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 58 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 15
PLK2 and PLK4 events 12
HIF-1-alpha transcription factor network 12
Syndecan-1-mediated signaling events 10
Signaling events mediated by the Hedgehog family 10
Ephrin B reverse signaling 8
IL23-mediated signaling events 8
Signaling events mediated by Stem cell factor receptor (c-Kit) 8
Glypican 1 network 7
TCR signaling in naïve CD8+ T cells 7
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 15 120 8 -0.125 0.054 1000 -1000 -0.003 -1000
PLK2 and PLK4 events 12 36 3 -0.101 0.01 1000 -1000 -0.002 -1000
HIF-1-alpha transcription factor network 12 941 76 -0.402 0.026 1000 -1000 -0.05 -1000
Syndecan-1-mediated signaling events 10 348 34 -0.155 0.018 1000 -1000 -0.014 -1000
Signaling events mediated by the Hedgehog family 10 534 52 -0.239 0.074 1000 -1000 -0.018 -1000
Ephrin B reverse signaling 8 405 48 -0.221 0.037 1000 -1000 -0.016 -1000
IL23-mediated signaling events 8 499 60 -0.481 0.017 1000 -1000 -0.036 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 8 689 78 -0.274 0.111 1000 -1000 -0.033 -1000
Glypican 1 network 7 344 48 -0.109 0.022 1000 -1000 -0.012 -1000
TCR signaling in naïve CD8+ T cells 7 653 93 -0.112 0.026 1000 -1000 -0.037 -1000
IGF1 pathway 7 430 57 -0.115 0.048 1000 -1000 -0.051 -1000
FOXM1 transcription factor network 7 361 51 -0.437 0.018 1000 -1000 -0.132 -1000
IL12-mediated signaling events 6 564 87 -0.328 0.029 1000 -1000 -0.095 -1000
Osteopontin-mediated events 6 234 38 -0.138 0.017 1000 -1000 -0.029 -1000
Noncanonical Wnt signaling pathway 6 170 26 -0.091 0.019 1000 -1000 -0.025 -1000
Nectin adhesion pathway 6 411 63 -0.146 0.032 1000 -1000 -0.048 -1000
Wnt signaling 6 46 7 -0.091 0.004 1000 -1000 -0.011 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 6 411 68 -0.302 0.159 1000 -1000 -0.045 -1000
Plasma membrane estrogen receptor signaling 6 580 86 -0.19 0.175 1000 -1000 -0.049 -1000
IL4-mediated signaling events 5 534 91 -0.617 0.401 1000 -1000 -0.142 -1000
BMP receptor signaling 5 470 81 -0.19 0.037 1000 -1000 -0.05 -1000
Endothelins 5 486 96 -0.209 0.018 1000 -1000 -0.04 -1000
TCGA08_p53 5 39 7 -0.091 0.062 1000 -1000 -0.002 -1000
Nongenotropic Androgen signaling 5 279 52 -0.105 0.051 1000 -1000 -0.029 -1000
LPA receptor mediated events 5 540 102 -0.147 0.018 1000 -1000 -0.056 -1000
Caspase cascade in apoptosis 4 340 74 -0.059 0.047 1000 -1000 -0.022 -1000
FOXA2 and FOXA3 transcription factor networks 4 229 46 -0.197 0.053 1000 -1000 -0.031 -1000
FAS signaling pathway (CD95) 4 223 47 -0.125 0.046 1000 -1000 -0.023 -1000
Signaling mediated by p38-alpha and p38-beta 4 198 44 -0.102 0.017 1000 -1000 -0.016 -1000
Canonical Wnt signaling pathway 4 211 51 -0.168 0.1 1000 -1000 -0.029 -1000
EPHB forward signaling 4 386 85 -0.099 0.063 1000 -1000 -0.057 -1000
Glypican 2 network 4 18 4 -0.028 0 1000 -1000 0 -1000
IL27-mediated signaling events 4 224 51 -0.19 0.082 1000 -1000 -0.045 -1000
IL6-mediated signaling events 4 318 75 -0.099 0.04 1000 -1000 -0.031 -1000
Syndecan-4-mediated signaling events 4 325 67 -0.123 0.026 1000 -1000 -0.022 -1000
Visual signal transduction: Rods 4 223 52 -0.117 0.036 1000 -1000 -0.048 -1000
LPA4-mediated signaling events 3 40 12 -0.02 0.01 1000 -1000 -0.009 -1000
Regulation of nuclear SMAD2/3 signaling 3 430 136 -0.427 0.091 1000 -1000 -0.029 -1000
Coregulation of Androgen receptor activity 3 232 76 -0.158 0.036 1000 -1000 -0.022 -1000
Visual signal transduction: Cones 3 122 38 -0.044 0.023 1000 -1000 -0.006 -1000
Thromboxane A2 receptor signaling 3 353 105 -0.095 0.045 1000 -1000 -0.044 -1000
Syndecan-2-mediated signaling events 3 246 69 -0.097 0.033 1000 -1000 -0.009 -1000
Signaling events mediated by PTP1B 3 233 76 -0.195 0.036 1000 -1000 -0.033 -1000
Presenilin action in Notch and Wnt signaling 3 201 61 -0.168 0.052 1000 -1000 -0.025 -1000
p75(NTR)-mediated signaling 3 393 125 -0.162 0.05 1000 -1000 -0.052 -1000
PDGFR-alpha signaling pathway 3 154 44 -0.142 0.03 1000 -1000 -0.012 -1000
amb2 Integrin signaling 3 257 82 -0.087 0.025 1000 -1000 -0.041 -1000
Ceramide signaling pathway 3 273 76 -0.103 0.038 1000 -1000 -0.018 -1000
TRAIL signaling pathway 3 178 48 -0.044 0.017 1000 -1000 -0.021 -1000
IL1-mediated signaling events 3 243 62 -0.08 0.044 1000 -1000 -0.047 -1000
HIF-2-alpha transcription factor network 3 134 43 -0.073 0.036 1000 -1000 -0.047 -1000
S1P1 pathway 3 134 36 -0.122 0.017 1000 -1000 -0.049 -1000
Signaling mediated by p38-gamma and p38-delta 3 48 15 -0.032 0.018 1000 -1000 -0.011 -1000
Integrins in angiogenesis 3 283 84 -0.114 0.033 1000 -1000 -0.053 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 3 172 45 -0.088 0.017 1000 -1000 -0.052 -1000
VEGFR1 specific signals 3 187 56 -0.038 0.017 1000 -1000 -0.021 -1000
Regulation of Androgen receptor activity 3 268 70 -0.208 0.024 1000 -1000 -0.033 -1000
Ras signaling in the CD4+ TCR pathway 3 58 17 -0.045 0.025 1000 -1000 -0.019 -1000
JNK signaling in the CD4+ TCR pathway 2 49 17 -0.044 0.017 1000 -1000 -0.016 -1000
a4b1 and a4b7 Integrin signaling 2 14 5 -0.01 0.01 1000 -1000 -0.004 -1000
Cellular roles of Anthrax toxin 2 116 39 -0.075 0.017 1000 -1000 -0.012 -1000
Arf6 signaling events 2 157 62 -0.028 0.018 1000 -1000 -0.007 -1000
Hedgehog signaling events mediated by Gli proteins 2 192 65 -0.402 0.047 1000 -1000 -0.044 -1000
Fc-epsilon receptor I signaling in mast cells 2 270 97 -0.103 0.029 1000 -1000 -0.045 -1000
PLK1 signaling events 2 177 85 -0.042 0.025 1000 -1000 -0.03 -1000
mTOR signaling pathway 2 115 53 -0.038 0.03 1000 -1000 -0.037 -1000
IFN-gamma pathway 2 187 68 -0.063 0.026 1000 -1000 -0.054 -1000
Glucocorticoid receptor regulatory network 2 339 114 -0.251 0.139 1000 -1000 -0.048 -1000
Paxillin-independent events mediated by a4b1 and a4b7 2 85 37 -0.038 0.026 1000 -1000 -0.013 -1000
Signaling events mediated by HDAC Class III 2 93 40 -0.059 0.043 1000 -1000 -0.009 -1000
Reelin signaling pathway 2 165 56 -0.047 0.041 1000 -1000 -0.045 -1000
Signaling events regulated by Ret tyrosine kinase 2 169 82 -0.051 0.024 1000 -1000 -0.051 -1000
S1P5 pathway 2 36 17 -0.05 0.017 1000 -1000 -0.008 -1000
ceramide signaling pathway 2 142 49 -0.06 0.02 1000 -1000 -0.02 -1000
Retinoic acid receptors-mediated signaling 2 147 58 -0.108 0.045 1000 -1000 -0.052 -1000
Syndecan-3-mediated signaling events 2 100 35 -0.123 0.041 1000 -1000 -0.026 -1000
IL2 signaling events mediated by PI3K 2 173 58 -0.127 0.019 1000 -1000 -0.048 -1000
Calcium signaling in the CD4+ TCR pathway 2 77 31 -0.095 0.02 1000 -1000 -0.031 -1000
Signaling events mediated by VEGFR1 and VEGFR2 2 321 125 -0.04 0.03 1000 -1000 -0.058 -1000
Stabilization and expansion of the E-cadherin adherens junction 2 189 74 -0.103 0.039 1000 -1000 -0.059 -1000
IL2 signaling events mediated by STAT5 2 65 22 -0.093 0.023 1000 -1000 -0.025 -1000
Class I PI3K signaling events 2 211 73 -0.052 0.032 1000 -1000 -0.027 -1000
BCR signaling pathway 2 237 99 -0.065 0.04 1000 -1000 -0.053 -1000
EGFR-dependent Endothelin signaling events 2 62 21 -0.042 0.026 1000 -1000 -0.036 -1000
Signaling events mediated by PRL 2 85 34 -0.073 0.026 1000 -1000 -0.019 -1000
E-cadherin signaling in keratinocytes 2 91 43 -0.037 0.021 1000 -1000 -0.017 -1000
p38 MAPK signaling pathway 2 90 44 -0.04 0.034 1000 -1000 -0.043 -1000
Aurora B signaling 2 153 67 -0.061 0.021 1000 -1000 -0.027 -1000
Canonical NF-kappaB pathway 1 59 39 -0.036 0.043 1000 -1000 -0.049 -1000
Signaling events mediated by HDAC Class II 1 106 75 -0.099 0.04 1000 -1000 -0.026 -1000
BARD1 signaling events 1 96 57 -0.055 0.041 1000 -1000 -0.014 -1000
Sphingosine 1-phosphate (S1P) pathway 1 41 28 -0.05 0.026 1000 -1000 -0.011 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 1 80 54 -0.085 0.048 1000 -1000 -0.053 -1000
Ephrin A reverse signaling 1 8 7 0 0.019 1000 -1000 -0.007 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 1 141 85 -0.144 0.049 1000 -1000 -0.043 -1000
Aurora A signaling 1 108 60 -0.04 0.039 1000 -1000 -0.013 -1000
Arf6 downstream pathway 1 63 43 -0.022 0.026 1000 -1000 -0.011 -1000
EPO signaling pathway 1 99 55 -0.082 0.035 1000 -1000 -0.045 -1000
RXR and RAR heterodimerization with other nuclear receptor 1 92 52 -0.126 0.043 1000 -1000 -0.026 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 1 152 83 -0.079 0.052 1000 -1000 -0.021 -1000
FoxO family signaling 1 79 64 -0.057 0.061 1000 -1000 -0.024 -1000
Paxillin-dependent events mediated by a4b1 1 60 36 -0.038 0.035 1000 -1000 -0.02 -1000
Atypical NF-kappaB pathway 1 58 31 -0.038 0.03 1000 -1000 -0.009 -1000
Regulation of p38-alpha and p38-beta 1 85 54 -0.058 0.041 1000 -1000 -0.031 -1000
TCGA08_rtk_signaling 1 38 26 -0.038 0.052 1000 -1000 -0.007 -1000
E-cadherin signaling in the nascent adherens junction 1 126 76 -0.038 0.035 1000 -1000 -0.054 -1000
Regulation of Telomerase 1 197 102 -0.099 0.047 1000 -1000 -0.068 -1000
Insulin Pathway 1 144 74 -0.099 0.054 1000 -1000 -0.047 -1000
S1P3 pathway 1 70 42 -0.048 0.026 1000 -1000 -0.015 -1000
Angiopoietin receptor Tie2-mediated signaling 1 131 88 -0.099 0.045 1000 -1000 -0.054 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 1 53 33 -0.132 0.049 1000 -1000 -0.017 -1000
Rapid glucocorticoid signaling 1 20 20 -0.006 0.017 1000 -1000 -0.004 -1000
Neurotrophic factor-mediated Trk receptor signaling 1 202 120 -0.065 0.052 1000 -1000 -0.044 -1000
PDGFR-beta signaling pathway 1 189 97 -0.055 0.044 1000 -1000 -0.049 -1000
S1P4 pathway 1 41 25 -0.05 0.026 1000 -1000 -0.012 -1000
E-cadherin signaling events 1 9 5 0.002 0.021 1000 -1000 -0.003 -1000
ErbB2/ErbB3 signaling events 0 56 65 -0.042 0.04 1000 -1000 -0.039 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0 22 23 -0.014 0.037 1000 -1000 -0.014 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0 28 34 -0.014 0.04 1000 -1000 -0.017 -1000
ErbB4 signaling events 0 64 69 -0.058 0.05 1000 -1000 -0.058 -1000
Circadian rhythm pathway 0 16 22 -0.024 0.044 1000 -1000 -0.02 -1000
Aurora C signaling 0 5 7 0 0.021 1000 -1000 -0.008 -1000
Insulin-mediated glucose transport 0 24 32 -0.057 0.036 1000 -1000 -0.017 -1000
Class I PI3K signaling events mediated by Akt 0 42 68 -0.057 0.05 1000 -1000 -0.023 -1000
Signaling events mediated by HDAC Class I 0 96 104 -0.052 0.045 1000 -1000 -0.026 -1000
Effects of Botulinum toxin 0 15 26 -0.02 0.036 1000 -1000 -0.012 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 8 27 -0.006 0.042 1000 -1000 -0.033 -1000
Arf6 trafficking events 0 32 71 -0.032 0.042 1000 -1000 -0.037 -1000
Class IB PI3K non-lipid kinase events 0 0 3 -0.017 0.017 1000 -1000 -0.003 -1000
Arf1 pathway 0 2 54 -0.002 0.037 1000 -1000 -0.009 -1000
Alternative NF-kappaB pathway 0 6 13 0 0.044 1000 -1000 -0.005 -1000
Total 381 24728 7203 -13.8165449518 5.3405760665 131000 -131000 -4.06018898464 -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 -0.004 0.077 -9999 0 -0.318 3 3
CDKN2C -0.02 0.111 -9999 0 -0.283 8 8
CDKN2A -0.125 0.168 -9999 0 -0.316 23 23
CCND2 0.037 0.073 0.138 16 -9999 0 16
RB1 -0.04 0.087 0.134 1 -0.157 17 18
CDK4 0.054 0.087 0.174 17 -9999 0 17
CDK6 0.033 0.095 0.162 14 -0.168 3 17
G1/S progression 0.04 0.087 0.157 17 -0.134 1 18
PLK2 and PLK4 events

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
PLK2 -0.101 0.177 -9999 0 -0.358 17 17
PLK4 0.01 0.058 -9999 0 -0.411 1 1
regulation of centriole replication -0.065 0.127 -9999 0 -0.242 18 18
HIF-1-alpha 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
PKM2 -0.311 0.445 -9999 0 -0.809 18 18
HDAC7 -0.001 0.007 -9999 0 -9999 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.239 0.355 -9999 0 -0.737 10 10
SMAD4 0.003 0.081 -9999 0 -0.409 2 2
ID2 -0.314 0.447 -9999 0 -0.816 18 18
AP1 -0.075 0.142 -9999 0 -0.271 18 18
ABCG2 -0.325 0.456 -9999 0 -0.817 19 19
HIF1A -0.037 0.075 -9999 0 -9999 0 0
TFF3 -0.402 0.505 -9999 0 -0.886 24 24
GATA2 -0.019 0.105 -9999 0 -0.342 5 5
AKT1 -0.041 0.079 -9999 0 -0.216 1 1
response to hypoxia -0.061 0.08 -9999 0 -0.183 4 4
MCL1 -0.313 0.45 -9999 0 -0.815 18 18
NDRG1 -0.326 0.457 -9999 0 -0.827 19 19
SERPINE1 -0.316 0.456 -9999 0 -0.824 18 18
FECH -0.314 0.446 -9999 0 -0.799 19 19
FURIN -0.311 0.445 -9999 0 -0.809 18 18
NCOA2 0.019 0.002 -9999 0 -9999 0 0
EP300 -0.043 0.116 -9999 0 -0.332 3 3
HMOX1 -0.33 0.459 -9999 0 -0.83 19 19
BHLHE40 -0.325 0.438 -9999 0 -0.815 18 18
BHLHE41 -0.325 0.438 -9999 0 -0.815 18 18
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.014 0.125 -9999 0 -0.294 4 4
ENG -0.013 0.109 -9999 0 -0.285 2 2
JUN -0.028 0.125 -9999 0 -0.376 6 6
RORA -0.341 0.457 -9999 0 -0.831 19 19
ABCB1 -0.085 0.1 -9999 0 -0.45 2 2
TFRC -0.335 0.462 -9999 0 -0.847 19 19
CXCR4 -0.339 0.452 -9999 0 -0.82 19 19
TF -0.32 0.449 -9999 0 -0.809 19 19
CITED2 -0.313 0.45 -9999 0 -0.815 18 18
HIF1A/ARNT -0.355 0.511 -9999 0 -0.976 15 15
LDHA -0.102 0.279 -9999 0 -1.238 3 3
ETS1 -0.313 0.45 -9999 0 -0.815 18 18
PGK1 -0.315 0.45 -9999 0 -0.818 18 18
NOS2 -0.325 0.438 -9999 0 -0.815 18 18
ITGB2 -0.322 0.451 -9999 0 -0.824 18 18
ALDOA -0.311 0.445 -9999 0 -0.809 18 18
Cbp/p300/CITED2 -0.313 0.464 -9999 0 -0.927 13 13
FOS -0.081 0.166 -9999 0 -0.358 14 14
HK2 -0.311 0.445 -9999 0 -0.809 18 18
SP1 0.026 0.005 -9999 0 -9999 0 0
GCK -0.084 0.276 -9999 0 -1.31 2 2
HK1 -0.311 0.445 -9999 0 -0.809 18 18
NPM1 -0.311 0.445 -9999 0 -0.809 18 18
EGLN1 -0.314 0.448 -9999 0 -0.816 18 18
CREB1 0.024 0.006 -9999 0 -9999 0 0
PGM1 -0.311 0.445 -9999 0 -0.809 18 18
SMAD3 0.005 0.071 -9999 0 -0.353 2 2
EDN1 -0.153 0.292 -9999 0 -1.018 4 4
IGFBP1 -0.321 0.452 -9999 0 -0.826 18 18
VEGFA -0.214 0.326 -9999 0 -0.621 13 13
HIF1A/JAB1 -0.013 0.069 -9999 0 -0.341 1 1
CP -0.39 0.478 -9999 0 -0.858 22 22
CXCL12 -0.338 0.447 -9999 0 -0.817 19 19
COPS5 0.011 0.058 -9999 0 -0.41 1 1
SMAD3/SMAD4 0.007 0.075 -9999 0 -0.256 4 4
BNIP3 -0.342 0.474 -9999 0 -0.86 19 19
EGLN3 -0.343 0.478 -9999 0 -0.889 18 18
CA9 -0.365 0.482 -9999 0 -0.879 20 20
TERT -0.311 0.445 -9999 0 -0.809 18 18
ENO1 -0.311 0.445 -9999 0 -0.809 18 18
PFKL -0.311 0.445 -9999 0 -0.809 18 18
NCOA1 0.018 0 -9999 0 -9999 0 0
ADM -0.349 0.462 -9999 0 -0.843 18 18
ARNT -0.038 0.074 -9999 0 -9999 0 0
HNF4A 0.019 0.018 -9999 0 -9999 0 0
ADFP -0.349 0.473 -9999 0 -0.845 21 21
SLC2A1 -0.209 0.324 -9999 0 -0.613 13 13
LEP -0.316 0.442 -9999 0 -0.809 18 18
HIF1A/ARNT/Cbp/p300 -0.26 0.364 -9999 0 -0.75 11 11
EPO -0.144 0.274 -9999 0 -0.585 6 6
CREBBP -0.038 0.108 -9999 0 -0.318 2 2
HIF1A/ARNT/Cbp/p300/HDAC7 -0.25 0.353 -9999 0 -0.709 12 12
PFKFB3 -0.326 0.463 -9999 0 -0.845 18 18
NT5E -0.351 0.463 -9999 0 -0.797 23 23
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.017 0 -9999 0 -9999 0 0
CCL5 -0.049 0.142 -9999 0 -0.344 10 10
SDCBP 0.01 0.058 -9999 0 -0.411 1 1
FGFR/FGF2/Syndecan-1 -0.139 0.163 -9999 0 -0.339 16 16
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 -0.136 0.167 -9999 0 -0.33 18 18
Syndecan-1/Syntenin -0.129 0.163 -9999 0 -0.329 16 16
MAPK3 -0.109 0.168 -9999 0 -0.323 13 13
HGF/MET 0.018 0.042 -9999 0 -0.194 2 2
TGFB1/TGF beta receptor Type II 0.017 0 -9999 0 -9999 0 0
BSG 0.01 0.058 -9999 0 -0.411 1 1
keratinocyte migration -0.134 0.164 -9999 0 -0.326 18 18
Syndecan-1/RANTES -0.155 0.178 -9999 0 -0.344 19 19
Syndecan-1/CD147 -0.12 0.179 -9999 0 -0.322 16 16
Syndecan-1/Syntenin/PIP2 -0.124 0.157 -9999 0 -0.318 16 16
LAMA5 -0.006 0.098 -9999 0 -0.411 3 3
positive regulation of cell-cell adhesion -0.122 0.154 -9999 0 -0.312 16 16
MMP7 -0.154 0.195 -9999 0 -0.369 24 24
HGF 0.012 0.043 -9999 0 -0.3 1 1
Syndecan-1/CASK -0.133 0.155 -9999 0 -0.323 16 16
Syndecan-1/HGF/MET -0.118 0.153 -9999 0 -0.298 17 17
regulation of cell adhesion -0.104 0.165 -9999 0 -0.349 10 10
HPSE -0.016 0.106 -9999 0 -0.344 5 5
positive regulation of cell migration -0.139 0.163 -9999 0 -0.339 16 16
SDC1 -0.14 0.164 -9999 0 -0.341 16 16
Syndecan-1/Collagen -0.139 0.163 -9999 0 -0.339 16 16
PPIB 0.01 0.058 -9999 0 -0.411 1 1
MET 0.012 0.043 -9999 0 -0.3 1 1
PRKACA 0.017 0 -9999 0 -9999 0 0
MMP9 -0.087 0.171 -9999 0 -0.359 15 15
MAPK1 -0.112 0.17 -9999 0 -0.321 14 14
homophilic cell adhesion -0.138 0.162 -9999 0 -0.336 16 16
MMP1 -0.081 0.161 -9999 0 -0.337 15 15
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.168 0.228 -9999 0 -0.556 11 11
IHH -0.239 0.212 -9999 0 -0.398 33 33
SHH Np/Cholesterol/GAS1 -0.075 0.119 -9999 0 -0.226 16 16
LRPAP1 0.017 0 -9999 0 -9999 0 0
dorsoventral neural tube patterning 0.074 0.118 0.225 16 -9999 0 16
SMO/beta Arrestin2 -0.158 0.205 -9999 0 -0.427 15 15
SMO -0.173 0.214 -9999 0 -0.454 15 15
AKT1 -0.096 0.166 -9999 0 -0.564 4 4
ARRB2 0.017 0 -9999 0 -9999 0 0
BOC -0.03 0.113 -9999 0 -0.3 8 8
ADRBK1 0.017 0 -9999 0 -9999 0 0
heart looping -0.171 0.211 -9999 0 -0.448 15 15
STIL -0.125 0.163 -9999 0 -0.354 14 14
DHH N/PTCH2 0.026 0 -9999 0 -9999 0 0
DHH N/PTCH1 -0.12 0.152 -9999 0 -0.368 10 10
PIK3CA 0.01 0.058 -9999 0 -0.411 1 1
DHH 0.017 0 -9999 0 -9999 0 0
PTHLH -0.2 0.266 -9999 0 -0.639 11 11
determination of left/right symmetry -0.171 0.211 -9999 0 -0.448 15 15
PIK3R1 -0.038 0.134 -9999 0 -0.355 8 8
skeletal system development -0.199 0.263 -9999 0 -0.633 11 11
IHH N/Hhip -0.182 0.158 -9999 0 -0.304 29 29
DHH N/Hhip -0.032 0.111 -9999 0 -0.237 12 12
mol:Cholesterol 0 0 -9999 0 -9999 0 0
heart development -0.171 0.211 -9999 0 -0.448 15 15
pancreas development -0.065 0.157 -9999 0 -0.355 12 12
HHAT -0.052 0.156 -9999 0 -0.398 9 9
PI3K -0.018 0.112 -9999 0 -0.268 8 8
EntrezGene:84976 0 0 -9999 0 -9999 0 0
GAS1 -0.107 0.179 -9999 0 -0.355 18 18
somite specification -0.171 0.211 -9999 0 -0.448 15 15
SHH Np/Cholesterol/PTCH1 -0.131 0.164 -9999 0 -0.351 15 15
SHH Np/Cholesterol/PTCH2 -0.01 0.084 -9999 0 -0.204 8 8
SHH Np/Cholesterol/Megalin -0.021 0.096 -9999 0 -0.222 8 8
SHH -0.026 0.11 -9999 0 -0.27 9 9
catabolic process -0.145 0.17 -9999 0 -0.406 11 11
SMO/Vitamin D3 -0.153 0.195 -9999 0 -0.412 15 15
SHH Np/Cholesterol/Hhip -0.053 0.112 -9999 0 -0.22 13 13
LRP2 -0.006 0.083 -9999 0 -0.3 4 4
receptor-mediated endocytosis -0.144 0.189 -9999 0 -0.419 12 12
SHH Np/Cholesterol/BOC -0.033 0.11 -9999 0 -0.258 8 8
SHH Np/Cholesterol/CDO -0.021 0.096 -9999 0 -0.222 8 8
mesenchymal cell differentiation 0.053 0.111 0.219 13 -9999 0 13
mol:Vitamin D3 -0.131 0.165 -9999 0 -0.353 15 15
IHH N/PTCH2 -0.123 0.126 -9999 0 -0.251 23 23
CDON -0.006 0.083 -9999 0 -0.3 4 4
IHH N/PTCH1 -0.145 0.173 -9999 0 -0.41 11 11
Megalin/LRPAP1 0.01 0.058 -9999 0 -0.194 4 4
PTCH2 0.017 0 -9999 0 -9999 0 0
SHH Np/Cholesterol -0.019 0.083 -9999 0 -0.203 9 9
PTCH1 -0.145 0.17 -9999 0 -0.407 11 11
HHIP -0.065 0.157 -9999 0 -0.355 12 12
Ephrin B reverse signaling

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
EFNB2 -0.014 0.099 -9999 0 -0.322 5 5
EPHB2 -0.019 0.107 -9999 0 -0.319 6 6
EFNB1 -0.033 0.116 -9999 0 -0.26 11 11
mol:GTP 0 0 -9999 0 -9999 0 0
Rac1/GDP -0.031 0.116 -9999 0 -0.277 5 5
Ephrin B2/EPHB1-2 -0.027 0.121 -9999 0 -0.289 7 7
neuron projection morphogenesis -0.046 0.099 -9999 0 -0.266 5 5
Ephrin B1/EPHB1-2/Tiam1 -0.04 0.123 -9999 0 -0.301 5 5
DNM1 0.01 0.058 -9999 0 -0.412 1 1
cell-cell signaling 0.001 0.003 -9999 0 -9999 0 0
MAP2K4 -0.141 0.245 -9999 0 -0.531 15 15
YES1 -0.213 0.348 -9999 0 -0.769 15 15
Ephrin B1/EPHB1-2/NCK2 -0.036 0.116 -9999 0 -0.286 4 4
PI3K -0.167 0.25 -9999 0 -0.516 17 17
mol:GDP -0.04 0.121 -9999 0 -0.299 5 5
ITGA2B 0.012 0.043 -9999 0 -0.3 1 1
endothelial cell proliferation 0.001 0.067 -9999 0 -0.184 6 6
FYN -0.221 0.351 -9999 0 -0.747 16 16
MAP3K7 -0.156 0.259 -9999 0 -0.568 15 15
FGR -0.21 0.343 -9999 0 -0.758 15 15
TIAM1 0.01 0.058 -9999 0 -0.411 1 1
PIK3R1 -0.038 0.134 -9999 0 -0.355 8 8
RGS3 0.017 0 -9999 0 -9999 0 0
cell adhesion -0.164 0.233 -9999 0 -0.488 17 17
LYN -0.214 0.347 -9999 0 -0.769 15 15
Ephrin B1/EPHB1-2/Src Family Kinases -0.204 0.317 -9999 0 -0.711 15 15
Ephrin B1/EPHB1-2 -0.18 0.275 -9999 0 -0.619 15 15
SRC -0.21 0.343 -9999 0 -0.758 15 15
ITGB3 -0.026 0.113 -9999 0 -0.315 7 7
EPHB1 -0.037 0.125 -9999 0 -0.314 9 9
EPHB4 0.01 0.058 -9999 0 -0.411 1 1
RAC1 0.017 0 -9999 0 -9999 0 0
Ephrin B2/EPHB4 0.001 0.067 -9999 0 -0.185 6 6
alphaIIb/beta3 Integrin -0.008 0.09 -9999 0 -0.232 7 7
BLK -0.214 0.343 -9999 0 -0.731 16 16
HCK -0.22 0.347 -9999 0 -0.772 15 15
regulation of stress fiber formation 0.037 0.114 0.284 4 -9999 0 4
MAPK8 -0.136 0.232 -9999 0 -0.5 15 15
Ephrin B1/EPHB1-2/RGS3 -0.036 0.116 -9999 0 -0.286 4 4
endothelial cell migration -0.141 0.23 -9999 0 -0.461 17 17
NCK2 0.017 0 -9999 0 -9999 0 0
PTPN13 -0.157 0.243 -9999 0 -0.478 19 19
regulation of focal adhesion formation 0.037 0.114 0.284 4 -9999 0 4
chemotaxis 0.037 0.114 0.284 4 -9999 0 4
PIK3CA 0.01 0.058 -9999 0 -0.411 1 1
Rac1/GTP -0.034 0.11 -9999 0 -0.271 5 5
angiogenesis -0.179 0.273 -9999 0 -0.615 15 15
LCK -0.219 0.344 -9999 0 -0.735 16 16
IL23-mediated signaling events

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
CCL2 -0.379 0.417 -9999 0 -1.031 10 10
IL23A -0.439 0.462 -9999 0 -1.08 14 14
NF kappa B1 p50/RelA/I kappa B alpha -0.345 0.371 -9999 0 -0.808 16 16
positive regulation of T cell mediated cytotoxicity -0.363 0.385 -9999 0 -0.867 14 14
ITGA3 -0.381 0.421 -9999 0 -0.975 12 12
IL17F -0.239 0.262 -9999 0 -0.599 11 11
IL12B -0.002 0.027 -9999 0 -9999 0 0
STAT1 (dimer) -0.367 0.372 -9999 0 -0.821 16 16
CD4 -0.324 0.349 -9999 0 -0.827 9 9
IL23 -0.422 0.441 -9999 0 -1.035 14 14
IL23R -0.044 0.07 -9999 0 -9999 0 0
IL1B -0.419 0.445 -9999 0 -0.997 16 16
T-helper cell lineage commitment 0 0 -9999 0 -9999 0 0
IL24 -0.324 0.349 -9999 0 -0.795 12 12
TYK2 -0.001 0.019 -9999 0 -9999 0 0
STAT4 0.017 0 -9999 0 -9999 0 0
STAT3 0.01 0.058 -9999 0 -0.41 1 1
IL18RAP -0.033 0.122 -9999 0 -0.325 8 8
IL12RB1 -0.009 0.063 -9999 0 -0.444 1 1
PIK3CA 0.01 0.058 -9999 0 -0.411 1 1
IL12Rbeta1/TYK2 -0.006 0.05 -9999 0 -0.32 1 1
IL23R/JAK2 -0.059 0.092 -9999 0 -9999 0 0
positive regulation of chronic inflammatory response -0.363 0.385 -9999 0 -0.867 14 14
natural killer cell activation 0.004 0.006 -9999 0 -9999 0 0
JAK2 -0.014 0.065 -9999 0 -0.313 2 2
PIK3R1 -0.037 0.134 -9999 0 -0.355 8 8
NFKB1 0.015 0.003 -9999 0 -9999 0 0
RELA 0.015 0.003 -9999 0 -9999 0 0
positive regulation of dendritic cell antigen processing and presentation -0.404 0.417 -9999 0 -0.944 16 16
ALOX12B -0.324 0.349 -9999 0 -0.827 9 9
CXCL1 -0.467 0.51 -9999 0 -1.133 16 16
T cell proliferation -0.363 0.385 -9999 0 -0.867 14 14
NFKBIA 0.007 0.059 -9999 0 -0.42 1 1
IL17A -0.188 0.22 -9999 0 -0.494 8 8
PI3K -0.349 0.373 -9999 0 -0.853 14 14
IFNG -0.024 0.036 -9999 0 -0.097 2 2
STAT3 (dimer) -0.327 0.359 -9999 0 -0.81 14 14
IL18R1 0.011 0.045 -9999 0 -0.312 1 1
IL23/IL23R/JAK2/TYK2/SOCS3 -0.205 0.232 -9999 0 -0.637 4 4
IL18/IL18R -0.02 0.118 -9999 0 -0.239 9 9
macrophage activation -0.024 0.017 -9999 0 -0.045 14 14
TNF -0.398 0.414 -9999 0 -0.918 16 16
STAT3/STAT4 -0.332 0.355 -9999 0 -0.801 14 14
STAT4 (dimer) -0.346 0.371 -9999 0 -0.834 14 14
IL18 -0.024 0.118 -9999 0 -0.355 6 6
IL19 -0.411 0.43 -9999 0 -0.942 15 15
STAT5A (dimer) -0.346 0.371 -9999 0 -0.834 14 14
STAT1 -0.032 0.118 -9999 0 -0.313 8 8
SOCS3 -0.012 0.106 -9999 0 -0.383 4 4
CXCL9 -0.481 0.466 -9999 0 -1.034 17 17
MPO -0.329 0.351 -9999 0 -0.84 9 9
positive regulation of humoral immune response -0.363 0.385 -9999 0 -0.867 14 14
IL23/IL23R/JAK2/TYK2 -0.371 0.394 -9999 0 -0.889 14 14
IL6 -0.366 0.371 -9999 0 -0.847 14 14
STAT5A 0.017 0 -9999 0 -9999 0 0
IL2 0.011 0.058 -9999 0 -0.402 1 1
positive regulation of tyrosine phosphorylation of STAT protein 0.004 0.006 -9999 0 -9999 0 0
CD3E -0.324 0.349 -9999 0 -0.827 9 9
keratinocyte proliferation -0.363 0.385 -9999 0 -0.867 14 14
NOS2 -0.332 0.348 -9999 0 -0.785 14 14
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.093 0.168 -9999 0 -0.378 11 11
CRKL -0.104 0.177 -9999 0 -0.406 11 11
HRAS -0.071 0.157 -9999 0 -0.332 11 11
mol:PIP3 -0.094 0.165 0.269 1 -0.345 12 13
SPRED1 0.01 0.058 -9999 0 -0.411 1 1
SPRED2 0.017 0 -9999 0 -9999 0 0
GAB1 -0.115 0.186 -9999 0 -0.416 12 12
FOXO3 -0.089 0.17 -9999 0 -0.376 11 11
AKT1 -0.102 0.182 -9999 0 -0.41 11 11
BAD -0.091 0.172 -9999 0 -0.37 12 12
megakaryocyte differentiation -0.123 0.185 -9999 0 -0.408 13 13
GSK3B -0.089 0.17 -9999 0 -0.376 11 11
RAF1 -0.054 0.136 -9999 0 -0.287 10 10
SHC1 0.017 0 -9999 0 -9999 0 0
STAT3 -0.111 0.186 -9999 0 -0.406 13 13
STAT1 -0.26 0.432 -9999 0 -0.892 15 15
HRAS/SPRED1 -0.055 0.133 -9999 0 -0.277 10 10
cell proliferation -0.112 0.181 -9999 0 -0.392 13 13
PIK3CA 0.009 0.058 -9999 0 -0.412 1 1
TEC 0.012 0.043 -9999 0 -0.3 1 1
RPS6KB1 -0.11 0.187 -9999 0 -0.4 13 13
HRAS/SPRED2 -0.052 0.134 -9999 0 -0.277 10 10
LYN/TEC/p62DOK -0.089 0.176 -9999 0 -0.387 11 11
MAPK3 -0.029 0.103 -9999 0 -0.222 5 5
STAP1 -0.109 0.185 -9999 0 -0.402 13 13
GRAP2 0.017 0 -9999 0 -9999 0 0
JAK2 -0.209 0.348 -9999 0 -0.72 15 15
STAT1 (dimer) -0.254 0.422 -9999 0 -0.872 15 15
mol:Gleevec 0.004 0.008 -9999 0 -9999 0 0
GRB2/SOCS1/VAV1 -0.112 0.189 -9999 0 -0.405 13 13
actin filament polymerization -0.111 0.179 -9999 0 -0.344 18 18
LYN 0.012 0.043 -9999 0 -0.3 1 1
STAP1/STAT5A (dimer) -0.142 0.251 -9999 0 -0.522 14 14
PIK3R1 -0.038 0.134 -9999 0 -0.355 8 8
CBL/CRKL/GRB2 -0.081 0.167 -9999 0 -0.362 11 11
PI3K -0.117 0.186 -9999 0 -0.383 15 15
PTEN -0.022 0.124 -9999 0 -0.41 5 5
SCF/KIT/EPO/EPOR -0.274 0.493 -9999 0 -1.174 11 11
MAPK8 -0.114 0.184 -9999 0 -0.4 13 13
STAT3 (dimer) -0.108 0.183 -9999 0 -0.399 13 13
positive regulation of transcription -0.022 0.087 -9999 0 -0.183 5 5
mol:GDP -0.082 0.166 -9999 0 -0.34 13 13
PIK3C2B -0.111 0.181 -9999 0 -0.406 12 12
CBL/CRKL -0.09 0.17 -9999 0 -0.378 11 11
FER -0.107 0.182 -9999 0 -0.406 12 12
SH2B3 -0.107 0.182 -9999 0 -0.406 12 12
PDPK1 -0.083 0.154 0.244 1 -0.319 12 13
SNAI2 -0.114 0.189 -9999 0 -0.422 12 12
positive regulation of cell proliferation -0.184 0.308 -9999 0 -0.638 15 15
KITLG -0.02 0.096 -9999 0 -0.315 5 5
cell motility -0.184 0.308 -9999 0 -0.638 15 15
PTPN6 0.016 0.058 -9999 0 -0.399 1 1
EPOR -0.068 0.159 -9999 0 -0.543 1 1
STAT5A (dimer) -0.147 0.254 -9999 0 -0.517 15 15
SOCS1 0.017 0 -9999 0 -9999 0 0
cell migration 0.111 0.18 0.398 12 -9999 0 12
SOS1 0.017 0 -9999 0 -9999 0 0
EPO 0.007 0.045 -9999 0 -0.315 1 1
VAV1 -0.047 0.138 -9999 0 -0.333 10 10
GRB10 -0.124 0.203 -9999 0 -0.452 12 12
PTPN11 0.022 0.008 -9999 0 -9999 0 0
SCF/KIT -0.119 0.191 -9999 0 -0.367 18 18
GO:0007205 0.006 0.01 -9999 0 -9999 0 0
MAP2K1 -0.037 0.112 -9999 0 -0.248 5 5
CBL 0.017 0 -9999 0 -9999 0 0
KIT -0.261 0.494 -9999 0 -1.26 10 10
MAP2K2 -0.037 0.112 -9999 0 -0.248 5 5
SHC/Grb2/SOS1 -0.084 0.177 -9999 0 -0.387 11 11
STAT5A -0.151 0.261 -9999 0 -0.531 15 15
GRB2 0.017 0 -9999 0 -9999 0 0
response to radiation -0.112 0.185 -9999 0 -0.413 12 12
SHC/GRAP2 0.026 0 -9999 0 -9999 0 0
PTPRO -0.126 0.189 -9999 0 -0.403 14 14
SH2B2 -0.113 0.182 -9999 0 -0.35 18 18
DOK1 0.017 0 -9999 0 -9999 0 0
MATK -0.113 0.183 -9999 0 -0.406 12 12
CREBBP -0.001 0.06 -9999 0 -9999 0 0
BCL2 -0.213 0.466 -9999 0 -1.297 8 8
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.017 0.107 -9999 0 -0.246 8 8
fibroblast growth factor receptor signaling pathway -0.017 0.106 -9999 0 -0.245 8 8
LAMA1 -0.034 0.124 -9999 0 -0.327 8 8
PRNP 0.012 0.043 -9999 0 -0.3 1 1
GPC1/SLIT2 -0.089 0.156 -9999 0 -0.271 21 21
SMAD2 0.012 0.067 -9999 0 -0.197 5 5
GPC1/PrPc/Cu2+ -0.004 0.078 -9999 0 -0.222 6 6
GPC1/Laminin alpha1 -0.035 0.139 -9999 0 -0.305 10 10
TDGF1 -0.089 0.174 -9999 0 -0.366 15 15
CRIPTO/GPC1 -0.077 0.146 -9999 0 -0.266 19 19
APP/GPC1 -0.002 0.089 -9999 0 -0.28 5 5
mol:NO 0 0 -9999 0 -9999 0 0
YES1 -0.057 0.122 -9999 0 -0.243 13 13
FLT1 -0.014 0.112 -9999 0 -0.411 4 4
GPC1/TGFB/TGFBR1/TGFBR2 0.011 0.076 -9999 0 -0.227 5 5
SERPINC1 0.012 0.043 -9999 0 -0.3 1 1
FYN -0.07 0.146 -9999 0 -0.273 14 14
FGR -0.057 0.122 -9999 0 -0.243 13 13
positive regulation of MAPKKK cascade -0.079 0.155 -9999 0 -0.3 14 14
SLIT2 -0.109 0.181 -9999 0 -0.361 18 18
GPC1/NRG -0.002 0.089 -9999 0 -0.28 5 5
NRG1 0.017 0 -9999 0 -9999 0 0
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.021 0.125 -9999 0 -0.272 10 10
LYN -0.06 0.127 -9999 0 -0.248 14 14
mol:Spermine -0.016 0.087 -9999 0 -0.288 5 5
cell growth -0.017 0.106 -9999 0 -0.245 8 8
BMP signaling pathway 0.022 0.124 0.41 5 -9999 0 5
SRC -0.057 0.122 -9999 0 -0.243 13 13
TGFBR1 0.017 0 -9999 0 -9999 0 0
mol:Cu2+ 0 0 -9999 0 -9999 0 0
PLA2G2A -0.016 0.106 -9999 0 -0.344 5 5
GPC1 -0.022 0.124 -9999 0 -0.411 5 5
TGFBR1 (dimer) 0.017 0 -9999 0 -9999 0 0
VEGFA -0.006 0.098 -9999 0 -0.411 3 3
BLK -0.065 0.124 -9999 0 -0.242 14 14
HCK -0.078 0.126 -9999 0 -0.24 16 16
FGF2 0.006 0.06 -9999 0 -0.3 2 2
FGFR1 -0.018 0.112 -9999 0 -0.366 5 5
VEGFR1 homodimer -0.014 0.112 -9999 0 -0.41 4 4
TGFBR2 0.017 0 -9999 0 -9999 0 0
cell death -0.002 0.089 -9999 0 -0.279 5 5
ATIII/GPC1 -0.006 0.101 -9999 0 -0.315 5 5
PLA2G2A/GPC1 -0.026 0.11 -9999 0 -0.254 10 10
LCK -0.079 0.128 -9999 0 -0.246 16 16
neuron differentiation -0.002 0.089 -9999 0 -0.279 5 5
PrPc/Cu2+ 0.009 0.029 -9999 0 -0.203 1 1
APP 0.017 0 -9999 0 -9999 0 0
TGFBR2 (dimer) 0.017 0 -9999 0 -9999 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.048 0.156 -9999 0 -0.329 9 9
FYN -0.078 0.188 -9999 0 -0.373 12 12
LAT/GRAP2/SLP76 -0.071 0.191 -9999 0 -0.392 12 12
IKBKB 0.017 0 -9999 0 -9999 0 0
AKT1 -0.056 0.154 -9999 0 -0.312 12 12
B2M 0.001 0.082 -9999 0 -0.416 2 2
IKBKG -0.011 0.056 -9999 0 -0.117 6 6
MAP3K8 -0.044 0.138 -9999 0 -0.349 9 9
mol:Ca2+ -0.01 0.021 -9999 0 -0.068 4 4
integrin-mediated signaling pathway 0.009 0.059 -9999 0 -0.233 3 3
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.086 0.208 -9999 0 -0.432 12 12
TRPV6 -0.009 0.075 -9999 0 -0.309 3 3
CD28 -0.017 0.107 -9999 0 -0.348 5 5
SHC1 -0.073 0.184 -9999 0 -0.376 11 11
receptor internalization -0.089 0.198 -9999 0 -0.362 14 14
PRF1 -0.047 0.147 -9999 0 -0.485 3 3
KRAS 0.017 0 -9999 0 -9999 0 0
GRB2 0.017 0 -9999 0 -9999 0 0
COT/AKT1 -0.056 0.13 -9999 0 -0.258 12 12
LAT -0.083 0.197 -9999 0 -0.403 12 12
EntrezGene:6955 0.001 0.003 -9999 0 -9999 0 0
CD3D -0.012 0.094 -9999 0 -0.306 5 5
CD3E 0.017 0.004 -9999 0 -9999 0 0
CD3G -0.041 0.135 -9999 0 -0.34 9 9
RASGRP2 -0.004 0.031 -9999 0 -0.182 1 1
RASGRP1 -0.06 0.155 -9999 0 -0.313 12 12
HLA-A -0.024 0.12 -9999 0 -0.36 6 6
RASSF5 0.017 0 -9999 0 -9999 0 0
RAP1A/GTP/RAPL 0.009 0.059 -9999 0 -0.234 3 3
mol:GTP 0 0 -9999 0 -9999 0 0
mol:GDP -0.003 0.052 -9999 0 -0.091 8 8
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.052 0.073 -9999 0 -0.172 12 12
PRKCA -0.04 0.112 -9999 0 -0.222 12 12
GRAP2 0.018 0 -9999 0 -9999 0 0
mol:IP3 -0.088 0.14 0.163 1 -0.323 12 13
EntrezGene:6957 0 0.003 -9999 0 -9999 0 0
TCR/CD3/MHC I/CD8 -0.06 0.14 -9999 0 -0.315 9 9
ORAI1 0.006 0.067 0.196 3 -0.248 2 5
CSK -0.072 0.18 -9999 0 -0.386 10 10
B7 family/CD28 -0.071 0.202 -9999 0 -0.413 12 12
CHUK 0.01 0.058 -9999 0 -0.411 1 1
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.087 0.202 -9999 0 -0.419 11 11
PTPN6 -0.073 0.18 -9999 0 -0.371 11 11
VAV1 -0.098 0.203 -9999 0 -0.403 13 13
Monovalent TCR/CD3 -0.052 0.13 -9999 0 -0.242 16 16
CBL 0.017 0 -9999 0 -9999 0 0
LCK -0.076 0.191 -9999 0 -0.399 11 11
PAG1 -0.08 0.187 -9999 0 -0.375 12 12
RAP1A -0.006 0.098 -9999 0 -0.411 3 3
TCR/CD3/MHC I/CD8/LCK -0.085 0.199 -9999 0 -0.413 11 11
CD80 0.017 0.002 -9999 0 -9999 0 0
CD86 -0.019 0.113 -9999 0 -0.368 5 5
PDK1/CARD11/BCL10/MALT1 -0.059 0.086 -9999 0 -0.19 14 14
HRAS 0.017 0 -9999 0 -9999 0 0
GO:0035030 -0.066 0.173 -9999 0 -0.36 12 12
CD8A 0 0.003 -9999 0 -9999 0 0
CD8B -0.03 0.125 -9999 0 -0.348 7 7
PTPRC -0.044 0.14 -9999 0 -0.352 9 9
PDK1/PKC theta -0.081 0.189 -9999 0 -0.366 14 14
CSK/PAG1 -0.071 0.178 -9999 0 -0.366 11 11
SOS1 0.017 0 -9999 0 -9999 0 0
peptide-MHC class I -0.014 0.112 -9999 0 -0.285 7 7
GRAP2/SLP76 -0.078 0.202 -9999 0 -0.431 11 11
STIM1 0.003 0.063 -9999 0 -0.42 1 1
RAS family/GTP -0.003 0.07 -9999 0 -0.137 4 4
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.093 0.208 -9999 0 -0.378 14 14
mol:DAG -0.083 0.124 -9999 0 -0.284 13 13
RAP1A/GDP -0.003 0.032 -9999 0 -0.093 3 3
PLCG1 0.01 0.058 -9999 0 -0.411 1 1
CD247 -0.083 0.174 -9999 0 -0.374 14 14
cytotoxic T cell degranulation -0.045 0.144 -9999 0 -0.473 3 3
RAP1A/GTP -0.007 0.019 -9999 0 -0.071 4 4
mol:PI-3-4-5-P3 -0.071 0.178 -9999 0 -0.367 12 12
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.109 0.176 0.181 1 -0.391 13 14
NRAS 0.012 0.043 -9999 0 -0.3 1 1
ZAP70 -0.02 0.107 -9999 0 -0.319 6 6
GRB2/SOS1 0.026 0 -9999 0 -9999 0 0
LAT/GRAP2/SLP76/VAV1 -0.112 0.176 -9999 0 -0.396 13 13
MALT1 -0.008 0.091 -9999 0 -0.327 4 4
TRAF6 0.002 0.081 -9999 0 -0.411 2 2
CD8 heterodimer -0.02 0.087 -9999 0 -0.24 7 7
CARD11 -0.006 0.083 -9999 0 -0.3 4 4
PRKCB -0.061 0.087 -9999 0 -0.203 13 13
PRKCE -0.039 0.102 -9999 0 -0.213 11 11
PRKCQ -0.099 0.21 -9999 0 -0.402 15 15
LCP2 -0.028 0.119 -9999 0 -0.331 7 7
BCL10 0.012 0.043 -9999 0 -0.3 1 1
regulation of survival gene product expression -0.046 0.135 -9999 0 -0.269 12 12
IKK complex -0.004 0.051 -9999 0 -0.092 5 5
RAS family/GDP -0.005 0.009 -9999 0 -9999 0 0
MAP3K14 -0.038 0.103 -9999 0 -0.201 11 11
PDPK1 -0.052 0.148 -9999 0 -0.296 12 12
TCR/CD3/MHC I/CD8/Fyn -0.077 0.185 -9999 0 -0.421 9 9
IGF1 pathway

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
NCK2 0.017 0 -9999 0 -9999 0 0
PTK2 0.017 0 -9999 0 -9999 0 0
CRKL -0.07 0.138 -9999 0 -0.271 14 14
GRB2/SOS1/SHC 0.036 0 -9999 0 -9999 0 0
HRAS 0.017 0 -9999 0 -9999 0 0
IRS1/Crk -0.085 0.146 -9999 0 -0.27 17 17
IGF-1R heterotetramer/IGF1/PTP1B -0.072 0.147 -9999 0 -0.289 14 14
AKT1 -0.07 0.136 -9999 0 -0.33 8 8
BAD -0.063 0.132 -9999 0 -0.323 8 8
mol:GTP 0 0 -9999 0 -9999 0 0
CRK -0.086 0.144 -9999 0 -0.27 17 17
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.069 0.14 -9999 0 -0.272 14 14
RAF1 -0.052 0.125 -9999 0 -0.367 3 3
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.054 0.137 -9999 0 -0.252 14 14
YWHAZ 0.017 0 -9999 0 -9999 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.082 0.15 -9999 0 -0.301 14 14
PIK3CA 0.01 0.058 -9999 0 -0.411 1 1
RPS6KB1 -0.074 0.14 -9999 0 -0.332 9 9
GNB2L1 0.01 0.058 -9999 0 -0.411 1 1
positive regulation of MAPKKK cascade -0.047 0.107 -9999 0 -0.32 3 3
PXN 0.017 0 -9999 0 -9999 0 0
PIK3R1 -0.038 0.134 -9999 0 -0.355 8 8
cell adhesion 0 0 -9999 0 -9999 0 0
GRB2/SOS1 0.026 0 -9999 0 -9999 0 0
HRAS/GTP -0.067 0.105 -9999 0 -0.315 6 6
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.034 0.119 -9999 0 -0.279 6 6
IGF-1R heterotetramer -0.062 0.156 -9999 0 -0.43 8 8
IGF-1R heterotetramer/IGF1/IRS/Nck -0.066 0.142 -9999 0 -0.272 14 14
Crk/p130 Cas/Paxillin -0.061 0.137 -9999 0 -0.339 7 7
IGF1R -0.062 0.157 -9999 0 -0.43 8 8
IGF1 -0.115 0.189 -9999 0 -0.385 17 17
IRS2/Crk -0.09 0.143 -9999 0 -0.246 21 21
PI3K -0.084 0.154 -9999 0 -0.359 9 9
apoptosis 0.048 0.119 0.279 8 -9999 0 8
HRAS/GDP 0.013 0 -9999 0 -9999 0 0
PRKCD -0.078 0.183 -9999 0 -0.401 11 11
RAF1/14-3-3 E -0.041 0.12 -9999 0 -0.362 3 3
BAD/14-3-3 -0.051 0.126 -9999 0 -0.296 8 8
PRKCZ -0.077 0.135 -9999 0 -0.321 9 9
Crk/p130 Cas/Paxillin/FAK1 -0.084 0.12 -9999 0 -0.306 10 10
PTPN1 0.012 0.043 -9999 0 -0.3 1 1
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.086 0.188 -9999 0 -0.374 14 14
BCAR1 0.017 0 -9999 0 -9999 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.068 0.157 -9999 0 -0.274 16 16
mol:GDP 0 0 -9999 0 -9999 0 0
SOS1 0.017 0 -9999 0 -9999 0 0
IRS1/NCK2 -0.068 0.139 -9999 0 -0.27 14 14
GRB10 -0.02 0.118 -9999 0 -0.389 5 5
PTPN11 -0.07 0.138 -9999 0 -0.271 14 14
IRS1 -0.082 0.148 -9999 0 -0.3 14 14
IRS2 -0.087 0.144 -9999 0 -0.265 18 18
IGF-1R heterotetramer/IGF1 -0.108 0.179 -9999 0 -0.311 21 21
GRB2 0.017 0 -9999 0 -9999 0 0
PDPK1 -0.079 0.143 -9999 0 -0.336 9 9
YWHAE 0.01 0.058 -9999 0 -0.411 1 1
PRKD1 -0.089 0.184 -9999 0 -0.386 13 13
SHC1 0.017 0 -9999 0 -9999 0 0
FOXM1 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
NFATC3 -0.265 0.466 -9999 0 -1.167 8 8
PLK1 0.016 0.047 -9999 0 -9999 0 0
BIRC5 -0.038 0.263 -9999 0 -1.351 2 2
HSPA1B -0.273 0.465 -9999 0 -1.174 8 8
MAP2K1 0.007 0.033 -9999 0 -9999 0 0
BRCA2 -0.274 0.481 -9999 0 -1.275 7 7
FOXM1 -0.41 0.835 -9999 0 -2.019 8 8
XRCC1 -0.265 0.466 -9999 0 -1.167 8 8
FOXM1B/p19 -0.419 0.491 -9999 0 -1.335 9 9
Cyclin D1/CDK4 -0.314 0.439 -9999 0 -1.058 9 9
CDC2 -0.288 0.502 -9999 0 -1.275 8 8
TGFA -0.362 0.449 -9999 0 -0.986 12 12
SKP2 -0.265 0.466 -9999 0 -1.167 8 8
CCNE1 -0.058 0.147 -9999 0 -0.344 11 11
CKS1B -0.267 0.467 -9999 0 -1.167 8 8
RB1 -0.225 0.311 -9999 0 -0.845 8 8
FOXM1C/SP1 -0.309 0.553 -9999 0 -1.42 8 8
AURKB -0.009 0.19 -9999 0 -1.353 1 1
CENPF -0.297 0.515 -9999 0 -1.276 9 9
CDK4 0.011 0.013 -9999 0 -9999 0 0
MYC -0.226 0.407 -9999 0 -0.984 8 8
CHEK2 0.007 0.033 -9999 0 -9999 0 0
ONECUT1 -0.319 0.454 -9999 0 -1.093 9 9
CDKN2A -0.134 0.176 -9999 0 -0.334 23 23
LAMA4 -0.267 0.466 -9999 0 -1.22 7 7
FOXM1B/HNF6 -0.381 0.563 -9999 0 -1.394 9 9
FOS -0.346 0.531 -9999 0 -1.201 12 12
SP1 0.018 0.001 -9999 0 -9999 0 0
CDC25B -0.273 0.475 -9999 0 -1.244 7 7
response to radiation -0.009 0.028 -9999 0 -9999 0 0
CENPB -0.265 0.466 -9999 0 -1.22 7 7
CENPA -0.287 0.5 -9999 0 -1.218 9 9
NEK2 -0.286 0.506 -9999 0 -1.309 8 8
HIST1H2BA -0.297 0.497 -9999 0 -1.163 10 10
CCNA2 -0.018 0.115 -9999 0 -0.425 4 4
EP300 0.01 0.058 -9999 0 -0.411 1 1
CCNB1/CDK1 -0.33 0.588 -9999 0 -1.629 7 7
CCNB2 -0.272 0.482 -9999 0 -1.215 8 8
CCNB1 -0.296 0.517 -9999 0 -1.327 8 8
ETV5 -0.36 0.536 -9999 0 -1.191 12 12
ESR1 -0.437 0.594 -9999 0 -1.147 20 20
CCND1 -0.32 0.453 -9999 0 -1.09 9 9
GSK3A 0.008 0.027 -9999 0 -9999 0 0
Cyclin A-E1/CDK1-2 -0.045 0.13 -9999 0 -0.277 9 9
CDK2 0.003 0.062 -9999 0 -0.313 2 2
G2/M transition of mitotic cell cycle -0.01 0.034 -9999 0 -9999 0 0
FOXM1B/Cbp/p300 -0.316 0.495 -9999 0 -1.33 8 8
GAS1 -0.369 0.524 -9999 0 -1.124 13 13
MMP2 -0.308 0.506 -9999 0 -1.271 9 9
RB1/FOXM1C -0.328 0.473 -9999 0 -1.103 10 10
CREBBP 0.017 0 -9999 0 -9999 0 0
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.014 0.097 -9999 0 -0.282 2 2
TBX21 -0.275 0.48 -9999 0 -0.965 14 14
B2M 0.003 0.081 -9999 0 -0.41 2 2
TYK2 0.006 0.025 -9999 0 -9999 0 0
IL12RB1 -0.002 0.066 -9999 0 -0.448 1 1
GADD45B -0.24 0.42 -9999 0 -0.891 12 12
IL12RB2 -0.007 0.077 -9999 0 -0.376 2 2
GADD45G -0.188 0.357 -9999 0 -0.856 7 7
natural killer cell activation -0.011 0.024 -9999 0 -9999 0 0
RELB 0.01 0.058 -9999 0 -0.411 1 1
RELA 0.017 0 -9999 0 -9999 0 0
IL18 -0.027 0.121 -9999 0 -0.362 6 6
IL2RA 0.01 0.058 -9999 0 -0.411 1 1
IFNG -0.047 0.128 -9999 0 -0.3 11 11
STAT3 (dimer) -0.183 0.35 -9999 0 -0.656 16 16
HLA-DRB5 -0.076 0.17 -9999 0 -0.393 12 12
FASLG -0.235 0.409 -9999 0 -0.829 14 14
NF kappa B2 p52/RelB -0.269 0.368 -9999 0 -0.763 17 17
CD4 0.015 0.007 -9999 0 -9999 0 0
SOCS1 0.017 0 -9999 0 -9999 0 0
EntrezGene:6955 -0.002 0.008 -9999 0 -9999 0 0
CD3D -0.014 0.094 -9999 0 -0.306 5 5
CD3E 0.016 0.007 -9999 0 -9999 0 0
CD3G -0.043 0.136 -9999 0 -0.344 9 9
IL12Rbeta2/JAK2 -0.007 0.087 -9999 0 -0.316 3 3
CCL3 -0.233 0.425 -9999 0 -0.896 12 12
CCL4 -0.328 0.574 -9999 0 -1.262 13 13
HLA-A -0.023 0.119 -9999 0 -0.354 6 6
IL18/IL18R -0.018 0.124 -9999 0 -0.281 6 6
NOS2 -0.208 0.37 -9999 0 -0.686 17 17
IL12/IL12R/TYK2/JAK2/SPHK2 -0.014 0.097 -9999 0 -0.282 2 2
IL1R1 -0.268 0.474 -9999 0 -0.968 14 14
IL4 0.029 0.024 -9999 0 -9999 0 0
JAK2 -0.006 0.067 -9999 0 -0.322 2 2
EntrezGene:6957 -0.001 0.007 -9999 0 -9999 0 0
TCR/CD3/MHC I/CD8 -0.063 0.145 -9999 0 -0.377 6 6
RAB7A -0.173 0.321 -9999 0 -0.683 9 9
lysosomal transport -0.164 0.308 -9999 0 -0.621 11 11
FOS -0.28 0.459 -9999 0 -0.984 13 13
STAT4 (dimer) -0.196 0.365 -9999 0 -0.676 16 16
STAT5A (dimer) -0.286 0.366 -9999 0 -0.774 17 17
GZMA -0.232 0.4 -9999 0 -0.764 17 17
GZMB -0.328 0.555 -9999 0 -1.11 16 16
HLX 0.017 0 -9999 0 -9999 0 0
LCK -0.259 0.44 -9999 0 -0.81 18 18
TCR/CD3/MHC II/CD4 -0.111 0.177 -9999 0 -0.34 17 17
IL2/IL2R 0.023 0.083 -9999 0 -0.294 3 3
MAPK14 -0.22 0.384 -9999 0 -0.767 13 13
CCR5 -0.222 0.404 -9999 0 -0.945 9 9
IL1B -0.037 0.131 -9999 0 -0.395 6 6
STAT6 -0.069 0.164 -9999 0 -0.335 7 7
STAT4 0.017 0 -9999 0 -9999 0 0
STAT3 0.01 0.058 -9999 0 -0.411 1 1
STAT1 -0.032 0.118 -9999 0 -0.313 8 8
NFKB1 0.017 0 -9999 0 -9999 0 0
NFKB2 0.017 0 -9999 0 -9999 0 0
IL12B 0.007 0.024 -9999 0 -9999 0 0
CD8A 0.001 0.003 -9999 0 -9999 0 0
CD8B -0.029 0.124 -9999 0 -0.346 7 7
T-helper 1 cell differentiation 0 0 -9999 0 -9999 0 0
natural killer cell mediated cytotoxicity 0.014 0.096 0.28 2 -9999 0 2
IL2RB -0.002 0.082 -9999 0 -0.337 3 3
proteasomal ubiquitin-dependent protein catabolic process -0.179 0.339 -9999 0 -0.625 16 16
IL2RG 0.012 0.043 -9999 0 -0.3 1 1
IL12 0.001 0.058 -9999 0 -0.267 1 1
STAT5A 0.017 0 -9999 0 -9999 0 0
CD247 -0.085 0.174 -9999 0 -0.375 14 14
IL2 0.01 0.058 -9999 0 -0.411 1 1
SPHK2 0.017 0 -9999 0 -9999 0 0
FRAP1 0.017 0 -9999 0 -9999 0 0
IL12A -0.008 0.071 -9999 0 -0.344 2 2
IL12/IL12R/TYK2/JAK2 -0.265 0.46 -9999 0 -0.869 17 17
MAP2K3 -0.215 0.385 -9999 0 -0.724 15 15
RIPK2 0.012 0.043 -9999 0 -0.3 1 1
MAP2K6 -0.239 0.399 -9999 0 -0.746 16 16
regulation of dendritic cell antigen processing and presentation 0 0 -9999 0 -9999 0 0
HLA-DRA -0.037 0.135 -9999 0 -0.382 7 7
IL18RAP -0.034 0.122 -9999 0 -0.323 8 8
IL12Rbeta1/TYK2 0.004 0.057 -9999 0 -0.331 1 1
EOMES 0.009 0.068 -9999 0 -9999 0 0
STAT1 (dimer) -0.211 0.35 -9999 0 -0.675 16 16
T cell proliferation -0.153 0.284 -9999 0 -0.527 15 15
T-helper 1 cell lineage commitment 0 0 -9999 0 -9999 0 0
IL18R1 0.009 0.042 -9999 0 -0.29 1 1
CD8-positive alpha-beta T cell lineage commitment 0 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelA -0.217 0.25 -9999 0 -0.577 13 13
ATF2 -0.198 0.356 -9999 0 -0.704 13 13
Osteopontin-mediated events

