Ovarian Serous Cystadenocarcinoma: PARADIGM pathway analysis of mRNA expression data
Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/Harvard Medical School)
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 69 significant pathways identified in this analysis.

Table 1.  Get Full Table Top 10 out of 131 pathways in order of significance.

Pathway.Name Avg.Num.Perturbations
FOXM1 transcription factor network 147
HIF-1-alpha transcription factor network 124
LPA receptor mediated events 106
TCGA08_retinoblastoma 96
Syndecan-1-mediated signaling events 92
Osteopontin-mediated events 90
Endothelins 88
PDGFR-alpha signaling pathway 85
Nectin adhesion pathway 79
Ephrin B reverse signaling 75
Results

The following list describes the columns found in Table 2.

  • Pathway.Name = Full pathway name of curated PARADIGM pathway

  • 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.

Pathway.Name 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 147 7507 51 -0.66 0.022 1000 -1000 -0.022 -1000
HIF-1-alpha transcription factor network 124 9435 76 -0.16 0.034 1000 -1000 -0.012 -1000
LPA receptor mediated events 106 10845 102 -0.086 0.023 1000 -1000 -0.021 -1000
TCGA08_retinoblastoma 96 770 8 -0.023 0.022 1000 -1000 -0.004 -1000
Syndecan-1-mediated signaling events 92 3134 34 -0.087 0.023 1000 -1000 0 -1000
Osteopontin-mediated events 90 3440 38 -0.22 0.023 1000 -1000 0 -1000
Endothelins 88 8493 96 -0.21 0.023 1000 -1000 -0.003 -1000
PDGFR-alpha signaling pathway 85 3748 44 -0.15 0.031 1000 -1000 0.003 -1000
Nectin adhesion pathway 79 4982 63 -0.081 0.033 1000 -1000 -0.024 -1000
Ephrin B reverse signaling 75 3622 48 -0.2 0.051 1000 -1000 -0.03 -1000
amb2 Integrin signaling 74 6146 82 -0.13 0.034 1000 -1000 0 -1000
TCGA08_p53 74 523 7 -0.069 0.019 1000 -1000 -0.002 -1000
Cellular roles of Anthrax toxin 71 2775 39 -0.1 0.022 1000 -1000 -0.003 -1000
Syndecan-4-mediated signaling events 70 4699 67 -0.11 0.027 1000 -1000 -0.008 -1000
Thromboxane A2 receptor signaling 69 7293 105 -0.21 0.052 1000 -1000 -0.028 -1000
PLK2 and PLK4 events 68 204 3 -0.002 0.016 1000 -1000 0.017 -1000
Fc-epsilon receptor I signaling in mast cells 63 6190 97 -0.088 0.026 1000 -1000 -0.02 -1000
Nongenotropic Androgen signaling 63 3300 52 -0.13 0.066 1000 -1000 -0.016 -1000
IL1-mediated signaling events 62 3871 62 -0.074 0.045 1000 -1000 0 -1000
BARD1 signaling events 60 3444 57 -0.035 0.027 1000 -1000 -0.032 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 59 5077 85 -0.17 0.023 1000 -1000 -0.013 -1000
IL4-mediated signaling events 59 5459 91 -0.33 0.17 1000 -1000 -0.11 -1000
IL23-mediated signaling events 59 3581 60 -0.27 0.025 1000 -1000 -0.002 -1000
TRAIL signaling pathway 57 2756 48 -0.038 0.023 1000 -1000 -0.001 -1000
Integrins in angiogenesis 57 4848 84 -0.056 0.033 1000 -1000 0 -1000
IL6-mediated signaling events 57 4300 75 -0.12 0.025 1000 -1000 -0.02 -1000
Noncanonical Wnt signaling pathway 56 1476 26 -0.033 0.026 1000 -1000 -0.016 -1000
PLK1 signaling events 51 4347 85 -0.063 0.025 1000 -1000 -0.002 -1000
a4b1 and a4b7 Integrin signaling 50 252 5 0.004 0.019 1000 -1000 0.019 -1000
IFN-gamma pathway 50 3436 68 -0.053 0.034 1000 -1000 -0.015 -1000
Caspase cascade in apoptosis 49 3686 74 -0.064 0.044 1000 -1000 -0.011 -1000
IGF1 pathway 49 2834 57 -0.021 0.035 1000 -1000 -0.013 -1000
Signaling events mediated by the Hedgehog family 47 2493 52 -0.083 0.034 1000 -1000 -0.016 -1000
EPHB forward signaling 47 4024 85 -0.028 0.036 1000 -1000 -0.019 -1000
Ras signaling in the CD4+ TCR pathway 47 799 17 -0.026 0.024 1000 -1000 0 -1000
Signaling events mediated by PTP1B 46 3554 76 -0.094 0.075 1000 -1000 -0.02 -1000
Wnt signaling 45 319 7 -0.033 0.022 1000 -1000 0.01 -1000
E-cadherin signaling in keratinocytes 45 1943 43 -0.012 0.026 1000 -1000 -0.01 -1000
BMP receptor signaling 44 3643 81 -0.074 0.049 1000 -1000 -0.018 -1000
Paxillin-independent events mediated by a4b1 and a4b7 44 1652 37 -0.041 0.033 1000 -1000 0 -1000
TCR signaling in naïve CD8+ T cells 44 4113 93 -0.05 0.033 1000 -1000 -0.021 -1000
Canonical Wnt signaling pathway 44 2289 51 -0.19 0.084 1000 -1000 -0.028 -1000
IL12-mediated signaling events 43 3765 87 -0.26 0.026 1000 -1000 -0.056 -1000
Circadian rhythm pathway 43 947 22 -0.08 0.024 1000 -1000 -0.007 -1000
Stabilization and expansion of the E-cadherin adherens junction 43 3202 74 -0.059 0.035 1000 -1000 -0.031 -1000
Aurora A signaling 42 2546 60 -0.064 0.037 1000 -1000 0 -1000
Syndecan-2-mediated signaling events 41 2889 69 -0.018 0.027 1000 -1000 0 -1000
Paxillin-dependent events mediated by a4b1 41 1500 36 -0.032 0.035 1000 -1000 -0.033 -1000
IL2 signaling events mediated by PI3K 40 2328 58 -0.11 0.023 1000 -1000 -0.012 -1000
FOXA2 and FOXA3 transcription factor networks 39 1826 46 -0.17 0.042 1000 -1000 -0.003 -1000
ceramide signaling pathway 39 1921 49 -0.014 0.038 1000 -1000 0 -1000
Reelin signaling pathway 38 2183 56 -0.018 0.055 1000 -1000 0 -1000
HIF-2-alpha transcription factor network 38 1654 43 -0.098 0.041 1000 -1000 -0.093 -1000
FoxO family signaling 38 2445 64 -0.27 0.041 1000 -1000 -0.012 -1000
Retinoic acid receptors-mediated signaling 38 2256 58 -0.098 0.029 1000 -1000 -0.008 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 38 1735 45 -0.06 0.038 1000 -1000 -0.003 -1000
E-cadherin signaling in the nascent adherens junction 37 2880 76 -0.059 0.041 1000 -1000 -0.023 -1000
Arf6 downstream pathway 36 1571 43 -0.027 0.031 1000 -1000 -0.024 -1000
BCR signaling pathway 36 3632 99 -0.057 0.032 1000 -1000 -0.022 -1000
Signaling events mediated by PRL 35 1195 34 -0.014 0.023 1000 -1000 -0.001 -1000
Aurora B signaling 34 2320 67 -0.065 0.033 1000 -1000 -0.008 -1000
Plasma membrane estrogen receptor signaling 33 2904 86 -0.055 0.051 1000 -1000 -0.026 -1000
TCGA08_rtk_signaling 32 852 26 -0.014 0.028 1000 -1000 -0.016 -1000
ErbB4 signaling events 31 2163 69 -0.068 0.046 1000 -1000 -0.013 -1000
p75(NTR)-mediated signaling 31 3881 125 -0.039 0.055 1000 -1000 -0.018 -1000
FAS signaling pathway (CD95) 31 1495 47 -0.054 0.042 1000 -1000 -0.009 -1000
ErbB2/ErbB3 signaling events 30 1996 65 -0.072 0.023 1000 -1000 -0.024 -1000
Signaling mediated by p38-gamma and p38-delta 29 438 15 -0.05 0.023 1000 -1000 0 -1000
Class I PI3K signaling events 29 2182 73 -0.008 0.041 1000 -1000 -0.004 -1000
RXR and RAR heterodimerization with other nuclear receptor 28 1497 52 -0.029 0.06 1000 -1000 -0.008 -1000
S1P3 pathway 28 1183 42 -0.054 0.03 1000 -1000 -0.001 -1000
E-cadherin signaling events 27 136 5 0.018 0.025 1000 -1000 0.02 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 26 1448 54 -0.015 0.029 1000 -1000 0 -1000
Ephrin A reverse signaling 26 186 7 0 0.023 1000 -1000 0 -1000
Nephrin/Neph1 signaling in the kidney podocyte 25 878 34 -0.023 0.049 1000 -1000 -0.021 -1000
EGFR-dependent Endothelin signaling events 25 540 21 0 0.041 1000 -1000 0 -1000
Regulation of Androgen receptor activity 25 1770 70 -0.095 0.033 1000 -1000 -0.013 -1000
Canonical NF-kappaB pathway 24 971 39 0 0.037 1000 -1000 0 -1000
Arf6 signaling events 24 1523 62 -0.017 0.036 1000 -1000 0 -1000
Regulation of Telomerase 24 2539 102 -0.13 0.046 1000 -1000 0 -1000
Glypican 1 network 23 1104 48 -0.021 0.039 1000 -1000 -0.018 -1000
EPO signaling pathway 23 1282 55 -0.006 0.058 1000 -1000 0 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 23 1607 68 -0.08 0.092 1000 -1000 -0.055 -1000
LPA4-mediated signaling events 22 266 12 0 0.014 1000 -1000 0 -1000
Glucocorticoid receptor regulatory network 22 2515 114 -0.13 0.046 1000 -1000 -0.023 -1000
IL2 signaling events mediated by STAT5 22 501 22 -0.077 0.032 1000 -1000 -0.002 -1000
Neurotrophic factor-mediated Trk receptor signaling 22 2743 120 -0.058 0.056 1000 -1000 -0.02 -1000
Coregulation of Androgen receptor activity 21 1671 76 -0.01 0.033 1000 -1000 -0.015 -1000
Presenilin action in Notch and Wnt signaling 21 1294 61 -0.18 0.042 1000 -1000 -0.017 -1000
Atypical NF-kappaB pathway 21 675 31 0 0.023 1000 -1000 -0.001 -1000
Signaling events mediated by VEGFR1 and VEGFR2 21 2651 125 -0.019 0.055 1000 -1000 -0.023 -1000
p38 MAPK signaling pathway 20 897 44 -0.012 0.043 1000 -1000 0 -1000
Regulation of nuclear SMAD2/3 signaling 19 2687 136 -0.13 0.071 1000 -1000 -0.036 -1000
mTOR signaling pathway 18 997 53 -0.015 0.032 1000 -1000 -0.016 -1000
Ceramide signaling pathway 18 1430 76 -0.012 0.044 1000 -1000 -0.003 -1000
Signaling events mediated by HDAC Class III 18 721 40 -0.036 0.042 1000 -1000 -0.025 -1000
S1P5 pathway 18 319 17 -0.007 0.023 1000 -1000 -0.009 -1000
PDGFR-beta signaling pathway 18 1829 97 -0.059 0.046 1000 -1000 -0.018 -1000
Signaling events mediated by HDAC Class I 17 1852 104 -0.036 0.052 1000 -1000 -0.027 -1000
Regulation of p38-alpha and p38-beta 17 945 54 -0.007 0.057 1000 -1000 0 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 17 571 33 -0.002 0.053 1000 -1000 0 -1000
Class IB PI3K non-lipid kinase events 17 51 3 -0.019 0.019 1000 -1000 -0.017 -1000
S1P4 pathway 17 434 25 -0.003 0.03 1000 -1000 0 -1000
Arf6 trafficking events 16 1186 71 -0.025 0.033 1000 -1000 -0.017 -1000
Hedgehog signaling events mediated by Gli proteins 14 916 65 -0.005 0.053 1000 -1000 -0.01 -1000
Class I PI3K signaling events mediated by Akt 14 1018 68 -0.026 0.047 1000 -1000 -0.01 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 14 1174 83 -0.006 0.048 1000 -1000 -0.015 -1000
Signaling mediated by p38-alpha and p38-beta 14 651 44 -0.008 0.033 1000 -1000 0 -1000
Calcium signaling in the CD4+ TCR pathway 14 436 31 -0.002 0.089 1000 -1000 -0.011 -1000
Signaling events regulated by Ret tyrosine kinase 13 1075 82 -0.008 0.056 1000 -1000 -0.026 -1000
S1P1 pathway 13 469 36 -0.001 0.028 1000 -1000 -0.016 -1000
Syndecan-3-mediated signaling events 13 475 35 -0.009 0.034 1000 -1000 -0.003 -1000
VEGFR1 specific signals 13 764 56 0 0.039 1000 -1000 0 -1000
Signaling events mediated by HDAC Class II 12 936 75 -0.034 0.059 1000 -1000 -0.014 -1000
JNK signaling in the CD4+ TCR pathway 12 207 17 -0.002 0.044 1000 -1000 0 -1000
Insulin Pathway 12 888 74 -0.012 0.063 1000 -1000 -0.016 -1000
Sphingosine 1-phosphate (S1P) pathway 11 333 28 0 0.037 1000 -1000 0 -1000
Insulin-mediated glucose transport 11 376 32 0 0.033 1000 -1000 0 -1000
Effects of Botulinum toxin 11 306 26 0 0.041 1000 -1000 0 -1000
IL27-mediated signaling events 11 561 51 -0.006 0.034 1000 -1000 -0.018 -1000
Sumoylation by RanBP2 regulates transcriptional repression 11 313 27 -0.013 0.047 1000 -1000 -0.014 -1000
Angiopoietin receptor Tie2-mediated signaling 11 1046 88 -0.029 0.057 1000 -1000 -0.041 -1000
Aurora C signaling 10 70 7 0 0.033 1000 -1000 0 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 9 229 23 -0.013 0.043 1000 -1000 0 -1000
Glypican 2 network 9 39 4 0.021 0.029 1000 -1000 0.018 -1000
Alternative NF-kappaB pathway 9 121 13 0 0.055 1000 -1000 0 -1000
Arf1 pathway 8 469 54 -0.01 0.032 1000 -1000 0 -1000
Rapid glucocorticoid signaling 7 146 20 0 0.025 1000 -1000 0 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 7 579 78 -0.013 0.037 1000 -1000 -0.012 -1000
Visual signal transduction: Rods 6 358 52 0 0.065 1000 -1000 0 -1000
Visual signal transduction: Cones 2 82 38 0 0.064 1000 -1000 0 -1000
Total 4791 276944 7203 -8.1 5.2 131000 -131000 -1.5 -131000
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.43 0.59 -10000 0 -1.1 193 193
PLK1 -0.062 0.29 -10000 0 -1.3 30 30
BIRC5 -0.061 0.29 -10000 0 -1.3 29 29
HSPA1B -0.44 0.59 -10000 0 -1.1 207 207
MAP2K1 0.001 0.044 -10000 0 -0.16 3 3
BRCA2 -0.44 0.6 -10000 0 -1.2 198 198
FOXM1 -0.66 0.96 -10000 0 -1.7 207 207
XRCC1 -0.43 0.59 -10000 0 -1.1 194 194
FOXM1B/p19 -0.54 0.66 -10000 0 -1.3 214 214
Cyclin D1/CDK4 -0.44 0.55 -10000 0 -1 227 227
CDC2 -0.5 0.67 -10000 0 -1.3 206 206
TGFA -0.39 0.52 -10000 0 -0.96 211 211
SKP2 -0.44 0.6 -10000 0 -1.2 190 190
CCNE1 -0.001 0.049 -10000 0 -0.13 70 70
CKS1B -0.44 0.6 -10000 0 -1.1 198 198
RB1 -0.36 0.45 -10000 0 -0.91 189 189
FOXM1C/SP1 -0.53 0.71 -10000 0 -1.3 212 212
AURKB -0.069 0.3 -10000 0 -1.3 32 32
CENPF -0.48 0.62 -10000 0 -1.2 212 212
CDK4 0.008 0.027 -10000 0 -0.14 9 9
MYC -0.39 0.52 -10000 0 -0.98 215 215
CHEK2 -0.003 0.051 -10000 0 -0.14 26 26
ONECUT1 -0.44 0.57 -10000 0 -1.1 212 212
CDKN2A 0.013 0.023 0.093 1 -0.13 12 13
LAMA4 -0.48 0.62 -10000 0 -1.2 218 218
FOXM1B/HNF6 -0.55 0.72 -10000 0 -1.4 214 214
FOS -0.52 0.64 -10000 0 -1.2 236 236
SP1 0.021 0.011 -10000 0 -0.037 12 12
CDC25B -0.44 0.59 -10000 0 -1.1 197 197
response to radiation -0.012 0.032 -10000 0 -10000 0 0
CENPB -0.43 0.59 -10000 0 -1.1 190 190
CENPA -0.43 0.59 -10000 0 -1.2 192 192
NEK2 -0.44 0.61 -10000 0 -1.2 193 193
HIST1H2BA -0.43 0.59 -10000 0 -1.1 191 191
CCNA2 0.01 0.034 -10000 0 -0.13 29 29
EP300 0.022 0.01 -10000 0 -0.12 2 2
CCNB1/CDK1 -0.58 0.78 -10000 0 -1.5 201 201
CCNB2 -0.46 0.62 -10000 0 -1.2 209 209
CCNB1 -0.48 0.65 -10000 0 -1.3 198 198
ETV5 -0.49 0.63 -10000 0 -1.2 219 219
ESR1 -0.47 0.61 -10000 0 -1.2 219 219
CCND1 -0.44 0.56 -10000 0 -1 230 230
GSK3A 0.003 0.042 -10000 0 -0.16 10 10
Cyclin A-E1/CDK1-2 -0.037 0.1 -10000 0 -0.17 159 159
CDK2 0.015 0.025 -10000 0 -0.13 14 14
G2/M transition of mitotic cell cycle -0.015 0.038 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.49 0.66 -10000 0 -1.3 207 207
GAS1 -0.44 0.6 -10000 0 -1.2 193 193
MMP2 -0.53 0.64 -10000 0 -1.2 244 244
RB1/FOXM1C -0.49 0.58 -10000 0 -1.1 227 227
CREBBP 0.021 0.015 -10000 0 -0.12 6 6
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.13 0.34 -9999 0 -0.55 171 171
HDAC7 -0.001 0.006 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.067 0.34 -9999 0 -0.56 120 120
SMAD4 0.023 0.007 -9999 0 -0.12 1 1
ID2 -0.13 0.34 -9999 0 -0.55 165 165
AP1 -0.03 0.087 -9999 0 -0.15 161 161
ABCG2 -0.13 0.34 -9999 0 -0.56 165 165
HIF1A -0.017 0.091 -9999 0 -0.12 164 164
TFF3 -0.13 0.34 -9999 0 -0.54 178 178
GATA2 0.019 0.023 -9999 0 -0.099 18 18
AKT1 -0.005 0.073 -9999 0 -0.1 117 117
response to hypoxia -0.021 0.064 -9999 0 -0.1 143 143
MCL1 -0.13 0.34 -9999 0 -0.55 167 167
NDRG1 -0.14 0.35 -9999 0 -0.56 176 176
SERPINE1 -0.14 0.33 -9999 0 -0.55 170 170
FECH -0.13 0.34 -9999 0 -0.56 164 164
FURIN -0.13 0.34 -9999 0 -0.54 171 171
NCOA2 0.023 0.013 -9999 0 -0.1 5 5
EP300 0 0.089 -9999 0 -0.2 33 33
HMOX1 -0.13 0.35 -9999 0 -0.56 173 173
BHLHE40 -0.14 0.33 -9999 0 -0.55 170 170
BHLHE41 -0.14 0.33 -9999 0 -0.55 170 170
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.034 0.12 -9999 0 -0.19 52 52
ENG 0.005 0.089 -9999 0 -0.2 40 40
JUN 0.014 0.033 -9999 0 -0.12 30 30
RORA -0.13 0.34 -9999 0 -0.55 164 164
ABCB1 -0.026 0.11 -9999 0 -0.78 4 4
TFRC -0.14 0.35 -9999 0 -0.55 182 182
CXCR4 -0.14 0.35 -9999 0 -0.55 184 184
TF -0.13 0.34 -9999 0 -0.55 166 166
CITED2 -0.13 0.34 -9999 0 -0.55 165 165
HIF1A/ARNT -0.084 0.44 -9999 0 -0.69 128 128
LDHA -0.09 0.3 -9999 0 -0.99 54 54
ETS1 -0.13 0.35 -9999 0 -0.56 173 173
PGK1 -0.13 0.35 -9999 0 -0.55 177 177
NOS2 -0.14 0.33 -9999 0 -0.55 170 170
ITGB2 -0.14 0.35 -9999 0 -0.56 179 179
ALDOA -0.13 0.34 -9999 0 -0.55 165 165
Cbp/p300/CITED2 -0.12 0.36 -9999 0 -0.62 141 141
FOS -0.006 0.054 -9999 0 -0.12 95 95
HK2 -0.13 0.34 -9999 0 -0.54 175 175
SP1 0.031 0.009 -9999 0 -0.11 1 1
GCK 0.002 0.12 -9999 0 -0.37 3 3
HK1 -0.13 0.34 -9999 0 -0.55 164 164
NPM1 -0.13 0.34 -9999 0 -0.54 171 171
EGLN1 -0.12 0.34 -9999 0 -0.54 171 171
CREB1 0.023 0.028 -9999 0 -0.075 42 42
PGM1 -0.13 0.34 -9999 0 -0.56 170 170
SMAD3 0.022 0.016 -9999 0 -0.12 7 7
EDN1 -0.037 0.19 -9999 0 -0.92 17 17
IGFBP1 -0.12 0.34 -9999 0 -0.55 166 166
VEGFA -0.093 0.29 -9999 0 -0.5 146 146
HIF1A/JAB1 -0.005 0.085 -9999 0 -0.15 99 99
CP -0.15 0.36 -9999 0 -0.57 183 183
CXCL12 -0.15 0.35 -9999 0 -0.56 182 182
COPS5 0.02 0.022 -9999 0 -0.11 13 13
SMAD3/SMAD4 0.029 0.032 -9999 0 -0.14 17 17
BNIP3 -0.14 0.34 -9999 0 -0.55 175 175
EGLN3 -0.15 0.35 -9999 0 -0.56 182 182
CA9 -0.15 0.34 -9999 0 -0.54 188 188
TERT -0.12 0.34 -9999 0 -0.55 164 164
ENO1 -0.13 0.34 -9999 0 -0.56 164 164
PFKL -0.13 0.34 -9999 0 -0.54 170 170
NCOA1 0.023 0.009 -9999 0 -0.12 2 2
ADM -0.14 0.34 -9999 0 -0.55 177 177
ARNT -0.009 0.07 -9999 0 -0.095 164 164
HNF4A 0.027 0.009 -9999 0 -0.12 2 2
ADFP -0.14 0.35 -9999 0 -0.56 182 182
SLC2A1 -0.097 0.29 -9999 0 -0.5 147 147
LEP -0.12 0.34 -9999 0 -0.55 164 164
HIF1A/ARNT/Cbp/p300 -0.077 0.34 -9999 0 -0.57 124 124
EPO -0.076 0.28 -9999 0 -0.55 97 97
CREBBP -0.002 0.09 -9999 0 -0.19 46 46
HIF1A/ARNT/Cbp/p300/HDAC7 -0.08 0.35 -9999 0 -0.57 131 131
PFKFB3 -0.13 0.34 -9999 0 -0.55 171 171
NT5E -0.16 0.36 -9999 0 -0.57 187 187
LPA receptor mediated events

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 -0.021 0.074 -10000 0 -0.13 138 138
NF kappa B1 p50/RelA/I kappa B alpha -0.015 0.092 -10000 0 -0.19 88 88
AP1 -0.058 0.074 -10000 0 -0.13 251 251
mol:PIP3 -0.051 0.063 -10000 0 -0.13 161 161
AKT1 -0.015 0.07 -10000 0 -0.16 54 54
PTK2B -0.028 0.066 -10000 0 -0.14 123 123
RHOA -0.009 0.054 -10000 0 -0.35 6 6
PIK3CB 0.015 0.03 -10000 0 -0.12 24 24
mol:Ca2+ -0.004 0.039 -10000 0 -0.12 31 31
MAGI3 0.018 0.026 -10000 0 -0.12 18 18
RELA 0.023 0.009 -10000 0 -0.12 2 2
apoptosis -0.035 0.07 -10000 0 -0.1 248 248
HRAS/GDP 0.017 0.008 -10000 0 -0.11 2 2
positive regulation of microtubule depolymerization -0.019 0.06 -10000 0 -0.12 127 127
NF kappa B1 p50/RelA -0.04 0.062 -10000 0 -0.13 141 141
endothelial cell migration -0.086 0.14 -10000 0 -0.23 247 247
ADCY4 -0.043 0.097 -10000 0 -0.2 135 135
ADCY5 -0.045 0.098 -10000 0 -0.2 141 141
ADCY6 -0.043 0.098 -10000 0 -0.2 134 134
ADCY7 -0.042 0.097 -10000 0 -0.2 134 134
ADCY1 -0.042 0.097 -10000 0 -0.2 134 134
ADCY2 -0.043 0.097 -10000 0 -0.2 135 135
ADCY3 -0.043 0.098 -10000 0 -0.2 135 135
ADCY8 -0.048 0.098 -10000 0 -0.2 138 138
ADCY9 -0.045 0.1 -10000 0 -0.2 141 141
GSK3B -0.024 0.064 -10000 0 -0.13 126 126
arachidonic acid secretion -0.041 0.091 -10000 0 -0.19 129 129
GNG2 0.02 0.018 -10000 0 -0.12 9 9
TRIP6 0.002 0.05 -10000 0 -0.25 19 19
GNAO1 -0.04 0.073 -10000 0 -0.1 275 275
HRAS 0.023 0.006 -10000 0 -0.12 1 1
NFKBIA -0.03 0.085 -10000 0 -0.21 71 71
GAB1 0.02 0.021 -10000 0 -0.12 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.023 0.22 -10000 0 -0.87 37 37
JUN 0.014 0.033 -10000 0 -0.12 30 30
LPA/LPA2/NHERF2 -0.01 0.035 -10000 0 -0.062 140 140
TIAM1 -0.041 0.26 -10000 0 -1 37 37
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
mol:IP3 -0.004 0.039 -10000 0 -0.12 31 31
PLCB3 -0.003 0.032 -10000 0 -0.079 28 28
FOS -0.005 0.053 -10000 0 -0.12 95 95
positive regulation of mitosis -0.041 0.091 -10000 0 -0.19 129 129
LPA/LPA1-2-3 -0.037 0.061 -10000 0 -0.098 247 247
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.022 0.011 -10000 0 -0.12 3 3
stress fiber formation -0.026 0.075 -10000 0 -0.14 140 140
GNAZ -0.035 0.071 -10000 0 -0.11 249 249
EGFR/PI3K-beta/Gab1 -0.053 0.065 -10000 0 -0.14 161 161
positive regulation of dendritic cell cytokine production -0.037 0.06 -10000 0 -0.098 247 247
LPA/LPA2/MAGI-3 -0.009 0.036 -10000 0 -0.063 136 136
ARHGEF1 -0.02 0.062 -10000 0 -0.12 128 128
GNAI2 -0.035 0.071 -10000 0 -0.11 248 248
GNAI3 -0.039 0.077 -10000 0 -0.11 248 248
GNAI1 -0.045 0.081 -10000 0 -0.12 270 270
LPA/LPA3 -0.021 0.031 -10000 0 -0.053 247 247
LPA/LPA2 -0.021 0.031 -10000 0 -0.052 247 247
LPA/LPA1 -0.052 0.082 -10000 0 -0.14 247 247
HB-EGF/EGFR -0.003 0.06 -10000 0 -0.13 77 77
HBEGF 0.004 0.039 -10000 0 -0.078 95 95
mol:DAG -0.004 0.039 -10000 0 -0.12 31 31
cAMP biosynthetic process -0.045 0.096 -10000 0 -0.2 135 135
NFKB1 0.021 0.013 -10000 0 -0.12 4 4
SRC 0.023 0.009 -10000 0 -0.12 2 2
GNB1 0.023 0.007 -10000 0 -0.12 1 1
LYN -0.03 0.089 -10000 0 -0.2 82 82
GNAQ -0.012 0.038 -10000 0 -0.063 143 143
LPAR2 0 0 -10000 0 -10000 0 0
LPAR3 0 0 -10000 0 -10000 0 0
LPAR1 -0.034 0.049 -10000 0 -0.084 247 247
IL8 -0.083 0.15 -10000 0 -0.35 100 100
PTK2 -0.029 0.063 -10000 0 -0.09 251 251
Rac1/GDP 0.016 0.015 -10000 0 -0.15 5 5
CASP3 -0.035 0.07 -10000 0 -0.1 248 248
EGFR 0.015 0.03 -10000 0 -0.12 25 25
PLCG1 -0.007 0.041 -10000 0 -0.066 135 135
PLD2 -0.026 0.06 -10000 0 -0.087 247 247
G12/G13 -0.019 0.073 -10000 0 -0.14 128 128
PI3K-beta -0.04 0.06 0.084 1 -0.19 49 50
cell migration -0.012 0.078 -10000 0 -0.23 50 50
SLC9A3R2 0.017 0.028 -10000 0 -0.12 22 22
PXN -0.027 0.076 -10000 0 -0.14 140 140
HRAS/GTP -0.042 0.093 -10000 0 -0.19 129 129
RAC1 0.023 0.002 -10000 0 -10000 0 0
MMP9 0 0.05 -10000 0 -0.12 81 81
PRKCE 0.021 0.017 -10000 0 -0.12 8 8
PRKCD -0.005 0.045 -10000 0 -0.13 39 39
Gi(beta/gamma) -0.043 0.096 -10000 0 -0.19 140 140
mol:LPA -0.034 0.049 -10000 0 -0.084 247 247
TRIP6/p130 Cas/FAK1/Paxillin -0.022 0.093 -10000 0 -0.16 140 140
MAPKKK cascade -0.041 0.091 -10000 0 -0.19 129 129
contractile ring contraction involved in cytokinesis -0.008 0.054 -10000 0 -0.35 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.009 0.029 -10000 0 -0.056 131 131
GNA15 -0.011 0.035 -10000 0 -0.063 128 128
GNA12 0.023 0.001 -10000 0 -10000 0 0
GNA13 0.022 0.009 -10000 0 -0.12 2 2
MAPT -0.019 0.061 -10000 0 -0.12 127 127
GNA11 -0.009 0.028 -10000 0 -0.054 134 134
Rac1/GTP -0.026 0.24 -10000 0 -0.92 37 37
MMP2 -0.086 0.14 -10000 0 -0.23 247 247
TCGA08_retinoblastoma

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
CDKN2B 0.017 0.017 -10000 0 -0.085 8 8
CDKN2C 0.008 0.044 -10000 0 -0.12 56 56
CDKN2A 0.014 0.023 -10000 0 -0.12 12 12
CCND2 0.015 0.052 0.12 107 -10000 0 107
RB1 -0.023 0.061 0.091 1 -0.12 135 136
CDK4 0.022 0.068 0.13 136 -0.12 17 153
CDK6 0.014 0.073 0.13 122 -0.13 39 161
G1/S progression 0.02 0.065 0.12 137 -10000 0 137
Syndecan-1-mediated signaling events

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
TGFB1 0.019 0.023 -9999 0 -0.12 14 14
CCL5 0.005 0.044 -9999 0 -0.12 60 60
SDCBP 0.021 0.01 -9999 0 -0.12 2 2
FGFR/FGF2/Syndecan-1 -0.083 0.12 -9999 0 -0.25 132 132
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.073 0.12 -9999 0 -0.24 139 139
Syndecan-1/Syntenin -0.076 0.13 -9999 0 -0.24 151 151
MAPK3 -0.06 0.12 -9999 0 -0.21 139 139
HGF/MET -0.017 0.074 -9999 0 -0.11 196 196
TGFB1/TGF beta receptor Type II 0.019 0.023 -9999 0 -0.12 14 14
BSG 0.022 0.013 -9999 0 -0.12 4 4
keratinocyte migration -0.072 0.12 -9999 0 -0.23 139 139
Syndecan-1/RANTES -0.087 0.14 -9999 0 -0.25 168 168
Syndecan-1/CD147 -0.062 0.12 -9999 0 -0.22 138 138
Syndecan-1/Syntenin/PIP2 -0.074 0.12 -9999 0 -0.23 153 153
LAMA5 0.019 0.025 -9999 0 -0.12 17 17
positive regulation of cell-cell adhesion -0.073 0.12 -9999 0 -0.22 153 153
MMP7 -0.022 0.06 -9999 0 -0.12 144 144
HGF 0.02 0.023 -9999 0 -0.12 14 14
Syndecan-1/CASK -0.079 0.12 -9999 0 -0.24 132 132
Syndecan-1/HGF/MET -0.087 0.13 -9999 0 -0.23 194 194
regulation of cell adhesion -0.058 0.11 -9999 0 -0.26 87 87
HPSE 0.014 0.034 -9999 0 -0.12 33 33
positive regulation of cell migration -0.083 0.12 -9999 0 -0.25 132 132
SDC1 -0.084 0.12 -9999 0 -0.25 132 132
Syndecan-1/Collagen -0.083 0.12 -9999 0 -0.25 132 132
PPIB 0.023 0.003 -9999 0 -10000 0 0
MET 0 0.047 -9999 0 -0.12 70 70
PRKACA 0.021 0.017 -9999 0 -0.12 8 8
MMP9 0 0.05 -9999 0 -0.12 81 81
MAPK1 -0.061 0.12 -9999 0 -0.24 109 109
homophilic cell adhesion -0.082 0.12 -9999 0 -0.25 132 132
MMP1 -0.007 0.058 -9999 0 -0.12 115 115
Osteopontin-mediated events

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
IKK alpha homodimer -0.047 0.11 -9999 0 -0.22 121 121
NF kappa B1 p50/RelA/I kappa B alpha -0.067 0.17 -9999 0 -0.33 131 131
alphaV/beta3 Integrin/Osteopontin/Src -0.038 0.11 -9999 0 -0.19 164 164
AP1 -0.12 0.16 -9999 0 -0.3 190 190
ILK -0.047 0.099 -9999 0 -0.22 103 103
bone resorption -0.041 0.11 -9999 0 -0.2 140 140
PTK2B 0.023 0.009 -9999 0 -0.12 2 2
PYK2/p130Cas -0.022 0.11 -9999 0 -0.2 117 117
ITGAV 0.008 0.035 -9999 0 -0.12 30 30
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.001 0.07 -9999 0 -0.15 80 80
alphaV/beta3 Integrin/Osteopontin -0.042 0.12 -9999 0 -0.19 171 171
MAP3K1 -0.05 0.1 -9999 0 -0.2 134 134
JUN 0.012 0.033 -9999 0 -0.12 30 30
MAPK3 -0.064 0.12 -9999 0 -0.25 139 139
MAPK1 -0.064 0.13 -9999 0 -0.25 140 140
Rac1/GDP 0.016 0.015 -9999 0 -0.15 5 5
NFKB1 0.021 0.013 -9999 0 -0.12 4 4
MAPK8 -0.053 0.1 -9999 0 -0.2 143 143
ITGB3 -0.001 0.048 -9999 0 -0.12 71 71
NFKBIA -0.081 0.16 -9999 0 -0.32 144 144
FOS -0.007 0.054 -9999 0 -0.12 95 95
CD44 0.011 0.038 -9999 0 -0.12 41 41
CHUK 0.021 0.013 -9999 0 -0.12 4 4
PLAU -0.22 0.4 -9999 0 -1 106 106
NF kappa B1 p50/RelA -0.068 0.17 -9999 0 -0.36 122 122
BCAR1 0.022 0.011 -9999 0 -0.12 3 3
RELA 0.023 0.009 -9999 0 -0.12 2 2
alphaV beta3 Integrin -0.027 0.088 -9999 0 -0.16 144 144
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.047 0.1 -9999 0 -0.2 134 134
VAV3 -0.055 0.11 -9999 0 -0.21 146 146
MAP3K14 -0.054 0.11 -9999 0 -0.2 152 152
ROCK2 0.019 0.021 -9999 0 -0.12 11 11
SPP1 0.008 0.034 -9999 0 -0.12 31 31
RAC1 0.023 0.002 -9999 0 -10000 0 0
Rac1/GTP -0.05 0.11 -9999 0 -0.2 145 145
MMP2 -0.13 0.16 -9999 0 -0.28 245 245
Endothelins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.075 0.13 0.27 6 -0.25 160 166
PTK2B 0.022 0.009 -10000 0 -0.12 2 2
mol:Ca2+ -0.041 0.16 -10000 0 -0.48 43 43
EDN1 -0.057 0.11 0.2 6 -0.18 191 197
EDN3 0.02 0.023 -10000 0 -0.12 14 14
EDN2 0.018 0.027 -10000 0 -0.12 20 20
HRAS/GDP -0.068 0.14 -10000 0 -0.31 101 101
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.05 0.11 0.2 3 -0.24 97 100
ADCY4 -0.059 0.11 0.2 6 -0.2 156 162
ADCY5 -0.062 0.11 0.2 5 -0.2 169 174
ADCY6 -0.058 0.11 0.2 6 -0.2 160 166
ADCY7 -0.058 0.11 0.2 6 -0.2 161 167
ADCY1 -0.058 0.11 0.2 6 -0.2 160 166
ADCY2 -0.059 0.11 0.2 6 -0.2 161 167
ADCY3 -0.059 0.11 0.2 6 -0.2 162 168
ADCY8 -0.067 0.11 0.2 4 -0.2 173 177
ADCY9 -0.06 0.11 0.2 6 -0.2 161 167
arachidonic acid secretion -0.13 0.23 -10000 0 -0.44 154 154
ETB receptor/Endothelin-1/Gq/GTP -0.022 0.082 -10000 0 -0.2 58 58
GNAO1 0.01 0.042 -10000 0 -0.12 51 51
HRAS 0.022 0.006 -10000 0 -0.12 1 1
ETA receptor/Endothelin-1/G12/GTP -0.053 0.14 0.32 6 -0.23 150 156
ETA receptor/Endothelin-1/Gs/GTP -0.051 0.13 0.3 6 -0.22 149 155
mol:GTP -0.001 0.006 -10000 0 -10000 0 0
COL3A1 -0.13 0.19 0.28 6 -0.35 200 206
EDNRB -0.012 0.054 -10000 0 -0.09 148 148
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.074 0.14 0.28 6 -0.27 139 145
CYSLTR1 -0.084 0.15 0.28 5 -0.28 149 154
SLC9A1 -0.043 0.088 0.19 6 -0.18 113 119
mol:GDP -0.08 0.15 0.21 2 -0.33 104 106
SLC9A3 -0.059 0.16 -10000 0 -0.42 53 53
RAF1 -0.092 0.18 -10000 0 -0.38 121 121
JUN -0.081 0.27 -10000 0 -0.83 55 55
JAK2 -0.082 0.14 0.27 6 -0.26 169 175
mol:IP3 -0.053 0.12 -10000 0 -0.26 83 83
ETA receptor/Endothelin-1 -0.086 0.17 0.36 6 -0.3 163 169
PLCB1 0.011 0.034 -10000 0 -0.12 32 32
PLCB2 0.019 0.018 -10000 0 -0.12 8 8
ETA receptor/Endothelin-3 -0.02 0.077 0.16 5 -0.13 130 135
FOS -0.17 0.34 -10000 0 -0.84 108 108
Gai/GDP 0.013 0.062 -10000 0 -0.47 3 3
CRK 0.021 0.016 -10000 0 -0.12 7 7
mol:Ca ++ -0.1 0.16 0.27 3 -0.32 155 158
BCAR1 0.023 0.011 -10000 0 -0.12 3 3
PRKCB1 -0.053 0.12 -10000 0 -0.26 83 83
GNAQ 0.019 0.017 -10000 0 -0.12 6 6
GNAZ 0.022 0.011 -10000 0 -0.12 3 3
GNAL 0.021 0.018 -10000 0 -0.12 9 9
Gs family/GDP -0.067 0.14 -10000 0 -0.3 104 104
ETA receptor/Endothelin-1/Gq/GTP -0.043 0.12 0.22 3 -0.24 93 96
MAPK14 -0.028 0.086 -10000 0 -0.2 76 76
TRPC6 -0.043 0.17 -10000 0 -0.51 40 40
GNAI2 0.022 0.011 -10000 0 -0.12 3 3
GNAI3 0.021 0.008 -10000 0 -0.12 1 1
GNAI1 0.012 0.035 -10000 0 -0.12 35 35
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.032 0.09 -10000 0 -0.21 74 74
ETB receptor/Endothelin-2 0.004 0.048 -10000 0 -0.12 38 38
ETB receptor/Endothelin-3 0.007 0.043 -10000 0 -0.11 25 25
ETB receptor/Endothelin-1 -0.05 0.1 0.17 5 -0.18 164 169
MAPK3 -0.16 0.3 -10000 0 -0.73 113 113
MAPK1 -0.16 0.31 -10000 0 -0.74 113 113
Rac1/GDP -0.068 0.14 -10000 0 -0.31 103 103
cAMP biosynthetic process -0.04 0.1 0.21 5 -0.2 118 123
MAPK8 -0.058 0.19 -10000 0 -0.51 69 69
SRC 0.023 0.009 -10000 0 -0.12 2 2
ETB receptor/Endothelin-1/Gi/GTP -0.034 0.095 -10000 0 -0.24 65 65
p130Cas/CRK/Src/PYK2 -0.055 0.15 -10000 0 -0.38 66 66
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.068 0.14 -10000 0 -0.31 102 102
COL1A2 -0.14 0.23 0.28 5 -0.46 164 169
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.023 0.08 0.16 5 -0.13 138 143
mol:DAG -0.053 0.12 -10000 0 -0.27 83 83
MAP2K2 -0.12 0.23 -10000 0 -0.54 117 117
MAP2K1 -0.12 0.23 -10000 0 -0.53 116 116
EDNRA -0.05 0.1 0.2 6 -0.17 187 193
positive regulation of muscle contraction -0.06 0.12 0.24 6 -0.22 152 158
Gq family/GDP -0.046 0.14 -10000 0 -0.31 89 89
HRAS/GTP -0.07 0.14 -10000 0 -0.31 98 98
PRKCH -0.053 0.12 -10000 0 -0.26 87 87
RAC1 0.023 0.002 -10000 0 -10000 0 0
PRKCA -0.058 0.12 -10000 0 -0.26 95 95
PRKCB -0.054 0.11 -10000 0 -0.26 88 88
PRKCE -0.052 0.12 -10000 0 -0.26 89 89
PRKCD -0.056 0.12 -10000 0 -0.26 94 94
PRKCG -0.051 0.12 -10000 0 -0.26 84 84
regulation of vascular smooth muscle contraction -0.21 0.4 -10000 0 -1 108 108
PRKCQ -0.059 0.12 -10000 0 -0.26 93 93
PLA2G4A -0.14 0.25 -10000 0 -0.48 154 154
GNA14 0.018 0.022 -10000 0 -0.12 11 11
GNA15 0.019 0.019 -10000 0 -0.12 8 8
GNA12 0.023 0.001 -10000 0 -10000 0 0
GNA11 0.021 0.015 -10000 0 -0.12 5 5
Rac1/GTP -0.054 0.14 0.32 6 -0.24 150 156
MMP1 0.019 0.14 0.23 5 -0.6 12 17
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.004 0.046 -10000 0 -0.13 59 59
PDGF/PDGFRA/CRKL -0.009 0.068 -10000 0 -0.11 156 156
positive regulation of JUN kinase activity 0.01 0.068 -10000 0 -0.1 115 115
CRKL 0.023 0.009 -10000 0 -0.12 2 2
PDGF/PDGFRA/Caveolin-3 -0.01 0.068 -10000 0 -0.13 122 122
AP1 -0.15 0.26 -10000 0 -0.64 114 114
mol:IP3 -0.007 0.046 -10000 0 -0.072 148 148
PLCG1 -0.007 0.046 -10000 0 -0.072 148 148
PDGF/PDGFRA/alphaV Integrin -0.037 0.094 -10000 0 -0.15 193 193
RAPGEF1 0.023 0 -10000 0 -10000 0 0
CRK 0.021 0.016 -10000 0 -0.12 7 7
mol:Ca2+ -0.011 0.053 -10000 0 -0.083 149 149
CAV3 0.022 0.011 -10000 0 -0.12 3 3
CAV1 0.012 0.039 -10000 0 -0.12 43 43
SHC/Grb2/SOS1 0.011 0.069 -10000 0 -0.1 115 115
PDGF/PDGFRA/Shf -0.009 0.068 -10000 0 -0.13 120 120
FOS -0.14 0.26 -10000 0 -0.63 114 114
JUN -0.019 0.045 0.26 4 -0.13 35 39
oligodendrocyte development -0.037 0.094 -10000 0 -0.15 193 193
GRB2 0.023 0.006 -10000 0 -0.12 1 1
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
mol:DAG -0.007 0.046 -10000 0 -0.072 148 148
PDGF/PDGFRA -0.004 0.046 -10000 0 -0.13 59 59
actin cytoskeleton reorganization -0.009 0.068 -10000 0 -0.12 154 154
SRF 0.024 0.022 -10000 0 -0.069 23 23
SHC1 0.023 0.001 -10000 0 -10000 0 0
PI3K -0.014 0.084 -10000 0 -0.13 153 153
PDGF/PDGFRA/Crk/C3G 0.007 0.061 -10000 0 -0.11 94 94
JAK1 0.003 0.032 -10000 0 -0.076 61 61
ELK1/SRF -0.011 0.066 -10000 0 -0.13 110 110
SHB 0.023 0.009 -10000 0 -0.12 2 2
SHF 0.023 0.009 -10000 0 -0.12 2 2
CSNK2A1 0.031 0.021 -10000 0 -0.1 6 6
GO:0007205 -0.023 0.072 -10000 0 -0.14 110 110
SOS1 0.017 0.027 -10000 0 -0.12 20 20
Ras protein signal transduction 0.01 0.068 -10000 0 -0.1 115 115
PDGF/PDGFRA/SHB -0.009 0.068 -10000 0 -0.12 154 154
PDGF/PDGFRA/Caveolin-1 -0.02 0.08 -10000 0 -0.13 181 181
ITGAV 0.013 0.032 -10000 0 -0.12 28 28
ELK1 -0.024 0.07 -10000 0 -0.12 146 146
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
PDGF/PDGFRA/Crk -0.01 0.068 -10000 0 -0.13 126 126
JAK-STAT cascade 0.004 0.032 -10000 0 -0.076 61 61
cell proliferation -0.009 0.067 -10000 0 -0.13 120 120
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.01 0.042 -9999 0 -0.12 52 52
alphaV beta3 Integrin -0.018 0.081 -9999 0 -0.12 191 191
PTK2 -0.073 0.15 -9999 0 -0.31 140 140
positive regulation of JNK cascade -0.052 0.11 -9999 0 -0.26 117 117
CDC42/GDP -0.044 0.17 -9999 0 -0.35 117 117
Rac1/GDP -0.043 0.17 -9999 0 -0.35 117 117
RAP1B 0.019 0.02 -9999 0 -0.12 10 10
RAP1A 0.021 0.012 -9999 0 -0.12 3 3
CTNNB1 0.022 0.008 -9999 0 -0.12 1 1
CDC42/GTP -0.044 0.15 -9999 0 -0.32 117 117
nectin-3/I-afadin -0.02 0.08 -9999 0 -0.12 200 200
RAPGEF1 -0.06 0.17 -9999 0 -0.38 115 115
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.073 0.19 -9999 0 -0.43 115 115
PDGFB-D/PDGFRB 0.01 0.042 -9999 0 -0.12 52 52
TLN1 -0.037 0.097 -9999 0 -0.23 88 88
Rap1/GTP -0.063 0.12 -9999 0 -0.28 117 117
IQGAP1 0.02 0.017 -9999 0 -0.12 7 7
Rap1/GTP/I-afadin 0.016 0.059 -9999 0 -0.11 85 85
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.02 0.08 -9999 0 -0.12 200 200
PVR 0.022 0.011 -9999 0 -0.12 3 3
Necl-5(dimer) 0.022 0.011 -9999 0 -0.12 3 3
mol:GDP -0.066 0.2 -9999 0 -0.43 116 116
MLLT4 0.014 0.032 -9999 0 -0.12 29 29
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
PI3K -0.009 0.085 -9999 0 -0.11 179 179
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.017 0.048 -9999 0 -0.11 68 68
positive regulation of lamellipodium assembly -0.059 0.12 -9999 0 -0.28 127 127
PVRL1 0.022 0.011 -9999 0 -0.12 3 3
PVRL3 0.003 0.046 -9999 0 -0.12 66 66
PVRL2 0.019 0.023 -9999 0 -0.12 15 15
PIK3R1 0.015 0.031 -9999 0 -0.12 27 27
CDH1 0.021 0.016 -9999 0 -0.12 6 6
CLDN1 -0.003 0.051 -9999 0 -0.12 87 87
JAM-A/CLDN1 -0.029 0.087 -9999 0 -0.12 216 216
SRC -0.081 0.21 -9999 0 -0.48 115 115
ITGB3 0.004 0.047 -9999 0 -0.12 68 68
nectin-1(dimer)/I-afadin/I-afadin 0.017 0.048 -9999 0 -0.11 68 68
FARP2 -0.063 0.19 -9999 0 -0.42 116 116
RAC1 0.023 0.002 -9999 0 -10000 0 0
CTNNA1 0.022 0.01 -9999 0 -0.12 2 2
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.003 0.072 -9999 0 -0.12 120 120
nectin-1/I-afadin 0.017 0.048 -9999 0 -0.11 68 68
nectin-2/I-afadin 0.013 0.054 -9999 0 -0.15 43 43
RAC1/GTP/IQGAP1/filamentous actin 0.017 0.044 -9999 0 -0.11 55 55
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.003 0.072 -9999 0 -0.12 119 119
CDC42/GTP/IQGAP1/filamentous actin 0.018 0.043 -9999 0 -0.11 54 54
F11R 0.023 0.007 -9999 0 -0.12 1 1
positive regulation of filopodium formation -0.052 0.11 -9999 0 -0.26 117 117
alphaV/beta3 Integrin/Talin -0.053 0.11 -9999 0 -0.22 142 142
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.013 0.054 -9999 0 -0.15 43 43
nectin-2(dimer)/I-afadin/I-afadin 0.013 0.054 -9999 0 -0.15 43 43
PIP5K1C -0.046 0.1 -9999 0 -0.25 93 93
VAV2 -0.076 0.21 -9999 0 -0.44 126 126
RAP1/GDP -0.044 0.16 -9999 0 -0.33 117 117
ITGAV 0.013 0.032 -9999 0 -0.12 28 28
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.007 0.074 -9999 0 -0.12 128 128
nectin-3(dimer)/I-afadin/I-afadin -0.02 0.08 -9999 0 -0.12 200 200
Rac1/GTP -0.051 0.16 -9999 0 -0.34 127 127
PTPRM -0.056 0.11 -9999 0 -0.2 168 168
E-cadherin/beta catenin/alpha catenin 0.033 0.07 -9999 0 -0.18 25 25
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.023 0.002 -9999 0 -10000 0 0
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.007 0.041 -10000 0 -0.12 50 50
EPHB2 0.022 0.021 -10000 0 -0.12 11 11
EFNB1 0.023 0.018 -10000 0 -0.068 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.045 0.055 -10000 0 -0.15 11 11
Ephrin B2/EPHB1-2 0.011 0.062 -10000 0 -0.1 101 101
neuron projection morphogenesis 0.029 0.046 -10000 0 -0.15 11 11
Ephrin B1/EPHB1-2/Tiam1 0.04 0.056 -10000 0 -0.1 48 48
DNM1 0.022 0.019 -10000 0 -0.12 10 10
cell-cell signaling 0.002 0.004 -10000 0 -10000 0 0
MAP2K4 -0.12 0.21 -10000 0 -0.47 149 149
YES1 -0.19 0.31 -10000 0 -0.71 149 149
Ephrin B1/EPHB1-2/NCK2 0.051 0.043 -10000 0 -0.094 24 24
PI3K -0.13 0.22 -10000 0 -0.47 154 154
mol:GDP 0.038 0.055 -10000 0 -0.1 48 48
ITGA2B 0.023 0.006 -10000 0 -0.12 1 1
endothelial cell proliferation 0.001 0.058 -10000 0 -0.1 124 124
FYN -0.2 0.31 -10000 0 -0.71 149 149
MAP3K7 -0.13 0.22 -10000 0 -0.5 149 149
FGR -0.18 0.31 -10000 0 -0.69 149 149
TIAM1 0.015 0.032 -10000 0 -0.12 28 28
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
RGS3 0.023 0 -10000 0 -10000 0 0
cell adhesion -0.12 0.2 -10000 0 -0.43 159 159
LYN -0.2 0.31 -10000 0 -0.71 149 149
Ephrin B1/EPHB1-2/Src Family Kinases -0.18 0.28 -10000 0 -0.64 149 149
Ephrin B1/EPHB1-2 -0.15 0.24 -10000 0 -0.54 149 149
SRC -0.18 0.31 -10000 0 -0.69 149 149
ITGB3 0.004 0.047 -10000 0 -0.12 68 68
EPHB1 0.018 0.032 -10000 0 -0.12 28 28
EPHB4 0.022 0.009 -10000 0 -0.12 2 2
RAC1 0.023 0.002 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.001 0.058 -10000 0 -0.1 124 124
alphaIIb/beta3 Integrin 0.01 0.053 -10000 0 -0.096 107 107
BLK -0.18 0.31 -10000 0 -0.7 149 149
HCK -0.19 0.31 -10000 0 -0.7 149 149
regulation of stress fiber formation -0.049 0.042 0.093 24 -10000 0 24
MAPK8 -0.12 0.2 -10000 0 -0.44 151 151
Ephrin B1/EPHB1-2/RGS3 0.051 0.043 -10000 0 -0.094 24 24
endothelial cell migration -0.12 0.18 -10000 0 -0.41 152 152
NCK2 0.023 0.006 -10000 0 -0.12 1 1
PTPN13 -0.013 0.058 -10000 0 -0.13 112 112
regulation of focal adhesion formation -0.049 0.042 0.093 24 -10000 0 24
chemotaxis -0.049 0.042 0.093 24 -10000 0 24
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
Rac1/GTP 0.038 0.051 -10000 0 -0.15 11 11
angiogenesis -0.15 0.23 -10000 0 -0.53 149 149
LCK -0.18 0.31 -10000 0 -0.69 149 149
amb2 Integrin 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
alphaM/beta2 Integrin/proMMP-2 -0.03 0.083 -9999 0 -0.12 213 213
alphaM/beta2 Integrin/GPIbA 0.022 0.059 -9999 0 -0.11 77 77
alphaM/beta2 Integrin/proMMP-9 -0.005 0.081 -9999 0 -0.13 132 132
PLAUR 0.018 0.024 -9999 0 -0.12 15 15
HMGB1 0.023 0.008 -9999 0 -0.032 9 9
alphaM/beta2 Integrin/Talin 0.015 0.069 -9999 0 -0.12 98 98
AGER 0.022 0.017 -9999 0 -0.11 7 7
RAP1A 0.021 0.012 -9999 0 -0.12 3 3
SELPLG 0.02 0.021 -9999 0 -0.12 12 12
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.034 0.07 -9999 0 -0.15 22 22
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 0 0.05 -9999 0 -0.12 81 81
CYR61 0.002 0.047 -9999 0 -0.12 70 70
TLN1 0.021 0.012 -9999 0 -0.12 3 3
Rap1/GTP -0.099 0.15 -9999 0 -0.28 176 176
RHOA 0.023 0.006 -9999 0 -0.12 1 1
P-selectin oligomer 0.018 0.027 -9999 0 -0.12 21 21
MYH2 -0.12 0.15 -9999 0 -0.28 208 208
MST1R 0.017 0.029 -9999 0 -0.12 23 23
leukocyte activation during inflammatory response 0.027 0.052 -9999 0 -0.091 76 76
APOB 0.022 0.011 -9999 0 -0.12 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.015 0.059 -9999 0 -0.12 128 128
JAM3 0.02 0.02 -9999 0 -0.12 11 11
GP1BA 0.022 0.012 -9999 0 -0.12 4 4
alphaM/beta2 Integrin/CTGF 0.003 0.073 -9999 0 -0.12 119 119
alphaM/beta2 Integrin -0.12 0.16 -9999 0 -0.33 158 158
JAM3 homodimer 0.02 0.02 -9999 0 -0.12 11 11
ICAM2 0.017 0.029 -9999 0 -0.12 23 23
ICAM1 0 0.048 -9999 0 -0.12 74 74
phagocytosis triggered by activation of immune response cell surface activating receptor -0.12 0.16 -9999 0 -0.33 158 158
cell adhesion 0.021 0.059 -9999 0 -0.11 77 77
NFKB1 0.021 0.072 -9999 0 -0.21 27 27
THY1 -0.003 0.049 -9999 0 -0.12 79 79
RhoA/GDP 0.016 0.016 -9999 0 -0.14 6 6
Lipoprotein(a) 0.03 0.014 -9999 0 -0.12 1 1
alphaM/beta2 Integrin/LRP/tPA -0.016 0.087 -9999 0 -0.12 203 203
IL6 0.007 0.094 -9999 0 -0.3 23 23
ITGB2 0.013 0.032 -9999 0 -0.098 37 37
elevation of cytosolic calcium ion concentration -0.016 0.1 -9999 0 -0.15 154 154
alphaM/beta2 Integrin/JAM2/JAM3 0.027 0.063 -9999 0 -0.1 83 83
JAM2 0.014 0.035 -9999 0 -0.12 35 35
alphaM/beta2 Integrin/ICAM1 0.004 0.088 -9999 0 -0.12 148 148
alphaM/beta2 Integrin/uPA/Plg -0.006 0.088 -9999 0 -0.13 143 143
RhoA/GTP -0.13 0.16 -9999 0 -0.3 216 216
positive regulation of phagocytosis -0.078 0.14 -9999 0 -0.26 169 169
Ron/MSP 0.027 0.031 -9999 0 -0.088 36 36
alphaM/beta2 Integrin/uPAR/uPA -0.015 0.1 -9999 0 -0.15 154 154
alphaM/beta2 Integrin/uPAR 0.012 0.077 -9999 0 -0.14 95 95
PLAU -0.007 0.055 -9999 0 -0.12 102 102
PLAT -0.001 0.049 -9999 0 -0.12 76 76
actin filament polymerization -0.12 0.14 -9999 0 -0.27 208 208
MST1 0.022 0.012 -9999 0 -0.12 4 4
alphaM/beta2 Integrin/lipoprotein(a) 0.031 0.054 -9999 0 -0.092 76 76
TNF 0.015 0.076 -9999 0 -0.26 16 16
RAP1B 0.019 0.02 -9999 0 -0.12 10 10
alphaM/beta2 Integrin/uPA -0.02 0.091 -9999 0 -0.14 168 168
fibrinolysis -0.007 0.086 -9999 0 -0.13 143 143
HCK 0.019 0.024 -9999 0 -0.12 15 15
dendritic cell antigen processing and presentation -0.12 0.16 -9999 0 -0.33 158 158
VTN 0.023 0.009 -9999 0 -0.12 2 2
alphaM/beta2 Integrin/CYR61 -0.01 0.08 -9999 0 -0.12 173 173
LPA 0.021 0.019 -9999 0 -0.12 10 10
LRP1 0.014 0.032 -9999 0 -0.12 29 29
cell migration -0.044 0.086 -9999 0 -0.13 235 235
FN1 -0.013 0.056 -9999 0 -0.12 114 114
alphaM/beta2 Integrin/Thy1 -0.026 0.085 -9999 0 -0.13 197 197
MPO 0.023 0.009 -9999 0 -0.12 2 2
KNG1 0.022 0.011 -9999 0 -0.12 3 3
RAP1/GDP 0.015 0.05 -9999 0 -0.12 61 61
ROCK1 -0.12 0.15 -9999 0 -0.28 208 208
ELA2 0.022 0.011 -9999 0 -0.12 3 3
PLG 0.023 0.009 -9999 0 -0.12 2 2
CTGF 0.012 0.036 -9999 0 -0.12 37 37
alphaM/beta2 Integrin/Hck 0.017 0.07 -9999 0 -0.13 89 89
ITGAM 0.021 0.019 -9999 0 -0.073 17 17
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.03 0.066 -9999 0 -0.11 81 81
HP -0.035 0.063 -9999 0 -0.12 193 193
leukocyte adhesion -0.009 0.088 -9999 0 -0.17 71 71
SELP 0.018 0.028 -9999 0 -0.12 21 21
TCGA08_p53

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
CDKN2A 0.007 0.013 -10000 0 -0.077 12 12
TP53 -0.051 0.11 0.18 14 -0.24 126 140
Senescence -0.069 0.12 0.18 14 -0.26 157 171
Apoptosis -0.069 0.12 0.18 14 -0.26 157 171
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.002 0.011 0.057 11 -0.084 4 15
MDM4 0.019 0.023 -10000 0 -0.12 14 14
Cellular roles of Anthrax toxin

