PARADIGM pathway analysis of mRNA expression data
Overview
Introduction

PAthway Representation and Analysis by Direct Inference on Graphical Models (PARADIGM) predicts the activity of a diverse set of molecular concepts such as genes, complexes, and processes. The predicted activities are called Inferred Pathway Levels (IPLs) and are derived from a probabilistic belief propagation strategy that incorporates multimodal data such as copy number and gene expression estimates with a concept's pathway context.

Summary

There were 44 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
FOXM1 transcription factor network 8
HIF-1-alpha transcription factor network 7
TCGA08_retinoblastoma 7
IL23-mediated signaling events 5
Osteopontin-mediated events 4
IL4-mediated signaling events 4
Fc-epsilon receptor I signaling in mast cells 4
Endothelins 4
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 4
EGFR-dependent Endothelin signaling events 4
Results

The following list describes the columns found in Table 2.

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

  • Avg.Num.Perturbations = Average number of samples with perturbations across the pathway concepts determined by a background permutation model (>2 standard deviations away from the permuted distribution)

  • Total.Perturbations = Total number of perturbed concepts across all samples (>2 standard deviations away from the permuted distribution)

  • Num.Entities = Number of concepts that belong to the pathway

  • Min.Mean.Truth = Minimum IPL for concepts in the pathway among real samples

  • Max.Mean.Truth = Maximum IPL for concepts in the pathway among real samples

  • Min.Mean.Within = Minimum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Max.Mean.Within = Maximum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Min.Mean.Any = Minimum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes)

  • Max.Mean.Any = Maximum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes).

Table 2.  Get Full Table This summary table provides a report of cancer type specific pathway perturbations. Click on the links in the first column to display more detailed results for each pathway.

Pathway.Name Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
FOXM1 transcription factor network 8 439 51 -0.74 0.019 1000 -1000 -0.174 -1000
HIF-1-alpha transcription factor network 7 558 76 -0.776 0.028 1000 -1000 -0.119 -1000
TCGA08_retinoblastoma 7 59 8 -0.246 0.092 1000 -1000 -0.021 -1000
IL23-mediated signaling events 5 317 60 -0.635 0.017 1000 -1000 -0.17 -1000
Osteopontin-mediated events 4 182 38 -0.425 0.016 1000 -1000 -0.128 -1000
IL4-mediated signaling events 4 448 91 -0.83 0.671 1000 -1000 -0.132 -1000
Fc-epsilon receptor I signaling in mast cells 4 404 97 -0.361 0.053 1000 -1000 -0.113 -1000
Endothelins 4 447 96 -0.385 0.016 1000 -1000 -0.076 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 4 296 68 -0.605 0.175 1000 -1000 -0.127 -1000
EGFR-dependent Endothelin signaling events 4 95 21 -0.257 0.016 1000 -1000 -0.087 -1000
IL12-mediated signaling events 3 271 87 -0.297 0.016 1000 -1000 -0.126 -1000
PLK2 and PLK4 events 3 10 3 -0.092 0.016 1000 -1000 -0.028 -1000
Visual signal transduction: Cones 3 132 38 -0.249 0.016 1000 -1000 -0.079 -1000
Signaling events mediated by the Hedgehog family 3 197 52 -0.35 0.212 1000 -1000 -0.109 -1000
Syndecan-2-mediated signaling events 3 217 69 -0.291 0.041 1000 -1000 -0.067 -1000
amb2 Integrin signaling 3 250 82 -0.25 0.016 1000 -1000 -0.113 -1000
Ephrin B reverse signaling 3 168 48 -0.246 0.116 1000 -1000 -0.094 -1000
Calcium signaling in the CD4+ TCR pathway 3 106 31 -0.357 0.026 1000 -1000 -0.089 -1000
IL27-mediated signaling events 3 183 51 -0.324 0.157 1000 -1000 -0.103 -1000
Wnt signaling 3 22 7 -0.201 0.016 1000 -1000 -0.032 -1000
Plasma membrane estrogen receptor signaling 3 263 86 -0.235 0.126 1000 -1000 -0.106 -1000
Caspase cascade in apoptosis 2 149 74 -0.133 0.067 1000 -1000 -0.048 -1000
Syndecan-1-mediated signaling events 2 90 34 -0.324 0.016 1000 -1000 -0.071 -1000
Noncanonical Wnt signaling pathway 2 56 26 -0.201 0.016 1000 -1000 -0.108 -1000
Thromboxane A2 receptor signaling 2 223 105 -0.175 0.027 1000 -1000 -0.091 -1000
Arf6 signaling events 2 179 62 -0.233 0.021 1000 -1000 -0.076 -1000
FOXA2 and FOXA3 transcription factor networks 2 112 46 -0.332 0.026 1000 -1000 -0.065 -1000
BMP receptor signaling 2 228 81 -0.412 0.04 1000 -1000 -0.12 -1000
Nectin adhesion pathway 2 169 63 -0.207 0.016 1000 -1000 -0.09 -1000
Glucocorticoid receptor regulatory network 2 264 114 -0.524 0.116 1000 -1000 -0.084 -1000
IL1-mediated signaling events 2 147 62 -0.215 0.074 1000 -1000 -0.116 -1000
TCGA08_p53 2 20 7 -0.188 0.084 1000 -1000 -0.019 -1000
FAS signaling pathway (CD95) 2 99 47 -0.235 0.028 1000 -1000 -0.062 -1000
Syndecan-3-mediated signaling events 2 101 35 -0.291 0.016 1000 -1000 -0.086 -1000
Signaling mediated by p38-alpha and p38-beta 2 109 44 -0.207 0.016 1000 -1000 -0.056 -1000
Integrins in angiogenesis 2 204 84 -0.266 0.016 1000 -1000 -0.119 -1000
EPHB forward signaling 2 197 85 -0.164 0.134 1000 -1000 -0.116 -1000
Glypican 2 network 2 9 4 -0.058 0 1000 -1000 -0.025 -1000
Signaling events mediated by VEGFR1 and VEGFR2 2 361 125 -0.225 0.016 1000 -1000 -0.132 -1000
IL6-mediated signaling events 2 176 75 -0.533 0.047 1000 -1000 -0.093 -1000
BCR signaling pathway 2 290 99 -0.27 0.051 1000 -1000 -0.117 -1000
Syndecan-4-mediated signaling events 2 136 67 -0.158 0.018 1000 -1000 -0.101 -1000
Visual signal transduction: Rods 2 149 52 -0.341 0.016 1000 -1000 -0.104 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 2 188 78 -0.179 0.072 1000 -1000 -0.092 -1000
Coregulation of Androgen receptor activity 1 89 76 -0.25 0.047 1000 -1000 -0.065 -1000
ErbB4 signaling events 1 103 69 -0.508 0.11 1000 -1000 -0.105 -1000
Sphingosine 1-phosphate (S1P) pathway 1 35 28 -0.076 0.016 1000 -1000 -0.058 -1000
Ephrin A reverse signaling 1 9 7 -0.026 0.007 1000 -1000 -0.044 -1000
Cellular roles of Anthrax toxin 1 68 39 -0.081 0.016 1000 -1000 -0.036 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 1 159 85 -0.131 0.016 1000 -1000 -0.097 -1000
Signaling events mediated by PTP1B 1 139 76 -0.223 0.092 1000 -1000 -0.093 -1000
Presenilin action in Notch and Wnt signaling 1 77 61 -0.275 0.039 1000 -1000 -0.094 -1000
p75(NTR)-mediated signaling 1 139 125 -0.307 0.04 1000 -1000 -0.104 -1000
Glypican 1 network 1 67 48 -0.078 0.025 1000 -1000 -0.06 -1000
PLK1 signaling events 1 96 85 -0.162 0.025 1000 -1000 -0.056 -1000
mTOR signaling pathway 1 74 53 -0.091 0.034 1000 -1000 -0.08 -1000
Ceramide signaling pathway 1 103 76 -0.133 0.052 1000 -1000 -0.068 -1000
Reelin signaling pathway 1 61 56 -0.104 0.024 1000 -1000 -0.107 -1000
TRAIL signaling pathway 1 90 48 -0.085 0.021 1000 -1000 -0.088 -1000
Signaling events regulated by Ret tyrosine kinase 1 94 82 -0.104 0.022 1000 -1000 -0.101 -1000
RXR and RAR heterodimerization with other nuclear receptor 1 61 52 -0.158 0.027 1000 -1000 -0.084 -1000
HIF-2-alpha transcription factor network 1 72 43 -0.293 0.154 1000 -1000 -0.107 -1000
S1P1 pathway 1 71 36 -0.202 0.016 1000 -1000 -0.087 -1000
TCR signaling in naïve CD8+ T cells 1 165 93 -0.145 0.022 1000 -1000 -0.097 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 1 65 45 -0.131 0.039 1000 -1000 -0.104 -1000
Canonical Wnt signaling pathway 1 68 51 -0.275 0.069 1000 -1000 -0.075 -1000
Effects of Botulinum toxin 1 35 26 -0.11 0.016 1000 -1000 -0.08 -1000
TCGA08_rtk_signaling 1 38 26 -0.175 0.029 1000 -1000 -0.023 -1000
LPA receptor mediated events 1 160 102 -0.259 0.016 1000 -1000 -0.085 -1000
Stabilization and expansion of the E-cadherin adherens junction 1 80 74 -0.183 0.04 1000 -1000 -0.119 -1000
Regulation of Telomerase 1 124 102 -0.234 0.054 1000 -1000 -0.113 -1000
IGF1 pathway 1 66 57 -0.075 0.031 1000 -1000 -0.115 -1000
Insulin Pathway 1 138 74 -0.216 0.019 1000 -1000 -0.111 -1000
VEGFR1 specific signals 1 63 56 -0.066 0.016 1000 -1000 -0.103 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 1 47 33 -0.292 0.033 1000 -1000 -0.095 -1000
Signaling events mediated by PRL 1 47 34 -0.172 0.029 1000 -1000 -0.057 -1000
E-cadherin signaling in keratinocytes 1 56 43 -0.175 0.03 1000 -1000 -0.086 -1000
Class IB PI3K non-lipid kinase events 1 3 3 -0.001 -1000 1000 -1000 -0.018 -1000
E-cadherin signaling events 1 9 5 -0.05 -0.001 1000 -1000 -0.058 -1000
Ras signaling in the CD4+ TCR pathway 1 22 17 -0.03 0.016 1000 -1000 -0.046 -1000
Aurora B signaling 1 107 67 -0.163 0.016 1000 -1000 -0.091 -1000
LPA4-mediated signaling events 0 7 12 0 0.026 1000 -1000 -0.029 -1000
ErbB2/ErbB3 signaling events 0 22 65 -0.025 0.057 1000 -1000 -0.087 -1000
Regulation of nuclear SMAD2/3 signaling 0 132 136 -0.231 0.2 1000 -1000 -0.085 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0 8 23 -0.025 0.047 1000 -1000 -0.091 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0 11 34 -0.093 0.043 1000 -1000 -0.08 -1000
Canonical NF-kappaB pathway 0 19 39 -0.071 0.075 1000 -1000 -0.103 -1000
Signaling events mediated by HDAC Class II 0 56 75 -0.235 0.038 1000 -1000 -0.07 -1000
BARD1 signaling events 0 29 57 -0.052 0.047 1000 -1000 -0.09 -1000
Circadian rhythm pathway 0 15 22 -0.175 0.054 1000 -1000 -0.053 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0 26 54 -0.065 0.033 1000 -1000 -0.127 -1000
JNK signaling in the CD4+ TCR pathway 0 7 17 -0.014 0.037 1000 -1000 -0.083 -1000
a4b1 and a4b7 Integrin signaling 0 0 5 0 0.016 1000 -1000 -0.048 -1000
Hedgehog signaling events mediated by Gli proteins 0 59 65 -0.321 0.055 1000 -1000 -0.076 -1000
Aurora A signaling 0 44 60 -0.119 0.041 1000 -1000 -0.08 -1000
Arf6 downstream pathway 0 17 43 -0.028 0.021 1000 -1000 -0.055 -1000
Aurora C signaling 0 5 7 -0.052 0 1000 -1000 -0.06 -1000
EPO signaling pathway 0 24 55 -0.047 0.07 1000 -1000 -0.11 -1000
Insulin-mediated glucose transport 0 5 32 -0.058 0.051 1000 -1000 -0.07 -1000
PDGFR-alpha signaling pathway 0 39 44 -0.122 0.046 1000 -1000 -0.084 -1000
IFN-gamma pathway 0 45 68 -0.19 0.032 1000 -1000 -0.126 -1000
Class I PI3K signaling events mediated by Akt 0 60 68 -0.058 0.041 1000 -1000 -0.088 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0 11 37 -0.033 0.043 1000 -1000 -0.071 -1000
Signaling events mediated by HDAC Class III 0 20 40 -0.158 0.029 1000 -1000 -0.058 -1000
S1P5 pathway 0 4 17 -0.016 0.016 1000 -1000 -0.057 -1000
ceramide signaling pathway 0 23 49 -0.133 0.031 1000 -1000 -0.054 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0 28 83 -0.058 0.079 1000 -1000 -0.102 -1000
Signaling events mediated by HDAC Class I 0 10 104 -0.086 0.069 1000 -1000 -0.088 -1000
FoxO family signaling 0 57 64 -0.244 0.073 1000 -1000 -0.078 -1000
Signaling mediated by p38-gamma and p38-delta 0 6 15 -0.031 0.029 1000 -1000 -0.041 -1000
Retinoic acid receptors-mediated signaling 0 53 58 -0.093 0.035 1000 -1000 -0.099 -1000
Paxillin-dependent events mediated by a4b1 0 12 36 -0.033 0.05 1000 -1000 -0.089 -1000
Atypical NF-kappaB pathway 0 6 31 -0.018 0.048 1000 -1000 -0.05 -1000
IL2 signaling events mediated by PI3K 0 32 58 -0.074 0.063 1000 -1000 -0.108 -1000
Regulation of p38-alpha and p38-beta 0 28 54 -0.11 0.046 1000 -1000 -0.074 -1000
Nongenotropic Androgen signaling 0 49 52 -0.033 0.027 1000 -1000 -0.084 -1000
E-cadherin signaling in the nascent adherens junction 0 63 76 -0.051 0.045 1000 -1000 -0.104 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 4 27 -0.022 0.041 1000 -1000 -0.074 -1000
IL2 signaling events mediated by STAT5 0 15 22 -0.073 0.039 1000 -1000 -0.051 -1000
Class I PI3K signaling events 0 43 73 -0.058 0.029 1000 -1000 -0.061 -1000
Arf6 trafficking events 0 25 71 -0.039 0.037 1000 -1000 -0.094 -1000
S1P3 pathway 0 26 42 -0.075 0.041 1000 -1000 -0.045 -1000
Angiopoietin receptor Tie2-mediated signaling 0 50 88 -0.183 0.08 1000 -1000 -0.141 -1000
Rapid glucocorticoid signaling 0 13 20 -0.035 0.016 1000 -1000 -0.051 -1000
Neurotrophic factor-mediated Trk receptor signaling 0 113 120 -0.168 0.164 1000 -1000 -0.098 -1000
PDGFR-beta signaling pathway 0 36 97 -0.075 0.056 1000 -1000 -0.107 -1000
S1P4 pathway 0 7 25 -0.016 0.025 1000 -1000 -0.062 -1000
p38 MAPK signaling pathway 0 36 44 -0.124 0.02 1000 -1000 -0.084 -1000
Arf1 pathway 0 5 54 -0.03 0.034 1000 -1000 -0.063 -1000
Alternative NF-kappaB pathway 0 4 13 -0.012 0.016 1000 -1000 -0.088 -1000
Regulation of Androgen receptor activity 0 61 70 -0.261 0.061 1000 -1000 -0.082 -1000
Total 167 13090 7203 -24.3814090675 -993.56866729 131000 -131000 -11.0476341771 -131000
FOXM1 transcription factor network

Figure 1.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 3.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.467 0.628 -9999 0 -1.153 12 12
PLK1 0.019 0.063 -9999 0 -9999 0 0
BIRC5 -0.154 0.474 -9999 0 -1.562 3 3
HSPA1B -0.477 0.628 -9999 0 -1.162 12 12
MAP2K1 0.011 0.041 -9999 0 -9999 0 0
BRCA2 -0.485 0.651 -9999 0 -1.2 12 12
FOXM1 -0.649 0.845 -9999 0 -1.598 12 12
XRCC1 -0.492 0.646 -9999 0 -1.166 13 13
FOXM1B/p19 -0.74 0.612 -9999 0 -1.317 15 15
Cyclin D1/CDK4 -0.503 0.595 -9999 0 -1.084 13 13
CDC2 -0.512 0.679 -9999 0 -1.259 12 12
TGFA -0.493 0.594 -9999 0 -1.037 14 14
SKP2 -0.477 0.641 -9999 0 -1.203 11 11
CCNE1 -0.056 0.18 -9999 0 -0.532 4 4
CKS1B -0.474 0.63 -9999 0 -1.175 11 11
RB1 -0.233 0.197 -9999 0 -0.634 2 2
FOXM1C/SP1 -0.554 0.721 -9999 0 -1.361 12 12
AURKB 0.004 0.115 -9999 0 -9999 0 0
CENPF -0.551 0.704 -9999 0 -1.341 12 12
CDK4 0.011 0.017 -9999 0 -9999 0 0
MYC -0.39 0.549 -9999 0 -0.994 11 11
CHEK2 -0.066 0.221 -9999 0 -0.635 4 4
ONECUT1 -0.549 0.648 -9999 0 -1.159 14 14
CDKN2A -0.252 0.349 -9999 0 -0.693 12 12
LAMA4 -0.483 0.647 -9999 0 -1.196 12 12
FOXM1B/HNF6 -0.685 0.8 -9999 0 -1.452 14 14
FOS -0.516 0.652 -9999 0 -1.185 13 13
SP1 0.017 0.001 -9999 0 -9999 0 0
CDC25B -0.467 0.628 -9999 0 -1.153 12 12
response to radiation -0.01 0.039 -9999 0 -9999 0 0
CENPB -0.467 0.628 -9999 0 -1.175 11 11
CENPA -0.563 0.717 -9999 0 -1.358 12 12
NEK2 -0.602 0.739 -9999 0 -1.341 14 14
HIST1H2BA -0.485 0.633 -9999 0 -1.179 12 12
CCNA2 -0.039 0.161 -9999 0 -0.54 3 3
EP300 0.016 0 -9999 0 -9999 0 0
CCNB1/CDK1 -0.632 0.822 -9999 0 -1.614 11 11
CCNB2 -0.477 0.641 -9999 0 -1.203 11 11
CCNB1 -0.559 0.738 -9999 0 -1.385 12 12
ETV5 -0.476 0.641 -9999 0 -1.2 11 11
ESR1 -0.594 0.68 -9999 0 -1.247 15 15
CCND1 -0.519 0.616 -9999 0 -1.12 13 13
GSK3A 0.018 0.03 -9999 0 -9999 0 0
Cyclin A-E1/CDK1-2 -0.047 0.184 -9999 0 -0.631 2 2
CDK2 0.012 0.011 -9999 0 -9999 0 0
G2/M transition of mitotic cell cycle -0.013 0.047 -9999 0 -9999 0 0
FOXM1B/Cbp/p300 -0.615 0.578 -9999 0 -1.289 12 12
GAS1 -0.563 0.691 -9999 0 -1.277 13 13
MMP2 -0.496 0.654 -9999 0 -1.21 12 12
RB1/FOXM1C -0.525 0.624 -9999 0 -1.142 13 13
CREBBP 0.016 0 -9999 0 -9999 0 0
HIF-1-alpha transcription factor network

Figure 2.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 4.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.52 0.692 -9999 0 -1.352 11 11
HDAC7 -0.001 0.013 -9999 0 -9999 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.392 0.45 -9999 0 -0.98 9 9
SMAD4 0.018 0.001 -9999 0 -9999 0 0
ID2 -0.532 0.696 -9999 0 -1.363 11 11
AP1 -0.1 0.257 -9999 0 -0.538 7 7
ABCG2 -0.539 0.719 -9999 0 -1.407 11 11
HIF1A -0.071 0.166 -9999 0 -0.617 2 2
TFF3 -0.675 0.724 -9999 0 -1.377 14 14
GATA2 0.015 0.01 -9999 0 -9999 0 0
AKT1 -0.047 0.095 -9999 0 -9999 0 0
response to hypoxia -0.072 0.103 -9999 0 -9999 0 0
MCL1 -0.525 0.701 -9999 0 -1.366 11 11
NDRG1 -0.584 0.726 -9999 0 -1.386 12 12
SERPINE1 -0.58 0.726 -9999 0 -1.397 12 12
FECH -0.524 0.699 -9999 0 -1.363 11 11
FURIN -0.541 0.692 -9999 0 -1.368 11 11
NCOA2 0.018 0.001 -9999 0 -9999 0 0
EP300 -0.045 0.142 -9999 0 -0.379 1 1
HMOX1 -0.553 0.721 -9999 0 -1.33 13 13
BHLHE40 -0.529 0.691 -9999 0 -1.361 11 11
BHLHE41 -0.529 0.691 -9999 0 -1.361 11 11
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.053 0.094 -9999 0 -9999 0 0
ENG 0.001 0.134 -9999 0 -9999 0 0
JUN -0.059 0.232 -9999 0 -0.78 3 3
RORA -0.52 0.692 -9999 0 -1.352 11 11
ABCB1 -0.094 0.08 -9999 0 -9999 0 0
TFRC -0.554 0.717 -9999 0 -1.411 11 11
CXCR4 -0.533 0.713 -9999 0 -1.39 11 11
TF -0.564 0.728 -9999 0 -1.392 12 12
CITED2 -0.538 0.716 -9999 0 -1.406 11 11
HIF1A/ARNT -0.776 0.951 -9999 0 -1.88 11 11
LDHA -0.051 0.049 -9999 0 -9999 0 0
ETS1 -0.541 0.697 -9999 0 -1.323 12 12
PGK1 -0.526 0.7 -9999 0 -1.371 11 11
NOS2 -0.529 0.691 -9999 0 -1.361 11 11
ITGB2 -0.537 0.721 -9999 0 -1.404 11 11
ALDOA -0.52 0.692 -9999 0 -1.352 11 11
Cbp/p300/CITED2 -0.564 0.689 -9999 0 -1.411 11 11
FOS -0.077 0.219 -9999 0 -0.578 5 5
HK2 -0.52 0.692 -9999 0 -1.352 11 11
SP1 0.028 0.001 -9999 0 -9999 0 0
GCK -0.107 0.351 -9999 0 -1.15 2 2
HK1 -0.52 0.692 -9999 0 -1.352 11 11
NPM1 -0.52 0.692 -9999 0 -1.352 11 11
EGLN1 -0.525 0.7 -9999 0 -1.368 11 11
CREB1 0.026 0 -9999 0 -9999 0 0
PGM1 -0.532 0.703 -9999 0 -1.366 11 11
SMAD3 0.018 0.001 -9999 0 -9999 0 0
EDN1 -0.183 0.435 -9999 0 -1.059 5 5
IGFBP1 -0.554 0.707 -9999 0 -1.402 11 11
VEGFA -0.291 0.452 -9999 0 -0.892 7 7
HIF1A/JAB1 -0.049 0.108 -9999 0 -0.447 2 2
CP -0.673 0.706 -9999 0 -1.536 11 11
CXCL12 -0.562 0.714 -9999 0 -1.357 12 12
COPS5 0.018 0.001 -9999 0 -9999 0 0
SMAD3/SMAD4 0 0 -9999 0 -9999 0 0
BNIP3 -0.537 0.712 -9999 0 -1.401 11 11
EGLN3 -0.65 0.761 -9999 0 -1.469 13 13
CA9 -0.572 0.703 -9999 0 -1.405 11 11
TERT -0.52 0.692 -9999 0 -1.352 11 11
ENO1 -0.52 0.692 -9999 0 -1.352 11 11
PFKL -0.52 0.692 -9999 0 -1.352 11 11
NCOA1 -0.008 0.137 -9999 0 -0.773 1 1
ADM -0.586 0.754 -9999 0 -1.452 12 12
ARNT -0.035 0.087 -9999 0 -9999 0 0
HNF4A 0.017 0.015 -9999 0 -9999 0 0
ADFP -0.556 0.743 -9999 0 -1.456 11 11
SLC2A1 -0.313 0.458 -9999 0 -0.955 6 6
LEP -0.541 0.701 -9999 0 -1.332 12 12
HIF1A/ARNT/Cbp/p300 -0.402 0.445 -9999 0 -0.981 9 9
EPO -0.179 0.341 -9999 0 -0.708 1 1
CREBBP -0.045 0.142 -9999 0 -0.379 1 1
HIF1A/ARNT/Cbp/p300/HDAC7 -0.416 0.44 -9999 0 -0.999 9 9
PFKFB3 -0.526 0.7 -9999 0 -1.371 11 11
NT5E -0.554 0.724 -9999 0 -1.371 12 12
TCGA08_retinoblastoma

Figure 3.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 5.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.028 0.156 -9999 0 -0.624 2 2
CDKN2C 0.036 0.03 -9999 0 -9999 0 0
CDKN2A -0.246 0.342 -9999 0 -0.68 12 12
CCND2 0.08 0.12 0.245 9 -9999 0 9
RB1 -0.087 0.129 -9999 0 -0.265 9 9
CDK4 0.092 0.134 0.28 9 -9999 0 9
CDK6 0.091 0.136 0.277 9 -9999 0 9
G1/S progression 0.074 0.137 0.265 9 -9999 0 9
IL23-mediated signaling events

Figure 4.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 6.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.433 0.557 -9999 0 -1.196 8 8
IL23A -0.517 0.633 -9999 0 -1.337 9 9
NF kappa B1 p50/RelA/I kappa B alpha -0.468 0.494 -9999 0 -1.137 9 9
positive regulation of T cell mediated cytotoxicity -0.461 0.599 -9999 0 -1.232 9 9
ITGA3 -0.475 0.6 -9999 0 -1.227 10 10
IL17F -0.235 0.362 -9999 0 -0.732 5 5
IL12B -0.025 0.169 -9999 0 -0.653 2 2
STAT1 (dimer) -0.445 0.586 -9999 0 -1.252 8 8
CD4 -0.387 0.511 -9999 0 -1.106 7 7
IL23 -0.511 0.594 -9999 0 -1.289 9 9
IL23R -0.026 0.097 -9999 0 -9999 0 0
IL1B -0.528 0.644 -9999 0 -1.259 12 12
T-helper cell lineage commitment 0 0 -9999 0 -9999 0 0
IL24 -0.387 0.511 -9999 0 -1.106 7 7
TYK2 0.009 0.022 -9999 0 -9999 0 0
STAT4 -0.001 0.094 -9999 0 -0.526 1 1
STAT3 0.017 0.001 -9999 0 -9999 0 0
IL18RAP -0.071 0.231 -9999 0 -0.67 4 4
IL12RB1 -0.016 0.143 -9999 0 -0.802 1 1
PIK3CA 0.017 0.001 -9999 0 -9999 0 0
IL12Rbeta1/TYK2 -0.013 0.113 -9999 0 -0.618 1 1
IL23R/JAK2 -0.031 0.122 -9999 0 -9999 0 0
positive regulation of chronic inflammatory response -0.461 0.599 -9999 0 -1.232 9 9
natural killer cell activation 0.003 0.009 -9999 0 -9999 0 0
JAK2 0.017 0.029 -9999 0 -9999 0 0
PIK3R1 -0.008 0.137 -9999 0 -0.773 1 1
NFKB1 0.014 0.005 -9999 0 -9999 0 0
RELA 0.014 0.005 -9999 0 -9999 0 0
positive regulation of dendritic cell antigen processing and presentation -0.473 0.558 -9999 0 -1.191 9 9
ALOX12B -0.387 0.511 -9999 0 -1.106 7 7
CXCL1 -0.635 0.676 -9999 0 -1.288 15 15
T cell proliferation -0.461 0.599 -9999 0 -1.232 9 9
NFKBIA 0.014 0.005 -9999 0 -9999 0 0
IL17A -0.185 0.316 -9999 0 -0.639 2 2
PI3K -0.454 0.493 -9999 0 -1.114 9 9
IFNG -0.047 0.063 -9999 0 -0.131 9 9
STAT3 (dimer) -0.419 0.461 -9999 0 -1.114 7 7
IL18R1 -0.061 0.202 -9999 0 -0.587 4 4
IL23/IL23R/JAK2/TYK2/SOCS3 -0.215 0.324 -9999 0 -0.89 2 2
IL18/IL18R -0.137 0.26 -9999 0 -0.583 7 7
macrophage activation -0.025 0.019 -9999 0 -0.047 5 5
TNF -0.47 0.595 -9999 0 -1.285 8 8
STAT3/STAT4 -0.463 0.495 -9999 0 -1.1 10 10
STAT4 (dimer) -0.443 0.576 -9999 0 -1.195 9 9
IL18 -0.077 0.244 -9999 0 -0.714 4 4
IL19 -0.402 0.538 -9999 0 -1.178 7 7
STAT5A (dimer) -0.436 0.57 -9999 0 -1.216 8 8
STAT1 -0.008 0.137 -9999 0 -0.773 1 1
SOCS3 -0.025 0.164 -9999 0 -0.65 2 2
CXCL9 -0.548 0.652 -9999 0 -1.282 12 12
MPO -0.399 0.519 -9999 0 -1.132 7 7
positive regulation of humoral immune response -0.461 0.599 -9999 0 -1.232 9 9
IL23/IL23R/JAK2/TYK2 -0.491 0.659 -9999 0 -1.384 8 8
IL6 -0.474 0.58 -9999 0 -1.23 9 9
STAT5A 0.016 0 -9999 0 -9999 0 0
IL2 -0.009 0.139 -9999 0 -0.78 1 1
positive regulation of tyrosine phosphorylation of STAT protein 0.003 0.009 -9999 0 -9999 0 0
CD3E -0.387 0.511 -9999 0 -1.106 7 7
keratinocyte proliferation -0.461 0.599 -9999 0 -1.232 9 9
NOS2 -0.397 0.51 -9999 0 -1.047 9 9
Osteopontin-mediated events

Figure 5.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 7.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.22 0.253 -9999 0 -0.578 6 6
NF kappa B1 p50/RelA/I kappa B alpha -0.205 0.257 -9999 0 -0.622 5 5
alphaV/beta3 Integrin/Osteopontin/Src -0.229 0.302 -9999 0 -0.564 13 13
AP1 -0.289 0.33 -9999 0 -0.761 7 7
ILK -0.227 0.256 -9999 0 -0.578 6 6
bone resorption -0.19 0.284 -9999 0 -0.847 3 3
PTK2B 0.016 0 -9999 0 -9999 0 0
PYK2/p130Cas -0.229 0.238 -9999 0 -0.872 2 2
ITGAV -0.035 0.196 -9999 0 -0.793 2 2
mol:GTP 0 0 -9999 0 -9999 0 0
CD44/Rho Family GTPase/ROCK2 -0.03 0.119 -9999 0 -0.478 2 2
alphaV/beta3 Integrin/Osteopontin -0.278 0.26 -9999 0 -0.566 11 11
MAP3K1 -0.241 0.258 -9999 0 -0.514 11 11
JUN -0.058 0.23 -9999 0 -0.774 3 3
MAPK3 -0.241 0.27 -9999 0 -0.631 6 6
MAPK1 -0.241 0.27 -9999 0 -0.631 6 6
Rac1/GDP 0 0 -9999 0 -9999 0 0
NFKB1 0.016 0 -9999 0 -9999 0 0
MAPK8 -0.22 0.248 -9999 0 -0.556 6 6
ITGB3 -0.113 0.247 -9999 0 -0.572 7 7
NFKBIA -0.24 0.28 -9999 0 -0.696 5 5
FOS -0.077 0.218 -9999 0 -0.576 5 5
CD44 -0.025 0.164 -9999 0 -0.65 2 2
CHUK 0.016 0 -9999 0 -9999 0 0
PLAU -0.425 0.496 -9999 0 -1.151 8 8
NF kappa B1 p50/RelA -0.247 0.228 -9999 0 -0.649 5 5
BCAR1 0.016 0 -9999 0 -9999 0 0
RELA 0.016 0 -9999 0 -9999 0 0
alphaV beta3 Integrin -0.13 0.216 -9999 0 -0.475 8 8
mol:GDP 0 0 -9999 0 -9999 0 0
SYK -0.242 0.284 -9999 0 -0.553 11 11
VAV3 -0.258 0.294 -9999 0 -0.643 8 8
MAP3K14 -0.244 0.269 -9999 0 -0.531 11 11
ROCK2 0.016 0 -9999 0 -9999 0 0
SPP1 -0.25 0.35 -9999 0 -0.693 12 12
RAC1 0.016 0 -9999 0 -9999 0 0
Rac1/GTP -0.25 0.249 -9999 0 -0.735 4 4
MMP2 -0.245 0.288 -9999 0 -0.68 7 7
IL4-mediated signaling events

Figure 6.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 8.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.567 0.551 -9999 0 -1.356 8 8
STAT6 (cleaved dimer) -0.589 0.555 -9999 0 -1.231 11 11
IGHG1 -0.197 0.17 -9999 0 -0.618 1 1
IGHG3 -0.555 0.526 -9999 0 -1.17 11 11
AKT1 -0.262 0.281 -9999 0 -0.812 4 4
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.175 0.194 -9999 0 -0.578 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.302 0.305 -9999 0 -0.873 4 4
THY1 -0.572 0.562 -9999 0 -1.377 8 8
MYB -0.018 0.131 -9999 0 -0.526 2 2
HMGA1 -0.001 0.094 -9999 0 -0.526 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.326 0.305 -9999 0 -0.834 5 5
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.272 0.312 -9999 0 -0.855 4 4
SP1 0.023 0.009 -9999 0 -9999 0 0
INPP5D 0 0 -9999 0 -9999 0 0
SOCS5 0.032 0.017 -9999 0 -9999 0 0
STAT6 (dimer)/ETS1 -0.582 0.57 -9999 0 -1.253 11 11
SOCS1 -0.34 0.326 -9999 0 -0.804 7 7
SOCS3 -0.29 0.343 -9999 0 -0.979 4 4
FCER2 -0.416 0.397 -9999 0 -1.086 5 5
PARP14 -0.007 0.138 -9999 0 -0.773 1 1
CCL17 -0.76 0.632 -9999 0 -1.386 14 14
GRB2 0.016 0 -9999 0 -9999 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.212 0.225 -9999 0 -0.814 2 2
T cell proliferation -0.571 0.577 -9999 0 -1.332 9 9
IL4R/JAK1 -0.575 0.576 -9999 0 -1.288 10 10
EGR2 -0.609 0.599 -9999 0 -1.433 9 9
JAK2 -0.009 0.021 -9999 0 -9999 0 0
JAK3 0.02 0.012 -9999 0 -9999 0 0
PIK3R1 -0.008 0.137 -9999 0 -0.773 1 1
JAK1 -0.018 0.135 -9999 0 -0.769 1 1
COL1A2 -0.258 0.408 -9999 0 -1.198 4 4
CCL26 -0.73 0.645 -9999 0 -1.41 13 13
IL4R -0.621 0.612 -9999 0 -1.377 10 10
PTPN6 0.029 0.012 -9999 0 -9999 0 0
IL13RA2 -0.73 0.668 -9999 0 -1.439 13 13
IL13RA1 -0.027 0.1 -9999 0 -0.57 1 1
IRF4 -0.219 0.417 -9999 0 -1.317 3 3
ARG1 -0.253 0.371 -9999 0 -1.076 4 4
CBL -0.296 0.292 -9999 0 -0.842 4 4
GTF3A 0 0.097 -9999 0 -0.52 1 1
PIK3CA 0.016 0 -9999 0 -9999 0 0
IL13RA1/JAK2 -0.028 0.077 -9999 0 -0.426 1 1
IRF4/BCL6 -0.213 0.387 -9999 0 -1.209 3 3
CD40LG -0.021 0.176 -9999 0 -0.699 2 2
MAPK14 -0.299 0.309 -9999 0 -0.821 5 5
mitosis -0.249 0.261 -9999 0 -0.753 4 4
STAT6 -0.741 0.864 -9999 0 -1.65 11 11
SPI1 -0.037 0.192 -9999 0 -0.769 2 2
RPS6KB1 -0.233 0.251 -9999 0 -0.778 3 3
STAT6 (dimer) -0.746 0.877 -9999 0 -1.663 11 11
STAT6 (dimer)/PARP14 -0.621 0.648 -9999 0 -1.417 10 10
mast cell activation 0.013 0.011 -9999 0 -9999 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.267 0.301 -9999 0 -0.877 4 4
FRAP1 -0.262 0.281 -9999 0 -0.812 4 4
LTA -0.567 0.551 -9999 0 -1.254 10 10
FES 0.016 0 -9999 0 -9999 0 0
T-helper 1 cell differentiation 0.671 0.691 1.451 11 -9999 0 11
CCL11 -0.687 0.664 -9999 0 -1.509 11 11
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.234 0.237 -9999 0 -0.678 4 4
IL2RG 0.02 0.012 -9999 0 -9999 0 0
IL10 -0.567 0.551 -9999 0 -1.254 10 10
IRS1 -0.099 0.272 -9999 0 -0.724 5 5
IRS2 -0.042 0.186 -9999 0 -0.608 3 3
IL4 -0.138 0.154 -9999 0 -0.713 1 1
IL5 -0.567 0.551 -9999 0 -1.3 9 9
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.45 0.394 -9999 0 -0.927 10 10
COL1A1 -0.38 0.533 -9999 0 -1.265 7 7
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -9999 0 0
IL4/IL4R/JAK1 -0.593 0.61 -9999 0 -1.471 8 8
IL2R gamma/JAK3 0.024 0.018 -9999 0 -9999 0 0
TFF3 -0.83 0.668 -9999 0 -1.542 13 13
ALOX15 -0.567 0.551 -9999 0 -1.356 8 8
MYBL1 -0.001 0.094 -9999 0 -0.526 1 1
T-helper 2 cell differentiation -0.469 0.456 -9999 0 -1.008 10 10
SHC1 -0.001 0.094 -9999 0 -0.526 1 1
CEBPB -0.007 0.112 -9999 0 -0.605 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.265 0.302 -9999 0 -0.914 3 3
mol:PI-3-4-5-P3 -0.263 0.281 -9999 0 -0.813 4 4
PI3K -0.278 0.31 -9999 0 -0.892 4 4
DOK2 -0.058 0.23 -9999 0 -0.773 3 3
ETS1 -0.011 0.159 -9999 0 -0.613 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.193 0.214 -9999 0 -0.763 2 2
ITGB3 -0.613 0.582 -9999 0 -1.397 9 9
PIGR -0.596 0.593 -9999 0 -1.472 8 8
IGHE 0.034 0.068 -9999 0 -9999 0 0
MAPKKK cascade -0.19 0.209 -9999 0 -0.742 2 2
BCL6 -0.009 0.138 -9999 0 -0.775 1 1
OPRM1 -0.6 0.563 -9999 0 -1.302 10 10
RETNLB -0.582 0.547 -9999 0 -1.275 10 10
SELP -0.589 0.571 -9999 0 -1.41 8 8
AICDA -0.56 0.523 -9999 0 -1.205 10 10
Fc-epsilon receptor I signaling in mast cells

Figure 7.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 9.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.001 0.094 -9999 0 -0.526 1 1
LAT2 -0.169 0.251 -9999 0 -0.632 5 5
AP1 -0.214 0.246 -9999 0 -0.587 7 7
mol:PIP3 -0.193 0.271 -9999 0 -0.663 5 5
IKBKB -0.089 0.144 -9999 0 -0.307 5 5
AKT1 -0.193 0.28 -9999 0 -0.684 5 5
IKBKG -0.089 0.144 -9999 0 -0.319 4 4
MS4A2 -0.245 0.343 -9999 0 -0.676 12 12
mol:Sphingosine-1-phosphate 0 0 -9999 0 -9999 0 0
PIK3CA 0.015 0.002 -9999 0 -9999 0 0
MAP3K1 -0.127 0.213 -9999 0 -0.524 4 4
mol:Ca2+ -0.139 0.198 -9999 0 -0.46 5 5
LYN 0.011 0.008 -9999 0 -9999 0 0
CBLB -0.167 0.248 -9999 0 -0.625 5 5
SHC1 -0.001 0.094 -9999 0 -0.526 1 1
RasGAP/p62DOK -0.06 0.145 -9999 0 -0.462 3 3
positive regulation of cell migration -0.005 0.106 -9999 0 -0.596 1 1
INPP5D 0 0 -9999 0 -9999 0 0
PLD2 -0.26 0.319 -9999 0 -0.595 12 12
PTPN13 -0.263 0.295 -9999 0 -0.591 12 12
PTPN11 0.008 0.011 -9999 0 -9999 0 0
GO:0007205 0 0 -9999 0 -9999 0 0
regulation of mast cell degranulation -0.103 0.184 -9999 0 -0.425 4 4
SYK -0.014 0.138 -9999 0 -0.781 1 1
GRB2 0.016 0.001 -9999 0 -9999 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.236 0.247 -9999 0 -0.693 5 5
LAT -0.167 0.248 -9999 0 -0.625 5 5
PAK2 -0.144 0.249 -9999 0 -0.57 5 5
NFATC2 -0.087 0.082 -9999 0 -9999 0 0
HRAS -0.17 0.285 -9999 0 -0.586 7 7
GAB2 0.016 0 -9999 0 -9999 0 0
PLA2G1B 0.032 0.044 -9999 0 -9999 0 0
Fc epsilon R1 -0.35 0.364 -9999 0 -0.696 14 14
Antigen/IgE/Fc epsilon R1 -0.323 0.341 -9999 0 -0.645 14 14
mol:GDP -0.185 0.308 -9999 0 -0.639 7 7
JUN -0.058 0.23 -9999 0 -0.773 3 3
mol:Ca++ 0 0 -9999 0 -9999 0 0
PIK3R1 -0.01 0.138 -9999 0 -0.78 1 1
FOS -0.076 0.218 -9999 0 -0.575 5 5
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.186 0.262 -9999 0 -0.57 7 7
CHUK -0.089 0.144 -9999 0 -0.319 4 4
KLRG1 -0.167 0.242 -9999 0 -0.605 5 5
VAV1 -0.181 0.261 -9999 0 -0.62 6 6
calcium-dependent protein kinase C activity 0 0 -9999 0 -9999 0 0
CBL -0.167 0.248 -9999 0 -0.625 5 5
negative regulation of mast cell degranulation -0.173 0.206 -9999 0 -0.557 5 5
BTK -0.193 0.329 -9999 0 -0.724 6 6
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.281 0.359 -9999 0 -0.645 13 13
GAB2/PI3K/SHP2 -0.252 0.293 -9999 0 -0.787 5 5
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.197 0.27 -9999 0 -0.719 5 5
RAF1 0.043 0.033 -9999 0 -9999 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.343 0.348 -9999 0 -0.683 14 14
FCER1G -0.006 0.143 -9999 0 -0.8 1 1
FCER1A -0.305 0.351 -9999 0 -0.667 15 15
Antigen/IgE/Fc epsilon R1/Fyn -0.299 0.322 -9999 0 -0.602 14 14
MAPK3 0.053 0.028 -9999 0 -9999 0 0
MAPK1 0.053 0.028 -9999 0 -9999 0 0
NFKB1 0.016 0 -9999 0 -9999 0 0
MAPK8 -0.019 0.064 -9999 0 -9999 0 0
DUSP1 -0.075 0.244 -9999 0 -0.712 4 4
NF-kappa-B/RelA -0.067 0.065 -9999 0 -9999 0 0
actin cytoskeleton reorganization -0.158 0.241 -9999 0 -0.607 5 5
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -9999 0 0
PI3K -0.182 0.25 -9999 0 -0.63 5 5
FER -0.167 0.248 -9999 0 -0.625 5 5
RELA 0.016 0 -9999 0 -9999 0 0
ITK -0.079 0.177 -9999 0 -0.742 2 2
SOS1 0.016 0 -9999 0 -9999 0 0
PLCG1 -0.182 0.301 -9999 0 -0.622 7 7
cytokine secretion -0.049 0.047 -9999 0 -9999 0 0
SPHK1 -0.214 0.26 -9999 0 -0.607 7 7
PTK2 -0.166 0.257 -9999 0 -0.645 5 5
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.249 0.263 -9999 0 -0.738 5 5
EDG1 -0.005 0.106 -9999 0 -0.597 1 1
mol:DAG -0.19 0.268 -9999 0 -0.612 6 6
MAP2K2 0.048 0.029 -9999 0 -9999 0 0
MAP2K1 0.048 0.029 -9999 0 -9999 0 0
MAP2K7 0.016 0 -9999 0 -9999 0 0
KLRG1/SHP2 -0.174 0.21 -9999 0 -0.609 4 4
MAP2K4 0.016 0.013 -9999 0 -9999 0 0
Fc epsilon R1/FcgammaRIIB -0.361 0.364 -9999 0 -0.718 14 14
mol:Choline -0.254 0.31 -9999 0 -0.582 12 12
SHC/Grb2/SOS1 -0.177 0.218 -9999 0 -0.554 6 6
FYN 0.016 0 -9999 0 -9999 0 0
DOK1 0.016 0 -9999 0 -9999 0 0
PXN -0.145 0.232 -9999 0 -0.578 5 5
HCLS1 -0.192 0.291 -9999 0 -0.646 6 6
PRKCB -0.137 0.196 -9999 0 -0.428 6 6
FCGR2B -0.067 0.225 -9999 0 -0.65 4 4
IGHE -0.006 0.009 -9999 0 -9999 0 0
KLRG1/SHIP -0.177 0.213 -9999 0 -0.574 5 5
LCP2 -0.009 0.138 -9999 0 -0.777 1 1
PLA2G4A -0.29 0.315 -9999 0 -0.617 12 12
RASA1 -0.001 0.094 -9999 0 -0.526 1 1
mol:Phosphatidic acid -0.254 0.31 -9999 0 -0.582 12 12
IKK complex -0.052 0.115 -9999 0 -0.255 1 1
WIPF1 0.016 0 -9999 0 -9999 0 0
Endothelins

Figure 8.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 10.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.063 0.304 -9999 0 -0.648 5 5
PTK2B 0.016 0.001 -9999 0 -9999 0 0
mol:Ca2+ -0.216 0.38 -9999 0 -0.808 7 7
EDN1 -0.071 0.325 -9999 0 -0.678 6 6
EDN3 -0.11 0.242 -9999 0 -0.561 7 7
EDN2 -0.341 0.348 -9999 0 -0.657 17 17
HRAS/GDP -0.085 0.244 -9999 0 -0.487 6 6
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.086 0.218 -9999 0 -0.411 7 7
ADCY4 -0.083 0.274 -9999 0 -0.639 5 5
ADCY5 -0.1 0.284 -9999 0 -0.637 6 6
ADCY6 -0.097 0.277 -9999 0 -0.639 5 5
ADCY7 -0.092 0.273 -9999 0 -0.639 5 5
ADCY1 -0.083 0.274 -9999 0 -0.639 5 5
ADCY2 -0.083 0.274 -9999 0 -0.639 5 5
ADCY3 -0.083 0.274 -9999 0 -0.639 5 5
ADCY8 -0.092 0.273 -9999 0 -0.639 5 5
ADCY9 -0.1 0.288 -9999 0 -0.637 6 6
arachidonic acid secretion -0.158 0.269 -9999 0 -0.549 8 8
ETB receptor/Endothelin-1/Gq/GTP -0.077 0.214 -9999 0 -0.437 6 6
GNAO1 0.016 0 -9999 0 -9999 0 0
HRAS 0.016 0.001 -9999 0 -9999 0 0
ETA receptor/Endothelin-1/G12/GTP -0.034 0.322 0.35 8 -0.61 5 13
ETA receptor/Endothelin-1/Gs/GTP -0.056 0.334 0.377 5 -0.633 6 11
mol:GTP -0.004 0.008 -9999 0 -9999 0 0
COL3A1 -0.094 0.389 -9999 0 -1.116 3 3
EDNRB 0.011 0.029 -9999 0 -9999 0 0
response to oxidative stress 0 0 -9999 0 -9999 0 0
CYSLTR2 -0.078 0.345 -9999 0 -0.944 3 3
CYSLTR1 -0.112 0.375 -9999 0 -0.898 4 4
SLC9A1 -0.025 0.161 0.215 4 -0.353 3 7
mol:GDP -0.101 0.259 -9999 0 -0.529 6 6
SLC9A3 -0.148 0.374 -9999 0 -0.826 6 6
RAF1 -0.094 0.232 -9999 0 -0.485 6 6
JUN -0.179 0.397 -9999 0 -1.216 3 3
JAK2 -0.063 0.304 -9999 0 -0.648 5 5
mol:IP3 -0.096 0.219 -9999 0 -0.44 6 6
ETA receptor/Endothelin-1 -0.051 0.39 0.454 6 -0.743 5 11
PLCB1 -0.035 0.191 -9999 0 -0.774 2 2
PLCB2 -0.011 0.137 -9999 0 -0.772 1 1
ETA receptor/Endothelin-3 -0.104 0.24 -9999 0 -0.586 5 5
FOS -0.095 0.279 -9999 0 -0.736 3 3
Gai/GDP -0.008 0.189 -9999 0 -0.982 1 1
CRK 0.016 0.001 -9999 0 -9999 0 0
mol:Ca ++ -0.144 0.336 -9999 0 -0.678 7 7
BCAR1 0.016 0.001 -9999 0 -9999 0 0
PRKCB1 -0.116 0.245 -9999 0 -0.52 6 6
GNAQ -0.004 0.01 -9999 0 -9999 0 0
GNAZ 0.016 0 -9999 0 -9999 0 0
GNAL -0.025 0.164 -9999 0 -0.65 2 2
Gs family/GDP -0.155 0.218 -9999 0 -0.524 7 7
ETA receptor/Endothelin-1/Gq/GTP -0.089 0.249 -9999 0 -0.483 6 6
MAPK14 -0.066 0.184 -9999 0 -0.501 3 3
TRPC6 -0.231 0.405 -9999 0 -0.868 7 7
GNAI2 -0.008 0.137 -9999 0 -0.773 1 1
GNAI3 0.016 0 -9999 0 -9999 0 0
GNAI1 -0.008 0.137 -9999 0 -0.773 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.078 0.195 -9999 0 -0.435 5 5
ETB receptor/Endothelin-2 -0.25 0.262 -9999 0 -0.485 17 17
ETB receptor/Endothelin-3 -0.077 0.177 -9999 0 -0.403 7 7
ETB receptor/Endothelin-1 -0.061 0.255 -9999 0 -0.646 4 4
MAPK3 -0.099 0.274 -9999 0 -0.646 4 4
MAPK1 -0.099 0.274 -9999 0 -0.646 4 4
Rac1/GDP -0.085 0.244 -9999 0 -0.487 6 6
cAMP biosynthetic process -0.068 0.253 -9999 0 -0.544 6 6
MAPK8 -0.167 0.339 -9999 0 -0.667 7 7
SRC 0.016 0.001 -9999 0 -9999 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.011 0.183 -9999 0 -0.629 2 2
p130Cas/CRK/Src/PYK2 -0.142 0.291 -9999 0 -0.577 7 7
mol:K + 0 0 -9999 0 -9999 0 0
G12/GDP -0.085 0.244 -9999 0 -0.487 6 6
COL1A2 -0.112 0.428 -9999 0 -1.222 3 3
EntrezGene:2778 0 0 -9999 0 -9999 0 0
ETA receptor/Endothelin-2 -0.269 0.304 -9999 0 -0.58 12 12
mol:DAG -0.096 0.219 -9999 0 -0.44 6 6
MAP2K2 -0.092 0.247 -9999 0 -0.539 5 5
MAP2K1 -0.092 0.247 -9999 0 -0.539 5 5
EDNRA -0.021 0.203 -9999 0 -0.538 2 2
positive regulation of muscle contraction -0.052 0.269 -9999 0 -0.7 3 3
Gq family/GDP -0.161 0.226 -9999 0 -0.545 6 6
HRAS/GTP -0.098 0.224 -9999 0 -0.467 6 6
PRKCH -0.095 0.229 -9999 0 -0.54 4 4
RAC1 0.016 0 -9999 0 -9999 0 0
PRKCA -0.109 0.239 -9999 0 -0.528 5 5
PRKCB -0.094 0.21 -9999 0 -0.425 6 6
PRKCE -0.086 0.21 -9999 0 -0.476 4 4
PRKCD -0.087 0.211 -9999 0 -0.478 4 4
PRKCG -0.101 0.228 -9999 0 -0.499 5 5
regulation of vascular smooth muscle contraction -0.109 0.312 -9999 0 -0.827 3 3
PRKCQ -0.086 0.21 -9999 0 -0.477 4 4
PLA2G4A -0.174 0.293 -9999 0 -0.601 8 8
GNA14 -0.079 0.243 -9999 0 -0.714 4 4
GNA15 -0.047 0.185 -9999 0 -0.61 3 3
GNA12 0.016 0 -9999 0 -9999 0 0
GNA11 0.011 0.009 -9999 0 -9999 0 0
Rac1/GTP -0.034 0.322 0.402 5 -0.741 3 8
MMP1 -0.385 0.514 -9999 0 -0.899 14 14
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

Figure 9.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 11.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.022 0.009 -9999 0 -9999 0 0
NFATC2 -0.095 0.274 -9999 0 -1.306 1 1
NFATC3 -0.051 0.108 -9999 0 -9999 0 0
CD40LG -0.486 0.51 -9999 0 -1.023 13 13
ITCH -0.062 0.141 -9999 0 -9999 0 0
CBLB -0.062 0.141 -9999 0 -9999 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.307 0.423 -9999 0 -1.266 4 4
JUNB 0.016 0 -9999 0 -9999 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.121 0.142 -9999 0 -9999 0 0
T cell anergy -0.133 0.24 -9999 0 -0.498 7 7
TLE4 -0.063 0.291 -9999 0 -1.558 1 1
Jun/NFAT1-c-4/p21SNFT -0.351 0.52 -9999 0 -1.311 6 6
AP-1/NFAT1-c-4 -0.593 0.681 -9999 0 -1.321 12 12
IKZF1 -0.063 0.291 -9999 0 -1.558 1 1
T-helper 2 cell differentiation -0.102 0.231 -9999 0 -0.759 2 2
AP-1/NFAT1 -0.189 0.344 -9999 0 -0.739 7 7
CALM1 -0.044 0.09 -9999 0 -9999 0 0
EGR2 -0.283 0.599 -9999 0 -1.457 5 5
EGR3 -0.371 0.69 -9999 0 -1.586 7 7
NFAT1/FOXP3 -0.05 0.211 -9999 0 -1.047 1 1
EGR1 -0.233 0.348 -9999 0 -0.704 11 11
JUN -0.08 0.225 -9999 0 -0.773 3 3
EGR4 -0.002 0.013 -9999 0 -9999 0 0
mol:Ca2+ -0.066 0.098 -9999 0 -9999 0 0
GBP3 -0.278 0.494 -9999 0 -0.99 10 10
FOSL1 -0.018 0.131 -9999 0 -0.526 2 2
NFAT1-c-4/MAF/IRF4 -0.313 0.451 -9999 0 -1.118 6 6
DGKA -0.047 0.211 -9999 0 -1.042 1 1
CREM 0.016 0.001 -9999 0 -9999 0 0
NFAT1-c-4/PPARG -0.364 0.524 -9999 0 -1.103 9 9
CTLA4 -0.031 0.183 -9999 0 -0.914 1 1
NFAT1-c-4 (dimer)/EGR1 -0.4 0.589 -9999 0 -1.323 8 8
NFAT1-c-4 (dimer)/EGR4 -0.28 0.464 -9999 0 -1.132 6 6
FOS -0.103 0.227 -9999 0 -0.621 5 5
IFNG -0.408 0.592 -9999 0 -1.333 8 8
T cell activation -0.204 0.373 -9999 0 -1.031 4 4
MAF -0.008 0.137 -9999 0 -0.771 1 1
T-helper 2 cell lineage commitment 0 0 -9999 0 -9999 0 0
activation-induced cell death of T cells 0.175 0.32 0.76 6 -9999 0 6
TNF -0.343 0.478 -9999 0 -1.08 8 8
FASLG -0.429 0.706 -9999 0 -1.398 10 10
TBX21 -0.113 0.271 -9999 0 -0.728 5 5
BATF3 0 0.001 -9999 0 -9999 0 0
PRKCQ 0.012 0.022 -9999 0 -9999 0 0
PTPN1 -0.047 0.211 -9999 0 -1.042 1 1
NFAT1-c-4/ICER1 -0.271 0.463 -9999 0 -1.127 6 6
GATA3 0.002 0.094 -9999 0 -0.522 1 1
T-helper 1 cell differentiation -0.389 0.556 -9999 0 -1.262 8 8
IL2RA -0.318 0.428 -9999 0 -1.067 6 6
T-helper 1 cell lineage commitment 0 0 -9999 0 -9999 0 0
CASP3 -0.047 0.211 -9999 0 -1.042 1 1
E2F1 0.008 0.094 -9999 0 -0.517 1 1
PPARG -0.158 0.308 -9999 0 -0.68 8 8
SLC3A2 -0.047 0.211 -9999 0 -1.042 1 1
IRF4 -0.084 0.237 -9999 0 -0.624 5 5
PTGS2 -0.552 0.558 -9999 0 -1.159 13 13
CSF2 -0.546 0.557 -9999 0 -1.108 14 14
JunB/Fra1/NFAT1-c-4 -0.267 0.45 -9999 0 -1.022 7 7
IL4 -0.106 0.24 -9999 0 -0.796 2 2
IL5 -0.465 0.501 -9999 0 -1.058 11 11
IL2 -0.211 0.389 -9999 0 -1.073 4 4
IL3 -0.048 0.06 -9999 0 -9999 0 0
RNF128 -0.263 0.382 -9999 0 -0.674 14 14
NFATC1 -0.176 0.322 -9999 0 -0.763 6 6
CDK4 0.12 0.219 0.727 1 -9999 0 1
PTPRK -0.047 0.211 -9999 0 -1.042 1 1
IL8 -0.605 0.543 -9999 0 -1.132 14 14
POU2F1 0.026 0 -9999 0 -9999 0 0
EGFR-dependent Endothelin signaling events

Figure 10.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 12.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.016 0 -9999 0 -9999 0 0
EGFR -0.175 0.312 -9999 0 -0.663 9 9
EGF/EGFR -0.257 0.287 -9999 0 -0.578 13 13
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.175 0.231 -9999 0 -0.519 8 8
mol:GTP 0 0 -9999 0 -9999 0 0
EDNRA -0.059 0.203 -9999 0 -0.588 4 4
response to oxidative stress 0 0 -9999 0 -9999 0 0
EGF -0.126 0.274 -9999 0 -0.632 7 7
EGF/EGFR dimer/SHC -0.208 0.269 -9999 0 -0.607 8 8
mol:GDP -0.172 0.228 -9999 0 -0.512 8 8
mol:Ca2+ 0 0 -9999 0 -9999 0 0
EDN1 -0.092 0.255 -9999 0 -0.674 5 5
GRB2/SOS1 0 0 -9999 0 -9999 0 0
HRAS/GTP -0.157 0.21 -9999 0 -0.623 3 3
SHC1 -0.001 0.094 -9999 0 -0.526 1 1
HRAS/GDP -0.16 0.213 -9999 0 -0.631 3 3
FRAP1 -0.13 0.24 -9999 0 -0.641 3 3
EGF/EGFR dimer -0.233 0.298 -9999 0 -0.533 14 14
SOS1 0.016 0 -9999 0 -9999 0 0
GRB2 0.016 0 -9999 0 -9999 0 0
ETA receptor/Endothelin-1 -0.131 0.217 -9999 0 -0.466 9 9
IL12-mediated signaling events

Figure 11.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 13.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.015 0.153 -9999 0 -0.62 1 1
TBX21 -0.206 0.526 -9999 0 -1.262 5 5
B2M 0.015 0.011 -9999 0 -9999 0 0
TYK2 0.016 0.02 -9999 0 -9999 0 0
IL12RB1 -0.009 0.143 -9999 0 -0.795 1 1
GADD45B -0.152 0.397 -9999 0 -1.11 3 3
IL12RB2 -0.068 0.204 -9999 0 -0.539 5 5
GADD45G -0.285 0.576 -9999 0 -1.207 8 8
natural killer cell activation 0 0.024 -9999 0 -9999 0 0
RELB -0.001 0.094 -9999 0 -0.526 1 1
RELA 0.016 0 -9999 0 -9999 0 0
IL18 -0.074 0.245 -9999 0 -0.712 4 4
IL2RA -0.075 0.244 -9999 0 -0.712 4 4
IFNG -0.192 0.316 -9999 0 -0.65 10 10
STAT3 (dimer) -0.125 0.352 -9999 0 -0.728 6 6
HLA-DRB5 -0.009 0.137 -9999 0 -0.773 1 1
FASLG -0.212 0.535 -9999 0 -1.08 7 7
NF kappa B2 p52/RelB -0.214 0.331 -9999 0 -0.819 6 6
CD4 0.015 0.006 -9999 0 -9999 0 0
SOCS1 0.016 0 -9999 0 -9999 0 0
EntrezGene:6955 -0.003 0.015 -9999 0 -9999 0 0
CD3D -0.028 0.167 -9999 0 -0.665 2 2
CD3E 0.014 0.012 -9999 0 -9999 0 0
CD3G -0.087 0.24 -9999 0 -0.632 5 5
IL12Rbeta2/JAK2 -0.037 0.156 -9999 0 -0.391 5 5
CCL3 -0.138 0.388 -9999 0 -0.876 5 5
CCL4 -0.159 0.403 -9999 0 -0.919 5 5
HLA-A -0.01 0.137 -9999 0 -0.772 1 1
IL18/IL18R -0.11 0.269 -9999 0 -0.561 7 7
NOS2 -0.148 0.37 -9999 0 -0.733 7 7
IL12/IL12R/TYK2/JAK2/SPHK2 -0.021 0.164 -9999 0 -0.511 2 2
IL1R1 -0.191 0.483 -9999 0 -1.073 6 6
IL4 -0.016 0.133 -9999 0 -0.525 2 2
JAK2 0.016 0.02 -9999 0 -9999 0 0
EntrezGene:6957 -0.003 0.014 -9999 0 -9999 0 0
TCR/CD3/MHC I/CD8 -0.091 0.288 -9999 0 -0.77 4 4
RAB7A -0.139 0.36 -9999 0 -0.825 4 4
lysosomal transport -0.13 0.343 -9999 0 -0.733 5 5
FOS -0.14 0.362 -9999 0 -0.847 5 5
STAT4 (dimer) -0.168 0.406 -9999 0 -0.843 6 6
STAT5A (dimer) -0.297 0.404 -9999 0 -0.916 8 8
GZMA -0.149 0.383 -9999 0 -0.776 7 7
GZMB -0.181 0.48 -9999 0 -1.051 6 6
HLX 0.016 0 -9999 0 -9999 0 0
LCK -0.169 0.43 -9999 0 -0.954 6 6
TCR/CD3/MHC II/CD4 -0.064 0.249 -9999 0 -0.632 4 4
IL2/IL2R -0.065 0.154 -9999 0 -0.453 4 4
MAPK14 -0.194 0.448 -9999 0 -0.912 7 7
CCR5 -0.153 0.409 -9999 0 -1.173 3 3
IL1B -0.152 0.301 -9999 0 -0.661 8 8
STAT6 -0.043 0.182 -9999 0 -0.429 3 3
STAT4 -0.001 0.094 -9999 0 -0.526 1 1
STAT3 0.016 0 -9999 0 -9999 0 0
STAT1 -0.008 0.137 -9999 0 -0.773 1 1
NFKB1 0.016 0 -9999 0 -9999 0 0
NFKB2 0.016 0 -9999 0 -9999 0 0
IL12B -0.023 0.166 -9999 0 -0.647 2 2
CD8A -0.002 0.014 -9999 0 -9999 0 0
CD8B -0.02 0.139 -9999 0 -0.555 2 2
T-helper 1 cell differentiation 0 0 -9999 0 -9999 0 0
natural killer cell mediated cytotoxicity 0.015 0.152 0.614 1 -9999 0 1
IL2RB 0.016 0 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.15 0.373 -9999 0 -0.762 6 6
IL2RG 0.016 0 -9999 0 -9999 0 0
IL12 -0.006 0.131 -9999 0 -0.611 1 1
STAT5A 0.016 0 -9999 0 -9999 0 0
CD247 -0.045 0.184 -9999 0 -0.605 3 3
IL2 -0.008 0.137 -9999 0 -0.773 1 1
SPHK2 -0.001 0.094 -9999 0 -0.526 1 1
FRAP1 0.016 0 -9999 0 -9999 0 0
IL12A 0.016 0.02 -9999 0 -9999 0 0
IL12/IL12R/TYK2/JAK2 -0.174 0.438 -9999 0 -0.887 7 7
MAP2K3 -0.193 0.442 -9999 0 -0.895 7 7
RIPK2 -0.018 0.131 -9999 0 -0.526 2 2
MAP2K6 -0.202 0.459 -9999 0 -0.934 7 7
regulation of dendritic cell antigen processing and presentation 0 0 -9999 0 -9999 0 0
HLA-DRA -0.01 0.137 -9999 0 -0.773 1 1
IL18RAP -0.066 0.226 -9999 0 -0.651 4 4
IL12Rbeta1/TYK2 0.003 0.115 -9999 0 -0.612 1 1
EOMES -0.062 0.27 -9999 0 -1.352 1 1
STAT1 (dimer) -0.233 0.443 -9999 0 -0.856 9 9
T cell proliferation -0.129 0.309 -9999 0 -0.604 7 7
T-helper 1 cell lineage commitment 0 0 -9999 0 -9999 0 0
IL18R1 -0.059 0.206 -9999 0 -0.596 4 4
CD8-positive alpha-beta T cell lineage commitment 0 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelA -0.241 0.287 -9999 0 -0.73 6 6
ATF2 -0.167 0.407 -9999 0 -0.819 7 7
PLK2 and PLK4 events

Figure 12.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 14.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.092 0.255 -9999 0 -0.674 5 5
PLK4 0.016 0 -9999 0 -9999 0 0
regulation of centriole replication -0.054 0.196 -9999 0 -0.499 5 5
Visual signal transduction: Cones