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
IKK alpha homodimer -0.049 0.146 -9999 0 -0.323 9 9
NF kappa B1 p50/RelA/I kappa B alpha -0.031 0.146 -9999 0 -0.327 7 7
alphaV/beta3 Integrin/Osteopontin/Src -0.071 0.148 -9999 0 -0.26 19 19
AP1 -0.134 0.183 -9999 0 -0.434 8 8
ILK -0.057 0.14 -9999 0 -0.312 9 9
bone resorption -0.045 0.147 -9999 0 -0.389 5 5
PTK2B 0.017 0 -9999 0 -9999 0 0
PYK2/p130Cas -0.044 0.16 -9999 0 -0.397 6 6
ITGAV -0.002 0.09 -9999 0 -0.368 3 3
mol:GTP 0 0 -9999 0 -9999 0 0
CD44/Rho Family GTPase/ROCK2 0.009 0.07 -9999 0 -0.28 3 3
alphaV/beta3 Integrin/Osteopontin -0.066 0.159 -9999 0 -0.342 10 10
MAP3K1 -0.075 0.156 -9999 0 -0.338 10 10
JUN -0.027 0.124 -9999 0 -0.374 6 6
MAPK3 -0.05 0.144 -9999 0 -0.363 6 6
MAPK1 -0.054 0.15 -9999 0 -0.365 7 7
Rac1/GDP 0.013 0 -9999 0 -9999 0 0
NFKB1 0.017 0 -9999 0 -9999 0 0
MAPK8 -0.074 0.156 -9999 0 -0.323 12 12
ITGB3 -0.024 0.112 -9999 0 -0.311 7 7
NFKBIA -0.049 0.154 -9999 0 -0.356 8 8
FOS -0.08 0.166 -9999 0 -0.357 14 14
CD44 0.002 0.081 -9999 0 -0.411 2 2
CHUK 0.01 0.058 -9999 0 -0.411 1 1
PLAU -0.093 0.282 -9999 0 -0.966 4 4
NF kappa B1 p50/RelA -0.03 0.154 -9999 0 -0.34 8 8
BCAR1 0.017 0 -9999 0 -9999 0 0
RELA 0.017 0 -9999 0 -9999 0 0
alphaV beta3 Integrin -0.015 0.102 -9999 0 -0.277 5 5
mol:GDP 0 0 -9999 0 -9999 0 0
SYK -0.071 0.169 -9999 0 -0.384 9 9
VAV3 -0.092 0.174 -9999 0 -0.366 11 11
MAP3K14 -0.058 0.146 -9999 0 -0.328 9 9
ROCK2 0.01 0.058 -9999 0 -0.411 1 1
SPP1 -0.105 0.18 -9999 0 -0.354 18 18
RAC1 0.017 0 -9999 0 -9999 0 0
Rac1/GTP -0.077 0.161 -9999 0 -0.378 8 8
MMP2 -0.138 0.182 -9999 0 -0.44 9 9
Noncanonical Wnt signaling pathway

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
NFATC2 0.01 0.058 -9999 0 -0.411 1 1
GNB1/GNG2 -0.071 0.211 -9999 0 -0.463 9 9
mol:DAG -0.064 0.191 -9999 0 -0.406 10 10
PLCG1 -0.067 0.2 -9999 0 -0.421 10 10
YES1 -0.08 0.213 -9999 0 -0.469 9 9
FZD3 -0.014 0.112 -9999 0 -0.411 4 4
FZD6 0.004 0.071 -9999 0 -0.355 2 2
G protein -0.062 0.2 -9999 0 -0.435 9 9
MAP3K7 -0.043 0.159 -9999 0 -0.347 9 9
mol:Ca2+ -0.062 0.184 -9999 0 -0.392 10 10
mol:IP3 -0.064 0.191 -9999 0 -0.406 10 10
NLK 0.019 0.021 -9999 0 -9999 0 0
GNB1 0.017 0 -9999 0 -9999 0 0
CAMK2A -0.053 0.172 -9999 0 -0.381 9 9
MAP3K7IP1 0.017 0 -9999 0 -9999 0 0
Noncanonical Wnts/FZD -0.091 0.226 -9999 0 -0.503 9 9
CSNK1A1 0.017 0 -9999 0 -9999 0 0
GNAS -0.08 0.213 -9999 0 -0.469 9 9
GO:0007205 -0.065 0.189 -9999 0 -0.405 10 10
WNT6 -0.02 0.106 -9999 0 -0.318 6 6
WNT4 0 0.073 -9999 0 -0.3 3 3
NFAT1/CK1 alpha -0.054 0.199 -9999 0 -0.448 8 8
GNG2 0.006 0.06 -9999 0 -0.3 2 2
WNT5A -0.05 0.152 -9999 0 -0.386 9 9
WNT11 -0.077 0.17 -9999 0 -0.377 13 13
CDC42 -0.07 0.201 -9999 0 -0.44 9 9
Nectin adhesion pathway

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
PDGFRB 0.002 0.081 -9999 0 -0.411 2 2
alphaV beta3 Integrin -0.019 0.103 -9999 0 -0.243 9 9
PTK2 -0.07 0.156 -9999 0 -0.375 9 9
positive regulation of JNK cascade -0.054 0.11 -9999 0 -0.28 10 10
CDC42/GDP -0.041 0.165 -9999 0 -0.375 10 10
Rac1/GDP -0.04 0.164 -9999 0 -0.37 10 10
RAP1B 0.017 0 -9999 0 -9999 0 0
RAP1A -0.006 0.098 -9999 0 -0.411 3 3
CTNNB1 0.002 0.081 -9999 0 -0.411 2 2
CDC42/GTP -0.063 0.135 -9999 0 -0.341 10 10
nectin-3/I-afadin -0.041 0.121 -9999 0 -0.254 13 13
RAPGEF1 -0.065 0.182 -9999 0 -0.424 10 10
mol:GTP 0 0 -9999 0 -9999 0 0
CRK -0.08 0.205 -9999 0 -0.485 10 10
PDGFB-D/PDGFRB 0.002 0.081 -9999 0 -0.41 2 2
TLN1 -0.072 0.142 -9999 0 -0.305 12 12
Rap1/GTP -0.07 0.123 -9999 0 -0.291 12 12
IQGAP1 0.017 0 -9999 0 -9999 0 0
Rap1/GTP/I-afadin 0.021 0.054 -9999 0 -0.204 3 3
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.041 0.121 -9999 0 -0.254 13 13
PVR 0.004 0.071 -9999 0 -0.355 2 2
Necl-5(dimer) 0.004 0.071 -9999 0 -0.355 2 2
mol:GDP -0.061 0.195 -9999 0 -0.457 10 10
MLLT4 0.017 0 -9999 0 -9999 0 0
PIK3CA 0.01 0.058 -9999 0 -0.411 1 1
PI3K -0.04 0.113 -9999 0 -0.191 15 15
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.02 0.041 -9999 0 -0.28 1 1
positive regulation of lamellipodium assembly -0.055 0.115 -9999 0 -0.293 10 10
PVRL1 0.01 0.058 -9999 0 -0.411 1 1
PVRL3 -0.077 0.17 -9999 0 -0.377 13 13
PVRL2 0.01 0.058 -9999 0 -0.411 1 1
PIK3R1 -0.038 0.134 -9999 0 -0.355 8 8
CDH1 0.01 0.058 -9999 0 -0.411 1 1
CLDN1 -0.146 0.193 -9999 0 -0.367 23 23
JAM-A/CLDN1 -0.096 0.146 -9999 0 -0.252 21 21
SRC -0.081 0.216 -9999 0 -0.522 10 10
ITGB3 -0.026 0.113 -9999 0 -0.315 7 7
nectin-1(dimer)/I-afadin/I-afadin 0.02 0.041 -9999 0 -0.28 1 1
FARP2 -0.059 0.189 -9999 0 -0.445 10 10
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) -0.03 0.114 -9999 0 -0.242 10 10
nectin-1/I-afadin 0.02 0.041 -9999 0 -0.28 1 1
nectin-2/I-afadin 0.02 0.041 -9999 0 -0.28 1 1
RAC1/GTP/IQGAP1/filamentous actin 0.024 0 -9999 0 -9999 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.027 0.107 -9999 0 -0.227 10 10
CDC42/GTP/IQGAP1/filamentous actin 0.024 0 -9999 0 -9999 0 0
F11R 0.017 0 -9999 0 -9999 0 0
positive regulation of filopodium formation -0.054 0.11 -9999 0 -0.28 10 10
alphaV/beta3 Integrin/Talin -0.079 0.142 -9999 0 -0.283 14 14
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.02 0.041 -9999 0 -0.28 1 1
nectin-2(dimer)/I-afadin/I-afadin 0.02 0.041 -9999 0 -0.28 1 1
PIP5K1C -0.084 0.151 -9999 0 -0.331 12 12
VAV2 -0.059 0.193 -9999 0 -0.453 10 10
RAP1/GDP -0.044 0.158 -9999 0 -0.347 10 10
ITGAV -0.004 0.09 -9999 0 -0.374 3 3
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.026 0.116 -9999 0 -0.252 9 9
nectin-3(dimer)/I-afadin/I-afadin -0.041 0.121 -9999 0 -0.254 13 13
Rac1/GTP -0.064 0.14 -9999 0 -0.353 10 10
PTPRM -0.1 0.164 -9999 0 -0.299 18 18
E-cadherin/beta catenin/alpha catenin 0.032 0.073 -9999 0 -0.359 1 1
adherens junction assembly 0 0 -9999 0 -9999 0 0
CDC42 0.017 0 -9999 0 -9999 0 0
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.091 0.226 -9999 0 -0.503 9 9
FZD6 0.004 0.071 -9999 0 -0.355 2 2
WNT6 -0.02 0.106 -9999 0 -0.318 6 6
WNT4 0 0.073 -9999 0 -0.3 3 3
FZD3 -0.014 0.112 -9999 0 -0.411 4 4
WNT5A -0.05 0.152 -9999 0 -0.386 9 9
WNT11 -0.077 0.17 -9999 0 -0.377 13 13
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.014 0.059 -9999 0 -0.401 1 1
NFATC2 -0.057 0.192 -9999 0 -0.474 6 6
NFATC3 -0.045 0.099 -9999 0 -0.251 5 5
CD40LG -0.263 0.345 -9999 0 -0.783 12 12
ITCH 0.011 0.077 -9999 0 -9999 0 0
CBLB 0.011 0.077 -9999 0 -9999 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.132 0.242 -9999 0 -0.751 3 3
JUNB 0.006 0.06 -9999 0 -0.299 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.001 0.093 -9999 0 -0.237 5 5
T cell anergy -0.014 0.123 -9999 0 -0.33 5 5
TLE4 -0.035 0.152 -9999 0 -0.432 3 3
Jun/NFAT1-c-4/p21SNFT -0.209 0.347 -9999 0 -0.81 10 10
AP-1/NFAT1-c-4 -0.278 0.385 -9999 0 -0.857 12 12
IKZF1 -0.025 0.152 -9999 0 -0.433 4 4
T-helper 2 cell differentiation -0.051 0.182 -9999 0 -0.536 1 1
AP-1/NFAT1 -0.105 0.159 -9999 0 -0.348 9 9
CALM1 0.007 0.054 -9999 0 -9999 0 0
EGR2 -0.23 0.46 -9999 0 -1.048 11 11
EGR3 -0.207 0.428 -9999 0 -1.293 5 5
NFAT1/FOXP3 -0.02 0.138 -9999 0 -0.371 3 3
EGR1 -0.062 0.15 -9999 0 -0.339 12 12
JUN -0.032 0.124 -9999 0 -0.377 6 6
EGR4 -0.001 0.009 -9999 0 -9999 0 0
mol:Ca2+ -0.01 0.055 -9999 0 -9999 0 0
GBP3 -0.085 0.265 -9999 0 -0.643 9 9
FOSL1 0.012 0.043 -9999 0 -0.3 1 1
NFAT1-c-4/MAF/IRF4 -0.17 0.355 -9999 0 -0.753 12 12
DGKA -0.019 0.141 -9999 0 -0.482 2 2
CREM 0.017 0.002 -9999 0 -9999 0 0
NFAT1-c-4/PPARG -0.251 0.373 -9999 0 -0.866 12 12
CTLA4 -0.012 0.117 -9999 0 -0.338 1 1
NFAT1-c-4 (dimer)/EGR1 -0.216 0.381 -9999 0 -0.854 12 12
NFAT1-c-4 (dimer)/EGR4 -0.191 0.363 -9999 0 -0.799 12 12
FOS -0.086 0.165 -9999 0 -0.359 14 14
IFNG -0.15 0.212 -9999 0 -0.517 6 6
T cell activation -0.155 0.263 -9999 0 -0.83 3 3
MAF -0.002 0.082 -9999 0 -0.336 3 3
T-helper 2 cell lineage commitment 0 0 -9999 0 -9999 0 0
activation-induced cell death of T cells 0.159 0.336 0.783 8 -9999 0 8
TNF -0.213 0.356 -9999 0 -0.803 12 12
FASLG -0.282 0.482 -9999 0 -1.127 11 11
TBX21 -0.069 0.162 -9999 0 -0.369 12 12
BATF3 0 0.001 -9999 0 -9999 0 0
PRKCQ -0.079 0.168 -9999 0 -0.359 14 14
PTPN1 -0.019 0.141 -9999 0 -0.483 2 2
NFAT1-c-4/ICER1 -0.185 0.358 -9999 0 -0.786 12 12
GATA3 -0.002 0.084 -9999 0 -0.298 4 4
T-helper 1 cell differentiation -0.148 0.209 -9999 0 -0.51 6 6
IL2RA -0.141 0.242 -9999 0 -0.694 4 4
T-helper 1 cell lineage commitment 0 0 -9999 0 -9999 0 0
CASP3 -0.016 0.13 -9999 0 -0.375 3 3
E2F1 -0.003 0.099 -9999 0 -0.349 4 4
PPARG -0.126 0.183 -9999 0 -0.352 21 21
SLC3A2 -0.016 0.13 -9999 0 -0.375 3 3
IRF4 0.006 0.06 -9999 0 -0.299 2 2
PTGS2 -0.292 0.339 -9999 0 -0.762 14 14
CSF2 -0.257 0.337 -9999 0 -0.764 12 12
JunB/Fra1/NFAT1-c-4 -0.166 0.36 -9999 0 -0.766 12 12
IL4 -0.053 0.186 -9999 0 -0.553 1 1
IL5 -0.252 0.332 -9999 0 -0.754 12 12
IL2 -0.158 0.27 -9999 0 -0.856 3 3
IL3 -0.031 0.059 -9999 0 -9999 0 0
RNF128 -0.034 0.173 -9999 0 -0.382 10 10
NFATC1 -0.16 0.338 -9999 0 -0.787 8 8
CDK4 0.093 0.19 0.66 1 -9999 0 1
PTPRK -0.032 0.172 -9999 0 -0.517 4 4
IL8 -0.302 0.359 -9999 0 -0.819 13 13
POU2F1 0.02 0.043 -9999 0 -0.295 1 1
Plasma membrane estrogen receptor 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
GNB1/GNG2 -0.026 0.106 -9999 0 -0.195 14 14
ER alpha/Gai/GDP/Gbeta gamma -0.082 0.188 -9999 0 -0.355 15 15
AKT1 -0.185 0.358 -9999 0 -0.77 14 14
PIK3CA 0.01 0.058 -9999 0 -0.411 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.19 0.366 -9999 0 -0.785 14 14
mol:Ca2+ -0.007 0.076 -9999 0 -0.254 3 3
IGF1R -0.042 0.143 -9999 0 -0.383 8 8
E2/ER alpha (dimer)/Striatin -0.063 0.133 -9999 0 -0.252 17 17
SHC1 0.017 0 -9999 0 -9999 0 0
apoptosis 0.175 0.338 0.73 14 -9999 0 14
RhoA/GTP -0.047 0.082 -9999 0 -0.31 2 2
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.111 0.165 -9999 0 -0.359 15 15
regulation of stress fiber formation 0.006 0.089 0.252 3 -9999 0 3
E2/ERA-ERB (dimer) -0.046 0.114 -9999 0 -0.229 15 15
KRAS 0.017 0 -9999 0 -9999 0 0
G13/GTP -0.041 0.103 -9999 0 -0.206 15 15
pseudopodium formation -0.006 0.089 -9999 0 -0.252 3 3
E2/ER alpha (dimer)/PELP1 -0.046 0.114 -9999 0 -0.229 15 15
GRB2 0.017 0 -9999 0 -9999 0 0
GNG2 0.006 0.06 -9999 0 -0.3 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 -0.101 0.225 -9999 0 -0.458 14 14
E2/ER beta (dimer) 0.013 0 -9999 0 -9999 0 0
mol:GDP -0.083 0.137 -9999 0 -0.312 14 14
mol:NADP -0.101 0.225 -9999 0 -0.458 14 14
PIK3R1 -0.038 0.134 -9999 0 -0.355 8 8
mol:IP3 -0.008 0.078 -9999 0 -0.263 3 3
IGF-1R heterotetramer -0.042 0.143 -9999 0 -0.382 8 8
PLCB1 -0.014 0.081 -9999 0 -0.276 3 3
PLCB2 -0.004 0.064 -9999 0 -0.31 1 1
IGF1 -0.103 0.18 -9999 0 -0.365 17 17
mol:L-citrulline -0.101 0.225 -9999 0 -0.458 14 14
RHOA 0.01 0.058 -9999 0 -0.411 1 1
Gai/GDP -0.018 0.115 -9999 0 -0.467 2 2
JNK cascade 0.013 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 -0.099 0.189 -9999 0 -0.403 15 15
Gq family/GDP/Gbeta gamma 0.019 0.043 -9999 0 -9999 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.027 0.11 -9999 0 -9999 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.111 0.165 -9999 0 -0.359 15 15
GNAZ -0.01 0.099 -9999 0 -0.355 4 4
E2/ER alpha (dimer) -0.069 0.133 -9999 0 -0.283 15 15
STRN -0.012 0.106 -9999 0 -0.383 4 4
GNAL 0.01 0.058 -9999 0 -0.411 1 1
PELP1 0.017 0 -9999 0 -9999 0 0
MAPK11 0.02 0 -9999 0 -9999 0 0
GNAI2 0.017 0 -9999 0 -9999 0 0
GNAI3 0.01 0.058 -9999 0 -0.411 1 1
GNAI1 -0.05 0.152 -9999 0 -0.386 9 9
HBEGF -0.1 0.178 -9999 0 -0.377 12 12
cAMP biosynthetic process -0.038 0.09 -9999 0 -0.18 15 15
SRC -0.072 0.18 -9999 0 -0.333 15 15
PI3K -0.018 0.112 -9999 0 -0.268 8 8
GNB1 0.017 0 -9999 0 -9999 0 0
G13/GDP/Gbeta gamma -0.043 0.14 -9999 0 -0.272 14 14
SOS1 0.017 0 -9999 0 -9999 0 0
IGF-1R heterotetramer/IGF1 -0.137 0.171 -9999 0 -0.377 16 16
Gs family/GTP -0.035 0.093 -9999 0 -0.182 15 15
EntrezGene:2778 0 0 -9999 0 -9999 0 0
RAS family/GTP 0.031 0.023 -9999 0 -9999 0 0
vasodilation -0.095 0.215 -9999 0 -0.438 14 14
mol:DAG -0.008 0.078 -9999 0 -0.263 3 3
Gs family/GDP/Gbeta gamma -0.073 0.115 -9999 0 -0.261 14 14
MSN -0.008 0.094 -9999 0 -0.269 3 3
Gq family/GTP -0.011 0.067 -9999 0 -0.25 2 2
mol:PI-3-4-5-P3 -0.181 0.348 -9999 0 -0.749 14 14
NRAS 0.012 0.043 -9999 0 -0.3 1 1
mol:E2 0 0 -9999 0 -9999 0 0
cell adhesion 0.095 0.215 0.438 14 -9999 0 14
GRB2/SOS1 0.026 0 -9999 0 -9999 0 0
RhoA/GDP -0.052 0.153 -9999 0 -0.304 14 14
NOS3 -0.107 0.237 -9999 0 -0.482 14 14
GNA11 0.017 0 -9999 0 -9999 0 0
MAPKKK cascade -0.119 0.259 -9999 0 -0.535 14 14
E2/ER alpha (dimer)/PELP1/Src -0.082 0.198 -9999 0 -0.378 15 15
ruffle organization -0.006 0.089 -9999 0 -0.252 3 3
ROCK2 -0.015 0.101 -9999 0 -0.297 3 3
GNA14 0.004 0.071 -9999 0 -0.355 2 2
GNA15 0.012 0.043 -9999 0 -0.3 1 1
GNA13 0.017 0 -9999 0 -9999 0 0
MMP9 -0.107 0.187 -9999 0 -0.403 12 12
MMP2 -0.092 0.181 -9999 0 -0.398 9 9
IL4-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
BCL2L1 -0.355 0.48 -9999 0 -1.163 9 9
STAT6 (cleaved dimer) -0.412 0.444 -9999 0 -1.101 12 12
IGHG1 -0.118 0.183 -9999 0 -0.422 2 2
IGHG3 -0.351 0.46 -9999 0 -1.059 11 11
AKT1 -0.189 0.309 -9999 0 -0.792 6 6
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.123 0.234 -9999 0 -0.652 4 4
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.208 0.325 -9999 0 -0.828 7 7
THY1 -0.366 0.503 -9999 0 -1.272 8 8
MYB -0.042 0.143 -9999 0 -0.383 8 8
HMGA1 0.012 0.043 -9999 0 -0.3 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.2 0.291 -9999 0 -0.642 8 8
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.198 0.314 -9999 0 -0.828 6 6
SP1 0.02 0.026 -9999 0 -0.16 1 1
INPP5D 0 0 -9999 0 -9999 0 0
SOCS5 0.017 0.059 -9999 0 -0.393 1 1
STAT6 (dimer)/ETS1 -0.352 0.489 -9999 0 -1.166 10 10
SOCS1 -0.234 0.344 -9999 0 -0.759 9 9
SOCS3 -0.199 0.358 -9999 0 -1.16 4 4
FCER2 -0.277 0.371 -9999 0 -0.915 5 5
PARP14 0.013 0.043 -9999 0 -0.298 1 1
CCL17 -0.372 0.492 -9999 0 -1.2 9 9
GRB2 0.017 0 -9999 0 -9999 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.145 0.242 -9999 0 -0.612 5 5
T cell proliferation -0.375 0.505 -9999 0 -1.206 10 10
IL4R/JAK1 -0.383 0.505 -9999 0 -1.21 10 10
EGR2 -0.449 0.583 -9999 0 -1.278 14 14
JAK2 -0.016 0.066 -9999 0 -0.301 2 2
JAK3 0.022 0.006 -9999 0 -9999 0 0
PIK3R1 -0.038 0.134 -9999 0 -0.355 8 8
JAK1 -0.034 0.133 -9999 0 -0.407 6 6
COL1A2 -0.167 0.334 -9999 0 -1.128 4 4
CCL26 -0.355 0.48 -9999 0 -1.201 8 8
IL4R -0.385 0.527 -9999 0 -1.275 9 9
PTPN6 0.018 0.058 -9999 0 -0.395 1 1
IL13RA2 -0.42 0.509 -9999 0 -1.157 12 12
IL13RA1 -0.004 0.036 -9999 0 -9999 0 0
IRF4 -0.076 0.203 -9999 0 -0.754 3 3
ARG1 -0.12 0.282 -9999 0 -1.336 2 2
CBL -0.185 0.274 -9999 0 -0.603 8 8
GTF3A 0.016 0.033 -9999 0 -9999 0 0
PIK3CA 0.01 0.058 -9999 0 -0.411 1 1
IL13RA1/JAK2 -0.011 0.063 -9999 0 -0.227 1 1
IRF4/BCL6 -0.069 0.189 -9999 0 -0.709 3 3
CD40LG 0.001 0.101 -9999 0 -0.413 3 3
MAPK14 -0.192 0.299 -9999 0 -0.731 6 6
mitosis -0.179 0.294 -9999 0 -0.742 6 6
STAT6 -0.407 0.564 -9999 0 -1.318 10 10
SPI1 -0.002 0.093 -9999 0 -0.369 3 3
RPS6KB1 -0.171 0.287 -9999 0 -0.683 7 7
STAT6 (dimer) -0.41 0.562 -9999 0 -1.318 10 10
STAT6 (dimer)/PARP14 -0.38 0.51 -9999 0 -1.212 10 10
mast cell activation 0.007 0.014 -9999 0 -9999 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.158 0.254 -9999 0 -0.625 4 4
FRAP1 -0.189 0.309 -9999 0 -0.792 6 6
LTA -0.372 0.497 -9999 0 -1.173 10 10
FES -0.014 0.112 -9999 0 -0.411 4 4
T-helper 1 cell differentiation 0.401 0.544 1.276 10 -9999 0 10
CCL11 -0.401 0.507 -9999 0 -1.159 12 12
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.171 0.265 -9999 0 -0.678 5 5
IL2RG 0.016 0.047 -9999 0 -0.327 1 1
IL10 -0.36 0.482 -9999 0 -1.13 10 10
IRS1 -0.02 0.118 -9999 0 -0.389 5 5
IRS2 -0.016 0.106 -9999 0 -0.344 5 5
IL4 -0.065 0.13 -9999 0 -9999 0 0
IL5 -0.355 0.48 -9999 0 -1.201 8 8
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.291 0.385 -9999 0 -0.877 9 9
COL1A1 -0.224 0.42 -9999 0 -1.144 7 7
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -9999 0 0
IL4/IL4R/JAK1 -0.383 0.513 -9999 0 -1.23 10 10
IL2R gamma/JAK3 0.026 0.038 -9999 0 -0.239 1 1
TFF3 -0.617 0.696 -9999 0 -1.426 21 21
ALOX15 -0.389 0.506 -9999 0 -1.167 11 11
MYBL1 0.017 0 -9999 0 -9999 0 0
T-helper 2 cell differentiation -0.314 0.403 -9999 0 -0.944 10 10
SHC1 0.017 0 -9999 0 -9999 0 0
CEBPB 0.013 0.05 -9999 0 -0.294 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.207 0.323 -9999 0 -0.794 8 8
mol:PI-3-4-5-P3 -0.189 0.309 -9999 0 -0.792 6 6
PI3K -0.201 0.327 -9999 0 -0.852 6 6
DOK2 0.004 0.071 -9999 0 -0.355 2 2
ETS1 0.02 0.042 -9999 0 -0.263 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.135 0.235 -9999 0 -0.572 6 6
ITGB3 -0.384 0.506 -9999 0 -1.239 9 9
PIGR -0.593 0.688 -9999 0 -1.404 20 20
IGHE 0.02 0.045 -9999 0 -9999 0 0
MAPKKK cascade -0.132 0.232 -9999 0 -0.562 6 6
BCL6 0.016 0 -9999 0 -9999 0 0
OPRM1 -0.355 0.48 -9999 0 -1.163 9 9
RETNLB -0.37 0.496 -9999 0 -1.173 10 10
SELP -0.371 0.499 -9999 0 -1.233 9 9
AICDA -0.365 0.492 -9999 0 -1.271 8 8
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.088 0.103 -9999 0 -0.195 18 18
SMAD6-7/SMURF1 0.031 0.035 -9999 0 -0.227 1 1
NOG -0.037 0.124 -9999 0 -0.312 9 9
SMAD9 -0.061 0.156 -9999 0 -0.512 5 5
SMAD4 0.002 0.081 -9999 0 -0.411 2 2
SMAD5 -0.029 0.072 -9999 0 -0.26 1 1
BMP7/USAG1 -0.19 0.184 -9999 0 -0.307 35 35
SMAD5/SKI -0.018 0.071 -9999 0 -0.242 1 1
SMAD1 0.017 0.073 -9999 0 -0.279 2 2
BMP2 -0.081 0.152 -9999 0 -0.313 16 16
SMAD1/SMAD1/SMAD4 -0.019 0.052 -9999 0 -9999 0 0
BMPR1A 0.01 0.058 -9999 0 -0.411 1 1
BMPR1B -0.012 0.092 -9999 0 -0.3 5 5
BMPR1A-1B/BAMBI -0.06 0.116 -9999 0 -0.188 23 23
AHSG 0.017 0 -9999 0 -9999 0 0
CER1 0.01 0.058 -9999 0 -0.411 1 1
BMP2-4/CER1 -0.082 0.138 -9999 0 -0.335 8 8
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.045 0.105 -9999 0 -0.352 2 2
BMP2-4 (homodimer) -0.106 0.152 -9999 0 -0.248 26 26
RGMB 0.017 0 -9999 0 -9999 0 0
BMP6/BMPR2/BMPR1A-1B -0.011 0.093 -9999 0 -0.213 5 5
RGMA -0.02 0.118 -9999 0 -0.389 5 5
SMURF1 0.017 0 -9999 0 -9999 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.053 0.102 -9999 0 -0.265 6 6
BMP2-4/USAG1 -0.16 0.159 -9999 0 -0.316 21 21
SMAD6/SMURF1/SMAD5 -0.018 0.071 -9999 0 -0.242 1 1
SOSTDC1 -0.127 0.191 -9999 0 -0.372 20 20
BMP7/BMPR2/BMPR1A-1B -0.078 0.101 -9999 0 -0.197 13 13
SKI 0.017 0 -9999 0 -9999 0 0
BMP6 (homodimer) -0.039 0.129 -9999 0 -0.324 9 9
HFE2 0.002 0.081 -9999 0 -0.411 2 2
ZFYVE16 0.017 0 -9999 0 -9999 0 0
MAP3K7 0.017 0 -9999 0 -9999 0 0
BMP2-4/CHRD -0.078 0.132 -9999 0 -0.329 7 7
SMAD5/SMAD5/SMAD4 -0.026 0.084 -9999 0 -0.292 2 2
MAPK1 0.01 0.058 -9999 0 -0.411 1 1
TAK1/TAB family -0.016 0.091 -9999 0 -0.404 1 1
BMP7 (homodimer) -0.158 0.186 -9999 0 -0.346 26 26
NUP214 0.017 0 -9999 0 -9999 0 0
BMP6/FETUA -0.014 0.09 -9999 0 -0.213 9 9
SMAD1/SKI 0.026 0.07 -9999 0 -0.261 2 2
SMAD6 0.017 0 -9999 0 -9999 0 0
CTDSP2 0.017 0 -9999 0 -9999 0 0
BMP2-4/FETUA -0.078 0.132 -9999 0 -0.329 7 7
MAP3K7IP1 0.017 0 -9999 0 -9999 0 0
GREM1 0.012 0.043 -9999 0 -0.3 1 1
BMPR2 (homodimer) 0.01 0.058 -9999 0 -0.41 1 1
GADD34/PP1CA 0.022 0.055 -9999 0 -0.227 2 2
BMPR1A-1B (homodimer) 0 0.074 -9999 0 -0.208 6 6
CHRDL1 -0.014 0.099 -9999 0 -0.322 5 5
ENDOFIN/SMAD1 0.026 0.07 -9999 0 -0.261 2 2
SMAD6-7/SMURF1/SMAD1 0.037 0.071 -9999 0 -9999 0 0
SMAD6/SMURF1 0.017 0 -9999 0 -9999 0 0
BAMBI -0.105 0.176 -9999 0 -0.349 18 18
SMURF2 -0.014 0.112 -9999 0 -0.411 4 4
BMP2-4/CHRDL1 -0.096 0.133 -9999 0 -0.316 9 9
BMP2-4/GREM1 -0.081 0.135 -9999 0 -0.327 8 8
SMAD7 0.01 0.058 -9999 0 -0.411 1 1
SMAD8A/SMAD8A/SMAD4 -0.056 0.152 -9999 0 -0.437 6 6
SMAD1/SMAD6 0.026 0.07 -9999 0 -0.261 2 2
TAK1/SMAD6 0.026 0 -9999 0 -9999 0 0
BMP7 -0.158 0.186 -9999 0 -0.347 26 26
BMP6 -0.039 0.129 -9999 0 -0.324 9 9
MAP3K7IP2 0.017 0 -9999 0 -9999 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.043 0.102 -9999 0 -0.249 7 7
PPM1A 0.017 0 -9999 0 -9999 0 0
SMAD1/SMURF2 0.012 0.096 -9999 0 -0.354 2 2
SMAD7/SMURF1 0.02 0.041 -9999 0 -0.28 1 1
CTDSPL 0.002 0.081 -9999 0 -0.411 2 2
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 -0.004 0.09 -9999 0 -0.374 3 3
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.068 0.115 -9999 0 -0.273 9 9
CHRD 0.017 0 -9999 0 -9999 0 0
BMPR2 0.01 0.058 -9999 0 -0.411 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.057 0.107 -9999 0 -0.278 6 6
BMP4 -0.079 0.157 -9999 0 -0.329 15 15
FST -0.03 0.124 -9999 0 -0.347 7 7
BMP2-4/NOG -0.109 0.137 -9999 0 -0.315 11 11
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.065 0.096 -9999 0 -0.178 13 13
Endothelins

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
AKT1 -0.004 0.135 0.281 1 -0.424 2 3
PTK2B 0.017 0.001 -9999 0 -9999 0 0
mol:Ca2+ -0.037 0.179 -9999 0 -0.497 3 3
EDN1 -0.032 0.146 0.22 1 -0.316 9 10
EDN3 -0.209 0.179 -9999 0 -0.342 34 34
EDN2 -0.093 0.18 -9999 0 -0.381 15 15
HRAS/GDP -0.039 0.123 -9999 0 -0.308 3 3
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.004 0.096 0.192 1 -0.319 1 2
ADCY4 -0.029 0.135 -9999 0 -0.378 5 5
ADCY5 -0.008 0.107 0.195 1 -0.345 2 3
ADCY6 -0.005 0.107 -9999 0 -0.345 2 2
ADCY7 -0.009 0.109 0.195 1 -0.345 2 3
ADCY1 -0.005 0.107 -9999 0 -0.345 2 2
ADCY2 -0.01 0.118 -9999 0 -0.41 2 2
ADCY3 -0.019 0.119 -9999 0 -0.442 2 2
ADCY8 -0.009 0.109 -9999 0 -0.345 2 2
ADCY9 -0.01 0.112 -9999 0 -0.331 3 3
arachidonic acid secretion -0.136 0.243 -9999 0 -0.523 12 12
ETB receptor/Endothelin-1/Gq/GTP -0.023 0.11 -9999 0 -0.303 5 5
GNAO1 0.017 0 -9999 0 -9999 0 0
HRAS 0.017 0.002 -9999 0 -9999 0 0
ETA receptor/Endothelin-1/G12/GTP 0.017 0.144 0.319 2 -0.39 2 4
ETA receptor/Endothelin-1/Gs/GTP 0.009 0.134 0.298 2 -0.369 2 4
mol:GTP -0.002 0.006 -9999 0 -9999 0 0
COL3A1 -0.024 0.177 0.281 1 -0.601 3 4
EDNRB -0.026 0.128 -9999 0 -0.412 5 5
response to oxidative stress 0 0 -9999 0 -9999 0 0
CYSLTR2 -0.019 0.157 0.281 1 -0.415 4 5
CYSLTR1 -0.013 0.145 0.281 1 -0.395 3 4
SLC9A1 0.003 0.083 0.199 1 -0.301 1 2
mol:GDP -0.049 0.127 -9999 0 -0.296 5 5
SLC9A3 -0.072 0.241 -9999 0 -0.637 7 7
RAF1 -0.064 0.162 -9999 0 -0.367 8 8
JUN -0.076 0.303 -9999 0 -0.92 5 5
JAK2 -0.01 0.143 0.281 1 -0.348 4 5
mol:IP3 -0.017 0.103 -9999 0 -0.275 3 3
ETA receptor/Endothelin-1 0.003 0.177 0.367 2 -0.426 3 5
PLCB1 -0.005 0.091 -9999 0 -0.378 3 3
PLCB2 0.016 0.004 -9999 0 -9999 0 0
ETA receptor/Endothelin-3 -0.134 0.161 -9999 0 -0.244 33 33
FOS -0.13 0.32 -9999 0 -0.902 7 7
Gai/GDP -0.015 0.111 -9999 0 -0.451 2 2
CRK -0.014 0.112 -9999 0 -0.411 4 4
mol:Ca ++ -0.031 0.16 0.257 1 -0.456 4 5
BCAR1 0.018 0.001 -9999 0 -9999 0 0
PRKCB1 -0.032 0.111 -9999 0 -0.266 4 4
GNAQ -0.002 0.007 -9999 0 -9999 0 0
GNAZ -0.01 0.099 -9999 0 -0.355 4 4
GNAL 0.01 0.058 -9999 0 -0.411 1 1
Gs family/GDP -0.048 0.111 -9999 0 -0.28 4 4
ETA receptor/Endothelin-1/Gq/GTP -0.002 0.105 0.212 1 -0.289 3 4
MAPK14 -0.013 0.094 -9999 0 -0.317 2 2
TRPC6 -0.039 0.184 -9999 0 -0.563 2 2
GNAI2 0.017 0 -9999 0 -9999 0 0
GNAI3 0.01 0.058 -9999 0 -0.411 1 1
GNAI1 -0.05 0.152 -9999 0 -0.386 9 9
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.021 0.1 -9999 0 -0.296 3 3
ETB receptor/Endothelin-2 -0.082 0.153 -9999 0 -0.301 16 16
ETB receptor/Endothelin-3 -0.161 0.15 -9999 0 -0.254 36 36
ETB receptor/Endothelin-1 -0.036 0.155 -9999 0 -0.371 7 7
MAPK3 -0.111 0.278 -9999 0 -0.764 7 7
MAPK1 -0.113 0.277 -9999 0 -0.764 7 7
Rac1/GDP -0.039 0.123 -9999 0 -0.308 3 3
cAMP biosynthetic process -0.005 0.121 -9999 0 -0.38 3 3
MAPK8 -0.044 0.199 -9999 0 -0.495 6 6
SRC 0.017 0.001 -9999 0 -9999 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.042 0.135 -9999 0 -0.322 8 8
p130Cas/CRK/Src/PYK2 -0.053 0.139 -9999 0 -0.322 4 4
mol:K + 0 0 -9999 0 -9999 0 0
G12/GDP -0.039 0.123 -9999 0 -0.308 3 3
COL1A2 -0.051 0.237 -9999 0 -0.606 6 6
EntrezGene:2778 0 0 -9999 0 -9999 0 0
ETA receptor/Endothelin-2 -0.056 0.146 -9999 0 -0.288 12 12
mol:DAG -0.018 0.103 -9999 0 -0.275 3 3
MAP2K2 -0.084 0.213 -9999 0 -0.557 7 7
MAP2K1 -0.084 0.213 -9999 0 -0.557 7 7
EDNRA 0.01 0.112 0.218 1 -0.421 2 3
positive regulation of muscle contraction 0.002 0.117 0.246 1 -0.363 2 3
Gq family/GDP -0.06 0.094 -9999 0 -0.253 4 4
HRAS/GTP -0.046 0.117 -9999 0 -0.266 6 6
PRKCH -0.03 0.119 -9999 0 -0.313 4 4
RAC1 0.017 0 -9999 0 -9999 0 0
PRKCA -0.021 0.105 -9999 0 -0.252 4 4
PRKCB -0.02 0.101 -9999 0 -0.25 4 4
PRKCE -0.019 0.098 -9999 0 -0.26 3 3
PRKCD -0.016 0.107 -9999 0 -0.27 4 4
PRKCG -0.014 0.102 -9999 0 -0.262 3 3
regulation of vascular smooth muscle contraction -0.15 0.37 -9999 0 -1.054 7 7
PRKCQ -0.059 0.114 -9999 0 -0.259 7 7
PLA2G4A -0.148 0.265 -9999 0 -0.571 12 12
GNA14 0.002 0.071 -9999 0 -0.354 2 2
GNA15 0.01 0.044 -9999 0 -0.306 1 1
GNA12 0.017 0 -9999 0 -9999 0 0
GNA11 0.016 0.006 -9999 0 -9999 0 0
Rac1/GTP 0.017 0.144 0.319 2 -0.39 2 4
MMP1 -0.094 0.254 0.258 1 -0.461 14 15
TCGA08_p53

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
CDKN2A -0.091 0.122 -9999 0 -0.229 23 23
TP53 -0.033 0.078 0.245 1 -0.36 1 2
Senescence -0.033 0.078 0.245 1 -0.359 1 2
Apoptosis -0.033 0.078 0.245 1 -0.359 1 2
Activated_Oncogenes 0 0 -9999 0 -9999 0 0
MDM2 0.062 0.084 0.207 7 -0.209 1 8
MDM4 0.004 0.071 -9999 0 -0.355 2 2
Nongenotropic Androgen 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
PTK2 0.012 0 -9999 0 -9999 0 0
GNB1/GNG2 -0.017 0.09 -9999 0 -0.205 7 7
regulation of S phase of mitotic cell cycle -0.034 0.131 -9999 0 -0.27 9 9
GNAO1 0.017 0 -9999 0 -9999 0 0
HRAS 0.017 0.001 -9999 0 -9999 0 0
SHBG/T-DHT 0.012 0 -9999 0 -9999 0 0
PELP1 0.017 0.001 -9999 0 -9999 0 0
AKT1 0.012 0 -9999 0 -9999 0 0
MAP2K1 -0.017 0.092 -9999 0 -0.271 3 3
T-DHT/AR -0.043 0.111 -9999 0 -0.259 11 11
G-protein coupled receptor activity 0 0 -9999 0 -9999 0 0
mol:GTP -0.001 0.003 -9999 0 -0.006 13 13
GNAI2 0.017 0 -9999 0 -9999 0 0
GNAI3 0.009 0.058 -9999 0 -0.411 1 1
GNAI1 -0.05 0.152 -9999 0 -0.386 9 9
mol:GDP -0.074 0.156 -9999 0 -0.404 8 8
cell proliferation -0.051 0.165 -9999 0 -0.379 9 9
PIK3CA 0.01 0.058 -9999 0 -0.411 1 1
FOS -0.105 0.278 -9999 0 -0.717 8 8
mol:Ca2+ -0.011 0.03 -9999 0 -0.065 9 9
MAPK3 -0.034 0.127 -9999 0 -0.317 5 5
MAPK1 -0.029 0.114 -9999 0 -0.319 4 4
PIK3R1 -0.038 0.134 -9999 0 -0.355 8 8
mol:IP3 -0.001 0.002 -9999 0 -0.003 14 14
cAMP biosynthetic process 0.015 0.023 0.096 1 -9999 0 1
GNG2 0.006 0.06 -9999 0 -0.3 2 2
potassium channel inhibitor activity -0.001 0.002 -9999 0 -0.003 14 14
HRAS/GTP -0.014 0.08 -9999 0 -0.182 8 8
actin cytoskeleton reorganization -0.002 0.075 -9999 0 -0.221 4 4
SRC 0.017 0.001 -9999 0 -9999 0 0
voltage-gated calcium channel activity -0.001 0.002 -9999 0 -0.003 14 14
PI3K -0.013 0.095 -9999 0 -0.225 8 8
apoptosis 0.051 0.163 0.382 9 -9999 0 9
T-DHT/AR/PELP1 -0.025 0.095 -9999 0 -0.209 11 11
HRAS/GDP -0.049 0.156 -9999 0 -0.379 8 8
CREB1 -0.056 0.173 -9999 0 -0.408 9 9
RAC1-CDC42/GTP 0.004 0.079 -9999 0 -0.224 4 4
AR -0.062 0.158 -9999 0 -0.372 11 11
GNB1 0.017 0 -9999 0 -9999 0 0
RAF1 -0.017 0.089 -9999 0 -0.259 3 3
RAC1-CDC42/GDP -0.037 0.153 -9999 0 -0.386 7 7
T-DHT/AR/PELP1/Src -0.013 0.088 -9999 0 -0.201 8 8
MAP2K2 -0.017 0.092 -9999 0 -0.271 3 3
T-DHT/AR/PELP1/Src/PI3K -0.035 0.133 -9999 0 -0.272 9 9
GNAZ -0.01 0.099 -9999 0 -0.355 4 4
SHBG 0.017 0 -9999 0 -9999 0 0
Gi family/GNB1/GNG2/GDP -0.015 0.114 -9999 0 -0.38 3 3
mol:T-DHT 0 0.001 -9999 0 -0.003 5 5
RAC1 0.017 0 -9999 0 -9999 0 0
GNRH1 -0.019 0.087 -9999 0 -0.26 6 6
Gi family/GTP -0.037 0.118 -9999 0 -0.249 9 9
CDC42 0.017 0 -9999 0 -9999 0 0
LPA receptor mediated events

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
GNB1/GNG2 -0.008 0.077 -9999 0 -0.205 4 4
NF kappa B1 p50/RelA/I kappa B alpha 0.004 0.075 -9999 0 -0.211 3 3
AP1 -0.081 0.099 -9999 0 -0.213 16 16
mol:PIP3 -0.062 0.106 -9999 0 -0.237 9 9
AKT1 -0.01 0.104 -9999 0 -0.302 3 3
PTK2B -0.011 0.058 -9999 0 -0.181 4 4
RHOA -0.005 0.087 -9999 0 -0.38 2 2
PIK3CB 0.004 0.071 -9999 0 -0.355 2 2
mol:Ca2+ -0.009 0.066 -9999 0 -0.169 7 7
MAGI3 0.002 0.081 -9999 0 -0.41 2 2
RELA 0.017 0 -9999 0 -9999 0 0
apoptosis -0.014 0.063 -9999 0 -0.135 11 11
HRAS/GDP 0.013 0 -9999 0 -9999 0 0
positive regulation of microtubule depolymerization -0.003 0.07 -9999 0 -0.206 4 4
NF kappa B1 p50/RelA -0.037 0.074 -9999 0 -0.254 4 4
endothelial cell migration -0.055 0.157 -9999 0 -0.354 11 11
ADCY4 -0.044 0.114 -9999 0 -0.281 6 6
ADCY5 -0.03 0.109 -9999 0 -0.297 5 5
ADCY6 -0.029 0.109 -9999 0 -0.297 5 5
ADCY7 -0.032 0.11 -9999 0 -0.297 5 5
ADCY1 -0.029 0.109 -9999 0 -0.297 5 5
ADCY2 -0.032 0.114 -9999 0 -0.323 5 5
ADCY3 -0.039 0.12 -9999 0 -0.337 5 5
ADCY8 -0.032 0.113 -9999 0 -0.289 6 6
ADCY9 -0.032 0.109 -9999 0 -0.297 5 5
GSK3B -0.004 0.056 -9999 0 -0.181 3 3
arachidonic acid secretion -0.022 0.103 -9999 0 -0.277 5 5
GNG2 0.006 0.06 -9999 0 -0.299 2 2
TRIP6 -0.018 0.101 -9999 0 -0.328 5 5
GNAO1 -0.016 0.074 -9999 0 -0.158 11 11
HRAS 0.017 0 -9999 0 -9999 0 0
NFKBIA -0.011 0.08 -9999 0 -0.22 5 5
GAB1 -0.002 0.082 -9999 0 -0.337 3 3
mol:GTP 0 0 -9999 0 -9999 0 0
lamellipodium assembly -0.003 0.167 -9999 0 -0.851 2 2
JUN -0.026 0.124 -9999 0 -0.374 6 6
LPA/LPA2/NHERF2 -0.02 0.071 -9999 0 -0.224 5 5
TIAM1 -0.03 0.19 -9999 0 -0.995 2 2
PIK3R1 -0.038 0.134 -9999 0 -0.355 8 8
mol:IP3 -0.01 0.067 -9999 0 -0.172 7 7
PLCB3 -0.014 0.072 -9999 0 -0.204 6 6
FOS -0.079 0.166 -9999 0 -0.355 14 14
positive regulation of mitosis -0.022 0.103 -9999 0 -0.277 5 5
LPA/LPA1-2-3 -0.025 0.064 -9999 0 -0.148 11 11
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 -0.003 0.058 -9999 0 -0.182 3 3
GNAZ -0.032 0.092 -9999 0 -0.184 13 13
EGFR/PI3K-beta/Gab1 -0.064 0.111 -9999 0 -0.246 9 9
positive regulation of dendritic cell cytokine production -0.025 0.064 -9999 0 -0.147 11 11
LPA/LPA2/MAGI-3 -0.008 0.059 -9999 0 -0.276 2 2
ARHGEF1 0.002 0.062 -9999 0 -0.169 3 3
GNAI2 -0.016 0.074 -9999 0 -0.158 11 11
GNAI3 -0.02 0.09 -9999 0 -0.179 11 11
GNAI1 -0.055 0.115 -9999 0 -0.204 18 18
LPA/LPA3 -0.014 0.033 -9999 0 -0.077 11 11
LPA/LPA2 -0.014 0.033 -9999 0 -0.077 11 11
LPA/LPA1 -0.032 0.087 -9999 0 -0.201 11 11
HB-EGF/EGFR -0.048 0.114 -9999 0 -0.243 10 10
HBEGF -0.05 0.12 -9999 0 -0.24 15 15
mol:DAG -0.01 0.067 -9999 0 -0.172 7 7
cAMP biosynthetic process -0.03 0.111 -9999 0 -0.301 5 5
NFKB1 0.017 0 -9999 0 -9999 0 0
SRC 0.017 0 -9999 0 -9999 0 0
GNB1 0.018 0.001 -9999 0 -9999 0 0
LYN -0.007 0.074 -9999 0 -0.215 4 4
GNAQ -0.009 0.025 -9999 0 -0.058 11 11
LPAR2 0 0.001 -9999 0 -9999 0 0
LPAR3 0 0.001 -9999 0 -9999 0 0
LPAR1 -0.021 0.052 -9999 0 -0.122 11 11
IL8 -0.147 0.18 -9999 0 -0.401 14 14
PTK2 -0.012 0.062 -9999 0 -0.131 11 11
Rac1/GDP 0.013 0 -9999 0 -9999 0 0
CASP3 -0.014 0.064 -9999 0 -0.135 11 11
EGFR -0.011 0.099 -9999 0 -0.355 4 4
PLCG1 -0.002 0.041 -9999 0 -0.179 2 2
PLD2 -0.012 0.062 -9999 0 -0.165 4 4
G12/G13 -0.002 0.069 -9999 0 -0.189 3 3
PI3K-beta -0.051 0.096 -9999 0 -0.349 3 3
cell migration 0.003 0.062 -9999 0 -0.243 2 2
SLC9A3R2 -0.018 0.112 -9999 0 -0.366 5 5
PXN -0.003 0.058 -9999 0 -0.185 3 3
HRAS/GTP -0.023 0.105 -9999 0 -0.283 5 5
RAC1 0.017 0 -9999 0 -9999 0 0
MMP9 -0.087 0.171 -9999 0 -0.359 15 15
PRKCE 0.004 0.071 -9999 0 -0.356 2 2
PRKCD -0.006 0.071 -9999 0 -0.185 6 6
Gi(beta/gamma) -0.027 0.111 -9999 0 -0.299 5 5
mol:LPA -0.021 0.052 -9999 0 -0.122 11 11
TRIP6/p130 Cas/FAK1/Paxillin -0.002 0.075 -9999 0 -0.222 1 1
MAPKKK cascade -0.022 0.103 -9999 0 -0.277 5 5
contractile ring contraction involved in cytokinesis -0.005 0.086 -9999 0 -0.377 2 2
mol:GDP 0 0 -9999 0 -9999 0 0
GNA14 -0.008 0.05 -9999 0 -0.215 2 2
GNA15 -0.003 0.031 -9999 0 -0.124 1 1
GNA12 0.017 0 -9999 0 -9999 0 0
GNA13 0.017 0 -9999 0 -9999 0 0
MAPT -0.004 0.071 -9999 0 -0.211 4 4
GNA11 -0.001 0.026 -9999 0 -9999 0 0
Rac1/GTP -0.003 0.177 -9999 0 -0.902 2 2
MMP2 -0.055 0.158 -9999 0 -0.355 11 11
Caspase cascade in apoptosis

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
TOP1 0.003 0.099 0.173 1 -0.207 7 8
ACTA1 -0.014 0.124 0.178 5 -0.262 9 14
NUMA1 -0.001 0.104 0.173 1 -0.209 8 9
SPTAN1 -0.005 0.12 0.188 2 -0.254 8 10
LIMK1 -0.011 0.118 0.199 1 -0.254 8 9
BIRC3 -0.059 0.154 -9999 0 -0.36 11 11
BIRC2 0.017 0 -9999 0 -9999 0 0
BAX 0.017 0 -9999 0 -9999 0 0
CASP10 -0.028 0.105 -9999 0 -0.236 10 10
CRMA 0 0 -9999 0 -9999 0 0
XIAP 0 0 -9999 0 -9999 0 0
PTK2 0.003 0.099 0.173 1 -0.207 7 8
DIABLO 0.017 0 -9999 0 -9999 0 0
apoptotic nuclear changes -0.005 0.119 0.182 3 -0.251 8 11
response to UV 0 0 -9999 0 -9999 0 0
CRADD -0.02 0.118 -9999 0 -0.389 5 5
GSN -0.021 0.129 0.189 2 -0.268 9 11
MADD 0.017 0 -9999 0 -9999 0 0
TFAP2A -0.036 0.145 -9999 0 -0.511 4 4
BID -0.012 0.067 -9999 0 -0.147 10 10
MAP3K1 -0.028 0.149 -9999 0 -0.505 4 4
TRADD 0.002 0.081 -9999 0 -0.411 2 2
mol:Ca2+ 0 0 -9999 0 -9999 0 0
APAF-1/Pro-Caspase 9 0.021 0.041 -9999 0 -0.28 1 1
mol:Activated DNA 0 0 -9999 0 -9999 0 0
ARHGDIB -0.008 0.126 0.199 1 -0.271 8 9
CASP9 0.018 0 -9999 0 -9999 0 0
DNA repair -0.017 0.082 0.393 1 -0.168 5 6
neuron apoptosis 0.022 0.017 -9999 0 -9999 0 0
mol:NAD 0 0 -9999 0 -9999 0 0
DNA fragmentation during apoptosis -0.004 0.12 0.196 1 -0.235 9 10
APAF1 0.01 0.058 -9999 0 -0.41 1 1
CASP6 0.008 0.064 -9999 0 -9999 0 0
TRAF2 0.017 0 -9999 0 -9999 0 0
ICAD/CAD -0.003 0.12 0.196 1 -0.239 9 10
CASP7 0.047 0.085 0.24 7 -9999 0 7
KRT18 -0.007 0.11 -9999 0 -0.557 2 2
apoptosis -0.022 0.124 0.221 1 -0.313 4 5
DFFA -0.005 0.12 0.199 1 -0.254 8 9
DFFB -0.009 0.124 0.199 1 -0.254 9 10
PARP1 0.017 0.083 0.169 5 -0.397 1 6
actin filament polymerization 0.006 0.11 0.232 8 -0.194 1 9
TNF -0.02 0.106 -9999 0 -0.318 6 6
CYCS -0.004 0.049 -9999 0 -0.127 1 1
SATB1 -0.048 0.091 -9999 0 -9999 0 0
SLK -0.005 0.12 0.199 1 -0.254 8 9
p15 BID/BAX -0.001 0.061 -9999 0 -9999 0 0
CASP2 -0.01 0.113 -9999 0 -0.372 3 3
JNK cascade 0.028 0.147 0.5 4 -9999 0 4
CASP3 -0.012 0.127 0.19 3 -0.275 8 11
LMNB2 0.007 0.07 -9999 0 -0.261 1 1
RIPK1 0.017 0 -9999 0 -9999 0 0
CASP4 0.002 0.081 -9999 0 -0.411 2 2
Mammalian IAPs/DIABLO -0.008 0.085 -9999 0 -0.205 6 6
negative regulation of DNA binding -0.036 0.143 -9999 0 -0.506 4 4
stress fiber formation -0.005 0.119 0.187 2 -0.251 8 10
GZMB -0.043 0.126 -9999 0 -0.274 12 12
CASP1 -0.02 0.109 -9999 0 -0.394 3 3
LMNB1 -0.004 0.084 -9999 0 -0.234 4 4
APP 0.022 0.017 -9999 0 -9999 0 0
TNFRSF1A 0.01 0.058 -9999 0 -0.411 1 1
response to stress 0 0 -9999 0 -9999 0 0
CASP8 0.012 0 -9999 0 -9999 0 0
VIM -0.027 0.125 0.199 3 -0.32 4 7
LMNA 0.007 0.07 -9999 0 -0.261 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.018 0.119 -9999 0 -0.352 4 4
LRDD 0.017 0 -9999 0 -9999 0 0
SREBF1 -0.012 0.119 0.177 1 -0.254 8 9
APAF-1/Caspase 9 0.011 0.058 -9999 0 -9999 0 0
nuclear fragmentation during apoptosis -0.001 0.103 0.172 1 -0.207 8 9
CFL2 -0.007 0.112 0.195 1 -0.237 8 9
GAS2 -0.056 0.135 -9999 0 -0.297 9 9
positive regulation of apoptosis 0.005 0.075 -9999 0 -0.251 2 2
PRF1 0.006 0.06 -9999 0 -0.299 2 2
FOXA2 and FOXA3 transcription factor networks

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ACADVL -0.064 0.355 -9999 0 -0.962 5 5
PCK1 -0.051 0.223 -9999 0 -0.65 1 1
HNF4A -0.068 0.384 -9999 0 -1.059 5 5
KCNJ11 -0.06 0.374 -9999 0 -0.976 5 5
AKT1 0.033 0.148 -9999 0 -0.439 2 2
response to starvation 0.002 0.012 -9999 0 -9999 0 0
DLK1 -0.081 0.403 -9999 0 -0.994 6 6
NKX2-1 0.053 0.24 0.523 2 -0.607 2 4
ACADM -0.084 0.394 -9999 0 -1.016 6 6
TAT -0.046 0.218 -9999 0 -0.759 1 1
CEBPB 0.015 0.043 -9999 0 -0.293 1 1
CEBPA 0.016 0.043 -9999 0 -0.293 1 1
TTR -0.197 0.345 -9999 0 -0.939 6 6
PKLR -0.064 0.355 -9999 0 -0.962 5 5
APOA1 -0.11 0.471 -9999 0 -1.324 5 5
CPT1C -0.141 0.421 -9999 0 -0.908 9 9
ALAS1 -0.055 0.328 -9999 0 -1.442 2 2
TFRC -0.168 0.46 -9999 0 -0.995 10 10
FOXF1 -0.017 0.097 -9999 0 -0.316 5 5
NF1 0.012 0.064 -9999 0 -0.405 1 1
HNF1A (dimer) -0.044 0.161 -9999 0 -0.373 10 10
CPT1A -0.064 0.355 -9999 0 -0.962 5 5
HMGCS1 -0.067 0.357 -9999 0 -0.962 5 5
NR3C1 0.014 0.067 -9999 0 -0.285 2 2
CPT1B -0.08 0.38 -9999 0 -0.965 6 6
chromatin remodeling 0 0 -9999 0 -9999 0 0
SP1 0.014 0.04 -9999 0 -0.224 1 1
GCK -0.08 0.377 -9999 0 -0.939 6 6
CREB1 0.024 0.017 -9999 0 -9999 0 0
IGFBP1 -0.053 0.293 -9999 0 -0.994 3 3
PDX1 -0.084 0.34 -9999 0 -0.981 4 4
UCP2 -0.101 0.416 -9999 0 -0.975 8 8
ALDOB -0.06 0.374 -9999 0 -0.976 5 5
AFP -0.131 0.146 -9999 0 -0.432 3 3
BDH1 -0.064 0.355 -9999 0 -0.962 5 5
HADH -0.064 0.39 -9999 0 -1.017 5 5
F2 -0.092 0.416 -9999 0 -1.126 5 5
HNF1A -0.044 0.162 -9999 0 -0.374 10 10
G6PC -0.028 0.131 -9999 0 -0.489 2 2
SLC2A2 -0.057 0.28 -9999 0 -0.769 2 2
INS 0.015 0.043 0.191 2 -9999 0 2
FOXA1 -0.197 0.193 -9999 0 -0.351 32 32
FOXA3 -0.069 0.183 -9999 0 -0.336 15 15
FOXA2 -0.068 0.44 -9999 0 -1.115 5 5
ABCC8 -0.079 0.395 -9999 0 -0.964 6 6
ALB -0.134 0.149 -9999 0 -0.464 2 2
FAS signaling pathway (CD95)