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
ANTXR1 0.007 0.043 -10000 0 -0.12 54 54
ANTXR2 0.013 0.036 -10000 0 -0.12 36 36
negative regulation of myeloid dendritic cell antigen processing and presentation -0.007 0.013 -10000 0 -0.034 102 102
monocyte activation -0.1 0.16 -10000 0 -0.35 156 156
MAP2K2 0.006 0.052 -10000 0 -0.66 3 3
MAP2K1 0 0.015 -10000 0 -0.031 80 80
MAP2K7 0 0.014 -10000 0 -0.048 17 17
MAP2K6 -0.005 0.024 -10000 0 -0.045 109 109
CYAA -0.016 0.048 -10000 0 -0.11 102 102
MAP2K4 -0.001 0.016 -10000 0 -0.029 105 105
IL1B -0.009 0.035 -10000 0 -0.073 94 94
Channel -0.003 0.06 -10000 0 -0.098 144 144
NLRP1 -0.001 0.015 -10000 0 -0.053 20 20
CALM1 0.022 0.014 -10000 0 -0.12 5 5
negative regulation of phagocytosis 0.001 0.054 -10000 0 -0.46 7 7
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.007 0.013 0.034 102 -10000 0 102
MAPK3 -0.001 0.015 -10000 0 -0.031 83 83
MAPK1 -0.001 0.019 -10000 0 -0.036 85 85
PGR -0.011 0.027 -10000 0 -0.044 195 195
PA/Cellular Receptors -0.004 0.066 -10000 0 -0.11 144 144
apoptosis -0.007 0.013 -10000 0 -0.034 102 102
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.002 0.058 -10000 0 -0.12 102 102
macrophage activation 0.003 0.018 -10000 0 -0.053 29 29
TNF 0.02 0.02 -10000 0 -0.12 11 11
VCAM1 -0.1 0.16 -10000 0 -0.36 156 156
platelet activation 0.001 0.054 -10000 0 -0.46 7 7
MAPKKK cascade 0.003 0.02 0.048 52 -10000 0 52
IL18 -0.011 0.039 -10000 0 -0.076 110 110
negative regulation of macrophage activation -0.007 0.013 -10000 0 -0.034 102 102
LEF -0.007 0.013 -10000 0 -0.034 102 102
CASP1 -0.005 0.024 -10000 0 -0.043 106 106
mol:cAMP 0.001 0.055 -10000 0 -0.46 7 7
necrosis -0.007 0.013 -10000 0 -0.034 102 102
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.001 0.056 -10000 0 -0.091 144 144
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.11 0.2 -10000 0 -0.37 177 177
Syndecan-4/Syndesmos -0.08 0.18 -10000 0 -0.4 102 102
positive regulation of JNK cascade -0.1 0.18 -10000 0 -0.37 128 128
Syndecan-4/ADAM12 -0.094 0.18 -10000 0 -0.39 111 111
CCL5 0.005 0.044 -10000 0 -0.12 60 60
Rac1/GDP 0.016 0.015 -10000 0 -0.15 5 5
DNM2 0.02 0.022 -10000 0 -0.12 13 13
ITGA5 0.013 0.036 -10000 0 -0.12 38 38
SDCBP 0.021 0.01 -10000 0 -0.12 2 2
PLG 0.027 0.011 0.068 1 -0.1 2 3
ADAM12 -0.01 0.06 -10000 0 -0.12 127 127
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.021 0.019 -10000 0 -0.12 10 10
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.008 0.009 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.088 0.18 -10000 0 -0.4 106 106
Syndecan-4/CXCL12/CXCR4 -0.11 0.19 -10000 0 -0.39 128 128
Syndecan-4/Laminin alpha3 -0.094 0.18 -10000 0 -0.41 110 110
MDK 0.021 0.014 -10000 0 -0.12 5 5
Syndecan-4/FZD7 -0.086 0.18 -10000 0 -0.4 105 105
Syndecan-4/Midkine -0.081 0.18 -10000 0 -0.4 105 105
FZD7 0.015 0.031 -10000 0 -0.12 27 27
Syndecan-4/FGFR1/FGF -0.068 0.17 -10000 0 -0.38 103 103
THBS1 -0.004 0.053 -10000 0 -0.12 92 92
integrin-mediated signaling pathway -0.098 0.18 -10000 0 -0.36 138 138
positive regulation of MAPKKK cascade -0.1 0.18 -10000 0 -0.37 128 128
Syndecan-4/TACI -0.079 0.18 -10000 0 -0.4 102 102
CXCR4 0.012 0.032 -10000 0 -0.12 29 29
cell adhesion -0.054 0.096 -10000 0 -0.19 165 165
Syndecan-4/Dynamin -0.081 0.18 -10000 0 -0.41 102 102
Syndecan-4/TSP1 -0.1 0.18 -10000 0 -0.35 151 151
Syndecan-4/GIPC -0.081 0.18 -10000 0 -0.4 102 102
Syndecan-4/RANTES -0.096 0.19 -10000 0 -0.38 133 133
ITGB1 0.021 0.015 -10000 0 -0.12 6 6
LAMA1 0 0.053 -10000 0 -0.12 89 89
LAMA3 0.006 0.043 -10000 0 -0.12 55 55
RAC1 0.023 0.002 -10000 0 -10000 0 0
PRKCA 0.001 0.052 0.08 3 -0.16 40 43
Syndecan-4/alpha-Actinin -0.082 0.18 -10000 0 -0.4 108 108
TFPI 0.018 0.026 -10000 0 -0.12 19 19
F2 0.02 0.016 -10000 0 -0.12 4 4
alpha5/beta1 Integrin 0.016 0.048 -10000 0 -0.1 76 76
positive regulation of cell adhesion -0.097 0.18 -10000 0 -0.4 113 113
ACTN1 0.022 0.011 -10000 0 -0.12 3 3
TNC -0.004 0.053 -10000 0 -0.12 93 93
Syndecan-4/CXCL12 -0.1 0.19 -10000 0 -0.37 141 141
FGF6 0.022 0.012 -10000 0 -0.12 4 4
RHOA 0.023 0.006 -10000 0 -0.12 1 1
CXCL12 -0.003 0.051 -10000 0 -0.12 86 86
TNFRSF13B 0.023 0 -10000 0 -10000 0 0
FGF2 0.023 0.009 -10000 0 -0.12 2 2
FGFR1 0.008 0.043 -10000 0 -0.12 54 54
Syndecan-4/PI-4-5-P2 -0.089 0.17 -10000 0 -0.4 102 102
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.012 0.056 -10000 0 -0.12 114 114
cell migration -0.005 0.005 -10000 0 -10000 0 0
PRKCD 0.023 0.019 -10000 0 -0.12 8 8
vasculogenesis -0.099 0.18 -10000 0 -0.34 151 151
SDC4 -0.09 0.18 -10000 0 -0.43 102 102
Syndecan-4/Tenascin C -0.1 0.18 -10000 0 -0.37 138 138
Syndecan-4/PI-4-5-P2/PKC alpha -0.006 0.007 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.085 0.18 -10000 0 -0.38 118 118
MMP9 0.001 0.051 -10000 0 -0.12 81 81
Rac1/GTP -0.054 0.098 -10000 0 -0.19 162 162
cytoskeleton organization -0.077 0.17 -10000 0 -0.39 102 102
GIPC1 0.019 0.023 -10000 0 -0.12 15 15
Syndecan-4/TFPI -0.081 0.18 -10000 0 -0.4 102 102
Thromboxane A2 receptor 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
TGM2 0.005 0.046 -10000 0 -0.12 65 65
GNB1/GNG2 -0.069 0.081 -10000 0 -0.18 194 194
AKT1 -0.055 0.11 -10000 0 -0.19 195 195
EGF 0.02 0.021 -10000 0 -0.12 12 12
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.026 0.029 -10000 0 -0.12 5 5
mol:Ca2+ -0.096 0.15 -10000 0 -0.29 196 196
LYN 0.024 0.031 -10000 0 -0.13 7 7
RhoA/GTP -0.036 0.069 -10000 0 -0.12 198 198
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.12 0.17 -10000 0 -0.34 196 196
GNG2 0.02 0.018 -10000 0 -0.12 9 9
ARRB2 0.022 0.014 -10000 0 -0.12 5 5
TP alpha/Gq family/GDP/G beta5/gamma2 0.028 0.047 -10000 0 -0.24 12 12
G beta5/gamma2 -0.091 0.11 -10000 0 -0.23 194 194
PRKCH -0.12 0.18 -10000 0 -0.35 196 196
DNM1 0.021 0.019 -10000 0 -0.12 10 10
TXA2/TP beta/beta Arrestin3 0.017 0.014 -10000 0 -10000 0 0
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
PTGDR 0.023 0.006 -10000 0 -0.12 1 1
G12 family/GTP -0.12 0.13 -10000 0 -0.29 197 197
ADRBK1 0.023 0.001 -10000 0 -10000 0 0
ADRBK2 0.015 0.032 -10000 0 -0.12 28 28
RhoA/GTP/ROCK1 0.027 0.021 -10000 0 -0.12 11 11
mol:GDP 0.05 0.12 0.26 65 -10000 0 65
mol:NADP 0.023 0 -10000 0 -10000 0 0
RAB11A 0.023 0.007 -10000 0 -0.12 1 1
PRKG1 0.018 0.026 -10000 0 -0.12 19 19
mol:IP3 -0.12 0.19 -10000 0 -0.36 196 196
cell morphogenesis 0.027 0.021 -10000 0 -0.12 11 11
PLCB2 -0.17 0.25 -10000 0 -0.49 196 196
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.026 0.029 -10000 0 -0.12 6 6
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.024 0.032 -10000 0 -0.15 6 6
RHOA 0.023 0.006 -10000 0 -0.12 1 1
PTGIR 0.023 0.002 -10000 0 -10000 0 0
PRKCB1 -0.13 0.19 -10000 0 -0.37 196 196
GNAQ 0.021 0.016 -10000 0 -0.12 6 6
mol:L-citrulline 0.023 0 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.18 0.26 -10000 0 -0.51 195 195
LCK 0.026 0.029 -10000 0 -0.11 5 5
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.042 0.026 -10000 0 -0.12 8 8
TXA2-R family/G12 family/GDP/G beta/gamma 0.028 0.061 -10000 0 -0.43 8 8
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.041 0.028 -10000 0 -0.16 2 2
MAPK14 -0.073 0.12 -10000 0 -0.22 197 197
TGM2/GTP -0.14 0.21 -10000 0 -0.4 203 203
MAPK11 -0.072 0.12 -10000 0 -0.22 196 196
ARHGEF1 -0.053 0.094 -10000 0 -0.17 197 197
GNAI2 0.022 0.011 -10000 0 -0.12 3 3
JNK cascade -0.13 0.19 -10000 0 -0.38 196 196
RAB11/GDP 0.023 0.007 -10000 0 -0.12 1 1
ICAM1 -0.11 0.16 -10000 0 -0.32 196 196
cAMP biosynthetic process -0.11 0.17 -10000 0 -0.33 200 200
Gq family/GTP/EBP50 0.017 0.042 -10000 0 -0.13 31 31
actin cytoskeleton reorganization 0.027 0.021 -10000 0 -0.12 11 11
SRC 0.026 0.029 -10000 0 -0.12 4 4
GNB5 0.023 0.009 -10000 0 -0.12 2 2
GNB1 0.023 0.007 -10000 0 -0.12 1 1
EGF/EGFR 0.018 0.057 -10000 0 -0.13 38 38
VCAM1 -0.12 0.17 -10000 0 -0.34 196 196
TP beta/Gq family/GDP/G beta5/gamma2 0.028 0.047 -10000 0 -0.24 12 12
platelet activation -0.094 0.16 -10000 0 -0.29 196 196
PGI2/IP 0.015 0.017 -10000 0 -0.15 6 6
PRKACA 0.021 0.023 -10000 0 -0.15 8 8
Gq family/GDP/G beta5/gamma2 0.027 0.046 -10000 0 -0.22 12 12
TXA2/TP beta/beta Arrestin2 0.016 0.033 -10000 0 -0.26 5 5
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.021 0.021 -10000 0 -0.14 8 8
mol:DAG -0.14 0.21 -10000 0 -0.41 196 196
EGFR 0.015 0.03 -10000 0 -0.12 25 25
TXA2/TP alpha -0.15 0.23 -10000 0 -0.45 199 199
Gq family/GTP 0.014 0.037 -10000 0 -0.14 25 25
YES1 0.024 0.032 -10000 0 -0.14 8 8
GNAI2/GTP 0.02 0.029 -10000 0 -0.12 6 6
PGD2/DP 0.017 0.004 -10000 0 -0.078 1 1
SLC9A3R1 0.016 0.031 -10000 0 -0.12 26 26
FYN 0.02 0.035 -10000 0 -0.14 12 12
mol:NO 0.023 0 -10000 0 -10000 0 0
GNA15 0.021 0.017 -10000 0 -0.12 8 8
PGK/cGMP 0.028 0.016 -10000 0 -0.057 19 19
RhoA/GDP 0.023 0.006 -10000 0 -0.12 1 1
TP alpha/TGM2/GDP/G beta/gamma 0.04 0.045 -10000 0 -0.15 7 7
NOS3 0.023 0 -10000 0 -10000 0 0
RAC1 0.023 0.002 -10000 0 -10000 0 0
PRKCA -0.12 0.18 -10000 0 -0.35 197 197
PRKCB -0.12 0.18 -10000 0 -0.34 196 196
PRKCE -0.12 0.18 -10000 0 -0.35 196 196
PRKCD -0.13 0.19 -10000 0 -0.37 196 196
PRKCG -0.13 0.19 -10000 0 -0.37 196 196
muscle contraction -0.16 0.24 -10000 0 -0.47 196 196
PRKCZ -0.11 0.17 -10000 0 -0.33 196 196
ARR3 0.023 0.006 -10000 0 -0.12 1 1
TXA2/TP beta 0.033 0.035 -10000 0 -0.13 7 7
PRKCQ -0.12 0.18 -10000 0 -0.35 197 197
MAPKKK cascade -0.15 0.22 -10000 0 -0.43 196 196
SELE -0.094 0.15 -10000 0 -0.28 194 194
TP beta/GNAI2/GDP/G beta/gamma 0.052 0.035 -10000 0 -0.2 2 2
ROCK1 0.022 0.009 -10000 0 -0.12 2 2
GNA14 0.02 0.02 -10000 0 -0.12 11 11
chemotaxis -0.21 0.3 -10000 0 -0.6 194 194
GNA12 0.023 0.001 -10000 0 -10000 0 0
GNA13 0.022 0.009 -10000 0 -0.12 2 2
GNA11 0.022 0.014 -10000 0 -0.12 5 5
Rac1/GTP 0.015 0.015 -10000 0 -0.15 5 5
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 -0.002 0.05 -9999 0 -0.12 81 81
PLK4 0.016 0.028 -9999 0 -0.12 22 22
regulation of centriole replication -0.002 0.047 -9999 0 -0.091 101 101
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.02 0.019 -9999 0 -0.12 10 10
LAT2 -0.033 0.11 -9999 0 -0.2 133 133
AP1 -0.068 0.18 -9999 0 -0.36 119 119
mol:PIP3 -0.037 0.14 -9999 0 -0.29 99 99
IKBKB -0.014 0.082 -9999 0 -0.17 99 99
AKT1 -0.025 0.071 -9999 0 -0.14 109 109
IKBKG -0.013 0.082 -9999 0 -0.16 99 99
MS4A2 0.026 0.014 -9999 0 -0.13 3 3
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
MAP3K1 -0.038 0.13 -9999 0 -0.29 92 92
mol:Ca2+ -0.026 0.11 -9999 0 -0.23 99 99
LYN 0.02 0.014 -9999 0 -0.12 4 4
CBLB -0.032 0.1 -9999 0 -0.2 127 127
SHC1 0.023 0.001 -9999 0 -10000 0 0
RasGAP/p62DOK -0.005 0.065 -9999 0 -0.1 132 132
positive regulation of cell migration 0.011 0.01 -9999 0 -0.077 7 7
INPP5D 0 0 -9999 0 -10000 0 0
PLD2 -0.008 0.051 -9999 0 -0.1 69 69
PTPN13 -0.088 0.2 -9999 0 -0.44 95 95
PTPN11 0.021 0.013 -9999 0 -0.12 3 3
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.035 0.11 -9999 0 -0.23 89 89
SYK 0.016 0.028 -9999 0 -0.12 20 20
GRB2 0.023 0.006 -9999 0 -0.12 1 1
LAT/PLCgamma1/GRB2/SLP76/GADs -0.062 0.12 -9999 0 -0.29 102 102
LAT -0.032 0.1 -9999 0 -0.2 131 131
PAK2 -0.043 0.14 -9999 0 -0.31 95 95
NFATC2 -0.003 0.061 -9999 0 -0.42 10 10
HRAS -0.047 0.15 -9999 0 -0.31 105 105
GAB2 0.007 0.041 -9999 0 -0.12 50 50
PLA2G1B 0.017 0.11 -9999 0 -0.92 8 8
Fc epsilon R1 0.003 0.062 -9999 0 -0.095 128 128
Antigen/IgE/Fc epsilon R1 0.006 0.055 -9999 0 -0.079 129 129
mol:GDP -0.057 0.17 -9999 0 -0.32 131 131
JUN 0.014 0.033 -9999 0 -0.12 30 30
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.015 0.031 -9999 0 -0.12 27 27
FOS -0.005 0.053 -9999 0 -0.12 95 95
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.037 0.11 -9999 0 -0.21 134 134
CHUK -0.017 0.085 -9999 0 -0.18 98 98
KLRG1 -0.015 0.088 -9999 0 -0.21 76 76
VAV1 -0.034 0.11 -9999 0 -0.21 127 127
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.032 0.1 -9999 0 -0.2 133 133
negative regulation of mast cell degranulation -0.026 0.086 -9999 0 -0.2 71 71
BTK -0.064 0.19 -9999 0 -0.42 91 91
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.035 0.1 -9999 0 -0.2 129 129
GAB2/PI3K/SHP2 -0.046 0.06 -9999 0 -0.14 115 115
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP 0.002 0.073 -9999 0 -0.23 40 40
RAF1 0.011 0.12 -9999 0 -0.99 8 8
Fc epsilon R1/FcgammaRIIB/SHIP -0.008 0.083 -9999 0 -0.13 146 146
FCER1G 0.002 0.044 -9999 0 -0.12 62 62
FCER1A 0.018 0.028 -9999 0 -0.12 20 20
Antigen/IgE/Fc epsilon R1/Fyn 0.002 0.066 -9999 0 -0.11 75 75
MAPK3 0.015 0.12 -9999 0 -0.93 8 8
MAPK1 0.014 0.12 -9999 0 -0.93 8 8
NFKB1 0.021 0.013 -9999 0 -0.12 4 4
MAPK8 -0.007 0.13 -9999 0 -0.53 26 26
DUSP1 -0.004 0.052 -9999 0 -0.12 90 90
NF-kappa-B/RelA -0.005 0.061 -9999 0 -0.12 92 92
actin cytoskeleton reorganization -0.066 0.2 -9999 0 -0.5 67 67
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.037 0.14 -9999 0 -0.3 95 95
FER -0.032 0.1 -9999 0 -0.2 130 130
RELA 0.023 0.009 -9999 0 -0.12 2 2
ITK -0.004 0.05 -9999 0 -0.32 8 8
SOS1 0.017 0.027 -9999 0 -0.12 20 20
PLCG1 -0.054 0.16 -9999 0 -0.3 133 133
cytokine secretion -0.005 0.044 -9999 0 -0.09 92 92
SPHK1 -0.033 0.1 -9999 0 -0.2 132 132
PTK2 -0.07 0.21 -9999 0 -0.53 67 67
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.062 0.13 -9999 0 -0.27 130 130
EDG1 0.011 0.01 -9999 0 -0.077 7 7
mol:DAG -0.035 0.14 -9999 0 -0.29 100 100
MAP2K2 0.01 0.12 -9999 0 -0.94 8 8
MAP2K1 0.013 0.11 -9999 0 -0.93 8 8
MAP2K7 0.022 0.012 -9999 0 -0.12 4 4
KLRG1/SHP2 -0.014 0.084 -9999 0 -0.21 63 63
MAP2K4 0.012 0.12 -9999 0 -0.84 11 11
Fc epsilon R1/FcgammaRIIB -0.009 0.09 -9999 0 -0.14 146 146
mol:Choline -0.008 0.05 -9999 0 -0.1 69 69
SHC/Grb2/SOS1 -0.011 0.12 -9999 0 -0.24 74 74
FYN 0.011 0.037 -9999 0 -0.12 40 40
DOK1 0.021 0.016 -9999 0 -0.12 7 7
PXN -0.06 0.19 -9999 0 -0.49 67 67
HCLS1 -0.035 0.12 -9999 0 -0.23 113 113
PRKCB -0.026 0.11 -9999 0 -0.2 125 125
FCGR2B 0.004 0.044 -9999 0 -0.12 60 60
IGHE -0.001 0.003 -9999 0 -10000 0 0
KLRG1/SHIP -0.027 0.087 -9999 0 -0.21 70 70
LCP2 0.013 0.033 -9999 0 -0.12 31 31
PLA2G4A -0.045 0.11 -9999 0 -0.22 131 131
RASA1 0.021 0.012 -9999 0 -0.12 3 3
mol:Phosphatidic acid -0.008 0.05 -9999 0 -0.1 69 69
IKK complex -0.006 0.068 -9999 0 -0.14 87 87
WIPF1 0.02 0.02 -9999 0 -0.12 11 11
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.01 0.009 -10000 0 -0.078 6 6
GNB1/GNG2 0.012 0.058 -10000 0 -0.1 94 94
regulation of S phase of mitotic cell cycle -0.018 0.085 -10000 0 -0.16 130 130
GNAO1 0.01 0.042 -10000 0 -0.12 51 51
HRAS 0.022 0.006 -10000 0 -0.12 1 1
SHBG/T-DHT 0.015 0.005 -10000 0 -0.062 2 2
PELP1 0.022 0.009 -10000 0 -0.12 2 2
AKT1 0.01 0.012 -10000 0 -0.077 10 10
MAP2K1 -0.013 0.061 -10000 0 -0.12 109 109
T-DHT/AR -0.013 0.059 -10000 0 -0.12 120 120
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.003 -10000 0 -0.007 103 103
GNAI2 0.022 0.011 -10000 0 -0.12 3 3
GNAI3 0.021 0.008 -10000 0 -0.12 1 1
GNAI1 0.012 0.035 -10000 0 -0.12 35 35
mol:GDP -0.047 0.096 -10000 0 -0.25 92 92
cell proliferation -0.063 0.16 -10000 0 -0.37 108 108
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
FOS -0.13 0.29 -10000 0 -0.7 107 107
mol:Ca2+ -0.008 0.022 -10000 0 -0.045 108 108
MAPK3 -0.042 0.11 -10000 0 -0.25 110 110
MAPK1 -0.032 0.1 -10000 0 -0.21 108 108
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
mol:IP3 -0.001 0.002 -10000 0 -0.003 172 172
cAMP biosynthetic process 0.01 0.015 0.058 17 -10000 0 17
GNG2 0.02 0.018 -10000 0 -0.12 9 9
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.003 172 172
HRAS/GTP 0.006 0.054 -10000 0 -0.092 86 86
actin cytoskeleton reorganization 0.016 0.047 -10000 0 -0.099 66 66
SRC 0.022 0.009 -10000 0 -0.13 2 2
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.003 172 172
PI3K 0.008 0.055 -10000 0 -0.1 96 96
apoptosis 0.066 0.17 0.38 113 -10000 0 113
T-DHT/AR/PELP1 0.002 0.053 -10000 0 -0.11 83 83
HRAS/GDP -0.027 0.1 -10000 0 -0.24 92 92
CREB1 -0.072 0.18 -10000 0 -0.4 113 113
RAC1-CDC42/GTP 0.023 0.051 -10000 0 -0.1 66 66
AR 0.008 0.039 -10000 0 -0.12 43 43
GNB1 0.023 0.007 -10000 0 -0.12 1 1
RAF1 -0.008 0.053 -10000 0 -0.13 32 32
RAC1-CDC42/GDP -0.014 0.1 -10000 0 -0.22 94 94
T-DHT/AR/PELP1/Src 0.014 0.053 -10000 0 -0.1 77 77
MAP2K2 -0.015 0.062 -10000 0 -0.12 113 113
T-DHT/AR/PELP1/Src/PI3K -0.018 0.086 -10000 0 -0.16 130 130
GNAZ 0.022 0.011 -10000 0 -0.12 3 3
SHBG 0.023 0.009 -10000 0 -0.12 2 2
Gi family/GNB1/GNG2/GDP 0.002 0.076 -10000 0 -0.26 26 26
mol:T-DHT -0.001 0.001 -10000 0 -0.003 85 85
RAC1 0.023 0.002 -10000 0 -10000 0 0
GNRH1 0.011 0.009 -10000 0 -0.077 6 6
Gi family/GTP -0.018 0.07 -10000 0 -0.15 95 95
CDC42 0.023 0.002 -10000 0 -10000 0 0
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.014 0.022 -10000 0 -0.14 11 11
PRKCZ 0.023 0 -10000 0 -10000 0 0
MAP3K7IP2 0.02 0.016 -10000 0 -0.12 6 6
ERC1 0.016 0.029 -10000 0 -0.12 24 24
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.063 0.15 -10000 0 -0.29 127 127
IRAK/TOLLIP 0.028 0.026 -10000 0 -0.1 15 15
IKBKB 0.022 0.015 -10000 0 -0.12 6 6
IKBKG 0.023 0.009 -10000 0 -0.12 2 2
IL1 alpha/IL1R2 0.014 0.048 -10000 0 -0.089 96 96
IL1A 0.017 0.029 -10000 0 -0.12 24 24
IL1B 0.002 0.039 -10000 0 -0.085 82 82
IRAK/TRAF6/p62/Atypical PKCs 0.036 0.059 -10000 0 -0.16 16 16
IL1R2 0.007 0.045 -10000 0 -0.12 62 62
IL1R1 0.003 0.046 -10000 0 -0.12 66 66
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.063 0.15 0.16 1 -0.28 137 138
TOLLIP 0.022 0.011 -10000 0 -0.12 3 3
TICAM2 0.021 0.014 -10000 0 -0.12 5 5
MAP3K3 0.023 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.033 0.051 -10000 0 -0.14 37 37
IKK complex/ELKS 0.024 0.092 -10000 0 -0.24 51 51
JUN 0.011 0.048 -10000 0 -0.16 29 29
MAP3K7 0.021 0.014 -10000 0 -0.12 5 5
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.051 0.12 -10000 0 -0.21 142 142
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.001 0.077 -10000 0 -0.11 134 134
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.003 0.087 -10000 0 -0.12 162 162
IL1 beta fragment/IL1R1/IL1RAP -0.056 0.1 -10000 0 -0.15 243 243
NFKB1 0.021 0.013 -10000 0 -0.12 4 4
MAPK8 0.013 0.051 -10000 0 -0.17 30 30
IRAK1 0.016 0.023 -10000 0 -0.087 23 23
IL1RN/IL1R1 -0.007 0.07 -10000 0 -0.11 159 159
IRAK4 0.019 0.02 -10000 0 -0.12 10 10
PRKCI 0.016 0.028 -10000 0 -0.12 22 22
TRAF6 0.022 0.009 -10000 0 -0.12 2 2
PI3K 0.007 0.065 -10000 0 -0.13 96 96
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.074 0.15 -10000 0 -0.3 137 137
CHUK 0.021 0.013 -10000 0 -0.12 4 4
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.056 0.1 -10000 0 -0.15 243 243
IL1 beta/IL1R2 -0.036 0.089 -10000 0 -0.15 181 181
IRAK/TRAF6/TAK1/TAB1/TAB2 0.045 0.057 -10000 0 -0.19 18 18
NF kappa B1 p50/RelA -0.05 0.11 -10000 0 -0.2 149 149
IRAK3 0.009 0.042 -10000 0 -0.12 52 52
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.05 0.12 -10000 0 -0.22 129 129
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.03 0.11 -10000 0 -0.18 154 154
IL1 alpha/IL1R1/IL1RAP -0.014 0.078 -10000 0 -0.13 131 131
RELA 0.023 0.009 -10000 0 -0.12 2 2
MAP3K7IP1 0.023 0 -10000 0 -10000 0 0
SQSTM1 0.021 0.014 -10000 0 -0.12 5 5
MYD88 0.023 0.006 -10000 0 -0.12 1 1
IRAK/TRAF6/MEKK3 0.039 0.031 -10000 0 -0.095 23 23
IL1RAP 0.009 0.039 -10000 0 -0.12 44 44
UBE2N 0.023 0.007 -10000 0 -0.12 1 1
IRAK/TRAF6 -0.046 0.098 -10000 0 -0.19 140 140
CASP1 0.006 0.04 -10000 0 -0.12 48 48
IL1RN/IL1R2 0.011 0.053 -10000 0 -0.094 105 105
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.045 0.1 -10000 0 -0.14 243 243
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.037 0.13 -10000 0 -0.27 106 106
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
IL1RN 0.019 0.024 -10000 0 -0.12 16 16
TRAF6/TAK1/TAB1/TAB2 0.041 0.054 -10000 0 -0.12 46 46
MAP2K6 0.014 0.051 -10000 0 -0.18 27 27
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.016 0.052 -10000 0 -0.12 70 70
ATM 0.018 0.022 -10000 0 -0.12 13 13
UBE2D3 0.023 0.001 -10000 0 -10000 0 0
PRKDC 0.021 0.015 -10000 0 -0.12 6 6
ATR 0.02 0.015 -10000 0 -0.12 5 5
UBE2L3 0.022 0.012 -10000 0 -0.12 4 4
FANCD2 -0.008 0.096 -10000 0 -0.24 69 69
protein ubiquitination -0.016 0.086 -10000 0 -0.11 211 211
XRCC5 0.021 0.01 -10000 0 -0.12 2 2
XRCC6 0.022 0.004 -10000 0 -10000 0 0
M/R/N Complex 0.023 0.065 -10000 0 -0.14 64 64
MRE11A 0.02 0.017 -10000 0 -0.12 7 7
DNA-PK 0.026 0.06 -10000 0 -0.14 60 60
FA complex/FANCD2/Ubiquitin 0.01 0.093 -10000 0 -0.32 27 27
FANCF 0.022 0.011 -10000 0 -0.12 3 3
BRCA1 0.015 0.03 -10000 0 -0.12 24 24
CCNE1 0.002 0.047 -10000 0 -0.12 70 70
CDK2/Cyclin E1 -0.016 0.075 -10000 0 -0.12 190 190
FANCG 0.021 0.016 -10000 0 -0.12 7 7
BRCA1/BACH1/BARD1 -0.001 0.071 -10000 0 -0.13 125 125
FANCE 0.023 0 -10000 0 -10000 0 0
FANCC 0.022 0.014 -10000 0 -0.12 5 5
NBN 0.02 0.015 -10000 0 -0.12 5 5
FANCA 0.021 0.019 -10000 0 -0.12 10 10
DNA repair -0.014 0.11 -10000 0 -0.3 47 47
BRCA1/BARD1/ubiquitin -0.001 0.071 -10000 0 -0.13 125 125
BARD1/DNA-PK 0.027 0.076 -10000 0 -0.14 80 80
FANCL 0.018 0.023 -10000 0 -0.12 14 14
mRNA polyadenylation -0.015 0.052 0.12 70 -10000 0 70
BRCA1/BARD1/CTIP/M/R/N Complex -0.035 0.14 -10000 0 -0.27 99 99
BRCA1/BACH1/BARD1/TopBP1 0.008 0.072 -10000 0 -0.13 104 104
BRCA1/BARD1/P53 -0.026 0.092 -10000 0 -0.12 252 252
BARD1/CSTF1/BRCA1 0.013 0.065 -10000 0 -0.12 94 94
BRCA1/BACH1 0.015 0.03 -10000 0 -0.12 24 24
BARD1 0.016 0.029 -10000 0 -0.12 23 23
PCNA 0.019 0.018 -10000 0 -0.12 8 8
BRCA1/BARD1/UbcH5C 0.015 0.063 -10000 0 -0.12 88 88
BRCA1/BARD1/UbcH7 0.013 0.065 -10000 0 -0.12 93 93
BRCA1/BARD1/RAD51/PCNA 0 0.085 -10000 0 -0.12 155 155
BARD1/DNA-PK/P53 -0.008 0.096 -10000 0 -0.2 59 59
BRCA1/BARD1/Ubiquitin -0.001 0.071 -10000 0 -0.13 125 125
BRCA1/BARD1/CTIP -0.011 0.083 -10000 0 -0.13 157 157
FA complex 0.018 0.074 -10000 0 -0.32 17 17
BARD1/EWS 0.018 0.049 -10000 0 -0.12 63 63
RBBP8 0.011 0.029 -10000 0 -0.077 47 47
TP53 0.011 0.029 -10000 0 -0.12 22 22
TOPBP1 0.021 0.016 -10000 0 -0.12 6 6
G1/S transition of mitotic cell cycle 0.027 0.091 0.12 252 -10000 0 252
BRCA1/BARD1 -0.013 0.09 -10000 0 -0.11 211 211
CSTF1 0.023 0.007 -10000 0 -0.12 1 1
BARD1/EWS-Fli1 0.002 0.045 -10000 0 -0.12 62 62
CDK2 0.018 0.023 -10000 0 -0.12 14 14
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.015 0.03 -10000 0 -0.12 25 25
RAD50 0.021 0.014 -10000 0 -0.12 5 5
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.001 0.071 -10000 0 -0.13 125 125
EWSR1 0.023 0.001 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.018 0.078 -10000 0 -0.12 192 192
CRKL -0.026 0.11 -10000 0 -0.33 33 33
mol:PIP3 -0.002 0.049 0.22 24 -10000 0 24
AKT1 0.004 0.039 0.17 23 -0.1 10 33
PTK2B 0.023 0.009 -10000 0 -0.12 2 2
RAPGEF1 -0.021 0.1 -10000 0 -0.32 31 31
RANBP10 0.023 0.009 -10000 0 -0.12 2 2
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
HGF/MET/SHIP2 -0.002 0.069 -10000 0 -0.11 122 122
MAP3K5 -0.014 0.1 -10000 0 -0.3 37 37
HGF/MET/CIN85/CBL/ENDOPHILINS 0.011 0.067 -10000 0 -0.097 126 126
AP1 -0.04 0.075 -10000 0 -0.14 166 166
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.023 0.001 -10000 0 -10000 0 0
apoptosis -0.17 0.32 -10000 0 -0.75 124 124
STAT3 (dimer) -0.022 0.099 -10000 0 -0.28 38 38
GAB1/CRKL/SHP2/PI3K -0.015 0.12 -10000 0 -0.29 57 57
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK -0.014 0.11 -10000 0 -0.31 33 33
PTPN11 0.022 0.011 -10000 0 -0.12 3 3
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.019 0.024 -10000 0 -0.12 16 16
PTEN 0.022 0.008 -10000 0 -0.12 1 1
ELK1 -0.021 0.058 0.25 12 -10000 0 12
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.016 0.082 -10000 0 -0.2 56 56
PAK1 0.002 0.042 0.16 22 -0.1 25 47
HGF/MET/RANBP10 0 0.067 -10000 0 -0.11 118 118
HRAS -0.084 0.21 -10000 0 -0.48 122 122
DOCK1 -0.026 0.11 -10000 0 -0.31 41 41
GAB1 -0.031 0.11 -10000 0 -0.34 35 35
CRK -0.026 0.11 -10000 0 -0.33 33 33
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.073 0.19 -10000 0 -0.42 122 122
JUN 0.014 0.033 -10000 0 -0.12 30 30
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.028 0.077 -10000 0 -0.16 123 123
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
cell morphogenesis -0.028 0.12 -10000 0 -0.27 68 68
GRB2/SHC -0.006 0.078 -10000 0 -0.14 128 128
FOS -0.005 0.053 -10000 0 -0.12 95 95
GLMN 0.004 0.013 0.076 7 -0.049 17 24
cell motility -0.021 0.058 0.25 12 -10000 0 12
HGF/MET/MUC20 -0.011 0.062 -10000 0 -0.092 196 196
cell migration -0.006 0.077 -10000 0 -0.14 128 128
GRB2 0.023 0.006 -10000 0 -0.12 1 1
CBL 0.023 0.006 -10000 0 -0.12 1 1
MET/RANBP10 -0.015 0.074 -10000 0 -0.12 187 187
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.02 0.092 -10000 0 -0.16 155 155
MET/MUC20 -0.028 0.068 -10000 0 -0.12 186 186
RAP1B -0.019 0.1 -10000 0 -0.3 35 35
RAP1A -0.019 0.1 -10000 0 -0.3 37 37
HGF/MET/RANBP9 -0.003 0.071 -10000 0 -0.12 126 126
RAF1 -0.077 0.2 -10000 0 -0.46 123 123
STAT3 -0.02 0.098 -10000 0 -0.16 148 148
cell proliferation -0.036 0.13 -10000 0 -0.26 125 125
RPS6KB1 -0.018 0.077 -10000 0 -0.26 37 37
MAPK3 -0.025 0.075 0.69 5 -10000 0 5
MAPK1 -0.021 0.092 0.7 8 -10000 0 8
RANBP9 0.021 0.014 -10000 0 -0.12 5 5
MAPK8 -0.015 0.12 -10000 0 -0.35 46 46
SRC -0.016 0.086 -10000 0 -0.25 30 30
PI3K -0.022 0.092 -10000 0 -0.16 132 132
MET/Glomulin -0.003 0.05 -10000 0 -0.097 95 95
SOS1 0.017 0.027 -10000 0 -0.12 20 20
MAP2K1 -0.068 0.19 -10000 0 -0.42 123 123
MET 0 0.047 -10000 0 -0.12 70 70
MAP4K1 -0.014 0.1 -10000 0 -0.33 28 28
PTK2 0.021 0.016 -10000 0 -0.12 6 6
MAP2K2 -0.07 0.19 -10000 0 -0.43 122 122
BAD 0.008 0.037 0.16 23 -0.1 7 30
MAP2K4 -0.011 0.097 -10000 0 -0.26 41 41
SHP2/GRB2/SOS1/GAB1 -0.029 0.12 -10000 0 -0.23 128 128
INPPL1 0.021 0.017 -10000 0 -0.12 8 8
PXN 0.022 0.014 -10000 0 -0.12 5 5
SH3KBP1 0.02 0.019 -10000 0 -0.12 10 10
HGS -0.022 0.071 -10000 0 -0.15 119 119
PLCgamma1/PKC 0.012 0.026 -10000 0 -0.1 26 26
HGF 0.02 0.023 -10000 0 -0.12 14 14
RASA1 0.021 0.012 -10000 0 -0.12 3 3
NCK1 0.02 0.019 -10000 0 -0.12 9 9
PTPRJ 0.02 0.019 -10000 0 -0.12 9 9
NCK/PLCgamma1 -0.014 0.085 -10000 0 -0.15 131 131
PDPK1 0.001 0.043 0.19 24 -0.11 9 33
HGF/MET/SHIP -0.011 0.062 -10000 0 -0.092 196 196
IL4-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
BCL2L1 -0.16 0.46 -10000 0 -1.1 84 84
STAT6 (cleaved dimer) -0.25 0.38 -10000 0 -0.96 100 100
IGHG1 -0.031 0.2 -10000 0 -0.43 31 31
IGHG3 -0.16 0.42 -10000 0 -0.95 90 90
AKT1 -0.12 0.34 -10000 0 -0.79 78 78
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.11 0.34 -10000 0 -0.88 66 66
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.13 0.37 -10000 0 -0.87 79 79
THY1 -0.33 0.62 -10000 0 -1.2 161 161
MYB 0.011 0.038 -10000 0 -0.12 41 41
HMGA1 0.012 0.037 -10000 0 -0.12 40 40
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.11 0.33 -10000 0 -0.7 89 89
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.13 0.37 -10000 0 -0.86 80 80
SP1 -0.002 0.049 -10000 0 -0.09 109 109
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.017 0.023 -10000 0 -0.088 3 3
STAT6 (dimer)/ETS1 -0.17 0.45 -10000 0 -0.98 95 95
SOCS1 -0.096 0.32 -10000 0 -0.66 86 86
SOCS3 -0.11 0.34 -10000 0 -0.92 52 52
FCER2 -0.099 0.33 -10000 0 -0.8 34 34
PARP14 0.014 0.032 -10000 0 -0.12 28 28
CCL17 -0.15 0.45 -10000 0 -1 80 80
GRB2 0.023 0.006 -10000 0 -0.12 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.078 0.27 -10000 0 -0.62 69 69
T cell proliferation -0.18 0.47 -10000 0 -1 97 97
IL4R/JAK1 -0.17 0.46 -10000 0 -1 93 93
EGR2 -0.15 0.45 -10000 0 -1 76 76
JAK2 0.014 0.05 -10000 0 -0.16 13 13
JAK3 0.023 0.016 -10000 0 -0.12 5 5
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
JAK1 0.024 0.021 -10000 0 -0.13 2 2
COL1A2 -0.24 0.54 -10000 0 -1.3 112 112
CCL26 -0.16 0.46 -10000 0 -1 85 85
IL4R -0.17 0.49 -10000 0 -1.1 89 89
PTPN6 0.023 0.018 -10000 0 -0.12 2 2
IL13RA2 -0.16 0.45 -10000 0 -1 79 79
IL13RA1 0.015 0.049 -10000 0 -0.13 12 12
IRF4 0.001 0.13 -10000 0 -0.85 2 2
ARG1 -0.001 0.16 -10000 0 -0.79 4 4
CBL -0.1 0.31 -10000 0 -0.66 89 89
GTF3A -0.013 0.055 -10000 0 -0.096 144 144
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
IL13RA1/JAK2 0.004 0.092 -10000 0 -0.17 73 73
IRF4/BCL6 -0.004 0.12 -10000 0 -0.84 2 2
CD40LG 0.031 0.012 -10000 0 -0.12 2 2
MAPK14 -0.11 0.33 -10000 0 -0.71 86 86
mitosis -0.11 0.32 -10000 0 -0.74 78 78
STAT6 -0.18 0.52 -10000 0 -1.1 88 88
SPI1 0.027 0.021 -10000 0 -0.12 12 12
RPS6KB1 -0.1 0.31 -10000 0 -0.71 80 80
STAT6 (dimer) -0.18 0.51 -10000 0 -1.1 87 87
STAT6 (dimer)/PARP14 -0.19 0.47 -10000 0 -1.1 92 92
mast cell activation 0.001 0.015 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.12 0.36 -10000 0 -0.83 79 79
FRAP1 -0.12 0.34 -10000 0 -0.79 78 78
LTA -0.15 0.45 -10000 0 -1 79 79
FES 0.022 0.011 -10000 0 -0.12 3 3
T-helper 1 cell differentiation 0.17 0.5 1.1 87 -10000 0 87
CCL11 -0.18 0.47 -10000 0 -1 93 93
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.12 0.35 -10000 0 -0.83 77 77
IL2RG 0 0.051 -10000 0 -0.12 82 82
IL10 -0.15 0.44 -10000 0 -1 77 77
IRS1 0.019 0.023 -10000 0 -0.12 14 14
IRS2 0.021 0.016 -10000 0 -0.12 7 7
IL4 0.003 0.14 -10000 0 -10000 0 0
IL5 -0.15 0.45 -10000 0 -1 79 79
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.14 0.43 -10000 0 -0.9 93 93
COL1A1 -0.3 0.6 -10000 0 -1.3 139 139
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.17 0.47 -10000 0 -1.1 82 82
IL2R gamma/JAK3 -0.008 0.072 -10000 0 -0.13 111 111
TFF3 -0.17 0.47 -10000 0 -1 89 89
ALOX15 -0.15 0.45 -10000 0 -1 81 81
MYBL1 0.017 0.028 -10000 0 -0.12 22 22
T-helper 2 cell differentiation -0.15 0.42 -10000 0 -0.89 98 98
SHC1 0.023 0.001 -10000 0 -10000 0 0
CEBPB 0.023 0.032 -10000 0 -0.12 29 29
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.12 0.37 -10000 0 -0.85 80 80
mol:PI-3-4-5-P3 -0.12 0.34 -10000 0 -0.79 78 78
PI3K -0.13 0.37 -10000 0 -0.87 78 78
DOK2 0.02 0.021 -10000 0 -0.12 12 12
ETS1 0.012 0.036 -10000 0 -0.12 27 27
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.074 0.26 -10000 0 -0.61 70 70
ITGB3 -0.2 0.51 -10000 0 -1.1 96 96
PIGR -0.18 0.46 -10000 0 -1.1 84 84
IGHE 0.001 0.06 0.16 17 -0.18 8 25
MAPKKK cascade -0.072 0.26 -10000 0 -0.59 70 70
BCL6 0.018 0.02 -10000 0 -0.12 10 10
OPRM1 -0.15 0.45 -10000 0 -1 74 74
RETNLB -0.15 0.45 -10000 0 -1.1 68 68
SELP -0.16 0.45 -10000 0 -1 77 77
AICDA -0.15 0.43 -10000 0 -0.98 77 77
IL23-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
CCL2 -0.27 0.57 -9999 0 -1.2 126 126
IL23A -0.2 0.5 -9999 0 -1.2 87 87
NF kappa B1 p50/RelA/I kappa B alpha -0.19 0.49 -9999 0 -1.1 92 92
positive regulation of T cell mediated cytotoxicity -0.22 0.56 -9999 0 -1.3 92 92
ITGA3 -0.24 0.54 -9999 0 -1.2 122 122
IL17F -0.11 0.32 -9999 0 -0.68 98 98
IL12B 0.016 0.04 -9999 0 -10000 0 0
STAT1 (dimer) -0.22 0.53 -9999 0 -1.2 98 98
CD4 -0.21 0.52 -9999 0 -1.2 101 101
IL23 -0.18 0.48 -9999 0 -1.1 87 87
IL23R 0.002 0.089 -9999 0 -10000 0 0
IL1B -0.22 0.54 -9999 0 -1.3 97 97
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 -0.18 0.46 -9999 0 -1.1 87 87
TYK2 0.013 0.034 -9999 0 -0.14 7 7
STAT4 0.02 0.02 -9999 0 -0.12 11 11
STAT3 0.022 0.011 -9999 0 -0.12 3 3
IL18RAP 0.022 0.018 -9999 0 -0.13 8 8
IL12RB1 0.015 0.03 -9999 0 -0.15 1 1
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
IL12Rbeta1/TYK2 0.021 0.04 -9999 0 -0.11 8 8
IL23R/JAK2 -0.001 0.12 -9999 0 -10000 0 0
positive regulation of chronic inflammatory response -0.22 0.56 -9999 0 -1.3 92 92
natural killer cell activation 0 0.008 -9999 0 -10000 0 0
JAK2 0.012 0.046 -9999 0 -0.13 16 16
PIK3R1 0.016 0.031 -9999 0 -0.12 27 27
NFKB1 0.021 0.013 -9999 0 -0.12 4 4
RELA 0.022 0.01 -9999 0 -0.12 2 2
positive regulation of dendritic cell antigen processing and presentation -0.17 0.45 -9999 0 -1.1 89 89
ALOX12B -0.18 0.46 -9999 0 -1.1 87 87
CXCL1 -0.23 0.52 -9999 0 -1.1 117 117
T cell proliferation -0.22 0.56 -9999 0 -1.3 92 92
NFKBIA 0.016 0.028 -9999 0 -0.12 21 21
IL17A -0.073 0.26 -9999 0 -0.54 93 93
PI3K -0.2 0.5 -9999 0 -1.2 95 95
IFNG -0.005 0.026 -9999 0 -10000 0 0
STAT3 (dimer) -0.18 0.48 -9999 0 -1.1 97 97
IL18R1 0.021 0.022 -9999 0 -0.12 13 13
IL23/IL23R/JAK2/TYK2/SOCS3 -0.086 0.28 -9999 0 -0.6 89 89
IL18/IL18R 0.015 0.061 -9999 0 -0.11 77 77
macrophage activation -0.009 0.021 -9999 0 -0.044 85 85
TNF -0.19 0.5 -9999 0 -1.2 87 87
STAT3/STAT4 -0.19 0.51 -9999 0 -1.2 94 94
STAT4 (dimer) -0.21 0.53 -9999 0 -1.2 92 92
IL18 0.004 0.046 -9999 0 -0.12 66 66
IL19 -0.18 0.47 -9999 0 -1.1 92 92
STAT5A (dimer) -0.21 0.53 -9999 0 -1.2 94 94
STAT1 0.014 0.031 -9999 0 -0.12 26 26
SOCS3 0.015 0.032 -9999 0 -0.12 28 28
CXCL9 -0.26 0.55 -9999 0 -1.2 128 128
MPO -0.18 0.46 -9999 0 -1.1 87 87
positive regulation of humoral immune response -0.22 0.56 -9999 0 -1.3 92 92
IL23/IL23R/JAK2/TYK2 -0.24 0.61 -9999 0 -1.4 92 92
IL6 -0.2 0.48 -9999 0 -1.1 91 91
STAT5A 0.022 0.013 -9999 0 -0.12 4 4
IL2 0.025 0.014 -9999 0 -0.13 3 3
positive regulation of tyrosine phosphorylation of STAT protein 0 0.008 -9999 0 -10000 0 0
CD3E -0.2 0.5 -9999 0 -1.2 92 92
keratinocyte proliferation -0.22 0.56 -9999 0 -1.3 92 92
NOS2 -0.18 0.46 -9999 0 -1.1 93 93
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.001 0.046 -9999 0 -0.12 67 67
positive regulation of NF-kappaB transcription factor activity -0.021 0.079 -9999 0 -0.12 202 202
MAP2K4 -0.008 0.086 -9999 0 -0.23 34 34
IKBKB 0.022 0.015 -9999 0 -0.12 6 6
TNFRSF10B 0.022 0.014 -9999 0 -0.12 5 5
TNFRSF10A 0.019 0.021 -9999 0 -0.12 12 12
SMPD1 -0.013 0.053 -9999 0 -0.1 129 129
IKBKG 0.023 0.009 -9999 0 -0.12 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.019 0.023 -9999 0 -0.12 15 15
TRAIL/TRAILR2 -0.02 0.078 -9999 0 -0.15 128 128
TRAIL/TRAILR3 -0.02 0.075 -9999 0 -0.14 126 126
TRAIL/TRAILR1 -0.025 0.082 -9999 0 -0.12 213 213
TRAIL/TRAILR4 -0.021 0.08 -9999 0 -0.12 202 202
TRAIL/TRAILR1/DAP3/GTP -0.006 0.069 -9999 0 -0.11 142 142
IKK complex 0.006 0.079 -9999 0 -0.28 32 32
RIPK1 0.022 0.011 -9999 0 -0.12 3 3
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0.014 0.021 -9999 0 -0.14 10 10
MAPK3 0.006 0.032 -9999 0 -0.074 71 71
MAP3K1 -0.008 0.087 -9999 0 -0.25 26 26
TRAILR4 (trimer) 0.019 0.023 -9999 0 -0.12 15 15
TRADD 0.023 0.006 -9999 0 -0.12 1 1
TRAILR1 (trimer) 0.019 0.021 -9999 0 -0.12 12 12
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.011 0.083 -9999 0 -0.27 18 18
CFLAR 0.022 0.011 -9999 0 -0.12 3 3
MAPK1 0.005 0.034 -9999 0 -0.076 73 73
TRAIL/TRAILR1/FADD/TRADD/RIP 0.015 0.073 -9999 0 -0.17 20 20
mol:ceramide -0.013 0.053 -9999 0 -0.1 129 129
FADD 0.023 0.009 -9999 0 -0.12 2 2
MAPK8 -0.007 0.084 -9999 0 -0.22 40 40
TRAF2 0.023 0 -9999 0 -10000 0 0
TRAILR3 (trimer) 0.019 0.025 -9999 0 -0.12 18 18
CHUK 0.021 0.013 -9999 0 -0.12 4 4
TRAIL/TRAILR1/FADD -0.007 0.074 -9999 0 -0.12 137 137
DAP3 0.023 0.007 -9999 0 -0.12 1 1
CASP10 -0.038 0.098 -9999 0 -0.2 122 122
JNK cascade -0.021 0.079 -9999 0 -0.12 202 202
TRAIL (trimer) 0.001 0.046 -9999 0 -0.12 67 67
TNFRSF10C 0.019 0.026 -9999 0 -0.12 18 18
TRAIL/TRAILR1/DAP3/GTP/FADD 0.004 0.069 -9999 0 -0.098 142 142
TRAIL/TRAILR2/FADD -0.002 0.071 -9999 0 -0.12 129 129
cell death -0.013 0.052 -9999 0 -0.1 129 129
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.007 0.079 -9999 0 -0.26 14 14
TRAILR2 (trimer) 0.022 0.014 -9999 0 -0.12 5 5
CASP8 -0.002 0.11 -9999 0 -0.66 15 15
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.019 0.071 -9999 0 -0.16 15 15
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.019 0.049 -9999 0 -0.12 58 58
alphaV beta3 Integrin -0.001 0.073 -9999 0 -0.13 107 107
PTK2 -0.029 0.13 -9999 0 -0.25 121 121
IGF1R 0.013 0.032 -9999 0 -0.12 28 28
PI4KB 0.022 0.014 -9999 0 -0.12 5 5
MFGE8 0.006 0.043 -9999 0 -0.12 56 56
SRC 0.023 0.009 -9999 0 -0.12 2 2
CDKN1B -0.006 0.085 -9999 0 -0.34 28 28
VEGFA 0.019 0.021 -9999 0 -0.12 11 11
ILK 0.013 0.04 -9999 0 -0.31 3 3
ROCK1 0.022 0.009 -9999 0 -0.12 2 2
AKT1 0.014 0.038 -9999 0 -0.28 3 3
PTK2B -0.011 0.063 -9999 0 -0.11 139 139
alphaV/beta3 Integrin/JAM-A 0.014 0.068 -9999 0 -0.1 114 114
CBL 0.023 0.006 -9999 0 -0.12 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.001 0.073 -9999 0 -0.13 107 107
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.013 0.07 -9999 0 -0.11 107 107
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.011 0.095 -9999 0 -0.25 51 51
alphaV/beta3 Integrin/Syndecan-1 -0.003 0.074 -9999 0 -0.13 113 113
PI4KA 0.021 0.016 -9999 0 -0.12 7 7
IGF-1R heterotetramer/IGF1/IRS1 -0.055 0.086 -9999 0 -0.16 152 152
PI4 Kinase 0.028 0.032 -9999 0 -0.12 24 24
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
alphaV/beta3 Integrin/Osteopontin -0.03 0.098 -9999 0 -0.16 164 164
RPS6KB1 -0.056 0.082 -9999 0 -0.16 163 163
TLN1 0.021 0.012 -9999 0 -0.12 3 3
MAPK3 -0.054 0.14 -9999 0 -0.34 102 102
GPR124 0.022 0.011 -9999 0 -0.12 3 3
MAPK1 -0.055 0.14 -9999 0 -0.34 102 102
PXN 0.022 0.014 -9999 0 -0.12 5 5
PIK3R1 0.015 0.031 -9999 0 -0.12 27 27
alphaV/beta3 Integrin/Tumstatin -0.001 0.073 -9999 0 -0.13 107 107
cell adhesion -0.03 0.097 -9999 0 -0.16 170 170
ANGPTL3 0.022 0.011 -9999 0 -0.12 3 3
VEGFR2 homodimer/VEGFA homodimer/Src 0.033 0.044 -9999 0 -0.11 38 38
IGF-1R heterotetramer 0.013 0.032 -9999 0 -0.12 28 28
Rac1/GDP 0.016 0.015 -9999 0 -0.15 5 5
TGFBR2 0.02 0.02 -9999 0 -0.12 11 11
ITGB3 0.004 0.047 -9999 0 -0.12 68 68
IGF1 0.007 0.045 -9999 0 -0.12 60 60
RAC1 0.023 0.002 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.001 0.073 -9999 0 -0.13 107 107
apoptosis 0.013 0.032 -9999 0 -0.12 28 28
CD47 0.021 0.012 -9999 0 -0.12 3 3
alphaV/beta3 Integrin/CD47 -0.009 0.084 -9999 0 -0.14 124 124
VCL 0.021 0.013 -9999 0 -0.12 4 4
alphaV/beta3 Integrin/Del1 -0.03 0.083 -9999 0 -0.14 161 161
CSF1 0.013 0.033 -9999 0 -0.12 31 31
PIK3C2A -0.012 0.1 -9999 0 -0.36 41 41
PI4 Kinase/Pyk2 0.001 0.059 -9999 0 -0.14 49 49
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.001 0.079 -9999 0 -0.12 139 139
FAK1/Vinculin -0.016 0.12 -9999 0 -0.22 97 97
alphaV beta3/Integrin/ppsTEM5 -0.001 0.073 -9999 0 -0.13 107 107
RHOA 0.023 0.006 -9999 0 -0.12 1 1
VTN 0.023 0.009 -9999 0 -0.12 2 2
BCAR1 0.022 0.011 -9999 0 -0.12 3 3
FGF2 0.023 0.009 -9999 0 -0.12 2 2
F11R 0.022 0.012 -9999 0 -0.12 3 3
alphaV/beta3 Integrin/Lactadherin -0.028 0.088 -9999 0 -0.14 170 170
alphaV/beta3 Integrin/TGFBR2 -0.006 0.079 -9999 0 -0.14 112 112
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.015 0.075 -9999 0 -0.12 112 112
HSP90AA1 0.023 0.003 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.005 0.074 -9999 0 -0.12 124 124
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.013 0.056 -9999 0 -0.12 114 114
alphaV/beta3 Integrin/Pyk2 0 0.072 -9999 0 -0.11 142 142
SDC1 0.021 0.018 -9999 0 -0.12 9 9
VAV3 -0.012 0.074 -9999 0 -0.14 118 118
PTPN11 0.022 0.011 -9999 0 -0.12 3 3
IRS1 0.019 0.023 -9999 0 -0.12 14 14
FAK1/Paxillin -0.014 0.11 -9999 0 -0.22 92 92
cell migration -0.011 0.11 -9999 0 -0.21 97 97
ITGAV 0.013 0.032 -9999 0 -0.12 28 28
PI3K 0.006 0.083 -9999 0 -0.17 61 61
SPP1 0.012 0.032 -9999 0 -0.12 28 28
KDR 0.021 0.019 -9999 0 -0.12 10 10
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.013 0.032 -9999 0 -0.12 28 28
COL4A3 0.023 0.009 -9999 0 -0.12 2 2
angiogenesis -0.056 0.16 -9999 0 -0.37 102 102
Rac1/GTP -0.007 0.075 -9999 0 -0.18 54 54
EDIL3 -0.007 0.057 -9999 0 -0.12 109 109
cell proliferation -0.006 0.079 -9999 0 -0.14 112 112
IL6-mediated signaling events

