Ovarian Serous Cystadenocarcinoma: PARADIGM pathway analysis of mRNA expression and copy number 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 107 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
PLK2 and PLK4 events 187
FOXM1 transcription factor network 143
HIF-1-alpha transcription factor network 103
TCGA08_p53 103
Ephrin B reverse signaling 96
Endothelins 92
LPA receptor mediated events 91
Osteopontin-mediated events 89
Wnt signaling 89
Syndecan-1-mediated signaling events 86
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
PLK2 and PLK4 events 187 561 3 -0.011 0.036 1000 -1000 -0.017 -1000
FOXM1 transcription factor network 143 7313 51 -0.52 0.038 1000 -1000 -0.014 -1000
HIF-1-alpha transcription factor network 103 7874 76 -0.048 0.097 1000 -1000 0 -1000
TCGA08_p53 103 727 7 -0.063 0.038 1000 -1000 -0.01 -1000
Ephrin B reverse signaling 96 4638 48 -0.2 0.08 1000 -1000 -0.054 -1000
Endothelins 92 8869 96 -0.18 0.044 1000 -1000 -0.025 -1000
LPA receptor mediated events 91 9351 102 -0.047 0.041 1000 -1000 -0.033 -1000
Osteopontin-mediated events 89 3408 38 -0.18 0.041 1000 -1000 -0.025 -1000
Wnt signaling 89 623 7 -0.019 0.041 1000 -1000 0.001 -1000
Syndecan-1-mediated signaling events 86 2949 34 -0.036 0.04 1000 -1000 -0.01 -1000
amb2 Integrin signaling 82 6781 82 -0.083 0.082 1000 -1000 -0.013 -1000
TRAIL signaling pathway 81 3923 48 -0.022 0.042 1000 -1000 -0.017 -1000
TCGA08_retinoblastoma 81 651 8 -0.012 0.029 1000 -1000 -0.005 -1000
PDGFR-alpha signaling pathway 80 3560 44 -0.12 0.051 1000 -1000 -0.017 -1000
Thromboxane A2 receptor signaling 78 8212 105 -0.15 0.071 1000 -1000 -0.02 -1000
Nectin adhesion pathway 78 4964 63 -0.083 0.063 1000 -1000 -0.015 -1000
Nongenotropic Androgen signaling 77 4047 52 -0.12 0.061 1000 -1000 -0.018 -1000
BARD1 signaling events 76 4338 57 -0.039 0.065 1000 -1000 -0.066 -1000
Syndecan-4-mediated signaling events 76 5144 67 -0.06 0.046 1000 -1000 -0.031 -1000
TCGA08_rtk_signaling 72 1894 26 -0.017 0.04 1000 -1000 -0.019 -1000
Signaling events mediated by the Hedgehog family 71 3742 52 -0.065 0.058 1000 -1000 -0.023 -1000
Paxillin-dependent events mediated by a4b1 70 2550 36 -0.066 0.069 1000 -1000 -0.052 -1000
Ras signaling in the CD4+ TCR pathway 69 1183 17 -0.002 0.054 1000 -1000 -0.004 -1000
Signaling events mediated by PTP1B 68 5180 76 -0.058 0.07 1000 -1000 -0.024 -1000
IL6-mediated signaling events 68 5114 75 -0.14 0.05 1000 -1000 -0.018 -1000
Integrins in angiogenesis 67 5683 84 -0.056 0.057 1000 -1000 -0.017 -1000
IL1-mediated signaling events 66 4126 62 -0.045 0.074 1000 -1000 -0.018 -1000
IL23-mediated signaling events 66 3975 60 -0.16 0.054 1000 -1000 -0.028 -1000
Cellular roles of Anthrax toxin 65 2546 39 -0.079 0.04 1000 -1000 -0.015 -1000
Signaling events mediated by PRL 65 2226 34 -0.018 0.04 1000 -1000 -0.028 -1000
Fc-epsilon receptor I signaling in mast cells 64 6296 97 -0.072 0.046 1000 -1000 -0.036 -1000
Canonical Wnt signaling pathway 64 3276 51 -0.18 0.099 1000 -1000 -0.021 -1000
IGF1 pathway 64 3674 57 -0.022 0.065 1000 -1000 -0.014 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 63 5423 85 -0.16 0.051 1000 -1000 -0.027 -1000
E-cadherin signaling in keratinocytes 63 2711 43 -0.026 0.05 1000 -1000 -0.005 -1000
IL2 signaling events mediated by STAT5 62 1370 22 -0.038 0.047 1000 -1000 -0.003 -1000
IL4-mediated signaling events 61 5569 91 -0.23 0.058 1000 -1000 -0.039 -1000
BMP receptor signaling 60 4902 81 -0.019 0.07 1000 -1000 -0.005 -1000
Syndecan-2-mediated signaling events 59 4075 69 0 0.063 1000 -1000 -0.011 -1000
a4b1 and a4b7 Integrin signaling 59 295 5 0.033 0.039 1000 -1000 0.038 -1000
FoxO family signaling 59 3827 64 -0.2 0.046 1000 -1000 -0.031 -1000
TCR signaling in naïve CD8+ T cells 59 5544 93 -0.082 0.087 1000 -1000 -0.024 -1000
IL12-mediated signaling events 58 5067 87 -0.19 0.061 1000 -1000 -0.019 -1000
Noncanonical Wnt signaling pathway 58 1533 26 -0.031 0.041 1000 -1000 -0.017 -1000
IFN-gamma pathway 57 3890 68 -0.058 0.063 1000 -1000 -0.029 -1000
HIF-2-alpha transcription factor network 57 2477 43 -0.061 0.069 1000 -1000 -0.085 -1000
E-cadherin signaling events 56 280 5 0.035 0.049 1000 -1000 0.038 -1000
Paxillin-independent events mediated by a4b1 and a4b7 55 2052 37 -0.02 0.07 1000 -1000 -0.013 -1000
EPHB forward signaling 55 4715 85 -0.055 0.16 1000 -1000 -0.037 -1000
FAS signaling pathway (CD95) 54 2565 47 -0.057 0.052 1000 -1000 -0.021 -1000
E-cadherin signaling in the nascent adherens junction 54 4162 76 -0.056 0.071 1000 -1000 -0.031 -1000
Retinoic acid receptors-mediated signaling 53 3123 58 -0.079 0.06 1000 -1000 -0.011 -1000
Plasma membrane estrogen receptor signaling 53 4576 86 -0.091 0.087 1000 -1000 -0.014 -1000
BCR signaling pathway 52 5178 99 -0.074 0.069 1000 -1000 -0.024 -1000
ErbB4 signaling events 50 3450 69 -0.07 0.056 1000 -1000 -0.03 -1000
Caspase cascade in apoptosis 49 3673 74 -0.11 0.051 1000 -1000 -0.021 -1000
Presenilin action in Notch and Wnt signaling 49 3007 61 -0.16 0.075 1000 -1000 -0.031 -1000
IL2 signaling events mediated by PI3K 49 2852 58 -0.064 0.041 1000 -1000 -0.018 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 49 2238 45 -0.058 0.075 1000 -1000 -0.017 -1000
Class I PI3K signaling events 49 3632 73 -0.015 0.05 1000 -1000 -0.016 -1000
Aurora B signaling 48 3227 67 -0.058 0.067 1000 -1000 -0.014 -1000
Circadian rhythm pathway 47 1050 22 -0.081 0.044 1000 -1000 -0.017 -1000
Arf6 signaling events 47 2935 62 0 0.082 1000 -1000 0 -1000
Regulation of Androgen receptor activity 47 3304 70 -0.081 0.064 1000 -1000 -0.016 -1000
PLK1 signaling events 46 3918 85 -0.046 0.051 1000 -1000 -0.013 -1000
Reelin signaling pathway 46 2588 56 -0.011 0.095 1000 -1000 -0.004 -1000
Stabilization and expansion of the E-cadherin adherens junction 46 3431 74 -0.076 0.066 1000 -1000 -0.055 -1000
EPO signaling pathway 45 2492 55 0 0.072 1000 -1000 -0.013 -1000
Regulation of Telomerase 44 4504 102 -0.11 0.071 1000 -1000 -0.017 -1000
Canonical NF-kappaB pathway 43 1703 39 -0.036 0.065 1000 -1000 -0.013 -1000
Arf6 downstream pathway 43 1855 43 -0.034 0.061 1000 -1000 -0.053 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 43 1445 33 -0.005 0.086 1000 -1000 -0.012 -1000
ErbB2/ErbB3 signaling events 42 2784 65 -0.033 0.047 1000 -1000 -0.046 -1000
p75(NTR)-mediated signaling 42 5285 125 -0.059 0.099 1000 -1000 -0.035 -1000
RXR and RAR heterodimerization with other nuclear receptor 42 2220 52 -0.038 0.095 1000 -1000 -0.023 -1000
Regulation of p38-alpha and p38-beta 41 2220 54 -0.029 0.091 1000 -1000 -0.002 -1000
EGFR-dependent Endothelin signaling events 40 860 21 -0.016 0.081 1000 -1000 -0.006 -1000
Insulin-mediated glucose transport 39 1253 32 -0.018 0.047 1000 -1000 -0.017 -1000
Neurotrophic factor-mediated Trk receptor signaling 39 4767 120 -0.052 0.09 1000 -1000 -0.024 -1000
Aurora A signaling 38 2296 60 -0.045 0.066 1000 -1000 -0.017 -1000
PDGFR-beta signaling pathway 38 3730 97 -0.036 0.084 1000 -1000 -0.035 -1000
p38 MAPK signaling pathway 38 1676 44 -0.044 0.072 1000 -1000 0 -1000
mTOR signaling pathway 37 2010 53 -0.053 0.057 1000 -1000 -0.019 -1000
Syndecan-3-mediated signaling events 36 1277 35 -0.013 0.073 1000 -1000 -0.014 -1000
S1P3 pathway 36 1552 42 -0.02 0.054 1000 -1000 -0.003 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 35 1905 54 -0.017 0.056 1000 -1000 -0.02 -1000
FOXA2 and FOXA3 transcription factor networks 35 1613 46 -0.12 0.056 1000 -1000 -0.012 -1000
ceramide signaling pathway 35 1733 49 -0.032 0.059 1000 -1000 -0.014 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 34 784 23 -0.017 0.066 1000 -1000 -0.001 -1000
Hedgehog signaling events mediated by Gli proteins 34 2229 65 0 0.076 1000 -1000 -0.007 -1000
Class I PI3K signaling events mediated by Akt 34 2350 68 -0.034 0.078 1000 -1000 -0.017 -1000
Class IB PI3K non-lipid kinase events 34 102 3 -0.039 0.039 1000 -1000 -0.038 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 33 2744 83 -0.013 0.071 1000 -1000 -0.015 -1000
Signaling events mediated by HDAC Class I 33 3444 104 -0.041 0.076 1000 -1000 -0.041 -1000
Signaling events mediated by VEGFR1 and VEGFR2 33 4242 125 -0.023 0.073 1000 -1000 -0.02 -1000
S1P4 pathway 33 829 25 -0.013 0.054 1000 -1000 -0.006 -1000
Ephrin A reverse signaling 32 228 7 -0.013 0.04 1000 -1000 -0.01 -1000
JNK signaling in the CD4+ TCR pathway 32 558 17 -0.007 0.079 1000 -1000 -0.009 -1000
Ceramide signaling pathway 32 2496 76 -0.019 0.081 1000 -1000 -0.017 -1000
S1P5 pathway 32 559 17 -0.007 0.041 1000 -1000 -0.02 -1000
Regulation of nuclear SMAD2/3 signaling 31 4259 136 -0.091 0.1 1000 -1000 -0.051 -1000
Signaling mediated by p38-gamma and p38-delta 31 466 15 -0.038 0.039 1000 -1000 -0.016 -1000
Atypical NF-kappaB pathway 31 989 31 -0.017 0.041 1000 -1000 -0.017 -1000
Insulin Pathway 30 2227 74 -0.026 0.1 1000 -1000 -0.028 -1000
VEGFR1 specific signals 30 1723 56 -0.027 0.045 1000 -1000 -0.018 -1000
Glypican 1 network 29 1420 48 -0.04 0.069 1000 -1000 -0.037 -1000
Signaling events regulated by Ret tyrosine kinase 29 2448 82 -0.009 0.092 1000 -1000 -0.021 -1000
Coregulation of Androgen receptor activity 28 2137 76 -0.011 0.052 1000 -1000 -0.013 -1000
Nephrin/Neph1 signaling in the kidney podocyte 28 965 34 -0.049 0.086 1000 -1000 -0.047 -1000
Sphingosine 1-phosphate (S1P) pathway 28 790 28 -0.019 0.054 1000 -1000 -0.017 -1000
Alternative NF-kappaB pathway 28 365 13 0 0.094 1000 -1000 0 -1000
LPA4-mediated signaling events 27 326 12 -0.015 0.055 1000 -1000 -0.014 -1000
Signaling events mediated by HDAC Class II 26 1952 75 -0.036 0.094 1000 -1000 -0.026 -1000
Glucocorticoid receptor regulatory network 26 2990 114 -0.11 0.077 1000 -1000 -0.044 -1000
Calcium signaling in the CD4+ TCR pathway 26 820 31 -0.038 0.084 1000 -1000 -0.026 -1000
Angiopoietin receptor Tie2-mediated signaling 26 2313 88 -0.045 0.077 1000 -1000 -0.049 -1000
IL27-mediated signaling events 25 1299 51 -0.008 0.08 1000 -1000 -0.028 -1000
Signaling events mediated by HDAC Class III 24 966 40 -0.064 0.072 1000 -1000 -0.058 -1000
Sumoylation by RanBP2 regulates transcriptional repression 24 664 27 -0.031 0.083 1000 -1000 -0.024 -1000
Arf1 pathway 24 1318 54 -0.01 0.052 1000 -1000 -0.009 -1000
S1P1 pathway 22 812 36 -0.001 0.044 1000 -1000 -0.004 -1000
Arf6 trafficking events 22 1563 71 -0.047 0.05 1000 -1000 -0.04 -1000
Rapid glucocorticoid signaling 21 429 20 -0.01 0.049 1000 -1000 -0.009 -1000
Signaling mediated by p38-alpha and p38-beta 20 887 44 -0.023 0.055 1000 -1000 -0.01 -1000
Effects of Botulinum toxin 20 544 26 -0.01 0.071 1000 -1000 -0.01 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 20 1363 68 -0.078 0.095 1000 -1000 -0.037 -1000
Aurora C signaling 18 128 7 0 0.063 1000 -1000 0 -1000
Glypican 2 network 18 72 4 0.04 0.055 1000 -1000 0.038 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 17 1381 78 -0.021 0.065 1000 -1000 -0.049 -1000
Visual signal transduction: Cones 15 603 38 -0.01 0.088 1000 -1000 -0.01 -1000
Visual signal transduction: Rods 14 739 52 -0.018 0.098 1000 -1000 -0.004 -1000
Total 6541 360740 7203 -7.1 8.4 131000 -131000 -2.6 -131000
PLK2 and PLK4 events

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
PLK2 0.026 0.02 -9999 0 0 216 216
PLK4 0.036 0.015 -9999 0 0 82 82
regulation of centriole replication -0.011 0.01 0 263 -9999 0 263
FOXM1 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
NFATC3 -0.35 0.6 -10000 0 -1.1 168 168
PLK1 -0.048 0.31 -10000 0 -1.2 34 34
BIRC5 -0.053 0.32 -10000 0 -1.3 35 35
HSPA1B -0.35 0.6 -10000 0 -1.1 178 178
MAP2K1 0.002 0.07 -10000 0 -10000 0 0
BRCA2 -0.36 0.61 -10000 0 -1.2 168 168
FOXM1 -0.52 0.88 -10000 0 -1.6 178 178
XRCC1 -0.35 0.6 -10000 0 -1.2 165 165
FOXM1B/p19 -0.44 0.66 -10000 0 -1.3 182 182
Cyclin D1/CDK4 -0.36 0.55 -10000 0 -1 182 182
CDC2 -0.41 0.68 -10000 0 -1.3 182 182
TGFA -0.32 0.52 -10000 0 -0.97 178 178
SKP2 -0.35 0.61 -10000 0 -1.2 163 163
CCNE1 0.02 0.029 -10000 0 -0.009 256 256
CKS1B -0.35 0.61 -10000 0 -1.2 167 167
RB1 -0.32 0.48 -10000 0 -0.97 167 167
FOXM1C/SP1 -0.44 0.71 -10000 0 -1.3 180 180
AURKB -0.1 0.4 -10000 0 -1.2 60 60
CENPF -0.39 0.63 -10000 0 -1.2 188 188
CDK4 0.007 0.044 0.11 3 -0.039 166 169
MYC -0.34 0.48 -10000 0 -0.95 184 184
CHEK2 0.005 0.065 -10000 0 -10000 0 0
ONECUT1 -0.36 0.58 -10000 0 -1.1 177 177
CDKN2A 0.026 0.02 0.089 2 -0.034 8 10
LAMA4 -0.39 0.63 -10000 0 -1.2 188 188
FOXM1B/HNF6 -0.45 0.71 -10000 0 -1.4 178 178
FOS -0.43 0.65 -10000 0 -1.2 218 218
SP1 0.036 0.022 -10000 0 -0.033 47 47
CDC25B -0.35 0.6 -10000 0 -1.1 168 168
response to radiation -0.006 0.036 0.087 9 -10000 0 9
CENPB -0.34 0.6 0.74 1 -1.1 167 168
CENPA -0.36 0.6 -10000 0 -1.1 168 168
NEK2 -0.37 0.62 -10000 0 -1.2 173 173
HIST1H2BA -0.35 0.6 0.74 1 -1.1 169 170
CCNA2 0.024 0.029 -10000 0 -0.011 202 202
EP300 0.037 0.014 -10000 0 0 72 72
CCNB1/CDK1 -0.49 0.79 -10000 0 -1.5 175 175
CCNB2 -0.38 0.63 0.8 1 -1.2 182 183
CCNB1 -0.39 0.66 -10000 0 -1.3 174 174
ETV5 -0.37 0.65 -10000 0 -1.2 194 194
ESR1 -0.4 0.62 -10000 0 -1.1 194 194
CCND1 -0.37 0.55 -10000 0 -1 186 186
GSK3A 0.005 0.062 0.15 3 -10000 0 3
Cyclin A-E1/CDK1-2 -0.007 0.11 -10000 0 -0.17 124 124
CDK2 0.028 0.028 -10000 0 -0.018 130 130
G2/M transition of mitotic cell cycle -0.007 0.043 0.094 10 -10000 0 10
FOXM1B/Cbp/p300 -0.41 0.66 -10000 0 -1.3 177 177
GAS1 -0.36 0.6 -10000 0 -1.1 173 173
MMP2 -0.43 0.65 -10000 0 -1.2 219 219
RB1/FOXM1C -0.41 0.59 0.67 1 -1.1 184 185
CREBBP 0.038 0.012 -10000 0 0 54 54
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 0.034 0.33 0.54 54 -0.52 90 144
HDAC7 -0.001 0.004 -10000 0 -0.037 1 1
HIF1A/ARNT/Cbp/p300/Src-1 0.03 0.32 0.57 19 -0.58 56 75
SMAD4 0.039 0.012 -10000 0 0 49 49
ID2 0.034 0.33 0.54 56 -0.52 89 145
AP1 0.006 0.084 -10000 0 -0.14 120 120
ABCG2 0.029 0.33 0.54 53 -0.52 89 142
HIF1A 0.031 0.1 0.2 44 -0.14 78 122
TFF3 0.011 0.32 0.53 43 -0.53 87 130
GATA2 0.04 0.019 -10000 0 -0.015 47 47
AKT1 0.042 0.097 0.21 43 -0.11 72 115
response to hypoxia 0.006 0.068 0.14 44 -0.1 59 103
MCL1 0.036 0.34 0.54 53 -0.53 90 143
NDRG1 -0.017 0.29 0.52 30 -0.56 76 106
SERPINE1 -0.01 0.3 0.53 32 -0.53 87 119
FECH 0.031 0.33 0.54 55 -0.53 88 143
FURIN 0.037 0.33 0.54 55 -0.52 90 145
NCOA2 0.038 0.015 -10000 0 -0.001 71 71
EP300 0.045 0.12 0.28 48 -0.23 21 69
HMOX1 0.022 0.33 0.54 47 -0.53 92 139
BHLHE40 -0.024 0.3 0.47 54 -0.52 90 144
BHLHE41 -0.024 0.3 0.47 54 -0.52 90 144
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.097 0.16 0.35 20 -0.21 29 49
ENG 0.02 0.11 0.26 18 -0.22 18 36
JUN 0.036 0.019 -10000 0 -0.005 90 90
RORA 0.034 0.33 0.54 55 -0.52 89 144
ABCB1 0.018 0.097 -10000 0 -0.55 4 4
TFRC -0.006 0.31 0.53 37 -0.54 86 123
CXCR4 0.01 0.33 0.53 47 -0.53 95 142
TF 0.028 0.32 0.54 52 -0.52 88 140
CITED2 0.032 0.33 0.53 54 -0.52 89 143
HIF1A/ARNT 0.018 0.38 -10000 0 -0.65 64 64
LDHA -0.048 0.3 -10000 0 -0.89 55 55
ETS1 0.012 0.33 0.52 43 -0.54 92 135
PGK1 0.032 0.34 0.54 56 -0.54 92 148
NOS2 -0.024 0.3 0.47 54 -0.52 90 144
ITGB2 0.012 0.33 0.54 47 -0.55 93 140
ALDOA 0.041 0.34 0.54 58 -0.53 89 147
Cbp/p300/CITED2 0.014 0.33 0.54 37 -0.58 76 113
FOS 0.027 0.022 -10000 0 -0.001 212 212
HK2 0.035 0.34 0.54 55 -0.53 90 145
SP1 0.048 0.008 -10000 0 -10000 0 0
GCK 0.067 0.15 0.48 13 -0.36 1 14
HK1 0.034 0.34 0.53 57 -0.52 90 147
NPM1 0.039 0.34 0.54 57 -0.52 90 147
EGLN1 0.04 0.33 0.54 58 -0.52 86 144
CREB1 0.035 0.041 -10000 0 -0.11 41 41
PGM1 0.028 0.34 0.54 51 -0.54 90 141
SMAD3 0.041 0.009 -10000 0 -10000 0 0
EDN1 0.035 0.21 0.43 7 -1 13 20
IGFBP1 0.041 0.34 0.53 58 -0.52 90 148
VEGFA -0.007 0.26 0.45 41 -0.47 75 116
HIF1A/JAB1 0.035 0.099 0.2 11 -0.16 64 75
CP -0.012 0.31 0.52 41 -0.55 88 129
CXCL12 -0.019 0.31 0.53 31 -0.53 94 125
COPS5 0.036 0.016 -10000 0 -0.049 1 1
SMAD3/SMAD4 0.053 0.033 -10000 0 -0.14 11 11
BNIP3 0.017 0.33 0.54 47 -0.54 90 137
EGLN3 -0.017 0.32 0.53 33 -0.54 98 131
CA9 -0.016 0.3 0.53 29 -0.53 89 118
TERT 0.022 0.32 0.53 49 -0.52 88 137
ENO1 0.035 0.34 0.54 56 -0.53 90 146
PFKL 0.038 0.34 0.54 55 -0.53 89 144
NCOA1 0.04 0.01 -10000 0 -0.001 29 29
ADM 0 0.31 0.53 31 -0.53 92 123
ARNT 0.031 0.098 0.2 40 -0.12 79 119
HNF4A 0.041 0.013 -10000 0 -10000 0 0
ADFP -0.002 0.32 0.53 40 -0.53 96 136
SLC2A1 0.005 0.28 0.48 32 -0.5 75 107
LEP 0.039 0.33 0.54 56 -0.53 86 142
HIF1A/ARNT/Cbp/p300 0.015 0.32 0.56 17 -0.6 58 75
EPO 0.031 0.28 0.5 29 -0.54 51 80
CREBBP 0.05 0.11 0.28 53 -0.22 14 67
HIF1A/ARNT/Cbp/p300/HDAC7 0.004 0.31 0.54 11 -0.59 58 69
PFKFB3 0.029 0.33 0.54 53 -0.54 88 141
NT5E -0.036 0.31 0.52 25 -0.54 99 124
TCGA08_p53

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
CDKN2A -0.007 0.005 0 175 -10000 0 175
TP53 -0.053 0.12 0.18 13 -0.24 148 161
Senescence -0.063 0.12 0.18 13 -0.24 150 163
Apoptosis -0.063 0.12 0.18 13 -0.24 150 163
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.006 0.038 0.3 8 -10000 0 8
MDM4 0.038 0.013 -10000 0 0 57 57
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.031 0.018 -10000 0 0 143 143
EPHB2 0.043 0.013 0.067 2 0 38 40
EFNB1 -0.001 0.024 0.029 208 -10000 0 208
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.077 0.066 0.23 1 -0.12 18 19
Ephrin B2/EPHB1-2 0.041 0.068 -10000 0 -0.1 77 77
neuron projection morphogenesis 0.052 0.051 -10000 0 -0.11 20 20
Ephrin B1/EPHB1-2/Tiam1 0.07 0.061 0.21 3 -0.11 29 32
DNM1 0.041 0.012 -10000 0 0 38 38
cell-cell signaling 0.003 0.006 0.025 1 -10000 0 1
MAP2K4 -0.13 0.21 0.23 3 -0.46 164 167
YES1 -0.2 0.33 -10000 0 -0.69 168 168
Ephrin B1/EPHB1-2/NCK2 0.08 0.052 0.21 4 -0.11 17 21
PI3K -0.11 0.23 -10000 0 -0.44 167 167
mol:GDP 0.068 0.06 0.2 3 -0.11 29 32
ITGA2B 0.04 0.009 -10000 0 0 30 30
endothelial cell proliferation 0.024 0.06 -10000 0 -0.11 83 83
FYN -0.2 0.33 -10000 0 -0.7 165 165
MAP3K7 -0.13 0.22 0.22 4 -0.48 160 164
FGR -0.19 0.32 -10000 0 -0.68 171 171
TIAM1 0.037 0.014 -10000 0 0 72 72
PIK3R1 0.034 0.017 -10000 0 0 107 107
RGS3 0.04 0.008 -10000 0 0 23 23
cell adhesion -0.11 0.21 -10000 0 -0.41 166 166
LYN -0.19 0.32 -10000 0 -0.69 163 163
Ephrin B1/EPHB1-2/Src Family Kinases -0.18 0.3 -10000 0 -0.62 170 170
Ephrin B1/EPHB1-2 -0.14 0.24 -10000 0 -0.53 151 151
SRC -0.18 0.32 -10000 0 -0.68 166 166
ITGB3 0.033 0.017 -10000 0 0 121 121
EPHB1 0.04 0.014 -10000 0 0 59 59
EPHB4 0.04 0.009 -10000 0 0 29 29
RAC1 0.039 0.01 -10000 0 0 33 33
Ephrin B2/EPHB4 0.025 0.061 -10000 0 -0.11 83 83
alphaIIb/beta3 Integrin 0.04 0.05 -10000 0 -0.14 34 34
BLK -0.19 0.32 -10000 0 -0.69 165 165
HCK -0.19 0.32 -10000 0 -0.68 165 165
regulation of stress fiber formation -0.077 0.051 0.11 17 -0.2 4 21
MAPK8 -0.14 0.21 0.24 1 -0.44 168 169
Ephrin B1/EPHB1-2/RGS3 0.08 0.052 0.21 4 -0.12 15 19
endothelial cell migration -0.11 0.18 0.19 5 -0.4 146 151
NCK2 0.042 0.004 -10000 0 0 6 6
PTPN13 0.022 0.022 -10000 0 0 276 276
regulation of focal adhesion formation -0.077 0.051 0.11 17 -0.2 4 21
chemotaxis -0.077 0.051 0.11 16 -0.2 4 20
PIK3CA 0.03 0.019 -10000 0 0 155 155
Rac1/GTP 0.066 0.059 0.2 1 -0.12 19 20
angiogenesis -0.14 0.24 -10000 0 -0.52 157 157
LCK -0.19 0.32 -10000 0 -0.68 170 170
Endothelins

Figure S6.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S6.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.004 0.14 0.22 42 -0.24 115 157
PTK2B 0.033 0.017 -10000 0 0 118 118
mol:Ca2+ -0.032 0.2 -10000 0 -0.61 22 22
EDN1 -0.005 0.1 0.22 8 -0.18 123 131
EDN3 0.036 0.014 -10000 0 0 77 77
EDN2 0.037 0.014 -10000 0 0 66 66
HRAS/GDP -0.051 0.19 0.27 2 -0.35 115 117
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.026 0.14 0.19 5 -0.26 101 106
ADCY4 0.01 0.13 0.2 77 -0.23 72 149
ADCY5 0.011 0.13 0.2 85 -0.23 72 157
ADCY6 0.008 0.14 0.2 88 -0.23 78 166
ADCY7 0.007 0.14 0.2 82 -0.23 74 156
ADCY1 0.009 0.14 0.2 77 -0.23 75 152
ADCY2 0.01 0.13 0.21 73 -0.23 65 138
ADCY3 0.009 0.14 0.2 82 -0.23 75 157
ADCY8 -0.002 0.11 0.21 43 -0.22 52 95
ADCY9 0.009 0.14 0.21 79 -0.23 78 157
arachidonic acid secretion -0.1 0.26 0.3 2 -0.5 135 137
ETB receptor/Endothelin-1/Gq/GTP 0 0.11 -10000 0 -0.24 60 60
GNAO1 0.034 0.016 -10000 0 0 101 101
HRAS 0.039 0.01 -10000 0 0 31 31
ETA receptor/Endothelin-1/G12/GTP -0.005 0.13 0.35 7 -0.22 124 131
ETA receptor/Endothelin-1/Gs/GTP -0.004 0.12 0.32 7 -0.2 123 130
mol:GTP 0 0.006 -10000 0 -0.027 1 1
COL3A1 -0.058 0.16 0.23 16 -0.35 119 135
EDNRB 0.021 0.054 0.091 4 -0.089 96 100
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.003 0.14 0.22 28 -0.24 115 143
CYSLTR1 -0.015 0.15 0.24 16 -0.26 110 126
SLC9A1 -0.016 0.085 0.2 7 -0.16 98 105
mol:GDP -0.064 0.19 0.25 4 -0.36 117 121
SLC9A3 -0.022 0.19 -10000 0 -0.56 25 25
RAF1 -0.076 0.22 0.26 7 -0.4 141 148
JUN -0.073 0.3 -10000 0 -0.84 56 56
JAK2 -0.008 0.14 0.22 30 -0.24 114 144
mol:IP3 -0.022 0.14 0.21 2 -0.3 82 84
ETA receptor/Endothelin-1 -0.027 0.15 0.39 6 -0.27 132 138
PLCB1 0.033 0.017 -10000 0 0 114 114
PLCB2 0.037 0.014 -10000 0 -0.005 52 52
ETA receptor/Endothelin-3 0.015 0.084 0.19 7 -0.13 106 113
FOS -0.14 0.36 0.33 2 -0.82 113 115
Gai/GDP -0.032 0.24 -10000 0 -0.69 59 59
CRK 0.038 0.012 -10000 0 0 51 51
mol:Ca ++ -0.031 0.19 0.25 29 -0.34 110 139
BCAR1 0.036 0.014 -10000 0 0 75 75
PRKCB1 -0.027 0.14 0.23 8 -0.3 87 95
GNAQ 0.035 0.022 -10000 0 -0.038 31 31
GNAZ 0.039 0.011 -10000 0 0 42 42
GNAL 0.04 0.009 -10000 0 0 26 26
Gs family/GDP -0.049 0.18 0.26 2 -0.34 108 110
ETA receptor/Endothelin-1/Gq/GTP -0.015 0.14 0.22 5 -0.26 82 87
MAPK14 -0.017 0.11 0.23 5 -0.24 70 75
TRPC6 -0.035 0.21 -10000 0 -0.66 20 20
GNAI2 0.041 0.007 -10000 0 0 15 15
GNAI3 0.039 0.011 -10000 0 0 45 45
GNAI1 0.035 0.016 -10000 0 0 95 95
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.011 0.11 -10000 0 -0.23 73 73
ETB receptor/Endothelin-2 0.031 0.054 -10000 0 -0.071 90 90
ETB receptor/Endothelin-3 0.032 0.051 -10000 0 -0.067 79 79
ETB receptor/Endothelin-1 0.007 0.11 0.2 5 -0.18 105 110
MAPK3 -0.13 0.34 0.31 3 -0.74 118 121
MAPK1 -0.14 0.35 0.31 3 -0.75 122 125
Rac1/GDP -0.051 0.18 0.28 1 -0.35 113 114
cAMP biosynthetic process 0.044 0.13 0.23 76 -0.22 29 105
MAPK8 -0.053 0.24 -10000 0 -0.58 67 67
SRC 0.039 0.01 -10000 0 0 36 36
ETB receptor/Endothelin-1/Gi/GTP -0.011 0.11 -10000 0 -0.26 62 62
p130Cas/CRK/Src/PYK2 -0.059 0.19 0.31 2 -0.42 84 86
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.05 0.19 0.26 3 -0.35 115 118
COL1A2 -0.075 0.21 0.27 5 -0.48 105 110
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.011 0.088 0.19 8 -0.13 127 135
mol:DAG -0.023 0.14 0.21 2 -0.3 83 85
MAP2K2 -0.099 0.27 0.29 4 -0.54 127 131
MAP2K1 -0.1 0.27 0.3 3 -0.56 126 129
EDNRA -0.003 0.1 0.22 8 -0.17 133 141
positive regulation of muscle contraction -0.014 0.12 0.22 22 -0.22 94 116
Gq family/GDP -0.013 0.19 0.28 1 -0.32 108 109
HRAS/GTP -0.053 0.18 0.24 3 -0.33 122 125
PRKCH -0.03 0.14 0.26 2 -0.29 92 94
RAC1 0.039 0.01 -10000 0 0 33 33
PRKCA -0.031 0.15 0.24 4 -0.3 91 95
PRKCB -0.027 0.14 0.2 1 -0.28 93 94
PRKCE -0.028 0.14 0.28 5 -0.29 85 90
PRKCD -0.031 0.14 0.24 3 -0.3 87 90
PRKCG -0.034 0.15 -10000 0 -0.3 90 90
regulation of vascular smooth muscle contraction -0.18 0.44 -10000 0 -1 112 112
PRKCQ -0.03 0.15 0.28 8 -0.31 85 93
PLA2G4A -0.11 0.28 0.3 2 -0.54 135 137
GNA14 0.036 0.022 -10000 0 -0.039 32 32
GNA15 0.034 0.022 -10000 0 -0.036 28 28
GNA12 0.04 0.01 -10000 0 0 32 32
GNA11 0.034 0.021 -10000 0 -0.036 29 29
Rac1/GTP -0.006 0.13 0.35 6 -0.22 120 126
MMP1 0.02 0.12 0.32 21 -0.58 10 31
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.021 0.081 -10000 0 -0.13 111 111
NF kappa B1 p50/RelA/I kappa B alpha -0.008 0.11 0.2 7 -0.22 69 76
AP1 -0.026 0.067 -10000 0 -0.12 172 172
mol:PIP3 -0.036 0.057 -10000 0 -0.13 125 125
AKT1 -0.003 0.094 0.24 18 -0.21 24 42
PTK2B -0.047 0.11 0.12 3 -0.19 182 185
RHOA 0.002 0.058 0.15 4 -0.3 8 12
PIK3CB 0.034 0.016 -10000 0 0 102 102
mol:Ca2+ -0.008 0.048 0.19 8 -0.13 23 31
MAGI3 0.04 0.009 -10000 0 0 30 30
RELA 0.041 0.006 -10000 0 0 10 10
apoptosis 0.002 0.069 0.072 123 -0.14 95 218
HRAS/GDP 0.029 0.01 -10000 0 -0.13 1 1
positive regulation of microtubule depolymerization -0.046 0.1 0.19 16 -0.2 115 131
NF kappa B1 p50/RelA -0.028 0.075 0.1 3 -0.16 113 116
endothelial cell migration -0.04 0.12 -10000 0 -0.3 99 99
ADCY4 -0.019 0.094 0.16 2 -0.2 99 101
ADCY5 -0.018 0.092 0.16 2 -0.19 103 105
ADCY6 -0.019 0.094 0.17 1 -0.2 103 104
ADCY7 -0.018 0.092 0.16 2 -0.19 100 102
ADCY1 -0.018 0.092 0.16 2 -0.2 99 101
ADCY2 -0.014 0.09 0.17 1 -0.2 90 91
ADCY3 -0.02 0.094 0.17 1 -0.2 105 106
ADCY8 -0.002 0.086 0.12 33 -0.18 82 115
ADCY9 -0.022 0.098 0.16 2 -0.2 107 109
GSK3B -0.046 0.11 0.21 15 -0.19 167 182
arachidonic acid secretion -0.029 0.098 0.14 2 -0.19 123 125
GNG2 0.039 0.01 -10000 0 0 34 34
TRIP6 0.012 0.052 -10000 0 -0.24 19 19
GNAO1 0.007 0.071 0.09 116 -0.14 87 203
HRAS 0.04 0.01 -10000 0 0 31 31
NFKBIA -0.03 0.091 0.17 9 -0.23 60 69
GAB1 0.038 0.012 -10000 0 0 51 51
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.011 0.26 -10000 0 -0.87 47 47
JUN 0.036 0.015 -10000 0 0 80 80
LPA/LPA2/NHERF2 0.015 0.037 -10000 0 -0.061 94 94
TIAM1 -0.037 0.3 -10000 0 -1 47 47
PIK3R1 0.034 0.016 -10000 0 0 107 107
mol:IP3 -0.004 0.044 0.19 8 -0.14 15 23
PLCB3 0.016 0.044 0.16 13 -0.061 91 104
FOS 0.026 0.02 -10000 0 0 207 207
positive regulation of mitosis -0.029 0.098 0.14 2 -0.19 123 125
LPA/LPA1-2-3 -0.017 0.049 -10000 0 -0.12 100 100
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.036 0.014 -10000 0 0 75 75
stress fiber formation -0.011 0.1 0.16 1 -0.25 47 48
GNAZ 0.008 0.073 0.091 122 -0.15 87 209
EGFR/PI3K-beta/Gab1 -0.025 0.066 -10000 0 -0.13 127 127
positive regulation of dendritic cell cytokine production -0.017 0.049 -10000 0 -0.12 100 100
LPA/LPA2/MAGI-3 0.016 0.037 -10000 0 -0.06 96 96
ARHGEF1 0.006 0.076 0.2 12 -0.14 90 102
GNAI2 0.006 0.076 0.091 126 -0.14 99 225
GNAI3 0.004 0.079 0.091 122 -0.15 98 220
GNAI1 0.003 0.079 0.091 119 -0.16 91 210
LPA/LPA3 -0.01 0.026 -10000 0 -0.065 100 100
LPA/LPA2 -0.01 0.025 -10000 0 -0.064 100 100
LPA/LPA1 -0.024 0.067 -10000 0 -0.17 100 100
HB-EGF/EGFR 0.023 0.052 -10000 0 -0.13 48 48
HBEGF -0.014 0.01 -10000 0 -10000 0 0
mol:DAG -0.004 0.044 0.19 8 -0.14 15 23
cAMP biosynthetic process -0.023 0.097 0.18 4 -0.2 95 99
NFKB1 0.036 0.015 -10000 0 0 83 83
SRC 0.039 0.01 -10000 0 0 36 36
GNB1 0.041 0.005 -10000 0 0 7 7
LYN -0.024 0.094 0.16 19 -0.22 63 82
GNAQ 0.009 0.032 0.043 124 -0.052 101 225
LPAR2 0 0.001 -10000 0 -10000 0 0
LPAR3 0 0 -10000 0 -10000 0 0
LPAR1 -0.017 0.04 -10000 0 -0.1 100 100
IL8 -0.023 0.18 0.25 8 -0.37 91 99
PTK2 0.006 0.06 0.094 79 -0.12 75 154
Rac1/GDP 0.029 0.01 -10000 0 -0.13 1 1
CASP3 0.002 0.069 0.072 123 -0.14 95 218
EGFR 0.037 0.014 -10000 0 0 72 72
PLCG1 0.006 0.037 -10000 0 -0.1 28 28
PLD2 0.016 0.066 0.094 124 -0.12 90 214
G12/G13 0.023 0.078 -10000 0 -0.14 100 100
PI3K-beta -0.025 0.074 0.13 1 -0.2 49 50
cell migration -0.008 0.086 -10000 0 -0.24 47 47
SLC9A3R2 0.038 0.012 -10000 0 0 54 54
PXN -0.011 0.1 0.16 1 -0.25 47 48
HRAS/GTP -0.028 0.099 0.14 2 -0.19 121 123
RAC1 0.039 0.01 -10000 0 0 33 33
MMP9 0.029 0.02 -10000 0 0 178 178
PRKCE 0.039 0.01 -10000 0 0 36 36
PRKCD -0.016 0.054 0.17 12 -0.15 25 37
Gi(beta/gamma) -0.02 0.1 0.16 1 -0.19 118 119
mol:LPA -0.017 0.04 -10000 0 -0.1 100 100
TRIP6/p130 Cas/FAK1/Paxillin -0.004 0.099 0.19 1 -0.23 48 49
MAPKKK cascade -0.029 0.098 0.14 2 -0.19 123 125
contractile ring contraction involved in cytokinesis 0.002 0.061 0.16 3 -0.29 10 13
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.008 0.032 0.043 125 -0.052 107 232
GNA15 0.009 0.031 0.043 117 -0.054 93 210
GNA12 0.04 0.01 -10000 0 0 32 32
GNA13 0.04 0.009 -10000 0 0 28 28
MAPT -0.047 0.1 0.19 16 -0.21 116 132
GNA11 0.008 0.032 0.043 118 -0.054 97 215
Rac1/GTP -0.014 0.28 -10000 0 -0.93 47 47
MMP2 -0.04 0.12 -10000 0 -0.3 99 99
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.011 0.13 0.2 10 -0.22 110 120
NF kappa B1 p50/RelA/I kappa B alpha -0.048 0.18 0.28 1 -0.35 120 121
alphaV/beta3 Integrin/Osteopontin/Src -0.007 0.11 -10000 0 -0.17 149 149
AP1 -0.044 0.18 0.27 2 -0.28 150 152
ILK -0.028 0.11 0.19 13 -0.24 71 84
bone resorption -0.04 0.1 0.2 2 -0.26 46 48
PTK2B 0.033 0.017 -10000 0 0 118 118
PYK2/p130Cas 0.005 0.12 -10000 0 -0.21 73 73
ITGAV 0.026 0.033 -10000 0 -0.048 65 65
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.029 0.068 -10000 0 -0.14 68 68
alphaV/beta3 Integrin/Osteopontin 0.005 0.13 -10000 0 -0.17 161 161
MAP3K1 -0.027 0.1 0.18 12 -0.24 69 81
JUN 0.036 0.015 -10000 0 0 80 80
MAPK3 -0.047 0.14 0.19 14 -0.28 112 126
MAPK1 -0.046 0.14 0.19 14 -0.28 111 125
Rac1/GDP 0.029 0.01 -10000 0 -0.13 1 1
NFKB1 0.036 0.015 -10000 0 0 83 83
MAPK8 -0.032 0.1 0.17 13 -0.23 77 90
ITGB3 0.023 0.034 -10000 0 -0.048 76 76
NFKBIA -0.064 0.16 0.19 12 -0.36 110 122
FOS 0.027 0.021 -10000 0 0 207 207
CD44 0.035 0.016 -10000 0 0 96 96
CHUK 0.038 0.012 -10000 0 0 52 52
PLAU -0.18 0.42 -10000 0 -1 107 107
NF kappa B1 p50/RelA -0.032 0.2 -10000 0 -0.4 107 107
BCAR1 0.036 0.014 -10000 0 0 75 75
RELA 0.041 0.006 -10000 0 0 10 10
alphaV beta3 Integrin 0.004 0.091 -10000 0 -0.14 127 127
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.029 0.1 0.19 12 -0.23 72 84
VAV3 -0.038 0.1 0.17 11 -0.23 88 99
MAP3K14 -0.026 0.12 0.2 13 -0.23 107 120
ROCK2 0.037 0.013 -10000 0 0 65 65
SPP1 0.025 0.031 -10000 0 -0.05 51 51
RAC1 0.039 0.01 -10000 0 0 33 33
Rac1/GTP -0.034 0.11 0.18 12 -0.22 88 100
MMP2 -0.087 0.14 0.2 1 -0.31 131 132
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.019 0.095 -9999 0 -0.29 39 39
FZD6 0.029 0.019 -9999 0 0 170 170
WNT6 0.041 0.006 -9999 0 0 13 13
WNT4 0.041 0.007 -9999 0 0 18 18
FZD3 0.029 0.019 -9999 0 0 168 168
WNT5A 0.035 0.015 -9999 0 0 91 91
WNT11 0.033 0.017 -9999 0 0 124 124
Syndecan-1-mediated signaling events

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
TGFB1 0.037 0.013 -10000 0 0 62 62
CCL5 0.03 0.019 -10000 0 0 161 161
SDCBP 0.036 0.014 -10000 0 0 75 75
FGFR/FGF2/Syndecan-1 -0.012 0.12 0.2 20 -0.33 42 62
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.013 0.13 0.23 15 -0.3 55 70
Syndecan-1/Syntenin -0.014 0.14 0.23 19 -0.29 66 85
MAPK3 -0.023 0.13 0.2 18 -0.29 56 74
HGF/MET 0.013 0.075 -10000 0 -0.14 105 105
TGFB1/TGF beta receptor Type II 0.037 0.013 -10000 0 0 62 62
BSG 0.037 0.014 -10000 0 0 71 71
keratinocyte migration -0.012 0.13 0.23 15 -0.3 55 70
Syndecan-1/RANTES -0.019 0.14 0.22 17 -0.3 74 91
Syndecan-1/CD147 -0.002 0.15 0.25 11 -0.3 56 67
Syndecan-1/Syntenin/PIP2 -0.015 0.14 0.21 19 -0.28 66 85
LAMA5 0.036 0.015 -10000 0 0 85 85
positive regulation of cell-cell adhesion -0.015 0.13 0.21 19 -0.28 66 85
MMP7 0.016 0.02 -10000 0 0 340 340
HGF 0.04 0.009 -10000 0 0 29 29
Syndecan-1/CASK -0.036 0.12 0.15 5 -0.29 62 67
Syndecan-1/HGF/MET -0.018 0.14 0.25 14 -0.29 68 82
regulation of cell adhesion -0.031 0.12 0.19 15 -0.29 55 70
HPSE 0.035 0.015 -10000 0 0 90 90
positive regulation of cell migration -0.012 0.12 0.2 20 -0.33 42 62
SDC1 -0.017 0.12 0.17 6 -0.34 37 43
Syndecan-1/Collagen -0.012 0.12 0.2 20 -0.33 42 62
PPIB 0.04 0.009 -10000 0 0 24 24
MET 0.027 0.02 -10000 0 0 198 198
PRKACA 0.035 0.015 -10000 0 0 89 89
MMP9 0.029 0.02 -10000 0 0 178 178
MAPK1 -0.022 0.13 0.21 16 -0.29 56 72
homophilic cell adhesion -0.012 0.13 0.2 28 -0.32 46 74
MMP1 0.03 0.019 -10000 0 0 159 159
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 0.006 0.085 -10000 0 -0.13 127 127
alphaM/beta2 Integrin/GPIbA 0.053 0.069 -10000 0 -0.12 60 60
alphaM/beta2 Integrin/proMMP-9 0.03 0.081 -10000 0 -0.13 82 82
PLAUR 0.036 0.014 -10000 0 0 77 77
HMGB1 0.041 0.016 -10000 0 -0.054 10 10
alphaM/beta2 Integrin/Talin 0.047 0.076 -10000 0 -0.12 75 75
AGER 0.041 0.016 -10000 0 -0.054 10 10
RAP1A 0.039 0.01 -10000 0 0 35 35
SELPLG 0.04 0.009 -10000 0 0 27 27
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.082 0.083 -10000 0 -0.18 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.029 0.02 -10000 0 0 178 178
CYR61 0.03 0.019 -10000 0 0 158 158
TLN1 0.039 0.012 -10000 0 0 46 46
Rap1/GTP -0.06 0.17 -10000 0 -0.31 139 139
RHOA 0.041 0.007 -10000 0 0 14 14
P-selectin oligomer 0.039 0.011 -10000 0 0 38 38
MYH2 -0.081 0.17 0.2 2 -0.33 139 141
MST1R 0.039 0.011 -10000 0 0 42 42
leukocyte activation during inflammatory response 0.058 0.065 -10000 0 -0.1 52 52
APOB 0.041 0.007 -10000 0 0 16 16
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.022 0.021 -10000 0 0 273 273
JAM3 0.038 0.012 -10000 0 0 55 55
GP1BA 0.039 0.01 -10000 0 0 36 36
alphaM/beta2 Integrin/CTGF 0.035 0.081 -10000 0 -0.12 97 97
alphaM/beta2 Integrin -0.063 0.17 -10000 0 -0.34 124 124
JAM3 homodimer 0.038 0.012 -10000 0 0 55 55
ICAM2 0.039 0.011 -10000 0 0 41 41
ICAM1 0.026 0.02 -10000 0 0 207 207
phagocytosis triggered by activation of immune response cell surface activating receptor -0.063 0.17 -10000 0 -0.33 125 125
cell adhesion 0.052 0.068 -10000 0 -0.12 60 60
NFKB1 0.022 0.075 0.26 4 -0.22 24 28
THY1 0.025 0.021 -10000 0 0 221 221
RhoA/GDP 0.03 0.012 -10000 0 -0.13 3 3
Lipoprotein(a) 0.05 0.018 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA 0.025 0.1 -10000 0 -0.13 139 139
IL6 -0.019 0.077 0.26 3 -0.43 10 13
ITGB2 0.034 0.022 -10000 0 -0.052 9 9
elevation of cytosolic calcium ion concentration 0.033 0.11 -10000 0 -0.16 104 104
alphaM/beta2 Integrin/JAM2/JAM3 0.067 0.075 -10000 0 -0.11 56 56
JAM2 0.038 0.013 -10000 0 0 57 57
alphaM/beta2 Integrin/ICAM1 0.052 0.1 -10000 0 -0.14 98 98
alphaM/beta2 Integrin/uPA/Plg 0.041 0.099 -10000 0 -0.15 93 93
RhoA/GTP -0.083 0.18 0.2 1 -0.34 146 147
positive regulation of phagocytosis -0.04 0.15 0.21 4 -0.3 103 107
Ron/MSP 0.054 0.029 -10000 0 -0.14 9 9
alphaM/beta2 Integrin/uPAR/uPA 0.035 0.11 -10000 0 -0.16 102 102
alphaM/beta2 Integrin/uPAR 0.045 0.081 -10000 0 -0.14 68 68
PLAU 0.026 0.02 -10000 0 0 214 214
PLAT 0.026 0.02 -10000 0 0 214 214
actin filament polymerization -0.077 0.16 0.2 2 -0.32 138 140
MST1 0.041 0.007 -10000 0 0 15 15
alphaM/beta2 Integrin/lipoprotein(a) 0.065 0.069 -10000 0 -0.1 52 52
TNF -0.01 0.073 0.26 4 -0.32 9 13
RAP1B 0.038 0.013 -10000 0 0 59 59
alphaM/beta2 Integrin/uPA 0.018 0.094 -10000 0 -0.15 102 102
fibrinolysis 0.039 0.097 -10000 0 -0.15 94 94
HCK 0.036 0.015 -10000 0 0 80 80
dendritic cell antigen processing and presentation -0.063 0.17 -10000 0 -0.33 125 125
VTN 0.04 0.009 -10000 0 0 24 24
alphaM/beta2 Integrin/CYR61 0.024 0.085 -10000 0 -0.12 111 111
LPA 0.038 0.013 -10000 0 0 56 56
LRP1 0.036 0.014 -10000 0 0 75 75
cell migration 0.019 0.094 0.19 14 -0.13 126 140
FN1 0.021 0.021 -10000 0 0 277 277
alphaM/beta2 Integrin/Thy1 0.007 0.092 -10000 0 -0.12 154 154
MPO 0.041 0.008 -10000 0 0 19 19
KNG1 0.034 0.017 -10000 0 0 109 109
RAP1/GDP 0.039 0.049 -10000 0 -0.12 42 42
ROCK1 -0.083 0.17 0.24 3 -0.33 146 149
ELA2 0.037 0.013 -10000 0 0 64 64
PLG 0.038 0.012 -10000 0 0 50 50
CTGF 0.034 0.017 -10000 0 0 112 112
alphaM/beta2 Integrin/Hck 0.05 0.071 -10000 0 -0.13 50 50
ITGAM 0.042 0.016 -10000 0 -0.054 10 10
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.073 0.076 -10000 0 -0.12 53 53
HP 0.01 0.018 -10000 0 0 429 429
leukocyte adhesion 0.019 0.11 -10000 0 -0.18 46 46
SELP 0.039 0.011 -10000 0 0 38 38
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.021 0.021 -10000 0 0 282 282
positive regulation of NF-kappaB transcription factor activity 0.002 0.066 -10000 0 -0.13 95 95
MAP2K4 -0.013 0.096 0.18 2 -0.26 41 43
IKBKB 0.039 0.011 -10000 0 0 43 43
TNFRSF10B 0.033 0.018 -10000 0 0 126 126
TNFRSF10A 0.031 0.018 -10000 0 0 141 141
SMPD1 -0.008 0.044 -10000 0 -0.1 92 92
IKBKG 0.042 0.003 -10000 0 0 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.032 0.018 -10000 0 0 137 137
TRAIL/TRAILR2 0.002 0.067 -10000 0 -0.13 96 96
TRAIL/TRAILR3 0.001 0.067 -10000 0 -0.13 100 100
TRAIL/TRAILR1 -0.001 0.068 -10000 0 -0.13 101 101
TRAIL/TRAILR4 0.002 0.067 -10000 0 -0.13 95 95
TRAIL/TRAILR1/DAP3/GTP 0.01 0.065 -10000 0 -0.1 99 99
IKK complex 0.021 0.089 -10000 0 -0.28 31 31
RIPK1 0.038 0.012 -10000 0 0 48 48
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.027 0.021 -10000 0 -0.13 9 9
MAPK3 -0.01 0.01 -10000 0 -10000 0 0
MAP3K1 -0.008 0.099 -10000 0 -0.28 39 39
TRAILR4 (trimer) 0.032 0.018 -10000 0 0 137 137
TRADD 0.036 0.014 -10000 0 0 76 76
TRAILR1 (trimer) 0.031 0.018 -10000 0 0 141 141
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.022 0.082 -10000 0 -0.18 95 95
CFLAR 0.04 0.008 -10000 0 0 21 21
MAPK1 -0.01 0.01 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP 0.026 0.082 -10000 0 -0.11 87 87
mol:ceramide -0.007 0.044 -10000 0 -0.1 92 92
FADD 0.04 0.008 -10000 0 0 21 21
MAPK8 -0.021 0.1 0.2 5 -0.26 51 56
TRAF2 0.04 0.009 -10000 0 0 29 29
TRAILR3 (trimer) 0.032 0.018 -10000 0 0 134 134
CHUK 0.038 0.012 -10000 0 0 52 52
TRAIL/TRAILR1/FADD 0.01 0.07 -10000 0 -0.12 98 98
DAP3 0.039 0.011 -10000 0 0 40 40
CASP10 -0.006 0.1 0.16 82 -0.2 79 161
JNK cascade 0.002 0.066 -10000 0 -0.13 95 95
TRAIL (trimer) 0.021 0.021 -10000 0 0 282 282
TNFRSF10C 0.032 0.018 -10000 0 0 134 134
TRAIL/TRAILR1/DAP3/GTP/FADD 0.021 0.073 -10000 0 -0.1 95 95
TRAIL/TRAILR2/FADD 0.013 0.069 -10000 0 -0.11 94 94
cell death -0.007 0.044 -10000 0 -0.1 92 92
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.022 0.082 -10000 0 -0.18 92 92
TRAILR2 (trimer) 0.032 0.018 -10000 0 0 126 126
CASP8 -0.001 0.11 -10000 0 -0.65 13 13
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.028 0.082 -10000 0 -0.11 81 81
TCGA08_retinoblastoma

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
CDKN2B 0.029 0.027 -10000 0 -0.046 42 42
CDKN2C 0.029 0.029 -10000 0 -0.046 45 45
CDKN2A 0.022 0.03 -10000 0 -0.039 61 61
CCND2 0.009 0.045 0.11 77 -0.12 2 79
RB1 -0.012 0.066 0.24 6 -0.14 83 89
CDK4 0.01 0.056 0.13 79 -0.12 19 98
CDK6 0.006 0.063 0.13 79 -0.12 43 122
G1/S progression 0.02 0.075 0.14 107 -0.23 8 115
PDGFR-alpha signaling pathway