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
SPTAN1 0.044 0.073 0.209 8 -9999 0 8
RFC1 0.044 0.073 0.209 8 -9999 0 8
PRKDC 0.044 0.073 0.209 8 -9999 0 8
RIPK1 0.018 0.002 -9999 0 -9999 0 0
CASP7 0.018 0.031 -9999 0 -9999 0 0
FASLG/FAS/FADD/FAF1 0.044 0.104 0.211 11 -0.21 2 13
MAP2K4 0.02 0.067 -9999 0 -9999 0 0
mol:ceramide 0.008 0.072 -9999 0 -0.3 1 1
GSN 0.027 0.093 0.21 7 -0.223 3 10
FASLG/FAS/FADD/FAF1/Caspase 8 0.045 0.095 0.222 2 -0.309 1 3
FAS -0.017 0.106 -9999 0 -0.343 5 5
BID 0.014 0.024 -9999 0 -9999 0 0
MAP3K1 0.022 0.059 -9999 0 -9999 0 0
MAP3K7 0.017 0.002 -9999 0 -9999 0 0
RB1 0.039 0.082 0.209 8 -0.223 1 9
CFLAR 0.01 0.058 -9999 0 -0.412 1 1
HGF/MET -0.057 0.129 -9999 0 -0.242 16 16
ARHGDIB 0.04 0.07 0.21 7 -9999 0 7
FADD 0.009 0.058 -9999 0 -0.41 1 1
actin filament polymerization -0.027 0.092 0.222 3 -0.209 7 10
NFKB1 0.004 0.038 -9999 0 -9999 0 0
MAPK8 0.014 0.094 -9999 0 -0.389 1 1
DFFA 0.044 0.073 0.209 8 -9999 0 8
DNA fragmentation during apoptosis 0.039 0.067 0.201 7 -9999 0 7
FAS/FADD/MET 0.007 0.081 -9999 0 -0.247 4 4
CFLAR/RIP1 0.021 0.042 -9999 0 -0.282 1 1
FAIM3 0 0.073 -9999 0 -0.3 3 3
FAF1 0.016 0.007 -9999 0 -9999 0 0
PARP1 0.04 0.07 0.21 7 -9999 0 7
DFFB 0.039 0.067 0.201 7 -9999 0 7
CHUK 0.006 0.044 -9999 0 -9999 0 0
FASLG -0.013 0.091 -9999 0 -0.298 5 5
FAS/FADD -0.004 0.083 -9999 0 -0.236 6 6
HGF 0.012 0.043 -9999 0 -0.3 1 1
LMNA 0.046 0.065 0.193 8 -9999 0 8
CASP6 0.044 0.073 0.209 8 -9999 0 8
CASP10 0.017 0.004 -9999 0 -9999 0 0
CASP3 0.044 0.089 0.244 8 -9999 0 8
PTPN13 -0.125 0.195 -9999 0 -0.387 19 19
CASP8 0.009 0.037 0.163 3 -9999 0 3
IL6 -0.008 0.106 -9999 0 -9999 0 0
MET 0.012 0.043 -9999 0 -0.3 1 1
ICAD/CAD 0.042 0.06 0.187 7 -9999 0 7
FASLG/FAS/FADD/FAF1/Caspase 10 0.008 0.073 -9999 0 -0.303 1 1
activation of caspase activity by cytochrome c 0.014 0.024 -9999 0 -9999 0 0
PAK2 0.044 0.073 0.208 8 -9999 0 8
BCL2 -0.058 0.159 -9999 0 -0.388 10 10
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.097 0.273 -9999 0 -0.957 4 4
MKNK1 0.017 0 -9999 0 -9999 0 0
MAPK14 -0.026 0.09 -9999 0 -0.27 4 4
ATF2/c-Jun -0.045 0.166 -9999 0 -0.458 6 6
MAPK11 -0.026 0.09 -9999 0 -0.27 4 4
MITF -0.028 0.108 -9999 0 -0.302 5 5
MAPKAPK5 -0.02 0.103 -9999 0 -0.316 4 4
KRT8 -0.033 0.111 -9999 0 -0.292 6 6
MAPKAPK3 0.017 0 -9999 0 -9999 0 0
MAPKAPK2 0.017 0 -9999 0 -9999 0 0
p38alpha-beta/CK2 -0.037 0.128 -9999 0 -0.368 5 5
CEBPB -0.023 0.104 -9999 0 -0.316 4 4
SLC9A1 -0.02 0.103 -9999 0 -0.316 4 4
mol:GDP 0 0 -9999 0 -9999 0 0
ATF2 -0.025 0.111 -9999 0 -0.301 5 5
p38alpha-beta/MNK1 -0.014 0.103 -9999 0 -0.305 4 4
JUN -0.045 0.165 -9999 0 -0.456 6 6
PPARGC1A -0.037 0.12 -9999 0 -0.336 5 5
USF1 -0.045 0.125 -9999 0 -0.337 6 6
RAB5/GDP/GDI1 -0.007 0.073 -9999 0 -0.222 4 4
NOS2 -0.029 0.103 -9999 0 -0.301 5 5
DDIT3 -0.036 0.117 -9999 0 -0.286 7 7
RAB5A 0.017 0 -9999 0 -9999 0 0
HSPB1 -0.024 0.099 -9999 0 -0.256 6 6
p38alpha-beta/HBP1 -0.02 0.107 -9999 0 -0.291 5 5
CREB1 -0.04 0.127 -9999 0 -0.412 4 4
RAB5/GDP 0.013 0 -9999 0 -9999 0 0
EIF4E -0.009 0.087 -9999 0 -0.26 4 4
RPS6KA4 -0.025 0.107 -9999 0 -0.302 5 5
PLA2G4A -0.1 0.139 -9999 0 -0.305 9 9
GDI1 -0.02 0.103 -9999 0 -0.316 4 4
TP53 -0.033 0.123 -9999 0 -0.389 4 4
RPS6KA5 -0.06 0.15 -9999 0 -0.35 8 8
ESR1 -0.102 0.182 -9999 0 -0.337 16 16
HBP1 0.01 0.058 -9999 0 -0.411 1 1
MEF2C -0.026 0.115 -9999 0 -0.333 5 5
MEF2A -0.025 0.107 -9999 0 -0.302 5 5
EIF4EBP1 -0.042 0.126 -9999 0 -0.412 4 4
KRT19 -0.057 0.144 -9999 0 -0.32 9 9
ELK4 -0.025 0.107 -9999 0 -0.302 5 5
ATF6 -0.02 0.103 -9999 0 -0.316 4 4
ATF1 -0.041 0.127 -9999 0 -0.412 4 4
p38alpha-beta/MAPKAPK2 -0.014 0.103 -9999 0 -0.305 4 4
p38alpha-beta/MAPKAPK3 -0.014 0.103 -9999 0 -0.305 4 4
Canonical Wnt signaling 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
HDAC1 0.026 0.023 -9999 0 -9999 0 0
AES 0.016 0.06 -9999 0 -0.4 1 1
FBXW11 0.017 0 -9999 0 -9999 0 0
mol:GTP 0 0.001 -9999 0 -9999 0 0
LRP6/FZD1 0.027 0.001 -9999 0 -9999 0 0
SMAD4 0.002 0.081 -9999 0 -0.411 2 2
DKK2 0.004 0.071 -9999 0 -0.355 2 2
TLE1 0.017 0.047 -9999 0 -0.304 1 1
MACF1 0.018 0.001 -9999 0 -9999 0 0
CTNNB1 0.07 0.101 0.252 4 -0.264 2 6
WIF1 -0.168 0.189 -9999 0 -0.353 27 27
beta catenin/RanBP3 0.078 0.164 0.435 5 -0.4 1 6
KREMEN2 -0.071 0.16 -9999 0 -0.351 13 13
DKK1 -0.152 0.179 -9999 0 -0.334 26 26
beta catenin/beta TrCP1 0.076 0.095 0.26 3 -0.256 1 4
FZD1 0.018 0.001 -9999 0 -9999 0 0
AXIN2 -0.083 0.269 -9999 0 -1.259 2 2
AXIN1 0.01 0.058 -9999 0 -0.411 1 1
RAN 0.01 0.058 -9999 0 -0.411 1 1
Axin1/APC/GSK3/beta catenin 0.046 0.076 -9999 0 -0.464 1 1
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.012 0.14 -9999 0 -0.371 4 4
Axin1/APC/GSK3 0.071 0.059 0.21 2 -9999 0 2
Axin1/APC/GSK3/beta catenin/Macf1 0.066 0.054 -9999 0 -0.245 1 1
HNF1A -0.046 0.158 -9999 0 -0.396 9 9
CTBP1 0.024 0.018 -9999 0 -9999 0 0
MYC 0.004 0.069 -9999 0 -9999 0 0
RANBP3 0.018 0.001 -9999 0 -9999 0 0
DKK2/LRP6/Kremen 2 -0.025 0.108 -9999 0 -0.249 7 7
NKD1 -0.077 0.154 -9999 0 -0.322 15 15
TCF4 -0.008 0.111 -9999 0 -0.396 4 4
TCF3 0.024 0.018 -9999 0 -9999 0 0
WNT1/LRP6/FZD1/Axin1 0.042 0.033 -9999 0 -0.199 1 1
Ran/GTP 0.008 0.041 -9999 0 -0.289 1 1
CtBP/CBP/TCF/TLE1/AES -0.003 0.164 0.355 3 -0.331 1 4
LEF1 -0.108 0.187 -9999 0 -0.367 18 18
DVL1 0.067 0.038 -9999 0 -9999 0 0
CSNK2A1 0.018 0 -9999 0 -9999 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.036 0.147 -9999 0 -0.39 5 5
DKK1/LRP6/Kremen 2 -0.115 0.143 -9999 0 -0.295 15 15
LRP6 0.018 0.001 -9999 0 -9999 0 0
CSNK1A1 0.026 0.023 -9999 0 -9999 0 0
NLK 0.01 0.043 -9999 0 -0.301 1 1
CCND1 -0.068 0.306 -9999 0 -1.277 3 3
WNT1 0.018 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 0.017 0.001 -9999 0 -9999 0 0
PPP2R5D 0.081 0.079 0.203 14 -9999 0 14
APC 0.036 0.03 -9999 0 -0.179 1 1
WNT1/LRP6/FZD1 0.1 0.077 0.214 13 -9999 0 13
CREBBP 0.024 0.018 -9999 0 -9999 0 0
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.003 0.07 -9999 0 -0.181 7 7
cell-cell adhesion 0.063 0.091 0.309 4 -9999 0 4
Ephrin B/EPHB2/RasGAP -0.022 0.116 -9999 0 -0.286 4 4
ITSN1 0.017 0 -9999 0 -9999 0 0
PIK3CA 0.01 0.058 -9999 0 -0.411 1 1
SHC1 0.017 0 -9999 0 -9999 0 0
Ephrin B1/EPHB3 -0.088 0.148 -9999 0 -0.251 22 22
Ephrin B1/EPHB1 -0.053 0.107 -9999 0 -0.195 19 19
HRAS/GDP -0.059 0.095 -9999 0 -0.276 6 6
Ephrin B/EPHB1/GRB7 -0.04 0.123 -9999 0 -0.276 6 6
Endophilin/SYNJ1 -0.03 0.103 -9999 0 -0.268 4 4
KRAS 0.017 0 -9999 0 -9999 0 0
Ephrin B/EPHB1/Src -0.032 0.113 -9999 0 -0.297 3 3
endothelial cell migration -0.014 0.094 -9999 0 -0.216 6 6
GRB2 0.017 0 -9999 0 -9999 0 0
GRB7 0 0.073 -9999 0 -0.3 3 3
PAK1 -0.03 0.106 -9999 0 -0.266 4 4
HRAS 0.017 0 -9999 0 -9999 0 0
RRAS -0.03 0.105 -9999 0 -0.272 4 4
DNM1 0.01 0.058 -9999 0 -0.411 1 1
cell-cell signaling 0 0 -9999 0 -9999 0 0
CRK -0.053 0.114 -9999 0 -0.291 5 5
lamellipodium assembly -0.063 0.091 -9999 0 -0.309 4 4
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.021 0.093 -9999 0 -0.365 1 1
PIK3R1 -0.038 0.134 -9999 0 -0.355 8 8
EPHB2 -0.02 0.106 -9999 0 -0.318 6 6
EPHB3 -0.099 0.182 -9999 0 -0.376 16 16
EPHB1 -0.037 0.124 -9999 0 -0.312 9 9
EPHB4 0.01 0.058 -9999 0 -0.411 1 1
mol:GDP -0.022 0.125 -9999 0 -0.28 6 6
Ephrin B/EPHB2 -0.032 0.115 -9999 0 -0.221 12 12
Ephrin B/EPHB3 -0.072 0.142 -9999 0 -0.252 16 16
JNK cascade -0.049 0.106 -9999 0 -0.251 4 4
Ephrin B/EPHB1 -0.041 0.111 -9999 0 -0.217 11 11
RAP1/GDP -0.015 0.128 -9999 0 -0.319 4 4
EFNB2 -0.014 0.099 -9999 0 -0.322 5 5
EFNB3 0.017 0 -9999 0 -9999 0 0
EFNB1 -0.058 0.159 -9999 0 -0.389 10 10
Ephrin B2/EPHB1-2 -0.03 0.12 -9999 0 -0.291 7 7
RAP1B 0.017 0 -9999 0 -9999 0 0
RAP1A -0.006 0.098 -9999 0 -0.411 3 3
CDC42/GTP -0.071 0.108 -9999 0 -0.396 3 3
Rap1/GTP -0.079 0.104 -9999 0 -0.317 6 6
axon guidance -0.003 0.069 -9999 0 -0.18 7 7
MAPK3 -0.007 0.083 -9999 0 -0.318 1 1
MAPK1 -0.011 0.085 -9999 0 -0.318 1 1
Rac1/GDP -0.012 0.119 -9999 0 -0.275 4 4
actin cytoskeleton reorganization -0.052 0.076 -9999 0 -0.268 3 3
CDC42/GDP -0.012 0.119 -9999 0 -0.275 4 4
PI3K -0.011 0.096 -9999 0 -0.218 6 6
EFNA5 0.01 0.058 -9999 0 -0.411 1 1
Ephrin B2/EPHB4 0.001 0.066 -9999 0 -0.184 6 6
Ephrin B/EPHB2/Intersectin/N-WASP -0.028 0.128 -9999 0 -0.691 1 1
CDC42 0.017 0 -9999 0 -9999 0 0
RAS family/GTP -0.059 0.084 -9999 0 -0.303 3 3
PTK2 0.023 0.028 -9999 0 -9999 0 0
MAP4K4 -0.05 0.107 -9999 0 -0.254 4 4
SRC 0.017 0 -9999 0 -9999 0 0
KALRN 0.004 0.071 -9999 0 -0.355 2 2
Intersectin/N-WASP 0.02 0.041 -9999 0 -0.28 1 1
neuron projection morphogenesis -0.02 0.114 -9999 0 -0.288 4 4
MAP2K1 -0.014 0.087 -9999 0 -0.339 1 1
WASL 0.009 0.058 -9999 0 -0.411 1 1
Ephrin B1/EPHB1-2/NCK1 -0.051 0.116 -9999 0 -0.215 14 14
cell migration -0.008 0.095 -9999 0 -0.35 1 1
NRAS 0.012 0.043 -9999 0 -0.3 1 1
SYNJ1 -0.03 0.105 -9999 0 -0.272 4 4
PXN 0.017 0 -9999 0 -9999 0 0
TF -0.032 0.11 -9999 0 -0.265 6 6
HRAS/GTP -0.039 0.111 -9999 0 -0.333 3 3
Ephrin B1/EPHB1-2 -0.056 0.113 -9999 0 -0.223 13 13
cell adhesion mediated by integrin 0.059 0.103 0.249 9 -9999 0 9
RAC1 0.017 0 -9999 0 -9999 0 0
mol:GTP -0.042 0.121 -9999 0 -0.306 5 5
RAC1-CDC42/GTP -0.096 0.106 -9999 0 -0.306 8 8
RASA1 0.017 0 -9999 0 -9999 0 0
RAC1-CDC42/GDP -0.005 0.116 -9999 0 -0.308 2 2
ruffle organization -0.038 0.119 -9999 0 -0.289 6 6
NCK1 0.01 0.058 -9999 0 -0.411 1 1
receptor internalization -0.027 0.101 -9999 0 -0.254 4 4
Ephrin B/EPHB2/KALRN -0.03 0.118 -9999 0 -0.286 4 4
ROCK1 -0.074 0.133 -9999 0 -0.252 16 16
RAS family/GDP -0.051 0.076 -9999 0 -0.268 3 3
Rac1/GTP -0.066 0.095 -9999 0 -0.325 4 4
Ephrin B/EPHB1/Src/Paxillin -0.029 0.1 -9999 0 -0.393 1 1
Glypican 2 network

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
MDK -0.028 0.129 -9999 0 -0.392 6 6
GPC2 0 0 -9999 0 -9999 0 0
GPC2/Midkine -0.019 0.091 -9999 0 -0.274 6 6
neuron projection morphogenesis -0.019 0.091 -9999 0 -0.273 6 6
IL27-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
TGFB1 0.026 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 0.082 0.247 0.744 5 -0.505 1 6
IL27/IL27R/JAK1 -0.129 0.351 0.47 1 -1.159 5 6
TBX21 -0.145 0.25 0.404 1 -0.575 9 10
IL12B 0.016 0.005 -9999 0 -9999 0 0
IL12A 0.001 0.049 -9999 0 -0.245 2 2
IL6ST 0.002 0.063 -9999 0 -0.312 2 2
IL27RA/JAK1 -0.115 0.367 -9999 0 -1.239 5 5
IL27 -0.038 0.137 -9999 0 -0.388 7 7
TYK2 0.014 0.015 -9999 0 -9999 0 0
T-helper cell lineage commitment 0.024 0.051 -9999 0 -9999 0 0
T-helper 2 cell differentiation 0.082 0.247 0.744 5 -0.505 1 6
T cell proliferation during immune response 0.082 0.247 0.744 5 -0.505 1 6
MAPKKK cascade -0.082 0.247 0.505 1 -0.744 5 6
STAT3 0.01 0.058 -9999 0 -0.411 1 1
STAT2 0.017 0 -9999 0 -9999 0 0
STAT1 -0.032 0.119 -9999 0 -0.316 8 8
IL12RB1 0.009 0.058 -9999 0 -0.411 1 1
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -9999 0 -9999 0 0
IL12RB2 -0.121 0.235 0.406 1 -0.57 8 9
IL27/IL27R/JAK2/TYK2 -0.084 0.252 0.506 1 -0.759 5 6
positive regulation of T cell mediated cytotoxicity -0.082 0.247 0.505 1 -0.744 5 6
STAT1 (dimer) -0.19 0.326 0.553 1 -0.983 6 7
JAK2 0.003 0.063 -9999 0 -0.309 2 2
JAK1 -0.031 0.135 -9999 0 -0.412 6 6
STAT2 (dimer) -0.072 0.237 0.439 1 -0.713 5 6
T cell proliferation -0.091 0.236 0.469 1 -0.71 5 6
IL12/IL12R/TYK2/JAK2 0.004 0.074 -9999 0 -9999 0 0
IL17A 0.024 0.051 -9999 0 -9999 0 0
mast cell activation 0.082 0.247 0.744 5 -0.505 1 6
IFNG -0.012 0.043 0.143 1 -0.092 4 5
T cell differentiation -0.007 0.008 -9999 0 -0.02 13 13
STAT3 (dimer) -0.076 0.237 0.439 1 -0.713 5 6
STAT5A (dimer) -0.072 0.237 0.439 1 -0.713 5 6
STAT4 (dimer) -0.072 0.237 0.439 1 -0.713 5 6
STAT4 0.017 0 -9999 0 -9999 0 0
T cell activation 0.003 0.038 0.123 5 -9999 0 5
IL27R/JAK2/TYK2 -0.085 0.322 0.412 1 -1.053 5 6
GATA3 0.011 0.097 -9999 0 -0.42 1 1
IL18 -0.017 0.082 -9999 0 -0.246 6 6
positive regulation of mast cell cytokine production -0.074 0.23 0.435 1 -0.694 5 6
IL27/EBI3 -0.028 0.112 0.186 1 -0.27 9 10
IL27RA -0.104 0.36 0.424 1 -1.214 5 6
IL6 -0.02 0.112 -9999 0 -0.289 8 8
STAT5A 0.017 0 -9999 0 -9999 0 0
monocyte differentiation -0.001 0.002 -9999 0 -9999 0 0
IL2 0.028 0.213 0.484 5 -1.152 1 6
IL1B -0.019 0.086 -9999 0 -0.26 6 6
EBI3 -0.002 0.083 -9999 0 -0.415 2 2
TNF -0.014 0.073 -9999 0 -0.217 6 6
IL6-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
BCL2L1 0.011 0.261 -9999 0 -0.746 3 3
CRP 0.011 0.261 -9999 0 -0.746 3 3
cell cycle arrest -0.003 0.295 -9999 0 -0.805 4 4
TIMP1 0.008 0.252 -9999 0 -0.654 4 4
IL6ST 0.01 0.062 -9999 0 -0.3 2 2
Rac1/GDP -0.033 0.18 0.259 1 -0.456 5 6
AP1 0.004 0.135 -9999 0 -0.302 1 1
GAB2 0.021 0.007 -9999 0 -9999 0 0
TNFSF11 -0.093 0.421 -9999 0 -0.955 9 9
HSP90B1 0.02 0.189 -9999 0 -1.284 1 1
GAB1 0 0.083 -9999 0 -0.34 3 3
MAPK14 -0.061 0.236 -9999 0 -0.561 7 7
AKT1 0.033 0.103 -9999 0 -0.58 1 1
FOXO1 0.037 0.098 -9999 0 -0.545 1 1
MAP2K6 -0.056 0.225 0.247 1 -0.516 7 8
mol:GTP 0 0.002 -9999 0 -9999 0 0
MAP2K4 -0.02 0.204 -9999 0 -0.543 4 4
MITF -0.02 0.184 0.261 1 -0.533 4 5
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 -0.098 0.345 -9999 0 -1.284 4 4
CEBPB 0.02 0.044 -9999 0 -0.297 1 1
GRB2/SOS1/GAB family/SHP2 0.03 0.096 0.241 1 -0.269 2 3
STAT3 -0.008 0.309 -9999 0 -0.856 4 4
STAT1 -0.02 0.134 -9999 0 -0.433 3 3
CEBPD -0.028 0.356 -9999 0 -0.999 5 5
PIK3CA 0.011 0.058 -9999 0 -0.41 1 1
PI3K -0.016 0.112 -9999 0 -0.266 8 8
JUN -0.026 0.124 -9999 0 -0.374 6 6
PIAS3/MITF -0.012 0.175 0.246 1 -0.502 4 5
MAPK11 -0.061 0.236 -9999 0 -0.561 7 7
STAT3 (dimer)/FOXO1 0.013 0.24 -9999 0 -0.624 3 3
GRB2/SOS1/GAB family -0.013 0.167 -9999 0 -0.43 5 5
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.048 0.176 -9999 0 -0.396 7 7
GRB2 0.02 0.004 -9999 0 -9999 0 0
JAK2 0.006 0.06 -9999 0 -0.3 2 2
LBP 0.03 0.229 -9999 0 -0.645 3 3
PIK3R1 -0.037 0.134 -9999 0 -0.354 8 8
JAK1 -0.028 0.138 -9999 0 -0.417 6 6
MYC 0.009 0.266 -9999 0 -0.784 3 3
FGG 0.011 0.261 -9999 0 -0.746 3 3
macrophage differentiation -0.003 0.295 -9999 0 -0.805 4 4
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.014 0.136 -9999 0 -0.306 7 7
JUNB 0.007 0.261 -9999 0 -0.707 4 4
FOS -0.079 0.166 -9999 0 -0.355 14 14
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.02 0.18 0.276 1 -0.483 4 5
STAT1/PIAS1 0 0.179 0.287 1 -0.381 6 7
GRB2/SOS1/GAB family/SHP2/PI3K 0.024 0.106 -9999 0 -0.621 1 1
STAT3 (dimer) -0.007 0.306 -9999 0 -0.849 4 4
PRKCD -0.016 0.233 -9999 0 -0.621 4 4
IL6R -0.022 0.12 -9999 0 -0.356 6 6
SOCS3 -0.083 0.308 -9999 0 -1.046 4 4
gp130 (dimer)/JAK1/JAK1/LMO4 -0.009 0.122 -9999 0 -0.254 9 9
Rac1/GTP -0.032 0.19 -9999 0 -0.477 5 5
HCK -0.017 0.113 -9999 0 -0.366 5 5
MAPKKK cascade 0.04 0.097 -9999 0 -0.35 1 1
bone resorption -0.08 0.393 -9999 0 -0.88 9 9
IRF1 0.009 0.261 -9999 0 -0.746 3 3
mol:GDP -0.039 0.181 0.266 1 -0.434 6 7
SOS1 0.02 0.007 -9999 0 -9999 0 0
VAV1 -0.039 0.184 0.267 1 -0.441 6 7
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.099 0.328 -9999 0 -0.736 8 8
PTPN11 0.023 0.033 -9999 0 -9999 0 0
IL6/IL6RA -0.031 0.113 -9999 0 -0.217 14 14
gp130 (dimer)/TYK2/TYK2/LMO4 0.016 0.077 -9999 0 -0.216 4 4
gp130 (dimer)/JAK2/JAK2/LMO4 0.01 0.089 -9999 0 -0.224 6 6
IL6 -0.026 0.117 -9999 0 -0.306 8 8
PIAS3 0.017 0 -9999 0 -9999 0 0
PTPRE -0.037 0.13 -9999 0 -0.368 7 7
PIAS1 0.017 0 -9999 0 -9999 0 0
RAC1 0.018 0.001 -9999 0 -9999 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0.002 0.121 0.24 2 -0.268 5 7
LMO4 -0.008 0.109 -9999 0 -0.389 4 4
STAT3 (dimer)/PIAS3 -0.015 0.284 -9999 0 -0.786 4 4
MCL1 0.037 0.101 -9999 0 -0.511 1 1
Syndecan-4-mediated signaling events

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
PTK2 0.004 0.063 -9999 0 -0.301 1 1
Syndecan-4/Syndesmos -0.042 0.154 -9999 0 -0.382 8 8
positive regulation of JNK cascade -0.079 0.169 -9999 0 -0.391 9 9
Syndecan-4/ADAM12 -0.046 0.161 -9999 0 -0.398 8 8
CCL5 -0.049 0.142 -9999 0 -0.344 10 10
Rac1/GDP 0.013 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 0.01 0.058 -9999 0 -0.411 1 1
PLG 0.007 0.061 -9999 0 -0.303 2 2
ADAM12 0.006 0.06 -9999 0 -0.3 2 2
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 -0.006 0.02 -9999 0 -9999 0 0
Syndecan-4/Laminin alpha1 -0.063 0.175 -9999 0 -0.443 8 8
Syndecan-4/CXCL12/CXCR4 -0.082 0.178 -9999 0 -0.412 9 9
Syndecan-4/Laminin alpha3 -0.057 0.166 -9999 0 -0.401 9 9
MDK -0.028 0.129 -9999 0 -0.392 6 6
Syndecan-4/FZD7 -0.103 0.177 -9999 0 -0.46 8 8
Syndecan-4/Midkine -0.062 0.152 -9999 0 -0.382 8 8
FZD7 -0.123 0.186 -9999 0 -0.361 20 20
Syndecan-4/FGFR1/FGF -0.052 0.157 -9999 0 -0.365 8 8
THBS1 0.017 0 -9999 0 -9999 0 0
integrin-mediated signaling pathway -0.057 0.173 -9999 0 -0.414 8 8
positive regulation of MAPKKK cascade -0.079 0.169 -9999 0 -0.391 9 9
Syndecan-4/TACI -0.042 0.154 -9999 0 -0.382 8 8
CXCR4 -0.042 0.143 -9999 0 -0.383 8 8
cell adhesion 0.016 0.042 -9999 0 -9999 0 0
Syndecan-4/Dynamin -0.042 0.154 -9999 0 -0.382 8 8
Syndecan-4/TSP1 -0.042 0.154 -9999 0 -0.382 8 8
Syndecan-4/GIPC -0.042 0.154 -9999 0 -0.382 8 8
Syndecan-4/RANTES -0.07 0.176 -9999 0 -0.427 8 8
ITGB1 0.017 0 -9999 0 -9999 0 0
LAMA1 -0.034 0.124 -9999 0 -0.327 8 8
LAMA3 -0.018 0.112 -9999 0 -0.366 5 5
RAC1 0.017 0 -9999 0 -9999 0 0
PRKCA 0.006 0.083 -9999 0 -0.392 2 2
Syndecan-4/alpha-Actinin -0.042 0.154 -9999 0 -0.382 8 8
TFPI 0 0.073 -9999 0 -0.3 3 3
F2 0.007 0.043 -9999 0 -0.3 1 1
alpha5/beta1 Integrin 0.026 0 -9999 0 -9999 0 0
positive regulation of cell adhesion -0.071 0.178 -9999 0 -0.437 9 9
ACTN1 0.017 0 -9999 0 -9999 0 0
TNC -0.024 0.119 -9999 0 -0.355 6 6
Syndecan-4/CXCL12 -0.066 0.162 -9999 0 -0.398 8 8
FGF6 0.004 0.071 -9999 0 -0.355 2 2
RHOA 0.01 0.058 -9999 0 -0.411 1 1
CXCL12 -0.038 0.134 -9999 0 -0.355 8 8
TNFRSF13B 0.017 0 -9999 0 -9999 0 0
FGF2 0.006 0.06 -9999 0 -0.3 2 2
FGFR1 -0.018 0.112 -9999 0 -0.366 5 5
Syndecan-4/PI-4-5-P2 -0.052 0.152 -9999 0 -0.388 8 8
mol:GDP 0 0 -9999 0 -9999 0 0
FN1 0.001 0.073 -9999 0 -0.301 3 3
cell migration -0.003 0.007 -9999 0 -9999 0 0
PRKCD 0.013 0.043 -9999 0 -0.297 1 1
vasculogenesis -0.04 0.15 -9999 0 -0.371 8 8
SDC4 -0.054 0.16 -9999 0 -0.408 8 8
Syndecan-4/Tenascin C -0.059 0.179 -9999 0 -0.428 8 8
Syndecan-4/PI-4-5-P2/PKC alpha -0.008 0.014 -9999 0 -9999 0 0
Syndecan-4/Syntenin -0.045 0.163 -9999 0 -0.405 8 8
MMP9 -0.086 0.172 -9999 0 -0.359 15 15
Rac1/GTP 0.016 0.043 -9999 0 -9999 0 0
cytoskeleton organization -0.04 0.15 -9999 0 -0.371 8 8
GIPC1 0.017 0 -9999 0 -9999 0 0
Syndecan-4/TFPI -0.049 0.154 -9999 0 -0.382 8 8
Visual signal transduction: Rods

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
mol:K + 0.002 0.081 -9999 0 -0.41 2 2
GNAT1/GTP 0.007 0.041 -9999 0 -0.288 1 1
Metarhodopsin II/Arrestin -0.025 0.087 -9999 0 -0.177 13 13
PDE6G/GNAT1/GTP -0.001 0.066 -9999 0 -0.17 7 7
mol:GTP 0 0 -9999 0 -9999 0 0
absorption of light 0 0 -9999 0 -9999 0 0
GNAT1 0.01 0.058 -9999 0 -0.411 1 1
GRK1 0 0 -9999 0 -9999 0 0
CNG Channel -0.05 0.08 -9999 0 -0.263 4 4
mol:Na + 0.014 0.066 -9999 0 -0.277 1 1
mol:ADP 0 0 -9999 0 -9999 0 0
RGS9-1/Gbeta5/R9AP -0.034 0.113 -9999 0 -0.264 7 7
mol:GDP 0 0 -9999 0 -9999 0 0
cGMP/CNG Channel 0.022 0.071 -9999 0 -0.283 1 1
CNGB1 0.017 0 -9999 0 -9999 0 0
RDH5 -0.02 0.106 -9999 0 -0.318 6 6
SAG -0.065 0.148 -9999 0 -0.325 13 13
mol:Ca2+ 0.015 0.078 -9999 0 -0.267 2 2
Na + (4 Units) -0.025 0.059 -9999 0 -0.263 2 2
RGS9 -0.024 0.106 -9999 0 -0.3 7 7
GNB1/GNGT1 -0.07 0.137 -9999 0 -0.261 18 18
GNAT1/GDP -0.023 0.1 -9999 0 -0.213 8 8
GUCY2D 0.017 0 -9999 0 -9999 0 0
GNGT1 -0.117 0.192 -9999 0 -0.386 18 18
GUCY2F 0.011 0.043 -9999 0 -0.3 1 1
GNB5 0 0.073 -9999 0 -0.3 3 3
mol:GMP (4 units) -0.014 0.092 -9999 0 -0.245 5 5
mol:11-cis-retinal -0.02 0.106 -9999 0 -0.318 6 6
mol:cGMP 0.036 0.042 -9999 0 -9999 0 0
GNB1 0.017 0 -9999 0 -9999 0 0
Rhodopsin 0 0.074 -9999 0 -0.208 6 6
SLC24A1 0.002 0.081 -9999 0 -0.411 2 2
CNGA1 -0.028 0.119 -9999 0 -0.331 7 7
Metarhodopsin II 0.011 0 -9999 0 -9999 0 0
mol:Ca ++ 0 0 -9999 0 -9999 0 0
GC1/GCAP Family 0.035 0.04 -9999 0 -9999 0 0
RGS9BP -0.044 0.138 -9999 0 -0.349 9 9
Metarhodopsin II/Transducin -0.044 0.1 -9999 0 -0.198 15 15
GCAP Family/Ca ++ 0.024 0.039 -9999 0 -9999 0 0
PDE6A/B -0.015 0.085 -9999 0 -0.194 10 10
mol:Pi -0.035 0.113 -9999 0 -0.263 7 7
mol:all-trans-retinal 0 0 -9999 0 -9999 0 0
Transducin -0.045 0.108 -9999 0 -0.204 15 15
PDE6B -0.041 0.123 -9999 0 -0.3 10 10
PDE6A 0.017 0 -9999 0 -9999 0 0
PDE6G -0.018 0.1 -9999 0 -0.3 6 6
RHO 0.017 0 -9999 0 -9999 0 0
PDE6 -0.048 0.135 -9999 0 -0.313 7 7
GUCA1A 0.012 0.043 -9999 0 -0.3 1 1
GC2/GCAP Family 0.032 0.046 -9999 0 -9999 0 0
GUCA1C 0.012 0.043 -9999 0 -0.3 1 1
GUCA1B 0.012 0.043 -9999 0 -0.3 1 1
LPA4-mediated signaling events

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
ADCY4 -0.02 0.082 -9999 0 -0.19 10 10
ADCY5 0.007 0.047 -9999 0 -0.184 3 3
ADCY6 0.01 0.041 -9999 0 -0.197 2 2
ADCY7 0.005 0.053 -9999 0 -0.209 3 3
ADCY1 0.01 0.041 -9999 0 -0.197 2 2
ADCY2 0.004 0.052 -9999 0 -0.178 4 4
ADCY3 -0.007 0.072 -9999 0 -0.209 6 6
ADCY8 0.005 0.053 -9999 0 -0.209 3 3
PRKCE 0.002 0.049 -9999 0 -0.246 2 2
ADCY9 0.004 0.052 -9999 0 -0.178 4 4
mol:DAG 0 0 -9999 0 -9999 0 0
cAMP biosynthetic process 0.001 0.059 -9999 0 -0.278 1 1
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.021 0.062 -9999 0 -0.411 1 1
HSPA8 -0.017 0.112 -9999 0 -0.414 4 4
SMAD3/SMAD4/ER alpha -0.061 0.159 0.216 1 -0.282 14 15
AKT1 0.018 0.009 -9999 0 -9999 0 0
GSC -0.427 0.609 -9999 0 -1.282 18 18
NKX2-5 -0.005 0.086 -9999 0 -0.307 4 4
muscle cell differentiation 0.048 0.166 0.367 8 -9999 0 8
SMAD2-3/SMAD4/SP1 -0.005 0.124 -9999 0 -0.267 6 6
SMAD4 -0.03 0.105 -9999 0 -0.299 5 5
CBFB 0.017 0 -9999 0 -9999 0 0
SAP18 0.016 0.002 -9999 0 -9999 0 0
Cbp/p300/MSG1 0.03 0.08 -9999 0 -0.227 3 3
SMAD3/SMAD4/VDR 0.034 0.095 -9999 0 -0.225 1 1
MYC 0.01 0.044 -9999 0 -0.305 1 1
CDKN2B -0.012 0.087 -9999 0 -9999 0 0
AP1 -0.055 0.171 -9999 0 -0.372 9 9
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.011 0.064 -9999 0 -9999 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.033 0.106 -9999 0 -0.275 4 4
SP3 0.02 0 -9999 0 -9999 0 0
CREB1 0.017 0 -9999 0 -9999 0 0
FOXH1 -0.018 0.052 -9999 0 -9999 0 0
SMAD3/SMAD4/GR 0.002 0.101 -9999 0 -0.254 4 4
GATA3 -0.002 0.083 -9999 0 -0.288 4 4
SKI/SIN3/HDAC complex/NCoR1 0.034 0.032 -9999 0 -9999 0 0
MEF2C/TIF2 -0.037 0.132 -9999 0 -0.649 1 1
endothelial cell migration -0.016 0.175 1.197 1 -9999 0 1
MAX 0.017 0.008 -9999 0 -9999 0 0
RBBP7 -0.009 0.091 -9999 0 -0.328 4 4
RBBP4 0.016 0.002 -9999 0 -9999 0 0
RUNX2 0.006 0.06 -9999 0 -0.3 2 2
RUNX3 -0.089 0.182 -9999 0 -0.395 14 14
RUNX1 -0.004 0.09 -9999 0 -0.374 3 3
CTBP1 0.017 0 -9999 0 -9999 0 0
NR3C1 0.005 0.061 -9999 0 -0.303 2 2
VDR -0.016 0.106 -9999 0 -0.344 5 5
CDKN1A -0.072 0.366 -9999 0 -1.185 5 5
KAT2B 0.004 0.006 -9999 0 -9999 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.055 0.141 -9999 0 -0.256 12 12
DCP1A 0.017 0 -9999 0 -9999 0 0
SKI 0.016 0.002 -9999 0 -9999 0 0
SERPINE1 0.015 0.177 -9999 0 -1.213 1 1
SMAD3/SMAD4/ATF2 0.009 0.087 -9999 0 -0.24 2 2
SMAD3/SMAD4/ATF3 0.002 0.098 -9999 0 -0.25 3 3
SAP30 0.016 0.002 -9999 0 -9999 0 0
Cbp/p300/PIAS3 0.061 0.059 -9999 0 -0.228 1 1
JUN -0.058 0.168 -9999 0 -0.389 8 8
SMAD3/SMAD4/IRF7 0.009 0.096 -9999 0 -0.254 3 3
TFE3 0.019 0.018 -9999 0 -9999 0 0
COL1A2 -0.032 0.207 -9999 0 -0.683 4 4
mesenchymal cell differentiation -0.002 0.098 0.24 4 -9999 0 4
DLX1 -0.032 0.118 -9999 0 -0.313 8 8
TCF3 0.017 0 -9999 0 -9999 0 0
FOS -0.084 0.167 -9999 0 -0.36 14 14
SMAD3/SMAD4/Max 0.008 0.089 -9999 0 -0.243 2 2
Cbp/p300/SNIP1 0.031 0.063 -9999 0 -0.223 3 3
ZBTB17 0.017 0.006 -9999 0 -9999 0 0
LAMC1 0.008 0.096 -9999 0 -0.341 2 2
TGIF2/HDAC complex/SMAD3/SMAD4 -0.012 0.113 -9999 0 -0.262 6 6
IRF7 0.013 0.045 -9999 0 -0.292 1 1
ESR1 -0.096 0.188 -9999 0 -0.397 15 15
HNF4A 0.017 0 -9999 0 -9999 0 0
MEF2C -0.048 0.138 -9999 0 -0.466 2 2
SMAD2-3/SMAD4 -0.018 0.106 -9999 0 -0.253 4 4
Cbp/p300/Src-1 0.048 0.046 -9999 0 -0.227 1 1
IGHV3OR16-13 -0.015 0.03 -9999 0 -9999 0 0
TGIF2/HDAC complex -0.014 0.112 -9999 0 -0.41 4 4
CREBBP 0.025 0.012 -9999 0 -9999 0 0
SKIL -0.022 0.113 -9999 0 -0.337 6 6
HDAC1 0.016 0.002 -9999 0 -9999 0 0
HDAC2 0.016 0.002 -9999 0 -9999 0 0
SNIP1 -0.001 0.081 -9999 0 -0.412 2 2
GCN5L2 0.027 0.014 -9999 0 -9999 0 0
SMAD3/SMAD4/TFE3 0.019 0.098 -9999 0 -0.276 2 2
MSG1/HSC70 -0.024 0.112 -9999 0 -0.284 8 8
SMAD2 -0.017 0.052 -9999 0 -9999 0 0
SMAD3 0.002 0.078 -9999 0 -0.298 2 2
SMAD3/E2F4-5/DP1/p107/SMAD4 0.001 0.094 -9999 0 -0.277 3 3
SMAD2/SMAD2/SMAD4 -0.009 0.055 -9999 0 -0.222 2 2
NCOR1 0.016 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 -0.005 0.088 -9999 0 -0.251 6 6
SMAD2-3/SMAD4/SP1/MIZ-1 0.008 0.118 -9999 0 -0.273 3 3
IFNB1 0.006 0.099 -9999 0 -0.497 1 1
SMAD3/SMAD4/MEF2C -0.035 0.145 -9999 0 -0.49 2 2
CITED1 -0.016 0.106 -9999 0 -0.344 5 5
SMAD2-3/SMAD4/ARC105 -0.004 0.096 -9999 0 -0.244 2 2
RBL1 0.017 0 -9999 0 -9999 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.02 0.072 -9999 0 -9999 0 0
RUNX1-3/PEBPB2 -0.041 0.132 -9999 0 -0.264 12 12
SMAD7 -0.049 0.191 -9999 0 -0.493 5 5
MYC/MIZ-1 0.019 0.034 -9999 0 -0.201 1 1
SMAD3/SMAD4 0.091 0.131 0.287 11 -9999 0 11
IL10 0.001 0.105 -9999 0 -0.295 3 3
PIASy/HDAC complex 0 0.058 -9999 0 -0.41 1 1
PIAS3 0.021 0.006 -9999 0 -9999 0 0
CDK2 0.014 0.06 -9999 0 -0.287 2 2
IL5 0.006 0.094 -9999 0 -0.339 1 1
CDK4 0.027 0.014 -9999 0 -9999 0 0
PIAS4 0 0.058 -9999 0 -0.41 1 1
ATF3 0.006 0.06 -9999 0 -0.3 2 2
SMAD3/SMAD4/SP1 0.004 0.119 -9999 0 -0.271 4 4
FOXG1 -0.13 0.196 -9999 0 -0.383 20 20
FOXO3 0.024 0.012 -9999 0 -9999 0 0
FOXO1 0.024 0.011 -9999 0 -9999 0 0
FOXO4 0.024 0.011 -9999 0 -9999 0 0
heart looping -0.047 0.136 -9999 0 -0.46 2 2
CEBPB 0.012 0.043 -9999 0 -0.298 1 1
SMAD3/SMAD4/DLX1 -0.022 0.116 -9999 0 -0.276 4 4
MYOD1 -0.026 0.124 -9999 0 -0.374 6 6
SMAD3/SMAD4/HNF4 0.009 0.087 -9999 0 -0.24 2 2
SMAD3/SMAD4/GATA3 0.007 0.114 -9999 0 -0.325 2 2
SnoN/SIN3/HDAC complex/NCoR1 -0.022 0.112 -9999 0 -0.336 6 6
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.036 0.146 -9999 0 -0.378 5 5
SMAD3/SMAD4/SP1-3 0.025 0.108 -9999 0 -0.258 2 2
MED15 0.017 0 -9999 0 -9999 0 0
SP1 0.007 0.044 -9999 0 -9999 0 0
SIN3B 0.016 0.002 -9999 0 -9999 0 0
SIN3A 0.016 0.002 -9999 0 -9999 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.046 0.142 -9999 0 -0.281 7 7
ITGB5 0.014 0.088 -9999 0 -0.235 1 1
TGIF/SIN3/HDAC complex/CtBP 0.031 0.054 -9999 0 -0.3 1 1
SMAD3/SMAD4/AR -0.04 0.145 -9999 0 -0.314 9 9
AR -0.062 0.158 -9999 0 -0.37 11 11
negative regulation of cell growth 0.003 0.107 -9999 0 -0.298 4 4
SMAD3/SMAD4/MYOD -0.018 0.122 -9999 0 -0.264 8 8
E2F5 -0.024 0.119 -9999 0 -0.355 6 6
E2F4 0.017 0 -9999 0 -9999 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.019 0.109 -9999 0 -0.227 2 2
SMAD2-3/SMAD4/FOXO1-3a-4 0.013 0.077 -9999 0 -9999 0 0
TFDP1 0.012 0.043 -9999 0 -0.3 1 1
SMAD3/SMAD4/AP1 -0.046 0.179 -9999 0 -0.394 8 8
SMAD3/SMAD4/RUNX2 0.002 0.099 -9999 0 -0.241 4 4
TGIF2 -0.014 0.112 -9999 0 -0.411 4 4
TGIF1 -0.004 0.09 -9999 0 -0.374 3 3
ATF2 0.017 0 -9999 0 -9999 0 0
Coregulation of Androgen receptor activity

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
NRIP1 -0.04 0.144 -9999 0 -0.382 8 8
SVIL 0.011 0.058 -9999 0 -0.41 1 1
ZNF318 0.014 0 -9999 0 -9999 0 0
JMJD2C 0.025 0 -9999 0 -9999 0 0
T-DHT/AR/Ubc9 -0.048 0.113 -9999 0 -0.273 8 8
CARM1 0.018 0 -9999 0 -9999 0 0
PRDX1 0.017 0 -9999 0 -9999 0 0
PELP1 0.017 0 -9999 0 -9999 0 0
CTNNB1 0.003 0.081 -9999 0 -0.41 2 2
AKT1 0.016 0 -9999 0 -9999 0 0
PTK2B 0.018 0 -9999 0 -9999 0 0
MED1 0.016 0 -9999 0 -9999 0 0
MAK -0.031 0.118 -9999 0 -0.334 7 7
response to oxidative stress 0 0 -9999 0 -9999 0 0
HIP1 0.019 0 -9999 0 -9999 0 0
GSN -0.013 0.112 -9999 0 -0.41 4 4
NCOA2 0.018 0 -9999 0 -9999 0 0
NCOA6 0.019 0 -9999 0 -9999 0 0
DNA-PK 0.032 0 -9999 0 -9999 0 0
NCOA4 0.01 0.058 -9999 0 -0.411 1 1
PIAS3 0.019 0 -9999 0 -9999 0 0
cell proliferation -0.057 0.132 -9999 0 -0.677 2 2
XRCC5 0.017 0 -9999 0 -9999 0 0
UBE3A 0.02 0 -9999 0 -9999 0 0
T-DHT/AR/SNURF -0.053 0.109 -9999 0 -0.239 11 11
FHL2 -0.119 0.296 -9999 0 -0.906 6 6
RANBP9 0.019 0 -9999 0 -9999 0 0
JMJD1A -0.006 0.079 -9999 0 -0.44 1 1
CDK6 -0.044 0.138 -9999 0 -0.349 9 9
TGFB1I1 0.005 0.071 -9999 0 -0.354 2 2
T-DHT/AR/CyclinD1 -0.065 0.135 -9999 0 -0.302 11 11
XRCC6 0.017 0 -9999 0 -9999 0 0
T-DHT/AR -0.06 0.143 -9999 0 -0.3 9 9
CTDSP1 0.018 0 -9999 0 -9999 0 0
CTDSP2 0.015 0 -9999 0 -9999 0 0
BRCA1 0.019 0 -9999 0 -9999 0 0
TCF4 -0.016 0.112 -9999 0 -0.412 4 4
CDKN2A -0.133 0.177 -9999 0 -0.335 23 23
SRF 0.003 0.046 -9999 0 -9999 0 0
NKX3-1 -0.047 0.111 -9999 0 -0.255 10 10
KLK3 0.036 0.045 -9999 0 -9999 0 0
TMF1 0.002 0.081 -9999 0 -0.411 2 2
HNRNPA1 0.008 0.058 -9999 0 -0.412 1 1
AOF2 0.019 0 -9999 0 -9999 0 0
APPL1 0.021 0 -9999 0 -9999 0 0
T-DHT/AR/Caspase 8 -0.044 0.111 -9999 0 -0.281 7 7
AR -0.077 0.164 -9999 0 -0.387 11 11
UBA3 0.001 0 -9999 0 -9999 0 0
PATZ1 0.016 0 -9999 0 -9999 0 0
PAWR 0.018 0 -9999 0 -9999 0 0
PRKDC 0.017 0 -9999 0 -9999 0 0
PA2G4 0.01 0.043 -9999 0 -0.301 1 1
UBE2I 0.01 0.058 -9999 0 -0.411 1 1
T-DHT/AR/Cyclin D3/CDK11 p58 -0.039 0.101 -9999 0 -0.254 7 7
RPS6KA3 0.011 0.058 -9999 0 -0.41 1 1
T-DHT/AR/ARA70 -0.047 0.121 -9999 0 -0.252 11 11
LATS2 0.01 0.043 -9999 0 -0.301 1 1
T-DHT/AR/PRX1 -0.039 0.101 -9999 0 -0.255 7 7
Cyclin D3/CDK11 p58 0.013 0 -9999 0 -9999 0 0
VAV3 -0.045 0.152 -9999 0 -0.41 8 8
KLK2 -0.001 0.057 -9999 0 -9999 0 0
CASP8 0.017 0 -9999 0 -9999 0 0
T-DHT/AR/TIF2/CARM1 -0.027 0.103 -9999 0 -0.247 7 7
TMPRSS2 -0.158 0.36 -9999 0 -0.848 11 11
CCND1 -0.023 0.118 -9999 0 -0.355 6 6
PIAS1 0.02 0 -9999 0 -9999 0 0
mol:T-DHT -0.015 0.032 -9999 0 -0.068 12 12
CDC2L1 0 0 -9999 0 -9999 0 0
PIAS4 0.013 0.058 -9999 0 -0.408 1 1
T-DHT/AR/CDK6 -0.079 0.13 -9999 0 -0.275 13 13
CMTM2 0.009 0.058 -9999 0 -0.411 1 1
SNURF 0 0 -9999 0 -9999 0 0
ZMIZ1 -0.003 0.05 -9999 0 -0.289 1 1
CCND3 0.017 0 -9999 0 -9999 0 0
TGIF1 -0.006 0.09 -9999 0 -0.375 3 3
FKBP4 0.019 0 -9999 0 -9999 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.021 0.042 -9999 0 -0.191 1 1
RGS9BP -0.044 0.138 -9999 0 -0.349 9 9
mol:GTP 0 0 -9999 0 -9999 0 0
GRK1 0 0 -9999 0 -9999 0 0
mol:Na + -0.011 0.082 -9999 0 -0.205 8 8
mol:ADP 0.006 0.04 -9999 0 -0.288 1 1
GNAT2 0.004 0.071 -9999 0 -0.355 2 2
RGS9-1/Gbeta5/R9AP -0.034 0.113 -9999 0 -0.264 7 7
mol:GDP 0 0 -9999 0 -9999 0 0
PDE6H/GNAT2/GTP -0.002 0.074 -9999 0 -0.209 6 6
GRK7 0.01 0.058 -9999 0 -0.411 1 1
CNGB3 -0.04 0.139 -9999 0 -0.369 8 8
Cone Metarhodopsin II/X-Arrestin 0.013 0 -9999 0 -9999 0 0
mol:Ca2+ -0.009 0.078 -9999 0 -0.205 6 6
Cone PDE6 -0.027 0.142 -9999 0 -0.362 6 6
Cone Metarhodopsin II 0.007 0.031 -9999 0 -0.217 1 1
Na + (4 Units) -0.002 0.081 -9999 0 -0.204 6 6
GNAT2/GDP -0.026 0.1 -9999 0 -0.213 8 8
GNB5 0 0.073 -9999 0 -0.3 3 3
mol:GMP (4 units) -0.001 0.079 -9999 0 -0.233 5 5
Cone Transducin 0.023 0.045 -9999 0 -0.204 1 1
SLC24A2 0.01 0.058 -9999 0 -0.411 1 1
GNB3/GNGT2 0.022 0.03 -9999 0 -0.194 1 1
GNB3 0.017 0 -9999 0 -9999 0 0
GNAT2/GTP 0.003 0.049 -9999 0 -0.245 2 2
CNGA3 0.017 0 -9999 0 -9999 0 0
ARR3 0.017 0 -9999 0 -9999 0 0
absorption of light 0 0 -9999 0 -9999 0 0
cGMP/Cone CNG Channel -0.011 0.083 -9999 0 -0.206 8 8
mol:Pi -0.035 0.113 -9999 0 -0.263 7 7
Cone CNG Channel -0.01 0.093 -9999 0 -0.184 10 10
mol:all-trans-retinal 0 0 -9999 0 -9999 0 0
mol:K + 0.01 0.058 -9999 0 -0.41 1 1
RGS9 -0.024 0.106 -9999 0 -0.3 7 7
PDE6C 0.01 0.058 -9999 0 -0.411 1 1
GNGT2 0.012 0.043 -9999 0 -0.3 1 1
mol:cGMP (4 units) 0 0 -9999 0 -9999 0 0
PDE6H -0.012 0.106 -9999 0 -0.383 4 4
Thromboxane A2 receptor signaling

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
TGM2 0.011 0.043 -9999 0 -0.3 1 1
GNB1/GNG2 -0.042 0.065 -9999 0 -0.171 9 9
AKT1 -0.014 0.095 -9999 0 -0.186 9 9
EGF -0.018 0.1 -9999 0 -0.3 6 6
mol:TXA2 0 0 -9999 0 -9999 0 0
FGR 0.041 0.013 -9999 0 -9999 0 0
mol:Ca2+ -0.032 0.133 -9999 0 -0.279 9 9
LYN 0.039 0.022 -9999 0 -9999 0 0
RhoA/GTP -0.029 0.046 -9999 0 -0.118 9 9
mol:PGI2 0 0 -9999 0 -9999 0 0
SYK -0.049 0.152 -9999 0 -0.323 10 10
GNG2 0.006 0.06 -9999 0 -0.299 2 2
ARRB2 0.017 0 -9999 0 -9999 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.024 0.038 -9999 0 -9999 0 0
G beta5/gamma2 -0.054 0.084 -9999 0 -0.222 9 9
PRKCH -0.05 0.151 -9999 0 -0.326 9 9
DNM1 0.01 0.058 -9999 0 -0.411 1 1
TXA2/TP beta/beta Arrestin3 0.009 0.025 -9999 0 -9999 0 0
mol:GTP 0 0.001 -9999 0 -9999 0 0
PTGDR 0.012 0.043 -9999 0 -0.299 1 1
G12 family/GTP -0.07 0.107 -9999 0 -0.284 9 9
ADRBK1 0.017 0 -9999 0 -9999 0 0
ADRBK2 0.017 0 -9999 0 -9999 0 0
RhoA/GTP/ROCK1 0.019 0.035 -9999 0 -0.234 1 1
mol:GDP 0.003 0.077 -9999 0 -9999 0 0
mol:NADP 0.011 0.043 -9999 0 -0.299 1 1
RAB11A 0.017 0 -9999 0 -9999 0 0
PRKG1 0.017 0 -9999 0 -9999 0 0
mol:IP3 -0.045 0.16 -9999 0 -0.347 9 9
cell morphogenesis 0.018 0.035 -9999 0 -0.233 1 1
PLCB2 -0.067 0.204 -9999 0 -0.462 9 9
mol:cGMP 0 0 -9999 0 -9999 0 0
BLK 0.036 0.033 -9999 0 -9999 0 0
mol:PDG2 0 0 -9999 0 -9999 0 0
HCK 0.027 0.048 -9999 0 -9999 0 0
RHOA 0.01 0.058 -9999 0 -0.411 1 1
PTGIR 0.017 0 -9999 0 -9999 0 0
PRKCB1 -0.052 0.162 -9999 0 -0.347 10 10
GNAQ 0 0 -9999 0 -9999 0 0
mol:L-citrulline 0.011 0.043 -9999 0 -0.299 1 1
TXA2/TXA2-R family -0.075 0.215 -9999 0 -0.493 9 9
LCK 0.025 0.048 -9999 0 -9999 0 0
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.038 0.014 -9999 0 -9999 0 0
TXA2-R family/G12 family/GDP/G beta/gamma 0.034 0.013 -9999 0 -9999 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.038 0.014 -9999 0 -9999 0 0
MAPK14 -0.025 0.107 -9999 0 -0.213 10 10
TGM2/GTP -0.051 0.175 -9999 0 -0.38 9 9
MAPK11 -0.025 0.107 -9999 0 -0.213 10 10
ARHGEF1 -0.013 0.084 -9999 0 -0.166 9 9
GNAI2 0.017 0 -9999 0 -9999 0 0
JNK cascade -0.051 0.166 -9999 0 -0.365 9 9
RAB11/GDP 0.017 0.001 -9999 0 -9999 0 0
ICAM1 -0.04 0.139 -9999 0 -0.291 10 10
cAMP biosynthetic process -0.044 0.148 -9999 0 -0.32 9 9
Gq family/GTP/EBP50 0.017 0.04 -9999 0 -0.249 1 1
actin cytoskeleton reorganization 0.018 0.035 -9999 0 -0.233 1 1
SRC 0.041 0.013 -9999 0 -9999 0 0
GNB5 0 0.073 -9999 0 -0.3 3 3
GNB1 0.017 0 -9999 0 -9999 0 0
EGF/EGFR 0.026 0.061 -9999 0 -0.217 1 1
VCAM1 -0.047 0.152 -9999 0 -0.326 10 10
TP beta/Gq family/GDP/G beta5/gamma2 0.024 0.038 -9999 0 -9999 0 0
platelet activation -0.03 0.14 -9999 0 -0.278 10 10
PGI2/IP 0.013 0.001 -9999 0 -9999 0 0
PRKACA 0.021 0.016 -9999 0 -9999 0 0
Gq family/GDP/G beta5/gamma2 0.023 0.037 -9999 0 -9999 0 0
TXA2/TP beta/beta Arrestin2 -0.009 0.06 -9999 0 -0.444 1 1
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -9999 0 0
TBXA2R 0.025 0.015 -9999 0 -9999 0 0
mol:DAG -0.053 0.177 -9999 0 -0.391 9 9
EGFR -0.01 0.099 -9999 0 -0.355 4 4
TXA2/TP alpha -0.061 0.193 -9999 0 -0.428 9 9
Gq family/GTP -0.006 0.031 -9999 0 -0.203 1 1
YES1 0.041 0.013 -9999 0 -9999 0 0
GNAI2/GTP -0.001 0.007 -9999 0 -9999 0 0
PGD2/DP 0.009 0.029 -9999 0 -0.202 1 1
SLC9A3R1 0.012 0.043 -9999 0 -0.3 1 1
FYN 0.031 0.041 -9999 0 -9999 0 0
mol:NO 0.011 0.043 -9999 0 -0.299 1 1
GNA15 0.012 0.043 -9999 0 -0.3 1 1
PGK/cGMP 0.02 0.025 -9999 0 -0.159 1 1
RhoA/GDP 0.009 0.057 -9999 0 -0.405 1 1
TP alpha/TGM2/GDP/G beta/gamma 0.043 0.035 -9999 0 -9999 0 0
NOS3 0.012 0.043 -9999 0 -0.299 1 1
RAC1 0.017 0 -9999 0 -9999 0 0
PRKCA -0.043 0.157 -9999 0 -0.338 9 9
PRKCB -0.042 0.153 -9999 0 -0.332 9 9
PRKCE -0.042 0.155 -9999 0 -0.334 9 9
PRKCD -0.047 0.163 -9999 0 -0.357 9 9
PRKCG -0.047 0.163 -9999 0 -0.358 9 9
muscle contraction -0.07 0.2 -9999 0 -0.44 10 10
PRKCZ -0.045 0.149 -9999 0 -0.324 9 9
ARR3 0.017 0 -9999 0 -9999 0 0
TXA2/TP beta 0.039 0.015 -9999 0 -9999 0 0
PRKCQ -0.066 0.16 -9999 0 -0.35 9 9
MAPKKK cascade -0.062 0.185 -9999 0 -0.415 9 9
SELE -0.051 0.15 -9999 0 -0.308 11 11
TP beta/GNAI2/GDP/G beta/gamma 0.045 0.031 -9999 0 -9999 0 0
ROCK1 0.017 0 -9999 0 -9999 0 0
GNA14 0.004 0.071 -9999 0 -0.355 2 2
chemotaxis -0.095 0.25 -9999 0 -0.589 9 9
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 0.013 0.001 -9999 0 -9999 0 0
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.006 0.065 -9999 0 -0.176 6 6
EPHB2 -0.02 0.106 -9999 0 -0.318 6 6
Syndecan-2/TACI 0.016 0.053 -9999 0 -0.2 3 3
LAMA1 -0.034 0.124 -9999 0 -0.327 8 8
Syndecan-2/alpha2 ITGB1 0.007 0.089 -9999 0 -0.207 5 5
HRAS 0.017 0 -9999 0 -9999 0 0
Syndecan-2/CASK 0.003 0.052 -9999 0 -0.207 3 3
ITGA5 0.017 0 -9999 0 -9999 0 0
BAX 0.019 0.062 -9999 0 -9999 0 0
EPB41 0.017 0 -9999 0 -9999 0 0
positive regulation of cell-cell adhesion 0.01 0.056 -9999 0 -0.185 4 4
LAMA3 -0.018 0.112 -9999 0 -0.366 5 5
EZR 0 0 -9999 0 -9999 0 0
mol:PI-4-5-P2 0 0 -9999 0 -9999 0 0
CAV2 0.01 0.058 -9999 0 -0.411 1 1
Syndecan-2/MMP2 -0.025 0.093 -9999 0 -0.179 14 14
RP11-540L11.1 0 0 -9999 0 -9999 0 0
alpha2 ITGB1 0.011 0.064 -9999 0 -0.251 3 3
dendrite morphogenesis -0.005 0.083 -9999 0 -0.199 8 8
Syndecan-2/GM-CSF 0.009 0.062 -9999 0 -0.189 4 4
determination of left/right symmetry 0.006 0.063 -9999 0 -0.249 3 3
Syndecan-2/PKC delta 0.012 0.058 -9999 0 -0.188 4 4
GNB2L1 0.01 0.058 -9999 0 -0.411 1 1
MAPK3 0.015 0.055 -9999 0 -0.195 2 2
MAPK1 0.011 0.062 -9999 0 -0.197 3 3
Syndecan-2/RACK1 0.021 0.054 -9999 0 -0.184 3 3
NF1 0.01 0.058 -9999 0 -0.411 1 1
FGFR/FGF/Syndecan-2 0.006 0.063 -9999 0 -0.249 3 3
ITGA2 -0.004 0.09 -9999 0 -0.374 3 3
MAPK8 0.011 0.069 -9999 0 -0.219 4 4
Syndecan-2/alpha2/beta1 Integrin 0 0.11 -9999 0 -0.27 6 6
Syndecan-2/Kininogen 0.012 0.058 -9999 0 -0.188 4 4
ITGB1 0.017 0 -9999 0 -9999 0 0
SRC 0.022 0.05 -9999 0 -0.168 3 3
Syndecan-2/CASK/Protein 4.1 0.014 0.048 -9999 0 -0.18 3 3
extracellular matrix organization 0.016 0.053 -9999 0 -0.199 3 3
actin cytoskeleton reorganization 0.006 0.065 -9999 0 -0.176 6 6
Syndecan-2/Caveolin-2/Ras 0.022 0.057 -9999 0 -0.196 3 3
Syndecan-2/Laminin alpha3 -0.005 0.082 -9999 0 -0.199 8 8
Syndecan-2/RasGAP 0.029 0.052 -9999 0 -9999 0 0
alpha5/beta1 Integrin 0.026 0 -9999 0 -9999 0 0
PRKCD 0.012 0.043 -9999 0 -0.3 1 1
Syndecan-2 dimer -0.005 0.084 -9999 0 -0.2 8 8
GO:0007205 0.004 0 -9999 0 -9999 0 0
DNA mediated transformation 0 0 -9999 0 -9999 0 0
Syndecan-2/RasGAP/Src 0.033 0.05 -9999 0 -9999 0 0
RHOA 0.01 0.058 -9999 0 -0.411 1 1
SDCBP 0.01 0.058 -9999 0 -0.411 1 1
TNFRSF13B 0.017 0 -9999 0 -9999 0 0
RASA1 0.017 0 -9999 0 -9999 0 0
alpha2/beta1 Integrin 0.011 0.064 -9999 0 -0.251 3 3
Syndecan-2/Synbindin 0.016 0.053 -9999 0 -0.2 3 3
TGFB1 0.017 0 -9999 0 -9999 0 0
CASP3 0.018 0.052 -9999 0 -0.195 2 2
FN1 0 0.073 -9999 0 -0.3 3 3
Syndecan-2/IL8 -0.05 0.12 -9999 0 -0.206 18 18
SDC2 0.006 0.063 -9999 0 -0.25 3 3
KNG1 0.012 0.043 -9999 0 -0.3 1 1
Syndecan-2/Neurofibromin 0.011 0.062 -9999 0 -0.207 4 4
TRAPPC4 0.017 0 -9999 0 -9999 0 0
CSF2 0.006 0.06 -9999 0 -0.3 2 2
Syndecan-2/TGFB1 0.016 0.053 -9999 0 -0.2 3 3
Syndecan-2/Syntenin/PI-4-5-P2 0.01 0.056 -9999 0 -0.186 4 4
Syndecan-2/Ezrin 0.01 0.056 -9999 0 -0.186 4 4
PRKACA 0.017 0.056 -9999 0 -0.196 3 3
angiogenesis -0.05 0.12 -9999 0 -0.206 18 18
MMP2 -0.053 0.142 -9999 0 -0.33 11 11
IL8 -0.097 0.171 -9999 0 -0.345 17 17
calcineurin-NFAT signaling pathway 0.016 0.053 -9999 0 -0.199 3 3
Signaling events mediated by PTP1B

