27 3 -0.35 1 4
MAP2K4 -0.004 0.049 0.22 1 -0.18 5 6
NSMAF 0.024 0.011 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.001 0.057 0.21 6 -0.18 9 15
EGF 0.017 0.012 -10000 0 -10000 0 0
mol:ceramide 0.009 0.055 -10000 0 -0.16 21 21
MADD 0.03 0.002 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.003 0.052 0.22 17 -10000 0 17
ASAH1 0.023 0.013 -10000 0 -10000 0 0
negative regulation of cell cycle 0.003 0.051 -10000 0 -0.18 10 10
cell proliferation -0.045 0.1 -10000 0 -0.27 25 25
BID 0.012 0.13 -10000 0 -0.56 13 13
MAP3K1 0.003 0.052 0.24 1 -0.18 10 11
EIF2A -0.006 0.052 0.21 1 -10000 0 1
TRADD 0.027 0.008 -10000 0 -10000 0 0
CRADD 0.028 0.021 -10000 0 -0.37 1 1
MAPK3 -0.002 0.059 0.27 2 -0.24 1 3
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.001 0.058 0.27 2 -10000 0 2
Cathepsin D/ceramide 0.024 0.057 -10000 0 -0.18 10 10
FADD 0.004 0.057 0.21 7 -10000 0 7
KSR1 0.005 0.056 0.2 5 -0.18 10 15
MAPK8 -0.022 0.096 -10000 0 -0.26 25 25
PRKRA 0.004 0.054 0.21 3 -0.18 10 13
PDGFA 0.027 0.008 -10000 0 -10000 0 0
TRAF2 0.029 0.005 -10000 0 -10000 0 0
IGF1 -0.13 0.2 -10000 0 -0.37 142 142
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process 0.009 0.055 -10000 0 -0.16 21 21
CTSD 0.029 0.003 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.039 0.014 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.047 0.11 -10000 0 -0.28 25 25
PRKCD 0.029 0.004 -10000 0 -10000 0 0
PRKCZ 0.014 0.071 -10000 0 -0.37 12 12
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.003 0.052 0.22 17 -10000 0 17
RelA/NF kappa B1 0.04 0.014 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.029 0.003 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.008 0.055 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.032 0.062 -10000 0 -0.22 17 17
mol:Sphingosine-1-phosphate -0.004 0.055 0.21 23 -10000 0 23
MAP2K1 -0.004 0.055 0.27 2 -10000 0 2
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.029 0.005 -10000 0 -10000 0 0
CYCS 0.011 0.039 0.16 1 -0.18 2 3
TNFRSF1A 0.028 0.006 -10000 0 -10000 0 0
NFKB1 0.027 0.009 -10000 0 -10000 0 0
TNFR1A/BAG4 0.031 0.039 -10000 0 -0.26 5 5
EIF2AK2 -0.001 0.052 0.19 4 -0.18 6 10
TNF-alpha/TNFR1A/FAN 0.037 0.05 -10000 0 -0.23 9 9
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.005 0.084 -10000 0 -0.28 23 23
MAP2K2 -0.003 0.058 0.21 5 -0.18 1 6
SMPD3 -0.011 0.12 0.21 11 -0.3 44 55
TNF 0.013 0.071 -10000 0 -0.37 12 12
PKC zeta/PAR4 0.03 0.056 -10000 0 -0.26 12 12
mol:PHOSPHOCHOLINE -0.039 0.079 -10000 0 -0.16 74 74
NF kappa B1/RelA/I kappa B alpha 0.061 0.061 -10000 0 -0.2 12 12
AIFM1 0.01 0.042 0.16 2 -0.18 2 4
BCL2 0.028 0.022 -10000 0 -0.37 1 1
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.018 0.065 0.37 10 -10000 0 10
PI3K Class IB/PDE3B 0.018 0.065 -10000 0 -0.37 10 10
PDE3B 0.018 0.065 -10000 0 -0.37 10 10
Syndecan-3-mediated signaling events

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
CTTN 0.029 0.006 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.027 0.12 -10000 0 -0.4 14 14
Syndecan-3/Neurocan 0.019 0.085 -10000 0 -0.38 13 13
POMC 0.026 0.036 -10000 0 -0.37 3 3
EGFR 0.019 0.062 -10000 0 -0.37 9 9
Syndecan-3/EGFR 0.026 0.093 -10000 0 -0.37 14 14
AGRP 0.021 0.01 -10000 0 -10000 0 0
NCSTN 0.023 0.013 -10000 0 -10000 0 0
PSENEN 0.029 0.004 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.029 0.004 -10000 0 -10000 0 0
APH1A 0.023 0.013 -10000 0 -10000 0 0
NCAN 0.025 0.007 -10000 0 -10000 0 0
long-term memory 0.042 0.088 -10000 0 -0.36 13 13
Syndecan-3/IL8 -0.006 0.12 -10000 0 -0.43 14 14
PSEN1 0.028 0.007 -10000 0 -10000 0 0
Src/Cortactin 0.041 0.011 -10000 0 -10000 0 0
FYN 0.028 0.008 -10000 0 -10000 0 0
limb bud formation -0.005 0.073 -10000 0 -0.4 12 12
MC4R 0.018 0.005 -10000 0 -10000 0 0
SRC 0.029 0.005 -10000 0 -10000 0 0
PTN -0.03 0.14 -10000 0 -0.37 53 53
FGFR/FGF/Syndecan-3 -0.005 0.073 -10000 0 -0.4 12 12
neuron projection morphogenesis -0.02 0.11 0.31 2 -0.41 13 15
Syndecan-3/AgRP 0.02 0.081 -10000 0 -0.36 13 13
Syndecan-3/AgRP/MC4R 0.033 0.083 -10000 0 -0.35 13 13
Fyn/Cortactin 0.039 0.014 -10000 0 -10000 0 0
SDC3 -0.005 0.074 -10000 0 -0.4 12 12
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration -0.006 0.12 -10000 0 -0.42 14 14
IL8 -0.051 0.16 -10000 0 -0.37 71 71
Syndecan-3/Fyn/Cortactin 0.043 0.09 -10000 0 -0.37 13 13
Syndecan-3/CASK -0.008 0.072 -10000 0 -0.37 13 13
alpha-MSH/MC4R 0.032 0.028 -10000 0 -0.26 3 3
Gamma Secretase 0.06 0.042 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.035 0.013 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.027 0.009 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.02 0.055 -10000 0 -0.37 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.026 0.01 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.019 0.031 -10000 0 -0.16 2 2
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.029 0.004 -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 0.029 0.006 -10000 0 -10000 0 0
FYN 0.028 0.008 -10000 0 -10000 0 0
MAP3K12 0.029 0.003 -10000 0 -10000 0 0
FGR 0.026 0.03 -10000 0 -0.37 2 2
p38 alpha/TAB1 -0.052 0.1 -10000 0 -0.27 47 47
PRKG1 0.009 0.084 -10000 0 -0.37 17 17
DUSP8 0.027 0.03 -10000 0 -0.37 2 2
PGK/cGMP/p38 alpha -0.024 0.12 0.19 1 -0.29 42 43
apoptosis -0.051 0.096 -10000 0 -0.26 47 47
RAL/GTP 0.039 0.007 -10000 0 -10000 0 0
LYN 0.025 0.011 -10000 0 -10000 0 0
DUSP1 -0.009 0.12 -10000 0 -0.37 34 34
PAK1 0.029 0.005 -10000 0 -10000 0 0
SRC 0.029 0.005 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.068 0.025 -10000 0 -10000 0 0
TRAF6 0.029 0.021 -10000 0 -0.37 1 1
RAC1 0.029 0.004 -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 0.029 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.037 0.011 -10000 0 -10000 0 0
MAPK11 -0.027 0.13 0.33 2 -0.33 30 32
BLK -0.022 0.12 -10000 0 -0.37 40 40
HCK 0.016 0.071 -10000 0 -0.37 12 12
MAP2K3 0.028 0.008 -10000 0 -10000 0 0
DUSP16 0.027 0.022 -10000 0 -0.37 1 1
DUSP10 0.019 0.043 -10000 0 -0.37 4 4
TRAF6/MEKK3 0.036 0.014 -10000 0 -0.2 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.023 0.13 0.29 2 -0.3 43 45
positive regulation of innate immune response -0.028 0.15 0.36 2 -0.4 30 32
LCK 0.017 0.065 -10000 0 -0.37 10 10
p38alpha-beta/MKP7 -0.018 0.15 0.36 2 -0.38 30 32
p38alpha-beta/MKP5 -0.016 0.14 0.25 1 -0.37 29 30
PGK/cGMP 0.008 0.059 -10000 0 -0.26 17 17
PAK2 0.029 0.003 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.03 0.16 0.36 2 -0.39 35 37
CDC42 0.028 0.007 -10000 0 -10000 0 0
RALB 0.029 0.003 -10000 0 -10000 0 0
RALA 0.029 0.004 -10000 0 -10000 0 0
PAK3 0.021 0.009 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.002 0.044 0.22 1 -0.37 1 2
adherens junction organization -0.01 0.067 -10000 0 -0.21 23 23
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.004 0.063 0.23 2 -0.28 6 8
FMN1 -0.009 0.069 -10000 0 -0.21 24 24
mol:IP3 -0.001 0.044 -10000 0 -0.32 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.006 0.068 -10000 0 -0.22 25 25
CTNNB1 0.03 0.004 -10000 0 -10000 0 0
AKT1 -0.001 0.051 -10000 0 -0.32 1 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.013 0.1 -10000 0 -0.32 25 25
CTNND1 0.029 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.007 0.049 -10000 0 -0.21 15 15
VASP -0.014 0.063 -10000 0 -0.21 24 24
ZYX -0.014 0.063 -10000 0 -0.21 25 25
JUB -0.01 0.063 -10000 0 -0.2 25 25
EGFR(dimer) 0.005 0.082 -10000 0 -0.24 24 24
E-cadherin/beta catenin-gamma catenin 0.038 0.066 -10000 0 -0.21 22 22
mol:PI-3-4-5-P3 0.023 0.063 -10000 0 -0.33 1 1
PIK3CA 0.029 0.022 -10000 0 -0.38 1 1
PI3K 0.024 0.064 -10000 0 -0.33 1 1
FYN -0.04 0.081 0.26 1 -0.26 13 14
mol:Ca2+ -0.001 0.043 -10000 0 -0.32 1 1
JUP 0.03 0.004 -10000 0 -10000 0 0
PIK3R1 0.028 0.03 -10000 0 -0.37 2 2
mol:DAG -0.001 0.044 -10000 0 -0.32 1 1
CDH1 0.003 0.095 -10000 0 -0.37 22 22
RhoA/GDP 0.007 0.065 0.23 3 -0.28 5 8
establishment of polarity of embryonic epithelium -0.013 0.062 -10000 0 -0.21 24 24
SRC 0.029 0.005 -10000 0 -10000 0 0
RAC1 0.029 0.004 -10000 0 -10000 0 0
RHOA 0.029 0.004 -10000 0 -10000 0 0
EGFR 0.019 0.062 -10000 0 -0.37 9 9
CASR -0.043 0.075 0.22 1 -0.26 8 9
RhoA/GTP 0.014 0.05 0.22 2 -0.3 1 3
AKT2 -0.001 0.052 -10000 0 -0.32 1 1
actin cable formation -0.015 0.069 -10000 0 -0.21 21 21
apoptosis 0 0.049 0.33 1 -0.22 1 2
CTNNA1 0.029 0.006 -10000 0 -10000 0 0
mol:GDP -0.023 0.054 0.23 2 -0.29 6 8
PIP5K1A -0.007 0.05 -10000 0 -0.21 15 15
PLCG1 -0.001 0.044 -10000 0 -0.33 1 1
Rac1/GTP 0.015 0.083 -10000 0 -0.22 24 24
homophilic cell adhesion -0.001 0.001 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.028 0.006 -10000 0 -10000 0 0
Jak2/Leptin Receptor 0.04 0.11 0.27 4 -0.33 12 16
PTP1B/AKT1 0.047 0.075 0.23 2 -0.31 6 8
FYN 0.028 0.008 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.041 0.079 0.24 2 -0.34 6 8
EGFR 0.02 0.064 -10000 0 -0.37 9 9
EGF/EGFR 0.034 0.069 -10000 0 -0.28 6 6
CSF1 0.024 0.042 -10000 0 -0.37 4 4
AKT1 0.029 0.008 -10000 0 -10000 0 0
INSR 0.03 0.005 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.048 0.082 0.26 1 -0.32 7 8
Insulin Receptor/Insulin 0.056 0.072 0.28 1 -0.3 5 6
HCK 0.016 0.071 -10000 0 -0.37 12 12
CRK 0.025 0.011 -10000 0 -10000 0 0
TYK2 0.033 0.075 0.28 2 -0.33 6 8
EGF 0.017 0.015 -10000 0 -10000 0 0
YES1 0.029 0.004 -10000 0 -10000 0 0
CAV1 0.045 0.085 0.24 5 -0.32 6 11
TXN 0.031 0.005 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.06 0.082 -10000 0 -0.32 6 6
cell migration -0.041 0.079 0.34 6 -0.24 2 8
STAT3 0.029 0.005 -10000 0 -10000 0 0
PRLR 0.018 0.069 -10000 0 -0.37 11 11
ITGA2B 0.026 0.011 -10000 0 -10000 0 0
CSF1R 0.019 0.062 -10000 0 -0.37 9 9
Prolactin Receptor/Prolactin 0.027 0.052 -10000 0 -0.26 10 10
FGR 0.026 0.03 -10000 0 -0.37 2 2
PTP1B/p130 Cas 0.052 0.075 0.26 1 -0.33 5 6
Crk/p130 Cas 0.058 0.078 0.26 1 -0.31 5 6
DOK1 0.04 0.076 0.23 3 -0.34 5 8
JAK2 0.038 0.094 0.24 3 -0.39 7 10
Jak2/Leptin Receptor/Leptin 0.015 0.13 -10000 0 -0.33 27 27
PIK3R1 0.027 0.03 -10000 0 -0.37 2 2
PTPN1 0.04 0.079 0.25 2 -0.34 6 8
LYN 0.025 0.011 -10000 0 -10000 0 0
CDH2 0.019 0.062 -10000 0 -0.37 9 9
SRC 0.039 0.069 -10000 0 -0.38 6 6
ITGB3 -0.001 0.11 -10000 0 -0.37 28 28
CAT1/PTP1B -0.036 0.15 0.24 2 -0.41 30 32
CAPN1 0.03 0.005 -10000 0 -10000 0 0
CSK 0.029 0.005 -10000 0 -10000 0 0
PI3K 0.061 0.076 -10000 0 -0.29 6 6
mol:H2O2 0.002 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.008 0.13 -10000 0 -0.33 35 35
negative regulation of transcription 0.039 0.094 0.24 3 -0.39 7 10
FCGR2A 0.023 0.013 -10000 0 -10000 0 0
FER 0.031 0.005 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.018 0.083 -10000 0 -0.27 28 28
BLK -0.022 0.12 -10000 0 -0.37 40 40
Insulin Receptor/Insulin/Shc 0.039 0.024 -10000 0 -10000 0 0
RHOA 0.03 0.004 -10000 0 -10000 0 0
LEPR -0.031 0.14 -10000 0 -0.36 56 56
BCAR1 0.027 0.008 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.028 0.006 -10000 0 -10000 0 0
mol:NADPH 0.002 0.003 -10000 0 -10000 0 0
TRPV6 -0.095 0.18 -10000 0 -0.39 69 69
PRL 0.019 0.008 -10000 0 -10000 0 0
SOCS3 -0.15 0.41 -10000 0 -1.2 52 52
SPRY2 0.024 0.043 -10000 0 -0.37 4 4
Insulin Receptor/Insulin/IRS1 0.051 0.012 -10000 0 -10000 0 0
CSF1/CSF1R 0.054 0.088 -10000 0 -0.31 8 8
Ras protein signal transduction -0.004 0.11 0.49 16 -10000 0 16
IRS1 0.03 0.003 -10000 0 -10000 0 0
INS 0.015 0.012 -10000 0 -10000 0 0
LEP 0.018 0.014 -10000 0 -10000 0 0
STAT5B 0.048 0.077 0.22 5 -0.3 7 12
STAT5A 0.048 0.077 0.22 5 -0.3 7 12
GRB2 0.028 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.047 0.079 0.26 1 -0.33 6 7
CSN2 -0.011 0.065 -10000 0 -10000 0 0
PIK3CA 0.028 0.021 -10000 0 -0.37 1 1
LAT 0.037 0.09 -10000 0 -0.46 9 9
YBX1 0.035 0.009 -10000 0 -10000 0 0
LCK 0.017 0.065 -10000 0 -0.37 10 10
SHC1 0.022 0.013 -10000 0 -10000 0 0
NOX4 0.019 0.016 -10000 0 -10000 0 0
Arf6 downstream 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
PLAUR 0.011 0.093 0.6 3 -0.97 2 5
regulation of axonogenesis -0.002 0.032 0.25 1 -0.19 3 4
myoblast fusion -0.023 0.047 0.38 2 -0.35 3 5
mol:GTP 0.02 0.037 0.22 3 -0.17 10 13