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
PDGFRA 0.018 0.036 -10000 0 -0.054 79 79
PDGF/PDGFRA/CRKL 0.015 0.07 -10000 0 -0.14 78 78
positive regulation of JUN kinase activity 0.048 0.083 -10000 0 -0.11 99 99
CRKL 0.039 0.011 -10000 0 0 38 38
PDGF/PDGFRA/Caveolin-3 0.014 0.072 -10000 0 -0.1 129 129
AP1 -0.12 0.26 -10000 0 -0.65 99 99
mol:IP3 -0.015 0.045 0.075 26 -0.095 80 106
PLCG1 -0.015 0.045 0.075 26 -0.095 80 106
PDGF/PDGFRA/alphaV Integrin -0.006 0.09 -10000 0 -0.16 128 128
RAPGEF1 0.04 0.008 -10000 0 0 23 23
CRK 0.038 0.012 -10000 0 0 51 51
mol:Ca2+ -0.015 0.045 0.075 26 -0.095 80 106
CAV3 0.04 0.008 -10000 0 0 22 22
CAV1 0.036 0.015 -10000 0 0 80 80
SHC/Grb2/SOS1 0.051 0.085 -10000 0 -0.12 99 99
PDGF/PDGFRA/Shf 0.014 0.071 -10000 0 -0.14 82 82
FOS -0.12 0.26 0.32 1 -0.64 98 99
JUN -0.033 0.043 0.23 3 -0.2 10 13
oligodendrocyte development -0.006 0.09 -10000 0 -0.16 128 128
GRB2 0.041 0.007 -10000 0 0 16 16
PIK3R1 0.034 0.017 -10000 0 0 107 107
mol:DAG -0.015 0.045 0.075 26 -0.095 80 106
PDGF/PDGFRA 0.018 0.036 -10000 0 -0.054 79 79
actin cytoskeleton reorganization 0.015 0.071 -10000 0 -0.1 127 127
SRF -0.007 0.024 0.033 124 -10000 0 124
SHC1 0.04 0.01 -10000 0 0 31 31
PI3K 0.012 0.08 -10000 0 -0.14 91 91
PDGF/PDGFRA/Crk/C3G 0.036 0.071 -10000 0 -0.12 82 82
JAK1 -0.01 0.02 0.027 43 -10000 0 43
ELK1/SRF -0.025 0.064 0.15 18 -0.16 56 74
SHB 0.041 0.007 -10000 0 0 17 17
SHF 0.039 0.011 -10000 0 0 40 40
CSNK2A1 0.036 0.031 0.084 1 -0.028 60 61
GO:0007205 -0.024 0.071 0.086 23 -0.2 60 83
SOS1 0.038 0.013 -10000 0 0 56 56
Ras protein signal transduction 0.048 0.083 -10000 0 -0.11 99 99
PDGF/PDGFRA/SHB 0.015 0.071 -10000 0 -0.1 127 127
PDGF/PDGFRA/Caveolin-1 0.013 0.074 -10000 0 -0.15 74 74
ITGAV 0.033 0.017 -10000 0 0 117 117
ELK1 -0.025 0.079 0.2 17 -0.18 65 82
PIK3CA 0.03 0.019 -10000 0 0 155 155
PDGF/PDGFRA/Crk 0.014 0.07 -10000 0 -0.14 79 79
JAK-STAT cascade -0.01 0.02 0.027 43 -10000 0 43
cell proliferation 0.014 0.07 -10000 0 -0.14 82 82
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 0.033 0.017 -10000 0 0 114 114
GNB1/GNG2 -0.064 0.086 -10000 0 -0.18 191 191
AKT1 -0.027 0.14 0.25 2 -0.23 76 78
EGF 0.038 0.012 -10000 0 0 52 52
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.004 0.06 0.21 11 -0.18 2 13
mol:Ca2+ -0.052 0.19 0.28 4 -0.29 197 201
LYN 0.001 0.057 0.22 9 -0.17 4 13
RhoA/GTP -0.019 0.088 0.14 5 -0.13 182 187
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.072 0.21 0.32 1 -0.34 192 193
GNG2 0.039 0.01 -10000 0 0 34 34
ARRB2 0.039 0.011 -10000 0 0 43 43
TP alpha/Gq family/GDP/G beta5/gamma2 -0.023 0.16 -10000 0 -0.52 46 46
G beta5/gamma2 -0.073 0.12 -10000 0 -0.24 189 189
PRKCH -0.072 0.22 0.33 1 -0.35 190 191
DNM1 0.039 0.011 -10000 0 0 38 38
TXA2/TP beta/beta Arrestin3 0.029 0.022 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR 0.041 0.006 -10000 0 0 12 12
G12 family/GTP -0.066 0.18 -10000 0 -0.3 190 190
ADRBK1 0.041 0.005 -10000 0 0 7 7
ADRBK2 0.036 0.015 -10000 0 0 84 84
RhoA/GTP/ROCK1 0.052 0.022 -10000 0 -0.11 8 8
mol:GDP 0.031 0.16 0.43 47 -0.23 1 48
mol:NADP 0.038 0.012 -10000 0 0 48 48
RAB11A 0.04 0.009 -10000 0 0 24 24
PRKG1 0.04 0.009 -10000 0 0 29 29
mol:IP3 -0.075 0.23 0.35 1 -0.37 197 198
cell morphogenesis 0.051 0.022 -10000 0 -0.11 8 8
PLCB2 -0.12 0.3 0.38 1 -0.5 196 197
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.001 0.053 0.22 8 -0.18 2 10
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.002 0.057 0.2 10 -0.18 3 13
RHOA 0.041 0.007 -10000 0 0 14 14
PTGIR 0.04 0.01 -10000 0 0 32 32
PRKCB1 -0.077 0.23 0.32 2 -0.37 192 194
GNAQ 0.038 0.012 -10000 0 0 49 49
mol:L-citrulline 0.038 0.012 -10000 0 0 48 48
TXA2/TXA2-R family -0.12 0.3 0.38 1 -0.52 191 192
LCK 0.003 0.058 0.2 13 -0.18 2 15
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.052 0.049 0.23 2 -0.15 8 10
TXA2-R family/G12 family/GDP/G beta/gamma 0.018 0.1 -10000 0 -0.42 27 27
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.048 0.05 0.2 4 -0.15 8 12
MAPK14 -0.04 0.15 0.23 6 -0.23 183 189
TGM2/GTP -0.085 0.25 0.4 1 -0.4 188 189
MAPK11 -0.048 0.14 0.22 5 -0.22 190 195
ARHGEF1 -0.029 0.12 0.2 10 -0.18 184 194
GNAI2 0.041 0.007 -10000 0 0 15 15
JNK cascade -0.077 0.23 0.33 2 -0.38 191 193
RAB11/GDP 0.04 0.009 -10000 0 0 24 24
ICAM1 -0.058 0.2 0.26 8 -0.32 184 192
cAMP biosynthetic process -0.07 0.21 0.33 1 -0.34 192 193
Gq family/GTP/EBP50 0.01 0.05 0.25 2 -0.14 45 47
actin cytoskeleton reorganization 0.051 0.022 -10000 0 -0.11 8 8
SRC 0.003 0.058 0.2 10 -0.18 2 12
GNB5 0.04 0.009 -10000 0 0 28 28
GNB1 0.041 0.005 -10000 0 0 7 7
EGF/EGFR 0.002 0.075 0.22 11 -0.2 13 24
VCAM1 -0.062 0.21 0.27 7 -0.33 190 197
TP beta/Gq family/GDP/G beta5/gamma2 -0.023 0.16 -10000 0 -0.52 46 46
platelet activation -0.057 0.19 0.29 3 -0.3 192 195
PGI2/IP 0.028 0.016 -10000 0 -0.13 5 5
PRKACA 0.019 0.023 -10000 0 -0.16 7 7
Gq family/GDP/G beta5/gamma2 -0.015 0.13 -10000 0 -0.44 39 39
TXA2/TP beta/beta Arrestin2 0.014 0.062 -10000 0 -0.3 15 15
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.004 0.024 0.11 6 -0.15 7 13
mol:DAG -0.089 0.26 0.36 1 -0.42 191 192
EGFR 0.037 0.014 -10000 0 0 72 72
TXA2/TP alpha -0.1 0.28 0.38 1 -0.46 192 193
Gq family/GTP -0.008 0.065 -10000 0 -0.18 65 65
YES1 0.002 0.057 0.2 10 -0.18 2 12
GNAI2/GTP 0.027 0.045 -10000 0 -0.14 12 12
PGD2/DP 0.03 0.005 -10000 0 -10000 0 0
SLC9A3R1 0.038 0.012 -10000 0 0 48 48
FYN 0.001 0.058 0.2 10 -0.16 8 18
mol:NO 0.038 0.012 -10000 0 0 48 48
GNA15 0.037 0.014 -10000 0 0 69 69
PGK/cGMP 0.049 0.019 -10000 0 -10000 0 0
RhoA/GDP 0.041 0.007 -10000 0 0 14 14
TP alpha/TGM2/GDP/G beta/gamma 0.06 0.063 0.26 1 -0.19 5 6
NOS3 0.038 0.012 -10000 0 0 48 48
RAC1 0.039 0.01 -10000 0 0 33 33
PRKCA -0.072 0.22 0.32 3 -0.36 189 192
PRKCB -0.07 0.22 0.29 2 -0.35 191 193
PRKCE -0.071 0.22 0.32 5 -0.36 189 194
PRKCD -0.081 0.23 0.3 3 -0.38 188 191
PRKCG -0.08 0.24 0.34 1 -0.38 192 193
muscle contraction -0.11 0.28 0.38 1 -0.48 192 193
PRKCZ -0.07 0.21 0.3 2 -0.34 191 193
ARR3 0.042 0.002 -10000 0 0 1 1
TXA2/TP beta 0.045 0.052 0.24 1 -0.14 9 10
PRKCQ -0.073 0.22 0.36 3 -0.36 184 187
MAPKKK cascade -0.1 0.26 0.36 1 -0.44 194 195
SELE -0.051 0.18 0.27 4 -0.29 191 195
TP beta/GNAI2/GDP/G beta/gamma 0.071 0.059 0.26 1 -0.19 4 5
ROCK1 0.041 0.007 -10000 0 0 14 14
GNA14 0.039 0.01 -10000 0 0 33 33
chemotaxis -0.15 0.34 0.39 1 -0.6 191 192
GNA12 0.04 0.01 -10000 0 0 32 32
GNA13 0.04 0.009 -10000 0 0 28 28
GNA11 0.037 0.013 -10000 0 0 61 61
Rac1/GTP 0.029 0.01 -10000 0 -0.13 1 1
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.037 0.013 -10000 0 0 64 64
alphaV beta3 Integrin 0.014 0.078 -10000 0 -0.15 93 93
PTK2 -0.044 0.14 -10000 0 -0.31 95 95
positive regulation of JNK cascade -0.032 0.14 -10000 0 -0.28 92 92
CDC42/GDP -0.039 0.2 -10000 0 -0.38 96 96
Rac1/GDP -0.041 0.19 -10000 0 -0.38 92 92
RAP1B 0.038 0.013 -10000 0 0 59 59
RAP1A 0.039 0.01 -10000 0 0 35 35
CTNNB1 0.04 0.01 -10000 0 0 31 31
CDC42/GTP -0.037 0.18 -10000 0 -0.34 91 91
nectin-3/I-afadin 0.01 0.076 -10000 0 -0.14 100 100
RAPGEF1 -0.056 0.18 -10000 0 -0.37 113 113
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.063 0.2 -10000 0 -0.41 116 116
PDGFB-D/PDGFRB 0.037 0.013 -10000 0 0 64 64
TLN1 -0.038 0.084 0.19 2 -0.25 59 61
Rap1/GTP -0.044 0.14 -10000 0 -0.29 117 117
IQGAP1 0.037 0.014 -10000 0 0 69 69
Rap1/GTP/I-afadin 0.043 0.066 -10000 0 -0.11 68 68
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.01 0.076 -10000 0 -0.14 100 100
PVR 0.04 0.009 -10000 0 0 27 27
Necl-5(dimer) 0.04 0.009 -10000 0 0 27 27
mol:GDP -0.067 0.22 -10000 0 -0.45 97 97
MLLT4 0.034 0.017 -10000 0 0 107 107
PIK3CA 0.03 0.019 -10000 0 0 155 155
PI3K 0.024 0.091 -10000 0 -0.13 91 91
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.042 0.047 -10000 0 -0.14 28 28
positive regulation of lamellipodium assembly -0.041 0.16 -10000 0 -0.3 95 95
PVRL1 0.04 0.008 -10000 0 0 21 21
PVRL3 0.029 0.019 -10000 0 0 174 174
PVRL2 0.039 0.011 -10000 0 0 44 44
PIK3R1 0.034 0.017 -10000 0 0 107 107
CDH1 0.035 0.016 -10000 0 0 98 98
CLDN1 0.023 0.021 -10000 0 0 259 259
JAM-A/CLDN1 0.013 0.089 -10000 0 -0.12 124 124
SRC -0.083 0.21 -10000 0 -0.44 123 123
ITGB3 0.033 0.017 -10000 0 0 121 121
nectin-1(dimer)/I-afadin/I-afadin 0.042 0.047 -10000 0 -0.14 28 28
FARP2 -0.059 0.22 -10000 0 -0.48 59 59
RAC1 0.039 0.01 -10000 0 0 33 33
CTNNA1 0.039 0.011 -10000 0 0 38 38
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.023 0.078 -10000 0 -0.12 100 100
nectin-1/I-afadin 0.042 0.047 -10000 0 -0.14 28 28
nectin-2/I-afadin 0.038 0.051 -10000 0 -0.14 33 33
RAC1/GTP/IQGAP1/filamentous actin 0.038 0.046 -10000 0 -0.11 42 42
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.025 0.078 -10000 0 -0.12 95 95
CDC42/GTP/IQGAP1/filamentous actin 0.04 0.046 -10000 0 -0.11 42 42
F11R 0.04 0.01 -10000 0 0 32 32
positive regulation of filopodium formation -0.032 0.14 -10000 0 -0.28 92 92
alphaV/beta3 Integrin/Talin -0.031 0.11 0.26 2 -0.22 99 101
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.051 -10000 0 -0.14 33 33
nectin-2(dimer)/I-afadin/I-afadin 0.038 0.051 -10000 0 -0.14 33 33
PIP5K1C -0.032 0.087 -10000 0 -0.17 118 118
VAV2 -0.075 0.24 -10000 0 -0.49 86 86
RAP1/GDP -0.039 0.18 -10000 0 -0.36 101 101
ITGAV 0.033 0.017 -10000 0 0 117 117
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.021 0.079 -10000 0 -0.12 101 101
nectin-3(dimer)/I-afadin/I-afadin 0.01 0.076 -10000 0 -0.14 100 100
Rac1/GTP -0.048 0.19 -10000 0 -0.37 95 95
PTPRM -0.029 0.097 -10000 0 -0.18 122 122
E-cadherin/beta catenin/alpha catenin 0.063 0.09 -10000 0 -0.13 57 57
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.04 0.009 -10000 0 0 24 24
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.007 0.005 0 205 -10000 0 205
GNB1/GNG2 0.041 0.07 -10000 0 -0.11 89 89
regulation of S phase of mitotic cell cycle -0.011 0.076 -10000 0 -0.17 90 90
GNAO1 0.034 0.016 -10000 0 0 101 101
HRAS 0.039 0.01 -10000 0 0 31 31
SHBG/T-DHT 0.027 0.007 -10000 0 -10000 0 0
PELP1 0.039 0.01 -10000 0 0 35 35
AKT1 -0.009 0.004 0.002 48 -10000 0 48
MAP2K1 -0.033 0.079 0.17 27 -0.17 80 107
T-DHT/AR 0.006 0.055 -10000 0 -0.13 79 79
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.007 103 103
GNAI2 0.041 0.007 -10000 0 0 15 15
GNAI3 0.039 0.011 -10000 0 0 45 45
GNAI1 0.035 0.016 -10000 0 0 95 95
mol:GDP -0.042 0.088 -10000 0 -0.26 71 71
cell proliferation -0.07 0.17 0.24 6 -0.39 108 114
PIK3CA 0.03 0.019 -10000 0 0 155 155
FOS -0.12 0.29 0.27 1 -0.7 105 106
mol:Ca2+ -0.006 0.021 -10000 0 -0.048 82 82
MAPK3 -0.052 0.13 0.21 8 -0.3 95 103
MAPK1 -0.042 0.14 -10000 0 -0.35 58 58
PIK3R1 0.034 0.017 -10000 0 0 107 107
mol:IP3 0 0.002 0.002 86 -0.004 103 189
cAMP biosynthetic process -0.001 0.024 0.18 5 -10000 0 5
GNG2 0.039 0.01 -10000 0 0 34 34
potassium channel inhibitor activity 0 0.002 0.002 86 -0.004 103 189
HRAS/GTP 0.025 0.078 -10000 0 -0.092 143 143
actin cytoskeleton reorganization 0.029 0.052 -10000 0 -0.11 46 46
SRC 0.039 0.01 -10000 0 0 36 36
voltage-gated calcium channel activity 0 0.002 0.002 86 -0.004 103 189
PI3K 0.023 0.052 -10000 0 -0.12 47 47
apoptosis 0.061 0.18 0.38 114 -0.22 5 119
T-DHT/AR/PELP1 0.025 0.058 -10000 0 -0.11 79 79
HRAS/GDP -0.006 0.11 -10000 0 -0.25 70 70
CREB1 -0.076 0.18 0.22 5 -0.41 114 119
RAC1-CDC42/GTP 0.038 0.059 -10000 0 -0.11 46 46
AR 0.033 0.017 -10000 0 0 122 122
GNB1 0.041 0.005 -10000 0 0 7 7
RAF1 -0.02 0.076 0.18 29 -0.18 17 46
RAC1-CDC42/GDP 0.017 0.12 0.19 3 -0.25 66 69
T-DHT/AR/PELP1/Src 0.039 0.066 -10000 0 -0.11 78 78
MAP2K2 -0.03 0.074 0.17 22 -0.17 70 92
T-DHT/AR/PELP1/Src/PI3K -0.012 0.077 -10000 0 -0.17 90 90
GNAZ 0.039 0.011 -10000 0 0 42 42
SHBG 0.039 0.01 -10000 0 0 34 34
Gi family/GNB1/GNG2/GDP -0.005 0.099 -10000 0 -0.3 34 34
mol:T-DHT 0 0.001 -10000 0 -0.003 31 31
RAC1 0.039 0.01 -10000 0 0 33 33
GNRH1 -0.008 0.005 0 125 -10000 0 125
Gi family/GTP -0.02 0.077 -10000 0 -0.19 70 70
CDC42 0.04 0.009 -10000 0 0 24 24
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.039 0.053 -10000 0 -0.14 38 38
ATM 0.037 0.014 -10000 0 0 73 73
UBE2D3 0.038 0.012 -10000 0 0 47 47
PRKDC 0.039 0.011 -10000 0 0 44 44
ATR 0.035 0.016 -10000 0 0 92 92
UBE2L3 0.039 0.011 -10000 0 0 40 40
FANCD2 -0.004 0.089 -10000 0 -0.25 58 58
protein ubiquitination 0.013 0.1 -10000 0 -0.13 156 156
XRCC5 0.039 0.011 -10000 0 0 39 39
XRCC6 0.037 0.014 -10000 0 0 69 69
M/R/N Complex 0.048 0.071 -10000 0 -0.14 52 52
MRE11A 0.038 0.012 -10000 0 0 54 54
DNA-PK 0.054 0.066 -10000 0 -0.14 46 46
FA complex/FANCD2/Ubiquitin -0.007 0.13 -10000 0 -0.41 34 34
FANCF 0.04 0.009 -10000 0 0 28 28
BRCA1 0.034 0.016 -10000 0 0 106 106
CCNE1 0.028 0.02 -10000 0 0 189 189
CDK2/Cyclin E1 0.01 0.077 -10000 0 -0.14 104 104
FANCG 0.04 0.008 -10000 0 0 22 22
BRCA1/BACH1/BARD1 0.027 0.068 -10000 0 -0.14 74 74
FANCE 0.041 0.007 -10000 0 0 18 18
FANCC 0.04 0.009 -10000 0 0 29 29
NBN 0.035 0.016 -10000 0 0 96 96
FANCA 0.035 0.016 -10000 0 0 94 94
DNA repair -0.02 0.13 0.26 15 -0.36 39 54
BRCA1/BARD1/ubiquitin 0.027 0.068 -10000 0 -0.14 74 74
BARD1/DNA-PK 0.065 0.082 -10000 0 -0.14 60 60
FANCL 0.038 0.012 -10000 0 0 55 55
mRNA polyadenylation -0.039 0.053 0.14 38 -10000 0 38
BRCA1/BARD1/CTIP/M/R/N Complex -0.025 0.14 0.16 3 -0.29 81 84
BRCA1/BACH1/BARD1/TopBP1 0.037 0.077 -10000 0 -0.13 81 81
BRCA1/BARD1/P53 0.002 0.1 -10000 0 -0.13 191 191
BARD1/CSTF1/BRCA1 0.037 0.072 -10000 0 -0.12 75 75
BRCA1/BACH1 0.034 0.016 -10000 0 0 106 106
BARD1 0.037 0.014 -10000 0 0 66 66
PCNA 0.034 0.016 -10000 0 0 100 100
BRCA1/BARD1/UbcH5C 0.041 0.072 -10000 0 -0.12 75 75
BRCA1/BARD1/UbcH7 0.042 0.071 -10000 0 -0.12 73 73
BRCA1/BARD1/RAD51/PCNA 0.035 0.095 -10000 0 -0.13 115 115
BARD1/DNA-PK/P53 0.019 0.12 -10000 0 -0.13 179 179
BRCA1/BARD1/Ubiquitin 0.027 0.068 -10000 0 -0.14 74 74
BRCA1/BARD1/CTIP 0.014 0.086 0.18 9 -0.13 124 133
FA complex 0.012 0.087 -10000 0 -0.3 26 26
BARD1/EWS 0.042 0.05 -10000 0 -0.13 35 35
RBBP8 -0.015 0.009 -10000 0 -10000 0 0
TP53 0.026 0.02 -10000 0 0 212 212
TOPBP1 0.038 0.013 -10000 0 0 59 59
G1/S transition of mitotic cell cycle 0 0.1 0.13 191 -10000 0 191
BRCA1/BARD1 0.018 0.11 -10000 0 -0.13 156 156
CSTF1 0.037 0.014 -10000 0 0 68 68
BARD1/EWS-Fli1 0.02 0.038 -10000 0 -0.13 34 34
CDK2 0.038 0.013 -10000 0 0 59 59
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.035 0.016 -10000 0 0 93 93
RAD50 0.039 0.011 -10000 0 0 42 42
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.027 0.068 -10000 0 -0.14 74 74
EWSR1 0.038 0.012 -10000 0 0 54 54
Syndecan-4-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
PTK2 -0.056 0.21 -10000 0 -0.34 164 164
Syndecan-4/Syndesmos -0.037 0.19 -10000 0 -0.4 88 88
positive regulation of JNK cascade -0.057 0.19 -10000 0 -0.38 102 102
Syndecan-4/ADAM12 -0.054 0.18 -10000 0 -0.41 85 85
CCL5 0.03 0.019 -10000 0 0 161 161
Rac1/GDP 0.029 0.01 -10000 0 -0.13 1 1
DNM2 0.037 0.014 -10000 0 0 72 72
ITGA5 0.038 0.013 -10000 0 0 58 58
SDCBP 0.036 0.014 -10000 0 0 75 75
PLG 0.031 0.03 -10000 0 -0.042 62 62
ADAM12 0.03 0.019 -10000 0 0 163 163
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.039 0.01 -10000 0 0 33 33
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.023 0.023 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.04 0.19 -10000 0 -0.39 89 89
Syndecan-4/CXCL12/CXCR4 -0.06 0.2 -10000 0 -0.4 102 102
Syndecan-4/Laminin alpha3 -0.047 0.19 -10000 0 -0.41 87 87
MDK 0.04 0.009 -10000 0 0 24 24
Syndecan-4/FZD7 -0.041 0.19 -10000 0 -0.41 87 87
Syndecan-4/Midkine -0.039 0.2 -10000 0 -0.4 90 90
FZD7 0.037 0.013 -10000 0 0 65 65
Syndecan-4/FGFR1/FGF -0.025 0.18 -10000 0 -0.38 80 80
THBS1 0.027 0.02 -10000 0 0 199 199
integrin-mediated signaling pathway -0.056 0.18 -10000 0 -0.4 89 89
positive regulation of MAPKKK cascade -0.057 0.19 -10000 0 -0.38 102 102
Syndecan-4/TACI -0.037 0.19 -10000 0 -0.4 90 90
CXCR4 0.033 0.017 -10000 0 0 117 117
cell adhesion -0.032 0.097 0.22 4 -0.2 127 131
Syndecan-4/Dynamin -0.036 0.19 -10000 0 -0.4 85 85
Syndecan-4/TSP1 -0.058 0.19 -10000 0 -0.41 92 92
Syndecan-4/GIPC -0.037 0.18 -10000 0 -0.39 85 85
Syndecan-4/RANTES -0.051 0.2 -10000 0 -0.41 95 95
ITGB1 0.039 0.011 -10000 0 0 38 38
LAMA1 0.034 0.017 -10000 0 0 108 108
LAMA3 0.031 0.018 -10000 0 0 147 147
RAC1 0.039 0.01 -10000 0 0 33 33
PRKCA 0.002 0.12 0.8 9 -10000 0 9
Syndecan-4/alpha-Actinin -0.039 0.2 -10000 0 -0.4 91 91
TFPI 0.039 0.01 -10000 0 0 35 35
F2 0.038 0.026 0.084 13 -0.038 48 61
alpha5/beta1 Integrin 0.046 0.045 -10000 0 -0.14 27 27
positive regulation of cell adhesion -0.056 0.17 0.24 1 -0.4 86 87
ACTN1 0.039 0.011 -10000 0 0 42 42
TNC 0.027 0.02 -10000 0 0 198 198
Syndecan-4/CXCL12 -0.057 0.2 -10000 0 -0.41 96 96
FGF6 0.037 0.014 -10000 0 0 73 73
RHOA 0.041 0.007 -10000 0 0 14 14
CXCL12 0.029 0.019 -10000 0 0 172 172
TNFRSF13B 0.039 0.011 -10000 0 0 42 42
FGF2 0.039 0.011 -10000 0 0 44 44
FGFR1 0.033 0.017 -10000 0 0 122 122
Syndecan-4/PI-4-5-P2 -0.06 0.18 -10000 0 -0.4 90 90
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.017 0.025 -10000 0 -0.039 28 28
cell migration -0.011 0.013 -10000 0 -10000 0 0
PRKCD 0.033 0.028 -10000 0 -0.041 51 51
vasculogenesis -0.056 0.18 -10000 0 -0.39 92 92
SDC4 -0.052 0.18 -10000 0 -0.42 82 82
Syndecan-4/Tenascin C -0.058 0.19 -10000 0 -0.42 89 89
Syndecan-4/PI-4-5-P2/PKC alpha -0.018 0.018 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.039 0.19 -10000 0 -0.4 88 88
MMP9 0.027 0.024 -10000 0 -0.04 17 17
Rac1/GTP -0.032 0.098 0.22 4 -0.2 126 130
cytoskeleton organization -0.035 0.18 -10000 0 -0.38 88 88
GIPC1 0.035 0.015 -10000 0 0 89 89
Syndecan-4/TFPI -0.04 0.19 -10000 0 -0.4 88 88
TCGA08_rtk_signaling

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
PDGFRA 0.03 0.019 -10000 0 0 156 156
HRAS 0.04 0.01 -10000 0 0 31 31
EGFR 0.037 0.014 -10000 0 0 72 72
AKT 0.017 0.092 0.23 6 -0.19 36 42
FOXO3 0 0 -10000 0 -10000 0 0
AKT1 0.039 0.011 -10000 0 0 38 38
FOXO1 0 0 -10000 0 -10000 0 0
AKT3 0.03 0.019 -10000 0 0 155 155
FOXO4 0 0 -10000 0 -10000 0 0
MET 0.027 0.02 -10000 0 0 198 198
PIK3CA 0.03 0.019 -10000 0 0 155 155
PIK3CB 0.034 0.016 -10000 0 0 102 102
NRAS 0.04 0.009 -10000 0 0 30 30
PIK3CG 0.033 0.017 -10000 0 0 118 118
PIK3R3 0.035 0.016 -10000 0 0 97 97
PIK3R2 0.037 0.013 -10000 0 0 63 63
NF1 0.034 0.016 -10000 0 0 101 101
RAS 0.005 0.078 0.15 35 -0.24 20 55
ERBB2 0.038 0.012 -10000 0 0 52 52
proliferation/survival/translation -0.017 0.086 0.21 32 -0.21 19 51
PI3K 0.003 0.088 0.18 18 -0.21 45 63
PIK3R1 0.034 0.017 -10000 0 0 107 107
KRAS 0.034 0.016 -10000 0 0 103 103
FOXO 0.037 0.054 0.17 20 -10000 0 20
AKT2 0.038 0.012 -10000 0 0 47 47
PTEN 0.039 0.011 -10000 0 0 38 38
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.065 0.18 -10000 0 -0.39 123 123
IHH 0.022 0.067 -10000 0 -0.099 128 128
SHH Np/Cholesterol/GAS1 0.027 0.027 -10000 0 -0.1 15 15
LRPAP1 0.036 0.014 -10000 0 0 77 77
dorsoventral neural tube patterning -0.027 0.027 0.1 15 -10000 0 15
SMO/beta Arrestin2 0.018 0.12 0.24 1 -0.2 106 107
SMO -0.002 0.11 -10000 0 -0.2 110 110
AKT1 -0.013 0.13 -10000 0 -0.4 35 35
ARRB2 0.039 0.011 -10000 0 0 43 43
BOC 0.036 0.015 -10000 0 0 85 85
ADRBK1 0.041 0.005 -10000 0 0 7 7
heart looping -0.001 0.11 0.19 3 -0.2 110 113
STIL 0 0.096 0.2 29 -0.17 103 132
DHH N/PTCH2 0.058 0.016 -10000 0 -10000 0 0
DHH N/PTCH1 0.003 0.11 -10000 0 -0.19 127 127
PIK3CA 0.03 0.019 -10000 0 0 155 155
DHH 0.041 0.006 -10000 0 0 13 13
PTHLH -0.032 0.17 -10000 0 -0.38 106 106
determination of left/right symmetry -0.001 0.11 0.19 3 -0.2 110 113
PIK3R1 0.034 0.017 -10000 0 0 107 107
skeletal system development -0.032 0.17 -10000 0 -0.38 106 106
IHH N/Hhip 0.035 0.055 -10000 0 -0.06 120 120
DHH N/Hhip 0.055 0.022 -10000 0 -0.14 1 1
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.001 0.11 0.19 3 -0.2 110 113
pancreas development 0.038 0.012 -10000 0 0 55 55
HHAT 0.04 0.008 -10000 0 0 23 23
PI3K 0.024 0.061 -10000 0 -0.15 47 47
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.037 0.014 -10000 0 0 68 68
somite specification -0.001 0.11 0.19 3 -0.2 110 113
SHH Np/Cholesterol/PTCH1 -0.006 0.085 -10000 0 -0.17 108 108
SHH Np/Cholesterol/PTCH2 0.032 0.017 -10000 0 -0.1 3 3
SHH Np/Cholesterol/Megalin 0.021 0.027 -10000 0 -0.1 14 14
SHH -0.018 0.007 -10000 0 -10000 0 0
catabolic process -0.036 0.096 -10000 0 -0.21 128 128
SMO/Vitamin D3 -0.006 0.1 0.2 19 -0.2 106 125
SHH Np/Cholesterol/Hhip 0.03 0.019 -10000 0 -0.1 4 4
LRP2 0.03 0.019 -10000 0 0 162 162
receptor-mediated endocytosis 0.002 0.1 0.19 21 -0.18 103 124
SHH Np/Cholesterol/BOC 0.025 0.029 -10000 0 -0.11 17 17
SHH Np/Cholesterol/CDO 0.023 0.035 -10000 0 -0.1 31 31
mesenchymal cell differentiation -0.03 0.019 0.1 4 -10000 0 4
mol:Vitamin D3 -0.012 0.089 0.2 26 -0.17 107 133
IHH N/PTCH2 0.039 0.054 -10000 0 -0.059 119 119
CDON 0.035 0.016 -10000 0 0 93 93
IHH N/PTCH1 -0.02 0.11 -10000 0 -0.21 128 128
Megalin/LRPAP1 0.029 0.053 -10000 0 -0.14 37 37
PTCH2 0.04 0.009 -10000 0 0 27 27
SHH Np/Cholesterol 0.034 0.047 0.2 42 -0.098 3 45
PTCH1 -0.036 0.096 -10000 0 -0.21 128 128
HHIP 0.038 0.012 -10000 0 0 55 55
Paxillin-dependent events mediated by a4b1

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
CRKL 0.039 0.011 -10000 0 0 38 38
Rac1/GDP 0.033 0.025 -10000 0 -0.024 66 66
DOCK1 0.037 0.013 -10000 0 0 62 62
ITGA4 0.035 0.015 -10000 0 0 88 88
RAC1 0.039 0.01 -10000 0 0 33 33
alpha4/beta7 Integrin 0.033 0.065 -10000 0 -0.14 65 65
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.038 0.012 -10000 0 0 51 51
alpha4/beta1 Integrin 0.047 0.062 -10000 0 -0.12 49 49
alpha4/beta7 Integrin/Paxillin 0.052 0.069 0.18 55 -0.12 50 105
lamellipodium assembly -0.029 0.15 -10000 0 -0.37 72 72
PIK3CA 0.03 0.019 -10000 0 0 155 155
PI3K 0.024 0.061 -10000 0 -0.15 47 47
ARF6 0.041 0.008 -10000 0 0 19 19
TLN1 0.039 0.012 -10000 0 0 46 46
PXN -0.017 0.008 -10000 0 -10000 0 0
PIK3R1 0.034 0.017 -10000 0 0 107 107
ARF6/GTP 0.062 0.071 -10000 0 -0.11 51 51
cell adhesion 0.061 0.077 0.2 47 -0.12 59 106
CRKL/CBL 0.055 0.021 -10000 0 -0.14 1 1
alpha4/beta1 Integrin/Paxillin 0.052 0.067 0.18 51 -0.11 48 99
ITGB1 0.039 0.011 -10000 0 0 38 38
ITGB7 0.039 0.011 -10000 0 0 40 40
ARF6/GDP 0.034 0.025 -10000 0 -0.024 66 66
alpha4/beta1 Integrin/Paxillin/VCAM1 0.025 0.094 0.2 28 -0.13 114 142
p130Cas/Crk/Dock1 0.056 0.054 -10000 0 -0.12 29 29
VCAM1 0.02 0.021 -10000 0 0 289 289
alpha4/beta1 Integrin/Paxillin/Talin 0.063 0.079 0.2 47 -0.12 59 106
alpha4/beta1 Integrin/Paxillin/GIT1 0.069 0.072 0.2 46 -0.11 48 94
BCAR1 0.036 0.014 -10000 0 0 75 75
mol:GDP -0.066 0.071 0.11 48 -0.2 46 94
CBL 0.04 0.008 -10000 0 0 23 23
PRKACA 0.035 0.015 -10000 0 0 89 89
GIT1 0.04 0.009 -10000 0 0 27 27
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.063 0.079 0.2 47 -0.12 59 106
Rac1/GTP -0.034 0.16 -10000 0 -0.41 72 72
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 0.015 0.15 -10000 0 -0.36 31 31
MAP3K8 0.04 0.009 -10000 0 0 21 21
FOS 0.014 0.11 -10000 0 -0.36 15 15
PRKCA 0.026 0.029 -10000 0 -0.015 169 169
PTPN7 0.031 0.032 0.071 1 -0.031 112 113
HRAS 0.039 0.01 -10000 0 0 31 31
PRKCB 0 0.007 0.01 94 -0.013 103 197
NRAS 0.04 0.01 -10000 0 0 30 30
RAS family/GTP 0.054 0.051 -10000 0 -0.11 29 29
MAPK3 0.03 0.081 -10000 0 -0.44 9 9
MAP2K1 0.001 0.096 0.16 3 -0.28 43 46
ELK1 0.028 0.032 -10000 0 -0.038 104 104
BRAF 0.001 0.072 -10000 0 -0.29 27 27
mol:GTP 0 0.002 0.002 90 -0.004 103 193
MAPK1 0.011 0.11 -10000 0 -0.39 30 30
RAF1 -0.002 0.078 -10000 0 -0.28 35 35
KRAS 0.034 0.016 -10000 0 0 103 103
Signaling events mediated by PTP1B

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
PDGFRB 0.037 0.013 -10000 0 0 64 64
Jak2/Leptin Receptor -0.017 0.14 -10000 0 -0.37 58 58
PTP1B/AKT1 -0.034 0.11 -10000 0 -0.23 91 91
FYN 0.034 0.016 -10000 0 0 104 104
p210 bcr-abl/PTP1B -0.052 0.11 -10000 0 -0.25 93 93
EGFR 0.036 0.017 -10000 0 -0.004 83 83
EGF/EGFR -0.025 0.12 -10000 0 -0.24 90 90
CSF1 0.035 0.015 -10000 0 0 89 89
AKT1 0.039 0.011 -10000 0 0 38 38
INSR 0.038 0.012 -10000 0 0 53 53
PTP1B/N-cadherin -0.053 0.12 -10000 0 -0.24 126 126
Insulin Receptor/Insulin -0.008 0.11 -10000 0 -0.21 68 68
HCK 0.036 0.015 -10000 0 0 80 80
CRK 0.038 0.012 -10000 0 0 51 51
TYK2 -0.036 0.12 0.23 22 -0.25 77 99
EGF 0.037 0.017 -10000 0 -0.007 68 68
YES1 0.038 0.013 -10000 0 0 57 57
CAV1 -0.035 0.11 0.19 1 -0.24 80 81
TXN 0.038 0.012 -10000 0 0 49 49
PTP1B/IRS1/GRB2 -0.028 0.13 -10000 0 -0.24 99 99
cell migration 0.052 0.11 0.25 93 -10000 0 93
STAT3 0.038 0.013 -10000 0 0 56 56
PRLR 0.038 0.017 -10000 0 -10000 0 0
ITGA2B 0.039 0.009 -10000 0 0 30 30
CSF1R 0.035 0.016 -10000 0 0 98 98
Prolactin Receptor/Prolactin 0.055 0.029 -10000 0 -10000 0 0
FGR 0.041 0.007 -10000 0 0 17 17
PTP1B/p130 Cas -0.036 0.12 -10000 0 -0.24 93 93
Crk/p130 Cas -0.029 0.12 -10000 0 -0.25 85 85
DOK1 -0.037 0.11 -10000 0 -0.25 69 69
JAK2 -0.03 0.14 -10000 0 -0.39 59 59
Jak2/Leptin Receptor/Leptin -0.024 0.14 0.26 1 -0.26 85 86
PIK3R1 0.034 0.017 -10000 0 0 107 107
PTPN1 -0.052 0.11 -10000 0 -0.26 93 93
LYN 0.036 0.015 -10000 0 0 83 83
CDH2 0.02 0.021 -10000 0 0 299 299
SRC 0.01 0.083 -10000 0 -0.5 10 10
ITGB3 0.032 0.017 -10000 0 0 121 121
CAT1/PTP1B -0.037 0.13 0.26 4 -0.28 73 77
CAPN1 0.039 0.009 -10000 0 0 25 25
CSK 0.04 0.008 -10000 0 0 21 21
PI3K -0.01 0.11 -10000 0 -0.21 65 65
mol:H2O2 0.002 0.005 0.03 1 -10000 0 1
STAT3 (dimer) -0.02 0.13 0.25 1 -0.25 83 84
negative regulation of transcription -0.029 0.14 -10000 0 -0.38 59 59
FCGR2A 0.032 0.018 -10000 0 0 129 129
FER 0.037 0.012 -10000 0 0 55 55
alphaIIb/beta3 Integrin 0.038 0.05 -10000 0 -0.14 34 34
BLK 0.033 0.017 -10000 0 0 117 117
Insulin Receptor/Insulin/Shc 0.068 0.037 -10000 0 -0.12 5 5
RHOA 0.04 0.007 -10000 0 0 14 14
LEPR 0.039 0.012 -10000 0 0 45 45
BCAR1 0.036 0.014 -10000 0 0 75 75
p210 bcr-abl/Grb2 0.041 0.007 -10000 0 0 16 16
mol:NADPH -0.001 0.002 -10000 0 -10000 0 0
TRPV6 -0.007 0.12 0.22 6 -0.3 44 50
PRL 0.042 0.012 -10000 0 -10000 0 0
SOCS3 -0.02 0.25 -10000 0 -1.1 26 26
SPRY2 0.023 0.021 -10000 0 0 247 247
Insulin Receptor/Insulin/IRS1 0.07 0.038 -10000 0 -0.12 8 8
CSF1/CSF1R -0.044 0.13 -10000 0 -0.26 106 106
Ras protein signal transduction 0.005 0.065 0.6 5 -10000 0 5
IRS1 0.04 0.008 -10000 0 0 22 22
INS 0.04 0.01 -10000 0 0 30 30
LEP 0.039 0.01 -10000 0 0 33 33
STAT5B -0.041 0.12 -10000 0 -0.26 93 93
STAT5A -0.042 0.12 -10000 0 -0.26 97 97
GRB2 0.041 0.007 -10000 0 0 16 16
PDGFB-D/PDGFRB -0.043 0.12 -10000 0 -0.24 100 100
CSN2 0.041 0.068 0.43 1 -10000 0 1
PIK3CA 0.03 0.019 -10000 0 0 155 155
LAT -0.058 0.19 -10000 0 -0.48 87 87
YBX1 0.048 0.02 -10000 0 -0.28 1 1
LCK 0.04 0.009 -10000 0 0 29 29
SHC1 0.04 0.01 -10000 0 0 31 31
NOX4 0.021 0.021 -10000 0 0 281 281
IL6-mediated signaling events

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
BCL2L1 -0.089 0.35 -10000 0 -0.79 86 86
CRP -0.082 0.33 0.49 2 -0.76 83 85
cell cycle arrest -0.12 0.39 -10000 0 -0.87 95 95
TIMP1 -0.1 0.36 -10000 0 -0.74 117 117
IL6ST 0.024 0.036 -10000 0 -0.041 86 86
Rac1/GDP -0.011 0.17 0.29 5 -0.36 68 73
AP1 -0.029 0.21 -10000 0 -0.47 78 78
GAB2 0.033 0.02 -10000 0 -0.001 143 143
TNFSF11 -0.087 0.33 -10000 0 -0.76 82 82
HSP90B1 0.012 0.092 -10000 0 -0.84 3 3
GAB1 0.039 0.014 -10000 0 -0.035 3 3
MAPK14 -0.024 0.16 0.24 2 -0.51 37 39
AKT1 -0.01 0.15 0.31 4 -0.46 34 38
FOXO1 -0.011 0.14 0.3 4 -0.43 34 38
MAP2K6 -0.02 0.15 0.22 4 -0.38 55 59
mol:GTP 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.032 0.21 0.3 8 -0.42 86 94
MITF -0.017 0.14 0.22 8 -0.32 68 76
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.037 0.014 -10000 0 0 66 66
A2M -0.12 0.4 -10000 0 -1.2 66 66
CEBPB 0.037 0.015 -10000 0 0 79 79
GRB2/SOS1/GAB family/SHP2 -0.009 0.16 0.28 6 -0.38 66 72
STAT3 -0.14 0.43 -10000 0 -0.96 95 95
STAT1 -0.069 0.28 -10000 0 -0.83 64 64
CEBPD -0.086 0.34 0.52 2 -0.78 82 84
PIK3CA 0.031 0.02 -10000 0 -0.001 158 158
PI3K 0.024 0.062 -10000 0 -0.15 48 48
JUN 0.036 0.015 -10000 0 0 80 80
PIAS3/MITF -0.006 0.15 0.24 4 -0.33 63 67
MAPK11 -0.023 0.16 0.24 2 -0.55 33 35
STAT3 (dimer)/FOXO1 -0.096 0.36 0.44 5 -0.72 109 114
GRB2/SOS1/GAB family 0.032 0.13 0.29 4 -0.27 34 38
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK 0.009 0.11 0.19 3 -0.25 53 56
GRB2 0.042 0.01 -10000 0 -0.006 19 19
JAK2 0.035 0.015 -10000 0 0 91 91
LBP -0.031 0.27 0.44 1 -0.57 76 77
PIK3R1 0.034 0.018 -10000 0 -0.043 3 3
JAK1 0.034 0.028 -10000 0 -0.044 55 55
MYC -0.071 0.42 0.5 10 -0.86 106 116
FGG -0.086 0.33 -10000 0 -0.76 82 82
macrophage differentiation -0.12 0.39 -10000 0 -0.87 95 95
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.05 0.1 -10000 0 -0.18 47 47
JUNB -0.1 0.39 0.5 4 -0.86 98 102
FOS 0.026 0.02 -10000 0 0 207 207
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.009 0.16 0.23 4 -0.34 70 74
STAT1/PIAS1 -0.019 0.18 0.29 2 -0.37 79 81
GRB2/SOS1/GAB family/SHP2/PI3K -0.011 0.16 -10000 0 -0.41 47 47
STAT3 (dimer) -0.14 0.41 -10000 0 -0.93 95 95
PRKCD -0.06 0.26 0.33 7 -0.54 97 104
IL6R 0.032 0.027 -10000 0 -0.043 46 46
SOCS3 -0.035 0.21 -10000 0 -0.97 22 22
gp130 (dimer)/JAK1/JAK1/LMO4 0.044 0.089 -10000 0 -0.14 61 61
Rac1/GTP -0.017 0.18 0.3 5 -0.38 76 81
HCK 0.036 0.015 -10000 0 0 80 80
MAPKKK cascade -0.024 0.22 -10000 0 -0.49 81 81
bone resorption -0.079 0.31 -10000 0 -0.72 82 82
IRF1 -0.14 0.42 -10000 0 -0.93 112 112
mol:GDP -0.02 0.15 0.24 6 -0.35 66 72
SOS1 0.039 0.015 -10000 0 -0.002 59 59
VAV1 -0.021 0.15 0.23 5 -0.36 66 71
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.012 0.17 -10000 0 -0.47 50 50
PTPN11 0 0.16 -10000 0 -0.78 22 22
IL6/IL6RA 0.029 0.063 -10000 0 -0.14 42 42
gp130 (dimer)/TYK2/TYK2/LMO4 0.05 0.066 -10000 0 -0.11 51 51
gp130 (dimer)/JAK2/JAK2/LMO4 0.043 0.075 -10000 0 -0.12 66 66
IL6 0.023 0.037 -10000 0 -0.042 87 87
PIAS3 0.04 0.008 -10000 0 0 23 23
PTPRE 0.027 0.038 0.1 11 -0.044 64 75
PIAS1 0.04 0.009 -10000 0 0 28 28
RAC1 0.04 0.01 -10000 0 0 33 33
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0.003 0.095 0.16 3 -0.24 46 49
LMO4 0.028 0.037 -10000 0 -0.041 99 99
STAT3 (dimer)/PIAS3 -0.1 0.4 -10000 0 -0.87 94 94
MCL1 -0.012 0.16 -10000 0 -0.68 16 16
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.029 0.013 -10000 0 -0.13 3 3
alphaV beta3 Integrin 0.029 0.079 -10000 0 -0.13 91 91
PTK2 -0.011 0.13 0.23 9 -0.28 64 73
IGF1R 0.033 0.017 -10000 0 0 118 118
PI4KB 0 0 -10000 0 -10000 0 0
MFGE8 0.031 0.018 -10000 0 0 142 142
SRC 0.039 0.01 -10000 0 0 36 36
CDKN1B 0.002 0.089 -10000 0 -0.32 34 34
VEGFA 0 0 -10000 0 -10000 0 0
ILK 0.015 0.059 -10000 0 -0.27 15 15
ROCK1 0.041 0.007 -10000 0 0 14 14
AKT1 0.006 0.055 0.21 5 -0.26 14 19
PTK2B -0.013 0.06 0.17 20 -0.18 11 31
alphaV/beta3 Integrin/JAM-A 0.041 0.08 0.2 10 -0.12 87 97
CBL 0.04 0.008 -10000 0 0 23 23
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.03 0.079 -10000 0 -0.13 91 91
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.057 0.085 -10000 0 -0.12 87 87
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.005 0.084 -10000 0 -0.21 49 49
alphaV/beta3 Integrin/Syndecan-1 0.029 0.079 -10000 0 -0.13 92 92
PI4KA 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.019 0.1 -10000 0 -0.14 172 172
PI4 Kinase 0 0 -10000 0 -10000 0 0
PIK3CA 0.03 0.019 -10000 0 0 155 155
alphaV/beta3 Integrin/Osteopontin 0.006 0.098 -10000 0 -0.15 128 128
RPS6KB1 -0.034 0.1 0.28 10 -0.26 16 26
TLN1 0.039 0.012 -10000 0 0 46 46
MAPK3 -0.05 0.16 0.23 1 -0.34 112 113
GPR124 0.037 0.013 -10000 0 0 63 63
MAPK1 -0.048 0.16 0.23 1 -0.35 109 110
PXN 0.041 0.007 -10000 0 0 14 14
PIK3R1 0.034 0.017 -10000 0 0 107 107
alphaV/beta3 Integrin/Tumstatin 0.031 0.08 -10000 0 -0.13 92 92
cell adhesion -0.001 0.1 -10000 0 -0.16 134 134
ANGPTL3 0.04 0.008 -10000 0 0 21 21
VEGFR2 homodimer/VEGFA homodimer/Src 0.05 0.02 -10000 0 -0.11 2 2
IGF-1R heterotetramer 0.033 0.017 -10000 0 0 118 118
Rac1/GDP 0.029 0.01 -10000 0 -0.13 1 1
TGFBR2 0.039 0.01 -10000 0 0 37 37
ITGB3 0.033 0.017 -10000 0 0 121 121
IGF1 0.036 0.015 -10000 0 0 84 84
RAC1 0.039 0.01 -10000 0 0 33 33
regulation of cell-matrix adhesion 0.029 0.076 -10000 0 -0.13 83 83
apoptosis 0.033 0.017 -10000 0 0 117 117
CD47 0.037 0.013 -10000 0 0 62 62
alphaV/beta3 Integrin/CD47 0.023 0.087 -10000 0 -0.14 103 103
VCL 0.039 0.01 -10000 0 0 35 35
alphaV/beta3 Integrin/Del1 0.006 0.082 -10000 0 -0.14 111 111
CSF1 0.035 0.015 -10000 0 0 89 89
PIK3C2A -0.005 0.1 -10000 0 -0.33 47 47
PI4 Kinase/Pyk2 0.006 0.055 -10000 0 -0.11 81 81
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.029 0.074 -10000 0 -0.12 94 94
FAK1/Vinculin 0.007 0.12 0.24 9 -0.24 56 65
alphaV beta3/Integrin/ppsTEM5 0.029 0.076 -10000 0 -0.13 83 83
RHOA 0.041 0.007 -10000 0 0 14 14
VTN 0.04 0.009 -10000 0 0 24 24
BCAR1 0.036 0.014 -10000 0 0 75 75
FGF2 0.039 0.011 -10000 0 0 44 44
F11R -0.018 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Lactadherin 0.008 0.088 -10000 0 -0.14 125 125
alphaV/beta3 Integrin/TGFBR2 0.027 0.084 -10000 0 -0.14 95 95
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.046 0.09 -10000 0 -0.13 95 95
HSP90AA1 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.026 0.077 -10000 0 -0.12 100 100
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.021 0.021 -10000 0 0 277 277
alphaV/beta3 Integrin/Pyk2 0.017 0.067 0.21 2 -0.11 87 89
SDC1 0.04 0.009 -10000 0 0 29 29
VAV3 -0.03 0.075 0.2 20 -0.21 38 58
PTPN11 0.04 0.009 -10000 0 0 27 27
IRS1 0.04 0.008 -10000 0 0 22 22
FAK1/Paxillin 0.009 0.12 0.23 9 -0.24 52 61
cell migration -0.001 0.11 0.22 8 -0.23 55 63
ITGAV 0.033 0.017 -10000 0 0 117 117
PI3K 0.028 0.091 -10000 0 -0.19 30 30
SPP1 0.03 0.019 -10000 0 0 154 154
KDR 0.04 0.009 -10000 0 0 29 29
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.033 0.017 -10000 0 0 117 117
COL4A3 0.041 0.005 -10000 0 0 7 7
angiogenesis -0.056 0.17 0.26 1 -0.37 113 114
Rac1/GTP -0.031 0.077 0.2 20 -0.2 38 58
EDIL3 0.027 0.02 -10000 0 0 202 202
cell proliferation 0.026 0.083 -10000 0 -0.14 95 95
IL1-mediated signaling events

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
UBC13/UEV1A 0.028 0.019 -10000 0 -0.13 8 8
PRKCZ 0.042 0 -10000 0 -10000 0 0
MAP3K7IP2 0.037 0.013 -10000 0 0 60 60
ERC1 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.034 0.13 -10000 0 -0.31 87 87
IRAK/TOLLIP 0.04 0.027 0.19 4 -0.1 11 15
IKBKB 0.039 0.011 -10000 0 0 43 43
IKBKG 0.042 0.003 -10000 0 0 2 2
IL1 alpha/IL1R2 0.047 0.039 -10000 0 -0.14 16 16
IL1A 0.04 0.01 -10000 0 0 31 31
IL1B -0.012 0.01 -10000 0 -10000 0 0
IRAK/TRAF6/p62/Atypical PKCs 0.048 0.077 0.22 2 -0.12 60 62
IL1R2 0.036 0.015 -10000 0 0 85 85
IL1R1 0.031 0.019 -10000 0 0 148 148
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.045 0.14 -10000 0 -0.36 70 70
TOLLIP 0.04 0.009 -10000 0 0 29 29
TICAM2 0.038 0.013 -10000 0 0 58 58
MAP3K3 0.041 0.007 -10000 0 0 17 17
TAK1/TAB1/TAB2 0.062 0.054 -10000 0 -0.14 24 24
IKK complex/ELKS 0.014 0.088 0.25 3 -0.27 26 29
JUN -0.033 0.062 0.15 27 -0.2 16 43
MAP3K7 0.038 0.012 -10000 0 0 47 47
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.001 0.12 0.22 2 -0.17 129 131
IL1 alpha/IL1R1/IL1RAP/MYD88 0.037 0.086 -10000 0 -0.12 96 96
PIK3R1 0.034 0.017 -10000 0 0 107 107
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.038 0.1 -10000 0 -0.14 103 103
IL1 beta fragment/IL1R1/IL1RAP -0.013 0.096 0.18 4 -0.15 145 149
NFKB1 0.036 0.015 -10000 0 0 83 83
MAPK8 -0.025 0.057 0.17 24 -0.2 15 39
IRAK1 0.016 0.014 -10000 0 -0.11 6 6
IL1RN/IL1R1 0.022 0.072 -10000 0 -0.14 85 85
IRAK4 0.037 0.014 -10000 0 0 72 72
PRKCI 0.027 0.02 -10000 0 0 197 197
TRAF6 0.04 0.008 -10000 0 0 22 22
PI3K 0.024 0.061 -10000 0 -0.15 47 47
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.036 0.15 -10000 0 -0.32 93 93
CHUK 0.038 0.012 -10000 0 0 52 52
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.013 0.096 0.18 4 -0.15 145 149
IL1 beta/IL1R2 -0.004 0.089 0.24 2 -0.15 133 135
IRAK/TRAF6/TAK1/TAB1/TAB2 0.072 0.068 0.22 1 -0.14 29 30
NF kappa B1 p50/RelA -0.015 0.11 -10000 0 -0.23 72 72
IRAK3 0.035 0.016 -10000 0 0 97 97
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.002 0.12 0.22 2 -0.17 140 142
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.016 0.099 -10000 0 -0.3 37 37
IL1 alpha/IL1R1/IL1RAP 0.015 0.078 -10000 0 -0.13 96 96
RELA 0.041 0.006 -10000 0 0 10 10
MAP3K7IP1 0.038 0.012 -10000 0 0 53 53
SQSTM1 0.038 0.012 -10000 0 0 49 49
MYD88 0.041 0.007 -10000 0 0 14 14
IRAK/TRAF6/MEKK3 0.061 0.037 0.2 4 -0.11 17 21
IL1RAP 0.027 0.02 -10000 0 0 196 196
UBE2N 0.04 0.008 -10000 0 0 20 20
IRAK/TRAF6 -0.022 0.096 -10000 0 -0.16 137 137
CASP1 0.028 0.02 -10000 0 0 192 192
IL1RN/IL1R2 0.041 0.049 -10000 0 -0.14 31 31
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.001 0.1 0.2 4 -0.15 142 146
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.021 0.13 0.21 1 -0.3 82 83
PIK3CA 0.03 0.019 -10000 0 0 155 155
IL1RN 0.039 0.011 -10000 0 0 39 39
TRAF6/TAK1/TAB1/TAB2 0.074 0.066 -10000 0 -0.14 29 29
MAP2K6 -0.021 0.059 0.19 24 -0.21 13 37
IL23-mediated 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
CCL2 -0.16 0.61 0.67 1 -1.2 120 121
IL23A -0.11 0.55 -10000 0 -1.2 81 81
NF kappa B1 p50/RelA/I kappa B alpha -0.11 0.55 -10000 0 -1.2 88 88
positive regulation of T cell mediated cytotoxicity -0.13 0.61 0.68 1 -1.4 88 89
ITGA3 -0.16 0.58 -10000 0 -1.1 121 121
IL17F -0.042 0.36 0.5 10 -0.71 88 98
IL12B 0.034 0.074 0.16 11 -0.079 9 20
STAT1 (dimer) -0.15 0.58 -10000 0 -1.3 87 87
CD4 -0.11 0.57 0.72 2 -1.2 96 98
IL23 -0.1 0.53 -10000 0 -1.2 82 82
IL23R 0.038 0.14 -10000 0 -1.2 3 3
IL1B -0.13 0.59 -10000 0 -1.3 94 94
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.095 0.52 -10000 0 -1.1 85 85
TYK2 0.025 0.056 0.13 1 -10000 0 1
STAT4 0.04 0.009 -10000 0 0 29 29
STAT3 0.038 0.013 -10000 0 0 56 56
IL18RAP 0.042 0.007 -10000 0 -10000 0 0
IL12RB1 0.024 0.057 0.13 1 -10000 0 1
PIK3CA 0.03 0.019 -10000 0 0 155 155
IL12Rbeta1/TYK2 0.037 0.07 -10000 0 -10000 0 0
IL23R/JAK2 0.051 0.18 -10000 0 -1.2 3 3
positive regulation of chronic inflammatory response -0.13 0.61 0.68 1 -1.4 88 89
natural killer cell activation -0.002 0.01 -10000 0 -10000 0 0
JAK2 0.032 0.07 0.16 11 -0.079 12 23
PIK3R1 0.034 0.017 -10000 0 0 107 107
NFKB1 0.038 0.016 -10000 0 0 83 83
RELA 0.043 0.008 -10000 0 0 10 10
positive regulation of dendritic cell antigen processing and presentation -0.091 0.5 -10000 0 -1.1 82 82
ALOX12B -0.098 0.52 -10000 0 -1.1 84 84
CXCL1 -0.13 0.57 -10000 0 -1.2 110 110
T cell proliferation -0.13 0.61 0.68 1 -1.4 88 89
NFKBIA 0.039 0.015 -10000 0 0 66 66
IL17A -0.03 0.29 0.45 6 -0.54 91 97
PI3K -0.15 0.53 -10000 0 -1.2 88 88
IFNG 0.007 0.04 0.1 5 -0.11 13 18
STAT3 (dimer) -0.14 0.5 -10000 0 -1.1 87 87
IL18R1 0.041 0.008 -10000 0 -10000 0 0
IL23/IL23R/JAK2/TYK2/SOCS3 -0.013 0.34 0.54 3 -0.65 76 79
IL18/IL18R 0.054 0.067 -10000 0 -0.11 62 62
macrophage activation -0.007 0.022 0.034 2 -0.045 79 81
TNF -0.11 0.55 -10000 0 -1.2 83 83
STAT3/STAT4 -0.12 0.56 -10000 0 -1.2 86 86
STAT4 (dimer) -0.13 0.58 -10000 0 -1.3 86 86
IL18 0.032 0.019 -10000 0 -10000 0 0
IL19 -0.096 0.52 -10000 0 -1.1 86 86
STAT5A (dimer) -0.13 0.58 -10000 0 -1.3 88 88
STAT1 0.034 0.017 -10000 0 0 108 108
SOCS3 0.037 0.014 -10000 0 0 67 67
CXCL9 -0.16 0.61 -10000 0 -1.2 124 124
MPO -0.096 0.52 -10000 0 -1.1 85 85
positive regulation of humoral immune response -0.13 0.61 0.68 1 -1.4 88 89
IL23/IL23R/JAK2/TYK2 -0.16 0.66 -10000 0 -1.5 88 88
IL6 -0.1 0.54 -10000 0 -1.2 87 87
STAT5A 0.038 0.012 -10000 0 0 51 51
IL2 0.039 0.017 -10000 0 -0.033 11 11
positive regulation of tyrosine phosphorylation of STAT protein -0.002 0.01 -10000 0 -10000 0 0
CD3E -0.11 0.54 0.69 1 -1.2 88 89
keratinocyte proliferation -0.13 0.61 0.68 1 -1.4 88 89
NOS2 -0.098 0.52 -10000 0 -1.1 91 91
Cellular roles of Anthrax toxin

