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 108 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 145
TCGA08_p53 104
HIF-1-alpha transcription factor network 96
Ephrin B reverse signaling 96
Endothelins 95
LPA receptor mediated events 92
Osteopontin-mediated events 89
Wnt signaling 89
Syndecan-1-mediated signaling events 88
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 145 7413 51 -0.52 0.038 1000 -1000 -0.011 -1000
TCGA08_p53 104 730 7 -0.063 0.038 1000 -1000 -0.009 -1000
HIF-1-alpha transcription factor network 96 7324 76 -0.048 0.096 1000 -1000 0 -1000
Ephrin B reverse signaling 96 4610 48 -0.2 0.08 1000 -1000 -0.057 -1000
Endothelins 95 9207 96 -0.18 0.044 1000 -1000 -0.015 -1000
LPA receptor mediated events 92 9475 102 -0.047 0.041 1000 -1000 -0.059 -1000
Osteopontin-mediated events 89 3417 38 -0.18 0.041 1000 -1000 -0.019 -1000
Wnt signaling 89 623 7 -0.019 0.041 1000 -1000 0.002 -1000
Syndecan-1-mediated signaling events 88 3000 34 -0.036 0.04 1000 -1000 -0.002 -1000
Nectin adhesion pathway 86 5476 63 -0.083 0.062 1000 -1000 -0.004 -1000
PDGFR-alpha signaling pathway 83 3662 44 -0.12 0.05 1000 -1000 -0.023 -1000
amb2 Integrin signaling 83 6813 82 -0.083 0.082 1000 -1000 -0.013 -1000
TCGA08_retinoblastoma 81 651 8 -0.012 0.029 1000 -1000 -0.003 -1000
LPA4-mediated signaling events 80 970 12 -0.015 0.054 1000 -1000 -0.014 -1000
Thromboxane A2 receptor signaling 80 8454 105 -0.15 0.071 1000 -1000 -0.019 -1000
TRAIL signaling pathway 78 3763 48 -0.022 0.042 1000 -1000 -0.025 -1000
Nongenotropic Androgen signaling 77 4038 52 -0.12 0.061 1000 -1000 -0.02 -1000
BARD1 signaling events 76 4340 57 -0.038 0.064 1000 -1000 -0.066 -1000
TCGA08_rtk_signaling 73 1918 26 -0.017 0.04 1000 -1000 -0.018 -1000
Ras signaling in the CD4+ TCR pathway 73 1248 17 -0.002 0.054 1000 -1000 0 -1000
Paxillin-dependent events mediated by a4b1 71 2560 36 -0.066 0.069 1000 -1000 -0.053 -1000
IL6-mediated signaling events 71 5363 75 -0.14 0.05 1000 -1000 -0.042 -1000
Integrins in angiogenesis 70 5895 84 -0.057 0.056 1000 -1000 -0.017 -1000
Syndecan-4-mediated signaling events 70 4737 67 -0.06 0.046 1000 -1000 -0.031 -1000
Signaling events mediated by the Hedgehog family 69 3628 52 -0.065 0.058 1000 -1000 -0.023 -1000
IL23-mediated signaling events 68 4114 60 -0.16 0.055 1000 -1000 -0.04 -1000
IL1-mediated signaling events 67 4190 62 -0.045 0.073 1000 -1000 -0.017 -1000
E-cadherin signaling in keratinocytes 67 2892 43 -0.026 0.05 1000 -1000 -0.007 -1000
FoxO family signaling 66 4224 64 -0.2 0.046 1000 -1000 -0.011 -1000
Signaling events mediated by PRL 66 2251 34 -0.018 0.04 1000 -1000 -0.023 -1000
Cellular roles of Anthrax toxin 65 2561 39 -0.078 0.04 1000 -1000 -0.014 -1000
Signaling events mediated by PTP1B 65 4983 76 -0.058 0.07 1000 -1000 -0.025 -1000
Fc-epsilon receptor I signaling in mast cells 64 6213 97 -0.072 0.046 1000 -1000 -0.034 -1000
Canonical Wnt signaling pathway 64 3293 51 -0.18 0.099 1000 -1000 -0.017 -1000
IGF1 pathway 64 3674 57 -0.022 0.065 1000 -1000 -0.017 -1000
IL12-mediated signaling events 63 5490 87 -0.19 0.061 1000 -1000 -0.024 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 63 5406 85 -0.16 0.051 1000 -1000 -0.027 -1000
IL2 signaling events mediated by STAT5 62 1367 22 -0.039 0.047 1000 -1000 -0.004 -1000
IL4-mediated signaling events 60 5526 91 -0.23 0.058 1000 -1000 -0.022 -1000
Noncanonical Wnt signaling pathway 59 1546 26 -0.032 0.041 1000 -1000 -0.03 -1000
a4b1 and a4b7 Integrin signaling 59 295 5 0.033 0.039 1000 -1000 0.037 -1000
BMP receptor signaling 59 4843 81 -0.02 0.07 1000 -1000 -0.011 -1000
TCR signaling in naïve CD8+ T cells 58 5484 93 -0.082 0.087 1000 -1000 -0.026 -1000
IFN-gamma pathway 57 3909 68 -0.058 0.063 1000 -1000 -0.03 -1000
EPHB forward signaling 57 4890 85 -0.055 0.16 1000 -1000 -0.037 -1000
E-cadherin signaling in the nascent adherens junction 56 4310 76 -0.057 0.071 1000 -1000 -0.027 -1000
E-cadherin signaling events 56 280 5 0.035 0.049 1000 -1000 0.037 -1000
Paxillin-independent events mediated by a4b1 and a4b7 55 2051 37 -0.02 0.07 1000 -1000 -0.012 -1000
Retinoic acid receptors-mediated signaling 55 3191 58 -0.079 0.06 1000 -1000 -0.007 -1000
BCR signaling pathway 55 5464 99 -0.075 0.069 1000 -1000 -0.025 -1000
Plasma membrane estrogen receptor signaling 55 4793 86 -0.09 0.086 1000 -1000 -0.014 -1000
FAS signaling pathway (CD95) 54 2582 47 -0.058 0.052 1000 -1000 -0.024 -1000
Syndecan-2-mediated signaling events 52 3642 69 0 0.063 1000 -1000 -0.01 -1000
IL2 signaling events mediated by PI3K 51 2983 58 -0.064 0.041 1000 -1000 -0.014 -1000
Class I PI3K signaling events 50 3660 73 -0.015 0.05 1000 -1000 -0.017 -1000
Caspase cascade in apoptosis 49 3643 74 -0.11 0.051 1000 -1000 -0.017 -1000
Presenilin action in Notch and Wnt signaling 49 3032 61 -0.16 0.075 1000 -1000 -0.026 -1000
HIF-2-alpha transcription factor network 49 2129 43 -0.061 0.069 1000 -1000 -0.071 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 49 2234 45 -0.058 0.075 1000 -1000 -0.015 -1000
Circadian rhythm pathway 48 1069 22 -0.081 0.044 1000 -1000 -0.023 -1000
Stabilization and expansion of the E-cadherin adherens junction 48 3578 74 -0.076 0.066 1000 -1000 -0.056 -1000
ErbB4 signaling events 47 3257 69 -0.07 0.056 1000 -1000 -0.029 -1000
EPO signaling pathway 47 2603 55 0 0.072 1000 -1000 -0.013 -1000
Aurora B signaling 47 3163 67 -0.058 0.067 1000 -1000 -0.023 -1000
Arf6 signaling events 46 2887 62 0 0.082 1000 -1000 0 -1000
Regulation of Androgen receptor activity 46 3287 70 -0.081 0.064 1000 -1000 -0.019 -1000
PLK1 signaling events 45 3862 85 -0.046 0.051 1000 -1000 -0.013 -1000
Regulation of Telomerase 45 4643 102 -0.11 0.071 1000 -1000 -0.016 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 44 1455 33 -0.005 0.086 1000 -1000 -0.009 -1000
Reelin signaling pathway 43 2435 56 -0.011 0.095 1000 -1000 -0.007 -1000
RXR and RAR heterodimerization with other nuclear receptor 43 2275 52 -0.038 0.095 1000 -1000 -0.016 -1000
Canonical NF-kappaB pathway 42 1653 39 -0.036 0.065 1000 -1000 -0.017 -1000
p75(NTR)-mediated signaling 42 5337 125 -0.059 0.099 1000 -1000 -0.035 -1000
Regulation of p38-alpha and p38-beta 41 2237 54 -0.029 0.091 1000 -1000 -0.003 -1000
mTOR signaling pathway 40 2121 53 -0.053 0.057 1000 -1000 -0.02 -1000
EGFR-dependent Endothelin signaling events 40 858 21 -0.016 0.081 1000 -1000 -0.004 -1000
Insulin-mediated glucose transport 39 1259 32 -0.018 0.047 1000 -1000 -0.017 -1000
Arf6 downstream pathway 38 1643 43 -0.034 0.061 1000 -1000 -0.048 -1000
Signaling mediated by p38-gamma and p38-delta 38 572 15 -0.038 0.039 1000 -1000 -0.017 -1000
Neurotrophic factor-mediated Trk receptor signaling 38 4670 120 -0.052 0.09 1000 -1000 -0.025 -1000
PDGFR-beta signaling pathway 38 3711 97 -0.036 0.083 1000 -1000 -0.035 -1000
ErbB2/ErbB3 signaling events 37 2466 65 -0.033 0.047 1000 -1000 -0.041 -1000
S1P5 pathway 37 639 17 -0.007 0.041 1000 -1000 -0.022 -1000
S1P3 pathway 37 1594 42 -0.02 0.054 1000 -1000 -0.009 -1000
p38 MAPK signaling pathway 37 1657 44 -0.043 0.072 1000 -1000 0 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 36 1976 54 -0.017 0.056 1000 -1000 -0.018 -1000
Syndecan-3-mediated signaling events 36 1274 35 -0.013 0.073 1000 -1000 -0.017 -1000
S1P4 pathway 36 904 25 -0.013 0.054 1000 -1000 -0.004 -1000
Aurora A signaling 35 2158 60 -0.046 0.066 1000 -1000 -0.017 -1000
ceramide signaling pathway 35 1761 49 -0.032 0.059 1000 -1000 -0.017 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 34 792 23 -0.017 0.066 1000 -1000 -0.003 -1000
Class I PI3K signaling events mediated by Akt 34 2327 68 -0.034 0.078 1000 -1000 -0.019 -1000
Class IB PI3K non-lipid kinase events 34 102 3 -0.039 0.039 1000 -1000 -0.038 -1000
JNK signaling in the CD4+ TCR pathway 33 575 17 -0.007 0.079 1000 -1000 0 -1000
Hedgehog signaling events mediated by Gli proteins 33 2178 65 0 0.076 1000 -1000 -0.02 -1000
Ceramide signaling pathway 33 2549 76 -0.019 0.081 1000 -1000 -0.017 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 33 2787 83 -0.013 0.071 1000 -1000 -0.016 -1000
Signaling events mediated by HDAC Class I 33 3477 104 -0.041 0.076 1000 -1000 -0.039 -1000
Regulation of nuclear SMAD2/3 signaling 32 4382 136 -0.091 0.1 1000 -1000 -0.053 -1000
Ephrin A reverse signaling 32 229 7 -0.013 0.04 1000 -1000 -0.005 -1000
Atypical NF-kappaB pathway 32 994 31 -0.016 0.041 1000 -1000 -0.017 -1000
FOXA2 and FOXA3 transcription factor networks 31 1471 46 -0.12 0.056 1000 -1000 -0.007 -1000
Signaling events mediated by VEGFR1 and VEGFR2 31 3877 125 -0.023 0.072 1000 -1000 -0.017 -1000
Coregulation of Androgen receptor activity 30 2283 76 -0.011 0.052 1000 -1000 -0.009 -1000
Glypican 1 network 29 1422 48 -0.04 0.069 1000 -1000 -0.038 -1000
Signaling events regulated by Ret tyrosine kinase 29 2384 82 -0.009 0.092 1000 -1000 -0.023 -1000
Insulin Pathway 29 2194 74 -0.026 0.1 1000 -1000 -0.026 -1000
Nephrin/Neph1 signaling in the kidney podocyte 28 964 34 -0.049 0.086 1000 -1000 -0.047 -1000
Sphingosine 1-phosphate (S1P) pathway 28 789 28 -0.019 0.054 1000 -1000 -0.017 -1000
Glucocorticoid receptor regulatory network 28 3234 114 -0.11 0.077 1000 -1000 -0.046 -1000
Alternative NF-kappaB pathway 28 366 13 0 0.094 1000 -1000 0 -1000
Signaling events mediated by HDAC Class II 26 1969 75 -0.036 0.094 1000 -1000 -0.025 -1000
Signaling mediated by p38-alpha and p38-beta 26 1182 44 -0.023 0.055 1000 -1000 -0.004 -1000
Calcium signaling in the CD4+ TCR pathway 26 830 31 -0.039 0.084 1000 -1000 -0.027 -1000
IL27-mediated signaling events 26 1370 51 -0.008 0.08 1000 -1000 -0.029 -1000
Angiopoietin receptor Tie2-mediated signaling 26 2375 88 -0.045 0.076 1000 -1000 -0.043 -1000
Signaling events mediated by HDAC Class III 25 1025 40 -0.064 0.072 1000 -1000 -0.055 -1000
Sumoylation by RanBP2 regulates transcriptional repression 24 663 27 -0.031 0.083 1000 -1000 -0.022 -1000
VEGFR1 specific signals 24 1393 56 -0.027 0.045 1000 -1000 -0.018 -1000
Arf1 pathway 24 1297 54 -0.01 0.052 1000 -1000 -0.009 -1000
S1P1 pathway 23 859 36 -0.001 0.044 1000 -1000 -0.011 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 22 1534 68 -0.078 0.095 1000 -1000 -0.026 -1000
Effects of Botulinum toxin 21 547 26 -0.01 0.071 1000 -1000 -0.009 -1000
Rapid glucocorticoid signaling 21 430 20 -0.01 0.049 1000 -1000 -0.009 -1000
Aurora C signaling 18 129 7 0 0.063 1000 -1000 -0.002 -1000
Glypican 2 network 18 72 4 0.04 0.055 1000 -1000 0.038 -1000
Arf6 trafficking events 18 1302 71 -0.047 0.05 1000 -1000 -0.036 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 18 1463 78 -0.021 0.065 1000 -1000 -0.027 -1000
Visual signal transduction: Cones 15 605 38 -0.01 0.088 1000 -1000 -0.01 -1000
Visual signal transduction: Rods 14 741 52 -0.018 0.098 1000 -1000 -0.004 -1000
Total 6630 363187 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 0 215 215
PLK4 0.036 0.015 -9999 0 0 83 83
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 -1.1 173 173
PLK1 -0.048 0.31 -10000 0 -1.2 34 34
BIRC5 -0.053 0.32 -10000 0 -1.3 35 35
HSPA1B -0.36 0.6 -10000 0 -1.1 182 182
MAP2K1 0.002 0.07 -10000 0 -10000 0 0
BRCA2 -0.36 0.61 -10000 0 -1.2 175 175
FOXM1 -0.52 0.88 -10000 0 -1.6 182 182
XRCC1 -0.35 0.6 -10000 0 -1.1 176 176
FOXM1B/p19 -0.44 0.66 -10000 0 -1.3 187 187
Cyclin D1/CDK4 -0.36 0.55 -10000 0 -1 191 191
CDC2 -0.42 0.68 -10000 0 -1.3 184 184
TGFA -0.32 0.52 0.63 1 -0.97 182 183
SKP2 -0.35 0.61 -10000 0 -1.1 174 174
CCNE1 0.02 0.029 -10000 0 -0.009 255 255
CKS1B -0.35 0.61 -10000 0 -1.2 171 171
RB1 -0.32 0.48 -10000 0 -0.97 170 170
FOXM1C/SP1 -0.44 0.71 -10000 0 -1.3 186 186
AURKB -0.1 0.4 -10000 0 -1.2 61 61
CENPF -0.39 0.63 -10000 0 -1.2 190 190
CDK4 0.007 0.044 0.11 3 -0.038 216 219
MYC -0.34 0.48 -10000 0 -0.94 189 189
CHEK2 0.005 0.065 -10000 0 -10000 0 0
ONECUT1 -0.36 0.58 -10000 0 -1.1 184 184
CDKN2A 0.026 0.02 0.089 2 -0.034 8 10
LAMA4 -0.39 0.63 -10000 0 -1.2 191 191
FOXM1B/HNF6 -0.46 0.71 -10000 0 -1.3 184 184
FOS -0.43 0.65 -10000 0 -1.2 223 223
SP1 0.036 0.022 -10000 0 -0.033 47 47
CDC25B -0.35 0.61 0.74 1 -1.1 175 176
response to radiation -0.006 0.036 0.088 9 -10000 0 9
CENPB -0.34 0.6 0.74 1 -1.1 168 169
CENPA -0.36 0.6 -10000 0 -1.1 171 171
NEK2 -0.37 0.62 -10000 0 -1.2 177 177
HIST1H2BA -0.35 0.6 0.74 1 -1.1 172 173
CCNA2 0.024 0.029 -10000 0 -0.033 67 67
EP300 0.036 0.014 -10000 0 0 73 73
CCNB1/CDK1 -0.49 0.79 -10000 0 -1.5 182 182
CCNB2 -0.38 0.63 0.8 1 -1.2 182 183
CCNB1 -0.39 0.66 -10000 0 -1.2 177 177
ETV5 -0.37 0.64 0.74 1 -1.1 204 205
ESR1 -0.4 0.62 -10000 0 -1.1 201 201
CCND1 -0.37 0.55 -10000 0 -1 193 193
GSK3A 0.005 0.062 0.15 3 -10000 0 3
Cyclin A-E1/CDK1-2 -0.007 0.11 0.21 1 -0.17 125 126
CDK2 0.029 0.028 -10000 0 -0.018 129 129
G2/M transition of mitotic cell cycle -0.007 0.044 0.095 10 -10000 0 10
FOXM1B/Cbp/p300 -0.41 0.66 -10000 0 -1.2 182 182
GAS1 -0.36 0.6 -10000 0 -1.1 175 175
MMP2 -0.43 0.65 -10000 0 -1.1 224 224
RB1/FOXM1C -0.41 0.59 0.67 1 -1.1 197 198
CREBBP 0.038 0.012 -10000 0 0 54 54
TCGA08_p53

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
CDKN2A -0.007 0.005 0 175 -10000 0 175
TP53 -0.053 0.12 0.18 13 -0.24 149 162
Senescence -0.063 0.12 0.18 13 -0.24 151 164
Apoptosis -0.063 0.12 0.18 13 -0.24 151 164
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
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 0.034 0.34 0.54 52 -0.54 85 137
HDAC7 -0.001 0.004 -10000 0 -0.037 1 1
HIF1A/ARNT/Cbp/p300/Src-1 0.03 0.32 0.57 15 -0.6 52 67
SMAD4 0.039 0.012 -10000 0 0 49 49
ID2 0.034 0.33 0.54 54 -0.54 84 138
AP1 0.006 0.085 -10000 0 -0.14 120 120
ABCG2 0.029 0.33 0.55 49 -0.54 83 132
HIF1A 0.031 0.1 0.2 43 -0.14 71 114
TFF3 0.01 0.32 0.54 39 -0.55 80 119
GATA2 0.04 0.019 -10000 0 -0.058 12 12
AKT1 0.042 0.097 0.22 34 -0.12 53 87
response to hypoxia 0.006 0.069 0.15 41 -0.11 47 88
MCL1 0.036 0.34 0.54 52 -0.53 88 140
NDRG1 -0.017 0.29 0.52 29 -0.56 75 104
SERPINE1 -0.01 0.3 0.54 30 -0.55 80 110
FECH 0.031 0.33 0.55 52 -0.55 83 135
FURIN 0.037 0.34 0.55 51 -0.54 85 136
NCOA2 0.038 0.015 -10000 0 -0.052 1 1
EP300 0.045 0.12 0.28 45 -0.24 20 65
HMOX1 0.021 0.33 0.54 46 -0.55 85 131
BHLHE40 -0.024 0.3 0.47 54 -0.53 87 141
BHLHE41 -0.024 0.3 0.47 54 -0.53 87 141
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.096 0.16 0.35 20 -0.21 30 50
ENG 0.02 0.11 0.27 16 -0.21 20 36
JUN 0.036 0.019 -10000 0 -0.005 90 90
RORA 0.034 0.33 0.55 49 -0.54 84 133
ABCB1 0.018 0.097 -10000 0 -0.55 4 4
TFRC -0.007 0.31 0.54 34 -0.57 77 111
CXCR4 0.009 0.33 0.54 44 -0.55 89 133
TF 0.027 0.33 0.54 49 -0.53 83 132
CITED2 0.032 0.33 0.54 51 -0.53 85 136
HIF1A/ARNT 0.018 0.38 -10000 0 -0.66 60 60
LDHA -0.048 0.3 -10000 0 -0.9 55 55
ETS1 0.011 0.33 0.53 40 -0.56 85 125
PGK1 0.032 0.34 0.54 55 -0.55 87 142
NOS2 -0.024 0.3 0.47 54 -0.53 87 141
ITGB2 0.012 0.34 0.55 42 -0.57 86 128
ALDOA 0.041 0.34 0.55 52 -0.54 85 137
Cbp/p300/CITED2 0.014 0.34 0.56 28 -0.6 73 101
FOS 0.027 0.022 -10000 0 -0.001 212 212
HK2 0.035 0.34 0.54 54 -0.54 88 142
SP1 0.048 0.008 -10000 0 -10000 0 0
GCK 0.066 0.15 0.52 6 -10000 0 6
HK1 0.034 0.34 0.54 54 -0.55 82 136
NPM1 0.039 0.34 0.54 54 -0.54 87 141
EGLN1 0.04 0.33 0.54 54 -0.54 81 135
CREB1 0.035 0.041 -10000 0 -0.11 41 41
PGM1 0.027 0.34 0.54 47 -0.56 85 132
SMAD3 0.041 0.009 -10000 0 0 24 24
EDN1 0.035 0.21 0.46 4 -1 13 17
IGFBP1 0.04 0.34 0.54 56 -0.54 84 140
VEGFA -0.007 0.26 0.46 36 -0.51 62 98
HIF1A/JAB1 0.035 0.099 0.19 15 -0.14 76 91
CP -0.013 0.32 0.52 38 -0.56 85 123
CXCL12 -0.019 0.31 0.53 29 -0.54 91 120
COPS5 0.036 0.016 -10000 0 -0.049 1 1
SMAD3/SMAD4 0.052 0.034 -10000 0 -0.14 12 12
BNIP3 0.017 0.33 0.54 44 -0.55 85 129
EGLN3 -0.017 0.32 0.54 32 -0.56 92 124
CA9 -0.016 0.3 0.55 26 -0.54 84 110
TERT 0.022 0.32 0.54 45 -0.54 82 127
ENO1 0.035 0.34 0.54 53 -0.54 87 140
PFKL 0.037 0.34 0.54 55 -0.54 85 140
NCOA1 0.04 0.01 -10000 0 -0.001 29 29
ADM -0.001 0.32 0.54 27 -0.56 83 110
ARNT 0.031 0.098 0.2 41 -0.12 75 116
HNF4A 0.041 0.013 -10000 0 -10000 0 0
ADFP -0.002 0.32 0.54 37 -0.54 90 127
SLC2A1 0.005 0.28 0.49 24 -0.54 65 89
LEP 0.039 0.33 0.55 51 -0.55 78 129
HIF1A/ARNT/Cbp/p300 0.015 0.32 0.57 13 -0.61 54 67
EPO 0.03 0.28 0.54 14 -0.56 44 58
CREBBP 0.05 0.11 0.28 47 -0.22 14 61
HIF1A/ARNT/Cbp/p300/HDAC7 0.005 0.31 0.54 9 -0.6 56 65
PFKFB3 0.029 0.34 0.55 49 -0.55 84 133
NT5E -0.036 0.31 0.52 25 -0.56 92 117
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 0.029 210 -10000 0 210
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.077 0.066 0.23 1 -0.12 19 20
Ephrin B2/EPHB1-2 0.041 0.069 -10000 0 -0.1 77 77
neuron projection morphogenesis 0.052 0.052 -10000 0 -0.11 21 21
Ephrin B1/EPHB1-2/Tiam1 0.07 0.061 0.23 1 -0.12 25 26
DNM1 0.041 0.012 -10000 0 0 38 38
cell-cell signaling 0.003 0.006 0.024 2 -10000 0 2
MAP2K4 -0.13 0.21 0.26 1 -0.46 163 164
YES1 -0.2 0.33 -10000 0 -0.69 168 168
Ephrin B1/EPHB1-2/NCK2 0.08 0.052 0.22 2 -0.11 17 19
PI3K -0.1 0.22 -10000 0 -0.44 165 165
mol:GDP 0.068 0.06 0.22 1 -0.12 26 27
ITGA2B 0.04 0.009 -10000 0 0 30 30
endothelial cell proliferation 0.024 0.061 -10000 0 -0.11 83 83
FYN -0.2 0.33 -10000 0 -0.7 166 166
MAP3K7 -0.13 0.23 0.23 1 -0.48 160 161
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 0 108 108
RGS3 0.04 0.008 -10000 0 0 23 23
cell adhesion -0.11 0.21 -10000 0 -0.42 162 162
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 34 34
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 -0.22 2 19
MAPK8 -0.14 0.21 0.24 1 -0.45 164 165
Ephrin B1/EPHB1-2/RGS3 0.08 0.052 0.22 2 -0.11 17 19
endothelial cell migration -0.11 0.18 0.19 3 -0.4 146 149
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 -0.22 2 19
chemotaxis -0.077 0.051 0.11 17 -0.22 2 19
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 0.21 56 -0.24 120 176
PTK2B 0.033 0.017 -10000 0 0 118 118
mol:Ca2+ -0.032 0.21 -10000 0 -0.55 36 36
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 -0.35 117 119
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.026 0.14 0.23 1 -0.26 101 102
ADCY4 0.01 0.14 0.2 87 -0.23 76 163
ADCY5 0.011 0.13 0.2 83 -0.22 76 159
ADCY6 0.008 0.14 0.21 79 -0.23 81 160
ADCY7 0.007 0.14 0.2 84 -0.23 79 163
ADCY1 0.009 0.14 0.2 78 -0.23 78 156
ADCY2 0.01 0.13 0.21 72 -0.23 68 140
ADCY3 0.009 0.14 0.2 89 -0.22 84 173
ADCY8 -0.002 0.11 0.21 43 -0.22 55 98
ADCY9 0.009 0.14 0.2 89 -0.23 81 170
arachidonic acid secretion -0.1 0.26 0.3 2 -0.49 136 138
ETB receptor/Endothelin-1/Gq/GTP 0 0.11 -10000 0 -0.23 62 62
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 -0.006 0.13 0.35 7 -0.21 129 136
ETA receptor/Endothelin-1/Gs/GTP -0.004 0.12 0.32 7 -0.19 131 138
mol:GTP 0 0.006 -10000 0 -0.025 3 3
COL3A1 -0.057 0.16 0.23 17 -0.34 123 140
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 27 -0.24 115 142
CYSLTR1 -0.015 0.15 0.2 43 -0.25 119 162
SLC9A1 -0.016 0.085 0.18 9 -0.15 136 145
mol:GDP -0.064 0.19 0.26 2 -0.36 117 119
SLC9A3 -0.022 0.19 -10000 0 -0.52 34 34
RAF1 -0.075 0.22 0.28 4 -0.4 140 144
JUN -0.073 0.3 -10000 0 -0.83 57 57
JAK2 -0.008 0.14 0.2 53 -0.24 123 176
mol:IP3 -0.023 0.14 0.21 2 -0.3 81 83
ETA receptor/Endothelin-1 -0.027 0.15 0.39 6 -0.27 136 142
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 -0.12 122 129
FOS -0.14 0.36 0.34 1 -0.84 110 111
Gai/GDP -0.032 0.24 -10000 0 -0.69 59 59
CRK 0.038 0.012 -10000 0 0 52 52
mol:Ca ++ -0.031 0.19 0.25 31 -0.34 113 144
BCAR1 0.036 0.014 -10000 0 0 76 76
PRKCB1 -0.027 0.14 0.25 5 -0.3 86 91
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 -0.05 0.18 0.26 2 -0.34 112 114
ETA receptor/Endothelin-1/Gq/GTP -0.015 0.14 0.22 5 -0.26 86 91
MAPK14 -0.017 0.11 0.24 4 -0.24 69 73
TRPC6 -0.034 0.21 -10000 0 -0.58 35 35
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 -0.24 68 68
ETB receptor/Endothelin-2 0.031 0.054 -10000 0 -0.071 91 91
ETB receptor/Endothelin-3 0.032 0.051 -10000 0 -0.067 81 81
ETB receptor/Endothelin-1 0.007 0.11 0.2 6 -0.17 118 124
MAPK3 -0.13 0.34 0.32 2 -0.76 114 116
MAPK1 -0.14 0.35 0.32 2 -0.75 120 122
Rac1/GDP -0.051 0.18 0.28 1 -0.35 114 115
cAMP biosynthetic process 0.044 0.13 0.23 82 -0.22 35 117
MAPK8 -0.053 0.24 -10000 0 -0.57 70 70
SRC 0.039 0.01 -10000 0 0 36 36
ETB receptor/Endothelin-1/Gi/GTP -0.011 0.11 -10000 0 -0.26 64 64
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 0.28 1 -0.35 114 115
COL1A2 -0.075 0.21 0.27 5 -0.48 108 113
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.011 0.088 0.19 8 -0.13 135 143
mol:DAG -0.023 0.14 0.21 2 -0.3 82 84
MAP2K2 -0.099 0.27 0.29 4 -0.55 125 129
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 0.19 35 -0.21 108 143
Gq family/GDP -0.013 0.19 0.28 1 -0.32 108 109
HRAS/GTP -0.053 0.18 0.24 3 -0.33 123 126
PRKCH -0.03 0.14 0.33 1 -0.29 92 93
RAC1 0.039 0.01 -10000 0 0 34 34
PRKCA -0.031 0.15 0.26 3 -0.3 91 94
PRKCB -0.027 0.14 0.2 1 -0.28 93 94
PRKCE -0.028 0.14 0.3 4 -0.29 86 90
PRKCD -0.031 0.14 0.24 3 -0.3 88 91
PRKCG -0.034 0.15 -10000 0 -0.3 90 90
regulation of vascular smooth muscle contraction -0.18 0.44 -10000 0 -1 111 111
PRKCQ -0.03 0.15 0.28 8 -0.3 87 95
PLA2G4A -0.11 0.28 0.3 2 -0.54 136 138
GNA14 0.036 0.021 -10000 0 -0.038 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 -0.21 131 137
MMP1 0.02 0.12 0.27 32 -0.58 10 42
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 -0.13 112 112
NF kappa B1 p50/RelA/I kappa B alpha -0.008 0.11 0.21 3 -0.22 67 70
AP1 -0.026 0.068 -10000 0 -0.12 172 172
mol:PIP3 -0.036 0.057 -10000 0 -0.13 126 126
AKT1 -0.002 0.094 0.24 18 -0.2 33 51
PTK2B -0.047 0.11 0.12 3 -0.18 186 189
RHOA 0.002 0.058 0.16 2 -0.3 8 10
PIK3CB 0.034 0.016 -10000 0 0 103 103
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 -0.18 157 173
NF kappa B1 p50/RelA -0.028 0.076 0.11 2 -0.16 113 115
endothelial cell migration -0.04 0.12 -10000 0 -0.3 99 99
ADCY4 -0.019 0.094 0.14 4 -0.2 102 106
ADCY5 -0.018 0.092 0.15 3 -0.19 103 106
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 0.14 4 -0.2 100 104
ADCY2 -0.014 0.09 0.12 9 -0.19 95 104
ADCY3 -0.02 0.094 0.14 2 -0.2 105 107
ADCY8 -0.002 0.086 0.17 1 -0.19 77 78
ADCY9 -0.022 0.098 0.15 3 -0.2 107 110
GSK3B -0.046 0.11 0.21 15 -0.18 182 197
arachidonic acid secretion -0.029 0.098 0.14 2 -0.19 124 126
GNG2 0.039 0.01 -10000 0 0 34 34
TRIP6 0.012 0.052 -10000 0 -0.24 19 19
GNAO1 0.006 0.071 0.09 116 -0.14 92 208
HRAS 0.04 0.01 -10000 0 0 31 31
NFKBIA -0.03 0.091 0.17 8 -0.24 54 62
GAB1 0.038 0.012 -10000 0 0 52 52
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 0.017 -10000 0 0 108 108
mol:IP3 -0.004 0.044 0.19 8 -0.14 15 23
PLCB3 0.016 0.044 0.16 13 -0.061 92 105
FOS 0.026 0.02 -10000 0 0 207 207
positive regulation of mitosis -0.029 0.098 0.14 2 -0.19 124 126
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 76 76
stress fiber formation -0.011 0.1 -10000 0 -0.25 47 47
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 -0.061 95 95
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 94 213
LPA/LPA3 -0.01 0.026 -10000 0 -0.065 100 100
LPA/LPA2 -0.01 0.025 -10000 0 -0.065 100 100
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 -0.013 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 99 103
NFKB1 0.036 0.015 -10000 0 0 84 84
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 0.17 14 -0.23 61 75
GNAQ 0.009 0.032 0.043 124 -0.053 101 225
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 0.26 4 -0.37 91 95
PTK2 0.006 0.061 0.094 80 -0.13 75 155
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 0.058 1 -0.083 42 43
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 51 52
cell migration -0.008 0.086 -10000 0 -0.24 46 46
SLC9A3R2 0.038 0.012 -10000 0 0 53 53
PXN -0.011 0.1 -10000 0 -0.25 47 47
HRAS/GTP -0.029 0.099 0.14 2 -0.19 122 124
RAC1 0.039 0.01 -10000 0 0 34 34
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 0.18 11 -0.15 25 36
Gi(beta/gamma) -0.02 0.1 0.16 1 -0.19 119 120
mol:LPA -0.017 0.04 -10000 0 -0.1 100 100
TRIP6/p130 Cas/FAK1/Paxillin -0.004 0.099 0.19 1 -0.22 57 58
MAPKKK cascade -0.029 0.098 0.14 2 -0.19 124 126
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 -0.18 163 179
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 -0.29 147 149
ILK -0.027 0.11 0.19 12 -0.24 71 83
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 13 -0.24 69 82
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 84 84
MAPK8 -0.032 0.1 0.16 16 -0.22 84 100
ITGB3 0.023 0.034 -10000 0 -0.048 76 76
NFKBIA -0.064 0.16 0.19 10 -0.36 110 120
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 76 76
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 0.17 16 -0.23 72 88
VAV3 -0.039 0.1 0.17 11 -0.23 89 100
MAP3K14 -0.024 0.12 0.2 13 -0.23 108 121
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 34 34
Rac1/GTP -0.034 0.11 0.18 12 -0.22 87 99
MMP2 -0.088 0.14 0.2 1 -0.31 127 128
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 0.096 -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 -0.29 58 73
Syndecan-1/Syntenin -0.014 0.14 0.23 19 -0.28 69 88
MAPK3 -0.023 0.13 0.2 21 -0.28 62 83
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 -0.29 58 73
Syndecan-1/RANTES -0.019 0.14 0.22 17 -0.29 77 94
Syndecan-1/CD147 -0.002 0.15 0.25 13 -0.29 61 74
Syndecan-1/Syntenin/PIP2 -0.016 0.14 0.21 19 -0.28 69 88
LAMA5 0.036 0.015 -10000 0 0 85 85
positive regulation of cell-cell adhesion -0.016 0.13 0.21 19 -0.27 69 88
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 63 68
Syndecan-1/HGF/MET -0.018 0.14 0.26 12 -0.28 75 87
regulation of cell adhesion -0.031 0.12 0.2 13 -0.28 59 72
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 5 -0.34 37 42
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 0.2 19 -0.28 62 81
homophilic cell adhesion -0.012 0.13 0.2 28 -0.32 47 75
MMP1 0.03 0.019 -10000 0 0 159 159
Nectin adhesion pathway