regulation of calcium-dependent cell-cell adhesion -0.038 0.071 0.22 21 -0.31 3 24
ARF1/GTP 0.032 0.031 0.21 3 -0.17 1 4
mol:GM1 0.007 0.028 0.2 3 -0.14 4 7
mol:Choline -0.017 0.048 0.18 3 -0.21 16 19
lamellipodium assembly 0.01 0.067 0.34 3 -0.36 8 11
MAPK3 0.017 0.047 0.39 3 -0.33 2 5
ARF6/GTP/NME1/Tiam1 0.038 0.072 0.32 3 -0.22 21 24
ARF1 0.024 0.012 -10000 0 -10000 0 0
ARF6/GDP 0.023 0.047 0.35 3 -0.38 2 5
ARF1/GDP 0.022 0.049 0.31 3 -0.28 3 6
ARF6 0.037 0.02 0.16 3 -0.14 2 5
RAB11A 0.029 0.004 -10000 0 -10000 0 0
TIAM1 0.007 0.089 -10000 0 -0.37 19 19
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.018 0.047 0.39 3 -0.33 2 5
actin filament bundle formation -0.03 0.054 0.3 4 -0.3 3 7
KALRN 0.011 0.031 -10000 0 -0.26 4 4
RAB11FIP3/RAB11A 0.041 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.03 0.055 0.3 3 -0.3 4 7
NME1 0.028 0.01 -10000 0 -10000 0 0
Rac1/GDP 0.032 0.052 0.3 3 -0.26 7 10
substrate adhesion-dependent cell spreading 0.02 0.037 0.22 3 -0.17 10 13
cortical actin cytoskeleton organization 0.01 0.067 0.35 3 -0.36 8 11
RAC1 0.029 0.004 -10000 0 -10000 0 0
liver development 0.02 0.037 0.22 3 -0.17 10 13
ARF6/GTP 0.02 0.037 0.22 3 -0.17 10 13
RhoA/GTP 0.037 0.033 0.21 3 -0.17 2 5
mol:GDP 0.011 0.058 0.4 3 -0.26 8 11
ARF6/GTP/RAB11FIP3/RAB11A 0.051 0.035 0.21 3 -0.15 2 5
RHOA 0.029 0.004 -10000 0 -10000 0 0
PLD1 0.001 0.066 0.21 3 -0.24 22 25
RAB11FIP3 0.028 0.007 -10000 0 -10000 0 0
tube morphogenesis 0.01 0.067 0.34 3 -0.36 8 11
ruffle organization 0.002 0.032 0.19 3 -0.25 1 4
regulation of epithelial cell migration 0.02 0.037 0.22 3 -0.17 10 13
PLD2 0.015 0.028 0.21 3 -0.17 2 5
PIP5K1A 0.002 0.032 0.19 3 -0.25 1 4
mol:Phosphatidic acid -0.017 0.048 0.18 3 -0.21 16 19
Rac1/GTP 0.01 0.067 0.35 3 -0.37 8 11
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.028 0.006 -10000 0 -10000 0 0
mol:PIP3 -0.015 0.024 -10000 0 -0.23 3 3
FRAP1 0.004 0.061 -10000 0 -0.47 5 5
AKT1 -0.012 0.045 0.17 1 -0.32 1 2
INSR 0.029 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.031 0.007 -10000 0 -10000 0 0
mol:GTP 0.02 0.049 -10000 0 -0.29 1 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.011 0.027 -10000 0 -0.16 2 2
TSC2 0.028 0.007 -10000 0 -10000 0 0
RHEB/GDP -0.023 0.039 -10000 0 -0.22 2 2
TSC1 0.029 0.005 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.024 0.021 -10000 0 -0.19 3 3
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.022 0.035 -10000 0 -0.17 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.028 0.006 -10000 0 -10000 0 0
RPS6KB1 0.016 0.053 -10000 0 -0.26 3 3
MAP3K5 -0.04 0.1 -10000 0 -0.26 62 62
PIK3R1 0.027 0.03 -10000 0 -0.37 2 2
apoptosis -0.04 0.1 -10000 0 -0.26 62 62
mol:LY294002 0 0 0.001 3 -0.001 3 6
EIF4B 0.011 0.05 0.24 1 -0.24 3 4
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.036 0.049 -10000 0 -0.22 3 3
eIF4E/eIF4G1/eIF4A1 0.011 0.04 -10000 0 -0.28 5 5
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.04 0.032 -10000 0 -0.2 5 5
mTOR/RHEB/GTP/Raptor/GBL -0.007 0.031 -10000 0 -0.16 2 2
FKBP1A 0.029 0.005 -10000 0 -10000 0 0
RHEB/GTP 0.028 0.047 -10000 0 -0.27 1 1
mol:Amino Acids 0 0 0.001 3 -0.001 3 6
FKBP12/Rapamycin 0.021 0.004 -10000 0 -10000 0 0
PDPK1 -0.018 0.028 -10000 0 -0.25 2 2
EIF4E 0.027 0.008 -10000 0 -10000 0 0
ASK1/PP5C -0.067 0.24 -10000 0 -0.57 66 66
mTOR/RHEB/GTP/Raptor/GBL/eIF4E -0.009 0.08 -10000 0 -0.24 34 34
TSC1/TSC2 0.023 0.053 -10000 0 -0.31 1 1
tumor necrosis factor receptor activity 0 0 0.001 3 -0.001 3 6
RPS6 0.029 0.006 -10000 0 -10000 0 0
PPP5C 0.029 0.005 -10000 0 -10000 0 0
EIF4G1 0.03 0.002 -10000 0 -10000 0 0
IRS1 0.005 0.019 -10000 0 -0.2 3 3
INS 0.018 0.004 -10000 0 -10000 0 0
PTEN 0.028 0.007 -10000 0 -10000 0 0
PDK2 -0.019 0.03 0.15 1 -0.23 3 4
EIF4EBP1 -0.14 0.38 -10000 0 -1 59 59
PIK3CA 0.029 0.021 -10000 0 -0.37 1 1
PPP2R5D 0.015 0.075 0.24 1 -0.42 5 6
peptide biosynthetic process -0.016 0.023 0.16 6 -10000 0 6
RHEB 0.029 0.006 -10000 0 -10000 0 0
EIF4A1 0.025 0.011 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.003 3 -0.003 3 6
EEF2 -0.016 0.023 0.16 6 -10000 0 6
eIF4E/4E-BP1 -0.12 0.36 -10000 0 -0.94 59 59
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.011 0.09 0.61 5 -10000 0 5
VDR 0.021 0.055 -10000 0 -0.37 7 7
FAM120B 0.027 0.009 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.016 0.073 0.41 1 -0.32 4 5
RXRs/LXRs/DNA/Oxysterols 0.025 0.11 0.5 1 -0.44 10 11
MED1 0.029 0.004 -10000 0 -10000 0 0
mol:9cRA 0 0.014 0.1 1 -0.087 2 3
RARs/THRs/DNA/Src-1 0.014 0.05 -10000 0 -0.2 19 19
RXRs/NUR77 0.022 0.1 0.3 1 -0.21 43 44
RXRs/PPAR 0.018 0.049 -10000 0 -0.22 5 5
NCOR2 0.029 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.016 0.038 -10000 0 -0.26 7 7
RARs/VDR/DNA/Vit D3 0.056 0.064 -10000 0 -0.2 20 20
RARA 0.029 0.003 -10000 0 -10000 0 0
NCOA1 0.03 0.003 -10000 0 -10000 0 0
VDR/VDR/DNA 0.021 0.055 -10000 0 -0.37 7 7
RARs/RARs/DNA/9cRA 0.039 0.052 -10000 0 -0.19 15 15
RARG 0.03 0.003 -10000 0 -10000 0 0
RPS6KB1 0.014 0.1 0.49 15 -10000 0 15
RARs/THRs/DNA/SMRT 0.013 0.052 -10000 0 -0.2 17 17
THRA 0.029 0.004 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.016 0.038 -10000 0 -0.26 7 7
RXRs/PPAR/9cRA/PGJ2/DNA 0.036 0.056 0.39 1 -0.2 4 5
NR1H4 0.018 0.065 -10000 0 -0.37 10 10
RXRs/LXRs/DNA 0.062 0.078 0.44 1 -10000 0 1
NR1H2 0.027 0.022 -10000 0 -10000 0 0
NR1H3 0.028 0.023 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.049 0.064 0.28 1 -0.19 8 9
NR4A1 -0.031 0.14 -10000 0 -0.37 55 55
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.026 0.064 0.2 1 -0.23 10 11
RXRG 0.013 0.045 -10000 0 -0.37 4 4
RXR alpha/CCPG 0.036 0.028 -10000 0 -0.26 1 1
RXRA 0.026 0.029 -10000 0 -0.37 1 1
RXRB 0.026 0.022 -10000 0 -10000 0 0
THRB 0.026 0.036 -10000 0 -0.37 3 3
PPARG 0.029 0.003 -10000 0 -10000 0 0
PPARD 0.027 0.009 -10000 0 -10000 0 0
TNF 0 0.19 0.63 1 -0.86 14 15
mol:Oxysterols 0 0.012 0.097 1 -0.075 2 3
cholesterol transport 0.025 0.11 0.5 1 -0.44 10 11
PPARA 0.028 0.006 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.013 0.079 -10000 0 -0.37 15 15
RXRs/NUR77/BCL2 -0.011 0.085 -10000 0 -0.21 44 44
SREBF1 0.013 0.11 0.45 1 -0.72 3 4
RXRs/RXRs/DNA/9cRA 0.036 0.056 0.39 1 -0.2 4 5
ABCA1 0.014 0.12 0.45 1 -0.73 5 6
RARs/THRs 0.071 0.065 -10000 0 -0.2 18 18
RXRs/FXR 0.049 0.075 0.3 1 -0.22 12 13
BCL2 0.028 0.022 -10000 0 -0.37 1 1
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.028 0.007 -10000 0 -10000 0 0
HDAC2 0.028 0.008 -10000 0 -10000 0 0
GNB1/GNG2 0.047 0.041 -10000 0 -0.22 6 6
forebrain development -0.014 0.13 -10000 0 -0.46 17 17
GNAO1 -0.14 0.2 -10000 0 -0.37 153 153
SMO/beta Arrestin2 0.031 0.038 -10000 0 -0.27 4 4
SMO 0.022 0.044 -10000 0 -0.37 4 4
ARRB2 0.024 0.014 -10000 0 -10000 0 0
GLI3/SPOP 0.037 0.056 0.25 2 -0.27 3 5
mol:GTP 0 0.002 -10000 0 -10000 0 0
GSK3B 0.03 0 -10000 0 -10000 0 0
GNAI2 0.027 0.013 -10000 0 -10000 0 0
SIN3/HDAC complex 0.066 0.027 -10000 0 -10000 0 0
GNAI1 0.025 0.031 -10000 0 -0.37 2 2
XPO1 0.027 0.016 -10000 0 -10000 0 0
GLI1/Su(fu) -0.009 0.14 -10000 0 -0.47 17 17
SAP30 0.027 0.008 -10000 0 -10000 0 0
mol:GDP 0.022 0.044 -10000 0 -0.37 4 4
MIM/GLI2A 0.023 0.018 -10000 0 -10000 0 0
IFT88 0.028 0.007 -10000 0 -10000 0 0
GNAI3 0.027 0.011 -10000 0 -10000 0 0
GLI2 0.008 0.06 -10000 0 -0.25 3 3
GLI3 0.022 0.054 0.25 2 -0.27 3 5
CSNK1D 0.028 0.007 -10000 0 -10000 0 0
CSNK1E 0.029 0.005 -10000 0 -10000 0 0
SAP18 0.028 0.007 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.028 0.007 -10000 0 -10000 0 0
GNG2 0.027 0.03 -10000 0 -0.37 2 2
Gi family/GTP -0.043 0.12 0.19 1 -0.21 86 87
SIN3B 0.029 0.004 -10000 0 -10000 0 0
SIN3A 0.029 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) 0.022 0.06 0.24 1 -0.32 5 6
GLI2/Su(fu) 0.012 0.065 -10000 0 -0.28 6 6
FOXA2 0.012 0.095 -10000 0 -0.79 4 4
neural tube patterning -0.014 0.13 -10000 0 -0.46 17 17
SPOP 0.029 0.003 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.019 0.047 -10000 0 -10000 0 0
GNB1 0.027 0.009 -10000 0 -10000 0 0
CSNK1G2 0.029 0.005 -10000 0 -10000 0 0
CSNK1G3 0.029 0.004 -10000 0 -10000 0 0
MTSS1 0.023 0.018 -10000 0 -10000 0 0
embryonic limb morphogenesis -0.014 0.13 -10000 0 -0.46 17 17
SUFU 0.014 0.022 -10000 0 -0.16 4 4
LGALS3 0.026 0.01 -10000 0 -10000 0 0
catabolic process 0.04 0.073 0.29 2 -0.33 3 5
GLI3A/CBP 0.037 0.038 0.19 16 -10000 0 16
KIF3A 0.029 0.006 -10000 0 -10000 0 0
GLI1 -0.015 0.13 -10000 0 -0.47 17 17
RAB23 0.028 0.008 -10000 0 -10000 0 0
CSNK1A1 0.029 0.005 -10000 0 -10000 0 0
IFT172 0.03 0.003 -10000 0 -10000 0 0
RBBP7 0.029 0.004 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.018 0.046 -10000 0 -10000 0 0
GNAZ 0.014 0.025 -10000 0 -0.37 1 1
RBBP4 0.028 0.007 -10000 0 -10000 0 0
CSNK1G1 0.029 0.004 -10000 0 -10000 0 0
PIAS1 0.029 0.004 -10000 0 -10000 0 0
PRKACA 0.029 0.004 -10000 0 -10000 0 0
GLI2/SPOP 0.023 0.062 -10000 0 -0.24 3 3
STK36 0.027 0.016 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.04 0.12 -10000 0 -0.29 27 27
PTCH1 -0.046 0.24 -10000 0 -1.1 18 18
MIM/GLI1 -0.006 0.12 -10000 0 -0.45 8 8
CREBBP 0.037 0.038 0.19 16 -10000 0 16
Su(fu)/SIN3/HDAC complex -0.008 0.1 -10000 0 -0.32 30 30
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.06 0.039 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.029 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.042 0.041 0.28 1 -10000 0 1
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.054 0.024 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.051 0.069 -10000 0 -0.22 11 11
CaM/Ca2+ 0.06 0.04 -10000 0 -10000 0 0
RAP1A 0.029 0.006 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.016 0.046 0.25 2 -10000 0 2
AKT1 -0.02 0.049 0.25 3 -0.35 1 4
MAP2K1 -0.019 0.044 0.27 3 -10000 0 3
MAP3K11 -0.014 0.046 0.27 3 -10000 0 3
IFNGR1 0.028 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.11 0.16 -10000 0 -0.27 148 148
Rap1/GTP -0.036 0.015 -10000 0 -10000 0 0
CRKL/C3G 0.042 0.009 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.075 0.041 -10000 0 -10000 0 0
CEBPB 0.002 0.085 0.37 1 -0.47 4 5
STAT3 0.029 0.004 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.043 0.18 -10000 0 -0.74 16 16
STAT1 -0.016 0.044 0.27 2 -10000 0 2
CALM1 0.028 0.007 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.019 0.02 -10000 0 -10000 0 0
PIK3CA 0.028 0.021 -10000 0 -0.37 1 1
STAT1 (dimer)/PIAS1 -0.017 0.05 0.26 3 -10000 0 3
CEBPB/PTGES2/Cbp/p300 0.027 0.061 -10000 0 -0.33 3 3
mol:Ca2+ 0.057 0.037 -10000 0 -10000 0 0
MAPK3 -0.011 0.13 -10000 0 -0.73 11 11
STAT1 (dimer) -0.055 0.1 -10000 0 -0.45 4 4
MAPK1 -0.004 0.11 -10000 0 -0.67 8 8
JAK2 0.029 0.009 -10000 0 -10000 0 0
PIK3R1 0.027 0.03 -10000 0 -0.37 2 2
JAK1 0.029 0.009 -10000 0 -10000 0 0
CAMK2D 0.027 0.008 -10000 0 -10000 0 0
DAPK1 0.002 0.07 0.32 1 -0.5 3 4
SMAD7 -0.032 0.045 0.24 1 -0.29 2 3
CBL/CRKL/C3G 0.023 0.049 0.28 2 -10000 0 2
PI3K 0.057 0.046 -10000 0 -0.37 1 1
IFNG 0.019 0.02 -10000 0 -10000 0 0
apoptosis -0.002 0.074 -10000 0 -0.42 7 7
CAMK2G 0.029 0.006 -10000 0 -10000 0 0
STAT3 (dimer) 0.029 0.004 -10000 0 -10000 0 0
CAMK2A 0.025 0.009 -10000 0 -10000 0 0
CAMK2B -0.16 0.2 -10000 0 -0.37 175 175
FRAP1 -0.02 0.044 0.24 3 -0.33 1 4
PRKCD -0.022 0.05 0.26 3 -0.36 1 4
RAP1B 0.029 0.004 -10000 0 -10000 0 0
negative regulation of cell growth -0.051 0.069 -10000 0 -0.22 11 11
PTPN2 0.029 0.004 -10000 0 -10000 0 0
EP300 0.029 0.004 -10000 0 -10000 0 0
IRF1 -0.019 0.05 0.38 1 -0.33 2 3
STAT1 (dimer)/PIASy -0.019 0.054 0.25 3 -0.23 3 6
SOCS1 -0.017 0.23 0.64 4 -1.1 16 20
mol:GDP -0.019 0.048 0.26 2 -10000 0 2
CASP1 -0.033 0.044 0.24 1 -0.23 3 4
PTGES2 0.029 0.004 -10000 0 -10000 0 0
IRF9 0.007 0.031 0.19 1 -0.16 1 2
mol:PI-3-4-5-P3 0.041 0.039 -10000 0 -0.36 1 1
RAP1/GDP -0.028 0.037 -10000 0 -10000 0 0
CBL -0.014 0.046 0.27 3 -10000 0 3
MAP3K1 -0.015 0.046 0.27 3 -10000 0 3
PIAS1 0.029 0.004 -10000 0 -10000 0 0
PIAS4 0.028 0.008 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.051 0.069 -10000 0 -0.22 11 11
PTPN11 -0.012 0.042 0.29 1 -10000 0 1
CREBBP 0.029 0.006 -10000 0 -10000 0 0
