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 68 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
HIF-1-alpha transcription factor network 15
Endothelins 14
VEGFR1 specific signals 11
Syndecan-1-mediated signaling events 10
HIF-2-alpha transcription factor network 10
TCR signaling in naïve CD8+ T cells 10
Signaling events mediated by VEGFR1 and VEGFR2 10
EGFR-dependent Endothelin signaling events 10
IL23-mediated signaling events 10
Arf6 signaling events 9
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
HIF-1-alpha transcription factor network 15 1187 76 -0.981 0.057 1000 -1000 -0.061 -1000
Endothelins 14 1362 96 -0.32 0.02 1000 -1000 -0.065 -1000
VEGFR1 specific signals 11 659 56 -0.265 0.02 1000 -1000 -0.049 -1000
Syndecan-1-mediated signaling events 10 369 34 -0.228 0.02 1000 -1000 -0.074 -1000
HIF-2-alpha transcription factor network 10 435 43 -0.347 0.227 1000 -1000 -0.059 -1000
TCR signaling in naïve CD8+ T cells 10 934 93 -0.214 0.023 1000 -1000 -0.076 -1000
Signaling events mediated by VEGFR1 and VEGFR2 10 1286 125 -0.309 0.02 1000 -1000 -0.124 -1000
EGFR-dependent Endothelin signaling events 10 217 21 -0.315 0.022 1000 -1000 -0.091 -1000
IL23-mediated signaling events 10 613 60 -0.557 0.021 1000 -1000 -0.127 -1000
Arf6 signaling events 9 558 62 -0.323 0.02 1000 -1000 -0.054 -1000
IL4-mediated signaling events 9 851 91 -0.606 0.424 1000 -1000 -0.106 -1000
FOXA2 and FOXA3 transcription factor networks 9 435 46 -0.53 0.035 1000 -1000 -0.028 -1000
Glypican 2 network 9 36 4 -0.071 0 1000 -1000 -0.014 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 9 674 68 -0.482 0.241 1000 -1000 -0.101 -1000
TCGA08_retinoblastoma 9 74 8 -0.075 0.05 1000 -1000 -0.016 -1000
IL12-mediated signaling events 8 763 87 -0.349 0.028 1000 -1000 -0.097 -1000
PLK2 and PLK4 events 8 25 3 -0.099 0.012 1000 -1000 -0.016 -1000
amb2 Integrin signaling 8 727 82 -0.223 0.02 1000 -1000 -0.098 -1000
Osteopontin-mediated events 7 274 38 -0.17 0.02 1000 -1000 -0.109 -1000
Thromboxane A2 receptor signaling 7 762 105 -0.247 0.02 1000 -1000 -0.075 -1000
Fc-epsilon receptor I signaling in mast cells 7 763 97 -0.237 0.046 1000 -1000 -0.096 -1000
IL6-mediated signaling events 7 581 75 -0.255 0.023 1000 -1000 -0.091 -1000
Angiopoietin receptor Tie2-mediated signaling 7 637 88 -0.322 0.023 1000 -1000 -0.12 -1000
Visual signal transduction: Rods 7 367 52 -0.417 0.038 1000 -1000 -0.097 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 7 614 78 -0.161 0.058 1000 -1000 -0.066 -1000
LPA4-mediated signaling events 6 79 12 -0.088 0.029 1000 -1000 -0.019 -1000
a4b1 and a4b7 Integrin signaling 6 32 5 -0.081 0.02 1000 -1000 -0.022 -1000
Glypican 1 network 6 304 48 -0.163 0.02 1000 -1000 -0.031 -1000
Syndecan-3-mediated signaling events 6 212 35 -0.247 0.03 1000 -1000 -0.052 -1000
Integrins in angiogenesis 6 583 84 -0.242 0.033 1000 -1000 -0.106 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 6 300 45 -0.266 0.02 1000 -1000 -0.094 -1000
Calcium signaling in the CD4+ TCR pathway 6 207 31 -0.319 0.032 1000 -1000 -0.072 -1000
IL27-mediated signaling events 6 349 51 -0.331 0.14 1000 -1000 -0.079 -1000
Syndecan-4-mediated signaling events 6 417 67 -0.24 0.054 1000 -1000 -0.107 -1000
E-cadherin signaling events 6 34 5 -0.096 0.02 1000 -1000 -0.021 -1000
Ephrin A reverse signaling 5 38 7 -0.066 0.012 1000 -1000 -0.024 -1000
Signaling events mediated by PTP1B 5 402 76 -0.251 0.072 1000 -1000 -0.088 -1000
BMP receptor signaling 5 416 81 -0.209 0.043 1000 -1000 -0.098 -1000
IFN-gamma pathway 5 354 68 -0.229 0.022 1000 -1000 -0.107 -1000
Nectin adhesion pathway 5 369 63 -0.146 0.027 1000 -1000 -0.081 -1000
Paxillin-independent events mediated by a4b1 and a4b7 5 206 37 -0.139 0.03 1000 -1000 -0.053 -1000
TRAIL signaling pathway 5 246 48 -0.091 0.02 1000 -1000 -0.081 -1000
S1P1 pathway 5 207 36 -0.194 0.02 1000 -1000 -0.079 -1000
FAS signaling pathway (CD95) 5 250 47 -0.191 0.025 1000 -1000 -0.044 -1000
Signaling mediated by p38-gamma and p38-delta 5 75 15 -0.105 0.021 1000 -1000 -0.028 -1000
Nongenotropic Androgen signaling 5 306 52 -0.124 0.052 1000 -1000 -0.074 -1000
Stabilization and expansion of the E-cadherin adherens junction 5 443 74 -0.247 0.077 1000 -1000 -0.102 -1000
Caspase cascade in apoptosis 4 352 74 -0.162 0.084 1000 -1000 -0.031 -1000
Nephrin/Neph1 signaling in the kidney podocyte 4 168 34 -0.096 0.02 1000 -1000 -0.068 -1000
ErbB4 signaling events 4 302 69 -0.106 0.065 1000 -1000 -0.103 -1000
Visual signal transduction: Cones 4 154 38 -0.139 0.02 1000 -1000 -0.076 -1000
Signaling events mediated by the Hedgehog family 4 252 52 -0.31 0.026 1000 -1000 -0.037 -1000
JNK signaling in the CD4+ TCR pathway 4 77 17 -0.089 0.02 1000 -1000 -0.031 -1000
Syndecan-2-mediated signaling events 4 302 69 -0.156 0.039 1000 -1000 -0.024 -1000
Cellular roles of Anthrax toxin 4 169 39 -0.094 0.02 1000 -1000 -0.032 -1000
p75(NTR)-mediated signaling 4 567 125 -0.329 0.045 1000 -1000 -0.117 -1000
PDGFR-alpha signaling pathway 4 203 44 -0.268 0.038 1000 -1000 -0.086 -1000
Ceramide signaling pathway 4 310 76 -0.247 0.093 1000 -1000 -0.046 -1000
IL1-mediated signaling events 4 301 62 -0.229 0.088 1000 -1000 -0.099 -1000
ceramide signaling pathway 4 208 49 -0.162 0.023 1000 -1000 -0.037 -1000
IL2 signaling events mediated by PI3K 4 237 58 -0.124 0.041 1000 -1000 -0.09 -1000
IL2 signaling events mediated by STAT5 4 90 22 -0.102 0.021 1000 -1000 -0.038 -1000
Regulation of Telomerase 4 419 102 -0.271 0.044 1000 -1000 -0.113 -1000
BCR signaling pathway 4 485 99 -0.157 0.048 1000 -1000 -0.105 -1000
IGF1 pathway 4 236 57 -0.085 0.034 1000 -1000 -0.112 -1000
Insulin Pathway 4 305 74 -0.148 0.02 1000 -1000 -0.102 -1000
E-cadherin signaling in keratinocytes 4 207 43 -0.108 0.021 1000 -1000 -0.08 -1000
FOXM1 transcription factor network 4 224 51 -0.189 0.181 1000 -1000 -0.13 -1000
Regulation of nuclear SMAD2/3 signaling 3 443 136 -0.202 0.197 1000 -1000 -0.059 -1000
Coregulation of Androgen receptor activity 3 285 76 -0.234 0.034 1000 -1000 -0.053 -1000
Presenilin action in Notch and Wnt signaling 3 230 61 -0.323 0.05 1000 -1000 -0.075 -1000
Glucocorticoid receptor regulatory network 3 437 114 -0.326 0.078 1000 -1000 -0.075 -1000
Reelin signaling pathway 3 215 56 -0.119 0.034 1000 -1000 -0.097 -1000
RXR and RAR heterodimerization with other nuclear receptor 3 206 52 -0.139 0.063 1000 -1000 -0.055 -1000
Ephrin B reverse signaling 3 172 48 -0.088 0.039 1000 -1000 -0.085 -1000
TCGA08_p53 3 22 7 -0.027 0.025 1000 -1000 -0.025 -1000
Signaling mediated by p38-alpha and p38-beta 3 157 44 -0.096 0.02 1000 -1000 -0.053 -1000
Canonical Wnt signaling pathway 3 170 51 -0.336 0.086 1000 -1000 -0.053 -1000
EPHB forward signaling 3 319 85 -0.087 0.072 1000 -1000 -0.111 -1000
Wnt signaling 3 25 7 -0.038 0.02 1000 -1000 -0.025 -1000
LPA receptor mediated events 3 353 102 -0.186 0.041 1000 -1000 -0.082 -1000
E-cadherin signaling in the nascent adherens junction 3 302 76 -0.115 0.03 1000 -1000 -0.092 -1000
S1P3 pathway 3 126 42 -0.172 0.05 1000 -1000 -0.028 -1000
Neurotrophic factor-mediated Trk receptor signaling 3 407 120 -0.253 0.102 1000 -1000 -0.1 -1000
Ras signaling in the CD4+ TCR pathway 3 67 17 -0.09 0.022 1000 -1000 -0.045 -1000
ErbB2/ErbB3 signaling events 2 186 65 -0.078 0.038 1000 -1000 -0.077 -1000
Canonical NF-kappaB pathway 2 105 39 -0.147 0.061 1000 -1000 -0.095 -1000
Sphingosine 1-phosphate (S1P) pathway 2 82 28 -0.071 0.023 1000 -1000 -0.027 -1000
Noncanonical Wnt signaling pathway 2 52 26 -0.038 0.024 1000 -1000 -0.049 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 2 251 85 -0.174 0.039 1000 -1000 -0.087 -1000
Hedgehog signaling events mediated by Gli proteins 2 165 65 -0.102 0.053 1000 -1000 -0.063 -1000
Aurora A signaling 2 140 60 -0.131 0.053 1000 -1000 -0.053 -1000
EPO signaling pathway 2 152 55 -0.135 0.021 1000 -1000 -0.111 -1000
mTOR signaling pathway 2 143 53 -0.123 0.045 1000 -1000 -0.068 -1000
Signaling events mediated by HDAC Class III 2 102 40 -0.159 0.029 1000 -1000 -0.051 -1000
Signaling events regulated by Ret tyrosine kinase 2 214 82 -0.169 0.02 1000 -1000 -0.093 -1000
FoxO family signaling 2 169 64 -0.269 0.071 1000 -1000 -0.056 -1000
Retinoic acid receptors-mediated signaling 2 154 58 -0.139 0.051 1000 -1000 -0.087 -1000
Paxillin-dependent events mediated by a4b1 2 106 36 -0.111 0.034 1000 -1000 -0.081 -1000
Atypical NF-kappaB pathway 2 81 31 -0.104 0.04 1000 -1000 -0.033 -1000
Regulation of p38-alpha and p38-beta 2 160 54 -0.106 0.039 1000 -1000 -0.057 -1000
TCGA08_rtk_signaling 2 71 26 -0.106 0.046 1000 -1000 -0.021 -1000
Class I PI3K signaling events 2 207 73 -0.104 0.026 1000 -1000 -0.063 -1000
Plasma membrane estrogen receptor signaling 2 231 86 -0.102 0.047 1000 -1000 -0.102 -1000
PDGFR-beta signaling pathway 2 279 97 -0.141 0.046 1000 -1000 -0.103 -1000
Signaling events mediated by PRL 2 99 34 -0.167 0.026 1000 -1000 -0.034 -1000
Class IB PI3K non-lipid kinase events 2 6 3 -0.005 0.005 1000 -1000 -0.016 -1000
p38 MAPK signaling pathway 2 95 44 -0.078 0.039 1000 -1000 -0.08 -1000
Alternative NF-kappaB pathway 2 38 13 -0.091 0.02 1000 -1000 -0.037 -1000