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
PDGFRB 0.037 0.013 -10000 0 0 64 64
alphaV beta3 Integrin 0.014 0.079 -10000 0 -0.15 93 93
PTK2 -0.045 0.14 -10000 0 -0.3 105 105
positive regulation of JNK cascade -0.032 0.14 -10000 0 -0.27 123 123
CDC42/GDP -0.039 0.2 -10000 0 -0.35 131 131
Rac1/GDP -0.041 0.19 -10000 0 -0.35 130 130
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 -0.32 123 123
nectin-3/I-afadin 0.009 0.077 -10000 0 -0.14 101 101
RAPGEF1 -0.056 0.18 -10000 0 -0.36 128 128
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.063 0.2 -10000 0 -0.4 130 130
PDGFB-D/PDGFRB 0.037 0.013 -10000 0 0 64 64
TLN1 -0.039 0.085 0.19 2 -0.25 60 62
Rap1/GTP -0.044 0.14 -10000 0 -0.28 132 132
IQGAP1 0.037 0.014 -10000 0 0 69 69
Rap1/GTP/I-afadin 0.042 0.066 -10000 0 -0.11 69 69
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.009 0.077 -10000 0 -0.14 101 101
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 -0.42 133 133
MLLT4 0.034 0.017 -10000 0 0 107 107
PIK3CA 0.03 0.019 -10000 0 0 155 155
PI3K 0.023 0.092 -10000 0 -0.13 100 100
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.041 0.048 -10000 0 -0.14 29 29
positive regulation of lamellipodium assembly -0.041 0.16 -10000 0 -0.28 136 136
PVRL1 0.04 0.008 -10000 0 0 22 22
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 0 108 108
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 -0.12 125 125
SRC -0.083 0.21 -10000 0 -0.44 134 134
ITGB3 0.033 0.017 -10000 0 0 121 121
nectin-1(dimer)/I-afadin/I-afadin 0.041 0.048 -10000 0 -0.14 29 29
FARP2 -0.059 0.22 -10000 0 -0.44 103 103
RAC1 0.039 0.01 -10000 0 0 34 34
CTNNA1 0.039 0.011 -10000 0 0 38 38
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.023 0.079 -10000 0 -0.12 101 101
nectin-1/I-afadin 0.041 0.048 -10000 0 -0.14 29 29
nectin-2/I-afadin 0.038 0.051 -10000 0 -0.14 34 34
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 0.024 0.078 -10000 0 -0.12 98 98
CDC42/GTP/IQGAP1/filamentous actin 0.04 0.047 -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 -0.27 123 123
alphaV/beta3 Integrin/Talin -0.031 0.11 0.26 2 -0.22 102 104
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.051 -10000 0 -0.14 34 34
nectin-2(dimer)/I-afadin/I-afadin 0.038 0.051 -10000 0 -0.14 34 34
PIP5K1C -0.032 0.087 -10000 0 -0.17 119 119
VAV2 -0.075 0.24 -10000 0 -0.44 139 139
RAP1/GDP -0.039 0.18 -10000 0 -0.34 130 130
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 -0.12 104 104
nectin-3(dimer)/I-afadin/I-afadin 0.009 0.077 -10000 0 -0.14 101 101
Rac1/GTP -0.048 0.19 -10000 0 -0.34 135 135
PTPRM -0.029 0.097 -10000 0 -0.18 123 123
E-cadherin/beta catenin/alpha catenin 0.062 0.09 -10000 0 -0.13 58 58
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.04 0.009 -10000 0 0 24 24
PDGFR-alpha 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
PDGFRA 0.018 0.036 -10000 0 -0.054 79 79
PDGF/PDGFRA/CRKL 0.014 0.07 -10000 0 -0.14 80 80
positive regulation of JUN kinase activity 0.048 0.083 -10000 0 -0.12 97 97
CRKL 0.039 0.011 -10000 0 0 38 38
PDGF/PDGFRA/Caveolin-3 0.014 0.072 -10000 0 -0.14 84 84
AP1 -0.12 0.26 -10000 0 -0.65 99 99
mol:IP3 -0.015 0.045 0.06 48 -0.096 81 129
PLCG1 -0.015 0.045 0.06 48 -0.096 81 129
PDGF/PDGFRA/alphaV Integrin -0.007 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 52 52
mol:Ca2+ -0.015 0.045 0.06 48 -0.096 81 129
CAV3 0.04 0.008 -10000 0 0 22 22
CAV1 0.036 0.015 -10000 0 0 80 80
SHC/Grb2/SOS1 0.05 0.084 -10000 0 -0.12 97 97
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 0.19 4 -0.2 11 15
oligodendrocyte development -0.007 0.09 -10000 0 -0.16 128 128
GRB2 0.041 0.007 -10000 0 0 17 17
PIK3R1 0.034 0.017 -10000 0 0 108 108
mol:DAG -0.015 0.045 0.06 48 -0.096 81 129
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 96 96
PDGF/PDGFRA/Crk/C3G 0.036 0.072 -10000 0 -0.12 82 82
JAK1 -0.01 0.02 0.028 44 -10000 0 44
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 41 41
CSNK2A1 0.036 0.031 -10000 0 -0.028 61 61
GO:0007205 -0.025 0.072 0.087 22 -0.19 65 87
SOS1 0.038 0.013 -10000 0 0 56 56
Ras protein signal transduction 0.048 0.083 -10000 0 -0.12 97 97
PDGF/PDGFRA/SHB 0.015 0.071 -10000 0 -0.1 127 127
PDGF/PDGFRA/Caveolin-1 0.012 0.074 -10000 0 -0.15 74 74
ITGAV 0.033 0.017 -10000 0 0 117 117
ELK1 -0.025 0.08 0.2 18 -0.18 65 83
PIK3CA 0.03 0.019 -10000 0 0 155 155
PDGF/PDGFRA/Crk 0.014 0.07 -10000 0 -0.1 120 120
JAK-STAT cascade -0.01 0.02 0.028 44 -10000 0 44
cell proliferation 0.013 0.07 -10000 0 -0.14 82 82
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.006 0.085 -10000 0 -0.12 134 134
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 83 83
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 -0.17 12 12
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 0 157 157
TLN1 0.039 0.012 -10000 0 0 46 46
Rap1/GTP -0.061 0.17 -10000 0 -0.3 145 145
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 0.21 1 -0.33 138 139
MST1R 0.039 0.011 -10000 0 0 42 42
leukocyte activation during inflammatory response 0.059 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 0.013 -10000 0 0 56 56
GP1BA 0.039 0.01 -10000 0 0 37 37
alphaM/beta2 Integrin/CTGF 0.035 0.081 -10000 0 -0.12 97 97
alphaM/beta2 Integrin -0.063 0.17 -10000 0 -0.33 126 126
JAM3 homodimer 0.038 0.013 -10000 0 0 56 56
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 -0.33 127 127
cell adhesion 0.052 0.069 -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 -0.16 105 105
alphaM/beta2 Integrin/JAM2/JAM3 0.067 0.075 -10000 0 -0.11 57 57
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 -0.34 147 148
positive regulation of phagocytosis -0.04 0.15 0.21 5 -0.28 118 123
Ron/MSP 0.054 0.029 -10000 0 -0.14 9 9
alphaM/beta2 Integrin/uPAR/uPA 0.035 0.11 -10000 0 -0.16 105 105
alphaM/beta2 Integrin/uPAR 0.045 0.082 -10000 0 -0.15 68 68
PLAU 0.026 0.02 -10000 0 0 214 214
PLAT 0.026 0.02 -10000 0 0 213 213
actin filament polymerization -0.077 0.16 0.2 1 -0.32 136 137
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 -0.15 104 104
fibrinolysis 0.039 0.097 -10000 0 -0.15 93 93
HCK 0.036 0.015 -10000 0 0 80 80
dendritic cell antigen processing and presentation -0.063 0.17 -10000 0 -0.33 127 127
VTN 0.04 0.009 -10000 0 0 24 24
alphaM/beta2 Integrin/CYR61 0.024 0.085 -10000 0 -0.12 112 112
LPA 0.038 0.012 -10000 0 0 55 55
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 0.093 -10000 0 -0.12 155 155
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 -0.33 144 147
ELA2 0.037 0.013 -10000 0 0 64 64
PLG 0.038 0.012 -10000 0 0 49 49
CTGF 0.034 0.017 -10000 0 0 112 112
alphaM/beta2 Integrin/Hck 0.05 0.071 -10000 0 -0.13 57 57
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 56 56
HP 0.01 0.018 -10000 0 0 429 429
leukocyte adhesion 0.019 0.11 -10000 0 -0.2 30 30
SELP 0.039 0.011 -10000 0 0 38 38
TCGA08_retinoblastoma

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
CDKN2B 0.029 0.027 -10000 0 -0.046 42 42
CDKN2C 0.029 0.029 -10000 0 -0.043 51 51
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 18 97
CDK6 0.006 0.063 0.14 79 -0.12 43 122
G1/S progression 0.02 0.075 0.15 102 -0.23 8 110
LPA4-mediated signaling events

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
ADCY4 -0.014 0.006 0 73 -10000 0 73
ADCY5 -0.014 0.006 0 86 -10000 0 86
ADCY6 -0.015 0.005 0 55 -10000 0 55
ADCY7 -0.014 0.006 0 77 -10000 0 77
ADCY1 -0.015 0.005 0 52 -10000 0 52
ADCY2 -0.014 0.006 0 95 -10000 0 95
ADCY3 -0.015 0.005 0 52 -10000 0 52
ADCY8 -0.008 0.008 0 283 -10000 0 283
PRKCE -0.01 0.003 0 36 -10000 0 36
ADCY9 -0.014 0.006 0 76 -10000 0 76
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.054 0.085 0.2 81 -0.2 4 85
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.21 158 160
EGF 0.038 0.012 -10000 0 0 53 53
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.005 0.06 0.22 8 -0.18 2 10
mol:Ca2+ -0.052 0.19 0.28 4 -0.29 207 211
LYN 0.002 0.057 0.22 8 -0.18 3 11
RhoA/GTP -0.019 0.088 0.14 5 -0.13 191 196
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.072 0.21 0.32 1 -0.34 193 194
GNG2 0.039 0.01 -10000 0 0 34 34
ARRB2 0.039 0.011 -10000 0 0 44 44
TP alpha/Gq family/GDP/G beta5/gamma2 -0.024 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 -0.35 198 199
DNM1 0.039 0.011 -10000 0 0 38 38
TXA2/TP beta/beta Arrestin3 0.029 0.023 -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 -0.3 198 198
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 -0.24 1 48
mol:NADP 0.038 0.012 -10000 0 0 49 49
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 -0.36 207 208
cell morphogenesis 0.051 0.022 -10000 0 -0.11 8 8
PLCB2 -0.12 0.3 0.38 1 -0.49 205 206
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.002 0.053 0.24 6 -0.18 2 8
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.003 0.057 0.22 7 -0.18 3 10
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 -0.37 200 202
GNAQ 0.038 0.012 -10000 0 0 49 49
mol:L-citrulline 0.038 0.012 -10000 0 0 49 49
TXA2/TXA2-R family -0.12 0.3 0.38 1 -0.51 192 193
LCK 0.004 0.058 0.23 7 -0.18 2 9
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 0.23 2 -0.15 8 10
MAPK14 -0.04 0.15 0.22 8 -0.23 185 193
TGM2/GTP -0.085 0.25 0.4 1 -0.39 204 205
MAPK11 -0.048 0.14 0.22 5 -0.22 193 198
ARHGEF1 -0.029 0.12 0.2 10 -0.18 190 200
GNAI2 0.041 0.007 -10000 0 0 15 15
JNK cascade -0.077 0.23 0.33 2 -0.38 192 194
RAB11/GDP 0.04 0.009 -10000 0 0 24 24
ICAM1 -0.058 0.2 0.27 7 -0.32 185 192
cAMP biosynthetic process -0.07 0.21 0.33 1 -0.33 209 210
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 0.22 7 -0.18 2 9
GNB5 0.04 0.009 -10000 0 0 29 29
GNB1 0.041 0.005 -10000 0 0 7 7
EGF/EGFR 0.002 0.075 0.22 11 -0.21 13 24
VCAM1 -0.062 0.21 0.27 7 -0.33 191 198
TP beta/Gq family/GDP/G beta5/gamma2 -0.024 0.16 -10000 0 -0.52 46 46
platelet activation -0.056 0.19 0.29 3 -0.29 198 201
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 0.013 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 -0.41 200 201
EGFR 0.037 0.014 -10000 0 0 72 72
TXA2/TP alpha -0.1 0.28 0.38 1 -0.45 205 206
Gq family/GTP -0.008 0.065 -10000 0 -0.18 61 61
YES1 0.002 0.057 0.2 10 -0.18 2 12
GNAI2/GTP 0.027 0.046 -10000 0 -0.14 9 9
PGD2/DP 0.03 0.005 -10000 0 -10000 0 0
SLC9A3R1 0.038 0.012 -10000 0 0 49 49
FYN 0.002 0.058 0.22 7 -0.17 5 12
mol:NO 0.038 0.012 -10000 0 0 49 49
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 -0.18 7 8
NOS3 0.038 0.012 -10000 0 0 49 49
RAC1 0.039 0.01 -10000 0 0 34 34
PRKCA -0.072 0.22 0.31 4 -0.35 199 203
PRKCB -0.07 0.22 0.29 2 -0.34 198 200
PRKCE -0.071 0.22 0.32 5 -0.36 189 194
PRKCD -0.08 0.23 0.3 3 -0.38 193 196
PRKCG -0.08 0.24 0.34 1 -0.38 200 201
muscle contraction -0.11 0.28 0.38 1 -0.47 197 198
PRKCZ -0.07 0.21 0.3 2 -0.34 192 194
ARR3 0.042 0.002 -10000 0 0 1 1
TXA2/TP beta 0.045 0.052 0.24 1 -0.2 2 3
PRKCQ -0.072 0.22 0.36 3 -0.35 190 193
MAPKKK cascade -0.099 0.26 0.36 1 -0.43 201 202
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 0.4 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
TRAIL signaling pathway

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
TNFSF10 0.021 0.021 -10000 0 0 282 282
positive regulation of NF-kappaB transcription factor activity 0.002 0.067 -10000 0 -0.13 95 95
MAP2K4 -0.013 0.096 0.18 2 -0.27 39 41
IKBKB 0.039 0.011 -10000 0 0 44 44
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 0.069 -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 0.02 0.091 -10000 0 -0.28 33 33
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 0.1 -10000 0 -0.28 38 38
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 0.083 -10000 0 -0.25 33 33
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 0.025 0.082 -10000 0 -0.11 68 68
mol:ceramide -0.007 0.044 -10000 0 -0.1 92 92
FADD 0.04 0.008 -10000 0 0 21 21
MAPK8 -0.022 0.1 0.2 5 -0.27 48 53
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 0.067 -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 -0.11 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 0.083 -10000 0 -0.24 35 35
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 62 62
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.007 0.005 0 204 -10000 0 204
GNB1/GNG2 0.041 0.07 -10000 0 -0.11 89 89
regulation of S phase of mitotic cell cycle -0.012 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 0.026 0.007 -10000 0 -10000 0 0
PELP1 0.039 0.01 -10000 0 0 36 36
AKT1 -0.009 0.004 0.002 47 -10000 0 47
MAP2K1 -0.033 0.079 0.17 27 -0.17 79 106
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 -0.27 64 64
cell proliferation -0.07 0.17 0.24 6 -0.39 106 112
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 93 101
MAPK1 -0.042 0.14 -10000 0 -0.32 72 72
PIK3R1 0.034 0.017 -10000 0 0 108 108
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 -0.093 143 143
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 48 48
apoptosis 0.061 0.18 0.39 112 -0.23 3 115
T-DHT/AR/PELP1 0.025 0.058 -10000 0 -0.11 79 79
HRAS/GDP -0.006 0.11 -10000 0 -0.26 68 68
CREB1 -0.076 0.18 0.24 2 -0.41 112 114
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 0.016 0.12 0.19 1 -0.26 63 64
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 68 90
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 35 35
Gi family/GNB1/GNG2/GDP -0.005 0.099 -10000 0 -0.29 36 36
mol:T-DHT 0 0.001 -10000 0 -0.003 31 31
RAC1 0.039 0.01 -10000 0 0 34 34
GNRH1 -0.008 0.004 0 125 -10000 0 125
Gi family/GTP -0.02 0.077 -10000 0 -0.18 72 72
CDC42 0.04 0.009 -10000 0 0 24 24
BARD1 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
BARD1/CSTF1 0.039 0.053 -10000 0 -0.14 38 38
ATM 0.036 0.014 -10000 0 0 73 73
UBE2D3 0.038 0.012 -10000 0 0 48 48
PRKDC 0.039 0.011 -10000 0 0 44 44
ATR 0.035 0.016 -10000 0 0 93 93
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 70 70
M/R/N Complex 0.048 0.071 -10000 0 -0.15 50 50
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 0.069 -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 0.25 18 -0.37 39 57
BRCA1/BARD1/ubiquitin 0.027 0.069 -10000 0 -0.14 74 74
BARD1/DNA-PK 0.064 0.082 -10000 0 -0.14 60 60
FANCL 0.038 0.012 -10000 0 0 55 55
mRNA polyadenylation -0.038 0.053 0.14 38 -10000 0 38
BRCA1/BARD1/CTIP/M/R/N Complex -0.025 0.14 0.17 2 -0.29 80 82
BRCA1/BACH1/BARD1/TopBP1 0.037 0.077 -10000 0 -0.13 81 81
BRCA1/BARD1/P53 0.002 0.1 -10000 0 -0.13 190 190
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 76 76
BRCA1/BARD1/UbcH7 0.042 0.072 -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 0.069 -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 0 213 213
TOPBP1 0.038 0.013 -10000 0 0 59 59
G1/S transition of mitotic cell cycle 0 0.1 0.13 190 -10000 0 190
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 0.069 -10000 0 -0.14 74 74
EWSR1 0.038 0.012 -10000 0 0 54 54
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 0 157 157
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 -0.18 38 44
FOXO3 0 0 -10000 0 -10000 0 0
AKT1 0.039 0.01 -10000 0 0 37 37
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 0 103 103
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 33 -0.2 22 55
PI3K 0.003 0.088 0.17 28 -0.21 47 75
PIK3R1 0.034 0.017 -10000 0 0 108 108
KRAS 0.034 0.016 -10000 0 0 103 103
FOXO 0.038 0.054 0.17 24 -10000 0 24
AKT2 0.038 0.012 -10000 0 0 47 47
PTEN 0.039 0.011 -10000 0 0 38 38
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 0.015 0.15 -10000 0 -0.26 86 86
MAP3K8 0.04 0.009 -10000 0 0 21 21
FOS 0.014 0.11 -10000 0 -0.31 23 23
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 45 48
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 86 -0.004 103 189
MAPK1 0.011 0.11 -10000 0 -0.37 34 34
RAF1 -0.002 0.078 -10000 0 -0.28 35 35
KRAS 0.034 0.016 -10000 0 0 103 103
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 34 34
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 52 52
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 -0.03 0.15 -10000 0 -0.36 74 74
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 0 108 108
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 0.051 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 -0.13 117 145
p130Cas/Crk/Dock1 0.055 0.054 -10000 0 -0.12 29 29
VCAM1 0.02 0.021 -10000 0 0 288 288
alpha4/beta1 Integrin/Paxillin/Talin 0.063 0.079 0.2 47 -0.12 59 106
alpha4/beta1 Integrin/Paxillin/GIT1 0.069 0.073 0.2 46 -0.11 48 94
BCAR1 0.036 0.014 -10000 0 0 76 76
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 -0.035 0.17 -10000 0 -0.4 74 74
IL6-mediated signaling events

Figure S23.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S23.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.089 0.35 0.47 1 -0.78 88 89
CRP -0.082 0.33 0.5 1 -0.76 82 83
cell cycle arrest -0.12 0.39 -10000 0 -0.85 99 99
TIMP1 -0.1 0.36 -10000 0 -0.74 117 117
IL6ST 0.024 0.036 -10000 0 -0.039 102 102
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 0.013 0.091 -10000 0 -1.1 2 2
GAB1 0.039 0.014 -10000 0 -0.002 55 55
MAPK14 -0.024 0.16 0.25 2 -0.51 38 40
AKT1 -0.01 0.15 0.31 4 -0.44 37 41
FOXO1 -0.011 0.14 0.3 4 -0.4 40 44
MAP2K6 -0.02 0.15 0.22 4 -0.37 56 60
mol:GTP 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.032 0.21 0.3 8 -0.42 88 96
MITF -0.017 0.14 0.22 8 -0.32 69 77
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 -0.01 0.16 0.3 3 -0.39 62 65
STAT3 -0.14 0.43 -10000 0 -0.94 99 99
STAT1 -0.069 0.28 -10000 0 -0.83 64 64
CEBPD -0.086 0.34 0.53 2 -0.78 83 85
PIK3CA 0.031 0.02 -10000 0 -0.001 158 158
PI3K 0.024 0.062 -10000 0 -0.15 49 49
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 0.25 2 -0.55 33 35
STAT3 (dimer)/FOXO1 -0.096 0.36 0.45 4 -0.71 111 115
GRB2/SOS1/GAB family 0.031 0.13 0.29 3 -0.28 33 36
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK 0.008 0.11 0.2 3 -0.25 57 60
GRB2 0.042 0.01 -10000 0 -0.005 20 20
JAK2 0.035 0.016 -10000 0 0 92 92
LBP -0.031 0.27 0.43 2 -0.56 80 82
PIK3R1 0.034 0.018 -10000 0 -0.001 111 111
JAK1 0.034 0.028 -10000 0 -0.044 55 55
MYC -0.071 0.42 0.52 6 -0.86 105 111
FGG -0.086 0.33 -10000 0 -0.74 87 87
macrophage differentiation -0.12 0.39 -10000 0 -0.85 99 99
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.049 0.1 -10000 0 -0.17 48 48
JUNB -0.1 0.39 0.52 3 -0.86 98 101
FOS 0.026 0.02 -10000 0 0 207 207
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.009 0.16 0.24 3 -0.34 70 73
STAT1/PIAS1 -0.019 0.18 0.29 2 -0.37 81 83
GRB2/SOS1/GAB family/SHP2/PI3K -0.011 0.16 -10000 0 -0.4 49 49
STAT3 (dimer) -0.14 0.41 -10000 0 -0.91 99 99
PRKCD -0.06 0.26 0.33 6 -0.53 100 106
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 -0.15 58 58
Rac1/GTP -0.017 0.18 0.3 5 -0.38 77 82
HCK 0.036 0.015 -10000 0 0 80 80
MAPKKK cascade -0.024 0.22 -10000 0 -0.5 80 80
bone resorption -0.079 0.31 -10000 0 -0.72 82 82
IRF1 -0.14 0.42 -10000 0 -0.92 114 114
mol:GDP -0.02 0.15 0.24 6 -0.35 67 73
SOS1 0.039 0.015 -10000 0 -0.002 59 59
VAV1 -0.021 0.15 0.23 5 -0.35 67 72
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.012 0.17 -10000 0 -0.46 53 53
PTPN11 0 0.16 -10000 0 -0.78 22 22
IL6/IL6RA 0.029 0.063 -10000 0 -0.14 43 43
gp130 (dimer)/TYK2/TYK2/LMO4 0.05 0.066 -10000 0 -0.12 45 45
gp130 (dimer)/JAK2/JAK2/LMO4 0.043 0.075 -10000 0 -0.12 66 66
IL6 0.023 0.037 -10000 0 -0.04 103 103
PIAS3 0.04 0.008 -10000 0 0 23 23
PTPRE 0.027 0.038 0.098 13 -0.045 55 68
PIAS1 0.04 0.009 -10000 0 0 28 28
RAC1 0.04 0.01 -10000 0 0 34 34
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0.004 0.095 -10000 0 -0.24 46 46
LMO4 0.028 0.037 -10000 0 -0.039 115 115
STAT3 (dimer)/PIAS3 -0.1 0.4 -10000 0 -0.85 98 98
MCL1 -0.012 0.16 0.36 1 -0.6 22 23
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.029 0.013 -10000 0 -0.13 3 3
alphaV beta3 Integrin 0.028 0.079 -10000 0 -0.13 91 91
PTK2 -0.011 0.13 0.23 9 -0.26 75 84
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 -0.014 0.06 0.17 19 -0.18 11 30
alphaV/beta3 Integrin/JAM-A 0.041 0.081 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 0.056 0.085 -10000 0 -0.12 87 87
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.005 0.084 -10000 0 -0.17 96 96
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 -0.15 151 151
PI4 Kinase 0 0 -10000 0 -10000 0 0
PIK3CA 0.03 0.019 -10000 0 0 155 155
alphaV/beta3 Integrin/Osteopontin 0.005 0.099 -10000 0 -0.15 128 128
RPS6KB1 -0.034 0.1 0.27 11 -0.2 56 67
TLN1 0.039 0.012 -10000 0 0 46 46
MAPK3 -0.052 0.16 0.23 1 -0.33 122 123
GPR124 0.037 0.013 -10000 0 0 63 63
MAPK1 -0.049 0.16 0.23 1 -0.34 115 116
PXN 0.041 0.007 -10000 0 0 14 14
PIK3R1 0.034 0.017 -10000 0 0 108 108
alphaV/beta3 Integrin/Tumstatin 0.031 0.08 -10000 0 -0.13 92 92
cell adhesion -0.001 0.1 -10000 0 -0.16 144 144
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 34 34
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 36 36
alphaV/beta3 Integrin/Del1 0.005 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 0.028 0.074 -10000 0 -0.12 94 94
FAK1/Vinculin 0.006 0.12 0.24 9 -0.23 74 83
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 76 76
FGF2 0.039 0.011 -10000 0 0 45 45
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 0.091 -10000 0 -0.13 96 96
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 0.066 0.21 1 -0.11 87 88
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 -0.23 72 81
cell migration -0.002 0.11 0.21 9 -0.22 73 82
ITGAV 0.033 0.017 -10000 0 0 117 117
PI3K 0.028 0.091 -10000 0 -0.15 73 73
SPP1 0.03 0.019 -10000 0 0 154 154
KDR 0.04 0.009 -10000 0 0 30 30
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 -0.057 0.17 0.25 2 -0.37 118 120
Rac1/GTP -0.032 0.078 0.2 20 -0.2 35 55
EDIL3 0.027 0.02 -10000 0 0 202 202
cell proliferation 0.026 0.084 -10000 0 -0.14 95 95
Syndecan-4-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
PTK2 -0.056 0.21 -10000 0 -0.34 164 164
Syndecan-4/Syndesmos -0.037 0.19 -10000 0 -0.42 77 77
positive regulation of JNK cascade -0.057 0.19 -10000 0 -0.41 84 84
Syndecan-4/ADAM12 -0.054 0.18 -10000 0 -0.43 74 74
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 0.04 0.01 -10000 0 0 32 32
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 -0.41 77 77
Syndecan-4/CXCL12/CXCR4 -0.06 0.2 -10000 0 -0.44 84 84
Syndecan-4/Laminin alpha3 -0.047 0.19 -10000 0 -0.43 76 76
MDK 0.04 0.009 -10000 0 0 24 24
Syndecan-4/FZD7 -0.041 0.19 -10000 0 -0.46 64 64
Syndecan-4/Midkine -0.039 0.2 -10000 0 -0.45 64 64
FZD7 0.037 0.013 -10000 0 0 65 65
Syndecan-4/FGFR1/FGF -0.025 0.18 -10000 0 -0.46 47 47
THBS1 0.027 0.02 -10000 0 0 199 199
integrin-mediated signaling pathway -0.055 0.18 -10000 0 -0.42 80 80
positive regulation of MAPKKK cascade -0.057 0.19 -10000 0 -0.41 84 84
Syndecan-4/TACI -0.037 0.19 -10000 0 -0.43 76 76
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 -0.035 0.19 -10000 0 -0.42 70 70
Syndecan-4/TSP1 -0.058 0.19 -10000 0 -0.44 76 76
Syndecan-4/GIPC -0.037 0.18 -10000 0 -0.43 67 67
Syndecan-4/RANTES -0.05 0.2 -10000 0 -0.43 81 81
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 34 34
PRKCA 0.002 0.12 0.87 8 -10000 0 8
Syndecan-4/alpha-Actinin -0.039 0.2 -10000 0 -0.43 76 76
TFPI 0.039 0.01 -10000 0 0 35 35
F2 0.038 0.026 0.085 2 -0.038 48 50
alpha5/beta1 Integrin 0.046 0.045 -10000 0 -0.14 27 27
positive regulation of cell adhesion -0.056 0.17 -10000 0 -0.41 76 76
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 -0.44 80 80
FGF6 0.036 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 45 45
FGFR1 0.033 0.017 -10000 0 0 122 122
Syndecan-4/PI-4-5-P2 -0.06 0.18 -10000 0 -0.42 78 78
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 -0.42 76 76
SDC4 -0.052 0.18 -10000 0 -0.45 71 71
Syndecan-4/Tenascin C -0.058 0.19 -10000 0 -0.44 79 79
Syndecan-4/PI-4-5-P2/PKC alpha -0.019 0.018 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.039 0.19 -10000 0 -0.44 71 71
MMP9 0.027 0.024 -10000 0 -0.04 17 17
Rac1/GTP -0.033 0.099 0.22 4 -0.2 127 131
cytoskeleton organization -0.035 0.18 -10000 0 -0.4 77 77
GIPC1 0.035 0.015 -10000 0 0 89 89
Syndecan-4/TFPI -0.04 0.19 -10000 0 -0.42 77 77
Signaling events mediated by the Hedgehog family