RAPGEF1 0.029 0.004 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.063 0.035 -10000 0 -0.21 2 2
HDAC3 0.029 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.02 0.004 -10000 0 -10000 0 0
GATA1/HDAC4 0.038 0.008 -10000 0 -10000 0 0
GATA1/HDAC5 0.038 0.009 -10000 0 -10000 0 0
GATA2/HDAC5 0.041 0.024 -10000 0 -0.26 2 2
HDAC5/BCL6/BCoR 0.057 0.013 -10000 0 -10000 0 0
HDAC9 0.009 0.087 -10000 0 -0.37 18 18
Glucocorticoid receptor/Hsp90/HDAC6 0.056 0.016 -10000 0 -10000 0 0
HDAC4/ANKRA2 0.042 0.018 -10000 0 -0.26 1 1
HDAC5/YWHAB 0.042 0.009 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.011 0.003 -10000 0 -10000 0 0
GATA2 0.027 0.03 -10000 0 -0.37 2 2
HDAC4/RFXANK 0.042 0.009 -10000 0 -10000 0 0
BCOR 0.029 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.028 0.006 -10000 0 -10000 0 0
HDAC5 0.029 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.037 0.027 -10000 0 -0.26 2 2
Histones 0.014 0.052 0.2 1 -0.18 16 17
ADRBK1 0.029 0.005 -10000 0 -10000 0 0
HDAC4 0.029 0.004 -10000 0 -10000 0 0
XPO1 0.03 0.003 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.042 0.018 -10000 0 -0.26 1 1
HDAC4/Ubc9 0.041 0.012 -10000 0 -10000 0 0
HDAC7 0.029 0.003 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.037 0.016 -10000 0 -10000 0 0
TUBA1B 0.03 0.003 -10000 0 -10000 0 0
HDAC6 0.03 0.002 -10000 0 -10000 0 0
HDAC5/RFXANK 0.042 0.009 -10000 0 -10000 0 0
CAMK4 -0.002 0.1 -10000 0 -0.37 27 27
Tubulin/HDAC6 0.054 0.019 -10000 0 -10000 0 0
SUMO1 0.03 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.029 0.005 -10000 0 -10000 0 0
GATA1 0.023 0.007 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.025 0.011 -10000 0 -10000 0 0
NR3C1 0.029 0.005 -10000 0 -10000 0 0
SUMO1/HDAC4 0.036 0.039 -10000 0 -0.24 2 2
SRF 0.027 0.009 -10000 0 -10000 0 0
HDAC4/YWHAB 0.042 0.009 -10000 0 -10000 0 0
Tubulin 0.04 0.014 -10000 0 -10000 0 0
HDAC4/14-3-3 E 0.037 0.016 -10000 0 -10000 0 0
GNB1 0.027 0.009 -10000 0 -10000 0 0
RANGAP1 0.029 0.005 -10000 0 -10000 0 0
BCL6/BCoR 0.043 0.007 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.057 0.015 -10000 0 -10000 0 0
HDAC4/SRF 0.035 0.069 -10000 0 -0.22 22 22
HDAC4/ER alpha -0.11 0.15 -10000 0 -0.26 178 178
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.014 0.052 0.2 1 -0.18 16 17
cell motility 0.053 0.019 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.028 0.007 -10000 0 -10000 0 0
HDAC7/HDAC3 0.043 0.008 -10000 0 -10000 0 0
BCL6 0.029 0.003 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.029 0.004 -10000 0 -10000 0 0
Hsp90/HDAC6 0.042 0.01 -10000 0 -10000 0 0
ESR1 -0.17 0.2 -10000 0 -0.37 178 178
HDAC6/HDAC11 0.043 0.008 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.036 0.039 -10000 0 -0.21 3 3
NPC 0.017 0.002 -10000 0 -10000 0 0
MEF2C 0.029 0.003 -10000 0 -10000 0 0
RAN 0.029 0.004 -10000 0 -10000 0 0
HDAC4/MEF2C 0.079 0.03 -10000 0 -10000 0 0
GNG2 0.027 0.03 -10000 0 -0.37 2 2
NCOR2 0.029 0.005 -10000 0 -10000 0 0
TUBB2A 0.027 0.009 -10000 0 -10000 0 0
HDAC11 0.029 0.005 -10000 0 -10000 0 0
HSP90AA1 0.028 0.007 -10000 0 -10000 0 0
RANBP2 0.03 0.003 -10000 0 -10000 0 0
ANKRA2 0.028 0.021 -10000 0 -0.37 1 1
RFXANK 0.029 0.005 -10000 0 -10000 0 0
nuclear import -0.029 0.014 -10000 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.029 0.005 -9999 0 -10000 0 0
ITGB7 0.024 0.047 -9999 0 -0.37 5 5
ITGA4 0.022 0.055 -9999 0 -0.37 7 7
alpha4/beta7 Integrin 0.034 0.054 -9999 0 -0.26 12 12
alpha4/beta1 Integrin 0.037 0.042 -9999 0 -0.26 7 7
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.001 0.15 -10000 0 -0.34 39 39
CaM/Ca2+ 0.021 0.005 -10000 0 -10000 0 0
AKT1 0.028 0.008 -10000 0 -10000 0 0
AKT2 0.029 0.005 -10000 0 -10000 0 0
STXBP4 0.029 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.016 0.16 0.23 1 -0.36 42 43
YWHAZ 0.022 0.013 -10000 0 -10000 0 0
CALM1 0.028 0.007 -10000 0 -10000 0 0
YWHAQ 0.03 0.003 -10000 0 -10000 0 0
TBC1D4 -0.018 0.023 -10000 0 -0.26 3 3
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.029 0.005 -10000 0 -10000 0 0
YWHAB 0.029 0.005 -10000 0 -10000 0 0
SNARE/Synip 0.048 0.024 -10000 0 -10000 0 0
YWHAG 0.029 0.004 -10000 0 -10000 0 0
ASIP 0.027 0.006 -10000 0 -10000 0 0
PRKCI 0.03 0.003 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.021 0.005 -10000 0 -10000 0 0
RHOQ 0.03 0.003 -10000 0 -10000 0 0
GYS1 0.004 0.01 0.2 1 -10000 0 1
PRKCZ 0.014 0.071 -10000 0 -0.37 12 12
TRIP10 0.029 0.004 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.039 0.006 -10000 0 -10000 0 0
AS160/14-3-3 0.062 0.081 0.18 62 -0.28 4 66
VAMP2 0.025 0.011 -10000 0 -10000 0 0
SLC2A4 -0.021 0.17 -10000 0 -0.4 42 42
STX4 0.029 0.005 -10000 0 -10000 0 0
GSK3B 0.017 0.005 -10000 0 -10000 0 0
SFN 0.011 0.014 -10000 0 -10000 0 0
LNPEP 0.029 0.003 -10000 0 -10000 0 0
YWHAE 0.025 0.011 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.029 0.003 -10000 0 -10000 0 0
NFATC1 0.001 0.083 0.26 1 -0.34 6 7
NFATC2 -0.039 0.083 -10000 0 -0.24 32 32
NFATC3 0.003 0.059 -10000 0 -0.31 12 12
YWHAE 0.025 0.011 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.009 0.08 -10000 0 -0.3 13 13
Exportin 1/Ran/NUP214 0.057 0.012 -10000 0 -10000 0 0
mol:DAG -0.001 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.006 0.089 -10000 0 -0.3 14 14
BCL2/BAX 0.041 0.019 -10000 0 -0.26 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 0.014 0.017 -10000 0 -10000 0 0
CaM/Ca2+ 0.014 0.017 -10000 0 -10000 0 0
BAX 0.029 0.005 -10000 0 -10000 0 0
MAPK14 0.026 0.01 -10000 0 -10000 0 0
BAD 0.029 0.004 -10000 0 -10000 0 0
CABIN1/MEF2D 0.005 0.073 -10000 0 -0.29 10 10
Calcineurin A alpha-beta B1/BCL2 0.028 0.022 -10000 0 -0.37 1 1
FKBP8 0.029 0.004 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.005 0.072 0.29 10 -10000 0 10
KPNB1 0.029 0.003 -10000 0 -10000 0 0
KPNA2 0.028 0.006 -10000 0 -10000 0 0
XPO1 0.029 0.003 -10000 0 -10000 0 0
SFN 0.011 0.014 -10000 0 -10000 0 0
MAP3K8 0.025 0.03 -10000 0 -0.37 2 2
NFAT4/CK1 alpha 0.007 0.049 0.17 3 -0.18 12 15
MEF2D/NFAT1/Cbp/p300 -0.03 0.12 -10000 0 -0.27 53 53
CABIN1 -0.009 0.081 -10000 0 -0.31 13 13
CALM1 0.022 0.018 -10000 0 -10000 0 0
RAN 0.029 0.004 -10000 0 -10000 0 0
MAP3K1 0.03 0.002 -10000 0 -10000 0 0
CAMK4 -0.002 0.1 -10000 0 -0.37 27 27
mol:Ca2+ -0.002 0.004 -10000 0 -10000 0 0
MAPK3 0.029 0.005 -10000 0 -10000 0 0
YWHAH 0.029 0.005 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.04 0.012 -10000 0 -10000 0 0
YWHAB 0.029 0.005 -10000 0 -10000 0 0
MAPK8 0.007 0.087 -10000 0 -0.37 18 18
MAPK9 0.028 0.006 -10000 0 -10000 0 0
YWHAG 0.029 0.004 -10000 0 -10000 0 0
FKBP1A 0.029 0.005 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.013 0.11 -10000 0 -0.33 16 16
PRKCH 0.028 0.006 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.03 0.03 -10000 0 -10000 0 0
CASP3 0.025 0.01 -10000 0 -10000 0 0
PIM1 0.027 0.008 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.015 0.011 -10000 0 -10000 0 0
apoptosis 0.02 0.015 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.034 0.063 -10000 0 -0.28 4 4
PRKCB -0.004 0.11 -10000 0 -0.37 30 30
PRKCE 0.028 0.021 -10000 0 -0.37 1 1
JNK2/NFAT4 -0.003 0.083 -10000 0 -0.18 60 60
BAD/BCL-XL 0.043 0.008 -10000 0 -10000 0 0
PRKCD 0.029 0.004 -10000 0 -10000 0 0
NUP214 0.029 0.004 -10000 0 -10000 0 0
PRKCZ 0.012 0.071 -10000 0 -0.37 12 12
PRKCA 0.028 0.006 -10000 0 -10000 0 0
PRKCG 0.021 0.007 -10000 0 -10000 0 0
PRKCQ 0.014 0.074 -10000 0 -0.37 13 13
FKBP38/BCL2 0.041 0.019 -10000 0 -0.26 1 1
EP300 0.021 0.021 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.029 0.005 -10000 0 -10000 0 0
NFATc/JNK1 0.008 0.094 0.26 1 -0.32 12 13
CaM/Ca2+/FKBP38 0.028 0.025 -10000 0 -10000 0 0
FKBP12/FK506 0.022 0.003 -10000 0 -10000 0 0
CSNK1A1 -0.016 0.008 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.009 0.069 -10000 0 -0.22 27 27
NFATc/ERK1 0.017 0.085 0.26 1 -0.35 4 5
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.009 0.099 -10000 0 -0.3 15 15
NR4A1 -0.049 0.17 -10000 0 -0.41 54 54
GSK3B 0.028 0.008 -10000 0 -10000 0 0
positive T cell selection 0.003 0.059 -10000 0 -0.31 12 12
NFAT1/CK1 alpha -0.029 0.064 -10000 0 -0.21 19 19
RCH1/ KPNB1 0.042 0.01 -10000 0 -10000 0 0
YWHAQ 0.03 0.003 -10000 0 -10000 0 0
PRKACA 0.028 0.007 -10000 0 -10000 0 0
AKAP5 0.028 0.007 -10000 0 -10000 0 0
MEF2D 0.015 0.021 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.022 0.013 -10000 0 -10000 0 0
NFATc/p38 alpha 0.008 0.08 -10000 0 -0.32 6 6
CREBBP 0.02 0.021 -10000 0 -10000 0 0
BCL2 0.028 0.022 -10000 0 -0.37 1 1
Retinoic acid receptors-mediated signaling

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
HDAC1 0.028 0.007 -10000 0 -10000 0 0
HDAC3 0.029 0.004 -10000 0 -10000 0 0
VDR 0.021 0.055 -10000 0 -0.37 7 7
Cbp/p300/PCAF 0.054 0.03 -10000 0 -0.23 3 3
EP300 0.029 0.004 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.014 0.059 0.18 2 -0.27 5 7
KAT2B 0.026 0.036 -10000 0 -0.37 3 3
MAPK14 0.027 0.009 -10000 0 -10000 0 0
AKT1 0.024 0.084 0.23 8 -0.22 10 18
RAR alpha/9cRA/Cyclin H 0.033 0.07 -10000 0 -0.22 2 2
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.004 0.055 -10000 0 -0.26 5 5
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0 0.002 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.014 0.08 -10000 0 -0.33 17 17
NCOR2 0.029 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.016 0.038 -10000 0 -0.26 7 7
RXRs/RARs/NRIP1/9cRA 0.027 0.077 -10000 0 -0.43 2 2
NCOA2 -0.013 0.11 -10000 0 -0.37 33 33
NCOA3 0.029 0.005 -10000 0 -10000 0 0
NCOA1 0.03 0.003 -10000 0 -10000 0 0
VDR/VDR/DNA 0.021 0.055 -10000 0 -0.37 7 7
RARG 0.03 0.004 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.039 0.007 -10000 0 -10000 0 0
MAPK3 0.029 0.006 -10000 0 -10000 0 0
MAPK1 0.029 0.004 -10000 0 -10000 0 0
MAPK8 0.01 0.087 -10000 0 -0.37 18 18
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.033 0.063 -10000 0 -0.3 1 1
RARA 0.004 0.047 -10000 0 -0.2 16 16
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.014 0.085 -10000 0 -0.32 15 15
PRKCA 0.029 0.009 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 0.028 0.077 -10000 0 -0.51 1 1
RXRG 0.022 0.052 -10000 0 -0.26 4 4
RXRA 0.006 0.049 0.21 1 -0.19 2 3
RXRB 0.016 0.017 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.016 0.038 -10000 0 -0.26 7 7
RBP1 -0.049 0.16 -10000 0 -0.37 71 71
CRBP1/9-cic-RA -0.033 0.11 -10000 0 -0.26 71 71
RARB 0.014 0.08 -10000 0 -0.37 15 15
PRKCG 0.021 0.009 -10000 0 -10000 0 0
MNAT1 0.028 0.006 -10000 0 -10000 0 0
RAR alpha/RXRs 0.024 0.08 0.34 1 -0.32 1 2
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.028 0.073 -10000 0 -0.43 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.008 0.069 0.22 2 -0.34 4 6
RXRs/RARs/NRIP1/9cRA/HDAC3 0.03 0.077 -10000 0 -0.51 1 1
positive regulation of DNA binding 0.025 0.064 -10000 0 -0.19 18 18
NRIP1 0.029 0.091 -10000 0 -1.1 1 1
RXRs/RARs 0.035 0.078 -10000 0 -0.34 2 2
RXRs/RXRs/DNA/9cRA 0.007 0.046 -10000 0 -0.3 1 1
PRKACA 0.029 0.004 -10000 0 -10000 0 0
CDK7 0.029 0.003 -10000 0 -10000 0 0
TFIIH 0.057 0.014 -10000 0 -10000 0 0
RAR alpha/9cRA 0.051 0.058 -10000 0 -10000 0 0
CCNH 0.029 0.003 -10000 0 -10000 0 0
CREBBP 0.028 0.006 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.049 0.024 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.019 0.082 -10000 0 -0.26 28 28
AKT1 0.002 0.098 -10000 0 -0.49 10 10
PTK2B -0.025 0.1 0.33 2 -0.52 7 9
VEGFR2 homodimer/Frs2 0.018 0.083 -10000 0 -0.49 9 9
CAV1 0.029 0.006 -10000 0 -10000 0 0
CALM1 0.028 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.031 0.079 -10000 0 -0.44 9 9
endothelial cell proliferation -0.002 0.1 0.3 1 -0.45 9 10
mol:Ca2+ -0.013 0.093 -10000 0 -0.44 9 9
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.044 0.081 -10000 0 -0.42 9 9
RP11-342D11.1 -0.026 0.07 -10000 0 -0.44 9 9
CDH5 0.026 0.022 -10000 0 -0.37 1 1
VEGFA homodimer 0.049 0.037 -10000 0 -10000 0 0
SHC1 0.022 0.013 -10000 0 -10000 0 0
SHC2 0.021 0.055 -10000 0 -0.37 7 7
HRAS/GDP 0.024 0.062 -10000 0 -0.34 7 7
SH2D2A 0.015 0.055 -10000 0 -0.37 7 7