Regulation of Androgen receptor activity 2 152 70 -0.211 0.063 1000 -1000 -0.074 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 1 27 23 -0.015 0.036 1000 -1000 -0.049 -1000
Signaling events mediated by HDAC Class II 1 104 75 -0.081 0.046 1000 -1000 -0.046 -1000
BARD1 signaling events 1 73 57 -0.031 0.054 1000 -1000 -0.08 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 1 89 54 -0.141 0.056 1000 -1000 -0.103 -1000
Arf6 downstream pathway 1 78 43 -0.052 0.027 1000 -1000 -0.039 -1000
PLK1 signaling events 1 98 85 -0.027 0.041 1000 -1000 -0.05 -1000
Insulin-mediated glucose transport 1 39 32 -0.041 0.039 1000 -1000 -0.056 -1000
Class I PI3K signaling events mediated by Akt 1 69 68 -0.054 0.069 1000 -1000 -0.068 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 1 139 83 -0.089 0.051 1000 -1000 -0.082 -1000
Signaling events mediated by HDAC Class I 1 150 104 -0.061 0.068 1000 -1000 -0.083 -1000
Effects of Botulinum toxin 1 43 26 -0.042 0.027 1000 -1000 -0.071 -1000
Arf6 trafficking events 1 92 71 -0.077 0.053 1000 -1000 -0.076 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 1 60 33 -0.147 0.06 1000 -1000 -0.073 -1000
Rapid glucocorticoid signaling 1 21 20 -0.03 0.02 1000 -1000 -0.019 -1000
Aurora B signaling 1 113 67 -0.076 0.04 1000 -1000 -0.08 -1000
Circadian rhythm pathway 0 21 22 -0.033 0.062 1000 -1000 -0.03 -1000
Aurora C signaling 0 6 7 -0.037 0.03 1000 -1000 -0.036 -1000
S1P5 pathway 0 10 17 -0.029 0.03 1000 -1000 -0.032 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 12 27 -0.009 0.046 1000 -1000 -0.058 -1000
S1P4 pathway 0 10 25 0 0.038 1000 -1000 -0.031 -1000
Arf1 pathway 0 21 54 -0.01 0.052 1000 -1000 -0.043 -1000
Total 547 35251 7203 -22.7128308403 6.1649503839 131000 -131000 -8.87127913399 -131000
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.299 0.861 -9999 0 -1.546 21 21
HDAC7 0.003 0.006 -9999 0 -9999 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.331 0.657 -9999 0 -1.229 22 22
SMAD4 0.012 0.085 -9999 0 -0.707 1 1
ID2 -0.317 0.891 -9999 0 -1.608 21 21
AP1 -0.179 0.323 -9999 0 -0.598 24 24
ABCG2 -0.359 0.865 -9999 0 -1.576 22 22
HIF1A -0.042 0.225 -9999 0 -0.703 6 6
TFF3 -0.333 0.895 -9999 0 -1.56 23 23
GATA2 -0.012 0.129 -9999 0 -0.543 4 4
AKT1 0.026 0.12 -9999 0 -9999 0 0
response to hypoxia 0 0.128 -9999 0 -0.244 1 1
MCL1 -0.31 0.873 -9999 0 -1.574 21 21
NDRG1 -0.335 0.913 -9999 0 -1.621 22 22
SERPINE1 -0.348 0.894 -9999 0 -1.631 21 21
FECH -0.299 0.861 -9999 0 -1.546 21 21
FURIN -0.299 0.861 -9999 0 -1.546 21 21
NCOA2 0.007 0.065 -9999 0 -0.523 1 1
EP300 0.051 0.198 -9999 0 -0.416 3 3
HMOX1 -0.328 0.883 -9999 0 -1.602 21 21
BHLHE40 -0.311 0.859 -9999 0 -1.515 22 22
BHLHE41 -0.311 0.859 -9999 0 -1.515 22 22
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.059 0.179 -9999 0 -0.52 7 7
ENG 0.048 0.222 -9999 0 -0.653 2 2
JUN -0.095 0.259 -9999 0 -0.669 12 12
RORA -0.309 0.879 -9999 0 -1.582 21 21
ABCB1 -0.398 0.641 -9999 0 -1.433 19 19
TFRC -0.301 0.864 -9999 0 -1.552 21 21
CXCR4 -0.331 0.909 -9999 0 -1.654 21 21
TF -0.313 0.865 -9999 0 -1.565 21 21
CITED2 -0.303 0.868 -9999 0 -1.561 21 21
HIF1A/ARNT -0.981 1.858 0.584 6 -3.255 23 29
LDHA -0.296 0.603 -9999 0 -1.574 13 13
ETS1 -0.315 0.886 -9999 0 -1.599 21 21
PGK1 -0.301 0.865 -9999 0 -1.554 21 21
NOS2 -0.311 0.859 -9999 0 -1.515 22 22
ITGB2 -0.325 0.901 -9999 0 -1.635 21 21
ALDOA -0.299 0.861 -9999 0 -1.546 21 21
Cbp/p300/CITED2 -0.298 0.883 -9999 0 -1.573 21 21
FOS -0.157 0.29 -9999 0 -0.617 20 20
HK2 -0.317 0.886 -9999 0 -1.595 21 21
SP1 0.019 0.035 -9999 0 -9999 0 0
GCK 0.048 0.333 -9999 0 -0.958 3 3
HK1 -0.301 0.865 -9999 0 -1.553 21 21
NPM1 -0.299 0.861 -9999 0 -1.546 21 21
EGLN1 -0.299 0.861 -9999 0 -1.546 21 21
CREB1 0.016 0.088 -9999 0 -0.717 1 1
PGM1 -0.299 0.861 -9999 0 -1.546 21 21
SMAD3 0.012 0.085 -9999 0 -0.705 1 1
EDN1 -0.218 0.642 -9999 0 -1.43 15 15
IGFBP1 -0.353 0.879 -9999 0 -1.564 22 22
VEGFA -0.191 0.707 -9999 0 -1.221 20 20
HIF1A/JAB1 -0.049 0.149 -9999 0 -0.521 6 6
CP -0.467 0.881 -9999 0 -1.644 23 23
CXCL12 -0.346 0.889 -9999 0 -1.551 23 23
COPS5 0.015 0.013 -9999 0 -9999 0 0
SMAD3/SMAD4 0.019 0.091 -9999 0 -0.522 2 2
BNIP3 -0.319 0.889 -9999 0 -1.57 22 22
EGLN3 -0.337 0.91 -9999 0 -1.655 21 21
CA9 -0.331 0.913 -9999 0 -1.655 21 21
TERT -0.303 0.868 -9999 0 -1.56 21 21
ENO1 -0.32 0.896 -9999 0 -1.617 21 21
PFKL -0.304 0.868 -9999 0 -1.562 21 21
NCOA1 0.018 0.006 -9999 0 -9999 0 0
ADM -0.324 0.895 -9999 0 -1.624 21 21
ARNT 0.023 0.106 -9999 0 -9999 0 0
HNF4A 0.014 0.086 -9999 0 -0.705 1 1
ADFP -0.349 0.917 -9999 0 -1.627 22 22
SLC2A1 -0.178 0.688 -9999 0 -1.187 20 20
LEP -0.324 0.872 -9999 0 -1.577 21 21
HIF1A/ARNT/Cbp/p300 -0.36 0.709 -9999 0 -1.291 23 23
EPO -0.12 0.482 -9999 0 -0.818 11 11
CREBBP 0.057 0.184 -9999 0 -0.314 2 2
HIF1A/ARNT/Cbp/p300/HDAC7 -0.407 0.792 -9999 0 -1.479 22 22
PFKFB3 -0.315 0.885 -9999 0 -1.6 21 21
NT5E -0.311 0.881 -9999 0 -1.587 21 21
Endothelins

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
AKT1 -0.173 0.41 -9999 0 -0.72 19 19
PTK2B 0.02 0.001 -9999 0 -9999 0 0
mol:Ca2+ -0.165 0.426 -9999 0 -0.91 15 15
EDN1 -0.147 0.331 -9999 0 -0.741 15 15
EDN3 -0.048 0.18 -9999 0 -0.523 9 9
EDN2 -0.288 0.331 -9999 0 -0.632 34 34
HRAS/GDP -0.19 0.427 -9999 0 -0.875 18 18
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.185 0.424 -9999 0 -0.825 18 18
ADCY4 -0.198 0.424 -9999 0 -0.929 14 14
ADCY5 -0.195 0.4 -9999 0 -0.821 16 16
ADCY6 -0.15 0.34 -9999 0 -0.742 13 13
ADCY7 -0.171 0.38 -9999 0 -0.871 12 12
ADCY1 -0.15 0.34 -9999 0 -0.742 13 13
ADCY2 -0.244 0.36 -9999 0 -0.708 21 21
ADCY3 -0.172 0.386 -9999 0 -0.823 14 14
ADCY8 -0.219 0.336 -9999 0 -0.689 18 18
ADCY9 -0.158 0.353 -9999 0 -0.761 13 13
arachidonic acid secretion -0.184 0.388 -9999 0 -0.766 19 19
ETB receptor/Endothelin-1/Gq/GTP -0.151 0.291 -9999 0 -0.549 20 20
GNAO1 0.02 0 -9999 0 -9999 0 0
HRAS 0.019 0.002 -9999 0 -9999 0 0
ETA receptor/Endothelin-1/G12/GTP -0.162 0.402 0.358 11 -0.744 16 27
ETA receptor/Endothelin-1/Gs/GTP -0.161 0.384 0.336 11 -0.799 13 24
mol:GTP -0.001 0.007 -9999 0 -9999 0 0
COL3A1 -0.213 0.466 -9999 0 -0.874 18 18
EDNRB -0.122 0.269 -9999 0 -0.66 14 14
response to oxidative stress 0 0 -9999 0 -9999 0 0
CYSLTR2 -0.223 0.447 -9999 0 -0.796 20 20
CYSLTR1 -0.182 0.421 -9999 0 -0.9 13 13
SLC9A1 -0.081 0.176 0.226 5 -0.39 10 15
mol:GDP -0.228 0.489 -9999 0 -1.009 18 18
SLC9A3 -0.283 0.505 -9999 0 -0.971 22 22
RAF1 -0.214 0.439 -9999 0 -0.901 18 18
JUN -0.204 0.494 -9999 0 -1.058 16 16
JAK2 -0.173 0.41 -9999 0 -0.875 13 13
mol:IP3 -0.212 0.423 -9999 0 -0.874 18 18
ETA receptor/Endothelin-1 -0.207 0.473 0.417 11 -0.819 19 30
PLCB1 -0.13 0.292 -9999 0 -0.698 15 15
PLCB2 0.018 0.006 -9999 0 -9999 0 0
ETA receptor/Endothelin-3 -0.122 0.249 -9999 0 -0.512 18 18
FOS -0.217 0.419 -9999 0 -0.863 17 17
Gai/GDP 0.01 0.158 -9999 0 -1.147 1 1
CRK 0 0.12 -9999 0 -0.709 2 2
mol:Ca ++ -0.304 0.542 -9999 0 -1.007 22 22
BCAR1 0.02 0.001 -9999 0 -9999 0 0
PRKCB1 -0.23 0.461 -9999 0 -0.932 19 19
GNAQ -0.001 0.008 -9999 0 -9999 0 0
GNAZ 0.012 0.064 -9999 0 -0.523 1 1
GNAL 0.01 0.085 -9999 0 -0.708 1 1
Gs family/GDP -0.227 0.37 -9999 0 -0.807 19 19
ETA receptor/Endothelin-1/Gq/GTP -0.154 0.372 -9999 0 -0.643 20 20
MAPK14 -0.165 0.341 -9999 0 -0.762 16 16
TRPC6 -0.184 0.464 -9999 0 -0.995 15 15
GNAI2 0.01 0.085 -9999 0 -0.708 1 1
GNAI3 0.02 0 -9999 0 -9999 0 0
GNAI1 0 0.12 -9999 0 -0.708 2 2
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.186 0.36 -9999 0 -0.815 16 16
ETB receptor/Endothelin-2 -0.294 0.325 -9999 0 -0.561 39 39
ETB receptor/Endothelin-3 -0.122 0.24 -9999 0 -0.478 21 21
ETB receptor/Endothelin-1 -0.21 0.31 -9999 0 -0.598 24 24
MAPK3 -0.23 0.448 -9999 0 -0.866 20 20
MAPK1 -0.23 0.448 -9999 0 -0.866 20 20
Rac1/GDP -0.187 0.428 -9999 0 -0.875 18 18
cAMP biosynthetic process -0.205 0.374 -9999 0 -0.8 16 16
MAPK8 -0.213 0.527 -9999 0 -1.134 15 15
SRC 0.02 0.001 -9999 0 -9999 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.075 0.197 -9999 0 -0.535 7 7
p130Cas/CRK/Src/PYK2 -0.204 0.488 -9999 0 -0.992 18 18
mol:K + 0 0 -9999 0 -9999 0 0
G12/GDP -0.187 0.428 -9999 0 -0.875 18 18
COL1A2 -0.32 0.516 -9999 0 -0.945 23 23
EntrezGene:2778 0 0 -9999 0 -9999 0 0
ETA receptor/Endothelin-2 -0.291 0.323 -9999 0 -0.587 32 32
mol:DAG -0.212 0.424 -9999 0 -0.876 18 18
MAP2K2 -0.21 0.42 -9999 0 -0.788 21 21
MAP2K1 -0.21 0.42 -9999 0 -0.788 21 21
EDNRA -0.105 0.287 -9999 0 -0.688 12 12
positive regulation of muscle contraction -0.148 0.369 -9999 0 -0.819 12 12
Gq family/GDP -0.216 0.407 -9999 0 -0.906 17 17
HRAS/GTP -0.217 0.451 -9999 0 -0.931 18 18
PRKCH -0.219 0.461 -9999 0 -0.932 18 18
RAC1 0.02 0 -9999 0 -9999 0 0
PRKCA -0.193 0.401 -9999 0 -0.825 18 18
PRKCB -0.203 0.399 -9999 0 -0.831 18 18
PRKCE -0.192 0.399 -9999 0 -0.82 18 18
PRKCD -0.213 0.433 -9999 0 -0.908 18 18
PRKCG -0.193 0.402 -9999 0 -0.827 18 18
regulation of vascular smooth muscle contraction -0.26 0.494 -9999 0 -1.038 17 17
PRKCQ -0.208 0.433 -9999 0 -0.885 18 18
PLA2G4A -0.215 0.443 -9999 0 -0.88 19 19
GNA14 -0.061 0.224 -9999 0 -0.691 8 8
GNA15 0.008 0.086 -9999 0 -0.715 1 1
GNA12 0.02 0 -9999 0 -9999 0 0
GNA11 -0.013 0.126 -9999 0 -0.53 4 4