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
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 0.015 -10000 0 0 78 78
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 99 100
SMO -0.002 0.11 -10000 0 -0.2 110 110
AKT1 -0.013 0.13 -10000 0 -0.39 36 36
ARRB2 0.039 0.011 -10000 0 0 44 44
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 -0.17 104 133
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 0 108 108
skeletal system development -0.032 0.17 -10000 0 -0.38 106 106
IHH N/Hhip 0.035 0.055 -10000 0 -0.085 4 4
DHH N/Hhip 0.054 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 0.013 -10000 0 0 56 56
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 -0.17 108 134
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 -0.21 129 129
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 -0.099 3 45
PTCH1 -0.036 0.096 -10000 0 -0.21 128 128
HHIP 0.038 0.013 -10000 0 0 56 56
IL23-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
CCL2 -0.16 0.61 0.68 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 86 86
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 -1.1 119 119
IL17F -0.042 0.36 0.49 12 -0.71 85 97
IL12B 0.034 0.074 0.16 11 -10000 0 11
STAT1 (dimer) -0.15 0.58 -10000 0 -1.3 87 87
CD4 -0.11 0.57 0.72 2 -1.2 95 97
IL23 -0.1 0.53 -10000 0 -1.2 81 81
IL23R 0.039 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 83 83
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 0 15 15
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 0.069 -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 17 -10000 0 17
PIK3R1 0.034 0.017 -10000 0 0 108 108
NFKB1 0.037 0.016 -10000 0 0 84 84
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 81 81
ALOX12B -0.098 0.52 -10000 0 -1.1 84 84
CXCL1 -0.13 0.57 -10000 0 -1.2 109 109
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 0.43 11 -0.55 86 97
PI3K -0.15 0.53 -10000 0 -1.2 86 86
IFNG 0.007 0.04 0.1 6 -0.11 14 20
STAT3 (dimer) -0.13 0.51 -10000 0 -1.1 84 84
IL18R1 0.041 0.008 -10000 0 0 20 20
IL23/IL23R/JAK2/TYK2/SOCS3 -0.013 0.34 0.54 3 -0.66 71 74
IL18/IL18R 0.055 0.067 -10000 0 -0.11 62 62
macrophage activation -0.007 0.022 0.034 2 -0.045 76 78
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 0 147 147
IL19 -0.095 0.52 -10000 0 -1.1 84 84
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 -1.2 123 123
MPO -0.096 0.52 -10000 0 -1.1 83 83
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 87 88
keratinocyte proliferation -0.13 0.61 0.68 1 -1.4 88 89
NOS2 -0.098 0.52 0.61 1 -1.1 88 89
IL1-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
UBC13/UEV1A 0.028 0.019 -10000 0 -0.13 8 8
PRKCZ 0.042 0 -10000 0 -10000 0 0
MAP3K7IP2 0.038 0.013 -10000 0 0 59 59
ERC1 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.034 0.14 -10000 0 -0.31 88 88
IRAK/TOLLIP 0.04 0.027 0.19 4 -0.1 11 15
IKBKB 0.039 0.011 -10000 0 0 44 44
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 73 73
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 0.089 0.26 3 -0.27 27 30
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 0.038 0.086 -10000 0 -0.12 95 95
PIK3R1 0.034 0.017 -10000 0 0 108 108
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.038 0.1 -10000 0 -0.14 102 102
IL1 beta fragment/IL1R1/IL1RAP -0.012 0.096 0.18 4 -0.15 144 148
NFKB1 0.036 0.015 -10000 0 0 84 84
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 0.17 2 -0.31 96 98
CHUK 0.038 0.012 -10000 0 0 52 52
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.012 0.096 0.18 4 -0.15 144 148
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 -0.18 124 124
IRAK3 0.035 0.016 -10000 0 0 97 97
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.003 0.12 0.22 2 -0.17 139 141
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.015 0.099 -10000 0 -0.2 104 104
IL1 alpha/IL1R1/IL1RAP 0.016 0.078 -10000 0 -0.13 95 95
RELA 0.041 0.006 -10000 0 0 10 10
MAP3K7IP1 0.038 0.012 -10000 0 0 54 54
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 -0.21 71 71
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 0.002 0.1 0.2 4 -0.15 141 145
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.021 0.13 0.21 1 -0.29 88 89
PIK3CA 0.03 0.019 -10000 0 0 155 155
IL1RN 0.039 0.011 -10000 0 0 39 39
TRAF6/TAK1/TAB1/TAB2 0.073 0.066 -10000 0 -0.14 29 29
MAP2K6 -0.021 0.059 0.19 24 -0.21 12 36
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.008 0.11 0.15 56 -0.28 44 100
adherens junction organization -0.026 0.13 0.18 8 -0.31 64 72
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.011 0.11 0.2 12 -0.26 34 46
FMN1 -0.023 0.12 0.15 7 -0.28 66 73
mol:IP3 0.003 0.098 0.16 60 -0.22 49 109
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 -0.25 46 56
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.011 0.15 -10000 0 -0.39 46 46
CTNND1 0.042 0.009 -10000 0 -0.002 18 18
mol:PI-4-5-P2 -0.02 0.12 0.17 8 -0.28 64 72
VASP -0.021 0.12 0.16 5 -0.28 65 70
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 71 72
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 -0.26 48 50
PIK3CA 0.03 0.02 -10000 0 -0.001 159 159
PI3K -0.004 0.11 0.22 2 -0.26 48 50
FYN -0.012 0.12 0.18 12 -0.27 69 81
mol:Ca2+ 0.003 0.096 0.16 60 -0.21 49 109
JUP 0.038 0.014 -10000 0 0 67 67
PIK3R1 0.035 0.018 -10000 0 0 109 109
mol:DAG 0.003 0.098 0.16 60 -0.22 49 109
CDH1 0.035 0.016 -10000 0 0 98 98
RhoA/GDP 0.013 0.11 0.22 12 -0.26 35 47
establishment of polarity of embryonic epithelium -0.02 0.12 0.17 6 -0.28 64 70
SRC 0.039 0.01 -10000 0 0 36 36
RAC1 0.039 0.01 -10000 0 0 34 34
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 -0.21 47 109
RhoA/GTP 0.015 0.1 0.2 4 -0.24 36 40
AKT2 -0.016 0.092 0.18 8 -0.24 48 56
actin cable formation -0.025 0.11 0.21 8 -0.28 61 69
apoptosis 0.001 0.11 0.26 47 -0.16 69 116
CTNNA1 0.041 0.012 -10000 0 -0.001 39 39
mol:GDP -0.005 0.1 0.16 58 -0.23 48 106
PIP5K1A -0.022 0.12 0.15 8 -0.28 65 73
PLCG1 0.002 0.1 0.16 60 -0.22 49 109
Rac1/GTP 0.004 0.13 -10000 0 -0.3 54 54
homophilic cell adhesion 0 0.004 -10000 0 -10000 0 0
FoxO family signaling

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
G6PC -0.002 0.065 -10000 0 -10000 0 0
PLK1 -0.15 0.38 -10000 0 -0.84 97 97
CDKN1B -0.046 0.2 0.4 2 -0.36 102 104
FOXO3 -0.14 0.35 -10000 0 -0.57 181 181
KAT2B -0.008 0.028 0.043 4 -0.045 191 195
FOXO1/SIRT1 0.015 0.078 -10000 0 -0.22 19 19
CAT -0.16 0.4 0.65 1 -0.88 96 97
CTNNB1 0.04 0.01 -10000 0 0 31 31
AKT1 0.012 0.056 -10000 0 -0.063 165 165
FOXO1 -0.005 0.07 -10000 0 -0.24 12 12
MAPK10 0 0.047 0.18 8 -0.12 28 36
mol:GTP 0 0.003 -10000 0 -10000 0 0
FOXO4 -0.025 0.12 0.24 2 -0.3 59 61
response to oxidative stress -0.007 0.03 0.061 1 -0.05 120 121
FOXO3A/SIRT1 -0.13 0.34 0.41 1 -0.54 190 191
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 -0.87 7 7
FOXO1/SKP2 0.012 0.075 -10000 0 -0.23 19 19
mol:GDP -0.007 0.03 0.061 1 -0.05 120 121
RAN 0.041 0.007 -10000 0 0 13 13
GADD45A -0.077 0.28 -10000 0 -0.83 48 48
YWHAQ 0.04 0.009 -10000 0 0 28 28
FOXO1/14-3-3 family 0.014 0.13 0.27 2 -0.34 42 44
MST1 0.011 0.056 -10000 0 -0.063 193 193
CSNK1D 0.04 0.009 -10000 0 0 28 28
CSNK1E 0.038 0.013 -10000 0 0 57 57
FOXO4/14-3-3 family 0.002 0.14 -10000 0 -0.39 40 40
YWHAB 0.038 0.012 -10000 0 0 52 52
MAPK8 0.001 0.052 0.18 12 -0.12 29 41
MAPK9 -0.001 0.052 0.19 11 -0.12 29 40
YWHAG 0.04 0.009 -10000 0 0 25 25
YWHAE 0.038 0.013 -10000 0 0 58 58
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 -0.65 102 102
RBL2 -0.12 0.33 -10000 0 -0.77 78 78
RAL/GDP 0.031 0.056 -10000 0 -0.092 54 54
CHUK 0.012 0.054 -10000 0 -0.063 173 173
Ran/GTP 0.027 0.019 -10000 0 -0.047 14 14
CSNK1G2 0.037 0.013 -10000 0 0 64 64
RAL/GTP 0.031 0.057 -10000 0 -0.084 63 63
CSNK1G1 0.041 0.008 -10000 0 0 19 19
FASLG 0.017 0.065 -10000 0 -1.2 1 1
SKP2 0.036 0.014 -10000 0 0 73 73
USP7 0.038 0.012 -10000 0 0 50 50
IKBKB 0.011 0.054 -10000 0 -0.062 182 182
CCNB1 -0.18 0.43 0.42 1 -0.94 110 111
FOXO1-3a-4/beta catenin -0.06 0.2 -10000 0 -0.38 105 105
proteasomal ubiquitin-dependent protein catabolic process 0.012 0.074 -10000 0 -0.23 19 19
CSNK1A1 0.04 0.009 -10000 0 0 26 26
SGK1 -0.008 0.028 0.043 4 -0.045 191 195
CSNK1G3 0.039 0.011 -10000 0 0 38 38
Ran/GTP/Exportin 1 0.046 0.038 -10000 0 -0.11 25 25
ZFAND5 -0.019 0.1 0.21 3 -0.25 56 59
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 53 53
CREBBP 0.04 0.013 -10000 0 -10000 0 0
FBXO32 -0.2 0.54 0.49 5 -1.1 144 149
BCL6 -0.13 0.35 -10000 0 -0.86 78 78
RALB 0.04 0.009 -10000 0 0 26 26
RALA 0.04 0.01 -10000 0 0 30 30
YWHAH 0.037 0.013 -10000 0 0 60 60
Signaling events mediated by PRL

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
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 18 18
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 0.097 -10000 0 -0.33 22 22
MAPK3 -0.012 0.01 0 236 -10000 0 236
PRL-2 /Rab GGTase beta 0.032 0.068 -10000 0 -0.14 72 72
MAPK1 -0.012 0.01 0 251 -10000 0 251
PTP4A1 -0.003 0.075 0.2 4 -0.61 7 11
PTP4A3 0.025 0.021 -10000 0 0 226 226
PTP4A2 0.04 0.01 -10000 0 0 31 31
ITGB1 -0.012 0.01 0 251 -10000 0 251
SRC 0.039 0.01 -10000 0 0 36 36
RAC1 -0.008 0.11 -10000 0 -0.36 45 45
Rab GGTase beta/Rab GGTase alpha 0.035 0.063 -10000 0 -0.14 63 63
PRL-1/ATF-5 0.016 0.097 0.3 3 -0.54 9 12
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 -0.34 44 46
PRL-1/alpha Tubulin -0.018 0.078 -10000 0 -0.54 9 9
PRL-3/alpha1 Integrin 0.011 0.067 -10000 0 -0.15 67 67
ROCK1 0.011 0.12 0.3 2 -0.34 44 46
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 0.2 6 -0.61 7 13
ATF5 0.038 0.012 -10000 0 0 54 54
Cellular roles of Anthrax toxin

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
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 -0.033 74 74
monocyte activation -0.076 0.17 -10000 0 -0.35 151 151
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 -0.037 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 0.056 -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 0.033 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 -0.033 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 -0.078 0.17 -10000 0 -0.35 149 149
platelet activation 0.003 0.078 -10000 0 -0.42 17 17
MAPKKK cascade 0.007 0.028 0.083 8 -0.07 23 31
IL18 -0.009 0.041 0.093 8 -0.093 73 81
negative regulation of macrophage activation -0.006 0.011 -10000 0 -0.033 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 -0.033 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 -0.1 74 74
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.037 0.013 -10000 0 0 64 64
Jak2/Leptin Receptor -0.017 0.14 -10000 0 -0.38 56 56
PTP1B/AKT1 -0.034 0.11 -10000 0 -0.24 80 80
FYN 0.034 0.016 -10000 0 0 103 103
p210 bcr-abl/PTP1B -0.052 0.11 0.17 1 -0.26 86 87
EGFR 0.036 0.017 -10000 0 -0.004 83 83
EGF/EGFR -0.025 0.12 -10000 0 -0.24 82 82
CSF1 0.035 0.015 -10000 0 0 89 89
AKT1 0.039 0.011 -10000 0 0 37 37
INSR 0.038 0.012 -10000 0 0 53 53
PTP1B/N-cadherin -0.053 0.12 -10000 0 -0.25 112 112
Insulin Receptor/Insulin -0.008 0.11 -10000 0 -0.22 64 64
HCK 0.036 0.015 -10000 0 0 80 80
CRK 0.038 0.012 -10000 0 0 52 52
TYK2 -0.036 0.12 0.22 24 -0.26 67 91
EGF 0.037 0.017 -10000 0 -0.007 69 69
YES1 0.038 0.013 -10000 0 0 57 57
CAV1 -0.035 0.11 0.19 1 -0.24 74 75
TXN 0.038 0.012 -10000 0 0 49 49
PTP1B/IRS1/GRB2 -0.027 0.13 -10000 0 -0.26 83 83
cell migration 0.052 0.11 0.26 86 -0.17 1 87
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 -0.25 84 84
Crk/p130 Cas -0.029 0.12 -10000 0 -0.25 81 81
DOK1 -0.037 0.11 -10000 0 -0.25 67 67
JAK2 -0.03 0.14 -10000 0 -0.39 58 58
Jak2/Leptin Receptor/Leptin -0.024 0.14 0.26 1 -0.28 68 69
PIK3R1 0.034 0.017 -10000 0 0 108 108
PTPN1 -0.052 0.12 0.17 1 -0.26 86 87
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 0.24 6 -0.29 69 75
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 -0.22 55 55
mol:H2O2 0.002 0.005 0.03 1 -10000 0 1
STAT3 (dimer) -0.02 0.13 0.25 1 -0.26 67 68
negative regulation of transcription -0.029 0.14 -10000 0 -0.39 58 58
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 76 76
p210 bcr-abl/Grb2 0.041 0.007 -10000 0 0 17 17
mol:NADPH -0.001 0.002 -10000 0 -10000 0 0
TRPV6 -0.007 0.12 0.22 8 -0.3 43 51
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 -0.28 87 87
Ras protein signal transduction 0.006 0.071 0.61 6 -10000 0 6
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 -0.27 83 83
STAT5A -0.043 0.12 -10000 0 -0.27 84 84
GRB2 0.041 0.007 -10000 0 0 17 17
PDGFB-D/PDGFRB -0.043 0.12 -10000 0 -0.25 87 87
CSN2 0.042 0.068 0.43 2 -10000 0 2
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
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.037 0.013 -10000 0 0 62 62
LAT2 -0.018 0.1 0.19 3 -0.21 87 90
AP1 -0.031 0.18 0.28 1 -0.42 67 68
mol:PIP3 -0.032 0.13 0.28 9 -0.31 69 78
IKBKB -0.013 0.088 0.21 21 -0.19 58 79
AKT1 0.015 0.12 0.27 51 -0.22 9 60
IKBKG -0.02 0.084 0.22 8 -0.19 60 68
MS4A2 0.046 0.012 0.071 30 -0.004 10 40
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 -0.32 63 66
mol:Ca2+ -0.022 0.11 0.23 13 -0.25 59 72
LYN 0.036 0.019 0.091 2 -0.003 92 94
CBLB -0.014 0.095 0.2 5 -0.22 73 78
SHC1 0.04 0.01 -10000 0 0 31 31
RasGAP/p62DOK 0.021 0.073 -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 -0.17 3 24
PTPN13 -0.055 0.2 -10000 0 -0.62 40 40
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 -0.31 33 54
SYK 0.037 0.017 0.091 2 -0.003 77 79
GRB2 0.041 0.007 -10000 0 0 17 17
LAT/PLCgamma1/GRB2/SLP76/GADs -0.023 0.13 0.18 1 -0.28 90 91
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 -0.095 110 110
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 65 69
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 0 108 108
FOS 0.026 0.02 -10000 0 0 207 207
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.009 0.1 0.15 1 -0.22 86 87
CHUK -0.021 0.085 0.22 8 -0.2 65 73
KLRG1 -0.015 0.079 0.18 4 -0.19 58 62
VAV1 -0.015 0.096 0.17 4 -0.22 75 79
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 -0.2 44 45
BTK -0.03 0.18 0.26 1 -0.51 49 50
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.026 0.11 -10000 0 -0.22 102 102
GAB2/PI3K/SHP2 -0.039 0.055 -10000 0 -0.15 73 73
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.003 0.069 -10000 0 -0.15 86 86
RAF1 0.013 0.16 -10000 0 -0.97 14 14
Fc epsilon R1/FcgammaRIIB/SHIP 0.033 0.092 -10000 0 -0.12 122 122
FCER1G 0.027 0.02 -10000 0 0 201 201
FCER1A 0.039 0.015 0.1 1 -0.005 48 49
Antigen/IgE/Fc epsilon R1/Fyn 0.04 0.077 -10000 0 -0.096 96 96
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 84 84
MAPK8 -0.033 0.22 -10000 0 -0.56 61 61
DUSP1 0.027 0.02 -10000 0 0 206 206
NF-kappa-B/RelA 0.001 0.068 0.14 15 -0.14 61 76
actin cytoskeleton reorganization -0.049 0.2 -10000 0 -0.71 31 31
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.017 0.13 0.26 3 -0.28 77 80
FER -0.015 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 0.25 5 -0.36 70 75
cytokine secretion -0.003 0.047 0.085 8 -0.1 63 71
SPHK1 -0.017 0.097 0.21 2 -0.21 84 86
PTK2 -0.052 0.21 -10000 0 -0.77 30 30
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.017 0.14 -10000 0 -0.29 89 89
EDG1 -0.01 0.002 -10000 0 -10000 0 0
mol:DAG -0.033 0.14 0.27 10 -0.31 73 83
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 37 74
MAP2K4 -0.072 0.32 -10000 0 -0.89 75 75
Fc epsilon R1/FcgammaRIIB 0.035 0.1 -10000 0 -0.14 122 122
mol:Choline -0.01 0.081 0.3 21 -0.16 3 24
SHC/Grb2/SOS1 0.023 0.13 -10000 0 -0.22 69 69
FYN 0.034 0.016 -10000 0 0 103 103
DOK1 0.04 0.009 -10000 0 0 24 24
PXN -0.052 0.19 -10000 0 -0.66 33 33
HCLS1 -0.01 0.099 0.19 7 -0.24 60 67
PRKCB -0.024 0.11 0.23 12 -0.24 69 81
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 -0.2 44 45
LCP2 0.034 0.016 -10000 0 0 102 102
PLA2G4A -0.007 0.092 0.18 9 -0.22 64 73
RASA1 0.037 0.014 -10000 0 0 71 71
mol:Phosphatidic acid -0.01 0.081 0.3 21 -0.16 3 24
IKK complex -0.015 0.073 0.22 11 -0.17 39 50
WIPF1 0 0 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.054 0.062 0.15 118 -0.033 29 147
AES 0.053 0.056 0.14 122 -0.032 14 136
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 47 47
TLE1 0.053 0.052 0.13 118 -0.033 12 130
MACF1 0.033 0.017 -10000 0 0 118 118
CTNNB1 0.033 0.12 0.29 28 -0.39 13 41
WIF1 0.04 0.01 -10000 0 -0.001 32 32
beta catenin/RanBP3 0.099 0.22 0.47 119 -0.4 8 127
KREMEN2 0.04 0.009 -10000 0 0 27 27
DKK1 0.039 0.011 -10000 0 0 44 44
beta catenin/beta TrCP1 0.054 0.12 0.3 28 -0.38 11 39
FZD1 0.041 0.007 -10000 0 0 17 17
AXIN2 -0.047 0.22 0.68 7 -0.79 28 35
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 8 -0.46 48 56
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 13 -0.27 9 22
HNF1A 0.019 0.051 0.09 137 -10000 0 137
CTBP1 0.053 0.053 0.14 114 -0.033 12 126
MYC 0.043 0.55 0.63 163 -1.1 74 237
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 0.14 118 -0.033 13 131
TCF3 0.053 0.055 0.14 121 -0.034 13 134
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 0.058 0.31 0.57 110 -0.39 28 138
LEF1 0.037 0.051 0.14 74 -0.033 13 87
DVL1 0.033 0.076 0.23 11 -0.29 14 25
CSNK2A1 0.038 0.013 -10000 0 0 54 54
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.066 0.19 -10000 0 -0.44 76 76
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 0.15 130 -0.033 30 160
NLK 0.031 0.025 -10000 0 -0.024 83 83
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 0.062 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 0.18 2 -0.22 9 11
CREBBP 0.054 0.055 0.14 122 -0.033 15 137
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.042 0.004 -10000 0 0 6 6
PTK2 0.027 0.02 -10000 0 0 204 204
CRKL -0.022 0.052 0.12 13 -0.13 71 84
GRB2/SOS1/SHC 0.065 0.051 -10000 0 -0.13 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 0.073 -10000 0 -0.12 75 75
AKT1 0 0.092 0.17 86 -0.17 15 101
BAD -0.007 0.085 0.16 83 -0.17 15 98
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.02 0.051 0.11 12 -0.13 66 78
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.011 0.069 0.2 4 -0.13 87 91
RAF1 0.016 0.12 0.28 12 -0.48 13 25
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.044 0.088 0.21 2 -0.13 89 91
YWHAZ 0.034 0.016 -10000 0 0 102 102
IGF-1R heterotetramer/IGF1/IRS1 0.018 0.068 0.18 2 -0.13 85 87
PIK3CA 0.03 0.019 -10000 0 0 155 155
RPS6KB1 0 0.096 0.18 92 -0.18 21 113
GNB2L1 0.041 0.005 -10000 0 0 7 7
positive regulation of MAPKKK cascade 0.014 0.11 0.27 16 -0.41 10 26
PXN 0.041 0.007 -10000 0 0 14 14
PIK3R1 0.034 0.017 -10000 0 0 108 108
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 0.091 -10000 0 -0.12 84 84
IGF-1R heterotetramer 0.033 0.024 0.1 2 -0.052 16 18
IGF-1R heterotetramer/IGF1/IRS/Nck 0.038 0.076 0.2 2 -0.13 84 86
Crk/p130 Cas/Paxillin 0.043 0.082 0.25 9 -0.13 71 80
IGF1R 0.034 0.024 0.1 2 -0.052 16 18
IGF1 0.027 0.035 0.1 2 -0.053 70 72
IRS2/Crk 0.009 0.055 0.17 1 -0.13 62 63
PI3K 0.024 0.083 0.21 2 -0.12 89 91
apoptosis -0.002 0.09 0.17 15 -0.18 67 82
HRAS/GDP 0.029 0.01 -10000 0 -0.13 1 1
PRKCD -0.011 0.093 0.21 6 -0.28 27 33
RAF1/14-3-3 E 0.032 0.11 0.29 12 -0.41 13 25
BAD/14-3-3 0.002 0.093 0.19 67 -0.17 15 82
PRKCZ 0.001 0.095 0.18 94 -0.17 15 109
Crk/p130 Cas/Paxillin/FAK1 0.01 0.08 0.18 22 -0.16 42 64
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 73 73
BCAR1 0.036 0.014 -10000 0 0 76 76
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.054 0.078 -10000 0 -0.11 77 77
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 85 101
GRB10 0.04 0.008 -10000 0 0 23 23
PTPN11 -0.021 0.052 0.11 13 -0.13 68 81
IRS1 0.004 0.062 0.13 17 -0.13 85 102
IRS2 -0.021 0.052 0.11 14 -0.13 71 85
IGF-1R heterotetramer/IGF1 0.02 0.076 0.17 1 -0.16 76 77
GRB2 0.041 0.007 -10000 0 0 17 17
PDPK1 0.008 0.099 0.19 92 -0.18 13 105
YWHAE 0.038 0.013 -10000 0 0 58 58
PRKD1 -0.012 0.097 0.21 7 -0.27 36 43
SHC1 0.04 0.01 -10000 0 0 31 31
IL12-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
IL12/IL12R/TYK2/JAK2/SOCS1 0.031 0.1 0.21 19 -0.24 29 48
TBX21 -0.029 0.28 -10000 0 -0.73 48 48
B2M 0.038 0.014 -10000 0 -10000 0 0
TYK2 0.025 0.044 -10000 0 -0.051 92 92
IL12RB1 0.024 0.045 -10000 0 -0.05 106 106
GADD45B -0.06 0.35 -10000 0 -0.9 63 63
IL12RB2 0.028 0.046 -10000 0 -0.051 91 91
GADD45G -0.031 0.3 0.43 1 -0.72 61 62
natural killer cell activation 0.002 0.021 0.046 12 -0.036 73 85
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) -0.027 0.29 -10000 0 -0.6 80 80
HLA-DRB5 0.02 0.028 -10000 0 -0.008 262 262
FASLG -0.026 0.28 0.53 1 -0.74 47 48
NF kappa B2 p52/RelB -0.015 0.29 -10000 0 -0.62 73 73
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 52 52
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 -0.04 57 57
IL12Rbeta2/JAK2 0.033 0.073 -10000 0 -0.14 31 31
CCL3 -0.046 0.33 -10000 0 -0.85 55 55
CCL4 -0.029 0.28 0.41 1 -0.61 73 74
HLA-A 0.038 0.014 -10000 0 -10000 0 0
IL18/IL18R 0.061 0.082 -10000 0 -0.12 78 78
NOS2 -0.027 0.27 0.38 2 -0.56 79 81
IL12/IL12R/TYK2/JAK2/SPHK2 0.031 0.1 0.21 19 -0.23 32 51
IL1R1 -0.11 0.43 -10000 0 -1 96 96
IL4 0.019 0.044 0.096 2 -0.057 29 31
JAK2 0.024 0.043 -10000 0 -0.052 84 84
EntrezGene:6957 -0.001 0.009 -10000 0 -0.025 18 18
TCR/CD3/MHC I/CD8 -0.012 0.12 -10000 0 -0.43 26 26
RAB7A -0.032 0.28 0.39 2 -0.58 83 85
lysosomal transport -0.028 0.26 0.38 2 -0.55 83 85
FOS -0.19 0.52 -10000 0 -1.1 127 127
STAT4 (dimer) -0.022 0.29 0.4 5 -0.6 81 86
STAT5A (dimer) -0.024 0.28 -10000 0 -0.62 69 69
GZMA -0.055 0.35 -10000 0 -0.93 55 55
GZMB -0.037 0.32 0.56 1 -0.83 52 53
HLX 0 0 -10000 0 -10000 0 0
LCK -0.036 0.29 0.42 2 -0.66 69 71
TCR/CD3/MHC II/CD4 -0.069 0.21 -10000 0 -0.38 132 132
IL2/IL2R 0.047 0.082 -10000 0 -0.11 94 94
MAPK14 -0.049 0.33 0.42 1 -0.71 81 82
CCR5 -0.021 0.25 0.35 3 -0.52 78 81
IL1B 0.023 0.042 -10000 0 -0.05 83 83
STAT6 0.012 0.14 0.23 1 -0.33 34 35
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 84 84
NFKB2 0.04 0.009 -10000 0 0 24 24
IL12B 0.027 0.046 -10000 0 -0.051 91 91
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 0.24 29 -0.21 19 48
IL2RB 0.036 0.014 -10000 0 0 75 75
proteasomal ubiquitin-dependent protein catabolic process -0.015 0.28 0.39 7 -0.56 81 88
IL2RG 0.028 0.02 -10000 0 0 183 183
IL12 0.024 0.072 -10000 0 -0.14 35 35
STAT5A 0.038 0.012 -10000 0 0 51 51
CD247 -0.001 0.009 -10000 0 -0.025 18 18
IL2 0.039 0.012 -10000 0 0 46 46
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 -0.05 81 81
IL12/IL12R/TYK2/JAK2 -0.045 0.3 0.42 1 -0.68 72 73
MAP2K3 -0.053 0.34 -10000 0 -0.75 79 79
RIPK2 0.033 0.017 -10000 0 0 125 125
MAP2K6 -0.056 0.32 0.41 1 -0.69 84 85
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 -0.086 6 6
EOMES 0.005 0.076 -10000 0 -0.52 9 9
STAT1 (dimer) -0.043 0.29 -10000 0 -0.61 81 81
T cell proliferation -0.021 0.24 0.35 5 -0.48 82 87
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 -0.03 0.25 0.35 1 -0.54 76 77
ATF2 -0.048 0.3 0.39 1 -0.66 82 83
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.011 0.076 -10000 0 -0.14 104 104
CRKL -0.032 0.14 0.33 1 -0.43 43 44
mol:PIP3 0.007 0.079 0.31 1 -0.83 4 5
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 42 43
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 -0.024 0.14 0.28 2 -0.4 45 47
HGF/MET/CIN85/CBL/ENDOPHILINS 0.051 0.085 -10000 0 -0.11 105 105
AP1 -0.004 0.082 0.16 10 -0.14 104 114
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 46 46
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK -0.01 0.15 0.29 3 -0.41 43 46
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 0.32 53 -10000 0 53
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.013 0.083 0.15 2 -0.22 46 48
PAK1 0.01 0.098 0.35 8 -0.69 4 12
HGF/MET/RANBP10 0.025 0.076 -10000 0 -0.12 104 104
HRAS -0.072 0.22 -10000 0 -0.48 118 118
DOCK1 -0.033 0.14 0.26 7 -0.42 43 50
GAB1 -0.029 0.15 0.25 1 -0.46 41 42
CRK -0.028 0.14 0.28 3 -0.42 43 46
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.056 0.19 -10000 0 -0.43 112 112
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 -10000 0 -0.16 103 103
PIK3R1 0.034 0.017 -10000 0 0 108 108
cell morphogenesis -0.009 0.15 0.27 30 -0.35 39 69
GRB2/SHC 0.018 0.096 0.19 3 -0.16 104 107
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 0.32 53 -10000 0 53
HGF/MET/MUC20 0.014 0.064 -10000 0 -0.11 105 105
cell migration 0.017 0.095 0.19 3 -0.16 104 107
GRB2 0.041 0.007 -10000 0 0 17 17
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 -0.29 21 21
MET/MUC20 -0.004 0.061 -10000 0 -0.13 107 107
RAP1B -0.034 0.13 0.27 2 -0.39 40 42
RAP1A -0.039 0.13 0.28 3 -0.4 43 46
HGF/MET/RANBP9 0.026 0.078 -10000 0 -0.12 102 102
RAF1 -0.072 0.21 -10000 0 -0.46 120 120
STAT3 -0.009 0.11 0.19 4 -0.3 34 38
cell proliferation -0.031 0.14 0.31 4 -0.3 77 81
RPS6KB1 -0.012 0.085 -10000 0 -0.27 41 41
MAPK3 -0.008 0.12 0.67 12 -10000 0 12
MAPK1 0.029 0.2 0.69 42 -10000 0 42
RANBP9 0.038 0.012 -10000 0 0 53 53
MAPK8 -0.022 0.15 -10000 0 -0.4 51 51
SRC -0.006 0.092 0.2 9 -0.26 29 38
PI3K 0 0.096 0.19 3 -0.18 95 98
MET/Glomulin 0.012 0.047 -10000 0 -0.12 47 47
SOS1 0.038 0.013 -10000 0 0 56 56
MAP2K1 -0.071 0.2 -10000 0 -0.44 118 118
MET 0.027 0.02 -10000 0 0 198 198
MAP4K1 -0.022 0.15 0.29 1 -0.44 42 43
PTK2 0.027 0.02 -10000 0 0 204 204
MAP2K2 -0.072 0.19 -10000 0 -0.43 119 119
BAD -0.003 0.079 0.34 2 -0.7 4 6
MAP2K4 -0.026 0.13 0.26 2 -0.38 44 46
SHP2/GRB2/SOS1/GAB1 -0.013 0.16 -10000 0 -0.37 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 80 80
PTPRJ 0.039 0.01 -10000 0 0 35 35
NCK/PLCgamma1 0.016 0.095 0.19 3 -0.16 99 102
PDPK1 0.002 0.076 -10000 0 -0.77 4 4
HGF/MET/SHIP 0.014 0.064 -10000 0 -0.11 105 105
IL2 signaling events mediated by STAT5

