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 37 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
TCGA08_retinoblastoma 9
Ephrin A reverse signaling 8
FOXM1 transcription factor network 8
E-cadherin signaling events 7
IL23-mediated signaling events 6
PLK2 and PLK4 events 5
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 5
IL12-mediated signaling events 4
Thromboxane A2 receptor signaling 4
Endothelins 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
TCGA08_retinoblastoma 9 74 8 -0.153 0.146 1000 -1000 -0.01 -1000
Ephrin A reverse signaling 8 61 7 -0.222 0 1000 -1000 -0.012 -1000
FOXM1 transcription factor network 8 416 51 -1.092 0.017 1000 -1000 -0.141 -1000
E-cadherin signaling events 7 39 5 -0.244 0.017 1000 -1000 -0.012 -1000
IL23-mediated signaling events 6 392 60 -0.733 0.019 1000 -1000 -0.116 -1000
PLK2 and PLK4 events 5 16 3 -0.084 -1000 1000 -1000 -0.009 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 5 383 68 -0.626 0.394 1000 -1000 -0.087 -1000
IL12-mediated signaling events 4 379 87 -0.492 0.111 1000 -1000 -0.1 -1000
Thromboxane A2 receptor signaling 4 430 105 -0.315 0.07 1000 -1000 -0.057 -1000
Endothelins 4 462 96 -0.363 0.039 1000 -1000 -0.053 -1000
Signaling events mediated by the Hedgehog family 3 181 52 -0.214 0.125 1000 -1000 -0.028 -1000
HIF-1-alpha transcription factor network 3 245 76 -0.227 0.04 1000 -1000 -0.072 -1000
PDGFR-alpha signaling pathway 3 163 44 -0.353 0.034 1000 -1000 -0.049 -1000
Calcium signaling in the CD4+ TCR pathway 3 93 31 -0.194 0.026 1000 -1000 -0.043 -1000
Nongenotropic Androgen signaling 3 165 52 -0.23 0.122 1000 -1000 -0.05 -1000
Signaling events mediated by VEGFR1 and VEGFR2 3 421 125 -0.179 0.03 1000 -1000 -0.095 -1000
Stabilization and expansion of the E-cadherin adherens junction 3 275 74 -0.244 0.122 1000 -1000 -0.07 -1000
E-cadherin signaling in the nascent adherens junction 3 250 76 -0.244 0.025 1000 -1000 -0.066 -1000
Aurora B signaling 3 221 67 -0.272 0.017 1000 -1000 -0.058 -1000
Syndecan-1-mediated signaling events 2 76 34 -0.308 0.017 1000 -1000 -0.039 -1000
Visual signal transduction: Cones 2 98 38 -0.113 0.025 1000 -1000 -0.019 -1000
Osteopontin-mediated events 2 83 38 -0.192 0.017 1000 -1000 -0.084 -1000
Arf6 signaling events 2 149 62 -0.15 0.027 1000 -1000 -0.018 -1000
BMP receptor signaling 2 163 81 -0.17 0.039 1000 -1000 -0.086 -1000
Fc-epsilon receptor I signaling in mast cells 2 222 97 -0.193 0.043 1000 -1000 -0.069 -1000
PLK1 signaling events 2 247 85 -0.24 0.025 1000 -1000 -0.04 -1000
IL1-mediated signaling events 2 157 62 -0.219 0.071 1000 -1000 -0.073 -1000
Signaling events regulated by Ret tyrosine kinase 2 168 82 -0.172 0.017 1000 -1000 -0.074 -1000
Ephrin B reverse signaling 2 143 48 -0.15 0.123 1000 -1000 -0.057 -1000
S1P1 pathway 2 79 36 -0.153 0.017 1000 -1000 -0.062 -1000
TCGA08_p53 2 19 7 -0.118 0.077 1000 -1000 -0.01 -1000
Effects of Botulinum toxin 2 66 26 -0.265 0.017 1000 -1000 -0.05 -1000
IL6-mediated signaling events 2 171 75 -0.193 0.068 1000 -1000 -0.056 -1000
Syndecan-4-mediated signaling events 2 169 67 -0.178 0.035 1000 -1000 -0.047 -1000
Rapid glucocorticoid signaling 2 40 20 -0.216 0.017 1000 -1000 -0.01 -1000
E-cadherin signaling in keratinocytes 2 98 43 -0.243 0.05 1000 -1000 -0.029 -1000
Ras signaling in the CD4+ TCR pathway 2 34 17 -0.072 0.021 1000 -1000 -0.015 -1000
LPA4-mediated signaling events 1 14 12 -0.081 0.022 1000 -1000 -0.012 -1000
Caspase cascade in apoptosis 1 87 74 -0.1 0.028 1000 -1000 -0.024 -1000
Regulation of nuclear SMAD2/3 signaling 1 234 136 -0.407 0.109 1000 -1000 -0.047 -1000
Coregulation of Androgen receptor activity 1 123 76 -0.203 0.037 1000 -1000 -0.024 -1000
ErbB4 signaling events 1 95 69 -0.229 0.072 1000 -1000 -0.083 -1000
BARD1 signaling events 1 63 57 -0.128 0.034 1000 -1000 -0.024 -1000
Sphingosine 1-phosphate (S1P) pathway 1 38 28 -0.084 0.025 1000 -1000 -0.017 -1000
Circadian rhythm pathway 1 22 22 -0.15 0.04 1000 -1000 -0.044 -1000
Noncanonical Wnt signaling pathway 1 32 26 -0.084 0.02 1000 -1000 -0.036 -1000
Syndecan-2-mediated signaling events 1 83 69 -0.135 0.04 1000 -1000 -0.03 -1000
a4b1 and a4b7 Integrin signaling 1 9 5 -0.034 0.017 1000 -1000 -0.012 -1000
Cellular roles of Anthrax toxin 1 77 39 -0.24 0.018 1000 -1000 -0.02 -1000
Presenilin action in Notch and Wnt signaling 1 93 61 -0.301 0.043 1000 -1000 -0.068 -1000
Aurora A signaling 1 102 60 -0.171 0.051 1000 -1000 -0.021 -1000
p75(NTR)-mediated signaling 1 188 125 -0.308 0.043 1000 -1000 -0.071 -1000
IL4-mediated signaling events 1 144 91 -0.523 0.261 1000 -1000 -0.116 -1000
Glypican 1 network 1 54 48 -0.107 0.032 1000 -1000 -0.025 -1000
amb2 Integrin signaling 1 143 82 -0.14 0.023 1000 -1000 -0.073 -1000
Nectin adhesion pathway 1 104 63 -0.244 0.026 1000 -1000 -0.059 -1000
Glucocorticoid receptor regulatory network 1 141 114 -0.31 0.069 1000 -1000 -0.048 -1000
Paxillin-independent events mediated by a4b1 and a4b7 1 68 37 -0.308 0.025 1000 -1000 -0.022 -1000
TRAIL signaling pathway 1 52 48 -0.026 0.035 1000 -1000 -0.069 -1000
RXR and RAR heterodimerization with other nuclear receptor 1 60 52 -0.271 0.05 1000 -1000 -0.05 -1000
FAS signaling pathway (CD95) 1 58 47 -0.107 0.047 1000 -1000 -0.035 -1000
Signaling mediated by p38-gamma and p38-delta 1 16 15 -0.12 0.03 1000 -1000 -0.017 -1000
Syndecan-3-mediated signaling events 1 53 35 -0.135 0.043 1000 -1000 -0.032 -1000
Signaling mediated by p38-alpha and p38-beta 1 84 44 -0.1 0.017 1000 -1000 -0.03 -1000
Integrins in angiogenesis 1 152 84 -0.164 0.031 1000 -1000 -0.081 -1000
TCR signaling in naïve CD8+ T cells 1 119 93 -0.12 0.028 1000 -1000 -0.056 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 1 55 45 -0.1 0.017 1000 -1000 -0.075 -1000
Canonical Wnt signaling pathway 1 68 51 -0.301 0.136 1000 -1000 -0.041 -1000
EPHB forward signaling 1 105 85 -0.15 0.06 1000 -1000 -0.076 -1000
Glypican 2 network 1 6 4 -0.012 0 1000 -1000 -0.008 -1000
IL27-mediated signaling events 1 56 51 -0.19 0.025 1000 -1000 -0.073 -1000
Wnt signaling 1 12 7 -0.084 0.017 1000 -1000 -0.02 -1000
LPA receptor mediated events 1 117 102 -0.193 0.036 1000 -1000 -0.062 -1000
IL2 signaling events mediated by STAT5 1 34 22 -0.179 0.078 1000 -1000 -0.024 -1000
Regulation of Telomerase 1 103 102 -0.194 0.049 1000 -1000 -0.093 -1000
BCR signaling pathway 1 187 99 -0.141 0.03 1000 -1000 -0.077 -1000
EGFR-dependent Endothelin signaling events 1 38 21 -0.099 0.025 1000 -1000 -0.067 -1000
Angiopoietin receptor Tie2-mediated signaling 1 140 88 -0.194 0.026 1000 -1000 -0.095 -1000
Neurotrophic factor-mediated Trk receptor signaling 1 162 120 -0.28 0.129 1000 -1000 -0.062 -1000
Visual signal transduction: Rods 1 100 52 -0.113 0.017 1000 -1000 -0.071 -1000
Signaling events mediated by PRL 1 67 34 -0.142 0.025 1000 -1000 -0.025 -1000
Class IB PI3K non-lipid kinase events 1 3 3 -0.002 0.002 1000 -1000 -0.002 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 1 131 78 -0.112 0.076 1000 -1000 -0.073 -1000
ErbB2/ErbB3 signaling events 0 47 65 -0.101 0.026 1000 -1000 -0.057 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0 7 23 -0.012 0.034 1000 -1000 -0.037 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0 1 34 -0.026 0.053 1000 -1000 -0.034 -1000
Canonical NF-kappaB pathway 0 28 39 -0.1 0.082 1000 -1000 -0.072 -1000
Signaling events mediated by HDAC Class II 0 35 75 -0.085 0.041 1000 -1000 -0.038 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0 30 54 -0.071 0.032 1000 -1000 -0.081 -1000
JNK signaling in the CD4+ TCR pathway 0 8 17 -0.019 0.034 1000 -1000 -0.018 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0 60 85 -0.194 0.049 1000 -1000 -0.064 -1000
Signaling events mediated by PTP1B 0 61 76 -0.101 0.034 1000 -1000 -0.064 -1000
Hedgehog signaling events mediated by Gli proteins 0 61 65 -0.048 0.043 1000 -1000 -0.052 -1000
Arf6 downstream pathway 0 12 43 -0.027 0.032 1000 -1000 -0.033 -1000
Aurora C signaling 0 3 7 -0.012 0.002 1000 -1000 -0.026 -1000
FOXA2 and FOXA3 transcription factor networks 0 16 46 -0.038 0.1 1000 -1000 -0.06 -1000
EPO signaling pathway 0 14 55 -0.049 0.052 1000 -1000 -0.077 -1000
Insulin-mediated glucose transport 0 13 32 -0.014 0.047 1000 -1000 -0.02 -1000
mTOR signaling pathway 0 14 53 -0.017 0.049 1000 -1000 -0.055 -1000
IFN-gamma pathway 0 64 68 -0.1 0.069 1000 -1000 -0.066 -1000
Class I PI3K signaling events mediated by Akt 0 18 68 -0.071 0.066 1000 -1000 -0.057 -1000
Ceramide signaling pathway 0 60 76 -0.1 0.025 1000 -1000 -0.031 -1000
Signaling events mediated by HDAC Class III 0 28 40 -0.188 0.097 1000 -1000 -0.025 -1000
Reelin signaling pathway 0 47 56 -0.113 0.038 1000 -1000 -0.068 -1000
S1P5 pathway 0 5 17 -0.02 0.025 1000 -1000 -0.014 -1000
ceramide signaling pathway 0 34 49 -0.099 0.025 1000 -1000 -0.033 -1000
HIF-2-alpha transcription factor network 0 28 43 -0.159 0.124 1000 -1000 -0.065 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0 66 83 -0.087 0.05 1000 -1000 -0.064 -1000
Signaling events mediated by HDAC Class I 0 60 104 -0.1 0.052 1000 -1000 -0.053 -1000
FoxO family signaling 0 21 64 -0.051 0.102 1000 -1000 -0.057 -1000
Retinoic acid receptors-mediated signaling 0 36 58 -0.12 0.063 1000 -1000 -0.069 -1000
Paxillin-dependent events mediated by a4b1 0 32 36 -0.308 0.034 1000 -1000 -0.059 -1000
Atypical NF-kappaB pathway 0 7 31 -0.056 0.038 1000 -1000 -0.03 -1000
IL2 signaling events mediated by PI3K 0 33 58 -0.048 0.066 1000 -1000 -0.071 -1000
Regulation of p38-alpha and p38-beta 0 39 54 -0.084 0.043 1000 -1000 -0.049 -1000
TCGA08_rtk_signaling 0 21 26 -0.092 0.035 1000 -1000 -0.016 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 3 27 -0.008 0.043 1000 -1000 -0.045 -1000
Class I PI3K signaling events 0 65 73 -0.121 0.037 1000 -1000 -0.044 -1000
Arf6 trafficking events 0 36 71 -0.113 0.066 1000 -1000 -0.057 -1000
IGF1 pathway 0 36 57 -0.07 0.051 1000 -1000 -0.076 -1000
Insulin Pathway 0 38 74 -0.107 0.054 1000 -1000 -0.076 -1000
Plasma membrane estrogen receptor signaling 0 56 86 -0.063 0.056 1000 -1000 -0.072 -1000
VEGFR1 specific signals 0 19 56 -0.07 0.048 1000 -1000 -0.035 -1000
S1P3 pathway 0 23 42 -0.063 0.051 1000 -1000 -0.02 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0 21 33 -0.164 0.05 1000 -1000 -0.031 -1000
PDGFR-beta signaling pathway 0 75 97 -0.092 0.044 1000 -1000 -0.069 -1000
S1P4 pathway 0 2 25 -0.005 0.032 1000 -1000 -0.02 -1000
p38 MAPK signaling pathway 0 43 44 -0.12 0.033 1000 -1000 -0.057 -1000
Arf1 pathway 0 2 54 -0.004 0.037 1000 -1000 -0.027 -1000
Alternative NF-kappaB pathway 0 6 13 -0.005 0.031 1000 -1000 -0.016 -1000
Regulation of Androgen receptor activity 0 60 70 -0.308 0.073 1000 -1000 -0.058 -1000
Total 169 12234 7203 -21.6660308048 -993.506384229 131000 -131000 -6.47300934113 -131000
TCGA08_retinoblastoma

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
CDKN2B -0.118 0.229 -9999 0 -0.499 7 7
CDKN2C -0.106 0.212 -9999 0 -0.421 8 8
CDKN2A -0.153 0.233 -9999 0 -0.447 10 10
CCND2 0.106 0.145 0.294 8 -9999 0 8
RB1 -0.109 0.16 -9999 0 -0.298 9 9
CDK4 0.146 0.164 0.288 13 -9999 0 13
CDK6 0.097 0.169 0.322 8 -0.163 2 10
G1/S progression 0.108 0.16 0.297 9 -9999 0 9
Ephrin A reverse signaling

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
MAPKKK cascade -0.148 0.206 -9999 0 -0.331 13 13
EFNA5 -0.026 0.153 -9999 0 -0.566 2 2
FYN -0.126 0.191 -9999 0 -0.392 7 7
neuron projection morphogenesis -0.148 0.206 -9999 0 -0.331 13 13
cell-cell signaling 0 0 -9999 0 -9999 0 0
Ephrin A5/EPHA5 -0.148 0.208 -9999 0 -0.332 13 13
EPHA5 -0.222 0.256 -9999 0 -0.479 13 13
FOXM1 transcription factor network

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
NFATC3 -0.542 0.681 -9999 0 -1.272 11 11
PLK1 0.011 0.06 -9999 0 -9999 0 0
BIRC5 -0.291 0.57 -9999 0 -1.449 5 5
HSPA1B -0.551 0.68 -9999 0 -1.28 11 11
MAP2K1 0.006 0.041 -9999 0 -9999 0 0
BRCA2 -0.598 0.714 -9999 0 -1.313 12 12
FOXM1 -1.092 1.477 -9999 0 -2.595 11 11
XRCC1 -0.542 0.681 -9999 0 -1.272 11 11
FOXM1B/p19 -0.779 0.701 -9999 0 -1.462 13 13
Cyclin D1/CDK4 -0.523 0.613 -9999 0 -1.114 12 12
CDC2 -0.621 0.772 -9999 0 -1.455 11 11
TGFA -0.519 0.601 -9999 0 -1.053 13 13
SKP2 -0.542 0.681 -9999 0 -1.272 11 11
CCNE1 0.014 0.009 -9999 0 -9999 0 0
CKS1B -0.547 0.682 -9999 0 -1.234 12 12
RB1 -0.292 0.314 -9999 0 -0.819 5 5
FOXM1C/SP1 -0.69 0.844 -9999 0 -1.619 11 11
AURKB -0.016 0.124 -9999 0 -0.402 2 2
CENPF -0.612 0.752 -9999 0 -1.432 11 11
CDK4 0.011 0.017 -9999 0 -9999 0 0
MYC -0.458 0.592 -9999 0 -1.088 11 11
CHEK2 -0.009 0.092 -9999 0 -0.429 1 1
ONECUT1 -0.563 0.658 -9999 0 -1.208 12 12
CDKN2A -0.167 0.242 -9999 0 -0.474 10 10
LAMA4 -0.546 0.686 -9999 0 -1.282 11 11
FOXM1B/HNF6 -0.753 0.87 -9999 0 -1.622 12 12
FOS -0.683 0.718 -9999 0 -1.319 14 14
SP1 0.017 0.001 -9999 0 -9999 0 0
CDC25B -0.542 0.681 -9999 0 -1.272 11 11
response to radiation -0.011 0.038 -9999 0 -9999 0 0
CENPB -0.542 0.681 -9999 0 -1.272 11 11
CENPA -0.612 0.754 -9999 0 -1.444 11 11
NEK2 -0.618 0.745 -9999 0 -1.327 13 13
HIST1H2BA -0.576 0.692 -9999 0 -1.263 12 12
CCNA2 -0.053 0.165 -9999 0 -0.44 4 4
EP300 0.017 0 -9999 0 -9999 0 0
CCNB1/CDK1 -0.726 0.892 -9999 0 -1.701 11 11
CCNB2 -0.599 0.741 -9999 0 -1.399 11 11
CCNB1 -0.597 0.738 -9999 0 -1.392 11 11
ETV5 -0.597 0.702 -9999 0 -1.349 11 11
ESR1 -0.548 0.679 -9999 0 -1.272 11 11
CCND1 -0.538 0.634 -9999 0 -1.15 12 12
GSK3A 0.009 0.035 -9999 0 -9999 0 0
Cyclin A-E1/CDK1-2 -0.058 0.195 -9999 0 -0.487 4 4
CDK2 -0.06 0.182 -9999 0 -0.487 4 4
G2/M transition of mitotic cell cycle -0.015 0.045 -9999 0 -9999 0 0
FOXM1B/Cbp/p300 -0.72 0.677 -9999 0 -1.485 11 11
GAS1 -0.617 0.706 -9999 0 -1.321 12 12
MMP2 -0.542 0.681 -9999 0 -1.272 11 11
RB1/FOXM1C -0.565 0.678 -9999 0 -1.235 12 12
CREBBP 0.017 0 -9999 0 -9999 0 0
E-cadherin 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
E-cadherin/beta catenin-gamma catenin -0.152 0.202 -9999 0 -0.395 9 9
E-cadherin/beta catenin -0.191 0.231 -9999 0 -0.391 14 14
CTNNB1 -0.026 0.153 -9999 0 -0.566 2 2
JUP 0.017 0 -9999 0 -9999 0 0
CDH1 -0.244 0.26 -9999 0 -0.486 14 14
IL23-mediated signaling 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
CCL2 -0.733 0.596 -9999 0 -1.254 13 13
IL23A -0.582 0.521 -9999 0 -1.114 10 10
NF kappa B1 p50/RelA/I kappa B alpha -0.521 0.464 -9999 0 -0.93 12 12
positive regulation of T cell mediated cytotoxicity -0.583 0.558 -9999 0 -1.037 13 13
ITGA3 -0.519 0.484 -9999 0 -0.946 12 12
IL17F -0.344 0.324 -9999 0 -0.669 7 7
IL12B -0.015 0.116 -9999 0 -0.596 1 1
STAT1 (dimer) -0.561 0.524 -9999 0 -0.989 13 13
CD4 -0.499 0.46 -9999 0 -1.072 6 6
IL23 -0.569 0.499 -9999 0 -1.071 10 10
IL23R -0.111 0.29 -9999 0 -1.53 1 1
IL1B -0.683 0.608 -9999 0 -1.257 12 12
T-helper cell lineage commitment 0 0 -9999 0 -9999 0 0
IL24 -0.499 0.46 -9999 0 -1.025 7 7
TYK2 -0.002 0.02 -9999 0 -9999 0 0
STAT4 -0.034 0.147 -9999 0 -0.441 3 3
STAT3 0.017 0.001 -9999 0 -9999 0 0
IL18RAP -0.025 0.124 -9999 0 -0.375 3 3
IL12RB1 -0.002 0.02 -9999 0 -9999 0 0
PIK3CA 0.017 0.001 -9999 0 -9999 0 0
IL12Rbeta1/TYK2 -0.003 0.025 -9999 0 -9999 0 0
IL23R/JAK2 -0.121 0.283 -9999 0 -1.47 1 1
positive regulation of chronic inflammatory response -0.583 0.558 -9999 0 -1.037 13 13
natural killer cell activation 0.008 0.015 0.077 1 -9999 0 1
JAK2 0.009 0.02 -9999 0 -9999 0 0
PIK3R1 -0.005 0.11 -9999 0 -0.566 1 1
NFKB1 0.014 0.004 -9999 0 -9999 0 0
RELA 0.014 0.004 -9999 0 -9999 0 0
positive regulation of dendritic cell antigen processing and presentation -0.541 0.469 -9999 0 -0.985 11 11
ALOX12B -0.499 0.46 -9999 0 -1.072 6 6
CXCL1 -0.61 0.511 -9999 0 -1.157 9 9
T cell proliferation -0.583 0.558 -9999 0 -1.037 13 13
NFKBIA 0.014 0.004 -9999 0 -9999 0 0
IL17A -0.242 0.261 -9999 0 -0.591 3 3
PI3K -0.548 0.475 -9999 0 -0.939 13 13
IFNG -0.022 0.039 0.147 1 -9999 0 1
STAT3 (dimer) -0.515 0.442 -9999 0 -0.877 13 13
IL18R1 0.019 0.003 -9999 0 -9999 0 0
IL23/IL23R/JAK2/TYK2/SOCS3 -0.295 0.282 -9999 0 -0.632 6 6
IL18/IL18R -0.072 0.15 -9999 0 -0.334 4 4
macrophage activation -0.028 0.017 -9999 0 -0.043 10 10
TNF -0.576 0.538 -9999 0 -1.077 11 11
STAT3/STAT4 -0.564 0.482 -9999 0 -0.94 14 14
STAT4 (dimer) -0.573 0.541 -9999 0 -1.015 13 13
IL18 -0.126 0.229 -9999 0 -0.47 8 8
IL19 -0.499 0.46 -9999 0 -1.072 6 6
STAT5A (dimer) -0.555 0.528 -9999 0 -0.989 13 13
STAT1 0.002 0.075 -9999 0 -0.378 1 1
SOCS3 -0.049 0.16 -9999 0 -0.425 4 4
CXCL9 -0.694 0.609 -9999 0 -1.294 12 12
MPO -0.532 0.5 -9999 0 -1.208 6 6
positive regulation of humoral immune response -0.583 0.558 -9999 0 -1.037 13 13
IL23/IL23R/JAK2/TYK2 -0.616 0.62 -9999 0 -1.105 13 13
IL6 -0.539 0.482 -9999 0 -0.987 11 11
STAT5A 0.017 0 -9999 0 -9999 0 0
IL2 0.009 0.075 -9999 0 -0.37 1 1
positive regulation of tyrosine phosphorylation of STAT protein 0.008 0.015 0.077 1 -9999 0 1
CD3E -0.499 0.46 -9999 0 -0.92 11 11
keratinocyte proliferation -0.583 0.558 -9999 0 -1.037 13 13
NOS2 -0.508 0.46 -9999 0 -0.895 13 13
PLK2 and PLK4 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
PLK2 -0.056 0.177 -9999 0 -0.472 4 4
PLK4 -0.07 0.187 -9999 0 -0.453 5 5
regulation of centriole replication -0.084 0.21 -9999 0 -0.398 7 7
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.023 0.007 -9999 0 -9999 0 0
NFATC2 -0.127 0.301 -9999 0 -0.732 4 4
NFATC3 -0.103 0.126 -9999 0 -0.278 5 5
CD40LG -0.522 0.578 -9999 0 -1.014 14 14
ITCH -0.06 0.133 -9999 0 -0.42 1 1
CBLB -0.067 0.155 -9999 0 -0.609 1 1
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.28 0.322 -9999 0 -0.867 4 4
JUNB -0.12 0.236 -9999 0 -0.513 7 7
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.088 0.156 -9999 0 -0.357 4 4
T cell anergy -0.126 0.21 -9999 0 -0.495 5 5
TLE4 -0.088 0.275 -9999 0 -0.974 2 2
Jun/NFAT1-c-4/p21SNFT -0.468 0.613 -9999 0 -0.988 13 13
AP-1/NFAT1-c-4 -0.626 0.747 -9999 0 -1.283 13 13
IKZF1 -0.1 0.25 -9999 0 -0.693 3 3
T-helper 2 cell differentiation -0.106 0.257 -9999 0 -0.805 2 2
AP-1/NFAT1 -0.214 0.358 -9999 0 -0.609 10 10
CALM1 -0.054 0.123 -9999 0 -0.534 1 1
EGR2 -0.559 0.745 -9999 0 -1.373 10 10
EGR3 -0.576 0.747 -9999 0 -1.397 10 10
NFAT1/FOXP3 -0.073 0.229 -9999 0 -0.765 2 2
EGR1 -0.217 0.264 -9999 0 -0.504 12 12
JUN -0.043 0.167 -9999 0 -0.504 3 3
EGR4 -0.003 0.012 -9999 0 -9999 0 0
mol:Ca2+ -0.054 0.085 -9999 0 -0.277 1 1
GBP3 -0.193 0.369 -9999 0 -0.796 6 6
FOSL1 0.017 0 -9999 0 -9999 0 0
NFAT1-c-4/MAF/IRF4 -0.443 0.582 -9999 0 -0.973 12 12
DGKA -0.073 0.229 -9999 0 -0.764 2 2
CREM 0.016 0.001 -9999 0 -9999 0 0
NFAT1-c-4/PPARG -0.49 0.606 -9999 0 -1.033 12 12
CTLA4 -0.055 0.195 -9999 0 -0.655 2 2
NFAT1-c-4 (dimer)/EGR1 -0.577 0.697 -9999 0 -1.186 13 13
NFAT1-c-4 (dimer)/EGR4 -0.477 0.607 -9999 0 -0.997 13 13
FOS -0.198 0.264 -9999 0 -0.509 11 11
IFNG -0.154 0.222 -9999 0 -0.803 2 2
T cell activation -0.278 0.402 -9999 0 -0.808 8 8
MAF -0.026 0.153 -9999 0 -0.565 2 2
T-helper 2 cell lineage commitment 0 0 -9999 0 -9999 0 0
activation-induced cell death of T cells 0.394 0.553 0.894 11 -9999 0 11
TNF -0.516 0.567 -9999 0 -1.035 13 13
FASLG -0.588 0.723 -9999 0 -1.36 11 11
TBX21 0.007 0.075 -9999 0 -0.37 1 1
BATF3 0 0 -9999 0 -9999 0 0
PRKCQ -0.003 0.11 -9999 0 -0.566 1 1
PTPN1 -0.073 0.229 -9999 0 -0.764 2 2
NFAT1-c-4/ICER1 -0.464 0.599 -9999 0 -1.017 12 12
GATA3 0.021 0.001 -9999 0 -9999 0 0
T-helper 1 cell differentiation -0.128 0.24 -9999 0 -0.787 2 2
IL2RA -0.293 0.307 -9999 0 -0.79 5 5
T-helper 1 cell lineage commitment 0 0 -9999 0 -9999 0 0
CASP3 -0.082 0.237 -9999 0 -0.764 2 2
E2F1 -0.019 0.124 -9999 0 -0.371 3 3
PPARG -0.041 0.166 -9999 0 -0.503 3 3
SLC3A2 -0.086 0.283 -9999 0 -0.947 2 2
IRF4 0.017 0 -9999 0 -9999 0 0
PTGS2 -0.538 0.586 -9999 0 -1.063 13 13
CSF2 -0.519 0.569 -9999 0 -1 14 14
JunB/Fra1/NFAT1-c-4 -0.481 0.632 -9999 0 -1.026 13 13
IL4 -0.111 0.268 -9999 0 -0.846 2 2
IL5 -0.512 0.559 -9999 0 -0.985 14 14
IL2 -0.284 0.41 -9999 0 -0.875 7 7
IL3 -0.06 0.057 -9999 0 -9999 0 0
RNF128 -0.184 0.27 -9999 0 -0.45 12 12
NFATC1 -0.398 0.562 -9999 0 -0.904 11 11
CDK4 0.204 0.266 0.654 3 -9999 0 3
PTPRK -0.086 0.283 -9999 0 -0.947 2 2
IL8 -0.558 0.6 -9999 0 -1.071 14 14
POU2F1 0.026 0 -9999 0 -9999 0 0
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.112 0.146 -9999 0 -0.291 8 8
TBX21 -0.381 0.455 -9999 0 -0.998 8 8
B2M -0.017 0.131 -9999 0 -0.471 2 2
TYK2 0.006 0.018 -9999 0 -9999 0 0
IL12RB1 0.006 0.018 -9999 0 -9999 0 0
GADD45B -0.461 0.526 -9999 0 -1.124 9 9
IL12RB2 -0.144 0.226 -9999 0 -0.455 9 9
GADD45G -0.296 0.342 -9999 0 -0.775 7 7
natural killer cell activation -0.009 0.018 -9999 0 -9999 0 0
RELB -0.005 0.11 -9999 0 -0.566 1 1
RELA 0.017 0 -9999 0 -9999 0 0
IL18 -0.134 0.233 -9999 0 -0.483 8 8
IL2RA -0.012 0.103 -9999 0 -0.378 2 2
IFNG 0.002 0.075 -9999 0 -0.378 1 1
STAT3 (dimer) -0.302 0.359 -9999 0 -0.791 8 8
HLA-DRB5 -0.132 0.249 -9999 0 -0.549 7 7
FASLG -0.388 0.45 -9999 0 -0.941 9 9
NF kappa B2 p52/RelB -0.395 0.446 -9999 0 -0.894 10 10
CD4 0.011 0.009 -9999 0 -9999 0 0
SOCS1 0.017 0 -9999 0 -9999 0 0
EntrezGene:6955 -0.003 0.009 -9999 0 -9999 0 0
CD3D 0.013 0.01 -9999 0 -9999 0 0
CD3E 0.013 0.009 -9999 0 -9999 0 0
CD3G 0.013 0.01 -9999 0 -9999 0 0
IL12Rbeta2/JAK2 -0.101 0.167 -9999 0 -0.326 9 9
CCL3 -0.441 0.531 -9999 0 -1.024 10 10
CCL4 -0.492 0.608 -9999 0 -1.274 9 9
HLA-A -0.017 0.131 -9999 0 -0.471 2 2
IL18/IL18R -0.086 0.161 -9999 0 -0.346 5 5
NOS2 -0.338 0.386 -9999 0 -0.76 10 10
IL12/IL12R/TYK2/JAK2/SPHK2 -0.112 0.146 -9999 0 -0.3 6 6
IL1R1 -0.396 0.485 -9999 0 -1.048 8 8
IL4 0.026 0.017 -9999 0 -9999 0 0
JAK2 0.006 0.018 -9999 0 -9999 0 0
EntrezGene:6957 -0.003 0.008 -9999 0 -9999 0 0
TCR/CD3/MHC I/CD8 0.012 0.094 -9999 0 -0.4 1 1
RAB7A -0.287 0.323 -9999 0 -0.759 6 6
lysosomal transport -0.272 0.306 -9999 0 -0.716 6 6
FOS -0.461 0.589 -9999 0 -1.064 11 11
STAT4 (dimer) -0.362 0.406 -9999 0 -0.896 8 8
STAT5A (dimer) -0.394 0.435 -9999 0 -0.885 10 10
GZMA -0.38 0.448 -9999 0 -0.841 11 11
GZMB -0.408 0.484 -9999 0 -1.06 8 8
HLX 0.017 0 -9999 0 -9999 0 0
LCK -0.411 0.501 -9999 0 -0.968 10 10
TCR/CD3/MHC II/CD4 -0.091 0.175 -9999 0 -0.349 7 7
IL2/IL2R 0.012 0.076 -9999 0 -9999 0 0
MAPK14 -0.359 0.406 -9999 0 -0.849 9 9
CCR5 -0.441 0.53 -9999 0 -1.014 10 10
IL1B -0.279 0.254 -9999 0 -0.479 16 16
STAT6 -0.152 0.269 -9999 0 -0.513 5 5
STAT4 -0.034 0.147 -9999 0 -0.441 3 3
STAT3 0.017 0 -9999 0 -9999 0 0
STAT1 0.002 0.075 -9999 0 -0.378 1 1
NFKB1 0.017 0 -9999 0 -9999 0 0
NFKB2 0.017 0 -9999 0 -9999 0 0
IL12B -0.012 0.113 -9999 0 -0.581 1 1
CD8A 0.002 0 -9999 0 -9999 0 0
CD8B 0.019 0 -9999 0 -9999 0 0
T-helper 1 cell differentiation 0 0 -9999 0 -9999 0 0
natural killer cell mediated cytotoxicity 0.111 0.145 0.289 8 -9999 0 8
IL2RB 0.002 0.075 -9999 0 -0.378 1 1
proteasomal ubiquitin-dependent protein catabolic process -0.33 0.364 -9999 0 -0.805 8 8
IL2RG 0.017 0 -9999 0 -9999 0 0
IL12 -0.102 0.182 -9999 0 -0.374 8 8
STAT5A 0.017 0 -9999 0 -9999 0 0
CD247 -0.016 0.102 -9999 0 -0.375 2 2
IL2 0.002 0.075 -9999 0 -0.378 1 1
SPHK2 0.017 0 -9999 0 -9999 0 0
FRAP1 0.017 0 -9999 0 -9999 0 0
IL12A -0.126 0.231 -9999 0 -0.508 7 7
IL12/IL12R/TYK2/JAK2 -0.451 0.553 -9999 0 -1.003 11 11
MAP2K3 -0.362 0.405 -9999 0 -0.846 9 9
RIPK2 0.002 0.075 -9999 0 -0.378 1 1
MAP2K6 -0.362 0.405 -9999 0 -0.846 9 9
regulation of dendritic cell antigen processing and presentation 0 0 -9999 0 -9999 0 0
HLA-DRA -0.076 0.189 -9999 0 -0.462 5 5
IL18RAP -0.031 0.123 -9999 0 -0.378 3 3
IL12Rbeta1/TYK2 0.008 0.029 -9999 0 -9999 0 0
EOMES 0.053 0.033 -9999 0 -9999 0 0
STAT1 (dimer) -0.304 0.344 -9999 0 -0.769 8 8
T cell proliferation -0.263 0.285 -9999 0 -0.626 8 8
T-helper 1 cell lineage commitment 0 0 -9999 0 -9999 0 0
IL18R1 0.012 0.009 -9999 0 -9999 0 0
CD8-positive alpha-beta T cell lineage commitment 0 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelA -0.321 0.297 -9999 0 -0.647 10 10
ATF2 -0.324 0.369 -9999 0 -0.772 9 9
Thromboxane A2 receptor signaling

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
TGM2 0.015 0.002 -9999 0 -9999 0 0
GNB1/GNG2 -0.104 0.07 -9999 0 -0.174 12 12
AKT1 -0.093 0.11 -9999 0 -0.201 5 5
EGF -0.012 0.103 -9999 0 -0.378 2 2
mol:TXA2 -0.001 0.001 -9999 0 -9999 0 0
FGR 0.038 0.03 -9999 0 -9999 0 0
mol:Ca2+ -0.144 0.15 -9999 0 -0.28 12 12
LYN 0.038 0.03 -9999 0 -9999 0 0
RhoA/GTP -0.072 0.061 -9999 0 -0.246 1 1
mol:PGI2 0 0 -9999 0 -9999 0 0
SYK -0.185 0.178 -9999 0 -0.342 13 13
GNG2 -0.02 0.131 -9999 0 -0.472 2 2
ARRB2 0.017 0 -9999 0 -9999 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.004 0.118 -9999 0 -0.376 2 2
G beta5/gamma2 -0.132 0.09 -9999 0 -0.224 11 11
PRKCH -0.172 0.176 -9999 0 -0.34 11 11
DNM1 -0.15 0.224 -9999 0 -0.435 10 10
TXA2/TP beta/beta Arrestin3 -0.045 0.062 -9999 0 -9999 0 0
mol:GTP -0.001 0.001 -9999 0 -9999 0 0
PTGDR -0.013 0.104 -9999 0 -0.379 2 2
G12 family/GTP -0.169 0.119 -9999 0 -0.288 12 12
ADRBK1 0.017 0 -9999 0 -9999 0 0
ADRBK2 0.017 0 -9999 0 -9999 0 0
RhoA/GTP/ROCK1 0.008 0.07 -9999 0 -0.347 1 1
mol:GDP 0.07 0.091 0.217 1 -9999 0 1
mol:NADP 0.016 0 -9999 0 -9999 0 0
RAB11A 0.017 0 -9999 0 -9999 0 0
PRKG1 0.016 0 -9999 0 -9999 0 0
mol:IP3 -0.181 0.181 -9999 0 -0.348 12 12
cell morphogenesis 0.008 0.069 -9999 0 -0.346 1 1
PLCB2 -0.242 0.233 -9999 0 -0.463 12 12
mol:cGMP -0.001 0.001 -9999 0 -9999 0 0
BLK 0.028 0.057 -9999 0 -9999 0 0
mol:PDG2 0 0 -9999 0 -9999 0 0
HCK 0.016 0.068 -9999 0 -9999 0 0
RHOA -0.005 0.11 -9999 0 -0.566 1 1
PTGIR 0.017 0 -9999 0 -9999 0 0
PRKCB1 -0.198 0.195 -9999 0 -0.374 12 12
GNAQ 0 0 -9999 0 -9999 0 0
mol:L-citrulline 0.016 0 -9999 0 -9999 0 0
TXA2/TXA2-R family -0.262 0.25 -9999 0 -0.503 12 12
LCK 0.038 0.03 -9999 0 -9999 0 0
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.034 0.033 -9999 0 -9999 0 0
TXA2-R family/G12 family/GDP/G beta/gamma 0.027 0.041 -9999 0 -9999 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.034 0.033 -9999 0 -9999 0 0
MAPK14 -0.117 0.123 -9999 0 -0.225 12 12
TGM2/GTP -0.199 0.202 -9999 0 -0.387 12 12
MAPK11 -0.117 0.123 -9999 0 -0.225 12 12
ARHGEF1 -0.082 0.095 -9999 0 -0.177 3 3
GNAI2 0.017 0 -9999 0 -9999 0 0
JNK cascade -0.193 0.192 -9999 0 -0.372 12 12
RAB11/GDP 0.018 0.001 -9999 0 -9999 0 0
ICAM1 -0.144 0.152 -9999 0 -0.282 12 12
cAMP biosynthetic process -0.17 0.171 -9999 0 -0.326 12 12
Gq family/GTP/EBP50 -0.017 0.125 -9999 0 -0.349 3 3
actin cytoskeleton reorganization 0.008 0.069 -9999 0 -0.346 1 1
SRC 0.038 0.03 -9999 0 -9999 0 0
GNB5 0.017 0 -9999 0 -9999 0 0
GNB1 0.017 0 -9999 0 -9999 0 0
EGF/EGFR 0.029 0.076 -9999 0 -9999 0 0
VCAM1 -0.211 0.198 -9999 0 -0.377 14 14
TP beta/Gq family/GDP/G beta5/gamma2 -0.004 0.118 -9999 0 -0.376 2 2
platelet activation -0.149 0.158 -9999 0 -0.291 12 12
PGI2/IP 0.012 0.001 -9999 0 -9999 0 0
PRKACA 0.013 0.039 -9999 0 -9999 0 0
Gq family/GDP/G beta5/gamma2 -0.005 0.115 -9999 0 -0.368 2 2
TXA2/TP beta/beta Arrestin2 -0.09 0.144 -9999 0 -0.458 3 3
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -9999 0 0
TBXA2R 0.02 0.037 -9999 0 -9999 0 0
mol:DAG -0.203 0.198 -9999 0 -0.388 12 12
EGFR -0.041 0.166 -9999 0 -0.503 3 3
TXA2/TP alpha -0.227 0.225 -9999 0 -0.438 12 12
Gq family/GTP -0.036 0.1 -9999 0 -0.301 3 3
YES1 0.028 0.058 -9999 0 -9999 0 0
GNAI2/GTP -0.006 0.02 -9999 0 -9999 0 0
PGD2/DP -0.009 0.072 -9999 0 -0.263 2 2
SLC9A3R1 -0.005 0.11 -9999 0 -0.566 1 1
FYN 0.038 0.03 -9999 0 -9999 0 0
mol:NO 0.016 0 -9999 0 -9999 0 0
GNA15 -0.005 0.11 -9999 0 -0.566 1 1
PGK/cGMP 0.022 0.001 -9999 0 -9999 0 0
RhoA/GDP -0.004 0.108 -9999 0 -0.556 1 1
TP alpha/TGM2/GDP/G beta/gamma 0.029 0.079 -9999 0 -9999 0 0
NOS3 0.016 0 -9999 0 -9999 0 0
RAC1 0.017 0 -9999 0 -9999 0 0
PRKCA -0.166 0.168 -9999 0 -0.325 11 11
PRKCB -0.176 0.171 -9999 0 -0.334 12 12
PRKCE -0.169 0.171 -9999 0 -0.331 11 11
PRKCD -0.201 0.197 -9999 0 -0.376 13 13
PRKCG -0.192 0.188 -9999 0 -0.363 12 12
muscle contraction -0.242 0.234 -9999 0 -0.466 12 12
PRKCZ -0.171 0.171 -9999 0 -0.329 12 12
ARR3 0.017 0 -9999 0 -9999 0 0
TXA2/TP beta 0.028 0.034 -9999 0 -9999 0 0
PRKCQ -0.177 0.18 -9999 0 -0.343 12 12
MAPKKK cascade -0.219 0.214 -9999 0 -0.42 12 12
SELE -0.158 0.153 -9999 0 -0.289 13 13
TP beta/GNAI2/GDP/G beta/gamma 0.029 0.079 -9999 0 -9999 0 0
ROCK1 0.017 0 -9999 0 -9999 0 0
GNA14 -0.063 0.193 -9999 0 -0.519 4 4
chemotaxis -0.315 0.294 -9999 0 -0.604 12 12
GNA12 0.017 0 -9999 0 -9999 0 0
GNA13 0.017 0 -9999 0 -9999 0 0
GNA11 0.017 0 -9999 0 -9999 0 0
Rac1/GTP 0.011 0.001 -9999 0 -9999 0 0
Endothelins

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
AKT1 -0.119 0.221 -9999 0 -0.533 4 4
PTK2B 0.002 0.075 -9999 0 -0.379 1 1
mol:Ca2+ -0.142 0.275 -9999 0 -0.713 4 4
EDN1 -0.138 0.239 -9999 0 -0.552 6 6
EDN3 -0.049 0.16 -9999 0 -0.425 4 4
EDN2 -0.005 0.11 -9999 0 -0.566 1 1
HRAS/GDP -0.166 0.246 -9999 0 -0.494 8 8
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.093 0.15 -9999 0 -0.36 4 4
ADCY4 -0.113 0.211 -9999 0 -0.464 6 6
ADCY5 -0.113 0.211 -9999 0 -0.464 6 6
ADCY6 -0.113 0.211 -9999 0 -0.464 6 6
ADCY7 -0.113 0.211 -9999 0 -0.464 6 6
ADCY1 -0.113 0.211 -9999 0 -0.464 6 6
ADCY2 -0.136 0.244 -9999 0 -0.539 6 6
ADCY3 -0.113 0.211 -9999 0 -0.464 6 6
ADCY8 -0.194 0.256 -9999 0 -0.486 10 10
ADCY9 -0.123 0.229 -9999 0 -0.511 6 6
arachidonic acid secretion -0.212 0.303 -9999 0 -0.554 10 10
ETB receptor/Endothelin-1/Gq/GTP -0.148 0.243 -9999 0 -0.47 8 8
GNAO1 0.017 0 -9999 0 -9999 0 0
HRAS 0.016 0.002 -9999 0 -9999 0 0
ETA receptor/Endothelin-1/G12/GTP -0.12 0.199 -9999 0 -0.492 4 4
ETA receptor/Endothelin-1/Gs/GTP -0.135 0.219 -9999 0 -0.495 6 6
mol:GTP -0.003 0.007 -9999 0 -9999 0 0
COL3A1 -0.2 0.298 -9999 0 -0.612 7 7
EDNRB -0.12 0.241 -9999 0 -0.516 7 7
response to oxidative stress 0 0 -9999 0 -9999 0 0
CYSLTR2 -0.132 0.261 -9999 0 -0.622 4 4
CYSLTR1 -0.118 0.219 -9999 0 -0.527 4 4
SLC9A1 -0.08 0.107 -9999 0 -0.291 3 3
mol:GDP -0.186 0.262 -9999 0 -0.535 8 8
SLC9A3 -0.207 0.332 -9999 0 -0.688 8 8
RAF1 -0.205 0.282 -9999 0 -0.532 10 10
JUN -0.158 0.325 -9999 0 -0.921 3 3
JAK2 -0.119 0.221 -9999 0 -0.533 4 4
mol:IP3 -0.135 0.215 -9999 0 -0.475 6 6
ETA receptor/Endothelin-1 -0.174 0.239 0.282 1 -0.506 7 8
PLCB1 0.015 0.003 -9999 0 -9999 0 0
PLCB2 -0.002 0.076 -9999 0 -0.386 1 1
ETA receptor/Endothelin-3 -0.072 0.18 -9999 0 -0.504 3 3
FOS -0.312 0.43 -9999 0 -0.814 10 10
Gai/GDP 0.009 0.061 -9999 0 -9999 0 0
CRK 0.016 0.001 -9999 0 -9999 0 0
mol:Ca ++ -0.214 0.281 -9999 0 -0.591 8 8
BCAR1 0.017 0.001 -9999 0 -9999 0 0
PRKCB1 -0.165 0.215 -9999 0 -0.471 7 7
GNAQ -0.004 0.009 -9999 0 -9999 0 0
GNAZ 0.017 0 -9999 0 -9999 0 0
GNAL -0.026 0.153 -9999 0 -0.566 2 2
Gs family/GDP -0.2 0.241 -9999 0 -0.534 8 8
ETA receptor/Endothelin-1/Gq/GTP -0.112 0.172 -9999 0 -0.367 6 6
MAPK14 -0.11 0.202 -9999 0 -0.447 6 6
TRPC6 -0.149 0.291 -9999 0 -0.756 4 4
GNAI2 0.017 0 -9999 0 -9999 0 0
GNAI3 0.017 0 -9999 0 -9999 0 0
GNAI1 -0.005 0.11 -9999 0 -0.566 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.126 0.212 -9999 0 -0.442 7 7
ETB receptor/Endothelin-2 -0.088 0.205 -9999 0 -0.445 6 6
ETB receptor/Endothelin-3 -0.12 0.199 -9999 0 -0.369 10 10
ETB receptor/Endothelin-1 -0.185 0.275 -9999 0 -0.535 9 9
MAPK3 -0.293 0.401 -9999 0 -0.768 10 10
MAPK1 -0.293 0.401 -9999 0 -0.768 10 10
Rac1/GDP -0.165 0.245 -9999 0 -0.492 8 8
cAMP biosynthetic process -0.121 0.231 -9999 0 -0.495 6 6
MAPK8 -0.139 0.25 -9999 0 -0.571 5 5
SRC 0.017 0.001 -9999 0 -9999 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.071 0.164 -9999 0 -0.335 6 6
p130Cas/CRK/Src/PYK2 -0.174 0.279 -9999 0 -0.589 7 7
mol:K + 0 0 -9999 0 -9999 0 0
G12/GDP -0.165 0.245 -9999 0 -0.52 7 7
COL1A2 -0.226 0.357 -9999 0 -0.815 6 6
EntrezGene:2778 0 0 -9999 0 -9999 0 0
ETA receptor/Endothelin-2 -0.045 0.142 -9999 0 -0.425 3 3
mol:DAG -0.135 0.215 -9999 0 -0.475 6 6
MAP2K2 -0.241 0.328 -9999 0 -0.63 10 10
MAP2K1 -0.241 0.328 -9999 0 -0.63 10 10
EDNRA -0.058 0.167 -9999 0 -0.593 2 2
positive regulation of muscle contraction -0.098 0.19 -9999 0 -0.459 4 4
Gq family/GDP -0.183 0.252 -9999 0 -0.559 7 7
HRAS/GTP -0.176 0.252 -9999 0 -0.512 8 8
PRKCH -0.138 0.217 -9999 0 -0.492 6 6
RAC1 0.017 0 -9999 0 -9999 0 0
PRKCA -0.127 0.208 -9999 0 -0.5 5 5
PRKCB -0.136 0.208 -9999 0 -0.432 7 7
PRKCE -0.127 0.207 -9999 0 -0.497 5 5
PRKCD -0.157 0.255 -9999 0 -0.573 6 6
PRKCG -0.143 0.212 -9999 0 -0.477 6 6
regulation of vascular smooth muscle contraction -0.363 0.503 -9999 0 -0.953 10 10
PRKCQ -0.138 0.235 -9999 0 -0.557 5 5
PLA2G4A -0.235 0.337 -9999 0 -0.612 10 10
GNA14 -0.066 0.195 -9999 0 -0.527 4 4
GNA15 -0.007 0.112 -9999 0 -0.575 1 1
GNA12 0.017 0 -9999 0 -9999 0 0
GNA11 0.014 0.007 -9999 0 -9999 0 0
Rac1/GTP -0.12 0.199 -9999 0 -0.492 4 4
MMP1 0.039 0.151 -9999 0 -9999 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.17 0.256 -9999 0 -0.55 6 6
IHH -0.021 0.057 -9999 0 -9999 0 0
SHH Np/Cholesterol/GAS1 -0.118 0.173 -9999 0 -0.359 7 7
LRPAP1 0.002 0.075 -9999 0 -0.378 1 1
dorsoventral neural tube patterning 0.117 0.172 0.357 7 -9999 0 7
SMO/beta Arrestin2 -0.087 0.191 -9999 0 -0.583 2 2
SMO -0.1 0.2 -9999 0 -0.62 2 2
AKT1 -0.032 0.099 -9999 0 -9999 0 0
ARRB2 0.017 0 -9999 0 -9999 0 0
BOC -0.063 0.193 -9999 0 -0.519 4 4
ADRBK1 0.017 0 -9999 0 -9999 0 0
heart looping -0.098 0.197 -9999 0 -0.609 2 2
STIL -0.131 0.198 -9999 0 -0.497 4 4
DHH N/PTCH2 0.025 0 -9999 0 -9999 0 0
DHH N/PTCH1 -0.077 0.157 -9999 0 -0.546 1 1
PIK3CA 0.017 0 -9999 0 -9999 0 0
DHH 0.017 0 -9999 0 -9999 0 0
PTHLH -0.214 0.346 -9999 0 -0.78 6 6
determination of left/right symmetry -0.098 0.197 -9999 0 -0.609 2 2
PIK3R1 -0.005 0.11 -9999 0 -0.566 1 1
skeletal system development -0.211 0.342 -9999 0 -0.771 6 6
IHH N/Hhip -0.143 0.205 -9999 0 -0.402 10 10
DHH N/Hhip -0.112 0.184 -9999 0 -0.344 10 10
mol:Cholesterol 0 0 -9999 0 -9999 0 0
heart development -0.098 0.197 -9999 0 -0.609 2 2
pancreas development -0.171 0.251 -9999 0 -0.49 10 10
HHAT -0.063 0.193 -9999 0 -0.519 4 4
PI3K 0.009 0.081 -9999 0 -0.406 1 1
EntrezGene:84976 0 0 -9999 0 -9999 0 0
GAS1 -0.157 0.234 -9999 0 -0.453 10 10
somite specification -0.098 0.197 -9999 0 -0.609 2 2
SHH Np/Cholesterol/PTCH1 -0.106 0.183 -9999 0 -0.473 3 3
SHH Np/Cholesterol/PTCH2 -0.023 0.114 -9999 0 -0.305 3 3
SHH Np/Cholesterol/Megalin -0.076 0.187 -9999 0 -0.476 4 4
SHH -0.042 0.148 -9999 0 -0.344 5 5
catabolic process -0.098 0.177 -9999 0 -0.61 1 1
SMO/Vitamin D3 -0.11 0.2 -9999 0 -0.465 4 4
SHH Np/Cholesterol/Hhip -0.126 0.199 -9999 0 -0.391 8 8
LRP2 -0.085 0.195 -9999 0 -0.441 6 6
receptor-mediated endocytosis -0.135 0.242 -9999 0 -0.596 4 4
SHH Np/Cholesterol/BOC -0.068 0.142 -9999 0 -0.306 6 6
SHH Np/Cholesterol/CDO -0.036 0.125 -9999 0 -0.306 4 4
mesenchymal cell differentiation 0.125 0.197 0.388 8 -9999 0 8
mol:Vitamin D3 -0.104 0.184 -9999 0 -0.473 3 3
IHH N/PTCH2 0.007 0.029 -9999 0 -9999 0 0
CDON -0.005 0.11 -9999 0 -0.566 1 1
IHH N/PTCH1 -0.098 0.178 -9999 0 -0.613 1 1
Megalin/LRPAP1 -0.056 0.165 -9999 0 -0.339 6 6
PTCH2 0.017 0 -9999 0 -9999 0 0
SHH Np/Cholesterol -0.034 0.113 -9999 0 -0.315 3 3
PTCH1 -0.099 0.177 -9999 0 -0.612 1 1
HHIP -0.171 0.251 -9999 0 -0.491 10 10
HIF-1-alpha transcription factor network

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
PKM2 -0.145 0.534 -9999 0 -1.177 4 4
HDAC7 0.002 0.002 -9999 0 -9999 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.128 0.384 -9999 0 -0.848 4 4
SMAD4 0.018 0 -9999 0 -9999 0 0
ID2 -0.156 0.542 -9999 0 -1.177 4 4
AP1 -0.168 0.249 -9999 0 -0.438 11 11
ABCG2 -0.162 0.56 -9999 0 -1.25 4 4
HIF1A 0.006 0.09 -9999 0 -9999 0 0
TFF3 -0.151 0.544 -9999 0 -1.217 4 4
GATA2 -0.024 0.13 -9999 0 -0.47 2 2
AKT1 0.001 0.101 -9999 0 -9999 0 0
response to hypoxia -0.023 0.105 -9999 0 -0.216 1 1
MCL1 -0.145 0.534 -9999 0 -1.177 4 4
NDRG1 -0.169 0.57 -9999 0 -1.29 4 4
SERPINE1 -0.151 0.54 -9999 0 -1.103 5 5
FECH -0.157 0.534 -9999 0 -1.177 4 4
FURIN -0.145 0.534 -9999 0 -1.177 4 4
NCOA2 0.019 0.001 -9999 0 -9999 0 0
EP300 0.017 0.146 -9999 0 -0.286 1 1
HMOX1 -0.209 0.591 -9999 0 -1.33 4 4
BHLHE40 -0.154 0.532 -9999 0 -1.185 4 4
BHLHE41 -0.154 0.532 -9999 0 -1.185 4 4
HIF1A/ARNT/SMAD3/SMAD4/SP1 0 0.142 -9999 0 -0.383 2 2
ENG 0.04 0.151 -9999 0 -9999 0 0
JUN -0.043 0.165 -9999 0 -0.503 3 3
RORA -0.145 0.534 -9999 0 -1.177 4 4
ABCB1 -0.094 0.271 -9999 0 -1.433 1 1
TFRC -0.151 0.544 -9999 0 -1.217 4 4
CXCR4 -0.212 0.579 -9999 0 -1.119 6 6
TF -0.186 0.571 -9999 0 -1.29 4 4
CITED2 -0.145 0.534 -9999 0 -1.177 4 4
HIF1A/ARNT -0.225 0.571 -9999 0 -1.236 5 5
LDHA -0.069 0.258 -9999 0 -1.369 1 1
ETS1 -0.145 0.534 -9999 0 -1.177 4 4
PGK1 -0.145 0.534 -9999 0 -1.177 4 4
NOS2 -0.154 0.532 -9999 0 -1.185 4 4
ITGB2 -0.189 0.569 -9999 0 -1.291 4 4
ALDOA -0.145 0.534 -9999 0 -1.177 4 4
Cbp/p300/CITED2 -0.146 0.542 -9999 0 -1.207 4 4
FOS -0.196 0.26 -9999 0 -0.501 11 11
HK2 -0.167 0.55 -9999 0 -1.02 6 6
SP1 0.027 0.005 -9999 0 -9999 0 0
GCK 0.018 0.231 -9999 0 -0.584 1 1
HK1 -0.145 0.534 -9999 0 -1.177 4 4
NPM1 -0.145 0.534 -9999 0 -1.177 4 4
EGLN1 -0.145 0.534 -9999 0 -1.177 4 4
CREB1 0.025 0.005 -9999 0 -9999 0 0
PGM1 -0.145 0.534 -9999 0 -1.177 4 4
SMAD3 -0.025 0.152 -9999 0 -0.564 2 2
EDN1 -0.22 0.462 -9999 0 -1.241 4 4
IGFBP1 -0.2 0.561 -9999 0 -1.25 4 4
VEGFA -0.053 0.4 -9999 0 -0.768 4 4
HIF1A/JAB1 0.007 0.049 -9999 0 -9999 0 0
CP -0.227 0.589 -9999 0 -1.161 6 6
CXCL12 -0.17 0.572 -9999 0 -1.301 4 4
COPS5 0.019 0.001 -9999 0 -9999 0 0
SMAD3/SMAD4 -0.004 0.113 -9999 0 -0.402 2 2
BNIP3 -0.145 0.534 -9999 0 -1.177 4 4
EGLN3 -0.179 0.559 -9999 0 -1.276 4 4
CA9 -0.145 0.534 -9999 0 -1.177 4 4
TERT -0.177 0.553 -9999 0 -1.128 5 5
ENO1 -0.157 0.541 -9999 0 -1.177 4 4
PFKL -0.145 0.534 -9999 0 -1.177 4 4
NCOA1 0.017 0.001 -9999 0 -9999 0 0
ADM -0.181 0.551 -9999 0 -1.214 4 4
ARNT 0.005 0.089 -9999 0 -9999 0 0
HNF4A 0.02 0.008 -9999 0 -9999 0 0
ADFP -0.151 0.54 -9999 0 -1.103 5 5
SLC2A1 -0.048 0.387 -9999 0 -0.733 4 4
LEP -0.145 0.534 -9999 0 -1.177 4 4
HIF1A/ARNT/Cbp/p300 -0.084 0.449 -9999 0 -0.888 4 4
EPO 0 0.314 -9999 0 -9999 0 0
CREBBP 0.017 0.146 -9999 0 -0.286 1 1
HIF1A/ARNT/Cbp/p300/HDAC7 -0.132 0.391 -9999 0 -0.87 4 4
PFKFB3 -0.161 0.553 -9999 0 -1.241 4 4
NT5E -0.172 0.563 -9999 0 -1.236 4 4
PDGFR-alpha signaling pathway

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
PDGFRA -0.105 0.214 -9999 0 -0.493 6 6
PDGF/PDGFRA/CRKL -0.059 0.153 -9999 0 -0.335 6 6
positive regulation of JUN kinase activity -0.023 0.117 -9999 0 -0.301 3 3
CRKL 0.017 0 -9999 0 -9999 0 0
PDGF/PDGFRA/Caveolin-3 -0.059 0.153 -9999 0 -0.335 6 6
AP1 -0.353 0.435 -9999 0 -0.897 10 10
mol:IP3 -0.072 0.161 -9999 0 -0.415 4 4
PLCG1 -0.072 0.162 -9999 0 -0.416 4 4
PDGF/PDGFRA/alphaV Integrin -0.075 0.166 -9999 0 -0.346 7 7
RAPGEF1 0.017 0 -9999 0 -9999 0 0
CRK 0.017 0 -9999 0 -9999 0 0
mol:Ca2+ -0.072 0.161 -9999 0 -0.414 4 4
CAV3 0.017 0 -9999 0 -9999 0 0
CAV1 -0.019 0.131 -9999 0 -0.472 2 2
SHC/Grb2/SOS1 -0.022 0.119 -9999 0 -0.303 3 3
PDGF/PDGFRA/Shf -0.059 0.153 -9999 0 -0.335 6 6
FOS -0.32 0.447 -9999 0 -0.88 10 10
JUN -0.066 0.135 -9999 0 -0.433 3 3
oligodendrocyte development -0.075 0.165 -9999 0 -0.345 7 7
GRB2 0.017 0 -9999 0 -9999 0 0
PIK3R1 -0.005 0.11 -9999 0 -0.566 1 1
mol:DAG -0.072 0.161 -9999 0 -0.415 4 4
PDGF/PDGFRA -0.104 0.214 -9999 0 -0.492 6 6
actin cytoskeleton reorganization -0.075 0.167 -9999 0 -0.348 7 7
SRF 0.034 0.012 -9999 0 -9999 0 0
SHC1 0.017 0 -9999 0 -9999 0 0
PI3K -0.051 0.143 -9999 0 -0.347 4 4
PDGF/PDGFRA/Crk/C3G -0.037 0.13 -9999 0 -0.344 3 3
JAK1 -0.069 0.156 -9999 0 -0.323 7 7
ELK1/SRF -0.024 0.124 -9999 0 -0.331 3 3
SHB -0.005 0.11 -9999 0 -0.566 1 1
SHF 0.017 0 -9999 0 -9999 0 0
CSNK2A1 0.031 0.023 -9999 0 -9999 0 0
GO:0007205 -0.075 0.166 -9999 0 -0.432 4 4
SOS1 0.017 0 -9999 0 -9999 0 0
Ras protein signal transduction -0.023 0.117 -9999 0 -0.301 3 3
PDGF/PDGFRA/SHB -0.075 0.168 -9999 0 -0.349 7 7
PDGF/PDGFRA/Caveolin-1 -0.086 0.17 -9999 0 -0.337 8 8
ITGAV -0.005 0.11 -9999 0 -0.566 1 1
ELK1 -0.068 0.153 -9999 0 -0.395 4 4
PIK3CA 0.017 0 -9999 0 -9999 0 0
PDGF/PDGFRA/Crk -0.059 0.153 -9999 0 -0.335 6 6
JAK-STAT cascade -0.069 0.156 -9999 0 -0.322 7 7
cell proliferation -0.059 0.153 -9999 0 -0.334 6 6
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.027 0.139 -9999 0 -0.404 3 3
NFATC2 0.007 0.073 -9999 0 -0.336 1 1
NFATC3 0.007 0.073 -9999 0 -0.336 1 1
CD40LG -0.143 0.315 -9999 0 -0.551 8 8
PTGS2 -0.16 0.331 -9999 0 -0.594 8 8
JUNB -0.12 0.236 -9999 0 -0.512 7 7
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.015 0.078 -9999 0 -0.409 1 1
CaM/Ca2+ -0.015 0.078 -9999 0 -0.409 1 1
CALM1 -0.005 0.11 -9999 0 -0.562 1 1
JUN -0.04 0.165 -9999 0 -0.498 3 3
mol:Ca2+ -0.003 0.011 -9999 0 -9999 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.011 0.005 -9999 0 -9999 0 0
FOSL1 0.017 0 -9999 0 -9999 0 0
CREM 0.016 0.001 -9999 0 -9999 0 0
Jun/NFAT1-c-4/p21SNFT -0.034 0.18 -9999 0 -0.455 3 3
FOS -0.194 0.263 -9999 0 -0.503 11 11
IFNG -0.124 0.284 -9999 0 -0.509 7 7
AP-1/NFAT1-c-4 -0.142 0.33 -9999 0 -0.6 7 7
FASLG -0.13 0.287 -9999 0 -0.553 6 6
NFAT1-c-4/ICER1 -0.039 0.106 -9999 0 -0.412 1 1
IL2RA -0.13 0.29 -9999 0 -0.522 7 7
FKBP12/FK506 0.012 0 -9999 0 -9999 0 0
CSF2 -0.139 0.302 -9999 0 -0.55 7 7
JunB/Fra1/NFAT1-c-4 -0.058 0.211 -9999 0 -0.565 3 3
IL4 -0.118 0.28 -9999 0 -0.526 6 6
IL2 -0.008 0.074 -9999 0 -0.382 1 1
IL3 -0.001 0.016 -9999 0 -9999 0 0
FKBP1A 0.017 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
Nongenotropic Androgen signaling