Figure S26.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S26.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.072 0.32 -10000 0 -0.76 73 73
CRP -0.063 0.3 -10000 0 -0.73 67 67
cell cycle arrest -0.09 0.36 -10000 0 -0.81 80 80
TIMP1 -0.11 0.35 -10000 0 -0.75 105 105
IL6ST 0.016 0.03 -10000 0 -0.087 31 31
Rac1/GDP -0.019 0.17 -10000 0 -0.36 77 77
AP1 -0.06 0.21 -10000 0 -0.47 91 91
GAB2 0.01 0.042 -10000 0 -0.12 50 50
TNFSF11 -0.063 0.3 -10000 0 -0.72 68 68
HSP90B1 0.007 0.18 -10000 0 -1.2 11 11
GAB1 0.022 0.022 -10000 0 -0.12 12 12
MAPK14 -0.031 0.17 -10000 0 -0.48 52 52
AKT1 -0.018 0.15 -10000 0 -0.4 48 48
FOXO1 -0.015 0.15 -10000 0 -0.39 46 46
MAP2K6 -0.03 0.16 -10000 0 -0.37 75 75
mol:GTP 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.028 0.2 -10000 0 -0.4 93 93
MITF -0.02 0.15 -10000 0 -0.34 74 74
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.021 0.016 -10000 0 -0.12 7 7
A2M -0.12 0.39 -10000 0 -1.2 63 63
CEBPB 0.023 0.036 -10000 0 -0.11 36 36
GRB2/SOS1/GAB family/SHP2 -0.03 0.18 0.25 5 -0.39 84 89
STAT3 -0.1 0.38 -10000 0 -0.89 79 79
STAT1 -0.088 0.28 -10000 0 -0.84 68 68
CEBPD -0.071 0.31 -10000 0 -0.75 69 69
PIK3CA 0.021 0.017 -10000 0 -0.12 7 7
PI3K 0.009 0.066 -10000 0 -0.15 71 71
JUN 0.014 0.033 -10000 0 -0.12 30 30
PIAS3/MITF -0.014 0.15 -10000 0 -0.32 75 75
MAPK11 -0.03 0.17 -10000 0 -0.48 53 53
STAT3 (dimer)/FOXO1 -0.086 0.34 -10000 0 -0.7 98 98
GRB2/SOS1/GAB family 0.003 0.12 0.22 6 -0.24 70 76
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.01 0.12 -10000 0 -0.25 84 84
GRB2 0.025 0.008 -10000 0 -0.12 1 1
JAK2 0.017 0.025 -10000 0 -0.12 16 16
LBP -0.038 0.25 -10000 0 -0.57 68 68
PIK3R1 0.016 0.031 -10000 0 -0.12 27 27
JAK1 0.022 0.015 -10000 0 -0.042 19 19
MYC -0.12 0.4 -10000 0 -0.88 105 105
FGG -0.063 0.3 -10000 0 -0.73 67 67
macrophage differentiation -0.09 0.36 -10000 0 -0.81 80 80
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.013 0.094 -10000 0 -0.15 97 97
JUNB -0.11 0.37 -10000 0 -0.86 89 89
FOS -0.005 0.053 -10000 0 -0.12 95 95
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.023 0.16 -10000 0 -0.36 74 74
STAT1/PIAS1 -0.031 0.18 -10000 0 -0.36 89 89
GRB2/SOS1/GAB family/SHP2/PI3K -0.024 0.16 -10000 0 -0.35 70 70
STAT3 (dimer) -0.099 0.38 -10000 0 -0.88 79 79
PRKCD -0.044 0.26 -10000 0 -0.51 94 94
IL6R 0.018 0.025 -10000 0 -0.092 20 20
SOCS3 -0.047 0.22 -10000 0 -0.94 27 27
gp130 (dimer)/JAK1/JAK1/LMO4 0.02 0.08 -10000 0 -0.14 82 82
Rac1/GTP -0.024 0.18 -10000 0 -0.39 79 79
HCK 0.019 0.024 -10000 0 -0.12 15 15
MAPKKK cascade -0.049 0.22 -10000 0 -0.5 92 92
bone resorption -0.057 0.29 -10000 0 -0.68 68 68
IRF1 -0.12 0.41 -10000 0 -0.94 97 97
mol:GDP -0.025 0.16 -10000 0 -0.35 79 79
SOS1 0.019 0.028 -10000 0 -0.12 20 20
VAV1 -0.025 0.16 -10000 0 -0.36 79 79
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.03 0.18 -10000 0 -0.46 68 68
PTPN11 -0.007 0.16 -10000 0 -0.83 19 19
IL6/IL6RA 0.007 0.063 -10000 0 -0.13 69 69
gp130 (dimer)/TYK2/TYK2/LMO4 0.025 0.061 -10000 0 -0.12 66 66
gp130 (dimer)/JAK2/JAK2/LMO4 0.014 0.076 -10000 0 -0.14 89 89
IL6 0.005 0.049 -10000 0 -0.11 83 83
PIAS3 0.02 0.022 -10000 0 -0.12 13 13
PTPRE 0.022 0.018 0.082 15 -10000 0 15
PIAS1 0.022 0.009 -10000 0 -0.12 2 2
RAC1 0.023 0.003 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.013 0.097 -10000 0 -0.21 77 77
LMO4 0.021 0.023 -10000 0 -0.068 20 20
STAT3 (dimer)/PIAS3 -0.087 0.35 -10000 0 -0.8 80 80
MCL1 -0.014 0.16 -10000 0 -0.74 13 13
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.02 0.019 -9999 0 -0.12 10 10
GNB1/GNG2 -0.012 0.11 -9999 0 -0.23 68 68
mol:DAG -0.018 0.095 -9999 0 -0.21 76 76
PLCG1 -0.019 0.097 -9999 0 -0.21 76 76
YES1 -0.029 0.1 -9999 0 -0.17 153 153
FZD3 0.013 0.032 -9999 0 -0.12 29 29
FZD6 0.017 0.023 -9999 0 -0.12 13 13
G protein -0.009 0.1 -9999 0 -0.22 68 68
MAP3K7 -0.014 0.084 -9999 0 -0.18 82 82
mol:Ca2+ -0.017 0.093 -9999 0 -0.2 76 76
mol:IP3 -0.018 0.095 -9999 0 -0.21 76 76
NLK 0.026 0.045 -9999 0 -0.98 1 1
GNB1 0.023 0.007 -9999 0 -0.12 1 1
CAMK2A -0.015 0.087 -9999 0 -0.19 76 76
MAP3K7IP1 0.023 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.033 0.1 -9999 0 -0.18 162 162
CSNK1A1 0.022 0.007 -9999 0 -0.12 1 1
GNAS -0.028 0.098 -9999 0 -0.16 162 162
GO:0007205 -0.021 0.093 -9999 0 -0.21 77 77
WNT6 0.022 0.011 -9999 0 -0.12 3 3
WNT4 0.022 0.011 -9999 0 -0.12 3 3
NFAT1/CK1 alpha -0.01 0.11 -9999 0 -0.22 82 82
GNG2 0.02 0.018 -9999 0 -0.12 9 9
WNT5A 0.014 0.031 -9999 0 -0.12 27 27
WNT11 0.002 0.051 -9999 0 -0.12 82 82
CDC42 -0.025 0.096 -9999 0 -0.24 63 63
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 0.012 0.057 0.18 50 -10000 0 50
BUB1B -0.028 0.1 -10000 0 -0.22 93 93
PLK1 -0.009 0.049 -10000 0 -0.1 96 96
PLK1S1 -0.003 0.022 0.027 4 -0.047 87 91
KIF2A -0.006 0.047 -10000 0 -0.11 77 77
regulation of mitotic centrosome separation -0.009 0.048 -10000 0 -0.1 96 96
GOLGA2 0.023 0.006 -10000 0 -0.12 1 1
Hec1/SPC24 -0.015 0.088 -10000 0 -0.15 136 136
WEE1 -0.014 0.076 -10000 0 -0.2 57 57
cytokinesis -0.053 0.14 -10000 0 -0.29 124 124
PP2A-alpha B56 -0.036 0.24 -10000 0 -0.7 61 61
AURKA -0.025 0.09 -10000 0 -0.24 77 77
PICH/PLK1 -0.024 0.1 -10000 0 -0.17 147 147
CENPE -0.005 0.046 -10000 0 -0.11 73 73
RhoA/GTP 0.016 0.016 -10000 0 -0.14 6 6
positive regulation of microtubule depolymerization -0.006 0.047 -10000 0 -0.11 77 77
PPP2CA 0.023 0.003 -10000 0 -10000 0 0
FZR1 0.023 0 -10000 0 -10000 0 0
TPX2 -0.034 0.099 -10000 0 -0.25 92 92
PAK1 0.016 0.029 -10000 0 -0.12 23 23
SPC24 0.016 0.029 -10000 0 -0.12 24 24
FBXW11 0.023 0.003 -10000 0 -10000 0 0
CLSPN 0 0.035 -10000 0 -0.28 3 3
GORASP1 0.023 0.006 -10000 0 -0.12 1 1
metaphase -0.001 0.004 -10000 0 -0.014 31 31
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.003 0.022 0.027 4 -0.047 87 91
G2 phase of mitotic cell cycle -0.001 0.003 -10000 0 -0.009 56 56
STAG2 0.02 0.02 -10000 0 -0.12 10 10
GRASP65/GM130/RAB1/GTP 0.017 0.031 -10000 0 -10000 0 0
spindle elongation -0.009 0.048 -10000 0 -0.1 96 96
ODF2 0.021 0.014 -10000 0 -0.12 5 5
BUB1 -0.063 0.25 -10000 0 -0.77 61 61
TPT1 0.001 0.035 -10000 0 -0.16 17 17
CDC25C -0.016 0.096 -10000 0 -0.37 34 34
CDC25B 0.015 0.025 -10000 0 -0.13 14 14
SGOL1 -0.012 0.057 -10000 0 -0.19 50 50
RHOA 0.023 0.006 -10000 0 -0.12 1 1
CCNB1/CDK1 -0.028 0.13 -10000 0 -0.24 138 138
CDC14B 0.011 0.004 -10000 0 -0.085 1 1
CDC20 0.016 0.027 -10000 0 -0.12 19 19
PLK1/PBIP1 -0.003 0.042 -10000 0 -0.096 73 73
mitosis 0.003 0.009 0.025 67 -0.009 5 72
FBXO5 -0.019 0.07 -10000 0 -0.16 87 87
CDC2 0.007 0.04 -10000 0 -0.12 46 46
NDC80 0.008 0.038 -10000 0 -0.12 43 43
metaphase plate congression 0 0.042 -10000 0 -0.16 21 21
ERCC6L -0.033 0.12 -10000 0 -0.23 135 135
NLP/gamma Tubulin -0.002 0.029 -10000 0 -0.08 49 49
microtubule cytoskeleton organization 0.001 0.035 -10000 0 -0.16 17 17
G2/M transition DNA damage checkpoint 0 0.002 0.01 16 -10000 0 16
PPP1R12A 0.022 0.008 -10000 0 -0.12 1 1
interphase 0 0.002 0.01 16 -10000 0 16
PLK1/PRC1-2 -0.015 0.095 -10000 0 -0.16 131 131
GRASP65/GM130/RAB1/GTP/PLK1 0.024 0.053 -10000 0 -0.11 50 50
RAB1A 0.023 0.004 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA -0.011 0.051 -10000 0 -0.11 91 91
mitotic prometaphase -0.001 0.003 0.02 6 -0.01 24 30
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.058 -10000 0 -0.26 14 14
microtubule-based process -0.01 0.072 -10000 0 -0.12 126 126
Golgi organization -0.009 0.048 -10000 0 -0.1 96 96
Cohesin/SA2 -0.003 0.054 -10000 0 -0.11 91 91
PPP1CB/MYPT1 0.024 0.039 -10000 0 -0.15 27 27
KIF20A 0.009 0.038 -10000 0 -0.12 43 43
APC/C/CDC20 -0.005 0.069 -10000 0 -0.13 101 101
PPP2R1A 0.022 0.009 -10000 0 -0.12 2 2
chromosome segregation -0.003 0.042 -10000 0 -0.095 73 73
PRC1 0.015 0.03 -10000 0 -0.12 25 25
ECT2 -0.021 0.072 -10000 0 -0.15 105 105
C13orf34 -0.01 0.05 -10000 0 -0.11 87 87
NUDC 0 0.042 -10000 0 -0.16 21 21
regulation of attachment of spindle microtubules to kinetochore -0.028 0.099 -10000 0 -0.22 93 93
spindle assembly -0.005 0.037 -10000 0 -0.079 88 88
spindle stabilization -0.003 0.022 0.027 4 -0.047 87 91
APC/C/HCDH1 0.025 0.007 -10000 0 -0.089 2 2
MKLP2/PLK1 -0.01 0.073 -10000 0 -0.12 126 126
CCNB1 0.014 0.028 -10000 0 -0.12 21 21
PPP1CB 0.022 0.003 -10000 0 -10000 0 0
BTRC 0.023 0.002 -10000 0 -10000 0 0
ROCK2 -0.016 0.095 -10000 0 -0.33 42 42
TUBG1 0 0.039 -10000 0 -0.17 18 18
G2/M transition of mitotic cell cycle -0.043 0.12 -10000 0 -0.23 138 138
MLF1IP 0.01 0.011 -10000 0 -0.079 8 8
INCENP 0.022 0.009 -10000 0 -0.12 2 2
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.021 0.015 -9999 0 -0.12 6 6
ITGB7 0.019 0.024 -9999 0 -0.12 15 15
ITGA4 0.015 0.03 -9999 0 -0.12 24 24
alpha4/beta7 Integrin 0.004 0.065 -9999 0 -0.13 106 106
alpha4/beta1 Integrin 0.006 0.063 -9999 0 -0.12 101 101
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.007 0.08 -10000 0 -0.13 103 103
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.023 0.009 -10000 0 -0.12 2 2
STAT1 (dimer)/Cbp/p300 -0.019 0.13 -10000 0 -0.22 125 125
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.007 0.081 -10000 0 -0.15 97 97
antigen processing and presentation of peptide antigen via MHC class I -0.053 0.093 -10000 0 -0.2 131 131
CaM/Ca2+ 0.01 0.077 -10000 0 -0.15 72 72
RAP1A 0.021 0.012 -10000 0 -0.12 3 3
STAT1 (dimer)/SHP2 -0.018 0.093 -10000 0 -0.19 95 95
AKT1 -0.014 0.081 -10000 0 -0.18 86 86
MAP2K1 -0.007 0.068 -10000 0 -0.15 76 76
MAP3K11 -0.007 0.067 -10000 0 -0.14 86 86
IFNGR1 0.016 0.026 -10000 0 -0.12 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.014 0.082 -10000 0 -0.29 27 27
Rap1/GTP -0.023 0.056 -10000 0 -0.16 59 59
CRKL/C3G 0.034 0.01 -10000 0 -0.14 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.023 0.079 -10000 0 -0.14 69 69
CEBPB -0.014 0.15 -10000 0 -0.41 52 52
STAT3 0.022 0.011 -10000 0 -0.12 3 3
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.018 0.11 -10000 0 -0.99 3 3
STAT1 -0.019 0.087 0.11 2 -0.19 84 86
CALM1 0.022 0.014 -10000 0 -0.12 5 5
IFN-gamma (dimer) 0.01 0.039 -10000 0 -0.12 41 41
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
STAT1 (dimer)/PIAS1 -0.015 0.091 -10000 0 -0.18 93 93
CEBPB/PTGES2/Cbp/p300 -0.036 0.11 -10000 0 -0.3 66 66
mol:Ca2+ 0.005 0.078 -10000 0 -0.13 102 102
MAPK3 -0.009 0.11 -10000 0 -0.53 13 13
STAT1 (dimer) -0.041 0.15 -10000 0 -0.28 129 129
MAPK1 -0.013 0.13 -10000 0 -0.59 16 16
JAK2 0.016 0.026 -10000 0 -0.13 16 16
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
JAK1 0.02 0.012 -10000 0 -0.12 2 2
CAMK2D 0.018 0.024 -10000 0 -0.12 16 16
DAPK1 -0.015 0.16 -10000 0 -0.48 48 48
SMAD7 -0.009 0.064 -10000 0 -0.13 88 88
CBL/CRKL/C3G 0.017 0.068 -10000 0 -0.15 49 49
PI3K -0.004 0.092 -10000 0 -0.18 90 90
IFNG 0.01 0.039 -10000 0 -0.12 41 41
apoptosis -0.018 0.13 0.22 1 -0.39 47 48
CAMK2G 0.023 0.006 -10000 0 -0.12 1 1
STAT3 (dimer) 0.022 0.011 -10000 0 -0.12 3 3
CAMK2A 0.023 0.006 -10000 0 -0.12 1 1
CAMK2B 0.023 0.009 -10000 0 -0.12 2 2
FRAP1 -0.012 0.077 -10000 0 -0.17 84 84
PRKCD -0.016 0.086 -10000 0 -0.19 85 85
RAP1B 0.019 0.02 -10000 0 -0.12 10 10
negative regulation of cell growth -0.053 0.093 -10000 0 -0.2 131 131
PTPN2 0.023 0.007 -10000 0 -0.12 1 1
EP300 0.022 0.01 -10000 0 -0.12 2 2
IRF1 -0.038 0.13 -10000 0 -0.27 110 110
STAT1 (dimer)/PIASy -0.015 0.089 0.19 3 -0.19 83 86
SOCS1 0.007 0.096 -10000 0 -1.2 3 3
mol:GDP 0.015 0.065 -10000 0 -0.14 53 53
CASP1 -0.031 0.095 -10000 0 -0.17 152 152
PTGES2 0.023 0.009 -10000 0 -0.12 2 2
IRF9 0.004 0.071 -10000 0 -0.14 77 77
mol:PI-3-4-5-P3 -0.013 0.085 -10000 0 -0.18 90 90
RAP1/GDP 0.006 0.073 -10000 0 -0.18 52 52
CBL -0.006 0.066 -10000 0 -0.14 82 82
MAP3K1 -0.008 0.071 -10000 0 -0.16 76 76
PIAS1 0.022 0.009 -10000 0 -0.12 2 2
PIAS4 0.023 0.001 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.053 0.093 -10000 0 -0.2 131 131
PTPN11 -0.01 0.067 -10000 0 -0.13 104 104
CREBBP 0.02 0.016 -10000 0 -0.12 6 6
RAPGEF1 0.023 0 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 0.004 0.11 0.17 9 -0.24 59 68
ACTA1 0.023 0.073 0.15 59 -0.19 21 80
NUMA1 0.001 0.11 0.16 17 -0.25 66 83
SPTAN1 0.019 0.077 0.15 60 -0.18 28 88
LIMK1 0.025 0.072 0.15 62 -0.2 16 78
BIRC3 -0.005 0.053 -10000 0 -0.12 94 94
BIRC2 0.021 0.013 -10000 0 -0.12 4 4
BAX 0.023 0 -10000 0 -10000 0 0
CASP10 0.005 0.036 -10000 0 -0.072 89 89
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 -0.008 0.14 0.16 17 -0.3 72 89
DIABLO 0.02 0.016 -10000 0 -0.12 6 6
apoptotic nuclear changes 0.019 0.076 0.15 60 -0.18 28 88
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.023 0.009 -10000 0 -0.12 2 2
GSN 0.021 0.074 0.15 57 -0.2 21 78
MADD 0.023 0.006 -10000 0 -0.12 1 1
TFAP2A -0.03 0.15 -10000 0 -0.48 48 48
BID 0.01 0.037 -10000 0 -0.22 5 5
MAP3K1 0.009 0.08 -10000 0 -0.36 20 20
TRADD 0.023 0.006 -10000 0 -0.12 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.025 0.041 -10000 0 -0.13 33 33
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.006 0.076 0.14 36 -0.2 28 64
CASP9 0.021 0.014 -10000 0 -0.12 5 5
DNA repair -0.023 0.074 0.26 22 -0.13 72 94
neuron apoptosis -0.026 0.16 -10000 0 -0.58 39 39
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.01 0.1 0.17 36 -0.21 55 91
APAF1 0.021 0.014 -10000 0 -0.12 5 5
CASP6 -0.055 0.25 -10000 0 -0.78 59 59
TRAF2 0.023 0 -10000 0 -10000 0 0
ICAD/CAD 0.028 0.069 0.15 60 -0.21 13 73
CASP7 0.044 0.077 0.19 104 -0.19 6 110
KRT18 -0.014 0.12 -10000 0 -0.56 22 22
apoptosis -0.006 0.13 0.17 43 -0.3 62 105
DFFA 0.025 0.072 0.15 60 -0.19 18 78
DFFB 0.025 0.072 0.15 62 -0.19 19 81
PARP1 0.024 0.074 0.13 72 -0.26 22 94
actin filament polymerization -0.025 0.069 0.19 15 -0.15 60 75
TNF 0.02 0.02 -10000 0 -0.12 11 11
CYCS -0.005 0.049 -10000 0 -0.19 26 26
SATB1 -0.064 0.24 -10000 0 -0.75 59 59
SLK 0.018 0.077 0.15 60 -0.19 23 83
p15 BID/BAX 0.016 0.044 -10000 0 -0.1 34 34
CASP2 0.008 0.066 -10000 0 -0.21 22 22
JNK cascade -0.009 0.079 0.36 20 -10000 0 20
CASP3 0.023 0.077 0.16 62 -0.2 19 81
LMNB2 -0.002 0.099 -10000 0 -0.26 62 62
RIPK1 0.022 0.011 -10000 0 -0.12 3 3
CASP4 0.015 0.029 -10000 0 -0.12 23 23
Mammalian IAPs/DIABLO -0.019 0.084 -10000 0 -0.13 157 157
negative regulation of DNA binding -0.03 0.15 -10000 0 -0.47 48 48
stress fiber formation 0.018 0.076 0.15 60 -0.18 23 83
GZMB 0.005 0.045 -10000 0 -0.1 79 79
CASP1 -0.064 0.14 -10000 0 -0.28 148 148
LMNB1 -0.028 0.14 -10000 0 -0.28 103 103
APP -0.026 0.16 -10000 0 -0.59 39 39
TNFRSF1A 0.021 0.016 -10000 0 -0.12 7 7
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.011 0.002 -10000 0 -10000 0 0
VIM -0.003 0.13 0.17 44 -0.31 60 104
LMNA -0.008 0.11 -10000 0 -0.27 73 73
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.006 0.07 -10000 0 -0.23 21 21
LRDD 0.022 0.015 -10000 0 -0.12 6 6
SREBF1 0.024 0.074 0.15 62 -0.2 17 79
APAF-1/Caspase 9 0.027 0.11 0.26 15 -0.75 8 23
nuclear fragmentation during apoptosis 0.001 0.11 0.16 17 -0.24 66 83
CFL2 0.025 0.07 0.15 60 -0.2 15 75
GAS2 0.023 0.072 0.15 61 -0.19 19 80
positive regulation of apoptosis -0.014 0.12 -10000 0 -0.3 67 67
PRF1 0.013 0.036 -10000 0 -0.12 37 37
IGF1 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
NCK2 0.023 0.006 -10000 0 -0.12 1 1
PTK2 0.021 0.016 -10000 0 -0.12 6 6
CRKL -0.005 0.054 -10000 0 -0.12 91 91
GRB2/SOS1/SHC 0.035 0.041 -10000 0 -0.12 30 30
HRAS 0.023 0.006 -10000 0 -0.12 1 1
IRS1/Crk -0.001 0.057 -10000 0 -0.12 88 88
IGF-1R heterotetramer/IGF1/PTP1B 0.008 0.062 -10000 0 -0.12 89 89
AKT1 -0.01 0.06 -10000 0 -0.11 108 108
BAD -0.007 0.057 -10000 0 -0.1 108 108
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.005 0.054 -10000 0 -0.12 91 91
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.003 0.062 -10000 0 -0.12 100 100
RAF1 -0.004 0.092 -10000 0 -0.48 12 12
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.01 0.07 -10000 0 -0.12 88 88
YWHAZ 0.023 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.004 0.063 -10000 0 -0.13 91 91
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
RPS6KB1 -0.011 0.063 -10000 0 -0.12 110 110
GNB2L1 0.023 0.003 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.007 0.079 0.2 7 -0.38 12 19
PXN 0.022 0.014 -10000 0 -0.12 5 5
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.021 0.045 -10000 0 -0.15 29 29
HRAS/GTP -0.002 0.052 -10000 0 -0.15 24 24
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.022 0.068 -10000 0 -0.15 22 22
IGF-1R heterotetramer 0.012 0.033 -10000 0 -0.12 29 29
IGF-1R heterotetramer/IGF1/IRS/Nck 0.008 0.062 -10000 0 -0.12 91 91
Crk/p130 Cas/Paxillin 0.021 0.06 -10000 0 -0.099 86 86
IGF1R 0.012 0.033 -10000 0 -0.12 29 29
IGF1 0.001 0.047 -10000 0 -0.12 62 62
IRS2/Crk 0.004 0.054 -10000 0 -0.11 86 86
PI3K 0 0.076 -10000 0 -0.12 141 141
apoptosis -0.003 0.057 0.12 57 -10000 0 57
HRAS/GDP 0.017 0.008 -10000 0 -0.11 2 2
PRKCD -0.015 0.093 -10000 0 -0.26 40 40
RAF1/14-3-3 E 0.007 0.084 -10000 0 -0.4 12 12
BAD/14-3-3 0.003 0.06 -10000 0 -0.12 57 57
PRKCZ -0.009 0.059 -10000 0 -0.11 107 107
Crk/p130 Cas/Paxillin/FAK1 0.004 0.069 -10000 0 -0.15 55 55
PTPN1 0.023 0.006 -10000 0 -0.12 1 1
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.016 0.095 -10000 0 -0.21 89 89
BCAR1 0.022 0.011 -10000 0 -0.12 3 3
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.019 0.061 -10000 0 -0.095 95 95
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.017 0.027 -10000 0 -0.12 20 20
IRS1/NCK2 0.002 0.058 -10000 0 -0.12 91 91
GRB10 0.022 0.014 -10000 0 -0.12 5 5
PTPN11 -0.006 0.057 -10000 0 -0.12 92 92
IRS1 -0.011 0.058 -10000 0 -0.13 91 91
IRS2 -0.005 0.054 -10000 0 -0.12 92 92
IGF-1R heterotetramer/IGF1 -0.012 0.076 -10000 0 -0.17 88 88
GRB2 0.023 0.006 -10000 0 -0.12 1 1
PDPK1 -0.011 0.064 -10000 0 -0.12 107 107
YWHAE 0.022 0.014 -10000 0 -0.12 5 5
PRKD1 -0.021 0.097 -10000 0 -0.25 53 53
SHC1 0.023 0.001 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.083 0.19 -10000 0 -0.4 135 135
IHH -0.002 0.048 -10000 0 -0.076 141 141
SHH Np/Cholesterol/GAS1 0.023 0.028 -10000 0 -0.098 16 16
LRPAP1 0.018 0.024 -10000 0 -0.12 15 15
dorsoventral neural tube patterning -0.022 0.028 0.097 16 -10000 0 16
SMO/beta Arrestin2 -0.01 0.11 -10000 0 -0.27 12 12
SMO -0.018 0.11 -10000 0 -0.3 9 9
AKT1 -0.017 0.11 -10000 0 -0.33 39 39
ARRB2 0.022 0.014 -10000 0 -0.12 5 5
BOC 0.011 0.039 -10000 0 -0.12 44 44
ADRBK1 0.023 0.001 -10000 0 -10000 0 0
heart looping -0.018 0.11 -10000 0 -0.3 9 9
STIL -0.016 0.082 -10000 0 -0.15 135 135
DHH N/PTCH2 0.034 0.011 -10000 0 -0.15 1 1
DHH N/PTCH1 -0.019 0.099 -10000 0 -0.18 136 136
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
DHH 0.022 0.011 -10000 0 -0.12 3 3
PTHLH -0.072 0.18 -10000 0 -0.38 135 135
determination of left/right symmetry -0.018 0.11 -10000 0 -0.3 9 9
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
skeletal system development -0.072 0.18 -10000 0 -0.37 135 135
IHH N/Hhip 0.016 0.039 -10000 0 -0.098 27 27
DHH N/Hhip 0.029 0.024 -10000 0 -0.073 28 28
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.018 0.11 -10000 0 -0.3 9 9
pancreas development 0.017 0.029 -10000 0 -0.12 24 24
HHAT 0.022 0.011 -10000 0 -0.12 3 3
PI3K 0.007 0.065 -10000 0 -0.13 96 96
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.014 0.035 -10000 0 -0.12 35 35
somite specification -0.018 0.11 -10000 0 -0.3 9 9
SHH Np/Cholesterol/PTCH1 -0.013 0.087 -10000 0 -0.15 136 136
SHH Np/Cholesterol/PTCH2 0.03 0.012 -10000 0 -0.1 3 3
SHH Np/Cholesterol/Megalin 0.007 0.039 -10000 0 -0.098 20 20
SHH 0.022 0.011 -10000 0 -0.086 5 5
catabolic process -0.033 0.11 -10000 0 -0.21 135 135
SMO/Vitamin D3 -0.01 0.097 -10000 0 -0.17 135 135
SHH Np/Cholesterol/Hhip 0.027 0.019 -10000 0 -0.099 3 3
LRP2 -0.016 0.064 -10000 0 -0.12 148 148
receptor-mediated endocytosis -0.02 0.098 -10000 0 -0.21 58 58
SHH Np/Cholesterol/BOC 0.02 0.033 -10000 0 -0.1 23 23
SHH Np/Cholesterol/CDO 0.018 0.036 -10000 0 -0.098 36 36
mesenchymal cell differentiation -0.027 0.019 0.099 3 -10000 0 3
mol:Vitamin D3 -0.011 0.088 -10000 0 -0.15 136 136
IHH N/PTCH2 0.021 0.032 -10000 0 -0.13 4 4
CDON 0.013 0.035 -10000 0 -0.12 35 35
IHH N/PTCH1 -0.028 0.11 -10000 0 -0.21 135 135
Megalin/LRPAP1 -0.011 0.065 -10000 0 -0.15 55 55
PTCH2 0.023 0.009 -10000 0 -0.12 2 2
SHH Np/Cholesterol 0.018 0.009 -10000 0 -0.1 2 2
PTCH1 -0.033 0.11 -10000 0 -0.21 135 135
HHIP 0.017 0.029 -10000 0 -0.12 24 24
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.011 0.049 -10000 0 -0.12 54 54
cell-cell adhesion 0.023 0.039 0.14 38 -10000 0 38
Ephrin B/EPHB2/RasGAP 0.016 0.076 -10000 0 -0.15 36 36
ITSN1 0.022 0.011 -10000 0 -0.12 3 3
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
SHC1 0.023 0.001 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.022 0.034 -10000 0 -0.087 46 46
Ephrin B1/EPHB1 0.024 0.027 -10000 0 -0.068 43 43
HRAS/GDP -0.002 0.07 -10000 0 -0.14 86 86
Ephrin B/EPHB1/GRB7 0.018 0.071 -10000 0 -0.096 119 119
Endophilin/SYNJ1 -0.001 0.052 -10000 0 -0.087 124 124
KRAS 0.014 0.034 -10000 0 -0.12 33 33
Ephrin B/EPHB1/Src 0.024 0.067 -10000 0 -0.14 19 19
endothelial cell migration 0.001 0.071 -10000 0 -0.11 145 145
GRB2 0.023 0.006 -10000 0 -0.12 1 1
GRB7 0.018 0.026 -10000 0 -0.12 18 18
PAK1 -0.003 0.057 -10000 0 -0.16 28 28
HRAS 0.023 0.006 -10000 0 -0.12 1 1
RRAS -0.006 0.056 -10000 0 -0.095 127 127
DNM1 0.021 0.019 -10000 0 -0.12 10 10
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0 0.049 -10000 0 -0.087 109 109
lamellipodium assembly -0.023 0.039 -10000 0 -0.14 38 38
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.019 0.051 -10000 0 -0.22 13 13
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
EPHB2 0.02 0.02 -10000 0 -0.12 11 11
EPHB3 0.019 0.024 -10000 0 -0.12 15 15
EPHB1 0.016 0.032 -10000 0 -0.12 28 28
EPHB4 0.022 0.009 -10000 0 -0.12 2 2
mol:GDP -0.01 0.079 -10000 0 -0.17 97 97
Ephrin B/EPHB2 0.012 0.066 -10000 0 -0.097 123 123
Ephrin B/EPHB3 0.011 0.065 -10000 0 -0.095 123 123
JNK cascade 0.015 0.045 -10000 0 -0.1 56 56
Ephrin B/EPHB1 0.013 0.063 -10000 0 -0.095 108 108
RAP1/GDP 0.001 0.084 -10000 0 -0.16 99 99
EFNB2 0.007 0.041 -10000 0 -0.12 50 50
EFNB3 0.018 0.026 -10000 0 -0.12 19 19
EFNB1 0.021 0.018 -10000 0 -0.12 9 9
Ephrin B2/EPHB1-2 0.006 0.061 -10000 0 -0.1 101 101
RAP1B 0.019 0.02 -10000 0 -0.12 10 10
RAP1A 0.021 0.012 -10000 0 -0.12 3 3
CDC42/GTP 0.008 0.077 -10000 0 -0.18 30 30
Rap1/GTP -0.028 0.045 -10000 0 -0.14 59 59
axon guidance 0.011 0.049 -10000 0 -0.12 54 54
MAPK3 0.008 0.063 -10000 0 -0.2 15 15
MAPK1 0.008 0.063 -10000 0 -0.2 16 16
Rac1/GDP 0.001 0.079 -10000 0 -0.16 86 86
actin cytoskeleton reorganization -0.025 0.045 -10000 0 -0.14 43 43
CDC42/GDP 0.001 0.079 -10000 0 -0.16 85 85
PI3K 0.004 0.074 -10000 0 -0.11 145 145
EFNA5 0.014 0.033 -10000 0 -0.12 30 30
Ephrin B2/EPHB4 0 0.058 -10000 0 -0.096 141 141
Ephrin B/EPHB2/Intersectin/N-WASP -0.005 0.08 -10000 0 -0.15 116 116
CDC42 0.023 0.002 -10000 0 -10000 0 0
RAS family/GTP -0.026 0.042 -10000 0 -0.13 53 53
PTK2 -0.001 0.051 -10000 0 -0.2 33 33
MAP4K4 0.015 0.045 -10000 0 -0.1 56 56
SRC 0.023 0.009 -10000 0 -0.12 2 2
KALRN 0.015 0.033 -10000 0 -0.12 30 30
Intersectin/N-WASP 0.031 0.022 -10000 0 -0.11 12 12
neuron projection morphogenesis 0.005 0.07 -10000 0 -0.16 42 42
MAP2K1 0.005 0.066 -10000 0 -0.2 15 15
WASL 0.023 0.009 -10000 0 -0.12 2 2
Ephrin B1/EPHB1-2/NCK1 0.036 0.056 -10000 0 -0.11 55 55
cell migration 0.002 0.077 -10000 0 -0.21 24 24
NRAS 0.022 0.011 -10000 0 -0.12 3 3
SYNJ1 -0.001 0.052 -10000 0 -0.088 124 124
PXN 0.022 0.014 -10000 0 -0.12 5 5
TF -0.001 0.049 -10000 0 -0.082 127 127
HRAS/GTP 0.01 0.063 -10000 0 -0.15 29 29
Ephrin B1/EPHB1-2 0.032 0.039 -10000 0 -0.11 26 26
cell adhesion mediated by integrin 0.014 0.047 0.1 102 -10000 0 102
RAC1 0.023 0.002 -10000 0 -10000 0 0
mol:GTP 0.011 0.069 -10000 0 -0.16 29 29
RAC1-CDC42/GTP -0.024 0.039 -10000 0 -0.13 39 39
RASA1 0.021 0.012 -10000 0 -0.12 3 3
RAC1-CDC42/GDP 0.009 0.08 -10000 0 -0.15 85 85
ruffle organization 0.004 0.057 -10000 0 -0.14 40 40
NCK1 0.02 0.019 -10000 0 -0.12 9 9
receptor internalization 0 0.049 -10000 0 -0.082 125 125
Ephrin B/EPHB2/KALRN 0.019 0.073 -10000 0 -0.13 39 39
ROCK1 0.017 0.028 -10000 0 -0.097 24 24
RAS family/GDP -0.028 0.049 -10000 0 -0.16 43 43
Rac1/GTP -0.024 0.041 -10000 0 -0.14 38 38
Ephrin B/EPHB1/Src/Paxillin 0 0.071 -10000 0 -0.24 11 11
Ras 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
ERK1-2/ELK1 -0.026 0.13 -9999 0 -0.25 110 110
MAP3K8 0.021 0.009 -9999 0 -0.12 2 2
FOS -0.014 0.093 -9999 0 -0.29 26 26
PRKCA 0.008 0.037 -9999 0 -0.12 40 40
PTPN7 0.017 0.013 -9999 0 -10000 0 0
HRAS 0.022 0.006 -9999 0 -0.12 1 1
PRKCB -0.003 0.006 -9999 0 -0.01 194 194
NRAS 0.021 0.012 -9999 0 -0.12 3 3
RAS family/GTP 0.024 0.043 -9999 0 -0.1 46 46
MAPK3 0.002 0.068 -9999 0 -0.44 6 6
MAP2K1 -0.017 0.091 -9999 0 -0.29 46 46
ELK1 0.015 0.02 -9999 0 -0.13 6 6
BRAF -0.016 0.086 -9999 0 -0.3 42 42
mol:GTP -0.001 0.002 -9999 0 -0.003 188 188
MAPK1 0 0.076 -9999 0 -0.44 9 9
RAF1 -0.017 0.085 -9999 0 -0.29 47 47
KRAS 0.013 0.034 -9999 0 -0.12 33 33
Signaling events mediated by PTP1B

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
PDGFRB 0.01 0.042 -10000 0 -0.12 52 52
Jak2/Leptin Receptor -0.043 0.13 0.21 1 -0.37 57 58
PTP1B/AKT1 -0.06 0.1 -10000 0 -0.23 97 97
FYN 0.011 0.037 -10000 0 -0.12 40 40
p210 bcr-abl/PTP1B -0.075 0.1 -10000 0 -0.26 98 98
EGFR 0.014 0.031 -10000 0 -0.13 25 25
EGF/EGFR -0.058 0.1 -10000 0 -0.23 106 106
CSF1 0.013 0.033 -10000 0 -0.12 31 31
AKT1 0.02 0.019 -10000 0 -0.12 10 10
INSR 0.021 0.017 -10000 0 -0.12 8 8
PTP1B/N-cadherin -0.094 0.12 -10000 0 -0.24 187 187
Insulin Receptor/Insulin -0.031 0.091 -10000 0 -0.21 73 73
HCK 0.019 0.024 -10000 0 -0.12 15 15
CRK 0.021 0.016 -10000 0 -0.12 7 7
TYK2 -0.068 0.1 -10000 0 -0.25 96 96
EGF 0.018 0.022 -10000 0 -0.13 12 12
YES1 0.02 0.018 -10000 0 -0.12 8 8
CAV1 -0.056 0.096 -10000 0 -0.23 92 92
TXN 0.019 0.015 -10000 0 -0.12 5 5
PTP1B/IRS1/GRB2 -0.055 0.11 -10000 0 -0.23 104 104
cell migration 0.075 0.1 0.26 98 -10000 0 98
STAT3 0.021 0.011 -10000 0 -0.12 3 3
PRLR 0.014 0.042 -10000 0 -0.12 53 53
ITGA2B 0.022 0.006 -10000 0 -0.13 1 1
CSF1R 0.014 0.031 -10000 0 -0.12 27 27
Prolactin Receptor/Prolactin 0.035 0.035 -10000 0 -0.18 2 2
FGR 0.023 0.006 -10000 0 -0.12 1 1
PTP1B/p130 Cas -0.063 0.1 -10000 0 -0.24 98 98
Crk/p130 Cas -0.052 0.1 -10000 0 -0.23 96 96
DOK1 -0.056 0.094 -10000 0 -0.24 82 82
JAK2 -0.052 0.13 -10000 0 -0.42 50 50
Jak2/Leptin Receptor/Leptin -0.056 0.12 -10000 0 -0.25 120 120
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
PTPN1 -0.075 0.1 -10000 0 -0.26 98 98
LYN 0.021 0.013 -10000 0 -0.12 4 4
CDH2 -0.015 0.057 -10000 0 -0.12 120 120
SRC -0.008 0.054 -10000 0 -0.61 2 2
ITGB3 0.003 0.047 -10000 0 -0.12 68 68
CAT1/PTP1B -0.058 0.12 -10000 0 -0.26 106 106
CAPN1 0.02 0.013 -10000 0 -0.12 4 4
CSK 0.023 0.009 -10000 0 -0.12 2 2
PI3K -0.033 0.1 -10000 0 -0.21 94 94
mol:H2O2 0.002 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.05 0.12 -10000 0 -0.24 116 116
negative regulation of transcription -0.05 0.13 -10000 0 -0.4 54 54
FCGR2A 0.013 0.031 -10000 0 -0.12 26 26
FER 0.019 0.018 -10000 0 -0.12 8 8
alphaIIb/beta3 Integrin 0.008 0.053 -10000 0 -0.098 107 107
BLK 0.022 0.015 -10000 0 -0.12 6 6
Insulin Receptor/Insulin/Shc 0.043 0.022 -10000 0 -0.11 7 7
RHOA 0.021 0.007 -10000 0 -0.13 1 1
LEPR 0.018 0.028 -10000 0 -0.12 21 21
BCAR1 0.022 0.011 -10000 0 -0.12 3 3
p210 bcr-abl/Grb2 0.023 0.006 -10000 0 -0.12 1 1
mol:NADPH -0.001 0.002 -10000 0 -10000 0 0
TRPV6 0 0.087 -10000 0 -0.22 42 42
PRL 0.027 0.013 -10000 0 -0.13 3 3
SOCS3 -0.031 0.23 -10000 0 -1.2 22 22
SPRY2 -0.009 0.055 -10000 0 -0.12 103 103
Insulin Receptor/Insulin/IRS1 0.039 0.03 -10000 0 -0.11 12 12
CSF1/CSF1R -0.077 0.13 -10000 0 -0.26 138 138
Ras protein signal transduction 0.029 0.034 0.11 17 -0.16 5 22
IRS1 0.019 0.023 -10000 0 -0.12 14 14
INS 0.022 0.011 -10000 0 -0.13 3 3
LEP 0.022 0.006 -10000 0 -0.12 1 1
STAT5B -0.06 0.1 -10000 0 -0.24 98 98
STAT5A -0.062 0.1 -10000 0 -0.24 102 102
GRB2 0.023 0.006 -10000 0 -0.12 1 1
PDGFB-D/PDGFRB -0.069 0.1 -10000 0 -0.24 109 109
CSN2 0.04 0.027 -10000 0 -10000 0 0
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
LAT -0.083 0.19 -10000 0 -0.5 87 87
YBX1 0.033 0.015 -10000 0 -0.18 2 2
LCK 0.022 0.015 -10000 0 -0.12 6 6
SHC1 0.023 0.001 -10000 0 -10000 0 0
NOX4 -0.021 0.062 -10000 0 -0.12 152 152
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.033 0.1 -9999 0 -0.18 162 162
FZD6 0.017 0.023 -9999 0 -0.12 13 13
WNT6 0.022 0.011 -9999 0 -0.12 3 3
WNT4 0.022 0.011 -9999 0 -0.12 3 3
FZD3 0.013 0.032 -9999 0 -0.12 29 29
WNT5A 0.014 0.031 -9999 0 -0.12 27 27
WNT11 0.002 0.051 -9999 0 -0.12 82 82
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.005 0.1 -10000 0 -0.22 79 79
adherens junction organization -0.007 0.12 -10000 0 -0.26 68 68
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.002 0.098 -10000 0 -0.24 50 50
FMN1 -0.002 0.11 -10000 0 -0.24 69 69
mol:IP3 -0.002 0.092 -10000 0 -0.21 64 64
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.004 0.11 -10000 0 -0.26 67 67
CTNNB1 0.022 0.008 -10000 0 -0.12 1 1
AKT1 0.001 0.097 -10000 0 -0.25 48 48
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.007 0.13 -10000 0 -0.36 47 47
CTNND1 0.023 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.001 0.1 -10000 0 -0.24 68 68
VASP -0.001 0.11 -10000 0 -0.25 68 68
ZYX -0.004 0.11 -10000 0 -0.25 69 69
JUB -0.005 0.11 -10000 0 -0.25 69 69
EGFR(dimer) -0.001 0.11 -10000 0 -0.25 71 71
E-cadherin/beta catenin-gamma catenin 0.026 0.052 -10000 0 -0.097 81 81
mol:PI-3-4-5-P3 0.003 0.1 -10000 0 -0.25 52 52
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
PI3K 0.004 0.11 -10000 0 -0.26 52 52
FYN -0.012 0.11 -10000 0 -0.27 67 67
mol:Ca2+ -0.002 0.09 -10000 0 -0.2 64 64
JUP 0.019 0.021 -10000 0 -0.12 12 12
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
mol:DAG -0.002 0.092 -10000 0 -0.21 64 64
CDH1 0.02 0.016 -10000 0 -0.12 6 6
RhoA/GDP 0.002 0.097 -10000 0 -0.24 49 49
establishment of polarity of embryonic epithelium -0.001 0.1 -10000 0 -0.24 68 68
SRC 0.023 0.009 -10000 0 -0.12 2 2
RAC1 0.023 0.002 -10000 0 -10000 0 0
RHOA 0.023 0.006 -10000 0 -0.12 1 1
EGFR 0.015 0.03 -10000 0 -0.12 25 25
CASR 0.001 0.086 -10000 0 -0.22 50 50
RhoA/GTP 0.006 0.089 -10000 0 -0.25 40 40
AKT2 0 0.097 -10000 0 -0.24 52 52
actin cable formation 0.001 0.1 -10000 0 -0.24 68 68
apoptosis 0.004 0.099 0.24 57 -10000 0 57
CTNNA1 0.022 0.01 -10000 0 -0.12 2 2
mol:GDP -0.006 0.097 -10000 0 -0.23 58 58
PIP5K1A -0.001 0.11 -10000 0 -0.25 68 68
PLCG1 -0.003 0.094 -10000 0 -0.21 63 63
Rac1/GTP 0.004 0.11 -10000 0 -0.24 70 70
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
BMP 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
BMP7/BMPR2/BMPR1A-1B/FS -0.035 0.091 -9999 0 -0.12 243 243
SMAD6-7/SMURF1 0.042 0.029 -9999 0 -0.13 11 11
NOG 0.017 0.029 -9999 0 -0.12 23 23
SMAD9 0.02 0.05 -9999 0 -0.42 3 3
SMAD4 0.022 0.007 -9999 0 -0.12 1 1
SMAD5 0 0.094 -9999 0 -0.27 39 39
BMP7/USAG1 -0.074 0.094 -9999 0 -0.13 369 369
SMAD5/SKI 0.011 0.094 -9999 0 -0.26 37 37
SMAD1 0.021 0.073 -9999 0 -0.28 26 26
BMP2 0.022 0.014 -9999 0 -0.12 5 5
SMAD1/SMAD1/SMAD4 -0.003 0.065 -9999 0 -0.25 27 27
BMPR1A 0.02 0.014 -9999 0 -0.12 4 4
BMPR1B 0.008 0.04 -9999 0 -0.12 48 48
BMPR1A-1B/BAMBI -0.026 0.087 -9999 0 -0.14 161 161
AHSG 0.023 0.009 -9999 0 -0.12 2 2
CER1 0.022 0.012 -9999 0 -0.12 4 4
BMP2-4/CER1 0.033 0.039 -9999 0 -0.12 16 16
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA 0.003 0.1 -9999 0 -0.25 54 54
BMP2-4 (homodimer) 0.02 0.041 -9999 0 -0.087 69 69
RGMB 0.023 0.009 -9999 0 -0.12 2 2
BMP6/BMPR2/BMPR1A-1B 0.013 0.076 -9999 0 -0.12 114 114
RGMA 0.021 0.017 -9999 0 -0.12 8 8
SMURF1 0.023 0.009 -9999 0 -0.12 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP 0.004 0.077 -9999 0 -0.17 74 74
BMP2-4/USAG1 -0.014 0.07 -9999 0 -0.12 118 118
SMAD6/SMURF1/SMAD5 0.011 0.094 -9999 0 -0.26 37 37
SOSTDC1 -0.018 0.062 -9999 0 -0.12 146 146
BMP7/BMPR2/BMPR1A-1B -0.033 0.093 -9999 0 -0.13 219 219
SKI 0.022 0.011 -9999 0 -0.12 3 3
BMP6 (homodimer) 0.02 0.023 -9999 0 -0.12 14 14
HFE2 0.023 0.009 -9999 0 -0.12 2 2
ZFYVE16 0.02 0.018 -9999 0 -0.12 8 8
MAP3K7 0.021 0.014 -9999 0 -0.12 5 5
BMP2-4/CHRD 0.033 0.038 -9999 0 -0.11 16 16
SMAD5/SMAD5/SMAD4 0.009 0.096 -9999 0 -0.27 39 39
MAPK1 0.021 0.016 -9999 0 -0.12 7 7
TAK1/TAB family 0.022 0.096 -9999 0 -0.21 54 54
BMP7 (homodimer) -0.009 0.055 -9999 0 -0.12 106 106
NUP214 0.023 0.007 -9999 0 -0.12 1 1
BMP6/FETUA 0.032 0.017 -9999 0 -0.071 16 16
SMAD1/SKI 0.033 0.072 -9999 0 -0.26 26 26
SMAD6 0.02 0.02 -9999 0 -0.12 11 11
CTDSP2 0.022 0.01 -9999 0 -0.12 2 2
BMP2-4/FETUA 0.033 0.039 -9999 0 -0.12 15 15
MAP3K7IP1 0.023 0 -9999 0 -10000 0 0
GREM1 0.008 0.044 -9999 0 -0.12 58 58
BMPR2 (homodimer) 0.021 0.014 -9999 0 -0.12 5 5
GADD34/PP1CA 0.03 0.047 -9999 0 -0.12 46 46
BMPR1A-1B (homodimer) -0.011 0.081 -9999 0 -0.13 154 154
CHRDL1 -0.008 0.055 -9999 0 -0.12 103 103
ENDOFIN/SMAD1 0.03 0.076 -9999 0 -0.27 27 27
SMAD6-7/SMURF1/SMAD1 0.049 0.076 -9999 0 -0.25 27 27
SMAD6/SMURF1 0.023 0.009 -9999 0 -0.12 2 2
BAMBI -0.004 0.054 -9999 0 -0.12 95 95
SMURF2 0.022 0.013 -9999 0 -0.12 4 4
BMP2-4/CHRDL1 -0.014 0.072 -9999 0 -0.12 135 135
BMP2-4/GREM1 0.023 0.049 -9999 0 -0.12 30 30
SMAD7 0.023 0.003 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 0.028 0.052 -9999 0 -0.3 6 6
SMAD1/SMAD6 0.033 0.073 -9999 0 -0.26 26 26
TAK1/SMAD6 0.027 0.035 -9999 0 -0.12 28 28
BMP7 -0.009 0.055 -9999 0 -0.12 106 106
BMP6 0.02 0.023 -9999 0 -0.12 14 14
MAP3K7IP2 0.02 0.016 -9999 0 -0.12 6 6
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 0.003 0.083 -9999 0 -0.21 48 48
PPM1A 0.023 0.001 -9999 0 -10000 0 0
SMAD1/SMURF2 0.031 0.075 -9999 0 -0.27 26 26
SMAD7/SMURF1 0.031 0.023 -9999 0 -0.13 11 11
CTDSPL 0.023 0.006 -9999 0 -0.12 1 1
PPP1CA 0.023 0.002 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0.022 0.011 -9999 0 -0.12 3 3
PPP1R15A 0.019 0.025 -9999 0 -0.12 17 17
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS 0.002 0.08 -9999 0 -0.21 51 51
CHRD 0.023 0.006 -9999 0 -0.12 1 1
BMPR2 0.021 0.014 -9999 0 -0.12 5 5
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.005 0.088 -9999 0 -0.24 43 43
BMP4 0.009 0.042 -9999 0 -0.12 52 52
FST 0.004 0.049 -9999 0 -0.12 73 73
BMP2-4/NOG 0.027 0.047 -9999 0 -0.12 33 33
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.023 0.091 -9999 0 -0.12 220 220
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.003 0.076 -9999 0 -0.17 89 89
CRKL 0.023 0.009 -9999 0 -0.12 2 2
Rac1/GDP 0.016 0.015 -9999 0 -0.15 5 5
DOCK1 0.019 0.02 -9999 0 -0.12 10 10
ITGA4 0.015 0.03 -9999 0 -0.12 24 24
alpha4/beta7 Integrin/MAdCAM1 0.032 0.059 -9999 0 -0.1 78 78
EPO 0.023 0.006 -9999 0 -0.12 1 1
alpha4/beta7 Integrin 0.004 0.065 -9999 0 -0.13 106 106
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.021 0.016 -9999 0 -0.12 7 7
alpha4/beta1 Integrin 0.006 0.063 -9999 0 -0.12 101 101
EPO/EPOR (dimer) 0.032 0.019 -9999 0 -0.08 15 15
lamellipodium assembly 0.004 0.087 -9999 0 -0.34 19 19
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
PI3K 0.007 0.065 -9999 0 -0.13 96 96
ARF6 0.023 0.003 -9999 0 -10000 0 0
JAK2 0.003 0.081 -9999 0 -0.18 73 73
PXN 0.022 0.014 -9999 0 -0.12 5 5
PIK3R1 0.015 0.031 -9999 0 -0.12 27 27
MADCAM1 0.023 0.006 -9999 0 -0.12 1 1
cell adhesion 0.03 0.058 -9999 0 -0.1 78 78
CRKL/CBL 0.033 0.013 -9999 0 -0.14 2 2
ITGB1 0.021 0.015 -9999 0 -0.12 6 6
SRC -0.038 0.074 -9999 0 -0.13 186 186
ITGB7 0.019 0.024 -9999 0 -0.12 15 15
RAC1 0.023 0.002 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.041 0.09 -9999 0 -0.15 186 186
p130Cas/Crk/Dock1 -0.021 0.075 -9999 0 -0.16 77 77
VCAM1 -0.019 0.06 -9999 0 -0.12 139 139
RHOA 0.023 0.006 -9999 0 -0.12 1 1
alpha4/beta1 Integrin/Paxillin/GIT1 0.033 0.057 -9999 0 -0.098 74 74
BCAR1 -0.033 0.068 -9999 0 -0.11 186 186
EPOR 0.02 0.021 -9999 0 -0.12 12 12
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.023 0.006 -9999 0 -0.12 1 1
GIT1 0.022 0.012 -9999 0 -0.12 4 4
Rac1/GTP 0.004 0.09 -9999 0 -0.35 19 19
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.004 0.14 -10000 0 -0.33 62 62
FYN -0.047 0.18 -10000 0 -0.4 86 86
LAT/GRAP2/SLP76 -0.009 0.15 -10000 0 -0.32 79 79
IKBKB 0.022 0.015 -10000 0 -0.12 6 6
AKT1 -0.009 0.13 -10000 0 -0.3 76 76
B2M 0.022 0.007 -10000 0 -10000 0 0
IKBKG 0.008 0.044 -10000 0 -0.087 73 73
MAP3K8 0.023 0.009 -10000 0 -0.12 2 2
mol:Ca2+ -0.004 0.011 -10000 0 -0.035 42 42
integrin-mediated signaling pathway 0.021 0.035 -10000 0 -0.096 44 44
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.023 0.18 -10000 0 -0.41 76 76
TRPV6 0.003 0.017 -10000 0 -0.13 6 6
CD28 0.022 0.011 -10000 0 -0.12 3 3
SHC1 -0.019 0.16 -10000 0 -0.4 63 63
receptor internalization -0.014 0.14 -10000 0 -0.35 63 63
PRF1 -0.019 0.18 -10000 0 -0.67 28 28
KRAS 0.014 0.034 -10000 0 -0.12 33 33
GRB2 0.023 0.006 -10000 0 -0.12 1 1
COT/AKT1 0.004 0.11 -10000 0 -0.24 76 76
LAT -0.019 0.16 -10000 0 -0.4 62 62
EntrezGene:6955 0 0.003 -10000 0 -0.022 2 2
CD3D 0.008 0.044 -10000 0 -0.12 56 56
CD3E 0.015 0.033 -10000 0 -0.13 29 29
CD3G 0.002 0.051 -10000 0 -0.12 78 78
RASGRP2 0.007 0.015 -10000 0 -10000 0 0
RASGRP1 -0.017 0.14 -10000 0 -0.29 87 87
HLA-A 0.02 0.019 -10000 0 -0.13 8 8
RASSF5 0.02 0.022 -10000 0 -0.12 13 13
RAP1A/GTP/RAPL 0.022 0.035 -10000 0 -0.096 44 44
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.009 0.05 -10000 0 -0.096 60 60
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.026 0.054 -10000 0 -0.14 82 82
PRKCA -0.005 0.08 -10000 0 -0.18 75 75
GRAP2 0.022 0.012 -10000 0 -0.12 4 4
mol:IP3 -0.044 0.098 0.098 3 -0.26 76 79
EntrezGene:6957 0 0.004 -10000 0 -0.023 2 2
TCR/CD3/MHC I/CD8 -0.014 0.13 -10000 0 -0.35 52 52
ORAI1 0 0.023 0.091 6 -0.15 7 13
CSK -0.019 0.16 -10000 0 -0.4 63 63
B7 family/CD28 -0.007 0.16 -10000 0 -0.35 73 73
CHUK 0.021 0.013 -10000 0 -0.12 4 4
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.026 0.17 -10000 0 -0.43 66 66
PTPN6 -0.023 0.16 -10000 0 -0.4 65 65
VAV1 -0.023 0.16 -10000 0 -0.39 69 69
Monovalent TCR/CD3 -0.015 0.095 -10000 0 -0.2 97 97
CBL 0.023 0.006 -10000 0 -0.12 1 1
LCK -0.036 0.17 -10000 0 -0.4 78 78
PAG1 -0.019 0.16 -10000 0 -0.4 62 62
RAP1A 0.021 0.012 -10000 0 -0.12 3 3
TCR/CD3/MHC I/CD8/LCK -0.028 0.17 -10000 0 -0.42 68 68
CD80 0.019 0.024 -10000 0 -0.12 15 15
CD86 0.013 0.034 -10000 0 -0.12 32 32
PDK1/CARD11/BCL10/MALT1 -0.027 0.066 -10000 0 -0.17 77 77
HRAS 0.023 0.006 -10000 0 -0.12 1 1
GO:0035030 -0.016 0.13 -10000 0 -0.3 73 73
CD8A 0.022 0.012 -10000 0 -0.13 3 3
CD8B 0.021 0.016 -10000 0 -0.13 6 6
PTPRC -0.004 0.051 -10000 0 -0.12 86 86
PDK1/PKC theta -0.016 0.15 -10000 0 -0.35 76 76
CSK/PAG1 -0.014 0.15 -10000 0 -0.39 62 62
SOS1 0.017 0.027 -10000 0 -0.12 20 20
peptide-MHC class I 0.012 0.073 -10000 0 -0.2 51 51
GRAP2/SLP76 -0.015 0.17 -10000 0 -0.37 79 79
STIM1 -0.002 0.032 -10000 0 -0.17 18 18
RAS family/GTP 0.007 0.07 -10000 0 -0.14 71 71
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.014 0.15 -10000 0 -0.37 63 63
mol:DAG -0.041 0.088 -10000 0 -0.23 81 81
RAP1A/GDP 0.005 0.026 -10000 0 -0.052 56 56
PLCG1 0.019 0.024 -10000 0 -0.12 16 16
CD247 0.023 0.004 -10000 0 -10000 0 0
cytotoxic T cell degranulation -0.017 0.18 -10000 0 -0.64 28 28
RAP1A/GTP -0.002 0.009 -10000 0 -0.037 25 25
mol:PI-3-4-5-P3 -0.015 0.15 -10000 0 -0.35 76 76
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.05 0.12 0.12 3 -0.33 75 78
NRAS 0.022 0.011 -10000 0 -0.12 3 3
ZAP70 0.023 0.006 -10000 0 -0.12 1 1
GRB2/SOS1 0.021 0.045 -10000 0 -0.15 29 29
LAT/GRAP2/SLP76/VAV1 -0.013 0.14 -10000 0 -0.33 76 76
MALT1 0.017 0.026 -10000 0 -0.12 19 19
TRAF6 0.022 0.009 -10000 0 -0.12 2 2
CD8 heterodimer 0.033 0.016 -10000 0 -0.08 8 8
CARD11 0.017 0.028 -10000 0 -0.12 22 22
PRKCB -0.03 0.063 -10000 0 -0.17 81 81
PRKCE 0 0.079 -10000 0 -0.17 75 75
PRKCQ -0.023 0.17 -10000 0 -0.38 78 78
LCP2 0.013 0.033 -10000 0 -0.12 31 31
BCL10 0.023 0.001 -10000 0 -10000 0 0
regulation of survival gene product expression -0.005 0.11 -10000 0 -0.26 76 76
IKK complex 0.007 0.044 -10000 0 -0.082 56 56
RAS family/GDP -0.006 0.01 -10000 0 -0.036 33 33
MAP3K14 0.008 0.087 -10000 0 -0.18 75 75
PDPK1 -0.007 0.12 -10000 0 -0.28 76 76
TCR/CD3/MHC I/CD8/Fyn -0.03 0.19 -10000 0 -0.48 65 65
Canonical Wnt signaling pathway

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
HDAC1 0.037 0.047 0.11 118 -0.089 10 128
AES 0.036 0.042 0.099 124 -0.11 10 134
FBXW11 0.023 0.003 -10000 0 -10000 0 0
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
LRP6/FZD1 0.018 0.047 -10000 0 -0.11 66 66
SMAD4 0.022 0.007 -10000 0 -0.12 1 1
DKK2 0.023 0.011 -10000 0 -0.12 3 3
TLE1 0.033 0.038 0.098 96 -0.11 8 104
MACF1 0.016 0.026 -10000 0 -0.12 18 18
CTNNB1 0.021 0.098 0.18 8 -0.31 27 35
WIF1 0.02 0.022 -10000 0 -0.12 13 13
beta catenin/RanBP3 0.084 0.19 0.38 135 -0.35 13 148
KREMEN2 0.022 0.012 -10000 0 -0.12 4 4
DKK1 0.015 0.034 -10000 0 -0.12 33 33
beta catenin/beta TrCP1 0.033 0.096 0.19 8 -0.3 26 34
FZD1 0.023 0.006 -10000 0 -0.12 1 1
AXIN2 -0.037 0.16 -10000 0 -0.82 11 11
AXIN1 0.023 0.011 -10000 0 -0.12 3 3
RAN 0.024 0.002 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.036 0.083 -10000 0 -0.48 10 10
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.024 0.11 0.24 8 -0.31 32 40
Axin1/APC/GSK3 0.027 0.06 -10000 0 -0.25 16 16
Axin1/APC/GSK3/beta catenin/Macf1 0.03 0.068 -10000 0 -0.25 18 18
HNF1A 0.037 0.038 0.1 107 -0.12 3 110
CTBP1 0.037 0.04 0.1 107 -0.11 7 114
MYC -0.17 0.44 -10000 0 -1.3 74 74
RANBP3 0.023 0.009 -10000 0 -0.12 2 2
DKK2/LRP6/Kremen 2 0.032 0.043 -10000 0 -0.11 32 32
NKD1 0.022 0.012 -10000 0 -0.12 4 4
TCF4 0.036 0.042 0.1 112 -0.093 8 120
TCF3 0.037 0.039 0.1 113 -0.12 5 118
WNT1/LRP6/FZD1/Axin1 0.044 0.044 -10000 0 -0.097 36 36
Ran/GTP 0.018 0.012 -10000 0 -0.14 3 3
CtBP/CBP/TCF/TLE1/AES 0.08 0.23 0.46 123 -0.36 12 135
LEF1 0.011 0.057 0.097 78 -0.11 75 153
DVL1 0.027 0.076 -10000 0 -0.32 19 19
CSNK2A1 0.022 0.015 -10000 0 -0.12 6 6
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.025 0.14 -10000 0 -0.31 62 62
DKK1/LRP6/Kremen 2 0.027 0.047 -10000 0 -0.11 34 34
LRP6 0.014 0.034 -10000 0 -0.12 32 32
CSNK1A1 0.04 0.044 0.11 124 -0.13 1 125
NLK 0.017 0.022 -10000 0 -0.13 11 11
CCND1 -0.19 0.45 -10000 0 -1.3 84 84
WNT1 0.023 0.009 -10000 0 -0.12 2 2
GSK3A 0.021 0.019 -10000 0 -0.12 10 10
GSK3B 0.022 0.011 -10000 0 -0.12 3 3
FRAT1 0.023 0.006 -10000 0 -0.12 1 1
PPP2R5D 0.018 0.044 -10000 0 -0.23 10 10
APC 0.022 0.033 -10000 0 -0.085 38 38
WNT1/LRP6/FZD1 0.018 0.056 -10000 0 -0.17 26 26
CREBBP 0.035 0.037 0.1 100 -0.1 5 105
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.001 0.094 -10000 0 -0.22 49 49
TBX21 -0.081 0.27 -10000 0 -0.72 57 57
B2M 0.024 0.006 -10000 0 -10000 0 0
TYK2 0.015 0.029 -10000 0 -0.13 7 7
IL12RB1 0.017 0.024 -10000 0 -0.12 1 1
GADD45B -0.09 0.32 -10000 0 -0.91 53 53
IL12RB2 0.014 0.033 -10000 0 -0.13 14 14
GADD45G -0.079 0.28 -10000 0 -0.73 60 60
natural killer cell activation -0.003 0.018 -10000 0 -0.041 39 39
RELB 0.022 0.011 -10000 0 -0.12 3 3
RELA 0.023 0.009 -10000 0 -0.12 2 2
IL18 0.004 0.047 -10000 0 -0.12 66 66
IL2RA 0.021 0.017 -10000 0 -0.12 8 8
IFNG 0.013 0.038 -10000 0 -0.12 41 41
STAT3 (dimer) -0.073 0.27 -10000 0 -0.59 87 87
HLA-DRB5 -0.014 0.058 -10000 0 -0.12 119 119
FASLG -0.083 0.28 -10000 0 -0.72 58 58
NF kappa B2 p52/RelB -0.077 0.27 -10000 0 -0.62 85 85
CD4 0.012 0.029 -10000 0 -0.13 21 21
SOCS1 0.016 0.031 -10000 0 -0.12 27 27
EntrezGene:6955 -0.002 0.008 -10000 0 -10000 0 0
CD3D 0.004 0.045 -10000 0 -0.13 56 56
CD3E 0.012 0.034 -10000 0 -0.12 29 29
CD3G -0.001 0.051 -10000 0 -0.13 78 78
IL12Rbeta2/JAK2 0.009 0.063 -10000 0 -0.15 51 51
CCL3 -0.1 0.32 -10000 0 -0.86 62 62
CCL4 -0.09 0.27 -10000 0 -0.62 85 85
HLA-A 0.021 0.018 -10000 0 -0.12 8 8
IL18/IL18R 0.025 0.076 -10000 0 -0.12 81 81
NOS2 -0.082 0.26 -10000 0 -0.58 87 87
IL12/IL12R/TYK2/JAK2/SPHK2 0.002 0.091 -10000 0 -0.23 41 41
IL1R1 -0.17 0.42 -10000 0 -1 97 97
IL4 0.026 0.021 -10000 0 -0.11 3 3
JAK2 0.012 0.033 -10000 0 -0.13 16 16
EntrezGene:6957 -0.001 0.007 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.01 0.12 -10000 0 -0.38 38 38
RAB7A -0.063 0.26 -10000 0 -0.68 58 58
lysosomal transport -0.058 0.25 -10000 0 -0.64 59 59
FOS -0.26 0.48 -10000 0 -1.1 134 134
STAT4 (dimer) -0.073 0.28 -10000 0 -0.62 83 83
STAT5A (dimer) -0.082 0.28 -10000 0 -0.61 89 89
GZMA -0.11 0.34 -10000 0 -0.88 68 68
GZMB -0.1 0.31 -10000 0 -0.79 65 65
HLX 0.023 0.006 -10000 0 -0.12 1 1
LCK -0.092 0.29 -10000 0 -0.65 85 85
TCR/CD3/MHC II/CD4 -0.11 0.21 -10000 0 -0.34 196 196
IL2/IL2R 0.013 0.068 -10000 0 -0.1 114 114
MAPK14 -0.084 0.3 -10000 0 -0.72 73 73
CCR5 -0.063 0.25 -10000 0 -0.71 40 40
IL1B 0.005 0.044 -10000 0 -0.12 45 45
STAT6 -0.025 0.14 -10000 0 -0.4 32 32
STAT4 0.02 0.02 -10000 0 -0.12 11 11
STAT3 0.022 0.011 -10000 0 -0.12 3 3
STAT1 0.014 0.031 -10000 0 -0.12 26 26
NFKB1 0.021 0.013 -10000 0 -0.12 4 4
NFKB2 0.023 0.009 -10000 0 -0.12 2 2
IL12B 0.018 0.023 -10000 0 -10000 0 0
CD8A 0.024 0.011 -10000 0 -0.12 3 3
CD8B 0.024 0.015 -10000 0 -0.12 6 6
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.001 0.093 0.22 49 -10000 0 49
IL2RB 0.019 0.024 -10000 0 -0.12 16 16
proteasomal ubiquitin-dependent protein catabolic process -0.065 0.26 -10000 0 -0.58 83 83
IL2RG -0.002 0.05 -10000 0 -0.12 82 82
IL12 0.004 0.063 -10000 0 -0.14 49 49
STAT5A 0.022 0.013 -10000 0 -0.12 4 4
CD247 0.021 0.01 -10000 0 -10000 0 0
IL2 0.022 0.011 -10000 0 -0.12 3 3
SPHK2 0.022 0.011 -10000 0 -0.12 3 3
FRAP1 0.022 0.013 -10000 0 -0.12 4 4
IL12A -0.001 0.051 -10000 0 -0.12 73 73
IL12/IL12R/TYK2/JAK2 -0.099 0.3 -10000 0 -0.69 85 85
MAP2K3 -0.078 0.29 -10000 0 -0.67 81 81
RIPK2 0.013 0.034 -10000 0 -0.12 32 32
MAP2K6 -0.096 0.3 -10000 0 -0.69 82 82
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.008 0.032 -10000 0 -0.13 24 24
IL18RAP 0.022 0.02 -10000 0 -0.12 8 8
IL12Rbeta1/TYK2 0.024 0.037 -10000 0 -0.12 5 5
EOMES 0.018 0.031 -10000 0 -10000 0 0
STAT1 (dimer) -0.097 0.28 -10000 0 -0.6 97 97
T cell proliferation -0.06 0.22 -10000 0 -0.49 85 85
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.021 0.024 -10000 0 -0.12 13 13
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.11 0.2 -10000 0 -0.53 85 85
ATF2 -0.076 0.28 -10000 0 -0.66 76 76
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification -0.068 0.31 -10000 0 -1 51 51
CLOCK 0.017 0.024 -10000 0 -0.052 49 49
TIMELESS/CRY2 -0.064 0.31 -10000 0 -1 50 50
DEC1/BMAL1 0.024 0.039 -10000 0 -0.14 26 26
ATR 0.02 0.015 -10000 0 -0.12 5 5
NR1D1 -0.01 0.11 -10000 0 -0.38 19 19
ARNTL 0.018 0.023 -10000 0 -0.048 46 46
TIMELESS -0.08 0.33 -10000 0 -1.1 50 50
NPAS2 0.002 0.049 -10000 0 -0.097 94 94
CRY2 0.023 0 -10000 0 -10000 0 0
mol:CO 0.001 0.042 0.13 50 -10000 0 50
CHEK1 0.012 0.035 -10000 0 -0.12 34 34
mol:HEME -0.001 0.042 -10000 0 -0.13 50 50
PER1 0.022 0.014 -10000 0 -0.12 5 5
BMAL/CLOCK/NPAS2 0 0.087 -10000 0 -0.12 157 157
BMAL1/CLOCK -0.033 0.19 -10000 0 -0.55 56 56
S phase of mitotic cell cycle -0.068 0.31 -10000 0 -1 51 51
TIMELESS/CHEK1/ATR -0.071 0.32 -10000 0 -1.1 51 51
mol:NADPH -0.001 0.042 -10000 0 -0.13 50 50
PER1/TIMELESS -0.064 0.31 -10000 0 -1.1 50 50
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.022 0.011 -10000 0 -0.12 3 3
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0 0.088 -10000 0 -0.18 86 86
epithelial cell differentiation 0.029 0.059 -10000 0 -0.12 67 67
CYFIP2 0.02 0.018 -10000 0 -0.12 8 8
ENAH 0.009 0.056 -10000 0 -0.13 51 51
EGFR 0.015 0.03 -10000 0 -0.12 25 25
EPHA2 0.02 0.022 -10000 0 -0.12 13 13
MYO6 0.01 0.057 -10000 0 -0.12 67 67
CTNNB1 0.022 0.008 -10000 0 -0.12 1 1
ABI1/Sra1/Nap1 0.03 0.05 -10000 0 -0.12 53 53
AQP5 -0.059 0.15 -10000 0 -0.32 122 122
CTNND1 0.023 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.015 0.049 -10000 0 -0.11 67 67
regulation of calcium-dependent cell-cell adhesion 0.014 0.05 -10000 0 -0.11 67 67
EGF 0.02 0.021 -10000 0 -0.12 12 12
NCKAP1 0.023 0.004 -10000 0 -10000 0 0
AQP3 0.012 0.076 -10000 0 -0.3 21 21
cortical microtubule organization 0.029 0.059 -10000 0 -0.12 67 67
GO:0000145 0.008 0.045 -10000 0 -0.1 67 67
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.033 0.061 -10000 0 -0.12 67 67
MLLT4 0.014 0.032 -10000 0 -0.12 29 29
ARF6/GDP -0.022 0.05 -10000 0 -0.17 43 43
ARF6 0.023 0.003 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.029 0.062 -10000 0 -0.11 75 75
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.015 0.058 -10000 0 -0.18 30 30
PVRL2 0.019 0.023 -10000 0 -0.12 15 15
ZYX 0.011 0.054 -10000 0 -0.12 67 67
ARF6/GTP 0.035 0.063 -10000 0 -0.17 18 18
CDH1 0.021 0.016 -10000 0 -0.12 6 6
EGFR/EGFR/EGF/EGF 0.015 0.062 -10000 0 -0.18 27 27
RhoA/GDP 0.03 0.058 -10000 0 -0.11 71 71
actin cytoskeleton organization 0.009 0.059 -10000 0 -0.13 67 67
IGF-1R heterotetramer 0.013 0.032 -10000 0 -0.12 28 28
GIT1 0.022 0.012 -10000 0 -0.12 4 4
IGF1R 0.013 0.032 -10000 0 -0.12 28 28
IGF1 0.007 0.045 -10000 0 -0.12 60 60
DIAPH1 -0.022 0.2 -10000 0 -0.56 70 70
Wnt receptor signaling pathway -0.029 0.059 0.12 67 -10000 0 67
RHOA 0.023 0.006 -10000 0 -0.12 1 1
RhoA/GTP -0.022 0.049 -10000 0 -0.17 42 42
CTNNA1 0.022 0.01 -10000 0 -0.12 2 2
VCL 0.009 0.061 -10000 0 -0.13 67 67
EFNA1 0.014 0.031 -10000 0 -0.12 26 26
LPP 0.012 0.054 -10000 0 -0.11 69 69
Ephrin A1/EPHA2 0.012 0.064 -10000 0 -0.19 28 28
SEC6/SEC8 -0.02 0.049 -10000 0 -0.19 32 32
MGAT3 0.014 0.051 -10000 0 -0.11 67 67
HGF/MET -0.006 0.071 -10000 0 -0.18 45 45
HGF 0.02 0.023 -10000 0 -0.12 14 14
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0 0.089 -10000 0 -0.18 86 86
actin cable formation 0.012 0.08 -10000 0 -0.19 49 49
KIAA1543 0.013 0.05 -10000 0 -0.11 67 67
KIFC3 0.015 0.05 -10000 0 -0.11 67 67
NCK1 0.02 0.019 -10000 0 -0.12 9 9
EXOC3 0.023 0.009 -10000 0 -0.12 2 2
ACTN1 0.013 0.057 -10000 0 -0.12 67 67
NCK1/GIT1 0.022 0.043 -10000 0 -0.12 45 45
mol:GDP 0.029 0.059 -10000 0 -0.12 67 67
EXOC4 0.022 0.007 -10000 0 -0.12 1 1
STX4 0.014 0.052 -10000 0 -0.11 67 67
PIP5K1C 0.015 0.05 -10000 0 -0.11 67 67
LIMA1 0.019 0.023 -10000 0 -0.12 14 14
ABI1 0.022 0.009 -10000 0 -0.12 2 2
ROCK1 0.011 0.06 -10000 0 -0.15 43 43
adherens junction assembly 0.022 0.059 -10000 0 -0.23 15 15
IGF-1R heterotetramer/IGF1 0 0.071 -10000 0 -0.17 47 47
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.013 0.054 -10000 0 -0.15 43 43
MET 0 0.047 -10000 0 -0.12 70 70
PLEKHA7 0.013 0.052 -10000 0 -0.11 67 67
mol:GTP 0.028 0.061 -10000 0 -0.11 75 75
establishment of epithelial cell apical/basal polarity 0.013 0.062 -10000 0 -0.18 34 34
cortical actin cytoskeleton stabilization 0 0.088 -10000 0 -0.18 86 86
regulation of cell-cell adhesion 0.009 0.059 -10000 0 -0.13 67 67
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0 0.089 -10000 0 -0.18 86 86
Aurora A signaling