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.023 0.1 -10000 0 -0.48 9 9
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.02 0.08 -10000 0 -0.35 13 13
VEGFR1 homodimer 0.027 0.008 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.042 0.077 -10000 0 -0.42 6 6
GRB10 -0.011 0.092 0.34 1 -0.44 8 9
PTPN11 0.029 0.003 -10000 0 -10000 0 0
GRB2 0.028 0.006 -10000 0 -10000 0 0
PAK1 0.029 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.05 0.086 -10000 0 -0.42 9 9
HRAS 0.029 0.004 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.006 0.084 -10000 0 -0.4 8 8
HIF1A 0.028 0.006 -10000 0 -10000 0 0
FRS2 0.029 0.004 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.042 0.079 -10000 0 -0.41 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.027 0.022 -10000 0 -0.37 1 1
Nck/Pak 0.043 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.029 0.082 -10000 0 -0.45 9 9
mol:GDP 0.032 0.07 -10000 0 -0.38 7 7
mol:NADP 0.011 0.096 -10000 0 -0.43 9 9
eNOS/Hsp90 0.025 0.092 -10000 0 -0.42 8 8
PIK3R1 0.027 0.03 -10000 0 -0.37 2 2
mol:IP3 -0.013 0.094 -10000 0 -0.45 9 9
HIF1A/ARNT 0.033 0.019 -10000 0 -10000 0 0
SHB 0.028 0.021 -10000 0 -0.37 1 1
VEGFA 0.026 0.01 -10000 0 -10000 0 0
VEGFC 0.027 0.009 -10000 0 -10000 0 0
FAK1/Vinculin 0.01 0.13 0.29 1 -0.54 10 11
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.029 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.029 0.11 -10000 0 -0.29 28 28
PTPN6 0.029 0.006 -10000 0 -10000 0 0
EPAS1 0.027 0.053 -10000 0 -0.3 9 9
mol:L-citrulline 0.011 0.096 -10000 0 -0.43 9 9
ITGAV 0.029 0.003 -10000 0 -10000 0 0
PIK3CA 0.028 0.021 -10000 0 -0.37 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.045 0.076 -10000 0 -0.41 8 8
VEGFR2 homodimer/VEGFA homodimer 0.032 0.087 -10000 0 -0.45 10 10
VEGFR2/3 heterodimer 0.017 0.086 -10000 0 -0.51 9 9
VEGFB 0.019 0.062 -10000 0 -0.37 9 9
MAPK11 -0.002 0.099 0.36 1 -0.46 9 10
VEGFR2 homodimer 0 0.09 -10000 0 -0.64 7 7
FLT1 0.027 0.008 -10000 0 -10000 0 0
NEDD4 0.028 0.03 -10000 0 -0.37 2 2
MAPK3 -0.011 0.095 0.34 1 -0.4 9 10
MAPK1 -0.012 0.095 0.34 1 -0.4 9 10
VEGFA145/NRP2 0.036 0.031 -10000 0 -0.26 3 3
VEGFR1/2 heterodimer 0.016 0.086 -10000 0 -0.5 9 9
KDR 0 0.091 -10000 0 -0.64 7 7
VEGFA165/NRP1/VEGFR2 homodimer 0.032 0.083 -10000 0 -0.39 11 11
SRC 0.029 0.005 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.011 0.096 0.35 1 -0.41 9 10
PI3K 0.004 0.1 -10000 0 -0.55 9 9
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.031 0.082 -10000 0 -0.46 9 9
FES -0.018 0.094 -10000 0 -0.48 8 8
GAB1 0.019 0.085 -10000 0 -0.46 8 8
VEGFR2 homodimer/VEGFA homodimer/Src 0.031 0.083 -10000 0 -0.46 9 9
CTNNB1 0.03 0.003 -10000 0 -10000 0 0
SOS1 0.03 0.002 -10000 0 -10000 0 0
ARNT 0.023 0.013 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.022 0.092 -10000 0 -0.4 8 8
VEGFR2 homodimer/VEGFA homodimer/Yes 0.03 0.082 -10000 0 -0.46 9 9
PI3K/GAB1 0.023 0.099 -10000 0 -0.47 9 9
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.054 0.082 -10000 0 -0.41 9 9
PRKACA 0.029 0.004 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.03 0.084 -10000 0 -0.47 9 9
HSP90AA1 0.028 0.007 -10000 0 -10000 0 0
CDC42 -0.013 0.094 -10000 0 -0.45 9 9
actin cytoskeleton reorganization 0.02 0.079 -10000 0 -0.35 13 13
PTK2 -0.001 0.12 0.29 1 -0.61 9 10
EDG1 -0.026 0.07 -10000 0 -0.44 9 9
mol:DAG -0.013 0.094 -10000 0 -0.45 9 9
CaM/Ca2+ -0.014 0.089 -10000 0 -0.42 9 9
MAP2K3 -0.016 0.09 0.34 1 -0.42 8 9
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.033 0.084 -10000 0 -0.44 9 9
PLCG1 -0.013 0.095 -10000 0 -0.45 9 9
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.044 0.085 -10000 0 -0.41 10 10
IQGAP1 0.029 0.005 -10000 0 -10000 0 0
YES1 0.029 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.031 0.078 -10000 0 -0.43 9 9
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.03 0.081 -10000 0 -0.45 9 9
cell migration 0.007 0.11 0.35 1 -0.56 8 9
mol:PI-3-4-5-P3 0.005 0.092 -10000 0 -0.51 9 9
FYN 0.028 0.008 -10000 0 -10000 0 0
VEGFB/NRP1 -0.016 0.089 -10000 0 -0.42 9 9
mol:NO 0.011 0.096 -10000 0 -0.43 9 9
PXN 0.029 0.003 -10000 0 -10000 0 0
HRAS/GTP -0.03 0.05 -10000 0 -0.37 6 6
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.023 0.08 -10000 0 -0.44 9 9
VHL 0.03 0.003 -10000 0 -10000 0 0
ITGB3 -0.002 0.11 -10000 0 -0.37 28 28
NOS3 0.009 0.11 -10000 0 -0.49 9 9
VEGFR2 homodimer/VEGFA homodimer/Sck 0.027 0.086 -10000 0 -0.37 14 14
RAC1 0.029 0.004 -10000 0 -10000 0 0
PRKCA -0.014 0.089 0.34 1 -0.41 8 9
PRKCB -0.026 0.1 0.34 1 -0.48 7 8
VCL 0.029 0.006 -10000 0 -10000 0 0
VEGFA165/NRP1 0.007 0.075 -10000 0 -0.44 9 9
VEGFR1/2 heterodimer/VEGFA homodimer 0.028 0.081 -10000 0 -0.45 9 9
VEGFA165/NRP2 0.036 0.031 -10000 0 -0.26 3 3
MAPKKK cascade 0.008 0.1 0.33 4 -0.4 5 9
NRP2 0.026 0.036 -10000 0 -0.37 3 3
VEGFC homodimer 0.027 0.009 -10000 0 -10000 0 0
NCK1 0.03 0.002 -10000 0 -10000 0 0
ROCK1 0.029 0.003 -10000 0 -10000 0 0
FAK1/Paxillin 0.01 0.13 0.29 1 -0.57 9 10
MAP3K13 -0.016 0.094 -10000 0 -0.45 9 9
PDPK1 -0.018 0.082 -10000 0 -0.45 9 9
IL2 signaling events mediated by STAT5

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
GAB2 0.029 0.005 -10000 0 -10000 0 0
ELF1 0.03 0.059 0.2 11 -0.33 7 18
CCNA2 0.013 0.015 -10000 0 -10000 0 0
PIK3CA 0.029 0.021 -10000 0 -0.37 1 1
JAK3 0.028 0.021 -10000 0 -0.37 1 1
PIK3R1 0.027 0.03 -10000 0 -0.37 2 2
JAK1 0.029 0.006 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.023 0.12 0.4 1 -0.44 13 14
SHC1 0.022 0.013 -10000 0 -10000 0 0
SP1 0.037 0.019 0.2 5 -10000 0 5
IL2RA 0.012 0.11 0.43 11 -0.54 7 18
IL2RB 0.001 0.1 -10000 0 -0.37 26 26
SOS1 0.03 0.002 -10000 0 -10000 0 0
IL2RG 0.024 0.047 -10000 0 -0.37 5 5
G1/S transition of mitotic cell cycle 0.043 0.18 0.35 7 -0.7 12 19
PTPN11 0.03 0.004 -10000 0 -10000 0 0
CCND2 -0.008 0.051 0.43 5 -10000 0 5
LCK 0.017 0.065 -10000 0 -0.37 10 10
GRB2 0.029 0.006 -10000 0 -10000 0 0
IL2 0.02 0.007 -10000 0 -10000 0 0
CDK6 0.003 0.097 -10000 0 -0.37 23 23
CCND3 0.029 0.12 0.38 1 -0.52 4 5
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.03 0.044 0.28 2 -10000 0 2
DAPP1 -0.046 0.14 0.26 1 -0.38 34 35
Src family/SYK family/BLNK-LAT/BTK-ITK -0.063 0.2 0.36 1 -0.51 40 41
mol:DAG -0.03 0.077 0.29 1 -0.22 22 23
HRAS 0.03 0.005 -10000 0 -10000 0 0
RAP1A 0.029 0.007 -10000 0 -10000 0 0
ARF5/GDP 0.011 0.077 -10000 0 -0.24 14 14
PLCG2 0.02 0.051 -10000 0 -0.37 6 6
PLCG1 0.029 0.004 -10000 0 -10000 0 0
ARF5 0.029 0.005 -10000 0 -10000 0 0
mol:GTP -0.029 0.024 0.3 1 -10000 0 1
ARF1/GTP -0.013 0.031 0.27 1 -10000 0 1
RHOA 0.029 0.004 -10000 0 -10000 0 0
YES1 0.029 0.004 -10000 0 -10000 0 0
RAP1A/GTP -0.029 0.019 0.15 2 -10000 0 2
ADAP1 -0.027 0.047 0.28 2 -0.2 6 8
ARAP3 -0.029 0.024 0.29 1 -10000 0 1
INPPL1 0.029 0.005 -10000 0 -10000 0 0
PREX1 0.029 0.005 -10000 0 -10000 0 0
ARHGEF6 0.029 0.004 -10000 0 -10000 0 0
ARHGEF7 0.028 0.007 -10000 0 -10000 0 0
ARF1 0.024 0.012 -10000 0 -10000 0 0
NRAS 0.029 0.006 -10000 0 -10000 0 0
FYN 0.028 0.008 -10000 0 -10000 0 0
ARF6 0.029 0.005 -10000 0 -10000 0 0
FGR 0.026 0.03 -10000 0 -0.37 2 2
mol:Ca2+ -0.017 0.041 0.14 4 -0.13 10 14
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.008 0.089 -10000 0 -0.37 19 19
ZAP70 0.025 0.042 -10000 0 -0.37 4 4
mol:IP3 -0.025 0.056 0.17 4 -0.17 14 18
LYN 0.025 0.011 -10000 0 -10000 0 0
ARF1/GDP 0.01 0.07 -10000 0 -0.25 13 13
RhoA/GDP -0.015 0.051 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.053 0.02 -10000 0 -10000 0 0
BLNK 0.019 0.062 -10000 0 -0.37 9 9
actin cytoskeleton reorganization -0.006 0.061 0.27 2 -0.29 3 5
SRC 0.029 0.005 -10000 0 -10000 0 0
PLEKHA2 -0.018 0.009 -10000 0 -10000 0 0
RAC1 0.029 0.004 -10000 0 -10000 0 0
PTEN 0.029 0.012 -10000 0 -10000 0 0
HSP90AA1 0.028 0.007 -10000 0 -10000 0 0
ARF6/GTP -0.032 0.038 0.28 2 -10000 0 2
RhoA/GTP -0.032 0.026 0.29 1 -10000 0 1
Src family/SYK family/BLNK-LAT -0.038 0.14 0.35 1 -0.38 36 37
BLK -0.022 0.12 -10000 0 -0.37 40 40
PDPK1 0.028 0.006 -10000 0 -10000 0 0
CYTH1 -0.029 0.035 0.28 2 -10000 0 2
HCK 0.016 0.071 -10000 0 -0.37 12 12
CYTH3 -0.029 0.036 0.28 2 -10000 0 2
CYTH2 -0.029 0.035 0.28 2 -10000 0 2
KRAS 0.03 0.006 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.01 0.084 -10000 0 -0.4 12 12
SGK1 -0.023 0.12 0.22 2 -0.37 32 34
INPP5D 0.029 0.003 -10000 0 -10000 0 0
mol:GDP -0.005 0.075 0.19 1 -0.26 15 16
SOS1 0.03 0.002 -10000 0 -10000 0 0
SYK 0.026 0.036 -10000 0 -0.37 3 3
ARF6/GDP -0.021 0.042 0.32 1 -10000 0 1
mol:PI-3-4-5-P3 -0.026 0.035 0.29 2 -10000 0 2
ARAP3/RAP1A/GTP -0.029 0.019 0.15 2 -10000 0 2
VAV1 0.013 0.079 -10000 0 -0.37 15 15
mol:PI-3-4-P2 -0.018 0.004 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.046 0.041 0.27 2 -10000 0 2
PLEKHA1 -0.02 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.01 0.078 -10000 0 -0.25 15 15
LAT 0.029 0.006 -10000 0 -10000 0 0
Rac1/GTP 0 0.071 -10000 0 -0.26 13 13
ITK -0.039 0.039 0.27 1 -0.2 14 15
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.042 0.1 0.33 1 -0.31 24 25
LCK 0.017 0.065 -10000 0 -0.37 10 10
BTK -0.032 0.04 0.28 2 -0.2 5 7
EGFR-dependent Endothelin signaling events

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
HRAS 0.029 0.004 -10000 0 -10000 0 0
EGFR 0.019 0.062 -10000 0 -0.37 9 9
EGF/EGFR 0.05 0.065 -10000 0 -0.18 16 16
EGF/EGFR dimer/SHC/GRB2/SOS1 0.063 0.064 -10000 0 -0.2 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.025 0.03 -10000 0 -0.37 2 2
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.017 0.012 -10000 0 -10000 0 0
EGF/EGFR dimer/SHC 0.026 0.039 -10000 0 -0.23 4 4
mol:GDP 0.057 0.059 -10000 0 -0.2 4 4
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.017 0.062 -10000 0 -0.37 9 9
GRB2/SOS1 0.042 0.009 -10000 0 -10000 0 0
HRAS/GTP 0.024 0.037 -10000 0 -0.19 4 4
SHC1 0.022 0.013 -10000 0 -10000 0 0
HRAS/GDP 0.054 0.056 -10000 0 -0.2 4 4
FRAP1 -0.001 0.051 0.12 50 -0.19 4 54
EGF/EGFR dimer 0.022 0.042 -10000 0 -0.26 6 6
SOS1 0.03 0.002 -10000 0 -10000 0 0
GRB2 0.028 0.006 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 0.028 0.054 -10000 0 -0.26 11 11
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.002 0.068 -10000 0 -0.32 4 4
PDGFB-D/PDGFRB/SLAP 0.024 0.048 -10000 0 -0.27 8 8
PDGFB-D/PDGFRB/APS/CBL 0.053 0.02 -10000 0 -10000 0 0
AKT1 -0.021 0.062 0.28 3 -0.31 1 4
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.006 0.072 -10000 0 -0.33 4 4
PIK3CA 0.028 0.021 -10000 0 -0.37 1 1
FGR -0.008 0.12 -10000 0 -0.44 20 20
mol:Ca2+ 0.011 0.073 -10000 0 -0.34 6 6
MYC -0.019 0.28 -10000 0 -0.75 41 41
SHC1 0.022 0.013 -10000 0 -10000 0 0
HRAS/GDP 0.017 0.05 0.16 15 -0.19 1 16
LRP1/PDGFRB/PDGFB 0.054 0.023 -10000 0 -0.22 1 1
GRB10 0.029 0.004 -10000 0 -10000 0 0
PTPN11 0.029 0.003 -10000 0 -10000 0 0
GO:0007205 0.01 0.074 -10000 0 -0.34 6 6
PTEN 0.028 0.007 -10000 0 -10000 0 0
GRB2 0.028 0.006 -10000 0 -10000 0 0
GRB7 0.024 0.042 -10000 0 -0.37 4 4
PDGFB-D/PDGFRB/SHP2 0.041 0.011 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0.041 0.012 -10000 0 -10000 0 0
cell cycle arrest 0.023 0.048 -10000 0 -0.27 8 8
HRAS 0.029 0.004 -10000 0 -10000 0 0
HIF1A -0.024 0.057 0.26 3 -0.29 1 4
GAB1 0.006 0.096 -10000 0 -0.41 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.003 0.092 0.28 2 -0.37 5 7
PDGFB-D/PDGFRB 0.047 0.036 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.041 0.011 -10000 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.002 0.086 -10000 0 -0.33 7 7
positive regulation of MAPKKK cascade 0.041 0.011 -10000 0 -10000 0 0
PIK3R1 0.027 0.03 -10000 0 -0.37 2 2
mol:IP3 0.011 0.074 -10000 0 -0.35 6 6
E5 -0.001 0.001 -10000 0 -10000 0 0
CSK 0.029 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.038 0.031 -10000 0 -0.27 3 3
SHB 0.028 0.021 -10000 0 -0.37 1 1
BLK -0.12 0.21 -10000 0 -0.42 111 111
PTPN2 0.025 0.017 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.041 0.013 -10000 0 -10000 0 0
BCAR1 0.027 0.008 -10000 0 -10000 0 0
VAV2 -0.003 0.12 -10000 0 -0.44 11 11
CBL 0.028 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.041 0.011 -10000 0 -10000 0 0