Figure 13.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 15.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.022 0.087 -9999 0 -0.438 1 1
RGS9BP -0.109 0.265 -9999 0 -0.65 6 6
mol:GTP 0 0 -9999 0 -9999 0 0
GRK1 0 0 -9999 0 -9999 0 0
mol:Na + -0.218 0.276 -9999 0 -0.498 14 14
mol:ADP -0.005 0.106 -9999 0 -0.596 1 1
GNAT2 0.016 0 -9999 0 -9999 0 0
RGS9-1/Gbeta5/R9AP -0.169 0.302 -9999 0 -0.686 7 7
mol:GDP 0 0 -9999 0 -9999 0 0
PDE6H/GNAT2/GTP -0.01 0.055 -9999 0 -0.314 1 1
GRK7 -0.009 0.137 -9999 0 -0.773 1 1
CNGB3 -0.077 0.218 -9999 0 -0.575 5 5
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -9999 0 0
mol:Ca2+ -0.18 0.266 -9999 0 -0.549 9 9
Cone PDE6 -0.193 0.335 -9999 0 -0.747 7 7
Cone Metarhodopsin II -0.015 0.084 -9999 0 -0.481 1 1
Na + (4 Units) -0.196 0.251 -9999 0 -0.545 9 9
GNAT2/GDP -0.146 0.265 -9999 0 -0.598 7 7
GNB5 -0.042 0.186 -9999 0 -0.608 3 3
mol:GMP (4 units) -0.029 0.143 -9999 0 -0.462 2 2
Cone Transducin -0.023 0.092 -9999 0 -0.462 1 1
SLC24A2 0.016 0 -9999 0 -9999 0 0
GNB3/GNGT2 -0.03 0.119 -9999 0 -0.478 2 2
GNB3 0.016 0 -9999 0 -9999 0 0
GNAT2/GTP 0 0 -9999 0 -9999 0 0
CNGA3 -0.249 0.349 -9999 0 -0.691 12 12
ARR3 0.016 0 -9999 0 -9999 0 0
absorption of light 0 0 -9999 0 -9999 0 0
cGMP/Cone CNG Channel -0.219 0.278 -9999 0 -0.501 14 14
mol:Pi -0.168 0.3 -9999 0 -0.681 7 7
Cone CNG Channel -0.223 0.286 -9999 0 -0.566 11 11
mol:all-trans-retinal 0 0 -9999 0 -9999 0 0
mol:K + 0.016 0 -9999 0 -9999 0 0
RGS9 -0.082 0.261 -9999 0 -0.773 4 4
PDE6C -0.068 0.224 -9999 0 -0.65 4 4
GNGT2 -0.025 0.164 -9999 0 -0.65 2 2
mol:cGMP (4 units) 0 0 -9999 0 -9999 0 0
PDE6H -0.001 0.094 -9999 0 -0.526 1 1
Signaling events mediated by the Hedgehog family

Figure 14.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 16.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.238 0.335 -9999 0 -0.845 4 4
IHH -0.027 0.061 -9999 0 -9999 0 0
SHH Np/Cholesterol/GAS1 -0.146 0.236 -9999 0 -0.517 8 8
LRPAP1 -0.001 0.094 -9999 0 -0.526 1 1
dorsoventral neural tube patterning 0.145 0.233 0.512 8 -9999 0 8
SMO/beta Arrestin2 -0.101 0.204 -9999 0 -0.862 1 1
SMO -0.115 0.215 -9999 0 -0.921 1 1
AKT1 -0.041 0.128 -9999 0 -0.525 1 1
ARRB2 0.016 0 -9999 0 -9999 0 0
BOC -0.001 0.094 -9999 0 -0.526 1 1
ADRBK1 0.016 0 -9999 0 -9999 0 0
heart looping -0.113 0.211 -9999 0 -0.897 1 1
STIL -0.151 0.247 -9999 0 -0.722 3 3
DHH N/PTCH2 0 0 -9999 0 -9999 0 0
DHH N/PTCH1 -0.098 0.183 -9999 0 -0.734 1 1
PIK3CA 0.016 0 -9999 0 -9999 0 0
DHH 0.016 0 -9999 0 -9999 0 0
PTHLH -0.35 0.467 -9999 0 -0.96 10 10
determination of left/right symmetry -0.113 0.211 -9999 0 -0.897 1 1
PIK3R1 -0.008 0.137 -9999 0 -0.773 1 1
skeletal system development -0.345 0.46 -9999 0 -0.945 10 10
IHH N/Hhip -0.227 0.288 -9999 0 -0.563 13 13
DHH N/Hhip -0.204 0.256 -9999 0 -0.503 13 13
mol:Cholesterol 0 0 -9999 0 -9999 0 0
heart development -0.113 0.211 -9999 0 -0.897 1 1
pancreas development -0.265 0.349 -9999 0 -0.677 13 13
HHAT -0.058 0.23 -9999 0 -0.773 3 3
PI3K -0.018 0.102 -9999 0 -0.586 1 1
EntrezGene:84976 0 0 -9999 0 -9999 0 0
GAS1 -0.141 0.302 -9999 0 -0.703 7 7
somite specification -0.113 0.211 -9999 0 -0.897 1 1
SHH Np/Cholesterol/PTCH1 -0.131 0.237 -9999 0 -0.81 2 2
SHH Np/Cholesterol/PTCH2 -0.058 0.152 -9999 0 -0.461 4 4
SHH Np/Cholesterol/Megalin -0.164 0.25 -9999 0 -0.551 8 8
SHH -0.048 0.203 -9999 0 -0.586 4 4
catabolic process -0.121 0.205 -9999 0 -0.807 1 1
SMO/Vitamin D3 -0.131 0.245 -9999 0 -0.813 2 2
SHH Np/Cholesterol/Hhip -0.214 0.287 -9999 0 -0.61 9 9
LRP2 -0.175 0.312 -9999 0 -0.663 9 9
receptor-mediated endocytosis -0.216 0.245 -9999 0 -0.771 4 4
SHH Np/Cholesterol/BOC -0.066 0.157 -9999 0 -0.461 4 4
SHH Np/Cholesterol/CDO -0.075 0.183 -9999 0 -0.529 4 4
mesenchymal cell differentiation 0.212 0.284 0.603 9 -9999 0 9
mol:Vitamin D3 -0.13 0.238 -9999 0 -0.809 2 2
IHH N/PTCH2 0.005 0.03 -9999 0 -9999 0 0
CDON -0.018 0.131 -9999 0 -0.526 2 2
IHH N/PTCH1 -0.122 0.206 -9999 0 -0.812 1 1
Megalin/LRPAP1 -0.149 0.23 -9999 0 -0.478 10 10
PTCH2 0.016 0 -9999 0 -9999 0 0
SHH Np/Cholesterol -0.059 0.156 -9999 0 -0.471 4 4
PTCH1 -0.122 0.205 -9999 0 -0.811 1 1
HHIP -0.266 0.35 -9999 0 -0.678 13 13
Syndecan-2-mediated signaling events

Figure 15.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 17.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.044 0.162 -9999 0 -0.371 6 6
EPHB2 -0.093 0.231 -9999 0 -0.567 6 6
Syndecan-2/TACI 0.02 0.058 -9999 0 -0.302 1 1
LAMA1 0.016 0 -9999 0 -9999 0 0
Syndecan-2/alpha2 ITGB1 -0.191 0.284 -9999 0 -0.516 12 12
HRAS 0.016 0 -9999 0 -9999 0 0
Syndecan-2/CASK -0.01 0.054 -9999 0 -0.312 1 1
ITGA5 -0.018 0.131 -9999 0 -0.526 2 2
BAX 0.041 0.053 -9999 0 -9999 0 0
EPB41 0.016 0 -9999 0 -9999 0 0
positive regulation of cell-cell adhesion -0.023 0.092 -9999 0 -0.46 1 1
LAMA3 -0.109 0.265 -9999 0 -0.65 6 6
EZR 0 0 -9999 0 -9999 0 0
mol:PI-4-5-P2 0 0 -9999 0 -9999 0 0
CAV2 -0.149 0.314 -9999 0 -0.738 7 7
Syndecan-2/MMP2 -0.017 0.131 -9999 0 -0.503 1 1
RP11-540L11.1 0 0 -9999 0 -9999 0 0
alpha2 ITGB1 -0.201 0.278 -9999 0 -0.586 11 11
dendrite morphogenesis -0.049 0.153 -9999 0 -0.332 7 7
Syndecan-2/GM-CSF -0.107 0.225 -9999 0 -0.459 9 9
determination of left/right symmetry 0.013 0.068 -9999 0 -0.368 1 1
Syndecan-2/PKC delta 0.02 0.058 -9999 0 -9999 0 0
GNB2L1 -0.001 0.094 -9999 0 -0.526 1 1
MAPK3 -0.086 0.207 -9999 0 -0.452 7 7
MAPK1 -0.086 0.207 -9999 0 -0.452 7 7
Syndecan-2/RACK1 -0.016 0.06 -9999 0 -9999 0 0
NF1 0.016 0 -9999 0 -9999 0 0
FGFR/FGF/Syndecan-2 0.013 0.068 -9999 0 -0.368 1 1
ITGA2 -0.255 0.375 -9999 0 -0.773 11 11
MAPK8 0.032 0.059 -9999 0 -9999 0 0
Syndecan-2/alpha2/beta1 Integrin -0.122 0.238 -9999 0 -0.445 11 11
Syndecan-2/Kininogen 0.02 0.058 -9999 0 -0.302 1 1
ITGB1 0.016 0 -9999 0 -9999 0 0
SRC 0.029 0.066 -9999 0 -9999 0 0
Syndecan-2/CASK/Protein 4.1 -0.009 0.048 -9999 0 -9999 0 0
extracellular matrix organization 0.02 0.058 -9999 0 -0.301 1 1
actin cytoskeleton reorganization -0.044 0.161 -9999 0 -0.369 6 6
Syndecan-2/Caveolin-2/Ras -0.072 0.198 -9999 0 -0.454 6 6
Syndecan-2/Laminin alpha3 -0.061 0.18 -9999 0 -0.39 7 7
Syndecan-2/RasGAP -0.022 0.067 -9999 0 -9999 0 0
alpha5/beta1 Integrin -0.023 0.09 -9999 0 -0.37 2 2
PRKCD 0.016 0 -9999 0 -9999 0 0
Syndecan-2 dimer -0.049 0.154 -9999 0 -0.333 7 7
GO:0007205 0.005 0 -9999 0 -9999 0 0
DNA mediated transformation 0 0 -9999 0 -9999 0 0
Syndecan-2/RasGAP/Src 0.029 0.078 -9999 0 -9999 0 0
RHOA 0.016 0 -9999 0 -9999 0 0
SDCBP -0.008 0.137 -9999 0 -0.773 1 1
TNFRSF13B 0.016 0 -9999 0 -9999 0 0
RASA1 -0.001 0.094 -9999 0 -0.526 1 1
alpha2/beta1 Integrin -0.201 0.278 -9999 0 -0.586 11 11
Syndecan-2/Synbindin 0.02 0.058 -9999 0 -0.302 1 1
TGFB1 0.016 0 -9999 0 -9999 0 0
CASP3 0.031 0.053 -9999 0 -9999 0 0
FN1 -0.084 0.238 -9999 0 -0.625 5 5
Syndecan-2/IL8 -0.181 0.255 -9999 0 -0.452 14 14
SDC2 0.013 0.069 -9999 0 -0.369 1 1
KNG1 0.016 0 -9999 0 -9999 0 0
Syndecan-2/Neurofibromin 0.02 0.058 -9999 0 -0.302 1 1
TRAPPC4 0.016 0 -9999 0 -9999 0 0
CSF2 -0.173 0.331 -9999 0 -0.742 8 8
Syndecan-2/TGFB1 0.02 0.058 -9999 0 -0.302 1 1
Syndecan-2/Syntenin/PI-4-5-P2 -0.023 0.092 -9999 0 -0.464 1 1
Syndecan-2/Ezrin -0.009 0.048 -9999 0 -0.273 1 1
PRKACA 0.031 0.053 -9999 0 -9999 0 0
angiogenesis -0.18 0.254 -9999 0 -0.45 14 14
MMP2 -0.042 0.186 -9999 0 -0.608 3 3
IL8 -0.291 0.357 -9999 0 -0.685 14 14
calcineurin-NFAT signaling pathway 0.02 0.058 -9999 0 -0.301 1 1
amb2 Integrin signaling

Figure 16.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 18.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.108 0.227 -9999 0 -0.624 4 4
alphaM/beta2 Integrin/GPIbA -0.1 0.218 -9999 0 -0.667 3 3
alphaM/beta2 Integrin/proMMP-9 -0.101 0.28 -9999 0 -0.731 4 4
PLAUR -0.042 0.186 -9999 0 -0.608 3 3
HMGB1 0.013 0.013 -9999 0 -9999 0 0
alphaM/beta2 Integrin/Talin -0.073 0.21 -9999 0 -0.667 3 3
AGER -0.222 0.353 -9999 0 -0.738 10 10
RAP1A 0.016 0 -9999 0 -9999 0 0
SELPLG -0.008 0.137 -9999 0 -0.773 1 1
mol:LDL 0 0 -9999 0 -9999 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.234 0.356 -9999 0 -0.674 10 10
mol:GTP 0 0 -9999 0 -9999 0 0
MMP9 -0.033 0.191 -9999 0 -0.773 2 2
CYR61 -0.082 0.261 -9999 0 -0.773 4 4
TLN1 0.016 0 -9999 0 -9999 0 0
Rap1/GTP -0.092 0.144 -9999 0 -0.651 1 1
RHOA 0.016 0 -9999 0 -9999 0 0
P-selectin oligomer -0.025 0.164 -9999 0 -0.648 2 2
MYH2 -0.088 0.188 -9999 0 -0.48 2 2
MST1R 0.016 0 -9999 0 -9999 0 0
leukocyte activation during inflammatory response -0.099 0.208 -9999 0 -0.497 6 6
APOB -0.058 0.23 -9999 0 -0.773 3 3
mol:GDP 0 0 -9999 0 -9999 0 0
complement component iC3b receptor activity 0 0 -9999 0 -9999 0 0
MMP2 -0.042 0.186 -9999 0 -0.608 3 3
JAM3 0.016 0 -9999 0 -9999 0 0
GP1BA -0.035 0.158 -9999 0 -0.526 3 3
alphaM/beta2 Integrin/CTGF -0.088 0.222 -9999 0 -0.624 4 4
alphaM/beta2 Integrin -0.087 0.193 -9999 0 -0.515 3 3
JAM3 homodimer 0.016 0 -9999 0 -9999 0 0
ICAM2 0.016 0 -9999 0 -9999 0 0
ICAM1 -0.025 0.164 -9999 0 -0.65 2 2
phagocytosis triggered by activation of immune response cell surface activating receptor -0.086 0.191 -9999 0 -0.509 3 3
cell adhesion -0.1 0.216 -9999 0 -0.663 3 3
NFKB1 -0.206 0.404 -9999 0 -0.903 6 6
THY1 -0.008 0.137 -9999 0 -0.773 1 1
RhoA/GDP 0 0 -9999 0 -9999 0 0
Lipoprotein(a) -0.048 0.149 -9999 0 -0.511 3 3
alphaM/beta2 Integrin/LRP/tPA -0.141 0.248 -9999 0 -0.682 4 4
IL6 -0.233 0.433 -9999 0 -0.987 6 6
ITGB2 -0.061 0.231 -9999 0 -0.779 3 3
elevation of cytosolic calcium ion concentration -0.232 0.372 -9999 0 -0.763 8 8
alphaM/beta2 Integrin/JAM2/JAM3 -0.084 0.257 -9999 0 -0.751 3 3
JAM2 -0.025 0.164 -9999 0 -0.65 2 2
alphaM/beta2 Integrin/ICAM1 -0.114 0.268 -9999 0 -0.808 3 3
alphaM/beta2 Integrin/uPA/Plg -0.208 0.325 -9999 0 -0.718 7 7
RhoA/GTP -0.085 0.177 -9999 0 -0.446 3 3
positive regulation of phagocytosis -0.107 0.223 -9999 0 -0.712 3 3
Ron/MSP -0.053 0.144 -9999 0 -0.586 1 1
alphaM/beta2 Integrin/uPAR/uPA -0.237 0.384 -9999 0 -0.779 8 8
alphaM/beta2 Integrin/uPAR -0.106 0.286 -9999 0 -0.756 4 4
PLAU -0.25 0.332 -9999 0 -0.64 13 13
PLAT -0.135 0.267 -9999 0 -0.588 8 8
actin filament polymerization -0.083 0.181 -9999 0 -0.459 2 2
MST1 -0.059 0.203 -9999 0 -0.588 4 4
alphaM/beta2 Integrin/lipoprotein(a) -0.1 0.212 -9999 0 -0.504 6 6
TNF -0.195 0.385 -9999 0 -0.888 6 6
RAP1B 0.016 0 -9999 0 -9999 0 0
alphaM/beta2 Integrin/uPA -0.23 0.347 -9999 0 -0.775 7 7
fibrinolysis -0.205 0.319 -9999 0 -0.707 7 7
HCK -0.008 0.137 -9999 0 -0.773 1 1
dendritic cell antigen processing and presentation -0.086 0.191 -9999 0 -0.509 3 3
VTN -0.008 0.137 -9999 0 -0.773 1 1
alphaM/beta2 Integrin/CYR61 -0.13 0.338 -9999 0 -0.96 4 4
LPA 0.016 0 -9999 0 -9999 0 0
LRP1 0.016 0 -9999 0 -9999 0 0
cell migration -0.118 0.273 -9999 0 -0.628 5 5
FN1 -0.084 0.238 -9999 0 -0.625 5 5
alphaM/beta2 Integrin/Thy1 -0.089 0.226 -9999 0 -0.64 4 4
MPO -0.018 0.131 -9999 0 -0.526 2 2
KNG1 0.016 0 -9999 0 -9999 0 0
RAP1/GDP 0 0 -9999 0 -9999 0 0
ROCK1 -0.072 0.168 -9999 0 -0.454 1 1
ELA2 -0.042 0.186 -9999 0 -0.608 3 3
PLG 0.016 0 -9999 0 -9999 0 0
CTGF -0.008 0.137 -9999 0 -0.773 1 1
alphaM/beta2 Integrin/Hck -0.086 0.272 -9999 0 -0.809 3 3
ITGAM -0.029 0.164 -9999 0 -0.651 2 2
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.098 0.264 -9999 0 -0.676 4 4
HP -0.118 0.259 -9999 0 -0.596 7 7
leukocyte adhesion -0.215 0.342 -9999 0 -0.85 5 5
SELP -0.025 0.164 -9999 0 -0.65 2 2
Ephrin B reverse signaling

Figure 17.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 19.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.068 0.197 -9999 0 -0.526 5 5
EPHB2 -0.094 0.231 -9999 0 -0.568 6 6
EFNB1 0.007 0.107 -9999 0 -0.588 1 1
mol:GTP 0 0 -9999 0 -9999 0 0
Rac1/GDP -0.117 0.178 -9999 0 -0.627 2 2
Ephrin B2/EPHB1-2 -0.153 0.24 -9999 0 -0.553 7 7
neuron projection morphogenesis -0.112 0.17 -9999 0 -0.599 2 2
Ephrin B1/EPHB1-2/Tiam1 -0.099 0.214 -9999 0 -0.595 3 3
DNM1 0.015 0.001 -9999 0 -9999 0 0
cell-cell signaling -0.001 0.003 -9999 0 -9999 0 0
MAP2K4 -0.115 0.234 -9999 0 -0.694 4 4
YES1 -0.174 0.306 -9999 0 -0.942 4 4
Ephrin B1/EPHB1-2/NCK2 -0.09 0.214 -9999 0 -0.595 3 3
PI3K -0.13 0.243 -9999 0 -0.652 5 5
mol:GDP -0.111 0.203 -9999 0 -0.587 3 3
ITGA2B -0.001 0.094 -9999 0 -0.526 1 1
endothelial cell proliferation -0.049 0.114 -9999 0 -0.313 5 5
FYN -0.174 0.306 -9999 0 -0.942 4 4
MAP3K7 -0.139 0.242 -9999 0 -0.742 4 4
FGR -0.174 0.304 -9999 0 -0.935 4 4
TIAM1 -0.001 0.094 -9999 0 -0.526 1 1
PIK3R1 -0.008 0.137 -9999 0 -0.773 1 1
RGS3 -0.008 0.137 -9999 0 -0.773 1 1
cell adhesion -0.171 0.281 -9999 0 -0.763 5 5
LYN -0.174 0.306 -9999 0 -0.942 4 4
Ephrin B1/EPHB1-2/Src Family Kinases -0.164 0.284 -9999 0 -0.877 4 4
Ephrin B1/EPHB1-2 -0.159 0.261 -9999 0 -0.804 4 4
SRC -0.174 0.304 -9999 0 -0.935 4 4
ITGB3 -0.11 0.242 -9999 0 -0.561 7 7
EPHB1 -0.102 0.248 -9999 0 -0.608 6 6
EPHB4 0.016 0 -9999 0 -9999 0 0
RAC1 0.016 0 -9999 0 -9999 0 0
Ephrin B2/EPHB4 -0.047 0.115 -9999 0 -0.315 5 5
alphaIIb/beta3 Integrin -0.099 0.176 -9999 0 -0.397 8 8
BLK -0.182 0.302 -9999 0 -0.938 4 4
HCK -0.18 0.303 -9999 0 -0.938 4 4
regulation of stress fiber formation 0.102 0.204 0.587 3 -9999 0 3
MAPK8 -0.1 0.223 -9999 0 -0.652 4 4
Ephrin B1/EPHB1-2/RGS3 -0.104 0.22 -9999 0 -0.553 4 4
endothelial cell migration -0.158 0.213 -9999 0 -0.597 5 5
NCK2 0.016 0 -9999 0 -9999 0 0
PTPN13 -0.246 0.331 -9999 0 -0.624 13 13
regulation of focal adhesion formation 0.102 0.204 0.587 3 -9999 0 3
chemotaxis 0.116 0.209 0.546 4 -9999 0 4
PIK3CA 0.016 0 -9999 0 -9999 0 0
Rac1/GTP -0.115 0.175 -9999 0 -0.618 2 2
angiogenesis -0.158 0.259 -9999 0 -0.798 4 4
LCK -0.179 0.306 -9999 0 -0.824 5 5
Calcium signaling in the CD4+ TCR pathway

Figure 18.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 20.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.003 0.043 -9999 0 -9999 0 0
NFATC2 -0.003 0.043 -9999 0 -9999 0 0
NFATC3 -0.003 0.043 -9999 0 -9999 0 0
CD40LG -0.283 0.396 -9999 0 -0.785 10 10
PTGS2 -0.357 0.434 -9999 0 -0.791 14 14
JUNB 0.016 0 -9999 0 -9999 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.013 0.018 -9999 0 -9999 0 0
CaM/Ca2+ -0.013 0.018 -9999 0 -9999 0 0
CALM1 0.009 0.013 -9999 0 -9999 0 0
JUN -0.065 0.231 -9999 0 -0.783 3 3
mol:Ca2+ -0.016 0.015 -9999 0 -9999 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.004 -9999 0 -9999 0 0
FOSL1 -0.018 0.131 -9999 0 -0.526 2 2
CREM 0.016 0.002 -9999 0 -9999 0 0
Jun/NFAT1-c-4/p21SNFT -0.149 0.173 -9999 0 -0.601 2 2
FOS -0.086 0.225 -9999 0 -0.603 5 5
IFNG -0.353 0.448 -9999 0 -0.824 13 13
AP-1/NFAT1-c-4 -0.342 0.468 -9999 0 -0.935 10 10
FASLG -0.313 0.434 -9999 0 -0.831 11 11
NFAT1-c-4/ICER1 -0.048 0.073 -9999 0 -9999 0 0
IL2RA -0.303 0.424 -9999 0 -0.848 10 10
FKBP12/FK506 0 0 -9999 0 -9999 0 0
CSF2 -0.349 0.442 -9999 0 -0.79 14 14
JunB/Fra1/NFAT1-c-4 -0.057 0.075 -9999 0 -9999 0 0
IL4 -0.28 0.385 -9999 0 -0.741 11 11
IL2 -0.042 0.267 -9999 0 -1.527 1 1
IL3 -0.006 0.021 -9999 0 -9999 0 0
FKBP1A 0.016 0 -9999 0 -9999 0 0
BATF3 0 0 -9999 0 -9999 0 0
mol:FK506 0 0 -9999 0 -9999 0 0
POU2F1 0.026 0 -9999 0 -9999 0 0
IL27-mediated signaling events

Figure 19.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 21.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.014 0.075 -9999 0 -0.402 1 1
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -9999 0 -9999 0 0
cytokine production during immune response 0.157 0.269 0.636 5 -0.456 1 6
IL27/IL27R/JAK1 -0.266 0.436 0.518 1 -1.451 3 4
TBX21 -0.222 0.346 0.509 1 -0.786 6 7
IL12B -0.029 0.165 -9999 0 -0.657 2 2
IL12A 0.011 0.007 -9999 0 -9999 0 0
IL6ST -0.022 0.133 -9999 0 -0.535 2 2
IL27RA/JAK1 -0.158 0.453 -9999 0 -1.501 3 3
IL27 -0.112 0.288 -9999 0 -0.781 5 5
TYK2 0.012 0.011 -9999 0 -9999 0 0
T-helper cell lineage commitment -0.067 0.283 -9999 0 -1.53 1 1
T-helper 2 cell differentiation 0.157 0.269 0.636 5 -0.456 1 6
T cell proliferation during immune response 0.157 0.269 0.636 5 -0.456 1 6
MAPKKK cascade -0.157 0.269 0.456 1 -0.636 5 6
STAT3 0.016 0 -9999 0 -9999 0 0
STAT2 0.016 0 -9999 0 -9999 0 0
STAT1 -0.009 0.137 -9999 0 -0.772 1 1
IL12RB1 -0.013 0.137 -9999 0 -0.774 1 1
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -9999 0 -9999 0 0
IL12RB2 -0.224 0.332 0.484 1 -0.739 6 7
IL27/IL27R/JAK2/TYK2 -0.16 0.273 0.457 1 -0.646 5 6
positive regulation of T cell mediated cytotoxicity -0.157 0.269 0.456 1 -0.636 5 6
STAT1 (dimer) -0.324 0.455 0.631 1 -1.301 4 5
JAK2 0.011 0.013 -9999 0 -9999 0 0
JAK1 -0.009 0.138 -9999 0 -0.774 1 1
STAT2 (dimer) -0.144 0.256 0.399 1 -0.649 4 5
T cell proliferation -0.217 0.279 -9999 0 -0.669 6 6
IL12/IL12R/TYK2/JAK2 -0.073 0.272 -9999 0 -1.417 1 1
IL17A -0.067 0.285 -9999 0 -1.539 1 1
mast cell activation 0.157 0.269 0.636 5 -0.456 1 6
IFNG -0.038 0.056 -9999 0 -0.124 6 6
T cell differentiation -0.011 0.014 0.033 1 -0.025 11 12
STAT3 (dimer) -0.144 0.256 0.399 1 -0.649 4 5
STAT5A (dimer) -0.144 0.256 0.399 1 -0.649 4 5
STAT4 (dimer) -0.153 0.254 0.399 1 -0.649 4 5
STAT4 -0.001 0.094 -9999 0 -0.526 1 1
T cell activation 0.006 0.045 0.107 5 -9999 0 5
IL27R/JAK2/TYK2 -0.179 0.379 -9999 0 -1.288 3 3
GATA3 0.041 0.091 -9999 0 -9999 0 0
IL18 -0.056 0.187 -9999 0 -0.544 4 4
positive regulation of mast cell cytokine production -0.141 0.251 0.396 1 -0.633 4 5
IL27/EBI3 -0.119 0.241 -9999 0 -0.567 7 7
IL27RA -0.169 0.441 0.435 1 -1.229 4 5
IL6 -0.129 0.254 -9999 0 -0.528 9 9
STAT5A 0.016 0 -9999 0 -9999 0 0
monocyte differentiation -0.002 0.003 -9999 0 -9999 0 0
IL2 0.035 0.297 0.503 3 -1.38 1 4
IL1B -0.113 0.225 -9999 0 -0.491 8 8
EBI3 -0.03 0.168 -9999 0 -0.666 2 2
TNF -0.018 0.125 -9999 0 -0.491 2 2
Wnt signaling

Figure 20.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 22.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.113 0.214 -9999 0 -0.557 4 4
FZD6 0.016 0 -9999 0 -9999 0 0
WNT6 0.016 0 -9999 0 -9999 0 0
WNT4 -0.201 0.308 -9999 0 -0.616 11 11
FZD3 -0.107 0.287 -9999 0 -0.773 5 5
WNT5A -0.008 0.137 -9999 0 -0.773 1 1
WNT11 -0.008 0.137 -9999 0 -0.773 1 1
Plasma membrane estrogen receptor signaling

Figure 21.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 23.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.145 0.185 -9999 0 -0.482 5 5
ER alpha/Gai/GDP/Gbeta gamma -0.082 0.19 -9999 0 -0.453 5 5
AKT1 -0.132 0.288 -9999 0 -0.838 4 4
PIK3CA 0.016 0 -9999 0 -9999 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.138 0.291 -9999 0 -0.85 4 4
mol:Ca2+ -0.114 0.197 -9999 0 -0.483 6 6
IGF1R -0.018 0.131 -9999 0 -0.526 2 2
E2/ER alpha (dimer)/Striatin -0.152 0.193 -9999 0 -0.375 13 13
SHC1 -0.001 0.094 -9999 0 -0.526 1 1
apoptosis 0.126 0.274 0.794 4 -9999 0 4
RhoA/GTP -0.139 0.163 -9999 0 -0.535 2 2
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.122 0.182 -9999 0 -0.539 4 4
regulation of stress fiber formation 0.083 0.173 0.525 2 -9999 0 2
E2/ERA-ERB (dimer) -0.162 0.193 -9999 0 -0.37 14 14
KRAS -0.018 0.131 -9999 0 -0.526 2 2
G13/GTP -0.147 0.176 -9999 0 -0.337 14 14
pseudopodium formation -0.083 0.173 -9999 0 -0.525 2 2
E2/ER alpha (dimer)/PELP1 -0.152 0.193 -9999 0 -0.375 13 13
GRB2 0.016 0 -9999 0 -9999 0 0
GNG2 -0.008 0.137 -9999 0 -0.773 1 1
GNAO1 0.016 0 -9999 0 -9999 0 0
HRAS 0.016 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
mol:NO -0.101 0.212 -9999 0 -0.58 4 4
E2/ER beta (dimer) -0.012 0.066 -9999 0 -0.382 1 1
mol:GDP -0.152 0.19 -9999 0 -0.528 5 5
mol:NADP -0.101 0.212 -9999 0 -0.58 4 4
PIK3R1 -0.008 0.137 -9999 0 -0.773 1 1
mol:IP3 -0.119 0.205 -9999 0 -0.505 6 6
IGF-1R heterotetramer -0.018 0.131 -9999 0 -0.525 2 2
PLCB1 -0.118 0.196 -9999 0 -0.481 6 6
PLCB2 -0.104 0.188 -9999 0 -0.54 4 4
IGF1 -0.001 0.094 -9999 0 -0.526 1 1
mol:L-citrulline -0.101 0.212 -9999 0 -0.58 4 4
RHOA 0.016 0 -9999 0 -9999 0 0
Gai/GDP -0.028 0.132 -9999 0 -0.678 1 1
JNK cascade -0.012 0.066 -9999 0 -0.381 1 1
BCAR1 0.016 0 -9999 0 -9999 0 0
ESR2 -0.001 0.094 -9999 0 -0.526 1 1
GNAQ 0 0 -9999 0 -9999 0 0
ESR1 -0.235 0.312 -9999 0 -0.602 13 13
Gq family/GDP/Gbeta gamma -0.045 0.158 -9999 0 -0.504 2 2
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.048 0.139 -9999 0 -0.48 1 1
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.129 0.198 -9999 0 -0.59 4 4
GNAZ 0.016 0 -9999 0 -9999 0 0
E2/ER alpha (dimer) -0.182 0.229 -9999 0 -0.448 13 13
STRN 0.016 0 -9999 0 -9999 0 0
GNAL -0.025 0.164 -9999 0 -0.65 2 2
PELP1 0.016 0 -9999 0 -9999 0 0
MAPK11 0.013 0.059 -9999 0 -0.313 1 1
GNAI2 -0.008 0.137 -9999 0 -0.773 1 1
GNAI3 0.016 0 -9999 0 -9999 0 0
GNAI1 -0.008 0.137 -9999 0 -0.773 1 1
HBEGF -0.089 0.217 -9999 0 -0.609 3 3
cAMP biosynthetic process -0.148 0.195 -9999 0 -0.512 5 5
SRC -0.069 0.182 -9999 0 -0.612 1 1
PI3K -0.018 0.102 -9999 0 -0.586 1 1
GNB1 0.016 0 -9999 0 -9999 0 0
G13/GDP/Gbeta gamma -0.144 0.182 -9999 0 -0.51 5 5
SOS1 0.016 0 -9999 0 -9999 0 0
IGF-1R heterotetramer/IGF1 -0.112 0.163 -9999 0 -0.585 2 2
Gs family/GTP -0.151 0.199 -9999 0 -0.523 5 5
EntrezGene:2778 0 0 -9999 0 -9999 0 0
RAS family/GTP -0.034 0.091 -9999 0 -9999 0 0
vasodilation -0.096 0.203 -9999 0 -0.55 4 4
mol:DAG -0.119 0.205 -9999 0 -0.505 6 6
Gs family/GDP/Gbeta gamma -0.143 0.202 -9999 0 -0.56 5 5
MSN -0.091 0.187 -9999 0 -0.581 2 2
Gq family/GTP -0.118 0.167 -9999 0 -0.462 5 5
mol:PI-3-4-5-P3 -0.133 0.278 -9999 0 -0.812 4 4
NRAS -0.018 0.131 -9999 0 -0.526 2 2
mol:E2 0 0 -9999 0 -9999 0 0
cell adhesion 0.096 0.203 0.55 4 -9999 0 4
GRB2/SOS1 0 0 -9999 0 -9999 0 0
RhoA/GDP -0.14 0.176 -9999 0 -0.531 4 4
NOS3 -0.107 0.223 -9999 0 -0.613 4 4
GNA11 0.016 0 -9999 0 -9999 0 0
MAPKKK cascade -0.084 0.241 -9999 0 -0.665 4 4
E2/ER alpha (dimer)/PELP1/Src -0.131 0.194 -9999 0 -0.571 4 4
ruffle organization -0.083 0.173 -9999 0 -0.525 2 2
ROCK2 -0.096 0.174 -9999 0 -0.487 2 2
GNA14 -0.075 0.244 -9999 0 -0.712 4 4
GNA15 -0.042 0.186 -9999 0 -0.608 3 3
GNA13 -0.001 0.094 -9999 0 -0.526 1 1
MMP9 -0.082 0.204 -9999 0 -0.617 2 2
MMP2 -0.085 0.21 -9999 0 -0.652 2 2
Caspase cascade in apoptosis

Figure 22.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 24.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.003 0.166 0.266 1 -0.419 3 4
ACTA1 -0.026 0.194 0.311 1 -0.505 3 4
NUMA1 -0.005 0.17 0.266 1 -0.419 3 4
SPTAN1 -0.007 0.196 0.309 1 -0.579 2 3
LIMK1 -0.022 0.195 -9999 0 -0.579 2 2
BIRC3 -0.133 0.288 -9999 0 -0.667 7 7
BIRC2 0.016 0 -9999 0 -9999 0 0
BAX 0.016 0 -9999 0 -9999 0 0
CASP10 -0.054 0.204 -9999 0 -0.594 3 3
CRMA 0 0 -9999 0 -9999 0 0
XIAP 0 0 -9999 0 -9999 0 0
PTK2 0.003 0.166 0.266 1 -0.419 3 4
DIABLO 0.016 0 -9999 0 -9999 0 0
apoptotic nuclear changes -0.006 0.193 0.308 1 -0.568 2 3
response to UV 0 0 -9999 0 -9999 0 0
CRADD 0.016 0 -9999 0 -9999 0 0
GSN -0.051 0.218 0.31 1 -0.503 4 5
MADD 0.016 0 -9999 0 -9999 0 0
TFAP2A -0.01 0.171 -9999 0 -0.895 1 1
BID -0.037 0.125 -9999 0 -0.3 5 5
MAP3K1 0.006 0.082 0.175 1 -0.198 1 2
TRADD 0.016 0 -9999 0 -9999 0 0
mol:Ca2+ 0 0 -9999 0 -9999 0 0
APAF-1/Pro-Caspase 9 0.011 0.013 -9999 0 -9999 0 0
mol:Activated DNA 0 0 -9999 0 -9999 0 0
ARHGDIB -0.031 0.203 0.309 1 -0.527 3 4
CASP9 0.017 0.001 -9999 0 -9999 0 0
DNA repair -0.011 0.132 0.367 2 -0.234 4 6
neuron apoptosis -0.022 0.167 -9999 0 -0.648 2 2
mol:NAD 0 0 -9999 0 -9999 0 0
DNA fragmentation during apoptosis -0.005 0.19 0.296 1 -0.555 2 3
APAF1 0.016 0 -9999 0 -9999 0 0
CASP6 0.016 0.112 -9999 0 -0.428 1 1
TRAF2 0.016 0 -9999 0 -9999 0 0
ICAD/CAD -0.007 0.193 -9999 0 -0.554 2 2
CASP7 0.067 0.124 0.309 6 -9999 0 6
KRT18 -0.013 0.113 -9999 0 -0.579 1 1
apoptosis -0.021 0.19 -9999 0 -0.587 2 2
DFFA -0.016 0.2 0.309 1 -0.579 2 3
DFFB -0.007 0.196 0.309 1 -0.579 2 3
PARP1 0.011 0.133 0.235 4 -0.371 2 6
actin filament polymerization 0.011 0.182 0.528 2 -9999 0 2
TNF -0.025 0.164 -9999 0 -0.65 2 2
CYCS -0.012 0.083 -9999 0 -0.217 2 2
SATB1 -0.003 0.156 -9999 0 -0.505 2 2
SLK -0.007 0.196 0.309 1 -0.579 2 3
p15 BID/BAX -0.025 0.112 -9999 0 -0.291 3 3
CASP2 0.01 0.097 -9999 0 -9999 0 0
JNK cascade -0.006 0.082 0.197 1 -0.175 1 2
CASP3 -0.017 0.207 0.325 1 -0.537 3 4
LMNB2 0.02 0.086 -9999 0 -9999 0 0
RIPK1 0.016 0 -9999 0 -9999 0 0
CASP4 -0.008 0.137 -9999 0 -0.774 1 1
Mammalian IAPs/DIABLO -0.084 0.164 -9999 0 -0.463 4 4
negative regulation of DNA binding -0.009 0.169 -9999 0 -0.88 1 1
stress fiber formation -0.006 0.193 0.308 1 -0.568 2 3
GZMB -0.076 0.232 -9999 0 -0.528 6 6
CASP1 -0.013 0.193 -9999 0 -1.087 1 1
LMNB1 0.02 0.078 -9999 0 -9999 0 0
APP -0.023 0.169 -9999 0 -0.656 2 2
TNFRSF1A 0.016 0 -9999 0 -9999 0 0
response to stress 0 0 -9999 0 -9999 0 0
CASP8 0.014 0 -9999 0 -9999 0 0
VIM -0.027 0.19 -9999 0 -0.591 2 2
LMNA 0.001 0.121 -9999 0 -0.361 2 2
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0 0.103 -9999 0 -9999 0 0
LRDD 0.016 0 -9999 0 -9999 0 0
SREBF1 -0.007 0.196 0.309 1 -0.579 2 3
APAF-1/Caspase 9 0.019 0.063 -9999 0 -9999 0 0
nuclear fragmentation during apoptosis -0.005 0.167 0.265 1 -0.412 3 4
CFL2 -0.012 0.186 -9999 0 -0.543 2 2
GAS2 -0.1 0.23 0.309 1 -0.477 6 7
positive regulation of apoptosis 0.014 0.093 -9999 0 -9999 0 0
PRF1 -0.076 0.218 -9999 0 -0.575 5 5
Syndecan-1-mediated signaling events

Figure 23.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 25.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.016 0 -9999 0 -9999 0 0
CCL5 -0.025 0.164 -9999 0 -0.65 2 2
SDCBP -0.008 0.137 -9999 0 -0.773 1 1
FGFR/FGF2/Syndecan-1 -0.138 0.198 -9999 0 -0.554 3 3
mol:PI-4-5-P2 0 0 -9999 0 -9999 0 0
RP11-540L11.1 0 0 -9999 0 -9999 0 0
Syndecan-1/Laminin-5 -0.132 0.187 -9999 0 -0.523 3 3
Syndecan-1/Syntenin -0.136 0.227 -9999 0 -0.663 3 3
MAPK3 -0.095 0.175 -9999 0 -0.465 3 3
HGF/MET -0.101 0.198 -9999 0 -0.462 7 7
TGFB1/TGF beta receptor Type II 0.016 0 -9999 0 -9999 0 0
BSG 0.016 0 -9999 0 -9999 0 0
keratinocyte migration -0.13 0.184 -9999 0 -0.515 3 3
Syndecan-1/RANTES -0.145 0.225 -9999 0 -0.663 3 3
Syndecan-1/CD147 -0.11 0.183 -9999 0 -0.499 3 3
Syndecan-1/Syntenin/PIP2 -0.155 0.201 -9999 0 -0.643 3 3
LAMA5 -0.001 0.094 -9999 0 -0.526 1 1
positive regulation of cell-cell adhesion -0.152 0.194 -9999 0 -0.622 3 3
MMP7 -0.042 0.186 -9999 0 -0.608 3 3
HGF 0.016 0 -9999 0 -9999 0 0
Syndecan-1/CASK -0.133 0.188 -9999 0 -0.532 3 3
Syndecan-1/HGF/MET -0.182 0.262 -9999 0 -0.642 5 5
regulation of cell adhesion -0.084 0.171 -9999 0 -9999 0 0
HPSE -0.008 0.137 -9999 0 -0.773 1 1
positive regulation of cell migration -0.138 0.198 -9999 0 -0.554 3 3
SDC1 -0.139 0.2 -9999 0 -0.56 3 3
Syndecan-1/Collagen -0.138 0.198 -9999 0 -0.554 3 3
PPIB 0.016 0 -9999 0 -9999 0 0
MET -0.126 0.274 -9999 0 -0.632 7 7
PRKACA 0.016 0 -9999 0 -9999 0 0
MMP9 -0.033 0.191 -9999 0 -0.773 2 2
MAPK1 -0.095 0.175 -9999 0 -0.465 3 3
homophilic cell adhesion -0.137 0.196 -9999 0 -0.549 3 3
MMP1 -0.324 0.352 -9999 0 -0.665 16 16
Noncanonical Wnt signaling pathway

Figure 24.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 26.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.016 0 -9999 0 -9999 0 0
GNB1/GNG2 -0.098 0.236 -9999 0 -0.595 4 4
mol:DAG -0.08 0.213 -9999 0 -0.675 2 2
PLCG1 -0.083 0.222 -9999 0 -0.709 2 2
YES1 -0.097 0.203 -9999 0 -0.519 4 4
FZD3 -0.107 0.287 -9999 0 -0.773 5 5
FZD6 0.016 0 -9999 0 -9999 0 0
G protein -0.093 0.226 -9999 0 -0.727 2 2
MAP3K7 -0.048 0.179 -9999 0 -0.647 1 1
mol:Ca2+ -0.076 0.206 -9999 0 -0.644 2 2
mol:IP3 -0.08 0.213 -9999 0 -0.675 2 2
NLK 0.014 0.038 -9999 0 -9999 0 0
GNB1 0.016 0 -9999 0 -9999 0 0
CAMK2A -0.062 0.193 -9999 0 -0.591 2 2
MAP3K7IP1 0.016 0 -9999 0 -9999 0 0
Noncanonical Wnts/FZD -0.113 0.214 -9999 0 -0.557 4 4
CSNK1A1 0.016 0 -9999 0 -9999 0 0
GNAS -0.106 0.202 -9999 0 -0.519 4 4
GO:0007205 -0.078 0.209 -9999 0 -0.66 2 2
WNT6 0.016 0 -9999 0 -9999 0 0
WNT4 -0.201 0.308 -9999 0 -0.616 11 11
NFAT1/CK1 alpha -0.106 0.156 -9999 0 -0.518 2 2
GNG2 -0.008 0.137 -9999 0 -0.773 1 1
WNT5A -0.008 0.137 -9999 0 -0.773 1 1
WNT11 -0.008 0.137 -9999 0 -0.773 1 1
CDC42 -0.083 0.194 -9999 0 -0.486 4 4
Thromboxane A2 receptor signaling

Figure 25.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 27.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.067 0.225 -9999 0 -0.651 4 4
GNB1/GNG2 -0.055 0.076 -9999 0 -0.218 3 3
AKT1 0.001 0.122 -9999 0 -9999 0 0
EGF -0.126 0.274 -9999 0 -0.632 7 7
mol:TXA2 0 0.001 -9999 0 -9999 0 0
FGR 0.027 0.091 -9999 0 -9999 0 0
mol:Ca2+ -0.026 0.176 -9999 0 -0.338 4 4
LYN 0.027 0.091 -9999 0 -9999 0 0
RhoA/GTP -0.033 0.051 -9999 0 -9999 0 0
mol:PGI2 0 0 -9999 0 -9999 0 0
SYK -0.03 0.199 -9999 0 -0.389 4 4
GNG2 -0.008 0.137 -9999 0 -0.774 1 1
ARRB2 0.016 0 -9999 0 -9999 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.04 0.166 -9999 0 -0.484 3 3
G beta5/gamma2 -0.076 0.104 -9999 0 -0.291 4 4
PRKCH -0.036 0.203 -9999 0 -0.451 3 3
DNM1 0.016 0 -9999 0 -9999 0 0
TXA2/TP beta/beta Arrestin3 -0.002 0.01 -9999 0 -9999 0 0
mol:GTP 0 0.002 -9999 0 -9999 0 0
PTGDR -0.025 0.164 -9999 0 -0.65 2 2
G12 family/GTP -0.085 0.126 -9999 0 -0.319 6 6
ADRBK1 0.016 0 -9999 0 -9999 0 0
ADRBK2 -0.001 0.094 -9999 0 -0.526 1 1
RhoA/GTP/ROCK1 0 0 -9999 0 -9999 0 0
mol:GDP 0.003 0.115 0.333 1 -9999 0 1
mol:NADP -0.042 0.185 -9999 0 -0.607 3 3
RAB11A 0.016 0 -9999 0 -9999 0 0
PRKG1 -0.009 0.138 -9999 0 -0.775 1 1
mol:IP3 -0.042 0.213 -9999 0 -0.394 7 7
cell morphogenesis 0 0 -9999 0 -9999 0 0
PLCB2 -0.074 0.278 -9999 0 -0.542 7 7
mol:cGMP 0 0.001 -9999 0 -9999 0 0
BLK 0.008 0.136 -9999 0 -0.575 1 1
mol:PDG2 0 0 -9999 0 -9999 0 0
HCK 0.016 0.136 -9999 0 -0.645 1 1
RHOA 0.016 0 -9999 0 -9999 0 0
PTGIR 0.016 0 -9999 0 -9999 0 0
PRKCB1 -0.05 0.221 -9999 0 -0.46 4 4
GNAQ 0 0 -9999 0 -9999 0 0
mol:L-citrulline -0.042 0.185 -9999 0 -0.607 3 3
TXA2/TXA2-R family -0.066 0.268 -9999 0 -0.54 6 6
LCK 0.014 0.111 -9999 0 -9999 0 0
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.011 0.054 -9999 0 -9999 0 0
TXA2-R family/G12 family/GDP/G beta/gamma 0.026 0.058 -9999 0 -9999 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.011 0.054 -9999 0 -9999 0 0
MAPK14 -0.004 0.141 -9999 0 -0.269 2 2
TGM2/GTP -0.059 0.255 -9999 0 -0.562 4 4
MAPK11 -0.004 0.141 -9999 0 -0.269 2 2
ARHGEF1 -0.002 0.108 -9999 0 -0.207 1 1
GNAI2 -0.008 0.137 -9999 0 -0.773 1 1
JNK cascade -0.037 0.208 -9999 0 -0.394 6 6
RAB11/GDP 0.016 0.002 -9999 0 -9999 0 0
ICAM1 -0.023 0.171 -9999 0 -0.375 3 3
cAMP biosynthetic process -0.043 0.202 -9999 0 -0.415 4 4
Gq family/GTP/EBP50 -0.025 0.12 -9999 0 -0.292 5 5
actin cytoskeleton reorganization 0 0 -9999 0 -9999 0 0
SRC 0.027 0.091 -9999 0 -9999 0 0
GNB5 -0.042 0.186 -9999 0 -0.608 3 3
GNB1 0.016 0 -9999 0 -9999 0 0
EGF/EGFR -0.011 0.118 -9999 0 -0.379 1 1
VCAM1 -0.025 0.176 -9999 0 -0.393 3 3
TP beta/Gq family/GDP/G beta5/gamma2 -0.04 0.166 -9999 0 -0.484 3 3
platelet activation -0.008 0.185 -9999 0 -0.326 4 4
PGI2/IP 0.007 0.006 -9999 0 -9999 0 0
PRKACA 0.008 0.076 -9999 0 -0.36 1 1
Gq family/GDP/G beta5/gamma2 -0.04 0.161 -9999 0 -0.463 3 3
TXA2/TP beta/beta Arrestin2 -0.001 0.006 -9999 0 -9999 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -9999 0 0
TBXA2R 0.018 0.072 -9999 0 -0.333 1 1
mol:DAG -0.05 0.23 -9999 0 -0.445 6 6
EGFR -0.175 0.312 -9999 0 -0.663 9 9
TXA2/TP alpha -0.068 0.27 -9999 0 -0.589 4 4
Gq family/GTP -0.045 0.109 -9999 0 -0.311 4 4
YES1 0.027 0.091 -9999 0 -9999 0 0
GNAI2/GTP -0.029 0.084 -9999 0 -0.365 1 1
PGD2/DP -0.024 0.123 -9999 0 -0.49 2 2
SLC9A3R1 -0.001 0.094 -9999 0 -0.526 1 1
FYN 0.027 0.091 -9999 0 -9999 0 0
mol:NO -0.042 0.185 -9999 0 -0.607 3 3
GNA15 -0.042 0.186 -9999 0 -0.608 3 3
PGK/cGMP -0.052 0.141 -9999 0 -0.413 4 4
RhoA/GDP 0.016 0.002 -9999 0 -9999 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.06 0.189 -9999 0 -1.014 1 1
NOS3 -0.042 0.185 -9999 0 -0.608 3 3
RAC1 0.016 0 -9999 0 -9999 0 0
PRKCA -0.045 0.203 -9999 0 -0.401 3 3
PRKCB -0.038 0.193 -9999 0 -0.367 6 6
PRKCE -0.032 0.195 -9999 0 -0.405 3 3
PRKCD -0.035 0.201 -9999 0 -0.402 4 4
PRKCG -0.046 0.22 -9999 0 -0.429 6 6
muscle contraction -0.056 0.255 -9999 0 -0.498 6 6
PRKCZ -0.031 0.186 -9999 0 -0.348 6 6
ARR3 0.016 0 -9999 0 -9999 0 0
TXA2/TP beta -0.02 0.065 -9999 0 -9999 0 0
PRKCQ -0.032 0.193 -9999 0 -0.396 3 3
MAPKKK cascade -0.057 0.241 -9999 0 -0.474 6 6
SELE -0.04 0.195 -9999 0 -0.394 5 5
TP beta/GNAI2/GDP/G beta/gamma -0.036 0.131 -9999 0 -0.667 1 1
ROCK1 0.016 0 -9999 0 -9999 0 0
GNA14 -0.075 0.244 -9999 0 -0.712 4 4
chemotaxis -0.075 0.292 -9999 0 -0.623 5 5
GNA12 0.016 0 -9999 0 -9999 0 0
GNA13 -0.001 0.094 -9999 0 -0.526 1 1
GNA11 0.016 0 -9999 0 -9999 0 0
Rac1/GTP 0.008 0.007 -9999 0 -9999 0 0
Arf6 signaling events

Figure 26.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 28.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.016 0.091 -9999 0 -0.521 1 1
ARNO/beta Arrestin1-2 -0.068 0.152 -9999 0 -0.433 4 4
EGFR -0.175 0.312 -9999 0 -0.664 9 9
EPHA2 -0.025 0.164 -9999 0 -0.65 2 2
USP6 0.016 0 -9999 0 -9999 0 0
IQSEC1 0.016 0 -9999 0 -9999 0 0
EGFR/EGFR/EGF/EGF -0.233 0.298 -9999 0 -0.533 14 14
ARRB2 0.021 0.002 -9999 0 -9999 0 0
mol:GTP 0.008 0.015 -9999 0 -9999 0 0
ARRB1 -0.001 0.094 -9999 0 -0.526 1 1
FBXO8 0.016 0 -9999 0 -9999 0 0
TSHR -0.001 0.094 -9999 0 -0.526 1 1
EGF -0.126 0.274 -9999 0 -0.632 7 7
somatostatin receptor activity 0 0 -9999 0 -0.001 4 4
ARAP2 0 0 -9999 0 0 4 4
mol:GDP -0.043 0.084 -9999 0 -0.242 3 3
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 3 3
ITGA2B -0.001 0.094 -9999 0 -0.526 1 1
ARF6 -0.001 0.094 -9999 0 -0.526 1 1
Ephrin A1/EPHA2/NCK1/GIT1 -0.037 0.117 -9999 0 -0.453 2 2
ADAP1 0 0 -9999 0 0 2 2
KIF13B -0.008 0.137 -9999 0 -0.773 1 1
HGF/MET -0.101 0.198 -9999 0 -0.463 7 7
PXN 0.016 0 -9999 0 -9999 0 0
ARF6/GTP -0.079 0.116 -9999 0 -0.275 4 4
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.199 0.26 -9999 0 -0.608 7 7
ADRB2 -0.116 0.281 -9999 0 -0.691 6 6
receptor agonist activity 0 0 -9999 0 0 3 3
actin filament binding 0 0 -9999 0 -0.001 4 4
SRC 0.016 0 -9999 0 -9999 0 0
ITGB3 -0.11 0.242 -9999 0 -0.561 7 7
GNAQ 0 0 -9999 0 -0.001 2 2
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 2 2
ARF6/GDP -0.003 0.058 -9999 0 -9999 0 0
ARF6/GDP/GULP/ACAP1 -0.089 0.154 -9999 0 -0.496 3 3
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.072 0.129 -9999 0 -0.453 1 1
ACAP1 0 0 -9999 0 -9999 0 0
ACAP2 0 0 -9999 0 0 5 5
LHCGR/beta Arrestin2 0.019 0.003 -9999 0 -9999 0 0
EFNA1 -0.008 0.137 -9999 0 -0.773 1 1
HGF 0.016 0 -9999 0 -9999 0 0
CYTH3 0 0 -9999 0 -0.001 3 3
CYTH2 -0.002 0.002 -9999 0 -0.004 5 5
NCK1 0.016 0 -9999 0 -9999 0 0
fibronectin binding 0 0 -9999 0 0 4 4
endosomal lumen acidification 0 0 -9999 0 0 4 4
microtubule-based process 0 0 -9999 0 -9999 0 0
GULP1 -0.076 0.218 -9999 0 -0.575 5 5
GNAQ/ARNO -0.002 0.003 -9999 0 -0.007 2 2
mol:Phosphatidic acid 0 0 -9999 0 0 5 5
PIP3-E -0.084 0.238 -9999 0 -0.625 5 5
MET -0.126 0.274 -9999 0 -0.632 7 7
GNA14 -0.075 0.244 -9999 0 -0.712 4 4
GNA15 -0.042 0.186 -9999 0 -0.608 3 3
GIT1 0.016 0 -9999 0 -9999 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 3 3
GNA11 0.016 0 -9999 0 -9999 0 0
LHCGR 0.016 0.003 -9999 0 -9999 0 0
AGTR1 -0.026 0.164 -9999 0 -0.65 2 2
desensitization of G-protein coupled receptor protein signaling pathway 0.019 0.003 -9999 0 -9999 0 0
IPCEF1/ARNO -0.189 0.257 -9999 0 -0.595 7 7
alphaIIb/beta3 Integrin -0.098 0.176 -9999 0 -0.397 8 8
FOXA2 and FOXA3 transcription factor networks

Figure 27.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 29.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.132 0.432 -9999 0 -1.223 2 2
PCK1 -0.144 0.285 -9999 0 -0.687 2 2
HNF4A -0.114 0.402 -9999 0 -0.947 3 3
KCNJ11 -0.116 0.407 -9999 0 -0.902 3 3
AKT1 0.01 0.159 -9999 0 -9999 0 0
response to starvation 0.002 0.013 -9999 0 -9999 0 0
DLK1 -0.182 0.464 -9999 0 -0.999 5 5
NKX2-1 -0.02 0.207 -9999 0 -9999 0 0
ACADM -0.113 0.378 -9999 0 -0.924 2 2
TAT -0.132 0.274 -9999 0 -0.741 1 1
CEBPB -0.002 0.098 -9999 0 -0.544 1 1
CEBPA -0.058 0.231 -9999 0 -0.774 3 3
TTR -0.332 0.507 -9999 0 -1.097 7 7
PKLR -0.113 0.378 -9999 0 -0.848 3 3
APOA1 -0.143 0.481 -9999 0 -1.331 2 2
CPT1C -0.203 0.469 -9999 0 -0.983 5 5
ALAS1 -0.02 0.213 -9999 0 -9999 0 0
TFRC -0.264 0.497 -9999 0 -1.175 5 5
FOXF1 0.001 0.003 -9999 0 -9999 0 0
NF1 0.026 0.001 -9999 0 -9999 0 0
HNF1A (dimer) 0.01 0.12 -9999 0 -0.631 1 1
CPT1A -0.144 0.425 -9999 0 -0.934 4 4
HMGCS1 -0.123 0.374 -9999 0 -0.924 2 2
NR3C1 0.018 0.043 -9999 0 -9999 0 0
CPT1B -0.113 0.378 -9999 0 -0.848 3 3
chromatin remodeling 0 0 -9999 0 -9999 0 0
SP1 0.022 0.016 -9999 0 -9999 0 0
GCK -0.157 0.416 -9999 0 -0.82 6 6
CREB1 0.021 0.024 -9999 0 -9999 0 0
IGFBP1 -0.081 0.344 -9999 0 -1.098 2 2
PDX1 -0.023 0.244 -9999 0 -9999 0 0
UCP2 -0.141 0.437 -9999 0 -1.142 3 3
ALDOB -0.149 0.441 -9999 0 -0.924 4 4
AFP -0.166 0.278 -9999 0 -1.033 2 2
BDH1 -0.145 0.421 -9999 0 -0.934 4 4
HADH -0.116 0.407 -9999 0 -0.975 2 2
F2 -0.118 0.422 -9999 0 -0.98 2 2
HNF1A 0.01 0.12 -9999 0 -0.632 1 1
G6PC -0.14 0.342 -9999 0 -0.986 3 3
SLC2A2 -0.081 0.376 -9999 0 -1.102 2 2
INS 0 0.108 -9999 0 -0.544 1 1
FOXA1 -0.061 0.206 -9999 0 -0.578 4 4
FOXA3 -0.263 0.36 -9999 0 -0.658 14 14
FOXA2 -0.136 0.476 -9999 0 -1.027 3 3
ABCC8 -0.174 0.475 -9999 0 -1.054 4 4
ALB -0.139 0.218 -9999 0 -0.932 1 1
BMP receptor signaling

Figure 28.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 30.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.044 0.135 -9999 0 -0.685 1 1
SMAD6-7/SMURF1 -0.025 0.1 -9999 0 -0.501 1 1
NOG -0.025 0.164 -9999 0 -0.65 2 2
SMAD9 -0.059 0.186 -9999 0 -0.595 3 3
SMAD4 0.016 0 -9999 0 -9999 0 0
SMAD5 -0.042 0.122 -9999 0 -0.476 1 1
BMP7/USAG1 -0.265 0.284 -9999 0 -0.53 16 16
SMAD5/SKI -0.031 0.116 -9999 0 -0.446 1 1
SMAD1 0.032 0.052 -9999 0 -9999 0 0
BMP2 -0.249 0.35 -9999 0 -0.691 12 12
SMAD1/SMAD1/SMAD4 -0.02 0.062 -9999 0 -9999 0 0
BMPR1A 0.016 0 -9999 0 -9999 0 0
BMPR1B -0.001 0.094 -9999 0 -0.526 1 1
BMPR1A-1B/BAMBI -0.113 0.176 -9999 0 -0.501 3 3
AHSG -0.008 0.137 -9999 0 -0.773 1 1
CER1 0.016 0 -9999 0 -9999 0 0
BMP2-4/CER1 -0.215 0.273 -9999 0 -0.595 9 9
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.055 0.164 -9999 0 -0.638 1 1
BMP2-4 (homodimer) -0.25 0.313 -9999 0 -0.684 9 9
RGMB 0.016 0 -9999 0 -9999 0 0
BMP6/BMPR2/BMPR1A-1B -0.07 0.138 -9999 0 -0.453 2 2
RGMA -0.008 0.137 -9999 0 -0.773 1 1
SMURF1 0.016 0 -9999 0 -9999 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.069 0.16 -9999 0 -0.506 2 2
BMP2-4/USAG1 -0.412 0.401 -9999 0 -0.777 15 15
SMAD6/SMURF1/SMAD5 -0.031 0.116 -9999 0 -0.446 1 1
SOSTDC1 -0.324 0.352 -9999 0 -0.665 16 16
BMP7/BMPR2/BMPR1A-1B -0.025 0.077 -9999 0 -9999 0 0
SKI 0.016 0 -9999 0 -9999 0 0
BMP6 (homodimer) -0.101 0.249 -9999 0 -0.607 6 6
HFE2 0.016 0 -9999 0 -9999 0 0
ZFYVE16 0.016 0 -9999 0 -9999 0 0
MAP3K7 0.016 0 -9999 0 -9999 0 0
BMP2-4/CHRD -0.242 0.281 -9999 0 -0.626 9 9
SMAD5/SMAD5/SMAD4 -0.031 0.116 -9999 0 -0.446 1 1
MAPK1 0.016 0 -9999 0 -9999 0 0
TAK1/TAB family -0.079 0.129 -9999 0 -0.499 2 2
BMP7 (homodimer) -0.018 0.131 -9999 0 -0.525 2 2
NUP214 0.016 0 -9999 0 -9999 0 0
BMP6/FETUA -0.101 0.198 -9999 0 -0.462 7 7
SMAD1/SKI 0.04 0.05 -9999 0 -9999 0 0
SMAD6 -0.008 0.137 -9999 0 -0.773 1 1
CTDSP2 0.016 0 -9999 0 -9999 0 0
BMP2-4/FETUA -0.229 0.299 -9999 0 -0.646 9 9
MAP3K7IP1 0.016 0 -9999 0 -9999 0 0
GREM1 -0.166 0.32 -9999 0 -0.712 8 8
BMPR2 (homodimer) 0.016 0 -9999 0 -9999 0 0
GADD34/PP1CA 0 0 -9999 0 -9999 0 0
BMPR1A-1B (homodimer) -0.012 0.064 -9999 0 -0.37 1 1
CHRDL1 -0.101 0.249 -9999 0 -0.608 6 6
ENDOFIN/SMAD1 0.04 0.05 -9999 0 -9999 0 0
SMAD6-7/SMURF1/SMAD1 -0.021 0.074 -9999 0 -9999 0 0
SMAD6/SMURF1 0.016 0 -9999 0 -9999 0 0
BAMBI -0.159 0.288 -9999 0 -0.608 9 9
SMURF2 -0.059 0.203 -9999 0 -0.588 4 4
BMP2-4/CHRDL1 -0.282 0.303 -9999 0 -0.659 10 10
BMP2-4/GREM1 -0.323 0.339 -9999 0 -0.68 13 13
SMAD7 -0.001 0.094 -9999 0 -0.526 1 1
SMAD8A/SMAD8A/SMAD4 -0.047 0.176 -9999 0 -0.553 3 3
SMAD1/SMAD6 0.04 0.05 -9999 0 -9999 0 0
TAK1/SMAD6 0 0 -9999 0 -9999 0 0
BMP7 -0.018 0.131 -9999 0 -0.526 2 2
BMP6 -0.101 0.249 -9999 0 -0.608 6 6
MAP3K7IP2 -0.008 0.137 -9999 0 -0.773 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.058 0.147 -9999 0 -0.578 1 1
PPM1A 0.016 0 -9999 0 -9999 0 0
SMAD1/SMURF2 0.001 0.127 -9999 0 -9999 0 0
SMAD7/SMURF1 -0.012 0.064 -9999 0 -0.37 1 1
CTDSPL -0.001 0.094 -9999 0 -0.526 1 1
PPP1CA 0.016 0 -9999 0 -9999 0 0
XIAP 0 0 -9999 0 -9999 0 0
CTDSP1 0.016 0 -9999 0 -9999 0 0
PPP1R15A 0.016 0 -9999 0 -9999 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.077 0.178 -9999 0 -0.487 3 3
CHRD -0.035 0.158 -9999 0 -0.526 3 3
BMPR2 0.016 0 -9999 0 -9999 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.081 0.177 -9999 0 -0.545 2 2
BMP4 -0.076 0.218 -9999 0 -0.575 5 5
FST -0.025 0.164 -9999 0 -0.65 2 2
BMP2-4/NOG -0.24 0.282 -9999 0 -0.587 11 11
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.022 0.07 -9999 0 -9999 0 0
Nectin adhesion pathway