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
GAB2 0.032 0.019 -10000 0 0 143 143
ELF1 0.047 0.023 -10000 0 -0.27 2 2
CCNA2 0.032 0.018 -10000 0 0 135 135
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 -0.001 110 110
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 0.001 0.14 0.24 1 -0.33 46 47
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 77 77
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 -0.039 0.18 0.28 5 -0.55 31 36
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 0.009 -10000 0 -0.003 19 19
IL2 0.039 0.013 -10000 0 -0.002 49 49
CDK6 0.032 0.018 -10000 0 0 129 129
CCND3 0.004 0.14 0.32 2 -0.53 15 17
IL4-mediated signaling events

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
BCL2L1 -0.066 0.49 -10000 0 -1 75 75
STAT6 (cleaved dimer) -0.11 0.45 -10000 0 -0.95 86 86
IGHG1 0.034 0.23 0.45 4 -0.68 8 12
IGHG3 -0.069 0.45 -10000 0 -0.91 83 83
AKT1 -0.055 0.37 -10000 0 -0.82 69 69
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.044 0.36 -10000 0 -0.87 66 66
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.051 0.4 -10000 0 -0.93 65 65
THY1 -0.23 0.66 0.78 1 -1.2 159 160
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 -10000 0 -0.75 68 68
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.055 0.4 -10000 0 -0.93 65 65
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 -0.086 2 2
STAT6 (dimer)/ETS1 -0.086 0.46 -10000 0 -0.96 81 81
SOCS1 -0.03 0.35 -10000 0 -0.66 67 67
SOCS3 -0.034 0.37 -10000 0 -0.89 49 49
FCER2 -0.032 0.39 -10000 0 -0.85 38 38
PARP14 0.033 0.019 -10000 0 -10000 0 0
CCL17 -0.062 0.47 -10000 0 -1 66 66
GRB2 0.041 0.007 -10000 0 0 17 17
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.011 0.3 -10000 0 -0.64 59 59
T cell proliferation -0.086 0.49 -10000 0 -1 87 87
IL4R/JAK1 -0.079 0.49 -10000 0 -1 83 83
EGR2 -0.059 0.48 -10000 0 -1 68 68
JAK2 0.033 0.073 0.18 2 -0.097 1 3
JAK3 0.034 0.026 -10000 0 -0.038 44 44
PIK3R1 0.034 0.017 -10000 0 0 108 108
JAK1 0.041 0.041 0.11 4 -0.041 7 11
COL1A2 -0.15 0.56 -10000 0 -1.3 108 108
CCL26 -0.072 0.49 -10000 0 -1.1 61 61
IL4R -0.068 0.52 -10000 0 -1.1 80 80
PTPN6 0.006 0.043 -10000 0 -0.074 2 2
IL13RA2 -0.061 0.47 -10000 0 -0.99 69 69
IL13RA1 0.036 0.076 0.18 6 -0.097 1 7
IRF4 0.058 0.15 -10000 0 -1.3 1 1
ARG1 0.05 0.19 -10000 0 -0.69 6 6
CBL -0.027 0.35 0.57 2 -0.71 67 69
GTF3A 0.013 0.08 -10000 0 -0.13 123 123
PIK3CA 0.03 0.019 -10000 0 0 155 155
IL13RA1/JAK2 0.043 0.12 0.25 5 -0.18 26 31
IRF4/BCL6 0.043 0.14 -10000 0 -1.2 1 1
CD40LG 0.049 0.01 -10000 0 -0.12 1 1
MAPK14 -0.029 0.36 -10000 0 -0.75 64 64
mitosis -0.046 0.35 -10000 0 -0.76 69 69
STAT6 -0.064 0.54 0.78 2 -1.1 80 82
SPI1 0.045 0.01 -10000 0 -10000 0 0
RPS6KB1 -0.05 0.34 -10000 0 -0.74 70 70
STAT6 (dimer) -0.062 0.54 0.78 2 -1.1 80 82
STAT6 (dimer)/PARP14 -0.1 0.48 -10000 0 -1 80 80
mast cell activation -0.004 0.019 -10000 0 -0.045 7 7
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.075 0.39 -10000 0 -0.91 68 68
FRAP1 -0.055 0.37 -10000 0 -0.82 69 69
LTA -0.06 0.47 -10000 0 -1 63 63
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 89 89
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.048 0.38 -10000 0 -0.89 66 66
IL2RG 0.027 0.025 -10000 0 -0.042 17 17
IL10 -0.058 0.48 -10000 0 -1 63 63
IRS1 0.04 0.008 -10000 0 0 22 22
IRS2 0.039 0.01 -10000 0 0 33 33
IL4 0.038 0.23 -10000 0 -0.93 14 14
IL5 -0.063 0.47 -10000 0 -0.99 71 71
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 77 77
IL2R gamma/JAK3 0.02 0.074 -10000 0 -0.13 92 92
TFF3 -0.067 0.49 -10000 0 -1 71 71
ALOX15 -0.062 0.47 -10000 0 -0.97 75 75
MYBL1 0.036 0.014 -10000 0 0 73 73
T-helper 2 cell differentiation -0.1 0.47 -10000 0 -0.94 91 91
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 -0.92 67 67
mol:PI-3-4-5-P3 -0.054 0.37 -10000 0 -0.82 69 69
PI3K -0.064 0.4 -10000 0 -0.9 69 69
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 -0.008 0.29 -10000 0 -0.61 63 63
ITGB3 -0.096 0.54 -10000 0 -1.1 90 90
PIGR -0.058 0.49 -10000 0 -1 73 73
IGHE -0.002 0.089 0.18 44 -0.18 25 69
MAPKKK cascade -0.007 0.29 -10000 0 -0.6 63 63
BCL6 0.03 0.018 -10000 0 0 146 146
OPRM1 -0.063 0.47 -10000 0 -0.99 71 71
RETNLB -0.056 0.48 -10000 0 -1 69 69
SELP -0.057 0.48 -10000 0 -0.98 73 73
AICDA -0.051 0.45 -10000 0 -0.97 62 62
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.036 0.015 -10000 0 0 78 78
GNB1/GNG2 0.015 0.12 0.23 1 -0.26 46 47
mol:DAG -0.006 0.1 0.2 7 -0.26 41 48
PLCG1 -0.007 0.1 0.21 6 -0.26 41 47
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 15 -0.23 40 55
mol:Ca2+ -0.006 0.1 0.2 7 -0.25 41 48
mol:IP3 -0.006 0.1 0.2 7 -0.26 41 48
NLK -0.032 0.27 -10000 0 -0.87 51 51
GNB1 0.041 0.005 -10000 0 0 7 7
CAMK2A -0.017 0.092 0.18 7 -0.24 41 48
MAP3K7IP1 0.038 0.012 -10000 0 0 54 54
Noncanonical Wnts/FZD -0.019 0.096 -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 0.19 7 -0.25 44 51
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 0.19 7 -0.26 43 50
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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
BMP receptor signaling

Figure S43.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S43.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.01 0.1 -10000 0 -0.14 134 134
SMAD6-7/SMURF1 0.07 0.04 -10000 0 -0.15 8 8
NOG 0.038 0.012 -10000 0 0 50 50
SMAD9 0.006 0.12 -10000 0 -0.43 36 36
SMAD4 0.038 0.012 -10000 0 0 49 49
SMAD5 -0.002 0.098 0.22 2 -0.28 36 38
BMP7/USAG1 -0.02 0.084 -10000 0 -0.16 134 134
SMAD5/SKI 0.011 0.11 0.24 1 -0.29 36 37
SMAD1 0.003 0.096 -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 49 49
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 -0.27 54 55
BMP2-4 (homodimer) 0.047 0.036 -10000 0 -0.14 11 11
RGMB 0.039 0.011 -10000 0 0 42 42
BMP6/BMPR2/BMPR1A-1B 0.05 0.085 -10000 0 -0.13 80 80
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 -0.25 30 32
BMP2-4/USAG1 0.022 0.07 -10000 0 -0.12 71 71
SMAD6/SMURF1/SMAD5 0.01 0.11 0.24 1 -0.29 36 37
SOSTDC1 0.023 0.021 -10000 0 0 255 255
BMP7/BMPR2/BMPR1A-1B 0.008 0.1 -10000 0 -0.14 153 153
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 0.046 -10000 0 -0.12 8 8
SMAD5/SMAD5/SMAD4 0.008 0.11 0.24 1 -0.29 35 36
MAPK1 0.039 0.012 -10000 0 0 46 46
TAK1/TAB family 0.032 0.12 -10000 0 -0.26 30 30
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 0.023 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 54 54
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 -0.41 41 41
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 0.038 0.013 -10000 0 0 59 59
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 0.002 0.084 -10000 0 -0.25 32 32
PPM1A 0.041 0.007 -10000 0 0 16 16
SMAD1/SMURF2 0.021 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 -0.26 32 32
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 31 31
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 0.05 -10000 0 -0.12 20 20
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.017 0.11 -10000 0 -0.14 143 143
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.014 0.15 0.25 17 -0.33 61 78
FYN -0.029 0.18 0.24 15 -0.4 80 95
LAT/GRAP2/SLP76 -0.003 0.15 0.24 6 -0.33 70 76
IKBKB 0.039 0.011 -10000 0 0 44 44
AKT1 -0.014 0.14 0.22 11 -0.32 73 84
B2M 0.037 0.017 -10000 0 -0.003 76 76
IKBKG -0.002 0.05 0.12 11 -0.11 49 60
MAP3K8 0.04 0.008 -10000 0 0 21 21
mol:Ca2+ -0.013 0.016 0.051 11 -0.042 45 56
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 10 -0.43 74 84
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 24 -0.38 62 86
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 17 17
COT/AKT1 0.005 0.12 0.22 10 -0.26 72 82
LAT -0.017 0.16 0.23 10 -0.38 64 74
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 11 -0.31 84 95
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 0.061 0.14 19 -0.11 35 54
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.019 0.065 -10000 0 -0.16 77 77
PRKCA -0.008 0.083 0.17 18 -0.19 56 74
GRAP2 0.038 0.013 -10000 0 0 57 57
mol:IP3 -0.016 0.11 -10000 0 -0.27 68 68
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 66 77
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 -0.39 73 76
PTPN6 -0.01 0.16 0.2 35 -0.36 68 103
VAV1 -0.018 0.16 0.21 12 -0.39 67 79
Monovalent TCR/CD3 -0.004 0.083 -10000 0 -0.21 66 66
CBL 0.04 0.008 -10000 0 0 23 23
LCK -0.018 0.18 0.23 16 -0.39 72 88
PAG1 -0.009 0.16 0.21 32 -0.38 63 95
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 78 82
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 1 -0.19 69 70
HRAS 0.04 0.01 -10000 0 0 31 31
GO:0035030 -0.013 0.13 0.19 17 -0.3 68 85
CD8A 0.042 0.01 -10000 0 -0.015 15 15
CD8B 0.001 0.004 -10000 0 -0.022 4 4
PTPRC 0.025 0.021 -10000 0 0 228 228
PDK1/PKC theta -0.021 0.16 0.25 9 -0.37 70 79
CSK/PAG1 -0.008 0.16 0.23 21 -0.39 57 78
SOS1 0.038 0.013 -10000 0 0 56 56
peptide-MHC class I 0.038 0.07 -10000 0 -0.18 45 45
GRAP2/SLP76 0.001 0.17 0.25 5 -0.38 71 76
STIM1 -0.022 0.075 1.1 1 -10000 0 1
RAS family/GTP 0.011 0.078 0.17 7 -0.15 55 62
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.018 0.15 0.17 3 -0.35 73 76
mol:DAG -0.028 0.09 -10000 0 -0.24 70 70
RAP1A/GDP 0.011 0.033 0.077 13 -0.06 39 52
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 -0.76 26 26
RAP1A/GTP 0.003 0.011 -10000 0 -0.045 8 8
mol:PI-3-4-5-P3 -0.018 0.16 0.23 11 -0.36 74 85
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.011 0.14 0.22 1 -0.34 65 66
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 0.26 3 -0.34 66 69
MALT1 0.036 0.014 -10000 0 0 76 76
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 71 71
PRKCE -0.005 0.085 0.18 21 -0.2 52 73
PRKCQ -0.023 0.17 0.24 8 -0.4 72 80
LCP2 0.034 0.016 -10000 0 0 102 102
BCL10 0.041 0.006 -10000 0 0 11 11
regulation of survival gene product expression -0.009 0.12 0.2 13 -0.27 73 86
IKK complex 0.004 0.05 0.13 22 -0.093 28 50
RAS family/GDP -0.002 0.014 -10000 0 -0.035 43 43
MAP3K14 -0.002 0.094 0.17 13 -0.21 68 81
PDPK1 -0.015 0.13 0.21 13 -0.3 72 85
TCR/CD3/MHC I/CD8/Fyn -0.037 0.2 -10000 0 -0.48 70 70
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 0.041 0.087 -10000 0 -0.14 68 68
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 81 86
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.041 0.081 -10000 0 -0.15 69 69
antigen processing and presentation of peptide antigen via MHC class I -0.025 0.093 -10000 0 -0.2 93 93
CaM/Ca2+ 0.044 0.088 -10000 0 -0.14 69 69
RAP1A 0.039 0.01 -10000 0 0 35 35
STAT1 (dimer)/SHP2 0 0.093 0.23 7 -0.17 81 88
AKT1 0.005 0.1 0.24 25 -0.22 30 55
MAP2K1 -0.028 0.066 0.19 4 -0.18 33 37
MAP3K11 -0.022 0.072 0.19 11 -0.18 29 40
IFNGR1 0.035 0.021 0.083 2 -0.005 111 113
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.01 0.1 -10000 0 -0.27 50 50
Rap1/GTP -0.044 0.057 0.073 8 -0.17 47 55
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 -0.029 0.16 0.28 1 -0.43 60 61
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 0.25 7 -0.21 49 56
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 0.093 0.25 6 -0.2 60 66
CEBPB/PTGES2/Cbp/p300 -0.011 0.12 -10000 0 -0.28 62 62
mol:Ca2+ 0.036 0.085 -10000 0 -0.14 69 69
MAPK3 -0.021 0.14 -10000 0 -0.65 15 15
STAT1 (dimer) -0.022 0.13 0.19 2 -0.28 84 86
MAPK1 -0.058 0.21 0.42 1 -0.72 44 45
JAK2 0.033 0.022 0.083 2 -0.007 114 116
PIK3R1 0.034 0.017 -10000 0 0 108 108
JAK1 0.036 0.022 0.082 1 -0.019 67 68
CAMK2D 0.036 0.015 -10000 0 0 82 82
DAPK1 -0.027 0.16 0.24 1 -0.46 52 53
SMAD7 -0.003 0.071 0.16 30 -0.13 54 84
CBL/CRKL/C3G 0.026 0.085 0.24 7 -0.17 33 40
PI3K 0.02 0.092 -10000 0 -0.17 63 63
IFNG 0.032 0.025 0.085 2 -0.017 103 105
apoptosis -0.022 0.15 -10000 0 -0.41 56 56
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 0.098 0.2 33 -0.21 34 67
PRKCD 0.002 0.11 0.23 32 -0.23 32 64
RAP1B 0.038 0.013 -10000 0 0 59 59
negative regulation of cell growth -0.025 0.093 -10000 0 -0.2 93 93
PTPN2 0.04 0.008 -10000 0 0 20 20
EP300 0.036 0.014 -10000 0 0 73 73
IRF1 -0.046 0.097 0.28 3 -0.28 57 60
STAT1 (dimer)/PIASy -0.029 0.087 0.22 8 -0.22 40 48
SOCS1 0.003 0.18 -10000 0 -1.1 15 15
mol:GDP 0.023 0.081 0.23 6 -0.16 33 39
CASP1 -0.023 0.08 0.16 14 -0.17 97 111
PTGES2 0.04 0.009 -10000 0 0 27 27
IRF9 -0.008 0.052 0.11 8 -0.12 55 63
mol:PI-3-4-5-P3 0.006 0.082 -10000 0 -0.17 66 66
RAP1/GDP 0.015 0.086 0.24 1 -0.17 54 55
CBL -0.021 0.072 0.22 9 -0.18 24 33
MAP3K1 -0.02 0.07 0.23 5 -0.18 29 34
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 93 93
PTPN11 -0.015 0.074 0.17 34 -0.17 31 65
CREBBP 0.038 0.013 -10000 0 0 54 54
RAPGEF1 0.04 0.008 -10000 0 0 23 23
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.035 0.048 -10000 0 -0.12 42 42
cell-cell adhesion 0.041 0.041 0.12 78 -10000 0 78
Ephrin B/EPHB2/RasGAP 0.053 0.096 -10000 0 -0.12 101 101
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 82 82
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 0.061 0.087 -10000 0 -0.12 77 77
endothelial cell migration 0.021 0.076 -10000 0 -0.12 99 99
GRB2 0.041 0.007 -10000 0 0 17 17
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 -0.12 78 78
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.007 0.072 -10000 0 -0.22 13 13
PIK3R1 0.034 0.017 -10000 0 0 108 108
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 -0.04 0.098 0.19 15 -0.23 73 88
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 0.1 0.28 51 -0.18 3 54
Ephrin B/EPHB1 0.049 0.075 -10000 0 -0.11 81 81
RAP1/GDP -0.026 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 71 71
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 -0.12 42 42
MAPK3 -0.003 0.069 0.2 6 -0.21 13 19
MAPK1 -0.001 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 73 73
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 -0.001 0.08 -10000 0 -0.16 98 98
CDC42 0.04 0.009 -10000 0 0 24 24
RAS family/GTP -0.041 0.049 0.051 9 -0.19 14 23
PTK2 0.16 0.26 0.56 165 -10000 0 165
MAP4K4 -0.003 0.1 0.28 51 -0.19 3 54
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 0.29 23 -0.21 15 38
MAP2K1 -0.001 0.066 0.21 2 -0.22 12 14
WASL 0.04 0.009 -10000 0 0 24 24
Ephrin B1/EPHB1-2/NCK1 0.076 0.065 -10000 0 -0.12 40 40
cell migration -0.009 0.091 0.23 12 -0.24 22 34
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 -0.22 14 26
RAC1 0.039 0.01 -10000 0 0 34 34
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 0.11 0.27 6 -0.21 75 81
ruffle organization -0.021 0.08 0.23 15 -0.24 2 17
NCK1 0.036 0.015 -10000 0 0 80 80
receptor internalization -0.03 0.055 0.17 11 -0.19 8 19
Ephrin B/EPHB2/KALRN 0.059 0.092 -10000 0 -0.12 88 88
ROCK1 0.02 0.089 0.19 111 -10000 0 111
RAS family/GDP -0.055 0.062 -10000 0 -0.16 109 109
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
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.042 0.15 -10000 0 -0.34 100 100
KLHL20 -0.016 0.1 0.2 14 -0.23 53 67
CYFIP2 0.038 0.012 -10000 0 0 47 47
Rac1/GDP -0.012 0.11 0.24 8 -0.25 50 58
ENAH -0.038 0.14 -10000 0 -0.34 92 92
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 0.15 8 -0.17 50 58
ABI1/Sra1/Nap1 -0.033 0.054 -10000 0 -0.15 68 68
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.068 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 -0.34 100 100
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 -0.14 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 69 69
DLG1 -0.044 0.15 -10000 0 -0.34 101 101
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.033 0.048 -10000 0 -0.14 59 59
MLLT4 0.034 0.017 -10000 0 0 107 107
ARF6/GTP/NME1/Tiam1 0.045 0.062 -10000 0 -0.11 58 58
PI3K -0.04 0.063 -10000 0 -0.18 56 56
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 0.063 0.15 20 -0.14 24 44
PIK3R1 0.034 0.017 -10000 0 0 108 108
CDH1 0.035 0.016 -10000 0 0 98 98
RhoA/GDP -0.013 0.11 0.22 5 -0.25 53 58
actin cytoskeleton organization -0.01 0.077 0.16 15 -0.17 52 67
CDC42/GDP -0.012 0.11 0.26 6 -0.25 50 56
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 0.039 0.01 -10000 0 0 34 34
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 53 60
CDC42/GTP/IQGAP1 0.04 0.047 -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 52 56
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 99 104
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 -0.35 90 90
regulation of cell-cell adhesion -0.008 0.064 0.11 11 -0.15 56 67
WASF2 -0.007 0.043 0.11 13 -0.091 52 65
Rap1/GTP 0.002 0.087 0.19 21 -0.19 51 72
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.071 0.083 -10000 0 -0.12 52 52
CCND1 -0.02 0.072 0.14 5 -0.15 99 104
VAV2 -0.051 0.22 -10000 0 -0.6 52 52
RAP1/GDP 0 0.098 0.21 21 -0.24 37 58
adherens junction assembly -0.039 0.14 -10000 0 -0.34 90 90
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 92 92
PIK3CA 0.03 0.019 -10000 0 0 155 155
Rac1/GTP -0.057 0.13 -10000 0 -0.35 67 67
E-cadherin/beta catenin/alpha catenin 0.052 0.066 -10000 0 -0.13 48 48
ITGAE 0.039 0.01 -10000 0 0 37 37
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.03 0.16 -10000 0 -0.34 100 100
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 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
PTK2 0.001 0.068 0.14 13 -0.19 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 0.074 -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 52 52
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 -0.34 20 21
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 0 108 108
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 -0.2 39 73
ITGB7 0.039 0.011 -10000 0 0 40 40
RAC1 0.039 0.01 -10000 0 0 34 34
alpha4/beta1 Integrin/VCAM1 -0.005 0.096 -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 0 288 288
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 0.036 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 -0.36 20 21
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 26 26
EP300 0.036 0.014 -10000 0 0 73 73
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.012 0.095 0.18 1 -0.25 51 52
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 72 -0.2 30 102
RAR alpha/9cRA/Cyclin H -0.002 0.12 -10000 0 -0.25 72 72
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.003 0.079 -10000 0 -0.21 52 52
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 -0.48 69 69
NCOA2 0.037 0.014 -10000 0 0 71 71
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 75 76
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 53 53
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 0 164 164
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 -0.015 0.16 0.27 2 -0.36 75 77
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.01 0.13 0.23 1 -0.3 61 62
proteasomal ubiquitin-dependent protein catabolic process -0.011 0.1 0.17 3 -0.26 51 54
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.043 0.2 -10000 0 -0.54 62 62
positive regulation of DNA binding -0.009 0.11 -10000 0 -0.23 73 73
NRIP1 -0.079 0.32 -10000 0 -0.97 55 55
RXRs/RARs -0.027 0.17 -10000 0 -0.39 77 77
RXRs/RXRs/DNA/9cRA -0.03 0.13 -10000 0 -0.32 79 79
PRKACA 0.035 0.015 -10000 0 0 89 89
CDK7 0.035 0.016 -10000 0 0 98 98
TFIIH 0.06 0.054 -10000 0 -0.14 25 25
RAR alpha/9cRA 0.037 0.087 -10000 0 -0.23 19 19
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
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.052 0.14 0.22 1 -0.34 73 74
IKBKB 0.017 0.099 0.26 11 -0.26 22 33
AKT1 0.024 0.093 0.22 48 -0.18 8 56
IKBKG 0.02 0.077 0.23 1 -0.26 10 11
CALM1 -0.012 0.12 0.2 10 -0.35 37 47
PIK3CA 0.03 0.019 -10000 0 0 155 155
MAP3K1 -0.045 0.16 -10000 0 -0.41 61 61
MAP3K7 0.038 0.012 -10000 0 0 47 47
mol:Ca2+ -0.011 0.12 0.2 5 -0.36 43 48
DOK1 0.04 0.009 -10000 0 0 24 24
AP-1 -0.027 0.096 -10000 0 -0.21 72 72
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 0.088 -10000 0 -0.27 37 37
CAMK2G -0.015 0.11 0.2 14 -0.33 39 53
CSNK2A1 0.038 0.012 -10000 0 0 54 54
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.02 0.063 -10000 0 -0.13 59 59
GO:0007205 -0.013 0.13 0.2 5 -0.36 44 49
SYK 0.037 0.014 -10000 0 0 70 70
ELK1 -0.017 0.12 0.22 3 -0.36 41 44
NFATC1 -0.029 0.11 0.2 3 -0.28 55 58
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 0.012 0.066 0.13 1 -0.13 81 82
HRAS -0.011 0.1 0.21 6 -0.28 45 51
NFKBIA 0.014 0.061 0.13 1 -0.12 71 72
NF-kappa-B/RelA/I kappa B beta 0.02 0.059 0.13 2 -0.1 75 77
RasGAP/Csk 0.057 0.088 -10000 0 -0.11 79 79
mol:GDP -0.012 0.12 0.2 5 -0.35 45 50
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 0.022 0.055 0.13 2 -0.1 66 68
GRB2 0.041 0.007 -10000 0 0 17 17
PI3K/BCAP/CD19 -0.027 0.15 -10000 0 -0.41 43 43
PIK3R1 0.034 0.017 -10000 0 0 108 108
mol:IP3 -0.008 0.12 0.21 5 -0.37 42 47
CSK 0.04 0.008 -10000 0 0 21 21
FOS -0.017 0.12 0.21 7 -0.33 47 54
CHUK -0.002 0.11 0.23 1 -0.29 53 54
IBTK 0.037 0.014 -10000 0 0 66 66
CARD11/BCL10/MALT1/TAK1 0.013 0.13 0.23 1 -0.3 44 45
PTPN6 -0.003 0.09 0.18 31 -0.27 28 59
RELA 0.041 0.006 -10000 0 0 10 10
BCL2A1 0.014 0.044 0.11 4 -0.079 69 73
VAV2 -0.022 0.12 -10000 0 -0.31 55 55
ubiquitin-dependent protein catabolic process 0.015 0.065 0.13 1 -0.12 81 82
BTK -0.037 0.25 -10000 0 -1.1 32 32
CD19 -0.019 0.095 -10000 0 -0.28 42 42
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 0.25 4 -0.36 61 65
SH3BP5 0.04 0.008 -10000 0 0 23 23
PIK3AP1 -0.01 0.13 0.23 6 -0.39 36 42
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.02 0.17 -10000 0 -0.49 45 45
RAF1 -0.015 0.095 0.24 5 -0.27 41 46
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 -0.21 68 68
RASA1 0.037 0.014 -10000 0 0 71 71
MAPK3 -0.02 0.085 0.22 7 -0.25 37 44
MAPK1 -0.018 0.083 0.22 8 -0.25 36 44
CD72/SHP1 0.025 0.12 0.26 31 -0.25 30 61
NFKB1 0.036 0.015 -10000 0 0 84 84
MAPK8 -0.043 0.14 -10000 0 -0.36 59 59
actin cytoskeleton organization -0.024 0.11 0.25 3 -0.28 55 58
NF-kappa-B/RelA 0.033 0.12 0.24 1 -0.22 75 76
Calcineurin 0.012 0.12 0.23 1 -0.31 40 41
PI3K -0.011 0.075 -10000 0 -0.24 22 22
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.001 0.12 0.23 4 -0.37 39 43
SOS1 0.038 0.013 -10000 0 0 56 56
Bam32/HPK1 -0.051 0.25 -10000 0 -0.68 63 63
DAPP1 -0.075 0.27 -10000 0 -0.76 63 63
cytokine secretion -0.027 0.1 0.2 3 -0.26 54 57
mol:DAG -0.008 0.12 0.21 5 -0.37 42 47
PLCG2 0.035 0.015 -10000 0 0 87 87
MAP2K1 -0.018 0.091 0.22 8 -0.27 38 46
B-cell antigen/BCR complex/FcgammaRIIB 0.037 0.071 -10000 0 -0.12 75 75
mol:PI-3-4-5-P3 0.011 0.094 0.22 39 -0.22 13 52
ETS1 -0.013 0.11 0.2 24 -0.32 40 64
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.069 0.083 -10000 0 -0.12 53 53
B-cell antigen/BCR complex/LYN -0.013 0.1 -10000 0 -0.28 44 44
MALT1 0.036 0.014 -10000 0 0 76 76
TRAF6 0.04 0.008 -10000 0 0 22 22
RAC1 -0.024 0.11 0.25 3 -0.3 53 56
B-cell antigen/BCR complex/LYN/SYK 0.054 0.11 0.33 15 -0.24 18 33
CARD11 -0.013 0.12 0.21 9 -0.36 41 50
FCGR2B 0.03 0.019 -10000 0 0 164 164
PPP3CA 0.037 0.013 -10000 0 0 61 61
BCL10 0.041 0.006 -10000 0 0 11 11
IKK complex 0.018 0.052 0.15 17 -0.11 14 31
PTPRC 0.025 0.021 -10000 0 0 228 228
PDPK1 0.015 0.083 0.19 51 -0.17 9 60
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 -0.075 72 74
Plasma membrane estrogen receptor 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
GNB1/GNG2 0.067 0.066 -10000 0 -0.11 55 55
ER alpha/Gai/GDP/Gbeta gamma -0.023 0.13 -10000 0 -0.3 78 78
AKT1 -0.09 0.27 -10000 0 -0.63 104 104
PIK3CA 0.03 0.019 -10000 0 0 155 155
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.089 0.28 -10000 0 -0.65 104 104
mol:Ca2+ -0.003 0.07 0.18 16 -0.28 21 37
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 0.086 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 0.23 1 -0.28 77 78
regulation of stress fiber formation 0.014 0.072 0.16 15 -0.16 41 56
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 0.16 41 -0.16 15 56
E2/ER alpha (dimer)/PELP1 0.036 0.047 -10000 0 -0.11 44 44
GRB2 0.041 0.007 -10000 0 0 17 17
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 83 83
E2/ER beta (dimer) 0.03 0.005 -10000 0 -10000 0 0
mol:GDP -0.005 0.079 0.14 3 -0.22 55 58
mol:NADP -0.038 0.16 -10000 0 -0.38 83 83
PIK3R1 0.034 0.017 -10000 0 0 108 108
mol:IP3 -0.001 0.067 0.18 10 -0.29 21 31
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 83 83
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 76 76
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 92 92
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 -0.006 0.14 0.24 2 -0.29 75 77
GNAZ 0.039 0.011 -10000 0 0 42 42
E2/ER alpha (dimer) 0.016 0.043 -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 36 36
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 18 -0.33 51 69
cAMP biosynthetic process 0.032 0.039 -10000 0 -0.092 41 41
SRC -0.022 0.13 0.22 21 -0.28 82 103
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 0.095 -10000 0 -0.19 61 61
SOS1 0.038 0.013 -10000 0 0 56 56
IGF-1R heterotetramer/IGF1 -0.038 0.1 -10000 0 -0.25 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 -0.36 83 83
mol:DAG -0.001 0.067 0.18 10 -0.29 21 31
Gs family/GDP/Gbeta gamma 0.003 0.081 -10000 0 -0.2 52 52
MSN -0.017 0.073 0.16 61 -0.17 17 78
Gq family/GTP 0.019 0.067 -10000 0 -0.28 22 22
mol:PI-3-4-5-P3 -0.085 0.27 -10000 0 -0.62 104 104
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 0.36 83 -10000 0 83
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 83 83
GNA11 0.037 0.013 -10000 0 0 61 61
MAPKKK cascade -0.028 0.19 -10000 0 -0.47 77 77
E2/ER alpha (dimer)/PELP1/Src -0.011 0.14 0.24 4 -0.29 80 84
ruffle organization -0.014 0.072 0.16 41 -0.16 15 56
ROCK2 -0.008 0.083 0.19 44 -0.17 8 52
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 -0.015 0.15 0.35 20 -0.3 67 87
MMP2 -0.019 0.13 0.24 5 -0.31 58 63
FAS signaling pathway (CD95)