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
PTK2 0.013 0.001 -9999 0 -9999 0 0
GNB1/GNG2 -0.082 0.134 -9999 0 -0.313 4 4
regulation of S phase of mitotic cell cycle -0.041 0.126 -9999 0 -0.338 3 3
GNAO1 0.017 0 -9999 0 -9999 0 0
HRAS 0.016 0.001 -9999 0 -9999 0 0
SHBG/T-DHT 0.011 0 -9999 0 -9999 0 0
PELP1 0.016 0.001 -9999 0 -9999 0 0
AKT1 0.013 0.001 -9999 0 -9999 0 0
MAP2K1 -0.065 0.133 -9999 0 -0.351 3 3
T-DHT/AR -0.109 0.163 -9999 0 -0.313 10 10
G-protein coupled receptor activity 0 0 -9999 0 -9999 0 0
mol:GTP -0.002 0.003 -9999 0 -0.005 11 11
GNAI2 0.017 0 -9999 0 -9999 0 0
GNAI3 0.017 0 -9999 0 -9999 0 0
GNAI1 -0.005 0.11 -9999 0 -0.567 1 1
mol:GDP -0.101 0.179 -9999 0 -0.551 3 3
cell proliferation -0.122 0.223 -9999 0 -0.458 7 7
PIK3CA 0.017 0 -9999 0 -9999 0 0
FOS -0.23 0.371 -9999 0 -0.765 8 8
mol:Ca2+ -0.014 0.021 -9999 0 -0.075 1 1
MAPK3 -0.095 0.18 -9999 0 -0.447 4 4
MAPK1 -0.058 0.112 -9999 0 -0.258 4 4
PIK3R1 -0.005 0.11 -9999 0 -0.566 1 1
mol:IP3 -0.001 0.002 -9999 0 -0.004 11 11
cAMP biosynthetic process 0.013 0.017 -9999 0 -9999 0 0
GNG2 -0.019 0.131 -9999 0 -0.472 2 2
potassium channel inhibitor activity -0.001 0.002 -9999 0 -0.004 11 11
HRAS/GTP -0.066 0.123 -9999 0 -0.326 3 3
actin cytoskeleton reorganization -0.01 0.05 -9999 0 -0.266 1 1
SRC 0.016 0.001 -9999 0 -9999 0 0
voltage-gated calcium channel activity -0.001 0.002 -9999 0 -0.004 11 11
PI3K 0.009 0.07 -9999 0 -0.345 1 1
apoptosis 0.122 0.217 0.43 8 -9999 0 8
T-DHT/AR/PELP1 -0.082 0.14 -9999 0 -0.257 10 10
HRAS/GDP -0.09 0.174 -9999 0 -0.527 3 3
CREB1 -0.133 0.232 -9999 0 -0.462 8 8
RAC1-CDC42/GTP 0.021 0.057 -9999 0 -0.27 1 1
AR -0.152 0.226 -9999 0 -0.438 10 10
GNB1 0.017 0 -9999 0 -9999 0 0
RAF1 -0.065 0.127 -9999 0 -0.338 3 3
RAC1-CDC42/GDP -0.06 0.175 -9999 0 -0.493 3 3
T-DHT/AR/PELP1/Src -0.067 0.13 -9999 0 -0.331 3 3
MAP2K2 -0.065 0.133 -9999 0 -0.351 3 3
T-DHT/AR/PELP1/Src/PI3K -0.042 0.127 -9999 0 -0.34 3 3
GNAZ 0.017 0 -9999 0 -9999 0 0
SHBG 0.017 0 -9999 0 -9999 0 0
Gi family/GNB1/GNG2/GDP 0.006 0.107 -9999 0 -0.502 1 1
mol:T-DHT 0 0.001 -9999 0 -0.002 6 6
RAC1 0.017 0 -9999 0 -9999 0 0
GNRH1 -0.013 0.095 -9999 0 -0.34 2 2
Gi family/GTP -0.019 0.071 -9999 0 -0.211 1 1
CDC42 0.017 0 -9999 0 -9999 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.017 0.122 -9999 0 -0.354 3 3
AKT1 -0.075 0.269 -9999 0 -0.555 5 5
PTK2B -0.114 0.258 -9999 0 -0.604 5 5
VEGFR2 homodimer/Frs2 -0.1 0.275 -9999 0 -0.735 4 4
CAV1 -0.019 0.131 -9999 0 -0.472 2 2
CALM1 -0.005 0.11 -9999 0 -0.566 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.104 0.262 -9999 0 -0.672 4 4
endothelial cell proliferation -0.071 0.249 -9999 0 -0.509 5 5
mol:Ca2+ -0.131 0.288 -9999 0 -0.575 7 7
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.089 0.251 -9999 0 -0.634 4 4
RP11-342D11.1 -0.14 0.287 -9999 0 -0.583 7 7
CDH5 -0.005 0.11 -9999 0 -0.566 1 1
VEGFA homodimer 0.03 0.051 -9999 0 -9999 0 0
SHC1 0.017 0 -9999 0 -9999 0 0
SHC2 0.017 0 -9999 0 -9999 0 0
HRAS/GDP -0.148 0.216 -9999 0 -0.538 5 5
SH2D2A 0.017 0 -9999 0 -9999 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.101 0.252 -9999 0 -0.527 5 5
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.104 0.262 -9999 0 -0.672 4 4
VEGFR1 homodimer 0.017 0 -9999 0 -9999 0 0
SHC/GRB2/SOS1 -0.165 0.241 -9999 0 -0.6 5 5
GRB10 -0.176 0.329 -9999 0 -0.637 8 8
PTPN11 0.017 0 -9999 0 -9999 0 0
GRB2 0.017 0 -9999 0 -9999 0 0
PAK1 -0.063 0.193 -9999 0 -0.519 4 4
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.109 0.305 -9999 0 -0.734 4 4
HRAS 0.017 0 -9999 0 -9999 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.054 0.18 -9999 0 -0.391 5 5
HIF1A 0.017 0 -9999 0 -9999 0 0
FRS2 0.017 0 -9999 0 -9999 0 0
oxygen and reactive oxygen species metabolic process -0.089 0.247 -9999 0 -0.625 4 4
mol:GTP 0 0 -9999 0 -9999 0 0
FLT4 0.017 0 -9999 0 -9999 0 0
Nck/Pak -0.033 0.142 -9999 0 -0.367 4 4
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.104 0.262 -9999 0 -0.672 4 4
mol:GDP -0.16 0.233 -9999 0 -0.58 5 5
mol:NADP -0.06 0.223 -9999 0 -0.449 5 5
eNOS/Hsp90 -0.049 0.211 -9999 0 -0.498 2 2
PIK3R1 -0.005 0.11 -9999 0 -0.566 1 1
mol:IP3 -0.133 0.292 -9999 0 -0.584 7 7
HIF1A/ARNT 0.025 0 -9999 0 -9999 0 0
SHB -0.005 0.11 -9999 0 -0.566 1 1
VEGFA -0.01 0.092 -9999 0 -0.453 1 1
VEGFC -0.005 0.11 -9999 0 -0.566 1 1
FAK1/Vinculin -0.097 0.271 -9999 0 -0.675 4 4
mol:Ca ++ 0 0 -9999 0 -9999 0 0
RHOA -0.005 0.11 -9999 0 -0.566 1 1
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.119 0.275 -9999 0 -0.642 5 5
PTPN6 -0.049 0.16 -9999 0 -0.425 4 4
EPAS1 -0.063 0.195 -9999 0 -0.466 4 4
mol:L-citrulline -0.06 0.223 -9999 0 -0.449 5 5
ITGAV -0.005 0.11 -9999 0 -0.566 1 1
PIK3CA 0.017 0 -9999 0 -9999 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.089 0.251 -9999 0 -0.634 4 4
VEGFR2 homodimer/VEGFA homodimer -0.151 0.315 -9999 0 -0.635 7 7
VEGFR2/3 heterodimer -0.1 0.275 -9999 0 -0.735 4 4
VEGFB 0.017 0 -9999 0 -9999 0 0
MAPK11 -0.132 0.296 -9999 0 -0.589 7 7
VEGFR2 homodimer -0.122 0.308 -9999 0 -0.83 4 4
FLT1 0.017 0 -9999 0 -9999 0 0
NEDD4 -0.025 0.12 -9999 0 -0.432 2 2
MAPK3 -0.115 0.265 -9999 0 -0.548 6 6
MAPK1 -0.115 0.265 -9999 0 -0.525 7 7
VEGFA145/NRP2 0.007 0.065 -9999 0 -0.312 1 1
VEGFR1/2 heterodimer -0.1 0.275 -9999 0 -0.735 4 4
KDR -0.122 0.31 -9999 0 -0.833 4 4
VEGFA165/NRP1/VEGFR2 homodimer -0.129 0.29 -9999 0 -0.576 7 7
SRC 0.017 0 -9999 0 -9999 0 0
platelet activating factor biosynthetic process -0.117 0.271 -9999 0 -0.559 6 6
PI3K -0.116 0.334 -9999 0 -0.698 5 5
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.104 0.262 -9999 0 -0.672 4 4
FES -0.145 0.326 -9999 0 -0.631 7 7
GAB1 -0.15 0.238 -9999 0 -0.656 4 4
VEGFR2 homodimer/VEGFA homodimer/Src -0.104 0.262 -9999 0 -0.672 4 4
CTNNB1 -0.026 0.153 -9999 0 -0.566 2 2
SOS1 0.017 0 -9999 0 -9999 0 0
ARNT 0.017 0 -9999 0 -9999 0 0
eNOS/Caveolin-1 -0.063 0.219 -9999 0 -0.562 2 2
VEGFR2 homodimer/VEGFA homodimer/Yes -0.115 0.294 -9999 0 -0.742 4 4
PI3K/GAB1 -0.076 0.276 -9999 0 -0.571 5 5
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.118 0.282 -9999 0 -0.652 5 5
PRKACA 0.017 0 -9999 0 -9999 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.093 0.291 -9999 0 -0.749 4 4
HSP90AA1 0.017 0 -9999 0 -9999 0 0
CDC42 -0.135 0.297 -9999 0 -0.593 7 7
actin cytoskeleton reorganization -0.104 0.259 -9999 0 -0.665 4 4
PTK2 -0.107 0.293 -9999 0 -0.737 4 4
EDG1 -0.168 0.348 -9999 0 -0.719 7 7
mol:DAG -0.133 0.292 -9999 0 -0.584 7 7
CaM/Ca2+ -0.125 0.296 -9999 0 -0.598 6 6
MAP2K3 -0.121 0.283 -9999 0 -0.582 6 6
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.179 0.341 -9999 0 -0.657 8 8
PLCG1 -0.135 0.297 -9999 0 -0.593 7 7
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.1 0.282 -9999 0 -0.703 4 4
IQGAP1 0.017 0 -9999 0 -9999 0 0
YES1 -0.005 0.11 -9999 0 -0.566 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.104 0.262 -9999 0 -0.672 4 4
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.14 0.259 -9999 0 -0.672 4 4
cell migration -0.063 0.251 -9999 0 -0.592 4 4
mol:PI-3-4-5-P3 -0.101 0.296 -9999 0 -0.621 5 5
FYN 0.017 0 -9999 0 -9999 0 0
VEGFB/NRP1 -0.125 0.273 -9999 0 -0.547 7 7
mol:NO -0.06 0.223 -9999 0 -0.449 5 5
PXN 0.017 0 -9999 0 -9999 0 0
HRAS/GTP -0.148 0.216 -9999 0 -0.538 5 5
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.179 0.34 -9999 0 -0.655 8 8
VHL 0.017 0 -9999 0 -9999 0 0
ITGB3 -0.019 0.131 -9999 0 -0.472 2 2
NOS3 -0.073 0.251 -9999 0 -0.512 5 5
VEGFR2 homodimer/VEGFA homodimer/Sck -0.104 0.262 -9999 0 -0.672 4 4
RAC1 0.017 0 -9999 0 -9999 0 0
PRKCA -0.116 0.274 -9999 0 -0.564 6 6
PRKCB -0.125 0.274 -9999 0 -0.547 7 7
VCL 0.002 0.075 -9999 0 -0.378 1 1
VEGFA165/NRP1 -0.14 0.289 -9999 0 -0.585 7 7
VEGFR1/2 heterodimer/VEGFA homodimer -0.104 0.262 -9999 0 -0.672 4 4
VEGFA165/NRP2 0.007 0.065 -9999 0 -0.312 1 1
MAPKKK cascade -0.123 0.29 -9999 0 -0.53 8 8
NRP2 0.017 0 -9999 0 -9999 0 0
VEGFC homodimer -0.005 0.11 -9999 0 -0.565 1 1
NCK1 0.017 0 -9999 0 -9999 0 0
ROCK1 0.017 0 -9999 0 -9999 0 0
FAK1/Paxillin -0.091 0.273 -9999 0 -0.675 4 4
MAP3K13 -0.135 0.297 -9999 0 -0.593 7 7
PDPK1 -0.078 0.26 -9999 0 -0.535 5 5
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.102 0.171 -9999 0 -0.305 9 9
epithelial cell differentiation -0.122 0.174 -9999 0 -0.33 9 9
CYFIP2 0.002 0.075 -9999 0 -0.378 1 1
ENAH -0.059 0.146 -9999 0 -0.412 2 2
EGFR -0.041 0.166 -9999 0 -0.503 3 3
EPHA2 0.002 0.075 -9999 0 -0.378 1 1
MYO6 -0.119 0.199 -9999 0 -0.34 9 9
CTNNB1 -0.026 0.153 -9999 0 -0.566 2 2
ABI1/Sra1/Nap1 0.026 0.044 -9999 0 -9999 0 0
AQP5 -0.125 0.134 -9999 0 -0.454 2 2
CTNND1 0.017 0 -9999 0 -9999 0 0
mol:PI-4-5-P2 -0.107 0.164 -9999 0 -0.304 9 9
regulation of calcium-dependent cell-cell adhesion -0.107 0.164 -9999 0 -0.304 9 9
EGF -0.012 0.103 -9999 0 -0.378 2 2
NCKAP1 0.017 0 -9999 0 -9999 0 0
AQP3 -0.116 0.133 -9999 0 -0.454 2 2
cortical microtubule organization -0.122 0.174 -9999 0 -0.33 9 9
GO:0000145 -0.103 0.156 -9999 0 -0.291 9 9
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.121 0.177 -9999 0 -0.333 9 9
MLLT4 -0.005 0.11 -9999 0 -0.566 1 1
ARF6/GDP -0.109 0.135 -9999 0 -0.47 2 2
ARF6 0.017 0 -9999 0 -9999 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.028 0.056 -9999 0 -9999 0 0
mol:Ca2+ 0 0 -9999 0 -9999 0 0
VASP -0.093 0.155 -9999 0 -0.445 2 2
PVRL2 -0.005 0.11 -9999 0 -0.566 1 1
ZYX -0.109 0.167 -9999 0 -0.309 9 9
ARF6/GTP 0.033 0.052 -9999 0 -9999 0 0
CDH1 -0.244 0.26 -9999 0 -0.486 14 14
EGFR/EGFR/EGF/EGF -0.158 0.153 -9999 0 -0.441 4 4
RhoA/GDP -0.138 0.181 -9999 0 -0.337 9 9
actin cytoskeleton organization -0.113 0.191 -9999 0 -0.482 3 3
IGF-1R heterotetramer 0.017 0 -9999 0 -9999 0 0
GIT1 0.017 0 -9999 0 -9999 0 0
IGF1R 0.017 0 -9999 0 -9999 0 0
IGF1 -0.005 0.11 -9999 0 -0.566 1 1
DIAPH1 0.002 0.046 -9999 0 -9999 0 0
Wnt receptor signaling pathway 0.122 0.174 0.33 9 -9999 0 9
RHOA -0.005 0.11 -9999 0 -0.566 1 1
RhoA/GTP -0.118 0.166 -9999 0 -0.58 2 2
CTNNA1 0.017 0 -9999 0 -9999 0 0
VCL -0.116 0.197 -9999 0 -0.498 3 3
EFNA1 0.002 0.075 -9999 0 -0.378 1 1
LPP -0.103 0.157 -9999 0 -0.456 2 2
Ephrin A1/EPHA2 -0.133 0.158 -9999 0 -0.548 2 2
SEC6/SEC8 -0.127 0.166 -9999 0 -0.492 3 3
MGAT3 -0.109 0.167 -9999 0 -0.309 9 9
HGF/MET -0.144 0.149 -9999 0 -0.413 4 4
HGF -0.027 0.124 -9999 0 -0.378 3 3
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.102 0.172 -9999 0 -0.307 9 9
actin cable formation -0.037 0.128 -9999 0 -0.426 1 1
KIAA1543 -0.138 0.226 -9999 0 -0.572 4 4
KIFC3 -0.109 0.167 -9999 0 -0.309 9 9
NCK1 0.017 0 -9999 0 -9999 0 0
EXOC3 0.017 0 -9999 0 -9999 0 0
ACTN1 -0.116 0.164 -9999 0 -0.309 9 9
NCK1/GIT1 0.025 0 -9999 0 -9999 0 0
mol:GDP -0.122 0.174 -9999 0 -0.33 9 9
EXOC4 0.017 0 -9999 0 -9999 0 0
STX4 -0.109 0.167 -9999 0 -0.309 9 9
PIP5K1C -0.109 0.167 -9999 0 -0.309 9 9
LIMA1 0.017 0 -9999 0 -9999 0 0
ABI1 0.017 0 -9999 0 -9999 0 0
ROCK1 -0.069 0.162 -9999 0 -0.481 2 2
adherens junction assembly -0.113 0.219 -9999 0 -0.537 4 4
IGF-1R heterotetramer/IGF1 -0.132 0.174 -9999 0 -0.599 2 2
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.007 0.113 -9999 0 -0.406 2 2
MET 0.002 0.075 -9999 0 -0.378 1 1
PLEKHA7 -0.109 0.167 -9999 0 -0.309 9 9
mol:GTP 0.026 0.055 -9999 0 -9999 0 0
establishment of epithelial cell apical/basal polarity -0.086 0.183 -9999 0 -0.465 3 3
cortical actin cytoskeleton stabilization -0.102 0.171 -9999 0 -0.305 9 9
regulation of cell-cell adhesion -0.113 0.191 -9999 0 -0.482 3 3
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.102 0.172 -9999 0 -0.307 9 9
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.17 0.244 -9999 0 -0.492 9 9
KLHL20 -0.063 0.071 -9999 0 -0.26 1 1
CYFIP2 0.002 0.075 -9999 0 -0.378 1 1
Rac1/GDP -0.077 0.158 -9999 0 -0.389 2 2
ENAH -0.174 0.251 -9999 0 -0.481 10 10
AP1M1 0.017 0 -9999 0 -9999 0 0
RAP1B 0.017 0 -9999 0 -9999 0 0
RAP1A 0.017 0 -9999 0 -9999 0 0
CTNNB1 -0.026 0.153 -9999 0 -0.566 2 2
CDC42/GTP -0.086 0.103 -9999 0 -0.329 2 2
ABI1/Sra1/Nap1 -0.043 0.05 -9999 0 -0.17 1 1
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.128 0.187 -9999 0 -0.353 9 9
RAPGEF1 -0.127 0.215 -9999 0 -0.412 9 9
CTNND1 0.017 0 -9999 0 -9999 0 0
regulation of calcium-dependent cell-cell adhesion -0.176 0.254 -9999 0 -0.513 9 9
CRK -0.146 0.232 -9999 0 -0.454 9 9
E-cadherin/gamma catenin/alpha catenin -0.128 0.163 -9999 0 -0.337 8 8
alphaE/beta7 Integrin 0.025 0 -9999 0 -9999 0 0
IQGAP1 0.017 0 -9999 0 -9999 0 0
NCKAP1 0.017 0 -9999 0 -9999 0 0
Rap1/GTP/I-afadin 0.02 0.064 -9999 0 -0.306 1 1
DLG1 -0.163 0.248 -9999 0 -0.492 9 9
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -9999 0 0
mol:PI-3-4-5-P3 -0.064 0.083 -9999 0 -0.275 2 2
MLLT4 -0.005 0.11 -9999 0 -0.566 1 1
ARF6/GTP/NME1/Tiam1 0.02 0.064 -9999 0 -0.306 1 1
PI3K -0.082 0.11 -9999 0 -0.369 2 2
ARF6 0.017 0 -9999 0 -9999 0 0
mol:Ca2+ 0 0 -9999 0 -9999 0 0
E-cadherin/gamma catenin -0.164 0.19 -9999 0 -0.34 14 14
TIAM1 -0.005 0.11 -9999 0 -0.566 1 1
E-cadherin(dimer)/Ca2+ -0.122 0.177 -9999 0 -0.333 9 9
AKT1 -0.045 0.059 -9999 0 -0.241 1 1
PIK3R1 -0.005 0.11 -9999 0 -0.566 1 1
CDH1 -0.244 0.26 -9999 0 -0.486 14 14
RhoA/GDP -0.083 0.178 -9999 0 -0.487 2 2
actin cytoskeleton organization -0.027 0.073 -9999 0 -0.187 1 1
CDC42/GDP -0.076 0.158 -9999 0 -0.389 2 2
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.083 0.12 -9999 0 -0.251 8 8
ITGB7 0.017 0 -9999 0 -9999 0 0
RAC1 0.017 0 -9999 0 -9999 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.129 0.187 -9999 0 -0.353 9 9
E-cadherin/Ca2+/beta catenin/alpha catenin -0.131 0.176 -9999 0 -0.341 9 9
mol:GDP -0.099 0.181 -9999 0 -0.468 2 2
CDC42/GTP/IQGAP1 0.023 0 -9999 0 -9999 0 0
JUP 0.017 0 -9999 0 -9999 0 0
p120 catenin/RhoA/GDP -0.085 0.178 -9999 0 -0.489 2 2
RAC1/GTP/IQGAP1 0.023 0 -9999 0 -9999 0 0
PIP5K1C/AP1M1 0.025 0 -9999 0 -9999 0 0
RHOA -0.005 0.11 -9999 0 -0.566 1 1
CDC42 0.017 0 -9999 0 -9999 0 0
CTNNA1 0.017 0 -9999 0 -9999 0 0
positive regulation of S phase of mitotic cell cycle -0.025 0.07 -9999 0 -0.168 3 3
NME1 0.017 0 -9999 0 -9999 0 0
clathrin coat assembly 0 0 -9999 0 -9999 0 0
TJP1 -0.163 0.248 -9999 0 -0.492 9 9
regulation of cell-cell adhesion -0.077 0.091 -9999 0 -0.287 2 2
WASF2 -0.021 0.027 -9999 0 -9999 0 0
Rap1/GTP -0.1 0.119 -9999 0 -0.381 2 2
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.09 0.142 -9999 0 -0.272 8 8
CCND1 -0.032 0.085 -9999 0 -0.208 3 3
VAV2 -0.139 0.231 -9999 0 -0.444 9 9
RAP1/GDP -0.072 0.149 -9999 0 -0.379 2 2
adherens junction assembly -0.157 0.239 -9999 0 -0.475 9 9
homophilic cell adhesion 0 0 -9999 0 -9999 0 0
ABI1 0.017 0 -9999 0 -9999 0 0
PIP5K1C 0.017 0 -9999 0 -9999 0 0
regulation of heterotypic cell-cell adhesion -0.1 0.171 -9999 0 -0.485 2 2
E-cadherin/beta catenin -0.149 0.165 -9999 0 -0.365 9 9
mol:GTP 0 0 -9999 0 -9999 0 0
SRC -0.165 0.246 -9999 0 -0.492 9 9
PIK3CA 0.017 0 -9999 0 -9999 0 0
Rac1/GTP -0.101 0.113 -9999 0 -0.439 1 1
E-cadherin/beta catenin/alpha catenin -0.152 0.202 -9999 0 -0.394 9 9
ITGAE 0.017 0 -9999 0 -9999 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.181 0.261 -9999 0 -0.526 9 9
Aurora B signaling

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
Condensin I complex -0.049 0.167 -9999 0 -0.362 5 5
STMN1 -0.015 0.119 -9999 0 -0.336 3 3
Aurora B/RasGAP/Survivin -0.08 0.178 -9999 0 -0.37 7 7
Chromosomal passenger complex/Cul3 protein complex -0.068 0.159 -9999 0 -0.289 8 8
BIRC5 -0.142 0.249 -9999 0 -0.517 8 8
DES -0.03 0.054 -9999 0 -9999 0 0
Aurora C/Aurora B/INCENP 0.005 0.07 -9999 0 -9999 0 0
Aurora B/TACC1 -0.007 0.115 -9999 0 -0.379 2 2
Aurora B/PP2A 0.005 0.074 -9999 0 -0.256 2 2
mol:GTP 0 0 -9999 0 -9999 0 0
CBX5 0.012 0.023 -9999 0 -9999 0 0
mitotic metaphase/anaphase transition 0.001 0.005 -9999 0 -9999 0 0
NDC80 -0.142 0.21 -9999 0 -0.388 11 11
Cul3 protein complex 0.012 0.081 -9999 0 -0.337 1 1
KIF2C -0.178 0.293 -9999 0 -0.462 11 11
PEBP1 -0.01 0.111 -9999 0 -0.574 1 1
KIF20A -0.121 0.238 -9999 0 -0.517 7 7
mol:GDP 0 0 -9999 0 -9999 0 0
Aurora B/RasGAP 0.005 0.074 -9999 0 -0.256 2 2
SEPT1 0.017 0 -9999 0 -9999 0 0
SMC2 -0.012 0.103 -9999 0 -0.378 2 2
SMC4 -0.056 0.153 -9999 0 -0.378 5 5
NSUN2/NPM1/Nucleolin -0.026 0.088 -9999 0 -9999 0 0
PSMA3 0.017 0 -9999 0 -9999 0 0
G2/M transition of mitotic cell cycle -0.001 0.004 -9999 0 -9999 0 0
H3F3B 0.007 0.047 -9999 0 -0.16 2 2
AURKB -0.013 0.107 -9999 0 -0.392 2 2
AURKC 0.002 0.075 -9999 0 -0.378 1 1
CDCA8 -0.091 0.201 -9999 0 -0.457 6 6
cytokinesis -0.251 0.385 -9999 0 -0.769 9 9
Aurora B/Septin1 -0.25 0.331 -9999 0 -0.7 9 9
AURKA -0.013 0.105 -9999 0 -0.383 2 2
INCENP 0.011 0.008 -9999 0 -9999 0 0
KLHL13 0.002 0.075 -9999 0 -0.378 1 1
BUB1 -0.218 0.251 -9999 0 -0.469 13 13
hSgo1/Aurora B/Survivin -0.091 0.205 -9999 0 -0.413 7 7
EVI5 0.015 0.003 -9999 0 -9999 0 0
RhoA/GTP -0.272 0.349 -9999 0 -0.7 10 10
SGOL1 -0.019 0.131 -9999 0 -0.472 2 2
CENPA -0.141 0.217 -9999 0 -0.434 9 9
NCAPG 0 0 -9999 0 -9999 0 0
Aurora B/HC8 Proteasome 0.005 0.074 -9999 0 -0.256 2 2
NCAPD2 -0.027 0.124 -9999 0 -0.378 3 3
Aurora B/PP1-gamma 0.005 0.074 -9999 0 -0.256 2 2
RHOA -0.005 0.11 -9999 0 -0.566 1 1
NCAPH -0.063 0.171 -9999 0 -0.416 5 5
NPM1 -0.009 0.059 -9999 0 -9999 0 0
RASA1 0.017 0 -9999 0 -9999 0 0
KLHL9 -0.005 0.11 -9999 0 -0.566 1 1
mitotic prometaphase -0.005 0.008 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.005 0.074 -9999 0 -0.255 2 2
PPP1CC 0.017 0 -9999 0 -9999 0 0
Centraspindlin -0.267 0.387 -9999 0 -0.743 10 10
RhoA/GDP -0.003 0.081 -9999 0 -0.415 1 1
NSUN2 -0.009 0.059 -9999 0 -9999 0 0
MYLK 0 0.056 -9999 0 -0.16 3 3
KIF23 -0.183 0.265 -9999 0 -0.522 10 10
VIM -0.128 0.21 -9999 0 -0.388 10 10
RACGAP1 -0.047 0.142 -9999 0 -0.387 4 4
mitosis 0 0 -9999 0 -9999 0 0
NCL -0.009 0.059 -9999 0 -9999 0 0
Chromosomal passenger complex -0.182 0.284 -9999 0 -0.556 9 9
Chromosomal passenger complex/EVI5 -0.128 0.209 -9999 0 -0.402 9 9
TACC1 -0.005 0.11 -9999 0 -0.566 1 1
PPP2R5D 0.017 0 -9999 0 -9999 0 0
CUL3 0.017 0 -9999 0 -9999 0 0
response to DNA damage stimulus 0 0 -9999 0 -9999 0 0
Syndecan-1-mediated signaling events

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
TGFB1 0.017 0 -9999 0 -9999 0 0
CCL5 0.002 0.075 -9999 0 -0.378 1 1
SDCBP 0.017 0 -9999 0 -9999 0 0
FGFR/FGF2/Syndecan-1 -0.153 0.127 -9999 0 -0.391 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 -0.137 0.121 -9999 0 -0.404 2 2
Syndecan-1/Syntenin -0.137 0.121 -9999 0 -0.404 2 2
MAPK3 -0.111 0.112 -9999 0 -0.45 1 1
HGF/MET -0.016 0.098 -9999 0 -0.252 4 4
TGFB1/TGF beta receptor Type II 0.017 0 -9999 0 -9999 0 0
BSG 0.017 0 -9999 0 -9999 0 0
keratinocyte migration -0.136 0.119 -9999 0 -0.399 2 2
Syndecan-1/RANTES -0.144 0.129 -9999 0 -0.372 4 4
Syndecan-1/CD147 -0.124 0.118 -9999 0 -0.48 1 1
Syndecan-1/Syntenin/PIP2 -0.132 0.117 -9999 0 -0.391 2 2
LAMA5 0.017 0 -9999 0 -9999 0 0
positive regulation of cell-cell adhesion -0.13 0.114 -9999 0 -0.383 2 2
MMP7 -0.308 0.259 -9999 0 -0.5 17 17
HGF -0.027 0.124 -9999 0 -0.378 3 3
Syndecan-1/CASK -0.146 0.12 -9999 0 -0.374 3 3
Syndecan-1/HGF/MET -0.15 0.129 -9999 0 -0.382 3 3
regulation of cell adhesion -0.101 0.109 -9999 0 -0.43 1 1
HPSE -0.041 0.166 -9999 0 -0.503 3 3
positive regulation of cell migration -0.153 0.127 -9999 0 -0.391 3 3
SDC1 -0.154 0.128 -9999 0 -0.395 3 3
Syndecan-1/Collagen -0.153 0.127 -9999 0 -0.391 3 3
PPIB 0.017 0 -9999 0 -9999 0 0
MET 0.002 0.075 -9999 0 -0.378 1 1
PRKACA 0.017 0 -9999 0 -9999 0 0
MMP9 -0.077 0.201 -9999 0 -0.491 5 5
MAPK1 -0.111 0.112 -9999 0 -0.45 1 1
homophilic cell adhesion -0.152 0.125 -9999 0 -0.388 3 3
MMP1 -0.027 0.124 -9999 0 -0.378 3 3
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.011 0.07 -9999 0 -0.288 1 1
RGS9BP -0.077 0.201 -9999 0 -0.491 5 5
mol:GTP 0 0 -9999 0 -9999 0 0
GRK1 0 0 -9999 0 -9999 0 0
mol:Na + -0.058 0.14 -9999 0 -0.288 7 7
mol:ADP 0.013 0 -9999 0 -9999 0 0
GNAT2 -0.019 0.131 -9999 0 -0.472 2 2
RGS9-1/Gbeta5/R9AP -0.104 0.208 -9999 0 -0.402 8 8
mol:GDP 0 0 -9999 0 -9999 0 0
PDE6H/GNAT2/GTP -0.017 0.097 -9999 0 -0.244 4 4
GRK7 0.017 0 -9999 0 -9999 0 0
CNGB3 -0.035 0.147 -9999 0 -0.441 3 3
Cone Metarhodopsin II/X-Arrestin 0.012 0 -9999 0 -9999 0 0
mol:Ca2+ -0.067 0.131 -9999 0 -0.305 4 4
Cone PDE6 -0.085 0.18 -9999 0 -0.33 8 8
Cone Metarhodopsin II 0.011 0 -9999 0 -9999 0 0
Na + (4 Units) -0.065 0.132 -9999 0 -0.304 4 4
GNAT2/GDP -0.098 0.193 -9999 0 -0.352 9 9
GNB5 0.017 0 -9999 0 -9999 0 0
mol:GMP (4 units) -0.006 0.088 -9999 0 -0.305 1 1
Cone Transducin 0.012 0.074 -9999 0 -0.306 1 1
SLC24A2 -0.027 0.124 -9999 0 -0.378 3 3
GNB3/GNGT2 0.025 0 -9999 0 -9999 0 0
GNB3 0.017 0 -9999 0 -9999 0 0
GNAT2/GTP -0.014 0.094 -9999 0 -0.339 2 2
CNGA3 -0.063 0.193 -9999 0 -0.519 4 4
ARR3 0.017 0 -9999 0 -9999 0 0
absorption of light 0 0 -9999 0 -9999 0 0
cGMP/Cone CNG Channel -0.058 0.141 -9999 0 -0.289 7 7
mol:Pi -0.103 0.207 -9999 0 -0.4 8 8
Cone CNG Channel -0.056 0.142 -9999 0 -0.283 6 6
mol:all-trans-retinal 0 0 -9999 0 -9999 0 0
mol:K + -0.027 0.124 -9999 0 -0.378 3 3
RGS9 -0.113 0.242 -9999 0 -0.566 6 6
PDE6C 0.017 0 -9999 0 -9999 0 0
GNGT2 0.017 0 -9999 0 -9999 0 0
mol:cGMP (4 units) 0 0 -9999 0 -9999 0 0
PDE6H -0.012 0.103 -9999 0 -0.378 2 2
Osteopontin-mediated events

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
IKK alpha homodimer -0.068 0.138 -9999 0 -0.321 1 1
NF kappa B1 p50/RelA/I kappa B alpha -0.032 0.132 -9999 0 -9999 0 0
alphaV/beta3 Integrin/Osteopontin/Src -0.111 0.183 -9999 0 -0.396 6 6
AP1 -0.148 0.196 -9999 0 -0.548 3 3
ILK -0.075 0.145 -9999 0 -9999 0 0
bone resorption -0.122 0.215 -9999 0 -0.529 4 4
PTK2B 0.002 0.075 -9999 0 -0.378 1 1
PYK2/p130Cas -0.094 0.167 -9999 0 -0.524 1 1
ITGAV 0 0.109 -9999 0 -0.555 1 1
mol:GTP 0 0 -9999 0 -9999 0 0
CD44/Rho Family GTPase/ROCK2 -0.054 0.151 -9999 0 -0.329 6 6
alphaV/beta3 Integrin/Osteopontin -0.095 0.162 -9999 0 -0.322 7 7
MAP3K1 -0.084 0.145 -9999 0 -0.327 1 1
JUN -0.041 0.166 -9999 0 -0.503 3 3
MAPK3 -0.066 0.141 -9999 0 -0.357 1 1
MAPK1 -0.066 0.141 -9999 0 -0.357 1 1
Rac1/GDP 0.012 0 -9999 0 -9999 0 0
NFKB1 0.017 0 -9999 0 -9999 0 0
MAPK8 -0.068 0.136 -9999 0 -0.302 1 1
ITGB3 -0.015 0.129 -9999 0 -0.461 2 2
NFKBIA -0.052 0.141 -9999 0 -0.371 1 1
FOS -0.192 0.259 -9999 0 -0.497 11 11
CD44 -0.092 0.208 -9999 0 -0.472 6 6
CHUK 0.017 0 -9999 0 -9999 0 0
PLAU -0.053 0.15 -9999 0 -0.535 1 1
NF kappa B1 p50/RelA -0.072 0.088 -9999 0 -9999 0 0
BCAR1 0.017 0 -9999 0 -9999 0 0
RELA 0.017 0 -9999 0 -9999 0 0
alphaV beta3 Integrin -0.008 0.119 -9999 0 -0.39 2 2
mol:GDP 0 0 -9999 0 -9999 0 0
SYK -0.116 0.184 -9999 0 -0.4 4 4
VAV3 -0.141 0.205 -9999 0 -0.505 4 4
MAP3K14 -0.082 0.147 -9999 0 -0.351 1 1
ROCK2 0.017 0 -9999 0 -9999 0 0
SPP1 -0.158 0.242 -9999 0 -0.464 10 10
RAC1 0.017 0 -9999 0 -9999 0 0
Rac1/GTP -0.122 0.189 -9999 0 -0.518 3 3
MMP2 -0.117 0.161 -9999 0 -0.557 1 1
Arf6 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
CENTA1/KIF3B 0.011 0 -9999 0 -9999 0 0
ARNO/beta Arrestin1-2 -0.043 0.111 -9999 0 -0.249 5 5
EGFR -0.041 0.166 -9999 0 -0.504 3 3
EPHA2 0.002 0.075 -9999 0 -0.378 1 1
USP6 0.017 0 -9999 0 -9999 0 0
IQSEC1 0.002 0.075 -9999 0 -0.379 1 1
EGFR/EGFR/EGF/EGF -0.036 0.156 -9999 0 -0.383 4 4
ARRB2 0 0.075 -9999 0 -0.341 1 1
mol:GTP 0.006 0.004 -9999 0 -9999 0 0
ARRB1 0.017 0 -9999 0 -9999 0 0
FBXO8 0.017 0 -9999 0 -9999 0 0
TSHR -0.071 0.164 -9999 0 -0.378 6 6
EGF -0.013 0.104 -9999 0 -0.379 2 2
somatostatin receptor activity 0 0 -9999 0 -0.001 4 4
ARAP2 0 0 -9999 0 0 5 5
mol:GDP -0.035 0.085 -9999 0 -0.259 2 2
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 5 5
ITGA2B 0.017 0 -9999 0 -9999 0 0
ARF6 0.017 0 -9999 0 -9999 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.027 0.056 -9999 0 -9999 0 0
ADAP1 0 0 -9999 0 0 2 2
KIF13B 0.017 0 -9999 0 -9999 0 0
HGF/MET -0.016 0.098 -9999 0 -0.252 4 4
PXN 0.017 0 -9999 0 -9999 0 0
ARF6/GTP -0.05 0.114 -9999 0 -0.261 4 4
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.027 0.14 -9999 0 -0.436 2 2
ADRB2 -0.106 0.232 -9999 0 -0.535 6 6
receptor agonist activity 0 0 -9999 0 0 3 3
actin filament binding 0 0 -9999 0 0 4 4
SRC 0.017 0 -9999 0 -9999 0 0
ITGB3 -0.019 0.131 -9999 0 -0.472 2 2
GNAQ 0 0 -9999 0 -0.001 3 3
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 2 2
ARF6/GDP 0.014 0.039 -9999 0 -9999 0 0
ARF6/GDP/GULP/ACAP1 -0.073 0.159 -9999 0 -0.34 6 6
alphaIIb/beta3 Integrin/paxillin/GIT1 0.023 0.075 -9999 0 -0.298 1 1
ACAP1 0 0 -9999 0 -9999 0 0
ACAP2 0 0 -9999 0 0 5 5
LHCGR/beta Arrestin2 -0.008 0.102 -9999 0 -0.473 1 1
EFNA1 0.002 0.075 -9999 0 -0.378 1 1
HGF -0.027 0.124 -9999 0 -0.378 3 3
CYTH3 0 0 -9999 0 -0.001 4 4
CYTH2 -0.001 0.002 -9999 0 -0.004 5 5
NCK1 0.017 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 -0.106 0.232 -9999 0 -0.535 6 6
GNAQ/ARNO -0.001 0.003 -9999 0 -0.007 3 3
mol:Phosphatidic acid 0 0 -9999 0 0 5 5
PIP3-E -0.15 0.242 -9999 0 -0.483 9 9
MET 0.002 0.075 -9999 0 -0.378 1 1
GNA14 -0.063 0.193 -9999 0 -0.519 4 4
GNA15 -0.005 0.11 -9999 0 -0.566 1 1
GIT1 0.017 0 -9999 0 -9999 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 3 3
GNA11 0.017 0 -9999 0 -9999 0 0
LHCGR -0.02 0.13 -9999 0 -0.472 2 2
AGTR1 0.017 0 -9999 0 -9999 0 0
desensitization of G-protein coupled receptor protein signaling pathway -0.008 0.102 -9999 0 -0.472 1 1
IPCEF1/ARNO -0.091 0.167 -9999 0 -0.331 7 7
alphaIIb/beta3 Integrin -0.001 0.095 -9999 0 -0.329 2 2
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS 0.016 0.099 -9999 0 -0.337 1 1
SMAD6-7/SMURF1 0.012 0.081 -9999 0 -0.337 1 1
NOG -0.034 0.147 -9999 0 -0.441 3 3
SMAD9 -0.005 0.063 -9999 0 -9999 0 0
SMAD4 0.017 0 -9999 0 -9999 0 0
SMAD5 -0.038 0.132 -9999 0 -0.408 2 2
BMP7/USAG1 -0.116 0.177 -9999 0 -0.322 11 11
SMAD5/SKI -0.027 0.127 -9999 0 -0.382 2 2
SMAD1 0.031 0.053 -9999 0 -9999 0 0
BMP2 -0.084 0.214 -9999 0 -0.529 5 5
SMAD1/SMAD1/SMAD4 -0.022 0.057 -9999 0 -9999 0 0
BMPR1A 0.017 0 -9999 0 -9999 0 0
BMPR1B -0.034 0.147 -9999 0 -0.441 3 3
BMPR1A-1B/BAMBI -0.006 0.098 -9999 0 -0.337 1 1
AHSG 0.017 0 -9999 0 -9999 0 0
CER1 0.002 0.075 -9999 0 -0.378 1 1
BMP2-4/CER1 -0.069 0.151 -9999 0 -0.337 5 5
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.061 0.191 -9999 0 -0.522 3 3
BMP2-4 (homodimer) -0.086 0.175 -9999 0 -0.348 8 8
RGMB -0.063 0.193 -9999 0 -0.519 4 4
BMP6/BMPR2/BMPR1A-1B -0.026 0.133 -9999 0 -0.315 4 4
RGMA -0.005 0.11 -9999 0 -0.566 1 1
SMURF1 0.017 0 -9999 0 -9999 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.066 0.16 -9999 0 -0.386 4 4
BMP2-4/USAG1 -0.17 0.188 -9999 0 -0.377 10 10
SMAD6/SMURF1/SMAD5 -0.027 0.127 -9999 0 -0.382 2 2
SOSTDC1 -0.164 0.243 -9999 0 -0.472 10 10
BMP7/BMPR2/BMPR1A-1B 0.008 0.105 -9999 0 -0.332 2 2
SKI 0.017 0 -9999 0 -9999 0 0
BMP6 (homodimer) -0.056 0.177 -9999 0 -0.471 4 4
HFE2 -0.005 0.11 -9999 0 -0.566 1 1
ZFYVE16 0.017 0 -9999 0 -9999 0 0
MAP3K7 0.017 0 -9999 0 -9999 0 0
BMP2-4/CHRD -0.06 0.15 -9999 0 -0.337 5 5
SMAD5/SMAD5/SMAD4 -0.027 0.127 -9999 0 -0.382 2 2
MAPK1 0.017 0 -9999 0 -9999 0 0
TAK1/TAB family -0.067 0.113 -9999 0 -0.343 3 3
BMP7 (homodimer) 0.002 0.075 -9999 0 -0.378 1 1
NUP214 0.002 0.075 -9999 0 -0.378 1 1
BMP6/FETUA -0.027 0.129 -9999 0 -0.329 4 4
SMAD1/SKI 0.039 0.051 -9999 0 -9999 0 0
SMAD6 0.002 0.075 -9999 0 -0.378 1 1
CTDSP2 0.017 0 -9999 0 -9999 0 0
BMP2-4/FETUA -0.06 0.15 -9999 0 -0.337 5 5
MAP3K7IP1 0.017 0 -9999 0 -9999 0 0
GREM1 -0.027 0.124 -9999 0 -0.378 3 3
BMPR2 (homodimer) 0.017 0 -9999 0 -9999 0 0
GADD34/PP1CA 0.034 0 -9999 0 -9999 0 0
BMPR1A-1B (homodimer) -0.011 0.106 -9999 0 -0.303 3 3
CHRDL1 -0.034 0.147 -9999 0 -0.441 3 3
ENDOFIN/SMAD1 0.039 0.051 -9999 0 -9999 0 0
SMAD6-7/SMURF1/SMAD1 0.036 0.086 -9999 0 -9999 0 0
SMAD6/SMURF1 0.017 0 -9999 0 -9999 0 0
BAMBI 0.002 0.075 -9999 0 -0.378 1 1
SMURF2 0.017 0 -9999 0 -9999 0 0
BMP2-4/CHRDL1 -0.09 0.174 -9999 0 -0.37 6 6
BMP2-4/GREM1 -0.084 0.183 -9999 0 -0.416 5 5
SMAD7 -0.005 0.11 -9999 0 -0.566 1 1
SMAD8A/SMAD8A/SMAD4 0.005 0.058 -9999 0 -9999 0 0
SMAD1/SMAD6 0.039 0.051 -9999 0 -9999 0 0
TAK1/SMAD6 0.025 0 -9999 0 -9999 0 0
BMP7 0.002 0.075 -9999 0 -0.378 1 1
BMP6 -0.056 0.177 -9999 0 -0.472 4 4
MAP3K7IP2 0.017 0 -9999 0 -9999 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.057 0.179 -9999 0 -0.47 3 3
PPM1A 0.017 0 -9999 0 -9999 0 0
SMAD1/SMURF2 0.039 0.051 -9999 0 -9999 0 0
SMAD7/SMURF1 0.009 0.081 -9999 0 -0.406 1 1
CTDSPL -0.005 0.11 -9999 0 -0.566 1 1
PPP1CA 0.017 0 -9999 0 -9999 0 0
XIAP 0 0 -9999 0 -9999 0 0
CTDSP1 0.017 0 -9999 0 -9999 0 0
PPP1R15A 0.017 0 -9999 0 -9999 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.062 0.166 -9999 0 -0.404 4 4
CHRD 0.017 0 -9999 0 -9999 0 0
BMPR2 0.017 0 -9999 0 -9999 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.069 0.17 -9999 0 -0.413 4 4
BMP4 -0.034 0.147 -9999 0 -0.441 3 3
FST 0.017 0 -9999 0 -9999 0 0
BMP2-4/NOG -0.09 0.178 -9999 0 -0.355 8 8
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.016 0.099 -9999 0 -0.305 2 2
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A -0.019 0.131 -9999 0 -0.472 2 2
LAT2 -0.051 0.175 -9999 0 -0.507 3 3
AP1 -0.159 0.206 -9999 0 -0.543 5 5
mol:PIP3 -0.056 0.208 -9999 0 -0.584 3 3
IKBKB -0.018 0.115 -9999 0 -0.294 3 3
AKT1 -0.023 0.143 -9999 0 -0.419 2 2
IKBKG -0.018 0.115 -9999 0 -0.294 3 3
MS4A2 -0.013 0.103 -9999 0 -0.376 2 2
mol:Sphingosine-1-phosphate 0 0 -9999 0 -9999 0 0
PIK3CA 0.016 0.001 -9999 0 -9999 0 0
MAP3K1 -0.039 0.177 -9999 0 -0.421 4 4
mol:Ca2+ -0.036 0.156 -9999 0 -0.42 3 3
LYN 0.016 0.005 -9999 0 -9999 0 0
CBLB -0.044 0.146 -9999 0 -0.387 3 3
SHC1 0.017 0 -9999 0 -9999 0 0
RasGAP/p62DOK -0.021 0.115 -9999 0 -0.306 3 3
positive regulation of cell migration -0.034 0.135 -9999 0 -0.415 3 3
INPP5D 0 0 -9999 0 -9999 0 0
PLD2 -0.046 0.134 -9999 0 -0.346 3 3
PTPN13 -0.079 0.159 -9999 0 -0.416 3 3
PTPN11 0.013 0.009 -9999 0 -9999 0 0
GO:0007205 0 0 -9999 0 -9999 0 0
regulation of mast cell degranulation 0.003 0.123 -9999 0 -0.336 2 2
SYK -0.057 0.182 -9999 0 -0.484 4 4
GRB2 0.017 0.001 -9999 0 -9999 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.101 0.183 -9999 0 -0.586 3 3
LAT -0.037 0.141 -9999 0 -0.387 3 3
PAK2 -0.047 0.197 -9999 0 -0.477 4 4
NFATC2 -0.027 0.043 -9999 0 -9999 0 0
HRAS -0.061 0.213 -9999 0 -0.528 4 4
GAB2 0.017 0 -9999 0 -9999 0 0
PLA2G1B 0.043 0.017 -9999 0 -9999 0 0
Fc epsilon R1 -0.082 0.163 -9999 0 -0.442 3 3
Antigen/IgE/Fc epsilon R1 -0.073 0.151 -9999 0 -0.408 3 3
mol:GDP -0.073 0.225 -9999 0 -0.565 4 4
JUN -0.041 0.166 -9999 0 -0.503 3 3
mol:Ca++ 0 0 -9999 0 -9999 0 0
PIK3R1 -0.005 0.111 -9999 0 -0.571 1 1
FOS -0.193 0.259 -9999 0 -0.498 11 11
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.048 0.148 -9999 0 -0.415 3 3
CHUK -0.018 0.115 -9999 0 -0.294 3 3
KLRG1 -0.045 0.143 -9999 0 -0.387 3 3
VAV1 -0.077 0.217 -9999 0 -0.557 4 4
calcium-dependent protein kinase C activity 0 0 -9999 0 -9999 0 0
CBL -0.037 0.141 -9999 0 -0.387 3 3
negative regulation of mast cell degranulation -0.043 0.133 -9999 0 -0.362 3 3
BTK -0.054 0.173 -9999 0 -0.491 3 3
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.105 0.174 -9999 0 -0.568 2 2
GAB2/PI3K/SHP2 -0.073 0.13 -9999 0 -0.46 2 2
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.055 0.169 -9999 0 -0.475 3 3
RAF1 0.031 0.021 -9999 0 -9999 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.134 0.172 -9999 0 -0.373 7 7
FCER1G -0.036 0.152 -9999 0 -0.457 3 3
FCER1A -0.093 0.19 -9999 0 -0.409 7 7
Antigen/IgE/Fc epsilon R1/Fyn -0.058 0.142 -9999 0 -0.374 3 3
MAPK3 0.041 0.018 -9999 0 -9999 0 0
MAPK1 0.041 0.018 -9999 0 -9999 0 0
NFKB1 0.017 0 -9999 0 -9999 0 0
MAPK8 0.014 0.05 -9999 0 -9999 0 0
DUSP1 -0.034 0.147 -9999 0 -0.441 3 3
NF-kappa-B/RelA -0.028 0.054 -9999 0 -9999 0 0
actin cytoskeleton reorganization -0.031 0.138 -9999 0 -0.43 2 2
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -9999 0 0
PI3K -0.099 0.215 -9999 0 -0.568 4 4
FER -0.037 0.141 -9999 0 -0.387 3 3
RELA 0.017 0 -9999 0 -9999 0 0
ITK -0.035 0.094 -9999 0 -0.469 1 1
SOS1 0.017 0 -9999 0 -9999 0 0
PLCG1 -0.068 0.224 -9999 0 -0.558 4 4
cytokine secretion -0.021 0.039 -9999 0 -9999 0 0
SPHK1 -0.088 0.173 -9999 0 -0.354 7 7
PTK2 -0.033 0.143 -9999 0 -0.448 2 2
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.109 0.2 -9999 0 -0.642 3 3
EDG1 -0.035 0.135 -9999 0 -0.416 3 3
mol:DAG -0.061 0.214 -9999 0 -0.608 3 3
MAP2K2 0.036 0.018 -9999 0 -9999 0 0
MAP2K1 0.036 0.018 -9999 0 -9999 0 0
MAP2K7 0.017 0 -9999 0 -9999 0 0
KLRG1/SHP2 -0.042 0.136 -9999 0 -0.367 3 3
MAP2K4 0.023 0.011 -9999 0 -9999 0 0
Fc epsilon R1/FcgammaRIIB -0.144 0.183 -9999 0 -0.397 7 7
mol:Choline -0.046 0.133 -9999 0 -0.342 3 3
SHC/Grb2/SOS1 -0.021 0.136 -9999 0 -0.407 2 2
FYN 0.017 0 -9999 0 -9999 0 0
DOK1 -0.026 0.153 -9999 0 -0.566 2 2
PXN -0.023 0.134 -9999 0 -0.411 2 2
HCLS1 -0.108 0.215 -9999 0 -0.564 4 4
PRKCB -0.039 0.155 -9999 0 -0.426 3 3
FCGR2B -0.128 0.229 -9999 0 -0.472 8 8
IGHE -0.002 0.007 -9999 0 -9999 0 0
KLRG1/SHIP -0.044 0.135 -9999 0 -0.369 3 3
LCP2 -0.013 0.104 -9999 0 -0.379 2 2
PLA2G4A -0.068 0.191 -9999 0 -0.539 3 3
RASA1 0.017 0 -9999 0 -9999 0 0
mol:Phosphatidic acid -0.046 0.133 -9999 0 -0.342 3 3
IKK complex 0.002 0.091 -9999 0 -0.21 3 3
WIPF1 0.017 0 -9999 0 -9999 0 0
PLK1 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
regulation of centriole-centriole cohesion 0.006 0.059 0.208 2 -9999 0 2
BUB1B -0.107 0.181 -9999 0 -0.322 10 10
PLK1 -0.017 0.055 -9999 0 -0.175 2 2
PLK1S1 -0.009 0.029 -9999 0 -0.091 2 2
KIF2A -0.006 0.05 -9999 0 -0.158 1 1
regulation of mitotic centrosome separation -0.017 0.055 -9999 0 -0.174 2 2
GOLGA2 0.017 0 -9999 0 -9999 0 0
Hec1/SPC24 -0.108 0.161 -9999 0 -0.292 11 11
WEE1 -0.042 0.099 -9999 0 -0.234 4 4
cytokinesis -0.12 0.223 -9999 0 -0.474 7 7
PP2A-alpha B56 -0.19 0.347 -9999 0 -0.819 6 6
AURKA -0.008 0.044 -9999 0 -0.163 1 1
PICH/PLK1 -0.108 0.215 -9999 0 -0.387 9 9
CENPE -0.063 0.148 -9999 0 -0.326 6 6
RhoA/GTP -0.003 0.081 -9999 0 -0.415 1 1
positive regulation of microtubule depolymerization -0.006 0.05 -9999 0 -0.157 1 1
PPP2CA 0.017 0 -9999 0 -9999 0 0
FZR1 0.017 0 -9999 0 -9999 0 0
TPX2 -0.081 0.132 -9999 0 -0.266 8 8
PAK1 -0.064 0.195 -9999 0 -0.526 4 4
SPC24 0 0 -9999 0 -9999 0 0
FBXW11 0.017 0 -9999 0 -9999 0 0
CLSPN -0.009 0.051 -9999 0 -0.168 2 2
GORASP1 0.017 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 -0.009 0.029 -9999 0 -0.091 2 2
G2 phase of mitotic cell cycle -0.001 0.002 -9999 0 -9999 0 0
STAG2 0.017 0 -9999 0 -9999 0 0
GRASP65/GM130/RAB1/GTP -0.003 0.02 -9999 0 -9999 0 0
spindle elongation -0.017 0.055 -9999 0 -0.174 2 2
ODF2 0.016 0.002 -9999 0 -9999 0 0
BUB1 -0.24 0.366 -9999 0 -0.906 6 6
TPT1 -0.002 0.029 -9999 0 -9999 0 0
CDC25C -0.084 0.174 -9999 0 -0.359 7 7
CDC25B 0.013 0.008 -9999 0 -9999 0 0
SGOL1 -0.006 0.059 -9999 0 -0.209 2 2
RHOA -0.005 0.11 -9999 0 -0.566 1 1
CCNB1/CDK1 -0.115 0.175 -9999 0 -0.375 8 8
CDC14B 0.013 0.001 -9999 0 -9999 0 0
CDC20 -0.056 0.153 -9999 0 -0.378 5 5
PLK1/PBIP1 -0.083 0.154 -9999 0 -0.317 8 8
mitosis 0 0.004 -9999 0 -9999 0 0
FBXO5 -0.045 0.112 -9999 0 -0.254 5 5
CDC2 -0.123 0.24 -9999 0 -0.522 7 7
NDC80 -0.186 0.252 -9999 0 -0.481 11 11
metaphase plate congression -0.002 0.03 -9999 0 -9999 0 0
ERCC6L -0.114 0.223 -9999 0 -0.427 8 8
NLP/gamma Tubulin -0.007 0.034 -9999 0 -0.104 2 2
microtubule cytoskeleton organization -0.002 0.029 -9999 0 -9999 0 0
G2/M transition DNA damage checkpoint 0.001 0.003 0.01 1 -9999 0 1
PPP1R12A 0.017 0.001 -9999 0 -9999 0 0
interphase 0.001 0.003 0.01 1 -9999 0 1
PLK1/PRC1-2 -0.13 0.2 -9999 0 -0.405 8 8
GRASP65/GM130/RAB1/GTP/PLK1 0.013 0.045 -9999 0 -9999 0 0
RAB1A 0.017 0 -9999 0 -9999 0 0
prophase 0 0 -9999 0 -9999 0 0
Aurora A/BORA -0.006 0.045 -9999 0 -0.154 1 1
mitotic prometaphase -0.001 0.001 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.039 -9999 0 -9999 0 0
microtubule-based process -0.078 0.164 -9999 0 -0.349 7 7
Golgi organization -0.017 0.055 -9999 0 -0.174 2 2
Cohesin/SA2 -0.006 0.045 -9999 0 -9999 0 0
PPP1CB/MYPT1 0.025 0.002 -9999 0 -9999 0 0
KIF20A -0.12 0.236 -9999 0 -0.512 7 7
APC/C/CDC20 -0.042 0.105 -9999 0 -0.241 5 5
PPP2R1A 0.017 0 -9999 0 -9999 0 0
chromosome segregation -0.082 0.152 -9999 0 -0.312 8 8
PRC1 -0.114 0.207 -9999 0 -0.425 8 8
ECT2 -0.035 0.101 -9999 0 -0.252 4 4
C13orf34 -0.008 0.048 -9999 0 -0.161 1 1
NUDC -0.002 0.03 -9999 0 -9999 0 0
regulation of attachment of spindle microtubules to kinetochore -0.106 0.179 -9999 0 -0.318 10 10
spindle assembly -0.011 0.046 -9999 0 -0.144 2 2
spindle stabilization -0.009 0.029 -9999 0 -0.091 2 2
APC/C/HCDH1 0.022 0.001 -9999 0 -9999 0 0
MKLP2/PLK1 -0.079 0.165 -9999 0 -0.352 7 7
CCNB1 -0.031 0.125 -9999 0 -0.385 3 3
PPP1CB 0.017 0.001 -9999 0 -9999 0 0
BTRC 0.017 0 -9999 0 -9999 0 0
ROCK2 -0.005 0.071 -9999 0 -0.335 1 1
TUBG1 -0.002 0.029 -9999 0 -9999 0 0
G2/M transition of mitotic cell cycle -0.119 0.167 -9999 0 -0.367 8 8
MLF1IP -0.104 0.185 -9999 0 -0.383 8 8
INCENP 0.012 0.006 -9999 0 -9999 0 0
IL1-mediated signaling events

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
UBC13/UEV1A 0.012 0 -9999 0 -9999 0 0
PRKCZ 0 0 -9999 0 -9999 0 0
MAP3K7IP2 0.017 0 -9999 0 -9999 0 0
ERC1 0.017 0 -9999 0 -9999 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.105 0.185 -9999 0 -0.603 2 2
IRAK/TOLLIP 0.031 0 -9999 0 -9999 0 0
IKBKB 0.017 0 -9999 0 -9999 0 0
IKBKG 0.017 0 -9999 0 -9999 0 0
IL1 alpha/IL1R2 -0.166 0.2 -9999 0 -0.344 14 14
IL1A -0.187 0.235 -9999 0 -0.441 12 12
IL1B -0.219 0.215 -9999 0 -0.363 17 17
IRAK/TRAF6/p62/Atypical PKCs 0.032 0.056 -9999 0 -9999 0 0
IL1R2 -0.048 0.183 -9999 0 -0.566 3 3
IL1R1 -0.005 0.11 -9999 0 -0.566 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.059 0.169 -9999 0 -0.496 2 2
TOLLIP 0.017 0 -9999 0 -9999 0 0
TICAM2 0 0 -9999 0 -9999 0 0
MAP3K3 0.017 0 -9999 0 -9999 0 0
TAK1/TAB1/TAB2 0.034 0 -9999 0 -9999 0 0
IKK complex/ELKS 0.071 0.019 -9999 0 -9999 0 0
JUN 0.033 0.079 -9999 0 -9999 0 0
MAP3K7 0.017 0 -9999 0 -9999 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.17 0.237 -9999 0 -0.48 6 6
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.118 0.165 -9999 0 -0.361 6 6
PIK3R1 -0.005 0.11 -9999 0 -0.566 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.102 0.157 -9999 0 -0.454 2 2
IL1 beta fragment/IL1R1/IL1RAP -0.195 0.219 -9999 0 -0.404 11 11
NFKB1 0.017 0 -9999 0 -9999 0 0
MAPK8 0.055 0 -9999 0 -9999 0 0
IRAK1 0.022 0 -9999 0 -9999 0 0
IL1RN/IL1R1 -0.001 0.095 -9999 0 -0.329 2 2
IRAK4 0.017 0 -9999 0 -9999 0 0
PRKCI 0.017 0 -9999 0 -9999 0 0
TRAF6 0.017 0 -9999 0 -9999 0 0
PI3K 0.009 0.081 -9999 0 -0.406 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.11 0.192 -9999 0 -0.515 3 3
CHUK 0.017 0 -9999 0 -9999 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.195 0.219 -9999 0 -0.404 11 11
IL1 beta/IL1R2 -0.214 0.224 -9999 0 -0.444 11 11
IRAK/TRAF6/TAK1/TAB1/TAB2 0.052 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelA -0.164 0.195 -9999 0 -0.572 3 3
IRAK3 -0.07 0.187 -9999 0 -0.453 5 5
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.169 0.202 -9999 0 -0.361 11 11
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.073 0.13 -9999 0 -0.379 2 2
IL1 alpha/IL1R1/IL1RAP -0.141 0.179 -9999 0 -0.403 6 6
RELA 0.017 0 -9999 0 -9999 0 0
MAP3K7IP1 0.017 0 -9999 0 -9999 0 0
SQSTM1 -0.005 0.11 -9999 0 -0.566 1 1
MYD88 0.017 0 -9999 0 -9999 0 0
IRAK/TRAF6/MEKK3 0.04 0 -9999 0 -9999 0 0
IL1RAP -0.049 0.16 -9999 0 -0.425 4 4
UBE2N 0.017 0 -9999 0 -9999 0 0
IRAK/TRAF6 -0.147 0.153 -9999 0 -0.465 3 3
CASP1 -0.049 0.16 -9999 0 -0.425 4 4
IL1RN/IL1R2 -0.033 0.142 -9999 0 -0.367 4 4
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.175 0.21 -9999 0 -0.461 6 6
TMEM189-UBE2V1 0 0 -9999 0 -9999 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.048 0.117 -9999 0 -0.352 2 2
PIK3CA 0.017 0 -9999 0 -9999 0 0
IL1RN 0.002 0.075 -9999 0 -0.378 1 1
TRAF6/TAK1/TAB1/TAB2 0.041 0 -9999 0 -9999 0 0
MAP2K6 0.049 0 -9999 0 -9999 0 0
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.053 0.147 -9999 0 -0.781 1 1
Crk/p130 Cas/Paxillin -0.065 0.103 -9999 0 -0.341 2 2
JUN -0.077 0.142 -9999 0 -0.369 2 2
HRAS 0.017 0 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.134 0.182 -9999 0 -0.369 8 8
RAP1A 0.017 0 -9999 0 -9999 0 0
FRS2 0.017 0 -9999 0 -9999 0 0
RAP1A/GDP 0.012 0 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.111 0.184 -9999 0 -0.369 7 7
EntrezGene:5979 0 0 -9999 0 -9999 0 0
PTPN11 0.017 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
CRK 0.017 0 -9999 0 -9999 0 0
RET9/GFRalpha1/GDNF/Enigma 0.007 0.089 -9999 0 -0.306 2 2
RHOA -0.005 0.11 -9999 0 -0.566 1 1
RAP1A/GTP -0.096 0.122 -9999 0 -0.289 6 6
GRB7 0.017 0 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF -0.087 0.159 -9999 0 -0.329 6 6
MAPKKK cascade -0.099 0.135 -9999 0 -0.45 2 2
BCAR1 0.017 0 -9999 0 -9999 0 0
RET9/GFRalpha1/GDNF/IRS1 0.007 0.089 -9999 0 -0.306 2 2
lamellipodium assembly -0.06 0.096 -9999 0 -0.32 2 2
RET51/GFRalpha1/GDNF/SHC -0.087 0.159 -9999 0 -0.329 6 6
PIK3CA 0.017 0 -9999 0 -9999 0 0
RET9/GFRalpha1/GDNF/SHC 0.007 0.089 -9999 0 -0.306 2 2
RET9/GFRalpha1/GDNF/Shank3 0.007 0.089 -9999 0 -0.306 2 2
MAPK3 -0.061 0.135 -9999 0 -0.406 1 1
DOK1 -0.026 0.153 -9999 0 -0.566 2 2
DOK6 -0.106 0.232 -9999 0 -0.535 6 6
PXN 0.017 0 -9999 0 -9999 0 0
neurite development -0.07 0.14 -9999 0 -0.36 2 2
DOK5 -0.07 0.207 -9999 0 -0.566 4 4
GFRA1 -0.026 0.153 -9999 0 -0.566 2 2
MAPK8 -0.059 0.139 -9999 0 -0.395 2 2
HRAS/GTP -0.118 0.157 -9999 0 -0.52 2 2
tube development 0.015 0.084 -9999 0 -0.28 2 2
MAPK1 -0.061 0.135 -9999 0 -0.406 1 1
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.016 0.073 -9999 0 -0.242 2 2
Rac1/GDP 0.012 0 -9999 0 -9999 0 0
SRC 0.017 0 -9999 0 -9999 0 0
PDLIM7 0.017 0 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.138 0.194 -9999 0 -0.356 10 10
SHC1 0.017 0 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.087 0.159 -9999 0 -0.329 6 6
RET51/GFRalpha1/GDNF/Dok5 -0.135 0.203 -9999 0 -0.398 8 8
PRKCA 0.017 0 -9999 0 -9999 0 0
HRAS/GDP 0.012 0 -9999 0 -9999 0 0
CREB1 -0.018 0.1 -9999 0 -0.316 2 2
PIK3R1 -0.005 0.11 -9999 0 -0.566 1 1
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.016 0.073 -9999 0 -0.242 2 2
RET51/GFRalpha1/GDNF/Grb7 -0.087 0.159 -9999 0 -0.329 6 6
mol:GDP 0 0 -9999 0 -9999 0 0
RET -0.172 0.235 -9999 0 -0.447 11 11
DOK4 0.017 0 -9999 0 -9999 0 0
JNK cascade -0.076 0.14 -9999 0 -0.362 2 2
RET9/GFRalpha1/GDNF/FRS2 0.007 0.089 -9999 0 -0.306 2 2
SHANK3 0.017 0 -9999 0 -9999 0 0
RASA1 0.017 0 -9999 0 -9999 0 0
NCK1 0.017 0 -9999 0 -9999 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.016 0.074 -9999 0 -0.244 2 2
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.052 0.123 -9999 0 -0.357 1 1
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.072 0.147 -9999 0 -0.426 2 2
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.053 0.127 -9999 0 -0.401 1 1
PI3K -0.047 0.171 -9999 0 -0.487 2 2
SOS1 0.017 0 -9999 0 -9999 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.016 0.084 -9999 0 -0.28 2 2
GRB10 -0.07 0.187 -9999 0 -0.453 5 5
activation of MAPKK activity -0.032 0.099 -9999 0 -0.321 1 1
RET51/GFRalpha1/GDNF/FRS2 -0.087 0.159 -9999 0 -0.329 6 6
GAB1 0.017 0 -9999 0 -9999 0 0
IRS1 0.017 0 -9999 0 -9999 0 0
IRS2 0.017 0 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.053 0.127 -9999 0 -0.401 1 1
RET51/GFRalpha1/GDNF/PKC alpha -0.087 0.159 -9999 0 -0.329 6 6
GRB2 0.017 0 -9999 0 -9999 0 0
PRKACA 0.017 0 -9999 0 -9999 0 0
GDNF 0.017 0 -9999 0 -9999 0 0
RAC1 0.017 0 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.087 0.159 -9999 0 -0.329 6 6
Rac1/GTP -0.07 0.113 -9999 0 -0.382 2 2
RET9/GFRalpha1/GDNF -0.004 0.097 -9999 0 -0.346 2 2
GFRalpha1/GDNF -0.007 0.113 -9999 0 -0.406 2 2
Ephrin B reverse signaling