Figure 29.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 31.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.016 0 -9999 0 -9999 0 0
alphaV beta3 Integrin -0.124 0.206 -9999 0 -0.442 9 9
PTK2 -0.138 0.231 -9999 0 -0.628 5 5
positive regulation of JNK cascade -0.059 0.115 -9999 0 -0.349 4 4
CDC42/GDP -0.039 0.18 -9999 0 -0.479 4 4
Rac1/GDP -0.036 0.178 -9999 0 -0.472 4 4
RAP1B 0.016 0 -9999 0 -9999 0 0
RAP1A 0.016 0 -9999 0 -9999 0 0
CTNNB1 -0.001 0.094 -9999 0 -0.526 1 1
CDC42/GTP -0.07 0.144 -9999 0 -0.435 4 4
nectin-3/I-afadin -0.108 0.21 -9999 0 -0.493 7 7
RAPGEF1 -0.057 0.201 -9999 0 -0.549 4 4
mol:GTP 0 0 -9999 0 -9999 0 0
CRK -0.077 0.231 -9999 0 -0.646 4 4
PDGFB-D/PDGFRB 0.016 0 -9999 0 -9999 0 0
TLN1 -0.025 0.126 -9999 0 -0.369 2 2
Rap1/GTP -0.061 0.123 -9999 0 -0.418 2 2
IQGAP1 0.016 0 -9999 0 -9999 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -9999 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.108 0.21 -9999 0 -0.493 7 7
PVR -0.018 0.131 -9999 0 -0.526 2 2
Necl-5(dimer) -0.018 0.131 -9999 0 -0.525 2 2
mol:GDP -0.059 0.221 -9999 0 -0.605 4 4
MLLT4 0.016 0 -9999 0 -9999 0 0
PIK3CA 0.016 0 -9999 0 -9999 0 0
PI3K -0.088 0.191 -9999 0 -0.527 4 4
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.018 0.102 -9999 0 -0.586 1 1
positive regulation of lamellipodium assembly -0.061 0.121 -9999 0 -0.367 4 4
PVRL1 -0.008 0.137 -9999 0 -0.773 1 1
PVRL3 -0.133 0.288 -9999 0 -0.667 7 7
PVRL2 0.016 0 -9999 0 -9999 0 0
PIK3R1 -0.008 0.137 -9999 0 -0.773 1 1
CDH1 -0.033 0.191 -9999 0 -0.773 2 2
CLDN1 -0.181 0.342 -9999 0 -0.773 8 8
JAM-A/CLDN1 -0.207 0.306 -9999 0 -0.583 10 10
SRC -0.126 0.243 -9999 0 -0.738 4 4
ITGB3 -0.11 0.242 -9999 0 -0.561 7 7
nectin-1(dimer)/I-afadin/I-afadin -0.018 0.102 -9999 0 -0.586 1 1
FARP2 -0.064 0.215 -9999 0 -0.594 4 4
RAC1 0.016 0 -9999 0 -9999 0 0
CTNNA1 0.016 0 -9999 0 -9999 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.11 0.184 -9999 0 -0.501 4 4
nectin-1/I-afadin -0.018 0.102 -9999 0 -0.586 1 1
nectin-2/I-afadin 0 0 -9999 0 -9999 0 0
RAC1/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -9999 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.107 0.191 -9999 0 -0.501 5 5
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -9999 0 0
F11R -0.008 0.137 -9999 0 -0.773 1 1
positive regulation of filopodium formation -0.059 0.115 -9999 0 -0.349 4 4
alphaV/beta3 Integrin/Talin -0.096 0.193 -9999 0 -0.602 2 2
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -9999 0 0
nectin-2(dimer)/I-afadin/I-afadin 0 0 -9999 0 -9999 0 0
PIP5K1C -0.038 0.134 -9999 0 -0.402 2 2
VAV2 -0.066 0.218 -9999 0 -0.606 4 4
RAP1/GDP -0.07 0.145 -9999 0 -0.439 4 4
ITGAV -0.033 0.191 -9999 0 -0.773 2 2
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.091 0.178 -9999 0 -0.501 4 4
nectin-3(dimer)/I-afadin/I-afadin -0.108 0.21 -9999 0 -0.493 7 7
Rac1/GTP -0.073 0.15 -9999 0 -0.453 4 4
PTPRM -0.053 0.146 -9999 0 -0.332 6 6
E-cadherin/beta catenin/alpha catenin -0.044 0.119 -9999 0 -9999 0 0
adherens junction assembly 0 0 -9999 0 -9999 0 0
CDC42 0.016 0 -9999 0 -9999 0 0
Glucocorticoid receptor regulatory network

Figure 30.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 32.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.007 0.115 -9999 0 -9999 0 0
SMARCC2 0.016 0 -9999 0 -9999 0 0
SMARCC1 0.016 0 -9999 0 -9999 0 0
TBX21 -0.119 0.385 -9999 0 -0.86 6 6
SUMO2 0.013 0.011 -9999 0 -9999 0 0
STAT1 (dimer) 0.002 0.137 -9999 0 -0.76 1 1
FKBP4 0.016 0 -9999 0 -9999 0 0
FKBP5 -0.092 0.255 -9999 0 -0.674 5 5
GR alpha/HSP90/FKBP51/HSP90 -0.008 0.201 0.367 1 -0.498 3 4
PRL 0.019 0.121 -9999 0 -9999 0 0
cortisol/GR alpha (dimer)/TIF2 0.095 0.318 0.718 4 -9999 0 4
RELA -0.063 0.103 -9999 0 -9999 0 0
FGG -0.278 0.488 0.557 4 -0.741 14 18
GR beta/TIF2 0.056 0.142 0.369 3 -9999 0 3
IFNG -0.381 0.523 -9999 0 -1.108 9 9
apoptosis -0.068 0.263 0.519 1 -0.612 1 2
CREB1 0.021 0.04 -9999 0 -9999 0 0
histone acetylation -0.002 0.147 -9999 0 -0.394 2 2
BGLAP -0.012 0.205 -9999 0 -0.861 1 1
GR/PKAc 0.046 0.166 0.349 2 -0.516 1 3
NF kappa B1 p50/RelA -0.118 0.186 -9999 0 -0.621 1 1
SMARCD1 0.016 0 -9999 0 -9999 0 0
MDM2 0.024 0.151 0.302 3 -0.524 1 4
GATA3 0.019 0.094 -9999 0 -0.503 1 1
AKT1 0.002 0.004 -9999 0 -9999 0 0
CSF2 -0.291 0.576 -9999 0 -1.344 7 7
GSK3B 0.013 0.011 -9999 0 -9999 0 0
NR1I3 -0.04 0.238 0.497 1 -9999 0 1
CSN2 0.029 0.217 0.478 2 -9999 0 2
BRG1/BAF155/BAF170/BAF60A -0.014 0.079 -9999 0 -0.453 1 1
NFATC1 0.015 0.053 -9999 0 -9999 0 0
POU2F1 0.026 0 -9999 0 -9999 0 0
CDKN1A 0.049 0.026 -9999 0 -9999 0 0
response to stress 0 0 -9999 0 -9999 0 0
response to UV -0.002 0.01 -9999 0 -9999 0 0
SFN -0.058 0.23 -9999 0 -0.773 3 3
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.04 0.258 0.358 1 -0.596 4 5
prolactin receptor activity 0 0 -9999 0 -9999 0 0
EGR1 -0.213 0.453 0.478 1 -0.905 8 9
JUN -0.169 0.242 -9999 0 -0.588 5 5
IL4 -0.026 0.191 -9999 0 -9999 0 0
CDK5R1 -0.026 0.165 -9999 0 -0.651 2 2
PRKACA 0.016 0 -9999 0 -9999 0 0
cortisol/GR alpha (monomer)/AP-1 -0.183 0.312 0.317 1 -0.713 5 6
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.006 0.187 0.358 1 -0.494 2 3
cortisol/GR alpha (monomer) 0.102 0.392 0.816 5 -9999 0 5
NCOA2 0.016 0 -9999 0 -9999 0 0
response to hypoxia 0 0 -9999 0 -9999 0 0
FOS -0.132 0.237 -9999 0 -0.654 5 5
AP-1/NFAT1-c-4 -0.323 0.361 -9999 0 -0.867 7 7
AFP -0.143 0.326 -9999 0 -1.188 2 2
SUV420H1 0.016 0 -9999 0 -9999 0 0
IRF1 0.059 0.165 0.525 1 -9999 0 1
TP53 0.044 0 -9999 0 -9999 0 0
PPP5C 0.016 0 -9999 0 -9999 0 0
KRT17 -0.188 0.297 -9999 0 -0.839 3 3
KRT14 -0.061 0.18 -9999 0 -0.611 1 1
TBP 0.024 0.024 -9999 0 -9999 0 0
CREBBP 0.026 0.044 -9999 0 -9999 0 0
HDAC1 0.002 0.004 -9999 0 -9999 0 0
HDAC2 0.034 0.036 -9999 0 -9999 0 0
AP-1 -0.325 0.363 -9999 0 -0.873 7 7
MAPK14 0.013 0.011 -9999 0 -9999 0 0
MAPK10 -0.004 0.097 -9999 0 -0.539 1 1
MAPK11 0.013 0.011 -9999 0 -9999 0 0
KRT5 -0.149 0.253 -9999 0 -0.728 3 3
interleukin-1 receptor activity 0.018 0.036 -9999 0 -9999 0 0
NCOA1 -0.005 0.138 -9999 0 -0.771 1 1
STAT1 0.002 0.137 -9999 0 -0.761 1 1
CGA -0.013 0.17 -9999 0 -9999 0 0
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.082 0.269 0.497 7 -9999 0 7
MAPK3 0.013 0.012 -9999 0 -9999 0 0
MAPK1 0.013 0.011 -9999 0 -9999 0 0
ICAM1 -0.162 0.374 -9999 0 -1.105 3 3
NFKB1 -0.063 0.103 -9999 0 -9999 0 0
MAPK8 -0.084 0.199 -9999 0 -0.498 4 4
MAPK9 0.013 0.011 -9999 0 -9999 0 0
cortisol/GR alpha (dimer) -0.076 0.269 0.523 1 -0.644 1 2
BAX 0.049 0.026 -9999 0 -9999 0 0
POMC -0.104 0.378 -9999 0 -1.201 2 2
EP300 0.028 0.047 -9999 0 -9999 0 0
cortisol/GR alpha (dimer)/p53 0.116 0.32 0.74 4 -9999 0 4
proteasomal ubiquitin-dependent protein catabolic process 0.007 0.122 0.242 1 -0.467 1 2
SGK1 0.051 0.072 0.277 1 -9999 0 1
IL13 -0.107 0.211 -9999 0 -0.641 1 1
IL6 -0.227 0.373 -9999 0 -0.801 7 7
PRKACG 0.016 0 -9999 0 -9999 0 0
IL5 -0.091 0.18 -9999 0 -9999 0 0
IL2 -0.191 0.354 -9999 0 -0.937 4 4
CDK5 0.015 0.005 -9999 0 -9999 0 0
PRKACB -0.025 0.164 -9999 0 -0.65 2 2
HSP90AA1 0.016 0 -9999 0 -9999 0 0
IL8 -0.467 0.565 -9999 0 -1.132 12 12
CDK5R1/CDK5 -0.024 0.122 -9999 0 -0.481 2 2
NF kappa B1 p50/RelA/PKAc -0.074 0.163 -9999 0 -9999 0 0
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.107 0.292 0.676 4 -9999 0 4
SMARCA4 -0.008 0.137 -9999 0 -0.773 1 1
chromatin remodeling 0.062 0.186 0.438 4 -9999 0 4
NF kappa B1 p50/RelA/Cbp -0.052 0.169 -9999 0 -0.491 1 1
JUN (dimer) -0.168 0.241 -9999 0 -0.586 5 5
YWHAH 0.016 0 -9999 0 -9999 0 0
VIPR1 -0.042 0.243 -9999 0 -0.709 3 3
NR3C1 0.066 0.23 0.563 4 -9999 0 4
NR4A1 -0.03 0.128 -9999 0 -0.447 2 2
TIF2/SUV420H1 0 0 -9999 0 -9999 0 0
MAPKKK cascade -0.068 0.263 0.519 1 -0.612 1 2
cortisol/GR alpha (dimer)/Src-1 0.089 0.35 0.727 4 -0.839 1 5
PBX1 0.026 0 -9999 0 -9999 0 0
POU1F1 0.009 0.094 -9999 0 -0.515 1 1
SELE -0.244 0.481 -9999 0 -1.191 5 5
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.062 0.187 0.439 4 -9999 0 4
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.107 0.292 0.676 4 -9999 0 4
mol:cortisol 0.049 0.241 0.501 5 -0.257 1 6
MMP1 -0.524 0.603 -9999 0 -1.08 15 15
IL1-mediated signaling events

Figure 31.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 33.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0 -9999 0 -9999 0 0
PRKCZ 0 0 -9999 0 -9999 0 0
MAP3K7IP2 -0.008 0.137 -9999 0 -0.773 1 1
ERC1 0.016 0 -9999 0 -9999 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.115 0.211 -9999 0 -0.599 4 4
IRAK/TOLLIP 0.032 0 -9999 0 -9999 0 0
IKBKB 0.016 0 -9999 0 -9999 0 0
IKBKG 0.016 0 -9999 0 -9999 0 0
IL1 alpha/IL1R2 -0.212 0.29 -9999 0 -0.662 8 8
IL1A -0.159 0.288 -9999 0 -0.608 9 9
IL1B -0.113 0.27 -9999 0 -0.539 8 8
IRAK/TRAF6/p62/Atypical PKCs -0.007 0.039 -9999 0 -9999 0 0
IL1R2 -0.118 0.259 -9999 0 -0.596 7 7
IL1R1 -0.033 0.191 -9999 0 -0.773 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.014 0.213 -9999 0 -0.589 2 2
TOLLIP 0.016 0 -9999 0 -9999 0 0
TICAM2 0 0 -9999 0 -9999 0 0
MAP3K3 0.016 0 -9999 0 -9999 0 0
TAK1/TAB1/TAB2 -0.016 0.087 -9999 0 -0.501 1 1
IKK complex/ELKS 0.074 0.028 -9999 0 -9999 0 0
JUN 0.003 0.162 -9999 0 -0.577 1 1
MAP3K7 0.016 0 -9999 0 -9999 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.172 0.29 -9999 0 -0.945 3 3
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.171 0.223 -9999 0 -0.516 7 7
PIK3R1 -0.008 0.137 -9999 0 -0.773 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.171 0.237 -9999 0 -0.853 2 2
IL1 beta fragment/IL1R1/IL1RAP -0.156 0.298 -9999 0 -0.642 7 7
NFKB1 0.016 0 -9999 0 -9999 0 0
MAPK8 0.033 0.093 -9999 0 -9999 0 0
IRAK1 0.024 0 -9999 0 -9999 0 0
IL1RN/IL1R1 -0.126 0.225 -9999 0 -0.505 8 8
IRAK4 -0.008 0.137 -9999 0 -0.773 1 1
PRKCI 0.016 0 -9999 0 -9999 0 0
TRAF6 0.016 0 -9999 0 -9999 0 0
PI3K -0.018 0.102 -9999 0 -0.586 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.093 0.245 -9999 0 -0.66 4 4
CHUK 0.016 0 -9999 0 -9999 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.156 0.298 -9999 0 -0.642 7 7
IL1 beta/IL1R2 -0.174 0.275 -9999 0 -0.584 8 8
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.012 0.067 -9999 0 -9999 0 0
NF kappa B1 p50/RelA -0.151 0.255 -9999 0 -0.835 3 3
IRAK3 -0.215 0.347 -9999 0 -0.724 10 10
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.177 0.278 -9999 0 -0.825 4 4
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.101 0.22 -9999 0 -0.769 2 2
IL1 alpha/IL1R1/IL1RAP -0.19 0.245 -9999 0 -0.567 7 7
RELA 0.016 0 -9999 0 -9999 0 0
MAP3K7IP1 0.016 0 -9999 0 -9999 0 0
SQSTM1 -0.001 0.094 -9999 0 -0.526 1 1
MYD88 0.016 0 -9999 0 -9999 0 0
IRAK/TRAF6/MEKK3 0.041 0 -9999 0 -9999 0 0
IL1RAP -0.075 0.244 -9999 0 -0.712 4 4
UBE2N 0.016 0 -9999 0 -9999 0 0
IRAK/TRAF6 -0.142 0.226 -9999 0 -0.671 4 4
CASP1 -0.008 0.137 -9999 0 -0.773 1 1
IL1RN/IL1R2 -0.181 0.26 -9999 0 -0.616 7 7
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.139 0.285 -9999 0 -0.852 3 3
TMEM189-UBE2V1 0 0 -9999 0 -9999 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.064 0.176 -9999 0 -0.617 2 2
PIK3CA 0.016 0 -9999 0 -9999 0 0
IL1RN -0.109 0.265 -9999 0 -0.65 6 6
TRAF6/TAK1/TAB1/TAB2 -0.013 0.07 -9999 0 -0.404 1 1
MAP2K6 0.025 0.097 -9999 0 -9999 0 0
TCGA08_p53

Figure 32.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 34.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.188 0.269 -9999 0 -0.526 12 12
TP53 -0.049 0.09 -9999 0 -9999 0 0
Senescence -0.049 0.09 -9999 0 -9999 0 0
Apoptosis -0.049 0.09 -9999 0 -9999 0 0
Activated_Oncogenes 0 0 -9999 0 -9999 0 0
MDM2 0.084 0.166 0.325 7 -0.43 1 8
MDM4 0.016 0 -9999 0 -9999 0 0
FAS signaling pathway (CD95)

Figure 33.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 35.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.018 0.056 -9999 0 -9999 0 0
RFC1 0.018 0.056 -9999 0 -9999 0 0
PRKDC 0.001 0.079 -9999 0 -0.352 1 1
RIPK1 0.018 0.004 -9999 0 -9999 0 0
CASP7 -0.029 0.043 -9999 0 -9999 0 0
FASLG/FAS/FADD/FAF1 -0.02 0.213 0.258 2 -0.42 5 7
MAP2K4 -0.056 0.181 -9999 0 -0.462 3 3
mol:ceramide -0.082 0.217 -9999 0 -0.493 5 5
GSN -0.028 0.16 -9999 0 -0.494 3 3
FASLG/FAS/FADD/FAF1/Caspase 8 -0.019 0.222 -9999 0 -0.475 4 4
FAS -0.102 0.273 -9999 0 -0.729 5 5
BID -0.032 0.125 -9999 0 -0.518 2 2
MAP3K1 -0.023 0.109 -9999 0 -9999 0 0
MAP3K7 0.014 0.006 -9999 0 -9999 0 0
RB1 0.018 0.056 -9999 0 -9999 0 0
CFLAR 0.001 0.095 -9999 0 -0.527 1 1
HGF/MET -0.23 0.263 -9999 0 -0.672 6 6
ARHGDIB -0.007 0.118 -9999 0 -0.496 1 1
FADD 0.014 0.007 -9999 0 -9999 0 0
actin filament polymerization 0.028 0.159 0.491 3 -9999 0 3
NFKB1 -0.05 0.084 -9999 0 -9999 0 0
MAPK8 -0.063 0.205 -9999 0 -0.531 3 3
DFFA 0.008 0.079 -9999 0 -0.305 1 1
DNA fragmentation during apoptosis 0.018 0.056 -9999 0 -9999 0 0
FAS/FADD/MET -0.156 0.27 -9999 0 -0.69 5 5
CFLAR/RIP1 0.005 0.069 -9999 0 -0.372 1 1
FAIM3 0.017 0.002 -9999 0 -9999 0 0
FAF1 0.014 0.007 -9999 0 -9999 0 0
PARP1 -0.013 0.137 -9999 0 -0.496 2 2
DFFB 0.018 0.056 -9999 0 -9999 0 0
CHUK -0.041 0.073 -9999 0 -9999 0 0
FASLG -0.111 0.267 -9999 0 -0.656 6 6
FAS/FADD -0.068 0.211 -9999 0 -0.551 5 5
HGF 0.016 0 -9999 0 -9999 0 0
LMNA -0.013 0.107 -9999 0 -0.454 1 1
CASP6 0.018 0.056 -9999 0 -9999 0 0
CASP10 0.014 0.007 -9999 0 -9999 0 0
CASP3 0.021 0.065 -9999 0 -9999 0 0
PTPN13 -0.235 0.312 -9999 0 -0.602 13 13
CASP8 0 0 -9999 0 -9999 0 0
IL6 -0.126 0.32 -9999 0 -0.776 4 4
MET -0.126 0.274 -9999 0 -0.632 7 7
ICAD/CAD 0.009 0.074 -9999 0 -9999 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 -0.084 0.22 -9999 0 -0.501 5 5
activation of caspase activity by cytochrome c -0.032 0.125 -9999 0 -0.516 2 2
PAK2 0.018 0.056 -9999 0 -9999 0 0
BCL2 -0.034 0.158 -9999 0 -0.525 3 3
Syndecan-3-mediated signaling events

Figure 34.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 36.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.016 0 -9999 0 -9999 0 0
Syndecan-3/Src/Cortactin -0.133 0.279 -9999 0 -0.883 3 3
Syndecan-3/Neurocan -0.052 0.191 -9999 0 -0.786 2 2
POMC -0.076 0.218 -9999 0 -0.575 5 5
EGFR -0.175 0.312 -9999 0 -0.663 9 9
Syndecan-3/EGFR -0.149 0.262 -9999 0 -0.576 7 7
AGRP -0.018 0.131 -9999 0 -0.526 2 2
NCSTN 0.016 0 -9999 0 -9999 0 0
PSENEN -0.001 0.094 -9999 0 -0.526 1 1
RP11-540L11.1 0 0 -9999 0 -9999 0 0
APH1B -0.001 0.094 -9999 0 -0.526 1 1
APH1A -0.001 0.094 -9999 0 -0.526 1 1
NCAN 0.016 0 -9999 0 -9999 0 0
long-term memory -0.048 0.177 -9999 0 -0.728 2 2
Syndecan-3/IL8 -0.21 0.238 -9999 0 -0.489 11 11
PSEN1 0.016 0 -9999 0 -9999 0 0
Src/Cortactin 0 0 -9999 0 -9999 0 0
FYN 0.016 0 -9999 0 -9999 0 0
limb bud formation -0.054 0.197 -9999 0 -0.81 2 2
MC4R 0.016 0 -9999 0 -9999 0 0
SRC 0.016 0 -9999 0 -9999 0 0
PTN -0.175 0.312 -9999 0 -0.663 9 9
FGFR/FGF/Syndecan-3 -0.054 0.2 -9999 0 -0.823 2 2
neuron projection morphogenesis -0.126 0.264 -9999 0 -0.835 3 3
Syndecan-3/AgRP -0.068 0.201 -9999 0 -0.786 2 2
Syndecan-3/AgRP/MC4R -0.065 0.192 -9999 0 -0.754 2 2
Fyn/Cortactin 0 0 -9999 0 -9999 0 0
SDC3 -0.055 0.204 -9999 0 -0.837 2 2
GO:0007205 0 0 -9999 0 -9999 0 0
positive regulation of leukocyte migration -0.207 0.234 -9999 0 -0.481 11 11
IL8 -0.291 0.357 -9999 0 -0.685 14 14
Syndecan-3/Fyn/Cortactin -0.049 0.184 -9999 0 -0.754 2 2
Syndecan-3/CASK -0.052 0.193 -9999 0 -0.794 2 2
alpha-MSH/MC4R -0.065 0.154 -9999 0 -0.413 5 5
Gamma Secretase -0.023 0.097 -9999 0 -0.512 1 1
Signaling mediated by p38-alpha and p38-beta

Figure 35.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 37.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.207 0.402 -9999 0 -1.087 4 4
MKNK1 0.016 0 -9999 0 -9999 0 0
MAPK14 -0.057 0.116 -9999 0 -9999 0 0
ATF2/c-Jun -0.094 0.28 -9999 0 -0.922 3 3
MAPK11 -0.057 0.116 -9999 0 -9999 0 0
MITF -0.051 0.137 -9999 0 -0.345 3 3
MAPKAPK5 -0.051 0.137 -9999 0 -0.345 3 3
KRT8 -0.073 0.148 -9999 0 -0.357 4 4
MAPKAPK3 0.016 0 -9999 0 -9999 0 0
MAPKAPK2 0.016 0 -9999 0 -9999 0 0
p38alpha-beta/CK2 -0.083 0.168 -9999 0 -0.426 4 4
CEBPB -0.06 0.138 -9999 0 -9999 0 0
SLC9A1 -0.051 0.137 -9999 0 -0.345 3 3
mol:GDP 0 0 -9999 0 -9999 0 0
ATF2 -0.057 0.149 -9999 0 -0.417 1 1
p38alpha-beta/MNK1 -0.05 0.134 -9999 0 -9999 0 0
JUN -0.093 0.278 -9999 0 -0.915 3 3
PPARGC1A -0.081 0.179 -9999 0 -0.416 5 5
USF1 -0.075 0.173 -9999 0 -0.433 4 4
RAB5/GDP/GDI1 -0.053 0.079 -9999 0 -9999 0 0
NOS2 -0.063 0.137 -9999 0 -0.343 4 4
DDIT3 -0.095 0.195 -9999 0 -0.433 6 6
RAB5A 0.016 0 -9999 0 -9999 0 0
HSPB1 -0.057 0.153 -9999 0 -0.474 2 2
p38alpha-beta/HBP1 -0.05 0.134 -9999 0 -9999 0 0
CREB1 -0.054 0.14 -9999 0 -0.357 3 3
RAB5/GDP 0 0 -9999 0 -9999 0 0
EIF4E -0.032 0.117 -9999 0 -9999 0 0
RPS6KA4 -0.051 0.137 -9999 0 -9999 0 0
PLA2G4A -0.177 0.23 -9999 0 -0.491 8 8
GDI1 -0.051 0.137 -9999 0 -0.345 3 3
TP53 -0.067 0.165 -9999 0 -0.431 3 3
RPS6KA5 -0.065 0.148 -9999 0 -0.357 4 4
ESR1 -0.182 0.193 -9999 0 -0.404 11 11
HBP1 0.016 0 -9999 0 -9999 0 0
MEF2C -0.104 0.222 -9999 0 -0.471 7 7
MEF2A -0.051 0.137 -9999 0 -0.345 3 3
EIF4EBP1 -0.054 0.14 -9999 0 -0.357 3 3
KRT19 -0.097 0.19 -9999 0 -0.444 5 5
ELK4 -0.073 0.148 -9999 0 -0.357 4 4
ATF6 -0.051 0.137 -9999 0 -0.345 3 3
ATF1 -0.054 0.14 -9999 0 -0.357 3 3
p38alpha-beta/MAPKAPK2 -0.05 0.134 -9999 0 -9999 0 0
p38alpha-beta/MAPKAPK3 -0.05 0.134 -9999 0 -9999 0 0
Integrins in angiogenesis

Figure 36.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 38.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.115 0.221 -9999 0 -0.524 7 7
alphaV beta3 Integrin -0.113 0.176 -9999 0 -0.501 3 3
PTK2 -0.151 0.26 -9999 0 -0.671 3 3
IGF1R -0.018 0.131 -9999 0 -0.526 2 2
PI4KB 0.016 0 -9999 0 -9999 0 0
MFGE8 0.016 0 -9999 0 -9999 0 0
SRC 0.016 0 -9999 0 -9999 0 0
CDKN1B -0.059 0.144 -9999 0 -0.795 1 1
VEGFA -0.008 0.137 -9999 0 -0.773 1 1
ILK -0.059 0.144 -9999 0 -0.795 1 1
ROCK1 0.016 0 -9999 0 -9999 0 0
AKT1 -0.02 0.147 -9999 0 -0.742 1 1
PTK2B -0.138 0.226 -9999 0 -0.841 1 1
alphaV/beta3 Integrin/JAM-A -0.085 0.232 -9999 0 -0.594 4 4
CBL 0.016 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
alphaV beta3 Integrin/ANGPTL3 -0.104 0.173 -9999 0 -0.501 3 3
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.09 0.162 -9999 0 -0.453 4 4
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.072 0.171 -9999 0 -0.542 2 2
alphaV/beta3 Integrin/Syndecan-1 -0.104 0.173 -9999 0 -0.501 3 3
PI4KA 0.016 0 -9999 0 -9999 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.198 0.247 -9999 0 -0.799 3 3
PI4 Kinase 0 0 -9999 0 -9999 0 0
PIK3CA 0.016 0 -9999 0 -9999 0 0
alphaV/beta3 Integrin/Osteopontin -0.266 0.252 -9999 0 -0.552 11 11
RPS6KB1 -0.152 0.248 -9999 0 -0.871 2 2
TLN1 0.016 0 -9999 0 -9999 0 0
MAPK3 -0.122 0.275 -9999 0 -0.895 3 3
GPR124 0.016 0 -9999 0 -9999 0 0
MAPK1 -0.122 0.275 -9999 0 -0.895 3 3
PXN 0.016 0 -9999 0 -9999 0 0
PIK3R1 -0.008 0.137 -9999 0 -0.773 1 1
alphaV/beta3 Integrin/Tumstatin -0.179 0.223 -9999 0 -0.548 6 6
cell adhesion -0.125 0.204 -9999 0 -0.6 3 3
ANGPTL3 0.016 0 -9999 0 -9999 0 0
VEGFR2 homodimer/VEGFA homodimer/Src -0.097 0.189 -9999 0 -0.501 5 5
IGF-1R heterotetramer -0.018 0.131 -9999 0 -0.525 2 2
Rac1/GDP 0 0 -9999 0 -9999 0 0
TGFBR2 0.016 0 -9999 0 -9999 0 0
ITGB3 -0.11 0.242 -9999 0 -0.561 7 7
IGF1 -0.001 0.094 -9999 0 -0.526 1 1
RAC1 0.016 0 -9999 0 -9999 0 0
regulation of cell-matrix adhesion -0.103 0.173 -9999 0 -0.499 3 3
apoptosis -0.033 0.19 -9999 0 -0.771 2 2
CD47 -0.058 0.23 -9999 0 -0.773 3 3
alphaV/beta3 Integrin/CD47 -0.15 0.235 -9999 0 -0.593 5 5
VCL -0.001 0.094 -9999 0 -0.526 1 1
alphaV/beta3 Integrin/Del1 -0.197 0.255 -9999 0 -0.566 9 9
CSF1 -0.001 0.094 -9999 0 -0.526 1 1
PIK3C2A -0.099 0.21 -9999 0 -0.721 3 3
PI4 Kinase/Pyk2 -0.149 0.197 -9999 0 -0.62 3 3
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.179 0.221 -9999 0 -0.516 7 7
FAK1/Vinculin -0.116 0.209 -9999 0 -0.501 3 3
alphaV beta3/Integrin/ppsTEM5 -0.104 0.173 -9999 0 -0.501 3 3
RHOA 0.016 0 -9999 0 -9999 0 0
VTN -0.008 0.137 -9999 0 -0.773 1 1
BCAR1 0.016 0 -9999 0 -9999 0 0
FGF2 -0.001 0.094 -9999 0 -0.526 1 1
F11R -0.003 0.126 -9999 0 -0.478 2 2
alphaV/beta3 Integrin/Lactadherin -0.104 0.173 -9999 0 -0.501 3 3
alphaV/beta3 Integrin/TGFBR2 -0.104 0.173 -9999 0 -0.501 3 3
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.037 0.117 -9999 0 -0.453 2 2
HSP90AA1 0.016 0 -9999 0 -9999 0 0
alphaV/beta3 Integrin/Talin -0.095 0.159 -9999 0 -0.462 3 3
mol:GDP 0 0 -9999 0 -9999 0 0
FN1 -0.084 0.238 -9999 0 -0.625 5 5
alphaV/beta3 Integrin/Pyk2 -0.138 0.227 -9999 0 -0.85 1 1
SDC1 0.016 0 -9999 0 -9999 0 0
VAV3 -0.031 0.157 -9999 0 -0.421 1 1
PTPN11 0.016 0 -9999 0 -9999 0 0
IRS1 -0.099 0.272 -9999 0 -0.724 5 5
FAK1/Paxillin -0.109 0.207 -9999 0 -0.501 3 3
cell migration -0.096 0.193 -9999 0 -0.444 3 3
ITGAV -0.033 0.191 -9999 0 -0.773 2 2
PI3K -0.116 0.235 -9999 0 -0.878 2 2
SPP1 -0.249 0.35 -9999 0 -0.691 12 12
KDR -0.116 0.281 -9999 0 -0.691 6 6
mol:PI-4-5-P2 0 0 -9999 0 -9999 0 0
alphaV/beta3 Integrin/Caspase 8 -0.033 0.191 -9999 0 -0.772 2 2
COL4A3 -0.109 0.265 -9999 0 -0.65 6 6
angiogenesis -0.113 0.276 -9999 0 -0.782 4 4
Rac1/GTP -0.062 0.123 -9999 0 -9999 0 0
EDIL3 -0.142 0.281 -9999 0 -0.619 8 8
cell proliferation -0.103 0.173 -9999 0 -0.499 3 3
EPHB forward signaling

Figure 37.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 39.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.081 0.159 -9999 0 -0.37 7 7
cell-cell adhesion 0.134 0.195 0.563 3 -9999 0 3
Ephrin B/EPHB2/RasGAP -0.112 0.202 -9999 0 -0.528 5 5
ITSN1 0.016 0 -9999 0 -9999 0 0
PIK3CA 0.016 0 -9999 0 -9999 0 0
SHC1 -0.001 0.094 -9999 0 -0.526 1 1
Ephrin B1/EPHB3 -0.032 0.124 -9999 0 -0.511 2 2
Ephrin B1/EPHB1 -0.086 0.194 -9999 0 -0.459 6 6
HRAS/GDP -0.096 0.156 -9999 0 -0.491 2 2
Ephrin B/EPHB1/GRB7 -0.109 0.181 -9999 0 -0.509 4 4
Endophilin/SYNJ1 -0.064 0.187 -9999 0 -0.445 5 5
KRAS -0.018 0.131 -9999 0 -0.526 2 2
Ephrin B/EPHB1/Src -0.109 0.181 -9999 0 -0.509 4 4
endothelial cell migration -0.052 0.111 -9999 0 -0.424 1 1
GRB2 0.016 0 -9999 0 -9999 0 0
GRB7 0.016 0 -9999 0 -9999 0 0
PAK1 -0.056 0.19 -9999 0 -0.479 3 3
HRAS 0.016 0 -9999 0 -9999 0 0
RRAS -0.079 0.198 -9999 0 -0.445 6 6
DNM1 0.016 0 -9999 0 -9999 0 0
cell-cell signaling 0 0 -9999 0 -9999 0 0
CRK -0.071 0.192 -9999 0 -0.485 4 4
lamellipodium assembly -0.134 0.195 -9999 0 -0.563 3 3
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.039 0.137 -9999 0 -0.419 1 1
PIK3R1 -0.008 0.137 -9999 0 -0.773 1 1
EPHB2 -0.093 0.231 -9999 0 -0.567 6 6
EPHB3 -0.008 0.137 -9999 0 -0.773 1 1
EPHB1 -0.101 0.249 -9999 0 -0.608 6 6
EPHB4 0.016 0 -9999 0 -9999 0 0
mol:GDP -0.088 0.153 -9999 0 -0.442 2 2
Ephrin B/EPHB2 -0.107 0.183 -9999 0 -0.484 5 5
Ephrin B/EPHB3 -0.066 0.13 -9999 0 -0.429 2 2
JNK cascade -0.095 0.222 -9999 0 -0.533 5 5
Ephrin B/EPHB1 -0.111 0.185 -9999 0 -0.518 4 4
RAP1/GDP -0.073 0.132 -9999 0 -0.417 1 1
EFNB2 -0.068 0.197 -9999 0 -0.526 5 5
EFNB3 0.016 0 -9999 0 -9999 0 0
EFNB1 -0.008 0.137 -9999 0 -0.773 1 1
Ephrin B2/EPHB1-2 -0.164 0.232 -9999 0 -0.555 7 7
RAP1B 0.016 0 -9999 0 -9999 0 0
RAP1A 0.016 0 -9999 0 -9999 0 0
CDC42/GTP -0.138 0.204 -9999 0 -0.596 3 3
Rap1/GTP -0.134 0.197 -9999 0 -0.572 3 3
axon guidance -0.081 0.158 -9999 0 -0.369 7 7
MAPK3 -0.016 0.124 -9999 0 -9999 0 0
MAPK1 -0.016 0.124 -9999 0 -9999 0 0
Rac1/GDP -0.041 0.162 -9999 0 -0.442 1 1
actin cytoskeleton reorganization -0.114 0.156 -9999 0 -0.468 3 3
CDC42/GDP -0.041 0.162 -9999 0 -0.442 1 1
PI3K -0.052 0.112 -9999 0 -0.429 1 1
EFNA5 -0.008 0.137 -9999 0 -0.773 1 1
Ephrin B2/EPHB4 -0.049 0.114 -9999 0 -0.314 5 5
Ephrin B/EPHB2/Intersectin/N-WASP -0.034 0.137 -9999 0 -9999 0 0
CDC42 0.016 0 -9999 0 -9999 0 0
RAS family/GTP -0.152 0.203 -9999 0 -0.617 3 3
PTK2 0.031 0.045 -9999 0 -9999 0 0
MAP4K4 -0.097 0.225 -9999 0 -0.54 5 5
SRC 0.016 0 -9999 0 -9999 0 0
KALRN 0.016 0 -9999 0 -9999 0 0
Intersectin/N-WASP 0 0 -9999 0 -9999 0 0
neuron projection morphogenesis -0.042 0.187 -9999 0 -9999 0 0
MAP2K1 -0.027 0.13 -9999 0 -0.388 1 1
WASL 0.016 0.003 -9999 0 -9999 0 0
Ephrin B1/EPHB1-2/NCK1 -0.132 0.209 -9999 0 -0.589 4 4
cell migration -0.02 0.138 -9999 0 -0.395 1 1
NRAS -0.018 0.131 -9999 0 -0.526 2 2
SYNJ1 -0.065 0.19 -9999 0 -0.453 5 5
PXN 0.016 0 -9999 0 -9999 0 0
TF -0.107 0.23 -9999 0 -0.516 6 6
HRAS/GTP -0.145 0.212 -9999 0 -0.525 6 6
Ephrin B1/EPHB1-2 -0.135 0.213 -9999 0 -0.598 4 4
cell adhesion mediated by integrin 0.048 0.119 0.398 1 -9999 0 1
RAC1 0.016 0 -9999 0 -9999 0 0
mol:GTP -0.157 0.229 -9999 0 -0.566 6 6
RAC1-CDC42/GTP -0.142 0.196 -9999 0 -0.566 3 3
RASA1 -0.001 0.094 -9999 0 -0.526 1 1
RAC1-CDC42/GDP -0.073 0.132 -9999 0 -9999 0 0
ruffle organization -0.085 0.231 -9999 0 -0.573 3 3
NCK1 0.016 0 -9999 0 -9999 0 0
receptor internalization -0.052 0.182 -9999 0 -0.457 3 3
Ephrin B/EPHB2/KALRN -0.104 0.179 -9999 0 -0.475 5 5
ROCK1 0.001 0.119 -9999 0 -0.46 2 2
RAS family/GDP -0.111 0.154 -9999 0 -0.5 2 2
Rac1/GTP -0.142 0.209 -9999 0 -0.607 3 3
Ephrin B/EPHB1/Src/Paxillin -0.039 0.142 -9999 0 -0.481 1 1
Glypican 2 network

Figure 38.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 40.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.058 0.23 -9999 0 -0.773 3 3
GPC2 0 0 -9999 0 -9999 0 0
GPC2/Midkine -0.056 0.174 -9999 0 -0.596 3 3
neuron projection morphogenesis -0.056 0.173 -9999 0 -0.594 3 3
Signaling events mediated by VEGFR1 and VEGFR2

Figure 39.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 41.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.124 0.206 -9999 0 -0.442 9 9
AKT1 -0.075 0.292 -9999 0 -0.641 6 6
PTK2B -0.173 0.303 -9999 0 -0.803 4 4
VEGFR2 homodimer/Frs2 -0.13 0.313 -9999 0 -0.866 4 4
CAV1 -0.058 0.23 -9999 0 -0.773 3 3
CALM1 0.016 0 -9999 0 -9999 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.168 0.27 -9999 0 -0.797 4 4
endothelial cell proliferation -0.063 0.252 -9999 0 -0.556 4 4
mol:Ca2+ -0.097 0.274 -9999 0 -0.71 4 4
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.143 0.252 -9999 0 -0.755 4 4
RP11-342D11.1 -0.107 0.273 -9999 0 -0.718 4 4
CDH5 -0.008 0.137 -9999 0 -0.773 1 1
VEGFA homodimer -0.028 0.098 -9999 0 -0.443 1 1
SHC1 -0.001 0.094 -9999 0 -0.526 1 1
SHC2 -0.082 0.261 -9999 0 -0.773 4 4
HRAS/GDP -0.129 0.199 -9999 0 -0.601 4 4
SH2D2A -0.042 0.186 -9999 0 -0.608 3 3
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.136 0.2 -9999 0 -0.572 4 4
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.182 0.266 -9999 0 -0.797 4 4
VEGFR1 homodimer -0.008 0.137 -9999 0 -0.772 1 1
SHC/GRB2/SOS1 -0.144 0.223 -9999 0 -0.674 4 4
GRB10 -0.129 0.306 -9999 0 -0.719 5 5
PTPN11 0.016 0 -9999 0 -9999 0 0
GRB2 0.016 0 -9999 0 -9999 0 0
PAK1 0.016 0 -9999 0 -9999 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.155 0.252 -9999 0 -0.687 5 5
HRAS 0.016 0 -9999 0 -9999 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.095 0.239 -9999 0 -0.758 2 2
HIF1A -0.018 0.131 -9999 0 -0.526 2 2
FRS2 -0.008 0.137 -9999 0 -0.773 1 1
oxygen and reactive oxygen species metabolic process -0.141 0.248 -9999 0 -0.742 4 4
mol:GTP 0 0 -9999 0 -9999 0 0
FLT4 0.016 0 -9999 0 -9999 0 0
Nck/Pak 0 0 -9999 0 -9999 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.154 0.267 -9999 0 -0.797 4 4
mol:GDP -0.14 0.215 -9999 0 -0.649 4 4
mol:NADP -0.063 0.219 -9999 0 -0.481 5 5
eNOS/Hsp90 -0.052 0.208 -9999 0 -0.474 1 1
PIK3R1 -0.008 0.137 -9999 0 -0.773 1 1
mol:IP3 -0.099 0.278 -9999 0 -0.722 4 4
HIF1A/ARNT -0.023 0.09 -9999 0 -0.37 2 2
SHB 0.016 0 -9999 0 -9999 0 0
VEGFA -0.012 0.137 -9999 0 -0.762 1 1
VEGFC -0.025 0.164 -9999 0 -0.65 2 2
FAK1/Vinculin -0.134 0.293 -9999 0 -0.785 4 4
mol:Ca ++ 0 0 -9999 0 -9999 0 0
RHOA 0.016 0 -9999 0 -9999 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.225 0.294 -9999 0 -0.761 6 6
PTPN6 0.016 0 -9999 0 -9999 0 0
EPAS1 -0.059 0.159 -9999 0 -0.495 1 1
mol:L-citrulline -0.063 0.219 -9999 0 -0.481 5 5
ITGAV -0.033 0.191 -9999 0 -0.773 2 2
PIK3CA 0.016 0 -9999 0 -9999 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.156 0.255 -9999 0 -0.755 4 4
VEGFR2 homodimer/VEGFA homodimer -0.169 0.264 -9999 0 -0.785 4 4
VEGFR2/3 heterodimer -0.113 0.307 -9999 0 -0.866 4 4
VEGFB 0.016 0 -9999 0 -9999 0 0
MAPK11 -0.103 0.283 -9999 0 -0.734 4 4
VEGFR2 homodimer -0.135 0.344 -9999 0 -0.968 4 4
FLT1 -0.008 0.137 -9999 0 -0.773 1 1
NEDD4 0.012 0.023 -9999 0 -9999 0 0
MAPK3 -0.09 0.254 -9999 0 -0.648 4 4
MAPK1 -0.09 0.254 -9999 0 -0.648 4 4
VEGFA145/NRP2 -0.05 0.155 -9999 0 -0.52 3 3
VEGFR1/2 heterodimer -0.13 0.313 -9999 0 -0.866 4 4
KDR -0.135 0.345 -9999 0 -0.973 4 4
VEGFA165/NRP1/VEGFR2 homodimer -0.121 0.29 -9999 0 -0.714 5 5
SRC 0.016 0 -9999 0 -9999 0 0
platelet activating factor biosynthetic process -0.091 0.26 -9999 0 -0.664 4 4
PI3K -0.085 0.302 -9999 0 -0.704 5 5
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.154 0.267 -9999 0 -0.797 4 4
FES -0.101 0.282 -9999 0 -0.734 4 4
GAB1 -0.164 0.292 -9999 0 -0.81 5 5
VEGFR2 homodimer/VEGFA homodimer/Src -0.154 0.267 -9999 0 -0.797 4 4
CTNNB1 -0.001 0.094 -9999 0 -0.526 1 1
SOS1 0.016 0 -9999 0 -9999 0 0
ARNT 0.016 0 -9999 0 -9999 0 0
eNOS/Caveolin-1 -0.085 0.236 -9999 0 -0.512 3 3
VEGFR2 homodimer/VEGFA homodimer/Yes -0.154 0.267 -9999 0 -0.797 4 4
PI3K/GAB1 -0.063 0.285 -9999 0 -0.634 5 5
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.146 0.243 -9999 0 -0.722 4 4
PRKACA 0.016 0 -9999 0 -9999 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.154 0.273 -9999 0 -0.805 4 4
HSP90AA1 0.016 0 -9999 0 -9999 0 0
CDC42 -0.101 0.282 -9999 0 -0.734 4 4
actin cytoskeleton reorganization -0.181 0.264 -9999 0 -0.788 4 4
PTK2 -0.146 0.321 -9999 0 -0.869 4 4
EDG1 -0.112 0.296 -9999 0 -0.719 5 5
mol:DAG -0.099 0.278 -9999 0 -0.722 4 4
CaM/Ca2+ -0.138 0.22 -9999 0 -0.659 4 4
MAP2K3 -0.113 0.288 -9999 0 -0.686 5 5
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.134 0.316 -9999 0 -0.749 5 5
PLCG1 -0.101 0.282 -9999 0 -0.734 4 4
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.143 0.252 -9999 0 -0.755 4 4
IQGAP1 0.016 0 -9999 0 -9999 0 0
YES1 0.016 0 -9999 0 -9999 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.154 0.267 -9999 0 -0.797 4 4
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.154 0.267 -9999 0 -0.797 4 4
cell migration -0.091 0.256 -9999 0 -0.639 4 4
mol:PI-3-4-5-P3 -0.075 0.279 -9999 0 -0.642 5 5
FYN 0.016 0 -9999 0 -9999 0 0
VEGFB/NRP1 -0.093 0.26 -9999 0 -0.675 4 4
mol:NO -0.063 0.219 -9999 0 -0.481 5 5
PXN 0.016 0 -9999 0 -9999 0 0
HRAS/GTP -0.129 0.2 -9999 0 -0.602 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.134 0.316 -9999 0 -0.749 5 5
VHL 0.016 0 -9999 0 -9999 0 0
ITGB3 -0.11 0.242 -9999 0 -0.561 7 7
NOS3 -0.076 0.243 -9999 0 -0.547 5 5
VEGFR2 homodimer/VEGFA homodimer/Sck -0.208 0.273 -9999 0 -0.797 4 4
RAC1 0.016 0 -9999 0 -9999 0 0
PRKCA -0.104 0.273 -9999 0 -0.667 4 4
PRKCB -0.092 0.261 -9999 0 -0.676 4 4
VCL -0.001 0.094 -9999 0 -0.526 1 1
VEGFA165/NRP1 -0.108 0.274 -9999 0 -0.72 4 4
VEGFR1/2 heterodimer/VEGFA homodimer -0.168 0.291 -9999 0 -0.812 5 5
VEGFA165/NRP2 -0.05 0.155 -9999 0 -0.52 3 3
MAPKKK cascade -0.088 0.268 -9999 0 -0.619 1 1
NRP2 -0.025 0.164 -9999 0 -0.65 2 2
VEGFC homodimer -0.025 0.164 -9999 0 -0.648 2 2
NCK1 0.016 0 -9999 0 -9999 0 0
ROCK1 0.016 0 -9999 0 -9999 0 0
FAK1/Paxillin -0.125 0.295 -9999 0 -0.785 4 4
MAP3K13 -0.129 0.301 -9999 0 -0.73 5 5
PDPK1 -0.087 0.295 -9999 0 -0.641 6 6
IL6-mediated signaling events

Figure 40.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 42.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.181 0.296 -9999 0 -0.77 1 1
CRP -0.181 0.296 -9999 0 -0.77 1 1
cell cycle arrest -0.22 0.328 -9999 0 -0.759 3 3
TIMP1 -0.145 0.287 -9999 0 -1.054 1 1
IL6ST -0.023 0.138 -9999 0 -0.556 2 2
Rac1/GDP -0.101 0.257 -9999 0 -0.683 3 3
AP1 -0.027 0.214 -9999 0 -0.63 3 3
GAB2 0.02 0.005 -9999 0 -9999 0 0
TNFSF11 -0.271 0.403 -9999 0 -0.881 6 6
HSP90B1 -0.04 0.26 -9999 0 -1.418 1 1
GAB1 -0.007 0.138 -9999 0 -0.773 1 1
MAPK14 -0.076 0.294 -9999 0 -0.855 3 3
AKT1 0.04 0.135 -9999 0 -0.65 1 1
FOXO1 0.047 0.128 -9999 0 -0.609 1 1
MAP2K6 -0.094 0.3 -9999 0 -0.852 3 3
mol:GTP -0.002 0.004 -9999 0 -9999 0 0
MAP2K4 -0.118 0.259 -9999 0 -0.65 3 3
MITF -0.089 0.268 -9999 0 -0.739 3 3
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -9999 0 0
TYK2 0.016 0 -9999 0 -9999 0 0
A2M -0.098 0.309 -9999 0 -1.497 1 1
CEBPB 0.009 0.095 -9999 0 -0.519 1 1
GRB2/SOS1/GAB family/SHP2 0.007 0.105 -9999 0 -9999 0 0
STAT3 -0.23 0.341 -9999 0 -0.809 3 3
STAT1 -0.039 0.161 -9999 0 -0.933 1 1
CEBPD -0.202 0.338 -9999 0 -0.965 2 2
PIK3CA 0.018 0.003 -9999 0 -9999 0 0
PI3K 0.008 0.111 -9999 0 -0.612 1 1
JUN -0.058 0.23 -9999 0 -0.773 3 3
PIAS3/MITF -0.076 0.251 -9999 0 -0.689 3 3
MAPK11 -0.076 0.294 -9999 0 -0.855 3 3
STAT3 (dimer)/FOXO1 -0.154 0.335 0.498 2 -0.935 2 4
GRB2/SOS1/GAB family -0.089 0.251 -9999 0 -0.928 2 2
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.106 0.315 -9999 0 -1.19 2 2
GRB2 0.018 0.005 -9999 0 -9999 0 0
JAK2 0.016 0 -9999 0 -9999 0 0
LBP -0.139 0.281 -9999 0 -0.636 3 3
PIK3R1 -0.008 0.141 -9999 0 -0.792 1 1
JAK1 -0.01 0.138 -9999 0 -0.778 1 1
MYC -0.181 0.296 -9999 0 -0.77 1 1
FGG -0.533 0.552 -9999 0 -1.023 16 16
macrophage differentiation -0.22 0.328 -9999 0 -0.759 3 3
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.119 0.216 -9999 0 -0.648 3 3
JUNB -0.176 0.287 -9999 0 -0.742 1 1
FOS -0.076 0.218 -9999 0 -0.575 5 5
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.104 0.285 0.365 2 -0.68 4 6
STAT1/PIAS1 -0.108 0.256 0.365 2 -0.803 2 4
GRB2/SOS1/GAB family/SHP2/PI3K 0.031 0.106 -9999 0 -0.47 1 1
STAT3 (dimer) -0.228 0.337 -9999 0 -0.795 3 3
PRKCD -0.137 0.27 -9999 0 -0.891 1 1
IL6R -0.035 0.192 -9999 0 -0.777 2 2
SOCS3 -0.072 0.328 -9999 0 -0.952 3 3
gp130 (dimer)/JAK1/JAK1/LMO4 -0.036 0.155 -9999 0 -0.467 3 3
Rac1/GTP -0.115 0.261 -9999 0 -0.693 3 3
HCK -0.008 0.137 -9999 0 -0.773 1 1
MAPKKK cascade 0.026 0.11 -9999 0 -9999 0 0
bone resorption -0.253 0.379 -9999 0 -0.816 6 6
IRF1 -0.181 0.296 -9999 0 -0.77 1 1
mol:GDP -0.107 0.269 -9999 0 -0.649 4 4
SOS1 0.019 0.005 -9999 0 -9999 0 0
VAV1 -0.109 0.276 -9999 0 -0.664 4 4
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.078 0.305 -9999 0 -0.766 4 4
PTPN11 -0.009 0.017 -9999 0 -9999 0 0
IL6/IL6RA -0.123 0.241 -9999 0 -0.48 9 9
gp130 (dimer)/TYK2/TYK2/LMO4 -0.022 0.124 -9999 0 -0.494 1 1
gp130 (dimer)/JAK2/JAK2/LMO4 -0.022 0.124 -9999 0 -0.494 1 1
IL6 -0.132 0.251 -9999 0 -0.56 8 8
PIAS3 0.016 0 -9999 0 -9999 0 0
PTPRE -0.075 0.265 -9999 0 -0.776 4 4
PIAS1 0.016 0 -9999 0 -9999 0 0
RAC1 0.015 0.002 -9999 0 -9999 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.053 0.177 0.318 2 -0.439 2 4
LMO4 -0.013 0.136 -9999 0 -0.768 1 1
STAT3 (dimer)/PIAS3 -0.245 0.292 0.456 2 -0.764 3 5
MCL1 0.027 0.24 -9999 0 -1.281 1 1
BCR signaling pathway

Figure 41.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 43.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.076 0.205 -9999 0 -0.408 8 8
IKBKB 0.006 0.1 -9999 0 -0.267 1 1
AKT1 -0.042 0.135 -9999 0 -0.304 3 3
IKBKG 0.008 0.105 -9999 0 -0.285 1 1
CALM1 -0.036 0.184 -9999 0 -0.494 3 3
PIK3CA 0.016 0 -9999 0 -9999 0 0
MAP3K1 -0.103 0.261 -9999 0 -0.65 5 5
MAP3K7 0.016 0 -9999 0 -9999 0 0
mol:Ca2+ -0.048 0.194 -9999 0 -0.455 5 5
DOK1 0.016 0 -9999 0 -9999 0 0
AP-1 -0.031 0.136 0.21 1 -0.271 4 5
LYN 0.016 0 -9999 0 -9999 0 0
BLNK -0.008 0.137 -9999 0 -0.773 1 1
SHC1 -0.001 0.094 -9999 0 -0.526 1 1
BCR complex -0.141 0.267 -9999 0 -0.565 8 8
CD22 -0.122 0.266 -9999 0 -0.762 4 4
CAMK2G -0.024 0.173 -9999 0 -0.452 3 3
CSNK2A1 0.016 0 -9999 0 -9999 0 0
INPP5D 0 0 -9999 0 -9999 0 0
SHC/GRB2/SOS1 -0.116 0.211 -9999 0 -0.738 2 2
GO:0007205 -0.049 0.196 -9999 0 -0.462 5 5
SYK -0.008 0.137 -9999 0 -0.774 1 1
ELK1 -0.037 0.186 -9999 0 -0.502 3 3
NFATC1 -0.059 0.253 -9999 0 -0.61 5 5
B-cell antigen/BCR complex -0.141 0.267 -9999 0 -0.565 8 8
PAG1/CSK -0.055 0.171 -9999 0 -0.586 3 3
NFKBIB 0.017 0.039 0.098 1 -9999 0 1
HRAS -0.038 0.19 -9999 0 -0.511 3 3
NFKBIA 0.017 0.038 0.098 1 -9999 0 1
NF-kappa-B/RelA/I kappa B beta 0.023 0.033 -9999 0 -9999 0 0
RasGAP/Csk -0.151 0.218 -9999 0 -0.483 8 8
mol:GDP -0.045 0.186 -9999 0 -0.434 5 5
PTEN 0.016 0 -9999 0 -9999 0 0
CD79B -0.083 0.261 -9999 0 -0.773 4 4
NF-kappa-B/RelA/I kappa B alpha 0.024 0.033 -9999 0 -9999 0 0
GRB2 0.016 0 -9999 0 -9999 0 0
PI3K/BCAP/CD19 -0.105 0.276 -9999 0 -0.625 6 6
PIK3R1 -0.008 0.137 -9999 0 -0.773 1 1
mol:IP3 -0.05 0.198 -9999 0 -0.468 5 5
CSK 0.016 0 -9999 0 -9999 0 0
FOS -0.069 0.215 -9999 0 -0.521 4 4
CHUK 0.008 0.105 -9999 0 -0.285 1 1
IBTK -0.008 0.137 -9999 0 -0.773 1 1
CARD11/BCL10/MALT1/TAK1 -0.072 0.16 -9999 0 -0.511 3 3
PTPN6 -0.112 0.247 -9999 0 -0.709 4 4
RELA 0.016 0 -9999 0 -9999 0 0
BCL2A1 -0.003 0.054 -9999 0 -0.119 3 3
VAV2 -0.166 0.352 -9999 0 -0.94 5 5
ubiquitin-dependent protein catabolic process 0.022 0.037 0.102 1 -9999 0 1
BTK -0.07 0.286 -9999 0 -1.176 2 2
CD19 -0.179 0.377 -9999 0 -0.996 5 5
MAP4K1 0.016 0 -9999 0 -9999 0 0
CD72 -0.084 0.238 -9999 0 -0.625 5 5
PAG1 -0.058 0.23 -9999 0 -0.773 3 3
MAPK14 -0.075 0.22 -9999 0 -0.528 5 5
SH3BP5 -0.075 0.244 -9999 0 -0.712 4 4
PIK3AP1 -0.087 0.225 -9999 0 -0.525 4 4
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.11 0.242 -9999 0 -0.663 4 4
RAF1 -0.026 0.18 -9999 0 -0.472 3 3
RasGAP/p62DOK/SHIP -0.145 0.211 -9999 0 -0.655 2 2
CD79A -0.084 0.238 -9999 0 -0.625 5 5
re-entry into mitotic cell cycle -0.03 0.135 0.211 1 -0.271 4 5
RASA1 -0.001 0.094 -9999 0 -0.526 1 1
MAPK3 -0.002 0.155 -9999 0 -0.394 2 2
MAPK1 -0.002 0.155 -9999 0 -0.394 2 2
CD72/SHP1 -0.119 0.262 -9999 0 -0.612 5 5
NFKB1 0.016 0 -9999 0 -9999 0 0
MAPK8 -0.075 0.22 -9999 0 -0.528 5 5
actin cytoskeleton organization -0.097 0.291 -9999 0 -0.733 5 5
NF-kappa-B/RelA 0.051 0.063 0.193 1 -9999 0 1
Calcineurin -0.091 0.15 -9999 0 -0.417 3 3
PI3K -0.129 0.222 -9999 0 -0.656 4 4
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.055 0.223 0.281 1 -0.53 5 6
SOS1 0.016 0 -9999 0 -9999 0 0
Bam32/HPK1 -0.213 0.373 -9999 0 -0.786 9 9
DAPP1 -0.27 0.411 -9999 0 -0.905 9 9
cytokine secretion -0.051 0.234 -9999 0 -0.557 5 5
mol:DAG -0.05 0.198 -9999 0 -0.468 5 5
PLCG2 -0.025 0.164 -9999 0 -0.65 2 2
MAP2K1 -0.014 0.169 -9999 0 -0.428 3 3
B-cell antigen/BCR complex/FcgammaRIIB -0.171 0.258 -9999 0 -0.571 8 8
mol:PI-3-4-5-P3 -0.091 0.147 -9999 0 -0.428 4 4
ETS1 -0.031 0.197 -9999 0 -0.525 3 3
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.128 0.237 -9999 0 -0.852 2 2
B-cell antigen/BCR complex/LYN -0.132 0.285 -9999 0 -0.814 4 4
MALT1 0.016 0 -9999 0 -9999 0 0
TRAF6 0.016 0 -9999 0 -9999 0 0
RAC1 -0.11 0.321 -9999 0 -0.814 5 5
B-cell antigen/BCR complex/LYN/SYK -0.136 0.237 -9999 0 -0.682 4 4
CARD11 -0.05 0.224 -9999 0 -0.633 3 3
FCGR2B -0.067 0.225 -9999 0 -0.65 4 4
PPP3CA -0.058 0.23 -9999 0 -0.773 3 3
BCL10 0.016 0 -9999 0 -9999 0 0
IKK complex 0.014 0.047 -9999 0 -9999 0 0
PTPRC -0.008 0.137 -9999 0 -0.773 1 1
PDPK1 -0.052 0.143 -9999 0 -0.305 4 4
PPP3CB 0.016 0 -9999 0 -9999 0 0
PPP3CC 0.016 0 -9999 0 -9999 0 0
POU2F2 0.023 0.024 -9999 0 -9999 0 0
Syndecan-4-mediated signaling events

Figure 42.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 44.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.031 0.173 -9999 0 -0.619 2 2
Syndecan-4/Syndesmos -0.015 0.172 -9999 0 -0.568 2 2
positive regulation of JNK cascade -0.125 0.206 -9999 0 -0.582 4 4
Syndecan-4/ADAM12 -0.062 0.255 -9999 0 -0.736 3 3
CCL5 -0.025 0.164 -9999 0 -0.65 2 2
Rac1/GDP 0 0 -9999 0 -9999 0 0
DNM2 0.016 0 -9999 0 -9999 0 0
ITGA5 -0.018 0.131 -9999 0 -0.526 2 2
SDCBP -0.008 0.137 -9999 0 -0.773 1 1
PLG 0.015 0.012 -9999 0 -9999 0 0
ADAM12 -0.075 0.244 -9999 0 -0.712 4 4
mol:GTP 0 0 -9999 0 -9999 0 0
NUDT16L1 0.016 0 -9999 0 -9999 0 0
mol:PI-4-5-P2 0 0 -9999 0 -9999 0 0
Syndecan-4/PKC alpha -0.019 0.038 -9999 0 -9999 0 0
Syndecan-4/Laminin alpha1 -0.015 0.172 -9999 0 -0.568 2 2
Syndecan-4/CXCL12/CXCR4 -0.086 0.247 -9999 0 -0.621 4 4
Syndecan-4/Laminin alpha3 -0.08 0.208 -9999 0 -0.568 2 2
MDK -0.058 0.23 -9999 0 -0.773 3 3
Syndecan-4/FZD7 -0.035 0.226 -9999 0 -0.687 3 3
Syndecan-4/Midkine -0.054 0.231 -9999 0 -0.76 2 2
FZD7 -0.025 0.164 -9999 0 -0.65 2 2
Syndecan-4/FGFR1/FGF -0.062 0.137 -9999 0 -0.517 2 2
THBS1 -0.033 0.191 -9999 0 -0.773 2 2
integrin-mediated signaling pathway -0.1 0.257 -9999 0 -0.698 3 3
positive regulation of MAPKKK cascade -0.125 0.206 -9999 0 -0.582 4 4
Syndecan-4/TACI -0.015 0.172 -9999 0 -0.568 2 2
CXCR4 -0.033 0.191 -9999 0 -0.773 2 2
cell adhesion -0.036 0.156 -9999 0 -0.381 5 5
Syndecan-4/Dynamin -0.015 0.172 -9999 0 -0.568 2 2
Syndecan-4/TSP1 -0.042 0.19 -9999 0 -0.568 2 2
Syndecan-4/GIPC -0.015 0.172 -9999 0 -0.568 2 2
Syndecan-4/RANTES -0.035 0.219 -9999 0 -0.76 2 2
ITGB1 0.016 0 -9999 0 -9999 0 0
LAMA1 0.016 0 -9999 0 -9999 0 0
LAMA3 -0.109 0.265 -9999 0 -0.65 6 6
RAC1 0.016 0 -9999 0 -9999 0 0
PRKCA -0.019 0.158 -9999 0 -0.598 2 2
Syndecan-4/alpha-Actinin -0.036 0.212 -9999 0 -0.608 3 3
TFPI -0.152 0.274 -9999 0 -0.581 9 9
F2 0.018 0.005 -9999 0 -9999 0 0
alpha5/beta1 Integrin -0.023 0.09 -9999 0 -0.37 2 2
positive regulation of cell adhesion -0.069 0.203 -9999 0 -0.544 2 2
ACTN1 -0.025 0.164 -9999 0 -0.65 2 2
TNC -0.158 0.308 -9999 0 -0.681 8 8
Syndecan-4/CXCL12 -0.072 0.205 -9999 0 -0.568 2 2
FGF6 0.016 0 -9999 0 -9999 0 0
RHOA 0.016 0 -9999 0 -9999 0 0
CXCL12 -0.092 0.255 -9999 0 -0.674 5 5
TNFRSF13B 0.016 0 -9999 0 -9999 0 0
FGF2 -0.001 0.094 -9999 0 -0.526 1 1
FGFR1 0.016 0 -9999 0 -9999 0 0
Syndecan-4/PI-4-5-P2 -0.025 0.171 -9999 0 -0.576 2 2
mol:GDP 0 0 -9999 0 -9999 0 0
FN1 -0.083 0.235 -9999 0 -0.618 5 5
cell migration -0.004 0.012 -9999 0 -9999 0 0
PRKCD 0.015 0.012 -9999 0 -9999 0 0
vasculogenesis -0.04 0.184 -9999 0 -0.546 2 2
SDC4 -0.026 0.181 -9999 0 -0.609 2 2
Syndecan-4/Tenascin C -0.105 0.269 -9999 0 -0.736 3 3
Syndecan-4/PI-4-5-P2/PKC alpha -0.015 0.03 -9999 0 -9999 0 0
Syndecan-4/Syntenin -0.027 0.218 -9999 0 -0.76 2 2
MMP9 -0.03 0.192 -9999 0 -0.775 2 2
Rac1/GTP -0.037 0.16 -9999 0 -0.391 5 5
cytoskeleton organization -0.014 0.166 -9999 0 -0.546 2 2
GIPC1 0.016 0 -9999 0 -9999 0 0
Syndecan-4/TFPI -0.099 0.234 -9999 0 -0.634 3 3
Visual signal transduction: Rods