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
SPTAN1 -0.025 0.06 0.18 4 -0.22 35 39
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 -0.57 20 20
FASLG/FAS/FADD/FAF1 0.022 0.082 0.15 103 -0.18 38 141
MAP2K4 0.002 0.12 0.32 4 -0.32 37 41
mol:ceramide 0.018 0.094 -10000 0 -0.29 23 23
GSN -0.023 0.061 0.2 4 -0.22 37 41
FASLG/FAS/FADD/FAF1/Caspase 8 0.027 0.091 0.2 19 -0.25 18 37
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 -0.38 27 34
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 23 -0.22 25 48
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 -0.05 0.24 -10000 0 -0.64 72 72
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 0.013 -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 -0.058 0.22 -10000 0 -0.61 71 71
FASLG 0.041 0.013 -10000 0 -0.012 29 29
FAS/FADD 0.036 0.062 -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 -0.019 0.06 0.14 2 -0.24 26 28
CASP10 0.037 0.017 -10000 0 -0.004 75 75
CASP3 -0.022 0.064 0.16 4 -0.24 41 45
PTPN13 0.021 0.021 -10000 0 0 276 276
CASP8 -0.031 0.02 0.26 2 -10000 0 2
IL6 -0.043 0.24 -10000 0 -0.73 37 37
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 -0.3 23 23
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
Syndecan-2-mediated signaling events

Figure S54.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S54.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -10000 0 -0.12 81 81
HRAS 0.04 0.01 -10000 0 0 31 31
Syndecan-2/CASK 0.001 0.028 -10000 0 -0.099 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 -0.098 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 0.057 -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 0.2 63 -10000 0 63
MAPK1 0.01 0.074 0.2 63 -10000 0 63
Syndecan-2/RACK1 0.041 0.048 -10000 0 -0.096 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 3 -0.11 51 54
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 0.051 -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 2 -0.099 53 55
alpha5/beta1 Integrin 0.046 0.045 -10000 0 -0.14 27 27
PRKCD 0.038 0.013 -10000 0 0 56 56
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 0.059 0.2 1 -0.17 1 2
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 0.057 -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 0.2 51 -0.18 1 52
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 0.038 -10000 0 -0.095 42 42
PRKACA 0 0.069 0.2 43 -0.18 3 46
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
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.012 0.17 -10000 0 -0.67 21 21
UGCG -0.008 0.15 -10000 0 -0.69 22 22
AKT1/mTOR/p70S6K/Hsp90/TERT -0.02 0.18 0.29 3 -0.37 79 82
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 -0.49 81 82
FRAP1 -0.056 0.26 0.4 1 -0.59 78 79
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 -0.077 82 91
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 52 52
CALM1 0.04 0.01 -10000 0 0 31 31
cell proliferation 0.003 0.18 0.26 11 -0.32 81 92
EIF3A 0 0 -10000 0 -10000 0 0
PI3K 0.021 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 0.031 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 84 84
MYC -0.035 0.35 0.41 13 -0.82 79 92
MYB -0.041 0.29 -10000 0 -1.1 39 39
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.028 0.17 0.25 3 -0.36 89 92
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 -0.35 89 93
Rac1/GDP 0.008 0.045 -10000 0 -0.11 47 47
T cell proliferation -0.029 0.16 0.25 5 -0.34 85 90
SHC1 0.037 0.016 -10000 0 -0.011 48 48
RAC1 0.039 0.01 -10000 0 0 34 34
positive regulation of cyclin-dependent protein kinase activity 0.002 0.02 0.032 47 -0.064 38 85
PRKCZ -0.031 0.17 0.25 5 -0.35 87 92
NF kappa B1 p50/RelA -0.03 0.24 0.4 1 -0.49 85 86
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.003 0.12 -10000 0 -0.34 41 41
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 -0.01 97 97
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 73 73
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 -0.018 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 85 90
GRB2 0.038 0.015 -10000 0 -0.017 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 -0.1 48 48
LCK 0.036 0.023 -10000 0 -0.04 36 36
BCL2 -0.032 0.2 0.4 1 -0.54 49 50
Class I PI3K signaling events

Figure S56.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S56.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.011 0.14 0.24 1 -0.34 51 52
mol:DAG 0.006 0.076 0.18 26 -0.17 29 55
HRAS 0.041 0.014 0.079 3 -0.005 36 39
RAP1A 0.041 0.012 0.069 4 -0.001 36 40
ARF5/GDP 0.017 0.096 -10000 0 -0.26 27 27
PLCG2 0.035 0.015 -10000 0 0 87 87
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 27 27
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 0 103 103
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 0.18 15 -0.11 7 22
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 0.21 14 -0.15 12 26
LYN 0.036 0.015 -10000 0 0 83 83
ARF1/GDP 0.018 0.096 -10000 0 -0.27 27 27
RhoA/GDP 0.036 0.083 0.19 47 -0.17 23 70
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 -0.27 18 35
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 34 34
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 25 25
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 7 9
SGK1 0.011 0.041 -10000 0 -0.16 8 8
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0 0.093 0.18 1 -0.27 30 31
SOS1 0.038 0.013 -10000 0 0 56 56
SYK 0.037 0.014 -10000 0 0 70 70
ARF6/GDP 0.002 0.079 0.17 57 -0.17 17 74
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 0.018 0.099 -10000 0 -0.26 30 30
LAT 0.041 0.006 -10000 0 0 13 13
Rac1/GTP -0.004 0.1 -10000 0 -0.27 47 47
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 0.2 20 -0.22 32 52
LCK 0.04 0.009 -10000 0 0 29 29
BTK -0.015 0.068 0.13 76 -0.2 9 85
Caspase cascade in apoptosis

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
TOP1 -0.013 0.14 0.25 5 -0.34 47 52
ACTA1 0.006 0.087 0.22 15 -0.25 16 31
NUMA1 -0.016 0.14 0.26 5 -0.32 53 58
SPTAN1 -0.001 0.087 0.22 14 -0.25 16 30
LIMK1 0.002 0.086 0.23 12 -0.25 14 26
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 -0.034 0.17 0.26 5 -0.39 69 74
DIABLO 0.037 0.013 -10000 0 0 63 63
apoptotic nuclear changes -0.002 0.086 0.22 14 -0.24 16 30
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.041 0.006 -10000 0 0 13 13
GSN -0.001 0.087 0.23 11 -0.27 14 25
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 0.11 0.24 43 -0.24 23 66
CASP9 0.04 0.009 -10000 0 0 26 26
DNA repair -0.013 0.081 0.26 26 -0.16 21 47
neuron apoptosis -0.037 0.2 -10000 0 -0.62 49 49
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.014 0.12 0.27 7 -0.32 32 39
APAF1 0.04 0.01 -10000 0 0 32 32
CASP6 -0.1 0.34 -10000 0 -0.85 91 91
TRAF2 0.04 0.009 -10000 0 0 29 29
ICAD/CAD 0 0.085 0.24 12 -0.25 11 23
CASP7 0.014 0.11 0.18 86 -0.27 25 111
KRT18 -0.016 0.15 -10000 0 -0.62 23 23
apoptosis -0.042 0.16 0.26 9 -0.37 79 88
DFFA 0.003 0.084 0.21 15 -0.25 13 28
DFFB 0.004 0.088 0.24 15 -0.26 12 27
PARP1 0.013 0.081 0.16 21 -0.26 26 47
actin filament polymerization 0.002 0.085 0.26 11 -0.24 13 24
TNF 0.04 0.009 -10000 0 0 26 26
CYCS 0.001 0.07 0.14 21 -0.21 36 57
SATB1 -0.11 0.32 -10000 0 -0.81 91 91
SLK -0.001 0.086 0.23 11 -0.25 16 27
p15 BID/BAX 0.032 0.05 0.16 3 -0.3 4 7
CASP2 0.005 0.089 0.24 20 -0.24 31 51
JNK cascade 0.026 0.14 0.37 68 -10000 0 68
CASP3 0.007 0.09 0.21 20 -0.25 16 36
LMNB2 -0.047 0.21 0.26 4 -0.46 84 88
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 0.23 11 -0.25 15 26
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 -0.4 87 94
APP -0.037 0.2 -10000 0 -0.63 49 49
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 -0.37 81 92
LMNA -0.017 0.15 0.26 5 -0.33 77 82
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.006 0.085 -10000 0 -0.24 36 36
LRDD 0.039 0.01 -10000 0 0 35 35
SREBF1 0.001 0.085 0.22 12 -0.26 13 25
APAF-1/Caspase 9 0.028 0.15 -10000 0 -0.64 20 20
nuclear fragmentation during apoptosis -0.016 0.13 0.26 5 -0.31 55 60
CFL2 -0.003 0.086 0.25 13 -0.26 12 25
GAS2 0.005 0.089 0.22 23 -0.25 15 38
positive regulation of apoptosis -0.041 0.18 0.25 7 -0.39 96 103
PRF1 0.037 0.013 -10000 0 0 61 61
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.015 0.16 -10000 0 -0.44 55 55
HDAC1 0.043 0.025 0.083 114 -0.003 61 175
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 0.083 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 45 45
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.071 0.22 -10000 0 -0.66 47 47
NICD/RBPSUH -0.013 0.15 -10000 0 -0.44 55 55
WIF1 0.04 0.01 -10000 0 0 31 31
NOTCH1 -0.004 0.15 -10000 0 -0.46 52 52
PSENEN 0.035 0.016 -10000 0 0 92 92
KREMEN2 0.04 0.009 -10000 0 0 27 27
DKK1 0.039 0.011 -10000 0 0 44 44
beta catenin/beta TrCP1 0.018 0.091 0.25 2 -0.34 12 14
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 0.013 0.099 0.19 79 -0.18 52 131
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 0.085 0.23 3 -0.34 12 15
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 56 75
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 0.013 0.16 -10000 0 -0.45 54 54
apoptosis -0.005 0.082 0.15 1 -0.17 91 92
Delta 1/NOTCHprecursor 0.01 0.16 -10000 0 -0.44 55 55
DLL1 0.038 0.012 -10000 0 0 52 52
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 -0.27 16 16
CSNK2A1 0.037 0.012 -10000 0 0 54 54
MAP3K7IP1 0.041 0.016 0.068 16 0 54 70
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 -0.36 17 18
DKK2 0.038 0.012 -10000 0 0 47 47
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 -0.45 54 54
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
HIF-2-alpha transcription factor network

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
MMP14 -0.054 0.3 -10000 0 -0.88 64 64
oxygen homeostasis 0.003 0.011 0.032 19 -0.025 3 22
TCEB2 0.04 0.008 -10000 0 0 23 23
TCEB1 0.038 0.012 -10000 0 0 50 50
VHL/Elongin B/Elongin C/HIF2A 0.04 0.13 0.28 10 -0.22 60 70
EPO 0.026 0.18 0.36 10 -0.37 31 41
FIH (dimer) 0.04 0.023 0.089 2 -0.035 34 36
APEX1 0.033 0.034 -10000 0 -0.039 40 40
SERPINE1 -0.008 0.16 0.36 9 -0.35 43 52
FLT1 -0.043 0.26 -10000 0 -0.7 70 70
ADORA2A 0.005 0.17 0.33 21 -0.34 39 60
germ cell development 0.008 0.18 0.35 20 -0.34 58 78
SLC11A2 0.011 0.19 0.34 17 -0.36 49 66
BHLHE40 0.012 0.18 0.33 21 -0.31 64 85
HIF1AN 0.04 0.023 0.089 2 -0.035 34 36
HIF2A/ARNT/SIRT1 0.04 0.16 0.31 12 -0.26 58 70
ETS1 0.043 0.025 0.12 1 -0.11 5 6
CITED2 0.014 0.15 -10000 0 -0.63 25 25
KDR -0.035 0.25 -10000 0 -0.71 63 63
PGK1 0.012 0.19 0.34 20 -0.37 51 71
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 -0.39 40 41
EPAS1 0.005 0.11 0.22 16 -0.22 69 85
SP1 0.034 0.05 -10000 0 -0.11 56 56
ABCG2 0.012 0.18 0.34 17 -0.35 44 61
EFNA1 0.001 0.19 0.34 14 -0.37 62 76
FXN 0.006 0.17 0.33 21 -0.34 41 62
POU5F1 0.006 0.18 0.34 19 -0.34 61 80
neuron apoptosis -0.061 0.22 0.38 40 -0.46 1 41
EP300 0.036 0.014 -10000 0 0 73 73
EGLN3 0.028 0.027 0.085 1 -0.035 22 23
EGLN2 0.04 0.023 0.091 2 -0.033 31 33
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 -0.04 34 34
SLC2A1 -0.012 0.18 0.35 10 -0.36 57 67
TWIST1 0.005 0.17 0.33 21 -0.32 50 71
ELK1 0.047 0.013 -10000 0 -0.088 3 3
HIF2A/ARNT/Cbp/p300 0.04 0.16 0.33 12 -0.27 50 62
VEGFA 0.012 0.18 0.33 21 -0.31 64 85
CREBBP 0.038 0.012 -10000 0 0 54 54
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.037 0.013 -10000 0 0 64 64
Caspase 8 (4 units) 0.036 0.094 -10000 0 -0.24 28 28
NEF 0.003 0.005 -10000 0 -0.1 1 1
NFKBIA 0.026 0.042 0.085 6 -0.068 78 84
BIRC3 -0.058 0.1 0.2 4 -0.28 89 93
CYCS -0.006 0.069 0.19 12 -0.25 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 0.23 6 -0.28 29 35
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 -0.18 119 119
TRADD 0.036 0.014 -10000 0 0 76 76
MAP3K5 0.037 0.014 -10000 0 0 69 69
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 -0.18 119 119
MAPK8 -0.01 0.16 -10000 0 -0.53 34 34
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 0.067 -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 -0.33 33 33
CHUK -0.002 0.1 0.23 7 -0.3 30 37
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.075 0.085 -10000 0 -0.13 58 58
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 0.085 6 -0.07 66 72
TNFR1A/BAG4/TNF-alpha 0.059 0.046 -10000 0 -0.12 15 15
CASP6 -0.045 0.23 -10000 0 -0.54 85 85
CASP7 -0.046 0.2 0.3 5 -0.4 111 116
RELA 0.027 0.044 0.081 6 -0.066 97 103
CASP2 0.038 0.012 -10000 0 0 51 51
CASP3 -0.056 0.2 0.29 6 -0.41 116 122
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 -0.32 29 35
APAF-1/Caspase 9 -0.028 0.11 0.18 2 -0.25 93 95
BCL2 -0.011 0.14 -10000 0 -0.48 33 33
Circadian rhythm pathway

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
chromatin modification -0.049 0.31 -10000 0 -1 49 49
CLOCK 0.032 0.032 -10000 0 -0.069 41 41
TIMELESS/CRY2 -0.051 0.31 -10000 0 -1 49 49
DEC1/BMAL1 0.044 0.047 -10000 0 -0.083 54 54
ATR 0.035 0.016 -10000 0 0 93 93
NR1D1 -0.016 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 42 42
BMAL/CLOCK/NPAS2 0.034 0.096 -10000 0 -0.14 112 112
BMAL1/CLOCK -0.04 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
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.003 0.07 -10000 0 -0.19 53 53
epithelial cell differentiation 0.056 0.069 -10000 0 -0.13 51 51
CYFIP2 0.038 0.012 -10000 0 0 47 47
ENAH -0.033 0.071 0.22 13 -0.22 4 17
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 0.059 -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 53 53
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 0.069 -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 -0.14 84 84
ARF6 0.041 0.008 -10000 0 0 19 19
Ephrin A1/EPHA2/NCK1/GIT1 0.06 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 -0.2 19 23
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 -0.56 74 74
Wnt receptor signaling pathway -0.056 0.069 0.13 51 -10000 0 51
RHOA 0.041 0.007 -10000 0 0 14 14
RhoA/GTP -0.049 0.045 -10000 0 -0.14 82 82
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 0.077 -10000 0 -0.13 74 74
SEC6/SEC8 -0.045 0.043 -10000 0 -0.14 70 70
MGAT3 -0.029 0.044 0.18 6 -0.2 12 18
HGF/MET 0.016 0.087 -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 0.097 0.26 26 -0.24 18 44
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 80 80
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 0.069 -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 51 59
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 0.085 0.26 12 -0.23 4 16
adherens junction assembly -0.05 0.13 -10000 0 -0.4 44 44
IGF-1R heterotetramer/IGF1 0.023 0.083 -10000 0 -0.13 94 94
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.051 -10000 0 -0.14 34 34
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
ErbB4 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
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 0 103 103
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 0.25 9 -0.57 35 44
PTPRZ1 0.039 0.01 -10000 0 0 36 36
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 0.11 4 -0.082 28 32
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 0.25 4 -0.56 40 44
ErbB4/ErbB2/betacellulin -0.028 0.18 -10000 0 -0.64 38 38
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 -0.82 39 39
NEDD4 0.038 0.039 0.11 7 -0.084 38 45
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 -0.023 0.16 0.27 7 -0.58 35 42
STAT1 (dimer) -0.034 0.21 -10000 0 -0.72 38 38
MAPK1 -0.024 0.16 0.27 7 -0.59 35 42
JAK2 0.035 0.016 -10000 0 0 92 92
ErbB4/ErbB2/neuregulin 1 beta -0.033 0.17 0.21 1 -0.64 37 38
NRG1 -0.008 0.032 0.045 21 -0.11 20 41
NRG3 0.035 0.016 -10000 0 0 92 92
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 -0.82 39 39
neural crest cell migration -0.032 0.17 0.21 1 -0.63 37 38
ERBB2 -0.008 0.033 0.049 25 -0.1 24 49
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 -0.037 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 -0.042 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 -10000 0 -0.8 38 38
ErbB4/EGFR/neuregulin 1 beta -0.027 0.18 -10000 0 -0.62 38 38
DLG4 0.039 0.01 -10000 0 0 34 34
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 0.038 0.013 -10000 0 0 59 59
STAT5B (dimer) -0.038 0.23 -10000 0 -0.81 38 38
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 -0.83 39 39
ERBB4 -0.048 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 17 17
ErbB4/ErbB2/neuregulin 4 -0.033 0.18 -10000 0 -0.64 38 38
glial cell differentiation 0.02 0.2 0.69 38 -10000 0 38
WWOX 0.037 0.014 -10000 0 0 71 71
cell proliferation -0.07 0.21 0.28 1 -0.61 58 59
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.029 0.14 0.36 1 -0.53 19 20
CRKL 0.025 0.085 0.18 114 -0.16 2 116
mol:DAG 0.044 0.073 0.22 4 -0.22 16 20
HRAS 0.018 0.097 0.25 40 -0.18 3 43
MAPK8 0.011 0.078 0.18 83 -0.13 5 88
RAP1A 0.024 0.085 0.18 114 -0.16 3 117
GAB1 0.023 0.083 0.18 107 -0.16 2 109
MAPK14 0.012 0.081 0.18 87 -0.13 5 92
EPO 0.045 0.015 0.083 5 -0.038 7 12
PLCG1 0.045 0.074 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 0.069 0.081 0.27 14 -0.16 6 20
EPO/EPOR (dimer) 0.057 0.033 -10000 0 -0.12 3 3
IRS2 0.024 0.084 0.18 111 -0.16 2 113
STAT1 0.036 0.096 0.24 4 -0.22 45 49
STAT5B 0.046 0.077 0.22 6 -0.21 22 28
cell proliferation 0.005 0.078 0.17 87 -0.14 6 93
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 -0.21 45 50
JAK2 0.039 0.02 0.082 7 -0.037 4 11
PIK3R1 0.034 0.017 -10000 0 0 108 108
EPO/EPOR (dimer)/JAK2 0.07 0.07 0.24 34 -0.1 26 60
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 0.073 0.22 4 -0.22 16 20
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.045 0.072 0.18 77 -0.14 4 81
SH2B3 0 0.008 0.032 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 67 -0.11 23 90
TEC/VAV2/GRB2 0.051 0.086 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 0.27 13 -0.16 6 19
SOS1 0.038 0.013 -10000 0 0 56 56
PLCG2 0.035 0.015 -10000 0 0 87 87
CRKL/CBL/C3G 0.072 0.077 0.23 44 -0.13 9 53
VAV2 0.022 0.083 0.18 105 -0.16 3 108
CBL 0.026 0.087 0.18 120 -0.19 2 122
SHC/Grb2/SOS1 0.038 0.057 0.17 2 -0.13 13 15
STAT5A 0.046 0.08 0.22 6 -0.22 22 28
GRB2 0.041 0.007 -10000 0 0 17 17
STAT5 (dimer) 0.063 0.092 0.28 4 -0.28 13 17
LYN/PLCgamma2 0.038 0.051 -10000 0 -0.13 36 36
PTPN11 0.04 0.009 -10000 0 0 27 27
BTK 0.024 0.085 0.18 113 -0.17 6 119
BCL2 0.028 0.12 0.33 2 -0.44 13 15
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.008 0.039 -10000 0 -0.11 62 62
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 49 49
BIRC5 0.037 0.014 -10000 0 -0.002 63 63
DES -0.047 0.28 -10000 0 -0.8 63 63
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 0.015 75 -10000 0 75
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 -0.48 81 81
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 -0.041 0.2 -10000 0 -0.56 62 62
PSMA3 0.037 0.013 -10000 0 0 60 60
G2/M transition of mitotic cell cycle -0.001 0.003 0.009 35 -0.008 19 54
H3F3B 0.002 0.057 -10000 0 -0.2 40 40
AURKB 0.038 0.016 -10000 0 0 81 81
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 -0.007 0.19 -10000 0 -0.4 76 76
AURKA -0.001 0.003 0.009 35 -0.008 19 54
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 63 63
EVI5 0.039 0.01 -10000 0 0 35 35
RhoA/GTP 0.002 0.17 -10000 0 -0.36 71 71
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 0.063 -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 -0.36 64 64
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 75 75
RhoA/GDP 0.03 0.012 -10000 0 -0.13 3 3
NSUN2 -0.012 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 0.034 12 -10000 0 12
RACGAP1 0.037 0.014 -10000 0 -0.004 54 54
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.028 0.12 -10000 0 -0.32 86 86
Chromosomal passenger complex -0.035 0.15 -10000 0 -0.35 68 68
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
Arf6 signaling events

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
CENTA1/KIF3B 0.022 0.012 -10000 0 -0.1 1 1
ARNO/beta Arrestin1-2 0.043 0.032 -10000 0 -0.089 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 36 36
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 68 68
TSHR 0.038 0.013 -10000 0 0 60 60
EGF 0.038 0.012 -10000 0 0 53 53
somatostatin receptor activity 0 0 0 6 -0.001 40 46
ARAP2 0 0 0 13 0 35 48
mol:GDP 0.013 0.071 0.15 2 -0.19 33 35
mol:PI-3-4-5-P3 0 0 0 7 0 36 43
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 0.06 0.077 -10000 0 -0.12 62 62
ADAP1 0 0 0 8 0 27 35
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 0.082 0.18 7 -0.21 39 46
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 35 44
actin filament binding 0 0 0 4 0 41 45
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 32 46
ARF6/GDP 0.01 0.077 0.2 7 -0.24 24 31
ARF6/GDP/GULP/ACAP1 0.029 0.084 -10000 0 -0.21 27 27
alphaIIb/beta3 Integrin/paxillin/GIT1 0.082 0.058 -10000 0 -0.11 34 34
ACAP1 0 0 0 4 0 1 5
ACAP2 0 0 0 8 0 35 43
LHCGR/beta Arrestin2 0.031 0.026 -10000 0 -0.063 32 32
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 11 -0.001 34 45
CYTH2 0 0.001 0.003 4 -0.004 38 42
NCK1 0.036 0.015 -10000 0 0 80 80
fibronectin binding 0 0 0 8 0 36 44
endosomal lumen acidification 0 0 0 10 0 20 30
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 8 0 35 43
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 37 50
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 0.031 0.026 -10000 0 -0.063 32 32
IPCEF1/ARNO 0.054 0.044 -10000 0 -0.086 36 36
alphaIIb/beta3 Integrin 0.04 0.05 -10000 0 -0.14 34 34
Regulation of Androgen receptor activity