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
PDGFRB 0.002 0.081 -9999 0 -0.411 2 2
Jak2/Leptin Receptor 0.015 0.078 -9999 0 -9999 0 0
PTP1B/AKT1 -0.01 0.095 -9999 0 -0.25 5 5
FYN -0.006 0.098 -9999 0 -0.411 3 3
p210 bcr-abl/PTP1B -0.023 0.104 -9999 0 -0.284 5 5
EGFR -0.011 0.098 -9999 0 -0.353 4 4
EGF/EGFR -0.03 0.11 -9999 0 -0.267 6 6
CSF1 0.017 0 -9999 0 -9999 0 0
AKT1 0.018 0.001 -9999 0 -9999 0 0
INSR 0.018 0.001 -9999 0 -9999 0 0
PTP1B/N-cadherin -0.111 0.148 -9999 0 -0.328 12 12
Insulin Receptor/Insulin 0.01 0.078 -9999 0 -0.255 1 1
HCK -0.018 0.112 -9999 0 -0.366 5 5
CRK -0.014 0.112 -9999 0 -0.411 4 4
TYK2 -0.015 0.099 -9999 0 -0.265 5 5
EGF -0.019 0.1 -9999 0 -0.302 6 6
YES1 0.017 0 -9999 0 -9999 0 0
CAV1 -0.009 0.091 -9999 0 -0.269 3 3
TXN 0.009 0.059 -9999 0 -0.417 1 1
PTP1B/IRS1/GRB2 -0.02 0.114 -9999 0 -0.263 6 6
cell migration 0.023 0.104 0.284 5 -9999 0 5
STAT3 0.009 0.058 -9999 0 -0.411 1 1
PRLR 0.019 0.026 -9999 0 -9999 0 0
ITGA2B 0.011 0.043 -9999 0 -0.302 1 1
CSF1R -0.016 0.106 -9999 0 -0.344 5 5
Prolactin Receptor/Prolactin 0.029 0.054 -9999 0 -0.289 1 1
FGR 0.017 0 -9999 0 -9999 0 0
PTP1B/p130 Cas -0.013 0.101 -9999 0 -0.265 5 5
Crk/p130 Cas -0.018 0.116 -9999 0 -0.347 3 3
DOK1 -0.009 0.101 -9999 0 -0.313 3 3
JAK2 0.006 0.072 -9999 0 -9999 0 0
Jak2/Leptin Receptor/Leptin -0.016 0.109 -9999 0 -0.276 2 2
PIK3R1 -0.038 0.134 -9999 0 -0.355 8 8
PTPN1 -0.025 0.103 -9999 0 -0.286 5 5
LYN 0.012 0.043 -9999 0 -0.3 1 1
CDH2 -0.195 0.181 -9999 0 -0.341 32 32
SRC 0.012 0.041 -9999 0 -9999 0 0
ITGB3 -0.026 0.113 -9999 0 -0.317 7 7
CAT1/PTP1B -0.019 0.116 -9999 0 -0.312 4 4
CAPN1 0.017 0.003 -9999 0 -9999 0 0
CSK 0.017 0 -9999 0 -9999 0 0
PI3K -0.014 0.093 -9999 0 -0.279 3 3
mol:H2O2 0.001 0.006 -9999 0 -9999 0 0
STAT3 (dimer) -0.016 0.109 -9999 0 -0.268 5 5
negative regulation of transcription 0.006 0.072 -9999 0 -9999 0 0
FCGR2A -0.006 0.083 -9999 0 -0.3 4 4
FER 0.017 0.004 -9999 0 -9999 0 0
alphaIIb/beta3 Integrin -0.009 0.09 -9999 0 -0.234 7 7
BLK 0.004 0.071 -9999 0 -0.355 2 2
Insulin Receptor/Insulin/Shc 0.036 0.002 -9999 0 -9999 0 0
RHOA 0.009 0.057 -9999 0 -0.403 1 1
LEPR 0.018 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 0.004 -9999 0 -9999 0 0
TRPV6 -0.005 0.112 -9999 0 -0.405 2 2
PRL 0.013 0.05 -9999 0 -0.294 1 1
SOCS3 -0.062 0.284 -9999 0 -1.222 3 3
SPRY2 -0.076 0.169 -9999 0 -0.371 13 13
Insulin Receptor/Insulin/IRS1 0.013 0.073 -9999 0 -0.229 4 4
CSF1/CSF1R -0.018 0.12 -9999 0 -0.311 5 5
Ras protein signal transduction 0.019 0.03 -9999 0 -9999 0 0
IRS1 -0.02 0.118 -9999 0 -0.389 5 5
INS 0.018 0.001 -9999 0 -9999 0 0
LEP 0.009 0.058 -9999 0 -0.411 1 1
STAT5B -0.009 0.098 -9999 0 -0.284 4 4
STAT5A -0.006 0.09 -9999 0 -0.262 3 3
GRB2 0.017 0 -9999 0 -9999 0 0
PDGFB-D/PDGFRB -0.02 0.115 -9999 0 -0.304 5 5
CSN2 0.009 0.175 -9999 0 -1.26 1 1
PIK3CA 0.01 0.058 -9999 0 -0.411 1 1
LAT -0.011 0.085 -9999 0 -0.347 2 2
YBX1 0.015 0.063 -9999 0 -0.402 1 1
LCK -0.022 0.113 -9999 0 -0.337 6 6
SHC1 0.017 0 -9999 0 -9999 0 0
NOX4 -0.006 0.099 -9999 0 -0.415 3 3
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.022 0.078 -9999 0 -0.511 1 1
HDAC1 0.016 0.009 -9999 0 -9999 0 0
AES 0.009 0.057 -9999 0 -0.408 1 1
FBXW11 0.017 0 -9999 0 -9999 0 0
DTX1 0.012 0.043 -9999 0 -0.3 1 1
LRP6/FZD1 0.026 0 -9999 0 -9999 0 0
TLE1 0.011 0.043 -9999 0 -0.301 1 1
AP1 -0.078 0.134 -9999 0 -0.285 12 12
NCSTN 0.017 0 -9999 0 -9999 0 0
ADAM10 0.004 0.071 -9999 0 -0.355 2 2
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.007 0.102 -9999 0 -0.436 1 1
NICD/RBPSUH 0.022 0.077 -9999 0 -0.5 1 1
WIF1 -0.168 0.189 -9999 0 -0.353 27 27
NOTCH1 0.013 0.08 -9999 0 -0.533 1 1
PSENEN 0.01 0.058 -9999 0 -0.412 1 1
KREMEN2 -0.071 0.16 -9999 0 -0.351 13 13
DKK1 -0.152 0.179 -9999 0 -0.334 26 26
beta catenin/beta TrCP1 0.032 0.073 -9999 0 -0.255 2 2
APH1B 0.004 0.071 -9999 0 -0.355 2 2
APH1A 0.017 0 -9999 0 -9999 0 0
AXIN1 -0.015 0.06 -9999 0 -0.393 1 1
CtBP/CBP/TCF1/TLE1/AES -0.005 0.087 -9999 0 -9999 0 0
PSEN1 0.017 0 -9999 0 -9999 0 0
FOS -0.079 0.166 -9999 0 -0.355 14 14
JUN -0.026 0.124 -9999 0 -0.374 6 6
MAP3K7 0.017 0.004 -9999 0 -9999 0 0
CTNNB1 0.024 0.076 -9999 0 -0.274 2 2
MAPK3 0.017 0 -9999 0 -9999 0 0
DKK2/LRP6/Kremen 2 -0.026 0.108 -9999 0 -0.249 7 7
HNF1A -0.052 0.156 -9999 0 -0.398 9 9
CTBP1 0.017 0.002 -9999 0 -9999 0 0
MYC 0.016 0.044 -9999 0 -9999 0 0
NKD1 -0.077 0.154 -9999 0 -0.322 15 15
FZD1 0.017 0 -9999 0 -9999 0 0
NOTCH1 precursor/Deltex homolog 1 0.02 0.079 -9999 0 -0.5 1 1
apoptosis -0.078 0.133 -9999 0 -0.283 12 12
Delta 1/NOTCHprecursor 0.022 0.077 -9999 0 -0.5 1 1
DLL1 0.017 0 -9999 0 -9999 0 0
PPARD 0.021 0.022 -9999 0 -9999 0 0
Gamma Secretase 0.041 0.049 -9999 0 -9999 0 0
APC -0.008 0.029 -9999 0 -0.177 1 1
DVL1 0.012 0.026 -9999 0 -9999 0 0
CSNK2A1 0.018 0.001 -9999 0 -9999 0 0
MAP3K7IP1 0.017 0.004 -9999 0 -9999 0 0
DKK1/LRP6/Kremen 2 -0.115 0.142 -9999 0 -0.295 15 15
LRP6 0.017 0 -9999 0 -9999 0 0
CSNK1A1 0.018 0.001 -9999 0 -9999 0 0
NLK 0.024 0.021 -9999 0 -9999 0 0
CCND1 -0.061 0.301 -9999 0 -1.267 3 3
WNT1 0.017 0 -9999 0 -9999 0 0
Axin1/APC/beta catenin 0.023 0.067 -9999 0 -0.292 1 1
DKK2 0.004 0.071 -9999 0 -0.355 2 2
NOTCH1 precursor/DVL1 0.022 0.071 -9999 0 -0.438 1 1
GSK3B 0.017 0.001 -9999 0 -9999 0 0
FRAT1 0.017 0.002 -9999 0 -9999 0 0
NOTCH/Deltex homolog 1 0.019 0.08 -9999 0 -0.511 1 1
PPP2R5D 0.052 0.073 0.219 3 -9999 0 3
MAPK1 0.01 0.058 -9999 0 -0.411 1 1
WNT1/LRP6/FZD1 -0.058 0.107 -9999 0 -0.197 13 13
RBPJ 0.017 0 -9999 0 -9999 0 0
CREBBP 0.018 0.007 -9999 0 -9999 0 0
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.015 0.058 -9999 0 -0.28 2 2
Necdin/E2F1 -0.021 0.122 -9999 0 -0.29 8 8
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.031 0.043 -9999 0 -0.185 1 1
NGF (dimer)/p75(NTR)/BEX1 -0.074 0.123 -9999 0 -0.217 22 22
NT-4/5 (dimer)/p75(NTR) 0.005 0.041 -9999 0 -0.203 2 2
IKBKB 0.017 0 -9999 0 -9999 0 0
AKT1 -0.005 0.083 -9999 0 -0.233 4 4
IKBKG 0.017 0 -9999 0 -9999 0 0
BDNF -0.065 0.157 -9999 0 -0.355 12 12
MGDIs/NGR/p75(NTR)/LINGO1 0.003 0.074 -9999 0 -0.227 1 1
FURIN 0.017 0 -9999 0 -9999 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.02 0.108 -9999 0 -0.248 8 8
LINGO1 0 0.073 -9999 0 -0.3 3 3
Sortilin/TRAF6/NRIF -0.012 0.039 -9999 0 -9999 0 0
proBDNF (dimer) -0.065 0.157 -9999 0 -0.355 12 12
NTRK1 -0.004 0.09 -9999 0 -0.374 3 3
RTN4R -0.008 0.091 -9999 0 -0.327 4 4
neuron apoptosis -0.012 0.104 -9999 0 -0.349 1 1
IRAK1 0.017 0 -9999 0 -9999 0 0
SHC1 0.013 0.034 -9999 0 -0.159 2 2
ARHGDIA 0.017 0 -9999 0 -9999 0 0
RhoA/GTP 0.007 0.041 -9999 0 -0.288 1 1
Gamma Secretase 0.041 0.048 -9999 0 -9999 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.024 0.091 -9999 0 -0.204 6 6
MAGEH1 -0.077 0.162 -9999 0 -0.347 14 14
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.005 0.07 -9999 0 -0.204 3 3
Mammalian IAPs/DIABLO -0.008 0.085 -9999 0 -0.204 6 6
proNGF (dimer) 0 0 -9999 0 -9999 0 0
MAGED1 0.01 0.058 -9999 0 -0.411 1 1
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 0.02 0.041 -9999 0 -0.191 1 1
NGF 0 0 -9999 0 -9999 0 0
cell cycle arrest 0.05 0.059 -9999 0 -9999 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.019 0.048 -9999 0 -0.19 2 2
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.007 0.059 -9999 0 -0.197 4 4
NCSTN 0.017 0 -9999 0 -9999 0 0
mol:GTP 0.017 0.034 -9999 0 -0.159 2 2
PSENEN 0.01 0.058 -9999 0 -0.411 1 1
mol:ceramide 0.02 0.03 -9999 0 -9999 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.017 0.049 -9999 0 -9999 0 0
p75(NTR)/beta APP 0.018 0.042 -9999 0 -0.194 2 2
BEX1 -0.137 0.196 -9999 0 -0.379 21 21
mol:GDP 0.002 0.033 -9999 0 -0.167 2 2
NGF (dimer) -0.067 0.107 -9999 0 -0.204 15 15
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.015 0.068 -9999 0 -0.197 1 1
PIK3R1 -0.038 0.134 -9999 0 -0.355 8 8
RAC1/GTP 0.015 0.029 -9999 0 -0.132 2 2
MYD88 0.017 0 -9999 0 -9999 0 0
CHUK 0.01 0.058 -9999 0 -0.411 1 1
NGF (dimer)/p75(NTR)/PKA 0.017 0.035 -9999 0 -0.159 2 2
RHOB 0.006 0.06 -9999 0 -0.3 2 2
RHOA 0.01 0.058 -9999 0 -0.411 1 1
MAGE-G1/E2F1 0.002 0.075 -9999 0 -0.228 5 5
NT3 (dimer) 0 0.073 -9999 0 -0.299 3 3
TP53 -0.013 0.092 -9999 0 -0.236 2 2
PRDM4 0.02 0.03 -9999 0 -9999 0 0
BDNF (dimer) -0.162 0.172 -9999 0 -0.305 26 26
PIK3CA 0.01 0.058 -9999 0 -0.411 1 1
SORT1 0.017 0 -9999 0 -9999 0 0
activation of caspase activity 0.028 0.041 -9999 0 -0.183 1 1
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.019 0.054 -9999 0 -0.204 2 2
RHOC 0.012 0.043 -9999 0 -0.3 1 1
XIAP 0 0 -9999 0 -9999 0 0
MAPK10 0.003 0.083 -9999 0 -0.34 1 1
DIABLO 0.017 0 -9999 0 -9999 0 0
SMPD2 0.02 0.03 -9999 0 -9999 0 0
APH1B 0.004 0.071 -9999 0 -0.355 2 2
APH1A 0.017 0 -9999 0 -9999 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.017 0.035 -9999 0 -0.159 2 2
PSEN1 0.017 0 -9999 0 -9999 0 0
APAF-1/Pro-Caspase 9 0.02 0.041 -9999 0 -0.28 1 1
NT3 (dimer)/p75(NTR) 0.006 0.064 -9999 0 -0.194 5 5
MAPK8 0.005 0.084 -9999 0 -0.287 1 1
MAPK9 0.005 0.087 -9999 0 -0.262 2 2
APAF1 0.01 0.058 -9999 0 -0.411 1 1
NTF3 0 0.073 -9999 0 -0.3 3 3
NTF4 0 0 -9999 0 -9999 0 0
NDN -0.024 0.119 -9999 0 -0.355 6 6
RAC1/GDP 0.013 0 -9999 0 -9999 0 0
RhoA-B-C/GDP 0.021 0.049 -9999 0 -9999 0 0
p75 CTF/Sortilin/TRAF6/NRIF 0.033 0.051 -9999 0 -0.197 2 2
RhoA-B-C/GTP 0.016 0.034 -9999 0 -0.158 2 2
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.006 0.1 -9999 0 -0.255 2 2
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.016 0.105 -9999 0 -0.213 10 10
PRKACB 0.017 0 -9999 0 -9999 0 0
proBDNF (dimer)/p75 ECD -0.037 0.113 -9999 0 -0.234 13 13
ChemicalAbstracts:86-01-1 0 0 -9999 0 -9999 0 0
BIRC3 -0.059 0.154 -9999 0 -0.36 11 11
BIRC2 0.017 0 -9999 0 -9999 0 0
neuron projection morphogenesis 0.014 0.098 0.15 12 -0.264 1 13
BAD 0.007 0.083 -9999 0 -0.256 1 1
RIPK2 0.012 0.043 -9999 0 -0.3 1 1
NGFR 0.006 0.06 -9999 0 -0.3 2 2
CYCS 0.022 0.04 -9999 0 -0.184 1 1
ADAM17 0.012 0.043 -9999 0 -0.3 1 1
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.016 0.058 -9999 0 -0.204 2 2
BCL2L11 0.008 0.083 -9999 0 -0.256 1 1
BDNF (dimer)/p75(NTR) -0.039 0.126 -9999 0 -0.268 12 12
PI3K -0.007 0.092 -9999 0 -0.257 4 4
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.025 0.048 -9999 0 -0.284 1 1
NDNL2 0.012 0.043 -9999 0 -0.3 1 1
YWHAE 0.01 0.058 -9999 0 -0.411 1 1
PRKCI 0.012 0.043 -9999 0 -0.3 1 1
NGF (dimer)/p75(NTR) 0.005 0.041 -9999 0 -0.203 2 2
ChemicalAbstracts:146-91-8 0 0 -9999 0 -9999 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.023 0.045 -9999 0 -0.204 1 1
TRAF6 0.002 0.081 -9999 0 -0.411 2 2
RAC1 0.017 0 -9999 0 -9999 0 0
PRKCZ 0 0 -9999 0 -9999 0 0
PLG 0.006 0.06 -9999 0 -0.3 2 2
oligodendrocyte cell fate commitment 0 0 -9999 0 -9999 0 0
CASP6 -0.013 0.087 -9999 0 -0.248 2 2
SQSTM1 0.01 0.058 -9999 0 -0.411 1 1
NGFRAP1 0.017 0 -9999 0 -9999 0 0
CASP3 0.01 0.079 -9999 0 -0.237 1 1
E2F1 -0.01 0.099 -9999 0 -0.355 4 4
CASP9 0.017 0 -9999 0 -9999 0 0
IKK complex -0.016 0.039 -9999 0 -9999 0 0
NGF (dimer)/TRKA -0.002 0.063 -9999 0 -0.26 3 3
MMP7 -0.154 0.195 -9999 0 -0.369 24 24
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.027 0.052 -9999 0 -0.185 2 2
MMP3 -0.105 0.176 -9999 0 -0.349 18 18
APAF-1/Caspase 9 -0.028 0.053 -9999 0 -0.238 1 1
PDGFR-alpha 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
PDGFRA -0.012 0.093 -9999 0 -0.386 3 3
PDGF/PDGFRA/CRKL 0.007 0.064 -9999 0 -0.252 3 3
positive regulation of JUN kinase activity 0.029 0.05 -9999 0 -0.198 2 2
CRKL 0.017 0 -9999 0 -9999 0 0
PDGF/PDGFRA/Caveolin-3 0.007 0.064 -9999 0 -0.252 3 3
AP1 -0.142 0.295 -9999 0 -0.738 9 9
mol:IP3 -0.01 0.079 -9999 0 -0.272 4 4
PLCG1 -0.01 0.079 -9999 0 -0.273 4 4
PDGF/PDGFRA/alphaV Integrin -0.009 0.09 -9999 0 -0.257 6 6
RAPGEF1 0.017 0 -9999 0 -9999 0 0
CRK -0.014 0.112 -9999 0 -0.411 4 4
mol:Ca2+ -0.01 0.079 -9999 0 -0.272 4 4
CAV3 0.017 0 -9999 0 -9999 0 0
CAV1 0.017 0 -9999 0 -9999 0 0
SHC/Grb2/SOS1 0.03 0.05 -9999 0 -0.198 2 2
PDGF/PDGFRA/Shf -0.002 0.093 -9999 0 -0.304 4 4
FOS -0.141 0.292 -9999 0 -0.728 9 9
JUN -0.04 0.087 -9999 0 -0.276 6 6
oligodendrocyte development -0.009 0.09 -9999 0 -0.257 6 6
GRB2 0.017 0 -9999 0 -9999 0 0
PIK3R1 -0.038 0.134 -9999 0 -0.355 8 8
mol:DAG -0.01 0.079 -9999 0 -0.272 4 4
PDGF/PDGFRA -0.012 0.093 -9999 0 -0.386 3 3
actin cytoskeleton reorganization 0.007 0.064 -9999 0 -0.251 3 3
SRF 0.027 0.009 -9999 0 -9999 0 0
SHC1 0.017 0 -9999 0 -9999 0 0
PI3K -0.019 0.108 -9999 0 -0.244 8 8
PDGF/PDGFRA/Crk/C3G 0 0.085 -9999 0 -0.23 6 6
JAK1 -0.031 0.112 -9999 0 -0.278 9 9
ELK1/SRF 0.017 0.06 -9999 0 -0.216 3 3
SHB 0.017 0 -9999 0 -9999 0 0
SHF 0.004 0.071 -9999 0 -0.355 2 2
CSNK2A1 0.025 0.017 -9999 0 -9999 0 0
GO:0007205 -0.013 0.085 -9999 0 -0.292 4 4
SOS1 0.017 0 -9999 0 -9999 0 0
Ras protein signal transduction 0.029 0.05 -9999 0 -0.198 2 2
PDGF/PDGFRA/SHB 0.007 0.064 -9999 0 -0.252 3 3
PDGF/PDGFRA/Caveolin-1 0.007 0.064 -9999 0 -0.252 3 3
ITGAV -0.004 0.09 -9999 0 -0.374 3 3
ELK1 -0.012 0.079 -9999 0 -0.288 3 3
PIK3CA 0.01 0.058 -9999 0 -0.411 1 1
PDGF/PDGFRA/Crk -0.016 0.1 -9999 0 -0.272 7 7
JAK-STAT cascade -0.03 0.112 -9999 0 -0.277 9 9
cell proliferation -0.002 0.093 -9999 0 -0.303 4 4
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.026 0.092 -9999 0 -0.213 5 5
alphaM/beta2 Integrin/GPIbA 0.013 0.067 -9999 0 -0.263 2 2
alphaM/beta2 Integrin/proMMP-9 -0.045 0.122 -9999 0 -0.253 11 11
PLAUR -0.022 0.113 -9999 0 -0.337 6 6
HMGB1 0.012 0.016 -9999 0 -9999 0 0
alphaM/beta2 Integrin/Talin 0.016 0.055 -9999 0 -0.219 1 1
AGER 0.012 0.016 -9999 0 -9999 0 0
RAP1A -0.006 0.098 -9999 0 -0.411 3 3
SELPLG 0.006 0.06 -9999 0 -0.3 2 2
mol:LDL 0 0 -9999 0 -9999 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.014 0.079 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
MMP9 -0.087 0.171 -9999 0 -0.359 15 15
CYR61 0.004 0.071 -9999 0 -0.355 2 2
TLN1 0.017 0 -9999 0 -9999 0 0
Rap1/GTP -0.022 0.061 -9999 0 -0.276 1 1
RHOA 0.01 0.058 -9999 0 -0.411 1 1
P-selectin oligomer 0.004 0.071 -9999 0 -0.355 2 2
MYH2 -0.011 0.1 -9999 0 -0.349 1 1
MST1R -0.022 0.124 -9999 0 -0.411 5 5
leukocyte activation during inflammatory response 0.022 0.046 -9999 0 -0.176 1 1
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 -0.053 0.142 -9999 0 -0.33 11 11
JAM3 -0.004 0.09 -9999 0 -0.374 3 3
GP1BA 0.012 0.043 -9999 0 -0.3 1 1
alphaM/beta2 Integrin/CTGF 0.005 0.073 -9999 0 -0.217 3 3
alphaM/beta2 Integrin 0.006 0.072 -9999 0 -0.21 1 1
JAM3 homodimer -0.004 0.09 -9999 0 -0.373 3 3
ICAM2 0.01 0.058 -9999 0 -0.411 1 1
ICAM1 -0.01 0.099 -9999 0 -0.355 4 4
phagocytosis triggered by activation of immune response cell surface activating receptor 0.006 0.072 -9999 0 -0.208 1 1
cell adhesion 0.013 0.067 -9999 0 -0.262 2 2
NFKB1 0.003 0.108 -9999 0 -0.302 3 3
THY1 0.004 0.071 -9999 0 -0.355 2 2
RhoA/GDP 0.007 0.041 -9999 0 -0.288 1 1
Lipoprotein(a) 0.024 0 -9999 0 -9999 0 0
alphaM/beta2 Integrin/LRP/tPA 0 0.086 -9999 0 -0.209 5 5
IL6 -0.011 0.136 -9999 0 -0.412 2 2
ITGB2 -0.013 0.09 -9999 0 -0.321 4 4
elevation of cytosolic calcium ion concentration -0.015 0.096 -9999 0 -0.215 6 6
alphaM/beta2 Integrin/JAM2/JAM3 -0.026 0.107 -9999 0 -0.233 7 7
JAM2 -0.059 0.145 -9999 0 -0.327 12 12
alphaM/beta2 Integrin/ICAM1 -0.025 0.126 -9999 0 -0.347 4 4
alphaM/beta2 Integrin/uPA/Plg 0.001 0.084 -9999 0 -0.19 5 5
RhoA/GTP 0.004 0.083 -9999 0 -9999 0 0
positive regulation of phagocytosis -0.001 0.108 -9999 0 -0.402 2 2
Ron/MSP -0.035 0.136 -9999 0 -0.305 10 10
alphaM/beta2 Integrin/uPAR/uPA -0.014 0.097 -9999 0 -0.216 6 6
alphaM/beta2 Integrin/uPAR -0.007 0.082 -9999 0 -0.211 4 4
PLAU -0.018 0.112 -9999 0 -0.366 5 5
PLAT -0.026 0.124 -9999 0 -0.374 6 6
actin filament polymerization -0.01 0.097 -9999 0 -0.336 1 1
MST1 -0.032 0.129 -9999 0 -0.363 7 7
alphaM/beta2 Integrin/lipoprotein(a) 0.025 0.048 -9999 0 -0.178 1 1
TNF -0.01 0.148 -9999 0 -0.48 3 3
RAP1B 0.017 0 -9999 0 -9999 0 0
alphaM/beta2 Integrin/uPA -0.005 0.083 -9999 0 -0.213 5 5
fibrinolysis 0 0.083 -9999 0 -0.189 5 5
HCK -0.018 0.112 -9999 0 -0.366 5 5
dendritic cell antigen processing and presentation 0.006 0.072 -9999 0 -0.208 1 1
VTN 0.017 0 -9999 0 -9999 0 0
alphaM/beta2 Integrin/CYR61 0.008 0.07 -9999 0 -0.217 3 3
LPA 0.017 0 -9999 0 -9999 0 0
LRP1 0.012 0.043 -9999 0 -0.3 1 1
cell migration -0.07 0.13 -9999 0 -0.255 14 14
FN1 0 0.073 -9999 0 -0.3 3 3
alphaM/beta2 Integrin/Thy1 0.008 0.071 -9999 0 -0.219 3 3
MPO 0.006 0.06 -9999 0 -0.3 2 2
KNG1 0.012 0.043 -9999 0 -0.3 1 1
RAP1/GDP 0.009 0.059 -9999 0 -0.234 3 3
ROCK1 0.01 0.079 -9999 0 -9999 0 0
ELA2 0.017 0 -9999 0 -9999 0 0
PLG 0.006 0.06 -9999 0 -0.3 2 2
CTGF -0.002 0.082 -9999 0 -0.337 3 3
alphaM/beta2 Integrin/Hck -0.004 0.098 -9999 0 -0.298 4 4
ITGAM 0.012 0.016 -9999 0 -9999 0 0
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.013 0.075 -9999 0 -0.229 3 3
HP -0.034 0.124 -9999 0 -0.327 8 8
leukocyte adhesion -0.022 0.128 -9999 0 -0.321 5 5
SELP 0.004 0.071 -9999 0 -0.355 2 2
Ceramide signaling pathway

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
SPHK2 -0.034 0.11 -9999 0 -0.237 12 12
MAP4K4 -0.021 0.126 -9999 0 -0.351 5 5
BAG4 0.012 0.043 -9999 0 -0.3 1 1
PKC zeta/ceramide 0.009 0.046 0.103 6 -9999 0 6
NFKBIA 0.01 0.058 -9999 0 -0.411 1 1
BIRC3 -0.059 0.154 -9999 0 -0.36 11 11
BAX 0.015 0.026 -9999 0 -9999 0 0
RIPK1 0.017 0 -9999 0 -9999 0 0
AKT1 0.014 0.008 -9999 0 -9999 0 0
BAD 0.014 0.053 0.118 6 -0.143 1 7
SMPD1 -0.01 0.09 -9999 0 -0.34 3 3
RB1 0.013 0.057 0.118 6 -0.207 1 7
FADD/Caspase 8 -0.01 0.123 -9999 0 -0.404 3 3
MAP2K4 0.007 0.06 -9999 0 -0.192 2 2
NSMAF 0.017 0 -9999 0 -9999 0 0
response to UV 0 0 -9999 0 -9999 0 0
RAF1 0.019 0.045 0.118 5 -9999 0 5
EGF -0.018 0.1 -9999 0 -0.3 6 6
mol:ceramide 0.011 0.052 0.12 6 -9999 0 6
MADD 0.017 0 -9999 0 -9999 0 0
response to oxidative stress 0 0 -9999 0 -9999 0 0
mol:Free Fatty acid -0.046 0.119 -9999 0 -0.243 14 14
ASAH1 0.002 0.081 -9999 0 -0.411 2 2
negative regulation of cell cycle 0.013 0.057 0.117 6 -0.205 1 7
cell proliferation -0.009 0.083 -9999 0 -0.215 2 2
BID -0.003 0.102 -9999 0 -0.352 3 3
MAP3K1 0.001 0.064 0.117 4 -0.208 2 6
EIF2A 0.013 0.065 -9999 0 -0.168 2 2
TRADD 0.002 0.081 -9999 0 -0.411 2 2
CRADD -0.02 0.118 -9999 0 -0.389 5 5
MAPK3 0.029 0.042 -9999 0 -9999 0 0
response to heat 0 0 -9999 0 -9999 0 0
MAPK1 0.027 0.046 -9999 0 -9999 0 0
Cathepsin D/ceramide 0.014 0.062 0.116 6 -0.197 2 8
FADD -0.022 0.126 -9999 0 -0.344 5 5
KSR1 0.017 0.049 0.118 6 -9999 0 6
MAPK8 0.006 0.065 0.117 4 -0.165 4 8
PRKRA 0.017 0.049 0.118 6 -9999 0 6
PDGFA -0.065 0.157 -9999 0 -0.355 12 12
TRAF2 0.017 0 -9999 0 -9999 0 0
IGF1 -0.103 0.18 -9999 0 -0.365 17 17
mol:GD3 0 0 -9999 0 -9999 0 0
ganglioside biosynthetic process 0.011 0.052 0.12 6 -9999 0 6
CTSD 0.004 0.071 -9999 0 -0.355 2 2
regulation of nitric oxide biosynthetic process 0.026 0 -9999 0 -9999 0 0
response to radiation 0 0 -9999 0 -9999 0 0
ERK1/PKC delta -0.009 0.088 -9999 0 -0.228 2 2
PRKCD 0.012 0.043 -9999 0 -0.3 1 1
PRKCZ 0 0 -9999 0 -9999 0 0
mol:GW4869 0 0 -9999 0 -9999 0 0
mol:sphingosine -0.046 0.119 -9999 0 -0.243 14 14
RelA/NF kappa B1 0.026 0 -9999 0 -9999 0 0
mol:glutathione 0 0 -9999 0 -9999 0 0
PAWR 0.017 0 -9999 0 -9999 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.026 0.13 -9999 0 -0.397 4 4
TNFR1A/BAG4/TNF-alpha 0.006 0.086 -9999 0 -0.451 1 1
mol:Sphingosine-1-phosphate -0.034 0.11 -9999 0 -0.236 12 12
MAP2K1 0.025 0.043 -9999 0 -9999 0 0
mol:C11AG 0 0 -9999 0 -9999 0 0
RELA 0.017 0 -9999 0 -9999 0 0
CYCS 0.038 0.057 0.151 7 -9999 0 7
TNFRSF1A 0.01 0.058 -9999 0 -0.411 1 1
NFKB1 0.017 0 -9999 0 -9999 0 0
TNFR1A/BAG4 0.016 0.05 -9999 0 -0.237 2 2
EIF2AK2 0.007 0.068 -9999 0 -0.182 2 2
TNF-alpha/TNFR1A/FAN 0.009 0.083 -9999 0 -0.451 1 1
response to hydrogen peroxide 0 0 -9999 0 -9999 0 0
CASP8 0.008 0.072 -9999 0 -0.281 1 1
MAP2K2 0.025 0.043 -9999 0 -9999 0 0
SMPD3 0.001 0.06 -9999 0 -0.216 2 2
TNF -0.02 0.106 -9999 0 -0.318 6 6
PKC zeta/PAR4 0.013 0 -9999 0 -9999 0 0
mol:PHOSPHOCHOLINE 0.018 0.052 0.1 11 -9999 0 11
NF kappa B1/RelA/I kappa B alpha 0.037 0.031 -9999 0 -0.185 1 1
AIFM1 0.033 0.062 0.156 6 -0.167 1 7
BCL2 -0.058 0.159 -9999 0 -0.389 10 10
TRAIL signaling pathway

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
TNFSF10 -0.044 0.138 -9999 0 -0.349 9 9
positive regulation of NF-kappaB transcription factor activity -0.029 0.105 -9999 0 -0.222 12 12
MAP2K4 0 0.093 -9999 0 -0.375 1 1
IKBKB 0.017 0 -9999 0 -9999 0 0
TNFRSF10B 0.004 0.071 -9999 0 -0.355 2 2
TNFRSF10A 0.017 0 -9999 0 -9999 0 0
SMPD1 -0.019 0.082 -9999 0 -0.203 7 7
IKBKG 0.017 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
TNFRSF10D 0 0.073 -9999 0 -0.3 3 3
TRAIL/TRAILR2 -0.027 0.106 -9999 0 -0.233 11 11
TRAIL/TRAILR3 -0.029 0.105 -9999 0 -0.223 12 12
TRAIL/TRAILR1 -0.017 0.098 -9999 0 -0.232 9 9
TRAIL/TRAILR4 -0.029 0.105 -9999 0 -0.223 12 12
TRAIL/TRAILR1/DAP3/GTP 0.001 0.076 -9999 0 -0.204 4 4
IKK complex 0.014 0.063 -9999 0 -0.304 1 1
RIPK1 0.017 0 -9999 0 -9999 0 0
response to oxidative stress 0 0 -9999 0 -9999 0 0
DAP3/GTP 0.013 0 -9999 0 -9999 0 0
MAPK3 -0.019 0.097 -9999 0 -0.232 9 9
MAP3K1 -0.006 0.098 -9999 0 -0.4 1 1
TRAILR4 (trimer) 0 0.073 -9999 0 -0.299 3 3
TRADD 0.002 0.081 -9999 0 -0.411 2 2
TRAILR1 (trimer) 0.017 0 -9999 0 -9999 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.001 0.078 -9999 0 -9999 0 0
CFLAR 0.01 0.058 -9999 0 -0.411 1 1
MAPK1 -0.025 0.103 -9999 0 -0.237 10 10
TRAIL/TRAILR1/FADD/TRADD/RIP 0.007 0.086 -9999 0 -9999 0 0
mol:ceramide -0.019 0.081 -9999 0 -0.202 7 7
FADD 0.01 0.058 -9999 0 -0.411 1 1
MAPK8 -0.005 0.094 -9999 0 -0.352 1 1
TRAF2 0.017 0 -9999 0 -9999 0 0
TRAILR3 (trimer) 0 0.073 -9999 0 -0.299 3 3
CHUK 0.01 0.058 -9999 0 -0.411 1 1
TRAIL/TRAILR1/FADD -0.006 0.089 -9999 0 -0.227 5 5
DAP3 0.017 0 -9999 0 -9999 0 0
CASP10 -0.011 0.091 -9999 0 -0.243 5 5
JNK cascade -0.029 0.105 -9999 0 -0.222 12 12
TRAIL (trimer) -0.044 0.138 -9999 0 -0.348 9 9
TNFRSF10C 0 0.073 -9999 0 -0.3 3 3
TRAIL/TRAILR1/DAP3/GTP/FADD 0.006 0.077 -9999 0 -0.185 5 5
TRAIL/TRAILR2/FADD -0.014 0.095 -9999 0 -0.227 6 6
cell death -0.019 0.081 -9999 0 -0.202 7 7
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.007 0.1 -9999 0 -0.494 1 1
TRAILR2 (trimer) 0.004 0.071 -9999 0 -0.355 2 2
CASP8 0.015 0.032 -9999 0 -9999 0 0
negative regulation of caspase activity 0 0 -9999 0 -9999 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0 0.098 -9999 0 -0.38 1 1
IL1-mediated signaling events

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
UBC13/UEV1A 0.013 0 -9999 0 -9999 0 0
PRKCZ 0 0 -9999 0 -9999 0 0
MAP3K7IP2 0.017 0 -9999 0 -9999 0 0
ERC1 0.01 0.058 -9999 0 -0.411 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.009 0.076 -9999 0 -0.327 1 1
IRAK/TOLLIP 0.029 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 -0.077 0.133 -9999 0 -0.24 21 21
IL1A -0.034 0.124 -9999 0 -0.327 8 8
IL1B -0.043 0.114 -9999 0 -0.231 14 14
IRAK/TRAF6/p62/Atypical PKCs 0.028 0.051 -9999 0 -0.165 3 3
IL1R2 -0.079 0.166 -9999 0 -0.355 14 14
IL1R1 -0.02 0.118 -9999 0 -0.389 5 5
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.009 0.097 -9999 0 -0.264 5 5
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 0.036 0 -9999 0 -9999 0 0
IKK complex/ELKS 0.044 0.071 -9999 0 -0.259 1 1
JUN -0.016 0.103 -9999 0 -0.311 3 3
MAP3K7 0.017 0 -9999 0 -9999 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.049 0.16 -9999 0 -0.387 7 7
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.014 0.109 -9999 0 -0.231 9 9
PIK3R1 -0.038 0.134 -9999 0 -0.355 8 8
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.004 0.104 -9999 0 -0.276 3 3
IL1 beta fragment/IL1R1/IL1RAP -0.041 0.126 -9999 0 -0.262 10 10
NFKB1 0.017 0 -9999 0 -9999 0 0
MAPK8 -0.003 0.088 -9999 0 -0.325 1 1
IRAK1 0.02 0 -9999 0 -9999 0 0
IL1RN/IL1R1 -0.029 0.105 -9999 0 -0.223 12 12
IRAK4 0.017 0 -9999 0 -9999 0 0
PRKCI 0.012 0.043 -9999 0 -0.3 1 1
TRAF6 0.002 0.081 -9999 0 -0.411 2 2
PI3K -0.018 0.112 -9999 0 -0.268 8 8
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.015 0.1 -9999 0 -0.329 3 3
CHUK 0.01 0.058 -9999 0 -0.411 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.041 0.126 -9999 0 -0.262 10 10
IL1 beta/IL1R2 -0.08 0.136 -9999 0 -0.275 13 13
IRAK/TRAF6/TAK1/TAB1/TAB2 0.044 0.04 -9999 0 -9999 0 0
NF kappa B1 p50/RelA -0.071 0.125 -9999 0 -0.347 7 7
IRAK3 0 0.073 -9999 0 -0.3 3 3
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.028 0.115 -9999 0 -0.32 4 4
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.007 0.089 -9999 0 -0.283 1 1
IL1 alpha/IL1R1/IL1RAP -0.028 0.118 -9999 0 -0.263 9 9
RELA 0.017 0 -9999 0 -9999 0 0
MAP3K7IP1 0.017 0 -9999 0 -9999 0 0
SQSTM1 0.01 0.058 -9999 0 -0.411 1 1
MYD88 0.017 0 -9999 0 -9999 0 0
IRAK/TRAF6/MEKK3 0.031 0.042 -9999 0 -0.185 2 2
IL1RAP -0.002 0.082 -9999 0 -0.337 3 3
UBE2N 0.017 0 -9999 0 -9999 0 0
IRAK/TRAF6 -0.052 0.085 -9999 0 -0.273 5 5
CASP1 -0.034 0.124 -9999 0 -0.327 8 8
IL1RN/IL1R2 -0.069 0.134 -9999 0 -0.245 19 19
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.029 0.121 -9999 0 -0.333 4 4
TMEM189-UBE2V1 0 0 -9999 0 -9999 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.003 0.097 -9999 0 -0.285 4 4
PIK3CA 0.01 0.058 -9999 0 -0.411 1 1
IL1RN -0.024 0.106 -9999 0 -0.3 7 7
TRAF6/TAK1/TAB1/TAB2 0.035 0.04 -9999 0 -9999 0 0
MAP2K6 -0.001 0.088 -9999 0 -0.347 1 1
HIF-2-alpha transcription factor network

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
MMP14 -0.017 0.157 -9999 0 -1.147 1 1
oxygen homeostasis 0.003 0.015 -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 0.017 0.143 -9999 0 -0.421 3 3
EPO 0.024 0.229 -9999 0 -0.463 5 5
FIH (dimer) 0.02 0.015 -9999 0 -9999 0 0
APEX1 0.02 0.018 -9999 0 -9999 0 0
SERPINE1 0.007 0.255 -9999 0 -0.541 6 6
FLT1 -0.073 0.282 -9999 0 -1.061 4 4
ADORA2A 0.007 0.236 -9999 0 -0.481 7 7
germ cell development -0.014 0.268 -9999 0 -0.577 6 6
SLC11A2 0.007 0.256 -9999 0 -0.563 6 6
BHLHE40 0.004 0.24 -9999 0 -0.515 6 6
HIF1AN 0.02 0.015 -9999 0 -9999 0 0
HIF2A/ARNT/SIRT1 0.018 0.182 -9999 0 -0.476 3 3
ETS1 0.024 0.046 -9999 0 -0.291 1 1
CITED2 -0.002 0.046 -9999 0 -9999 0 0
KDR -0.005 0.052 -9999 0 -9999 0 0
PGK1 0.008 0.246 -9999 0 -0.509 6 6
SIRT1 0.018 0.001 -9999 0 -9999 0 0
response to hypoxia 0 0.001 -9999 0 -9999 0 0
HIF2A/ARNT 0.028 0.284 -9999 0 -0.585 6 6
EPAS1 0.001 0.158 -9999 0 -0.428 4 4
SP1 0.025 0.003 -9999 0 -9999 0 0
ABCG2 -0.002 0.265 -9999 0 -0.556 7 7
EFNA1 -0.008 0.276 -9999 0 -0.615 6 6
FXN 0.01 0.233 -9999 0 -0.493 6 6
POU5F1 -0.017 0.276 -9999 0 -0.6 6 6
neuron apoptosis -0.027 0.278 0.57 6 -9999 0 6
EP300 0.01 0.058 -9999 0 -0.411 1 1
EGLN3 -0.055 0.16 -9999 0 -0.385 10 10
EGLN2 0.012 0.06 -9999 0 -0.411 1 1
EGLN1 0.014 0.047 -9999 0 -0.312 1 1
VHL/Elongin B/Elongin C 0.036 0 -9999 0 -9999 0 0
VHL 0.017 0 -9999 0 -9999 0 0
ARNT 0.02 0.018 -9999 0 -9999 0 0
SLC2A1 0.003 0.245 -9999 0 -0.506 7 7
TWIST1 -0.009 0.25 -9999 0 -0.491 8 8
ELK1 0.025 0.003 -9999 0 -9999 0 0
HIF2A/ARNT/Cbp/p300 0.017 0.182 -9999 0 -0.474 3 3
VEGFA -0.001 0.258 -9999 0 -0.499 8 8
CREBBP 0.017 0 -9999 0 -9999 0 0
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer -0.002 0.105 -9999 0 -0.292 6 6
PDGFRB 0 0.081 -9999 0 -0.413 2 2
SPHK1 -0.028 0.102 -9999 0 -0.738 1 1
mol:S1P -0.032 0.092 -9999 0 -0.643 1 1
S1P1/S1P/Gi -0.064 0.158 -9999 0 -0.351 9 9
GNAO1 0.015 0.006 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/PLCgamma1 -0.058 0.152 -9999 0 -0.341 8 8
PLCG1 -0.06 0.157 -9999 0 -0.348 9 9
mol:GTP 0 0 -9999 0 -9999 0 0
PDGFB-D/PDGFRB 0 0.081 -9999 0 -0.412 2 2
GNAI2 0.015 0.006 -9999 0 -9999 0 0
GNAI3 0.007 0.058 -9999 0 -0.416 1 1
GNAI1 -0.052 0.152 -9999 0 -0.389 9 9
mol:GDP 0 0 -9999 0 -9999 0 0
EDG1 -0.016 0.147 -9999 0 -0.509 4 4
S1P1/S1P -0.037 0.136 -9999 0 -0.41 5 5
negative regulation of cAMP metabolic process -0.062 0.155 -9999 0 -0.343 9 9
MAPK3 -0.077 0.188 -9999 0 -0.436 9 9
calcium-dependent phospholipase C activity -0.002 0.003 -9999 0 -9999 0 0
Rac1/GDP 0.013 0 -9999 0 -9999 0 0
RhoA/GDP 0.007 0.041 -9999 0 -0.288 1 1
KDR 0.011 0.04 -9999 0 -9999 0 0
PLCB2 -0.027 0.124 -9999 0 -0.365 5 5
RAC1 0.017 0 -9999 0 -9999 0 0
RhoA/GTP -0.056 0.104 -9999 0 -0.348 5 5
receptor internalization -0.035 0.127 -9999 0 -0.384 5 5
PTGS2 -0.122 0.288 -9999 0 -0.816 6 6
Rac1/GTP -0.053 0.101 -9999 0 -0.348 5 5
RHOA 0.01 0.058 -9999 0 -0.411 1 1
VEGFA -0.014 0.112 -9999 0 -0.442 3 3
negative regulation of T cell proliferation -0.062 0.155 -9999 0 -0.343 9 9
GO:0007205 0 0 -9999 0 -9999 0 0
GNAZ -0.012 0.099 -9999 0 -0.358 4 4
MAPK1 -0.08 0.195 -9999 0 -0.456 9 9
S1P1/S1P/PDGFB-D/PDGFRB -0.04 0.142 -9999 0 -0.405 5 5
ABCC1 0.009 0.057 -9999 0 -0.409 1 1
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.022 0.034 -9999 0 -0.226 1 1
SNTA1 -0.018 0.1 -9999 0 -0.3 6 6
response to hypoxia 0 0 -9999 0 -9999 0 0
STMN1 0.014 0.053 -9999 0 -0.227 2 2
MAPK12 -0.026 0.095 -9999 0 -0.211 9 9
CCND1 -0.032 0.113 -9999 0 -0.38 4 4
p38 gamma/SNTA1 -0.031 0.101 -9999 0 -0.279 3 3
MAP2K3 0.01 0.058 -9999 0 -0.411 1 1
PKN1 0.012 0.043 -9999 0 -0.3 1 1
G2/M transition checkpoint -0.025 0.094 -9999 0 -0.21 9 9
MAP2K6 -0.022 0.091 -9999 0 -0.223 8 8
MAPT -0.001 0.072 -9999 0 -0.258 3 3
MAPK13 0.018 0.041 -9999 0 -0.28 1 1
hyperosmotic response 0 0 -9999 0 -9999 0 0
ZAK 0.016 0.019 -9999 0 -9999 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.009 0.07 -9999 0 -0.28 3 3
alphaV beta3 Integrin -0.01 0.093 -9999 0 -0.248 4 4
PTK2 0.005 0.124 -9999 0 -0.413 2 2
IGF1R -0.042 0.143 -9999 0 -0.383 8 8
PI4KB 0.017 0 -9999 0 -9999 0 0
MFGE8 -0.008 0.091 -9999 0 -0.327 4 4
SRC 0.017 0 -9999 0 -9999 0 0
CDKN1B -0.041 0.154 -9999 0 -0.449 6 6
VEGFA -0.006 0.098 -9999 0 -0.411 3 3
ILK 0.013 0.039 -9999 0 -9999 0 0
ROCK1 0.017 0 -9999 0 -9999 0 0
AKT1 0.019 0.036 -9999 0 -9999 0 0
PTK2B -0.005 0.092 -9999 0 -0.315 2 2
alphaV/beta3 Integrin/JAM-A 0.01 0.08 -9999 0 -0.255 1 1
CBL 0.017 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
alphaV beta3 Integrin/ANGPTL3 -0.008 0.093 -9999 0 -0.244 5 5
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.073 0.159 -9999 0 -0.286 15 15
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.001 0.104 -9999 0 -0.421 2 2
alphaV/beta3 Integrin/Syndecan-1 -0.013 0.098 -9999 0 -0.241 6 6
PI4KA 0.017 0 -9999 0 -9999 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.114 0.148 -9999 0 -0.384 10 10
PI4 Kinase 0.026 0 -9999 0 -9999 0 0
PIK3CA 0.01 0.058 -9999 0 -0.411 1 1
alphaV/beta3 Integrin/Osteopontin -0.074 0.156 -9999 0 -0.306 14 14
RPS6KB1 -0.085 0.16 -9999 0 -0.37 10 10
TLN1 0.017 0 -9999 0 -9999 0 0
MAPK3 -0.032 0.112 -9999 0 -0.32 4 4
GPR124 0.002 0.081 -9999 0 -0.411 2 2
MAPK1 -0.036 0.112 -9999 0 -0.32 4 4
PXN 0.017 0 -9999 0 -9999 0 0
PIK3R1 -0.038 0.134 -9999 0 -0.355 8 8
alphaV/beta3 Integrin/Tumstatin -0.01 0.104 -9999 0 -0.274 5 5
cell adhesion -0.019 0.11 -9999 0 -0.315 3 3
ANGPTL3 0.01 0.058 -9999 0 -0.411 1 1
VEGFR2 homodimer/VEGFA homodimer/Src 0.021 0.06 -9999 0 -0.227 3 3
IGF-1R heterotetramer -0.042 0.143 -9999 0 -0.382 8 8
Rac1/GDP 0.013 0 -9999 0 -9999 0 0
TGFBR2 0.017 0 -9999 0 -9999 0 0
ITGB3 -0.026 0.113 -9999 0 -0.315 7 7
IGF1 -0.103 0.18 -9999 0 -0.365 17 17
RAC1 0.017 0 -9999 0 -9999 0 0
regulation of cell-matrix adhesion -0.013 0.097 -9999 0 -0.24 6 6
apoptosis -0.004 0.09 -9999 0 -0.373 3 3
CD47 -0.004 0.09 -9999 0 -0.374 3 3
alphaV/beta3 Integrin/CD47 -0.015 0.111 -9999 0 -0.274 7 7
VCL 0.01 0.058 -9999 0 -0.411 1 1
alphaV/beta3 Integrin/Del1 -0.026 0.106 -9999 0 -0.238 8 8
CSF1 0.017 0 -9999 0 -9999 0 0
PIK3C2A 0.006 0.065 -9999 0 -0.371 1 1
PI4 Kinase/Pyk2 -0.029 0.062 -9999 0 -0.313 1 1
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.003 0.103 -9999 0 -0.246 6 6
FAK1/Vinculin 0.014 0.105 -9999 0 -0.328 2 2
alphaV beta3/Integrin/ppsTEM5 -0.013 0.098 -9999 0 -0.241 6 6
RHOA 0.01 0.058 -9999 0 -0.411 1 1
VTN 0.017 0 -9999 0 -9999 0 0
BCAR1 0.017 0 -9999 0 -9999 0 0
FGF2 0.006 0.06 -9999 0 -0.3 2 2
F11R 0.015 0.041 -9999 0 -0.194 2 2
alphaV/beta3 Integrin/Lactadherin -0.018 0.103 -9999 0 -0.256 6 6
alphaV/beta3 Integrin/TGFBR2 -0.003 0.089 -9999 0 -0.248 4 4
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.033 0.051 -9999 0 -0.197 2 2
HSP90AA1 0.002 0.081 -9999 0 -0.411 2 2
alphaV/beta3 Integrin/Talin -0.001 0.08 -9999 0 -0.224 4 4
mol:GDP 0 0 -9999 0 -9999 0 0
FN1 0 0.073 -9999 0 -0.3 3 3
alphaV/beta3 Integrin/Pyk2 0.001 0.095 -9999 0 -0.317 2 2
SDC1 0.002 0.081 -9999 0 -0.411 2 2
VAV3 -0.005 0.085 -9999 0 -9999 0 0
PTPN11 0.017 0 -9999 0 -9999 0 0
IRS1 -0.02 0.118 -9999 0 -0.389 5 5
FAK1/Paxillin 0.015 0.105 -9999 0 -0.328 2 2
cell migration 0.02 0.098 -9999 0 -0.358 1 1
ITGAV -0.004 0.09 -9999 0 -0.374 3 3
PI3K -0.01 0.112 -9999 0 -0.295 5 5
SPP1 -0.107 0.179 -9999 0 -0.355 18 18
KDR 0.017 0 -9999 0 -9999 0 0
mol:PI-4-5-P2 0 0 -9999 0 -9999 0 0
alphaV/beta3 Integrin/Caspase 8 -0.004 0.09 -9999 0 -0.373 3 3
COL4A3 0.004 0.071 -9999 0 -0.355 2 2
angiogenesis -0.025 0.112 -9999 0 -0.343 3 3
Rac1/GTP 0.004 0.08 -9999 0 -9999 0 0
EDIL3 -0.02 0.118 -9999 0 -0.389 5 5
cell proliferation -0.003 0.088 -9999 0 -0.248 4 4
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.012 0.043 -9999 0 -0.3 1 1
Caspase 8 (4 units) -0.012 0.103 -9999 0 -0.338 3 3
NEF -0.004 0.028 -9999 0 -9999 0 0
NFKBIA -0.005 0.066 -9999 0 -0.405 1 1
BIRC3 -0.043 0.169 -9999 0 -0.363 11 11
CYCS -0.011 0.094 -9999 0 -0.283 3 3
RIPK1 0.017 0 -9999 0 -9999 0 0
CD247 -0.088 0.18 -9999 0 -0.388 14 14
MAP2K7 -0.011 0.11 -9999 0 -0.428 2 2
protein ubiquitination 0.001 0.121 -9999 0 -0.311 5 5
CRADD -0.02 0.118 -9999 0 -0.389 5 5
DAXX 0.017 0 -9999 0 -9999 0 0
FAS -0.016 0.106 -9999 0 -0.344 5 5
BID -0.018 0.098 -9999 0 -0.303 3 3
NF-kappa-B/RelA/I kappa B alpha -0.005 0.101 -9999 0 -0.223 7 7
TRADD 0.002 0.081 -9999 0 -0.411 2 2
MAP3K5 -0.012 0.106 -9999 0 -0.383 4 4
CFLAR 0.01 0.058 -9999 0 -0.411 1 1
FADD 0.01 0.058 -9999 0 -0.411 1 1
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.005 0.102 -9999 0 -0.224 7 7
MAPK8 -0.011 0.115 -9999 0 -0.377 3 3
APAF1 0.01 0.058 -9999 0 -0.411 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 -0.025 0.103 -9999 0 -0.324 3 3
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.013 0.148 -9999 0 -0.385 6 6
CHUK -0.001 0.13 -9999 0 -0.339 5 5
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.015 0.09 -9999 0 -0.38 1 1
TCRz/NEF -0.063 0.139 -9999 0 -0.27 16 16
TNF -0.02 0.106 -9999 0 -0.318 6 6
FASLG -0.057 0.145 -9999 0 -0.282 14 14
NFKB1 0.003 0.036 -9999 0 -9999 0 0
TNFR1A/BAG4/TNF-alpha 0.006 0.086 -9999 0 -0.451 1 1
CASP6 0.001 0.124 -9999 0 -0.535 2 2
CASP7 -0.038 0.196 -9999 0 -0.453 8 8
RELA 0.003 0.036 -9999 0 -9999 0 0
CASP2 0.017 0 -9999 0 -9999 0 0
CASP3 -0.038 0.196 -9999 0 -0.434 9 9
TNFRSF1A 0.01 0.058 -9999 0 -0.411 1 1
TNFR1A/BAG4 0.016 0.05 -9999 0 -0.237 2 2
CASP8 0.017 0 -9999 0 -9999 0 0
CASP9 0.017 0 -9999 0 -9999 0 0
MAP3K14 -0.006 0.137 -9999 0 -0.352 6 6
APAF-1/Caspase 9 -0.068 0.129 -9999 0 -0.34 8 8
BCL2 -0.035 0.137 -9999 0 -0.359 5 5
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer -0.007 0.158 -9999 0 -0.565 4 4
VEGFR1 homodimer/NRP1 -0.02 0.156 -9999 0 -0.572 4 4
mol:DAG -0.006 0.146 -9999 0 -0.51 4 4
VEGFR1 homodimer/NRP1/VEGFR 121 -0.019 0.164 -9999 0 -0.572 4 4
CaM/Ca2+ 0.004 0.14 -9999 0 -0.479 4 4
HIF1A 0.003 0.087 -9999 0 -0.304 4 4
GAB1 -0.002 0.082 -9999 0 -0.337 3 3
AKT1 -0.016 0.162 -9999 0 -0.49 5 5
PLCG1 -0.006 0.147 -9999 0 -0.514 4 4
NOS3 0.006 0.143 -9999 0 -0.429 5 5
CBL 0.017 0 -9999 0 -9999 0 0
mol:NO 0.007 0.138 -9999 0 -0.413 5 5
FLT1 -0.018 0.18 -9999 0 -0.653 4 4
PGF 0.017 0 -9999 0 -9999 0 0
VEGFR1 homodimer/NRP2/VEGFR121 -0.019 0.168 -9999 0 -0.566 4 4
CALM1 0.017 0 -9999 0 -9999 0 0
PIK3CA 0.01 0.058 -9999 0 -0.411 1 1
eNOS/Hsp90 0.012 0.144 -9999 0 -0.432 5 5
endothelial cell proliferation -0.013 0.153 -9999 0 -0.474 5 5
mol:Ca2+ -0.005 0.145 -9999 0 -0.506 4 4
MAPK3 -0.002 0.133 -9999 0 -0.443 4 4
MAPK1 -0.006 0.14 -9999 0 -0.424 5 5
PIK3R1 -0.038 0.134 -9999 0 -0.355 8 8
PLGF homodimer 0.017 0 -9999 0 -9999 0 0
PRKACA 0.017 0 -9999 0 -9999 0 0
RP11-342D11.1 0 0 -9999 0 -9999 0 0
CAV1 0.017 0 -9999 0 -9999 0 0
VEGFA homodimer -0.006 0.098 -9999 0 -0.41 3 3
VEGFR1 homodimer/VEGFA homodimer -0.02 0.177 -9999 0 -0.616 4 4
platelet activating factor biosynthetic process 0 0.135 -9999 0 -0.406 5 5
PI3K -0.017 0.167 -9999 0 -0.499 5 5
PRKCA -0.008 0.14 -9999 0 -0.471 4 4
PRKCB -0.007 0.136 -9999 0 -0.477 4 4
VEGFR1 homodimer/PLGF homodimer -0.007 0.158 -9999 0 -0.565 4 4
VEGFA -0.006 0.098 -9999 0 -0.411 3 3
VEGFB 0.017 0 -9999 0 -9999 0 0
mol:IP3 -0.006 0.146 -9999 0 -0.51 4 4
RASA1 -0.001 0.145 -9999 0 -0.514 4 4
NRP2 -0.002 0.082 -9999 0 -0.337 3 3
VEGFR1 homodimer -0.018 0.179 -9999 0 -0.651 4 4
VEGFB homodimer 0.017 0 -9999 0 -9999 0 0
NCK1 0.01 0.058 -9999 0 -0.411 1 1
eNOS/Caveolin-1 0.016 0.135 -9999 0 -0.397 5 5
PTPN11 0.017 0 -9999 0 -9999 0 0
mol:PI-3-4-5-P3 -0.018 0.165 -9999 0 -0.493 5 5
mol:L-citrulline 0.007 0.138 -9999 0 -0.413 5 5
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.001 0.161 -9999 0 -0.533 4 4
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.012 0.167 -9999 0 -0.566 4 4
CD2AP 0.01 0.058 -9999 0 -0.411 1 1
PI3K/GAB1 -0.017 0.17 -9999 0 -0.51 5 5
PDPK1 -0.017 0.154 -9999 0 -0.464 5 5
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.008 0.166 -9999 0 -0.566 4 4
mol:NADP 0.007 0.138 -9999 0 -0.413 5 5
HSP90AA1 0.002 0.081 -9999 0 -0.411 2 2
ubiquitin-dependent protein catabolic process -0.002 0.158 -9999 0 -0.526 4 4
VEGFR1 homodimer/NRP2 -0.019 0.162 -9999 0 -0.565 4 4
Regulation of Androgen receptor activity

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
HDAC1 0.02 0.029 -9999 0 -0.194 1 1
SMARCC1 0.011 0.012 -9999 0 -9999 0 0
REL 0.003 0.071 -9999 0 -0.356 2 2
HDAC7 -0.049 0.153 -9999 0 -0.367 7 7
JUN -0.026 0.124 -9999 0 -0.374 6 6
EP300 0.01 0.058 -9999 0 -0.411 1 1
KAT2B 0 0 -9999 0 -9999 0 0
KAT5 0 0 -9999 0 -9999 0 0
MAPK14 -0.032 0.117 -9999 0 -0.273 10 10
FOXO1 0.018 0 -9999 0 -9999 0 0
T-DHT/AR -0.041 0.167 -9999 0 -0.385 7 7
MAP2K6 -0.059 0.162 -9999 0 -0.395 10 10
BRM/BAF57 0.005 0.08 -9999 0 -0.279 4 4
MAP2K4 0.017 0.005 -9999 0 -9999 0 0
SMARCA2 -0.014 0.112 -9999 0 -0.41 4 4
PDE9A -0.027 0.159 -9999 0 -0.955 1 1
NCOA2 0.018 0 -9999 0 -9999 0 0
CEBPA 0.011 0.043 -9999 0 -0.3 1 1
EHMT2 0.012 0.043 -9999 0 -0.299 1 1
cell proliferation -0.034 0.163 -9999 0 -0.333 9 9
NR0B1 -0.055 0.146 -9999 0 -0.34 11 11
EGR1 -0.061 0.149 -9999 0 -0.336 12 12
RXRs/9cRA 0.018 0.063 -9999 0 -0.203 4 4
AR/RACK1/Src -0.014 0.118 -9999 0 -0.271 6 6
AR/GR -0.038 0.127 -9999 0 -0.331 6 6
GNB2L1 0.01 0.058 -9999 0 -0.41 1 1
PKN1 0.012 0.043 -9999 0 -0.299 1 1
RCHY1 -0.006 0.098 -9999 0 -0.411 3 3
epidermal growth factor receptor activity 0 0 -9999 0 -9999 0 0
MAPK8 0.01 0.058 -9999 0 -0.28 2 2
T-DHT/AR/TIF2/CARM1 -0.011 0.12 -9999 0 -0.281 6 6
SRC -0.014 0.094 -9999 0 -0.218 5 5
NR3C1 0.006 0.06 -9999 0 -0.3 2 2
KLK3 -0.124 0.148 -9999 0 -0.461 3 3
APPBP2 0.016 0.007 -9999 0 -9999 0 0
TRIM24 0.018 0 -9999 0 -9999 0 0
T-DHT/AR/TIP60 -0.037 0.118 -9999 0 -0.252 11 11
TMPRSS2 -0.177 0.417 -9999 0 -1.04 10 10
RXRG -0.006 0.098 -9999 0 -0.41 3 3
mol:9cRA 0 0 -9999 0 -9999 0 0
RXRA 0.01 0.058 -9999 0 -0.41 1 1
RXRB 0.018 0 -9999 0 -9999 0 0
CARM1 0.018 0 -9999 0 -9999 0 0
NR2C2 0.018 0 -9999 0 -9999 0 0
KLK2 0.009 0.1 -9999 0 -9999 0 0
AR -0.044 0.136 -9999 0 -0.303 9 9
SENP1 0.012 0.043 -9999 0 -0.299 1 1
HSP90AA1 0.002 0.081 -9999 0 -0.411 2 2
MDM2 0.01 0.043 -9999 0 -0.301 1 1
SRY 0.002 0.071 -9999 0 -0.356 2 2
GATA2 -0.016 0.106 -9999 0 -0.344 5 5
MYST2 0.017 0 -9999 0 -9999 0 0
HOXB13 -0.208 0.2 -9999 0 -0.377 31 31
T-DHT/AR/RACK1/Src -0.02 0.12 -9999 0 -0.272 7 7
positive regulation of transcription -0.016 0.106 -9999 0 -0.344 5 5
DNAJA1 -0.022 0.118 -9999 0 -0.39 5 5
proteasomal ubiquitin-dependent protein catabolic process 0.008 0.084 -9999 0 -0.325 3 3
NCOA1 0.024 0.004 -9999 0 -9999 0 0
SPDEF -0.12 0.198 -9999 0 -0.398 18 18
T-DHT/AR/TIF2 0 0.08 -9999 0 -0.209 2 2
T-DHT/AR/Hsp90 -0.034 0.132 -9999 0 -0.333 6 6
GSK3B 0.017 0.002 -9999 0 -9999 0 0
NR2C1 0.017 0 -9999 0 -9999 0 0
mol:T-DHT -0.022 0.102 -9999 0 -0.213 11 11
SIRT1 0.018 0 -9999 0 -9999 0 0
ZMIZ2 0.016 0 -9999 0 -9999 0 0
POU2F1 0.012 0.053 -9999 0 -0.291 1 1
T-DHT/AR/DAX-1 -0.06 0.145 -9999 0 -0.331 8 8
CREBBP 0.018 0 -9999 0 -9999 0 0
SMARCE1 0.018 0 -9999 0 -9999 0 0
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.028 0.143 -9999 0 -0.317 8 8
MAP3K8 -0.045 0.138 -9999 0 -0.35 9 9
FOS -0.015 0.1 -9999 0 -0.328 2 2
PRKCA -0.001 0.082 -9999 0 -0.416 2 2
PTPN7 0.014 0.009 -9999 0 -9999 0 0
HRAS 0.017 0.001 -9999 0 -9999 0 0
PRKCB -0.002 0.006 -9999 0 -0.013 14 14
NRAS 0.011 0.043 -9999 0 -0.299 1 1
RAS family/GTP 0.025 0.025 -9999 0 -9999 0 0
MAPK3 0.004 0.053 -9999 0 -9999 0 0
MAP2K1 -0.014 0.092 -9999 0 -0.321 3 3
ELK1 0.014 0.009 -9999 0 -9999 0 0
BRAF 0.002 0.075 -9999 0 -0.365 2 2
mol:GTP -0.001 0.002 -9999 0 -0.004 14 14
MAPK1 -0.005 0.086 -9999 0 -0.5 1 1
RAF1 -0.001 0.078 -9999 0 -0.365 2 2
KRAS 0.017 0.001 -9999 0 -9999 0 0
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 0.007 0.094 -9999 0 -0.238 6 6
MAP4K1 0.017 0 -9999 0 -9999 0 0
MAP3K8 -0.044 0.138 -9999 0 -0.349 9 9
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 -0.007 0.118 -9999 0 -0.402 3 3
JUN -0.026 0.143 -9999 0 -0.698 2 2
MAP3K7 0.008 0.09 -9999 0 -0.339 2 2
GRAP2 0.017 0 -9999 0 -9999 0 0
CRK -0.014 0.112 -9999 0 -0.411 4 4
MAP2K4 -0.008 0.11 -9999 0 -0.293 5 5
LAT -0.008 0.091 -9999 0 -0.327 4 4
LCP2 -0.028 0.119 -9999 0 -0.331 7 7
MAPK8 -0.012 0.128 -9999 0 -0.642 2 2
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.002 0.096 -9999 0 -0.365 2 2
LAT/GRAP2/SLP76/HPK1/HIP-55 0.016 0.089 -9999 0 -0.255 3 3
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.017 0 -9999 0 -9999 0 0
ITGB7 0.01 0.058 -9999 0 -0.411 1 1
ITGA4 -0.01 0.099 -9999 0 -0.355 4 4
alpha4/beta7 Integrin 0.001 0.08 -9999 0 -0.246 5 5
alpha4/beta1 Integrin 0.007 0.07 -9999 0 -0.237 4 4
Cellular roles of Anthrax toxin