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
Aurora A/GADD45A 0.001 0.074 -10000 0 -0.18 70 70
BIRC5 0.018 0.023 -10000 0 -0.12 14 14
NFKBIA 0.013 0.039 0.11 8 -0.18 15 23
CPEB1 0.02 0.023 -10000 0 -0.12 14 14
AKT1 0.018 0.027 0.11 8 -0.1 12 20
NDEL1 0.023 0.006 -10000 0 -0.12 1 1
Aurora A/BRCA1 -0.006 0.069 -10000 0 -0.13 110 110
NDEL1/TACC3 0.006 0.075 -10000 0 -0.16 74 74
GADD45A 0.014 0.032 -10000 0 -0.12 29 29
GSK3B 0.021 0.013 0.071 9 -0.12 3 12
PAK1/Aurora A 0.003 0.071 -10000 0 -0.17 69 69
MDM2 0.02 0.02 -10000 0 -0.12 11 11
JUB 0.018 0.024 -10000 0 -0.12 15 15
TPX2 0.017 0.017 -10000 0 -0.071 16 16
TP53 -0.064 0.13 -10000 0 -0.25 179 179
DLG7 0.012 0.026 0.11 2 -0.11 8 10
AURKAIP1 0.02 0.021 -10000 0 -0.12 12 12
ARHGEF7 0.023 0.006 -10000 0 -0.12 1 1
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.006 0.08 -10000 0 -0.17 74 74
G2/M transition of mitotic cell cycle -0.006 0.069 -10000 0 -0.13 110 110
AURKA -0.004 0.078 0.14 4 -0.2 67 71
AURKB 0.003 0.064 -10000 0 -0.27 23 23
CDC25B 0.006 0.067 -10000 0 -0.25 29 29
G2/M transition checkpoint -0.001 0.067 -10000 0 -0.14 91 91
mRNA polyadenylation 0.006 0.061 -10000 0 -0.15 67 67
Aurora A/CPEB 0.006 0.061 -10000 0 -0.15 67 67
Aurora A/TACC1/TRAP/chTOG 0.006 0.091 -10000 0 -0.18 76 76
BRCA1 0.015 0.03 -10000 0 -0.12 24 24
centrosome duplication 0.003 0.071 -10000 0 -0.17 69 69
regulation of centrosome cycle 0.005 0.074 -10000 0 -0.16 74 74
spindle assembly 0.005 0.09 -10000 0 -0.18 76 76
TDRD7 0.014 0.031 -10000 0 -0.12 27 27
Aurora A/RasGAP/Survivin 0.005 0.082 -10000 0 -0.16 81 81
CENPA 0.012 0.044 -10000 0 -0.31 9 9
Aurora A/PP2A 0.007 0.068 -10000 0 -0.16 67 67
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process -0.025 0.096 -10000 0 -0.25 67 67
negative regulation of DNA binding -0.063 0.13 -10000 0 -0.25 179 179
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.034 0.01 -10000 0 -0.071 5 5
RASA1 0.021 0.012 -10000 0 -0.12 3 3
Ajuba/Aurora A -0.001 0.068 -10000 0 -0.14 91 91
mitotic prometaphase 0.002 0.018 0.073 32 -10000 0 32
proteasomal ubiquitin-dependent protein catabolic process -0.004 0.077 0.14 4 -0.2 67 71
TACC1 0.014 0.035 -10000 0 -0.12 34 34
TACC3 0.014 0.032 -10000 0 -0.12 29 29
Aurora A/Antizyme1 0.005 0.077 -10000 0 -0.16 76 76
Aurora A/RasGAP 0.005 0.073 -10000 0 -0.18 67 67
OAZ1 0.017 0.025 -10000 0 -0.12 17 17
RAN 0.023 0.002 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.02 0.019 0.074 5 -0.12 8 13
GIT1 0.022 0.012 -10000 0 -0.12 4 4
GIT1/beta-PIX/PAK1 0.037 0.036 -10000 0 -0.11 21 21
Importin alpha/Importin beta/TPX2 0.017 0.017 -10000 0 -0.071 16 16
PPP2R5D 0.022 0.014 -10000 0 -0.12 5 5
Aurora A/TPX2 -0.003 0.082 -10000 0 -0.2 74 74
PAK1 0.016 0.029 -10000 0 -0.12 23 23
CKAP5 0.021 0.013 -10000 0 -0.12 4 4
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.018 0.069 -9999 0 -0.16 81 81
EPHB2 0.02 0.02 -9999 0 -0.12 11 11
Syndecan-2/TACI 0.014 0.043 -9999 0 -0.11 47 47
LAMA1 0 0.053 -9999 0 -0.12 89 89
Syndecan-2/alpha2 ITGB1 -0.007 0.08 -9999 0 -0.17 58 58
HRAS 0.023 0.006 -9999 0 -0.12 1 1
Syndecan-2/CASK -0.001 0.039 -9999 0 -0.11 47 47
ITGA5 0.013 0.036 -9999 0 -0.12 38 38
BAX 0.025 0.021 -9999 0 -10000 0 0
EPB41 0.02 0.019 -9999 0 -0.12 9 9
positive regulation of cell-cell adhesion 0.004 0.05 -9999 0 -0.1 84 84
LAMA3 0.006 0.043 -9999 0 -0.12 55 55
EZR 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.01 0.039 -9999 0 -0.12 45 45
Syndecan-2/MMP2 -0.016 0.066 -9999 0 -0.16 68 68
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 0.007 0.061 -9999 0 -0.12 105 105
dendrite morphogenesis 0.01 0.049 -9999 0 -0.12 49 49
Syndecan-2/GM-CSF 0.014 0.043 -9999 0 -0.11 48 48
determination of left/right symmetry 0.011 0.025 -9999 0 -0.067 50 50
Syndecan-2/PKC delta 0.01 0.049 -9999 0 -0.12 54 54
GNB2L1 0.023 0.003 -9999 0 -10000 0 0
MAPK3 0.014 0.039 -9999 0 -0.094 48 48
MAPK1 0.013 0.039 -9999 0 -0.096 48 48
Syndecan-2/RACK1 0.024 0.043 -9999 0 -0.087 54 54
NF1 0.018 0.02 -9999 0 -0.12 10 10
FGFR/FGF/Syndecan-2 0.011 0.025 -9999 0 -0.067 50 50
ITGA2 0.011 0.038 -9999 0 -0.12 41 41
MAPK8 0.02 0.023 -9999 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin 0.005 0.07 -9999 0 -0.13 58 58
Syndecan-2/Kininogen 0.014 0.043 -9999 0 -0.11 47 47
ITGB1 0.021 0.015 -9999 0 -0.12 6 6
SRC 0.017 0.036 -9999 0 -0.091 10 10
Syndecan-2/CASK/Protein 4.1 0.009 0.045 -9999 0 -0.1 61 61
extracellular matrix organization 0.01 0.049 -9999 0 -0.12 53 53
actin cytoskeleton reorganization -0.018 0.069 -9999 0 -0.16 81 81
Syndecan-2/Caveolin-2/Ras 0.009 0.062 -9999 0 -0.11 95 95
Syndecan-2/Laminin alpha3 -0.001 0.06 -9999 0 -0.14 62 62
Syndecan-2/RasGAP 0.027 0.051 -9999 0 -0.15 7 7
alpha5/beta1 Integrin 0.016 0.048 -9999 0 -0.1 76 76
PRKCD 0.02 0.018 -9999 0 -0.12 8 8
Syndecan-2 dimer 0.011 0.049 -9999 0 -0.12 49 49
GO:0007205 0.004 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.026 0.047 -9999 0 -0.14 7 7
RHOA 0.023 0.006 -9999 0 -0.12 1 1
SDCBP 0.021 0.01 -9999 0 -0.12 2 2
TNFRSF13B 0.023 0 -9999 0 -10000 0 0
RASA1 0.021 0.012 -9999 0 -0.12 3 3
alpha2/beta1 Integrin 0.007 0.061 -9999 0 -0.12 105 105
Syndecan-2/Synbindin 0.006 0.05 -9999 0 -0.12 56 56
TGFB1 0.019 0.023 -9999 0 -0.12 14 14
CASP3 0.01 0.043 -9999 0 -0.1 54 54
FN1 -0.013 0.056 -9999 0 -0.12 114 114
Syndecan-2/IL8 0.001 0.055 -9999 0 -0.13 61 61
SDC2 0.011 0.025 -9999 0 -0.067 50 50
KNG1 0.022 0.011 -9999 0 -0.12 3 3
Syndecan-2/Neurofibromin 0.007 0.051 -9999 0 -0.13 52 52
TRAPPC4 0.016 0.025 -9999 0 -0.12 16 16
CSF2 0.023 0.009 -9999 0 -0.12 2 2
Syndecan-2/TGFB1 0.01 0.049 -9999 0 -0.12 53 53
Syndecan-2/Syntenin/PI-4-5-P2 0.004 0.05 -9999 0 -0.1 84 84
Syndecan-2/Ezrin 0.012 0.04 -9999 0 -0.097 51 51
PRKACA 0.008 0.045 -9999 0 -0.11 53 53
angiogenesis 0.001 0.055 -9999 0 -0.13 61 61
MMP2 -0.015 0.059 -9999 0 -0.12 128 128
IL8 0.004 0.047 -9999 0 -0.12 69 69
calcineurin-NFAT signaling pathway 0.014 0.043 -9999 0 -0.11 47 47
Paxillin-dependent events mediated by a4b1

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
CRKL 0.023 0.009 -10000 0 -0.12 2 2
Rac1/GDP 0.021 0.007 -10000 0 -10000 0 0
DOCK1 0.019 0.02 -10000 0 -0.12 10 10
ITGA4 0.015 0.03 -10000 0 -0.12 24 24
RAC1 0.023 0.002 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.004 0.065 -10000 0 -0.13 106 106
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.021 0.016 -10000 0 -0.12 7 7
alpha4/beta1 Integrin 0.02 0.059 -10000 0 -0.12 75 75
alpha4/beta7 Integrin/Paxillin 0.021 0.055 -10000 0 -0.1 79 79
lamellipodium assembly 0.001 0.12 -10000 0 -0.3 63 63
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
PI3K 0.007 0.065 -10000 0 -0.13 96 96
ARF6 0.023 0.003 -10000 0 -10000 0 0
TLN1 0.021 0.012 -10000 0 -0.12 3 3
PXN 0.021 0.014 -10000 0 -0.071 13 13
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
ARF6/GTP 0.031 0.051 -10000 0 -0.13 11 11
cell adhesion 0.026 0.062 -10000 0 -0.098 96 96
CRKL/CBL 0.033 0.013 -10000 0 -0.14 2 2
alpha4/beta1 Integrin/Paxillin 0.022 0.053 -10000 0 -0.1 76 76
ITGB1 0.021 0.015 -10000 0 -0.12 6 6
ITGB7 0.019 0.024 -10000 0 -0.12 15 15
ARF6/GDP 0.02 0.008 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.022 0.082 -10000 0 -0.12 187 187
p130Cas/Crk/Dock1 0.035 0.04 -10000 0 -0.11 34 34
VCAM1 -0.019 0.06 -10000 0 -0.12 139 139
alpha4/beta1 Integrin/Paxillin/Talin 0.027 0.063 -10000 0 -0.098 96 96
alpha4/beta1 Integrin/Paxillin/GIT1 0.034 0.055 -10000 0 -0.09 76 76
BCAR1 0.022 0.011 -10000 0 -0.12 3 3
mol:GDP -0.032 0.054 0.09 76 -10000 0 76
CBL 0.023 0.006 -10000 0 -0.12 1 1
PRKACA 0.021 0.017 -10000 0 -0.12 8 8
GIT1 0.022 0.012 -10000 0 -0.12 4 4
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.027 0.063 -10000 0 -0.098 96 96
Rac1/GTP -0.001 0.13 -10000 0 -0.33 62 62
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.02 0.16 -10000 0 -0.69 21 21
UGCG -0.001 0.079 -10000 0 -0.73 5 5
AKT1/mTOR/p70S6K/Hsp90/TERT -0.031 0.16 -10000 0 -0.32 101 101
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.001 0.078 -10000 0 -0.71 5 5
mol:DAG -0.043 0.2 -10000 0 -0.89 29 29
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.04 0.18 -10000 0 -0.38 98 98
FRAP1 -0.053 0.2 -10000 0 -0.43 98 98
FOXO3 -0.053 0.2 -10000 0 -0.41 105 105
AKT1 -0.058 0.21 -10000 0 -0.44 103 103
GAB2 0.007 0.041 -10000 0 -0.12 50 50
SMPD1 0.006 0.042 -10000 0 -0.52 1 1
SGMS1 -0.029 0.16 -10000 0 -0.68 29 29
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 -0.005 0.05 -10000 0 -0.13 67 67
CALM1 0.022 0.014 -10000 0 -0.12 5 5
cell proliferation -0.039 0.16 -10000 0 -0.32 96 96
EIF3A 0.022 0.004 -10000 0 -10000 0 0
PI3K 0.008 0.067 -10000 0 -0.15 67 67
RPS6KB1 -0.031 0.18 -10000 0 -0.82 23 23
mol:sphingomyelin -0.043 0.2 -10000 0 -0.89 29 29
natural killer cell activation -0.001 0.003 -10000 0 -0.011 23 23
JAK3 0.022 0.016 -10000 0 -0.12 5 5
PIK3R1 0.015 0.033 -10000 0 -0.12 29 29
JAK1 0.022 0.013 -10000 0 -0.05 10 10
NFKB1 0.021 0.013 -10000 0 -0.12 4 4
MYC -0.11 0.32 -10000 0 -0.85 80 80
MYB -0.064 0.29 -10000 0 -1.1 41 41
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.039 0.16 -10000 0 -0.32 104 104
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.008 0.17 -10000 0 -0.76 23 23
mol:PI-3-4-5-P3 -0.037 0.15 -10000 0 -0.31 104 104
Rac1/GDP 0.008 0.051 -10000 0 -0.12 66 66
T cell proliferation -0.032 0.14 -10000 0 -0.29 104 104
SHC1 0.022 0.004 -10000 0 -10000 0 0
RAC1 0.023 0.002 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.001 0.019 -10000 0 -0.064 41 41
PRKCZ -0.033 0.15 -10000 0 -0.3 104 104
NF kappa B1 p50/RelA -0.035 0.19 -10000 0 -0.38 104 104
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.016 0.12 -10000 0 -0.32 51 51
HSP90AA1 0.023 0.003 -10000 0 -10000 0 0
RELA 0.023 0.009 -10000 0 -0.12 2 2
IL2RA 0.02 0.018 -10000 0 -0.12 8 8
IL2RB 0.019 0.025 -10000 0 -0.091 24 24
TERT 0.023 0 -10000 0 -10000 0 0
E2F1 -0.016 0.13 -10000 0 -0.42 44 44
SOS1 0.016 0.027 -10000 0 -0.12 20 20
RPS6 0.023 0.002 -10000 0 -10000 0 0
mol:cAMP 0 0.009 0.031 39 -10000 0 39
PTPN11 0.021 0.012 -10000 0 -0.12 3 3
IL2RG -0.002 0.051 -10000 0 -0.11 90 90
actin cytoskeleton organization -0.032 0.14 -10000 0 -0.29 104 104
GRB2 0.022 0.007 -10000 0 -0.12 1 1
IL2 0.023 0.014 -10000 0 -0.054 13 13
PIK3CA 0.02 0.019 -10000 0 -0.073 15 15
Rac1/GTP 0.02 0.057 -10000 0 -0.11 66 66
LCK 0.022 0.017 -10000 0 -0.067 15 15
BCL2 -0.033 0.17 -10000 0 -0.41 59 59
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.056 0.28 -10000 0 -0.62 65 65
PCK1 -0.16 0.41 -10000 0 -1 87 87
HNF4A -0.11 0.36 -10000 0 -0.73 113 113
KCNJ11 -0.012 0.27 -10000 0 -0.63 41 41
AKT1 -0.004 0.16 -10000 0 -0.31 50 50
response to starvation -0.019 0.045 -10000 0 -0.12 76 76
DLK1 -0.028 0.28 -10000 0 -0.64 50 50
NKX2-1 -0.01 0.15 -10000 0 -0.49 2 2
ACADM -0.069 0.3 -10000 0 -0.64 79 79
TAT -0.025 0.2 -10000 0 -0.56 18 18
CEBPB 0.021 0.032 -10000 0 -0.11 30 30
CEBPA 0.029 0.015 -10000 0 -0.1 6 6
TTR 0.011 0.16 -10000 0 -0.75 5 5
PKLR -0.045 0.27 -10000 0 -0.6 56 56
APOA1 -0.17 0.49 -10000 0 -1 115 115
CPT1C -0.052 0.27 -10000 0 -0.62 56 56
ALAS1 -0.012 0.19 -10000 0 -0.93 5 5
TFRC -0.1 0.4 -10000 0 -0.94 85 85
FOXF1 0.015 0.012 -10000 0 -0.11 5 5
NF1 0.024 0.026 -10000 0 -0.13 12 12
HNF1A (dimer) 0.042 0.019 -10000 0 -0.13 5 5
CPT1A -0.064 0.29 -10000 0 -0.63 77 77
HMGCS1 -0.059 0.29 -10000 0 -0.64 66 66
NR3C1 0.035 0.017 -10000 0 -0.11 5 5
CPT1B -0.047 0.27 -10000 0 -0.6 58 58
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.029 0.013 -10000 0 -0.14 2 2
GCK -0.045 0.27 -10000 0 -0.59 58 58
CREB1 -0.009 0.07 -10000 0 -0.17 77 77
IGFBP1 -0.014 0.16 -10000 0 -0.54 6 6
PDX1 0.028 0.17 -10000 0 -0.76 4 4
UCP2 -0.093 0.33 -10000 0 -0.68 95 95
ALDOB -0.012 0.27 -10000 0 -0.6 47 47
AFP 0.017 0.051 -10000 0 -0.32 2 2
BDH1 -0.07 0.3 -10000 0 -0.64 77 77
HADH -0.021 0.28 -10000 0 -0.64 48 48
F2 -0.066 0.34 -10000 0 -0.78 53 53
HNF1A 0.042 0.019 -10000 0 -0.13 5 5
G6PC 0.025 0.076 -10000 0 -0.42 1 1
SLC2A2 0.021 0.18 -10000 0 -0.66 2 2
INS 0.009 0.012 0.16 1 -0.14 2 3
FOXA1 0.035 0.03 -10000 0 -0.17 4 4
FOXA3 0.002 0.097 -10000 0 -0.19 78 78
FOXA2 -0.008 0.32 -10000 0 -0.67 53 53
ABCC8 -0.012 0.27 -10000 0 -0.62 41 41
ALB 0.017 0.051 -10000 0 -0.3 3 3
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.012 0.11 -10000 0 -0.21 118 118
BAG4 0.022 0.012 -10000 0 -0.12 4 4
BAD 0.007 0.036 -10000 0 -0.11 20 20
NFKBIA 0.016 0.028 -10000 0 -0.12 21 21
BIRC3 -0.005 0.053 -10000 0 -0.12 94 94
BAX 0.007 0.036 -10000 0 -0.11 19 19
EnzymeConsortium:3.1.4.12 0 0.027 -10000 0 -0.061 46 46
IKBKB -0.009 0.11 -10000 0 -0.2 119 119
MAP2K2 0.013 0.036 -10000 0 -0.099 27 27
MAP2K1 0.015 0.033 -10000 0 -0.098 21 21
SMPD1 0.005 0.028 -10000 0 -0.092 17 17
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.005 0.12 -10000 0 -0.2 119 119
MAP2K4 0.008 0.039 -10000 0 -0.1 33 33
protein ubiquitination -0.012 0.11 -10000 0 -0.2 119 119
EnzymeConsortium:2.7.1.37 0.017 0.034 -10000 0 -0.093 25 25
response to UV 0 0 -10000 0 -0.001 13 13
RAF1 0.011 0.035 -10000 0 -0.1 24 24
CRADD 0.023 0.009 -10000 0 -0.12 2 2
mol:ceramide 0.003 0.038 -10000 0 -0.11 25 25
I-kappa-B-alpha/RELA/p50/ubiquitin 0.018 0.041 -10000 0 -0.097 61 61
MADD 0.023 0.006 -10000 0 -0.12 1 1
MAP3K1 0.004 0.04 -10000 0 -0.1 39 39
TRADD 0.023 0.006 -10000 0 -0.12 1 1
RELA/p50 0.023 0.009 -10000 0 -0.12 2 2
MAPK3 0.017 0.035 -10000 0 -0.099 22 22
MAPK1 0.016 0.037 -10000 0 -0.1 26 26
p50/RELA/I-kappa-B-alpha 0.018 0.049 -10000 0 -0.12 61 61
FADD -0.01 0.11 -10000 0 -0.2 118 118
KSR1 0.008 0.036 -10000 0 -0.11 20 20
MAPK8 0.008 0.042 -10000 0 -0.11 39 39
TRAF2 0.024 0.001 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK -0.013 0.11 -10000 0 -0.2 119 119
TNF R/SODD 0.027 0.034 -10000 0 -0.11 29 29
TNF 0.02 0.02 -10000 0 -0.12 11 11
CYCS 0.006 0.038 0.097 1 -0.11 22 23
IKBKG -0.009 0.11 -10000 0 -0.19 119 119
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.014 0.12 -10000 0 -0.22 118 118
RELA 0.023 0.009 -10000 0 -0.12 2 2
RIPK1 0.022 0.011 -10000 0 -0.12 3 3
AIFM1 0.001 0.044 0.097 1 -0.12 38 39
TNF/TNF R/SODD 0.038 0.034 -10000 0 -0.11 20 20
TNFRSF1A 0.021 0.016 -10000 0 -0.12 7 7
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.005 0.13 -10000 0 -0.67 17 17
NSMAF -0.011 0.11 -10000 0 -0.21 118 118
response to hydrogen peroxide 0 0 -10000 0 -0.001 13 13
BCL2 0.016 0.031 -10000 0 -0.12 27 27
Reelin signaling pathway

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
CDK5R1/CDK5 0.022 0.042 -9999 0 -0.1 52 52
VLDLR 0.01 0.038 -9999 0 -0.12 41 41
CRKL 0.023 0.009 -9999 0 -0.12 2 2
LRPAP1 0.018 0.024 -9999 0 -0.12 15 15
FYN 0.011 0.037 -9999 0 -0.12 40 40
ITGA3 0.012 0.034 -9999 0 -0.12 33 33
RELN/VLDLR/Fyn -0.006 0.073 -9999 0 -0.13 102 102
MAPK8IP1/MKK7/MAP3K11/JNK1 0.055 0.042 -9999 0 -0.093 31 31
AKT1 -0.015 0.078 -9999 0 -0.15 113 113
MAP2K7 0.022 0.012 -9999 0 -0.12 4 4
RAPGEF1 0.023 0 -9999 0 -10000 0 0
DAB1 0.022 0.011 -9999 0 -0.12 3 3
RELN/LRP8/DAB1 0.025 0.042 -9999 0 -0.11 21 21
LRPAP1/LRP8 0.015 0.054 -9999 0 -0.15 45 45
RELN/LRP8/DAB1/Fyn 0.02 0.056 -9999 0 -0.096 63 63
DAB1/alpha3/beta1 Integrin -0.006 0.069 -9999 0 -0.14 60 60
long-term memory 0.016 0.062 -9999 0 -0.13 20 20
DAB1/LIS1 0.016 0.067 -9999 0 -0.14 25 25
DAB1/CRLK/C3G 0.012 0.057 -9999 0 -0.13 21 21
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
DAB1/NCK2 0.019 0.067 -9999 0 -0.14 22 22
ARHGEF2 0.022 0.009 -9999 0 -0.12 2 2
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A 0.001 0.052 -9999 0 -0.12 86 86
CDK5R1 0.023 0.006 -9999 0 -0.12 1 1
RELN 0.001 0.053 -9999 0 -0.12 88 88
PIK3R1 0.015 0.031 -9999 0 -0.12 27 27
RELN/LRP8/Fyn 0.009 0.061 -9999 0 -0.12 62 62
GRIN2A/RELN/LRP8/DAB1/Fyn 0.015 0.066 -9999 0 -0.11 42 42
MAPK8 0.021 0.015 -9999 0 -0.12 6 6
RELN/VLDLR/DAB1 0.011 0.055 -9999 0 -0.1 69 69
ITGB1 0.021 0.015 -9999 0 -0.12 6 6
MAP1B -0.006 0.056 -9999 0 -0.11 96 96
RELN/LRP8 0.015 0.058 -9999 0 -0.12 53 53
GRIN2B/RELN/LRP8/DAB1/Fyn 0.029 0.061 -9999 0 -0.11 23 23
PI3K 0.007 0.065 -9999 0 -0.13 96 96
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin 0.004 0.063 -9999 0 -0.14 72 72
RAP1A 0.005 0.05 -9999 0 -0.13 26 26
PAFAH1B1 0.021 0.018 -9999 0 -0.12 9 9
MAPK8IP1 0.017 0.029 -9999 0 -0.12 24 24
CRLK/C3G 0.034 0.01 -9999 0 -0.14 1 1
GRIN2B 0.021 0.019 -9999 0 -0.12 10 10
NCK2 0.023 0.006 -9999 0 -0.12 1 1
neuron differentiation 0.017 0.057 -9999 0 -0.18 23 23
neuron adhesion -0.004 0.061 -9999 0 -0.13 67 67
LRP8 0.02 0.021 -9999 0 -0.12 12 12
GSK3B -0.011 0.074 -9999 0 -0.14 114 114
RELN/VLDLR/DAB1/Fyn 0.006 0.066 -9999 0 -0.1 103 103
MAP3K11 0.022 0.014 -9999 0 -0.12 5 5
RELN/VLDLR/DAB1/P13K -0.018 0.083 -9999 0 -0.16 112 112
CDK5 0.015 0.032 -9999 0 -0.12 28 28
MAPT 0.01 0.016 -9999 0 -0.094 5 5
neuron migration -0.014 0.079 -9999 0 -0.19 52 52
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.017 0.057 -9999 0 -0.18 23 23
RELN/VLDLR 0.007 0.071 -9999 0 -0.11 119 119
HIF-2-alpha transcription factor network

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
MMP14 -0.098 0.3 -10000 0 -0.93 63 63
oxygen homeostasis 0.001 0.01 -10000 0 -10000 0 0
TCEB2 0.023 0.006 -10000 0 -0.12 1 1
TCEB1 0.022 0.011 -10000 0 -0.12 3 3
VHL/Elongin B/Elongin C/HIF2A 0.008 0.11 -10000 0 -0.21 61 61
EPO 0.004 0.19 -10000 0 -0.38 49 49
FIH (dimer) 0.023 0.013 -10000 0 -0.12 1 1
APEX1 0.02 0.026 -10000 0 -0.12 11 11
SERPINE1 -0.015 0.19 -10000 0 -0.39 56 56
FLT1 -0.027 0.23 -10000 0 -0.76 46 46
ADORA2A -0.01 0.17 -10000 0 -0.38 52 52
germ cell development -0.018 0.2 -10000 0 -0.37 78 78
SLC11A2 -0.011 0.19 -10000 0 -0.39 63 63
BHLHE40 -0.013 0.18 -10000 0 -0.36 68 68
HIF1AN 0.023 0.013 -10000 0 -0.12 1 1
HIF2A/ARNT/SIRT1 0.012 0.14 -10000 0 -0.26 56 56
ETS1 0.027 0.037 -10000 0 -0.11 33 33
CITED2 0.025 0.079 -10000 0 -0.86 3 3
KDR -0.027 0.22 -10000 0 -0.74 46 46
PGK1 -0.013 0.2 -10000 0 -0.4 71 71
SIRT1 0.023 0.003 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.022 0.23 -10000 0 -0.44 52 52
EPAS1 -0.009 0.11 -10000 0 -0.21 90 90
SP1 0.016 0.034 -10000 0 -0.077 59 59
ABCG2 -0.007 0.19 -10000 0 -0.39 57 57
EFNA1 -0.019 0.2 -10000 0 -0.4 76 76
FXN -0.011 0.17 -10000 0 -0.38 52 52
POU5F1 -0.02 0.2 -10000 0 -0.38 78 78
neuron apoptosis -0.021 0.23 0.43 52 -10000 0 52
EP300 0.022 0.01 -10000 0 -0.12 2 2
EGLN3 -0.001 0.051 -10000 0 -0.12 84 84
EGLN2 0.023 0.014 -10000 0 -0.12 2 2
EGLN1 0.023 0.014 -10000 0 -0.12 2 2
VHL/Elongin B/Elongin C 0.041 0.029 -10000 0 -0.12 15 15
VHL 0.021 0.016 -10000 0 -0.12 7 7
ARNT 0.023 0.021 -10000 0 -0.12 4 4
SLC2A1 -0.024 0.19 -10000 0 -0.4 70 70
TWIST1 -0.011 0.17 -10000 0 -0.38 53 53
ELK1 0.028 0.019 -10000 0 -0.1 9 9
HIF2A/ARNT/Cbp/p300 0.008 0.15 -10000 0 -0.28 59 59
VEGFA -0.013 0.2 -10000 0 -0.41 63 63
CREBBP 0.021 0.015 -10000 0 -0.12 6 6
FoxO family signaling

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
G6PC 0.023 0.06 -9999 0 -0.41 1 1
PLK1 -0.15 0.36 -9999 0 -0.86 82 82
CDKN1B -0.05 0.19 -9999 0 -0.36 108 108
FOXO3 -0.13 0.32 -9999 0 -0.61 127 127
KAT2B -0.011 0.027 -9999 0 -0.046 187 187
FOXO1/SIRT1 0.025 0.065 -9999 0 -0.24 15 15
CAT -0.16 0.38 -9999 0 -0.97 74 74
CTNNB1 0.022 0.008 -9999 0 -0.12 1 1
AKT1 0.009 0.038 -9999 0 -0.065 51 51
FOXO1 0.016 0.066 -9999 0 -0.27 11 11
MAPK10 0.013 0.042 -9999 0 -0.098 45 45
mol:GTP 0 0.003 -9999 0 -10000 0 0
FOXO4 0.011 0.13 -9999 0 -0.34 41 41
response to oxidative stress -0.008 0.029 -9999 0 -0.052 105 105
FOXO3A/SIRT1 -0.14 0.3 -9999 0 -0.58 132 132
XPO1 0.022 0.01 -9999 0 -0.12 2 2
EP300 0.024 0.01 -9999 0 -0.12 2 2
BCL2L11 0.005 0.086 -9999 0 -1.3 2 2
FOXO1/SKP2 0.022 0.069 -9999 0 -0.24 19 19
mol:GDP -0.008 0.029 -9999 0 -0.052 105 105
RAN 0.024 0.003 -9999 0 -10000 0 0
GADD45A -0.081 0.27 -9999 0 -0.79 51 51
YWHAQ 0.023 0.003 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.041 0.086 -9999 0 -0.27 21 21
MST1 0.007 0.034 -9999 0 -0.056 47 47
CSNK1D 0.023 0.001 -9999 0 -10000 0 0
CSNK1E 0.022 0.015 -9999 0 -0.12 6 6
FOXO4/14-3-3 family 0.013 0.12 -9999 0 -0.35 29 29
YWHAB 0.023 0.007 -9999 0 -0.12 1 1
MAPK8 0.016 0.042 -9999 0 -0.1 38 38
MAPK9 0.015 0.042 -9999 0 -0.11 35 35
YWHAG 0.02 0.022 -9999 0 -0.12 13 13
YWHAE 0.022 0.014 -9999 0 -0.12 5 5
YWHAZ 0.023 0.003 -9999 0 -10000 0 0
SIRT1 0.02 0.008 -9999 0 -10000 0 0
SOD2 -0.092 0.3 -9999 0 -0.67 90 90
RBL2 -0.083 0.27 -9999 0 -0.7 53 53
RAL/GDP 0.019 0.043 -9999 0 -0.13 27 27
CHUK 0.007 0.034 -9999 0 -0.058 44 44
Ran/GTP 0.017 0.014 -9999 0 -0.14 3 3
CSNK1G2 0.022 0.011 -9999 0 -0.12 3 3
RAL/GTP 0.022 0.044 -9999 0 -0.12 28 28
CSNK1G1 0.023 0.009 -9999 0 -0.12 2 2
FASLG 0.007 0.068 -9999 0 -1.2 1 1
SKP2 0.018 0.024 -9999 0 -0.12 16 16
USP7 0.02 0.02 -9999 0 -0.12 10 10
IKBKB 0.007 0.036 -9999 0 -0.055 65 65
CCNB1 -0.18 0.42 -9999 0 -1 89 89
FOXO1-3a-4/beta catenin -0.036 0.21 -9999 0 -0.39 98 98
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.068 -9999 0 -0.24 19 19
CSNK1A1 0.022 0.007 -9999 0 -0.12 1 1
SGK1 -0.011 0.027 -9999 0 -0.046 187 187
CSNK1G3 0.022 0.007 -9999 0 -0.12 1 1
Ran/GTP/Exportin 1 0.027 0.032 -9999 0 -0.11 26 26
ZFAND5 0.019 0.12 -9999 0 -0.57 8 8
SFN 0.014 0.032 -9999 0 -0.12 29 29
CDK2 0.022 0.023 -9999 0 -0.12 14 14
FOXO3A/14-3-3 -0.005 0.13 -9999 0 -0.33 47 47
CREBBP 0.025 0.016 -9999 0 -0.12 6 6
FBXO32 -0.27 0.5 -9999 0 -1.1 147 147
BCL6 -0.12 0.34 -9999 0 -0.87 67 67
RALB 0.023 0.008 -9999 0 -0.12 1 1
RALA 0.023 0.009 -9999 0 -0.12 2 2
YWHAH 0.021 0.014 -9999 0 -0.12 5 5
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.019 0.02 -10000 0 -0.12 10 10
HDAC3 0.023 0.002 -10000 0 -10000 0 0
VDR 0.019 0.022 -10000 0 -0.12 13 13
Cbp/p300/PCAF 0.02 0.043 -10000 0 -0.13 41 41
EP300 0.022 0.01 -10000 0 -0.12 2 2
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.001 0.095 -10000 0 -0.22 64 64
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.023 0.007 -10000 0 -0.12 1 1
AKT1 0.019 0.089 0.17 78 -0.21 28 106
RAR alpha/9cRA/Cyclin H -0.016 0.12 -10000 0 -0.22 106 106
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.002 0.081 -10000 0 -0.21 54 54
CDC2 0.006 0.04 -10000 0 -0.12 46 46
response to UV -0.001 0.008 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.006 0.062 -10000 0 -0.15 52 52
NCOR2 0.019 0.023 -10000 0 -0.12 15 15
VDR/VDR/Vit D3 0.008 0.035 -10000 0 -0.12 36 36
RXRs/RARs/NRIP1/9cRA -0.044 0.19 -10000 0 -0.48 72 72
NCOA2 0.021 0.013 -10000 0 -0.12 4 4
NCOA3 0.021 0.012 -10000 0 -0.12 3 3
NCOA1 0.022 0.009 -10000 0 -0.12 2 2
VDR/VDR/DNA 0.019 0.022 -10000 0 -0.12 13 13
RARG 0.02 0.016 -10000 0 -0.12 6 6
RAR gamma1/9cRA 0.024 0.028 -10000 0 -0.11 18 18
MAPK3 0.02 0.015 -10000 0 -0.12 5 5
MAPK1 0.021 0.016 -10000 0 -0.12 7 7
MAPK8 0.019 0.018 -10000 0 -0.12 6 6
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.036 0.14 -10000 0 -0.31 96 96
RARA 0.01 0.056 -10000 0 -0.19 27 27
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0 0.086 -10000 0 -0.21 56 56
PRKCA 0.008 0.043 -10000 0 -0.089 76 76
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.063 0.21 -10000 0 -0.54 74 74
RXRG -0.006 0.07 -10000 0 -0.19 52 52
RXRA -0.034 0.11 -10000 0 -0.21 98 98
RXRB 0.003 0.064 -10000 0 -0.19 39 39
VDR/Vit D3/DNA 0.008 0.035 -10000 0 -0.12 36 36
RBP1 0.01 0.035 -10000 0 -0.12 35 35
CRBP1/9-cic-RA -0.019 0.065 -10000 0 -0.13 138 138
RARB 0.012 0.036 -10000 0 -0.12 33 33
PRKCG 0.018 0.025 -10000 0 -0.054 47 47
MNAT1 0.023 0.007 -10000 0 -0.12 1 1
RAR alpha/RXRs -0.021 0.16 -10000 0 -0.36 81 81
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.016 0.13 -10000 0 -0.28 79 79
proteasomal ubiquitin-dependent protein catabolic process -0.01 0.099 -10000 0 -0.25 51 51
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.06 0.21 -10000 0 -0.54 73 73
positive regulation of DNA binding -0.02 0.11 -10000 0 -0.2 106 106
NRIP1 -0.098 0.32 -10000 0 -0.98 59 59
RXRs/RARs -0.048 0.17 -10000 0 -0.4 93 93
RXRs/RXRs/DNA/9cRA -0.042 0.14 -10000 0 -0.32 95 95
PRKACA 0.021 0.017 -10000 0 -0.12 8 8
CDK7 0.018 0.023 -10000 0 -0.12 14 14
TFIIH 0.029 0.053 -10000 0 -0.13 46 46
RAR alpha/9cRA 0.023 0.071 -10000 0 -0.2 26 26
CCNH 0.02 0.022 -10000 0 -0.12 13 13
CREBBP 0.021 0.015 -10000 0 -0.12 6 6
RAR gamma2/9cRA 0.025 0.05 -10000 0 -0.18 16 16
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.022 0.012 -9999 0 -0.12 4 4
Caspase 8 (4 units) 0.023 0.084 -9999 0 -0.25 34 34
NEF 0.005 0.007 -9999 0 -0.066 5 5
NFKBIA -0.001 0.039 -9999 0 -0.066 109 109
BIRC3 -0.058 0.13 -9999 0 -0.21 206 206
CYCS 0.013 0.071 -9999 0 -0.23 29 29
RIPK1 0.022 0.011 -9999 0 -0.12 3 3
CD247 0.028 0.008 -9999 0 -0.11 1 1
MAP2K7 0.018 0.091 -9999 0 -0.38 16 16
protein ubiquitination 0.021 0.067 -9999 0 -0.18 29 29
CRADD 0.023 0.009 -9999 0 -0.12 2 2
DAXX 0.022 0.012 -9999 0 -0.12 4 4
FAS 0.016 0.025 -9999 0 -0.12 17 17
BID 0.021 0.065 -9999 0 -0.24 28 28
NF-kappa-B/RelA/I kappa B alpha -0.021 0.11 -9999 0 -0.18 146 146
TRADD 0.023 0.006 -9999 0 -0.12 1 1
MAP3K5 0.018 0.025 -9999 0 -0.12 17 17
CFLAR 0.022 0.011 -9999 0 -0.12 3 3
FADD 0.023 0.009 -9999 0 -0.12 2 2
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.021 0.11 -9999 0 -0.18 146 146
MAPK8 0.02 0.09 -9999 0 -0.36 17 17
APAF1 0.021 0.014 -9999 0 -0.12 5 5
TRAF1 0.023 0.001 -9999 0 -10000 0 0
TRAF2 0.023 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.019 0.068 -9999 0 -0.26 27 27
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.019 0.075 -9999 0 -0.21 34 34
CHUK 0.021 0.071 -9999 0 -0.2 29 29
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.038 0.068 -9999 0 -0.11 81 81
TCRz/NEF 0.028 0.014 -9999 0 -0.16 2 2
TNF 0.02 0.02 -9999 0 -0.12 11 11
FASLG 0.029 0.021 -9999 0 -0.33 1 1
NFKB1 0.004 0.031 -9999 0 -0.059 71 71
TNFR1A/BAG4/TNF-alpha 0.038 0.034 -9999 0 -0.11 20 20
CASP6 -0.041 0.21 -9999 0 -0.53 79 79
CASP7 -0.058 0.19 -9999 0 -0.41 117 117
RELA 0.003 0.032 -9999 0 -0.05 102 102
CASP2 0.022 0.009 -9999 0 -0.12 2 2
CASP3 -0.06 0.2 -9999 0 -0.41 118 118
TNFRSF1A 0.021 0.016 -9999 0 -0.12 7 7
TNFR1A/BAG4 0.027 0.034 -9999 0 -0.11 29 29
CASP8 0.023 0.004 -9999 0 -10000 0 0
CASP9 0.022 0.014 -9999 0 -0.12 5 5
MAP3K14 0.022 0.071 -9999 0 -0.2 33 33
APAF-1/Caspase 9 -0.028 0.12 -9999 0 -0.22 126 126
BCL2 0.02 0.087 -9999 0 -0.34 17 17
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.009 0.13 -9999 0 -0.41 49 49
KLHL20 -0.012 0.085 -9999 0 -0.18 79 79
CYFIP2 0.02 0.018 -9999 0 -0.12 8 8
Rac1/GDP 0.012 0.091 -9999 0 -0.22 55 55
ENAH -0.01 0.13 -9999 0 -0.4 50 50
AP1M1 0.021 0.017 -9999 0 -0.12 8 8
RAP1B 0.019 0.02 -9999 0 -0.12 10 10
RAP1A 0.021 0.012 -9999 0 -0.12 3 3
CTNNB1 0.022 0.008 -9999 0 -0.12 1 1
CDC42/GTP 0.011 0.07 -9999 0 -0.2 34 34
ABI1/Sra1/Nap1 -0.028 0.049 -9999 0 -0.13 84 84
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.038 0.055 -9999 0 -0.1 63 63
RAPGEF1 0 0.11 -9999 0 -0.34 49 49
CTNND1 0.023 0.004 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.01 0.13 -9999 0 -0.41 49 49
CRK -0.005 0.12 -9999 0 -0.37 49 49
E-cadherin/gamma catenin/alpha catenin 0.025 0.06 -9999 0 -0.13 61 61
alphaE/beta7 Integrin 0.026 0.035 -9999 0 -0.14 18 18
IQGAP1 0.02 0.017 -9999 0 -0.12 7 7
NCKAP1 0.023 0.004 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.015 0.059 -9999 0 -0.11 85 85
DLG1 -0.01 0.13 -9999 0 -0.41 49 49
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.022 0.05 -9999 0 -0.16 53 53
MLLT4 0.014 0.032 -9999 0 -0.12 29 29
ARF6/GTP/NME1/Tiam1 0.018 0.056 -9999 0 -0.11 71 71
PI3K -0.028 0.065 -9999 0 -0.2 52 52
ARF6 0.023 0.003 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin 0.017 0.054 -9999 0 -0.13 61 61
TIAM1 0.015 0.032 -9999 0 -0.12 28 28
E-cadherin(dimer)/Ca2+ 0.033 0.061 -9999 0 -0.12 67 67
AKT1 0.005 0.049 -9999 0 -0.13 44 44
PIK3R1 0.015 0.031 -9999 0 -0.12 27 27
CDH1 0.02 0.016 -9999 0 -0.12 6 6
RhoA/GDP 0.013 0.091 -9999 0 -0.22 55 55
actin cytoskeleton organization -0.007 0.064 -9999 0 -0.13 79 79
CDC42/GDP 0.013 0.091 -9999 0 -0.22 54 54
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.001 0.08 -9999 0 -0.19 66 66
ITGB7 0.019 0.024 -9999 0 -0.12 15 15
RAC1 0.023 0.002 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.036 0.065 -9999 0 -0.13 67 67
E-cadherin/Ca2+/beta catenin/alpha catenin 0.023 0.049 -9999 0 -0.11 64 64
mol:GDP 0.001 0.1 -9999 0 -0.26 54 54
CDC42/GTP/IQGAP1 0.018 0.043 -9999 0 -0.11 54 54
JUP 0.019 0.021 -9999 0 -0.12 12 12
p120 catenin/RhoA/GDP 0.017 0.094 -9999 0 -0.23 53 53
RAC1/GTP/IQGAP1 0.017 0.044 -9999 0 -0.11 55 55
PIP5K1C/AP1M1 0.033 0.014 -9999 0 -0.14 1 1
RHOA 0.023 0.006 -9999 0 -0.12 1 1
CDC42 0.023 0.002 -9999 0 -10000 0 0
CTNNA1 0.022 0.01 -9999 0 -0.12 2 2
positive regulation of S phase of mitotic cell cycle -0.014 0.063 -9999 0 -0.12 127 127
NME1 0.015 0.03 -9999 0 -0.12 24 24
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.011 0.14 -9999 0 -0.42 51 51
regulation of cell-cell adhesion -0.018 0.05 -9999 0 -0.18 34 34
WASF2 -0.002 0.036 -9999 0 -0.073 79 79
Rap1/GTP 0.013 0.08 -9999 0 -0.23 33 33
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.041 0.064 -9999 0 -0.1 76 76
CCND1 -0.018 0.076 -9999 0 -0.14 126 126
VAV2 -0.019 0.17 -9999 0 -0.46 65 65
RAP1/GDP 0.016 0.087 -9999 0 -0.25 34 34
adherens junction assembly -0.01 0.13 -9999 0 -0.4 51 51
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.022 0.009 -9999 0 -0.12 2 2
PIP5K1C 0.023 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.033 0.064 -9999 0 -0.17 23 23
E-cadherin/beta catenin 0.008 0.056 -9999 0 -0.23 28 28
mol:GTP 0 0 -9999 0 -10000 0 0
SRC -0.008 0.13 -9999 0 -0.4 49 49
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
Rac1/GTP -0.059 0.11 -9999 0 -0.3 77 77
E-cadherin/beta catenin/alpha catenin 0.026 0.058 -9999 0 -0.13 64 64
ITGAE 0.023 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.011 0.14 -9999 0 -0.42 49 49
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR -0.027 0.22 -10000 0 -0.83 37 37
regulation of axonogenesis -0.005 0.059 0.18 43 -10000 0 43
myoblast fusion 0 0.1 0.38 37 -10000 0 37
mol:GTP 0 0.065 -10000 0 -0.22 44 44
regulation of calcium-dependent cell-cell adhesion -0.007 0.087 0.21 53 -10000 0 53
ARF1/GTP 0.013 0.055 -10000 0 -0.16 45 45
mol:GM1 -0.002 0.048 -10000 0 -0.16 43 43
mol:Choline 0.004 0.051 -10000 0 -0.15 45 45
lamellipodium assembly -0.006 0.12 -10000 0 -0.41 44 44
MAPK3 0.005 0.085 -10000 0 -0.28 44 44
ARF6/GTP/NME1/Tiam1 0.008 0.088 -10000 0 -0.21 53 53
ARF1 0.018 0.028 -10000 0 -0.12 21 21
ARF6/GDP 0 0.1 -10000 0 -0.38 37 37
ARF1/GDP 0.005 0.1 -10000 0 -0.33 44 44
ARF6 0.016 0.035 -10000 0 -0.12 35 35
RAB11A 0.023 0.007 -10000 0 -0.12 1 1
TIAM1 0.014 0.034 -10000 0 -0.13 28 28
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.004 0.087 -10000 0 -0.28 45 45
actin filament bundle formation -0.007 0.1 0.34 44 -10000 0 44
KALRN 0.002 0.08 -10000 0 -0.29 37 37
RAB11FIP3/RAB11A 0.031 0.023 -10000 0 -0.13 11 11
RhoA/GDP 0.007 0.1 -10000 0 -0.34 44 44
NME1 0.014 0.031 -10000 0 -0.12 24 24
Rac1/GDP 0.007 0.1 -10000 0 -0.34 44 44
substrate adhesion-dependent cell spreading 0 0.065 -10000 0 -0.22 44 44
cortical actin cytoskeleton organization -0.007 0.12 -10000 0 -0.41 44 44
RAC1 0.023 0.002 -10000 0 -10000 0 0
liver development 0 0.065 -10000 0 -0.22 44 44
ARF6/GTP 0 0.065 -10000 0 -0.22 44 44
RhoA/GTP 0.016 0.056 -10000 0 -0.17 44 44
mol:GDP -0.005 0.11 -10000 0 -0.36 44 44
ARF6/GTP/RAB11FIP3/RAB11A 0.029 0.052 -10000 0 -0.13 50 50
RHOA 0.023 0.006 -10000 0 -0.12 1 1
PLD1 0 0.059 -10000 0 -0.18 43 43
RAB11FIP3 0.022 0.011 -10000 0 -0.12 3 3
tube morphogenesis -0.006 0.12 -10000 0 -0.41 44 44
ruffle organization 0.005 0.059 -10000 0 -0.18 43 43
regulation of epithelial cell migration 0 0.065 -10000 0 -0.22 44 44
PLD2 0.01 0.05 -10000 0 -0.16 44 44
PIP5K1A 0.005 0.059 -10000 0 -0.18 43 43
mol:Phosphatidic acid 0.004 0.051 -10000 0 -0.15 45 45
Rac1/GTP -0.007 0.12 -10000 0 -0.41 44 44
BCR signaling pathway

Figure S59.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S59.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.024 0.11 -10000 0 -0.25 76 76
IKBKB 0.013 0.077 0.18 15 -0.22 30 45
AKT1 -0.008 0.06 0.14 11 -0.15 45 56
IKBKG 0.012 0.068 0.16 1 -0.2 31 32
CALM1 -0.008 0.1 0.16 4 -0.28 51 55
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
MAP3K1 -0.029 0.13 -10000 0 -0.33 63 63
MAP3K7 0.021 0.014 -10000 0 -0.12 5 5
mol:Ca2+ -0.012 0.11 0.16 4 -0.3 51 55
DOK1 0.021 0.016 -10000 0 -0.12 7 7
AP-1 -0.014 0.077 0.14 1 -0.18 72 73
LYN 0.02 0.013 -10000 0 -0.12 4 4
BLNK 0.014 0.033 -10000 0 -0.12 31 31
SHC1 0.023 0.001 -10000 0 -10000 0 0
BCR complex 0.028 0.026 -10000 0 -0.14 3 3
CD22 -0.04 0.1 -10000 0 -0.28 57 57
CAMK2G -0.003 0.099 0.15 4 -0.28 44 48
CSNK2A1 0.021 0.015 -10000 0 -0.12 6 6
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.001 0.052 -10000 0 -0.14 37 37
GO:0007205 -0.012 0.11 0.16 4 -0.3 51 55
SYK 0.016 0.027 -10000 0 -0.12 20 20
ELK1 -0.008 0.1 0.16 4 -0.29 50 54
NFATC1 -0.014 0.084 0.16 1 -0.22 55 56
B-cell antigen/BCR complex 0.028 0.026 -10000 0 -0.14 3 3
PAG1/CSK 0.032 0.02 -10000 0 -0.1 12 12
NFKBIB 0.008 0.045 -10000 0 -0.13 46 46
HRAS -0.001 0.087 0.14 1 -0.25 43 44
NFKBIA 0.011 0.041 -10000 0 -0.12 36 36
NF-kappa-B/RelA/I kappa B beta 0.014 0.043 -10000 0 -0.12 42 42
RasGAP/Csk 0.023 0.067 -10000 0 -0.11 22 22
mol:GDP -0.011 0.11 0.15 4 -0.29 52 56
PTEN 0.022 0.008 -10000 0 -0.12 1 1
CD79B 0.023 0.006 -10000 0 -0.12 1 1
NF-kappa-B/RelA/I kappa B alpha 0.014 0.04 -10000 0 -0.11 42 42
GRB2 0.023 0.006 -10000 0 -0.12 1 1
PI3K/BCAP/CD19 -0.029 0.13 -10000 0 -0.37 54 54
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
mol:IP3 -0.012 0.11 0.16 4 -0.3 51 55
CSK 0.023 0.009 -10000 0 -0.12 2 2
FOS -0.023 0.11 0.15 2 -0.29 56 58
CHUK -0.004 0.096 0.16 1 -0.25 57 58
IBTK 0.02 0.016 -10000 0 -0.12 6 6
CARD11/BCL10/MALT1/TAK1 0.006 0.1 0.19 1 -0.24 54 55
PTPN6 -0.036 0.095 -10000 0 -0.26 58 58
RELA 0.023 0.009 -10000 0 -0.12 2 2
BCL2A1 0.009 0.034 -10000 0 -0.078 54 54
VAV2 -0.031 0.11 -10000 0 -0.31 55 55
ubiquitin-dependent protein catabolic process 0.012 0.045 -10000 0 -0.12 46 46
BTK -0.05 0.25 -10000 0 -1.1 32 32
CD19 -0.032 0.095 -10000 0 -0.29 41 41
MAP4K1 0.02 0.023 -10000 0 -0.12 14 14
CD72 0.023 0.006 -10000 0 -0.12 1 1
PAG1 0.022 0.014 -10000 0 -0.12 5 5
MAPK14 -0.021 0.11 -10000 0 -0.28 63 63
SH3BP5 0.021 0.015 -10000 0 -0.12 6 6
PIK3AP1 -0.009 0.11 0.17 4 -0.33 45 49
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.012 0.13 -10000 0 -0.3 81 81
RAF1 0.002 0.083 0.13 2 -0.24 42 44
RasGAP/p62DOK/SHIP 0.015 0.062 -10000 0 -0.11 24 24
CD79A 0.016 0.032 -10000 0 -0.12 28 28
re-entry into mitotic cell cycle -0.014 0.076 0.14 1 -0.18 72 73
RASA1 0.021 0.012 -10000 0 -0.12 3 3
MAPK3 0.009 0.074 0.13 3 -0.21 36 39
MAPK1 0.008 0.074 0.13 3 -0.22 36 39
CD72/SHP1 -0.026 0.095 -10000 0 -0.24 56 56
NFKB1 0.021 0.013 -10000 0 -0.12 4 4
MAPK8 -0.022 0.11 -10000 0 -0.29 63 63
actin cytoskeleton organization -0.024 0.098 -10000 0 -0.28 55 55
NF-kappa-B/RelA 0.022 0.096 -10000 0 -0.23 52 52
Calcineurin 0.014 0.098 -10000 0 -0.25 47 47
PI3K -0.038 0.075 -10000 0 -0.23 51 51
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.012 0.11 0.17 4 -0.34 42 46
SOS1 0.017 0.027 -10000 0 -0.12 20 20
Bam32/HPK1 -0.042 0.18 -10000 0 -0.55 46 46
DAPP1 -0.057 0.19 -10000 0 -0.61 46 46
cytokine secretion -0.012 0.08 0.16 1 -0.21 55 56
mol:DAG -0.012 0.11 0.16 4 -0.3 51 55
PLCG2 0.02 0.02 -10000 0 -0.12 11 11
MAP2K1 0.006 0.079 0.13 3 -0.22 39 42
B-cell antigen/BCR complex/FcgammaRIIB 0.009 0.063 -10000 0 -0.11 99 99
mol:PI-3-4-5-P3 -0.034 0.057 0.095 1 -0.18 48 49
ETS1 -0.006 0.098 0.15 2 -0.27 50 52
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.029 0.069 -10000 0 -0.17 20 20
B-cell antigen/BCR complex/LYN -0.037 0.1 -10000 0 -0.31 41 41
MALT1 0.017 0.026 -10000 0 -0.12 19 19
TRAF6 0.022 0.009 -10000 0 -0.12 2 2
RAC1 -0.026 0.1 -10000 0 -0.29 55 55
B-cell antigen/BCR complex/LYN/SYK -0.004 0.091 -10000 0 -0.22 51 51
CARD11 -0.009 0.11 0.16 4 -0.29 51 55
FCGR2B 0.004 0.044 -10000 0 -0.12 60 60
PPP3CA 0.021 0.014 -10000 0 -0.12 5 5
BCL10 0.023 0.001 -10000 0 -10000 0 0
IKK complex 0.012 0.039 0.1 16 -0.092 30 46
PTPRC -0.004 0.051 -10000 0 -0.12 86 86
PDPK1 -0.01 0.054 0.13 13 -0.13 50 63
PPP3CB 0.023 0.003 -10000 0 -10000 0 0
PPP3CC 0.022 0.011 -10000 0 -0.12 3 3
POU2F2 0.012 0.033 -10000 0 -0.075 53 53
Signaling events mediated by PRL