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
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 0.093 0.18 14 -0.22 74 88
JUN 0.036 0.015 -10000 0 0 80 80
EP300 0.037 0.014 -10000 0 0 73 73
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 87 93
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 0 135 135
PDE9A -0.081 0.32 -10000 0 -0.83 82 82
NCOA2 0.037 0.014 -10000 0 0 71 71
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 0.28 15 -0.3 34 49
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 20 53
AR/GR -0.012 0.093 0.2 2 -0.19 78 80
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 -0.054 2 9
T-DHT/AR/TIF2/CARM1 0.004 0.088 0.25 5 -0.21 26 31
SRC -0.015 0.068 0.17 45 -0.16 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 0.084 5 -0.16 63 68
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 0.077 0.23 5 -0.26 9 14
AR -0.019 0.079 0.15 11 -0.19 71 82
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 -0.23 22 55
positive regulation of transcription 0.039 0.01 -10000 0 0 35 35
DNAJA1 0.031 0.026 -10000 0 -0.02 109 109
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.089 0.17 21 -0.26 49 70
NCOA1 0.041 0.035 0.12 1 -0.18 12 13
SPDEF 0.038 0.015 -10000 0 0 72 72
T-DHT/AR/TIF2 -0.012 0.095 0.2 11 -0.24 49 60
T-DHT/AR/Hsp90 -0.035 0.059 0.084 5 -0.16 63 68
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 -0.02 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 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
regulation of centriole-centriole cohesion 0.008 0.054 0.17 51 -0.097 2 53
BUB1B -0.024 0.082 0.12 1 -0.2 77 78
PLK1 -0.001 0.037 0.076 5 -0.097 44 49
PLK1S1 -0.001 0.021 0.048 5 -0.054 41 46
KIF2A -0.001 0.033 0.067 5 -0.088 44 49
regulation of mitotic centrosome separation -0.001 0.037 0.076 5 -0.098 43 48
GOLGA2 0.04 0.009 -10000 0 0 26 26
Hec1/SPC24 -0.01 0.025 -10000 0 -0.072 58 58
WEE1 -0.012 0.088 -10000 0 -0.33 28 28
cytokinesis -0.038 0.13 0.14 4 -0.29 97 101
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 0.073 1 -0.16 107 108
CENPE -0.007 0.035 0.21 1 -0.13 20 21
RhoA/GTP 0.03 0.012 -10000 0 -0.13 3 3
positive regulation of microtubule depolymerization -0.001 0.033 0.067 5 -0.087 44 49
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 -0.24 90 90
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 0.048 5 -0.054 41 46
G2 phase of mitotic cell cycle -0.001 0.003 0.012 16 -10000 0 16
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 -0.098 43 48
ODF2 0.04 0.009 -10000 0 0 27 27
BUB1 -0.046 0.25 -10000 0 -0.72 65 65
TPT1 -0.002 0.051 -10000 0 -0.19 33 33
CDC25C -0.007 0.089 -10000 0 -0.33 37 37
CDC25B 0.024 0.03 -10000 0 -0.03 106 106
SGOL1 -0.008 0.054 0.097 2 -0.17 51 53
RHOA 0.041 0.007 -10000 0 0 14 14
CCNB1/CDK1 0.004 0.13 -10000 0 -0.21 119 119
CDC14B -0.01 0.005 0.011 30 -10000 0 30
CDC20 0.034 0.016 -10000 0 0 104 104
PLK1/PBIP1 -0.003 0.032 -10000 0 -0.1 34 34
mitosis -0.001 0.003 0.014 10 -0.011 7 17
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 -0.2 115 115
NLP/gamma Tubulin -0.001 0.032 0.066 3 -0.086 48 51
microtubule cytoskeleton organization -0.002 0.051 -10000 0 -0.19 33 33
G2/M transition DNA damage checkpoint 0 0.003 0.012 10 -10000 0 10
PPP1R12A 0.04 0.01 -10000 0 0 31 31
interphase 0 0.003 0.012 10 -10000 0 10
PLK1/PRC1-2 0.014 0.083 -10000 0 -0.15 94 94
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 0.062 10 -0.067 40 50
mitotic prometaphase -0.001 0.004 0.019 19 -0.01 8 27
proteasomal ubiquitin-dependent protein catabolic process -0.002 0.066 -10000 0 -0.22 26 26
microtubule-based process 0.014 0.052 -10000 0 -0.14 38 38
Golgi organization -0.001 0.037 0.076 5 -0.098 43 48
Cohesin/SA2 0.014 0.047 0.11 1 -0.098 59 60
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 40 41
PPP2R1A 0.039 0.011 -10000 0 0 42 42
chromosome segregation -0.003 0.032 -10000 0 -0.1 34 34
PRC1 0.036 0.015 -10000 0 0 82 82
ECT2 0.037 0.12 0.21 140 -0.15 53 193
C13orf34 0 0.029 0.067 7 -0.075 42 49
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 77 78
spindle assembly -0.001 0.034 0.072 10 -0.09 41 51
spindle stabilization -0.001 0.021 0.048 5 -0.054 41 46
APC/C/HCDH1 0.032 0.012 -10000 0 -10000 0 0
MKLP2/PLK1 0.014 0.052 -10000 0 -0.14 38 38
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 -0.2 33 33
G2/M transition of mitotic cell cycle -0.035 0.1 0.13 16 -0.21 114 130
MLF1IP -0.008 0.007 0.014 8 -10000 0 8
INCENP 0.041 0.005 -10000 0 0 5 5
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 -0.48 34 34
RAD9A 0.042 0.004 -10000 0 0 6 6
AP1 0.002 0.084 -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 -0.26 32 37
EGF 0.038 0.013 -10000 0 0 53 53
SMG5 0 0 -10000 0 -10000 0 0
SMG6 0 0 -10000 0 -10000 0 0
SP3/HDAC2 0.045 0.043 -10000 0 -0.078 18 18
TERT/c-Abl -0.019 0.18 -10000 0 -0.46 34 34
SAP18 0.039 0.01 -10000 0 0 34 34
MRN complex 0.048 0.071 -10000 0 -0.15 50 50
WT1 0.029 0.027 -10000 0 -0.033 68 68
WRN 0.033 0.017 -10000 0 0 124 124
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 75 75
Telomerase/Nucleolin -0.018 0.18 -10000 0 -0.43 41 41
Mad/Max 0.055 0.024 -10000 0 -10000 0 0
TERT -0.032 0.18 -10000 0 -0.5 31 31
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 0.095 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 -0.29 21 21
CDKN1B -0.002 0.083 0.2 4 -0.19 65 69
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 70 70
SAP30 0.038 0.013 -10000 0 0 55 55
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 0.082 -10000 0 -0.16 82 82
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 -0.26 18 18
IRF1 0.029 0.041 0.11 1 -0.14 21 22
ESR1 0.035 0.016 -10000 0 0 92 92
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 0.004 0.084 0.18 6 -0.27 26 32
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.004 0.085 0.18 6 -0.28 25 31
HDAC1 0.038 0.013 -10000 0 0 56 56
HDAC2 0.03 0.03 -10000 0 -0.04 74 74
ATM 0.009 0.066 -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 41 41
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 -0.49 28 28
NR2F2 0.04 0.013 -10000 0 0 38 38
MAPK3 -0.016 0.015 0.022 51 -0.04 7 58
MAPK1 -0.015 0.015 0.022 47 -0.04 7 54
TGFB1/TGF beta receptor Type II 0.037 0.013 -10000 0 0 62 62
NFKB1 0.036 0.015 -10000 0 0 84 84
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 0 268 268
IL2 0.03 0.031 -10000 0 -0.042 74 74
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 -0.46 37 37
SP1/HDAC2 0.043 0.05 -10000 0 -0.1 20 20
PINX1 0.033 0.017 -10000 0 0 123 123
Telomerase/EST1A -0.025 0.17 -10000 0 -0.43 36 36
Smad3/Myc 0.015 0.038 -10000 0 -0.15 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 -0.43 36 36
Telomerase/AKT1/mTOR/p70S6K -0.001 0.1 -10000 0 -0.32 29 29
SIN3B 0.037 0.013 -10000 0 0 65 65
YWHAE 0.038 0.013 -10000 0 0 58 58
Telomerase/EST1B -0.025 0.17 -10000 0 -0.43 36 36
response to DNA damage stimulus 0.001 0.035 0.063 3 -0.11 49 52
MRN complex/TRF2/Rap1 0.065 0.081 -10000 0 -0.13 47 47
TRF2/WRN 0.038 0.041 -10000 0 -0.11 21 21
Telomerase/hnRNP C1/C2 -0.025 0.17 -10000 0 -0.43 36 36
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
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HIF3A 0.038 0.012 -10000 0 0 54 54
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.04 0.008 -10000 0 0 23 23
TCEB1 0.038 0.012 -10000 0 0 50 50
HIF1A/p53 0 0.086 0.22 1 -0.27 34 35
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 29 29
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 23 24
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 -0.29 21 24
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 24 25
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 0 213 213
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.024 0.12 -10000 0 -0.54 23 23
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 71 71
HIF1A/p19ARF 0.004 0.085 -10000 0 -0.29 29 29
Reelin signaling 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
CDK5R1/CDK5 0.046 0.041 -10000 0 -0.14 20 20
VLDLR 0.032 0.018 -10000 0 0 129 129
CRKL 0.039 0.011 -10000 0 0 38 38
LRPAP1 0.036 0.015 -10000 0 0 78 78
FYN 0.034 0.016 -10000 0 0 103 103
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 0.039 -10000 0 -0.11 5 5
LRPAP1/LRP8 0.041 0.053 -10000 0 -0.14 36 36
RELN/LRP8/DAB1/Fyn 0.066 0.056 -10000 0 -0.1 31 31
DAB1/alpha3/beta1 Integrin 0.029 0.082 -10000 0 -0.18 10 10
long-term memory 0.073 0.071 0.22 7 -0.11 28 35
DAB1/LIS1 0.058 0.082 -10000 0 -0.18 2 2
DAB1/CRLK/C3G 0.046 0.073 -10000 0 -0.18 2 2
PIK3CA 0.03 0.019 -10000 0 0 155 155
DAB1/NCK2 0.064 0.083 -10000 0 -0.12 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 0 111 111
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 0 108 108
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 -0.11 37 37
ITGB1 0.039 0.011 -10000 0 0 38 38
MAP1B 0 0.066 0.22 25 -0.2 5 30
RELN/LRP8 0.049 0.055 -10000 0 -0.12 28 28
GRIN2B/RELN/LRP8/DAB1/Fyn 0.077 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 -0.002 0.097 0.3 27 -10000 0 27
PAFAH1B1 0.038 0.012 -10000 0 0 49 49
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 -0.22 9 10
neuron adhesion -0.011 0.1 0.28 33 -0.25 1 34
LRP8 0.039 0.011 -10000 0 0 39 39
GSK3B -0.005 0.076 0.18 8 -0.16 61 69
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 -0.16 64 64
CDK5 0.036 0.015 -10000 0 0 83 83
MAPT -0.009 0.034 0.68 1 -10000 0 1
neuron migration 0.004 0.099 0.29 22 -0.24 14 36
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.022 0.057 0.17 1 -0.21 8 9
RELN/VLDLR 0.053 0.073 -10000 0 -0.11 57 57
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.038 0.19 0.33 7 -0.98 21 28
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 -0.046 51 52
RARs/THRs/DNA/Src-1 -0.004 0.095 -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 12 12
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 45 46
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 0.15 2 -0.14 8 10
RXRG 0.032 0.031 0.1 1 -0.055 44 45
RXR alpha/CCPG 0.026 0.022 -10000 0 -0.039 42 42
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 0.027 1 -0.041 59 60
cholesterol transport 0.016 0.13 -10000 0 -0.34 55 55
PPARA 0.034 0.016 -10000 0 0 104 104
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.036 0.015 -10000 0 0 80 80
RXRs/NUR77/BCL2 0.021 0.047 -10000 0 -0.14 24 24
SREBF1 0.007 0.12 -10000 0 -0.38 32 32
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 0.07 0.092 -10000 0 -0.12 82 82
RXRs/FXR 0.088 0.068 0.3 1 -0.11 30 31
BCL2 0.036 0.014 -10000 0 0 76 76
Canonical NF-kappaB pathway

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
FBXW11 0.036 0.028 0.091 2 -0.07 31 33
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.009 0.13 0.24 4 -0.27 65 69
ERC1 0 0 -10000 0 -10000 0 0
RIP2/NOD2 0.015 0.041 -10000 0 -0.13 41 41
NFKBIA -0.036 0.067 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 44 44
RIPK2 0.033 0.017 -10000 0 0 125 125
IKBKG -0.005 0.11 -10000 0 -0.3 50 50
IKK complex/A20 0.033 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 0.003 0.13 -10000 0 -0.35 39 39
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 -0.31 38 38
BCL10/MALT1/TRAF6 0.065 0.047 -10000 0 -0.12 21 21
NOD2 0 0 -10000 0 -10000 0 0
NFKB1 0.032 0.028 0.084 1 -0.072 26 27
RELA 0.036 0.028 0.097 1 -0.069 34 35
MALT1 0.036 0.014 -10000 0 0 76 76
cIAP1/UbcH5C 0.04 0.053 -10000 0 -0.14 38 38
ATM 0.036 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 48 48
TNF 0.04 0.009 -10000 0 0 26 26
NF kappa B1 p50/RelA 0.057 0.082 -10000 0 -0.15 62 62
BCL10 0.041 0.006 -10000 0 0 11 11
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 0.091 2 -0.07 31 33
TNFRSF1A 0.036 0.015 -10000 0 0 84 84
IKK complex 0.019 0.13 -10000 0 -0.33 38 38
CYLD 0.038 0.012 -10000 0 0 51 51
IKK complex/PKC alpha 0.023 0.13 -10000 0 -0.32 39 39
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 44 44
AKT1 0.016 0.09 0.19 101 -0.18 6 107
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 46 47
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 0.087 -10000 0 -0.12 66 66
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.055 0.058 -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 -0.11 23 23
PSENEN 0.035 0.016 -10000 0 0 92 92
mol:ceramide -0.021 0.028 0.19 3 -10000 0 3
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.011 0.091 -10000 0 -0.33 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 0.075 -10000 0 -0.1 173 173
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.064 0.037 -10000 0 -0.11 8 8
PIK3R1 0.034 0.017 -10000 0 0 108 108
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 -0.11 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 0.22 7 -0.19 19 26
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 0.064 0.24 7 -0.22 14 21
MAPK9 -0.02 0.061 0.22 7 -0.2 16 23
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 0.076 -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 48 48
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 0.23 6 -0.21 27 33
RIPK2 0.033 0.017 -10000 0 0 125 125
NGFR 0.04 0.009 -10000 0 0 28 28
CYCS -0.026 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 0.23 6 -0.21 27 33
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 58 58
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 34 34
PRKCZ 0.042 0 -10000 0 -10000 0 0
PLG 0.038 0.012 -10000 0 0 49 49
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 0.013 0.045 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 -0.22 32 36
E2F1 0.038 0.012 -10000 0 0 49 49
CASP9 0.04 0.009 -10000 0 0 26 26
IKK complex 0.046 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 -0.2 51 51
Regulation of p38-alpha and p38-beta

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
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 0 103 103
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 0.19 2 -0.26 54 56
PRKG1 0.04 0.009 -10000 0 0 29 29
DUSP8 0.04 0.009 -10000 0 0 28 28
PGK/cGMP/p38 alpha -0.003 0.11 0.18 1 -0.26 55 56
apoptosis 0.001 0.11 0.18 2 -0.25 54 56
RAL/GTP 0.046 0.037 -10000 0 -0.12 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 34 34
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 64 66
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 -0.099 7 7
MAP3K7IP1 0.038 0.012 -10000 0 0 54 54
MAPK14 -0.011 0.12 0.19 3 -0.27 59 62
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 0.24 2 -0.33 52 54
p38alpha-beta/MKP5 -0.018 0.14 0.24 2 -0.33 56 58
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 62 63
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
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0.04 0.009 -10000 0 0 25 25
MKNK1 0.04 0.009 -10000 0 0 25 25
mol:PIP3 -0.013 0.038 0.2 1 -0.18 11 12
FRAP1 0.028 0.1 -10000 0 -0.43 22 22
AKT1 0.018 0.081 0.17 100 -0.17 10 110
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 -0.16 11 39
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.006 0.052 -10000 0 -0.18 32 32
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 0.16 1 -0.21 29 30
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0 0 -10000 0 -10000 0 0
RPS6KB1 0.029 0.11 0.24 19 -0.31 28 47
MAP3K5 -0.009 0.066 0.2 5 -0.22 46 51
PIK3R1 0.034 0.017 -10000 0 0 108 108
apoptosis -0.009 0.066 0.2 5 -0.22 46 51
mol:LY294002 0 0 0.001 3 -0.001 6 9
EIF4B 0.024 0.1 0.25 17 -0.29 28 45
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.037 0.098 0.22 18 -0.25 32 50
eIF4E/eIF4G1/eIF4A1 0.012 0.062 -10000 0 -0.27 20 20
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.028 0.053 -10000 0 -0.17 13 13
mTOR/RHEB/GTP/Raptor/GBL 0.028 0.075 0.2 20 -0.18 25 45
FKBP1A 0.039 0.012 -10000 0 0 50 50
RHEB/GTP 0.052 0.084 0.22 18 -0.16 13 31
mol:Amino Acids 0 0 0.001 3 -0.001 6 9
FKBP12/Rapamycin 0.028 0.013 -10000 0 -0.13 2 2
PDPK1 0.006 0.075 0.16 91 -0.17 11 102
EIF4E 0.039 0.011 -10000 0 0 43 43
ASK1/PP5C 0.013 0.2 -10000 0 -0.56 52 52
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.001 0.12 -10000 0 -0.46 20 20
TSC1/TSC2 0.057 0.095 0.25 28 -0.18 10 38
tumor necrosis factor receptor activity 0 0 0.001 6 -0.001 3 9
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 0.03 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 64 64
EIF4A1 0.039 0.011 -10000 0 0 39 39
mol:Rapamycin 0 0.001 0.003 108 -0.002 4 112
EEF2 -0.014 0.032 0.19 11 -10000 0 11
eIF4E/4E-BP1 -0.032 0.29 -10000 0 -0.98 46 46
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 0.059 -10000 0 -0.099 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 86 86
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.038 0.012 -10000 0 0 53 53
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 0.061 -10000 0 -0.11 49 49
SHC1 0.04 0.01 -10000 0 0 31 31
HRAS/GDP 0.069 0.073 -10000 0 -0.12 44 44
FRAP1 -0.016 0.073 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 17 17
ETA receptor/Endothelin-1 0.037 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 4 -0.28 36 40
CaM/Ca2+ 0.028 0.016 -10000 0 -0.13 5 5
AKT1 0.039 0.01 -10000 0 0 37 37
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 0.013 0.12 0.22 8 -0.3 36 44
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 0.037 0.013 -10000 0 0 60 60
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 0.21 1 -0.25 23 24
VAMP2 0.037 0.014 -10000 0 0 67 67
SLC2A4 0.011 0.13 0.24 5 -0.33 36 41
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 58 58
Arf6 downstream pathway

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
PLAUR -0.028 0.2 -10000 0 -0.81 35 35
regulation of axonogenesis -0.002 0.051 0.22 21 -10000 0 21
myoblast fusion -0.011 0.1 0.35 38 -10000 0 38
mol:GTP 0.017 0.067 -10000 0 -0.2 46 46
regulation of calcium-dependent cell-cell adhesion -0.034 0.089 0.2 43 -10000 0 43
ARF1/GTP 0.038 0.06 -10000 0 -0.16 42 42
mol:GM1 0.003 0.047 -10000 0 -0.15 46 46
mol:Choline 0.001 0.04 0.093 1 -0.16 28 29
lamellipodium assembly -0.013 0.12 -10000 0 -0.4 46 46
MAPK3 0.01 0.085 -10000 0 -0.28 41 41
ARF6/GTP/NME1/Tiam1 0.035 0.09 -10000 0 -0.2 43 43
ARF1 0.038 0.012 -10000 0 0 50 50
ARF6/GDP 0.011 0.1 -10000 0 -0.35 38 38
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 -0.046 29 29
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.012 0.079 -10000 0 -0.28 35 35
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 -0.012 121 121
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 46 46
cortical actin cytoskeleton organization -0.013 0.12 -10000 0 -0.41 46 46
RAC1 0.039 0.01 -10000 0 0 34 34
liver development 0.017 0.067 -10000 0 -0.2 46 46
ARF6/GTP 0.017 0.067 -10000 0 -0.2 46 46
RhoA/GTP 0.041 0.063 -10000 0 -0.16 46 46
mol:GDP -0.004 0.098 -10000 0 -0.35 39 39
ARF6/GTP/RAB11FIP3/RAB11A 0.061 0.067 -10000 0 -0.14 48 48
RHOA 0.041 0.007 -10000 0 0 14 14
PLD1 0.008 0.049 -10000 0 -0.18 31 31
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 -0.22 21 21
regulation of epithelial cell migration 0.017 0.067 -10000 0 -0.2 46 46
PLD2 0.015 0.049 -10000 0 -0.15 40 40
PIP5K1A 0.002 0.052 -10000 0 -0.22 21 21
mol:Phosphatidic acid 0.001 0.04 0.093 1 -0.16 28 29
Rac1/GTP -0.014 0.12 -10000 0 -0.41 46 46
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.018 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 0.044 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 0.15 17 -0.19 16 33
MAPK13 -0.017 0.008 0 98 -10000 0 98
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.003 0.05 -10000 0 -0.2 32 32
Neurotrophic factor-mediated Trk receptor signaling

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
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 -0.28 21 21
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 81 81
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 -0.088 1 1
neuron apoptosis -0.03 0.1 0.26 29 -0.22 4 33
SHC 2-3/Grb2 0.031 0.11 0.24 3 -0.28 29 32
SHC1 0.04 0.01 -10000 0 0 31 31
SHC2 0.007 0.12 0.21 3 -0.37 41 44
SHC3 0.025 0.088 0.22 2 -0.38 17 19
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 0.23 23 -0.19 24 47
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 -0.13 26 26
GRB2 0.041 0.007 -10000 0 0 17 17
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 0.035 0.015 -10000 0 0 87 87
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 52 52
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.028 0.062 0.2 4 -0.18 8 12
mol:GDP 0.043 0.11 0.27 25 -0.27 25 50
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.022 0.03 -10000 0 -0.13 19 19
RIT1/GDP 0.043 0.084 0.23 17 -0.19 25 42
TIAM1 0.037 0.014 -10000 0 0 72 72
PIK3R1 0.034 0.017 -10000 0 0 108 108
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 -0.14 16 16
FRS2 family/SHP2 0.067 0.051 -10000 0 -0.12 29 29
SHC/GRB2/SOS1/GAB1 0.078 0.062 -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 28 45
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 0.005 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 0.069 0.053 0.21 1 -0.11 9 10
ABL1 0.039 0.011 -10000 0 0 41 41
SH2B family/GRB2/SOS1 0.047 0.047 -10000 0 -0.14 28 28
Rap1/GTP 0.007 0.11 -10000 0 -0.27 50 50
STAT3 0.004 0.11 -10000 0 -0.27 75 75
axon guidance 0.047 0.041 -10000 0 -0.11 9 9
MAPK3 -0.008 0.047 0.19 28 -10000 0 28
MAPK1 -0.007 0.046 0.19 27 -10000 0 27
CDC42/GDP 0.049 0.087 0.23 26 -0.19 23 49
NTF3 0.031 0.018 -10000 0 0 147 147
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.048 0.022 -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 52 52
GAB1 0.038 0.012 -10000 0 0 52 52
RASGRF1 0.01 0.053 0.15 10 -0.17 10 20
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 0.3 3 -0.35 26 29
Rac1/GDP 0.048 0.087 0.23 26 -0.19 22 48
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 -0.011 0.072 0.19 48 -0.19 3 51
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 0.076 -10000 0 -0.13 43 43
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 34 34
PRKCZ 0.042 0 -10000 0 -10000 0 0
MAPKKK cascade 0.026 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 79 79
RAS family/GDP -0.009 0.038 -10000 0 -0.13 28 28
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
PDGFR-beta 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
S1P1/Sphingosine-1-phosphate 0.061 0.1 0.29 21 -0.31 9 30
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 0.024 0.11 0.25 47 -0.18 1 48
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.045 0.094 0.27 20 -0.33 10 30
PIK3CA 0.03 0.019 -10000 0 0 155 155
FGR 0.023 0.092 0.27 8 -0.39 13 21
mol:Ca2+ 0.027 0.087 0.25 18 -0.36 10 28
MYC 0.004 0.28 0.35 18 -0.66 75 93
SHC1 0.04 0.01 -10000 0 0 31 31
HRAS/GDP 0.038 0.059 0.19 43 -0.11 17 60
LRP1/PDGFRB/PDGFB 0.055 0.057 -10000 0 -0.12 36 36
GRB10 0.04 0.008 -10000 0 0 23 23
PTPN11 0.04 0.009 -10000 0 0 27 27
GO:0007205 0.026 0.088 0.25 17 -0.37 10 27
PTEN 0.039 0.011 -10000 0 0 38 38
GRB2 0.041 0.007 -10000 0 0 17 17
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 0.01 0.096 0.23 45 -0.2 6 51
GAB1 0.023 0.1 0.28 9 -0.29 16 25
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.025 0.11 0.28 21 -0.28 15 36
PDGFB-D/PDGFRB 0.057 0.052 -10000 0 -0.13 5 5
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 31 46
positive regulation of MAPKKK cascade 0.047 0.043 -10000 0 -0.14 22 22
PIK3R1 0.034 0.017 -10000 0 0 108 108
mol:IP3 0.027 0.088 0.25 17 -0.37 10 27
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 0.26 7 -0.36 96 103
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 76 76
VAV2 0.01 0.13 0.28 13 -0.32 42 55
CBL 0.04 0.008 -10000 0 0 23 23
PDGFB-D/PDGFRB/DEP1 0.047 0.04 -10000 0 -0.14 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 0.27 7 -0.46 13 20
ABL1 0.019 0.091 0.24 19 -0.24 17 36
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 0.32 29 -0.59 75 104
SLA 0.027 0.02 -10000 0 0 206 206
actin cytoskeleton reorganization 0.01 0.095 0.22 70 -0.18 1 71
SRC 0.026 0.058 0.32 3 -10000 0 3
PI3K -0.027 0.036 -10000 0 -0.12 25 25
PDGFB-D/PDGFRB/GRB7/SHC 0.063 0.042 -10000 0 -0.12 8 8
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.046 0.096 0.27 20 -0.34 10 30
LYN 0.001 0.12 0.3 4 -0.43 32 36
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 18 18
SPHK1 0.042 0.009 -10000 0 0 20 20
EDG1 0.042 0.007 -10000 0 0 12 12
mol:DAG 0.027 0.088 0.25 17 -0.37 10 27
PLCG1 0.027 0.09 0.25 17 -0.38 10 27
NHERF/PDGFRB 0.061 0.047 -10000 0 -0.12 17 17
YES1 0.003 0.12 0.26 5 -0.42 33 38
cell migration 0.059 0.047 -10000 0 -0.12 17 17
SHC/Grb2/SOS1 0.083 0.073 -10000 0 -0.13 17 17
SLC9A3R2 0.038 0.012 -10000 0 0 53 53
SLC9A3R1 0.038 0.012 -10000 0 0 49 49
NHERF1-2/PDGFRB/PTEN 0.079 0.057 -10000 0 -0.12 25 25
FYN -0.014 0.14 0.26 5 -0.38 57 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 57 57
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 0.18 61 -0.18 4 65
RASA1 0.003 0.064 0.19 45 -0.16 2 47
NCK1 0.036 0.015 -10000 0 0 80 80
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 0.02 0.09 0.24 19 -0.24 17 36
STAT1-3-5/STAT1-3-5 0.05 0.08 -10000 0 -0.16 15 15
Bovine Papilomavirus E5/PDGFRB 0.026 0.019 -10000 0 -0.13 3 3
PTPRJ 0.039 0.01 -10000 0 0 35 35
ErbB2/ErbB3 signaling events

Figure S83.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S83.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.013 0.01 0.02 19 -10000 0 19
RAS family/GTP 0.017 0.1 0.26 2 -0.22 29 31
NFATC4 -0.017 0.082 0.26 19 -0.18 4 23
ERBB2IP 0.036 0.015 -10000 0 -0.002 74 74
HSP90 (dimer) 0 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.001 0.079 0.2 1 -0.16 52 53
JUN 0.009 0.086 0.2 7 -10000 0 7
HRAS 0.04 0.01 -10000 0 0 31 31
DOCK7 -0.024 0.082 0.24 12 -0.21 10 22
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.037 0.08 0.22 15 -0.12 66 81
AKT1 -0.005 0.012 0.021 29 -10000 0 29
BAD -0.015 0.007 0.012 13 -10000 0 13
MAPK10 -0.008 0.07 0.2 24 -0.14 4 28
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.001 0.085 0.21 1 -0.17 52 53
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 23 -0.18 9 32
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.029 0.24 0.42 2 -0.59 47 49
FOS -0.033 0.22 0.35 6 -0.4 127 133
NRAS 0.04 0.01 -10000 0 0 30 30
mol:Ca2+ -0.001 0.079 0.2 1 -0.16 52 53
MAPK3 -0.01 0.19 0.37 4 -0.49 41 45
MAPK1 -0.024 0.2 0.37 4 -0.52 45 49
JAK2 -0.022 0.079 0.25 9 -0.24 6 15
NF2 0.004 0.075 -10000 0 -0.7 6 6
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.001 0.073 0.18 3 -0.18 63 66
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 0.22 5 -0.22 74 79
MAPK9 -0.011 0.071 0.21 22 -0.17 4 26
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 34 34
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 0.047 11 -0.12 3 14
FRAP1 -0.014 0.007 0.012 13 -10000 0 13
RAC1-CDC42/GTP -0.03 0.056 0.09 19 -0.14 40 59
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 35 40
myelination -0.01 0.097 0.26 32 -0.2 4 36
PPP3CB -0.02 0.079 0.23 12 -0.2 4 16
KRAS 0.034 0.016 -10000 0 0 103 103
RAC1-CDC42/GDP 0.02 0.099 -10000 0 -0.18 46 46
NRG2 0.041 0.007 -10000 0 0 14 14
mol:GDP -0.001 0.073 0.18 3 -0.18 63 66
SOS1 0.038 0.013 -10000 0 0 56 56
MAP2K2 -0.006 0.11 0.25 23 -0.23 39 62
SRC 0.039 0.01 -10000 0 0 36 36
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.021 0.085 0.24 13 -0.21 9 22
MAP2K1 -0.017 0.19 0.38 1 -0.51 32 33
heart morphogenesis -0.001 0.079 0.2 1 -0.16 52 53
RAS family/GDP 0.025 0.1 0.3 1 -0.21 28 29
GRB2 0.041 0.007 -10000 0 0 17 17
PRKACA 0.008 0.084 -10000 0 -0.73 7 7
CHRNE 0.008 0.023 0.068 3 -10000 0 3
HSP90AA1 0 0 -10000 0 -10000 0 0
activation of caspase activity 0.005 0.012 -10000 0 -0.021 29 29
nervous system development -0.001 0.079 0.2 1 -0.16 52 53
CDC42 0.04 0.009 -10000 0 0 24 24
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.007 0.085 0.17 76 -10000 0 76
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 -0.17 76 76
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 0.079 -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
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 0.007 0.081 -10000 0 -0.18 59 59
GNAO1 0.033 0.024 -10000 0 -0.05 20 20
S1P/S1P3/G12/G13 0.047 0.032 -10000 0 -0.066 25 25
AKT1 0.015 0.1 -10000 0 -0.45 21 21
AKT3 -0.02 0.23 -10000 0 -0.97 27 27
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 -0.029 37 37
GNAI3 0.038 0.021 -10000 0 -0.047 20 20
GNAI1 0.034 0.022 -10000 0 -0.007 112 112
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.001 0.007 -10000 0 -0.03 24 24
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0.041 0.006 -10000 0 0 12 12
mol:Ca2+ -0.001 0.1 0.16 1 -0.27 49 50
MAPK3 -0.009 0.096 0.21 1 -0.26 50 51
MAPK1 -0.004 0.089 0.14 1 -0.26 41 42
JAK2 -0.018 0.11 0.18 5 -0.29 55 60
CXCR4 -0.01 0.099 0.21 2 -0.27 49 51
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 0.21 16 -0.26 45 61
S1P/S1P3/Gi 0 0.1 0.16 1 -0.27 48 49
RAC1 0.039 0.01 -10000 0 0 34 34
RhoA/GTP 0.01 0.11 -10000 0 -0.25 50 50
VEGFA 0.003 0.011 0.018 93 -0.038 23 116
S1P/S1P2/Gi -0.002 0.089 0.14 1 -0.18 81 82
VEGFR1 homodimer/VEGFA homodimer 0.036 0.032 -10000 0 -0.088 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 -0.047 21 21
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 49 49
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.019 0.053 -10000 0 -0.13 47 47
TRAF2/ASK1 0.044 0.035 -10000 0 -0.11 20 20
ATM 0.036 0.014 -10000 0 0 73 73
MAP2K3 -0.041 0.16 -10000 0 -0.33 100 100
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.043 0.14 0.21 2 -0.36 63 65
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 0.036 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 49 49
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 -0.28 20 26
RAC1/OSM/MEKK3 0.072 0.026 -10000 0 -0.11 1 1
TRAF2 0.04 0.009 -10000 0 0 29 29
RAC1/OSM/MEKK3/MKK3 -0.009 0.14 -10000 0 -0.29 81 81
TRAF6 0.01 0.041 -10000 0 -0.2 21 21
RAC1 0.039 0.01 -10000 0 0 34 34
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 0 142 142
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 54 54
MAPK14 0.04 0.009 -10000 0 0 28 28
MAP3K7IP2 0.038 0.013 -10000 0 0 59 59
MAP3K5 0.037 0.014 -10000 0 0 69 69
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 -10000 0 -0.15 33 33
GADD45/MTK1/MTK1 0.055 0.069 -10000 0 -0.11 58 58
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.039 0.011 -10000 0 0 41 41
VLDLR 0.032 0.018 -10000 0 0 129 129
LRPAP1 0.036 0.015 -10000 0 0 78 78
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 61 61
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.001 0.068 0.21 35 -0.19 1 36
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 81 81
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.041 0.053 -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 58 58
NDEL1/14-3-3 E 0.035 0.084 0.28 26 -0.17 7 33
MAP1B -0.002 0.049 0.18 3 -0.19 34 37
RAC1 0.012 0.043 -10000 0 -0.59 1 1
p35/CDK5 -0.006 0.071 0.19 37 -0.18 1 38
RELN 0.034 0.017 -10000 0 0 110 110
PAFAH/LIS1 0.024 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 0.024 0.079 0.2 17 -0.19 13 30
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.001 0.096 -10000 0 -0.22 67 67
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.007 0.081 0.22 45 -0.16 5 50
LIS1/IQGAP1 0.03 0.026 -10000 0 -0.15 5 5
RHOA 0.012 0.044 0.12 25 -0.12 29 54
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 0.012 0.061 0.18 1 -0.15 38 39
NDEL1/Katanin 60/Dynein heavy chain 0.043 0.093 0.29 24 -0.18 11 35
LRP8 0.039 0.011 -10000 0 0 39 39
NDEL1/Katanin 60 0.033 0.084 0.25 36 -0.17 11 47
P39/CDK5 -0.006 0.073 0.19 39 -0.18 1 40
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 -0.19 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 0.065 0.2 20 -0.11 33 53
RELN/VLDLR 0.053 0.073 -10000 0 -0.11 57 57
CDC42 0.012 0.049 -10000 0 -0.45 3 3
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.039 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 0.081 -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 0 103 103
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 0.072 -9999 0 -0.4 11 11
Syndecan-3/AgRP 0.03 0.074 -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 0.04 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 0.087 -9999 0 -0.12 66 66
S1P4 pathway

Figure S89.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S89.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.17 74 74
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 -0.17 74 74
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 0.063 -10000 0 -0.16 58 58
S1P/S1P5/Gi -0.005 0.079 -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 0.19 16 -0.17 1 17
S1P/S1P4/Gi -0.005 0.079 -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 -0.099 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
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.042 0.041 0.17 3 -0.16 10 13
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 0.011 -10000 0 0 38 38
Aurora A/BRCA1 0.027 0.05 0.15 3 -0.1 53 56
NDEL1/TACC3 0.045 0.051 0.17 2 -0.16 7 9
GADD45A 0.036 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 -0.17 9 12
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 -0.046 0.12 0.16 2 -0.24 142 144
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 27 27
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.048 0.054 0.18 2 -0.17 7 9
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 45 45
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 -0.18 14 16
BRCA1 0.034 0.016 -10000 0 0 106 106
centrosome duplication 0.042 0.041 0.17 3 -0.17 9 12
regulation of centrosome cycle 0.044 0.05 0.17 2 -0.16 7 9
spindle assembly 0.053 0.074 0.21 2 -0.17 14 16
TDRD7 0.035 0.016 -10000 0 0 92 92
Aurora A/RasGAP/Survivin 0.044 0.073 0.2 4 -0.16 10 14
CENPA 0.008 0.055 -10000 0 -0.33 12 12
Aurora A/PP2A 0.046 0.039 0.17 3 -0.15 9 12
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process -0.013 0.06 0.15 9 -0.2 17 26
negative regulation of DNA binding -0.045 0.12 0.16 2 -0.24 142 144
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 62 -10000 0 62
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 10 13
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 0.034 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 -0.19 9 11
PAK1 0.037 0.014 -10000 0 0 70 70
CKAP5 0.039 0.011 -10000 0 0 45 45
ceramide signaling pathway