Rac1/GTP -0.162 0.401 0.358 11 -0.741 16 27
MMP1 -0.133 0.47 -9999 0 -0.869 18 18
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer -0.167 0.419 -9999 0 -0.963 15 15
VEGFR1 homodimer/NRP1 -0.181 0.417 -9999 0 -0.974 15 15
mol:DAG -0.229 0.399 -9999 0 -0.937 15 15
VEGFR1 homodimer/NRP1/VEGFR 121 -0.238 0.516 -9999 0 -1.204 15 15
CaM/Ca2+ -0.209 0.383 -9999 0 -0.889 15 15
HIF1A -0.098 0.275 -9999 0 -0.554 16 16
GAB1 -0.02 0.167 -9999 0 -0.708 4 4
AKT1 -0.2 0.417 -9999 0 -0.92 16 16
PLCG1 -0.233 0.406 -9999 0 -0.953 15 15
NOS3 -0.171 0.373 -9999 0 -0.821 16 16
CBL 0.02 0 -9999 0 -9999 0 0
mol:NO -0.159 0.35 -9999 0 -0.769 16 16
FLT1 -0.193 0.464 -9999 0 -1.076 15 15
PGF -0.141 0.263 -9999 0 -0.56 20 20
VEGFR1 homodimer/NRP2/VEGFR121 -0.226 0.517 -9999 0 -1.195 15 15
CALM1 0.02 0 -9999 0 -9999 0 0
PIK3CA 0.02 0 -9999 0 -9999 0 0
eNOS/Hsp90 -0.149 0.349 -9999 0 -0.781 15 15
endothelial cell proliferation -0.203 0.387 -9999 0 -0.898 15 15
mol:Ca2+ -0.226 0.393 -9999 0 -0.922 15 15
MAPK3 -0.18 0.351 -9999 0 -0.805 15 15
MAPK1 -0.18 0.351 -9999 0 -0.805 15 15
PIK3R1 -0.038 0.194 -9999 0 -0.677 6 6
PLGF homodimer -0.141 0.262 -9999 0 -0.559 20 20
PRKACA 0.02 0 -9999 0 -9999 0 0
RP11-342D11.1 0 0 -9999 0 -9999 0 0
CAV1 -0.031 0.185 -9999 0 -0.708 5 5
VEGFA homodimer -0.131 0.295 -9999 0 -0.707 15 15
VEGFR1 homodimer/VEGFA homodimer -0.25 0.544 -9999 0 -1.268 15 15
platelet activating factor biosynthetic process -0.165 0.34 -9999 0 -0.771 15 15
PI3K -0.239 0.444 -9999 0 -0.996 16 16
PRKCA -0.202 0.371 -9999 0 -0.861 15 15
PRKCB -0.213 0.37 -9999 0 -0.871 15 15
VEGFR1 homodimer/PLGF homodimer -0.265 0.434 -9999 0 -0.961 17 17
VEGFA -0.132 0.296 -9999 0 -0.708 15 15
VEGFB 0.02 0 -9999 0 -9999 0 0
mol:IP3 -0.229 0.399 -9999 0 -0.937 15 15
RASA1 -0.143 0.393 -9999 0 -0.889 15 15
NRP2 0.02 0 -9999 0 -9999 0 0
VEGFR1 homodimer -0.192 0.461 -9999 0 -1.069 15 15
VEGFB homodimer 0.02 0 -9999 0 -9999 0 0
NCK1 0.01 0.085 -9999 0 -0.708 1 1
eNOS/Caveolin-1 -0.165 0.374 -9999 0 -0.809 16 16
PTPN11 0.02 0 -9999 0 -9999 0 0
mol:PI-3-4-5-P3 -0.233 0.427 -9999 0 -0.965 16 16
mol:L-citrulline -0.159 0.35 -9999 0 -0.769 16 16
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.209 0.5 -9999 0 -1.099 16 16
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.23 0.529 -9999 0 -1.215 15 15
CD2AP 0.012 0.064 -9999 0 -0.523 1 1
PI3K/GAB1 -0.234 0.455 -9999 0 -1.015 16 16
PDPK1 -0.212 0.412 -9999 0 -0.914 16 16
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.226 0.517 -9999 0 -1.195 15 15
mol:NADP -0.159 0.35 -9999 0 -0.769 16 16
HSP90AA1 0.005 0.089 -9999 0 -0.523 2 2
ubiquitin-dependent protein catabolic process -0.202 0.481 -9999 0 -1.061 16 16
VEGFR1 homodimer/NRP2 -0.167 0.419 -9999 0 -0.963 15 15
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 0.02 0 -9999 0 -9999 0 0
CCL5 -0.096 0.25 -9999 0 -0.623 13 13
SDCBP 0.002 0.106 -9999 0 -0.616 2 2
FGFR/FGF2/Syndecan-1 -0.186 0.251 -9999 0 -0.573 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 -0.168 0.241 -9999 0 -0.54 16 16
Syndecan-1/Syntenin -0.177 0.26 -9999 0 -0.579 16 16
MAPK3 -0.157 0.245 -9999 0 -0.567 13 13
HGF/MET -0.02 0.155 -9999 0 -0.481 7 7
TGFB1/TGF beta receptor Type II 0.02 0 -9999 0 -9999 0 0
BSG -0.033 0.161 -9999 0 -0.523 7 7
keratinocyte migration -0.165 0.236 -9999 0 -0.531 16 16
Syndecan-1/RANTES -0.228 0.297 -9999 0 -0.634 19 19
Syndecan-1/CD147 -0.177 0.261 -9999 0 -0.57 16 16
Syndecan-1/Syntenin/PIP2 -0.171 0.252 -9999 0 -0.561 16 16
LAMA5 0.02 0 -9999 0 -9999 0 0
positive regulation of cell-cell adhesion -0.189 0.224 -9999 0 -0.545 16 16
MMP7 -0.179 0.305 -9999 0 -0.632 22 22
HGF -0.023 0.159 -9999 0 -0.597 5 5
Syndecan-1/CASK -0.18 0.239 -9999 0 -0.55 16 16
Syndecan-1/HGF/MET -0.185 0.276 -9999 0 -0.602 17 17
regulation of cell adhesion -0.142 0.238 -9999 0 -0.585 10 10
HPSE -0.043 0.194 -9999 0 -0.629 7 7
positive regulation of cell migration -0.186 0.251 -9999 0 -0.573 16 16
SDC1 -0.188 0.254 -9999 0 -0.58 16 16
Syndecan-1/Collagen -0.186 0.251 -9999 0 -0.573 16 16
PPIB 0.02 0 -9999 0 -9999 0 0
MET -0.005 0.122 -9999 0 -0.585 3 3
PRKACA 0.02 0 -9999 0 -9999 0 0
MMP9 -0.149 0.266 -9999 0 -0.559 21 21
MAPK1 -0.157 0.245 -9999 0 -0.567 13 13
homophilic cell adhesion -0.184 0.248 -9999 0 -0.566 16 16
MMP1 -0.141 0.283 -9999 0 -0.626 18 18
HIF-2-alpha transcription factor network

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
MMP14 -0.021 0.181 -9999 0 -1.507 1 1
oxygen homeostasis 0.002 0.021 -9999 0 -9999 0 0
TCEB2 0.02 0 -9999 0 -9999 0 0
TCEB1 0.02 0 -9999 0 -9999 0 0
VHL/Elongin B/Elongin C/HIF2A -0.122 0.275 -9999 0 -0.595 16 16
EPO -0.189 0.455 -9999 0 -0.792 21 21
FIH (dimer) 0.012 0.089 -9999 0 -0.715 1 1
APEX1 0.024 0.019 -9999 0 -9999 0 0
SERPINE1 -0.199 0.571 -9999 0 -1.002 22 22
FLT1 -0.347 0.688 -9999 0 -1.619 16 16
ADORA2A -0.163 0.501 -9999 0 -0.917 19 19
germ cell development -0.147 0.505 -9999 0 -0.936 18 18
SLC11A2 -0.146 0.519 -9999 0 -0.939 19 19
BHLHE40 -0.159 0.518 -9999 0 -0.93 20 20
HIF1AN 0.012 0.089 -9999 0 -0.716 1 1
HIF2A/ARNT/SIRT1 -0.126 0.396 -9999 0 -0.766 16 16
ETS1 -0.036 0.224 -9999 0 -0.718 7 7
CITED2 -0.04 0.239 -9999 0 -1.432 2 2
KDR -0.291 0.621 -9999 0 -1.539 14 14
PGK1 -0.149 0.526 -9999 0 -0.975 18 18
SIRT1 0.008 0.085 -9999 0 -0.708 1 1
response to hypoxia -0.003 0.007 -9999 0 -9999 0 0
HIF2A/ARNT -0.264 0.721 -9999 0 -1.305 20 20
EPAS1 -0.099 0.356 -9999 0 -0.7 16 16
SP1 0.031 0.004 -9999 0 -9999 0 0
ABCG2 -0.214 0.537 -9999 0 -0.979 20 20
EFNA1 -0.185 0.581 -9999 0 -1.101 18 18
FXN -0.153 0.496 -9999 0 -0.905 19 19
POU5F1 -0.165 0.536 -9999 0 -1.006 18 18
neuron apoptosis 0.227 0.639 1.165 20 -9999 0 20
EP300 0.01 0.085 -9999 0 -0.708 1 1
EGLN3 -0.144 0.311 -9999 0 -0.699 17 17
EGLN2 0.022 0.02 -9999 0 -9999 0 0
EGLN1 0.022 0.02 -9999 0 -9999 0 0
VHL/Elongin B/Elongin C 0.041 0 -9999 0 -9999 0 0
VHL 0.02 0 -9999 0 -9999 0 0
ARNT 0.023 0.019 -9999 0 -9999 0 0
SLC2A1 -0.187 0.545 -9999 0 -1.019 19 19
TWIST1 -0.168 0.511 -9999 0 -0.901 21 21
ELK1 0.031 0.005 -9999 0 -9999 0 0
HIF2A/ARNT/Cbp/p300 -0.17 0.349 -9999 0 -0.764 16 16
VEGFA -0.198 0.602 -9999 0 -1.168 18 18
CREBBP 0.02 0 -9999 0 -9999 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.148 0.241 -9999 0 -0.576 16 16
FYN -0.168 0.406 -9999 0 -0.771 19 19
LAT/GRAP2/SLP76 -0.182 0.297 -9999 0 -0.686 17 17
IKBKB 0.02 0 -9999 0 -9999 0 0
AKT1 -0.073 0.247 -9999 0 -0.486 17 17
B2M 0.018 0.008 -9999 0 -9999 0 0
IKBKG -0.039 0.063 -9999 0 -0.177 8 8
MAP3K8 -0.089 0.257 -9999 0 -0.691 11 11
mol:Ca2+ -0.016 0.04 -9999 0 -0.121 8 8
integrin-mediated signaling pathway -0.011 0.127 -9999 0 -0.429 6 6
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.137 0.367 -9999 0 -0.75 17 17
TRPV6 -0.01 0.131 -9999 0 -0.601 3 3
CD28 -0.054 0.211 -9999 0 -0.644 8 8
SHC1 -0.139 0.353 -9999 0 -0.722 17 17
receptor internalization -0.176 0.402 -9999 0 -0.806 18 18
PRF1 -0.14 0.329 -9999 0 -0.773 12 12
KRAS 0.02 0 -9999 0 -9999 0 0
GRB2 0.01 0.085 -9999 0 -0.708 1 1
COT/AKT1 -0.078 0.242 -9999 0 -0.479 16 16
LAT -0.159 0.376 -9999 0 -0.779 17 17
EntrezGene:6955 -0.001 0.005 -9999 0 -9999 0 0
CD3D -0.093 0.243 -9999 0 -0.603 13 13
CD3E 0.01 0.066 -9999 0 -0.539 1 1
CD3G -0.158 0.292 -9999 0 -0.623 20 20
RASGRP2 -0.015 0.072 -9999 0 -0.196 9 9
RASGRP1 -0.071 0.265 -9999 0 -0.535 15 15
HLA-A 0.017 0.009 -9999 0 -9999 0 0
RASSF5 -0.028 0.177 -9999 0 -0.671 5 5
RAP1A/GTP/RAPL -0.011 0.128 -9999 0 -0.431 6 6
mol:GTP 0 0 -9999 0 -9999 0 0
mol:GDP 0.008 0.085 -9999 0 -0.146 10 10
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.075 0.115 -9999 0 -0.293 13 13
PRKCA -0.075 0.121 -9999 0 -0.296 15 15
GRAP2 0 0.12 -9999 0 -0.708 2 2
mol:IP3 -0.124 0.207 -9999 0 -0.501 15 15
EntrezGene:6957 -0.001 0.006 -9999 0 -9999 0 0
TCR/CD3/MHC I/CD8 -0.14 0.329 -9999 0 -0.671 16 16
ORAI1 -0.008 0.122 0.329 3 -0.386 5 8
CSK -0.144 0.361 -9999 0 -0.736 17 17
B7 family/CD28 -0.214 0.353 -9999 0 -0.768 18 18
CHUK 0.02 0 -9999 0 -9999 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.181 0.423 -9999 0 -0.839 18 18
PTPN6 -0.149 0.363 -9999 0 -0.722 18 18
VAV1 -0.156 0.392 -9999 0 -0.795 17 17
Monovalent TCR/CD3 -0.162 0.349 -9999 0 -0.666 19 19
CBL 0.02 0 -9999 0 -9999 0 0
LCK -0.162 0.399 -9999 0 -0.761 19 19
PAG1 -0.165 0.384 -9999 0 -0.741 19 19
RAP1A 0.01 0.085 -9999 0 -0.708 1 1
TCR/CD3/MHC I/CD8/LCK -0.185 0.424 -9999 0 -0.846 18 18
CD80 0.004 0.09 -9999 0 -0.527 2 2
CD86 -0.009 0.136 -9999 0 -0.653 3 3
PDK1/CARD11/BCL10/MALT1 -0.093 0.142 -9999 0 -0.363 13 13
HRAS 0.02 0 -9999 0 -9999 0 0
GO:0035030 -0.122 0.309 -9999 0 -0.611 18 18
CD8A -0.001 0.006 -9999 0 -9999 0 0
CD8B -0.11 0.245 -9999 0 -0.565 16 16
PTPRC -0.069 0.237 -9999 0 -0.693 9 9
PDK1/PKC theta -0.092 0.307 -9999 0 -0.604 17 17
CSK/PAG1 -0.149 0.367 -9999 0 -0.741 17 17
SOS1 0.02 0 -9999 0 -9999 0 0
peptide-MHC class I 0.023 0.016 -9999 0 -9999 0 0
GRAP2/SLP76 -0.203 0.344 -9999 0 -0.759 18 18
STIM1 -0.026 0.144 -9999 0 -0.54 5 5
RAS family/GTP 0.008 0.111 -9999 0 -0.194 9 9
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.198 0.448 -9999 0 -0.89 18 18
mol:DAG -0.113 0.182 -9999 0 -0.434 16 16
RAP1A/GDP 0.004 0.041 -9999 0 -0.138 1 1