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
EFNB2 0.002 0.075 -9999 0 -0.378 1 1
EPHB2 -0.042 0.141 -9999 0 -0.379 4 4
EFNB1 -0.094 0.161 -9999 0 -0.297 10 10
mol:GTP 0 0 -9999 0 -9999 0 0
Rac1/GDP -0.119 0.179 -9999 0 -0.466 3 3
Ephrin B2/EPHB1-2 -0.068 0.153 -9999 0 -0.341 5 5
neuron projection morphogenesis -0.134 0.152 -9999 0 -0.446 3 3
Ephrin B1/EPHB1-2/Tiam1 -0.135 0.191 -9999 0 -0.505 3 3
DNM1 -0.15 0.223 -9999 0 -0.434 10 10
cell-cell signaling -0.001 0.002 -9999 0 -9999 0 0
MAP2K4 -0.065 0.195 -9999 0 -0.602 3 3
YES1 -0.115 0.265 -9999 0 -0.844 3 3
Ephrin B1/EPHB1-2/NCK2 -0.124 0.162 -9999 0 -0.409 3 3
PI3K -0.074 0.204 -9999 0 -0.537 4 4
mol:GDP -0.134 0.188 -9999 0 -0.498 3 3
ITGA2B 0.017 0 -9999 0 -9999 0 0
endothelial cell proliferation 0.014 0.044 -9999 0 -0.21 1 1
FYN -0.108 0.266 -9999 0 -0.844 3 3
MAP3K7 -0.078 0.205 -9999 0 -0.644 3 3
FGR -0.107 0.261 -9999 0 -0.83 3 3
TIAM1 -0.005 0.11 -9999 0 -0.566 1 1
PIK3R1 -0.005 0.11 -9999 0 -0.566 1 1
RGS3 0.017 0 -9999 0 -9999 0 0
cell adhesion -0.071 0.191 -9999 0 -0.482 4 4
LYN -0.108 0.266 -9999 0 -0.844 3 3
Ephrin B1/EPHB1-2/Src Family Kinases -0.105 0.246 -9999 0 -0.786 3 3
Ephrin B1/EPHB1-2 -0.098 0.219 -9999 0 -0.7 3 3
SRC -0.107 0.261 -9999 0 -0.83 3 3
ITGB3 -0.019 0.131 -9999 0 -0.472 2 2
EPHB1 -0.092 0.226 -9999 0 -0.566 5 5
EPHB4 0.017 0 -9999 0 -9999 0 0
RAC1 0.017 0 -9999 0 -9999 0 0
Ephrin B2/EPHB4 0.014 0.044 -9999 0 -0.21 1 1
alphaIIb/beta3 Integrin -0.001 0.095 -9999 0 -0.329 2 2
BLK -0.114 0.262 -9999 0 -0.835 3 3
HCK -0.118 0.261 -9999 0 -0.835 3 3
regulation of stress fiber formation 0.123 0.16 0.405 3 -9999 0 3
MAPK8 -0.054 0.186 -9999 0 -0.566 3 3
Ephrin B1/EPHB1-2/RGS3 -0.124 0.162 -9999 0 -0.321 8 8
endothelial cell migration -0.066 0.175 -9999 0 -0.539 3 3
NCK2 0.017 0 -9999 0 -9999 0 0
PTPN13 -0.116 0.241 -9999 0 -0.501 7 7
regulation of focal adhesion formation 0.123 0.16 0.405 3 -9999 0 3
chemotaxis 0.123 0.16 0.318 8 -9999 0 8
PIK3CA 0.017 0 -9999 0 -9999 0 0
Rac1/GTP -0.131 0.162 -9999 0 -0.459 3 3
angiogenesis -0.097 0.217 -9999 0 -0.696 3 3
LCK -0.107 0.261 -9999 0 -0.83 3 3
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer -0.088 0.191 -9999 0 -0.39 7 7
PDGFRB 0.017 0.003 -9999 0 -9999 0 0
SPHK1 -0.121 0.274 -9999 0 -0.767 4 4
mol:S1P -0.105 0.241 -9999 0 -0.67 4 4
S1P1/S1P/Gi -0.063 0.139 -9999 0 -0.425 1 1
GNAO1 0.015 0.008 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/PLCgamma1 -0.038 0.123 -9999 0 -0.387 1 1
PLCG1 -0.05 0.13 -9999 0 -0.404 1 1
mol:GTP 0 0 -9999 0 -9999 0 0
PDGFB-D/PDGFRB 0.016 0.003 -9999 0 -9999 0 0
GNAI2 0.015 0.008 -9999 0 -9999 0 0
GNAI3 0.015 0.006 -9999 0 -9999 0 0
GNAI1 -0.007 0.11 -9999 0 -0.569 1 1
mol:GDP 0 0 -9999 0 -9999 0 0
EDG1 -0.112 0.253 -9999 0 -0.723 3 3
S1P1/S1P -0.151 0.237 -9999 0 -0.509 7 7
negative regulation of cAMP metabolic process -0.061 0.136 -9999 0 -0.414 1 1
MAPK3 -0.074 0.175 -9999 0 -0.543 2 2
calcium-dependent phospholipase C activity 0 0.004 -9999 0 -9999 0 0
Rac1/GDP 0.012 0 -9999 0 -9999 0 0
RhoA/GDP -0.003 0.081 -9999 0 -0.415 1 1
KDR -0.097 0.209 -9999 0 -0.517 5 5
PLCB2 -0.133 0.212 -9999 0 -0.446 7 7
RAC1 0.017 0 -9999 0 -9999 0 0
RhoA/GTP -0.153 0.187 -9999 0 -0.421 8 8
receptor internalization -0.14 0.219 -9999 0 -0.471 7 7
PTGS2 -0.115 0.289 -9999 0 -1.028 2 2
Rac1/GTP -0.144 0.18 -9999 0 -0.422 7 7
RHOA -0.005 0.11 -9999 0 -0.566 1 1
VEGFA -0.015 0.12 -9999 0 -0.572 1 1
negative regulation of T cell proliferation -0.061 0.136 -9999 0 -0.414 1 1
GO:0007205 0 0 -9999 0 -9999 0 0
GNAZ 0.015 0.006 -9999 0 -9999 0 0
MAPK1 -0.074 0.175 -9999 0 -0.543 2 2
S1P1/S1P/PDGFB-D/PDGFRB -0.138 0.231 -9999 0 -0.548 5 5
ABCC1 0.016 0.002 -9999 0 -9999 0 0
TCGA08_p53

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
CDKN2A -0.118 0.177 -9999 0 -0.34 10 10
TP53 -0.055 0.093 -9999 0 -0.418 1 1
Senescence -0.055 0.093 -9999 0 -0.417 1 1
Apoptosis -0.055 0.093 -9999 0 -0.417 1 1
Activated_Oncogenes 0 0 -9999 0 -9999 0 0
MDM2 0.077 0.105 0.261 5 -9999 0 5
MDM4 0.002 0.075 -9999 0 -0.378 1 1
Effects of Botulinum toxin

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
STX1A -0.058 0.121 -9999 0 -0.263 7 7
UniProt:P19321 0 0 -9999 0 -9999 0 0
RIMS1/UNC13B -0.011 0.106 -9999 0 -0.303 3 3
STXBP1 0.002 0.075 -9999 0 -0.378 1 1
ACh/CHRNA1 -0.011 0.039 -9999 0 -9999 0 0
RAB3GAP2/RIMS1/UNC13B 0.003 0.091 -9999 0 -0.337 1 1
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 0.002 0.075 -9999 0 -0.378 1 1
mol:ACh -0.029 0.051 -9999 0 -0.123 5 5
RAB3GAP2 0.017 0 -9999 0 -9999 0 0
STX1A/SNAP25/VAMP2 -0.081 0.111 -9999 0 -0.411 2 2
UniProt:P10844 0 0 -9999 0 -9999 0 0
muscle contraction -0.011 0.039 -9999 0 -9999 0 0
UNC13B -0.019 0.131 -9999 0 -0.472 2 2
CHRNA1 0.017 0 -9999 0 -9999 0 0
UniProt:P10845 0 0 -9999 0 -9999 0 0
ACh/Synaptotagmin 1 -0.19 0.194 -9999 0 -0.354 15 15
SNAP25 -0.049 0.121 -9999 0 -0.304 5 5
VAMP2 0.008 0 -9999 0 -9999 0 0
SYT1 -0.265 0.261 -9999 0 -0.491 15 15
UniProt:Q00496 0 0 -9999 0 -9999 0 0
STXIA/STXBP1 -0.045 0.12 -9999 0 -0.239 7 7
STX1A/SNAP25 fragment 1/VAMP2 -0.081 0.111 -9999 0 -0.411 2 2
IL6-mediated signaling events

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
BCL2L1 -0.033 0.353 -9999 0 -0.792 4 4
CRP -0.033 0.353 -9999 0 -0.792 4 4
cell cycle arrest -0.068 0.417 -9999 0 -0.975 4 4
TIMP1 -0.031 0.324 -9999 0 -0.776 3 3
IL6ST -0.002 0.113 -9999 0 -0.574 1 1
Rac1/GDP -0.055 0.24 -9999 0 -0.621 3 3
AP1 -0.051 0.195 -9999 0 -0.51 2 2
GAB2 0.019 0.004 -9999 0 -9999 0 0
TNFSF11 -0.033 0.353 -9999 0 -0.858 3 3
HSP90B1 0.044 0.061 -9999 0 -9999 0 0
GAB1 0.018 0.002 -9999 0 -9999 0 0
MAPK14 -0.05 0.202 -9999 0 -0.597 2 2
AKT1 0.063 0.04 -9999 0 -9999 0 0
FOXO1 0.068 0.039 -9999 0 -9999 0 0
MAP2K6 -0.044 0.191 -9999 0 -0.556 2 2
mol:GTP 0.001 0.002 -9999 0 -9999 0 0
MAP2K4 -0.037 0.264 -9999 0 -0.663 3 3
MITF -0.03 0.187 -9999 0 -0.405 4 4
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -9999 0 0
TYK2 0.017 0 -9999 0 -9999 0 0
A2M -0.028 0.263 -9999 0 -1.368 1 1
CEBPB 0.027 0.001 -9999 0 -9999 0 0
GRB2/SOS1/GAB family/SHP2 0.027 0.06 -9999 0 -9999 0 0
STAT3 -0.09 0.443 -9999 0 -1.053 4 4
STAT1 -0.008 0.03 -9999 0 -9999 0 0
CEBPD -0.117 0.514 -9999 0 -1.169 5 5
PIK3CA 0.019 0 -9999 0 -9999 0 0
PI3K 0.013 0.082 -9999 0 -0.404 1 1
JUN -0.041 0.166 -9999 0 -0.503 3 3
PIAS3/MITF -0.021 0.177 -9999 0 -0.416 3 3
MAPK11 -0.05 0.202 -9999 0 -0.597 2 2
STAT3 (dimer)/FOXO1 0.018 0.356 -9999 0 -0.823 3 3
GRB2/SOS1/GAB family -0.056 0.146 -9999 0 -0.721 1 1
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.052 0.207 -9999 0 -0.495 3 3
GRB2 0.018 0.002 -9999 0 -9999 0 0
JAK2 0.017 0 -9999 0 -9999 0 0
LBP 0 0.292 -9999 0 -0.666 3 3
PIK3R1 -0.003 0.11 -9999 0 -0.565 1 1
JAK1 0.002 0.073 -9999 0 -0.367 1 1
MYC -0.045 0.386 -9999 0 -0.871 4 4
FGG -0.033 0.353 -9999 0 -0.792 4 4
macrophage differentiation -0.068 0.417 -9999 0 -0.975 4 4
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.04 0.166 -9999 0 -0.406 3 3
JUNB -0.122 0.484 -9999 0 -1.082 5 5
FOS -0.193 0.259 -9999 0 -0.498 11 11
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.04 0.197 -9999 0 -0.436 4 4
STAT1/PIAS1 -0.019 0.195 -9999 0 -0.42 4 4
GRB2/SOS1/GAB family/SHP2/PI3K 0.05 0.042 -9999 0 -9999 0 0
STAT3 (dimer) -0.089 0.44 -9999 0 -1.045 4 4
PRKCD -0.058 0.366 -9999 0 -0.972 3 3
IL6R -0.02 0.131 -9999 0 -0.47 2 2
SOCS3 -0.076 0.262 -9999 0 -1.135 1 1
gp130 (dimer)/JAK1/JAK1/LMO4 -0.01 0.135 -9999 0 -0.359 3 3
Rac1/GTP -0.053 0.253 -9999 0 -0.654 3 3
HCK -0.034 0.147 -9999 0 -0.441 3 3
MAPKKK cascade 0.046 0.049 -9999 0 -9999 0 0
bone resorption -0.026 0.335 -9999 0 -0.742 4 4
IRF1 -0.033 0.353 -9999 0 -0.792 4 4
mol:GDP -0.069 0.244 -9999 0 -0.5 5 5
SOS1 0.018 0.004 -9999 0 -9999 0 0
VAV1 -0.071 0.249 -9999 0 -0.509 5 5
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.056 0.174 -9999 0 -0.509 2 2
PTPN11 -0.002 0.017 -9999 0 -9999 0 0
IL6/IL6RA -0.049 0.138 -9999 0 -0.273 7 7
gp130 (dimer)/TYK2/TYK2/LMO4 -0.004 0.125 -9999 0 -0.351 3 3
gp130 (dimer)/JAK2/JAK2/LMO4 -0.004 0.125 -9999 0 -0.351 3 3
IL6 -0.054 0.155 -9999 0 -0.377 5 5
PIAS3 0.017 0 -9999 0 -9999 0 0
PTPRE 0.013 0.02 -9999 0 -9999 0 0
PIAS1 0.017 0 -9999 0 -9999 0 0
RAC1 0.018 0.002 -9999 0 -9999 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.035 0.147 -9999 0 -0.371 3 3
LMO4 -0.024 0.157 -9999 0 -0.576 2 2
STAT3 (dimer)/PIAS3 -0.059 0.406 -9999 0 -0.943 4 4
MCL1 0.068 0.037 -9999 0 -9999 0 0
Syndecan-4-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
PTK2 0.001 0.095 -9999 0 -0.456 1 1
Syndecan-4/Syndesmos -0.068 0.192 -9999 0 -0.477 4 4
positive regulation of JNK cascade -0.145 0.225 -9999 0 -0.499 6 6
Syndecan-4/ADAM12 -0.074 0.206 -9999 0 -0.518 4 4
CCL5 0.002 0.075 -9999 0 -0.378 1 1
Rac1/GDP 0.012 0 -9999 0 -9999 0 0
DNM2 0.017 0 -9999 0 -9999 0 0
ITGA5 0.017 0 -9999 0 -9999 0 0
SDCBP 0.017 0 -9999 0 -9999 0 0
PLG 0.018 0.005 -9999 0 -9999 0 0
ADAM12 0.002 0.075 -9999 0 -0.378 1 1
mol:GTP 0 0 -9999 0 -9999 0 0
NUDT16L1 0.017 0 -9999 0 -9999 0 0
mol:PI-4-5-P2 0 0 -9999 0 -9999 0 0
Syndecan-4/PKC alpha -0.014 0.02 -9999 0 -9999 0 0
Syndecan-4/Laminin alpha1 -0.078 0.221 -9999 0 -0.542 4 4
Syndecan-4/CXCL12/CXCR4 -0.152 0.238 -9999 0 -0.529 6 6
Syndecan-4/Laminin alpha3 -0.075 0.191 -9999 0 -0.477 4 4
MDK -0.012 0.103 -9999 0 -0.378 2 2
Syndecan-4/FZD7 -0.161 0.241 -9999 0 -0.565 5 5
Syndecan-4/Midkine -0.081 0.2 -9999 0 -0.477 4 4
FZD7 -0.178 0.26 -9999 0 -0.51 10 10
Syndecan-4/FGFR1/FGF -0.107 0.208 -9999 0 -0.48 2 2
THBS1 0.017 0 -9999 0 -9999 0 0
integrin-mediated signaling pathway -0.108 0.225 -9999 0 -0.512 5 5
positive regulation of MAPKKK cascade -0.145 0.225 -9999 0 -0.499 6 6
Syndecan-4/TACI -0.068 0.192 -9999 0 -0.477 4 4
CXCR4 -0.127 0.246 -9999 0 -0.539 7 7
cell adhesion 0.035 0.005 -9999 0 -9999 0 0
Syndecan-4/Dynamin -0.068 0.192 -9999 0 -0.477 4 4
Syndecan-4/TSP1 -0.068 0.192 -9999 0 -0.477 4 4
Syndecan-4/GIPC -0.068 0.192 -9999 0 -0.477 4 4
Syndecan-4/RANTES -0.074 0.206 -9999 0 -0.518 4 4
ITGB1 0.017 0 -9999 0 -9999 0 0
LAMA1 -0.005 0.11 -9999 0 -0.566 1 1
LAMA3 0.002 0.075 -9999 0 -0.378 1 1
RAC1 0.017 0 -9999 0 -9999 0 0
PRKCA 0.029 0.038 -9999 0 -9999 0 0
Syndecan-4/alpha-Actinin -0.075 0.191 -9999 0 -0.477 4 4
TFPI -0.114 0.207 -9999 0 -0.425 8 8
F2 0.013 0.009 -9999 0 -9999 0 0
alpha5/beta1 Integrin 0.025 0 -9999 0 -9999 0 0
positive regulation of cell adhesion -0.074 0.213 -9999 0 -0.519 4 4
ACTN1 0.002 0.075 -9999 0 -0.378 1 1
TNC -0.077 0.201 -9999 0 -0.491 5 5
Syndecan-4/CXCL12 -0.096 0.212 -9999 0 -0.479 5 5
FGF6 -0.026 0.153 -9999 0 -0.566 2 2
RHOA -0.005 0.11 -9999 0 -0.566 1 1
CXCL12 -0.041 0.166 -9999 0 -0.503 3 3
TNFRSF13B 0.017 0 -9999 0 -9999 0 0
FGF2 -0.063 0.193 -9999 0 -0.519 4 4
FGFR1 0.017 0 -9999 0 -9999 0 0
Syndecan-4/PI-4-5-P2 -0.078 0.191 -9999 0 -0.485 4 4
mol:GDP 0 0 -9999 0 -9999 0 0
FN1 0.018 0.005 -9999 0 -9999 0 0
cell migration 0 0.009 -9999 0 -9999 0 0
PRKCD -0.04 0.163 -9999 0 -0.494 3 3
vasculogenesis -0.066 0.186 -9999 0 -0.461 4 4
SDC4 -0.081 0.201 -9999 0 -0.51 4 4
Syndecan-4/Tenascin C -0.112 0.233 -9999 0 -0.533 5 5
Syndecan-4/PI-4-5-P2/PKC alpha -0.011 0.016 -9999 0 -9999 0 0
Syndecan-4/Syntenin -0.068 0.192 -9999 0 -0.477 4 4
MMP9 -0.078 0.2 -9999 0 -0.49 5 5
Rac1/GTP 0.035 0.005 -9999 0 -9999 0 0
cytoskeleton organization -0.066 0.186 -9999 0 -0.461 4 4
GIPC1 0.017 0 -9999 0 -9999 0 0
Syndecan-4/TFPI -0.126 0.255 -9999 0 -0.577 5 5
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.012 0.132 -9999 0 -0.436 2 2
MAPK9 0.01 0 -9999 0 -9999 0 0
adrenocorticotropin secretion -0.153 0.167 -9999 0 -0.306 14 14
GNB1/GNG2 0.001 0.081 -9999 0 -0.278 2 2
GNB1 0.017 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 0.01 0 -9999 0 -9999 0 0
Gs family/GTP -0.014 0.087 -9999 0 -0.323 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 0.022 0.084 2 -9999 0 2
GNAL -0.026 0.153 -9999 0 -0.566 2 2
GNG2 -0.019 0.131 -9999 0 -0.472 2 2
CRH -0.216 0.232 -9999 0 -0.432 14 14
mol:cortisol 0 0 -9999 0 -9999 0 0
MAPK8 0.01 0 -9999 0 -9999 0 0
MAPK11 0.01 0 -9999 0 -9999 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.039 0.148 -9999 0 -0.675 1 1
adherens junction organization -0.097 0.191 -9999 0 -0.59 2 2
mol:GTP 0 0 -9999 0 -9999 0 0
Rac1/GDP -0.053 0.149 -9999 0 -0.616 1 1
FMN1 -0.095 0.189 -9999 0 -0.31 9 9
mol:IP3 -0.044 0.143 -9999 0 -0.654 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.1 0.2 -9999 0 -0.326 9 9
CTNNB1 -0.023 0.154 -9999 0 -0.567 2 2
AKT1 -0.048 0.154 -9999 0 -0.684 1 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.153 0.272 -9999 0 -0.479 9 9
CTNND1 0.016 0.004 -9999 0 -9999 0 0
mol:PI-4-5-P2 -0.085 0.184 -9999 0 -0.559 2 2
VASP -0.087 0.19 -9999 0 -0.577 2 2
ZYX -0.087 0.19 -9999 0 -0.577 2 2
JUB -0.105 0.192 -9999 0 -0.467 3 3
EGFR(dimer) -0.115 0.197 -9999 0 -0.517 3 3
E-cadherin/beta catenin-gamma catenin -0.147 0.195 -9999 0 -0.378 9 9
mol:PI-3-4-5-P3 -0.059 0.162 -9999 0 -0.5 2 2
PIK3CA 0.016 0.003 -9999 0 -9999 0 0
PI3K -0.06 0.167 -9999 0 -0.514 2 2
FYN -0.027 0.136 -9999 0 -0.625 1 1
mol:Ca2+ -0.043 0.139 -9999 0 -0.633 1 1
JUP 0.021 0.005 -9999 0 -9999 0 0
PIK3R1 -0.006 0.113 -9999 0 -0.582 1 1
mol:DAG -0.044 0.143 -9999 0 -0.654 1 1
CDH1 -0.243 0.259 -9999 0 -0.484 14 14
RhoA/GDP -0.062 0.184 -9999 0 -0.851 1 1
establishment of polarity of embryonic epithelium -0.085 0.184 -9999 0 -0.559 2 2
SRC 0.017 0 -9999 0 -9999 0 0
RAC1 0.017 0 -9999 0 -9999 0 0
RHOA -0.005 0.11 -9999 0 -0.566 1 1
EGFR -0.041 0.166 -9999 0 -0.503 3 3
CASR -0.04 0.132 -9999 0 -0.59 1 1
RhoA/GTP -0.041 0.168 -9999 0 -0.813 1 1
AKT2 -0.054 0.157 -9999 0 -0.684 1 1
actin cable formation -0.085 0.184 -9999 0 -0.56 2 2
apoptosis 0.05 0.151 0.677 1 -9999 0 1
CTNNA1 0.016 0.004 -9999 0 -9999 0 0
mol:GDP -0.066 0.159 -9999 0 -0.677 1 1
PIP5K1A -0.087 0.19 -9999 0 -0.577 2 2
PLCG1 -0.046 0.147 -9999 0 -0.676 1 1
Rac1/GTP -0.1 0.18 -9999 0 -0.467 3 3
homophilic cell adhesion -0.001 0.004 -9999 0 -9999 0 0
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.072 0.175 -9999 0 -0.325 7 7
MAP3K8 -0.022 0.131 -9999 0 -0.476 2 2
FOS -0.032 0.109 -9999 0 -0.273 1 1
PRKCA 0.011 0.009 -9999 0 -9999 0 0
PTPN7 -0.003 0.078 -9999 0 -0.397 1 1
HRAS 0.016 0.002 -9999 0 -9999 0 0
PRKCB -0.006 0.009 -9999 0 -0.016 11 11
NRAS 0.016 0.002 -9999 0 -9999 0 0
RAS family/GTP 0.021 0.017 -9999 0 -9999 0 0
MAPK3 -0.007 0.062 -9999 0 -9999 0 0
MAP2K1 -0.001 0.062 -9999 0 -0.235 1 1
ELK1 0.01 0.011 -9999 0 -9999 0 0
BRAF 0.012 0.024 -9999 0 -9999 0 0
mol:GTP -0.002 0.003 -9999 0 -0.005 11 11
MAPK1 -0.007 0.062 -9999 0 -9999 0 0
RAF1 0.012 0.024 -9999 0 -9999 0 0
KRAS 0.016 0.002 -9999 0 -9999 0 0
LPA4-mediated signaling events

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
ADCY4 0.022 0 -9999 0 -9999 0 0
ADCY5 0.022 0 -9999 0 -9999 0 0
ADCY6 0.022 0 -9999 0 -9999 0 0
ADCY7 0.022 0 -9999 0 -9999 0 0
ADCY1 0.022 0 -9999 0 -9999 0 0
ADCY2 -0.009 0.09 -9999 0 -0.255 3 3
ADCY3 0.022 0 -9999 0 -9999 0 0
ADCY8 -0.081 0.15 -9999 0 -0.286 9 9
PRKCE 0.013 0 -9999 0 -9999 0 0
ADCY9 0.008 0.07 -9999 0 -0.347 1 1
mol:DAG 0 0 -9999 0 -9999 0 0
cAMP biosynthetic process -0.016 0.085 -9999 0 -0.304 1 1
Caspase cascade in apoptosis

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
TOP1 0.022 0.086 -9999 0 -0.27 1 1
ACTA1 -0.003 0.096 -9999 0 -0.349 1 1
NUMA1 0.022 0.086 -9999 0 -0.27 1 1
SPTAN1 0.022 0.104 0.243 1 -0.346 1 2
LIMK1 0.022 0.104 0.243 1 -0.346 1 2
BIRC3 -0.056 0.177 -9999 0 -0.472 4 4
BIRC2 0.017 0 -9999 0 -9999 0 0
BAX 0.017 0 -9999 0 -9999 0 0
CASP10 0.002 0.09 -9999 0 -0.337 1 1
CRMA 0 0 -9999 0 -9999 0 0
XIAP 0 0 -9999 0 -9999 0 0
PTK2 0.022 0.086 -9999 0 -0.27 1 1
DIABLO 0.017 0 -9999 0 -9999 0 0
apoptotic nuclear changes 0.022 0.103 0.242 1 -0.341 1 2
response to UV 0 0 -9999 0 -9999 0 0
CRADD 0.017 0 -9999 0 -9999 0 0
GSN -0.032 0.119 -9999 0 -0.298 3 3
MADD 0.017 0 -9999 0 -9999 0 0
TFAP2A -0.084 0.195 -9999 0 -0.611 3 3
BID 0.006 0.056 -9999 0 -0.192 1 1
MAP3K1 0.014 0.048 -9999 0 -9999 0 0
TRADD 0.017 0 -9999 0 -9999 0 0
mol:Ca2+ 0 0 -9999 0 -9999 0 0
APAF-1/Pro-Caspase 9 -0.022 0.135 -9999 0 -0.405 3 3
mol:Activated DNA 0 0 -9999 0 -9999 0 0
ARHGDIB 0.008 0.112 0.243 1 -0.346 1 2
CASP9 -0.026 0.152 -9999 0 -0.565 2 2
DNA repair -0.021 0.069 -9999 0 -0.195 2 2
neuron apoptosis 0.025 0.015 -9999 0 -9999 0 0
mol:NAD 0 0 -9999 0 -9999 0 0
DNA fragmentation during apoptosis 0.027 0.1 -9999 0 -0.324 1 1
APAF1 -0.005 0.11 -9999 0 -0.566 1 1
CASP6 0.017 0.056 -9999 0 -9999 0 0
TRAF2 0.017 0 -9999 0 -9999 0 0
ICAD/CAD 0.028 0.1 0.239 1 -0.328 1 2
CASP7 0.026 0.089 0.271 2 -9999 0 2
KRT18 0.017 0.018 -9999 0 -9999 0 0
apoptosis -0.033 0.118 -9999 0 -9999 0 0
DFFA 0.022 0.104 0.243 1 -0.346 1 2
DFFB 0.022 0.104 0.243 1 -0.346 1 2
PARP1 0.021 0.07 0.196 2 -9999 0 2
actin filament polymerization -0.029 0.098 0.317 1 -0.237 1 2
TNF -0.1 0.201 -9999 0 -0.432 7 7
CYCS 0.019 0.043 -9999 0 -9999 0 0
SATB1 0.018 0.058 -9999 0 -9999 0 0
SLK 0.022 0.104 0.243 1 -0.346 1 2
p15 BID/BAX 0.014 0.05 -9999 0 -9999 0 0
CASP2 -0.008 0.096 -9999 0 -0.35 1 1
JNK cascade -0.014 0.047 -9999 0 -9999 0 0
CASP3 0.015 0.111 0.253 1 -0.373 1 2
LMNB2 0.009 0.063 -9999 0 -9999 0 0
RIPK1 0.017 0 -9999 0 -9999 0 0
CASP4 0.017 0 -9999 0 -9999 0 0
Mammalian IAPs/DIABLO -0.008 0.101 -9999 0 -0.306 2 2
negative regulation of DNA binding -0.084 0.193 -9999 0 -0.604 3 3
stress fiber formation 0.022 0.103 0.242 1 -0.341 1 2
GZMB -0.01 0.107 -9999 0 -0.304 3 3
CASP1 -0.013 0.085 -9999 0 -0.342 1 1
LMNB1 -0.016 0.094 -9999 0 -0.296 1 1
APP 0.025 0.015 -9999 0 -9999 0 0
TNFRSF1A -0.019 0.131 -9999 0 -0.472 2 2
response to stress 0 0 -9999 0 -9999 0 0
CASP8 0.013 0 -9999 0 -9999 0 0
VIM -0.041 0.12 -9999 0 -0.283 1 1
LMNA -0.011 0.098 -9999 0 -0.383 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.017 0.101 -9999 0 -0.378 1 1
LRDD 0.017 0 -9999 0 -9999 0 0
SREBF1 -0.061 0.134 -9999 0 -0.29 5 5
APAF-1/Caspase 9 -0.055 0.2 -9999 0 -0.722 2 2
nuclear fragmentation during apoptosis 0.022 0.085 -9999 0 -0.267 1 1
CFL2 0.028 0.099 -9999 0 -0.323 1 1
GAS2 -0.01 0.137 0.243 1 -0.385 2 3
positive regulation of apoptosis -0.01 0.08 -9999 0 -0.227 1 1
PRF1 0.017 0 -9999 0 -9999 0 0
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.031 0.02 -9999 0 -9999 0 0
HSPA8 0.013 0.005 -9999 0 -9999 0 0
SMAD3/SMAD4/ER alpha -0.06 0.14 -9999 0 -0.441 2 2
AKT1 0.001 0.029 -9999 0 -9999 0 0
GSC -0.407 0.645 -9999 0 -1.396 8 8
NKX2-5 0.001 0.075 -9999 0 -0.374 1 1
muscle cell differentiation 0.109 0.217 0.744 2 -9999 0 2
SMAD2-3/SMAD4/SP1 -0.114 0.183 -9999 0 -0.445 4 4
SMAD4 -0.06 0.09 -9999 0 -0.274 1 1
CBFB 0.017 0 -9999 0 -9999 0 0
SAP18 0.016 0.002 -9999 0 -9999 0 0
Cbp/p300/MSG1 0.009 0.111 -9999 0 -0.292 1 1
SMAD3/SMAD4/VDR -0.023 0.155 -9999 0 -0.475 2 2
MYC 0.011 0.092 -9999 0 -0.44 1 1
CDKN2B -0.284 0.531 -9999 0 -1.378 5 5
AP1 -0.163 0.292 -9999 0 -0.521 8 8
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.012 0.074 -9999 0 -9999 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.085 0.157 -9999 0 -0.373 3 3
SP3 0.01 0.022 -9999 0 -9999 0 0
CREB1 0.017 0 -9999 0 -9999 0 0
FOXH1 -0.013 0.049 -9999 0 -9999 0 0
SMAD3/SMAD4/GR -0.058 0.133 -9999 0 -0.442 2 2
GATA3 0.015 0.029 -9999 0 -9999 0 0
SKI/SIN3/HDAC complex/NCoR1 0.027 0.057 -9999 0 -9999 0 0
MEF2C/TIF2 -0.06 0.182 -9999 0 -0.536 2 2
endothelial cell migration -0.042 0.082 -9999 0 -9999 0 0
MAX 0.016 0.005 -9999 0 -9999 0 0
RBBP7 0.015 0.002 -9999 0 -9999 0 0
RBBP4 0.016 0.002 -9999 0 -9999 0 0
RUNX2 0.017 0 -9999 0 -9999 0 0
RUNX3 0.017 0 -9999 0 -9999 0 0
RUNX1 -0.056 0.177 -9999 0 -0.472 4 4
CTBP1 0.017 0 -9999 0 -9999 0 0
NR3C1 0.016 0.005 -9999 0 -9999 0 0
VDR -0.026 0.153 -9999 0 -0.566 2 2
CDKN1A -0.315 0.506 -9999 0 -1.195 6 6
KAT2B 0.004 0.006 -9999 0 -9999 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.076 0.157 -9999 0 -0.375 3 3
DCP1A 0.017 0 -9999 0 -9999 0 0
SKI 0.016 0.002 -9999 0 -9999 0 0
SERPINE1 0.041 0.083 -9999 0 -9999 0 0
SMAD3/SMAD4/ATF2 -0.057 0.132 -9999 0 -0.439 2 2
SMAD3/SMAD4/ATF3 -0.089 0.152 -9999 0 -0.437 3 3
SAP30 0.015 0.002 -9999 0 -9999 0 0
Cbp/p300/PIAS3 0.071 0.048 -9999 0 -9999 0 0
JUN -0.163 0.288 -9999 0 -0.514 8 8
SMAD3/SMAD4/IRF7 -0.052 0.143 -9999 0 -0.485 2 2
TFE3 0.019 0.02 -9999 0 -9999 0 0
COL1A2 -0.096 0.221 -9999 0 -0.482 5 5
mesenchymal cell differentiation 0.057 0.131 0.437 2 -9999 0 2
DLX1 0.002 0.075 -9999 0 -0.378 1 1
TCF3 0.002 0.075 -9999 0 -0.378 1 1
FOS -0.205 0.275 -9999 0 -0.526 11 11
SMAD3/SMAD4/Max -0.058 0.133 -9999 0 -0.442 2 2
Cbp/p300/SNIP1 0.047 0.016 -9999 0 -9999 0 0
ZBTB17 0.026 0.022 -9999 0 -9999 0 0
LAMC1 -0.042 0.129 -9999 0 -0.357 3 3
TGIF2/HDAC complex/SMAD3/SMAD4 -0.057 0.132 -9999 0 -0.439 2 2
IRF7 0.019 0.011 -9999 0 -9999 0 0
ESR1 0.006 0.071 -9999 0 -0.351 1 1
HNF4A 0.017 0 -9999 0 -9999 0 0
MEF2C -0.073 0.191 -9999 0 -0.572 2 2
SMAD2-3/SMAD4 -0.091 0.161 -9999 0 -0.441 3 3
Cbp/p300/Src-1 0.055 0.029 -9999 0 -9999 0 0
IGHV3OR16-13 -0.014 0.032 -9999 0 -9999 0 0
TGIF2/HDAC complex 0.017 0 -9999 0 -9999 0 0
CREBBP 0.026 0.012 -9999 0 -9999 0 0
SKIL 0.017 0 -9999 0 -9999 0 0
HDAC1 -0.006 0.11 -9999 0 -0.569 1 1
HDAC2 -0.006 0.11 -9999 0 -0.566 1 1
SNIP1 0.014 0.004 -9999 0 -9999 0 0
GCN5L2 0.027 0.013 -9999 0 -9999 0 0
SMAD3/SMAD4/TFE3 -0.049 0.136 -9999 0 -0.43 2 2
MSG1/HSC70 -0.041 0.12 -9999 0 -0.286 5 5
SMAD2 -0.027 0.058 -9999 0 -9999 0 0
SMAD3 -0.068 0.171 -9999 0 -0.643 2 2
SMAD3/E2F4-5/DP1/p107/SMAD4 -0.019 0.103 -9999 0 -0.305 2 2
SMAD2/SMAD2/SMAD4 -0.016 0.037 -9999 0 -9999 0 0
NCOR1 0.015 0.002 -9999 0 -9999 0 0
NCOA2 0.017 0 -9999 0 -9999 0 0
NCOA1 0.017 0 -9999 0 -9999 0 0
MYOD/E2A 0.015 0.052 -9999 0 -0.252 1 1
SMAD2-3/SMAD4/SP1/MIZ-1 -0.099 0.175 -9999 0 -0.456 3 3
IFNB1 -0.043 0.149 -9999 0 -0.514 2 2
SMAD3/SMAD4/MEF2C -0.103 0.234 -9999 0 -0.707 2 2
CITED1 -0.063 0.171 -9999 0 -0.415 5 5
SMAD2-3/SMAD4/ARC105 -0.068 0.146 -9999 0 -0.387 3 3
RBL1 0.002 0.075 -9999 0 -0.378 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.103 0.222 -9999 0 -0.529 5 5
RUNX1-3/PEBPB2 -0.011 0.111 -9999 0 -0.337 2 2
SMAD7 -0.173 0.304 -9999 0 -0.705 5 5
MYC/MIZ-1 0.034 0.073 -9999 0 -0.243 1 1
SMAD3/SMAD4 0.065 0.136 0.288 1 -0.333 1 2
IL10 -0.045 0.136 -9999 0 -0.361 3 3
PIASy/HDAC complex 0.008 0.011 -9999 0 -9999 0 0
PIAS3 0.021 0.006 -9999 0 -9999 0 0
CDK2 -0.046 0.174 -9999 0 -0.453 4 4
IL5 -0.052 0.149 -9999 0 -0.392 3 3
CDK4 0.027 0.013 -9999 0 -9999 0 0
PIAS4 0.008 0.011 -9999 0 -9999 0 0
ATF3 -0.034 0.147 -9999 0 -0.441 3 3
SMAD3/SMAD4/SP1 -0.107 0.164 -9999 0 -0.43 4 4
FOXG1 -0.086 0.224 -9999 0 -0.556 5 5
FOXO3 0.005 0.039 -9999 0 -9999 0 0
FOXO1 0.005 0.038 -9999 0 -9999 0 0
FOXO4 0.005 0.038 -9999 0 -9999 0 0
heart looping -0.072 0.188 -9999 0 -0.564 2 2
CEBPB 0.01 0.015 -9999 0 -9999 0 0
SMAD3/SMAD4/DLX1 -0.065 0.141 -9999 0 -0.398 3 3
MYOD1 0.017 0 -9999 0 -9999 0 0
SMAD3/SMAD4/HNF4 -0.057 0.132 -9999 0 -0.439 2 2
SMAD3/SMAD4/GATA3 -0.056 0.142 -9999 0 -0.427 2 2
SnoN/SIN3/HDAC complex/NCoR1 0.017 0 -9999 0 -9999 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.063 0.16 -9999 0 -0.44 3 3
SMAD3/SMAD4/SP1-3 -0.093 0.163 -9999 0 -0.403 4 4
MED15 0.017 0 -9999 0 -9999 0 0
SP1 -0.027 0.057 -9999 0 -9999 0 0
SIN3B 0.015 0.002 -9999 0 -9999 0 0
SIN3A 0.016 0.002 -9999 0 -9999 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.065 0.163 -9999 0 -0.424 2 2
ITGB5 -0.112 0.196 -9999 0 -0.523 3 3
TGIF/SIN3/HDAC complex/CtBP 0.015 0.075 -9999 0 -9999 0 0
SMAD3/SMAD4/AR -0.158 0.209 -9999 0 -0.482 6 6
AR -0.15 0.224 -9999 0 -0.435 10 10
negative regulation of cell growth -0.042 0.128 -9999 0 -0.388 2 2
SMAD3/SMAD4/MYOD -0.057 0.132 -9999 0 -0.439 2 2
E2F5 0.017 0 -9999 0 -9999 0 0
E2F4 0.017 0 -9999 0 -9999 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.029 0.12 -9999 0 -0.365 1 1
SMAD2-3/SMAD4/FOXO1-3a-4 -0.089 0.172 -9999 0 -0.378 6 6
TFDP1 0.017 0 -9999 0 -9999 0 0
SMAD3/SMAD4/AP1 -0.164 0.299 -9999 0 -0.528 8 8
SMAD3/SMAD4/RUNX2 -0.057 0.132 -9999 0 -0.439 2 2
TGIF2 0.017 0 -9999 0 -9999 0 0
TGIF1 -0.056 0.177 -9999 0 -0.472 4 4
ATF2 0.017 0 -9999 0 -9999 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.019 0 -9999 0 -9999 0 0
SVIL -0.054 0.178 -9999 0 -0.471 4 4
ZNF318 0.013 0 -9999 0 -9999 0 0
JMJD2C -0.018 0.154 -9999 0 -0.562 2 2
T-DHT/AR/Ubc9 -0.087 0.138 -9999 0 -0.338 4 4
CARM1 0.017 0 -9999 0 -9999 0 0
PRDX1 -0.07 0.207 -9999 0 -0.566 4 4
PELP1 0.016 0 -9999 0 -9999 0 0
CTNNB1 -0.025 0.153 -9999 0 -0.565 2 2
AKT1 0.016 0 -9999 0 -9999 0 0
PTK2B 0.003 0.075 -9999 0 -0.377 1 1
MED1 0.016 0 -9999 0 -9999 0 0
MAK -0.002 0.075 -9999 0 -0.383 1 1
response to oxidative stress 0 0 -9999 0 -9999 0 0
HIP1 0.019 0 -9999 0 -9999 0 0
GSN -0.082 0.214 -9999 0 -0.527 5 5
NCOA2 0.017 0 -9999 0 -9999 0 0
NCOA6 0.019 0 -9999 0 -9999 0 0
DNA-PK 0.03 0 -9999 0 -9999 0 0
NCOA4 0.017 0 -9999 0 -9999 0 0
PIAS3 0.018 0 -9999 0 -9999 0 0
cell proliferation -0.026 0.047 -9999 0 -9999 0 0
XRCC5 0.016 0 -9999 0 -9999 0 0
UBE3A 0.02 0 -9999 0 -9999 0 0
T-DHT/AR/SNURF -0.097 0.137 -9999 0 -0.26 10 10
FHL2 -0.128 0.293 -9999 0 -1.048 2 2
RANBP9 0.019 0 -9999 0 -9999 0 0
JMJD1A 0.017 0.028 -9999 0 -9999 0 0
CDK6 -0.179 0.244 -9999 0 -0.464 11 11
TGFB1I1 0.019 0 -9999 0 -9999 0 0
T-DHT/AR/CyclinD1 -0.116 0.158 -9999 0 -0.376 5 5
XRCC6 0.016 0 -9999 0 -9999 0 0
T-DHT/AR -0.092 0.148 -9999 0 -0.358 4 4
CTDSP1 0.017 0 -9999 0 -9999 0 0
CTDSP2 0.014 0 -9999 0 -9999 0 0
BRCA1 0.019 0 -9999 0 -9999 0 0
TCF4 -0.007 0.11 -9999 0 -0.568 1 1
CDKN2A -0.166 0.243 -9999 0 -0.474 10 10
SRF 0.003 0.043 -9999 0 -9999 0 0
NKX3-1 -0.032 0.064 -9999 0 -9999 0 0
KLK3 0.037 0.036 -9999 0 -9999 0 0
TMF1 0.017 0 -9999 0 -9999 0 0
HNRNPA1 0.015 0 -9999 0 -9999 0 0
AOF2 0.019 0 -9999 0 -9999 0 0
APPL1 0.024 0 -9999 0 -9999 0 0
T-DHT/AR/Caspase 8 -0.088 0.138 -9999 0 -0.339 4 4
AR -0.157 0.222 -9999 0 -0.435 10 10
UBA3 0.001 0 -9999 0 -9999 0 0
PATZ1 0.015 0 -9999 0 -9999 0 0
PAWR -0.019 0.131 -9999 0 -0.472 2 2
PRKDC 0.016 0 -9999 0 -9999 0 0
PA2G4 0.015 0 -9999 0 -9999 0 0
UBE2I 0.017 0 -9999 0 -9999 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.078 0.126 -9999 0 -0.308 4 4
RPS6KA3 0.019 0 -9999 0 -9999 0 0
T-DHT/AR/ARA70 -0.086 0.138 -9999 0 -0.338 4 4
LATS2 0.001 0.075 -9999 0 -0.38 1 1
T-DHT/AR/PRX1 -0.128 0.169 -9999 0 -0.364 7 7
Cyclin D3/CDK11 p58 0.012 0 -9999 0 -9999 0 0
VAV3 -0.061 0.193 -9999 0 -0.518 4 4
KLK2 -0.043 0.133 -9999 0 -0.509 1 1
CASP8 0.016 0 -9999 0 -9999 0 0
T-DHT/AR/TIF2/CARM1 -0.067 0.127 -9999 0 -0.322 3 3
TMPRSS2 -0.042 0.114 -9999 0 -9999 0 0
CCND1 -0.034 0.147 -9999 0 -0.44 3 3
PIAS1 0.02 0 -9999 0 -9999 0 0
mol:T-DHT -0.009 0.023 -9999 0 -0.069 1 1
CDC2L1 0 0 -9999 0 -9999 0 0
PIAS4 0.021 0 -9999 0 -9999 0 0
T-DHT/AR/CDK6 -0.203 0.188 -9999 0 -0.412 9 9
CMTM2 0.016 0 -9999 0 -9999 0 0
SNURF 0 0 -9999 0 -9999 0 0
ZMIZ1 0.01 0.02 -9999 0 -9999 0 0
CCND3 0.017 0 -9999 0 -9999 0 0
TGIF1 -0.057 0.177 -9999 0 -0.474 4 4
FKBP4 0.019 0 -9999 0 -9999 0 0
ErbB4 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
ErbB4/ErbB4/HBEGF/HBEGF -0.013 0.148 -9999 0 -0.669 1 1
epithelial cell differentiation -0.058 0.136 -9999 0 -0.628 1 1
ITCH 0.019 0.024 -9999 0 -9999 0 0
WWP1 -0.029 0.26 -9999 0 -1.328 1 1
FYN 0.017 0 -9999 0 -9999 0 0
EGFR -0.041 0.166 -9999 0 -0.503 3 3
PRL 0.017 0 -9999 0 -9999 0 0
neuron projection morphogenesis 0.003 0.124 -9999 0 -0.458 1 1
PTPRZ1 -0.005 0.11 -9999 0 -0.566 1 1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.012 0.134 -9999 0 -0.514 1 1
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.044 0.15 -9999 0 -0.6 1 1
ADAM17 0.019 0.024 -9999 0 -9999 0 0
ErbB4/ErbB4 -0.012 0.157 -9999 0 -0.741 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.092 0.171 -9999 0 -0.52 2 2
NCOR1 0.017 0 -9999 0 -9999 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.032 0.143 -9999 0 -0.564 1 1
GRIN2B -0.088 0.169 -9999 0 -0.476 2 2
ErbB4/ErbB2/betacellulin -0.124 0.168 -9999 0 -0.47 2 2
STAT1 0.002 0.075 -9999 0 -0.378 1 1
HBEGF 0.002 0.075 -9999 0 -0.378 1 1
PRLR -0.026 0.153 -9999 0 -0.566 2 2
E4ICDs/ETO2 -0.044 0.177 -9999 0 -0.47 3 3
axon guidance -0.031 0.166 -9999 0 -0.767 1 1
NEDD4 -0.011 0.106 -9999 0 -0.377 2 2
Prolactin receptor/Prolactin receptor/Prolactin -0.007 0.113 -9999 0 -0.406 2 2
CBFA2T3 -0.048 0.183 -9999 0 -0.566 3 3
ErbB4/ErbB2/HBEGF -0.002 0.128 -9999 0 -0.564 1 1
MAPK3 -0.005 0.127 -9999 0 -0.479 1 1
STAT1 (dimer) -0.013 0.143 -9999 0 -0.666 1 1
MAPK1 -0.005 0.127 -9999 0 -0.479 1 1
JAK2 0.017 0 -9999 0 -9999 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.04 0.143 -9999 0 -0.564 1 1
NRG1 -0.036 0.14 -9999 0 -0.319 5 5
NRG3 -0.136 0.222 -9999 0 -0.441 9 9
NRG2 0.017 0 -9999 0 -9999 0 0
NRG4 0.017 0 -9999 0 -9999 0 0
heart development -0.031 0.166 -9999 0 -0.767 1 1
neural crest cell migration -0.039 0.141 -9999 0 -0.557 1 1
ERBB2 0.018 0.056 -9999 0 -0.256 1 1
WWOX/E4ICDs -0.005 0.141 -9999 0 -0.669 1 1
SHC1 0.017 0 -9999 0 -9999 0 0
ErbB4/EGFR/neuregulin 4 -0.027 0.152 -9999 0 -0.624 1 1
apoptosis 0.072 0.163 0.492 2 -9999 0 2
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.005 0.141 -9999 0 -0.669 1 1
ErbB4/ErbB2/epiregulin -0.006 0.132 -9999 0 -0.564 1 1
ErbB4/ErbB4/betacellulin/betacellulin -0.148 0.195 -9999 0 -0.497 3 3
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.006 0.145 -9999 0 -0.567 1 1
MDM2 -0.003 0.142 -9999 0 -0.669 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.033 0.138 -9999 0 -0.527 1 1
STAT5A -0.021 0.159 -9999 0 -0.73 1 1
ErbB4/EGFR/neuregulin 1 beta -0.062 0.16 -9999 0 -0.564 1 1
DLG4 0.017 0 -9999 0 -9999 0 0
GRB2/SHC 0.025 0 -9999 0 -9999 0 0
E4ICDs/TAB2/NCoR1 0.005 0.133 -9999 0 -0.624 1 1
STAT5A (dimer) -0.061 0.149 -9999 0 -0.691 1 1
MAP3K7IP2 0.017 0 -9999 0 -9999 0 0
STAT5B (dimer) -0.021 0.159 -9999 0 -0.73 1 1
LRIG1 -0.026 0.153 -9999 0 -0.566 2 2
EREG -0.005 0.11 -9999 0 -0.566 1 1
BTC -0.229 0.263 -9999 0 -0.494 13 13
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.031 0.168 -9999 0 -0.777 1 1
ERBB4 -0.012 0.157 -9999 0 -0.745 1 1
STAT5B 0.017 0 -9999 0 -9999 0 0
YAP1 0.009 0.036 -9999 0 -9999 0 0
GRB2 0.017 0 -9999 0 -9999 0 0
ErbB4/ErbB2/neuregulin 4 0.006 0.123 -9999 0 -0.564 1 1
glial cell differentiation -0.005 0.132 0.617 1 -9999 0 1
WWOX 0.017 0 -9999 0 -9999 0 0
cell proliferation -0.136 0.193 -9999 0 -0.513 3 3
BARD1 signaling events

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
BARD1/CSTF1 0.009 0.081 -9999 0 -0.406 1 1
ATM 0.017 0 -9999 0 -9999 0 0
UBE2D3 0.017 0 -9999 0 -9999 0 0
PRKDC 0.017 0 -9999 0 -9999 0 0
ATR 0.017 0 -9999 0 -9999 0 0
UBE2L3 0.017 0 -9999 0 -9999 0 0
FANCD2 0.024 0.034 -9999 0 -9999 0 0
protein ubiquitination -0.003 0.133 -9999 0 -0.415 2 2
XRCC5 0.017 0 -9999 0 -9999 0 0
XRCC6 0.017 0 -9999 0 -9999 0 0
M/R/N Complex 0.034 0 -9999 0 -9999 0 0
MRE11A 0.017 0 -9999 0 -9999 0 0
DNA-PK 0.034 0 -9999 0 -9999 0 0
FA complex/FANCD2/Ubiquitin 0.023 0.099 -9999 0 -0.312 1 1
FANCF 0.017 0 -9999 0 -9999 0 0
BRCA1 0.017 0 -9999 0 -9999 0 0
CCNE1 0.017 0 -9999 0 -9999 0 0
CDK2/Cyclin E1 -0.027 0.129 -9999 0 -0.329 4 4
FANCG 0.002 0.075 -9999 0 -0.378 1 1
BRCA1/BACH1/BARD1 0.009 0.081 -9999 0 -0.406 1 1
FANCE 0.017 0 -9999 0 -9999 0 0
FANCC 0.002 0.075 -9999 0 -0.378 1 1
NBN 0.017 0 -9999 0 -9999 0 0
FANCA -0.027 0.124 -9999 0 -0.378 3 3
DNA repair -0.037 0.193 -9999 0 -0.547 2 2
BRCA1/BARD1/ubiquitin 0.009 0.081 -9999 0 -0.406 1 1
BARD1/DNA-PK 0.031 0.064 -9999 0 -0.298 1 1
FANCL -0.012 0.103 -9999 0 -0.378 2 2
mRNA polyadenylation -0.009 0.081 0.405 1 -9999 0 1
BRCA1/BARD1/CTIP/M/R/N Complex 0.029 0.058 -9999 0 -9999 0 0
BRCA1/BACH1/BARD1/TopBP1 0.021 0.07 -9999 0 -0.337 1 1
BRCA1/BARD1/P53 0.01 0.096 -9999 0 -0.298 2 2
BARD1/CSTF1/BRCA1 0.021 0.07 -9999 0 -0.337 1 1
BRCA1/BACH1 0.017 0 -9999 0 -9999 0 0
BARD1 -0.005 0.11 -9999 0 -0.566 1 1
PCNA -0.012 0.103 -9999 0 -0.378 2 2
BRCA1/BARD1/UbcH5C 0.021 0.07 -9999 0 -0.337 1 1
BRCA1/BARD1/UbcH7 0.021 0.07 -9999 0 -0.337 1 1
BRCA1/BARD1/RAD51/PCNA -0.066 0.159 -9999 0 -0.317 7 7
BARD1/DNA-PK/P53 0.019 0.091 -9999 0 -9999 0 0
BRCA1/BARD1/Ubiquitin 0.009 0.081 -9999 0 -0.406 1 1
BRCA1/BARD1/CTIP 0.013 0.082 -9999 0 -0.298 1 1
FA complex 0.016 0.09 -9999 0 -0.299 1 1
BARD1/EWS 0.009 0.081 -9999 0 -0.406 1 1
RBBP8 0.006 0.073 -9999 0 -0.252 2 2
TP53 -0.019 0.131 -9999 0 -0.472 2 2
TOPBP1 0.017 0 -9999 0 -9999 0 0
G1/S transition of mitotic cell cycle -0.009 0.095 0.296 2 -9999 0 2
BRCA1/BARD1 0 0.136 -9999 0 -0.42 2 2
CSTF1 0.017 0 -9999 0 -9999 0 0
BARD1/EWS-Fli1 -0.003 0.081 -9999 0 -0.415 1 1
CDK2 -0.056 0.177 -9999 0 -0.472 4 4
UniProt:Q9BZD1 0 0 -9999 0 -9999 0 0
RAD51 -0.128 0.229 -9999 0 -0.472 8 8
RAD50 0.017 0 -9999 0 -9999 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.009 0.081 -9999 0 -0.406 1 1
EWSR1 0.017 0 -9999 0 -9999 0 0
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.017 0 -9999 0 -9999 0 0
SPHK1 -0.084 0.214 -9999 0 -0.529 5 5
GNAI2 0.017 0 -9999 0 -9999 0 0
mol:S1P -0.025 0.112 -9999 0 -0.284 4 4
GNAO1 0.017 0 -9999 0 -9999 0 0
mol:Sphinganine-1-P -0.048 0.158 -9999 0 -0.375 5 5
growth factor activity 0 0 -9999 0 -9999 0 0
S1P/S1P2/G12/G13 -0.001 0.083 -9999 0 -9999 0 0
GNAI3 0.017 0 -9999 0 -9999 0 0
G12/G13 0.025 0 -9999 0 -9999 0 0
S1PR3 0 0 -9999 0 -9999 0 0
S1PR2 0 0 -9999 0 -9999 0 0
EDG1 -0.048 0.183 -9999 0 -0.566 3 3
S1P1/S1P -0.052 0.135 -9999 0 -0.274 7 7
S1PR5 0 0 -9999 0 -9999 0 0
S1PR4 0 0 -9999 0 -9999 0 0
GNAI1 -0.005 0.11 -9999 0 -0.566 1 1
S1P/S1P5/G12 -0.012 0.087 -9999 0 -0.215 4 4
S1P/S1P3/Gq -0.037 0.155 -9999 0 -0.4 3 3
S1P/S1P4/Gi 0.013 0.083 -9999 0 -0.364 1 1
GNAQ 0 0 -9999 0 -9999 0 0
GNAZ 0.017 0 -9999 0 -9999 0 0
GNA14 -0.063 0.193 -9999 0 -0.519 4 4
GNA15 -0.005 0.11 -9999 0 -0.566 1 1
GNA12 0.017 0 -9999 0 -9999 0 0
GNA13 0.017 0 -9999 0 -9999 0 0
GNA11 0.017 0 -9999 0 -9999 0 0
ABCC1 0.017 0 -9999 0 -9999 0 0
Circadian rhythm pathway

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
chromatin modification -0.041 0.155 -9999 0 -0.512 1 1
CLOCK 0.02 0.002 -9999 0 -9999 0 0
TIMELESS/CRY2 0.017 0.104 -9999 0 -9999 0 0
DEC1/BMAL1 -0.021 0.138 -9999 0 -0.411 3 3
ATR 0.017 0 -9999 0 -9999 0 0
NR1D1 0.04 0.05 -9999 0 -9999 0 0
ARNTL -0.002 0.116 -9999 0 -0.591 1 1
TIMELESS 0.033 0.086 -9999 0 -9999 0 0
NPAS2 0.02 0.002 -9999 0 -9999 0 0
CRY2 -0.019 0.131 -9999 0 -0.472 2 2
mol:CO -0.014 0.014 -9999 0 -9999 0 0
CHEK1 -0.15 0.242 -9999 0 -0.483 9 9
mol:HEME 0.014 0.014 -9999 0 -9999 0 0
PER1 0.017 0 -9999 0 -9999 0 0
BMAL/CLOCK/NPAS2 0.038 0.084 -9999 0 -0.393 1 1
BMAL1/CLOCK 0.027 0.128 -9999 0 -0.558 1 1
S phase of mitotic cell cycle -0.041 0.155 -9999 0 -0.512 1 1
TIMELESS/CHEK1/ATR -0.041 0.157 -9999 0 -0.52 1 1
mol:NADPH 0.014 0.014 -9999 0 -9999 0 0
PER1/TIMELESS 0.037 0.079 -9999 0 -9999 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -9999 0 0
DEC1 -0.026 0.153 -9999 0 -0.566 2 2
Noncanonical Wnt signaling pathway