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
MAP4K4 -0.023 0.13 0.25 3 -0.37 44 47
BAG4 0.037 0.013 -10000 0 0 64 64
BAD -0.008 0.048 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 26 34
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 -0.01 0.04 0.14 5 -0.15 8 13
MAP2K1 -0.012 0.045 0.16 9 -0.15 9 18
SMPD1 -0.003 0.037 0.097 1 -0.11 33 34
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.014 0.14 0.25 10 -0.36 45 55
MAP2K4 -0.01 0.041 0.14 1 -0.14 21 22
protein ubiquitination -0.029 0.13 0.23 3 -0.38 40 43
EnzymeConsortium:2.7.1.37 -0.013 0.044 0.15 5 -0.16 7 12
response to UV 0 0 0.002 7 -0.002 3 10
RAF1 -0.01 0.044 0.14 5 -0.14 16 21
CRADD 0.041 0.006 -10000 0 0 13 13
mol:ceramide -0.004 0.047 0.1 4 -0.13 37 41
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 0.12 1 -0.13 31 32
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 0.16 4 -0.16 10 14
MAPK1 -0.012 0.052 0.15 6 -0.16 24 30
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 43 53
KSR1 -0.007 0.042 0.11 2 -0.13 26 28
MAPK8 -0.016 0.043 0.17 3 -0.14 12 15
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 0.12 7 -0.14 21 28
IKBKG -0.03 0.13 0.23 3 -0.37 41 44
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.018 0.14 -10000 0 -0.38 44 44
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 8 -0.14 21 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 -0.38 41 56
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 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
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 -0.38 84 84
SMAD4/Ubc9/PIASy 0.066 0.042 -10000 0 -0.13 11 11
SMAD2/SMAD2/SMAD4 0.046 0.086 0.28 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 0.054 0.2 5 -0.17 14 19
MAP3K1 0.036 0.014 -10000 0 0 77 77
TRAP-1/SMAD4 0.049 0.044 -10000 0 -0.14 24 24
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 27 27
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
Class I PI3K signaling events mediated by Akt

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 -0.016 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 0.092 0.21 40 -0.3 27 67
CDKN1A 0.009 0.084 0.21 14 -0.3 30 44
FRAP1 0.04 0.009 -10000 0 0 27 27
PRKDC 0.039 0.011 -10000 0 0 44 44
FOXO3 0.006 0.079 -10000 0 -0.29 33 33
AKT1 0.007 0.08 -10000 0 -0.31 30 30
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 0.079 -10000 0 -0.29 33 33
AKT1/ASK1 0.028 0.088 -10000 0 -0.28 35 35
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 0.086 0.28 35 -10000 0 35
TSC1 0.003 0.078 0.23 2 -0.3 30 32
YWHAZ 0.034 0.016 -10000 0 0 102 102
AKT1/RAF1 0.035 0.093 -10000 0 -0.3 33 33
EP300 0.036 0.014 -10000 0 0 73 73
mol:GDP 0.006 0.081 -10000 0 -0.3 33 33
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 69 69
MAPKAP1 0.04 0.009 -10000 0 0 27 27
negative regulation of cell cycle -0.027 0.083 0.32 11 -0.22 2 13
YWHAH 0.037 0.013 -10000 0 0 60 60
AKT1S1 0.008 0.081 0.22 11 -0.3 27 38
CASP9 0.002 0.079 -10000 0 -0.3 31 31
YWHAB 0.038 0.012 -10000 0 0 52 52
p27Kip1/KPNA1 0.037 0.11 0.27 10 -0.3 32 42
GBL 0.04 0.009 -10000 0 0 25 25
PDK1/Src/Hsp90 0.05 0.021 -10000 0 -0.11 3 3
YWHAE 0.038 0.013 -10000 0 0 58 58
SRC 0.039 0.01 -10000 0 0 36 36
AKT2/p21CIP1 0.012 0.075 0.21 14 -0.26 29 43
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.022 0.091 -10000 0 -0.35 26 26
CHUK 0.001 0.08 -10000 0 -0.31 31 31
BAD/BCL-XL 0.028 0.086 -10000 0 -0.3 28 28
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 25 25
MDM2 0.006 0.087 0.2 13 -0.3 33 46
MAPKKK cascade -0.034 0.092 0.3 33 -10000 0 33
MDM2/Cbp/p300 0.039 0.1 0.32 3 -0.3 33 36
TSC1/TSC2 -0.003 0.082 0.29 4 -0.29 33 37
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.1 0.31 3 -0.29 33 36
glucose import -0.003 0.034 0.21 11 -0.16 3 14
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.023 0.087 0.28 1 -0.29 15 16
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.003 0.032 0.21 10 -0.16 3 13
GSK3A 0.005 0.078 0.22 3 -0.3 29 32
FOXO1 0.006 0.079 -10000 0 -0.29 33 33
GSK3B 0.007 0.088 0.21 16 -0.3 33 49
SFN 0.036 0.015 -10000 0 0 86 86
G1/S transition of mitotic cell cycle 0.007 0.094 0.29 11 -0.3 32 43
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 64 64
CREBBP 0.038 0.012 -10000 0 0 54 54
Class IB PI3K non-lipid kinase events

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
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
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.07 0.067 -10000 0 -0.11 45 45
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 0.062 -10000 0 -0.23 19 19
JUN -0.007 0.11 0.24 2 -0.51 23 25
MAP3K7 0.005 0.064 0.21 5 -0.21 21 26
GRAP2 0.038 0.013 -10000 0 0 57 57
CRK 0.038 0.012 -10000 0 0 52 52
MAP2K4 -0.005 0.078 0.23 1 -0.27 25 26
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 0.015 0.067 -10000 0 -0.21 20 20
LAT/GRAP2/SLP76/HPK1/HIP-55 0.079 0.077 -10000 0 -0.11 45 45
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.038 0.013 -10000 0 0 56 56
HDAC2 0.038 0.012 -10000 0 0 47 47
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 44 44
GLI3/SPOP 0.02 0.13 -10000 0 -0.36 28 28
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) 0.02 0.11 -10000 0 -0.41 24 24
SAP30 0.038 0.012 -10000 0 0 55 55
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 0.016 0.073 0.19 6 -0.21 24 30
GLI3 0.003 0.12 0.23 2 -0.38 27 29
CSNK1D 0.04 0.009 -10000 0 0 28 28
CSNK1E 0.038 0.013 -10000 0 0 57 57
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 0.24 2 -0.33 33 35
GLI2/Su(fu) 0.024 0.083 0.19 5 -0.25 23 28
FOXA2 0.025 0.094 -10000 0 -0.61 9 9
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 -0.37 27 27
GLI3A/CBP 0.047 0.015 -10000 0 -10000 0 0
KIF3A 0.038 0.012 -10000 0 0 51 51
GLI1 0.013 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 -0.24 17 18
STK36 0.04 0.011 -10000 0 -0.003 33 33
Gi family/GNB1/GNG2/GDP 0 0.086 -10000 0 -0.26 33 33
PTCH1 0.014 0.1 -10000 0 -0.35 28 28
MIM/GLI1 0.026 0.099 -10000 0 -0.37 17 17
CREBBP 0.047 0.015 -10000 0 -10000 0 0
Su(fu)/SIN3/HDAC complex 0.004 0.11 0.18 7 -0.31 37 44
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.019 0.005 0 42 -10000 0 42
MAP4K4 -0.002 0.081 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 -0.17 9 9
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 0.19 3 -0.18 8 11
FADD/Caspase 8 -0.004 0.11 0.25 8 -0.31 37 45
MAP2K4 -0.006 0.028 -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 53 53
mol:ceramide 0.006 0.027 -10000 0 -0.18 9 9
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 0.19 3 -0.18 8 11
cell proliferation 0.026 0.051 0.2 5 -0.18 7 12
BID 0.02 0.095 -10000 0 -0.62 4 4
MAP3K1 -0.001 0.027 -10000 0 -0.18 8 8
EIF2A 0.009 0.079 0.18 75 -0.19 12 87
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 0.17 6 -0.19 7 13
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.009 0.044 0.17 6 -0.17 8 14
Cathepsin D/ceramide 0.03 0.032 -10000 0 -0.17 9 9
FADD -0.001 0.084 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 -0.2 19 19
PRKRA 0.004 0.044 0.2 17 -0.17 8 25
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 -0.18 9 9
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 0.21 5 -0.2 6 11
PRKCD 0.038 0.013 -10000 0 0 56 56
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 0.005 0 42 -10000 0 42
MAP2K1 -0.009 0.036 0.17 12 -0.17 7 19
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 4 -0.19 11 15
TNFRSF1A 0.036 0.015 -10000 0 0 84 84
NFKB1 0.036 0.015 -10000 0 0 84 84
TNFR1A/BAG4 0.044 0.038 -10000 0 -0.13 14 14
EIF2AK2 -0.001 0.057 0.19 30 -0.17 11 41
TNF-alpha/TNFR1A/FAN 0.059 0.052 -10000 0 -0.14 21 21
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.005 0.14 -10000 0 -0.4 45 45
MAP2K2 -0.008 0.033 0.16 7 -0.18 8 15
SMPD3 -0.004 0.1 0.19 6 -0.29 53 59
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 0.12 3 -0.14 9 12
NF kappa B1/RelA/I kappa B alpha 0.081 0.083 -10000 0 -0.12 62 62
AIFM1 0.01 0.042 0.13 4 -0.17 12 16
BCL2 0.036 0.014 -10000 0 0 76 76
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.038 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 -0.092 4 4
YWHAE 0.038 0.013 -10000 0 0 58 58
Calcineurin A alpha-beta B1/CABIN1 -0.003 0.086 0.17 4 -0.26 27 31
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 0.028 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 -0.25 25 25
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 25 -10000 0 25
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 -0.12 19 21
MEF2D/NFAT1/Cbp/p300 0.071 0.091 0.24 3 -0.18 20 23
CABIN1 -0.003 0.086 0.17 4 -0.27 27 31
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 0.037 0.013 -10000 0 0 60 60
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 -0.28 23 25
PRKCH 0.039 0.011 -10000 0 0 41 41
CABIN1/Cbp/p300 0.044 0.052 -10000 0 -0.16 26 26
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 -10000 0 -0.2 11 11
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 56 56
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 0.015 -10000 0 0 73 73
PRKCB1 0.038 0.012 -10000 0 0 48 48
CSNK2A1 0.038 0.012 -10000 0 0 54 54
NFATc/JNK1 0.032 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 -0.043 17 23
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 26 26
NR4A1 0.017 0.075 0.2 21 -0.22 21 42
GSK3B 0.041 0.009 -10000 0 0 26 26
positive T cell selection 0.026 0.016 -10000 0 -0.092 4 4
NFAT1/CK1 alpha 0.023 0.047 0.13 5 -0.18 11 16
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 0.034 0.11 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 S99.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA 0.051 0.093 -10000 0 -0.2 35 35
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 -0.29 30 31
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 -0.15 25 25
FKBP3 0.039 0.01 -10000 0 0 34 34
Histones 0.069 0.087 0.24 1 -0.2 24 25
YY1/LSF 0.012 0.083 -10000 0 -0.22 45 45
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 0.061 -10000 0 -0.18 39 39
I kappa B alpha/HDAC1 0.031 0.09 0.22 1 -0.23 48 49
SAP18 0.039 0.01 -10000 0 0 34 34
RELA 0.017 0.086 0.22 3 -0.26 26 29
HDAC1/Smad7 0.062 0.053 -10000 0 -0.12 33 33
RANGAP1 0.038 0.013 -10000 0 0 57 57
HDAC3/TR2 0.047 0.061 0.22 1 -0.2 21 22
NuRD/MBD3 Complex 0.01 0.098 -10000 0 -0.29 32 32
NF kappa B1 p50/RelA 0.023 0.1 0.25 1 -0.26 37 38
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 30 30
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 55 55
SAP30 0.038 0.012 -10000 0 0 55 55
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.037 0.013 -10000 0 0 61 61
YY1/HDAC3 0.016 0.078 -10000 0 -0.24 30 30
YY1/HDAC2 0.015 0.077 -10000 0 -0.21 41 41
YY1/HDAC1 0.012 0.079 -10000 0 -0.22 41 41
NuRD/MBD2 Complex (MeCP1) 0.011 0.097 -10000 0 -0.29 29 29
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 27 27
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 -0.19 20 21
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 -0.27 42 50
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 47 47
YY1 0.005 0.057 -10000 0 -0.24 25 25
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 33 33
NFKB1 0.036 0.015 -10000 0 0 84 84
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.04 0.009 -10000 0 0 30 30
YY1/LSF/HDAC1 0.022 0.092 -10000 0 -0.21 48 48
YY1/SAP30/HDAC1 0.025 0.085 -10000 0 -0.2 42 42
EP300 0.036 0.014 -10000 0 0 73 73
STAT3 (dimer non-phopshorylated) 0.009 0.066 -10000 0 -0.24 33 33
proteasomal ubiquitin-dependent protein catabolic process 0.009 0.071 -10000 0 -0.27 30 30
histone deacetylation 0.011 0.096 -10000 0 -0.29 29 29
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 -0.3 26 26
NuRD Complex 0.004 0.1 0.19 8 -0.28 39 47
positive regulation of chromatin silencing 0.065 0.085 0.23 1 -0.2 24 25
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 25 25
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 0.062 -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 26 26
NuRD/MBD2/PRMT5 Complex 0.011 0.097 -10000 0 -0.29 29 29
Ran/GTP/Exportin 1 0.038 0.071 0.18 1 -0.18 36 37
NF kappa B/RelA/I kappa B alpha 0.016 0.083 -10000 0 -0.28 27 27
SIN3/HDAC complex/NCoR1 -0.001 0.096 0.17 1 -0.25 45 46
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 42 42
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.037 0.016 0.079 1 -0.057 3 4
HSPA8 0.039 0.01 -10000 0 0 34 34
SMAD3/SMAD4/ER alpha 0.065 0.092 0.23 38 -0.16 23 61
AKT1 0.04 0.017 -10000 0 -0.098 5 5
GSC 0.008 0.096 -10000 0 -1.2 2 2
NKX2-5 0.039 0.017 -10000 0 -0.053 13 13
muscle cell differentiation -0.04 0.11 0.29 15 -10000 0 15
SMAD2-3/SMAD4/SP1 0.072 0.12 -10000 0 -0.19 12 12
SMAD4 0.036 0.046 -10000 0 -0.1 15 15
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 24 24
SMAD3/SMAD4/VDR 0.074 0.1 -10000 0 -0.19 17 17
MYC 0.021 0.022 0.12 4 -0.044 2 6
CDKN2B -0.044 0.16 -10000 0 -1.2 6 6
AP1 0.004 0.092 -10000 0 -0.23 38 38
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.001 0.13 0.2 3 -0.31 53 56
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.012 0.063 -10000 0 -0.2 34 34
SP3 0.037 0.024 0.08 2 -0.053 34 36
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 -0.27 37 43
MEF2C/TIF2 0.023 0.068 0.26 6 -0.22 15 21
endothelial cell migration -0.031 0.1 0.91 5 -10000 0 5
MAX 0.029 0.027 0.098 3 -0.03 94 97
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 0.013 -10000 0 0 56 56
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 0.081 0.06 -10000 0 -0.28 2 2
DCP1A 0.04 0.008 -10000 0 0 20 20
SKI 0.042 0.003 -10000 0 0 3 3
SERPINE1 0.03 0.1 -10000 0 -0.92 5 5
SMAD3/SMAD4/ATF2 0.064 0.075 -10000 0 -0.16 16 16
SMAD3/SMAD4/ATF3 0.061 0.068 -10000 0 -0.13 11 11
SAP30 0.038 0.012 -10000 0 0 55 55
Cbp/p300/PIAS3 0.061 0.059 -10000 0 -0.14 29 29
JUN -0.002 0.087 0.18 4 -0.24 36 40
SMAD3/SMAD4/IRF7 0.071 0.071 -10000 0 -0.14 9 9
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 0.13 13 -10000 0 13
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 28 28
SMAD3/SMAD4/Max 0.063 0.068 -10000 0 -0.14 7 7
Cbp/p300/SNIP1 0.058 0.057 -10000 0 -0.14 25 25
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 0.075 -10000 0 -0.15 17 17
IRF7 0.041 0.012 0.087 1 -10000 0 1
ESR1 0.046 0.036 0.12 91 0 92 183
HNF4A 0.038 0.012 -10000 0 0 47 47
MEF2C -0.003 0.061 0.22 13 -0.23 15 28
SMAD2-3/SMAD4 0.071 0.074 -10000 0 -0.14 7 7
Cbp/p300/Src-1 0.058 0.062 -10000 0 -0.14 34 34
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 47 47
SNIP1 0.039 0.011 -10000 0 0 38 38
GCN5L2 0.039 0.013 -10000 0 -0.045 3 3
SMAD3/SMAD4/TFE3 0.078 0.083 -10000 0 -0.16 25 25
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 17 18
SMAD2/SMAD2/SMAD4 -0.01 0.061 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 71 71
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 -0.2 7 7
IFNB1 0.012 0.052 0.27 3 -0.16 2 5
SMAD3/SMAD4/MEF2C 0.052 0.084 0.28 2 -0.22 15 17
CITED1 0.039 0.01 -10000 0 0 35 35
SMAD2-3/SMAD4/ARC105 0.068 0.068 -10000 0 -0.12 6 6
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 -0.37 31 31
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 26 27
IL10 0.022 0.061 0.22 19 -10000 0 19
PIASy/HDAC complex 0.037 0.014 -10000 0 -0.037 5 5
PIAS3 0.04 0.01 -10000 0 -0.004 26 26
CDK2 0.038 0.015 -10000 0 -0.043 3 3
IL5 0.022 0.06 0.22 17 -0.15 1 18
CDK4 0.038 0.015 -10000 0 -0.002 63 63
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 31 31
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 13 -0.23 15 28
CEBPB 0.036 0.018 -10000 0 -0.061 5 5
SMAD3/SMAD4/DLX1 0.068 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 -0.13 12 12
SMAD3/SMAD4/GATA3 0.078 0.071 -10000 0 -0.14 4 4
SnoN/SIN3/HDAC complex/NCoR1 0.025 0.021 -10000 0 0 228 228
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.085 0.085 -10000 0 -0.18 1 1
SMAD3/SMAD4/SP1-3 0.07 0.12 -10000 0 -0.21 26 26
MED15 0 0 -10000 0 -10000 0 0
SP1 0.018 0.067 -10000 0 -0.1 126 126
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 -0.27 33 46
TGIF/SIN3/HDAC complex/CtBP 0.007 0.089 -10000 0 -0.28 30 30
SMAD3/SMAD4/AR 0.042 0.091 -10000 0 -0.15 46 46
AR 0.033 0.017 -10000 0 0 122 122
negative regulation of cell growth 0.018 0.074 -10000 0 -0.24 18 18
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 52 52
SMAD3/SMAD4/AP1 0.033 0.11 0.26 3 -0.23 38 41
SMAD3/SMAD4/RUNX2 0.065 0.07 -10000 0 -0.13 12 12
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
Ephrin A reverse 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
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 26 26
Atypical NF-kappaB pathway

Figure S102.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S102.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.055 0.027 -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 30 30
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 0.026 0.04 -10000 0 -0.12 30 30
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 0.04 -10000 0 -0.12 31 31
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.027 0.04 -10000 0 -0.12 32 32
PIK3CA 0.03 0.019 -10000 0 0 155 155
NF kappa B1 p50 dimer 0.019 0.041 -10000 0 -0.14 31 31
PIK3R1 0.034 0.017 -10000 0 0 108 108
NFKB1 -0.016 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 -0.22 22 22
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 44 44
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 22 22
NF kappa B1 p105/c-Rel 0.027 0.038 -10000 0 -0.12 30 30
LCK 0.04 0.009 -10000 0 0 29 29
BCL3 0.039 0.011 -10000 0 0 40 40
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.034 0.25 0.49 2 -0.58 51 53
PCK1 -0.092 0.4 -10000 0 -1.1 72 72
HNF4A -0.067 0.34 0.57 5 -0.76 83 88
KCNJ11 -0.003 0.23 0.53 1 -0.57 22 23
AKT1 0.006 0.17 -10000 0 -0.35 25 25
response to starvation -0.015 0.045 -10000 0 -0.12 79 79
DLK1 0.006 0.24 0.64 3 -0.57 22 25
NKX2-1 -0.002 0.15 0.36 3 -0.32 24 27
ACADM -0.049 0.27 0.54 1 -0.6 64 65
TAT -0.023 0.19 -10000 0 -0.53 21 21
CEBPB 0.039 0.017 -10000 0 -0.064 2 2
CEBPA 0.042 0.016 -10000 0 -0.066 1 1
TTR 0.042 0.17 0.52 2 -0.92 4 6
PKLR -0.021 0.25 0.45 2 -0.57 39 41
APOA1 -0.12 0.47 -10000 0 -1.1 93 93
CPT1C -0.026 0.24 0.49 1 -0.58 42 43
ALAS1 -0.005 0.18 -10000 0 -0.64 9 9
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 -0.04 0.27 0.53 1 -0.6 59 60
HMGCS1 -0.032 0.26 0.5 3 -0.59 57 60
NR3C1 0.048 0.015 -10000 0 -10000 0 0
CPT1B -0.033 0.24 -10000 0 -0.58 43 43
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 -0.57 43 46
CREB1 0.021 0.095 -10000 0 -0.21 74 74
IGFBP1 -0.001 0.15 -10000 0 -0.49 5 5
PDX1 0.014 0.14 0.4 1 -0.3 22 23
UCP2 -0.055 0.3 0.48 10 -0.65 82 92
ALDOB -0.003 0.23 -10000 0 -0.56 22 22
AFP 0.015 0.049 -10000 0 -10000 0 0
BDH1 -0.053 0.27 -10000 0 -0.6 67 67
HADH -0.003 0.23 -10000 0 -0.51 37 37
F2 -0.029 0.31 -10000 0 -0.73 37 37
HNF1A 0.009 0.001 -10000 0 -10000 0 0
G6PC 0.028 0.088 -10000 0 -10000 0 0
SLC2A2 0.034 0.16 -10000 0 -10000 0 0
INS 0.03 0.013 0.18 1 -0.062 2 3
FOXA1 0.056 0.016 -10000 0 -10000 0 0
FOXA3 0.022 0.12 -10000 0 -0.21 104 104
FOXA2 0.016 0.29 -10000 0 -0.6 33 33
ABCC8 -0.003 0.23 0.53 1 -0.57 21 22
ALB 0.016 0.05 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.014 0.079 -10000 0 -0.15 93 93
AKT1 0.013 0.11 0.28 12 -0.3 20 32
PTK2B -0.012 0.077 0.19 23 -0.32 7 30
VEGFR2 homodimer/Frs2 0.033 0.057 -10000 0 -0.37 4 4
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 -0.36 4 4
endothelial cell proliferation 0.035 0.098 0.28 16 -0.29 9 25
mol:Ca2+ 0.019 0.063 0.2 22 -0.28 8 30
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 78 78
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 0.051 0.085 0.31 1 -0.37 6 7
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.035 0.053 -10000 0 -0.28 5 5
VEGFR1 homodimer 0.04 0.01 -10000 0 0 31 31
SHC/GRB2/SOS1 0.072 0.085 -10000 0 -0.25 11 11
GRB10 0.019 0.069 0.2 22 -0.34 9 31
PTPN11 0.04 0.009 -10000 0 0 27 27
GRB2 0.041 0.007 -10000 0 0 17 17
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 0.044 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 -0.27 7 7
mol:GDP 0.056 0.076 -10000 0 -0.24 11 11
mol:NADP 0.038 0.082 0.31 5 -0.34 7 12
eNOS/Hsp90 0.035 0.077 0.29 5 -0.32 7 12
PIK3R1 0.034 0.017 -10000 0 0 108 108
mol:IP3 0.019 0.064 0.2 22 -0.28 8 30
HIF1A/ARNT 0.05 0.045 -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 80 80
FAK1/Vinculin 0.012 0.13 0.28 7 -0.29 43 50
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 -0.27 3 3
mol:L-citrulline 0.038 0.082 0.31 5 -0.34 7 12
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 0.043 0.062 -10000 0 -0.29 8 8
VEGFR2/3 heterodimer 0.034 0.058 -10000 0 -0.33 5 5
VEGFB 0.039 0.011 -10000 0 0 42 42
MAPK11 -0.004 0.069 0.24 7 -0.31 9 16
VEGFR2 homodimer 0.022 0.044 -10000 0 -0.38 5 5
FLT1 0.04 0.01 -10000 0 0 31 31
NEDD4 0.041 0.014 -10000 0 -0.054 5 5
MAPK3 -0.002 0.073 0.25 11 -0.28 8 19
MAPK1 -0.002 0.074 0.26 10 -0.3 7 17
VEGFA145/NRP2 0.016 0.045 -10000 0 -0.12 49 49
VEGFR1/2 heterodimer 0.034 0.058 -10000 0 -0.29 7 7
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 0.27 9 -0.3 7 16
PI3K 0.012 0.082 0.26 3 -0.28 13 16
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.025 0.063 -10000 0 -0.25 10 10
FES 0.02 0.065 0.2 24 -0.27 8 32
GAB1 0.019 0.083 0.26 5 -0.31 16 21
VEGFR2 homodimer/VEGFA homodimer/Src 0.035 0.053 -10000 0 -0.28 5 5
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 0.044 0.084 0.33 3 -0.33 8 11
VEGFR2 homodimer/VEGFA homodimer/Yes 0.028 0.062 -10000 0 -0.27 8 8
PI3K/GAB1 0.024 0.11 0.27 5 -0.32 18 23
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.048 0.084 -10000 0 -0.21 12 12
PRKACA 0.035 0.015 -10000 0 0 89 89
VEGFR2/3 heterodimer/VEGFC homodimer 0.05 0.068 -10000 0 -0.29 6 6
HSP90AA1 0 0 -10000 0 -10000 0 0
CDC42 0.019 0.064 0.2 24 -0.28 8 32
actin cytoskeleton reorganization 0.034 0.053 -10000 0 -0.28 5 5
PTK2 -0.005 0.11 0.25 2 -0.3 38 40
EDG1 0.02 0.062 0.2 22 -0.27 8 30
mol:DAG 0.019 0.064 0.2 22 -0.28 8 30
CaM/Ca2+ 0.033 0.066 0.25 2 -0.27 8 10
MAP2K3 -0.008 0.059 0.19 21 -0.33 5 26
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.047 0.073 0.24 5 -0.34 9 14
PLCG1 0.019 0.064 0.2 22 -0.29 8 30
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 -0.28 7 7
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.033 0.053 -10000 0 -0.31 5 5
cell migration 0 0.13 0.26 8 -0.34 36 44
mol:PI-3-4-5-P3 0.012 0.078 0.25 3 -0.27 13 16
FYN 0.034 0.016 -10000 0 0 103 103
VEGFB/NRP1 0.026 0.062 0.2 20 -0.24 10 30
mol:NO 0.038 0.082 0.31 5 -0.34 7 12
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 0.038 0.087 0.31 5 -0.38 7 12
VEGFR2 homodimer/VEGFA homodimer/Sck 0.031 0.056 -10000 0 -0.32 5 5
RAC1 0.039 0.01 -10000 0 0 34 34
PRKCA -0.008 0.065 0.19 25 -0.24 12 37
PRKCB -0.007 0.06 0.18 24 -0.33 5 29
VCL 0.039 0.01 -10000 0 0 36 36
VEGFA165/NRP1 0.01 0.055 0.17 19 -0.26 8 27
VEGFR1/2 heterodimer/VEGFA homodimer 0.034 0.057 -10000 0 -0.28 7 7
VEGFA165/NRP2 0.016 0.045 -10000 0 -0.12 49 49
MAPKKK cascade -0.023 0.07 0.19 24 -0.33 8 32
NRP2 0.035 0.016 -10000 0 0 94 94
VEGFC homodimer 0.036 0.015 -10000 0 0 80 80
NCK1 0.036 0.015 -10000 0 0 80 80
ROCK1 0.041 0.007 -10000 0 0 14 14
FAK1/Paxillin 0.015 0.12 0.28 7 -0.29 39 46
MAP3K13 0.014 0.062 0.2 20 -0.27 9 29
PDPK1 -0.003 0.067 0.24 3 -0.24 11 14
Coregulation of Androgen receptor activity