Figure 43.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 45.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 + 0.016 0 -9999 0 -9999 0 0
GNAT1/GTP -0.031 0.121 -9999 0 -0.489 2 2
Metarhodopsin II/Arrestin -0.045 0.124 -9999 0 -0.363 4 4
PDE6G/GNAT1/GTP -0.055 0.132 -9999 0 -0.511 1 1
mol:GTP 0 0 -9999 0 -9999 0 0
absorption of light 0 0 -9999 0 -9999 0 0
GNAT1 -0.025 0.164 -9999 0 -0.65 2 2
GRK1 0 0 -9999 0 -9999 0 0
CNG Channel -0.132 0.182 -9999 0 -0.791 1 1
mol:Na + -0.091 0.203 -9999 0 -0.769 2 2
mol:ADP 0 0 -9999 0 -9999 0 0
RGS9-1/Gbeta5/R9AP -0.169 0.302 -9999 0 -0.686 7 7
mol:GDP 0 0 -9999 0 -9999 0 0
cGMP/CNG Channel -0.094 0.213 -9999 0 -0.808 2 2
CNGB1 0.016 0 -9999 0 -9999 0 0
RDH5 -0.001 0.094 -9999 0 -0.526 1 1
SAG -0.059 0.203 -9999 0 -0.588 4 4
mol:Ca2+ -0.033 0.218 -9999 0 -0.736 2 2
Na + (4 Units) -0.083 0.185 -9999 0 -0.705 2 2
RGS9 -0.082 0.261 -9999 0 -0.773 4 4
GNB1/GNGT1 -0.257 0.254 -9999 0 -0.586 9 9
GNAT1/GDP -0.168 0.28 -9999 0 -0.61 8 8
GUCY2D 0.016 0 -9999 0 -9999 0 0
GNGT1 -0.341 0.348 -9999 0 -0.657 17 17
GUCY2F -0.058 0.23 -9999 0 -0.773 3 3
GNB5 -0.042 0.186 -9999 0 -0.608 3 3
mol:GMP (4 units) -0.092 0.22 -9999 0 -0.514 5 5
mol:11-cis-retinal -0.001 0.094 -9999 0 -0.525 1 1
mol:cGMP -0.034 0.218 -9999 0 -0.655 3 3
GNB1 0.016 0 -9999 0 -9999 0 0
Rhodopsin -0.012 0.064 -9999 0 -0.369 1 1
SLC24A1 0.016 0 -9999 0 -9999 0 0
CNGA1 -0.052 0.179 -9999 0 -0.526 4 4
Metarhodopsin II 0 0 -9999 0 -9999 0 0
mol:Ca ++ 0 0 -9999 0 -9999 0 0
GC1/GCAP Family -0.039 0.107 -9999 0 -0.453 1 1
RGS9BP -0.109 0.265 -9999 0 -0.65 6 6
Metarhodopsin II/Transducin -0.133 0.15 -9999 0 -0.323 10 10
GCAP Family/Ca ++ -0.04 0.11 -9999 0 -0.462 1 1
PDE6A/B -0.103 0.217 -9999 0 -0.55 6 6
mol:Pi -0.168 0.3 -9999 0 -0.681 7 7
mol:all-trans-retinal 0 0 -9999 0 -9999 0 0
Transducin -0.222 0.197 -9999 0 -0.462 10 10
PDE6B -0.124 0.295 -9999 0 -0.732 6 6
PDE6A 0.016 0 -9999 0 -9999 0 0
PDE6G -0.035 0.158 -9999 0 -0.526 3 3
RHO 0.016 0 -9999 0 -9999 0 0
PDE6 -0.227 0.315 -9999 0 -0.906 4 4
GUCA1A -0.001 0.094 -9999 0 -0.526 1 1
GC2/GCAP Family -0.082 0.214 -9999 0 -0.695 3 3
GUCA1C -0.001 0.094 -9999 0 -0.526 1 1
GUCA1B -0.025 0.164 -9999 0 -0.65 2 2
Signaling events mediated by Stem cell factor receptor (c-Kit)

Figure 44.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 46.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.075 0.17 -9999 0 -9999 0 0
CRKL -0.089 0.179 -9999 0 -0.404 4 4
HRAS -0.033 0.145 -9999 0 -9999 0 0
mol:PIP3 -0.112 0.22 0.305 1 -0.546 4 5
SPRED1 -0.033 0.191 -9999 0 -0.773 2 2
SPRED2 -0.025 0.164 -9999 0 -0.65 2 2
GAB1 -0.088 0.18 -9999 0 -0.429 4 4
FOXO3 -0.079 0.18 -9999 0 -0.419 4 4
AKT1 -0.095 0.192 -9999 0 -0.44 6 6
BAD -0.079 0.18 -9999 0 -0.419 4 4
megakaryocyte differentiation -0.136 0.241 -9999 0 -0.507 8 8
GSK3B -0.079 0.18 -9999 0 -0.419 4 4
RAF1 -0.017 0.126 -9999 0 -9999 0 0
SHC1 -0.001 0.094 -9999 0 -0.526 1 1
STAT3 -0.074 0.173 -9999 0 -0.411 4 4
STAT1 -0.152 0.35 -9999 0 -0.933 4 4
HRAS/SPRED1 -0.041 0.148 -9999 0 -0.441 1 1
cell proliferation -0.072 0.17 -9999 0 -0.431 3 3
PIK3CA 0.016 0.001 -9999 0 -9999 0 0
TEC 0.016 0 -9999 0 -9999 0 0
RPS6KB1 -0.084 0.181 -9999 0 -0.416 5 5
HRAS/SPRED2 -0.036 0.147 -9999 0 -0.503 1 1
LYN/TEC/p62DOK -0.093 0.135 -9999 0 -9999 0 0
MAPK3 0.003 0.098 -9999 0 -9999 0 0
STAP1 -0.102 0.203 -9999 0 -0.471 5 5
GRAP2 0.016 0 -9999 0 -9999 0 0
JAK2 -0.179 0.269 -9999 0 -0.791 4 4
STAT1 (dimer) -0.148 0.343 -9999 0 -0.912 4 4
mol:Gleevec 0.002 0.007 -9999 0 -9999 0 0
GRB2/SOCS1/VAV1 -0.104 0.141 -9999 0 -0.399 3 3
actin filament polymerization -0.082 0.17 -9999 0 -0.378 6 6
LYN 0.016 0 -9999 0 -9999 0 0
STAP1/STAT5A (dimer) -0.111 0.246 -9999 0 -0.613 4 4
PIK3R1 -0.009 0.138 -9999 0 -0.776 1 1
CBL/CRKL/GRB2 -0.065 0.165 -9999 0 -9999 0 0
PI3K -0.084 0.202 -9999 0 -0.496 4 4
PTEN 0.016 0 -9999 0 -9999 0 0
SCF/KIT/EPO/EPOR -0.168 0.419 -9999 0 -1.285 3 3
MAPK8 -0.074 0.173 -9999 0 -0.44 3 3
STAT3 (dimer) -0.072 0.17 -9999 0 -0.403 4 4
positive regulation of transcription 0.007 0.086 -9999 0 -9999 0 0
mol:GDP -0.088 0.115 -9999 0 -9999 0 0
PIK3C2B -0.128 0.245 -9999 0 -0.547 6 6
CBL/CRKL -0.075 0.17 -9999 0 -9999 0 0
FER -0.074 0.173 -9999 0 -0.44 3 3
SH2B3 -0.087 0.205 -9999 0 -0.517 4 4
PDPK1 -0.126 0.249 -9999 0 -0.539 6 6
SNAI2 -0.113 0.207 -9999 0 -0.525 4 4
positive regulation of cell proliferation -0.112 0.268 -9999 0 -0.685 4 4
KITLG -0.034 0.193 -9999 0 -0.78 2 2
cell motility -0.112 0.268 -9999 0 -0.685 4 4
PTPN6 0.013 0.015 -9999 0 -9999 0 0
EPOR -0.014 0.116 -9999 0 -9999 0 0
STAT5A (dimer) -0.093 0.229 -9999 0 -0.569 4 4
SOCS1 0.016 0 -9999 0 -9999 0 0
cell migration 0.072 0.17 0.431 3 -9999 0 3
SOS1 0.016 0 -9999 0 -9999 0 0
EPO 0.012 0.01 -9999 0 -9999 0 0
VAV1 -0.008 0.137 -9999 0 -0.773 1 1
GRB10 -0.104 0.211 -9999 0 -0.505 5 5
PTPN11 0.018 0.007 -9999 0 -9999 0 0
SCF/KIT -0.09 0.18 -9999 0 -0.404 6 6
GO:0007205 0.003 0.01 -9999 0 -9999 0 0
MAP2K1 -0.002 0.106 -9999 0 -9999 0 0
CBL 0.016 0 -9999 0 -9999 0 0
KIT -0.171 0.438 -9999 0 -1.2 4 4
MAP2K2 -0.002 0.106 -9999 0 -9999 0 0
SHC/Grb2/SOS1 -0.099 0.135 -9999 0 -0.399 3 3
STAT5A -0.096 0.235 -9999 0 -0.586 4 4
GRB2 0.016 0 -9999 0 -9999 0 0
response to radiation -0.11 0.203 -9999 0 -0.513 4 4
SHC/GRAP2 -0.012 0.064 -9999 0 -0.37 1 1
PTPRO -0.14 0.246 -9999 0 -0.518 8 8
SH2B2 -0.083 0.173 -9999 0 -0.385 6 6
DOK1 0.016 0 -9999 0 -9999 0 0
MATK -0.074 0.173 -9999 0 -0.44 3 3
CREBBP 0.032 0.022 -9999 0 -9999 0 0
BCL2 -0.042 0.175 -9999 0 -9999 0 0
Coregulation of Androgen receptor activity

Figure 45.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 47.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.006 0.138 -9999 0 -0.772 1 1
SVIL -0.007 0.137 -9999 0 -0.772 1 1
ZNF318 0.012 0 -9999 0 -9999 0 0
JMJD2C 0.026 0 -9999 0 -9999 0 0
T-DHT/AR/Ubc9 -0.034 0.114 -9999 0 -0.493 1 1
CARM1 0.016 0 -9999 0 -9999 0 0
PRDX1 -0.001 0.094 -9999 0 -0.526 1 1
PELP1 0.015 0 -9999 0 -9999 0 0
CTNNB1 0.001 0.094 -9999 0 -0.524 1 1
AKT1 0.015 0 -9999 0 -9999 0 0
PTK2B 0.017 0 -9999 0 -9999 0 0
MED1 -0.027 0.164 -9999 0 -0.65 2 2
MAK -0.022 0.131 -9999 0 -0.53 2 2
response to oxidative stress 0 0 -9999 0 -9999 0 0
HIP1 0.001 0.094 -9999 0 -0.524 1 1
GSN -0.056 0.23 -9999 0 -0.772 3 3
NCOA2 0.016 0 -9999 0 -9999 0 0
NCOA6 0.018 0 -9999 0 -9999 0 0
DNA-PK -0.016 0.088 -9999 0 -0.505 1 1
NCOA4 0.016 0 -9999 0 -9999 0 0
PIAS3 0.018 0 -9999 0 -9999 0 0
cell proliferation -0.039 0.088 -9999 0 -0.355 2 2
XRCC5 0.015 0 -9999 0 -9999 0 0
UBE3A 0.019 0 -9999 0 -9999 0 0
T-DHT/AR/SNURF -0.045 0.114 -9999 0 -0.404 2 2
FHL2 -0.21 0.427 -9999 0 -0.904 8 8
RANBP9 0.018 0 -9999 0 -9999 0 0
JMJD1A -0.006 0.061 -9999 0 -9999 0 0
CDK6 0.016 0 -9999 0 -9999 0 0
TGFB1I1 -0.007 0.138 -9999 0 -0.772 1 1
T-DHT/AR/CyclinD1 -0.07 0.158 -9999 0 -0.538 2 2
XRCC6 0.015 0 -9999 0 -9999 0 0
T-DHT/AR -0.061 0.153 -9999 0 -0.482 1 1
CTDSP1 0.017 0 -9999 0 -9999 0 0
CTDSP2 0.013 0 -9999 0 -9999 0 0
BRCA1 0.001 0.094 -9999 0 -0.523 1 1
TCF4 0.014 0 -9999 0 -9999 0 0
CDKN2A -0.25 0.35 -9999 0 -0.692 12 12
SRF -0.007 0.058 -9999 0 -9999 0 0
NKX3-1 -0.072 0.103 -9999 0 -0.28 3 3
KLK3 0.047 0.055 -9999 0 -9999 0 0
TMF1 0.017 0 -9999 0 -9999 0 0
HNRNPA1 0.015 0 -9999 0 -9999 0 0
AOF2 0.018 0 -9999 0 -9999 0 0
APPL1 0.007 0.107 -9999 0 -0.589 1 1
T-DHT/AR/Caspase 8 -0.037 0.113 -9999 0 -0.494 1 1
AR -0.047 0.16 -9999 0 -0.636 2 2
UBA3 0.001 0 -9999 0 -9999 0 0
PATZ1 0.015 0 -9999 0 -9999 0 0
PAWR -0.033 0.191 -9999 0 -0.773 2 2
PRKDC -0.009 0.137 -9999 0 -0.775 1 1
PA2G4 0.014 0 -9999 0 -9999 0 0
UBE2I 0.016 0 -9999 0 -9999 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.04 0.112 -9999 0 -0.454 1 1
RPS6KA3 0.018 0 -9999 0 -9999 0 0
T-DHT/AR/ARA70 -0.034 0.114 -9999 0 -0.493 1 1
LATS2 0.015 0 -9999 0 -9999 0 0
T-DHT/AR/PRX1 -0.041 0.118 -9999 0 -0.407 2 2
Cyclin D3/CDK11 p58 -0.012 0.066 -9999 0 -0.382 1 1
VAV3 -0.058 0.203 -9999 0 -0.586 4 4
KLK2 0.006 0.062 -9999 0 -9999 0 0
CASP8 0.016 0 -9999 0 -9999 0 0
T-DHT/AR/TIF2/CARM1 -0.018 0.105 -9999 0 -0.443 1 1
TMPRSS2 -0.233 0.49 -9999 0 -1.153 7 7
CCND1 -0.042 0.185 -9999 0 -0.607 3 3
PIAS1 0.019 0 -9999 0 -9999 0 0
mol:T-DHT -0.027 0.048 -9999 0 -0.086 12 12
CDC2L1 0 0 -9999 0 -9999 0 0
PIAS4 0.02 0 -9999 0 -9999 0 0
T-DHT/AR/CDK6 -0.035 0.114 -9999 0 -0.493 1 1
CMTM2 -0.001 0.094 -9999 0 -0.526 1 1
SNURF 0 0 -9999 0 -9999 0 0
ZMIZ1 -0.006 0.041 -9999 0 -9999 0 0
CCND3 -0.001 0.094 -9999 0 -0.526 1 1
TGIF1 -0.01 0.137 -9999 0 -0.775 1 1
FKBP4 0.018 0 -9999 0 -9999 0 0
ErbB4 signaling events

Figure 46.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 48.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.004 0.114 -9999 0 -0.466 1 1
epithelial cell differentiation -0.029 0.067 -9999 0 -9999 0 0
ITCH 0.023 0.015 -9999 0 -9999 0 0
WWP1 0.024 0.057 -9999 0 -9999 0 0
FYN 0.016 0 -9999 0 -9999 0 0
EGFR -0.175 0.312 -9999 0 -0.663 9 9
PRL 0.016 0 -9999 0 -9999 0 0
neuron projection morphogenesis 0.055 0.091 -9999 0 -9999 0 0
PTPRZ1 -0.277 0.322 -9999 0 -0.608 15 15
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.019 0.081 -9999 0 -9999 0 0
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.021 0.069 -9999 0 -9999 0 0
ADAM17 0.023 0.015 -9999 0 -9999 0 0
ErbB4/ErbB4 0.019 0.072 -9999 0 -9999 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.018 0.168 -9999 0 -0.517 3 3
NCOR1 0.016 0 -9999 0 -9999 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.028 0.064 -9999 0 -9999 0 0
GRIN2B 0.021 0.087 -9999 0 -9999 0 0
ErbB4/ErbB2/betacellulin -0.03 0.158 -9999 0 -0.414 4 4
STAT1 -0.008 0.137 -9999 0 -0.773 1 1
HBEGF -0.025 0.164 -9999 0 -0.65 2 2
PRLR -0.018 0.131 -9999 0 -0.526 2 2
E4ICDs/ETO2 0.012 0.079 -9999 0 -9999 0 0
axon guidance 0.075 0.105 -9999 0 -9999 0 0
NEDD4 0.023 0.015 -9999 0 -9999 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.023 0.09 -9999 0 -0.37 2 2
CBFA2T3 -0.001 0.094 -9999 0 -0.526 1 1
ErbB4/ErbB2/HBEGF 0.005 0.108 -9999 0 -9999 0 0
MAPK3 0.046 0.093 -9999 0 -9999 0 0
STAT1 (dimer) 0.006 0.104 -9999 0 -0.467 1 1
MAPK1 0.046 0.093 -9999 0 -9999 0 0
JAK2 0.016 0 -9999 0 -9999 0 0
ErbB4/ErbB2/neuregulin 1 beta 0.019 0.078 -9999 0 -9999 0 0
NRG1 0.02 0.072 -9999 0 -0.376 1 1
NRG3 -0.05 0.209 -9999 0 -0.691 3 3
NRG2 -0.001 0.094 -9999 0 -0.526 1 1
NRG4 -0.001 0.094 -9999 0 -0.526 1 1
heart development 0.075 0.105 -9999 0 -9999 0 0
neural crest cell migration 0.019 0.078 -9999 0 -9999 0 0
ERBB2 0.02 0.072 -9999 0 -0.376 1 1
WWOX/E4ICDs 0.022 0.06 -9999 0 -9999 0 0
SHC1 -0.001 0.094 -9999 0 -0.526 1 1
ErbB4/EGFR/neuregulin 4 -0.09 0.197 -9999 0 -0.422 7 7
apoptosis 0.11 0.163 0.591 3 -9999 0 3
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.012 0.079 -9999 0 -9999 0 0
ErbB4/ErbB2/epiregulin -0.269 0.193 -9999 0 -0.57 3 3
ErbB4/ErbB4/betacellulin/betacellulin -0.042 0.171 -9999 0 -0.466 4 4
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.041 0.087 -9999 0 -9999 0 0
MDM2 0.012 0.128 -9999 0 -0.636 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.012 0.045 -9999 0 -9999 0 0
STAT5A 0.079 0.098 -9999 0 -9999 0 0
ErbB4/EGFR/neuregulin 1 beta -0.081 0.183 -9999 0 -9999 0 0
DLG4 0.016 0 -9999 0 -9999 0 0
GRB2/SHC -0.012 0.064 -9999 0 -0.37 1 1
E4ICDs/TAB2/NCoR1 0.016 0.109 -9999 0 -0.512 1 1
STAT5A (dimer) -0.03 0.07 -9999 0 -9999 0 0
MAP3K7IP2 -0.008 0.137 -9999 0 -0.773 1 1
STAT5B (dimer) 0.073 0.094 -9999 0 -9999 0 0
LRIG1 -0.033 0.191 -9999 0 -0.773 2 2
EREG -0.508 0.298 -9999 0 -0.655 25 25
BTC -0.082 0.261 -9999 0 -0.773 4 4
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.075 0.106 -9999 0 -9999 0 0
ERBB4 0.019 0.072 -9999 0 -9999 0 0
STAT5B 0.016 0 -9999 0 -9999 0 0
YAP1 -0.012 0.04 -9999 0 -9999 0 0
GRB2 0.016 0 -9999 0 -9999 0 0
ErbB4/ErbB2/neuregulin 4 0.019 0.092 -9999 0 -9999 0 0
glial cell differentiation 0.029 0.093 0.507 1 -9999 0 1
WWOX 0.016 0 -9999 0 -9999 0 0
cell proliferation -0.007 0.191 -9999 0 -0.802 1 1
Sphingosine 1-phosphate (S1P) pathway

Figure 47.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 49.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.001 0.094 -9999 0 -0.526 1 1
SPHK1 -0.076 0.218 -9999 0 -0.575 5 5
GNAI2 -0.008 0.137 -9999 0 -0.773 1 1
mol:S1P -0.029 0.103 -9999 0 -0.348 1 1
GNAO1 0.016 0 -9999 0 -9999 0 0
mol:Sphinganine-1-P -0.053 0.173 -9999 0 -0.406 6 6
growth factor activity 0 0 -9999 0 -9999 0 0
S1P/S1P2/G12/G13 -0.04 0.085 -9999 0 -0.387 1 1
GNAI3 0.016 0 -9999 0 -9999 0 0
G12/G13 -0.012 0.064 -9999 0 -0.37 1 1
S1PR3 0 0 -9999 0 -9999 0 0
S1PR2 0 0 -9999 0 -9999 0 0
EDG1 -0.008 0.137 -9999 0 -0.773 1 1
S1P1/S1P -0.032 0.119 -9999 0 -0.488 1 1
S1PR5 0 0 -9999 0 -9999 0 0
S1PR4 0 0 -9999 0 -9999 0 0
GNAI1 -0.008 0.137 -9999 0 -0.773 1 1
S1P/S1P5/G12 -0.036 0.067 -9999 0 -9999 0 0
S1P/S1P3/Gq -0.049 0.152 -9999 0 -0.399 4 4
S1P/S1P4/Gi 0.004 0.094 -9999 0 -0.328 2 2
GNAQ 0 0 -9999 0 -9999 0 0
GNAZ 0.016 0 -9999 0 -9999 0 0
GNA14 -0.075 0.244 -9999 0 -0.712 4 4
GNA15 -0.042 0.186 -9999 0 -0.608 3 3
GNA12 0.016 0 -9999 0 -9999 0 0
GNA13 -0.001 0.094 -9999 0 -0.526 1 1
GNA11 0.016 0 -9999 0 -9999 0 0
ABCC1 -0.018 0.131 -9999 0 -0.526 2 2
Ephrin A reverse signaling

Figure 48.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 50.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.026 0.102 -9999 0 -0.411 2 2
EFNA5 -0.008 0.137 -9999 0 -0.773 1 1
FYN 0.007 0.099 -9999 0 -0.46 1 1
neuron projection morphogenesis -0.026 0.102 -9999 0 -0.411 2 2
cell-cell signaling 0 0 -9999 0 -9999 0 0
Ephrin A5/EPHA5 -0.026 0.103 -9999 0 -0.412 2 2
EPHA5 -0.001 0.094 -9999 0 -0.526 1 1
Cellular roles of Anthrax toxin

Figure 49.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 51.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.025 0.164 -9999 0 -0.65 2 2
ANTXR2 -0.025 0.164 -9999 0 -0.65 2 2
negative regulation of myeloid dendritic cell antigen processing and presentation -0.01 0.027 -9999 0 -0.08 4 4
monocyte activation -0.04 0.213 -9999 0 -0.783 2 2
MAP2K2 -0.004 0.01 -9999 0 -9999 0 0
MAP2K1 -0.008 0.022 -9999 0 -9999 0 0
MAP2K7 -0.008 0.022 -9999 0 -9999 0 0
MAP2K6 -0.025 0.068 -9999 0 -0.273 2 2
CYAA -0.028 0.128 -9999 0 -0.355 4 4
MAP2K4 -0.008 0.022 -9999 0 -9999 0 0
IL1B -0.081 0.171 -9999 0 -0.363 8 8
Channel -0.047 0.129 -9999 0 -0.378 4 4
NLRP1 -0.008 0.022 -9999 0 -9999 0 0
CALM1 0.016 0 -9999 0 -9999 0 0
negative regulation of phagocytosis -0.011 0.031 -9999 0 -9999 0 0
mol:Ca2+ 0 0 -9999 0 -9999 0 0
regulation of endothelial cell proliferation 0.01 0.027 0.08 4 -9999 0 4
MAPK3 -0.008 0.022 -9999 0 -9999 0 0
MAPK1 -0.008 0.022 -9999 0 -9999 0 0
PGR -0.008 0.022 -9999 0 -9999 0 0
PA/Cellular Receptors -0.052 0.141 -9999 0 -0.412 4 4
apoptosis -0.01 0.027 -9999 0 -0.08 4 4
LOC728358 0 0 -9999 0 -9999 0 0
Lethal toxin (unfolded) -0.026 0.126 -9999 0 -0.347 4 4
macrophage activation 0.015 0.026 -9999 0 -9999 0 0
TNF -0.025 0.164 -9999 0 -0.65 2 2
VCAM1 -0.04 0.217 -9999 0 -0.794 2 2
platelet activation -0.011 0.031 -9999 0 -9999 0 0
MAPKKK cascade -0.005 0.032 -9999 0 -9999 0 0
IL18 -0.041 0.145 -9999 0 -0.408 4 4
negative regulation of macrophage activation -0.01 0.027 -9999 0 -0.08 4 4
LEF -0.01 0.027 -9999 0 -0.081 4 4
CASP1 -0.01 0.024 -9999 0 -9999 0 0
mol:cAMP -0.011 0.031 -9999 0 -9999 0 0
necrosis -0.01 0.027 -9999 0 -0.08 4 4
intracellular pH reduction 0 0 -9999 0 -9999 0 0
PAGA 0 0 -9999 0 -9999 0 0
Edema toxin (unfolded) -0.027 0.129 -9999 0 -0.357 4 4
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -9999 0 -9999 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

Figure 50.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 52.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.101 0.198 -9999 0 -0.462 7 7
CRKL -0.034 0.145 -9999 0 -0.401 2 2
mol:PIP3 -0.023 0.012 -9999 0 -9999 0 0
AKT1 -0.041 0.138 -9999 0 -0.469 3 3
PTK2B 0.016 0 -9999 0 -9999 0 0
RAPGEF1 -0.023 0.138 -9999 0 -0.374 2 2
RANBP10 -0.025 0.164 -9999 0 -0.65 2 2
PIK3CA 0.016 0 -9999 0 -9999 0 0
HGF/MET/SHIP2 -0.101 0.181 -9999 0 -0.501 4 4
MAP3K5 -0.005 0.124 -9999 0 -9999 0 0
HGF/MET/CIN85/CBL/ENDOPHILINS -0.084 0.152 -9999 0 -0.453 3 3
AP1 -0.116 0.231 -9999 0 -0.487 7 7
mol:SU11274 0 0 -9999 0 -9999 0 0
SHC1 -0.001 0.094 -9999 0 -0.526 1 1
apoptosis -0.1 0.261 -9999 0 -0.883 3 3
STAT3 (dimer) -0.005 0.11 -9999 0 -9999 0 0
GAB1/CRKL/SHP2/PI3K -0.067 0.142 -9999 0 -0.633 1 1
INPP5D 0 0 -9999 0 -9999 0 0
CBL/CRK -0.009 0.124 -9999 0 -0.378 1 1
PTPN11 0.016 0 -9999 0 -9999 0 0
GO:0007205 0 0 -9999 0 -9999 0 0
PLCG1 0.016 0 -9999 0 -9999 0 0
PTEN 0.016 0 -9999 0 -9999 0 0
ELK1 -0.05 0.099 -9999 0 -0.228 7 7
mol:SU5416 0 0 -9999 0 -9999 0 0
SHP2/GRB2/SOS1GAB1 -0.03 0.058 -9999 0 -9999 0 0
PAK1 -0.03 0.131 -9999 0 -0.437 3 3
HGF/MET/RANBP10 -0.11 0.184 -9999 0 -0.501 4 4
HRAS -0.053 0.227 -9999 0 -0.717 3 3
DOCK1 -0.023 0.138 -9999 0 -0.374 2 2
GAB1 -0.03 0.136 -9999 0 -0.353 4 4
CRK -0.02 0.13 -9999 0 -0.406 1 1
mol:PHA665752 0 0 -9999 0 -9999 0 0
mol:GDP -0.087 0.199 -9999 0 -0.673 3 3
JUN -0.058 0.23 -9999 0 -0.773 3 3
EntrezGene:200958 0 0 -9999 0 -9999 0 0
HGF/MET -0.039 0.118 -9999 0 -0.347 3 3
PIK3R1 -0.008 0.137 -9999 0 -0.773 1 1
cell morphogenesis -0.001 0.161 -9999 0 -0.607 1 1
GRB2/SHC -0.024 0.113 -9999 0 -9999 0 0
FOS -0.076 0.218 -9999 0 -0.575 5 5
GLMN 0 0 -9999 0 -9999 0 0
cell motility -0.05 0.098 -9999 0 -0.228 7 7
HGF/MET/MUC20 -0.087 0.171 -9999 0 -0.398 7 7
cell migration -0.024 0.111 -9999 0 -9999 0 0
GRB2 0.016 0 -9999 0 -9999 0 0
CBL 0.016 0 -9999 0 -9999 0 0
MET/RANBP10 -0.131 0.217 -9999 0 -0.466 9 9
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.016 0.116 -9999 0 -9999 0 0
MET/MUC20 -0.104 0.202 -9999 0 -0.474 7 7
RAP1B -0.012 0.132 -9999 0 -9999 0 0
RAP1A -0.012 0.132 -9999 0 -9999 0 0
HGF/MET/RANBP9 -0.085 0.167 -9999 0 -0.501 3 3
RAF1 -0.04 0.213 -9999 0 -0.663 3 3
STAT3 -0.006 0.111 -9999 0 -9999 0 0
cell proliferation -0.016 0.157 -9999 0 -0.437 3 3
RPS6KB1 -0.005 0.045 -9999 0 -9999 0 0
MAPK3 -0.052 0.09 -9999 0 -9999 0 0
MAPK1 -0.052 0.09 -9999 0 -9999 0 0
RANBP9 0.016 0 -9999 0 -9999 0 0
MAPK8 0.016 0.116 -9999 0 -9999 0 0
SRC -0.005 0.109 -9999 0 -9999 0 0
PI3K -0.029 0.156 -9999 0 -0.723 1 1
MET/Glomulin -0.08 0.186 -9999 0 -0.419 7 7
SOS1 0.016 0 -9999 0 -9999 0 0
MAP2K1 -0.027 0.198 -9999 0 -0.602 3 3
MET -0.126 0.274 -9999 0 -0.632 7 7
MAP4K1 -0.016 0.131 -9999 0 -0.375 1 1
PTK2 0.016 0 -9999 0 -9999 0 0
MAP2K2 -0.027 0.198 -9999 0 -0.602 3 3
BAD -0.03 0.131 -9999 0 -0.437 3 3
MAP2K4 0.005 0.116 -9999 0 -9999 0 0
SHP2/GRB2/SOS1/GAB1 -0.073 0.145 -9999 0 -0.454 3 3
INPPL1 -0.008 0.137 -9999 0 -0.773 1 1
PXN 0.016 0 -9999 0 -9999 0 0
SH3KBP1 -0.001 0.094 -9999 0 -0.526 1 1
HGS -0.027 0.111 -9999 0 -0.315 3 3
PLCgamma1/PKC 0 0 -9999 0 -9999 0 0
HGF 0.016 0 -9999 0 -9999 0 0
RASA1 -0.001 0.094 -9999 0 -0.526 1 1
NCK1 0.016 0 -9999 0 -9999 0 0
PTPRJ 0.016 0 -9999 0 -9999 0 0
NCK/PLCgamma1 -0.012 0.105 -9999 0 -9999 0 0
PDPK1 -0.055 0.146 -9999 0 -0.51 3 3
HGF/MET/SHIP -0.087 0.171 -9999 0 -0.398 7 7
Signaling events mediated by PTP1B

Figure 51.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 53.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.016 0 -9999 0 -9999 0 0
Jak2/Leptin Receptor -0.074 0.137 -9999 0 -0.514 2 2
PTP1B/AKT1 -0.077 0.109 -9999 0 -9999 0 0
FYN 0.016 0 -9999 0 -9999 0 0
p210 bcr-abl/PTP1B -0.092 0.121 -9999 0 -0.295 5 5
EGFR -0.18 0.315 -9999 0 -0.672 9 9
EGF/EGFR -0.223 0.253 -9999 0 -0.614 8 8
CSF1 -0.001 0.094 -9999 0 -0.526 1 1
AKT1 0.015 0.004 -9999 0 -9999 0 0
INSR -0.034 0.192 -9999 0 -0.776 2 2
PTP1B/N-cadherin -0.096 0.13 -9999 0 -0.428 1 1
Insulin Receptor/Insulin -0.09 0.131 -9999 0 -0.463 2 2
HCK -0.008 0.137 -9999 0 -0.773 1 1
CRK 0.016 0 -9999 0 -9999 0 0
TYK2 -0.079 0.115 -9999 0 -9999 0 0
EGF -0.131 0.276 -9999 0 -0.638 7 7
YES1 0.016 0 -9999 0 -9999 0 0
CAV1 -0.129 0.186 -9999 0 -0.426 7 7
TXN 0.011 0.006 -9999 0 -9999 0 0
PTP1B/IRS1/GRB2 -0.128 0.222 -9999 0 -0.658 4 4
cell migration 0.092 0.121 0.295 5 -9999 0 5
STAT3 0.016 0.001 -9999 0 -9999 0 0
PRLR -0.012 0.131 -9999 0 -0.519 2 2
ITGA2B -0.003 0.094 -9999 0 -0.527 1 1
CSF1R 0.016 0 -9999 0 -9999 0 0
Prolactin Receptor/Prolactin 0.013 0.096 -9999 0 -0.36 2 2
FGR 0.016 0 -9999 0 -9999 0 0
PTP1B/p130 Cas -0.079 0.115 -9999 0 -9999 0 0
Crk/p130 Cas -0.066 0.112 -9999 0 -9999 0 0
DOK1 -0.067 0.109 -9999 0 -9999 0 0
JAK2 -0.037 0.083 -9999 0 -0.299 1 1
Jak2/Leptin Receptor/Leptin -0.122 0.169 -9999 0 -0.596 2 2
PIK3R1 -0.008 0.137 -9999 0 -0.773 1 1
PTPN1 -0.093 0.122 -9999 0 -0.298 5 5
LYN 0.016 0 -9999 0 -9999 0 0
CDH2 -0.018 0.131 -9999 0 -0.526 2 2
SRC -0.017 0.047 -9999 0 -9999 0 0
ITGB3 -0.112 0.242 -9999 0 -0.563 7 7
CAT1/PTP1B -0.056 0.126 -9999 0 -9999 0 0
CAPN1 -0.028 0.164 -9999 0 -0.651 2 2
CSK 0.016 0 -9999 0 -9999 0 0
PI3K -0.087 0.156 -9999 0 -0.562 2 2
mol:H2O2 -0.003 0.006 -9999 0 -9999 0 0
STAT3 (dimer) -0.109 0.172 -9999 0 -0.514 3 3
negative regulation of transcription -0.036 0.082 -9999 0 -0.296 1 1
FCGR2A -0.082 0.261 -9999 0 -0.773 4 4
FER 0.011 0.006 -9999 0 -9999 0 0
alphaIIb/beta3 Integrin -0.098 0.178 -9999 0 -0.399 8 8
BLK -0.025 0.164 -9999 0 -0.65 2 2
Insulin Receptor/Insulin/Shc -0.05 0.138 -9999 0 -0.501 2 2
RHOA 0.013 0.005 -9999 0 -9999 0 0
LEPR -0.059 0.202 -9999 0 -0.584 4 4
BCAR1 0.016 0 -9999 0 -9999 0 0
p210 bcr-abl/Grb2 0.016 0 -9999 0 -9999 0 0
mol:NADPH -0.004 0.004 -9999 0 -9999 0 0
TRPV6 0.016 0.091 -9999 0 -9999 0 0
PRL 0.022 0.003 -9999 0 -9999 0 0
SOCS3 -0.037 0.274 -9999 0 -1.482 1 1
SPRY2 -0.038 0.193 -9999 0 -0.784 2 2
Insulin Receptor/Insulin/IRS1 -0.114 0.202 -9999 0 -0.505 6 6
CSF1/CSF1R -0.075 0.113 -9999 0 -9999 0 0
Ras protein signal transduction 0.047 0.035 -9999 0 -9999 0 0
IRS1 -0.099 0.272 -9999 0 -0.724 5 5
INS -0.002 0.095 -9999 0 -0.528 1 1
LEP -0.035 0.158 -9999 0 -0.526 3 3
STAT5B -0.065 0.104 -9999 0 -0.32 1 1
STAT5A -0.065 0.104 -9999 0 -0.32 1 1
GRB2 0.016 0 -9999 0 -9999 0 0
PDGFB-D/PDGFRB -0.079 0.115 -9999 0 -0.301 1 1
CSN2 0.048 0.039 -9999 0 -9999 0 0
PIK3CA 0.016 0 -9999 0 -9999 0 0
LAT -0.091 0.217 -9999 0 -0.645 4 4
YBX1 0.024 0.002 -9999 0 -9999 0 0
LCK -0.008 0.137 -9999 0 -0.773 1 1
SHC1 -0.001 0.094 -9999 0 -0.526 1 1
NOX4 -0.155 0.314 -9999 0 -0.744 7 7
Presenilin action in Notch and Wnt signaling

Figure 52.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 54.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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) -0.01 0.042 -9999 0 -9999 0 0
HDAC1 0.014 0.009 -9999 0 -9999 0 0
AES -0.009 0.137 -9999 0 -0.773 1 1
FBXW11 0.016 0 -9999 0 -9999 0 0
DTX1 0.016 0 -9999 0 -9999 0 0
LRP6/FZD1 -0.03 0.119 -9999 0 -0.478 2 2
TLE1 0.015 0.001 -9999 0 -9999 0 0
AP1 -0.059 0.179 -9999 0 -0.497 3 3
NCSTN 0.016 0 -9999 0 -9999 0 0
ADAM10 0.016 0 -9999 0 -9999 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.023 0.087 -9999 0 -9999 0 0
NICD/RBPSUH -0.001 0.015 -9999 0 -9999 0 0
WIF1 -0.192 0.316 -9999 0 -0.65 10 10
NOTCH1 -0.004 0.016 -9999 0 -9999 0 0
PSENEN -0.001 0.094 -9999 0 -0.526 1 1
KREMEN2 -0.052 0.179 -9999 0 -0.526 4 4
DKK1 -0.275 0.34 -9999 0 -0.65 14 14
beta catenin/beta TrCP1 0.032 0.035 -9999 0 -9999 0 0
APH1B -0.001 0.094 -9999 0 -0.525 1 1
APH1A -0.001 0.094 -9999 0 -0.526 1 1
AXIN1 0.006 0.047 -9999 0 -9999 0 0
CtBP/CBP/TCF1/TLE1/AES 0.017 0.109 -9999 0 -0.563 1 1
PSEN1 0.016 0 -9999 0 -9999 0 0
FOS -0.076 0.218 -9999 0 -0.575 5 5
JUN -0.058 0.23 -9999 0 -0.773 3 3
MAP3K7 0.015 0.004 -9999 0 -9999 0 0
CTNNB1 0.024 0.037 -9999 0 -9999 0 0
MAPK3 0.016 0 -9999 0 -9999 0 0
DKK2/LRP6/Kremen 2 -0.054 0.128 -9999 0 -0.501 1 1
HNF1A -0.002 0.094 -9999 0 -0.526 1 1
CTBP1 0.015 0.002 -9999 0 -9999 0 0
MYC 0.025 0.021 -9999 0 -9999 0 0
NKD1 -0.05 0.208 -9999 0 -0.688 3 3
FZD1 -0.025 0.164 -9999 0 -0.649 2 2
NOTCH1 precursor/Deltex homolog 1 -0.001 0.015 -9999 0 -9999 0 0
apoptosis -0.058 0.178 -9999 0 -0.494 3 3
Delta 1/NOTCHprecursor -0.009 0.044 -9999 0 -9999 0 0
DLL1 -0.001 0.094 -9999 0 -0.526 1 1
PPARD 0.025 0.021 -9999 0 -9999 0 0
Gamma Secretase -0.023 0.097 -9999 0 -0.511 1 1
APC 0.006 0.047 -9999 0 -9999 0 0
DVL1 -0.018 0.03 -9999 0 -9999 0 0
CSNK2A1 0.016 0.003 -9999 0 -9999 0 0
MAP3K7IP1 0.015 0.004 -9999 0 -9999 0 0
DKK1/LRP6/Kremen 2 -0.213 0.223 -9999 0 -0.542 7 7
LRP6 0.016 0 -9999 0 -9999 0 0
CSNK1A1 0.016 0.003 -9999 0 -9999 0 0
NLK 0.022 0.036 -9999 0 -9999 0 0
CCND1 -0.047 0.284 -9999 0 -1.484 1 1
WNT1 -0.008 0.137 -9999 0 -0.774 1 1
Axin1/APC/beta catenin 0.039 0.049 -9999 0 -9999 0 0
DKK2 -0.008 0.137 -9999 0 -0.773 1 1
NOTCH1 precursor/DVL1 -0.004 0.016 -9999 0 -9999 0 0
GSK3B 0.016 0.001 -9999 0 -9999 0 0
FRAT1 -0.001 0.094 -9999 0 -0.526 1 1
NOTCH/Deltex homolog 1 -0.003 0.012 -9999 0 -9999 0 0
PPP2R5D 0.02 0.084 0.308 2 -9999 0 2
MAPK1 0.016 0 -9999 0 -9999 0 0
WNT1/LRP6/FZD1 -0.149 0.237 -9999 0 -0.572 6 6
RBPJ 0.016 0 -9999 0 -9999 0 0
CREBBP 0.019 0.006 -9999 0 -9999 0 0
p75(NTR)-mediated signaling

Figure 53.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 55.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0 -9999 0 -9999 0 0
Necdin/E2F1 -0.048 0.153 -9999 0 -0.514 3 3
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.027 0.104 -9999 0 -0.429 2 2
NGF (dimer)/p75(NTR)/BEX1 -0.02 0.076 -9999 0 -0.314 2 2
NT-4/5 (dimer)/p75(NTR) 0 0 -9999 0 -9999 0 0
IKBKB 0.016 0 -9999 0 -9999 0 0
AKT1 0.025 0.081 -9999 0 -0.426 1 1
IKBKG 0.016 0 -9999 0 -9999 0 0
BDNF -0.118 0.259 -9999 0 -0.596 7 7
MGDIs/NGR/p75(NTR)/LINGO1 -0.025 0.1 -9999 0 -0.501 1 1
FURIN -0.035 0.158 -9999 0 -0.526 3 3
proBDNF (dimer)/p75(NTR)/Sortilin -0.079 0.155 -9999 0 -0.501 2 2
LINGO1 -0.001 0.094 -9999 0 -0.526 1 1
Sortilin/TRAF6/NRIF -0.02 0.082 -9999 0 -9999 0 0
proBDNF (dimer) -0.118 0.258 -9999 0 -0.595 7 7
NTRK1 0.016 0 -9999 0 -9999 0 0
RTN4R -0.008 0.137 -9999 0 -0.773 1 1
neuron apoptosis -0.003 0.141 -9999 0 -0.5 1 1
IRAK1 0.016 0 -9999 0 -9999 0 0
SHC1 0.013 0.059 -9999 0 -9999 0 0
ARHGDIA 0.016 0 -9999 0 -9999 0 0
RhoA/GTP 0 0 -9999 0 -9999 0 0
Gamma Secretase -0.023 0.097 -9999 0 -0.512 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.017 0.067 -9999 0 -9999 0 0
MAGEH1 -0.018 0.131 -9999 0 -0.526 2 2
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.029 0.112 -9999 0 -0.462 2 2
Mammalian IAPs/DIABLO -0.084 0.164 -9999 0 -0.462 4 4
proNGF (dimer) 0 0 -9999 0 -9999 0 0
MAGED1 0.016 0 -9999 0 -9999 0 0
APP -0.05 0.209 -9999 0 -0.691 3 3
NT-4/5 (dimer) 0 0 -9999 0 -9999 0 0
ZNF274 0.016 0 -9999 0 -9999 0 0
RhoA/GDP/RHOGDI 0.031 0 -9999 0 -9999 0 0
NGF 0 0 -9999 0 -9999 0 0
cell cycle arrest 0.009 0.033 -9999 0 -9999 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.027 0.046 -9999 0 -9999 0 0
NT-4/5 (dimer)/p75(NTR)/TRAF6 0 0 -9999 0 -9999 0 0
NCSTN 0.016 0 -9999 0 -9999 0 0
mol:GTP -0.026 0.102 -9999 0 -0.411 2 2
PSENEN -0.001 0.094 -9999 0 -0.526 1 1
mol:ceramide 0.032 0 -9999 0 -9999 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.026 0.046 -9999 0 -9999 0 0
p75(NTR)/beta APP -0.048 0.153 -9999 0 -0.514 3 3
BEX1 -0.018 0.131 -9999 0 -0.526 2 2
mol:GDP 0.011 0 -9999 0 -9999 0 0
NGF (dimer) -0.057 0.123 -9999 0 -0.462 1 1
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.022 0.09 -9999 0 -0.453 1 1
PIK3R1 -0.008 0.137 -9999 0 -0.773 1 1
RAC1/GTP 0 0 -9999 0 -9999 0 0
MYD88 0.016 0 -9999 0 -9999 0 0
CHUK 0.016 0 -9999 0 -9999 0 0
NGF (dimer)/p75(NTR)/PKA -0.026 0.103 -9999 0 -0.412 2 2
RHOB 0.016 0 -9999 0 -9999 0 0
RHOA 0.016 0 -9999 0 -9999 0 0
MAGE-G1/E2F1 -0.012 0.064 -9999 0 -0.37 1 1
NT3 (dimer) -0.025 0.164 -9999 0 -0.648 2 2
TP53 -0.014 0.139 -9999 0 -9999 0 0
PRDM4 0.032 0 -9999 0 -9999 0 0
BDNF (dimer) -0.278 0.253 -9999 0 -0.567 11 11
PIK3CA 0.016 0 -9999 0 -9999 0 0
SORT1 0.016 0 -9999 0 -9999 0 0
activation of caspase activity -0.027 0.103 -9999 0 -0.424 2 2
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0 0 -9999 0 -9999 0 0
RHOC 0.016 0 -9999 0 -9999 0 0
XIAP 0 0 -9999 0 -9999 0 0
MAPK10 -0.003 0.12 -9999 0 -9999 0 0
DIABLO 0.016 0 -9999 0 -9999 0 0
SMPD2 0.032 0 -9999 0 -9999 0 0
APH1B -0.001 0.094 -9999 0 -0.526 1 1
APH1A -0.001 0.094 -9999 0 -0.526 1 1
proNGF (dimer)/p75(NTR)/Sortilin 0 0 -9999 0 -9999 0 0
PSEN1 0.016 0 -9999 0 -9999 0 0
APAF-1/Pro-Caspase 9 0 0 -9999 0 -9999 0 0
NT3 (dimer)/p75(NTR) -0.03 0.119 -9999 0 -0.478 2 2
MAPK8 0.002 0.119 -9999 0 -9999 0 0
MAPK9 0.002 0.119 -9999 0 -9999 0 0
APAF1 0.016 0 -9999 0 -9999 0 0
NTF3 -0.025 0.164 -9999 0 -0.65 2 2
NTF4 0 0 -9999 0 -9999 0 0
NDN -0.033 0.191 -9999 0 -0.773 2 2
RAC1/GDP 0 0 -9999 0 -9999 0 0
RhoA-B-C/GDP -0.019 0.077 -9999 0 -0.392 1 1
p75 CTF/Sortilin/TRAF6/NRIF 0 0 -9999 0 -9999 0 0
RhoA-B-C/GTP -0.026 0.102 -9999 0 -0.409 2 2
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.064 0.126 -9999 0 -0.42 2 2
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.07 0.138 -9999 0 -0.453 2 2
PRKACB -0.025 0.164 -9999 0 -0.65 2 2
proBDNF (dimer)/p75 ECD -0.094 0.184 -9999 0 -0.432 7 7
ChemicalAbstracts:86-01-1 0 0 -9999 0 -9999 0 0
BIRC3 -0.133 0.288 -9999 0 -0.667 7 7
BIRC2 0.016 0 -9999 0 -9999 0 0
neuron projection morphogenesis -0.03 0.131 -9999 0 -0.504 2 2
BAD 0.006 0.121 -9999 0 -9999 0 0
RIPK2 -0.018 0.131 -9999 0 -0.526 2 2
NGFR 0.016 0 -9999 0 -9999 0 0
CYCS 0.04 0 -9999 0 -9999 0 0
ADAM17 0.016 0 -9999 0 -9999 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.017 0.067 -9999 0 -9999 0 0
BCL2L11 0.006 0.121 -9999 0 -9999 0 0
BDNF (dimer)/p75(NTR) -0.094 0.184 -9999 0 -0.432 7 7
PI3K -0.014 0.08 -9999 0 -0.462 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0 0 -9999 0 -9999 0 0
NDNL2 0.016 0 -9999 0 -9999 0 0
YWHAE 0.016 0 -9999 0 -9999 0 0
PRKCI 0.016 0 -9999 0 -9999 0 0
NGF (dimer)/p75(NTR) 0 0 -9999 0 -9999 0 0
ChemicalAbstracts:146-91-8 0 0 -9999 0 -9999 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0 0 -9999 0 -9999 0 0
TRAF6 0.016 0 -9999 0 -9999 0 0
RAC1 0.016 0 -9999 0 -9999 0 0
PRKCZ 0 0 -9999 0 -9999 0 0
PLG 0.016 0 -9999 0 -9999 0 0
oligodendrocyte cell fate commitment 0 0 -9999 0 -9999 0 0
CASP6 -0.028 0.131 -9999 0 -0.39 2 2
SQSTM1 -0.001 0.094 -9999 0 -0.526 1 1
NGFRAP1 -0.033 0.191 -9999 0 -0.773 2 2
CASP3 0.009 0.115 -9999 0 -9999 0 0
E2F1 -0.001 0.094 -9999 0 -0.526 1 1
CASP9 0.016 0 -9999 0 -9999 0 0
IKK complex -0.005 0.017 -9999 0 -9999 0 0
NGF (dimer)/TRKA 0 0 -9999 0 -9999 0 0
MMP7 -0.042 0.186 -9999 0 -0.608 3 3
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0 0 -9999 0 -9999 0 0
MMP3 -0.307 0.354 -9999 0 -0.674 15 15
APAF-1/Caspase 9 -0.054 0.108 -9999 0 -9999 0 0
Glypican 1 network

Figure 54.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 56.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.035 0.111 -9999 0 -0.501 1 1
fibroblast growth factor receptor signaling pathway -0.034 0.111 -9999 0 -0.499 1 1
LAMA1 0.016 0 -9999 0 -9999 0 0
PRNP -0.008 0.137 -9999 0 -0.773 1 1
GPC1/SLIT2 -0.066 0.179 -9999 0 -0.532 4 4
SMAD2 0.007 0.111 -9999 0 -0.45 1 1
GPC1/PrPc/Cu2+ -0.042 0.133 -9999 0 -0.445 3 3
GPC1/Laminin alpha1 -0.03 0.119 -9999 0 -0.586 1 1
TDGF1 -0.001 0.094 -9999 0 -0.526 1 1
CRIPTO/GPC1 -0.041 0.133 -9999 0 -0.442 3 3
APP/GPC1 -0.078 0.186 -9999 0 -0.499 5 5
mol:NO 0 0 -9999 0 -9999 0 0
YES1 -0.003 0.121 -9999 0 -0.5 1 1
FLT1 -0.008 0.137 -9999 0 -0.773 1 1
GPC1/TGFB/TGFBR1/TGFBR2 -0.025 0.1 -9999 0 -0.501 1 1
SERPINC1 -0.001 0.094 -9999 0 -0.526 1 1
FYN -0.003 0.121 -9999 0 -0.5 1 1
FGR -0.003 0.121 -9999 0 -0.5 1 1
positive regulation of MAPKKK cascade 0.007 0.125 -9999 0 -0.481 1 1
SLIT2 -0.033 0.191 -9999 0 -0.773 2 2
GPC1/NRG -0.041 0.133 -9999 0 -0.586 1 1
NRG1 -0.001 0.094 -9999 0 -0.526 1 1
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.055 0.191 -9999 0 -0.731 2 2
LYN -0.003 0.121 -9999 0 -0.5 1 1
mol:Spermine -0.017 0.125 -9999 0 -0.489 2 2
cell growth -0.034 0.111 -9999 0 -0.499 1 1
BMP signaling pathway 0.025 0.164 0.648 2 -9999 0 2
SRC -0.003 0.121 -9999 0 -0.5 1 1
TGFBR1 0.016 0 -9999 0 -9999 0 0
mol:Cu2+ 0 0 -9999 0 -9999 0 0
PLA2G2A 0.016 0 -9999 0 -9999 0 0
GPC1 -0.025 0.164 -9999 0 -0.65 2 2
TGFBR1 (dimer) 0.016 0 -9999 0 -9999 0 0
VEGFA -0.008 0.137 -9999 0 -0.773 1 1
BLK -0.03 0.156 -9999 0 -0.501 2 2
HCK -0.02 0.149 -9999 0 -0.501 2 2
FGF2 -0.001 0.094 -9999 0 -0.526 1 1
FGFR1 0.016 0 -9999 0 -9999 0 0
VEGFR1 homodimer -0.008 0.137 -9999 0 -0.772 1 1
TGFBR2 0.016 0 -9999 0 -9999 0 0
cell death -0.078 0.186 -9999 0 -0.498 5 5
ATIII/GPC1 -0.041 0.133 -9999 0 -0.442 3 3
PLA2G2A/GPC1 -0.03 0.119 -9999 0 -0.478 2 2
LCK -0.02 0.149 -9999 0 -0.501 2 2
neuron differentiation -0.041 0.132 -9999 0 -0.584 1 1
PrPc/Cu2+ -0.019 0.104 -9999 0 -0.596 1 1
APP -0.05 0.209 -9999 0 -0.691 3 3
TGFBR2 (dimer) 0.016 0 -9999 0 -9999 0 0
PLK1 signaling events

Figure 55.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 57.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.014 0.007 -9999 0 -9999 0 0
BUB1B -0.025 0.13 -9999 0 -0.375 3 3
PLK1 0.007 0.027 -9999 0 -9999 0 0
PLK1S1 0.004 0.015 -9999 0 -9999 0 0
KIF2A 0.017 0.024 -9999 0 -9999 0 0
regulation of mitotic centrosome separation 0.007 0.027 -9999 0 -9999 0 0
GOLGA2 -0.058 0.23 -9999 0 -0.773 3 3
Hec1/SPC24 0.001 0.09 -9999 0 -0.489 1 1
WEE1 -0.001 0.058 -9999 0 -9999 0 0
cytokinesis 0.006 0.084 -9999 0 -0.341 1 1
PP2A-alpha B56 -0.112 0.315 -9999 0 -0.816 5 5
AURKA 0.004 0.033 -9999 0 -9999 0 0
PICH/PLK1 -0.07 0.204 -9999 0 -0.448 6 6
CENPE -0.002 0.078 -9999 0 -0.291 2 2
RhoA/GTP 0 0 -9999 0 -9999 0 0
positive regulation of microtubule depolymerization 0.017 0.024 -9999 0 -9999 0 0
PPP2CA 0.016 0 -9999 0 -9999 0 0
FZR1 0.016 0 -9999 0 -9999 0 0
TPX2 -0.006 0.064 -9999 0 -0.22 2 2
PAK1 0.016 0.001 -9999 0 -9999 0 0
SPC24 0 0 -9999 0 -9999 0 0
FBXW11 0.016 0 -9999 0 -9999 0 0
CLSPN 0.012 0.015 -9999 0 -9999 0 0
GORASP1 0.016 0 -9999 0 -9999 0 0
metaphase 0.001 0.002 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
NLP 0.004 0.015 -9999 0 -9999 0 0
G2 phase of mitotic cell cycle -0.001 0.002 -9999 0 -9999 0 0
STAG2 0.016 0 -9999 0 -9999 0 0
GRASP65/GM130/RAB1/GTP -0.04 0.103 -9999 0 -0.357 1 1
spindle elongation 0.007 0.027 -9999 0 -9999 0 0
ODF2 0.015 0.004 -9999 0 -9999 0 0
BUB1 -0.162 0.333 -9999 0 -0.907 5 5
TPT1 0.002 0.051 -9999 0 -0.273 1 1
CDC25C -0.003 0.053 -9999 0 -0.182 1 1
CDC25B 0.014 0.007 -9999 0 -9999 0 0
SGOL1 0.014 0.007 -9999 0 -9999 0 0
RHOA 0.016 0 -9999 0 -9999 0 0
CCNB1/CDK1 -0.093 0.189 -9999 0 -0.476 6 6
CDC14B -0.005 0.108 -9999 0 -0.606 1 1
CDC20 -0.008 0.137 -9999 0 -0.773 1 1
PLK1/PBIP1 -0.04 0.12 -9999 0 -0.404 3 3
mitosis 0.001 0.008 0.03 2 -9999 0 2
FBXO5 -0.005 0.071 -9999 0 -0.331 1 1
CDC2 -0.003 0.096 -9999 0 -0.537 1 1
NDC80 -0.008 0.137 -9999 0 -0.773 1 1
metaphase plate congression 0.01 0.017 -9999 0 -9999 0 0
ERCC6L -0.077 0.215 -9999 0 -0.484 6 6
NLP/gamma Tubulin 0.006 0.02 -9999 0 -9999 0 0
microtubule cytoskeleton organization 0.002 0.051 -9999 0 -0.272 1 1
G2/M transition DNA damage checkpoint 0 0.001 -9999 0 -9999 0 0
PPP1R12A 0.016 0.001 -9999 0 -9999 0 0
interphase 0 0.001 -9999 0 -9999 0 0
PLK1/PRC1-2 -0.009 0.122 -9999 0 -0.417 2 2
GRASP65/GM130/RAB1/GTP/PLK1 -0.046 0.133 -9999 0 -0.398 4 4
RAB1A -0.008 0.137 -9999 0 -0.773 1 1
prophase 0 0 -9999 0 -9999 0 0
Aurora A/BORA 0.012 0.025 -9999 0 -9999 0 0
mitotic prometaphase -0.001 0.001 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.058 -9999 0 -9999 0 0
microtubule-based process -0.002 0.081 -9999 0 -0.306 2 2
Golgi organization 0.007 0.027 -9999 0 -9999 0 0
Cohesin/SA2 -0.005 0.01 -9999 0 -9999 0 0
PPP1CB/MYPT1 0.002 0.007 -9999 0 -9999 0 0
KIF20A -0.018 0.131 -9999 0 -0.526 2 2
APC/C/CDC20 0.001 0.095 -9999 0 -0.512 1 1
PPP2R1A 0.016 0 -9999 0 -9999 0 0
chromosome segregation -0.039 0.118 -9999 0 -0.397 3 3
PRC1 -0.018 0.131 -9999 0 -0.526 2 2
ECT2 -0.011 0.089 -9999 0 -0.28 3 3
C13orf34 0.013 0.023 -9999 0 -9999 0 0
NUDC 0.01 0.017 -9999 0 -9999 0 0
regulation of attachment of spindle microtubules to kinetochore -0.025 0.128 -9999 0 -0.37 3 3
spindle assembly 0.007 0.024 -9999 0 -9999 0 0
spindle stabilization 0.004 0.014 -9999 0 -9999 0 0
APC/C/HCDH1 0.006 0.093 -9999 0 -0.515 1 1
MKLP2/PLK1 -0.002 0.082 -9999 0 -0.308 2 2
CCNB1 -0.141 0.305 -9999 0 -0.709 7 7
PPP1CB 0.016 0.001 -9999 0 -9999 0 0
BTRC 0.016 0 -9999 0 -9999 0 0
ROCK2 0.02 0.018 -9999 0 -9999 0 0
TUBG1 0.007 0.026 -9999 0 -9999 0 0
G2/M transition of mitotic cell cycle -0.086 0.189 -9999 0 -0.464 6 6
MLF1IP -0.036 0.163 -9999 0 -0.533 3 3
INCENP 0.013 0.006 -9999 0 -9999 0 0
mTOR signaling pathway

Figure 56.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 58.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.016 0 -9999 0 -9999 0 0
MKNK1 0.016 0 -9999 0 -9999 0 0
mol:PIP3 -0.059 0.129 -9999 0 -0.352 5 5
FRAP1 0.009 0.056 -9999 0 -9999 0 0
AKT1 -0.043 0.15 -9999 0 -0.608 1 1
INSR -0.033 0.191 -9999 0 -0.773 2 2
Insulin Receptor/Insulin -0.042 0.133 -9999 0 -0.445 3 3
mol:GTP -0.081 0.154 -9999 0 -0.488 3 3
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.018 0.064 -9999 0 -0.362 1 1
TSC2 -0.009 0.137 -9999 0 -0.773 1 1
RHEB/GDP -0.077 0.138 -9999 0 -0.44 3 3
TSC1 -0.033 0.191 -9999 0 -0.774 2 2
Insulin Receptor/IRS1 -0.068 0.171 -9999 0 -0.418 6 6
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.022 0.076 -9999 0 -0.431 1 1
mol:GDP 0 0 -9999 0 -9999 0 0
EIF3A 0.016 0 -9999 0 -9999 0 0
RPS6KB1 0.002 0.084 -9999 0 -0.34 1 1
MAP3K5 0.013 0.004 -9999 0 -9999 0 0
PIK3R1 -0.009 0.138 -9999 0 -0.775 1 1
apoptosis 0.013 0.004 -9999 0 -9999 0 0
mol:LY294002 0 0.001 -9999 0 -0.002 5 5
EIF4B 0.012 0.076 -9999 0 -9999 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.022 0.054 -9999 0 -9999 0 0
eIF4E/eIF4G1/eIF4A1 -0.013 0.062 -9999 0 -0.352 1 1
KIAA1303 0.016 0 -9999 0 -9999 0 0
PI3K -0.039 0.149 -9999 0 -0.376 5 5
mTOR/RHEB/GTP/Raptor/GBL 0.007 0.091 -9999 0 -9999 0 0
FKBP1A 0.016 0.001 -9999 0 -9999 0 0
RHEB/GTP -0.077 0.136 -9999 0 -0.432 3 3
mol:Amino Acids 0 0.001 -9999 0 -0.002 5 5
FKBP12/Rapamycin 0.01 0.006 -9999 0 -9999 0 0
PDPK1 -0.091 0.181 -9999 0 -0.534 3 3
EIF4E 0.016 0 -9999 0 -9999 0 0
ASK1/PP5C 0.026 0.044 -9999 0 -9999 0 0
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.034 0.041 -9999 0 -9999 0 0
TSC1/TSC2 -0.088 0.169 -9999 0 -0.535 3 3
tumor necrosis factor receptor activity 0 0.001 0.002 5 -9999 0 5
RPS6 0.016 0 -9999 0 -9999 0 0
PPP5C 0.016 0 -9999 0 -9999 0 0
EIF4G1 -0.008 0.137 -9999 0 -0.773 1 1
IRS1 -0.052 0.151 -9999 0 -0.39 5 5
INS -0.001 0.094 -9999 0 -0.526 1 1
PTEN 0.016 0.001 -9999 0 -9999 0 0
PDK2 -0.053 0.117 -9999 0 -0.406 1 1
EIF4EBP1 0.017 0.004 -9999 0 -9999 0 0
PIK3CA 0.016 0.001 -9999 0 -9999 0 0
PPP2R5D 0.018 0.053 -9999 0 -9999 0 0
peptide biosynthetic process -0.008 0.127 -9999 0 -0.456 2 2
RHEB -0.001 0.094 -9999 0 -0.525 1 1
EIF4A1 0.016 0 -9999 0 -9999 0 0
mol:Rapamycin 0 0.001 -9999 0 -0.004 1 1
EEF2 -0.009 0.128 -9999 0 -0.46 2 2
eIF4E/4E-BP1 0.025 0.003 -9999 0 -9999 0 0
Ceramide signaling pathway

Figure 57.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 59.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.051 0.22 -9999 0 -0.606 4 4
MAP4K4 -0.009 0.137 -9999 0 -0.513 1 1
BAG4 0.016 0 -9999 0 -9999 0 0
PKC zeta/ceramide -0.008 0.072 0.188 2 -9999 0 2
NFKBIA 0.016 0 -9999 0 -9999 0 0
BIRC3 -0.133 0.288 -9999 0 -0.667 7 7
BAX 0.008 0.041 -9999 0 -9999 0 0
RIPK1 0.016 0 -9999 0 -9999 0 0
AKT1 0.026 0.012 -9999 0 -9999 0 0
BAD 0.004 0.076 0.214 2 -9999 0 2
SMPD1 -0.012 0.099 -9999 0 -0.251 4 4
RB1 0.004 0.076 0.214 2 -9999 0 2
FADD/Caspase 8 0.014 0.105 -9999 0 -9999 0 0
MAP2K4 0.004 0.072 0.225 1 -9999 0 1
NSMAF -0.008 0.137 -9999 0 -0.773 1 1
response to UV 0 0 -9999 0 -9999 0 0
RAF1 0.012 0.072 -9999 0 -9999 0 0
EGF -0.126 0.274 -9999 0 -0.632 7 7
mol:ceramide -0.007 0.083 0.185 4 -9999 0 4
MADD 0.016 0 -9999 0 -9999 0 0
response to oxidative stress 0 0 -9999 0 -9999 0 0
mol:Free Fatty acid -0.061 0.21 -9999 0 -0.542 5 5
ASAH1 -0.008 0.137 -9999 0 -0.773 1 1
negative regulation of cell cycle 0.003 0.076 0.214 2 -9999 0 2
cell proliferation 0.009 0.048 -9999 0 -9999 0 0
BID -0.05 0.214 -9999 0 -0.644 3 3
MAP3K1 -0.005 0.076 0.214 2 -9999 0 2
EIF2A 0.005 0.095 -9999 0 -9999 0 0
TRADD 0.016 0 -9999 0 -9999 0 0
CRADD 0.016 0 -9999 0 -9999 0 0
MAPK3 0.026 0.068 -9999 0 -9999 0 0
response to heat 0 0 -9999 0 -9999 0 0
MAPK1 0.026 0.068 -9999 0 -9999 0 0
Cathepsin D/ceramide -0.026 0.14 0.2 2 -0.492 2 4
FADD -0.001 0.111 -9999 0 -9999 0 0
KSR1 0.004 0.076 0.214 2 -9999 0 2
MAPK8 0.007 0.067 0.207 2 -9999 0 2
PRKRA 0.004 0.076 0.214 2 -9999 0 2
PDGFA -0.075 0.244 -9999 0 -0.712 4 4
TRAF2 0.016 0 -9999 0 -9999 0 0
IGF1 -0.001 0.094 -9999 0 -0.526 1 1
mol:GD3 0 0 -9999 0 -9999 0 0
ganglioside biosynthetic process -0.007 0.083 0.198 3 -9999 0 3
CTSD -0.033 0.191 -9999 0 -0.773 2 2
regulation of nitric oxide biosynthetic process 0 0 -9999 0 -9999 0 0
response to radiation 0 0 -9999 0 -9999 0 0
ERK1/PKC delta 0.01 0.051 -9999 0 -9999 0 0
PRKCD 0.016 0 -9999 0 -9999 0 0
PRKCZ 0 0 -9999 0 -9999 0 0
mol:GW4869 0 0 -9999 0 -9999 0 0
mol:sphingosine -0.061 0.21 -9999 0 -0.542 5 5
RelA/NF kappa B1 0 0 -9999 0 -9999 0 0
mol:glutathione 0 0 -9999 0 -9999 0 0
PAWR -0.033 0.191 -9999 0 -0.773 2 2
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.011 0.118 -9999 0 -9999 0 0
TNFR1A/BAG4/TNF-alpha -0.025 0.1 -9999 0 -0.501 1 1
mol:Sphingosine-1-phosphate -0.051 0.219 -9999 0 -0.604 4 4
MAP2K1 0.021 0.069 -9999 0 -9999 0 0
mol:C11AG 0 0 -9999 0 -9999 0 0
RELA 0.016 0 -9999 0 -9999 0 0
CYCS 0.016 0.06 0.173 1 -9999 0 1
TNFRSF1A 0.016 0 -9999 0 -9999 0 0
NFKB1 0.016 0 -9999 0 -9999 0 0
TNFR1A/BAG4 0 0 -9999 0 -9999 0 0
EIF2AK2 0.004 0.087 0.225 1 -0.264 1 2
TNF-alpha/TNFR1A/FAN -0.041 0.13 -9999 0 -0.501 2 2
response to hydrogen peroxide 0 0 -9999 0 -9999 0 0
CASP8 0.018 0.069 -9999 0 -9999 0 0
MAP2K2 0.021 0.069 -9999 0 -9999 0 0
SMPD3 -0.001 0.081 -9999 0 -9999 0 0
TNF -0.025 0.164 -9999 0 -0.65 2 2
PKC zeta/PAR4 -0.037 0.144 -9999 0 -0.596 2 2
mol:PHOSPHOCHOLINE 0.052 0.11 0.226 8 -9999 0 8
NF kappa B1/RelA/I kappa B alpha -0.027 0.103 -9999 0 -0.427 2 2
AIFM1 0.016 0.06 0.173 1 -9999 0 1
BCL2 -0.035 0.158 -9999 0 -0.526 3 3
Reelin signaling pathway