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
NFATC2 0.017 0 -9999 0 -9999 0 0
GNB1/GNG2 -0.044 0.155 -9999 0 -0.595 1 1
mol:DAG -0.033 0.143 -9999 0 -0.537 1 1
PLCG1 -0.034 0.147 -9999 0 -0.557 1 1
YES1 -0.048 0.162 -9999 0 -0.499 2 2
FZD3 -0.005 0.11 -9999 0 -0.566 1 1
FZD6 -0.019 0.131 -9999 0 -0.472 2 2
G protein -0.034 0.149 -9999 0 -0.561 1 1
MAP3K7 -0.053 0.143 -9999 0 -0.385 2 2
mol:Ca2+ -0.032 0.139 -9999 0 -0.518 1 1
mol:IP3 -0.033 0.143 -9999 0 -0.537 1 1
NLK 0.02 0.013 -9999 0 -9999 0 0
GNB1 0.017 0 -9999 0 -9999 0 0
CAMK2A -0.065 0.153 -9999 0 -0.389 3 3
MAP3K7IP1 0.017 0 -9999 0 -9999 0 0
Noncanonical Wnts/FZD -0.048 0.157 -9999 0 -0.662 1 1
CSNK1A1 0.017 0 -9999 0 -9999 0 0
GNAS -0.037 0.149 -9999 0 -0.621 1 1
GO:0007205 -0.033 0.141 -9999 0 -0.528 1 1
WNT6 0.017 0 -9999 0 -9999 0 0
WNT4 -0.027 0.124 -9999 0 -0.378 3 3
NFAT1/CK1 alpha -0.02 0.15 -9999 0 -0.548 1 1
GNG2 -0.019 0.131 -9999 0 -0.472 2 2
WNT5A -0.084 0.214 -9999 0 -0.529 5 5
WNT11 0.017 0 -9999 0 -9999 0 0
CDC42 -0.038 0.155 -9999 0 -0.468 2 2
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.016 0.069 -9999 0 -0.335 1 1
EPHB2 -0.042 0.14 -9999 0 -0.378 4 4
Syndecan-2/TACI 0.016 0.069 -9999 0 -0.335 1 1
LAMA1 -0.005 0.11 -9999 0 -0.566 1 1
Syndecan-2/alpha2 ITGB1 0.017 0.11 -9999 0 -0.363 2 2
HRAS 0.017 0 -9999 0 -9999 0 0
Syndecan-2/CASK 0.004 0.068 -9999 0 -0.344 1 1
ITGA5 0.017 0 -9999 0 -9999 0 0
BAX 0.033 0.062 -9999 0 -9999 0 0
EPB41 0.002 0.075 -9999 0 -0.378 1 1
positive regulation of cell-cell adhesion 0.015 0.062 -9999 0 -0.303 1 1
LAMA3 0.002 0.075 -9999 0 -0.378 1 1
EZR 0 0 -9999 0 -9999 0 0
mol:PI-4-5-P2 0 0 -9999 0 -9999 0 0
CAV2 0.017 0 -9999 0 -9999 0 0
Syndecan-2/MMP2 0.016 0.069 -9999 0 -0.335 1 1
RP11-540L11.1 0 0 -9999 0 -9999 0 0
alpha2 ITGB1 0.009 0.081 -9999 0 -0.406 1 1
dendrite morphogenesis -0.018 0.102 -9999 0 -0.334 1 1
Syndecan-2/GM-CSF -0.011 0.115 -9999 0 -0.337 3 3
determination of left/right symmetry 0.008 0.081 -9999 0 -0.403 1 1
Syndecan-2/PKC delta -0.019 0.12 -9999 0 -0.337 3 3
GNB2L1 0.017 0 -9999 0 -9999 0 0
MAPK3 0 0.105 -9999 0 -0.297 3 3
MAPK1 0 0.105 -9999 0 -0.297 3 3
Syndecan-2/RACK1 0.025 0.06 -9999 0 -0.278 1 1
NF1 0.017 0 -9999 0 -9999 0 0
FGFR/FGF/Syndecan-2 0.008 0.081 -9999 0 -0.403 1 1
ITGA2 -0.005 0.11 -9999 0 -0.566 1 1
MAPK8 0.025 0.069 -9999 0 -0.328 1 1
Syndecan-2/alpha2/beta1 Integrin 0.012 0.101 -9999 0 -0.272 3 3
Syndecan-2/Kininogen 0.016 0.069 -9999 0 -0.335 1 1
ITGB1 0.017 0 -9999 0 -9999 0 0
SRC 0.031 0.056 -9999 0 -9999 0 0
Syndecan-2/CASK/Protein 4.1 0.007 0.073 -9999 0 -0.304 1 1
extracellular matrix organization 0.016 0.069 -9999 0 -0.334 1 1
actin cytoskeleton reorganization 0.016 0.069 -9999 0 -0.334 1 1
Syndecan-2/Caveolin-2/Ras 0.026 0.063 -9999 0 -0.296 1 1
Syndecan-2/Laminin alpha3 0.008 0.08 -9999 0 -0.335 1 1
Syndecan-2/RasGAP 0.033 0.057 -9999 0 -0.259 1 1
alpha5/beta1 Integrin 0.025 0 -9999 0 -9999 0 0
PRKCD -0.041 0.166 -9999 0 -0.503 3 3
Syndecan-2 dimer -0.018 0.103 -9999 0 -0.335 1 1
GO:0007205 0.004 0 -9999 0 -9999 0 0
DNA mediated transformation 0 0 -9999 0 -9999 0 0
Syndecan-2/RasGAP/Src 0.04 0.056 -9999 0 -9999 0 0
RHOA -0.005 0.11 -9999 0 -0.566 1 1
SDCBP 0.017 0 -9999 0 -9999 0 0
TNFRSF13B 0.017 0 -9999 0 -9999 0 0
RASA1 0.017 0 -9999 0 -9999 0 0
alpha2/beta1 Integrin 0.009 0.081 -9999 0 -0.406 1 1
Syndecan-2/Synbindin 0.016 0.069 -9999 0 -0.335 1 1
TGFB1 0.017 0 -9999 0 -9999 0 0
CASP3 -0.015 0.113 -9999 0 -0.297 3 3
FN1 0.017 0 -9999 0 -9999 0 0
Syndecan-2/IL8 -0.077 0.156 -9999 0 -0.338 6 6
SDC2 0.008 0.081 -9999 0 -0.404 1 1
KNG1 0.017 0 -9999 0 -9999 0 0
Syndecan-2/Neurofibromin 0.016 0.069 -9999 0 -0.335 1 1
TRAPPC4 0.017 0 -9999 0 -9999 0 0
CSF2 -0.026 0.153 -9999 0 -0.566 2 2
Syndecan-2/TGFB1 0.016 0.069 -9999 0 -0.335 1 1
Syndecan-2/Syntenin/PI-4-5-P2 0.015 0.063 -9999 0 -0.304 1 1
Syndecan-2/Ezrin 0.003 0.087 -9999 0 -0.306 2 2
PRKACA 0.025 0.063 -9999 0 -0.295 1 1
angiogenesis -0.077 0.156 -9999 0 -0.336 6 6
MMP2 0.017 0 -9999 0 -9999 0 0
IL8 -0.135 0.239 -9999 0 -0.496 8 8
calcineurin-NFAT signaling pathway 0.016 0.069 -9999 0 -0.334 1 1
a4b1 and a4b7 Integrin 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
ITGB1 0.017 0 -9999 0 -9999 0 0
ITGB7 0.017 0 -9999 0 -9999 0 0
ITGA4 -0.034 0.147 -9999 0 -0.441 3 3
alpha4/beta7 Integrin -0.011 0.106 -9999 0 -0.303 3 3
alpha4/beta1 Integrin -0.011 0.106 -9999 0 -0.303 3 3
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 0.017 0 -9999 0 -9999 0 0
ANTXR2 -0.005 0.11 -9999 0 -0.566 1 1
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.014 -9999 0 -0.074 1 1
monocyte activation -0.238 0.226 -9999 0 -0.423 14 14
MAP2K2 0.014 0.008 -9999 0 -9999 0 0
MAP2K1 -0.002 0.011 -9999 0 -9999 0 0
MAP2K7 -0.002 0.011 -9999 0 -9999 0 0
MAP2K6 -0.002 0.011 -9999 0 -9999 0 0
CYAA 0.005 0.059 -9999 0 -0.295 1 1
MAP2K4 -0.002 0.011 -9999 0 -9999 0 0
IL1B -0.13 0.132 -9999 0 -0.231 16 16
Channel 0.009 0.064 -9999 0 -0.315 1 1
NLRP1 -0.002 0.011 -9999 0 -9999 0 0
CALM1 -0.005 0.11 -9999 0 -0.566 1 1
negative regulation of phagocytosis -0.007 0.105 -9999 0 -0.533 1 1
mol:Ca2+ 0 0 -9999 0 -9999 0 0
regulation of endothelial cell proliferation 0.003 0.014 0.074 1 -9999 0 1
MAPK3 -0.002 0.011 -9999 0 -9999 0 0
MAPK1 -0.002 0.011 -9999 0 -9999 0 0
PGR -0.013 0.058 -9999 0 -0.302 1 1
PA/Cellular Receptors 0.009 0.07 -9999 0 -0.346 1 1
apoptosis -0.003 0.014 -9999 0 -0.074 1 1
LOC728358 0 0 -9999 0 -9999 0 0
Lethal toxin (unfolded) 0.009 0.06 -9999 0 -0.296 1 1
macrophage activation 0.018 0.013 -9999 0 -9999 0 0
TNF -0.1 0.201 -9999 0 -0.432 7 7
VCAM1 -0.24 0.228 -9999 0 -0.426 14 14
platelet activation -0.007 0.105 -9999 0 -0.533 1 1
MAPKKK cascade -0.015 0.014 -9999 0 -9999 0 0
IL18 -0.061 0.121 -9999 0 -0.241 8 8
negative regulation of macrophage activation -0.003 0.014 -9999 0 -0.074 1 1
LEF -0.003 0.014 -9999 0 -0.074 1 1
CASP1 -0.006 0.019 -9999 0 -0.082 1 1
mol:cAMP -0.023 0.102 -9999 0 -0.538 1 1
necrosis -0.003 0.014 -9999 0 -0.074 1 1
intracellular pH reduction 0 0 -9999 0 -9999 0 0
PAGA 0 0 -9999 0 -9999 0 0
Edema toxin (unfolded) 0.009 0.06 -9999 0 -0.296 1 1
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -9999 0 -9999 0 0
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.001 0.004 -9999 0 -9999 0 0
HDAC1 -0.005 0.111 -9999 0 -0.57 1 1
AES 0.017 0.003 -9999 0 -9999 0 0
FBXW11 0.017 0 -9999 0 -9999 0 0
DTX1 0.017 0 -9999 0 -9999 0 0
LRP6/FZD1 0.015 0.053 -9999 0 -0.254 1 1
TLE1 -0.02 0.131 -9999 0 -0.473 2 2
AP1 -0.104 0.183 -9999 0 -0.372 7 7
NCSTN 0.017 0 -9999 0 -9999 0 0
ADAM10 0.017 0 -9999 0 -9999 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.006 0.086 -9999 0 -9999 0 0
NICD/RBPSUH 0.04 0.006 -9999 0 -9999 0 0
WIF1 -0.301 0.255 -9999 0 -0.489 17 17
NOTCH1 -0.001 0.003 -9999 0 -9999 0 0
PSENEN 0.017 0 -9999 0 -9999 0 0
KREMEN2 -0.063 0.171 -9999 0 -0.416 5 5
DKK1 -0.136 0.222 -9999 0 -0.441 9 9
beta catenin/beta TrCP1 -0.009 0.112 -9999 0 -0.372 2 2
APH1B 0.002 0.075 -9999 0 -0.379 1 1
APH1A 0.017 0 -9999 0 -9999 0 0
AXIN1 0.002 0.012 -9999 0 -9999 0 0
CtBP/CBP/TCF1/TLE1/AES 0.009 0.144 -9999 0 -0.682 1 1
PSEN1 0.017 0 -9999 0 -9999 0 0
FOS -0.193 0.259 -9999 0 -0.498 11 11
JUN -0.041 0.166 -9999 0 -0.503 3 3
MAP3K7 0.017 0.005 -9999 0 -9999 0 0
CTNNB1 -0.019 0.117 -9999 0 -0.398 2 2
MAPK3 0.017 0 -9999 0 -9999 0 0
DKK2/LRP6/Kremen 2 -0.014 0.104 -9999 0 -0.337 1 1
HNF1A 0.017 0.003 -9999 0 -9999 0 0
CTBP1 0.017 0.003 -9999 0 -9999 0 0
MYC -0.028 0.264 -9999 0 -1.371 1 1
NKD1 -0.027 0.124 -9999 0 -0.378 3 3
FZD1 0.002 0.075 -9999 0 -0.38 1 1
NOTCH1 precursor/Deltex homolog 1 0.04 0.006 -9999 0 -9999 0 0
apoptosis -0.103 0.182 -9999 0 -0.37 7 7
Delta 1/NOTCHprecursor 0.04 0.006 -9999 0 -9999 0 0
DLL1 0.017 0 -9999 0 -9999 0 0
PPARD 0.02 0.031 -9999 0 -9999 0 0
Gamma Secretase 0.043 0.039 -9999 0 -9999 0 0
APC 0.002 0.012 -9999 0 -9999 0 0
DVL1 -0.006 0.033 -9999 0 -9999 0 0
CSNK2A1 0.017 0.002 -9999 0 -9999 0 0
MAP3K7IP1 0.017 0.005 -9999 0 -9999 0 0
DKK1/LRP6/Kremen 2 -0.105 0.171 -9999 0 -0.391 5 5
LRP6 0.017 0 -9999 0 -9999 0 0
CSNK1A1 0.017 0.002 -9999 0 -9999 0 0
NLK 0.03 0.013 -9999 0 -9999 0 0
CCND1 -0.052 0.276 -9999 0 -1.371 1 1
WNT1 0.017 0 -9999 0 -9999 0 0
Axin1/APC/beta catenin 0.007 0.07 -9999 0 -9999 0 0
DKK2 0.017 0 -9999 0 -9999 0 0
NOTCH1 precursor/DVL1 0.009 0.011 -9999 0 -9999 0 0
GSK3B 0.017 0.001 -9999 0 -9999 0 0
FRAT1 0.017 0.002 -9999 0 -9999 0 0
NOTCH/Deltex homolog 1 0.001 0.004 -9999 0 -9999 0 0
PPP2R5D 0.012 0.063 0.203 2 -9999 0 2
MAPK1 0.017 0 -9999 0 -9999 0 0
WNT1/LRP6/FZD1 -0.146 0.144 -9999 0 -0.298 10 10
RBPJ 0.017 0 -9999 0 -9999 0 0
CREBBP 0.018 0.008 -9999 0 -9999 0 0
Aurora A signaling

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
Aurora A/GADD45A 0.023 0.112 -9999 0 -0.444 1 1
BIRC5 -0.135 0.239 -9999 0 -0.496 8 8
NFKBIA 0.049 0.056 -9999 0 -9999 0 0
CPEB1 -0.019 0.131 -9999 0 -0.472 2 2
AKT1 0.049 0.056 -9999 0 -9999 0 0
NDEL1 0.017 0 -9999 0 -9999 0 0
Aurora A/BRCA1 0.04 0.046 -9999 0 -9999 0 0
NDEL1/TACC3 -0.052 0.126 -9999 0 -0.259 2 2
GADD45A -0.019 0.131 -9999 0 -0.472 2 2
GSK3B 0.032 0.023 -9999 0 -9999 0 0
PAK1/Aurora A -0.005 0.132 -9999 0 -0.326 3 3
MDM2 0.017 0 -9999 0 -9999 0 0
JUB -0.019 0.131 -9999 0 -0.472 2 2
TPX2 -0.121 0.185 -9999 0 -0.336 11 11
TP53 0.03 0.082 -9999 0 -0.303 1 1
DLG7 -0.077 0.149 -9999 0 -0.278 9 9
AURKAIP1 0.017 0 -9999 0 -9999 0 0
ARHGEF7 -0.026 0.153 -9999 0 -0.566 2 2
G2 phase of mitotic cell cycle 0 0 -9999 0 -9999 0 0
Aurora A/NDEL1/TACC3 -0.055 0.134 -9999 0 -0.276 2 2
G2/M transition of mitotic cell cycle 0.039 0.046 -9999 0 -9999 0 0
AURKA 0.05 0.073 -9999 0 -9999 0 0
AURKB -0.039 0.075 -9999 0 -0.173 2 2
CDC25B 0.042 0.06 -9999 0 -9999 0 0
G2/M transition checkpoint 0.019 0.088 -9999 0 -0.304 1 1
mRNA polyadenylation 0.019 0.072 -9999 0 -0.24 1 1
Aurora A/CPEB 0.019 0.072 -9999 0 -0.241 1 1
Aurora A/TACC1/TRAP/chTOG 0.048 0.09 -9999 0 -0.37 1 1
BRCA1 0.017 0 -9999 0 -9999 0 0
centrosome duplication -0.005 0.131 -9999 0 -0.325 3 3
regulation of centrosome cycle -0.052 0.124 -9999 0 -0.257 2 2
spindle assembly 0.046 0.089 -9999 0 -0.366 1 1
TDRD7 0.017 0 -9999 0 -9999 0 0
Aurora A/RasGAP/Survivin -0.022 0.119 -9999 0 -9999 0 0
CENPA -0.068 0.119 -9999 0 -0.233 9 9
Aurora A/PP2A 0.044 0.052 -9999 0 -9999 0 0
meiosis 0 0 -9999 0 -9999 0 0
protein catabolic process -0.021 0.089 -9999 0 -9999 0 0
negative regulation of DNA binding 0.03 0.082 -9999 0 -0.302 1 1
prophase 0 0 -9999 0 -9999 0 0
GIT1/beta-PIX -0.007 0.113 -9999 0 -0.406 2 2
RASA1 0.017 0 -9999 0 -9999 0 0
Ajuba/Aurora A 0.02 0.089 -9999 0 -0.306 1 1
mitotic prometaphase 0 0.009 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.05 0.073 -9999 0 -9999 0 0
TACC1 -0.005 0.11 -9999 0 -0.566 1 1
TACC3 -0.171 0.251 -9999 0 -0.491 10 10
Aurora A/Antizyme1 0.051 0.047 -9999 0 -9999 0 0
Aurora A/RasGAP 0.044 0.052 -9999 0 -9999 0 0
OAZ1 0.017 0 -9999 0 -9999 0 0
RAN 0.017 0 -9999 0 -9999 0 0
mitosis 0 0 -9999 0 -9999 0 0
PRKACA 0.032 0.023 -9999 0 -9999 0 0
GIT1 0.017 0 -9999 0 -9999 0 0
GIT1/beta-PIX/PAK1 -0.041 0.171 -9999 0 -0.417 4 4
Importin alpha/Importin beta/TPX2 -0.121 0.184 -9999 0 -0.336 11 11
PPP2R5D 0.017 0 -9999 0 -9999 0 0
Aurora A/TPX2 -0.063 0.134 -9999 0 -0.276 2 2
PAK1 -0.063 0.193 -9999 0 -0.519 4 4
CKAP5 0.017 0 -9999 0 -9999 0 0
p75(NTR)-mediated 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
Sortilin/TRAF6 0.025 0 -9999 0 -9999 0 0
Necdin/E2F1 -0.019 0.138 -9999 0 -0.375 3 3
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.021 0.07 -9999 0 -0.28 1 1
NGF (dimer)/p75(NTR)/BEX1 -0.013 0.104 -9999 0 -0.3 3 3
NT-4/5 (dimer)/p75(NTR) -0.014 0.094 -9999 0 -0.339 2 2
IKBKB 0.017 0 -9999 0 -9999 0 0
AKT1 0.006 0.088 -9999 0 -0.278 2 2
IKBKG 0.017 0 -9999 0 -9999 0 0
BDNF -0.093 0.188 -9999 0 -0.405 7 7
MGDIs/NGR/p75(NTR)/LINGO1 -0.059 0.167 -9999 0 -0.377 5 5
FURIN 0.017 0 -9999 0 -9999 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.054 0.129 -9999 0 -0.337 2 2
LINGO1 -0.026 0.153 -9999 0 -0.566 2 2
Sortilin/TRAF6/NRIF -0.004 0.021 -9999 0 -9999 0 0
proBDNF (dimer) -0.092 0.188 -9999 0 -0.405 7 7
NTRK1 0.017 0 -9999 0 -9999 0 0
RTN4R -0.056 0.177 -9999 0 -0.472 4 4
neuron apoptosis -0.031 0.114 -9999 0 -9999 0 0
IRAK1 0.017 0 -9999 0 -9999 0 0
SHC1 0 0.08 -9999 0 -0.345 1 1
ARHGDIA 0.017 0 -9999 0 -9999 0 0
RhoA/GTP -0.003 0.081 -9999 0 -0.415 1 1
Gamma Secretase 0.043 0.038 -9999 0 -9999 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.004 0.082 -9999 0 -0.306 1 1
MAGEH1 0.002 0.075 -9999 0 -0.378 1 1
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0 0.095 -9999 0 -0.306 2 2
Mammalian IAPs/DIABLO -0.008 0.101 -9999 0 -0.306 2 2
proNGF (dimer) 0 0 -9999 0 -9999 0 0
MAGED1 0.017 0 -9999 0 -9999 0 0
APP 0.017 0 -9999 0 -9999 0 0
NT-4/5 (dimer) 0 0 -9999 0 -9999 0 0
ZNF274 0.017 0 -9999 0 -9999 0 0
RhoA/GDP/RHOGDI 0 0.089 -9999 0 -0.287 2 2
NGF 0 0 -9999 0 -9999 0 0
cell cycle arrest -0.01 0.068 0.161 1 -0.263 1 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.017 0.079 -9999 0 -0.364 1 1
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.001 0.081 -9999 0 -0.278 2 2
NCSTN 0.017 0 -9999 0 -9999 0 0
mol:GTP 0 0.081 -9999 0 -0.345 1 1
PSENEN 0.017 0 -9999 0 -9999 0 0
mol:ceramide 0.009 0.073 -9999 0 -0.303 1 1
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.013 0.079 -9999 0 -0.303 1 1
p75(NTR)/beta APP -0.001 0.095 -9999 0 -0.329 2 2
BEX1 -0.005 0.11 -9999 0 -0.566 1 1
mol:GDP -0.012 0.08 -9999 0 -0.286 2 2
NGF (dimer) -0.153 0.15 -9999 0 -0.306 11 11
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.043 0.154 -9999 0 -0.336 5 5
PIK3R1 -0.005 0.11 -9999 0 -0.566 1 1
RAC1/GTP 0.001 0.069 -9999 0 -0.296 1 1
MYD88 0.017 0 -9999 0 -9999 0 0
CHUK 0.017 0 -9999 0 -9999 0 0
NGF (dimer)/p75(NTR)/PKA 0.001 0.081 -9999 0 -0.346 1 1
RHOB -0.005 0.11 -9999 0 -0.566 1 1
RHOA -0.005 0.11 -9999 0 -0.566 1 1
MAGE-G1/E2F1 -0.006 0.087 -9999 0 -0.252 3 3
NT3 (dimer) 0.017 0 -9999 0 -9999 0 0
TP53 -0.038 0.128 -9999 0 -0.429 1 1
PRDM4 0.009 0.073 -9999 0 -0.305 1 1
BDNF (dimer) -0.221 0.191 -9999 0 -0.361 15 15
PIK3CA 0.017 0 -9999 0 -9999 0 0
SORT1 0.017 0 -9999 0 -9999 0 0
activation of caspase activity 0.017 0.069 -9999 0 -0.278 1 1
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.012 0.074 -9999 0 -0.306 1 1
RHOC 0.017 0 -9999 0 -9999 0 0
XIAP 0 0 -9999 0 -9999 0 0
MAPK10 -0.001 0.106 -9999 0 -0.396 1 1
DIABLO 0.017 0 -9999 0 -9999 0 0
SMPD2 0.009 0.073 -9999 0 -0.305 1 1
APH1B 0.002 0.075 -9999 0 -0.378 1 1
APH1A 0.017 0 -9999 0 -9999 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.001 0.081 -9999 0 -0.278 2 2
PSEN1 0.017 0 -9999 0 -9999 0 0
APAF-1/Pro-Caspase 9 -0.023 0.135 -9999 0 -0.406 3 3
NT3 (dimer)/p75(NTR) -0.001 0.095 -9999 0 -0.329 2 2
MAPK8 0.008 0.09 -9999 0 -9999 0 0
MAPK9 0.008 0.09 -9999 0 -9999 0 0
APAF1 -0.005 0.11 -9999 0 -0.566 1 1
NTF3 0.017 0 -9999 0 -9999 0 0
NTF4 0 0 -9999 0 -9999 0 0
NDN -0.005 0.11 -9999 0 -0.566 1 1
RAC1/GDP 0.012 0 -9999 0 -9999 0 0
RhoA-B-C/GDP -0.033 0.082 -9999 0 -9999 0 0
p75 CTF/Sortilin/TRAF6/NRIF 0.043 0 -9999 0 -9999 0 0
RhoA-B-C/GTP 0 0.08 -9999 0 -0.343 1 1
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.026 0.111 -9999 0 -0.272 2 2
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.037 0.118 -9999 0 -0.298 2 2
PRKACB 0.017 0 -9999 0 -9999 0 0
proBDNF (dimer)/p75 ECD -0.053 0.134 -9999 0 -0.274 7 7
ChemicalAbstracts:86-01-1 0 0 -9999 0 -9999 0 0
BIRC3 -0.056 0.177 -9999 0 -0.472 4 4
BIRC2 0.017 0 -9999 0 -9999 0 0
neuron projection morphogenesis -0.015 0.087 0.19 1 -0.304 1 2
BAD 0.012 0.097 -9999 0 -0.329 1 1
RIPK2 0.002 0.075 -9999 0 -0.378 1 1
NGFR -0.019 0.131 -9999 0 -0.472 2 2
CYCS 0.017 0.069 -9999 0 -0.279 1 1
ADAM17 0.017 0 -9999 0 -9999 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.005 0.106 -9999 0 -0.494 1 1
BCL2L11 0.012 0.097 -9999 0 -0.329 1 1
BDNF (dimer)/p75(NTR) -0.079 0.151 -9999 0 -0.286 9 9
PI3K 0 0.095 -9999 0 -0.306 2 2
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.012 0.074 -9999 0 -0.306 1 1
NDNL2 0.017 0 -9999 0 -9999 0 0
YWHAE 0.017 0 -9999 0 -9999 0 0
PRKCI 0.017 0 -9999 0 -9999 0 0
NGF (dimer)/p75(NTR) -0.014 0.094 -9999 0 -0.339 2 2
ChemicalAbstracts:146-91-8 0 0 -9999 0 -9999 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.012 0.074 -9999 0 -0.306 1 1
TRAF6 0.017 0 -9999 0 -9999 0 0
RAC1 0.017 0 -9999 0 -9999 0 0
PRKCZ 0 0 -9999 0 -9999 0 0
PLG 0.017 0 -9999 0 -9999 0 0
oligodendrocyte cell fate commitment 0 0 -9999 0 -9999 0 0
CASP6 -0.041 0.107 -9999 0 -0.293 2 2
SQSTM1 -0.005 0.11 -9999 0 -0.566 1 1
NGFRAP1 0.017 0 -9999 0 -9999 0 0
CASP3 0.013 0.091 -9999 0 -0.31 1 1
E2F1 -0.027 0.124 -9999 0 -0.378 3 3
CASP9 -0.026 0.153 -9999 0 -0.566 2 2
IKK complex -0.015 0.05 -9999 0 -9999 0 0
NGF (dimer)/TRKA 0.012 0 -9999 0 -9999 0 0
MMP7 -0.308 0.259 -9999 0 -0.5 17 17
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.021 0.07 -9999 0 -0.28 1 1
MMP3 -0.027 0.124 -9999 0 -0.378 3 3
APAF-1/Caspase 9 -0.058 0.114 -9999 0 -0.39 2 2
IL4-mediated signaling events

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
BCL2L1 -0.234 0.378 -9999 0 -1.168 1 1
STAT6 (cleaved dimer) -0.269 0.322 -9999 0 -0.826 5 5
IGHG1 -0.088 0.167 -9999 0 -0.416 1 1
IGHG3 -0.237 0.361 -9999 0 -0.818 5 5
AKT1 -0.088 0.212 -9999 0 -9999 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.078 0.163 -9999 0 -9999 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.089 0.199 -9999 0 -9999 0 0
THY1 -0.275 0.45 -9999 0 -1.196 3 3
MYB -0.042 0.14 -9999 0 -0.378 4 4
HMGA1 0.017 0 -9999 0 -9999 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.124 0.233 -9999 0 -0.597 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.095 0.199 -9999 0 -9999 0 0
SP1 0.022 0.01 -9999 0 -9999 0 0
INPP5D 0 0 -9999 0 -9999 0 0
SOCS5 0.023 0.014 -9999 0 -9999 0 0
STAT6 (dimer)/ETS1 -0.225 0.346 -9999 0 -0.889 3 3
SOCS1 -0.15 0.261 -9999 0 -0.713 1 1
SOCS3 -0.141 0.3 -9999 0 -1.348 1 1
FCER2 -0.233 0.332 -9999 0 -0.799 2 2
PARP14 0.004 0.075 -9999 0 -0.378 1 1
CCL17 -0.254 0.362 -9999 0 -1.168 1 1
GRB2 0.017 0 -9999 0 -9999 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.069 0.17 -9999 0 -9999 0 0
T cell proliferation -0.218 0.376 -9999 0 -0.925 3 3
IL4R/JAK1 -0.254 0.36 -9999 0 -0.859 4 4
EGR2 -0.466 0.615 -9999 0 -1.384 7 7
JAK2 0.011 0.032 -9999 0 -9999 0 0
JAK3 0.021 0.008 -9999 0 -9999 0 0
PIK3R1 -0.005 0.11 -9999 0 -0.566 1 1
JAK1 -0.001 0.077 -9999 0 -0.387 1 1
COL1A2 -0.147 0.335 -9999 0 -0.875 3 3
CCL26 -0.241 0.374 -9999 0 -1.168 1 1
IL4R -0.247 0.397 -9999 0 -0.95 3 3
PTPN6 -0.043 0.161 -9999 0 -0.422 4 4
IL13RA2 -0.523 0.611 -9999 0 -1.228 10 10
IL13RA1 -0.088 0.203 -9999 0 -0.499 5 5
IRF4 -0.057 0.198 -9999 0 -0.666 2 2
ARG1 -0.158 0.41 -9999 0 -1.519 2 2
CBL -0.111 0.219 -9999 0 -0.591 1 1
GTF3A 0.009 0.032 -9999 0 -9999 0 0
PIK3CA 0.017 0 -9999 0 -9999 0 0
IL13RA1/JAK2 -0.059 0.148 -9999 0 -0.344 5 5
IRF4/BCL6 -0.051 0.184 -9999 0 -0.624 2 2
CD40LG -0.032 0.168 -9999 0 -0.5 3 3
MAPK14 -0.123 0.234 -9999 0 -0.797 1 1
mitosis -0.084 0.206 -9999 0 -9999 0 0
STAT6 -0.265 0.421 -9999 0 -0.936 5 5
SPI1 -0.047 0.153 -9999 0 -0.402 4 4
RPS6KB1 -0.074 0.2 -9999 0 -9999 0 0
STAT6 (dimer) -0.265 0.42 -9999 0 -0.935 5 5
STAT6 (dimer)/PARP14 -0.25 0.403 -9999 0 -0.902 5 5
mast cell activation 0.005 0.013 -9999 0 -9999 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.101 0.196 -9999 0 -9999 0 0
FRAP1 -0.088 0.212 -9999 0 -9999 0 0
LTA -0.24 0.381 -9999 0 -1.168 1 1
FES -0.005 0.11 -9999 0 -0.566 1 1
T-helper 1 cell differentiation 0.261 0.415 0.923 5 -9999 0 5
CCL11 -0.287 0.461 -9999 0 -1.278 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.091 0.207 -9999 0 -0.545 1 1
IL2RG 0.021 0.008 -9999 0 -9999 0 0
IL10 -0.24 0.381 -9999 0 -1.168 1 1
IRS1 0.017 0 -9999 0 -9999 0 0
IRS2 0.017 0 -9999 0 -9999 0 0
IL4 -0.039 0.115 -9999 0 -9999 0 0
IL5 -0.246 0.377 -9999 0 -1.168 1 1
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.221 0.346 -9999 0 -0.816 3 3
COL1A1 -0.239 0.415 -9999 0 -1.469 2 2
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -9999 0 0
IL4/IL4R/JAK1 -0.253 0.366 -9999 0 -1.189 1 1
IL2R gamma/JAK3 0.027 0.015 -9999 0 -9999 0 0
TFF3 -0.24 0.387 -9999 0 -1.035 2 2
ALOX15 -0.234 0.378 -9999 0 -1.168 1 1
MYBL1 0.017 0 -9999 0 -9999 0 0
T-helper 2 cell differentiation -0.2 0.322 -9999 0 -0.762 3 3
SHC1 0.017 0 -9999 0 -9999 0 0
CEBPB 0.013 0.034 -9999 0 -9999 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.089 0.204 -9999 0 -0.505 1 1
mol:PI-3-4-5-P3 -0.088 0.212 -9999 0 -9999 0 0
PI3K -0.092 0.219 -9999 0 -9999 0 0
DOK2 -0.041 0.166 -9999 0 -0.503 3 3
ETS1 0.023 0.013 -9999 0 -9999 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.06 0.162 -9999 0 -9999 0 0
ITGB3 -0.271 0.438 -9999 0 -1.312 2 2
PIGR -0.239 0.392 -9999 0 -1.31 1 1
IGHE 0.018 0.035 -9999 0 -9999 0 0
MAPKKK cascade -0.059 0.161 -9999 0 -9999 0 0
BCL6 0.016 0 -9999 0 -9999 0 0
OPRM1 -0.265 0.438 -9999 0 -1.312 2 2
RETNLB -0.234 0.378 -9999 0 -1.168 1 1
SELP -0.234 0.378 -9999 0 -1.168 1 1
AICDA -0.227 0.362 -9999 0 -1.129 1 1
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 -0.016 0.122 -9999 0 -0.337 3 3
fibroblast growth factor receptor signaling pathway -0.016 0.121 -9999 0 -0.336 3 3
LAMA1 -0.005 0.11 -9999 0 -0.566 1 1
PRNP -0.005 0.11 -9999 0 -0.566 1 1
GPC1/SLIT2 -0.064 0.155 -9999 0 -0.318 7 7
SMAD2 0.031 0.039 -9999 0 -9999 0 0
GPC1/PrPc/Cu2+ 0.009 0.07 -9999 0 -0.346 1 1
GPC1/Laminin alpha1 0.009 0.081 -9999 0 -0.406 1 1
TDGF1 0.017 0 -9999 0 -9999 0 0
CRIPTO/GPC1 0.025 0 -9999 0 -9999 0 0
APP/GPC1 0.025 0 -9999 0 -9999 0 0
mol:NO 0 0 -9999 0 -9999 0 0
YES1 0.019 0.07 -9999 0 -0.338 1 1
FLT1 0.017 0 -9999 0 -9999 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.026 0.044 -9999 0 -9999 0 0
SERPINC1 0.017 0 -9999 0 -9999 0 0
FYN 0.032 0 -9999 0 -9999 0 0
FGR 0.032 0 -9999 0 -9999 0 0
positive regulation of MAPKKK cascade 0.03 0.095 -9999 0 -0.37 1 1
SLIT2 -0.107 0.214 -9999 0 -0.459 7 7
GPC1/NRG -0.038 0.135 -9999 0 -0.313 5 5
NRG1 -0.07 0.187 -9999 0 -0.453 5 5
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.026 0.044 -9999 0 -9999 0 0
LYN 0.032 0 -9999 0 -9999 0 0
mol:Spermine 0.013 0 -9999 0 -9999 0 0
cell growth -0.016 0.121 -9999 0 -0.336 3 3
BMP signaling pathway -0.017 0 -9999 0 -9999 0 0
SRC 0.032 0 -9999 0 -9999 0 0
TGFBR1 0.002 0.075 -9999 0 -0.378 1 1
mol:Cu2+ 0 0 -9999 0 -9999 0 0
PLA2G2A 0.017 0 -9999 0 -9999 0 0
GPC1 0.017 0 -9999 0 -9999 0 0
TGFBR1 (dimer) 0.002 0.075 -9999 0 -0.378 1 1
VEGFA 0.002 0.075 -9999 0 -0.378 1 1
BLK 0.019 0.07 -9999 0 -0.338 1 1
HCK 0.001 0.09 -9999 0 -0.338 1 1
FGF2 -0.063 0.193 -9999 0 -0.519 4 4
FGFR1 0.017 0 -9999 0 -9999 0 0
VEGFR1 homodimer 0.017 0 -9999 0 -9999 0 0
TGFBR2 0.017 0 -9999 0 -9999 0 0
cell death 0.025 0 -9999 0 -9999 0 0
ATIII/GPC1 0.025 0 -9999 0 -9999 0 0
PLA2G2A/GPC1 0.025 0 -9999 0 -9999 0 0
LCK 0.032 0 -9999 0 -9999 0 0
neuron differentiation -0.038 0.135 -9999 0 -0.313 5 5
PrPc/Cu2+ -0.003 0.081 -9999 0 -0.415 1 1
APP 0.017 0 -9999 0 -9999 0 0
TGFBR2 (dimer) 0.017 0 -9999 0 -9999 0 0
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.056 0.167 -9999 0 -0.531 2 2
alphaM/beta2 Integrin/GPIbA -0.056 0.167 -9999 0 -0.435 3 3
alphaM/beta2 Integrin/proMMP-9 -0.113 0.197 -9999 0 -0.458 5 5
PLAUR 0.017 0 -9999 0 -9999 0 0
HMGB1 0.007 0.017 -9999 0 -9999 0 0
alphaM/beta2 Integrin/Talin -0.056 0.167 -9999 0 -0.435 3 3
AGER 0.007 0.017 -9999 0 -9999 0 0
RAP1A 0.017 0 -9999 0 -9999 0 0
SELPLG -0.063 0.171 -9999 0 -0.416 5 5
mol:LDL 0 0 -9999 0 -9999 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.073 0.181 -9999 0 -0.547 2 2
mol:GTP 0 0 -9999 0 -9999 0 0
MMP9 -0.077 0.201 -9999 0 -0.491 5 5
CYR61 -0.12 0.236 -9999 0 -0.512 7 7
TLN1 0.017 0 -9999 0 -9999 0 0
Rap1/GTP -0.042 0.145 -9999 0 -0.763 1 1
RHOA -0.005 0.11 -9999 0 -0.566 1 1
P-selectin oligomer 0.017 0 -9999 0 -9999 0 0
MYH2 -0.004 0.173 -9999 0 -0.837 1 1
MST1R 0.017 0 -9999 0 -9999 0 0
leukocyte activation during inflammatory response -0.037 0.146 -9999 0 -0.454 2 2
APOB 0.017 0 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
complement component iC3b receptor activity 0 0 -9999 0 -9999 0 0
MMP2 0.017 0 -9999 0 -9999 0 0
JAM3 0.017 0 -9999 0 -9999 0 0
GP1BA 0.017 0 -9999 0 -9999 0 0
alphaM/beta2 Integrin/CTGF -0.082 0.168 -9999 0 -0.435 3 3
alphaM/beta2 Integrin -0.023 0.183 -9999 0 -0.901 1 1
JAM3 homodimer 0.017 0 -9999 0 -9999 0 0
ICAM2 -0.005 0.11 -9999 0 -0.566 1 1
ICAM1 -0.005 0.11 -9999 0 -0.566 1 1
phagocytosis triggered by activation of immune response cell surface activating receptor -0.023 0.18 -9999 0 -0.886 1 1
cell adhesion -0.056 0.166 -9999 0 -0.433 3 3
NFKB1 -0.095 0.214 -9999 0 -0.536 3 3
THY1 -0.034 0.147 -9999 0 -0.441 3 3
RhoA/GDP -0.003 0.081 -9999 0 -0.415 1 1
Lipoprotein(a) 0.023 0 -9999 0 -9999 0 0
alphaM/beta2 Integrin/LRP/tPA -0.072 0.191 -9999 0 -0.491 3 3
IL6 -0.108 0.222 -9999 0 -0.586 3 3
ITGB2 -0.095 0.193 -9999 0 -0.446 6 6
elevation of cytosolic calcium ion concentration -0.045 0.167 -9999 0 -0.453 3 3
alphaM/beta2 Integrin/JAM2/JAM3 -0.037 0.157 -9999 0 -0.484 2 2
JAM2 0.017 0 -9999 0 -9999 0 0
alphaM/beta2 Integrin/ICAM1 -0.044 0.195 -9999 0 -0.592 2 2
alphaM/beta2 Integrin/uPA/Plg -0.044 0.168 -9999 0 -0.457 3 3
RhoA/GTP -0.007 0.187 -9999 0 -0.923 1 1
positive regulation of phagocytosis -0.077 0.2 -9999 0 -1.011 1 1
Ron/MSP 0.015 0.052 -9999 0 -0.252 1 1
alphaM/beta2 Integrin/uPAR/uPA -0.044 0.168 -9999 0 -0.457 3 3
alphaM/beta2 Integrin/uPAR -0.056 0.167 -9999 0 -0.531 2 2
PLAU 0.002 0.075 -9999 0 -0.378 1 1
PLAT -0.049 0.16 -9999 0 -0.425 4 4
actin filament polymerization -0.002 0.162 -9999 0 -0.78 1 1
MST1 0.002 0.075 -9999 0 -0.378 1 1
alphaM/beta2 Integrin/lipoprotein(a) -0.036 0.149 -9999 0 -0.46 2 2
TNF -0.14 0.291 -9999 0 -0.803 3 3
RAP1B 0.017 0 -9999 0 -9999 0 0
alphaM/beta2 Integrin/uPA -0.064 0.18 -9999 0 -0.504 3 3
fibrinolysis -0.045 0.167 -9999 0 -0.453 3 3
HCK -0.034 0.147 -9999 0 -0.441 3 3
dendritic cell antigen processing and presentation -0.023 0.18 -9999 0 -0.886 1 1
VTN 0.017 0 -9999 0 -9999 0 0
alphaM/beta2 Integrin/CYR61 -0.139 0.212 -9999 0 -0.43 7 7
LPA 0.017 0 -9999 0 -9999 0 0
LRP1 0.017 0 -9999 0 -9999 0 0
cell migration -0.092 0.184 -9999 0 -0.413 5 5
FN1 0.017 0 -9999 0 -9999 0 0
alphaM/beta2 Integrin/Thy1 -0.087 0.177 -9999 0 -0.38 5 5
MPO -0.034 0.147 -9999 0 -0.441 3 3
KNG1 0.017 0 -9999 0 -9999 0 0
RAP1/GDP 0.023 0 -9999 0 -9999 0 0
ROCK1 0.003 0.172 -9999 0 -0.837 1 1
ELA2 0.017 0 -9999 0 -9999 0 0
PLG 0.017 0 -9999 0 -9999 0 0
CTGF -0.027 0.124 -9999 0 -0.378 3 3
alphaM/beta2 Integrin/Hck -0.083 0.229 -9999 0 -0.48 5 5
ITGAM -0.015 0.115 -9999 0 -0.593 1 1
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.08 0.18 -9999 0 -0.395 5 5
HP 0.002 0.075 -9999 0 -0.378 1 1
leukocyte adhesion -0.094 0.153 -9999 0 -0.738 1 1
SELP 0.017 0 -9999 0 -9999 0 0
Nectin adhesion 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
PDGFRB 0.017 0 -9999 0 -9999 0 0
alphaV beta3 Integrin -0.017 0.122 -9999 0 -0.354 3 3
PTK2 -0.009 0.154 -9999 0 -0.488 2 2
positive regulation of JNK cascade -0.026 0.082 -9999 0 -0.311 2 2
CDC42/GDP 0.024 0.129 -9999 0 -0.417 2 2
Rac1/GDP 0.026 0.128 -9999 0 -0.412 2 2
RAP1B 0.017 0 -9999 0 -9999 0 0
RAP1A 0.017 0 -9999 0 -9999 0 0
CTNNB1 -0.026 0.153 -9999 0 -0.566 2 2
CDC42/GTP -0.03 0.101 -9999 0 -0.381 2 2
nectin-3/I-afadin -0.007 0.113 -9999 0 -0.406 2 2
RAPGEF1 0.015 0.142 -9999 0 -0.47 2 2
mol:GTP 0 0 -9999 0 -9999 0 0
CRK 0.005 0.16 -9999 0 -0.543 2 2
PDGFB-D/PDGFRB 0.017 0 -9999 0 -9999 0 0
TLN1 -0.022 0.158 -9999 0 -0.43 3 3
Rap1/GTP -0.025 0.087 -9999 0 -0.328 2 2
IQGAP1 0.017 0 -9999 0 -9999 0 0
Rap1/GTP/I-afadin 0.02 0.064 -9999 0 -0.306 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.007 0.113 -9999 0 -0.406 2 2
PVR 0.017 0 -9999 0 -9999 0 0
Necl-5(dimer) 0.017 0 -9999 0 -9999 0 0
mol:GDP 0.015 0.155 -9999 0 -0.515 2 2
MLLT4 -0.005 0.11 -9999 0 -0.566 1 1
PIK3CA 0.017 0 -9999 0 -9999 0 0
PI3K 0.014 0.101 -9999 0 -9999 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.009 0.081 -9999 0 -0.406 1 1
positive regulation of lamellipodium assembly -0.025 0.086 -9999 0 -0.326 2 2
PVRL1 0.017 0 -9999 0 -9999 0 0
PVRL3 -0.005 0.11 -9999 0 -0.566 1 1
PVRL2 -0.005 0.11 -9999 0 -0.566 1 1
PIK3R1 -0.005 0.11 -9999 0 -0.566 1 1
CDH1 -0.244 0.26 -9999 0 -0.486 14 14
CLDN1 -0.005 0.11 -9999 0 -0.566 1 1
JAM-A/CLDN1 -0.014 0.141 -9999 0 -0.345 4 4
SRC -0.006 0.176 -9999 0 -0.61 2 2
ITGB3 -0.019 0.131 -9999 0 -0.472 2 2
nectin-1(dimer)/I-afadin/I-afadin 0.009 0.081 -9999 0 -0.406 1 1
FARP2 0.008 0.151 -9999 0 -0.508 2 2
RAC1 0.017 0 -9999 0 -9999 0 0
CTNNA1 0.017 0 -9999 0 -9999 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.007 0.097 -9999 0 -0.337 2 2
nectin-1/I-afadin 0.009 0.081 -9999 0 -0.406 1 1
nectin-2/I-afadin -0.007 0.113 -9999 0 -0.406 2 2
RAC1/GTP/IQGAP1/filamentous actin 0.023 0 -9999 0 -9999 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.007 0.097 -9999 0 -0.337 2 2
CDC42/GTP/IQGAP1/filamentous actin 0.023 0 -9999 0 -9999 0 0
F11R -0.019 0.131 -9999 0 -0.472 2 2
positive regulation of filopodium formation -0.026 0.082 -9999 0 -0.311 2 2
alphaV/beta3 Integrin/Talin -0.03 0.179 -9999 0 -0.476 3 3
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.007 0.113 -9999 0 -0.406 2 2
nectin-2(dimer)/I-afadin/I-afadin -0.007 0.113 -9999 0 -0.406 2 2
PIP5K1C -0.032 0.167 -9999 0 -0.465 3 3
VAV2 0.01 0.153 -9999 0 -0.518 2 2
RAP1/GDP -0.026 0.102 -9999 0 -0.384 2 2
ITGAV -0.005 0.11 -9999 0 -0.566 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.007 0.117 -9999 0 -0.337 3 3
nectin-3(dimer)/I-afadin/I-afadin -0.007 0.113 -9999 0 -0.406 2 2
Rac1/GTP -0.03 0.105 -9999 0 -0.397 2 2
PTPRM -0.045 0.18 -9999 0 -0.436 4 4
E-cadherin/beta catenin/alpha catenin -0.124 0.209 -9999 0 -0.559 3 3
adherens junction assembly 0 0 -9999 0 -9999 0 0
CDC42 0.017 0 -9999 0 -9999 0 0
Glucocorticoid receptor regulatory network

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
PCK2 -0.006 0.013 -9999 0 -9999 0 0
SMARCC2 0.017 0 -9999 0 -9999 0 0
SMARCC1 0.017 0 -9999 0 -9999 0 0
TBX21 0.005 0.096 -9999 0 -0.346 1 1
SUMO2 0.018 0.011 -9999 0 -9999 0 0
STAT1 (dimer) 0.012 0.074 -9999 0 -0.367 1 1
FKBP4 0.017 0 -9999 0 -9999 0 0
FKBP5 -0.236 0.269 -9999 0 -0.508 13 13
GR alpha/HSP90/FKBP51/HSP90 -0.117 0.165 -9999 0 -0.35 6 6
PRL 0.031 0.063 -9999 0 -9999 0 0
cortisol/GR alpha (dimer)/TIF2 0.051 0.155 0.539 1 -9999 0 1
RELA -0.032 0.094 -9999 0 -9999 0 0
FGG 0.055 0.138 0.471 1 -9999 0 1
GR beta/TIF2 0.036 0.071 0.267 1 -9999 0 1
IFNG -0.06 0.159 -9999 0 -0.506 1 1
apoptosis 0.047 0.222 0.525 2 -9999 0 2
CREB1 0.014 0.071 -9999 0 -0.348 1 1
histone acetylation 0.009 0.063 -9999 0 -0.284 1 1
BGLAP 0.026 0.066 -9999 0 -9999 0 0
GR/PKAc 0.053 0.063 -9999 0 -9999 0 0
NF kappa B1 p50/RelA -0.056 0.171 -9999 0 -0.413 3 3
SMARCD1 0.017 0 -9999 0 -9999 0 0
MDM2 0.026 0.062 0.228 1 -9999 0 1
GATA3 0.028 0.025 -9999 0 -9999 0 0
AKT1 0.008 0.002 -9999 0 -9999 0 0
CSF2 -0.076 0.321 -9999 0 -1.191 2 2
GSK3B 0.018 0.011 -9999 0 -9999 0 0
NR1I3 0.061 0.205 0.504 2 -9999 0 2
CSN2 0.048 0.12 0.396 1 -9999 0 1
BRG1/BAF155/BAF170/BAF60A 0.043 0 -9999 0 -9999 0 0
NFATC1 -0.03 0.166 -9999 0 -0.492 3 3
POU2F1 0.026 0 -9999 0 -9999 0 0
CDKN1A -0.31 0.552 -9999 0 -1.426 5 5
response to stress 0 0 -9999 0 -9999 0 0
response to UV 0.002 0.012 -9999 0 -9999 0 0
SFN 0.017 0 -9999 0 -9999 0 0
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.094 0.153 -9999 0 -0.32 4 4
prolactin receptor activity 0 0 -9999 0 -9999 0 0
EGR1 -0.157 0.396 0.486 1 -0.745 7 8
JUN 0.013 0.124 -9999 0 -0.33 2 2
IL4 -0.008 0.127 -9999 0 -0.46 1 1
CDK5R1 0.017 0.006 -9999 0 -9999 0 0
PRKACA 0.017 0 -9999 0 -9999 0 0
cortisol/GR alpha (monomer)/AP-1 -0.09 0.161 -9999 0 -0.455 3 3
GR alpha/HSP90/FKBP51/HSP90/PP5C -0.094 0.153 -9999 0 -0.32 4 4
cortisol/GR alpha (monomer) 0.052 0.181 0.628 1 -9999 0 1
NCOA2 0.017 0 -9999 0 -9999 0 0
response to hypoxia 0 0 -9999 0 -9999 0 0
FOS -0.18 0.262 -9999 0 -0.487 11 11
AP-1/NFAT1-c-4 -0.09 0.23 -9999 0 -0.514 3 3
AFP 0.027 0.105 -9999 0 -9999 0 0
SUV420H1 0.017 0 -9999 0 -9999 0 0
IRF1 0.052 0.1 -9999 0 -9999 0 0
TP53 -0.122 0.249 -9999 0 -0.55 6 6
PPP5C 0.017 0 -9999 0 -9999 0 0
KRT17 -0.06 0.167 -9999 0 -9999 0 0
KRT14 -0.007 0.075 -9999 0 -9999 0 0
TBP 0.028 0 -9999 0 -9999 0 0
CREBBP 0.007 0.024 -9999 0 -9999 0 0
HDAC1 -0.006 0.114 -9999 0 -0.573 1 1
HDAC2 -0.001 0.114 -9999 0 -0.568 1 1
AP-1 -0.09 0.23 -9999 0 -0.513 3 3
MAPK14 0.018 0.011 -9999 0 -9999 0 0
MAPK10 -0.012 0.105 -9999 0 -0.379 2 2
MAPK11 0.018 0.011 -9999 0 -9999 0 0
KRT5 -0.052 0.151 -9999 0 -0.506 1 1
interleukin-1 receptor activity 0.004 0.023 -9999 0 -9999 0 0
NCOA1 0.02 0.001 -9999 0 -9999 0 0
STAT1 0.012 0.074 -9999 0 -0.368 1 1
CGA -0.015 0.228 -9999 0 -1.129 1 1
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.031 0.154 0.508 2 -9999 0 2
MAPK3 0.018 0.013 -9999 0 -9999 0 0
MAPK1 0.018 0.011 -9999 0 -9999 0 0
ICAM1 -0.077 0.272 -9999 0 -1.275 1 1
NFKB1 -0.032 0.094 -9999 0 -0.256 1 1
MAPK8 0.03 0.073 -9999 0 -9999 0 0
MAPK9 0.018 0.011 -9999 0 -9999 0 0
cortisol/GR alpha (dimer) 0.026 0.226 0.529 2 -9999 0 2
BAX -0.071 0.163 -9999 0 -9999 0 0
POMC -0.103 0.388 -9999 0 -1.436 2 2
EP300 0.007 0.025 -9999 0 -9999 0 0
cortisol/GR alpha (dimer)/p53 -0.027 0.2 -9999 0 -0.57 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.057 -9999 0 -9999 0 0
SGK1 0.022 0.04 -9999 0 -9999 0 0
IL13 -0.021 0.125 -9999 0 -9999 0 0
IL6 -0.098 0.233 -9999 0 -0.566 4 4
PRKACG 0.017 0 -9999 0 -9999 0 0
IL5 -0.032 0.15 -9999 0 -9999 0 0
IL2 -0.062 0.172 -9999 0 -0.525 2 2
CDK5 0.017 0.006 -9999 0 -9999 0 0
PRKACB 0.017 0 -9999 0 -9999 0 0
HSP90AA1 0.017 0 -9999 0 -9999 0 0
IL8 -0.227 0.46 -9999 0 -1.028 6 6
CDK5R1/CDK5 0.023 0.018 -9999 0 -9999 0 0
NF kappa B1 p50/RelA/PKAc -0.007 0.128 -9999 0 -0.343 1 1
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.069 0.148 0.517 1 -9999 0 1
SMARCA4 0.017 0 -9999 0 -9999 0 0
chromatin remodeling 0.056 0.098 0.356 1 -9999 0 1
NF kappa B1 p50/RelA/Cbp -0.025 0.141 -9999 0 -0.381 1 1
JUN (dimer) 0.013 0.124 -9999 0 -0.329 2 2
YWHAH 0.002 0.075 -9999 0 -0.378 1 1
VIPR1 0.016 0.068 -9999 0 -9999 0 0
NR3C1 0.04 0.104 0.389 1 -9999 0 1
NR4A1 -0.035 0.171 -9999 0 -0.516 3 3
TIF2/SUV420H1 0.025 0 -9999 0 -9999 0 0
MAPKKK cascade 0.047 0.222 0.525 2 -9999 0 2
cortisol/GR alpha (dimer)/Src-1 0.054 0.157 0.547 1 -9999 0 1
PBX1 0.026 0 -9999 0 -9999 0 0
POU1F1 0.011 0.075 -9999 0 -0.369 1 1
SELE -0.099 0.227 -9999 0 -0.61 3 3
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.056 0.098 0.356 1 -9999 0 1
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.069 0.148 0.517 1 -9999 0 1
mol:cortisol 0.02 0.108 0.376 1 -9999 0 1
MMP1 -0.045 0.11 -9999 0 -9999 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.006 0.093 -9999 0 -0.38 1 1
CRKL 0.017 0 -9999 0 -9999 0 0
Rac1/GDP 0.012 0 -9999 0 -9999 0 0
DOCK1 0.017 0 -9999 0 -9999 0 0
ITGA4 -0.034 0.147 -9999 0 -0.441 3 3
alpha4/beta7 Integrin/MAdCAM1 -0.021 0.132 -9999 0 -0.392 2 2
EPO 0.017 0 -9999 0 -9999 0 0
alpha4/beta7 Integrin -0.011 0.106 -9999 0 -0.303 3 3
mol:GTP 0 0 -9999 0 -9999 0 0
CRK 0.017 0 -9999 0 -9999 0 0
alpha4/beta1 Integrin -0.011 0.106 -9999 0 -0.303 3 3
EPO/EPOR (dimer) 0.025 0 -9999 0 -9999 0 0
lamellipodium assembly 0.019 0.06 -9999 0 -0.28 1 1
PIK3CA 0.017 0 -9999 0 -9999 0 0
PI3K 0.009 0.081 -9999 0 -0.406 1 1
ARF6 0.017 0 -9999 0 -9999 0 0
JAK2 0.019 0.066 -9999 0 -9999 0 0
PXN 0.017 0 -9999 0 -9999 0 0
PIK3R1 -0.005 0.11 -9999 0 -0.566 1 1
MADCAM1 -0.027 0.124 -9999 0 -0.378 3 3
cell adhesion -0.021 0.131 -9999 0 -0.389 2 2
CRKL/CBL 0.025 0 -9999 0 -9999 0 0
ITGB1 0.017 0 -9999 0 -9999 0 0
SRC -0.171 0.166 -9999 0 -0.328 12 12
ITGB7 0.017 0 -9999 0 -9999 0 0
RAC1 0.017 0 -9999 0 -9999 0 0
alpha4/beta1 Integrin/VCAM1 -0.197 0.183 -9999 0 -0.37 12 12
p130Cas/Crk/Dock1 -0.123 0.146 -9999 0 -0.399 2 2
VCAM1 -0.308 0.259 -9999 0 -0.5 17 17
RHOA -0.005 0.11 -9999 0 -0.566 1 1
alpha4/beta1 Integrin/Paxillin/GIT1 0.015 0.083 -9999 0 -0.298 1 1
BCAR1 -0.151 0.156 -9999 0 -0.448 2 2
EPOR 0.017 0 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
CBL 0.017 0 -9999 0 -9999 0 0
GIT1 0.017 0 -9999 0 -9999 0 0
Rac1/GTP 0.019 0.061 -9999 0 -0.287 1 1
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 -0.026 0.153 -9999 0 -0.566 2 2
positive regulation of NF-kappaB transcription factor activity -0.023 0.135 -9999 0 -0.405 3 3
MAP2K4 0.028 0.09 -9999 0 -0.349 1 1
IKBKB 0.017 0 -9999 0 -9999 0 0
TNFRSF10B -0.005 0.11 -9999 0 -0.566 1 1
TNFRSF10A 0.017 0 -9999 0 -9999 0 0
SMPD1 -0.005 0.084 -9999 0 -0.269 2 2
IKBKG 0.017 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
TNFRSF10D -0.005 0.11 -9999 0 -0.566 1 1
TRAIL/TRAILR2 -0.02 0.165 -9999 0 -0.578 2 2
TRAIL/TRAILR3 -0.017 0.122 -9999 0 -0.354 3 3
TRAIL/TRAILR1 -0.007 0.113 -9999 0 -0.406 2 2
TRAIL/TRAILR4 -0.023 0.135 -9999 0 -0.406 3 3
TRAIL/TRAILR1/DAP3/GTP 0.007 0.089 -9999 0 -0.306 2 2
IKK complex -0.011 0.041 -9999 0 -9999 0 0
RIPK1 0.017 0 -9999 0 -9999 0 0
response to oxidative stress 0 0 -9999 0 -9999 0 0
DAP3/GTP 0.012 0 -9999 0 -9999 0 0
MAPK3 -0.006 0.113 -9999 0 -0.405 2 2
MAP3K1 0.021 0.095 -9999 0 -0.375 1 1
TRAILR4 (trimer) -0.005 0.11 -9999 0 -0.565 1 1
TRADD 0.017 0 -9999 0 -9999 0 0
TRAILR1 (trimer) 0.017 0 -9999 0 -9999 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.024 0.073 -9999 0 -9999 0 0
CFLAR 0.017 0 -9999 0 -9999 0 0
MAPK1 -0.006 0.113 -9999 0 -0.405 2 2
TRAIL/TRAILR1/FADD/TRADD/RIP 0.026 0.084 -9999 0 -9999 0 0
mol:ceramide -0.005 0.083 -9999 0 -0.268 2 2
FADD 0.017 0 -9999 0 -9999 0 0
MAPK8 0.035 0.086 -9999 0 -0.326 1 1
TRAF2 0.017 0 -9999 0 -9999 0 0
TRAILR3 (trimer) 0.002 0.075 -9999 0 -0.378 1 1
CHUK 0.017 0 -9999 0 -9999 0 0
TRAIL/TRAILR1/FADD 0.007 0.097 -9999 0 -0.337 2 2
DAP3 0.017 0 -9999 0 -9999 0 0
CASP10 -0.022 0.128 0.269 1 -0.429 2 3
JNK cascade -0.023 0.135 -9999 0 -0.405 3 3
TRAIL (trimer) -0.026 0.152 -9999 0 -0.565 2 2
TNFRSF10C 0.002 0.075 -9999 0 -0.378 1 1
TRAIL/TRAILR1/DAP3/GTP/FADD 0.016 0.084 -9999 0 -0.28 2 2
TRAIL/TRAILR2/FADD -0.005 0.146 -9999 0 -0.497 2 2
cell death -0.005 0.083 -9999 0 -0.267 2 2
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.014 0.113 -9999 0 -0.494 1 1
TRAILR2 (trimer) -0.005 0.11 -9999 0 -0.565 1 1
CASP8 0.01 0.035 -9999 0 -9999 0 0
negative regulation of caspase activity 0 0 -9999 0 -9999 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.015 0.13 -9999 0 -0.568 1 1
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.027 0.024 -9999 0 -9999 0 0
VDR -0.026 0.153 -9999 0 -0.566 2 2
FAM120B 0.017 0 -9999 0 -9999 0 0
RXRs/LXRs/DNA/9cRA -0.067 0.155 -9999 0 -0.425 2 2
RXRs/LXRs/DNA/Oxysterols -0.125 0.254 -9999 0 -0.462 8 8
MED1 0.017 0 -9999 0 -9999 0 0
mol:9cRA -0.018 0.03 -9999 0 -9999 0 0
RARs/THRs/DNA/Src-1 0.044 0 -9999 0 -9999 0 0
RXRs/NUR77 -0.013 0.085 -9999 0 -0.286 1 1
RXRs/PPAR -0.015 0.089 -9999 0 -0.344 1 1
NCOR2 0.017 0 -9999 0 -9999 0 0
VDR/VDR/Vit D3 -0.019 0.112 -9999 0 -0.415 2 2
RARs/VDR/DNA/Vit D3 0.016 0.084 -9999 0 -0.28 2 2
RARA 0.017 0 -9999 0 -9999 0 0
NCOA1 0.017 0 -9999 0 -9999 0 0
VDR/VDR/DNA -0.026 0.152 -9999 0 -0.565 2 2
RARs/RARs/DNA/9cRA 0.021 0.016 -9999 0 -9999 0 0
RARG 0.017 0 -9999 0 -9999 0 0
RPS6KB1 0.033 0.03 -9999 0 -9999 0 0
RARs/THRs/DNA/SMRT 0.044 0 -9999 0 -9999 0 0
THRA 0.017 0 -9999 0 -9999 0 0
mol:Bile acids 0 0 -9999 0 -9999 0 0
VDR/Vit D3/DNA -0.019 0.112 -9999 0 -0.415 2 2
RXRs/PPAR/9cRA/PGJ2/DNA -0.03 0.088 -9999 0 -9999 0 0
NR1H4 -0.056 0.153 -9999 0 -0.378 5 5
RXRs/LXRs/DNA -0.024 0.111 -9999 0 -9999 0 0
NR1H2 0.005 0.023 -9999 0 -9999 0 0
NR1H3 0.002 0.027 -9999 0 -9999 0 0
RXRs/VDR/DNA/Vit D3 -0.023 0.11 -9999 0 -0.348 2 2
NR4A1 -0.005 0.11 -9999 0 -0.566 1 1
mol:ATRA 0 0 -9999 0 -9999 0 0
RXRs/FXR/9cRA/MED1 -0.031 0.06 -9999 0 -9999 0 0
RXRG -0.025 0.1 -9999 0 -0.37 2 2
RXR alpha/CCPG 0.015 0.017 -9999 0 -9999 0 0
RXRA 0.005 0.023 -9999 0 -9999 0 0
RXRB 0.002 0.027 -9999 0 -9999 0 0
THRB 0.017 0 -9999 0 -9999 0 0
PPARG -0.041 0.166 -9999 0 -0.503 3 3
PPARD 0.017 0 -9999 0 -9999 0 0
TNF -0.178 0.367 -9999 0 -1.019 3 3
mol:Oxysterols -0.015 0.026 -9999 0 -9999 0 0
cholesterol transport -0.123 0.251 -9999 0 -0.457 8 8
PPARA 0.017 0 -9999 0 -9999 0 0
mol:Vit D3 0 0 -9999 0 -9999 0 0
RARB 0.017 0 -9999 0 -9999 0 0
RXRs/NUR77/BCL2 -0.01 0.077 -9999 0 -0.236 2 2
SREBF1 -0.271 0.471 -9999 0 -0.956 8 8
RXRs/RXRs/DNA/9cRA -0.03 0.088 -9999 0 -9999 0 0
ABCA1 -0.126 0.305 -9999 0 -1.002 2 2
RARs/THRs 0.05 0 -9999 0 -9999 0 0
RXRs/FXR -0.04 0.087 -9999 0 -9999 0 0
BCL2 -0.019 0.131 -9999 0 -0.472 2 2
FAS signaling pathway (CD95)