LCK -0.016 0.13 -10000 0 -0.44 27 27
PDGFRB 0.023 0.019 -10000 0 -10000 0 0
ACP1 0.03 0.003 -10000 0 -10000 0 0
HCK 0.004 0.1 -10000 0 -0.48 12 12
ABL1 -0.003 0.095 -10000 0 -0.36 10 10
PDGFB-D/PDGFRB/CBL 0.003 0.1 -10000 0 -0.42 7 7
PTPN1 0.024 0.017 -10000 0 -10000 0 0
SNX15 0.029 0.005 -10000 0 -10000 0 0
STAT3 0.029 0.004 -10000 0 -10000 0 0
STAT1 0.029 0.003 -10000 0 -10000 0 0
cell proliferation -0.01 0.25 0.32 1 -0.66 41 42
SLA 0.013 0.059 -10000 0 -0.37 8 8
actin cytoskeleton reorganization -0.023 0.047 0.33 1 -10000 0 1
SRC 0.017 0.044 -10000 0 -10000 0 0
PI3K -0.036 0.026 -10000 0 -0.22 4 4
PDGFB-D/PDGFRB/GRB7/SHC 0.041 0.032 -10000 0 -0.23 1 1
SH2B2 0.029 0.006 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.006 0.073 -10000 0 -0.34 4 4
LYN 0.009 0.062 -10000 0 -0.42 4 4
LRP1 0.028 0.021 -10000 0 -0.37 1 1
SOS1 0.03 0.002 -10000 0 -10000 0 0
STAT5B 0.029 0.004 -10000 0 -10000 0 0
STAT5A 0.029 0.004 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.068 0.052 -10000 0 -0.18 1 1
SPHK1 0.018 0.048 -10000 0 -0.38 5 5
EDG1 0 0.003 -10000 0 -10000 0 0
mol:DAG 0.011 0.074 -10000 0 -0.35 6 6
PLCG1 0.01 0.075 -10000 0 -0.35 6 6
NHERF/PDGFRB 0.049 0.033 -10000 0 -0.23 3 3
YES1 0.01 0.083 -10000 0 -0.59 5 5
cell migration 0.049 0.033 -10000 0 -0.23 3 3
SHC/Grb2/SOS1 0.055 0.053 -10000 0 -10000 0 0
SLC9A3R2 0.026 0.03 -10000 0 -0.37 2 2
SLC9A3R1 0.027 0.022 -10000 0 -0.37 1 1
NHERF1-2/PDGFRB/PTEN 0.063 0.041 -10000 0 -0.2 3 3
FYN -0.009 0.11 -10000 0 -0.39 25 25
DOK1 -0.009 0.053 0.17 22 -10000 0 22
HRAS/GTP 0.022 0.003 -10000 0 -10000 0 0
PDGFB 0.029 0.005 -10000 0 -10000 0 0
RAC1 -0.023 0.17 0.32 1 -0.46 40 41
PRKCD -0.008 0.053 0.17 29 -10000 0 29
FER -0.011 0.05 0.17 18 -10000 0 18
MAPKKK cascade 0.032 0.1 0.35 15 -10000 0 15
RASA1 -0.012 0.052 0.17 17 -0.21 2 19
NCK1 0.03 0.002 -10000 0 -10000 0 0
NCK2 0.028 0.021 -10000 0 -0.37 1 1
p62DOK/Csk -0.004 0.055 0.17 21 -10000 0 21
PDGFB-D/PDGFRB/SHB 0.041 0.012 -10000 0 -10000 0 0
chemotaxis -0.003 0.094 -10000 0 -0.36 10 10
STAT1-3-5/STAT1-3-5 0.059 0.043 -10000 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.017 0.014 -10000 0 -10000 0 0
PTPRJ 0.03 0.002 -10000 0 -10000 0 0
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.049 0.038 -10000 0 -10000 0 0
epithelial cell differentiation 0.01 0.07 -10000 0 -10000 0 0
ITCH 0.029 0.013 -10000 0 -10000 0 0
WWP1 0.055 0.084 -10000 0 -10000 0 0
FYN 0.028 0.008 -10000 0 -10000 0 0
EGFR 0.019 0.062 -10000 0 -0.37 9 9
PRL 0.017 0.007 -10000 0 -10000 0 0
neuron projection morphogenesis 0 0.12 0.35 8 -10000 0 8
PTPRZ1 0.024 0.008 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.015 0.092 -10000 0 -10000 0 0
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.03 0.09 -10000 0 -0.24 1 1
ADAM17 0.029 0.013 -10000 0 -10000 0 0
ErbB4/ErbB4 0.039 0.045 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.017 0.081 -10000 0 -0.3 2 2
NCOR1 0.026 0.01 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.031 0.095 -10000 0 -10000 0 0
GRIN2B -0.045 0.085 0.23 2 -10000 0 2
ErbB4/ErbB2/betacellulin 0.038 0.04 -10000 0 -10000 0 0
STAT1 0.029 0.003 -10000 0 -10000 0 0
HBEGF 0.027 0.03 -10000 0 -0.37 2 2
PRLR 0.016 0.068 -10000 0 -0.37 11 11
E4ICDs/ETO2 0.029 0.069 -10000 0 -10000 0 0
axon guidance -0.001 0.063 -10000 0 -10000 0 0
NEDD4 0.026 0.032 -10000 0 -0.37 2 2
Prolactin receptor/Prolactin receptor/Prolactin 0.023 0.05 -10000 0 -0.26 10 10
CBFA2T3 -0.014 0.12 -10000 0 -0.37 37 37
ErbB4/ErbB2/HBEGF 0.041 0.04 -10000 0 -10000 0 0
MAPK3 -0.008 0.11 0.33 6 -10000 0 6
STAT1 (dimer) 0.05 0.036 -10000 0 -10000 0 0
MAPK1 -0.008 0.11 0.33 6 -10000 0 6
JAK2 0.028 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.042 0.092 -10000 0 -0.35 2 2
NRG1 -0.091 0.12 -10000 0 -0.27 116 116
NRG3 -0.036 0.14 -10000 0 -0.37 56 56
NRG2 0.022 0.012 -10000 0 -10000 0 0
NRG4 -0.029 0.14 -10000 0 -0.37 52 52
heart development -0.001 0.063 -10000 0 -10000 0 0
neural crest cell migration -0.042 0.092 -10000 0 -0.34 2 2
ERBB2 -0.015 0.036 -10000 0 -0.27 6 6
WWOX/E4ICDs 0.047 0.037 -10000 0 -10000 0 0
SHC1 0.022 0.013 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.025 0.09 -10000 0 -0.32 2 2
apoptosis 0.017 0.13 0.34 42 -10000 0 42
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.038 0.039 -10000 0 -10000 0 0
ErbB4/ErbB2/epiregulin 0.033 0.039 -10000 0 -10000 0 0
ErbB4/ErbB4/betacellulin/betacellulin 0.045 0.039 -10000 0 -10000 0 0
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.062 0.061 -10000 0 -10000 0 0
MDM2 0.028 0.043 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.038 0.093 -10000 0 -0.21 1 1
STAT5A 0.002 0.067 0.3 1 -10000 0 1
ErbB4/EGFR/neuregulin 1 beta -0.035 0.099 -10000 0 -0.34 3 3
DLG4 0.025 0.011 -10000 0 -10000 0 0
GRB2/SHC 0.032 0.02 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.04 0.035 -10000 0 -10000 0 0
STAT5A (dimer) 0.018 0.08 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.013 0.071 -10000 0 -10000 0 0
LRIG1 0.029 0.004 -10000 0 -10000 0 0
EREG 0.022 0.011 -10000 0 -10000 0 0
BTC 0.025 0.009 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.002 0.062 -10000 0 -10000 0 0
ERBB4 0.039 0.045 -10000 0 -10000 0 0
STAT5B 0.029 0.004 -10000 0 -10000 0 0
YAP1 0.021 0.071 -10000 0 -0.36 11 11
GRB2 0.028 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.012 0.079 -10000 0 -10000 0 0
glial cell differentiation -0.039 0.035 -10000 0 -10000 0 0
WWOX 0.027 0.009 -10000 0 -10000 0 0
cell proliferation -0.063 0.11 -10000 0 -0.37 6 6
Canonical NF-kappaB 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
FBXW11 0.029 0.005 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.01 0.11 -9999 0 -0.3 22 22
ERC1 0.029 0.006 -9999 0 -10000 0 0
RIP2/NOD2 0.028 0.037 -9999 0 -0.26 4 4
NFKBIA -0.019 0.017 -9999 0 -10000 0 0
BIRC2 0.029 0.006 -9999 0 -10000 0 0
IKBKB 0.026 0.01 -9999 0 -10000 0 0
RIPK2 0.023 0.013 -9999 0 -10000 0 0
IKBKG 0.018 0.087 -9999 0 -0.39 11 11
IKK complex/A20 0.029 0.12 -9999 0 -0.37 20 20
NEMO/A20/RIP2 0.023 0.013 -9999 0 -10000 0 0
XPO1 0.03 0.003 -9999 0 -10000 0 0
NEMO/ATM 0.024 0.12 -9999 0 -0.39 22 22
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.029 0.004 -9999 0 -10000 0 0
Exportin 1/RanGTP 0.039 0.007 -9999 0 -10000 0 0
IKK complex/ELKS 0.024 0.11 -9999 0 -0.36 22 22
BCL10/MALT1/TRAF6 0.056 0.021 -9999 0 -0.23 1 1
NOD2 0.024 0.042 -9999 0 -0.37 4 4
NFKB1 0.028 0.009 -9999 0 -10000 0 0
RELA 0.03 0.005 -9999 0 -10000 0 0
MALT1 0.029 0.006 -9999 0 -10000 0 0
cIAP1/UbcH5C 0.039 0.014 -9999 0 -10000 0 0
ATM 0.029 0.006 -9999 0 -10000 0 0
TNF/TNFR1A 0.028 0.056 -9999 0 -0.26 12 12
TRAF6 0.029 0.021 -9999 0 -0.37 1 1
PRKCA 0.028 0.006 -9999 0 -10000 0 0
CHUK 0.029 0.005 -9999 0 -10000 0 0
UBE2D3 0.027 0.009 -9999 0 -10000 0 0
TNF 0.013 0.071 -9999 0 -0.37 12 12
NF kappa B1 p50/RelA 0.057 0.022 -9999 0 -10000 0 0
BCL10 0.029 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.019 0.017 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.029 0.005 -9999 0 -10000 0 0
TNFRSF1A 0.028 0.006 -9999 0 -10000 0 0
IKK complex 0.028 0.12 -9999 0 -0.38 22 22
CYLD 0.028 0.007 -9999 0 -10000 0 0
IKK complex/PKC alpha 0.036 0.12 -9999 0 -0.38 21 21
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.043 0.029 -10000 0 -0.18 4 4
RGS9BP 0.026 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.017 0.004 -10000 0 -10000 0 0
mol:Na + 0.019 0.013 -10000 0 -10000 0 0
mol:ADP -0.017 0.004 -10000 0 -10000 0 0
GNAT2 0.027 0.007 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.043 0.049 -10000 0 -0.23 10 10
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.03 0.009 -10000 0 -10000 0 0
GRK7 0.021 0.006 -10000 0 -10000 0 0
CNGB3 0.015 0.011 -10000 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0.015 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0.034 0.084 0.17 101 -10000 0 101
Cone PDE6 0.067 0.058 -10000 0 -0.2 10 10
Cone Metarhodopsin II 0.024 0.007 -10000 0 -10000 0 0
Na + (4 Units) 0.024 0.018 -10000 0 -10000 0 0
GNAT2/GDP 0.058 0.051 -10000 0 -0.2 10 10
GNB5 0.029 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.015 0.019 0.17 3 -10000 0 3
Cone Transducin 0.047 0.031 -10000 0 -0.2 4 4
SLC24A2 0.017 0.004 -10000 0 -10000 0 0
GNB3/GNGT2 0.036 0.033 -10000 0 -0.26 4 4
GNB3 0.026 0.008 -10000 0 -10000 0 0
GNAT2/GTP 0.02 0.005 -10000 0 -10000 0 0
CNGA3 0.019 0.004 -10000 0 -10000 0 0
ARR3 0.02 0.005 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.019 0.013 -10000 0 -10000 0 0
mol:Pi 0.043 0.049 -10000 0 -0.23 10 10
Cone CNG Channel 0.042 0.037 -10000 0 -10000 0 0
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.017 0.004 -10000 0 -10000 0 0
RGS9 0.017 0.065 -10000 0 -0.37 10 10
PDE6C 0.022 0.009 -10000 0 -10000 0 0
GNGT2 0.025 0.042 -10000 0 -0.37 4 4
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.018 0.005 -10000 0 -10000 0 0
ceramide signaling pathway

Figure S110.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S110.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.012 0.079 -10000 0 -0.5 1 1
BAG4 0.019 0.047 -10000 0 -0.37 5 5
BAD 0.007 0.038 -10000 0 -0.16 1 1
NFKBIA 0.029 0.004 -10000 0 -10000 0 0
BIRC3 0.026 0.022 -10000 0 -0.37 1 1
BAX 0.008 0.041 0.18 3 -0.16 1 4
EnzymeConsortium:3.1.4.12 0.005 0.025 0.073 5 -0.11 1 6
IKBKB 0.006 0.083 0.32 6 -0.48 1 7
MAP2K2 0.003 0.053 0.26 6 -0.16 1 7
MAP2K1 0.001 0.05 0.24 5 -0.16 1 6
SMPD1 0.006 0.027 -10000 0 -0.11 3 3
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.018 0.087 0.28 4 -0.32 4 8
MAP2K4 0.006 0.038 0.22 2 -10000 0 2
protein ubiquitination 0.007 0.084 0.27 1 -0.5 1 2
EnzymeConsortium:2.7.1.37 0 0.054 0.25 6 -0.17 1 7
response to UV 0 0.001 0.003 6 -10000 0 6
RAF1 0.005 0.05 0.25 5 -0.16 1 6
CRADD 0.028 0.021 -10000 0 -0.37 1 1
mol:ceramide 0.011 0.04 0.12 14 -0.16 1 15
I-kappa-B-alpha/RELA/p50/ubiquitin 0.039 0.008 -10000 0 -10000 0 0
MADD 0.03 0.002 -10000 0 -10000 0 0
MAP3K1 0.007 0.043 0.2 3 -0.16 1 4
TRADD 0.027 0.008 -10000 0 -10000 0 0
RELA/p50 0.029 0.005 -10000 0 -10000 0 0
MAPK3 0.003 0.058 0.26 5 -0.19 5 10
MAPK1 0.003 0.054 0.26 5 -0.18 2 7
p50/RELA/I-kappa-B-alpha 0.042 0.009 -10000 0 -10000 0 0
FADD 0.017 0.082 0.27 3 -0.5 1 4
KSR1 0.008 0.047 0.2 7 -0.16 1 8
MAPK8 -0.008 0.048 0.26 1 -0.19 3 4
TRAF2 0.029 0.005 -10000 0 -10000 0 0
response to radiation 0 0 0.002 3 -10000 0 3
CHUK 0.005 0.076 -10000 0 -0.48 1 1
TNF R/SODD 0.031 0.039 -10000 0 -0.26 5 5
TNF 0.013 0.072 -10000 0 -0.37 12 12
CYCS 0.008 0.038 0.15 2 -0.16 1 3
IKBKG 0.008 0.085 0.31 3 -0.48 1 4
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.008 0.074 -10000 0 -0.53 1 1
RELA 0.029 0.005 -10000 0 -10000 0 0
RIPK1 0.027 0.009 -10000 0 -10000 0 0
AIFM1 0.007 0.04 0.14 2 -0.16 1 3
TNF/TNF R/SODD 0.032 0.062 -10000 0 -0.22 17 17
TNFRSF1A 0.028 0.006 -10000 0 -10000 0 0
response to heat 0 0 0.002 3 -10000 0 3
CASP8 0.02 0.1 -10000 0 -0.55 11 11
NSMAF 0.03 0.096 0.26 7 -0.5 1 8
response to hydrogen peroxide 0 0.001 0.003 6 -10000 0 6
BCL2 0.028 0.022 -10000 0 -0.37 1 1
Paxillin-dependent events mediated by a4b1

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
CRKL 0.029 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.03 0.013 -10000 0 -10000 0 0
DOCK1 0.019 0.059 -10000 0 -0.37 8 8
ITGA4 0.022 0.055 -10000 0 -0.37 7 7
RAC1 0.029 0.004 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.034 0.054 -10000 0 -0.26 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.025 0.011 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.051 0.041 -10000 0 -0.22 7 7
alpha4/beta7 Integrin/Paxillin 0.036 0.046 -10000 0 -0.2 12 12
lamellipodium assembly 0.003 0.071 -10000 0 -0.5 4 4
PIK3CA 0.028 0.021 -10000 0 -0.37 1 1
PI3K 0.041 0.032 -10000 0 -0.37 2 2
ARF6 0.029 0.005 -10000 0 -10000 0 0
TLN1 0.029 0.005 -10000 0 -10000 0 0
PXN -0.018 0.003 -10000 0 -10000 0 0
PIK3R1 0.027 0.03 -10000 0 -0.37 2 2
ARF6/GTP 0.054 0.039 -10000 0 -0.18 6 6
cell adhesion 0.054 0.041 -10000 0 -0.19 7 7
CRKL/CBL 0.041 0.011 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.039 0.036 -10000 0 -0.2 7 7