Figure 58.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 60.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.03 0.119 -9999 0 -0.478 2 2
VLDLR -0.018 0.131 -9999 0 -0.526 2 2
CRKL -0.008 0.137 -9999 0 -0.773 1 1
LRPAP1 -0.001 0.094 -9999 0 -0.526 1 1
FYN 0.016 0 -9999 0 -9999 0 0
ITGA3 -0.092 0.255 -9999 0 -0.674 5 5
RELN/VLDLR/Fyn -0.035 0.111 -9999 0 -0.501 1 1
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.026 0.102 -9999 0 -9999 0 0
AKT1 0.015 0.089 -9999 0 -9999 0 0
MAP2K7 0.016 0 -9999 0 -9999 0 0
RAPGEF1 0.016 0 -9999 0 -9999 0 0
DAB1 0.016 0 -9999 0 -9999 0 0
RELN/LRP8/DAB1 -0.04 0.11 -9999 0 -0.462 1 1
LRPAP1/LRP8 -0.046 0.122 -9999 0 -0.37 4 4
RELN/LRP8/DAB1/Fyn -0.037 0.101 -9999 0 -0.429 1 1
DAB1/alpha3/beta1 Integrin -0.104 0.214 -9999 0 -0.788 2 2
long-term memory -0.062 0.126 -9999 0 -0.485 1 1
DAB1/LIS1 -0.056 0.138 -9999 0 -0.481 2 2
DAB1/CRLK/C3G -0.066 0.176 -9999 0 -0.786 1 1
PIK3CA 0.016 0 -9999 0 -9999 0 0
DAB1/NCK2 -0.056 0.139 -9999 0 -0.485 2 2
ARHGEF2 -0.033 0.191 -9999 0 -0.773 2 2
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -9999 0 0
GRIN2A -0.018 0.131 -9999 0 -0.526 2 2
CDK5R1 -0.025 0.164 -9999 0 -0.65 2 2
RELN -0.008 0.137 -9999 0 -0.773 1 1
PIK3R1 -0.008 0.137 -9999 0 -0.773 1 1
RELN/LRP8/Fyn -0.044 0.121 -9999 0 -0.501 1 1
GRIN2A/RELN/LRP8/DAB1/Fyn -0.051 0.109 -9999 0 -9999 0 0
MAPK8 0.016 0 -9999 0 -9999 0 0
RELN/VLDLR/DAB1 -0.032 0.102 -9999 0 -0.462 1 1
ITGB1 0.016 0 -9999 0 -9999 0 0
MAP1B -0.078 0.192 -9999 0 -0.444 3 3
RELN/LRP8 -0.054 0.128 -9999 0 -0.501 1 1
GRIN2B/RELN/LRP8/DAB1/Fyn -0.051 0.109 -9999 0 -9999 0 0
PI3K -0.018 0.102 -9999 0 -0.586 1 1
mol:PP2 0 0 -9999 0 -9999 0 0
alpha3/beta1 Integrin -0.078 0.186 -9999 0 -0.499 5 5
RAP1A -0.001 0.185 -9999 0 -0.722 1 1
PAFAH1B1 0.016 0 -9999 0 -9999 0 0
MAPK8IP1 0.016 0 -9999 0 -9999 0 0
CRLK/C3G -0.018 0.102 -9999 0 -0.586 1 1
GRIN2B -0.018 0.131 -9999 0 -0.526 2 2
NCK2 0.016 0 -9999 0 -9999 0 0
neuron differentiation 0.019 0.08 -9999 0 -9999 0 0
neuron adhesion -0.034 0.238 -9999 0 -0.677 3 3
LRP8 -0.035 0.158 -9999 0 -0.526 3 3
GSK3B 0.024 0.085 -9999 0 -9999 0 0
RELN/VLDLR/DAB1/Fyn -0.029 0.094 -9999 0 -0.429 1 1
MAP3K11 0.016 0 -9999 0 -9999 0 0
RELN/VLDLR/DAB1/P13K 0.005 0.094 -9999 0 -9999 0 0
CDK5 0.016 0 -9999 0 -9999 0 0
MAPT -0.016 0.13 -9999 0 -0.731 1 1
neuron migration 0.014 0.139 -9999 0 -9999 0 0
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.019 0.081 -9999 0 -9999 0 0
RELN/VLDLR -0.065 0.159 -9999 0 -0.516 3 3
TRAIL signaling pathway

Figure 59.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 61.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.058 0.23 -9999 0 -0.773 3 3
positive regulation of NF-kappaB transcription factor activity -0.078 0.186 -9999 0 -0.498 5 5
MAP2K4 0.012 0.103 -9999 0 -9999 0 0
IKBKB 0.016 0 -9999 0 -9999 0 0
TNFRSF10B -0.008 0.137 -9999 0 -0.773 1 1
TNFRSF10A -0.025 0.164 -9999 0 -0.65 2 2
SMPD1 -0.037 0.151 -9999 0 -0.371 5 5
IKBKG 0.016 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
TNFRSF10D -0.018 0.131 -9999 0 -0.526 2 2
TRAIL/TRAILR2 -0.073 0.194 -9999 0 -0.586 4 4
TRAIL/TRAILR3 -0.085 0.2 -9999 0 -0.542 5 5
TRAIL/TRAILR1 -0.085 0.2 -9999 0 -0.542 5 5
TRAIL/TRAILR4 -0.078 0.186 -9999 0 -0.499 5 5
TRAIL/TRAILR1/DAP3/GTP -0.066 0.157 -9999 0 -0.462 4 4
IKK complex -0.023 0.053 -9999 0 -9999 0 0
RIPK1 0.016 0 -9999 0 -9999 0 0
response to oxidative stress 0 0 -9999 0 -9999 0 0
DAP3/GTP 0 0 -9999 0 -9999 0 0
MAPK3 -0.029 0.179 -9999 0 -0.584 3 3
MAP3K1 0.003 0.108 -9999 0 -9999 0 0
TRAILR4 (trimer) -0.018 0.131 -9999 0 -0.525 2 2
TRADD 0.016 0 -9999 0 -9999 0 0
TRAILR1 (trimer) -0.025 0.164 -9999 0 -0.648 2 2
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.003 0.119 -9999 0 -9999 0 0
CFLAR -0.001 0.094 -9999 0 -0.526 1 1
MAPK1 -0.029 0.179 -9999 0 -0.584 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP -0.06 0.142 -9999 0 -9999 0 0
mol:ceramide -0.037 0.151 -9999 0 -0.369 5 5
FADD 0.016 0 -9999 0 -9999 0 0
MAPK8 0.021 0.098 -9999 0 -9999 0 0
TRAF2 0.016 0 -9999 0 -9999 0 0
TRAILR3 (trimer) -0.025 0.164 -9999 0 -0.648 2 2
CHUK 0.016 0 -9999 0 -9999 0 0
TRAIL/TRAILR1/FADD -0.072 0.171 -9999 0 -0.501 4 4
DAP3 0.016 0 -9999 0 -9999 0 0
CASP10 -0.051 0.163 -9999 0 -0.48 3 3
JNK cascade -0.078 0.186 -9999 0 -0.498 5 5
TRAIL (trimer) -0.058 0.23 -9999 0 -0.772 3 3
TNFRSF10C -0.025 0.164 -9999 0 -0.65 2 2
TRAIL/TRAILR1/DAP3/GTP/FADD -0.061 0.146 -9999 0 -0.429 4 4
TRAIL/TRAILR2/FADD -0.063 0.166 -9999 0 -0.501 4 4
cell death -0.037 0.15 -9999 0 -0.368 5 5
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.003 0.117 -9999 0 -9999 0 0
TRAILR2 (trimer) -0.008 0.137 -9999 0 -0.772 1 1
CASP8 0.008 0.059 -9999 0 -9999 0 0
negative regulation of caspase activity 0 0 -9999 0 -9999 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.052 0.139 -9999 0 -9999 0 0
Signaling events regulated by Ret tyrosine kinase

Figure 60.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 62.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.009 0.026 -9999 0 -9999 0 0
Crk/p130 Cas/Paxillin -0.078 0.125 -9999 0 -9999 0 0
JUN -0.011 0.157 -9999 0 -0.546 1 1
HRAS 0.016 0 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.07 0.138 -9999 0 -0.453 2 2
RAP1A 0.016 0 -9999 0 -9999 0 0
FRS2 -0.008 0.137 -9999 0 -0.773 1 1
RAP1A/GDP 0 0 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.039 0.107 -9999 0 -0.453 1 1
EntrezGene:5979 0 0 -9999 0 -9999 0 0
PTPN11 0.016 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
CRK 0.016 0 -9999 0 -9999 0 0
RET9/GFRalpha1/GDNF/Enigma -0.014 0.08 -9999 0 -0.462 1 1
RHOA 0.016 0 -9999 0 -9999 0 0
RAP1A/GTP -0.068 0.161 -9999 0 -0.815 1 1
GRB7 0.016 0 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF -0.039 0.107 -9999 0 -0.453 1 1
MAPKKK cascade -0.029 0.078 -9999 0 -9999 0 0
BCAR1 0.016 0 -9999 0 -9999 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.081 0.171 -9999 0 -0.462 5 5
lamellipodium assembly -0.077 0.12 -9999 0 -0.359 2 2
RET51/GFRalpha1/GDNF/SHC -0.047 0.114 -9999 0 -0.453 1 1
PIK3CA 0.016 0 -9999 0 -9999 0 0
RET9/GFRalpha1/GDNF/SHC -0.023 0.092 -9999 0 -0.462 1 1
RET9/GFRalpha1/GDNF/Shank3 -0.014 0.08 -9999 0 -0.462 1 1
MAPK3 -0.02 0.168 -9999 0 -0.76 1 1
DOK1 0.016 0 -9999 0 -9999 0 0
DOK6 -0.092 0.255 -9999 0 -0.674 5 5
PXN 0.016 0 -9999 0 -9999 0 0
neurite development -0.025 0.166 -9999 0 -0.695 1 1
DOK5 -0.093 0.231 -9999 0 -0.567 6 6
GFRA1 -0.008 0.137 -9999 0 -0.773 1 1
MAPK8 0.022 0.08 -9999 0 -9999 0 0
HRAS/GTP -0.035 0.091 -9999 0 -0.415 1 1
tube development -0.013 0.075 -9999 0 -0.429 1 1
MAPK1 -0.02 0.168 -9999 0 -0.76 1 1
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.017 0.085 -9999 0 -0.313 2 2
Rac1/GDP 0 0 -9999 0 -9999 0 0
SRC 0.016 0 -9999 0 -9999 0 0
PDLIM7 0.016 0 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.091 0.174 -9999 0 -0.486 4 4
SHC1 -0.001 0.094 -9999 0 -0.526 1 1
RET51/GFRalpha1/GDNF/Dok4 -0.078 0.18 -9999 0 -0.898 1 1
RET51/GFRalpha1/GDNF/Dok5 -0.095 0.185 -9999 0 -0.575 3 3
PRKCA -0.025 0.164 -9999 0 -0.65 2 2
HRAS/GDP 0 0 -9999 0 -9999 0 0
CREB1 0.022 0.078 -9999 0 -0.34 1 1
PIK3R1 -0.008 0.137 -9999 0 -0.773 1 1
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.011 0.09 -9999 0 -0.313 2 2
RET51/GFRalpha1/GDNF/Grb7 -0.039 0.107 -9999 0 -0.453 1 1
mol:GDP 0 0 -9999 0 -9999 0 0
RET -0.035 0.158 -9999 0 -0.526 3 3
DOK4 -0.059 0.203 -9999 0 -0.588 4 4
JNK cascade -0.01 0.154 -9999 0 -0.533 1 1
RET9/GFRalpha1/GDNF/FRS2 -0.029 0.112 -9999 0 -0.462 2 2
SHANK3 0.016 0 -9999 0 -9999 0 0
RASA1 -0.001 0.094 -9999 0 -0.526 1 1
NCK1 0.016 0 -9999 0 -9999 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.022 0.069 -9999 0 -0.316 1 1
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.007 0.098 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.012 0.085 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.012 0.085 -9999 0 -9999 0 0
PI3K -0.061 0.217 -9999 0 -0.532 3 3
SOS1 0.016 0 -9999 0 -9999 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.013 0.075 -9999 0 -0.429 1 1
GRB10 -0.042 0.186 -9999 0 -0.608 3 3
activation of MAPKK activity 0.011 0.09 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF/FRS2 -0.053 0.129 -9999 0 -0.453 2 2
GAB1 -0.008 0.137 -9999 0 -0.773 1 1
IRS1 -0.099 0.272 -9999 0 -0.724 5 5
IRS2 -0.042 0.186 -9999 0 -0.608 3 3
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.001 0.101 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF/PKC alpha -0.062 0.16 -9999 0 -0.589 2 2
GRB2 0.016 0 -9999 0 -9999 0 0
PRKACA 0.016 0 -9999 0 -9999 0 0
GDNF 0.016 0 -9999 0 -9999 0 0
RAC1 0.016 0 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.104 0.194 -9999 0 -0.507 5 5
Rac1/GTP -0.09 0.143 -9999 0 -0.433 2 2
RET9/GFRalpha1/GDNF -0.016 0.089 -9999 0 -0.511 1 1
GFRalpha1/GDNF -0.018 0.102 -9999 0 -0.586 1 1
RXR and RAR heterodimerization with other nuclear receptor

Figure 61.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 63.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.013 0.025 -9999 0 -9999 0 0
VDR -0.058 0.23 -9999 0 -0.773 3 3
FAM120B 0.016 0 -9999 0 -9999 0 0
RXRs/LXRs/DNA/9cRA 0.018 0.123 -9999 0 -9999 0 0
RXRs/LXRs/DNA/Oxysterols 0.017 0.15 -9999 0 -9999 0 0
MED1 -0.025 0.164 -9999 0 -0.65 2 2
mol:9cRA 0.002 0.019 -9999 0 -9999 0 0
RARs/THRs/DNA/Src-1 0.008 0.106 -9999 0 -9999 0 0
RXRs/NUR77 0 0.138 -9999 0 -0.438 2 2
RXRs/PPAR -0.05 0.155 -9999 0 -0.47 1 1
NCOR2 0.016 0 -9999 0 -9999 0 0
VDR/VDR/Vit D3 -0.056 0.174 -9999 0 -0.596 3 3
RARs/VDR/DNA/Vit D3 -0.054 0.142 -9999 0 -0.429 4 4
RARA 0.016 0 -9999 0 -9999 0 0
NCOA1 -0.008 0.137 -9999 0 -0.773 1 1
VDR/VDR/DNA -0.058 0.23 -9999 0 -0.772 3 3
RARs/RARs/DNA/9cRA 0.015 0.082 -9999 0 -0.434 1 1
RARG 0.016 0 -9999 0 -9999 0 0
RPS6KB1 0.018 0.036 -9999 0 -9999 0 0
RARs/THRs/DNA/SMRT 0.019 0.09 -9999 0 -9999 0 0
THRA -0.025 0.164 -9999 0 -0.65 2 2
mol:Bile acids 0 0 -9999 0 -9999 0 0
VDR/Vit D3/DNA -0.056 0.174 -9999 0 -0.596 3 3
RXRs/PPAR/9cRA/PGJ2/DNA -0.001 0.134 -9999 0 -0.441 2 2
NR1H4 -0.059 0.203 -9999 0 -0.588 4 4
RXRs/LXRs/DNA 0.024 0.134 -9999 0 -9999 0 0
NR1H2 0.02 0.013 -9999 0 -9999 0 0
NR1H3 0.02 0.016 -9999 0 -9999 0 0
RXRs/VDR/DNA/Vit D3 -0.036 0.173 -9999 0 -0.416 5 5
NR4A1 -0.001 0.094 -9999 0 -0.526 1 1
mol:ATRA 0 0 -9999 0 -9999 0 0
RXRs/FXR/9cRA/MED1 -0.026 0.123 -9999 0 -0.44 1 1
RXRG -0.047 0.208 -9999 0 -0.683 3 3
RXR alpha/CCPG 0.026 0.01 -9999 0 -9999 0 0
RXRA 0.02 0.013 -9999 0 -9999 0 0
RXRB 0.019 0.016 -9999 0 -9999 0 0
THRB 0.016 0 -9999 0 -9999 0 0
PPARG -0.158 0.308 -9999 0 -0.681 8 8
PPARD 0.016 0 -9999 0 -9999 0 0
TNF -0.006 0.253 -9999 0 -1.173 1 1
mol:Oxysterols 0.003 0.017 -9999 0 -9999 0 0
cholesterol transport 0.017 0.149 -9999 0 -9999 0 0
PPARA 0.016 0 -9999 0 -9999 0 0
mol:Vit D3 0 0 -9999 0 -9999 0 0
RARB -0.008 0.137 -9999 0 -0.773 1 1
RXRs/NUR77/BCL2 -0.011 0.102 -9999 0 -9999 0 0
SREBF1 0.027 0.139 -9999 0 -9999 0 0
RXRs/RXRs/DNA/9cRA 0 0.134 -9999 0 -0.441 2 2
ABCA1 -0.025 0.314 -9999 0 -1.173 2 2
RARs/THRs -0.034 0.108 -9999 0 -9999 0 0
RXRs/FXR -0.035 0.165 -9999 0 -0.439 3 3
BCL2 -0.035 0.158 -9999 0 -0.526 3 3
HIF-2-alpha transcription factor network

Figure 62.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 64.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.055 0.221 -9999 0 -1.168 1 1
oxygen homeostasis -0.001 0.016 -9999 0 -9999 0 0
TCEB2 0.016 0 -9999 0 -9999 0 0
TCEB1 0.016 0 -9999 0 -9999 0 0
VHL/Elongin B/Elongin C/HIF2A -0.108 0.134 -9999 0 -0.472 1 1
EPO -0.102 0.271 -9999 0 -0.816 1 1
FIH (dimer) 0.015 0.017 -9999 0 -9999 0 0
APEX1 0.014 0.015 -9999 0 -9999 0 0
SERPINE1 -0.205 0.393 -9999 0 -0.824 7 7
FLT1 -0.093 0.284 -9999 0 -1.1 2 2
ADORA2A -0.135 0.311 -9999 0 -0.893 2 2
germ cell development -0.128 0.298 -9999 0 -0.959 1 1
SLC11A2 -0.148 0.333 -9999 0 -0.971 2 2
BHLHE40 -0.143 0.309 -9999 0 -0.76 3 3
HIF1AN 0.015 0.017 -9999 0 -9999 0 0
HIF2A/ARNT/SIRT1 -0.136 0.174 -9999 0 -0.656 1 1
ETS1 -0.019 0.166 -9999 0 -0.642 2 2
CITED2 -0.078 0.296 -9999 0 -1.216 2 2
KDR -0.215 0.423 -9999 0 -1.131 5 5
PGK1 -0.141 0.322 -9999 0 -0.93 2 2
SIRT1 0.017 0 -9999 0 -9999 0 0
response to hypoxia 0 0 -9999 0 -9999 0 0
HIF2A/ARNT -0.161 0.377 -9999 0 -0.947 3 3
EPAS1 -0.116 0.192 -9999 0 -0.556 1 1
SP1 0.022 0.019 -9999 0 -9999 0 0
ABCG2 -0.171 0.349 -9999 0 -0.816 4 4
EFNA1 -0.148 0.325 -9999 0 -0.875 2 2
FXN -0.128 0.299 -9999 0 -0.983 1 1
POU5F1 -0.134 0.309 -9999 0 -1.027 1 1
neuron apoptosis 0.154 0.36 0.895 3 -9999 0 3
EP300 0.016 0 -9999 0 -9999 0 0
EGLN3 -0.293 0.342 -9999 0 -0.646 15 15
EGLN2 0.016 0.015 -9999 0 -9999 0 0
EGLN1 -0.002 0.1 -9999 0 -0.549 1 1
VHL/Elongin B/Elongin C 0 0 -9999 0 -9999 0 0
VHL 0.016 0 -9999 0 -9999 0 0
ARNT 0.014 0.016 -9999 0 -9999 0 0
SLC2A1 -0.158 0.328 -9999 0 -0.965 2 2
TWIST1 -0.2 0.371 -9999 0 -0.856 5 5
ELK1 0.022 0.019 -9999 0 -9999 0 0
HIF2A/ARNT/Cbp/p300 -0.134 0.172 -9999 0 -0.65 1 1
VEGFA -0.142 0.335 -9999 0 -1.283 1 1
CREBBP 0.016 0 -9999 0 -9999 0 0
S1P1 pathway

Figure 63.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 65.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.122 0.219 -9999 0 -0.573 5 5
PDGFRB 0.014 0.005 -9999 0 -9999 0 0
SPHK1 -0.067 0.171 -9999 0 -0.961 1 1
mol:S1P -0.077 0.157 -9999 0 -0.855 1 1
S1P1/S1P/Gi -0.105 0.227 -9999 0 -0.679 3 3
GNAO1 0.012 0.008 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/PLCgamma1 -0.078 0.193 -9999 0 -0.619 2 2
PLCG1 -0.091 0.208 -9999 0 -0.61 3 3
mol:GTP 0 0 -9999 0 -9999 0 0
PDGFB-D/PDGFRB 0.014 0.005 -9999 0 -9999 0 0
GNAI2 -0.013 0.138 -9999 0 -0.778 1 1
GNAI3 0.011 0.008 -9999 0 -9999 0 0
GNAI1 -0.013 0.137 -9999 0 -0.773 1 1
mol:GDP 0 0 -9999 0 -9999 0 0
EDG1 -0.095 0.238 -9999 0 -0.547 6 6
S1P1/S1P -0.122 0.238 -9999 0 -0.715 3 3
negative regulation of cAMP metabolic process -0.101 0.219 -9999 0 -0.653 3 3
MAPK3 -0.129 0.263 -9999 0 -0.649 5 5
calcium-dependent phospholipase C activity -0.002 0.004 -9999 0 -9999 0 0
Rac1/GDP 0 0 -9999 0 -9999 0 0
RhoA/GDP 0 0 -9999 0 -9999 0 0
KDR -0.118 0.277 -9999 0 -0.68 6 6
PLCB2 -0.111 0.208 -9999 0 -0.605 3 3
RAC1 0.016 0 -9999 0 -9999 0 0
RhoA/GTP -0.117 0.176 -9999 0 -0.566 3 3
receptor internalization -0.135 0.199 -9999 0 -0.644 3 3
PTGS2 -0.202 0.381 -9999 0 -0.985 5 5
Rac1/GTP -0.117 0.176 -9999 0 -0.566 3 3
RHOA 0.016 0 -9999 0 -9999 0 0
VEGFA -0.011 0.141 -9999 0 -0.77 1 1
negative regulation of T cell proliferation -0.101 0.219 -9999 0 -0.653 3 3
GO:0007205 0 0 -9999 0 -9999 0 0
GNAZ 0.011 0.008 -9999 0 -9999 0 0
MAPK1 -0.129 0.263 -9999 0 -0.649 5 5
S1P1/S1P/PDGFB-D/PDGFRB -0.118 0.242 -9999 0 -0.724 3 3
ABCC1 -0.019 0.13 -9999 0 -0.523 2 2
TCR signaling in naïve CD8+ T cells

Figure 64.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 66.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.07 0.147 -9999 0 -0.519 2 2
FYN -0.044 0.208 -9999 0 -0.586 3 3
LAT/GRAP2/SLP76 -0.075 0.171 -9999 0 -0.624 2 2
IKBKB 0.016 0 -9999 0 -9999 0 0
AKT1 -0.027 0.178 -9999 0 -0.483 3 3
B2M 0.015 0.007 -9999 0 -9999 0 0
IKBKG -0.022 0.046 -9999 0 -9999 0 0
MAP3K8 -0.008 0.137 -9999 0 -0.773 1 1
mol:Ca2+ -0.001 0.01 -9999 0 -9999 0 0
integrin-mediated signaling pathway -0.016 0.089 -9999 0 -0.509 1 1
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.036 0.229 -9999 0 -0.654 3 3
TRPV6 0.003 0.005 -9999 0 -9999 0 0
CD28 -0.051 0.21 -9999 0 -0.694 3 3
SHC1 -0.05 0.211 -9999 0 -0.598 3 3
receptor internalization -0.053 0.228 -9999 0 -0.665 3 3
PRF1 -0.106 0.314 -9999 0 -0.78 4 4
KRAS -0.018 0.131 -9999 0 -0.526 2 2
GRB2 0.016 0 -9999 0 -9999 0 0
COT/AKT1 -0.021 0.147 -9999 0 -0.365 3 3
LAT -0.042 0.211 -9999 0 -0.597 3 3
EntrezGene:6955 -0.001 0.007 -9999 0 -9999 0 0
CD3D -0.027 0.165 -9999 0 -0.653 2 2
CD3E 0.015 0.007 -9999 0 -9999 0 0
CD3G -0.085 0.24 -9999 0 -0.632 5 5
RASGRP2 0.004 0.042 -9999 0 -0.196 1 1
RASGRP1 0.003 0.16 -9999 0 -0.418 3 3
HLA-A -0.01 0.139 -9999 0 -0.781 1 1
RASSF5 -0.008 0.137 -9999 0 -0.773 1 1
RAP1A/GTP/RAPL -0.016 0.089 -9999 0 -0.511 1 1
mol:GTP 0 0 -9999 0 -9999 0 0
mol:GDP 0.022 0.057 -9999 0 -0.143 1 1
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.044 0.082 -9999 0 -0.272 2 2
PRKCA -0.047 0.089 -9999 0 -0.291 2 2
GRAP2 0.016 0 -9999 0 -9999 0 0
mol:IP3 -0.06 0.134 -9999 0 -0.441 3 3
EntrezGene:6957 -0.001 0.007 -9999 0 -9999 0 0
TCR/CD3/MHC I/CD8 -0.049 0.193 -9999 0 -0.459 5 5
ORAI1 0.004 0.006 -9999 0 -9999 0 0
CSK -0.045 0.209 -9999 0 -0.591 3 3
B7 family/CD28 -0.145 0.245 -9999 0 -0.715 4 4
CHUK 0.016 0 -9999 0 -9999 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.058 0.236 -9999 0 -0.685 3 3
PTPN6 -0.048 0.215 -9999 0 -0.616 3 3
VAV1 -0.052 0.239 -9999 0 -0.712 3 3
Monovalent TCR/CD3 -0.06 0.214 -9999 0 -0.51 5 5
CBL 0.016 0 -9999 0 -9999 0 0
LCK -0.048 0.216 -9999 0 -0.619 3 3
PAG1 -0.073 0.227 -9999 0 -0.591 3 3
RAP1A 0.016 0 -9999 0 -9999 0 0
TCR/CD3/MHC I/CD8/LCK -0.063 0.24 -9999 0 -0.703 3 3
CD80 -0.026 0.165 -9999 0 -0.653 2 2
CD86 -0.026 0.164 -9999 0 -0.649 2 2
PDK1/CARD11/BCL10/MALT1 -0.054 0.099 -9999 0 -0.334 2 2
HRAS 0.016 0 -9999 0 -9999 0 0
GO:0035030 -0.078 0.233 -9999 0 -0.59 4 4
CD8A -0.001 0.007 -9999 0 -9999 0 0
CD8B -0.019 0.131 -9999 0 -0.524 2 2
PTPRC -0.009 0.138 -9999 0 -0.778 1 1
PDK1/PKC theta -0.034 0.211 -9999 0 -0.558 3 3
CSK/PAG1 -0.064 0.218 -9999 0 -0.553 3 3
SOS1 0.016 0 -9999 0 -9999 0 0
peptide-MHC class I 0 0.108 -9999 0 -0.595 1 1
GRAP2/SLP76 -0.089 0.2 -9999 0 -0.631 3 3
STIM1 0.003 0.006 -9999 0 -9999 0 0
RAS family/GTP 0.015 0.078 -9999 0 -9999 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.057 0.24 -9999 0 -0.707 3 3
mol:DAG -0.054 0.119 -9999 0 -0.394 3 3
RAP1A/GDP 0.012 0.025 -9999 0 -9999 0 0
PLCG1 0.016 0 -9999 0 -9999 0 0
CD247 -0.044 0.187 -9999 0 -0.613 3 3
cytotoxic T cell degranulation -0.1 0.299 -9999 0 -0.689 5 5
RAP1A/GTP -0.004 0.013 -9999 0 -0.069 1 1
mol:PI-3-4-5-P3 -0.023 0.192 -9999 0 -0.532 3 3
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.076 0.174 -9999 0 -0.577 3 3
NRAS -0.018 0.131 -9999 0 -0.526 2 2
ZAP70 0.016 0.001 -9999 0 -9999 0 0
GRB2/SOS1 0 0 -9999 0 -9999 0 0
LAT/GRAP2/SLP76/VAV1 -0.077 0.176 -9999 0 -0.582 3 3
MALT1 0.016 0 -9999 0 -9999 0 0
TRAF6 0.016 0 -9999 0 -9999 0 0
CD8 heterodimer -0.014 0.095 -9999 0 -0.379 2 2
CARD11 -0.008 0.137 -9999 0 -0.773 1 1
PRKCB -0.038 0.083 -9999 0 -0.272 3 3
PRKCE -0.035 0.082 -9999 0 -0.291 2 2
PRKCQ -0.025 0.219 -9999 0 -0.618 3 3
LCP2 -0.008 0.137 -9999 0 -0.773 1 1
BCL10 0.016 0 -9999 0 -9999 0 0
regulation of survival gene product expression -0.018 0.153 -9999 0 -0.402 3 3
IKK complex 0.019 0.057 -9999 0 -9999 0 0
RAS family/GDP -0.009 0.019 -9999 0 -0.067 1 1
MAP3K14 -0.005 0.116 -9999 0 -0.34 1 1
PDPK1 -0.037 0.193 -9999 0 -0.45 4 4
TCR/CD3/MHC I/CD8/Fyn -0.049 0.214 -9999 0 -0.68 2 2
HIV-1 Nef: Negative effector of Fas and TNF-alpha

Figure 65.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 67.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.016 0 -9999 0 -9999 0 0
Caspase 8 (4 units) -0.081 0.137 -9999 0 -0.444 2 2
NEF -0.023 0.067 -9999 0 -9999 0 0
NFKBIA -0.004 0.048 -9999 0 -9999 0 0
BIRC3 -0.098 0.299 -9999 0 -0.648 7 7
CYCS -0.056 0.174 -9999 0 -0.415 3 3
RIPK1 0.016 0 -9999 0 -9999 0 0
CD247 -0.07 0.227 -9999 0 -0.724 3 3
MAP2K7 -0.015 0.13 -9999 0 -0.496 1 1
protein ubiquitination 0.039 0.094 -9999 0 -9999 0 0
CRADD 0.016 0 -9999 0 -9999 0 0
DAXX 0.016 0 -9999 0 -9999 0 0
FAS -0.099 0.272 -9999 0 -0.724 5 5
BID -0.068 0.182 -9999 0 -0.445 3 3
NF-kappa-B/RelA/I kappa B alpha -0.062 0.12 -9999 0 -9999 0 0
TRADD 0.016 0 -9999 0 -9999 0 0
MAP3K5 0.016 0 -9999 0 -9999 0 0
CFLAR -0.001 0.094 -9999 0 -0.526 1 1
FADD 0.016 0 -9999 0 -9999 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.063 0.12 -9999 0 -9999 0 0
MAPK8 -0.005 0.123 -9999 0 -0.458 1 1
APAF1 0.016 0 -9999 0 -9999 0 0
TRAF1 -0.025 0.164 -9999 0 -0.65 2 2
TRAF2 0.016 0 -9999 0 -9999 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.052 0.171 -9999 0 -0.381 4 4
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.021 0.112 -9999 0 -9999 0 0
CHUK 0.039 0.099 -9999 0 -9999 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.06 0.142 -9999 0 -0.42 4 4
TCRz/NEF -0.1 0.218 -9999 0 -0.537 5 5
TNF -0.025 0.164 -9999 0 -0.65 2 2
FASLG -0.131 0.346 -9999 0 -0.799 6 6
NFKB1 -0.004 0.048 -9999 0 -9999 0 0
TNFR1A/BAG4/TNF-alpha -0.025 0.1 -9999 0 -0.501 1 1
CASP6 -0.054 0.103 -9999 0 -9999 0 0
CASP7 -0.074 0.262 -9999 0 -0.614 5 5
RELA -0.004 0.048 -9999 0 -9999 0 0
CASP2 0.016 0 -9999 0 -9999 0 0
CASP3 -0.074 0.262 -9999 0 -0.614 5 5
TNFRSF1A 0.016 0 -9999 0 -9999 0 0
TNFR1A/BAG4 0 0 -9999 0 -9999 0 0
CASP8 0.016 0 -9999 0 -9999 0 0
CASP9 0.016 0 -9999 0 -9999 0 0
MAP3K14 0.03 0.106 -9999 0 -9999 0 0
APAF-1/Caspase 9 -0.131 0.192 -9999 0 -0.562 4 4
BCL2 -0.018 0.152 -9999 0 -0.641 1 1
Canonical Wnt signaling pathway

Figure 66.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 68.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.009 0.024 -9999 0 -9999 0 0
AES -0.015 0.138 -9999 0 -0.777 1 1
FBXW11 0.016 0 -9999 0 -9999 0 0
mol:GTP 0 0.001 -9999 0 -9999 0 0
LRP6/FZD1 -0.029 0.119 -9999 0 -0.476 2 2
SMAD4 0.016 0 -9999 0 -9999 0 0
DKK2 -0.008 0.137 -9999 0 -0.773 1 1
TLE1 0.009 0.021 -9999 0 -9999 0 0
MACF1 -0.008 0.137 -9999 0 -0.774 1 1
CTNNB1 0.044 0.087 -9999 0 -9999 0 0
WIF1 -0.192 0.316 -9999 0 -0.649 10 10
beta catenin/RanBP3 0.02 0.108 0.402 1 -9999 0 1
KREMEN2 -0.052 0.179 -9999 0 -0.525 4 4
DKK1 -0.275 0.34 -9999 0 -0.65 14 14
beta catenin/beta TrCP1 0.051 0.082 -9999 0 -9999 0 0
FZD1 -0.025 0.164 -9999 0 -0.648 2 2
AXIN2 -0.037 0.279 -9999 0 -1.563 1 1
AXIN1 0.017 0.001 -9999 0 -9999 0 0
RAN 0.016 0.001 -9999 0 -9999 0 0
Axin1/APC/GSK3/beta catenin 0.021 0.035 -9999 0 -9999 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.069 0.136 -9999 0 -0.631 1 1
Axin1/APC/GSK3 0.017 0.056 -9999 0 -9999 0 0
Axin1/APC/GSK3/beta catenin/Macf1 0.033 0.112 -9999 0 -9999 0 0
HNF1A -0.008 0.096 -9999 0 -0.53 1 1
CTBP1 0.009 0.022 -9999 0 -9999 0 0
MYC 0.006 0.066 -9999 0 -9999 0 0
RANBP3 0.016 0.001 -9999 0 -9999 0 0
DKK2/LRP6/Kremen 2 -0.053 0.128 -9999 0 -0.502 1 1
NKD1 -0.05 0.209 -9999 0 -0.691 3 3
TCF4 0.008 0.022 -9999 0 -9999 0 0
TCF3 0.009 0.022 -9999 0 -9999 0 0
WNT1/LRP6/FZD1/Axin1 -0.035 0.116 -9999 0 -0.448 2 2
Ran/GTP 0.002 0.005 -9999 0 -9999 0 0
CtBP/CBP/TCF/TLE1/AES 0.029 0.144 0.453 2 -9999 0 2
LEF1 -0.009 0.097 -9999 0 -0.532 1 1
DVL1 0.046 0.051 -9999 0 -9999 0 0
CSNK2A1 0.016 0 -9999 0 -9999 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.059 0.145 -9999 0 -0.607 1 1
DKK1/LRP6/Kremen 2 -0.213 0.223 -9999 0 -0.542 7 7
LRP6 0.016 0.001 -9999 0 -9999 0 0
CSNK1A1 0.009 0.024 -9999 0 -9999 0 0
NLK -0.001 0.097 -9999 0 -0.54 1 1
CCND1 -0.06 0.3 -9999 0 -1.57 1 1
WNT1 -0.008 0.137 -9999 0 -0.77 1 1
GSK3A 0.017 0.001 -9999 0 -9999 0 0
GSK3B 0.016 0.001 -9999 0 -9999 0 0
FRAT1 -0.001 0.094 -9999 0 -0.526 1 1
PPP2R5D 0.056 0.099 0.355 3 -9999 0 3
APC 0.013 0.12 -9999 0 -0.41 2 2
WNT1/LRP6/FZD1 0.048 0.122 0.278 3 -9999 0 3
CREBBP 0.009 0.022 -9999 0 -9999 0 0
Effects of Botulinum toxin

Figure 67.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 69.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
STX1A 0.002 0.069 -9999 0 -0.382 1 1
UniProt:P19321 0 0 -9999 0 -9999 0 0
RIMS1/UNC13B -0.048 0.153 -9999 0 -0.514 3 3
STXBP1 -0.018 0.131 -9999 0 -0.526 2 2
ACh/CHRNA1 -0.015 0.114 -9999 0 -0.439 2 2
RAB3GAP2/RIMS1/UNC13B -0.041 0.13 -9999 0 -0.501 2 2
mol:Ca2+ 0 0 -9999 0 -9999 0 0
UniProt:P30996 0 0 -9999 0 -9999 0 0
UniProt:Q60393 0 0 -9999 0 -9999 0 0
CST086 0 0 -9999 0 -9999 0 0
RIMS1 -0.001 0.094 -9999 0 -0.526 1 1
mol:ACh 0.004 0.026 -9999 0 -9999 0 0
RAB3GAP2 0.016 0 -9999 0 -9999 0 0
STX1A/SNAP25/VAMP2 -0.051 0.124 -9999 0 -0.572 1 1
UniProt:P10844 0 0 -9999 0 -9999 0 0
muscle contraction -0.015 0.114 -9999 0 -0.437 2 2
UNC13B -0.033 0.191 -9999 0 -0.773 2 2
CHRNA1 -0.025 0.164 -9999 0 -0.65 2 2
UniProt:P10845 0 0 -9999 0 -9999 0 0
ACh/Synaptotagmin 1 -0.07 0.167 -9999 0 -0.373 7 7
SNAP25 -0.004 0.05 -9999 0 -0.199 2 2
VAMP2 0.008 0 -9999 0 -9999 0 0
SYT1 -0.11 0.242 -9999 0 -0.561 7 7
UniProt:Q00496 0 0 -9999 0 -9999 0 0
STXIA/STXBP1 -0.009 0.098 -9999 0 -9999 0 0
STX1A/SNAP25 fragment 1/VAMP2 -0.051 0.124 -9999 0 -0.572 1 1
TCGA08_rtk_signaling

Figure 68.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 70.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.016 0 -9999 0 -9999 0 0
HRAS 0.016 0 -9999 0 -9999 0 0
EGFR -0.175 0.312 -9999 0 -0.663 9 9
AKT 0.018 0.059 -9999 0 -0.277 1 1
FOXO3 0.016 0 -9999 0 -9999 0 0
AKT1 0.016 0 -9999 0 -9999 0 0
FOXO1 0.016 0 -9999 0 -9999 0 0
AKT3 0.016 0 -9999 0 -9999 0 0
FOXO4 0.016 0 -9999 0 -9999 0 0
MET -0.126 0.274 -9999 0 -0.632 7 7
PIK3CA 0.016 0 -9999 0 -9999 0 0
PIK3CB -0.008 0.137 -9999 0 -0.773 1 1
NRAS -0.018 0.131 -9999 0 -0.526 2 2
PIK3CG -0.008 0.137 -9999 0 -0.773 1 1
PIK3R3 -0.059 0.203 -9999 0 -0.588 4 4
PIK3R2 0.016 0 -9999 0 -9999 0 0
NF1 0.016 0 -9999 0 -9999 0 0
RAS -0.06 0.107 -9999 0 -0.269 3 3
ERBB2 -0.001 0.094 -9999 0 -0.526 1 1
proliferation/survival/translation -0.01 0.077 0.318 1 -9999 0 1
PI3K -0.056 0.126 -9999 0 -0.305 4 4
PIK3R1 -0.008 0.137 -9999 0 -0.773 1 1
KRAS -0.018 0.131 -9999 0 -0.526 2 2
FOXO 0.029 0.039 -9999 0 -9999 0 0
AKT2 -0.001 0.094 -9999 0 -0.526 1 1
PTEN 0.016 0 -9999 0 -9999 0 0
LPA receptor mediated events

Figure 69.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 71.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.032 0.133 -9999 0 -0.73 1 1
NF kappa B1 p50/RelA/I kappa B alpha 0.004 0.073 -9999 0 -9999 0 0
AP1 -0.099 0.182 -9999 0 -0.479 4 4
mol:PIP3 -0.133 0.206 -9999 0 -0.47 7 7
AKT1 -0.003 0.161 -9999 0 -0.481 3 3
PTK2B -0.001 0.057 -9999 0 -0.185 2 2
RHOA -0.007 0.109 -9999 0 -0.369 2 2
PIK3CB -0.008 0.137 -9999 0 -0.771 1 1
mol:Ca2+ -0.011 0.095 -9999 0 -0.403 1 1
MAGI3 -0.05 0.209 -9999 0 -0.691 3 3
RELA 0.016 0 -9999 0 -9999 0 0
apoptosis -0.002 0.066 -9999 0 -0.258 1 1
HRAS/GDP 0 0 -9999 0 -9999 0 0
positive regulation of microtubule depolymerization 0.004 0.086 -9999 0 -0.382 1 1
NF kappa B1 p50/RelA -0.035 0.085 -9999 0 -9999 0 0
endothelial cell migration -0.036 0.195 -9999 0 -0.622 3 3
ADCY4 0.01 0.088 -9999 0 -9999 0 0
ADCY5 0.003 0.096 -9999 0 -9999 0 0
ADCY6 0.003 0.094 -9999 0 -9999 0 0
ADCY7 0.006 0.089 -9999 0 -9999 0 0
ADCY1 0.01 0.088 -9999 0 -9999 0 0
ADCY2 0.01 0.088 -9999 0 -9999 0 0
ADCY3 0.01 0.088 -9999 0 -9999 0 0
ADCY8 0.006 0.089 -9999 0 -9999 0 0
ADCY9 0.003 0.097 -9999 0 -0.28 1 1
GSK3B 0.008 0.054 -9999 0 -9999 0 0
arachidonic acid secretion 0.012 0.1 -9999 0 -0.349 1 1
GNG2 -0.009 0.137 -9999 0 -0.772 1 1
TRIP6 0.003 0.092 -9999 0 -0.502 1 1
GNAO1 -0.001 0.079 -9999 0 -0.304 1 1
HRAS 0.016 0 -9999 0 -9999 0 0
NFKBIA 0.004 0.083 -9999 0 -9999 0 0
GAB1 -0.008 0.137 -9999 0 -0.773 1 1
mol:GTP 0 0 -9999 0 -9999 0 0
lamellipodium assembly 0 0.033 -9999 0 -9999 0 0
JUN -0.058 0.23 -9999 0 -0.774 3 3
LPA/LPA2/NHERF2 -0.024 0.092 -9999 0 -0.517 1 1
TIAM1 -0.002 0.037 -9999 0 -9999 0 0
PIK3R1 -0.008 0.137 -9999 0 -0.771 1 1
mol:IP3 -0.011 0.097 -9999 0 -0.411 1 1
PLCB3 0.002 0.088 -9999 0 -0.466 1 1
FOS -0.076 0.218 -9999 0 -0.576 5 5
positive regulation of mitosis 0.012 0.1 -9999 0 -0.349 1 1
LPA/LPA1-2-3 -0.021 0.068 -9999 0 -0.229 3 3
mol:Ca ++ 0 0 -9999 0 -9999 0 0
JNK cascade 0 0.001 -9999 0 -9999 0 0
BCAR1 0.016 0 -9999 0 -9999 0 0
stress fiber formation 0.007 0.058 -9999 0 -0.2 1 1
GNAZ -0.001 0.079 -9999 0 -0.304 1 1
EGFR/PI3K-beta/Gab1 -0.14 0.218 -9999 0 -0.495 7 7
positive regulation of dendritic cell cytokine production -0.021 0.067 -9999 0 -0.228 3 3
LPA/LPA2/MAGI-3 -0.05 0.142 -9999 0 -0.475 3 3
ARHGEF1 0.01 0.099 -9999 0 -0.436 1 1
GNAI2 -0.018 0.118 -9999 0 -0.405 2 2
GNAI3 -0.001 0.079 -9999 0 -0.304 1 1
GNAI1 -0.018 0.118 -9999 0 -0.407 2 2
LPA/LPA3 -0.011 0.033 -9999 0 -0.113 3 3
LPA/LPA2 -0.011 0.033 -9999 0 -0.112 3 3
LPA/LPA1 -0.028 0.089 -9999 0 -0.302 3 3
HB-EGF/EGFR -0.158 0.257 -9999 0 -0.567 7 7
HBEGF -0.038 0.223 -9999 0 -0.675 3 3
mol:DAG -0.011 0.097 -9999 0 -0.411 1 1
cAMP biosynthetic process 0.009 0.101 -9999 0 -0.344 1 1
NFKB1 0.016 0 -9999 0 -9999 0 0
SRC 0.016 0 -9999 0 -9999 0 0
GNB1 0.016 0.001 -9999 0 -9999 0 0
LYN 0.004 0.083 -9999 0 -9999 0 0
GNAQ -0.005 0.026 -9999 0 -0.085 3 3
LPAR2 -0.001 0.001 -9999 0 -9999 0 0
LPAR3 -0.001 0.001 -9999 0 -9999 0 0
LPAR1 -0.011 0.053 -9999 0 -0.175 3 3
IL8 -0.259 0.265 -9999 0 -0.504 16 16
PTK2 -0.001 0.066 -9999 0 -0.256 1 1
Rac1/GDP 0 0 -9999 0 -9999 0 0
CASP3 -0.002 0.066 -9999 0 -0.26 1 1
EGFR -0.176 0.312 -9999 0 -0.664 9 9
PLCG1 -0.019 0.073 -9999 0 -0.182 4 4
PLD2 -0.001 0.066 -9999 0 -0.256 1 1
G12/G13 -0.029 0.097 -9999 0 -0.472 1 1
PI3K-beta -0.063 0.169 -9999 0 -0.57 3 3
cell migration -0.006 0.033 -9999 0 -9999 0 0
SLC9A3R2 -0.009 0.137 -9999 0 -0.774 1 1
PXN 0.007 0.059 -9999 0 -0.203 1 1
HRAS/GTP 0.012 0.102 -9999 0 -0.357 1 1
RAC1 0.016 0 -9999 0 -9999 0 0
MMP9 -0.034 0.191 -9999 0 -0.774 2 2
PRKCE 0.016 0 -9999 0 -9999 0 0
PRKCD -0.002 0.093 -9999 0 -0.385 1 1
Gi(beta/gamma) 0.008 0.112 -9999 0 -0.459 1 1
mol:LPA -0.012 0.053 -9999 0 -0.175 3 3
TRIP6/p130 Cas/FAK1/Paxillin -0.017 0.065 -9999 0 -9999 0 0
MAPKKK cascade 0.012 0.1 -9999 0 -0.349 1 1
contractile ring contraction involved in cytokinesis -0.007 0.108 -9999 0 -0.365 2 2
mol:GDP 0 0 -9999 0 -9999 0 0
GNA14 -0.043 0.137 -9999 0 -0.388 4 4
GNA15 -0.024 0.1 -9999 0 -0.32 3 3
GNA12 0.016 0 -9999 0 -9999 0 0
GNA13 -0.001 0.094 -9999 0 -0.526 1 1
MAPT 0.003 0.088 -9999 0 -0.394 1 1
GNA11 0.005 0.026 -9999 0 -9999 0 0
Rac1/GTP 0 0.034 -9999 0 -9999 0 0
MMP2 -0.037 0.196 -9999 0 -0.626 3 3
Stabilization and expansion of the E-cadherin adherens junction

Figure 70.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 72.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.011 0.089 -9999 0 -9999 0 0
epithelial cell differentiation -0.034 0.109 -9999 0 -0.424 2 2
CYFIP2 -0.008 0.137 -9999 0 -0.773 1 1
ENAH 0.008 0.154 -9999 0 -0.556 1 1
EGFR -0.175 0.312 -9999 0 -0.663 9 9
EPHA2 -0.025 0.164 -9999 0 -0.65 2 2
MYO6 0.011 0.116 -9999 0 -9999 0 0
CTNNB1 -0.001 0.094 -9999 0 -0.526 1 1
ABI1/Sra1/Nap1 -0.016 0.087 -9999 0 -0.501 1 1
AQP5 -0.176 0.283 -9999 0 -0.642 8 8
CTNND1 0.016 0 -9999 0 -9999 0 0
mol:PI-4-5-P2 0.011 0.114 -9999 0 -9999 0 0
regulation of calcium-dependent cell-cell adhesion -0.01 0.173 -9999 0 -0.596 2 2
EGF -0.126 0.274 -9999 0 -0.632 7 7
NCKAP1 0.016 0 -9999 0 -9999 0 0
AQP3 -0.119 0.246 -9999 0 -0.724 4 4
cortical microtubule organization -0.034 0.109 -9999 0 -0.424 2 2
GO:0000145 0.011 0.109 -9999 0 -9999 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.035 0.111 -9999 0 -0.429 2 2
MLLT4 0.016 0 -9999 0 -9999 0 0
ARF6/GDP -0.056 0.112 -9999 0 -9999 0 0
ARF6 -0.001 0.094 -9999 0 -0.526 1 1
Ephrin A1/EPHA2/NCK1/GIT1 -0.037 0.117 -9999 0 -0.453 2 2
mol:Ca2+ 0 0 -9999 0 -9999 0 0
VASP -0.003 0.137 -9999 0 -9999 0 0
PVRL2 0.016 0 -9999 0 -9999 0 0
ZYX -0.006 0.145 -9999 0 -0.493 1 1
ARF6/GTP -0.041 0.112 -9999 0 -9999 0 0
CDH1 -0.033 0.191 -9999 0 -0.773 2 2
EGFR/EGFR/EGF/EGF -0.183 0.221 -9999 0 -0.687 3 3
RhoA/GDP -0.032 0.102 -9999 0 -0.395 2 2
actin cytoskeleton organization 0.012 0.117 -9999 0 -9999 0 0
IGF-1R heterotetramer -0.018 0.131 -9999 0 -0.525 2 2
GIT1 0.016 0 -9999 0 -9999 0 0
IGF1R -0.018 0.131 -9999 0 -0.526 2 2
IGF1 -0.001 0.094 -9999 0 -0.526 1 1
DIAPH1 -0.021 0.13 -9999 0 -0.742 1 1
Wnt receptor signaling pathway 0.034 0.109 0.424 2 -9999 0 2
RHOA 0.016 0 -9999 0 -9999 0 0
RhoA/GTP -0.051 0.111 -9999 0 -9999 0 0
CTNNA1 0.016 0 -9999 0 -9999 0 0
VCL 0.011 0.12 -9999 0 -9999 0 0
EFNA1 -0.008 0.137 -9999 0 -0.773 1 1
LPP -0.015 0.151 -9999 0 -9999 0 0
Ephrin A1/EPHA2 -0.061 0.132 -9999 0 -9999 0 0
SEC6/SEC8 -0.035 0.109 -9999 0 -9999 0 0
MGAT3 -0.011 0.177 -9999 0 -0.611 2 2
HGF/MET -0.095 0.188 -9999 0 -0.63 2 2
HGF 0.016 0 -9999 0 -9999 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.011 0.09 -9999 0 -9999 0 0
actin cable formation 0.025 0.125 -9999 0 -9999 0 0
KIAA1543 0.02 0.111 -9999 0 -9999 0 0
KIFC3 0.011 0.116 -9999 0 -0.4 2 2
NCK1 0.016 0 -9999 0 -9999 0 0
EXOC3 -0.001 0.094 -9999 0 -0.526 1 1
ACTN1 -0.012 0.142 -9999 0 -9999 0 0
NCK1/GIT1 0 0 -9999 0 -9999 0 0
mol:GDP -0.034 0.109 -9999 0 -0.424 2 2
EXOC4 0.016 0 -9999 0 -9999 0 0
STX4 0.011 0.116 -9999 0 -9999 0 0
PIP5K1C 0.011 0.116 -9999 0 -9999 0 0
LIMA1 0.016 0 -9999 0 -9999 0 0
ABI1 0.016 0 -9999 0 -9999 0 0
ROCK1 0.019 0.126 -9999 0 -9999 0 0
adherens junction assembly 0.04 0.108 -9999 0 -9999 0 0
IGF-1R heterotetramer/IGF1 -0.05 0.11 -9999 0 -9999 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -9999 0 0
MET -0.126 0.274 -9999 0 -0.632 7 7
PLEKHA7 0.011 0.116 -9999 0 -9999 0 0
mol:GTP -0.036 0.116 -9999 0 -0.449 2 2
establishment of epithelial cell apical/basal polarity 0.037 0.125 -9999 0 -9999 0 0
cortical actin cytoskeleton stabilization 0.011 0.089 -9999 0 -9999 0 0
regulation of cell-cell adhesion 0.012 0.117 -9999 0 -9999 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.011 0.09 -9999 0 -9999 0 0
Regulation of Telomerase

Figure 71.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 73.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.045 0.159 -9999 0 -0.596 1 1
RAD9A 0.016 0 -9999 0 -9999 0 0
AP1 -0.096 0.256 -9999 0 -0.531 7 7
IFNAR2 0.017 0.006 -9999 0 -9999 0 0
AKT1 -0.079 0.198 -9999 0 -0.65 2 2
ER alpha/Oestrogen -0.174 0.235 -9999 0 -0.447 13 13
NFX1/SIN3/HDAC complex 0.049 0.045 -9999 0 -9999 0 0
EGF -0.125 0.274 -9999 0 -0.632 7 7
SMG5 0.016 0 -9999 0 -9999 0 0
SMG6 0.016 0 -9999 0 -9999 0 0
SP3/HDAC2 0.027 0.009 -9999 0 -9999 0 0
TERT/c-Abl -0.049 0.143 -9999 0 -0.554 1 1
SAP18 0.017 0.001 -9999 0 -9999 0 0
MRN complex 0 0 -9999 0 -9999 0 0
WT1 -0.108 0.265 -9999 0 -0.647 6 6
WRN 0.016 0 -9999 0 -9999 0 0
SP1 0.019 0.006 -9999 0 -9999 0 0
SP3 0.017 0.002 -9999 0 -9999 0 0
TERF2IP -0.001 0.094 -9999 0 -0.526 1 1
Telomerase/Nucleolin -0.055 0.11 -9999 0 -9999 0 0
Mad/Max 0.025 0.008 -9999 0 -9999 0 0
TERT -0.047 0.162 -9999 0 -0.61 1 1
CCND1 -0.067 0.261 -9999 0 -1.27 1 1
MAX 0.017 0.003 -9999 0 -9999 0 0
RBBP7 0.017 0.001 -9999 0 -9999 0 0
RBBP4 0.017 0.001 -9999 0 -9999 0 0
TERF2 0.003 0.018 -9999 0 -9999 0 0
PTGES3 0.016 0 -9999 0 -9999 0 0
SIN3A 0.017 0.001 -9999 0 -9999 0 0
Telomerase/911 0.042 0.026 -9999 0 -9999 0 0
CDKN1B -0.085 0.206 -9999 0 -0.478 5 5
RAD1 0.016 0 -9999 0 -9999 0 0
XRCC5 0.016 0 -9999 0 -9999 0 0
XRCC6 0.016 0 -9999 0 -9999 0 0
SAP30 0.017 0.001 -9999 0 -9999 0 0
TRF2/PARP2 -0.014 0.097 -9999 0 -0.549 1 1
UBE3A 0.017 0.002 -9999 0 -9999 0 0
JUN -0.057 0.23 -9999 0 -0.773 3 3
E6 0.001 0.002 -9999 0 -9999 0 0
HPV-16 E6/E6AP 0.014 0.004 -9999 0 -9999 0 0
FOS -0.075 0.219 -9999 0 -0.575 5 5
IFN-gamma/IRF1 -0.128 0.231 -9999 0 -0.567 5 5
PARP2 -0.008 0.137 -9999 0 -0.773 1 1
BLM -0.001 0.094 -9999 0 -0.526 1 1
Telomerase 0.036 0.062 -9999 0 -9999 0 0
IRF1 0.022 0.005 -9999 0 -9999 0 0
ESR1 -0.234 0.312 -9999 0 -0.602 13 13
KU/TER 0 0 -9999 0 -9999 0 0
ATM/TRF2 0.008 0.094 -9999 0 -0.518 1 1
ubiquitin-dependent protein catabolic process 0.054 0.049 -9999 0 -9999 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.054 0.049 -9999 0 -9999 0 0
HDAC1 0.017 0.001 -9999 0 -9999 0 0
HDAC2 0.018 0.006 -9999 0 -9999 0 0
ATM -0.017 0.094 -9999 0 -0.54 1 1
SMAD3 0.028 0.003 -9999 0 -9999 0 0
ABL1 0.016 0 -9999 0 -9999 0 0
MXD1 0.017 0.003 -9999 0 -9999 0 0
MRE11A 0.016 0 -9999 0 -9999 0 0
HUS1 0.016 0 -9999 0 -9999 0 0
RPS6KB1 0.016 0 -9999 0 -9999 0 0
TERT/NF kappa B1/14-3-3 -0.073 0.192 -9999 0 -0.719 2 2
NR2F2 -0.01 0.138 -9999 0 -0.775 1 1
MAPK3 0.01 0.107 -9999 0 -0.584 1 1
MAPK1 0.01 0.107 -9999 0 -0.584 1 1
TGFB1/TGF beta receptor Type II 0.016 0.001 -9999 0 -9999 0 0
NFKB1 0.016 0 -9999 0 -9999 0 0
HNRNPC 0.016 0 -9999 0 -9999 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.017 0.094 -9999 0 -0.539 1 1
NBN 0.016 0 -9999 0 -9999 0 0
EGFR -0.174 0.312 -9999 0 -0.662 9 9
mol:Oestrogen 0 0.001 -9999 0 -9999 0 0
EGF/EGFR -0.219 0.308 -9999 0 -0.532 14 14
MYC 0.016 0.005 -9999 0 -9999 0 0
IL2 -0.006 0.138 -9999 0 -0.772 1 1
KU 0 0 -9999 0 -9999 0 0
RAD50 0.016 0 -9999 0 -9999 0 0
HSP90AA1 0.016 0 -9999 0 -9999 0 0
TGFB1 0.016 0.001 -9999 0 -9999 0 0
TRF2/BLM -0.008 0.062 -9999 0 -0.341 1 1
FRAP1 0.016 0 -9999 0 -9999 0 0
KU/TERT -0.025 0.15 -9999 0 -0.547 1 1
SP1/HDAC2 0.03 0.01 -9999 0 -9999 0 0
PINX1 0.016 0 -9999 0 -9999 0 0
Telomerase/EST1A -0.055 0.11 -9999 0 -0.494 1 1
Smad3/Myc 0.032 0.002 -9999 0 -9999 0 0
911 complex 0 0 -9999 0 -9999 0 0
IFNG -0.183 0.313 -9999 0 -0.636 10 10
Telomerase/PinX1 -0.055 0.11 -9999 0 -0.494 1 1
Telomerase/AKT1/mTOR/p70S6K -0.004 0.15 -9999 0 -0.77 1 1
SIN3B 0.017 0.001 -9999 0 -9999 0 0
YWHAE 0.016 0 -9999 0 -9999 0 0
Telomerase/EST1B -0.055 0.11 -9999 0 -0.494 1 1
response to DNA damage stimulus 0 0.026 -9999 0 -9999 0 0
MRN complex/TRF2/Rap1 -0.004 0.045 -9999 0 -9999 0 0
TRF2/WRN 0.003 0.016 -9999 0 -9999 0 0
Telomerase/hnRNP C1/C2 -0.055 0.11 -9999 0 -9999 0 0
E2F1 0 0.094 -9999 0 -0.524 1 1
ZNFX1 -0.008 0.137 -9999 0 -0.773 1 1
PIF1 0.016 0 -9999 0 -9999 0 0
NCL 0.016 0 -9999 0 -9999 0 0
DKC1 0.016 0 -9999 0 -9999 0 0
telomeric DNA binding 0 0 -9999 0 -9999 0 0
IGF1 pathway

Figure 72.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 74.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.016 0 -9999 0 -9999 0 0
PTK2 0.016 0 -9999 0 -9999 0 0
CRKL -0.056 0.15 -9999 0 -0.45 1 1
GRB2/SOS1/SHC -0.009 0.053 -9999 0 -9999 0 0
HRAS 0.016 0 -9999 0 -9999 0 0
IRS1/Crk -0.041 0.133 -9999 0 -0.328 4 4
IGF-1R heterotetramer/IGF1/PTP1B -0.032 0.077 -9999 0 -9999 0 0
AKT1 -0.06 0.189 -9999 0 -0.752 1 1
BAD -0.047 0.178 -9999 0 -0.686 1 1
mol:GTP 0 0 -9999 0 -9999 0 0
CRK -0.041 0.133 -9999 0 -0.326 4 4
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.041 0.133 -9999 0 -9999 0 0
RAF1 -0.043 0.18 -9999 0 -0.673 1 1
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.029 0.127 -9999 0 -9999 0 0
YWHAZ 0.016 0 -9999 0 -9999 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.056 0.143 -9999 0 -0.364 4 4
PIK3CA 0.016 0 -9999 0 -9999 0 0
RPS6KB1 -0.06 0.189 -9999 0 -0.752 1 1
GNB2L1 -0.001 0.094 -9999 0 -0.526 1 1
positive regulation of MAPKKK cascade -0.038 0.153 -9999 0 -0.545 1 1
PXN 0.016 0 -9999 0 -9999 0 0
PIK3R1 -0.008 0.137 -9999 0 -0.773 1 1
cell adhesion 0 0 -9999 0 -9999 0 0
GRB2/SOS1 0 0 -9999 0 -9999 0 0
HRAS/GTP -0.059 0.109 -9999 0 -9999 0 0
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.029 0.092 -9999 0 -0.473 1 1
IGF-1R heterotetramer -0.03 0.129 -9999 0 -0.517 2 2
IGF-1R heterotetramer/IGF1/IRS/Nck -0.041 0.133 -9999 0 -0.328 4 4
Crk/p130 Cas/Paxillin -0.056 0.101 -9999 0 -9999 0 0
IGF1R -0.03 0.129 -9999 0 -0.517 2 2
IGF1 -0.015 0.095 -9999 0 -0.517 1 1
IRS2/Crk -0.06 0.171 -9999 0 -0.439 3 3
PI3K -0.043 0.143 -9999 0 -0.42 1 1
apoptosis 0.031 0.155 0.564 1 -9999 0 1
HRAS/GDP 0 0 -9999 0 -9999 0 0
PRKCD 0.002 0.084 -9999 0 -9999 0 0
RAF1/14-3-3 E -0.027 0.157 -9999 0 -0.552 1 1
BAD/14-3-3 -0.034 0.165 -9999 0 -0.613 1 1
PRKCZ -0.069 0.189 -9999 0 -0.507 3 3
Crk/p130 Cas/Paxillin/FAK1 -0.075 0.132 -9999 0 -0.6 1 1
PTPN1 0.016 0 -9999 0 -9999 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.008 0.089 -9999 0 -9999 0 0
BCAR1 0.016 0 -9999 0 -9999 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.069 0.148 -9999 0 -0.529 2 2
mol:GDP 0 0 -9999 0 -9999 0 0
SOS1 0.016 0 -9999 0 -9999 0 0
IRS1/NCK2 -0.041 0.133 -9999 0 -0.327 4 4
GRB10 -0.042 0.186 -9999 0 -0.608 3 3
PTPN11 -0.041 0.133 -9999 0 -9999 0 0
IRS1 -0.056 0.144 -9999 0 -0.365 4 4
IRS2 -0.073 0.179 -9999 0 -0.469 3 3
IGF-1R heterotetramer/IGF1 -0.031 0.114 -9999 0 -0.364 3 3
GRB2 0.016 0 -9999 0 -9999 0 0
PDPK1 -0.073 0.199 -9999 0 -0.536 3 3
YWHAE 0.016 0 -9999 0 -9999 0 0
PRKD1 -0.026 0.145 -9999 0 -0.483 2 2
SHC1 -0.001 0.094 -9999 0 -0.526 1 1
Insulin Pathway