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
ANTXR1 0.033 0.017 -10000 0 0 120 120
ANTXR2 0.035 0.015 -10000 0 0 91 91
negative regulation of myeloid dendritic cell antigen processing and presentation -0.006 0.011 -10000 0 -0.032 74 74
monocyte activation -0.076 0.17 -10000 0 -0.35 152 152
MAP2K2 -0.039 0.18 -10000 0 -0.58 56 56
MAP2K1 -0.011 0.011 0.007 39 -0.037 69 108
MAP2K7 -0.01 0.011 0.007 38 -0.036 69 107
MAP2K6 -0.009 0.012 0.007 34 -0.039 60 94
CYAA -0.022 0.032 -10000 0 -0.1 73 73
MAP2K4 -0.01 0.012 0.007 33 -0.038 68 101
IL1B -0.012 0.041 0.1 9 -0.09 82 91
Channel 0.023 0.055 -10000 0 -0.11 74 74
NLRP1 -0.006 0.01 -10000 0 -0.03 74 74
CALM1 0.04 0.01 -10000 0 0 31 31
negative regulation of phagocytosis 0.003 0.078 -10000 0 -0.42 17 17
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.006 0.011 0.032 74 -10000 0 74
MAPK3 -0.011 0.011 0.007 38 -0.037 72 110
MAPK1 -0.01 0.011 0.007 37 -0.037 66 103
PGR -0.008 0.011 0.007 36 -0.037 51 87
PA/Cellular Receptors 0.023 0.061 -10000 0 -0.12 73 73
apoptosis -0.006 0.011 -10000 0 -0.032 74 74
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.022 0.055 -10000 0 -0.11 74 74
macrophage activation -0.012 0.021 0.17 3 -0.11 1 4
TNF 0.04 0.009 -10000 0 0 26 26
VCAM1 -0.079 0.17 -10000 0 -0.35 150 150
platelet activation 0.003 0.078 -10000 0 -0.42 17 17
MAPKKK cascade 0.007 0.028 0.083 8 -0.087 6 14
IL18 -0.009 0.041 0.093 8 -0.093 73 81
negative regulation of macrophage activation -0.006 0.011 -10000 0 -0.032 74 74
LEF -0.006 0.011 -10000 0 -0.033 74 74
CASP1 0 0.012 0.018 34 -0.031 49 83
mol:cAMP 0 0.077 -10000 0 -0.43 17 17
necrosis -0.006 0.011 -10000 0 -0.032 74 74
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.023 0.053 -10000 0 -0.099 74 74
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 0.028 0.02 -10000 0 0 189 189
mol:Halofuginone 0.002 0.022 -10000 0 -0.17 9 9
ITGA1 0.033 0.017 -10000 0 0 124 124
CDKN1A 0.02 0.08 -10000 0 -0.36 17 17
PRL-3/alpha Tubulin 0.01 0.039 -10000 0 -0.13 36 36
mol:Ca2+ -0.003 0.071 0.26 35 -10000 0 35
AGT 0.039 0.011 -10000 0 0 44 44
CCNA2 -0.016 0.088 -10000 0 -0.62 7 7
TUBA1B 0 0 -10000 0 -10000 0 0
EGR1 0.007 0.043 -10000 0 -0.32 9 9
CDK2/Cyclin E1 0.025 0.096 -10000 0 -0.36 18 18
MAPK3 -0.012 0.01 0 237 -10000 0 237
PRL-2 /Rab GGTase beta 0.032 0.068 -10000 0 -0.14 72 72
MAPK1 -0.012 0.01 0 252 -10000 0 252
PTP4A1 -0.003 0.075 -10000 0 -0.61 7 7
PTP4A3 0.025 0.021 -10000 0 0 227 227
PTP4A2 0.04 0.01 -10000 0 0 31 31
ITGB1 -0.012 0.01 0 252 -10000 0 252
SRC 0.039 0.01 -10000 0 0 36 36
RAC1 -0.007 0.11 -10000 0 -0.36 42 42
Rab GGTase beta/Rab GGTase alpha 0.035 0.063 -10000 0 -0.14 63 63
PRL-1/ATF-5 0.016 0.097 0.32 2 -0.54 9 11
RABGGTA 0.04 0.009 -10000 0 0 26 26
BCAR1 -0.003 0.068 0.26 32 -10000 0 32
RHOC -0.005 0.11 -10000 0 -0.36 42 42
RHOA -0.008 0.11 -10000 0 -0.36 46 46
cell motility 0.011 0.12 0.3 2 -0.35 39 41
PRL-1/alpha Tubulin -0.018 0.077 -10000 0 -0.54 9 9
PRL-3/alpha1 Integrin 0.011 0.066 -10000 0 -0.15 67 67
ROCK1 0.011 0.12 0.3 2 -0.36 39 41
RABGGTB 0.036 0.015 -10000 0 0 84 84
CDK2 0.038 0.013 -10000 0 0 59 59
mitosis -0.002 0.076 -10000 0 -0.61 7 7
ATF5 0.038 0.012 -10000 0 0 54 54
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.037 0.013 -10000 0 0 62 62
LAT2 -0.018 0.099 0.2 3 -0.21 86 89
AP1 -0.031 0.18 0.28 1 -0.42 67 68
mol:PIP3 -0.032 0.13 0.25 14 -0.29 80 94
IKBKB -0.013 0.088 0.2 24 -0.19 59 83
AKT1 0.015 0.12 0.25 66 -0.22 10 76
IKBKG -0.02 0.083 0.19 12 -0.19 66 78
MS4A2 0.046 0.012 0.07 39 -0.004 10 49
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.03 0.019 -10000 0 0 155 155
MAP3K1 -0.033 0.13 0.22 3 -0.31 67 70
mol:Ca2+ -0.023 0.11 0.22 15 -0.24 69 84
LYN 0.036 0.019 0.091 2 -0.003 93 95
CBLB -0.014 0.095 0.2 5 -0.21 73 78
SHC1 0.04 0.01 -10000 0 0 31 31
RasGAP/p62DOK 0.022 0.072 -10000 0 -0.11 107 107
positive regulation of cell migration -0.01 0.002 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.01 0.081 0.3 21 -0.16 5 26
PTPN13 -0.056 0.2 -10000 0 -0.7 31 31
PTPN11 0.04 0.02 0.11 2 -0.033 23 25
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.006 0.13 0.31 21 -0.33 28 49
SYK 0.037 0.017 0.091 2 -0.003 77 79
GRB2 0.041 0.007 -10000 0 0 16 16
LAT/PLCgamma1/GRB2/SLP76/GADs -0.023 0.13 0.18 1 -0.28 92 93
LAT -0.017 0.095 -10000 0 -0.21 81 81
PAK2 -0.031 0.14 0.21 5 -0.32 71 76
NFATC2 0.004 0.054 -10000 0 -0.4 9 9
HRAS -0.027 0.14 0.22 5 -0.32 76 81
GAB2 0.031 0.018 -10000 0 0 141 141
PLA2G1B 0.01 0.15 -10000 0 -0.88 14 14
Fc epsilon R1 0.034 0.071 -10000 0 -0.094 110 110
Antigen/IgE/Fc epsilon R1 0.037 0.063 -10000 0 -0.081 101 101
mol:GDP -0.024 0.16 0.25 4 -0.38 66 70
JUN 0.036 0.015 -10000 0 0 80 80
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.034 0.017 -10000 0 0 107 107
FOS 0.026 0.02 -10000 0 0 207 207
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.009 0.1 -10000 0 -0.22 86 86
CHUK -0.022 0.085 0.2 10 -0.19 69 79
KLRG1 -0.015 0.079 0.18 4 -0.22 42 46
VAV1 -0.015 0.096 0.18 3 -0.22 75 78
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.017 0.097 0.2 3 -0.21 83 86
negative regulation of mast cell degranulation -0.02 0.073 0.13 1 -0.21 41 42
BTK -0.03 0.18 0.26 1 -0.5 50 51
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.026 0.11 -10000 0 -0.22 104 104
GAB2/PI3K/SHP2 -0.039 0.055 -10000 0 -0.15 67 67
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.002 0.065 -10000 0 -0.15 83 83
RAF1 0.012 0.16 -10000 0 -0.97 14 14
Fc epsilon R1/FcgammaRIIB/SHIP 0.033 0.092 -10000 0 -0.12 121 121
FCER1G 0.027 0.02 0.066 1 0 201 202
FCER1A 0.039 0.015 0.1 1 -0.006 49 50
Antigen/IgE/Fc epsilon R1/Fyn 0.04 0.077 -10000 0 -0.094 102 102
MAPK3 0.011 0.15 -10000 0 -0.89 14 14
MAPK1 0.004 0.15 -10000 0 -0.9 14 14
NFKB1 0.036 0.015 -10000 0 0 83 83
MAPK8 -0.033 0.22 -10000 0 -0.57 57 57
DUSP1 0.027 0.02 -10000 0 0 206 206
NF-kappa-B/RelA 0.001 0.068 0.14 16 -0.14 63 79
actin cytoskeleton reorganization -0.049 0.2 -10000 0 -0.73 29 29
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.017 0.13 0.26 3 -0.28 77 80
FER -0.016 0.094 -10000 0 -0.22 76 76
RELA 0.041 0.006 -10000 0 0 10 10
ITK -0.002 0.058 -10000 0 -0.28 17 17
SOS1 0.038 0.013 -10000 0 0 56 56
PLCG1 -0.026 0.15 0.24 6 -0.36 70 76
cytokine secretion -0.003 0.047 0.083 11 -0.1 64 75
SPHK1 -0.017 0.097 0.21 2 -0.21 84 86
PTK2 -0.053 0.21 -10000 0 -0.78 29 29
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.017 0.14 0.19 1 -0.28 95 96
EDG1 -0.01 0.002 -10000 0 -10000 0 0
mol:DAG -0.034 0.14 0.26 12 -0.31 73 85
MAP2K2 0.003 0.15 -10000 0 -0.9 14 14
MAP2K1 0.004 0.15 -10000 0 -0.91 14 14
MAP2K7 0.039 0.011 -10000 0 0 43 43
KLRG1/SHP2 0.013 0.091 0.2 37 -0.21 36 73
MAP2K4 -0.072 0.32 -10000 0 -0.89 75 75
Fc epsilon R1/FcgammaRIIB 0.035 0.099 -10000 0 -0.14 122 122
mol:Choline -0.01 0.081 0.3 21 -0.16 5 26
SHC/Grb2/SOS1 0.023 0.13 -10000 0 -0.22 80 80
FYN 0.034 0.016 -10000 0 0 104 104
DOK1 0.04 0.009 -10000 0 0 24 24
PXN -0.052 0.19 -10000 0 -0.71 29 29
HCLS1 -0.01 0.099 0.19 7 -0.24 60 67
PRKCB -0.024 0.11 0.22 14 -0.24 72 86
FCGR2B 0.03 0.019 -10000 0 0 164 164
IGHE 0 0.007 0.048 2 -10000 0 2
KLRG1/SHIP -0.02 0.075 0.13 1 -0.21 41 42
LCP2 0.034 0.016 -10000 0 0 102 102
PLA2G4A -0.007 0.092 0.17 11 -0.22 64 75
RASA1 0.037 0.014 -10000 0 0 71 71
mol:Phosphatidic acid -0.01 0.081 0.3 21 -0.16 5 26
IKK complex -0.015 0.073 0.19 18 -0.16 45 63
WIPF1 0 0 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.054 0.062 0.15 115 -0.033 29 144
AES 0.053 0.056 0.14 121 -0.032 14 135
FBXW11 0.04 0.009 -10000 0 0 25 25
mol:GTP 0.001 0.003 0.033 1 -10000 0 1
LRP6/FZD1 0.041 0.049 -10000 0 -0.14 32 32
SMAD4 0.038 0.012 -10000 0 0 49 49
DKK2 0.039 0.012 -10000 0 0 46 46
TLE1 0.053 0.052 0.14 110 -0.033 12 122
MACF1 0.033 0.017 -10000 0 0 118 118
CTNNB1 0.033 0.12 0.29 28 -0.38 13 41
WIF1 0.04 0.01 -10000 0 -0.001 32 32
beta catenin/RanBP3 0.099 0.22 0.47 118 -0.43 7 125
KREMEN2 0.04 0.009 -10000 0 0 28 28
DKK1 0.039 0.011 -10000 0 0 44 44
beta catenin/beta TrCP1 0.054 0.12 0.3 28 -0.37 12 40
FZD1 0.041 0.007 -10000 0 0 17 17
AXIN2 -0.047 0.22 0.68 7 -0.81 27 34
AXIN1 0.042 0.004 -10000 0 0 4 4
RAN 0.042 0.007 0.076 1 0 13 14
Axin1/APC/GSK3/beta catenin 0.047 0.087 0.41 1 -0.55 7 8
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.025 0.17 0.32 9 -0.41 60 69
Axin1/APC/GSK3 0.03 0.07 0.21 15 -0.24 11 26
Axin1/APC/GSK3/beta catenin/Macf1 0.022 0.088 0.28 14 -0.27 10 24
HNF1A 0.019 0.051 0.092 132 -10000 0 132
CTBP1 0.053 0.053 0.14 111 -0.033 12 123
MYC 0.044 0.55 0.63 164 -1.1 74 238
RANBP3 0.04 0.011 0.076 1 0 40 41
DKK2/LRP6/Kremen 2 0.057 0.054 -10000 0 -0.12 29 29
NKD1 0.038 0.012 -10000 0 0 49 49
TCF4 0.055 0.059 0.15 115 -0.033 13 128
TCF3 0.053 0.055 0.14 117 -0.034 13 130
WNT1/LRP6/FZD1/Axin1 0.08 0.061 -10000 0 -0.11 31 31
Ran/GTP 0.031 0.013 0.1 1 -0.12 3 4
CtBP/CBP/TCF/TLE1/AES 0.059 0.31 0.62 95 -0.41 23 118
LEF1 0.037 0.051 0.14 75 -0.033 13 88
DVL1 0.033 0.076 0.25 8 -0.34 10 18
CSNK2A1 0.038 0.013 -10000 0 0 54 54
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.066 0.19 -10000 0 -0.42 82 82
DKK1/LRP6/Kremen 2 0.056 0.054 -10000 0 -0.12 28 28
LRP6 0.034 0.017 -10000 0 0 107 107
CSNK1A1 0.059 0.065 0.15 128 -0.033 30 158
NLK 0.031 0.025 -10000 0 -0.024 84 84
CCND1 -0.18 0.51 0.71 17 -1.2 96 113
WNT1 0.041 0.006 -10000 0 0 13 13
GSK3A 0.039 0.011 0.065 1 0 38 39
GSK3B 0.04 0.009 -10000 0 0 26 26
FRAT1 0.04 0.009 -10000 0 -0.002 25 25
PPP2R5D 0.035 0.061 0.24 2 -0.29 12 14
APC -0.005 0.082 0.21 61 -10000 0 61
WNT1/LRP6/FZD1 0.019 0.062 0.15 6 -0.16 30 36
CREBBP 0.054 0.055 0.14 114 -0.033 15 129
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.042 0.004 -10000 0 0 6 6
PTK2 0.027 0.02 -10000 0 0 205 205
CRKL -0.022 0.052 0.12 13 -0.13 70 83
GRB2/SOS1/SHC 0.065 0.051 -10000 0 -0.12 26 26
HRAS 0.04 0.01 -10000 0 0 31 31
IRS1/Crk 0.011 0.057 -10000 0 -0.12 75 75
IGF-1R heterotetramer/IGF1/PTP1B 0.034 0.072 -10000 0 -0.12 81 81
AKT1 0 0.091 0.17 85 -0.18 14 99
BAD -0.007 0.085 0.16 81 -0.18 13 94
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.02 0.05 0.11 12 -0.13 65 77
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.011 0.068 0.2 4 -0.13 95 99
RAF1 0.016 0.12 0.28 12 -0.46 14 26
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.044 0.088 0.21 2 -0.13 97 99
YWHAZ 0.034 0.016 -10000 0 0 102 102
IGF-1R heterotetramer/IGF1/IRS1 0.019 0.067 0.18 2 -0.13 84 86
PIK3CA 0.03 0.019 -10000 0 0 155 155
RPS6KB1 0 0.095 0.18 89 -0.19 20 109
GNB2L1 0.041 0.005 -10000 0 0 7 7
positive regulation of MAPKKK cascade 0.014 0.11 0.27 15 -0.39 11 26
PXN 0.041 0.007 -10000 0 0 14 14
PIK3R1 0.034 0.017 -10000 0 0 107 107
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.047 0.047 -10000 0 -0.14 28 28
HRAS/GTP 0.014 0.068 -10000 0 -0.13 82 82
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.061 0.09 -10000 0 -0.12 85 85
IGF-1R heterotetramer 0.033 0.024 0.1 2 -0.051 16 18
IGF-1R heterotetramer/IGF1/IRS/Nck 0.038 0.075 0.2 2 -0.13 84 86
Crk/p130 Cas/Paxillin 0.043 0.082 0.25 9 -0.13 72 81
IGF1R 0.034 0.024 0.1 2 -0.052 16 18
IGF1 0.027 0.035 0.1 2 -0.053 68 70
IRS2/Crk 0.009 0.054 0.17 1 -0.12 70 71
PI3K 0.024 0.083 0.21 2 -0.12 89 91
apoptosis -0.002 0.09 0.17 9 -0.22 29 38
HRAS/GDP 0.029 0.01 -10000 0 -0.13 1 1
PRKCD -0.011 0.093 0.21 6 -0.21 70 76
RAF1/14-3-3 E 0.031 0.11 0.29 12 -0.4 14 26
BAD/14-3-3 0.002 0.093 0.23 29 -0.18 9 38
PRKCZ 0.002 0.095 0.18 92 -0.18 13 105
Crk/p130 Cas/Paxillin/FAK1 0.01 0.08 0.2 13 -0.16 42 55
PTPN1 0.038 0.012 -10000 0 0 54 54
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.011 0.094 -10000 0 -0.21 82 82
BCAR1 0.036 0.014 -10000 0 0 75 75
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.055 0.078 -10000 0 -0.11 76 76
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.038 0.013 -10000 0 0 56 56
IRS1/NCK2 0.025 0.069 0.14 16 -0.12 84 100
GRB10 0.04 0.009 -10000 0 0 24 24
PTPN11 -0.021 0.052 0.11 13 -0.13 67 80
IRS1 0.004 0.062 0.13 17 -0.13 84 101
IRS2 -0.021 0.052 0.11 14 -0.13 70 84
IGF-1R heterotetramer/IGF1 0.02 0.075 0.16 2 -0.16 75 77
GRB2 0.041 0.007 -10000 0 0 16 16
PDPK1 0.008 0.099 0.19 90 -0.18 13 103
YWHAE 0.038 0.013 -10000 0 0 57 57
PRKD1 -0.012 0.097 0.21 7 -0.22 75 82
SHC1 0.04 0.01 -10000 0 0 31 31
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.011 0.076 -10000 0 -0.14 104 104
CRKL -0.032 0.14 0.33 1 -0.43 42 43
mol:PIP3 0.007 0.079 0.29 2 -0.82 4 6
AKT1 0.001 0.081 0.38 2 -0.73 4 6
PTK2B 0.033 0.017 -10000 0 0 118 118
RAPGEF1 -0.034 0.14 0.31 1 -0.41 41 42
RANBP10 0.036 0.014 -10000 0 0 77 77
PIK3CA 0.03 0.019 -10000 0 0 155 155
HGF/MET/SHIP2 0.029 0.078 -10000 0 -0.12 102 102
MAP3K5 -0.023 0.14 0.28 2 -0.4 44 46
HGF/MET/CIN85/CBL/ENDOPHILINS 0.051 0.085 -10000 0 -0.11 105 105
AP1 -0.003 0.081 0.16 9 -0.14 104 113
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.04 0.01 -10000 0 0 31 31
apoptosis -0.16 0.36 -10000 0 -0.77 138 138
STAT3 (dimer) -0.01 0.11 0.19 4 -0.29 38 42
GAB1/CRKL/SHP2/PI3K -0.012 0.15 -10000 0 -0.39 45 45
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK -0.009 0.15 0.29 3 -0.41 42 45
PTPN11 0.04 0.009 -10000 0 0 27 27
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.038 0.012 -10000 0 0 50 50
PTEN 0.039 0.011 -10000 0 0 38 38
ELK1 0.014 0.12 0.34 44 -10000 0 44
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.013 0.083 0.15 2 -0.22 48 50
PAK1 0.01 0.098 0.34 9 -0.69 4 13
HGF/MET/RANBP10 0.025 0.076 -10000 0 -0.11 104 104
HRAS -0.072 0.22 -10000 0 -0.48 118 118
DOCK1 -0.032 0.14 0.26 6 -0.41 42 48
GAB1 -0.028 0.15 0.25 1 -0.46 40 41
CRK -0.028 0.14 0.28 3 -0.42 42 45
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.056 0.19 -10000 0 -0.43 110 110
JUN 0.036 0.015 -10000 0 0 80 80
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.02 0.072 0.096 2 -0.16 103 105
PIK3R1 0.034 0.017 -10000 0 0 107 107
cell morphogenesis -0.009 0.15 0.26 34 -0.35 40 74
GRB2/SHC 0.018 0.096 0.19 3 -0.16 106 109
FOS 0.026 0.02 -10000 0 0 207 207
GLMN 0.005 0.007 0.069 7 -10000 0 7
cell motility 0.013 0.12 0.34 44 -10000 0 44
HGF/MET/MUC20 0.015 0.063 -10000 0 -0.11 105 105
cell migration 0.017 0.095 0.19 3 -0.16 106 109
GRB2 0.041 0.007 -10000 0 0 16 16
CBL 0.04 0.008 -10000 0 0 23 23
MET/RANBP10 0.01 0.073 -10000 0 -0.13 105 105
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.017 0.081 -10000 0 -0.18 81 81
MET/MUC20 -0.004 0.061 -10000 0 -0.13 107 107
RAP1B -0.033 0.13 0.27 2 -0.39 39 41
RAP1A -0.038 0.13 0.28 3 -0.4 42 45
HGF/MET/RANBP9 0.026 0.078 -10000 0 -0.12 102 102
RAF1 -0.072 0.21 -10000 0 -0.46 119 119
STAT3 -0.008 0.11 0.19 4 -0.3 34 38
cell proliferation -0.031 0.14 0.28 6 -0.31 76 82
RPS6KB1 -0.012 0.085 -10000 0 -0.32 30 30
MAPK3 -0.008 0.12 0.67 12 -10000 0 12
MAPK1 0.029 0.2 0.71 40 -10000 0 40
RANBP9 0.038 0.012 -10000 0 0 53 53
MAPK8 -0.022 0.15 -10000 0 -0.42 46 46
SRC -0.006 0.092 0.2 9 -0.25 29 38
PI3K 0 0.096 0.19 3 -0.18 93 96
MET/Glomulin 0.012 0.047 -10000 0 -0.12 48 48
SOS1 0.038 0.013 -10000 0 0 56 56
MAP2K1 -0.071 0.2 -10000 0 -0.44 116 116
MET 0.027 0.02 -10000 0 0 198 198
MAP4K1 -0.022 0.15 0.29 1 -0.44 41 42
PTK2 0.027 0.02 -10000 0 0 205 205
MAP2K2 -0.072 0.19 -10000 0 -0.43 118 118
BAD -0.003 0.079 0.34 2 -0.7 4 6
MAP2K4 -0.025 0.13 0.26 2 -0.37 44 46
SHP2/GRB2/SOS1/GAB1 -0.012 0.16 -10000 0 -0.36 53 53
INPPL1 0.04 0.009 -10000 0 0 30 30
PXN 0.041 0.007 -10000 0 0 14 14
SH3KBP1 0.041 0.007 -10000 0 0 16 16
HGS -0.026 0.071 0.084 2 -0.16 112 114
PLCgamma1/PKC 0.026 0.022 -10000 0 -0.13 10 10
HGF 0.04 0.009 -10000 0 0 29 29
RASA1 0.037 0.014 -10000 0 0 71 71
NCK1 0.036 0.015 -10000 0 0 79 79
PTPRJ 0.039 0.01 -10000 0 0 35 35
NCK/PLCgamma1 0.016 0.094 0.19 3 -0.17 97 100
PDPK1 0.001 0.076 0.26 1 -0.77 4 5
HGF/MET/SHIP 0.015 0.063 -10000 0 -0.11 105 105
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.008 0.11 0.15 55 -0.29 39 94
adherens junction organization -0.026 0.13 0.18 8 -0.35 52 60
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.011 0.11 0.21 9 -0.28 30 39
FMN1 -0.023 0.12 0.15 7 -0.28 65 72
mol:IP3 0.003 0.098 0.16 60 -0.26 33 93
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.014 0.13 0.17 5 -0.29 65 70
CTNNB1 0.041 0.011 0.069 3 0 31 34
AKT1 -0.015 0.092 0.19 10 -0.26 43 53
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.011 0.15 -10000 0 -0.38 51 51
CTNND1 0.042 0.009 -10000 0 -0.002 18 18
mol:PI-4-5-P2 -0.02 0.12 0.2 4 -0.28 64 68
VASP -0.021 0.12 0.16 5 -0.28 64 69
ZYX -0.016 0.11 0.15 9 -0.29 51 60
JUB -0.022 0.12 0.15 8 -0.29 64 72
EGFR(dimer) -0.005 0.13 0.2 1 -0.28 70 71
E-cadherin/beta catenin-gamma catenin 0.05 0.06 -10000 0 -0.11 46 46
mol:PI-3-4-5-P3 -0.004 0.1 0.22 2 -0.27 43 45
PIK3CA 0.03 0.02 -10000 0 -0.001 159 159
PI3K -0.003 0.11 0.22 2 -0.27 43 45
FYN -0.013 0.12 0.2 8 -0.28 61 69
mol:Ca2+ 0.003 0.096 0.16 60 -0.26 33 93
JUP 0.038 0.014 -10000 0 0 67 67
PIK3R1 0.035 0.018 -10000 0 0 108 108
mol:DAG 0.003 0.098 0.16 60 -0.26 33 93
CDH1 0.035 0.016 -10000 0 0 98 98
RhoA/GDP 0.013 0.11 0.22 9 -0.28 31 40
establishment of polarity of embryonic epithelium -0.02 0.12 0.2 3 -0.28 64 67
SRC 0.039 0.01 -10000 0 0 36 36
RAC1 0.039 0.01 -10000 0 0 33 33
RHOA 0.041 0.007 -10000 0 0 14 14
EGFR 0.037 0.014 -10000 0 0 72 72
CASR -0.004 0.093 0.15 62 -0.25 33 95
RhoA/GTP 0.015 0.1 0.2 4 -0.25 32 36
AKT2 -0.016 0.092 0.18 8 -0.25 44 52
actin cable formation -0.025 0.11 0.22 6 -0.28 61 67
apoptosis 0.001 0.11 0.28 42 -0.17 63 105
CTNNA1 0.041 0.012 -10000 0 -0.001 39 39
mol:GDP -0.005 0.1 0.16 58 -0.28 32 90
PIP5K1A -0.022 0.12 0.15 8 -0.29 64 72
PLCG1 0.002 0.099 0.16 60 -0.27 33 93
Rac1/GTP 0.004 0.13 -10000 0 -0.3 53 53
homophilic cell adhesion 0 0.004 -10000 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.032 0.019 -10000 0 0 143 143
ELF1 0.047 0.023 -10000 0 -0.26 2 2
CCNA2 0.032 0.018 -10000 0 0 134 134
PIK3CA 0.031 0.019 -10000 0 0 155 155
JAK3 0.038 0.013 -10000 0 -0.001 56 56
PIK3R1 0.034 0.017 -10000 0 -0.001 109 109
JAK1 0.04 0.011 -10000 0 -0.002 36 36
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.002 0.14 0.24 3 -0.33 46 49
SHC1 0.04 0.01 -10000 0 -0.001 32 32
SP1 0.044 0.043 -10000 0 -0.28 9 9
IL2RA 0.02 0.032 -10000 0 -0.49 2 2
IL2RB 0.037 0.015 -10000 0 -0.001 76 76
SOS1 0.038 0.013 -10000 0 -0.001 58 58
IL2RG 0.029 0.02 -10000 0 0 184 184
G1/S transition of mitotic cell cycle -0.038 0.18 0.28 5 -0.47 41 46
PTPN11 0.04 0.011 -10000 0 -0.004 31 31
CCND2 0.012 0.058 -10000 0 -0.49 7 7
LCK 0.04 0.011 -10000 0 -0.004 33 33
GRB2 0.041 0.008 -10000 0 -0.003 18 18
IL2 0.039 0.013 -10000 0 -0.002 48 48
CDK6 0.032 0.018 -10000 0 0 129 129
CCND3 0.004 0.14 -10000 0 -0.56 13 13
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.067 0.49 -10000 0 -1 71 71
STAT6 (cleaved dimer) -0.11 0.45 -10000 0 -0.95 86 86
IGHG1 0.034 0.23 0.44 5 -0.45 24 29
IGHG3 -0.069 0.45 -10000 0 -0.91 83 83
AKT1 -0.055 0.37 0.5 1 -0.82 70 71
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.045 0.36 0.45 1 -0.86 68 69
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.051 0.4 -10000 0 -0.93 66 66
THY1 -0.23 0.66 0.77 1 -1.2 161 162
MYB 0.034 0.017 -10000 0 0 111 111
HMGA1 0.037 0.014 -10000 0 0 72 72
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.025 0.37 0.53 2 -0.75 68 70
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.056 0.4 -10000 0 -0.92 67 67
SP1 0.022 0.073 -10000 0 -0.13 104 104
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.001 0.05 -10000 0 -0.084 3 3
STAT6 (dimer)/ETS1 -0.087 0.46 -10000 0 -0.96 80 80
SOCS1 -0.031 0.35 0.52 1 -0.66 66 67
SOCS3 -0.034 0.37 -10000 0 -0.88 51 51
FCER2 -0.032 0.39 -10000 0 -0.76 65 65
PARP14 0.033 0.019 -10000 0 -10000 0 0
CCL17 -0.063 0.47 -10000 0 -0.99 71 71
GRB2 0.041 0.007 -10000 0 0 16 16
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.011 0.3 -10000 0 -0.65 57 57
T cell proliferation -0.086 0.49 -10000 0 -1 84 84
IL4R/JAK1 -0.079 0.49 -10000 0 -1 80 80
EGR2 -0.059 0.48 0.71 1 -0.98 77 78
JAK2 0.033 0.073 0.17 3 -10000 0 3
JAK3 0.034 0.026 -10000 0 -0.04 36 36
PIK3R1 0.034 0.017 -10000 0 0 107 107
JAK1 0.04 0.041 0.11 4 -0.042 6 10
COL1A2 -0.15 0.56 -10000 0 -1.3 108 108
CCL26 -0.073 0.49 -10000 0 -1 73 73
IL4R -0.069 0.52 -10000 0 -1.1 76 76
PTPN6 0.006 0.043 -10000 0 -0.074 2 2
IL13RA2 -0.061 0.47 -10000 0 -1 67 67
IL13RA1 0.036 0.076 0.17 8 -10000 0 8
IRF4 0.058 0.15 -10000 0 -1.3 1 1
ARG1 0.049 0.19 -10000 0 -0.69 6 6
CBL -0.027 0.35 0.57 2 -0.7 68 70
GTF3A 0.013 0.079 -10000 0 -0.13 123 123
PIK3CA 0.03 0.019 -10000 0 0 155 155
IL13RA1/JAK2 0.042 0.12 0.25 4 -0.18 25 29
IRF4/BCL6 0.043 0.14 -10000 0 -1.2 1 1
CD40LG 0.049 0.01 -10000 0 -0.12 1 1
MAPK14 -0.03 0.36 -10000 0 -0.76 63 63
mitosis -0.046 0.35 0.5 1 -0.76 70 71
STAT6 -0.065 0.54 0.78 2 -1.1 80 82
SPI1 0.045 0.01 -10000 0 -10000 0 0
RPS6KB1 -0.05 0.34 0.47 1 -0.74 71 72
STAT6 (dimer) -0.063 0.54 0.78 2 -1.1 80 82
STAT6 (dimer)/PARP14 -0.1 0.48 -10000 0 -1 82 82
mast cell activation -0.004 0.019 -10000 0 -0.043 10 10
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.076 0.39 -10000 0 -0.91 69 69
FRAP1 -0.055 0.37 0.5 1 -0.82 70 71
LTA -0.061 0.47 -10000 0 -1 61 61
FES 0.04 0.008 -10000 0 0 22 22
T-helper 1 cell differentiation 0.058 0.53 1.1 80 -0.78 2 82
CCL11 -0.096 0.5 -10000 0 -1.1 82 82
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.048 0.38 -10000 0 -0.89 66 66
IL2RG 0.027 0.025 -10000 0 -0.045 13 13
IL10 -0.058 0.48 -10000 0 -1 67 67
IRS1 0.04 0.008 -10000 0 0 22 22
IRS2 0.039 0.01 -10000 0 0 33 33
IL4 0.037 0.23 -10000 0 -0.93 14 14
IL5 -0.064 0.47 -10000 0 -1 59 59
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.047 0.46 0.7 2 -0.88 84 86
COL1A1 -0.22 0.65 -10000 0 -1.3 143 143
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.085 0.49 -10000 0 -1.1 65 65
IL2R gamma/JAK3 0.02 0.074 -10000 0 -0.13 92 92
TFF3 -0.068 0.49 -10000 0 -1 73 73
ALOX15 -0.063 0.47 -10000 0 -1 67 67
MYBL1 0.037 0.014 -10000 0 0 73 73
T-helper 2 cell differentiation -0.1 0.47 -10000 0 -0.93 93 93
SHC1 0.04 0.01 -10000 0 0 31 31
CEBPB 0.04 0.016 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.052 0.4 -10000 0 -0.9 69 69
mol:PI-3-4-5-P3 -0.054 0.37 0.5 1 -0.82 70 71
PI3K -0.064 0.4 -10000 0 -0.89 70 70
DOK2 0.032 0.018 -10000 0 0 135 135
ETS1 0.001 0.047 -10000 0 -0.099 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.009 0.29 -10000 0 -0.62 62 62
ITGB3 -0.096 0.54 -10000 0 -1.1 89 89
PIGR -0.059 0.49 -10000 0 -1 74 74
IGHE -0.002 0.089 0.18 46 -0.18 26 72
MAPKKK cascade -0.007 0.29 0.41 1 -0.6 62 63
BCL6 0.03 0.018 -10000 0 0 146 146
OPRM1 -0.063 0.47 -10000 0 -1 67 67
RETNLB -0.056 0.48 -10000 0 -0.98 73 73
SELP -0.058 0.48 -10000 0 -1 68 68
AICDA -0.052 0.45 -10000 0 -0.93 73 73
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.01 0.1 -10000 0 -0.13 144 144
SMAD6-7/SMURF1 0.07 0.04 -10000 0 -0.15 8 8
NOG 0.038 0.012 -10000 0 0 50 50
SMAD9 0.005 0.12 -10000 0 -0.42 38 38
SMAD4 0.038 0.012 -10000 0 0 49 49
SMAD5 -0.002 0.098 0.2 3 -0.28 38 41
BMP7/USAG1 -0.019 0.084 -10000 0 -0.16 134 134
SMAD5/SKI 0.011 0.11 0.24 1 -0.28 40 41
SMAD1 0.003 0.095 -10000 0 -0.3 33 33
BMP2 0.038 0.012 -10000 0 0 49 49
SMAD1/SMAD1/SMAD4 0.027 0.1 -10000 0 -0.29 32 32
BMPR1A 0.037 0.013 -10000 0 0 65 65
BMPR1B 0.031 0.019 -10000 0 0 153 153
BMPR1A-1B/BAMBI 0.007 0.088 -10000 0 -0.14 121 121
AHSG 0.034 0.017 -10000 0 0 109 109
CER1 0.038 0.012 -10000 0 0 48 48
BMP2-4/CER1 0.06 0.045 -10000 0 -0.12 11 11
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.008 0.11 0.19 1 -0.26 58 59
BMP2-4 (homodimer) 0.047 0.035 -10000 0 -0.14 11 11
RGMB 0.039 0.011 -10000 0 0 42 42
BMP6/BMPR2/BMPR1A-1B 0.051 0.085 -10000 0 -0.13 82 82
RGMA 0.039 0.01 -10000 0 0 34 34
SMURF1 0.041 0.008 -10000 0 0 19 19
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP 0.002 0.081 0.17 2 -0.24 34 36
BMP2-4/USAG1 0.022 0.069 -10000 0 -0.12 71 71
SMAD6/SMURF1/SMAD5 0.01 0.11 0.24 1 -0.28 40 41
SOSTDC1 0.023 0.021 -10000 0 0 254 254
BMP7/BMPR2/BMPR1A-1B 0.009 0.1 -10000 0 -0.14 154 154
SKI 0.042 0.003 -10000 0 0 3 3
BMP6 (homodimer) 0.037 0.013 -10000 0 0 63 63
HFE2 0.041 0.005 -10000 0 0 8 8
ZFYVE16 0.035 0.016 -10000 0 0 93 93
MAP3K7 0.038 0.012 -10000 0 0 47 47
BMP2-4/CHRD 0.052 0.045 -10000 0 -0.12 8 8
SMAD5/SMAD5/SMAD4 0.008 0.11 0.24 1 -0.28 39 40
MAPK1 0.039 0.012 -10000 0 0 46 46
TAK1/TAB family 0.032 0.12 -10000 0 -0.25 34 34
BMP7 (homodimer) 0.022 0.021 -10000 0 0 271 271
NUP214 0.039 0.01 -10000 0 0 33 33
BMP6/FETUA 0.045 0.028 -10000 0 -10000 0 0
SMAD1/SKI 0.024 0.1 -10000 0 -0.29 35 35
SMAD6 0.04 0.01 -10000 0 0 32 32
CTDSP2 0.039 0.011 -10000 0 0 42 42
BMP2-4/FETUA 0.053 0.045 -10000 0 -0.12 8 8
MAP3K7IP1 0.038 0.012 -10000 0 0 53 53
GREM1 0.035 0.016 -10000 0 0 98 98
BMPR2 (homodimer) 0.04 0.009 -10000 0 0 29 29
GADD34/PP1CA 0.057 0.056 -10000 0 -0.12 35 35
BMPR1A-1B (homodimer) 0.016 0.078 -10000 0 -0.15 90 90
CHRDL1 0.026 0.02 -10000 0 0 213 213
ENDOFIN/SMAD1 0.019 0.1 -10000 0 -0.28 34 34
SMAD6-7/SMURF1/SMAD1 0.049 0.11 -10000 0 -0.29 31 31
SMAD6/SMURF1 0.04 0.008 -10000 0 0 19 19
BAMBI 0.029 0.019 -10000 0 0 172 172
SMURF2 0.039 0.01 -10000 0 0 35 35
BMP2-4/CHRDL1 0.019 0.077 -10000 0 -0.12 102 102
BMP2-4/GREM1 0.052 0.049 -10000 0 -0.12 16 16
SMAD7 0.039 0.011 -10000 0 0 45 45
SMAD8A/SMAD8A/SMAD4 0.019 0.13 -10000 0 -0.4 42 42
SMAD1/SMAD6 0.023 0.1 -10000 0 -0.29 33 33
TAK1/SMAD6 0.052 0.036 -10000 0 -0.14 15 15
BMP7 0.022 0.021 -10000 0 0 271 271
BMP6 0.037 0.013 -10000 0 0 63 63
MAP3K7IP2 0.037 0.013 -10000 0 0 60 60
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 0.002 0.084 -10000 0 -0.24 35 35
PPM1A 0.041 0.007 -10000 0 0 16 16
SMAD1/SMURF2 0.022 0.1 -10000 0 -0.29 34 34
SMAD7/SMURF1 0.053 0.029 -10000 0 -0.14 8 8
CTDSPL 0.041 0.006 -10000 0 0 10 10
PPP1CA 0.041 0.006 -10000 0 0 13 13
XIAP 0 0 -10000 0 -10000 0 0
CTDSP1 0.041 0.006 -10000 0 0 13 13
PPP1R15A 0.039 0.011 -10000 0 0 44 44
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS 0.001 0.087 -10000 0 -0.24 41 41
CHRD 0.033 0.017 -10000 0 0 116 116
BMPR2 0.04 0.009 -10000 0 0 29 29
BMP2-4/BMPR2/BMPR1A-1B/RGM 0 0.087 -10000 0 -0.26 30 30
BMP4 0.036 0.014 -10000 0 0 75 75
FST 0.033 0.017 -10000 0 0 120 120
BMP2-4/NOG 0.058 0.049 -10000 0 -0.12 20 20
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.017 0.11 -10000 0 -0.13 150 150
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.007 0.051 -10000 0 -0.15 40 40
EPHB2 0.039 0.011 -10000 0 0 38 38
Syndecan-2/TACI 0.026 0.041 -10000 0 -0.11 39 39
LAMA1 0.034 0.017 -10000 0 0 108 108
Syndecan-2/alpha2 ITGB1 0.041 0.086 0.19 39 -0.12 81 120
HRAS 0.04 0.01 -10000 0 0 31 31
Syndecan-2/CASK 0.001 0.028 -10000 0 -0.098 40 40
ITGA5 0.038 0.013 -10000 0 0 58 58
BAX 0.02 0.064 -10000 0 -10000 0 0
EPB41 0.039 0.01 -10000 0 0 35 35
positive regulation of cell-cell adhesion 0.017 0.046 -10000 0 -0.097 67 67
LAMA3 0.031 0.018 -10000 0 0 147 147
EZR 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.033 0.017 -10000 0 0 114 114
Syndecan-2/MMP2 0.008 0.052 -10000 0 -0.16 40 40
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.035 0.056 -10000 0 -0.14 43 43
dendrite morphogenesis 0.025 0.043 -10000 0 -0.12 38 38
Syndecan-2/GM-CSF 0.027 0.041 -10000 0 -0.11 39 39
determination of left/right symmetry 0.01 0.007 -10000 0 -10000 0 0
Syndecan-2/PKC delta 0.024 0.041 -10000 0 -0.11 38 38
GNB2L1 0.041 0.005 -10000 0 0 7 7
MAPK3 0.009 0.074 0.15 104 -0.1 37 141
MAPK1 0.01 0.074 0.2 63 -0.1 36 99
Syndecan-2/RACK1 0.041 0.048 -10000 0 -0.095 44 44
NF1 0.034 0.016 -10000 0 0 101 101
FGFR/FGF/Syndecan-2 0.01 0.007 -10000 0 -10000 0 0
ITGA2 0.033 0.017 -10000 0 0 118 118
MAPK8 0 0.02 -10000 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin 0.054 0.076 0.19 43 -0.11 52 95
Syndecan-2/Kininogen 0.022 0.039 -10000 0 -0.11 35 35
ITGB1 0.039 0.011 -10000 0 0 38 38
SRC 0.006 0.073 0.19 65 -0.17 1 66
Syndecan-2/CASK/Protein 4.1 0.023 0.038 -10000 0 -0.094 43 43
extracellular matrix organization 0.024 0.042 -10000 0 -0.11 36 36
actin cytoskeleton reorganization 0.007 0.05 -10000 0 -0.15 40 40
Syndecan-2/Caveolin-2/Ras 0.03 0.06 -10000 0 -0.11 64 64
Syndecan-2/Laminin alpha3 0.018 0.045 -10000 0 -0.13 34 34
Syndecan-2/RasGAP 0.063 0.069 0.18 48 -0.097 57 105
alpha5/beta1 Integrin 0.046 0.045 -10000 0 -0.14 27 27
PRKCD 0.038 0.013 -10000 0 0 57 57
Syndecan-2 dimer 0.025 0.043 -10000 0 -0.12 38 38
GO:0007205 0.003 0.001 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.038 0.058 0.2 1 -0.1 50 51
RHOA 0.041 0.007 -10000 0 0 14 14
SDCBP 0.036 0.014 -10000 0 0 75 75
TNFRSF13B 0.039 0.011 -10000 0 0 42 42
RASA1 0.037 0.014 -10000 0 0 71 71
alpha2/beta1 Integrin 0.035 0.056 -10000 0 -0.14 43 43
Syndecan-2/Synbindin 0.021 0.043 -10000 0 -0.12 39 39
TGFB1 0.037 0.013 -10000 0 0 62 62
CASP3 0.004 0.07 0.15 85 -0.1 47 132
FN1 0.021 0.021 -10000 0 0 277 277
Syndecan-2/IL8 0.018 0.044 -10000 0 -0.12 37 37
SDC2 0.01 0.007 -10000 0 -10000 0 0
KNG1 0.034 0.017 -10000 0 0 109 109
Syndecan-2/Neurofibromin 0.023 0.042 -10000 0 -0.12 35 35
TRAPPC4 0.034 0.016 -10000 0 0 102 102
CSF2 0.04 0.009 -10000 0 0 25 25
Syndecan-2/TGFB1 0.024 0.042 -10000 0 -0.11 36 36
Syndecan-2/Syntenin/PI-4-5-P2 0.017 0.046 -10000 0 -0.098 67 67
Syndecan-2/Ezrin 0.024 0.037 -10000 0 -0.094 42 42
PRKACA 0 0.069 0.2 43 -0.1 62 105
angiogenesis 0.018 0.044 -10000 0 -0.12 37 37
MMP2 0.022 0.021 -10000 0 0 273 273
IL8 0.032 0.018 -10000 0 0 139 139
calcineurin-NFAT signaling pathway 0.025 0.041 -10000 0 -0.11 39 39
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.039 0.011 -9999 0 0 38 38
ITGB7 0.039 0.011 -9999 0 0 40 40
ITGA4 0.035 0.015 -9999 0 0 88 88
alpha4/beta7 Integrin 0.033 0.065 -9999 0 -0.14 65 65
alpha4/beta1 Integrin 0.033 0.064 -9999 0 -0.14 64 64
FoxO family signaling

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
G6PC -0.002 0.065 -10000 0 -10000 0 0
PLK1 -0.15 0.38 -10000 0 -0.97 74 74
CDKN1B -0.046 0.2 0.4 2 -0.38 83 85
FOXO3 -0.14 0.35 -10000 0 -0.58 173 173
KAT2B -0.008 0.028 0.043 4 -0.046 178 182
FOXO1/SIRT1 0.015 0.078 -10000 0 -0.23 15 15
CAT -0.16 0.4 0.49 4 -0.88 96 100
CTNNB1 0.04 0.01 -10000 0 0 31 31
AKT1 0.012 0.056 -10000 0 -0.072 81 81
FOXO1 -0.005 0.07 0.24 1 -0.26 9 10
MAPK10 0 0.048 0.18 9 -0.12 27 36
mol:GTP 0 0.003 -10000 0 -10000 0 0
FOXO4 -0.025 0.12 0.24 2 -0.32 50 52
response to oxidative stress -0.007 0.03 0.061 1 -0.054 94 95
FOXO3A/SIRT1 -0.13 0.34 0.41 1 -0.55 182 183
XPO1 0.039 0.011 -10000 0 0 39 39
EP300 0.038 0.015 -10000 0 -10000 0 0
BCL2L11 0.01 0.11 -10000 0 -1 5 5
FOXO1/SKP2 0.012 0.075 -10000 0 -0.24 15 15
mol:GDP -0.007 0.03 0.061 1 -0.054 94 95
RAN 0.041 0.007 -10000 0 0 13 13
GADD45A -0.077 0.28 -10000 0 -0.86 44 44
YWHAQ 0.04 0.009 -10000 0 0 28 28
FOXO1/14-3-3 family 0.014 0.13 0.24 1 -0.34 40 41
MST1 0.011 0.056 -10000 0 -0.063 185 185
CSNK1D 0.04 0.009 -10000 0 0 28 28
CSNK1E 0.038 0.013 -10000 0 0 56 56
FOXO4/14-3-3 family 0.002 0.14 -10000 0 -0.42 34 34
YWHAB 0.038 0.012 -10000 0 0 52 52
MAPK8 0.001 0.053 0.19 13 -0.12 29 42
MAPK9 0 0.053 0.19 12 -0.13 26 38
YWHAG 0.04 0.009 -10000 0 0 25 25
YWHAE 0.038 0.013 -10000 0 0 57 57
YWHAZ 0.034 0.016 -10000 0 0 102 102
SIRT1 0.037 0.018 0.12 2 -0.035 24 26
SOD2 -0.12 0.3 -10000 0 -0.69 88 88
RBL2 -0.12 0.33 -10000 0 -0.78 78 78
RAL/GDP 0.031 0.056 -10000 0 -0.11 37 37
CHUK 0.012 0.054 -10000 0 -0.063 166 166
Ran/GTP 0.027 0.019 -10000 0 -0.1 4 4
CSNK1G2 0.037 0.013 -10000 0 0 64 64
RAL/GTP 0.031 0.057 -10000 0 -0.099 42 42
CSNK1G1 0.041 0.008 -10000 0 0 19 19
FASLG 0.017 0.065 -10000 0 -1.2 1 1
SKP2 0.037 0.014 -10000 0 0 73 73
USP7 0.038 0.012 -10000 0 0 50 50
IKBKB 0.011 0.054 -10000 0 -0.063 178 178
CCNB1 -0.18 0.43 -10000 0 -0.99 100 100
FOXO1-3a-4/beta catenin -0.06 0.2 -10000 0 -0.4 89 89
proteasomal ubiquitin-dependent protein catabolic process 0.012 0.074 -10000 0 -0.24 15 15
CSNK1A1 0.04 0.009 -10000 0 0 26 26
SGK1 -0.008 0.028 0.043 4 -0.046 178 182
CSNK1G3 0.039 0.011 -10000 0 0 38 38
Ran/GTP/Exportin 1 0.046 0.038 -10000 0 -0.098 29 29
ZFAND5 -0.018 0.1 0.21 3 -0.27 49 52
SFN 0.036 0.015 -10000 0 0 86 86
CDK2 0.04 0.014 -10000 0 -10000 0 0
FOXO3A/14-3-3 -0.006 0.14 -10000 0 -0.35 51 51
CREBBP 0.04 0.013 -10000 0 -10000 0 0
FBXO32 -0.2 0.54 0.56 2 -1.1 138 140
BCL6 -0.13 0.35 -10000 0 -0.96 62 62
RALB 0.04 0.009 -10000 0 0 26 26
RALA 0.04 0.01 -10000 0 0 30 30
YWHAH 0.038 0.013 -10000 0 0 59 59
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.014 0.15 0.24 19 -0.33 61 80
FYN -0.029 0.18 0.24 16 -0.39 81 97
LAT/GRAP2/SLP76 -0.003 0.15 0.23 7 -0.33 70 77
IKBKB 0.039 0.011 -10000 0 0 43 43
AKT1 -0.014 0.14 0.22 11 -0.32 73 84
B2M 0.038 0.017 -10000 0 -0.003 75 75
IKBKG -0.002 0.05 0.13 9 -0.11 48 57
MAP3K8 0.04 0.008 -10000 0 0 21 21
mol:Ca2+ -0.014 0.015 0.047 10 -0.042 45 55
integrin-mediated signaling pathway 0.045 0.035 -10000 0 -0.11 22 22
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.026 0.18 0.24 11 -0.43 74 85
TRPV6 0.087 0.34 1.3 43 -10000 0 43
CD28 0.041 0.007 -10000 0 0 16 16
SHC1 -0.01 0.16 0.22 25 -0.38 62 87
receptor internalization -0.016 0.14 0.17 3 -0.34 72 75
PRF1 -0.009 0.21 -10000 0 -0.81 25 25
KRAS 0.034 0.016 -10000 0 0 103 103
GRB2 0.041 0.007 -10000 0 0 16 16
COT/AKT1 0.005 0.12 0.22 10 -0.26 71 81
LAT -0.017 0.16 0.22 11 -0.37 67 78
EntrezGene:6955 0.001 0.003 -10000 0 -0.023 3 3
CD3D 0.034 0.018 -10000 0 -0.001 111 111
CD3E 0.037 0.016 -10000 0 -0.001 80 80
CD3G 0.032 0.02 -10000 0 -0.002 136 136
RASGRP2 0.008 0.019 -10000 0 -0.14 2 2
RASGRP1 -0.021 0.15 0.22 13 -0.31 84 97
HLA-A 0.038 0.015 -10000 0 -0.002 67 67
RASSF5 0.039 0.01 -10000 0 0 34 34
RAP1A/GTP/RAPL 0.046 0.035 -10000 0 -0.11 22 22
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.014 0.06 0.14 25 -0.11 45 70
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.019 0.065 -10000 0 -0.16 77 77
PRKCA -0.008 0.083 0.17 18 -0.2 55 73
GRAP2 0.038 0.013 -10000 0 0 56 56
mol:IP3 -0.016 0.11 -10000 0 -0.27 65 65
EntrezGene:6957 0.001 0.004 -10000 0 -0.022 2 2
TCR/CD3/MHC I/CD8 -0.01 0.12 -10000 0 -0.36 45 45
ORAI1 -0.082 0.28 -10000 0 -1.1 43 43
CSK -0.014 0.16 0.23 11 -0.38 65 76
B7 family/CD28 0.027 0.16 0.27 6 -0.36 63 69
CHUK 0.038 0.012 -10000 0 0 52 52
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.023 0.17 0.21 3 -0.4 72 75
PTPN6 -0.01 0.16 0.2 35 -0.35 72 107
VAV1 -0.018 0.16 0.21 12 -0.39 67 79
Monovalent TCR/CD3 -0.004 0.083 -10000 0 -0.21 65 65
CBL 0.04 0.008 -10000 0 0 23 23
LCK -0.018 0.18 0.23 19 -0.39 72 91
PAG1 -0.009 0.16 0.21 33 -0.38 65 98
RAP1A 0.039 0.01 -10000 0 0 35 35
TCR/CD3/MHC I/CD8/LCK -0.022 0.17 0.2 4 -0.37 79 83
CD80 0.04 0.01 -10000 0 0 35 35
CD86 0.035 0.016 -10000 0 0 102 102
PDK1/CARD11/BCL10/MALT1 -0.007 0.085 0.12 2 -0.2 68 70
HRAS 0.04 0.01 -10000 0 0 31 31
GO:0035030 -0.013 0.13 0.18 18 -0.3 68 86
CD8A 0.042 0.01 -10000 0 -0.015 15 15
CD8B 0.001 0.004 -10000 0 -0.022 3 3
PTPRC 0.025 0.021 -10000 0 0 228 228
PDK1/PKC theta -0.02 0.16 0.26 9 -0.37 69 78
CSK/PAG1 -0.008 0.16 0.24 19 -0.39 57 76
SOS1 0.038 0.013 -10000 0 0 56 56
peptide-MHC class I 0.038 0.07 -10000 0 -0.18 46 46
GRAP2/SLP76 0.001 0.17 0.25 6 -0.38 71 77
STIM1 -0.022 0.075 1.1 1 -10000 0 1
RAS family/GTP 0.011 0.078 0.16 15 -0.16 52 67
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.017 0.15 0.17 3 -0.36 72 75
mol:DAG -0.028 0.09 -10000 0 -0.24 70 70
RAP1A/GDP 0.011 0.033 0.073 17 -0.057 48 65
PLCG1 0.038 0.012 -10000 0 0 50 50
CD247 0.001 0.003 -10000 0 -0.023 3 3
cytotoxic T cell degranulation -0.007 0.2 -10000 0 -0.77 25 25
RAP1A/GTP 0.003 0.011 -10000 0 -0.036 19 19
mol:PI-3-4-5-P3 -0.018 0.16 0.22 13 -0.36 74 87
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.011 0.14 0.22 1 -0.34 61 62
NRAS 0.04 0.009 -10000 0 0 30 30
ZAP70 0.041 0.006 -10000 0 0 10 10
GRB2/SOS1 0.047 0.047 -10000 0 -0.14 28 28
LAT/GRAP2/SLP76/VAV1 -0.012 0.14 0.24 5 -0.34 65 70
MALT1 0.036 0.014 -10000 0 0 77 77
TRAF6 0.04 0.008 -10000 0 0 22 22
CD8 heterodimer 0.031 0.012 -10000 0 -0.04 6 6
CARD11 0.038 0.013 -10000 0 0 56 56
PRKCB -0.028 0.062 -10000 0 -0.17 70 70
PRKCE -0.005 0.085 0.17 26 -0.2 52 78
PRKCQ -0.023 0.17 0.23 9 -0.4 72 81
LCP2 0.034 0.016 -10000 0 0 102 102
BCL10 0.041 0.006 -10000 0 0 12 12
regulation of survival gene product expression -0.009 0.12 0.2 14 -0.27 73 87
IKK complex 0.004 0.05 0.13 21 -0.093 26 47
RAS family/GDP -0.002 0.014 -10000 0 -0.035 43 43
MAP3K14 -0.002 0.094 0.16 17 -0.21 69 86
PDPK1 -0.015 0.13 0.21 14 -0.3 72 86
TCR/CD3/MHC I/CD8/Fyn -0.037 0.2 -10000 0 -0.48 70 70
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 0.03 0.1 0.21 19 -0.23 31 50
TBX21 -0.029 0.28 -10000 0 -0.76 41 41
B2M 0.038 0.014 -10000 0 -10000 0 0
TYK2 0.024 0.044 -10000 0 -0.053 71 71
IL12RB1 0.024 0.045 -10000 0 -0.054 76 76
GADD45B -0.06 0.35 -10000 0 -0.97 54 54
IL12RB2 0.028 0.046 -10000 0 -0.055 54 54
GADD45G -0.032 0.3 -10000 0 -0.81 46 46
natural killer cell activation 0.002 0.021 0.047 11 -0.038 56 67
RELB 0.04 0.009 -10000 0 0 27 27
RELA 0.041 0.006 -10000 0 0 10 10
IL18 0.03 0.025 -10000 0 -0.042 20 20
IL2RA 0.039 0.011 -10000 0 0 45 45
IFNG 0.037 0.013 -10000 0 0 60 60
STAT3 (dimer) -0.028 0.29 -10000 0 -0.63 71 71
HLA-DRB5 0.02 0.028 -10000 0 -0.008 262 262
FASLG -0.026 0.28 0.53 1 -0.74 46 47
NF kappa B2 p52/RelB -0.015 0.29 -10000 0 -0.62 71 71
CD4 0.025 0.028 -10000 0 -0.012 189 189
SOCS1 0.038 0.012 -10000 0 0 50 50
EntrezGene:6955 -0.001 0.01 -10000 0 -0.026 54 54
CD3D 0.027 0.03 -10000 0 -0.039 65 65
CD3E 0.029 0.029 -10000 0 -0.037 67 67
CD3G 0.026 0.029 -10000 0 -0.041 57 57
IL12Rbeta2/JAK2 0.033 0.073 -10000 0 -0.15 26 26
CCL3 -0.046 0.33 -10000 0 -0.85 56 56
CCL4 -0.029 0.28 0.4 2 -0.62 72 74
HLA-A 0.038 0.014 -10000 0 -10000 0 0
IL18/IL18R 0.061 0.082 -10000 0 -0.12 73 73
NOS2 -0.027 0.27 0.37 3 -0.58 75 78
IL12/IL12R/TYK2/JAK2/SPHK2 0.03 0.1 0.21 19 -0.23 32 51
IL1R1 -0.11 0.43 -10000 0 -1 96 96
IL4 0.019 0.044 0.099 1 -0.062 16 17
JAK2 0.024 0.043 -10000 0 -0.053 72 72
EntrezGene:6957 -0.001 0.009 -10000 0 -0.025 20 20
TCR/CD3/MHC I/CD8 -0.012 0.12 -10000 0 -0.43 26 26
RAB7A -0.033 0.28 0.39 1 -0.61 75 76
lysosomal transport -0.028 0.26 0.38 2 -0.58 75 77
FOS -0.19 0.52 -10000 0 -1.1 128 128
STAT4 (dimer) -0.022 0.29 0.42 2 -0.64 70 72
STAT5A (dimer) -0.024 0.28 -10000 0 -0.63 66 66
GZMA -0.055 0.35 -10000 0 -0.89 60 60
GZMB -0.037 0.32 0.56 1 -0.85 50 51
HLX 0 0 -10000 0 -10000 0 0
LCK -0.036 0.29 0.41 3 -0.66 68 71
TCR/CD3/MHC II/CD4 -0.069 0.2 -10000 0 -0.38 132 132
IL2/IL2R 0.047 0.082 -10000 0 -0.11 94 94
MAPK14 -0.05 0.33 -10000 0 -0.74 75 75
CCR5 -0.021 0.25 0.36 2 -0.54 73 75
IL1B 0.023 0.042 -10000 0 -0.058 34 34
STAT6 0.011 0.14 -10000 0 -0.56 12 12
STAT4 0.04 0.009 -10000 0 0 29 29
STAT3 0.038 0.013 -10000 0 0 56 56
STAT1 0.034 0.017 -10000 0 0 108 108
NFKB1 0.036 0.015 -10000 0 0 83 83
NFKB2 0.04 0.009 -10000 0 0 24 24
IL12B 0.027 0.046 -10000 0 -0.056 54 54
CD8A 0.043 0.005 -10000 0 -10000 0 0
CD8B 0.001 0 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.031 0.1 0.23 31 -0.21 20 51
IL2RB 0.036 0.014 -10000 0 0 74 74
proteasomal ubiquitin-dependent protein catabolic process -0.016 0.28 0.39 5 -0.59 70 75
IL2RG 0.028 0.02 -10000 0 0 183 183
IL12 0.024 0.072 -10000 0 -0.15 31 31
STAT5A 0.038 0.012 -10000 0 0 51 51
CD247 -0.001 0.009 -10000 0 -0.025 19 19
IL2 0.039 0.011 -10000 0 0 45 45
SPHK2 0.04 0.009 -10000 0 0 25 25
FRAP1 0.04 0.009 -10000 0 0 27 27
IL12A 0.019 0.041 -10000 0 -0.053 60 60
IL12/IL12R/TYK2/JAK2 -0.045 0.3 0.42 1 -0.7 69 70
MAP2K3 -0.053 0.34 -10000 0 -0.78 72 72
RIPK2 0.033 0.017 -10000 0 0 125 125
MAP2K6 -0.056 0.32 -10000 0 -0.71 80 80
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.024 0.029 -10000 0 -0.011 206 206
IL18RAP 0.04 0.019 -10000 0 -0.042 24 24
IL12Rbeta1/TYK2 0.039 0.058 -10000 0 -0.091 2 2
EOMES 0.005 0.076 -10000 0 -0.52 9 9
STAT1 (dimer) -0.043 0.29 -10000 0 -0.63 74 74
T cell proliferation -0.021 0.24 0.37 3 -0.5 74 77
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.04 0.019 -10000 0 -0.042 23 23
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.031 0.25 -10000 0 -0.57 68 68
ATF2 -0.048 0.3 -10000 0 -0.68 76 76
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.036 0.015 -10000 0 0 78 78
GNB1/GNG2 0.015 0.12 0.23 2 -0.26 46 48
mol:DAG -0.006 0.1 0.22 5 -0.26 41 46
PLCG1 -0.007 0.1 0.22 5 -0.26 41 46
YES1 -0.017 0.095 0.2 1 -0.27 44 45
FZD3 0.029 0.019 -10000 0 0 168 168
FZD6 0.029 0.019 -10000 0 0 170 170
G protein 0.029 0.13 0.25 40 -0.27 39 79
MAP3K7 -0.026 0.086 0.17 14 -0.23 40 54
mol:Ca2+ -0.006 0.1 0.21 5 -0.25 41 46
mol:IP3 -0.006 0.1 0.22 5 -0.26 41 46
NLK -0.031 0.27 -10000 0 -0.86 51 51
GNB1 0.041 0.005 -10000 0 0 7 7
CAMK2A -0.017 0.091 0.19 6 -0.24 40 46
MAP3K7IP1 0.038 0.012 -10000 0 0 53 53
Noncanonical Wnts/FZD -0.019 0.095 -10000 0 -0.29 39 39
CSNK1A1 0.04 0.009 -10000 0 0 26 26
GNAS -0.01 0.1 0.2 21 -0.28 37 58
GO:0007205 -0.013 0.096 0.2 6 -0.25 43 49
WNT6 0.041 0.006 -10000 0 0 13 13
WNT4 0.041 0.007 -10000 0 0 18 18
NFAT1/CK1 alpha 0.005 0.12 0.29 9 -0.27 40 49
GNG2 0.039 0.01 -10000 0 0 34 34
WNT5A 0.035 0.015 -10000 0 0 91 91
WNT11 0.033 0.017 -10000 0 0 124 124
CDC42 -0.019 0.095 0.2 6 -0.26 43 49
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.04 0.087 -10000 0 -0.14 66 66
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.039 0.011 -10000 0 0 38 38
STAT1 (dimer)/Cbp/p300 0.005 0.12 0.29 5 -0.22 77 82
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.041 0.081 -10000 0 -0.15 68 68
antigen processing and presentation of peptide antigen via MHC class I -0.025 0.093 -10000 0 -0.2 86 86
CaM/Ca2+ 0.043 0.088 -10000 0 -0.14 62 62
RAP1A 0.039 0.01 -10000 0 0 35 35
STAT1 (dimer)/SHP2 0 0.093 0.23 7 -0.19 60 67
AKT1 0.005 0.1 0.21 34 -0.22 30 64
MAP2K1 -0.028 0.066 0.14 25 -0.18 34 59
MAP3K11 -0.022 0.072 0.17 21 -0.18 29 50
IFNGR1 0.034 0.021 0.083 2 -0.005 112 114
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.01 0.1 -10000 0 -0.28 47 47
Rap1/GTP -0.044 0.057 0.073 8 -0.17 46 54
CRKL/C3G 0.056 0.018 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.063 0.091 -10000 0 -0.14 62 62
CEBPB -0.03 0.16 0.28 1 -0.44 55 56
STAT3 0.038 0.013 -10000 0 0 56 56
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.048 0.16 -10000 0 -0.77 15 15
STAT1 -0.028 0.082 0.22 10 -0.21 47 57
CALM1 0.04 0.01 -10000 0 0 31 31
IFN-gamma (dimer) 0.032 0.025 0.085 2 -0.017 103 105
PIK3CA 0.03 0.019 -10000 0 0 155 155
STAT1 (dimer)/PIAS1 -0.009 0.092 0.25 6 -0.2 50 56
CEBPB/PTGES2/Cbp/p300 -0.011 0.12 -10000 0 -0.3 55 55
mol:Ca2+ 0.036 0.085 -10000 0 -0.14 67 67
MAPK3 -0.021 0.14 -10000 0 -0.67 14 14
STAT1 (dimer) -0.022 0.13 0.18 5 -0.28 81 86
MAPK1 -0.058 0.21 0.42 1 -0.74 42 43
JAK2 0.033 0.022 0.083 2 -0.007 113 115
PIK3R1 0.034 0.017 -10000 0 0 107 107
JAK1 0.036 0.022 0.082 1 -0.019 67 68
CAMK2D 0.036 0.015 -10000 0 0 81 81
DAPK1 -0.027 0.16 -10000 0 -0.48 48 48
SMAD7 -0.003 0.07 0.16 30 -0.13 44 74
CBL/CRKL/C3G 0.025 0.085 0.24 7 -0.17 33 40
PI3K 0.02 0.092 -10000 0 -0.18 57 57
IFNG 0.032 0.025 0.086 2 -0.017 103 105
apoptosis -0.023 0.15 -10000 0 -0.42 53 53
CAMK2G 0.04 0.008 -10000 0 0 23 23
STAT3 (dimer) 0.038 0.013 -10000 0 0 56 56
CAMK2A 0.041 0.006 -10000 0 0 12 12
CAMK2B 0.041 0.007 -10000 0 0 18 18
FRAP1 -0.004 0.097 0.16 76 -0.21 33 109
PRKCD 0.002 0.11 0.22 34 -0.23 31 65
RAP1B 0.038 0.013 -10000 0 0 59 59
negative regulation of cell growth -0.025 0.093 -10000 0 -0.2 86 86
PTPN2 0.04 0.008 -10000 0 0 20 20
EP300 0.037 0.014 -10000 0 0 72 72
IRF1 -0.046 0.097 0.22 6 -0.28 56 62
STAT1 (dimer)/PIASy -0.03 0.087 0.21 10 -0.22 39 49
SOCS1 0.002 0.18 -10000 0 -1.1 15 15
mol:GDP 0.022 0.081 0.22 7 -0.16 33 40
CASP1 -0.023 0.079 0.16 13 -0.17 97 110
PTGES2 0.04 0.009 -10000 0 0 27 27
IRF9 -0.008 0.052 0.11 9 -0.13 47 56
mol:PI-3-4-5-P3 0.006 0.081 -10000 0 -0.18 57 57
RAP1/GDP 0.015 0.086 0.24 1 -0.18 47 48
CBL -0.021 0.072 0.17 27 -0.18 24 51
MAP3K1 -0.02 0.07 0.17 18 -0.18 29 47
PIAS1 0.04 0.009 -10000 0 0 28 28
PIAS4 0.038 0.012 -10000 0 0 55 55
antigen processing and presentation of peptide antigen via MHC class II -0.025 0.093 -10000 0 -0.2 86 86
PTPN11 -0.015 0.074 0.17 34 -0.17 30 64
CREBBP 0.038 0.013 -10000 0 0 54 54
RAPGEF1 0.04 0.008 -10000 0 0 23 23
HIF-2-alpha transcription factor network