PLCG1 0.02 0 -9999 0 -9999 0 0
CD247 -0.14 0.291 -9999 0 -0.658 17 17
cytotoxic T cell degranulation -0.134 0.316 -9999 0 -0.741 12 12
RAP1A/GTP -0.012 0.026 -9999 0 -0.074 10 10
mol:PI-3-4-5-P3 -0.099 0.293 -9999 0 -0.589 17 17
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.166 0.281 -9999 0 -0.68 15 15
NRAS 0.005 0.089 -9999 0 -0.523 2 2
ZAP70 -0.006 0.123 -9999 0 -0.587 3 3
GRB2/SOS1 0.022 0.065 -9999 0 -0.526 1 1
LAT/GRAP2/SLP76/VAV1 -0.173 0.28 -9999 0 -0.649 17 17
MALT1 -0.031 0.185 -9999 0 -0.708 5 5
TRAF6 0.02 0 -9999 0 -9999 0 0
CD8 heterodimer -0.08 0.183 -9999 0 -0.417 16 16
CARD11 -0.05 0.188 -9999 0 -0.544 9 9
PRKCB -0.079 0.122 -9999 0 -0.295 16 16
PRKCE -0.075 0.121 -9999 0 -0.296 15 15
PRKCQ -0.121 0.349 -9999 0 -0.705 17 17
LCP2 -0.068 0.235 -9999 0 -0.687 9 9
BCL10 0.01 0.085 -9999 0 -0.708 1 1
regulation of survival gene product expression -0.055 0.211 -9999 0 -0.405 17 17
IKK complex 0.019 0.076 -9999 0 -9999 0 0
RAS family/GDP -0.008 0.016 -9999 0 -0.076 2 2
MAP3K14 -0.073 0.232 -9999 0 -0.474 15 15
PDPK1 -0.065 0.238 -9999 0 -0.462 17 17
TCR/CD3/MHC I/CD8/Fyn -0.162 0.374 -9999 0 -0.79 16 16
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.023 0.152 -9999 0 -0.446 8 8
AKT1 -0.1 0.408 -9999 0 -0.828 16 16
PTK2B -0.187 0.51 -9999 0 -1.154 14 14
VEGFR2 homodimer/Frs2 -0.132 0.4 -9999 0 -1.076 10 10
CAV1 -0.031 0.185 -9999 0 -0.708 5 5
CALM1 0.02 0 -9999 0 -9999 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.205 0.529 -9999 0 -1.258 13 13
endothelial cell proliferation -0.069 0.375 -9999 0 -0.76 15 15
mol:Ca2+ -0.206 0.548 -9999 0 -1.21 15 15
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.184 0.509 -9999 0 -1.198 13 13
RP11-342D11.1 -0.218 0.545 -9999 0 -1.216 15 15
CDH5 -0.018 0.157 -9999 0 -0.662 4 4
VEGFA homodimer -0.065 0.225 -9999 0 -0.467 16 16
SHC1 0.02 0 -9999 0 -9999 0 0
SHC2 -0.063 0.223 -9999 0 -0.646 9 9
HRAS/GDP -0.222 0.402 -9999 0 -0.965 15 15
SH2D2A -0.119 0.263 -9999 0 -0.604 16 16
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.195 0.343 -9999 0 -0.839 15 15
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.279 0.564 -9999 0 -1.244 16 16
VEGFR1 homodimer -0.131 0.295 -9999 0 -0.707 15 15
SHC/GRB2/SOS1 -0.276 0.513 -9999 0 -1.211 15 15
GRB10 -0.236 0.597 -9999 0 -1.231 17 17
PTPN11 0.02 0 -9999 0 -9999 0 0
GRB2 0.01 0.085 -9999 0 -0.708 1 1
PAK1 0.012 0.064 -9999 0 -0.523 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.249 0.481 -9999 0 -1.207 13 13
HRAS 0.02 0 -9999 0 -9999 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.103 0.334 -9999 0 -0.687 16 16
HIF1A -0.028 0.16 -9999 0 -0.554 6 6
FRS2 0.02 0 -9999 0 -9999 0 0
oxygen and reactive oxygen species metabolic process -0.238 0.454 -9999 0 -1.149 13 13
mol:GTP 0 0 -9999 0 -9999 0 0
FLT4 0.02 0 -9999 0 -9999 0 0
Nck/Pak 0.017 0.079 -9999 0 -0.446 2 2
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.266 0.61 -9999 0 -1.34 16 16
mol:GDP -0.251 0.46 -9999 0 -1.097 15 15
mol:NADP -0.064 0.325 -9999 0 -0.663 15 15
eNOS/Hsp90 -0.053 0.312 -9999 0 -0.63 15 15
PIK3R1 -0.038 0.194 -9999 0 -0.677 6 6
mol:IP3 -0.219 0.576 -9999 0 -1.27 15 15
HIF1A/ARNT -0.005 0.118 -9999 0 -0.393 6 6
SHB 0.02 0 -9999 0 -9999 0 0
VEGFA -0.129 0.297 -9999 0 -0.708 15 15
VEGFC -0.071 0.241 -9999 0 -0.708 9 9
FAK1/Vinculin -0.149 0.471 -9999 0 -1.046 14 14
mol:Ca ++ 0 0 -9999 0 -9999 0 0
RHOA 0.01 0.085 -9999 0 -0.708 1 1
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.216 0.558 -9999 0 -1.22 15 15
PTPN6 0.02 0 -9999 0 -9999 0 0
EPAS1 -0.125 0.34 -9999 0 -0.737 15 15
mol:L-citrulline -0.064 0.325 -9999 0 -0.663 15 15
ITGAV 0 0.12 -9999 0 -0.708 2 2
PIK3CA 0.02 0 -9999 0 -9999 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.188 0.519 -9999 0 -1.22 13 13
VEGFR2 homodimer/VEGFA homodimer -0.274 0.682 -9999 0 -1.5 15 15
VEGFR2/3 heterodimer -0.132 0.4 -9999 0 -1.076 10 10
VEGFB 0.02 0 -9999 0 -9999 0 0
MAPK11 -0.224 0.59 -9999 0 -1.304 15 15
VEGFR2 homodimer -0.152 0.44 -9999 0 -1.028 13 13
FLT1 -0.132 0.296 -9999 0 -0.708 15 15
NEDD4 -0.048 0.217 -9999 0 -0.709 7 7
MAPK3 -0.166 0.474 -9999 0 -1.037 15 15
MAPK1 -0.166 0.474 -9999 0 -1.037 15 15
VEGFA145/NRP2 -0.084 0.227 -9999 0 -0.526 15 15
VEGFR1/2 heterodimer -0.218 0.523 -9999 0 -1.256 13 13
KDR -0.154 0.443 -9999 0 -1.035 13 13
VEGFA165/NRP1/VEGFR2 homodimer -0.226 0.591 -9999 0 -1.302 15 15
SRC 0.02 0 -9999 0 -9999 0 0
platelet activating factor biosynthetic process -0.175 0.496 -9999 0 -1.087 15 15
PI3K -0.202 0.57 -9999 0 -1.229 16 16
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.209 0.541 -9999 0 -1.282 13 13
FES -0.239 0.62 -9999 0 -1.369 15 15
GAB1 -0.309 0.54 -9999 0 -1.244 17 17
VEGFR2 homodimer/VEGFA homodimer/Src -0.205 0.529 -9999 0 -1.258 13 13
CTNNB1 0.02 0 -9999 0 -9999 0 0
SOS1 0.02 0 -9999 0 -9999 0 0
ARNT 0.02 0 -9999 0 -9999 0 0
eNOS/Caveolin-1 -0.063 0.325 -9999 0 -0.655 15 15
VEGFR2 homodimer/VEGFA homodimer/Yes -0.205 0.529 -9999 0 -1.258 13 13
PI3K/GAB1 -0.103 0.419 -9999 0 -0.855 16 16
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.241 0.463 -9999 0 -1.164 13 13
PRKACA 0.02 0 -9999 0 -9999 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.163 0.444 -9999 0 -1.092 12 12
HSP90AA1 0.005 0.089 -9999 0 -0.523 2 2
CDC42 -0.235 0.612 -9999 0 -1.346 15 15
actin cytoskeleton reorganization -0.27 0.543 -9999 0 -1.203 16 16
PTK2 -0.192 0.545 -9999 0 -1.229 14 14
EDG1 -0.24 0.611 -9999 0 -1.3 16 16
mol:DAG -0.219 0.576 -9999 0 -1.27 15 15
CaM/Ca2+ -0.255 0.464 -9999 0 -1.108 15 15
MAP2K3 -0.22 0.58 -9999 0 -1.25 16 16
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.266 0.667 -9999 0 -1.366 17 17
PLCG1 -0.235 0.612 -9999 0 -1.346 15 15
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.184 0.509 -9999 0 -1.198 13 13
IQGAP1 0.02 0 -9999 0 -9999 0 0
YES1 0.02 0 -9999 0 -9999 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.205 0.529 -9999 0 -1.258 13 13
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.205 0.529 -9999 0 -1.258 13 13
cell migration -0.076 0.38 -9999 0 -0.821 13 13
mol:PI-3-4-5-P3 -0.155 0.478 -9999 0 -1.015 16 16
FYN -0.101 0.271 -9999 0 -0.708 12 12
VEGFB/NRP1 -0.19 0.504 -9999 0 -1.115 15 15
mol:NO -0.064 0.325 -9999 0 -0.663 15 15
PXN 0.02 0 -9999 0 -9999 0 0
HRAS/GTP -0.224 0.408 -9999 0 -0.978 15 15
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.266 0.665 -9999 0 -1.363 17 17
VHL 0.02 0 -9999 0 -9999 0 0
ITGB3 -0.03 0.169 -9999 0 -0.585 6 6
NOS3 -0.09 0.379 -9999 0 -0.792 15 15
VEGFR2 homodimer/VEGFA homodimer/Sck -0.245 0.584 -9999 0 -1.4 13 13
RAC1 0.02 0 -9999 0 -9999 0 0
PRKCA -0.178 0.507 -9999 0 -1.109 15 15
PRKCB -0.189 0.506 -9999 0 -1.118 15 15
VCL 0.02 0 -9999 0 -9999 0 0
VEGFA165/NRP1 -0.234 0.582 -9999 0 -1.296 15 15
VEGFR1/2 heterodimer/VEGFA homodimer -0.279 0.641 -9999 0 -1.349 17 17
VEGFA165/NRP2 -0.084 0.227 -9999 0 -0.526 15 15
MAPKKK cascade -0.146 0.475 -9999 0 -0.976 16 16
NRP2 0.02 0 -9999 0 -9999 0 0
VEGFC homodimer -0.071 0.24 -9999 0 -0.707 9 9
NCK1 0.01 0.085 -9999 0 -0.708 1 1
ROCK1 0.02 0 -9999 0 -9999 0 0
FAK1/Paxillin -0.149 0.471 -9999 0 -1.046 14 14
MAP3K13 -0.25 0.625 -9999 0 -1.353 16 16
PDPK1 -0.109 0.406 -9999 0 -0.835 16 16
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.02 0 -9999 0 -9999 0 0
EGFR -0.106 0.26 -9999 0 -0.629 14 14
EGF/EGFR -0.315 0.371 -9999 0 -0.654 30 30
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.163 0.241 -9999 0 -0.667 7 7
mol:GTP 0 0 -9999 0 -9999 0 0
EDNRA -0.094 0.256 -9999 0 -0.662 12 12
response to oxidative stress 0 0 -9999 0 -9999 0 0
EGF -0.247 0.304 -9999 0 -0.581 32 32
EGF/EGFR dimer/SHC -0.207 0.255 -9999 0 -0.542 19 19
mol:GDP -0.188 0.213 -9999 0 -0.656 7 7
mol:Ca2+ 0 0 -9999 0 -9999 0 0
EDN1 -0.132 0.296 -9999 0 -0.708 15 15
GRB2/SOS1 0.022 0.065 -9999 0 -0.526 1 1
HRAS/GTP -0.17 0.195 -9999 0 -0.606 7 7
SHC1 0.02 0 -9999 0 -9999 0 0
HRAS/GDP -0.173 0.198 -9999 0 -0.613 7 7
FRAP1 -0.145 0.228 -9999 0 -0.624 7 7
EGF/EGFR dimer -0.254 0.289 -9999 0 -0.495 39 39
SOS1 0.02 0 -9999 0 -9999 0 0
GRB2 0.01 0.085 -9999 0 -0.708 1 1
ETA receptor/Endothelin-1 -0.159 0.337 -9999 0 -0.686 19 19
IL23-mediated signaling events

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
CCL2 -0.438 0.611 -9999 0 -1.318 19 19
IL23A -0.345 0.516 -9999 0 -1.155 15 15
NF kappa B1 p50/RelA/I kappa B alpha -0.359 0.479 -9999 0 -1.131 16 16
positive regulation of T cell mediated cytotoxicity -0.375 0.574 -9999 0 -1.247 16 16
ITGA3 -0.386 0.57 -9999 0 -1.372 13 13
IL17F -0.182 0.343 -9999 0 -0.748 10 10
IL12B -0.006 0.114 -9999 0 -0.655 2 2
STAT1 (dimer) -0.383 0.57 -9999 0 -1.296 15 15
CD4 -0.311 0.475 -9999 0 -1.099 13 13
IL23 -0.341 0.501 -9999 0 -1.163 13 13
IL23R -0.027 0.129 -9999 0 -0.593 2 2
IL1B -0.402 0.589 -9999 0 -1.296 17 17
T-helper cell lineage commitment 0 0 -9999 0 -9999 0 0
IL24 -0.311 0.475 -9999 0 -1.145 11 11
TYK2 0.01 0.02 -9999 0 -9999 0 0
STAT4 -0.061 0.229 -9999 0 -0.708 8 8
STAT3 0.011 0.085 -9999 0 -0.708 1 1
IL18RAP -0.082 0.239 -9999 0 -0.674 10 10
IL12RB1 0.01 0.02 -9999 0 -9999 0 0
PIK3CA 0.021 0.001 -9999 0 -9999 0 0
IL12Rbeta1/TYK2 0.004 0.023 -9999 0 -9999 0 0
IL23R/JAK2 -0.035 0.14 -9999 0 -0.577 2 2