ITGB1 0.029 0.005 -10000 0 -10000 0 0
ITGB7 0.024 0.047 -10000 0 -0.37 5 5
ARF6/GDP 0.03 0.013 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.043 0.07 -10000 0 -0.22 21 21
p130Cas/Crk/Dock1 0.044 0.043 -10000 0 -0.22 7 7
VCAM1 0.006 0.091 -10000 0 -0.37 20 20
alpha4/beta1 Integrin/Paxillin/Talin 0.056 0.041 -10000 0 -0.19 7 7
alpha4/beta1 Integrin/Paxillin/GIT1 0.057 0.042 -10000 0 -0.2 7 7
BCAR1 0.027 0.008 -10000 0 -10000 0 0
mol:GDP -0.055 0.041 0.2 7 -10000 0 7
CBL 0.028 0.006 -10000 0 -10000 0 0
PRKACA 0.029 0.004 -10000 0 -10000 0 0
GIT1 0.029 0.003 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.056 0.041 -10000 0 -0.19 7 7
Rac1/GTP 0.003 0.079 -10000 0 -0.57 4 4
Aurora A 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
Aurora A/GADD45A 0.029 0.05 -10000 0 -0.23 1 1
BIRC5 0.01 0.014 -10000 0 -10000 0 0
NFKBIA -0.004 0.031 0.24 1 -10000 0 1
CPEB1 0.022 0.008 -10000 0 -10000 0 0
AKT1 -0.004 0.032 0.24 2 -10000 0 2
NDEL1 0.025 0.011 -10000 0 -10000 0 0
Aurora A/BRCA1 0.026 0.043 -10000 0 -10000 0 0
NDEL1/TACC3 0.035 0.037 -10000 0 -10000 0 0
GADD45A 0.025 0.037 -10000 0 -0.37 3 3
GSK3B -0.001 0.027 -10000 0 -10000 0 0
PAK1/Aurora A 0.031 0.049 -10000 0 -10000 0 0
MDM2 0.029 0.004 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.01 0.074 0.21 45 -10000 0 45
TP53 0.012 0.066 -10000 0 -0.2 25 25
DLG7 0.001 0.026 0.12 13 -10000 0 13
AURKAIP1 0.027 0.009 -10000 0 -10000 0 0
ARHGEF7 0.028 0.007 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.037 0.039 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.025 0.043 -10000 0 -10000 0 0
AURKA 0.005 0.034 0.18 1 -10000 0 1
AURKB 0.009 0.036 0.1 16 -0.14 11 27
CDC25B 0.022 0.039 -10000 0 -10000 0 0
G2/M transition checkpoint -0.002 0.012 -10000 0 -10000 0 0
mRNA polyadenylation 0.021 0.04 -10000 0 -10000 0 0
Aurora A/CPEB 0.021 0.041 -10000 0 -10000 0 0
Aurora A/TACC1/TRAP/chTOG 0.061 0.043 -10000 0 -10000 0 0
BRCA1 0.029 0.005 -10000 0 -10000 0 0
centrosome duplication 0.03 0.049 -10000 0 -10000 0 0
regulation of centrosome cycle 0.034 0.036 -10000 0 -10000 0 0
spindle assembly 0.059 0.041 -10000 0 -10000 0 0
TDRD7 0.029 0.004 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.068 0.055 -10000 0 -10000 0 0
CENPA 0.015 0.024 -10000 0 -10000 0 0
Aurora A/PP2A 0.029 0.049 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.024 0.044 0.19 3 -10000 0 3
negative regulation of DNA binding 0.007 0.074 -10000 0 -0.2 34 34
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.041 0.011 -10000 0 -10000 0 0
RASA1 0.027 0.03 -10000 0 -0.37 2 2
Ajuba/Aurora A -0.002 0.012 -10000 0 -10000 0 0
mitotic prometaphase 0.008 0.023 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.005 0.034 0.18 1 -10000 0 1
TACC1 0.024 0.011 -10000 0 -10000 0 0
TACC3 0.025 0.011 -10000 0 -10000 0 0
Aurora A/Antizyme1 0.047 0.042 -10000 0 -10000 0 0
Aurora A/RasGAP 0.03 0.052 -10000 0 -0.23 1 1
OAZ1 0.029 0.005 -10000 0 -10000 0 0
RAN 0.029 0.004 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.001 0.026 -10000 0 -10000 0 0
GIT1 0.029 0.003 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.055 0.018 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.01 0.074 0.21 45 -10000 0 45
PPP2R5D 0.027 0.009 -10000 0 -10000 0 0
Aurora A/TPX2 0.037 0.075 0.23 31 -10000 0 31
PAK1 0.029 0.005 -10000 0 -10000 0 0
CKAP5 0.03 0.002 -10000 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.024 0.047 -10000 0 -0.37 5 5
positive regulation of NF-kappaB transcription factor activity 0.028 0.042 -10000 0 -0.26 6 6
MAP2K4 0.009 0.045 -10000 0 -0.26 2 2
IKBKB 0.026 0.01 -10000 0 -10000 0 0
TNFRSF10B 0.023 0.012 -10000 0 -10000 0 0
TNFRSF10A 0.02 0.038 -10000 0 -0.37 3 3
SMPD1 0.007 0.02 -10000 0 -0.16 5 5
IKBKG 0.029 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.022 0.024 -10000 0 -0.37 1 1
TRAIL/TRAILR2 0.029 0.039 -10000 0 -0.26 5 5
TRAIL/TRAILR3 0.029 0.04 -10000 0 -0.26 5 5
TRAIL/TRAILR1 0.027 0.047 -10000 0 -0.26 8 8
TRAIL/TRAILR4 0.028 0.042 -10000 0 -0.26 6 6
TRAIL/TRAILR1/DAP3/GTP 0.029 0.043 -10000 0 -0.2 7 7
IKK complex 0.004 0.068 -10000 0 -0.21 1 1
RIPK1 0.027 0.009 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.017 0.009 -10000 0 -10000 0 0
MAPK3 -0.021 0.029 -10000 0 -0.26 5 5
MAP3K1 0.01 0.044 -10000 0 -0.23 2 2
TRAILR4 (trimer) 0.022 0.024 -10000 0 -0.37 1 1
TRADD 0.027 0.008 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.02 0.038 -10000 0 -0.37 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.003 0.051 -10000 0 -0.2 8 8
CFLAR 0.03 0.003 -10000 0 -10000 0 0
MAPK1 -0.021 0.029 -10000 0 -0.26 5 5
TRAIL/TRAILR1/FADD/TRADD/RIP 0.049 0.058 -10000 0 -0.2 8 8
mol:ceramide 0.007 0.02 -10000 0 -0.16 5 5
FADD 0.028 0.006 -10000 0 -10000 0 0
MAPK8 -0.012 0.066 -10000 0 -0.26 7 7
TRAF2 0.029 0.005 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.023 0.013 -10000 0 -10000 0 0
CHUK 0.029 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.038 0.048 -10000 0 -0.23 8 8
DAP3 0.023 0.013 -10000 0 -10000 0 0
CASP10 -0.006 0.05 0.25 2 -0.25 5 7
JNK cascade 0.028 0.042 -10000 0 -0.26 6 6
TRAIL (trimer) 0.024 0.047 -10000 0 -0.37 5 5
TNFRSF10C 0.023 0.013 -10000 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP/FADD 0.035 0.048 -10000 0 -0.2 7 7
TRAIL/TRAILR2/FADD 0.04 0.041 -10000 0 -0.23 5 5
cell death 0.007 0.02 -10000 0 -0.16 5 5
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.001 0.048 -10000 0 -0.2 5 5
TRAILR2 (trimer) 0.023 0.012 -10000 0 -10000 0 0
CASP8 0.021 0.049 -10000 0 -0.6 2 2
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.052 0.054 -10000 0 -0.2 5 5
Atypical NF-kappaB pathway

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
BCL3/RelA 0.042 0.009 -10000 0 -10000 0 0
FBXW11 0.029 0.005 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.015 0.042 -10000 0 -0.22 11 11
NF kappa B1 p50/RelA/I kappa B alpha 0.017 0.053 -10000 0 -0.25 4 4
NFKBIA 0.013 0.049 -10000 0 -0.22 8 8
MAPK14 0.027 0.009 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.022 0.012 -10000 0 -10000 0 0
ARRB2 0.01 0.005 -10000 0 -10000 0 0
REL 0.016 0.071 -10000 0 -0.37 12 12
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.022 0.012 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.022 0.012 -10000 0 -10000 0 0
PIK3CA 0.028 0.021 -10000 0 -0.37 1 1
NF kappa B1 p50 dimer -0.011 0.017 -10000 0 -10000 0 0
PIK3R1 0.027 0.03 -10000 0 -0.37 2 2
NFKB1 -0.015 0.008 -10000 0 -10000 0 0
RELA 0.029 0.005 -10000 0 -10000 0 0
positive regulation of anti-apoptosis -0.001 0.053 -10000 0 -0.23 12 12
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.014 0.058 -10000 0 -0.25 6 6
SRC 0.029 0.005 -10000 0 -10000 0 0
PI3K 0.041 0.032 -10000 0 -0.37 2 2
NF kappa B1 p50/RelA 0.002 0.05 -10000 0 -0.24 11 11
IKBKB 0.026 0.01 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.029 0.005 -10000 0 -10000 0 0
SYK 0.026 0.036 -10000 0 -0.37 3 3
I kappa B alpha/PIK3R1 0.02 0.062 0.2 1 -0.24 7 8
cell death 0.013 0.056 -10000 0 -0.24 6 6
NF kappa B1 p105/c-Rel 0.015 0.042 -10000 0 -0.22 11 11
LCK 0.017 0.065 -10000 0 -0.37 10 10
BCL3 0.029 0.004 -10000 0 -10000 0 0
Insulin 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
CBL/APS/CAP 0.054 0.027 -10000 0 -0.19 1 1
TC10/GTP 0.044 0.03 -10000 0 -0.19 1 1
Insulin Receptor/Insulin/IRS1/Shp2 0.069 0.019 -10000 0 -10000 0 0
HRAS 0.029 0.004 -10000 0 -10000 0 0
APS homodimer 0.029 0.006 -10000 0 -10000 0 0
GRB14 0.023 0.051 -10000 0 -0.37 6 6
FOXO3 -0.044 0.2 -10000 0 -0.62 38 38
AKT1 -0.033 0.042 -10000 0 -0.33 1 1
INSR 0.031 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.058 0.028 0.21 2 -10000 0 2
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.029 0.004 -10000 0 -10000 0 0
SORBS1 0.027 0.03 -10000 0 -0.37 2 2
CRK 0.025 0.011 -10000 0 -10000 0 0
PTPN1 -0.014 0.022 -10000 0 -10000 0 0
CAV1 -0.018 0.022 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II/C3G 0.07 0.041 -10000 0 -0.2 1 1
Insulin Receptor/Insulin/IRS1/NCK2 0.069 0.024 -10000 0 -0.22 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.055 0.03 -10000 0 -0.27 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.018 0.041 -10000 0 -0.31 4 4
RPS6KB1 -0.036 0.037 -10000 0 -0.31 1 1
PARD6A 0.027 0.008 -10000 0 -10000 0 0
CBL 0.028 0.006 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.016 0.034 -10000 0 -0.58 1 1
PIK3R1 0.027 0.03 -10000 0 -0.37 2 2
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.036 0.043 -10000 0 -0.31 1 1
HRAS/GTP -0.027 0.02 -10000 0 -10000 0 0
Insulin Receptor 0.031 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.06 0.04 -10000 0 -10000 0 0
PRKCI 0.028 0.051 -10000 0 -0.3 8 8
Insulin Receptor/Insulin/GRB14/PDK1 0.026 0.041 -10000 0 -0.21 8 8
SHC1 0.022 0.013 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.049 0.038 -10000 0 -0.51 1 1
PI3K 0.067 0.033 -10000 0 -0.28 2 2
NCK2 0.028 0.021 -10000 0 -0.37 1 1
RHOQ 0.03 0.003 -10000 0 -10000 0 0
mol:H2O2 -0.003 0.002 -10000 0 -10000 0 0
HRAS/GDP 0.022 0.003 -10000 0 -10000 0 0
AKT2 -0.033 0.045 -10000 0 -0.33 1 1
PRKCZ -0.018 0.14 -10000 0 -0.36 48 48
SH2B2 0.029 0.006 -10000 0 -10000 0 0
SHC/SHIP -0.017 0.022 -10000 0 -10000 0 0
F2RL2 -0.011 0.12 -10000 0 -0.37 36 36
TRIP10 0.029 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.037 0.024 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.039 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.06 0.04 -10000 0 -10000 0 0
RAPGEF1 0.029 0.004 -10000 0 -10000 0 0
RASA1 0.027 0.03 -10000 0 -0.37 2 2
NCK1 0.03 0.002 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.062 0.035 -10000 0 -0.21 1 1
TC10/GDP 0.022 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.052 0.034 -10000 0 -10000 0 0
INPP5D -0.019 0.023 -10000 0 -10000 0 0
SOS1 0.03 0.002 -10000 0 -10000 0 0
SGK1 -0.059 0.22 -10000 0 -0.71 38 38
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.029 0.003 -10000 0 -10000 0 0
IRS1 0.03 0.003 -10000 0 -10000 0 0
p62DOK/RasGAP 0.049 0.038 -10000 0 -0.51 1 1
INS 0.019 0.008 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.019 0.023 -10000 0 -10000 0 0
GRB2 0.028 0.006 -10000 0 -10000 0 0
EIF4EBP1 -0.032 0.039 -10000 0 -0.31 1 1
PTPRA 0.031 0.006 -10000 0 -10000 0 0
PIK3CA 0.028 0.021 -10000 0 -0.37 1 1
TC10/GTP/CIP4 0.039 0.006 -10000 0 -10000 0 0
PDPK1 0.028 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.016 0.019 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.05 0.013 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS3 0.037 0.011 -10000 0 -10000 0 0
Par3/Par6 0.041 0.08 -10000 0 -0.19 36 36
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.042 0.074 -9999 0 -0.26 13 13
Ran/GTP/Exportin 1/HDAC1 -0.019 0.005 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.028 0.073 -9999 0 -0.26 14 14
SUMO1 0.03 0.003 -9999 0 -10000 0 0
ZFPM1 0.025 0.031 -9999 0 -0.37 2 2
NPC/RanGAP1/SUMO1/Ubc9 0.011 0.003 -9999 0 -10000 0 0
FKBP3 0.029 0.004 -9999 0 -10000 0 0
Histones 0.057 0.052 -9999 0 -10000 0 0
YY1/LSF 0.016 0.055 -9999 0 -0.22 11 11
SMG5 0.023 0.013 -9999 0 -10000 0 0
RAN 0.029 0.004 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 0.011 0.044 -9999 0 -0.2 12 12
I kappa B alpha/HDAC1 0.032 0.042 -9999 0 -10000 0 0
SAP18 0.028 0.007 -9999 0 -10000 0 0
RELA 0.013 0.057 -9999 0 -0.19 12 12
HDAC1/Smad7 0.053 0.024 -9999 0 -0.23 1 1
RANGAP1 0.029 0.005 -9999 0 -10000 0 0
HDAC3/TR2 0.034 0.044 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.017 0.063 -9999 0 -0.25 8 8
NF kappa B1 p50/RelA 0.026 0.069 -9999 0 -0.25 9 9
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.027 0.03 -9999 0 -0.37 2 2
GATA1 0.023 0.007 -9999 0 -10000 0 0
Mad/Max 0.042 0.011 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.009 0.086 -9999 0 -0.27 18 18
RBBP7 0.029 0.004 -9999 0 -10000 0 0
NPC 0.017 0.002 -9999 0 -10000 0 0
RBBP4 0.028 0.007 -9999 0 -10000 0 0
MAX 0.028 0.007 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.029 0.005 -9999 0 -10000 0 0
NFKBIA 0.012 0.032 -9999 0 -10000 0 0