Figure 73.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 75.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.109 0.195 -9999 0 -0.475 5 5
TC10/GTP -0.024 0.094 -9999 0 -0.388 2 2
Insulin Receptor/Insulin/IRS1/Shp2 -0.1 0.178 -9999 0 -0.448 6 6
HRAS 0.016 0 -9999 0 -9999 0 0
APS homodimer 0 0 -9999 0 -9999 0 0
GRB14 -0.183 0.324 -9999 0 -0.691 9 9
FOXO3 -0.032 0.036 -9999 0 -9999 0 0
AKT1 -0.161 0.268 -9999 0 -0.692 4 4
INSR -0.031 0.19 -9999 0 -0.768 2 2
Insulin Receptor/Insulin 0.019 0.113 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
GRB10 -0.042 0.186 -9999 0 -0.608 3 3
SORBS1 -0.033 0.191 -9999 0 -0.773 2 2
CRK 0.016 0 -9999 0 -9999 0 0
PTPN1 0.017 0.111 -9999 0 -9999 0 0
CAV1 -0.103 0.275 -9999 0 -0.58 7 7
CBL/APS/CAP/Crk-II/C3G -0.027 0.104 -9999 0 -0.429 2 2
Insulin Receptor/Insulin/IRS1/NCK2 -0.1 0.178 -9999 0 -0.448 6 6
mol:GDP 0 0 -9999 0 -9999 0 0
mol:PI-3-4-5-P3 -0.1 0.18 -9999 0 -0.445 5 5
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.04 0.18 -9999 0 -0.601 2 2
RPS6KB1 -0.137 0.244 -9999 0 -0.61 4 4
PARD6A -0.042 0.186 -9999 0 -0.608 3 3
CBL 0.016 0 -9999 0 -9999 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -9999 0 0
DOK1 0.014 0.031 -9999 0 -9999 0 0
PIK3R1 -0.008 0.137 -9999 0 -0.773 1 1
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.176 0.215 -9999 0 -0.631 4 4
HRAS/GTP -0.08 0.133 -9999 0 -9999 0 0
Insulin Receptor -0.031 0.19 -9999 0 -0.766 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.099 0.165 -9999 0 -0.425 4 4
PRKCI -0.043 0.049 -9999 0 -9999 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.216 0.263 -9999 0 -0.767 4 4
SHC1 -0.001 0.094 -9999 0 -0.526 1 1
negative regulation of MAPKKK cascade 0.005 0.049 -9999 0 -9999 0 0
PI3K -0.101 0.183 -9999 0 -0.453 5 5
NCK2 0.016 0 -9999 0 -9999 0 0
RHOQ 0.016 0 -9999 0 -9999 0 0
mol:H2O2 -0.004 0.012 -9999 0 -9999 0 0
HRAS/GDP 0 0 -9999 0 -9999 0 0
AKT2 -0.17 0.265 -9999 0 -0.692 4 4
PRKCZ -0.048 0.054 -9999 0 -9999 0 0
SH2B2 0 0 -9999 0 -9999 0 0
SHC/SHIP -0.068 0.176 -9999 0 -0.397 6 6
F2RL2 -0.008 0.137 -9999 0 -0.773 1 1
TRIP10 0.016 0 -9999 0 -9999 0 0
Insulin Receptor/Insulin/Shc -0.044 0.119 -9999 0 -0.432 2 2
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -9999 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 -0.038 0.106 -9999 0 -9999 0 0
RAPGEF1 0.016 0 -9999 0 -9999 0 0
RASA1 -0.001 0.094 -9999 0 -0.526 1 1
NCK1 0.016 0 -9999 0 -9999 0 0
CBL/APS/CAP/Crk-II -0.029 0.112 -9999 0 -0.462 2 2
TC10/GDP 0 0 -9999 0 -9999 0 0
Insulin Receptor/Insulin/SHC/GRB10 -0.074 0.145 -9999 0 -0.435 3 3
INPP5D -0.072 0.183 -9999 0 -0.428 6 6
SOS1 0.016 0 -9999 0 -9999 0 0
SGK1 -0.018 0.019 -9999 0 -9999 0 0
mol:cAMP 0 0 -9999 0 -9999 0 0
PTPN11 0.016 0 -9999 0 -9999 0 0
IRS1 -0.099 0.272 -9999 0 -0.724 5 5
p62DOK/RasGAP 0.005 0.05 -9999 0 -9999 0 0
INS 0 0.093 -9999 0 -0.517 1 1
mol:PI-3-4-P2 -0.072 0.182 -9999 0 -0.424 6 6
GRB2 0.016 0 -9999 0 -9999 0 0
EIF4EBP1 -0.137 0.244 -9999 0 -0.61 4 4
PTPRA 0.016 0.01 -9999 0 -9999 0 0
PIK3CA 0.016 0 -9999 0 -9999 0 0
TC10/GTP/CIP4 0 0 -9999 0 -9999 0 0
PDPK1 -0.058 0.23 -9999 0 -0.773 3 3
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.034 0.14 -9999 0 -9999 0 0
Insulin Receptor/Insulin/IRS1 -0.102 0.183 -9999 0 -0.458 6 6
Insulin Receptor/Insulin/IRS3 -0.048 0.151 -9999 0 -0.507 3 3
Par3/Par6 -0.042 0.117 -9999 0 -0.429 2 2
VEGFR1 specific signals

Figure 74.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 76.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.009 0.176 -9999 0 -0.882 1 1
VEGFR1 homodimer/NRP1 -0.021 0.175 -9999 0 -0.891 1 1
mol:DAG -0.005 0.168 -9999 0 -0.805 1 1
VEGFR1 homodimer/NRP1/VEGFR 121 -0.055 0.224 -9999 0 -1.25 1 1
CaM/Ca2+ 0.004 0.16 -9999 0 -0.762 1 1
HIF1A -0.02 0.144 -9999 0 -0.462 3 3
GAB1 -0.008 0.137 -9999 0 -0.773 1 1
AKT1 -0.034 0.222 -9999 0 -0.754 2 2
PLCG1 -0.005 0.17 -9999 0 -0.814 1 1
NOS3 -0.014 0.185 -9999 0 -0.64 2 2
CBL 0.016 0 -9999 0 -9999 0 0
mol:NO -0.012 0.178 -9999 0 -0.611 2 2
FLT1 -0.018 0.198 -9999 0 -0.99 1 1
PGF -0.001 0.094 -9999 0 -0.526 1 1
VEGFR1 homodimer/NRP2/VEGFR121 -0.035 0.257 -9999 0 -0.887 2 2
CALM1 0.016 0 -9999 0 -9999 0 0
PIK3CA 0.016 0 -9999 0 -9999 0 0
eNOS/Hsp90 -0.003 0.172 -9999 0 -0.584 2 2
endothelial cell proliferation -0.014 0.166 -9999 0 -0.764 1 1
mol:Ca2+ -0.005 0.166 -9999 0 -0.795 1 1
MAPK3 -0.008 0.169 -9999 0 -0.699 1 1
MAPK1 -0.008 0.169 -9999 0 -0.699 1 1
PIK3R1 -0.008 0.137 -9999 0 -0.773 1 1
PLGF homodimer -0.001 0.094 -9999 0 -0.525 1 1
PRKACA 0.016 0 -9999 0 -9999 0 0
RP11-342D11.1 0 0 -9999 0 -9999 0 0
CAV1 -0.058 0.23 -9999 0 -0.773 3 3
VEGFA homodimer -0.008 0.137 -9999 0 -0.772 1 1
VEGFR1 homodimer/VEGFA homodimer -0.022 0.245 -9999 0 -1.314 1 1
platelet activating factor biosynthetic process 0.001 0.164 -9999 0 -0.671 1 1
PI3K -0.011 0.177 -9999 0 -0.772 1 1
PRKCA -0.018 0.177 -9999 0 -0.744 1 1
PRKCB -0.004 0.157 -9999 0 -0.753 1 1
VEGFR1 homodimer/PLGF homodimer -0.019 0.182 -9999 0 -0.882 1 1
VEGFA -0.008 0.137 -9999 0 -0.773 1 1
VEGFB 0.016 0 -9999 0 -9999 0 0
mol:IP3 -0.005 0.168 -9999 0 -0.805 1 1
RASA1 -0.005 0.17 -9999 0 -0.814 1 1
NRP2 -0.025 0.164 -9999 0 -0.65 2 2
VEGFR1 homodimer -0.018 0.198 -9999 0 -0.985 1 1
VEGFB homodimer 0.016 0 -9999 0 -9999 0 0
NCK1 0.016 0 -9999 0 -9999 0 0
eNOS/Caveolin-1 -0.041 0.221 -9999 0 -0.566 4 4
PTPN11 0.016 0 -9999 0 -9999 0 0
mol:PI-3-4-5-P3 -0.058 0.157 -9999 0 -0.758 1 1
mol:L-citrulline -0.012 0.178 -9999 0 -0.611 2 2
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0 0.224 -9999 0 -1.187 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.011 0.233 -9999 0 -1.242 1 1
CD2AP 0.016 0 -9999 0 -9999 0 0
PI3K/GAB1 -0.066 0.16 -9999 0 -0.726 1 1
PDPK1 -0.042 0.226 -9999 0 -0.759 2 2
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.011 0.233 -9999 0 -1.242 1 1
mol:NADP -0.012 0.178 -9999 0 -0.611 2 2
HSP90AA1 0.016 0 -9999 0 -9999 0 0
ubiquitin-dependent protein catabolic process -0.05 0.205 -9999 0 -1.149 1 1
VEGFR1 homodimer/NRP2 -0.035 0.213 -9999 0 -0.654 3 3
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

Figure 75.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 77.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.001 0.094 -9999 0 -0.526 1 1
oxygen homeostasis 0 0 -9999 0 -9999 0 0
TCEB2 0.016 0 -9999 0 -9999 0 0
TCEB1 0.016 0 -9999 0 -9999 0 0
HIF1A/p53 -0.019 0.066 -9999 0 -9999 0 0
HIF1A -0.029 0.068 -9999 0 -9999 0 0
COPS5 0.016 0 -9999 0 -9999 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0 0 -9999 0 -9999 0 0
FIH (dimer) 0.016 0 -9999 0 -9999 0 0
CDKN2A -0.249 0.35 -9999 0 -0.691 12 12
ARNT/IPAS -0.012 0.064 -9999 0 -0.37 1 1
HIF1AN 0.016 0 -9999 0 -9999 0 0
GNB2L1 -0.001 0.094 -9999 0 -0.526 1 1
HIF1A/ARNT -0.019 0.066 -9999 0 -9999 0 0
CUL2 0.016 0 -9999 0 -9999 0 0
OS9 -0.001 0.094 -9999 0 -0.526 1 1
RACK1/Elongin B/Elongin C -0.009 0.053 -9999 0 -9999 0 0
response to hypoxia 0 0 -9999 0 -9999 0 0
HIF1A/Hsp90 -0.019 0.066 -9999 0 -9999 0 0
PHD1-3/OS9 -0.182 0.184 -9999 0 -0.453 7 7
HIF1A/RACK1/Elongin B/Elongin C -0.036 0.062 -9999 0 -9999 0 0
VHL 0.016 0 -9999 0 -9999 0 0
HSP90AA1 0.016 0 -9999 0 -9999 0 0
HIF1A/JAB1 -0.019 0.066 -9999 0 -9999 0 0
EGLN3 -0.292 0.339 -9999 0 -0.641 15 15
EGLN2 0.016 0 -9999 0 -9999 0 0
EGLN1 -0.001 0.094 -9999 0 -0.526 1 1
TP53 0.016 0 -9999 0 -9999 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.033 0.016 -9999 0 -9999 0 0
ARNT 0.016 0 -9999 0 -9999 0 0
ARD1A 0.016 0 -9999 0 -9999 0 0
RBX1 0.016 0 -9999 0 -9999 0 0
HIF1A/p19ARF -0.16 0.171 -9999 0 -0.403 8 8
Signaling events mediated by PRL

Figure 76.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 78.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.052 0.179 -9999 0 -0.526 4 4
mol:Halofuginone 0.003 0.014 -9999 0 -9999 0 0
ITGA1 -0.035 0.158 -9999 0 -0.526 3 3
CDKN1A -0.026 0.1 -9999 0 -0.306 1 1
PRL-3/alpha Tubulin -0.018 0.102 -9999 0 -0.586 1 1
mol:Ca2+ -0.118 0.228 -9999 0 -0.542 7 7
AGT -0.141 0.302 -9999 0 -0.703 7 7
CCNA2 -0.143 0.297 -9999 0 -0.991 2 2
TUBA1B -0.008 0.137 -9999 0 -0.773 1 1
EGR1 -0.172 0.297 -9999 0 -0.558 11 11
CDK2/Cyclin E1 -0.04 0.118 -9999 0 -9999 0 0
MAPK3 0.029 0 -9999 0 -9999 0 0
PRL-2 /Rab GGTase beta 0 0 -9999 0 -9999 0 0
MAPK1 0.029 0 -9999 0 -9999 0 0
PTP4A1 -0.134 0.307 -9999 0 -1.413 1 1
PTP4A3 0.016 0 -9999 0 -9999 0 0
PTP4A2 0.016 0 -9999 0 -9999 0 0
ITGB1 0.029 0 -9999 0 -9999 0 0
SRC 0.016 0 -9999 0 -9999 0 0
RAC1 -0.026 0.1 -9999 0 -9999 0 0
Rab GGTase beta/Rab GGTase alpha 0 0 -9999 0 -9999 0 0
PRL-1/ATF-5 -0.117 0.287 -9999 0 -1.312 1 1
RABGGTA 0.016 0 -9999 0 -9999 0 0
BCAR1 0 0 -9999 0 -9999 0 0
RHOC -0.026 0.1 -9999 0 -9999 0 0
RHOA -0.026 0.1 -9999 0 -0.306 1 1
cell motility -0.025 0.108 -9999 0 -0.332 1 1
PRL-1/alpha Tubulin -0.132 0.29 -9999 0 -1.312 1 1
PRL-3/alpha1 Integrin -0.035 0.108 -9999 0 -0.37 3 3
ROCK1 -0.026 0.109 -9999 0 -0.334 1 1
RABGGTB 0.016 0 -9999 0 -9999 0 0
CDK2 0.016 0 -9999 0 -9999 0 0
mitosis -0.132 0.301 -9999 0 -1.371 1 1
ATF5 0.016 0 -9999 0 -9999 0 0
E-cadherin signaling in keratinocytes

Figure 77.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 79.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.026 0.122 -9999 0 -0.584 1 1
adherens junction organization 0.007 0.123 -9999 0 -0.549 1 1
mol:GTP 0 0 -9999 0 -9999 0 0
Rac1/GDP -0.056 0.181 -9999 0 -0.518 1 1
FMN1 0.007 0.121 -9999 0 -0.551 1 1
mol:IP3 0.02 0.113 -9999 0 -0.559 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.007 0.127 -9999 0 -0.578 1 1
CTNNB1 0 0.094 -9999 0 -0.525 1 1
AKT1 0.026 0.119 -9999 0 -0.579 1 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.002 0.147 -9999 0 -0.537 2 2
CTNND1 0.017 0.003 -9999 0 -9999 0 0
mol:PI-4-5-P2 0.017 0.119 -9999 0 -0.528 1 1
VASP 0.016 0.121 -9999 0 -0.542 1 1
ZYX 0 0.142 -9999 0 -0.456 2 2
JUB -0.006 0.145 -9999 0 -0.466 2 2
EGFR(dimer) -0.087 0.2 -9999 0 -0.44 6 6
E-cadherin/beta catenin-gamma catenin -0.05 0.136 -9999 0 -0.492 2 2
mol:PI-3-4-5-P3 -0.03 0.112 -9999 0 -0.621 1 1
PIK3CA 0.017 0.003 -9999 0 -9999 0 0
PI3K -0.031 0.115 -9999 0 -0.638 1 1
FYN 0.008 0.125 -9999 0 -0.461 1 1
mol:Ca2+ 0.021 0.11 -9999 0 -0.544 1 1
JUP 0 0.094 -9999 0 -0.525 1 1
PIK3R1 -0.008 0.139 -9999 0 -0.78 1 1
mol:DAG 0.02 0.113 -9999 0 -0.559 1 1
CDH1 -0.033 0.192 -9999 0 -0.776 2 2
RhoA/GDP -0.056 0.181 -9999 0 -0.477 2 2
establishment of polarity of embryonic epithelium 0.017 0.119 -9999 0 -0.528 1 1
SRC 0.016 0 -9999 0 -9999 0 0
RAC1 0.016 0 -9999 0 -9999 0 0
RHOA 0.016 0 -9999 0 -9999 0 0
EGFR -0.175 0.312 -9999 0 -0.663 9 9
CASR -0.008 0.14 -9999 0 -0.507 1 1
RhoA/GTP -0.022 0.088 -9999 0 -0.492 1 1
AKT2 0.018 0.133 -9999 0 -0.579 1 1
actin cable formation 0.016 0.118 -9999 0 -0.527 1 1
apoptosis 0.03 0.107 0.582 1 -9999 0 1
CTNNA1 0.017 0.003 -9999 0 -9999 0 0
mol:GDP -0.07 0.193 -9999 0 -0.52 2 2
PIP5K1A 0.016 0.121 -9999 0 -0.542 1 1
PLCG1 0.02 0.116 -9999 0 -0.576 1 1
Rac1/GTP -0.11 0.16 -9999 0 -0.49 2 2
homophilic cell adhesion 0.001 0.003 -9999 0 -9999 0 0
Class IB PI3K non-lipid kinase events

Figure 78.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 80.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.001 0.094 0.524 1 -9999 0 1
PI3K Class IB/PDE3B -0.001 0.094 -9999 0 -0.525 1 1
PDE3B -0.001 0.094 -9999 0 -0.526 1 1
E-cadherin signaling events

Figure 79.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 81.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.05 0.138 -9999 0 -0.501 2 2
E-cadherin/beta catenin -0.048 0.153 -9999 0 -0.514 3 3
CTNNB1 -0.001 0.094 -9999 0 -0.526 1 1
JUP -0.001 0.094 -9999 0 -0.526 1 1
CDH1 -0.033 0.191 -9999 0 -0.773 2 2
Ras signaling in the CD4+ TCR pathway

Figure 80.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 82.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.003 0.149 -9999 0 -0.625 1 1
MAP3K8 -0.01 0.137 -9999 0 -0.773 1 1
FOS 0.009 0.108 -9999 0 -0.468 1 1
PRKCA -0.026 0.166 -9999 0 -0.655 2 2
PTPN7 0.016 0.007 -9999 0 -9999 0 0
HRAS 0.016 0.001 -9999 0 -9999 0 0
PRKCB -0.001 0.006 -9999 0 -0.014 5 5
NRAS -0.018 0.131 -9999 0 -0.525 2 2
RAS family/GTP -0.009 0.102 -9999 0 -9999 0 0
MAPK3 0.015 0.06 -9999 0 -9999 0 0
MAP2K1 -0.005 0.123 -9999 0 -0.598 1 1
ELK1 0.016 0.004 -9999 0 -9999 0 0
BRAF -0.03 0.103 -9999 0 -0.564 1 1
mol:GTP 0 0.002 -9999 0 -0.004 5 5
MAPK1 0.015 0.06 -9999 0 -9999 0 0
RAF1 -0.03 0.103 -9999 0 -0.564 1 1
KRAS -0.018 0.132 -9999 0 -0.528 2 2
Aurora B signaling

Figure 81.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 83.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.015 0.072 -9999 0 -9999 0 0
STMN1 -0.061 0.213 -9999 0 -0.595 4 4
Aurora B/RasGAP/Survivin -0.075 0.19 -9999 0 -0.532 4 4
Chromosomal passenger complex/Cul3 protein complex -0.029 0.128 -9999 0 -0.332 1 1
BIRC5 -0.095 0.26 -9999 0 -0.688 5 5
DES -0.037 0.116 -9999 0 -0.564 1 1
Aurora C/Aurora B/INCENP -0.011 0.098 -9999 0 -0.467 1 1
Aurora B/TACC1 0.001 0.058 -9999 0 -9999 0 0
Aurora B/PP2A 0 0.068 -9999 0 -0.371 1 1
mol:GTP 0 0 -9999 0 -9999 0 0
CBX5 0.005 0.064 -9999 0 -0.286 1 1
mitotic metaphase/anaphase transition 0 0.004 -9999 0 -9999 0 0
NDC80 -0.003 0.128 -9999 0 -0.485 2 2
Cul3 protein complex -0.056 0.178 -9999 0 -0.596 3 3
KIF2C -0.126 0.227 -9999 0 -0.452 9 9
PEBP1 0.014 0.006 -9999 0 -9999 0 0
KIF20A -0.018 0.131 -9999 0 -0.525 2 2
mol:GDP 0 0 -9999 0 -9999 0 0
Aurora B/RasGAP -0.013 0.094 -9999 0 -0.374 2 2
SEPT1 0.016 0 -9999 0 -9999 0 0
SMC2 -0.001 0.094 -9999 0 -0.526 1 1
SMC4 0.016 0 -9999 0 -9999 0 0
NSUN2/NPM1/Nucleolin 0 0.08 -9999 0 -9999 0 0
PSMA3 0.016 0 -9999 0 -9999 0 0
G2/M transition of mitotic cell cycle 0.002 0.006 -9999 0 -9999 0 0
H3F3B -0.014 0.144 -9999 0 -0.555 2 2
AURKB 0.001 0.097 -9999 0 -0.537 1 1
AURKC -0.008 0.137 -9999 0 -0.773 1 1
CDCA8 0.013 0.006 -9999 0 -9999 0 0
cytokinesis -0.142 0.262 -9999 0 -0.76 4 4
Aurora B/Septin1 -0.124 0.241 -9999 0 -0.788 3 3
AURKA -0.016 0.132 -9999 0 -0.527 2 2
INCENP 0.013 0.006 -9999 0 -9999 0 0
KLHL13 -0.025 0.164 -9999 0 -0.65 2 2
BUB1 -0.143 0.304 -9999 0 -0.707 7 7
hSgo1/Aurora B/Survivin -0.059 0.173 -9999 0 -0.493 4 4
EVI5 0.016 0.002 -9999 0 -9999 0 0
RhoA/GTP -0.146 0.248 -9999 0 -0.738 4 4
SGOL1 0.016 0 -9999 0 -9999 0 0
CENPA -0.068 0.155 -9999 0 -0.402 4 4
NCAPG 0 0 -9999 0 -9999 0 0
Aurora B/HC8 Proteasome 0 0.068 -9999 0 -0.371 1 1
NCAPD2 -0.018 0.131 -9999 0 -0.526 2 2
Aurora B/PP1-gamma 0 0.068 -9999 0 -0.371 1 1
RHOA 0.016 0 -9999 0 -9999 0 0
NCAPH 0.016 0 -9999 0 -9999 0 0
NPM1 -0.008 0.051 -9999 0 -9999 0 0
RASA1 -0.001 0.094 -9999 0 -0.526 1 1
KLHL9 -0.033 0.191 -9999 0 -0.773 2 2
mitotic prometaphase -0.002 0.005 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0.068 -9999 0 -0.37 1 1
PPP1CC 0.016 0 -9999 0 -9999 0 0
Centraspindlin -0.163 0.273 -9999 0 -0.733 5 5
RhoA/GDP 0 0 -9999 0 -9999 0 0
NSUN2 -0.016 0.063 -9999 0 -9999 0 0
MYLK 0 0.089 -9999 0 -0.428 1 1
KIF23 -0.151 0.298 -9999 0 -0.655 8 8
VIM -0.064 0.228 -9999 0 -0.566 5 5
RACGAP1 -0.004 0.096 -9999 0 -0.539 1 1
mitosis 0 0 -9999 0 -9999 0 0
NCL -0.008 0.051 -9999 0 -9999 0 0
Chromosomal passenger complex -0.06 0.173 -9999 0 -0.455 4 4
Chromosomal passenger complex/EVI5 -0.044 0.172 -9999 0 -0.472 4 4
TACC1 0.016 0 -9999 0 -9999 0 0
PPP2R5D 0.016 0 -9999 0 -9999 0 0
CUL3 0.016 0 -9999 0 -9999 0 0
response to DNA damage stimulus 0 0 -9999 0 -9999 0 0
LPA4-mediated signaling events

Figure 82.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 84.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.025 0 -9999 0 -9999 0 0
ADCY5 0.003 0.082 -9999 0 -0.314 2 2
ADCY6 0.008 0.093 -9999 0 -0.513 1 1
ADCY7 0.014 0.059 -9999 0 -0.314 1 1
ADCY1 0.025 0 -9999 0 -9999 0 0
ADCY2 0.025 0 -9999 0 -9999 0 0
ADCY3 0.025 0 -9999 0 -9999 0 0
ADCY8 0.014 0.059 -9999 0 -0.314 1 1
PRKCE 0.014 0 -9999 0 -9999 0 0
ADCY9 0.003 0.082 -9999 0 -0.314 2 2
mol:DAG 0 0 -9999 0 -9999 0 0
cAMP biosynthetic process 0.026 0.05 -9999 0 -9999 0 0
ErbB2/ErbB3 signaling events

Figure 83.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 85.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.026 0.003 -9999 0 -9999 0 0
RAS family/GTP 0.005 0.11 -9999 0 -9999 0 0
NFATC4 0.048 0.049 -9999 0 -9999 0 0
ERBB2IP 0.015 0.002 -9999 0 -9999 0 0
HSP90 (dimer) 0.016 0 -9999 0 -9999 0 0
mammary gland morphogenesis 0.027 0.061 -9999 0 -9999 0 0
JUN 0.05 0.071 -9999 0 -9999 0 0
HRAS 0.016 0.001 -9999 0 -9999 0 0
DOCK7 0.033 0.061 -9999 0 -9999 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.025 0.102 -9999 0 -0.538 1 1
AKT1 0.015 0.002 -9999 0 -9999 0 0
BAD 0.025 0.001 -9999 0 -9999 0 0
MAPK10 -0.006 0.034 -9999 0 -9999 0 0
mol:GTP 0 0.002 -9999 0 -9999 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.029 0.065 -9999 0 -9999 0 0
RAF1 0.018 0.117 -9999 0 -9999 0 0
ErbB2/ErbB3/neuregulin 2 -0.017 0.097 -9999 0 -0.559 1 1
STAT3 0.001 0.004 -9999 0 -9999 0 0
cell migration 0.055 0.04 -9999 0 -9999 0 0
mol:PI-3-4-5-P3 0 0.001 -9999 0 -9999 0 0
cell proliferation -0.016 0.257 -9999 0 -0.618 4 4
FOS -0.003 0.197 -9999 0 -0.553 1 1
NRAS -0.018 0.131 -9999 0 -0.525 2 2
mol:Ca2+ 0.027 0.061 -9999 0 -9999 0 0
MAPK3 -0.002 0.208 -9999 0 -0.654 1 1
MAPK1 -0.002 0.208 -9999 0 -0.654 1 1
JAK2 0.033 0.061 -9999 0 -9999 0 0
NF2 0 0.001 -9999 0 -9999 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.023 0.072 -9999 0 -0.367 1 1
NRG1 0 0.095 -9999 0 -0.528 1 1
GRB2/SOS1 0 0 -9999 0 -9999 0 0
MAPK8 0.04 0.052 -9999 0 -9999 0 0
MAPK9 -0.002 0.025 -9999 0 -9999 0 0
ERBB2 -0.012 0.067 -9999 0 -0.387 1 1
ERBB3 0.016 0.002 -9999 0 -9999 0 0
SHC1 -0.001 0.095 -9999 0 -0.529 1 1
RAC1 0.016 0 -9999 0 -9999 0 0
apoptosis 0 0.006 -9999 0 -9999 0 0
STAT3 (dimer) 0.007 0.011 -9999 0 -9999 0 0
RNF41 0.034 0.004 -9999 0 -9999 0 0
FRAP1 0.025 0.001 -9999 0 -9999 0 0
RAC1-CDC42/GTP -0.008 0.03 -9999 0 -9999 0 0
ErbB2/ErbB2/HSP90 (dimer) -0.01 0.055 -9999 0 -9999 0 0
CHRNA1 0.002 0.201 -9999 0 -0.556 2 2
myelination 0.057 0.049 -9999 0 -9999 0 0
PPP3CB 0.032 0.057 -9999 0 -9999 0 0
KRAS -0.018 0.131 -9999 0 -0.526 2 2
RAC1-CDC42/GDP 0.038 0.064 -9999 0 -9999 0 0
NRG2 -0.001 0.094 -9999 0 -0.526 1 1
mol:GDP 0.023 0.072 -9999 0 -0.365 1 1
SOS1 0.016 0.001 -9999 0 -9999 0 0
MAP2K2 0.022 0.123 -9999 0 -9999 0 0
SRC 0.016 0 -9999 0 -9999 0 0
mol:cAMP 0 0.001 -9999 0 -9999 0 0
PTPN11 0.032 0.06 -9999 0 -9999 0 0
MAP2K1 0.006 0.174 -9999 0 -0.56 1 1
heart morphogenesis 0.027 0.061 -9999 0 -9999 0 0
RAS family/GDP 0.005 0.108 -9999 0 -9999 0 0
GRB2 0.016 0.001 -9999 0 -9999 0 0
PRKACA -0.001 0.002 -9999 0 -9999 0 0
CHRNE 0.025 0.019 -9999 0 -9999 0 0
HSP90AA1 0.016 0 -9999 0 -9999 0 0
activation of caspase activity -0.015 0.002 -9999 0 -9999 0 0
nervous system development 0.027 0.061 -9999 0 -9999 0 0
CDC42 0.016 0 -9999 0 -9999 0 0
Regulation of nuclear SMAD2/3 signaling

Figure 84.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 86.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.018 0.015 -9999 0 -9999 0 0
HSPA8 0.016 0.005 -9999 0 -9999 0 0
SMAD3/SMAD4/ER alpha -0.145 0.212 -9999 0 -0.49 5 5
AKT1 0.017 0.015 -9999 0 -9999 0 0
GSC -0.087 0.319 -9999 0 -1.025 2 2
NKX2-5 0.01 0.025 -9999 0 -9999 0 0
muscle cell differentiation 0.045 0.128 0.599 1 -9999 0 1
SMAD2-3/SMAD4/SP1 0.012 0.14 -9999 0 -0.467 1 1
SMAD4 0.001 0.08 -9999 0 -0.374 1 1
CBFB 0.016 0 -9999 0 -9999 0 0
SAP18 0.016 0.002 -9999 0 -9999 0 0
Cbp/p300/MSG1 -0.045 0.161 -9999 0 -0.514 2 2
SMAD3/SMAD4/VDR -0.041 0.173 -9999 0 -0.555 2 2
MYC 0.016 0.016 -9999 0 -9999 0 0
CDKN2B -0.022 0.284 -9999 0 -1.515 1 1
AP1 -0.059 0.3 -9999 0 -0.932 3 3
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.058 0.051 -9999 0 -9999 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.016 0.1 -9999 0 -9999 0 0
SP3 0.015 0.021 -9999 0 -9999 0 0
CREB1 0.016 0 -9999 0 -9999 0 0
FOXH1 0.001 0.036 -9999 0 -9999 0 0
SMAD3/SMAD4/GR -0.001 0.081 -9999 0 -0.368 1 1
GATA3 0.01 0.092 -9999 0 -0.504 1 1
SKI/SIN3/HDAC complex/NCoR1 0.052 0.027 -9999 0 -9999 0 0
MEF2C/TIF2 -0.049 0.25 -9999 0 -0.748 3 3
endothelial cell migration 0.2 0.503 1.488 4 -9999 0 4
MAX 0.023 0.02 -9999 0 -9999 0 0
RBBP7 0.016 0.002 -9999 0 -9999 0 0
RBBP4 0.016 0.002 -9999 0 -9999 0 0
RUNX2 -0.001 0.094 -9999 0 -0.526 1 1
RUNX3 -0.025 0.164 -9999 0 -0.65 2 2
RUNX1 -0.025 0.164 -9999 0 -0.65 2 2
CTBP1 0.016 0 -9999 0 -9999 0 0
NR3C1 0.023 0.02 -9999 0 -9999 0 0
VDR -0.058 0.23 -9999 0 -0.773 3 3
CDKN1A 0.062 0.09 -9999 0 -9999 0 0
KAT2B -0.002 0.009 -9999 0 -9999 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.017 0.123 -9999 0 -0.443 1 1
DCP1A 0.016 0 -9999 0 -9999 0 0
SKI 0.016 0.002 -9999 0 -9999 0 0
SERPINE1 -0.205 0.513 -9999 0 -1.521 4 4
SMAD3/SMAD4/ATF2 -0.003 0.076 -9999 0 -9999 0 0
SMAD3/SMAD4/ATF3 -0.017 0.11 -9999 0 -0.457 1 1
SAP30 0.016 0.002 -9999 0 -9999 0 0
Cbp/p300/PIAS3 0.021 0.043 -9999 0 -9999 0 0
JUN -0.048 0.303 -9999 0 -0.93 3 3
SMAD3/SMAD4/IRF7 -0.001 0.076 -9999 0 -9999 0 0
TFE3 -0.008 0.097 -9999 0 -0.51 1 1
COL1A2 -0.031 0.311 -9999 0 -1.096 2 2
mesenchymal cell differentiation 0.016 0.089 0.364 1 -9999 0 1
DLX1 -0.001 0.094 -9999 0 -0.526 1 1
TCF3 0.016 0 -9999 0 -9999 0 0
FOS -0.076 0.225 -9999 0 -0.579 5 5
SMAD3/SMAD4/Max -0.001 0.081 -9999 0 -0.368 1 1
Cbp/p300/SNIP1 0.012 0.022 -9999 0 -9999 0 0
ZBTB17 0.016 0.013 -9999 0 -9999 0 0
LAMC1 -0.011 0.233 -9999 0 -0.872 2 2
TGIF2/HDAC complex/SMAD3/SMAD4 -0.003 0.076 -9999 0 -0.365 1 1
IRF7 0.021 0.001 -9999 0 -9999 0 0
ESR1 -0.231 0.316 -9999 0 -0.602 13 13
HNF4A 0.016 0 -9999 0 -9999 0 0
MEF2C -0.048 0.268 -9999 0 -0.713 4 4
SMAD2-3/SMAD4 -0.031 0.103 -9999 0 -0.453 1 1
Cbp/p300/Src-1 0.001 0.095 -9999 0 -0.502 1 1
IGHV3OR16-13 -0.01 0.031 -9999 0 -9999 0 0
TGIF2/HDAC complex 0.016 0 -9999 0 -9999 0 0
CREBBP 0.017 0.011 -9999 0 -9999 0 0
SKIL 0.016 0 -9999 0 -9999 0 0
HDAC1 0.016 0.002 -9999 0 -9999 0 0
HDAC2 0.016 0.002 -9999 0 -9999 0 0
SNIP1 0.016 0.004 -9999 0 -9999 0 0
GCN5L2 -0.025 0.168 -9999 0 -0.666 2 2
SMAD3/SMAD4/TFE3 -0.023 0.128 -9999 0 -0.543 1 1
MSG1/HSC70 -0.066 0.172 -9999 0 -0.453 5 5
SMAD2 -0.014 0.1 -9999 0 -0.532 1 1
SMAD3 0.017 0.058 -9999 0 -9999 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.045 0.056 -9999 0 -9999 0 0
SMAD2/SMAD2/SMAD4 -0.002 0.043 -9999 0 -9999 0 0
NCOR1 0.016 0.002 -9999 0 -9999 0 0
NCOA2 0.016 0 -9999 0 -9999 0 0
NCOA1 -0.008 0.137 -9999 0 -0.773 1 1
MYOD/E2A -0.012 0.064 -9999 0 -9999 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.022 0.132 -9999 0 -0.428 1 1
IFNB1 0.057 0.079 -9999 0 -9999 0 0
SMAD3/SMAD4/MEF2C -0.049 0.274 -9999 0 -0.808 3 3
CITED1 -0.084 0.238 -9999 0 -0.625 5 5
SMAD2-3/SMAD4/ARC105 -0.021 0.091 -9999 0 -0.396 1 1
RBL1 0.016 0 -9999 0 -9999 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.035 0.118 -9999 0 -0.517 1 1
RUNX1-3/PEBPB2 -0.05 0.138 -9999 0 -0.501 2 2
SMAD7 -0.029 0.239 -9999 0 -0.857 1 1
MYC/MIZ-1 0.008 0.033 -9999 0 -9999 0 0
SMAD3/SMAD4 -0.029 0.191 0.315 1 -0.489 2 3
IL10 0.054 0.093 -9999 0 -9999 0 0
PIASy/HDAC complex 0.017 0.014 -9999 0 -9999 0 0
PIAS3 0.015 0.007 -9999 0 -9999 0 0
CDK2 0.017 0.011 -9999 0 -9999 0 0
IL5 0.054 0.093 -9999 0 -9999 0 0
CDK4 0.017 0.012 -9999 0 -9999 0 0
PIAS4 0.017 0.014 -9999 0 -9999 0 0
ATF3 -0.008 0.137 -9999 0 -0.773 1 1
SMAD3/SMAD4/SP1 -0.006 0.112 -9999 0 -0.445 1 1
FOXG1 -0.07 0.197 -9999 0 -0.528 5 5
FOXO3 0.03 0.02 -9999 0 -9999 0 0
FOXO1 0.03 0.02 -9999 0 -9999 0 0
FOXO4 0.03 0.02 -9999 0 -9999 0 0
heart looping -0.046 0.264 -9999 0 -0.701 4 4
CEBPB 0 0.094 -9999 0 -0.523 1 1
SMAD3/SMAD4/DLX1 -0.015 0.091 -9999 0 -0.365 1 1
MYOD1 -0.001 0.094 -9999 0 -0.526 1 1
SMAD3/SMAD4/HNF4 -0.003 0.076 -9999 0 -0.365 1 1
SMAD3/SMAD4/GATA3 -0.009 0.087 -9999 0 -9999 0 0
SnoN/SIN3/HDAC complex/NCoR1 0.016 0 -9999 0 -9999 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.04 0.157 -9999 0 -0.731 1 1
SMAD3/SMAD4/SP1-3 0.021 0.141 -9999 0 -0.554 1 1
MED15 0.016 0 -9999 0 -9999 0 0
SP1 0.008 0.047 -9999 0 -9999 0 0
SIN3B 0.016 0.002 -9999 0 -9999 0 0
SIN3A 0.016 0.002 -9999 0 -9999 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.019 0.152 -9999 0 -0.555 1 1
ITGB5 0.017 0.23 -9999 0 -0.825 2 2
TGIF/SIN3/HDAC complex/CtBP 0.052 0.043 -9999 0 -9999 0 0
SMAD3/SMAD4/AR -0.026 0.119 -9999 0 -0.453 1 1
AR -0.025 0.164 -9999 0 -0.65 2 2
negative regulation of cell growth 0.035 0.075 -9999 0 -9999 0 0
SMAD3/SMAD4/MYOD -0.012 0.09 -9999 0 -9999 0 0
E2F5 0.016 0 -9999 0 -9999 0 0
E2F4 0.016 0 -9999 0 -9999 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.007 0.1 -9999 0 -9999 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 0.033 0.092 -9999 0 -9999 0 0
TFDP1 0.016 0 -9999 0 -9999 0 0
SMAD3/SMAD4/AP1 -0.061 0.307 -9999 0 -0.954 3 3
SMAD3/SMAD4/RUNX2 -0.015 0.09 -9999 0 -0.365 1 1
TGIF2 0.016 0 -9999 0 -9999 0 0
TGIF1 -0.008 0.137 -9999 0 -0.773 1 1
ATF2 0.016 0 -9999 0 -9999 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

Figure 85.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 87.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.016 0 -9999 0 -9999 0 0
SMAD2 0.017 0.022 -9999 0 -9999 0 0
SMAD3 0.047 0.027 -9999 0 -9999 0 0
SMAD3/SMAD4 0.03 0.105 -9999 0 -0.375 2 2
SMAD4/Ubc9/PIASy 0 0 -9999 0 -9999 0 0
SMAD2/SMAD2/SMAD4 -0.025 0.093 -9999 0 -9999 0 0
PPM1A 0.016 0 -9999 0 -9999 0 0
CALM1 0.016 0 -9999 0 -9999 0 0
SMAD2/SMAD4 0.025 0.019 -9999 0 -9999 0 0
MAP3K1 -0.001 0.094 -9999 0 -0.526 1 1
TRAP-1/SMAD4 -0.018 0.102 -9999 0 -0.586 1 1
MAPK3 0.016 0 -9999 0 -9999 0 0
MAPK1 0.016 0 -9999 0 -9999 0 0
NUP214 0.016 0 -9999 0 -9999 0 0
CTDSP1 0.016 0 -9999 0 -9999 0 0
CTDSP2 0.016 0 -9999 0 -9999 0 0
CTDSPL -0.001 0.094 -9999 0 -0.526 1 1
KPNB1 0.016 0 -9999 0 -9999 0 0
TGFBRAP1 -0.008 0.137 -9999 0 -0.773 1 1
UBE2I 0.016 0 -9999 0 -9999 0 0
NUP153 -0.008 0.137 -9999 0 -0.773 1 1
KPNA2 -0.008 0.137 -9999 0 -0.773 1 1
PIAS4 0.016 0 -9999 0 -9999 0 0
Nephrin/Neph1 signaling in the kidney podocyte

Figure 86.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 88.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
positive regulation of NF-kappaB transcription factor activity 0.023 0.088 0.363 2 -9999 0 2
KIRREL 0.016 0.009 -9999 0 -9999 0 0
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.023 0.088 -9999 0 -0.363 2 2
PLCG1 0.016 0 -9999 0 -9999 0 0
ARRB2 0.016 0 -9999 0 -9999 0 0
WASL 0.016 0.003 -9999 0 -9999 0 0
Nephrin/NEPH1/podocin/CD2AP -0.015 0.059 -9999 0 -9999 0 0
ChemicalAbstracts:57-88-5 0 0 -9999 0 -9999 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.035 0.045 -9999 0 -9999 0 0
FYN 0.018 0.061 -9999 0 -9999 0 0
mol:Ca2+ -0.015 0.059 -9999 0 -9999 0 0
mol:DAG -0.015 0.059 -9999 0 -9999 0 0
NPHS2 0.016 0.009 -9999 0 -9999 0 0
mol:IP3 -0.015 0.059 -9999 0 -9999 0 0
regulation of endocytosis 0.027 0.058 -9999 0 -9999 0 0
Nephrin/NEPH1/podocin/Cholesterol -0.016 0.062 -9999 0 -9999 0 0
establishment of cell polarity -0.023 0.088 -9999 0 -0.363 2 2
Nephrin/NEPH1/podocin/NCK1-2 -0.013 0.051 -9999 0 -9999 0 0
Nephrin/NEPH1/beta Arrestin2 0.028 0.059 -9999 0 -9999 0 0
NPHS1 -0.016 0.13 -9999 0 -0.518 2 2
Nephrin/NEPH1/podocin 0.019 0.062 -9999 0 -9999 0 0
TJP1 0.016 0 -9999 0 -9999 0 0
NCK1 0.016 0 -9999 0 -9999 0 0
NCK2 0.016 0 -9999 0 -9999 0 0
heterophilic cell adhesion 0 0 -9999 0 -9999 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.015 0.059 -9999 0 -9999 0 0
CD2AP 0.016 0 -9999 0 -9999 0 0
Nephrin/NEPH1/podocin/GRB2 -0.015 0.059 -9999 0 -9999 0 0
GRB2 0.016 0 -9999 0 -9999 0 0
homophilic cell adhesion 0 0 -9999 0 -9999 0 0
TRPC6 -0.093 0.179 -9999 0 -0.47 3 3
cytoskeleton organization 0.043 0.056 -9999 0 -9999 0 0
Nephrin/NEPH1 -0.016 0.061 -9999 0 -9999 0 0
Nephrin/NEPH1/ZO-1 -0.017 0.067 -9999 0 -9999 0 0
Canonical NF-kappaB pathway

Figure 87.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 89.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.02 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.075 0.071 -9999 0 -9999 0 0
ERC1 0.016 0 -9999 0 -9999 0 0
RIP2/NOD2 -0.071 0.171 -9999 0 -0.456 5 5
NFKBIA 0.058 0 -9999 0 -9999 0 0
BIRC2 0.016 0 -9999 0 -9999 0 0
IKBKB 0.016 0 -9999 0 -9999 0 0
RIPK2 -0.018 0.131 -9999 0 -0.526 2 2
IKBKG -0.024 0.062 -9999 0 -9999 0 0
IKK complex/A20 -0.036 0.089 -9999 0 -9999 0 0
NEMO/A20/RIP2 -0.018 0.131 -9999 0 -0.525 2 2
XPO1 0.016 0 -9999 0 -9999 0 0
NEMO/ATM 0.019 0.105 -9999 0 -9999 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -9999 0 0
RAN 0.016 0 -9999 0 -9999 0 0
Exportin 1/RanGTP 0 0 -9999 0 -9999 0 0
IKK complex/ELKS -0.017 0.046 -9999 0 -9999 0 0
BCL10/MALT1/TRAF6 0 0 -9999 0 -9999 0 0
NOD2 -0.05 0.209 -9999 0 -0.691 3 3
NFKB1 0.02 0 -9999 0 -9999 0 0
RELA 0.02 0 -9999 0 -9999 0 0
MALT1 0.016 0 -9999 0 -9999 0 0
cIAP1/UbcH5C 0 0 -9999 0 -9999 0 0
ATM -0.008 0.137 -9999 0 -0.773 1 1
TNF/TNFR1A -0.03 0.119 -9999 0 -0.478 2 2
TRAF6 0.016 0 -9999 0 -9999 0 0
PRKCA -0.025 0.164 -9999 0 -0.65 2 2
CHUK 0.016 0 -9999 0 -9999 0 0
UBE2D3 0.016 0 -9999 0 -9999 0 0
TNF -0.025 0.164 -9999 0 -0.65 2 2
NF kappa B1 p50/RelA 0 0 -9999 0 -9999 0 0
BCL10 0.016 0 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.058 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0 -9999 0 -9999 0 0
TNFRSF1A 0.016 0 -9999 0 -9999 0 0
IKK complex 0.041 0.075 -9999 0 -9999 0 0
CYLD 0.016 0 -9999 0 -9999 0 0
IKK complex/PKC alpha -0.036 0.089 -9999 0 -9999 0 0
Signaling events mediated by HDAC Class II

Figure 88.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 90.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.014 0.079 -9999 0 -0.453 1 1
HDAC3 0.016 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -9999 0 0
GATA1/HDAC4 0 0 -9999 0 -9999 0 0
GATA1/HDAC5 0 0 -9999 0 -9999 0 0
GATA2/HDAC5 0 0 -9999 0 -9999 0 0
HDAC5/BCL6/BCoR -0.016 0.087 -9999 0 -0.501 1 1
HDAC9 -0.008 0.137 -9999 0 -0.773 1 1
Glucocorticoid receptor/Hsp90/HDAC6 -0.009 0.053 -9999 0 -9999 0 0
HDAC4/ANKRA2 0 0 -9999 0 -9999 0 0
HDAC5/YWHAB 0 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.027 0 -9999 0 -9999 0 0
GATA2 0.016 0 -9999 0 -9999 0 0
HDAC4/RFXANK 0 0 -9999 0 -9999 0 0
BCOR 0.016 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
HDAC10 0.016 0 -9999 0 -9999 0 0
HDAC5 0.016 0 -9999 0 -9999 0 0
GNB1/GNG2 -0.018 0.102 -9999 0 -0.586 1 1
Histones 0.029 0.057 -9999 0 -9999 0 0
ADRBK1 0.016 0 -9999 0 -9999 0 0
HDAC4 0.016 0 -9999 0 -9999 0 0
XPO1 0.016 0 -9999 0 -9999 0 0
HDAC5/ANKRA2 0 0 -9999 0 -9999 0 0
HDAC4/Ubc9 0 0 -9999 0 -9999 0 0
HDAC7 0 0 -9999 0 -9999 0 0
HDAC5/14-3-3 E 0 0 -9999 0 -9999 0 0
TUBA1B -0.008 0.137 -9999 0 -0.773 1 1
HDAC6 -0.001 0.094 -9999 0 -0.526 1 1
HDAC5/RFXANK 0 0 -9999 0 -9999 0 0
CAMK4 0.016 0 -9999 0 -9999 0 0
Tubulin/HDAC6 -0.071 0.206 -9999 0 -0.655 3 3
SUMO1 0.016 0 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 0 0
YWHAB 0.016 0 -9999 0 -9999 0 0
GATA1 0.016 0 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
YWHAE 0.016 0 -9999 0 -9999 0 0
NR3C1 0.016 0 -9999 0 -9999 0 0
SUMO1/HDAC4 0.038 0 -9999 0 -9999 0 0
SRF 0.016 0 -9999 0 -9999 0 0
HDAC4/YWHAB 0 0 -9999 0 -9999 0 0
Tubulin -0.07 0.228 -9999 0 -0.746 3 3
HDAC4/14-3-3 E 0 0 -9999 0 -9999 0 0
GNB1 0.016 0 -9999 0 -9999 0 0
RANGAP1 0.016 0 -9999 0 -9999 0 0
BCL6/BCoR -0.018 0.102 -9999 0 -0.586 1 1
HDAC4/HDAC3/SMRT (N-CoR2) 0 0 -9999 0 -9999 0 0
HDAC4/SRF 0 0 -9999 0 -9999 0 0
HDAC4/ER alpha -0.177 0.223 -9999 0 -0.436 13 13
EntrezGene:23225 0 0 -9999 0 -9999 0 0
positive regulation of chromatin silencing 0.029 0.057 -9999 0 -9999 0 0
cell motility -0.07 0.205 -9999 0 -0.65 3 3
EntrezGene:23636 0 0 -9999 0 -9999 0 0
UBE2I 0.016 0 -9999 0 -9999 0 0
HDAC7/HDAC3 0 0 -9999 0 -9999 0 0
BCL6 -0.008 0.137 -9999 0 -0.773 1 1
HDAC4/CaMK II delta B 0.016 0 -9999 0 -9999 0 0
Hsp90/HDAC6 -0.012 0.064 -9999 0 -0.37 1 1
ESR1 -0.235 0.312 -9999 0 -0.602 13 13
HDAC6/HDAC11 -0.012 0.064 -9999 0 -0.37 1 1
Ran/GTP/Exportin 1 0 0 -9999 0 -9999 0 0
NPC 0 0 -9999 0 -9999 0 0
MEF2C -0.075 0.244 -9999 0 -0.712 4 4
RAN 0.016 0 -9999 0 -9999 0 0
HDAC4/MEF2C -0.047 0.127 -9999 0 -0.42 3 3
GNG2 -0.008 0.137 -9999 0 -0.773 1 1
NCOR2 0.016 0 -9999 0 -9999 0 0
TUBB2A -0.058 0.23 -9999 0 -0.773 3 3
HDAC11 0.016 0 -9999 0 -9999 0 0
HSP90AA1 0.016 0 -9999 0 -9999 0 0
RANBP2 0.016 0 -9999 0 -9999 0 0
ANKRA2 0.016 0 -9999 0 -9999 0 0
RFXANK 0.016 0 -9999 0 -9999 0 0
nuclear import -0.037 0 -9999 0 -9999 0 0
BARD1 signaling events

Figure 89.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 91.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0 -9999 0 -9999 0 0
ATM -0.008 0.137 -9999 0 -0.773 1 1
UBE2D3 0.016 0 -9999 0 -9999 0 0
PRKDC -0.008 0.137 -9999 0 -0.773 1 1
ATR 0.016 0 -9999 0 -9999 0 0
UBE2L3 0.016 0 -9999 0 -9999 0 0
FANCD2 0.018 0.078 -9999 0 -0.416 1 1
protein ubiquitination -0.05 0.108 -9999 0 -9999 0 0
XRCC5 0.016 0 -9999 0 -9999 0 0
XRCC6 0.016 0 -9999 0 -9999 0 0
M/R/N Complex 0 0 -9999 0 -9999 0 0
MRE11A 0.016 0 -9999 0 -9999 0 0
DNA-PK -0.016 0.087 -9999 0 -0.501 1 1
FA complex/FANCD2/Ubiquitin -0.007 0.044 -9999 0 -9999 0 0
FANCF 0.016 0 -9999 0 -9999 0 0
BRCA1 -0.001 0.094 -9999 0 -0.526 1 1
CCNE1 -0.052 0.179 -9999 0 -0.526 4 4
CDK2/Cyclin E1 -0.046 0.122 -9999 0 -0.37 4 4
FANCG 0.016 0 -9999 0 -9999 0 0
BRCA1/BACH1/BARD1 -0.012 0.064 -9999 0 -0.37 1 1
FANCE 0.016 0 -9999 0 -9999 0 0
FANCC 0.016 0 -9999 0 -9999 0 0
NBN 0.016 0 -9999 0 -9999 0 0
FANCA -0.008 0.137 -9999 0 -0.773 1 1
DNA repair 0.047 0.106 -9999 0 -9999 0 0
BRCA1/BARD1/ubiquitin -0.012 0.064 -9999 0 -0.37 1 1
BARD1/DNA-PK -0.014 0.079 -9999 0 -0.453 1 1
FANCL 0.016 0 -9999 0 -9999 0 0
mRNA polyadenylation 0 0 -9999 0 -9999 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.016 0.112 -9999 0 -0.534 1 1
BRCA1/BACH1/BARD1/TopBP1 -0.009 0.053 -9999 0 -9999 0 0
BRCA1/BARD1/P53 -0.008 0.046 -9999 0 -9999 0 0
BARD1/CSTF1/BRCA1 -0.009 0.053 -9999 0 -9999 0 0
BRCA1/BACH1 -0.001 0.094 -9999 0 -0.525 1 1
BARD1 0.016 0 -9999 0 -9999 0 0
PCNA 0.016 0 -9999 0 -9999 0 0
BRCA1/BARD1/UbcH5C -0.009 0.053 -9999 0 -9999 0 0
BRCA1/BARD1/UbcH7 -0.009 0.053 -9999 0 -9999 0 0
BRCA1/BARD1/RAD51/PCNA -0.025 0.105 -9999 0 -0.548 1 1
BARD1/DNA-PK/P53 -0.013 0.073 -9999 0 -9999 0 0
BRCA1/BARD1/Ubiquitin -0.012 0.064 -9999 0 -0.37 1 1
BRCA1/BARD1/CTIP -0.009 0.136 -9999 0 -0.452 2 2
FA complex 0.04 0.061 -9999 0 -9999 0 0
BARD1/EWS 0 0 -9999 0 -9999 0 0
RBBP8 -0.022 0.161 -9999 0 -0.514 3 3
TP53 0.016 0 -9999 0 -9999 0 0
TOPBP1 0.016 0 -9999 0 -9999 0 0
G1/S transition of mitotic cell cycle 0.008 0.046 -9999 0 -9999 0 0
BRCA1/BARD1 -0.05 0.109 -9999 0 -9999 0 0
CSTF1 0.016 0 -9999 0 -9999 0 0
BARD1/EWS-Fli1 0 0 -9999 0 -9999 0 0
CDK2 0.016 0 -9999 0 -9999 0 0
UniProt:Q9BZD1 0 0 -9999 0 -9999 0 0
RAD51 -0.018 0.131 -9999 0 -0.526 2 2
RAD50 0.016 0 -9999 0 -9999 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.012 0.064 -9999 0 -0.37 1 1
EWSR1 0.016 0 -9999 0 -9999 0 0
Circadian rhythm pathway

Figure 90.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 92.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.047 0.178 -9999 0 -9999 0 0
CLOCK 0.02 0 -9999 0 -9999 0 0
TIMELESS/CRY2 0.054 0.011 -9999 0 -9999 0 0
DEC1/BMAL1 -0.011 0.148 -9999 0 -0.583 2 2
ATR 0.016 0 -9999 0 -9999 0 0
NR1D1 0.052 0.013 -9999 0 -9999 0 0
ARNTL 0.02 0 -9999 0 -9999 0 0
TIMELESS 0.052 0.013 -9999 0 -9999 0 0
NPAS2 0.004 0.094 -9999 0 -0.519 1 1
CRY2 0.016 0 -9999 0 -9999 0 0
mol:CO -0.018 0 -9999 0 -9999 0 0
CHEK1 -0.175 0.312 -9999 0 -0.663 9 9
mol:HEME 0.018 0 -9999 0 -9999 0 0
PER1 -0.008 0.137 -9999 0 -0.773 1 1
BMAL/CLOCK/NPAS2 0.044 0.06 -9999 0 -9999 0 0
BMAL1/CLOCK 0.046 0.074 -9999 0 -9999 0 0
S phase of mitotic cell cycle -0.047 0.178 -9999 0 -9999 0 0
TIMELESS/CHEK1/ATR -0.047 0.181 -9999 0 -9999 0 0
mol:NADPH 0.018 0 -9999 0 -9999 0 0
PER1/TIMELESS 0.038 0.085 -9999 0 -9999 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -9999 0 0
DEC1 -0.033 0.191 -9999 0 -0.773 2 2
Lissencephaly gene (LIS1) in neuronal migration and development

Figure 91.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 93.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.016 0 -9999 0 -9999 0 0
VLDLR -0.018 0.131 -9999 0 -0.526 2 2
LRPAP1 -0.001 0.094 -9999 0 -0.526 1 1
NUDC 0.016 0 -9999 0 -9999 0 0
RELN/LRP8 -0.054 0.128 -9999 0 -0.501 1 1
CaM/Ca2+ 0 0 -9999 0 -9999 0 0
KATNA1 0.016 0 -9999 0 -9999 0 0
GO:0030286 0 0 -9999 0 -9999 0 0
ABL1 -0.012 0.128 -9999 0 -0.45 1 1
IQGAP1/CaM 0 0 -9999 0 -9999 0 0
DAB1 0.016 0 -9999 0 -9999 0 0
IQGAP1 0.016 0 -9999 0 -9999 0 0
PLA2G7 -0.025 0.164 -9999 0 -0.65 2 2
CALM1 0.016 0 -9999 0 -9999 0 0
DYNLT1 0.016 0 -9999 0 -9999 0 0
mol:Ca2+ 0 0 -9999 0 -9999 0 0
LRPAP1/LRP8 -0.046 0.122 -9999 0 -0.37 4 4
UniProt:Q4QZ09 0 0 -9999 0 -9999 0 0
CLIP1 0.016 0 -9999 0 -9999 0 0
CDK5R1 -0.025 0.164 -9999 0 -0.65 2 2
LIS1/Poliovirus Protein 3A 0.021 0 -9999 0 -9999 0 0
CDK5R2 0.016 0 -9999 0 -9999 0 0
mol:PP1 0 0 -9999 0 -9999 0 0
RELN/VLDLR/DAB1 -0.035 0.111 -9999 0 -0.501 1 1
YWHAE 0.016 0 -9999 0 -9999 0 0
NDEL1/14-3-3 E 0.015 0.116 -9999 0 -9999 0 0
MAP1B -0.059 0.127 -9999 0 -0.37 4 4
RAC1 0 0 -9999 0 -9999 0 0
p35/CDK5 -0.014 0.139 -9999 0 -9999 0 0
RELN -0.008 0.137 -9999 0 -0.773 1 1
PAFAH/LIS1 0.006 0.108 -9999 0 -0.502 1 1
LIS1/CLIP170 0.033 0 -9999 0 -9999 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.03 0.063 -9999 0 -9999 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 0.03 0.07 -9999 0 -9999 0 0
GO:0005869 0 0 -9999 0 -9999 0 0
NDEL1 0.005 0.121 -9999 0 -9999 0 0
LIS1/IQGAP1 0.033 0 -9999 0 -9999 0 0
RHOA 0 0 -9999 0 -9999 0 0
PAFAH1B1 0.029 0 -9999 0 -9999 0 0
PAFAH1B3 0.016 0 -9999 0 -9999 0 0
PAFAH1B2 0.016 0 -9999 0 -9999 0 0
MAP1B/LIS1/Dynein heavy chain -0.01 0.09 -9999 0 -9999 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.04 0.081 -9999 0 -9999 0 0
LRP8 -0.035 0.158 -9999 0 -0.526 3 3
NDEL1/Katanin 60 0.015 0.116 -9999 0 -9999 0 0
P39/CDK5 0.009 0.115 -9999 0 -9999 0 0
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.033 0 -9999 0 -9999 0 0
CDK5 0 0.12 -9999 0 -9999 0 0
PPP2R5D 0.016 0 -9999 0 -9999 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -9999 0 0
CSNK2A1 0.016 0 -9999 0 -9999 0 0
RELN/VLDLR/DAB1/LIS1 0.017 0.105 -9999 0 -9999 0 0
RELN/VLDLR -0.065 0.159 -9999 0 -0.516 3 3
CDC42 0 0 -9999 0 -9999 0 0
JNK signaling in the CD4+ TCR pathway

Figure 92.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 94.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.014 0.079 -9999 0 -0.453 1 1
MAP4K1 0.016 0 -9999 0 -9999 0 0
MAP3K8 -0.008 0.137 -9999 0 -0.773 1 1
PRKCB 0 0 -9999 0 -9999 0 0
DBNL 0.016 0 -9999 0 -9999 0 0
CRKL -0.008 0.137 -9999 0 -0.773 1 1
MAP3K1 0.028 0.093 -9999 0 -9999 0 0
JUN -0.011 0.142 -9999 0 -0.446 3 3
MAP3K7 0.037 0.081 -9999 0 -9999 0 0
GRAP2 0.016 0 -9999 0 -9999 0 0
CRK 0.016 0 -9999 0 -9999 0 0
MAP2K4 0.035 0.103 -9999 0 -9999 0 0
LAT 0.016 0 -9999 0 -9999 0 0
LCP2 -0.008 0.137 -9999 0 -0.773 1 1
MAPK8 0.024 0.028 -9999 0 -9999 0 0
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.029 0.085 -9999 0 -9999 0 0
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.013 0.073 -9999 0 -9999 0 0
a4b1 and a4b7 Integrin signaling

Figure 93.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 95.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.016 0 -9999 0 -9999 0 0
ITGB7 0.016 0 -9999 0 -9999 0 0
ITGA4 0.016 0 -9999 0 -9999 0 0
alpha4/beta7 Integrin 0 0 -9999 0 -9999 0 0
alpha4/beta1 Integrin 0 0 -9999 0 -9999 0 0
Hedgehog signaling events mediated by Gli proteins

Figure 94.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 96.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.001 -9999 0 -9999 0 0
HDAC2 0.017 0.001 -9999 0 -9999 0 0
GNB1/GNG2 -0.025 0.101 -9999 0 -0.508 1 1
forebrain development -0.045 0.184 -9999 0 -0.504 2 2
GNAO1 0.014 0.006 -9999 0 -9999 0 0
SMO/beta Arrestin2 0.009 0.069 -9999 0 -0.367 1 1
SMO -0.003 0.094 -9999 0 -0.523 1 1
ARRB2 0.014 0.007 -9999 0 -9999 0 0
GLI3/SPOP -0.027 0.222 -9999 0 -1.124 1 1
mol:GTP -0.001 0.004 -9999 0 -9999 0 0
GSK3B 0.016 0 -9999 0 -9999 0 0
GNAI2 -0.011 0.137 -9999 0 -0.772 1 1
SIN3/HDAC complex 0.014 0.023 -9999 0 -9999 0 0
GNAI1 -0.01 0.138 -9999 0 -0.779 1 1
XPO1 0.015 0.009 -9999 0 -9999 0 0
GLI1/Su(fu) -0.099 0.183 -9999 0 -0.676 2 2
SAP30 0.017 0.001 -9999 0 -9999 0 0
mol:GDP -0.003 0.094 -9999 0 -0.523 1 1
MIM/GLI2A -0.025 0.177 -9999 0 -0.707 2 2
IFT88 0.016 0 -9999 0 -9999 0 0
GNAI3 0.014 0.006 -9999 0 -9999 0 0
GLI2 0.042 0.06 -9999 0 -9999 0 0
GLI3 -0.039 0.241 -9999 0 -1.236 1 1
CSNK1D 0.016 0 -9999 0 -9999 0 0
CSNK1E 0.016 0 -9999 0 -9999 0 0
SAP18 0.017 0.001 -9999 0 -9999 0 0
embryonic digit morphogenesis 0.016 0 -9999 0 -9999 0 0
GNG2 -0.008 0.137 -9999 0 -0.773 1 1
Gi family/GTP 0.01 0.089 -9999 0 -9999 0 0
SIN3B 0.017 0.001 -9999 0 -9999 0 0
SIN3A 0.017 0.001 -9999 0 -9999 0 0
GLI3/Su(fu) -0.035 0.203 -9999 0 -0.897 1 1
GLI2/Su(fu) 0.015 0.112 -9999 0 -9999 0 0
FOXA2 -0.321 0.539 -9999 0 -1.231 8 8
neural tube patterning -0.045 0.184 -9999 0 -0.504 2 2
SPOP 0.016 0 -9999 0 -9999 0 0
Su(fu)/PIAS1 -0.003 0.118 -9999 0 -0.444 2 2
GNB1 0.016 0 -9999 0 -9999 0 0
CSNK1G2 0.016 0 -9999 0 -9999 0 0
CSNK1G3 0.016 0 -9999 0 -9999 0 0
MTSS1 -0.025 0.178 -9999 0 -0.708 2 2
embryonic limb morphogenesis -0.045 0.184 -9999 0 -0.504 2 2
SUFU -0.009 0.129 -9999 0 -0.493 2 2
LGALS3 -0.033 0.191 -9999 0 -0.773 2 2
catabolic process 0.005 0.185 -9999 0 -0.876 1 1
GLI3A/CBP 0.007 0.065 -9999 0 -9999 0 0
KIF3A -0.05 0.209 -9999 0 -0.691 3 3
GLI1 -0.046 0.187 -9999 0 -0.516 2 2
RAB23 -0.008 0.137 -9999 0 -0.773 1 1
CSNK1A1 0.016 0 -9999 0 -9999 0 0
IFT172 -0.033 0.191 -9999 0 -0.773 2 2
RBBP7 0.017 0.001 -9999 0 -9999 0 0
Su(fu)/Galectin3 -0.032 0.161 -9999 0 -0.449 4 4
GNAZ 0.014 0.006 -9999 0 -9999 0 0
RBBP4 0.017 0.001 -9999 0 -9999 0 0
CSNK1G1 0.016 0 -9999 0 -9999 0 0
PIAS1 0.016 0 -9999 0 -9999 0 0
PRKACA 0.016 0 -9999 0 -9999 0 0
GLI2/SPOP 0.047 0.056 -9999 0 -9999 0 0
STK36 -0.034 0.192 -9999 0 -0.777 2 2
Gi family/GNB1/GNG2/GDP 0.011 0.094 -9999 0 -9999 0 0
PTCH1 -0.056 0.258 -9999 0 -1.184 1 1
MIM/GLI1 -0.128 0.312 -9999 0 -0.642 7 7
CREBBP 0.007 0.064 -9999 0 -9999 0 0
Su(fu)/SIN3/HDAC complex 0.055 0.035 -9999 0 -9999 0 0
Aurora A signaling