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
SPTAN1 0.01 0.058 0.243 1 -9999 0 1
RFC1 0.01 0.058 0.243 1 -9999 0 1
PRKDC 0.01 0.058 0.243 1 -9999 0 1
RIPK1 0.017 0.002 -9999 0 -9999 0 0
CASP7 -0.008 0.022 -9999 0 -9999 0 0
FASLG/FAS/FADD/FAF1 0.019 0.094 0.212 3 -0.264 1 4
MAP2K4 0.025 0.077 -9999 0 -9999 0 0
mol:ceramide 0.02 0.075 -9999 0 -9999 0 0
GSN -0.047 0.13 0.243 1 -0.33 4 5
FASLG/FAS/FADD/FAF1/Caspase 8 0.035 0.078 -9999 0 -9999 0 0
FAS -0.007 0.11 -9999 0 -0.565 1 1
BID 0.002 0.043 -9999 0 -0.217 1 1
MAP3K1 0.02 0.056 -9999 0 -9999 0 0
MAP3K7 0.016 0.002 -9999 0 -9999 0 0
RB1 0.01 0.058 0.243 1 -9999 0 1
CFLAR 0.017 0.002 -9999 0 -9999 0 0
HGF/MET -0.074 0.162 -9999 0 -0.365 5 5
ARHGDIB -0.005 0.08 0.243 1 -9999 0 1
FADD 0.015 0.007 -9999 0 -9999 0 0
actin filament polymerization 0.047 0.129 0.329 4 -0.243 1 5
NFKB1 -0.021 0.039 -9999 0 -9999 0 0
MAPK8 0.024 0.096 -9999 0 -9999 0 0
DFFA 0.01 0.058 0.243 1 -9999 0 1
DNA fragmentation during apoptosis 0.01 0.058 0.243 1 -9999 0 1
FAS/FADD/MET 0.009 0.082 -9999 0 -0.335 1 1
CFLAR/RIP1 0.025 0.006 -9999 0 -9999 0 0
FAIM3 0.017 0.001 -9999 0 -9999 0 0
FAF1 0.015 0.007 -9999 0 -9999 0 0
PARP1 0.003 0.082 0.243 1 -0.316 1 2
DFFB 0.01 0.058 0.243 1 -9999 0 1
CHUK -0.017 0.032 -9999 0 -9999 0 0
FASLG -0.014 0.105 -9999 0 -0.386 2 2
FAS/FADD 0.006 0.081 -9999 0 -0.404 1 1
HGF -0.027 0.124 -9999 0 -0.378 3 3
LMNA -0.015 0.116 0.224 1 -0.297 3 4
CASP6 0.003 0.082 0.243 1 -0.316 1 2
CASP10 0.015 0.007 -9999 0 -9999 0 0
CASP3 0.012 0.068 0.287 1 -9999 0 1
PTPN13 -0.107 0.214 -9999 0 -0.459 7 7
CASP8 0 0 -9999 0 -9999 0 0
IL6 -0.022 0.143 -9999 0 -9999 0 0
MET 0.002 0.075 -9999 0 -0.378 1 1
ICAD/CAD 0.01 0.054 0.227 1 -9999 0 1
FASLG/FAS/FADD/FAF1/Caspase 10 0.02 0.076 -9999 0 -9999 0 0
activation of caspase activity by cytochrome c 0.002 0.043 -9999 0 -0.216 1 1
PAK2 0.01 0.058 0.244 1 -9999 0 1
BCL2 -0.019 0.131 -9999 0 -0.472 2 2
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.033 0 -9999 0 -9999 0 0
SNTA1 -0.12 0.236 -9999 0 -0.512 7 7
response to hypoxia 0 0 -9999 0 -9999 0 0
STMN1 0.016 0.061 -9999 0 -9999 0 0
MAPK12 0.016 0.067 -9999 0 -0.297 1 1
CCND1 -0.007 0.089 -9999 0 -0.407 1 1
p38 gamma/SNTA1 -0.047 0.16 -9999 0 -0.322 6 6
MAP2K3 0.017 0 -9999 0 -9999 0 0
PKN1 0.017 0 -9999 0 -9999 0 0
G2/M transition checkpoint 0.016 0.066 -9999 0 -0.295 1 1
MAP2K6 0.022 0.028 -9999 0 -9999 0 0
MAPT 0.03 0.023 -9999 0 -9999 0 0
MAPK13 0.026 0 -9999 0 -9999 0 0
hyperosmotic response 0 0 -9999 0 -9999 0 0
ZAK 0.014 0.034 -9999 0 -9999 0 0
Syndecan-3-mediated signaling events

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
CTTN 0.002 0.075 -9999 0 -0.378 1 1
Syndecan-3/Src/Cortactin 0.018 0.116 -9999 0 -0.534 1 1
Syndecan-3/Neurocan -0.005 0.127 -9999 0 -0.428 2 2
POMC -0.026 0.153 -9999 0 -0.566 2 2
EGFR -0.041 0.166 -9999 0 -0.503 3 3
Syndecan-3/EGFR -0.022 0.177 -9999 0 -0.567 2 2
AGRP 0.002 0.075 -9999 0 -0.378 1 1
NCSTN 0.017 0 -9999 0 -9999 0 0
PSENEN 0.017 0 -9999 0 -9999 0 0
RP11-540L11.1 0 0 -9999 0 -9999 0 0
APH1B 0.002 0.075 -9999 0 -0.378 1 1
APH1A 0.017 0 -9999 0 -9999 0 0
NCAN -0.005 0.11 -9999 0 -0.566 1 1
long-term memory 0.009 0.116 -9999 0 -0.542 1 1
Syndecan-3/IL8 -0.071 0.158 -9999 0 -0.326 6 6
PSEN1 0.017 0 -9999 0 -9999 0 0
Src/Cortactin 0.015 0.052 -9999 0 -0.252 1 1
FYN 0.017 0 -9999 0 -9999 0 0
limb bud formation -0.023 0.114 -9999 0 -0.605 1 1
MC4R -0.034 0.147 -9999 0 -0.441 3 3
SRC 0.017 0 -9999 0 -9999 0 0
PTN 0.017 0 -9999 0 -9999 0 0
FGFR/FGF/Syndecan-3 -0.024 0.115 -9999 0 -0.612 1 1
neuron projection morphogenesis 0.013 0.122 -9999 0 -0.512 1 1
Syndecan-3/AgRP 0 0.12 -9999 0 -0.581 1 1
Syndecan-3/AgRP/MC4R -0.015 0.131 -9999 0 -0.556 1 1
Fyn/Cortactin 0.015 0.052 -9999 0 -0.252 1 1
SDC3 -0.024 0.117 -9999 0 -0.619 1 1
GO:0007205 0 0 -9999 0 -9999 0 0
positive regulation of leukocyte migration -0.07 0.155 -9999 0 -0.322 6 6
IL8 -0.135 0.239 -9999 0 -0.496 8 8
Syndecan-3/Fyn/Cortactin 0.01 0.119 -9999 0 -0.556 1 1
Syndecan-3/CASK -0.023 0.111 -9999 0 -0.588 1 1
alpha-MSH/MC4R -0.043 0.147 -9999 0 -0.344 5 5
Gamma Secretase 0.043 0.038 -9999 0 -9999 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.1 0.306 -9999 0 -1.082 2 2
MKNK1 -0.005 0.11 -9999 0 -0.566 1 1
MAPK14 -0.025 0.091 -9999 0 -0.281 2 2
ATF2/c-Jun -0.054 0.2 -9999 0 -0.564 3 3
MAPK11 -0.025 0.091 -9999 0 -0.281 2 2
MITF -0.016 0.107 -9999 0 -0.329 2 2
MAPKAPK5 -0.016 0.107 -9999 0 -0.329 2 2
KRT8 -0.016 0.107 -9999 0 -0.329 2 2
MAPKAPK3 -0.005 0.11 -9999 0 -0.566 1 1
MAPKAPK2 0.017 0 -9999 0 -9999 0 0
p38alpha-beta/CK2 -0.035 0.132 -9999 0 -0.416 2 2
CEBPB -0.016 0.107 -9999 0 -0.329 2 2
SLC9A1 -0.016 0.107 -9999 0 -0.329 2 2
mol:GDP 0 0 -9999 0 -9999 0 0
ATF2 -0.021 0.115 -9999 0 -0.315 2 2
p38alpha-beta/MNK1 -0.027 0.123 -9999 0 -0.332 3 3
JUN -0.054 0.199 -9999 0 -0.562 3 3
PPARGC1A -0.056 0.135 -9999 0 -0.319 4 4
USF1 -0.016 0.107 -9999 0 -0.329 2 2
RAB5/GDP/GDI1 -0.012 0.081 -9999 0 -9999 0 0
NOS2 -0.026 0.107 -9999 0 -0.34 2 2
DDIT3 -0.016 0.107 -9999 0 -0.329 2 2
RAB5A 0.002 0.075 -9999 0 -0.378 1 1
HSPB1 -0.011 0.094 -9999 0 -9999 0 0
p38alpha-beta/HBP1 -0.012 0.105 -9999 0 -0.322 2 2
CREB1 -0.018 0.113 -9999 0 -0.345 2 2
RAB5/GDP 0.002 0.052 -9999 0 -0.263 1 1
EIF4E -0.016 0.106 -9999 0 -9999 0 0
RPS6KA4 -0.016 0.107 -9999 0 -0.329 2 2
PLA2G4A -0.052 0.147 -9999 0 -0.342 4 4
GDI1 -0.016 0.107 -9999 0 -0.329 2 2
TP53 -0.039 0.132 -9999 0 -0.408 2 2
RPS6KA5 -0.029 0.12 -9999 0 -0.322 3 3
ESR1 -0.023 0.109 -9999 0 -0.329 2 2
HBP1 0.017 0 -9999 0 -9999 0 0
MEF2C -0.036 0.141 -9999 0 -0.345 4 4
MEF2A -0.016 0.107 -9999 0 -0.329 2 2
EIF4EBP1 -0.018 0.113 -9999 0 -0.345 2 2
KRT19 -0.016 0.107 -9999 0 -0.329 2 2
ELK4 -0.029 0.12 -9999 0 -0.322 3 3
ATF6 -0.016 0.107 -9999 0 -0.329 2 2
ATF1 -0.018 0.113 -9999 0 -0.345 2 2
p38alpha-beta/MAPKAPK2 -0.012 0.105 -9999 0 -0.322 2 2
p38alpha-beta/MAPKAPK3 -0.027 0.123 -9999 0 -0.332 3 3
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.059 0.161 -9999 0 -0.354 6 6
alphaV beta3 Integrin -0.049 0.183 -9999 0 -0.415 5 5
PTK2 -0.079 0.235 -9999 0 -0.512 5 5
IGF1R 0.017 0 -9999 0 -9999 0 0
PI4KB 0.017 0 -9999 0 -9999 0 0
MFGE8 0.017 0 -9999 0 -9999 0 0
SRC 0.017 0 -9999 0 -9999 0 0
CDKN1B 0.002 0.071 -9999 0 -9999 0 0
VEGFA 0.002 0.075 -9999 0 -0.378 1 1
ILK 0.002 0.071 -9999 0 -9999 0 0
ROCK1 0.017 0 -9999 0 -9999 0 0
AKT1 0.011 0.066 -9999 0 -9999 0 0
PTK2B -0.053 0.162 -9999 0 -0.45 2 2
alphaV/beta3 Integrin/JAM-A -0.042 0.186 -9999 0 -0.49 3 3
CBL 0.017 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
alphaV beta3 Integrin/ANGPTL3 -0.002 0.105 -9999 0 -0.337 2 2
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.031 0.064 -9999 0 -0.298 1 1
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.022 0.134 -9999 0 -0.33 3 3
alphaV/beta3 Integrin/Syndecan-1 -0.002 0.105 -9999 0 -0.337 2 2
PI4KA 0.002 0.075 -9999 0 -0.378 1 1
IGF-1R heterotetramer/IGF1/IRS1 -0.067 0.151 -9999 0 -0.517 2 2
PI4 Kinase 0.015 0.052 -9999 0 -0.252 1 1
PIK3CA 0.017 0 -9999 0 -9999 0 0
alphaV/beta3 Integrin/Osteopontin -0.114 0.161 -9999 0 -0.337 7 7
RPS6KB1 -0.011 0.163 -9999 0 -0.481 2 2
TLN1 0.017 0 -9999 0 -9999 0 0
MAPK3 -0.055 0.252 -9999 0 -0.607 4 4
GPR124 0.002 0.075 -9999 0 -0.378 1 1
MAPK1 -0.055 0.252 -9999 0 -0.607 4 4
PXN 0.017 0 -9999 0 -9999 0 0
PIK3R1 -0.005 0.11 -9999 0 -0.566 1 1
alphaV/beta3 Integrin/Tumstatin -0.002 0.105 -9999 0 -0.337 2 2
cell adhesion 0.009 0.098 -9999 0 -0.311 2 2
ANGPTL3 0.017 0 -9999 0 -9999 0 0
VEGFR2 homodimer/VEGFA homodimer/Src -0.038 0.139 -9999 0 -0.337 4 4
IGF-1R heterotetramer 0.017 0 -9999 0 -9999 0 0
Rac1/GDP 0.012 0 -9999 0 -9999 0 0
TGFBR2 0.017 0 -9999 0 -9999 0 0
ITGB3 -0.019 0.131 -9999 0 -0.472 2 2
IGF1 -0.005 0.11 -9999 0 -0.566 1 1
RAC1 0.017 0 -9999 0 -9999 0 0
regulation of cell-matrix adhesion -0.011 0.11 -9999 0 -0.336 2 2
apoptosis -0.005 0.11 -9999 0 -0.564 1 1
CD47 0.017 0 -9999 0 -9999 0 0
alphaV/beta3 Integrin/CD47 -0.002 0.105 -9999 0 -0.337 2 2
VCL 0.002 0.075 -9999 0 -0.378 1 1
alphaV/beta3 Integrin/Del1 -0.088 0.164 -9999 0 -0.337 7 7
CSF1 0.002 0.075 -9999 0 -0.378 1 1
PIK3C2A 0.002 0.071 -9999 0 -9999 0 0
PI4 Kinase/Pyk2 -0.106 0.17 -9999 0 -0.463 4 4
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.054 0.174 -9999 0 -0.361 6 6
FAK1/Vinculin -0.056 0.189 -9999 0 -0.416 4 4
alphaV beta3/Integrin/ppsTEM5 -0.011 0.111 -9999 0 -0.337 2 2
RHOA -0.005 0.11 -9999 0 -0.566 1 1
VTN 0.017 0 -9999 0 -9999 0 0
BCAR1 0.017 0 -9999 0 -9999 0 0
FGF2 -0.063 0.193 -9999 0 -0.519 4 4
F11R -0.055 0.188 -9999 0 -0.413 5 5
alphaV/beta3 Integrin/Lactadherin -0.002 0.105 -9999 0 -0.337 2 2
alphaV/beta3 Integrin/TGFBR2 -0.002 0.105 -9999 0 -0.337 2 2
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.023 0.075 -9999 0 -0.298 1 1
HSP90AA1 0.017 0 -9999 0 -9999 0 0
alphaV/beta3 Integrin/Talin 0 0.095 -9999 0 -0.306 2 2
mol:GDP 0 0 -9999 0 -9999 0 0
FN1 0.017 0 -9999 0 -9999 0 0
alphaV/beta3 Integrin/Pyk2 -0.051 0.164 -9999 0 -0.452 2 2
SDC1 0.017 0 -9999 0 -9999 0 0
VAV3 -0.017 0.118 -9999 0 -9999 0 0
PTPN11 0.017 0 -9999 0 -9999 0 0
IRS1 0.017 0 -9999 0 -9999 0 0
FAK1/Paxillin -0.051 0.187 -9999 0 -0.416 4 4
cell migration -0.042 0.174 -9999 0 -0.391 3 3
ITGAV -0.005 0.11 -9999 0 -0.566 1 1
PI3K -0.081 0.183 -9999 0 -0.645 2 2
SPP1 -0.164 0.243 -9999 0 -0.472 10 10
KDR -0.084 0.214 -9999 0 -0.529 5 5
mol:PI-4-5-P2 0 0 -9999 0 -9999 0 0
alphaV/beta3 Integrin/Caspase 8 -0.005 0.11 -9999 0 -0.565 1 1
COL4A3 0.017 0 -9999 0 -9999 0 0
angiogenesis -0.05 0.249 -9999 0 -0.601 4 4
Rac1/GTP -0.007 0.109 -9999 0 -9999 0 0
EDIL3 -0.12 0.236 -9999 0 -0.512 7 7
cell proliferation -0.002 0.104 -9999 0 -0.336 2 2
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.022 0.098 -9999 0 -0.465 1 1
FYN -0.021 0.167 -9999 0 -0.438 3 3
LAT/GRAP2/SLP76 -0.045 0.109 -9999 0 -0.384 2 2
IKBKB 0.017 0 -9999 0 -9999 0 0
AKT1 -0.007 0.133 -9999 0 -0.322 3 3
B2M -0.019 0.132 -9999 0 -0.476 2 2
IKBKG -0.007 0.036 -9999 0 -9999 0 0
MAP3K8 -0.019 0.131 -9999 0 -0.472 2 2
mol:Ca2+ -0.005 0.023 -9999 0 -0.12 1 1
integrin-mediated signaling pathway 0.023 0 -9999 0 -9999 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.024 0.179 -9999 0 -0.454 3 3
TRPV6 0.008 0.03 -9999 0 -9999 0 0
CD28 -0.056 0.178 -9999 0 -0.473 4 4
SHC1 0.003 0.137 -9999 0 -0.584 1 1
receptor internalization 0.015 0.103 -9999 0 -0.419 1 1
PRF1 0.028 0.082 -9999 0 -9999 0 0
KRAS 0.017 0 -9999 0 -9999 0 0
GRB2 0.017 0 -9999 0 -9999 0 0
COT/AKT1 -0.006 0.14 -9999 0 -0.331 3 3
LAT 0.003 0.137 -9999 0 -0.584 1 1
EntrezGene:6955 0.001 0.002 -9999 0 -9999 0 0
CD3D 0.018 0.002 -9999 0 -9999 0 0
CD3E 0.018 0.003 -9999 0 -9999 0 0
CD3G 0.018 0.002 -9999 0 -9999 0 0
RASGRP2 0.008 0.018 -9999 0 -9999 0 0
RASGRP1 -0.01 0.132 -9999 0 -0.316 3 3
HLA-A -0.018 0.132 -9999 0 -0.477 2 2
RASSF5 0.017 0 -9999 0 -9999 0 0
RAP1A/GTP/RAPL 0.023 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
mol:GDP 0.017 0.047 -9999 0 -0.103 1 1
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.025 0.054 -9999 0 -0.204 1 1
PRKCA -0.033 0.075 -9999 0 -0.218 3 3
GRAP2 -0.005 0.11 -9999 0 -0.566 1 1
mol:IP3 -0.058 0.115 -9999 0 -0.346 3 3
EntrezGene:6957 0.001 0.002 -9999 0 -9999 0 0
TCR/CD3/MHC I/CD8 0.017 0.089 -9999 0 -0.38 1 1
ORAI1 -0.013 0.08 -9999 0 -0.42 1 1
CSK 0 0.14 -9999 0 -0.6 1 1
B7 family/CD28 -0.058 0.199 -9999 0 -0.582 2 2
CHUK 0.017 0 -9999 0 -9999 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.007 0.151 -9999 0 -0.662 1 1
PTPN6 -0.027 0.168 -9999 0 -0.444 3 3
VAV1 -0.033 0.204 -9999 0 -0.527 3 3
Monovalent TCR/CD3 0.023 0.035 -9999 0 -9999 0 0
CBL 0.017 0 -9999 0 -9999 0 0
LCK -0.023 0.166 -9999 0 -0.437 3 3
PAG1 0 0.14 -9999 0 -0.6 1 1
RAP1A 0.017 0 -9999 0 -9999 0 0
TCR/CD3/MHC I/CD8/LCK -0.013 0.155 -9999 0 -0.682 1 1
CD80 0.016 0.002 -9999 0 -9999 0 0
CD86 -0.12 0.236 -9999 0 -0.513 7 7
PDK1/CARD11/BCL10/MALT1 -0.031 0.065 -9999 0 -0.247 1 1
HRAS 0.017 0 -9999 0 -9999 0 0
GO:0035030 -0.049 0.17 -9999 0 -0.486 2 2
CD8A 0.001 0.002 -9999 0 -9999 0 0
CD8B 0.018 0.003 -9999 0 -9999 0 0
PTPRC -0.078 0.181 -9999 0 -0.411 6 6
PDK1/PKC theta -0.009 0.161 -9999 0 -0.389 3 3
CSK/PAG1 0.005 0.138 -9999 0 -0.587 1 1
SOS1 0.017 0 -9999 0 -9999 0 0
peptide-MHC class I -0.021 0.174 -9999 0 -0.62 2 2
GRAP2/SLP76 -0.048 0.128 -9999 0 -0.444 2 2
STIM1 -0.019 0.11 -9999 0 -0.578 1 1
RAS family/GTP 0.025 0.058 -9999 0 -0.151 1 1
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.015 0.106 -9999 0 -0.436 1 1
mol:DAG -0.053 0.104 -9999 0 -0.314 3 3
RAP1A/GDP 0.01 0.021 -9999 0 -9999 0 0
PLCG1 0.017 0 -9999 0 -9999 0 0
CD247 -0.012 0.103 -9999 0 -0.377 2 2
cytotoxic T cell degranulation 0.028 0.081 -9999 0 -9999 0 0
RAP1A/GTP -0.001 0.004 -9999 0 -9999 0 0
mol:PI-3-4-5-P3 -0.016 0.154 -9999 0 -0.382 3 3
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.071 0.145 -9999 0 -0.438 3 3
NRAS 0.017 0 -9999 0 -9999 0 0
ZAP70 0.017 0 -9999 0 -9999 0 0
GRB2/SOS1 0.025 0 -9999 0 -9999 0 0
LAT/GRAP2/SLP76/VAV1 -0.07 0.15 -9999 0 -0.444 3 3
MALT1 0.017 0 -9999 0 -9999 0 0
TRAF6 0.017 0 -9999 0 -9999 0 0
CD8 heterodimer 0.014 0.005 -9999 0 -9999 0 0
CARD11 0.002 0.075 -9999 0 -0.378 1 1
PRKCB -0.038 0.074 -9999 0 -0.223 3 3
PRKCE -0.033 0.075 -9999 0 -0.24 2 2
PRKCQ -0.021 0.177 -9999 0 -0.44 3 3
LCP2 -0.013 0.103 -9999 0 -0.378 2 2
BCL10 0.017 0 -9999 0 -9999 0 0
regulation of survival gene product expression -0.002 0.117 -9999 0 -0.277 3 3
IKK complex 0.026 0.049 -9999 0 -9999 0 0
RAS family/GDP -0.002 0.005 -9999 0 -9999 0 0
MAP3K14 0 0.108 -9999 0 -0.284 2 2
PDPK1 -0.003 0.128 -9999 0 -0.305 3 3
TCR/CD3/MHC I/CD8/Fyn 0.006 0.144 -9999 0 -0.658 1 1
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.002 0.075 -9999 0 -0.378 1 1
Caspase 8 (4 units) 0.007 0.137 -9999 0 -0.592 1 1
NEF -0.002 0.03 -9999 0 -9999 0 0
NFKBIA 0.006 0.035 -9999 0 -9999 0 0
BIRC3 -0.025 0.188 -9999 0 -0.581 2 2
CYCS 0.006 0.136 -9999 0 -0.559 1 1
RIPK1 0.017 0 -9999 0 -9999 0 0
CD247 -0.016 0.123 -9999 0 -0.436 2 2
MAP2K7 0.003 0.156 -9999 0 -0.701 1 1
protein ubiquitination 0.009 0.113 -9999 0 -0.419 1 1
CRADD 0.017 0 -9999 0 -9999 0 0
DAXX 0.017 0 -9999 0 -9999 0 0
FAS -0.005 0.11 -9999 0 -0.566 1 1
BID -0.002 0.143 -9999 0 -0.435 2 2
NF-kappa-B/RelA/I kappa B alpha 0.007 0.098 -9999 0 -9999 0 0
TRADD 0.017 0 -9999 0 -9999 0 0
MAP3K5 -0.026 0.153 -9999 0 -0.566 2 2
CFLAR 0.017 0 -9999 0 -9999 0 0
FADD 0.017 0 -9999 0 -9999 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.007 0.099 -9999 0 -9999 0 0
MAPK8 0.012 0.146 -9999 0 -0.643 1 1
APAF1 -0.005 0.11 -9999 0 -0.566 1 1
TRAF1 0.017 0 -9999 0 -9999 0 0
TRAF2 0.017 0 -9999 0 -9999 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.004 0.147 -9999 0 -0.465 2 2
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.005 0.137 -9999 0 -0.575 1 1
CHUK 0.007 0.121 -9999 0 -0.46 1 1
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.015 0.13 -9999 0 -0.42 2 2
TCRz/NEF -0.012 0.111 -9999 0 -0.359 2 2
TNF -0.1 0.201 -9999 0 -0.432 7 7
FASLG -0.012 0.139 -9999 0 -0.468 2 2
NFKB1 0.006 0.035 -9999 0 -9999 0 0
TNFR1A/BAG4/TNF-alpha -0.066 0.156 -9999 0 -0.403 3 3
CASP6 0.015 0.131 -9999 0 -0.551 1 1
CASP7 -0.002 0.208 -9999 0 -0.548 3 3
RELA 0.006 0.035 -9999 0 -9999 0 0
CASP2 0.017 0 -9999 0 -9999 0 0
CASP3 -0.002 0.21 -9999 0 -0.548 3 3
TNFRSF1A -0.019 0.131 -9999 0 -0.472 2 2
TNFR1A/BAG4 -0.011 0.106 -9999 0 -0.303 3 3
CASP8 0.017 0 -9999 0 -9999 0 0
CASP9 -0.026 0.153 -9999 0 -0.566 2 2
MAP3K14 -0.002 0.132 -9999 0 -0.521 1 1
APAF-1/Caspase 9 -0.076 0.157 -9999 0 -0.49 3 3
BCL2 0.004 0.141 -9999 0 -0.576 1 1
Canonical Wnt signaling pathway

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
HDAC1 -0.003 0.113 -9999 0 -0.569 1 1
AES 0.018 0.018 -9999 0 -9999 0 0
FBXW11 0.017 0 -9999 0 -9999 0 0
mol:GTP 0 0.001 -9999 0 -9999 0 0
LRP6/FZD1 0.016 0.053 -9999 0 -0.253 1 1
SMAD4 0.017 0 -9999 0 -9999 0 0
DKK2 0.017 0 -9999 0 -9999 0 0
TLE1 -0.019 0.133 -9999 0 -0.476 2 2
MACF1 0.017 0 -9999 0 -9999 0 0
CTNNB1 0.083 0.098 -9999 0 -9999 0 0
WIF1 -0.301 0.254 -9999 0 -0.488 17 17
beta catenin/RanBP3 0.029 0.111 0.405 1 -9999 0 1
KREMEN2 -0.063 0.171 -9999 0 -0.416 5 5
DKK1 -0.136 0.222 -9999 0 -0.441 9 9
beta catenin/beta TrCP1 0.088 0.093 -9999 0 -9999 0 0
FZD1 0.003 0.075 -9999 0 -0.379 1 1
AXIN2 0.012 0.062 -9999 0 -9999 0 0
AXIN1 0.018 0.001 -9999 0 -9999 0 0
RAN 0.017 0.001 -9999 0 -9999 0 0
Axin1/APC/GSK3/beta catenin 0.04 0.038 -9999 0 -9999 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.065 0.114 -9999 0 -9999 0 0
Axin1/APC/GSK3 0.05 0.046 -9999 0 -9999 0 0
Axin1/APC/GSK3/beta catenin/Macf1 0.077 0.044 -9999 0 -9999 0 0
HNF1A 0.017 0.018 -9999 0 -9999 0 0
CTBP1 0.017 0.018 -9999 0 -9999 0 0
MYC -0.034 0.271 -9999 0 -1.391 1 1
RANBP3 0.017 0.001 -9999 0 -9999 0 0
DKK2/LRP6/Kremen 2 -0.014 0.104 -9999 0 -0.337 1 1
NKD1 -0.028 0.124 -9999 0 -0.379 3 3
TCF4 -0.004 0.109 -9999 0 -0.551 1 1
TCF3 0.003 0.078 -9999 0 -0.384 1 1
WNT1/LRP6/FZD1/Axin1 0.038 0.041 -9999 0 -9999 0 0
Ran/GTP 0.013 0.002 -9999 0 -9999 0 0
CtBP/CBP/TCF/TLE1/AES 0.005 0.156 0.397 2 -0.5 1 3
LEF1 -0.04 0.137 -9999 0 -0.365 4 4
DVL1 0.081 0.04 -9999 0 -9999 0 0
CSNK2A1 0.017 0 -9999 0 -9999 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.059 0.135 -9999 0 -9999 0 0
DKK1/LRP6/Kremen 2 -0.104 0.172 -9999 0 -0.39 5 5
LRP6 0.017 0.001 -9999 0 -9999 0 0
CSNK1A1 0.019 0.021 -9999 0 -9999 0 0
NLK 0.016 0.005 -9999 0 -9999 0 0
CCND1 -0.054 0.285 -9999 0 -1.416 1 1
WNT1 0.017 0.001 -9999 0 -9999 0 0
GSK3A 0.018 0.001 -9999 0 -9999 0 0
GSK3B 0.017 0.001 -9999 0 -9999 0 0
FRAT1 0.016 0.001 -9999 0 -9999 0 0
PPP2R5D 0.064 0.056 0.247 1 -9999 0 1
APC 0.04 0.037 -9999 0 -9999 0 0
WNT1/LRP6/FZD1 0.136 0.098 0.241 10 -9999 0 10
CREBBP 0.017 0.018 -9999 0 -9999 0 0
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.039 0.119 -9999 0 -0.255 6 6
cell-cell adhesion 0.06 0.097 0.36 1 -9999 0 1
Ephrin B/EPHB2/RasGAP 0.013 0.078 -9999 0 -9999 0 0
ITSN1 0.017 0 -9999 0 -9999 0 0
PIK3CA 0.017 0 -9999 0 -9999 0 0
SHC1 0.017 0 -9999 0 -9999 0 0
Ephrin B1/EPHB3 0.009 0.07 -9999 0 -0.346 1 1
Ephrin B1/EPHB1 -0.045 0.143 -9999 0 -0.346 5 5
HRAS/GDP -0.035 0.083 -9999 0 -9999 0 0
Ephrin B/EPHB1/GRB7 -0.017 0.127 -9999 0 -0.272 5 5
Endophilin/SYNJ1 0.008 0.071 -9999 0 -9999 0 0
KRAS 0.017 0 -9999 0 -9999 0 0
Ephrin B/EPHB1/Src -0.017 0.127 -9999 0 -0.272 5 5
endothelial cell migration 0.017 0.068 -9999 0 -0.278 1 1
GRB2 0.017 0 -9999 0 -9999 0 0
GRB7 0.017 0 -9999 0 -9999 0 0
PAK1 -0.051 0.153 -9999 0 -0.459 2 2
HRAS 0.017 0 -9999 0 -9999 0 0
RRAS 0.008 0.072 -9999 0 -9999 0 0
DNM1 -0.15 0.224 -9999 0 -0.435 10 10
cell-cell signaling 0 0 -9999 0 -9999 0 0
CRK -0.02 0.119 -9999 0 -0.259 5 5
lamellipodium assembly -0.06 0.097 -9999 0 -0.36 1 1
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.009 0.108 -9999 0 -9999 0 0
PIK3R1 -0.005 0.11 -9999 0 -0.566 1 1
EPHB2 -0.042 0.14 -9999 0 -0.378 4 4
EPHB3 -0.005 0.11 -9999 0 -0.566 1 1
EPHB1 -0.091 0.226 -9999 0 -0.566 5 5
EPHB4 0.017 0 -9999 0 -9999 0 0
mol:GDP -0.003 0.089 -9999 0 -9999 0 0
Ephrin B/EPHB2 0.003 0.077 -9999 0 -9999 0 0
Ephrin B/EPHB3 0.021 0.07 -9999 0 -0.28 1 1
JNK cascade -0.042 0.142 -9999 0 -0.445 1 1
Ephrin B/EPHB1 -0.027 0.127 -9999 0 -0.28 5 5
RAP1/GDP 0.014 0.083 -9999 0 -9999 0 0
EFNB2 0.002 0.075 -9999 0 -0.378 1 1
EFNB3 0.017 0 -9999 0 -9999 0 0
EFNB1 0.017 0 -9999 0 -9999 0 0
Ephrin B2/EPHB1-2 -0.069 0.154 -9999 0 -0.344 5 5
RAP1B 0.017 0 -9999 0 -9999 0 0
RAP1A 0.017 0 -9999 0 -9999 0 0
CDC42/GTP -0.06 0.097 -9999 0 -0.365 1 1
Rap1/GTP -0.058 0.095 -9999 0 -0.36 1 1
axon guidance -0.039 0.119 -9999 0 -0.254 6 6
MAPK3 0.008 0.098 -9999 0 -9999 0 0
MAPK1 0.008 0.098 -9999 0 -9999 0 0
Rac1/GDP 0.006 0.085 -9999 0 -9999 0 0
actin cytoskeleton reorganization -0.04 0.067 -9999 0 -9999 0 0
CDC42/GDP 0.006 0.085 -9999 0 -9999 0 0
PI3K 0.021 0.07 -9999 0 -0.28 1 1
EFNA5 -0.026 0.153 -9999 0 -0.566 2 2
Ephrin B2/EPHB4 0.014 0.044 -9999 0 -0.21 1 1
Ephrin B/EPHB2/Intersectin/N-WASP 0.02 0.051 -9999 0 -9999 0 0
CDC42 0.017 0 -9999 0 -9999 0 0
RAS family/GTP -0.057 0.093 -9999 0 -0.351 1 1
PTK2 0.023 0.036 -9999 0 -9999 0 0
MAP4K4 -0.042 0.143 -9999 0 -0.45 1 1
SRC 0.017 0 -9999 0 -9999 0 0
KALRN -0.042 0.14 -9999 0 -0.378 4 4
Intersectin/N-WASP 0.025 0 -9999 0 -9999 0 0
neuron projection morphogenesis -0.036 0.137 -9999 0 -0.445 1 1
MAP2K1 0 0.102 -9999 0 -9999 0 0
WASL 0.017 0 -9999 0 -9999 0 0
Ephrin B1/EPHB1-2/NCK1 -0.051 0.155 -9999 0 -0.336 5 5
cell migration 0.003 0.111 -9999 0 -9999 0 0
NRAS 0.017 0 -9999 0 -9999 0 0
SYNJ1 0.008 0.072 -9999 0 -9999 0 0
PXN 0.017 0 -9999 0 -9999 0 0
TF -0.03 0.108 -9999 0 -9999 0 0
HRAS/GTP -0.065 0.104 -9999 0 -0.387 1 1
Ephrin B1/EPHB1-2 -0.061 0.154 -9999 0 -0.344 5 5
cell adhesion mediated by integrin -0.004 0.043 -9999 0 -9999 0 0
RAC1 0.017 0 -9999 0 -9999 0 0
mol:GTP -0.036 0.136 -9999 0 -0.416 1 1
RAC1-CDC42/GTP -0.067 0.118 -9999 0 -0.406 2 2
RASA1 0.017 0 -9999 0 -9999 0 0
RAC1-CDC42/GDP 0.014 0.083 -9999 0 -9999 0 0
ruffle organization -0.013 0.124 -9999 0 -0.36 1 1
NCK1 0.017 0 -9999 0 -9999 0 0
receptor internalization -0.063 0.126 -9999 0 -0.304 2 2
Ephrin B/EPHB2/KALRN -0.016 0.108 -9999 0 -0.337 1 1
ROCK1 0.017 0.063 -9999 0 -0.305 1 1
RAS family/GDP -0.034 0.059 -9999 0 -9999 0 0
Rac1/GTP -0.063 0.101 -9999 0 -0.381 1 1
Ephrin B/EPHB1/Src/Paxillin -0.012 0.109 -9999 0 -9999 0 0
Glypican 2 network

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
MDK -0.012 0.103 -9999 0 -0.378 2 2
GPC2 0 0 -9999 0 -9999 0 0
GPC2/Midkine -0.008 0.072 -9999 0 -0.263 2 2
neuron projection morphogenesis -0.008 0.072 -9999 0 -0.262 2 2
IL27-mediated signaling events

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
TGFB1 0.027 0 -9999 0 -9999 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -9999 0 -9999 0 0
cytokine production during immune response -0.016 0.069 -9999 0 -9999 0 0
IL27/IL27R/JAK1 -0.006 0.086 -9999 0 -9999 0 0
TBX21 -0.032 0.128 -9999 0 -9999 0 0
IL12B -0.005 0.11 -9999 0 -0.566 1 1
IL12A -0.081 0.164 -9999 0 -0.35 7 7
IL6ST -0.006 0.111 -9999 0 -0.57 1 1
IL27RA/JAK1 0.009 0.051 -9999 0 -9999 0 0
IL27 0.001 0.074 -9999 0 -0.375 1 1
TYK2 0.018 0.007 -9999 0 -9999 0 0
T-helper cell lineage commitment 0.017 0.066 -9999 0 -9999 0 0
T-helper 2 cell differentiation -0.016 0.069 -9999 0 -9999 0 0
T cell proliferation during immune response -0.016 0.069 -9999 0 -9999 0 0
MAPKKK cascade 0.016 0.069 -9999 0 -9999 0 0
STAT3 0.017 0 -9999 0 -9999 0 0
STAT2 0.017 0 -9999 0 -9999 0 0
STAT1 0 0.077 -9999 0 -0.391 1 1
IL12RB1 0.017 0.001 -9999 0 -9999 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -9999 0 -9999 0 0
IL12RB2 -0.088 0.198 -9999 0 -0.48 3 3
IL27/IL27R/JAK2/TYK2 0.016 0.069 -9999 0 -9999 0 0
positive regulation of T cell mediated cytotoxicity 0.016 0.069 -9999 0 -9999 0 0
STAT1 (dimer) -0.086 0.11 -9999 0 -9999 0 0
JAK2 0.017 0.007 -9999 0 -9999 0 0
JAK1 0.001 0.074 -9999 0 -0.378 1 1
STAT2 (dimer) 0.025 0.064 -9999 0 -9999 0 0
T cell proliferation -0.006 0.093 -9999 0 -9999 0 0
IL12/IL12R/TYK2/JAK2 -0.027 0.153 -9999 0 -0.709 1 1
IL17A 0.003 0.063 -9999 0 -9999 0 0
mast cell activation -0.016 0.069 -9999 0 -9999 0 0
IFNG 0.005 0.021 -9999 0 -9999 0 0
T cell differentiation -0.003 0.005 -9999 0 -9999 0 0
STAT3 (dimer) 0.025 0.064 -9999 0 -9999 0 0
STAT5A (dimer) 0.025 0.064 -9999 0 -9999 0 0
STAT4 (dimer) -0.001 0.102 -9999 0 -9999 0 0
STAT4 -0.034 0.147 -9999 0 -0.441 3 3
T cell activation -0.009 0.003 -9999 0 -9999 0 0
IL27R/JAK2/TYK2 0.024 0.071 -9999 0 -9999 0 0
GATA3 0.012 0.024 -9999 0 -9999 0 0
IL18 -0.091 0.166 -9999 0 -0.34 8 8
positive regulation of mast cell cytokine production 0.025 0.064 -9999 0 -9999 0 0
IL27/EBI3 0.01 0.052 -9999 0 -0.247 1 1
IL27RA 0.004 0.031 -9999 0 -9999 0 0
IL6 -0.046 0.153 -9999 0 -0.366 5 5
STAT5A 0.017 0 -9999 0 -9999 0 0
monocyte differentiation 0 0.001 -9999 0 -9999 0 0
IL2 -0.008 0.052 -9999 0 -9999 0 0
IL1B -0.19 0.179 -9999 0 -0.33 16 16
EBI3 0.015 0.007 -9999 0 -9999 0 0
TNF -0.07 0.145 -9999 0 -0.307 7 7
Wnt signaling

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
Noncanonical Wnts/FZD -0.048 0.157 -9999 0 -0.662 1 1
FZD6 -0.019 0.131 -9999 0 -0.472 2 2
WNT6 0.017 0 -9999 0 -9999 0 0
WNT4 -0.027 0.124 -9999 0 -0.378 3 3
FZD3 -0.005 0.11 -9999 0 -0.566 1 1
WNT5A -0.084 0.214 -9999 0 -0.529 5 5
WNT11 0.017 0 -9999 0 -9999 0 0
LPA receptor mediated events

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
GNB1/GNG2 0.011 0.074 -9999 0 -0.307 1 1
NF kappa B1 p50/RelA/I kappa B alpha -0.012 0.104 -9999 0 -0.299 1 1
AP1 -0.121 0.168 -9999 0 -0.351 8 8
mol:PIP3 -0.031 0.076 -9999 0 -9999 0 0
AKT1 0.005 0.097 -9999 0 -0.351 1 1
PTK2B 0.003 0.035 -9999 0 -9999 0 0
RHOA -0.019 0.094 -9999 0 -0.336 1 1
PIK3CB 0.017 0.001 -9999 0 -9999 0 0
mol:Ca2+ -0.027 0.102 -9999 0 -0.248 4 4
MAGI3 -0.084 0.214 -9999 0 -0.529 5 5
RELA 0.017 0 -9999 0 -9999 0 0
apoptosis 0.012 0.032 -9999 0 -9999 0 0
HRAS/GDP 0.012 0 -9999 0 -9999 0 0
positive regulation of microtubule depolymerization 0.018 0.032 -9999 0 -9999 0 0
NF kappa B1 p50/RelA -0.059 0.114 -9999 0 -0.385 2 2
endothelial cell migration 0.023 0.001 -9999 0 -9999 0 0
ADCY4 0.036 0.034 -9999 0 -9999 0 0
ADCY5 0.036 0.034 -9999 0 -9999 0 0
ADCY6 0.036 0.034 -9999 0 -9999 0 0
ADCY7 0.036 0.034 -9999 0 -9999 0 0
ADCY1 0.036 0.034 -9999 0 -9999 0 0
ADCY2 0.023 0.051 -9999 0 -9999 0 0
ADCY3 0.036 0.034 -9999 0 -9999 0 0
ADCY8 -0.012 0.078 -9999 0 -9999 0 0
ADCY9 0.029 0.049 -9999 0 -9999 0 0
GSK3B 0.011 0.033 -9999 0 -9999 0 0
arachidonic acid secretion 0.036 0.05 -9999 0 -9999 0 0
GNG2 -0.02 0.131 -9999 0 -0.473 2 2
TRIP6 0.017 0.034 -9999 0 -9999 0 0
GNAO1 0.023 0.001 -9999 0 -9999 0 0
HRAS 0.017 0 -9999 0 -9999 0 0
NFKBIA -0.025 0.115 -9999 0 -0.331 2 2
GAB1 0.017 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
lamellipodium assembly -0.004 0.182 -9999 0 -0.931 1 1
JUN -0.041 0.166 -9999 0 -0.504 3 3
LPA/LPA2/NHERF2 -0.034 0.12 -9999 0 -0.316 4 4
TIAM1 -0.035 0.211 -9999 0 -1.108 1 1
PIK3R1 -0.005 0.109 -9999 0 -0.563 1 1
mol:IP3 -0.028 0.104 -9999 0 -0.252 4 4
PLCB3 -0.021 0.109 -9999 0 -0.309 3 3
FOS -0.193 0.26 -9999 0 -0.498 11 11
positive regulation of mitosis 0.036 0.05 -9999 0 -9999 0 0
LPA/LPA1-2-3 0.007 0.006 -9999 0 -9999 0 0
mol:Ca ++ 0 0 -9999 0 -9999 0 0
JNK cascade 0 0.001 -9999 0 -9999 0 0
BCAR1 0.017 0 -9999 0 -9999 0 0
stress fiber formation 0.017 0.023 -9999 0 -9999 0 0
GNAZ 0.023 0.001 -9999 0 -9999 0 0
EGFR/PI3K-beta/Gab1 -0.032 0.079 -9999 0 -9999 0 0
positive regulation of dendritic cell cytokine production 0.001 0.003 -9999 0 -9999 0 0
LPA/LPA2/MAGI-3 -0.048 0.134 -9999 0 -0.324 5 5
ARHGEF1 0.036 0.003 -9999 0 -9999 0 0
GNAI2 0.023 0.001 -9999 0 -9999 0 0
GNAI3 0.023 0.001 -9999 0 -9999 0 0
GNAI1 0.009 0.069 -9999 0 -0.342 1 1
LPA/LPA3 0 0 -9999 0 -9999 0 0
LPA/LPA2 0 0 -9999 0 -9999 0 0
LPA/LPA1 0 0 -9999 0 -9999 0 0
HB-EGF/EGFR -0.071 0.187 -9999 0 -0.466 4 4
HBEGF -0.053 0.152 -9999 0 -0.329 6 6
mol:DAG -0.028 0.104 -9999 0 -0.252 4 4
cAMP biosynthetic process 0.033 0.036 -9999 0 -9999 0 0
NFKB1 0.017 0 -9999 0 -9999 0 0
SRC 0.017 0 -9999 0 -9999 0 0
GNB1 0.017 0.001 -9999 0 -9999 0 0
LYN -0.025 0.115 -9999 0 -0.331 2 2
GNAQ 0.004 0.002 -9999 0 -9999 0 0
LPAR2 0 0.001 -9999 0 -9999 0 0
LPAR3 0 0.001 -9999 0 -9999 0 0
LPAR1 0.006 0.001 -9999 0 -9999 0 0
IL8 -0.175 0.227 -9999 0 -0.44 10 10
PTK2 0.02 0.003 -9999 0 -9999 0 0
Rac1/GDP 0.012 0 -9999 0 -9999 0 0
CASP3 0.012 0.032 -9999 0 -9999 0 0
EGFR -0.042 0.166 -9999 0 -0.503 3 3
PLCG1 -0.004 0.064 -9999 0 -0.166 3 3
PLD2 0.02 0.003 -9999 0 -9999 0 0
G12/G13 0.031 0.002 -9999 0 -9999 0 0
PI3K-beta -0.041 0.088 -9999 0 -0.405 1 1
cell migration 0.024 0.059 -9999 0 -0.269 1 1
SLC9A3R2 -0.063 0.193 -9999 0 -0.519 4 4
PXN 0.017 0.023 -9999 0 -9999 0 0
HRAS/GTP 0.036 0.051 -9999 0 -9999 0 0
RAC1 0.017 0 -9999 0 -9999 0 0
MMP9 -0.078 0.201 -9999 0 -0.491 5 5
PRKCE 0.017 0 -9999 0 -9999 0 0
PRKCD -0.047 0.147 -9999 0 -0.329 5 5
Gi(beta/gamma) 0.028 0.082 -9999 0 -0.383 1 1
mol:LPA 0.006 0.001 -9999 0 -9999 0 0
TRIP6/p130 Cas/FAK1/Paxillin 0.036 0.023 -9999 0 -9999 0 0
MAPKKK cascade 0.036 0.05 -9999 0 -9999 0 0
contractile ring contraction involved in cytokinesis -0.019 0.094 -9999 0 -0.333 1 1
mol:GDP 0 0 -9999 0 -9999 0 0
GNA14 -0.029 0.103 -9999 0 -0.269 4 4
GNA15 0.001 0.06 -9999 0 -0.306 1 1
GNA12 0.017 0 -9999 0 -9999 0 0
GNA13 0.017 0 -9999 0 -9999 0 0
MAPT 0.019 0.032 -9999 0 -9999 0 0
GNA11 0.013 0.002 -9999 0 -9999 0 0
Rac1/GTP -0.005 0.194 -9999 0 -0.995 1 1
MMP2 0.023 0.001 -9999 0 -9999 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.018 0 -9999 0 -9999 0 0
ELF1 0.012 0.054 -9999 0 -9999 0 0
CCNA2 -0.049 0.16 -9999 0 -0.425 4 4
PIK3CA 0.018 0 -9999 0 -9999 0 0
JAK3 0.018 0 -9999 0 -9999 0 0
PIK3R1 -0.004 0.11 -9999 0 -0.565 1 1
JAK1 0.003 0.075 -9999 0 -0.377 1 1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.073 0.048 -9999 0 -9999 0 0
SHC1 0.018 0 -9999 0 -9999 0 0
SP1 -0.019 0.086 -9999 0 -9999 0 0
IL2RA 0.009 0.1 -9999 0 -9999 0 0
IL2RB 0.003 0.075 -9999 0 -0.377 1 1
SOS1 0.018 0 -9999 0 -9999 0 0
IL2RG 0.018 0 -9999 0 -9999 0 0
G1/S transition of mitotic cell cycle -0.146 0.215 -9999 0 -0.419 9 9
PTPN11 0.018 0 -9999 0 -9999 0 0
CCND2 -0.048 0.158 -9999 0 -0.344 6 6
LCK 0.018 0 -9999 0 -9999 0 0
GRB2 0.018 0 -9999 0 -9999 0 0
IL2 0.003 0.075 -9999 0 -0.377 1 1
CDK6 -0.179 0.243 -9999 0 -0.464 11 11
CCND3 0.078 0.045 -9999 0 -9999 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.104 0.414 -9999 0 -1.235 3 3
RAD9A 0.017 0 -9999 0 -9999 0 0
AP1 -0.163 0.249 -9999 0 -0.434 11 11
IFNAR2 0.016 0.007 -9999 0 -9999 0 0
AKT1 0.013 0.046 -9999 0 -9999 0 0
ER alpha/Oestrogen 0.002 0.053 -9999 0 -0.268 1 1
NFX1/SIN3/HDAC complex 0.034 0.059 -9999 0 -9999 0 0
EGF -0.013 0.103 -9999 0 -0.377 2 2
SMG5 0.017 0 -9999 0 -9999 0 0
SMG6 0.017 0 -9999 0 -9999 0 0
SP3/HDAC2 0.008 0.082 -9999 0 -0.402 1 1
TERT/c-Abl -0.099 0.373 -9999 0 -1.121 3 3
SAP18 0.016 0.002 -9999 0 -9999 0 0
MRN complex 0.034 0 -9999 0 -9999 0 0
WT1 0.016 0.007 -9999 0 -9999 0 0
WRN 0.017 0 -9999 0 -9999 0 0
SP1 0.015 0.012 -9999 0 -9999 0 0
SP3 0.016 0.006 -9999 0 -9999 0 0
TERF2IP 0.017 0 -9999 0 -9999 0 0
Telomerase/Nucleolin -0.122 0.302 -9999 0 -0.964 3 3
Mad/Max 0.023 0.011 -9999 0 -9999 0 0
TERT -0.115 0.443 -9999 0 -1.326 3 3
CCND1 -0.094 0.379 -9999 0 -1.094 3 3
MAX 0.016 0.006 -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
TERF2 0.015 0 -9999 0 -9999 0 0
PTGES3 0.017 0 -9999 0 -9999 0 0
SIN3A 0.016 0.002 -9999 0 -9999 0 0
Telomerase/911 0.042 0.04 -9999 0 -9999 0 0
CDKN1B 0.034 0.043 -9999 0 -9999 0 0
RAD1 0.017 0 -9999 0 -9999 0 0
XRCC5 0.017 0 -9999 0 -9999 0 0
XRCC6 0.017 0 -9999 0 -9999 0 0
SAP30 0.016 0.002 -9999 0 -9999 0 0
TRF2/PARP2 0.025 0 -9999 0 -9999 0 0
UBE3A 0.016 0.005 -9999 0 -9999 0 0
JUN -0.042 0.166 -9999 0 -0.504 3 3
E6 -0.001 0.005 -9999 0 -9999 0 0
HPV-16 E6/E6AP 0.012 0.008 -9999 0 -9999 0 0
FOS -0.194 0.259 -9999 0 -0.498 11 11
IFN-gamma/IRF1 0.023 0.053 -9999 0 -9999 0 0
PARP2 0.017 0 -9999 0 -9999 0 0
BLM -0.106 0.232 -9999 0 -0.535 6 6
Telomerase -0.005 0.04 -9999 0 -9999 0 0
IRF1 0.021 0.008 -9999 0 -9999 0 0
ESR1 0.002 0.075 -9999 0 -0.382 1 1
KU/TER 0.025 0 -9999 0 -9999 0 0
ATM/TRF2 0.026 0 -9999 0 -9999 0 0
ubiquitin-dependent protein catabolic process 0.039 0.062 -9999 0 -9999 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.039 0.063 -9999 0 -9999 0 0
HDAC1 -0.005 0.11 -9999 0 -0.566 1 1
HDAC2 -0.006 0.11 -9999 0 -0.563 1 1
ATM 0 0 -9999 0 -9999 0 0
SMAD3 -0.005 0.112 -9999 0 -0.399 2 2
ABL1 0.017 0 -9999 0 -9999 0 0
MXD1 0.016 0.006 -9999 0 -9999 0 0
MRE11A 0.017 0 -9999 0 -9999 0 0
HUS1 0.017 0 -9999 0 -9999 0 0
RPS6KB1 0.017 0 -9999 0 -9999 0 0
TERT/NF kappa B1/14-3-3 -0.084 0.356 -9999 0 -1.061 3 3
NR2F2 -0.047 0.162 -9999 0 -0.428 4 4
MAPK3 0.015 0.053 -9999 0 -0.249 1 1
MAPK1 0.015 0.053 -9999 0 -0.249 1 1
TGFB1/TGF beta receptor Type II 0.017 0.002 -9999 0 -9999 0 0
NFKB1 0.017 0 -9999 0 -9999 0 0
HNRNPC 0.017 0 -9999 0 -9999 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0 -9999 0 -9999 0 0
NBN 0.017 0 -9999 0 -9999 0 0
EGFR -0.042 0.166 -9999 0 -0.502 3 3
mol:Oestrogen -0.001 0.004 -9999 0 -9999 0 0
EGF/EGFR -0.037 0.155 -9999 0 -0.38 4 4
MYC -0.006 0.11 -9999 0 -0.565 1 1
IL2 0.001 0.075 -9999 0 -0.375 1 1
KU 0.025 0 -9999 0 -9999 0 0
RAD50 0.017 0 -9999 0 -9999 0 0
HSP90AA1 0.017 0 -9999 0 -9999 0 0
TGFB1 0.017 0.002 -9999 0 -9999 0 0
TRF2/BLM -0.059 0.158 -9999 0 -0.351 6 6
FRAP1 0.017 0 -9999 0 -9999 0 0
KU/TERT -0.079 0.38 -9999 0 -1.117 3 3
SP1/HDAC2 0.008 0.083 -9999 0 -0.401 1 1
PINX1 0.017 0 -9999 0 -9999 0 0
Telomerase/EST1A -0.122 0.302 -9999 0 -0.964 3 3
Smad3/Myc -0.008 0.115 -9999 0 -0.333 3 3
911 complex 0.034 0 -9999 0 -9999 0 0
IFNG 0.007 0.073 -9999 0 -0.365 1 1
Telomerase/PinX1 -0.122 0.302 -9999 0 -0.964 3 3
Telomerase/AKT1/mTOR/p70S6K 0.031 0.078 -9999 0 -9999 0 0
SIN3B 0.016 0.002 -9999 0 -9999 0 0
YWHAE 0.017 0 -9999 0 -9999 0 0
Telomerase/EST1B -0.122 0.302 -9999 0 -0.964 3 3
response to DNA damage stimulus 0.004 0 -9999 0 -9999 0 0
MRN complex/TRF2/Rap1 0.049 0 -9999 0 -9999 0 0
TRF2/WRN 0.025 0 -9999 0 -9999 0 0
Telomerase/hnRNP C1/C2 -0.122 0.302 -9999 0 -0.964 3 3
E2F1 -0.028 0.127 -9999 0 -0.387 3 3
ZNFX1 0.016 0.002 -9999 0 -9999 0 0
PIF1 0.002 0.075 -9999 0 -0.378 1 1
NCL 0.017 0 -9999 0 -9999 0 0
DKC1 0.017 0 -9999 0 -9999 0 0
telomeric DNA binding 0 0 -9999 0 -9999 0 0
BCR signaling pathway

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
JUN -0.042 0.139 -9999 0 -0.448 2 2
IKBKB -0.002 0.084 -9999 0 -9999 0 0
AKT1 -0.036 0.093 -9999 0 -0.241 2 2
IKBKG -0.004 0.082 -9999 0 -9999 0 0
CALM1 -0.066 0.169 -9999 0 -0.432 3 3
PIK3CA 0.017 0 -9999 0 -9999 0 0
MAP3K1 -0.039 0.135 -9999 0 -0.454 2 2
MAP3K7 0.017 0 -9999 0 -9999 0 0
mol:Ca2+ -0.067 0.146 0.217 1 -0.344 4 5
DOK1 -0.026 0.153 -9999 0 -0.566 2 2
AP-1 -0.059 0.116 -9999 0 -0.253 5 5
LYN 0.017 0 -9999 0 -9999 0 0
BLNK -0.121 0.218 -9999 0 -0.449 8 8
SHC1 0.017 0 -9999 0 -9999 0 0
BCR complex -0.001 0.095 -9999 0 -0.329 2 2
CD22 -0.071 0.109 -9999 0 -0.397 2 2
CAMK2G -0.07 0.16 -9999 0 -0.474 2 2
CSNK2A1 0.017 0 -9999 0 -9999 0 0
INPP5D 0 0 -9999 0 -9999 0 0
SHC/GRB2/SOS1 -0.088 0.127 -9999 0 -0.49 1 1
GO:0007205 -0.068 0.148 0.217 1 -0.349 4 5
SYK -0.056 0.177 -9999 0 -0.472 4 4
ELK1 -0.057 0.141 -9999 0 -0.391 2 2
NFATC1 -0.056 0.144 -9999 0 -0.363 4 4
B-cell antigen/BCR complex -0.001 0.095 -9999 0 -0.329 2 2
PAG1/CSK 0.025 0 -9999 0 -9999 0 0
NFKBIB 0.009 0.031 -9999 0 -9999 0 0
HRAS -0.051 0.14 -9999 0 -0.361 2 2
NFKBIA 0.009 0.031 -9999 0 -9999 0 0
NF-kappa-B/RelA/I kappa B beta 0.015 0.027 -9999 0 -9999 0 0
RasGAP/Csk -0.047 0.131 -9999 0 -9999 0 0
mol:GDP -0.064 0.143 0.207 1 -0.332 4 5
PTEN 0.017 0 -9999 0 -9999 0 0
CD79B -0.019 0.131 -9999 0 -0.472 2 2
NF-kappa-B/RelA/I kappa B alpha 0.016 0.026 -9999 0 -9999 0 0
GRB2 0.017 0 -9999 0 -9999 0 0
PI3K/BCAP/CD19 -0.081 0.183 -9999 0 -0.472 4 4
PIK3R1 -0.005 0.11 -9999 0 -0.566 1 1
mol:IP3 -0.068 0.149 0.219 1 -0.352 4 5
CSK 0.017 0 -9999 0 -9999 0 0
FOS -0.141 0.213 -9999 0 -0.517 5 5
CHUK -0.004 0.082 -9999 0 -9999 0 0
IBTK 0.017 0 -9999 0 -9999 0 0
CARD11/BCL10/MALT1/TAK1 -0.066 0.109 -9999 0 -0.324 2 2
PTPN6 -0.075 0.156 -9999 0 -0.51 2 2
RELA 0.017 0 -9999 0 -9999 0 0
BCL2A1 0.001 0.041 -9999 0 -0.102 2 2
VAV2 -0.056 0.131 -9999 0 -0.437 2 2
ubiquitin-dependent protein catabolic process 0.014 0.03 -9999 0 -9999 0 0
BTK -0.015 0.052 -9999 0 -9999 0 0
CD19 -0.066 0.111 -9999 0 -0.397 2 2
MAP4K1 0.017 0 -9999 0 -9999 0 0
CD72 -0.012 0.103 -9999 0 -0.378 2 2
PAG1 0.017 0 -9999 0 -9999 0 0
MAPK14 -0.026 0.119 -9999 0 -0.385 2 2
SH3BP5 -0.005 0.11 -9999 0 -0.566 1 1
PIK3AP1 -0.073 0.161 -9999 0 -0.392 4 4
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.073 0.18 -9999 0 -0.443 4 4
RAF1 -0.04 0.133 -9999 0 -0.335 2 2
RasGAP/p62DOK/SHIP -0.071 0.153 -9999 0 -0.548 1 1
CD79A 0.017 0 -9999 0 -9999 0 0
re-entry into mitotic cell cycle -0.059 0.115 -9999 0 -0.252 5 5
RASA1 0.017 0 -9999 0 -9999 0 0
MAPK3 -0.019 0.117 -9999 0 -0.301 1 1
MAPK1 -0.019 0.117 -9999 0 -0.301 1 1
CD72/SHP1 -0.075 0.161 -9999 0 -0.446 3 3
NFKB1 0.017 0 -9999 0 -9999 0 0
MAPK8 -0.026 0.119 -9999 0 -0.385 2 2
actin cytoskeleton organization -0.042 0.117 -9999 0 -0.378 2 2
NF-kappa-B/RelA 0.03 0.059 -9999 0 -9999 0 0
Calcineurin -0.069 0.122 -9999 0 -0.423 2 2
PI3K -0.101 0.154 -9999 0 -0.395 5 5
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.071 0.157 0.244 1 -0.374 4 5
SOS1 0.017 0 -9999 0 -9999 0 0
Bam32/HPK1 -0.077 0.222 -9999 0 -0.774 2 2
DAPP1 -0.111 0.249 -9999 0 -0.906 2 2
cytokine secretion -0.052 0.136 -9999 0 -0.34 4 4
mol:DAG -0.068 0.149 0.219 1 -0.352 4 5
PLCG2 -0.049 0.16 -9999 0 -0.425 4 4
MAP2K1 -0.03 0.126 -9999 0 -0.338 1 1
B-cell antigen/BCR complex/FcgammaRIIB -0.078 0.152 -9999 0 -0.337 5 5
mol:PI-3-4-5-P3 -0.077 0.109 -9999 0 -0.312 3 3
ETS1 -0.057 0.148 -9999 0 -0.425 2 2
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.079 0.173 -9999 0 -0.414 3 3
B-cell antigen/BCR complex/LYN -0.067 0.112 -9999 0 -0.425 2 2
MALT1 0.017 0 -9999 0 -9999 0 0
TRAF6 0.017 0 -9999 0 -9999 0 0
RAC1 -0.044 0.123 -9999 0 -0.4 2 2
B-cell antigen/BCR complex/LYN/SYK -0.107 0.184 -9999 0 -0.481 4 4
CARD11 -0.063 0.15 -9999 0 -0.374 3 3
FCGR2B -0.128 0.229 -9999 0 -0.472 8 8
PPP3CA 0.017 0 -9999 0 -9999 0 0
BCL10 0.017 0 -9999 0 -9999 0 0
IKK complex 0.009 0.039 -9999 0 -9999 0 0
PTPRC -0.078 0.18 -9999 0 -0.41 6 6
PDPK1 -0.035 0.087 -9999 0 -0.228 2 2
PPP3CB 0.017 0 -9999 0 -9999 0 0
PPP3CC 0.017 0 -9999 0 -9999 0 0
POU2F2 0.013 0.026 -9999 0 -9999 0 0
EGFR-dependent Endothelin signaling events