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
CCNE1 0.002 0.047 -10000 0 -0.12 70 70
mol:Halofuginone 0.003 0.025 -10000 0 -0.18 10 10
ITGA1 0.014 0.03 -10000 0 -0.12 24 24
CDKN1A 0.014 0.059 -10000 0 -0.29 18 18
PRL-3/alpha Tubulin 0.014 0.051 -10000 0 -0.1 83 83
mol:Ca2+ 0.018 0.076 0.28 41 -10000 0 41
AGT 0.02 0.02 -10000 0 -0.12 11 11
CCNA2 -0.001 0.094 -10000 0 -0.67 10 10
TUBA1B 0.023 0 -10000 0 -10000 0 0
EGR1 -0.002 0.06 -10000 0 -0.34 12 12
CDK2/Cyclin E1 0.006 0.074 -10000 0 -0.25 25 25
MAPK3 0.014 0.027 -10000 0 -0.072 46 46
PRL-2 /Rab GGTase beta 0.009 0.063 -10000 0 -0.15 73 73
MAPK1 0.013 0.031 -10000 0 -0.083 47 47
PTP4A1 0.001 0.092 -10000 0 -0.57 12 12
PTP4A3 0.011 0.038 -10000 0 -0.12 42 42
PTP4A2 0.022 0.009 -10000 0 -0.12 2 2
ITGB1 0.013 0.028 -10000 0 -0.074 48 48
SRC 0.023 0.009 -10000 0 -0.12 2 2
RAC1 -0.014 0.11 -10000 0 -0.34 54 54
Rab GGTase beta/Rab GGTase alpha 0.012 0.058 -10000 0 -0.14 66 66
PRL-1/ATF-5 -0.003 0.095 -10000 0 -0.57 11 11
RABGGTA 0.023 0.006 -10000 0 -0.12 1 1
BCAR1 0.02 0.076 0.28 41 -10000 0 41
RHOC -0.013 0.11 -10000 0 -0.35 51 51
RHOA -0.014 0.11 -10000 0 -0.34 54 54
cell motility -0.011 0.11 -10000 0 -0.32 56 56
PRL-1/alpha Tubulin 0 0.094 -10000 0 -0.61 10 10
PRL-3/alpha1 Integrin -0.012 0.08 -10000 0 -0.13 161 161
ROCK1 -0.012 0.11 -10000 0 -0.32 56 56
RABGGTB 0.017 0.022 -10000 0 -0.12 12 12
CDK2 0.018 0.023 -10000 0 -0.12 14 14
mitosis 0.001 0.091 -10000 0 -0.57 12 12
ATF5 0.018 0.027 -10000 0 -0.12 20 20
Aurora B 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
Condensin I complex -0.05 0.17 -9999 0 -0.34 101 101
STMN1 0.019 0.019 -9999 0 -0.069 23 23
Aurora B/RasGAP/Survivin 0.018 0.072 -9999 0 -0.16 70 70
Chromosomal passenger complex/Cul3 protein complex -0.001 0.087 -9999 0 -0.26 44 44
BIRC5 0.018 0.023 -9999 0 -0.12 14 14
DES -0.029 0.23 -9999 0 -0.95 32 32
Aurora C/Aurora B/INCENP 0.033 0.039 -9999 0 -0.11 32 32
Aurora B/TACC1 0.014 0.048 -9999 0 -0.13 42 42
Aurora B/PP2A 0.02 0.048 -9999 0 -0.14 36 36
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.005 0.061 -9999 0 -0.2 49 49
mitotic metaphase/anaphase transition 0.002 0.005 -9999 0 -10000 0 0
NDC80 0.009 0.032 -9999 0 -0.081 55 55
Cul3 protein complex 0.016 0.056 -9999 0 -0.11 58 58
KIF2C -0.065 0.21 -9999 0 -0.47 94 94
PEBP1 0.022 0.008 -9999 0 -0.12 1 1
KIF20A 0.009 0.038 -9999 0 -0.12 43 43
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP 0.012 0.058 -9999 0 -0.15 59 59
SEPT1 0.022 0.014 -9999 0 -0.12 5 5
SMC2 0.015 0.03 -9999 0 -0.12 25 25
SMC4 0.018 0.025 -9999 0 -0.12 17 17
NSUN2/NPM1/Nucleolin -0.024 0.17 -9999 0 -0.66 33 33
PSMA3 0.019 0.021 -9999 0 -0.12 11 11
G2/M transition of mitotic cell cycle 0 0.003 -9999 0 -10000 0 0
H3F3B -0.001 0.065 -9999 0 -0.21 47 47
AURKB 0.018 0.027 -9999 0 -0.12 19 19
AURKC 0.023 0.006 -9999 0 -0.12 1 1
CDCA8 0.019 0.021 -9999 0 -0.12 11 11
cytokinesis -0.04 0.2 -9999 0 -0.46 75 75
Aurora B/Septin1 -0.022 0.19 -9999 0 -0.43 73 73
AURKA 0.015 0.028 -9999 0 -0.12 21 21
INCENP 0.021 0.011 -9999 0 -0.12 2 2
KLHL13 -0.001 0.053 -9999 0 -0.12 89 89
BUB1 0.017 0.026 -9999 0 -0.12 17 17
hSgo1/Aurora B/Survivin 0.011 0.078 -9999 0 -0.16 77 77
EVI5 0.021 0.016 -9999 0 -0.12 6 6
RhoA/GTP -0.022 0.18 -9999 0 -0.38 80 80
SGOL1 0.016 0.028 -9999 0 -0.12 22 22
CENPA -0.036 0.17 -9999 0 -0.35 88 88
NCAPG 0.01 0.037 -9999 0 -0.12 39 39
Aurora B/HC8 Proteasome 0.009 0.063 -9999 0 -0.14 73 73
NCAPD2 0.015 0.03 -9999 0 -0.12 25 25
Aurora B/PP1-gamma 0.012 0.059 -9999 0 -0.15 61 61
RHOA 0.023 0.006 -9999 0 -0.12 1 1
NCAPH 0.019 0.02 -9999 0 -0.12 10 10
NPM1 -0.01 0.12 -9999 0 -0.41 39 39
RASA1 0.021 0.012 -9999 0 -0.12 3 3
KLHL9 0.023 0.007 -9999 0 -0.12 1 1
mitotic prometaphase -0.001 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.008 0.063 -9999 0 -0.14 73 73
PPP1CC 0.022 0.005 -9999 0 -10000 0 0
Centraspindlin -0.032 0.19 -9999 0 -0.39 89 89
RhoA/GDP 0.016 0.016 -9999 0 -0.14 6 6
NSUN2 -0.01 0.11 -9999 0 -0.39 40 40
MYLK -0.005 0.066 -9999 0 -0.21 50 50
KIF23 0.013 0.034 -9999 0 -0.12 32 32
VIM 0.016 0.028 -9999 0 -0.09 28 28
RACGAP1 0.017 0.025 -9999 0 -0.12 16 16
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.02 0.12 -9999 0 -0.37 57 57
Chromosomal passenger complex -0.035 0.17 -9999 0 -0.33 93 93
Chromosomal passenger complex/EVI5 0.032 0.084 -9999 0 -0.16 73 73
TACC1 0.014 0.035 -9999 0 -0.12 34 34
PPP2R5D 0.022 0.014 -9999 0 -0.12 5 5
CUL3 0.023 0.004 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.036 0.049 -10000 0 -0.094 62 62
ER alpha/Gai/GDP/Gbeta gamma 0.006 0.094 -10000 0 -0.26 53 53
AKT1 -0.054 0.23 -10000 0 -0.6 78 78
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.055 0.23 -10000 0 -0.61 78 78
mol:Ca2+ 0.011 0.069 -10000 0 -0.25 30 30
IGF1R 0.013 0.032 -10000 0 -0.12 28 28
E2/ER alpha (dimer)/Striatin 0.014 0.047 -10000 0 -0.1 72 72
SHC1 0.023 0.001 -10000 0 -10000 0 0
apoptosis 0.051 0.22 0.57 78 -10000 0 78
RhoA/GTP -0.016 0.034 -10000 0 -0.15 17 17
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.008 0.1 -10000 0 -0.25 59 59
regulation of stress fiber formation -0.007 0.049 0.14 38 -10000 0 38
E2/ERA-ERB (dimer) 0.018 0.041 -10000 0 -0.099 59 59
KRAS 0.014 0.034 -10000 0 -0.12 33 33
G13/GTP 0.014 0.041 -10000 0 -0.091 72 72
pseudopodium formation 0.007 0.049 -10000 0 -0.14 38 38
E2/ER alpha (dimer)/PELP1 0.018 0.041 -10000 0 -0.12 43 43
GRB2 0.023 0.006 -10000 0 -0.12 1 1
GNG2 0.02 0.018 -10000 0 -0.12 9 9
GNAO1 0.01 0.042 -10000 0 -0.12 51 51
HRAS 0.023 0.006 -10000 0 -0.12 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.012 0.13 -10000 0 -0.32 69 69
E2/ER beta (dimer) 0.017 0.004 -10000 0 -0.077 1 1
mol:GDP 0.002 0.075 -10000 0 -0.24 44 44
mol:NADP -0.012 0.13 -10000 0 -0.32 69 69
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
mol:IP3 0.01 0.071 -10000 0 -0.26 30 30
IGF-1R heterotetramer 0.013 0.032 -10000 0 -0.12 28 28
PLCB1 0.009 0.072 -10000 0 -0.26 30 30
PLCB2 0.016 0.069 -10000 0 -0.26 28 28
IGF1 0.007 0.045 -10000 0 -0.12 60 60
mol:L-citrulline -0.012 0.13 -10000 0 -0.32 69 69
RHOA 0.023 0.006 -10000 0 -0.12 1 1
Gai/GDP 0.023 0.057 -10000 0 -0.53 2 2
JNK cascade 0.017 0.004 -10000 0 -0.077 1 1
BCAR1 0.022 0.011 -10000 0 -0.12 3 3
ESR2 0.023 0.006 -10000 0 -0.12 1 1
GNAQ 0.021 0.016 -10000 0 -0.12 6 6
ESR1 0.018 0.024 -10000 0 -0.12 15 15
Gq family/GDP/Gbeta gamma 0.031 0.062 -10000 0 -0.3 16 16
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.017 0.086 -10000 0 -0.51 8 8
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.008 0.1 -10000 0 -0.25 59 59
GNAZ 0.022 0.011 -10000 0 -0.12 3 3
E2/ER alpha (dimer) 0.002 0.045 -10000 0 -0.13 58 58
STRN 0.022 0.013 -10000 0 -0.12 4 4
GNAL 0.021 0.018 -10000 0 -0.12 9 9
PELP1 0.023 0.009 -10000 0 -0.12 2 2
MAPK11 0.021 0.003 -10000 0 -0.057 1 1
GNAI2 0.022 0.011 -10000 0 -0.12 3 3
GNAI3 0.021 0.008 -10000 0 -0.12 1 1
GNAI1 0.012 0.035 -10000 0 -0.12 35 35
HBEGF -0.025 0.1 -10000 0 -0.25 66 66
cAMP biosynthetic process 0.016 0.032 -10000 0 -0.086 44 44
SRC 0.004 0.096 -10000 0 -0.25 62 62
PI3K 0.007 0.065 -10000 0 -0.13 96 96
GNB1 0.023 0.007 -10000 0 -0.12 1 1
G13/GDP/Gbeta gamma 0.023 0.076 -10000 0 -0.2 46 46
SOS1 0.017 0.027 -10000 0 -0.12 20 20
IGF-1R heterotetramer/IGF1 -0.038 0.072 -10000 0 -0.22 66 66
Gs family/GTP 0.022 0.035 -10000 0 -0.087 44 44
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.03 0.043 -10000 0 -0.11 38 38
vasodilation -0.011 0.12 -10000 0 -0.31 69 69
mol:DAG 0.01 0.071 -10000 0 -0.26 30 30
Gs family/GDP/Gbeta gamma 0.005 0.068 -10000 0 -0.2 46 46
MSN 0.007 0.051 -10000 0 -0.15 38 38
Gq family/GTP 0.015 0.073 -10000 0 -0.27 28 28
mol:PI-3-4-5-P3 -0.053 0.22 -10000 0 -0.59 78 78
NRAS 0.022 0.011 -10000 0 -0.12 3 3
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.011 0.12 0.31 69 -10000 0 69
GRB2/SOS1 0.021 0.045 -10000 0 -0.15 29 29
RhoA/GDP 0.014 0.076 -10000 0 -0.22 46 46
NOS3 -0.013 0.13 -10000 0 -0.34 69 69
GNA11 0.022 0.014 -10000 0 -0.12 5 5
MAPKKK cascade -0.005 0.15 -10000 0 -0.43 55 55
E2/ER alpha (dimer)/PELP1/Src 0.003 0.1 -10000 0 -0.26 59 59
ruffle organization 0.007 0.049 -10000 0 -0.14 38 38
ROCK2 0.01 0.049 -10000 0 -0.15 23 23
GNA14 0.02 0.02 -10000 0 -0.12 11 11
GNA15 0.021 0.017 -10000 0 -0.12 8 8
GNA13 0.022 0.009 -10000 0 -0.12 2 2
MMP9 -0.012 0.099 -10000 0 -0.26 60 60
MMP2 -0.018 0.1 -10000 0 -0.26 65 65
TCGA08_rtk_signaling

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
PDGFRA 0.004 0.044 -10000 0 -0.12 59 59
HRAS 0.023 0.006 -10000 0 -0.12 1 1
EGFR 0.015 0.03 -10000 0 -0.12 25 25
AKT 0 0.065 0.14 5 -0.13 79 84
FOXO3 0.021 0.017 -10000 0 -0.12 8 8
AKT1 0.021 0.019 -10000 0 -0.12 10 10
FOXO1 0.023 0.009 -10000 0 -0.12 2 2
AKT3 -0.004 0.056 -10000 0 -0.12 102 102
FOXO4 0.023 0 -10000 0 -10000 0 0
MET 0 0.047 -10000 0 -0.12 70 70
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
PIK3CB 0.015 0.03 -10000 0 -0.12 24 24
NRAS 0.022 0.011 -10000 0 -0.12 3 3
PIK3CG 0.011 0.037 -10000 0 -0.12 39 39
PIK3R3 0.012 0.036 -10000 0 -0.12 37 37
PIK3R2 0.017 0.03 -10000 0 -0.12 25 25
NF1 0.018 0.02 -10000 0 -0.12 10 10
RAS 0.005 0.061 0.15 33 -0.13 56 89
ERBB2 0.02 0.021 -10000 0 -0.12 12 12
proliferation/survival/translation 0.002 0.074 0.23 36 -10000 0 36
PI3K -0.014 0.075 0.13 9 -0.14 110 119
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
KRAS 0.014 0.034 -10000 0 -0.12 33 33
FOXO 0.028 0.037 0.14 9 -0.05 3 12
AKT2 0.019 0.025 -10000 0 -0.12 17 17
PTEN 0.022 0.008 -10000 0 -0.12 1 1
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.046 0.2 -10000 0 -0.79 33 33
epithelial cell differentiation -0.037 0.19 -10000 0 -0.65 40 40
ITCH 0.027 0.027 0.085 4 -0.072 28 32
WWP1 -0.051 0.28 -10000 0 -1.2 33 33
FYN 0.011 0.037 -10000 0 -0.12 40 40
EGFR 0.015 0.03 -10000 0 -0.12 25 25
PRL 0.022 0.011 -10000 0 -0.12 3 3
neuron projection morphogenesis -0.015 0.16 -10000 0 -0.53 39 39
PTPRZ1 0.021 0.018 -10000 0 -0.12 9 9
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.007 0.18 -10000 0 -0.59 39 39
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.035 0.18 -10000 0 -0.66 39 39
ADAM17 0.023 0.031 0.085 1 -0.087 33 34
ErbB4/ErbB4 -0.035 0.21 -10000 0 -0.8 37 37
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.053 0.2 -10000 0 -0.8 33 33
NCOR1 0.022 0.009 -10000 0 -0.12 2 2
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.037 0.18 -10000 0 -0.62 42 42
GRIN2B -0.035 0.17 -10000 0 -0.59 42 42
ErbB4/ErbB2/betacellulin -0.04 0.18 -10000 0 -0.64 40 40
STAT1 0.014 0.031 -10000 0 -0.12 26 26
HBEGF 0.018 0.026 -10000 0 -0.12 19 19
PRLR 0.01 0.042 -10000 0 -0.12 53 53
E4ICDs/ETO2 -0.044 0.2 -10000 0 -0.79 33 33
axon guidance -0.06 0.23 -10000 0 -0.81 40 40
NEDD4 0.024 0.034 0.085 6 -0.082 41 47
Prolactin receptor/Prolactin receptor/Prolactin 0.024 0.032 -10000 0 -0.15 2 2
CBFA2T3 0.023 0.006 -10000 0 -0.12 1 1
ErbB4/ErbB2/HBEGF -0.031 0.18 -10000 0 -0.64 38 38
MAPK3 -0.016 0.16 -10000 0 -0.55 39 39
STAT1 (dimer) -0.056 0.21 -10000 0 -0.75 38 38
MAPK1 -0.016 0.16 -10000 0 -0.55 39 39
JAK2 0.017 0.025 -10000 0 -0.12 16 16
ErbB4/ErbB2/neuregulin 1 beta -0.03 0.18 -10000 0 -0.64 39 39
NRG1 0.021 0.027 -10000 0 -0.07 30 30
NRG3 0.005 0.048 -10000 0 -0.12 72 72
NRG2 0.023 0.006 -10000 0 -0.12 1 1
NRG4 0.001 0.047 -10000 0 -0.12 70 70
heart development -0.06 0.23 -10000 0 -0.81 40 40
neural crest cell migration -0.03 0.18 -10000 0 -0.62 39 39
ERBB2 0.021 0.027 -10000 0 -0.067 32 32
WWOX/E4ICDs -0.044 0.2 -10000 0 -0.79 33 33
SHC1 0.023 0.001 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.068 0.2 -10000 0 -0.63 46 46
apoptosis 0.046 0.19 0.66 41 -10000 0 41
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.044 0.2 -10000 0 -0.79 33 33
ErbB4/ErbB2/epiregulin -0.03 0.18 -10000 0 -0.64 39 39
ErbB4/ErbB4/betacellulin/betacellulin -0.054 0.2 -10000 0 -0.77 35 35
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.027 0.19 -10000 0 -0.64 39 39
MDM2 -0.032 0.2 -10000 0 -0.74 37 37
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.024 0.17 -10000 0 -0.58 40 40
STAT5A -0.055 0.22 -10000 0 -0.76 41 41
ErbB4/EGFR/neuregulin 1 beta -0.035 0.18 -10000 0 -0.63 40 40
DLG4 0.023 0.009 -10000 0 -0.12 2 2
GRB2/SHC 0.033 0.019 -10000 0 -0.14 6 6
E4ICDs/TAB2/NCoR1 -0.04 0.2 -10000 0 -0.72 37 37
STAT5A (dimer) -0.037 0.21 -10000 0 -0.73 40 40
MAP3K7IP2 0.02 0.016 -10000 0 -0.12 6 6
STAT5B (dimer) -0.05 0.22 -10000 0 -0.78 40 40
LRIG1 0.01 0.037 -10000 0 -0.12 40 40
EREG 0.021 0.017 -10000 0 -0.12 8 8
BTC 0.01 0.039 -10000 0 -0.12 43 43
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.06 0.23 -10000 0 -0.82 40 40
ERBB4 -0.033 0.21 -10000 0 -0.8 37 37
STAT5B 0.023 0.006 -10000 0 -0.12 1 1
YAP1 0.002 0.077 -10000 0 -0.5 11 11
GRB2 0.023 0.006 -10000 0 -0.12 1 1
ErbB4/ErbB2/neuregulin 4 -0.049 0.18 -10000 0 -0.55 51 51
glial cell differentiation 0.039 0.2 0.71 37 -10000 0 37
WWOX 0.023 0.006 -10000 0 -0.12 1 1
cell proliferation -0.068 0.21 -10000 0 -0.57 62 62
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.02 0.048 -10000 0 -0.13 49 49
Necdin/E2F1 0.016 0.046 -10000 0 -0.089 84 84
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.039 0.048 -10000 0 -0.098 51 51
NGF (dimer)/p75(NTR)/BEX1 -0.008 0.054 -10000 0 -0.075 210 210
NT-4/5 (dimer)/p75(NTR) 0.016 0.013 -10000 0 -0.085 9 9
IKBKB 0.022 0.015 -10000 0 -0.12 6 6
AKT1 0.009 0.045 -10000 0 -0.1 63 63
IKBKG 0.023 0.009 -10000 0 -0.12 2 2
BDNF 0.022 0.011 -10000 0 -0.12 3 3
MGDIs/NGR/p75(NTR)/LINGO1 0.04 0.031 -10000 0 -0.12 13 13
FURIN 0.02 0.02 -10000 0 -0.12 11 11
proBDNF (dimer)/p75(NTR)/Sortilin 0.035 0.042 -10000 0 -0.12 33 33
LINGO1 0.018 0.026 -10000 0 -0.12 19 19
Sortilin/TRAF6/NRIF 0.003 0.054 -10000 0 -0.17 24 24
proBDNF (dimer) 0.022 0.011 -10000 0 -0.12 3 3
NTRK1 0.023 0.006 -10000 0 -0.12 1 1
RTN4R 0.021 0.018 -10000 0 -0.12 9 9
neuron apoptosis -0.039 0.12 -10000 0 -0.36 34 34
IRAK1 0.019 0.023 -10000 0 -0.12 14 14
SHC1 0.019 0.011 -10000 0 -0.063 9 9
ARHGDIA 0.016 0.032 -10000 0 -0.12 29 29
RhoA/GTP 0.016 0.016 -10000 0 -0.14 6 6
Gamma Secretase 0.034 0.067 -10000 0 -0.18 14 14
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.025 0.05 -10000 0 -0.11 59 59
MAGEH1 0.018 0.024 -10000 0 -0.12 16 16
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.021 0.051 -10000 0 -0.11 53 53
Mammalian IAPs/DIABLO -0.019 0.083 -10000 0 -0.13 157 157
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.02 0.019 -10000 0 -0.12 10 10
APP 0.022 0.008 -10000 0 -0.12 1 1
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.023 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.029 0.028 -10000 0 -0.1 12 12
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest 0.023 0.042 0.098 60 -0.099 33 93
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.01 0.063 -10000 0 -0.16 60 60
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.027 0.023 -10000 0 -0.091 19 19
NCSTN 0.022 0.012 -10000 0 -0.12 4 4
mol:GTP 0.022 0.034 -10000 0 -0.12 26 26
PSENEN 0.016 0.03 -10000 0 -0.12 24 24
mol:ceramide 0.016 0.034 -10000 0 -0.11 33 33
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.004 0.091 -10000 0 -0.3 31 31
p75(NTR)/beta APP 0.023 0.043 -10000 0 -0.14 33 33
BEX1 -0.017 0.062 -10000 0 -0.12 145 145
mol:GDP 0.006 0.01 -10000 0 -0.068 9 9
NGF (dimer) -0.028 0.064 -10000 0 -0.1 197 197
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.046 0.041 -10000 0 -0.11 21 21
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
RAC1/GTP 0.025 0.016 -10000 0 -0.073 13 13
MYD88 0.023 0.006 -10000 0 -0.12 1 1
CHUK 0.021 0.013 -10000 0 -0.12 4 4
NGF (dimer)/p75(NTR)/PKA 0.022 0.034 -10000 0 -0.12 26 26
RHOB 0.022 0.014 -10000 0 -0.12 5 5
RHOA 0.023 0.006 -10000 0 -0.12 1 1
MAGE-G1/E2F1 0.032 0.018 -10000 0 -0.14 3 3
NT3 (dimer) -0.003 0.056 -10000 0 -0.12 101 101
TP53 0.011 0.047 -10000 0 -0.18 23 23
PRDM4 0.017 0.032 -10000 0 -0.1 33 33
BDNF (dimer) -0.021 0.069 -10000 0 -0.096 203 203
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
SORT1 0.02 0.018 -10000 0 -0.12 8 8
activation of caspase activity 0.034 0.046 -10000 0 -0.098 51 51
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.032 0.042 -10000 0 -0.11 40 40
RHOC 0.023 0.002 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 0.022 0.054 -10000 0 -0.18 20 20
DIABLO 0.02 0.016 -10000 0 -0.12 6 6
SMPD2 0.016 0.034 -10000 0 -0.11 33 33
APH1B 0.014 0.032 -10000 0 -0.12 29 29
APH1A 0.023 0.009 -10000 0 -0.12 2 2
proNGF (dimer)/p75(NTR)/Sortilin 0.021 0.038 -10000 0 -0.1 45 45
PSEN1 0.022 0.008 -10000 0 -0.12 1 1
APAF-1/Pro-Caspase 9 0.025 0.041 -10000 0 -0.13 33 33
NT3 (dimer)/p75(NTR) 0.011 0.048 -10000 0 -0.078 118 118
MAPK8 0.022 0.058 -10000 0 -0.2 21 21
MAPK9 0.022 0.054 -10000 0 -0.18 20 20
APAF1 0.021 0.014 -10000 0 -0.12 5 5
NTF3 -0.003 0.056 -10000 0 -0.12 101 101
NTF4 0 0 -10000 0 -10000 0 0
NDN 0.007 0.044 -10000 0 -0.12 59 59
RAC1/GDP 0.016 0.015 -10000 0 -0.15 5 5
RhoA-B-C/GDP 0.04 0.035 -10000 0 -0.15 4 4
p75 CTF/Sortilin/TRAF6/NRIF 0.037 0.059 -10000 0 -0.12 62 62
RhoA-B-C/GTP 0.022 0.034 -10000 0 -0.12 26 26
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.055 0.045 -10000 0 -0.18 5 5
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.045 0.046 -10000 0 -0.1 40 40
PRKACB 0.019 0.02 -10000 0 -0.12 11 11
proBDNF (dimer)/p75 ECD 0.022 0.045 -10000 0 -0.15 33 33
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.005 0.053 -10000 0 -0.12 94 94
BIRC2 0.021 0.013 -10000 0 -0.12 4 4
neuron projection morphogenesis 0.003 0.055 0.1 46 -0.14 34 80
BAD 0.021 0.06 -10000 0 -0.2 19 19
RIPK2 0.013 0.034 -10000 0 -0.12 32 32
NGFR 0.021 0.017 -10000 0 -0.12 8 8
CYCS 0.015 0.042 -10000 0 -0.11 47 47
ADAM17 0.019 0.021 -10000 0 -0.12 11 11
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.024 0.05 -10000 0 -0.11 54 54
BCL2L11 0.021 0.06 -10000 0 -0.2 20 20
BDNF (dimer)/p75(NTR) 0.032 0.017 -10000 0 -0.14 2 2
PI3K 0.021 0.054 -10000 0 -0.11 63 63
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.033 0.038 -10000 0 -0.1 35 35
NDNL2 0.023 0.009 -10000 0 -0.12 2 2
YWHAE 0.022 0.014 -10000 0 -0.12 5 5
PRKCI 0.016 0.028 -10000 0 -0.12 22 22
NGF (dimer)/p75(NTR) 0.016 0.013 -10000 0 -0.085 9 9
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.029 0.046 -10000 0 -0.11 47 47
TRAF6 0.022 0.009 -10000 0 -0.12 2 2
RAC1 0.023 0.002 -10000 0 -10000 0 0
PRKCZ 0.023 0 -10000 0 -10000 0 0
PLG 0.023 0.009 -10000 0 -0.12 2 2
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 0.013 0.05 -10000 0 -0.16 33 33
SQSTM1 0.021 0.014 -10000 0 -0.12 5 5
NGFRAP1 0.022 0.009 -10000 0 -0.12 2 2
CASP3 0.021 0.059 -10000 0 -0.19 20 20
E2F1 0.021 0.016 -10000 0 -0.12 7 7
CASP9 0.022 0.014 -10000 0 -0.12 5 5
IKK complex 0.021 0.08 -10000 0 -0.22 33 33
NGF (dimer)/TRKA 0.017 0.004 -10000 0 -0.077 1 1
MMP7 -0.022 0.06 -10000 0 -0.12 144 144
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.042 0.042 -10000 0 -0.097 40 40
MMP3 0.017 0.029 -10000 0 -0.12 23 23
APAF-1/Caspase 9 -0.037 0.061 -10000 0 -0.16 86 86
FAS signaling pathway (CD95)

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
SPTAN1 0.003 0.039 0.15 3 -0.26 10 13
RFC1 0.003 0.04 0.16 4 -0.26 10 14
PRKDC 0.003 0.039 0.16 4 -0.25 10 14
RIPK1 0.022 0.011 -10000 0 -0.12 3 3
CASP7 0.002 0.091 0.2 2 -0.43 17 19
FASLG/FAS/FADD/FAF1 0.036 0.085 0.16 118 -0.17 42 160
MAP2K4 -0.001 0.11 -10000 0 -0.3 41 41
mol:ceramide 0.005 0.094 -10000 0 -0.27 34 34
GSN 0.002 0.038 0.16 1 -0.26 10 11
FASLG/FAS/FADD/FAF1/Caspase 8 0.042 0.09 0.18 1 -0.25 18 19
FAS 0.016 0.026 -10000 0 -0.12 17 17
BID 0.005 0.017 0.25 2 -10000 0 2
MAP3K1 0.001 0.093 0.17 2 -0.29 34 36
MAP3K7 0.021 0.014 -10000 0 -0.12 5 5
RB1 0.001 0.041 0.16 4 -0.25 11 15
CFLAR 0.022 0.011 -10000 0 -0.12 3 3
HGF/MET -0.054 0.089 -10000 0 -0.14 247 247
ARHGDIB -0.002 0.043 0.16 3 -0.28 10 13
FADD 0.022 0.01 -10000 0 -0.12 2 2
actin filament polymerization -0.002 0.038 0.25 10 -0.16 1 11
NFKB1 -0.037 0.2 -10000 0 -0.74 38 38
MAPK8 -0.001 0.12 -10000 0 -0.35 36 36
DFFA 0.003 0.04 0.16 4 -0.25 11 15
DNA fragmentation during apoptosis 0.003 0.04 0.16 4 -0.25 11 15
FAS/FADD/MET -0.014 0.082 -10000 0 -0.13 164 164
CFLAR/RIP1 0.03 0.027 -10000 0 -0.12 16 16
FAIM3 0.022 0.012 -10000 0 -0.12 4 4
FAF1 0.021 0.015 -10000 0 -0.12 5 5
PARP1 0.004 0.037 0.16 4 -0.24 10 14
DFFB 0.003 0.04 0.16 4 -0.25 11 15
CHUK -0.034 0.19 -10000 0 -0.71 38 38
FASLG 0.022 0.014 -10000 0 -0.13 4 4
FAS/FADD 0.012 0.056 -10000 0 -0.13 67 67
HGF 0.02 0.023 -10000 0 -0.12 14 14
LMNA 0 0.047 0.14 4 -0.25 14 18
CASP6 -0.003 0.05 0.16 4 -0.29 12 16
CASP10 0.018 0.02 -10000 0 -0.12 10 10
CASP3 -0.002 0.046 0.18 4 -0.28 11 15
PTPN13 -0.012 0.056 -10000 0 -0.12 112 112
CASP8 -0.005 0.018 0.28 2 -10000 0 2
IL6 -0.038 0.21 -10000 0 -0.75 35 35
MET 0 0.047 -10000 0 -0.12 70 70
ICAD/CAD 0.007 0.038 0.15 2 -0.21 13 15
FASLG/FAS/FADD/FAF1/Caspase 10 0.005 0.095 -10000 0 -0.28 34 34
activation of caspase activity by cytochrome c 0.005 0.017 0.25 2 -10000 0 2
PAK2 0.003 0.04 0.16 4 -0.25 11 15
BCL2 0.016 0.031 -10000 0 -0.12 27 27
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.012 0.012 -10000 0 -0.057 15 15
RAS family/GTP 0.004 0.084 -10000 0 -0.18 52 52
NFATC4 0.001 0.053 0.18 6 -0.14 21 27
ERBB2IP 0.021 0.019 -10000 0 -0.12 9 9
HSP90 (dimer) 0.023 0.003 -10000 0 -10000 0 0
mammary gland morphogenesis 0 0.066 0.19 7 -0.14 44 51
JUN 0.004 0.07 -10000 0 -10000 0 0
HRAS 0.023 0.006 -10000 0 -0.12 1 1
DOCK7 -0.005 0.066 0.19 6 -0.16 45 51
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.017 0.061 0.21 7 -0.1 88 95
AKT1 0.01 0.012 -10000 0 -0.078 10 10
BAD 0.013 0.011 -10000 0 -0.057 13 13
MAPK10 0.002 0.045 0.14 6 -0.1 41 47
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.001 0.071 0.2 7 -0.15 43 50
RAF1 -0.005 0.085 -10000 0 -0.18 55 55
ErbB2/ErbB3/neuregulin 2 0.004 0.054 -10000 0 -0.11 88 88
STAT3 -0.003 0.17 -10000 0 -0.93 19 19
cell migration 0.001 0.053 0.16 5 -0.13 37 42
mol:PI-3-4-5-P3 0 0.001 -10000 0 -10000 0 0
cell proliferation -0.063 0.21 -10000 0 -0.52 66 66
FOS -0.072 0.2 -10000 0 -0.41 127 127
NRAS 0.021 0.011 -10000 0 -0.12 3 3
mol:Ca2+ 0 0.066 0.19 7 -0.14 44 51
MAPK3 -0.04 0.17 -10000 0 -0.48 45 45
MAPK1 -0.042 0.17 -10000 0 -0.47 51 51
JAK2 -0.005 0.065 0.19 6 -0.16 41 47
NF2 0.013 0.046 -10000 0 -0.73 2 2
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.012 0.051 0.13 8 -0.16 28 36
NRG1 0.02 0.017 -10000 0 -0.12 8 8
GRB2/SOS1 0.021 0.045 -10000 0 -0.15 29 29
MAPK8 -0.012 0.092 0.18 6 -0.19 97 103
MAPK9 0.003 0.044 0.14 5 -0.11 35 40
ERBB2 0 0.048 0.27 15 -0.093 7 22
ERBB3 0.013 0.031 -10000 0 -0.12 26 26
SHC1 0.023 0.001 -10000 0 -10000 0 0
RAC1 0.023 0.002 -10000 0 -10000 0 0
apoptosis -0.009 0.017 0.19 2 -10000 0 2
STAT3 (dimer) -0.002 0.17 -10000 0 -0.91 19 19
RNF41 0.013 0.012 -10000 0 -0.047 17 17
FRAP1 0.013 0.011 -10000 0 -0.057 14 14
RAC1-CDC42/GTP -0.006 0.05 -10000 0 -0.13 41 41
ErbB2/ErbB2/HSP90 (dimer) 0.012 0.028 -10000 0 -0.14 14 14
CHRNA1 -0.025 0.14 -10000 0 -0.35 47 47
myelination 0 0.053 0.18 6 -0.15 20 26
PPP3CB -0.001 0.058 0.18 6 -0.14 33 39
KRAS 0.014 0.034 -10000 0 -0.12 33 33
RAC1-CDC42/GDP 0.017 0.074 -10000 0 -0.13 83 83
NRG2 0.023 0.006 -10000 0 -0.12 1 1
mol:GDP 0.012 0.051 0.13 8 -0.16 28 36
SOS1 0.017 0.027 -10000 0 -0.12 20 20
MAP2K2 -0.01 0.09 -10000 0 -0.19 71 71
SRC 0.023 0.009 -10000 0 -0.12 2 2
mol:cAMP 0 0.001 -10000 0 -10000 0 0
PTPN11 -0.002 0.063 0.19 5 -0.16 35 40
MAP2K1 -0.043 0.16 -10000 0 -0.42 47 47
heart morphogenesis 0 0.066 0.19 7 -0.14 44 51
RAS family/GDP 0.012 0.085 -10000 0 -0.18 48 48
GRB2 0.023 0.006 -10000 0 -0.12 1 1
PRKACA 0.01 0.048 -10000 0 -0.77 2 2
CHRNE 0.01 0.019 -10000 0 -10000 0 0
HSP90AA1 0.023 0.003 -10000 0 -10000 0 0
activation of caspase activity -0.01 0.012 0.078 10 -10000 0 10
nervous system development 0 0.066 0.19 7 -0.14 44 51
CDC42 0.023 0.002 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.019 0.016 -9999 0 -0.058 18 18
SNTA1 0.023 0.009 -9999 0 -0.12 2 2
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.017 0.021 -9999 0 -0.074 21 21
MAPK12 0.01 0.027 -9999 0 -0.059 36 36
CCND1 -0.05 0.14 -9999 0 -0.34 97 97
p38 gamma/SNTA1 0.005 0.057 -9999 0 -0.16 40 40
MAP2K3 0.023 0.006 -9999 0 -0.12 1 1
PKN1 0.016 0.031 -9999 0 -0.12 26 26
G2/M transition checkpoint 0.003 0.044 -9999 0 -0.15 36 36
MAP2K6 0.008 0.028 -9999 0 -0.05 79 79
MAPT 0.007 0.039 -9999 0 -0.13 28 28
MAPK13 0.019 0.019 -9999 0 -0.079 17 17
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK -0.001 0.058 -9999 0 -0.21 37 37
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0.005 0.042 -10000 0 -0.11 49 49
DAPP1 0.005 0.08 -10000 0 -0.25 27 27
Src family/SYK family/BLNK-LAT/BTK-ITK 0 0.12 -10000 0 -0.33 42 42
mol:DAG 0.015 0.066 0.16 14 -0.15 38 52
HRAS 0.023 0.008 -10000 0 -0.13 1 1
RAP1A 0.022 0.012 -10000 0 -0.12 3 3
ARF5/GDP 0.003 0.086 -10000 0 -0.2 65 65
PLCG2 0.02 0.02 -10000 0 -0.12 11 11
PLCG1 0.019 0.024 -10000 0 -0.12 16 16
ARF5 0.02 0.018 -10000 0 -0.12 9 9
mol:GTP -0.006 0.038 -10000 0 -0.11 54 54
ARF1/GTP 0.003 0.05 0.16 21 -0.12 41 62
RHOA 0.023 0.006 -10000 0 -0.12 1 1
YES1 0.02 0.018 -10000 0 -0.12 8 8
RAP1A/GTP 0.012 0.05 0.17 22 -0.12 38 60
ADAP1 -0.005 0.036 -10000 0 -0.1 54 54
ARAP3 -0.006 0.038 -10000 0 -0.11 54 54
INPPL1 0.021 0.017 -10000 0 -0.12 8 8
PREX1 0.021 0.017 -10000 0 -0.12 8 8
ARHGEF6 0.014 0.032 -10000 0 -0.12 28 28
ARHGEF7 0.023 0.006 -10000 0 -0.12 1 1
ARF1 0.018 0.028 -10000 0 -0.12 21 21
NRAS 0.022 0.012 -10000 0 -0.12 3 3
FYN 0.011 0.037 -10000 0 -0.12 40 40
ARF6 0.023 0.003 -10000 0 -10000 0 0
FGR 0.023 0.006 -10000 0 -0.12 1 1
mol:Ca2+ 0.012 0.038 0.092 14 -0.078 37 51
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.015 0.032 -10000 0 -0.12 28 28
ZAP70 0.023 0.006 -10000 0 -0.12 1 1
mol:IP3 0.013 0.05 0.11 14 -0.11 38 52
LYN 0.021 0.013 -10000 0 -0.12 4 4
ARF1/GDP 0.002 0.088 -10000 0 -0.2 63 63
RhoA/GDP 0.014 0.067 0.17 19 -0.15 45 64
PDK1/Src/Hsp90 0.041 0.032 -10000 0 -0.12 19 19
BLNK 0.014 0.033 -10000 0 -0.12 31 31
actin cytoskeleton reorganization 0.005 0.087 0.19 17 -0.23 40 57
SRC 0.023 0.009 -10000 0 -0.12 2 2
PLEKHA2 0.013 0.011 -10000 0 -0.057 12 12
RAC1 0.023 0.002 -10000 0 -10000 0 0
PTEN 0.022 0.009 -10000 0 -0.12 1 1
HSP90AA1 0.023 0.003 -10000 0 -10000 0 0
ARF6/GTP 0.006 0.042 -10000 0 -0.11 47 47
RhoA/GTP 0.013 0.052 0.17 22 -0.11 41 63
Src family/SYK family/BLNK-LAT 0.006 0.097 -10000 0 -0.29 31 31
BLK 0.022 0.015 -10000 0 -0.12 6 6
PDPK1 0.023 0.007 -10000 0 -0.12 1 1
CYTH1 -0.005 0.036 -10000 0 -0.1 54 54
HCK 0.019 0.024 -10000 0 -0.12 15 15
CYTH3 -0.005 0.036 -10000 0 -0.1 54 54
CYTH2 -0.005 0.036 -10000 0 -0.1 54 54
KRAS 0.014 0.035 -10000 0 -0.12 33 33
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.015 0.054 0.13 22 -0.21 20 42
SGK1 0.008 0.05 -10000 0 -0.21 20 20
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP -0.008 0.086 -10000 0 -0.21 62 62
SOS1 0.017 0.027 -10000 0 -0.12 20 20
SYK 0.016 0.027 -10000 0 -0.12 20 20
ARF6/GDP 0.008 0.064 0.17 19 -0.15 47 66
mol:PI-3-4-5-P3 -0.004 0.039 0.085 1 -0.11 54 55
ARAP3/RAP1A/GTP 0.012 0.05 0.17 22 -0.12 38 60
VAV1 0.02 0.02 -10000 0 -0.12 10 10
mol:PI-3-4-P2 0.01 0.011 -10000 0 -0.077 8 8
RAS family/GTP/PI3K Class I 0.026 0.058 0.19 22 -0.11 54 76
PLEKHA1 0.013 0.012 -10000 0 -0.057 15 15
Rac1/GDP 0.004 0.087 -10000 0 -0.2 60 60
LAT 0.022 0.011 -10000 0 -0.12 3 3
Rac1/GTP -0.001 0.1 -10000 0 -0.24 71 71
ITK -0.002 0.04 -10000 0 -0.1 58 58
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.014 0.083 0.19 14 -0.2 39 53
LCK 0.022 0.015 -10000 0 -0.12 6 6
BTK -0.003 0.043 -10000 0 -0.11 56 56
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.021 0.2 -10000 0 -0.97 24 24
VDR 0.019 0.022 -10000 0 -0.12 13 13
FAM120B 0.022 0.011 -10000 0 -0.12 3 3
RXRs/LXRs/DNA/9cRA 0.025 0.095 -10000 0 -0.24 54 54
RXRs/LXRs/DNA/Oxysterols 0.019 0.13 -10000 0 -0.35 59 59
MED1 0.021 0.014 -10000 0 -0.12 5 5
mol:9cRA 0.002 0.016 -10000 0 -0.047 49 49
RARs/THRs/DNA/Src-1 -0.003 0.087 -10000 0 -0.29 24 24
RXRs/NUR77 0.033 0.067 -10000 0 -0.13 27 27
RXRs/PPAR 0.032 0.039 -10000 0 -0.17 4 4
NCOR2 0.019 0.023 -10000 0 -0.12 15 15
VDR/VDR/Vit D3 0.008 0.035 -10000 0 -0.12 36 36
RARs/VDR/DNA/Vit D3 0.029 0.056 -10000 0 -0.1 66 66
RARA 0.023 0 -10000 0 -10000 0 0
NCOA1 0.022 0.009 -10000 0 -0.12 2 2
VDR/VDR/DNA 0.019 0.022 -10000 0 -0.12 13 13
RARs/RARs/DNA/9cRA 0.025 0.045 -10000 0 -0.094 57 57
RARG 0.021 0.015 -10000 0 -0.12 6 6
RPS6KB1 -0.004 0.091 -10000 0 -0.32 39 39
RARs/THRs/DNA/SMRT -0.002 0.083 -10000 0 -0.16 101 101
THRA 0.022 0.015 -10000 0 -0.12 6 6
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.008 0.035 -10000 0 -0.12 36 36
RXRs/PPAR/9cRA/PGJ2/DNA 0.041 0.074 0.27 14 -0.16 15 29
NR1H4 0.021 0.017 -10000 0 -0.12 8 8
RXRs/LXRs/DNA 0.06 0.085 -10000 0 -0.16 54 54
NR1H2 0.021 0.027 -10000 0 -0.091 17 17
NR1H3 0.02 0.029 -10000 0 -0.056 52 52
RXRs/VDR/DNA/Vit D3 0.039 0.059 -10000 0 -0.13 23 23
NR4A1 0.003 0.049 -10000 0 -0.12 74 74
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.022 0.049 -10000 0 -0.21 9 9
RXRG 0.006 0.05 -10000 0 -0.12 70 70
RXR alpha/CCPG 0.031 0.026 -10000 0 -0.12 9 9
RXRA 0.021 0.025 -10000 0 -0.11 10 10
RXRB 0.024 0.02 -10000 0 -0.04 5 5
THRB 0.011 0.036 -10000 0 -0.12 36 36
PPARG 0.018 0.028 -10000 0 -0.12 22 22
PPARD 0.023 0.009 -10000 0 -0.12 2 2
TNF 0.022 0.13 -10000 0 -0.4 22 22
mol:Oxysterols 0.001 0.015 -10000 0 -0.041 58 58
cholesterol transport 0.02 0.13 -10000 0 -0.34 59 59
PPARA 0.022 0.012 -10000 0 -0.12 4 4
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.013 0.034 -10000 0 -0.12 33 33
RXRs/NUR77/BCL2 0.013 0.045 -10000 0 -0.15 23 23
SREBF1 0.022 0.13 -10000 0 -0.51 8 8
RXRs/RXRs/DNA/9cRA 0.041 0.073 0.26 14 -0.16 15 29
ABCA1 -0.029 0.27 -10000 0 -0.83 56 56
RARs/THRs 0.027 0.072 -10000 0 -0.1 104 104
RXRs/FXR 0.049 0.057 -10000 0 -0.12 15 15
BCL2 0.016 0.031 -10000 0 -0.12 27 27
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 0.01 0.042 -9999 0 -0.12 52 52
mol:S1P -0.002 0.007 -9999 0 -0.029 24 24
S1P1/S1P/Gi 0.008 0.065 -9999 0 -0.22 31 31
GNAO1 0.008 0.043 -9999 0 -0.12 51 51
S1P/S1P3/G12/G13 0.024 0.024 -9999 0 -0.097 16 16
AKT1 0.006 0.059 -9999 0 -0.42 5 5
AKT3 -0.054 0.23 -9999 0 -0.86 32 32
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.01 0.042 -9999 0 -0.12 52 52
GNAI2 0.02 0.014 -9999 0 -0.12 3 3
GNAI3 0.02 0.012 -9999 0 -0.12 1 1
GNAI1 0.01 0.036 -9999 0 -0.12 35 35
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 -0.002 0.008 -9999 0 -0.016 92 92
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0.021 0.016 -9999 0 -0.12 7 7
mol:Ca2+ -0.016 0.088 -9999 0 -0.24 49 49
MAPK3 -0.012 0.084 -9999 0 -0.22 52 52
MAPK1 -0.013 0.085 -9999 0 -0.22 51 51
JAK2 -0.023 0.1 -9999 0 -0.26 66 66
CXCR4 -0.021 0.092 -9999 0 -0.24 62 62
FLT1 0.019 0.019 -9999 0 -0.053 23 23
RhoA/GDP 0.016 0.016 -9999 0 -0.14 6 6
Rac1/GDP 0.016 0.015 -9999 0 -0.15 5 5
SRC -0.012 0.083 -9999 0 -0.23 45 45
S1P/S1P3/Gi -0.016 0.089 -9999 0 -0.24 49 49
RAC1 0.023 0.002 -9999 0 -10000 0 0
RhoA/GTP -0.005 0.085 -9999 0 -0.22 46 46
VEGFA 0.017 0.024 -9999 0 -0.072 25 25
S1P/S1P2/Gi -0.011 0.076 -9999 0 -0.15 106 106
VEGFR1 homodimer/VEGFA homodimer 0.016 0.055 -9999 0 -0.14 53 53
RHOA 0.023 0.006 -9999 0 -0.12 1 1
S1P/S1P3/Gq 0.014 0.045 -9999 0 -0.15 34 34
GNAQ 0.021 0.016 -9999 0 -0.12 6 6
GNAZ 0.02 0.014 -9999 0 -0.04 15 15
G12/G13 0.03 0.028 -9999 0 -0.13 16 16
GNA14 0.02 0.02 -9999 0 -0.12 11 11
GNA15 0.021 0.017 -9999 0 -0.12 8 8
GNA12 0.023 0.001 -9999 0 -10000 0 0
GNA13 0.022 0.009 -9999 0 -0.12 2 2
GNA11 0.022 0.014 -9999 0 -0.12 5 5
Rac1/GTP -0.005 0.085 -9999 0 -0.22 46 46
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.025 0.057 -9999 0 -0.12 63 63
E-cadherin/beta catenin 0.018 0.053 -9999 0 -0.14 54 54
CTNNB1 0.022 0.008 -9999 0 -0.12 1 1
JUP 0.019 0.021 -9999 0 -0.12 12 12
CDH1 0.021 0.016 -9999 0 -0.12 6 6
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.021 0.014 -10000 0 -0.12 5 5
VLDLR 0.01 0.038 -10000 0 -0.12 41 41
LRPAP1 0.018 0.024 -10000 0 -0.12 15 15
NUDC 0.022 0.011 -10000 0 -0.12 3 3
RELN/LRP8 0.015 0.058 -10000 0 -0.12 53 53
CaM/Ca2+ 0.014 0.02 -10000 0 -0.12 12 12
KATNA1 0.02 0.02 -10000 0 -0.12 10 10
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.006 0.047 -10000 0 -0.11 53 53
IQGAP1/CaM 0.016 0.054 -10000 0 -0.13 63 63
DAB1 0.022 0.011 -10000 0 -0.12 3 3
IQGAP1 0.02 0.017 -10000 0 -0.12 7 7
PLA2G7 0.004 0.045 -10000 0 -0.12 61 61
CALM1 0.022 0.014 -10000 0 -0.12 5 5
DYNLT1 0.018 0.023 -10000 0 -0.12 14 14
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.015 0.054 -10000 0 -0.15 45 45
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.023 0.009 -10000 0 -0.12 2 2
CDK5R1 0.023 0.006 -10000 0 -0.12 1 1
LIS1/Poliovirus Protein 3A 0.012 0.023 -10000 0 -0.086 26 26
CDK5R2 0.022 0.011 -10000 0 -0.12 3 3
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.01 0.06 -10000 0 -0.12 69 69
YWHAE 0.022 0.014 -10000 0 -0.12 5 5
NDEL1/14-3-3 E 0.023 0.055 -10000 0 -0.16 20 20
MAP1B -0.015 0.059 0.2 3 -0.19 47 50
RAC1 0.014 0.048 -10000 0 -0.36 7 7
p35/CDK5 0.008 0.054 -10000 0 -0.15 22 22
RELN 0.001 0.053 -10000 0 -0.12 88 88
PAFAH/LIS1 0.015 0.038 -10000 0 -0.065 85 85
LIS1/CLIP170 0.029 0.028 -10000 0 -0.083 28 28
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain 0.016 0.063 -10000 0 -0.16 37 37
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.014 0.098 -10000 0 -0.21 93 93
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.011 0.052 -10000 0 -0.16 18 18
LIS1/IQGAP1 0.025 0.034 -10000 0 -0.16 13 13
RHOA 0.014 0.048 -10000 0 -0.32 8 8
PAFAH1B1 0.02 0.015 -10000 0 -0.071 15 15
PAFAH1B3 0.014 0.032 -10000 0 -0.12 29 29
PAFAH1B2 0.022 0.013 -10000 0 -0.12 4 4
MAP1B/LIS1/Dynein heavy chain 0.009 0.054 0.13 3 -0.13 54 57
NDEL1/Katanin 60/Dynein heavy chain 0.025 0.065 -10000 0 -0.17 25 25
LRP8 0.02 0.021 -10000 0 -0.12 12 12
NDEL1/Katanin 60 0.021 0.056 -10000 0 -0.16 23 23
P39/CDK5 0.008 0.053 -10000 0 -0.14 22 22
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.028 0.029 -10000 0 -0.13 11 11
CDK5 0.004 0.043 -10000 0 -0.099 56 56
PPP2R5D 0.022 0.014 -10000 0 -0.12 5 5
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.025 0.023 -10000 0 -0.11 11 11
CSNK2A1 0.021 0.015 -10000 0 -0.12 6 6
RELN/VLDLR/DAB1/LIS1 0.021 0.059 -10000 0 -0.092 81 81
RELN/VLDLR 0.007 0.071 -10000 0 -0.11 119 119
CDC42 0.015 0.04 -10000 0 -0.27 7 7
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0.017 0.04 -9999 0 -0.12 38 38
EFNA5 0.014 0.033 -9999 0 -0.12 30 30
FYN 0.007 0.043 -9999 0 -0.12 40 40
neuron projection morphogenesis 0.017 0.04 -9999 0 -0.12 38 38
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 0.017 0.041 -9999 0 -0.12 38 38
EPHA5 0.023 0.009 -9999 0 -0.12 2 2
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.023 0.042 0.11 47 -10000 0 47
KIRREL 0.018 0.028 -10000 0 -0.12 20 20
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.023 0.043 -10000 0 -0.11 47 47
PLCG1 0.019 0.024 -10000 0 -0.12 16 16
ARRB2 0.022 0.014 -10000 0 -0.12 5 5
WASL 0.023 0.009 -10000 0 -0.12 2 2
Nephrin/NEPH1/podocin/CD2AP 0.036 0.056 -10000 0 -0.11 64 64
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.021 0.053 -10000 0 -0.13 53 53
FYN 0.014 0.034 -10000 0 -0.11 26 26
mol:Ca2+ 0.041 0.047 -10000 0 -0.11 38 38
mol:DAG 0.042 0.048 -10000 0 -0.11 38 38
NPHS2 0.022 0.014 -10000 0 -0.082 7 7
mol:IP3 0.042 0.048 -10000 0 -0.11 38 38
regulation of endocytosis 0.031 0.045 -10000 0 -0.098 32 32
Nephrin/NEPH1/podocin/Cholesterol 0.034 0.035 -10000 0 -0.098 28 28
establishment of cell polarity 0.023 0.042 -10000 0 -0.11 47 47
Nephrin/NEPH1/podocin/NCK1-2 0.049 0.054 -10000 0 -0.095 56 56
Nephrin/NEPH1/beta Arrestin2 0.033 0.046 -10000 0 -0.099 32 32
NPHS1 0.021 0.02 -10000 0 -0.13 9 9
Nephrin/NEPH1/podocin 0.025 0.045 -10000 0 -0.11 28 28
TJP1 0.021 0.01 -10000 0 -0.12 2 2
NCK1 0.02 0.019 -10000 0 -0.12 9 9
NCK2 0.023 0.006 -10000 0 -0.12 1 1
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.043 0.048 -10000 0 -0.11 38 38
CD2AP 0.02 0.017 -10000 0 -0.12 7 7
Nephrin/NEPH1/podocin/GRB2 0.047 0.042 -10000 0 -0.11 28 28
GRB2 0.023 0.006 -10000 0 -0.12 1 1
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.019 0.029 -10000 0 -0.087 27 27
cytoskeleton organization 0.022 0.047 -10000 0 -0.13 30 30
Nephrin/NEPH1 0.022 0.029 -10000 0 -0.072 47 47
Nephrin/NEPH1/ZO-1 0.027 0.055 -10000 0 -0.13 55 55
EGFR-dependent Endothelin signaling events

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
HRAS 0.023 0.006 -9999 0 -0.12 1 1
EGFR 0.015 0.03 -9999 0 -0.12 25 25
EGF/EGFR 0.013 0.053 -9999 0 -0.092 80 80
EGF/EGFR dimer/SHC/GRB2/SOS1 0.041 0.058 -9999 0 -0.15 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.014 0.035 -9999 0 -0.12 34 34
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF 0.02 0.021 -9999 0 -0.12 12 12
EGF/EGFR dimer/SHC 0.03 0.046 -9999 0 -0.11 40 40
mol:GDP 0.036 0.056 -9999 0 -0.15 12 12
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.009 0.043 -9999 0 -0.12 54 54
GRB2/SOS1 0.021 0.045 -9999 0 -0.15 29 29
HRAS/GTP 0.023 0.045 -9999 0 -0.16 9 9
SHC1 0.023 0.001 -9999 0 -10000 0 0
HRAS/GDP 0.036 0.052 -9999 0 -0.16 9 9
FRAP1 0.016 0.044 -9999 0 -0.14 14 14
EGF/EGFR dimer 0.016 0.05 -9999 0 -0.11 73 73
SOS1 0.017 0.027 -9999 0 -0.12 20 20
GRB2 0.023 0.006 -9999 0 -0.12 1 1
ETA receptor/Endothelin-1 0.008 0.056 -9999 0 -0.096 115 115
Regulation of Androgen receptor activity

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 0.02 0.015 -9999 0 -0.07 13 13
SMARCC1 0 0.17 -9999 0 -1.1 13 13
REL 0.021 0.014 -9999 0 -0.12 5 5
HDAC7 -0.018 0.096 -9999 0 -0.19 87 87
JUN 0.014 0.033 -9999 0 -0.12 30 30
EP300 0.022 0.01 -9999 0 -0.12 2 2
KAT2B 0 0 -9999 0 -10000 0 0
KAT5 0 0 -9999 0 -10000 0 0
MAPK14 0.013 0.025 -9999 0 -0.071 34 34
FOXO1 0.023 0.009 -9999 0 -0.12 2 2
T-DHT/AR -0.001 0.11 -9999 0 -0.21 79 79
MAP2K6 0.012 0.035 -9999 0 -0.12 33 33
BRM/BAF57 0.007 0.062 -9999 0 -0.14 71 71
MAP2K4 0.022 0.012 -9999 0 -0.12 3 3
SMARCA2 0.012 0.036 -9999 0 -0.12 36 36
PDE9A -0.095 0.31 -9999 0 -0.86 79 79
NCOA2 0.022 0.013 -9999 0 -0.12 4 4
CEBPA 0.022 0.014 -9999 0 -0.12 5 5
EHMT2 0.023 0.009 -9999 0 -0.12 2 2
cell proliferation -0.011 0.11 -9999 0 -0.26 53 53
NR0B1 0.013 0.038 -9999 0 -0.12 41 41
EGR1 -0.005 0.054 -9999 0 -0.12 99 99
RXRs/9cRA 0.033 0.033 -9999 0 -0.096 4 4
AR/RACK1/Src 0.011 0.073 -9999 0 -0.18 41 41
AR/GR -0.013 0.085 -9999 0 -0.17 101 101
GNB2L1 0.023 0.003 -9999 0 -10000 0 0
PKN1 0.016 0.031 -9999 0 -0.12 26 26
RCHY1 0.018 0.022 -9999 0 -0.12 13 13
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
MAPK8 0.018 0.018 -9999 0 -0.074 9 9
T-DHT/AR/TIF2/CARM1 0.01 0.084 -9999 0 -0.16 66 66
SRC 0.015 0.027 -9999 0 -0.073 13 13
NR3C1 0.021 0.015 -9999 0 -0.12 5 5
KLK3 0.004 0.047 -9999 0 -10000 0 0
APPBP2 0.019 0.017 -9999 0 -0.12 6 6
TRIM24 0.023 0.014 -9999 0 -0.12 5 5
T-DHT/AR/TIP60 -0.014 0.071 -9999 0 -0.17 59 59
TMPRSS2 0.002 0.092 -9999 0 -0.68 4 4
RXRG 0.006 0.047 -9999 0 -0.12 68 68
mol:9cRA 0 0 -9999 0 -0.003 1 1
RXRA 0.021 0.017 -9999 0 -0.12 8 8
RXRB 0.023 0 -9999 0 -10000 0 0
CARM1 0.019 0.026 -9999 0 -0.12 19 19
NR2C2 0.023 0.006 -9999 0 -0.12 1 1
KLK2 0.019 0.072 -9999 0 -0.25 14 14
AR -0.01 0.074 -9999 0 -0.16 94 94
SENP1 0.022 0.011 -9999 0 -0.12 3 3
HSP90AA1 0.023 0.003 -9999 0 -10000 0 0
MDM2 0.018 0.02 -9999 0 -0.12 11 11
SRY 0.021 0.008 -9999 0 -0.11 2 2
GATA2 0.02 0.022 -9999 0 -0.12 13 13
MYST2 0.022 0.011 -9999 0 -0.12 3 3
HOXB13 0.02 0.026 -9999 0 -0.12 19 19
T-DHT/AR/RACK1/Src 0.006 0.074 -9999 0 -0.18 47 47
positive regulation of transcription 0.02 0.022 -9999 0 -0.12 13 13
DNAJA1 0.02 0.012 -9999 0 -0.13 2 2
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.09 -9999 0 -0.28 48 48
NCOA1 0.025 0.032 -9999 0 -0.16 15 15
SPDEF 0.012 0.042 -9999 0 -0.12 50 50
T-DHT/AR/TIF2 -0.006 0.088 -9999 0 -0.21 64 64
T-DHT/AR/Hsp90 -0.003 0.078 -9999 0 -0.19 53 53
GSK3B 0.022 0.011 -9999 0 -0.12 3 3
NR2C1 0.021 0.01 -9999 0 -0.12 2 2
mol:T-DHT 0.013 0.028 -9999 0 -0.068 17 17
SIRT1 0.023 0.003 -9999 0 -10000 0 0
ZMIZ2 0.02 0.014 -9999 0 -0.12 5 5
POU2F1 0.017 0.041 -9999 0 -0.077 78 78
T-DHT/AR/DAX-1 -0.007 0.077 -9999 0 -0.17 65 65
CREBBP 0.021 0.015 -9999 0 -0.12 6 6
SMARCE1 0.023 0.011 -9999 0 -0.12 3 3
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.019 0.02 -9999 0 -0.05 35 35
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.013 0.11 -9999 0 -0.26 54 54
ERC1 0.016 0.029 -9999 0 -0.12 24 24
RIP2/NOD2 0.013 0.053 -9999 0 -0.14 48 48
NFKBIA 0.001 0.087 -9999 0 -0.22 60 60
BIRC2 0.021 0.013 -9999 0 -0.12 4 4
IKBKB 0.022 0.015 -9999 0 -0.12 6 6
RIPK2 0.013 0.034 -9999 0 -0.12 32 32
IKBKG 0.012 0.091 -9999 0 -0.32 29 29
IKK complex/A20 0.037 0.096 -9999 0 -0.27 35 35
NEMO/A20/RIP2 0.013 0.034 -9999 0 -0.12 32 32
XPO1 0.022 0.01 -9999 0 -0.12 2 2
NEMO/ATM 0.017 0.1 -9999 0 -0.3 39 39
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.023 0.002 -9999 0 -10000 0 0
Exportin 1/RanGTP 0.025 0.03 -9999 0 -0.11 26 26
IKK complex/ELKS 0.021 0.094 -9999 0 -0.28 35 35
BCL10/MALT1/TRAF6 0.034 0.043 -9999 0 -0.12 31 31
NOD2 0.023 0.006 -9999 0 -0.12 1 1
NFKB1 0.017 0.023 -9999 0 -0.064 31 31
RELA 0.019 0.022 -9999 0 -0.061 29 29
MALT1 0.017 0.026 -9999 0 -0.12 19 19
cIAP1/UbcH5C 0.021 0.047 -9999 0 -0.14 41 41
ATM 0.018 0.022 -9999 0 -0.12 13 13
TNF/TNFR1A 0.025 0.036 -9999 0 -0.11 37 37
TRAF6 0.022 0.009 -9999 0 -0.12 2 2
PRKCA 0.011 0.037 -9999 0 -0.12 40 40
CHUK 0.021 0.013 -9999 0 -0.12 4 4
UBE2D3 0.023 0.001 -9999 0 -10000 0 0
TNF 0.02 0.02 -9999 0 -0.12 11 11
NF kappa B1 p50/RelA 0.029 0.075 -9999 0 -0.15 75 75
BCL10 0.023 0.001 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.001 0.086 -9999 0 -0.22 60 60
beta TrCP1/SCF ubiquitin ligase complex 0.019 0.02 -9999 0 -0.051 35 35
TNFRSF1A 0.021 0.016 -9999 0 -0.12 7 7
IKK complex 0.029 0.098 -9999 0 -0.29 35 35
CYLD 0.023 0.007 -9999 0 -0.12 1 1
IKK complex/PKC alpha 0.024 0.1 -9999 0 -0.28 38 38
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.013 0.017 -9999 0 -0.078 18 18
ARNO/beta Arrestin1-2 0.029 0.019 -9999 0 -0.077 11 11
EGFR 0.015 0.03 -9999 0 -0.12 25 25
EPHA2 0.02 0.022 -9999 0 -0.12 13 13
USP6 0.023 0.006 -9999 0 -0.12 1 1
IQSEC1 0.023 0.006 -9999 0 -0.12 1 1
EGFR/EGFR/EGF/EGF 0.016 0.05 -9999 0 -0.11 73 73
ARRB2 0.017 0.018 -9999 0 -0.2 3 3
mol:GTP 0.003 0.006 -9999 0 -0.04 1 1
ARRB1 0.02 0.022 -9999 0 -0.12 13 13
FBXO8 0.022 0.011 -9999 0 -0.12 3 3
TSHR 0.013 0.038 -9999 0 -0.12 41 41
EGF 0.02 0.021 -9999 0 -0.12 12 12
somatostatin receptor activity 0 0 -9999 0 0 27 27
ARAP2 0 0 -9999 0 0 26 26
mol:GDP 0.015 0.046 -9999 0 -0.16 25 25
mol:PI-3-4-5-P3 0 0 -9999 0 0 27 27
ITGA2B 0.023 0.006 -9999 0 -0.12 1 1
ARF6 0.023 0.003 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.029 0.062 -9999 0 -0.11 75 75
ADAP1 0 0 -9999 0 0 26 26
KIF13B 0.02 0.022 -9999 0 -0.12 13 13
HGF/MET -0.017 0.074 -9999 0 -0.11 196 196
PXN 0.022 0.014 -9999 0 -0.12 5 5
ARF6/GTP 0.022 0.059 -9999 0 -0.2 27 27
EGFR/EGFR/EGF/EGF/ARFGEP100 0.03 0.046 -9999 0 -0.11 40 40
ADRB2 0.023 0.006 -9999 0 -0.12 1 1
receptor agonist activity 0 0 -9999 0 0 27 27
actin filament binding 0 0 -9999 0 0 27 27
SRC 0.023 0.009 -9999 0 -0.12 2 2
ITGB3 0.004 0.047 -9999 0 -0.12 68 68
GNAQ 0.021 0.016 -9999 0 -0.12 6 6
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 26 26
ARF6/GDP 0.021 0.05 -9999 0 -0.25 11 11
ARF6/GDP/GULP/ACAP1 0.017 0.061 -9999 0 -0.16 29 29
alphaIIb/beta3 Integrin/paxillin/GIT1 0.036 0.05 -9999 0 -0.096 39 39
ACAP1 0 0 -9999 0 0 8 8
ACAP2 0 0 -9999 0 0 26 26
LHCGR/beta Arrestin2 0.023 0.016 -9999 0 -0.14 3 3
EFNA1 0.014 0.031 -9999 0 -0.12 26 26
HGF 0.02 0.023 -9999 0 -0.12 14 14
CYTH3 0 0 -9999 0 -0.001 27 27
CYTH2 0 0.001 -9999 0 -0.004 27 27
NCK1 0.02 0.019 -9999 0 -0.12 9 9
fibronectin binding 0 0 -9999 0 0 28 28
endosomal lumen acidification 0 0 -9999 0 0 15 15
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 0.005 0.045 -9999 0 -0.12 63 63
GNAQ/ARNO 0.015 0.007 -9999 0 -0.047 6 6
mol:Phosphatidic acid 0 0 -9999 0 0 26 26
PIP3-E 0.018 0.028 -9999 0 -0.12 22 22
MET 0 0.047 -9999 0 -0.12 70 70
GNA14 0.02 0.02 -9999 0 -0.12 11 11
GNA15 0.021 0.017 -9999 0 -0.12 8 8
GIT1 0.022 0.012 -9999 0 -0.12 4 4
mol:PI-4-5-P2 0 0 -9999 0 -0.001 26 26
GNA11 0.022 0.014 -9999 0 -0.12 5 5
LHCGR 0.022 0.014 -9999 0 -0.12 5 5
AGTR1 0.022 0.012 -9999 0 -0.12 4 4
desensitization of G-protein coupled receptor protein signaling pathway 0.023 0.016 -9999 0 -0.14 3 3
IPCEF1/ARNO 0.026 0.038 -9999 0 -0.084 41 41
alphaIIb/beta3 Integrin 0.01 0.053 -9999 0 -0.096 107 107
Regulation of Telomerase