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
MMP14 -0.054 0.3 -10000 0 -0.88 64 64
oxygen homeostasis 0.003 0.011 0.034 16 -0.024 4 20
TCEB2 0.04 0.009 -10000 0 0 24 24
TCEB1 0.038 0.012 -10000 0 0 49 49
VHL/Elongin B/Elongin C/HIF2A 0.04 0.13 0.29 9 -0.22 55 64
EPO 0.026 0.18 0.36 10 -0.34 42 52
FIH (dimer) 0.04 0.023 0.089 2 -0.035 34 36
APEX1 0.033 0.034 -10000 0 -0.034 90 90
SERPINE1 -0.008 0.16 0.36 8 -0.32 65 73
FLT1 -0.044 0.26 -10000 0 -0.68 76 76
ADORA2A 0.005 0.17 0.33 19 -0.31 62 81
germ cell development 0.008 0.18 0.36 17 -0.32 75 92
SLC11A2 0.011 0.19 0.35 13 -0.33 69 82
BHLHE40 0.012 0.18 0.33 20 -0.31 68 88
HIF1AN 0.04 0.023 0.089 2 -0.035 34 36
HIF2A/ARNT/SIRT1 0.04 0.16 0.31 11 -0.26 59 70
ETS1 0.043 0.025 0.12 1 -0.11 5 6
CITED2 0.013 0.15 -10000 0 -0.63 26 26
KDR -0.033 0.25 -10000 0 -0.69 66 66
PGK1 0.011 0.19 0.36 15 -0.34 71 86
SIRT1 0.041 0.008 -10000 0 0 20 20
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.062 0.23 0.46 1 -0.35 64 65
EPAS1 0.005 0.11 0.22 16 -0.22 68 84
SP1 0.034 0.05 -10000 0 -0.11 56 56
ABCG2 0.012 0.18 0.35 15 -0.32 64 79
EFNA1 0.001 0.19 0.35 12 -0.36 72 84
FXN 0.006 0.17 0.33 20 -0.31 63 83
POU5F1 0.006 0.18 0.35 15 -0.32 75 90
neuron apoptosis -0.061 0.22 0.34 64 -0.46 1 65
EP300 0.037 0.014 -10000 0 0 72 72
EGLN3 0.028 0.027 0.085 1 -0.035 22 23
EGLN2 0.04 0.023 0.087 3 -0.033 31 34
EGLN1 0.039 0.024 0.089 2 -0.035 33 35
VHL/Elongin B/Elongin C 0.069 0.039 -10000 0 -0.12 11 11
VHL 0.04 0.009 -10000 0 0 28 28
ARNT 0.035 0.033 -10000 0 -0.035 88 88
SLC2A1 -0.012 0.18 0.35 10 -0.34 76 86
TWIST1 0.004 0.17 0.33 21 -0.31 63 84
ELK1 0.047 0.013 -10000 0 -0.088 3 3
HIF2A/ARNT/Cbp/p300 0.04 0.16 0.33 12 -0.27 52 64
VEGFA 0.012 0.18 0.33 20 -0.31 68 88
CREBBP 0.038 0.012 -10000 0 0 54 54
E-cadherin 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
E-cadherin/beta catenin-gamma catenin 0.049 0.064 -9999 0 -0.13 48 48
E-cadherin/beta catenin 0.04 0.052 -9999 0 -0.14 36 36
CTNNB1 0.04 0.01 -9999 0 0 31 31
JUP 0.037 0.014 -9999 0 0 67 67
CDH1 0.035 0.016 -9999 0 0 98 98
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.001 0.068 0.14 13 -0.18 56 69
CRKL 0.039 0.011 -10000 0 0 38 38
Rac1/GDP 0.029 0.01 -10000 0 -0.13 1 1
DOCK1 0.037 0.013 -10000 0 0 62 62
ITGA4 0.035 0.015 -10000 0 0 88 88
alpha4/beta7 Integrin/MAdCAM1 0.067 0.073 -10000 0 -0.11 66 66
EPO 0.04 0.008 -10000 0 0 20 20
alpha4/beta7 Integrin 0.033 0.065 -10000 0 -0.14 65 65
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.038 0.012 -10000 0 0 51 51
alpha4/beta1 Integrin 0.033 0.064 -10000 0 -0.14 64 64
EPO/EPOR (dimer) 0.052 0.025 -10000 0 -0.14 2 2
lamellipodium assembly 0.017 0.11 0.21 1 -0.33 22 23
PIK3CA 0.03 0.019 -10000 0 0 155 155
PI3K 0.024 0.061 -10000 0 -0.15 47 47
ARF6 0.041 0.008 -10000 0 0 19 19
JAK2 0.007 0.067 -10000 0 -0.18 53 53
PXN 0.041 0.007 -10000 0 0 14 14
PIK3R1 0.034 0.017 -10000 0 0 107 107
MADCAM1 0.037 0.013 -10000 0 0 64 64
cell adhesion 0.065 0.072 -10000 0 -0.11 66 66
CRKL/CBL 0.055 0.021 -10000 0 -0.14 1 1
ITGB1 0.039 0.011 -10000 0 0 38 38
SRC -0.018 0.089 0.18 34 -0.19 39 73
ITGB7 0.039 0.011 -10000 0 0 40 40
RAC1 0.039 0.01 -10000 0 0 33 33
alpha4/beta1 Integrin/VCAM1 -0.005 0.095 -10000 0 -0.14 153 153
p130Cas/Crk/Dock1 0.012 0.098 0.23 17 -0.18 44 61
VCAM1 0.02 0.021 -10000 0 0 289 289
RHOA 0.041 0.007 -10000 0 0 14 14
alpha4/beta1 Integrin/Paxillin/GIT1 0.07 0.073 -10000 0 -0.11 63 63
BCAR1 -0.02 0.08 0.17 29 -0.18 39 68
EPOR 0.037 0.014 -10000 0 0 73 73
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.04 0.008 -10000 0 0 23 23
GIT1 0.04 0.009 -10000 0 0 27 27
Rac1/GTP 0.017 0.11 0.21 1 -0.35 21 22
EPHB forward signaling

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
Ephrin A5/EPHB2 0.035 0.048 -10000 0 -0.12 42 42
cell-cell adhesion 0.041 0.041 0.18 12 -10000 0 12
Ephrin B/EPHB2/RasGAP 0.053 0.096 -10000 0 -0.12 93 93
ITSN1 0.04 0.008 -10000 0 0 22 22
PIK3CA 0.03 0.019 -10000 0 0 155 155
SHC1 0.04 0.01 -10000 0 0 31 31
Ephrin B1/EPHB3 0.037 0.038 -10000 0 -0.11 22 22
Ephrin B1/EPHB1 0.048 0.024 -10000 0 -0.11 5 5
HRAS/GDP -0.019 0.11 -10000 0 -0.18 130 130
Ephrin B/EPHB1/GRB7 0.058 0.089 -10000 0 -0.12 78 78
Endophilin/SYNJ1 -0.025 0.059 0.19 12 -0.2 6 18
KRAS 0.034 0.016 -10000 0 0 103 103
Ephrin B/EPHB1/Src 0.062 0.087 -10000 0 -0.12 75 75
endothelial cell migration 0.021 0.076 -10000 0 -0.12 99 99
GRB2 0.041 0.007 -10000 0 0 16 16
GRB7 0.037 0.013 -10000 0 0 63 63
PAK1 -0.018 0.071 0.18 29 -0.2 9 38
HRAS 0.04 0.01 -10000 0 0 31 31
RRAS -0.025 0.058 0.19 9 -0.2 11 20
DNM1 0.039 0.011 -10000 0 0 38 38
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.011 0.071 0.19 34 -0.18 4 38
lamellipodium assembly -0.041 0.041 -10000 0 -0.18 12 12
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.007 0.072 -10000 0 -0.22 13 13
PIK3R1 0.034 0.017 -10000 0 0 107 107
EPHB2 0.039 0.011 -10000 0 0 38 38
EPHB3 0.032 0.018 -10000 0 0 135 135
EPHB1 0.038 0.013 -10000 0 0 59 59
EPHB4 0.04 0.009 -10000 0 0 29 29
mol:GDP -0.041 0.098 0.19 14 -0.23 70 84
Ephrin B/EPHB2 0.048 0.08 -10000 0 -0.11 96 96
Ephrin B/EPHB3 0.035 0.076 -10000 0 -0.11 88 88
JNK cascade -0.003 0.099 0.28 50 -0.18 3 53
Ephrin B/EPHB1 0.049 0.075 -10000 0 -0.11 81 81
RAP1/GDP -0.025 0.12 0.29 4 -0.22 83 87
EFNB2 0.031 0.018 -10000 0 0 143 143
EFNB3 0.037 0.014 -10000 0 0 70 70
EFNB1 0.041 0.007 -10000 0 0 16 16
Ephrin B2/EPHB1-2 0.036 0.067 -10000 0 -0.11 77 77
RAP1B 0.038 0.013 -10000 0 0 59 59
RAP1A 0.039 0.01 -10000 0 0 35 35
CDC42/GTP 0.029 0.099 -10000 0 -0.16 84 84
Rap1/GTP -0.045 0.05 0.062 2 -0.19 16 18
axon guidance 0.035 0.047 -10000 0 -0.11 42 42
MAPK3 -0.003 0.069 0.2 6 -0.21 12 18
MAPK1 -0.002 0.068 0.2 6 -0.21 13 19
Rac1/GDP -0.03 0.11 0.26 7 -0.21 75 82
actin cytoskeleton reorganization -0.051 0.06 -10000 0 -0.16 72 72
CDC42/GDP -0.029 0.11 0.26 6 -0.22 77 83
PI3K 0.025 0.08 -10000 0 -0.12 99 99
EFNA5 0.034 0.016 -10000 0 0 103 103
Ephrin B2/EPHB4 0.023 0.061 -10000 0 -0.11 83 83
Ephrin B/EPHB2/Intersectin/N-WASP 0 0.079 -10000 0 -0.16 98 98
CDC42 0.04 0.009 -10000 0 0 24 24
RAS family/GTP -0.041 0.049 -10000 0 -0.19 14 14
PTK2 0.16 0.26 0.56 166 -0.18 1 167
MAP4K4 -0.003 0.1 0.28 50 -0.19 3 53
SRC 0.039 0.01 -10000 0 0 36 36
KALRN 0.038 0.012 -10000 0 0 54 54
Intersectin/N-WASP 0.056 0.025 -10000 0 -0.14 6 6
neuron projection morphogenesis -0.017 0.094 0.28 23 -0.21 14 37
MAP2K1 -0.001 0.065 0.21 2 -0.22 12 14
WASL 0.04 0.008 -10000 0 0 23 23
Ephrin B1/EPHB1-2/NCK1 0.076 0.065 -10000 0 -0.12 40 40
cell migration -0.009 0.09 0.23 12 -0.24 19 31
NRAS 0.04 0.009 -10000 0 0 30 30
SYNJ1 -0.025 0.06 0.19 12 -0.2 6 18
PXN 0.041 0.007 -10000 0 0 14 14
TF -0.029 0.054 0.17 11 -0.2 6 17
HRAS/GTP 0.033 0.081 -10000 0 -0.12 86 86
Ephrin B1/EPHB1-2 0.062 0.043 -10000 0 -0.11 18 18
cell adhesion mediated by integrin 0.009 0.064 0.17 12 -0.2 16 28
RAC1 0.039 0.01 -10000 0 0 33 33
mol:GTP 0.037 0.083 -10000 0 -0.12 87 87
RAC1-CDC42/GTP -0.04 0.046 -10000 0 -0.19 10 10
RASA1 0.037 0.014 -10000 0 0 71 71
RAC1-CDC42/GDP -0.018 0.12 0.27 6 -0.21 75 81
ruffle organization -0.021 0.08 0.23 14 -0.24 2 16
NCK1 0.036 0.015 -10000 0 0 79 79
receptor internalization -0.03 0.055 0.17 11 -0.19 8 19
Ephrin B/EPHB2/KALRN 0.06 0.092 -10000 0 -0.12 84 84
ROCK1 0.02 0.089 0.19 111 -10000 0 111
RAS family/GDP -0.055 0.062 -10000 0 -0.16 108 108
Rac1/GTP -0.039 0.046 0.051 4 -0.18 12 16
Ephrin B/EPHB1/Src/Paxillin 0.004 0.072 -10000 0 -0.15 78 78
FAS signaling pathway (CD95)

Figure S50.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S50.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPTAN1 -0.025 0.059 0.2 3 -0.22 35 38
RFC1 -0.023 0.06 0.17 3 -0.22 35 38
PRKDC -0.019 0.068 0.21 13 -0.21 38 51
RIPK1 0.038 0.012 -10000 0 0 48 48
CASP7 0.002 0.12 -10000 0 -0.56 21 21
FASLG/FAS/FADD/FAF1 0.022 0.082 0.15 103 -0.17 38 141
MAP2K4 0.002 0.12 0.32 4 -0.32 38 42
mol:ceramide 0.018 0.094 -10000 0 -0.27 28 28
GSN -0.023 0.061 0.2 4 -0.22 37 41
FASLG/FAS/FADD/FAF1/Caspase 8 0.027 0.091 0.21 16 -0.25 18 34
FAS 0.035 0.018 -10000 0 -0.002 105 105
BID -0.034 0.024 0.23 2 -0.13 12 14
MAP3K1 -0.001 0.11 0.25 7 -0.35 31 38
MAP3K7 0.039 0.012 -10000 0 0 47 47
RB1 -0.025 0.061 0.18 2 -0.22 35 37
CFLAR 0.04 0.008 -10000 0 0 21 21
HGF/MET -0.014 0.092 -10000 0 -0.14 168 168
ARHGDIB -0.012 0.074 0.23 22 -0.22 25 47
FADD 0.041 0.012 -10000 0 -0.01 28 28
actin filament polymerization 0.023 0.06 0.21 37 -0.2 4 41
NFKB1 -0.049 0.24 -10000 0 -0.64 71 71
MAPK8 -0.002 0.12 0.34 3 -0.36 31 34
DFFA -0.021 0.064 0.2 7 -0.21 40 47
DNA fragmentation during apoptosis -0.021 0.062 0.2 7 -0.21 38 45
FAS/FADD/MET 0.017 0.09 -10000 0 -0.13 129 129
CFLAR/RIP1 0.052 0.031 -10000 0 -0.15 8 8
FAIM3 0.04 0.009 -10000 0 0 26 26
FAF1 0.041 0.014 -10000 0 -0.044 7 7
PARP1 -0.02 0.067 0.22 13 -0.21 36 49
DFFB -0.021 0.062 0.2 7 -0.21 38 45
CHUK -0.057 0.22 -10000 0 -0.62 70 70
FASLG 0.041 0.013 -10000 0 -0.043 8 8
FAS/FADD 0.036 0.061 -10000 0 -0.14 56 56
HGF 0.04 0.009 -10000 0 0 29 29
LMNA -0.019 0.068 0.19 17 -0.22 30 47
CASP6 -0.02 0.06 0.14 2 -0.24 27 29
CASP10 0.037 0.017 -10000 0 -0.004 75 75
CASP3 -0.022 0.064 0.16 4 -0.23 41 45
PTPN13 0.021 0.021 -10000 0 0 276 276
CASP8 -0.031 0.02 0.26 2 -10000 0 2
IL6 -0.042 0.24 -10000 0 -0.78 31 31
MET 0.027 0.02 -10000 0 0 198 198
ICAD/CAD -0.024 0.061 0.19 11 -0.2 40 51
FASLG/FAS/FADD/FAF1/Caspase 10 0.018 0.095 -10000 0 -0.27 28 28
activation of caspase activity by cytochrome c -0.034 0.024 0.23 2 -0.13 12 14
PAK2 -0.024 0.06 0.14 2 -0.22 39 41
BCL2 0.036 0.014 -10000 0 0 76 76
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.041 0.15 -10000 0 -0.34 100 100
KLHL20 -0.016 0.1 0.2 14 -0.23 52 66
CYFIP2 0.038 0.012 -10000 0 0 47 47
Rac1/GDP -0.012 0.11 0.26 6 -0.25 50 56
ENAH -0.038 0.14 -10000 0 -0.33 98 98
AP1M1 0.036 0.014 -10000 0 0 77 77
RAP1B 0.038 0.013 -10000 0 0 59 59
RAP1A 0.039 0.01 -10000 0 0 35 35
CTNNB1 0.04 0.01 -10000 0 0 31 31
CDC42/GTP 0.003 0.079 0.16 4 -0.21 27 31
ABI1/Sra1/Nap1 -0.033 0.054 -10000 0 -0.15 66 66
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.069 0.068 -10000 0 -0.11 43 43
RAPGEF1 -0.035 0.13 0.28 3 -0.31 83 86
CTNND1 0.041 0.007 -10000 0 0 17 17
regulation of calcium-dependent cell-cell adhesion -0.029 0.15 -10000 0 -0.34 102 102
CRK -0.033 0.13 0.25 1 -0.32 83 84
E-cadherin/gamma catenin/alpha catenin 0.05 0.065 -10000 0 -0.14 42 42
alphaE/beta7 Integrin 0.05 0.038 -10000 0 -0.13 17 17
IQGAP1 0.037 0.014 -10000 0 0 69 69
NCKAP1 0.04 0.01 -10000 0 0 31 31
Rap1/GTP/I-afadin 0.043 0.066 -10000 0 -0.11 68 68
DLG1 -0.044 0.15 -10000 0 -0.34 103 103
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.033 0.048 -10000 0 -0.15 55 55
MLLT4 0.034 0.017 -10000 0 0 107 107
ARF6/GTP/NME1/Tiam1 0.045 0.062 -10000 0 -0.11 59 59
PI3K -0.04 0.062 -10000 0 -0.2 42 42
ARF6 0.041 0.008 -10000 0 0 19 19
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.038 0.052 -10000 0 -0.15 30 30
TIAM1 0.037 0.014 -10000 0 0 72 72
E-cadherin(dimer)/Ca2+ 0.062 0.072 -10000 0 -0.13 51 51
AKT1 -0.008 0.062 0.16 15 -0.16 17 32
PIK3R1 0.034 0.017 -10000 0 0 107 107
CDH1 0.035 0.016 -10000 0 0 98 98
RhoA/GDP -0.013 0.11 0.22 5 -0.25 52 57
actin cytoskeleton organization -0.01 0.077 0.16 15 -0.17 50 65
CDC42/GDP -0.012 0.11 0.26 6 -0.25 49 55
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.002 0.073 -10000 0 -0.2 55 55
ITGB7 0.039 0.011 -10000 0 0 40 40
RAC1 0.04 0.01 -10000 0 0 33 33
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.067 0.078 -10000 0 -0.14 51 51
E-cadherin/Ca2+/beta catenin/alpha catenin 0.046 0.056 -10000 0 -0.11 48 48
mol:GDP -0.031 0.11 0.24 7 -0.28 52 59
CDC42/GTP/IQGAP1 0.04 0.046 -10000 0 -0.11 42 42
JUP 0.037 0.014 -10000 0 0 67 67
p120 catenin/RhoA/GDP -0.001 0.12 0.24 4 -0.26 48 52
RAC1/GTP/IQGAP1 0.038 0.046 -10000 0 -0.11 42 42
PIP5K1C/AP1M1 0.049 0.026 -10000 0 -0.14 1 1
RHOA 0.041 0.007 -10000 0 0 14 14
CDC42 0.04 0.009 -10000 0 0 24 24
CTNNA1 0.039 0.011 -10000 0 0 38 38
positive regulation of S phase of mitotic cell cycle -0.016 0.059 0.12 5 -0.12 96 101
NME1 0.035 0.015 -10000 0 0 91 91
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.039 0.15 -10000 0 -0.34 93 93
regulation of cell-cell adhesion -0.008 0.064 -10000 0 -0.15 50 50
WASF2 -0.007 0.043 0.11 13 -0.095 42 55
Rap1/GTP 0.002 0.087 0.2 9 -0.24 24 33
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.071 0.083 -10000 0 -0.12 52 52
CCND1 -0.02 0.071 0.14 5 -0.15 96 101
VAV2 -0.051 0.22 -10000 0 -0.61 50 50
RAP1/GDP 0 0.098 0.23 10 -0.25 31 41
adherens junction assembly -0.038 0.14 -10000 0 -0.34 93 93
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.04 0.009 -10000 0 0 26 26
PIP5K1C 0.038 0.012 -10000 0 0 54 54
regulation of heterotypic cell-cell adhesion 0.045 0.076 0.22 5 -0.13 60 65
E-cadherin/beta catenin 0.007 0.042 0.15 1 -0.23 14 15
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.037 0.14 -10000 0 -0.33 94 94
PIK3CA 0.03 0.019 -10000 0 0 155 155
Rac1/GTP -0.056 0.13 -10000 0 -0.35 64 64
E-cadherin/beta catenin/alpha catenin 0.052 0.065 -10000 0 -0.13 48 48
ITGAE 0.039 0.01 -10000 0 0 36 36
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.03 0.16 -10000 0 -0.34 102 102
Retinoic acid receptors-mediated signaling

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
HDAC1 0.038 0.013 -10000 0 0 56 56
HDAC3 0.041 0.007 -10000 0 0 15 15
VDR 0.038 0.013 -10000 0 0 56 56
Cbp/p300/PCAF 0.04 0.044 -10000 0 -0.14 25 25
EP300 0.037 0.014 -10000 0 0 72 72
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.012 0.094 0.18 1 -0.26 47 48
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.04 0.009 -10000 0 0 28 28
AKT1 0.01 0.091 0.17 73 -0.2 30 103
RAR alpha/9cRA/Cyclin H -0.002 0.12 -10000 0 -0.25 66 66
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.003 0.079 -10000 0 -0.22 45 45
CDC2 0.026 0.024 -10000 0 -0.005 199 199
response to UV -0.001 0.008 -10000 0 -0.026 41 41
RAR alpha/Jnk1 0.017 0.068 -10000 0 -0.16 41 41
NCOR2 0.04 0.009 -10000 0 0 28 28
VDR/VDR/Vit D3 0.023 0.031 -10000 0 -0.13 22 22
RXRs/RARs/NRIP1/9cRA -0.037 0.19 -10000 0 -0.51 60 60
NCOA2 0.037 0.014 -10000 0 0 70 70
NCOA3 0.036 0.015 -10000 0 0 83 83
NCOA1 0.04 0.009 -10000 0 0 28 28
VDR/VDR/DNA 0.038 0.013 -10000 0 0 56 56
RARG 0.036 0.021 -10000 0 -0.018 68 68
RAR gamma1/9cRA 0.042 0.033 -10000 0 -0.11 14 14
MAPK3 0.036 0.022 -10000 0 -0.026 59 59
MAPK1 0.039 0.012 -10000 0 0 46 46
MAPK8 0.035 0.024 -10000 0 -0.025 70 70
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.013 0.14 0.26 1 -0.32 72 73
RARA 0.007 0.054 -10000 0 -0.16 42 42
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.005 0.083 -10000 0 -0.22 52 52
PRKCA 0.031 0.031 -10000 0 -0.072 34 34
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.044 0.2 -10000 0 -0.55 61 61
RXRG 0.016 0.057 -10000 0 -0.2 29 29
RXRA -0.027 0.097 -10000 0 -0.24 51 51
RXRB 0.013 0.059 -10000 0 -0.2 33 33
VDR/Vit D3/DNA 0.023 0.031 -10000 0 -0.13 22 22
RBP1 0.03 0.019 -10000 0 0 163 163
CRBP1/9-cic-RA 0.002 0.057 -10000 0 -0.13 89 89
RARB 0.032 0.026 -10000 0 -0.015 118 118
PRKCG 0.036 0.032 -10000 0 -0.071 44 44
MNAT1 0.04 0.008 -10000 0 0 22 22
RAR alpha/RXRs -0.016 0.16 0.27 2 -0.36 73 75
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.01 0.13 0.23 1 -0.32 44 45
proteasomal ubiquitin-dependent protein catabolic process -0.011 0.1 0.18 1 -0.26 47 48
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.043 0.2 -10000 0 -0.55 61 61
positive regulation of DNA binding -0.009 0.11 -10000 0 -0.24 69 69
NRIP1 -0.079 0.32 -10000 0 -0.96 56 56
RXRs/RARs -0.027 0.17 -10000 0 -0.4 76 76
RXRs/RXRs/DNA/9cRA -0.03 0.13 -10000 0 -0.33 76 76
PRKACA 0.035 0.015 -10000 0 0 89 89
CDK7 0.035 0.016 -10000 0 0 97 97
TFIIH 0.06 0.054 -10000 0 -0.14 25 25
RAR alpha/9cRA 0.037 0.087 -10000 0 -0.23 18 18
CCNH 0.037 0.014 -10000 0 0 68 68
CREBBP 0.038 0.012 -10000 0 0 54 54
RAR gamma2/9cRA 0.044 0.061 -10000 0 -0.13 34 34
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.067 0.066 -10000 0 -0.1 55 55
ER alpha/Gai/GDP/Gbeta gamma -0.023 0.13 -10000 0 -0.32 64 64
AKT1 -0.091 0.27 -10000 0 -0.64 104 104
PIK3CA 0.03 0.019 -10000 0 0 155 155
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.09 0.28 -10000 0 -0.65 105 105
mol:Ca2+ -0.003 0.07 0.18 16 -0.27 22 38
IGF1R 0.033 0.017 -10000 0 0 118 118
E2/ER alpha (dimer)/Striatin 0.035 0.051 -10000 0 -0.11 52 52
SHC1 0.04 0.01 -10000 0 0 31 31
apoptosis 0.087 0.26 0.61 104 -10000 0 104
RhoA/GTP 0.014 0.049 -10000 0 -0.11 62 62
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.006 0.14 -10000 0 -0.28 76 76
regulation of stress fiber formation 0.014 0.072 0.16 15 -0.19 20 35
E2/ERA-ERB (dimer) 0.037 0.047 -10000 0 -0.11 44 44
KRAS 0.034 0.016 -10000 0 0 103 103
G13/GTP 0.033 0.046 -10000 0 -0.1 53 53
pseudopodium formation -0.014 0.072 0.19 20 -0.16 15 35
E2/ER alpha (dimer)/PELP1 0.036 0.047 -10000 0 -0.11 44 44
GRB2 0.041 0.007 -10000 0 0 16 16
GNG2 0.039 0.01 -10000 0 0 34 34
GNAO1 0.034 0.016 -10000 0 0 101 101
HRAS 0.04 0.01 -10000 0 0 31 31
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.038 0.16 -10000 0 -0.38 81 81
E2/ER beta (dimer) 0.03 0.005 -10000 0 -10000 0 0
mol:GDP -0.005 0.08 0.14 3 -0.22 56 59
mol:NADP -0.038 0.16 -10000 0 -0.38 81 81
PIK3R1 0.034 0.017 -10000 0 0 107 107
mol:IP3 -0.001 0.067 0.18 10 -0.28 22 32
IGF-1R heterotetramer 0.033 0.017 -10000 0 0 118 118
PLCB1 0.005 0.064 -10000 0 -0.29 21 21
PLCB2 0.007 0.062 -10000 0 -0.28 22 22
IGF1 0.036 0.015 -10000 0 0 84 84
mol:L-citrulline -0.038 0.16 -10000 0 -0.38 81 81
RHOA 0.041 0.007 -10000 0 0 14 14
Gai/GDP -0.02 0.2 -10000 0 -0.58 59 59
JNK cascade 0.03 0.005 -10000 0 -10000 0 0
BCAR1 0.036 0.014 -10000 0 0 75 75
ESR2 0.041 0.007 -10000 0 0 18 18
GNAQ 0.038 0.012 -10000 0 0 49 49
ESR1 0.035 0.016 -10000 0 0 93 93
Gq family/GDP/Gbeta gamma -0.037 0.22 -10000 0 -0.62 67 67
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.021 0.11 -10000 0 -0.64 11 11
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.007 0.14 -10000 0 -0.29 73 73
GNAZ 0.039 0.011 -10000 0 0 42 42
E2/ER alpha (dimer) 0.016 0.042 -10000 0 -0.13 44 44
STRN 0.04 0.009 -10000 0 0 30 30
GNAL 0.04 0.009 -10000 0 0 26 26
PELP1 0.039 0.01 -10000 0 0 35 35
MAPK11 0.013 0.008 0.069 1 -10000 0 1
GNAI2 0.041 0.007 -10000 0 0 15 15
GNAI3 0.039 0.011 -10000 0 0 45 45
GNAI1 0.035 0.016 -10000 0 0 95 95
HBEGF -0.015 0.14 0.31 17 -0.33 49 66
cAMP biosynthetic process 0.032 0.039 -10000 0 -0.092 41 41
SRC -0.022 0.13 0.22 19 -0.3 66 85
PI3K 0.024 0.061 -10000 0 -0.15 47 47
GNB1 0.041 0.005 -10000 0 0 7 7
G13/GDP/Gbeta gamma 0.04 0.096 -10000 0 -0.19 62 62
SOS1 0.038 0.013 -10000 0 0 56 56
IGF-1R heterotetramer/IGF1 -0.038 0.1 -10000 0 -0.24 74 74
Gs family/GTP 0.041 0.044 -10000 0 -0.093 41 41
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.054 0.05 -10000 0 -0.11 29 29
vasodilation -0.036 0.16 -10000 0 -0.37 81 81
mol:DAG -0.001 0.067 0.18 10 -0.28 22 32
Gs family/GDP/Gbeta gamma 0.003 0.081 -10000 0 -0.2 53 53
MSN -0.016 0.073 0.2 18 -0.17 15 33
Gq family/GTP 0.019 0.067 -10000 0 -0.28 22 22
mol:PI-3-4-5-P3 -0.086 0.27 -10000 0 -0.62 105 105
NRAS 0.04 0.009 -10000 0 0 30 30
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.036 0.16 0.37 81 -10000 0 81
GRB2/SOS1 0.047 0.047 -10000 0 -0.14 28 28
RhoA/GDP 0.014 0.09 -10000 0 -0.22 56 56
NOS3 -0.041 0.17 -10000 0 -0.4 80 80
GNA11 0.037 0.013 -10000 0 0 61 61
MAPKKK cascade -0.029 0.19 -10000 0 -0.46 78 78
E2/ER alpha (dimer)/PELP1/Src -0.012 0.14 0.24 2 -0.29 78 80
ruffle organization -0.014 0.072 0.19 20 -0.16 15 35
ROCK2 -0.008 0.083 0.22 22 -0.17 4 26
GNA14 0.039 0.01 -10000 0 0 33 33
GNA15 0.037 0.014 -10000 0 0 69 69
GNA13 0.04 0.009 -10000 0 0 28 28
MMP9 -0.016 0.15 0.37 18 -0.32 53 71
MMP2 -0.019 0.13 0.24 4 -0.34 44 48
BCR signaling pathway

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
JUN -0.052 0.14 -10000 0 -0.34 71 71
IKBKB 0.017 0.099 0.26 11 -0.27 19 30
AKT1 0.024 0.093 0.22 48 -0.19 6 54
IKBKG 0.02 0.077 0.23 1 -0.26 10 11
CALM1 -0.012 0.12 0.2 10 -0.34 40 50
PIK3CA 0.03 0.019 -10000 0 0 155 155
MAP3K1 -0.045 0.16 -10000 0 -0.47 44 44
MAP3K7 0.038 0.012 -10000 0 0 47 47
mol:Ca2+ -0.01 0.12 0.2 5 -0.35 44 49
DOK1 0.04 0.009 -10000 0 0 24 24
AP-1 -0.027 0.096 -10000 0 -0.22 64 64
LYN 0.036 0.015 -10000 0 0 83 83
BLNK 0.037 0.014 -10000 0 0 70 70
SHC1 0.04 0.01 -10000 0 0 31 31
BCR complex 0.053 0.025 -10000 0 -0.13 3 3
CD22 -0.011 0.087 -10000 0 -0.27 36 36
CAMK2G -0.015 0.11 0.2 14 -0.34 38 52
CSNK2A1 0.038 0.012 -10000 0 0 54 54
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.021 0.063 -10000 0 -0.13 59 59
GO:0007205 -0.012 0.13 0.21 4 -0.35 46 50
SYK 0.037 0.014 -10000 0 0 70 70
ELK1 -0.016 0.12 0.22 3 -0.35 43 46
NFATC1 -0.029 0.11 0.21 2 -0.29 46 48
B-cell antigen/BCR complex 0.053 0.025 -10000 0 -0.13 3 3
PAG1/CSK 0.053 0.027 -10000 0 -0.14 5 5
NFKBIB 0.013 0.066 0.13 1 -0.13 78 79
HRAS -0.011 0.1 0.25 3 -0.28 42 45
NFKBIA 0.015 0.061 0.13 1 -0.12 70 71
NF-kappa-B/RelA/I kappa B beta 0.021 0.059 0.13 2 -0.11 46 48
RasGAP/Csk 0.057 0.088 -10000 0 -0.11 79 79
mol:GDP -0.012 0.12 0.21 4 -0.35 45 49
PTEN 0.039 0.011 -10000 0 0 38 38
CD79B 0.04 0.008 -10000 0 0 19 19
NF-kappa-B/RelA/I kappa B alpha 0.023 0.055 0.13 3 -0.11 46 49
GRB2 0.041 0.007 -10000 0 0 16 16
PI3K/BCAP/CD19 -0.026 0.15 -10000 0 -0.42 40 40
PIK3R1 0.034 0.016 -10000 0 0 107 107
mol:IP3 -0.008 0.12 0.2 5 -0.36 43 48
CSK 0.04 0.008 -10000 0 0 21 21
FOS -0.017 0.12 0.21 7 -0.33 48 55
CHUK -0.002 0.11 0.23 1 -0.29 50 51
IBTK 0.037 0.014 -10000 0 0 66 66
CARD11/BCL10/MALT1/TAK1 0.013 0.13 0.23 1 -0.31 43 44
PTPN6 -0.003 0.09 0.18 31 -0.27 27 58
RELA 0.041 0.006 -10000 0 0 10 10
BCL2A1 0.015 0.044 0.11 3 -0.084 50 53
VAV2 -0.022 0.12 -10000 0 -0.32 51 51
ubiquitin-dependent protein catabolic process 0.016 0.065 0.13 1 -0.12 77 78
BTK -0.037 0.25 -10000 0 -1.1 32 32
CD19 -0.019 0.095 -10000 0 -0.28 41 41
MAP4K1 0.039 0.012 -10000 0 0 46 46
CD72 0.04 0.008 -10000 0 0 20 20
PAG1 0.038 0.012 -10000 0 0 53 53
MAPK14 -0.038 0.14 0.3 1 -0.4 45 46
SH3BP5 0.04 0.008 -10000 0 0 23 23
PIK3AP1 -0.01 0.12 0.24 4 -0.4 35 39
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.02 0.17 -10000 0 -0.45 51 51
RAF1 -0.015 0.095 0.24 5 -0.28 40 45
RasGAP/p62DOK/SHIP 0.045 0.078 -10000 0 -0.11 81 81
CD79A 0.037 0.013 -10000 0 0 60 60
re-entry into mitotic cell cycle -0.027 0.095 -10000 0 -0.22 61 61
RASA1 0.037 0.014 -10000 0 0 71 71
MAPK3 -0.02 0.084 0.22 7 -0.26 35 42
MAPK1 -0.018 0.083 0.22 8 -0.25 33 41
CD72/SHP1 0.025 0.12 0.28 21 -0.26 27 48
NFKB1 0.036 0.015 -10000 0 0 83 83
MAPK8 -0.043 0.14 -10000 0 -0.4 45 45
actin cytoskeleton organization -0.024 0.11 0.24 3 -0.3 47 50
NF-kappa-B/RelA 0.034 0.12 -10000 0 -0.24 56 56
Calcineurin 0.012 0.12 0.22 2 -0.3 42 44
PI3K -0.011 0.075 -10000 0 -0.26 18 18
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.001 0.12 0.22 4 -0.37 39 43
SOS1 0.038 0.013 -10000 0 0 56 56
Bam32/HPK1 -0.05 0.25 -10000 0 -0.68 62 62
DAPP1 -0.074 0.27 -10000 0 -0.76 62 62
cytokine secretion -0.027 0.1 0.21 2 -0.28 44 46
mol:DAG -0.008 0.12 0.2 5 -0.36 43 48
PLCG2 0.036 0.015 -10000 0 0 86 86
MAP2K1 -0.018 0.091 0.23 7 -0.27 38 45
B-cell antigen/BCR complex/FcgammaRIIB 0.037 0.071 -10000 0 -0.12 75 75
mol:PI-3-4-5-P3 0.012 0.094 0.22 35 -0.23 10 45
ETS1 -0.013 0.11 0.24 10 -0.32 40 50
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.069 0.083 -10000 0 -0.12 51 51
B-cell antigen/BCR complex/LYN -0.013 0.1 -10000 0 -0.29 43 43
MALT1 0.036 0.014 -10000 0 0 77 77
TRAF6 0.04 0.008 -10000 0 0 22 22
RAC1 -0.024 0.11 0.25 3 -0.31 46 49
B-cell antigen/BCR complex/LYN/SYK 0.054 0.11 0.34 14 -0.24 16 30
CARD11 -0.013 0.12 0.22 8 -0.34 44 52
FCGR2B 0.03 0.019 -10000 0 0 164 164
PPP3CA 0.037 0.013 -10000 0 0 60 60
BCL10 0.041 0.006 -10000 0 0 12 12
IKK complex 0.018 0.052 0.15 23 -0.12 13 36
PTPRC 0.025 0.021 -10000 0 0 228 228
PDPK1 0.015 0.083 0.2 48 -0.17 7 55
PPP3CB 0.04 0.01 -10000 0 0 31 31
PPP3CC 0.033 0.017 -10000 0 0 117 117
POU2F2 0.014 0.042 0.12 2 -0.08 51 53
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.028 0.2 -10000 0 -0.72 37 37
epithelial cell differentiation -0.027 0.19 -10000 0 -0.67 37 37
ITCH 0.039 0.037 0.1 8 -0.099 26 34
WWP1 -0.064 0.27 -10000 0 -1.1 33 33
FYN 0.034 0.016 -10000 0 0 104 104
EGFR 0.037 0.014 -10000 0 0 72 72
PRL 0.039 0.011 -10000 0 0 39 39
neuron projection morphogenesis -0.043 0.16 0.24 10 -0.57 35 45
PTPRZ1 0.039 0.01 -10000 0 0 35 35
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.004 0.18 0.29 1 -0.61 36 37
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.034 0.18 -10000 0 -0.65 38 38
ADAM17 0.038 0.035 0.1 5 -0.082 28 33
ErbB4/ErbB4 -0.05 0.21 -10000 0 -0.79 36 36
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.03 0.2 -10000 0 -0.71 37 37
NCOR1 0.037 0.013 -10000 0 0 61 61
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.027 0.18 -10000 0 -0.58 42 42
GRIN2B -0.035 0.16 0.24 5 -0.56 41 46
ErbB4/ErbB2/betacellulin -0.028 0.18 -10000 0 -0.63 39 39
STAT1 0.034 0.017 -10000 0 0 108 108
HBEGF 0.04 0.01 -10000 0 0 32 32
PRLR 0.035 0.015 -10000 0 0 88 88
E4ICDs/ETO2 -0.031 0.2 -10000 0 -0.72 37 37
axon guidance -0.056 0.23 -10000 0 -0.79 41 41
NEDD4 0.038 0.039 0.11 8 -0.084 38 46
Prolactin receptor/Prolactin receptor/Prolactin 0.049 0.025 -10000 0 -10000 0 0
CBFA2T3 0.036 0.015 -10000 0 0 81 81
ErbB4/ErbB2/HBEGF -0.022 0.18 -10000 0 -0.63 38 38
MAPK3 -0.024 0.16 0.27 7 -0.57 36 43
STAT1 (dimer) -0.034 0.21 -10000 0 -0.72 38 38
MAPK1 -0.024 0.16 0.27 7 -0.57 36 43
JAK2 0.035 0.015 -10000 0 0 91 91
ErbB4/ErbB2/neuregulin 1 beta -0.033 0.17 0.21 1 -0.64 37 38
NRG1 -0.008 0.032 0.035 103 -0.11 20 123
NRG3 0.035 0.015 -10000 0 0 91 91
NRG2 0.041 0.007 -10000 0 0 14 14
NRG4 0.029 0.019 -10000 0 0 171 171
heart development -0.056 0.23 -10000 0 -0.79 41 41
neural crest cell migration -0.032 0.17 0.21 1 -0.63 37 38
ERBB2 -0.008 0.033 0.036 121 -0.1 24 145
WWOX/E4ICDs -0.03 0.2 -10000 0 -0.72 37 37
SHC1 0.04 0.01 -10000 0 0 31 31
ErbB4/EGFR/neuregulin 4 -0.036 0.2 -10000 0 -0.7 37 37
apoptosis 0.031 0.19 0.62 44 -10000 0 44
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.026 0.2 -10000 0 -0.72 37 37
ErbB4/ErbB2/epiregulin -0.02 0.18 -10000 0 -0.63 38 38
ErbB4/ErbB4/betacellulin/betacellulin -0.035 0.2 -10000 0 -0.73 37 37
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.005 0.2 -10000 0 -0.64 36 36
MDM2 -0.041 0.19 0.28 9 -0.72 33 42
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.02 0.16 -10000 0 -0.57 38 38
STAT5A -0.057 0.22 0.24 1 -0.79 39 40
ErbB4/EGFR/neuregulin 1 beta -0.027 0.18 -10000 0 -0.62 38 38
DLG4 0.039 0.01 -10000 0 0 33 33
GRB2/SHC 0.056 0.024 -10000 0 -0.14 5 5
E4ICDs/TAB2/NCoR1 -0.02 0.2 -10000 0 -0.7 38 38
STAT5A (dimer) -0.022 0.22 -10000 0 -0.75 37 37
MAP3K7IP2 0.037 0.013 -10000 0 0 60 60
STAT5B (dimer) -0.038 0.23 -10000 0 -0.79 39 39
LRIG1 0.033 0.017 -10000 0 0 119 119
EREG 0.039 0.011 -10000 0 0 45 45
BTC 0.034 0.017 -10000 0 0 111 111
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.06 0.23 -10000 0 -0.8 41 41
ERBB4 -0.047 0.2 -10000 0 -0.84 32 32
STAT5B 0.039 0.011 -10000 0 0 43 43
YAP1 0.007 0.1 -10000 0 -0.52 17 17
GRB2 0.041 0.007 -10000 0 0 16 16
ErbB4/ErbB2/neuregulin 4 -0.032 0.18 -10000 0 -0.63 38 38
glial cell differentiation 0.02 0.2 0.69 38 -10000 0 38
WWOX 0.037 0.014 -10000 0 0 70 70
cell proliferation -0.07 0.21 0.28 1 -0.6 60 61
Caspase cascade in apoptosis

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
TOP1 -0.013 0.14 0.25 5 -0.32 54 59
ACTA1 0.006 0.087 0.22 15 -0.25 16 31
NUMA1 -0.016 0.14 0.26 5 -0.32 51 56
SPTAN1 -0.001 0.087 0.22 13 -0.25 15 28
LIMK1 0.002 0.086 0.23 11 -0.26 13 24
BIRC3 0.026 0.02 -10000 0 0 218 218
BIRC2 0.036 0.014 -10000 0 0 75 75
BAX 0.04 0.008 -10000 0 0 22 22
CASP10 -0.011 0.025 0.058 54 -10000 0 54
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 -0.033 0.17 0.26 4 -0.42 57 61
DIABLO 0.037 0.013 -10000 0 0 63 63
apoptotic nuclear changes -0.002 0.086 0.22 13 -0.25 15 28
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.041 0.006 -10000 0 0 13 13
GSN -0.001 0.086 0.22 13 -0.27 14 27
MADD 0.041 0.006 -10000 0 0 11 11
TFAP2A -0.031 0.21 -10000 0 -0.59 51 51
BID 0.007 0.035 0.13 23 -0.094 26 49
MAP3K1 -0.027 0.14 -10000 0 -0.38 68 68
TRADD 0.036 0.014 -10000 0 0 76 76
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.051 0.041 -10000 0 -0.15 19 19
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.009 0.1 0.24 45 -0.24 23 68
CASP9 0.04 0.009 -10000 0 0 26 26
DNA repair -0.013 0.081 0.25 27 -0.16 23 50
neuron apoptosis -0.036 0.2 -10000 0 -0.63 48 48
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.014 0.12 0.26 8 -0.32 31 39
APAF1 0.04 0.01 -10000 0 0 32 32
CASP6 -0.1 0.34 -10000 0 -0.85 90 90
TRAF2 0.04 0.009 -10000 0 0 29 29
ICAD/CAD 0 0.085 0.22 17 -0.25 12 29
CASP7 0.014 0.11 0.18 86 -0.26 27 113
KRT18 -0.015 0.14 -10000 0 -0.6 23 23
apoptosis -0.042 0.16 0.26 9 -0.38 77 86
DFFA 0.003 0.084 0.22 13 -0.24 14 27
DFFB 0.004 0.088 0.23 18 -0.26 13 31
PARP1 0.013 0.081 0.16 23 -0.25 27 50
actin filament polymerization 0.002 0.085 0.25 12 -0.24 13 25
TNF 0.04 0.009 -10000 0 0 26 26
CYCS 0.001 0.07 0.16 13 -0.22 33 46
SATB1 -0.11 0.32 -10000 0 -0.81 90 90
SLK -0.001 0.086 0.22 12 -0.25 15 27
p15 BID/BAX 0.032 0.05 0.16 3 -0.3 4 7
CASP2 0.006 0.089 0.24 21 -0.24 30 51
JNK cascade 0.026 0.14 0.37 68 -10000 0 68
CASP3 0.007 0.09 0.21 19 -0.25 16 35
LMNB2 -0.047 0.21 0.24 7 -0.41 108 115
RIPK1 0.038 0.012 -10000 0 0 48 48
CASP4 0.034 0.017 -10000 0 0 107 107
Mammalian IAPs/DIABLO 0.012 0.089 -10000 0 -0.13 132 132
negative regulation of DNA binding -0.03 0.2 -10000 0 -0.58 51 51
stress fiber formation -0.002 0.086 0.22 12 -0.25 15 27
GZMB -0.016 0.009 0 133 -10000 0 133
CASP1 -0.012 0.07 -10000 0 -0.2 68 68
LMNB1 -0.048 0.2 0.26 7 -0.41 85 92
APP -0.037 0.2 -10000 0 -0.65 47 47
TNFRSF1A 0.036 0.015 -10000 0 0 84 84
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.01 0.002 0 28 -10000 0 28
VIM -0.036 0.16 0.27 11 -0.38 79 90
LMNA -0.017 0.15 0.23 12 -0.32 85 97
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.006 0.085 -10000 0 -0.25 33 33
LRDD 0.039 0.01 -10000 0 0 35 35
SREBF1 0.001 0.085 0.24 9 -0.26 13 22
APAF-1/Caspase 9 0.028 0.15 -10000 0 -0.64 20 20
nuclear fragmentation during apoptosis -0.015 0.13 0.26 5 -0.32 51 56
CFL2 -0.003 0.086 0.25 13 -0.26 12 25
GAS2 0.005 0.089 0.22 23 -0.25 14 37
positive regulation of apoptosis -0.04 0.18 0.23 15 -0.38 101 116
PRF1 0.037 0.013 -10000 0 0 61 61
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.016 0.16 -10000 0 -0.44 55 55
HDAC1 0.043 0.025 0.084 107 -0.003 61 168
AES 0.039 0.016 0.08 17 0 68 85
FBXW11 0.04 0.009 -10000 0 0 25 25
DTX1 0.041 0.005 -10000 0 0 8 8
LRP6/FZD1 0.041 0.049 -10000 0 -0.14 32 32
TLE1 0.04 0.015 0.077 15 -0.001 52 67
AP1 -0.005 0.082 0.15 1 -0.18 91 92
NCSTN 0.04 0.008 -10000 0 0 24 24
ADAM10 0.039 0.011 -10000 0 0 44 44
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.072 0.22 -10000 0 -0.68 45 45
NICD/RBPSUH -0.012 0.15 -10000 0 -0.44 54 54
WIF1 0.04 0.01 -10000 0 0 31 31
NOTCH1 -0.003 0.15 -10000 0 -0.46 51 51
PSENEN 0.035 0.016 -10000 0 0 92 92
KREMEN2 0.04 0.009 -10000 0 0 28 28
DKK1 0.039 0.011 -10000 0 0 44 44
beta catenin/beta TrCP1 0.018 0.091 0.24 2 -0.38 9 11
APH1B 0.036 0.015 -10000 0 0 83 83
APH1A 0.041 0.006 -10000 0 0 10 10
AXIN1 0.002 0.067 -10000 0 -0.41 4 4
CtBP/CBP/TCF1/TLE1/AES 0.014 0.097 0.19 79 -0.18 51 130
PSEN1 0.039 0.01 -10000 0 0 35 35
FOS 0.026 0.02 -10000 0 0 207 207
JUN 0.036 0.015 -10000 0 0 80 80
MAP3K7 0.041 0.015 0.069 15 0 47 62
CTNNB1 0.001 0.084 0.24 2 -0.37 9 11
MAPK3 0.041 0.007 -10000 0 0 17 17
DKK2/LRP6/Kremen 2 0.056 0.054 -10000 0 -0.12 29 29
HNF1A 0.002 0.008 0.037 19 -10000 0 19
CTBP1 0.04 0.015 0.08 19 0 55 74
MYC -0.16 0.42 -10000 0 -1.2 76 76
NKD1 0.039 0.012 -10000 0 0 49 49
FZD1 0.041 0.007 -10000 0 0 17 17
NOTCH1 precursor/Deltex homolog 1 0.014 0.16 -10000 0 -0.44 56 56
apoptosis -0.005 0.082 0.15 1 -0.17 91 92
Delta 1/NOTCHprecursor 0.01 0.15 -10000 0 -0.44 55 55
DLL1 0.038 0.012 -10000 0 0 53 53
PPARD 0.008 0.076 -10000 0 -1 2 2
Gamma Secretase 0.072 0.086 -10000 0 -0.12 66 66
APC -0.021 0.12 -10000 0 -0.42 34 34
DVL1 0.018 0.058 -10000 0 -0.31 11 11
CSNK2A1 0.037 0.012 -10000 0 0 54 54
MAP3K7IP1 0.041 0.015 0.068 16 0 53 69
DKK1/LRP6/Kremen 2 0.055 0.053 -10000 0 -0.12 28 28
LRP6 0.034 0.016 -10000 0 0 107 107
CSNK1A1 0.039 0.009 -10000 0 0 26 26
NLK 0.027 0.043 -10000 0 -0.22 12 12
CCND1 -0.15 0.44 -10000 0 -1.2 82 82
WNT1 0.041 0.006 -10000 0 0 13 13
Axin1/APC/beta catenin 0.003 0.11 0.28 1 -0.38 14 15
DKK2 0.039 0.012 -10000 0 0 46 46
NOTCH1 precursor/DVL1 0.015 0.15 -10000 0 -0.4 50 50
GSK3B 0.041 0.009 -10000 0 0 26 26
FRAT1 0.041 0.009 -10000 0 0 24 24
NOTCH/Deltex homolog 1 0.019 0.16 -10000 0 -0.44 56 56
PPP2R5D 0.021 0.053 -10000 0 -0.29 11 11
MAPK1 0.039 0.012 -10000 0 0 46 46
WNT1/LRP6/FZD1 0.075 0.061 -10000 0 -0.11 31 31
RBPJ 0 0 -10000 0 -10000 0 0
CREBBP 0.03 0.024 -10000 0 -0.017 83 83
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.012 0.17 -10000 0 -0.78 16 16
UGCG -0.007 0.15 -10000 0 -0.69 22 22
AKT1/mTOR/p70S6K/Hsp90/TERT -0.02 0.18 0.28 3 -0.38 74 77
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.006 0.15 -10000 0 -0.68 22 22
mol:DAG -0.008 0.029 0.17 13 -10000 0 13
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.038 0.23 0.37 1 -0.53 70 71
FRAP1 -0.056 0.26 0.4 1 -0.62 70 71
FOXO3 -0.055 0.26 0.37 1 -0.53 94 95
AKT1 -0.064 0.28 -10000 0 -0.58 94 94
GAB2 0.03 0.02 -10000 0 -0.002 152 152
SMPD1 0 0.12 -10000 0 -0.59 19 19
SGMS1 -0.003 0.038 0.065 9 -0.078 79 88
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 -0.02 0.035 -10000 0 -0.12 47 47
CALM1 0.04 0.01 -10000 0 0 31 31
cell proliferation 0.003 0.18 0.23 22 -0.32 82 104
EIF3A 0 0 -10000 0 -10000 0 0
PI3K 0.022 0.064 -10000 0 -0.14 54 54
RPS6KB1 -0.023 0.2 -10000 0 -0.83 29 29
mol:sphingomyelin -0.008 0.029 0.17 13 -10000 0 13
natural killer cell activation -0.001 0.004 -10000 0 -0.013 40 40
JAK3 0.035 0.022 -10000 0 -0.046 23 23
PIK3R1 0.032 0.023 -10000 0 -0.041 24 24
JAK1 0.037 0.02 -10000 0 -0.043 22 22
NFKB1 0.036 0.015 -10000 0 0 83 83
MYC -0.035 0.35 0.38 21 -0.81 80 101
MYB -0.041 0.29 -10000 0 -1.1 38 38
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.028 0.17 0.25 3 -0.36 87 90
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.005 0.19 -10000 0 -0.77 29 29
mol:PI-3-4-5-P3 -0.025 0.17 0.27 4 -0.36 87 91
Rac1/GDP 0.008 0.045 -10000 0 -0.12 44 44
T cell proliferation -0.029 0.16 0.25 5 -0.34 83 88
SHC1 0.037 0.016 -10000 0 -0.011 48 48
RAC1 0.039 0.01 -10000 0 0 33 33
positive regulation of cyclin-dependent protein kinase activity 0.002 0.02 0.032 47 -0.065 38 85
PRKCZ -0.031 0.17 0.25 5 -0.36 84 89
NF kappa B1 p50/RelA -0.03 0.24 0.4 1 -0.52 75 76
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.003 0.12 -10000 0 -0.35 38 38
HSP90AA1 0 0 -10000 0 -10000 0 0
RELA 0.041 0.006 -10000 0 0 10 10
IL2RA 0.036 0.017 -10000 0 -0.009 63 63
IL2RB 0.034 0.022 -10000 0 -0.045 22 22
TERT 0.037 0.014 -10000 0 0 68 68
E2F1 -0.001 0.12 -10000 0 -0.41 40 40
SOS1 0.035 0.018 -10000 0 -0.008 74 74
RPS6 0.039 0.011 -10000 0 0 41 41
mol:cAMP -0.001 0.01 0.032 35 -0.017 46 81
PTPN11 0.036 0.02 -10000 0 -0.019 62 62
IL2RG 0.026 0.026 -10000 0 -0.042 27 27
actin cytoskeleton organization -0.029 0.16 0.25 5 -0.34 83 88
GRB2 0.038 0.016 -10000 0 -0.018 36 36
IL2 0.035 0.023 -10000 0 -0.04 35 35
PIK3CA 0.028 0.024 -10000 0 -0.043 22 22
Rac1/GTP 0.031 0.062 -10000 0 -0.11 44 44
LCK 0.036 0.023 -10000 0 -0.04 36 36
BCL2 -0.032 0.2 0.4 1 -0.57 42 43
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.037 0.013 -10000 0 0 64 64
Caspase 8 (4 units) 0.035 0.094 -10000 0 -0.24 28 28
NEF 0.003 0.005 -10000 0 -0.1 1 1
NFKBIA 0.026 0.042 0.1 1 -0.068 78 79
BIRC3 -0.058 0.1 0.2 4 -0.28 89 93
CYCS -0.006 0.069 0.19 12 -0.24 19 31
RIPK1 0.038 0.012 -10000 0 0 48 48
CD247 0.003 0.005 -10000 0 -0.1 1 1
MAP2K7 -0.006 0.17 -10000 0 -0.55 36 36
protein ubiquitination -0.001 0.098 0.22 7 -0.27 34 41
CRADD 0.041 0.006 -10000 0 0 13 13
DAXX 0.041 0.008 -10000 0 0 19 19
FAS 0.035 0.016 -10000 0 0 99 99
BID 0.001 0.063 0.16 2 -0.17 52 54
NF-kappa-B/RelA/I kappa B alpha 0.029 0.12 -10000 0 -0.18 118 118
TRADD 0.036 0.014 -10000 0 0 76 76
MAP3K5 0.037 0.014 -10000 0 0 70 70
CFLAR 0.04 0.008 -10000 0 0 21 21
FADD 0.04 0.008 -10000 0 0 21 21
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.029 0.12 -10000 0 -0.18 118 118
MAPK8 -0.01 0.16 -10000 0 -0.52 35 35
APAF1 0.04 0.01 -10000 0 0 32 32
TRAF1 0.04 0.008 -10000 0 0 22 22
TRAF2 0.04 0.009 -10000 0 0 29 29
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.011 0.066 -10000 0 -0.17 51 51
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.005 0.11 -10000 0 -0.32 36 36
CHUK -0.002 0.1 0.23 7 -0.3 33 40
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.075 0.085 -10000 0 -0.12 60 60
TCRz/NEF 0.01 0.008 -10000 0 -0.17 1 1
TNF 0.04 0.009 -10000 0 0 26 26
FASLG 0.022 0.014 -10000 0 -0.3 1 1
NFKB1 0.027 0.041 0.1 1 -0.07 66 67
TNFR1A/BAG4/TNF-alpha 0.059 0.046 -10000 0 -0.12 15 15
CASP6 -0.045 0.23 -10000 0 -0.53 88 88
CASP7 -0.046 0.2 0.3 5 -0.4 112 117
RELA 0.027 0.044 -10000 0 -0.066 97 97
CASP2 0.038 0.012 -10000 0 0 52 52
CASP3 -0.057 0.2 0.3 5 -0.41 115 120
TNFRSF1A 0.036 0.015 -10000 0 0 84 84
TNFR1A/BAG4 0.044 0.038 -10000 0 -0.13 14 14
CASP8 0.04 0.009 -10000 0 0 28 28
CASP9 0.04 0.009 -10000 0 0 26 26
MAP3K14 0.007 0.11 0.25 6 -0.3 32 38
APAF-1/Caspase 9 -0.027 0.11 0.19 1 -0.25 93 94
BCL2 -0.012 0.14 -10000 0 -0.48 34 34
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.012 0.073 0.15 79 -0.18 6 85
DAPP1 -0.006 0.1 0.22 5 -0.26 39 44
Src family/SYK family/BLNK-LAT/BTK-ITK -0.012 0.14 -10000 0 -0.35 48 48
mol:DAG 0.005 0.076 0.18 20 -0.18 19 39
HRAS 0.041 0.014 0.076 4 -0.005 36 40
RAP1A 0.041 0.012 0.069 4 -0.001 36 40
ARF5/GDP 0.017 0.096 -10000 0 -0.24 36 36
PLCG2 0.036 0.015 -10000 0 0 86 86
PLCG1 0.038 0.012 -10000 0 0 50 50
ARF5 0.039 0.011 -10000 0 0 44 44
mol:GTP -0.012 0.067 0.14 80 -0.18 5 85
ARF1/GTP 0.001 0.064 0.14 85 -0.17 5 90
RHOA 0.041 0.007 -10000 0 0 14 14
YES1 0.038 0.013 -10000 0 0 57 57
RAP1A/GTP -0.008 0.076 0.16 80 -0.18 5 85
ADAP1 -0.014 0.061 0.13 74 -0.18 5 79
ARAP3 -0.012 0.066 0.14 80 -0.18 5 85
INPPL1 0.04 0.009 -10000 0 0 30 30
PREX1 0.037 0.013 -10000 0 0 64 64
ARHGEF6 0.037 0.013 -10000 0 0 65 65
ARHGEF7 0.04 0.009 -10000 0 0 28 28
ARF1 0.038 0.012 -10000 0 0 50 50
NRAS 0.042 0.011 0.069 3 0 30 33
FYN 0.034 0.016 -10000 0 0 104 104
ARF6 0.041 0.008 -10000 0 0 19 19
FGR 0.041 0.007 -10000 0 0 17 17
mol:Ca2+ 0.002 0.05 0.16 19 -0.12 6 25
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.037 0.014 -10000 0 0 72 72
ZAP70 0.041 0.006 -10000 0 0 10 10
mol:IP3 -0.002 0.062 0.2 16 -0.15 11 27
LYN 0.036 0.015 -10000 0 0 83 83
ARF1/GDP 0.017 0.096 -10000 0 -0.25 34 34
RhoA/GDP 0.036 0.083 0.22 12 -0.17 22 34
PDK1/Src/Hsp90 0.05 0.021 -10000 0 -0.11 3 3
BLNK 0.037 0.014 -10000 0 0 70 70
actin cytoskeleton reorganization 0.009 0.093 0.23 17 -0.24 27 44
SRC 0.039 0.01 -10000 0 0 36 36
PLEKHA2 -0.014 0.006 -10000 0 -10000 0 0
RAC1 0.039 0.01 -10000 0 0 33 33
PTEN 0.031 0.028 -10000 0 -0.03 80 80
HSP90AA1 0 0 -10000 0 -10000 0 0
ARF6/GTP -0.011 0.075 0.15 84 -0.18 5 89
RhoA/GTP -0.01 0.079 0.16 86 -0.18 6 92
Src family/SYK family/BLNK-LAT 0 0.098 -10000 0 -0.28 32 32
BLK 0.033 0.017 -10000 0 0 117 117
PDPK1 0.04 0.009 -10000 0 0 26 26
CYTH1 -0.014 0.061 0.13 74 -0.18 5 79
HCK 0.036 0.015 -10000 0 0 80 80
CYTH3 -0.014 0.061 0.13 74 -0.18 5 79
CYTH2 -0.014 0.061 0.13 74 -0.18 5 79
KRAS 0.034 0.018 0.091 1 -0.001 107 108
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.011 0.043 0.16 2 -0.16 8 10
SGK1 0.011 0.042 -10000 0 -0.17 8 8
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0 0.093 0.18 1 -0.26 36 37
SOS1 0.038 0.013 -10000 0 0 56 56
SYK 0.037 0.014 -10000 0 0 70 70
ARF6/GDP 0.002 0.078 0.17 52 -0.18 14 66
mol:PI-3-4-5-P3 -0.014 0.065 0.14 74 -0.18 5 79
ARAP3/RAP1A/GTP -0.008 0.076 0.16 80 -0.18 5 85
VAV1 0.037 0.014 -10000 0 0 68 68
mol:PI-3-4-P2 -0.01 0.002 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.044 0.066 0.22 29 -0.12 39 68
PLEKHA1 -0.015 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.099 -10000 0 -0.25 37 37
LAT 0.041 0.006 -10000 0 0 13 13
Rac1/GTP -0.004 0.1 -10000 0 -0.28 46 46
ITK -0.014 0.065 0.13 76 -0.18 6 82
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0 0.092 0.21 17 -0.23 27 44
LCK 0.04 0.009 -10000 0 0 29 29
BTK -0.015 0.068 0.13 76 -0.2 9 85
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 -0.008 0.038 -10000 0 -0.11 61 61
STMN1 -0.011 0.016 0.028 18 -10000 0 18
Aurora B/RasGAP/Survivin 0.045 0.075 -10000 0 -0.16 52 52
Chromosomal passenger complex/Cul3 protein complex -0.006 0.092 -10000 0 -0.24 50 50
BIRC5 0.037 0.014 -10000 0 -0.002 63 63
DES -0.046 0.27 -10000 0 -0.8 62 62
Aurora C/Aurora B/INCENP 0.063 0.048 -10000 0 -0.12 28 28
Aurora B/TACC1 0.036 0.04 -10000 0 -0.1 29 29
Aurora B/PP2A 0.044 0.05 -10000 0 -0.14 31 31
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 -0.011 0.063 -10000 0 -0.16 78 78
mitotic metaphase/anaphase transition 0.002 0.006 0.013 109 -10000 0 109
NDC80 -0.004 0.01 0.02 12 -10000 0 12
Cul3 protein complex 0.05 0.06 -10000 0 -0.12 42 42
KIF2C -0.058 0.19 -10000 0 -0.49 80 80
PEBP1 -0.001 0.003 -10000 0 -0.011 39 39
KIF20A 0.033 0.018 -10000 0 0 133 133
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.036 0.058 -10000 0 -0.14 45 45
SEPT1 0.041 0.007 -10000 0 0 16 16
SMC2 0 0 -10000 0 -10000 0 0
SMC4 0 0 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.04 0.19 0.25 1 -0.56 62 63
PSMA3 0.037 0.013 -10000 0 0 60 60
G2/M transition of mitotic cell cycle -0.001 0.003 0.009 34 -0.008 19 53
H3F3B 0.002 0.057 -10000 0 -0.2 40 40
AURKB 0.038 0.016 -10000 0 0 80 80
AURKC 0.042 0.002 -10000 0 0 1 1
CDCA8 0.036 0.016 -10000 0 -0.005 69 69
cytokinesis -0.032 0.18 0.2 1 -0.45 69 70
Aurora B/Septin1 -0.006 0.19 0.22 1 -0.38 83 84
AURKA -0.001 0.003 0.009 34 -0.008 19 53
INCENP 0.039 0.016 -10000 0 -0.03 27 27
KLHL13 0.033 0.017 -10000 0 0 121 121
BUB1 0.037 0.015 -10000 0 0 78 78
hSgo1/Aurora B/Survivin 0.04 0.079 -10000 0 -0.15 64 64
EVI5 0.039 0.01 -10000 0 0 36 36
RhoA/GTP 0.003 0.17 -10000 0 -0.35 74 74
SGOL1 0.036 0.014 -10000 0 0 74 74
CENPA -0.017 0.12 -10000 0 -0.3 61 61
NCAPG 0 0 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.032 0.066 -10000 0 -0.14 63 63
NCAPD2 0 0 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.037 0.062 -10000 0 -0.14 55 55
RHOA 0.041 0.007 -10000 0 0 14 14
NCAPH 0 0 -10000 0 -10000 0 0
NPM1 -0.024 0.14 -10000 0 -0.34 74 74
RASA1 0.037 0.014 -10000 0 0 71 71
KLHL9 0.039 0.011 -10000 0 0 42 42
mitotic prometaphase -0.001 0.003 -10000 0 -0.011 39 39
proteasomal ubiquitin-dependent protein catabolic process 0.032 0.066 -10000 0 -0.14 63 63
PPP1CC 0.039 0.01 -10000 0 0 36 36
Centraspindlin -0.011 0.17 -10000 0 -0.37 76 76
RhoA/GDP 0.03 0.012 -10000 0 -0.13 3 3
NSUN2 -0.011 0.12 -10000 0 -0.33 66 66
MYLK 0.001 0.057 -10000 0 -0.2 41 41
KIF23 0.035 0.016 -10000 0 0 98 98
VIM -0.01 0.016 0.031 17 -10000 0 17
RACGAP1 0.037 0.014 -10000 0 -0.004 54 54
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.027 0.12 -10000 0 -0.31 86 86
Chromosomal passenger complex -0.035 0.15 -10000 0 -0.34 73 73
Chromosomal passenger complex/EVI5 0.067 0.098 -10000 0 -0.17 57 57
TACC1 0.035 0.016 -10000 0 0 93 93
PPP2R5D 0.04 0.009 -10000 0 0 29 29
CUL3 0.04 0.008 -10000 0 0 21 21
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification -0.049 0.31 -10000 0 -1 49 49
CLOCK 0.032 0.032 -10000 0 -0.07 41 41
TIMELESS/CRY2 -0.051 0.31 -10000 0 -1 49 49
DEC1/BMAL1 0.044 0.047 -10000 0 -0.11 27 27
ATR 0.035 0.016 -10000 0 0 92 92
NR1D1 -0.017 0.12 -10000 0 -0.64 3 3
ARNTL 0.032 0.032 -10000 0 -0.068 43 43
TIMELESS -0.081 0.32 -10000 0 -1.1 49 49
NPAS2 0.027 0.031 -10000 0 -0.068 38 38
CRY2 0.042 0.004 -10000 0 0 5 5
mol:CO 0.001 0.041 0.13 49 -10000 0 49
CHEK1 0.033 0.017 -10000 0 0 120 120
mol:HEME -0.001 0.041 -10000 0 -0.13 49 49
PER1 0.039 0.011 -10000 0 0 41 41
BMAL/CLOCK/NPAS2 0.034 0.096 -10000 0 -0.13 122 122
BMAL1/CLOCK -0.039 0.2 -10000 0 -0.59 51 51
S phase of mitotic cell cycle -0.049 0.31 -10000 0 -1 49 49
TIMELESS/CHEK1/ATR -0.052 0.32 -10000 0 -1.1 49 49
mol:NADPH -0.001 0.041 -10000 0 -0.13 49 49
PER1/TIMELESS -0.053 0.31 -10000 0 -1 49 49
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.04 0.009 -10000 0 0 26 26
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.022 0.012 -10000 0 -0.1 1 1
ARNO/beta Arrestin1-2 0.043 0.032 -10000 0 -0.085 9 9
EGFR 0.037 0.014 -10000 0 0 72 72
EPHA2 0.039 0.01 -10000 0 0 35 35
USP6 0.039 0.01 -10000 0 0 35 35
IQSEC1 0.041 0.007 -10000 0 0 14 14
EGFR/EGFR/EGF/EGF 0.041 0.051 -10000 0 -0.13 37 37
ARRB2 0.016 0.017 -10000 0 -0.2 3 3
mol:GTP 0.001 0.014 -10000 0 -0.061 11 11
ARRB1 0.038 0.012 -10000 0 0 49 49
FBXO8 0.037 0.014 -10000 0 0 67 67
TSHR 0.038 0.013 -10000 0 0 60 60
EGF 0.038 0.012 -10000 0 0 52 52
somatostatin receptor activity 0 0 0 7 0 43 50
ARAP2 0 0 0 14 0 36 50
mol:GDP 0.013 0.071 0.15 2 -0.18 37 39
mol:PI-3-4-5-P3 0 0 0 7 0 37 44
ITGA2B 0.04 0.009 -10000 0 0 30 30
ARF6 0.041 0.008 -10000 0 0 19 19
Ephrin A1/EPHA2/NCK1/GIT1 0.061 0.077 -10000 0 -0.12 62 62
ADAP1 0 0 0 8 0 29 37
KIF13B 0.034 0.017 -10000 0 0 112 112
HGF/MET 0.013 0.075 -10000 0 -0.14 105 105
PXN 0.041 0.007 -10000 0 0 14 14
ARF6/GTP 0.015 0.081 0.18 8 -0.21 40 48
EGFR/EGFR/EGF/EGF/ARFGEP100 0.06 0.055 -10000 0 -0.12 35 35
ADRB2 0.041 0.006 -10000 0 0 13 13
receptor agonist activity 0 0 0 9 0 36 45
actin filament binding 0 0 0 7 0 44 51
SRC 0.039 0.01 -10000 0 0 36 36
ITGB3 0.033 0.017 -10000 0 0 121 121
GNAQ 0.038 0.012 -10000 0 0 49 49
EFA6/PI-4-5-P2 0 0 0.001 14 -0.001 36 50
ARF6/GDP 0.01 0.077 0.18 9 -0.22 29 38
ARF6/GDP/GULP/ACAP1 0.029 0.084 -10000 0 -0.2 30 30
alphaIIb/beta3 Integrin/paxillin/GIT1 0.082 0.058 -10000 0 -0.11 34 34
ACAP1 0 0 0 5 0 1 6
ACAP2 0 0 0 9 0 36 45
LHCGR/beta Arrestin2 0.032 0.025 -10000 0 -0.063 31 31
EFNA1 0.034 0.017 -10000 0 0 107 107
HGF 0.04 0.009 -10000 0 0 29 29
CYTH3 0 0 0.001 12 -0.001 34 46
CYTH2 0 0.001 0.003 4 -0.004 40 44
NCK1 0.036 0.015 -10000 0 0 79 79
fibronectin binding 0 0 0 8 0 37 45
endosomal lumen acidification 0 0 0 12 0 25 37
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 0.032 0.018 -10000 0 0 129 129
GNAQ/ARNO 0.027 0.009 -10000 0 0 49 49
mol:Phosphatidic acid 0 0 0 9 0 36 45
PIP3-E 0.038 0.012 -10000 0 0 52 52
MET 0.027 0.02 -10000 0 0 198 198
GNA14 0.04 0.01 -10000 0 0 33 33
GNA15 0.037 0.014 -10000 0 0 69 69
GIT1 0.04 0.009 -10000 0 0 27 27
mol:PI-4-5-P2 0 0 0.001 13 -0.001 40 53
GNA11 0.037 0.013 -10000 0 0 61 61
LHCGR 0.04 0.009 -10000 0 0 25 25
AGTR1 0.037 0.014 -10000 0 0 68 68
desensitization of G-protein coupled receptor protein signaling pathway 0.032 0.025 -10000 0 -0.063 31 31
IPCEF1/ARNO 0.054 0.044 -10000 0 -0.087 35 35
alphaIIb/beta3 Integrin 0.04 0.05 -10000 0 -0.14 34 34
Regulation of Androgen receptor activity