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
HRAS 0.017 0 -9999 0 -9999 0 0
EGFR -0.041 0.166 -9999 0 -0.503 3 3
EGF/EGFR -0.085 0.164 -9999 0 -0.346 6 6
EGF/EGFR dimer/SHC/GRB2/SOS1 0.005 0.119 -9999 0 -0.454 1 1
mol:GTP 0 0 -9999 0 -9999 0 0
EDNRA -0.019 0.131 -9999 0 -0.472 2 2
response to oxidative stress 0 0 -9999 0 -9999 0 0
EGF -0.012 0.103 -9999 0 -0.378 2 2
EGF/EGFR dimer/SHC -0.018 0.136 -9999 0 -0.436 2 2
mol:GDP 0.001 0.117 -9999 0 -0.449 1 1
mol:Ca2+ 0 0 -9999 0 -9999 0 0
EDN1 -0.099 0.22 -9999 0 -0.503 6 6
GRB2/SOS1 0.025 0 -9999 0 -9999 0 0
HRAS/GTP -0.034 0.093 -9999 0 -0.412 1 1
SHC1 0.017 0 -9999 0 -9999 0 0
HRAS/GDP -0.035 0.095 -9999 0 -0.42 1 1
FRAP1 0.008 0.112 -9999 0 -0.425 1 1
EGF/EGFR dimer -0.035 0.156 -9999 0 -0.382 4 4
SOS1 0.017 0 -9999 0 -9999 0 0
GRB2 0.017 0 -9999 0 -9999 0 0
ETA receptor/Endothelin-1 -0.086 0.175 -9999 0 -0.348 8 8
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.105 0.297 -9999 0 -1.033 2 2
NCK1/PAK1/Dok-R -0.094 0.136 -9999 0 -0.471 2 2
NCK1/Dok-R -0.096 0.298 -9999 0 -1.054 2 2
PIK3CA 0.017 0.001 -9999 0 -9999 0 0
mol:beta2-estradiol 0.008 0.054 0.238 1 -9999 0 1
RELA 0.017 0 -9999 0 -9999 0 0
SHC1 0.016 0.001 -9999 0 -9999 0 0
Rac/GDP 0.012 0 -9999 0 -9999 0 0
F2 0.026 0.055 0.258 1 -9999 0 1
TNIP2 -0.019 0.131 -9999 0 -0.472 2 2
NF kappa B/RelA -0.072 0.285 -9999 0 -0.988 2 2
FN1 0.017 0 -9999 0 -9999 0 0
PLD2 -0.082 0.304 -9999 0 -1.098 2 2
PTPN11 0.017 0 -9999 0 -9999 0 0
GRB14 -0.107 0.214 -9999 0 -0.459 7 7
ELK1 -0.059 0.279 -9999 0 -0.989 2 2
GRB7 0.017 0 -9999 0 -9999 0 0
PAK1 -0.063 0.193 -9999 0 -0.519 4 4
Tie2/Ang1/alpha5/beta1 Integrin -0.058 0.291 -9999 0 -1.032 2 2
CDKN1A -0.194 0.354 -9999 0 -0.815 6 6
ITGA5 0.017 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
RasGAP/Dok-R -0.096 0.298 -9999 0 -1.054 2 2
CRK 0.017 0 -9999 0 -9999 0 0
mol:NO -0.068 0.219 -9999 0 -0.719 2 2
PLG -0.082 0.304 -9999 0 -1.098 2 2
mol:GDP 0 0 -9999 0 -9999 0 0
chemokinesis -0.085 0.274 -9999 0 -0.956 2 2
GRB2 0.017 0 -9999 0 -9999 0 0
PIK3R1 -0.006 0.111 -9999 0 -0.57 1 1
ANGPT2 -0.055 0.145 -9999 0 -9999 0 0
BMX -0.089 0.31 -9999 0 -1.098 2 2
ANGPT1 -0.079 0.253 -9999 0 -1.252 1 1
tube development -0.106 0.254 -9999 0 -0.724 3 3
ANGPT4 0.016 0.003 -9999 0 -9999 0 0
response to hypoxia -0.008 0.021 -9999 0 -9999 0 0
Tie2/Ang1/GRB14 -0.142 0.312 -9999 0 -1.127 2 2
alpha5/beta1 Integrin 0.025 0 -9999 0 -9999 0 0
FGF2 -0.062 0.193 -9999 0 -0.518 4 4
STAT5A (dimer) -0.163 0.343 -9999 0 -0.952 3 3
mol:L-citrulline -0.068 0.219 -9999 0 -0.719 2 2
AGTR1 0.016 0.006 -9999 0 -9999 0 0
MAPK14 -0.1 0.33 -9999 0 -1.202 2 2
Tie2/SHP2 -0.041 0.239 -9999 0 -1.158 1 1
TEK -0.055 0.263 -9999 0 -1.283 1 1
RPS6KB1 -0.088 0.279 -9999 0 -0.974 2 2
Angiotensin II/AT1 0.011 0.01 -9999 0 -9999 0 0
Tie2/Ang1/GRB2 -0.081 0.312 -9999 0 -1.127 2 2
MAPK3 -0.067 0.283 -9999 0 -1.01 2 2
MAPK1 -0.067 0.283 -9999 0 -1.01 2 2
Tie2/Ang1/GRB7 -0.081 0.312 -9999 0 -1.127 2 2
NFKB1 0.017 0 -9999 0 -9999 0 0
MAPK8 -0.082 0.304 -9999 0 -1.098 2 2
PI3K -0.117 0.342 -9999 0 -1.224 2 2
FES -0.111 0.368 -9999 0 -1.334 2 2
Crk/Dok-R -0.096 0.298 -9999 0 -1.054 2 2
Tie2/Ang1/ABIN2 -0.099 0.317 -9999 0 -1.127 2 2
blood circulation 0 0 -9999 0 -9999 0 0
negative regulation of caspase activity -0.092 0.262 -9999 0 -0.896 2 2
STAT5A 0.015 0.003 -9999 0 -9999 0 0
mol:ROS 0 0 -9999 0 -9999 0 0
PTK2 -0.088 0.279 -9999 0 -0.974 2 2
Tie2/Ang2 -0.155 0.354 -9999 0 -1.044 3 3
Tie2/Ang1 -0.095 0.324 -9999 0 -1.18 2 2
FOXO1 -0.1 0.271 -9999 0 -0.91 2 2
ELF1 0.018 0.023 -9999 0 -9999 0 0
ELF2 -0.087 0.304 -9999 0 -1.097 2 2
mol:Choline -0.079 0.292 -9999 0 -1.051 2 2
cell migration -0.048 0.07 -9999 0 -0.245 2 2
FYN -0.122 0.29 -9999 0 -0.84 3 3
DOK2 -0.041 0.166 -9999 0 -0.503 3 3
negative regulation of cell cycle -0.17 0.314 -9999 0 -0.717 6 6
ETS1 0.01 0.052 -9999 0 -9999 0 0
PXN -0.064 0.23 -9999 0 -0.775 2 2
ITGB1 0.017 0 -9999 0 -9999 0 0
NOS3 -0.08 0.248 -9999 0 -0.836 2 2
RAC1 0.017 0 -9999 0 -9999 0 0
TNF -0.108 0.201 -9999 0 -0.398 8 8
MAPKKK cascade -0.079 0.292 -9999 0 -1.051 2 2
RASA1 0.017 0 -9999 0 -9999 0 0
Tie2/Ang1/Shc -0.096 0.309 -9999 0 -1.134 2 2
NCK1 0.017 0 -9999 0 -9999 0 0
vasculogenesis -0.06 0.197 -9999 0 -0.636 2 2
mol:Phosphatidic acid -0.079 0.292 -9999 0 -1.051 2 2
mol:Angiotensin II -0.001 0.006 -9999 0 -9999 0 0
mol:NADP -0.068 0.219 -9999 0 -0.719 2 2
Rac1/GTP -0.107 0.243 -9999 0 -0.894 2 2
MMP2 -0.082 0.304 -9999 0 -1.098 2 2
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.017 0 -9999 0 -9999 0 0
RAS family/GTP/Tiam1 0.03 0.05 -9999 0 -9999 0 0
NT3 (dimer)/TRKC 0.025 0 -9999 0 -9999 0 0
NT3 (dimer)/TRKB -0.04 0.151 -9999 0 -0.403 3 3
SHC/Grb2/SOS1/GAB1/PI3K 0.034 0.053 -9999 0 -9999 0 0
RAPGEF1 0.017 0 -9999 0 -9999 0 0
BDNF -0.093 0.188 -9999 0 -0.405 7 7
PIK3CA 0.017 0 -9999 0 -9999 0 0
DYNLT1 0.017 0 -9999 0 -9999 0 0
NTRK1 0.017 0 -9999 0 -9999 0 0
NTRK2 -0.07 0.187 -9999 0 -0.453 5 5
NTRK3 0.017 0 -9999 0 -9999 0 0
NT-4/5 (dimer)/TRKB -0.051 0.15 -9999 0 -0.311 6 6
neuron apoptosis 0.129 0.197 0.57 3 -9999 0 3
SHC 2-3/Grb2 -0.141 0.218 -9999 0 -0.635 3 3
SHC1 0.017 0 -9999 0 -9999 0 0
SHC2 -0.045 0.073 -9999 0 -0.308 1 1
SHC3 -0.198 0.27 -9999 0 -0.656 6 6
STAT3 (dimer) -0.002 0.085 -9999 0 -0.338 1 1
NT3 (dimer)/TRKA 0.012 0.081 -9999 0 -0.337 1 1
RIN/GDP -0.048 0.1 -9999 0 -9999 0 0
GIPC1 0.017 0 -9999 0 -9999 0 0
KRAS 0.017 0 -9999 0 -9999 0 0
DNAJA3 0 0.075 -9999 0 -0.312 1 1
RIN/GTP -0.202 0.187 -9999 0 -0.349 16 16
CCND1 -0.023 0.181 -9999 0 -0.494 3 3
MAGED1 0.017 0 -9999 0 -9999 0 0
PTPN11 0.017 0 -9999 0 -9999 0 0
RICS 0.017 0 -9999 0 -9999 0 0
NT-4/5 (dimer) 0 0 -9999 0 -9999 0 0
SHC/GRB2/SOS1 0.034 0 -9999 0 -9999 0 0
GRB2 0.017 0 -9999 0 -9999 0 0
NGF (dimer)/TRKA/MATK -0.035 0.125 -9999 0 -0.291 5 5
TRKA/NEDD4-2 -0.033 0.142 -9999 0 -0.367 4 4
ELMO1 0.017 0 -9999 0 -9999 0 0
RhoG/GTP/ELMO1/DOCK1 0.023 0 -9999 0 -9999 0 0
NGF 0 0 -9999 0 -9999 0 0
HRAS 0.017 0 -9999 0 -9999 0 0
DOCK1 0.017 0 -9999 0 -9999 0 0
GAB2 0.017 0 -9999 0 -9999 0 0
RIT2 -0.28 0.256 -9999 0 -0.484 16 16
RIT1 0.017 0 -9999 0 -9999 0 0
FRS2 0.017 0 -9999 0 -9999 0 0
DNM1 -0.15 0.224 -9999 0 -0.435 10 10
mol:GTP 0 0 -9999 0 -9999 0 0
CRK 0.017 0 -9999 0 -9999 0 0
SH2B1 (homopentamer) 0 0 -9999 0 -9999 0 0
RhoG/GTP 0.001 0.073 -9999 0 -0.303 1 1
mol:GDP 0.064 0.036 -9999 0 -9999 0 0
NGF (dimer) 0 0 -9999 0 -9999 0 0
RhoG/GDP 0.012 0 -9999 0 -9999 0 0
RIT1/GDP 0.056 0.028 -9999 0 -9999 0 0
TIAM1 -0.005 0.11 -9999 0 -0.566 1 1
PIK3R1 -0.005 0.11 -9999 0 -0.566 1 1
BDNF (dimer)/TRKB -0.092 0.156 -9999 0 -0.403 3 3
KIDINS220/CRKL/C3G 0.025 0 -9999 0 -9999 0 0
SHC/RasGAP 0.025 0 -9999 0 -9999 0 0
FRS2 family/SHP2 0.034 0 -9999 0 -9999 0 0
SHC/GRB2/SOS1/GAB1 0.043 0 -9999 0 -9999 0 0
RIT1/GTP 0.012 0 -9999 0 -9999 0 0
NT3 (dimer) 0.017 0 -9999 0 -9999 0 0
RAP1/GDP -0.001 0.004 -9999 0 -9999 0 0
KIDINS220/CRKL 0.017 0 -9999 0 -9999 0 0
BDNF (dimer) -0.092 0.188 -9999 0 -0.405 7 7
ubiquitin-dependent protein catabolic process -0.027 0.12 -9999 0 -0.311 4 4
Schwann cell development -0.018 0.019 -9999 0 -9999 0 0
EHD4 0.002 0.075 -9999 0 -0.378 1 1
FRS2 family/GRB2/SOS1 0.043 0 -9999 0 -9999 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.047 0 -9999 0 -9999 0 0
RAP1B 0.017 0 -9999 0 -9999 0 0
RAP1A 0.017 0 -9999 0 -9999 0 0
CDC42/GTP -0.072 0.097 -9999 0 -0.397 1 1
ABL1 0.017 0 -9999 0 -9999 0 0
SH2B family/GRB2/SOS1 0.025 0 -9999 0 -9999 0 0
Rap1/GTP 0.007 0.067 -9999 0 -9999 0 0
STAT3 -0.002 0.085 -9999 0 -0.337 1 1
axon guidance -0.07 0.094 -9999 0 -0.382 1 1
MAPK3 -0.023 0.113 -9999 0 -0.305 3 3
MAPK1 -0.023 0.113 -9999 0 -0.305 3 3
CDC42/GDP 0.056 0.028 -9999 0 -9999 0 0
NTF3 0.017 0 -9999 0 -9999 0 0
NTF4 0 0 -9999 0 -9999 0 0
NGF (dimer)/TRKA/FAIM -0.032 0.131 -9999 0 -0.346 4 4
PI3K 0.009 0.081 -9999 0 -0.406 1 1
FRS3 0.017 0 -9999 0 -9999 0 0
FAIM -0.07 0.207 -9999 0 -0.566 4 4
GAB1 0.017 0 -9999 0 -9999 0 0
RASGRF1 -0.057 0.139 -9999 0 -0.316 5 5
SOS1 0.017 0 -9999 0 -9999 0 0
MCF2L 0.032 0 -9999 0 -9999 0 0
RGS19 0.017 0 -9999 0 -9999 0 0
CDC42 0.017 0 -9999 0 -9999 0 0
RAS family/GTP 0.036 0.057 -9999 0 -9999 0 0
Rac1/GDP 0.056 0.028 -9999 0 -9999 0 0
NGF (dimer)/TRKA/GRIT 0.023 0 -9999 0 -9999 0 0
neuron projection morphogenesis 0.004 0.087 -9999 0 -9999 0 0
NGF (dimer)/TRKA/NEDD4-2 -0.027 0.121 -9999 0 -0.312 4 4
MAP2K1 0.045 0 -9999 0 -9999 0 0
NGFR -0.019 0.131 -9999 0 -0.472 2 2
NGF (dimer)/TRKA/GIPC/GAIP -0.028 0.094 -9999 0 -0.242 3 3
RAS family/GTP/PI3K 0.027 0.053 -9999 0 -0.242 1 1
FRS2 family/SHP2/GRB2/SOS1 0.05 0 -9999 0 -9999 0 0
NRAS 0.017 0 -9999 0 -9999 0 0
GRB2/SOS1 0.025 0 -9999 0 -9999 0 0
PRKCI 0.017 0 -9999 0 -9999 0 0
ChemicalAbstracts:146-91-8 0 0 -9999 0 -9999 0 0
RAC1 0.017 0 -9999 0 -9999 0 0
PRKCZ 0 0 -9999 0 -9999 0 0
MAPKKK cascade -0.079 0.165 -9999 0 -0.443 4 4
RASA1 0.017 0 -9999 0 -9999 0 0
TRKA/c-Abl 0.025 0 -9999 0 -9999 0 0
SQSTM1 -0.005 0.11 -9999 0 -0.566 1 1
BDNF (dimer)/TRKB/GIPC -0.065 0.144 -9999 0 -0.361 3 3
NGF (dimer)/TRKA/p62/Atypical PKCs 0.018 0.06 -9999 0 -0.288 1 1
MATK -0.077 0.201 -9999 0 -0.491 5 5
NEDD4L -0.063 0.193 -9999 0 -0.519 4 4
RAS family/GDP 0 0.002 -9999 0 -9999 0 0
NGF (dimer)/TRKA -0.024 0.074 -9999 0 -0.335 1 1
Rac1/GTP -0.041 0.072 -9999 0 -0.251 1 1
FRS2 family/SHP2/CRK family 0.05 0 -9999 0 -9999 0 0
Visual signal transduction: Rods

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
mol:K + 0.017 0 -9999 0 -9999 0 0
GNAT1/GTP 0.002 0.052 -9999 0 -0.263 1 1
Metarhodopsin II/Arrestin 0.001 0.081 -9999 0 -0.278 2 2
PDE6G/GNAT1/GTP 0.014 0.044 -9999 0 -0.21 1 1
mol:GTP 0 0 -9999 0 -9999 0 0
absorption of light 0 0 -9999 0 -9999 0 0
GNAT1 0.002 0.075 -9999 0 -0.378 1 1
GRK1 0 0 -9999 0 -9999 0 0
CNG Channel -0.037 0.081 -9999 0 -9999 0 0
mol:Na + -0.087 0.16 -9999 0 -0.501 3 3
mol:ADP 0 0 -9999 0 -9999 0 0
RGS9-1/Gbeta5/R9AP -0.104 0.208 -9999 0 -0.402 8 8
mol:GDP 0 0 -9999 0 -9999 0 0
cGMP/CNG Channel -0.089 0.165 -9999 0 -0.517 3 3
CNGB1 0.017 0 -9999 0 -9999 0 0
RDH5 0.002 0.075 -9999 0 -0.378 1 1
SAG -0.019 0.131 -9999 0 -0.472 2 2
mol:Ca2+ -0.04 0.177 -9999 0 -0.481 3 3
Na + (4 Units) -0.08 0.149 -9999 0 -0.467 3 3
RGS9 -0.113 0.242 -9999 0 -0.566 6 6
GNB1/GNGT1 -0.007 0.113 -9999 0 -0.406 2 2
GNAT1/GDP -0.087 0.18 -9999 0 -0.338 8 8
GUCY2D 0.017 0 -9999 0 -9999 0 0
GNGT1 -0.026 0.153 -9999 0 -0.566 2 2
GUCY2F -0.027 0.124 -9999 0 -0.378 3 3
GNB5 0.017 0 -9999 0 -9999 0 0
mol:GMP (4 units) 0.007 0.089 -9999 0 -0.28 2 2
mol:11-cis-retinal 0.002 0.075 -9999 0 -0.378 1 1
mol:cGMP -0.051 0.171 -9999 0 -0.542 2 2
GNB1 0.017 0 -9999 0 -9999 0 0
Rhodopsin 0.015 0.052 -9999 0 -0.252 1 1
SLC24A1 0.017 0 -9999 0 -9999 0 0
CNGA1 -0.019 0.131 -9999 0 -0.472 2 2
Metarhodopsin II 0.011 0 -9999 0 -9999 0 0
mol:Ca ++ 0 0 -9999 0 -9999 0 0
GC1/GCAP Family -0.039 0.178 -9999 0 -0.484 3 3
RGS9BP -0.077 0.201 -9999 0 -0.491 5 5
Metarhodopsin II/Transducin 0.004 0.076 -9999 0 -0.251 2 2
GCAP Family/Ca ++ -0.05 0.177 -9999 0 -0.492 3 3
PDE6A/B -0.007 0.113 -9999 0 -0.406 2 2
mol:Pi -0.103 0.207 -9999 0 -0.4 8 8
mol:all-trans-retinal 0 0 -9999 0 -9999 0 0
Transducin 0 0.095 -9999 0 -0.306 2 2
PDE6B -0.026 0.153 -9999 0 -0.566 2 2
PDE6A 0.017 0 -9999 0 -9999 0 0
PDE6G 0.017 0 -9999 0 -9999 0 0
RHO 0.017 0 -9999 0 -9999 0 0
PDE6 -0.085 0.209 -9999 0 -0.511 4 4
GUCA1A -0.034 0.147 -9999 0 -0.441 3 3
GC2/GCAP Family -0.063 0.18 -9999 0 -0.484 3 3
GUCA1C -0.049 0.16 -9999 0 -0.425 4 4
GUCA1B -0.019 0.131 -9999 0 -0.472 2 2
Signaling events mediated by PRL

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
CCNE1 0.017 0 -9999 0 -9999 0 0
mol:Halofuginone 0.005 0.001 -9999 0 -9999 0 0
ITGA1 -0.063 0.171 -9999 0 -0.416 5 5
CDKN1A -0.135 0.22 -9999 0 -0.547 5 5
PRL-3/alpha Tubulin 0.015 0.052 -9999 0 -0.252 1 1
mol:Ca2+ -0.107 0.188 0.195 1 -0.385 8 9
AGT -0.142 0.249 -9999 0 -0.519 8 8
CCNA2 -0.105 0.17 -9999 0 -0.501 2 2
TUBA1B 0.017 0 -9999 0 -9999 0 0
EGR1 -0.139 0.193 -9999 0 -0.348 12 12
CDK2/Cyclin E1 -0.14 0.218 -9999 0 -0.491 6 6
MAPK3 0.016 0.053 -9999 0 -0.252 1 1
PRL-2 /Rab GGTase beta 0.025 0 -9999 0 -9999 0 0
MAPK1 0.016 0.053 -9999 0 -0.252 1 1
PTP4A1 -0.086 0.149 -9999 0 -9999 0 0
PTP4A3 0.002 0.075 -9999 0 -0.378 1 1
PTP4A2 0.017 0 -9999 0 -9999 0 0
ITGB1 0.016 0.053 -9999 0 -0.252 1 1
SRC 0.017 0 -9999 0 -9999 0 0
RAC1 -0.024 0.068 -9999 0 -9999 0 0
Rab GGTase beta/Rab GGTase alpha 0.025 0 -9999 0 -9999 0 0
PRL-1/ATF-5 -0.08 0.138 -9999 0 -9999 0 0
RABGGTA 0.017 0 -9999 0 -9999 0 0
BCAR1 0.007 0.037 0.196 1 -9999 0 1
RHOC -0.024 0.068 -9999 0 -9999 0 0
RHOA -0.044 0.137 -9999 0 -0.657 1 1
cell motility -0.031 0.093 -9999 0 -0.342 1 1
PRL-1/alpha Tubulin -0.072 0.139 -9999 0 -9999 0 0
PRL-3/alpha1 Integrin -0.042 0.129 -9999 0 -0.278 6 6
ROCK1 -0.031 0.094 -9999 0 -0.344 1 1
RABGGTB 0.017 0 -9999 0 -9999 0 0
CDK2 -0.056 0.177 -9999 0 -0.472 4 4
mitosis -0.086 0.148 -9999 0 -9999 0 0
ATF5 0.002 0.075 -9999 0 -0.378 1 1
Class IB PI3K non-lipid kinase 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
cAMP biosynthetic process -0.002 0.074 0.377 1 -9999 0 1
PI3K Class IB/PDE3B 0.002 0.075 -9999 0 -0.378 1 1
PDE3B 0.002 0.075 -9999 0 -0.378 1 1
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.014 0.139 -9999 0 -0.37 1 1
CRKL -0.023 0.146 -9999 0 -0.359 2 2
HRAS -0.021 0.14 -9999 0 -9999 0 0
mol:PIP3 -0.048 0.147 -9999 0 -0.337 3 3
SPRED1 -0.034 0.147 -9999 0 -0.441 3 3
SPRED2 -0.026 0.153 -9999 0 -0.566 2 2
GAB1 -0.032 0.153 -9999 0 -0.384 2 2
FOXO3 -0.044 0.147 -9999 0 -0.335 2 2
AKT1 -0.055 0.156 -9999 0 -0.351 3 3
BAD -0.044 0.147 -9999 0 -0.335 2 2
megakaryocyte differentiation -0.084 0.209 -9999 0 -0.417 6 6
GSK3B -0.044 0.147 -9999 0 -0.335 2 2
RAF1 -0.008 0.12 -9999 0 -9999 0 0
SHC1 0.017 0 -9999 0 -9999 0 0
STAT3 -0.032 0.153 -9999 0 -0.384 2 2
STAT1 -0.085 0.314 -9999 0 -1.011 2 2
HRAS/SPRED1 -0.029 0.134 -9999 0 -9999 0 0
cell proliferation -0.031 0.151 -9999 0 -0.377 2 2
PIK3CA 0.017 0.001 -9999 0 -9999 0 0
TEC 0.017 0 -9999 0 -9999 0 0
RPS6KB1 -0.042 0.155 -9999 0 -0.347 3 3
HRAS/SPRED2 -0.026 0.137 -9999 0 -0.378 1 1
LYN/TEC/p62DOK -0.035 0.169 -9999 0 -0.437 2 2
MAPK3 0.008 0.093 -9999 0 -9999 0 0
STAP1 -0.039 0.169 -9999 0 -0.47 2 2
GRAP2 -0.005 0.11 -9999 0 -0.566 1 1
JAK2 -0.066 0.255 -9999 0 -0.761 2 2
STAT1 (dimer) -0.082 0.308 -9999 0 -0.986 2 2
mol:Gleevec 0 0.007 -9999 0 -9999 0 0
GRB2/SOCS1/VAV1 -0.055 0.168 -9999 0 -0.448 3 3
actin filament polymerization -0.039 0.15 -9999 0 -0.384 2 2
LYN 0.017 0 -9999 0 -9999 0 0
STAP1/STAT5A (dimer) -0.04 0.209 -9999 0 -0.606 2 2
PIK3R1 -0.005 0.11 -9999 0 -0.567 1 1
CBL/CRKL/GRB2 -0.005 0.136 -9999 0 -0.353 1 1
PI3K -0.035 0.17 -9999 0 -0.444 2 2
PTEN 0.017 0 -9999 0 -9999 0 0
SCF/KIT/EPO/EPOR -0.112 0.349 -9999 0 -1.208 2 2
MAPK8 -0.032 0.153 -9999 0 -0.384 2 2
STAT3 (dimer) -0.031 0.151 -9999 0 -0.377 2 2
positive regulation of transcription 0.011 0.081 -9999 0 -9999 0 0
mol:GDP -0.033 0.149 -9999 0 -0.382 2 2
PIK3C2B -0.039 0.162 -9999 0 -0.366 3 3
CBL/CRKL -0.013 0.139 -9999 0 -0.37 1 1
FER -0.032 0.153 -9999 0 -0.384 2 2
SH2B3 -0.032 0.153 -9999 0 -0.384 2 2
PDPK1 -0.038 0.139 -9999 0 -0.325 2 2
SNAI2 -0.052 0.179 -9999 0 -0.422 3 3
positive regulation of cell proliferation -0.054 0.232 -9999 0 -0.676 2 2
KITLG -0.041 0.168 -9999 0 -0.506 3 3
cell motility -0.054 0.232 -9999 0 -0.676 2 2
PTPN6 -0.047 0.159 -9999 0 -0.422 4 4
EPOR 0.007 0.105 -9999 0 -9999 0 0
STAT5A (dimer) -0.041 0.198 -9999 0 -0.541 2 2
SOCS1 0.017 0 -9999 0 -9999 0 0
cell migration 0.076 0.191 0.441 4 -9999 0 4
SOS1 0.017 0 -9999 0 -9999 0 0
EPO 0.015 0.008 -9999 0 -9999 0 0
VAV1 -0.07 0.187 -9999 0 -0.453 5 5
GRB10 -0.075 0.174 -9999 0 -0.392 4 4
PTPN11 0.017 0.007 -9999 0 -9999 0 0
SCF/KIT -0.041 0.162 -9999 0 -0.41 2 2
GO:0007205 0.002 0.008 -9999 0 -9999 0 0
MAP2K1 0.003 0.101 -9999 0 -9999 0 0
CBL 0.017 0 -9999 0 -9999 0 0
KIT -0.095 0.362 -9999 0 -1.296 2 2
MAP2K2 0.003 0.101 -9999 0 -9999 0 0
SHC/Grb2/SOS1 -0.014 0.145 -9999 0 -0.389 1 1
STAT5A -0.043 0.202 -9999 0 -0.557 2 2
GRB2 0.017 0 -9999 0 -9999 0 0
response to radiation -0.05 0.176 -9999 0 -0.414 3 3
SHC/GRAP2 0.009 0.081 -9999 0 -0.406 1 1
PTPRO -0.086 0.212 -9999 0 -0.425 6 6
SH2B2 -0.04 0.153 -9999 0 -0.391 2 2
DOK1 -0.026 0.153 -9999 0 -0.566 2 2
MATK -0.078 0.194 -9999 0 -0.45 4 4
CREBBP 0.034 0.021 -9999 0 -9999 0 0
BCL2 -0.039 0.266 -9999 0 -1.277 1 1
ErbB2/ErbB3 signaling events

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
USP8 0.02 0.004 -9999 0 -9999 0 0
RAS family/GTP -0.004 0.09 -9999 0 -9999 0 0
NFATC4 -0.008 0.085 -9999 0 -9999 0 0
ERBB2IP 0.003 0.075 -9999 0 -0.38 1 1
HSP90 (dimer) 0.017 0 -9999 0 -9999 0 0
mammary gland morphogenesis -0.026 0.105 -9999 0 -9999 0 0
JUN 0.015 0.081 -9999 0 -9999 0 0
HRAS 0.017 0.001 -9999 0 -9999 0 0
DOCK7 -0.078 0.15 -9999 0 -0.359 3 3
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.045 0.118 -9999 0 -0.293 2 2
AKT1 0.012 0.003 -9999 0 -9999 0 0
BAD 0.021 0.002 -9999 0 -9999 0 0
MAPK10 -0.035 0.094 -9999 0 -0.243 1 1
mol:GTP -0.001 0.002 -9999 0 -9999 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.027 0.112 -9999 0 -9999 0 0
RAF1 0.003 0.099 -9999 0 -9999 0 0
ErbB2/ErbB3/neuregulin 2 -0.014 0.085 -9999 0 -9999 0 0
STAT3 0.009 0.01 -9999 0 -9999 0 0
cell migration -0.022 0.092 -9999 0 -9999 0 0
mol:PI-3-4-5-P3 -0.001 0.002 -9999 0 -9999 0 0
cell proliferation -0.067 0.26 -9999 0 -0.69 2 2
FOS -0.101 0.271 -9999 0 -0.485 8 8
NRAS 0.017 0.001 -9999 0 -9999 0 0
mol:Ca2+ -0.026 0.105 -9999 0 -9999 0 0
MAPK3 -0.034 0.196 -9999 0 -0.495 2 2
MAPK1 -0.034 0.196 -9999 0 -0.495 2 2
JAK2 -0.021 0.099 -9999 0 -9999 0 0
NF2 0.002 0.004 -9999 0 -9999 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.025 0.093 -9999 0 -0.266 2 2
NRG1 -0.071 0.187 -9999 0 -0.455 5 5
GRB2/SOS1 0.025 0.001 -9999 0 -9999 0 0
MAPK8 -0.032 0.106 -9999 0 -0.259 2 2
MAPK9 -0.026 0.087 -9999 0 -9999 0 0
ERBB2 -0.003 0.065 0.198 1 -0.272 1 2
ERBB3 -0.042 0.14 -9999 0 -0.378 4 4
SHC1 0.016 0.001 -9999 0 -9999 0 0
RAC1 0.017 0 -9999 0 -9999 0 0
apoptosis -0.005 0.009 -9999 0 -9999 0 0
STAT3 (dimer) 0.023 0.007 -9999 0 -9999 0 0
RNF41 0.026 0.007 -9999 0 -9999 0 0
FRAP1 0.021 0.002 -9999 0 -9999 0 0
RAC1-CDC42/GTP -0.074 0.09 -9999 0 -0.254 3 3
ErbB2/ErbB2/HSP90 (dimer) 0.008 0.051 -9999 0 -9999 0 0
CHRNA1 -0.014 0.159 -9999 0 -0.363 2 2
myelination 0.002 0.084 -9999 0 -9999 0 0
PPP3CB -0.019 0.094 -9999 0 -9999 0 0
KRAS 0.017 0.001 -9999 0 -9999 0 0
RAC1-CDC42/GDP -0.004 0.082 -9999 0 -9999 0 0
NRG2 0.017 0 -9999 0 -9999 0 0
mol:GDP -0.025 0.093 -9999 0 -0.265 2 2
SOS1 0.017 0.001 -9999 0 -9999 0 0
MAP2K2 0.005 0.108 -9999 0 -9999 0 0
SRC 0.017 0 -9999 0 -9999 0 0
mol:cAMP -0.001 0.001 -9999 0 -9999 0 0
PTPN11 -0.021 0.098 -9999 0 -9999 0 0
MAP2K1 -0.044 0.193 -9999 0 -0.408 4 4
heart morphogenesis -0.026 0.105 -9999 0 -9999 0 0
RAS family/GDP 0.002 0.087 -9999 0 -9999 0 0
GRB2 0.017 0.001 -9999 0 -9999 0 0
PRKACA -0.002 0.005 -9999 0 -9999 0 0
CHRNE 0.015 0.021 -9999 0 -9999 0 0
HSP90AA1 0.017 0 -9999 0 -9999 0 0
activation of caspase activity -0.012 0.003 -9999 0 -9999 0 0
nervous system development -0.026 0.105 -9999 0 -9999 0 0
CDC42 0.017 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 0.017 0 -9999 0 -9999 0 0
SMAD2 0.003 0.057 -9999 0 -0.24 1 1
SMAD3 0.021 0.075 -9999 0 -9999 0 0
SMAD3/SMAD4 0.033 0.042 -9999 0 -9999 0 0
SMAD4/Ubc9/PIASy 0.034 0 -9999 0 -9999 0 0
SMAD2/SMAD2/SMAD4 0.018 0.077 -9999 0 -9999 0 0
PPM1A 0.017 0 -9999 0 -9999 0 0
CALM1 -0.005 0.11 -9999 0 -0.566 1 1
SMAD2/SMAD4 0.013 0.052 -9999 0 -9999 0 0
MAP3K1 0.002 0.075 -9999 0 -0.378 1 1
TRAP-1/SMAD4 0.025 0 -9999 0 -9999 0 0
MAPK3 0.017 0 -9999 0 -9999 0 0
MAPK1 0.017 0 -9999 0 -9999 0 0
NUP214 0.002 0.075 -9999 0 -0.378 1 1
CTDSP1 0.017 0 -9999 0 -9999 0 0
CTDSP2 0.017 0 -9999 0 -9999 0 0
CTDSPL -0.005 0.11 -9999 0 -0.566 1 1
KPNB1 0.017 0 -9999 0 -9999 0 0
TGFBRAP1 0.017 0 -9999 0 -9999 0 0
UBE2I 0.017 0 -9999 0 -9999 0 0
NUP153 0.017 0 -9999 0 -9999 0 0
KPNA2 -0.012 0.103 -9999 0 -0.378 2 2
PIAS4 0.017 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 -0.026 0 -9999 0 -9999 0 0
KIRREL 0.018 0 -9999 0 -9999 0 0
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.026 0 -9999 0 -9999 0 0
PLCG1 0.017 0 -9999 0 -9999 0 0
ARRB2 0.017 0 -9999 0 -9999 0 0
WASL 0.017 0 -9999 0 -9999 0 0
Nephrin/NEPH1/podocin/CD2AP 0.042 0 -9999 0 -9999 0 0
ChemicalAbstracts:57-88-5 0 0 -9999 0 -9999 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.045 0 -9999 0 -9999 0 0
FYN 0.031 0 -9999 0 -9999 0 0
mol:Ca2+ 0.04 0 -9999 0 -9999 0 0
mol:DAG 0.041 0 -9999 0 -9999 0 0
NPHS2 0.018 0 -9999 0 -9999 0 0
mol:IP3 0.041 0 -9999 0 -9999 0 0
regulation of endocytosis 0.042 0 -9999 0 -9999 0 0
Nephrin/NEPH1/podocin/Cholesterol 0.031 0 -9999 0 -9999 0 0
establishment of cell polarity 0.026 0 -9999 0 -9999 0 0
Nephrin/NEPH1/podocin/NCK1-2 0.05 0 -9999 0 -9999 0 0
Nephrin/NEPH1/beta Arrestin2 0.044 0 -9999 0 -9999 0 0
NPHS1 0.018 0 -9999 0 -9999 0 0
Nephrin/NEPH1/podocin 0.035 0 -9999 0 -9999 0 0
TJP1 0.017 0 -9999 0 -9999 0 0
NCK1 0.017 0 -9999 0 -9999 0 0
NCK2 0.017 0 -9999 0 -9999 0 0
heterophilic cell adhesion 0 0 -9999 0 -9999 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.042 0 -9999 0 -9999 0 0
CD2AP 0.017 0 -9999 0 -9999 0 0
Nephrin/NEPH1/podocin/GRB2 0.042 0 -9999 0 -9999 0 0
GRB2 0.017 0 -9999 0 -9999 0 0
homophilic cell adhesion 0 0 -9999 0 -9999 0 0
TRPC6 0.008 0.081 -9999 0 -0.298 1 1
cytoskeleton organization 0.053 0 -9999 0 -9999 0 0
Nephrin/NEPH1 0.022 0 -9999 0 -9999 0 0
Nephrin/NEPH1/ZO-1 0.035 0 -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 0.021 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.082 0.045 -9999 0 -9999 0 0
ERC1 0.017 0 -9999 0 -9999 0 0
RIP2/NOD2 -0.022 0.115 -9999 0 -0.29 4 4
NFKBIA 0.051 0 -9999 0 -9999 0 0
BIRC2 0.017 0 -9999 0 -9999 0 0
IKBKB 0.017 0 -9999 0 -9999 0 0
RIPK2 0.002 0.075 -9999 0 -0.378 1 1
IKBKG 0.028 0.067 -9999 0 -9999 0 0
IKK complex/A20 -0.02 0.115 -9999 0 -9999 0 0
NEMO/A20/RIP2 0.002 0.075 -9999 0 -0.378 1 1
XPO1 0.017 0 -9999 0 -9999 0 0
NEMO/ATM 0.036 0.064 -9999 0 -9999 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -9999 0 0
RAN 0.017 0 -9999 0 -9999 0 0
Exportin 1/RanGTP 0.023 0 -9999 0 -9999 0 0
IKK complex/ELKS -0.012 0.037 -9999 0 -9999 0 0
BCL10/MALT1/TRAF6 0.034 0 -9999 0 -9999 0 0
NOD2 -0.034 0.147 -9999 0 -0.441 3 3
NFKB1 0.021 0 -9999 0 -9999 0 0
RELA 0.021 0 -9999 0 -9999 0 0
MALT1 0.017 0 -9999 0 -9999 0 0
cIAP1/UbcH5C 0.025 0 -9999 0 -9999 0 0
ATM 0.017 0 -9999 0 -9999 0 0
TNF/TNFR1A -0.084 0.16 -9999 0 -0.303 9 9
TRAF6 0.017 0 -9999 0 -9999 0 0
PRKCA 0.017 0 -9999 0 -9999 0 0
CHUK 0.017 0 -9999 0 -9999 0 0
UBE2D3 0.017 0 -9999 0 -9999 0 0
TNF -0.1 0.201 -9999 0 -0.432 7 7
NF kappa B1 p50/RelA 0.048 0 -9999 0 -9999 0 0
BCL10 0.017 0 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.051 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.021 0 -9999 0 -9999 0 0
TNFRSF1A -0.019 0.131 -9999 0 -0.472 2 2
IKK complex 0.044 0.063 -9999 0 -9999 0 0
CYLD 0.002 0.075 -9999 0 -0.378 1 1
IKK complex/PKC alpha 0.05 0.061 -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 0.023 0.075 -9999 0 -0.298 1 1
HDAC3 0.017 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -9999 0 0
GATA1/HDAC4 0.025 0 -9999 0 -9999 0 0
GATA1/HDAC5 0.025 0 -9999 0 -9999 0 0
GATA2/HDAC5 -0.001 0.095 -9999 0 -0.329 2 2
HDAC5/BCL6/BCoR 0.034 0 -9999 0 -9999 0 0
HDAC9 0.002 0.075 -9999 0 -0.378 1 1
Glucocorticoid receptor/Hsp90/HDAC6 0.034 0 -9999 0 -9999 0 0
HDAC4/ANKRA2 0.025 0 -9999 0 -9999 0 0
HDAC5/YWHAB 0.025 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.025 0 -9999 0 -9999 0 0
GATA2 -0.019 0.131 -9999 0 -0.472 2 2
HDAC4/RFXANK 0.025 0 -9999 0 -9999 0 0
BCOR 0.017 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
HDAC10 0.017 0 -9999 0 -9999 0 0
HDAC5 0.017 0 -9999 0 -9999 0 0
GNB1/GNG2 -0.001 0.095 -9999 0 -0.329 2 2
Histones 0.036 0.021 -9999 0 -9999 0 0
ADRBK1 0.017 0 -9999 0 -9999 0 0
HDAC4 0.017 0 -9999 0 -9999 0 0
XPO1 0.017 0 -9999 0 -9999 0 0
HDAC5/ANKRA2 0.025 0 -9999 0 -9999 0 0
HDAC4/Ubc9 0.025 0 -9999 0 -9999 0 0
HDAC7 0 0 -9999 0 -9999 0 0
HDAC5/14-3-3 E 0.025 0 -9999 0 -9999 0 0
TUBA1B 0.017 0 -9999 0 -9999 0 0
HDAC6 0.017 0 -9999 0 -9999 0 0
HDAC5/RFXANK 0.025 0 -9999 0 -9999 0 0
CAMK4 -0.085 0.195 -9999 0 -0.441 6 6
Tubulin/HDAC6 -0.011 0.111 -9999 0 -0.337 2 2
SUMO1 0.017 0 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 0 0
YWHAB 0.017 0 -9999 0 -9999 0 0
GATA1 0.017 0 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
YWHAE 0.017 0 -9999 0 -9999 0 0
NR3C1 0.017 0 -9999 0 -9999 0 0
SUMO1/HDAC4 0.037 0 -9999 0 -9999 0 0
SRF 0.017 0 -9999 0 -9999 0 0
HDAC4/YWHAB 0.025 0 -9999 0 -9999 0 0
Tubulin -0.027 0.129 -9999 0 -0.329 4 4
HDAC4/14-3-3 E 0.025 0 -9999 0 -9999 0 0
GNB1 0.017 0 -9999 0 -9999 0 0
RANGAP1 0.017 0 -9999 0 -9999 0 0
BCL6/BCoR 0.025 0 -9999 0 -9999 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.034 0 -9999 0 -9999 0 0
HDAC4/SRF -0.028 0.12 -9999 0 -0.337 2 2
HDAC4/ER alpha 0.015 0.052 -9999 0 -0.252 1 1
EntrezGene:23225 0 0 -9999 0 -9999 0 0
positive regulation of chromatin silencing 0.036 0.021 -9999 0 -9999 0 0
cell motility -0.011 0.11 -9999 0 -0.336 2 2
EntrezGene:23636 0 0 -9999 0 -9999 0 0
UBE2I 0.017 0 -9999 0 -9999 0 0
HDAC7/HDAC3 0.012 0 -9999 0 -9999 0 0
BCL6 0.017 0 -9999 0 -9999 0 0
HDAC4/CaMK II delta B 0.017 0 -9999 0 -9999 0 0
Hsp90/HDAC6 0.025 0 -9999 0 -9999 0 0
ESR1 0.002 0.075 -9999 0 -0.378 1 1
HDAC6/HDAC11 0.025 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0.041 0 -9999 0 -9999 0 0
NPC 0.01 0 -9999 0 -9999 0 0
MEF2C -0.019 0.131 -9999 0 -0.472 2 2
RAN 0.017 0 -9999 0 -9999 0 0
HDAC4/MEF2C 0.031 0.071 -9999 0 -0.272 1 1
GNG2 -0.019 0.131 -9999 0 -0.472 2 2
NCOR2 0.017 0 -9999 0 -9999 0 0
TUBB2A -0.056 0.177 -9999 0 -0.472 4 4
HDAC11 0.017 0 -9999 0 -9999 0 0
HSP90AA1 0.017 0 -9999 0 -9999 0 0
RANBP2 0.017 0 -9999 0 -9999 0 0
ANKRA2 0.017 0 -9999 0 -9999 0 0
RFXANK 0.017 0 -9999 0 -9999 0 0
nuclear import -0.036 0 -9999 0 -9999 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.017 0 -9999 0 -9999 0 0
VLDLR -0.027 0.124 -9999 0 -0.378 3 3
LRPAP1 0.002 0.075 -9999 0 -0.378 1 1
NUDC 0.017 0 -9999 0 -9999 0 0
RELN/LRP8 -0.035 0.107 -9999 0 -9999 0 0
CaM/Ca2+ -0.003 0.081 -9999 0 -0.415 1 1
KATNA1 0.017 0 -9999 0 -9999 0 0
GO:0030286 0 0 -9999 0 -9999 0 0
ABL1 -0.023 0.095 -9999 0 -9999 0 0
IQGAP1/CaM 0.009 0.081 -9999 0 -0.406 1 1
DAB1 0.017 0 -9999 0 -9999 0 0
IQGAP1 0.017 0 -9999 0 -9999 0 0
PLA2G7 -0.063 0.193 -9999 0 -0.519 4 4
CALM1 -0.005 0.11 -9999 0 -0.566 1 1
DYNLT1 0.017 0 -9999 0 -9999 0 0
mol:Ca2+ 0 0 -9999 0 -9999 0 0
LRPAP1/LRP8 0.004 0.073 -9999 0 -0.252 2 2
UniProt:Q4QZ09 0 0 -9999 0 -9999 0 0
CLIP1 -0.005 0.11 -9999 0 -0.566 1 1
CDK5R1 0.017 0 -9999 0 -9999 0 0
LIS1/Poliovirus Protein 3A 0.02 0 -9999 0 -9999 0 0
CDK5R2 0.017 0 -9999 0 -9999 0 0
mol:PP1 0 0 -9999 0 -9999 0 0
RELN/VLDLR/DAB1 -0.044 0.11 -9999 0 -9999 0 0
YWHAE 0.017 0 -9999 0 -9999 0 0
NDEL1/14-3-3 E 0.017 0.077 -9999 0 -9999 0 0
MAP1B 0 0 -9999 0 -9999 0 0
RAC1 0.026 0 -9999 0 -9999 0 0
p35/CDK5 -0.003 0.085 -9999 0 -9999 0 0
RELN -0.071 0.164 -9999 0 -0.378 6 6
PAFAH/LIS1 -0.017 0.121 -9999 0 -0.337 3 3
LIS1/CLIP170 0.018 0.07 -9999 0 -0.337 1 1
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.018 0.028 -9999 0 -9999 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 0.003 0.059 -9999 0 -9999 0 0
GO:0005869 0 0 -9999 0 -9999 0 0
NDEL1 0.008 0.08 -9999 0 -9999 0 0
LIS1/IQGAP1 0.032 0 -9999 0 -9999 0 0
RHOA 0.009 0.083 -9999 0 -0.413 1 1
PAFAH1B1 0.026 0 -9999 0 -9999 0 0
PAFAH1B3 0.002 0.075 -9999 0 -0.378 1 1
PAFAH1B2 0.017 0 -9999 0 -9999 0 0
MAP1B/LIS1/Dynein heavy chain 0.031 0 -9999 0 -9999 0 0
NDEL1/Katanin 60/Dynein heavy chain 0.024 0.075 -9999 0 -9999 0 0
LRP8 0.002 0.075 -9999 0 -0.378 1 1
NDEL1/Katanin 60 0.017 0.077 -9999 0 -9999 0 0
P39/CDK5 -0.003 0.085 -9999 0 -9999 0 0
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.032 0 -9999 0 -9999 0 0
CDK5 -0.013 0.089 -9999 0 -9999 0 0
PPP2R5D 0.017 0 -9999 0 -9999 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.016 0.06 -9999 0 -0.288 1 1
CSNK2A1 0.017 0 -9999 0 -9999 0 0
RELN/VLDLR/DAB1/LIS1 -0.017 0.095 -9999 0 -9999 0 0
RELN/VLDLR -0.042 0.13 -9999 0 -0.365 2 2
CDC42 0.026 0 -9999 0 -9999 0 0
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 0.015 0.083 -9999 0 -0.298 1 1
MAP4K1 0.017 0 -9999 0 -9999 0 0
MAP3K8 -0.019 0.131 -9999 0 -0.472 2 2
PRKCB 0 0 -9999 0 -9999 0 0
DBNL 0.017 0 -9999 0 -9999 0 0
CRKL 0.017 0 -9999 0 -9999 0 0
MAP3K1 0.027 0.066 -9999 0 -9999 0 0
JUN -0.001 0.085 -9999 0 -0.271 2 2
MAP3K7 0.034 0.058 -9999 0 -9999 0 0
GRAP2 -0.005 0.11 -9999 0 -0.566 1 1
CRK 0.017 0 -9999 0 -9999 0 0
MAP2K4 0.031 0.063 -9999 0 -9999 0 0
LAT 0.017 0 -9999 0 -9999 0 0
LCP2 -0.012 0.103 -9999 0 -0.378 2 2
MAPK8 0.022 0.019 -9999 0 -9999 0 0
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.027 0.061 -9999 0 -9999 0 0
LAT/GRAP2/SLP76/HPK1/HIP-55 0.023 0.078 -9999 0 -9999 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.015 0.052 -9999 0 -0.252 1 1
CRKL 0.027 0.043 -9999 0 -9999 0 0
mol:PIP3 -0.024 0.007 -9999 0 -9999 0 0
AKT1 0 0.006 -9999 0 -9999 0 0
PTK2B 0.002 0.075 -9999 0 -0.378 1 1
RAPGEF1 0.034 0.041 -9999 0 -9999 0 0
RANBP10 0.017 0 -9999 0 -9999 0 0
PIK3CA 0.017 0 -9999 0 -9999 0 0
HGF/MET/SHIP2 0 0.083 -9999 0 -9999 0 0
MAP3K5 0.024 0.09 -9999 0 -0.308 1 1
HGF/MET/CIN85/CBL/ENDOPHILINS -0.001 0.096 -9999 0 -0.298 1 1
AP1 -0.144 0.223 -9999 0 -0.387 11 11
mol:SU11274 0 0 -9999 0 -9999 0 0
SHC1 0.017 0 -9999 0 -9999 0 0
apoptosis -0.194 0.326 -9999 0 -0.732 7 7
STAT3 (dimer) 0.028 0.057 -9999 0 -9999 0 0
GAB1/CRKL/SHP2/PI3K 0.038 0.062 -9999 0 -9999 0 0
INPP5D 0 0 -9999 0 -9999 0 0
CBL/CRK 0.036 0.042 -9999 0 -9999 0 0
PTPN11 0.017 0 -9999 0 -9999 0 0
GO:0007205 0 0 -9999 0 -9999 0 0
PLCG1 0.017 0 -9999 0 -9999 0 0
PTEN 0.017 0 -9999 0 -9999 0 0
ELK1 -0.006 0.029 -9999 0 -0.151 1 1
mol:SU5416 0 0 -9999 0 -9999 0 0
SHP2/GRB2/SOS1GAB1 0.022 0.034 -9999 0 -9999 0 0
PAK1 -0.034 0.101 -9999 0 -0.304 3 3
HGF/MET/RANBP10 0 0.083 -9999 0 -9999 0 0
HRAS 0.024 0.052 -9999 0 -9999 0 0
DOCK1 0.034 0.041 -9999 0 -9999 0 0
GAB1 0.02 0.045 -9999 0 -9999 0 0
CRK 0.027 0.043 -9999 0 -9999 0 0
mol:PHA665752 0 0 -9999 0 -9999 0 0
mol:GDP 0.019 0.052 -9999 0 -9999 0 0
JUN -0.041 0.166 -9999 0 -0.503 3 3
EntrezGene:200958 0 0 -9999 0 -9999 0 0
HGF/MET -0.003 0.046 -9999 0 -9999 0 0
PIK3R1 -0.005 0.11 -9999 0 -0.566 1 1
cell morphogenesis 0.049 0.068 -9999 0 -9999 0 0
GRB2/SHC 0.017 0.042 -9999 0 -9999 0 0
FOS -0.193 0.259 -9999 0 -0.498 11 11
GLMN 0 0 -9999 0 -9999 0 0
cell motility -0.006 0.029 -9999 0 -0.151 1 1
HGF/MET/MUC20 -0.012 0.083 -9999 0 -0.21 4 4
cell migration 0.017 0.042 -9999 0 -9999 0 0
GRB2 0.017 0 -9999 0 -9999 0 0
CBL 0.017 0 -9999 0 -9999 0 0
MET/RANBP10 0.015 0.052 -9999 0 -0.252 1 1
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.02 0.062 -9999 0 -9999 0 0
MET/MUC20 0.002 0.052 -9999 0 -0.263 1 1
RAP1B 0.041 0.039 -9999 0 -9999 0 0
RAP1A 0.041 0.039 -9999 0 -9999 0 0
HGF/MET/RANBP9 0 0.083 -9999 0 -9999 0 0
RAF1 0.031 0.049 -9999 0 -9999 0 0
STAT3 0.028 0.057 -9999 0 -9999 0 0
cell proliferation 0.036 0.06 -9999 0 -9999 0 0
RPS6KB1 0.008 0.019 -9999 0 -9999 0 0
MAPK3 -0.012 0.026 -9999 0 -9999 0 0
MAPK1 -0.012 0.026 -9999 0 -9999 0 0
RANBP9 0.017 0 -9999 0 -9999 0 0
MAPK8 0.042 0.082 -9999 0 -9999 0 0
SRC 0.027 0.058 -9999 0 -9999 0 0
PI3K 0.006 0.069 -9999 0 -0.27 1 1
MET/Glomulin 0.007 0.045 -9999 0 -0.225 1 1
SOS1 0.017 0 -9999 0 -9999 0 0
MAP2K1 0.038 0.047 -9999 0 -9999 0 0
MET 0.002 0.075 -9999 0 -0.378 1 1
MAP4K1 0.038 0.041 -9999 0 -9999 0 0
PTK2 0.017 0 -9999 0 -9999 0 0
MAP2K2 0.038 0.047 -9999 0 -9999 0 0
BAD 0.007 0.005 -9999 0 -9999 0 0
MAP2K4 0.031 0.084 -9999 0 -9999 0 0
SHP2/GRB2/SOS1/GAB1 -0.008 0.024 -9999 0 -9999 0 0
INPPL1 0.017 0 -9999 0 -9999 0 0
PXN 0.017 0 -9999 0 -9999 0 0
SH3KBP1 -0.005 0.11 -9999 0 -0.566 1 1
HGS 0.006 0.043 -9999 0 -9999 0 0
PLCgamma1/PKC 0.012 0 -9999 0 -9999 0 0
HGF -0.027 0.124 -9999 0 -0.378 3 3
RASA1 0.017 0 -9999 0 -9999 0 0
NCK1 0.017 0 -9999 0 -9999 0 0
PTPRJ 0.002 0.075 -9999 0 -0.378 1 1
NCK/PLCgamma1 0.019 0.044 -9999 0 -9999 0 0
PDPK1 -0.011 0.006 -9999 0 -9999 0 0
HGF/MET/SHIP -0.012 0.083 -9999 0 -0.21 4 4
Signaling events mediated by PTP1B

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
PDGFRB 0.017 0 -9999 0 -9999 0 0
Jak2/Leptin Receptor 0.005 0.102 -9999 0 -0.384 1 1
PTP1B/AKT1 -0.016 0.076 -9999 0 -9999 0 0
FYN 0.017 0 -9999 0 -9999 0 0
p210 bcr-abl/PTP1B -0.028 0.082 -9999 0 -9999 0 0
EGFR -0.042 0.169 -9999 0 -0.511 3 3
EGF/EGFR -0.047 0.138 -9999 0 -0.393 3 3
CSF1 0.002 0.075 -9999 0 -0.378 1 1
AKT1 0.017 0.001 -9999 0 -9999 0 0
INSR 0.017 0.001 -9999 0 -9999 0 0
PTP1B/N-cadherin -0.017 0.079 -9999 0 -9999 0 0
Insulin Receptor/Insulin 0.004 0.064 -9999 0 -9999 0 0
HCK -0.034 0.147 -9999 0 -0.441 3 3
CRK 0.017 0 -9999 0 -9999 0 0
TYK2 -0.018 0.078 -9999 0 -9999 0 0
EGF -0.014 0.106 -9999 0 -0.39 2 2
YES1 -0.005 0.11 -9999 0 -0.566 1 1
CAV1 -0.023 0.097 -9999 0 -0.25 1 1
TXN 0.015 0.002 -9999 0 -9999 0 0
PTP1B/IRS1/GRB2 -0.007 0.077 -9999 0 -9999 0 0
cell migration 0.028 0.082 -9999 0 -9999 0 0
STAT3 0.017 0.001 -9999 0 -9999 0 0
PRLR -0.02 0.153 -9999 0 -0.561 2 2
ITGA2B 0.016 0.001 -9999 0 -9999 0 0
CSF1R 0.017 0 -9999 0 -9999 0 0
Prolactin Receptor/Prolactin 0.008 0.116 -9999 0 -0.398 2 2
FGR 0.017 0 -9999 0 -9999 0 0
PTP1B/p130 Cas -0.017 0.079 -9999 0 -9999 0 0
Crk/p130 Cas -0.007 0.077 -9999 0 -9999 0 0
DOK1 -0.021 0.115 -9999 0 -0.366 2 2
JAK2 -0.005 0.101 -9999 0 -0.412 1 1
Jak2/Leptin Receptor/Leptin -0.056 0.121 -9999 0 -0.4 2 2
PIK3R1 -0.005 0.11 -9999 0 -0.566 1 1
PTPN1 -0.028 0.083 -9999 0 -9999 0 0
LYN 0.017 0 -9999 0 -9999 0 0
CDH2 0.017 0 -9999 0 -9999 0 0
SRC 0.009 0.034 -9999 0 -9999 0 0
ITGB3 -0.02 0.131 -9999 0 -0.473 2 2
CAT1/PTP1B -0.006 0.126 -9999 0 -0.386 2 2
CAPN1 0.001 0.074 -9999 0 -0.378 1 1
CSK 0.017 0 -9999 0 -9999 0 0
PI3K -0.019 0.087 -9999 0 -0.426 1 1
mol:H2O2 0 0.004 -9999 0 -9999 0 0
STAT3 (dimer) -0.054 0.124 -9999 0 -0.412 2 2
negative regulation of transcription -0.007 0.1 -9999 0 -0.407 1 1
FCGR2A -0.07 0.187 -9999 0 -0.453 5 5
FER 0.015 0.002 -9999 0 -9999 0 0
alphaIIb/beta3 Integrin -0.003 0.095 -9999 0 -0.33 2 2
BLK -0.005 0.11 -9999 0 -0.566 1 1
Insulin Receptor/Insulin/Shc 0.034 0.002 -9999 0 -9999 0 0
RHOA -0.006 0.111 -9999 0 -0.572 1 1
LEPR 0.017 0.003 -9999 0 -9999 0 0
BCAR1 0.017 0 -9999 0 -9999 0 0
p210 bcr-abl/Grb2 0.017 0 -9999 0 -9999 0 0
mol:NADPH -0.001 0.002 -9999 0 -9999 0 0
TRPV6 0.017 0.116 -9999 0 -0.384 2 2
PRL 0.023 0.004 -9999 0 -9999 0 0
SOCS3 -0.074 0.271 -9999 0 -1.33 1 1
SPRY2 -0.035 0.147 -9999 0 -0.443 3 3
Insulin Receptor/Insulin/IRS1 0.034 0.002 -9999 0 -9999 0 0
CSF1/CSF1R -0.014 0.083 -9999 0 -9999 0 0
Ras protein signal transduction 0.025 0.026 -9999 0 -9999 0 0
IRS1 0.017 0 -9999 0 -9999 0 0
INS 0.017 0.001 -9999 0 -9999 0 0
LEP 0.017 0.001 -9999 0 -9999 0 0
STAT5B -0.013 0.082 -9999 0 -0.281 1 1
STAT5A -0.013 0.082 -9999 0 -0.281 1 1
GRB2 0.017 0 -9999 0 -9999 0 0
PDGFB-D/PDGFRB -0.017 0.079 -9999 0 -9999 0 0
CSN2 0.027 0.047 -9999 0 -9999 0 0
PIK3CA 0.017 0 -9999 0 -9999 0 0
LAT -0.04 0.124 -9999 0 -0.446 2 2
YBX1 0.004 0.109 -9999 0 -0.553 1 1
LCK 0.017 0 -9999 0 -9999 0 0
SHC1 0.017 0 -9999 0 -9999 0 0
NOX4 -0.101 0.203 -9999 0 -0.435 7 7
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 -0.005 0.11 -9999 0 -0.566 1 1
HDAC2 -0.005 0.11 -9999 0 -0.566 1 1
GNB1/GNG2 -0.009 0.132 -9999 0 -0.435 2 2
forebrain development -0.024 0.218 -9999 0 -0.539 3 3
GNAO1 0.017 0.004 -9999 0 -9999 0 0
SMO/beta Arrestin2 0.001 0.096 -9999 0 -0.328 2 2
SMO -0.019 0.131 -9999 0 -0.471 2 2
ARRB2 0.017 0.004 -9999 0 -9999 0 0
GLI3/SPOP 0.008 0.149 -9999 0 -0.687 1 1
mol:GTP 0 0.003 -9999 0 -9999 0 0
GSK3B 0.017 0 -9999 0 -9999 0 0
GNAI2 0.017 0.004 -9999 0 -9999 0 0
SIN3/HDAC complex 0.043 0.004 -9999 0 -9999 0 0
GNAI1 -0.005 0.11 -9999 0 -0.566 1 1
XPO1 0.019 0.005 -9999 0 -9999 0 0
GLI1/Su(fu) -0.02 0.217 -9999 0 -0.661 2 2
SAP30 0.017 0.001 -9999 0 -9999 0 0
mol:GDP -0.019 0.13 -9999 0 -0.471 2 2
MIM/GLI2A -0.025 0.148 -9999 0 -0.435 3 3
IFT88 0.017 0 -9999 0 -9999 0 0
GNAI3 0.017 0.004 -9999 0 -9999 0 0
GLI2 0.015 0.086 -9999 0 -0.265 1 1
GLI3 -0.002 0.156 -9999 0 -0.732 1 1
CSNK1D 0.017 0 -9999 0 -9999 0 0
CSNK1E 0.002 0.075 -9999 0 -0.378 1 1
SAP18 0.017 0.001 -9999 0 -9999 0 0
embryonic digit morphogenesis 0.017 0 -9999 0 -9999 0 0
GNG2 -0.019 0.131 -9999 0 -0.472 2 2
Gi family/GTP 0.02 0.086 -9999 0 -0.316 1 1
SIN3B 0.017 0.001 -9999 0 -9999 0 0
SIN3A 0.017 0.001 -9999 0 -9999 0 0
GLI3/Su(fu) 0.01 0.135 -9999 0 -0.41 2 2
GLI2/Su(fu) 0.016 0.11 -9999 0 -9999 0 0
FOXA2 -0.042 0.148 -9999 0 -0.777 1 1
neural tube patterning -0.024 0.218 -9999 0 -0.539 3 3
SPOP 0.017 0 -9999 0 -9999 0 0
Su(fu)/PIAS1 0.014 0.082 -9999 0 -0.337 1 1
GNB1 0.017 0 -9999 0 -9999 0 0
CSNK1G2 0.017 0 -9999 0 -9999 0 0
CSNK1G3 0.017 0 -9999 0 -9999 0 0
MTSS1 -0.025 0.148 -9999 0 -0.436 3 3
embryonic limb morphogenesis -0.024 0.218 -9999 0 -0.539 3 3
SUFU 0.006 0.09 -9999 0 -0.378 1 1
LGALS3 -0.048 0.183 -9999 0 -0.566 3 3
catabolic process 0.014 0.152 -9999 0 -0.563 1 1
GLI3A/CBP -0.007 0.101 -9999 0 -0.337 2 2
KIF3A 0.017 0 -9999 0 -9999 0 0
GLI1 -0.025 0.224 -9999 0 -0.555 3 3
RAB23 0.017 0 -9999 0 -9999 0 0
CSNK1A1 0.017 0 -9999 0 -9999 0 0
IFT172 -0.026 0.153 -9999 0 -0.566 2 2
RBBP7 0.017 0.001 -9999 0 -9999 0 0
Su(fu)/Galectin3 -0.022 0.154 -9999 0 -0.408 3 3
GNAZ 0.017 0.004 -9999 0 -9999 0 0
RBBP4 0.017 0.001 -9999 0 -9999 0 0
CSNK1G1 0.017 0 -9999 0 -9999 0 0
PIAS1 0.017 0 -9999 0 -9999 0 0
PRKACA 0.017 0 -9999 0 -9999 0 0
GLI2/SPOP 0.023 0.081 -9999 0 -9999 0 0
STK36 -0.003 0.11 -9999 0 -0.565 1 1
Gi family/GNB1/GNG2/GDP 0.014 0.135 -9999 0 -0.625 1 1
PTCH1 -0.044 0.282 -9999 0 -0.935 2 2
MIM/GLI1 -0.028 0.222 -9999 0 -0.848 1 1
CREBBP -0.007 0.101 -9999 0 -0.337 2 2
Su(fu)/SIN3/HDAC complex 0.033 0.064 -9999 0 -9999 0 0
Arf6 downstream pathway