Figure 95.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 97.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.008 0.123 -9999 0 -0.486 1 1
BIRC5 -0.092 0.255 -9999 0 -0.674 5 5
NFKBIA 0.041 0.065 -9999 0 -9999 0 0
CPEB1 -0.025 0.164 -9999 0 -0.65 2 2
AKT1 0.041 0.065 -9999 0 -9999 0 0
NDEL1 0.016 0 -9999 0 -9999 0 0
Aurora A/BRCA1 0.002 0.072 -9999 0 -9999 0 0
NDEL1/TACC3 0.014 0.056 -9999 0 -9999 0 0
GADD45A -0.025 0.164 -9999 0 -0.65 2 2
GSK3B 0.026 0.021 -9999 0 -9999 0 0
PAK1/Aurora A 0.035 0.061 -9999 0 -9999 0 0
MDM2 -0.008 0.137 -9999 0 -0.773 1 1
JUB -0.025 0.164 -9999 0 -0.65 2 2
TPX2 -0.016 0.141 -9999 0 -0.443 3 3
TP53 0.029 0.082 -9999 0 -0.349 1 1
DLG7 -0.119 0.223 -9999 0 -0.47 8 8
AURKAIP1 0.016 0 -9999 0 -9999 0 0
ARHGEF7 0.016 0 -9999 0 -9999 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -9999 0 0
Aurora A/NDEL1/TACC3 0.015 0.059 -9999 0 -9999 0 0
G2/M transition of mitotic cell cycle 0.002 0.072 -9999 0 -9999 0 0
AURKA 0.037 0.081 -9999 0 -9999 0 0
AURKB -0.033 0.057 -9999 0 -9999 0 0
CDC25B 0.033 0.068 -9999 0 -9999 0 0
G2/M transition checkpoint -0.012 0.11 -9999 0 -0.458 1 1
mRNA polyadenylation -0.012 0.11 -9999 0 -0.458 1 1
Aurora A/CPEB -0.012 0.111 -9999 0 -0.462 1 1
Aurora A/TACC1/TRAP/chTOG 0.017 0.058 -9999 0 -9999 0 0
BRCA1 -0.001 0.094 -9999 0 -0.526 1 1
centrosome duplication 0.035 0.061 -9999 0 -9999 0 0
regulation of centrosome cycle 0.014 0.054 -9999 0 -9999 0 0
spindle assembly 0.017 0.057 -9999 0 -9999 0 0
TDRD7 0.016 0 -9999 0 -9999 0 0
Aurora A/RasGAP/Survivin -0.07 0.137 -9999 0 -0.404 2 2
CENPA -0.038 0.103 -9999 0 -0.255 5 5
Aurora A/PP2A 0.035 0.061 -9999 0 -9999 0 0
meiosis 0 0 -9999 0 -9999 0 0
protein catabolic process -0.041 0.126 -9999 0 -9999 0 0
negative regulation of DNA binding 0.029 0.082 -9999 0 -0.348 1 1
prophase 0 0 -9999 0 -9999 0 0
GIT1/beta-PIX 0 0 -9999 0 -9999 0 0
RASA1 -0.001 0.094 -9999 0 -0.526 1 1
Ajuba/Aurora A -0.012 0.111 -9999 0 -0.462 1 1
mitotic prometaphase 0 0.01 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.081 -9999 0 -9999 0 0
TACC1 0.016 0 -9999 0 -9999 0 0
TACC3 0.016 0 -9999 0 -9999 0 0
Aurora A/Antizyme1 0.015 0.059 -9999 0 -9999 0 0
Aurora A/RasGAP 0.025 0.104 -9999 0 -0.484 1 1
OAZ1 0.016 0 -9999 0 -9999 0 0
RAN 0.016 0 -9999 0 -9999 0 0
mitosis 0 0 -9999 0 -9999 0 0
PRKACA 0.026 0.021 -9999 0 -9999 0 0
GIT1 0.016 0 -9999 0 -9999 0 0
GIT1/beta-PIX/PAK1 0 0 -9999 0 -9999 0 0
Importin alpha/Importin beta/TPX2 -0.016 0.141 -9999 0 -0.442 3 3
PPP2R5D 0.016 0 -9999 0 -9999 0 0
Aurora A/TPX2 0.011 0.124 -9999 0 -0.452 1 1
PAK1 0.016 0 -9999 0 -9999 0 0
CKAP5 0.016 0 -9999 0 -9999 0 0
Arf6 downstream pathway

Figure 96.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 98.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.023 0.25 -9999 0 -1.238 1 1
regulation of axonogenesis -0.021 0.045 -9999 0 -9999 0 0
myoblast fusion 0.009 0.098 0.424 1 -9999 0 1
mol:GTP -0.023 0.064 -9999 0 -9999 0 0
regulation of calcium-dependent cell-cell adhesion -0.011 0.082 -9999 0 -9999 0 0
ARF1/GTP -0.016 0.043 -9999 0 -9999 0 0
mol:GM1 -0.005 0.052 -9999 0 -9999 0 0
mol:Choline 0.02 0.045 -9999 0 -9999 0 0
lamellipodium assembly -0.028 0.098 -9999 0 -0.461 1 1
MAPK3 0.004 0.089 -9999 0 -0.346 1 1
ARF6/GTP/NME1/Tiam1 0.012 0.082 -9999 0 -9999 0 0
ARF1 0.016 0 -9999 0 -9999 0 0
ARF6/GDP -0.01 0.099 -9999 0 -0.426 1 1
ARF1/GDP 0.004 0.092 -9999 0 -0.385 1 1
ARF6 -0.01 0.093 -9999 0 -0.501 1 1
RAB11A 0.016 0 -9999 0 -9999 0 0
TIAM1 0 0.094 -9999 0 -0.522 1 1
fibronectin binding 0 0 -9999 0 -9999 0 0
MAPK1 0.004 0.089 -9999 0 -0.346 1 1
actin filament bundle formation -0.001 0.091 0.384 1 -9999 0 1
KALRN -0.022 0.073 -9999 0 -0.325 1 1
RAB11FIP3/RAB11A 0 0 -9999 0 -9999 0 0
RhoA/GDP 0.001 0.092 -9999 0 -0.387 1 1
NME1 0.017 0.006 -9999 0 -9999 0 0
Rac1/GDP 0.001 0.092 -9999 0 -0.387 1 1
substrate adhesion-dependent cell spreading -0.023 0.064 -9999 0 -9999 0 0
cortical actin cytoskeleton organization -0.028 0.099 -9999 0 -0.464 1 1
RAC1 0.016 0 -9999 0 -9999 0 0
liver development -0.023 0.064 -9999 0 -9999 0 0
ARF6/GTP -0.023 0.064 -9999 0 -9999 0 0
RhoA/GTP -0.016 0.043 -9999 0 -9999 0 0
mol:GDP -0.028 0.094 -9999 0 -0.427 1 1
ARF6/GTP/RAB11FIP3/RAB11A -0.012 0.033 -9999 0 -9999 0 0
RHOA 0.016 0 -9999 0 -9999 0 0
PLD1 0.008 0.052 -9999 0 -9999 0 0
RAB11FIP3 0.016 0 -9999 0 -9999 0 0
tube morphogenesis -0.028 0.098 -9999 0 -0.461 1 1
ruffle organization 0.021 0.045 -9999 0 -9999 0 0
regulation of epithelial cell migration -0.023 0.064 -9999 0 -9999 0 0
PLD2 0.008 0.052 -9999 0 -9999 0 0
PIP5K1A 0.021 0.046 -9999 0 -9999 0 0
mol:Phosphatidic acid 0.02 0.045 -9999 0 -9999 0 0
Rac1/GTP -0.028 0.099 -9999 0 -0.465 1 1
Aurora C signaling

Figure 97.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 99.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.016 0 -9999 0 -9999 0 0
Aurora C/Aurora B/INCENP -0.023 0.092 -9999 0 -0.462 1 1
metaphase 0 0 -9999 0 -9999 0 0
mitosis 0 0 -9999 0 -9999 0 0
H3F3B -0.052 0.189 -9999 0 -0.773 2 2
AURKB -0.001 0.094 -9999 0 -0.526 1 1
AURKC -0.008 0.137 -9999 0 -0.773 1 1
EPO signaling pathway

Figure 98.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 100.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.064 0.113 -9999 0 -9999 0 0
CRKL 0.03 0.115 -9999 0 -0.427 1 1
mol:DAG 0.052 0.073 -9999 0 -9999 0 0
HRAS 0.052 0.106 -9999 0 -9999 0 0
MAPK8 0.044 0.016 -9999 0 -9999 0 0
RAP1A 0.044 0.087 -9999 0 -0.427 1 1
GAB1 0.03 0.115 -9999 0 -0.427 1 1
MAPK14 0.044 0.016 -9999 0 -9999 0 0
EPO 0.018 0.01 -9999 0 -9999 0 0
PLCG1 0.053 0.074 -9999 0 -9999 0 0
EPOR/TRPC2/IP3 Receptors 0.018 0.01 -9999 0 -9999 0 0
RAPGEF1 0.016 0 -9999 0 -9999 0 0
EPO/EPOR (dimer)/SOCS3 0.007 0.113 -9999 0 -0.518 1 1
GAB1/SHC/GRB2/SOS1 -0.027 0.087 -9999 0 -9999 0 0
EPO/EPOR (dimer) 0.028 0.015 -9999 0 -9999 0 0
IRS2 0.012 0.128 -9999 0 -0.427 1 1
STAT1 0.044 0.122 -9999 0 -9999 0 0
STAT5B 0.056 0.084 -9999 0 -9999 0 0
cell proliferation 0.052 0.017 -9999 0 -9999 0 0
GAB1/SHIP/PIK3R1/SHP2/SHC -0.037 0.133 -9999 0 -0.695 1 1
TEC 0.044 0.087 -9999 0 -0.427 1 1
SOCS3 -0.025 0.164 -9999 0 -0.65 2 2
STAT1 (dimer) 0.044 0.12 -9999 0 -9999 0 0
JAK2 0.018 0.008 -9999 0 -9999 0 0
PIK3R1 -0.008 0.137 -9999 0 -0.773 1 1
EPO/EPOR (dimer)/JAK2 0.051 0.094 -9999 0 -0.457 1 1
EPO/EPOR 0.028 0.015 -9999 0 -9999 0 0
LYN 0.017 0.006 -9999 0 -9999 0 0
TEC/VAV2 0.054 0.085 -9999 0 -9999 0 0
elevation of cytosolic calcium ion concentration 0.018 0.01 -9999 0 -9999 0 0
SHC1 -0.001 0.094 -9999 0 -0.526 1 1
EPO/EPOR (dimer)/LYN 0.044 0.018 -9999 0 -9999 0 0
mol:IP3 0.052 0.073 -9999 0 -9999 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.047 0.151 -9999 0 -0.778 1 1
SH2B3 -0.006 0.139 -9999 0 -0.78 1 1
NFKB1 0.044 0.016 -9999 0 -9999 0 0
EPO/EPOR (dimer)/JAK2/SOCS3 -0.003 0.077 0.318 1 -9999 0 1
PTPN6 0.035 0.09 -9999 0 -0.453 1 1
TEC/VAV2/GRB2 0.059 0.083 -9999 0 -9999 0 0
EPOR 0.018 0.01 -9999 0 -9999 0 0
INPP5D 0 0 -9999 0 -9999 0 0
mol:GDP -0.027 0.088 -9999 0 -9999 0 0
SOS1 0.016 0 -9999 0 -9999 0 0
PLCG2 -0.025 0.164 -9999 0 -0.65 2 2
CRKL/CBL/C3G 0.046 0.109 -9999 0 -9999 0 0
VAV2 0.044 0.087 -9999 0 -0.427 1 1
CBL 0.044 0.087 -9999 0 -0.427 1 1
SHC/Grb2/SOS1 -0.018 0.074 -9999 0 -9999 0 0
STAT5A 0.056 0.084 -9999 0 -9999 0 0
GRB2 0.016 0 -9999 0 -9999 0 0
STAT5 (dimer) 0.07 0.112 -9999 0 -9999 0 0
LYN/PLCgamma2 -0.008 0.124 -9999 0 -0.477 2 2
PTPN11 0.016 0 -9999 0 -9999 0 0
BTK 0.017 0.174 -9999 0 -0.846 1 1
BCL2 0.042 0.172 -9999 0 -0.621 1 1
Insulin-mediated glucose transport

Figure 99.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 101.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.002 0.006 -9999 0 -9999 0 0
CaM/Ca2+ 0 0 -9999 0 -9999 0 0
AKT1 0.016 0 -9999 0 -9999 0 0
AKT2 -0.001 0.094 -9999 0 -0.526 1 1
STXBP4 0.016 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
mol:glucose 0.05 0.034 -9999 0 -9999 0 0
YWHAZ 0.016 0 -9999 0 -9999 0 0
CALM1 0.016 0 -9999 0 -9999 0 0
YWHAQ 0.016 0 -9999 0 -9999 0 0
TBC1D4 0.009 0.107 -9999 0 -0.587 1 1
mol:Ca2+ 0 0 -9999 0 -9999 0 0
YWHAH 0.016 0 -9999 0 -9999 0 0
YWHAB 0.016 0 -9999 0 -9999 0 0
SNARE/Synip 0 0 -9999 0 -9999 0 0
YWHAG 0.016 0 -9999 0 -9999 0 0
ASIP 0 0 -9999 0 -9999 0 0
PRKCI 0.016 0 -9999 0 -9999 0 0
AS160/CaM/Ca2+ 0 0 -9999 0 -9999 0 0
RHOQ 0.016 0 -9999 0 -9999 0 0
GYS1 0.033 0.037 -9999 0 -9999 0 0
PRKCZ 0 0 -9999 0 -9999 0 0
TRIP10 0.016 0 -9999 0 -9999 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -9999 0 0
AS160/14-3-3 0.025 0.09 -9999 0 -9999 0 0
VAMP2 0.016 0 -9999 0 -9999 0 0
SLC2A4 0.051 0.035 -9999 0 -9999 0 0
STX4 0.016 0 -9999 0 -9999 0 0
GSK3B 0.025 0.044 -9999 0 -9999 0 0
SFN -0.058 0.23 -9999 0 -0.773 3 3
LNPEP 0.016 0 -9999 0 -9999 0 0
YWHAE 0.016 0 -9999 0 -9999 0 0
PDGFR-alpha signaling pathway

Figure 100.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 102.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.013 0.011 -9999 0 -9999 0 0
PDGF/PDGFRA/CRKL -0.016 0.104 -9999 0 -0.594 1 1
positive regulation of JUN kinase activity -0.009 0.049 -9999 0 -9999 0 0
CRKL -0.008 0.137 -9999 0 -0.773 1 1
PDGF/PDGFRA/Caveolin-3 0.002 0.004 -9999 0 -9999 0 0
AP1 -0.122 0.278 -9999 0 -1.367 1 1
mol:IP3 0.023 0.021 -9999 0 -9999 0 0
PLCG1 0.023 0.021 -9999 0 -9999 0 0
PDGF/PDGFRA/alphaV Integrin -0.036 0.146 -9999 0 -0.6 2 2
RAPGEF1 0.016 0 -9999 0 -9999 0 0
CRK 0.016 0 -9999 0 -9999 0 0
mol:Ca2+ 0.023 0.021 -9999 0 -9999 0 0
CAV3 0.016 0 -9999 0 -9999 0 0
CAV1 -0.058 0.23 -9999 0 -0.773 3 3
SHC/Grb2/SOS1 -0.009 0.049 -9999 0 -9999 0 0
PDGF/PDGFRA/Shf -0.079 0.192 -9999 0 -0.516 5 5
FOS -0.074 0.286 -9999 0 -1.286 1 1
JUN -0.063 0.18 -9999 0 -0.62 3 3
oligodendrocyte development -0.036 0.145 -9999 0 -0.599 2 2
GRB2 0.016 0 -9999 0 -9999 0 0
PIK3R1 -0.008 0.137 -9999 0 -0.773 1 1
mol:DAG 0.023 0.021 -9999 0 -9999 0 0
PDGF/PDGFRA 0.013 0.011 -9999 0 -9999 0 0
actin cytoskeleton reorganization 0.002 0.004 -9999 0 -9999 0 0
SRF 0.029 0.008 -9999 0 -9999 0 0
SHC1 -0.001 0.094 -9999 0 -0.526 1 1
PI3K -0.016 0.09 -9999 0 -0.517 1 1
PDGF/PDGFRA/Crk/C3G 0 0 -9999 0 -9999 0 0
JAK1 0.007 0.111 -9999 0 -0.608 1 1
ELK1/SRF 0.046 0.008 -9999 0 -9999 0 0
SHB 0.016 0 -9999 0 -9999 0 0
SHF -0.092 0.255 -9999 0 -0.674 5 5
CSNK2A1 0.011 0.021 -9999 0 -9999 0 0
GO:0007205 0.023 0.024 -9999 0 -9999 0 0
SOS1 0.016 0 -9999 0 -9999 0 0
Ras protein signal transduction -0.009 0.049 -9999 0 -9999 0 0
PDGF/PDGFRA/SHB 0.002 0.004 -9999 0 -9999 0 0
PDGF/PDGFRA/Caveolin-1 -0.054 0.175 -9999 0 -0.598 3 3
ITGAV -0.033 0.191 -9999 0 -0.773 2 2
ELK1 0.025 0.035 -9999 0 -9999 0 0
PIK3CA 0.016 0 -9999 0 -9999 0 0
PDGF/PDGFRA/Crk 0.002 0.004 -9999 0 -9999 0 0
JAK-STAT cascade 0.007 0.11 -9999 0 -0.606 1 1
cell proliferation -0.079 0.191 -9999 0 -0.514 5 5
IFN-gamma pathway

Figure 101.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 103.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.08 0.178 -9999 0 -9999 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -9999 0 0
CRKL -0.008 0.137 -9999 0 -0.773 1 1
STAT1 (dimer)/Cbp/p300 -0.041 0.165 -9999 0 -9999 0 0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.037 0.098 -9999 0 -0.499 1 1
antigen processing and presentation of peptide antigen via MHC class I -0.056 0.102 -9999 0 -0.506 1 1
CaM/Ca2+ -0.102 0.142 -9999 0 -9999 0 0
RAP1A 0.016 0 -9999 0 -9999 0 0
STAT1 (dimer)/SHP2 -0.079 0.178 -9999 0 -9999 0 0
AKT1 -0.055 0.186 -9999 0 -0.686 1 1
MAP2K1 -0.06 0.165 -9999 0 -9999 0 0
MAP3K11 -0.066 0.17 -9999 0 -9999 0 0
IFNGR1 -0.009 0.093 -9999 0 -0.518 1 1
mol:GTP 0 0 -9999 0 -9999 0 0
CaM/Ca2+/CAMKII -0.065 0.114 -9999 0 -0.469 1 1
Rap1/GTP -0.081 0.109 -9999 0 -9999 0 0
CRKL/C3G -0.018 0.102 -9999 0 -0.586 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.118 0.163 -9999 0 -9999 0 0
CEBPB -0.017 0.173 -9999 0 -0.528 1 1
STAT3 0.016 0 -9999 0 -9999 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.066 0.17 -9999 0 -9999 0 0
STAT1 -0.079 0.177 -9999 0 -9999 0 0
CALM1 0.016 0 -9999 0 -9999 0 0
IFN-gamma (dimer) -0.19 0.313 -9999 0 -0.642 10 10
PIK3CA 0.016 0 -9999 0 -9999 0 0
STAT1 (dimer)/PIAS1 -0.066 0.17 -9999 0 -9999 0 0
CEBPB/PTGES2/Cbp/p300 -0.044 0.074 -9999 0 -9999 0 0
mol:Ca2+ -0.084 0.173 -9999 0 -9999 0 0
MAPK3 -0.033 0.154 -9999 0 -9999 0 0
STAT1 (dimer) -0.078 0.158 -9999 0 -0.836 1 1
MAPK1 -0.033 0.154 -9999 0 -9999 0 0
JAK2 0.007 0.016 -9999 0 -9999 0 0
PIK3R1 -0.008 0.137 -9999 0 -0.774 1 1
JAK1 -0.016 0.136 -9999 0 -0.769 1 1
CAMK2D -0.001 0.094 -9999 0 -0.525 1 1
DAPK1 0.005 0.137 -9999 0 -0.471 1 1
SMAD7 0.012 0.088 -9999 0 -9999 0 0
CBL/CRKL/C3G -0.101 0.133 -9999 0 -9999 0 0
PI3K -0.109 0.173 -9999 0 -0.762 1 1
IFNG -0.19 0.314 -9999 0 -0.643 10 10
apoptosis -0.005 0.115 -9999 0 -0.346 1 1
CAMK2G 0.016 0 -9999 0 -9999 0 0
STAT3 (dimer) 0.016 0 -9999 0 -9999 0 0
CAMK2A 0.016 0 -9999 0 -9999 0 0
CAMK2B -0.059 0.203 -9999 0 -0.588 4 4
FRAP1 -0.041 0.174 -9999 0 -0.617 1 1
PRKCD -0.055 0.189 -9999 0 -0.701 1 1
RAP1B 0.016 0 -9999 0 -9999 0 0
negative regulation of cell growth -0.056 0.102 -9999 0 -0.506 1 1
PTPN2 0.016 0 -9999 0 -9999 0 0
EP300 0.017 0 -9999 0 -9999 0 0
IRF1 -0.011 0.139 -9999 0 -9999 0 0
STAT1 (dimer)/PIASy -0.072 0.168 -9999 0 -9999 0 0
SOCS1 0.015 0.018 -9999 0 -9999 0 0
mol:GDP -0.097 0.128 -9999 0 -9999 0 0
CASP1 0.012 0.099 -9999 0 -0.403 1 1
PTGES2 0.016 0 -9999 0 -9999 0 0
IRF9 0.032 0.064 -9999 0 -9999 0 0
mol:PI-3-4-5-P3 -0.106 0.167 -9999 0 -0.727 1 1
RAP1/GDP -0.082 0.109 -9999 0 -9999 0 0
CBL -0.067 0.17 -9999 0 -9999 0 0
MAP3K1 -0.074 0.171 -9999 0 -9999 0 0
PIAS1 0.016 0 -9999 0 -9999 0 0
PIAS4 0.016 0 -9999 0 -9999 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.056 0.102 -9999 0 -0.506 1 1
PTPN11 -0.08 0.176 -9999 0 -9999 0 0
CREBBP 0.017 0 -9999 0 -9999 0 0
RAPGEF1 0.016 0 -9999 0 -9999 0 0
Class I PI3K signaling events mediated by Akt

Figure 102.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 104.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -9999 0 -9999 0 0
BAD/BCL-XL/YWHAZ 0.041 0 -9999 0 -9999 0 0
CDKN1B 0.017 0.144 -9999 0 -0.75 1 1
CDKN1A 0.017 0.144 -9999 0 -0.75 1 1
FRAP1 0.016 0 -9999 0 -9999 0 0
PRKDC -0.008 0.137 -9999 0 -0.773 1 1
FOXO3 0.017 0.144 -9999 0 -0.75 1 1
AKT1 -0.033 0.141 -9999 0 -0.8 1 1
BAD 0.016 0 -9999 0 -9999 0 0
AKT3 -0.021 0.131 -9999 0 -0.427 3 3
mol:GTP 0 0 -9999 0 -9999 0 0
FOXO4 0.017 0.144 -9999 0 -0.75 1 1
AKT1/ASK1 -0.03 0.128 -9999 0 -0.729 1 1
BAD/YWHAZ 0 0 -9999 0 -9999 0 0
RICTOR 0.016 0 -9999 0 -9999 0 0
RAF1 0.016 0 -9999 0 -9999 0 0
JNK cascade 0.029 0.123 0.696 1 -9999 0 1
TSC1 -0.011 0.186 -9999 0 -0.566 3 3
YWHAZ 0.016 0 -9999 0 -9999 0 0
AKT1/RAF1 0.016 0.144 -9999 0 -0.75 1 1
EP300 0.016 0 -9999 0 -9999 0 0
mol:GDP -0.033 0.138 -9999 0 -0.782 1 1
mol:PI-3-4-5-P3 0 0 -9999 0 -9999 0 0
TSC2 0.003 0.173 -9999 0 -0.651 2 2
YWHAQ 0.016 0 -9999 0 -9999 0 0
TBC1D4 -0.03 0.145 -9999 0 -0.395 4 4
MAP3K5 0.016 0 -9999 0 -9999 0 0
MAPKAP1 0.016 0 -9999 0 -9999 0 0
negative regulation of cell cycle -0.035 0.063 -9999 0 -9999 0 0
YWHAH 0.016 0 -9999 0 -9999 0 0
AKT1S1 0.017 0.144 -9999 0 -0.75 1 1
CASP9 0.017 0.144 -9999 0 -0.75 1 1
YWHAB 0.016 0 -9999 0 -9999 0 0
p27Kip1/KPNA1 0.026 0.136 -9999 0 -0.698 1 1
GBL 0.016 0 -9999 0 -9999 0 0
PDK1/Src/Hsp90 -0.047 0.146 -9999 0 -0.501 3 3
YWHAE 0.016 0 -9999 0 -9999 0 0
SRC 0.016 0 -9999 0 -9999 0 0
AKT2/p21CIP1 -0.047 0.159 -9999 0 -0.838 1 1
KIAA1303 0.016 0 -9999 0 -9999 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.033 0.043 -9999 0 -9999 0 0
CHUK 0.017 0.144 -9999 0 -0.75 1 1
BAD/BCL-XL 0.034 0.136 -9999 0 -0.69 1 1
mTORC2 0 0 -9999 0 -9999 0 0
AKT2 -0.028 0.136 -9999 0 -0.427 3 3
FOXO1-3a-4/14-3-3 family 0.037 0.103 -9999 0 -0.405 1 1
PDPK1 -0.058 0.23 -9999 0 -0.773 3 3
MDM2 0.003 0.16 -9999 0 -0.573 2 2
MAPKKK cascade -0.016 0.139 0.727 1 -9999 0 1
MDM2/Cbp/p300 0.021 0.148 -9999 0 -0.669 1 1
TSC1/TSC2 -0.015 0.202 -9999 0 -0.592 3 3
proteasomal ubiquitin-dependent protein catabolic process -0.036 0.123 -9999 0 -0.628 1 1
glucose import -0.017 0.132 -9999 0 -0.351 4 4
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.037 0.081 -9999 0 -0.374 1 1
response to stress 0 0 -9999 0 -9999 0 0
SLC2A4 -0.017 0.133 -9999 0 -0.45 1 1
GSK3A 0.017 0.144 -9999 0 -0.75 1 1
FOXO1 0.017 0.144 -9999 0 -0.75 1 1
GSK3B 0.017 0.144 -9999 0 -0.75 1 1
SFN -0.058 0.23 -9999 0 -0.773 3 3
G1/S transition of mitotic cell cycle 0.026 0.14 -9999 0 -0.721 1 1
p27Kip1/14-3-3 family 0.032 0.079 -9999 0 -9999 0 0
PRKACA 0.016 0 -9999 0 -9999 0 0
KPNA1 0.016 0 -9999 0 -9999 0 0
HSP90AA1 0.016 0 -9999 0 -9999 0 0
YWHAG 0.016 0 -9999 0 -9999 0 0
RHEB -0.001 0.094 -9999 0 -0.526 1 1
CREBBP 0.016 0 -9999 0 -9999 0 0
Paxillin-independent events mediated by a4b1 and a4b7

Figure 103.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 105.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.039 0 -9999 0 -9999 0 0
CRKL -0.008 0.137 -9999 0 -0.773 1 1
Rac1/GDP 0 0 -9999 0 -9999 0 0
DOCK1 0.016 0 -9999 0 -9999 0 0
ITGA4 0.016 0 -9999 0 -9999 0 0
alpha4/beta7 Integrin/MAdCAM1 0 0 -9999 0 -9999 0 0
EPO 0.016 0 -9999 0 -9999 0 0
alpha4/beta7 Integrin 0 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
CRK 0.016 0 -9999 0 -9999 0 0
alpha4/beta1 Integrin 0 0 -9999 0 -9999 0 0
EPO/EPOR (dimer) 0 0 -9999 0 -9999 0 0
lamellipodium assembly -0.022 0.077 -9999 0 -9999 0 0
PIK3CA 0.016 0 -9999 0 -9999 0 0
PI3K -0.018 0.102 -9999 0 -0.586 1 1
ARF6 -0.001 0.094 -9999 0 -0.526 1 1
JAK2 0.043 0 -9999 0 -9999 0 0
PXN 0.016 0 -9999 0 -9999 0 0
PIK3R1 -0.008 0.137 -9999 0 -0.773 1 1
MADCAM1 0.016 0 -9999 0 -9999 0 0
cell adhesion 0 0 -9999 0 -9999 0 0
CRKL/CBL -0.018 0.102 -9999 0 -0.586 1 1
ITGB1 0.016 0 -9999 0 -9999 0 0
SRC 0.011 0.119 -9999 0 -0.45 2 2
ITGB7 0.016 0 -9999 0 -9999 0 0
RAC1 0.016 0 -9999 0 -9999 0 0
alpha4/beta1 Integrin/VCAM1 -0.031 0.121 -9999 0 -0.501 2 2
p130Cas/Crk/Dock1 0.038 0.104 -9999 0 -9999 0 0
VCAM1 -0.033 0.191 -9999 0 -0.773 2 2
RHOA 0.016 0 -9999 0 -9999 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0 0 -9999 0 -9999 0 0
BCAR1 0.021 0.112 -9999 0 -9999 0 0
EPOR 0.016 0 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
CBL 0.016 0 -9999 0 -9999 0 0
GIT1 0.016 0 -9999 0 -9999 0 0
Rac1/GTP -0.022 0.079 -9999 0 -9999 0 0
Signaling events mediated by HDAC Class III

Figure 104.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 106.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.016 0 -9999 0 -9999 0 0
HDAC4 0.016 0 -9999 0 -9999 0 0
induction of apoptosis 0 0 -9999 0 -9999 0 0
regulation of S phase of mitotic cell cycle -0.011 0 -9999 0 -9999 0 0
CDKN1A 0 0 -9999 0 -9999 0 0
KAT2B 0 0 -9999 0 -9999 0 0
BAX 0.016 0 -9999 0 -9999 0 0
FOXO3 0 0 -9999 0 -9999 0 0
FOXO1 0.016 0 -9999 0 -9999 0 0
FOXO4 0.029 0 -9999 0 -9999 0 0
response to UV 0 0 -9999 0 -9999 0 0
XRCC6 0.016 0 -9999 0 -9999 0 0
TAT 0.016 0 -9999 0 -9999 0 0
mol:Lysophosphatidic acid 0 0 -9999 0 -9999 0 0
MYOD1 0.002 0.069 -9999 0 -0.382 1 1
PPARGC1A -0.033 0.191 -9999 0 -0.773 2 2
FHL2 -0.158 0.308 -9999 0 -0.681 8 8
response to nutrient levels 0 0 -9999 0 -9999 0 0
KU70/SIRT1 0 0 -9999 0 -9999 0 0
HIST2H4A 0.011 0 -9999 0 -9999 0 0
SIRT1/FOXO3a 0 0 -9999 0 -9999 0 0
SIRT1 0 0 -9999 0 -9999 0 0
response to hypoxia 0 0 -9999 0 -9999 0 0
SIRT1/MEF2D/HDAC4 0 0 -9999 0 -9999 0 0
SIRT1/Histone H1b -0.014 0.056 -9999 0 -9999 0 0
apoptosis 0 0 -9999 0 -9999 0 0
SIRT1/PGC1A -0.032 0.124 -9999 0 -0.513 2 2
p53/SIRT1 0 0 -9999 0 -9999 0 0
SIRT1/FOXO4 0 0 -9999 0 -9999 0 0
FOXO1/FHL2/SIRT1 -0.098 0.176 -9999 0 -0.463 5 5
HIST1H1E 0.01 0.074 -9999 0 -0.349 1 1
SIRT1/p300 0 0 -9999 0 -9999 0 0
muscle cell differentiation 0.01 0.055 -9999 0 -9999 0 0
TP53 0 0 -9999 0 -9999 0 0
KU70/SIRT1/BAX 0 0 -9999 0 -9999 0 0
CREBBP 0.016 0 -9999 0 -9999 0 0
MEF2D 0.016 0 -9999 0 -9999 0 0
HIV-1 Tat/SIRT1 0 0 -9999 0 -9999 0 0
ACSS2 0.013 0.069 -9999 0 -0.372 1 1
SIRT1/PCAF/MYOD -0.01 0.055 -9999 0 -9999 0 0
S1P5 pathway

Figure 105.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 107.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -9999 0 0
telencephalon oligodendrocyte cell migration 0.016 0.061 -9999 0 -9999 0 0
GNAI2 -0.008 0.137 -9999 0 -0.773 1 1
S1P/S1P5/G12 0 0 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
GNAO1 0.016 0 -9999 0 -9999 0 0
RhoA/GTP -0.016 0.062 -9999 0 -9999 0 0
negative regulation of cAMP metabolic process 0.016 0.078 -9999 0 -0.315 1 1
GNAZ 0.016 0 -9999 0 -9999 0 0
GNAI3 0.016 0 -9999 0 -9999 0 0
GNA12 0.016 0 -9999 0 -9999 0 0
S1PR5 0 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
S1P/S1P5/Gi 0.016 0.079 -9999 0 -0.318 1 1
RhoA/GDP 0 0 -9999 0 -9999 0 0
RHOA 0.016 0 -9999 0 -9999 0 0
GNAI1 -0.008 0.137 -9999 0 -0.773 1 1
ceramide signaling pathway

Figure 106.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 108.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.014 0.152 -9999 0 -0.48 1 1
BAG4 0.016 0 -9999 0 -9999 0 0
BAD 0.009 0.06 -9999 0 -9999 0 0
NFKBIA 0.016 0 -9999 0 -9999 0 0
BIRC3 -0.133 0.288 -9999 0 -0.667 7 7
BAX 0.009 0.06 -9999 0 -9999 0 0
EnzymeConsortium:3.1.4.12 0.002 0.034 -9999 0 -9999 0 0
IKBKB -0.003 0.145 -9999 0 -0.445 1 1
MAP2K2 0.026 0.054 -9999 0 -9999 0 0
MAP2K1 0.026 0.054 -9999 0 -9999 0 0
SMPD1 -0.006 0.074 -9999 0 -0.261 2 2
GO:0005551 0 0 -9999 0 -9999 0 0
FADD/Caspase 8 0.004 0.129 -9999 0 -9999 0 0
MAP2K4 0.011 0.068 -9999 0 -9999 0 0
protein ubiquitination -0.002 0.146 -9999 0 -0.448 1 1
EnzymeConsortium:2.7.1.37 0.031 0.056 -9999 0 -9999 0 0
response to UV 0 0.001 -9999 0 -9999 0 0
RAF1 0.019 0.057 -9999 0 -9999 0 0
CRADD 0.016 0 -9999 0 -9999 0 0
mol:ceramide 0 0.063 -9999 0 -0.19 1 1
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -9999 0 -9999 0 0
MADD 0.016 0 -9999 0 -9999 0 0
MAP3K1 0.002 0.072 -9999 0 -0.218 1 1
TRADD 0.016 0 -9999 0 -9999 0 0
RELA/p50 0.016 0 -9999 0 -9999 0 0
MAPK3 0.03 0.054 -9999 0 -9999 0 0
MAPK1 0.03 0.054 -9999 0 -9999 0 0
p50/RELA/I-kappa-B-alpha 0 0 -9999 0 -9999 0 0
FADD -0.006 0.132 -9999 0 -9999 0 0
KSR1 0.01 0.06 -9999 0 -9999 0 0
MAPK8 0.02 0.065 -9999 0 -9999 0 0
TRAF2 0.016 0.001 -9999 0 -9999 0 0
response to radiation 0 0 -9999 0 -9999 0 0
CHUK -0.003 0.145 -9999 0 -0.445 1 1
TNF R/SODD 0.006 0.01 -9999 0 -9999 0 0
TNF -0.025 0.164 -9999 0 -0.65 2 2
CYCS 0.017 0.06 -9999 0 -9999 0 0
IKBKG -0.003 0.145 -9999 0 -0.445 1 1
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.016 0.138 -9999 0 -9999 0 0
RELA 0.016 0 -9999 0 -9999 0 0
RIPK1 0.016 0.001 -9999 0 -9999 0 0
AIFM1 0.017 0.06 -9999 0 -9999 0 0
TNF/TNF R/SODD -0.023 0.101 -9999 0 -0.501 1 1
TNFRSF1A 0.016 0.001 -9999 0 -9999 0 0
response to heat 0 0 -9999 0 -9999 0 0
CASP8 0.02 0.037 -9999 0 -9999 0 0
NSMAF -0.017 0.17 -9999 0 -0.696 1 1
response to hydrogen peroxide 0 0.001 -9999 0 -9999 0 0
BCL2 -0.035 0.158 -9999 0 -0.526 3 3
Role of Calcineurin-dependent NFAT signaling in lymphocytes

Figure 107.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 109.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -9999 0 -9999 0 0
NFATC1 0.058 0.038 -9999 0 -9999 0 0
NFATC2 0.042 0.033 -9999 0 -9999 0 0
NFATC3 0.019 0.003 -9999 0 -9999 0 0
YWHAE 0.016 0 -9999 0 -9999 0 0
Calcineurin A alpha-beta B1/CABIN1 0.007 0.097 -9999 0 -9999 0 0
Exportin 1/Ran/NUP214 0 0 -9999 0 -9999 0 0
mol:DAG 0 0.001 -9999 0 -9999 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.025 0.057 -9999 0 -9999 0 0
BCL2/BAX -0.035 0.108 -9999 0 -0.37 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 0.014 0.003 -9999 0 -9999 0 0
CaM/Ca2+ 0.014 0.003 -9999 0 -9999 0 0
BAX 0.016 0 -9999 0 -9999 0 0
MAPK14 0.016 0.003 -9999 0 -9999 0 0
BAD 0.016 0 -9999 0 -9999 0 0
CABIN1/MEF2D 0.015 0.091 -9999 0 -9999 0 0
Calcineurin A alpha-beta B1/BCL2 -0.035 0.158 -9999 0 -0.525 3 3
FKBP8 0.016 0 -9999 0 -9999 0 0
activation-induced cell death of T cells -0.015 0.09 -9999 0 -9999 0 0
KPNB1 0.016 0 -9999 0 -9999 0 0
KPNA2 -0.008 0.137 -9999 0 -0.773 1 1
XPO1 0.016 0 -9999 0 -9999 0 0
SFN -0.058 0.23 -9999 0 -0.773 3 3
MAP3K8 -0.008 0.137 -9999 0 -0.773 1 1
NFAT4/CK1 alpha 0.029 0.049 -9999 0 -9999 0 0
MEF2D/NFAT1/Cbp/p300 0.068 0.056 -9999 0 -9999 0 0
CABIN1 0.007 0.097 -9999 0 -9999 0 0
CALM1 0.017 0.002 -9999 0 -9999 0 0
RAN 0.016 0 -9999 0 -9999 0 0
MAP3K1 -0.001 0.094 -9999 0 -0.526 1 1
CAMK4 0.016 0 -9999 0 -9999 0 0
mol:Ca2+ 0.001 0.003 -9999 0 -9999 0 0
MAPK3 0.016 0 -9999 0 -9999 0 0
YWHAH 0.016 0 -9999 0 -9999 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.034 0.177 -9999 0 -0.585 3 3
YWHAB 0.016 0 -9999 0 -9999 0 0
MAPK8 0.016 0.003 -9999 0 -9999 0 0
MAPK9 0.016 0 -9999 0 -9999 0 0
YWHAG 0.016 0 -9999 0 -9999 0 0
FKBP1A 0.016 0 -9999 0 -9999 0 0
NFAT1-c-4/YWHAQ 0.079 0.033 -9999 0 -9999 0 0
PRKCH -0.001 0.094 -9999 0 -0.526 1 1
CABIN1/Cbp/p300 0 0.001 -9999 0 -9999 0 0
CASP3 0.016 0.003 -9999 0 -9999 0 0
PIM1 0.016 0 -9999 0 -9999 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.012 0.002 -9999 0 -9999 0 0
apoptosis -0.011 0.035 -9999 0 -9999 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.031 0.072 -9999 0 -9999 0 0
PRKCB 0 0 -9999 0 -9999 0 0
PRKCE 0.016 0 -9999 0 -9999 0 0
JNK2/NFAT4 0.027 0.003 -9999 0 -9999 0 0
BAD/BCL-XL 0 0 -9999 0 -9999 0 0
PRKCD 0.016 0 -9999 0 -9999 0 0
NUP214 0.016 0 -9999 0 -9999 0 0
PRKCZ 0.001 0.002 -9999 0 -9999 0 0
PRKCA -0.025 0.164 -9999 0 -0.65 2 2
PRKCG -0.008 0.137 -9999 0 -0.773 1 1
PRKCQ 0.016 0 -9999 0 -9999 0 0
FKBP38/BCL2 -0.035 0.108 -9999 0 -9999 0 0
EP300 0.017 0.002 -9999 0 -9999 0 0
PRKCB1 -0.033 0.191 -9999 0 -0.773 2 2
CSNK2A1 0.016 0 -9999 0 -9999 0 0
NFATc/JNK1 0.064 0.038 -9999 0 -9999 0 0
CaM/Ca2+/FKBP38 0.023 0.004 -9999 0 -9999 0 0
FKBP12/FK506 0 0 -9999 0 -9999 0 0
CSNK1A1 0.025 0.004 -9999 0 -9999 0 0
CaM/Ca2+/CAMK IV 0.023 0.004 -9999 0 -9999 0 0
NFATc/ERK1 0.065 0.036 -9999 0 -9999 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.025 0.058 -9999 0 -9999 0 0
NR4A1 0.065 0.091 -9999 0 -9999 0 0
GSK3B 0.016 0.003 -9999 0 -9999 0 0
positive T cell selection 0.019 0.003 -9999 0 -9999 0 0
NFAT1/CK1 alpha -0.004 0.017 -9999 0 -9999 0 0
RCH1/ KPNB1 -0.018 0.102 -9999 0 -0.586 1 1
YWHAQ 0.016 0 -9999 0 -9999 0 0
PRKACA 0.016 0.003 -9999 0 -9999 0 0
AKAP5 -0.058 0.23 -9999 0 -0.773 3 3
MEF2D 0.017 0.002 -9999 0 -9999 0 0
mol:FK506 0 0 -9999 0 -9999 0 0
YWHAZ 0.016 0 -9999 0 -9999 0 0
NFATc/p38 alpha 0.064 0.038 -9999 0 -9999 0 0
CREBBP 0.017 0.002 -9999 0 -9999 0 0
BCL2 -0.035 0.158 -9999 0 -0.526 3 3
Signaling events mediated by HDAC Class I

Figure 108.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 110.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.021 0.087 -9999 0 -0.46 1 1
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.039 0.085 -9999 0 -9999 0 0
SUMO1 0.016 0 -9999 0 -9999 0 0
ZFPM1 0.016 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.027 0 -9999 0 -9999 0 0
FKBP3 -0.001 0.094 -9999 0 -0.526 1 1
Histones -0.009 0.035 -9999 0 -9999 0 0
YY1/LSF 0.032 0 -9999 0 -9999 0 0
SMG5 0.016 0 -9999 0 -9999 0 0
RAN 0.016 0 -9999 0 -9999 0 0
I kappa B alpha/HDAC3 0.024 0.076 -9999 0 -9999 0 0
I kappa B alpha/HDAC1 0.027 0.054 -9999 0 -9999 0 0
SAP18 0.016 0 -9999 0 -9999 0 0
RELA 0.032 0.067 -9999 0 -9999 0 0
HDAC1/Smad7 -0.009 0.053 -9999 0 -9999 0 0
RANGAP1 0.016 0 -9999 0 -9999 0 0
HDAC3/TR2 0.027 0.054 -9999 0 -9999 0 0
NuRD/MBD3 Complex 0.056 0.023 -9999 0 -9999 0 0
NF kappa B1 p50/RelA 0.036 0.062 -9999 0 -9999 0 0
EntrezGene:23225 0 0 -9999 0 -9999 0 0
GATA2 0.016 0 -9999 0 -9999 0 0
GATA1 0.016 0 -9999 0 -9999 0 0
Mad/Max 0 0 -9999 0 -9999 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.069 0.024 -9999 0 -9999 0 0
RBBP7 0.016 0 -9999 0 -9999 0 0
NPC 0 0 -9999 0 -9999 0 0
RBBP4 0.016 0 -9999 0 -9999 0 0
MAX 0.016 0 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 0 0
FBXW11 0.016 0 -9999 0 -9999 0 0
NFKBIA 0.021 0.06 -9999 0 -9999 0 0
KAT2B 0 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
SIN3/HDAC complex 0.055 0 -9999 0 -9999 0 0
SIN3 complex 0 0 -9999 0 -9999 0 0
SMURF1 0.016 0 -9999 0 -9999 0 0
CHD3 -0.001 0.094 -9999 0 -0.526 1 1
SAP30 0.016 0 -9999 0 -9999 0 0
EntrezGene:23636 0 0 -9999 0 -9999 0 0
NCOR1 0.016 0 -9999 0 -9999 0 0
YY1/HDAC3 0.036 0.05 -9999 0 -9999 0 0
YY1/HDAC2 0.032 0 -9999 0 -9999 0 0
YY1/HDAC1 0.032 0 -9999 0 -9999 0 0
NuRD/MBD2 Complex (MeCP1) 0.056 0.023 -9999 0 -9999 0 0
PPARG -0.086 0.14 -9999 0 -0.417 1 1
HDAC8/hEST1B 0 0 -9999 0 -9999 0 0
UBE2I 0.016 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -9999 0 0
TNFRSF1A 0.016 0 -9999 0 -9999 0 0
HDAC3/SMRT (N-CoR2) 0.027 0.054 -9999 0 -9999 0 0
MBD3L2 0.016 0.003 -9999 0 -9999 0 0
ubiquitin-dependent protein catabolic process -0.009 0.053 -9999 0 -9999 0 0
CREBBP 0.016 0 -9999 0 -9999 0 0
NuRD/MBD3/MBD3L2 Complex 0.065 0.024 -9999 0 -9999 0 0
HDAC1 0.016 0 -9999 0 -9999 0 0
HDAC3 0.021 0.06 -9999 0 -9999 0 0
HDAC2 0.016 0 -9999 0 -9999 0 0
YY1 0.029 0 -9999 0 -9999 0 0
HDAC8 0.016 0 -9999 0 -9999 0 0
SMAD7 -0.001 0.094 -9999 0 -0.526 1 1
NCOR2 0.016 0 -9999 0 -9999 0 0
MXD1 0.016 0 -9999 0 -9999 0 0
STAT3 0.032 0 -9999 0 -9999 0 0
NFKB1 0.016 0 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.016 0 -9999 0 -9999 0 0
YY1/LSF/HDAC1 0.04 0 -9999 0 -9999 0 0
YY1/SAP30/HDAC1 0.04 0 -9999 0 -9999 0 0
EP300 0.016 0 -9999 0 -9999 0 0
STAT3 (dimer non-phopshorylated) 0.032 0 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.06 -9999 0 -9999 0 0
histone deacetylation 0.056 0.023 -9999 0 -9999 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.039 0.05 -9999 0 -9999 0 0
nuclear export 0 0 -9999 0 -9999 0 0
PRKACA 0.016 0 -9999 0 -9999 0 0
GATAD2B 0.016 0 -9999 0 -9999 0 0
GATAD2A 0.016 0 -9999 0 -9999 0 0
GATA2/HDAC3 0.027 0.054 -9999 0 -9999 0 0
GATA1/HDAC1 0 0 -9999 0 -9999 0 0
GATA1/HDAC3 0.027 0.054 -9999 0 -9999 0 0
CHD4 0.016 0 -9999 0 -9999 0 0
TNF-alpha/TNFR1A -0.03 0.119 -9999 0 -0.478 2 2
SIN3/HDAC complex/Mad/Max 0.06 0 -9999 0 -9999 0 0
NuRD Complex 0.066 0.024 -9999 0 -9999 0 0
positive regulation of chromatin silencing -0.008 0.035 -9999 0 -9999 0 0
SIN3B 0.016 0 -9999 0 -9999 0 0
MTA2 0.016 0 -9999 0 -9999 0 0
SIN3A 0.016 0 -9999 0 -9999 0 0
XPO1 0.016 0 -9999 0 -9999 0 0
SUMO1/HDAC1 0.038 0 -9999 0 -9999 0 0
HDAC complex 0 0 -9999 0 -9999 0 0
GATA1/Fog1 0 0 -9999 0 -9999 0 0
FKBP25/HDAC1/HDAC2 -0.009 0.053 -9999 0 -9999 0 0
TNF -0.025 0.164 -9999 0 -0.65 2 2
negative regulation of cell growth 0.06 0 -9999 0 -9999 0 0
NuRD/MBD2/PRMT5 Complex 0.056 0.023 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -9999 0 0
NF kappa B/RelA/I kappa B alpha 0.032 0.088 -9999 0 -0.408 1 1
SIN3/HDAC complex/NCoR1 0.057 0 -9999 0 -9999 0 0
TFCP2 0.016 0 -9999 0 -9999 0 0
NR2C1 0.016 0 -9999 0 -9999 0 0
MBD3 0.016 0 -9999 0 -9999 0 0
MBD2 0.016 0 -9999 0 -9999 0 0
FoxO family signaling

Figure 109.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 111.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.016 0.258 -9999 0 -1.42 1 1
PLK1 -0.078 0.231 -9999 0 -9999 0 0
CDKN1B 0.05 0.154 -9999 0 -9999 0 0
FOXO3 -0.095 0.251 -9999 0 -0.718 2 2
KAT2B -0.009 0.025 -9999 0 -0.06 1 1
FOXO1/SIRT1 0.034 0.081 -9999 0 -9999 0 0
CAT -0.078 0.231 -9999 0 -9999 0 0
CTNNB1 -0.001 0.094 -9999 0 -0.526 1 1
AKT1 0.014 0.026 -9999 0 -9999 0 0
FOXO1 0.043 0.085 -9999 0 -0.427 1 1
MAPK10 -0.004 0.114 -9999 0 -0.414 1 1
mol:GTP 0.002 0.004 -9999 0 -9999 0 0
FOXO4 0.06 0.126 -9999 0 -9999 0 0
response to oxidative stress -0.005 0.031 -9999 0 -0.08 2 2
FOXO3A/SIRT1 -0.105 0.203 -9999 0 -0.604 2 2
XPO1 0.017 0.001 -9999 0 -9999 0 0
EP300 0.018 0.01 -9999 0 -9999 0 0
BCL2L11 0.012 0.039 -9999 0 -9999 0 0
FOXO1/SKP2 0.026 0.103 -9999 0 -9999 0 0
mol:GDP -0.005 0.031 -9999 0 -0.08 2 2
RAN 0.018 0.002 -9999 0 -9999 0 0
GADD45A -0.002 0.245 -9999 0 -1.085 1 1
YWHAQ 0.016 0 -9999 0 -9999 0 0
FOXO1/14-3-3 family 0.073 0.064 -9999 0 -9999 0 0
MST1 -0.065 0.206 -9999 0 -0.596 4 4
CSNK1D 0.016 0 -9999 0 -9999 0 0
CSNK1E 0.016 0 -9999 0 -9999 0 0
FOXO4/14-3-3 family 0.035 0.103 -9999 0 -9999 0 0
YWHAB 0.016 0 -9999 0 -9999 0 0
MAPK8 0.006 0.106 -9999 0 -0.413 1 1
MAPK9 0.005 0.106 -9999 0 -0.414 1 1
YWHAG 0.016 0 -9999 0 -9999 0 0
YWHAE 0.016 0 -9999 0 -9999 0 0
YWHAZ 0.016 0 -9999 0 -9999 0 0
SIRT1 0.019 0.022 -9999 0 -9999 0 0
SOD2 0.025 0.204 -9999 0 -0.699 1 1
RBL2 -0.055 0.291 -9999 0 -1.402 1 1
RAL/GDP -0.017 0.121 -9999 0 -0.378 3 3
CHUK 0.012 0.02 -9999 0 -9999 0 0
Ran/GTP 0.016 0.005 -9999 0 -9999 0 0
CSNK1G2 0.016 0 -9999 0 -9999 0 0
RAL/GTP -0.003 0.115 -9999 0 -0.342 3 3
CSNK1G1 0.016 0 -9999 0 -9999 0 0
FASLG -0.169 0.46 -9999 0 -0.992 6 6
SKP2 -0.018 0.131 -9999 0 -0.526 2 2
USP7 0.017 0.003 -9999 0 -9999 0 0
IKBKB 0.012 0.02 -9999 0 -9999 0 0
CCNB1 -0.244 0.513 -9999 0 -1.164 7 7
FOXO1-3a-4/beta catenin 0.026 0.199 -9999 0 -0.443 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.103 -9999 0 -9999 0 0
CSNK1A1 0.016 0 -9999 0 -9999 0 0
SGK1 -0.009 0.025 -9999 0 -0.06 1 1
CSNK1G3 0.016 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0.027 0.01 -9999 0 -9999 0 0
ZFAND5 0.068 0.111 -9999 0 -9999 0 0
SFN -0.058 0.23 -9999 0 -0.773 3 3
CDK2 0.019 0.015 -9999 0 -9999 0 0
FOXO3A/14-3-3 0.017 0.085 -9999 0 -9999 0 0
CREBBP 0.019 0.015 -9999 0 -9999 0 0
FBXO32 -0.183 0.387 -9999 0 -1.01 4 4
BCL6 -0.064 0.275 -9999 0 -0.865 2 2
RALB -0.041 0.185 -9999 0 -0.606 3 3
RALA 0.017 0.002 -9999 0 -9999 0 0
YWHAH 0.016 0 -9999 0 -9999 0 0
Signaling mediated by p38-gamma and p38-delta

Figure 110.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 112.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.037 0 -9999 0 -9999 0 0
SNTA1 0.016 0 -9999 0 -9999 0 0
response to hypoxia 0 0 -9999 0 -9999 0 0
STMN1 -0.031 0.178 -9999 0 -0.503 4 4
MAPK12 0.003 0.093 -9999 0 -9999 0 0
CCND1 -0.017 0.133 -9999 0 -0.692 1 1
p38 gamma/SNTA1 0.012 0.087 -9999 0 -9999 0 0
MAP2K3 0.016 0 -9999 0 -9999 0 0
PKN1 0.016 0 -9999 0 -9999 0 0
G2/M transition checkpoint 0.004 0.092 -9999 0 -9999 0 0
MAP2K6 0.003 0.087 -9999 0 -9999 0 0
MAPT 0.013 0.103 -9999 0 -0.541 1 1
MAPK13 0.029 0 -9999 0 -9999 0 0
hyperosmotic response 0 0 -9999 0 -9999 0 0
ZAK 0.014 0.044 -9999 0 -9999 0 0
Retinoic acid receptors-mediated signaling

Figure 111.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 113.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.016 0 -9999 0 -9999 0 0
HDAC3 0.016 0 -9999 0 -9999 0 0
VDR -0.058 0.23 -9999 0 -0.773 3 3
Cbp/p300/PCAF 0 0 -9999 0 -9999 0 0
EP300 0.016 0 -9999 0 -9999 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.035 0.052 -9999 0 -9999 0 0
KAT2B 0 0 -9999 0 -9999 0 0
MAPK14 0.016 0 -9999 0 -9999 0 0
AKT1 0.023 0.048 -9999 0 -9999 0 0
RAR alpha/9cRA/Cyclin H -0.027 0.075 -9999 0 -9999 0 0
mol:9cRA 0 0 -9999 0 -9999 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.021 0.075 -9999 0 -9999 0 0
CDC2 0 0.094 -9999 0 -0.525 1 1
response to UV 0.001 0.005 -9999 0 -9999 0 0
RAR alpha/Jnk1 -0.017 0.058 -9999 0 -9999 0 0
NCOR2 0.016 0 -9999 0 -9999 0 0
VDR/VDR/Vit D3 -0.056 0.174 -9999 0 -0.596 3 3
RXRs/RARs/NRIP1/9cRA 0.004 0.181 -9999 0 -0.524 3 3
NCOA2 0.016 0 -9999 0 -9999 0 0
NCOA3 0.016 0 -9999 0 -9999 0 0
NCOA1 -0.008 0.137 -9999 0 -0.773 1 1
VDR/VDR/DNA -0.058 0.23 -9999 0 -0.772 3 3
RARG 0.017 0.003 -9999 0 -9999 0 0
RAR gamma1/9cRA 0 0 -9999 0 -9999 0 0
MAPK3 0.017 0.003 -9999 0 -9999 0 0
MAPK1 0.016 0 -9999 0 -9999 0 0
MAPK8 0.017 0.003 -9999 0 -9999 0 0
mol:Vit D3 0 0 -9999 0 -9999 0 0
RXRs/VDR/DNA/Vit D3 -0.093 0.18 -9999 0 -0.554 3 3
RARA 0.011 0.084 -9999 0 -0.286 2 2
negative regulation of phosphoinositide 3-kinase cascade 0 0 -9999 0 -9999 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.03 0.059 -9999 0 -9999 0 0
PRKCA -0.023 0.164 -9999 0 -0.646 2 2
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.007 0.187 -9999 0 -0.548 3 3
RXRG -0.037 0.178 -9999 0 -0.477 4 4
RXRA 0.017 0.092 -9999 0 -9999 0 0
RXRB -0.001 0.116 -9999 0 -0.413 2 2
VDR/Vit D3/DNA -0.056 0.174 -9999 0 -0.596 3 3
RBP1 -0.025 0.164 -9999 0 -0.65 2 2
CRBP1/9-cic-RA -0.031 0.121 -9999 0 -0.489 2 2
RARB -0.006 0.138 -9999 0 -0.773 1 1
PRKCG -0.006 0.138 -9999 0 -0.772 1 1
MNAT1 0.016 0 -9999 0 -9999 0 0
RAR alpha/RXRs 0.005 0.178 -9999 0 -0.596 2 2
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.017 0.142 -9999 0 -0.45 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.03 0.072 -9999 0 -9999 0 0
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.007 0.187 -9999 0 -0.548 3 3
positive regulation of DNA binding -0.026 0.071 -9999 0 -9999 0 0
NRIP1 -0.026 0.269 -9999 0 -0.914 2 2
RXRs/RARs -0.009 0.17 -9999 0 -0.492 3 3
RXRs/RXRs/DNA/9cRA -0.061 0.159 -9999 0 -0.625 2 2
PRKACA 0.016 0 -9999 0 -9999 0 0
CDK7 0.016 0 -9999 0 -9999 0 0
TFIIH 0 0 -9999 0 -9999 0 0
RAR alpha/9cRA -0.012 0.04 -9999 0 -9999 0 0
CCNH 0.016 0 -9999 0 -9999 0 0
CREBBP 0.016 0 -9999 0 -9999 0 0
RAR gamma2/9cRA 0 0 -9999 0 -9999 0 0
Paxillin-dependent events mediated by a4b1

Figure 112.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 114.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.008 0.137 -9999 0 -0.773 1 1
Rac1/GDP 0 0 -9999 0 -9999 0 0
DOCK1 0.016 0 -9999 0 -9999 0 0
ITGA4 0.016 0 -9999 0 -9999 0 0
RAC1 0.016 0 -9999 0 -9999 0 0
alpha4/beta7 Integrin 0 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
CRK 0.016 0 -9999 0 -9999 0 0
alpha4/beta1 Integrin 0 0 -9999 0 -9999 0 0
alpha4/beta7 Integrin/Paxillin 0.041 0 -9999 0 -9999 0 0
lamellipodium assembly -0.017 0.081 -9999 0 -0.443 1 1
PIK3CA 0.016 0 -9999 0 -9999 0 0
PI3K -0.018 0.102 -9999 0 -0.586 1 1
ARF6 -0.001 0.094 -9999 0 -0.526 1 1
TLN1 0.016 0 -9999 0 -9999 0 0
PXN 0.029 0 -9999 0 -9999 0 0
PIK3R1 -0.008 0.137 -9999 0 -0.773 1 1
ARF6/GTP -0.007 0.037 -9999 0 -9999 0 0
cell adhesion 0 0 -9999 0 -9999 0 0
CRKL/CBL -0.018 0.102 -9999 0 -0.586 1 1
alpha4/beta1 Integrin/Paxillin 0.041 0 -9999 0 -9999 0 0
ITGB1 0.016 0 -9999 0 -9999 0 0
ITGB7 0.016 0 -9999 0 -9999 0 0
ARF6/GDP -0.016 0.09 -9999 0 -0.518 1 1
alpha4/beta1 Integrin/Paxillin/VCAM1 0.02 0.114 -9999 0 -0.42 2 2
p130Cas/Crk/Dock1 0 0 -9999 0 -9999 0 0
VCAM1 -0.033 0.191 -9999 0 -0.773 2 2
alpha4/beta1 Integrin/Paxillin/Talin 0.05 0 -9999 0 -9999 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.05 0 -9999 0 -9999 0 0
BCAR1 0.016 0 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
CBL 0.016 0 -9999 0 -9999 0 0
PRKACA 0.016 0 -9999 0 -9999 0 0
GIT1 0.016 0 -9999 0 -9999 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.05 0 -9999 0 -9999 0 0
Rac1/GTP -0.019 0.09 -9999 0 -0.495 1 1
Atypical NF-kappaB pathway

Figure 113.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 115.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0 -9999 0 -9999 0 0
FBXW11 0.016 0 -9999 0 -9999 0 0
NF kappa B1 p50/c-Rel 0.023 0.059 -9999 0 -9999 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.044 0.064 -9999 0 -9999 0 0
NFKBIA 0.019 0.072 -9999 0 -9999 0 0
MAPK14 0.016 0 -9999 0 -9999 0 0
NF kappa B1 p105/p50 0.033 0 -9999 0 -9999 0 0
ARRB2 0.022 0 -9999 0 -9999 0 0
REL -0.001 0.094 -9999 0 -0.526 1 1
response to oxidative stress 0 0 -9999 0 -9999 0 0
BCL3/NF kappa B1 p50 0.033 0 -9999 0 -9999 0 0
response to UV 0 0 -9999 0 -9999 0 0
NF kappa B1 p105/RelA 0.033 0 -9999 0 -9999 0 0
PIK3CA 0.016 0 -9999 0 -9999 0 0
NF kappa B1 p50 dimer 0.025 0 -9999 0 -9999 0 0
PIK3R1 -0.008 0.137 -9999 0 -0.773 1 1
NFKB1 0.029 0 -9999 0 -9999 0 0
RELA 0.016 0 -9999 0 -9999 0 0
positive regulation of anti-apoptosis 0.027 0.071 -9999 0 -9999 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.048 0.062 -9999 0 -9999 0 0
SRC 0.016 0 -9999 0 -9999 0 0
PI3K -0.018 0.102 -9999 0 -0.586 1 1
NF kappa B1 p50/RelA 0.027 0.071 -9999 0 -9999 0 0
IKBKB 0.016 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -9999 0 0
SYK -0.008 0.137 -9999 0 -0.773 1 1
I kappa B alpha/PIK3R1 0.012 0.102 -9999 0 -0.416 1 1
cell death 0.046 0.06 -9999 0 -9999 0 0
NF kappa B1 p105/c-Rel 0.023 0.059 -9999 0 -9999 0 0
LCK -0.008 0.137 -9999 0 -0.773 1 1
BCL3 0.016 0 -9999 0 -9999 0 0
IL2 signaling events mediated by PI3K

Figure 114.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 116.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.044 0.137 -9999 0 -0.626 1 1
UGCG 0.02 0.046 -9999 0 -9999 0 0
AKT1/mTOR/p70S6K/Hsp90/TERT 0.063 0.113 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
mol:glucosylceramide 0.02 0.045 -9999 0 -9999 0 0
mol:DAG -0.017 0.084 -9999 0 -9999 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.038 0.097 -9999 0 -0.478 1 1
FRAP1 0.054 0.158 -9999 0 -0.56 1 1
FOXO3 0.058 0.135 -9999 0 -0.452 1 1
AKT1 0.049 0.142 -9999 0 -0.491 1 1
GAB2 0.017 0.003 -9999 0 -9999 0 0
SMPD1 -0.003 0.131 -9999 0 -0.694 1 1
SGMS1 0 0.077 -9999 0 -9999 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -9999 0 0
mol:Ca2+ 0 0 -9999 0 -9999 0 0
mol:GDP 0.01 0.094 -9999 0 -0.512 1 1
CALM1 0.016 0 -9999 0 -9999 0 0
cell proliferation 0.031 0.087 -9999 0 -0.315 1 1
EIF3A 0.016 0 -9999 0 -9999 0 0
PI3K 0.011 0.108 -9999 0 -0.587 1 1
RPS6KB1 0.024 0.041 -9999 0 -9999 0 0
mol:sphingomyelin -0.017 0.084 -9999 0 -9999 0 0
natural killer cell activation 0.001 0.002 -9999 0 -9999 0 0
JAK3 0.02 0.002 -9999 0 -9999 0 0
PIK3R1 -0.005 0.138 -9999 0 -0.774 1 1
JAK1 -0.005 0.138 -9999 0 -0.774 1 1
NFKB1 0.016 0 -9999 0 -9999 0 0
MYC 0.06 0.125 -9999 0 -9999 0 0
MYB 0.009 0.117 -9999 0 -9999 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.043 0.138 -9999 0 -0.438 1 1
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.041 0.037 -9999 0 -9999 0 0
mol:PI-3-4-5-P3 0.043 0.135 -9999 0 -0.428 1 1
Rac1/GDP 0.019 0.087 -9999 0 -0.461 1 1
T cell proliferation 0.042 0.128 -9999 0 -0.401 1 1
SHC1 0 0.094 -9999 0 -0.524 1 1
RAC1 0.016 0 -9999 0 -9999 0 0
positive regulation of cyclin-dependent protein kinase activity 0.004 0.012 -9999 0 -0.044 2 2
PRKCZ 0.041 0.131 -9999 0 -0.416 1 1
NF kappa B1 p50/RelA -0.033 0.097 -9999 0 -0.471 1 1
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.032 0.149 -9999 0 -0.695 1 1
HSP90AA1 0.016 0 -9999 0 -9999 0 0
RELA 0.016 0 -9999 0 -9999 0 0
IL2RA -0.074 0.243 -9999 0 -0.71 4 4
IL2RB 0.02 0.002 -9999 0 -9999 0 0
TERT 0.016 0 -9999 0 -9999 0 0
E2F1 0.016 0.073 -9999 0 -9999 0 0
SOS1 0.017 0.003 -9999 0 -9999 0 0
RPS6 0.016 0 -9999 0 -9999 0 0
mol:cAMP -0.002 0.006 0.021 2 -9999 0 2
PTPN11 0.017 0.003 -9999 0 -9999 0 0
IL2RG 0.02 0.002 -9999 0 -9999 0 0
actin cytoskeleton organization 0.042 0.128 -9999 0 -0.401 1 1
GRB2 0.017 0.003 -9999 0 -9999 0 0
IL2 -0.005 0.137 -9999 0 -0.77 1 1
PIK3CA 0.02 0.002 -9999 0 -9999 0 0
Rac1/GTP 0.028 0.085 -9999 0 -0.44 1 1
LCK -0.005 0.138 -9999 0 -0.77 1 1
BCL2 0.046 0.18 -9999 0 -0.617 1 1
Regulation of p38-alpha and p38-beta