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
HDAC1 -0.017 0.007 -10000 0 -10000 0 0
SMARCC1 -0.014 0.18 -10000 0 -1.1 14 14
REL 0.04 0.008 -10000 0 0 20 20
HDAC7 -0.045 0.092 0.18 14 -0.21 85 99
JUN 0.036 0.015 -10000 0 0 80 80
EP300 0.037 0.014 -10000 0 0 72 72
KAT2B 0 0 -10000 0 -10000 0 0
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 -0.012 0.022 0.063 15 -0.05 1 16
FOXO1 0 0 -10000 0 -10000 0 0
T-DHT/AR -0.002 0.12 0.28 6 -0.22 88 94
MAP2K6 0.029 0.025 -10000 0 -0.011 148 148
BRM/BAF57 0.032 0.059 -10000 0 -0.13 53 53
MAP2K4 0.032 0.024 -10000 0 -0.014 106 106
SMARCA2 0.032 0.018 -10000 0 0 134 134
PDE9A -0.081 0.32 -10000 0 -0.83 82 82
NCOA2 0.037 0.014 -10000 0 0 70 70
CEBPA 0.037 0.014 -10000 0 0 67 67
EHMT2 0.041 0.007 -10000 0 0 18 18
cell proliferation -0.014 0.12 0.27 17 -0.28 42 59
NR0B1 0.039 0.011 -10000 0 0 38 38
EGR1 0.028 0.02 -10000 0 0 194 194
RXRs/9cRA 0.064 0.035 -10000 0 -0.1 3 3
AR/RACK1/Src -0.013 0.094 0.21 33 -0.22 22 55
AR/GR -0.012 0.093 0.2 2 -0.19 86 88
GNB2L1 0.042 0.005 -10000 0 0 7 7
PKN1 0.035 0.016 -10000 0 0 99 99
RCHY1 0.037 0.014 -10000 0 0 72 72
epidermal growth factor receptor activity 0 0 0.003 1 -10000 0 1
MAPK8 -0.013 0.021 0.051 7 -0.059 1 8
T-DHT/AR/TIF2/CARM1 0.004 0.088 0.23 10 -0.19 33 43
SRC -0.015 0.068 0.17 45 -0.15 7 52
NR3C1 0.039 0.012 -10000 0 0 46 46
KLK3 0.005 0.072 -10000 0 -10000 0 0
APPBP2 0.031 0.026 -10000 0 -0.034 65 65
TRIM24 0.039 0.012 -10000 0 0 44 44
T-DHT/AR/TIP60 -0.035 0.059 0.088 4 -0.16 66 70
TMPRSS2 0.016 0.11 -10000 0 -0.58 11 11
RXRG 0.036 0.015 -10000 0 0 86 86
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.04 0.01 -10000 0 0 33 33
RXRB 0.041 0.007 -10000 0 0 17 17
CARM1 0.037 0.014 -10000 0 0 69 69
NR2C2 0.041 0.007 -10000 0 0 16 16
KLK2 0 0.076 0.23 5 -0.24 13 18
AR -0.019 0.079 0.15 14 -0.18 80 94
SENP1 0.039 0.01 -10000 0 0 35 35
HSP90AA1 0 0 -10000 0 -10000 0 0
MDM2 0.038 0.01 -10000 0 0 35 35
SRY 0.041 0.002 -10000 0 0 2 2
GATA2 0.039 0.01 -10000 0 0 35 35
MYST2 0.04 0.009 -10000 0 0 27 27
HOXB13 0.04 0.011 -10000 0 0 38 38
T-DHT/AR/RACK1/Src -0.016 0.097 0.22 33 -0.22 23 56
positive regulation of transcription 0.039 0.01 -10000 0 0 35 35
DNAJA1 0.031 0.026 -10000 0 -0.034 64 64
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.089 0.17 21 -0.26 49 70
NCOA1 0.041 0.035 -10000 0 -0.18 12 12
SPDEF 0.038 0.015 -10000 0 0 72 72
T-DHT/AR/TIF2 -0.012 0.094 0.2 11 -0.24 49 60
T-DHT/AR/Hsp90 -0.035 0.059 0.088 4 -0.16 68 72
GSK3B 0.04 0.009 -10000 0 0 26 26
NR2C1 0.039 0.011 -10000 0 0 41 41
mol:T-DHT -0.023 0.052 0.18 14 -0.16 8 22
SIRT1 0.041 0.008 -10000 0 0 20 20
ZMIZ2 -0.001 0.001 -10000 0 -0.012 2 2
POU2F1 0.034 0.056 0.12 4 -0.1 73 77
T-DHT/AR/DAX-1 -0.021 0.082 0.2 20 -0.21 25 45
CREBBP 0.038 0.012 -10000 0 0 54 54
SMARCE1 0.039 0.011 -10000 0 0 43 43
PLK1 signaling events

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
regulation of centriole-centriole cohesion 0.008 0.054 0.17 51 -0.092 3 54
BUB1B -0.024 0.082 0.12 1 -0.2 73 74
PLK1 -0.001 0.037 0.073 6 -0.098 43 49
PLK1S1 -0.001 0.021 0.044 8 -0.054 41 49
KIF2A -0.001 0.033 0.067 5 -0.089 42 47
regulation of mitotic centrosome separation -0.001 0.037 0.076 5 -0.099 42 47
GOLGA2 0.04 0.009 -10000 0 0 26 26
Hec1/SPC24 -0.01 0.025 -10000 0 -0.077 51 51
WEE1 -0.012 0.088 -10000 0 -0.33 29 29
cytokinesis -0.038 0.13 0.15 3 -0.3 90 93
PP2A-alpha B56 -0.008 0.25 -10000 0 -0.68 65 65
AURKA -0.001 0.023 0.05 9 -0.062 35 44
PICH/PLK1 -0.032 0.069 0.067 3 -0.16 106 109
CENPE -0.007 0.035 0.21 1 -0.13 19 20
RhoA/GTP 0.03 0.012 -10000 0 -0.13 3 3
positive regulation of microtubule depolymerization -0.001 0.033 0.067 5 -0.089 42 47
PPP2CA 0.04 0.009 -10000 0 0 26 26
FZR1 0.038 0.013 -10000 0 0 56 56
TPX2 -0.025 0.099 -10000 0 -0.25 89 89
PAK1 0.037 0.014 -10000 0 0 70 70
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.04 0.009 -10000 0 0 25 25
CLSPN 0.009 0.037 -10000 0 -0.26 7 7
GORASP1 0.041 0.006 -10000 0 0 10 10
metaphase 0 0.004 0.016 13 -0.013 26 39
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.001 0.021 0.044 8 -0.054 41 49
G2 phase of mitotic cell cycle -0.001 0.003 0.011 19 -10000 0 19
STAG2 0.039 0.01 -10000 0 0 35 35
GRASP65/GM130/RAB1/GTP 0.016 0.069 -10000 0 -0.62 5 5
spindle elongation -0.001 0.037 0.076 5 -0.099 42 47
ODF2 0.04 0.009 -10000 0 0 27 27
BUB1 -0.046 0.25 -10000 0 -0.72 65 65
TPT1 -0.002 0.052 -10000 0 -0.19 34 34
CDC25C -0.007 0.089 -10000 0 -0.33 37 37
CDC25B 0.024 0.03 -10000 0 -0.031 106 106
SGOL1 -0.008 0.054 0.092 3 -0.17 51 54
RHOA 0.041 0.007 -10000 0 0 14 14
CCNB1/CDK1 0.004 0.12 -10000 0 -0.2 124 124
CDC14B -0.01 0.005 0.011 27 -10000 0 27
CDC20 0.034 0.016 -10000 0 0 104 104
PLK1/PBIP1 -0.003 0.032 -10000 0 -0.1 33 33
mitosis -0.001 0.003 0.011 17 -0.01 12 29
FBXO5 -0.015 0.063 0.1 4 -0.16 64 68
CDC2 0.028 0.022 -10000 0 -0.029 16 16
NDC80 0 0 -10000 0 -10000 0 0
metaphase plate congression 0.002 0.054 -10000 0 -0.25 20 20
ERCC6L -0.03 0.098 -10000 0 -0.2 119 119
NLP/gamma Tubulin -0.001 0.032 0.066 3 -0.084 50 53
microtubule cytoskeleton organization -0.002 0.052 -10000 0 -0.19 34 34
G2/M transition DNA damage checkpoint 0 0.003 0.01 22 -10000 0 22
PPP1R12A 0.04 0.01 -10000 0 0 31 31
interphase 0 0.003 0.01 22 -10000 0 22
PLK1/PRC1-2 0.014 0.083 -10000 0 -0.16 83 83
GRASP65/GM130/RAB1/GTP/PLK1 0.051 0.06 -10000 0 -0.12 35 35
RAB1A 0.04 0.009 -10000 0 0 29 29
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA -0.001 0.026 0.058 13 -0.066 40 53
mitotic prometaphase -0.001 0.004 0.019 19 -10000 0 19
proteasomal ubiquitin-dependent protein catabolic process -0.002 0.066 -10000 0 -0.23 24 24
microtubule-based process 0.014 0.052 -10000 0 -0.14 36 36
Golgi organization -0.001 0.037 0.076 5 -0.099 42 47
Cohesin/SA2 0.014 0.047 0.11 1 -0.1 56 57
PPP1CB/MYPT1 0.05 0.042 -10000 0 -0.14 23 23
KIF20A 0.032 0.018 -10000 0 0 133 133
APC/C/CDC20 0.017 0.051 0.098 1 -0.13 39 40
PPP2R1A 0.039 0.011 -10000 0 0 42 42
chromosome segregation -0.003 0.032 -10000 0 -0.1 33 33
PRC1 0.036 0.015 -10000 0 0 82 82
ECT2 0.037 0.12 0.21 141 -0.14 56 197
C13orf34 0 0.029 0.06 12 -0.077 40 52
NUDC 0.002 0.054 -10000 0 -0.25 20 20
regulation of attachment of spindle microtubules to kinetochore -0.024 0.081 0.12 1 -0.2 73 74
spindle assembly -0.001 0.034 0.068 13 -0.09 41 54
spindle stabilization -0.001 0.02 0.043 8 -0.054 41 49
APC/C/HCDH1 0.032 0.012 -10000 0 -10000 0 0
MKLP2/PLK1 0.014 0.052 -10000 0 -0.14 36 36
CCNB1 0.026 0.027 -10000 0 -0.03 63 63
PPP1CB 0.04 0.01 -10000 0 0 33 33
BTRC 0.04 0.008 -10000 0 0 21 21
ROCK2 -0.006 0.095 -10000 0 -0.33 40 40
TUBG1 -0.002 0.054 -10000 0 -0.19 36 36
G2/M transition of mitotic cell cycle -0.035 0.1 0.13 16 -0.21 114 130
MLF1IP -0.008 0.007 0.011 49 -10000 0 49
INCENP 0.041 0.005 -10000 0 0 5 5
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.046 0.041 -10000 0 -0.13 20 20
VLDLR 0.032 0.018 -10000 0 0 128 128
CRKL 0.039 0.011 -10000 0 0 38 38
LRPAP1 0.036 0.014 -10000 0 0 77 77
FYN 0.034 0.016 -10000 0 0 104 104
ITGA3 0.034 0.016 -10000 0 0 104 104
RELN/VLDLR/Fyn 0.032 0.067 -10000 0 -0.13 51 51
MAPK8IP1/MKK7/MAP3K11/JNK1 0.095 0.061 -10000 0 -0.11 17 17
AKT1 0 0.075 -10000 0 -0.17 60 60
MAP2K7 0.039 0.011 -10000 0 0 43 43
RAPGEF1 0.04 0.008 -10000 0 0 23 23
DAB1 0.04 0.009 -10000 0 0 27 27
RELN/LRP8/DAB1 0.059 0.038 -10000 0 -0.1 5 5
LRPAP1/LRP8 0.041 0.052 -10000 0 -0.14 36 36
RELN/LRP8/DAB1/Fyn 0.066 0.056 -10000 0 -0.1 32 32
DAB1/alpha3/beta1 Integrin 0.029 0.082 -10000 0 -0.12 85 85
long-term memory 0.073 0.071 0.22 7 -0.11 28 35
DAB1/LIS1 0.058 0.082 -10000 0 -0.11 54 54
DAB1/CRLK/C3G 0.046 0.073 -10000 0 -0.12 52 52
PIK3CA 0.03 0.019 -10000 0 0 155 155
DAB1/NCK2 0.064 0.083 -10000 0 -0.11 55 55
ARHGEF2 0.039 0.01 -10000 0 0 37 37
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.034 0.017 -10000 0 0 112 112
CDK5R1 0.04 0.009 -10000 0 0 30 30
RELN 0.034 0.017 -10000 0 0 110 110
PIK3R1 0.034 0.017 -10000 0 0 107 107
RELN/LRP8/Fyn 0.045 0.057 -10000 0 -0.12 32 32
GRIN2A/RELN/LRP8/DAB1/Fyn 0.076 0.069 -10000 0 -0.11 31 31
MAPK8 0.04 0.009 -10000 0 0 30 30
RELN/VLDLR/DAB1 0.042 0.054 -10000 0 -0.1 37 37
ITGB1 0.039 0.011 -10000 0 0 38 38
MAP1B 0 0.065 0.22 24 -0.2 5 29
RELN/LRP8 0.049 0.055 -10000 0 -0.12 28 28
GRIN2B/RELN/LRP8/DAB1/Fyn 0.076 0.068 -10000 0 -0.11 26 26
PI3K 0.024 0.061 -10000 0 -0.15 47 47
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.03 0.066 -10000 0 -0.14 69 69
RAP1A -0.003 0.097 0.3 27 -10000 0 27
PAFAH1B1 0.038 0.012 -10000 0 0 48 48
MAPK8IP1 0.04 0.009 -10000 0 0 30 30
CRLK/C3G 0.056 0.018 -10000 0 -10000 0 0
GRIN2B 0.037 0.014 -10000 0 0 71 71
NCK2 0.042 0.004 -10000 0 0 6 6
neuron differentiation 0.023 0.059 0.17 1 -0.21 10 11
neuron adhesion -0.011 0.1 0.31 24 -0.25 1 25
LRP8 0.039 0.011 -10000 0 0 39 39
GSK3B -0.004 0.076 0.18 8 -0.18 43 51
RELN/VLDLR/DAB1/Fyn 0.051 0.068 -10000 0 -0.12 50 50
MAP3K11 0.041 0.006 -10000 0 0 12 12
RELN/VLDLR/DAB1/P13K -0.004 0.068 -10000 0 -0.17 60 60
CDK5 0.036 0.015 -10000 0 0 82 82
MAPT -0.009 0.034 0.68 1 -10000 0 1
neuron migration 0.003 0.097 0.26 28 -0.24 16 44
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.022 0.057 0.17 1 -0.2 9 10
RELN/VLDLR 0.053 0.073 -10000 0 -0.11 57 57
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.003 0.07 -10000 0 -0.19 53 53
epithelial cell differentiation 0.056 0.068 -10000 0 -0.13 51 51
CYFIP2 0.038 0.012 -10000 0 0 47 47
ENAH -0.033 0.071 0.22 12 -0.22 4 16
EGFR 0.037 0.014 -10000 0 0 72 72
EPHA2 0.039 0.01 -10000 0 0 35 35
MYO6 -0.03 0.048 0.18 7 -0.21 17 24
CTNNB1 0.04 0.01 -10000 0 0 31 31
ABI1/Sra1/Nap1 0.061 0.058 -10000 0 -0.12 41 41
AQP5 -0.076 0.14 0.18 4 -0.37 98 102
CTNND1 0.041 0.007 -10000 0 0 17 17
mol:PI-4-5-P2 -0.03 0.043 0.18 6 -0.2 12 18
regulation of calcium-dependent cell-cell adhesion -0.028 0.043 0.18 6 -0.2 12 18
EGF 0.038 0.012 -10000 0 0 52 52
NCKAP1 0.04 0.01 -10000 0 0 31 31
AQP3 -0.024 0.058 0.18 4 -0.29 15 19
cortical microtubule organization 0.056 0.068 -10000 0 -0.13 51 51
GO:0000145 -0.03 0.039 0.16 6 -0.19 12 18
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.062 0.072 -10000 0 -0.13 51 51
MLLT4 0.034 0.017 -10000 0 0 107 107
ARF6/GDP -0.05 0.046 -10000 0 -0.19 24 24
ARF6 0.041 0.008 -10000 0 0 19 19
Ephrin A1/EPHA2/NCK1/GIT1 0.061 0.077 -10000 0 -0.12 62 62
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.017 0.048 0.2 4 -0.21 15 19
PVRL2 0.039 0.011 -10000 0 0 44 44
ZYX -0.028 0.039 0.18 5 -0.2 8 13
ARF6/GTP 0.066 0.083 -10000 0 -0.12 64 64
CDH1 0.035 0.016 -10000 0 0 98 98
EGFR/EGFR/EGF/EGF 0.037 0.075 -10000 0 -0.13 66 66
RhoA/GDP 0.056 0.072 -10000 0 -0.12 53 53
actin cytoskeleton organization -0.032 0.048 0.16 6 -0.23 16 22
IGF-1R heterotetramer 0.033 0.017 -10000 0 0 118 118
GIT1 0.04 0.009 -10000 0 0 27 27
IGF1R 0.033 0.017 -10000 0 0 118 118
IGF1 0.036 0.015 -10000 0 0 84 84
DIAPH1 -0.002 0.22 -10000 0 -0.58 60 60
Wnt receptor signaling pathway -0.056 0.068 0.13 51 -10000 0 51
RHOA 0.041 0.007 -10000 0 0 14 14
RhoA/GTP -0.049 0.045 -10000 0 -0.19 23 23
CTNNA1 0.039 0.011 -10000 0 0 38 38
VCL -0.033 0.049 0.16 6 -0.24 16 22
EFNA1 0.034 0.017 -10000 0 0 107 107
LPP -0.029 0.044 0.17 6 -0.2 14 20
Ephrin A1/EPHA2 0.032 0.076 -10000 0 -0.13 74 74
SEC6/SEC8 -0.045 0.043 -10000 0 -0.14 68 68
MGAT3 -0.029 0.044 0.18 6 -0.2 12 18
HGF/MET 0.016 0.086 -10000 0 -0.13 113 113
HGF 0.04 0.009 -10000 0 0 29 29
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.003 0.07 -10000 0 -0.19 53 53
actin cable formation 0.002 0.096 0.26 24 -0.25 14 38
KIAA1543 -0.033 0.043 0.17 6 -0.2 13 19
KIFC3 -0.032 0.041 0.18 5 -0.2 12 17
NCK1 0.036 0.015 -10000 0 0 79 79
EXOC3 0.041 0.005 -10000 0 0 8 8
ACTN1 -0.031 0.049 0.18 7 -0.22 16 23
NCK1/GIT1 0.044 0.047 -10000 0 -0.14 30 30
mol:GDP 0.056 0.068 -10000 0 -0.13 51 51
EXOC4 0.038 0.012 -10000 0 0 49 49
STX4 -0.029 0.034 0.036 8 -0.12 49 57
PIP5K1C -0.031 0.043 0.18 6 -0.2 12 18
LIMA1 0 0 -10000 0 -10000 0 0
ABI1 0.04 0.009 -10000 0 0 26 26
ROCK1 -0.026 0.084 0.24 15 -0.23 4 19
adherens junction assembly -0.051 0.13 -10000 0 -0.39 46 46
IGF-1R heterotetramer/IGF1 0.023 0.083 -10000 0 -0.13 93 93
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.051 -10000 0 -0.14 33 33
MET 0.027 0.02 -10000 0 0 198 198
PLEKHA7 -0.031 0.045 0.18 7 -0.2 14 21
mol:GTP 0.058 0.075 -10000 0 -0.12 62 62
establishment of epithelial cell apical/basal polarity -0.038 0.056 0.14 25 -0.2 16 41
cortical actin cytoskeleton stabilization 0.003 0.07 -10000 0 -0.19 53 53
regulation of cell-cell adhesion -0.032 0.048 0.16 6 -0.23 16 22
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.003 0.07 -10000 0 -0.19 53 53
EPO signaling pathway

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
BCL2L1 0.029 0.14 0.36 1 -0.57 16 17
CRKL 0.024 0.085 0.18 113 -0.16 2 115
mol:DAG 0.044 0.072 0.22 4 -0.22 16 20
HRAS 0.018 0.096 0.25 39 -0.18 3 42
MAPK8 0.011 0.078 0.18 83 -0.13 6 89
RAP1A 0.024 0.084 0.18 113 -0.16 3 116
GAB1 0.023 0.083 0.18 107 -0.16 2 109
MAPK14 0.012 0.081 0.18 87 -0.14 2 89
EPO 0.045 0.015 0.083 5 -0.038 7 12
PLCG1 0.044 0.073 0.22 4 -0.22 16 20
EPOR/TRPC2/IP3 Receptors 0.04 0.019 0.082 4 -0.038 6 10
RAPGEF1 0.04 0.008 -10000 0 0 23 23
EPO/EPOR (dimer)/SOCS3 0.064 0.051 -10000 0 -0.13 16 16
GAB1/SHC/GRB2/SOS1 0.07 0.081 0.26 15 -0.16 6 21
EPO/EPOR (dimer) 0.057 0.033 -10000 0 -0.12 3 3
IRS2 0.023 0.084 0.18 110 -0.16 2 112
STAT1 0.036 0.096 0.24 4 -0.26 23 27
STAT5B 0.046 0.077 0.22 6 -0.21 20 26
cell proliferation 0.005 0.078 0.17 87 -0.15 3 90
GAB1/SHIP/PIK3R1/SHP2/SHC 0.036 0.061 0.16 3 -0.17 5 8
TEC 0.018 0.081 0.18 96 -0.18 8 104
SOCS3 0.037 0.014 -10000 0 0 67 67
STAT1 (dimer) 0.036 0.095 0.24 5 -0.26 23 28
JAK2 0.039 0.02 0.082 6 -0.037 4 10
PIK3R1 0.034 0.017 -10000 0 0 107 107
EPO/EPOR (dimer)/JAK2 0.07 0.07 0.24 34 -0.1 25 59
EPO/EPOR 0.057 0.033 -10000 0 -0.12 3 3
LYN 0.036 0.018 -10000 0 -0.037 9 9
TEC/VAV2 0.032 0.076 0.22 28 -0.17 11 39
elevation of cytosolic calcium ion concentration 0.04 0.019 0.082 4 -0.038 6 10
SHC1 0.04 0.01 -10000 0 0 31 31
EPO/EPOR (dimer)/LYN 0.062 0.062 -10000 0 -0.12 31 31
mol:IP3 0.044 0.072 0.22 4 -0.22 16 20
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.045 0.072 0.21 38 -0.16 2 40
SH2B3 0 0.008 0.031 11 -10000 0 11
NFKB1 0.008 0.076 0.18 70 -0.18 5 75
EPO/EPOR (dimer)/JAK2/SOCS3 0.016 0.047 0.21 2 -0.16 28 30
PTPN6 0.033 0.062 0.17 66 -0.11 22 88
TEC/VAV2/GRB2 0.051 0.085 0.23 33 -0.17 11 44
EPOR 0.04 0.019 0.083 4 -0.038 6 10
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.068 0.081 0.26 15 -0.16 6 21
SOS1 0.038 0.013 -10000 0 0 56 56
PLCG2 0.036 0.015 -10000 0 0 86 86
CRKL/CBL/C3G 0.072 0.076 0.23 44 -0.16 4 48
VAV2 0.021 0.083 0.18 104 -0.16 3 107
CBL 0.025 0.087 0.18 119 -0.19 2 121
SHC/Grb2/SOS1 0.039 0.057 0.17 2 -0.12 20 22
STAT5A 0.046 0.08 0.24 4 -0.22 22 26
GRB2 0.041 0.007 -10000 0 0 16 16
STAT5 (dimer) 0.063 0.092 0.28 4 -0.28 13 17
LYN/PLCgamma2 0.038 0.05 -10000 0 -0.13 35 35
PTPN11 0.04 0.009 -10000 0 0 27 27
BTK 0.023 0.085 0.18 112 -0.17 6 118
BCL2 0.028 0.12 0.36 1 -0.47 10 11
Regulation of Telomerase

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
Telomerase catalytic core complex -0.03 0.18 -10000 0 -0.51 25 25
RAD9A 0.042 0.004 -10000 0 0 6 6
AP1 0.002 0.083 -10000 0 -0.15 115 115
IFNAR2 0.03 0.027 -10000 0 -0.033 70 70
AKT1 0.013 0.038 -10000 0 -0.15 6 6
ER alpha/Oestrogen 0.013 0.044 -10000 0 -0.13 44 44
NFX1/SIN3/HDAC complex 0.001 0.084 0.17 5 -0.25 35 40
EGF 0.038 0.012 -10000 0 0 52 52
SMG5 0 0 -10000 0 -10000 0 0
SMG6 0 0 -10000 0 -10000 0 0
SP3/HDAC2 0.044 0.043 -10000 0 -0.13 6 6
TERT/c-Abl -0.02 0.18 -10000 0 -0.49 25 25
SAP18 0.039 0.01 -10000 0 0 34 34
MRN complex 0.048 0.071 -10000 0 -0.14 52 52
WT1 0.029 0.027 -10000 0 -0.033 68 68
WRN 0.033 0.017 -10000 0 0 123 123
SP1 0.032 0.031 -10000 0 -0.041 79 79
SP3 0.041 0.008 -10000 0 -0.002 14 14
TERF2IP 0.036 0.014 -10000 0 0 74 74
Telomerase/Nucleolin -0.019 0.18 -10000 0 -0.46 30 30
Mad/Max 0.055 0.025 -10000 0 -10000 0 0
TERT -0.033 0.18 -10000 0 -0.53 21 21
CCND1 -0.11 0.37 -10000 0 -0.97 81 81
MAX 0.04 0.009 -10000 0 -0.003 18 18
RBBP7 0.04 0.009 -10000 0 0 26 26
RBBP4 0.038 0.012 -10000 0 0 46 46
TERF2 0.035 0.021 0.094 44 0 79 123
PTGES3 0.038 0.013 -10000 0 0 56 56
SIN3A 0.04 0.009 -10000 0 0 28 28
Telomerase/911 0.024 0.081 -10000 0 -0.28 22 22
CDKN1B -0.002 0.083 0.2 4 -0.33 22 26
RAD1 0.038 0.013 -10000 0 0 57 57
XRCC5 0.039 0.011 -10000 0 0 39 39
XRCC6 0.037 0.014 -10000 0 0 69 69
SAP30 0.038 0.012 -10000 0 0 54 54
TRF2/PARP2 0.049 0.035 -10000 0 -0.13 9 9
UBE3A 0.041 0.006 -10000 0 0 7 7
JUN 0.036 0.015 -10000 0 0 81 81
E6 0 0.004 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.023 0.027 -10000 0 -0.13 7 7
FOS 0.026 0.021 -10000 0 0 210 210
IFN-gamma/IRF1 0.025 0.081 -10000 0 -0.16 81 81
PARP2 0.04 0.009 -10000 0 0 30 30
BLM 0.037 0.014 -10000 0 0 67 67
Telomerase 0.004 0.061 -10000 0 -0.25 20 20
IRF1 0.029 0.041 0.11 1 -0.14 21 22
ESR1 0.035 0.016 -10000 0 0 93 93
KU/TER 0.043 0.054 -10000 0 -0.16 31 31
ATM/TRF2 0.037 0.056 -10000 0 -0.14 41 41
ubiquitin-dependent protein catabolic process 0.003 0.084 0.18 6 -0.26 28 34
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.004 0.085 0.18 5 -0.27 27 32
HDAC1 0.038 0.013 -10000 0 0 56 56
HDAC2 0.03 0.03 -10000 0 -0.04 74 74
ATM 0.009 0.065 -10000 0 -0.24 32 32
SMAD3 -0.013 0.016 0.025 70 -10000 0 70
ABL1 0.039 0.011 -10000 0 0 40 40
MXD1 0.04 0.009 -10000 0 -0.002 19 19
MRE11A 0.038 0.012 -10000 0 0 54 54
HUS1 0.04 0.008 -10000 0 0 20 20
RPS6KB1 0.039 0.011 -10000 0 0 38 38
TERT/NF kappa B1/14-3-3 -0.008 0.19 -10000 0 -0.54 16 16
NR2F2 0.039 0.013 -10000 0 0 39 39
MAPK3 -0.016 0.015 0.022 51 -10000 0 51
MAPK1 -0.015 0.015 0.022 47 -0.04 2 49
TGFB1/TGF beta receptor Type II 0.037 0.013 -10000 0 0 62 62
NFKB1 0.036 0.015 -10000 0 0 83 83
HNRNPC 0 0 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.009 0.065 -10000 0 -0.24 32 32
NBN 0.035 0.016 -10000 0 0 96 96
EGFR 0.036 0.014 -10000 0 0 72 72
mol:Oestrogen 0 0.002 -10000 0 -10000 0 0
EGF/EGFR 0.04 0.052 -10000 0 -0.14 37 37
MYC 0.022 0.021 -10000 0 0 269 269
IL2 0.03 0.031 -10000 0 -0.042 75 75
KU 0.043 0.054 -10000 0 -0.16 31 31
RAD50 0.039 0.011 -10000 0 0 42 42
HSP90AA1 0 0 -10000 0 -10000 0 0
TGFB1 0.037 0.013 -10000 0 0 62 62
TRF2/BLM 0.043 0.044 -10000 0 -0.13 21 21
FRAP1 0.04 0.009 -10000 0 0 27 27
KU/TERT -0.012 0.19 -10000 0 -0.49 26 26
SP1/HDAC2 0.043 0.05 -10000 0 -0.093 24 24
PINX1 0.033 0.017 -10000 0 0 123 123
Telomerase/EST1A -0.025 0.16 -10000 0 -0.45 29 29
Smad3/Myc 0.015 0.038 -10000 0 -0.14 19 19
911 complex 0.071 0.037 -10000 0 -0.12 9 9
IFNG 0.034 0.036 0.11 2 -0.11 26 28
Telomerase/PinX1 -0.025 0.17 -10000 0 -0.44 30 30
Telomerase/AKT1/mTOR/p70S6K -0.001 0.1 -10000 0 -0.29 37 37
SIN3B 0.037 0.013 -10000 0 0 65 65
YWHAE 0.038 0.013 -10000 0 0 57 57
Telomerase/EST1B -0.025 0.16 -10000 0 -0.45 29 29
response to DNA damage stimulus 0.001 0.035 0.063 3 -0.11 49 52
MRN complex/TRF2/Rap1 0.065 0.08 -10000 0 -0.13 47 47
TRF2/WRN 0.038 0.041 -10000 0 -0.11 20 20
Telomerase/hnRNP C1/C2 -0.025 0.16 -10000 0 -0.45 29 29
E2F1 0.031 0.027 -10000 0 -0.033 69 69
ZNFX1 0 0.001 -10000 0 -10000 0 0
PIF1 0 0 -10000 0 -10000 0 0
NCL 0.04 0.009 -10000 0 0 30 30
DKC1 0.04 0.008 -10000 0 0 20 20
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.036 0.028 0.087 3 -0.07 31 34
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.008 0.13 0.24 4 -0.27 70 74
ERC1 0 0 -10000 0 -10000 0 0
RIP2/NOD2 0.015 0.041 -10000 0 -0.13 41 41
NFKBIA -0.036 0.066 0.25 3 -0.28 30 33
BIRC2 0.036 0.014 -10000 0 0 75 75
IKBKB 0.039 0.011 -10000 0 0 43 43
RIPK2 0.033 0.017 -10000 0 0 125 125
IKBKG -0.005 0.11 -10000 0 -0.3 50 50
IKK complex/A20 0.034 0.12 -10000 0 -0.31 31 31
NEMO/A20/RIP2 0.033 0.017 -10000 0 0 125 125
XPO1 0.039 0.011 -10000 0 0 39 39
NEMO/ATM 0.004 0.13 -10000 0 -0.31 52 52
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.041 0.006 -10000 0 0 13 13
Exportin 1/RanGTP 0.047 0.035 -10000 0 -0.11 24 24
IKK complex/ELKS 0.006 0.11 -10000 0 -0.28 49 49
BCL10/MALT1/TRAF6 0.065 0.047 -10000 0 -0.12 20 20
NOD2 0 0 -10000 0 -10000 0 0
NFKB1 0.032 0.028 0.084 1 -0.072 26 27
RELA 0.037 0.028 0.097 1 -0.069 34 35
MALT1 0.036 0.014 -10000 0 0 77 77
cIAP1/UbcH5C 0.04 0.053 -10000 0 -0.14 38 38
ATM 0.037 0.014 -10000 0 0 73 73
TNF/TNFR1A 0.047 0.038 -10000 0 -0.14 15 15
TRAF6 0.04 0.008 -10000 0 0 22 22
PRKCA 0.035 0.015 -10000 0 0 90 90
CHUK 0.038 0.012 -10000 0 0 52 52
UBE2D3 0.038 0.012 -10000 0 0 47 47
TNF 0.04 0.009 -10000 0 0 26 26
NF kappa B1 p50/RelA 0.057 0.081 -10000 0 -0.15 62 62
BCL10 0.041 0.006 -10000 0 0 12 12
proteasomal ubiquitin-dependent protein catabolic process -0.036 0.066 0.25 3 -0.28 30 33
beta TrCP1/SCF ubiquitin ligase complex 0.036 0.028 0.087 3 -0.07 31 34
TNFRSF1A 0.036 0.015 -10000 0 0 84 84
IKK complex 0.02 0.13 -10000 0 -0.3 49 49
CYLD 0.038 0.012 -10000 0 0 51 51
IKK complex/PKC alpha 0.023 0.13 -10000 0 -0.3 48 48
Arf6 downstream 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
PLAUR -0.028 0.2 -10000 0 -0.81 35 35
regulation of axonogenesis -0.002 0.051 0.2 29 -10000 0 29
myoblast fusion -0.011 0.1 0.35 38 -0.16 1 39
mol:GTP 0.017 0.067 -10000 0 -0.2 48 48
regulation of calcium-dependent cell-cell adhesion -0.034 0.089 0.15 87 -10000 0 87
ARF1/GTP 0.038 0.06 -10000 0 -0.15 45 45
mol:GM1 0.003 0.047 -10000 0 -0.15 48 48
mol:Choline 0 0.041 0.093 1 -0.15 30 31
lamellipodium assembly -0.013 0.12 -10000 0 -0.4 46 46
MAPK3 0.01 0.085 -10000 0 -0.28 42 42
ARF6/GTP/NME1/Tiam1 0.035 0.09 -10000 0 -0.15 87 87
ARF1 0.038 0.012 -10000 0 0 50 50
ARF6/GDP 0.011 0.1 0.16 1 -0.35 38 39
ARF1/GDP 0.014 0.1 -10000 0 -0.3 46 46
ARF6 0.042 0.046 -10000 0 -0.13 35 35
RAB11A 0.04 0.009 -10000 0 0 24 24
TIAM1 0.032 0.023 -10000 0 -0.013 100 100
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.012 0.079 -10000 0 -0.27 36 36
actin filament bundle formation -0.025 0.11 0.31 48 -10000 0 48
KALRN 0.003 0.075 -10000 0 -0.26 38 38
RAB11FIP3/RAB11A 0.058 0.023 -10000 0 -0.14 6 6
RhoA/GDP 0.026 0.11 -10000 0 -0.31 48 48
NME1 0.031 0.024 -10000 0 -0.012 120 120
Rac1/GDP 0.025 0.11 -10000 0 -0.31 47 47
substrate adhesion-dependent cell spreading 0.017 0.067 -10000 0 -0.2 48 48
cortical actin cytoskeleton organization -0.013 0.12 -10000 0 -0.41 45 45
RAC1 0.039 0.01 -10000 0 0 33 33
liver development 0.017 0.067 -10000 0 -0.2 48 48
ARF6/GTP 0.017 0.067 -10000 0 -0.2 48 48
RhoA/GTP 0.041 0.063 -10000 0 -0.16 48 48
mol:GDP -0.004 0.098 -10000 0 -0.35 39 39
ARF6/GTP/RAB11FIP3/RAB11A 0.061 0.067 -10000 0 -0.14 51 51
RHOA 0.041 0.007 -10000 0 0 14 14
PLD1 0.008 0.049 -10000 0 -0.17 32 32
RAB11FIP3 0.042 0.003 -10000 0 0 3 3
tube morphogenesis -0.013 0.12 -10000 0 -0.4 46 46
ruffle organization 0.002 0.051 -10000 0 -0.2 29 29
regulation of epithelial cell migration 0.017 0.067 -10000 0 -0.2 48 48
PLD2 0.015 0.05 -10000 0 -0.15 43 43
PIP5K1A 0.002 0.052 -10000 0 -0.2 29 29
mol:Phosphatidic acid 0 0.041 0.093 1 -0.15 30 31
Rac1/GTP -0.014 0.12 -10000 0 -0.41 46 46
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HIF3A 0.038 0.012 -10000 0 0 54 54
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.04 0.009 -10000 0 0 24 24
TCEB1 0.038 0.012 -10000 0 0 49 49
HIF1A/p53 0 0.086 0.22 1 -0.28 32 33
HIF1A -0.001 0.072 0.16 3 -0.32 17 20
COPS5 0.036 0.015 -10000 0 0 86 86
VHL/Elongin B/Elongin C/RBX1/CUL2 0.086 0.071 -10000 0 -0.12 26 26
FIH (dimer) 0.04 0.009 -10000 0 0 25 25
CDKN2A 0.029 0.019 -10000 0 0 175 175
ARNT/IPAS 0.054 0.025 -10000 0 -0.14 4 4
HIF1AN 0.04 0.009 -10000 0 0 25 25
GNB2L1 0.041 0.005 -10000 0 0 7 7
HIF1A/ARNT 0.015 0.085 0.22 1 -0.29 22 23
CUL2 0.039 0.01 -10000 0 0 36 36
OS9 0.039 0.011 -10000 0 0 38 38
RACK1/Elongin B/Elongin C 0.071 0.038 -10000 0 -0.12 11 11
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 -0.005 0.073 0.15 3 -0.3 20 23
PHD1-3/OS9 0.053 0.08 -10000 0 -0.11 86 86
HIF1A/RACK1/Elongin B/Elongin C 0.048 0.09 -10000 0 -0.29 19 19
VHL 0.04 0.009 -10000 0 0 28 28
HSP90AA1 0 0 -10000 0 -10000 0 0
HIF1A/JAB1 0.012 0.08 0.22 1 -0.28 23 24
EGLN3 0.028 0.02 -10000 0 0 187 187
EGLN2 0.04 0.009 -10000 0 0 29 29
EGLN1 0.039 0.01 -10000 0 0 36 36
TP53 0.026 0.02 -10000 0 0 212 212
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.024 0.12 -10000 0 -0.53 24 24
ARNT 0.041 0.006 -10000 0 0 12 12
ARD1A 0.04 0.01 -10000 0 0 31 31
RBX1 0.037 0.014 -10000 0 0 70 70
HIF1A/p19ARF 0.004 0.085 -10000 0 -0.29 28 28
ErbB2/ErbB3 signaling events

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
USP8 -0.013 0.01 0.018 24 -10000 0 24
RAS family/GTP 0.017 0.1 0.26 2 -0.22 29 31
NFATC4 -0.017 0.081 0.2 33 -0.16 9 42
ERBB2IP 0.036 0.015 -10000 0 -0.002 73 73
HSP90 (dimer) 0 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.001 0.079 0.18 12 -0.15 58 70
JUN 0.009 0.086 0.2 9 -10000 0 9
HRAS 0.04 0.01 -10000 0 0 31 31
DOCK7 -0.024 0.082 0.2 22 -0.2 13 35
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.037 0.08 0.21 20 -0.12 69 89
AKT1 -0.005 0.012 0.018 53 -10000 0 53
BAD -0.015 0.007 0.012 13 -10000 0 13
MAPK10 -0.008 0.071 0.2 26 -0.14 7 33
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0 0.085 0.2 12 -0.16 58 70
RAF1 0.008 0.11 0.26 26 -0.23 30 56
ErbB2/ErbB3/neuregulin 2 0.028 0.074 0.19 35 -0.12 76 111
STAT3 -0.027 0.25 -10000 0 -0.91 42 42
cell migration -0.008 0.073 0.22 24 -0.18 10 34
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.029 0.23 0.41 3 -0.56 55 58
FOS -0.033 0.22 0.34 7 -0.4 127 134
NRAS 0.04 0.01 -10000 0 0 30 30
mol:Ca2+ -0.001 0.079 0.18 12 -0.15 58 70
MAPK3 -0.01 0.19 0.36 5 -0.48 44 49
MAPK1 -0.024 0.2 0.37 4 -0.49 51 55
JAK2 -0.023 0.078 0.19 21 -0.21 9 30
NF2 0.004 0.075 -10000 0 -0.7 6 6
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.002 0.073 0.18 3 -0.17 65 68
NRG1 0.035 0.016 -10000 0 0 93 93
GRB2/SOS1 0.047 0.047 -10000 0 -0.14 28 28
MAPK8 -0.019 0.11 0.2 10 -0.22 76 86
MAPK9 -0.01 0.072 0.2 25 -0.15 9 34
ERBB2 -0.024 0.041 0.26 10 -10000 0 10
ERBB3 0.033 0.018 -10000 0 0 124 124
SHC1 0.04 0.01 -10000 0 0 31 31
RAC1 0.039 0.01 -10000 0 0 33 33
apoptosis 0.005 0.027 0.18 1 -0.21 7 8
STAT3 (dimer) -0.023 0.25 -10000 0 -0.88 42 42
RNF41 -0.017 0.016 0.045 12 -0.12 3 15
FRAP1 -0.014 0.007 0.012 13 -10000 0 13
RAC1-CDC42/GTP -0.031 0.056 0.087 27 -0.14 51 78
ErbB2/ErbB2/HSP90 (dimer) -0.024 0.015 0.017 4 -0.12 5 9
CHRNA1 0.006 0.15 0.35 5 -0.36 37 42
myelination -0.01 0.097 0.26 34 -0.2 4 38
PPP3CB -0.02 0.079 0.18 29 -0.18 10 39
KRAS 0.034 0.016 -10000 0 0 103 103
RAC1-CDC42/GDP 0.02 0.099 0.21 3 -0.17 65 68
NRG2 0.041 0.007 -10000 0 0 14 14
mol:GDP -0.002 0.072 0.18 3 -0.17 65 68
SOS1 0.038 0.013 -10000 0 0 56 56
MAP2K2 -0.006 0.11 0.25 23 -0.23 44 67
SRC 0.039 0.01 -10000 0 0 36 36
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.022 0.085 0.19 26 -0.2 10 36
MAP2K1 -0.017 0.19 0.38 1 -0.54 27 28
heart morphogenesis -0.001 0.079 0.18 12 -0.15 58 70
RAS family/GDP 0.025 0.1 0.27 2 -0.22 26 28
GRB2 0.041 0.007 -10000 0 0 16 16
PRKACA 0.008 0.084 -10000 0 -0.73 7 7
CHRNE 0.008 0.023 0.071 2 -10000 0 2
HSP90AA1 0 0 -10000 0 -10000 0 0
activation of caspase activity 0.005 0.012 -10000 0 -0.018 52 52
nervous system development -0.001 0.079 0.18 12 -0.15 58 70
CDC42 0.04 0.009 -10000 0 0 24 24
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.046 0.051 -10000 0 -0.14 35 35
Necdin/E2F1 0.045 0.041 -10000 0 -0.14 17 17
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.072 0.061 -10000 0 -0.11 42 42
NGF (dimer)/p75(NTR)/BEX1 0.022 0.053 -10000 0 -0.11 63 63
NT-4/5 (dimer)/p75(NTR) 0.029 0.009 -10000 0 -0.13 1 1
IKBKB 0.039 0.011 -10000 0 0 43 43
AKT1 0.015 0.09 0.19 100 -0.18 6 106
IKBKG 0.042 0.003 -10000 0 0 2 2
BDNF 0.04 0.008 -10000 0 0 23 23
MGDIs/NGR/p75(NTR)/LINGO1 0.049 0.022 -10000 0 -0.11 3 3
FURIN 0.04 0.01 -10000 0 0 32 32
proBDNF (dimer)/p75(NTR)/Sortilin 0.066 0.049 -10000 0 -0.12 26 26
LINGO1 0 0 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.02 0.071 -10000 0 -0.13 79 79
proBDNF (dimer) 0.04 0.008 -10000 0 0 23 23
NTRK1 0.039 0.01 -10000 0 0 35 35
RTN4R 0.038 0.012 -10000 0 0 54 54
neuron apoptosis -0.059 0.13 0.36 1 -0.38 45 46
IRAK1 0.041 0.007 -10000 0 0 18 18
SHC1 0.017 0.01 0.069 8 -0.11 1 9
ARHGDIA 0.038 0.012 -10000 0 0 55 55
RhoA/GTP 0.03 0.012 -10000 0 -0.13 3 3
Gamma Secretase 0.073 0.086 -10000 0 -0.12 66 66
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.055 0.057 -10000 0 -0.11 51 51
MAGEH1 0.039 0.011 -10000 0 0 45 45
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.054 0.054 -10000 0 -0.1 41 41
Mammalian IAPs/DIABLO 0.012 0.089 -10000 0 -0.13 132 132
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.04 0.009 -10000 0 0 26 26
APP 0.038 0.012 -10000 0 0 51 51
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.042 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.047 0.027 0.19 1 -0.11 7 8
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest -0.017 0.041 0.2 3 -10000 0 3
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.01 0.062 -10000 0 -0.16 50 50
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.05 0.023 -10000 0 -0.11 7 7
NCSTN 0.04 0.009 -10000 0 0 24 24
mol:GTP 0.045 0.035 -10000 0 -0.1 23 23
PSENEN 0.035 0.016 -10000 0 0 92 92
mol:ceramide -0.021 0.027 0.19 3 -10000 0 3
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.011 0.091 -10000 0 -0.32 20 20
p75(NTR)/beta APP 0.047 0.045 -10000 0 -0.14 28 28
BEX1 0.027 0.02 -10000 0 0 205 205
mol:GDP -0.008 0.004 -10000 0 -0.1 1 1
NGF (dimer) -0.004 0.074 -10000 0 -0.1 173 173
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.064 0.037 -10000 0 -0.1 8 8
PIK3R1 0.034 0.017 -10000 0 0 107 107
RAC1/GTP 0.044 0.016 -10000 0 -0.091 1 1
MYD88 0.041 0.007 -10000 0 0 14 14
CHUK 0.038 0.012 -10000 0 0 52 52
NGF (dimer)/p75(NTR)/PKA 0.045 0.035 -10000 0 -0.1 23 23
RHOB 0.04 0.008 -10000 0 0 21 21
RHOA 0.041 0.007 -10000 0 0 14 14
MAGE-G1/E2F1 0.053 0.025 -10000 0 -0.14 2 2
NT3 (dimer) 0.031 0.018 -10000 0 0 147 147
TP53 -0.023 0.048 0.21 9 -0.18 13 22
PRDM4 -0.022 0.028 0.19 3 -10000 0 3
BDNF (dimer) 0.019 0.091 -10000 0 -0.11 166 166
PIK3CA 0.03 0.019 -10000 0 0 155 155
SORT1 0.039 0.012 -10000 0 0 46 46
activation of caspase activity 0.065 0.057 -10000 0 -0.11 42 42
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.062 0.049 -10000 0 -0.11 33 33
RHOC 0.041 0.006 -10000 0 0 12 12
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 -0.016 0.057 0.24 5 -0.21 11 16
DIABLO 0.037 0.013 -10000 0 0 63 63
SMPD2 -0.021 0.028 0.19 3 -10000 0 3
APH1B 0.036 0.015 -10000 0 0 83 83
APH1A 0.041 0.006 -10000 0 0 10 10
proNGF (dimer)/p75(NTR)/Sortilin 0.044 0.038 -10000 0 -0.11 27 27
PSEN1 0.039 0.01 -10000 0 0 35 35
APAF-1/Pro-Caspase 9 0.051 0.041 -10000 0 -0.15 19 19
NT3 (dimer)/p75(NTR) 0.041 0.037 -10000 0 -0.14 10 10
MAPK8 -0.02 0.063 0.26 5 -0.25 10 15
MAPK9 -0.02 0.061 0.24 5 -0.23 10 15
APAF1 0.04 0.01 -10000 0 0 32 32
NTF3 0.031 0.018 -10000 0 0 147 147
NTF4 0 0 -10000 0 -10000 0 0
NDN 0.036 0.014 -10000 0 0 77 77
RAC1/GDP 0.029 0.01 -10000 0 -0.13 1 1
RhoA-B-C/GDP 0.074 0.05 -10000 0 -0.1 27 27
p75 CTF/Sortilin/TRAF6/NRIF 0.075 0.075 -10000 0 -0.13 57 57
RhoA-B-C/GTP 0.044 0.034 -10000 0 -0.1 23 23
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.099 0.065 -10000 0 -0.11 32 32
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.084 0.059 -10000 0 -0.12 32 32
PRKACB 0.038 0.012 -10000 0 0 49 49
proBDNF (dimer)/p75 ECD 0.046 0.047 -10000 0 -0.14 31 31
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.026 0.02 -10000 0 0 218 218
BIRC2 0.036 0.014 -10000 0 0 75 75
neuron projection morphogenesis -0.019 0.05 0.16 3 -0.16 25 28
BAD -0.024 0.068 0.26 4 -0.22 21 25
RIPK2 0.033 0.017 -10000 0 0 125 125
NGFR 0.04 0.009 -10000 0 0 28 28
CYCS -0.025 0.033 0.19 2 -0.18 5 7
ADAM17 0.038 0.013 -10000 0 0 57 57
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.05 0.056 -10000 0 -0.11 44 44
BCL2L11 -0.025 0.068 0.26 4 -0.22 21 25
BDNF (dimer)/p75(NTR) 0.057 0.019 -10000 0 -0.14 1 1
PI3K 0.035 0.06 -10000 0 -0.12 48 48
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.061 0.047 -10000 0 -0.1 28 28
NDNL2 0.039 0.011 -10000 0 0 39 39
YWHAE 0.038 0.013 -10000 0 0 57 57
PRKCI 0.027 0.02 -10000 0 0 197 197
NGF (dimer)/p75(NTR) 0.029 0.009 -10000 0 -0.13 1 1
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.06 0.053 -10000 0 -0.11 40 40
TRAF6 0.04 0.008 -10000 0 0 22 22
RAC1 0.039 0.01 -10000 0 0 33 33
PRKCZ 0.042 0 -10000 0 -10000 0 0
PLG 0.038 0.012 -10000 0 0 50 50
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 0.013 0.044 0.16 6 -0.17 24 30
SQSTM1 0.038 0.012 -10000 0 0 49 49
NGFRAP1 0.041 0.007 -10000 0 0 16 16
CASP3 -0.027 0.072 0.26 4 -0.24 24 28
E2F1 0.038 0.012 -10000 0 0 49 49
CASP9 0.04 0.009 -10000 0 0 26 26
IKK complex 0.047 0.099 -10000 0 -0.26 20 20
NGF (dimer)/TRKA 0.029 0.007 -10000 0 -10000 0 0
MMP7 0.016 0.02 -10000 0 0 340 340
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.079 0.054 -10000 0 -0.11 33 33
MMP3 0.038 0.013 -10000 0 0 59 59
APAF-1/Caspase 9 -0.056 0.061 -10000 0 -0.19 51 51
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.038 0.19 0.35 2 -0.98 21 23
VDR 0.038 0.013 -10000 0 0 56 56
FAM120B 0 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.023 0.091 -10000 0 -0.24 47 47
RXRs/LXRs/DNA/Oxysterols 0.016 0.13 -10000 0 -0.34 55 55
MED1 0 0 -10000 0 -10000 0 0
mol:9cRA 0.001 0.016 0.057 1 -0.047 50 51
RARs/THRs/DNA/Src-1 -0.004 0.094 -10000 0 -0.18 113 113
RXRs/NUR77 0.079 0.072 0.3 1 -0.11 37 38
RXRs/PPAR 0.026 0.056 -10000 0 -0.16 13 13
NCOR2 0.04 0.009 -10000 0 0 28 28
VDR/VDR/Vit D3 0.023 0.031 -10000 0 -0.13 22 22
RARs/VDR/DNA/Vit D3 0.064 0.069 -10000 0 -0.11 59 59
RARA 0.039 0.01 -10000 0 0 35 35
NCOA1 0.04 0.009 -10000 0 0 28 28
VDR/VDR/DNA 0.038 0.013 -10000 0 0 56 56
RARs/RARs/DNA/9cRA 0.052 0.053 -10000 0 -0.1 46 46
RARG 0.04 0.009 -10000 0 0 27 27
RPS6KB1 -0.018 0.1 0.56 5 -0.42 22 27
RARs/THRs/DNA/SMRT -0.003 0.09 -10000 0 -0.17 110 110
THRA 0.039 0.011 -10000 0 0 40 40
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.023 0.031 -10000 0 -0.13 22 22
RXRs/PPAR/9cRA/PGJ2/DNA 0.071 0.077 0.31 12 -0.15 33 45
NR1H4 0.041 0.007 -10000 0 0 16 16
RXRs/LXRs/DNA 0.095 0.1 0.32 1 -0.2 34 35
NR1H2 0.034 0.032 -10000 0 -0.059 52 52
NR1H3 0.035 0.034 -10000 0 -0.065 54 54
RXRs/VDR/DNA/Vit D3 0.072 0.071 0.28 1 -0.11 43 44
NR4A1 0.034 0.016 -10000 0 0 103 103
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.023 0.042 0.14 3 -0.14 8 11
RXRG 0.032 0.031 0.1 1 -0.055 44 45
RXR alpha/CCPG 0.026 0.022 -10000 0 -0.042 20 20
RXRA 0.035 0.031 0.1 1 -0.057 50 51
RXRB 0.036 0.034 0.1 1 -0.062 56 57
THRB 0.034 0.017 -10000 0 0 108 108
PPARG 0.039 0.01 -10000 0 0 37 37
PPARD 0.04 0.008 -10000 0 0 21 21
TNF 0.008 0.13 -10000 0 -0.52 9 9
mol:Oxysterols 0 0.015 -10000 0 -0.041 59 59
cholesterol transport 0.016 0.13 -10000 0 -0.34 55 55
PPARA 0.034 0.016 -10000 0 0 103 103
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.036 0.015 -10000 0 0 80 80
RXRs/NUR77/BCL2 0.02 0.047 -10000 0 -0.14 22 22
SREBF1 0.007 0.12 -10000 0 -0.49 10 10
RXRs/RXRs/DNA/9cRA 0.071 0.077 0.31 12 -0.15 33 45
ABCA1 -0.035 0.26 -10000 0 -0.8 54 54
RARs/THRs 0.071 0.092 -10000 0 -0.12 82 82
RXRs/FXR 0.088 0.068 0.3 1 -0.11 29 30
BCL2 0.036 0.014 -10000 0 0 76 76
Regulation of p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
RIP1/MEKK3 0.049 0.023 -10000 0 -0.11 5 5
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.038 0.012 -10000 0 0 48 48
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.034 0.016 -10000 0 0 100 100
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.037 0.013 -10000 0 0 61 61
RAC1-CDC42/GTP/PAK family 0.007 0.049 -10000 0 -0.15 34 34
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.038 0.013 -10000 0 0 57 57
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.041 0.007 -10000 0 0 17 17
FYN 0.034 0.016 -10000 0 0 104 104
MAP3K12 0.041 0.007 -10000 0 0 14 14
FGR 0.041 0.007 -10000 0 0 17 17
p38 alpha/TAB1 0.002 0.12 -10000 0 -0.27 51 51
PRKG1 0.04 0.009 -10000 0 0 29 29
DUSP8 0.04 0.009 -10000 0 0 28 28
PGK/cGMP/p38 alpha -0.004 0.11 -10000 0 -0.26 55 55
apoptosis 0.001 0.11 -10000 0 -0.26 51 51
RAL/GTP 0.046 0.037 -10000 0 -0.11 25 25
LYN 0.036 0.015 -10000 0 0 83 83
DUSP1 0.027 0.02 -10000 0 0 206 206
PAK1 0.037 0.014 -10000 0 0 70 70
SRC 0.039 0.01 -10000 0 0 36 36
RAC1/OSM/MEKK3/MKK3 0.091 0.04 -10000 0 -0.11 1 1
TRAF6 0.04 0.008 -10000 0 0 22 22
RAC1 0.039 0.01 -10000 0 0 33 33
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.041 0.007 -10000 0 0 17 17
RAC1-CDC42/GTP 0.05 0.023 -10000 0 -0.13 4 4
MAPK11 -0.028 0.12 0.2 2 -0.29 65 67
BLK 0.033 0.017 -10000 0 0 117 117
HCK 0.036 0.015 -10000 0 0 80 80
MAP2K3 0.038 0.012 -10000 0 0 47 47
DUSP16 0.036 0.015 -10000 0 0 86 86
DUSP10 0.034 0.017 -10000 0 0 109 109
TRAF6/MEKK3 0.049 0.021 -10000 0 -0.098 7 7
MAP3K7IP1 0.038 0.012 -10000 0 0 53 53
MAPK14 -0.011 0.12 0.19 2 -0.28 55 57
positive regulation of innate immune response -0.024 0.14 0.23 2 -0.34 57 59
LCK 0.04 0.009 -10000 0 0 29 29
p38alpha-beta/MKP7 -0.013 0.14 0.25 1 -0.33 51 52
p38alpha-beta/MKP5 -0.018 0.14 0.24 2 -0.32 58 60
PGK/cGMP 0.029 0.007 -10000 0 -10000 0 0
PAK2 0.04 0.009 -10000 0 0 25 25
p38alpha-beta/MKP1 -0.029 0.14 0.25 1 -0.33 61 62
CDC42 0.04 0.009 -10000 0 0 24 24
RALB 0.04 0.009 -10000 0 0 26 26
RALA 0.04 0.009 -10000 0 0 30 30
PAK3 0.037 0.013 -10000 0 0 62 62
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.04 0.01 -10000 0 0 31 31
EGFR 0.037 0.014 -10000 0 0 72 72
EGF/EGFR 0.046 0.058 -10000 0 -0.098 55 55
EGF/EGFR dimer/SHC/GRB2/SOS1 0.081 0.077 -10000 0 -0.11 49 49
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.036 0.015 -10000 0 0 85 85
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.038 0.012 -10000 0 0 52 52
EGF/EGFR dimer/SHC 0.058 0.055 -10000 0 -0.12 33 33
mol:GDP 0.073 0.073 -10000 0 -0.11 49 49
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.035 0.016 -10000 0 0 99 99
GRB2/SOS1 0.047 0.047 -10000 0 -0.14 28 28
HRAS/GTP 0.048 0.06 -10000 0 -0.11 49 49
SHC1 0.04 0.01 -10000 0 0 31 31
HRAS/GDP 0.069 0.073 -10000 0 -0.11 49 49
FRAP1 -0.016 0.072 0.2 40 -0.18 4 44
EGF/EGFR dimer 0.041 0.051 -10000 0 -0.13 37 37
SOS1 0.038 0.013 -10000 0 0 56 56
GRB2 0.041 0.007 -10000 0 0 16 16
ETA receptor/Endothelin-1 0.038 0.047 -10000 0 -0.14 25 25
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.025 0.12 0.25 3 -0.28 35 38
CaM/Ca2+ 0.028 0.016 -10000 0 -0.13 5 5
AKT1 0.039 0.011 -10000 0 0 38 38
AKT2 0.038 0.012 -10000 0 0 47 47
STXBP4 0.038 0.012 -10000 0 0 47 47
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.014 0.12 0.22 8 -0.3 35 43
YWHAZ 0.034 0.016 -10000 0 0 102 102
CALM1 0.04 0.01 -10000 0 0 31 31
YWHAQ 0.04 0.009 -10000 0 0 28 28
TBC1D4 -0.018 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.038 0.013 -10000 0 0 59 59
YWHAB 0.038 0.012 -10000 0 0 52 52
SNARE/Synip 0.045 0.029 -10000 0 -0.11 9 9
YWHAG 0.04 0.009 -10000 0 0 25 25
ASIP 0.037 0.013 -10000 0 0 60 60
PRKCI 0.027 0.02 -10000 0 0 197 197
AS160/CaM/Ca2+ 0.028 0.016 -10000 0 -0.13 5 5
RHOQ 0.039 0.01 -10000 0 0 33 33
GYS1 0.009 0.029 0.25 4 -0.17 6 10
PRKCZ 0.042 0 -10000 0 -10000 0 0
TRIP10 0.038 0.012 -10000 0 0 47 47
TC10/GTP/CIP4/Exocyst 0.047 0.029 -10000 0 -0.11 12 12
AS160/14-3-3 0.021 0.081 0.2 1 -0.25 23 24
VAMP2 0.037 0.014 -10000 0 0 66 66
SLC2A4 0.012 0.13 0.24 5 -0.33 35 40
STX4 0 0 -10000 0 -10000 0 0
GSK3B 0.024 0.025 -10000 0 -0.2 6 6
SFN 0.036 0.015 -10000 0 0 86 86
LNPEP 0.036 0.015 -10000 0 0 86 86
YWHAE 0.038 0.013 -10000 0 0 57 57
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.039 0.011 -10000 0 0 38 38
RAS family/GTP/Tiam1 0.012 0.06 -10000 0 -0.16 38 38
NT3 (dimer)/TRKC 0.04 0.036 -10000 0 -0.14 8 8
NT3 (dimer)/TRKB 0.056 0.045 -10000 0 -0.12 10 10
SHC/Grb2/SOS1/GAB1/PI3K -0.001 0.08 -10000 0 -0.19 63 63
RAPGEF1 0.04 0.008 -10000 0 0 23 23
BDNF 0.04 0.008 -10000 0 0 23 23
PIK3CA 0.03 0.019 -10000 0 0 155 155
DYNLT1 0.036 0.015 -10000 0 0 82 82
NTRK1 0.039 0.01 -10000 0 0 35 35
NTRK2 0.039 0.01 -10000 0 0 36 36
NTRK3 0.038 0.012 -10000 0 0 49 49
NT-4/5 (dimer)/TRKB 0.051 0.018 -10000 0 -0.087 1 1
neuron apoptosis -0.03 0.1 0.26 27 -0.23 3 30
SHC 2-3/Grb2 0.031 0.11 -10000 0 -0.28 27 27
SHC1 0.04 0.01 -10000 0 0 31 31
SHC2 0.007 0.12 0.22 2 -0.37 41 43
SHC3 0.025 0.088 -10000 0 -0.38 17 17
STAT3 (dimer) 0.003 0.11 -10000 0 -0.27 75 75
NT3 (dimer)/TRKA 0.054 0.046 -10000 0 -0.12 10 10
RIN/GDP 0.047 0.086 0.22 31 -0.19 24 55
GIPC1 0.035 0.015 -10000 0 0 89 89
KRAS 0.034 0.016 -10000 0 0 103 103
DNAJA3 0.01 0.052 0.15 10 -0.16 9 19
RIN/GTP 0.029 0.008 -10000 0 -10000 0 0
CCND1 -0.048 0.17 -10000 0 -0.49 74 74
MAGED1 0.04 0.009 -10000 0 0 26 26
PTPN11 0.04 0.009 -10000 0 0 27 27
RICS 0.037 0.014 -10000 0 0 71 71
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.065 0.051 -10000 0 -0.12 26 26
GRB2 0.041 0.007 -10000 0 0 16 16
NGF (dimer)/TRKA/MATK 0.048 0.02 -10000 0 -10000 0 0
TRKA/NEDD4-2 0.047 0.038 -10000 0 -0.14 15 15
ELMO1 0.036 0.015 -10000 0 0 86 86
RhoG/GTP/ELMO1/DOCK1 0.034 0.048 -10000 0 -0.11 44 44
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.04 0.01 -10000 0 0 31 31
DOCK1 0.037 0.013 -10000 0 0 62 62
GAB2 0.031 0.018 -10000 0 0 141 141
RIT2 0.039 0.01 -10000 0 0 37 37
RIT1 0.038 0.012 -10000 0 0 48 48
FRS2 0.039 0.011 -10000 0 0 40 40
DNM1 0.039 0.011 -10000 0 0 38 38
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.038 0.012 -10000 0 0 51 51
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.028 0.061 0.2 4 -0.16 11 15
mol:GDP 0.043 0.11 0.26 26 -0.27 25 51
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.022 0.03 -10000 0 -0.13 19 19
RIT1/GDP 0.042 0.084 0.22 22 -0.19 27 49
TIAM1 0.037 0.014 -10000 0 0 72 72
PIK3R1 0.034 0.017 -10000 0 0 107 107
BDNF (dimer)/TRKB 0.071 0.032 -10000 0 -0.12 1 1
KIDINS220/CRKL/C3G 0.056 0.018 -10000 0 -10000 0 0
SHC/RasGAP 0.048 0.038 -10000 0 -0.13 16 16
FRS2 family/SHP2 0.067 0.05 -10000 0 -0.12 29 29
SHC/GRB2/SOS1/GAB1 0.079 0.061 -10000 0 -0.12 32 32
RIT1/GTP 0.025 0.026 -10000 0 -0.13 15 15
NT3 (dimer) 0.031 0.018 -10000 0 0 147 147
RAP1/GDP 0.033 0.074 0.18 17 -0.17 29 46
KIDINS220/CRKL 0.039 0.011 -10000 0 0 38 38
BDNF (dimer) 0.04 0.008 -10000 0 0 23 23
ubiquitin-dependent protein catabolic process 0.042 0.033 -10000 0 -0.11 15 15
Schwann cell development -0.007 0.011 -10000 0 -0.044 11 11
EHD4 0.039 0.011 -10000 0 0 38 38
FRS2 family/GRB2/SOS1 0.081 0.062 -10000 0 -0.12 33 33
FRS2 family/SHP2/CRK family/C3G/GAB2 0.006 0.084 -10000 0 -0.21 37 37
RAP1B 0.038 0.013 -10000 0 0 59 59
RAP1A 0.039 0.01 -10000 0 0 35 35
CDC42/GTP 0.068 0.053 0.18 28 -0.11 9 37
ABL1 0.039 0.011 -10000 0 0 40 40
SH2B family/GRB2/SOS1 0.047 0.047 -10000 0 -0.14 28 28
Rap1/GTP 0.007 0.11 -10000 0 -0.26 55 55
STAT3 0.004 0.11 -10000 0 -0.27 75 75
axon guidance 0.046 0.041 -10000 0 -0.11 9 9
MAPK3 -0.008 0.047 0.19 28 -10000 0 28
MAPK1 -0.008 0.046 0.19 27 -10000 0 27
CDC42/GDP 0.049 0.087 0.22 32 -0.19 24 56
NTF3 0.031 0.018 -10000 0 0 147 147
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.049 0.021 -10000 0 -0.11 2 2
PI3K 0.024 0.061 -10000 0 -0.15 47 47
FRS3 0.04 0.008 -10000 0 0 23 23
FAIM 0.038 0.012 -10000 0 0 51 51
GAB1 0.038 0.012 -10000 0 0 51 51
RASGRF1 0.01 0.053 0.16 9 -0.17 10 19
SOS1 0.038 0.013 -10000 0 0 56 56
MCF2L 0.005 0.061 0.18 41 -0.12 8 49
RGS19 0.036 0.015 -10000 0 0 78 78
CDC42 0.04 0.009 -10000 0 0 24 24
RAS family/GTP 0.035 0.12 0.29 4 -0.34 30 34
Rac1/GDP 0.048 0.087 0.22 30 -0.18 26 56
NGF (dimer)/TRKA/GRIT 0.042 0.036 -10000 0 -0.11 20 20
neuron projection morphogenesis -0.052 0.25 -10000 0 -0.84 43 43
NGF (dimer)/TRKA/NEDD4-2 0.043 0.033 -10000 0 -0.11 15 15
MAP2K1 -0.012 0.071 0.19 47 -0.19 3 50
NGFR 0.04 0.009 -10000 0 0 28 28
NGF (dimer)/TRKA/GIPC/GAIP 0.015 0.04 -10000 0 -0.15 23 23
RAS family/GTP/PI3K -0.004 0.072 -10000 0 -0.19 52 52
FRS2 family/SHP2/GRB2/SOS1 0.09 0.077 -10000 0 -0.13 44 44
NRAS 0.04 0.009 -10000 0 0 30 30
GRB2/SOS1 0.047 0.047 -10000 0 -0.14 28 28
PRKCI 0.027 0.02 -10000 0 0 197 197
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.039 0.01 -10000 0 0 33 33
PRKCZ 0.042 0 -10000 0 -10000 0 0
MAPKKK cascade 0.027 0.047 -10000 0 -0.5 2 2
RASA1 0.037 0.014 -10000 0 0 71 71
TRKA/c-Abl 0.052 0.033 -10000 0 -0.14 11 11
SQSTM1 0.038 0.012 -10000 0 0 49 49
BDNF (dimer)/TRKB/GIPC 0.071 0.059 -10000 0 -0.11 21 21
NGF (dimer)/TRKA/p62/Atypical PKCs 0.048 0.069 -10000 0 -0.11 52 52
MATK 0.038 0.013 -10000 0 0 59 59
NEDD4L 0.036 0.015 -10000 0 0 80 80
RAS family/GDP -0.009 0.038 -10000 0 -0.13 29 29
NGF (dimer)/TRKA 0.015 0.052 0.16 6 -0.17 10 16
Rac1/GTP -0.003 0.048 -10000 0 -0.16 15 15
FRS2 family/SHP2/CRK family 0.088 0.069 -10000 0 -0.11 26 26
Aurora A signaling