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
ANTXR1 0.01 0.058 -9999 0 -0.411 1 1
ANTXR2 -0.006 0.098 -9999 0 -0.411 3 3
negative regulation of myeloid dendritic cell antigen processing and presentation -0.004 0.014 -9999 0 -0.054 4 4
monocyte activation -0.04 0.126 -9999 0 -0.379 6 6
MAP2K2 0.012 0.008 -9999 0 -9999 0 0
MAP2K1 0.006 0.014 -9999 0 -9999 0 0
MAP2K7 0.006 0.014 -9999 0 -9999 0 0
MAP2K6 -0.03 0.077 -9999 0 -0.188 10 10
CYAA -0.002 0.055 -9999 0 -0.196 4 4
MAP2K4 0.006 0.014 -9999 0 -9999 0 0
IL1B -0.017 0.06 -9999 0 -0.169 6 6
Channel 0.005 0.061 -9999 0 -0.211 4 4
NLRP1 0 0.037 -9999 0 -0.169 2 2
CALM1 0.017 0 -9999 0 -9999 0 0
negative regulation of phagocytosis 0.01 0.018 -9999 0 -9999 0 0
mol:Ca2+ 0 0 -9999 0 -9999 0 0
regulation of endothelial cell proliferation 0.004 0.014 0.054 4 -9999 0 4
MAPK3 0.006 0.014 -9999 0 -9999 0 0
MAPK1 0.003 0.031 -9999 0 -0.201 1 1
PGR -0.075 0.101 -9999 0 -0.194 22 22
PA/Cellular Receptors 0.005 0.068 -9999 0 -0.234 4 4
apoptosis -0.004 0.014 -9999 0 -0.054 4 4
LOC728358 0 0 -9999 0 -9999 0 0
Lethal toxin (unfolded) 0.005 0.058 -9999 0 -0.201 4 4
macrophage activation 0.009 0.03 -9999 0 -0.186 1 1
TNF -0.02 0.106 -9999 0 -0.318 6 6
VCAM1 -0.04 0.126 -9999 0 -0.381 6 6
platelet activation 0.01 0.018 -9999 0 -9999 0 0
MAPKKK cascade 0 0.025 -9999 0 -9999 0 0
IL18 -0.015 0.063 -9999 0 -0.176 6 6
negative regulation of macrophage activation -0.004 0.014 -9999 0 -0.054 4 4
LEF -0.004 0.014 -9999 0 -0.055 4 4
CASP1 -0.001 0.023 -9999 0 -0.088 2 2
mol:cAMP 0.01 0.018 -9999 0 -9999 0 0
necrosis -0.004 0.014 -9999 0 -0.054 4 4
intracellular pH reduction 0 0 -9999 0 -9999 0 0
PAGA 0 0 -9999 0 -9999 0 0
Edema toxin (unfolded) 0.006 0.057 -9999 0 -0.197 4 4
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -9999 0 -9999 0 0
Arf6 signaling events

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
CENTA1/KIF3B -0.001 0.053 -9999 0 -0.216 3 3
ARNO/beta Arrestin1-2 0.007 0.049 -9999 0 -0.167 1 1
EGFR -0.01 0.099 -9999 0 -0.355 4 4
EPHA2 -0.028 0.129 -9999 0 -0.392 6 6
USP6 0.017 0 -9999 0 -9999 0 0
IQSEC1 0.01 0.058 -9999 0 -0.411 1 1
EGFR/EGFR/EGF/EGF -0.018 0.093 -9999 0 -0.211 10 10
ARRB2 0.016 0.019 -9999 0 -9999 0 0
mol:GTP 0.001 0.025 -9999 0 -0.158 1 1
ARRB1 0.017 0 -9999 0 -9999 0 0
FBXO8 -0.004 0.09 -9999 0 -0.374 3 3
TSHR 0.004 0.071 -9999 0 -0.355 2 2
EGF -0.018 0.1 -9999 0 -0.299 6 6
somatostatin receptor activity 0 0 -9999 0 0 2 2
ARAP2 0 0 -9999 0 0 1 1
mol:GDP 0.013 0.051 -9999 0 -0.209 2 2
mol:PI-3-4-5-P3 0 0 -9999 0 0 2 2
ITGA2B 0.012 0.043 -9999 0 -0.3 1 1
ARF6 0.017 0 -9999 0 -9999 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.01 0.124 -9999 0 -0.268 9 9
ADAP1 0 0 -9999 0 0 1 1
KIF13B -0.004 0.09 -9999 0 -0.374 3 3
HGF/MET 0.018 0.042 -9999 0 -0.194 2 2
PXN 0.017 0 -9999 0 -9999 0 0
ARF6/GTP 0.014 0.059 -9999 0 -0.2 2 2
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.007 0.085 -9999 0 -0.172 11 11
ADRB2 -0.026 0.113 -9999 0 -0.315 7 7
receptor agonist activity 0 0 -9999 0 0 2 2
actin filament binding 0 0 -9999 0 0 2 2
SRC 0.017 0 -9999 0 -9999 0 0
ITGB3 -0.026 0.113 -9999 0 -0.315 7 7
GNAQ 0 0 -9999 0 -0.001 2 2
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 2 2
ARF6/GDP 0.012 0.054 -9999 0 -0.153 2 2
ARF6/GDP/GULP/ACAP1 0.012 0.068 -9999 0 -0.192 2 2
alphaIIb/beta3 Integrin/paxillin/GIT1 0.014 0.077 -9999 0 -0.224 3 3
ACAP1 0 0 -9999 0 -9999 0 0
ACAP2 0 0 -9999 0 0 1 1
LHCGR/beta Arrestin2 0.016 0.026 -9999 0 -0.173 1 1
EFNA1 -0.022 0.124 -9999 0 -0.411 5 5
HGF 0.012 0.043 -9999 0 -0.3 1 1
CYTH3 0 0 -9999 0 0 2 2
CYTH2 0 0.001 -9999 0 -0.004 2 2
NCK1 0.01 0.058 -9999 0 -0.411 1 1
fibronectin binding 0 0 -9999 0 0 2 2
endosomal lumen acidification 0 0 -9999 0 0 2 2
microtubule-based process 0 0 -9999 0 -9999 0 0
GULP1 -0.02 0.118 -9999 0 -0.389 5 5
GNAQ/ARNO 0.001 0.002 -9999 0 -0.005 2 2
mol:Phosphatidic acid 0 0 -9999 0 0 1 1
PIP3-E -0.018 0.112 -9999 0 -0.366 5 5
MET 0.012 0.043 -9999 0 -0.3 1 1
GNA14 0.004 0.071 -9999 0 -0.355 2 2
GNA15 0.012 0.043 -9999 0 -0.3 1 1
GIT1 0.01 0.058 -9999 0 -0.411 1 1
mol:PI-4-5-P2 0 0 -9999 0 -0.001 2 2
GNA11 0.017 0 -9999 0 -9999 0 0
LHCGR 0.011 0.043 -9999 0 -0.299 1 1
AGTR1 0.012 0.043 -9999 0 -0.3 1 1
desensitization of G-protein coupled receptor protein signaling pathway 0.016 0.026 -9999 0 -0.173 1 1
IPCEF1/ARNO -0.013 0.081 -9999 0 -0.166 8 8
alphaIIb/beta3 Integrin -0.007 0.09 -9999 0 -0.232 7 7
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.018 0.001 -9999 0 -9999 0 0
HDAC2 0.018 0.001 -9999 0 -9999 0 0
GNB1/GNG2 0.007 0.072 -9999 0 -0.229 2 2
forebrain development -0.113 0.252 -9999 0 -0.607 8 8
GNAO1 0.016 0.003 -9999 0 -9999 0 0
SMO/beta Arrestin2 -0.003 0.076 -9999 0 -0.234 5 5
SMO -0.019 0.107 -9999 0 -0.349 5 5
ARRB2 0.016 0.004 -9999 0 -9999 0 0
GLI3/SPOP -0.012 0.131 -9999 0 -0.447 3 3
mol:GTP -0.001 0.003 -9999 0 -9999 0 0
GSK3B 0.017 0 -9999 0 -9999 0 0
GNAI2 0.016 0.003 -9999 0 -9999 0 0
SIN3/HDAC complex 0.047 0.004 -9999 0 -9999 0 0
GNAI1 -0.051 0.152 -9999 0 -0.387 9 9
XPO1 0.014 0.009 -9999 0 -9999 0 0
GLI1/Su(fu) -0.096 0.248 -9999 0 -0.664 6 6
SAP30 0.018 0.001 -9999 0 -9999 0 0
mol:GDP -0.019 0.107 -9999 0 -0.348 5 5
MIM/GLI2A -0.038 0.118 -9999 0 -0.378 5 5
IFT88 0.002 0.081 -9999 0 -0.411 2 2
GNAI3 0.008 0.058 -9999 0 -0.41 1 1
GLI2 0.035 0.045 -9999 0 -0.217 1 1
GLI3 -0.022 0.135 -9999 0 -0.413 4 4
CSNK1D 0.012 0.043 -9999 0 -0.3 1 1
CSNK1E 0.017 0 -9999 0 -9999 0 0
SAP18 0.018 0.001 -9999 0 -9999 0 0
embryonic digit morphogenesis 0.002 0.081 -9999 0 -0.41 2 2
GNG2 0.006 0.06 -9999 0 -0.3 2 2
Gi family/GTP -0.032 0.128 -9999 0 -0.357 5 5
SIN3B 0.018 0.001 -9999 0 -9999 0 0
SIN3A 0.018 0.001 -9999 0 -9999 0 0
GLI3/Su(fu) -0.01 0.126 -9999 0 -0.379 4 4
GLI2/Su(fu) 0.03 0.085 -9999 0 -0.43 1 1
FOXA2 -0.402 0.509 -9999 0 -1.031 21 21
neural tube patterning -0.113 0.252 -9999 0 -0.607 8 8
SPOP 0.017 0 -9999 0 -9999 0 0
Su(fu)/PIAS1 0.01 0.089 -9999 0 -0.397 2 2
GNB1 0.017 0 -9999 0 -9999 0 0
CSNK1G2 0.01 0.058 -9999 0 -0.411 1 1
CSNK1G3 0.017 0 -9999 0 -9999 0 0
MTSS1 -0.038 0.118 -9999 0 -0.379 5 5
embryonic limb morphogenesis -0.113 0.252 -9999 0 -0.607 8 8
SUFU -0.001 0.096 -9999 0 -0.439 2 2
LGALS3 -0.004 0.09 -9999 0 -0.374 3 3
catabolic process 0.012 0.12 -9999 0 -0.329 4 4
GLI3A/CBP -0.029 0.107 -9999 0 -0.306 5 5
KIF3A 0.004 0.071 -9999 0 -0.355 2 2
GLI1 -0.116 0.261 -9999 0 -0.67 7 7
RAB23 -0.012 0.106 -9999 0 -0.383 4 4
CSNK1A1 0.017 0 -9999 0 -9999 0 0
IFT172 0.002 0.081 -9999 0 -0.411 2 2
RBBP7 -0.008 0.091 -9999 0 -0.327 4 4
Su(fu)/Galectin3 -0.001 0.099 -9999 0 -0.397 2 2
GNAZ -0.011 0.099 -9999 0 -0.357 4 4
RBBP4 0.018 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 0.041 0.043 -9999 0 -9999 0 0
STK36 -0.002 0.081 -9999 0 -0.411 2 2
Gi family/GNB1/GNG2/GDP -0.02 0.125 -9999 0 -0.376 4 4
PTCH1 -0.093 0.225 -9999 0 -0.661 5 5
MIM/GLI1 -0.198 0.348 -9999 0 -0.571 21 21
CREBBP -0.029 0.107 -9999 0 -0.306 5 5
Su(fu)/SIN3/HDAC complex 0.04 0.039 -9999 0 -9999 0 0
Fc-epsilon receptor I signaling in mast cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A 0.012 0.043 -9999 0 -0.3 1 1
LAT2 -0.015 0.081 -9999 0 -0.384 1 1
AP1 -0.062 0.14 -9999 0 -0.357 6 6
mol:PIP3 -0.048 0.115 -9999 0 -0.285 4 4
IKBKB -0.019 0.072 -9999 0 -0.171 3 3
AKT1 -0.033 0.103 -9999 0 -0.293 3 3
IKBKG -0.019 0.072 -9999 0 -0.171 3 3
MS4A2 0.015 0.002 -9999 0 -9999 0 0
mol:Sphingosine-1-phosphate 0 0 -9999 0 -9999 0 0
PIK3CA 0.009 0.058 -9999 0 -0.413 1 1
MAP3K1 -0.026 0.11 -9999 0 -0.294 5 5
mol:Ca2+ -0.036 0.094 -9999 0 -0.238 3 3
LYN 0.012 0.043 -9999 0 -0.298 1 1
CBLB -0.014 0.08 -9999 0 -0.382 1 1
SHC1 0.017 0 -9999 0 -9999 0 0
RasGAP/p62DOK 0.024 0.039 -9999 0 -9999 0 0
positive regulation of cell migration -0.009 0.074 -9999 0 -0.267 4 4
INPP5D 0 0 -9999 0 -9999 0 0
PLD2 -0.031 0.095 -9999 0 -0.196 9 9
PTPN13 -0.065 0.119 -9999 0 -0.345 4 4
PTPN11 0.014 0.007 -9999 0 -9999 0 0
GO:0007205 0 0 -9999 0 -9999 0 0
regulation of mast cell degranulation -0.013 0.085 -9999 0 -0.302 1 1
SYK -0.012 0.108 -9999 0 -0.393 4 4
GRB2 0.017 0 -9999 0 -9999 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.078 0.095 -9999 0 -0.277 6 6
LAT -0.026 0.084 -9999 0 -0.382 1 1
PAK2 -0.021 0.099 -9999 0 -0.352 2 2
NFATC2 -0.014 0.067 -9999 0 -0.428 1 1
HRAS -0.03 0.105 -9999 0 -0.331 3 3
GAB2 0.017 0 -9999 0 -9999 0 0
PLA2G1B 0.029 0.027 -9999 0 -9999 0 0
Fc epsilon R1 -0.041 0.105 -9999 0 -0.24 7 7
Antigen/IgE/Fc epsilon R1 -0.036 0.094 -9999 0 -0.215 7 7
mol:GDP -0.038 0.114 -9999 0 -0.341 4 4
JUN -0.026 0.124 -9999 0 -0.374 6 6
mol:Ca++ 0 0 -9999 0 -9999 0 0
PIK3R1 -0.038 0.134 -9999 0 -0.355 8 8
FOS -0.079 0.166 -9999 0 -0.355 14 14
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.021 0.085 -9999 0 -0.407 1 1
CHUK -0.022 0.072 -9999 0 -0.171 3 3
KLRG1 -0.02 0.085 -9999 0 -0.398 1 1
VAV1 -0.042 0.107 -9999 0 -0.339 3 3
calcium-dependent protein kinase C activity 0 0 -9999 0 -9999 0 0
CBL -0.014 0.08 -9999 0 -0.382 1 1
negative regulation of mast cell degranulation -0.02 0.079 -9999 0 -0.372 1 1
BTK -0.025 0.11 -9999 0 -0.476 2 2
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.048 0.108 -9999 0 -0.344 2 2
GAB2/PI3K/SHP2 -0.067 0.089 -9999 0 -0.272 5 5
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.024 0.088 -9999 0 -0.281 2 2
RAF1 0.02 0.028 -9999 0 -9999 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.06 0.112 -9999 0 -0.217 13 13
FCER1G 0.015 0.002 -9999 0 -9999 0 0
FCER1A -0.103 0.174 -9999 0 -0.345 18 18
Antigen/IgE/Fc epsilon R1/Fyn -0.036 0.104 -9999 0 -0.215 9 9
MAPK3 0.029 0.024 -9999 0 -9999 0 0
MAPK1 0.027 0.031 -9999 0 -9999 0 0
NFKB1 0.017 0 -9999 0 -9999 0 0
MAPK8 -0.002 0.11 -9999 0 -0.534 2 2
DUSP1 0 0.073 -9999 0 -0.3 3 3
NF-kappa-B/RelA -0.022 0.032 -9999 0 -9999 0 0
actin cytoskeleton reorganization -0.01 0.08 -9999 0 -0.378 1 1
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -9999 0 0
PI3K -0.046 0.113 -9999 0 -0.38 2 2
FER -0.014 0.08 -9999 0 -0.382 1 1
RELA 0.017 0 -9999 0 -9999 0 0
ITK -0.012 0.057 -9999 0 -0.228 2 2
SOS1 0.017 0 -9999 0 -9999 0 0
PLCG1 -0.039 0.114 -9999 0 -0.362 3 3
cytokine secretion -0.017 0.023 -9999 0 -9999 0 0
SPHK1 -0.023 0.088 -9999 0 -0.32 2 2
PTK2 -0.011 0.082 -9999 0 -0.392 1 1
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.071 0.091 -9999 0 -0.298 4 4
EDG1 -0.009 0.074 -9999 0 -0.267 4 4
mol:DAG -0.042 0.111 -9999 0 -0.299 3 3
MAP2K2 0.025 0.025 -9999 0 -9999 0 0
MAP2K1 0.025 0.025 -9999 0 -9999 0 0
MAP2K7 0.017 0 -9999 0 -9999 0 0
KLRG1/SHP2 -0.019 0.084 -9999 0 -0.391 1 1
MAP2K4 0.023 0.008 -9999 0 -9999 0 0
Fc epsilon R1/FcgammaRIIB -0.065 0.121 -9999 0 -0.233 13 13
mol:Choline -0.031 0.094 -9999 0 -0.194 9 9
SHC/Grb2/SOS1 0.004 0.081 -9999 0 -0.351 1 1
FYN -0.006 0.098 -9999 0 -0.411 3 3
DOK1 0.017 0 -9999 0 -9999 0 0
PXN -0.004 0.078 -9999 0 -0.362 1 1
HCLS1 -0.05 0.095 -9999 0 -0.382 1 1
PRKCB -0.034 0.091 -9999 0 -0.235 3 3
FCGR2B -0.057 0.15 -9999 0 -0.35 11 11
IGHE -0.001 0.003 -9999 0 -9999 0 0
KLRG1/SHIP -0.02 0.08 -9999 0 -0.379 1 1
LCP2 -0.028 0.119 -9999 0 -0.331 7 7
PLA2G4A -0.09 0.131 -9999 0 -0.349 7 7
RASA1 0.017 0 -9999 0 -9999 0 0
mol:Phosphatidic acid -0.031 0.094 -9999 0 -0.194 9 9
IKK complex -0.007 0.059 -9999 0 -0.144 1 1
WIPF1 0.017 0 -9999 0 -9999 0 0
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.005 0.03 0.208 1 -9999 0 1
BUB1B -0.019 0.114 -9999 0 -0.325 6 6
PLK1 0.007 0.032 -9999 0 -0.109 3 3
PLK1S1 0.005 0.015 -9999 0 -0.047 3 3
KIF2A 0.009 0.043 -9999 0 -0.17 2 2
regulation of mitotic centrosome separation 0.007 0.032 -9999 0 -0.108 3 3
GOLGA2 0.017 0 -9999 0 -9999 0 0
Hec1/SPC24 -0.008 0.086 -9999 0 -0.244 6 6
WEE1 0.009 0.049 -9999 0 -0.182 2 2
cytokinesis -0.007 0.128 -9999 0 -0.513 3 3
PP2A-alpha B56 -0.018 0.233 -9999 0 -0.796 4 4
AURKA -0.002 0.065 -9999 0 -0.263 3 3
PICH/PLK1 -0.004 0.125 -9999 0 -0.368 4 4
CENPE -0.006 0.083 -9999 0 -0.253 5 5
RhoA/GTP 0.007 0.041 -9999 0 -0.288 1 1
positive regulation of microtubule depolymerization 0.009 0.043 -9999 0 -0.169 2 2
PPP2CA 0.017 0 -9999 0 -9999 0 0
FZR1 0.017 0 -9999 0 -9999 0 0
TPX2 -0.018 0.092 -9999 0 -0.276 6 6
PAK1 0.017 0.001 -9999 0 -9999 0 0
SPC24 0 0 -9999 0 -9999 0 0
FBXW11 0.017 0 -9999 0 -9999 0 0
CLSPN -0.005 0.074 -9999 0 -0.302 3 3
GORASP1 0.01 0.058 -9999 0 -0.411 1 1
metaphase 0 0.001 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
NLP 0.005 0.015 -9999 0 -0.047 3 3
G2 phase of mitotic cell cycle -0.001 0.003 -9999 0 -0.011 3 3
STAG2 0.017 0 -9999 0 -9999 0 0
GRASP65/GM130/RAB1/GTP 0.009 0.085 -9999 0 -0.567 1 1
spindle elongation 0.007 0.032 -9999 0 -0.108 3 3
ODF2 0.017 0.003 -9999 0 -9999 0 0
BUB1 -0.042 0.255 -9999 0 -0.887 4 4
TPT1 0.006 0.038 -9999 0 -0.249 1 1
CDC25C -0.003 0.083 -9999 0 -0.414 2 2
CDC25B -0.002 0.082 -9999 0 -0.337 3 3
SGOL1 0.005 0.03 -9999 0 -0.208 1 1
RHOA 0.01 0.058 -9999 0 -0.411 1 1
CCNB1/CDK1 0.004 0.108 -9999 0 -0.338 4 4
CDC14B 0.011 0.002 -9999 0 -9999 0 0
CDC20 -0.014 0.112 -9999 0 -0.411 4 4
PLK1/PBIP1 0.001 0.068 -9999 0 -0.274 3 3
mitosis 0.001 0.008 0.035 3 -9999 0 3
FBXO5 0.008 0.034 -9999 0 -0.111 2 2
CDC2 0.009 0.06 -9999 0 -0.43 1 1
NDC80 -0.03 0.135 -9999 0 -0.411 6 6
metaphase plate congression 0.011 0.019 -9999 0 -9999 0 0
ERCC6L -0.007 0.136 -9999 0 -0.405 4 4
NLP/gamma Tubulin 0.009 0.016 -9999 0 -9999 0 0
microtubule cytoskeleton organization 0.006 0.038 -9999 0 -0.248 1 1
G2/M transition DNA damage checkpoint 0 0.001 -9999 0 -9999 0 0
PPP1R12A 0.009 0.058 -9999 0 -0.414 1 1
interphase 0 0.001 -9999 0 -9999 0 0
PLK1/PRC1-2 0.005 0.102 -9999 0 -0.393 3 3
GRASP65/GM130/RAB1/GTP/PLK1 0.025 0.048 -9999 0 -0.174 2 2
RAB1A 0.01 0.058 -9999 0 -0.411 1 1
prophase 0 0 -9999 0 -9999 0 0
Aurora A/BORA 0.003 0.05 -9999 0 -0.163 4 4
mitotic prometaphase 0 0.001 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.043 -9999 0 -9999 0 0
microtubule-based process 0.004 0.073 -9999 0 -0.281 3 3
Golgi organization 0.007 0.032 -9999 0 -0.108 3 3
Cohesin/SA2 0.014 0.028 -9999 0 -0.108 1 1
PPP1CB/MYPT1 0.013 0.058 -9999 0 -0.284 2 2
KIF20A -0.006 0.098 -9999 0 -0.411 3 3
APC/C/CDC20 0 0.078 -9999 0 -0.26 4 4
PPP2R1A 0.017 0 -9999 0 -9999 0 0
chromosome segregation 0.001 0.067 -9999 0 -0.27 3 3
PRC1 -0.004 0.09 -9999 0 -0.374 3 3
ECT2 0.006 0.045 -9999 0 -0.146 3 3
C13orf34 0.004 0.049 -9999 0 -0.156 4 4
NUDC 0.011 0.019 -9999 0 -9999 0 0
regulation of attachment of spindle microtubules to kinetochore -0.018 0.113 -9999 0 -0.321 6 6
spindle assembly 0.009 0.023 -9999 0 -0.074 3 3
spindle stabilization 0.005 0.015 -9999 0 -0.047 3 3
APC/C/HCDH1 0.021 0.001 -9999 0 -9999 0 0
MKLP2/PLK1 0.004 0.073 -9999 0 -0.283 3 3
CCNB1 -0.006 0.101 -9999 0 -0.423 3 3
PPP1CB 0.009 0.058 -9999 0 -0.413 1 1
BTRC 0.017 0 -9999 0 -9999 0 0
ROCK2 0.008 0.063 -9999 0 -0.275 2 2
TUBG1 0.011 0.015 -9999 0 -9999 0 0
G2/M transition of mitotic cell cycle -0.029 0.095 -9999 0 -0.331 4 4
MLF1IP -0.005 0.07 -9999 0 -0.294 3 3
INCENP 0.009 0.059 -9999 0 -0.421 1 1
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0.017 0 -9999 0 -9999 0 0
MKNK1 0.017 0 -9999 0 -9999 0 0
mol:PIP3 -0.026 0.098 0.235 3 -0.211 7 10
FRAP1 0.016 0.037 -9999 0 -9999 0 0
AKT1 -0.002 0.09 0.211 3 -0.194 4 7
INSR 0.017 0 -9999 0 -9999 0 0
Insulin Receptor/Insulin 0.024 0 -9999 0 -9999 0 0
mol:GTP 0.003 0.066 -9999 0 -9999 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.01 0.032 -9999 0 -0.219 1 1
TSC2 0.017 0 -9999 0 -9999 0 0
RHEB/GDP -0.026 0.055 -9999 0 -0.293 1 1
TSC1 0.018 0 -9999 0 -9999 0 0
Insulin Receptor/IRS1 -0.005 0.083 -9999 0 -0.294 4 4
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.012 0.038 -9999 0 -0.254 1 1
mol:GDP 0 0 -9999 0 -9999 0 0
EIF3A 0.017 0 -9999 0 -9999 0 0
RPS6KB1 0.01 0.087 0.175 3 -0.441 1 4
MAP3K5 -0.011 0.08 -9999 0 -0.284 4 4
PIK3R1 -0.038 0.134 -9999 0 -0.355 8 8
apoptosis -0.011 0.08 -9999 0 -0.283 4 4
mol:LY294002 0 0 -9999 0 -0.001 5 5
EIF4B 0.016 0.078 0.172 3 -0.378 1 4
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.014 0.066 -9999 0 -0.351 1 1
eIF4E/eIF4G1/eIF4A1 -0.001 0.008 -9999 0 -9999 0 0
KIAA1303 0.017 0 -9999 0 -9999 0 0
PI3K -0.021 0.104 -9999 0 -0.242 8 8
mTOR/RHEB/GTP/Raptor/GBL 0.03 0.065 0.172 3 -0.269 1 4
FKBP1A 0.018 0.001 -9999 0 -9999 0 0
RHEB/GTP 0.003 0.071 -9999 0 -0.302 1 1
mol:Amino Acids 0 0 -9999 0 -0.001 5 5
FKBP12/Rapamycin 0.013 0.003 -9999 0 -9999 0 0
PDPK1 -0.008 0.093 0.213 3 -0.213 4 7
EIF4E 0.017 0 -9999 0 -9999 0 0
ASK1/PP5C -0.006 0.142 -9999 0 -0.577 3 3
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.026 0.061 -9999 0 -0.395 1 1
TSC1/TSC2 0.016 0.085 0.206 3 -9999 0 3
tumor necrosis factor receptor activity 0 0 0.001 5 -9999 0 5
RPS6 0.017 0 -9999 0 -9999 0 0
PPP5C 0.017 0 -9999 0 -9999 0 0
EIF4G1 0.017 0 -9999 0 -9999 0 0
IRS1 -0.017 0.087 -9999 0 -0.321 4 4
INS 0.017 0 -9999 0 -9999 0 0
PTEN -0.022 0.124 -9999 0 -0.409 5 5
PDK2 -0.008 0.093 0.213 3 -0.213 4 7
EIF4EBP1 0.011 0.033 -9999 0 -9999 0 0
PIK3CA 0.01 0.058 -9999 0 -0.412 1 1
PPP2R5D 0.021 0.036 -9999 0 -9999 0 0
peptide biosynthetic process 0.026 0 -9999 0 -9999 0 0
RHEB 0.004 0.071 -9999 0 -0.355 2 2
EIF4A1 0.017 0 -9999 0 -9999 0 0
mol:Rapamycin 0 0.001 0.003 4 -0.002 1 5
EEF2 0.026 0 -9999 0 -9999 0 0
eIF4E/4E-BP1 0.02 0.029 -9999 0 -9999 0 0
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.018 0.102 -9999 0 -0.328 2 2
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 -0.014 0.118 -9999 0 -0.335 4 4
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.014 0.102 -9999 0 -0.246 8 8
antigen processing and presentation of peptide antigen via MHC class I -0.041 0.083 -9999 0 -0.258 5 5
CaM/Ca2+ -0.013 0.094 -9999 0 -0.303 2 2
RAP1A -0.006 0.098 -9999 0 -0.411 3 3
STAT1 (dimer)/SHP2 -0.037 0.111 -9999 0 -0.349 3 3
AKT1 -0.032 0.112 -9999 0 -0.331 4 4
MAP2K1 -0.025 0.106 -9999 0 -0.301 4 4
MAP3K11 -0.018 0.093 -9999 0 -0.307 2 2
IFNGR1 0 0.073 -9999 0 -0.37 2 2
mol:GTP 0 0 -9999 0 -9999 0 0
CaM/Ca2+/CAMKII 0.014 0.053 -9999 0 -9999 0 0
Rap1/GTP -0.038 0.063 -9999 0 -0.242 3 3
CRKL/C3G 0.026 0 -9999 0 -9999 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.016 0.107 -9999 0 -0.344 2 2
CEBPB -0.022 0.148 -9999 0 -0.365 5 5
STAT3 0.01 0.058 -9999 0 -0.411 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.002 0.098 -9999 0 -9999 0 0
STAT1 -0.04 0.109 -9999 0 -0.349 3 3
CALM1 0.017 0 -9999 0 -9999 0 0
IFN-gamma (dimer) -0.049 0.128 -9999 0 -0.301 11 11
PIK3CA 0.01 0.058 -9999 0 -0.411 1 1
STAT1 (dimer)/PIAS1 -0.029 0.106 -9999 0 -0.327 3 3
CEBPB/PTGES2/Cbp/p300 -0.063 0.13 -9999 0 -0.383 5 5
mol:Ca2+ -0.019 0.1 -9999 0 -0.324 2 2
MAPK3 -0.02 0.117 -9999 0 -0.392 1 1
STAT1 (dimer) -0.053 0.114 -9999 0 -0.353 5 5
MAPK1 -0.034 0.165 -9999 0 -0.543 3 3
JAK2 0.001 0.063 -9999 0 -0.313 2 2
PIK3R1 -0.038 0.134 -9999 0 -0.355 8 8
JAK1 -0.032 0.135 -9999 0 -0.412 6 6
CAMK2D 0.017 0 -9999 0 -9999 0 0
DAPK1 -0.014 0.146 -9999 0 -0.576 2 2
SMAD7 -0.002 0.065 -9999 0 -0.172 3 3
CBL/CRKL/C3G 0 0.089 -9999 0 -0.274 2 2
PI3K -0.04 0.118 -9999 0 -0.357 4 4
IFNG -0.049 0.128 -9999 0 -0.302 11 11
apoptosis -0.015 0.118 -9999 0 -0.445 2 2
CAMK2G 0.017 0 -9999 0 -9999 0 0
STAT3 (dimer) 0.01 0.058 -9999 0 -0.41 1 1
CAMK2A 0.017 0 -9999 0 -9999 0 0
CAMK2B -0.012 0.092 -9999 0 -0.3 5 5
FRAP1 -0.024 0.105 -9999 0 -0.304 4 4
PRKCD -0.034 0.113 -9999 0 -0.333 4 4
RAP1B 0.017 0 -9999 0 -9999 0 0
negative regulation of cell growth -0.041 0.083 -9999 0 -0.258 5 5
PTPN2 0.017 0 -9999 0 -9999 0 0
EP300 0.01 0.058 -9999 0 -0.41 1 1
IRF1 -0.004 0.102 -9999 0 -0.359 2 2
STAT1 (dimer)/PIASy -0.036 0.11 -9999 0 -0.319 4 4
SOCS1 0.025 0.004 -9999 0 -9999 0 0
mol:GDP -0.002 0.085 -9999 0 -0.264 2 2
CASP1 -0.016 0.089 -9999 0 -0.2 8 8
PTGES2 0.017 0 -9999 0 -9999 0 0
IRF9 -0.006 0.107 -9999 0 -0.276 6 6
mol:PI-3-4-5-P3 -0.063 0.098 -9999 0 -0.347 4 4
RAP1/GDP -0.037 0.065 -9999 0 -0.247 3 3
CBL -0.018 0.092 -9999 0 -0.306 2 2
MAP3K1 -0.032 0.11 -9999 0 -0.321 4 4
PIAS1 0.017 0 -9999 0 -9999 0 0
PIAS4 0.009 0.058 -9999 0 -0.411 1 1
antigen processing and presentation of peptide antigen via MHC class II -0.041 0.083 -9999 0 -0.258 5 5
PTPN11 -0.026 0.096 -9999 0 -0.325 2 2
CREBBP 0.018 0 -9999 0 -9999 0 0
RAPGEF1 0.017 0 -9999 0 -9999 0 0
Glucocorticoid receptor regulatory network

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
PCK2 -0.009 0.119 -9999 0 -0.842 1 1
SMARCC2 0.017 0 -9999 0 -9999 0 0
SMARCC1 0.017 0 -9999 0 -9999 0 0
TBX21 -0.098 0.219 -9999 0 -0.522 9 9
SUMO2 0.014 0.044 -9999 0 -0.299 1 1
STAT1 (dimer) -0.024 0.123 -9999 0 -0.317 8 8
FKBP4 0.017 0 -9999 0 -9999 0 0
FKBP5 -0.018 0.112 -9999 0 -0.366 5 5
GR alpha/HSP90/FKBP51/HSP90 0.039 0.105 0.227 2 -0.246 2 4
PRL -0.015 0.089 -9999 0 -9999 0 0
cortisol/GR alpha (dimer)/TIF2 0.134 0.165 0.433 8 -9999 0 8
RELA -0.038 0.081 -9999 0 -0.246 1 1
FGG 0.11 0.136 0.381 5 -9999 0 5
GR beta/TIF2 0.066 0.079 0.24 2 -9999 0 2
IFNG -0.191 0.176 -9999 0 -0.53 6 6
apoptosis 0.061 0.21 0.504 4 -0.528 1 5
CREB1 0.025 0.021 -9999 0 -9999 0 0
histone acetylation -0.034 0.088 -9999 0 -0.295 2 2
BGLAP -0.018 0.077 -9999 0 -9999 0 0
GR/PKAc 0.081 0.065 0.233 1 -9999 0 1
NF kappa B1 p50/RelA -0.062 0.146 -9999 0 -0.391 4 4
SMARCD1 0.017 0 -9999 0 -9999 0 0
MDM2 0.048 0.065 0.177 5 -9999 0 5
GATA3 0.01 0.084 -9999 0 -0.288 4 4
AKT1 0.013 0.019 -9999 0 -9999 0 0
CSF2 -0.04 0.086 -9999 0 -9999 0 0
GSK3B 0.02 0.01 -9999 0 -9999 0 0
NR1I3 0.068 0.192 0.483 4 -9999 0 4
CSN2 0.087 0.132 0.342 2 -0.43 1 3
BRG1/BAF155/BAF170/BAF60A 0.045 0 -9999 0 -9999 0 0
NFATC1 0.012 0.081 -9999 0 -0.402 2 2
POU2F1 0.018 0.044 -9999 0 -0.291 1 1
CDKN1A -0.1 0.388 -9999 0 -1.298 5 5
response to stress 0 0 -9999 0 -9999 0 0
response to UV 0.003 0.011 -9999 0 -9999 0 0
SFN -0.057 0.15 -9999 0 -0.35 11 11
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.012 0.131 0.233 1 -0.272 5 6
prolactin receptor activity 0 0 -9999 0 -9999 0 0
EGR1 0.013 0.281 0.465 4 -0.792 4 8
JUN -0.117 0.159 -9999 0 -0.414 7 7
IL4 -0.028 0.093 -9999 0 -9999 0 0
CDK5R1 0.019 0.005 -9999 0 -9999 0 0
PRKACA 0.017 0 -9999 0 -9999 0 0
cortisol/GR alpha (monomer)/AP-1 -0.101 0.16 0.204 4 -0.342 10 14
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.051 0.098 0.233 1 -0.247 1 2
cortisol/GR alpha (monomer) 0.139 0.191 0.49 8 -9999 0 8
NCOA2 0.017 0 -9999 0 -9999 0 0
response to hypoxia 0 0 -9999 0 -9999 0 0
FOS -0.124 0.162 -9999 0 -0.38 14 14
AP-1/NFAT1-c-4 -0.224 0.216 -9999 0 -0.632 7 7
AFP -0.063 0.129 -9999 0 -0.523 1 1
SUV420H1 0.017 0 -9999 0 -9999 0 0
IRF1 0.062 0.134 -9999 0 -0.377 2 2
TP53 -0.016 0.152 -9999 0 -0.442 6 6
PPP5C 0.017 0 -9999 0 -9999 0 0
KRT17 -0.251 0.333 -9999 0 -0.891 9 9
KRT14 -0.025 0.079 -9999 0 -9999 0 0
TBP 0.028 0 -9999 0 -9999 0 0
CREBBP 0.007 0.006 -9999 0 -9999 0 0
HDAC1 0.011 0.001 -9999 0 -9999 0 0
HDAC2 0.016 0.005 -9999 0 -9999 0 0
AP-1 -0.226 0.217 -9999 0 -0.636 7 7
MAPK14 0.02 0.01 -9999 0 -9999 0 0
MAPK10 -0.005 0.093 -9999 0 -0.328 4 4
MAPK11 0.02 0.01 -9999 0 -9999 0 0
KRT5 -0.239 0.227 -9999 0 -0.722 5 5
interleukin-1 receptor activity -0.001 0.005 -9999 0 -9999 0 0
NCOA1 0.019 0.009 -9999 0 -9999 0 0
STAT1 -0.024 0.124 -9999 0 -0.318 8 8
CGA -0.023 0.079 -9999 0 -9999 0 0
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.036 0.087 -9999 0 -9999 0 0
MAPK3 0.02 0.011 -9999 0 -9999 0 0
MAPK1 0.012 0.058 -9999 0 -0.408 1 1
ICAM1 -0.116 0.235 -9999 0 -0.89 3 3
NFKB1 -0.038 0.081 -9999 0 -0.232 2 2
MAPK8 -0.071 0.115 -9999 0 -0.317 6 6
MAPK9 0.004 0.082 -9999 0 -0.414 2 2
cortisol/GR alpha (dimer) 0.059 0.215 0.508 4 -0.552 1 5
BAX -0.008 0.118 -9999 0 -9999 0 0
POMC -0.097 0.205 -9999 0 -1.32 1 1
EP300 -0.001 0.058 -9999 0 -0.418 1 1
cortisol/GR alpha (dimer)/p53 0.111 0.189 0.451 7 -0.392 1 8
proteasomal ubiquitin-dependent protein catabolic process 0.029 0.051 -9999 0 -9999 0 0
SGK1 0.022 0.047 -9999 0 -0.236 1 1
IL13 -0.108 0.137 -9999 0 -0.543 1 1
IL6 -0.116 0.188 -9999 0 -0.503 4 4
PRKACG 0.017 0 -9999 0 -9999 0 0
IL5 -0.097 0.119 -9999 0 -9999 0 0
IL2 -0.163 0.207 -9999 0 -0.892 2 2
CDK5 0.019 0.005 -9999 0 -9999 0 0
PRKACB 0.017 0 -9999 0 -9999 0 0
HSP90AA1 0.002 0.081 -9999 0 -0.411 2 2
IL8 -0.206 0.345 -9999 0 -0.847 10 10
CDK5R1/CDK5 0.029 0.012 -9999 0 -9999 0 0
NF kappa B1 p50/RelA/PKAc -0.014 0.112 -9999 0 -0.298 2 2
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.126 0.165 0.42 8 -0.338 1 9
SMARCA4 0.017 0 -9999 0 -9999 0 0
chromatin remodeling 0.095 0.096 0.295 4 -9999 0 4
NF kappa B1 p50/RelA/Cbp -0.039 0.122 -9999 0 -0.351 3 3
JUN (dimer) -0.116 0.159 -9999 0 -0.413 7 7
YWHAH 0.017 0 -9999 0 -9999 0 0
VIPR1 -0.021 0.076 -9999 0 -9999 0 0
NR3C1 0.075 0.115 0.304 5 -0.289 1 6
NR4A1 -0.001 0.079 -9999 0 -0.477 1 1
TIF2/SUV420H1 0.026 0 -9999 0 -9999 0 0
MAPKKK cascade 0.061 0.21 0.504 4 -0.528 1 5
cortisol/GR alpha (dimer)/Src-1 0.137 0.169 0.441 8 -9999 0 8
PBX1 0.01 0.072 -9999 0 -0.348 2 2
POU1F1 0.024 0.013 -9999 0 -9999 0 0
SELE -0.161 0.27 -9999 0 -0.703 7 7
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.095 0.096 0.296 4 -9999 0 4
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.126 0.165 0.42 8 -0.338 1 9
mol:cortisol 0.067 0.105 0.285 6 -9999 0 6
MMP1 -0.197 0.325 -9999 0 -0.696 12 12
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.011 0.072 -9999 0 -0.256 3 3
CRKL 0.017 0 -9999 0 -9999 0 0
Rac1/GDP 0.013 0 -9999 0 -9999 0 0
DOCK1 0.012 0.043 -9999 0 -0.3 1 1
ITGA4 -0.01 0.099 -9999 0 -0.355 4 4
alpha4/beta7 Integrin/MAdCAM1 0.018 0.073 -9999 0 -0.197 4 4
EPO 0.012 0.043 -9999 0 -0.3 1 1
alpha4/beta7 Integrin 0.001 0.08 -9999 0 -0.246 5 5
mol:GTP 0 0 -9999 0 -9999 0 0
CRK -0.014 0.112 -9999 0 -0.411 4 4
alpha4/beta1 Integrin 0.007 0.07 -9999 0 -0.237 4 4
EPO/EPOR (dimer) 0.014 0.05 -9999 0 -0.194 3 3
lamellipodium assembly 0.005 0.087 -9999 0 -0.331 2 2
PIK3CA 0.01 0.058 -9999 0 -0.411 1 1
PI3K -0.018 0.112 -9999 0 -0.268 8 8
ARF6 0.017 0 -9999 0 -9999 0 0
JAK2 0.012 0.058 -9999 0 -9999 0 0
PXN 0.017 0 -9999 0 -9999 0 0
PIK3R1 -0.038 0.134 -9999 0 -0.355 8 8
MADCAM1 0.012 0.043 -9999 0 -0.3 1 1
cell adhesion 0.016 0.072 -9999 0 -0.196 4 4
CRKL/CBL 0.026 0 -9999 0 -9999 0 0
ITGB1 0.017 0 -9999 0 -9999 0 0
SRC -0.008 0.093 -9999 0 -0.232 6 6
ITGB7 0.01 0.058 -9999 0 -0.411 1 1
RAC1 0.017 0 -9999 0 -9999 0 0
alpha4/beta1 Integrin/VCAM1 -0.012 0.106 -9999 0 -0.264 6 6
p130Cas/Crk/Dock1 0 0.101 -9999 0 -0.338 2 2
VCAM1 -0.034 0.134 -9999 0 -0.379 7 7
RHOA 0.01 0.058 -9999 0 -0.411 1 1
alpha4/beta1 Integrin/Paxillin/GIT1 0.025 0.063 -9999 0 -0.197 3 3
BCAR1 -0.002 0.087 -9999 0 -0.375 1 1
EPOR 0.006 0.06 -9999 0 -0.3 2 2
mol:GDP 0 0 -9999 0 -9999 0 0
CBL 0.017 0 -9999 0 -9999 0 0
GIT1 0.01 0.058 -9999 0 -0.411 1 1
Rac1/GTP 0.005 0.089 -9999 0 -0.34 2 2
Signaling events mediated by HDAC Class III

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
EP300 0.01 0.058 -9999 0 -0.411 1 1
HDAC4 0.012 0.043 -9999 0 -0.3 1 1
induction of apoptosis 0 0 -9999 0 -9999 0 0
regulation of S phase of mitotic cell cycle -0.02 0.035 -9999 0 -0.129 5 5
CDKN1A -0.052 0.184 -9999 0 -0.551 6 6
KAT2B 0 0 -9999 0 -9999 0 0
BAX 0.017 0 -9999 0 -9999 0 0
FOXO3 0.001 0.049 0.357 1 -9999 0 1
FOXO1 0.017 0 -9999 0 -9999 0 0
FOXO4 0.019 0.035 -9999 0 -0.235 1 1
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 -0.019 0.086 -9999 0 -0.26 6 6
PPARGC1A -0.018 0.1 -9999 0 -0.3 6 6
FHL2 -0.059 0.154 -9999 0 -0.36 11 11
response to nutrient levels 0 0 -9999 0 -9999 0 0
KU70/SIRT1 0.035 0.036 -9999 0 -9999 0 0
HIST2H4A 0.02 0.035 0.129 5 -9999 0 5
SIRT1/FOXO3a 0.021 0.049 0.247 1 -9999 0 1
SIRT1 0.03 0.052 0.189 5 -9999 0 5
response to hypoxia 0 0 -9999 0 -9999 0 0
SIRT1/MEF2D/HDAC4 0.04 0.042 -9999 0 -9999 0 0
SIRT1/Histone H1b 0.025 0.067 -9999 0 -0.195 3 3
apoptosis -0.043 0.033 -9999 0 -9999 0 0
SIRT1/PGC1A 0.009 0.053 -9999 0 -0.161 3 3
p53/SIRT1 0.043 0.115 0.342 6 -0.284 1 7
SIRT1/FOXO4 0.035 0.049 -9999 0 -0.195 1 1
FOXO1/FHL2/SIRT1 -0.002 0.086 -9999 0 -0.206 4 4
HIST1H1E 0.007 0.061 -9999 0 -0.235 3 3
SIRT1/p300 0.029 0.056 -9999 0 -0.282 1 1
muscle cell differentiation 0 0.073 0.206 5 -0.132 3 8
TP53 0.022 0.079 0.189 5 -0.414 1 6
KU70/SIRT1/BAX 0.043 0.033 -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 0.035 0.036 -9999 0 -9999 0 0
ACSS2 0.032 0.035 -9999 0 -9999 0 0
SIRT1/PCAF/MYOD 0 0.074 0.133 3 -0.206 5 8
Reelin signaling pathway

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
CDK5R1/CDK5 0.026 0 -9999 0 -9999 0 0
VLDLR -0.038 0.144 -9999 0 -0.411 7 7
CRKL 0.017 0 -9999 0 -9999 0 0
LRPAP1 0.017 0 -9999 0 -9999 0 0
FYN -0.006 0.098 -9999 0 -0.411 3 3
ITGA3 -0.012 0.106 -9999 0 -0.383 4 4
RELN/VLDLR/Fyn -0.024 0.117 -9999 0 -0.249 10 10
MAPK8IP1/MKK7/MAP3K11/JNK1 0.041 0.048 -9999 0 -0.178 2 2
AKT1 -0.025 0.123 -9999 0 -0.463 2 2
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 0.012 0.082 -9999 0 -0.301 3 3
LRPAP1/LRP8 0.011 0.064 -9999 0 -0.251 3 3
RELN/LRP8/DAB1/Fyn 0.009 0.105 -9999 0 -0.279 5 5
DAB1/alpha3/beta1 Integrin -0.046 0.086 -9999 0 -0.304 3 3
long-term memory -0.005 0.115 -9999 0 -0.394 2 2
DAB1/LIS1 0.004 0.098 -9999 0 -0.296 2 2
DAB1/CRLK/C3G -0.035 0.074 -9999 0 -0.284 2 2
PIK3CA 0.01 0.058 -9999 0 -0.411 1 1
DAB1/NCK2 0.004 0.099 -9999 0 -0.299 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 0.017 0 -9999 0 -9999 0 0
CDK5R1 0.017 0 -9999 0 -9999 0 0
RELN -0.002 0.082 -9999 0 -0.337 3 3
PIK3R1 -0.038 0.134 -9999 0 -0.355 8 8
RELN/LRP8/Fyn -0.002 0.12 -9999 0 -0.331 5 5
GRIN2A/RELN/LRP8/DAB1/Fyn 0.019 0.107 -9999 0 -0.273 5 5
MAPK8 0.002 0.081 -9999 0 -0.411 2 2
RELN/VLDLR/DAB1 -0.008 0.088 -9999 0 -0.204 8 8
ITGB1 0.017 0 -9999 0 -9999 0 0
MAP1B -0.047 0.105 -9999 0 -0.309 2 2
RELN/LRP8 0.012 0.089 -9999 0 -0.33 3 3
GRIN2B/RELN/LRP8/DAB1/Fyn -0.01 0.121 -9999 0 -0.231 9 9
PI3K -0.018 0.112 -9999 0 -0.268 8 8
mol:PP2 0 0 -9999 0 -9999 0 0
alpha3/beta1 Integrin 0.005 0.075 -9999 0 -0.259 4 4
RAP1A -0.002 0.101 -9999 0 -0.285 3 3
PAFAH1B1 0.017 0 -9999 0 -9999 0 0
MAPK8IP1 0.012 0.043 -9999 0 -0.3 1 1
CRLK/C3G 0.026 0 -9999 0 -9999 0 0
GRIN2B -0.038 0.134 -9999 0 -0.355 8 8
NCK2 0.017 0 -9999 0 -9999 0 0
neuron differentiation 0.015 0.094 -9999 0 -0.528 1 1
neuron adhesion 0.002 0.104 -9999 0 -0.299 3 3
LRP8 -0.004 0.09 -9999 0 -0.374 3 3
GSK3B -0.018 0.117 -9999 0 -0.435 2 2
RELN/VLDLR/DAB1/Fyn -0.01 0.101 -9999 0 -0.205 10 10
MAP3K11 0.017 0 -9999 0 -9999 0 0
RELN/VLDLR/DAB1/P13K -0.033 0.13 -9999 0 -0.246 11 11
CDK5 0.017 0 -9999 0 -9999 0 0
MAPT 0 0.067 -9999 0 -0.324 2 2
neuron migration -0.007 0.124 -9999 0 -0.463 2 2
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.015 0.095 -9999 0 -0.533 1 1
RELN/VLDLR -0.008 0.11 -9999 0 -0.226 10 10
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.009 0.068 -9999 0 -0.448 1 1
Crk/p130 Cas/Paxillin -0.051 0.084 -9999 0 -0.3 3 3
JUN -0.008 0.091 -9999 0 -0.345 2 2
HRAS 0.017 0 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.019 0.112 -9999 0 -0.273 6 6
RAP1A -0.006 0.098 -9999 0 -0.411 3 3
FRS2 0.017 0 -9999 0 -9999 0 0
RAP1A/GDP -0.004 0.069 -9999 0 -0.288 3 3
RET51/GFRalpha1/GDNF/DOK1 0.001 0.082 -9999 0 -0.278 1 1
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 -0.014 0.112 -9999 0 -0.411 4 4
RET9/GFRalpha1/GDNF/Enigma 0.015 0.053 -9999 0 -9999 0 0
RHOA 0.01 0.058 -9999 0 -0.411 1 1
RAP1A/GTP -0.015 0.096 -9999 0 -0.227 6 6
GRB7 0 0.073 -9999 0 -0.3 3 3
RET51/GFRalpha1/GDNF 0.001 0.082 -9999 0 -0.278 1 1
MAPKKK cascade -0.021 0.039 -9999 0 -9999 0 0
BCAR1 0.017 0 -9999 0 -9999 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.006 0.08 -9999 0 -0.204 4 4
lamellipodium assembly -0.044 0.069 -9999 0 -0.21 6 6
RET51/GFRalpha1/GDNF/SHC 0.001 0.082 -9999 0 -0.278 1 1
PIK3CA 0.01 0.058 -9999 0 -0.411 1 1
RET9/GFRalpha1/GDNF/SHC 0.015 0.053 -9999 0 -9999 0 0
RET9/GFRalpha1/GDNF/Shank3 0.015 0.053 -9999 0 -9999 0 0
MAPK3 -0.012 0.09 -9999 0 -0.265 3 3
DOK1 0.017 0 -9999 0 -9999 0 0
DOK6 -0.047 0.138 -9999 0 -0.333 10 10
PXN 0.017 0 -9999 0 -9999 0 0
neurite development -0.017 0.106 -9999 0 -0.295 4 4
DOK5 -0.006 0.083 -9999 0 -0.3 4 4
GFRA1 -0.018 0.1 -9999 0 -0.3 6 6
MAPK8 0.006 0.074 -9999 0 -0.366 1 1
HRAS/GTP 0.006 0.065 -9999 0 -0.223 1 1
tube development 0.021 0.05 -9999 0 -9999 0 0
MAPK1 -0.016 0.099 -9999 0 -0.286 4 4
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.022 0.034 -9999 0 -9999 0 0
Rac1/GDP 0.013 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 -0.022 0.117 -9999 0 -0.286 6 6
SHC1 0.017 0 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.008 0.096 -9999 0 -0.273 3 3
RET51/GFRalpha1/GDNF/Dok5 -0.011 0.1 -9999 0 -0.349 2 2
PRKCA 0.002 0.081 -9999 0 -0.411 2 2
HRAS/GDP 0.013 0 -9999 0 -9999 0 0
CREB1 0.022 0.039 -9999 0 -9999 0 0
PIK3R1 -0.038 0.134 -9999 0 -0.355 8 8
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.014 0.051 -9999 0 -0.184 2 2
RET51/GFRalpha1/GDNF/Grb7 -0.008 0.1 -9999 0 -0.278 4 4
mol:GDP 0 0 -9999 0 -9999 0 0
RET -0.03 0.113 -9999 0 -0.3 8 8
DOK4 0.002 0.081 -9999 0 -0.411 2 2
JNK cascade -0.008 0.089 -9999 0 -0.339 2 2
RET9/GFRalpha1/GDNF/FRS2 0.015 0.053 -9999 0 -9999 0 0
SHANK3 0.017 0 -9999 0 -9999 0 0
RASA1 0.017 0 -9999 0 -9999 0 0
NCK1 0.01 0.058 -9999 0 -0.411 1 1
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.022 0.034 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.012 0.051 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.008 0.057 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.012 0.051 -9999 0 -9999 0 0
PI3K -0.028 0.124 -9999 0 -0.301 6 6
SOS1 0.017 0 -9999 0 -9999 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.024 0.051 -9999 0 -9999 0 0
GRB10 -0.02 0.118 -9999 0 -0.389 5 5
activation of MAPKK activity 0.016 0.044 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF/FRS2 0.001 0.082 -9999 0 -0.278 1 1
GAB1 -0.002 0.082 -9999 0 -0.337 3 3
IRS1 -0.02 0.118 -9999 0 -0.389 5 5
IRS2 -0.016 0.106 -9999 0 -0.344 5 5
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.004 0.062 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF/PKC alpha -0.008 0.089 -9999 0 -0.224 3 3
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 -0.02 0.108 -9999 0 -0.272 5 5
Rac1/GTP -0.051 0.08 -9999 0 -0.251 5 5
RET9/GFRalpha1/GDNF 0.003 0.058 -9999 0 -0.159 6 6
GFRalpha1/GDNF 0.002 0.069 -9999 0 -0.194 6 6
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -9999 0 0
telencephalon oligodendrocyte cell migration 0.009 0.111 0.478 2 -9999 0 2
GNAI2 0.017 0 -9999 0 -9999 0 0
S1P/S1P5/G12 0.012 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 -0.009 0.114 -9999 0 -0.49 2 2
negative regulation of cAMP metabolic process -0.015 0.106 -9999 0 -0.234 8 8
GNAZ -0.01 0.099 -9999 0 -0.355 4 4
GNAI3 0.01 0.058 -9999 0 -0.411 1 1
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 -0.016 0.106 -9999 0 -0.236 8 8
RhoA/GDP 0.007 0.041 -9999 0 -0.288 1 1
RHOA 0.01 0.058 -9999 0 -0.411 1 1
GNAI1 -0.05 0.152 -9999 0 -0.386 9 9
ceramide signaling pathway

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
MAP4K4 -0.022 0.141 -9999 0 -0.394 5 5
BAG4 0.012 0.043 -9999 0 -0.3 1 1
BAD -0.001 0.065 -9999 0 -0.217 3 3
NFKBIA 0.01 0.058 -9999 0 -0.411 1 1
BIRC3 -0.06 0.154 -9999 0 -0.36 11 11
BAX 0.001 0.059 -9999 0 -0.221 2 2
EnzymeConsortium:3.1.4.12 -0.003 0.034 -9999 0 -0.095 4 4
IKBKB -0.015 0.134 -9999 0 -0.367 5 5
MAP2K2 0.009 0.061 -9999 0 -0.289 1 1
MAP2K1 0.009 0.061 -9999 0 -0.289 1 1
SMPD1 -0.005 0.062 -9999 0 -0.28 2 2
GO:0005551 0 0 -9999 0 -9999 0 0
FADD/Caspase 8 -0.015 0.137 -9999 0 -0.392 4 4
MAP2K4 -0.006 0.073 -9999 0 -0.179 6 6
protein ubiquitination -0.016 0.137 -9999 0 -0.373 5 5
EnzymeConsortium:2.7.1.37 0.008 0.066 -9999 0 -0.315 1 1
response to UV 0 0.001 -9999 0 -0.003 1 1
RAF1 0.004 0.062 -9999 0 -0.224 2 2
CRADD -0.02 0.119 -9999 0 -0.39 5 5
mol:ceramide -0.005 0.062 -9999 0 -0.181 4 4
I-kappa-B-alpha/RELA/p50/ubiquitin 0.019 0.035 -9999 0 -0.234 1 1
MADD 0.018 0 -9999 0 -9999 0 0
MAP3K1 -0.012 0.076 -9999 0 -0.194 6 6
TRADD 0.002 0.081 -9999 0 -0.412 2 2
RELA/p50 0.017 0 -9999 0 -9999 0 0
MAPK3 0.012 0.06 -9999 0 -0.283 1 1
MAPK1 0.01 0.063 -9999 0 -0.283 1 1
p50/RELA/I-kappa-B-alpha 0.02 0.041 -9999 0 -0.28 1 1
FADD -0.023 0.139 -9999 0 -0.408 4 4
KSR1 0.001 0.061 -9999 0 -0.173 4 4
MAPK8 -0.006 0.077 -9999 0 -0.224 3 3
TRAF2 0.018 0 -9999 0 -9999 0 0
response to radiation 0 0 -9999 0 -0.002 1 1
CHUK -0.018 0.138 -9999 0 -0.356 6 6
TNF R/SODD 0.016 0.05 -9999 0 -0.237 2 2
TNF -0.02 0.106 -9999 0 -0.318 6 6
CYCS 0.017 0.065 0.127 4 -0.194 2 6
IKBKG -0.015 0.134 -9999 0 -0.367 5 5
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.027 0.143 -9999 0 -0.435 4 4
RELA 0.017 0 -9999 0 -9999 0 0
RIPK1 0.018 0 -9999 0 -9999 0 0
AIFM1 0.014 0.068 0.127 4 -0.182 3 7
TNF/TNF R/SODD 0.006 0.086 -9999 0 -0.451 1 1
TNFRSF1A 0.01 0.058 -9999 0 -0.411 1 1
response to heat 0 0 -9999 0 -0.002 1 1
CASP8 0.018 0.034 -9999 0 -9999 0 0
NSMAF -0.019 0.135 -9999 0 -0.403 4 4
response to hydrogen peroxide 0 0.001 -9999 0 -0.003 1 1
BCL2 -0.058 0.159 -9999 0 -0.389 10 10
Retinoic acid receptors-mediated signaling

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
HDAC1 0.017 0 -9999 0 -9999 0 0
HDAC3 0.017 0 -9999 0 -9999 0 0
VDR -0.016 0.106 -9999 0 -0.344 5 5
Cbp/p300/PCAF 0.019 0.035 -9999 0 -0.234 1 1
EP300 0.01 0.058 -9999 0 -0.411 1 1
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.022 0.048 -9999 0 -9999 0 0
KAT2B 0 0 -9999 0 -9999 0 0
MAPK14 0.017 0 -9999 0 -9999 0 0
AKT1 0.045 0.088 0.196 10 -0.192 1 11
RAR alpha/9cRA/Cyclin H 0.01 0.105 -9999 0 -0.329 2 2
mol:9cRA 0 0 -9999 0 -9999 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.017 0.049 -9999 0 -9999 0 0
CDC2 0.009 0.058 -9999 0 -0.41 1 1
response to UV -0.002 0.009 -9999 0 -9999 0 0
RAR alpha/Jnk1 -0.002 0.088 -9999 0 -0.321 3 3
NCOR2 0.017 0 -9999 0 -9999 0 0
VDR/VDR/Vit D3 -0.01 0.074 -9999 0 -0.237 5 5
RXRs/RARs/NRIP1/9cRA -0.023 0.203 -9999 0 -0.504 7 7
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 -0.016 0.106 -9999 0 -0.344 5 5
RARG 0.016 0.006 -9999 0 -9999 0 0
RAR gamma1/9cRA 0.022 0.008 -9999 0 -9999 0 0
MAPK3 0.016 0.006 -9999 0 -9999 0 0
MAPK1 0.01 0.058 -9999 0 -0.411 1 1
MAPK8 0 0.083 -9999 0 -0.42 2 2
mol:Vit D3 0 0 -9999 0 -9999 0 0
RXRs/VDR/DNA/Vit D3 -0.026 0.149 -9999 0 -0.453 3 3
RARA 0.003 0.074 -9999 0 -0.232 4 4
negative regulation of phosphoinositide 3-kinase cascade 0 0 -9999 0 -9999 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.017 0.049 -9999 0 -9999 0 0
PRKCA -0.002 0.084 -9999 0 -0.418 2 2
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.046 0.219 -9999 0 -0.546 8 8
RXRG -0.007 0.089 -9999 0 -0.267 5 5
RXRA -0.003 0.097 -9999 0 -0.283 3 3
RXRB 0.01 0.064 -9999 0 -0.277 2 2
VDR/Vit D3/DNA -0.01 0.074 -9999 0 -0.237 5 5
RBP1 -0.086 0.183 -9999 0 -0.411 13 13
CRBP1/9-cic-RA -0.06 0.129 -9999 0 -0.288 13 13
RARB 0.003 0.071 -9999 0 -0.354 2 2
PRKCG 0.014 0.018 -9999 0 -9999 0 0
MNAT1 0.017 0 -9999 0 -9999 0 0
RAR alpha/RXRs 0.013 0.16 -9999 0 -0.364 6 6
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.012 0.129 -9999 0 -0.367 3 3
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.064 -9999 0 -0.235 1 1
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.046 0.219 -9999 0 -0.546 8 8
positive regulation of DNA binding -0.036 0.079 -9999 0 -0.312 2 2
NRIP1 -0.108 0.38 -9999 0 -1.057 7 7
RXRs/RARs -0.03 0.171 -9999 0 -0.416 8 8
RXRs/RXRs/DNA/9cRA -0.02 0.143 -9999 0 -0.334 8 8
PRKACA 0.017 0 -9999 0 -9999 0 0
CDK7 0.017 0 -9999 0 -9999 0 0
TFIIH 0.036 0 -9999 0 -9999 0 0
RAR alpha/9cRA 0.031 0.052 -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
Syndecan-3-mediated signaling events