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
Telomerase catalytic core complex -0.047 0.18 -10000 0 -0.46 52 52
RAD9A 0.023 0 -10000 0 -10000 0 0
AP1 -0.031 0.087 -10000 0 -0.15 158 158
IFNAR2 0.018 0.02 -10000 0 -0.13 8 8
AKT1 0.012 0.041 -10000 0 -0.17 7 7
ER alpha/Oestrogen 0.002 0.046 -10000 0 -0.13 58 58
NFX1/SIN3/HDAC complex 0.009 0.089 -10000 0 -0.25 39 39
EGF 0.02 0.022 -10000 0 -0.13 12 12
SMG5 0.022 0.011 -10000 0 -0.12 3 3
SMG6 0.022 0.011 -10000 0 -0.12 3 3
SP3/HDAC2 0.026 0.031 -10000 0 -0.13 13 13
TERT/c-Abl -0.042 0.17 -10000 0 -0.43 54 54
SAP18 0.023 0.003 -10000 0 -10000 0 0
MRN complex 0.023 0.065 -10000 0 -0.14 64 64
WT1 0.019 0.016 -10000 0 -0.12 5 5
WRN 0.019 0.02 -10000 0 -0.12 10 10
SP1 0.02 0.015 -10000 0 -0.14 1 1
SP3 0.023 0.003 -10000 0 -10000 0 0
TERF2IP 0.023 0.009 -10000 0 -0.12 2 2
Telomerase/Nucleolin -0.033 0.17 -10000 0 -0.4 58 58
Mad/Max 0.032 0.015 -10000 0 -0.074 8 8
TERT -0.048 0.18 -10000 0 -0.48 44 44
CCND1 -0.13 0.37 -10000 0 -0.98 83 83
MAX 0.023 0.004 -10000 0 -10000 0 0
RBBP7 0.021 0.012 -10000 0 -0.12 3 3
RBBP4 0.021 0.014 -10000 0 -0.12 5 5
TERF2 0.025 0.017 0.082 38 -0.12 1 39
PTGES3 0.014 0.036 -10000 0 -0.12 36 36
SIN3A 0.021 0.014 -10000 0 -0.12 5 5
Telomerase/911 0.017 0.096 -10000 0 -0.34 27 27
CDKN1B -0.015 0.095 -10000 0 -0.32 34 34
RAD1 0.02 0.021 -10000 0 -0.12 12 12
XRCC5 0.021 0.01 -10000 0 -0.12 2 2
XRCC6 0.022 0.004 -10000 0 -10000 0 0
SAP30 0.023 0.001 -10000 0 -10000 0 0
TRF2/PARP2 0.03 0.032 -10000 0 -0.09 30 30
UBE3A 0.023 0.004 -10000 0 -10000 0 0
JUN 0.014 0.033 -10000 0 -0.12 30 30
E6 -0.001 0.003 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.013 0.021 -10000 0 -0.15 8 8
FOS -0.006 0.053 -10000 0 -0.12 95 95
IFN-gamma/IRF1 -0.007 0.086 -10000 0 -0.16 112 112
PARP2 0.018 0.026 -10000 0 -0.12 18 18
BLM 0.015 0.032 -10000 0 -0.12 28 28
Telomerase 0.013 0.1 -10000 0 -0.41 23 23
IRF1 0.004 0.058 -10000 0 -0.14 62 62
ESR1 0.017 0.024 -10000 0 -0.12 15 15
KU/TER 0.018 0.058 -10000 0 -0.17 44 44
ATM/TRF2 0.02 0.049 -10000 0 -0.13 51 51
ubiquitin-dependent protein catabolic process 0.013 0.088 -10000 0 -0.26 33 33
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.013 0.09 -10000 0 -0.26 33 33
HDAC1 0.019 0.02 -10000 0 -0.12 10 10
HDAC2 0.017 0.024 -10000 0 -0.12 12 12
ATM -0.012 0.067 0.14 1 -0.22 50 51
SMAD3 0.019 0.019 -10000 0 -0.072 21 21
ABL1 0.022 0.007 -10000 0 -0.12 1 1
MXD1 0.021 0.018 -10000 0 -0.12 8 8
MRE11A 0.02 0.017 -10000 0 -0.12 7 7
HUS1 0.023 0 -10000 0 -10000 0 0
RPS6KB1 0.021 0.014 -10000 0 -0.12 5 5
TERT/NF kappa B1/14-3-3 -0.024 0.17 -10000 0 -0.43 37 37
NR2F2 0.023 0.014 -10000 0 -0.12 4 4
MAPK3 0.021 0.016 -10000 0 -0.091 8 8
MAPK1 0.02 0.017 -10000 0 -0.087 10 10
TGFB1/TGF beta receptor Type II 0.019 0.023 -10000 0 -0.12 14 14
NFKB1 0.021 0.013 -10000 0 -0.12 4 4
HNRNPC 0.022 0.012 -10000 0 -0.12 4 4
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.012 0.067 0.14 1 -0.21 50 51
NBN 0.02 0.015 -10000 0 -0.12 5 5
EGFR 0.015 0.03 -10000 0 -0.12 25 25
mol:Oestrogen 0 0.002 -10000 0 -10000 0 0
EGF/EGFR 0.015 0.051 -10000 0 -0.11 73 73
MYC 0.015 0.028 -10000 0 -0.12 20 20
IL2 0.02 0.017 -10000 0 -0.12 3 3
KU 0.018 0.058 -10000 0 -0.17 44 44
RAD50 0.021 0.014 -10000 0 -0.12 5 5
HSP90AA1 0.023 0.003 -10000 0 -10000 0 0
TGFB1 0.019 0.023 -10000 0 -0.12 14 14
TRF2/BLM 0.024 0.043 -10000 0 -0.095 57 57
FRAP1 0.022 0.013 -10000 0 -0.12 4 4
KU/TERT -0.035 0.18 -10000 0 -0.43 55 55
SP1/HDAC2 0.025 0.038 -10000 0 -0.14 19 19
PINX1 0.021 0.017 -10000 0 -0.12 8 8
Telomerase/EST1A -0.029 0.17 -10000 0 -0.39 57 57
Smad3/Myc 0.016 0.046 -10000 0 -0.15 29 29
911 complex 0.043 0.024 -10000 0 -0.11 9 9
IFNG 0.009 0.047 -10000 0 -0.11 68 68
Telomerase/PinX1 -0.032 0.17 -10000 0 -0.4 56 56
Telomerase/AKT1/mTOR/p70S6K 0.004 0.11 -10000 0 -0.37 26 26
SIN3B 0.022 0.015 -10000 0 -0.12 6 6
YWHAE 0.022 0.014 -10000 0 -0.12 5 5
Telomerase/EST1B -0.03 0.17 -10000 0 -0.39 57 57
response to DNA damage stimulus -0.004 0.03 0.052 1 -0.12 38 39
MRN complex/TRF2/Rap1 0.046 0.06 -10000 0 -0.11 54 54
TRF2/WRN 0.024 0.042 -10000 0 -0.11 47 47
Telomerase/hnRNP C1/C2 -0.029 0.17 -10000 0 -0.4 56 56
E2F1 0.02 0.018 -10000 0 -0.12 7 7
ZNFX1 0.018 0.022 -10000 0 -0.12 12 12
PIF1 0.023 0.006 -10000 0 -0.12 1 1
NCL 0.022 0.008 -10000 0 -0.12 1 1
DKC1 0.022 0.011 -10000 0 -0.12 3 3
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.029 0.045 -10000 0 -0.11 31 31
fibroblast growth factor receptor signaling pathway 0.028 0.044 -10000 0 -0.11 31 31
LAMA1 0 0.053 -10000 0 -0.12 89 89
PRNP 0.021 0.015 -10000 0 -0.12 5 5
GPC1/SLIT2 -0.011 0.07 -10000 0 -0.11 175 175
SMAD2 0.024 0.028 -10000 0 -0.1 18 18
GPC1/PrPc/Cu2+ 0.021 0.036 -10000 0 -0.099 45 45
GPC1/Laminin alpha1 0.015 0.043 -10000 0 -0.076 101 101
TDGF1 0.022 0.015 -10000 0 -0.12 6 6
CRIPTO/GPC1 0.032 0.017 -10000 0 -0.076 14 14
APP/GPC1 0.023 0.043 -10000 0 -0.13 41 41
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.024 0.016 -10000 0 -0.11 1 1
FLT1 0.022 0.014 -10000 0 -0.12 5 5
GPC1/TGFB/TGFBR1/TGFBR2 0.039 0.033 -10000 0 -0.11 18 18
SERPINC1 0.023 0.009 -10000 0 -0.12 2 2
FYN 0.019 0.024 -10000 0 -0.11 1 1
FGR 0.026 0.014 -10000 0 -0.11 1 1
positive regulation of MAPKKK cascade 0.016 0.052 -10000 0 -0.18 17 17
SLIT2 0.001 0.047 -10000 0 -0.12 71 71
GPC1/NRG 0.031 0.019 -10000 0 -0.081 15 15
NRG1 0.021 0.017 -10000 0 -0.12 8 8
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.032 0.046 -10000 0 -0.12 41 41
LYN 0.024 0.015 -10000 0 -0.11 1 1
mol:Spermine 0.011 0.01 -10000 0 -0.077 7 7
cell growth 0.028 0.044 -10000 0 -0.11 31 31
BMP signaling pathway -0.021 0.016 0.12 7 -10000 0 7
SRC 0.026 0.015 -10000 0 -0.11 2 2
TGFBR1 0.022 0.011 -10000 0 -0.12 3 3
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A 0.011 0.041 -10000 0 -0.12 48 48
GPC1 0.021 0.016 -10000 0 -0.12 7 7
TGFBR1 (dimer) 0.022 0.011 -10000 0 -0.12 3 3
VEGFA 0.019 0.021 -10000 0 -0.12 11 11
BLK 0.025 0.016 -10000 0 -0.11 2 2
HCK 0.023 0.019 -10000 0 -0.17 1 1
FGF2 0.023 0.009 -10000 0 -0.12 2 2
FGFR1 0.008 0.043 -10000 0 -0.12 54 54
VEGFR1 homodimer 0.022 0.014 -10000 0 -0.12 5 5
TGFBR2 0.02 0.02 -10000 0 -0.12 11 11
cell death 0.023 0.043 -10000 0 -0.13 41 41
ATIII/GPC1 0.033 0.015 -10000 0 -0.078 10 10
PLA2G2A/GPC1 0.023 0.034 -10000 0 -0.076 57 57
LCK 0.025 0.016 -10000 0 -0.17 1 1
neuron differentiation 0.031 0.019 -10000 0 -0.08 15 15
PrPc/Cu2+ 0.007 0.039 -10000 0 -0.14 37 37
APP 0.022 0.008 -10000 0 -0.12 1 1
TGFBR2 (dimer) 0.02 0.02 -10000 0 -0.12 11 11
EPO signaling pathway

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
BCL2L1 0.015 0.15 -9999 0 -0.44 39 39
CRKL 0.029 0.037 -9999 0 -0.1 8 8
mol:DAG 0.026 0.075 -9999 0 -0.19 46 46
HRAS 0.032 0.045 -9999 0 -0.14 11 11
MAPK8 0.021 0.041 -9999 0 -0.11 43 43
RAP1A 0.026 0.045 -9999 0 -0.17 14 14
GAB1 0.027 0.038 -9999 0 -0.11 10 10
MAPK14 0.022 0.041 -9999 0 -0.11 44 44
EPO 0.025 0.008 -9999 0 -0.12 1 1
PLCG1 0.026 0.076 -9999 0 -0.2 46 46
EPOR/TRPC2/IP3 Receptors 0.022 0.022 -9999 0 -0.12 12 12
RAPGEF1 0.023 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.035 0.043 -9999 0 -0.11 29 29
GAB1/SHC/GRB2/SOS1 0.042 0.052 -9999 0 -0.14 11 11
EPO/EPOR (dimer) 0.034 0.022 -9999 0 -0.082 15 15
IRS2 0.028 0.038 -9999 0 -0.11 9 9
STAT1 0.02 0.1 -9999 0 -0.25 55 55
STAT5B 0.032 0.076 -9999 0 -0.18 51 51
cell proliferation 0.02 0.038 -9999 0 -0.1 44 44
GAB1/SHIP/PIK3R1/SHP2/SHC 0.022 0.046 -9999 0 -0.12 18 18
TEC 0.02 0.045 -9999 0 -0.13 22 22
SOCS3 0.015 0.032 -9999 0 -0.12 28 28
STAT1 (dimer) 0.021 0.098 -9999 0 -0.25 55 55
JAK2 0.019 0.025 -9999 0 -0.12 16 16
PIK3R1 0.015 0.031 -9999 0 -0.12 27 27
EPO/EPOR (dimer)/JAK2 0.058 0.054 -9999 0 -0.12 8 8
EPO/EPOR 0.034 0.022 -9999 0 -0.082 15 15
LYN 0.022 0.014 -9999 0 -0.12 4 4
TEC/VAV2 0.021 0.059 -9999 0 -0.12 31 31
elevation of cytosolic calcium ion concentration 0.022 0.022 -9999 0 -0.12 12 12
SHC1 0.023 0.001 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.039 0.052 -9999 0 -0.13 43 43
mol:IP3 0.026 0.075 -9999 0 -0.19 46 46
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.029 0.047 -9999 0 -0.14 15 15
SH2B3 0.024 0.004 -9999 0 -10000 0 0
NFKB1 0.018 0.053 -9999 0 -0.15 43 43
EPO/EPOR (dimer)/JAK2/SOCS3 -0.006 0.06 -9999 0 -0.17 64 64
PTPN6 0.025 0.038 -9999 0 -0.09 27 27
TEC/VAV2/GRB2 0.029 0.062 -9999 0 -0.12 32 32
EPOR 0.022 0.022 -9999 0 -0.12 12 12
INPP5D 0 0 -9999 0 -10000 0 0
mol:GDP 0.042 0.053 -9999 0 -0.14 11 11
SOS1 0.017 0.027 -9999 0 -0.12 20 20
PLCG2 0.02 0.02 -9999 0 -0.12 11 11
CRKL/CBL/C3G 0.053 0.042 -9999 0 -0.13 4 4
VAV2 0.027 0.037 -9999 0 -0.1 8 8
CBL 0.029 0.038 -9999 0 -0.12 8 8
SHC/Grb2/SOS1 0.03 0.045 -9999 0 -0.13 16 16
STAT5A 0.03 0.079 -9999 0 -0.19 53 53
GRB2 0.023 0.006 -9999 0 -0.12 1 1
STAT5 (dimer) 0.049 0.088 -9999 0 -0.23 33 33
LYN/PLCgamma2 0.02 0.05 -9999 0 -0.13 54 54
PTPN11 0.022 0.011 -9999 0 -0.12 3 3
BTK 0.022 0.047 -9999 0 -0.15 20 20
BCL2 0.019 0.12 -9999 0 -0.37 34 34
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.028 0.018 -10000 0 -0.098 7 7
NFATC2 0.016 0.19 -10000 0 -0.4 56 56
NFATC3 0.06 0.059 0.26 28 -0.24 2 30
CD40LG 0.043 0.14 -10000 0 -0.53 5 5
ITCH 0.026 0.064 -10000 0 -0.28 17 17
CBLB 0.023 0.073 -10000 0 -0.25 29 29
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment 0.038 0.15 -10000 0 -0.49 13 13
JUNB 0.007 0.042 -10000 0 -0.12 52 52
CaM/Ca2+/Calcineurin A alpha-beta B1 0.034 0.059 -10000 0 -0.18 33 33
T cell anergy 0.012 0.087 -10000 0 -0.31 29 29
TLE4 -0.016 0.18 -10000 0 -0.41 75 75
Jun/NFAT1-c-4/p21SNFT 0.08 0.15 -10000 0 -0.56 4 4
AP-1/NFAT1-c-4 0.08 0.2 -10000 0 -0.62 4 4
IKZF1 0.019 0.13 -10000 0 -0.27 49 49
T-helper 2 cell differentiation 0.023 0.14 -10000 0 -0.48 5 5
AP-1/NFAT1 0.007 0.15 -10000 0 -0.26 78 78
CALM1 0.027 0.037 -10000 0 -0.11 32 32
EGR2 0.067 0.15 -10000 0 -0.86 3 3
EGR3 0.068 0.14 0.51 11 -0.48 4 15
NFAT1/FOXP3 0.038 0.14 -10000 0 -0.27 51 51
EGR1 -0.005 0.054 -10000 0 -0.12 99 99
JUN 0.019 0.035 -10000 0 -0.12 31 31
EGR4 0.023 0.014 -10000 0 -0.13 5 5
mol:Ca2+ 0.006 0.03 -10000 0 -0.12 26 26
GBP3 -0.06 0.23 -10000 0 -0.45 131 131
FOSL1 0.021 0.018 -10000 0 -0.12 9 9
NFAT1-c-4/MAF/IRF4 0.092 0.14 -10000 0 -0.57 3 3
DGKA 0.012 0.14 -10000 0 -0.31 57 57
CREM 0.021 0.012 -10000 0 -0.12 4 4
NFAT1-c-4/PPARG 0.081 0.14 -10000 0 -0.57 4 4
CTLA4 0.018 0.11 -10000 0 -0.22 53 53
NFAT1-c-4 (dimer)/EGR1 0.053 0.15 -10000 0 -0.56 5 5
NFAT1-c-4 (dimer)/EGR4 0.088 0.14 -10000 0 -0.56 4 4
FOS 0 0.053 -10000 0 -0.11 96 96
IFNG 0.017 0.14 -10000 0 -0.42 10 10
T cell activation 0.027 0.11 -10000 0 -0.44 2 2
MAF 0.023 0.012 -10000 0 -0.12 4 4
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.07 0.13 0.61 3 -0.5 22 25
TNF 0.037 0.14 -10000 0 -0.51 6 6
FASLG 0.056 0.15 -10000 0 -0.98 3 3
TBX21 0.026 0.018 -10000 0 -0.13 3 3
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ 0.019 0.03 -10000 0 -0.12 25 25
PTPN1 0.019 0.13 -10000 0 -0.28 49 49
NFAT1-c-4/ICER1 0.081 0.14 -10000 0 -0.56 4 4
GATA3 0.024 0.021 -10000 0 -0.12 11 11
T-helper 1 cell differentiation 0.017 0.14 -10000 0 -0.42 10 10
IL2RA 0.04 0.15 -10000 0 -0.45 15 15
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.015 0.14 -10000 0 -0.31 52 52
E2F1 0.017 0.045 -10000 0 -0.15 36 36
PPARG 0.018 0.028 -10000 0 -0.12 22 22
SLC3A2 0.013 0.14 -10000 0 -0.33 43 43
IRF4 0.019 0.025 -10000 0 -0.12 17 17
PTGS2 0.035 0.15 -10000 0 -0.6 4 4
CSF2 0.043 0.14 -10000 0 -0.53 5 5
JunB/Fra1/NFAT1-c-4 0.071 0.15 -10000 0 -0.5 6 6
IL4 0.022 0.14 -10000 0 -0.5 4 4
IL5 0.042 0.14 -10000 0 -0.56 4 4
IL2 0.027 0.11 -10000 0 -0.45 2 2
IL3 0.012 0.04 -10000 0 -0.38 3 3
RNF128 0.026 0.051 -10000 0 -0.25 7 7
NFATC1 0.071 0.13 0.5 22 -0.62 3 25
CDK4 -0.08 0.28 -10000 0 -1.2 29 29
PTPRK -0.007 0.18 -10000 0 -0.43 60 60
IL8 0.029 0.15 -10000 0 -0.54 6 6
POU2F1 0.031 0.007 -10000 0 -0.12 1 1
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.012 0.014 -9999 0 -0.057 22 22
ADCY5 0.009 0.02 -9999 0 -0.06 42 42
ADCY6 0.013 0.01 -9999 0 -0.057 11 11
ADCY7 0.014 0.009 -9999 0 -0.057 8 8
ADCY1 0.013 0.013 -9999 0 -0.067 12 12
ADCY2 0.012 0.013 -9999 0 -0.057 18 18
ADCY3 0.012 0.013 -9999 0 -0.057 18 18
ADCY8 0.002 0.03 -9999 0 -0.061 99 99
PRKCE 0.01 0.011 -9999 0 -0.077 8 8
ADCY9 0.012 0.015 -9999 0 -0.064 17 17
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process 0.012 0.032 -9999 0 -0.18 11 11
Glucocorticoid receptor regulatory network

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
PCK2 -0.011 0.059 -10000 0 -0.7 2 2
SMARCC2 0.022 0.012 -10000 0 -0.12 4 4
SMARCC1 0.023 0.003 -10000 0 -10000 0 0
TBX21 0.042 0.047 -10000 0 -0.31 1 1
SUMO2 0.021 0.005 -10000 0 -10000 0 0
STAT1 (dimer) -0.007 0.08 -10000 0 -0.17 94 94
FKBP4 0.02 0.02 -10000 0 -0.12 10 10
FKBP5 0.006 0.043 -10000 0 -0.12 56 56
GR alpha/HSP90/FKBP51/HSP90 -0.013 0.082 0.24 1 -0.22 31 32
PRL 0.045 0.057 -10000 0 -0.5 1 1
cortisol/GR alpha (dimer)/TIF2 -0.02 0.11 0.48 2 -0.34 3 5
RELA -0.02 0.075 -10000 0 -0.15 117 117
FGG -0.016 0.1 0.45 1 -0.32 3 4
GR beta/TIF2 -0.006 0.07 0.23 2 -0.2 23 25
IFNG -0.003 0.12 -10000 0 -0.45 4 4
apoptosis -0.052 0.16 -10000 0 -0.45 32 32
CREB1 0.033 0.008 -10000 0 -10000 0 0
histone acetylation 0.028 0.081 0.28 7 -0.35 12 19
BGLAP 0.042 0.075 -10000 0 -0.68 3 3
GR/PKAc 0.028 0.063 0.23 2 -0.16 14 16
NF kappa B1 p50/RelA -0.044 0.14 -10000 0 -0.26 139 139
SMARCD1 0.021 0.018 -10000 0 -0.12 9 9
MDM2 -0.003 0.047 -10000 0 -0.22 9 9
GATA3 0.037 0.022 -10000 0 -0.12 11 11
AKT1 0.015 0.022 0.15 2 -0.13 10 12
CSF2 0.03 0.055 -10000 0 -10000 0 0
GSK3B 0.02 0.012 -10000 0 -0.13 3 3
NR1I3 -0.038 0.15 -10000 0 -0.5 7 7
CSN2 -0.015 0.093 0.39 1 -0.29 3 4
BRG1/BAF155/BAF170/BAF60A 0.041 0.052 -10000 0 -0.11 45 45
NFATC1 0.033 0.013 -10000 0 -0.11 3 3
POU2F1 0.031 0.008 -10000 0 -0.11 1 1
CDKN1A -0.041 0.12 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.002 0.004 -10000 0 -10000 0 0
SFN 0.014 0.032 -10000 0 -0.12 29 29
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.007 0.086 0.24 1 -0.2 46 47
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.11 0.28 -10000 0 -0.72 92 92
JUN 0.021 0.089 -10000 0 -0.29 8 8
IL4 0.046 0.048 -10000 0 -10000 0 0
CDK5R1 0.022 0.007 -10000 0 -0.12 1 1
PRKACA 0.021 0.017 -10000 0 -0.12 8 8
cortisol/GR alpha (monomer)/AP-1 -0.043 0.079 0.19 12 -0.2 66 78
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.006 0.079 0.24 1 -0.2 29 30
cortisol/GR alpha (monomer) -0.039 0.12 0.55 2 -0.38 3 5
NCOA2 0.021 0.013 -10000 0 -0.12 4 4
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.014 0.079 -10000 0 -0.14 134 134
AP-1/NFAT1-c-4 -0.012 0.15 -10000 0 -0.38 33 33
AFP 0.017 0.083 -10000 0 -0.56 1 1
SUV420H1 0.021 0.015 -10000 0 -0.12 6 6
IRF1 -0.095 0.24 -10000 0 -0.6 86 86
TP53 0.026 0.033 -10000 0 -10000 0 0
PPP5C 0.022 0.014 -10000 0 -0.12 5 5
KRT17 -0.011 0.15 -10000 0 -0.75 11 11
KRT14 -0.006 0.2 0.48 8 -1.1 15 23
TBP 0.031 0.026 -10000 0 -0.2 5 5
CREBBP 0.023 0.052 0.3 15 -0.13 5 20
HDAC1 0.013 0.02 -10000 0 -0.13 10 10
HDAC2 0.018 0.021 -10000 0 -0.12 12 12
AP-1 -0.012 0.15 -10000 0 -0.37 39 39
MAPK14 0.02 0.008 -10000 0 -0.13 1 1
MAPK10 0.011 0.037 -10000 0 -0.13 38 38
MAPK11 0.021 0.004 -10000 0 -10000 0 0
KRT5 -0.07 0.26 -10000 0 -0.89 46 46
interleukin-1 receptor activity -0.002 0.001 -10000 0 -10000 0 0
NCOA1 0.024 0.01 -10000 0 -0.08 4 4
STAT1 -0.007 0.08 -10000 0 -0.17 94 94
CGA 0.043 0.059 -10000 0 -0.51 1 1
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.046 0.11 0.28 7 -0.34 37 44
MAPK3 0.019 0.015 -10000 0 -0.13 5 5
MAPK1 0.019 0.017 -10000 0 -0.12 7 7
ICAM1 -0.13 0.32 -10000 0 -0.79 102 102
NFKB1 -0.031 0.097 -10000 0 -0.18 133 133
MAPK8 0.033 0.076 -10000 0 -0.23 9 9
MAPK9 0.019 0.012 -10000 0 -0.12 3 3
cortisol/GR alpha (dimer) -0.055 0.17 -10000 0 -0.47 32 32
BAX -0.039 0.12 -10000 0 -10000 0 0
POMC 0.029 0.082 -10000 0 -10000 0 0
EP300 0.023 0.047 0.29 14 -0.13 1 15
cortisol/GR alpha (dimer)/p53 -0.045 0.12 0.5 1 -0.36 5 6
proteasomal ubiquitin-dependent protein catabolic process -0.006 0.058 0.26 15 -0.21 7 22
SGK1 0.001 0.1 0.34 14 -0.32 31 45
IL13 0.021 0.089 -10000 0 -0.52 1 1
IL6 -0.028 0.15 -10000 0 -0.66 14 14
PRKACG 0.023 0.009 -10000 0 -0.12 2 2
IL5 0.025 0.089 -10000 0 -10000 0 0
IL2 0.004 0.11 -10000 0 -0.46 2 2
CDK5 0.014 0.032 -10000 0 -0.12 28 28
PRKACB 0.019 0.02 -10000 0 -0.12 11 11
HSP90AA1 0.023 0.003 -10000 0 -10000 0 0
IL8 -0.055 0.22 -10000 0 -0.76 40 40
CDK5R1/CDK5 0.019 0.042 -10000 0 -0.11 52 52
NF kappa B1 p50/RelA/PKAc -0.002 0.12 -10000 0 -0.19 114 114
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 -0.01 0.11 0.4 2 -0.36 1 3
SMARCA4 0.015 0.031 -10000 0 -0.12 27 27
chromatin remodeling -0.009 0.092 0.27 2 -0.32 14 16
NF kappa B1 p50/RelA/Cbp -0.02 0.13 0.34 8 -0.25 80 88
JUN (dimer) 0.021 0.089 -10000 0 -0.29 8 8
YWHAH 0.021 0.014 -10000 0 -0.12 5 5
VIPR1 0.043 0.045 -10000 0 -10000 0 0
NR3C1 -0.015 0.081 0.32 2 -0.33 10 12
NR4A1 0.01 0.048 -10000 0 -10000 0 0
TIF2/SUV420H1 0.02 0.048 -10000 0 -0.13 50 50
MAPKKK cascade -0.052 0.16 -10000 0 -0.45 32 32
cortisol/GR alpha (dimer)/Src-1 -0.013 0.11 0.49 2 -0.32 2 4
PBX1 0.029 0.014 -10000 0 -0.11 4 4
POU1F1 0.03 0.014 -10000 0 -0.13 4 4
SELE -0.006 0.11 -10000 0 -0.41 3 3
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A -0.009 0.092 0.27 2 -0.32 14 16
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.01 0.11 0.4 2 -0.36 1 3
mol:cortisol -0.027 0.065 0.3 2 -10000 0 2
MMP1 -0.038 0.16 -10000 0 -0.95 12 12
IL2 signaling events mediated by STAT5

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GAB2 0.008 0.041 -9999 0 -0.12 50 50
ELF1 0.032 0.023 -9999 0 -0.2 3 3
CCNA2 0.013 0.032 -9999 0 -0.12 29 29
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
JAK3 0.022 0.014 -9999 0 -0.12 5 5
PIK3R1 0.016 0.031 -9999 0 -0.12 27 27
JAK1 0.022 0.01 -9999 0 -0.12 2 2
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.006 0.13 -9999 0 -0.31 53 53
SHC1 0.024 0.002 -9999 0 -10000 0 0
SP1 0.012 0.055 -9999 0 -0.25 11 11
IL2RA 0.03 0.037 -9999 0 -0.49 2 2
IL2RB 0.019 0.024 -9999 0 -0.12 16 16
SOS1 0.018 0.027 -9999 0 -0.12 20 20
IL2RG -0.001 0.05 -9999 0 -0.12 82 82
G1/S transition of mitotic cell cycle -0.077 0.17 -9999 0 -0.35 105 105
PTPN11 0.022 0.011 -9999 0 -0.12 3 3
CCND2 -0.001 0.088 -9999 0 -0.48 10 10
LCK 0.022 0.015 -9999 0 -0.12 6 6
GRB2 0.023 0.007 -9999 0 -0.12 1 1
IL2 0.023 0.011 -9999 0 -0.12 3 3
CDK6 0.008 0.04 -9999 0 -0.12 46 46
CCND3 -0.004 0.14 -9999 0 -0.48 20 20
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.023 0.009 -10000 0 -0.12 2 2
RAS family/GTP/Tiam1 0 0.066 -10000 0 -0.16 64 64
NT3 (dimer)/TRKC 0.007 0.051 -10000 0 -0.082 132 132
NT3 (dimer)/TRKB 0.023 0.047 -10000 0 -0.12 19 19
SHC/Grb2/SOS1/GAB1/PI3K 0.003 0.087 -10000 0 -0.31 22 22
RAPGEF1 0.023 0 -10000 0 -10000 0 0
BDNF 0.022 0.011 -10000 0 -0.12 3 3
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
DYNLT1 0.018 0.023 -10000 0 -0.12 14 14
NTRK1 0.023 0.006 -10000 0 -0.12 1 1
NTRK2 0.019 0.026 -10000 0 -0.12 18 18
NTRK3 0.015 0.033 -10000 0 -0.12 31 31
NT-4/5 (dimer)/TRKB 0.027 0.02 -10000 0 -0.064 25 25
neuron apoptosis -0.043 0.036 -10000 0 -10000 0 0
SHC 2-3/Grb2 0.045 0.038 -10000 0 -10000 0 0
SHC1 0.023 0.001 -10000 0 -10000 0 0
SHC2 0.027 0.034 -10000 0 -10000 0 0
SHC3 0.027 0.034 -10000 0 -10000 0 0
STAT3 (dimer) -0.02 0.1 -10000 0 -0.19 137 137
NT3 (dimer)/TRKA 0.025 0.044 -10000 0 -0.13 11 11
RIN/GDP 0.03 0.061 -10000 0 -0.19 26 26
GIPC1 0.019 0.023 -10000 0 -0.12 15 15
KRAS 0.014 0.034 -10000 0 -0.12 33 33
DNAJA3 0.009 0.042 0.16 13 -0.14 8 21
RIN/GTP 0.017 0.007 -10000 0 -0.077 3 3
CCND1 -0.058 0.18 -10000 0 -0.48 85 85
MAGED1 0.02 0.019 -10000 0 -0.12 10 10
PTPN11 0.022 0.011 -10000 0 -0.12 3 3
RICS 0.017 0.027 -10000 0 -0.12 20 20
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.035 0.041 -10000 0 -0.12 30 30
GRB2 0.023 0.006 -10000 0 -0.12 1 1
NGF (dimer)/TRKA/MATK 0.031 0.01 -10000 0 -0.12 1 1
TRKA/NEDD4-2 0.022 0.043 -10000 0 -0.11 50 50
ELMO1 0.01 0.041 -10000 0 -0.12 49 49
RhoG/GTP/ELMO1/DOCK1 0.009 0.049 -10000 0 -0.12 53 53
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.023 0.006 -10000 0 -0.12 1 1
DOCK1 0.019 0.02 -10000 0 -0.12 10 10
GAB2 0.007 0.041 -10000 0 -0.12 50 50
RIT2 0.022 0.011 -10000 0 -0.12 3 3
RIT1 0.021 0.014 -10000 0 -0.12 5 5
FRS2 0.019 0.024 -10000 0 -0.12 15 15
DNM1 0.021 0.019 -10000 0 -0.12 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.021 0.016 -10000 0 -0.12 7 7
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.006 0.044 0.13 3 -0.14 12 15
mol:GDP 0.027 0.083 -10000 0 -0.28 26 26
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.003 0.039 -10000 0 -0.097 69 69
RIT1/GDP 0.029 0.064 -10000 0 -0.2 26 26
TIAM1 0.015 0.032 -10000 0 -0.12 28 28
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
BDNF (dimer)/TRKB 0.043 0.021 -10000 0 -0.11 3 3
KIDINS220/CRKL/C3G 0.034 0.01 -10000 0 -0.14 1 1
SHC/RasGAP 0.025 0.039 -10000 0 -0.13 32 32
FRS2 family/SHP2 0.035 0.041 -10000 0 -0.12 30 30
SHC/GRB2/SOS1/GAB1 0.043 0.047 -10000 0 -0.1 41 41
RIT1/GTP 0.012 0.028 -10000 0 -0.13 20 20
NT3 (dimer) -0.003 0.056 -10000 0 -0.12 101 101
RAP1/GDP 0.017 0.056 -10000 0 -0.17 28 28
KIDINS220/CRKL 0.023 0.009 -10000 0 -0.12 2 2
BDNF (dimer) 0.022 0.011 -10000 0 -0.12 3 3
ubiquitin-dependent protein catabolic process 0.02 0.035 -10000 0 -0.09 50 50
Schwann cell development -0.004 0.009 -10000 0 -0.057 2 2
EHD4 0.023 0.001 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.042 0.05 -10000 0 -0.11 38 38
FRS2 family/SHP2/CRK family/C3G/GAB2 0.012 0.065 -10000 0 -0.21 19 19
RAP1B 0.019 0.02 -10000 0 -0.12 10 10
RAP1A 0.021 0.012 -10000 0 -0.12 3 3
CDC42/GTP 0.031 0.04 -10000 0 -0.15 4 4
ABL1 0.022 0.007 -10000 0 -0.12 1 1
SH2B family/GRB2/SOS1 0.021 0.045 -10000 0 -0.15 29 29
Rap1/GTP 0.023 0.081 -10000 0 -0.26 34 34
STAT3 -0.02 0.1 -10000 0 -0.19 137 137
axon guidance 0.02 0.034 -10000 0 -0.15 4 4
MAPK3 0.024 0.013 -10000 0 -0.21 1 1
MAPK1 0.024 0.014 -10000 0 -0.21 1 1
CDC42/GDP 0.03 0.062 -10000 0 -0.19 26 26
NTF3 -0.003 0.056 -10000 0 -0.12 101 101
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.03 0.012 -10000 0 -0.073 7 7
PI3K 0.007 0.065 -10000 0 -0.13 96 96
FRS3 0.023 0.009 -10000 0 -0.12 2 2
FAIM 0.022 0.012 -10000 0 -0.12 4 4
GAB1 0.02 0.021 -10000 0 -0.12 12 12
RASGRF1 0.01 0.041 0.16 13 -0.14 8 21
SOS1 0.017 0.027 -10000 0 -0.12 20 20
MCF2L 0.008 0.039 -10000 0 -0.12 19 19
RGS19 0.023 0 -10000 0 -10000 0 0
CDC42 0.023 0.002 -10000 0 -10000 0 0
RAS family/GTP 0.018 0.11 -10000 0 -0.36 32 32
Rac1/GDP 0.03 0.062 -10000 0 -0.19 26 26
NGF (dimer)/TRKA/GRIT 0.022 0.034 -10000 0 -0.089 47 47
neuron projection morphogenesis -0.04 0.18 -10000 0 -0.72 25 25
NGF (dimer)/TRKA/NEDD4-2 0.021 0.036 -10000 0 -0.09 50 50
MAP2K1 0.022 0.035 -10000 0 -0.089 41 41
NGFR 0.021 0.017 -10000 0 -0.12 8 8
NGF (dimer)/TRKA/GIPC/GAIP 0.019 0.048 -10000 0 -0.14 42 42
RAS family/GTP/PI3K -0.003 0.084 -10000 0 -0.18 87 87
FRS2 family/SHP2/GRB2/SOS1 0.047 0.058 -10000 0 -0.21 11 11
NRAS 0.022 0.011 -10000 0 -0.12 3 3
GRB2/SOS1 0.021 0.045 -10000 0 -0.15 29 29
PRKCI 0.016 0.028 -10000 0 -0.12 22 22
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.023 0.002 -10000 0 -10000 0 0
PRKCZ 0.023 0 -10000 0 -10000 0 0
MAPKKK cascade 0.027 0.033 -10000 0 -0.4 2 2
RASA1 0.021 0.012 -10000 0 -0.12 3 3
TRKA/c-Abl 0.029 0.031 -10000 0 -0.14 18 18
SQSTM1 0.021 0.014 -10000 0 -0.12 5 5
BDNF (dimer)/TRKB/GIPC 0.041 0.049 -10000 0 -0.1 42 42
NGF (dimer)/TRKA/p62/Atypical PKCs 0.033 0.053 -10000 0 -0.097 67 67
MATK 0.022 0.014 -10000 0 -0.12 5 5
NEDD4L 0.017 0.027 -10000 0 -0.12 20 20
RAS family/GDP -0.013 0.034 -10000 0 -0.13 31 31
NGF (dimer)/TRKA 0.003 0.036 -10000 0 -0.15 8 8
Rac1/GTP -0.017 0.041 -10000 0 -0.14 33 33
FRS2 family/SHP2/CRK family 0.056 0.042 -10000 0 -0.13 6 6
Coregulation of Androgen receptor activity

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
NRIP1 0.014 0.035 -9999 0 -0.12 35 35
SVIL 0.016 0.031 -9999 0 -0.12 26 26
ZNF318 0.018 0.014 -9999 0 -0.12 5 5
JMJD2C 0.029 0.016 -9999 0 -0.12 6 6
T-DHT/AR/Ubc9 0.017 0.057 -9999 0 -0.11 84 84
CARM1 0.018 0.026 -9999 0 -0.12 19 19
PRDX1 0.022 0.004 -9999 0 -10000 0 0
PELP1 0.022 0.009 -9999 0 -0.12 2 2
CTNNB1 0.023 0.008 -9999 0 -0.12 1 1
AKT1 0.02 0.019 -9999 0 -0.12 10 10
PTK2B 0.023 0.009 -9999 0 -0.12 2 2
MED1 0.02 0.014 -9999 0 -0.12 5 5
MAK 0.008 0.04 -9999 0 -0.12 47 47
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.022 0.019 -9999 0 -0.12 9 9
GSN 0.023 0.012 -9999 0 -0.12 3 3
NCOA2 0.021 0.013 -9999 0 -0.12 4 4
NCOA6 0.023 0.014 -9999 0 -0.12 5 5
DNA-PK 0.023 0.06 -9999 0 -0.14 60 60
NCOA4 0.023 0.004 -9999 0 -10000 0 0
PIAS3 0.021 0.022 -9999 0 -0.12 13 13
cell proliferation 0.004 0.045 -9999 0 -0.5 2 2
XRCC5 0.021 0.01 -9999 0 -0.12 2 2
UBE3A 0.025 0.003 -9999 0 -10000 0 0
T-DHT/AR/SNURF 0.016 0.058 -9999 0 -0.11 84 84
FHL2 0.018 0.078 -9999 0 -0.67 5 5
RANBP9 0.023 0.014 -9999 0 -0.12 5 5
JMJD1A 0.033 0.024 -9999 0 -0.12 6 6
CDK6 0.008 0.04 -9999 0 -0.12 46 46
TGFB1I1 0.024 0.012 -9999 0 -0.12 4 4
T-DHT/AR/CyclinD1 -0.01 0.079 -9999 0 -0.12 152 152
XRCC6 0.022 0.004 -9999 0 -10000 0 0
T-DHT/AR 0.027 0.076 -9999 0 -0.18 20 20
CTDSP1 0.023 0.011 -9999 0 -0.12 3 3
CTDSP2 0.02 0.009 -9999 0 -0.12 2 2
BRCA1 0.016 0.03 -9999 0 -0.12 24 24
TCF4 0.019 0.017 -9999 0 -0.12 8 8
CDKN2A 0.013 0.022 -9999 0 -0.12 12 12
SRF 0.024 0.03 -9999 0 -0.12 23 23
NKX3-1 0.013 0.086 -9999 0 -0.29 34 34
KLK3 0.013 0.04 -9999 0 -10000 0 0
TMF1 0.022 0.012 -9999 0 -0.12 3 3
HNRNPA1 0.022 0.002 -9999 0 -10000 0 0
AOF2 0.024 0.009 -9999 0 -0.12 2 2
APPL1 0.019 0.014 -9999 0 -0.073 12 12
T-DHT/AR/Caspase 8 0.012 0.061 -9999 0 -0.11 96 96
AR 0.015 0.039 -9999 0 -0.11 44 44
UBA3 0.001 0 -9999 0 -10000 0 0
PATZ1 0.021 0.012 -9999 0 -0.12 4 4
PAWR 0.023 0.009 -9999 0 -0.12 2 2
PRKDC 0.02 0.015 -9999 0 -0.12 6 6
PA2G4 0.021 0.009 -9999 0 -0.12 2 2
UBE2I 0.023 0.001 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.015 0.054 -9999 0 -0.099 86 86
RPS6KA3 0.019 0.023 -9999 0 -0.12 13 13
T-DHT/AR/ARA70 0.014 0.062 -9999 0 -0.11 99 99
LATS2 0.022 0.006 -9999 0 -0.12 1 1
T-DHT/AR/PRX1 0.012 0.055 -9999 0 -0.099 94 94
Cyclin D3/CDK11 p58 0.014 0.019 -9999 0 -0.1 14 14
VAV3 0.011 0.038 -9999 0 -0.12 41 41
KLK2 0.016 0.072 -9999 0 -0.28 24 24
CASP8 0.022 0.004 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.023 0.065 -9999 0 -0.1 101 101
TMPRSS2 0.005 0.099 -9999 0 -0.4 10 10
CCND1 0.006 0.042 -9999 0 -0.12 54 54
PIAS1 0.025 0.009 -9999 0 -0.12 2 2
mol:T-DHT 0.006 0.007 -9999 0 -0.047 3 3
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.026 0.002 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.008 0.078 -9999 0 -0.13 136 136
CMTM2 0.023 0.006 -9999 0 -0.12 1 1
SNURF 0.021 0.017 -9999 0 -0.12 8 8
ZMIZ1 0.022 0.031 -9999 0 -0.11 26 26
CCND3 0.021 0.018 -9999 0 -0.12 9 9
TGIF1 0.022 0.001 -9999 0 -10000 0 0
FKBP4 0.022 0.02 -9999 0 -0.12 10 10
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.015 0.12 -10000 0 -0.48 29 29
HDAC1 0.027 0.027 0.092 18 -0.1 10 28
AES 0.023 0.021 0.065 1 -0.12 10 11
FBXW11 0.023 0.003 -10000 0 -10000 0 0
DTX1 0.023 0.009 -10000 0 -0.12 2 2
LRP6/FZD1 0.018 0.047 -10000 0 -0.11 66 66
TLE1 0.022 0.02 0.075 1 -0.11 10 11
AP1 -0.004 0.071 -10000 0 -0.2 46 46
NCSTN 0.022 0.012 -10000 0 -0.12 4 4
ADAM10 0.022 0.013 -10000 0 -0.12 4 4
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.056 0.18 -10000 0 -0.48 52 52
NICD/RBPSUH 0.013 0.12 -10000 0 -0.48 29 29
WIF1 0.02 0.022 -10000 0 -0.12 13 13
NOTCH1 0.001 0.12 -10000 0 -0.51 29 29
PSENEN 0.016 0.03 -10000 0 -0.12 24 24
KREMEN2 0.022 0.012 -10000 0 -0.12 4 4
DKK1 0.015 0.034 -10000 0 -0.12 33 33
beta catenin/beta TrCP1 -0.005 0.081 -10000 0 -0.28 30 30
APH1B 0.014 0.032 -10000 0 -0.12 29 29
APH1A 0.023 0.009 -10000 0 -0.12 2 2
AXIN1 -0.001 0.046 0.19 4 -0.18 28 32
CtBP/CBP/TCF1/TLE1/AES 0.038 0.094 0.26 21 -0.27 9 30
PSEN1 0.022 0.008 -10000 0 -0.12 1 1
FOS -0.005 0.053 -10000 0 -0.12 95 95
JUN 0.014 0.033 -10000 0 -0.12 30 30
MAP3K7 0.024 0.017 -10000 0 -0.12 5 5
CTNNB1 -0.016 0.078 -10000 0 -0.28 29 29
MAPK3 0.022 0.014 -10000 0 -0.12 5 5
DKK2/LRP6/Kremen 2 0.032 0.043 -10000 0 -0.11 32 32
HNF1A 0.024 0.014 0.063 2 -0.12 4 6
CTBP1 0.024 0.018 0.065 1 -0.12 7 8
MYC -0.15 0.42 -10000 0 -1.2 73 73
NKD1 0.023 0.012 -10000 0 -0.12 4 4
FZD1 0.023 0.006 -10000 0 -0.12 1 1
NOTCH1 precursor/Deltex homolog 1 0.014 0.12 -10000 0 -0.48 29 29
apoptosis -0.004 0.071 -10000 0 -0.2 46 46
Delta 1/NOTCHprecursor 0.013 0.12 -10000 0 -0.48 29 29
DLL1 0.022 0.012 -10000 0 -0.12 4 4
PPARD 0.001 0.045 -10000 0 -10000 0 0
Gamma Secretase 0.033 0.067 -10000 0 -0.15 21 21
APC -0.004 0.057 0.19 4 -0.24 18 22
DVL1 0.017 0.066 -10000 0 -0.3 20 20
CSNK2A1 0.021 0.015 -10000 0 -0.12 6 6
MAP3K7IP1 0.026 0.008 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.027 0.047 -10000 0 -0.11 34 34
LRP6 0.014 0.034 -10000 0 -0.12 32 32
CSNK1A1 0.022 0.007 -10000 0 -0.12 1 1
NLK 0.029 0.042 -10000 0 -0.22 11 11
CCND1 -0.18 0.43 -10000 0 -1.2 82 82
WNT1 0.023 0.009 -10000 0 -0.12 2 2
Axin1/APC/beta catenin -0.001 0.086 0.2 3 -0.28 27 30
DKK2 0.022 0.011 -10000 0 -0.12 3 3
NOTCH1 precursor/DVL1 0.014 0.13 -10000 0 -0.44 34 34
GSK3B 0.023 0.011 -10000 0 -0.12 3 3
FRAT1 0.024 0.007 -10000 0 -0.12 1 1
NOTCH/Deltex homolog 1 0.016 0.12 -10000 0 -0.48 29 29
PPP2R5D 0.009 0.041 -10000 0 -0.25 7 7
MAPK1 0.021 0.016 -10000 0 -0.12 7 7
WNT1/LRP6/FZD1 0.042 0.045 -10000 0 -0.096 37 37
RBPJ 0.023 0.006 -10000 0 -0.12 1 1
CREBBP 0.017 0.018 -10000 0 -0.12 6 6
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.03 0.026 -9999 0 -0.094 21 21
FBXW11 0.023 0.003 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.022 0.04 -9999 0 -0.11 41 41
NF kappa B1 p50/RelA/I kappa B alpha 0.018 0.073 -9999 0 -0.21 28 28
NFKBIA 0.001 0.066 -9999 0 -0.22 23 23
MAPK14 0.023 0.007 -9999 0 -0.12 1 1
NF kappa B1 p105/p50 0.022 0.042 -9999 0 -0.12 40 40
ARRB2 0.014 0.035 -9999 0 -0.2 14 14
REL 0.022 0.014 -9999 0 -0.12 5 5
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.02 0.042 -9999 0 -0.097 56 56
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.022 0.04 -9999 0 -0.098 52 52
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
NF kappa B1 p50 dimer 0.012 0.044 -9999 0 -0.13 48 48
PIK3R1 0.015 0.031 -9999 0 -0.12 27 27
NFKB1 0.02 0.014 -9999 0 -0.071 10 10
RELA 0.023 0.009 -9999 0 -0.12 2 2
positive regulation of anti-apoptosis 0.013 0.051 -9999 0 -0.2 9 9
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.02 0.075 -9999 0 -0.2 35 35
SRC 0.023 0.009 -9999 0 -0.12 2 2
PI3K 0.007 0.065 -9999 0 -0.13 96 96
NF kappa B1 p50/RelA 0.013 0.052 -9999 0 -0.2 9 9
IKBKB 0.022 0.015 -9999 0 -0.12 6 6
beta TrCP1/SCF ubiquitin ligase complex 0.023 0.003 -9999 0 -10000 0 0
SYK 0.016 0.027 -9999 0 -0.12 20 20
I kappa B alpha/PIK3R1 0.008 0.069 -9999 0 -0.21 27 27
cell death 0.02 0.072 -9999 0 -0.19 35 35
NF kappa B1 p105/c-Rel 0.022 0.04 -9999 0 -0.11 41 41
LCK 0.022 0.015 -9999 0 -0.12 6 6
BCL3 0.02 0.023 -9999 0 -0.12 14 14
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.018 0.081 -9999 0 -0.12 191 191
AKT1 0.019 0.12 -9999 0 -0.31 34 34
PTK2B -0.005 0.081 -9999 0 -0.2 49 49
VEGFR2 homodimer/Frs2 0.025 0.058 -9999 0 -0.29 7 7
CAV1 0.012 0.039 -9999 0 -0.12 43 43
CALM1 0.022 0.014 -9999 0 -0.12 5 5
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.03 0.073 -9999 0 -0.24 17 17
endothelial cell proliferation 0.026 0.1 -9999 0 -0.29 27 27
mol:Ca2+ 0.027 0.068 -9999 0 -0.23 18 18
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.036 0.083 -9999 0 -0.22 28 28
RP11-342D11.1 0.019 0.062 -9999 0 -0.23 17 17
CDH5 0.022 0.014 -9999 0 -0.12 5 5
VEGFA homodimer 0.038 0.057 -9999 0 -0.1 69 69
SHC1 0.023 0.001 -9999 0 -10000 0 0
SHC2 0.023 0.009 -9999 0 -0.12 2 2
HRAS/GDP 0.03 0.061 -9999 0 -0.24 12 12
SH2D2A 0.023 0.009 -9999 0 -0.12 2 2
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.054 0.083 -9999 0 -0.31 10 10
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.036 0.07 -9999 0 -0.24 16 16
VEGFR1 homodimer 0.022 0.014 -9999 0 -0.12 5 5
SHC/GRB2/SOS1 0.055 0.078 -9999 0 -0.26 12 12
GRB10 0.029 0.073 -9999 0 -0.34 11 11
PTPN11 0.022 0.011 -9999 0 -0.12 3 3
GRB2 0.023 0.006 -9999 0 -0.12 1 1
PAK1 0.016 0.029 -9999 0 -0.12 23 23
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.04 0.087 -9999 0 -0.21 31 31
HRAS 0.023 0.006 -9999 0 -0.12 1 1
VEGF/Rho/ROCK1/Integrin Complex -0.019 0.12 -9999 0 -0.3 64 64
HIF1A 0.022 0.01 -9999 0 -0.12 2 2
FRS2 0.019 0.024 -9999 0 -0.12 15 15
oxygen and reactive oxygen species metabolic process 0.034 0.081 -9999 0 -0.22 28 28
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.023 0.009 -9999 0 -0.12 2 2
Nck/Pak 0.013 0.056 -9999 0 -0.12 81 81
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.021 0.08 -9999 0 -0.22 24 24
mol:GDP 0.041 0.071 -9999 0 -0.25 12 12
mol:NADP 0.037 0.071 -9999 0 -0.28 10 10
eNOS/Hsp90 0.045 0.071 -9999 0 -0.26 10 10
PIK3R1 0.015 0.031 -9999 0 -0.12 27 27
mol:IP3 0.027 0.068 -9999 0 -0.24 18 18
HIF1A/ARNT 0.024 0.042 -9999 0 -0.14 34 34
SHB 0.023 0.009 -9999 0 -0.12 2 2
VEGFA 0.022 0.021 -9999 0 -0.099 14 14
VEGFC 0.018 0.028 -9999 0 -0.12 21 21
FAK1/Vinculin -0.007 0.13 -9999 0 -0.34 43 43
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.023 0.006 -9999 0 -0.12 1 1
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.007 0.095 -9999 0 -0.21 47 47
PTPN6 0.023 0.009 -9999 0 -0.12 2 2
EPAS1 0.025 0.04 -9999 0 -0.13 27 27
mol:L-citrulline 0.037 0.071 -9999 0 -0.28 10 10
ITGAV 0.013 0.032 -9999 0 -0.12 28 28
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.042 0.074 -9999 0 -0.21 20 20
VEGFR2 homodimer/VEGFA homodimer 0.047 0.079 -9999 0 -0.25 17 17
VEGFR2/3 heterodimer 0.028 0.057 -9999 0 -0.28 7 7
VEGFB 0.015 0.033 -9999 0 -0.12 30 30
MAPK11 0.022 0.069 -9999 0 -0.25 17 17
VEGFR2 homodimer 0.028 0.052 -9999 0 -0.34 7 7
FLT1 0.022 0.014 -9999 0 -0.12 5 5
NEDD4 0.023 0.022 -9999 0 -0.1 15 15
MAPK3 0.014 0.064 -9999 0 -0.23 17 17
MAPK1 0.013 0.065 -9999 0 -0.24 17 17
VEGFA145/NRP2 0.001 0.072 -9999 0 -0.13 123 123
VEGFR1/2 heterodimer 0.027 0.059 -9999 0 -0.27 9 9
KDR 0.028 0.052 -9999 0 -0.34 7 7
VEGFA165/NRP1/VEGFR2 homodimer 0.032 0.084 -9999 0 -0.21 30 30
SRC 0.023 0.009 -9999 0 -0.12 2 2
platelet activating factor biosynthetic process 0.014 0.066 -9999 0 -0.23 18 18
PI3K 0.034 0.099 -9999 0 -0.29 24 24
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.027 0.076 -9999 0 -0.22 21 21
FES 0.029 0.066 -9999 0 -0.23 17 17
GAB1 0.026 0.095 -9999 0 -0.3 25 25
VEGFR2 homodimer/VEGFA homodimer/Src 0.036 0.07 -9999 0 -0.24 16 16
CTNNB1 0.022 0.008 -9999 0 -0.12 1 1
SOS1 0.017 0.027 -9999 0 -0.12 20 20
ARNT 0.022 0.012 -9999 0 -0.12 4 4
eNOS/Caveolin-1 0.039 0.075 -9999 0 -0.27 12 12
VEGFR2 homodimer/VEGFA homodimer/Yes 0.028 0.076 -9999 0 -0.22 22 22
PI3K/GAB1 0.027 0.12 -9999 0 -0.33 32 32
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.035 0.083 -9999 0 -0.19 30 30
PRKACA 0.021 0.017 -9999 0 -0.12 8 8
VEGFR2/3 heterodimer/VEGFC homodimer 0.036 0.06 -9999 0 -0.28 8 8
HSP90AA1 0.023 0.003 -9999 0 -10000 0 0
CDC42 0.029 0.066 -9999 0 -0.23 17 17
actin cytoskeleton reorganization 0.035 0.07 -9999 0 -0.23 16 16
PTK2 -0.016 0.13 -9999 0 -0.34 48 48
EDG1 0.03 0.068 -9999 0 -0.28 11 11
mol:DAG 0.027 0.068 -9999 0 -0.24 18 18
CaM/Ca2+ 0.033 0.068 -9999 0 -0.2 22 22
MAP2K3 0.023 0.065 -9999 0 -0.21 21 21
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.052 0.084 -9999 0 -0.35 11 11
PLCG1 0.027 0.069 -9999 0 -0.24 18 18
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.048 0.069 -9999 0 -0.22 16 16
IQGAP1 0.02 0.017 -9999 0 -0.12 7 7
YES1 0.02 0.018 -9999 0 -0.12 8 8
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.031 0.075 -9999 0 -0.24 20 20
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.035 0.071 -9999 0 -0.24 16 16
cell migration -0.002 0.14 -9999 0 -0.34 55 55
mol:PI-3-4-5-P3 0.034 0.095 -9999 0 -0.28 24 24
FYN 0.011 0.037 -9999 0 -0.12 40 40
VEGFB/NRP1 0.026 0.064 -9999 0 -0.21 19 19
mol:NO 0.037 0.071 -9999 0 -0.28 10 10
PXN 0.022 0.014 -9999 0 -0.12 5 5
HRAS/GTP -0.013 0.043 -9999 0 -0.24 12 12
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.048 0.078 -9999 0 -0.35 11 11
VHL 0.021 0.016 -9999 0 -0.12 7 7
ITGB3 0.004 0.047 -9999 0 -0.12 68 68
NOS3 0.037 0.076 -9999 0 -0.31 10 10
VEGFR2 homodimer/VEGFA homodimer/Sck 0.036 0.07 -9999 0 -0.24 16 16
RAC1 0.023 0.002 -9999 0 -10000 0 0
PRKCA 0.02 0.063 -9999 0 -0.22 20 20
PRKCB 0.02 0.062 -9999 0 -0.22 18 18
VCL 0.021 0.013 -9999 0 -0.12 4 4
VEGFA165/NRP1 0.033 0.065 -9999 0 -0.23 17 17
VEGFR1/2 heterodimer/VEGFA homodimer 0.034 0.073 -9999 0 -0.24 18 18
VEGFA165/NRP2 0.001 0.072 -9999 0 -0.13 123 123
MAPKKK cascade 0.048 0.074 -9999 0 -0.27 14 14
NRP2 0.011 0.036 -9999 0 -0.12 38 38
VEGFC homodimer 0.018 0.027 -9999 0 -0.12 21 21
NCK1 0.02 0.019 -9999 0 -0.12 9 9
ROCK1 0.022 0.009 -9999 0 -0.12 2 2
FAK1/Paxillin -0.005 0.13 -9999 0 -0.32 49 49
MAP3K13 0.024 0.069 -9999 0 -0.23 19 19
PDPK1 0.029 0.085 -9999 0 -0.25 24 24
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.008 0.054 -9999 0 -0.15 53 53
TRAF2/ASK1 0.022 0.033 -9999 0 -0.091 42 42
ATM 0.018 0.022 -9999 0 -0.12 13 13
MAP2K3 -0.002 0.12 -9999 0 -0.32 65 65
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.012 0.12 -9999 0 -0.26 74 74
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G 0.015 0.033 -9999 0 -0.12 30 30
TXN -0.003 0.051 -9999 0 -0.21 33 33
CALM1 0.022 0.014 -9999 0 -0.12 5 5
GADD45A 0.014 0.032 -9999 0 -0.12 29 29
GADD45B 0.016 0.029 -9999 0 -0.12 24 24
MAP3K1 0.021 0.015 -9999 0 -0.12 6 6
MAP3K6 0.022 0.012 -9999 0 -0.12 4 4
MAP3K7 0.021 0.014 -9999 0 -0.12 5 5
MAP3K4 0.023 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 0.023 0.041 -9999 0 -0.11 47 47
TAK1/TAB family -0.002 0.072 -9999 0 -0.32 25 25
RAC1/OSM/MEKK3 0.043 0.015 -9999 0 -0.097 6 6
TRAF2 0.023 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.016 0.1 -9999 0 -0.25 64 64
TRAF6 0.004 0.058 -9999 0 -0.21 36 36
RAC1 0.023 0.002 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B 0.023 0.009 -9999 0 -0.12 2 2
CCM2 0.023 0.001 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.029 0.019 -9999 0 -0.093 13 13
MAPK11 0.023 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.033 0.037 -9999 0 -0.1 32 32
OSM/MEKK3 0.034 0.007 -9999 0 -0.14 1 1
TAOK1 -0.001 0.067 -9999 0 -0.22 43 43
TAOK2 0.003 0.056 -9999 0 -0.2 38 38
TAOK3 -0.003 0.067 -9999 0 -0.21 50 50
MAP3K7IP1 0.023 0 -9999 0 -10000 0 0
MAPK14 0.023 0.007 -9999 0 -0.12 1 1
MAP3K7IP2 0.02 0.016 -9999 0 -0.12 6 6
MAP3K5 0.018 0.025 -9999 0 -0.12 17 17
MAP3K10 0.022 0.015 -9999 0 -0.12 6 6
MAP3K3 0.023 0 -9999 0 -10000 0 0
TRX/ASK1 0.009 0.051 -9999 0 -0.14 48 48
GADD45/MTK1/MTK1 0.025 0.057 -9999 0 -0.095 79 79
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.02 0.011 -10000 0 -0.12 2 2
HSPA8 0.023 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.061 0.084 0.2 44 -0.14 29 73
AKT1 0.023 0.021 -10000 0 -0.1 15 15
GSC 0.024 0.078 -10000 0 -1.2 2 2
NKX2-5 0.022 0.015 -10000 0 -0.12 3 3
muscle cell differentiation -0.039 0.08 0.28 19 -10000 0 19
SMAD2-3/SMAD4/SP1 0.048 0.094 -10000 0 -0.23 19 19
SMAD4 0.024 0.039 -10000 0 -0.13 14 14
CBFB 0.022 0.009 -10000 0 -0.12 2 2
SAP18 0.023 0.003 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.026 0.052 -10000 0 -0.14 37 37
SMAD3/SMAD4/VDR 0.047 0.073 -10000 0 -0.16 30 30
MYC 0.013 0.029 0.098 5 -0.13 20 25
CDKN2B 0.03 0.12 -10000 0 -1.2 5 5
AP1 0.005 0.1 -10000 0 -0.22 67 67
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.006 0.12 -10000 0 -0.31 49 49
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.039 0.055 -10000 0 -0.28 10 10
SP3 0.02 0.015 -10000 0 -0.041 10 10
CREB1 0.023 0.003 -10000 0 -10000 0 0
FOXH1 0.024 0.018 -10000 0 -0.11 6 6
SMAD3/SMAD4/GR 0.036 0.07 0.18 1 -0.15 35 36
GATA3 0.026 0.021 -10000 0 -0.12 11 11
SKI/SIN3/HDAC complex/NCoR1 0.02 0.078 -10000 0 -0.25 27 27
MEF2C/TIF2 0.042 0.064 -10000 0 -0.2 24 24
endothelial cell migration 0.014 0.11 1.2 3 -10000 0 3
MAX 0.023 0.006 0.074 3 -10000 0 3
RBBP7 0.022 0.012 -10000 0 -0.12 3 3
RBBP4 0.021 0.014 -10000 0 -0.12 5 5
RUNX2 0.019 0.023 -10000 0 -0.12 15 15
RUNX3 0.018 0.028 -10000 0 -0.12 22 22
RUNX1 0.019 0.022 -10000 0 -0.12 13 13
CTBP1 0.021 0.016 -10000 0 -0.12 7 7
NR3C1 0.021 0.016 0.074 3 -0.13 5 8
VDR 0.019 0.022 -10000 0 -0.12 13 13
CDKN1A 0.017 0.065 -10000 0 -0.53 1 1
KAT2B -0.001 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.055 0.053 -10000 0 -0.21 9 9
DCP1A 0.023 0.001 -10000 0 -10000 0 0
SKI 0.023 0.011 -10000 0 -0.12 3 3
SERPINE1 -0.014 0.11 -10000 0 -1.2 3 3
SMAD3/SMAD4/ATF2 0.041 0.064 -10000 0 -0.19 18 18
SMAD3/SMAD4/ATF3 0.035 0.062 -10000 0 -0.15 18 18
SAP30 0.023 0.001 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.027 0.051 0.14 2 -0.14 38 40
JUN -0.008 0.098 -10000 0 -0.22 66 66
SMAD3/SMAD4/IRF7 0.051 0.058 -10000 0 -0.18 12 12
TFE3 0.018 0.032 -10000 0 -0.084 41 41
COL1A2 -0.13 0.26 -10000 0 -0.64 112 112
mesenchymal cell differentiation -0.041 0.057 0.15 15 -10000 0 15
DLX1 0.021 0.017 -10000 0 -0.12 8 8
TCF3 0.022 0.014 -10000 0 -0.12 5 5
FOS -0.004 0.055 -10000 0 -0.12 101 101
SMAD3/SMAD4/Max 0.046 0.056 0.18 1 -0.16 9 10
Cbp/p300/SNIP1 0.033 0.047 -10000 0 -0.13 36 36
ZBTB17 0.022 0.006 0.081 5 -10000 0 5
LAMC1 0.021 0.083 -10000 0 -0.26 36 36
TGIF2/HDAC complex/SMAD3/SMAD4 0.04 0.061 -10000 0 -0.16 20 20
IRF7 0.024 0.017 -10000 0 -0.12 7 7
ESR1 0.033 0.037 0.098 100 -0.13 10 110
HNF4A 0.023 0.009 -10000 0 -0.12 2 2
MEF2C 0.034 0.061 -10000 0 -0.22 23 23
SMAD2-3/SMAD4 0.05 0.063 -10000 0 -0.19 10 10
Cbp/p300/Src-1 0.029 0.053 -10000 0 -0.14 46 46
IGHV3OR16-13 0.005 0.075 -10000 0 -0.49 12 12
TGIF2/HDAC complex 0.021 0.013 -10000 0 -0.12 4 4
CREBBP 0.02 0.016 -10000 0 -0.13 6 6
SKIL 0.011 0.035 -10000 0 -0.12 35 35
HDAC1 0.02 0.02 -10000 0 -0.12 10 10
HDAC2 0.02 0.021 -10000 0 -0.12 12 12
SNIP1 0.023 0.011 -10000 0 -0.12 3 3
GCN5L2 0.021 0.013 -10000 0 -0.12 4 4
SMAD3/SMAD4/TFE3 0.047 0.072 -10000 0 -0.16 37 37
MSG1/HSC70 0.027 0.032 -10000 0 -0.082 42 42
SMAD2 0.027 0.015 -10000 0 -0.073 5 5
SMAD3 0.022 0.036 -10000 0 -0.1 21 21
SMAD3/E2F4-5/DP1/p107/SMAD4 0.024 0.067 -10000 0 -0.18 32 32
SMAD2/SMAD2/SMAD4 -0.001 0.043 0.12 2 -0.2 16 18
NCOR1 0.022 0.009 -10000 0 -0.12 2 2
NCOA2 0.021 0.013 -10000 0 -0.12 4 4
NCOA1 0.022 0.009 -10000 0 -0.12 2 2
MYOD/E2A 0.032 0.016 -10000 0 -0.077 12 12
SMAD2-3/SMAD4/SP1/MIZ-1 0.061 0.091 -10000 0 -0.23 15 15
IFNB1 0.035 0.044 -10000 0 -0.18 7 7
SMAD3/SMAD4/MEF2C 0.059 0.076 -10000 0 -0.23 19 19
CITED1 0.014 0.035 -10000 0 -0.12 35 35
SMAD2-3/SMAD4/ARC105 0.062 0.061 -10000 0 -0.19 8 8
RBL1 0.019 0.022 -10000 0 -0.12 13 13
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.042 0.067 -10000 0 -0.4 8 8
RUNX1-3/PEBPB2 0.035 0.04 -10000 0 -0.12 27 27
SMAD7 -0.003 0.14 -10000 0 -0.43 26 26
MYC/MIZ-1 0.003 0.063 0.17 5 -0.15 73 78
SMAD3/SMAD4 -0.018 0.098 0.29 2 -0.3 37 39
IL10 0.039 0.044 -10000 0 -0.18 7 7
PIASy/HDAC complex 0.024 0.004 -10000 0 -10000 0 0
PIAS3 0.019 0.022 -10000 0 -0.12 13 13
CDK2 0.017 0.023 -10000 0 -0.12 14 14
IL5 0.039 0.044 -10000 0 -0.2 6 6
CDK4 0.018 0.019 -10000 0 -0.12 9 9
PIAS4 0.024 0.004 -10000 0 -10000 0 0
ATF3 0.011 0.04 -10000 0 -0.12 47 47
SMAD3/SMAD4/SP1 0.027 0.09 -10000 0 -0.21 30 30
FOXG1 0.02 0.019 -10000 0 -0.12 10 10
FOXO3 0.023 0.02 -10000 0 -0.07 23 23
FOXO1 0.025 0.017 -10000 0 -0.071 17 17
FOXO4 0.025 0.016 -10000 0 -0.072 15 15
heart looping 0.034 0.06 -10000 0 -0.22 23 23
CEBPB 0.017 0.033 -10000 0 -0.12 30 30
SMAD3/SMAD4/DLX1 0.044 0.055 -10000 0 -0.16 13 13
MYOD1 0.022 0.015 -10000 0 -0.12 6 6
SMAD3/SMAD4/HNF4 0.045 0.053 -10000 0 -0.16 10 10
SMAD3/SMAD4/GATA3 0.059 0.059 -10000 0 -0.2 7 7
SnoN/SIN3/HDAC complex/NCoR1 0.011 0.035 -10000 0 -0.12 35 35
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.058 0.062 -10000 0 -0.14 14 14
SMAD3/SMAD4/SP1-3 0.042 0.097 -10000 0 -0.21 34 34
MED15 0.022 0.012 -10000 0 -0.12 4 4
SP1 -0.004 0.053 -10000 0 -0.093 112 112
SIN3B 0.022 0.015 -10000 0 -0.12 6 6
SIN3A 0.022 0.014 -10000 0 -0.12 5 5
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.071 0.061 -10000 0 -0.18 14 14
ITGB5 0.007 0.094 -10000 0 -0.28 39 39
TGIF/SIN3/HDAC complex/CtBP 0.022 0.078 -10000 0 -0.27 22 22
SMAD3/SMAD4/AR 0.016 0.077 -10000 0 -0.15 49 49
AR 0.009 0.038 -10000 0 -0.12 43 43
negative regulation of cell growth 0.026 0.073 -10000 0 -0.22 29 29
SMAD3/SMAD4/MYOD 0.044 0.055 -10000 0 -0.17 11 11
E2F5 0.02 0.02 -10000 0 -0.12 11 11
E2F4 0.022 0.012 -10000 0 -0.12 4 4
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.069 0.058 -10000 0 -0.18 9 9
SMAD2-3/SMAD4/FOXO1-3a-4 0.041 0.061 -10000 0 -0.31 10 10
TFDP1 0.019 0.023 -10000 0 -0.12 14 14
SMAD3/SMAD4/AP1 0.012 0.11 -10000 0 -0.25 52 52
SMAD3/SMAD4/RUNX2 0.041 0.057 -10000 0 -0.15 15 15
TGIF2 0.021 0.013 -10000 0 -0.12 4 4
TGIF1 0.023 0 -10000 0 -10000 0 0
ATF2 0.022 0.004 -10000 0 -10000 0 0
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0.023 0.009 -10000 0 -0.12 2 2
MKNK1 0.023 0.006 -10000 0 -0.12 1 1
mol:PIP3 -0.005 0.043 -10000 0 -0.14 31 31
FRAP1 0.01 0.072 -10000 0 -0.42 13 13
AKT1 0.006 0.057 0.18 19 -0.14 34 53
INSR 0.021 0.017 -10000 0 -0.12 8 8
Insulin Receptor/Insulin 0.028 0.019 -10000 0 -0.077 17 17
mol:GTP 0.022 0.057 0.18 18 -0.13 26 44
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.015 0.045 -10000 0 -0.17 32 32
TSC2 0.021 0.017 -10000 0 -0.12 8 8
RHEB/GDP 0.008 0.047 -10000 0 -0.12 35 35
TSC1 0.023 0.006 -10000 0 -0.12 1 1
Insulin Receptor/IRS1 0.02 0.029 -10000 0 -0.22 6 6
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.01 0.061 -10000 0 -0.2 31 31
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.022 0.004 -10000 0 -10000 0 0
RPS6KB1 0.006 0.085 0.16 14 -0.3 29 43
MAP3K5 -0.004 0.058 -10000 0 -0.27 25 25
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
apoptosis -0.004 0.058 -10000 0 -0.27 25 25
mol:LY294002 0 0 0 11 -0.001 6 17
EIF4B 0.008 0.079 0.16 14 -0.26 31 45
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.021 0.078 0.16 12 -0.24 31 43
eIF4E/eIF4G1/eIF4A1 -0.007 0.042 -10000 0 -0.25 14 14
KIAA1303 0.023 0.009 -10000 0 -0.12 2 2
PI3K 0.016 0.053 -10000 0 -0.11 66 66
mTOR/RHEB/GTP/Raptor/GBL 0.026 0.054 0.16 16 -0.15 26 42
FKBP1A 0.022 0.012 -10000 0 -0.12 4 4
RHEB/GTP 0.019 0.053 0.14 3 -0.13 33 36
mol:Amino Acids 0 0 0 11 -0.001 6 17
FKBP12/Rapamycin 0.016 0.014 -10000 0 -0.11 7 7
PDPK1 0.005 0.052 0.18 17 -0.15 20 37
EIF4E 0.023 0.001 -10000 0 -10000 0 0
ASK1/PP5C 0.005 0.14 -10000 0 -0.49 38 38
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.032 0.061 -10000 0 -0.3 18 18
TSC1/TSC2 0.025 0.061 0.19 18 -0.14 26 44
tumor necrosis factor receptor activity 0 0 0.001 6 0 11 17
RPS6 0.023 0.002 -10000 0 -10000 0 0
PPP5C 0.022 0.014 -10000 0 -0.12 5 5
EIF4G1 0.023 0.004 -10000 0 -10000 0 0
IRS1 0.006 0.028 -10000 0 -0.27 5 5
INS 0.022 0.011 -10000 0 -0.12 3 3
PTEN 0.022 0.008 -10000 0 -0.12 1 1
PDK2 0.004 0.054 0.18 17 -0.16 24 41
EIF4EBP1 0.011 0.1 -10000 0 -1.1 5 5
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
PPP2R5D 0.014 0.066 -10000 0 -0.37 13 13
peptide biosynthetic process 0.022 0.018 -10000 0 -0.11 6 6
RHEB 0.019 0.022 -10000 0 -0.12 13 13
EIF4A1 0.023 0.007 -10000 0 -0.12 1 1
mol:Rapamycin 0 0.001 0.003 20 -0.002 17 37
EEF2 0.023 0.018 -10000 0 -0.12 6 6
eIF4E/4E-BP1 0.023 0.098 -10000 0 -1 5 5
Ceramide signaling pathway