positive regulation of chronic inflammatory response -0.375 0.574 -9999 0 -1.247 16 16
natural killer cell activation 0.004 0.011 0.052 2 -9999 0 2
JAK2 0.013 0.027 -9999 0 -9999 0 0
PIK3R1 -0.037 0.194 -9999 0 -0.677 6 6
NFKB1 0.019 0.004 -9999 0 -9999 0 0
RELA 0.019 0.004 -9999 0 -9999 0 0
positive regulation of dendritic cell antigen processing and presentation -0.323 0.471 -9999 0 -1.086 13 13
ALOX12B -0.311 0.475 -9999 0 -1.099 13 13
CXCL1 -0.557 0.633 -9999 0 -1.295 26 26
T cell proliferation -0.375 0.574 -9999 0 -1.247 16 16
NFKBIA -0.012 0.147 -9999 0 -0.717 3 3
IL17A -0.121 0.292 -9999 0 -0.611 8 8
PI3K -0.375 0.496 -9999 0 -1.121 18 18
IFNG -0.052 0.059 -9999 0 -0.124 14 14
STAT3 (dimer) -0.338 0.464 -9999 0 -1.086 16 16
IL18R1 -0.128 0.287 -9999 0 -0.711 14 14
IL23/IL23R/JAK2/TYK2/SOCS3 -0.171 0.316 -9999 0 -0.897 5 5
IL18/IL18R -0.175 0.372 -9999 0 -0.739 19 19
macrophage activation -0.019 0.018 -9999 0 -0.045 10 10
TNF -0.34 0.512 -9999 0 -1.189 13 13
STAT3/STAT4 -0.387 0.507 -9999 0 -1.176 17 17
STAT4 (dimer) -0.379 0.577 -9999 0 -1.316 15 15
IL18 -0.079 0.22 -9999 0 -0.589 11 11
IL19 -0.311 0.475 -9999 0 -1.099 13 13
STAT5A (dimer) -0.357 0.542 -9999 0 -1.244 14 14
STAT1 -0.056 0.216 -9999 0 -0.662 8 8
SOCS3 -0.028 0.177 -9999 0 -0.671 5 5
CXCL9 -0.453 0.618 -9999 0 -1.35 19 19
MPO -0.317 0.481 -9999 0 -1.069 15 15
positive regulation of humoral immune response -0.375 0.574 -9999 0 -1.247 16 16
IL23/IL23R/JAK2/TYK2 -0.419 0.706 -9999 0 -1.476 15 15
IL6 -0.429 0.543 -9999 0 -1.17 19 19
STAT5A 0.012 0.064 -9999 0 -0.523 1 1
IL2 -0.006 0.12 -9999 0 -0.706 2 2
positive regulation of tyrosine phosphorylation of STAT protein 0.004 0.011 0.052 2 -9999 0 2
CD3E -0.314 0.477 -9999 0 -1.078 14 14
keratinocyte proliferation -0.375 0.574 -9999 0 -1.247 16 16
NOS2 -0.323 0.474 -9999 0 -1.043 16 16
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B -0.014 0.093 -9999 0 -0.323 6 6
ARNO/beta Arrestin1-2 -0.023 0.09 -9999 0 -0.413 3 3
EGFR -0.106 0.26 -9999 0 -0.629 14 14
EPHA2 -0.018 0.157 -9999 0 -0.662 4 4
USP6 0.02 0 -9999 0 -9999 0 0
IQSEC1 0.02 0 -9999 0 -9999 0 0
EGFR/EGFR/EGF/EGF -0.254 0.289 -9999 0 -0.495 39 39
ARRB2 0.019 0.041 -9999 0 -9999 0 0
mol:GTP 0.006 0.031 -9999 0 -0.234 1 1
ARRB1 0.01 0.085 -9999 0 -0.708 1 1
FBXO8 0.012 0.064 -9999 0 -0.523 1 1
TSHR -0.003 0.109 -9999 0 -0.524 3 3
EGF -0.247 0.304 -9999 0 -0.581 32 32
somatostatin receptor activity 0 0 -9999 0 -0.001 13 13
ARAP2 0 0 -9999 0 0 14 14
mol:GDP -0.083 0.123 -9999 0 -0.331 11 11
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 14 14
ITGA2B 0.02 0 -9999 0 -9999 0 0
ARF6 0.02 0 -9999 0 -9999 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.053 0.25 -9999 0 -0.577 11 11
ADAP1 0 0 -9999 0 0 12 12
KIF13B -0.025 0.15 -9999 0 -0.523 6 6
HGF/MET -0.02 0.155 -9999 0 -0.481 7 7
PXN 0.02 0 -9999 0 -9999 0 0
ARF6/GTP -0.097 0.138 -9999 0 -0.35 13 13
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.207 0.255 -9999 0 -0.542 19 19
ADRB2 -0.015 0.147 -9999 0 -0.616 4 4
receptor agonist activity 0 0 -9999 0 0 13 13
actin filament binding 0 0 -9999 0 -0.001 14 14
SRC 0.02 0 -9999 0 -9999 0 0
ITGB3 -0.03 0.169 -9999 0 -0.585 6 6
GNAQ 0 0 -9999 0 -0.001 12 12
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 12 12
ARF6/GDP -0.019 0.104 -9999 0 -0.369 3 3
ARF6/GDP/GULP/ACAP1 -0.148 0.186 -9999 0 -0.405 21 21
alphaIIb/beta3 Integrin/paxillin/GIT1 0.016 0.112 -9999 0 -0.396 3 3
ACAP1 0 0 -9999 0 -9999 0 0
ACAP2 0 0 -9999 0 0 14 14
LHCGR/beta Arrestin2 0.014 0.057 -9999 0 -0.322 2 2
EFNA1 -0.099 0.266 -9999 0 -0.693 12 12
HGF -0.023 0.159 -9999 0 -0.597 5 5
CYTH3 0 0 -9999 0 -0.001 13 13
CYTH2 -0.002 0.002 -9999 0 -0.005 14 14
NCK1 0.01 0.085 -9999 0 -0.708 1 1
fibronectin binding 0 0 -9999 0 0 12 12
endosomal lumen acidification 0 0 -9999 0 -0.001 14 14
microtubule-based process 0 0 -9999 0 -9999 0 0
GULP1 -0.159 0.283 -9999 0 -0.594 21 21
GNAQ/ARNO -0.002 0.003 -9999 0 -0.008 12 12
mol:Phosphatidic acid 0 0 -9999 0 0 14 14
PIP3-E -0.048 0.195 -9999 0 -0.593 8 8
MET -0.005 0.122 -9999 0 -0.585 3 3
GNA14 -0.058 0.223 -9999 0 -0.685 8 8
GNA15 0.01 0.085 -9999 0 -0.708 1 1
GIT1 0.01 0.085 -9999 0 -0.708 1 1
mol:PI-4-5-P2 0 0 -9999 0 -0.001 13 13
GNA11 -0.01 0.125 -9999 0 -0.524 4 4
LHCGR 0.005 0.089 -9999 0 -0.523 2 2
AGTR1 -0.323 0.314 -9999 0 -0.597 40 40
desensitization of G-protein coupled receptor protein signaling pathway 0.014 0.057 -9999 0 -0.321 2 2
IPCEF1/ARNO -0.194 0.223 -9999 0 -0.455 24 24
alphaIIb/beta3 Integrin -0.008 0.126 -9999 0 -0.42 6 6
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.344 0.712 -9999 0 -1.475 17 17
STAT6 (cleaved dimer) -0.477 0.648 -9999 0 -1.402 21 21
IGHG1 -0.057 0.248 -9999 0 -0.47 3 3
IGHG3 -0.345 0.672 -9999 0 -1.318 20 20
AKT1 -0.101 0.391 -9999 0 -0.908 7 7
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.047 0.27 -9999 0 -0.625 5 5
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.135 0.443 -9999 0 -1.132 7 7
THY1 -0.384 0.77 -9999 0 -1.627 17 17
MYB -0.005 0.122 -9999 0 -0.585 3 3
HMGA1 0.02 0 -9999 0 -9999 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.125 0.381 -9999 0 -0.679 15 15
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.134 0.44 -9999 0 -1.21 6 6
SP1 0.023 0.021 -9999 0 -9999 0 0
INPP5D 0 0 -9999 0 -9999 0 0
SOCS5 0.009 0.084 -9999 0 -0.67 1 1
STAT6 (dimer)/ETS1 -0.42 0.703 -9999 0 -1.496 19 19
SOCS1 -0.158 0.458 -9999 0 -0.849 17 17
SOCS3 -0.125 0.443 -9999 0 -1.332 5 5
FCER2 -0.198 0.533 -9999 0 -1.112 11 11
PARP14 -0.028 0.186 -9999 0 -0.708 5 5
CCL17 -0.381 0.732 -9999 0 -1.494 18 18
GRB2 0.01 0.085 -9999 0 -0.708 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.078 0.327 -9999 0 -0.886 5 5
T cell proliferation -0.374 0.767 -9999 0 -1.613 17 17
IL4R/JAK1 -0.39 0.77 -9999 0 -1.638 17 17
EGR2 -0.396 0.773 -9999 0 -1.59 18 18
JAK2 0.02 0.044 -9999 0 -9999 0 0
JAK3 0.025 0.01 -9999 0 -9999 0 0
PIK3R1 -0.038 0.194 -9999 0 -0.677 6 6
JAK1 -0.017 0.168 -9999 0 -0.703 4 4
COL1A2 -0.199 0.506 -9999 0 -1.129 12 12
CCL26 -0.375 0.733 -9999 0 -1.507 18 18
IL4R -0.41 0.833 -9999 0 -1.749 17 17
PTPN6 0.024 0.017 -9999 0 -9999 0 0
IL13RA2 -0.453 0.796 -9999 0 -1.574 21 21
IL13RA1 0.02 0.044 -9999 0 -9999 0 0
IRF4 -0.01 0.227 -9999 0 -0.953 2 2
ARG1 -0.058 0.288 -9999 0 -0.814 5 5
CBL -0.107 0.36 -9999 0 -0.705 9 9
GTF3A -0.005 0.089 -9999 0 -0.615 1 1
PIK3CA 0.02 0 -9999 0 -9999 0 0
IL13RA1/JAK2 0.027 0.069 -9999 0 -9999 0 0
IRF4/BCL6 -0.049 0.265 -9999 0 -0.786 4 4
CD40LG 0.013 0.122 -9999 0 -0.707 2 2
MAPK14 -0.112 0.386 -9999 0 -0.795 9 9
mitosis -0.091 0.369 -9999 0 -0.836 7 7
STAT6 -0.479 0.94 -9999 0 -1.854 19 19
SPI1 -0.033 0.187 -9999 0 -0.595 7 7
RPS6KB1 -0.078 0.357 -9999 0 -0.837 6 6
STAT6 (dimer) -0.478 0.943 -9999 0 -1.857 19 19
STAT6 (dimer)/PARP14 -0.415 0.815 -9999 0 -1.596 20 20
mast cell activation 0.001 0.021 -9999 0 -9999 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.1 0.37 -9999 0 -0.796 9 9
FRAP1 -0.101 0.391 -9999 0 -0.908 7 7
LTA -0.344 0.712 -9999 0 -1.474 17 17
FES 0.01 0.085 -9999 0 -0.708 1 1
T-helper 1 cell differentiation 0.424 0.853 1.644 20 -9999 0 20
CCL11 -0.355 0.696 -9999 0 -1.457 17 17
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.082 0.334 -9999 0 -0.728 7 7
IL2RG 0.002 0.111 -9999 0 -0.528 3 3
IL10 -0.344 0.713 -9999 0 -1.474 17 17
IRS1 -0.018 0.138 -9999 0 -0.523 5 5
IRS2 -0.04 0.171 -9999 0 -0.523 8 8
IL4 -0.005 0.18 -9999 0 -9999 0 0
IL5 -0.342 0.708 -9999 0 -1.464 17 17
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.22 0.527 -9999 0 -1 17 17
COL1A1 -0.349 0.625 -9999 0 -1.351 16 16
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -9999 0 0
IL4/IL4R/JAK1 -0.404 0.805 -9999 0 -1.715 17 17
IL2R gamma/JAK3 0.02 0.084 -9999 0 -0.372 3 3
TFF3 -0.407 0.79 -9999 0 -1.612 19 19
ALOX15 -0.351 0.724 -9999 0 -1.502 17 17
MYBL1 -0.003 0.109 -9999 0 -0.523 3 3
T-helper 2 cell differentiation -0.253 0.575 -9999 0 -1.141 16 16
SHC1 0.02 0 -9999 0 -9999 0 0
CEBPB 0.012 0.09 -9999 0 -0.514 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.135 0.444 -9999 0 -1.161 7 7
mol:PI-3-4-5-P3 -0.101 0.391 -9999 0 -0.909 7 7
PI3K -0.114 0.421 -9999 0 -1.009 7 7
DOK2 -0.038 0.194 -9999 0 -0.677 6 6
ETS1 -0.047 0.205 -9999 0 -0.67 7 7
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.07 0.328 -9999 0 -1.014 4 4
ITGB3 -0.366 0.737 -9999 0 -1.551 17 17
PIGR -0.606 0.834 -9999 0 -1.476 32 32
IGHE 0.006 0.073 -9999 0 -9999 0 0
MAPKKK cascade -0.067 0.32 -9999 0 -0.978 4 4
BCL6 -0.06 0.221 -9999 0 -0.683 8 8
OPRM1 -0.342 0.708 -9999 0 -1.464 17 17
RETNLB -0.354 0.723 -9999 0 -1.475 18 18
SELP -0.375 0.737 -9999 0 -1.496 18 18
AICDA -0.372 0.703 -9999 0 -1.435 18 18
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.294 0.61 -9999 0 -1.288 17 17
PCK1 -0.296 0.555 -9999 0 -1.259 14 14
HNF4A -0.285 0.592 -9999 0 -1.25 16 16
KCNJ11 -0.277 0.616 -9999 0 -1.336 15 15
AKT1 -0.084 0.217 -9999 0 -0.436 11 11
response to starvation -0.006 0.03 -9999 0 -9999 0 0
DLK1 -0.268 0.595 -9999 0 -1.246 16 16
NKX2-1 -0.053 0.226 -9999 0 -0.952 1 1
ACADM -0.278 0.587 -9999 0 -1.204 17 17
TAT -0.072 0.24 -9999 0 -0.687 1 1