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
CTTN 0.017 0 -9999 0 -9999 0 0
Syndecan-3/Src/Cortactin -0.045 0.122 -9999 0 -0.468 2 2
Syndecan-3/Neurocan 0.002 0.105 -9999 0 -0.508 2 2
POMC -0.032 0.118 -9999 0 -0.313 8 8
EGFR -0.01 0.099 -9999 0 -0.355 4 4
Syndecan-3/EGFR -0.011 0.112 -9999 0 -0.508 2 2
AGRP 0.017 0 -9999 0 -9999 0 0
NCSTN 0.017 0 -9999 0 -9999 0 0
PSENEN 0.01 0.058 -9999 0 -0.411 1 1
RP11-540L11.1 0 0 -9999 0 -9999 0 0
APH1B 0.004 0.071 -9999 0 -0.355 2 2
APH1A 0.017 0 -9999 0 -9999 0 0
NCAN 0.017 0 -9999 0 -9999 0 0
long-term memory 0 0.108 -9999 0 -0.476 2 2
Syndecan-3/IL8 -0.052 0.14 -9999 0 -0.505 3 3
PSEN1 0.017 0 -9999 0 -9999 0 0
Src/Cortactin 0.026 0 -9999 0 -9999 0 0
FYN -0.006 0.098 -9999 0 -0.411 3 3
limb bud formation -0.026 0.103 -9999 0 -0.53 2 2
MC4R 0.004 0.071 -9999 0 -0.355 2 2
SRC 0.017 0 -9999 0 -9999 0 0
PTN -0.123 0.186 -9999 0 -0.361 20 20
FGFR/FGF/Syndecan-3 -0.026 0.104 -9999 0 -0.536 2 2
neuron projection morphogenesis -0.041 0.116 -9999 0 -0.45 2 2
Syndecan-3/AgRP 0.002 0.105 -9999 0 -0.508 2 2
Syndecan-3/AgRP/MC4R 0.006 0.122 -9999 0 -0.579 2 2
Fyn/Cortactin 0.009 0.07 -9999 0 -0.28 3 3
SDC3 -0.027 0.105 -9999 0 -0.541 2 2
GO:0007205 0 0 -9999 0 -9999 0 0
positive regulation of leukocyte migration -0.051 0.138 -9999 0 -0.496 3 3
IL8 -0.097 0.171 -9999 0 -0.345 17 17
Syndecan-3/Fyn/Cortactin 0 0.11 -9999 0 -0.487 2 2
Syndecan-3/CASK -0.025 0.099 -9999 0 -0.514 2 2
alpha-MSH/MC4R -0.018 0.093 -9999 0 -0.211 10 10
Gamma Secretase 0.041 0.048 -9999 0 -9999 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.005 0.107 -9999 0 -9999 0 0
UGCG -0.038 0.174 -9999 0 -0.632 4 4
AKT1/mTOR/p70S6K/Hsp90/TERT -0.02 0.168 -9999 0 -0.355 8 8
mol:GTP 0 0 -9999 0 -9999 0 0
mol:glucosylceramide -0.037 0.172 -9999 0 -0.624 4 4
mol:DAG -0.004 0.13 -9999 0 -0.91 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.072 0.16 -9999 0 -0.387 10 10
FRAP1 -0.037 0.213 -9999 0 -0.447 10 10
FOXO3 -0.004 0.145 -9999 0 -0.369 4 4
AKT1 -0.012 0.153 -9999 0 -0.378 5 5
GAB2 0.017 0.003 -9999 0 -9999 0 0
SMPD1 -0.012 0.131 -9999 0 -0.654 2 2
SGMS1 0 0.096 -9999 0 -0.661 1 1
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 -0.017 0.094 -9999 0 -0.224 8 8
CALM1 0.017 0 -9999 0 -9999 0 0
cell proliferation -0.017 0.123 -9999 0 -0.383 3 3
EIF3A 0.017 0 -9999 0 -9999 0 0
PI3K -0.014 0.113 -9999 0 -0.267 8 8
RPS6KB1 -0.022 0.164 -9999 0 -1.101 1 1
mol:sphingomyelin -0.004 0.13 -9999 0 -0.91 1 1
natural killer cell activation -0.001 0.003 -9999 0 -9999 0 0
JAK3 0.019 0.003 -9999 0 -9999 0 0
PIK3R1 -0.036 0.135 -9999 0 -0.354 8 8
JAK1 -0.028 0.135 -9999 0 -0.41 6 6
NFKB1 0.017 0 -9999 0 -9999 0 0
MYC -0.001 0.141 -9999 0 -0.416 2 2
MYB -0.127 0.384 -9999 0 -1.18 6 6
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.003 0.125 -9999 0 -0.352 3 3
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.001 0.151 -9999 0 -0.99 1 1
mol:PI-3-4-5-P3 -0.002 0.123 -9999 0 -0.344 3 3
Rac1/GDP -0.005 0.087 -9999 0 -0.256 4 4
T cell proliferation -0.002 0.116 -9999 0 -0.324 3 3
SHC1 0.017 0.003 -9999 0 -9999 0 0
RAC1 0.017 0 -9999 0 -9999 0 0
positive regulation of cyclin-dependent protein kinase activity -0.003 0.022 -9999 0 -0.054 8 8
PRKCZ -0.003 0.119 -9999 0 -0.335 3 3
NF kappa B1 p50/RelA -0.017 0.19 -9999 0 -0.422 7 7
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.015 0.116 -9999 0 -0.354 3 3
HSP90AA1 0.002 0.081 -9999 0 -0.411 2 2
RELA 0.017 0 -9999 0 -9999 0 0
IL2RA 0.009 0.058 -9999 0 -0.41 1 1
IL2RB 0 0.082 -9999 0 -0.336 3 3
TERT 0.017 0 -9999 0 -9999 0 0
E2F1 -0.051 0.18 -9999 0 -0.467 8 8
SOS1 0.017 0.003 -9999 0 -9999 0 0
RPS6 0.017 0 -9999 0 -9999 0 0
mol:cAMP 0.001 0.01 0.026 7 -9999 0 7
PTPN11 0.017 0.003 -9999 0 -9999 0 0
IL2RG 0.013 0.044 -9999 0 -0.304 1 1
actin cytoskeleton organization -0.002 0.116 -9999 0 -0.324 3 3
GRB2 0.017 0.003 -9999 0 -9999 0 0
IL2 0.011 0.058 -9999 0 -0.409 1 1
PIK3CA 0.011 0.058 -9999 0 -0.409 1 1
Rac1/GTP 0.003 0.086 -9999 0 -0.242 4 4
LCK -0.02 0.113 -9999 0 -0.335 6 6
BCL2 -0.09 0.33 -9999 0 -0.792 9 9
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 0.005 0.057 -9999 0 -0.259 2 2
NFATC2 0.01 0.042 -9999 0 -0.248 1 1
NFATC3 0.015 0.023 -9999 0 -9999 0 0
CD40LG -0.068 0.184 -9999 0 -0.483 5 5
PTGS2 -0.095 0.202 -9999 0 -0.494 6 6
JUNB 0.006 0.06 -9999 0 -0.3 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.01 0.014 -9999 0 -9999 0 0
CaM/Ca2+ 0.01 0.014 -9999 0 -9999 0 0
CALM1 0.016 0.007 -9999 0 -9999 0 0
JUN -0.027 0.123 -9999 0 -0.37 6 6
mol:Ca2+ -0.004 0.009 -9999 0 -9999 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.011 0.005 -9999 0 -9999 0 0
FOSL1 0.012 0.043 -9999 0 -0.3 1 1
CREM 0.017 0.002 -9999 0 -9999 0 0
Jun/NFAT1-c-4/p21SNFT -0.014 0.118 -9999 0 -0.305 3 3
FOS -0.08 0.165 -9999 0 -0.353 14 14
IFNG -0.083 0.194 -9999 0 -0.448 7 7
AP-1/NFAT1-c-4 -0.06 0.199 -9999 0 -0.512 4 4
FASLG -0.069 0.188 -9999 0 -0.466 6 6
NFAT1-c-4/ICER1 0.012 0.079 -9999 0 -0.225 2 2
IL2RA -0.061 0.17 -9999 0 -0.43 5 5
FKBP12/FK506 0.013 0 -9999 0 -9999 0 0
CSF2 -0.062 0.168 -9999 0 -0.417 5 5
JunB/Fra1/NFAT1-c-4 0.018 0.086 -9999 0 -0.244 2 2
IL4 -0.057 0.165 -9999 0 -0.437 4 4
IL2 -0.012 0.16 -9999 0 -1.177 1 1
IL3 0.011 0.02 -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 0.02 0.043 -9999 0 -0.295 1 1
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.019 0.103 -9999 0 -0.243 9 9
AKT1 -0.012 0.171 -9999 0 -0.46 4 4
PTK2B -0.006 0.117 -9999 0 -0.305 3 3
VEGFR2 homodimer/Frs2 0.025 0.057 -9999 0 -0.275 1 1
CAV1 0.017 0 -9999 0 -9999 0 0
CALM1 0.017 0 -9999 0 -9999 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.017 0.096 -9999 0 -0.285 2 2
endothelial cell proliferation 0.007 0.147 -9999 0 -0.389 4 4
mol:Ca2+ 0.005 0.132 -9999 0 -0.375 4 4
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.027 0.092 -9999 0 -0.262 2 2
RP11-342D11.1 -0.001 0.129 -9999 0 -0.381 4 4
CDH5 -0.006 0.098 -9999 0 -0.411 3 3
VEGFA homodimer 0.03 0.058 -9999 0 -0.204 3 3
SHC1 0.017 0 -9999 0 -9999 0 0
SHC2 -0.035 0.118 -9999 0 -0.3 9 9
HRAS/GDP -0.037 0.089 -9999 0 -0.316 4 4
SH2D2A 0 0.073 -9999 0 -0.3 3 3
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.021 0.125 -9999 0 -0.344 3 3
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.007 0.099 -9999 0 -0.285 2 2
VEGFR1 homodimer -0.014 0.112 -9999 0 -0.41 4 4
SHC/GRB2/SOS1 0.024 0.126 -9999 0 -0.346 4 4
GRB10 -0.01 0.184 -9999 0 -0.493 6 6
PTPN11 0.017 0 -9999 0 -9999 0 0
GRB2 0.017 0 -9999 0 -9999 0 0
PAK1 0.017 0 -9999 0 -9999 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.015 0.128 -9999 0 -0.355 4 4
HRAS 0.017 0 -9999 0 -9999 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.006 0.115 -9999 0 -0.363 3 3
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 0.025 0.09 -9999 0 -0.259 2 2
mol:GTP 0 0 -9999 0 -9999 0 0
FLT4 0.017 0 -9999 0 -9999 0 0
Nck/Pak 0.02 0.041 -9999 0 -0.28 1 1
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.004 0.105 -9999 0 -0.285 2 2
mol:GDP -0.04 0.096 -9999 0 -0.338 4 4
mol:NADP 0.02 0.114 -9999 0 -0.311 3 3
eNOS/Hsp90 0.023 0.117 -9999 0 -0.316 3 3
PIK3R1 -0.038 0.134 -9999 0 -0.355 8 8
mol:IP3 0.005 0.133 -9999 0 -0.379 4 4
HIF1A/ARNT 0.026 0 -9999 0 -9999 0 0
SHB 0.017 0 -9999 0 -9999 0 0
VEGFA -0.011 0.103 -9999 0 -0.421 3 3
VEGFC -0.024 0.119 -9999 0 -0.355 6 6
FAK1/Vinculin 0.008 0.124 -9999 0 -0.426 1 1
mol:Ca ++ 0 0 -9999 0 -9999 0 0
RHOA 0.01 0.058 -9999 0 -0.411 1 1
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.005 0.127 -9999 0 -0.327 3 3
PTPN6 0.01 0.058 -9999 0 -0.411 1 1
EPAS1 0.009 0.078 -9999 0 -0.36 2 2
mol:L-citrulline 0.02 0.114 -9999 0 -0.311 3 3
ITGAV -0.004 0.09 -9999 0 -0.374 3 3
PIK3CA 0.01 0.058 -9999 0 -0.411 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.027 0.092 -9999 0 -0.262 2 2
VEGFR2 homodimer/VEGFA homodimer 0.009 0.145 -9999 0 -0.414 4 4
VEGFR2/3 heterodimer 0.025 0.057 -9999 0 -0.275 1 1
VEGFB 0.017 0 -9999 0 -9999 0 0
MAPK11 0.009 0.14 -9999 0 -0.403 4 4
VEGFR2 homodimer 0.018 0.069 -9999 0 -0.335 1 1
FLT1 -0.014 0.112 -9999 0 -0.411 4 4
NEDD4 0.013 0.026 -9999 0 -9999 0 0
MAPK3 0.005 0.121 -9999 0 -0.339 4 4
MAPK1 0.003 0.124 -9999 0 -0.339 4 4
VEGFA145/NRP2 -0.007 0.093 -9999 0 -0.263 6 6
VEGFR1/2 heterodimer 0.006 0.092 -9999 0 -0.306 2 2
KDR 0.018 0.069 -9999 0 -0.336 1 1
VEGFA165/NRP1/VEGFR2 homodimer 0.007 0.145 -9999 0 -0.415 4 4
SRC 0.017 0 -9999 0 -9999 0 0
platelet activating factor biosynthetic process 0.005 0.125 -9999 0 -0.348 4 4
PI3K -0.017 0.178 -9999 0 -0.559 3 3
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.012 0.099 -9999 0 -0.285 2 2
FES -0.008 0.138 -9999 0 -0.383 4 4
GAB1 -0.009 0.163 -9999 0 -0.604 2 2
VEGFR2 homodimer/VEGFA homodimer/Src 0.017 0.096 -9999 0 -0.285 2 2
CTNNB1 0.002 0.081 -9999 0 -0.411 2 2
SOS1 0.017 0 -9999 0 -9999 0 0
ARNT 0.017 0 -9999 0 -9999 0 0
eNOS/Caveolin-1 0.027 0.11 -9999 0 -0.307 2 2
VEGFR2 homodimer/VEGFA homodimer/Yes 0.017 0.096 -9999 0 -0.285 2 2
PI3K/GAB1 -0.018 0.186 -9999 0 -0.483 5 5
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.029 0.092 -9999 0 -9999 0 0
PRKACA 0.017 0 -9999 0 -9999 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.012 0.079 -9999 0 -9999 0 0
HSP90AA1 0.002 0.081 -9999 0 -0.411 2 2
CDC42 0.009 0.133 -9999 0 -0.383 4 4
actin cytoskeleton reorganization 0.007 0.099 -9999 0 -0.283 2 2
PTK2 0 0.129 -9999 0 -0.394 2 2
EDG1 -0.006 0.176 -9999 0 -0.504 5 5
mol:DAG 0.005 0.133 -9999 0 -0.379 4 4
CaM/Ca2+ 0.012 0.124 -9999 0 -0.344 4 4
MAP2K3 0.01 0.14 -9999 0 -0.406 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.001 0.19 -9999 0 -0.5 6 6
PLCG1 0.005 0.135 -9999 0 -0.383 4 4
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.027 0.092 -9999 0 -0.262 2 2
IQGAP1 0.017 0 -9999 0 -9999 0 0
YES1 0.017 0 -9999 0 -9999 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.017 0.096 -9999 0 -0.285 2 2
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.012 0.099 -9999 0 -0.285 2 2
cell migration 0.02 0.134 -9999 0 -0.384 1 1
mol:PI-3-4-5-P3 -0.014 0.167 -9999 0 -0.516 3 3
FYN -0.006 0.098 -9999 0 -0.411 3 3
VEGFB/NRP1 0.009 0.124 -9999 0 -0.356 4 4
mol:NO 0.02 0.114 -9999 0 -0.311 3 3
PXN 0.017 0 -9999 0 -9999 0 0
HRAS/GTP -0.037 0.089 -9999 0 -0.314 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.004 0.189 -9999 0 -0.498 6 6
VHL 0.017 0 -9999 0 -9999 0 0
ITGB3 -0.026 0.113 -9999 0 -0.315 7 7
NOS3 0.018 0.123 -9999 0 -0.363 2 2
VEGFR2 homodimer/VEGFA homodimer/Sck -0.011 0.107 -9999 0 -0.285 2 2
RAC1 0.017 0 -9999 0 -9999 0 0
PRKCA 0.002 0.128 -9999 0 -0.351 4 4
PRKCB 0.002 0.124 -9999 0 -0.357 4 4
VCL 0.01 0.058 -9999 0 -0.411 1 1
VEGFA165/NRP1 0.004 0.132 -9999 0 -0.383 4 4
VEGFR1/2 heterodimer/VEGFA homodimer 0 0.126 -9999 0 -0.398 3 3
VEGFA165/NRP2 -0.007 0.093 -9999 0 -0.263 6 6
MAPKKK cascade 0.02 0.162 -9999 0 -0.435 5 5
NRP2 -0.002 0.082 -9999 0 -0.337 3 3
VEGFC homodimer -0.024 0.118 -9999 0 -0.355 6 6
NCK1 0.01 0.058 -9999 0 -0.411 1 1
ROCK1 0.017 0 -9999 0 -9999 0 0
FAK1/Paxillin 0.009 0.124 -9999 0 -0.368 2 2
MAP3K13 0.009 0.133 -9999 0 -0.383 4 4
PDPK1 -0.008 0.151 -9999 0 -0.456 3 3
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.013 0.065 -9999 0 -0.189 5 5
epithelial cell differentiation 0.025 0.051 -9999 0 -0.183 3 3
CYFIP2 -0.014 0.112 -9999 0 -0.411 4 4
ENAH 0.007 0.093 -9999 0 -0.25 4 4
EGFR -0.01 0.099 -9999 0 -0.355 4 4
EPHA2 -0.028 0.129 -9999 0 -0.392 6 6
MYO6 0.007 0.08 -9999 0 -0.364 1 1
CTNNB1 0.002 0.081 -9999 0 -0.411 2 2
ABI1/Sra1/Nap1 0.011 0.076 -9999 0 -0.227 5 5
AQP5 0.011 0.115 -9999 0 -0.424 3 3
CTNND1 0.017 0 -9999 0 -9999 0 0
mol:PI-4-5-P2 0.025 0.046 -9999 0 -9999 0 0
regulation of calcium-dependent cell-cell adhesion -0.04 0.108 -9999 0 -0.329 2 2
EGF -0.018 0.1 -9999 0 -0.3 6 6
NCKAP1 0.01 0.058 -9999 0 -0.411 1 1
AQP3 -0.019 0.137 -9999 0 -0.411 5 5
cortical microtubule organization 0.025 0.051 -9999 0 -0.183 3 3
GO:0000145 0.021 0.044 -9999 0 -9999 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.029 0.052 -9999 0 -0.185 3 3
MLLT4 0.017 0 -9999 0 -9999 0 0
ARF6/GDP -0.04 0.086 -9999 0 -0.302 4 4
ARF6 0.017 0 -9999 0 -9999 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.01 0.124 -9999 0 -0.268 9 9
mol:Ca2+ 0 0 -9999 0 -9999 0 0
VASP 0.027 0.067 -9999 0 -0.373 1 1
PVRL2 0.01 0.058 -9999 0 -0.411 1 1
ZYX 0.025 0.047 -9999 0 -9999 0 0
ARF6/GTP -0.002 0.116 -9999 0 -0.374 3 3
CDH1 0.01 0.058 -9999 0 -0.411 1 1
EGFR/EGFR/EGF/EGF -0.03 0.071 -9999 0 -0.318 2 2
RhoA/GDP 0.023 0.066 -9999 0 -0.363 1 1
actin cytoskeleton organization 0.009 0.087 -9999 0 -0.339 2 2
IGF-1R heterotetramer -0.042 0.143 -9999 0 -0.382 8 8
GIT1 0.01 0.058 -9999 0 -0.411 1 1
IGF1R -0.042 0.143 -9999 0 -0.383 8 8
IGF1 -0.103 0.18 -9999 0 -0.365 17 17
DIAPH1 -0.049 0.172 -9999 0 -0.58 5 5
Wnt receptor signaling pathway -0.025 0.051 0.183 3 -9999 0 3
RHOA 0.01 0.058 -9999 0 -0.411 1 1
RhoA/GTP -0.043 0.097 -9999 0 -0.341 4 4
CTNNA1 0.017 0 -9999 0 -9999 0 0
VCL 0.009 0.089 -9999 0 -0.347 2 2
EFNA1 -0.022 0.124 -9999 0 -0.411 5 5
LPP 0.029 0.045 -9999 0 -9999 0 0
Ephrin A1/EPHA2 -0.042 0.092 -9999 0 -0.349 3 3
SEC6/SEC8 -0.013 0.04 -9999 0 -9999 0 0
MGAT3 -0.04 0.109 -9999 0 -0.334 2 2
HGF/MET -0.012 0.04 -9999 0 -9999 0 0
HGF 0.012 0.043 -9999 0 -0.3 1 1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.013 0.065 -9999 0 -0.19 5 5
actin cable formation 0.022 0.089 -9999 0 -0.351 1 1
KIAA1543 0.029 0.045 -9999 0 -9999 0 0
KIFC3 0.018 0.057 -9999 0 -9999 0 0
NCK1 0.01 0.058 -9999 0 -0.411 1 1
EXOC3 0.017 0 -9999 0 -9999 0 0
ACTN1 0.025 0.047 -9999 0 -9999 0 0
NCK1/GIT1 0.015 0.058 -9999 0 -0.28 2 2
mol:GDP 0.025 0.051 -9999 0 -0.183 3 3
EXOC4 0.01 0.058 -9999 0 -0.411 1 1
STX4 0.025 0.047 -9999 0 -9999 0 0
PIP5K1C 0.025 0.047 -9999 0 -9999 0 0
LIMA1 0.002 0.081 -9999 0 -0.411 2 2
ABI1 0.017 0 -9999 0 -9999 0 0
ROCK1 0.006 0.104 -9999 0 -0.298 4 4
adherens junction assembly 0.033 0.066 -9999 0 -0.305 1 1
IGF-1R heterotetramer/IGF1 -0.075 0.103 -9999 0 -0.325 5 5
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.02 0.041 -9999 0 -0.28 1 1
MET 0.012 0.043 -9999 0 -0.3 1 1
PLEKHA7 0.025 0.047 -9999 0 -9999 0 0
mol:GTP -0.011 0.123 -9999 0 -0.266 9 9
establishment of epithelial cell apical/basal polarity 0.039 0.054 -9999 0 -9999 0 0
cortical actin cytoskeleton stabilization 0.013 0.065 -9999 0 -0.189 5 5
regulation of cell-cell adhesion 0.009 0.087 -9999 0 -0.339 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.013 0.065 -9999 0 -0.19 5 5
IL2 signaling events mediated by STAT5

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
GAB2 0.018 0 -9999 0 -9999 0 0
ELF1 -0.01 0.118 -9999 0 -0.379 5 5
CCNA2 -0.014 0.112 -9999 0 -0.411 4 4
PIK3CA 0.01 0.058 -9999 0 -0.41 1 1
JAK3 0.018 0 -9999 0 -9999 0 0
PIK3R1 -0.037 0.134 -9999 0 -0.355 8 8
JAK1 -0.029 0.135 -9999 0 -0.41 6 6
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.014 0.114 -9999 0 -0.403 2 2
SHC1 0.018 0 -9999 0 -9999 0 0
SP1 -0.018 0.099 -9999 0 -0.304 4 4
IL2RA -0.001 0.119 -9999 0 -0.652 1 1
IL2RB -0.001 0.082 -9999 0 -0.336 3 3
SOS1 0.018 0 -9999 0 -9999 0 0
IL2RG 0.012 0.043 -9999 0 -0.299 1 1
G1/S transition of mitotic cell cycle -0.093 0.224 -9999 0 -0.723 4 4
PTPN11 0.018 0 -9999 0 -9999 0 0
CCND2 -0.053 0.196 -9999 0 -0.431 10 10
LCK -0.021 0.113 -9999 0 -0.336 6 6
GRB2 0.018 0 -9999 0 -9999 0 0
IL2 0.01 0.058 -9999 0 -0.41 1 1
CDK6 -0.044 0.138 -9999 0 -0.349 9 9
CCND3 0.023 0.103 -9999 0 -9999 0 0
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0.03 0.063 0.209 4 -9999 0 4
DAPP1 -0.013 0.089 -9999 0 -0.296 2 2
Src family/SYK family/BLNK-LAT/BTK-ITK -0.026 0.162 -9999 0 -0.386 6 6
mol:DAG 0.001 0.092 0.184 2 -0.207 4 6
HRAS 0.018 0.004 -9999 0 -9999 0 0
RAP1A -0.005 0.096 -9999 0 -0.401 3 3
ARF5/GDP -0.002 0.084 -9999 0 -0.258 2 2
PLCG2 -0.042 0.143 -9999 0 -0.383 8 8
PLCG1 0.01 0.058 -9999 0 -0.411 1 1
ARF5 0.017 0 -9999 0 -9999 0 0
mol:GTP 0.007 0.065 0.201 4 -9999 0 4
ARF1/GTP 0.008 0.062 0.197 4 -9999 0 4
RHOA 0.01 0.058 -9999 0 -0.411 1 1
YES1 0.017 0 -9999 0 -9999 0 0
RAP1A/GTP 0.024 0.063 0.197 4 -0.169 2 6
ADAP1 0.007 0.062 0.193 4 -9999 0 4
ARAP3 0.007 0.064 0.2 4 -9999 0 4
INPPL1 0.01 0.058 -9999 0 -0.411 1 1
PREX1 -0.052 0.156 -9999 0 -0.398 9 9
ARHGEF6 0.017 0 -9999 0 -9999 0 0
ARHGEF7 0.017 0 -9999 0 -9999 0 0
ARF1 0.017 0 -9999 0 -9999 0 0
NRAS 0.013 0.043 -9999 0 -0.298 1 1
FYN -0.006 0.098 -9999 0 -0.411 3 3
ARF6 0.017 0 -9999 0 -9999 0 0
FGR 0.017 0 -9999 0 -9999 0 0
mol:Ca2+ 0.003 0.048 -9999 0 -9999 0 0
mol:IP4 0 0 -9999 0 -9999 0 0
TIAM1 0.01 0.058 -9999 0 -0.411 1 1
ZAP70 -0.02 0.106 -9999 0 -0.318 6 6
mol:IP3 -0.002 0.064 -9999 0 -0.165 3 3
LYN 0.012 0.043 -9999 0 -0.3 1 1
ARF1/GDP -0.002 0.084 -9999 0 -0.229 3 3
RhoA/GDP 0.019 0.071 0.208 3 -9999 0 3
PDK1/Src/Hsp90 0.026 0.05 -9999 0 -0.227 2 2
BLNK -0.006 0.098 -9999 0 -0.411 3 3
actin cytoskeleton reorganization 0.007 0.096 0.212 3 -0.259 2 5
SRC 0.017 0 -9999 0 -9999 0 0
PLEKHA2 0.013 0.034 -9999 0 -0.233 1 1
RAC1 0.017 0 -9999 0 -9999 0 0
PTEN -0.022 0.117 -9999 0 -0.387 5 5
HSP90AA1 0.002 0.081 -9999 0 -0.411 2 2
ARF6/GTP 0.03 0.063 0.209 4 -9999 0 4
RhoA/GTP 0.026 0.068 0.198 4 -0.193 1 5
Src family/SYK family/BLNK-LAT -0.024 0.136 -9999 0 -0.4 4 4
BLK 0.004 0.071 -9999 0 -0.355 2 2
PDPK1 0.017 0 -9999 0 -9999 0 0
CYTH1 0.007 0.062 0.193 4 -9999 0 4
HCK -0.018 0.112 -9999 0 -0.366 5 5
CYTH3 0.007 0.062 0.193 4 -9999 0 4
CYTH2 0.007 0.062 0.193 4 -9999 0 4
KRAS 0.018 0.004 -9999 0 -9999 0 0
GO:0030676 0 0 -9999 0 -9999 0 0
FOXO3 0.028 0.056 -9999 0 -9999 0 0
SGK1 0.001 0.058 0.159 4 -0.189 1 5
INPP5D 0 0 -9999 0 -9999 0 0
mol:GDP -0.011 0.087 -9999 0 -0.246 3 3
SOS1 0.017 0 -9999 0 -9999 0 0
SYK -0.012 0.106 -9999 0 -0.383 4 4
ARF6/GDP 0.02 0.067 0.211 3 -9999 0 3
mol:PI-3-4-5-P3 0.01 0.072 0.231 4 -9999 0 4
ARAP3/RAP1A/GTP 0.024 0.063 0.198 4 -0.169 2 6
VAV1 -0.047 0.138 -9999 0 -0.333 10 10
mol:PI-3-4-P2 0.006 0.04 -9999 0 -0.288 1 1
RAS family/GTP/PI3K Class I 0.032 0.059 0.18 4 -0.167 2 6
PLEKHA1 0.005 0.053 -9999 0 -0.209 3 3
Rac1/GDP -0.002 0.084 -9999 0 -0.258 2 2
LAT -0.008 0.091 -9999 0 -0.327 4 4
Rac1/GTP -0.011 0.102 -9999 0 -0.33 3 3
ITK 0.014 0.076 0.2 4 -9999 0 4
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.006 0.12 0.21 2 -0.29 4 6
LCK -0.022 0.113 -9999 0 -0.337 6 6
BTK 0.022 0.069 0.2 4 -0.172 1 5
BCR signaling pathway

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
JUN -0.022 0.103 -9999 0 -0.279 3 3
IKBKB 0.006 0.081 -9999 0 -0.267 2 2
AKT1 0.009 0.081 0.19 4 -0.198 1 5
IKBKG 0.005 0.083 -9999 0 -0.277 2 2
CALM1 -0.006 0.087 -9999 0 -0.281 3 3
PIK3CA 0.01 0.058 -9999 0 -0.411 1 1
MAP3K1 -0.017 0.12 -9999 0 -0.372 4 4
MAP3K7 0.017 0 -9999 0 -9999 0 0
mol:Ca2+ -0.015 0.09 -9999 0 -0.301 3 3
DOK1 0.017 0 -9999 0 -9999 0 0
AP-1 -0.023 0.079 -9999 0 -0.177 2 2
LYN 0.012 0.043 -9999 0 -0.3 1 1
BLNK -0.006 0.098 -9999 0 -0.411 3 3
SHC1 0.017 0 -9999 0 -9999 0 0
BCR complex 0.012 0.058 -9999 0 -0.222 3 3
CD22 -0.016 0.096 -9999 0 -0.326 2 2
CAMK2G 0 0.082 -9999 0 -0.289 2 2
CSNK2A1 0.017 0 -9999 0 -9999 0 0
INPP5D 0 0 -9999 0 -9999 0 0
SHC/GRB2/SOS1 -0.025 0.05 -9999 0 -9999 0 0
GO:0007205 -0.015 0.091 -9999 0 -0.305 3 3
SYK -0.012 0.106 -9999 0 -0.383 4 4
ELK1 -0.007 0.088 -9999 0 -0.285 3 3
NFATC1 0.002 0.113 -9999 0 -0.47 2 2
B-cell antigen/BCR complex 0.012 0.058 -9999 0 -0.222 3 3
PAG1/CSK 0.002 0.075 -9999 0 -0.228 5 5
NFKBIB 0.014 0.031 -9999 0 -9999 0 0
HRAS 0 0.079 -9999 0 -0.27 2 2
NFKBIA 0.014 0.03 -9999 0 -9999 0 0
NF-kappa-B/RelA/I kappa B beta 0.019 0.026 -9999 0 -9999 0 0
RasGAP/Csk 0.002 0.09 -9999 0 -0.254 1 1
mol:GDP -0.013 0.089 -9999 0 -0.294 3 3
PTEN -0.022 0.124 -9999 0 -0.411 5 5
CD79B 0.004 0.071 -9999 0 -0.355 2 2
NF-kappa-B/RelA/I kappa B alpha 0.019 0.026 -9999 0 -9999 0 0
GRB2 0.017 0 -9999 0 -9999 0 0
PI3K/BCAP/CD19 -0.024 0.132 -9999 0 -0.371 4 4
PIK3R1 -0.038 0.134 -9999 0 -0.355 8 8
mol:IP3 -0.015 0.092 -9999 0 -0.307 3 3
CSK 0.017 0 -9999 0 -9999 0 0
FOS -0.041 0.116 -9999 0 -0.327 4 4
CHUK -0.001 0.092 -9999 0 -0.259 4 4
IBTK 0.01 0.058 -9999 0 -0.411 1 1
CARD11/BCL10/MALT1/TAK1 -0.015 0.106 -9999 0 -0.366 3 3
PTPN6 -0.013 0.094 -9999 0 -0.39 1 1
RELA 0.017 0 -9999 0 -9999 0 0
BCL2A1 0.015 0.027 -9999 0 -0.092 1 1
VAV2 -0.005 0.09 -9999 0 -0.413 1 1
ubiquitin-dependent protein catabolic process 0.018 0.03 -9999 0 -9999 0 0
BTK -0.017 0.14 -9999 0 -1.028 1 1
CD19 -0.012 0.093 -9999 0 -0.415 1 1
MAP4K1 0.017 0 -9999 0 -9999 0 0
CD72 -0.024 0.119 -9999 0 -0.355 6 6
PAG1 -0.016 0.106 -9999 0 -0.344 5 5
MAPK14 -0.007 0.107 -9999 0 -0.32 4 4
SH3BP5 -0.024 0.119 -9999 0 -0.355 6 6
PIK3AP1 -0.011 0.093 -9999 0 -0.311 3 3
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.034 0.116 -9999 0 -0.337 4 4
RAF1 0.004 0.077 -9999 0 -0.251 2 2
RasGAP/p62DOK/SHIP -0.003 0.084 -9999 0 -0.243 1 1
CD79A 0.012 0.043 -9999 0 -0.3 1 1
re-entry into mitotic cell cycle -0.023 0.079 -9999 0 -0.176 2 2
RASA1 0.017 0 -9999 0 -9999 0 0
MAPK3 0.016 0.069 -9999 0 -0.212 1 1
MAPK1 0.013 0.071 -9999 0 -0.212 1 1
CD72/SHP1 -0.021 0.103 -9999 0 -0.364 1 1
NFKB1 0.017 0 -9999 0 -9999 0 0
MAPK8 -0.014 0.112 -9999 0 -0.307 5 5
actin cytoskeleton organization 0.002 0.082 -9999 0 -0.36 1 1
NF-kappa-B/RelA 0.04 0.056 -9999 0 -9999 0 0
Calcineurin -0.008 0.087 -9999 0 -0.259 3 3
PI3K -0.051 0.091 -9999 0 -0.352 2 2
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.016 0.097 -9999 0 -0.332 3 3
SOS1 0.017 0 -9999 0 -9999 0 0
Bam32/HPK1 -0.05 0.188 -9999 0 -0.659 4 4
DAPP1 -0.065 0.207 -9999 0 -0.74 4 4
cytokine secretion 0.003 0.107 -9999 0 -0.436 2 2
mol:DAG -0.015 0.092 -9999 0 -0.307 3 3
PLCG2 -0.042 0.143 -9999 0 -0.383 8 8
MAP2K1 0.01 0.073 -9999 0 -0.23 2 2
B-cell antigen/BCR complex/FcgammaRIIB -0.021 0.103 -9999 0 -0.239 7 7
mol:PI-3-4-5-P3 -0.023 0.095 0.233 4 -0.273 1 5
ETS1 0.004 0.086 -9999 0 -0.322 2 2
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.01 0.084 -9999 0 -9999 0 0
B-cell antigen/BCR complex/LYN -0.015 0.094 -9999 0 -0.338 2 2
MALT1 -0.008 0.091 -9999 0 -0.327 4 4
TRAF6 0.002 0.081 -9999 0 -0.41 2 2
RAC1 0.001 0.085 -9999 0 -0.38 1 1
B-cell antigen/BCR complex/LYN/SYK -0.007 0.1 -9999 0 -0.307 2 2
CARD11 -0.017 0.093 -9999 0 -0.284 3 3
FCGR2B -0.057 0.15 -9999 0 -0.35 11 11
PPP3CA 0.002 0.081 -9999 0 -0.411 2 2
BCL10 0.012 0.043 -9999 0 -0.299 1 1
IKK complex 0.013 0.041 -9999 0 -0.112 2 2
PTPRC -0.044 0.138 -9999 0 -0.349 9 9
PDPK1 0.006 0.076 0.179 4 -0.186 1 5
PPP3CB 0.017 0 -9999 0 -9999 0 0
PPP3CC -0.012 0.106 -9999 0 -0.383 4 4
POU2F2 0.017 0.023 -9999 0 -9999 0 0
EGFR-dependent Endothelin 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
HRAS 0.017 0 -9999 0 -9999 0 0
EGFR -0.01 0.099 -9999 0 -0.355 4 4
EGF/EGFR -0.03 0.083 -9999 0 -0.176 6 6
EGF/EGFR dimer/SHC/GRB2/SOS1 0.019 0.07 -9999 0 -0.178 2 2
mol:GTP 0 0 -9999 0 -9999 0 0
EDNRA 0.004 0.071 -9999 0 -0.355 2 2
response to oxidative stress 0 0 -9999 0 -9999 0 0
EGF -0.018 0.1 -9999 0 -0.3 6 6
EGF/EGFR dimer/SHC -0.002 0.08 -9999 0 -0.167 10 10
mol:GDP 0.015 0.068 -9999 0 -0.177 2 2
mol:Ca2+ 0 0 -9999 0 -9999 0 0
EDN1 -0.042 0.134 -9999 0 -0.337 9 9
GRB2/SOS1 0.026 0 -9999 0 -9999 0 0
HRAS/GTP -0.02 0.044 -9999 0 -9999 0 0
SHC1 0.017 0 -9999 0 -9999 0 0
HRAS/GDP 0.017 0.062 -9999 0 -9999 0 0
FRAP1 0.014 0.062 -9999 0 -9999 0 0
EGF/EGFR dimer -0.018 0.093 -9999 0 -0.211 10 10
SOS1 0.017 0 -9999 0 -9999 0 0
GRB2 0.017 0 -9999 0 -9999 0 0
ETA receptor/Endothelin-1 -0.025 0.103 -9999 0 -0.225 11 11
Signaling events mediated by PRL

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
CCNE1 -0.055 0.146 -9999 0 -0.34 11 11
mol:Halofuginone 0.006 0.001 -9999 0 -9999 0 0
ITGA1 -0.028 0.119 -9999 0 -0.331 7 7
CDKN1A -0.023 0.121 -9999 0 -0.38 5 5
PRL-3/alpha Tubulin 0.026 0 -9999 0 -9999 0 0
mol:Ca2+ -0.061 0.105 -9999 0 -0.236 14 14
AGT -0.073 0.155 -9999 0 -0.331 14 14
CCNA2 -0.014 0.092 -9999 0 -0.373 1 1
TUBA1B 0.017 0 -9999 0 -9999 0 0
EGR1 -0.028 0.103 -9999 0 -0.217 12 12
CDK2/Cyclin E1 -0.042 0.13 -9999 0 -0.308 8 8
MAPK3 0.023 0 -9999 0 -9999 0 0
PRL-2 /Rab GGTase beta 0.026 0 -9999 0 -9999 0 0
MAPK1 0.018 0.041 -9999 0 -0.281 1 1
PTP4A1 -0.005 0.076 -9999 0 -9999 0 0
PTP4A3 0.017 0 -9999 0 -9999 0 0
PTP4A2 0.017 0 -9999 0 -9999 0 0
ITGB1 0.023 0 -9999 0 -9999 0 0
SRC 0.017 0 -9999 0 -9999 0 0
RAC1 0.017 0.037 -9999 0 -9999 0 0
Rab GGTase beta/Rab GGTase alpha 0.026 0 -9999 0 -9999 0 0
PRL-1/ATF-5 -0.001 0.079 -9999 0 -9999 0 0
RABGGTA 0.017 0 -9999 0 -9999 0 0
BCAR1 0 0 -9999 0 -9999 0 0
RHOC 0.014 0.044 -9999 0 -9999 0 0
RHOA 0.009 0.062 -9999 0 -0.355 1 1
cell motility 0.017 0.047 -9999 0 -9999 0 0
PRL-1/alpha Tubulin 0.005 0.072 -9999 0 -9999 0 0
PRL-3/alpha1 Integrin -0.006 0.083 -9999 0 -0.218 7 7
ROCK1 0.017 0.047 -9999 0 -9999 0 0
RABGGTB 0.017 0 -9999 0 -9999 0 0
CDK2 0.006 0.06 -9999 0 -0.3 2 2
mitosis -0.005 0.076 -9999 0 -9999 0 0
ATF5 0.006 0.06 -9999 0 -0.3 2 2
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.006 0.136 -9999 0 -0.576 2 2
adherens junction organization 0.009 0.096 -9999 0 -0.365 3 3
mol:GTP 0 0 -9999 0 -9999 0 0
Rac1/GDP 0.008 0.135 -9999 0 -0.538 2 2
FMN1 0.01 0.092 -9999 0 -0.338 3 3
mol:IP3 0.003 0.122 -9999 0 -0.515 2 2
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.011 0.096 -9999 0 -0.354 3 3
CTNNB1 0.001 0.082 -9999 0 -0.417 2 2
AKT1 0.01 0.118 -9999 0 -0.494 2 2
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.019 0.097 -9999 0 -0.375 3 3
CTNND1 0.017 0.003 -9999 0 -9999 0 0
mol:PI-4-5-P2 0.014 0.091 -9999 0 -0.396 2 2
VASP 0.008 0.104 -9999 0 -0.396 3 3
ZYX 0.016 0.092 -9999 0 -0.405 2 2
JUB 0.003 0.1 -9999 0 -0.405 2 2
EGFR(dimer) 0.008 0.121 -9999 0 -0.437 3 3
E-cadherin/beta catenin-gamma catenin 0.021 0.058 -9999 0 -0.218 3 3
mol:PI-3-4-5-P3 0.005 0.125 -9999 0 -0.528 2 2
PIK3CA 0.009 0.061 -9999 0 -0.433 1 1
PI3K 0.005 0.128 -9999 0 -0.544 2 2
FYN -0.008 0.136 -9999 0 -0.356 5 5
mol:Ca2+ 0.003 0.118 -9999 0 -0.499 2 2
JUP 0.017 0.001 -9999 0 -9999 0 0
PIK3R1 -0.037 0.135 -9999 0 -0.357 8 8
mol:DAG 0.003 0.122 -9999 0 -0.515 2 2
CDH1 0.009 0.058 -9999 0 -0.41 1 1
RhoA/GDP 0.005 0.151 -9999 0 -0.609 2 2
establishment of polarity of embryonic epithelium 0.008 0.102 -9999 0 -0.388 3 3
SRC 0.017 0 -9999 0 -9999 0 0
RAC1 0.017 0 -9999 0 -9999 0 0
RHOA 0.01 0.058 -9999 0 -0.411 1 1
EGFR -0.01 0.099 -9999 0 -0.355 4 4
CASR 0.001 0.115 -9999 0 -0.466 2 2
RhoA/GTP 0.008 0.127 -9999 0 -0.531 2 2
AKT2 0.01 0.118 -9999 0 -0.494 2 2
actin cable formation 0.007 0.101 -9999 0 -0.385 3 3
apoptosis -0.006 0.119 0.502 2 -9999 0 2
CTNNA1 0.017 0.003 -9999 0 -9999 0 0
mol:GDP -0.003 0.146 -9999 0 -0.47 3 3
PIP5K1A 0.014 0.093 -9999 0 -0.405 2 2
PLCG1 0.002 0.126 -9999 0 -0.533 2 2
Rac1/GTP 0.015 0.112 -9999 0 -0.397 3 3
homophilic cell adhesion 0 0.003 -9999 0 -9999 0 0
p38 MAPK signaling 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
TRAF6/ASK1 0 0.065 -9999 0 -0.192 5 5
TRAF2/ASK1 0.006 0.063 -9999 0 -0.215 4 4
ATM 0.017 0 -9999 0 -9999 0 0
MAP2K3 -0.002 0.113 -9999 0 -0.355 4 4
response to stress 0 0 -9999 0 -9999 0 0
MAP2K6 -0.035 0.14 -9999 0 -0.341 7 7
hyperosmotic response 0 0 -9999 0 -9999 0 0
response to oxidative stress 0 0 -9999 0 -9999 0 0
GADD45G 0.004 0.071 -9999 0 -0.355 2 2
TXN 0.004 0.04 -9999 0 -0.285 1 1
CALM1 0.017 0 -9999 0 -9999 0 0
GADD45A -0.04 0.139 -9999 0 -0.369 8 8
GADD45B -0.032 0.129 -9999 0 -0.363 7 7
MAP3K1 -0.014 0.112 -9999 0 -0.411 4 4
MAP3K6 0.017 0 -9999 0 -9999 0 0
MAP3K7 0.017 0 -9999 0 -9999 0 0
MAP3K4 0.01 0.058 -9999 0 -0.411 1 1
mol:Ca2+ 0 0 -9999 0 -9999 0 0
ASK1/ASK2 0.005 0.075 -9999 0 -0.259 4 4
TAK1/TAB family 0.008 0.026 -9999 0 -9999 0 0
RAC1/OSM/MEKK3 0.034 0 -9999 0 -9999 0 0
TRAF2 0.017 0 -9999 0 -9999 0 0
RAC1/OSM/MEKK3/MKK3 -0.025 0.075 -9999 0 -0.269 4 4
TRAF6 0.008 0.055 -9999 0 -0.275 2 2
RAC1 0.017 0 -9999 0 -9999 0 0
mol:LPS 0 0 -9999 0 -9999 0 0
CAMK2B -0.012 0.092 -9999 0 -0.3 5 5
CCM2 0.017 0 -9999 0 -9999 0 0
CaM/Ca2+/CAMKIIB 0.007 0.053 -9999 0 -0.159 5 5
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 0.002 0.081 -9999 0 -0.253 3 3
OSM/MEKK3 0.026 0 -9999 0 -9999 0 0
TAOK1 0.002 0.054 -9999 0 -0.275 1 1
TAOK2 0.019 0 -9999 0 -9999 0 0
TAOK3 0.016 0.019 -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 -0.012 0.106 -9999 0 -0.383 4 4
MAP3K10 0.004 0.071 -9999 0 -0.355 2 2
MAP3K3 0.017 0 -9999 0 -9999 0 0
TRX/ASK1 -0.002 0.069 -9999 0 -0.215 5 5
GADD45/MTK1/MTK1 -0.024 0.112 -9999 0 -0.214 12 12
Aurora B signaling

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
Condensin I complex 0.001 0.082 -9999 0 -0.296 2 2
STMN1 0.008 0.066 -9999 0 -0.261 3 3
Aurora B/RasGAP/Survivin 0.018 0.082 -9999 0 -0.36 2 2
Chromosomal passenger complex/Cul3 protein complex -0.025 0.148 -9999 0 -0.516 3 3
BIRC5 -0.005 0.095 -9999 0 -0.39 3 3
DES -0.048 0.18 -9999 0 -0.727 3 3
Aurora C/Aurora B/INCENP 0.021 0.072 -9999 0 -0.324 2 2
Aurora B/TACC1 0.016 0.044 -9999 0 -0.204 2 2
Aurora B/PP2A 0.021 0.044 -9999 0 -0.298 1 1
mol:GTP 0 0 -9999 0 -9999 0 0
CBX5 0.005 0.053 -9999 0 -0.209 3 3
mitotic metaphase/anaphase transition 0 0.003 -9999 0 -9999 0 0
NDC80 -0.015 0.116 -9999 0 -0.33 6 6
Cul3 protein complex -0.016 0.094 -9999 0 -0.227 5 5
KIF2C -0.054 0.237 -9999 0 -0.578 7 7
PEBP1 0.017 0.004 -9999 0 -9999 0 0
KIF20A -0.007 0.1 -9999 0 -0.418 3 3
mol:GDP 0 0 -9999 0 -9999 0 0
Aurora B/RasGAP 0.021 0.044 -9999 0 -0.298 1 1
SEPT1 0.017 0 -9999 0 -9999 0 0
SMC2 -0.014 0.112 -9999 0 -0.411 4 4
SMC4 0.006 0.06 -9999 0 -0.3 2 2
NSUN2/NPM1/Nucleolin 0.012 0.119 -9999 0 -0.828 1 1
PSMA3 0.017 0 -9999 0 -9999 0 0
G2/M transition of mitotic cell cycle 0 0.003 -9999 0 -9999 0 0
H3F3B 0.013 0.042 -9999 0 -0.289 1 1
AURKB 0.01 0.062 -9999 0 -0.443 1 1
AURKC 0.01 0.058 -9999 0 -0.411 1 1
CDCA8 -0.013 0.111 -9999 0 -0.401 4 4
cytokinesis -0.019 0.219 -9999 0 -0.663 4 4
Aurora B/Septin1 -0.003 0.2 -9999 0 -0.598 4 4
AURKA -0.007 0.099 -9999 0 -0.414 3 3
INCENP 0.009 0.063 -9999 0 -0.447 1 1
KLHL13 -0.061 0.149 -9999 0 -0.337 12 12
BUB1 -0.015 0.114 -9999 0 -0.416 4 4
hSgo1/Aurora B/Survivin 0.014 0.092 -9999 0 -0.442 2 2
EVI5 0.017 0.002 -9999 0 -9999 0 0
RhoA/GTP -0.015 0.214 -9999 0 -0.537 5 5
SGOL1 0.01 0.058 -9999 0 -0.411 1 1
CENPA -0.031 0.238 -9999 0 -0.584 5 5
NCAPG 0 0 -9999 0 -9999 0 0
Aurora B/HC8 Proteasome 0.021 0.044 -9999 0 -0.298 1 1
NCAPD2 0.017 0 -9999 0 -9999 0 0
Aurora B/PP1-gamma 0.009 0.072 -9999 0 -0.289 3 3
RHOA 0.01 0.058 -9999 0 -0.411 1 1
NCAPH 0.002 0.081 -9999 0 -0.411 2 2
NPM1 0.01 0.076 -9999 0 -0.534 1 1
RASA1 0.017 0 -9999 0 -9999 0 0
KLHL9 0.01 0.058 -9999 0 -0.411 1 1
mitotic prometaphase 0 0.005 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.044 -9999 0 -0.298 1 1
PPP1CC 0.002 0.081 -9999 0 -0.411 2 2
Centraspindlin -0.022 0.25 -9999 0 -0.619 5 5
RhoA/GDP 0.007 0.041 -9999 0 -0.288 1 1
NSUN2 0.01 0.076 -9999 0 -0.534 1 1
MYLK 0.008 0.057 -9999 0 -0.281 2 2
KIF23 -0.012 0.108 -9999 0 -0.39 4 4
VIM -0.061 0.133 -9999 0 -0.264 16 16
RACGAP1 0.003 0.073 -9999 0 -0.364 2 2
mitosis 0 0 -9999 0 -9999 0 0
NCL 0.01 0.076 -9999 0 -0.534 1 1
Chromosomal passenger complex -0.024 0.238 -9999 0 -0.689 4 4
Chromosomal passenger complex/EVI5 0.015 0.135 -9999 0 -0.419 3 3
TACC1 0.012 0.043 -9999 0 -0.3 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
Canonical NF-kappaB pathway

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
FBXW11 0.019 0.013 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.043 0.081 -9999 0 -0.323 1 1
ERC1 0.01 0.058 -9999 0 -0.411 1 1
RIP2/NOD2 -0.016 0.102 -9999 0 -0.259 8 8
NFKBIA 0.034 0.065 -9999 0 -0.438 1 1
BIRC2 0.017 0 -9999 0 -9999 0 0
IKBKB 0.017 0 -9999 0 -9999 0 0
RIPK2 0.012 0.043 -9999 0 -0.3 1 1
IKBKG 0.004 0.121 -9999 0 -0.745 1 1
IKK complex/A20 0.009 0.127 -9999 0 -0.48 2 2
NEMO/A20/RIP2 0.012 0.043 -9999 0 -0.299 1 1
XPO1 0.017 0 -9999 0 -9999 0 0
NEMO/ATM 0.014 0.116 -9999 0 -0.702 1 1
tumor necrosis factor receptor activity 0 0 -9999 0 -9999 0 0
RAN 0.01 0.058 -9999 0 -0.411 1 1
Exportin 1/RanGTP 0.019 0.035 -9999 0 -0.234 1 1
IKK complex/ELKS -0.031 0.093 -9999 0 -0.625 1 1
BCL10/MALT1/TRAF6 0.008 0.081 -9999 0 -0.248 4 4
NOD2 -0.036 0.139 -9999 0 -0.395 7 7
NFKB1 0.019 0.013 -9999 0 -9999 0 0
RELA 0.019 0.013 -9999 0 -9999 0 0
MALT1 -0.008 0.091 -9999 0 -0.327 4 4
cIAP1/UbcH5C 0.026 0 -9999 0 -9999 0 0
ATM 0.017 0 -9999 0 -9999 0 0
TNF/TNFR1A -0.005 0.096 -9999 0 -0.25 6 6
TRAF6 0.002 0.081 -9999 0 -0.411 2 2
PRKCA 0.002 0.081 -9999 0 -0.411 2 2
CHUK 0.01 0.058 -9999 0 -0.411 1 1
UBE2D3 0.017 0 -9999 0 -9999 0 0
TNF -0.02 0.106 -9999 0 -0.318 6 6
NF kappa B1 p50/RelA 0.043 0.037 -9999 0 -0.225 1 1
BCL10 0.012 0.043 -9999 0 -0.3 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.034 0.064 -9999 0 -0.435 1 1
beta TrCP1/SCF ubiquitin ligase complex 0.019 0.013 -9999 0 -9999 0 0
TNFRSF1A 0.01 0.058 -9999 0 -0.411 1 1
IKK complex 0.019 0.116 -9999 0 -0.677 1 1
CYLD 0.01 0.058 -9999 0 -0.411 1 1
IKK complex/PKC alpha 0.018 0.116 -9999 0 -0.65 1 1
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.039 0.033 -9999 0 -9999 0 0
HDAC3 0.017 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 -0.005 0.039 -9999 0 -0.286 1 1
GATA1/HDAC4 0.016 0.05 -9999 0 -0.237 2 2
GATA1/HDAC5 0.02 0.041 -9999 0 -0.28 1 1
GATA2/HDAC5 0.002 0.075 -9999 0 -0.228 5 5
HDAC5/BCL6/BCoR 0.036 0 -9999 0 -9999 0 0
HDAC9 0.017 0 -9999 0 -9999 0 0
Glucocorticoid receptor/Hsp90/HDAC6 0.019 0.06 -9999 0 -0.227 2 2
HDAC4/ANKRA2 0.022 0.03 -9999 0 -0.194 1 1
HDAC5/YWHAB 0.026 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.019 0.027 -9999 0 -0.175 1 1
GATA2 -0.016 0.106 -9999 0 -0.344 5 5
HDAC4/RFXANK 0.016 0.05 -9999 0 -0.237 2 2
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 0.018 0.042 -9999 0 -0.194 2 2
Histones 0.029 0.027 -9999 0 -9999 0 0
ADRBK1 0.017 0 -9999 0 -9999 0 0
HDAC4 0.012 0.043 -9999 0 -0.3 1 1
XPO1 0.017 0 -9999 0 -9999 0 0
HDAC5/ANKRA2 0.026 0 -9999 0 -9999 0 0
HDAC4/Ubc9 0.016 0.05 -9999 0 -0.237 2 2
HDAC7 0 0 -9999 0 -9999 0 0
HDAC5/14-3-3 E 0.02 0.041 -9999 0 -0.28 1 1
TUBA1B 0.017 0 -9999 0 -9999 0 0
HDAC6 0.017 0 -9999 0 -9999 0 0
HDAC5/RFXANK 0.02 0.041 -9999 0 -0.28 1 1
CAMK4 -0.01 0.099 -9999 0 -0.355 4 4
Tubulin/HDAC6 0.009 0.071 -9999 0 -0.227 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 0.01 0.058 -9999 0 -0.411 1 1
EntrezGene:8021 0 0 -9999 0 -9999 0 0
YWHAE 0.01 0.058 -9999 0 -0.411 1 1
NR3C1 0.006 0.06 -9999 0 -0.3 2 2
SUMO1/HDAC4 0.03 0.032 -9999 0 -9999 0 0
SRF 0.017 0 -9999 0 -9999 0 0
HDAC4/YWHAB 0.022 0.03 -9999 0 -0.194 1 1
Tubulin -0.006 0.083 -9999 0 -0.218 7 7
HDAC4/14-3-3 E 0.016 0.05 -9999 0 -0.237 2 2
GNB1 0.017 0 -9999 0 -9999 0 0
RANGAP1 0.017 0 -9999 0 -9999 0 0
BCL6/BCoR 0.026 0 -9999 0 -9999 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.032 0.025 -9999 0 -9999 0 0
HDAC4/SRF 0.015 0.064 -9999 0 -0.227 2 2
HDAC4/ER alpha -0.061 0.142 -9999 0 -0.286 15 15
EntrezGene:23225 0 0 -9999 0 -9999 0 0
positive regulation of chromatin silencing 0.028 0.027 -9999 0 -9999 0 0
cell motility 0.008 0.071 -9999 0 -0.226 2 2
EntrezGene:23636 0 0 -9999 0 -9999 0 0
UBE2I 0.01 0.058 -9999 0 -0.411 1 1
HDAC7/HDAC3 0.013 0 -9999 0 -9999 0 0
BCL6 0.017 0 -9999 0 -9999 0 0
HDAC4/CaMK II delta B 0.012 0.043 -9999 0 -0.299 1 1
Hsp90/HDAC6 0.015 0.058 -9999 0 -0.28 2 2
ESR1 -0.099 0.189 -9999 0 -0.403 15 15
HDAC6/HDAC11 0.014 0.05 -9999 0 -0.194 3 3
Ran/GTP/Exportin 1 0.032 0.036 -9999 0 -9999 0 0
NPC 0.01 0 -9999 0 -9999 0 0
MEF2C 0.01 0.058 -9999 0 -0.411 1 1
RAN 0.01 0.058 -9999 0 -0.411 1 1
HDAC4/MEF2C 0.04 0.048 -9999 0 -9999 0 0
GNG2 0.006 0.06 -9999 0 -0.3 2 2
NCOR2 0.017 0 -9999 0 -9999 0 0
TUBB2A -0.028 0.119 -9999 0 -0.331 7 7
HDAC11 0 0.073 -9999 0 -0.3 3 3
HSP90AA1 0.002 0.081 -9999 0 -0.411 2 2
RANBP2 0.017 0 -9999 0 -9999 0 0
ANKRA2 0.017 0 -9999 0 -9999 0 0
RFXANK 0.01 0.058 -9999 0 -0.411 1 1
nuclear import -0.026 0.04 0.233 1 -9999 0 1
BARD1 signaling events

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
BARD1/CSTF1 0.016 0.05 -9999 0 -0.237 2 2
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 0.028 0 -9999 0 -9999 0 0
protein ubiquitination -0.003 0.087 -9999 0 -0.252 1 1
XRCC5 0.017 0 -9999 0 -9999 0 0
XRCC6 0.017 0 -9999 0 -9999 0 0
M/R/N Complex 0.026 0.05 -9999 0 -0.227 2 2
MRE11A 0.017 0 -9999 0 -9999 0 0
DNA-PK 0.036 0 -9999 0 -9999 0 0
FA complex/FANCD2/Ubiquitin 0.017 0.074 -9999 0 -0.271 1 1
FANCF -0.014 0.112 -9999 0 -0.411 4 4
BRCA1 0.017 0 -9999 0 -9999 0 0
CCNE1 -0.055 0.146 -9999 0 -0.34 11 11
CDK2/Cyclin E1 -0.033 0.107 -9999 0 -0.22 13 13
FANCG 0.017 0 -9999 0 -9999 0 0
BRCA1/BACH1/BARD1 0.016 0.05 -9999 0 -0.237 2 2
FANCE 0.006 0.06 -9999 0 -0.3 2 2
FANCC 0.017 0 -9999 0 -9999 0 0
NBN 0.01 0.058 -9999 0 -0.411 1 1
FANCA -0.014 0.099 -9999 0 -0.322 5 5
DNA repair 0.006 0.109 -9999 0 -0.383 2 2
BRCA1/BARD1/ubiquitin 0.016 0.05 -9999 0 -0.237 2 2
BARD1/DNA-PK 0.037 0.04 -9999 0 -0.197 1 1
FANCL 0.006 0.06 -9999 0 -0.3 2 2
mRNA polyadenylation -0.016 0.05 0.236 2 -9999 0 2
BRCA1/BARD1/CTIP/M/R/N Complex 0.027 0.048 -9999 0 -9999 0 0
BRCA1/BACH1/BARD1/TopBP1 0.024 0.058 -9999 0 -0.27 2 2
BRCA1/BARD1/P53 0.033 0.051 -9999 0 -0.197 2 2
BARD1/CSTF1/BRCA1 0.027 0.043 -9999 0 -0.227 1 1
BRCA1/BACH1 0.017 0 -9999 0 -9999 0 0
BARD1 0.004 0.071 -9999 0 -0.355 2 2
PCNA -0.004 0.09 -9999 0 -0.374 3 3
BRCA1/BARD1/UbcH5C 0.027 0.043 -9999 0 -0.227 1 1
BRCA1/BARD1/UbcH7 0.027 0.043 -9999 0 -0.227 1 1
BRCA1/BARD1/RAD51/PCNA 0.008 0.09 -9999 0 -0.207 8 8
BARD1/DNA-PK/P53 0.041 0.048 -9999 0 -9999 0 0
BRCA1/BARD1/Ubiquitin 0.016 0.05 -9999 0 -0.237 2 2
BRCA1/BARD1/CTIP 0.029 0.044 -9999 0 -0.197 1 1
FA complex 0.009 0.075 -9999 0 -0.251 1 1
BARD1/EWS 0.016 0.05 -9999 0 -0.237 2 2
RBBP8 0.019 0.029 -9999 0 -0.194 1 1
TP53 0.01 0.058 -9999 0 -0.411 1 1
TOPBP1 0.012 0.043 -9999 0 -0.3 1 1
G1/S transition of mitotic cell cycle -0.031 0.05 0.196 2 -9999 0 2
BRCA1/BARD1 0.001 0.09 -9999 0 -0.255 1 1
CSTF1 0.017 0 -9999 0 -9999 0 0
BARD1/EWS-Fli1 0.003 0.049 -9999 0 -0.245 2 2
CDK2 0.006 0.06 -9999 0 -0.3 2 2
UniProt:Q9BZD1 0 0 -9999 0 -9999 0 0
RAD51 -0.014 0.112 -9999 0 -0.411 4 4
RAD50 0.01 0.058 -9999 0 -0.411 1 1
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.016 0.05 -9999 0 -0.237 2 2
EWSR1 0.017 0 -9999 0 -9999 0 0
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.017 0 -9999 0 -9999 0 0
SPHK1 -0.002 0.082 -9999 0 -0.337 3 3
GNAI2 0.017 0 -9999 0 -9999 0 0
mol:S1P 0.01 0.053 -9999 0 -0.235 2 2
GNAO1 0.017 0 -9999 0 -9999 0 0
mol:Sphinganine-1-P 0.01 0.057 -9999 0 -0.223 3 3
growth factor activity 0 0 -9999 0 -9999 0 0
S1P/S1P2/G12/G13 0.026 0.04 -9999 0 -9999 0 0
GNAI3 0.01 0.058 -9999 0 -0.411 1 1
G12/G13 0.026 0 -9999 0 -9999 0 0
S1PR3 0 0 -9999 0 -9999 0 0
S1PR2 0 0 -9999 0 -9999 0 0
EDG1 -0.012 0.106 -9999 0 -0.383 4 4
S1P1/S1P 0.001 0.073 -9999 0 -0.207 5 5
S1PR5 0 0 -9999 0 -9999 0 0
S1PR4 0 0 -9999 0 -9999 0 0
GNAI1 -0.05 0.152 -9999 0 -0.386 9 9
S1P/S1P5/G12 0.016 0.042 -9999 0 -0.176 2 2
S1P/S1P3/Gq 0.015 0.062 -9999 0 -0.395 1 1
S1P/S1P4/Gi -0.013 0.108 -9999 0 -0.361 3 3
GNAQ 0 0 -9999 0 -9999 0 0
GNAZ -0.01 0.099 -9999 0 -0.355 4 4
GNA14 0.004 0.071 -9999 0 -0.355 2 2
GNA15 0.012 0.043 -9999 0 -0.3 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 0.01 0.058 -9999 0 -0.411 1 1
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.017 0 -9999 0 -9999 0 0
VLDLR -0.038 0.144 -9999 0 -0.411 7 7
LRPAP1 0.017 0 -9999 0 -9999 0 0
NUDC 0.017 0 -9999 0 -9999 0 0
RELN/LRP8 0.012 0.089 -9999 0 -0.33 3 3
CaM/Ca2+ 0.013 0 -9999 0 -9999 0 0
KATNA1 0.017 0 -9999 0 -9999 0 0
GO:0030286 0 0 -9999 0 -9999 0 0
ABL1 0.012 0.08 -9999 0 -0.293 3 3
IQGAP1/CaM 0.026 0 -9999 0 -9999 0 0
DAB1 0.017 0 -9999 0 -9999 0 0
IQGAP1 0.017 0 -9999 0 -9999 0 0
PLA2G7 -0.085 0.168 -9999 0 -0.351 15 15
CALM1 0.017 0 -9999 0 -9999 0 0
DYNLT1 0.017 0 -9999 0 -9999 0 0
mol:Ca2+ 0 0 -9999 0 -9999 0 0
LRPAP1/LRP8 0.011 0.064 -9999 0 -0.251 3 3
UniProt:Q4QZ09 0 0 -9999 0 -9999 0 0
CLIP1 0.017 0 -9999 0 -9999 0 0
CDK5R1 0.017 0 -9999 0 -9999 0 0
LIS1/Poliovirus Protein 3A 0.017 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 -0.01 0.097 -9999 0 -0.227 8 8
YWHAE 0.01 0.058 -9999 0 -0.411 1 1
NDEL1/14-3-3 E 0.038 0.07 -9999 0 -0.305 1 1
MAP1B -0.032 0.081 -9999 0 -0.252 5 5
RAC1 0.023 0 -9999 0 -9999 0 0
p35/CDK5 0.026 0.072 -9999 0 -0.292 2 2
RELN -0.002 0.082 -9999 0 -0.337 3 3
PAFAH/LIS1 -0.03 0.099 -9999 0 -0.227 7 7
LIS1/CLIP170 0.03 0 -9999 0 -9999 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.01 0.04 -9999 0 -0.239 1 1
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 0.003 0.088 -9999 0 -9999 0 0
GO:0005869 0 0 -9999 0 -9999 0 0
NDEL1 0.032 0.068 -9999 0 -0.327 1 1
LIS1/IQGAP1 0.03 0 -9999 0 -9999 0 0
RHOA 0.016 0.051 -9999 0 -0.353 1 1
PAFAH1B1 0.023 0 -9999 0 -9999 0 0
PAFAH1B3 0.017 0 -9999 0 -9999 0 0
PAFAH1B2 0.017 0 -9999 0 -9999 0 0
MAP1B/LIS1/Dynein heavy chain 0.001 0.056 -9999 0 -9999 0 0
NDEL1/Katanin 60/Dynein heavy chain 0.048 0.065 -9999 0 -0.291 1 1
LRP8 -0.004 0.09 -9999 0 -0.374 3 3
NDEL1/Katanin 60 0.041 0.066 -9999 0 -0.305 1 1
P39/CDK5 0.026 0.072 -9999 0 -0.292 2 2
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.03 0 -9999 0 -9999 0 0
CDK5 0.017 0.075 -9999 0 -0.314 2 2
PPP2R5D 0.017 0 -9999 0 -9999 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.026 0 -9999 0 -9999 0 0
CSNK2A1 0.017 0 -9999 0 -9999 0 0
RELN/VLDLR/DAB1/LIS1 0.009 0.084 -9999 0 -9999 0 0
RELN/VLDLR -0.008 0.11 -9999 0 -0.226 10 10
CDC42 0.023 0 -9999 0 -9999 0 0
Ephrin A reverse signaling