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
PLAUR 0.047 0.01 -9999 0 -9999 0 0
regulation of axonogenesis -0.012 0.058 -9999 0 -9999 0 0
myoblast fusion -0.017 0.028 -9999 0 -9999 0 0
mol:GTP 0.01 0.009 -9999 0 -9999 0 0
regulation of calcium-dependent cell-cell adhesion -0.027 0.068 0.317 1 -9999 0 1
ARF1/GTP 0.021 0.006 -9999 0 -9999 0 0
mol:GM1 0.01 0.008 -9999 0 -9999 0 0
mol:Choline 0.001 0.087 -9999 0 -0.32 1 1
lamellipodium assembly -0.004 0.028 -9999 0 -9999 0 0
MAPK3 0.032 0.008 -9999 0 -9999 0 0
ARF6/GTP/NME1/Tiam1 0.028 0.068 -9999 0 -0.318 1 1
ARF1 0.017 0 -9999 0 -9999 0 0
ARF6/GDP 0.017 0.028 -9999 0 -9999 0 0
ARF1/GDP 0.026 0.026 -9999 0 -9999 0 0
ARF6 0.014 0.006 -9999 0 -9999 0 0
RAB11A 0.017 0 -9999 0 -9999 0 0
TIAM1 -0.003 0.11 -9999 0 -0.565 1 1
fibronectin binding 0 0 -9999 0 -9999 0 0
MAPK1 0.032 0.008 -9999 0 -9999 0 0
actin filament bundle formation -0.013 0.054 0.238 1 -9999 0 1
KALRN -0.021 0.06 -9999 0 -9999 0 0
RAB11FIP3/RAB11A 0.025 0 -9999 0 -9999 0 0
RhoA/GDP 0.014 0.055 -9999 0 -0.239 1 1
NME1 0.019 0.001 -9999 0 -9999 0 0
Rac1/GDP 0.023 0.023 -9999 0 -9999 0 0
substrate adhesion-dependent cell spreading 0.01 0.009 -9999 0 -9999 0 0
cortical actin cytoskeleton organization -0.004 0.028 -9999 0 -9999 0 0
RAC1 0.017 0 -9999 0 -9999 0 0
liver development 0.01 0.009 -9999 0 -9999 0 0
ARF6/GTP 0.01 0.009 -9999 0 -9999 0 0
RhoA/GTP 0.008 0.075 -9999 0 -0.374 1 1
mol:GDP -0.003 0.026 -9999 0 -9999 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0.031 0.008 -9999 0 -9999 0 0
RHOA -0.005 0.11 -9999 0 -0.566 1 1
PLD1 -0.01 0.099 -9999 0 -0.283 3 3
RAB11FIP3 0.017 0 -9999 0 -9999 0 0
tube morphogenesis -0.004 0.028 -9999 0 -9999 0 0
ruffle organization 0.012 0.058 -9999 0 -9999 0 0
regulation of epithelial cell migration 0.01 0.009 -9999 0 -9999 0 0
PLD2 0.023 0.007 -9999 0 -9999 0 0
PIP5K1A 0.012 0.059 -9999 0 -9999 0 0
mol:Phosphatidic acid 0.001 0.087 -9999 0 -0.32 1 1
Rac1/GTP -0.004 0.028 -9999 0 -9999 0 0
Aurora C 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
INCENP 0.017 0 -9999 0 -9999 0 0
Aurora C/Aurora B/INCENP 0.009 0.067 -9999 0 -9999 0 0
metaphase 0 0 -9999 0 -9999 0 0
mitosis 0 0 -9999 0 -9999 0 0
H3F3B -0.005 0.016 -9999 0 -9999 0 0
AURKB -0.012 0.103 -9999 0 -0.378 2 2
AURKC 0.002 0.075 -9999 0 -0.378 1 1
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.075 0.209 -9999 0 -9999 0 0
PCK1 0.1 0.123 -9999 0 -9999 0 0
HNF4A 0.09 0.21 -9999 0 -9999 0 0
KCNJ11 0.074 0.254 -9999 0 -9999 0 0
AKT1 0.035 0.146 -9999 0 -9999 0 0
response to starvation 0.007 0.004 -9999 0 -9999 0 0
DLK1 0.08 0.237 -9999 0 -9999 0 0
NKX2-1 0.032 0.189 -9999 0 -9999 0 0
ACADM 0.075 0.209 -9999 0 -9999 0 0
TAT 0.087 0.136 -9999 0 -9999 0 0
CEBPB 0.023 0.006 -9999 0 -9999 0 0
CEBPA -0.033 0.167 -9999 0 -0.497 3 3
TTR 0.078 0.186 -9999 0 -0.587 1 1
PKLR 0.075 0.209 -9999 0 -9999 0 0
APOA1 0.092 0.236 -9999 0 -9999 0 0
CPT1C 0.075 0.209 -9999 0 -9999 0 0
ALAS1 0.059 0.159 -9999 0 -9999 0 0
TFRC 0.1 0.184 -9999 0 -9999 0 0
FOXF1 -0.006 0.114 -9999 0 -0.573 1 1
NF1 0.026 0.001 -9999 0 -9999 0 0
HNF1A (dimer) 0.036 0.022 -9999 0 -9999 0 0
CPT1A 0.008 0.304 -9999 0 -0.737 2 2
HMGCS1 0.002 0.317 -9999 0 -0.885 2 2
NR3C1 0.003 0.051 -9999 0 -9999 0 0
CPT1B 0.075 0.209 -9999 0 -9999 0 0
chromatin remodeling 0 0 -9999 0 -9999 0 0
SP1 0.021 0.022 -9999 0 -9999 0 0
GCK 0.06 0.217 -9999 0 -9999 0 0
CREB1 0.03 0 -9999 0 -9999 0 0
IGFBP1 -0.038 0.313 -9999 0 -1.297 1 1
PDX1 0.086 0.147 -9999 0 -9999 0 0
UCP2 0.037 0.301 -9999 0 -1.081 1 1
ALDOB 0.08 0.237 -9999 0 -9999 0 0
AFP 0.06 0.018 -9999 0 -9999 0 0
BDH1 0.037 0.293 -9999 0 -0.914 1 1
HADH 0.08 0.237 -9999 0 -9999 0 0
F2 0.092 0.236 -9999 0 -9999 0 0
HNF1A 0.036 0.022 -9999 0 -9999 0 0
G6PC 0.065 0.077 -9999 0 -9999 0 0
SLC2A2 0.09 0.168 -9999 0 -9999 0 0
INS 0.034 0.054 -9999 0 -9999 0 0
FOXA1 0.04 0.028 -9999 0 -9999 0 0
FOXA3 0.07 0.015 -9999 0 -9999 0 0
FOXA2 0.092 0.289 -9999 0 -9999 0 0
ABCC8 -0.022 0.421 -9999 0 -0.914 4 4
ALB 0.06 0.018 -9999 0 -9999 0 0
EPO signaling pathway

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
BCL2L1 0.051 0.092 -9999 0 -9999 0 0
CRKL 0.024 0.071 -9999 0 -9999 0 0
mol:DAG 0.036 0.059 -9999 0 -9999 0 0
HRAS 0.049 0.062 -9999 0 -9999 0 0
MAPK8 0.039 0.014 -9999 0 -9999 0 0
RAP1A 0.024 0.071 -9999 0 -9999 0 0
GAB1 0.024 0.071 -9999 0 -9999 0 0
MAPK14 0.039 0.014 -9999 0 -9999 0 0
EPO 0.017 0.008 -9999 0 -9999 0 0
PLCG1 0.036 0.06 -9999 0 -9999 0 0
EPOR/TRPC2/IP3 Receptors 0.017 0.008 -9999 0 -9999 0 0
RAPGEF1 0.017 0 -9999 0 -9999 0 0
EPO/EPOR (dimer)/SOCS3 -0.008 0.102 -9999 0 -0.349 1 1
GAB1/SHC/GRB2/SOS1 -0.015 0.038 -9999 0 -9999 0 0
EPO/EPOR (dimer) 0.026 0.014 -9999 0 -9999 0 0
IRS2 0.024 0.071 -9999 0 -9999 0 0
STAT1 0.036 0.086 -9999 0 -9999 0 0
STAT5B 0.039 0.067 -9999 0 -9999 0 0
cell proliferation 0.045 0.013 -9999 0 -9999 0 0
GAB1/SHIP/PIK3R1/SHP2/SHC -0.022 0.05 -9999 0 -9999 0 0
TEC 0.024 0.071 -9999 0 -9999 0 0
SOCS3 -0.049 0.16 -9999 0 -0.425 4 4
STAT1 (dimer) 0.036 0.085 -9999 0 -9999 0 0
JAK2 0.017 0.007 -9999 0 -9999 0 0
PIK3R1 -0.005 0.11 -9999 0 -0.566 1 1
EPO/EPOR (dimer)/JAK2 0.032 0.082 -9999 0 -9999 0 0
EPO/EPOR 0.026 0.014 -9999 0 -9999 0 0
LYN 0.018 0.004 -9999 0 -9999 0 0
TEC/VAV2 0.034 0.07 -9999 0 -9999 0 0
elevation of cytosolic calcium ion concentration 0.017 0.008 -9999 0 -9999 0 0
SHC1 0.017 0 -9999 0 -9999 0 0
EPO/EPOR (dimer)/LYN 0.042 0.015 -9999 0 -9999 0 0
mol:IP3 0.036 0.059 -9999 0 -9999 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.018 0.081 -9999 0 -9999 0 0
SH2B3 0.017 0.007 -9999 0 -9999 0 0
NFKB1 0.039 0.014 -9999 0 -9999 0 0
EPO/EPOR (dimer)/JAK2/SOCS3 -0.013 0.051 -9999 0 -9999 0 0
PTPN6 0.015 0.074 -9999 0 -9999 0 0
TEC/VAV2/GRB2 0.04 0.069 -9999 0 -9999 0 0
EPOR 0.017 0.008 -9999 0 -9999 0 0
INPP5D 0 0 -9999 0 -9999 0 0
mol:GDP -0.015 0.039 -9999 0 -9999 0 0
SOS1 0.017 0 -9999 0 -9999 0 0
PLCG2 -0.049 0.16 -9999 0 -0.425 4 4
CRKL/CBL/C3G 0.04 0.069 -9999 0 -9999 0 0
VAV2 0.024 0.071 -9999 0 -9999 0 0
CBL 0.024 0.071 -9999 0 -9999 0 0
SHC/Grb2/SOS1 -0.018 0.042 -9999 0 -9999 0 0
STAT5A 0.039 0.067 -9999 0 -9999 0 0
GRB2 0.017 0 -9999 0 -9999 0 0
STAT5 (dimer) 0.052 0.09 -9999 0 -9999 0 0
LYN/PLCgamma2 -0.021 0.115 -9999 0 -0.404 1 1
PTPN11 0.017 0 -9999 0 -9999 0 0
BTK -0.004 0.109 -9999 0 -0.289 2 2
BCL2 0.024 0.192 -9999 0 -0.853 1 1
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.002 0.097 -9999 0 -0.324 1 1
CaM/Ca2+ -0.003 0.081 -9999 0 -0.415 1 1
AKT1 0.017 0 -9999 0 -9999 0 0
AKT2 0.002 0.075 -9999 0 -0.378 1 1
STXBP4 0.017 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
mol:glucose -0.011 0.104 -9999 0 -0.355 1 1
YWHAZ 0.017 0 -9999 0 -9999 0 0
CALM1 -0.005 0.11 -9999 0 -0.566 1 1
YWHAQ 0.017 0 -9999 0 -9999 0 0
TBC1D4 0.026 0 -9999 0 -9999 0 0
mol:Ca2+ 0 0 -9999 0 -9999 0 0
YWHAH 0.002 0.075 -9999 0 -0.378 1 1
YWHAB 0.017 0 -9999 0 -9999 0 0
SNARE/Synip 0.034 0 -9999 0 -9999 0 0
YWHAG 0.002 0.075 -9999 0 -0.378 1 1
ASIP 0 0 -9999 0 -9999 0 0
PRKCI 0.017 0 -9999 0 -9999 0 0
AS160/CaM/Ca2+ -0.003 0.081 -9999 0 -0.415 1 1
RHOQ 0.002 0.075 -9999 0 -0.378 1 1
GYS1 0.03 0.028 -9999 0 -9999 0 0
PRKCZ 0 0 -9999 0 -9999 0 0
TRIP10 -0.005 0.11 -9999 0 -0.566 1 1
TC10/GTP/CIP4/Exocyst 0.001 0.081 -9999 0 -0.278 2 2
AS160/14-3-3 0.047 0.04 -9999 0 -9999 0 0
VAMP2 0.017 0 -9999 0 -9999 0 0
SLC2A4 -0.014 0.113 -9999 0 -0.392 1 1
STX4 0.017 0 -9999 0 -9999 0 0
GSK3B 0.024 0.034 -9999 0 -9999 0 0
SFN 0.017 0 -9999 0 -9999 0 0
LNPEP 0.017 0 -9999 0 -9999 0 0
YWHAE 0.017 0 -9999 0 -9999 0 0
mTOR signaling pathway

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
GBL 0.017 0 -9999 0 -9999 0 0
MKNK1 -0.005 0.11 -9999 0 -0.566 1 1
mol:PIP3 -0.01 0.051 -9999 0 -0.269 1 1
FRAP1 0.022 0.022 -9999 0 -9999 0 0
AKT1 0.023 0.054 -9999 0 -0.254 1 1
INSR 0.017 0 -9999 0 -9999 0 0
Insulin Receptor/Insulin 0.023 0 -9999 0 -9999 0 0
mol:GTP 0.035 0.047 -9999 0 -9999 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.003 0.014 -9999 0 -9999 0 0
TSC2 0.017 0 -9999 0 -9999 0 0
RHEB/GDP -0.007 0.036 -9999 0 -9999 0 0
TSC1 0.017 0 -9999 0 -9999 0 0
Insulin Receptor/IRS1 0.021 0.001 -9999 0 -9999 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.003 0.016 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
EIF3A 0.017 0 -9999 0 -9999 0 0
RPS6KB1 0.031 0.037 -9999 0 -9999 0 0
MAP3K5 -0.017 0.102 -9999 0 -0.376 2 2
PIK3R1 -0.005 0.11 -9999 0 -0.566 1 1
apoptosis -0.017 0.101 -9999 0 -0.376 2 2
mol:LY294002 0 0 -9999 0 -9999 0 0
EIF4B 0.037 0.034 -9999 0 -9999 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.033 0.056 -9999 0 -9999 0 0
eIF4E/eIF4G1/eIF4A1 -0.007 0.031 -9999 0 -9999 0 0
KIAA1303 0.017 0 -9999 0 -9999 0 0
PI3K 0.02 0.058 -9999 0 -0.276 1 1
mTOR/RHEB/GTP/Raptor/GBL 0.049 0.031 -9999 0 -9999 0 0
FKBP1A 0.017 0.001 -9999 0 -9999 0 0
RHEB/GTP -0.007 0.035 -9999 0 -9999 0 0
mol:Amino Acids 0 0 -9999 0 -9999 0 0
FKBP12/Rapamycin 0.013 0.002 -9999 0 -9999 0 0
PDPK1 -0.009 0.047 -9999 0 -0.251 1 1
EIF4E 0.017 0 -9999 0 -9999 0 0
ASK1/PP5C -0.012 0.167 -9999 0 -0.603 2 2
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.041 0.001 -9999 0 -9999 0 0
TSC1/TSC2 0.039 0.051 -9999 0 -9999 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -9999 0 0
RPS6 -0.005 0.11 -9999 0 -0.566 1 1
PPP5C 0.017 0 -9999 0 -9999 0 0
EIF4G1 0.017 0 -9999 0 -9999 0 0
IRS1 0.011 0.002 -9999 0 -9999 0 0
INS 0.017 0 -9999 0 -9999 0 0
PTEN 0.016 0.001 -9999 0 -9999 0 0
PDK2 -0.009 0.047 -9999 0 -0.251 1 1
EIF4EBP1 0.016 0 -9999 0 -9999 0 0
PIK3CA 0.017 0 -9999 0 -9999 0 0
PPP2R5D 0.029 0.02 -9999 0 -9999 0 0
peptide biosynthetic process 0.029 0 -9999 0 -9999 0 0
RHEB 0.017 0 -9999 0 -9999 0 0
EIF4A1 0.017 0 -9999 0 -9999 0 0
mol:Rapamycin 0 0 -9999 0 -9999 0 0
EEF2 0.029 0 -9999 0 -9999 0 0
eIF4E/4E-BP1 0.025 0 -9999 0 -9999 0 0
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.034 0.066 -9999 0 -0.296 1 1
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -9999 0 0
CRKL 0.017 0 -9999 0 -9999 0 0
STAT1 (dimer)/Cbp/p300 0.061 0.067 -9999 0 -9999 0 0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.026 0.053 -9999 0 -0.241 1 1
antigen processing and presentation of peptide antigen via MHC class I -0.071 0.125 -9999 0 -0.321 4 4
CaM/Ca2+ 0.017 0.083 -9999 0 -0.265 2 2
RAP1A 0.017 0 -9999 0 -9999 0 0
STAT1 (dimer)/SHP2 0.033 0.071 -9999 0 -0.273 1 1
AKT1 0.038 0.076 -9999 0 -9999 0 0
MAP2K1 0.035 0.068 -9999 0 -9999 0 0
MAP3K11 0.036 0.062 -9999 0 -0.273 1 1
IFNGR1 0.017 0.007 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
CaM/Ca2+/CAMKII -0.085 0.245 -9999 0 -0.662 3 3
Rap1/GTP -0.007 0.037 -9999 0 -9999 0 0
CRKL/C3G 0.025 0 -9999 0 -9999 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.038 0.07 -9999 0 -0.319 1 1
CEBPB 0.04 0.132 -9999 0 -0.373 2 2
STAT3 0.017 0 -9999 0 -9999 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.046 0.064 -9999 0 -9999 0 0
STAT1 0.031 0.07 -9999 0 -0.272 1 1
CALM1 -0.005 0.11 -9999 0 -0.566 1 1
IFN-gamma (dimer) 0.003 0.079 -9999 0 -0.398 1 1
PIK3CA 0.017 0 -9999 0 -9999 0 0
STAT1 (dimer)/PIAS1 0.04 0.068 -9999 0 -9999 0 0
CEBPB/PTGES2/Cbp/p300 -0.033 0.076 -9999 0 -9999 0 0
mol:Ca2+ 0.03 0.065 -9999 0 -0.293 1 1
MAPK3 0.041 0.073 -9999 0 -9999 0 0
STAT1 (dimer) -0.1 0.196 -9999 0 -0.482 4 4
MAPK1 0.041 0.073 -9999 0 -9999 0 0
JAK2 0.017 0.007 -9999 0 -9999 0 0
PIK3R1 -0.005 0.11 -9999 0 -0.566 1 1
JAK1 0.003 0.079 -9999 0 -0.398 1 1
CAMK2D -0.005 0.11 -9999 0 -0.566 1 1
DAPK1 0.021 0.185 -9999 0 -0.613 2 2
SMAD7 -0.004 0.1 -9999 0 -0.266 2 2
CBL/CRKL/C3G 0.052 0.058 -9999 0 -9999 0 0
PI3K -0.019 0.066 -9999 0 -9999 0 0
IFNG 0.003 0.079 -9999 0 -0.398 1 1
apoptosis 0.009 0.138 -9999 0 -0.452 2 2
CAMK2G -0.019 0.131 -9999 0 -0.472 2 2
STAT3 (dimer) 0.017 0 -9999 0 -9999 0 0
CAMK2A -0.078 0.18 -9999 0 -0.41 6 6
CAMK2B -0.084 0.214 -9999 0 -0.529 5 5
FRAP1 0.045 0.072 -9999 0 -9999 0 0
PRKCD 0.012 0.132 -9999 0 -0.499 1 1
RAP1B 0.017 0 -9999 0 -9999 0 0
negative regulation of cell growth -0.071 0.125 -9999 0 -0.321 4 4
PTPN2 0.017 0 -9999 0 -9999 0 0
EP300 0.017 0 -9999 0 -9999 0 0
IRF1 0.069 0.056 -9999 0 -9999 0 0
STAT1 (dimer)/PIASy 0.035 0.067 -9999 0 -9999 0 0
SOCS1 0.004 0.011 -9999 0 -9999 0 0
mol:GDP 0.047 0.055 -9999 0 -9999 0 0
CASP1 -0.016 0.12 -9999 0 -0.285 3 3
PTGES2 0.017 0 -9999 0 -9999 0 0
IRF9 0.031 0.09 -9999 0 -0.237 2 2
mol:PI-3-4-5-P3 -0.018 0.064 -9999 0 -9999 0 0
RAP1/GDP -0.007 0.037 -9999 0 -9999 0 0
CBL 0.036 0.061 -9999 0 -0.274 1 1
MAP3K1 0.029 0.07 -9999 0 -0.273 1 1
PIAS1 0.017 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 -0.071 0.125 -9999 0 -0.321 4 4
PTPN11 0.029 0.064 -9999 0 -0.293 1 1
CREBBP 0.017 0 -9999 0 -9999 0 0
RAPGEF1 0.017 0 -9999 0 -9999 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.026 0 -9999 0 -9999 0 0
BAD/BCL-XL/YWHAZ 0.041 0 -9999 0 -9999 0 0
CDKN1B 0.045 0.015 -9999 0 -9999 0 0
CDKN1A -0.045 0.127 -9999 0 -0.327 1 1
FRAP1 0.017 0 -9999 0 -9999 0 0
PRKDC 0.017 0 -9999 0 -9999 0 0
FOXO3 0.045 0.015 -9999 0 -9999 0 0
AKT1 -0.002 0.008 -9999 0 -9999 0 0
BAD 0.017 0 -9999 0 -9999 0 0
AKT3 0.02 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
FOXO4 0.045 0.015 -9999 0 -9999 0 0
AKT1/ASK1 0.022 0.086 -9999 0 -0.318 1 1
BAD/YWHAZ 0.034 0 -9999 0 -9999 0 0
RICTOR -0.005 0.11 -9999 0 -0.566 1 1
RAF1 0.017 0 -9999 0 -9999 0 0
JNK cascade -0.021 0.084 0.309 1 -9999 0 1
TSC1 0.045 0.015 -9999 0 -9999 0 0
YWHAZ 0.017 0 -9999 0 -9999 0 0
AKT1/RAF1 0.046 0.015 -9999 0 -9999 0 0
EP300 0.017 0 -9999 0 -9999 0 0
mol:GDP 0.038 0.016 -9999 0 -9999 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -9999 0 0
TSC2 0.045 0.015 -9999 0 -9999 0 0
YWHAQ 0.017 0 -9999 0 -9999 0 0
TBC1D4 0.022 0.028 -9999 0 -9999 0 0
MAP3K5 -0.026 0.153 -9999 0 -0.566 2 2
MAPKAP1 0.017 0 -9999 0 -9999 0 0
negative regulation of cell cycle -0.038 0.033 -9999 0 -9999 0 0
YWHAH 0.002 0.075 -9999 0 -0.378 1 1
AKT1S1 0.045 0.015 -9999 0 -9999 0 0
CASP9 0.023 0.079 -9999 0 -9999 0 0
YWHAB 0.017 0 -9999 0 -9999 0 0
p27Kip1/KPNA1 0.053 0.015 -9999 0 -9999 0 0
GBL 0.017 0 -9999 0 -9999 0 0
PDK1/Src/Hsp90 0.034 0 -9999 0 -9999 0 0
YWHAE 0.017 0 -9999 0 -9999 0 0
SRC 0.017 0 -9999 0 -9999 0 0
AKT2/p21CIP1 -0.071 0.098 -9999 0 -0.299 1 1
KIAA1303 0.017 0 -9999 0 -9999 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.043 0.008 -9999 0 -9999 0 0
CHUK 0.045 0.015 -9999 0 -9999 0 0
BAD/BCL-XL 0.061 0.015 -9999 0 -9999 0 0
mTORC2 0.031 0.064 -9999 0 -0.298 1 1
AKT2 0.014 0.034 -9999 0 -9999 0 0
FOXO1-3a-4/14-3-3 family 0.066 0.028 -9999 0 -9999 0 0
PDPK1 0.017 0 -9999 0 -9999 0 0
MDM2 0.045 0.015 -9999 0 -9999 0 0
MAPKKK cascade -0.045 0.015 -9999 0 -9999 0 0
MDM2/Cbp/p300 0.06 0.015 -9999 0 -9999 0 0
TSC1/TSC2 0.051 0.015 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.057 0.014 -9999 0 -9999 0 0
glucose import -0.043 0.125 -9999 0 -0.295 4 4
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.054 0.015 -9999 0 -9999 0 0
response to stress 0 0 -9999 0 -9999 0 0
SLC2A4 -0.043 0.125 -9999 0 -0.297 4 4
GSK3A 0.045 0.015 -9999 0 -9999 0 0
FOXO1 0.045 0.015 -9999 0 -9999 0 0
GSK3B 0.045 0.015 -9999 0 -9999 0 0
SFN 0.017 0 -9999 0 -9999 0 0
G1/S transition of mitotic cell cycle 0.051 0.015 -9999 0 -9999 0 0
p27Kip1/14-3-3 family 0.049 0.044 -9999 0 -9999 0 0
PRKACA 0.017 0 -9999 0 -9999 0 0
KPNA1 0.017 0 -9999 0 -9999 0 0
HSP90AA1 0.017 0 -9999 0 -9999 0 0
YWHAG 0.002 0.075 -9999 0 -0.378 1 1
RHEB 0.017 0 -9999 0 -9999 0 0
CREBBP 0.017 0 -9999 0 -9999 0 0
Ceramide signaling pathway

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
SPHK2 0.006 0.073 -9999 0 -9999 0 0
MAP4K4 -0.02 0.12 -9999 0 -0.499 1 1
BAG4 0.002 0.075 -9999 0 -0.378 1 1
PKC zeta/ceramide -0.007 0.03 -9999 0 -9999 0 0
NFKBIA 0.017 0 -9999 0 -9999 0 0
BIRC3 -0.056 0.177 -9999 0 -0.472 4 4
BAX 0.006 0.017 -9999 0 -9999 0 0
RIPK1 0.017 0 -9999 0 -9999 0 0
AKT1 0.021 0.007 -9999 0 -9999 0 0
BAD 0.002 0.032 -9999 0 -9999 0 0
SMPD1 -0.023 0.077 -9999 0 -0.198 3 3
RB1 0.002 0.032 -9999 0 -9999 0 0
FADD/Caspase 8 -0.005 0.116 -9999 0 -0.474 1 1
MAP2K4 0.003 0.046 -9999 0 -0.173 1 1
NSMAF 0.017 0 -9999 0 -9999 0 0
response to UV 0 0 -9999 0 -9999 0 0
RAF1 0.01 0.03 -9999 0 -9999 0 0
EGF -0.012 0.103 -9999 0 -0.378 2 2
mol:ceramide -0.007 0.034 -9999 0 -9999 0 0
MADD 0.017 0 -9999 0 -9999 0 0
response to oxidative stress 0 0 -9999 0 -9999 0 0
mol:Free Fatty acid -0.011 0.134 -9999 0 -0.484 2 2
ASAH1 -0.012 0.103 -9999 0 -0.378 2 2
negative regulation of cell cycle 0.002 0.031 -9999 0 -9999 0 0
cell proliferation -0.006 0.105 -9999 0 -0.457 1 1
BID -0.012 0.09 -9999 0 -0.313 1 1
MAP3K1 -0.005 0.048 -9999 0 -0.19 1 1
EIF2A 0.011 0.044 -9999 0 -9999 0 0
TRADD 0.017 0 -9999 0 -9999 0 0
CRADD 0.017 0 -9999 0 -9999 0 0
MAPK3 0.022 0.028 -9999 0 -9999 0 0
response to heat 0 0 -9999 0 -9999 0 0
MAPK1 0.022 0.028 -9999 0 -9999 0 0
Cathepsin D/ceramide -0.003 0.031 -9999 0 -9999 0 0
FADD -0.02 0.12 -9999 0 -0.499 1 1
KSR1 0.002 0.032 -9999 0 -9999 0 0
MAPK8 0.006 0.037 -9999 0 -9999 0 0
PRKRA 0.002 0.032 -9999 0 -9999 0 0
PDGFA -0.012 0.103 -9999 0 -0.378 2 2
TRAF2 0.017 0 -9999 0 -9999 0 0
IGF1 -0.005 0.11 -9999 0 -0.566 1 1
mol:GD3 0 0 -9999 0 -9999 0 0
ganglioside biosynthetic process -0.007 0.034 -9999 0 -9999 0 0
CTSD 0.002 0.075 -9999 0 -0.378 1 1
regulation of nitric oxide biosynthetic process 0.025 0 -9999 0 -9999 0 0
response to radiation 0 0 -9999 0 -9999 0 0
ERK1/PKC delta 0.003 0.119 -9999 0 -0.497 1 1
PRKCD -0.041 0.166 -9999 0 -0.503 3 3
PRKCZ 0 0 -9999 0 -9999 0 0
mol:GW4869 0 0 -9999 0 -9999 0 0
mol:sphingosine -0.011 0.134 -9999 0 -0.484 2 2
RelA/NF kappa B1 0.025 0 -9999 0 -9999 0 0
mol:glutathione 0 0 -9999 0 -9999 0 0
PAWR -0.019 0.131 -9999 0 -0.472 2 2
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.03 0.126 -9999 0 -0.533 1 1
TNFR1A/BAG4/TNF-alpha -0.066 0.156 -9999 0 -0.403 3 3
mol:Sphingosine-1-phosphate 0.006 0.073 -9999 0 -9999 0 0
MAP2K1 0.018 0.029 -9999 0 -9999 0 0
mol:C11AG 0 0 -9999 0 -9999 0 0
RELA 0.017 0 -9999 0 -9999 0 0
CYCS 0.014 0.048 0.226 1 -9999 0 1
TNFRSF1A -0.019 0.131 -9999 0 -0.472 2 2
NFKB1 0.017 0 -9999 0 -9999 0 0
TNFR1A/BAG4 -0.011 0.106 -9999 0 -0.303 3 3
EIF2AK2 0.01 0.03 -9999 0 -9999 0 0
TNF-alpha/TNFR1A/FAN -0.059 0.137 -9999 0 -0.337 3 3
response to hydrogen peroxide 0 0 -9999 0 -9999 0 0
CASP8 0.006 0.07 -9999 0 -9999 0 0
MAP2K2 0.018 0.029 -9999 0 -9999 0 0
SMPD3 -0.019 0.084 -9999 0 -0.292 1 1
TNF -0.1 0.201 -9999 0 -0.432 7 7
PKC zeta/PAR4 -0.014 0.094 -9999 0 -0.339 2 2
mol:PHOSPHOCHOLINE -0.006 0.048 -9999 0 -9999 0 0
NF kappa B1/RelA/I kappa B alpha 0.021 0.07 -9999 0 -0.279 1 1
AIFM1 0.014 0.048 0.226 1 -9999 0 1
BCL2 -0.019 0.131 -9999 0 -0.472 2 2
Signaling events mediated by HDAC Class III

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
EP300 0.017 0 -9999 0 -9999 0 0
HDAC4 0.017 0 -9999 0 -9999 0 0
induction of apoptosis 0 0 -9999 0 -9999 0 0
regulation of S phase of mitotic cell cycle -0.038 0.043 -9999 0 -9999 0 0
CDKN1A -0.188 0.297 -9999 0 -0.766 5 5
KAT2B 0 0 -9999 0 -9999 0 0
BAX 0.017 0 -9999 0 -9999 0 0
FOXO3 0 0 -9999 0 -9999 0 0
FOXO1 0.017 0 -9999 0 -9999 0 0
FOXO4 0.027 0 -9999 0 -9999 0 0
response to UV 0 0 -9999 0 -9999 0 0
XRCC6 0.017 0 -9999 0 -9999 0 0
TAT 0.017 0 -9999 0 -9999 0 0
mol:Lysophosphatidic acid 0 0 -9999 0 -9999 0 0
MYOD1 0.013 0 -9999 0 -9999 0 0
PPARGC1A -0.056 0.177 -9999 0 -0.472 4 4
FHL2 -0.085 0.195 -9999 0 -0.441 6 6
response to nutrient levels 0 0 -9999 0 -9999 0 0
KU70/SIRT1 0.056 0.05 -9999 0 -9999 0 0
HIST2H4A 0.038 0.043 -9999 0 -9999 0 0
SIRT1/FOXO3a 0.036 0.052 -9999 0 -9999 0 0
SIRT1 0.06 0.071 -9999 0 -9999 0 0
response to hypoxia 0 0 -9999 0 -9999 0 0
SIRT1/MEF2D/HDAC4 0.062 0.045 -9999 0 -9999 0 0
SIRT1/Histone H1b 0.058 0.059 -9999 0 -9999 0 0
apoptosis -0.061 0.045 -9999 0 -9999 0 0
SIRT1/PGC1A 0.001 0.117 -9999 0 -0.256 4 4
p53/SIRT1 0.097 0.182 0.377 5 -0.409 1 6
SIRT1/FOXO4 0.063 0.051 -9999 0 -9999 0 0
FOXO1/FHL2/SIRT1 -0.001 0.121 -9999 0 -0.278 2 2
HIST1H1E 0.021 0.028 -9999 0 -9999 0 0
SIRT1/p300 0.056 0.05 -9999 0 -9999 0 0
muscle cell differentiation -0.04 0.054 -9999 0 -9999 0 0
TP53 0.026 0.142 -9999 0 -0.568 1 1
KU70/SIRT1/BAX 0.062 0.045 -9999 0 -9999 0 0
CREBBP 0.017 0 -9999 0 -9999 0 0
MEF2D 0.017 0 -9999 0 -9999 0 0
HIV-1 Tat/SIRT1 0.056 0.05 -9999 0 -9999 0 0
ACSS2 0.052 0.044 -9999 0 -9999 0 0
SIRT1/PCAF/MYOD 0.04 0.054 -9999 0 -9999 0 0
Reelin signaling pathway

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
CDK5R1/CDK5 0.025 0 -9999 0 -9999 0 0
VLDLR -0.027 0.124 -9999 0 -0.378 3 3
CRKL 0.017 0 -9999 0 -9999 0 0
LRPAP1 0.002 0.075 -9999 0 -0.378 1 1
FYN 0.017 0 -9999 0 -9999 0 0
ITGA3 -0.005 0.11 -9999 0 -0.566 1 1
RELN/VLDLR/Fyn -0.044 0.11 -9999 0 -9999 0 0
MAPK8IP1/MKK7/MAP3K11/JNK1 0.038 0.061 -9999 0 -9999 0 0
AKT1 -0.008 0.071 -9999 0 -9999 0 0
MAP2K7 0.017 0 -9999 0 -9999 0 0
RAPGEF1 0.017 0 -9999 0 -9999 0 0
DAB1 0.017 0 -9999 0 -9999 0 0
RELN/LRP8/DAB1 -0.022 0.093 -9999 0 -9999 0 0
LRPAP1/LRP8 0.004 0.073 -9999 0 -0.252 2 2
RELN/LRP8/DAB1/Fyn -0.012 0.087 -9999 0 -9999 0 0
DAB1/alpha3/beta1 Integrin -0.063 0.093 -9999 0 -0.298 2 2
long-term memory -0.073 0.176 -9999 0 -0.416 4 4
DAB1/LIS1 -0.026 0.114 -9999 0 -0.313 2 2
DAB1/CRLK/C3G -0.054 0.087 -9999 0 -0.298 2 2
PIK3CA 0.017 0 -9999 0 -9999 0 0
DAB1/NCK2 -0.025 0.115 -9999 0 -0.315 2 2
ARHGEF2 0.017 0 -9999 0 -9999 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -9999 0 0
GRIN2A -0.012 0.103 -9999 0 -0.378 2 2
CDK5R1 0.017 0 -9999 0 -9999 0 0
RELN -0.071 0.164 -9999 0 -0.378 6 6
PIK3R1 -0.005 0.11 -9999 0 -0.566 1 1
RELN/LRP8/Fyn -0.026 0.103 -9999 0 -9999 0 0
GRIN2A/RELN/LRP8/DAB1/Fyn -0.016 0.108 -9999 0 -0.337 1 1
MAPK8 0.017 0 -9999 0 -9999 0 0
RELN/VLDLR/DAB1 -0.038 0.1 -9999 0 -9999 0 0
ITGB1 0.017 0 -9999 0 -9999 0 0
MAP1B -0.025 0.099 -9999 0 -0.3 1 1
RELN/LRP8 -0.035 0.107 -9999 0 -9999 0 0
GRIN2B/RELN/LRP8/DAB1/Fyn -0.07 0.163 -9999 0 -0.415 3 3
PI3K 0.009 0.081 -9999 0 -0.406 1 1
mol:PP2 0 0 -9999 0 -9999 0 0
alpha3/beta1 Integrin 0.009 0.081 -9999 0 -0.406 1 1
RAP1A -0.007 0.107 -9999 0 -9999 0 0
PAFAH1B1 0.017 0 -9999 0 -9999 0 0
MAPK8IP1 -0.005 0.11 -9999 0 -0.566 1 1
CRLK/C3G 0.025 0 -9999 0 -9999 0 0
GRIN2B -0.113 0.225 -9999 0 -0.486 7 7
NCK2 0.017 0 -9999 0 -9999 0 0
neuron differentiation 0.02 0.057 -9999 0 -9999 0 0
neuron adhesion -0.002 0.11 -9999 0 -9999 0 0
LRP8 0.002 0.075 -9999 0 -0.378 1 1
GSK3B 0 0.068 -9999 0 -9999 0 0
RELN/VLDLR/DAB1/Fyn -0.026 0.094 -9999 0 -9999 0 0
MAP3K11 0.017 0 -9999 0 -9999 0 0
RELN/VLDLR/DAB1/P13K -0.018 0.076 -9999 0 -0.242 1 1
CDK5 0.017 0 -9999 0 -9999 0 0
MAPT 0.013 0.017 -9999 0 -9999 0 0
neuron migration 0.015 0.088 -9999 0 -9999 0 0
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.02 0.058 -9999 0 -9999 0 0
RELN/VLDLR -0.042 0.13 -9999 0 -0.365 2 2
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 -0.02 0.067 0.255 1 -9999 0 1
GNAI2 0.017 0 -9999 0 -9999 0 0
S1P/S1P5/G12 0.011 0 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
GNAO1 0.017 0 -9999 0 -9999 0 0
RhoA/GTP 0.02 0.069 -9999 0 -0.259 1 1
negative regulation of cAMP metabolic process 0.025 0.045 -9999 0 -9999 0 0
GNAZ 0.017 0 -9999 0 -9999 0 0
GNAI3 0.017 0 -9999 0 -9999 0 0
GNA12 0.017 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 0.025 0.045 -9999 0 -9999 0 0
RhoA/GDP -0.003 0.081 -9999 0 -0.415 1 1
RHOA -0.005 0.11 -9999 0 -0.566 1 1
GNAI1 -0.005 0.11 -9999 0 -0.566 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 -0.016 0.12 -9999 0 -0.437 1 1
BAG4 0.002 0.075 -9999 0 -0.378 1 1
BAD 0.007 0.042 -9999 0 -9999 0 0
NFKBIA 0.017 0 -9999 0 -9999 0 0
BIRC3 -0.056 0.177 -9999 0 -0.472 4 4
BAX 0.007 0.042 -9999 0 -9999 0 0
EnzymeConsortium:3.1.4.12 -0.003 0.031 -9999 0 -0.102 1 1
IKBKB -0.007 0.114 -9999 0 -0.406 1 1
MAP2K2 0.019 0.042 -9999 0 -9999 0 0
MAP2K1 0.019 0.042 -9999 0 -9999 0 0
SMPD1 0 0.036 -9999 0 -9999 0 0
GO:0005551 0 0 -9999 0 -9999 0 0
FADD/Caspase 8 -0.007 0.117 -9999 0 -0.417 1 1
MAP2K4 0.008 0.053 -9999 0 -9999 0 0
protein ubiquitination -0.006 0.116 -9999 0 -0.412 1 1
EnzymeConsortium:2.7.1.37 0.022 0.046 -9999 0 -9999 0 0
response to UV 0 0.001 -9999 0 -9999 0 0
RAF1 0.014 0.043 -9999 0 -9999 0 0
CRADD 0.017 0 -9999 0 -9999 0 0
mol:ceramide -0.001 0.044 -9999 0 -0.141 1 1
I-kappa-B-alpha/RELA/p50/ubiquitin 0.023 0 -9999 0 -9999 0 0
MADD 0.017 0 -9999 0 -9999 0 0
MAP3K1 0.001 0.055 -9999 0 -0.176 1 1
TRADD 0.017 0 -9999 0 -9999 0 0
RELA/p50 0.017 0 -9999 0 -9999 0 0
MAPK3 0.023 0.042 -9999 0 -9999 0 0
MAPK1 0.023 0.042 -9999 0 -9999 0 0
p50/RELA/I-kappa-B-alpha 0.025 0 -9999 0 -9999 0 0
FADD -0.016 0.12 -9999 0 -0.437 1 1
KSR1 0.007 0.043 -9999 0 -9999 0 0
MAPK8 0.016 0.05 -9999 0 -9999 0 0
TRAF2 0.017 0.001 -9999 0 -9999 0 0
response to radiation 0 0 -9999 0 -9999 0 0
CHUK -0.007 0.114 -9999 0 -0.406 1 1
TNF R/SODD -0.011 0.106 -9999 0 -0.303 3 3
TNF -0.099 0.201 -9999 0 -0.432 7 7
CYCS 0.014 0.045 -9999 0 -9999 0 0
IKBKG -0.007 0.114 -9999 0 -0.406 1 1
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.025 0.126 -9999 0 -0.466 1 1
RELA 0.017 0 -9999 0 -9999 0 0
RIPK1 0.017 0.001 -9999 0 -9999 0 0
AIFM1 0.014 0.045 -9999 0 -9999 0 0
TNF/TNF R/SODD -0.066 0.156 -9999 0 -0.403 3 3
TNFRSF1A -0.019 0.131 -9999 0 -0.472 2 2
response to heat 0 0 -9999 0 -9999 0 0
CASP8 0.016 0.032 -9999 0 -9999 0 0
NSMAF -0.016 0.118 -9999 0 -0.431 1 1
response to hydrogen peroxide 0 0.001 -9999 0 -9999 0 0
BCL2 -0.019 0.131 -9999 0 -0.472 2 2
HIF-2-alpha transcription factor network

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
MMP14 -0.005 0.069 -9999 0 -9999 0 0
oxygen homeostasis 0.01 0.012 -9999 0 -9999 0 0
TCEB2 0.017 0 -9999 0 -9999 0 0
TCEB1 0.017 0 -9999 0 -9999 0 0
VHL/Elongin B/Elongin C/HIF2A -0.009 0.113 -9999 0 -0.509 1 1
EPO 0.121 0.19 -9999 0 -0.516 1 1
FIH (dimer) 0.026 0.012 -9999 0 -9999 0 0
APEX1 0.026 0.014 -9999 0 -9999 0 0
SERPINE1 0.104 0.208 -9999 0 -0.579 1 1
FLT1 -0.007 0.053 -9999 0 -9999 0 0
ADORA2A 0.101 0.201 -9999 0 -0.56 1 1
germ cell development 0.111 0.199 -9999 0 -0.559 1 1
SLC11A2 0.098 0.224 -9999 0 -0.579 1 1
BHLHE40 0.102 0.202 -9999 0 -0.587 1 1
HIF1AN 0.027 0.012 -9999 0 -9999 0 0
HIF2A/ARNT/SIRT1 0.079 0.172 -9999 0 -0.558 1 1
ETS1 0.02 0.035 -9999 0 -9999 0 0
CITED2 0.007 0.02 -9999 0 -9999 0 0
KDR -0.159 0.393 -9999 0 -1.086 4 4
PGK1 0.111 0.203 -9999 0 -0.579 1 1
SIRT1 0.017 0 -9999 0 -9999 0 0
response to hypoxia 0.001 0 -9999 0 -9999 0 0
HIF2A/ARNT 0.124 0.233 -9999 0 -0.674 1 1
EPAS1 0.05 0.161 -9999 0 -0.593 1 1
SP1 0.025 0.005 -9999 0 -9999 0 0
ABCG2 0.091 0.221 -9999 0 -0.579 1 1
EFNA1 0.105 0.224 -9999 0 -0.736 1 1
FXN 0.108 0.197 -9999 0 -0.56 1 1
POU5F1 0.111 0.203 -9999 0 -0.579 1 1
neuron apoptosis -0.121 0.228 0.655 1 -9999 0 1
EP300 0.017 0 -9999 0 -9999 0 0
EGLN3 -0.046 0.181 -9999 0 -0.47 4 4
EGLN2 0.027 0.012 -9999 0 -9999 0 0
EGLN1 0.027 0.012 -9999 0 -9999 0 0
VHL/Elongin B/Elongin C 0.034 0 -9999 0 -9999 0 0
VHL 0.017 0 -9999 0 -9999 0 0
ARNT 0.026 0.014 -9999 0 -9999 0 0
SLC2A1 0.108 0.197 -9999 0 -0.56 1 1
TWIST1 0.096 0.217 -9999 0 -0.56 1 1
ELK1 0.026 0 -9999 0 -9999 0 0
HIF2A/ARNT/Cbp/p300 0.079 0.171 -9999 0 -0.556 1 1
VEGFA 0.105 0.213 -9999 0 -0.579 1 1
CREBBP 0.017 0 -9999 0 -9999 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.017 0 -9999 0 -9999 0 0
NFATC1 0.017 0.105 -9999 0 -9999 0 0
NFATC2 0.023 0.075 -9999 0 -0.331 1 1
NFATC3 0.009 0.043 -9999 0 -0.212 1 1
YWHAE 0.017 0 -9999 0 -9999 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.021 0.154 -9999 0 -0.709 1 1
Exportin 1/Ran/NUP214 0.026 0.044 -9999 0 -9999 0 0
mol:DAG 0 0.001 -9999 0 -9999 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.086 0.173 -9999 0 -0.562 2 2
BCL2/BAX -0.001 0.095 -9999 0 -0.406 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.002 0.081 -9999 0 -0.415 1 1
CaM/Ca2+ -0.002 0.081 -9999 0 -0.415 1 1
BAX 0.017 0 -9999 0 -9999 0 0
MAPK14 0.017 0.001 -9999 0 -9999 0 0
BAD 0.017 0 -9999 0 -9999 0 0
CABIN1/MEF2D -0.012 0.147 -9999 0 -0.675 1 1
Calcineurin A alpha-beta B1/BCL2 -0.019 0.13 -9999 0 -0.471 2 2
FKBP8 0.017 0 -9999 0 -9999 0 0
activation-induced cell death of T cells 0.012 0.145 0.662 1 -9999 0 1
KPNB1 0.017 0 -9999 0 -9999 0 0
KPNA2 -0.012 0.103 -9999 0 -0.378 2 2
XPO1 0.017 0 -9999 0 -9999 0 0
SFN 0.017 0 -9999 0 -9999 0 0
MAP3K8 -0.019 0.131 -9999 0 -0.472 2 2
NFAT4/CK1 alpha 0.015 0.074 -9999 0 -0.315 1 1
MEF2D/NFAT1/Cbp/p300 0.05 0.092 -9999 0 -0.293 1 1
CABIN1 -0.022 0.155 -9999 0 -0.719 1 1
CALM1 -0.005 0.11 -9999 0 -0.565 1 1
RAN 0.017 0 -9999 0 -9999 0 0
MAP3K1 0.002 0.075 -9999 0 -0.378 1 1
CAMK4 -0.085 0.195 -9999 0 -0.441 6 6
mol:Ca2+ 0.001 0.003 -9999 0 -9999 0 0
MAPK3 0.017 0 -9999 0 -9999 0 0
YWHAH 0.002 0.075 -9999 0 -0.378 1 1
Calcineurin A alpha-beta B1/AKAP79/PKA 0.009 0.082 -9999 0 -0.408 1 1
YWHAB 0.017 0 -9999 0 -9999 0 0
MAPK8 0.017 0.002 -9999 0 -9999 0 0
MAPK9 0.017 0 -9999 0 -9999 0 0
YWHAG 0.002 0.075 -9999 0 -0.378 1 1
FKBP1A 0.017 0 -9999 0 -9999 0 0
NFAT1-c-4/YWHAQ 0.034 0.117 -9999 0 -0.43 1 1
PRKCH -0.005 0.11 -9999 0 -0.566 1 1
CABIN1/Cbp/p300 0.026 0.004 -9999 0 -9999 0 0
CASP3 0.002 0.076 -9999 0 -0.385 1 1
PIM1 0.017 0 -9999 0 -9999 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.012 0.002 -9999 0 -9999 0 0
apoptosis -0.007 0.026 -9999 0 -9999 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.036 0.051 -9999 0 -9999 0 0
PRKCB 0 0 -9999 0 -9999 0 0
PRKCE 0.017 0 -9999 0 -9999 0 0
JNK2/NFAT4 0.019 0.039 -9999 0 -9999 0 0
BAD/BCL-XL 0.025 0 -9999 0 -9999 0 0
PRKCD -0.041 0.166 -9999 0 -0.503 3 3
NUP214 0.002 0.075 -9999 0 -0.378 1 1
PRKCZ 0 0.002 -9999 0 -9999 0 0
PRKCA 0.017 0 -9999 0 -9999 0 0
PRKCG -0.012 0.103 -9999 0 -0.378 2 2
PRKCQ -0.005 0.11 -9999 0 -0.566 1 1
FKBP38/BCL2 -0.001 0.095 -9999 0 -0.329 2 2
EP300 0.017 0.002 -9999 0 -9999 0 0
PRKCB1 -0.063 0.171 -9999 0 -0.416 5 5
CSNK2A1 0.017 0 -9999 0 -9999 0 0
NFATc/JNK1 0.025 0.101 -9999 0 -9999 0 0
CaM/Ca2+/FKBP38 0.01 0.07 -9999 0 -0.345 1 1
FKBP12/FK506 0.012 0 -9999 0 -9999 0 0
CSNK1A1 0.01 0.069 -9999 0 -0.344 1 1
CaM/Ca2+/CAMK IV -0.052 0.132 -9999 0 -0.267 7 7
NFATc/ERK1 0.026 0.101 -9999 0 -9999 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.087 0.173 -9999 0 -0.562 2 2
NR4A1 0.041 0.129 -9999 0 -0.55 1 1
GSK3B 0.017 0.002 -9999 0 -9999 0 0
positive T cell selection 0.009 0.043 -9999 0 -0.211 1 1
NFAT1/CK1 alpha 0.018 0.095 -9999 0 -0.452 1 1
RCH1/ KPNB1 0.004 0.073 -9999 0 -0.252 2 2
YWHAQ 0.017 0 -9999 0 -9999 0 0
PRKACA 0.017 0.001 -9999 0 -9999 0 0
AKAP5 -0.005 0.11 -9999 0 -0.566 1 1
MEF2D 0.017 0.002 -9999 0 -9999 0 0
mol:FK506 0 0 -9999 0 -9999 0 0
YWHAZ 0.017 0 -9999 0 -9999 0 0
NFATc/p38 alpha 0.025 0.101 -9999 0 -9999 0 0
CREBBP 0.017 0.002 -9999 0 -9999 0 0
BCL2 -0.019 0.131 -9999 0 -0.472 2 2
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.064 0.105 -9999 0 -0.32 3 3
Ran/GTP/Exportin 1/HDAC1 -0.009 0.047 -9999 0 -0.247 1 1
NF kappa B1 p50/RelA/I kappa B alpha -0.015 0.115 -9999 0 -0.291 3 3
SUMO1 0.017 0 -9999 0 -9999 0 0
ZFPM1 0.017 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.025 0 -9999 0 -9999 0 0
FKBP3 0.017 0 -9999 0 -9999 0 0
Histones -0.011 0.095 -9999 0 -9999 0 0
YY1/LSF 0.031 0 -9999 0 -9999 0 0
SMG5 0.017 0 -9999 0 -9999 0 0
RAN 0.017 0 -9999 0 -9999 0 0
I kappa B alpha/HDAC3 -0.025 0.101 -9999 0 -0.252 3 3
I kappa B alpha/HDAC1 -0.021 0.09 -9999 0 -0.294 1 1
SAP18 0.017 0 -9999 0 -9999 0 0
RELA -0.015 0.093 -9999 0 -9999 0 0
HDAC1/Smad7 0.007 0.097 -9999 0 -0.337 2 2
RANGAP1 0.017 0 -9999 0 -9999 0 0
HDAC3/TR2 -0.009 0.073 -9999 0 -9999 0 0
NuRD/MBD3 Complex 0.041 0.054 -9999 0 -9999 0 0
NF kappa B1 p50/RelA -0.006 0.085 -9999 0 -9999 0 0
EntrezGene:23225 0 0 -9999 0 -9999 0 0
GATA2 -0.019 0.131 -9999 0 -0.472 2 2
GATA1 0.017 0 -9999 0 -9999 0 0
Mad/Max 0.025 0 -9999 0 -9999 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.052 0.057 -9999 0 -9999 0 0
RBBP7 0.017 0 -9999 0 -9999 0 0
NPC 0.01 0 -9999 0 -9999 0 0
RBBP4 0.017 0 -9999 0 -9999 0 0
MAX 0.017 0 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 0 0
FBXW11 0.017 0 -9999 0 -9999 0 0
NFKBIA -0.02 0.082 -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 0.033 0.062 -9999 0 -9999 0 0
SIN3 complex 0.043 0 -9999 0 -9999 0 0
SMURF1 0.017 0 -9999 0 -9999 0 0
CHD3 0.017 0 -9999 0 -9999 0 0
SAP30 0.017 0 -9999 0 -9999 0 0
EntrezGene:23636 0 0 -9999 0 -9999 0 0
NCOR1 0.017 0 -9999 0 -9999 0 0
YY1/HDAC3 0.001 0.068 -9999 0 -9999 0 0
YY1/HDAC2 0.018 0.067 -9999 0 -0.325 1 1
YY1/HDAC1 0.018 0.067 -9999 0 -0.325 1 1
NuRD/MBD2 Complex (MeCP1) 0.037 0.056 -9999 0 -9999 0 0
PPARG -0.061 0.171 -9999 0 -0.402 4 4
HDAC8/hEST1B 0.034 0 -9999 0 -9999 0 0
UBE2I 0.017 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.017 0 -9999 0 -9999 0 0
TNFRSF1A -0.019 0.131 -9999 0 -0.472 2 2
HDAC3/SMRT (N-CoR2) -0.009 0.073 -9999 0 -9999 0 0
MBD3L2 -0.048 0.183 -9999 0 -0.566 3 3
ubiquitin-dependent protein catabolic process 0.006 0.097 -9999 0 -0.336 2 2
CREBBP 0.017 0 -9999 0 -9999 0 0
NuRD/MBD3/MBD3L2 Complex 0.024 0.087 -9999 0 -9999 0 0
HDAC1 -0.005 0.11 -9999 0 -0.566 1 1
HDAC3 -0.02 0.082 -9999 0 -9999 0 0
HDAC2 -0.005 0.11 -9999 0 -0.566 1 1
YY1 0.027 0 -9999 0 -9999 0 0
HDAC8 0.017 0 -9999 0 -9999 0 0
SMAD7 -0.005 0.11 -9999 0 -0.566 1 1
NCOR2 0.017 0 -9999 0 -9999 0 0
MXD1 0.017 0 -9999 0 -9999 0 0
STAT3 0.031 0 -9999 0 -9999 0 0
NFKB1 0.017 0 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.017 0 -9999 0 -9999 0 0
YY1/LSF/HDAC1 0.028 0.062 -9999 0 -0.291 1 1
YY1/SAP30/HDAC1 0.028 0.062 -9999 0 -0.291 1 1
EP300 0.017 0 -9999 0 -9999 0 0
STAT3 (dimer non-phopshorylated) 0.031 0 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.02 0.081 -9999 0 -9999 0 0
histone deacetylation 0.037 0.055 -9999 0 -9999 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.004 0.068 -9999 0 -9999 0 0
nuclear export -0.034 0 -9999 0 -9999 0 0
PRKACA 0.017 0 -9999 0 -9999 0 0
GATAD2B 0.017 0 -9999 0 -9999 0 0
GATAD2A 0.017 0 -9999 0 -9999 0 0
GATA2/HDAC3 -0.028 0.106 -9999 0 -0.396 1 1
GATA1/HDAC1 0.009 0.081 -9999 0 -0.406 1 1
GATA1/HDAC3 -0.009 0.073 -9999 0 -9999 0 0
CHD4 0.017 0 -9999 0 -9999 0 0
TNF-alpha/TNFR1A -0.084 0.16 -9999 0 -0.303 9 9
SIN3/HDAC complex/Mad/Max 0.041 0.054 -9999 0 -9999 0 0
NuRD Complex 0.044 0.063 -9999 0 -9999 0 0
positive regulation of chromatin silencing -0.012 0.093 -9999 0 -9999 0 0
SIN3B 0.017 0 -9999 0 -9999 0 0
MTA2 0.017 0 -9999 0 -9999 0 0
SIN3A 0.017 0 -9999 0 -9999 0 0
XPO1 0.017 0 -9999 0 -9999 0 0
SUMO1/HDAC1 0.026 0.058 -9999 0 -0.269 1 1
HDAC complex 0.018 0.089 -9999 0 -0.298 2 2
GATA1/Fog1 0.025 0 -9999 0 -9999 0 0
FKBP25/HDAC1/HDAC2 0.007 0.097 -9999 0 -0.337 2 2
TNF -0.1 0.201 -9999 0 -0.432 7 7
negative regulation of cell growth 0.041 0.054 -9999 0 -9999 0 0
NuRD/MBD2/PRMT5 Complex 0.037 0.056 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0.041 0 -9999 0 -9999 0 0
NF kappa B/RelA/I kappa B alpha -0.024 0.119 -9999 0 -0.31 3 3
SIN3/HDAC complex/NCoR1 0.037 0.058 -9999 0 -9999 0 0
TFCP2 0.017 0 -9999 0 -9999 0 0
NR2C1 0.017 0 -9999 0 -9999 0 0
MBD3 0.017 0 -9999 0 -9999 0 0
MBD2 0.002 0.075 -9999 0 -0.378 1 1
FoxO family signaling