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
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 36 36
CTNNB1 0.04 0.01 -9999 0 -10000 0 0
AKT1 0.039 0.01 -9999 0 0 37 37
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 71 71
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 0.079 -9999 0 -0.12 129 129
XRCC6 0.036 0.014 -9999 0 0 70 70
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 59 59
CDKN2A 0.028 0.019 -9999 0 0 175 175
SRF 0.043 0.021 -9999 0 -0.14 4 4
NKX3-1 0.014 0.082 -9999 0 -0.3 30 30
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 27 27
T-DHT/AR/Cyclin D3/CDK11 p58 0.034 0.058 -9999 0 -0.095 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 72 72
TMPRSS2 0.013 0.09 -9999 0 -0.31 35 35
CCND1 0.031 0.018 -9999 0 0 144 144
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 0.017 0.076 -9999 0 -0.12 119 119
CMTM2 0.036 0.014 -9999 0 0 75 75
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
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 31 31
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 -0.2 15 30
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 45 45
FGFR1 0.033 0.017 -10000 0 0 122 122
VEGFR1 homodimer 0.04 0.01 -10000 0 0 31 31
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 0.003 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 52 52
RET9/GFRalpha1/GDNF/Enigma 0.063 0.035 -10000 0 -0.11 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 76 76
RET9/GFRalpha1/GDNF/IRS1 0.063 0.036 -10000 0 -0.11 5 5
lamellipodium assembly 0.03 0.051 -10000 0 -0.2 3 3
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 -0.11 2 2
RET9/GFRalpha1/GDNF/Shank3 0.066 0.031 -10000 0 -0.11 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 0.001 0.06 0.2 15 -0.2 5 20
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 -0.24 8 8
HRAS/GTP 0.081 0.048 -10000 0 -0.15 4 4
tube development 0.064 0.03 0.24 5 -0.1 2 7
MAPK1 -0.009 0.062 0.18 40 -10000 0 40
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.021 0.046 -10000 0 -0.16 28 28
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 -0.38 5 5
PIK3R1 0.034 0.017 -10000 0 0 108 108
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.024 0.035 -10000 0 -0.15 11 11
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 52 52
JNK cascade 0.003 0.061 0.19 4 -0.23 11 15
RET9/GFRalpha1/GDNF/FRS2 0.06 0.041 -10000 0 -0.11 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 80 80
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.023 0.038 -10000 0 -0.14 21 21
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.027 0.049 -10000 0 -0.16 27 27
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.016 0.058 -10000 0 -0.16 34 34
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.028 0.043 -10000 0 -0.15 22 22
PI3K 0.043 0.064 0.23 6 -0.24 3 9
SOS1 0.038 0.013 -10000 0 0 56 56
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.086 0.034 -10000 0 -0.1 2 2
GRB10 0.04 0.008 -10000 0 0 23 23
activation of MAPKK activity 0.029 0.053 0.16 1 -0.26 7 8
RET51/GFRalpha1/GDNF/FRS2 0.086 0.047 -10000 0 -0.11 12 12
GAB1 0.038 0.012 -10000 0 0 52 52
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 -0.17 2 2
RET51/GFRalpha1/GDNF/PKC alpha 0.078 0.056 -10000 0 -0.11 27 27
GRB2 0.041 0.007 -10000 0 0 17 17
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 34 34
RET51/GFRalpha1/GDNF/IRS1 0.091 0.039 -10000 0 -0.11 5 5
Rac1/GTP 0.042 0.064 0.2 4 -0.23 3 7
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
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.06 0.041 -10000 0 -0.11 11 11
TC10/GTP 0.05 0.036 -10000 0 -0.1 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 0.022 10 -0.037 5 15
AKT1 0.016 0.098 0.23 40 -0.18 3 43
INSR 0.042 0.016 0.082 13 0 53 66
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 0.008 -10000 0 0 23 23
SORBS1 0.039 0.011 -10000 0 0 40 40
CRK 0.038 0.012 -10000 0 0 52 52
PTPN1 -0.005 0.042 0.15 36 -10000 0 36
CAV1 -0.007 0.042 0.17 17 -10000 0 17
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 46 46
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.026 0.097 0.22 1 -0.31 36 37
RPS6KB1 0.005 0.09 0.2 42 -0.18 8 50
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 0 108 108
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.049 0.082 0.2 24 -0.18 13 37
HRAS/GTP -0.026 0.033 0.049 1 -0.11 24 25
Insulin Receptor 0.042 0.016 0.082 13 0 53 66
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.1 0.062 -10000 0 -0.11 11 11
PRKCI -0.006 0.13 -10000 0 -0.38 52 52
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 46 46
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 0.23 30 -0.18 3 33
PRKCZ 0.036 0.09 -10000 0 -0.34 22 22
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.007 0.041 0.15 18 -10000 0 18
F2RL2 0.036 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 80 80
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 -0.091 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 0.083 18 0 30 48
mol:PI-3-4-P2 -0.012 0.019 0.045 27 -0.09 8 35
GRB2 0.041 0.007 -10000 0 0 17 17
EIF4EBP1 0.003 0.08 0.19 31 -0.17 2 33
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 25 25
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.029 0.059 -10000 0 -0.15 30 30
Insulin Receptor/Insulin/IRS1 0.071 0.038 -10000 0 -0.099 8 8
Insulin Receptor/Insulin/IRS3 0.059 0.03 0.14 1 -0.14 3 4
Par3/Par6 0.067 0.051 -10000 0 -0.1 14 14
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 44 44
WASL 0.04 0.009 -10000 0 0 24 24
Nephrin/NEPH1/podocin/CD2AP 0.073 0.071 -10000 0 -0.12 41 41
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 60 -0.18 3 63
mol:Ca2+ 0.075 0.064 -10000 0 -0.13 25 25
mol:DAG 0.077 0.065 -10000 0 -0.13 25 25
NPHS2 0.043 0.02 -10000 0 -0.043 19 19
mol:IP3 0.077 0.065 -10000 0 -0.13 25 25
regulation of endocytosis 0.053 0.059 -10000 0 -0.12 20 20
Nephrin/NEPH1/podocin/Cholesterol 0.064 0.048 0.18 1 -0.11 18 19
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 80 80
NCK2 0.042 0.004 -10000 0 0 6 6
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.078 0.066 -10000 0 -0.13 25 25
CD2AP 0.037 0.014 -10000 0 0 67 67
Nephrin/NEPH1/podocin/GRB2 0.085 0.059 -10000 0 -0.12 18 18
GRB2 0.041 0.007 -10000 0 0 17 17
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.005 0.071 0.17 67 -0.12 3 70
cytoskeleton organization 0.013 0.054 0.25 4 -0.16 14 18
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 12 12
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
Glucocorticoid receptor regulatory network

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
PCK2 -0.02 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 0.015 -10000 0 -0.016 39 39
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 -0.035 0.074 0.19 3 -0.21 21 24
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 0.013 0.097 -10000 0 -0.16 126 126
FGG -0.055 0.11 0.31 6 -0.32 1 7
GR beta/TIF2 -0.033 0.079 0.22 2 -0.24 7 9
IFNG 0.047 0.1 -10000 0 -10000 0 0
apoptosis -0.055 0.17 -10000 0 -0.42 66 66
CREB1 0.049 0.009 -10000 0 -10000 0 0
histone acetylation 0.022 0.083 0.29 10 -0.34 8 18
BGLAP 0.045 0.091 0.3 1 -0.89 3 4
GR/PKAc 0.032 0.085 0.24 1 -0.16 24 25
NF kappa B1 p50/RelA 0.01 0.17 -10000 0 -0.3 114 114
SMARCD1 0.041 0.008 -10000 0 0 19 19
MDM2 -0.013 0.047 0.13 7 -0.24 7 14
GATA3 0.05 0.014 -10000 0 -10000 0 0
AKT1 0.035 0.016 0.17 2 -0.052 7 9
CSF2 0.012 0.054 -10000 0 -10000 0 0
GSK3B 0.037 0.015 -10000 0 -0.012 43 43
NR1I3 -0.043 0.16 -10000 0 -0.44 20 20
CSN2 -0.05 0.097 0.27 5 -0.3 2 7
BRG1/BAF155/BAF170/BAF60A 0.077 0.065 -10000 0 -0.13 32 32
NFATC1 0.043 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 -0.19 31 32
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 -0.27 4 13
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 -0.041 0.07 0.2 13 -0.21 32 45
GR alpha/HSP90/FKBP51/HSP90/PP5C -0.017 0.081 0.21 2 -0.19 21 23
cortisol/GR alpha (monomer) -0.071 0.13 0.39 5 -0.38 2 7
NCOA2 0.037 0.014 -10000 0 0 71 71
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS 0.032 0.054 -10000 0 -0.12 29 29
AP-1/NFAT1-c-4 0.039 0.14 -10000 0 -0.37 20 20
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 0.29 1 -0.56 90 91
TP53 0.036 0.028 -10000 0 -10000 0 0
PPP5C 0.04 0.01 -10000 0 0 32 32
KRT17 0.029 0.16 -10000 0 -0.72 12 12
KRT14 0.026 0.17 0.5 8 -1.1 10 18
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 47 47
AP-1 0.038 0.14 -10000 0 -0.38 20 20
MAPK14 0.037 0.016 -10000 0 -0.03 19 19
MAPK10 0.033 0.021 -10000 0 -0.03 30 30
MAPK11 0.029 0.021 -10000 0 -0.03 16 16
KRT5 -0.006 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 -0.061 0.11 0.29 3 -0.34 42 45
MAPK3 0.036 0.019 -10000 0 -0.03 34 34
MAPK1 0.035 0.018 -10000 0 -0.01 67 67
ICAM1 -0.076 0.32 -10000 0 -0.77 93 93
NFKB1 0.006 0.11 -10000 0 -0.2 110 110
MAPK8 0.049 0.083 0.57 1 -0.23 4 5
MAPK9 0.036 0.017 -10000 0 -0.011 61 61
cortisol/GR alpha (dimer) -0.057 0.18 -10000 0 -0.44 67 67
BAX -0.048 0.12 -10000 0 -0.43 2 2
POMC 0.056 0.094 0.49 2 -10000 0 2
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 46 55
IL13 0.049 0.092 -10000 0 -10000 0 0
IL6 0.013 0.16 -10000 0 -0.62 18 18
PRKACG 0.041 0.005 -10000 0 0 9 9
IL5 0.048 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 83 83
PRKACB 0.038 0.012 -10000 0 0 48 48
HSP90AA1 0 0 -10000 0 -10000 0 0
IL8 -0.013 0.23 -10000 0 -0.79 37 37
CDK5R1/CDK5 0.045 0.041 -10000 0 -0.13 20 20
NF kappa B1 p50/RelA/PKAc 0.043 0.15 -10000 0 -0.22 89 89
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 -0.31 16 20
NF kappa B1 p50/RelA/Cbp 0.024 0.16 0.42 6 -0.25 111 117
JUN (dimer) 0.04 0.098 0.34 9 -0.27 4 13
YWHAH 0.037 0.013 -10000 0 0 60 60
VIPR1 0.041 0.057 0.4 1 -10000 0 1
NR3C1 -0.047 0.092 0.26 3 -0.32 6 9
NR4A1 0.038 0.018 -10000 0 -10000 0 0
TIF2/SUV420H1 0.042 0.052 -10000 0 -0.14 36 36
MAPKKK cascade -0.055 0.17 -10000 0 -0.42 66 66
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 -0.031 0.092 0.25 4 -0.31 17 21
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.043 0.11 0.36 4 -0.32 1 5
mol:cortisol -0.043 0.066 0.2 6 -10000 0 6
MMP1 0.009 0.18 -10000 0 -0.76 23 23
Alternative NF-kappaB pathway

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
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 84 84
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
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 0.05 -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 -0.12 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 0.059 -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 -0.15 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 0 141 141
HDAC5 0.04 0.01 -10000 0 0 32 32
GNB1/GNG2 0.053 0.038 -10000 0 -0.14 19 19
Histones -0.006 0.071 -10000 0 -0.19 39 39
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 58 58
NR3C1 0.039 0.012 -10000 0 0 46 46
SUMO1/HDAC4 0.041 0.062 -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 57 57
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 -0.19 39 39
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 27 27
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 92 92
HDAC6/HDAC11 0.056 0.026 -10000 0 -0.14 7 7
Ran/GTP/Exportin 1 0.038 0.071 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 -0.11 20 20
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
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0.015 0.12 -10000 0 -0.62 14 14
MKNK1 0.04 0.009 -10000 0 0 25 25
MAPK14 0.042 0.053 0.16 2 -0.13 36 38
ATF2/c-Jun -0.02 0.1 -10000 0 -0.31 43 43
MAPK11 0.031 0.054 -10000 0 -0.13 33 33
MITF 0.019 0.061 -10000 0 -0.28 16 16
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 -0.26 14 14
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 -0.18 31 31
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 -0.17 37 37
CREB1 -0.005 0.098 -10000 0 -0.2 98 98
RAB5/GDP 0.03 0.012 -10000 0 -0.13 3 3
EIF4E -0.007 0.064 0.19 22 -0.3 9 31
RPS6KA4 0.02 0.056 -10000 0 -0.28 14 14
PLA2G4A -0.01 0.06 0.2 11 -0.31 11 22
GDI1 0.017 0.062 -10000 0 -0.25 22 22
TP53 0.002 0.064 0.2 1 -0.3 17 18
RPS6KA5 0.018 0.059 -10000 0 -0.25 19 19
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 21 21
MEF2A 0.017 0.058 -10000 0 -0.25 18 18
EIF4EBP1 -0.001 0.092 -10000 0 -0.2 82 82
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 0.098 -10000 0 -0.2 95 95
p38alpha-beta/MAPKAPK2 0.053 0.077 -10000 0 -0.24 16 16
p38alpha-beta/MAPKAPK3 0.055 0.076 -10000 0 -0.25 14 14
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 0.2 3 -0.093 3 6
CD40LG 0.034 0.1 0.29 22 -0.24 1 23
PTGS2 0.014 0.09 0.3 12 -0.27 5 17
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 -10000 0 -0.1 2 2
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 -0.14 1 9
FOS 0.028 0.022 0.099 1 0 207 208
IFNG 0.024 0.097 0.31 15 -0.24 1 16
AP-1/NFAT1-c-4 0.084 0.12 -10000 0 -0.23 3 3
FASLG 0.031 0.1 0.29 20 -0.24 2 22
NFAT1-c-4/ICER1 0.053 0.058 0.21 8 -0.12 1 9
IL2RA 0.031 0.1 0.31 18 -0.25 2 20
FKBP12/FK506 0.028 0.013 -10000 0 -0.13 2 2
CSF2 0.033 0.1 0.29 21 -0.24 1 22
JunB/Fra1/NFAT1-c-4 0.048 0.074 0.23 4 -0.16 5 9
IL4 0.032 0.1 0.3 20 -0.24 1 21
IL2 -0.039 0.23 -10000 0 -0.86 41 41
IL3 0.026 0.12 -10000 0 -0.58 21 21
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
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.49 11 -10000 0 11
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 0.006 0.061 0.2 20 -0.18 31 51
T-helper 2 cell differentiation -0.003 0.11 0.49 11 -10000 0 11
T cell proliferation during immune response -0.003 0.11 0.49 11 -10000 0 11
MAPKKK cascade 0.003 0.11 -10000 0 -0.49 11 11
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 -0.5 11 11
positive regulation of T cell mediated cytotoxicity 0.003 0.11 -10000 0 -0.49 11 11
STAT1 (dimer) 0.063 0.13 -10000 0 -0.81 3 3
JAK2 0.037 0.018 -10000 0 -0.037 1 1
JAK1 0.039 0.01 -10000 0 0 34 34
STAT2 (dimer) 0.02 0.13 -10000 0 -0.45 14 14
T cell proliferation 0.005 0.11 0.34 2 -0.46 12 14
IL12/IL12R/TYK2/JAK2 0.015 0.17 -10000 0 -0.7 26 26
IL17A 0.008 0.056 0.2 18 -0.17 28 46
mast cell activation -0.003 0.11 0.49 11 -10000 0 11
IFNG 0.013 0.03 0.1 1 -0.095 7 8
T cell differentiation -0.001 0.003 0.014 1 -0.017 6 7
STAT3 (dimer) 0.025 0.13 -10000 0 -0.43 14 14
STAT5A (dimer) 0.025 0.13 -10000 0 -0.45 13 13
STAT4 (dimer) 0.024 0.13 -10000 0 -0.46 12 12
STAT4 0.04 0.009 -10000 0 0 29 29
T cell activation -0.008 0.011 0.12 1 -0.046 32 33
IL27R/JAK2/TYK2 0.053 0.1 -10000 0 -0.94 3 3
GATA3 0.015 0.12 0.63 19 -10000 0 19
IL18 -0.006 0.006 0.002 178 -10000 0 178
positive regulation of mast cell cytokine production 0.025 0.13 -10000 0 -0.42 14 14
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 0 111 111
STAT5A 0.038 0.012 -10000 0 0 51 51
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.008 0.042 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 0.006 65 -10000 0 65
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 0.015 0.17 -10000 0 -0.68 14 14
NCK1/PAK1/Dok-R -0.029 0.072 -10000 0 -0.33 15 15
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 -0.079 4 4
TNIP2 0.038 0.012 -10000 0 0 49 49
NF kappa B/RelA 0.076 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 0.12 -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 52 52
mol:NO 0.03 0.15 0.37 1 -0.5 16 17
PLG 0.031 0.076 -10000 0 -0.9 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.027 0.14 -10000 0 -0.75 6 6
GRB2 0.041 0.007 -10000 0 0 17 17
PIK3R1 0.034 0.017 -10000 0 0 108 108
ANGPT2 -0.045 0.29 -10000 0 -1 38 38
BMX 0.032 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 0.033 2 -0.062 2 4
Tie2/Ang1/GRB14 0.054 0.089 -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 45 45
STAT5A (dimer) 0.015 0.24 -10000 0 -0.8 39 39
mol:L-citrulline 0.03 0.15 0.37 1 -0.5 16 17
AGTR1 0.033 0.025 -10000 0 -0.016 103 103
MAPK14 0.041 0.12 -10000 0 -1 4 4
Tie2/SHP2 0.038 0.11 -10000 0 -0.76 3 3
TEK 0.03 0.11 -10000 0 -0.69 4 4
RPS6KB1 0.016 0.16 -10000 0 -0.66 11 11
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 84 84
MAPK8 0.031 0.08 -10000 0 -0.9 2 2
PI3K 0.017 0.16 -10000 0 -0.82 8 8
FES 0.043 0.11 -10000 0 -1 2 2
Crk/Dok-R 0.056 0.095 -10000 0 -0.88 2 2
Tie2/Ang1/ABIN2 0.056 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 -0.6 16 16
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 -0.67 8 8
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 -0.6 39 39
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 -0.017 0.047 -10000 0 -0.18 18 18
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 -0.54 10 11
ITGB1 0.039 0.011 -10000 0 0 38 38
NOS3 0.026 0.16 -10000 0 -0.58 14 14
RAC1 0.039 0.01 -10000 0 0 34 34
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 0.059 0.091 -10000 0 -0.91 2 2
NCK1 0.036 0.015 -10000 0 0 80 80
vasculogenesis 0.031 0.14 0.36 2 -0.41 27 29
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 0.03 0.15 0.37 1 -0.5 16 17
Rac1/GTP 0.029 0.15 -10000 0 -0.67 8 8
MMP2 0.033 0.087 -10000 0 -0.9 2 2
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 0.036 0.014 -10000 0 0 73 73
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 0.035 -10000 0 -0.18 19 19
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.037 0.014 -10000 0 0 70 70
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 0.046 0.041 -10000 0 -0.17 15 15
HIST2H4A -0.013 0.004 -10000 0 -10000 0 0
SIRT1/FOXO3a 0.036 0.048 0.15 58 -0.21 6 64
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 68 68
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 0.09 -10000 0 -0.15 163 163
SIRT1/FOXO4 0.009 0.075 -10000 0 -0.15 84 84
FOXO1/FHL2/SIRT1 0.046 0.025 -10000 0 -0.1 12 12
HIST1H1E -0.005 0.07 -10000 0 -0.21 53 53
SIRT1/p300 0.044 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 0.031 -10000 0 -0.13 8 8
ACSS2 -0.021 0.009 0.03 2 -10000 0 2
SIRT1/PCAF/MYOD 0.018 0.024 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 0.039 -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 0.062 -10000 0 -0.18 18 18
SUMO1/HDAC1 0.037 0.065 -10000 0 -0.18 25 25
RANGAP1 0.038 0.013 -10000 0 0 57 57
MDM2/SUMO1/SUMO1 0.083 0.056 -10000 0 -0.12 20 20
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.009 0.035 -10000 0 -0.15 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 27 27
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
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.034 0.054 -10000 0 -0.4 5 5
VEGFR1 homodimer/NRP1 0.008 0.046 -10000 0 -0.4 5 5
mol:DAG -0.024 0.039 0.19 1 -0.31 6 7
VEGFR1 homodimer/NRP1/VEGFR 121 0.007 0.042 -10000 0 -0.36 5 5
CaM/Ca2+ 0.025 0.053 -10000 0 -0.28 7 7
HIF1A 0.045 0.033 -10000 0 -0.28 5 5
GAB1 0.038 0.012 -10000 0 0 52 52
AKT1 0.001 0.09 0.23 6 -0.27 16 22
PLCG1 -0.024 0.04 0.2 1 -0.31 6 7
NOS3 0.026 0.071 0.32 3 -0.28 7 10
CBL 0.04 0.008 -10000 0 0 23 23
mol:NO 0.028 0.072 0.29 5 -0.27 7 12
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 -0.31 8 8
CALM1 0.04 0.01 -10000 0 0 31 31
PIK3CA 0.03 0.019 -10000 0 0 155 155
eNOS/Hsp90 0.021 0.069 0.3 3 -0.27 7 10
endothelial cell proliferation -0.003 0.066 0.29 2 -0.31 9 11
mol:Ca2+ -0.023 0.039 0.19 1 -0.31 6 7
MAPK3 -0.027 0.056 0.16 17 -0.28 6 23
MAPK1 -0.026 0.054 0.16 14 -0.25 9 23
PIK3R1 0.034 0.017 -10000 0 0 108 108
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 -0.4 5 5
platelet activating factor biosynthetic process -0.027 0.058 0.32 1 -0.3 5 6
PI3K 0.039 0.08 -10000 0 -0.24 16 16
PRKCA -0.021 0.046 0.22 4 -0.27 8 12
PRKCB -0.022 0.036 0.18 1 -0.29 6 7
VEGFR1 homodimer/PLGF homodimer 0.035 0.054 -10000 0 -0.4 5 5
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 80 80
eNOS/Caveolin-1 0.043 0.082 0.3 4 -0.27 7 11
PTPN11 0.04 0.009 -10000 0 0 27 27
mol:PI-3-4-5-P3 0.037 0.079 -10000 0 -0.24 16 16
mol:L-citrulline 0.028 0.072 0.29 5 -0.27 7 12
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.041 0.066 -10000 0 -0.27 10 10
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.024 0.058 -10000 0 -0.28 10 10
CD2AP 0.037 0.014 -10000 0 0 67 67
PI3K/GAB1 0.044 0.088 -10000 0 -0.24 17 17
PDPK1 0.001 0.091 0.17 85 -0.31 7 92
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.028 0.056 -10000 0 -0.28 10 10
mol:NADP 0.028 0.072 0.29 5 -0.27 7 12
HSP90AA1 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.04 0.065 -10000 0 -0.26 10 10
VEGFR1 homodimer/NRP2 0.028 0.058 -10000 0 -0.34 8 8
Arf1 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
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 0.045 -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 -0.12 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 0.012 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 0.079 25 -10000 0 25
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 0.011 0.06 1 -0.077 4 5
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 0.05 16 -0.1 2 18
Rac/GTP 0.029 0.011 -10000 0 -0.13 1 1
ARF1/GTP/GGA3/ARF-GAP1 0.044 0.026 -10000 0 -0.1 1 1
ARFIP2 0.035 0.019 -10000 0 -0.041 28 28
COPA 0.04 0.009 -10000 0 0 29 29
RAC1 0.039 0.01 -10000 0 0 34 34
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 0.008 -10000 0 0 19 19
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 0.012 6 -0.02 1 7
ARF1/GTP/GGA3 0.049 0.021 -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 -0.34 6 6
PLD2 0.01 0.016 0.08 25 -10000 0 25
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 0.079 25 -10000 0 25
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 0.041 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 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
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 0.022 0.09 -10000 0 -0.3 27 27
GNAO1 0.034 0.018 -10000 0 -0.002 108 108
PDGFB-D/PDGFRB/PLCgamma1 0.011 0.11 0.22 15 -0.27 38 53
PLCG1 0.006 0.097 0.21 12 -0.29 31 43
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 0.022 0.089 -10000 0 -0.3 27 27
MAPK3 0.009 0.1 -10000 0 -0.38 24 24
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 34 34
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 -0.65 17 17
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 0.022 0.089 -10000 0 -0.3 27 27
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 -0.41 21 21
S1P1/S1P/PDGFB-D/PDGFRB 0.034 0.072 -10000 0 -0.26 9 9
ABCC1 0.041 0.009 -10000 0 0 26 26
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.047 0.012 -10000 0 -0.085 3 3
NFATC2 0.048 0.18 0.41 5 -0.39 35 40
NFATC3 0.069 0.067 0.29 26 -0.26 2 28
CD40LG 0.083 0.15 0.49 5 -0.48 4 9
ITCH 0.021 0.057 0.2 6 -0.23 20 26
CBLB 0.019 0.061 0.2 6 -0.25 22 28
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment 0.047 0.14 0.38 2 -0.54 6 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 0.27 5 -0.41 47 52
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 -0.53 3 3
IKZF1 0.023 0.11 0.22 19 -0.26 35 54
T-helper 2 cell differentiation 0.035 0.14 0.45 2 -0.49 1 3
AP-1/NFAT1 0.038 0.14 0.32 2 -0.26 31 33
CALM1 0.042 0.036 -10000 0 -0.12 21 21
EGR2 0.06 0.16 0.54 11 -0.83 3 14
EGR3 0.053 0.14 0.56 7 -0.51 2 9
NFAT1/FOXP3 0.059 0.14 0.33 3 -0.28 32 35
EGR1 0.028 0.021 0.073 1 0 196 197
JUN 0.04 0.026 0.14 2 -0.048 7 9
EGR4 0.041 0.009 -10000 0 -0.004 20 20
mol:Ca2+ 0.005 0.022 -10000 0 -0.1 22 22
GBP3 -0.019 0.21 0.3 9 -0.46 91 100
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 7 -0.31 29 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 29 30
NFAT1-c-4 (dimer)/EGR1 0.062 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 -0.042 8 10
IFNG 0.036 0.13 -10000 0 -0.46 8 8
T cell activation 0.054 0.12 0.6 1 -10000 0 1
MAF 0.036 0.015 -10000 0 0 84 84
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.06 0.13 0.57 3 -0.49 26 29
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 0.096 1 -10000 0 1
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 -0.29 28 31
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 -0.45 8 8
IL2RA 0.05 0.15 0.39 1 -0.48 8 9
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.022 0.12 0.27 3 -0.32 28 31
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 -0.32 30 35
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 0.48 6 -0.48 4 10
JunB/Fra1/NFAT1-c-4 0.077 0.15 -10000 0 -0.46 3 3
IL4 0.034 0.14 -10000 0 -0.51 1 1
IL5 0.078 0.15 0.47 5 -0.48 4 9
IL2 0.054 0.12 0.6 1 -10000 0 1
IL3 0.037 0.079 -10000 0 -0.4 14 14
RNF128 0.023 0.045 0.2 7 -0.16 22 29
NFATC1 0.06 0.13 0.5 25 -0.57 3 28
CDK4 -0.078 0.28 0.39 1 -1.2 28 29
PTPRK 0.013 0.15 0.28 5 -0.4 43 48
IL8 0.048 0.14 0.55 4 -0.46 5 9
POU2F1 0.046 0.01 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
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 32 34
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 0.056 0.058 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 32 34
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 67 67
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 0.056 0.058 0.18 2 -0.13 5 7
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0 142 142
Aurora C signaling

Figure S126.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S126.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.042 0.004 -9999 0 0 5 5
Aurora C/Aurora B/INCENP 0.063 0.046 -9999 0 -0.11 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 81 81
AURKC 0.042 0.002 -9999 0 0 1 1
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK 0.04 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
Arf6 trafficking events

Figure S128.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S128.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 0.039 0.01 -10000 0 0 33 33
CLTC 0.015 0.089 0.22 2 -0.45 12 14
calcium ion-dependent exocytosis 0.017 0.045 0.18 2 -0.18 7 9
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 -0.36 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 0.004 0.035 -10000 0 -0.2 5 5
CTNND1 -0.006 0.072 0.18 57 -0.2 3 60
DNM2 0.037 0.014 -10000 0 0 72 72
mol:PI-4-5-P2 0.017 0.056 0.18 5 -0.24 12 17
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 0.004 0.035 -10000 0 -0.2 5 5
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 0.008 0.064 -10000 0 -0.36 11 11
ASAP2/amphiphysin II 0.048 0.024 -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 -0.38 10 10
clathrin-independent pinocytosis 0.028 0.019 -10000 0 -0.13 8 8
MAPK8IP3 0.04 0.009 -10000 0 0 27 27
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 -0.36 27 27
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 0.35 12 -10000 0 12
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 -10000 0 -0.18 8 8
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 0.23 3 -0.38 11 14
JIP4/KLC1 0.045 0.03 -10000 0 -0.098 18 18
EXOC1 0.038 0.012 -10000 0 0 47 47
exocyst 0.008 0.1 -10000 0 -0.37 27 27
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 -0.45 12 14
IL2RA 0.013 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 0.038 0.081 -10000 0 -0.32 13 13
EXOC6 0.038 0.012 -10000 0 0 55 55
PLD1 0 0.05 -10000 0 -0.2 29 29
PLD2 0.014 0.029 -10000 0 -0.19 5 5
EXOC5 0.04 0.009 -10000 0 0 27 27
PIP5K1C 0.012 0.05 0.17 4 -0.24 10 14
SDC1 0.01 0.061 -10000 0 -0.36 10 10
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 -10000 0 -0.36 12 12
mol:Phosphatidic acid 0.004 0.035 -10000 0 -0.2 5 5
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 1 -0.42 13 14
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 0.21 1 -0.43 12 13
RALA 0.04 0.009 -10000 0 0 30 30
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.021 0.091 -10000 0 -0.4 11 11
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 0.01 0.068 0.27 6 -0.4 2 8
CRKL 0.014 0.065 0.42 1 -0.42 2 3
HRAS 0.029 0.081 0.25 1 -0.33 4 5
mol:PIP3 0.023 0.089 0.36 1 -0.33 9 10
SPRED1 0.035 0.015 -10000 0 0 90 90
SPRED2 0.04 0.009 -10000 0 0 24 24
GAB1 0.018 0.061 -10000 0 -0.44 2 2
FOXO3 0.021 0.091 0.3 2 -0.36 13 15
AKT1 0.022 0.096 0.37 1 -0.39 13 14
BAD 0.017 0.092 0.35 1 -0.37 13 14
megakaryocyte differentiation 0.023 0.059 0.25 2 -0.3 1 3
GSK3B 0.021 0.098 0.32 8 -0.36 13 21
RAF1 0.021 0.076 0.27 5 -0.27 5 10
SHC1 0.04 0.01 -10000 0 0 31 31
STAT3 0.018 0.061 0.28 2 -0.44 2 4
STAT1 0.032 0.11 -10000 0 -0.87 3 3
HRAS/SPRED1 0.033 0.083 0.28 1 -0.31 4 5
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 0 115 115
RPS6KB1 0.021 0.099 0.3 1 -0.38 11 12
HRAS/SPRED2 0.04 0.084 0.28 1 -0.28 5 6
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 57 57
JAK2 0.029 0.11 -10000 0 -0.73 3 3
STAT1 (dimer) 0.031 0.12 -10000 0 -0.85 3 3
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 -10000 0 -0.5 5 5
PIK3R1 0.034 0.017 -10000 0 0 108 108
CBL/CRKL/GRB2 0.044 0.083 0.42 1 -0.43 2 3
PI3K 0.023 0.1 0.32 1 -0.35 12 13
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 0.063 0.25 2 -0.44 2 4
STAT3 (dimer) 0.02 0.063 0.28 2 -0.43 2 4
positive regulation of transcription 0.016 0.058 0.21 7 -0.2 5 12
mol:GDP 0.036 0.086 0.27 1 -0.3 5 6
PIK3C2B 0.019 0.066 0.26 3 -0.44 2 5
CBL/CRKL 0.03 0.077 0.42 1 -0.44 2 3
FER 0.018 0.061 0.26 1 -0.44 2 3
SH2B3 0.023 0.061 0.25 2 -0.43 2 4
PDPK1 0.022 0.087 0.28 5 -0.3 8 13
SNAI2 0.023 0.068 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 0.01 0.17 -10000 0 -0.56 31 31
STAT5A (dimer) 0.021 0.1 -10000 0 -0.51 5 5
SOCS1 0.038 0.012 -10000 0 0 50 50
cell migration -0.017 0.06 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 0.063 0.26 1 -0.44 2 3
PTPN11 0.038 0.011 -10000 0 -0.004 31 31
SCF/KIT 0.027 0.065 0.28 1 -0.45 2 3
GO:0007205 -0.002 0.004 -10000 0 -10000 0 0
MAP2K1 0.014 0.067 0.23 9 -0.24 3 12
CBL 0.04 0.008 -10000 0 0 23 23
KIT 0.017 0.16 -10000 0 -0.68 7 7
MAP2K2 0.013 0.063 0.23 5 -0.23 4 9
SHC/Grb2/SOS1 0.065 0.094 -10000 0 -0.33 4 4
STAT5A 0.023 0.1 -10000 0 -0.53 5 5
GRB2 0.041 0.007 -10000 0 0 17 17
response to radiation 0.027 0.071 0.26 6 -0.5 2 8
SHC/GRAP2 0.053 0.024 -10000 0 -0.14 1 1
PTPRO 0.02 0.056 0.25 2 -0.3 1 3
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 0.06 0.26 1 -0.44 2 3
CREBBP 0.059 0.029 0.15 3 -0.15 3 6
BCL2 -0.021 0.23 -10000 0 -0.64 40 40
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 51 51
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 29 29
mol:GMP (4 units) -0.002 0.06 0.19 49 -10000 0 49
Cone Transducin 0.067 0.031 -10000 0 -0.11 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 + 0.07 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 49 49
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 37 37
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 29 29
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 0.031 -10000 0 -0.14 7 7
SLC24A1 0.04 0.008 -10000 0 0 20 20
CNGA1 0.041 0.008 -10000 0 0 19 19
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 -0.11 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 -0.11 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/1708758/2.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/1768822/1.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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