KAT2B 0.026 0.036 -9999 0 -0.37 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.008 0.044 -9999 0 -0.36 1 1
SIN3 complex 0.066 0.027 -9999 0 -10000 0 0
SMURF1 0.029 0.006 -9999 0 -10000 0 0
CHD3 0.024 0.012 -9999 0 -10000 0 0
SAP30 0.027 0.008 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.026 0.01 -9999 0 -10000 0 0
YY1/HDAC3 0.009 0.048 -9999 0 -0.21 1 1
YY1/HDAC2 0.018 0.048 -9999 0 -0.2 9 9
YY1/HDAC1 0.019 0.048 -9999 0 -0.21 9 9
NuRD/MBD2 Complex (MeCP1) 0.018 0.059 -9999 0 -0.25 5 5
PPARG 0.016 0.069 -9999 0 -0.3 11 11
HDAC8/hEST1B 0.045 0.027 -9999 0 -10000 0 0
UBE2I 0.028 0.007 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.029 0.005 -9999 0 -10000 0 0
TNFRSF1A 0.028 0.006 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.034 0.042 -9999 0 -10000 0 0
MBD3L2 0.018 0.003 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.052 0.024 -9999 0 -0.23 1 1
CREBBP 0.028 0.006 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.015 0.077 -9999 0 -0.26 13 13
HDAC1 0.028 0.007 -9999 0 -10000 0 0
HDAC3 0.013 0.032 -9999 0 -10000 0 0
HDAC2 0.028 0.008 -9999 0 -10000 0 0
YY1 0.012 0.022 -9999 0 -0.23 3 3
HDAC8 0.03 0.002 -9999 0 -10000 0 0
SMAD7 0.026 0.03 -9999 0 -0.37 2 2
NCOR2 0.029 0.005 -9999 0 -10000 0 0
MXD1 0.03 0.003 -9999 0 -10000 0 0
STAT3 0.017 0.005 -9999 0 -10000 0 0
NFKB1 0.027 0.009 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.03 0.003 -9999 0 -10000 0 0
YY1/LSF/HDAC1 0.031 0.056 -9999 0 -0.2 11 11
YY1/SAP30/HDAC1 0.032 0.05 -9999 0 -0.18 9 9
EP300 0.029 0.004 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.017 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.012 0.032 -9999 0 -10000 0 0
histone deacetylation 0.018 0.059 -9999 0 -0.25 5 5
STAT3 (dimer non-phopshorylated)/HDAC3 0.022 0.045 -9999 0 -0.22 1 1
nuclear export -0.044 0.026 -9999 0 -10000 0 0
PRKACA 0.029 0.004 -9999 0 -10000 0 0
GATAD2B 0.022 0.013 -9999 0 -10000 0 0
GATAD2A 0.029 0.004 -9999 0 -10000 0 0
GATA2/HDAC3 0.033 0.047 -9999 0 -10000 0 0
GATA1/HDAC1 0.037 0.011 -9999 0 -10000 0 0
GATA1/HDAC3 0.03 0.043 -9999 0 -10000 0 0
CHD4 0.029 0.006 -9999 0 -10000 0 0
TNF-alpha/TNFR1A 0.028 0.056 -9999 0 -0.26 12 12
SIN3/HDAC complex/Mad/Max -0.001 0.073 -9999 0 -0.27 17 17
NuRD Complex 0.015 0.078 -9999 0 -0.27 10 10
positive regulation of chromatin silencing 0.055 0.05 -9999 0 -10000 0 0
SIN3B 0.029 0.004 -9999 0 -10000 0 0
MTA2 0.029 0.004 -9999 0 -10000 0 0
SIN3A 0.029 0.004 -9999 0 -10000 0 0
XPO1 0.03 0.003 -9999 0 -10000 0 0
SUMO1/HDAC1 0.037 0.035 -9999 0 -0.21 3 3
HDAC complex 0.067 0.026 -9999 0 -10000 0 0
GATA1/Fog1 0.033 0.026 -9999 0 -0.26 2 2
FKBP25/HDAC1/HDAC2 0.053 0.02 -9999 0 -10000 0 0
TNF 0.013 0.071 -9999 0 -0.37 12 12
negative regulation of cell growth -0.001 0.073 -9999 0 -0.27 17 17
NuRD/MBD2/PRMT5 Complex 0.018 0.059 -9999 0 -0.25 5 5
Ran/GTP/Exportin 1 0.036 0.039 -9999 0 -0.21 3 3
NF kappa B/RelA/I kappa B alpha 0.002 0.065 -9999 0 -0.26 17 17
SIN3/HDAC complex/NCoR1 -0.012 0.086 -9999 0 -0.28 25 25
TFCP2 0.027 0.03 -9999 0 -0.37 2 2
NR2C1 0.029 0.003 -9999 0 -10000 0 0
MBD3 0.029 0.004 -9999 0 -10000 0 0
MBD2 0.029 0.006 -9999 0 -10000 0 0
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 0.017 0.052 -10000 0 -0.37 6 6
CLTC 0.008 0.061 -10000 0 -0.37 8 8
calcium ion-dependent exocytosis 0.002 0.039 -10000 0 -0.17 7 7
Dynamin 2/GTP 0.025 0.011 0.15 2 -10000 0 2
EXOC4 0.028 0.006 -10000 0 -10000 0 0
CD59 0.003 0.05 -10000 0 -0.33 7 7
CPE -0.013 0.012 -10000 0 -0.22 1 1
CTNNB1 0.03 0.003 -10000 0 -10000 0 0
membrane fusion 0.003 0.031 -10000 0 -10000 0 0
CTNND1 -0.016 0.036 0.17 13 -10000 0 13
DNM2 0.029 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.003 0.038 0.21 1 -0.22 4 5
TSHR -0.014 0.004 -10000 0 -10000 0 0
INS 0.007 0.045 -10000 0 -0.45 3 3
BIN1 0.028 0.021 -10000 0 -0.37 1 1
mol:Choline 0.003 0.031 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP -0.014 0.004 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.029 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.025 0.011 0.15 2 -10000 0 2
JUP 0.003 0.049 -10000 0 -0.33 7 7
ASAP2/amphiphysin II 0.054 0.019 -10000 0 -0.2 1 1
ARF6/GTP 0.021 0.004 -10000 0 -10000 0 0
CDH1 -0.006 0.062 -10000 0 -0.26 13 13
clathrin-independent pinocytosis 0.021 0.004 -10000 0 -10000 0 0
MAPK8IP3 0.028 0.007 -10000 0 -10000 0 0
positive regulation of endocytosis 0.021 0.004 -10000 0 -10000 0 0
EXOC2 0.027 0.009 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.015 0.04 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.029 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.021 0.074 0.31 8 -10000 0 8
positive regulation of phagocytosis -0.013 0.005 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.037 0.011 -10000 0 -10000 0 0
ACAP1 0.006 0.041 -10000 0 -0.21 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.001 0.053 -10000 0 -0.31 8 8
clathrin heavy chain/ACAP1 0.005 0.054 0.25 2 -0.31 7 9
JIP4/KLC1 0.051 0.018 -10000 0 -10000 0 0
EXOC1 0.029 0.006 -10000 0 -10000 0 0
exocyst 0.015 0.04 -10000 0 -10000 0 0
RALA/GTP 0.022 0.003 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.038 0.009 -10000 0 -10000 0 0
receptor recycling 0.021 0.004 -10000 0 -10000 0 0
CTNNA1 -0.016 0.035 0.17 12 -10000 0 12
NME1 -0.014 0.004 -10000 0 -10000 0 0
clathrin coat assembly 0.011 0.063 -10000 0 -0.36 8 8
IL2RA 0.007 0.054 -10000 0 -0.32 6 6
VAMP3 -0.013 0.005 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.013 0.061 -10000 0 -0.29 7 7
EXOC6 0.029 0.006 -10000 0 -10000 0 0
PLD1 -0.004 0.058 -10000 0 -0.24 20 20
PLD2 0.009 0.006 -10000 0 -10000 0 0
EXOC5 0.029 0.006 -10000 0 -10000 0 0
PIP5K1C 0.003 0.037 0.21 1 -0.23 4 5
SDC1 0.002 0.053 -10000 0 -0.33 7 7
ARF6/GDP 0.025 0.012 0.16 2 -10000 0 2
EXOC7 0.029 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.023 0.077 -10000 0 -0.32 8 8
mol:Phosphatidic acid 0.003 0.031 -10000 0 -10000 0 0
endocytosis -0.052 0.018 0.2 1 -10000 0 1
SCAMP2 0.029 0.005 -10000 0 -10000 0 0
ADRB2 -0.01 0.085 0.24 1 -0.42 7 8
EXOC3 0.028 0.007 -10000 0 -10000 0 0
ASAP2 0.029 0.003 -10000 0 -10000 0 0
Dynamin 2/GDP 0.031 0.017 0.17 3 -10000 0 3
KLC1 0.028 0.008 -10000 0 -10000 0 0
AVPR2 0.018 0.077 0.37 1 -0.35 8 9
RALA 0.029 0.004 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.013 0.074 -10000 0 -0.32 6 6
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.015 0.071 -9999 0 -0.37 12 12
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.028 0.006 -9999 0 -10000 0 0
TCEB1 0.023 0.012 -9999 0 -10000 0 0
HIF1A/p53 0.026 0.056 -9999 0 -0.27 7 7
HIF1A 0.011 0.052 -9999 0 -0.29 7 7
COPS5 0.024 0.012 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.061 0.042 -9999 0 -10000 0 0
FIH (dimer) 0.029 0.005 -9999 0 -10000 0 0
CDKN2A 0.008 0.013 -9999 0 -10000 0 0
ARNT/IPAS 0.023 0.052 -9999 0 -0.26 10 10
HIF1AN 0.029 0.005 -9999 0 -10000 0 0
GNB2L1 0.029 0.006 -9999 0 -10000 0 0
HIF1A/ARNT 0.016 0.052 -9999 0 -0.28 7 7
CUL2 0.029 0.006 -9999 0 -10000 0 0
OS9 0.029 0.004 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.043 0.028 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.029 0.059 -9999 0 -0.27 8 8
PHD1-3/OS9 0.06 0.055 -9999 0 -0.2 6 6
HIF1A/RACK1/Elongin B/Elongin C 0.037 0.065 -9999 0 -0.27 7 7
VHL 0.03 0.003 -9999 0 -10000 0 0
HSP90AA1 0.028 0.007 -9999 0 -10000 0 0
HIF1A/JAB1 0.021 0.06 -9999 0 -0.27 8 8
EGLN3 0.016 0.065 -9999 0 -0.37 10 10
EGLN2 0.029 0.005 -9999 0 -10000 0 0
EGLN1 0.024 0.012 -9999 0 -10000 0 0
TP53 0.025 0.011 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.034 0.065 -9999 0 -0.64 3 3
ARNT 0.023 0.013 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.029 0.004 -9999 0 -10000 0 0
HIF1A/p19ARF 0.007 0.034 -9999 0 -0.26 1 1
Arf1 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
coatomer protein complex 0.003 0.021 0.16 4 -10000 0 4
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.023 0.057 0.14 46 -0.19 6 52
AP2 0.043 0.008 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.035 0.016 -10000 0 -10000 0 0
CLTB 0.029 0.006 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.012 0.009 -10000 0 -10000 0 0
CD4 -0.003 0.11 -10000 0 -0.37 29 29
CLTA 0.029 0.005 -10000 0 -10000 0 0
mol:GTP -0.002 0.003 -10000 0 -10000 0 0
ARFGAP1 -0.009 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.004 0.012 -10000 0 -10000 0 0
ARF1/GTP 0.027 0.021 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.004 0.019 0.16 3 -10000 0 3
mol:Choline 0.004 0.012 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.025 0.014 -10000 0 -10000 0 0
DDEF1 0.003 0.012 -10000 0 -10000 0 0
ARF1/GDP 0 0.02 -10000 0 -0.11 4 4
AP2M1 0.029 0.003 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.007 0.013 -10000 0 -10000 0 0
Rac/GTP 0.025 0.009 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.032 0.02 -10000 0 -10000 0 0
ARFIP2 0.01 0.029 -10000 0 -10000 0 0
COPA 0.023 0.013 -10000 0 -10000 0 0
RAC1 0.029 0.004 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.01 0.031 0.15 1 -10000 0 1
ARF1/GTP/ARHGAP10 0.017 0.01 -10000 0 -10000 0 0
GGA3 0.028 0.006 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.02 0.015 -10000 0 -10000 0 0
AP2A1 0.029 0.005 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.009 0.01 -10000 0 -10000 0 0
ARF1/GDP/Membrin 0.02 0.02 -10000 0 -10000 0 0
Arfaptin 2/Rac/GDP 0.032 0.018 -10000 0 -10000 0 0
CYTH2 0.035 0.012 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.032 0.019 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.022 0.003 -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 0.048 -10000 0 -0.17 17 17
PLD2 0.004 0.012 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE -0.009 0.002 -10000 0 -10000 0 0
PIP5K1A 0.004 0.012 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.008 0.028 -10000 0 -0.13 4 4
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.004 0.012 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 -0.009 0.002 -10000 0 -10000 0 0
GOSR2 0.009 0.009 -10000 0 -10000 0 0
USO1 0.003 0.045 -10000 0 -0.32 7 7
GBF1 0.009 0.009 -10000 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0.032 0.019 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.034 0.078 -10000 0 -0.23 29 29
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.029 0.006 -9999 0 -10000 0 0
SMAD2 -0.005 0.037 -9999 0 -0.26 1 1
SMAD3 0.006 0.029 -9999 0 -10000 0 0
SMAD3/SMAD4 0.033 0.04 -9999 0 -0.36 3 3
SMAD4/Ubc9/PIASy 0.054 0.019 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.046 0.052 -9999 0 -0.23 1 1
PPM1A 0.028 0.006 -9999 0 -10000 0 0
CALM1 0.028 0.007 -9999 0 -10000 0 0
SMAD2/SMAD4 0.012 0.038 -9999 0 -0.24 1 1
MAP3K1 0.03 0.002 -9999 0 -10000 0 0
TRAP-1/SMAD4 0.026 0.069 -9999 0 -0.26 19 19
MAPK3 0.029 0.005 -9999 0 -10000 0 0
MAPK1 0.029 0.004 -9999 0 -10000 0 0
NUP214 0.029 0.004 -9999 0 -10000 0 0
CTDSP1 0.029 0.003 -9999 0 -10000 0 0
CTDSP2 0.029 0.004 -9999 0 -10000 0 0
CTDSPL 0.03 0.003 -9999 0 -10000 0 0
KPNB1 0.029 0.003 -9999 0 -10000 0 0
TGFBRAP1 0.009 0.089 -9999 0 -0.37 19 19
UBE2I 0.028 0.007 -9999 0 -10000 0 0
NUP153 0.027 0.009 -9999 0 -10000 0 0
KPNA2 0.028 0.006 -9999 0 -10000 0 0
PIAS4 0.029 0.005 -9999 0 -10000 0 0
Arf6 signaling events

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
CENTA1/KIF3B 0.01 0.066 -10000 0 -0.22 1 1
ARNO/beta Arrestin1-2 -0.036 0.22 -10000 0 -0.8 1 1
EGFR 0.028 0.008 -10000 0 -10000 0 0
EPHA2 -0.003 0.1 -10000 0 -0.37 1 1
USP6 0.019 0.014 -10000 0 -10000 0 0
IQSEC1 0.03 0 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.025 0.019 -10000 0 -10000 0 0
ARRB2 0.006 0.004 -10000 0 -10000 0 0
mol:GTP -0.023 0.067 -10000 0 -0.17 2 2
ARRB1 0.03 0 -10000 0 -10000 0 0
FBXO8 0.03 0 -10000 0 -10000 0 0
TSHR 0.024 0.011 -10000 0 -10000 0 0
EGF 0.016 0.011 -10000 0 -10000 0 0
somatostatin receptor activity 0 0 0.001 1 -0.001 1 2
ARAP2 0.028 0.008 -10000 0 -10000 0 0
mol:GDP -0.056 0.12 0.19 1 -0.23 3 4
mol:PI-3-4-5-P3 0 0 0.001 1 -0.001 1 2
ITGA2B 0.023 0.009 -10000 0 -10000 0 0
ARF6 0.03 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.03 0.079 -10000 0 -0.21 1 1