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
Aurora A/GADD45A 0.042 0.041 0.17 3 -0.15 11 14
BIRC5 0.037 0.013 -10000 0 0 60 60
NFKBIA -0.004 0.028 0.25 1 -0.18 6 7
CPEB1 0.039 0.01 -10000 0 0 34 34
AKT1 -0.003 0.042 0.26 9 -0.18 7 16
NDEL1 0.039 0.01 -10000 0 0 37 37
Aurora A/BRCA1 0.027 0.05 0.15 3 -0.1 53 56
NDEL1/TACC3 0.045 0.051 0.17 2 -0.11 31 33
GADD45A 0.037 0.014 -10000 0 0 73 73
GSK3B 0.039 0.012 0.091 15 0 26 41
PAK1/Aurora A 0.042 0.042 0.17 3 -0.16 10 13
MDM2 0.039 0.01 -10000 0 0 35 35
JUB 0.037 0.013 -10000 0 0 60 60
TPX2 -0.015 0.009 -10000 0 -10000 0 0
TP53 -0.045 0.12 0.16 2 -0.24 141 143
DLG7 -0.002 0.025 0.17 2 -0.17 3 5
AURKAIP1 0 0 -10000 0 -10000 0 0
ARHGEF7 0.04 0.009 -10000 0 0 28 28
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.048 0.054 0.18 2 -0.12 31 33
G2/M transition of mitotic cell cycle 0.026 0.049 0.15 3 -0.1 53 56
AURKA 0.01 0.03 0.13 13 -0.2 7 20
AURKB 0 0.063 -10000 0 -0.2 44 44
CDC25B 0.005 0.045 -10000 0 -0.22 18 18
G2/M transition checkpoint 0.033 0.044 0.15 3 -0.11 31 34
mRNA polyadenylation 0.039 0.035 0.15 2 -0.14 10 12
Aurora A/CPEB 0.039 0.036 0.15 2 -0.14 10 12
Aurora A/TACC1/TRAP/chTOG 0.055 0.075 0.21 2 -0.17 16 18
BRCA1 0.034 0.016 -10000 0 0 106 106
centrosome duplication 0.042 0.041 0.17 3 -0.16 10 13
regulation of centrosome cycle 0.044 0.05 0.17 2 -0.11 31 33
spindle assembly 0.053 0.073 0.21 2 -0.16 16 18
TDRD7 0.035 0.016 -10000 0 0 93 93
Aurora A/RasGAP/Survivin 0.044 0.073 0.2 6 -0.1 70 76
CENPA 0.009 0.055 -10000 0 -0.33 12 12
Aurora A/PP2A 0.046 0.039 0.17 3 -0.15 10 13
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process -0.014 0.059 0.16 6 -0.2 17 23
negative regulation of DNA binding -0.045 0.12 0.16 2 -0.24 141 143
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.057 0.018 -10000 0 -10000 0 0
RASA1 0.037 0.014 -10000 0 0 71 71
Ajuba/Aurora A 0.034 0.044 0.15 3 -0.11 31 34
mitotic prometaphase 0.003 0.025 0.074 61 -10000 0 61
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.03 0.13 13 -0.2 7 20
TACC1 0.035 0.016 -10000 0 0 93 93
TACC3 0.034 0.017 -10000 0 0 112 112
Aurora A/Antizyme1 0.029 0.044 0.15 2 -0.1 36 38
Aurora A/RasGAP 0.042 0.042 0.17 3 -0.16 11 14
OAZ1 0.034 0.017 -10000 0 0 107 107
RAN 0.041 0.006 -10000 0 0 13 13
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.035 0.017 0.091 14 0 89 103
GIT1 0.04 0.009 -10000 0 0 27 27
GIT1/beta-PIX/PAK1 0.066 0.044 -10000 0 -0.12 15 15
Importin alpha/Importin beta/TPX2 -0.015 0.009 -10000 0 -10000 0 0
PPP2R5D 0.04 0.009 -10000 0 0 29 29
Aurora A/TPX2 0.018 0.037 0.15 2 -0.18 10 12
PAK1 0.037 0.014 -10000 0 0 70 70
CKAP5 0.039 0.011 -10000 0 0 45 45
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.061 0.1 0.31 17 -0.31 9 26
PDGFB-D/PDGFRB/SLAP 0.032 0.038 -10000 0 -0.14 10 10
PDGFB-D/PDGFRB/APS/CBL 0.048 0.024 -10000 0 -0.11 4 4
AKT1 0.023 0.1 0.25 46 -10000 0 46
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.045 0.094 0.27 18 -0.33 10 28
PIK3CA 0.03 0.019 -10000 0 0 155 155
FGR 0.023 0.092 0.28 7 -0.39 13 20
mol:Ca2+ 0.027 0.087 0.25 15 -0.36 10 25
MYC 0.004 0.28 0.34 21 -0.66 76 97
SHC1 0.04 0.01 -10000 0 0 31 31
HRAS/GDP 0.038 0.059 0.19 43 -0.11 18 61
LRP1/PDGFRB/PDGFB 0.054 0.057 -10000 0 -0.12 36 36
GRB10 0.04 0.009 -10000 0 0 24 24
PTPN11 0.04 0.009 -10000 0 0 27 27
GO:0007205 0.026 0.088 0.26 14 -0.37 10 24
PTEN 0.039 0.011 -10000 0 0 38 38
GRB2 0.041 0.007 -10000 0 0 16 16
GRB7 0.037 0.013 -10000 0 0 63 63
PDGFB-D/PDGFRB/SHP2 0.047 0.043 -10000 0 -0.14 22 22
PDGFB-D/PDGFRB/GRB10 0.051 0.034 -10000 0 -0.15 9 9
cell cycle arrest 0.032 0.038 -10000 0 -0.14 10 10
HRAS 0.04 0.01 -10000 0 0 31 31
HIF1A 0.009 0.096 0.23 43 -0.2 6 49
GAB1 0.023 0.1 0.28 9 -0.28 18 27
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.025 0.11 0.27 24 -0.26 19 43
PDGFB-D/PDGFRB 0.057 0.052 -10000 0 -0.12 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.048 0.042 -10000 0 -0.14 22 22
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.054 0.12 0.33 15 -0.25 34 49
positive regulation of MAPKKK cascade 0.047 0.043 -10000 0 -0.14 22 22
PIK3R1 0.034 0.017 -10000 0 0 107 107
mol:IP3 0.027 0.088 0.26 14 -0.37 10 24
E5 0 0.002 -10000 0 -10000 0 0
CSK 0.04 0.009 -10000 0 -0.003 23 23
PDGFB-D/PDGFRB/GRB7 0.047 0.034 -10000 0 -0.14 8 8
SHB 0.041 0.007 -10000 0 0 17 17
BLK -0.036 0.16 0.3 4 -0.36 96 100
PTPN2 0.039 0.015 -10000 0 -0.014 36 36
PDGFB-D/PDGFRB/SNX15 0.054 0.025 -10000 0 -0.14 3 3
BCAR1 0.036 0.014 -10000 0 0 75 75
VAV2 0.01 0.13 0.28 13 -0.32 46 59
CBL 0.04 0.008 -10000 0 0 23 23
PDGFB-D/PDGFRB/DEP1 0.047 0.04 -10000 0 -0.13 19 19
LCK 0.028 0.079 0.27 8 -0.38 6 14
PDGFRB 0.036 0.019 -10000 0 -0.007 81 81
ACP1 0.04 0.009 -10000 0 0 26 26
HCK 0.016 0.095 0.3 4 -0.46 13 17
ABL1 0.019 0.091 0.24 19 -0.24 19 38
PDGFB-D/PDGFRB/CBL 0.023 0.1 0.27 8 -0.34 15 23
PTPN1 0.036 0.017 -10000 0 -0.007 70 70
SNX15 0.041 0.005 -10000 0 0 7 7
STAT3 0.038 0.013 -10000 0 0 56 56
STAT1 0.034 0.017 -10000 0 0 108 108
cell proliferation 0.012 0.26 0.31 31 -0.59 76 107
SLA 0.026 0.02 -10000 0 0 207 207
actin cytoskeleton reorganization 0.009 0.095 0.22 69 -0.18 1 70
SRC 0.026 0.057 0.32 3 -10000 0 3
PI3K -0.027 0.036 -10000 0 -0.13 13 13
PDGFB-D/PDGFRB/GRB7/SHC 0.062 0.043 -10000 0 -0.12 8 8
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.046 0.096 0.28 17 -0.34 10 27
LYN 0.001 0.12 0.29 5 -0.42 33 38
LRP1 0.036 0.014 -10000 0 0 75 75
SOS1 0.038 0.013 -10000 0 0 56 56
STAT5B 0.039 0.011 -10000 0 0 43 43
STAT5A 0.038 0.012 -10000 0 0 51 51
NCK1-2/p130 Cas 0.075 0.075 -10000 0 -0.12 19 19
SPHK1 0.042 0.009 -10000 0 0 20 20
EDG1 0.042 0.007 -10000 0 0 13 13
mol:DAG 0.027 0.088 0.26 14 -0.37 10 24
PLCG1 0.026 0.09 0.26 14 -0.38 10 24
NHERF/PDGFRB 0.06 0.048 -10000 0 -0.12 17 17
YES1 0.003 0.12 0.26 5 -0.42 33 38
cell migration 0.059 0.048 -10000 0 -0.12 17 17
SHC/Grb2/SOS1 0.084 0.073 -10000 0 -0.13 24 24
SLC9A3R2 0.038 0.012 -10000 0 0 54 54
SLC9A3R1 0.038 0.012 -10000 0 0 48 48
NHERF1-2/PDGFRB/PTEN 0.079 0.057 -10000 0 -0.12 25 25
FYN -0.015 0.14 0.27 4 -0.38 58 62
DOK1 0.006 0.069 0.19 56 -10000 0 56
HRAS/GTP 0.029 0.01 -10000 0 -0.13 1 1
PDGFB 0.038 0.013 -10000 0 0 56 56
RAC1 -0.032 0.24 0.29 12 -0.54 77 89
PRKCD 0.004 0.068 0.2 51 -10000 0 51
FER 0.004 0.066 0.19 49 -10000 0 49
MAPKKK cascade -0.002 0.08 0.19 58 -0.18 4 62
RASA1 0.004 0.064 0.19 45 -10000 0 45
NCK1 0.036 0.015 -10000 0 0 79 79
NCK2 0.042 0.004 -10000 0 0 6 6
p62DOK/Csk 0.056 0.056 0.2 58 -0.11 11 69
PDGFB-D/PDGFRB/SHB 0.053 0.026 -10000 0 -0.14 3 3
chemotaxis 0.019 0.09 0.24 19 -0.23 19 38
STAT1-3-5/STAT1-3-5 0.05 0.08 -10000 0 -0.13 50 50
Bovine Papilomavirus E5/PDGFRB 0.026 0.019 -10000 0 -0.13 3 3
PTPRJ 0.039 0.01 -10000 0 0 35 35
p38 MAPK 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
TRAF6/ASK1 0.019 0.053 -10000 0 -0.15 33 33
TRAF2/ASK1 0.044 0.035 -10000 0 -0.11 20 20
ATM 0.037 0.014 -10000 0 0 73 73
MAP2K3 -0.042 0.16 -10000 0 -0.32 105 105
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.044 0.14 0.21 2 -0.32 80 82
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.037 0.013 -10000 0 0 61 61
TXN 0.009 0.003 -10000 0 -10000 0 0
CALM1 0.04 0.01 -10000 0 0 31 31
GADD45A 0.037 0.014 -10000 0 0 73 73
GADD45B 0.035 0.016 -10000 0 0 99 99
MAP3K1 0.036 0.014 -10000 0 0 77 77
MAP3K6 0.04 0.008 -10000 0 0 22 22
MAP3K7 0.038 0.012 -10000 0 0 47 47
MAP3K4 0.038 0.012 -10000 0 0 50 50
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.048 0.041 -10000 0 -0.14 20 20
TAK1/TAB family 0.017 0.067 0.17 6 -0.29 18 24
RAC1/OSM/MEKK3 0.072 0.026 -10000 0 -0.1 1 1
TRAF2 0.04 0.009 -10000 0 0 29 29
RAC1/OSM/MEKK3/MKK3 -0.01 0.14 -10000 0 -0.28 94 94
TRAF6 0.009 0.041 -10000 0 -0.2 21 21
RAC1 0.039 0.01 -10000 0 0 33 33
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.041 0.007 -10000 0 0 18 18
CCM2 0.041 0.007 -10000 0 0 17 17
CaM/Ca2+/CAMKIIB 0.051 0.019 -10000 0 -0.11 3 3
MAPK11 0.031 0.018 -10000 0 0 141 141
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.062 0.044 -10000 0 -0.1 22 22
OSM/MEKK3 0.059 0.014 -10000 0 -10000 0 0
TAOK1 0.003 0.054 -10000 0 -0.2 38 38
TAOK2 0.004 0.053 -10000 0 -0.2 36 36
TAOK3 0 0.059 -10000 0 -0.2 46 46
MAP3K7IP1 0.038 0.012 -10000 0 0 53 53
MAPK14 0.04 0.009 -10000 0 0 28 28
MAP3K7IP2 0.037 0.013 -10000 0 0 60 60
MAP3K5 0.037 0.014 -10000 0 0 70 70
MAP3K10 0.039 0.011 -10000 0 0 41 41
MAP3K3 0.041 0.007 -10000 0 0 17 17
TRX/ASK1 0.023 0.046 0.11 1 -0.15 33 34
GADD45/MTK1/MTK1 0.055 0.068 -10000 0 -0.11 57 57
mTOR signaling pathway

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
GBL 0.04 0.009 -10000 0 0 26 26
MKNK1 0.04 0.009 -10000 0 0 25 25
mol:PIP3 -0.013 0.038 0.2 1 -0.17 12 13
FRAP1 0.028 0.1 -10000 0 -0.43 22 22
AKT1 0.017 0.08 0.17 98 -0.18 7 105
INSR 0.038 0.012 -10000 0 0 53 53
Insulin Receptor/Insulin 0.048 0.023 -10000 0 -0.11 4 4
mol:GTP 0.051 0.088 0.23 28 -0.18 7 35
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.006 0.052 -10000 0 -0.19 26 26
TSC2 0.039 0.01 -10000 0 0 35 35
RHEB/GDP 0.029 0.068 0.16 6 -0.16 13 19
TSC1 0.04 0.009 -10000 0 0 28 28
Insulin Receptor/IRS1 0.034 0.033 -10000 0 -0.23 7 7
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.012 0.071 -10000 0 -0.23 23 23
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0 0 -10000 0 -10000 0 0
RPS6KB1 0.029 0.11 0.26 14 -0.33 24 38
MAP3K5 -0.009 0.066 0.2 5 -0.22 47 52
PIK3R1 0.034 0.017 -10000 0 0 107 107
apoptosis -0.009 0.066 0.2 5 -0.22 47 52
mol:LY294002 0 0 0.001 4 -0.001 6 10
EIF4B 0.024 0.1 0.26 14 -0.3 25 39
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.037 0.098 0.23 14 -0.28 25 39
eIF4E/eIF4G1/eIF4A1 0.012 0.062 -10000 0 -0.26 20 20
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.028 0.053 -10000 0 -0.16 16 16
mTOR/RHEB/GTP/Raptor/GBL 0.028 0.074 0.2 20 -0.18 23 43
FKBP1A 0.039 0.012 -10000 0 0 50 50
RHEB/GTP 0.051 0.084 0.22 18 -0.16 13 31
mol:Amino Acids 0 0 0.001 4 -0.001 6 10
FKBP12/Rapamycin 0.028 0.013 -10000 0 -0.13 2 2
PDPK1 0.006 0.074 0.16 90 -0.17 11 101
EIF4E 0.039 0.011 -10000 0 0 42 42
ASK1/PP5C 0.012 0.2 -10000 0 -0.56 53 53
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.001 0.12 -10000 0 -0.46 21 21
TSC1/TSC2 0.057 0.095 0.25 28 -0.19 7 35
tumor necrosis factor receptor activity 0 0 0.001 6 -0.001 4 10
RPS6 0.039 0.011 -10000 0 0 41 41
PPP5C 0.04 0.01 -10000 0 0 32 32
EIF4G1 0.032 0.018 -10000 0 0 129 129
IRS1 0.01 0.03 -10000 0 -0.24 7 7
INS 0.04 0.009 -10000 0 0 30 30
PTEN 0.039 0.011 -10000 0 0 38 38
PDK2 0.006 0.073 0.16 86 -0.17 10 96
EIF4EBP1 -0.053 0.3 -10000 0 -1.1 46 46
PIK3CA 0.03 0.019 -10000 0 0 155 155
PPP2R5D 0.029 0.1 0.28 6 -0.38 22 28
peptide biosynthetic process -0.014 0.032 0.19 11 -10000 0 11
RHEB 0.037 0.013 -10000 0 0 65 65
EIF4A1 0.039 0.011 -10000 0 0 38 38
mol:Rapamycin 0 0.001 0.004 41 -0.002 4 45
EEF2 -0.014 0.032 0.19 11 -10000 0 11
eIF4E/4E-BP1 -0.033 0.29 -10000 0 -0.98 46 46
Syndecan-3-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
CTTN 0.039 0.01 -9999 0 0 34 34
Syndecan-3/Src/Cortactin 0.026 0.094 -9999 0 -0.38 13 13
Syndecan-3/Neurocan 0.002 0.066 -9999 0 -0.42 13 13
POMC 0.041 0.007 -9999 0 0 17 17
EGFR 0.037 0.014 -9999 0 0 72 72
Syndecan-3/EGFR 0.03 0.074 -9999 0 -0.42 13 13
AGRP 0.036 0.014 -9999 0 0 76 76
NCSTN 0.04 0.009 -9999 0 0 24 24
PSENEN 0.035 0.016 -9999 0 0 92 92
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.036 0.015 -9999 0 0 83 83
APH1A 0.041 0.006 -9999 0 0 10 10
NCAN 0 0 -9999 0 -10000 0 0
long-term memory 0.038 0.08 -9999 0 -0.39 13 13
Syndecan-3/IL8 0.023 0.074 -9999 0 -0.42 13 13
PSEN1 0.039 0.01 -9999 0 0 35 35
Src/Cortactin 0.052 0.032 -9999 0 -0.14 10 10
FYN 0.034 0.016 -9999 0 0 104 104
limb bud formation 0.003 0.068 -9999 0 -0.43 13 13
MC4R 0 0 -9999 0 -10000 0 0
SRC 0.039 0.01 -9999 0 0 36 36
PTN 0.023 0.021 -9999 0 0 253 253
FGFR/FGF/Syndecan-3 0.003 0.069 -9999 0 -0.43 13 13
neuron projection morphogenesis -0.013 0.071 -9999 0 -0.37 13 13
Syndecan-3/AgRP 0.03 0.073 -9999 0 -0.42 13 13
Syndecan-3/AgRP/MC4R 0.028 0.071 -9999 0 -0.41 13 13
Fyn/Cortactin 0.037 0.055 -9999 0 -0.14 44 44
SDC3 0.003 0.07 -9999 0 -0.44 13 13
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration 0.023 0.073 -9999 0 -0.42 13 13
IL8 0.032 0.018 -9999 0 0 139 139
Syndecan-3/Fyn/Cortactin 0.039 0.082 -9999 0 -0.4 13 13
Syndecan-3/CASK 0.002 0.066 -9999 0 -0.42 13 13
alpha-MSH/MC4R 0.03 0.005 -9999 0 -10000 0 0
Gamma Secretase 0.073 0.086 -9999 0 -0.12 66 66
S1P3 pathway

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
PDGFRB 0.037 0.013 -10000 0 0 64 64
mol:S1P 0.001 0.007 -10000 0 -0.028 24 24
S1P1/S1P/Gi 0.006 0.081 -10000 0 -0.26 23 23
GNAO1 0.033 0.024 -10000 0 -0.008 121 121
S1P/S1P3/G12/G13 0.047 0.032 -10000 0 -0.065 25 25
AKT1 0.015 0.1 -10000 0 -0.44 22 22
AKT3 -0.02 0.23 -10000 0 -0.95 28 28
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.037 0.013 -10000 0 0 64 64
GNAI2 0.04 0.02 -10000 0 -0.049 22 22
GNAI3 0.038 0.021 -10000 0 -0.047 20 20
GNAI1 0.034 0.022 -10000 0 -0.046 17 17
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.001 0.007 0.012 1 -0.03 24 25
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0.041 0.006 -10000 0 0 13 13
mol:Ca2+ -0.001 0.1 0.16 1 -0.27 49 50
MAPK3 -0.009 0.096 0.18 2 -0.26 51 53
MAPK1 -0.004 0.089 0.14 1 -0.26 40 41
JAK2 -0.018 0.11 0.19 3 -0.29 55 58
CXCR4 -0.01 0.098 0.19 3 -0.27 49 52
FLT1 0.04 0.023 -10000 0 -0.059 20 20
RhoA/GDP 0.03 0.012 -10000 0 -0.13 3 3
Rac1/GDP 0.029 0.01 -10000 0 -0.13 1 1
SRC -0.002 0.099 0.22 15 -0.27 43 58
S1P/S1P3/Gi 0 0.1 0.16 1 -0.27 48 49
RAC1 0.039 0.01 -10000 0 0 33 33
RhoA/GTP 0.01 0.11 -10000 0 -0.26 47 47
VEGFA 0.003 0.011 0.018 98 -0.038 23 121
S1P/S1P2/Gi -0.002 0.089 -10000 0 -0.24 42 42
VEGFR1 homodimer/VEGFA homodimer 0.036 0.032 -10000 0 -0.087 25 25
RHOA 0.041 0.007 -10000 0 0 14 14
S1P/S1P3/Gq 0.018 0.037 -10000 0 -0.14 25 25
GNAQ 0.038 0.012 -10000 0 0 49 49
GNAZ 0.038 0.021 -10000 0 -0.016 63 63
G12/G13 0.054 0.03 -10000 0 -0.14 9 9
GNA14 0.039 0.01 -10000 0 0 33 33
GNA15 0.037 0.014 -10000 0 0 69 69
GNA12 0.04 0.01 -10000 0 0 32 32
GNA13 0.04 0.009 -10000 0 0 28 28
GNA11 0.037 0.013 -10000 0 0 61 61
Rac1/GTP 0.009 0.1 -10000 0 -0.25 48 48
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.039 0.011 -10000 0 0 42 42
VLDLR 0.032 0.018 -10000 0 0 128 128
LRPAP1 0.036 0.014 -10000 0 0 77 77
NUDC 0.04 0.009 -10000 0 0 26 26
RELN/LRP8 0.049 0.055 -10000 0 -0.12 28 28
CaM/Ca2+ 0.028 0.016 -10000 0 -0.13 5 5
KATNA1 0.037 0.013 -10000 0 0 62 62
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.001 0.068 0.21 34 -0.19 1 35
IQGAP1/CaM 0.041 0.056 -10000 0 -0.14 45 45
DAB1 0.04 0.009 -10000 0 0 27 27
IQGAP1 0.037 0.014 -10000 0 0 69 69
PLA2G7 0.03 0.019 -10000 0 0 157 157
CALM1 0.04 0.01 -10000 0 0 31 31
DYNLT1 0.036 0.015 -10000 0 0 82 82
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.041 0.052 -10000 0 -0.14 36 36
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0 0 -10000 0 -10000 0 0
CDK5R1 0.04 0.009 -10000 0 0 30 30
LIS1/Poliovirus Protein 3A -0.015 0.013 -10000 0 -0.13 5 5
CDK5R2 0.041 0.006 -10000 0 0 11 11
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.043 0.059 -10000 0 -0.12 37 37
YWHAE 0.038 0.013 -10000 0 0 57 57
NDEL1/14-3-3 E 0.036 0.084 0.29 24 -0.17 7 31
MAP1B -0.002 0.049 0.18 3 -0.18 34 37
RAC1 0.012 0.043 -10000 0 -0.59 1 1
p35/CDK5 -0.007 0.07 0.21 25 -0.18 1 26
RELN 0.034 0.017 -10000 0 0 110 110
PAFAH/LIS1 0.025 0.027 -10000 0 -0.15 5 5
LIS1/CLIP170 -0.015 0.013 -10000 0 -0.13 5 5
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain 0.025 0.079 0.2 17 -0.19 13 30
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.001 0.096 -10000 0 -0.21 73 73
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.007 0.081 0.21 52 -0.16 5 57
LIS1/IQGAP1 0.03 0.026 -10000 0 -0.15 5 5
RHOA 0.012 0.044 0.12 25 -0.45 2 27
PAFAH1B1 -0.017 0.008 -10000 0 -10000 0 0
PAFAH1B3 0.035 0.016 -10000 0 0 92 92
PAFAH1B2 0.04 0.01 -10000 0 0 31 31
MAP1B/LIS1/Dynein heavy chain 0.011 0.061 0.18 1 -0.15 38 39
NDEL1/Katanin 60/Dynein heavy chain 0.043 0.092 0.28 27 -0.18 11 38
LRP8 0.039 0.011 -10000 0 0 39 39
NDEL1/Katanin 60 0.033 0.084 0.29 23 -0.17 11 34
P39/CDK5 -0.007 0.072 0.21 27 -0.18 1 28
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.033 0.025 -10000 0 -0.15 5 5
CDK5 -0.01 0.054 0.19 20 -0.18 1 21
PPP2R5D 0.04 0.009 -10000 0 0 29 29
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.012 0.011 -10000 0 -0.11 5 5
CSNK2A1 0.038 0.012 -10000 0 0 54 54
RELN/VLDLR/DAB1/LIS1 0.056 0.064 -10000 0 -0.11 33 33
RELN/VLDLR 0.053 0.073 -10000 0 -0.11 57 57
CDC42 0.012 0.049 -10000 0 -0.45 3 3
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.035 0.25 0.48 2 -0.56 58 60
PCK1 -0.092 0.4 -10000 0 -1.1 72 72
HNF4A -0.067 0.34 0.57 5 -0.76 85 90
KCNJ11 -0.003 0.23 0.53 1 -0.54 30 31
AKT1 0.005 0.17 -10000 0 -0.33 34 34
response to starvation -0.015 0.045 -10000 0 -0.12 78 78
DLK1 0.005 0.24 0.64 3 -0.57 22 25
NKX2-1 -0.002 0.15 0.36 3 -0.31 32 35
ACADM -0.049 0.27 0.54 1 -0.59 69 70
TAT -0.023 0.19 -10000 0 -0.55 19 19
CEBPB 0.039 0.017 -10000 0 -0.064 2 2
CEBPA 0.042 0.016 -10000 0 -0.066 1 1
TTR 0.041 0.17 0.55 1 -0.92 4 5
PKLR -0.022 0.25 0.45 2 -0.55 45 47
APOA1 -0.12 0.47 -10000 0 -1.1 93 93
CPT1C -0.027 0.24 0.46 2 -0.55 51 53
ALAS1 -0.005 0.18 -10000 0 -0.62 10 10
TFRC -0.054 0.38 -10000 0 -0.94 69 69
FOXF1 0.035 0.015 -10000 0 -10000 0 0
NF1 0.039 0.02 -10000 0 -0.16 1 1
HNF1A (dimer) 0.009 0.001 -10000 0 -10000 0 0
CPT1A -0.041 0.27 0.48 2 -0.59 61 63
HMGCS1 -0.033 0.26 0.48 5 -0.58 62 67
NR3C1 0.048 0.015 -10000 0 -10000 0 0
CPT1B -0.034 0.24 -10000 0 -0.54 55 55
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.041 0.006 -10000 0 -10000 0 0
GCK -0.029 0.24 0.48 3 -0.54 54 57
CREB1 0.021 0.095 -10000 0 -0.21 74 74
IGFBP1 -0.001 0.15 -10000 0 -0.5 4 4
PDX1 0.013 0.14 0.4 1 -0.29 28 29
UCP2 -0.055 0.3 0.48 9 -0.64 83 92
ALDOB -0.003 0.23 -10000 0 -0.53 31 31
AFP 0.015 0.049 -10000 0 -10000 0 0
BDH1 -0.054 0.27 -10000 0 -0.59 72 72
HADH -0.003 0.23 -10000 0 -0.48 51 51
F2 -0.03 0.31 -10000 0 -0.7 47 47
HNF1A 0.009 0.001 -10000 0 -10000 0 0
G6PC 0.028 0.088 -10000 0 -10000 0 0
SLC2A2 0.033 0.16 -10000 0 -0.43 1 1
INS 0.03 0.013 0.18 1 -0.063 1 2
FOXA1 0.056 0.016 -10000 0 -10000 0 0
FOXA3 0.022 0.12 -10000 0 -0.21 94 94
FOXA2 0.016 0.29 -10000 0 -0.56 48 48
ABCC8 -0.003 0.23 0.53 1 -0.53 30 31
ALB 0.015 0.049 -10000 0 -10000 0 0
ceramide signaling pathway

Figure S88.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S88.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.023 0.13 0.25 3 -0.38 42 45
BAG4 0.037 0.013 -10000 0 0 64 64
BAD -0.008 0.047 0.17 5 -0.14 30 35
NFKBIA 0.037 0.014 -10000 0 0 66 66
BIRC3 0.026 0.02 -10000 0 0 218 218
BAX -0.007 0.047 0.14 8 -0.14 27 35
EnzymeConsortium:3.1.4.12 -0.003 0.032 0.074 3 -0.085 37 40
IKBKB -0.024 0.13 0.23 11 -0.36 40 51
MAP2K2 -0.009 0.04 0.15 3 -0.15 8 11
MAP2K1 -0.012 0.045 0.17 7 -0.15 7 14
SMPD1 -0.003 0.037 0.097 1 -0.1 36 37
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.014 0.14 0.25 10 -0.37 43 53
MAP2K4 -0.01 0.041 0.14 1 -0.13 22 23
protein ubiquitination -0.029 0.13 0.24 2 -0.38 40 42
EnzymeConsortium:2.7.1.37 -0.013 0.044 0.15 4 -0.16 7 11
response to UV 0 0 0.002 7 -0.002 3 10
RAF1 -0.01 0.044 0.15 4 -0.14 19 23
CRADD 0.041 0.006 -10000 0 0 13 13
mol:ceramide -0.004 0.047 0.12 2 -0.13 38 40
I-kappa-B-alpha/RELA/p50/ubiquitin 0.042 0.044 -10000 0 -0.11 37 37
MADD 0.041 0.006 -10000 0 0 11 11
MAP3K1 -0.008 0.044 0.11 2 -0.13 34 36
TRADD 0.036 0.014 -10000 0 0 76 76
RELA/p50 0.041 0.006 -10000 0 0 10 10
MAPK3 -0.008 0.045 0.17 3 -0.16 8 11
MAPK1 -0.012 0.052 0.16 4 -0.17 20 24
p50/RELA/I-kappa-B-alpha 0.045 0.051 -10000 0 -0.14 37 37
FADD -0.018 0.14 0.24 10 -0.37 41 51
KSR1 -0.007 0.042 0.12 1 -0.13 26 27
MAPK8 -0.016 0.043 0.17 3 -0.14 15 18
TRAF2 0.04 0.009 -10000 0 0 29 29
response to radiation 0 0 -10000 0 -10000 0 0
CHUK -0.032 0.13 0.23 3 -0.36 46 49
TNF R/SODD 0.044 0.038 -10000 0 -0.13 14 14
TNF 0.04 0.009 -10000 0 0 26 26
CYCS -0.007 0.049 0.14 4 -0.14 21 25
IKBKG -0.03 0.13 0.24 2 -0.38 38 40
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.018 0.14 -10000 0 -0.4 40 40
RELA 0.041 0.006 -10000 0 0 10 10
RIPK1 0.038 0.012 -10000 0 0 48 48
AIFM1 -0.006 0.047 0.12 7 -0.14 22 29
TNF/TNF R/SODD 0.059 0.046 -10000 0 -0.12 15 15
TNFRSF1A 0.036 0.015 -10000 0 0 84 84
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.019 0.13 -10000 0 -0.65 19 19
NSMAF -0.015 0.14 0.25 15 -0.41 35 50
response to hydrogen peroxide 0 0 0.002 7 -0.002 3 10
BCL2 0.036 0.014 -10000 0 0 76 76
Regulation of cytoplasmic and nuclear SMAD2/3 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
SMAD4 0.038 0.012 -10000 0 0 49 49
SMAD2 0.008 0.054 0.19 8 -0.2 9 17
SMAD3 0.014 0.054 0.22 2 -0.3 4 6
SMAD3/SMAD4 -0.017 0.16 -10000 0 -0.39 79 79
SMAD4/Ubc9/PIASy 0.066 0.042 -10000 0 -0.13 10 10
SMAD2/SMAD2/SMAD4 0.046 0.086 0.27 1 -0.19 10 11
PPM1A 0.041 0.007 -10000 0 0 16 16
CALM1 0.04 0.01 -10000 0 0 31 31
SMAD2/SMAD4 0.026 0.053 0.22 3 -0.17 14 17
MAP3K1 0.036 0.014 -10000 0 0 77 77
TRAP-1/SMAD4 0.049 0.043 -10000 0 -0.14 23 23
MAPK3 0.041 0.007 -10000 0 0 17 17
MAPK1 0.039 0.012 -10000 0 0 46 46
NUP214 0.039 0.01 -10000 0 0 33 33
CTDSP1 0.041 0.006 -10000 0 0 13 13
CTDSP2 0.039 0.011 -10000 0 0 42 42
CTDSPL 0.041 0.006 -10000 0 0 10 10
KPNB1 0.04 0.01 -10000 0 0 31 31
TGFBRAP1 0.04 0.008 -10000 0 0 20 20
UBE2I 0.04 0.009 -10000 0 0 28 28
NUP153 0.037 0.014 -10000 0 0 67 67
KPNA2 0.036 0.015 -10000 0 0 86 86
PIAS4 0.038 0.012 -10000 0 0 55 55
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.038 0.013 -10000 0 0 56 56
HDAC2 0.038 0.012 -10000 0 0 48 48
GNB1/GNG2 0.071 0.042 -10000 0 -0.12 18 18
forebrain development 0.014 0.11 -10000 0 -0.38 28 28
GNAO1 0.035 0.016 -10000 0 0 101 101
SMO/beta Arrestin2 0.054 0.026 -10000 0 -0.14 4 4
SMO 0.04 0.01 -10000 0 -0.001 33 33
ARRB2 0.039 0.011 -10000 0 0 43 43
GLI3/SPOP 0.021 0.13 0.23 3 -0.34 33 36
mol:GTP 0 0.001 -10000 0 -10000 0 0
GSK3B 0.04 0.009 -10000 0 0 26 26
GNAI2 0.041 0.007 -10000 0 0 15 15
SIN3/HDAC complex 0.076 0.054 -10000 0 -0.12 10 10
GNAI1 0.035 0.016 -10000 0 0 95 95
XPO1 0.039 0.012 -10000 0 -0.002 42 42
GLI1/Su(fu) 0.021 0.11 -10000 0 -0.42 23 23
SAP30 0.038 0.012 -10000 0 0 54 54
mol:GDP 0.04 0.01 -10000 0 -0.001 33 33
MIM/GLI2A 0.032 0.026 -10000 0 -0.12 2 2
IFT88 0.037 0.014 -10000 0 0 70 70
GNAI3 0.039 0.011 -10000 0 0 45 45
GLI2 0.017 0.072 0.19 6 -0.21 24 30
GLI3 0.003 0.12 0.22 6 -0.35 33 39
CSNK1D 0.04 0.009 -10000 0 0 28 28
CSNK1E 0.038 0.013 -10000 0 0 56 56
SAP18 0.039 0.01 -10000 0 0 34 34
embryonic digit morphogenesis 0.037 0.014 -10000 0 0 70 70
GNG2 0.039 0.01 -10000 0 0 34 34
Gi family/GTP 0.002 0.076 -10000 0 -0.24 29 29
SIN3B 0.037 0.013 -10000 0 0 65 65
SIN3A 0.04 0.009 -10000 0 0 28 28
GLI3/Su(fu) 0.017 0.12 0.23 3 -0.32 36 39
GLI2/Su(fu) 0.024 0.082 0.19 5 -0.22 31 36
FOXA2 0.024 0.097 -10000 0 -0.57 12 12
neural tube patterning 0.014 0.11 -10000 0 -0.38 28 28
SPOP 0.04 0.009 -10000 0 0 27 27
Su(fu)/PIAS1 0.04 0.06 0.21 1 -0.18 27 28
GNB1 0.041 0.005 -10000 0 0 7 7
CSNK1G2 0.037 0.013 -10000 0 0 64 64
CSNK1G3 0.039 0.011 -10000 0 0 38 38
MTSS1 0.032 0.026 -10000 0 -0.12 2 2
embryonic limb morphogenesis 0.014 0.11 -10000 0 -0.38 28 28
SUFU 0.023 0.039 -10000 0 -0.24 10 10
LGALS3 0.037 0.014 -10000 0 0 70 70
catabolic process 0.026 0.13 -10000 0 -0.33 38 38
GLI3A/CBP 0.047 0.015 -10000 0 -10000 0 0
KIF3A 0.038 0.012 -10000 0 0 51 51
GLI1 0.014 0.11 -10000 0 -0.39 28 28
RAB23 0.041 0.007 -10000 0 0 15 15
CSNK1A1 0.04 0.009 -10000 0 0 26 26
IFT172 0.04 0.009 -10000 0 0 28 28
RBBP7 0.04 0.009 -10000 0 0 26 26
Su(fu)/Galectin3 0.037 0.058 0.21 1 -0.18 25 26
GNAZ 0.039 0.011 -10000 0 0 42 42
RBBP4 0.038 0.012 -10000 0 0 46 46
CSNK1G1 0.041 0.008 -10000 0 0 19 19
PIAS1 0.04 0.009 -10000 0 0 28 28
PRKACA 0.035 0.015 -10000 0 0 89 89
GLI2/SPOP 0.034 0.08 0.21 1 -0.22 25 26
STK36 0.04 0.011 -10000 0 -0.003 33 33
Gi family/GNB1/GNG2/GDP 0 0.086 -10000 0 -0.26 31 31
PTCH1 0.014 0.1 -10000 0 -0.35 28 28
MIM/GLI1 0.026 0.099 -10000 0 -0.36 19 19
CREBBP 0.047 0.015 -10000 0 -10000 0 0
Su(fu)/SIN3/HDAC complex 0.004 0.11 0.18 7 -0.3 39 46
Class I PI3K signaling events mediated by Akt