Figure S95.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S95.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.02 0.016 -10000 0 -0.076 15 15
MAP4K4 0.003 0.068 -10000 0 -0.22 21 21
BAG4 0.022 0.012 -10000 0 -0.12 4 4
PKC zeta/ceramide 0.013 0.009 0.071 7 -10000 0 7
NFKBIA 0.016 0.028 -10000 0 -0.12 21 21
BIRC3 -0.005 0.053 -10000 0 -0.12 94 94
BAX 0.01 0.005 -10000 0 -10000 0 0
RIPK1 0.022 0.011 -10000 0 -0.12 3 3
AKT1 0.007 0.021 -10000 0 -0.13 12 12
BAD 0.001 0.01 0.063 7 -0.055 3 10
SMPD1 0.009 0.036 -10000 0 -0.12 25 25
RB1 -0.012 0.033 0.064 4 -0.092 78 82
FADD/Caspase 8 0.003 0.095 -10000 0 -0.24 48 48
MAP2K4 0 0.023 0.069 5 -0.092 28 33
NSMAF 0.021 0.014 -10000 0 -0.12 5 5
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.004 0.015 0.069 5 -0.097 7 12
EGF 0.02 0.021 -10000 0 -0.12 12 12
mol:ceramide -0.004 0.01 0.063 7 -10000 0 7
MADD 0.023 0.006 -10000 0 -0.12 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.018 0.022 -10000 0 -0.085 20 20
ASAH1 0.021 0.017 -10000 0 -0.12 7 7
negative regulation of cell cycle -0.012 0.033 0.063 4 -0.091 78 82
cell proliferation 0.017 0.041 -10000 0 -0.12 14 14
BID 0.009 0.079 -10000 0 -0.36 11 11
MAP3K1 -0.003 0.021 0.063 7 -0.09 23 30
EIF2A -0.007 0.043 0.071 1 -0.11 59 60
TRADD 0.023 0.006 -10000 0 -0.12 1 1
CRADD 0.023 0.009 -10000 0 -0.12 2 2
MAPK3 0.009 0.021 -10000 0 -0.1 12 12
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.008 0.024 0.074 2 -0.11 15 17
Cathepsin D/ceramide 0.011 0.013 0.07 6 -0.056 9 15
FADD 0.004 0.068 -10000 0 -0.22 20 20
KSR1 0.001 0.01 0.068 5 -0.055 3 8
MAPK8 0.005 0.039 -10000 0 -0.19 17 17
PRKRA -0.002 0.02 0.068 5 -0.099 17 22
PDGFA 0.02 0.022 -10000 0 -0.12 13 13
TRAF2 0.023 0 -10000 0 -10000 0 0
IGF1 0.007 0.045 -10000 0 -0.12 60 60
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.004 0.01 0.063 7 -10000 0 7
CTSD 0.02 0.02 -10000 0 -0.12 11 11
regulation of nitric oxide biosynthetic process 0.021 0.046 -10000 0 -0.13 47 47
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.019 0.043 -10000 0 -0.13 14 14
PRKCD 0.02 0.018 -10000 0 -0.12 8 8
PRKCZ 0.023 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.018 0.022 -10000 0 -0.085 20 20
RelA/NF kappa B1 0.021 0.047 -10000 0 -0.13 47 47
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.023 0.009 -10000 0 -0.12 2 2
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.001 0.073 -10000 0 -0.24 19 19
TNFR1A/BAG4/TNF-alpha 0.038 0.034 -10000 0 -0.11 20 20
mol:Sphingosine-1-phosphate 0.02 0.016 -10000 0 -0.076 15 15
MAP2K1 0.007 0.016 0.07 5 -0.094 9 14
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.023 0.009 -10000 0 -0.12 2 2
CYCS 0.004 0.024 0.13 2 -0.12 14 16
TNFRSF1A 0.021 0.016 -10000 0 -0.12 7 7
NFKB1 0.021 0.013 -10000 0 -0.12 4 4
TNFR1A/BAG4 0.027 0.034 -10000 0 -0.11 29 29
EIF2AK2 -0.008 0.036 0.069 5 -0.1 53 58
TNF-alpha/TNFR1A/FAN 0.033 0.047 -10000 0 -0.13 34 34
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.003 0.12 -10000 0 -0.4 39 39
MAP2K2 0.005 0.019 0.07 4 -0.094 11 15
SMPD3 0.011 0.041 -10000 0 -0.16 15 15
TNF 0.02 0.02 -10000 0 -0.12 11 11
PKC zeta/PAR4 0.034 0.012 -10000 0 -0.11 4 4
mol:PHOSPHOCHOLINE -0.008 0.016 0.092 5 -10000 0 5
NF kappa B1/RelA/I kappa B alpha 0.044 0.059 -10000 0 -0.096 72 72
AIFM1 -0.005 0.036 0.13 1 -0.12 44 45
BCL2 0.016 0.031 -10000 0 -0.12 27 27
Signaling events mediated by HDAC Class III

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
EP300 0.022 0.01 -10000 0 -0.12 2 2
HDAC4 0.023 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.008 0.002 -10000 0 -10000 0 0
CDKN1A 0.034 0.04 -10000 0 -10000 0 0
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.023 0 -10000 0 -10000 0 0
FOXO3 0.003 0.05 0.26 19 -10000 0 19
FOXO1 0.023 0.009 -10000 0 -0.12 2 2
FOXO4 0.009 0.064 -10000 0 -0.22 34 34
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.022 0.004 -10000 0 -10000 0 0
TAT 0.023 0.009 -10000 0 -0.12 2 2
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.011 0.009 -10000 0 -0.077 6 6
PPARGC1A 0.014 0.035 -10000 0 -0.12 35 35
FHL2 0.02 0.02 -10000 0 -0.12 11 11
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.022 0.045 -10000 0 -0.18 25 25
HIST2H4A 0.008 0.002 -10000 0 -10000 0 0
SIRT1/FOXO3a 0.014 0.037 0.2 19 -0.089 5 24
SIRT1 0.019 0.004 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.042 0.021 -10000 0 -0.11 10 10
SIRT1/Histone H1b 0.005 0.071 -10000 0 -0.17 69 69
apoptosis -0.036 0.039 0.14 25 -10000 0 25
SIRT1/PGC1A 0.021 0.029 -10000 0 -0.074 44 44
p53/SIRT1 -0.035 0.081 -10000 0 -0.15 173 173
SIRT1/FOXO4 0.017 0.058 -10000 0 -0.19 34 34
FOXO1/FHL2/SIRT1 0.037 0.026 -10000 0 -0.1 14 14
HIST1H1E -0.005 0.079 -10000 0 -0.2 69 69
SIRT1/p300 0.022 0.04 -10000 0 -0.14 32 32
muscle cell differentiation -0.014 0.02 0.12 11 -10000 0 11
TP53 0.007 0.029 -10000 0 -0.13 22 22
KU70/SIRT1/BAX 0.036 0.039 -10000 0 -0.14 25 25
CREBBP 0.021 0.015 -10000 0 -0.12 6 6
MEF2D 0.023 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.028 0.024 -10000 0 -0.14 10 10
ACSS2 0.018 0.01 -10000 0 -0.074 6 6
SIRT1/PCAF/MYOD 0.014 0.02 -10000 0 -0.12 11 11
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.007 0.066 0.21 23 -10000 0 23
GNAI2 0.022 0.011 -10000 0 -0.12 3 3
S1P/S1P5/G12 0.016 0.006 -10000 0 -0.12 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.01 0.042 -10000 0 -0.12 51 51
RhoA/GTP 0.007 0.067 -10000 0 -0.21 23 23
negative regulation of cAMP metabolic process -0.003 0.068 -10000 0 -0.15 86 86
GNAZ 0.022 0.011 -10000 0 -0.12 3 3
GNAI3 0.021 0.008 -10000 0 -0.12 1 1
GNA12 0.023 0.001 -10000 0 -10000 0 0
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.003 0.069 -10000 0 -0.15 86 86
RhoA/GDP 0.016 0.016 -10000 0 -0.14 6 6
RHOA 0.023 0.006 -10000 0 -0.12 1 1
GNAI1 0.012 0.035 -10000 0 -0.12 35 35
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.025 0.07 -9999 0 -0.26 11 11
PDGFB-D/PDGFRB/SLAP 0.02 0.039 -9999 0 -0.088 45 45
PDGFB-D/PDGFRB/APS/CBL 0.022 0.028 -9999 0 -0.12 4 4
AKT1 0.008 0.053 -9999 0 -0.12 45 45
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.019 0.068 -9999 0 -0.28 11 11
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
FGR 0.014 0.04 -9999 0 -0.18 6 6
mol:Ca2+ 0.011 0.065 -9999 0 -0.3 11 11
MYC -0.059 0.26 -9999 0 -0.71 74 74
SHC1 0.023 0.001 -9999 0 -10000 0 0
HRAS/GDP 0.026 0.038 -9999 0 -0.1 15 15
LRP1/PDGFRB/PDGFB 0.024 0.053 -9999 0 -0.11 57 57
GRB10 0.022 0.014 -9999 0 -0.12 5 5
PTPN11 0.022 0.011 -9999 0 -0.12 3 3
GO:0007205 0.011 0.066 -9999 0 -0.3 11 11
PTEN 0.022 0.008 -9999 0 -0.12 1 1
GRB2 0.023 0.006 -9999 0 -0.12 1 1
GRB7 0.018 0.026 -9999 0 -0.12 18 18
PDGFB-D/PDGFRB/SHP2 0.017 0.045 -9999 0 -0.14 22 22
PDGFB-D/PDGFRB/GRB10 0.021 0.039 -9999 0 -0.1 27 27
cell cycle arrest 0.02 0.039 -9999 0 -0.088 45 45
HRAS 0.023 0.006 -9999 0 -0.12 1 1
HIF1A 0.007 0.054 -9999 0 -0.13 52 52
GAB1 0.006 0.08 -9999 0 -0.29 14 14
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.006 0.078 -9999 0 -0.24 22 22
PDGFB-D/PDGFRB 0.032 0.039 -9999 0 -0.13 10 10
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.016 0.047 -9999 0 -0.15 25 25
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.018 0.086 -9999 0 -0.22 32 32
positive regulation of MAPKKK cascade 0.017 0.045 -9999 0 -0.14 22 22
PIK3R1 0.015 0.031 -9999 0 -0.12 27 27
mol:IP3 0.011 0.066 -9999 0 -0.3 11 11
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.023 0.009 -9999 0 -0.12 2 2
PDGFB-D/PDGFRB/GRB7 0.017 0.046 -9999 0 -0.11 37 37
SHB 0.023 0.009 -9999 0 -0.12 2 2
BLK 0.014 0.039 -9999 0 -0.2 4 4
PTPN2 0.022 0.008 -9999 0 -0.13 1 1
PDGFB-D/PDGFRB/SNX15 0.024 0.033 -9999 0 -0.1 8 8
BCAR1 0.022 0.011 -9999 0 -0.12 3 3
VAV2 -0.004 0.11 -9999 0 -0.26 55 55
CBL 0.023 0.006 -9999 0 -0.12 1 1
PDGFB-D/PDGFRB/DEP1 0.017 0.046 -9999 0 -0.09 81 81
LCK 0.014 0.039 -9999 0 -10000 0 0
PDGFRB 0.01 0.043 -9999 0 -0.12 52 52
ACP1 0.021 0.014 -9999 0 -0.12 5 5
HCK -0.001 0.091 -9999 0 -0.42 19 19
ABL1 0.007 0.068 -9999 0 -0.24 14 14
PDGFB-D/PDGFRB/CBL 0.007 0.082 -9999 0 -0.33 11 11
PTPN1 0.022 0.007 -9999 0 -0.13 1 1
SNX15 0.023 0 -9999 0 -10000 0 0
STAT3 0.022 0.011 -9999 0 -0.12 3 3
STAT1 0.014 0.031 -9999 0 -0.12 26 26
cell proliferation -0.049 0.23 -9999 0 -0.62 75 75
SLA 0.02 0.019 -9999 0 -0.12 10 10
actin cytoskeleton reorganization 0.031 0.041 -9999 0 -0.15 7 7
SRC 0.015 0.038 -9999 0 -0.2 1 1
PI3K -0.021 0.04 -9999 0 -0.14 43 43
PDGFB-D/PDGFRB/GRB7/SHC 0.03 0.042 -9999 0 -0.13 17 17
SH2B2 0 0 -9999 0 -10000 0 0
PLCgamma1/SPHK1 0.019 0.07 -9999 0 -0.28 11 11
LYN -0.021 0.13 -9999 0 -0.42 48 48
LRP1 0.014 0.032 -9999 0 -0.12 29 29
SOS1 0.017 0.027 -9999 0 -0.12 20 20
STAT5B 0.023 0.006 -9999 0 -0.12 1 1
STAT5A 0.022 0.013 -9999 0 -0.12 4 4
NCK1-2/p130 Cas 0.046 0.052 -9999 0 -0.12 15 15
SPHK1 0.022 0.015 -9999 0 -0.12 6 6
EDG1 0.022 0.016 -9999 0 -0.12 7 7
mol:DAG 0.011 0.066 -9999 0 -0.3 11 11
PLCG1 0.011 0.068 -9999 0 -0.31 11 11
NHERF/PDGFRB 0.024 0.049 -9999 0 -0.12 28 28
YES1 -0.011 0.12 -9999 0 -0.46 31 31
cell migration 0.024 0.049 -9999 0 -0.12 28 28
SHC/Grb2/SOS1 0.044 0.051 -9999 0 -0.16 8 8
SLC9A3R2 0.017 0.028 -9999 0 -0.12 22 22
SLC9A3R1 0.016 0.031 -9999 0 -0.12 26 26
NHERF1-2/PDGFRB/PTEN 0.031 0.056 -9999 0 -0.1 50 50
FYN -0.021 0.12 -9999 0 -0.41 41 41
DOK1 0.021 0.029 -9999 0 -0.11 10 10
HRAS/GTP 0.017 0.008 -9999 0 -0.11 2 2
PDGFB 0.022 0.011 -9999 0 -0.12 3 3
RAC1 -0.022 0.16 -9999 0 -0.4 81 81
PRKCD 0.019 0.031 -9999 0 -0.12 11 11
FER 0.02 0.03 -9999 0 -0.11 11 11
MAPKKK cascade -0.007 0.028 -9999 0 -0.15 8 8
RASA1 0.02 0.03 -9999 0 -0.12 10 10
NCK1 0.02 0.019 -9999 0 -0.12 9 9
NCK2 0.023 0.006 -9999 0 -0.12 1 1
p62DOK/Csk 0.032 0.033 -9999 0 -0.093 16 16
PDGFB-D/PDGFRB/SHB 0.023 0.033 -9999 0 -0.074 57 57
chemotaxis 0.007 0.067 -9999 0 -0.24 14 14
STAT1-3-5/STAT1-3-5 0.021 0.058 -9999 0 -0.14 22 22
Bovine Papilomavirus E5/PDGFRB 0.007 0.03 -9999 0 -0.081 55 55
PTPRJ 0.02 0.019 -9999 0 -0.12 9 9
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.032 0.075 -10000 0 -0.2 35 35
Ran/GTP/Exportin 1/HDAC1 -0.012 0.04 -10000 0 -0.12 54 54
NF kappa B1 p50/RelA/I kappa B alpha 0.019 0.091 -10000 0 -0.26 40 40
SUMO1 0.023 0.009 -10000 0 -0.12 2 2
ZFPM1 0.022 0.011 -10000 0 -0.12 3 3
NPC/RanGAP1/SUMO1/Ubc9 0.015 0.037 -10000 0 -0.14 30 30
FKBP3 0.021 0.013 -10000 0 -0.12 4 4
Histones 0.04 0.067 -10000 0 -0.22 18 18
YY1/LSF 0.017 0.063 -10000 0 -0.21 34 34
SMG5 0.022 0.011 -10000 0 -0.12 3 3
RAN 0.023 0.002 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.016 0.066 -10000 0 -0.17 49 49
I kappa B alpha/HDAC1 0.011 0.084 -10000 0 -0.24 48 48
SAP18 0.023 0.003 -10000 0 -10000 0 0
RELA 0.017 0.076 -10000 0 -0.22 36 36
HDAC1/Smad7 0.034 0.042 -10000 0 -0.11 39 39
RANGAP1 0.023 0.006 -10000 0 -0.12 1 1
HDAC3/TR2 0.031 0.046 -10000 0 -0.24 11 11
NuRD/MBD3 Complex 0.013 0.099 -10000 0 -0.32 32 32
NF kappa B1 p50/RelA 0.022 0.079 -10000 0 -0.21 44 44
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.02 0.022 -10000 0 -0.12 13 13
GATA1 0.023 0.006 -10000 0 -0.12 1 1
Mad/Max 0.033 0.012 -10000 0 -0.071 8 8
NuRD/MBD3 Complex/GATA1/Fog1 0.025 0.094 -10000 0 -0.29 32 32
RBBP7 0.022 0.011 -10000 0 -0.12 3 3
NPC 0.009 0.023 -10000 0 -0.096 27 27
RBBP4 0.021 0.014 -10000 0 -0.12 5 5
MAX 0.023 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.023 0.003 -10000 0 -10000 0 0
NFKBIA 0.004 0.083 -10000 0 -0.26 43 43
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.015 0.082 -10000 0 -0.3 22 22
SIN3 complex 0.052 0.032 -10000 0 -0.098 20 20
SMURF1 0.023 0.009 -10000 0 -0.12 2 2
CHD3 0.021 0.016 -10000 0 -0.12 7 7
SAP30 0.023 0 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.022 0.009 -10000 0 -0.12 2 2
YY1/HDAC3 0.023 0.065 -10000 0 -0.25 19 19
YY1/HDAC2 0.018 0.059 -10000 0 -0.19 34 34
YY1/HDAC1 0.017 0.059 -10000 0 -0.2 34 34
NuRD/MBD2 Complex (MeCP1) 0.013 0.098 -10000 0 -0.31 32 32
PPARG 0.021 0.062 -10000 0 -0.2 35 35
HDAC8/hEST1B 0.037 0.039 -10000 0 -0.12 28 28
UBE2I 0.023 0.001 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.023 0.003 -10000 0 -10000 0 0
TNFRSF1A 0.021 0.016 -10000 0 -0.12 7 7
HDAC3/SMRT (N-CoR2) 0.031 0.046 -10000 0 -0.25 10 10
MBD3L2 0.022 0.011 -10000 0 -0.12 3 3
ubiquitin-dependent protein catabolic process 0.034 0.041 -10000 0 -0.11 39 39
CREBBP 0.021 0.015 -10000 0 -0.12 6 6
NuRD/MBD3/MBD3L2 Complex 0.023 0.095 -10000 0 -0.3 32 32
HDAC1 0.019 0.02 -10000 0 -0.12 10 10
HDAC3 0.023 0.044 -10000 0 -0.26 9 9
HDAC2 0.02 0.021 -10000 0 -0.12 12 12
YY1 0.008 0.064 -10000 0 -0.22 34 34
HDAC8 0.021 0.013 -10000 0 -0.12 4 4
SMAD7 0.023 0.003 -10000 0 -10000 0 0
NCOR2 0.019 0.023 -10000 0 -0.12 15 15
MXD1 0.021 0.017 -10000 0 -0.12 8 8
STAT3 0.006 0.078 -10000 0 -0.23 48 48
NFKB1 0.021 0.013 -10000 0 -0.12 4 4
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.022 0.01 -10000 0 -0.12 2 2
YY1/LSF/HDAC1 0.019 0.072 -10000 0 -0.19 41 41
YY1/SAP30/HDAC1 0.025 0.062 -10000 0 -0.17 35 35
EP300 0.022 0.01 -10000 0 -0.12 2 2
STAT3 (dimer non-phopshorylated) 0.006 0.078 -10000 0 -0.23 48 48
proteasomal ubiquitin-dependent protein catabolic process 0.004 0.082 -10000 0 -0.26 43 43
histone deacetylation 0.013 0.097 -10000 0 -0.31 32 32
STAT3 (dimer non-phopshorylated)/HDAC3 0.02 0.077 -10000 0 -0.26 24 24
nuclear export -0.036 0.038 0.12 28 -10000 0 28
PRKACA 0.021 0.017 -10000 0 -0.12 8 8
GATAD2B 0.022 0.009 -10000 0 -0.12 2 2
GATAD2A 0.02 0.022 -10000 0 -0.12 13 13
GATA2/HDAC3 0.032 0.047 -10000 0 -0.25 10 10
GATA1/HDAC1 0.023 0.042 -10000 0 -0.12 40 40
GATA1/HDAC3 0.033 0.044 -10000 0 -0.24 10 10
CHD4 0.022 0.009 -10000 0 -0.12 2 2
TNF-alpha/TNFR1A 0.025 0.036 -10000 0 -0.11 37 37
SIN3/HDAC complex/Mad/Max 0.022 0.077 -10000 0 -0.27 22 22
NuRD Complex 0.024 0.095 -10000 0 -0.3 32 32
positive regulation of chromatin silencing 0.038 0.065 -10000 0 -0.22 18 18
SIN3B 0.022 0.015 -10000 0 -0.12 6 6
MTA2 0.023 0.002 -10000 0 -10000 0 0
SIN3A 0.022 0.014 -10000 0 -0.12 5 5
XPO1 0.022 0.01 -10000 0 -0.12 2 2
SUMO1/HDAC1 0.029 0.048 -10000 0 -0.19 13 13
HDAC complex 0.034 0.064 -10000 0 -0.12 66 66
GATA1/Fog1 0.034 0.01 -10000 0 -0.097 3 3
FKBP25/HDAC1/HDAC2 0.027 0.054 -10000 0 -0.12 54 54
TNF 0.02 0.02 -10000 0 -0.12 11 11
negative regulation of cell growth 0.022 0.077 -10000 0 -0.27 22 22
NuRD/MBD2/PRMT5 Complex 0.013 0.098 -10000 0 -0.31 32 32
Ran/GTP/Exportin 1 0.034 0.049 -10000 0 -0.15 30 30
NF kappa B/RelA/I kappa B alpha 0.018 0.08 -10000 0 -0.27 31 31
SIN3/HDAC complex/NCoR1 0.019 0.079 -10000 0 -0.26 28 28
TFCP2 0.021 0.014 -10000 0 -0.12 5 5
NR2C1 0.022 0.01 -10000 0 -0.12 2 2
MBD3 0.023 0.009 -10000 0 -0.12 2 2
MBD2 0.023 0 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.03 0.016 -9999 0 -0.12 6 6
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.022 0.011 -9999 0 -0.12 3 3
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.013 0.034 -9999 0 -0.12 33 33
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.022 0.011 -9999 0 -0.12 3 3
RAC1-CDC42/GTP/PAK family 0.007 0.055 -9999 0 -0.15 50 50
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.02 0.018 -9999 0 -0.12 8 8
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.023 0 -9999 0 -10000 0 0
FYN 0.011 0.037 -9999 0 -0.12 40 40
MAP3K12 0.022 0.011 -9999 0 -0.12 3 3
FGR 0.023 0.006 -9999 0 -0.12 1 1
p38 alpha/TAB1 0.019 0.083 -9999 0 -0.2 45 45
PRKG1 0.018 0.026 -9999 0 -0.12 19 19
DUSP8 0.023 0.006 -9999 0 -0.12 1 1
PGK/cGMP/p38 alpha 0.013 0.08 -9999 0 -0.2 45 45
apoptosis 0.018 0.08 -9999 0 -0.19 45 45
RAL/GTP 0.024 0.033 -9999 0 -0.11 29 29
LYN 0.021 0.013 -9999 0 -0.12 4 4
DUSP1 -0.004 0.052 -9999 0 -0.12 90 90
PAK1 0.016 0.029 -9999 0 -0.12 23 23
SRC 0.023 0.009 -9999 0 -0.12 2 2
RAC1/OSM/MEKK3/MKK3 0.057 0.021 -9999 0 -0.093 11 11
TRAF6 0.022 0.009 -9999 0 -0.12 2 2
RAC1 0.023 0.002 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.023 0.001 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0.03 0.019 -9999 0 -0.13 7 7
MAPK11 0.004 0.1 -9999 0 -0.27 42 42
BLK 0.022 0.015 -9999 0 -0.12 6 6
HCK 0.019 0.024 -9999 0 -0.12 15 15
MAP2K3 0.023 0.006 -9999 0 -0.12 1 1
DUSP16 0.018 0.026 -9999 0 -0.12 18 18
DUSP10 0.012 0.036 -9999 0 -0.12 36 36
TRAF6/MEKK3 0.028 0.017 -9999 0 -0.093 11 11
MAP3K7IP1 0.023 0 -9999 0 -10000 0 0
MAPK14 0.01 0.087 -9999 0 -0.22 45 45
positive regulation of innate immune response 0.007 0.11 -9999 0 -0.29 44 44
LCK 0.022 0.015 -9999 0 -0.12 6 6
p38alpha-beta/MKP7 0.013 0.11 -9999 0 -0.28 46 46
p38alpha-beta/MKP5 0.005 0.12 -9999 0 -0.27 56 56
PGK/cGMP 0.014 0.017 -9999 0 -0.077 19 19
PAK2 0.022 0.011 -9999 0 -0.12 3 3
p38alpha-beta/MKP1 -0.007 0.12 -9999 0 -0.27 65 65
CDC42 0.023 0.002 -9999 0 -10000 0 0
RALB 0.022 0.007 -9999 0 -0.12 1 1
RALA 0.022 0.009 -9999 0 -0.12 2 2
PAK3 0.008 0.044 -9999 0 -0.12 59 59
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.016 0.032 -9999 0 -0.12 28 28
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.023 0.006 -9999 0 -0.12 1 1
TCEB1 0.022 0.011 -9999 0 -0.12 3 3
HIF1A/p53 0.002 0.061 -9999 0 -0.2 32 32
HIF1A 0.007 0.047 -9999 0 -0.19 22 22
COPS5 0.019 0.022 -9999 0 -0.12 12 12
VHL/Elongin B/Elongin C/RBX1/CUL2 0.053 0.049 -9999 0 -0.097 48 48
FIH (dimer) 0.023 0.006 -9999 0 -0.12 1 1
CDKN2A 0.014 0.023 -9999 0 -0.12 12 12
ARNT/IPAS 0.027 0.028 -9999 0 -0.14 4 4
HIF1AN 0.023 0.006 -9999 0 -0.12 1 1
GNB2L1 0.023 0.003 -9999 0 -10000 0 0
HIF1A/ARNT 0.014 0.055 -9999 0 -0.18 23 23
CUL2 0.022 0.011 -9999 0 -0.12 3 3
OS9 0.022 0.009 -9999 0 -0.12 2 2
RACK1/Elongin B/Elongin C 0.043 0.024 -9999 0 -0.11 13 13
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.014 0.056 -9999 0 -0.19 24 24
PHD1-3/OS9 0.014 0.066 -9999 0 -0.097 112 112
HIF1A/RACK1/Elongin B/Elongin C 0.035 0.057 -9999 0 -0.18 21 21
VHL 0.021 0.016 -9999 0 -0.12 7 7
HSP90AA1 0.023 0.003 -9999 0 -10000 0 0
HIF1A/JAB1 0.011 0.057 -9999 0 -0.19 25 25
EGLN3 -0.002 0.051 -9999 0 -0.12 84 84
EGLN2 0.023 0.009 -9999 0 -0.12 2 2
EGLN1 0.023 0.009 -9999 0 -0.12 2 2
TP53 0.011 0.029 -9999 0 -0.12 22 22
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.027 0.091 -9999 0 -0.52 14 14
ARNT 0.022 0.012 -9999 0 -0.12 4 4
ARD1A 0.018 0.025 -9999 0 -0.12 17 17
RBX1 0.022 0.011 -9999 0 -0.12 3 3
HIF1A/p19ARF 0.004 0.063 -9999 0 -0.21 29 29
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.019 0.025 0.12 17 -10000 0 17
PI3K Class IB/PDE3B 0.019 0.025 -10000 0 -0.12 17 17
PDE3B 0.019 0.025 -10000 0 -0.12 17 17
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 0.01 0.042 -9999 0 -0.12 51 51
CDC42/GTP 0.008 0.067 -9999 0 -0.21 22 22
PLCG1 -0.001 0.065 -9999 0 -0.22 23 23
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.022 0.011 -9999 0 -0.12 3 3
GNAI3 0.021 0.008 -9999 0 -0.12 1 1
G12/G13 0.03 0.028 -9999 0 -0.13 16 16
cell migration 0.007 0.065 -9999 0 -0.21 22 22
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
MAPK3 0 0.066 -9999 0 -0.21 25 25
MAPK1 0 0.066 -9999 0 -0.21 25 25
S1P/S1P5/Gi -0.003 0.069 -9999 0 -0.15 86 86
GNAI1 0.012 0.035 -9999 0 -0.12 35 35
CDC42/GDP 0.016 0.012 -9999 0 -0.15 3 3
S1P/S1P5/G12 0.016 0.006 -9999 0 -0.12 1 1
RHOA 0.021 0.02 -9999 0 -0.1 14 14
S1P/S1P4/Gi -0.003 0.069 -9999 0 -0.15 86 86
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.022 0.011 -9999 0 -0.12 3 3
S1P/S1P4/G12/G13 0.026 0.021 -9999 0 -0.096 16 16
GNA12 0.023 0.001 -9999 0 -10000 0 0
GNA13 0.022 0.009 -9999 0 -0.12 2 2
CDC42 0.023 0.002 -9999 0 -10000 0 0
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 0.023 0.006 -10000 0 -0.12 1 1
CLTC 0.005 0.082 -10000 0 -0.39 15 15
calcium ion-dependent exocytosis 0.01 0.043 -10000 0 -0.15 22 22
Dynamin 2/GTP 0.014 0.044 -10000 0 -0.11 53 53
EXOC4 0.022 0.007 -10000 0 -0.12 1 1
CD59 0.009 0.061 -10000 0 -0.37 11 11
CPE 0.009 0.028 -10000 0 -0.066 58 58
CTNNB1 0.022 0.008 -10000 0 -0.12 1 1
membrane fusion 0.015 0.036 -10000 0 -0.15 22 22
CTNND1 0.012 0.041 -10000 0 -0.099 52 52
DNM2 0.02 0.022 -10000 0 -0.12 13 13
mol:PI-4-5-P2 0.015 0.048 -10000 0 -0.27 12 12
TSHR 0.013 0.026 -10000 0 -0.069 49 49
INS 0.018 0.017 -10000 0 -10000 0 0
BIN1 0.022 0.012 -10000 0 -0.12 4 4
mol:Choline 0.015 0.036 -10000 0 -0.15 22 22
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.014 0.022 -10000 0 -0.072 30 30
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.023 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0.014 0.043 -10000 0 -0.1 53 53
JUP 0.006 0.066 -10000 0 -0.38 12 12
ASAP2/amphiphysin II 0.027 0.02 -10000 0 -0.1 12 12
ARF6/GTP 0.015 0.021 -10000 0 -0.15 9 9
CDH1 0.005 0.069 -10000 0 -0.4 11 11
clathrin-independent pinocytosis 0.015 0.021 -10000 0 -0.15 9 9
MAPK8IP3 0.023 0.006 -10000 0 -0.12 1 1
positive regulation of endocytosis 0.015 0.021 -10000 0 -0.15 9 9
EXOC2 0.022 0.013 -10000 0 -0.12 4 4
substrate adhesion-dependent cell spreading 0.011 0.1 -10000 0 -0.28 50 50
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.021 0.015 -10000 0 -0.12 6 6
regulation of calcium-dependent cell-cell adhesion -0.014 0.079 0.32 16 -10000 0 16
positive regulation of phagocytosis 0.018 0.016 -10000 0 -0.11 8 8
ARF6/GTP/JIP3 0.029 0.019 -10000 0 -0.11 10 10
ACAP1 0.014 0.032 -10000 0 -0.13 22 22
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.01 0.06 -10000 0 -0.39 10 10
clathrin heavy chain/ACAP1 0.011 0.066 -10000 0 -0.3 16 16
JIP4/KLC1 0.033 0.039 -10000 0 -0.11 37 37
EXOC1 0.021 0.012 -10000 0 -0.12 3 3
exocyst 0.011 0.11 -10000 0 -0.28 50 50
RALA/GTP 0.014 0.021 -10000 0 -0.13 11 11
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.025 0.029 -10000 0 -0.12 21 21
receptor recycling 0.015 0.021 -10000 0 -0.15 9 9
CTNNA1 0.012 0.04 -10000 0 -0.098 52 52
NME1 0.014 0.022 -10000 0 -0.072 30 30
clathrin coat assembly 0.005 0.081 -10000 0 -0.38 15 15
IL2RA 0.01 0.06 -10000 0 -0.38 10 10
VAMP3 0.019 0.016 -10000 0 -0.12 8 8
GLUT4/clathrin heavy chain/ACAP1 0.019 0.065 -10000 0 -0.29 15 15
EXOC6 0.021 0.012 -10000 0 -0.12 3 3
PLD1 0.002 0.057 -10000 0 -0.19 40 40
PLD2 0.018 0.028 -10000 0 -0.19 6 6
EXOC5 0.022 0.011 -10000 0 -0.12 3 3
PIP5K1C 0.015 0.048 -10000 0 -0.27 12 12
SDC1 0.009 0.061 -10000 0 -0.37 11 11
ARF6/GDP 0.012 0.041 -10000 0 -0.098 63 63
EXOC7 0.023 0.001 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.016 0.082 -10000 0 -0.33 16 16
mol:Phosphatidic acid 0.015 0.036 -10000 0 -0.15 22 22
endocytosis -0.025 0.02 0.1 12 -10000 0 12
SCAMP2 0.023 0.009 -10000 0 -0.12 2 2
ADRB2 0.009 0.078 -10000 0 -0.36 15 15
EXOC3 0.023 0.009 -10000 0 -0.12 2 2
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.016 0.044 -10000 0 -0.1 53 53
KLC1 0.021 0.013 -10000 0 -0.12 4 4
AVPR2 0.008 0.079 -10000 0 -0.36 16 16
RALA 0.022 0.009 -10000 0 -0.12 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.015 0.087 -10000 0 -0.32 19 19
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.019 0.02 -9999 0 -0.12 10 10
HDAC2 0.019 0.021 -9999 0 -0.12 12 12
GNB1/GNG2 0.04 0.034 -9999 0 -0.11 23 23
forebrain development 0.027 0.11 -9999 0 -0.37 29 29
GNAO1 0.011 0.042 -9999 0 -0.12 51 51
SMO/beta Arrestin2 0.035 0.021 -9999 0 -0.13 6 6
SMO 0.024 0.011 -9999 0 -0.12 3 3
ARRB2 0.023 0.014 -9999 0 -0.12 5 5
GLI3/SPOP 0.006 0.11 -9999 0 -0.3 36 36
mol:GTP 0.001 0.001 -9999 0 -10000 0 0
GSK3B 0.022 0.011 -9999 0 -0.12 3 3
GNAI2 0.023 0.011 -9999 0 -0.12 3 3
SIN3/HDAC complex 0.051 0.032 -9999 0 -0.098 20 20
GNAI1 0.013 0.035 -9999 0 -0.12 35 35
XPO1 0.025 0.01 -9999 0 -0.12 2 2
GLI1/Su(fu) 0.034 0.11 -9999 0 -0.38 27 27
SAP30 0.023 0 -9999 0 -10000 0 0
mol:GDP 0.024 0.011 -9999 0 -0.12 3 3
MIM/GLI2A 0.022 0.034 -9999 0 -0.11 31 31
IFT88 0.016 0.03 -9999 0 -0.12 25 25
GNAI3 0.022 0.009 -9999 0 -0.12 1 1
GLI2 0.036 0.043 -9999 0 -0.23 8 8
GLI3 -0.005 0.11 -9999 0 -0.32 34 34
CSNK1D 0.023 0.001 -9999 0 -10000 0 0
CSNK1E 0.022 0.015 -9999 0 -0.12 6 6
SAP18 0.023 0.003 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.016 0.03 -9999 0 -0.12 25 25
GNG2 0.02 0.018 -9999 0 -0.12 9 9
Gi family/GTP 0.009 0.07 -9999 0 -0.14 86 86
SIN3B 0.021 0.015 -9999 0 -0.12 6 6
SIN3A 0.021 0.014 -9999 0 -0.12 5 5
GLI3/Su(fu) 0.015 0.1 -9999 0 -0.33 27 27
GLI2/Su(fu) 0.053 0.045 -9999 0 -0.22 9 9
FOXA2 0.028 0.085 -9999 0 -0.74 5 5
neural tube patterning 0.027 0.11 -9999 0 -0.37 29 29
SPOP 0.022 0.011 -9999 0 -0.12 3 3
Su(fu)/PIAS1 0.036 0.041 -9999 0 -0.2 13 13
GNB1 0.023 0.007 -9999 0 -0.12 1 1
CSNK1G2 0.022 0.011 -9999 0 -0.12 3 3
CSNK1G3 0.022 0.007 -9999 0 -0.12 1 1
MTSS1 0.022 0.034 -9999 0 -0.11 31 31
embryonic limb morphogenesis 0.027 0.11 -9999 0 -0.37 29 29
SUFU 0.026 0.041 -9999 0 -0.22 12 12
LGALS3 0.018 0.023 -9999 0 -0.12 14 14
catabolic process 0.032 0.1 -9999 0 -0.32 24 24
GLI3A/CBP 0.033 0.022 -9999 0 -0.14 7 7
KIF3A 0.019 0.021 -9999 0 -0.12 12 12
GLI1 0.027 0.11 -9999 0 -0.4 25 25
RAB23 0.022 0.011 -9999 0 -0.12 3 3
CSNK1A1 0.022 0.007 -9999 0 -0.12 1 1
IFT172 0.021 0.014 -9999 0 -0.12 5 5
RBBP7 0.021 0.011 -9999 0 -0.12 3 3
Su(fu)/Galectin3 0.031 0.044 -9999 0 -0.19 16 16
GNAZ 0.023 0.011 -9999 0 -0.12 3 3
RBBP4 0.021 0.014 -9999 0 -0.12 5 5
CSNK1G1 0.023 0.009 -9999 0 -0.12 2 2
PIAS1 0.022 0.009 -9999 0 -0.12 2 2
PRKACA 0.021 0.017 -9999 0 -0.12 8 8
GLI2/SPOP 0.045 0.044 -9999 0 -0.23 8 8
STK36 0.022 0.022 -9999 0 -0.12 12 12
Gi family/GNB1/GNG2/GDP 0.009 0.077 -9999 0 -0.22 31 31
PTCH1 0.033 0.11 -9999 0 -0.51 10 10
MIM/GLI1 0.043 0.11 -9999 0 -0.4 23 23
CREBBP 0.033 0.022 -9999 0 -0.14 7 7
Su(fu)/SIN3/HDAC complex 0.02 0.094 -9999 0 -0.31 28 28
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.02 0.016 -10000 0 -0.071 16 16
BAD/BCL-XL/YWHAZ 0.039 0.031 -10000 0 -0.096 22 22
CDKN1B 0.013 0.076 -10000 0 -0.34 22 22
CDKN1A 0.017 0.075 -10000 0 -0.34 22 22
FRAP1 0.022 0.013 -10000 0 -0.12 4 4
PRKDC 0.021 0.015 -10000 0 -0.12 6 6
FOXO3 0.016 0.076 -10000 0 -0.33 23 23
AKT1 0.014 0.077 -10000 0 -0.35 22 22
BAD 0.022 0.011 -10000 0 -0.12 3 3
AKT3 -0.006 0.055 -10000 0 -0.2 32 32
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.018 0.074 -10000 0 -0.33 22 22
AKT1/ASK1 0.019 0.077 -10000 0 -0.33 22 22
BAD/YWHAZ 0.043 0.025 -10000 0 -0.11 11 11
RICTOR 0.02 0.017 -10000 0 -0.12 7 7
RAF1 0.023 0.003 -10000 0 -10000 0 0
JNK cascade -0.018 0.075 0.32 22 -10000 0 22
TSC1 0.017 0.074 -10000 0 -0.33 22 22
YWHAZ 0.023 0.003 -10000 0 -10000 0 0
AKT1/RAF1 0.026 0.079 -10000 0 -0.34 23 23
EP300 0.022 0.01 -10000 0 -0.12 2 2
mol:GDP 0.014 0.077 -10000 0 -0.35 22 22
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.016 0.074 -10000 0 -0.33 22 22
YWHAQ 0.023 0.003 -10000 0 -10000 0 0
TBC1D4 0.018 0.014 -10000 0 -0.04 28 28
MAP3K5 0.018 0.025 -10000 0 -0.12 17 17
MAPKAP1 0.023 0.002 -10000 0 -10000 0 0
negative regulation of cell cycle -0.018 0.071 0.23 22 -10000 0 22
YWHAH 0.021 0.014 -10000 0 -0.12 5 5
AKT1S1 0.017 0.074 -10000 0 -0.33 22 22
CASP9 0.016 0.075 -10000 0 -0.34 22 22
YWHAB 0.023 0.007 -10000 0 -0.12 1 1
p27Kip1/KPNA1 0.021 0.081 -10000 0 -0.32 24 24
GBL 0.023 0.009 -10000 0 -0.12 2 2
PDK1/Src/Hsp90 0.041 0.032 -10000 0 -0.12 19 19
YWHAE 0.022 0.014 -10000 0 -0.12 5 5
SRC 0.023 0.009 -10000 0 -0.12 2 2
AKT2/p21CIP1 0.022 0.07 -10000 0 -0.29 23 23
KIAA1303 0.023 0.009 -10000 0 -0.12 2 2
mTOR/RHEB/GTP/Raptor/GBL 0.026 0.072 -10000 0 -0.34 17 17
CHUK 0.014 0.078 -10000 0 -0.34 23 23
BAD/BCL-XL 0.035 0.077 -10000 0 -0.32 22 22
mTORC2 0.047 0.043 -10000 0 -0.1 38 38
AKT2 0.014 0.029 -10000 0 -0.2 8 8
FOXO1-3a-4/14-3-3 family 0.024 0.088 -10000 0 -0.28 25 25
PDPK1 0.023 0.007 -10000 0 -0.12 1 1
MDM2 0.015 0.078 -10000 0 -0.35 22 22
MAPKKK cascade -0.026 0.077 0.33 23 -10000 0 23
MDM2/Cbp/p300 0.032 0.087 -10000 0 -0.34 22 22
TSC1/TSC2 0.018 0.073 -10000 0 -0.32 22 22
proteasomal ubiquitin-dependent protein catabolic process 0.03 0.083 -10000 0 -0.33 22 22
glucose import 0.018 0.023 -10000 0 -0.14 8 8
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.027 0.071 -10000 0 -0.25 21 21
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 0.02 0.012 -10000 0 -0.031 29 29
GSK3A 0.016 0.076 -10000 0 -0.34 22 22
FOXO1 0.017 0.074 -10000 0 -0.33 22 22
GSK3B 0.017 0.076 -10000 0 -0.34 22 22
SFN 0.014 0.032 -10000 0 -0.12 29 29
G1/S transition of mitotic cell cycle 0.019 0.075 -10000 0 -0.33 22 22
p27Kip1/14-3-3 family 0.029 0.078 -10000 0 -0.33 17 17
PRKACA 0.021 0.017 -10000 0 -0.12 8 8
KPNA1 0.023 0.003 -10000 0 -10000 0 0
HSP90AA1 0.023 0.003 -10000 0 -10000 0 0
YWHAG 0.02 0.022 -10000 0 -0.12 13 13
RHEB 0.019 0.022 -10000 0 -0.12 13 13
CREBBP 0.021 0.015 -10000 0 -0.12 6 6
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.021 0.017 -10000 0 -0.12 8 8
NFATC1 0.03 0.065 -10000 0 -0.25 14 14
NFATC2 0.02 0.048 -10000 0 -0.16 20 20
NFATC3 0.024 0.022 -10000 0 -0.24 2 2
YWHAE 0.022 0.014 -10000 0 -0.12 5 5
Calcineurin A alpha-beta B1/CABIN1 -0.006 0.08 -10000 0 -0.22 37 37
Exportin 1/Ran/NUP214 0.037 0.039 -10000 0 -0.11 34 34
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.015 0.079 -10000 0 -0.22 27 27
BCL2/BAX 0.029 0.025 -10000 0 -0.076 29 29
CaM/Ca2+/Calcineurin A alpha-beta B1 0.013 0.021 -10000 0 -0.12 12 12
CaM/Ca2+ 0.013 0.021 -10000 0 -0.12 12 12
BAX 0.023 0 -10000 0 -10000 0 0
MAPK14 0.022 0.007 -10000 0 -0.12 1 1
BAD 0.022 0.011 -10000 0 -0.12 3 3
CABIN1/MEF2D 0.006 0.08 -10000 0 -0.21 37 37
Calcineurin A alpha-beta B1/BCL2 0.016 0.031 -10000 0 -0.12 27 27
FKBP8 0.016 0.031 -10000 0 -0.12 27 27
activation-induced cell death of T cells -0.006 0.079 0.2 37 -10000 0 37
KPNB1 0.022 0.009 -10000 0 -0.12 2 2
KPNA2 0.017 0.024 -10000 0 -0.12 15 15
XPO1 0.022 0.01 -10000 0 -0.12 2 2
SFN 0.014 0.032 -10000 0 -0.12 29 29
MAP3K8 0.022 0.009 -10000 0 -0.12 2 2
NFAT4/CK1 alpha 0.03 0.038 -10000 0 -0.13 18 18
MEF2D/NFAT1/Cbp/p300 0.04 0.079 -10000 0 -0.16 43 43
CABIN1 -0.006 0.081 -10000 0 -0.22 37 37
CALM1 0.021 0.014 -10000 0 -0.12 5 5
RAN 0.023 0.002 -10000 0 -10000 0 0
MAP3K1 0.021 0.015 -10000 0 -0.12 6 6
CAMK4 0.016 0.031 -10000 0 -0.12 27 27
mol:Ca2+ 0 0.003 -10000 0 -10000 0 0
MAPK3 0.022 0.014 -10000 0 -0.12 5 5
YWHAH 0.021 0.014 -10000 0 -0.12 5 5
Calcineurin A alpha-beta B1/AKAP79/PKA 0.032 0.017 -10000 0 -0.14 2 2
YWHAB 0.023 0.007 -10000 0 -0.12 1 1
MAPK8 0.021 0.015 -10000 0 -0.12 6 6
MAPK9 0.021 0.012 -10000 0 -0.12 3 3
YWHAG 0.02 0.022 -10000 0 -0.12 13 13
FKBP1A 0.022 0.012 -10000 0 -0.12 4 4
NFAT1-c-4/YWHAQ 0.048 0.071 -10000 0 -0.29 10 10
PRKCH 0.019 0.024 -10000 0 -0.12 15 15
CABIN1/Cbp/p300 0.02 0.052 -10000 0 -0.16 41 41
CASP3 0.022 0.009 -10000 0 -0.12 2 2
PIM1 0.02 0.023 -10000 0 -0.12 14 14
Calcineurin A alpha-beta B1/FKBP12/FK506 0.014 0.012 -10000 0 -0.087 7 7
apoptosis 0.019 0.036 0.14 2 -0.21 11 13
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.017 0.07 -10000 0 -0.29 13 13
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.021 0.017 -10000 0 -0.12 8 8
JNK2/NFAT4 0.034 0.024 -10000 0 -0.2 3 3
BAD/BCL-XL 0.029 0.028 -10000 0 -0.11 22 22
PRKCD 0.02 0.018 -10000 0 -0.12 8 8
NUP214 0.022 0.007 -10000 0 -0.12 1 1
PRKCZ 0.023 0.001 -10000 0 -10000 0 0
PRKCA 0.011 0.037 -10000 0 -0.12 40 40
PRKCG 0.021 0.016 -10000 0 -0.12 7 7
PRKCQ 0.015 0.03 -10000 0 -0.12 24 24
FKBP38/BCL2 0.023 0.035 -10000 0 -0.14 7 7
EP300 0.022 0.01 -10000 0 -0.12 2 2
PRKCB1 0.014 0.035 -10000 0 -0.12 35 35
CSNK2A1 0.021 0.015 -10000 0 -0.12 6 6
NFATc/JNK1 0.039 0.068 -10000 0 -0.24 18 18
CaM/Ca2+/FKBP38 0.024 0.028 -10000 0 -0.12 10 10
FKBP12/FK506 0.016 0.014 -10000 0 -0.11 7 7
CSNK1A1 0.017 0.017 -10000 0 -0.085 12 12
CaM/Ca2+/CAMK IV 0.023 0.028 -10000 0 -0.072 41 41
NFATc/ERK1 0.04 0.066 -10000 0 -0.24 14 14
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.014 0.08 -10000 0 -0.22 28 28
NR4A1 0.017 0.082 -10000 0 -0.19 44 44
GSK3B 0.022 0.011 -10000 0 -0.12 3 3
positive T cell selection 0.024 0.022 -10000 0 -0.24 2 2
NFAT1/CK1 alpha 0.021 0.044 -10000 0 -0.16 18 18
RCH1/ KPNB1 0.01 0.061 -10000 0 -0.13 82 82
YWHAQ 0.023 0.003 -10000 0 -10000 0 0
PRKACA 0.021 0.017 -10000 0 -0.12 8 8
AKAP5 0.023 0.009 -10000 0 -0.12 2 2
MEF2D 0.023 0.002 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.023 0.003 -10000 0 -10000 0 0
NFATc/p38 alpha 0.041 0.067 -10000 0 -0.24 17 17
CREBBP 0.021 0.016 -10000 0 -0.12 6 6
BCL2 0.016 0.031 -10000 0 -0.12 27 27
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0.005 0.12 -9999 0 -0.82 9 9
MKNK1 0.023 0.006 -9999 0 -0.12 1 1
MAPK14 0.015 0.049 -9999 0 -0.2 15 15
ATF2/c-Jun -0.006 0.11 -9999 0 -0.36 42 42
MAPK11 0.015 0.049 -9999 0 -0.21 14 14
MITF 0.018 0.062 -9999 0 -0.29 14 14
MAPKAPK5 0.02 0.058 -9999 0 -0.27 14 14
KRT8 0.016 0.065 -9999 0 -0.28 20 20
MAPKAPK3 0.022 0.012 -9999 0 -0.12 4 4
MAPKAPK2 0.023 0.009 -9999 0 -0.12 2 2
p38alpha-beta/CK2 0.019 0.072 -9999 0 -0.28 15 15
CEBPB 0.016 0.063 -9999 0 -0.3 14 14
SLC9A1 0.019 0.059 -9999 0 -0.29 13 13
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 0.016 0.07 -9999 0 -0.27 18 18
p38alpha-beta/MNK1 0.033 0.063 -9999 0 -0.27 11 11
JUN -0.008 0.11 -9999 0 -0.36 42 42
PPARGC1A 0.016 0.06 -9999 0 -0.29 13 13
USF1 0.019 0.059 -9999 0 -0.26 16 16
RAB5/GDP/GDI1 0.018 0.052 -9999 0 -0.19 19 19
NOS2 0.011 0.056 -9999 0 -0.24 18 18
DDIT3 0.015 0.06 -9999 0 -0.26 17 17
RAB5A 0.023 0.006 -9999 0 -0.12 1 1
HSPB1 0.019 0.045 -9999 0 -0.24 11 11
p38alpha-beta/HBP1 0.025 0.069 -9999 0 -0.24 15 15
CREB1 0.019 0.071 -9999 0 -0.3 21 21
RAB5/GDP 0.016 0.014 -9999 0 -0.13 5 5
EIF4E 0.02 0.049 -9999 0 -0.23 11 11
RPS6KA4 0.02 0.057 -9999 0 -0.28 13 13
PLA2G4A 0 0.06 -9999 0 -0.23 18 18
GDI1 0.017 0.062 -9999 0 -0.26 19 19
TP53 0.005 0.066 -9999 0 -0.3 17 17
RPS6KA5 0.018 0.059 -9999 0 -0.25 17 17
ESR1 0.01 0.076 -9999 0 -0.29 27 27
HBP1 0.022 0.005 -9999 0 -10000 0 0
MEF2C 0.016 0.068 -9999 0 -0.28 19 19
MEF2A 0.019 0.061 -9999 0 -0.28 15 15
EIF4EBP1 0.019 0.068 -9999 0 -0.28 20 20
KRT19 0.009 0.075 -9999 0 -0.28 25 25
ELK4 0.021 0.056 -9999 0 -0.27 13 13
ATF6 0.018 0.064 -9999 0 -0.32 14 14
ATF1 0.019 0.07 -9999 0 -0.3 20 20
p38alpha-beta/MAPKAPK2 0.033 0.061 -9999 0 -0.27 10 10
p38alpha-beta/MAPKAPK3 0.033 0.061 -9999 0 -0.28 9 9
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 0.025 0.021 -9999 0 -0.089 14 14
NFATC2 0.024 0.022 -9999 0 -0.072 21 21
NFATC3 0.026 0.02 -9999 0 -0.083 14 14
CD40LG 0.045 0.079 -9999 0 -0.22 13 13
PTGS2 0.037 0.089 -9999 0 -0.22 22 22
JUNB 0.007 0.042 -9999 0 -0.12 52 52
CaM/Ca2+/Calcineurin A alpha-beta B1 0.019 0.021 -9999 0 -0.12 12 12
CaM/Ca2+ 0.019 0.021 -9999 0 -0.12 12 12
CALM1 0.024 0.014 -9999 0 -0.12 5 5
JUN 0.017 0.033 -9999 0 -0.12 30 30
mol:Ca2+ 0.002 0.003 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.016 0.012 -9999 0 -0.086 7 7
FOSL1 0.021 0.018 -9999 0 -0.12 9 9
CREM 0.021 0.012 -9999 0 -0.12 4 4
Jun/NFAT1-c-4/p21SNFT 0.062 0.06 -9999 0 -0.17 9 9
FOS -0.002 0.053 -9999 0 -0.12 95 95
IFNG 0.041 0.085 -9999 0 -0.24 14 14
AP-1/NFAT1-c-4 0.089 0.12 -9999 0 -0.24 13 13
FASLG 0.044 0.08 -9999 0 -0.22 12 12
NFAT1-c-4/ICER1 0.052 0.038 -9999 0 -0.13 8 8
IL2RA 0.043 0.081 -9999 0 -0.22 14 14
FKBP12/FK506 0.016 0.014 -9999 0 -0.11 7 7
CSF2 0.044 0.079 -9999 0 -0.22 12 12
JunB/Fra1/NFAT1-c-4 0.046 0.06 -9999 0 -0.14 18 18
IL4 0.044 0.079 -9999 0 -0.23 11 11
IL2 0.008 0.015 -9999 0 -10000 0 0
IL3 0.039 0.05 -9999 0 -0.61 3 3
FKBP1A 0.022 0.012 -9999 0 -0.12 4 4
BATF3 0 0 -9999 0 -10000 0 0
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.031 0.007 -9999 0 -0.12 1 1
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.008 0.098 -9999 0 -0.39 31 31
Crk/p130 Cas/Paxillin -0.007 0.025 -9999 0 -0.16 5 5
JUN 0.012 0.06 -9999 0 -0.21 22 22
HRAS 0.023 0.006 -9999 0 -0.12 1 1
RET51/GFRalpha1/GDNF/GRB10 0.045 0.039 -9999 0 -0.1 11 11
RAP1A 0.021 0.012 -9999 0 -0.12 3 3
FRS2 0.019 0.024 -9999 0 -0.12 15 15
RAP1A/GDP 0.009 0.034 -9999 0 -0.14 28 28
RET51/GFRalpha1/GDNF/DOK1 0.045 0.039 -9999 0 -0.11 9 9
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.022 0.011 -9999 0 -0.12 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.021 0.016 -9999 0 -0.12 7 7
RET9/GFRalpha1/GDNF/Enigma 0.034 0.032 -9999 0 -0.11 7 7
RHOA 0.023 0.006 -9999 0 -0.12 1 1
RAP1A/GTP 0.039 0.042 -9999 0 -0.12 10 10
GRB7 0.018 0.026 -9999 0 -0.12 18 18
RET51/GFRalpha1/GDNF 0.046 0.037 -9999 0 -0.097 8 8
MAPKKK cascade 0.037 0.037 -9999 0 -0.18 5 5
BCAR1 0.022 0.011 -9999 0 -0.12 3 3
RET9/GFRalpha1/GDNF/IRS1 0.033 0.033 -9999 0 -0.1 10 10
lamellipodium assembly 0.025 0.043 -9999 0 -0.18 6 6
RET51/GFRalpha1/GDNF/SHC 0.047 0.035 -9999 0 -0.096 5 5
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
RET9/GFRalpha1/GDNF/SHC 0.036 0.027 -9999 0 -0.099 3 3
RET9/GFRalpha1/GDNF/Shank3 0.036 0.027 -9999 0 -0.1 3 3
MAPK3 0.022 0.033 -9999 0 -0.14 7 7
DOK1 0.021 0.016 -9999 0 -0.12 7 7
DOK6 0.023 0.009 -9999 0 -0.12 2 2
PXN 0.022 0.014 -9999 0 -0.12 5 5
neurite development 0.028 0.039 -9999 0 -0.17 10 10
DOK5 -0.008 0.054 -9999 0 -0.12 102 102
GFRA1 0.01 0.041 -9999 0 -0.12 50 50
MAPK8 0.014 0.061 -9999 0 -0.23 17 17
HRAS/GTP 0.042 0.041 -9999 0 -0.15 9 9
tube development 0.038 0.03 -9999 0 -0.12 6 6
MAPK1 0.021 0.033 -9999 0 -0.14 7 7
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.018 0.055 -9999 0 -0.3 8 8
Rac1/GDP 0.016 0.015 -9999 0 -0.15 5 5
SRC 0.023 0.009 -9999 0 -0.12 2 2
PDLIM7 0.02 0.021 -9999 0 -0.12 12 12
RET51/GFRalpha1/GDNF/Dok6 0.056 0.036 -9999 0 -0.14 1 1
SHC1 0.023 0.001 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.047 0.035 -9999 0 -0.098 7 7
RET51/GFRalpha1/GDNF/Dok5 -0.003 0.072 -9999 0 -0.1 144 144
PRKCA 0.011 0.037 -9999 0 -0.12 40 40
HRAS/GDP 0.017 0.008 -9999 0 -0.11 2 2
CREB1 0.021 0.071 -9999 0 -0.39 10 10
PIK3R1 0.015 0.031 -9999 0 -0.12 27 27
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.024 0.034 -9999 0 -0.14 17 17
RET51/GFRalpha1/GDNF/Grb7 0.041 0.044 -9999 0 -0.11 18 18
mol:GDP 0 0 -9999 0 -10000 0 0
RET 0.019 0.026 -9999 0 -0.12 18 18
DOK4 0.022 0.012 -9999 0 -0.12 4 4
JNK cascade 0.01 0.063 -9999 0 -0.2 28 28
RET9/GFRalpha1/GDNF/FRS2 0.031 0.036 -9999 0 -0.1 17 17
SHANK3 0.023 0.006 -9999 0 -0.12 1 1
RASA1 0.021 0.012 -9999 0 -0.12 3 3
NCK1 0.02 0.019 -9999 0 -0.12 9 9
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.019 0.048 -9999 0 -0.26 5 5
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.023 0.055 -9999 0 -0.29 8 8
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.014 0.065 -9999 0 -0.16 60 60
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.024 0.049 -9999 0 -0.25 6 6
PI3K 0.035 0.052 -9999 0 -0.22 6 6
SOS1 0.017 0.027 -9999 0 -0.12 20 20
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.045 0.032 -9999 0 -0.12 6 6
GRB10 0.022 0.014 -9999 0 -0.12 5 5
activation of MAPKK activity 0.022 0.056 -9999 0 -0.29 9 9
RET51/GFRalpha1/GDNF/FRS2 0.042 0.043 -9999 0 -0.097 19 19
GAB1 0.02 0.021 -9999 0 -0.12 12 12
IRS1 0.019 0.023 -9999 0 -0.12 14 14
IRS2 0.021 0.016 -9999 0 -0.12 7 7
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.03 0.036 -9999 0 -0.21 2 2
RET51/GFRalpha1/GDNF/PKC alpha 0.03 0.053 -9999 0 -0.097 46 46
GRB2 0.023 0.006 -9999 0 -0.12 1 1
PRKACA 0.021 0.017 -9999 0 -0.12 8 8
GDNF 0.023 0.009 -9999 0 -0.12 2 2
RAC1 0.023 0.002 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.044 0.039 -9999 0 -0.096 13 13
Rac1/GTP 0.032 0.05 -9999 0 -0.21 6 6
RET9/GFRalpha1/GDNF 0.023 0.026 -9999 0 -0.12 2 2
GFRalpha1/GDNF 0.025 0.032 -9999 0 -0.14 2 2
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.029 0.054 -9999 0 -0.15 39 39
PDGFRB 0.01 0.042 -9999 0 -0.12 52 52
SPHK1 0.001 0.015 -9999 0 -10000 0 0
mol:S1P 0.015 0.027 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.023 0.07 -9999 0 -0.31 13 13
GNAO1 0.01 0.042 -9999 0 -0.12 51 51
PDGFB-D/PDGFRB/PLCgamma1 0.009 0.086 -9999 0 -0.26 25 25
PLCG1 0.021 0.07 -9999 0 -0.28 17 17
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.01 0.042 -9999 0 -0.12 52 52
GNAI2 0.022 0.011 -9999 0 -0.12 3 3
GNAI3 0.022 0.009 -9999 0 -0.12 1 1
GNAI1 0.012 0.035 -9999 0 -0.12 35 35
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.023 0.047 -9999 0 -0.19 9 9
S1P1/S1P 0.025 0.052 -9999 0 -0.2 11 11
negative regulation of cAMP metabolic process 0.023 0.069 -9999 0 -0.3 13 13
MAPK3 0.021 0.09 -9999 0 -0.42 14 14
calcium-dependent phospholipase C activity -0.001 0.001 -9999 0 -10000 0 0
Rac1/GDP 0.016 0.015 -9999 0 -0.15 5 5
RhoA/GDP 0.016 0.016 -9999 0 -0.14 6 6
KDR 0.025 0.022 -9999 0 -0.11 12 12
PLCB2 0.026 0.049 -9999 0 -0.19 9 9
RAC1 0.023 0.002 -9999 0 -10000 0 0
RhoA/GTP 0.021 0.046 -9999 0 -0.19 11 11
receptor internalization 0.024 0.05 -9999 0 -0.19 11 11
PTGS2 0.001 0.14 -9999 0 -0.92 9 9
Rac1/GTP 0.021 0.045 -9999 0 -0.19 9 9
RHOA 0.023 0.006 -9999 0 -0.12 1 1
VEGFA 0.023 0.022 -9999 0 -0.12 12 12
negative regulation of T cell proliferation 0.023 0.069 -9999 0 -0.3 13 13
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.022 0.011 -9999 0 -0.12 3 3
MAPK1 0.021 0.091 -9999 0 -0.42 14 14
S1P1/S1P/PDGFB-D/PDGFRB 0.028 0.065 -9999 0 -0.24 11 11
ABCC1 0.021 0.018 -9999 0 -0.12 8 8
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.022 0.011 -9999 0 -0.12 3 3
Syndecan-3/Src/Cortactin -0.001 0.076 -9999 0 -0.33 10 10
Syndecan-3/Neurocan 0.02 0.052 -9999 0 -0.47 5 5
POMC 0.022 0.011 -9999 0 -0.12 3 3
EGFR 0.015 0.03 -9999 0 -0.12 25 25
Syndecan-3/EGFR 0.016 0.054 -9999 0 -0.47 5 5
AGRP 0.023 0 -9999 0 -10000 0 0
NCSTN 0.022 0.012 -9999 0 -0.12 4 4
PSENEN 0.016 0.03 -9999 0 -0.12 24 24
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.014 0.032 -9999 0 -0.12 29 29
APH1A 0.023 0.009 -9999 0 -0.12 2 2
NCAN 0.022 0.011 -9999 0 -0.12 3 3
long-term memory 0.017 0.065 -9999 0 -0.36 8 8
Syndecan-3/IL8 0.011 0.056 -9999 0 -0.49 5 5
PSEN1 0.022 0.008 -9999 0 -0.12 1 1
Src/Cortactin 0.03 0.027 -9999 0 -0.14 12 12
FYN 0.011 0.037 -9999 0 -0.12 40 40
limb bud formation 0.006 0.052 -9999 0 -0.49 5 5
MC4R 0 0 -9999 0 -10000 0 0
SRC 0.023 0.009 -9999 0 -0.12 2 2
PTN -0.009 0.055 -9999 0 -0.12 106 106
FGFR/FGF/Syndecan-3 0.006 0.052 -9999 0 -0.49 5 5
neuron projection morphogenesis -0.006 0.068 -9999 0 -0.36 8 8
Syndecan-3/AgRP 0.021 0.051 -9999 0 -0.47 5 5
Syndecan-3/AgRP/MC4R 0.019 0.049 -9999 0 -0.45 5 5
Fyn/Cortactin 0.011 0.056 -9999 0 -0.14 51 51
SDC3 0.006 0.052 -9999 0 -0.5 5 5
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration 0.011 0.055 -9999 0 -0.48 5 5
IL8 0.004 0.047 -9999 0 -0.12 69 69
Syndecan-3/Fyn/Cortactin 0.018 0.066 -9999 0 -0.37 8 8
Syndecan-3/CASK 0.005 0.049 -9999 0 -0.47 5 5
alpha-MSH/MC4R 0.017 0.007 -9999 0 -0.077 3 3
Gamma Secretase 0.034 0.067 -9999 0 -0.18 14 14
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.026 0.057 -9999 0 -0.28 10 10
VEGFR1 homodimer/NRP1 0.014 0.05 -9999 0 -0.4 5 5
mol:DAG 0.022 0.05 -9999 0 -0.26 10 10
VEGFR1 homodimer/NRP1/VEGFR 121 0.019 0.06 -9999 0 -0.29 10 10
CaM/Ca2+ 0.032 0.053 -9999 0 -0.23 12 12
HIF1A 0.029 0.033 -9999 0 -0.23 7 7
GAB1 0.02 0.021 -9999 0 -0.12 12 12
AKT1 0.014 0.072 -9999 0 -0.23 28 28
PLCG1 0.022 0.05 -9999 0 -0.26 10 10
NOS3 0.029 0.061 -9999 0 -0.26 12 12
CBL 0.023 0.006 -9999 0 -0.12 1 1
mol:NO 0.029 0.059 -9999 0 -0.26 12 12
FLT1 0.027 0.05 -9999 0 -0.47 5 5
PGF 0.021 0.018 -9999 0 -0.12 9 9
VEGFR1 homodimer/NRP2/VEGFR121 0.015 0.077 -9999 0 -0.24 22 22
CALM1 0.022 0.014 -9999 0 -0.12 5 5
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
eNOS/Hsp90 0.039 0.063 -9999 0 -0.25 14 14
endothelial cell proliferation 0.006 0.068 -9999 0 -0.26 19 19
mol:Ca2+ 0.022 0.05 -9999 0 -0.26 10 10
MAPK3 0.016 0.045 -9999 0 -0.21 12 12
MAPK1 0.016 0.046 -9999 0 -0.2 14 14
PIK3R1 0.015 0.031 -9999 0 -0.12 27 27
PLGF homodimer 0.021 0.018 -9999 0 -0.12 9 9
PRKACA 0.021 0.017 -9999 0 -0.12 8 8
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 0.012 0.039 -9999 0 -0.12 43 43
VEGFA homodimer 0.019 0.021 -9999 0 -0.12 11 11
VEGFR1 homodimer/VEGFA homodimer 0.026 0.06 -9999 0 -0.32 10 10
platelet activating factor biosynthetic process 0.017 0.044 -9999 0 -0.2 13 13
PI3K 0.032 0.074 -9999 0 -0.23 22 22
PRKCA 0.016 0.047 -9999 0 -0.23 11 11
PRKCB 0.016 0.045 -9999 0 -0.24 10 10
VEGFR1 homodimer/PLGF homodimer 0.029 0.054 -9999 0 -0.36 6 6
VEGFA 0.019 0.021 -9999 0 -0.12 11 11
VEGFB 0.015 0.033 -9999 0 -0.12 30 30
mol:IP3 0.022 0.05 -9999 0 -0.26 10 10
RASA1 0.02 0.052 -9999 0 -0.24 14 14
NRP2 0.011 0.036 -9999 0 -0.12 38 38
VEGFR1 homodimer 0.027 0.05 -9999 0 -0.47 5 5
VEGFB homodimer 0.015 0.033 -9999 0 -0.12 30 30
NCK1 0.02 0.019 -9999 0 -0.12 9 9
eNOS/Caveolin-1 0.034 0.064 -9999 0 -0.25 13 13
PTPN11 0.022 0.011 -9999 0 -0.12 3 3
mol:PI-3-4-5-P3 0.03 0.073 -9999 0 -0.23 22 22
mol:L-citrulline 0.029 0.059 -9999 0 -0.26 12 12
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.034 0.073 -9999 0 -0.23 18 18
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.024 0.072 -9999 0 -0.26 17 17
CD2AP 0.02 0.017 -9999 0 -0.12 7 7
PI3K/GAB1 0.037 0.077 -9999 0 -0.22 25 25
PDPK1 0.015 0.063 -9999 0 -0.22 24 24
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.028 0.07 -9999 0 -0.25 19 19
mol:NADP 0.029 0.059 -9999 0 -0.26 12 12
HSP90AA1 0.023 0.003 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.033 0.071 -9999 0 -0.23 18 18
VEGFR1 homodimer/NRP2 0.02 0.061 -9999 0 -0.3 11 11
Signaling events mediated by HDAC Class II