ADAP1 -0.001 0.1 -10000 0 -0.37 1 1
KIF13B 0.023 0.012 -10000 0 -10000 0 0
HGF/MET -0.14 0.15 -10000 0 -0.26 8 8
PXN 0.03 0 -10000 0 -10000 0 0
ARF6/GTP -0.046 0.12 0.25 1 -0.2 3 4
EGFR/EGFR/EGF/EGF/ARFGEP100 0.036 0.027 -10000 0 -10000 0 0
ADRB2 0.03 0 -10000 0 -10000 0 0
receptor agonist activity 0 0 -10000 0 0 2 2
actin filament binding 0 0 0.001 1 0 2 3
SRC 0.03 0 -10000 0 -10000 0 0
ITGB3 0.028 0.008 -10000 0 -10000 0 0
GNAQ 0.03 0 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.002 1 -0.001 1 2
ARF6/GDP -0.12 0.24 0.22 1 -0.39 5 6
ARF6/GDP/GULP/ACAP1 -0.051 0.13 -10000 0 -0.21 1 1
alphaIIb/beta3 Integrin/paxillin/GIT1 0.069 0.019 -10000 0 -10000 0 0
ACAP1 0.019 0.014 -10000 0 -10000 0 0
ACAP2 0.03 0 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 -0.001 0.029 -10000 0 -10000 0 0
EFNA1 0.026 0.01 -10000 0 -10000 0 0
HGF -0.2 0.19 -10000 0 -0.37 8 8
CYTH3 -0.009 0.002 -10000 0 -10000 0 0
CYTH2 -0.05 0.26 -10000 0 -0.98 1 1
NCK1 0.03 0 -10000 0 -10000 0 0
fibronectin binding 0 0 0.001 1 0 3 4
endosomal lumen acidification 0 0 0.001 1 0 3 4
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.03 0.14 -10000 0 -0.37 2 2
GNAQ/ARNO -0.03 0.24 -10000 0 -0.91 1 1
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
PIP3-E 0 0 0 1 -10000 0 1
MET 0.025 0.01 -10000 0 -10000 0 0
GNA14 0.001 0.1 -10000 0 -0.37 1 1
GNA15 0.028 0.008 -10000 0 -10000 0 0
GIT1 0.03 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 1 -0.001 1 2
GNA11 -0.001 0.1 -10000 0 -0.37 1 1
LHCGR 0.015 0.006 -10000 0 -10000 0 0
AGTR1 0.001 0.1 -10000 0 -0.37 1 1
desensitization of G-protein coupled receptor protein signaling pathway -0.001 0.029 -10000 0 -10000 0 0
IPCEF1/ARNO -0.029 0.22 -10000 0 -0.83 1 1
alphaIIb/beta3 Integrin 0.038 0.011 -10000 0 -10000 0 0
VEGFR1 specific signals

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR1 homodimer/VEGFB homodimer 0.022 0.041 -10000 0 -0.22 9 9
VEGFR1 homodimer/NRP1 -0.01 0.004 -10000 0 -10000 0 0
mol:DAG -0.016 0.026 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0.023 0.012 -10000 0 -10000 0 0
CaM/Ca2+ -0.019 0.027 -10000 0 -10000 0 0
HIF1A 0.033 0.008 -10000 0 -10000 0 0
GAB1 0.028 0.008 -10000 0 -10000 0 0
AKT1 -0.016 0.035 -10000 0 -0.38 1 1
PLCG1 -0.016 0.026 -10000 0 -10000 0 0
NOS3 0.001 0.061 -10000 0 -0.46 4 4
CBL 0.028 0.006 -10000 0 -10000 0 0
mol:NO 0.001 0.069 0.54 1 -0.49 3 4
FLT1 -0.013 0.005 -10000 0 -10000 0 0
PGF 0.027 0.008 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2/VEGFR121 0.037 0.03 -10000 0 -0.21 1 1
CALM1 0.028 0.007 -10000 0 -10000 0 0
PIK3CA 0.028 0.021 -10000 0 -0.37 1 1
eNOS/Hsp90 0.015 0.062 -10000 0 -0.46 3 3
endothelial cell proliferation -0.013 0.062 0.32 2 -0.27 2 4
mol:Ca2+ -0.016 0.026 -10000 0 -10000 0 0
MAPK3 -0.022 0.029 0.34 1 -10000 0 1
MAPK1 -0.022 0.029 0.34 1 -10000 0 1
PIK3R1 0.027 0.03 -10000 0 -0.37 2 2
PLGF homodimer 0.027 0.008 -10000 0 -10000 0 0
PRKACA 0.029 0.004 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.029 0.006 -10000 0 -10000 0 0
VEGFA homodimer 0.026 0.01 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.025 0.014 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.019 0.047 0.32 2 -10000 0 2
PI3K 0.057 0.038 -10000 0 -0.28 2 2
PRKCA -0.019 0.03 0.35 1 -10000 0 1
PRKCB -0.031 0.055 0.35 1 -10000 0 1
VEGFR1 homodimer/PLGF homodimer 0.028 0.011 -10000 0 -10000 0 0
VEGFA 0.026 0.01 -10000 0 -10000 0 0
VEGFB 0.019 0.062 -10000 0 -0.37 9 9
mol:IP3 -0.016 0.026 -10000 0 -10000 0 0
RASA1 -0.024 0.039 -10000 0 -10000 0 0
NRP2 0.026 0.036 -10000 0 -0.37 3 3
VEGFR1 homodimer -0.013 0.005 -10000 0 -10000 0 0
VEGFB homodimer 0.019 0.062 -10000 0 -0.37 9 9
NCK1 0.03 0.002 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.01 0.072 0.52 1 -0.43 4 5
PTPN11 0.029 0.003 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.055 0.037 -10000 0 -0.28 2 2
mol:L-citrulline 0.001 0.069 0.54 1 -0.49 3 4
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.051 0.03 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.039 0.021 -10000 0 -10000 0 0
CD2AP 0.027 0.008 -10000 0 -10000 0 0
PI3K/GAB1 0.063 0.044 -10000 0 -0.36 1 1
PDPK1 -0.021 0.046 0.51 1 -0.35 1 2
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.038 0.021 -10000 0 -10000 0 0
mol:NADP 0.001 0.069 0.54 1 -0.49 3 4
HSP90AA1 0.028 0.007 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.049 0.029 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.027 0.024 -10000 0 -0.21 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 0.037 0.029 -10000 0 -0.19 2 2
MAPK9 0.006 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.005 0.022 0.2 4 -10000 0 4
GNB1/GNG2 0.034 0.023 -10000 0 -0.22 2 2
GNB1 0.027 0.009 -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 0.006 0.002 -10000 0 -10000 0 0
Gs family/GTP 0.016 0.007 -10000 0 -10000 0 0
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 0.001 -10000 0 -10000 0 0
GNAL 0.024 0.011 -10000 0 -10000 0 0
GNG2 0.027 0.03 -10000 0 -0.37 2 2
CRH 0.016 0.009 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 -0.007 0.059 -10000 0 -0.27 18 18
MAPK11 0.006 0.002 -10000 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 0.039 0.013 -10000 0 -10000 0 0
ATM 0.029 0.006 -10000 0 -10000 0 0
UBE2D3 0.027 0.009 -10000 0 -10000 0 0
PRKDC 0.025 0.011 -10000 0 -10000 0 0
ATR 0.03 0.003 -10000 0 -10000 0 0
UBE2L3 0.029 0.005 -10000 0 -10000 0 0
FANCD2 0.052 0.06 -10000 0 -10000 0 0
protein ubiquitination 0.089 0.049 -10000 0 -10000 0 0
XRCC5 0.029 0.003 -10000 0 -10000 0 0
XRCC6 0.029 0.005 -10000 0 -10000 0 0
M/R/N Complex 0.042 0.028 -10000 0 -10000 0 0
MRE11A 0.029 0.006 -10000 0 -10000 0 0
DNA-PK 0.049 0.024 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.027 0.081 -10000 0 -0.49 5 5
FANCF 0.03 0.003 -10000 0 -10000 0 0
BRCA1 0.029 0.005 -10000 0 -10000 0 0
CCNE1 0.019 0.014 -10000 0 -10000 0 0
CDK2/Cyclin E1 0.028 0.021 -10000 0 -10000 0 0
FANCG 0.029 0.005 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.04 0.013 -10000 0 -10000 0 0
FANCE 0.027 0.009 -10000 0 -10000 0 0
FANCC 0.028 0.021 -10000 0 -0.37 1 1
NBN 0.023 0.013 -10000 0 -10000 0 0
FANCA 0.027 0.009 -10000 0 -10000 0 0
DNA repair 0.063 0.13 0.34 28 -0.36 4 32
BRCA1/BARD1/ubiquitin 0.04 0.013 -10000 0 -10000 0 0
BARD1/DNA-PK 0.065 0.037 -10000 0 -10000 0 0
FANCL 0.03 0.003 -10000 0 -10000 0 0
mRNA polyadenylation -0.039 0.013 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.029 0.052 -10000 0 -0.21 8 8
BRCA1/BACH1/BARD1/TopBP1 0.054 0.018 -10000 0 -10000 0 0
BRCA1/BARD1/P53 0.065 0.035 -10000 0 -10000 0 0
BARD1/CSTF1/BRCA1 0.053 0.019 -10000 0 -10000 0 0
BRCA1/BACH1 0.029 0.005 -10000 0 -10000 0 0
BARD1 0.027 0.008 -10000 0 -10000 0 0
PCNA 0.029 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.05 0.022 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.054 0.018 -10000 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.089 0.048 -10000 0 -10000 0 0
BARD1/DNA-PK/P53 0.062 0.047 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin 0.04 0.013 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP 0.046 0.024 -10000 0 -10000 0 0
FA complex 0.02 0.027 -10000 0 -10000 0 0
BARD1/EWS 0.04 0.012 -10000 0 -10000 0 0
RBBP8 -0.018 0.004 -10000 0 -10000 0 0
TP53 0.025 0.011 -10000 0 -10000 0 0
TOPBP1 0.03 0.003 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.063 0.034 -10000 0 -10000 0 0
BRCA1/BARD1 0.097 0.053 -10000 0 -10000 0 0
CSTF1 0.029 0.005 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.02 0.006 -10000 0 -10000 0 0
CDK2 0.029 0.003 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.021 0.014 -10000 0 -10000 0 0
RAD50 0.029 0.006 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.04 0.013 -10000 0 -10000 0 0
EWSR1 0.029 0.005 -10000 0 -10000 0 0
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.044 0.027 -10000 0 -10000 0 0
CLOCK 0.028 0.022 -10000 0 -0.37 1 1
TIMELESS/CRY2 0.03 0.025 -10000 0 -10000 0 0
DEC1/BMAL1 0.035 0.008 -10000 0 -10000 0 0
ATR 0.03 0.003 -10000 0 -10000 0 0
NR1D1 0.008 0.063 -10000 0 -1.2 1 1
ARNTL 0.03 0.006 -10000 0 -10000 0 0
TIMELESS 0.01 0.021 -10000 0 -10000 0 0
NPAS2 0.029 0.022 -10000 0 -0.37 1 1
CRY2 0.03 0.003 -10000 0 -10000 0 0
mol:CO -0.004 0.007 0.13 1 -10000 0 1
CHEK1 0.028 0.007 -10000 0 -10000 0 0
mol:HEME 0.004 0.007 -10000 0 -0.13 1 1
PER1 0.025 0.011 -10000 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.061 0.029 -10000 0 -0.2 3 3
BMAL1/CLOCK 0.006 0.071 -10000 0 -0.8 1 1
S phase of mitotic cell cycle 0.044 0.027 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.045 0.027 -10000 0 -10000 0 0
mol:NADPH 0.004 0.007 -10000 0 -0.13 1 1
PER1/TIMELESS 0.026 0.025 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.017 0.003 -10000 0 -10000 0 0
Aurora C signaling

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
INCENP 0.029 0.005 -9999 0 -9999 0 0
Aurora C/Aurora B/INCENP 0.022 0.028 -9999 0 -9999 0 0
metaphase 0 0 -9999 0 -9999 0 0
mitosis 0 0 -9999 0 -9999 0 0
H3F3B 0.005 0.006 -9999 0 -9999 0 0
AURKB 0.012 0.015 -9999 0 -9999 0 0
AURKC 0.029 0.005 -9999 0 -9999 0 0
Glypican 2 network

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
MDK 0.013 0.015 -9999 0 -9999 0 0
GPC2 0.025 0.011 -9999 0 -9999 0 0
GPC2/Midkine 0.017 0.021 -9999 0 -9999 0 0
neuron projection morphogenesis 0.017 0.021 -9999 0 -9999 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.028 0.007 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.021 0.008 -9999 0 -10000 0 0
MDM2/SUMO1 0.036 0.039 -9999 0 -0.21 3 3
HDAC4 0.029 0.004 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.02 0.008 -9999 0 -10000 0 0
SUMO1 0.03 0.003 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.009 0.015 -9999 0 -0.26 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 -0.003 0.028 -9999 0 -0.25 2 2
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.029 0.004 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.03 0.003 -9999 0 -10000 0 0
SUMO1/HDAC4 0.036 0.039 -9999 0 -0.24 2 2
SUMO1/HDAC1 0.037 0.035 -9999 0 -0.21 3 3
RANGAP1 0.029 0.005 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.072 0.019 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.011 0.003 -9999 0 -10000 0 0
Ran/GTP 0.022 0.035 -9999 0 -0.21 3 3
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.029 0.004 -9999 0 -10000 0 0
UBE2I 0.028 0.007 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.017 0.034 -9999 0 -0.21 3 3
NPC 0.017 0.002 -9999 0 -10000 0 0
PIAS2 0.029 0.005 -9999 0 -10000 0 0
PIAS1 0.029 0.004 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Alternative NF-kappaB 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
IKK alpha homodimer 0.042 0.01 -9999 0 -9999 0 0
FBXW11 0.029 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 0.029 0.005 -9999 0 -9999 0 0
CHUK 0.029 0.005 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.08 0.027 -9999 0 -9999 0 0
NFKB1 0.027 0.009 -9999 0 -9999 0 0
MAP3K14 0.029 0.004 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.04 0.014 -9999 0 -9999 0 0
RELB 0.029 0.005 -9999 0 -9999 0 0
NFKB2 0.029 0.005 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.038 0.009 -9999 0 -9999 0 0
regulation of B cell activation 0.038 0.009 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7156 rows and 4 out of 364 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.ZS.A9CG TCGA.ZS.A9CF TCGA.ZS.A9CE TCGA.ZS.A9CD
109_MAP3K5 -0.1 -0.27 -0.16 0.053
47_PPARGC1A 0.03 0 0.03 0.03
105_BMP4 0.03 0.03 0.03 0.03
105_BMP6 0.03 0.03 0.03 0.03
105_BMP7 0.03 0.03 0.03 0.018
105_BMP2 0.03 0.03 0.03 0.03
131_RELN/VLDLR 0.16 -0.19 0.069 0.077
30_TGFB1/TGF beta receptor Type II 0.029 -0.03 -0.041 0.03
84_STAT5B 0.085 0.12 0.026 0.026
84_STAT5A 0.085 0.12 0.026 0.026
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/LIHC-TP/19437975/LIHC-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/LIHC-TP/19775320/GDAC_Gistic2Report_19782236/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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