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
BCL2L1 -0.016 0.009 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.064 0.063 0.18 81 -0.11 18 99
CDKN1B 0.017 0.093 0.21 39 -0.3 28 67
CDKN1A 0.008 0.085 0.21 14 -0.3 31 45
FRAP1 0.04 0.009 -10000 0 0 27 27
PRKDC 0.039 0.011 -10000 0 0 44 44
FOXO3 0.006 0.08 -10000 0 -0.29 34 34
AKT1 0.006 0.081 -10000 0 -0.31 31 31
BAD 0.041 0.005 -10000 0 0 9 9
AKT3 0.005 0.043 -10000 0 -0.2 23 23
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.006 0.08 -10000 0 -0.29 34 34
AKT1/ASK1 0.027 0.089 -10000 0 -0.28 36 36
BAD/YWHAZ 0.056 0.044 -10000 0 -0.12 7 7
RICTOR 0.037 0.014 -10000 0 0 68 68
RAF1 0.04 0.008 -10000 0 0 21 21
JNK cascade -0.026 0.087 0.28 36 -10000 0 36
TSC1 0.002 0.079 0.23 2 -0.3 31 33
YWHAZ 0.034 0.016 -10000 0 0 102 102
AKT1/RAF1 0.034 0.094 -10000 0 -0.3 34 34
EP300 0.037 0.014 -10000 0 0 72 72
mol:GDP 0.005 0.082 -10000 0 -0.3 34 34
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.001 0.08 -10000 0 -0.3 34 34
YWHAQ 0.04 0.009 -10000 0 0 28 28
TBC1D4 0.007 0.028 0.24 5 -0.17 3 8
MAP3K5 0.037 0.014 -10000 0 0 70 70
MAPKAP1 0.04 0.009 -10000 0 0 27 27
negative regulation of cell cycle -0.027 0.084 0.32 11 -0.22 2 13
YWHAH 0.038 0.013 -10000 0 0 59 59
AKT1S1 0.008 0.082 0.22 11 -0.3 28 39
CASP9 0.002 0.08 -10000 0 -0.3 32 32
YWHAB 0.038 0.012 -10000 0 0 52 52
p27Kip1/KPNA1 0.036 0.11 0.27 10 -0.3 33 43
GBL 0.04 0.009 -10000 0 0 26 26
PDK1/Src/Hsp90 0.05 0.021 -10000 0 -0.11 3 3
YWHAE 0.038 0.013 -10000 0 0 57 57
SRC 0.039 0.01 -10000 0 0 36 36
AKT2/p21CIP1 0.011 0.077 0.21 14 -0.26 28 42
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.021 0.093 -10000 0 -0.35 27 27
CHUK 0 0.081 -10000 0 -0.31 32 32
BAD/BCL-XL 0.027 0.087 -10000 0 -0.3 29 29
mTORC2 0.078 0.062 -10000 0 -0.12 33 33
AKT2 0.016 0.017 -10000 0 -0.2 3 3
FOXO1-3a-4/14-3-3 family 0.028 0.1 0.24 2 -0.37 13 15
PDPK1 0.04 0.009 -10000 0 0 26 26
MDM2 0.005 0.088 0.2 13 -0.3 34 47
MAPKKK cascade -0.034 0.093 0.3 34 -10000 0 34
MDM2/Cbp/p300 0.039 0.1 0.32 3 -0.3 34 37
TSC1/TSC2 -0.003 0.081 0.29 4 -0.29 33 37
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.1 0.31 3 -0.29 34 37
glucose import -0.003 0.034 0.21 11 -0.16 3 14
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.022 0.088 0.28 1 -0.29 17 18
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.003 0.032 0.21 10 -0.16 3 13
GSK3A 0.004 0.08 0.22 3 -0.3 30 33
FOXO1 0.006 0.08 -10000 0 -0.29 34 34
GSK3B 0.006 0.089 0.21 16 -0.3 34 50
SFN 0.036 0.015 -10000 0 0 86 86
G1/S transition of mitotic cell cycle 0.006 0.095 0.31 9 -0.3 33 42
p27Kip1/14-3-3 family 0.023 0.078 -10000 0 -0.31 12 12
PRKACA 0.035 0.015 -10000 0 0 89 89
KPNA1 0.039 0.01 -10000 0 0 33 33
HSP90AA1 0 0 -10000 0 -10000 0 0
YWHAG 0.04 0.009 -10000 0 0 25 25
RHEB 0.037 0.013 -10000 0 0 65 65
CREBBP 0.038 0.012 -10000 0 0 54 54
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.039 0.01 0 34 -9999 0 34
PI3K Class IB/PDE3B 0.039 0.01 -9999 0 0 34 34
PDE3B 0.039 0.01 -9999 0 0 34 34
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.038 0.012 -10000 0 0 51 51
NFATC1 0.019 0.1 0.25 3 -0.31 20 23
NFATC2 0.027 0.058 0.17 9 -0.21 11 20
NFATC3 0.026 0.016 -10000 0 -10000 0 0
YWHAE 0.038 0.013 -10000 0 0 57 57
Calcineurin A alpha-beta B1/CABIN1 -0.004 0.086 0.18 1 -0.27 26 27
Exportin 1/Ran/NUP214 0.067 0.052 -10000 0 -0.12 33 33
mol:DAG 0.001 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.027 0.097 -10000 0 -0.24 21 21
BCL2/BAX 0.051 0.026 -10000 0 -0.14 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.029 0.019 -10000 0 -0.13 5 5
CaM/Ca2+ 0.029 0.019 -10000 0 -0.13 5 5
BAX 0.04 0.008 -10000 0 0 22 22
MAPK14 0.04 0.009 -10000 0 0 28 28
BAD 0.041 0.005 -10000 0 0 9 9
CABIN1/MEF2D 0.013 0.09 -10000 0 -0.26 24 24
Calcineurin A alpha-beta B1/BCL2 0.036 0.014 -10000 0 0 76 76
FKBP8 0.036 0.014 -10000 0 0 74 74
activation-induced cell death of T cells -0.013 0.089 0.25 24 -10000 0 24
KPNB1 0.04 0.01 -10000 0 0 31 31
KPNA2 0.036 0.015 -10000 0 0 86 86
XPO1 0.039 0.011 -10000 0 0 39 39
SFN 0.036 0.015 -10000 0 0 86 86
MAP3K8 0.041 0.008 -10000 0 0 21 21
NFAT4/CK1 alpha 0.028 0.045 0.19 2 -0.13 18 20
MEF2D/NFAT1/Cbp/p300 0.071 0.09 0.24 2 -0.2 12 14
CABIN1 -0.003 0.086 0.18 1 -0.27 26 27
CALM1 0.04 0.01 -10000 0 0 31 31
RAN 0.041 0.006 -10000 0 0 13 13
MAP3K1 0.036 0.014 -10000 0 0 77 77
CAMK4 0.037 0.013 -10000 0 0 64 64
mol:Ca2+ 0.001 0.004 -10000 0 -10000 0 0
MAPK3 0.041 0.007 -10000 0 0 17 17
YWHAH 0.038 0.013 -10000 0 0 59 59
Calcineurin A alpha-beta B1/AKAP79/PKA 0.051 0.027 -10000 0 -0.14 2 2
YWHAB 0.038 0.012 -10000 0 0 52 52
MAPK8 0.04 0.01 -10000 0 0 30 30
MAPK9 0.039 0.011 -10000 0 0 39 39
YWHAG 0.04 0.009 -10000 0 0 25 25
FKBP1A 0.038 0.012 -10000 0 0 50 50
NFAT1-c-4/YWHAQ 0.035 0.11 0.27 2 -0.3 20 22
PRKCH 0.039 0.011 -10000 0 0 41 41
CABIN1/Cbp/p300 0.044 0.051 -10000 0 -0.16 25 25
CASP3 0.037 0.014 -10000 0 0 67 67
PIM1 0.039 0.011 -10000 0 0 45 45
Calcineurin A alpha-beta B1/FKBP12/FK506 0.026 0.012 -10000 0 -0.1 2 2
apoptosis 0.019 0.037 0.13 1 -0.2 11 12
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.026 0.076 -10000 0 -0.27 17 17
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.039 0.01 -10000 0 0 36 36
JNK2/NFAT4 0.026 0.068 -10000 0 -0.14 68 68
BAD/BCL-XL 0.053 0.032 -10000 0 -0.14 11 11
PRKCD 0.038 0.013 -10000 0 0 57 57
NUP214 0.04 0.01 -10000 0 0 33 33
PRKCZ 0.043 0.002 -10000 0 -10000 0 0
PRKCA 0.035 0.015 -10000 0 0 90 90
PRKCG 0.041 0.005 -10000 0 0 7 7
PRKCQ 0.035 0.016 -10000 0 0 92 92
FKBP38/BCL2 0.046 0.03 -10000 0 -0.14 3 3
EP300 0.037 0.014 -10000 0 0 72 72
PRKCB1 0.038 0.012 -10000 0 0 48 48
CSNK2A1 0.038 0.012 -10000 0 0 54 54
NFATc/JNK1 0.033 0.11 0.26 2 -0.3 20 22
CaM/Ca2+/FKBP38 0.047 0.027 -10000 0 -0.13 4 4
FKBP12/FK506 0.028 0.013 -10000 0 -0.13 2 2
CSNK1A1 0.017 0.017 0.093 6 -0.07 6 12
CaM/Ca2+/CAMK IV 0.048 0.028 -10000 0 -0.11 7 7
NFATc/ERK1 0.035 0.11 0.26 3 -0.3 18 21
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.025 0.099 -10000 0 -0.24 24 24
NR4A1 0.018 0.076 0.2 22 -0.22 21 43
GSK3B 0.041 0.009 -10000 0 0 26 26
positive T cell selection 0.025 0.016 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.023 0.047 0.12 7 -0.18 11 18
RCH1/ KPNB1 0.035 0.064 -10000 0 -0.14 60 60
YWHAQ 0.04 0.009 -10000 0 0 28 28
PRKACA 0.036 0.016 -10000 0 0 89 89
AKAP5 0.041 0.008 -10000 0 0 19 19
MEF2D 0.041 0.01 -10000 0 0 28 28
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.034 0.016 -10000 0 0 102 102
NFATc/p38 alpha 0.035 0.1 0.26 3 -0.29 20 23
CREBBP 0.039 0.013 -10000 0 0 54 54
BCL2 0.036 0.014 -10000 0 0 76 76
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.052 0.093 -10000 0 -0.23 26 26
Ran/GTP/Exportin 1/HDAC1 -0.03 0.032 -10000 0 -0.12 48 48
NF kappa B1 p50/RelA/I kappa B alpha 0.026 0.1 0.24 1 -0.3 28 29
SUMO1 0.041 0.006 -10000 0 0 13 13
ZFPM1 0.036 0.015 -10000 0 0 86 86
NPC/RanGAP1/SUMO1/Ubc9 0.009 0.035 -10000 0 -0.14 25 25
FKBP3 0.039 0.01 -10000 0 0 34 34
Histones 0.069 0.087 -10000 0 -0.22 19 19
YY1/LSF 0.012 0.084 0.19 1 -0.22 45 46
SMG5 0 0 -10000 0 -10000 0 0
RAN 0.041 0.006 -10000 0 0 13 13
I kappa B alpha/HDAC3 0.016 0.06 -10000 0 -0.18 39 39
I kappa B alpha/HDAC1 0.031 0.09 0.22 1 -0.22 50 51
SAP18 0.039 0.01 -10000 0 0 34 34
RELA 0.018 0.086 0.22 3 -0.37 13 16
HDAC1/Smad7 0.062 0.053 -10000 0 -0.12 33 33
RANGAP1 0.038 0.013 -10000 0 0 56 56
HDAC3/TR2 0.047 0.061 0.22 1 -0.2 19 20
NuRD/MBD3 Complex 0.01 0.098 0.17 5 -0.28 33 38
NF kappa B1 p50/RelA 0.023 0.1 0.25 1 -0.28 32 33
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.039 0.01 -10000 0 0 35 35
GATA1 0.042 0.002 -10000 0 0 1 1
Mad/Max 0.059 0.014 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.005 0.1 -10000 0 -0.27 38 38
RBBP7 0.04 0.009 -10000 0 0 26 26
NPC 0.02 0.022 -10000 0 -0.085 23 23
RBBP4 0.039 0.012 -10000 0 0 46 46
MAX 0.041 0.007 -10000 0 0 16 16
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.04 0.009 -10000 0 0 25 25
NFKBIA 0.009 0.071 -10000 0 -0.27 30 30
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.006 0.091 -10000 0 -0.28 31 31
SIN3 complex 0.076 0.054 -10000 0 -0.12 10 10
SMURF1 0.041 0.008 -10000 0 0 19 19
CHD3 0.038 0.012 -10000 0 0 54 54
SAP30 0.038 0.012 -10000 0 0 54 54
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.037 0.013 -10000 0 0 61 61
YY1/HDAC3 0.017 0.077 -10000 0 -0.23 30 30
YY1/HDAC2 0.016 0.078 0.19 1 -0.21 41 42
YY1/HDAC1 0.012 0.08 0.19 1 -0.22 41 42
NuRD/MBD2 Complex (MeCP1) 0.011 0.098 -10000 0 -0.29 30 30
PPARG 0.031 0.067 0.2 6 -0.2 24 30
HDAC8/hEST1B 0.042 0.036 -10000 0 -0.11 20 20
UBE2I 0.04 0.009 -10000 0 0 28 28
beta TrCP1/SCF ubiquitin ligase complex 0.04 0.009 -10000 0 0 25 25
TNFRSF1A 0.036 0.015 -10000 0 0 84 84
HDAC3/SMRT (N-CoR2) 0.048 0.06 0.22 1 -0.2 18 19
MBD3L2 0.039 0.011 -10000 0 0 40 40
ubiquitin-dependent protein catabolic process 0.061 0.053 -10000 0 -0.12 33 33
CREBBP 0.038 0.012 -10000 0 0 54 54
NuRD/MBD3/MBD3L2 Complex 0.008 0.1 0.19 8 -0.28 39 47
HDAC1 0.038 0.013 -10000 0 0 56 56
HDAC3 0.022 0.038 -10000 0 -0.29 5 5
HDAC2 0.038 0.012 -10000 0 0 48 48
YY1 0.006 0.056 -10000 0 -0.24 24 24
HDAC8 0.04 0.009 -10000 0 0 26 26
SMAD7 0.039 0.011 -10000 0 0 45 45
NCOR2 0.04 0.009 -10000 0 0 28 28
MXD1 0.041 0.007 -10000 0 0 18 18
STAT3 0.009 0.066 -10000 0 -0.24 32 32
NFKB1 0.036 0.015 -10000 0 0 83 83
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.04 0.009 -10000 0 0 30 30
YY1/LSF/HDAC1 0.022 0.093 0.2 1 -0.21 48 49
YY1/SAP30/HDAC1 0.025 0.086 0.2 1 -0.2 42 43
EP300 0.037 0.014 -10000 0 0 72 72
STAT3 (dimer non-phopshorylated) 0.009 0.066 -10000 0 -0.24 32 32
proteasomal ubiquitin-dependent protein catabolic process 0.009 0.071 -10000 0 -0.27 30 30
histone deacetylation 0.011 0.097 -10000 0 -0.29 30 30
STAT3 (dimer non-phopshorylated)/HDAC3 0.021 0.084 -10000 0 -0.28 22 22
nuclear export -0.041 0.036 0.11 20 -10000 0 20
PRKACA 0.035 0.015 -10000 0 0 89 89
GATAD2B 0.038 0.012 -10000 0 0 52 52
GATAD2A 0.038 0.013 -10000 0 0 59 59
GATA2/HDAC3 0.048 0.059 0.22 1 -0.2 18 19
GATA1/HDAC1 0.049 0.044 -10000 0 -0.14 27 27
GATA1/HDAC3 0.051 0.06 0.22 1 -0.2 18 19
CHD4 0.036 0.015 -10000 0 0 79 79
TNF-alpha/TNFR1A 0.047 0.038 -10000 0 -0.14 15 15
SIN3/HDAC complex/Mad/Max 0.01 0.092 -10000 0 -0.29 27 27
NuRD Complex 0.004 0.1 0.19 8 -0.27 40 48
positive regulation of chromatin silencing 0.065 0.085 -10000 0 -0.21 19 19
SIN3B 0.037 0.013 -10000 0 0 65 65
MTA2 0.041 0.005 -10000 0 0 9 9
SIN3A 0.04 0.009 -10000 0 0 28 28
XPO1 0.039 0.011 -10000 0 0 39 39
SUMO1/HDAC1 0.037 0.065 -10000 0 -0.18 26 26
HDAC complex 0.072 0.078 -10000 0 -0.14 55 55
GATA1/Fog1 0.053 0.022 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.057 0.061 -10000 0 -0.13 44 44
TNF 0.04 0.009 -10000 0 0 26 26
negative regulation of cell growth 0.01 0.091 -10000 0 -0.29 27 27
NuRD/MBD2/PRMT5 Complex 0.011 0.098 -10000 0 -0.29 30 30
Ran/GTP/Exportin 1 0.038 0.072 0.18 1 -0.18 36 37
NF kappa B/RelA/I kappa B alpha 0.016 0.083 -10000 0 -0.29 24 24
SIN3/HDAC complex/NCoR1 -0.001 0.096 0.17 1 -0.25 47 48
TFCP2 0.039 0.01 -10000 0 0 37 37
NR2C1 0.039 0.011 -10000 0 0 41 41
MBD3 0.037 0.014 -10000 0 0 67 67
MBD2 0.039 0.011 -10000 0 0 43 43
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.014 0.078 -10000 0 -0.15 93 93
AKT1 0.013 0.1 0.28 12 -0.3 20 32
PTK2B -0.012 0.078 0.19 24 -0.21 29 53
VEGFR2 homodimer/Frs2 0.033 0.057 -10000 0 -0.14 39 39
CAV1 0.036 0.015 -10000 0 0 80 80
CALM1 0.04 0.01 -10000 0 0 31 31
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.031 0.058 -10000 0 -0.31 5 5
endothelial cell proliferation 0.035 0.098 0.26 27 -0.27 11 38
mol:Ca2+ 0.019 0.063 0.2 24 -0.28 8 32
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.046 0.078 -10000 0 -0.21 20 20
RP11-342D11.1 -0.006 0.057 0.17 22 -0.26 8 30
CDH5 0.036 0.015 -10000 0 0 79 79
VEGFA homodimer 0.065 0.049 -10000 0 -0.11 33 33
SHC1 0.04 0.01 -10000 0 0 31 31
SHC2 0.037 0.013 -10000 0 0 64 64
HRAS/GDP 0.039 0.069 -10000 0 -0.24 11 11
SH2D2A 0.039 0.01 -10000 0 0 33 33
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.052 0.084 0.28 3 -0.33 9 12
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.035 0.053 -10000 0 -0.26 6 6
VEGFR1 homodimer 0.04 0.01 -10000 0 0 32 32
SHC/GRB2/SOS1 0.073 0.085 -10000 0 -0.25 11 11
GRB10 0.019 0.069 0.2 24 -0.34 9 33
PTPN11 0.04 0.009 -10000 0 0 27 27
GRB2 0.041 0.007 -10000 0 0 16 16
PAK1 0.037 0.014 -10000 0 0 70 70
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.051 0.089 -10000 0 -0.21 22 22
HRAS 0.04 0.01 -10000 0 0 31 31
VEGF/Rho/ROCK1/Integrin Complex -0.014 0.11 -10000 0 -0.25 79 79
HIF1A 0.039 0.011 -10000 0 0 42 42
FRS2 0.039 0.011 -10000 0 0 40 40
oxygen and reactive oxygen species metabolic process 0.045 0.077 -10000 0 -0.21 20 20
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.04 0.008 -10000 0 0 21 21
Nck/Pak 0.036 0.056 -10000 0 -0.14 43 43
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.023 0.062 -10000 0 -0.25 8 8
mol:GDP 0.056 0.076 -10000 0 -0.24 11 11
mol:NADP 0.038 0.081 0.27 10 -0.3 11 21
eNOS/Hsp90 0.035 0.076 0.26 9 -0.28 11 20
PIK3R1 0.034 0.017 -10000 0 0 107 107
mol:IP3 0.019 0.064 0.2 24 -0.28 8 32
HIF1A/ARNT 0.05 0.044 -10000 0 -0.14 25 25
SHB 0.041 0.007 -10000 0 0 17 17
VEGFA 0.002 0.004 -10000 0 -0.037 6 6
VEGFC 0.036 0.015 -10000 0 0 79 79
FAK1/Vinculin 0.013 0.13 0.27 8 -0.27 52 60
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.041 0.007 -10000 0 0 14 14
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.023 0.088 -10000 0 -0.21 33 33
PTPN6 0.037 0.014 -10000 0 0 67 67
EPAS1 0.043 0.031 -10000 0 -0.15 7 7
mol:L-citrulline 0.038 0.081 0.27 10 -0.3 11 21
ITGAV 0.033 0.017 -10000 0 0 117 117
PIK3CA 0.03 0.019 -10000 0 0 155 155
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.054 0.07 -10000 0 -0.29 6 6
VEGFR2 homodimer/VEGFA homodimer 0.044 0.062 -10000 0 -0.29 8 8
VEGFR2/3 heterodimer 0.034 0.058 -10000 0 -0.14 40 40
VEGFB 0.039 0.011 -10000 0 0 42 42
MAPK11 -0.004 0.07 0.21 14 -0.29 11 25
VEGFR2 homodimer 0.022 0.044 -10000 0 -0.38 5 5
FLT1 0.04 0.01 -10000 0 0 32 32
NEDD4 0.041 0.014 -10000 0 -0.054 5 5
MAPK3 -0.002 0.073 0.19 36 -0.28 8 44
MAPK1 -0.002 0.074 0.19 38 -0.3 7 45
VEGFA145/NRP2 0.016 0.045 -10000 0 -0.12 49 49
VEGFR1/2 heterodimer 0.034 0.058 -10000 0 -0.14 40 40
KDR 0.022 0.044 -10000 0 -0.38 5 5
VEGFA165/NRP1/VEGFR2 homodimer 0.033 0.073 -10000 0 -0.21 20 20
SRC 0.039 0.01 -10000 0 0 36 36
platelet activating factor biosynthetic process 0 0.077 0.2 32 -0.3 7 39
PI3K 0.012 0.081 0.26 3 -0.28 13 16
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.025 0.063 -10000 0 -0.24 11 11
FES 0.02 0.065 0.2 27 -0.27 8 35
GAB1 0.019 0.084 0.26 5 -0.31 16 21
VEGFR2 homodimer/VEGFA homodimer/Src 0.035 0.053 -10000 0 -0.26 6 6
CTNNB1 0.04 0.01 -10000 0 0 31 31
SOS1 0.038 0.013 -10000 0 0 56 56
ARNT 0.041 0.006 -10000 0 0 12 12
eNOS/Caveolin-1 0.045 0.083 0.29 6 -0.3 11 17
VEGFR2 homodimer/VEGFA homodimer/Yes 0.028 0.062 -10000 0 -0.25 9 9
PI3K/GAB1 0.024 0.11 0.26 8 -0.31 20 28
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.049 0.084 -10000 0 -0.21 12 12
PRKACA 0.035 0.015 -10000 0 0 89 89
VEGFR2/3 heterodimer/VEGFC homodimer 0.051 0.067 -10000 0 -0.29 6 6
HSP90AA1 0 0 -10000 0 -10000 0 0
CDC42 0.019 0.064 0.2 26 -0.28 8 34
actin cytoskeleton reorganization 0.034 0.052 -10000 0 -0.25 6 6
PTK2 -0.004 0.11 0.25 2 -0.28 46 48
EDG1 0.02 0.062 0.2 22 -0.27 8 30
mol:DAG 0.019 0.064 0.2 24 -0.28 8 32
CaM/Ca2+ 0.033 0.065 0.2 19 -0.27 8 27
MAP2K3 -0.009 0.059 0.19 21 -0.26 9 30
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.047 0.073 0.24 5 -0.34 9 14
PLCG1 0.019 0.064 0.2 24 -0.29 8 32
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.059 0.064 -10000 0 -0.27 5 5
IQGAP1 0.037 0.014 -10000 0 0 69 69
YES1 0.038 0.013 -10000 0 0 57 57
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.031 0.061 -10000 0 -0.26 8 8
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.033 0.053 -10000 0 -0.28 6 6
cell migration 0 0.13 0.26 8 -0.33 40 48
mol:PI-3-4-5-P3 0.012 0.078 0.25 3 -0.27 13 16
FYN 0.034 0.016 -10000 0 0 104 104
VEGFB/NRP1 0.026 0.062 0.19 24 -0.24 10 34
mol:NO 0.038 0.081 0.27 10 -0.3 11 21
PXN 0.041 0.007 -10000 0 0 14 14
HRAS/GTP 0.017 0.057 -10000 0 -0.24 11 11
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.026 0.062 -10000 0 -0.34 9 9
VHL 0.04 0.009 -10000 0 0 28 28
ITGB3 0.033 0.017 -10000 0 0 121 121
NOS3 0.039 0.086 0.3 7 -0.33 11 18
VEGFR2 homodimer/VEGFA homodimer/Sck 0.031 0.055 -10000 0 -0.28 6 6
RAC1 0.039 0.01 -10000 0 0 33 33
PRKCA -0.008 0.065 0.19 25 -0.22 15 40
PRKCB -0.007 0.059 0.18 25 -0.27 8 33
VCL 0.039 0.01 -10000 0 0 35 35
VEGFA165/NRP1 0.01 0.055 0.17 19 -0.26 8 27
VEGFR1/2 heterodimer/VEGFA homodimer 0.034 0.057 -10000 0 -0.26 8 8
VEGFA165/NRP2 0.016 0.045 -10000 0 -0.12 49 49
MAPKKK cascade -0.023 0.07 0.19 23 -0.33 8 31
NRP2 0.035 0.016 -10000 0 0 94 94
VEGFC homodimer 0.036 0.015 -10000 0 0 79 79
NCK1 0.036 0.015 -10000 0 0 79 79
ROCK1 0.041 0.007 -10000 0 0 14 14
FAK1/Paxillin 0.015 0.12 0.27 8 -0.29 40 48
MAP3K13 0.014 0.062 0.2 22 -0.26 9 31
PDPK1 -0.003 0.067 0.24 3 -0.24 11 14
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.034 0.016 -10000 0 0 101 101
CDC42/GTP 0.007 0.085 -10000 0 -0.22 36 36
PLCG1 -0.013 0.072 -10000 0 -0.18 69 69
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.041 0.007 -10000 0 0 15 15
GNAI3 0.039 0.011 -10000 0 0 45 45
G12/G13 0.054 0.03 -10000 0 -0.14 9 9
cell migration 0.007 0.084 -10000 0 -0.22 36 36
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
MAPK3 -0.013 0.073 -10000 0 -0.18 68 68
MAPK1 -0.006 0.062 -10000 0 -0.16 58 58
S1P/S1P5/Gi -0.005 0.078 -10000 0 -0.18 70 70
GNAI1 0.035 0.016 -10000 0 0 95 95
CDC42/GDP 0.029 0.014 -10000 0 -0.13 4 4
S1P/S1P5/G12 0.027 0.007 -10000 0 -10000 0 0
RHOA -0.012 0.038 0.18 17 -0.17 1 18
S1P/S1P4/Gi -0.005 0.078 -10000 0 -0.18 70 70
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.039 0.011 -10000 0 0 42 42
S1P/S1P4/G12/G13 0.047 0.024 -10000 0 -0.098 9 9
GNA12 0.04 0.01 -10000 0 0 32 32
GNA13 0.04 0.009 -10000 0 0 28 28
CDC42 0.04 0.009 -10000 0 0 24 24
Ephrin A reverse signaling

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
MAPKKK cascade 0.037 0.041 -10000 0 -0.11 31 31
EFNA5 0.034 0.016 -10000 0 0 103 103
FYN -0.013 0.036 0.18 7 -10000 0 7
neuron projection morphogenesis 0.037 0.041 -10000 0 -0.11 31 31
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.038 0.042 -10000 0 -0.11 31 31
EPHA5 0.04 0.009 -10000 0 0 25 25
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 0.07 0.067 -10000 0 -0.11 43 43
MAP4K1 0.039 0.012 -10000 0 0 46 46
MAP3K8 0.04 0.008 -10000 0 0 21 21
PRKCB 0 0 -10000 0 -10000 0 0
DBNL 0.041 0.007 -10000 0 0 17 17
CRKL 0.039 0.011 -10000 0 0 38 38
MAP3K1 0.004 0.061 -10000 0 -0.23 18 18
JUN -0.007 0.11 0.25 1 -0.51 23 24
MAP3K7 0.005 0.064 0.21 5 -0.22 19 24
GRAP2 0.038 0.013 -10000 0 0 56 56
CRK 0.038 0.012 -10000 0 0 51 51
MAP2K4 -0.005 0.078 0.23 1 -0.28 23 24
LAT 0.041 0.006 -10000 0 0 13 13
LCP2 0.034 0.016 -10000 0 0 102 102
MAPK8 -0.003 0.12 -10000 0 -0.55 23 23
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.016 0.066 -10000 0 -0.22 18 18
LAT/GRAP2/SLP76/HPK1/HIP-55 0.079 0.077 -10000 0 -0.12 40 40
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.019 0.006 0 42 -10000 0 42
MAP4K4 -0.002 0.08 0.2 2 -0.25 28 30
BAG4 0.037 0.013 -10000 0 0 64 64
PKC zeta/ceramide 0.032 0.031 -10000 0 -0.18 8 8
NFKBIA 0.037 0.014 -10000 0 0 66 66
BIRC3 0.026 0.02 -10000 0 0 218 218
BAX 0.012 0.058 -10000 0 -0.34 14 14
RIPK1 0.038 0.012 -10000 0 0 48 48
AKT1 0.001 0.12 0.67 17 -10000 0 17
BAD 0.001 0.03 0.18 4 -0.18 8 12
SMPD1 0.01 0.06 0.16 17 -0.17 25 42
RB1 -0.006 0.038 0.22 2 -0.18 8 10
FADD/Caspase 8 -0.004 0.11 0.25 8 -0.31 37 45
MAP2K4 -0.006 0.027 -10000 0 -0.18 7 7
NSMAF 0.038 0.012 -10000 0 0 54 54
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.005 0.033 0.18 7 -0.18 8 15
EGF 0.038 0.012 -10000 0 0 52 52
mol:ceramide 0.006 0.027 -10000 0 -0.19 8 8
MADD 0.041 0.006 -10000 0 0 11 11
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.016 0.009 0 142 -10000 0 142
ASAH1 0.032 0.018 -10000 0 0 128 128
negative regulation of cell cycle -0.006 0.038 0.22 2 -0.18 8 10
cell proliferation 0.026 0.051 0.21 1 -0.19 6 7
BID 0.02 0.095 -10000 0 -0.5 7 7
MAP3K1 -0.001 0.027 -10000 0 -0.18 7 7
EIF2A 0.009 0.079 0.18 71 -0.2 8 79
TRADD 0.036 0.014 -10000 0 0 76 76
CRADD 0.041 0.006 -10000 0 0 13 13
MAPK3 -0.003 0.037 0.18 5 -0.19 5 10
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.009 0.044 0.17 5 -0.18 5 10
Cathepsin D/ceramide 0.03 0.032 -10000 0 -0.18 8 8
FADD -0.001 0.083 0.21 6 -0.25 28 34
KSR1 -0.001 0.026 -10000 0 -0.18 8 8
MAPK8 0.008 0.048 -10000 0 -0.21 14 14
PRKRA 0.004 0.044 0.2 17 -0.18 7 24
PDGFA 0.041 0.007 -10000 0 0 18 18
TRAF2 0.04 0.009 -10000 0 0 29 29
IGF1 0.036 0.015 -10000 0 0 84 84
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process 0.006 0.027 -10000 0 -0.19 8 8
CTSD 0.038 0.012 -10000 0 0 54 54
regulation of nitric oxide biosynthetic process 0.043 0.05 -10000 0 -0.14 36 36
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.029 0.054 0.22 1 -0.2 6 7
PRKCD 0.038 0.013 -10000 0 0 57 57
PRKCZ 0.042 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.016 0.009 0 142 -10000 0 142
RelA/NF kappa B1 0.043 0.05 -10000 0 -0.14 36 36
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.041 0.007 -10000 0 0 18 18
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.005 0.086 -10000 0 -0.26 28 28
TNFR1A/BAG4/TNF-alpha 0.059 0.046 -10000 0 -0.12 15 15
mol:Sphingosine-1-phosphate -0.019 0.006 0 42 -10000 0 42
MAP2K1 -0.009 0.036 0.17 11 -0.18 5 16
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.041 0.006 -10000 0 0 10 10
CYCS 0.009 0.05 0.14 3 -0.19 11 14
TNFRSF1A 0.036 0.015 -10000 0 0 84 84
NFKB1 0.036 0.015 -10000 0 0 83 83
TNFR1A/BAG4 0.044 0.038 -10000 0 -0.13 14 14
EIF2AK2 -0.001 0.057 0.19 30 -0.18 10 40
TNF-alpha/TNFR1A/FAN 0.059 0.052 -10000 0 -0.13 21 21
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.005 0.14 -10000 0 -0.4 47 47
MAP2K2 -0.008 0.033 0.17 6 -0.18 6 12
SMPD3 -0.004 0.1 0.2 5 -0.3 49 54
TNF 0.04 0.009 -10000 0 0 26 26
PKC zeta/PAR4 0.06 0.016 -10000 0 -0.14 2 2
mol:PHOSPHOCHOLINE 0.004 0.035 0.14 1 -0.14 8 9
NF kappa B1/RelA/I kappa B alpha 0.081 0.083 -10000 0 -0.12 62 62
AIFM1 0.01 0.042 0.14 1 -0.17 11 12
BCL2 0.036 0.014 -10000 0 0 76 76
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.007 0.085 0.22 36 -10000 0 36
GNAI2 0.041 0.007 -10000 0 0 15 15
S1P/S1P5/G12 0.027 0.007 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.034 0.016 -10000 0 0 101 101
RhoA/GTP 0.007 0.086 -10000 0 -0.23 36 36
negative regulation of cAMP metabolic process -0.005 0.078 -10000 0 -0.18 70 70
GNAZ 0.039 0.011 -10000 0 0 42 42
GNAI3 0.039 0.011 -10000 0 0 45 45
GNA12 0.04 0.01 -10000 0 0 32 32
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.005 0.078 -10000 0 -0.18 70 70
RhoA/GDP 0.03 0.012 -10000 0 -0.13 3 3
RHOA 0.041 0.007 -10000 0 0 14 14
GNAI1 0.035 0.016 -10000 0 0 95 95
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.037 0.016 -10000 0 -0.057 3 3
HSPA8 0.039 0.01 -10000 0 0 34 34
SMAD3/SMAD4/ER alpha 0.065 0.092 0.26 10 -0.17 16 26
AKT1 0.04 0.017 -10000 0 -0.098 5 5
GSC 0.008 0.096 -10000 0 -0.95 3 3
NKX2-5 0.039 0.017 -10000 0 -0.053 13 13
muscle cell differentiation -0.04 0.11 0.29 14 -10000 0 14
SMAD2-3/SMAD4/SP1 0.072 0.12 -10000 0 -0.22 6 6
SMAD4 0.036 0.046 -10000 0 -0.1 14 14
CBFB 0.036 0.015 -10000 0 0 82 82
SAP18 0.039 0.01 -10000 0 0 34 34
Cbp/p300/MSG1 0.06 0.056 -10000 0 -0.14 23 23
SMAD3/SMAD4/VDR 0.074 0.1 -10000 0 -0.2 14 14
MYC 0.021 0.022 0.12 4 -0.044 2 6
CDKN2B -0.045 0.16 -10000 0 -0.77 13 13
AP1 0.004 0.091 -10000 0 -0.24 36 36
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.001 0.13 0.2 3 -0.3 55 58
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.012 0.063 -10000 0 -0.2 35 35
SP3 0.037 0.024 0.08 2 -0.038 47 49
CREB1 0.041 0.008 -10000 0 0 19 19
FOXH1 0.041 0.019 -10000 0 -0.059 17 17
SMAD3/SMAD4/GR 0.054 0.079 -10000 0 -0.14 24 24
GATA3 0.042 0.012 -10000 0 -10000 0 0
SKI/SIN3/HDAC complex/NCoR1 0.004 0.096 0.17 6 -0.26 39 45
MEF2C/TIF2 0.023 0.068 0.34 2 -0.22 14 16
endothelial cell migration -0.031 0.1 1 4 -10000 0 4
MAX 0.029 0.027 0.098 3 -0.036 78 81
RBBP7 0.04 0.009 -10000 0 0 26 26
RBBP4 0.038 0.012 -10000 0 0 46 46
RUNX2 0.039 0.011 -10000 0 0 45 45
RUNX3 0.039 0.01 -10000 0 0 33 33
RUNX1 0.039 0.01 -10000 0 0 33 33
CTBP1 0.038 0.012 -10000 0 0 55 55
NR3C1 0.027 0.028 0.098 3 -0.036 78 81
VDR 0.038 0.013 -10000 0 0 56 56
CDKN1A 0.012 0.076 -10000 0 -0.61 3 3
KAT2B 0 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.082 0.059 -10000 0 -0.28 2 2
DCP1A 0.04 0.008 -10000 0 0 21 21
SKI 0.042 0.003 -10000 0 0 3 3
SERPINE1 0.03 0.1 -10000 0 -1 4 4
SMAD3/SMAD4/ATF2 0.064 0.075 -10000 0 -0.16 16 16
SMAD3/SMAD4/ATF3 0.061 0.068 -10000 0 -0.14 9 9
SAP30 0.038 0.012 -10000 0 0 54 54
Cbp/p300/PIAS3 0.061 0.058 -10000 0 -0.14 28 28
JUN -0.001 0.087 0.19 3 -0.24 34 37
SMAD3/SMAD4/IRF7 0.071 0.07 -10000 0 -0.14 8 8
TFE3 0.038 0.033 0.11 1 -0.081 37 38
COL1A2 -0.091 0.26 -10000 0 -0.62 103 103
mesenchymal cell differentiation -0.064 0.07 0.14 10 -10000 0 10
DLX1 0.041 0.008 -10000 0 0 19 19
TCF3 0.037 0.014 -10000 0 0 71 71
FOS 0.025 0.029 -10000 0 -0.051 27 27
SMAD3/SMAD4/Max 0.063 0.067 -10000 0 -0.14 7 7
Cbp/p300/SNIP1 0.058 0.056 -10000 0 -0.14 24 24
ZBTB17 0.039 0.012 0.1 4 -0.042 4 8
LAMC1 0.009 0.073 -10000 0 -0.26 25 25
TGIF2/HDAC complex/SMAD3/SMAD4 0.062 0.074 -10000 0 -0.15 17 17
IRF7 0.041 0.012 0.087 1 -10000 0 1
ESR1 0.046 0.037 0.12 91 0 93 184
HNF4A 0.038 0.012 -10000 0 0 47 47
MEF2C -0.003 0.061 0.22 11 -0.24 13 24
SMAD2-3/SMAD4 0.071 0.074 -10000 0 -0.14 6 6
Cbp/p300/Src-1 0.058 0.061 -10000 0 -0.14 33 33
IGHV3OR16-13 0.009 0.061 -10000 0 -0.43 10 10
TGIF2/HDAC complex 0.038 0.012 -10000 0 0 54 54
CREBBP 0.038 0.014 -10000 0 -0.045 2 2
SKIL 0.025 0.021 -10000 0 0 228 228
HDAC1 0.038 0.013 -10000 0 0 56 56
HDAC2 0.038 0.012 -10000 0 0 48 48
SNIP1 0.039 0.011 -10000 0 0 38 38
GCN5L2 0.039 0.013 -10000 0 -0.045 3 3
SMAD3/SMAD4/TFE3 0.079 0.083 -10000 0 -0.16 24 24
MSG1/HSC70 0.053 0.027 -10000 0 -0.14 5 5
SMAD2 0.039 0.025 -10000 0 -0.064 20 20
SMAD3 0.035 0.046 -10000 0 -0.096 19 19
SMAD3/E2F4-5/DP1/p107/SMAD4 0.02 0.066 0.18 1 -0.2 18 19
SMAD2/SMAD2/SMAD4 -0.009 0.06 0.17 7 -0.18 41 48
NCOR1 0.037 0.013 -10000 0 0 61 61
NCOA2 0.037 0.014 -10000 0 0 70 70
NCOA1 0.04 0.009 -10000 0 0 28 28
MYOD/E2A 0.052 0.024 -10000 0 -0.14 1 1
SMAD2-3/SMAD4/SP1/MIZ-1 0.082 0.12 -10000 0 -0.23 4 4
IFNB1 0.012 0.052 0.23 5 -0.16 2 7
SMAD3/SMAD4/MEF2C 0.052 0.084 0.3 1 -0.23 14 15
CITED1 0.039 0.01 -10000 0 0 35 35
SMAD2-3/SMAD4/ARC105 0.068 0.068 -10000 0 -0.13 4 4
RBL1 0.037 0.013 -10000 0 0 61 61
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.024 0.074 -10000 0 -0.4 7 7
RUNX1-3/PEBPB2 0.064 0.044 -10000 0 -0.11 14 14
SMAD7 -0.003 0.14 -10000 0 -0.4 26 26
MYC/MIZ-1 0.017 0.059 0.2 4 -0.14 54 58
SMAD3/SMAD4 -0.006 0.1 0.26 1 -0.35 25 26
IL10 0.022 0.061 0.22 18 -10000 0 18
PIASy/HDAC complex 0.037 0.014 -10000 0 -0.037 5 5
PIAS3 0.04 0.01 -10000 0 -0.035 3 3
CDK2 0.038 0.015 -10000 0 -0.043 3 3
IL5 0.022 0.06 0.23 14 -10000 0 14
CDK4 0.038 0.015 -10000 0 -0.045 3 3
PIAS4 0.037 0.015 -10000 0 -0.037 5 5
ATF3 0.037 0.014 -10000 0 0 69 69
SMAD3/SMAD4/SP1 0.054 0.11 -10000 0 -0.18 27 27
FOXG1 -0.001 0.001 -10000 0 -10000 0 0
FOXO3 0.01 0.012 -10000 0 -0.11 5 5
FOXO1 0.01 0.012 -10000 0 -0.11 5 5
FOXO4 0.01 0.012 -10000 0 -0.11 5 5
heart looping -0.003 0.061 0.22 11 -0.23 13 24
CEBPB 0.036 0.018 -10000 0 -0.004 84 84
SMAD3/SMAD4/DLX1 0.069 0.067 -10000 0 -0.14 7 7
MYOD1 0.04 0.008 -10000 0 0 20 20
SMAD3/SMAD4/HNF4 0.065 0.068 -10000 0 -0.14 7 7
SMAD3/SMAD4/GATA3 0.078 0.071 -10000 0 -0.17 1 1
SnoN/SIN3/HDAC complex/NCoR1 0.025 0.021 -10000 0 0 228 228
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.085 0.084 -10000 0 -0.16 2 2
SMAD3/SMAD4/SP1-3 0.07 0.12 -10000 0 -0.21 25 25
MED15 0 0 -10000 0 -10000 0 0
SP1 0.018 0.066 -10000 0 -0.1 121 121
SIN3B 0.037 0.013 -10000 0 0 65 65
SIN3A 0.04 0.009 -10000 0 0 28 28
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.1 0.073 -10000 0 -0.17 12 12
ITGB5 -0.006 0.094 0.21 13 -0.26 34 47
TGIF/SIN3/HDAC complex/CtBP 0.007 0.089 -10000 0 -0.26 34 34
SMAD3/SMAD4/AR 0.042 0.091 -10000 0 -0.16 32 32
AR 0.033 0.017 -10000 0 0 122 122
negative regulation of cell growth 0.019 0.074 -10000 0 -0.25 17 17
SMAD3/SMAD4/MYOD 0.068 0.068 -10000 0 -0.14 7 7
E2F5 0.037 0.014 -10000 0 0 71 71
E2F4 0.036 0.015 -10000 0 0 79 79
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.098 0.081 -10000 0 -0.16 5 5
SMAD2-3/SMAD4/FOXO1-3a-4 0.025 0.052 -10000 0 -0.29 7 7
TFDP1 0.038 0.012 -10000 0 0 53 53
SMAD3/SMAD4/AP1 0.033 0.11 -10000 0 -0.24 35 35
SMAD3/SMAD4/RUNX2 0.065 0.07 -10000 0 -0.14 10 10
TGIF2 0.038 0.012 -10000 0 0 54 54
TGIF1 0 0 -10000 0 -10000 0 0
ATF2 0.04 0.01 -10000 0 0 31 31
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.019 0.015 0.058 14 -10000 0 14
SNTA1 0.039 0.011 -10000 0 0 44 44
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.018 0.016 0.058 14 -10000 0 14
MAPK12 -0.008 0.043 0.21 7 -0.16 17 24
CCND1 -0.038 0.13 -10000 0 -0.37 72 72
p38 gamma/SNTA1 0.023 0.071 0.22 12 -0.17 31 43
MAP2K3 0.038 0.012 -10000 0 0 47 47
PKN1 0.035 0.016 -10000 0 0 99 99
G2/M transition checkpoint -0.008 0.043 0.21 7 -0.16 17 24
MAP2K6 0.004 0.047 0.24 6 -0.17 22 28
MAPT 0 0.054 0.16 9 -0.19 16 25
MAPK13 -0.017 0.008 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.003 0.05 -10000 0 -0.2 32 32
Atypical NF-kappaB 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
BCL3/RelA 0.055 0.026 -10000 0 -0.16 5 5
FBXW11 0.04 0.009 -10000 0 0 25 25
NF kappa B1 p50/c-Rel 0.027 0.038 -10000 0 -0.12 29 29
NF kappa B1 p50/RelA/I kappa B alpha 0.021 0.076 -10000 0 -0.22 22 22
NFKBIA 0.006 0.062 -10000 0 -0.15 50 50
MAPK14 0.04 0.009 -10000 0 0 28 28
NF kappa B1 p105/p50 0.027 0.039 -10000 0 -0.12 29 29
ARRB2 0.014 0.028 -10000 0 -0.2 9 9
REL 0.04 0.008 -10000 0 0 20 20
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.025 0.039 -10000 0 -0.12 30 30
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.027 0.039 -10000 0 -0.12 31 31
PIK3CA 0.03 0.019 -10000 0 0 155 155
NF kappa B1 p50 dimer 0.019 0.041 0.1 4 -0.14 31 35
PIK3R1 0.034 0.017 -10000 0 0 107 107
NFKB1 -0.017 0.009 -10000 0 -10000 0 0
RELA 0.041 0.006 -10000 0 0 10 10
positive regulation of anti-apoptosis 0.013 0.051 0.14 2 -0.18 12 14
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.024 0.082 -10000 0 -0.23 21 21
SRC 0.039 0.01 -10000 0 0 36 36
PI3K 0.024 0.061 -10000 0 -0.15 47 47
NF kappa B1 p50/RelA 0.013 0.052 0.14 2 -0.18 12 14
IKBKB 0.039 0.011 -10000 0 0 43 43
beta TrCP1/SCF ubiquitin ligase complex 0.04 0.009 -10000 0 0 25 25
SYK 0.037 0.014 -10000 0 0 70 70
I kappa B alpha/PIK3R1 0.018 0.068 0.19 1 -0.22 14 15
cell death 0.02 0.077 -10000 0 -0.22 21 21
NF kappa B1 p105/c-Rel 0.027 0.038 -10000 0 -0.12 29 29
LCK 0.04 0.009 -10000 0 0 29 29
BCL3 0.039 0.011 -10000 0 0 40 40
Insulin Pathway

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
CBL/APS/CAP 0.06 0.041 -10000 0 -0.11 11 11
TC10/GTP 0.05 0.036 -10000 0 -0.11 10 10
Insulin Receptor/Insulin/IRS1/Shp2 0.089 0.058 -10000 0 -0.12 23 23
HRAS 0.04 0.01 -10000 0 0 31 31
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 0.038 0.012 -10000 0 0 53 53
FOXO3 -0.005 0.009 0.021 11 -0.037 5 16
AKT1 0.015 0.098 0.23 40 -0.18 3 43
INSR 0.042 0.016 0.081 15 0 53 68
Insulin Receptor/Insulin 0.081 0.053 0.24 28 -0.1 3 31
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.04 0.009 -10000 0 0 24 24
SORBS1 0.039 0.011 -10000 0 0 40 40
CRK 0.038 0.012 -10000 0 0 51 51
PTPN1 -0.005 0.042 0.15 36 -10000 0 36
CAV1 -0.007 0.042 0.17 18 -10000 0 18
CBL/APS/CAP/Crk-II/C3G 0.08 0.043 -10000 0 -0.11 6 6
Insulin Receptor/Insulin/IRS1/NCK2 0.096 0.046 -10000 0 -0.11 8 8
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.041 0.064 -10000 0 -0.11 44 44
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.026 0.097 0.22 1 -0.31 36 37
RPS6KB1 0.004 0.089 0.19 46 -0.18 8 54
PARD6A 0.036 0.015 -10000 0 0 81 81
CBL 0.04 0.008 -10000 0 0 23 23
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.022 0.081 -10000 0 -0.69 7 7
PIK3R1 0.034 0.017 -10000 0 0 107 107
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.049 0.082 0.2 18 -0.18 13 31
HRAS/GTP -0.026 0.033 0.046 11 -0.11 24 35
Insulin Receptor 0.042 0.016 0.081 15 0 53 68
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.1 0.062 -10000 0 -0.11 12 12
PRKCI -0.006 0.13 -10000 0 -0.38 56 56
Insulin Receptor/Insulin/GRB14/PDK1 0.02 0.053 -10000 0 -0.12 44 44
SHC1 0.04 0.01 -10000 0 0 31 31
negative regulation of MAPKKK cascade 0.046 0.084 -10000 0 -0.56 7 7
PI3K 0.051 0.073 -10000 0 -0.11 43 43
NCK2 0.042 0.004 -10000 0 0 6 6
RHOQ 0.039 0.01 -10000 0 0 33 33
mol:H2O2 -0.001 0.005 0.035 3 -10000 0 3
HRAS/GDP 0.029 0.01 -10000 0 -0.13 1 1
AKT2 0.015 0.095 0.22 37 -0.18 3 40
PRKCZ 0.036 0.09 -10000 0 -0.32 29 29
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.007 0.041 0.15 18 -10000 0 18
F2RL2 0.037 0.014 -10000 0 0 73 73
TRIP10 0.038 0.012 -10000 0 0 47 47
Insulin Receptor/Insulin/Shc 0.07 0.037 -10000 0 -0.098 5 5
TC10/GTP/CIP4/Exocyst 0.047 0.029 -10000 0 -0.11 12 12
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.093 0.071 -10000 0 -0.11 26 26
RAPGEF1 0.04 0.008 -10000 0 0 23 23
RASA1 0.037 0.014 -10000 0 0 71 71
NCK1 0.036 0.015 -10000 0 0 79 79
CBL/APS/CAP/Crk-II 0.065 0.036 -10000 0 -0.12 6 6
TC10/GDP 0.027 0.02 -10000 0 -0.13 8 8
Insulin Receptor/Insulin/SHC/GRB10 0.088 0.053 -10000 0 -0.11 11 11
INPP5D -0.012 0.019 0.045 27 -0.09 8 35
SOS1 0.038 0.013 -10000 0 0 56 56
SGK1 -0.004 0.004 -10000 0 -10000 0 0
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.04 0.009 -10000 0 0 27 27
IRS1 0.04 0.008 -10000 0 0 22 22
p62DOK/RasGAP 0.047 0.085 -10000 0 -0.56 7 7
INS 0.044 0.014 0.082 19 0 30 49
mol:PI-3-4-P2 -0.012 0.019 0.045 27 -0.09 8 35
GRB2 0.041 0.007 -10000 0 0 16 16
EIF4EBP1 0.002 0.08 0.18 37 -0.17 2 39
PTPRA 0.042 0.014 0.082 5 0 47 52
PIK3CA 0.03 0.019 -10000 0 0 155 155
TC10/GTP/CIP4 0.047 0.029 -10000 0 -0.11 12 12
PDPK1 0.04 0.009 -10000 0 0 26 26
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.029 0.059 0.16 1 -0.15 30 31
Insulin Receptor/Insulin/IRS1 0.071 0.038 -10000 0 -0.099 8 8
Insulin Receptor/Insulin/IRS3 0.059 0.03 -10000 0 -0.14 3 3
Par3/Par6 0.067 0.051 -10000 0 -0.1 14 14
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.034 0.054 -10000 0 -0.18 24 24
VEGFR1 homodimer/NRP1 0.008 0.046 -10000 0 -0.16 28 28
mol:DAG -0.024 0.039 0.19 1 -0.31 6 7
VEGFR1 homodimer/NRP1/VEGFR 121 0.007 0.042 -10000 0 -0.14 28 28
CaM/Ca2+ 0.025 0.052 0.2 1 -0.28 7 8
HIF1A 0.045 0.033 -10000 0 -0.28 5 5
GAB1 0.038 0.012 -10000 0 0 51 51
AKT1 0.001 0.089 0.23 6 -0.27 16 22
PLCG1 -0.024 0.04 0.2 1 -0.31 6 7
NOS3 0.026 0.071 0.3 4 -0.27 9 13
CBL 0.04 0.008 -10000 0 0 23 23
mol:NO 0.028 0.072 0.27 6 -0.26 9 15
FLT1 0.019 0.044 -10000 0 -0.49 4 4
PGF 0.04 0.009 -10000 0 0 27 27
VEGFR1 homodimer/NRP2/VEGFR121 0.018 0.062 -10000 0 -0.13 66 66
CALM1 0.04 0.01 -10000 0 0 31 31
PIK3CA 0.03 0.019 -10000 0 0 155 155
eNOS/Hsp90 0.021 0.068 0.28 4 -0.25 9 13
endothelial cell proliferation -0.003 0.066 0.22 6 -0.29 11 17
mol:Ca2+ -0.023 0.039 0.19 1 -0.31 6 7
MAPK3 -0.027 0.056 0.16 17 -0.25 9 26
MAPK1 -0.026 0.054 0.16 14 -0.25 9 23
PIK3R1 0.034 0.017 -10000 0 0 107 107
PLGF homodimer 0.04 0.009 -10000 0 0 27 27
PRKACA 0.035 0.015 -10000 0 0 89 89
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.036 0.015 -10000 0 0 80 80
VEGFA homodimer 0 0 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.008 0.046 -10000 0 -0.16 28 28
platelet activating factor biosynthetic process -0.027 0.058 0.15 24 -0.25 8 32
PI3K 0.039 0.08 -10000 0 -0.24 17 17
PRKCA -0.021 0.046 0.22 4 -0.26 8 12
PRKCB -0.022 0.036 0.18 1 -0.29 6 7
VEGFR1 homodimer/PLGF homodimer 0.035 0.054 -10000 0 -0.17 27 27
VEGFA 0 0 -10000 0 -10000 0 0
VEGFB 0.039 0.011 -10000 0 0 42 42
mol:IP3 -0.024 0.039 0.19 1 -0.31 6 7
RASA1 -0.021 0.045 0.2 2 -0.34 6 8
NRP2 0.035 0.016 -10000 0 0 94 94
VEGFR1 homodimer 0.019 0.044 -10000 0 -0.49 4 4
VEGFB homodimer 0.039 0.011 -10000 0 0 42 42
NCK1 0.036 0.015 -10000 0 0 79 79
eNOS/Caveolin-1 0.043 0.081 0.3 4 -0.26 9 13
PTPN11 0.04 0.009 -10000 0 0 27 27
mol:PI-3-4-5-P3 0.037 0.079 -10000 0 -0.23 17 17
mol:L-citrulline 0.028 0.072 0.27 6 -0.26 9 15
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.041 0.066 -10000 0 -0.17 23 23
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.024 0.058 -10000 0 -0.14 44 44
CD2AP 0.037 0.014 -10000 0 0 67 67
PI3K/GAB1 0.044 0.088 -10000 0 -0.24 17 17
PDPK1 0 0.09 0.17 84 -0.31 7 91
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.028 0.056 -10000 0 -0.14 42 42
mol:NADP 0.028 0.072 0.27 6 -0.26 9 15
HSP90AA1 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.039 0.065 -10000 0 -0.17 23 23
VEGFR1 homodimer/NRP2 0.028 0.058 -10000 0 -0.18 27 27
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.056 0.05 -10000 0 -0.11 21 21
fibroblast growth factor receptor signaling pathway 0.055 0.049 -10000 0 -0.11 21 21
LAMA1 0.034 0.017 -10000 0 0 108 108
PRNP 0.036 0.014 -10000 0 0 77 77
GPC1/SLIT2 0.018 0.072 -10000 0 -0.14 91 91
SMAD2 -0.021 0.035 0.2 7 -0.19 1 8
GPC1/PrPc/Cu2+ 0.039 0.043 -10000 0 -0.11 35 35
GPC1/Laminin alpha1 0.046 0.032 -10000 0 -0.14 6 6
TDGF1 0.041 0.006 -10000 0 0 12 12
CRIPTO/GPC1 0.058 0.017 -10000 0 -0.14 1 1
APP/GPC1 0.047 0.046 -10000 0 -0.14 29 29
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.018 0.025 0.19 5 -0.12 1 6
FLT1 0.04 0.01 -10000 0 0 32 32
GPC1/TGFB/TGFBR1/TGFBR2 0.069 0.043 -10000 0 -0.12 17 17
SERPINC1 0.04 0.008 -10000 0 0 23 23
FYN -0.016 0.026 0.19 5 -0.12 1 6
FGR -0.019 0.025 0.19 5 -0.12 1 6
positive regulation of MAPKKK cascade 0.005 0.072 0.21 15 -0.21 12 27
SLIT2 0.028 0.02 -10000 0 0 184 184
GPC1/NRG 0.049 0.026 -10000 0 -0.14 1 1
NRG1 0.035 0.016 -10000 0 0 93 93
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.05 0.023 -10000 0 -0.11 6 6
LYN -0.017 0.025 0.19 5 -0.12 1 6
mol:Spermine -0.01 0.002 -10000 0 -10000 0 0
cell growth 0.055 0.049 -10000 0 -0.11 21 21
BMP signaling pathway -0.04 0.009 0 26 -10000 0 26
SRC -0.019 0.025 0.19 5 -0.12 1 6
TGFBR1 0.04 0.009 -10000 0 0 25 25
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A 0.037 0.014 -10000 0 0 69 69
GPC1 0.04 0.009 -10000 0 0 26 26
TGFBR1 (dimer) 0.04 0.009 -10000 0 0 25 25
VEGFA 0 0 -10000 0 -10000 0 0
BLK -0.016 0.024 0.19 4 -0.12 1 5
HCK -0.017 0.025 0.19 5 -10000 0 5
FGF2 0.039 0.011 -10000 0 0 44 44
FGFR1 0.033 0.017 -10000 0 0 122 122
VEGFR1 homodimer 0.04 0.01 -10000 0 0 32 32
TGFBR2 0.039 0.01 -10000 0 0 37 37
cell death 0.046 0.046 -10000 0 -0.14 29 29
ATIII/GPC1 0.057 0.019 -10000 0 -0.14 1 1
PLA2G2A/GPC1 0.051 0.026 -10000 0 -0.14 3 3
LCK -0.019 0.025 0.19 5 -10000 0 5
neuron differentiation 0.049 0.026 -10000 0 -0.14 1 1
PrPc/Cu2+ 0.019 0.038 -10000 0 -0.13 34 34
APP 0.038 0.012 -10000 0 0 51 51
TGFBR2 (dimer) 0.039 0.01 -10000 0 0 37 37
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.017 0.085 -10000 0 -0.38 21 21
Crk/p130 Cas/Paxillin 0.005 0.039 -10000 0 -0.18 5 5
JUN 0.002 0.062 0.19 4 -0.23 11 15
HRAS 0.04 0.01 -10000 0 0 31 31
RET51/GFRalpha1/GDNF/GRB10 0.09 0.04 -10000 0 -0.11 5 5
RAP1A 0.039 0.01 -10000 0 0 35 35
FRS2 0.039 0.011 -10000 0 0 40 40
RAP1A/GDP 0.024 0.03 -10000 0 -0.13 21 21
RET51/GFRalpha1/GDNF/DOK1 0.09 0.04 -10000 0 -0.11 5 5
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.04 0.009 -10000 0 0 27 27
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.038 0.012 -10000 0 0 51 51
RET9/GFRalpha1/GDNF/Enigma 0.063 0.035 -10000 0 -0.1 2 2
RHOA 0.041 0.007 -10000 0 0 14 14
RAP1A/GTP 0.075 0.051 -10000 0 -0.1 15 15
GRB7 0.037 0.013 -10000 0 0 63 63
RET51/GFRalpha1/GDNF 0.078 0.047 -10000 0 -0.11 3 3
MAPKKK cascade 0.048 0.046 -10000 0 -0.15 4 4
BCAR1 0.036 0.014 -10000 0 0 75 75
RET9/GFRalpha1/GDNF/IRS1 0.063 0.036 -10000 0 -0.1 5 5
lamellipodium assembly 0.03 0.051 0.14 1 -0.18 4 5
RET51/GFRalpha1/GDNF/SHC 0.089 0.039 -10000 0 -0.11 2 2
PIK3CA 0.03 0.019 -10000 0 0 155 155
RET9/GFRalpha1/GDNF/SHC 0.063 0.035 -10000 0 -0.1 2 2
RET9/GFRalpha1/GDNF/Shank3 0.066 0.031 -10000 0 -0.1 1 1
MAPK3 -0.008 0.066 0.18 43 -10000 0 43
DOK1 0.04 0.009 -10000 0 0 24 24
DOK6 0.037 0.013 -10000 0 0 61 61
PXN 0.041 0.007 -10000 0 0 14 14
neurite development 0.002 0.06 0.2 15 -0.21 4 19
DOK5 0.022 0.021 -10000 0 0 269 269
GFRA1 0.037 0.013 -10000 0 0 62 62
MAPK8 0.012 0.06 -10000 0 -0.16 34 34
HRAS/GTP 0.081 0.048 -10000 0 -0.15 4 4
tube development 0.063 0.029 0.24 4 -0.1 2 6
MAPK1 -0.009 0.062 0.18 40 -10000 0 40
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.021 0.047 -10000 0 -0.16 29 29
Rac1/GDP 0.029 0.01 -10000 0 -0.13 1 1
SRC 0.039 0.01 -10000 0 0 36 36
PDLIM7 0.039 0.01 -10000 0 0 36 36
RET51/GFRalpha1/GDNF/Dok6 0.092 0.055 -10000 0 -0.11 1 1
SHC1 0.04 0.01 -10000 0 0 31 31
RET51/GFRalpha1/GDNF/Dok4 0.086 0.041 -10000 0 -0.11 1 1
RET51/GFRalpha1/GDNF/Dok5 0.041 0.079 -10000 0 -0.11 85 85
PRKCA 0.035 0.015 -10000 0 0 90 90
HRAS/GDP 0.029 0.01 -10000 0 -0.13 1 1
CREB1 0.036 0.063 -10000 0 -0.32 7 7
PIK3R1 0.034 0.017 -10000 0 0 107 107
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.024 0.034 -10000 0 -0.14 12 12
RET51/GFRalpha1/GDNF/Grb7 0.085 0.043 -10000 0 -0.11 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.041 0.007 -10000 0 0 17 17
DOK4 0.038 0.012 -10000 0 0 53 53
JNK cascade 0.003 0.061 0.19 4 -0.23 11 15
RET9/GFRalpha1/GDNF/FRS2 0.06 0.041 -10000 0 -0.1 12 12
SHANK3 0.042 0.002 -10000 0 0 1 1
RASA1 0.037 0.014 -10000 0 0 71 71
NCK1 0.036 0.015 -10000 0 0 79 79
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.023 0.038 -10000 0 -0.14 25 25
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.026 0.05 -10000 0 -0.16 28 28
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.016 0.057 -10000 0 -0.16 34 34
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.028 0.043 -10000 0 -0.15 22 22
PI3K 0.042 0.064 0.22 7 -0.24 3 10
SOS1 0.038 0.013 -10000 0 0 56 56
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.086 0.033 -10000 0 -0.1 2 2
GRB10 0.04 0.009 -10000 0 0 24 24
activation of MAPKK activity 0.029 0.053 0.16 1 -0.16 29 30
RET51/GFRalpha1/GDNF/FRS2 0.086 0.047 -10000 0 -0.11 12 12
GAB1 0.038 0.012 -10000 0 0 51 51
IRS1 0.04 0.008 -10000 0 0 22 22
IRS2 0.039 0.01 -10000 0 0 33 33
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.03 0.037 -10000 0 -0.14 11 11
RET51/GFRalpha1/GDNF/PKC alpha 0.078 0.056 -10000 0 -0.11 27 27
GRB2 0.041 0.007 -10000 0 0 16 16
PRKACA 0.035 0.015 -10000 0 0 89 89
GDNF 0.039 0.011 -10000 0 0 40 40
RAC1 0.039 0.01 -10000 0 0 33 33
RET51/GFRalpha1/GDNF/IRS1 0.091 0.039 -10000 0 -0.11 5 5
Rac1/GTP 0.042 0.063 0.19 5 -0.21 4 9
RET9/GFRalpha1/GDNF 0.047 0.022 -10000 0 -0.11 1 1
GFRalpha1/GDNF 0.051 0.025 -10000 0 -0.14 1 1
Coregulation of Androgen receptor activity