CEBPB -0.009 0.092 -9999 0 -0.525 2 2
CEBPA -0.02 0.127 -9999 0 -0.599 3 3
TTR -0.235 0.488 -9999 0 -1.175 12 12
PKLR -0.316 0.59 -9999 0 -1.175 19 19
APOA1 -0.304 0.638 -9999 0 -1.387 15 15
CPT1C -0.294 0.611 -9999 0 -1.27 17 17
ALAS1 -0.11 0.325 -9999 0 -0.872 7 7
TFRC -0.106 0.308 -9999 0 -0.814 3 3
FOXF1 -0.07 0.214 -9999 0 -0.671 8 8
NF1 0.025 0.02 -9999 0 -9999 0 0
HNF1A (dimer) -0.046 0.169 -9999 0 -0.678 4 4
CPT1A -0.264 0.561 -9999 0 -1.25 14 14
HMGCS1 -0.258 0.555 -9999 0 -1.237 14 14
NR3C1 0.018 0.043 -9999 0 -9999 0 0
CPT1B -0.272 0.585 -9999 0 -1.232 16 16
chromatin remodeling 0 0 -9999 0 -9999 0 0
SP1 0.024 0.031 -9999 0 -9999 0 0
GCK -0.273 0.576 -9999 0 -1.196 17 17
CREB1 -0.039 0.111 -9999 0 -0.698 1 1
IGFBP1 -0.155 0.332 -9999 0 -0.793 9 9
PDX1 -0.134 0.403 -9999 0 -1.268 5 5
UCP2 -0.28 0.577 -9999 0 -1.192 17 17
ALDOB -0.53 0.767 -9999 0 -1.415 27 27
AFP 0.003 0.153 -9999 0 -1.125 1 1
BDH1 -0.312 0.617 -9999 0 -1.315 17 17
HADH -0.258 0.588 -9999 0 -1.225 16 16
F2 -0.287 0.606 -9999 0 -1.341 14 14
HNF1A -0.046 0.169 -9999 0 -0.679 4 4
G6PC -0.179 0.344 -9999 0 -0.776 10 10
SLC2A2 -0.459 0.819 -9999 0 -1.809 18 18
INS 0.035 0.054 -9999 0 -9999 0 0
FOXA1 0.006 0.117 -9999 0 -0.519 3 3
FOXA3 -0.004 0.134 -9999 0 -0.61 2 2
FOXA2 -0.303 0.679 -9999 0 -1.409 16 16
ABCC8 -0.282 0.608 -9999 0 -1.283 16 16
ALB 0.015 0.082 -9999 0 -9999 0 0
Glypican 2 network

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
MDK -0.071 0.203 -9999 0 -0.523 12 12
GPC2 0 0 -9999 0 -9999 0 0
GPC2/Midkine -0.051 0.147 -9999 0 -0.38 12 12
neuron projection morphogenesis -0.051 0.147 -9999 0 -0.379 12 12
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.021 0.031 -9999 0 -9999 0 0
NFATC2 -0.138 0.365 -9999 0 -0.855 11 11
NFATC3 -0.044 0.091 -9999 0 -9999 0 0
CD40LG -0.379 0.512 -9999 0 -1.134 18 18
ITCH -0.006 0.152 -9999 0 -0.579 2 2
CBLB -0.019 0.209 -9999 0 -1.045 2 2
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.323 0.486 -9999 0 -1.138 15 15
JUNB 0.002 0.106 -9999 0 -0.616 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.075 0.153 -9999 0 -0.679 2 2
T cell anergy -0.082 0.32 -9999 0 -0.666 13 13
TLE4 -0.086 0.295 -9999 0 -0.793 8 8
Jun/NFAT1-c-4/p21SNFT -0.35 0.586 -9999 0 -1.232 18 18
AP-1/NFAT1-c-4 -0.482 0.686 -9999 0 -1.457 19 19
IKZF1 -0.123 0.387 -9999 0 -1.033 9 9
T-helper 2 cell differentiation -0.105 0.286 -9999 0 -0.924 4 4
AP-1/NFAT1 -0.251 0.434 -9999 0 -0.852 19 19
CALM1 -0.005 0.09 -9999 0 -9999 0 0
EGR2 -0.3 0.611 -9999 0 -1.3 15 15
EGR3 -0.276 0.551 -9999 0 -1.272 12 12
NFAT1/FOXP3 -0.097 0.298 -9999 0 -0.753 9 9
EGR1 -0.167 0.279 -9999 0 -0.569 23 23
JUN -0.1 0.256 -9999 0 -0.665 12 12
EGR4 0.001 0.008 -9999 0 -9999 0 0
mol:Ca2+ -0.028 0.097 -9999 0 -0.342 2 2
GBP3 -0.251 0.5 -9999 0 -1.01 20 20
FOSL1 0.02 0 -9999 0 -9999 0 0
NFAT1-c-4/MAF/IRF4 -0.306 0.569 -9999 0 -1.227 16 16
DGKA -0.086 0.295 -9999 0 -0.84 7 7
CREM 0.012 0.064 -9999 0 -0.525 1 1
NFAT1-c-4/PPARG -0.338 0.526 -9999 0 -1.246 14 14
CTLA4 -0.076 0.299 -9999 0 -0.79 8 8
NFAT1-c-4 (dimer)/EGR1 -0.373 0.567 -9999 0 -1.207 18 18
NFAT1-c-4 (dimer)/EGR4 -0.292 0.534 -9999 0 -1.216 14 14
FOS -0.162 0.285 -9999 0 -0.612 20 20
IFNG -0.42 0.556 -9999 0 -1.203 19 19
T cell activation -0.231 0.432 -9999 0 -1.013 13 13
MAF -0.08 0.252 -9999 0 -0.708 10 10
T-helper 2 cell lineage commitment 0 0 -9999 0 -9999 0 0
activation-induced cell death of T cells 0.241 0.516 1.136 13 -9999 0 13
TNF -0.299 0.458 -9999 0 -1.086 14 14
FASLG -0.451 0.732 -9999 0 -1.71 15 15
TBX21 -0.148 0.279 -9999 0 -0.662 16 16
BATF3 0 0.001 -9999 0 -9999 0 0
PRKCQ -0.025 0.151 -9999 0 -0.634 4 4
PTPN1 -0.082 0.287 -9999 0 -0.798 7 7
NFAT1-c-4/ICER1 -0.319 0.51 -9999 0 -1.206 14 14
GATA3 -0.005 0.125 -9999 0 -0.521 4 4
T-helper 1 cell differentiation -0.383 0.536 -9999 0 -1.138 19 19
IL2RA -0.322 0.469 -9999 0 -1.058 16 16
T-helper 1 cell lineage commitment 0 0 -9999 0 -9999 0 0
CASP3 -0.087 0.293 -9999 0 -0.777 8 8
E2F1 0.022 0.064 -9999 0 -0.515 1 1
PPARG -0.031 0.169 -9999 0 -0.584 6 6
SLC3A2 -0.086 0.302 -9999 0 -0.787 8 8
IRF4 0.013 0.064 -9999 0 -0.523 1 1
PTGS2 -0.408 0.536 -9999 0 -1.109 22 22
CSF2 -0.371 0.509 -9999 0 -1.125 18 18
JunB/Fra1/NFAT1-c-4 -0.273 0.506 -9999 0 -1.115 15 15
IL4 -0.111 0.3 -9999 0 -0.987 4 4
IL5 -0.371 0.509 -9999 0 -1.125 18 18
IL2 -0.239 0.45 -9999 0 -1.052 13 13
IL3 -0.035 0.053 -9999 0 -9999 0 0
RNF128 -0.118 0.351 -9999 0 -0.763 16 16
NFATC1 -0.244 0.526 -9999 0 -1.153 13 13
CDK4 0.137 0.263 0.711 6 -9999 0 6
PTPRK -0.109 0.374 -9999 0 -0.997 8 8
IL8 -0.454 0.541 -9999 0 -1.177 20 20
POU2F1 0.032 0 -9999 0 -9999 0 0
TCGA08_retinoblastoma

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
CDKN2B -0.004 0.114 -9999 0 -0.669 2 2
CDKN2C -0.075 0.24 -9999 0 -0.671 10 10
CDKN2A -0.029 0.187 -9999 0 -0.643 6 6
CCND2 0.032 0.11 0.243 10 -0.2 1 11
RB1 -0.023 0.127 0.188 1 -0.269 10 11
CDK4 0.05 0.127 0.283 11 -9999 0 11
CDK6 0.04 0.131 0.28 10 -0.237 2 12
G1/S progression 0.023 0.127 0.268 10 -0.188 1 11
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.009 0.144 -9999 0 -0.538 2 2
TBX21 -0.243 0.605 -9999 0 -1.369 14 14
B2M 0.014 0.012 -9999 0 -9999 0 0
TYK2 0.021 0.022 -9999 0 -9999 0 0
IL12RB1 0.021 0.022 -9999 0 -9999 0 0
GADD45B -0.173 0.506 -9999 0 -1.16 13 13
IL12RB2 -0.1 0.227 -9999 0 -0.522 16 16
GADD45G -0.194 0.527 -9999 0 -1.12 15 15
natural killer cell activation 0.001 0.027 -9999 0 -9999 0 0
RELB 0 0.12 -9999 0 -0.708 2 2
RELA 0.02 0 -9999 0 -9999 0 0
IL18 -0.072 0.225 -9999 0 -0.595 11 11
IL2RA -0.091 0.251 -9999 0 -0.646 12 12
IFNG -0.229 0.291 -9999 0 -0.559 31 31
STAT3 (dimer) -0.121 0.42 -9999 0 -0.916 13 13
HLA-DRB5 -0.024 0.167 -9999 0 -0.71 4 4
FASLG -0.274 0.618 -9999 0 -1.371 15 15
NF kappa B2 p52/RelB -0.252 0.447 -9999 0 -1.128 13 13
CD4 0.017 0.009 -9999 0 -9999 0 0
SOCS1 0.002 0.106 -9999 0 -0.616 2 2
EntrezGene:6955 -0.009 0.016 -9999 0 -9999 0 0
CD3D -0.1 0.243 -9999 0 -0.61 13 13
CD3E 0.003 0.065 -9999 0 -0.535 1 1
CD3G -0.166 0.294 -9999 0 -0.635 20 20
IL12Rbeta2/JAK2 -0.057 0.17 -9999 0 -0.37 15 15
CCL3 -0.189 0.522 -9999 0 -1.151 14 14
CCL4 -0.172 0.505 -9999 0 -1.133 13 13
HLA-A 0.015 0.012 -9999 0 -9999 0 0
IL18/IL18R -0.137 0.398 -9999 0 -0.741 19 19
NOS2 -0.178 0.497 -9999 0 -0.999 16 16
IL12/IL12R/TYK2/JAK2/SPHK2 0 0.117 -9999 0 -0.368 1 1
IL1R1 -0.189 0.514 -9999 0 -1.133 14 14
IL4 0.022 0.024 -9999 0 -9999 0 0
JAK2 0.021 0.022 -9999 0 -9999 0 0
EntrezGene:6957 -0.009 0.015 -9999 0 -9999 0 0
TCR/CD3/MHC I/CD8 -0.349 0.638 -9999 0 -1.047 25 25
RAB7A -0.104 0.402 -9999 0 -0.866 13 13
lysosomal transport -0.093 0.38 -9999 0 -0.789 14 14
FOS -0.31 0.582 -9999 0 -1.277 16 16
STAT4 (dimer) -0.176 0.539 -9999 0 -1.088 16 16
STAT5A (dimer) -0.324 0.457 -9999 0 -0.951 21 21
GZMA -0.173 0.475 -9999 0 -1.038 14 14
GZMB -0.186 0.531 -9999 0 -1.214 13 13
HLX -0.056 0.216 -9999 0 -0.662 8 8
LCK -0.247 0.596 -9999 0 -1.192 17 17
TCR/CD3/MHC II/CD4 -0.196 0.403 -9999 0 -0.744 19 19
IL2/IL2R -0.081 0.257 -9999 0 -0.616 11 11
MAPK14 -0.171 0.524 -9999 0 -1.145 14 14
CCR5 -0.224 0.563 -9999 0 -1.082 18 18
IL1B -0.117 0.275 -9999 0 -0.642 15 15
STAT6 -0.06 0.233 -9999 0 -0.616 6 6
STAT4 -0.061 0.229 -9999 0 -0.708 8 8
STAT3 0.01 0.085 -9999 0 -0.708 1 1
STAT1 -0.056 0.216 -9999 0 -0.662 8 8
NFKB1 0.02 0 -9999 0 -9999 0 0
NFKB2 0.002 0.106 -9999 0 -0.616 2 2
IL12B 0.005 0.11 -9999 0 -0.623 2 2
CD8A -0.006 0.015 -9999 0 -9999 0 0
CD8B -0.114 0.248 -9999 0 -0.574 16 16
T-helper 1 cell differentiation 0 0 -9999 0 -9999 0 0
natural killer cell mediated cytotoxicity 0.008 0.143 0.533 2 -9999 0 2
IL2RB -0.051 0.216 -9999 0 -0.708 7 7
proteasomal ubiquitin-dependent protein catabolic process -0.141 0.467 -9999 0 -0.932 16 16
IL2RG -0.003 0.109 -9999 0 -0.523 3 3
IL12 0.02 0.092 -9999 0 -0.462 2 2
STAT5A 0.012 0.064 -9999 0 -0.523 1 1
CD247 -0.148 0.293 -9999 0 -0.67 17 17
IL2 0 0.12 -9999 0 -0.708 2 2
SPHK2 0.02 0 -9999 0 -9999 0 0
FRAP1 0.02 0 -9999 0 -9999 0 0
IL12A 0.021 0.022 -9999 0 -9999 0 0
IL12/IL12R/TYK2/JAK2 -0.246 0.68 -9999 0 -1.397 14 14
MAP2K3 -0.188 0.549 -9999 0 -1.156 15 15
RIPK2 0.012 0.064 -9999 0 -0.523 1 1
MAP2K6 -0.18 0.529 -9999 0 -1.119 15 15
regulation of dendritic cell antigen processing and presentation 0 0 -9999 0 -9999 0 0
HLA-DRA -0.014 0.145 -9999 0 -0.71 3 3
IL18RAP -0.075 0.246 -9999 0 -0.683 10 10
IL12Rbeta1/TYK2 0.028 0.034 -9999 0 -9999 0 0
EOMES -0.29 0.523 -9999 0 -1.424 11 11
STAT1 (dimer) -0.232 0.453 -9999 0 -0.909 19 19
T cell proliferation -0.105 0.375 -9999 0 -0.757 15 15
T-helper 1 cell lineage commitment 0 0 -9999 0 -9999 0 0
IL18R1 -0.121 0.293 -9999 0 -0.716 14 14
CD8-positive alpha-beta T cell lineage commitment 0 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelA -0.227 0.35 -9999 0 -0.842 16 16
ATF2 -0.137 0.467 -9999 0 -1.004 14 14
PLK2 and PLK4 events

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
PLK2 -0.099 0.266 -9999 0 -0.693 12 12
PLK4 0.012 0.064 -9999 0 -0.523 1 1
regulation of centriole replication -0.061 0.217 -9999 0 -0.538 12 12
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.128 0.286 -9999 0 -0.746 11 11
alphaM/beta2 Integrin/GPIbA -0.134 0.282 -9999 0 -0.67 14 14