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
MAPKKK cascade 0.019 0.035 -9999 0 -0.233 1 1
EFNA5 0.01 0.058 -9999 0 -0.411 1 1
FYN 0.009 0.06 -9999 0 -0.204 4 4
neuron projection morphogenesis 0.019 0.035 -9999 0 -0.233 1 1
cell-cell signaling 0 0 -9999 0 -9999 0 0
Ephrin A5/EPHA5 0.019 0.035 -9999 0 -0.234 1 1
EPHA5 0.017 0 -9999 0 -9999 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.022 0.03 -9999 0 -0.194 1 1
CRKL 0.027 0.059 -9999 0 -0.348 1 1
mol:PIP3 0.016 0.116 0.377 5 -9999 0 5
AKT1 0.023 0.082 0.28 5 -9999 0 5
PTK2B 0.017 0 -9999 0 -9999 0 0
RAPGEF1 0.032 0.056 -9999 0 -0.326 1 1
RANBP10 0.017 0 -9999 0 -9999 0 0
PIK3CA 0.01 0.058 -9999 0 -0.411 1 1
HGF/MET/SHIP2 0.024 0.049 -9999 0 -0.227 1 1
MAP3K5 0.024 0.078 -9999 0 -0.362 1 1
HGF/MET/CIN85/CBL/ENDOPHILINS 0.023 0.063 -9999 0 -0.197 2 2
AP1 -0.062 0.124 -9999 0 -0.232 18 18
mol:SU11274 0 0 -9999 0 -9999 0 0
SHC1 0.017 0 -9999 0 -9999 0 0
apoptosis -0.144 0.289 -9999 0 -0.704 11 11
STAT3 (dimer) 0.039 0.019 -9999 0 -9999 0 0
GAB1/CRKL/SHP2/PI3K 0.022 0.107 -9999 0 -0.634 1 1
INPP5D 0 0 -9999 0 -9999 0 0
CBL/CRK 0.022 0.088 -9999 0 -0.503 1 1
PTPN11 0.017 0 -9999 0 -9999 0 0
GO:0007205 0 0 -9999 0 -9999 0 0
PLCG1 0.01 0.058 -9999 0 -0.411 1 1
PTEN -0.022 0.124 -9999 0 -0.411 5 5
ELK1 0.002 0.042 0.289 1 -9999 0 1
mol:SU5416 0 0 -9999 0 -9999 0 0
SHP2/GRB2/SOS1GAB1 0.028 0.025 -9999 0 -9999 0 0
PAK1 0.028 0.076 0.265 5 -9999 0 5
HGF/MET/RANBP10 0.029 0.035 -9999 0 -9999 0 0
HRAS 0.037 0.026 -9999 0 -9999 0 0
DOCK1 0.029 0.058 -9999 0 -0.326 1 1
GAB1 0.022 0.061 -9999 0 -0.37 1 1
CRK 0.012 0.091 -9999 0 -0.535 1 1
mol:PHA665752 0 0 -9999 0 -9999 0 0
mol:GDP 0.033 0.028 -9999 0 -9999 0 0
JUN -0.026 0.124 -9999 0 -0.374 6 6
EntrezGene:200958 0 0 -9999 0 -9999 0 0
HGF/MET 0.013 0.033 -9999 0 -0.202 1 1
PIK3R1 -0.038 0.134 -9999 0 -0.355 8 8
cell morphogenesis 0.034 0.082 -9999 0 -0.414 1 1
GRB2/SHC 0.033 0.03 -9999 0 -0.167 1 1
FOS -0.079 0.166 -9999 0 -0.355 14 14
GLMN 0.006 0.014 -9999 0 -9999 0 0
cell motility 0.002 0.042 0.288 1 -9999 0 1
HGF/MET/MUC20 0.017 0.035 -9999 0 -0.159 2 2
cell migration 0.032 0.03 -9999 0 -0.165 1 1
GRB2 0.017 0 -9999 0 -9999 0 0
CBL 0.017 0 -9999 0 -9999 0 0
MET/RANBP10 0.022 0.03 -9999 0 -0.194 1 1
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.036 0.02 -9999 0 -9999 0 0
MET/MUC20 0.009 0.029 -9999 0 -0.203 1 1
RAP1B 0.037 0.053 -9999 0 -0.303 1 1
RAP1A 0.027 0.082 -9999 0 -0.481 1 1
HGF/MET/RANBP9 0.029 0.035 -9999 0 -9999 0 0
RAF1 0.039 0.031 -9999 0 -9999 0 0
STAT3 0.04 0.019 -9999 0 -9999 0 0
cell proliferation 0.049 0.031 -9999 0 -9999 0 0
RPS6KB1 0.01 0.041 -9999 0 -0.267 1 1
MAPK3 -0.009 0.016 -9999 0 -9999 0 0
MAPK1 0.006 0.117 0.852 1 -9999 0 1
RANBP9 0.017 0 -9999 0 -9999 0 0
MAPK8 0.019 0.134 -9999 0 -0.579 2 2
SRC 0.04 0.019 -9999 0 -9999 0 0
PI3K 0.002 0.079 -9999 0 -0.203 5 5
MET/Glomulin 0.014 0.027 -9999 0 -0.171 1 1
SOS1 0.017 0 -9999 0 -9999 0 0
MAP2K1 0.044 0.029 -9999 0 -9999 0 0
MET 0.012 0.043 -9999 0 -0.3 1 1
MAP4K1 0.031 0.066 -9999 0 -0.391 1 1
PTK2 0.017 0 -9999 0 -9999 0 0
MAP2K2 0.044 0.029 -9999 0 -9999 0 0
BAD 0.025 0.079 0.265 5 -9999 0 5
MAP2K4 0.029 0.073 -9999 0 -0.329 1 1
SHP2/GRB2/SOS1/GAB1 -0.009 0.042 -9999 0 -0.284 1 1
INPPL1 0.01 0.058 -9999 0 -0.411 1 1
PXN 0.017 0 -9999 0 -9999 0 0
SH3KBP1 -0.01 0.099 -9999 0 -0.355 4 4
HGS 0.018 0.03 -9999 0 -0.181 1 1
PLCgamma1/PKC 0.007 0.041 -9999 0 -0.288 1 1
HGF 0.012 0.043 -9999 0 -0.3 1 1
RASA1 0.017 0 -9999 0 -9999 0 0
NCK1 0.01 0.058 -9999 0 -0.411 1 1
PTPRJ 0.012 0.043 -9999 0 -0.3 1 1
NCK/PLCgamma1 0.027 0.057 -9999 0 -0.246 2 2
PDPK1 0.019 0.093 0.31 5 -9999 0 5
HGF/MET/SHIP 0.017 0.035 -9999 0 -0.159 2 2
Aurora A signaling

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
Aurora A/GADD45A -0.01 0.104 -9999 0 -0.257 7 7
BIRC5 -0.004 0.09 -9999 0 -0.374 3 3
NFKBIA 0.017 0.058 -9999 0 -0.22 2 2
CPEB1 0 0.073 -9999 0 -0.3 3 3
AKT1 0.021 0.048 -9999 0 -0.215 1 1
NDEL1 0.017 0 -9999 0 -9999 0 0
Aurora A/BRCA1 0.021 0.043 -9999 0 -0.193 1 1
NDEL1/TACC3 0.012 0.075 -9999 0 -0.227 3 3
GADD45A -0.04 0.139 -9999 0 -0.369 8 8
GSK3B 0.02 0.013 -9999 0 -9999 0 0
PAK1/Aurora A 0.023 0.048 -9999 0 -0.215 1 1
MDM2 0.012 0.043 -9999 0 -0.3 1 1
JUB -0.012 0.106 -9999 0 -0.383 4 4
TPX2 -0.02 0.105 -9999 0 -0.27 8 8
TP53 0.019 0.055 -9999 0 -0.268 1 1
DLG7 -0.005 0.096 -9999 0 -0.279 5 5
AURKAIP1 0.017 0 -9999 0 -9999 0 0
ARHGEF7 0.017 0 -9999 0 -9999 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -9999 0 0
Aurora A/NDEL1/TACC3 0.012 0.079 -9999 0 -0.241 3 3
G2/M transition of mitotic cell cycle 0.02 0.042 -9999 0 -0.192 1 1
AURKA 0.017 0.059 -9999 0 -0.267 1 1
AURKB -0.005 0.091 -9999 0 -0.275 4 4
CDC25B 0.005 0.061 -9999 0 -0.224 2 2
G2/M transition checkpoint 0.005 0.064 -9999 0 -0.198 3 3
mRNA polyadenylation 0.011 0.055 -9999 0 -0.192 1 1
Aurora A/CPEB 0.012 0.055 -9999 0 -0.193 1 1
Aurora A/TACC1/TRAP/chTOG 0.039 0.047 -9999 0 -9999 0 0
BRCA1 0.017 0 -9999 0 -9999 0 0
centrosome duplication 0.023 0.047 -9999 0 -0.215 1 1
regulation of centrosome cycle 0.011 0.074 -9999 0 -0.225 3 3
spindle assembly 0.038 0.046 -9999 0 -9999 0 0
TDRD7 0.017 0 -9999 0 -9999 0 0
Aurora A/RasGAP/Survivin 0.028 0.066 -9999 0 -0.295 1 1
CENPA -0.012 0.113 -9999 0 -0.38 4 4
Aurora A/PP2A 0.023 0.048 -9999 0 -0.215 1 1
meiosis 0 0 -9999 0 -9999 0 0
protein catabolic process 0.013 0.076 -9999 0 -0.252 3 3
negative regulation of DNA binding 0.019 0.055 -9999 0 -0.267 1 1
prophase 0 0 -9999 0 -9999 0 0
GIT1/beta-PIX 0.02 0.041 -9999 0 -0.28 1 1
RASA1 0.017 0 -9999 0 -9999 0 0
Ajuba/Aurora A 0.005 0.065 -9999 0 -0.199 3 3
mitotic prometaphase 0 0.007 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.059 -9999 0 -0.267 1 1
TACC1 0.012 0.043 -9999 0 -0.3 1 1
TACC3 -0.02 0.118 -9999 0 -0.389 5 5
Aurora A/Antizyme1 0.032 0.044 -9999 0 -0.187 1 1
Aurora A/RasGAP 0.023 0.048 -9999 0 -0.215 1 1
OAZ1 0.017 0 -9999 0 -9999 0 0
RAN 0.01 0.058 -9999 0 -0.411 1 1
mitosis 0 0 -9999 0 -9999 0 0
PRKACA 0.02 0.013 -9999 0 -9999 0 0
GIT1 0.01 0.058 -9999 0 -0.411 1 1
GIT1/beta-PIX/PAK1 0.031 0.035 -9999 0 -0.227 1 1
Importin alpha/Importin beta/TPX2 -0.02 0.104 -9999 0 -0.269 8 8
PPP2R5D 0.017 0 -9999 0 -9999 0 0
Aurora A/TPX2 -0.004 0.093 -9999 0 -0.237 6 6
PAK1 0.017 0 -9999 0 -9999 0 0
CKAP5 0.017 0 -9999 0 -9999 0 0
Arf6 downstream 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
PLAUR -0.018 0.208 -9999 0 -0.99 2 2
regulation of axonogenesis -0.017 0.035 -9999 0 -9999 0 0
myoblast fusion 0.006 0.09 0.337 3 -9999 0 3
mol:GTP -0.002 0.048 -9999 0 -0.185 2 2
regulation of calcium-dependent cell-cell adhesion -0.022 0.06 0.208 2 -9999 0 2
ARF1/GTP 0.013 0.037 -9999 0 -0.157 1 1
mol:GM1 0 0.036 -9999 0 -0.165 1 1
mol:Choline 0.018 0.032 -9999 0 -9999 0 0
lamellipodium assembly -0.003 0.095 -9999 0 -0.347 3 3
MAPK3 0.009 0.069 -9999 0 -0.25 2 2
ARF6/GTP/NME1/Tiam1 0.022 0.061 -9999 0 -0.209 2 2
ARF1 0.017 0 -9999 0 -9999 0 0
ARF6/GDP -0.006 0.091 -9999 0 -0.338 3 3
ARF1/GDP 0.004 0.084 -9999 0 -0.305 3 3
ARF6 0.009 0.028 -9999 0 -9999 0 0
RAB11A 0.017 0 -9999 0 -9999 0 0
TIAM1 0.009 0.058 -9999 0 -0.41 1 1
fibronectin binding 0 0 -9999 0 -9999 0 0
MAPK1 0.003 0.094 -9999 0 -0.411 2 2
actin filament bundle formation 0.001 0.1 0.371 3 -9999 0 3
KALRN -0.004 0.081 -9999 0 -0.297 3 3
RAB11FIP3/RAB11A 0.026 0 -9999 0 -9999 0 0
RhoA/GDP -0.001 0.101 -9999 0 -0.374 3 3
NME1 0.017 0.007 -9999 0 -9999 0 0
Rac1/GDP 0.003 0.084 -9999 0 -0.306 3 3
substrate adhesion-dependent cell spreading -0.002 0.048 -9999 0 -0.184 2 2
cortical actin cytoskeleton organization -0.003 0.095 -9999 0 -0.349 3 3
RAC1 0.017 0 -9999 0 -9999 0 0
liver development -0.002 0.048 -9999 0 -0.184 2 2
ARF6/GTP -0.002 0.048 -9999 0 -0.185 2 2
RhoA/GTP 0.008 0.059 -9999 0 -0.248 2 2
mol:GDP -0.006 0.091 -9999 0 -0.34 3 3
ARF6/GTP/RAB11FIP3/RAB11A 0.024 0.034 -9999 0 -9999 0 0
RHOA 0.01 0.058 -9999 0 -0.411 1 1
PLD1 0.011 0.037 -9999 0 -9999 0 0
RAB11FIP3 0.017 0 -9999 0 -9999 0 0
tube morphogenesis -0.003 0.095 -9999 0 -0.347 3 3
ruffle organization 0.017 0.035 -9999 0 -9999 0 0
regulation of epithelial cell migration -0.002 0.048 -9999 0 -0.184 2 2
PLD2 0.011 0.037 -9999 0 -0.157 1 1
PIP5K1A 0.017 0.035 -9999 0 -9999 0 0
mol:Phosphatidic acid 0.018 0.032 -9999 0 -9999 0 0
Rac1/GTP -0.003 0.095 -9999 0 -0.35 3 3
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.004 0.148 -9999 0 -0.421 2 2
CRKL 0.018 0.058 -9999 0 -9999 0 0
mol:DAG 0.015 0.077 -9999 0 -9999 0 0
HRAS 0.03 0.066 -9999 0 -0.236 1 1
MAPK8 0.011 0.062 -9999 0 -0.2 2 2
RAP1A 0.006 0.073 -9999 0 -0.21 1 1
GAB1 0.009 0.075 -9999 0 -0.296 1 1
MAPK14 0.02 0.046 -9999 0 -9999 0 0
EPO 0.011 0.045 -9999 0 -0.31 1 1
PLCG1 0.015 0.078 -9999 0 -9999 0 0
EPOR/TRPC2/IP3 Receptors 0.005 0.061 -9999 0 -0.302 2 2
RAPGEF1 0.017 0 -9999 0 -9999 0 0
EPO/EPOR (dimer)/SOCS3 0.006 0.085 -9999 0 -0.264 4 4
GAB1/SHC/GRB2/SOS1 0.027 0.069 -9999 0 -0.252 1 1
EPO/EPOR (dimer) 0.014 0.054 -9999 0 -0.203 3 3
IRS2 0.002 0.079 -9999 0 -0.235 2 2
STAT1 -0.009 0.127 -9999 0 -0.321 4 4
STAT5B 0.011 0.109 -9999 0 -0.522 1 1
cell proliferation 0.017 0.057 -9999 0 -0.178 2 2
GAB1/SHIP/PIK3R1/SHP2/SHC -0.037 0.068 -9999 0 -0.25 3 3
TEC 0.015 0.06 -9999 0 -9999 0 0
SOCS3 -0.012 0.106 -9999 0 -0.383 4 4
STAT1 (dimer) -0.008 0.126 -9999 0 -0.315 4 4
JAK2 0.006 0.059 -9999 0 -0.294 2 2
PIK3R1 -0.038 0.134 -9999 0 -0.355 8 8
EPO/EPOR (dimer)/JAK2 0.03 0.072 -9999 0 -0.174 2 2
EPO/EPOR 0.014 0.054 -9999 0 -0.203 3 3
LYN 0.01 0.043 -9999 0 -0.298 1 1
TEC/VAV2 0.025 0.061 -9999 0 -9999 0 0
elevation of cytosolic calcium ion concentration 0.005 0.061 -9999 0 -0.301 2 2
SHC1 0.017 0 -9999 0 -9999 0 0
EPO/EPOR (dimer)/LYN 0.024 0.057 -9999 0 -0.172 3 3
mol:IP3 0.015 0.077 -9999 0 -9999 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.015 0.097 -9999 0 -0.224 5 5
SH2B3 0.017 0.006 -9999 0 -9999 0 0
NFKB1 0.02 0.046 -9999 0 -9999 0 0
EPO/EPOR (dimer)/JAK2/SOCS3 -0.005 0.053 -9999 0 -0.181 2 2
PTPN6 0.014 0.057 -9999 0 -0.173 2 2
TEC/VAV2/GRB2 0.032 0.06 -9999 0 -9999 0 0
EPOR 0.005 0.061 -9999 0 -0.302 2 2
INPP5D 0 0 -9999 0 -9999 0 0
mol:GDP 0.026 0.069 -9999 0 -0.256 1 1
SOS1 0.017 0 -9999 0 -9999 0 0
PLCG2 -0.042 0.143 -9999 0 -0.383 8 8
CRKL/CBL/C3G 0.035 0.059 -9999 0 -9999 0 0
VAV2 0.018 0.058 -9999 0 -9999 0 0
CBL 0.018 0.058 -9999 0 -9999 0 0
SHC/Grb2/SOS1 -0.015 0.033 -9999 0 -9999 0 0
STAT5A 0.017 0.086 -9999 0 -0.226 1 1
GRB2 0.017 0 -9999 0 -9999 0 0
STAT5 (dimer) 0.014 0.14 -9999 0 -0.42 2 2
LYN/PLCgamma2 -0.021 0.105 -9999 0 -0.252 9 9
PTPN11 0.017 0 -9999 0 -9999 0 0
BTK 0.011 0.064 -9999 0 -9999 0 0
BCL2 -0.082 0.316 -9999 0 -0.815 8 8
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.005 0.041 -9999 0 -9999 0 0
VDR -0.016 0.106 -9999 0 -0.344 5 5
FAM120B 0.002 0.081 -9999 0 -0.411 2 2
RXRs/LXRs/DNA/9cRA 0.022 0.091 -9999 0 -0.284 1 1
RXRs/LXRs/DNA/Oxysterols 0.021 0.112 -9999 0 -0.335 3 3
MED1 0.017 0 -9999 0 -9999 0 0
mol:9cRA 0.001 0.014 -9999 0 -9999 0 0
RARs/THRs/DNA/Src-1 0.03 0.044 -9999 0 -9999 0 0
RXRs/NUR77 0.031 0.071 -9999 0 -0.229 1 1
RXRs/PPAR -0.038 0.102 -9999 0 -0.228 4 4
NCOR2 0.017 0 -9999 0 -9999 0 0
VDR/VDR/Vit D3 -0.01 0.074 -9999 0 -0.237 5 5
RARs/VDR/DNA/Vit D3 0.017 0.065 -9999 0 -0.185 3 3
RARA 0.017 0 -9999 0 -9999 0 0
NCOA1 0.017 0 -9999 0 -9999 0 0
VDR/VDR/DNA -0.016 0.106 -9999 0 -0.344 5 5
RARs/RARs/DNA/9cRA 0.025 0.038 -9999 0 -0.2 1 1
RARG 0.017 0 -9999 0 -9999 0 0
RPS6KB1 0.005 0.059 -9999 0 -0.391 1 1
RARs/THRs/DNA/SMRT 0.03 0.044 -9999 0 -9999 0 0
THRA 0.01 0.058 -9999 0 -0.411 1 1
mol:Bile acids 0 0 -9999 0 -9999 0 0
VDR/Vit D3/DNA -0.01 0.074 -9999 0 -0.237 5 5
RXRs/PPAR/9cRA/PGJ2/DNA 0.021 0.076 -9999 0 -0.253 1 1
NR1H4 0.01 0.058 -9999 0 -0.411 1 1
RXRs/LXRs/DNA 0.043 0.084 -9999 0 -0.245 1 1
NR1H2 0.019 0.012 -9999 0 -9999 0 0
NR1H3 0.019 0.014 -9999 0 -9999 0 0
RXRs/VDR/DNA/Vit D3 0.011 0.081 -9999 0 -0.215 1 1
NR4A1 0.017 0 -9999 0 -9999 0 0
mol:ATRA 0 0 -9999 0 -9999 0 0
RXRs/FXR/9cRA/MED1 0.014 0.064 -9999 0 -9999 0 0
RXRG -0.005 0.098 -9999 0 -0.406 3 3
RXR alpha/CCPG 0.01 0.071 -9999 0 -0.282 3 3
RXRA 0.011 0.061 -9999 0 -0.426 1 1
RXRB 0.019 0.014 -9999 0 -9999 0 0
THRB 0.017 0 -9999 0 -9999 0 0
PPARG -0.126 0.184 -9999 0 -0.353 21 21
PPARD 0.017 0 -9999 0 -9999 0 0
TNF 0.004 0.175 -9999 0 -0.672 2 2
mol:Oxysterols 0.002 0.012 -9999 0 -9999 0 0
cholesterol transport 0.021 0.111 -9999 0 -0.332 3 3
PPARA 0.017 0 -9999 0 -9999 0 0
mol:Vit D3 0 0 -9999 0 -9999 0 0
RARB 0.004 0.071 -9999 0 -0.355 2 2
RXRs/NUR77/BCL2 -0.021 0.111 -9999 0 -0.314 3 3
SREBF1 0.014 0.163 -9999 0 -0.935 1 1
RXRs/RXRs/DNA/9cRA 0.021 0.076 -9999 0 -0.253 1 1
ABCA1 0.025 0.108 -9999 0 -9999 0 0
RARs/THRs 0.041 0.048 -9999 0 -9999 0 0
RXRs/FXR 0.026 0.077 -9999 0 -0.229 1 1
BCL2 -0.058 0.159 -9999 0 -0.389 10 10
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.017 0 -9999 0 -9999 0 0
NFATC1 0.037 0.057 -9999 0 -9999 0 0
NFATC2 0.017 0.058 -9999 0 -0.213 2 2
NFATC3 0.016 0 -9999 0 -9999 0 0
YWHAE 0.01 0.058 -9999 0 -0.411 1 1
Calcineurin A alpha-beta B1/CABIN1 -0.036 0.109 -9999 0 -0.314 4 4
Exportin 1/Ran/NUP214 0.031 0.035 -9999 0 -0.227 1 1
mol:DAG 0 0 -9999 0 -9999 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.023 0.104 -9999 0 -0.285 4 4
BCL2/BAX -0.027 0.113 -9999 0 -0.263 10 10
CaM/Ca2+/Calcineurin A alpha-beta B1 0.015 0 -9999 0 -9999 0 0
CaM/Ca2+ 0.015 0 -9999 0 -9999 0 0
BAX 0.017 0 -9999 0 -9999 0 0
MAPK14 0.018 0 -9999 0 -9999 0 0
BAD 0.012 0.043 -9999 0 -0.3 1 1
CABIN1/MEF2D -0.026 0.104 -9999 0 -0.328 3 3
Calcineurin A alpha-beta B1/BCL2 -0.058 0.159 -9999 0 -0.388 10 10
FKBP8 0.012 0.043 -9999 0 -0.3 1 1
activation-induced cell death of T cells 0.026 0.103 0.324 3 -9999 0 3
KPNB1 0.017 0 -9999 0 -9999 0 0
KPNA2 0.017 0 -9999 0 -9999 0 0
XPO1 0.018 0 -9999 0 -9999 0 0
SFN -0.057 0.15 -9999 0 -0.35 11 11
MAP3K8 -0.043 0.138 -9999 0 -0.349 9 9
NFAT4/CK1 alpha 0.019 0.055 -9999 0 -0.177 4 4
MEF2D/NFAT1/Cbp/p300 0.051 0.065 -9999 0 -0.237 1 1
CABIN1 -0.037 0.109 -9999 0 -0.317 4 4
CALM1 0.018 0 -9999 0 -9999 0 0
RAN 0.01 0.058 -9999 0 -0.411 1 1
MAP3K1 -0.014 0.112 -9999 0 -0.411 4 4
CAMK4 -0.01 0.099 -9999 0 -0.355 4 4
mol:Ca2+ 0.001 0 -9999 0 -9999 0 0
MAPK3 0.017 0 -9999 0 -9999 0 0
YWHAH 0.017 0 -9999 0 -9999 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.02 0.041 -9999 0 -0.28 1 1
YWHAB 0.017 0 -9999 0 -9999 0 0
MAPK8 0.002 0.081 -9999 0 -0.41 2 2
MAPK9 0.002 0.081 -9999 0 -0.411 2 2
YWHAG 0.017 0 -9999 0 -9999 0 0
FKBP1A 0.017 0 -9999 0 -9999 0 0
NFAT1-c-4/YWHAQ 0.052 0.056 -9999 0 -9999 0 0
PRKCH -0.02 0.118 -9999 0 -0.389 5 5
CABIN1/Cbp/p300 0.022 0.041 -9999 0 -0.279 1 1
CASP3 0.018 0 -9999 0 -9999 0 0
PIM1 0.006 0.06 -9999 0 -0.3 2 2
Calcineurin A alpha-beta B1/FKBP12/FK506 0.013 0 -9999 0 -9999 0 0
apoptosis -0.014 0.04 -9999 0 -0.225 1 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.017 0.057 -9999 0 -9999 0 0
PRKCB 0 0 -9999 0 -9999 0 0
PRKCE 0.004 0.071 -9999 0 -0.355 2 2
JNK2/NFAT4 0.017 0.043 -9999 0 -0.203 2 2
BAD/BCL-XL 0.022 0.03 -9999 0 -0.194 1 1
PRKCD 0.012 0.043 -9999 0 -0.3 1 1
NUP214 0.018 0 -9999 0 -9999 0 0
PRKCZ 0.001 0 -9999 0 -9999 0 0
PRKCA 0.002 0.081 -9999 0 -0.411 2 2
PRKCG 0.017 0 -9999 0 -9999 0 0
PRKCQ -0.079 0.166 -9999 0 -0.355 14 14
FKBP38/BCL2 -0.031 0.121 -9999 0 -0.281 10 10
EP300 0.01 0.058 -9999 0 -0.41 1 1
PRKCB1 -0.024 0.119 -9999 0 -0.355 6 6
CSNK2A1 0.017 0 -9999 0 -9999 0 0
NFATc/JNK1 0.042 0.064 -9999 0 -9999 0 0
CaM/Ca2+/FKBP38 0.022 0.025 -9999 0 -0.159 1 1
FKBP12/FK506 0.013 0 -9999 0 -9999 0 0
CSNK1A1 0.021 0 -9999 0 -9999 0 0
CaM/Ca2+/CAMK IV 0.009 0.059 -9999 0 -0.196 4 4
NFATc/ERK1 0.046 0.055 -9999 0 -9999 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.024 0.103 -9999 0 -0.286 4 4
NR4A1 0.046 0.057 -9999 0 -9999 0 0
GSK3B 0.018 0 -9999 0 -9999 0 0
positive T cell selection 0.016 0 -9999 0 -9999 0 0
NFAT1/CK1 alpha 0.02 0.043 -9999 0 -0.184 1 1
RCH1/ KPNB1 0.026 0 -9999 0 -9999 0 0
YWHAQ 0.017 0 -9999 0 -9999 0 0
PRKACA 0.018 0 -9999 0 -9999 0 0
AKAP5 0.009 0.058 -9999 0 -0.411 1 1
MEF2D 0.018 0 -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 0.046 0.055 -9999 0 -9999 0 0
CREBBP 0.018 0 -9999 0 -9999 0 0
BCL2 -0.058 0.159 -9999 0 -0.389 10 10
FoxO family signaling

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
G6PC 0.046 0.027 -9999 0 -9999 0 0
PLK1 0.033 0.158 -9999 0 -9999 0 0
CDKN1B 0.001 0.2 -9999 0 -0.439 7 7
FOXO3 0.029 0.17 -9999 0 -0.434 3 3
KAT2B 0.005 0.018 -9999 0 -0.045 4 4
FOXO1/SIRT1 0.035 0.033 -9999 0 -9999 0 0
CAT 0.002 0.266 -9999 0 -1.14 2 2
CTNNB1 0.002 0.081 -9999 0 -0.411 2 2
AKT1 0.026 0.019 -9999 0 -9999 0 0
FOXO1 0.041 0.03 -9999 0 -9999 0 0
MAPK10 0.021 0.049 -9999 0 -0.164 2 2
mol:GTP 0.001 0.003 -9999 0 -9999 0 0
FOXO4 0.047 0.135 -9999 0 -0.759 1 1
response to oxidative stress 0.009 0.02 -9999 0 -0.045 3 3
FOXO3A/SIRT1 0.004 0.155 -9999 0 -0.412 3 3
XPO1 0.018 0.001 -9999 0 -9999 0 0
EP300 0.012 0.058 -9999 0 -0.409 1 1
BCL2L11 0.03 0.027 -9999 0 -9999 0 0
FOXO1/SKP2 0.045 0.027 -9999 0 -9999 0 0
mol:GDP 0.009 0.02 -9999 0 -0.045 3 3
RAN 0.01 0.058 -9999 0 -0.413 1 1
GADD45A -0.03 0.305 -9999 0 -0.934 5 5
YWHAQ 0.017 0 -9999 0 -9999 0 0
FOXO1/14-3-3 family 0.048 0.069 -9999 0 -0.285 1 1
MST1 -0.027 0.13 -9999 0 -0.357 7 7
CSNK1D 0.012 0.043 -9999 0 -0.3 1 1
CSNK1E 0.017 0 -9999 0 -9999 0 0
FOXO4/14-3-3 family 0.017 0.088 -9999 0 -9999 0 0
YWHAB 0.017 0 -9999 0 -9999 0 0
MAPK8 0.026 0.048 -9999 0 -0.199 2 2
MAPK9 0.025 0.047 -9999 0 -0.197 2 2
YWHAG 0.017 0 -9999 0 -9999 0 0
YWHAE 0.01 0.058 -9999 0 -0.411 1 1
YWHAZ 0.017 0 -9999 0 -9999 0 0
SIRT1 0.012 0.008 -9999 0 -9999 0 0
SOD2 0.05 0.186 -9999 0 -0.955 1 1
RBL2 0.048 0.132 -9999 0 -9999 0 0
RAL/GDP 0.032 0.017 -9999 0 -9999 0 0
CHUK 0.015 0.06 -9999 0 -0.4 1 1
Ran/GTP 0.01 0.042 -9999 0 -0.292 1 1
CSNK1G2 0.01 0.058 -9999 0 -0.411 1 1
RAL/GTP 0.036 0.022 -9999 0 -9999 0 0
CSNK1G1 0.017 0 -9999 0 -9999 0 0
FASLG 0.004 0.098 -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 0.022 0.018 -9999 0 -9999 0 0
CCNB1 -0.01 0.302 -9999 0 -1.145 3 3
FOXO1-3a-4/beta catenin 0.061 0.144 -9999 0 -0.431 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.045 0.027 -9999 0 -9999 0 0
CSNK1A1 0.017 0 -9999 0 -9999 0 0
SGK1 0.005 0.018 -9999 0 -0.045 4 4
CSNK1G3 0.017 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0.022 0.037 -9999 0 -0.239 1 1
ZFAND5 0.053 0.112 -9999 0 -0.558 1 1
SFN -0.057 0.15 -9999 0 -0.35 11 11
CDK2 0.009 0.06 -9999 0 -0.296 2 2
FOXO3A/14-3-3 0.024 0.088 -9999 0 -9999 0 0
CREBBP 0.021 0.001 -9999 0 -9999 0 0
FBXO32 0.013 0.219 -9999 0 -1.09 1 1
BCL6 0.048 0.132 -9999 0 -9999 0 0
RALB 0.018 0.002 -9999 0 -9999 0 0
RALA 0.018 0.002 -9999 0 -9999 0 0
YWHAH 0.017 0 -9999 0 -9999 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.017 0 -9999 0 -9999 0 0
Rac1/GDP 0.013 0.009 -9999 0 -9999 0 0
DOCK1 0.012 0.043 -9999 0 -0.3 1 1
ITGA4 -0.01 0.099 -9999 0 -0.355 4 4
RAC1 0.017 0 -9999 0 -9999 0 0
alpha4/beta7 Integrin 0.001 0.08 -9999 0 -0.246 5 5
mol:GTP 0 0 -9999 0 -9999 0 0
CRK -0.014 0.112 -9999 0 -0.411 4 4
alpha4/beta1 Integrin 0.019 0.06 -9999 0 -0.227 2 2
alpha4/beta7 Integrin/Paxillin 0.02 0.062 -9999 0 -0.197 3 3
lamellipodium assembly -0.006 0.148 -9999 0 -0.469 4 4
PIK3CA 0.01 0.058 -9999 0 -0.411 1 1
PI3K -0.018 0.112 -9999 0 -0.268 8 8
ARF6 0.017 0 -9999 0 -9999 0 0
TLN1 0.017 0 -9999 0 -9999 0 0
PXN 0.023 0 -9999 0 -9999 0 0
PIK3R1 -0.038 0.134 -9999 0 -0.355 8 8
ARF6/GTP 0.029 0.053 -9999 0 -9999 0 0
cell adhesion 0.033 0.051 -9999 0 -9999 0 0
CRKL/CBL 0.026 0 -9999 0 -9999 0 0
alpha4/beta1 Integrin/Paxillin 0.025 0.054 -9999 0 -0.197 2 2
ITGB1 0.017 0 -9999 0 -9999 0 0
ITGB7 0.01 0.058 -9999 0 -0.411 1 1
ARF6/GDP 0.013 0.009 -9999 0 -9999 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.008 0.092 -9999 0 -0.38 1 1
p130Cas/Crk/Dock1 0.013 0.072 -9999 0 -0.227 4 4
VCAM1 -0.034 0.134 -9999 0 -0.379 7 7
alpha4/beta1 Integrin/Paxillin/Talin 0.035 0.052 -9999 0 -9999 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.03 0.059 -9999 0 -9999 0 0
BCAR1 0.017 0 -9999 0 -9999 0 0
mol:GDP -0.029 0.058 -9999 0 -9999 0 0
CBL 0.017 0 -9999 0 -9999 0 0
PRKACA 0.017 0 -9999 0 -9999 0 0
GIT1 0.01 0.058 -9999 0 -0.411 1 1
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.035 0.052 -9999 0 -9999 0 0
Rac1/GTP -0.011 0.168 -9999 0 -0.534 4 4
Atypical NF-kappaB pathway

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
BCL3/RelA -0.001 0.084 -9999 0 -0.263 5 5
FBXW11 0.017 0 -9999 0 -9999 0 0
NF kappa B1 p50/c-Rel 0.022 0.042 -9999 0 -0.227 1 1
NF kappa B1 p50/RelA/I kappa B alpha 0.022 0.075 -9999 0 -0.375 1 1
NFKBIA -0.002 0.082 -9999 0 -0.222 5 5
MAPK14 0.017 0 -9999 0 -9999 0 0
NF kappa B1 p105/p50 0.03 0 -9999 0 -9999 0 0
ARRB2 0.019 0 -9999 0 -9999 0 0
REL 0.004 0.071 -9999 0 -0.355 2 2
response to oxidative stress 0 0 -9999 0 -9999 0 0
BCL3/NF kappa B1 p50 0.008 0.071 -9999 0 -0.227 4 4
response to UV 0 0 -9999 0 -9999 0 0
NF kappa B1 p105/RelA 0.03 0 -9999 0 -9999 0 0
PIK3CA 0.01 0.058 -9999 0 -0.411 1 1
NF kappa B1 p50 dimer 0.022 0 -9999 0 -9999 0 0
PIK3R1 -0.038 0.134 -9999 0 -0.355 8 8
NFKB1 0.023 0 -9999 0 -9999 0 0
RELA 0.017 0 -9999 0 -9999 0 0
positive regulation of anti-apoptosis 0.01 0.06 -9999 0 -9999 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.026 0.074 -9999 0 -0.364 1 1
SRC 0.017 0 -9999 0 -9999 0 0
PI3K -0.018 0.112 -9999 0 -0.268 8 8
NF kappa B1 p50/RelA 0.01 0.06 -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 -0.012 0.106 -9999 0 -0.383 4 4
I kappa B alpha/PIK3R1 -0.019 0.094 -9999 0 -0.22 5 5
cell death 0.025 0.071 -9999 0 -0.349 1 1
NF kappa B1 p105/c-Rel 0.022 0.042 -9999 0 -0.227 1 1
LCK -0.022 0.113 -9999 0 -0.337 6 6
BCL3 -0.02 0.118 -9999 0 -0.389 5 5
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.024 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 -0.058 0.159 -9999 0 -0.389 10 10
mol:GTP 0 0 -9999 0 -9999 0 0
MAP2K4 0.017 0 -9999 0 -9999 0 0
RAC1-CDC42/GTP/PAK family 0.025 0.017 -9999 0 -9999 0 0
response to UV 0 0 -9999 0 -9999 0 0
YES1 0.017 0 -9999 0 -9999 0 0
interleukin-1 receptor activity 0 0 -9999 0 -9999 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -9999 0 0
MAP3K3 0.017 0 -9999 0 -9999 0 0
FYN -0.006 0.098 -9999 0 -0.411 3 3
MAP3K12 0.004 0.071 -9999 0 -0.355 2 2
FGR 0.017 0 -9999 0 -9999 0 0
p38 alpha/TAB1 0.004 0.1 -9999 0 -0.269 4 4
PRKG1 0.017 0 -9999 0 -9999 0 0
DUSP8 -0.006 0.098 -9999 0 -0.411 3 3
PGK/cGMP/p38 alpha -0.036 0.075 -9999 0 -0.261 4 4
apoptosis 0.003 0.096 -9999 0 -0.259 4 4
RAL/GTP 0.024 0 -9999 0 -9999 0 0
LYN 0.012 0.043 -9999 0 -0.3 1 1
DUSP1 0 0.073 -9999 0 -0.3 3 3
PAK1 0.017 0 -9999 0 -9999 0 0
SRC 0.017 0 -9999 0 -9999 0 0
RAC1/OSM/MEKK3/MKK3 0.041 0.033 -9999 0 -0.197 1 1
TRAF6 0.002 0.081 -9999 0 -0.411 2 2
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 0.024 0 -9999 0 -9999 0 0
MAPK11 -0.016 0.136 -9999 0 -0.359 5 5
BLK 0.004 0.071 -9999 0 -0.355 2 2
HCK -0.018 0.112 -9999 0 -0.366 5 5
MAP2K3 0.01 0.058 -9999 0 -0.411 1 1
DUSP16 0.017 0 -9999 0 -9999 0 0
DUSP10 0.017 0 -9999 0 -9999 0 0
TRAF6/MEKK3 0.014 0.044 -9999 0 -0.211 2 2
MAP3K7IP1 0.017 0 -9999 0 -9999 0 0
MAPK14 -0.003 0.107 -9999 0 -0.295 4 4
positive regulation of innate immune response -0.014 0.149 -9999 0 -0.387 5 5
LCK -0.022 0.113 -9999 0 -0.337 6 6
p38alpha-beta/MKP7 -0.006 0.144 -9999 0 -0.366 5 5
p38alpha-beta/MKP5 -0.006 0.144 -9999 0 -0.366 5 5
PGK/cGMP 0.013 0 -9999 0 -9999 0 0
PAK2 0.017 0 -9999 0 -9999 0 0
p38alpha-beta/MKP1 -0.012 0.147 -9999 0 -0.346 6 6
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 0.006 0.06 -9999 0 -0.3 2 2
TCGA08_rtk_signaling

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
PDGFRA -0.004 0.09 -9999 0 -0.374 3 3
HRAS 0.017 0 -9999 0 -9999 0 0
EGFR -0.01 0.099 -9999 0 -0.355 4 4
AKT 0.043 0.04 -9999 0 -9999 0 0
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 0.012 0.043 -9999 0 -0.3 1 1
PIK3CA 0.01 0.058 -9999 0 -0.411 1 1
PIK3CB 0.004 0.071 -9999 0 -0.355 2 2
NRAS 0.012 0.043 -9999 0 -0.3 1 1
PIK3CG 0.017 0 -9999 0 -9999 0 0
PIK3R3 -0.004 0.09 -9999 0 -0.374 3 3
PIK3R2 0.017 0 -9999 0 -9999 0 0
NF1 0.01 0.058 -9999 0 -0.411 1 1
RAS 0.01 0.055 0.188 1 -9999 0 1
ERBB2 -0.002 0.082 -9999 0 -0.337 3 3
proliferation/survival/translation -0.033 0.043 -9999 0 -9999 0 0
PI3K 0.014 0.071 0.165 4 -0.176 1 5
PIK3R1 -0.038 0.134 -9999 0 -0.355 8 8
KRAS 0.017 0 -9999 0 -9999 0 0
FOXO 0.052 0.041 -9999 0 -9999 0 0
AKT2 0.017 0 -9999 0 -9999 0 0
PTEN -0.022 0.124 -9999 0 -0.411 5 5
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.012 0.121 -9999 0 -0.48 3 3
KLHL20 0.024 0.067 -9999 0 -9999 0 0
CYFIP2 -0.014 0.112 -9999 0 -0.411 4 4
Rac1/GDP 0.026 0.109 -9999 0 -0.469 2 2
ENAH 0.006 0.124 -9999 0 -0.48 3 3
AP1M1 0.017 0 -9999 0 -9999 0 0
RAP1B 0.017 0 -9999 0 -9999 0 0
RAP1A -0.006 0.098 -9999 0 -0.411 3 3
CTNNB1 0.002 0.081 -9999 0 -0.411 2 2
CDC42/GTP -0.023 0.08 -9999 0 -0.403 2 2
ABI1/Sra1/Nap1 -0.019 0.038 -9999 0 -0.178 1 1
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.019 0.086 -9999 0 -0.24 5 5
RAPGEF1 0.012 0.133 -9999 0 -0.504 3 3
CTNND1 0.017 0 -9999 0 -9999 0 0
regulation of calcium-dependent cell-cell adhesion 0.007 0.124 -9999 0 -0.499 3 3
CRK 0.005 0.146 -9999 0 -0.559 3 3
E-cadherin/gamma catenin/alpha catenin 0.031 0.035 -9999 0 -0.227 1 1
alphaE/beta7 Integrin 0.009 0.07 -9999 0 -0.28 3 3
IQGAP1 0.017 0 -9999 0 -9999 0 0
NCKAP1 0.01 0.058 -9999 0 -0.411 1 1
Rap1/GTP/I-afadin 0.021 0.054 -9999 0 -0.204 3 3
DLG1 0.01 0.122 -9999 0 -0.48 3 3
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -9999 0 0
mol:PI-3-4-5-P3 -0.025 0.068 -9999 0 -0.346 2 2
MLLT4 0.017 0 -9999 0 -9999 0 0
ARF6/GTP/NME1/Tiam1 0.029 0.032 -9999 0 -0.204 1 1
PI3K -0.032 0.093 -9999 0 -0.478 2 2
ARF6 0.017 0 -9999 0 -9999 0 0
mol:Ca2+ 0 0 -9999 0 -9999 0 0
E-cadherin/gamma catenin 0.02 0.041 -9999 0 -0.28 1 1
TIAM1 0.01 0.058 -9999 0 -0.411 1 1
E-cadherin(dimer)/Ca2+ 0.029 0.052 -9999 0 -0.185 3 3
AKT1 -0.014 0.05 -9999 0 -0.244 2 2
PIK3R1 -0.038 0.134 -9999 0 -0.355 8 8
CDH1 0.009 0.058 -9999 0 -0.411 1 1
RhoA/GDP 0.024 0.12 -9999 0 -0.533 2 2
actin cytoskeleton organization 0.02 0.051 -9999 0 -9999 0 0
CDC42/GDP 0.026 0.109 -9999 0 -0.469 2 2
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.023 0.03 -9999 0 -0.198 1 1
ITGB7 0.01 0.058 -9999 0 -0.411 1 1
RAC1 0.017 0 -9999 0 -9999 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.031 0.055 -9999 0 -0.197 3 3
E-cadherin/Ca2+/beta catenin/alpha catenin 0.019 0.051 -9999 0 -0.191 3 3
mol:GDP 0.016 0.127 -9999 0 -0.46 3 3
CDC42/GTP/IQGAP1 0.024 0 -9999 0 -9999 0 0
JUP 0.017 0 -9999 0 -9999 0 0
p120 catenin/RhoA/GDP 0.024 0.121 -9999 0 -0.536 2 2
RAC1/GTP/IQGAP1 0.024 0 -9999 0 -9999 0 0
PIP5K1C/AP1M1 0.026 0 -9999 0 -9999 0 0
RHOA 0.01 0.058 -9999 0 -0.411 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 0.008 0.061 -9999 0 -0.148 6 6
NME1 0.017 0 -9999 0 -9999 0 0
clathrin coat assembly 0 0 -9999 0 -9999 0 0
TJP1 0.012 0.121 -9999 0 -0.48 3 3
regulation of cell-cell adhesion -0.02 0.069 -9999 0 -0.347 2 2
WASF2 -0.008 0.022 -9999 0 -9999 0 0
Rap1/GTP 0.02 0.107 -9999 0 -0.469 2 2
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.035 0.06 -9999 0 -9999 0 0
CCND1 0.008 0.074 -9999 0 -0.181 6 6
VAV2 0.021 0.118 -9999 0 -0.514 2 2
RAP1/GDP 0.021 0.115 -9999 0 -0.504 2 2
adherens junction assembly 0.013 0.117 -9999 0 -0.464 3 3
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 0.03 0.078 -9999 0 -0.359 1 1
E-cadherin/beta catenin 0.009 0.044 -9999 0 -0.299 1 1
mol:GTP 0 0 -9999 0 -9999 0 0
SRC 0.012 0.121 -9999 0 -0.48 3 3
PIK3CA 0.01 0.058 -9999 0 -0.411 1 1
Rac1/GTP -0.032 0.072 -9999 0 -0.269 2 2
E-cadherin/beta catenin/alpha catenin 0.021 0.06 -9999 0 -0.227 3 3
ITGAE 0.002 0.081 -9999 0 -0.411 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.006 0.127 -9999 0 -0.511 3 3
Regulation of Telomerase

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
Telomerase catalytic core complex -0.023 0.139 -9999 0 -0.497 1 1
RAD9A 0.017 0 -9999 0 -9999 0 0
AP1 -0.07 0.143 -9999 0 -0.268 18 18
IFNAR2 0.018 0.005 -9999 0 -9999 0 0
AKT1 -0.027 0.088 -9999 0 -0.25 2 2
ER alpha/Oestrogen -0.069 0.133 -9999 0 -0.282 15 15
NFX1/SIN3/HDAC complex 0.041 0.033 -9999 0 -9999 0 0
EGF -0.017 0.1 -9999 0 -0.3 6 6
SMG5 0.017 0 -9999 0 -9999 0 0
SMG6 0.017 0 -9999 0 -9999 0 0
SP3/HDAC2 0.028 0.008 -9999 0 -9999 0 0
TERT/c-Abl -0.013 0.132 -9999 0 -0.463 1 1
SAP18 0.018 0.001 -9999 0 -9999 0 0
MRN complex 0.026 0.05 -9999 0 -0.227 2 2
WT1 -0.098 0.175 -9999 0 -0.352 17 17
WRN 0.017 0 -9999 0 -9999 0 0
SP1 0.019 0.007 -9999 0 -9999 0 0
SP3 0.018 0.002 -9999 0 -9999 0 0
TERF2IP 0.017 0 -9999 0 -9999 0 0
Telomerase/Nucleolin -0.042 0.104 -9999 0 -0.419 1 1
Mad/Max 0.027 0.007 -9999 0 -9999 0 0
TERT -0.024 0.141 -9999 0 -0.507 1 1
CCND1 -0.057 0.266 -9999 0 -1.054 3 3
MAX 0.018 0.002 -9999 0 -9999 0 0
RBBP7 -0.008 0.091 -9999 0 -0.327 4 4
RBBP4 0.018 0.001 -9999 0 -9999 0 0
TERF2 0.016 0 -9999 0 -9999 0 0
PTGES3 0.017 0 -9999 0 -9999 0 0
SIN3A 0.018 0.001 -9999 0 -9999 0 0
Telomerase/911 0.022 0.081 -9999 0 -0.486 1 1
CDKN1B -0.071 0.197 -9999 0 -0.468 9 9
RAD1 0.01 0.058 -9999 0 -0.411 1 1
XRCC5 0.017 0 -9999 0 -9999 0 0
XRCC6 0.017 0 -9999 0 -9999 0 0
SAP30 0.018 0.001 -9999 0 -9999 0 0
TRF2/PARP2 0.026 0 -9999 0 -9999 0 0
UBE3A 0.018 0.002 -9999 0 -9999 0 0
JUN -0.025 0.124 -9999 0 -0.374 6 6
E6 0 0.002 -9999 0 -9999 0 0
HPV-16 E6/E6AP 0.014 0.005 -9999 0 -9999 0 0
FOS -0.079 0.166 -9999 0 -0.356 14 14
IFN-gamma/IRF1 -0.049 0.139 -9999 0 -0.328 7 7
PARP2 0.017 0 -9999 0 -9999 0 0
BLM -0.022 0.124 -9999 0 -0.411 5 5
Telomerase 0.023 0.086 -9999 0 -0.345 2 2
IRF1 -0.004 0.065 -9999 0 -0.292 1 1
ESR1 -0.099 0.189 -9999 0 -0.403 15 15
KU/TER 0.026 0 -9999 0 -9999 0 0
ATM/TRF2 0.027 0 -9999 0 -9999 0 0
ubiquitin-dependent protein catabolic process 0.047 0.03 -9999 0 -9999 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.047 0.031 -9999 0 -9999 0 0
HDAC1 0.018 0.001 -9999 0 -9999 0 0
HDAC2 0.019 0.006 -9999 0 -9999 0 0
ATM 0 0 -9999 0 -9999 0 0
SMAD3 0.013 0.05 -9999 0 -0.239 2 2
ABL1 0.017 0 -9999 0 -9999 0 0
MXD1 0.018 0.002 -9999 0 -9999 0 0
MRE11A 0.017 0 -9999 0 -9999 0 0
HUS1 0.017 0 -9999 0 -9999 0 0
RPS6KB1 0.01 0.058 -9999 0 -0.411 1 1
TERT/NF kappa B1/14-3-3 -0.018 0.135 -9999 0 -9999 0 0
NR2F2 -0.015 0.112 -9999 0 -0.41 4 4
MAPK3 0.019 0.041 -9999 0 -0.278 1 1
MAPK1 0.013 0.057 -9999 0 -0.279 2 2
TGFB1/TGF beta receptor Type II 0.017 0.001 -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 0.01 0.058 -9999 0 -0.411 1 1
EGFR -0.01 0.099 -9999 0 -0.354 4 4
mol:Oestrogen 0 0.001 -9999 0 -9999 0 0
EGF/EGFR -0.017 0.093 -9999 0 -0.211 10 10
MYC 0.012 0.043 -9999 0 -0.298 1 1
IL2 0.011 0.058 -9999 0 -0.408 1 1
KU 0.026 0 -9999 0 -9999 0 0
RAD50 0.01 0.058 -9999 0 -0.411 1 1
HSP90AA1 0.002 0.081 -9999 0 -0.411 2 2
TGFB1 0.017 0.001 -9999 0 -9999 0 0
TRF2/BLM -0.001 0.082 -9999 0 -0.257 5 5
FRAP1 0.017 0 -9999 0 -9999 0 0
KU/TERT -0.006 0.133 -9999 0 -0.459 1 1
SP1/HDAC2 0.029 0.012 -9999 0 -9999 0 0
PINX1 0.01 0.058 -9999 0 -0.411 1 1
Telomerase/EST1A -0.042 0.104 -9999 0 -0.419 1 1
Smad3/Myc 0.019 0.058 -9999 0 -0.271 2 2
911 complex 0.031 0.035 -9999 0 -0.227 1 1
IFNG -0.064 0.142 -9999 0 -0.322 11 11
Telomerase/PinX1 -0.045 0.105 -9999 0 -0.419 1 1
Telomerase/AKT1/mTOR/p70S6K 0.001 0.091 -9999 0 -0.3 3 3
SIN3B 0.018 0.001 -9999 0 -9999 0 0
YWHAE 0.01 0.058 -9999 0 -0.411 1 1
Telomerase/EST1B -0.042 0.104 -9999 0 -0.419 1 1
response to DNA damage stimulus 0.004 0 -9999 0 -9999 0 0
MRN complex/TRF2/Rap1 0.042 0.042 -9999 0 -9999 0 0
TRF2/WRN 0.026 0 -9999 0 -9999 0 0
Telomerase/hnRNP C1/C2 -0.042 0.104 -9999 0 -0.419 1 1
E2F1 -0.009 0.099 -9999 0 -0.354 4 4
ZNFX1 0.018 0.001 -9999 0 -9999 0 0
PIF1 0.017 0 -9999 0 -9999 0 0
NCL 0.017 0 -9999 0 -9999 0 0
DKC1 0.006 0.06 -9999 0 -0.3 2 2
telomeric DNA binding 0 0 -9999 0 -9999 0 0
Insulin Pathway

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
CBL/APS/CAP -0.018 0.054 -9999 0 -0.179 5 5
TC10/GTP -0.019 0.05 -9999 0 -9999 0 0
Insulin Receptor/Insulin/IRS1/Shp2 0.025 0.069 -9999 0 -0.202 4 4
HRAS 0.017 0 -9999 0 -9999 0 0
APS homodimer 0 0 -9999 0 -9999 0 0
GRB14 -0.099 0.174 -9999 0 -0.352 17 17
FOXO3 0.001 0.025 -9999 0 -9999 0 0
AKT1 -0.04 0.106 -9999 0 -0.266 5 5
INSR 0.019 0.005 -9999 0 -9999 0 0
Insulin Receptor/Insulin 0.047 0.045 -9999 0 -0.28 1 1
mol:GTP 0 0 -9999 0 -9999 0 0
GRB10 -0.02 0.118 -9999 0 -0.389 5 5
SORBS1 0.006 0.06 -9999 0 -0.3 2 2
CRK -0.014 0.112 -9999 0 -0.411 4 4
PTPN1 0.031 0.042 -9999 0 -0.278 1 1
CAV1 0.014 0.06 -9999 0 -0.186 4 4
CBL/APS/CAP/Crk-II/C3G 0.019 0.065 -9999 0 -0.185 4 4
Insulin Receptor/Insulin/IRS1/NCK2 0.025 0.069 -9999 0 -0.202 4 4
mol:GDP 0 0 -9999 0 -9999 0 0
mol:PI-3-4-5-P3 -0.01 0.09 -9999 0 -0.363 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.029 0.052 -9999 0 -9999 0 0
RPS6KB1 -0.035 0.105 -9999 0 -0.252 6 6
PARD6A -0.004 0.09 -9999 0 -0.374 3 3
CBL 0.017 0 -9999 0 -9999 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -9999 0 0
DOK1 0.007 0.021 -9999 0 -9999 0 0
PIK3R1 -0.038 0.134 -9999 0 -0.355 8 8
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.061 0.08 -9999 0 -0.245 6 6
HRAS/GTP -0.012 0.038 -9999 0 -9999 0 0
Insulin Receptor 0.019 0.005 -9999 0 -9999 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.034 0.065 -9999 0 -0.18 4 4
PRKCI -0.02 0.058 -9999 0 -0.391 1 1
Insulin Receptor/Insulin/GRB14/PDK1 -0.074 0.091 -9999 0 -0.287 5 5
SHC1 0.017 0 -9999 0 -9999 0 0
negative regulation of MAPKKK cascade 0.033 0.032 -9999 0 -9999 0 0
PI3K -0.004 0.095 -9999 0 -0.368 1 1
NCK2 0.017 0 -9999 0 -9999 0 0
RHOQ 0.01 0.058 -9999 0 -0.411 1 1
mol:H2O2 -0.001 0.005 -9999 0 -9999 0 0
HRAS/GDP 0.013 0 -9999 0 -9999 0 0
AKT2 -0.04 0.106 -9999 0 -0.266 5 5
PRKCZ -0.026 0.058 -9999 0 -0.397 1 1
SH2B2 0 0 -9999 0 -9999 0 0
SHC/SHIP 0.013 0.057 -9999 0 -0.175 4 4
F2RL2 0.012 0.043 -9999 0 -0.3 1 1
TRIP10 0.012 0.043 -9999 0 -0.3 1 1
Insulin Receptor/Insulin/Shc 0.035 0.007 -9999 0 -9999 0 0
TC10/GTP/CIP4/Exocyst 0.016 0.042 -9999 0 -0.197 2 2
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.054 0.004 -9999 0 -9999 0 0
RAPGEF1 0.017 0 -9999 0 -9999 0 0
RASA1 0.017 0 -9999 0 -9999 0 0
NCK1 0.01 0.058 -9999 0 -0.411 1 1
CBL/APS/CAP/Crk-II 0.01 0.068 -9999 0 -0.204 4 4
TC10/GDP 0.007 0.041 -9999 0 -0.288 1 1
Insulin Receptor/Insulin/SHC/GRB10 0.025 0.069 -9999 0 -0.202 4 4
INPP5D 0.002 0.059 -9999 0 -0.192 4 4
SOS1 0.017 0 -9999 0 -9999 0 0
SGK1 -0.008 0.01 -9999 0 -9999 0 0
mol:cAMP 0 0 -9999 0 -9999 0 0
PTPN11 0.017 0 -9999 0 -9999 0 0
IRS1 -0.02 0.118 -9999 0 -0.389 5 5
p62DOK/RasGAP 0.033 0.032 -9999 0 -9999 0 0
INS 0.019 0.005 -9999 0 -9999 0 0
mol:PI-3-4-P2 0.002 0.058 -9999 0 -0.191 4 4
GRB2 0.017 0 -9999 0 -9999 0 0
EIF4EBP1 -0.037 0.106 -9999 0 -0.266 5 5
PTPRA 0.019 0.005 -9999 0 -9999 0 0
PIK3CA 0.01 0.058 -9999 0 -0.411 1 1
TC10/GTP/CIP4 0.016 0.042 -9999 0 -0.197 2 2
PDPK1 0.017 0 -9999 0 -9999 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.023 0.059 -9999 0 -9999 0 0
Insulin Receptor/Insulin/IRS1 0.014 0.068 -9999 0 -0.209 4 4
Insulin Receptor/Insulin/IRS3 0.028 0.008 -9999 0 -9999 0 0
Par3/Par6 0.02 0.062 -9999 0 -0.184 3 3
S1P3 pathway