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
G6PC 0.031 0.079 -9999 0 -9999 0 0
PLK1 0.049 0.159 -9999 0 -9999 0 0
CDKN1B 0.085 0.12 -9999 0 -9999 0 0
FOXO3 0.042 0.172 -9999 0 -0.526 1 1
KAT2B 0.004 0.02 -9999 0 -0.052 1 1
FOXO1/SIRT1 -0.004 0.072 -9999 0 -9999 0 0
CAT 0.018 0.285 -9999 0 -1.294 1 1
CTNNB1 -0.026 0.153 -9999 0 -0.566 2 2
AKT1 0.026 0.019 -9999 0 -9999 0 0
FOXO1 0.024 0.087 -9999 0 -9999 0 0
MAPK10 0.028 0.053 -9999 0 -9999 0 0
mol:GTP 0.002 0.002 -9999 0 -9999 0 0
FOXO4 0.098 0.055 -9999 0 -9999 0 0
response to oxidative stress 0.01 0.02 -9999 0 -0.045 1 1
FOXO3A/SIRT1 -0.033 0.13 -9999 0 -0.498 1 1
XPO1 0.017 0.001 -9999 0 -9999 0 0
EP300 0.02 0.001 -9999 0 -9999 0 0
BCL2L11 0.035 0.028 -9999 0 -9999 0 0
FOXO1/SKP2 0.028 0.079 -9999 0 -9999 0 0
mol:GDP 0.01 0.02 -9999 0 -0.045 1 1
RAN 0.018 0.002 -9999 0 -9999 0 0
GADD45A 0.046 0.214 -9999 0 -0.927 1 1
YWHAQ 0.017 0 -9999 0 -9999 0 0
FOXO1/14-3-3 family 0.074 0.038 -9999 0 -9999 0 0
MST1 0.006 0.074 -9999 0 -0.36 1 1
CSNK1D 0.017 0 -9999 0 -9999 0 0
CSNK1E 0.002 0.075 -9999 0 -0.378 1 1
FOXO4/14-3-3 family 0.06 0.044 -9999 0 -9999 0 0
YWHAB 0.017 0 -9999 0 -9999 0 0
MAPK8 0.043 0.014 -9999 0 -9999 0 0
MAPK9 0.042 0.013 -9999 0 -9999 0 0
YWHAG 0.002 0.075 -9999 0 -0.378 1 1
YWHAE 0.017 0 -9999 0 -9999 0 0
YWHAZ 0.017 0 -9999 0 -9999 0 0
SIRT1 0.014 0.009 -9999 0 -9999 0 0
SOD2 0.092 0.136 -9999 0 -9999 0 0
RBL2 0.073 0.119 -9999 0 -9999 0 0
RAL/GDP 0.034 0.017 -9999 0 -9999 0 0
CHUK 0.021 0.019 -9999 0 -9999 0 0
Ran/GTP 0.016 0.005 -9999 0 -9999 0 0
CSNK1G2 0.017 0 -9999 0 -9999 0 0
RAL/GTP 0.04 0.02 -9999 0 -9999 0 0
CSNK1G1 0.017 0 -9999 0 -9999 0 0
FASLG 0.011 0.095 -9999 0 -9999 0 0
SKP2 0.017 0 -9999 0 -9999 0 0
USP7 0.018 0.002 -9999 0 -9999 0 0
IKBKB 0.021 0.019 -9999 0 -9999 0 0
CCNB1 0.031 0.177 -9999 0 -9999 0 0
FOXO1-3a-4/beta catenin 0.102 0.144 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.028 0.078 -9999 0 -9999 0 0
CSNK1A1 0.017 0 -9999 0 -9999 0 0
SGK1 0.004 0.02 -9999 0 -0.052 1 1
CSNK1G3 0.017 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0.029 0.008 -9999 0 -9999 0 0
ZFAND5 0.1 0.05 -9999 0 -9999 0 0
SFN 0.017 0 -9999 0 -9999 0 0
CDK2 -0.051 0.177 -9999 0 -0.466 4 4
FOXO3A/14-3-3 0.061 0.05 -9999 0 -9999 0 0
CREBBP 0.021 0.001 -9999 0 -9999 0 0
FBXO32 -0.028 0.359 -9999 0 -0.982 3 3
BCL6 0.073 0.119 -9999 0 -9999 0 0
RALB 0.018 0.001 -9999 0 -9999 0 0
RALA 0.018 0.001 -9999 0 -9999 0 0
YWHAH 0.002 0.075 -9999 0 -0.378 1 1
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 -0.005 0.11 -9999 0 -0.566 1 1
HDAC3 0.017 0 -9999 0 -9999 0 0
VDR -0.026 0.153 -9999 0 -0.566 2 2
Cbp/p300/PCAF 0.023 0 -9999 0 -9999 0 0
EP300 0.017 0 -9999 0 -9999 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.047 0.013 -9999 0 -9999 0 0
KAT2B 0 0 -9999 0 -9999 0 0
MAPK14 0.017 0 -9999 0 -9999 0 0
AKT1 0.063 0.068 0.223 3 -9999 0 3
RAR alpha/9cRA/Cyclin H -0.023 0.049 -9999 0 -9999 0 0
mol:9cRA 0 0 -9999 0 -9999 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.043 0.013 -9999 0 -9999 0 0
CDC2 -0.12 0.236 -9999 0 -0.512 7 7
response to UV 0.002 0 -9999 0 -9999 0 0
RAR alpha/Jnk1 0.023 0.026 -9999 0 -9999 0 0
NCOR2 0.017 0 -9999 0 -9999 0 0
VDR/VDR/Vit D3 -0.019 0.112 -9999 0 -0.415 2 2
RXRs/RARs/NRIP1/9cRA 0.052 0.059 -9999 0 -9999 0 0
NCOA2 0.017 0 -9999 0 -9999 0 0
NCOA3 0.017 0 -9999 0 -9999 0 0
NCOA1 0.017 0 -9999 0 -9999 0 0
VDR/VDR/DNA -0.026 0.152 -9999 0 -0.565 2 2
RARG 0.018 0 -9999 0 -9999 0 0
RAR gamma1/9cRA 0.024 0 -9999 0 -9999 0 0
MAPK3 0.018 0 -9999 0 -9999 0 0
MAPK1 0.017 0 -9999 0 -9999 0 0
MAPK8 0.018 0 -9999 0 -9999 0 0
mol:Vit D3 0 0 -9999 0 -9999 0 0
RXRs/VDR/DNA/Vit D3 -0.007 0.101 -9999 0 -9999 0 0
RARA 0.028 0.033 -9999 0 -9999 0 0
negative regulation of phosphoinositide 3-kinase cascade 0 0 -9999 0 -9999 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.043 0.013 -9999 0 -9999 0 0
PRKCA 0.021 0 -9999 0 -9999 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 0.034 0.057 -9999 0 -9999 0 0
RXRG 0.01 0.064 -9999 0 -9999 0 0
RXRA -0.011 0.106 -9999 0 -0.326 1 1
RXRB 0.023 0.047 -9999 0 -9999 0 0
VDR/Vit D3/DNA -0.019 0.112 -9999 0 -0.415 2 2
RBP1 -0.107 0.214 -9999 0 -0.459 7 7
CRBP1/9-cic-RA -0.076 0.154 -9999 0 -0.328 7 7
RARB 0.02 0 -9999 0 -9999 0 0
PRKCG -0.008 0.104 -9999 0 -0.375 2 2
MNAT1 0.017 0 -9999 0 -9999 0 0
RAR alpha/RXRs 0.055 0.093 -9999 0 -9999 0 0
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.057 0.055 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.049 0.022 -9999 0 -9999 0 0
RXRs/RARs/NRIP1/9cRA/HDAC3 0.037 0.057 -9999 0 -9999 0 0
positive regulation of DNA binding -0.022 0.047 -9999 0 -9999 0 0
NRIP1 0.04 0.05 -9999 0 -9999 0 0
RXRs/RARs 0.033 0.054 -9999 0 -9999 0 0
RXRs/RXRs/DNA/9cRA 0.004 0.084 -9999 0 -9999 0 0
PRKACA 0.017 0 -9999 0 -9999 0 0
CDK7 0.017 0 -9999 0 -9999 0 0
TFIIH 0.034 0 -9999 0 -9999 0 0
RAR alpha/9cRA -0.002 0.007 -9999 0 -9999 0 0
CCNH 0.017 0 -9999 0 -9999 0 0
CREBBP 0.017 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 0.017 0 -9999 0 -9999 0 0
Rac1/GDP 0.005 0.014 -9999 0 -9999 0 0
DOCK1 0.017 0 -9999 0 -9999 0 0
ITGA4 -0.034 0.147 -9999 0 -0.441 3 3
RAC1 0.017 0 -9999 0 -9999 0 0
alpha4/beta7 Integrin -0.011 0.106 -9999 0 -0.303 3 3
mol:GTP 0 0 -9999 0 -9999 0 0
CRK 0.017 0 -9999 0 -9999 0 0
alpha4/beta1 Integrin 0.003 0.091 -9999 0 -0.337 1 1
alpha4/beta7 Integrin/Paxillin 0.013 0.082 -9999 0 -0.298 1 1
lamellipodium assembly -0.009 0.076 -9999 0 -0.387 1 1
PIK3CA 0.017 0 -9999 0 -9999 0 0
PI3K 0.009 0.081 -9999 0 -0.406 1 1
ARF6 0.017 0 -9999 0 -9999 0 0
TLN1 0.017 0 -9999 0 -9999 0 0
PXN 0.026 0 -9999 0 -9999 0 0
PIK3R1 -0.005 0.11 -9999 0 -0.566 1 1
ARF6/GTP -0.019 0.056 -9999 0 -9999 0 0
cell adhesion 0.021 0.077 -9999 0 -9999 0 0
CRKL/CBL 0.025 0 -9999 0 -9999 0 0
alpha4/beta1 Integrin/Paxillin 0.013 0.082 -9999 0 -0.298 1 1
ITGB1 0.017 0 -9999 0 -9999 0 0
ITGB7 0.017 0 -9999 0 -9999 0 0
ARF6/GDP 0.005 0.014 -9999 0 -9999 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.152 0.16 -9999 0 -0.454 2 2
p130Cas/Crk/Dock1 0.034 0 -9999 0 -9999 0 0
VCAM1 -0.308 0.259 -9999 0 -0.5 17 17
alpha4/beta1 Integrin/Paxillin/Talin 0.023 0.078 -9999 0 -9999 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.023 0.078 -9999 0 -9999 0 0
BCAR1 0.017 0 -9999 0 -9999 0 0
mol:GDP -0.021 0.077 -9999 0 -9999 0 0
CBL 0.017 0 -9999 0 -9999 0 0
PRKACA 0.017 0 -9999 0 -9999 0 0
GIT1 0.017 0 -9999 0 -9999 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.023 0.078 -9999 0 -9999 0 0
Rac1/GTP -0.011 0.084 -9999 0 -0.428 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 0.025 0 -9999 0 -9999 0 0
FBXW11 0.017 0 -9999 0 -9999 0 0
NF kappa B1 p50/c-Rel 0.032 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.033 0.06 -9999 0 -9999 0 0
NFKBIA 0.008 0.067 -9999 0 -9999 0 0
MAPK14 0.017 0 -9999 0 -9999 0 0
NF kappa B1 p105/p50 0.032 0 -9999 0 -9999 0 0
ARRB2 0.02 0 -9999 0 -9999 0 0
REL 0.017 0 -9999 0 -9999 0 0
response to oxidative stress 0 0 -9999 0 -9999 0 0
BCL3/NF kappa B1 p50 0.032 0 -9999 0 -9999 0 0
response to UV 0 0 -9999 0 -9999 0 0
NF kappa B1 p105/RelA 0.032 0 -9999 0 -9999 0 0
PIK3CA 0.017 0 -9999 0 -9999 0 0
NF kappa B1 p50 dimer 0.024 0 -9999 0 -9999 0 0
PIK3R1 -0.005 0.11 -9999 0 -0.566 1 1
NFKB1 0.026 0 -9999 0 -9999 0 0
RELA 0.017 0 -9999 0 -9999 0 0
positive regulation of anti-apoptosis 0.017 0.065 -9999 0 -9999 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.038 0.059 -9999 0 -9999 0 0
SRC 0.017 0 -9999 0 -9999 0 0
PI3K 0.009 0.081 -9999 0 -0.406 1 1
NF kappa B1 p50/RelA 0.017 0.065 -9999 0 -9999 0 0
IKBKB 0.017 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.017 0 -9999 0 -9999 0 0
SYK -0.056 0.177 -9999 0 -0.472 4 4
I kappa B alpha/PIK3R1 0.006 0.108 -9999 0 -0.482 1 1
cell death 0.036 0.057 -9999 0 -9999 0 0
NF kappa B1 p105/c-Rel 0.032 0 -9999 0 -9999 0 0
LCK 0.017 0 -9999 0 -9999 0 0
BCL3 0.017 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 0.055 0.051 -9999 0 -9999 0 0
UGCG 0.027 0.023 -9999 0 -9999 0 0
AKT1/mTOR/p70S6K/Hsp90/TERT 0.036 0.113 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
mol:glucosylceramide 0.027 0.023 -9999 0 -9999 0 0
mol:DAG -0.002 0.015 -9999 0 -9999 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.037 0.104 -9999 0 -0.353 2 2
FRAP1 0.056 0.135 -9999 0 -0.406 1 1
FOXO3 0.062 0.107 -9999 0 -9999 0 0
AKT1 0.056 0.112 -9999 0 -0.347 1 1
GAB2 0.017 0.004 -9999 0 -9999 0 0
SMPD1 0.022 0.043 -9999 0 -9999 0 0
SGMS1 0.022 0.043 -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 0.069 -9999 0 -0.342 1 1
CALM1 -0.005 0.11 -9999 0 -0.566 1 1
cell proliferation 0.039 0.069 -9999 0 -0.235 1 1
EIF3A 0.017 0 -9999 0 -9999 0 0
PI3K 0.014 0.082 -9999 0 -0.403 1 1
RPS6KB1 0.017 0.041 -9999 0 -9999 0 0
mol:sphingomyelin -0.002 0.015 -9999 0 -9999 0 0
natural killer cell activation 0 0.003 -9999 0 -0.012 1 1
JAK3 0.02 0.003 -9999 0 -9999 0 0
PIK3R1 -0.002 0.11 -9999 0 -0.564 1 1
JAK1 0.005 0.074 -9999 0 -0.374 1 1
NFKB1 0.017 0 -9999 0 -9999 0 0
MYC 0.039 0.207 -9999 0 -0.951 1 1
MYB -0.021 0.144 -9999 0 -9999 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.059 0.078 -9999 0 -9999 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.024 0.072 -9999 0 -9999 0 0
mol:PI-3-4-5-P3 0.058 0.077 -9999 0 -9999 0 0
Rac1/GDP 0.019 0.064 -9999 0 -0.302 1 1
T cell proliferation 0.056 0.074 -9999 0 -9999 0 0
SHC1 0.017 0.004 -9999 0 -9999 0 0
RAC1 0.017 0 -9999 0 -9999 0 0
positive regulation of cyclin-dependent protein kinase activity 0.001 0.014 -9999 0 -0.032 4 4
PRKCZ 0.056 0.075 -9999 0 -9999 0 0
NF kappa B1 p50/RelA 0.066 0.121 -9999 0 -9999 0 0
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.048 0.056 -9999 0 -9999 0 0
HSP90AA1 0.017 0 -9999 0 -9999 0 0
RELA 0.017 0 -9999 0 -9999 0 0
IL2RA -0.013 0.105 -9999 0 -0.382 2 2
IL2RB 0.005 0.074 -9999 0 -0.374 1 1
TERT -0.048 0.183 -9999 0 -0.566 3 3
E2F1 -0.008 0.102 -9999 0 -0.304 2 2
SOS1 0.017 0.004 -9999 0 -9999 0 0
RPS6 -0.005 0.11 -9999 0 -0.566 1 1
mol:cAMP -0.001 0.007 0.016 4 -9999 0 4
PTPN11 0.017 0.004 -9999 0 -9999 0 0
IL2RG 0.02 0.003 -9999 0 -9999 0 0
actin cytoskeleton organization 0.056 0.074 -9999 0 -9999 0 0
GRB2 0.017 0.004 -9999 0 -9999 0 0
IL2 0.005 0.074 -9999 0 -0.374 1 1
PIK3CA 0.019 0.004 -9999 0 -9999 0 0
Rac1/GTP 0.028 0.063 -9999 0 -0.285 1 1
LCK 0.02 0.003 -9999 0 -9999 0 0
BCL2 0.038 0.205 -9999 0 -0.874 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 0.023 0 -9999 0 -9999 0 0
response to insulin stimulus 0 0 -9999 0 -9999 0 0
RIPK1 0.017 0 -9999 0 -9999 0 0
response to stress 0 0 -9999 0 -9999 0 0
MAP2K6 0.017 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
MAP2K4 0.017 0 -9999 0 -9999 0 0
RAC1-CDC42/GTP/PAK family -0.039 0.109 -9999 0 -0.209 7 7
response to UV 0 0 -9999 0 -9999 0 0
YES1 -0.005 0.11 -9999 0 -0.566 1 1
interleukin-1 receptor activity 0 0 -9999 0 -9999 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -9999 0 0
MAP3K3 0.017 0 -9999 0 -9999 0 0
FYN 0.017 0 -9999 0 -9999 0 0
MAP3K12 0.017 0 -9999 0 -9999 0 0
FGR 0.017 0 -9999 0 -9999 0 0
p38 alpha/TAB1 0.037 0.104 -9999 0 -0.454 1 1
PRKG1 0.017 0 -9999 0 -9999 0 0
DUSP8 -0.005 0.11 -9999 0 -0.566 1 1
PGK/cGMP/p38 alpha -0.02 0.086 -9999 0 -0.44 1 1
apoptosis -0.009 0.089 -9999 0 -0.433 1 1
RAL/GTP 0.023 0 -9999 0 -9999 0 0
LYN 0.017 0 -9999 0 -9999 0 0
DUSP1 -0.034 0.147 -9999 0 -0.441 3 3
PAK1 -0.063 0.193 -9999 0 -0.519 4 4
SRC 0.017 0 -9999 0 -9999 0 0
RAC1/OSM/MEKK3/MKK3 0.043 0 -9999 0 -9999 0 0
TRAF6 0.017 0 -9999 0 -9999 0 0
RAC1 0.017 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 0.017 0 -9999 0 -9999 0 0
RAC1-CDC42/GTP 0.023 0 -9999 0 -9999 0 0
MAPK11 0.025 0.132 -9999 0 -0.586 1 1
BLK -0.005 0.11 -9999 0 -0.566 1 1
HCK -0.034 0.147 -9999 0 -0.441 3 3
MAP2K3 0.017 0 -9999 0 -9999 0 0
DUSP16 0.002 0.075 -9999 0 -0.378 1 1
DUSP10 -0.056 0.177 -9999 0 -0.472 4 4
TRAF6/MEKK3 0.022 0 -9999 0 -9999 0 0
MAP3K7IP1 0.017 0 -9999 0 -9999 0 0
MAPK14 0.031 0.112 -9999 0 -0.498 1 1
positive regulation of innate immune response 0.034 0.142 -9999 0 -0.628 1 1
LCK 0.017 0 -9999 0 -9999 0 0
p38alpha-beta/MKP7 0.036 0.137 -9999 0 -0.59 1 1
p38alpha-beta/MKP5 0.01 0.152 -9999 0 -0.59 1 1
PGK/cGMP 0.012 0 -9999 0 -9999 0 0
PAK2 0.017 0 -9999 0 -9999 0 0
p38alpha-beta/MKP1 0.02 0.152 -9999 0 -0.59 1 1
CDC42 0.017 0 -9999 0 -9999 0 0
RALB 0.017 0 -9999 0 -9999 0 0
RALA 0.017 0 -9999 0 -9999 0 0
PAK3 -0.084 0.214 -9999 0 -0.529 5 5
TCGA08_rtk_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
PDGFRA -0.092 0.208 -9999 0 -0.472 6 6
HRAS 0.017 0 -9999 0 -9999 0 0
EGFR -0.041 0.166 -9999 0 -0.503 3 3
AKT 0.022 0.052 -9999 0 -0.207 1 1
FOXO3 0.017 0 -9999 0 -9999 0 0
AKT1 0.017 0 -9999 0 -9999 0 0
FOXO1 0.017 0 -9999 0 -9999 0 0
AKT3 0.017 0 -9999 0 -9999 0 0
FOXO4 0.017 0 -9999 0 -9999 0 0
MET 0.002 0.075 -9999 0 -0.378 1 1
PIK3CA 0.017 0 -9999 0 -9999 0 0
PIK3CB 0.017 0 -9999 0 -9999 0 0
NRAS 0.017 0 -9999 0 -9999 0 0
PIK3CG -0.027 0.124 -9999 0 -0.378 3 3
PIK3R3 0.017 0 -9999 0 -9999 0 0
PIK3R2 0.017 0 -9999 0 -9999 0 0
NF1 0.017 0 -9999 0 -9999 0 0
RAS -0.019 0.092 -9999 0 -0.288 2 2
ERBB2 0.002 0.075 -9999 0 -0.378 1 1
proliferation/survival/translation -0.034 0.024 -9999 0 -9999 0 0
PI3K -0.013 0.08 -9999 0 -0.232 2 2
PIK3R1 -0.005 0.11 -9999 0 -0.566 1 1
KRAS 0.017 0 -9999 0 -9999 0 0
FOXO 0.035 0.036 -9999 0 -9999 0 0
AKT2 0.002 0.075 -9999 0 -0.378 1 1
PTEN 0.017 0 -9999 0 -9999 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 -0.005 0.11 -9999 0 -0.566 1 1
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -9999 0 0
MDM2/SUMO1 0.037 0 -9999 0 -9999 0 0
HDAC4 0.017 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 -0.008 0.043 -9999 0 -0.225 1 1
SUMO1 0.017 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1 0.02 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
XPO1 0.032 0 -9999 0 -9999 0 0
EntrezGene:23636 0 0 -9999 0 -9999 0 0
RAN 0.017 0 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.017 0 -9999 0 -9999 0 0
SUMO1/HDAC4 0.037 0 -9999 0 -9999 0 0
SUMO1/HDAC1 0.026 0.058 -9999 0 -0.269 1 1
RANGAP1 0.017 0 -9999 0 -9999 0 0
MDM2/SUMO1/SUMO1 0.043 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.025 0 -9999 0 -9999 0 0
Ran/GTP 0.032 0 -9999 0 -9999 0 0
EntrezGene:23225 0 0 -9999 0 -9999 0 0
MDM2 0.017 0 -9999 0 -9999 0 0
UBE2I 0.017 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0.039 0 -9999 0 -9999 0 0
NPC 0.01 0 -9999 0 -9999 0 0
PIAS2 0.017 0 -9999 0 -9999 0 0
PIAS1 0.017 0 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 0 0
Class I PI3K signaling events

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
ARF5/GTP 0 0 -9999 0 -9999 0 0
DAPP1 -0.003 0.122 -9999 0 -0.385 2 2
Src family/SYK family/BLNK-LAT/BTK-ITK -0.031 0.209 -9999 0 -0.559 3 3
mol:DAG 0.002 0.105 -9999 0 -0.257 2 2
HRAS 0.017 0 -9999 0 -9999 0 0
RAP1A 0.017 0 -9999 0 -9999 0 0
ARF5/GDP -0.022 0.141 -9999 0 -0.441 2 2
PLCG2 -0.049 0.16 -9999 0 -0.425 4 4
PLCG1 0.017 0 -9999 0 -9999 0 0
ARF5 0.017 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
ARF1/GTP 0 0 -9999 0 -9999 0 0
RHOA -0.005 0.11 -9999 0 -0.566 1 1
YES1 -0.005 0.11 -9999 0 -0.566 1 1
RAP1A/GTP 0.024 0 -9999 0 -9999 0 0
ADAP1 0 0 -9999 0 -9999 0 0
ARAP3 0 0 -9999 0 -9999 0 0
INPPL1 0.017 0 -9999 0 -9999 0 0
PREX1 -0.063 0.193 -9999 0 -0.519 4 4
ARHGEF6 0.017 0 -9999 0 -9999 0 0
ARHGEF7 -0.026 0.153 -9999 0 -0.566 2 2
ARF1 0.017 0 -9999 0 -9999 0 0
NRAS 0.017 0 -9999 0 -9999 0 0
FYN 0.017 0 -9999 0 -9999 0 0
ARF6 0.017 0 -9999 0 -9999 0 0
FGR 0.017 0 -9999 0 -9999 0 0
mol:Ca2+ 0.012 0.057 -9999 0 -9999 0 0
mol:IP4 0 0 -9999 0 -9999 0 0
TIAM1 -0.005 0.11 -9999 0 -0.566 1 1
ZAP70 0.017 0 -9999 0 -9999 0 0
mol:IP3 0.011 0.076 -9999 0 -0.186 1 1
LYN 0.017 0 -9999 0 -9999 0 0
ARF1/GDP -0.022 0.141 -9999 0 -0.441 2 2
RhoA/GDP 0 0.116 -9999 0 -0.547 1 1
PDK1/Src/Hsp90 0.034 0 -9999 0 -9999 0 0
BLNK -0.121 0.218 -9999 0 -0.449 8 8
actin cytoskeleton reorganization -0.013 0.156 -9999 0 -0.502 2 2
SRC 0.017 0 -9999 0 -9999 0 0
PLEKHA2 0.013 0.044 -9999 0 -0.21 1 1
RAC1 0.017 0 -9999 0 -9999 0 0
PTEN 0.013 0 -9999 0 -9999 0 0
HSP90AA1 0.017 0 -9999 0 -9999 0 0
ARF6/GTP 0 0 -9999 0 -9999 0 0
RhoA/GTP 0.02 0.055 -9999 0 -0.26 1 1
Src family/SYK family/BLNK-LAT -0.032 0.187 -9999 0 -0.497 3 3
BLK -0.005 0.11 -9999 0 -0.566 1 1
PDPK1 0.017 0 -9999 0 -9999 0 0
CYTH1 0 0 -9999 0 -9999 0 0
HCK -0.034 0.147 -9999 0 -0.441 3 3
CYTH3 0 0 -9999 0 -9999 0 0
CYTH2 0 0 -9999 0 -9999 0 0
KRAS 0.017 0 -9999 0 -9999 0 0
GO:0030676 0 0 -9999 0 -9999 0 0
FOXO3 0.037 0 -9999 0 -9999 0 0
SGK1 0 0 -9999 0 -9999 0 0
INPP5D 0 0 -9999 0 -9999 0 0
mol:GDP -0.033 0.147 -9999 0 -0.472 2 2
SOS1 0.017 0 -9999 0 -9999 0 0
SYK -0.056 0.177 -9999 0 -0.472 4 4
ARF6/GDP -0.02 0.061 -9999 0 -0.293 1 1
mol:PI-3-4-5-P3 0 0 -9999 0 -9999 0 0
ARAP3/RAP1A/GTP 0.024 0 -9999 0 -9999 0 0
VAV1 -0.07 0.187 -9999 0 -0.453 5 5
mol:PI-3-4-P2 0.013 0 -9999 0 -9999 0 0
RAS family/GTP/PI3K Class I 0.032 0 -9999 0 -9999 0 0
PLEKHA1 0.022 0 -9999 0 -9999 0 0
Rac1/GDP -0.022 0.141 -9999 0 -0.441 2 2
LAT 0.017 0 -9999 0 -9999 0 0
Rac1/GTP -0.042 0.19 -9999 0 -0.647 2 2
ITK -0.015 0.056 -9999 0 -0.261 1 1
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.007 0.14 -9999 0 -0.332 3 3
LCK 0.017 0 -9999 0 -9999 0 0
BTK -0.022 0.052 -9999 0 -9999 0 0
Arf6 trafficking events

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
SLC2A4 -0.113 0.225 -9999 0 -0.486 7 7
CLTC 0.034 0.013 -9999 0 -9999 0 0
calcium ion-dependent exocytosis 0.019 0.038 -9999 0 -9999 0 0
Dynamin 2/GTP 0.029 0 -9999 0 -9999 0 0
EXOC4 0.017 0 -9999 0 -9999 0 0
CD59 0.019 0.045 -9999 0 -9999 0 0
CPE -0.014 0.104 -9999 0 -0.301 3 3
CTNNB1 -0.026 0.153 -9999 0 -0.566 2 2
membrane fusion 0.017 0.04 -9999 0 -9999 0 0
CTNND1 0.036 0 -9999 0 -9999 0 0
DNM2 0.017 0 -9999 0 -9999 0 0
mol:PI-4-5-P2 0.03 0.021 -9999 0 -9999 0 0
TSHR -0.029 0.096 -9999 0 -0.21 6 6
INS 0.021 0.008 -9999 0 -9999 0 0
BIN1 0.017 0 -9999 0 -9999 0 0
mol:Choline 0.017 0.04 -9999 0 -9999 0 0
growth hormone secretagogue receptor activity 0 0 -9999 0 -9999 0 0
mol:GDP 0.022 0 -9999 0 -9999 0 0
membrane depolarization 0 0 -9999 0 -9999 0 0
ARF6 0.017 0 -9999 0 -9999 0 0
mol:Ca2+ 0.029 0 -9999 0 -9999 0 0
JUP 0.028 0.018 -9999 0 -9999 0 0
ASAP2/amphiphysin II 0.022 0 -9999 0 -9999 0 0
ARF6/GTP 0.012 0 -9999 0 -9999 0 0
CDH1 -0.065 0.101 -9999 0 -0.276 1 1
clathrin-independent pinocytosis 0.012 0 -9999 0 -9999 0 0
MAPK8IP3 0.017 0 -9999 0 -9999 0 0
positive regulation of endocytosis 0.012 0 -9999 0 -9999 0 0
EXOC2 0.017 0 -9999 0 -9999 0 0
substrate adhesion-dependent cell spreading 0.05 0 -9999 0 -9999 0 0
insulin receptor binding 0 0 -9999 0 -9999 0 0
SPAG9 0.017 0 -9999 0 -9999 0 0
regulation of calcium-dependent cell-cell adhesion 0.066 0.101 0.357 2 -9999 0 2
positive regulation of phagocytosis 0.022 0 -9999 0 -9999 0 0
ARF6/GTP/JIP3 0.023 0 -9999 0 -9999 0 0
ACAP1 0.017 0.032 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
CHRM2 -0.01 0.08 -9999 0 -0.276 1 1
clathrin heavy chain/ACAP1 0.035 0.025 -9999 0 -9999 0 0
JIP4/KLC1 0.032 0 -9999 0 -9999 0 0
EXOC1 0.017 0 -9999 0 -9999 0 0
exocyst 0.051 0 -9999 0 -9999 0 0
RALA/GTP 0.012 0 -9999 0 -9999 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.023 0 -9999 0 -9999 0 0
receptor recycling 0.012 0 -9999 0 -9999 0 0
CTNNA1 0.036 0 -9999 0 -9999 0 0
NME1 0.022 0 -9999 0 -9999 0 0
clathrin coat assembly 0.033 0.012 -9999 0 -9999 0 0
IL2RA 0.019 0.038 -9999 0 -9999 0 0
VAMP3 0.022 0 -9999 0 -9999 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.05 0.086 -9999 0 -0.233 4 4
EXOC6 0.017 0 -9999 0 -9999 0 0
PLD1 0.006 0.064 -9999 0 -0.274 1 1
PLD2 0.026 0 -9999 0 -9999 0 0
EXOC5 0.017 0 -9999 0 -9999 0 0
PIP5K1C 0.03 0.022 -9999 0 -9999 0 0
SDC1 0.028 0.018 -9999 0 -9999 0 0
ARF6/GDP 0.022 0 -9999 0 -9999 0 0
EXOC7 0.017 0 -9999 0 -9999 0 0
E-cadherin/beta catenin -0.068 0.104 -9999 0 -0.368 2 2
mol:Phosphatidic acid 0.017 0.04 -9999 0 -9999 0 0
endocytosis -0.021 0 -9999 0 -9999 0 0
SCAMP2 0.017 0 -9999 0 -9999 0 0
ADRB2 -0.022 0.123 -9999 0 -0.268 5 5
EXOC3 0.017 0 -9999 0 -9999 0 0
ASAP2 0 0 -9999 0 -9999 0 0
Dynamin 2/GDP 0.031 0 -9999 0 -9999 0 0
KLC1 0.017 0 -9999 0 -9999 0 0
AVPR2 0.029 0.056 -9999 0 -9999 0 0
RALA 0.017 0 -9999 0 -9999 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.056 0.095 -9999 0 -0.334 2 2
IGF1 pathway

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
NCK2 0.017 0 -9999 0 -9999 0 0
PTK2 0.017 0 -9999 0 -9999 0 0
CRKL 0.02 0.057 -9999 0 -0.272 1 1
GRB2/SOS1/SHC 0.034 0 -9999 0 -9999 0 0
HRAS 0.017 0 -9999 0 -9999 0 0
IRS1/Crk 0.021 0.058 -9999 0 -0.272 1 1
IGF-1R heterotetramer/IGF1/PTP1B 0.019 0.066 -9999 0 -0.315 1 1
AKT1 0.031 0.1 -9999 0 -0.478 1 1
BAD 0.037 0.094 -9999 0 -0.443 1 1
mol:GTP 0 0 -9999 0 -9999 0 0
CRK 0.02 0.057 -9999 0 -0.272 1 1
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.021 0.058 -9999 0 -0.273 1 1
RAF1 0.044 0.09 -9999 0 -0.413 1 1
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.032 0.056 -9999 0 -9999 0 0
YWHAZ 0.017 0 -9999 0 -9999 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.013 0.062 -9999 0 -0.305 1 1
PIK3CA 0.017 0 -9999 0 -9999 0 0
RPS6KB1 0.031 0.1 -9999 0 -0.478 1 1
GNB2L1 0.017 0 -9999 0 -9999 0 0
positive regulation of MAPKKK cascade 0.037 0.077 -9999 0 -0.357 1 1
PXN 0.017 0 -9999 0 -9999 0 0
PIK3R1 -0.005 0.11 -9999 0 -0.566 1 1
cell adhesion 0 0 -9999 0 -9999 0 0
GRB2/SOS1 0.025 0 -9999 0 -9999 0 0
HRAS/GTP -0.008 0.041 -9999 0 -9999 0 0
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.039 0.054 -9999 0 -9999 0 0
IGF-1R heterotetramer 0.015 0.014 -9999 0 -9999 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck 0.023 0.058 -9999 0 -0.273 1 1
Crk/p130 Cas/Paxillin 0.038 0.053 -9999 0 -9999 0 0
IGF1R 0.015 0.014 -9999 0 -9999 0 0
IGF1 -0.004 0.112 -9999 0 -0.575 1 1
IRS2/Crk 0.029 0.055 -9999 0 -9999 0 0
PI3K 0.021 0.111 -9999 0 -0.543 1 1
apoptosis -0.044 0.083 0.379 1 -9999 0 1
HRAS/GDP 0.012 0 -9999 0 -9999 0 0
PRKCD 0.005 0.142 -9999 0 -0.637 1 1
RAF1/14-3-3 E 0.051 0.079 -9999 0 -0.353 1 1
BAD/14-3-3 0.046 0.088 -9999 0 -0.403 1 1
PRKCZ 0.022 0.099 -9999 0 -0.485 1 1
Crk/p130 Cas/Paxillin/FAK1 -0.015 0.075 -9999 0 -0.398 1 1
PTPN1 0.017 0 -9999 0 -9999 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.027 0.079 -9999 0 -0.378 1 1
BCAR1 0.017 0 -9999 0 -9999 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.022 0.122 -9999 0 -0.319 2 2
mol:GDP 0 0 -9999 0 -9999 0 0
SOS1 0.017 0 -9999 0 -9999 0 0
IRS1/NCK2 0.021 0.057 -9999 0 -0.271 1 1
GRB10 -0.07 0.187 -9999 0 -0.453 5 5
PTPN11 0.02 0.057 -9999 0 -0.272 1 1
IRS1 0.011 0.062 -9999 0 -0.304 1 1
IRS2 0.02 0.057 -9999 0 -0.272 1 1
IGF-1R heterotetramer/IGF1 0.007 0.084 -9999 0 -0.421 1 1
GRB2 0.017 0 -9999 0 -9999 0 0
PDPK1 0.024 0.105 -9999 0 -0.511 1 1
YWHAE 0.017 0 -9999 0 -9999 0 0
PRKD1 0.034 0.075 -9999 0 -0.351 1 1
SHC1 0.017 0 -9999 0 -9999 0 0
Insulin Pathway

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
CBL/APS/CAP -0.005 0.026 -9999 0 -9999 0 0
TC10/GTP -0.01 0.036 -9999 0 -9999 0 0
Insulin Receptor/Insulin/IRS1/Shp2 0.046 0 -9999 0 -9999 0 0
HRAS 0.017 0 -9999 0 -9999 0 0
APS homodimer 0 0 -9999 0 -9999 0 0
GRB14 -0.107 0.214 -9999 0 -0.459 7 7
FOXO3 -0.008 0.014 -9999 0 -9999 0 0
AKT1 -0.003 0.106 -9999 0 -9999 0 0
INSR 0.019 0 -9999 0 -9999 0 0
Insulin Receptor/Insulin 0.054 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
GRB10 -0.07 0.187 -9999 0 -0.453 5 5
SORBS1 0.002 0.075 -9999 0 -0.378 1 1
CRK 0.017 0 -9999 0 -9999 0 0
PTPN1 0.046 0 -9999 0 -9999 0 0
CAV1 0.019 0.071 -9999 0 -0.284 1 1
CBL/APS/CAP/Crk-II/C3G 0.033 0.038 -9999 0 -9999 0 0
Insulin Receptor/Insulin/IRS1/NCK2 0.046 0 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
mol:PI-3-4-5-P3 -0.01 0.049 -9999 0 -9999 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.053 0 -9999 0 -9999 0 0
RPS6KB1 0.006 0.1 -9999 0 -9999 0 0
PARD6A 0.017 0 -9999 0 -9999 0 0
CBL 0.017 0 -9999 0 -9999 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -9999 0 0
DOK1 -0.045 0.216 -9999 0 -0.8 2 2
PIK3R1 -0.005 0.11 -9999 0 -0.566 1 1
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.039 0.066 -9999 0 -9999 0 0
HRAS/GTP 0 0 -9999 0 -9999 0 0
Insulin Receptor 0.019 0 -9999 0 -9999 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.053 0 -9999 0 -9999 0 0
PRKCI -0.033 0.107 -9999 0 -0.567 1 1
Insulin Receptor/Insulin/GRB14/PDK1 -0.052 0.086 -9999 0 -9999 0 0
SHC1 0.017 0 -9999 0 -9999 0 0
negative regulation of MAPKKK cascade -0.013 0.188 -9999 0 -0.676 2 2
PI3K 0.034 0.058 -9999 0 -9999 0 0
NCK2 0.017 0 -9999 0 -9999 0 0
RHOQ 0.002 0.075 -9999 0 -0.378 1 1
mol:H2O2 0 0 -9999 0 -9999 0 0
HRAS/GDP 0.012 0 -9999 0 -9999 0 0
AKT2 -0.009 0.107 -9999 0 -9999 0 0
PRKCZ -0.036 0.109 -9999 0 -0.574 1 1
SH2B2 0 0 -9999 0 -9999 0 0
SHC/SHIP 0.036 0 -9999 0 -9999 0 0
F2RL2 -0.041 0.166 -9999 0 -0.503 3 3
TRIP10 -0.005 0.11 -9999 0 -0.566 1 1
Insulin Receptor/Insulin/Shc 0.035 0 -9999 0 -9999 0 0
TC10/GTP/CIP4/Exocyst 0.001 0.081 -9999 0 -0.278 2 2
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.053 0 -9999 0 -9999 0 0
RAPGEF1 0.017 0 -9999 0 -9999 0 0
RASA1 0.017 0 -9999 0 -9999 0 0
NCK1 0.017 0 -9999 0 -9999 0 0
CBL/APS/CAP/Crk-II 0.025 0.04 -9999 0 -9999 0 0
TC10/GDP 0.002 0.052 -9999 0 -0.263 1 1
Insulin Receptor/Insulin/SHC/GRB10 -0.004 0.109 -9999 0 -0.304 2 2
INPP5D 0.027 0 -9999 0 -9999 0 0
SOS1 0.017 0 -9999 0 -9999 0 0
SGK1 -0.006 0.009 -9999 0 -9999 0 0
mol:cAMP 0 0 -9999 0 -9999 0 0
PTPN11 0.017 0 -9999 0 -9999 0 0
IRS1 0.017 0 -9999 0 -9999 0 0
p62DOK/RasGAP -0.013 0.191 -9999 0 -0.685 2 2
INS 0.019 0 -9999 0 -9999 0 0
mol:PI-3-4-P2 0.027 0 -9999 0 -9999 0 0
GRB2 0.017 0 -9999 0 -9999 0 0
EIF4EBP1 0.006 0.1 -9999 0 -9999 0 0
PTPRA 0.019 0 -9999 0 -9999 0 0
PIK3CA 0.017 0 -9999 0 -9999 0 0
TC10/GTP/CIP4 0.001 0.081 -9999 0 -0.278 2 2
PDPK1 0.017 0 -9999 0 -9999 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.046 0 -9999 0 -9999 0 0
Insulin Receptor/Insulin/IRS1 0.035 0 -9999 0 -9999 0 0
Insulin Receptor/Insulin/IRS3 0.028 0 -9999 0 -9999 0 0
Par3/Par6 -0.01 0.109 -9999 0 -0.28 3 3
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.014 0.093 -9999 0 -0.313 2 2
ER alpha/Gai/GDP/Gbeta gamma 0.027 0.111 -9999 0 -0.494 1 1
AKT1 0.031 0.057 -9999 0 -9999 0 0
PIK3CA 0.017 0 -9999 0 -9999 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K 0.027 0.058 -9999 0 -9999 0 0
mol:Ca2+ -0.023 0.162 -9999 0 -0.459 3 3
IGF1R 0.017 0 -9999 0 -9999 0 0
E2/ER alpha (dimer)/Striatin 0.014 0.044 -9999 0 -0.21 1 1
SHC1 0.017 0 -9999 0 -9999 0 0
apoptosis -0.031 0.056 -9999 0 -9999 0 0
RhoA/GTP -0.014 0.05 -9999 0 -9999 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.021 0.081 -9999 0 -0.401 1 1
regulation of stress fiber formation -0.03 0.065 -9999 0 -9999 0 0
E2/ERA-ERB (dimer) 0.014 0.044 -9999 0 -0.21 1 1
KRAS 0.017 0 -9999 0 -9999 0 0
G13/GTP 0.014 0.04 -9999 0 -0.188 1 1
pseudopodium formation 0.03 0.065 -9999 0 -9999 0 0
E2/ER alpha (dimer)/PELP1 0.014 0.044 -9999 0 -0.21 1 1
GRB2 0.017 0 -9999 0 -9999 0 0
GNG2 -0.019 0.131 -9999 0 -0.472 2 2
GNAO1 0.017 0 -9999 0 -9999 0 0
HRAS 0.017 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
mol:NO 0.043 0.069 -9999 0 -9999 0 0
E2/ER beta (dimer) 0.012 0 -9999 0 -9999 0 0
mol:GDP -0.005 0.024 -9999 0 -9999 0 0
mol:NADP 0.043 0.069 -9999 0 -9999 0 0
PIK3R1 -0.005 0.11 -9999 0 -0.566 1 1
mol:IP3 -0.025 0.169 -9999 0 -0.48 3 3
IGF-1R heterotetramer 0.017 0 -9999 0 -9999 0 0
PLCB1 -0.027 0.172 -9999 0 -0.5 3 3
PLCB2 -0.034 0.173 -9999 0 -0.5 3 3
IGF1 -0.005 0.11 -9999 0 -0.566 1 1
mol:L-citrulline 0.043 0.069 -9999 0 -9999 0 0
RHOA -0.005 0.11 -9999 0 -0.566 1 1
Gai/GDP 0.037 0.047 -9999 0 -9999 0 0
JNK cascade 0.012 0 -9999 0 -9999 0 0
BCAR1 0.017 0 -9999 0 -9999 0 0
ESR2 0.017 0 -9999 0 -9999 0 0
GNAQ 0 0 -9999 0 -9999 0 0
ESR1 0.002 0.075 -9999 0 -0.378 1 1
Gq family/GDP/Gbeta gamma -0.019 0.159 -9999 0 -0.51 2 2
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.042 0.032 -9999 0 -9999 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.021 0.081 -9999 0 -0.401 1 1
GNAZ 0.017 0 -9999 0 -9999 0 0
E2/ER alpha (dimer) 0.002 0.052 -9999 0 -0.263 1 1
STRN 0.017 0 -9999 0 -9999 0 0
GNAL -0.026 0.153 -9999 0 -0.566 2 2
PELP1 0.017 0 -9999 0 -9999 0 0
MAPK11 0.022 0 -9999 0 -9999 0 0
GNAI2 0.017 0 -9999 0 -9999 0 0
GNAI3 0.017 0 -9999 0 -9999 0 0
GNAI1 -0.005 0.11 -9999 0 -0.566 1 1
HBEGF 0.02 0.109 -9999 0 -0.422 1 1
cAMP biosynthetic process -0.026 0.076 -9999 0 -0.273 2 2
SRC 0.034 0.106 -9999 0 -0.463 1 1
PI3K 0.009 0.081 -9999 0 -0.406 1 1
GNB1 0.017 0 -9999 0 -9999 0 0
G13/GDP/Gbeta gamma -0.018 0.065 -9999 0 -9999 0 0
SOS1 0.017 0 -9999 0 -9999 0 0
IGF-1R heterotetramer/IGF1 -0.023 0.07 -9999 0 -0.318 1 1
Gs family/GTP -0.005 0.084 -9999 0 -0.277 2 2
EntrezGene:2778 0 0 -9999 0 -9999 0 0
RAS family/GTP 0.033 0 -9999 0 -9999 0 0
vasodilation 0.043 0.067 -9999 0 -9999 0 0
mol:DAG -0.025 0.169 -9999 0 -0.48 3 3
Gs family/GDP/Gbeta gamma -0.033 0.1 -9999 0 -0.442 1 1
MSN 0.031 0.068 -9999 0 -9999 0 0
Gq family/GTP -0.038 0.181 -9999 0 -0.533 3 3
mol:PI-3-4-5-P3 0.027 0.057 -9999 0 -9999 0 0
NRAS 0.017 0 -9999 0 -9999 0 0
mol:E2 0 0 -9999 0 -9999 0 0
cell adhesion -0.043 0.067 -9999 0 -9999 0 0
GRB2/SOS1 0.025 0 -9999 0 -9999 0 0
RhoA/GDP -0.013 0.049 -9999 0 -9999 0 0
NOS3 0.043 0.071 -9999 0 -9999 0 0
GNA11 0.017 0 -9999 0 -9999 0 0
MAPKKK cascade 0.056 0.061 -9999 0 -9999 0 0
E2/ER alpha (dimer)/PELP1/Src -0.022 0.085 -9999 0 -0.423 1 1
ruffle organization 0.03 0.065 -9999 0 -9999 0 0
ROCK2 0.037 0.059 -9999 0 -9999 0 0
GNA14 -0.063 0.193 -9999 0 -0.519 4 4
GNA15 -0.005 0.11 -9999 0 -0.566 1 1
GNA13 0.017 0 -9999 0 -9999 0 0
MMP9 -0.004 0.131 -9999 0 -0.43 1 1
MMP2 0.041 0.101 -9999 0 -0.43 1 1
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.039 0 -9999 0 -9999 0 0
VEGFR1 homodimer/NRP1 0.027 0 -9999 0 -9999 0 0
mol:DAG -0.002 0.104 -9999 0 -9999 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0.028 0.039 -9999 0 -9999 0 0
CaM/Ca2+ -0.005 0.11 -9999 0 -9999 0 0
HIF1A 0.027 0 -9999 0 -9999 0 0
GAB1 0.017 0 -9999 0 -9999 0 0
AKT1 0.012 0.108 -9999 0 -9999 0 0
PLCG1 -0.002 0.104 -9999 0 -9999 0 0
NOS3 0.014 0.119 -9999 0 -9999 0 0
CBL 0.017 0 -9999 0 -9999 0 0
mol:NO 0.015 0.116 -9999 0 -9999 0 0
FLT1 0.036 0 -9999 0 -9999 0 0
PGF -0.07 0.187 -9999 0 -0.453 5 5
VEGFR1 homodimer/NRP2/VEGFR121 0.04 0.04 -9999 0 -9999 0 0
CALM1 -0.005 0.11 -9999 0 -0.566 1 1
PIK3CA 0.017 0 -9999 0 -9999 0 0
eNOS/Hsp90 0.023 0.114 -9999 0 -9999 0 0
endothelial cell proliferation 0.006 0.104 -9999 0 -9999 0 0
mol:Ca2+ -0.002 0.103 -9999 0 -9999 0 0
MAPK3 0.014 0.092 -9999 0 -9999 0 0
MAPK1 0.014 0.092 -9999 0 -9999 0 0
PIK3R1 -0.005 0.11 -9999 0 -0.566 1 1
PLGF homodimer -0.07 0.187 -9999 0 -0.453 5 5
PRKACA 0.017 0 -9999 0 -9999 0 0
RP11-342D11.1 0 0 -9999 0 -9999 0 0
CAV1 -0.019 0.131 -9999 0 -0.472 2 2
VEGFA homodimer 0.002 0.075 -9999 0 -0.378 1 1
VEGFR1 homodimer/VEGFA homodimer 0.031 0.044 -9999 0 -9999 0 0
platelet activating factor biosynthetic process 0.021 0.089 -9999 0 -9999 0 0
PI3K -0.002 0.112 -9999 0 -9999 0 0
PRKCA 0.006 0.097 -9999 0 -9999 0 0
PRKCB -0.003 0.096 -9999 0 -9999 0 0
VEGFR1 homodimer/PLGF homodimer -0.014 0.115 -9999 0 -0.33 2 2
VEGFA 0.002 0.075 -9999 0 -0.378 1 1
VEGFB 0.017 0 -9999 0 -9999 0 0
mol:IP3 -0.002 0.104 -9999 0 -9999 0 0
RASA1 0.046 0 -9999 0 -9999 0 0
NRP2 0.017 0 -9999 0 -9999 0 0
VEGFR1 homodimer 0.036 0 -9999 0 -9999 0 0
VEGFB homodimer 0.017 0 -9999 0 -9999 0 0
NCK1 0.017 0 -9999 0 -9999 0 0
eNOS/Caveolin-1 0.007 0.144 -9999 0 -0.498 1 1
PTPN11 0.017 0 -9999 0 -9999 0 0
mol:PI-3-4-5-P3 -0.003 0.11 -9999 0 -9999 0 0
mol:L-citrulline 0.015 0.116 -9999 0 -9999 0 0
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.048 0.038 -9999 0 -9999 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.04 0.04 -9999 0 -9999 0 0
CD2AP 0.017 0 -9999 0 -9999 0 0
PI3K/GAB1 0.006 0.107 -9999 0 -9999 0 0
PDPK1 0.003 0.104 -9999 0 -9999 0 0
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.04 0.04 -9999 0 -9999 0 0
mol:NADP 0.015 0.116 -9999 0 -9999 0 0
HSP90AA1 0.017 0 -9999 0 -9999 0 0
ubiquitin-dependent protein catabolic process 0.047 0.037 -9999 0 -9999 0 0
VEGFR1 homodimer/NRP2 0.039 0 -9999 0 -9999 0 0
S1P3 pathway

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
PDGFRB 0.017 0 -9999 0 -9999 0 0
mol:S1P 0.002 0 -9999 0 -9999 0 0
S1P1/S1P/Gi 0.011 0.089 -9999 0 -9999 0 0
GNAO1 0.019 0 -9999 0 -9999 0 0
S1P/S1P3/G12/G13 0.025 0 -9999 0 -9999 0 0
AKT1 0.037 0.019 -9999 0 -9999 0 0
AKT3 0.051 0.031 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
PDGFB-D/PDGFRB 0.017 0 -9999 0 -9999 0 0
GNAI2 0.019 0 -9999 0 -9999 0 0
GNAI3 0.019 0 -9999 0 -9999 0 0
GNAI1 -0.003 0.11 -9999 0 -0.565 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 -0.048 0.183 -9999 0 -0.566 3 3
mol:Ca2+ 0.038 0.045 -9999 0 -9999 0 0
MAPK3 0.044 0.043 -9999 0 -9999 0 0
MAPK1 0.044 0.043 -9999 0 -9999 0 0
JAK2 0.006 0.08 -9999 0 -9999 0 0
CXCR4 -0.032 0.132 -9999 0 -0.258 6 6
FLT1 0.02 0 -9999 0 -9999 0 0
RhoA/GDP -0.003 0.081 -9999 0 -0.415 1 1
Rac1/GDP 0.012 0 -9999 0 -9999 0 0
SRC 0.044 0.043 -9999 0 -9999 0 0
S1P/S1P3/Gi 0.038 0.045 -9999 0 -9999 0 0
RAC1 0.017 0 -9999 0 -9999 0 0
RhoA/GTP 0.031 0.069 -9999 0 -0.249 1 1
VEGFA 0.006 0.075 -9999 0 -0.376 1 1
S1P/S1P2/Gi 0.033 0.045 -9999 0 -9999 0 0
VEGFR1 homodimer/VEGFA homodimer 0.024 0.053 -9999 0 -0.248 1 1
RHOA -0.005 0.11 -9999 0 -0.566 1 1
S1P/S1P3/Gq -0.022 0.124 -9999 0 -0.345 3 3
GNAQ 0 0 -9999 0 -9999 0 0
GNAZ 0.019 0 -9999 0 -9999 0 0
G12/G13 0.025 0 -9999 0 -9999 0 0
GNA14 -0.063 0.193 -9999 0 -0.519 4 4
GNA15 -0.005 0.11 -9999 0 -0.566 1 1
GNA12 0.017 0 -9999 0 -9999 0 0
GNA13 0.017 0 -9999 0 -9999 0 0
GNA11 0.017 0 -9999 0 -9999 0 0
Rac1/GTP 0.042 0.041 -9999 0 -9999 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.002 0.075 -9999 0 -0.378 1 1
oxygen homeostasis 0 0 -9999 0 -9999 0 0
TCEB2 0.017 0 -9999 0 -9999 0 0
TCEB1 0.017 0 -9999 0 -9999 0 0
HIF1A/p53 0.015 0.067 -9999 0 -9999 0 0
HIF1A 0.023 0.03 -9999 0 -9999 0 0
COPS5 0.017 0 -9999 0 -9999 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.05 0 -9999 0 -9999 0 0
FIH (dimer) 0.017 0 -9999 0 -9999 0 0
CDKN2A -0.164 0.243 -9999 0 -0.472 10 10
ARNT/IPAS 0.015 0.052 -9999 0 -0.252 1 1
HIF1AN 0.017 0 -9999 0 -9999 0 0
GNB2L1 0.017 0 -9999 0 -9999 0 0
HIF1A/ARNT 0.032 0.03 -9999 0 -9999 0 0
CUL2 0.017 0 -9999 0 -9999 0 0
OS9 0.017 0 -9999 0 -9999 0 0
RACK1/Elongin B/Elongin C 0.034 0 -9999 0 -9999 0 0
response to hypoxia 0 0 -9999 0 -9999 0 0
HIF1A/Hsp90 0.032 0.03 -9999 0 -9999 0 0
PHD1-3/OS9 0.002 0.102 -9999 0 -0.298 2 2
HIF1A/RACK1/Elongin B/Elongin C 0.046 0.027 -9999 0 -9999 0 0
VHL 0.017 0 -9999 0 -9999 0 0
HSP90AA1 0.017 0 -9999 0 -9999 0 0
HIF1A/JAB1 0.032 0.03 -9999 0 -9999 0 0
EGLN3 -0.056 0.177 -9999 0 -0.472 4 4
EGLN2 0.017 0 -9999 0 -9999 0 0
EGLN1 0.017 0 -9999 0 -9999 0 0
TP53 -0.019 0.131 -9999 0 -0.472 2 2
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.045 0.008 -9999 0 -9999 0 0
ARNT 0.017 0 -9999 0 -9999 0 0
ARD1A 0.017 0 -9999 0 -9999 0 0
RBX1 0.017 0 -9999 0 -9999 0 0
HIF1A/p19ARF -0.055 0.124 -9999 0 -0.306 1 1
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 -0.031 0.142 -9999 0 -0.339 1 1
PDGFB-D/PDGFRB/SLAP -0.056 0.152 -9999 0 -0.332 6 6
PDGFB-D/PDGFRB/APS/CBL 0.022 0.005 -9999 0 -9999 0 0
AKT1 0.01 0.105 -9999 0 -9999 0 0
mol:PI-4-5-P2 0 0 -9999 0 -9999 0 0
mol:Sphingosine-1-phosphate -0.01 0.12 -9999 0 -0.338 1 1
PIK3CA 0.017 0 -9999 0 -9999 0 0
FGR 0.006 0.048 -9999 0 -9999 0 0
mol:Ca2+ 0.025 0.046 -9999 0 -9999 0 0
MYC 0.013 0.175 -9999 0 -0.829 1 1
SHC1 0.017 0 -9999 0 -9999 0 0
HRAS/GDP 0.042 0.009 -9999 0 -9999 0 0
LRP1/PDGFRB/PDGFB 0.033 0.007 -9999 0 -9999 0 0
GRB10 -0.07 0.187 -9999 0 -0.453 5 5
PTPN11 0.017 0 -9999 0 -9999 0 0
GO:0007205 0.025 0.046 -9999 0 -9999 0 0
PTEN 0.017 0 -9999 0 -9999 0 0
GRB2 0.017 0 -9999 0 -9999 0 0
GRB7 0.017 0 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/SHP2 0.024 0.006 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/GRB10 -0.039 0.137 -9999 0 -0.408 2 2
cell cycle arrest -0.056 0.152 -9999 0 -0.331 6 6
HRAS 0.017 0 -9999 0 -9999 0 0
HIF1A 0.018 0.097 -9999 0 -9999 0 0
GAB1 0.014 0.08 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
DNM2 0.01 0.091 -9999 0 -9999 0 0
PDGFB-D/PDGFRB 0.027 0.018 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.008 0.081 -9999 0 -0.406 1 1
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.071 0.133 -9999 0 -0.433 1 1
positive regulation of MAPKKK cascade 0.024 0.006 -9999 0 -9999 0 0
PIK3R1 -0.005 0.11 -9999 0 -0.566 1 1
mol:IP3 0.025 0.046 -9999 0 -9999 0 0
E5 0 0.002 -9999 0 -9999 0 0
CSK 0.017 0.002 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/GRB7 0.024 0.006 -9999 0 -9999 0 0
SHB -0.005 0.11 -9999 0 -0.566 1 1
BLK -0.012 0.109 -9999 0 -0.51 1 1
PTPN2 0.017 0.004 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/SNX15 0.024 0.006 -9999 0 -9999 0 0
BCAR1 0.017 0 -9999 0 -9999 0 0
VAV2 0.013 0.097 -9999 0 -0.338 1 1
CBL 0.017 0 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/DEP1 0.014 0.053 -9999 0 -0.257 1 1
LCK 0.006 0.048 -9999 0 -9999 0 0
PDGFRB 0.016 0.005 -9999 0 -9999 0 0
ACP1 -0.005 0.11 -9999 0 -0.566 1 1
HCK -0.023 0.088 -9999 0 -0.409 1 1
ABL1 0.021 0.062 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/CBL 0.018 0.074 -9999 0 -9999 0 0
PTPN1 0.017 0.004 -9999 0 -9999 0 0
SNX15 0.017 0 -9999 0 -9999 0 0
STAT3 0.017 0 -9999 0 -9999 0 0
STAT1 0.002 0.075 -9999 0 -0.378 1 1
cell proliferation 0.016 0.155 -9999 0 -0.722 1 1
SLA -0.092 0.208 -9999 0 -0.472 6 6
actin cytoskeleton reorganization 0.044 0.057 -9999 0 -9999 0 0
SRC 0.007 0.048 -9999 0 -9999 0 0
PI3K -0.045 0.087 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/GRB7/SHC 0.033 0.007 -9999 0 -9999 0 0
SH2B2 0 0 -9999 0 -9999 0 0
PLCgamma1/SPHK1 -0.01 0.123 -9999 0 -0.347 1 1
LYN 0.006 0.048 -9999 0 -9999 0 0
LRP1 0.017 0 -9999 0 -9999 0 0
SOS1 0.017 0 -9999 0 -9999 0 0
STAT5B 0.017 0 -9999 0 -9999 0 0
STAT5A 0.017 0 -9999 0 -9999 0 0
NCK1-2/p130 Cas 0.038 0.025 -9999 0 -9999 0 0
SPHK1 -0.084 0.215 -9999 0 -0.529 5 5
EDG1 -0.048 0.183 -9999 0 -0.566 3 3
mol:DAG 0.025 0.046 -9999 0 -9999 0 0
PLCG1 0.025 0.047 -9999 0 -9999 0 0
NHERF/PDGFRB -0.031 0.136 -9999 0 -0.34 4 4
YES1 -0.015 0.084 -9999 0 -0.395 1 1
cell migration -0.031 0.136 -9999 0 -0.339 4 4
SHC/Grb2/SOS1 0.038 0.025 -9999 0 -9999 0 0
SLC9A3R2 -0.063 0.193 -9999 0 -0.519 4 4
SLC9A3R1 -0.005 0.11 -9999 0 -0.566 1 1
NHERF1-2/PDGFRB/PTEN -0.016 0.125 -9999 0 -0.3 4 4
FYN 0.007 0.047 -9999 0 -9999 0 0
DOK1 0.011 0.09 -9999 0 -0.305 2 2
HRAS/GTP 0.012 0 -9999 0 -9999 0 0
PDGFB 0.017 0 -9999 0 -9999 0 0
RAC1 0.018 0.124 -9999 0 -0.518 1 1
PRKCD 0.003 0.097 -9999 0 -0.306 2 2
FER 0.037 0.009 -9999 0 -9999 0 0
MAPKKK cascade 0 0 -9999 0 -9999 0 0
RASA1 0.037 0.009 -9999 0 -9999 0 0
NCK1 0.017 0 -9999 0 -9999 0 0
NCK2 0.017 0 -9999 0 -9999 0 0
p62DOK/Csk 0.022 0.084 -9999 0 -0.275 2 2
PDGFB-D/PDGFRB/SHB 0.008 0.082 -9999 0 -0.409 1 1
chemotaxis 0.021 0.061 -9999 0 -9999 0 0
STAT1-3-5/STAT1-3-5 -0.005 0.025 -9999 0 -9999 0 0
Bovine Papilomavirus E5/PDGFRB 0.011 0.006 -9999 0 -9999 0 0
PTPRJ 0.002 0.075 -9999 0 -0.378 1 1
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 0.017 0 -9999 0 -9999 0 0
CDC42/GTP 0.031 0.041 -9999 0 -9999 0 0
PLCG1 0.032 0.043 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
GNAI2 0.017 0 -9999 0 -9999 0 0
GNAI3 0.017 0 -9999 0 -9999 0 0
G12/G13 0.025 0 -9999 0 -9999 0 0
cell migration 0.03 0.041 -9999 0 -9999 0 0
S1PR5 0 0 -9999 0 -9999 0 0
S1PR4 0 0 -9999 0 -9999 0 0
MAPK3 0.032 0.043 -9999 0 -9999 0 0
MAPK1 0.032 0.043 -9999 0 -9999 0 0
S1P/S1P5/Gi 0.025 0.045 -9999 0 -9999 0 0
GNAI1 -0.005 0.11 -9999 0 -0.566 1 1
CDC42/GDP 0.012 0 -9999 0 -9999 0 0
S1P/S1P5/G12 0.011 0 -9999 0 -9999 0 0
RHOA 0.016 0.06 -9999 0 -0.289 1 1
S1P/S1P4/Gi 0.025 0.045 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
GNAZ 0.017 0 -9999 0 -9999 0 0
S1P/S1P4/G12/G13 0.022 0 -9999 0 -9999 0 0
GNA12 0.017 0 -9999 0 -9999 0 0
GNA13 0.017 0 -9999 0 -9999 0 0
CDC42 0.017 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 0.082 -9999 0 -0.289 2 2
TRAF2/ASK1 -0.004 0.097 -9999 0 -0.346 2 2
ATM 0.017 0 -9999 0 -9999 0 0
MAP2K3 0.023 0.081 -9999 0 -0.264 1 1
response to stress 0 0 -9999 0 -9999 0 0
MAP2K6 0.011 0.12 -9999 0 -0.4 2 2
hyperosmotic response 0 0 -9999 0 -9999 0 0
response to oxidative stress 0 0 -9999 0 -9999 0 0
GADD45G 0.017 0 -9999 0 -9999 0 0
TXN 0.01 0 -9999 0 -9999 0 0
CALM1 -0.005 0.11 -9999 0 -0.566 1 1
GADD45A -0.019 0.131 -9999 0 -0.472 2 2
GADD45B -0.12 0.236 -9999 0 -0.512 7 7
MAP3K1 0.002 0.075 -9999 0 -0.378 1 1
MAP3K6 0.017 0 -9999 0 -9999 0 0
MAP3K7 0.017 0 -9999 0 -9999 0 0
MAP3K4 0.017 0 -9999 0 -9999 0 0
mol:Ca2+ 0 0 -9999 0 -9999 0 0
ASK1/ASK2 -0.007 0.113 -9999 0 -0.406 2 2
TAK1/TAB family 0 0 -9999 0 -9999 0 0
RAC1/OSM/MEKK3 0.033 0 -9999 0 -9999 0 0
TRAF2 0.017 0 -9999 0 -9999 0 0
RAC1/OSM/MEKK3/MKK3 -0.013 0.049 -9999 0 -9999 0 0
TRAF6 0.02 0 -9999 0 -9999 0 0
RAC1 0.017 0 -9999 0 -9999 0 0
mol:LPS 0 0 -9999 0 -9999 0 0
CAMK2B -0.084 0.214 -9999 0 -0.529 5 5
CCM2 0.017 0 -9999 0 -9999 0 0
CaM/Ca2+/CAMKIIB -0.052 0.17 -9999 0 -0.426 4 4
MAPK11 0.017 0 -9999 0 -9999 0 0
response to DNA damage stimulus 0 0 -9999 0 -9999 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.06 0.206 -9999 0 -0.426 5 5
OSM/MEKK3 0.025 0 -9999 0 -9999 0 0
TAOK1 0.02 0 -9999 0 -9999 0 0
TAOK2 0.02 0 -9999 0 -9999 0 0
TAOK3 0.02 0 -9999 0 -9999 0 0
MAP3K7IP1 0.017 0 -9999 0 -9999 0 0
MAPK14 0.017 0 -9999 0 -9999 0 0
MAP3K7IP2 0.017 0 -9999 0 -9999 0 0
MAP3K5 -0.026 0.153 -9999 0 -0.566 2 2
MAP3K10 0.017 0 -9999 0 -9999 0 0
MAP3K3 0.017 0 -9999 0 -9999 0 0
TRX/ASK1 -0.007 0.094 -9999 0 -0.339 2 2
GADD45/MTK1/MTK1 -0.052 0.159 -9999 0 -0.34 5 5
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 -0.004 0.022 -9999 0 -9999 0 0
EntrezGene:79658 0 0 -9999 0 -9999 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.017 0.022 -9999 0 -9999 0 0
AP2 0.025 0 -9999 0 -9999 0 0
mol:DAG 0 0 -9999 0 -9999 0 0
Arfaptin 2/Rac/GTP 0.023 0 -9999 0 -9999 0 0
CLTB 0.002 0.075 -9999 0 -0.378 1 1
coatomer protein complex/ARF1/GTP/ER cargo protein 0.024 0.025 -9999 0 -9999 0 0
CD4 0.017 0 -9999 0 -9999 0 0
CLTA 0.017 0 -9999 0 -9999 0 0
mol:GTP 0.001 0 -9999 0 -9999 0 0
ARFGAP1 0.013 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 0.028 0.012 -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 -9999 0 -9999 0 0
ARF1/GDP 0.009 0 -9999 0 -9999 0 0
AP2M1 0.017 0 -9999 0 -9999 0 0
EntrezGene:1313 0 0 -9999 0 -9999 0 0
actin filament polymerization 0.019 0 -9999 0 -9999 0 0
Rac/GTP 0.013 0 -9999 0 -9999 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.03 0 -9999 0 -9999 0 0
ARFIP2 0.015 0 -9999 0 -9999 0 0
COPA 0.017 0 -9999 0 -9999 0 0
RAC1 0.017 0 -9999 0 -9999 0 0
ARF1/GTP/coatomer protein complex 0.025 0.015 -9999 0 -9999 0 0
ARF1/GTP/ARHGAP10 0.01 0 -9999 0 -9999 0 0
GGA3 0.017 0 -9999 0 -9999 0 0
ARF1/GTP/Membrin 0.018 0 -9999 0 -9999 0 0
AP2A1 0.017 0 -9999 0 -9999 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.027 0.021 -9999 0 -9999 0 0
ARF1/GDP/Membrin 0.02 0 -9999 0 -9999 0 0
Arfaptin 2/Rac/GDP 0.022 0 -9999 0 -9999 0 0
CYTH2 0.001 0 -9999 0 -9999 0 0
ARF1/GTP/GGA3 0.022 0 -9999 0 -9999 0 0
mol:ATP 0 0 -9999 0 -9999 0 0
Rac/GDP 0.012 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 0.037 0.021 -9999 0 -9999 0 0
PLD2 0 0 -9999 0 -9999 0 0
ARF-GAP1/v-SNARE 0.013 0 -9999 0 -9999 0 0
PIP5K1A 0 0 -9999 0 -9999 0 0
ARF1/GTP/Membrin/GBF1/p115 -0.003 0.016 -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 0.013 0 -9999 0 -9999 0 0
GOSR2 0.015 0 -9999 0 -9999 0 0
USO1 0.015 0 -9999 0 -9999 0 0
GBF1 -0.001 0.082 -9999 0 -0.417 1 1
ARF1/GTP/Arfaptin 2 0.023 0 -9999 0 -9999 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.034 0 -9999 0 -9999 0 0
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 0.015 0.052 -9999 0 -0.252 1 1
FBXW11 0.017 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 0.017 0 -9999 0 -9999 0 0
CHUK 0.017 0 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.031 0.071 -9999 0 -9999 0 0
NFKB1 0.017 0 -9999 0 -9999 0 0
MAP3K14 0.002 0.075 -9999 0 -0.378 1 1
NF kappa B1 p50/RelB 0.009 0.081 -9999 0 -0.406 1 1
RELB -0.005 0.11 -9999 0 -0.566 1 1
NFKB2 0.017 0 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.009 0.07 -9999 0 -0.346 1 1
regulation of B cell activation 0.009 0.069 -9999 0 -0.345 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 0.011 0.082 -9999 0 -0.406 1 1
SMARCC1 0.017 0.018 -9999 0 -9999 0 0
REL 0.016 0 -9999 0 -9999 0 0
HDAC7 0.044 0.044 -9999 0 -9999 0 0
JUN -0.04 0.166 -9999 0 -0.503 3 3
EP300 0.017 0 -9999 0 -9999 0 0
KAT2B 0 0 -9999 0 -9999 0 0
KAT5 0 0 -9999 0 -9999 0 0
MAPK14 0.031 0.007 -9999 0 -9999 0 0
FOXO1 0.017 0 -9999 0 -9999 0 0
T-DHT/AR 0.056 0.05 -9999 0 -9999 0 0
MAP2K6 0.019 0.003 -9999 0 -9999 0 0
BRM/BAF57 0.027 0 -9999 0 -9999 0 0
MAP2K4 0.019 0.003 -9999 0 -9999 0 0
SMARCA2 0.018 0 -9999 0 -9999 0 0
PDE9A 0.002 0.062 -9999 0 -9999 0 0
NCOA2 0.018 0 -9999 0 -9999 0 0
CEBPA -0.041 0.166 -9999 0 -0.504 3 3
EHMT2 0.017 0 -9999 0 -9999 0 0
cell proliferation 0.073 0.065 -9999 0 -9999 0 0
NR0B1 -0.308 0.259 -9999 0 -0.5 17 17
EGR1 -0.213 0.265 -9999 0 -0.502 12 12
RXRs/9cRA 0.019 0.056 -9999 0 -9999 0 0
AR/RACK1/Src 0.051 0.033 -9999 0 -9999 0 0
AR/GR -0.007 0.084 -9999 0 -9999 0 0
GNB2L1 0.017 0 -9999 0 -9999 0 0
PKN1 0.017 0 -9999 0 -9999 0 0
RCHY1 -0.005 0.11 -9999 0 -0.566 1 1
epidermal growth factor receptor activity 0.001 0 -9999 0 -9999 0 0
MAPK8 0.031 0.007 -9999 0 -9999 0 0
T-DHT/AR/TIF2/CARM1 0.053 0.035 -9999 0 -9999 0 0
SRC 0.052 0.014 -9999 0 -9999 0 0
NR3C1 0.017 0 -9999 0 -9999 0 0
KLK3 0 0.085 -9999 0 -9999 0 0
APPBP2 0.018 0.003 -9999 0 -9999 0 0
TRIM24 -0.004 0.11 -9999 0 -0.565 1 1
T-DHT/AR/TIP60 -0.004 0.014 -9999 0 -9999 0 0
TMPRSS2 -0.026 0.109 -9999 0 -9999 0 0
RXRG -0.012 0.103 -9999 0 -0.378 2 2
mol:9cRA 0 0 -9999 0 -9999 0 0
RXRA 0.017 0 -9999 0 -9999 0 0
RXRB 0.017 0 -9999 0 -9999 0 0
CARM1 0.017 0 -9999 0 -9999 0 0
NR2C2 0.017 0 -9999 0 -9999 0 0
KLK2 0.068 0.029 -9999 0 -9999 0 0
AR -0.016 0.095 -9999 0 -0.236 3 3
SENP1 0.017 0 -9999 0 -9999 0 0
HSP90AA1 0.017 0 -9999 0 -9999 0 0
MDM2 0.015 0 -9999 0 -9999 0 0
SRY -0.059 0.177 -9999 0 -0.474 4 4
GATA2 -0.019 0.131 -9999 0 -0.472 2 2
MYST2 0.017 0 -9999 0 -9999 0 0
HOXB13 0.004 0.075 -9999 0 -0.376 1 1
T-DHT/AR/RACK1/Src 0.047 0.034 -9999 0 -9999 0 0
positive regulation of transcription -0.019 0.13 -9999 0 -0.471 2 2
DNAJA1 0.018 0.003 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.081 -9999 0 -0.317 1 1
NCOA1 0.022 0.002 -9999 0 -9999 0 0
SPDEF 0.019 0 -9999 0 -9999 0 0
T-DHT/AR/TIF2 0.045 0.029 -9999 0 -9999 0 0
T-DHT/AR/Hsp90 0.036 0.035 -9999 0 -9999 0 0
GSK3B 0.018 0.002 -9999 0 -9999 0 0
NR2C1 0.016 0 -9999 0 -9999 0 0
mol:T-DHT 0.046 0.016 -9999 0 -9999 0 0
SIRT1 0.017 0 -9999 0 -9999 0 0
ZMIZ2 0.015 0 -9999 0 -9999 0 0
POU2F1 0.03 0.011 -9999 0 -9999 0 0
T-DHT/AR/DAX-1 -0.133 0.148 -9999 0 -0.31 7 7
CREBBP 0.017 0 -9999 0 -9999 0 0
SMARCE1 0.018 0 -9999 0 -9999 0 0
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/LGG/463526/1.GDAC_MergeDataFiles.Finished/LGG.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)