alphaM/beta2 Integrin/proMMP-9 -0.213 0.326 -9999 0 -0.602 22 22
PLAUR -0.013 0.136 -9999 0 -0.57 4 4
HMGB1 0.013 0.017 -9999 0 -9999 0 0
alphaM/beta2 Integrin/Talin -0.115 0.273 -9999 0 -0.722 11 11
AGER 0.013 0.017 -9999 0 -9999 0 0
RAP1A 0.01 0.085 -9999 0 -0.708 1 1
SELPLG -0.01 0.145 -9999 0 -0.708 3 3
mol:LDL 0 0 -9999 0 -9999 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.14 0.258 -9999 0 -0.765 9 9
mol:GTP 0 0 -9999 0 -9999 0 0
MMP9 -0.149 0.266 -9999 0 -0.559 21 21
CYR61 -0.109 0.265 -9999 0 -0.642 14 14
TLN1 0.02 0 -9999 0 -9999 0 0
Rap1/GTP -0.127 0.251 -9999 0 -0.657 11 11
RHOA 0.01 0.085 -9999 0 -0.708 1 1
P-selectin oligomer -0.046 0.201 -9999 0 -0.654 7 7
MYH2 -0.058 0.231 -9999 0 -0.514 11 11
MST1R -0.003 0.109 -9999 0 -0.523 3 3
leukocyte activation during inflammatory response -0.164 0.238 -9999 0 -0.603 12 12
APOB -0.01 0.124 -9999 0 -0.523 4 4
mol:GDP 0 0 -9999 0 -9999 0 0
complement component iC3b receptor activity 0 0 -9999 0 -9999 0 0
MMP2 -0.003 0.109 -9999 0 -0.523 3 3
JAM3 -0.051 0.216 -9999 0 -0.708 7 7
GP1BA -0.013 0.136 -9999 0 -0.57 4 4
alphaM/beta2 Integrin/CTGF -0.132 0.281 -9999 0 -0.715 12 12
alphaM/beta2 Integrin -0.102 0.317 -9999 0 -0.662 14 14
JAM3 homodimer -0.051 0.215 -9999 0 -0.707 7 7
ICAM2 -0.02 0.167 -9999 0 -0.708 4 4
ICAM1 -0.089 0.257 -9999 0 -0.691 11 11
phagocytosis triggered by activation of immune response cell surface activating receptor -0.099 0.31 -9999 0 -0.65 14 14
cell adhesion -0.133 0.28 -9999 0 -0.665 14 14
NFKB1 -0.108 0.3 -9999 0 -0.772 9 9
THY1 -0.068 0.235 -9999 0 -0.687 9 9
RhoA/GDP 0.007 0.065 -9999 0 -0.538 1 1
Lipoprotein(a) -0.064 0.153 -9999 0 -0.318 19 19
alphaM/beta2 Integrin/LRP/tPA -0.114 0.325 -9999 0 -0.672 16 16
IL6 -0.179 0.375 -9999 0 -0.822 13 13
ITGB2 -0.106 0.267 -9999 0 -0.7 12 12
elevation of cytosolic calcium ion concentration -0.169 0.345 -9999 0 -0.766 14 14
alphaM/beta2 Integrin/JAM2/JAM3 -0.145 0.354 -9999 0 -0.689 17 17
JAM2 -0.043 0.194 -9999 0 -0.629 7 7
alphaM/beta2 Integrin/ICAM1 -0.168 0.411 -9999 0 -0.968 13 13
alphaM/beta2 Integrin/uPA/Plg -0.206 0.345 -9999 0 -0.774 14 14
RhoA/GTP -0.074 0.247 -9999 0 -0.561 11 11
positive regulation of phagocytosis -0.151 0.311 -9999 0 -0.805 12 12
Ron/MSP -0.05 0.184 -9999 0 -0.447 12 12
alphaM/beta2 Integrin/uPAR/uPA -0.142 0.368 -9999 0 -0.78 14 14
alphaM/beta2 Integrin/uPAR -0.134 0.292 -9999 0 -0.723 12 12
PLAU -0.081 0.24 -9999 0 -0.641 11 11
PLAT -0.058 0.222 -9999 0 -0.685 8 8
actin filament polymerization -0.054 0.219 -9999 0 -0.487 11 11
MST1 -0.068 0.209 -9999 0 -0.557 11 11
alphaM/beta2 Integrin/lipoprotein(a) -0.146 0.257 -9999 0 -0.613 12 12
TNF -0.093 0.295 -9999 0 -0.765 8 8
RAP1B 0.01 0.085 -9999 0 -0.708 1 1
alphaM/beta2 Integrin/uPA -0.171 0.359 -9999 0 -0.814 14 14
fibrinolysis -0.223 0.325 -9999 0 -0.762 14 14
HCK 0 0.12 -9999 0 -0.708 2 2
dendritic cell antigen processing and presentation -0.099 0.31 -9999 0 -0.65 14 14
VTN 0.02 0 -9999 0 -9999 0 0
alphaM/beta2 Integrin/CYR61 -0.188 0.371 -9999 0 -0.856 14 14
LPA -0.096 0.227 -9999 0 -0.536 15 15
LRP1 0.02 0 -9999 0 -9999 0 0
cell migration -0.177 0.332 -9999 0 -0.732 14 14
FN1 -0.013 0.136 -9999 0 -0.57 4 4
alphaM/beta2 Integrin/Thy1 -0.167 0.348 -9999 0 -0.779 15 15
MPO 0.005 0.089 -9999 0 -0.523 2 2
KNG1 -0.048 0.18 -9999 0 -0.523 9 9
RAP1/GDP 0.015 0.105 -9999 0 -0.871 1 1
ROCK1 -0.058 0.231 -9999 0 -0.514 11 11
ELA2 0.02 0 -9999 0 -9999 0 0
PLG -0.123 0.24 -9999 0 -0.523 19 19
CTGF -0.01 0.124 -9999 0 -0.523 4 4
alphaM/beta2 Integrin/Hck -0.126 0.309 -9999 0 -0.755 12 12
ITGAM -0.058 0.215 -9999 0 -0.711 7 7
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.12 0.377 -9999 0 -0.859 12 12
HP -0.046 0.187 -9999 0 -0.57 8 8
leukocyte adhesion -0.216 0.376 -9999 0 -0.939 13 13
SELP -0.046 0.202 -9999 0 -0.655 7 7
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.099 0.299 -9999 0 -0.689 11 11
NF kappa B1 p50/RelA/I kappa B alpha -0.084 0.33 -9999 0 -0.742 11 11
alphaV/beta3 Integrin/Osteopontin/Src -0.098 0.19 -9999 0 -0.433 17 17
AP1 -0.143 0.335 -9999 0 -0.811 10 10
ILK -0.046 0.219 -9999 0 -0.603 6 6
bone resorption -0.031 0.255 -9999 0 -0.623 8 8
PTK2B 0.02 0 -9999 0 -9999 0 0
PYK2/p130Cas -0.038 0.229 -9999 0 -0.604 7 7
ITGAV 0.004 0.118 -9999 0 -0.693 2 2
mol:GTP 0 0 -9999 0 -9999 0 0
CD44/Rho Family GTPase/ROCK2 -0.002 0.119 -9999 0 -0.43 5 5
alphaV/beta3 Integrin/Osteopontin -0.111 0.216 -9999 0 -0.533 13 13
MAP3K1 -0.054 0.225 -9999 0 -0.557 8 8
JUN -0.093 0.256 -9999 0 -0.662 12 12
MAPK3 -0.103 0.309 -9999 0 -0.69 12 12
MAPK1 -0.103 0.309 -9999 0 -0.69 12 12
Rac1/GDP 0.015 0 -9999 0 -9999 0 0
NFKB1 0.02 0 -9999 0 -9999 0 0
MAPK8 -0.038 0.214 -9999 0 -0.57 6 6
ITGB3 -0.026 0.17 -9999 0 -0.582 6 6
NFKBIA -0.117 0.369 -9999 0 -0.817 12 12
FOS -0.156 0.289 -9999 0 -0.615 20 20
CD44 -0.003 0.109 -9999 0 -0.523 3 3
CHUK 0.02 0 -9999 0 -9999 0 0
PLAU -0.17 0.461 -9999 0 -1.143 11 11
NF kappa B1 p50/RelA -0.139 0.238 -9999 0 -0.634 11 11
BCAR1 0.02 0 -9999 0 -9999 0 0
RELA 0.02 0 -9999 0 -9999 0 0
alphaV beta3 Integrin -0.041 0.143 -9999 0 -0.438 8 8
mol:GDP 0 0 -9999 0 -9999 0 0
SYK -0.062 0.248 -9999 0 -0.638 8 8
VAV3 -0.067 0.272 -9999 0 -0.683 9 9
MAP3K14 -0.117 0.317 -9999 0 -0.71 12 12
ROCK2 0 0.12 -9999 0 -0.708 2 2
SPP1 -0.103 0.254 -9999 0 -0.593 15 15
RAC1 0.02 0 -9999 0 -9999 0 0
Rac1/GTP -0.052 0.25 -9999 0 -0.653 8 8
MMP2 -0.107 0.274 -9999 0 -0.655 9 9
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 -0.083 0.247 -9999 0 -0.659 11 11
GNB1/GNG2 -0.06 0.091 -9999 0 -0.216 15 15
AKT1 0.012 0.145 -9999 0 -0.224 11 11
EGF -0.247 0.304 -9999 0 -0.581 32 32
mol:TXA2 0 0.001 -9999 0 -9999 0 0
FGR 0.016 0.142 -9999 0 -0.622 2 2
mol:Ca2+ -0.012 0.206 -9999 0 -0.335 18 18
LYN 0.016 0.142 -9999 0 -0.622 2 2
RhoA/GTP -0.042 0.062 -9999 0 -0.248 1 1
mol:PGI2 0 0.001 -9999 0 -9999 0 0
SYK -0.019 0.236 -9999 0 -0.397 17 17
GNG2 0.02 0 -9999 0 -9999 0 0
ARRB2 0.02 0 -9999 0 -9999 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.001 0.12 -9999 0 -0.669 1 1
G beta5/gamma2 -0.081 0.126 -9999 0 -0.308 14 14
PRKCH -0.039 0.254 -9999 0 -0.47 14 14
DNM1 -0.053 0.195 -9999 0 -0.564 9 9
TXA2/TP beta/beta Arrestin3 -0.024 0.06 -9999 0 -0.273 2 2
mol:GTP 0.001 0.002 -9999 0 -9999 0 0
PTGDR -0.081 0.24 -9999 0 -0.641 11 11
G12 family/GTP -0.098 0.142 -9999 0 -0.326 19 19
ADRBK1 0.02 0 -9999 0 -9999 0 0
ADRBK2 0 0.12 -9999 0 -0.708 2 2
RhoA/GTP/ROCK1 0.014 0.057 -9999 0 -0.456 1 1
mol:GDP 0.012 0.181 0.406 9 -9999 0 9
mol:NADP 0.005 0.089 -9999 0 -0.524 2 2
RAB11A 0.01 0.085 -9999 0 -0.708 1 1
PRKG1 0.02 0 -9999 0 -9999 0 0
mol:IP3 -0.031 0.249 -9999 0 -0.421 19 19
cell morphogenesis 0.012 0.057 -9999 0 -0.454 1 1
PLCB2 -0.069 0.33 -9999 0 -0.588 19 19
mol:cGMP 0 0.001 -9999 0 -9999 0 0
BLK 0.01 0.145 -9999 0 -0.622 2 2
mol:PDG2 0 0.001 -9999 0 -9999 0 0
HCK 0.01 0.165 -9999 0 -0.642 3 3
RHOA 0.01 0.085 -9999 0 -0.708 1 1
PTGIR 0 0.12 -9999 0 -0.709 2 2
PRKCB1 -0.048 0.276 -9999 0 -0.483 18 18
GNAQ 0 0 -9999 0 -9999 0 0
mol:L-citrulline 0.005 0.089 -9999 0 -0.524 2 2
TXA2/TXA2-R family -0.07 0.333 -9999 0 -0.598 19 19
LCK -0.039 0.197 -9999 0 -0.613 5 5
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.049 0.116 -9999 0 -0.683 1 1
TXA2-R family/G12 family/GDP/G beta/gamma 0.016 0.135 -9999 0 -1.068 1 1
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.049 0.116 -9999 0 -0.683 1 1
MAPK14 0.009 0.166 -9999 0 -0.269 10 10
TGM2/GTP -0.053 0.3 -9999 0 -0.559 15 15
MAPK11 0.009 0.166 -9999 0 -0.265 12 12
ARHGEF1 0.006 0.129 -9999 0 -0.202 2 2
GNAI2 0.01 0.085 -9999 0 -0.708 1 1
JNK cascade -0.03 0.253 -9999 0 -0.427 19 19
RAB11/GDP 0.01 0.084 -9999 0 -0.698 1 1
ICAM1 -0.024 0.22 -9999 0 -0.397 14 14
cAMP biosynthetic process -0.03 0.236 -9999 0 -0.415 16 16
Gq family/GTP/EBP50 -0.009 0.101 -9999 0 -0.384 2 2
actin cytoskeleton reorganization 0.012 0.057 -9999 0 -0.454 1 1
SRC 0.016 0.142 -9999 0 -0.622 2 2
GNB5 0.012 0.064 -9999 0 -0.524 1 1
GNB1 0.01 0.085 -9999 0 -0.708 1 1
EGF/EGFR -0.045 0.172 -9999 0 -0.403 10 10
VCAM1 -0.03 0.229 -9999 0 -0.39 19 19
TP beta/Gq family/GDP/G beta5/gamma2 -0.001 0.12 -9999 0 -0.669 1 1
platelet activation 0.009 0.217 -9999 0 -0.343 14 14
PGI2/IP 0 0.091 -9999 0 -0.539 2 2
PRKACA -0.027 0.152 -9999 0 -0.397 8 8
Gq family/GDP/G beta5/gamma2 -0.005 0.125 -9999 0 -0.707 1 1
TXA2/TP beta/beta Arrestin2 -0.038 0.114 -9999 0 -0.609 2 2
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -9999 0 0
TBXA2R -0.02 0.15 -9999 0 -0.368 9 9
mol:DAG -0.042 0.272 -9999 0 -0.469 19 19
EGFR -0.106 0.26 -9999 0 -0.629 14 14
TXA2/TP alpha -0.059 0.32 -9999 0 -0.59 16 16
Gq family/GTP -0.036 0.088 -9999 0 -0.264 8 8
YES1 0.016 0.142 -9999 0 -0.622 2 2
GNAI2/GTP -0.051 0.151 -9999 0 -0.79 2 2
PGD2/DP -0.061 0.181 -9999 0 -0.481 11 11
SLC9A3R1 0.01 0.085 -9999 0 -0.708 1 1
FYN -0.036 0.223 -9999 0 -0.616 7 7
mol:NO 0.005 0.089 -9999 0 -0.524 2 2
GNA15 0.01 0.085 -9999 0 -0.708 1 1
PGK/cGMP 0.018 0.056 -9999 0 -0.313 2 2
RhoA/GDP 0.01 0.084 -9999 0 -0.7 1 1
TP alpha/TGM2/GDP/G beta/gamma -0.042 0.222 -9999 0 -0.753 4 4
NOS3 0.005 0.09 -9999 0 -0.525 2 2
RAC1 0.02 0 -9999 0 -9999 0 0