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
PDGFRB 0.002 0.081 -9999 0 -0.411 2 2
mol:S1P 0.002 0 -9999 0 -9999 0 0
S1P1/S1P/Gi -0.022 0.13 -9999 0 -0.448 3 3
GNAO1 0.019 0 -9999 0 -9999 0 0
S1P/S1P3/G12/G13 0.026 0 -9999 0 -9999 0 0
AKT1 0.003 0.087 -9999 0 -0.388 2 2
AKT3 0.001 0.089 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
PDGFB-D/PDGFRB 0.002 0.081 -9999 0 -0.41 2 2
GNAI2 0.019 0 -9999 0 -9999 0 0
GNAI3 0.011 0.058 -9999 0 -0.41 1 1
GNAI1 -0.048 0.152 -9999 0 -0.385 9 9
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 -0.012 0.106 -9999 0 -0.383 4 4
mol:Ca2+ -0.004 0.106 -9999 0 -0.425 2 2
MAPK3 0.002 0.101 -9999 0 -0.4 2 2
MAPK1 -0.002 0.117 -9999 0 -0.496 2 2
JAK2 -0.012 0.108 -9999 0 -0.318 4 4
CXCR4 -0.027 0.121 -9999 0 -0.355 4 4
FLT1 -0.011 0.113 -9999 0 -0.41 4 4
RhoA/GDP 0.007 0.041 -9999 0 -0.288 1 1
Rac1/GDP 0.013 0 -9999 0 -9999 0 0
SRC 0.002 0.101 -9999 0 -0.4 2 2
S1P/S1P3/Gi -0.005 0.107 -9999 0 -0.429 2 2
RAC1 0.017 0 -9999 0 -9999 0 0
RhoA/GTP 0.001 0.114 -9999 0 -0.48 2 2
VEGFA -0.003 0.099 -9999 0 -0.41 3 3
S1P/S1P2/Gi -0.009 0.106 -9999 0 -0.432 2 2
VEGFR1 homodimer/VEGFA homodimer -0.005 0.116 -9999 0 -0.32 6 6
RHOA 0.01 0.058 -9999 0 -0.411 1 1
S1P/S1P3/Gq 0.014 0.036 -9999 0 -0.204 1 1
GNAQ 0 0 -9999 0 -9999 0 0
GNAZ -0.009 0.099 -9999 0 -0.354 4 4
G12/G13 0.026 0 -9999 0 -9999 0 0
GNA14 0.004 0.071 -9999 0 -0.355 2 2
GNA15 0.012 0.043 -9999 0 -0.3 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 0.004 0.098 -9999 0 -0.387 2 2
Angiopoietin receptor Tie2-mediated 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
AKT1 0.01 0.182 -9999 0 -0.85 1 1
NCK1/PAK1/Dok-R -0.032 0.087 -9999 0 -0.412 2 2
NCK1/Dok-R 0.03 0.166 -9999 0 -0.763 2 2
PIK3CA 0.009 0.058 -9999 0 -0.41 1 1
mol:beta2-estradiol -0.009 0.015 -9999 0 -9999 0 0
RELA 0.017 0 -9999 0 -9999 0 0
SHC1 0.018 0.002 -9999 0 -9999 0 0
Rac/GDP 0.013 0 -9999 0 -9999 0 0
F2 0.001 0.047 -9999 0 -0.316 1 1
TNIP2 0.017 0 -9999 0 -9999 0 0
NF kappa B/RelA 0.045 0.138 -9999 0 -0.843 1 1
FN1 0 0.073 -9999 0 -0.3 3 3
PLD2 0.03 0.146 -9999 0 -0.928 1 1
PTPN11 0.017 0 -9999 0 -9999 0 0
GRB14 -0.099 0.174 -9999 0 -0.352 17 17
ELK1 0.035 0.144 -9999 0 -0.864 1 1
GRB7 0 0.073 -9999 0 -0.3 3 3
PAK1 0.017 0 -9999 0 -9999 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0.038 0.145 -9999 0 -0.872 1 1
CDKN1A -0.019 0.273 -9999 0 -0.76 6 6
ITGA5 0.017 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
RasGAP/Dok-R 0.033 0.153 -9999 0 -0.895 1 1
CRK -0.014 0.112 -9999 0 -0.411 4 4
mol:NO 0.019 0.149 -9999 0 -0.516 2 2
PLG 0.025 0.148 -9999 0 -0.928 1 1
mol:GDP 0 0 -9999 0 -9999 0 0
chemokinesis 0.025 0.163 -9999 0 -0.805 1 1
GRB2 0.017 0 -9999 0 -9999 0 0
PIK3R1 -0.038 0.134 -9999 0 -0.355 8 8
ANGPT2 0.008 0.178 -9999 0 -1.205 1 1
BMX 0.008 0.157 -9999 0 -0.928 1 1
ANGPT1 0.021 0.063 -9999 0 -9999 0 0
tube development 0.004 0.2 -9999 0 -0.754 2 2
ANGPT4 0.018 0.002 -9999 0 -9999 0 0
response to hypoxia 0.002 0.011 -9999 0 -9999 0 0
Tie2/Ang1/GRB14 -0.022 0.159 -9999 0 -0.942 1 1
alpha5/beta1 Integrin 0.026 0 -9999 0 -9999 0 0
FGF2 0.005 0.06 -9999 0 -0.3 2 2
STAT5A (dimer) -0.001 0.259 -9999 0 -0.83 3 3
mol:L-citrulline 0.019 0.149 -9999 0 -0.516 2 2
AGTR1 0.012 0.043 -9999 0 -0.298 1 1
MAPK14 0.025 0.17 -9999 0 -1.06 1 1
Tie2/SHP2 0.007 0.166 -9999 0 -0.698 2 2
TEK 0 0.183 -9999 0 -0.773 2 2
RPS6KB1 0.011 0.176 -9999 0 -0.819 1 1
Angiotensin II/AT1 0.012 0.03 -9999 0 -0.2 1 1
Tie2/Ang1/GRB2 0.03 0.149 -9999 0 -0.942 1 1
MAPK3 0.034 0.138 -9999 0 -0.865 1 1
MAPK1 0.031 0.147 -9999 0 -0.865 1 1
Tie2/Ang1/GRB7 0.022 0.153 -9999 0 -0.942 1 1
NFKB1 0.017 0 -9999 0 -9999 0 0
MAPK8 0.023 0.157 -9999 0 -0.928 1 1
PI3K 0.006 0.19 -9999 0 -0.966 1 1
FES -0.001 0.187 -9999 0 -1.05 1 1
Crk/Dok-R 0.019 0.175 -9999 0 -0.763 2 2
Tie2/Ang1/ABIN2 0.03 0.149 -9999 0 -0.942 1 1
blood circulation 0 0 -9999 0 -9999 0 0
negative regulation of caspase activity 0.013 0.169 -9999 0 -0.761 1 1
STAT5A 0.017 0.002 -9999 0 -9999 0 0
mol:ROS 0 0 -9999 0 -9999 0 0
PTK2 0.014 0.17 -9999 0 -0.819 1 1
Tie2/Ang2 -0.005 0.259 -9999 0 -1.099 2 2
Tie2/Ang1 0.026 0.154 -9999 0 -0.988 1 1
FOXO1 0.013 0.181 -9999 0 -0.684 2 2
ELF1 -0.007 0.114 -9999 0 -0.407 4 4
ELF2 0.029 0.146 -9999 0 -0.942 1 1
mol:Choline 0.03 0.142 -9999 0 -0.897 1 1
cell migration -0.017 0.046 -9999 0 -0.215 2 2
FYN -0.001 0.224 -9999 0 -0.878 2 2
DOK2 0.004 0.071 -9999 0 -0.355 2 2
negative regulation of cell cycle -0.011 0.245 -9999 0 -0.674 6 6
ETS1 0.02 0.045 -9999 0 -0.29 1 1
PXN 0.022 0.151 -9999 0 -0.678 1 1
ITGB1 0.017 0 -9999 0 -9999 0 0
NOS3 0.016 0.163 -9999 0 -0.718 1 1
RAC1 0.017 0 -9999 0 -9999 0 0
TNF -0.011 0.109 -9999 0 -0.314 6 6
MAPKKK cascade 0.03 0.142 -9999 0 -0.897 1 1
RASA1 0.017 0 -9999 0 -9999 0 0
Tie2/Ang1/Shc 0.031 0.15 -9999 0 -0.945 1 1
NCK1 0.01 0.058 -9999 0 -0.411 1 1
vasculogenesis 0.021 0.139 -9999 0 -0.467 2 2
mol:Phosphatidic acid 0.03 0.142 -9999 0 -0.897 1 1
mol:Angiotensin II 0.001 0.005 -9999 0 -9999 0 0
mol:NADP 0.019 0.149 -9999 0 -0.516 2 2
Rac1/GTP 0.01 0.159 -9999 0 -0.765 1 1
MMP2 -0.002 0.159 -9999 0 -0.928 1 1
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.012 0.043 -9999 0 -0.3 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 0.022 0.046 -9999 0 -0.226 1 1
HIF1A 0.016 0.031 -9999 0 -9999 0 0
COPS5 0.01 0.058 -9999 0 -0.411 1 1
VHL/Elongin B/Elongin C/RBX1/CUL2 0.049 0.022 -9999 0 -9999 0 0
FIH (dimer) 0.017 0 -9999 0 -9999 0 0
CDKN2A -0.132 0.177 -9999 0 -0.333 23 23
ARNT/IPAS 0.022 0.03 -9999 0 -0.194 1 1
HIF1AN 0.017 0 -9999 0 -9999 0 0
GNB2L1 0.01 0.058 -9999 0 -0.411 1 1
HIF1A/ARNT 0.026 0.032 -9999 0 -9999 0 0
CUL2 0.012 0.043 -9999 0 -0.3 1 1
OS9 0.017 0 -9999 0 -9999 0 0
RACK1/Elongin B/Elongin C 0.031 0.035 -9999 0 -0.227 1 1
response to hypoxia 0 0 -9999 0 -9999 0 0
HIF1A/Hsp90 0.018 0.047 -9999 0 -9999 0 0
PHD1-3/OS9 -0.004 0.109 -9999 0 -0.242 8 8
HIF1A/RACK1/Elongin B/Elongin C 0.036 0.045 -9999 0 -9999 0 0
VHL 0.017 0 -9999 0 -9999 0 0
HSP90AA1 0.002 0.081 -9999 0 -0.411 2 2
HIF1A/JAB1 0.022 0.04 -9999 0 -9999 0 0
EGLN3 -0.058 0.159 -9999 0 -0.389 10 10
EGLN2 0.01 0.058 -9999 0 -0.411 1 1
EGLN1 0.012 0.043 -9999 0 -0.3 1 1
TP53 0.01 0.058 -9999 0 -0.411 1 1
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.04 0.017 -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 -0.041 0.088 -9999 0 -9999 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.021 0.042 -9999 0 -0.191 1 1
MAPK9 -0.002 0.056 -9999 0 -0.285 2 2
adrenocorticotropin secretion -0.004 0.056 -9999 0 -0.203 4 4
GNB1/GNG2 0.017 0.035 -9999 0 -0.159 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 0.009 0 -9999 0 -9999 0 0
Gs family/GTP 0.007 0.031 -9999 0 -0.217 1 1
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 0.001 0.008 0.061 1 -9999 0 1
GNAL 0.01 0.058 -9999 0 -0.411 1 1
GNG2 0.006 0.06 -9999 0 -0.3 2 2
CRH -0.006 0.083 -9999 0 -0.3 4 4
mol:cortisol 0 0 -9999 0 -9999 0 0
MAPK8 -0.002 0.056 -9999 0 -0.285 2 2
MAPK11 0.009 0 -9999 0 -9999 0 0
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.017 0 -9999 0 -9999 0 0
RAS family/GTP/Tiam1 0.024 0.038 -9999 0 -9999 0 0
NT3 (dimer)/TRKC 0.01 0.058 -9999 0 -0.194 4 4
NT3 (dimer)/TRKB -0.003 0.076 -9999 0 -9999 0 0
SHC/Grb2/SOS1/GAB1/PI3K 0.002 0.112 -9999 0 -0.691 1 1
RAPGEF1 0.017 0 -9999 0 -9999 0 0
BDNF -0.065 0.157 -9999 0 -0.355 12 12
PIK3CA 0.01 0.058 -9999 0 -0.411 1 1
DYNLT1 0.017 0 -9999 0 -9999 0 0
NTRK1 -0.004 0.09 -9999 0 -0.374 3 3
NTRK2 -0.018 0.1 -9999 0 -0.3 6 6
NTRK3 0.012 0.043 -9999 0 -0.3 1 1
NT-4/5 (dimer)/TRKB -0.003 0.065 -9999 0 -0.159 8 8
neuron apoptosis 0.048 0.108 0.327 3 -9999 0 3
SHC 2-3/Grb2 -0.052 0.115 -9999 0 -0.354 3 3
SHC1 0.017 0 -9999 0 -9999 0 0
SHC2 -0.039 0.096 -9999 0 -0.45 1 1
SHC3 -0.05 0.12 -9999 0 -0.439 3 3
STAT3 (dimer) -0.009 0.114 -9999 0 -0.374 4 4
NT3 (dimer)/TRKA 0.006 0.083 -9999 0 -0.305 2 2
RIN/GDP 0.041 0.039 -9999 0 -9999 0 0
GIPC1 0.017 0 -9999 0 -9999 0 0
KRAS 0.017 0 -9999 0 -9999 0 0
DNAJA3 -0.007 0.068 0.21 1 -0.206 1 2
RIN/GTP 0.013 0 -9999 0 -9999 0 0
CCND1 -0.028 0.182 -9999 0 -0.636 4 4
MAGED1 0.01 0.058 -9999 0 -0.411 1 1
PTPN11 0.017 0 -9999 0 -9999 0 0
RICS 0.01 0.058 -9999 0 -0.411 1 1
NT-4/5 (dimer) 0 0 -9999 0 -9999 0 0
SHC/GRB2/SOS1 0.036 0 -9999 0 -9999 0 0
GRB2 0.017 0 -9999 0 -9999 0 0
NGF (dimer)/TRKA/MATK 0.003 0.08 -9999 0 -0.253 4 4
TRKA/NEDD4-2 -0.001 0.084 -9999 0 -0.263 5 5
ELMO1 0.012 0.043 -9999 0 -0.3 1 1
RhoG/GTP/ELMO1/DOCK1 0.017 0.035 -9999 0 -0.159 2 2
NGF 0 0 -9999 0 -9999 0 0
HRAS 0.017 0 -9999 0 -9999 0 0
DOCK1 0.012 0.043 -9999 0 -0.3 1 1
GAB2 0.017 0 -9999 0 -9999 0 0
RIT2 0.017 0 -9999 0 -9999 0 0
RIT1 0.017 0 -9999 0 -9999 0 0
FRS2 0.017 0 -9999 0 -9999 0 0
DNM1 0.01 0.058 -9999 0 -0.411 1 1
mol:GTP 0 0 -9999 0 -9999 0 0
CRK -0.014 0.112 -9999 0 -0.411 4 4
SH2B1 (homopentamer) 0 0 -9999 0 -9999 0 0
RhoG/GTP -0.006 0.072 0.199 1 -0.211 2 3
mol:GDP 0.044 0.05 -9999 0 -9999 0 0
NGF (dimer) 0 0 -9999 0 -9999 0 0
RhoG/GDP 0.009 0.029 -9999 0 -0.203 1 1
RIT1/GDP 0.041 0.039 -9999 0 -9999 0 0
TIAM1 0.01 0.058 -9999 0 -0.411 1 1
PIK3R1 -0.038 0.134 -9999 0 -0.355 8 8
BDNF (dimer)/TRKB -0.035 0.102 -9999 0 -0.227 6 6
KIDINS220/CRKL/C3G 0.026 0 -9999 0 -9999 0 0
SHC/RasGAP 0.026 0 -9999 0 -9999 0 0
FRS2 family/SHP2 0.036 0 -9999 0 -9999 0 0
SHC/GRB2/SOS1/GAB1 0.034 0.046 -9999 0 -0.197 1 1
RIT1/GTP 0.013 0 -9999 0 -9999 0 0
NT3 (dimer) 0 0.073 -9999 0 -0.299 3 3
RAP1/GDP -0.008 0.031 -9999 0 -0.154 1 1
KIDINS220/CRKL 0.017 0 -9999 0 -9999 0 0
BDNF (dimer) -0.065 0.157 -9999 0 -0.355 12 12
ubiquitin-dependent protein catabolic process 0.001 0.071 -9999 0 -0.218 5 5
Schwann cell development -0.013 0.016 -9999 0 -9999 0 0
EHD4 0.017 0 -9999 0 -9999 0 0
FRS2 family/GRB2/SOS1 0.045 0 -9999 0 -9999 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.028 0.052 -9999 0 -9999 0 0
RAP1B 0.017 0 -9999 0 -9999 0 0
RAP1A -0.006 0.098 -9999 0 -0.411 3 3
CDC42/GTP -0.024 0.083 -9999 0 -0.276 1 1
ABL1 0.017 0 -9999 0 -9999 0 0
SH2B family/GRB2/SOS1 0.026 0 -9999 0 -9999 0 0
Rap1/GTP 0.003 0.094 -9999 0 -0.378 2 2
STAT3 -0.009 0.114 -9999 0 -0.374 4 4
axon guidance -0.048 0.062 -9999 0 -0.267 1 1
MAPK3 0.008 0.072 -9999 0 -0.308 2 2
MAPK1 0.003 0.077 -9999 0 -0.273 3 3
CDC42/GDP 0.041 0.039 -9999 0 -9999 0 0
NTF3 0 0.073 -9999 0 -0.3 3 3
NTF4 0 0 -9999 0 -9999 0 0
NGF (dimer)/TRKA/FAIM 0.006 0.063 -9999 0 -0.215 4 4
PI3K -0.018 0.112 -9999 0 -0.268 8 8
FRS3 0.017 0 -9999 0 -9999 0 0
FAIM 0.01 0.058 -9999 0 -0.411 1 1
GAB1 -0.002 0.082 -9999 0 -0.337 3 3
RASGRF1 -0.036 0.091 0.21 1 -0.204 5 6
SOS1 0.017 0 -9999 0 -9999 0 0
MCF2L 0.006 0.075 -9999 0 -0.305 2 2
RGS19 0.017 0 -9999 0 -9999 0 0
CDC42 0.017 0 -9999 0 -9999 0 0
RAS family/GTP 0.037 0.04 -9999 0 -9999 0 0
Rac1/GDP 0.041 0.039 -9999 0 -9999 0 0
NGF (dimer)/TRKA/GRIT 0.006 0.063 -9999 0 -0.215 4 4
neuron projection morphogenesis -0.02 0.152 -9999 0 -0.971 1 1
NGF (dimer)/TRKA/NEDD4-2 0.001 0.071 -9999 0 -0.219 5 5
MAP2K1 0.028 0.04 -9999 0 -9999 0 0
NGFR 0.006 0.06 -9999 0 -0.3 2 2
NGF (dimer)/TRKA/GIPC/GAIP 0.019 0.053 -9999 0 -9999 0 0
RAS family/GTP/PI3K 0.003 0.08 -9999 0 -0.401 1 1
FRS2 family/SHP2/GRB2/SOS1 0.052 0 -9999 0 -9999 0 0
NRAS 0.012 0.043 -9999 0 -0.3 1 1
GRB2/SOS1 0.026 0 -9999 0 -9999 0 0
PRKCI 0.012 0.043 -9999 0 -0.3 1 1
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 -0.03 0.1 -9999 0 -0.408 3 3
RASA1 0.017 0 -9999 0 -9999 0 0
TRKA/c-Abl 0.011 0.064 -9999 0 -0.251 3 3
SQSTM1 0.01 0.058 -9999 0 -0.411 1 1
BDNF (dimer)/TRKB/GIPC -0.02 0.095 -9999 0 -0.197 6 6
NGF (dimer)/TRKA/p62/Atypical PKCs 0.013 0.058 -9999 0 -0.191 3 3
MATK 0.004 0.071 -9999 0 -0.355 2 2
NEDD4L 0.002 0.081 -9999 0 -0.411 2 2
RAS family/GDP -0.004 0.014 -9999 0 -9999 0 0
NGF (dimer)/TRKA -0.014 0.072 0.218 1 -0.207 3 4
Rac1/GTP -0.028 0.046 -9999 0 -0.194 1 1
FRS2 family/SHP2/CRK family 0.035 0.06 -9999 0 -9999 0 0
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.005 0.109 -9999 0 -0.311 3 3
PDGFB-D/PDGFRB/SLAP 0.011 0.064 -9999 0 -0.251 3 3
PDGFB-D/PDGFRB/APS/CBL 0.015 0.048 -9999 0 -0.231 2 2
AKT1 -0.013 0.111 -9999 0 -0.31 4 4
mol:PI-4-5-P2 0 0 -9999 0 -9999 0 0
mol:Sphingosine-1-phosphate 0.007 0.102 -9999 0 -0.335 3 3
PIK3CA 0.01 0.058 -9999 0 -0.411 1 1
FGR -0.009 0.053 -9999 0 -9999 0 0
mol:Ca2+ 0.005 0.097 -9999 0 -0.351 3 3
MYC 0.025 0.088 -9999 0 -9999 0 0
SHC1 0.017 0 -9999 0 -9999 0 0
HRAS/GDP 0.03 0.044 -9999 0 -9999 0 0
LRP1/PDGFRB/PDGFB 0.023 0.055 -9999 0 -0.224 2 2
GRB10 -0.02 0.118 -9999 0 -0.389 5 5
PTPN11 0.017 0 -9999 0 -9999 0 0
GO:0007205 0.005 0.098 -9999 0 -0.356 3 3
PTEN -0.022 0.124 -9999 0 -0.411 5 5
GRB2 0.017 0 -9999 0 -9999 0 0
GRB7 0 0.073 -9999 0 -0.3 3 3
PDGFB-D/PDGFRB/SHP2 0.015 0.058 -9999 0 -0.278 2 2
PDGFB-D/PDGFRB/GRB10 -0.012 0.1 -9999 0 -0.269 7 7
cell cycle arrest 0.011 0.064 -9999 0 -0.25 3 3
HRAS 0.017 0 -9999 0 -9999 0 0
HIF1A -0.006 0.101 -9999 0 -0.293 3 3
GAB1 0.004 0.096 -9999 0 -0.363 2 2
mol:GTP 0 0 -9999 0 -9999 0 0
DNM2 0.007 0.093 -9999 0 -0.328 2 2
PDGFB-D/PDGFRB 0.024 0.057 -9999 0 -0.231 2 2
mol:GDP 0 0 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.015 0.058 -9999 0 -0.278 2 2
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.007 0.108 -9999 0 -0.286 4 4
positive regulation of MAPKKK cascade 0.015 0.057 -9999 0 -0.277 2 2
PIK3R1 -0.038 0.134 -9999 0 -0.355 8 8
mol:IP3 0.005 0.099 -9999 0 -0.358 3 3
E5 0 0.001 -9999 0 -9999 0 0
CSK 0.017 0.001 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/GRB7 0.003 0.075 -9999 0 -0.229 5 5
SHB 0.017 0 -9999 0 -9999 0 0
BLK -0.019 0.084 -9999 0 -0.477 1 1
PTPN2 0.018 0.002 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/SNX15 0.015 0.058 -9999 0 -0.278 2 2
BCAR1 0.017 0 -9999 0 -9999 0 0
VAV2 0.008 0.099 -9999 0 -0.353 2 2
CBL 0.017 0 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/DEP1 0.011 0.064 -9999 0 -0.251 3 3
LCK -0.035 0.1 -9999 0 -0.354 4 4
PDGFRB 0.002 0.082 -9999 0 -0.413 2 2
ACP1 0.017 0 -9999 0 -9999 0 0
HCK -0.041 0.13 -9999 0 -0.523 3 3
ABL1 0.005 0.084 -9999 0 -0.303 2 2
PDGFB-D/PDGFRB/CBL 0.003 0.105 -9999 0 -0.431 2 2
PTPN1 0.012 0.044 -9999 0 -0.306 1 1
SNX15 0.017 0 -9999 0 -9999 0 0
STAT3 0.01 0.058 -9999 0 -0.411 1 1
STAT1 -0.032 0.118 -9999 0 -0.313 8 8
cell proliferation 0.026 0.083 -9999 0 -0.313 1 1
SLA 0.012 0.043 -9999 0 -0.3 1 1
actin cytoskeleton reorganization 0.038 0.051 -9999 0 -9999 0 0
SRC -0.009 0.053 -9999 0 -9999 0 0
PI3K -0.055 0.1 -9999 0 -0.342 4 4
PDGFB-D/PDGFRB/GRB7/SHC 0.016 0.064 -9999 0 -0.224 2 2
SH2B2 0 0 -9999 0 -9999 0 0
PLCgamma1/SPHK1 0.006 0.105 -9999 0 -0.344 3 3
LYN -0.011 0.054 -9999 0 -9999 0 0
LRP1 0.012 0.043 -9999 0 -0.3 1 1
SOS1 0.017 0 -9999 0 -9999 0 0
STAT5B 0.01 0.058 -9999 0 -0.411 1 1
STAT5A 0.017 0 -9999 0 -9999 0 0
NCK1-2/p130 Cas 0.039 0.055 -9999 0 -9999 0 0
SPHK1 -0.002 0.082 -9999 0 -0.338 3 3
EDG1 -0.012 0.106 -9999 0 -0.384 4 4
mol:DAG 0.005 0.099 -9999 0 -0.358 3 3
PLCG1 0.004 0.1 -9999 0 -0.366 3 3
NHERF/PDGFRB 0.002 0.092 -9999 0 -0.259 5 5
YES1 -0.009 0.053 -9999 0 -9999 0 0
cell migration 0.001 0.092 -9999 0 -0.258 5 5
SHC/Grb2/SOS1 0.044 0.047 -9999 0 -9999 0 0
SLC9A3R2 -0.018 0.112 -9999 0 -0.366 5 5
SLC9A3R1 0.012 0.043 -9999 0 -0.3 1 1
NHERF1-2/PDGFRB/PTEN -0.009 0.104 -9999 0 -0.213 10 10
FYN -0.037 0.124 -9999 0 -0.397 5 5
DOK1 0.022 0.049 -9999 0 -0.198 2 2
HRAS/GTP 0.013 0 -9999 0 -9999 0 0
PDGFB 0.017 0 -9999 0 -9999 0 0
RAC1 0.018 0.097 -9999 0 -0.317 2 2
PRKCD 0.019 0.054 -9999 0 -0.198 2 2
FER 0.022 0.049 -9999 0 -0.198 2 2
MAPKKK cascade -0.008 0.033 -9999 0 -9999 0 0
RASA1 0.022 0.049 -9999 0 -0.198 2 2
NCK1 0.01 0.058 -9999 0 -0.411 1 1
NCK2 0.017 0 -9999 0 -9999 0 0
p62DOK/Csk 0.031 0.046 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/SHB 0.015 0.058 -9999 0 -0.278 2 2
chemotaxis 0.006 0.082 -9999 0 -0.296 2 2
STAT1-3-5/STAT1-3-5 -0.018 0.066 -9999 0 -0.234 1 1
Bovine Papilomavirus E5/PDGFRB 0.002 0.057 -9999 0 -0.289 2 2
PTPRJ 0.012 0.043 -9999 0 -0.3 1 1
S1P4 pathway

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
mol:S1P 0 0 -9999 0 -9999 0 0
GNAO1 0.017 0 -9999 0 -9999 0 0
CDC42/GTP -0.005 0.098 -9999 0 -0.397 2 2
PLCG1 -0.012 0.117 -9999 0 -0.506 2 2
mol:GTP 0 0 -9999 0 -9999 0 0
GNAI2 0.017 0 -9999 0 -9999 0 0
GNAI3 0.01 0.058 -9999 0 -0.411 1 1
G12/G13 0.026 0 -9999 0 -9999 0 0
cell migration -0.006 0.096 -9999 0 -0.389 2 2
S1PR5 0 0 -9999 0 -9999 0 0
S1PR4 0 0 -9999 0 -9999 0 0
MAPK3 -0.009 0.101 -9999 0 -0.41 2 2
MAPK1 -0.012 0.117 -9999 0 -0.506 2 2
S1P/S1P5/Gi -0.016 0.106 -9999 0 -0.236 8 8
GNAI1 -0.05 0.152 -9999 0 -0.386 9 9
CDC42/GDP 0.013 0 -9999 0 -9999 0 0
S1P/S1P5/G12 0.012 0 -9999 0 -9999 0 0
RHOA 0.021 0.029 -9999 0 -0.191 1 1
S1P/S1P4/Gi -0.016 0.106 -9999 0 -0.236 8 8
mol:GDP 0 0 -9999 0 -9999 0 0
GNAZ -0.01 0.099 -9999 0 -0.355 4 4
S1P/S1P4/G12/G13 0.023 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
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.021 0.06 -9999 0 -0.227 3 3
E-cadherin/beta catenin 0.009 0.07 -9999 0 -0.28 3 3
CTNNB1 0.002 0.081 -9999 0 -0.411 2 2
JUP 0.017 0 -9999 0 -9999 0 0
CDH1 0.01 0.058 -9999 0 -0.411 1 1
ErbB2/ErbB3 signaling events

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
USP8 0.018 0.002 -9999 0 -9999 0 0
RAS family/GTP 0.033 0.051 -9999 0 -9999 0 0
NFATC4 0.027 0.04 -9999 0 -9999 0 0
ERBB2IP 0.017 0.001 -9999 0 -9999 0 0
HSP90 (dimer) 0.002 0.081 -9999 0 -0.41 2 2
mammary gland morphogenesis 0.018 0.051 -9999 0 -9999 0 0
JUN 0.026 0.071 -9999 0 -9999 0 0
HRAS 0.017 0.001 -9999 0 -9999 0 0
DOCK7 0.021 0.048 -9999 0 -9999 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.017 0.056 -9999 0 -0.193 2 2
AKT1 0.012 0.001 -9999 0 -9999 0 0
BAD 0.015 0.024 -9999 0 -0.16 1 1
MAPK10 0.022 0.035 -9999 0 -9999 0 0
mol:GTP -0.001 0.002 -9999 0 -9999 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.02 0.055 -9999 0 -9999 0 0
RAF1 0.03 0.064 -9999 0 -9999 0 0
ErbB2/ErbB3/neuregulin 2 -0.003 0.066 -9999 0 -0.211 2 2
STAT3 0.009 0.126 -9999 0 -0.905 1 1
cell migration 0.022 0.05 -9999 0 -0.191 1 1
mol:PI-3-4-5-P3 0 0.001 -9999 0 -9999 0 0
cell proliferation -0.021 0.21 -9999 0 -0.56 4 4
FOS -0.042 0.212 -9999 0 -0.411 11 11
NRAS 0.011 0.043 -9999 0 -0.299 1 1
mol:Ca2+ 0.018 0.051 -9999 0 -9999 0 0
MAPK3 0.002 0.16 -9999 0 -0.424 4 4
MAPK1 -0.003 0.161 -9999 0 -0.424 4 4
JAK2 0.016 0.053 -9999 0 -9999 0 0
NF2 0.019 0.005 -9999 0 -9999 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.02 0.039 -9999 0 -0.203 1 1
NRG1 0.017 0.002 -9999 0 -9999 0 0
GRB2/SOS1 0.026 0.001 -9999 0 -9999 0 0
MAPK8 0.015 0.069 -9999 0 -0.215 3 3
MAPK9 0.023 0.04 -9999 0 -9999 0 0
ERBB2 -0.013 0.056 -9999 0 -0.239 3 3
ERBB3 0.004 0.071 -9999 0 -0.357 2 2
SHC1 0.017 0.001 -9999 0 -9999 0 0
RAC1 0.017 0 -9999 0 -9999 0 0
apoptosis -0.014 0.018 -9999 0 -9999 0 0
STAT3 (dimer) 0.009 0.123 -9999 0 -0.883 1 1
RNF41 0.023 0.003 -9999 0 -9999 0 0
FRAP1 0.018 0.001 -9999 0 -9999 0 0
RAC1-CDC42/GTP -0.007 0.025 -9999 0 -9999 0 0
ErbB2/ErbB2/HSP90 (dimer) -0.007 0.066 -9999 0 -0.211 5 5
CHRNA1 0.011 0.133 -9999 0 -0.349 1 1
myelination 0.032 0.039 -9999 0 -9999 0 0
PPP3CB 0.02 0.046 -9999 0 -9999 0 0
KRAS 0.017 0.001 -9999 0 -9999 0 0
RAC1-CDC42/GDP 0.037 0.036 -9999 0 -9999 0 0
NRG2 0 0.073 -9999 0 -0.3 3 3
mol:GDP 0.02 0.039 -9999 0 -0.203 1 1
SOS1 0.017 0.001 -9999 0 -9999 0 0
MAP2K2 0.03 0.074 -9999 0 -9999 0 0
SRC 0.017 0 -9999 0 -9999 0 0
mol:cAMP 0 0.001 -9999 0 -9999 0 0
PTPN11 0.023 0.047 -9999 0 -9999 0 0
MAP2K1 0.001 0.142 -9999 0 -0.384 1 1
heart morphogenesis 0.018 0.051 -9999 0 -9999 0 0
RAS family/GDP 0.04 0.045 -9999 0 -9999 0 0
GRB2 0.017 0.001 -9999 0 -9999 0 0
PRKACA 0 0.002 -9999 0 -9999 0 0
CHRNE 0.016 0.019 -9999 0 -9999 0 0
HSP90AA1 0.002 0.081 -9999 0 -0.411 2 2
activation of caspase activity -0.012 0.001 -9999 0 -9999 0 0
nervous system development 0.018 0.051 -9999 0 -9999 0 0
CDC42 0.017 0 -9999 0 -9999 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.002 0.081 -9999 0 -0.411 2 2
SMAD2 0.01 0.058 -9999 0 -0.198 3 3
SMAD3 0.025 0.054 -9999 0 -9999 0 0
SMAD3/SMAD4 0.037 0.043 -9999 0 -9999 0 0
SMAD4/Ubc9/PIASy 0.016 0.069 -9999 0 -0.227 4 4
SMAD2/SMAD2/SMAD4 0.036 0.061 -9999 0 -9999 0 0
PPM1A 0.017 0 -9999 0 -9999 0 0
CALM1 0.017 0 -9999 0 -9999 0 0
SMAD2/SMAD4 0.011 0.066 -9999 0 -0.198 2 2
MAP3K1 -0.014 0.112 -9999 0 -0.411 4 4
TRAP-1/SMAD4 0.015 0.058 -9999 0 -0.28 2 2
MAPK3 0.017 0 -9999 0 -9999 0 0
MAPK1 0.01 0.058 -9999 0 -0.411 1 1
NUP214 0.017 0 -9999 0 -9999 0 0
CTDSP1 0.017 0 -9999 0 -9999 0 0
CTDSP2 0.017 0 -9999 0 -9999 0 0
CTDSPL 0.002 0.081 -9999 0 -0.411 2 2
KPNB1 0.017 0 -9999 0 -9999 0 0
TGFBRAP1 0.017 0 -9999 0 -9999 0 0
UBE2I 0.01 0.058 -9999 0 -0.411 1 1
NUP153 0.017 0 -9999 0 -9999 0 0
KPNA2 0.017 0 -9999 0 -9999 0 0
PIAS4 0.01 0.058 -9999 0 -0.411 1 1
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.014 0.051 0.236 2 -9999 0 2
KIRREL 0.009 0.058 -9999 0 -0.412 1 1
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.014 0.051 -9999 0 -0.237 2 2
PLCG1 0.01 0.058 -9999 0 -0.411 1 1
ARRB2 0.017 0 -9999 0 -9999 0 0
WASL 0.009 0.058 -9999 0 -0.411 1 1
Nephrin/NEPH1/podocin/CD2AP 0.031 0.051 -9999 0 -0.204 2 2
ChemicalAbstracts:57-88-5 0 0 -9999 0 -9999 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.025 0.053 -9999 0 -9999 0 0
FYN 0.02 0.034 -9999 0 -0.187 1 1
mol:Ca2+ 0.029 0.05 -9999 0 -0.202 2 2
mol:DAG 0.03 0.051 -9999 0 -0.203 2 2
NPHS2 0.016 0.01 -9999 0 -9999 0 0
mol:IP3 0.03 0.051 -9999 0 -0.203 2 2
regulation of endocytosis 0.027 0.05 -9999 0 -9999 0 0
Nephrin/NEPH1/podocin/Cholesterol 0.022 0.039 -9999 0 -0.197 1 1
establishment of cell polarity 0.014 0.051 -9999 0 -0.236 2 2
Nephrin/NEPH1/podocin/NCK1-2 0.04 0.047 -9999 0 -0.19 1 1
Nephrin/NEPH1/beta Arrestin2 0.028 0.051 -9999 0 -9999 0 0
NPHS1 0.011 0.043 -9999 0 -0.295 1 1
Nephrin/NEPH1/podocin 0.02 0.053 -9999 0 -0.188 1 1
TJP1 0.017 0 -9999 0 -9999 0 0
NCK1 0.01 0.058 -9999 0 -0.411 1 1
NCK2 0.017 0 -9999 0 -9999 0 0
heterophilic cell adhesion 0 0 -9999 0 -9999 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.031 0.051 -9999 0 -0.204 2 2
CD2AP 0.01 0.058 -9999 0 -0.411 1 1
Nephrin/NEPH1/podocin/GRB2 0.036 0.038 -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 0.007 0.055 -9999 0 -9999 0 0
cytoskeleton organization 0.03 0.049 -9999 0 -9999 0 0
Nephrin/NEPH1 0.014 0.035 -9999 0 -0.192 1 1
Nephrin/NEPH1/ZO-1 0.028 0.04 -9999 0 -0.213 1 1
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.023 0.044 -9999 0 -9999 0 0
epithelial cell differentiation -0.017 0.046 -9999 0 -9999 0 0
ITCH 0.023 0.011 -9999 0 -9999 0 0
WWP1 0.022 0.04 -9999 0 -9999 0 0
FYN -0.006 0.098 -9999 0 -0.411 3 3
EGFR -0.01 0.099 -9999 0 -0.355 4 4
PRL 0.012 0.043 -9999 0 -0.3 1 1
neuron projection morphogenesis 0.05 0.032 -9999 0 -9999 0 0
PTPRZ1 -0.006 0.083 -9999 0 -0.3 4 4
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.05 0.035 -9999 0 -9999 0 0
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.025 0.038 -9999 0 -9999 0 0
ADAM17 0.016 0.045 -9999 0 -0.298 1 1
ErbB4/ErbB4 0.018 0.052 -9999 0 -9999 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.012 0.06 -9999 0 -9999 0 0
NCOR1 0.017 0 -9999 0 -9999 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.022 0.064 -9999 0 -9999 0 0
GRIN2B 0 0.08 -9999 0 -9999 0 0
ErbB4/ErbB2/betacellulin -0.011 0.086 -9999 0 -9999 0 0
STAT1 -0.032 0.118 -9999 0 -0.313 8 8
HBEGF 0.017 0 -9999 0 -9999 0 0
PRLR 0.017 0 -9999 0 -9999 0 0
E4ICDs/ETO2 0.003 0.067 -9999 0 -9999 0 0
axon guidance 0.002 0.072 -9999 0 -9999 0 0
NEDD4 0.023 0.011 -9999 0 -9999 0 0
Prolactin receptor/Prolactin receptor/Prolactin 0.022 0.03 -9999 0 -0.194 1 1
CBFA2T3 -0.02 0.106 -9999 0 -0.318 6 6
ErbB4/ErbB2/HBEGF 0.024 0.054 -9999 0 -9999 0 0
MAPK3 0.047 0.032 -9999 0 -9999 0 0
STAT1 (dimer) -0.003 0.078 -9999 0 -9999 0 0
MAPK1 0.046 0.032 -9999 0 -9999 0 0
JAK2 0.006 0.06 -9999 0 -0.3 2 2
ErbB4/ErbB2/neuregulin 1 beta 0.021 0.053 -9999 0 -9999 0 0
NRG1 0.023 0.03 -9999 0 -0.187 1 1
NRG3 -0.002 0.082 -9999 0 -0.337 3 3
NRG2 0 0.073 -9999 0 -0.3 3 3
NRG4 0.012 0.043 -9999 0 -0.3 1 1
heart development 0.002 0.072 -9999 0 -9999 0 0
neural crest cell migration 0.021 0.052 -9999 0 -9999 0 0
ERBB2 0.009 0.065 -9999 0 -0.216 4 4
WWOX/E4ICDs 0.023 0.044 -9999 0 -9999 0 0
SHC1 0.017 0 -9999 0 -9999 0 0
ErbB4/EGFR/neuregulin 4 0.015 0.064 -9999 0 -9999 0 0
apoptosis -0.014 0.059 -9999 0 -9999 0 0
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.014 0.055 -9999 0 -9999 0 0
ErbB4/ErbB2/epiregulin 0.018 0.058 -9999 0 -9999 0 0
ErbB4/ErbB4/betacellulin/betacellulin -0.016 0.09 -9999 0 -9999 0 0
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.041 0.057 -9999 0 -9999 0 0
MDM2 0.02 0.048 -9999 0 -9999 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.031 0.029 -9999 0 -9999 0 0
STAT5A 0.009 0.068 -9999 0 -9999 0 0
ErbB4/EGFR/neuregulin 1 beta 0.02 0.057 -9999 0 -9999 0 0
DLG4 0.017 0 -9999 0 -9999 0 0
GRB2/SHC 0.026 0 -9999 0 -9999 0 0
E4ICDs/TAB2/NCoR1 0.032 0.042 -9999 0 -9999 0 0
STAT5A (dimer) 0.024 0.068 -9999 0 -9999 0 0
MAP3K7IP2 0.017 0 -9999 0 -9999 0 0
STAT5B (dimer) 0.007 0.073 -9999 0 -9999 0 0
LRIG1 -0.058 0.159 -9999 0 -0.389 10 10
EREG 0.006 0.06 -9999 0 -0.3 2 2
BTC -0.052 0.156 -9999 0 -0.398 9 9
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.003 0.072 -9999 0 -9999 0 0
ERBB4 0.018 0.052 -9999 0 -9999 0 0
STAT5B 0.01 0.058 -9999 0 -0.411 1 1
YAP1 0.018 0.009 -9999 0 -9999 0 0
GRB2 0.017 0 -9999 0 -9999 0 0
ErbB4/ErbB2/neuregulin 4 0.021 0.056 -9999 0 -9999 0 0
glial cell differentiation -0.031 0.042 -9999 0 -9999 0 0
WWOX 0.017 0 -9999 0 -9999 0 0
cell proliferation -0.012 0.095 -9999 0 -9999 0 0
Circadian rhythm 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
chromatin modification 0.031 0.06 -9999 0 -9999 0 0
CLOCK 0.021 0 -9999 0 -9999 0 0
TIMELESS/CRY2 0.044 0.014 -9999 0 -9999 0 0
DEC1/BMAL1 0.013 0.064 -9999 0 -0.248 3 3
ATR 0.017 0 -9999 0 -9999 0 0
NR1D1 0.039 0.016 -9999 0 -9999 0 0
ARNTL 0.005 0.081 -9999 0 -0.406 2 2
TIMELESS 0.039 0.016 -9999 0 -9999 0 0
NPAS2 0.009 0.06 -9999 0 -0.294 2 2
CRY2 0.017 0 -9999 0 -9999 0 0
mol:CO -0.014 0 -9999 0 -9999 0 0
CHEK1 -0.024 0.119 -9999 0 -0.355 6 6
mol:HEME 0.014 0 -9999 0 -9999 0 0
PER1 0.017 0 -9999 0 -9999 0 0
BMAL/CLOCK/NPAS2 0.036 0.062 -9999 0 -0.217 2 2
BMAL1/CLOCK 0.044 0.061 -9999 0 -9999 0 0
S phase of mitotic cell cycle 0.031 0.06 -9999 0 -9999 0 0
TIMELESS/CHEK1/ATR 0.032 0.061 -9999 0 -9999 0 0
mol:NADPH 0.014 0 -9999 0 -9999 0 0
PER1/TIMELESS 0.044 0.014 -9999 0 -9999 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -9999 0 0
DEC1 0.011 0.043 -9999 0 -0.3 1 1
Aurora C 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
INCENP 0.01 0.058 -9999 0 -0.411 1 1
Aurora C/Aurora B/INCENP 0.021 0.068 -9999 0 -0.309 2 2
metaphase 0 0 -9999 0 -9999 0 0
mitosis 0 0 -9999 0 -9999 0 0
H3F3B 0.014 0.021 -9999 0 -9999 0 0
AURKB 0.01 0.058 -9999 0 -0.411 1 1
AURKC 0.01 0.058 -9999 0 -0.411 1 1
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.03 0.056 -9999 0 -0.195 1 1
CaM/Ca2+ 0.013 0 -9999 0 -9999 0 0
AKT1 0.017 0 -9999 0 -9999 0 0
AKT2 0.017 0 -9999 0 -9999 0 0
STXBP4 0.017 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
mol:glucose 0.028 0.043 -9999 0 -9999 0 0
YWHAZ 0.017 0 -9999 0 -9999 0 0
CALM1 0.017 0 -9999 0 -9999 0 0
YWHAQ 0.017 0 -9999 0 -9999 0 0
TBC1D4 0.007 0.07 -9999 0 -0.281 3 3
mol:Ca2+ 0 0 -9999 0 -9999 0 0
YWHAH 0.017 0 -9999 0 -9999 0 0
YWHAB 0.017 0 -9999 0 -9999 0 0
SNARE/Synip 0.036 0 -9999 0 -9999 0 0
YWHAG 0.017 0 -9999 0 -9999 0 0
ASIP 0 0 -9999 0 -9999 0 0
PRKCI 0.012 0.043 -9999 0 -0.3 1 1
AS160/CaM/Ca2+ 0.013 0 -9999 0 -9999 0 0
RHOQ 0.01 0.058 -9999 0 -0.411 1 1
GYS1 0.031 0 -9999 0 -9999 0 0
PRKCZ 0 0 -9999 0 -9999 0 0
TRIP10 0.012 0.043 -9999 0 -0.3 1 1
TC10/GTP/CIP4/Exocyst 0.016 0.042 -9999 0 -0.197 2 2
AS160/14-3-3 0.009 0.067 -9999 0 -9999 0 0
VAMP2 0.017 0 -9999 0 -9999 0 0
SLC2A4 0.029 0.046 -9999 0 -9999 0 0
STX4 0.017 0 -9999 0 -9999 0 0
GSK3B 0.028 0 -9999 0 -9999 0 0
SFN -0.057 0.15 -9999 0 -0.35 11 11
LNPEP -0.004 0.09 -9999 0 -0.374 3 3
YWHAE 0.01 0.058 -9999 0 -0.411 1 1
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.023 0 -9999 0 -9999 0 0
BAD/BCL-XL/YWHAZ 0.037 0.023 -9999 0 -9999 0 0
CDKN1B 0.009 0.071 -9999 0 -9999 0 0
CDKN1A 0.015 0.071 -9999 0 -0.258 1 1
FRAP1 0.017 0 -9999 0 -9999 0 0
PRKDC 0.017 0 -9999 0 -9999 0 0
FOXO3 0.036 0.021 -9999 0 -9999 0 0
AKT1 0.031 0.022 -9999 0 -9999 0 0
BAD 0.012 0.043 -9999 0 -0.3 1 1
AKT3 0.019 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
FOXO4 0.036 0.021 -9999 0 -9999 0 0
AKT1/ASK1 0.024 0.058 -9999 0 -0.251 1 1
BAD/YWHAZ 0.032 0.025 -9999 0 -9999 0 0
RICTOR 0.017 0 -9999 0 -9999 0 0
RAF1 0.012 0.043 -9999 0 -0.3 1 1
JNK cascade -0.023 0.056 0.245 1 -9999 0 1
TSC1 0.036 0.021 -9999 0 -9999 0 0
YWHAZ 0.017 0 -9999 0 -9999 0 0
AKT1/RAF1 0.037 0.029 -9999 0 -9999 0 0
EP300 0.01 0.058 -9999 0 -0.411 1 1
mol:GDP 0.031 0.022 -9999 0 -9999 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -9999 0 0
TSC2 0.036 0.021 -9999 0 -9999 0 0
YWHAQ 0.017 0 -9999 0 -9999 0 0
TBC1D4 0.01 0.056 -9999 0 -0.223 3 3
MAP3K5 -0.012 0.106 -9999 0 -0.383 4 4
MAPKAP1 0.01 0.058 -9999 0 -0.411 1 1
negative regulation of cell cycle -0.022 0.049 -9999 0 -9999 0 0
YWHAH 0.017 0 -9999 0 -9999 0 0
AKT1S1 0.036 0.021 -9999 0 -9999 0 0
CASP9 0.036 0.021 -9999 0 -9999 0 0
YWHAB 0.017 0 -9999 0 -9999 0 0
p27Kip1/KPNA1 0.018 0.069 -9999 0 -9999 0 0
GBL 0.017 0 -9999 0 -9999 0 0
PDK1/Src/Hsp90 0.026 0.05 -9999 0 -0.227 2 2
YWHAE 0.01 0.058 -9999 0 -0.411 1 1
SRC 0.017 0 -9999 0 -9999 0 0
AKT2/p21CIP1 0.019 0.069 -9999 0 -0.255 1 1
KIAA1303 0.017 0 -9999 0 -9999 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.031 0.061 -9999 0 -0.4 1 1
CHUK 0.032 0.034 -9999 0 -9999 0 0
BAD/BCL-XL 0.05 0.028 -9999 0 -9999 0 0
mTORC2 0.041 0.033 -9999 0 -0.197 1 1
AKT2 0.019 0 -9999 0 -9999 0 0
FOXO1-3a-4/14-3-3 family 0.038 0.054 -9999 0 -9999 0 0
PDPK1 0.017 0 -9999 0 -9999 0 0
MDM2 0.034 0.028 -9999 0 -9999 0 0
MAPKKK cascade -0.037 0.028 -9999 0 -9999 0 0
MDM2/Cbp/p300 0.047 0.037 -9999 0 -9999 0 0
TSC1/TSC2 0.041 0.02 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.045 0.036 -9999 0 -9999 0 0
glucose import 0.009 0.073 -9999 0 -0.263 3 3
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.042 0.043 -9999 0 -0.252 1 1
response to stress 0 0 -9999 0 -9999 0 0
SLC2A4 0.009 0.073 -9999 0 -0.265 3 3
GSK3A 0.036 0.021 -9999 0 -9999 0 0
FOXO1 0.036 0.021 -9999 0 -9999 0 0
GSK3B 0.036 0.021 -9999 0 -9999 0 0
SFN -0.057 0.15 -9999 0 -0.35 11 11
G1/S transition of mitotic cell cycle 0.041 0.02 -9999 0 -9999 0 0
p27Kip1/14-3-3 family 0.018 0.06 -9999 0 -9999 0 0
PRKACA 0.017 0 -9999 0 -9999 0 0
KPNA1 0.017 0 -9999 0 -9999 0 0
HSP90AA1 0.002 0.081 -9999 0 -0.411 2 2
YWHAG 0.017 0 -9999 0 -9999 0 0
RHEB 0.004 0.071 -9999 0 -0.355 2 2
CREBBP 0.017 0 -9999 0 -9999 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.024 0.078 -9999 0 -0.434 1 1
Ran/GTP/Exportin 1/HDAC1 -0.003 0.022 -9999 0 -0.162 1 1
NF kappa B1 p50/RelA/I kappa B alpha 0.027 0.072 -9999 0 -0.379 1 1
SUMO1 0.017 0 -9999 0 -9999 0 0
ZFPM1 0.002 0.081 -9999 0 -0.411 2 2
NPC/RanGAP1/SUMO1/Ubc9 0.019 0.027 -9999 0 -0.175 1 1
FKBP3 0.01 0.058 -9999 0 -0.411 1 1
Histones 0.038 0.049 -9999 0 -9999 0 0
YY1/LSF 0.021 0.044 -9999 0 -0.204 2 2
SMG5 0.017 0 -9999 0 -9999 0 0
RAN 0.01 0.058 -9999 0 -0.411 1 1
I kappa B alpha/HDAC3 0.015 0.065 -9999 0 -0.325 1 1
I kappa B alpha/HDAC1 0.018 0.059 -9999 0 -0.245 2 2
SAP18 0.017 0 -9999 0 -9999 0 0
RELA 0.02 0.059 -9999 0 -0.287 1 1
HDAC1/Smad7 0.031 0.035 -9999 0 -0.227 1 1
RANGAP1 0.017 0 -9999 0 -9999 0 0
HDAC3/TR2 0.024 0.043 -9999 0 -0.218 1 1
NuRD/MBD3 Complex 0.031 0.045 -9999 0 -9999 0 0
NF kappa B1 p50/RelA 0.027 0.055 -9999 0 -0.259 1 1
EntrezGene:23225 0 0 -9999 0 -9999 0 0
GATA2 -0.016 0.106 -9999 0 -0.344 5 5
GATA1 0.01 0.058 -9999 0 -0.411 1 1
Mad/Max 0.026 0 -9999 0 -9999 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.03 0.075 -9999 0 -0.368 1 1
RBBP7 -0.008 0.091 -9999 0 -0.327 4 4
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 0.01 0.064 -9999 0 -0.278 2 2
KAT2B 0 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
SIN3/HDAC complex 0.037 0.033 -9999 0 -9999 0 0
SIN3 complex 0.045 0 -9999 0 -9999 0 0
SMURF1 0.017 0 -9999 0 -9999 0 0
CHD3 0.006 0.06 -9999 0 -0.3 2 2
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 0.026 0.046 -9999 0 -9999 0 0
YY1/HDAC2 0.026 0.03 -9999 0 -0.193 1 1
YY1/HDAC1 0.026 0.03 -9999 0 -0.193 1 1
NuRD/MBD2 Complex (MeCP1) 0.032 0.041 -9999 0 -9999 0 0
PPARG -0.052 0.127 -9999 0 -0.274 11 11
HDAC8/hEST1B 0.031 0.035 -9999 0 -0.227 1 1
UBE2I 0.01 0.058 -9999 0 -0.411 1 1
beta TrCP1/SCF ubiquitin ligase complex 0.017 0 -9999 0 -9999 0 0
TNFRSF1A 0.01 0.058 -9999 0 -0.411 1 1
HDAC3/SMRT (N-CoR2) 0.024 0.043 -9999 0 -0.218 1 1
MBD3L2 -0.005 0.09 -9999 0 -0.374 3 3
ubiquitin-dependent protein catabolic process 0.03 0.035 -9999 0 -0.226 1 1
CREBBP 0.017 0 -9999 0 -9999 0 0
NuRD/MBD3/MBD3L2 Complex 0.029 0.058 -9999 0 -9999 0 0
HDAC1 0.017 0 -9999 0 -9999 0 0
HDAC3 0.016 0.047 -9999 0 -0.249 1 1
HDAC2 0.017 0 -9999 0 -9999 0 0
YY1 0.019 0.035 -9999 0 -0.235 1 1
HDAC8 0.01 0.058 -9999 0 -0.411 1 1
SMAD7 0.01 0.058 -9999 0 -0.411 1 1
NCOR2 0.017 0 -9999 0 -9999 0 0
MXD1 0.017 0 -9999 0 -9999 0 0
STAT3 0.017 0.055 -9999 0 -0.265 2 2
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 0.031 0.041 -9999 0 -0.19 1 1
YY1/SAP30/HDAC1 0.035 0.028 -9999 0 -9999 0 0
EP300 0.01 0.058 -9999 0 -0.411 1 1
STAT3 (dimer non-phopshorylated) 0.017 0.055 -9999 0 -0.265 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.064 -9999 0 -0.277 2 2
histone deacetylation 0.032 0.04 -9999 0 -9999 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.024 0.055 -9999 0 -9999 0 0
nuclear export -0.03 0.035 0.226 1 -9999 0 1
PRKACA 0.017 0 -9999 0 -9999 0 0
GATAD2B 0.017 0 -9999 0 -9999 0 0
GATAD2A 0.012 0.043 -9999 0 -0.3 1 1
GATA2/HDAC3 0.007 0.067 -9999 0 -0.201 3 3
GATA1/HDAC1 0.02 0.041 -9999 0 -0.28 1 1
GATA1/HDAC3 0.02 0.052 -9999 0 -0.205 2 2
CHD4 0.017 0 -9999 0 -9999 0 0
TNF-alpha/TNFR1A -0.005 0.096 -9999 0 -0.25 6 6
SIN3/HDAC complex/Mad/Max 0.043 0.029 -9999 0 -9999 0 0
NuRD Complex 0.036 0.05 -9999 0 -9999 0 0
positive regulation of chromatin silencing 0.036 0.048 -9999 0 -9999 0 0
SIN3B 0.017 0 -9999 0 -9999 0 0
MTA2 0.004 0.071 -9999 0 -0.355 2 2
SIN3A 0.017 0 -9999 0 -9999 0 0
XPO1 0.017 0 -9999 0 -9999 0 0
SUMO1/HDAC1 0.033 0.026 -9999 0 -9999 0 0
HDAC complex 0.031 0.051 -9999 0 -0.197 1 1
GATA1/Fog1 0.009 0.07 -9999 0 -0.28 3 3
FKBP25/HDAC1/HDAC2 0.031 0.035 -9999 0 -0.227 1 1
TNF -0.02 0.106 -9999 0 -0.318 6 6
negative regulation of cell growth 0.043 0.028 -9999 0 -9999 0 0
NuRD/MBD2/PRMT5 Complex 0.032 0.041 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0.032 0.036 -9999 0 -9999 0 0
NF kappa B/RelA/I kappa B alpha 0.019 0.074 -9999 0 -0.4 1 1
SIN3/HDAC complex/NCoR1 0.04 0.029 -9999 0 -9999 0 0
TFCP2 0.01 0.058 -9999 0 -0.411 1 1
NR2C1 0.017 0 -9999 0 -9999 0 0
MBD3 0.01 0.058 -9999 0 -0.411 1 1
MBD2 0.012 0.043 -9999 0 -0.3 1 1
Effects of Botulinum toxin

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
STX1A 0.012 0 -9999 0 -9999 0 0
UniProt:P19321 0 0 -9999 0 -9999 0 0
RIMS1/UNC13B 0.026 0 -9999 0 -9999 0 0
STXBP1 0.017 0 -9999 0 -9999 0 0
ACh/CHRNA1 0.017 0.013 -9999 0 -9999 0 0
RAB3GAP2/RIMS1/UNC13B 0.036 0 -9999 0 -9999 0 0
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 0.017 0 -9999 0 -9999 0 0
mol:ACh 0.006 0.017 -9999 0 -0.104 1 1
RAB3GAP2 0.017 0 -9999 0 -9999 0 0
STX1A/SNAP25/VAMP2 0.036 0.021 -9999 0 -9999 0 0
UniProt:P10844 0 0 -9999 0 -9999 0 0
muscle contraction 0.017 0.013 -9999 0 -9999 0 0
UNC13B 0.017 0 -9999 0 -9999 0 0
CHRNA1 0.017 0 -9999 0 -9999 0 0
UniProt:P10845 0 0 -9999 0 -9999 0 0
ACh/Synaptotagmin 1 -0.006 0.068 -9999 0 -0.192 6 6
SNAP25 0.001 0.038 -9999 0 -0.182 2 2
VAMP2 0.007 0 -9999 0 -9999 0 0
SYT1 -0.02 0.106 -9999 0 -0.318 6 6
UniProt:Q00496 0 0 -9999 0 -9999 0 0
STXIA/STXBP1 0.022 0 -9999 0 -9999 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.036 0.021 -9999 0 -9999 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.017 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 -0.006 0.037 -9999 0 -0.264 1 1
MDM2/SUMO1 0.03 0.032 -9999 0 -9999 0 0
HDAC4 0.012 0.043 -9999 0 -0.3 1 1
Ran/GTP/Exportin 1/HDAC1 -0.004 0.022 -9999 0 -9999 0 0
SUMO1 0.017 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1 0.018 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
XPO1 0.024 0.025 -9999 0 -9999 0 0
EntrezGene:23636 0 0 -9999 0 -9999 0 0
RAN 0.01 0.058 -9999 0 -0.411 1 1
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.017 0 -9999 0 -9999 0 0
SUMO1/HDAC4 0.03 0.032 -9999 0 -9999 0 0
SUMO1/HDAC1 0.033 0.026 -9999 0 -9999 0 0
RANGAP1 0.017 0 -9999 0 -9999 0 0
MDM2/SUMO1/SUMO1 0.042 0.023 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.019 0.027 -9999 0 -0.175 1 1
Ran/GTP 0.023 0.036 -9999 0 -0.162 2 2
EntrezGene:23225 0 0 -9999 0 -9999 0 0
MDM2 0.012 0.043 -9999 0 -0.3 1 1
UBE2I 0.01 0.058 -9999 0 -0.411 1 1
Ran/GTP/Exportin 1 0.029 0.035 -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
Arf6 trafficking events

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
SLC2A4 0.004 0.071 -9999 0 -0.355 2 2
CLTC 0.027 0.036 -9999 0 -9999 0 0
calcium ion-dependent exocytosis 0.028 0 -9999 0 -9999 0 0
Dynamin 2/GTP 0.028 0 -9999 0 -9999 0 0
EXOC4 0.01 0.058 -9999 0 -0.411 1 1
CD59 0.025 0.027 -9999 0 -9999 0 0
CPE -0.009 0.072 -9999 0 -0.178 8 8
CTNNB1 0.002 0.081 -9999 0 -0.411 2 2
membrane fusion 0.027 0 -9999 0 -9999 0 0
CTNND1 0.031 0 -9999 0 -9999 0 0
DNM2 0.017 0 -9999 0 -9999 0 0
mol:PI-4-5-P2 0.033 0 -9999 0 -9999 0 0
TSHR 0.012 0.042 -9999 0 -0.197 2 2
INS 0.022 0 -9999 0 -9999 0 0
BIN1 0.012 0.043 -9999 0 -0.3 1 1
mol:Choline 0.027 0 -9999 0 -9999 0 0
growth hormone secretagogue receptor activity 0 0 -9999 0 -9999 0 0
mol:GDP 0.02 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+ 0.027 0 -9999 0 -9999 0 0
JUP 0.03 0 -9999 0 -9999 0 0
ASAP2/amphiphysin II 0.019 0.022 -9999 0 -0.142 1 1
ARF6/GTP 0.013 0 -9999 0 -9999 0 0
CDH1 0.026 0.024 -9999 0 -9999 0 0
clathrin-independent pinocytosis 0.013 0 -9999 0 -9999 0 0
MAPK8IP3 -0.005 0.09 -9999 0 -0.374 3 3
positive regulation of endocytosis 0.013 0 -9999 0 -9999 0 0
EXOC2 0.017 0 -9999 0 -9999 0 0
substrate adhesion-dependent cell spreading 0.032 0.056 -9999 0 -0.2 3 3
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 -0.032 0.04 -9999 0 -9999 0 0
positive regulation of phagocytosis 0.02 0 -9999 0 -9999 0 0
ARF6/GTP/JIP3 0.011 0.054 -9999 0 -0.209 3 3
ACAP1 0.024 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
CHRM2 0.023 0.024 -9999 0 -9999 0 0
clathrin heavy chain/ACAP1 0.033 0.024 -9999 0 -9999 0 0
JIP4/KLC1 0.034 0 -9999 0 -9999 0 0
EXOC1 0.017 0 -9999 0 -9999 0 0
exocyst 0.032 0.057 -9999 0 -0.202 3 3
RALA/GTP 0.013 0 -9999 0 -9999 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.024 0 -9999 0 -9999 0 0
receptor recycling 0.013 0 -9999 0 -9999 0 0
CTNNA1 0.031 0 -9999 0 -9999 0 0
NME1 0.02 0 -9999 0 -9999 0 0
clathrin coat assembly 0.027 0.036 -9999 0 -9999 0 0
IL2RA 0.026 0.024 -9999 0 -9999 0 0
VAMP3 0.02 0 -9999 0 -9999 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.007 0.027 -9999 0 -9999 0 0
EXOC6 0.002 0.081 -9999 0 -0.411 2 2
PLD1 0.023 0 -9999 0 -9999 0 0
PLD2 0.023 0 -9999 0 -9999 0 0
EXOC5 0.017 0 -9999 0 -9999 0 0
PIP5K1C 0.033 0 -9999 0 -9999 0 0
SDC1 0.023 0.034 -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 0.034 0.041 -9999 0 -9999 0 0
mol:Phosphatidic acid 0.027 0 -9999 0 -9999 0 0
endocytosis -0.019 0.022 0.142 1 -9999 0 1
SCAMP2 0.017 0 -9999 0 -9999 0 0
ADRB2 0.013 0.058 -9999 0 -9999 0 0
EXOC3 0.017 0 -9999 0 -9999 0 0
ASAP2 0 0 -9999 0 -9999 0 0
Dynamin 2/GDP 0.029 0 -9999 0 -9999 0 0
KLC1 0.017 0 -9999 0 -9999 0 0
AVPR2 0.024 0.045 -9999 0 -9999 0 0
RALA 0.017 0 -9999 0 -9999 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.042 0.039 -9999 0 -9999 0 0
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.017 0 -9999 0 -9999 0 0
PI3K Class IB/PDE3B 0.017 0 -9999 0 -9999 0 0
PDE3B 0.017 0 -9999 0 -9999 0 0
Arf1 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
coatomer protein complex 0.021 0.001 -9999 0 -9999 0 0
EntrezGene:79658 0 0 -9999 0 -9999 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.014 0.022 -9999 0 -9999 0 0
AP2 0.026 0 -9999 0 -9999 0 0
mol:DAG 0 0 -9999 0 -9999 0 0
Arfaptin 2/Rac/GTP 0.025 0.001 -9999 0 -9999 0 0
CLTB 0.017 0 -9999 0 -9999 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.026 0 -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 0.001 -9999 0 -9999 0 0
ARFGAP1 0.012 0 -9999 0 -9999 0 0
mol:PI-4-5-P2 0.008 0.014 -9999 0 -9999 0 0
ARF1/GTP 0.008 0.012 -9999 0 -9999 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.026 0.001 -9999 0 -9999 0 0
mol:Choline 0.008 0.014 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
ARF1 0.017 0 -9999 0 -9999 0 0
DDEF1 0.008 0.014 -9999 0 -9999 0 0
ARF1/GDP 0.007 0.005 -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 0.017 0 -9999 0 -9999 0 0
Rac/GTP 0.014 0 -9999 0 -9999 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.029 0 -9999 0 -9999 0 0
ARFIP2 0.016 0.002 -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 0.024 0.005 -9999 0 -9999 0 0
ARF1/GTP/ARHGAP10 0.011 0 -9999 0 -9999 0 0
GGA3 0.017 0 -9999 0 -9999 0 0
ARF1/GTP/Membrin 0.017 0.008 -9999 0 -9999 0 0
AP2A1 0.017 0 -9999 0 -9999 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.028 0.001 -9999 0 -9999 0 0
ARF1/GDP/Membrin 0.019 0.007 -9999 0 -9999 0 0
Arfaptin 2/Rac/GDP 0.023 0.002 -9999 0 -9999 0 0
CYTH2 0 0.001 -9999 0 -9999 0 0
ARF1/GTP/GGA3 0.023 0 -9999 0 -9999 0 0
mol:ATP 0 0 -9999 0 -9999 0 0
Rac/GDP 0.013 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 -9999 0 -9999 0 0
PLD2 0.008 0.014 -9999 0 -9999 0 0
ARF-GAP1/v-SNARE 0.012 0 -9999 0 -9999 0 0
PIP5K1A 0.008 0.015 -9999 0 -9999 0 0
ARF1/GTP/Membrin/GBF1/p115 0.014 0.02 -9999 0 -9999 0 0
mol:Phosphatic acid 0 0 -9999 0 -9999 0 0
mol:Phosphatidic acid 0.008 0.014 -9999 0 -9999 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.012 0 -9999 0 -9999 0 0
GOSR2 0.013 0.007 -9999 0 -9999 0 0
USO1 -0.002 0.076 -9999 0 -0.386 2 2
GBF1 0.013 0.007 -9999 0 -9999 0 0
ARF1/GTP/Arfaptin 2 0.024 0.001 -9999 0 -9999 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.036 0 -9999 0 -9999 0 0
Alternative NF-kappaB pathway

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
IKK alpha homodimer 0.02 0.041 -9999 0 -0.28 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 0.01 0.058 -9999 0 -0.411 1 1
NF kappa B2 p100/RelB 0.044 0.043 -9999 0 -9999 0 0
NFKB1 0.017 0 -9999 0 -9999 0 0
MAP3K14 0.017 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.02 0.041 -9999 0 -0.28 1 1
RELB 0.01 0.058 -9999 0 -0.411 1 1
NFKB2 0.017 0 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.019 0.035 -9999 0 -0.234 1 1
regulation of B cell activation 0.019 0.035 -9999 0 -0.233 1 1
Methods & Data
Input

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

  • Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/UCEC/463053/1.GDAC_MergeDataFiles.Finished/UCEC.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)