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 0.052 0.033 -10000 0 -0.098 21 21
HDAC3 0.023 0.002 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.007 0.028 -10000 0 -0.11 36 36
GATA1/HDAC4 0.034 0.004 -10000 0 -0.071 1 1
GATA1/HDAC5 0.034 0.004 -10000 0 -0.071 1 1
GATA2/HDAC5 0.032 0.016 -10000 0 -0.071 13 13
HDAC5/BCL6/BCoR 0.034 0.044 -10000 0 -0.12 41 41
HDAC9 0.015 0.032 -10000 0 -0.12 28 28
Glucocorticoid receptor/Hsp90/HDAC6 0.031 0.047 -10000 0 -0.12 45 45
HDAC4/ANKRA2 0.028 0.031 -10000 0 -0.11 26 26
HDAC5/YWHAB 0.032 0.02 -10000 0 -0.13 8 8
NPC/RanGAP1/SUMO1/Ubc9 0.015 0.037 -10000 0 -0.14 30 30
GATA2 0.02 0.022 -10000 0 -0.12 13 13
HDAC4/RFXANK 0.025 0.037 -10000 0 -0.11 37 37
BCOR 0.023 0.007 -10000 0 -0.12 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.023 0 -10000 0 -10000 0 0
HDAC5 0.023 0 -10000 0 -10000 0 0
GNB1/GNG2 0.026 0.035 -10000 0 -0.12 30 30
Histones 0.026 0.035 -10000 0 -0.12 26 26
ADRBK1 0.023 0.001 -10000 0 -10000 0 0
HDAC4 0.023 0 -10000 0 -10000 0 0
XPO1 0.022 0.01 -10000 0 -0.12 2 2
HDAC5/ANKRA2 0.028 0.031 -10000 0 -0.11 26 26
HDAC4/Ubc9 0.034 0.007 -10000 0 -0.14 1 1
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.031 0.023 -10000 0 -0.11 13 13
TUBA1B 0.023 0 -10000 0 -10000 0 0
HDAC6 0.019 0.023 -10000 0 -0.12 15 15
HDAC5/RFXANK 0.025 0.037 -10000 0 -0.11 37 37
CAMK4 0.016 0.031 -10000 0 -0.12 27 27
Tubulin/HDAC6 0.043 0.02 -10000 0 -10000 0 0
SUMO1 0.023 0.009 -10000 0 -0.12 2 2
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.023 0.007 -10000 0 -0.12 1 1
GATA1 0.023 0.006 -10000 0 -0.12 1 1
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.022 0.014 -10000 0 -0.12 5 5
NR3C1 0.021 0.015 -10000 0 -0.12 5 5
SUMO1/HDAC4 0.036 0.035 -10000 0 -0.17 6 6
SRF 0.018 0.026 -10000 0 -0.12 19 19
HDAC4/YWHAB 0.032 0.02 -10000 0 -0.13 8 8
Tubulin 0.033 0.012 -10000 0 -0.071 8 8
HDAC4/14-3-3 E 0.031 0.023 -10000 0 -0.11 13 13
GNB1 0.023 0.007 -10000 0 -0.12 1 1
RANGAP1 0.023 0.006 -10000 0 -0.12 1 1
BCL6/BCoR 0.019 0.05 -10000 0 -0.15 41 41
HDAC4/HDAC3/SMRT (N-CoR2) 0.043 0.022 -10000 0 -0.11 6 6
HDAC4/SRF 0.038 0.03 -10000 0 -0.12 5 5
HDAC4/ER alpha 0.018 0.049 -10000 0 -0.12 58 58
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.026 0.035 -10000 0 -0.12 26 26
cell motility 0.043 0.019 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.023 0.001 -10000 0 -10000 0 0
HDAC7/HDAC3 0.016 0.012 -10000 0 -0.15 3 3
BCL6 0.019 0.02 -10000 0 -0.12 10 10
HDAC4/CaMK II delta B 0.023 0 -10000 0 -10000 0 0
Hsp90/HDAC6 0.028 0.031 -10000 0 -0.1 28 28
ESR1 0.018 0.024 -10000 0 -0.12 15 15
HDAC6/HDAC11 0.029 0.028 -10000 0 -0.095 26 26
Ran/GTP/Exportin 1 0.034 0.049 -10000 0 -0.15 30 30
NPC 0.009 0.023 -10000 0 -0.096 27 27
MEF2C 0.02 0.02 -10000 0 -0.12 11 11
RAN 0.023 0.002 -10000 0 -10000 0 0
HDAC4/MEF2C 0.059 0.037 -10000 0 -0.091 22 22
GNG2 0.02 0.018 -10000 0 -0.12 9 9
NCOR2 0.019 0.023 -10000 0 -0.12 15 15
TUBB2A 0.021 0.017 -10000 0 -0.12 8 8
HDAC11 0.022 0.012 -10000 0 -0.12 4 4
HSP90AA1 0.023 0.003 -10000 0 -10000 0 0
RANBP2 0.022 0.01 -10000 0 -0.12 2 2
ANKRA2 0.02 0.021 -10000 0 -0.12 12 12
RFXANK 0.018 0.024 -10000 0 -0.12 16 16
nuclear import -0.034 0.033 0.16 14 -10000 0 14
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 0.036 0.054 -9999 0 -0.1 60 60
MAP4K1 0.02 0.023 -9999 0 -0.12 14 14
MAP3K8 0.023 0.009 -9999 0 -0.12 2 2
PRKCB 0 0 -9999 0 -10000 0 0
DBNL 0.023 0.006 -9999 0 -0.12 1 1
CRKL 0.023 0.009 -9999 0 -0.12 2 2
MAP3K1 0.021 0.053 -9999 0 -0.19 9 9
JUN -0.002 0.093 -9999 0 -0.5 17 17
MAP3K7 0.021 0.051 -9999 0 -0.19 7 7
GRAP2 0.022 0.012 -9999 0 -0.12 4 4
CRK 0.021 0.016 -9999 0 -0.12 7 7
MAP2K4 0.021 0.057 -9999 0 -0.2 13 13
LAT 0.022 0.011 -9999 0 -0.12 3 3
LCP2 0.013 0.033 -9999 0 -0.12 31 31
MAPK8 0.004 0.095 -9999 0 -0.52 17 17
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.031 0.037 -9999 0 -0.2 9 9
LAT/GRAP2/SLP76/HPK1/HIP-55 0.044 0.056 -9999 0 -0.14 11 11
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.034 0.028 -9999 0 -0.12 6 6
TC10/GTP 0.031 0.024 -9999 0 -0.17 1 1
Insulin Receptor/Insulin/IRS1/Shp2 0.049 0.042 -9999 0 -0.1 29 29
HRAS 0.023 0.006 -9999 0 -0.12 1 1
APS homodimer 0 0 -9999 0 -10000 0 0
GRB14 0.013 0.036 -9999 0 -0.12 38 38
FOXO3 0.009 0.065 -9999 0 -0.6 6 6
AKT1 0.015 0.048 -9999 0 -0.13 28 28
INSR 0.023 0.017 -9999 0 -0.12 8 8
Insulin Receptor/Insulin 0.06 0.028 -9999 0 -0.16 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.022 0.014 -9999 0 -0.12 5 5
SORBS1 0.02 0.021 -9999 0 -0.12 12 12
CRK 0.021 0.016 -9999 0 -0.12 7 7
PTPN1 0.026 0.021 -9999 0 -0.16 3 3
CAV1 0.02 0.027 -9999 0 -0.091 13 13
CBL/APS/CAP/Crk-II/C3G 0.051 0.024 -9999 0 -0.1 7 7
Insulin Receptor/Insulin/IRS1/NCK2 0.055 0.03 -9999 0 -0.09 13 13
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.025 0.052 -9999 0 -0.094 69 69
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.038 0.053 -9999 0 -0.3 12 12
RPS6KB1 0.014 0.05 -9999 0 -0.14 32 32
PARD6A 0.023 0.009 -9999 0 -0.12 2 2
CBL 0.023 0.006 -9999 0 -0.12 1 1
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0.009 0.074 -9999 0 -0.68 6 6
PIK3R1 0.015 0.031 -9999 0 -0.12 27 27
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.026 0.056 -9999 0 -0.16 22 22
HRAS/GTP -0.007 0.02 -9999 0 -0.12 6 6
Insulin Receptor 0.023 0.017 -9999 0 -0.12 8 8
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.063 0.034 -9999 0 -0.09 12 12
PRKCI -0.012 0.13 -9999 0 -0.38 63 63
Insulin Receptor/Insulin/GRB14/PDK1 0.007 0.046 -9999 0 -0.14 25 25
SHC1 0.023 0.001 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0.021 0.079 -9999 0 -0.38 13 13
PI3K 0.033 0.057 -9999 0 -0.095 69 69
NCK2 0.023 0.006 -9999 0 -0.12 1 1
RHOQ 0.021 0.017 -9999 0 -0.12 8 8
mol:H2O2 0 0.002 -9999 0 -10000 0 0
HRAS/GDP 0.017 0.008 -9999 0 -0.11 2 2
AKT2 0.015 0.049 -9999 0 -0.13 27 27
PRKCZ 0.028 0.063 -9999 0 -0.36 13 13
SH2B2 0 0 -9999 0 -10000 0 0
SHC/SHIP 0.025 0.02 -9999 0 -0.079 13 13
F2RL2 0.019 0.023 -9999 0 -0.12 15 15
TRIP10 0.021 0.018 -9999 0 -0.12 9 9
Insulin Receptor/Insulin/Shc 0.044 0.02 -9999 0 -0.095 7 7
TC10/GTP/CIP4/Exocyst 0.026 0.027 -9999 0 -0.12 14 14
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.057 0.046 -9999 0 -0.16 5 5
RAPGEF1 0.023 0 -9999 0 -10000 0 0
RASA1 0.021 0.012 -9999 0 -0.12 3 3
NCK1 0.02 0.019 -9999 0 -0.12 9 9
CBL/APS/CAP/Crk-II 0.04 0.024 -9999 0 -0.11 7 7
TC10/GDP 0.014 0.022 -9999 0 -0.11 16 16
Insulin Receptor/Insulin/SHC/GRB10 0.056 0.029 -9999 0 -0.092 15 15
INPP5D 0.012 0.018 -9999 0 -0.086 12 12
SOS1 0.017 0.027 -9999 0 -0.12 20 20
SGK1 -0.002 0.004 -9999 0 -10000 0 0
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.022 0.011 -9999 0 -0.12 3 3
IRS1 0.019 0.023 -9999 0 -0.12 14 14
p62DOK/RasGAP 0.021 0.08 -9999 0 -0.38 13 13
INS 0.024 0.011 -9999 0 -0.12 3 3
mol:PI-3-4-P2 0.011 0.018 -9999 0 -0.085 12 12
GRB2 0.023 0.006 -9999 0 -0.12 1 1
EIF4EBP1 0.015 0.046 -9999 0 -0.12 31 31
PTPRA 0.024 0.012 -9999 0 -0.12 4 4
PIK3CA 0.02 0.017 -9999 0 -0.12 7 7
TC10/GTP/CIP4 0.026 0.027 -9999 0 -0.12 14 14
PDPK1 0.023 0.007 -9999 0 -0.12 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.027 0.048 -9999 0 -0.22 5 5
Insulin Receptor/Insulin/IRS1 0.04 0.027 -9999 0 -0.094 12 12
Insulin Receptor/Insulin/IRS3 0.034 0.024 -9999 0 -0.13 7 7
Par3/Par6 0.045 0.032 -9999 0 -0.089 18 18
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.022 0.011 -9999 0 -0.12 3 3
SPHK1 0.022 0.015 -9999 0 -0.12 6 6
GNAI2 0.022 0.011 -9999 0 -0.12 3 3
mol:S1P 0.019 0.029 -9999 0 -0.18 11 11
GNAO1 0.01 0.042 -9999 0 -0.12 51 51
mol:Sphinganine-1-P 0.022 0.012 -9999 0 -0.071 9 9
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.037 0.033 -9999 0 -0.14 12 12
GNAI3 0.021 0.008 -9999 0 -0.12 1 1
G12/G13 0.03 0.028 -9999 0 -0.13 16 16
S1PR3 0 0 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0.021 0.016 -9999 0 -0.12 7 7
S1P1/S1P 0.028 0.028 -9999 0 -0.14 12 12
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
GNAI1 0.012 0.035 -9999 0 -0.12 35 35
S1P/S1P5/G12 0.026 0.024 -9999 0 -0.13 12 12
S1P/S1P3/Gq 0.022 0.057 -9999 0 -0.22 26 26
S1P/S1P4/Gi 0.002 0.074 -9999 0 -0.16 86 86
GNAQ 0.021 0.016 -9999 0 -0.12 6 6
GNAZ 0.022 0.011 -9999 0 -0.12 3 3
GNA14 0.02 0.02 -9999 0 -0.12 11 11
GNA15 0.021 0.017 -9999 0 -0.12 8 8
GNA12 0.023 0.001 -9999 0 -10000 0 0
GNA13 0.022 0.009 -9999 0 -0.12 2 2
GNA11 0.022 0.014 -9999 0 -0.12 5 5
ABCC1 0.021 0.017 -9999 0 -0.12 8 8
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.021 0.074 -10000 0 -0.21 24 24
CaM/Ca2+ 0.014 0.02 -10000 0 -0.12 12 12
AKT1 0.021 0.019 -10000 0 -0.12 10 10
AKT2 0.019 0.025 -10000 0 -0.12 17 17
STXBP4 0.018 0.026 -10000 0 -0.12 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.015 0.067 0.18 6 -0.2 19 25
YWHAZ 0.023 0.003 -10000 0 -10000 0 0
CALM1 0.022 0.014 -10000 0 -0.12 5 5
YWHAQ 0.023 0.003 -10000 0 -10000 0 0
TBC1D4 0.02 0.017 -10000 0 -0.071 20 20
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.021 0.014 -10000 0 -0.12 5 5
YWHAB 0.023 0.007 -10000 0 -0.12 1 1
SNARE/Synip 0.033 0.041 -10000 0 -0.13 19 19
YWHAG 0.02 0.022 -10000 0 -0.12 13 13
ASIP 0.021 0.015 -10000 0 -0.12 6 6
PRKCI 0.016 0.028 -10000 0 -0.12 22 22
AS160/CaM/Ca2+ 0.014 0.02 -10000 0 -0.12 12 12
RHOQ 0.021 0.017 -10000 0 -0.12 8 8
GYS1 0.025 0.017 -10000 0 -0.22 1 1
PRKCZ 0.023 0 -10000 0 -10000 0 0
TRIP10 0.021 0.018 -10000 0 -0.12 9 9
TC10/GTP/CIP4/Exocyst 0.026 0.027 -10000 0 -0.12 14 14
AS160/14-3-3 0.024 0.064 -10000 0 -0.26 17 17
VAMP2 0.015 0.033 -10000 0 -0.12 30 30
SLC2A4 0.015 0.072 0.18 6 -0.23 16 22
STX4 0.022 0.012 -10000 0 -0.12 4 4
GSK3B 0.023 0.03 -10000 0 -0.2 7 7
SFN 0.014 0.032 -10000 0 -0.12 29 29
LNPEP 0.016 0.027 -10000 0 -0.12 20 20
YWHAE 0.022 0.014 -10000 0 -0.12 5 5
Effects of Botulinum toxin

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
STX1A 0.011 0.006 -9999 0 -0.077 3 3
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B 0.032 0.016 -9999 0 -0.085 10 10
STXBP1 0.02 0.02 -9999 0 -0.12 11 11
ACh/CHRNA1 0.013 0.025 -9999 0 -0.063 49 49
RAB3GAP2/RIMS1/UNC13B 0.041 0.029 -9999 0 -0.11 16 16
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 0.023 0.006 -9999 0 -0.12 1 1
mol:ACh 0.005 0.01 -9999 0 -0.074 3 3
RAB3GAP2 0.022 0.009 -9999 0 -0.12 2 2
STX1A/SNAP25/VAMP2 0.039 0.031 -9999 0 -0.1 8 8
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction 0.013 0.025 -9999 0 -0.063 49 49
UNC13B 0.021 0.016 -9999 0 -0.12 7 7
CHRNA1 0.011 0.04 -9999 0 -0.12 47 47
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 0.015 0.023 -9999 0 -0.062 39 39
SNAP25 0.004 0.017 -9999 0 -0.19 1 1
VAMP2 0.004 0.016 -9999 0 -0.18 2 2
SYT1 0.014 0.036 -9999 0 -0.12 36 36
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 0.024 0.013 -9999 0 -0.057 14 14
STX1A/SNAP25 fragment 1/VAMP2 0.039 0.031 -9999 0 -0.1 8 8
IL27-mediated signaling events

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
TGFB1 0.025 0.035 -10000 0 -0.4 2 2
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response -0.002 0.086 0.35 19 -10000 0 19
IL27/IL27R/JAK1 0.029 0.089 -10000 0 -0.95 2 2
TBX21 0 0.077 -10000 0 -0.53 3 3
IL12B 0.024 0.002 -10000 0 -10000 0 0
IL12A 0 0.029 -10000 0 -0.077 70 70
IL6ST 0.016 0.027 -10000 0 -0.12 19 19
IL27RA/JAK1 0.012 0.073 -10000 0 -1.1 2 2
IL27 0.023 0.004 -10000 0 -10000 0 0
TYK2 0.021 0.017 -10000 0 -0.12 7 7
T-helper cell lineage commitment 0.013 0.09 -10000 0 -1.2 2 2
T-helper 2 cell differentiation -0.002 0.086 0.35 19 -10000 0 19
T cell proliferation during immune response -0.002 0.086 0.35 19 -10000 0 19
MAPKKK cascade 0.002 0.086 -10000 0 -0.35 19 19
STAT3 0.022 0.011 -10000 0 -0.12 3 3
STAT2 0.02 0.019 -10000 0 -0.12 9 9
STAT1 0.014 0.031 -10000 0 -0.12 26 26
IL12RB1 0.023 0.006 -10000 0 -0.12 1 1
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0 0.08 -10000 0 -0.55 3 3
IL27/IL27R/JAK2/TYK2 0.002 0.086 -10000 0 -0.35 19 19
positive regulation of T cell mediated cytotoxicity 0.002 0.086 -10000 0 -0.35 19 19
STAT1 (dimer) 0.015 0.11 -10000 0 -0.92 2 2
JAK2 0.016 0.025 -10000 0 -0.12 16 16
JAK1 0.022 0.01 -10000 0 -0.12 2 2
STAT2 (dimer) 0.004 0.094 -10000 0 -0.36 17 17
T cell proliferation 0 0.084 -10000 0 -0.34 17 17
IL12/IL12R/TYK2/JAK2 0.026 0.066 -10000 0 -0.72 1 1
IL17A 0.013 0.09 -10000 0 -1.2 2 2
mast cell activation -0.002 0.086 0.35 19 -10000 0 19
IFNG 0.003 0.021 -10000 0 -0.068 6 6
T cell differentiation -0.001 0.003 -10000 0 -0.02 3 3
STAT3 (dimer) 0.004 0.094 -10000 0 -0.36 16 16
STAT5A (dimer) 0.006 0.091 -10000 0 -0.35 16 16
STAT4 (dimer) 0.006 0.091 -10000 0 -0.35 16 16
STAT4 0.02 0.02 -10000 0 -0.12 11 11
T cell activation -0.006 0.011 0.12 2 -10000 0 2
IL27R/JAK2/TYK2 0.009 0.094 -10000 0 -0.98 2 2
GATA3 0.014 0.029 -10000 0 -10000 0 0
IL18 0 0.028 -10000 0 -0.077 66 66
positive regulation of mast cell cytokine production 0.004 0.092 -10000 0 -0.36 16 16
IL27/EBI3 0.034 0.009 -10000 0 -10000 0 0
IL27RA -0.001 0.076 -10000 0 -1.1 2 2
IL6 0.012 0.054 -10000 0 -0.33 3 3
STAT5A 0.022 0.013 -10000 0 -0.12 4 4
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 0.005 0.041 0.46 2 -10000 0 2
IL1B 0.003 0.024 -10000 0 -0.077 45 45
EBI3 0.023 0.008 -10000 0 -0.12 1 1
TNF 0.01 0.012 -10000 0 -0.077 11 11
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.019 0.02 -9999 0 -0.12 10 10
Ran/GTP/Exportin 1/HDAC4 -0.008 0.033 -9999 0 -0.15 26 26
MDM2/SUMO1 0.032 0.041 -9999 0 -0.18 8 8
HDAC4 0.023 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.013 0.043 -9999 0 -0.17 30 30
SUMO1 0.023 0.009 -9999 0 -0.12 2 2
NPC/RanGAP1/SUMO1 0.01 0.036 -9999 0 -0.14 29 29
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.02 0.03 -9999 0 -0.13 17 17
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.023 0.002 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.022 0.01 -9999 0 -0.12 2 2
SUMO1/HDAC4 0.036 0.035 -9999 0 -0.17 6 6
SUMO1/HDAC1 0.029 0.048 -9999 0 -0.19 13 13
RANGAP1 0.023 0.006 -9999 0 -0.12 1 1
MDM2/SUMO1/SUMO1 0.047 0.043 -9999 0 -0.11 31 31
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.015 0.037 -9999 0 -0.14 30 30
Ran/GTP 0.026 0.036 -9999 0 -0.12 30 30
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.02 0.02 -9999 0 -0.12 11 11
UBE2I 0.023 0.001 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.025 0.047 -9999 0 -0.15 30 30
NPC 0.009 0.023 -9999 0 -0.096 27 27
PIAS2 0.021 0.017 -9999 0 -0.12 8 8
PIAS1 0.022 0.009 -9999 0 -0.12 2 2
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.022 0.17 -9999 0 -0.68 14 14
NCK1/PAK1/Dok-R -0.028 0.072 -9999 0 -0.32 15 15
NCK1/Dok-R 0.049 0.087 -9999 0 -0.84 2 2
PIK3CA 0.019 0.017 -9999 0 -0.12 7 7
mol:beta2-estradiol -0.008 0.012 -9999 0 -10000 0 0
RELA 0.023 0.009 -9999 0 -0.12 2 2
SHC1 0.024 0.002 -9999 0 -10000 0 0
Rac/GDP 0.016 0.015 -9999 0 -0.15 5 5
F2 0.014 0.02 -9999 0 -0.14 4 4
TNIP2 0.021 0.017 -9999 0 -0.12 8 8
NF kappa B/RelA 0.057 0.087 -9999 0 -0.79 2 2
FN1 -0.013 0.056 -9999 0 -0.12 114 114
PLD2 0.041 0.076 -9999 0 -0.87 2 2
PTPN11 0.022 0.011 -9999 0 -0.12 3 3
GRB14 0.013 0.036 -9999 0 -0.12 38 38
ELK1 0.044 0.074 -9999 0 -0.82 2 2
GRB7 0.018 0.026 -9999 0 -0.12 18 18
PAK1 0.016 0.029 -9999 0 -0.12 23 23
Tie2/Ang1/alpha5/beta1 Integrin 0.013 0.1 -9999 0 -0.7 3 3
CDKN1A 0.027 0.18 -9999 0 -0.61 41 41
ITGA5 0.013 0.036 -9999 0 -0.12 38 38
mol:GTP 0 0 -9999 0 -10000 0 0
RasGAP/Dok-R 0.051 0.084 -9999 0 -0.84 2 2
CRK 0.021 0.016 -9999 0 -0.12 7 7
mol:NO 0.03 0.14 -9999 0 -0.5 17 17
PLG 0.041 0.077 -9999 0 -0.87 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
chemokinesis 0.036 0.14 -9999 0 -0.74 6 6
GRB2 0.023 0.006 -9999 0 -0.12 1 1
PIK3R1 0.015 0.031 -9999 0 -0.12 27 27
ANGPT2 -0.029 0.27 -9999 0 -1 39 39
BMX 0.041 0.077 -9999 0 -0.87 2 2
ANGPT1 0.022 0.048 -9999 0 -10000 0 0
tube development 0.009 0.2 -9999 0 -0.69 41 41
ANGPT4 0.023 0.01 -9999 0 -0.12 2 2
response to hypoxia 0.002 0.008 -9999 0 -0.061 2 2
Tie2/Ang1/GRB14 0.043 0.083 -9999 0 -0.88 2 2
alpha5/beta1 Integrin 0.016 0.048 -9999 0 -0.1 76 76
FGF2 0.023 0.01 -9999 0 -0.12 2 2
STAT5A (dimer) 0.024 0.23 -9999 0 -0.78 41 41
mol:L-citrulline 0.03 0.14 -9999 0 -0.5 17 17
AGTR1 0.021 0.017 -9999 0 -0.12 4 4
MAPK14 0.037 0.12 -9999 0 -1 4 4
Tie2/SHP2 0.036 0.083 -9999 0 -0.67 4 4
TEK 0.033 0.088 -9999 0 -0.72 4 4
RPS6KB1 0.025 0.15 -9999 0 -0.71 9 9
Angiotensin II/AT1 0.016 0.018 -9999 0 -0.079 4 4
Tie2/Ang1/GRB2 0.048 0.081 -9999 0 -0.88 2 2
MAPK3 0.042 0.073 -9999 0 -0.81 2 2
MAPK1 0.041 0.074 -9999 0 -0.81 2 2
Tie2/Ang1/GRB7 0.045 0.083 -9999 0 -0.88 2 2
NFKB1 0.021 0.013 -9999 0 -0.12 4 4
MAPK8 0.039 0.077 -9999 0 -0.87 2 2
PI3K 0.024 0.16 -9999 0 -0.92 6 6
FES 0.045 0.097 -9999 0 -1 2 2
Crk/Dok-R 0.055 0.082 -9999 0 -0.84 2 2
Tie2/Ang1/ABIN2 0.047 0.081 -9999 0 -0.88 2 2
blood circulation 0 0 -9999 0 -10000 0 0
negative regulation of caspase activity 0.024 0.16 -9999 0 -0.58 17 17
STAT5A 0.022 0.013 -9999 0 -0.12 4 4
mol:ROS 0 0 -9999 0 -10000 0 0
PTK2 0.024 0.15 -9999 0 -0.74 7 7
Tie2/Ang2 0.002 0.27 -9999 0 -0.93 41 41
Tie2/Ang1 0.04 0.081 -9999 0 -0.92 2 2
FOXO1 0.02 0.18 -9999 0 -0.6 41 41
ELF1 0.03 0.014 -9999 0 -0.098 3 3
ELF2 0.041 0.078 -9999 0 -0.88 2 2
mol:Choline 0.041 0.075 -9999 0 -0.84 2 2
cell migration -0.02 0.045 -9999 0 -0.18 19 19
FYN 0.003 0.23 -9999 0 -0.79 41 41
DOK2 0.02 0.021 -9999 0 -0.12 12 12
negative regulation of cell cycle 0.029 0.17 -9999 0 -0.55 41 41
ETS1 0.022 0.035 -9999 0 -0.12 27 27
PXN 0.028 0.14 -9999 0 -0.57 9 9
ITGB1 0.021 0.015 -9999 0 -0.12 6 6
NOS3 0.028 0.15 -9999 0 -0.56 17 17
RAC1 0.023 0.002 -9999 0 -10000 0 0
TNF 0.028 0.025 -9999 0 -0.12 11 11
MAPKKK cascade 0.041 0.075 -9999 0 -0.84 2 2
RASA1 0.021 0.012 -9999 0 -0.12 3 3
Tie2/Ang1/Shc 0.049 0.082 -9999 0 -0.88 2 2
NCK1 0.02 0.019 -9999 0 -0.12 9 9
vasculogenesis 0.031 0.13 -9999 0 -0.45 17 17
mol:Phosphatidic acid 0.041 0.075 -9999 0 -0.84 2 2
mol:Angiotensin II -0.001 0.009 -9999 0 -10000 0 0
mol:NADP 0.03 0.14 -9999 0 -0.5 17 17
Rac1/GTP 0.03 0.14 -9999 0 -0.66 8 8
MMP2 0.015 0.083 -9999 0 -0.87 2 2
Aurora C 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
INCENP 0.023 0.009 -9999 0 -0.12 2 2
Aurora C/Aurora B/INCENP 0.033 0.036 -9999 0 -0.097 32 32
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.003 0.069 -9999 0 -0.39 16 16
AURKB 0.017 0.027 -9999 0 -0.12 19 19
AURKC 0.023 0.006 -9999 0 -0.12 1 1
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.022 0.007 -10000 0 -0.12 1 1
SMAD2 0.015 0.036 0.19 2 -0.16 9 11
SMAD3 0.027 0.046 -10000 0 -0.29 4 4
SMAD3/SMAD4 -0.013 0.16 -10000 0 -0.37 81 81
SMAD4/Ubc9/PIASy 0.043 0.027 -10000 0 -0.12 15 15
SMAD2/SMAD2/SMAD4 0.034 0.063 0.17 2 -0.17 18 20
PPM1A 0.023 0.001 -10000 0 -10000 0 0
CALM1 0.022 0.014 -10000 0 -0.12 5 5
SMAD2/SMAD4 0.027 0.032 0.16 2 -0.14 8 10
MAP3K1 0.021 0.015 -10000 0 -0.12 6 6
TRAP-1/SMAD4 0.025 0.041 -10000 0 -0.14 30 30
MAPK3 0.022 0.014 -10000 0 -0.12 5 5
MAPK1 0.021 0.016 -10000 0 -0.12 7 7
NUP214 0.023 0.007 -10000 0 -0.12 1 1
CTDSP1 0.022 0.011 -10000 0 -0.12 3 3
CTDSP2 0.022 0.01 -10000 0 -0.12 2 2
CTDSPL 0.023 0.006 -10000 0 -0.12 1 1
KPNB1 0.022 0.009 -10000 0 -0.12 2 2
TGFBRAP1 0.022 0.007 -10000 0 -0.12 1 1
UBE2I 0.023 0.001 -10000 0 -10000 0 0
NUP153 0.02 0.019 -10000 0 -0.12 9 9
KPNA2 0.017 0.024 -10000 0 -0.12 15 15
PIAS4 0.023 0 -10000 0 -10000 0 0
Glypican 2 network

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
MDK 0.021 0.014 -9999 0 -0.12 5 5
GPC2 0.023 0.009 -9999 0 -0.12 2 2
GPC2/Midkine 0.029 0.031 -9999 0 -0.14 16 16
neuron projection morphogenesis 0.029 0.031 -9999 0 -0.14 16 16
Alternative NF-kappaB pathway

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
IKK alpha homodimer 0.024 0.04 -9999 0 -0.14 30 30
FBXW11 0.023 0.003 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.023 0.003 -9999 0 -10000 0 0
CHUK 0.021 0.013 -9999 0 -0.12 4 4
NF kappa B2 p100/RelB 0.055 0.045 -9999 0 -0.16 5 5
NFKB1 0.021 0.013 -9999 0 -0.12 4 4
MAP3K14 0.023 0.006 -9999 0 -0.12 1 1
NF kappa B1 p50/RelB 0.02 0.048 -9999 0 -0.13 48 48
RELB 0.022 0.011 -9999 0 -0.12 3 3
NFKB2 0.023 0.009 -9999 0 -0.12 2 2
NF kappa B2 p52/RelB 0.029 0.02 -9999 0 -0.1 12 12
regulation of B cell activation 0.028 0.02 -9999 0 -0.1 12 12
Arf1 pathway

Figure S127.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S127.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.019 0.009 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.008 0.035 -9999 0 -0.14 14 14
AP2 0.025 0.04 -9999 0 -0.13 33 33
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.03 0.016 -9999 0 -0.089 10 10
CLTB 0.022 0.014 -9999 0 -0.12 5 5
coatomer protein complex/ARF1/GTP/ER cargo protein 0.02 0.034 -9999 0 -0.16 16 16
CD4 0.016 0.028 -9999 0 -0.12 21 21
CLTA 0.023 0.006 -9999 0 -0.12 1 1
mol:GTP 0 0.002 -9999 0 -10000 0 0
ARFGAP1 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.009 0.009 -9999 0 -0.047 5 5
ARF1/GTP 0.011 0.015 -9999 0 -0.12 2 2
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.02 0.026 -9999 0 -0.15 11 11
mol:Choline 0.009 0.008 -9999 0 -0.046 5 5
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.017 0.028 -9999 0 -0.12 21 21
DDEF1 0.008 0.012 -9999 0 -0.2 1 1
ARF1/GDP 0.009 0.005 -9999 0 -0.063 1 1
AP2M1 0.022 0.005 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0.013 0.019 -9999 0 -0.11 7 7
Rac/GTP 0.016 0.016 -9999 0 -0.15 5 5
ARF1/GTP/GGA3/ARF-GAP1 0.032 0.019 -9999 0 -0.091 3 3
ARFIP2 0.021 0.014 -9999 0 -0.12 5 5
COPA 0.023 0.007 -9999 0 -0.12 1 1
RAC1 0.023 0.002 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.018 0.035 -9999 0 -0.21 11 11
ARF1/GTP/ARHGAP10 0.011 0.016 -9999 0 -0.066 23 23
GGA3 0.022 0.015 -9999 0 -0.12 6 6
ARF1/GTP/Membrin 0.019 0.018 -9999 0 -0.18 2 2
AP2A1 0.021 0.017 -9999 0 -0.12 8 8
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.021 0.033 -9999 0 -0.16 16 16
ARF1/GDP/Membrin 0.021 0.019 -9999 0 -0.29 1 1
Arfaptin 2/Rac/GDP 0.029 0.016 -9999 0 -0.087 10 10
CYTH2 0 0.002 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0.026 0.021 -9999 0 -0.08 9 9
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0.016 0.015 -9999 0 -0.15 5 5
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.006 0.077 -9999 0 -0.26 22 22
PLD2 0.009 0.008 -9999 0 -0.046 5 5
ARF-GAP1/v-SNARE 0.012 0 -9999 0 -10000 0 0
PIP5K1A 0.009 0.009 -9999 0 -0.047 5 5
ARF1/GTP/Membrin/GBF1/p115 0.011 0.028 -9999 0 -0.1 14 14
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0.009 0.008 -9999 0 -0.046 5 5
KDEL Receptor/Ligand/ARF-GAP1 0.012 0 -9999 0 -10000 0 0
GOSR2 0.015 0.016 -9999 0 -0.36 1 1
USO1 -0.01 0.093 -9999 0 -0.36 37 37
GBF1 0.001 0.07 -9999 0 -0.36 21 21
ARF1/GTP/Arfaptin 2 0.027 0.021 -9999 0 -0.062 27 27
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.02 0.062 -9999 0 -0.13 74 74
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.034 0.029 -10000 0 -0.093 20 20
MAPK9 0 0.045 -10000 0 -0.21 25 25
adrenocorticotropin secretion 0.011 0.006 -10000 0 -0.077 3 3
GNB1/GNG2 0.025 0.029 -10000 0 -0.095 30 30
GNB1 0.023 0.007 -10000 0 -0.12 1 1
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 0.03 -10000 0 -0.21 11 11
Gs family/GTP 0.014 0.009 -10000 0 -0.055 9 9
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0 0.002 0.017 9 -10000 0 9
GNAL 0.021 0.018 -10000 0 -0.12 9 9
GNG2 0.02 0.018 -10000 0 -0.12 9 9
CRH 0.022 0.011 -10000 0 -0.12 3 3
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.003 0.038 -10000 0 -0.21 17 17
MAPK11 0.01 0 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 0.016 0.057 -10000 0 -0.29 4 4
CRKL 0.014 0.059 -10000 0 -0.31 4 4
HRAS 0.032 0.067 -10000 0 -0.26 7 7
mol:PIP3 0.004 0.067 0.22 4 -0.32 4 8
SPRED1 0.019 0.016 -10000 0 -0.12 6 6
SPRED2 0.022 0.014 -10000 0 -0.12 5 5
GAB1 0.011 0.061 -10000 0 -0.3 5 5
FOXO3 0.019 0.063 -10000 0 -0.31 6 6
AKT1 0.017 0.064 -10000 0 -0.34 5 5
BAD 0.021 0.061 -10000 0 -0.32 5 5
megakaryocyte differentiation 0.013 0.059 -10000 0 -0.32 4 4
GSK3B 0.02 0.062 -10000 0 -0.33 5 5
RAF1 0.031 0.06 -10000 0 -0.25 6 6
SHC1 0.023 0.001 -10000 0 -10000 0 0
STAT3 0.011 0.062 -10000 0 -0.3 6 6
STAT1 0.013 0.12 -10000 0 -0.72 5 5
HRAS/SPRED1 0.031 0.067 -10000 0 -0.24 8 8
cell proliferation 0.012 0.06 -10000 0 -0.3 6 6
PIK3CA 0.02 0.017 -10000 0 -0.12 7 7
TEC 0.01 0.038 -10000 0 -0.12 43 43
RPS6KB1 0.01 0.077 -10000 0 -0.28 14 14
HRAS/SPRED2 0.037 0.063 -10000 0 -0.22 8 8
LYN/TEC/p62DOK 0.013 0.085 -10000 0 -0.27 15 15
MAPK3 0.03 0.052 -10000 0 -0.26 4 4
STAP1 0.012 0.06 -10000 0 -0.3 5 5
GRAP2 0.022 0.012 -10000 0 -0.12 4 4
JAK2 0.005 0.12 -10000 0 -0.51 12 12
STAT1 (dimer) 0.008 0.13 -10000 0 -0.7 5 5
mol:Gleevec -0.001 0.003 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.031 0.074 -10000 0 -0.29 6 6
actin filament polymerization 0.009 0.059 -10000 0 -0.3 5 5
LYN 0.021 0.013 -10000 0 -0.12 4 4
STAP1/STAT5A (dimer) 0.013 0.09 -10000 0 -0.41 7 7
PIK3R1 0.015 0.031 -10000 0 -0.12 27 27
CBL/CRKL/GRB2 0.034 0.063 -10000 0 -0.34 3 3
PI3K 0.017 0.089 -10000 0 -0.29 16 16
PTEN 0.022 0.008 -10000 0 -0.12 1 1
SCF/KIT/EPO/EPOR 0.032 0.13 -10000 0 -1.3 2 2
MAPK8 0.012 0.061 -10000 0 -0.31 6 6
STAT3 (dimer) 0.012 0.061 -10000 0 -0.3 6 6
positive regulation of transcription 0.028 0.045 -10000 0 -0.21 4 4
mol:GDP 0.031 0.072 -10000 0 -0.28 6 6
PIK3C2B 0.011 0.061 -10000 0 -0.3 5 5
CBL/CRKL 0.025 0.061 -10000 0 -0.36 3 3
FER 0.012 0.06 -10000 0 -0.3 5 5
SH2B3 0.013 0.06 -10000 0 -0.33 4 4
PDPK1 0.007 0.066 0.21 4 -0.26 7 11
SNAI2 0.002 0.065 -10000 0 -0.34 6 6
positive regulation of cell proliferation 0.008 0.11 -10000 0 -0.48 8 8
KITLG 0.02 0.029 -10000 0 -0.12 21 21
cell motility 0.008 0.11 -10000 0 -0.48 8 8
PTPN6 0.021 0.01 -10000 0 -0.12 2 2
EPOR 0.015 0.13 -10000 0 -0.55 22 22
STAT5A (dimer) 0.011 0.094 -10000 0 -0.41 8 8
SOCS1 0.016 0.031 -10000 0 -0.12 27 27
cell migration -0.013 0.059 0.32 4 -10000 0 4
SOS1 0.017 0.027 -10000 0 -0.12 20 20
EPO 0.024 0.008 -10000 0 -0.13 1 1
VAV1 0.02 0.02 -10000 0 -0.12 10 10
GRB10 0.012 0.062 -10000 0 -0.31 6 6
PTPN11 0.021 0.012 -10000 0 -0.12 3 3
SCF/KIT 0.009 0.062 -10000 0 -0.32 5 5
GO:0007205 -0.001 0.004 -10000 0 -10000 0 0
MAP2K1 0.03 0.051 -10000 0 -0.2 6 6
CBL 0.023 0.006 -10000 0 -0.12 1 1
KIT 0.007 0.12 -10000 0 -0.72 4 4
MAP2K2 0.028 0.053 -10000 0 -0.18 8 8
SHC/Grb2/SOS1 0.033 0.071 -10000 0 -0.32 4 4
STAT5A 0.01 0.096 -10000 0 -0.42 8 8
GRB2 0.023 0.006 -10000 0 -0.12 1 1
response to radiation 0.002 0.064 -10000 0 -0.34 6 6
SHC/GRAP2 0.034 0.011 -10000 0 -0.085 5 5
PTPRO 0.013 0.06 -10000 0 -0.33 4 4
SH2B2 0.008 0.059 -10000 0 -0.31 5 5
DOK1 0.021 0.016 -10000 0 -0.12 7 7
MATK 0.013 0.06 -10000 0 -0.33 4 4
CREBBP 0.036 0.031 -10000 0 -0.12 9 9
BCL2 0.009 0.15 -10000 0 -0.62 23 23
Visual signal transduction: Rods

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:K + 0.023 0.009 -9999 0 -0.12 2 2
GNAT1/GTP 0.017 0.006 -9999 0 -0.077 2 2
Metarhodopsin II/Arrestin 0.031 0.007 -9999 0 -0.057 4 4
PDE6G/GNAT1/GTP 0.025 0.024 -9999 0 -0.12 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.023 0.009 -9999 0 -0.12 2 2
GRK1 0 0 -9999 0 -10000 0 0
CNG Channel 0.039 0.024 -9999 0 -0.13 2 2
mol:Na + 0.052 0.02 -9999 0 -0.31 1 1
mol:ADP 0 0 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.042 0.023 -9999 0 -0.11 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel 0.065 0.021 -9999 0 -0.32 1 1
CNGB1 0.023 0.006 -9999 0 -0.12 1 1
RDH5 0.011 0.041 -9999 0 -0.12 48 48
SAG 0.022 0.011 -9999 0 -0.12 3 3
mol:Ca2+ 0.04 0.018 -9999 0 -0.3 1 1
Na + (4 Units) 0.042 0.018 -9999 0 -0.29 1 1
RGS9 0.017 0.029 -9999 0 -0.12 23 23
GNB1/GNGT1 0.03 0.027 -9999 0 -0.1 20 20
GNAT1/GDP 0.05 0.022 -9999 0 -0.089 2 2
GUCY2D 0.022 0.011 -9999 0 -0.12 3 3
GNGT1 0.02 0.023 -9999 0 -0.12 14 14
GUCY2F 0.023 0.006 -9999 0 -0.12 1 1
GNB5 0.023 0.009 -9999 0 -0.12 2 2
mol:GMP (4 units) 0.031 0.023 -9999 0 -0.1 4 4
mol:11-cis-retinal 0.011 0.04 -9999 0 -0.12 48 48
mol:cGMP 0.057 0.019 -9999 0 -0.12 4 4
GNB1 0.023 0.007 -9999 0 -0.12 1 1
Rhodopsin 0.023 0.035 -9999 0 -0.08 57 57
SLC24A1 0.023 0.009 -9999 0 -0.12 2 2
CNGA1 0.022 0.014 -9999 0 -0.12 5 5
Metarhodopsin II 0.015 0.003 -9999 0 -0.055 1 1
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family 0.058 0.019 -9999 0 -0.12 4 4
RGS9BP 0.022 0.011 -9999 0 -0.12 3 3
Metarhodopsin II/Transducin 0.025 0.022 -9999 0 -0.15 7 7
GCAP Family/Ca ++ 0.043 0.015 -9999 0 -0.12 4 4
PDE6A/B 0.033 0.014 -9999 0 -0.071 10 10
mol:Pi 0.042 0.022 -9999 0 -0.11 2 2
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin 0.041 0.023 -9999 0 -0.11 8 8
PDE6B 0.022 0.015 -9999 0 -0.12 6 6
PDE6A 0.022 0.012 -9999 0 -0.12 4 4
PDE6G 0.014 0.035 -9999 0 -0.12 35 35
RHO 0.023 0.006 -9999 0 -0.12 1 1
PDE6 0.056 0.035 -9999 0 -0.15 2 2
GUCA1A 0.022 0.011 -9999 0 -0.12 3 3
GC2/GCAP Family 0.058 0.018 -9999 0 -0.12 4 4
GUCA1C 0.022 0.012 -9999 0 -0.12 4 4
GUCA1B 0.023 0.006 -9999 0 -0.12 1 1
Visual signal transduction: Cones

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Cone Metarhodopsin II/Cone Transducin 0.04 0.013 -9999 0 -0.09 2 2
RGS9BP 0.022 0.011 -9999 0 -0.12 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0 0 -9999 0 -10000 0 0
mol:Na + 0.031 0.004 -9999 0 -0.057 1 1
mol:ADP 0.011 0.004 -9999 0 -0.077 1 1
GNAT2 0.023 0 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.042 0.023 -9999 0 -0.11 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.031 0.004 -9999 0 -10000 0 0
GRK7 0.023 0.006 -9999 0 -0.12 1 1
CNGB3 0.023 0.006 -9999 0 -0.12 1 1
Cone Metarhodopsin II/X-Arrestin 0.017 0.004 -9999 0 -0.077 1 1
mol:Ca2+ 0.025 0.008 -9999 0 -0.1 1 1
Cone PDE6 0.064 0.024 -9999 0 -0.11 2 2
Cone Metarhodopsin II 0.015 0.003 -9999 0 -0.055 1 1
Na + (4 Units) 0.043 0.01 -9999 0 -0.1 1 1
GNAT2/GDP 0.05 0.021 -9999 0 -0.089 2 2
GNB5 0.023 0.009 -9999 0 -0.12 2 2
mol:GMP (4 units) 0.026 0.005 -9999 0 -0.1 1 1
Cone Transducin 0.043 0.014 -9999 0 -0.097 2 2
SLC24A2 0.022 0.014 -9999 0 -0.12 5 5
GNB3/GNGT2 0.032 0.016 -9999 0 -0.085 10 10
GNB3 0.022 0.011 -9999 0 -0.12 3 3
GNAT2/GTP 0.017 0 -9999 0 -10000 0 0
CNGA3 0.023 0 -9999 0 -10000 0 0
ARR3 0.023 0.006 -9999 0 -0.12 1 1
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel 0.031 0.004 -9999 0 -0.057 1 1
mol:Pi 0.042 0.022 -9999 0 -0.11 2 2
Cone CNG Channel 0.057 0.008 -9999 0 -0.14 1 1
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + 0.022 0.014 -9999 0 -0.12 5 5
RGS9 0.017 0.029 -9999 0 -0.12 23 23
PDE6C 0.023 0.006 -9999 0 -0.12 1 1
GNGT2 0.022 0.014 -9999 0 -0.12 5 5
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.023 0.006 -9999 0 -0.12 1 1
Methods & Data
Input

  • Expression Data Normalization = Tumor samples were used to median center the expression data used in this analysis.

  • Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/OV/1551648/2.GDAC_MergeDataFiles.Finished/OV.exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data.data.txt

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

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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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