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
NRIP1 0.037 0.015 -9999 0 -10000 0 0
SVIL 0.037 0.015 -9999 0 -10000 0 0
ZNF318 0.037 0.01 -9999 0 -0.035 2 2
JMJD2C 0.043 0.015 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 0.037 0.062 -9999 0 -0.1 77 77
CARM1 0.037 0.014 -9999 0 0 69 69
PRDX1 0.039 0.01 -9999 0 0 36 36
PELP1 0.039 0.01 -9999 0 0 35 35
CTNNB1 0.04 0.01 -9999 0 -10000 0 0
AKT1 0.039 0.01 -9999 0 0 38 38
PTK2B 0.034 0.017 -9999 0 -10000 0 0
MED1 -0.001 0 -9999 0 -10000 0 0
MAK 0.033 0.015 -9999 0 -0.034 1 1
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.041 0.01 -9999 0 -10000 0 0
GSN 0.04 0.012 -9999 0 -10000 0 0
NCOA2 0.037 0.014 -9999 0 0 70 70
NCOA6 0.04 0.012 -9999 0 -10000 0 0
DNA-PK 0.052 0.066 -9999 0 -0.14 46 46
NCOA4 0.04 0.008 -9999 0 0 23 23
PIAS3 0.041 0.009 -9999 0 -10000 0 0
cell proliferation 0.018 0.048 -9999 0 -0.42 6 6
XRCC5 0.039 0.011 -9999 0 0 39 39
UBE3A 0.043 0.005 -9999 0 -10000 0 0
T-DHT/AR/SNURF 0.038 0.063 -9999 0 -0.11 79 79
FHL2 0.025 0.069 -9999 0 -0.61 5 5
RANBP9 0.039 0.013 -9999 0 -10000 0 0
JMJD1A 0.052 0.019 -9999 0 -0.14 1 1
CDK6 0.032 0.018 -9999 0 0 129 129
TGFB1I1 0.042 0.006 -9999 0 -10000 0 0
T-DHT/AR/CyclinD1 0.013 0.078 -9999 0 -0.12 129 129
XRCC6 0.036 0.014 -9999 0 0 69 69
T-DHT/AR 0.036 0.057 -9999 0 -0.1 71 71
CTDSP1 0.041 0.006 -9999 0 0 13 13
CTDSP2 0.037 0.011 -9999 0 -10000 0 0
BRCA1 0.035 0.017 -9999 0 -10000 0 0
TCF4 0.036 0.013 -9999 0 0 60 60
CDKN2A 0.028 0.019 -9999 0 0 175 175
SRF 0.043 0.021 -9999 0 -0.14 4 4
NKX3-1 0.015 0.081 -9999 0 -0.3 29 29
KLK3 0.004 0.048 -9999 0 -10000 0 0
TMF1 0.039 0.011 -9999 0 0 38 38
HNRNPA1 -0.001 0 -9999 0 -10000 0 0
AOF2 0.041 0.009 -9999 0 -10000 0 0
APPL1 -0.011 0.003 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 0.033 0.065 -9999 0 -0.11 89 89
AR 0.037 0.02 -9999 0 -0.043 1 1
UBA3 0 0 -9999 0 -10000 0 0
PATZ1 -0.001 0 -9999 0 -10000 0 0
PAWR 0.041 0.007 -9999 0 0 18 18
PRKDC 0.038 0.011 -9999 0 0 44 44
PA2G4 0.039 0.008 -9999 0 0 25 25
UBE2I 0.04 0.009 -9999 0 0 28 28
T-DHT/AR/Cyclin D3/CDK11 p58 0.034 0.058 -9999 0 -0.094 81 81
RPS6KA3 0.038 0.014 -9999 0 -10000 0 0
T-DHT/AR/ARA70 0.035 0.066 -9999 0 -0.11 90 90
LATS2 0.039 0.009 -9999 0 0 28 28
T-DHT/AR/PRX1 0.031 0.06 -9999 0 -0.095 90 90
Cyclin D3/CDK11 p58 0.028 0.016 -9999 0 -0.13 5 5
VAV3 0.034 0.017 -9999 0 -10000 0 0
KLK2 0.021 0.065 -9999 0 -0.3 17 17
CASP8 0.04 0.009 -9999 0 0 28 28
T-DHT/AR/TIF2/CARM1 0.045 0.071 -9999 0 -0.11 70 70
TMPRSS2 0.013 0.09 -9999 0 -0.31 35 35
CCND1 0.031 0.018 -9999 0 -10000 0 0
PIAS1 0.041 0.01 -9999 0 -10000 0 0
mol:T-DHT 0.005 0.005 -9999 0 -0.032 3 3
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.04 0.013 -9999 0 -10000 0 0
T-DHT/AR/CDK6 0.018 0.076 -9999 0 -0.12 119 119
CMTM2 0.036 0.014 -9999 0 0 76 76
SNURF 0.041 0.006 -9999 0 0 10 10
ZMIZ1 0.005 0.005 -9999 0 -0.032 3 3
CCND3 0.039 0.01 -9999 0 0 33 33
TGIF1 -0.001 0 -9999 0 -10000 0 0
FKBP4 0.037 0.016 -9999 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.049 0.045 0.15 18 -10000 0 18
KIRREL 0.041 0.017 0.084 2 -0.037 2 4
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.049 0.045 -10000 0 -0.15 18 18
PLCG1 0.038 0.012 -10000 0 0 50 50
ARRB2 0.039 0.011 -10000 0 0 43 43
WASL 0.04 0.008 -10000 0 0 23 23
Nephrin/NEPH1/podocin/CD2AP 0.073 0.071 0.21 1 -0.12 41 42
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.031 0.057 -10000 0 -0.14 31 31
FYN 0.003 0.065 0.17 58 -0.18 3 61
mol:Ca2+ 0.075 0.064 0.2 1 -0.13 25 26
mol:DAG 0.077 0.065 0.21 1 -0.13 25 26
NPHS2 0.043 0.02 -10000 0 -0.043 19 19
mol:IP3 0.077 0.065 0.21 1 -0.13 25 26
regulation of endocytosis 0.054 0.058 -10000 0 -0.12 20 20
Nephrin/NEPH1/podocin/Cholesterol 0.064 0.049 0.17 2 -0.11 18 20
establishment of cell polarity 0.049 0.045 -10000 0 -0.15 18 18
Nephrin/NEPH1/podocin/NCK1-2 0.086 0.078 -10000 0 -0.11 38 38
Nephrin/NEPH1/beta Arrestin2 0.056 0.06 -10000 0 -0.12 20 20
NPHS1 0.04 0.022 0.084 5 -0.044 17 22
Nephrin/NEPH1/podocin 0.055 0.056 0.22 1 -0.12 19 20
TJP1 0.037 0.013 -10000 0 0 64 64
NCK1 0.036 0.015 -10000 0 0 79 79
NCK2 0.042 0.004 -10000 0 0 6 6
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.079 0.066 0.21 1 -0.13 25 26
CD2AP 0.037 0.014 -10000 0 0 67 67
Nephrin/NEPH1/podocin/GRB2 0.085 0.059 0.21 1 -0.12 19 20
GRB2 0.041 0.007 -10000 0 0 16 16
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.005 0.071 0.18 65 -0.12 3 68
cytoskeleton organization 0.013 0.054 0.25 4 -0.16 15 19
Nephrin/NEPH1 0.042 0.034 -10000 0 -0.096 18 18
Nephrin/NEPH1/ZO-1 0.055 0.062 -10000 0 -0.13 37 37
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.04 0.009 -10000 0 0 25 25
SPHK1 0.04 0.008 -10000 0 0 20 20
GNAI2 0.041 0.007 -10000 0 0 15 15
mol:S1P 0.015 0.029 -10000 0 -0.17 12 12
GNAO1 0.034 0.016 -10000 0 0 101 101
mol:Sphinganine-1-P -0.019 0.006 -10000 0 -10000 0 0
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.051 0.048 0.19 1 -0.15 13 14
GNAI3 0.039 0.011 -10000 0 0 45 45
G12/G13 0.054 0.03 -10000 0 -0.14 9 9
S1PR3 0 0 -10000 0 -10000 0 0
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0.041 0.006 -10000 0 0 13 13
S1P1/S1P 0.037 0.042 0.19 1 -0.15 12 13
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
GNAI1 0.035 0.016 -10000 0 0 95 95
S1P/S1P5/G12 0.032 0.038 -10000 0 -0.14 12 12
S1P/S1P3/Gq 0.015 0.079 0.17 1 -0.26 36 37
S1P/S1P4/Gi -0.009 0.09 -10000 0 -0.27 39 39
GNAQ 0.038 0.012 -10000 0 0 49 49
GNAZ 0.039 0.011 -10000 0 0 42 42
GNA14 0.039 0.01 -10000 0 0 33 33
GNA15 0.037 0.014 -10000 0 0 69 69
GNA12 0.04 0.01 -10000 0 0 32 32
GNA13 0.04 0.009 -10000 0 0 28 28
GNA11 0.037 0.013 -10000 0 0 61 61
ABCC1 0.04 0.009 -10000 0 0 26 26
Alternative NF-kappaB 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
IKK alpha homodimer 0.047 0.045 -9999 0 -0.14 27 27
FBXW11 0.04 0.009 -9999 0 0 25 25
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.04 0.009 -9999 0 0 25 25
CHUK 0.038 0.012 -9999 0 0 52 52
NF kappa B2 p100/RelB 0.094 0.067 -9999 0 -0.12 30 30
NFKB1 0.036 0.015 -9999 0 0 83 83
MAP3K14 0.04 0.009 -9999 0 0 29 29
NF kappa B1 p50/RelB 0.042 0.05 -9999 0 -0.14 35 35
RELB 0.04 0.009 -9999 0 0 27 27
NFKB2 0.04 0.009 -9999 0 0 24 24
NF kappa B2 p52/RelB 0.051 0.022 -9999 0 -0.13 4 4
regulation of B cell activation 0.05 0.022 -9999 0 -0.13 4 4
LPA4-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
ADCY4 -0.014 0.006 -10000 0 -10000 0 0
ADCY5 -0.014 0.006 0 86 -10000 0 86
ADCY6 -0.015 0.005 -10000 0 -10000 0 0
ADCY7 -0.014 0.006 -10000 0 -10000 0 0
ADCY1 -0.015 0.005 0 52 -10000 0 52
ADCY2 -0.014 0.006 -10000 0 -10000 0 0
ADCY3 -0.015 0.005 -10000 0 -10000 0 0
ADCY8 -0.008 0.008 -10000 0 -10000 0 0
PRKCE -0.01 0.003 0 36 -10000 0 36
ADCY9 -0.014 0.006 0 77 -10000 0 77
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.055 0.085 0.22 71 -0.2 4 75
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.09 0.049 -10000 0 -0.11 20 20
HDAC3 0.041 0.007 -10000 0 0 15 15
Ran/GTP/Exportin 1/HDAC4 -0.027 0.024 -10000 0 -0.11 33 33
GATA1/HDAC4 0.06 0.01 -10000 0 -10000 0 0
GATA1/HDAC5 0.059 0.015 -10000 0 -10000 0 0
GATA2/HDAC5 0.055 0.02 -10000 0 -10000 0 0
HDAC5/BCL6/BCoR 0.051 0.058 -10000 0 -0.12 36 36
HDAC9 0.035 0.015 -10000 0 0 88 88
Glucocorticoid receptor/Hsp90/HDAC6 0.045 0.039 -10000 0 -0.11 30 30
HDAC4/ANKRA2 0.049 0.033 -10000 0 -0.14 9 9
HDAC5/YWHAB 0.051 0.03 -10000 0 -0.14 7 7
NPC/RanGAP1/SUMO1/Ubc9 0.009 0.035 -10000 0 -0.14 25 25
GATA2 0.039 0.01 -10000 0 0 35 35
HDAC4/RFXANK 0.047 0.041 -10000 0 -0.14 20 20
BCOR 0.041 0.005 -10000 0 0 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.031 0.018 -10000 0 0 140 140
HDAC5 0.04 0.01 -10000 0 0 32 32
GNB1/GNG2 0.053 0.037 -10000 0 -0.14 19 19
Histones -0.006 0.07 -10000 0 -0.2 32 32
ADRBK1 0.041 0.005 -10000 0 0 7 7
HDAC4 0.041 0.007 -10000 0 0 15 15
XPO1 0.039 0.011 -10000 0 0 39 39
HDAC5/ANKRA2 0.048 0.033 -10000 0 -0.13 9 9
HDAC4/Ubc9 0.057 0.018 -10000 0 -0.14 1 1
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.052 0.03 -10000 0 -0.14 8 8
TUBA1B 0 0 -10000 0 -10000 0 0
HDAC6 0.041 0.007 -10000 0 0 15 15
HDAC5/RFXANK 0.046 0.042 -10000 0 -0.14 21 21
CAMK4 0.037 0.013 -10000 0 0 64 64
Tubulin/HDAC6 0.05 0.018 -10000 0 -10000 0 0
SUMO1 0.041 0.006 -10000 0 0 13 13
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.038 0.012 -10000 0 0 52 52
GATA1 0.042 0.002 -10000 0 0 1 1
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.038 0.013 -10000 0 0 57 57
NR3C1 0.039 0.012 -10000 0 0 46 46
SUMO1/HDAC4 0.041 0.063 -10000 0 -0.18 18 18
SRF 0.039 0.011 -10000 0 0 42 42
HDAC4/YWHAB 0.053 0.029 -10000 0 -0.14 7 7
Tubulin 0.028 0.009 -10000 0 -10000 0 0
HDAC4/14-3-3 E 0.052 0.03 -10000 0 -0.14 8 8
GNB1 0.041 0.005 -10000 0 0 7 7
RANGAP1 0.038 0.013 -10000 0 0 56 56
BCL6/BCoR 0.036 0.053 -10000 0 -0.14 36 36
HDAC4/HDAC3/SMRT (N-CoR2) 0.075 0.033 -10000 0 -0.12 7 7
HDAC4/SRF 0.068 0.034 -10000 0 -0.12 1 1
HDAC4/ER alpha 0.04 0.054 -10000 0 -0.14 43 43
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing -0.006 0.07 -10000 0 -0.2 32 32
cell motility 0.05 0.017 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.04 0.009 -10000 0 0 28 28
HDAC7/HDAC3 0.029 0.012 -10000 0 -0.13 3 3
BCL6 0.031 0.018 -10000 0 0 146 146
HDAC4/CaMK II delta B 0.041 0.007 -10000 0 0 15 15
Hsp90/HDAC6 0.03 0.005 -10000 0 -10000 0 0
ESR1 0.035 0.016 -10000 0 0 93 93
HDAC6/HDAC11 0.056 0.026 -10000 0 -0.14 7 7
Ran/GTP/Exportin 1 0.038 0.072 0.18 1 -0.18 36 37
NPC 0.02 0.022 -10000 0 -0.085 23 23
MEF2C 0.036 0.014 -10000 0 0 75 75
RAN 0.041 0.006 -10000 0 0 13 13
HDAC4/MEF2C 0.094 0.063 -10000 0 -0.12 18 18
GNG2 0.039 0.01 -10000 0 0 34 34
NCOR2 0.04 0.009 -10000 0 0 28 28
TUBB2A 0.038 0.012 -10000 0 0 47 47
HDAC11 0.04 0.008 -10000 0 0 23 23
HSP90AA1 0 0 -10000 0 -10000 0 0
RANBP2 0.04 0.009 -10000 0 0 30 30
ANKRA2 0.035 0.015 -10000 0 0 87 87
RFXANK 0.036 0.014 -10000 0 0 77 77
nuclear import -0.036 0.041 0.18 14 -10000 0 14
Glucocorticoid receptor regulatory network

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
PCK2 -0.021 0.075 -10000 0 -0.37 12 12
SMARCC2 0.04 0.009 -10000 0 0 25 25
SMARCC1 0.04 0.008 -10000 0 0 21 21
TBX21 0.04 0.058 0.41 1 -10000 0 1
SUMO2 0.037 0.016 -10000 0 -0.03 21 21
STAT1 (dimer) 0.022 0.064 -10000 0 -0.18 46 46
FKBP4 0.036 0.015 -10000 0 0 86 86
FKBP5 0.031 0.018 -10000 0 0 147 147
GR alpha/HSP90/FKBP51/HSP90 -0.034 0.074 0.19 3 -0.21 20 23
PRL 0.049 0.068 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 -0.059 0.12 0.38 3 -0.35 1 4
RELA 0.012 0.097 -10000 0 -0.16 128 128
FGG -0.055 0.11 0.33 3 -0.32 1 4
GR beta/TIF2 -0.033 0.079 0.22 2 -0.23 7 9
IFNG 0.047 0.1 -10000 0 -10000 0 0
apoptosis -0.054 0.17 -10000 0 -0.46 37 37
CREB1 0.049 0.009 -10000 0 -10000 0 0
histone acetylation 0.023 0.083 0.29 10 -0.39 6 16
BGLAP 0.045 0.091 0.29 2 -0.89 3 5
GR/PKAc 0.032 0.085 0.24 1 -0.16 24 25
NF kappa B1 p50/RelA 0.01 0.17 -10000 0 -0.3 117 117
SMARCD1 0.041 0.008 -10000 0 0 19 19
MDM2 -0.013 0.047 0.14 4 -0.24 7 11
GATA3 0.05 0.014 -10000 0 -10000 0 0
AKT1 0.035 0.015 0.17 2 -0.052 6 8
CSF2 0.012 0.054 -10000 0 -10000 0 0
GSK3B 0.037 0.015 -10000 0 -0.03 18 18
NR1I3 -0.042 0.16 -10000 0 -0.46 13 13
CSN2 -0.05 0.097 0.29 2 -0.31 1 3
BRG1/BAF155/BAF170/BAF60A 0.077 0.065 -10000 0 -0.13 32 32
NFATC1 0.044 0.017 -10000 0 -10000 0 0
POU2F1 0.046 0.01 -10000 0 -10000 0 0
CDKN1A -0.041 0.12 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.001 0.005 -10000 0 -10000 0 0
SFN 0.036 0.015 -10000 0 0 86 86
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.025 0.082 0.22 1 -0.2 26 27
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.11 0.28 -10000 0 -0.7 92 92
JUN 0.041 0.098 0.34 9 -0.32 1 10
IL4 0.042 0.057 -10000 0 -10000 0 0
CDK5R1 0.039 0.01 -10000 0 0 30 30
PRKACA 0.035 0.015 -10000 0 0 89 89
cortisol/GR alpha (monomer)/AP-1 -0.04 0.07 0.2 13 -0.22 23 36
GR alpha/HSP90/FKBP51/HSP90/PP5C -0.017 0.081 0.21 2 -0.2 19 21
cortisol/GR alpha (monomer) -0.071 0.13 0.4 4 -0.4 1 5
NCOA2 0.037 0.014 -10000 0 0 70 70
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS 0.032 0.054 -10000 0 -0.13 21 21
AP-1/NFAT1-c-4 0.038 0.14 -10000 0 -0.38 16 16
AFP 0.03 0.095 -10000 0 -10000 0 0
SUV420H1 0.04 0.009 -10000 0 0 30 30
IRF1 -0.1 0.22 -10000 0 -0.56 89 89
TP53 0.036 0.028 -10000 0 -10000 0 0
PPP5C 0.04 0.01 -10000 0 0 32 32
KRT17 0.028 0.16 -10000 0 -0.74 11 11
KRT14 0.025 0.17 0.48 9 -1.1 10 19
TBP 0.044 0.032 -10000 0 -0.34 3 3
CREBBP 0.029 0.051 0.34 11 -10000 0 11
HDAC1 0.033 0.012 -10000 0 -0.059 2 2
HDAC2 0.037 0.011 -10000 0 0 48 48
AP-1 0.038 0.14 -10000 0 -0.38 16 16
MAPK14 0.037 0.016 -10000 0 -0.03 21 21
MAPK10 0.032 0.021 -10000 0 -0.03 32 32
MAPK11 0.029 0.021 -10000 0 -0.03 17 17
KRT5 -0.007 0.26 -10000 0 -0.83 44 44
interleukin-1 receptor activity -0.001 0 -10000 0 -10000 0 0
NCOA1 0.041 0.012 -10000 0 -0.068 2 2
STAT1 0.022 0.064 -10000 0 -0.18 46 46
CGA 0.046 0.064 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.06 0.11 0.29 3 -0.35 37 40
MAPK3 0.036 0.019 -10000 0 -0.03 36 36
MAPK1 0.035 0.018 -10000 0 -0.03 24 24
ICAM1 -0.077 0.32 -10000 0 -0.77 93 93
NFKB1 0.006 0.11 -10000 0 -0.2 113 113
MAPK8 0.049 0.083 0.57 1 -0.23 4 5
MAPK9 0.035 0.018 -10000 0 -0.031 25 25
cortisol/GR alpha (dimer) -0.057 0.18 -10000 0 -0.47 40 40
BAX -0.048 0.12 -10000 0 -0.43 2 2
POMC 0.056 0.094 0.51 1 -10000 0 1
EP300 0.027 0.047 0.33 9 -10000 0 9
cortisol/GR alpha (dimer)/p53 -0.078 0.12 0.37 4 -10000 0 4
proteasomal ubiquitin-dependent protein catabolic process -0.025 0.047 0.25 5 -0.22 7 12
SGK1 -0.025 0.11 0.34 9 -0.3 45 54
IL13 0.049 0.092 -10000 0 -10000 0 0
IL6 0.012 0.16 -10000 0 -0.62 18 18
PRKACG 0.041 0.006 -10000 0 0 10 10
IL5 0.047 0.096 -10000 0 -10000 0 0
IL2 0.038 0.12 -10000 0 -0.56 4 4
CDK5 0.035 0.015 -10000 0 0 82 82
PRKACB 0.038 0.012 -10000 0 0 49 49
HSP90AA1 0 0 -10000 0 -10000 0 0
IL8 -0.014 0.23 -10000 0 -0.8 37 37
CDK5R1/CDK5 0.045 0.041 -10000 0 -0.13 20 20
NF kappa B1 p50/RelA/PKAc 0.042 0.15 -10000 0 -0.22 95 95
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 -0.043 0.11 0.36 4 -0.32 1 5
SMARCA4 0.035 0.015 -10000 0 0 90 90
chromatin remodeling -0.03 0.092 0.25 4 -0.28 25 29
NF kappa B1 p50/RelA/Cbp 0.024 0.16 0.42 6 -0.25 108 114
JUN (dimer) 0.041 0.098 0.34 9 -0.31 1 10
YWHAH 0.038 0.013 -10000 0 0 59 59
VIPR1 0.041 0.057 0.4 1 -10000 0 1
NR3C1 -0.047 0.092 0.26 3 -0.31 6 9
NR4A1 0.038 0.018 -10000 0 -10000 0 0
TIF2/SUV420H1 0.043 0.051 -10000 0 -0.14 36 36
MAPKKK cascade -0.054 0.17 -10000 0 -0.46 37 37
cortisol/GR alpha (dimer)/Src-1 -0.055 0.12 0.38 4 -0.35 1 5
PBX1 0.044 0.013 -10000 0 -10000 0 0
POU1F1 0.046 0.009 -10000 0 -10000 0 0
SELE 0.022 0.12 -10000 0 -0.36 5 5
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A -0.03 0.092 0.25 4 -0.28 26 30
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.043 0.11 0.36 4 -0.32 1 5
mol:cortisol -0.043 0.066 0.21 3 -10000 0 3
MMP1 0.009 0.18 -10000 0 -0.78 22 22
Calcium 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
NFATC1 0.02 0.024 0.21 3 -0.093 3 6
NFATC2 0.021 0.024 0.22 3 -0.11 3 6
NFATC3 0.021 0.024 0.17 4 -0.093 3 7
CD40LG 0.034 0.1 0.29 22 -0.24 1 23
PTGS2 0.014 0.09 0.32 10 -0.27 5 15
JUNB 0.03 0.019 -10000 0 0 160 160
CaM/Ca2+/Calcineurin A alpha-beta B1 0.032 0.017 -10000 0 -0.1 4 4
CaM/Ca2+ 0.032 0.017 -10000 0 -0.1 4 4
CALM1 0.042 0.011 -10000 0 -0.001 32 32
JUN 0.038 0.016 0.099 1 0 81 82
mol:Ca2+ 0.001 0.003 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.027 0.012 0.064 1 -0.1 2 3
FOSL1 0.041 0.007 -10000 0 0 15 15
CREM 0.04 0.008 -10000 0 0 20 20
Jun/NFAT1-c-4/p21SNFT 0.056 0.069 0.24 8 -10000 0 8
FOS 0.028 0.022 0.099 1 0 207 208
IFNG 0.024 0.097 0.31 14 -0.24 1 15
AP-1/NFAT1-c-4 0.084 0.12 -10000 0 -0.23 3 3
FASLG 0.031 0.1 0.3 19 -0.24 2 21
NFAT1-c-4/ICER1 0.053 0.058 0.22 7 -10000 0 7
IL2RA 0.031 0.1 0.32 17 -0.24 2 19
FKBP12/FK506 0.028 0.013 -10000 0 -0.13 2 2
CSF2 0.033 0.1 0.29 22 -0.24 1 23
JunB/Fra1/NFAT1-c-4 0.048 0.074 0.23 4 -0.18 3 7
IL4 0.032 0.1 0.29 20 -0.24 1 21
IL2 -0.038 0.23 -10000 0 -0.86 40 40
IL3 0.026 0.12 -10000 0 -0.6 19 19
FKBP1A 0.038 0.012 -10000 0 0 50 50
BATF3 0 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.046 0.01 -10000 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 0.015 0.17 -10000 0 -0.7 13 13
NCK1/PAK1/Dok-R -0.03 0.072 -10000 0 -0.34 14 14
NCK1/Dok-R 0.05 0.098 -10000 0 -0.88 2 2
PIK3CA 0.03 0.019 -10000 0 0 155 155
mol:beta2-estradiol -0.008 0.008 -10000 0 -10000 0 0
RELA 0.041 0.006 -10000 0 0 10 10
SHC1 0.04 0.01 -10000 0 0 31 31
Rac/GDP 0.029 0.01 -10000 0 -0.13 1 1
F2 0.01 0.038 -10000 0 -0.084 1 1
TNIP2 0.038 0.012 -10000 0 0 48 48
NF kappa B/RelA 0.077 0.1 -10000 0 -0.84 2 2
FN1 0.021 0.021 -10000 0 0 277 277
PLD2 0.033 0.077 -10000 0 -0.9 2 2
PTPN11 0.04 0.009 -10000 0 0 27 27
GRB14 0.038 0.012 -10000 0 0 53 53
ELK1 0.032 0.078 -10000 0 -0.85 2 2
GRB7 0.037 0.013 -10000 0 0 63 63
PAK1 0.037 0.014 -10000 0 0 70 70
Tie2/Ang1/alpha5/beta1 Integrin 0.037 0.11 -10000 0 -0.86 2 2
CDKN1A 0.014 0.19 -10000 0 -0.62 39 39
ITGA5 0.038 0.013 -10000 0 0 58 58
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.054 0.096 -10000 0 -0.88 2 2
CRK 0.038 0.012 -10000 0 0 51 51
mol:NO 0.029 0.15 0.37 1 -0.54 12 13
PLG 0.031 0.076 -10000 0 -0.9 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.028 0.14 -10000 0 -0.75 6 6
GRB2 0.041 0.007 -10000 0 0 16 16
PIK3R1 0.034 0.017 -10000 0 0 107 107
ANGPT2 -0.045 0.29 -10000 0 -1 38 38
BMX 0.031 0.077 -10000 0 -0.9 2 2
ANGPT1 0.03 0.054 -10000 0 -10000 0 0
tube development -0.002 0.21 -10000 0 -0.7 39 39
ANGPT4 0.035 0.021 -10000 0 -0.012 82 82
response to hypoxia 0.001 0.008 -10000 0 -0.062 2 2
Tie2/Ang1/GRB14 0.054 0.09 -10000 0 -0.91 2 2
alpha5/beta1 Integrin 0.046 0.045 -10000 0 -0.14 27 27
FGF2 0.039 0.012 -10000 0 0 44 44
STAT5A (dimer) 0.014 0.24 -10000 0 -0.8 39 39
mol:L-citrulline 0.029 0.15 0.37 1 -0.54 12 13
AGTR1 0.033 0.025 -10000 0 -0.016 103 103
MAPK14 0.041 0.12 -10000 0 -1 4 4
Tie2/SHP2 0.037 0.11 -10000 0 -0.76 3 3
TEK 0.03 0.11 -10000 0 -0.8 3 3
RPS6KB1 0.016 0.16 -10000 0 -0.7 9 9
Angiotensin II/AT1 0.025 0.024 -10000 0 -0.057 35 35
Tie2/Ang1/GRB2 0.058 0.091 -10000 0 -0.91 2 2
MAPK3 0.028 0.075 -10000 0 -0.85 2 2
MAPK1 0.027 0.074 -10000 0 -0.85 2 2
Tie2/Ang1/GRB7 0.054 0.09 -10000 0 -0.91 2 2
NFKB1 0.036 0.015 -10000 0 0 83 83
MAPK8 0.031 0.08 -10000 0 -0.9 2 2
PI3K 0.017 0.16 -10000 0 -0.93 6 6
FES 0.043 0.11 -10000 0 -1 2 2
Crk/Dok-R 0.057 0.095 -10000 0 -0.88 2 2
Tie2/Ang1/ABIN2 0.055 0.091 -10000 0 -0.91 2 2
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.019 0.16 -10000 0 -0.63 13 13
STAT5A 0.038 0.012 -10000 0 0 51 51
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.061 0.18 -10000 0 -0.73 6 6
Tie2/Ang2 -0.013 0.27 -10000 0 -0.95 39 39
Tie2/Ang1 0.043 0.082 -10000 0 -0.94 2 2
FOXO1 0.015 0.18 -10000 0 -0.61 38 38
ELF1 0.047 0.019 -10000 0 -0.13 2 2
ELF2 0.04 0.079 -10000 0 -0.9 2 2
mol:Choline 0.033 0.076 -10000 0 -0.87 2 2
cell migration -0.016 0.047 -10000 0 -0.19 14 14
FYN -0.01 0.23 -10000 0 -0.8 39 39
DOK2 0.032 0.018 -10000 0 0 135 135
negative regulation of cell cycle 0.017 0.18 -10000 0 -0.56 39 39
ETS1 0.043 0.021 -10000 0 -10000 0 0
PXN 0.061 0.17 0.4 1 -0.57 8 9
ITGB1 0.039 0.011 -10000 0 0 38 38
NOS3 0.026 0.16 -10000 0 -0.61 12 12
RAC1 0.039 0.01 -10000 0 0 33 33
TNF 0.049 0.014 -10000 0 -10000 0 0
MAPKKK cascade 0.033 0.076 -10000 0 -0.87 2 2
RASA1 0.037 0.014 -10000 0 0 71 71
Tie2/Ang1/Shc 0.058 0.091 -10000 0 -0.91 2 2
NCK1 0.036 0.015 -10000 0 0 79 79
vasculogenesis 0.031 0.14 0.36 2 -0.49 12 14
mol:Phosphatidic acid 0.033 0.076 -10000 0 -0.87 2 2
mol:Angiotensin II 0 0.008 -10000 0 -0.033 30 30
mol:NADP 0.029 0.15 0.37 1 -0.54 12 13
Rac1/GTP 0.029 0.15 -10000 0 -0.7 7 7
MMP2 0.033 0.087 -10000 0 -0.9 2 2
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.037 0.013 -10000 0 0 62 62
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response -0.003 0.11 0.53 9 -10000 0 9
IL27/IL27R/JAK1 0.08 0.12 -10000 0 -0.91 3 3
TBX21 0.004 0.1 0.36 5 -0.57 3 8
IL12B 0.042 0.008 -10000 0 0 20 20
IL12A -0.006 0.006 0.013 26 -10000 0 26
IL6ST 0.036 0.018 -10000 0 -0.032 2 2
IL27RA/JAK1 0.049 0.11 -10000 0 -1.1 3 3
IL27 0.043 0.009 -10000 0 -0.036 3 3
TYK2 0.039 0.016 -10000 0 -0.036 3 3
T-helper cell lineage commitment 0.007 0.061 0.2 21 -0.18 30 51
T-helper 2 cell differentiation -0.003 0.11 0.53 9 -10000 0 9
T cell proliferation during immune response -0.003 0.11 0.53 9 -10000 0 9
MAPKKK cascade 0.003 0.11 -10000 0 -0.53 9 9
STAT3 0.038 0.013 -10000 0 0 56 56
STAT2 0.039 0.011 -10000 0 0 43 43
STAT1 0.034 0.017 -10000 0 0 108 108
IL12RB1 0.039 0.012 -10000 0 0 49 49
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.002 0.1 0.36 2 -0.55 3 5
IL27/IL27R/JAK2/TYK2 0.003 0.12 -10000 0 -0.54 9 9
positive regulation of T cell mediated cytotoxicity 0.003 0.11 -10000 0 -0.53 9 9
STAT1 (dimer) 0.063 0.13 -10000 0 -0.81 3 3
JAK2 0.037 0.017 -10000 0 -0.037 1 1
JAK1 0.039 0.01 -10000 0 0 34 34
STAT2 (dimer) 0.02 0.13 -10000 0 -0.49 11 11
T cell proliferation 0.005 0.11 0.34 2 -0.57 7 9
IL12/IL12R/TYK2/JAK2 0.015 0.17 -10000 0 -0.7 26 26
IL17A 0.009 0.056 0.2 19 -0.18 26 45
mast cell activation -0.003 0.11 0.53 9 -10000 0 9
IFNG 0.013 0.03 0.1 1 -0.095 7 8
T cell differentiation -0.001 0.003 0.014 1 -0.022 3 4
STAT3 (dimer) 0.025 0.13 -10000 0 -0.48 10 10
STAT5A (dimer) 0.025 0.13 -10000 0 -0.55 8 8
STAT4 (dimer) 0.024 0.13 -10000 0 -0.51 9 9
STAT4 0.04 0.009 -10000 0 0 29 29
T cell activation -0.008 0.012 0.12 1 -0.048 27 28
IL27R/JAK2/TYK2 0.053 0.1 -10000 0 -0.94 3 3
GATA3 0.015 0.12 0.62 19 -10000 0 19
IL18 -0.007 0.006 0.002 178 -10000 0 178
positive regulation of mast cell cytokine production 0.025 0.13 -10000 0 -0.46 11 11
IL27/EBI3 0.059 0.022 -10000 0 -10000 0 0
IL27RA 0.024 0.12 -10000 0 -1.1 3 3
IL6 0.034 0.017 -10000 0 0 112 112
STAT5A 0.038 0.012 -10000 0 0 51 51
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.008 0.041 0.48 3 -10000 0 3
IL1B -0.007 0.006 0.002 149 -10000 0 149
EBI3 0.039 0.014 -10000 0 -0.037 1 1
TNF -0.008 0.005 0.01 39 -10000 0 39
Signaling events mediated by HDAC Class III

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
EP300 0.037 0.014 -10000 0 0 72 72
HDAC4 0.041 0.007 -10000 0 0 15 15
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.013 0.004 -10000 0 -10000 0 0
CDKN1A 0.024 0.066 0.29 19 -10000 0 19
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.04 0.008 -10000 0 0 22 22
FOXO3 0.002 0.042 0.25 15 -10000 0 15
FOXO1 0 0 -10000 0 -10000 0 0
FOXO4 0.005 0.034 -10000 0 -0.18 18 18
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.037 0.014 -10000 0 0 69 69
TAT 0.036 0.014 -10000 0 0 75 75
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.01 0.002 -10000 0 -10000 0 0
PPARGC1A 0.038 0.012 -10000 0 0 55 55
FHL2 0.04 0.008 -10000 0 0 20 20
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.047 0.041 -10000 0 -0.17 15 15
HIST2H4A -0.013 0.004 -10000 0 -10000 0 0
SIRT1/FOXO3a 0.036 0.048 0.2 16 -0.21 6 22
SIRT1 0.037 0.008 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.072 0.034 -10000 0 -0.12 8 8
SIRT1/Histone H1b 0.005 0.091 -10000 0 -0.2 67 67
apoptosis -0.064 0.045 0.14 15 -10000 0 15
SIRT1/PGC1A 0.046 0.026 -10000 0 -0.11 8 8
p53/SIRT1 -0.01 0.089 -10000 0 -0.15 163 163
SIRT1/FOXO4 0.01 0.075 -10000 0 -0.16 74 74
FOXO1/FHL2/SIRT1 0.046 0.024 -10000 0 -0.1 12 12
HIST1H1E -0.004 0.07 -10000 0 -0.21 52 52
SIRT1/p300 0.045 0.042 -10000 0 -0.14 23 23
muscle cell differentiation -0.018 0.023 0.11 9 -0.21 2 11
TP53 0.024 0.019 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.065 0.046 -10000 0 -0.14 15 15
CREBBP 0.038 0.012 -10000 0 0 54 54
MEF2D 0.04 0.009 -10000 0 0 28 28
HIV-1 Tat/SIRT1 0.048 0.03 -10000 0 -0.13 8 8
ACSS2 -0.021 0.009 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.018 0.023 0.21 2 -0.11 9 11
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.038 0.013 -10000 0 0 56 56
Ran/GTP/Exportin 1/HDAC4 -0.029 0.033 -10000 0 -0.14 34 34
MDM2/SUMO1 0.039 0.062 -10000 0 -0.18 19 19
HDAC4 0.041 0.007 -10000 0 0 15 15
Ran/GTP/Exportin 1/HDAC1 -0.031 0.04 -10000 0 -0.14 48 48
SUMO1 0.041 0.006 -10000 0 0 13 13
NPC/RanGAP1/SUMO1 0.008 0.033 -10000 0 -0.14 24 24
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.001 0.04 -10000 0 -0.17 15 15
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.041 0.006 -10000 0 0 13 13
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.04 0.009 -10000 0 0 30 30
SUMO1/HDAC4 0.041 0.063 -10000 0 -0.18 18 18
SUMO1/HDAC1 0.037 0.065 -10000 0 -0.18 26 26
RANGAP1 0.038 0.013 -10000 0 0 56 56
MDM2/SUMO1/SUMO1 0.083 0.056 -10000 0 -0.12 20 20
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.009 0.035 -10000 0 -0.14 25 25
Ran/GTP 0.023 0.058 0.17 1 -0.15 36 37
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.039 0.01 -10000 0 0 35 35
UBE2I 0.04 0.009 -10000 0 0 28 28
Ran/GTP/Exportin 1 0.019 0.068 0.2 14 -0.18 36 50
NPC 0.02 0.022 -10000 0 -0.085 23 23
PIAS2 0.038 0.012 -10000 0 0 51 51
PIAS1 0.04 0.009 -10000 0 0 28 28
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Arf1 pathway

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
coatomer protein complex 0.022 0.047 0.15 65 -0.12 1 66
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.013 0.031 0.12 1 -0.13 6 7
AP2 0.038 0.044 -10000 0 -0.14 22 22
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.052 0.019 -10000 0 -0.11 1 1
CLTB 0.04 0.009 -10000 0 0 27 27
coatomer protein complex/ARF1/GTP/ER cargo protein 0.019 0.03 -10000 0 -0.15 14 14
CD4 0.032 0.018 -10000 0 0 132 132
CLTA 0.04 0.008 -10000 0 0 20 20
mol:GTP -0.003 0.003 0.013 6 -0.02 1 7
ARFGAP1 -0.009 0.004 0 77 -10000 0 77
mol:PI-4-5-P2 0.01 0.016 0.079 24 -10000 0 24
ARF1/GTP 0.023 0.012 0.079 1 -0.14 1 2
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.025 0.055 0.17 59 -0.17 4 63
mol:Choline 0.01 0.016 0.08 24 -10000 0 24
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.039 0.012 -10000 0 0 50 50
DDEF1 0.005 0.012 0.08 12 -10000 0 12
ARF1/GDP 0.006 0.01 0.06 1 -0.074 3 4
AP2M1 0.032 0.018 -10000 0 0 137 137
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.01 0.016 0.049 16 -0.1 2 18
Rac/GTP 0.029 0.01 -10000 0 -0.13 1 1
ARF1/GTP/GGA3/ARF-GAP1 0.045 0.025 -10000 0 -0.1 1 1
ARFIP2 0.035 0.019 -10000 0 -0.041 27 27
COPA 0.04 0.009 -10000 0 0 29 29
RAC1 0.039 0.01 -10000 0 0 33 33
ARF1/GTP/coatomer protein complex 0.013 0.04 0.14 1 -0.19 12 13
ARF1/GTP/ARHGAP10 0.024 0.01 -10000 0 -0.11 1 1
GGA3 0.041 0.007 -10000 0 0 18 18
ARF1/GTP/Membrin 0.023 0.05 -10000 0 -0.22 21 21
AP2A1 0.039 0.011 -10000 0 0 43 43
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.011 0.033 -10000 0 -0.16 14 14
ARF1/GDP/Membrin 0.025 0.057 -10000 0 -0.25 21 21
Arfaptin 2/Rac/GDP 0.051 0.019 -10000 0 -0.11 1 1
CYTH2 -0.003 0.003 0.013 6 -0.02 1 7
ARF1/GTP/GGA3 0.049 0.02 -10000 0 -0.12 2 2
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.029 0.01 -10000 0 -0.13 1 1
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.008 0.055 -10000 0 -0.16 34 34
PLD2 0.01 0.016 0.08 24 -10000 0 24
ARF-GAP1/v-SNARE -0.009 0.004 0 77 -10000 0 77
PIP5K1A 0.01 0.016 0.08 24 -10000 0 24
ARF1/GTP/Membrin/GBF1/p115 0.018 0.025 -10000 0 -0.075 17 17
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.01 0.016 0.08 24 -10000 0 24
KDEL Receptor/Ligand/ARF-GAP1 -0.009 0.004 0 77 -10000 0 77
GOSR2 0.011 0.052 -10000 0 -0.31 14 14
USO1 0.004 0.008 0.04 25 -0.029 1 26
GBF1 0.005 0.07 -10000 0 -0.34 22 22
ARF1/GTP/Arfaptin 2 0.05 0.02 -10000 0 -0.12 1 1
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.038 0.061 -10000 0 -0.13 38 38
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.038 0.017 -10000 0 -0.13 3 3
PDGFRB 0.037 0.014 -10000 0 0 64 64
SPHK1 0.014 0.073 -10000 0 -0.61 7 7
mol:S1P 0.013 0.067 -10000 0 -0.51 7 7
S1P1/S1P/Gi 0.021 0.09 -10000 0 -0.32 23 23
GNAO1 0.034 0.018 -10000 0 -0.002 108 108
PDGFB-D/PDGFRB/PLCgamma1 0.01 0.11 0.26 4 -0.28 32 36
PLCG1 0.008 0.094 0.21 12 -0.3 25 37
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.037 0.014 -10000 0 0 64 64
GNAI2 0.041 0.012 -10000 0 -0.013 24 24
GNAI3 0.039 0.015 -10000 0 -0.005 53 53
GNAI1 0.035 0.018 -10000 0 -0.002 102 102
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 0.026 0.024 0.2 6 -0.12 3 9
S1P1/S1P 0.023 0.061 -10000 0 -0.32 8 8
negative regulation of cAMP metabolic process 0.021 0.089 -10000 0 -0.32 23 23
MAPK3 0.009 0.1 -10000 0 -0.44 17 17
calcium-dependent phospholipase C activity 0 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.029 0.01 -10000 0 -0.13 1 1
RhoA/GDP 0.03 0.012 -10000 0 -0.13 3 3
KDR 0.044 0.011 -10000 0 -10000 0 0
PLCB2 0.017 0.059 -10000 0 -0.29 8 8
RAC1 0.039 0.01 -10000 0 0 33 33
RhoA/GTP 0.024 0.056 -10000 0 -0.27 9 9
receptor internalization 0.021 0.058 -10000 0 -0.3 8 8
PTGS2 -0.001 0.15 -10000 0 -0.72 14 14
Rac1/GTP 0.022 0.055 -10000 0 -0.28 8 8
RHOA 0.041 0.007 -10000 0 0 14 14
VEGFA 0.004 0.002 -10000 0 -10000 0 0
negative regulation of T cell proliferation 0.021 0.089 -10000 0 -0.32 23 23
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.039 0.015 -10000 0 -0.006 51 51
MAPK1 0.01 0.11 -10000 0 -0.47 16 16
S1P1/S1P/PDGFB-D/PDGFRB 0.034 0.072 0.22 2 -0.24 11 13
ABCC1 0.041 0.009 -10000 0 0 26 26
Arf6 trafficking events

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
SLC2A4 0.04 0.01 -10000 0 0 32 32
CLTC 0.015 0.089 0.22 2 -0.43 13 15
calcium ion-dependent exocytosis 0.017 0.045 0.18 2 -0.16 12 14
Dynamin 2/GTP 0.021 0.042 -10000 0 -0.11 45 45
EXOC4 0.038 0.012 -10000 0 0 49 49
CD59 0.01 0.062 -10000 0 -0.35 11 11
CPE 0.012 0.013 -10000 0 -0.11 4 4
CTNNB1 0.04 0.01 -10000 0 0 31 31
membrane fusion 0.005 0.035 0.11 6 -0.11 35 41
CTNND1 -0.006 0.072 0.18 57 -0.18 4 61
DNM2 0.037 0.014 -10000 0 0 72 72
mol:PI-4-5-P2 0.017 0.056 0.18 6 -0.23 13 19
TSHR 0.014 0.015 -10000 0 -0.11 7 7
INS 0.006 0.1 -10000 0 -0.44 26 26
BIN1 0.041 0.007 -10000 0 0 18 18
mol:Choline 0.005 0.035 0.11 6 -0.11 35 41
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.014 0.014 -10000 0 -0.11 5 5
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.041 0.008 -10000 0 0 19 19
mol:Ca2+ 0.021 0.042 -10000 0 -0.11 45 45
JUP 0.009 0.064 -10000 0 -0.33 13 13
ASAP2/amphiphysin II 0.048 0.023 -10000 0 -0.098 11 11
ARF6/GTP 0.028 0.019 -10000 0 -0.13 8 8
CDH1 0.007 0.064 -10000 0 -0.36 11 11
clathrin-independent pinocytosis 0.028 0.019 -10000 0 -0.13 8 8
MAPK8IP3 0.04 0.009 -10000 0 0 28 28
positive regulation of endocytosis 0.028 0.019 -10000 0 -0.13 8 8
EXOC2 0.041 0.006 -10000 0 0 13 13
substrate adhesion-dependent cell spreading 0.009 0.1 -10000 0 -0.27 47 47
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.039 0.011 -10000 0 0 42 42
regulation of calcium-dependent cell-cell adhesion -0.035 0.086 0.28 18 -0.21 9 27
positive regulation of phagocytosis 0.015 0.015 -10000 0 -0.11 7 7
ARF6/GTP/JIP3 0.05 0.024 -10000 0 -0.11 8 8
ACAP1 0.005 0.034 0.11 6 -0.18 8 14
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.013 0.061 -10000 0 -0.34 11 11
clathrin heavy chain/ACAP1 0.015 0.078 0.21 6 -0.35 13 19
JIP4/KLC1 0.045 0.03 -10000 0 -0.098 18 18
EXOC1 0.039 0.012 -10000 0 0 46 46
exocyst 0.009 0.1 -10000 0 -0.28 47 47
RALA/GTP 0.027 0.021 -10000 0 -0.13 9 9
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.047 0.032 -10000 0 -0.11 18 18
receptor recycling 0.028 0.019 -10000 0 -0.13 8 8
CTNNA1 -0.006 0.071 0.18 55 -0.2 3 58
NME1 0.014 0.014 -10000 0 -0.11 5 5
clathrin coat assembly 0.015 0.089 0.22 2 -0.43 13 15
IL2RA 0.014 0.061 0.22 1 -0.35 10 11
VAMP3 0.015 0.015 -10000 0 -0.11 7 7
GLUT4/clathrin heavy chain/ACAP1 0.039 0.081 0.2 4 -0.32 13 17
EXOC6 0.038 0.012 -10000 0 0 55 55
PLD1 0.001 0.05 0.11 7 -0.19 29 36
PLD2 0.015 0.029 0.11 13 -0.11 19 32
EXOC5 0.04 0.009 -10000 0 0 27 27
PIP5K1C 0.013 0.05 0.16 6 -0.22 11 17
SDC1 0.011 0.061 -10000 0 -0.34 11 11
ARF6/GDP 0.025 0.04 -10000 0 -0.12 38 38
EXOC7 0.041 0.006 -10000 0 0 12 12
E-cadherin/beta catenin 0.038 0.089 0.22 9 -0.29 18 27
mol:Phosphatidic acid 0.005 0.035 0.11 6 -0.11 35 41
endocytosis -0.047 0.023 0.098 11 -10000 0 11
SCAMP2 0.04 0.008 -10000 0 0 23 23
ADRB2 0.008 0.087 0.21 4 -0.39 15 19
EXOC3 0.041 0.005 -10000 0 0 8 8
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.026 0.046 0.19 5 -0.11 45 50
KLC1 0 0 -10000 0 -10000 0 0
AVPR2 0.008 0.086 0.2 2 -0.4 14 16
RALA 0.04 0.009 -10000 0 0 30 30
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.021 0.091 0.22 2 -0.3 19 21
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.063 0.035 -9999 0 -0.098 17 17
MAPK9 0.009 0.002 -9999 0 0 39 39
adrenocorticotropin secretion -0.01 0.003 0 44 -10000 0 44
GNB1/GNG2 0.049 0.032 -9999 0 -0.11 19 19
GNB1 0.041 0.005 -9999 0 0 7 7
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
MAPK14 0.009 0.002 -9999 0 0 28 28
Gs family/GTP 0.026 0.006 -9999 0 -10000 0 0
EntrezGene:2778 0 0 -9999 0 -10000 0 0
vasopressin secretion 0 0 -9999 0 -10000 0 0
G-protein coupled receptor activity 0 0 -9999 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
glutamate secretion 0.002 0 -9999 0 -10000 0 0
GNAL 0.04 0.009 -9999 0 0 26 26
GNG2 0.039 0.01 -9999 0 0 34 34
CRH 0.039 0.011 -9999 0 0 44 44
mol:cortisol 0 0 -9999 0 -10000 0 0
MAPK8 0.009 0.002 -9999 0 0 30 30
MAPK11 0.007 0.004 -9999 0 0 141 141
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0.015 0.12 -10000 0 -0.85 9 9
MKNK1 0.04 0.009 -10000 0 0 25 25
MAPK14 0.042 0.053 0.17 1 -0.26 10 11
ATF2/c-Jun -0.02 0.1 -10000 0 -0.31 43 43
MAPK11 0.031 0.054 -10000 0 -0.14 30 30
MITF 0.019 0.061 -10000 0 -0.29 15 15
MAPKAPK5 0.019 0.058 -10000 0 -0.26 17 17
KRT8 0.016 0.061 -10000 0 -0.23 24 24
MAPKAPK3 0.041 0.006 -10000 0 0 13 13
MAPKAPK2 0.04 0.008 -10000 0 0 23 23
p38alpha-beta/CK2 0.042 0.078 -10000 0 -0.31 14 14
CEBPB 0.021 0.053 -10000 0 -0.28 10 10
SLC9A1 0.02 0.056 -10000 0 -0.28 14 14
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.014 0.074 0.23 1 -0.24 28 29
p38alpha-beta/MNK1 0.053 0.077 -10000 0 -0.32 10 10
JUN -0.023 0.1 -10000 0 -0.31 43 43
PPARGC1A 0.022 0.054 -10000 0 -0.28 12 12
USF1 0.018 0.058 -10000 0 -0.26 17 17
RAB5/GDP/GDI1 0.005 0.077 -10000 0 -0.2 26 26
NOS2 0.014 0.055 -10000 0 -0.28 14 14
DDIT3 0.016 0.061 -10000 0 -0.22 25 25
RAB5A 0.041 0.006 -10000 0 0 13 13
HSPB1 0.002 0.05 0.28 2 -0.23 16 18
p38alpha-beta/HBP1 0.045 0.084 -10000 0 -0.21 25 25
CREB1 -0.005 0.099 -10000 0 -0.3 19 19
RAB5/GDP 0.03 0.012 -10000 0 -0.13 3 3
EIF4E -0.007 0.064 0.19 23 -0.3 9 32
RPS6KA4 0.02 0.056 -10000 0 -0.28 14 14
PLA2G4A -0.009 0.059 0.2 11 -0.35 9 20
GDI1 0.017 0.061 -10000 0 -0.25 21 21
TP53 0.001 0.063 -10000 0 -0.36 12 12
RPS6KA5 0.018 0.059 -10000 0 -0.25 18 18
ESR1 0.007 0.075 -10000 0 -0.22 44 44
HBP1 0.038 0.012 -10000 0 0 50 50
MEF2C 0.015 0.068 -10000 0 -0.28 20 20
MEF2A 0.017 0.058 -10000 0 -0.25 18 18
EIF4EBP1 0 0.092 -10000 0 -0.29 18 18
KRT19 0.007 0.08 -10000 0 -0.22 47 47
ELK4 0.019 0.057 -10000 0 -0.27 15 15
ATF6 0.018 0.056 -10000 0 -0.26 16 16
ATF1 -0.005 0.099 -10000 0 -0.29 20 20
p38alpha-beta/MAPKAPK2 0.053 0.077 -10000 0 -0.29 11 11
p38alpha-beta/MAPKAPK3 0.055 0.076 -10000 0 -0.33 9 9
Effects of Botulinum toxin

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
STX1A -0.01 0.002 0 13 -10000 0 13
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.057 0.019 -10000 0 -0.14 2 2
STXBP1 0.039 0.011 -10000 0 0 41 41
ACh/CHRNA1 0.029 0.025 0.092 2 -0.051 31 33
RAB3GAP2/RIMS1/UNC13B 0.071 0.04 -10000 0 -0.12 14 14
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.041 0.007 -10000 0 0 15 15
mol:ACh 0.004 0.025 0.073 35 -0.085 5 40
RAB3GAP2 0.039 0.01 -10000 0 0 37 37
STX1A/SNAP25/VAMP2 0.057 0.057 0.18 2 -0.13 5 7
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.029 0.025 0.092 2 -0.051 31 33
UNC13B 0.04 0.009 -10000 0 0 25 25
CHRNA1 0.038 0.013 -10000 0 0 59 59
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.03 0.026 0.092 2 -0.051 32 34
SNAP25 0.006 0.002 -10000 0 0 71 71
VAMP2 0.005 0.002 -10000 0 0 66 66
SYT1 0.038 0.012 -10000 0 0 47 47
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.034 0.011 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.057 0.057 0.18 2 -0.13 5 7
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.047 0.012 -10000 0 -0.072 4 4
NFATC2 0.048 0.18 0.41 5 -0.38 37 42
NFATC3 0.069 0.067 0.29 26 -0.26 2 28
CD40LG 0.083 0.15 0.49 5 -0.46 5 10
ITCH 0.021 0.057 0.2 6 -0.22 22 28
CBLB 0.019 0.061 0.2 6 -0.24 24 30
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment 0.047 0.14 0.38 1 -0.52 7 8
JUNB 0.03 0.019 -10000 0 0 160 160
CaM/Ca2+/Calcineurin A alpha-beta B1 0.043 0.051 -10000 0 -0.18 24 24
T cell anergy 0.002 0.071 0.27 6 -0.29 20 26
TLE4 0.01 0.16 0.28 4 -0.41 47 51
Jun/NFAT1-c-4/p21SNFT 0.082 0.15 -10000 0 -0.46 3 3
AP-1/NFAT1-c-4 0.092 0.19 -10000 0 -0.52 4 4
IKZF1 0.023 0.11 0.22 19 -0.25 37 56
T-helper 2 cell differentiation 0.035 0.14 0.45 2 -0.49 1 3
AP-1/NFAT1 0.038 0.14 0.33 1 -0.25 41 42
CALM1 0.042 0.036 -10000 0 -0.11 25 25
EGR2 0.06 0.16 0.51 19 -0.66 5 24
EGR3 0.053 0.14 0.57 6 -0.51 2 8
NFAT1/FOXP3 0.059 0.14 0.33 3 -0.27 34 37
EGR1 0.028 0.021 -10000 0 -0.035 2 2
JUN 0.04 0.026 0.14 2 -0.052 5 7
EGR4 0.041 0.009 -10000 0 -0.004 20 20
mol:Ca2+ 0.005 0.022 -10000 0 -0.1 23 23
GBP3 -0.018 0.21 0.3 9 -0.46 90 99
FOSL1 0.041 0.007 -10000 0 0 15 15
NFAT1-c-4/MAF/IRF4 0.095 0.15 -10000 0 -0.46 3 3
DGKA 0.026 0.12 0.3 6 -0.31 30 36
CREM 0.04 0.008 -10000 0 -0.002 21 21
NFAT1-c-4/PPARG 0.084 0.14 -10000 0 -0.5 2 2
CTLA4 0.027 0.1 0.23 1 -0.24 31 32
NFAT1-c-4 (dimer)/EGR1 0.063 0.15 -10000 0 -0.51 3 3
NFAT1-c-4 (dimer)/EGR4 0.091 0.15 -10000 0 -0.48 3 3
FOS 0.029 0.029 0.14 2 -0.043 6 8
IFNG 0.036 0.13 -10000 0 -0.49 6 6
T cell activation 0.054 0.12 0.6 1 -10000 0 1
MAF 0.036 0.015 -10000 0 0 83 83
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.06 0.13 0.56 3 -0.51 22 25
TNF 0.047 0.13 0.44 3 -0.47 4 7
FASLG 0.05 0.17 0.7 1 -1 3 4
TBX21 0.047 0.013 -10000 0 -10000 0 0
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ 0.037 0.018 -10000 0 -0.12 1 1
PTPN1 0.027 0.12 0.32 3 -0.28 33 36
NFAT1-c-4/ICER1 0.085 0.14 -10000 0 -0.48 3 3
GATA3 0.042 0.011 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.039 0.13 -10000 0 -0.48 6 6
IL2RA 0.05 0.15 0.39 1 -0.46 9 10
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.022 0.12 -10000 0 -0.32 28 28
E2F1 0.032 0.05 -10000 0 -0.18 27 27
PPARG 0.039 0.01 -10000 0 -10000 0 0
SLC3A2 0.025 0.13 0.29 5 -0.31 33 38
IRF4 0.041 0.008 -10000 0 0 19 19
PTGS2 0.056 0.14 0.68 1 -0.5 4 5
CSF2 0.078 0.15 0.49 5 -0.46 5 10
JunB/Fra1/NFAT1-c-4 0.077 0.15 -10000 0 -0.46 3 3
IL4 0.034 0.14 0.45 2 -0.51 1 3
IL5 0.078 0.15 0.48 4 -0.46 5 9
IL2 0.054 0.12 0.6 1 -10000 0 1
IL3 0.036 0.079 -10000 0 -0.42 8 8
RNF128 0.023 0.045 0.2 7 -0.15 24 31
NFATC1 0.06 0.13 0.51 22 -0.57 3 25
CDK4 -0.078 0.28 -10000 0 -1.2 28 28
PTPRK 0.012 0.15 0.28 5 -0.39 45 50
IL8 0.048 0.14 0.55 4 -0.46 5 9
POU2F1 0.046 0.01 -10000 0 -10000 0 0
Aurora C signaling

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
INCENP 0.042 0.004 -9999 0 0 5 5
Aurora C/Aurora B/INCENP 0.063 0.046 -9999 0 -0.1 28 28
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.005 0.065 -9999 0 -0.39 14 14
AURKB 0.036 0.015 -9999 0 0 80 80
AURKC 0.042 0.002 -9999 0 0 1 1
Glypican 2 network

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
MDK 0.04 0.009 -9999 0 0 24 24
GPC2 0.04 0.008 -9999 0 0 22 22
GPC2/Midkine 0.055 0.032 -9999 0 -0.14 13 13
neuron projection morphogenesis 0.054 0.032 -9999 0 -0.14 13 13
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 0.011 0.067 0.28 5 -0.4 2 7
CRKL 0.014 0.062 -10000 0 -0.42 2 2
HRAS 0.028 0.08 0.25 1 -0.33 4 5
mol:PIP3 0.023 0.089 0.36 1 -0.37 5 6
SPRED1 0.035 0.015 -10000 0 0 90 90
SPRED2 0.04 0.009 -10000 0 0 24 24
GAB1 0.019 0.06 -10000 0 -0.44 2 2
FOXO3 0.021 0.092 0.35 1 -0.39 11 12
AKT1 0.021 0.097 0.37 1 -0.42 11 12
BAD 0.017 0.093 0.35 1 -0.39 11 12
megakaryocyte differentiation 0.023 0.059 0.24 3 -0.3 1 4
GSK3B 0.021 0.099 0.33 7 -0.39 11 18
RAF1 0.021 0.075 0.26 6 -0.29 4 10
SHC1 0.04 0.01 -10000 0 0 31 31
STAT3 0.019 0.06 0.26 3 -0.44 2 5
STAT1 0.032 0.11 -10000 0 -1 2 2
HRAS/SPRED1 0.034 0.083 0.26 3 -0.31 4 7
cell proliferation 0.018 0.062 0.25 2 -0.43 2 4
PIK3CA 0.03 0.019 -10000 0 0 155 155
TEC 0.033 0.017 -10000 0 0 114 114
RPS6KB1 0.021 0.099 0.3 1 -0.4 9 10
HRAS/SPRED2 0.04 0.083 0.26 3 -0.28 5 8
LYN/TEC/p62DOK 0.041 0.097 -10000 0 -0.38 3 3
MAPK3 0.016 0.065 0.22 7 -0.24 5 12
STAP1 0.023 0.061 0.25 2 -0.43 2 4
GRAP2 0.038 0.013 -10000 0 0 56 56
JAK2 0.029 0.11 -10000 0 -0.88 2 2
STAT1 (dimer) 0.031 0.11 -10000 0 -1 2 2
mol:Gleevec -0.002 0.003 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.062 0.092 -10000 0 -0.38 3 3
actin filament polymerization 0.024 0.061 0.25 2 -0.42 2 4
LYN 0.036 0.015 -10000 0 0 83 83
STAP1/STAT5A (dimer) 0.017 0.099 0.3 1 -0.5 5 6
PIK3R1 0.034 0.017 -10000 0 0 107 107
CBL/CRKL/GRB2 0.044 0.083 0.42 1 -0.43 2 3
PI3K 0.024 0.1 0.32 1 -0.39 8 9
PTEN 0.039 0.011 -10000 0 0 38 38
SCF/KIT/EPO/EPOR 0.061 0.14 -10000 0 -1.3 2 2
MAPK8 0.018 0.062 0.24 3 -0.44 2 5
STAT3 (dimer) 0.02 0.062 0.26 3 -0.43 2 5
positive regulation of transcription 0.016 0.057 0.21 7 -0.2 4 11
mol:GDP 0.037 0.085 0.27 1 -0.32 4 5
PIK3C2B 0.019 0.065 0.26 3 -0.44 2 5
CBL/CRKL 0.03 0.076 0.42 1 -0.44 2 3
FER 0.019 0.061 0.24 2 -0.44 2 4
SH2B3 0.023 0.061 0.25 2 -0.43 2 4
PDPK1 0.022 0.086 0.29 4 -0.36 3 7
SNAI2 0.024 0.067 0.25 4 -0.51 2 6
positive regulation of cell proliferation 0.02 0.11 -10000 0 -0.7 3 3
KITLG 0.044 0.015 -10000 0 -0.041 3 3
cell motility 0.02 0.11 -10000 0 -0.7 3 3
PTPN6 0.033 0.017 -10000 0 -0.005 80 80
EPOR 0.009 0.17 -10000 0 -0.7 8 8
STAT5A (dimer) 0.021 0.1 -10000 0 -0.51 5 5
SOCS1 0.038 0.012 -10000 0 0 50 50
cell migration -0.018 0.059 0.43 2 -0.26 1 3
SOS1 0.038 0.013 -10000 0 0 56 56
EPO 0.043 0.011 -10000 0 -0.035 3 3
VAV1 0.037 0.014 -10000 0 0 68 68
GRB10 0.018 0.062 0.26 1 -0.44 2 3
PTPN11 0.038 0.011 -10000 0 -0.004 31 31
SCF/KIT 0.027 0.064 0.26 2 -0.45 2 4
GO:0007205 -0.002 0.004 -10000 0 -0.023 1 1
MAP2K1 0.014 0.067 0.23 9 -0.24 3 12
CBL 0.04 0.008 -10000 0 0 23 23
KIT 0.018 0.16 -10000 0 -0.77 4 4
MAP2K2 0.013 0.062 0.22 7 -0.23 4 11
SHC/Grb2/SOS1 0.065 0.093 -10000 0 -0.36 3 3
STAT5A 0.023 0.099 -10000 0 -0.53 5 5
GRB2 0.041 0.007 -10000 0 0 16 16
response to radiation 0.027 0.071 0.26 6 -0.5 2 8
SHC/GRAP2 0.053 0.023 -10000 0 -0.14 1 1
PTPRO 0.02 0.055 0.24 3 -0.3 1 4
SH2B2 0.023 0.061 0.25 2 -0.43 2 4
DOK1 0.04 0.009 -10000 0 0 24 24
MATK 0.018 0.059 0.26 1 -0.44 2 3
CREBBP 0.059 0.029 0.15 1 -0.15 3 4
BCL2 -0.021 0.23 -10000 0 -0.84 9 9
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.062 0.028 -10000 0 -0.098 1 1
RGS9BP 0.037 0.013 -10000 0 0 62 62
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
mol:Na + 0.05 0.017 -10000 0 -10000 0 0
mol:ADP -0.01 0.003 -10000 0 -10000 0 0
GNAT2 0.041 0.005 -10000 0 0 8 8
RGS9-1/Gbeta5/R9AP 0.067 0.035 -10000 0 -0.12 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.05 0.018 -10000 0 -10000 0 0
GRK7 0.038 0.012 -10000 0 0 50 50
CNGB3 0.038 0.012 -10000 0 0 53 53
Cone Metarhodopsin II/X-Arrestin 0.031 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.003 0.057 0.19 43 -10000 0 43
Cone PDE6 0.088 0.057 -10000 0 -0.11 1 1
Cone Metarhodopsin II 0.024 0.008 -10000 0 -10000 0 0
Na + (4 Units) 0.066 0.03 -10000 0 -10000 0 0
GNAT2/GDP 0.08 0.039 -10000 0 -0.1 1 1
GNB5 0.04 0.009 -10000 0 0 28 28
mol:GMP (4 units) -0.002 0.06 0.19 49 -10000 0 49
Cone Transducin 0.067 0.031 -10000 0 -0.1 1 1
SLC24A2 0.039 0.011 -10000 0 0 41 41
GNB3/GNGT2 0.052 0.024 -10000 0 -0.14 1 1
GNB3 0.037 0.014 -10000 0 0 66 66
GNAT2/GTP 0.031 0.004 -10000 0 -10000 0 0
CNGA3 0.041 0.005 -10000 0 0 7 7
ARR3 0.042 0.002 -10000 0 0 1 1
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.051 0.018 -10000 0 -10000 0 0
mol:Pi 0.066 0.035 -10000 0 -0.12 1 1
Cone CNG Channel 0.079 0.046 -10000 0 -10000 0 0
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.039 0.011 -10000 0 0 41 41
RGS9 0.039 0.011 -10000 0 0 39 39
PDE6C 0.04 0.009 -10000 0 0 24 24
GNGT2 0.04 0.009 -10000 0 0 25 25
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.038 0.013 -10000 0 0 59 59
Visual signal transduction: Rods

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
mol:K + 0.04 0.008 -10000 0 0 20 20
GNAT1/GTP 0.03 0.005 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.053 0.013 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.049 0.021 -10000 0 -0.11 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.041 0.007 -10000 0 0 15 15
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel 0.069 0.037 -10000 0 -0.11 2 2
mol:Na + 0.069 0.042 -10000 0 -0.11 1 1
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.067 0.035 -10000 0 -0.12 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.086 0.05 -10000 0 -0.11 1 1
CNGB1 0.038 0.012 -10000 0 0 50 50
RDH5 0.037 0.014 -10000 0 0 72 72
SAG 0.041 0.006 -10000 0 0 10 10
mol:Ca2+ -0.018 0.082 0.33 21 -10000 0 21
Na + (4 Units) 0.056 0.038 -10000 0 -0.11 1 1
RGS9 0.039 0.011 -10000 0 0 39 39
GNB1/GNGT1 0.057 0.023 -10000 0 -0.14 5 5
GNAT1/GDP 0.079 0.039 -10000 0 -0.1 1 1
GUCY2D 0.039 0.01 -10000 0 0 36 36
GNGT1 0.04 0.009 -10000 0 0 29 29
GUCY2F 0.042 0.002 -10000 0 0 1 1
GNB5 0.04 0.009 -10000 0 0 28 28
mol:GMP (4 units) 0.04 0.025 0.17 13 -0.1 2 15
mol:11-cis-retinal 0.037 0.014 -10000 0 0 72 72
mol:cGMP 0.077 0.034 0.2 2 -0.11 1 3
GNB1 0.041 0.005 -10000 0 0 7 7
Rhodopsin 0.05 0.03 -10000 0 -0.14 7 7
SLC24A1 0.04 0.008 -10000 0 0 20 20
CNGA1 0.041 0.007 -10000 0 0 18 18
Metarhodopsin II 0.026 0.005 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.093 0.038 -10000 0 -0.11 1 1
RGS9BP 0.037 0.013 -10000 0 0 62 62
Metarhodopsin II/Transducin 0.025 0.019 -10000 0 -0.14 6 6
GCAP Family/Ca ++ 0.073 0.024 -10000 0 -0.1 1 1
PDE6A/B 0.059 0.013 -10000 0 -10000 0 0
mol:Pi 0.066 0.035 -10000 0 -0.12 1 1
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.073 0.027 -10000 0 -0.1 5 5
PDE6B 0.041 0.005 -10000 0 0 7 7
PDE6A 0.041 0.008 -10000 0 0 19 19
PDE6G 0.038 0.013 -10000 0 0 58 58
RHO 0.04 0.008 -10000 0 0 23 23
PDE6 0.096 0.054 -10000 0 -0.15 2 2
GUCA1A 0.04 0.009 -10000 0 0 25 25
GC2/GCAP Family 0.098 0.031 -10000 0 -0.11 1 1
GUCA1C 0.04 0.009 -10000 0 0 28 28
GUCA1B 0.04 0.008 -10000 0 0 23 23
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/1669117/2.GDAC_MergeDataFiles.Finished/OV.exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data.data.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/writeReducedSegments/OV/1676920/1.GetReducedSegments.Finished/OV.RS.tsv

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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