Figure 115.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 117.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0 -9999 0 -9999 0 0
response to insulin stimulus 0 0 -9999 0 -9999 0 0
RIPK1 0.016 0 -9999 0 -9999 0 0
response to stress 0 0 -9999 0 -9999 0 0
MAP2K6 -0.018 0.131 -9999 0 -0.526 2 2
mol:GTP 0 0 -9999 0 -9999 0 0
MAP2K4 0.016 0 -9999 0 -9999 0 0
RAC1-CDC42/GTP/PAK family -0.005 0.077 -9999 0 -9999 0 0
response to UV 0 0 -9999 0 -9999 0 0
YES1 0.016 0 -9999 0 -9999 0 0
interleukin-1 receptor activity 0 0 -9999 0 -9999 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -9999 0 0
MAP3K3 0.016 0 -9999 0 -9999 0 0
FYN 0.016 0 -9999 0 -9999 0 0
MAP3K12 0.016 0 -9999 0 -9999 0 0
FGR 0.016 0 -9999 0 -9999 0 0
p38 alpha/TAB1 -0.014 0.044 -9999 0 -9999 0 0
PRKG1 -0.008 0.137 -9999 0 -0.773 1 1
DUSP8 -0.008 0.137 -9999 0 -0.773 1 1
PGK/cGMP/p38 alpha -0.029 0.097 -9999 0 -0.531 1 1
apoptosis -0.016 0.041 -9999 0 -9999 0 0
RAL/GTP -0.036 0.114 -9999 0 -0.38 3 3
LYN 0.016 0 -9999 0 -9999 0 0
DUSP1 -0.075 0.244 -9999 0 -0.712 4 4
PAK1 0.016 0 -9999 0 -9999 0 0
SRC 0.016 0 -9999 0 -9999 0 0
RAC1/OSM/MEKK3/MKK3 0 0 -9999 0 -9999 0 0
TRAF6 0.016 0 -9999 0 -9999 0 0
RAC1 0.016 0 -9999 0 -9999 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -9999 0 0
mol:LPS 0 0 -9999 0 -9999 0 0
mol:cGMP 0 0 -9999 0 -9999 0 0
CCM2 0.016 0 -9999 0 -9999 0 0
RAC1-CDC42/GTP 0 0 -9999 0 -9999 0 0
MAPK11 0.03 0.098 -9999 0 -9999 0 0
BLK -0.025 0.164 -9999 0 -0.65 2 2
HCK -0.008 0.137 -9999 0 -0.773 1 1
MAP2K3 0.016 0 -9999 0 -9999 0 0
DUSP16 0.016 0 -9999 0 -9999 0 0
DUSP10 -0.008 0.137 -9999 0 -0.773 1 1
TRAF6/MEKK3 0 0 -9999 0 -9999 0 0
MAP3K7IP1 0.016 0 -9999 0 -9999 0 0
MAPK14 0.037 0.074 -9999 0 -9999 0 0
positive regulation of innate immune response 0.039 0.106 -9999 0 -9999 0 0
LCK -0.008 0.137 -9999 0 -0.773 1 1
p38alpha-beta/MKP7 0.046 0.103 -9999 0 -9999 0 0
p38alpha-beta/MKP5 0.033 0.118 -9999 0 -9999 0 0
PGK/cGMP -0.019 0.104 -9999 0 -0.596 1 1
PAK2 0.016 0 -9999 0 -9999 0 0
p38alpha-beta/MKP1 0.001 0.154 -9999 0 -9999 0 0
CDC42 0.016 0 -9999 0 -9999 0 0
RALB -0.042 0.186 -9999 0 -0.608 3 3
RALA 0.016 0 -9999 0 -9999 0 0
PAK3 -0.11 0.242 -9999 0 -0.561 7 7
Nongenotropic Androgen signaling

Figure 116.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 118.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.014 0 -9999 0 -9999 0 0
GNB1/GNG2 -0.033 0.121 -9999 0 -0.461 2 2
regulation of S phase of mitotic cell cycle 0.01 0.089 -9999 0 -9999 0 0
GNAO1 0.016 0 -9999 0 -9999 0 0
HRAS 0.016 0.001 -9999 0 -9999 0 0
SHBG/T-DHT 0.002 0.004 -9999 0 -9999 0 0
PELP1 0.016 0.001 -9999 0 -9999 0 0
AKT1 0.014 0 -9999 0 -9999 0 0
MAP2K1 0.026 0.087 -9999 0 -9999 0 0
T-DHT/AR -0.029 0.122 -9999 0 -0.488 2 2
G-protein coupled receptor activity 0 0 -9999 0 -9999 0 0
mol:GTP -0.001 0.002 -9999 0 -0.006 5 5
GNAI2 -0.009 0.137 -9999 0 -0.773 1 1
GNAI3 0.016 0 -9999 0 -9999 0 0
GNAI1 -0.009 0.137 -9999 0 -0.773 1 1
mol:GDP -0.033 0.113 -9999 0 -0.57 1 1
cell proliferation 0.024 0.124 -9999 0 -9999 0 0
PIK3CA 0.016 0 -9999 0 -9999 0 0
FOS -0.016 0.209 -9999 0 -0.856 1 1
mol:Ca2+ -0.006 0.017 -9999 0 -9999 0 0
MAPK3 0.027 0.103 -9999 0 -9999 0 0
MAPK1 0.017 0.067 -9999 0 -9999 0 0
PIK3R1 -0.008 0.137 -9999 0 -0.773 1 1
mol:IP3 0 0.002 -9999 0 -0.004 5 5
cAMP biosynthetic process 0.007 0.018 -9999 0 -9999 0 0
GNG2 -0.008 0.137 -9999 0 -0.773 1 1
potassium channel inhibitor activity 0 0.002 -9999 0 -0.004 5 5
HRAS/GTP -0.021 0.08 -9999 0 -0.406 1 1
actin cytoskeleton reorganization -0.013 0.07 -9999 0 -0.404 1 1
SRC 0.016 0.001 -9999 0 -9999 0 0
voltage-gated calcium channel activity 0 0.002 -9999 0 -0.004 5 5
PI3K -0.015 0.089 -9999 0 -0.511 1 1
apoptosis -0.015 0.118 0.37 1 -9999 0 1
T-DHT/AR/PELP1 -0.024 0.103 -9999 0 -0.51 1 1
HRAS/GDP -0.03 0.105 -9999 0 -0.533 1 1
CREB1 0.014 0.124 -9999 0 -0.395 1 1
RAC1-CDC42/GTP -0.013 0.071 -9999 0 -0.411 1 1
AR -0.026 0.164 -9999 0 -0.649 2 2
GNB1 0.016 0 -9999 0 -9999 0 0
RAF1 0.019 0.088 -9999 0 -9999 0 0
RAC1-CDC42/GDP -0.027 0.1 -9999 0 -0.509 1 1
T-DHT/AR/PELP1/Src -0.02 0.093 -9999 0 -0.46 1 1
MAP2K2 0.026 0.087 -9999 0 -9999 0 0
T-DHT/AR/PELP1/Src/PI3K 0.01 0.09 -9999 0 -9999 0 0
GNAZ 0.016 0 -9999 0 -9999 0 0
SHBG 0.016 0 -9999 0 -9999 0 0
Gi family/GNB1/GNG2/GDP 0.019 0.113 -9999 0 -0.486 1 1
mol:T-DHT 0 0.001 -9999 0 -0.002 5 5
RAC1 0.016 0 -9999 0 -9999 0 0
GNRH1 -0.005 0.106 -9999 0 -0.597 1 1
Gi family/GTP 0.004 0.078 -9999 0 -9999 0 0
CDC42 0.016 0 -9999 0 -9999 0 0
E-cadherin signaling in the nascent adherens junction

Figure 117.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 119.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.008 0.149 -9999 0 -0.549 2 2
KLHL20 -0.028 0.055 -9999 0 -9999 0 0
CYFIP2 -0.008 0.137 -9999 0 -0.773 1 1
Rac1/GDP 0.045 0.101 -9999 0 -9999 0 0
ENAH -0.019 0.175 -9999 0 -0.549 2 2
AP1M1 0.016 0 -9999 0 -9999 0 0
RAP1B 0.016 0 -9999 0 -9999 0 0
RAP1A 0.016 0 -9999 0 -9999 0 0
CTNNB1 -0.001 0.094 -9999 0 -0.526 1 1
CDC42/GTP -0.02 0.064 -9999 0 -9999 0 0
ABI1/Sra1/Nap1 -0.023 0.046 -9999 0 -9999 0 0
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.051 0.137 -9999 0 -0.452 3 3
RAPGEF1 0.027 0.13 -9999 0 -0.458 2 2
CTNND1 0.016 0 -9999 0 -9999 0 0
regulation of calcium-dependent cell-cell adhesion -0.042 0.141 -9999 0 -0.573 2 2
CRK 0.018 0.14 -9999 0 -0.506 2 2
E-cadherin/gamma catenin/alpha catenin -0.041 0.13 -9999 0 -0.501 2 2
alphaE/beta7 Integrin -0.018 0.102 -9999 0 -0.586 1 1
IQGAP1 0.016 0 -9999 0 -9999 0 0
NCKAP1 0.016 0 -9999 0 -9999 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -9999 0 0
DLG1 0.008 0.149 -9999 0 -0.549 2 2
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -9999 0 0
mol:PI-3-4-5-P3 -0.019 0.066 -9999 0 -0.333 1 1
MLLT4 0.016 0 -9999 0 -9999 0 0
ARF6/GTP/NME1/Tiam1 -0.015 0.067 -9999 0 -9999 0 0
PI3K -0.025 0.089 -9999 0 -0.456 1 1
ARF6 -0.001 0.094 -9999 0 -0.526 1 1
mol:Ca2+ 0 0 -9999 0 -9999 0 0
E-cadherin/gamma catenin -0.048 0.153 -9999 0 -0.514 3 3
TIAM1 -0.001 0.094 -9999 0 -0.526 1 1
E-cadherin(dimer)/Ca2+ -0.035 0.111 -9999 0 -0.429 2 2
AKT1 -0.013 0.046 -9999 0 -9999 0 0
PIK3R1 -0.008 0.137 -9999 0 -0.773 1 1
CDH1 -0.033 0.191 -9999 0 -0.773 2 2
RhoA/GDP 0.045 0.101 -9999 0 -9999 0 0
actin cytoskeleton organization -0.021 0.041 -9999 0 -9999 0 0
CDC42/GDP 0.045 0.101 -9999 0 -9999 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.003 0.091 -9999 0 -0.323 2 2
ITGB7 0.016 0 -9999 0 -9999 0 0
RAC1 0.016 0 -9999 0 -9999 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.037 0.117 -9999 0 -0.452 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin -0.035 0.113 -9999 0 -0.438 2 2
mol:GDP 0.038 0.116 -9999 0 -9999 0 0
CDC42/GTP/IQGAP1 0 0 -9999 0 -9999 0 0
JUP -0.001 0.094 -9999 0 -0.526 1 1
p120 catenin/RhoA/GDP -0.024 0.081 -9999 0 -9999 0 0
RAC1/GTP/IQGAP1 0 0 -9999 0 -9999 0 0
PIP5K1C/AP1M1 0 0 -9999 0 -9999 0 0
RHOA 0.016 0 -9999 0 -9999 0 0
CDC42 0.016 0 -9999 0 -9999 0 0
CTNNA1 0.016 0 -9999 0 -9999 0 0
positive regulation of S phase of mitotic cell cycle 0.009 0.079 -9999 0 -0.212 3 3
NME1 0.016 0 -9999 0 -9999 0 0
clathrin coat assembly 0 0 -9999 0 -9999 0 0
TJP1 0.008 0.149 -9999 0 -0.549 2 2
regulation of cell-cell adhesion -0.017 0.057 -9999 0 -9999 0 0
WASF2 -0.011 0.023 -9999 0 -9999 0 0
Rap1/GTP -0.023 0.074 -9999 0 -9999 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.047 0.127 -9999 0 -0.42 3 3
CCND1 0.008 0.097 -9999 0 -0.265 3 3
VAV2 0.021 0.14 -9999 0 -0.5 2 2
RAP1/GDP -0.018 0.08 -9999 0 -9999 0 0
adherens junction assembly 0.009 0.144 -9999 0 -0.529 2 2
homophilic cell adhesion 0 0 -9999 0 -9999 0 0
ABI1 0.016 0 -9999 0 -9999 0 0
PIP5K1C 0.016 0 -9999 0 -9999 0 0
regulation of heterotypic cell-cell adhesion -0.008 0.142 -9999 0 -9999 0 0
E-cadherin/beta catenin -0.031 0.115 -9999 0 -0.477 2 2
mol:GTP 0 0 -9999 0 -9999 0 0
SRC 0.004 0.148 -9999 0 -0.548 2 2
PIK3CA 0.016 0 -9999 0 -9999 0 0
Rac1/GTP -0.044 0.087 -9999 0 -9999 0 0
E-cadherin/beta catenin/alpha catenin -0.041 0.13 -9999 0 -0.501 2 2
ITGAE -0.008 0.137 -9999 0 -0.773 1 1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.043 0.145 -9999 0 -0.588 2 2
Sumoylation by RanBP2 regulates transcriptional repression

Figure 118.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 120.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.016 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -9999 0 0
MDM2/SUMO1 0.024 0.079 -9999 0 -0.415 1 1
HDAC4 0.016 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -9999 0 0
SUMO1 0.016 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1 0.021 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
XPO1 0.036 0 -9999 0 -9999 0 0
EntrezGene:23636 0 0 -9999 0 -9999 0 0
RAN 0.016 0 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.016 0 -9999 0 -9999 0 0
SUMO1/HDAC4 0.038 0 -9999 0 -9999 0 0
SUMO1/HDAC1 0.038 0 -9999 0 -9999 0 0
RANGAP1 0.016 0 -9999 0 -9999 0 0
MDM2/SUMO1/SUMO1 -0.022 0.09 -9999 0 -0.453 1 1
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.027 0 -9999 0 -9999 0 0
Ran/GTP 0.034 0 -9999 0 -9999 0 0
EntrezGene:23225 0 0 -9999 0 -9999 0 0
MDM2 -0.008 0.137 -9999 0 -0.773 1 1
UBE2I 0.016 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0.041 0 -9999 0 -9999 0 0
NPC 0 0 -9999 0 -9999 0 0
PIAS2 -0.001 0.094 -9999 0 -0.526 1 1
PIAS1 0.016 0 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 0 0
IL2 signaling events mediated by STAT5

Figure 119.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 121.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.017 0.003 -9999 0 -9999 0 0
ELF1 -0.019 0.123 -9999 0 -0.373 3 3
CCNA2 -0.035 0.158 -9999 0 -0.526 3 3
PIK3CA 0.017 0.003 -9999 0 -9999 0 0
JAK3 0.017 0.003 -9999 0 -9999 0 0
PIK3R1 -0.008 0.137 -9999 0 -0.773 1 1
JAK1 -0.008 0.137 -9999 0 -0.773 1 1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.034 0.136 -9999 0 -9999 0 0
SHC1 0 0.094 -9999 0 -0.525 1 1
SP1 0.026 0 -9999 0 -9999 0 0
IL2RA -0.073 0.308 -9999 0 -0.861 4 4
IL2RB 0.017 0.003 -9999 0 -9999 0 0
SOS1 0.017 0.003 -9999 0 -9999 0 0
IL2RG 0.017 0.003 -9999 0 -9999 0 0
G1/S transition of mitotic cell cycle 0.031 0.075 -9999 0 -9999 0 0
PTPN11 0.017 0.003 -9999 0 -9999 0 0
CCND2 0.039 0 -9999 0 -9999 0 0
LCK -0.008 0.137 -9999 0 -0.773 1 1
GRB2 0.017 0.003 -9999 0 -9999 0 0
IL2 -0.008 0.137 -9999 0 -0.773 1 1
CDK6 0.016 0 -9999 0 -9999 0 0
CCND3 0.038 0.139 -9999 0 -9999 0 0
Class I PI3K signaling events

Figure 120.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 122.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.037 0.092 -9999 0 -0.388 1 1
DAPP1 -0.014 0.125 -9999 0 -0.423 1 1
Src family/SYK family/BLNK-LAT/BTK-ITK 0.004 0.185 -9999 0 -0.523 3 3
mol:DAG 0.024 0.104 -9999 0 -0.253 1 1
HRAS 0.015 0.004 -9999 0 -9999 0 0
RAP1A 0.015 0.004 -9999 0 -9999 0 0
ARF5/GDP 0.01 0.092 -9999 0 -0.388 1 1
PLCG2 -0.025 0.164 -9999 0 -0.65 2 2
PLCG1 0.016 0 -9999 0 -9999 0 0
ARF5 -0.008 0.137 -9999 0 -0.773 1 1
mol:GTP -0.028 0.073 -9999 0 -9999 0 0
ARF1/GTP -0.026 0.068 -9999 0 -9999 0 0
RHOA 0.016 0 -9999 0 -9999 0 0
YES1 0.016 0 -9999 0 -9999 0 0
RAP1A/GTP -0.027 0.072 -9999 0 -9999 0 0
ADAP1 -0.026 0.07 -9999 0 -9999 0 0
ARAP3 -0.027 0.072 -9999 0 -9999 0 0
INPPL1 -0.008 0.137 -9999 0 -0.773 1 1
PREX1 -0.008 0.137 -9999 0 -0.773 1 1
ARHGEF6 0.016 0 -9999 0 -9999 0 0
ARHGEF7 0.016 0 -9999 0 -9999 0 0
ARF1 0.016 0 -9999 0 -9999 0 0
NRAS -0.018 0.13 -9999 0 -0.523 2 2
FYN 0.016 0 -9999 0 -9999 0 0
ARF6 -0.001 0.094 -9999 0 -0.526 1 1
FGR 0.016 0 -9999 0 -9999 0 0
mol:Ca2+ 0.026 0.057 -9999 0 -9999 0 0
mol:IP4 0 0 -9999 0 -9999 0 0
TIAM1 -0.001 0.094 -9999 0 -0.526 1 1
ZAP70 0.016 0 -9999 0 -9999 0 0
mol:IP3 0.029 0.076 -9999 0 -9999 0 0
LYN 0.016 0 -9999 0 -9999 0 0
ARF1/GDP 0.024 0.058 -9999 0 -9999 0 0
RhoA/GDP -0.026 0.059 -9999 0 -9999 0 0
PDK1/Src/Hsp90 -0.047 0.146 -9999 0 -0.501 3 3
BLNK -0.008 0.137 -9999 0 -0.773 1 1
actin cytoskeleton reorganization 0.02 0.086 -9999 0 -9999 0 0
SRC 0.016 0 -9999 0 -9999 0 0
PLEKHA2 0.008 0.093 -9999 0 -0.509 1 1
RAC1 0.016 0 -9999 0 -9999 0 0
PTEN 0.005 0.012 -9999 0 -9999 0 0
HSP90AA1 0.016 0 -9999 0 -9999 0 0
ARF6/GTP -0.032 0.075 -9999 0 -9999 0 0
RhoA/GTP -0.025 0.067 -9999 0 -9999 0 0
Src family/SYK family/BLNK-LAT 0.028 0.117 -9999 0 -0.449 1 1
BLK -0.025 0.164 -9999 0 -0.65 2 2
PDPK1 -0.058 0.23 -9999 0 -0.773 3 3
CYTH1 -0.026 0.07 -9999 0 -9999 0 0
HCK -0.008 0.137 -9999 0 -0.773 1 1
CYTH3 -0.026 0.07 -9999 0 -9999 0 0
CYTH2 -0.026 0.07 -9999 0 -9999 0 0
KRAS -0.018 0.13 -9999 0 -0.523 2 2
GO:0030676 0 0 -9999 0 -9999 0 0
FOXO3 -0.037 0.091 -9999 0 -0.421 1 1
SGK1 -0.041 0.1 -9999 0 -0.46 1 1
INPP5D 0 0 -9999 0 -9999 0 0
mol:GDP 0.015 0.06 -9999 0 -9999 0 0
SOS1 0.016 0 -9999 0 -9999 0 0
SYK -0.008 0.137 -9999 0 -0.773 1 1
ARF6/GDP -0.032 0.066 -9999 0 -9999 0 0
mol:PI-3-4-5-P3 -0.028 0.073 -9999 0 -9999 0 0
ARAP3/RAP1A/GTP -0.028 0.073 -9999 0 -9999 0 0
VAV1 -0.008 0.137 -9999 0 -0.773 1 1
mol:PI-3-4-P2 -0.005 0.106 -9999 0 -0.596 1 1
RAS family/GTP/PI3K Class I -0.001 0.085 -9999 0 -9999 0 0
PLEKHA1 0.008 0.093 -9999 0 -0.509 1 1
Rac1/GDP 0.024 0.058 -9999 0 -9999 0 0
LAT 0.016 0 -9999 0 -9999 0 0
Rac1/GTP 0.026 0.07 -9999 0 -9999 0 0
ITK -0.05 0.112 -9999 0 -0.401 2 2
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.02 0.137 -9999 0 -0.352 2 2
LCK -0.008 0.137 -9999 0 -0.773 1 1
BTK -0.05 0.112 -9999 0 -0.401 2 2
Arf6 trafficking events

Figure 121.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 123.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.016 0 -9999 0 -9999 0 0
CLTC 0.026 0.058 -9999 0 -9999 0 0
calcium ion-dependent exocytosis 0.029 0.028 -9999 0 -9999 0 0
Dynamin 2/GTP -0.009 0.048 -9999 0 -9999 0 0
EXOC4 0.016 0 -9999 0 -9999 0 0
CD59 0.01 0.081 -9999 0 -9999 0 0
CPE -0.035 0.141 -9999 0 -0.354 5 5
CTNNB1 -0.001 0.094 -9999 0 -0.526 1 1
membrane fusion 0.028 0.028 -9999 0 -9999 0 0
CTNND1 0.031 0.05 -9999 0 -9999 0 0
DNM2 0.016 0 -9999 0 -9999 0 0
mol:PI-4-5-P2 0.033 0.044 -9999 0 -9999 0 0
TSHR 0.002 0.082 -9999 0 -0.314 2 2
INS 0.017 0.035 -9999 0 -9999 0 0
BIN1 0.016 0 -9999 0 -9999 0 0
mol:Choline 0.028 0.028 -9999 0 -9999 0 0
growth hormone secretagogue receptor activity 0 0 -9999 0 -9999 0 0
mol:GDP 0.013 0.058 -9999 0 -0.312 1 1
membrane depolarization 0 0 -9999 0 -9999 0 0
ARF6 -0.001 0.094 -9999 0 -0.526 1 1
mol:Ca2+ -0.009 0.047 -9999 0 -9999 0 0
JUP 0.023 0.052 -9999 0 -9999 0 0
ASAP2/amphiphysin II -0.009 0.049 -9999 0 -0.284 1 1
ARF6/GTP -0.012 0.066 -9999 0 -0.382 1 1
CDH1 0.01 0.081 -9999 0 -9999 0 0
clathrin-independent pinocytosis -0.012 0.066 -9999 0 -0.381 1 1
MAPK8IP3 0.016 0 -9999 0 -9999 0 0
positive regulation of endocytosis -0.012 0.066 -9999 0 -0.381 1 1
EXOC2 0.016 0 -9999 0 -9999 0 0
substrate adhesion-dependent cell spreading 0.037 0.057 -9999 0 -9999 0 0
insulin receptor binding 0 0 -9999 0 -9999 0 0
SPAG9 0.016 0 -9999 0 -9999 0 0
regulation of calcium-dependent cell-cell adhesion 0.022 0.059 -9999 0 -9999 0 0
positive regulation of phagocytosis 0.013 0.058 -9999 0 -9999 0 0
ARF6/GTP/JIP3 -0.01 0.055 -9999 0 -0.314 1 1
ACAP1 0.025 0.024 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
CHRM2 0.009 0.075 -9999 0 -9999 0 0
clathrin heavy chain/ACAP1 0.033 0.051 -9999 0 -9999 0 0
JIP4/KLC1 -0.009 0.048 -9999 0 -9999 0 0
EXOC1 0.016 0 -9999 0 -9999 0 0
exocyst 0.037 0.057 -9999 0 -9999 0 0
RALA/GTP 0 0 -9999 0 -9999 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex -0.01 0.055 -9999 0 -9999 0 0
receptor recycling -0.012 0.066 -9999 0 -0.381 1 1
CTNNA1 0.031 0.05 -9999 0 -9999 0 0
NME1 0.013 0.059 -9999 0 -0.313 1 1
clathrin coat assembly 0.025 0.057 -9999 0 -9999 0 0
IL2RA -0.004 0.096 -9999 0 -9999 0 0
VAMP3 0.013 0.059 -9999 0 -9999 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.009 0.036 -9999 0 -9999 0 0
EXOC6 0.016 0 -9999 0 -9999 0 0
PLD1 -0.003 0.019 -9999 0 -9999 0 0
PLD2 -0.003 0.019 -9999 0 -9999 0 0
EXOC5 0.016 0 -9999 0 -9999 0 0
PIP5K1C 0.033 0.045 -9999 0 -9999 0 0
SDC1 0.028 0.045 -9999 0 -9999 0 0
ARF6/GDP 0.012 0.059 -9999 0 -0.314 1 1
EXOC7 -0.008 0.137 -9999 0 -0.773 1 1
E-cadherin/beta catenin -0.023 0.061 -9999 0 -9999 0 0
mol:Phosphatidic acid 0.028 0.028 -9999 0 -9999 0 0
endocytosis 0.009 0.049 0.282 1 -9999 0 1
SCAMP2 0.016 0 -9999 0 -9999 0 0
ADRB2 -0.039 0.158 -9999 0 -0.396 4 4
EXOC3 -0.001 0.094 -9999 0 -0.526 1 1
ASAP2 0 0 -9999 0 -9999 0 0
Dynamin 2/GDP 0.022 0.053 -9999 0 -9999 0 0
KLC1 0.016 0 -9999 0 -9999 0 0
AVPR2 0.025 0.071 -9999 0 -9999 0 0
RALA 0.016 0 -9999 0 -9999 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.02 0.052 -9999 0 -9999 0 0
S1P3 pathway

Figure 122.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 124.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.016 0 -9999 0 -9999 0 0
mol:S1P 0.002 0 -9999 0 -9999 0 0
S1P1/S1P/Gi 0.016 0.144 -9999 0 -0.709 1 1
GNAO1 0.019 0 -9999 0 -9999 0 0
S1P/S1P3/G12/G13 0.015 0.054 -9999 0 -0.283 1 1
AKT1 0.034 0.032 -9999 0 -9999 0 0
AKT3 0.041 0.074 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
PDGFB-D/PDGFRB 0.016 0 -9999 0 -9999 0 0
GNAI2 -0.006 0.137 -9999 0 -0.772 1 1
GNAI3 0.018 0 -9999 0 -9999 0 0
GNAI1 -0.006 0.137 -9999 0 -0.772 1 1
mol:GDP 0 0 -9999 0 -9999 0 0
S1PR3 0.002 0 -9999 0 -9999 0 0
S1PR2 0 0 -9999 0 -9999 0 0
EDG1 -0.008 0.137 -9999 0 -0.773 1 1
mol:Ca2+ 0.03 0.078 -9999 0 -0.302 1 1
MAPK3 0.038 0.075 -9999 0 -9999 0 0
MAPK1 0.038 0.075 -9999 0 -9999 0 0
JAK2 0.028 0.091 -9999 0 -9999 0 0
CXCR4 0.009 0.13 -9999 0 -0.406 2 2
FLT1 -0.005 0.138 -9999 0 -0.773 1 1
RhoA/GDP 0 0 -9999 0 -9999 0 0
Rac1/GDP 0 0 -9999 0 -9999 0 0
SRC 0.038 0.075 -9999 0 -9999 0 0
S1P/S1P3/Gi 0.03 0.079 -9999 0 -0.304 1 1
RAC1 0.016 0 -9999 0 -9999 0 0
RhoA/GTP 0.034 0.071 -9999 0 -9999 0 0
VEGFA -0.005 0.138 -9999 0 -0.773 1 1
S1P/S1P2/Gi 0.024 0.079 -9999 0 -0.311 1 1
VEGFR1 homodimer/VEGFA homodimer 0.001 0.191 -9999 0 -1.064 1 1
RHOA 0.016 0 -9999 0 -9999 0 0
S1P/S1P3/Gq -0.036 0.138 -9999 0 -0.374 4 4
GNAQ 0 0 -9999 0 -9999 0 0
GNAZ 0.018 0 -9999 0 -9999 0 0
G12/G13 -0.012 0.064 -9999 0 -0.37 1 1
GNA14 -0.075 0.244 -9999 0 -0.712 4 4
GNA15 -0.042 0.186 -9999 0 -0.608 3 3
GNA12 0.016 0 -9999 0 -9999 0 0
GNA13 -0.001 0.094 -9999 0 -0.526 1 1
GNA11 0.016 0 -9999 0 -9999 0 0
Rac1/GTP 0.034 0.071 -9999 0 -9999 0 0
Angiopoietin receptor Tie2-mediated signaling

Figure 123.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 125.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.066 0.169 -9999 0 -9999 0 0
NCK1/PAK1/Dok-R -0.037 0.101 -9999 0 -0.45 1 1
NCK1/Dok-R 0.032 0.163 -9999 0 -9999 0 0
PIK3CA 0.016 0 -9999 0 -9999 0 0
mol:beta2-estradiol -0.015 0.004 -9999 0 -9999 0 0
RELA 0.016 0 -9999 0 -9999 0 0
SHC1 0 0.094 -9999 0 -0.524 1 1
Rac/GDP 0 0 -9999 0 -9999 0 0
F2 0.003 0.009 -9999 0 -9999 0 0
TNIP2 0.016 0 -9999 0 -9999 0 0
NF kappa B/RelA -0.011 0.036 -9999 0 -9999 0 0
FN1 -0.084 0.238 -9999 0 -0.625 5 5
PLD2 0.069 0.071 -9999 0 -9999 0 0
PTPN11 0.016 0 -9999 0 -9999 0 0
GRB14 -0.183 0.324 -9999 0 -0.691 9 9
ELK1 0.08 0.066 -9999 0 -9999 0 0
GRB7 0.016 0 -9999 0 -9999 0 0
PAK1 0.016 0 -9999 0 -9999 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.068 0.164 -9999 0 -9999 0 0
CDKN1A 0.063 0.197 -9999 0 -0.674 2 2
ITGA5 -0.018 0.131 -9999 0 -0.526 2 2
mol:GTP 0 0 -9999 0 -9999 0 0
RasGAP/Dok-R 0.024 0.166 -9999 0 -9999 0 0
CRK 0.016 0 -9999 0 -9999 0 0
mol:NO 0.047 0.162 -9999 0 -9999 0 0
PLG 0.069 0.071 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
chemokinesis 0.067 0.136 -9999 0 -9999 0 0
GRB2 0.016 0 -9999 0 -9999 0 0
PIK3R1 -0.008 0.138 -9999 0 -0.773 1 1
ANGPT2 -0.025 0.333 -9999 0 -1.286 2 2
BMX 0.046 0.111 -9999 0 -9999 0 0
ANGPT1 0.025 0.088 -9999 0 -9999 0 0
tube development 0.053 0.221 -9999 0 -0.78 2 2
ANGPT4 -0.008 0.138 -9999 0 -0.775 1 1
response to hypoxia 0.004 0.009 -9999 0 -9999 0 0
Tie2/Ang1/GRB14 -0.045 0.181 -9999 0 -9999 0 0
alpha5/beta1 Integrin -0.023 0.09 -9999 0 -0.37 2 2
FGF2 -0.001 0.095 -9999 0 -0.528 1 1
STAT5A (dimer) 0.055 0.254 -9999 0 -0.904 2 2
mol:L-citrulline 0.047 0.162 -9999 0 -9999 0 0
AGTR1 -0.025 0.168 -9999 0 -0.665 2 2
MAPK14 0.069 0.095 -9999 0 -9999 0 0
Tie2/SHP2 -0.003 0.01 -9999 0 -9999 0 0
TEK 0.058 0.036 -9999 0 -9999 0 0
RPS6KB1 0.072 0.143 -9999 0 -9999 0 0
Angiotensin II/AT1 -0.016 0.13 -9999 0 -0.513 2 2
Tie2/Ang1/GRB2 0.066 0.071 -9999 0 -9999 0 0
MAPK3 0.075 0.068 -9999 0 -9999 0 0
MAPK1 0.075 0.068 -9999 0 -9999 0 0
Tie2/Ang1/GRB7 0.066 0.071 -9999 0 -9999 0 0
NFKB1 0.016 0 -9999 0 -9999 0 0
MAPK8 0.069 0.071 -9999 0 -9999 0 0
PI3K 0.064 0.154 -9999 0 -9999 0 0
FES 0.068 0.096 -9999 0 -9999 0 0
Crk/Dok-R 0.032 0.163 -9999 0 -9999 0 0
Tie2/Ang1/ABIN2 0.066 0.071 -9999 0 -9999 0 0
blood circulation 0 0 -9999 0 -9999 0 0
negative regulation of caspase activity 0.067 0.159 -9999 0 -9999 0 0
STAT5A 0.017 0 -9999 0 -9999 0 0
mol:ROS 0 0 -9999 0 -9999 0 0
PTK2 0.072 0.143 -9999 0 -9999 0 0
Tie2/Ang2 0.03 0.305 -9999 0 -1.132 2 2
Tie2/Ang1 0.063 0.075 -9999 0 -9999 0 0
FOXO1 0.064 0.188 -9999 0 -0.706 1 1
ELF1 0.028 0.002 -9999 0 -9999 0 0
ELF2 0.064 0.072 -9999 0 -9999 0 0
mol:Choline 0.069 0.07 -9999 0 -9999 0 0
cell migration -0.031 0.06 -9999 0 -9999 0 0
FYN 0.048 0.253 -9999 0 -0.909 2 2
DOK2 -0.058 0.23 -9999 0 -0.773 3 3
negative regulation of cell cycle 0.065 0.18 -9999 0 -0.607 2 2
ETS1 -0.012 0.166 -9999 0 -0.644 2 2
PXN 0.079 0.13 -9999 0 -9999 0 0
ITGB1 0.016 0 -9999 0 -9999 0 0
NOS3 0.045 0.174 -9999 0 -9999 0 0
RAC1 0.016 0 -9999 0 -9999 0 0
TNF -0.011 0.167 -9999 0 -0.646 2 2
MAPKKK cascade 0.069 0.07 -9999 0 -9999 0 0
RASA1 -0.001 0.094 -9999 0 -0.526 1 1
Tie2/Ang1/Shc 0.06 0.085 -9999 0 -9999 0 0
NCK1 0.016 0 -9999 0 -9999 0 0
vasculogenesis 0.048 0.152 -9999 0 -9999 0 0
mol:Phosphatidic acid 0.069 0.07 -9999 0 -9999 0 0
mol:Angiotensin II 0.001 0.006 -9999 0 -9999 0 0
mol:NADP 0.047 0.162 -9999 0 -9999 0 0
Rac1/GTP -0.031 0.101 -9999 0 -9999 0 0
MMP2 0.038 0.151 -9999 0 -9999 0 0
Rapid glucocorticoid signaling

Figure 124.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 126.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.035 0.157 -9999 0 -0.87 1 1
MAPK9 0.011 0 -9999 0 -9999 0 0
adrenocorticotropin secretion -0.011 0.096 -9999 0 -0.382 2 2
GNB1/GNG2 -0.016 0.089 -9999 0 -0.511 1 1
GNB1 0.016 0 -9999 0 -9999 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
MAPK14 0.011 0 -9999 0 -9999 0 0
Gs family/GTP -0.024 0.097 -9999 0 -0.388 2 2
EntrezGene:2778 0 0 -9999 0 -9999 0 0
vasopressin secretion 0 0 -9999 0 -9999 0 0
G-protein coupled receptor activity 0 0 -9999 0 -9999 0 0
ChemicalAbstracts:86-01-1 0 0 -9999 0 -9999 0 0
glutamate secretion 0.006 0.023 0.094 2 -9999 0 2
GNAL -0.025 0.164 -9999 0 -0.65 2 2
GNG2 -0.008 0.137 -9999 0 -0.773 1 1
CRH -0.018 0.131 -9999 0 -0.526 2 2
mol:cortisol 0 0 -9999 0 -9999 0 0
MAPK8 0.011 0 -9999 0 -9999 0 0
MAPK11 0.011 0 -9999 0 -9999 0 0
Neurotrophic factor-mediated Trk receptor signaling

Figure 125.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 127.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.008 0.137 -9999 0 -0.773 1 1
RAS family/GTP/Tiam1 -0.003 0.09 -9999 0 -9999 0 0
NT3 (dimer)/TRKC -0.039 0.165 -9999 0 -0.626 2 2
NT3 (dimer)/TRKB -0.043 0.152 -9999 0 -0.784 1 1
SHC/Grb2/SOS1/GAB1/PI3K 0.019 0.09 -9999 0 -9999 0 0
RAPGEF1 0.016 0 -9999 0 -9999 0 0
BDNF -0.118 0.259 -9999 0 -0.596 7 7
PIK3CA 0.016 0 -9999 0 -9999 0 0
DYNLT1 0.016 0 -9999 0 -9999 0 0
NTRK1 0.016 0 -9999 0 -9999 0 0
NTRK2 -0.018 0.131 -9999 0 -0.526 2 2
NTRK3 -0.001 0.094 -9999 0 -0.526 1 1
NT-4/5 (dimer)/TRKB -0.02 0.076 -9999 0 -0.314 2 2
neuron apoptosis 0.164 0.211 0.498 8 -9999 0 8
SHC 2-3/Grb2 -0.155 0.254 -9999 0 -0.551 8 8
SHC1 -0.001 0.094 -9999 0 -0.526 1 1
SHC2 -0.106 0.208 -9999 0 -0.637 4 4
SHC3 -0.168 0.267 -9999 0 -0.744 5 5
STAT3 (dimer) -0.003 0.092 -9999 0 -0.373 1 1
NT3 (dimer)/TRKA -0.025 0.1 -9999 0 -0.501 1 1
RIN/GDP 0.028 0.082 -9999 0 -9999 0 0
GIPC1 0.016 0 -9999 0 -9999 0 0
KRAS -0.018 0.131 -9999 0 -0.526 2 2
DNAJA3 -0.007 0.038 -9999 0 -9999 0 0
RIN/GTP 0 0 -9999 0 -9999 0 0
CCND1 -0.026 0.214 -9999 0 -0.649 3 3
MAGED1 0.016 0 -9999 0 -9999 0 0
PTPN11 0.016 0 -9999 0 -9999 0 0
RICS -0.008 0.137 -9999 0 -0.773 1 1
NT-4/5 (dimer) 0 0 -9999 0 -9999 0 0
SHC/GRB2/SOS1 -0.009 0.053 -9999 0 -9999 0 0
GRB2 0.016 0 -9999 0 -9999 0 0
NGF (dimer)/TRKA/MATK 0 0 -9999 0 -9999 0 0
TRKA/NEDD4-2 -0.023 0.09 -9999 0 -0.37 2 2
ELMO1 -0.008 0.137 -9999 0 -0.773 1 1
RhoG/GTP/ELMO1/DOCK1 -0.016 0.089 -9999 0 -0.511 1 1
NGF 0 0 -9999 0 -9999 0 0
HRAS 0.016 0 -9999 0 -9999 0 0
DOCK1 0.016 0 -9999 0 -9999 0 0
GAB2 0.016 0 -9999 0 -9999 0 0
RIT2 0.016 0 -9999 0 -9999 0 0
RIT1 -0.025 0.164 -9999 0 -0.65 2 2
FRS2 -0.008 0.137 -9999 0 -0.773 1 1
DNM1 0.016 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
CRK 0.016 0 -9999 0 -9999 0 0
SH2B1 (homopentamer) 0 0 -9999 0 -9999 0 0
RhoG/GTP -0.019 0.079 -9999 0 -0.406 1 1
mol:GDP 0.024 0.115 -9999 0 -9999 0 0
NGF (dimer) 0 0 -9999 0 -9999 0 0
RhoG/GDP -0.019 0.104 -9999 0 -0.596 1 1
RIT1/GDP 0.013 0.103 -9999 0 -9999 0 0
TIAM1 -0.001 0.094 -9999 0 -0.526 1 1
PIK3R1 -0.008 0.137 -9999 0 -0.773 1 1
BDNF (dimer)/TRKB -0.098 0.162 -9999 0 -0.501 2 2
KIDINS220/CRKL/C3G -0.018 0.102 -9999 0 -0.586 1 1
SHC/RasGAP -0.023 0.09 -9999 0 -9999 0 0
FRS2 family/SHP2 -0.016 0.087 -9999 0 -0.501 1 1
SHC/GRB2/SOS1/GAB1 -0.022 0.09 -9999 0 -0.453 1 1
RIT1/GTP -0.031 0.121 -9999 0 -0.489 2 2
NT3 (dimer) -0.025 0.164 -9999 0 -0.648 2 2
RAP1/GDP -0.018 0.048 -9999 0 -9999 0 0
KIDINS220/CRKL -0.008 0.137 -9999 0 -0.772 1 1
BDNF (dimer) -0.118 0.258 -9999 0 -0.595 7 7
ubiquitin-dependent protein catabolic process -0.02 0.076 -9999 0 -0.313 2 2
Schwann cell development -0.025 0.029 -9999 0 -9999 0 0
EHD4 0.016 0 -9999 0 -9999 0 0
FRS2 family/GRB2/SOS1 -0.014 0.079 -9999 0 -0.453 1 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.031 0.078 -9999 0 -9999 0 0
RAP1B 0.016 0 -9999 0 -9999 0 0
RAP1A 0.016 0 -9999 0 -9999 0 0
CDC42/GTP -0.092 0.173 -9999 0 -0.83 1 1
ABL1 0.016 0 -9999 0 -9999 0 0
SH2B family/GRB2/SOS1 0 0 -9999 0 -9999 0 0
Rap1/GTP -0.042 0.087 -9999 0 -0.456 1 1
STAT3 -0.003 0.092 -9999 0 -0.373 1 1
axon guidance -0.088 0.164 -9999 0 -0.775 1 1
MAPK3 0.032 0 -9999 0 -9999 0 0
MAPK1 0.032 0 -9999 0 -9999 0 0
CDC42/GDP 0.028 0.082 -9999 0 -9999 0 0
NTF3 -0.025 0.164 -9999 0 -0.65 2 2
NTF4 0 0 -9999 0 -9999 0 0
NGF (dimer)/TRKA/FAIM 0 0 -9999 0 -9999 0 0
PI3K -0.018 0.102 -9999 0 -0.586 1 1
FRS3 0.016 0 -9999 0 -9999 0 0
FAIM 0.016 0 -9999 0 -9999 0 0
GAB1 -0.008 0.137 -9999 0 -0.773 1 1
RASGRF1 -0.114 0.192 -9999 0 -0.452 7 7
SOS1 0.016 0 -9999 0 -9999 0 0
MCF2L -0.001 0.152 -9999 0 -0.78 1 1
RGS19 0.016 0 -9999 0 -9999 0 0
CDC42 0.016 0 -9999 0 -9999 0 0
RAS family/GTP -0.003 0.097 -9999 0 -9999 0 0
Rac1/GDP 0.028 0.082 -9999 0 -9999 0 0
NGF (dimer)/TRKA/GRIT -0.016 0.089 -9999 0 -0.511 1 1
neuron projection morphogenesis 0.022 0.059 -9999 0 -9999 0 0
NGF (dimer)/TRKA/NEDD4-2 -0.02 0.076 -9999 0 -0.314 2 2
MAP2K1 0.026 0.094 -9999 0 -0.417 1 1
NGFR 0.016 0 -9999 0 -9999 0 0
NGF (dimer)/TRKA/GIPC/GAIP 0.039 0 -9999 0 -9999 0 0
RAS family/GTP/PI3K 0.004 0.085 -9999 0 -0.313 1 1
FRS2 family/SHP2/GRB2/SOS1 -0.013 0.073 -9999 0 -0.42 1 1
NRAS -0.018 0.131 -9999 0 -0.526 2 2
GRB2/SOS1 0 0 -9999 0 -9999 0 0
PRKCI 0.016 0 -9999 0 -9999 0 0
ChemicalAbstracts:146-91-8 0 0 -9999 0 -9999 0 0
RAC1 0.016 0 -9999 0 -9999 0 0
PRKCZ 0 0 -9999 0 -9999 0 0
MAPKKK cascade -0.038 0.045 -9999 0 -9999 0 0
RASA1 -0.001 0.094 -9999 0 -0.526 1 1
TRKA/c-Abl 0 0 -9999 0 -9999 0 0
SQSTM1 -0.001 0.094 -9999 0 -0.526 1 1
BDNF (dimer)/TRKB/GIPC -0.086 0.144 -9999 0 -0.453 2 2
NGF (dimer)/TRKA/p62/Atypical PKCs -0.008 0.045 -9999 0 -9999 0 0
MATK 0.016 0 -9999 0 -9999 0 0
NEDD4L -0.018 0.131 -9999 0 -0.526 2 2
RAS family/GDP -0.028 0.051 -9999 0 -9999 0 0
NGF (dimer)/TRKA -0.007 0.041 -9999 0 -9999 0 0
Rac1/GTP -0.079 0.109 -9999 0 -0.333 2 2
FRS2 family/SHP2/CRK family -0.026 0.102 -9999 0 -9999 0 0
PDGFR-beta signaling pathway

Figure 126.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 128.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.003 0.14 -9999 0 -0.443 2 2
PDGFB-D/PDGFRB/SLAP -0.011 0.125 -9999 0 -0.481 2 2
PDGFB-D/PDGFRB/APS/CBL 0.001 0.004 -9999 0 -9999 0 0
AKT1 0.043 0.102 -9999 0 -9999 0 0
mol:PI-4-5-P2 0 0 -9999 0 -9999 0 0
mol:Sphingosine-1-phosphate 0.006 0.12 -9999 0 -0.454 1 1
PIK3CA 0.016 0 -9999 0 -9999 0 0
FGR -0.001 0.015 -9999 0 -9999 0 0
mol:Ca2+ 0.035 0.043 -9999 0 -9999 0 0
MYC 0.056 0.068 -9999 0 -9999 0 0
SHC1 -0.001 0.094 -9999 0 -0.526 1 1
HRAS/GDP 0.038 0.048 -9999 0 -9999 0 0
LRP1/PDGFRB/PDGFB -0.01 0.053 -9999 0 -9999 0 0
GRB10 -0.042 0.186 -9999 0 -0.608 3 3
PTPN11 0.016 0 -9999 0 -9999 0 0
GO:0007205 0.034 0.043 -9999 0 -9999 0 0
PTEN 0.016 0 -9999 0 -9999 0 0
GRB2 0.016 0 -9999 0 -9999 0 0
GRB7 0.016 0 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/SHP2 0.021 0.01 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/GRB10 -0.023 0.139 -9999 0 -0.445 3 3
cell cycle arrest -0.011 0.125 -9999 0 -0.48 2 2
HRAS 0.016 0 -9999 0 -9999 0 0
HIF1A 0.035 0.107 -9999 0 -9999 0 0
GAB1 0.027 0.079 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
DNM2 0.028 0.088 -9999 0 -9999 0 0
PDGFB-D/PDGFRB 0.004 0.012 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.021 0.01 -9999 0 -9999 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.046 0.124 -9999 0 -0.474 2 2
positive regulation of MAPKKK cascade 0.021 0.01 -9999 0 -9999 0 0
PIK3R1 -0.008 0.137 -9999 0 -0.773 1 1
mol:IP3 0.035 0.043 -9999 0 -9999 0 0
E5 0 0.002 -9999 0 -9999 0 0
CSK 0.015 0.001 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/GRB7 0.021 0.01 -9999 0 -9999 0 0
SHB 0.016 0 -9999 0 -9999 0 0
BLK -0.025 0.105 -9999 0 -0.583 1 1
PTPN2 0.017 0.002 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/SNX15 0.021 0.01 -9999 0 -9999 0 0
BCAR1 0.016 0 -9999 0 -9999 0 0
VAV2 0.035 0.086 -9999 0 -9999 0 0
CBL 0.016 0 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/DEP1 0.021 0.01 -9999 0 -9999 0 0
LCK -0.025 0.142 -9999 0 -0.814 1 1
PDGFRB 0.016 0.005 -9999 0 -9999 0 0
ACP1 0.016 0 -9999 0 -9999 0 0
HCK -0.024 0.143 -9999 0 -0.814 1 1
ABL1 0.03 0.062 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/CBL 0.031 0.072 -9999 0 -9999 0 0
PTPN1 0.017 0.002 -9999 0 -9999 0 0
SNX15 0.016 0 -9999 0 -9999 0 0
STAT3 0.016 0 -9999 0 -9999 0 0
STAT1 -0.008 0.137 -9999 0 -0.773 1 1
cell proliferation 0.055 0.065 -9999 0 -9999 0 0
SLA -0.025 0.164 -9999 0 -0.65 2 2
actin cytoskeleton reorganization 0.054 0.026 -9999 0 -9999 0 0
SRC -0.001 0.014 -9999 0 -9999 0 0
PI3K -0.028 0.09 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/GRB7/SHC -0.009 0.053 -9999 0 -9999 0 0
SH2B2 0 0 -9999 0 -9999 0 0
PLCgamma1/SPHK1 0.006 0.123 -9999 0 -0.469 1 1
LYN 0 0.014 -9999 0 -9999 0 0
LRP1 0.016 0 -9999 0 -9999 0 0
SOS1 0.016 0 -9999 0 -9999 0 0
STAT5B 0.016 0 -9999 0 -9999 0 0
STAT5A 0.016 0 -9999 0 -9999 0 0
NCK1-2/p130 Cas 0.002 0.01 -9999 0 -9999 0 0
SPHK1 -0.075 0.218 -9999 0 -0.574 5 5
EDG1 -0.008 0.138 -9999 0 -0.775 1 1
mol:DAG 0.035 0.043 -9999 0 -9999 0 0
PLCG1 0.035 0.044 -9999 0 -9999 0 0
NHERF/PDGFRB -0.025 0.101 -9999 0 -0.503 1 1
YES1 -0.001 0.014 -9999 0 -9999 0 0
cell migration -0.025 0.1 -9999 0 -0.5 1 1
SHC/Grb2/SOS1 -0.005 0.04 -9999 0 -9999 0 0
SLC9A3R2 -0.008 0.137 -9999 0 -0.773 1 1
SLC9A3R1 -0.001 0.094 -9999 0 -0.526 1 1
NHERF1-2/PDGFRB/PTEN -0.018 0.092 -9999 0 -0.453 1 1
FYN 0 0.014 -9999 0 -9999 0 0
DOK1 0.041 0.004 -9999 0 -9999 0 0
HRAS/GTP 0 0 -9999 0 -9999 0 0
PDGFB -0.001 0.094 -9999 0 -0.526 1 1
RAC1 0.051 0.08 -9999 0 -9999 0 0
PRKCD 0.042 0.005 -9999 0 -9999 0 0
FER 0.042 0.005 -9999 0 -9999 0 0
MAPKKK cascade -0.003 0.045 -9999 0 -9999 0 0
RASA1 0.032 0.054 -9999 0 -9999 0 0
NCK1 0.016 0 -9999 0 -9999 0 0
NCK2 0.016 0 -9999 0 -9999 0 0
p62DOK/Csk 0.014 0.022 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/SHB 0.021 0.01 -9999 0 -9999 0 0
chemotaxis 0.03 0.061 -9999 0 -9999 0 0
STAT1-3-5/STAT1-3-5 -0.012 0.068 -9999 0 -9999 0 0
Bovine Papilomavirus E5/PDGFRB 0.011 0.006 -9999 0 -9999 0 0
PTPRJ 0.016 0 -9999 0 -9999 0 0
S1P4 pathway

Figure 127.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 129.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -9999 0 0
GNAO1 0.016 0 -9999 0 -9999 0 0
CDC42/GTP -0.016 0.062 -9999 0 -9999 0 0
PLCG1 0.025 0.075 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
GNAI2 -0.008 0.137 -9999 0 -0.773 1 1
GNAI3 0.016 0 -9999 0 -9999 0 0
G12/G13 -0.012 0.064 -9999 0 -0.37 1 1
cell migration -0.016 0.061 -9999 0 -9999 0 0
S1PR5 0 0 -9999 0 -9999 0 0
S1PR4 0 0 -9999 0 -9999 0 0
MAPK3 0.025 0.075 -9999 0 -9999 0 0
MAPK1 0.025 0.075 -9999 0 -9999 0 0
S1P/S1P5/Gi 0.016 0.079 -9999 0 -0.318 1 1
GNAI1 -0.008 0.137 -9999 0 -0.773 1 1
CDC42/GDP 0 0 -9999 0 -9999 0 0
S1P/S1P5/G12 0 0 -9999 0 -9999 0 0
RHOA 0.021 0.05 -9999 0 -9999 0 0
S1P/S1P4/Gi 0.016 0.079 -9999 0 -0.318 1 1
mol:GDP 0 0 -9999 0 -9999 0 0
GNAZ 0.016 0 -9999 0 -9999 0 0
S1P/S1P4/G12/G13 -0.009 0.05 -9999 0 -0.285 1 1
GNA12 0.016 0 -9999 0 -9999 0 0
GNA13 -0.001 0.094 -9999 0 -0.526 1 1
CDC42 0.016 0 -9999 0 -9999 0 0
p38 MAPK signaling pathway

Figure 128.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 130.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.01 0.055 -9999 0 -0.315 1 1
TRAF2/ASK1 0 0 -9999 0 -9999 0 0
ATM -0.008 0.137 -9999 0 -0.773 1 1
MAP2K3 0.015 0.107 -9999 0 -0.401 1 1
response to stress 0 0 -9999 0 -9999 0 0
MAP2K6 0.011 0.108 -9999 0 -0.351 2 2
hyperosmotic response 0 0 -9999 0 -9999 0 0
response to oxidative stress 0 0 -9999 0 -9999 0 0
GADD45G -0.124 0.295 -9999 0 -0.732 6 6
TXN 0.011 0 -9999 0 -9999 0 0
CALM1 0.016 0 -9999 0 -9999 0 0
GADD45A -0.025 0.164 -9999 0 -0.65 2 2
GADD45B -0.025 0.164 -9999 0 -0.65 2 2
MAP3K1 -0.001 0.094 -9999 0 -0.526 1 1
MAP3K6 0.016 0 -9999 0 -9999 0 0
MAP3K7 0.016 0 -9999 0 -9999 0 0
MAP3K4 0.016 0 -9999 0 -9999 0 0
mol:Ca2+ 0 0 -9999 0 -9999 0 0
ASK1/ASK2 0 0 -9999 0 -9999 0 0
TAK1/TAB family -0.016 0.089 -9999 0 -0.511 1 1
RAC1/OSM/MEKK3 0 0 -9999 0 -9999 0 0
TRAF2 0.016 0 -9999 0 -9999 0 0
RAC1/OSM/MEKK3/MKK3 -0.022 0.065 -9999 0 -9999 0 0
TRAF6 0.008 0.078 -9999 0 -0.427 1 1
RAC1 0.016 0 -9999 0 -9999 0 0
mol:LPS 0 0 -9999 0 -9999 0 0
CAMK2B -0.059 0.203 -9999 0 -0.588 4 4
CCM2 0.016 0 -9999 0 -9999 0 0
CaM/Ca2+/CAMKIIB -0.045 0.124 -9999 0 -0.511 1 1
MAPK11 0.016 0 -9999 0 -9999 0 0
response to DNA damage stimulus 0 0 -9999 0 -9999 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.04 0.11 -9999 0 -0.462 1 1
OSM/MEKK3 0 0 -9999 0 -9999 0 0
TAOK1 0.008 0.078 -9999 0 -0.427 1 1
TAOK2 0.008 0.078 -9999 0 -0.427 1 1
TAOK3 -0.021 0.131 -9999 0 -0.428 3 3
MAP3K7IP1 0.016 0 -9999 0 -9999 0 0
MAPK14 0.016 0 -9999 0 -9999 0 0
MAP3K7IP2 -0.008 0.137 -9999 0 -0.773 1 1
MAP3K5 0.016 0 -9999 0 -9999 0 0
MAP3K10 0.016 0 -9999 0 -9999 0 0
MAP3K3 0.016 0 -9999 0 -9999 0 0
TRX/ASK1 0.02 0 -9999 0 -9999 0 0
GADD45/MTK1/MTK1 -0.118 0.254 -9999 0 -0.586 6 6
Arf1 pathway

Figure 129.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 131.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0 -9999 0 -9999 0 0
EntrezGene:79658 0 0 -9999 0 -9999 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.022 0 -9999 0 -9999 0 0
AP2 -0.03 0.119 -9999 0 -0.478 2 2
mol:DAG 0 0 -9999 0 -9999 0 0
Arfaptin 2/Rac/GTP 0 0 -9999 0 -9999 0 0
CLTB 0.016 0 -9999 0 -9999 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.031 0 -9999 0 -9999 0 0
CD4 0.016 0 -9999 0 -9999 0 0
CLTA 0.016 0 -9999 0 -9999 0 0
mol:GTP 0.001 0 -9999 0 -9999 0 0
ARFGAP1 0.014 0 -9999 0 -9999 0 0
mol:PI-4-5-P2 0 0 -9999 0 -9999 0 0
ARF1/GTP 0 0 -9999 0 -9999 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.034 0 -9999 0 -9999 0 0
mol:Choline 0 0 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
ARF1 0.016 0 -9999 0 -9999 0 0
DDEF1 0 0.002 -9999 0 -9999 0 0
ARF1/GDP 0 0.001 -9999 0 -9999 0 0
AP2M1 -0.025 0.164 -9999 0 -0.65 2 2
EntrezGene:1313 0 0 -9999 0 -9999 0 0
actin filament polymerization 0.02 0 -9999 0 -9999 0 0
Rac/GTP 0 0 -9999 0 -9999 0 0
ARF1/GTP/GGA3/ARF-GAP1 0 0 -9999 0 -9999 0 0
ARFIP2 0.014 0 -9999 0 -9999 0 0
COPA 0.016 0 -9999 0 -9999 0 0
RAC1 0.016 0 -9999 0 -9999 0 0
ARF1/GTP/coatomer protein complex 0.03 0 -9999 0 -9999 0 0
ARF1/GTP/ARHGAP10 0 0 -9999 0 -9999 0 0
GGA3 0.016 0 -9999 0 -9999 0 0
ARF1/GTP/Membrin 0 0 -9999 0 -9999 0 0
AP2A1 0.016 0 -9999 0 -9999 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.034 0 -9999 0 -9999 0 0
ARF1/GDP/Membrin 0.02 0 -9999 0 -9999 0 0
Arfaptin 2/Rac/GDP 0 0 -9999 0 -9999 0 0
CYTH2 0.001 0 -9999 0 -9999 0 0
ARF1/GTP/GGA3 0 0 -9999 0 -9999 0 0
mol:ATP 0 0 -9999 0 -9999 0 0
Rac/GDP 0 0 -9999 0 -9999 0 0
mol:Brefeldin A 0 0 -9999 0 -9999 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.03 0.058 -9999 0 -9999 0 0
PLD2 0 0 -9999 0 -9999 0 0
ARF-GAP1/v-SNARE 0.014 0 -9999 0 -9999 0 0
PIP5K1A 0 0 -9999 0 -9999 0 0
ARF1/GTP/Membrin/GBF1/p115 0 0 -9999 0 -9999 0 0
mol:Phosphatic acid 0 0 -9999 0 -9999 0 0
mol:Phosphatidic acid 0 0 -9999 0 -9999 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.014 0 -9999 0 -9999 0 0
GOSR2 0 0 -9999 0 -9999 0 0
USO1 0 0 -9999 0 -9999 0 0
GBF1 0 0 -9999 0 -9999 0 0
ARF1/GTP/Arfaptin 2 0 0 -9999 0 -9999 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex -0.025 0.1 -9999 0 -0.501 1 1
Alternative NF-kappaB pathway

Figure 130.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 132.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0 -9999 0 -9999 0 0
FBXW11 0.016 0 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -9999 0 0
CHUK 0.016 0 -9999 0 -9999 0 0
NF kappa B2 p100/RelB -0.007 0.042 -9999 0 -9999 0 0
NFKB1 0.016 0 -9999 0 -9999 0 0
MAP3K14 0.016 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelB -0.012 0.064 -9999 0 -0.37 1 1
RELB -0.001 0.094 -9999 0 -0.526 1 1
NFKB2 0.016 0 -9999 0 -9999 0 0
NF kappa B2 p52/RelB -0.01 0.055 -9999 0 -0.314 1 1
regulation of B cell activation -0.01 0.054 -9999 0 -0.313 1 1
Regulation of Androgen receptor activity

Figure 131.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 133.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.029 0 -9999 0 -9999 0 0
SMARCC1 -0.003 0.075 -9999 0 -9999 0 0
REL -0.002 0.094 -9999 0 -0.527 1 1
HDAC7 0.018 0.114 -9999 0 -9999 0 0
JUN -0.057 0.23 -9999 0 -0.773 3 3
EP300 0.016 0 -9999 0 -9999 0 0
KAT2B 0 0 -9999 0 -9999 0 0
KAT5 0 0 -9999 0 -9999 0 0
MAPK14 0.004 0.096 -9999 0 -9999 0 0
FOXO1 0.016 0 -9999 0 -9999 0 0
T-DHT/AR 0.026 0.124 -9999 0 -9999 0 0
MAP2K6 -0.018 0.13 -9999 0 -0.519 2 2
BRM/BAF57 0.013 0.069 -9999 0 -0.368 1 1
MAP2K4 0.016 0.007 -9999 0 -9999 0 0
SMARCA2 0.017 0 -9999 0 -9999 0 0
PDE9A -0.061 0.239 -9999 0 -1.359 1 1
NCOA2 0.017 0 -9999 0 -9999 0 0
CEBPA -0.058 0.23 -9999 0 -0.774 3 3
EHMT2 0.017 0 -9999 0 -9999 0 0
cell proliferation 0.051 0.121 -9999 0 -9999 0 0
NR0B1 -0.161 0.266 -9999 0 -0.55 10 10
EGR1 -0.231 0.349 -9999 0 -0.705 11 11
RXRs/9cRA -0.007 0.129 -9999 0 -0.461 2 2
AR/RACK1/Src 0.037 0.082 -9999 0 -9999 0 0
AR/GR 0.023 0.068 -9999 0 -9999 0 0
GNB2L1 0 0.094 -9999 0 -0.525 1 1
PKN1 0.016 0 -9999 0 -9999 0 0
RCHY1 0.016 0 -9999 0 -9999 0 0
epidermal growth factor receptor activity 0.001 0 -9999 0 -9999 0 0
MAPK8 0.028 0.016 -9999 0 -9999 0 0
T-DHT/AR/TIF2/CARM1 0.043 0.075 -9999 0 -9999 0 0
SRC 0.034 0.072 -9999 0 -9999 0 0
NR3C1 0.016 0 -9999 0 -9999 0 0
KLK3 -0.005 0.098 -9999 0 -9999 0 0
APPBP2 0.015 0.008 -9999 0 -9999 0 0
TRIM24 0.001 0.094 -9999 0 -0.524 1 1
T-DHT/AR/TIP60 -0.025 0.052 -9999 0 -9999 0 0
TMPRSS2 -0.261 0.504 -9999 0 -1.212 7 7
RXRG -0.05 0.209 -9999 0 -0.69 3 3
mol:9cRA 0 0 -9999 0 -9999 0 0
RXRA 0.016 0 -9999 0 -9999 0 0
RXRB 0.016 0 -9999 0 -9999 0 0
CARM1 0.017 0 -9999 0 -9999 0 0
NR2C2 0.016 0 -9999 0 -9999 0 0
KLK2 0.061 0.065 -9999 0 -9999 0 0
AR 0.019 0.078 -9999 0 -9999 0 0
SENP1 0.016 0 -9999 0 -9999 0 0
HSP90AA1 0.016 0 -9999 0 -9999 0 0
MDM2 -0.01 0.137 -9999 0 -0.774 1 1
SRY -0.044 0.185 -9999 0 -0.61 3 3
GATA2 0.016 0 -9999 0 -9999 0 0
MYST2 0.016 0 -9999 0 -9999 0 0
HOXB13 -0.04 0.186 -9999 0 -0.606 3 3
T-DHT/AR/RACK1/Src 0.032 0.083 -9999 0 -9999 0 0
positive regulation of transcription 0.016 0 -9999 0 -9999 0 0
DNAJA1 0.015 0.008 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.071 -9999 0 -0.373 1 1
NCOA1 -0.003 0.143 -9999 0 -0.801 1 1
SPDEF -0.056 0.231 -9999 0 -0.773 3 3
T-DHT/AR/TIF2 0.048 0.048 -9999 0 -9999 0 0
T-DHT/AR/Hsp90 0.027 0.076 -9999 0 -9999 0 0
GSK3B 0.016 0.003 -9999 0 -9999 0 0
NR2C1 0.016 0 -9999 0 -9999 0 0
mol:T-DHT 0.022 0.08 -9999 0 -9999 0 0
SIRT1 0.016 0 -9999 0 -9999 0 0
ZMIZ2 0.014 0 -9999 0 -9999 0 0
POU2F1 0.023 0.033 -9999 0 -9999 0 0
T-DHT/AR/DAX-1 -0.066 0.186 -9999 0 -0.556 2 2
CREBBP 0.016 0 -9999 0 -9999 0 0
SMARCE1 0 0.094 -9999 0 -0.525 1 1
Methods & Data
Input

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

  • Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/LUAD/760651/1.GDAC_MergeDataFiles.Finished/LUAD.transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data.txt

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

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

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)