PRKCA -0.022 0.229 -9999 0 -0.392 16 16
PRKCB -0.029 0.228 -9999 0 -0.386 19 19
PRKCE -0.021 0.23 -9999 0 -0.389 17 17
PRKCD -0.038 0.259 -9999 0 -0.45 18 18
PRKCG -0.031 0.244 -9999 0 -0.413 19 19
muscle contraction -0.055 0.313 -9999 0 -0.55 19 19
PRKCZ -0.023 0.226 -9999 0 -0.376 19 19
ARR3 0.02 0 -9999 0 -9999 0 0
TXA2/TP beta -0.016 0.174 -9999 0 -0.826 2 2
PRKCQ -0.032 0.246 -9999 0 -0.416 19 19
MAPKKK cascade -0.058 0.301 -9999 0 -0.532 19 19
SELE -0.027 0.22 -9999 0 -0.363 19 19
TP beta/GNAI2/GDP/G beta/gamma 0.005 0.18 -9999 0 -1.235 1 1
ROCK1 0.02 0 -9999 0 -9999 0 0
GNA14 -0.058 0.222 -9999 0 -0.685 8 8
chemotaxis -0.081 0.358 -9999 0 -0.653 19 19
GNA12 0.02 0 -9999 0 -9999 0 0
GNA13 0.01 0.085 -9999 0 -0.708 1 1
GNA11 -0.01 0.124 -9999 0 -0.523 4 4
Rac1/GTP 0.012 0.007 -9999 0 -9999 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A -0.068 0.235 -9999 0 -0.687 9 9
LAT2 -0.103 0.314 -9999 0 -0.881 8 8
AP1 -0.208 0.305 -9999 0 -0.713 15 15
mol:PIP3 -0.101 0.313 -9999 0 -0.764 11 11
IKBKB -0.033 0.157 -9999 0 -0.334 11 11
AKT1 -0.121 0.318 -9999 0 -0.711 13 13
IKBKG -0.033 0.157 -9999 0 -0.334 11 11
MS4A2 -0.129 0.281 -9999 0 -0.648 16 16
mol:Sphingosine-1-phosphate 0 0 -9999 0 -9999 0 0
PIK3CA 0.019 0.002 -9999 0 -9999 0 0
MAP3K1 -0.061 0.279 -9999 0 -0.689 10 10
mol:Ca2+ -0.06 0.22 -9999 0 -0.512 11 11
LYN 0.017 0.008 -9999 0 -9999 0 0
CBLB -0.107 0.307 -9999 0 -0.791 10 10
SHC1 0.02 0 -9999 0 -9999 0 0
RasGAP/p62DOK -0.005 0.132 -9999 0 -0.407 7 7
positive regulation of cell migration -0.053 0.183 -9999 0 -0.538 9 9
INPP5D 0 0 -9999 0 -9999 0 0
PLD2 -0.183 0.401 -9999 0 -0.724 19 19
PTPN13 -0.085 0.279 -9999 0 -0.742 9 9
PTPN11 0.016 0.012 -9999 0 -9999 0 0
GO:0007205 0 0 -9999 0 -9999 0 0
regulation of mast cell degranulation -0.039 0.205 -9999 0 -0.426 11 11
SYK -0.008 0.125 -9999 0 -0.601 3 3
GRB2 0.01 0.086 -9999 0 -0.712 1 1
LAT/PLCgamma1/GRB2/SLP76/GADs -0.167 0.293 -9999 0 -0.81 11 11
LAT -0.124 0.354 -9999 0 -0.952 9 9
PAK2 -0.086 0.32 -9999 0 -0.806 10 10
NFATC2 -0.058 0.169 -9999 0 -1.355 1 1
HRAS -0.117 0.381 -9999 0 -0.913 11 11
GAB2 0.02 0 -9999 0 -9999 0 0
PLA2G1B 0.046 0.024 -9999 0 -9999 0 0
Fc epsilon R1 -0.182 0.337 -9999 0 -0.763 14 14
Antigen/IgE/Fc epsilon R1 -0.17 0.317 -9999 0 -0.714 14 14
mol:GDP -0.131 0.397 -9999 0 -0.966 11 11
JUN -0.094 0.256 -9999 0 -0.662 12 12
mol:Ca++ 0 0 -9999 0 -9999 0 0
PIK3R1 -0.039 0.194 -9999 0 -0.68 6 6
FOS -0.157 0.289 -9999 0 -0.616 20 20
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.115 0.314 -9999 0 -0.734 11 11
CHUK -0.033 0.157 -9999 0 -0.334 11 11
KLRG1 -0.112 0.302 -9999 0 -0.752 10 10
VAV1 -0.13 0.364 -9999 0 -0.876 11 11
calcium-dependent protein kinase C activity 0 0 -9999 0 -9999 0 0
CBL -0.097 0.295 -9999 0 -0.831 8 8
negative regulation of mast cell degranulation -0.104 0.271 -9999 0 -0.681 10 10
BTK -0.142 0.41 -9999 0 -1.067 10 10
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.162 0.391 -9999 0 -0.67 18 18
GAB2/PI3K/SHP2 -0.201 0.338 -9999 0 -0.829 13 13
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.094 0.273 -9999 0 -0.791 8 8
RAF1 0.032 0.028 -9999 0 -9999 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.225 0.378 -9999 0 -0.697 20 20
FCER1G -0.044 0.2 -9999 0 -0.645 7 7
FCER1A -0.097 0.262 -9999 0 -0.677 12 12
Antigen/IgE/Fc epsilon R1/Fyn -0.222 0.379 -9999 0 -0.709 20 20
MAPK3 0.046 0.023 -9999 0 -9999 0 0
MAPK1 0.046 0.023 -9999 0 -9999 0 0
NFKB1 0.02 0 -9999 0 -9999 0 0
MAPK8 -0.013 0.163 -9999 0 -0.676 3 3
DUSP1 -0.051 0.216 -9999 0 -0.708 7 7
NF-kappa-B/RelA -0.045 0.069 -9999 0 -9999 0 0
actin cytoskeleton reorganization -0.089 0.283 -9999 0 -0.799 8 8
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -9999 0 0
PI3K -0.161 0.324 -9999 0 -0.882 10 10
FER -0.097 0.295 -9999 0 -0.831 8 8
RELA 0.02 0 -9999 0 -9999 0 0
ITK -0.082 0.199 -9999 0 -0.645 7 7
SOS1 0.02 0 -9999 0 -9999 0 0
PLCG1 -0.123 0.387 -9999 0 -0.942 11 11
cytokine secretion -0.033 0.05 -9999 0 -9999 0 0
SPHK1 -0.139 0.343 -9999 0 -0.725 14 14
PTK2 -0.097 0.308 -9999 0 -0.87 8 8
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.17 0.304 -9999 0 -0.825 11 11
EDG1 -0.053 0.184 -9999 0 -0.539 9 9
mol:DAG -0.121 0.313 -9999 0 -0.675 14 14
MAP2K2 0.04 0.024 -9999 0 -9999 0 0
MAP2K1 0.04 0.024 -9999 0 -9999 0 0
MAP2K7 -0.01 0.145 -9999 0 -0.708 3 3
KLRG1/SHP2 -0.139 0.266 -9999 0 -0.745 9 9
MAP2K4 -0.017 0.219 -9999 0 -1.062 3 3
Fc epsilon R1/FcgammaRIIB -0.237 0.395 -9999 0 -0.733 20 20
mol:Choline -0.176 0.38 -9999 0 -0.695 19 19
SHC/Grb2/SOS1 -0.122 0.268 -9999 0 -0.799 8 8
FYN -0.101 0.271 -9999 0 -0.708 12 12
DOK1 0.02 0 -9999 0 -9999 0 0
PXN -0.075 0.271 -9999 0 -0.756 8 8
HCLS1 -0.144 0.381 -9999 0 -0.847 13 13
PRKCB -0.069 0.217 -9999 0 -0.486 12 12
FCGR2B -0.114 0.274 -9999 0 -0.668 14 14
IGHE -0.004 0.011 -9999 0 -9999 0 0
KLRG1/SHIP -0.107 0.283 -9999 0 -0.707 10 10
LCP2 -0.069 0.236 -9999 0 -0.69 9 9
PLA2G4A -0.153 0.355 -9999 0 -0.758 14 14
RASA1 0.02 0 -9999 0 -9999 0 0
mol:Phosphatidic acid -0.176 0.38 -9999 0 -0.695 19 19
IKK complex -0.003 0.125 -9999 0 -0.25 7 7
WIPF1 0.01 0.085 -9999 0 -0.708 1 1
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.118 0.398 -9999 0 -0.971 9 9
CRP -0.119 0.393 -9999 0 -0.953 9 9
cell cycle arrest -0.176 0.484 -9999 0 -1.096 12 12
TIMP1 -0.122 0.411 -9999 0 -0.954 11 11
IL6ST -0.027 0.189 -9999 0 -0.719 5 5
Rac1/GDP -0.115 0.333 -9999 0 -0.795 11 11
AP1 -0.097 0.296 -9999 0 -0.698 10 10
GAB2 0.023 0.009 -9999 0 -9999 0 0
TNFSF11 -0.152 0.403 -9999 0 -0.929 10 10
HSP90B1 -0.017 0.273 -9999 0 -1.514 2 2
GAB1 -0.019 0.167 -9999 0 -0.706 4 4
MAPK14 -0.096 0.31 -9999 0 -0.846 8 8
AKT1 0.011 0.244 -9999 0 -0.816 4 4
FOXO1 0.002 0.259 -9999 0 -0.859 5 5
MAP2K6 -0.106 0.307 -9999 0 -0.738 10 10
mol:GTP 0 0.003 -9999 0 -9999 0 0
MAP2K4 -0.101 0.356 -9999 0 -0.809 11 11
MITF -0.101 0.29 -9999 0 -0.743 9 9
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -9999 0 0
TYK2 0.02 0 -9999 0 -9999 0 0
A2M -0.255 0.608 -9999 0 -1.551 13 13
CEBPB 0.015 0.091 -9999 0 -0.519 2 2
GRB2/SOS1/GAB family/SHP2 0.002 0.162 -9999 0 -0.686 2 2
STAT3 -0.206 0.543 -9999 0 -1.243 12 12
STAT1 -0.114 0.343 -9999 0 -0.994 8 8
CEBPD -0.144 0.453 -9999 0 -1.113 10 10
PIK3CA 0.021 0.005 -9999 0 -9999 0 0
PI3K -0.012 0.149 -9999 0 -0.504 6 6
JUN -0.094 0.256 -9999 0 -0.662 12 12
PIAS3/MITF -0.085 0.274 -9999 0 -0.693 9 9
MAPK11 -0.096 0.31 -9999 0 -0.846 8 8
STAT3 (dimer)/FOXO1 -0.13 0.501 -9999 0 -1.126 11 11
GRB2/SOS1/GAB family -0.13 0.282 -9999 0 -0.853 8 8
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.125 0.325 -9999 0 -0.843 9 9
GRB2 0.011 0.086 -9999 0 -0.71 1 1
JAK2 0.02 0 -9999 0 -9999 0 0
LBP -0.133 0.378 -9999 0 -0.755 13 13
PIK3R1 -0.038 0.195 -9999 0 -0.68 6 6
JAK1 -0.02 0.17 -9999 0 -0.719 4 4
MYC -0.155 0.474 -9999 0 -1.194 10 10
FGG -0.149 0.41 -9999 0 -0.906 11 11
macrophage differentiation -0.176 0.484 -9999 0 -1.096 12 12
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.157 0.245 -9999 0 -0.69 8 8
JUNB -0.125 0.391 -9999 0 -0.888 11 11
FOS -0.157 0.289 -9999 0 -0.616 20 20
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.122 0.305 -9999 0 -0.683 12 12
STAT1/PIAS1 -0.111 0.302 -9999 0 -0.729 10 10
GRB2/SOS1/GAB family/SHP2/PI3K 0.006 0.221 -9999 0 -0.77 4 4
STAT3 (dimer) -0.202 0.535 -9999 0 -1.225 12 12
PRKCD -0.122 0.434 -9999 0 -0.966 12 12
IL6R -0.07 0.248 -9999 0 -0.726 9 9
SOCS3 -0.108 0.362 -9999 0 -1.088 7 7
gp130 (dimer)/JAK1/JAK1/LMO4 -0.027 0.201 -9999 0 -0.503 10 10
Rac1/GTP -0.119 0.352 -9999 0 -0.833 11 11
HCK 0 0.119 -9999 0 -0.705 2 2
MAPKKK cascade 0.011 0.196 -9999 0 -0.71 3 3
bone resorption -0.14 0.38 -9999 0 -0.835 11 11
IRF1 -0.18 0.502 -9999 0 -1.135 13 13
mol:GDP -0.133 0.344 -9999 0 -0.837 11 11
SOS1 0.023 0.008 -9999 0 -9999 0 0
VAV1 -0.138 0.354 -9999 0 -0.862 11 11
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.138 0.384 -9999 0 -0.976 9 9
PTPN11 -0.007 0.024 -9999 0 -9999 0 0
IL6/IL6RA -0.164 0.263 -9999 0 -0.464 29 29
gp130 (dimer)/TYK2/TYK2/LMO4 -0.006 0.149 -9999 0 -0.451 7 7
gp130 (dimer)/JAK2/JAK2/LMO4 -0.006 0.149 -9999 0 -0.451 7 7
IL6 -0.151 0.276 -9999 0 -0.574 21 21
PIAS3 0.02 0 -9999 0 -9999 0 0
PTPRE -0.045 0.197 -9999 0 -0.696 6 6
PIAS1 0.02 0 -9999 0 -9999 0 0
RAC1 0.021 0.002 -9999 0 -9999 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.081 0.176 -9999 0 -0.401 10 10
LMO4 0.003 0.119 -9999 0 -0.696 2 2
STAT3 (dimer)/PIAS3 -0.245 0.41 -9999 0 -1.055 12 12
MCL1 -0.012 0.328 -9999 0 -1.271 4 4
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.076 0.413 -9999 0 -0.934 12 12
NCK1/PAK1/Dok-R -0.089 0.171 -9999 0 -0.45 12 12
NCK1/Dok-R -0.081 0.422 -9999 0 -1.114 9 9
PIK3CA 0.02 0.001 -9999 0 -9999 0 0
mol:beta2-estradiol -0.002 0.039 -9999 0 -9999 0 0
RELA 0.02 0 -9999 0 -9999 0 0
SHC1 0.02 0.002 -9999 0 -9999 0 0
Rac/GDP 0.015 0 -9999 0 -9999 0 0
F2 -0.027 0.158 -9999 0 -0.529 6 6
TNIP2 -0.01 0.124 -9999 0 -0.523 4 4
NF kappa B/RelA -0.138 0.318 -9999 0 -1.048 7 7
FN1 -0.013 0.136 -9999 0 -0.57 4 4
PLD2 -0.074 0.424 -9999 0 -1.196 8 8
PTPN11 0.02 0 -9999 0 -9999 0 0
GRB14 -0.139 0.269 -9999 0 -0.582 19 19
ELK1 -0.047 0.383 -9999 0 -1.06 8 8
GRB7 0.012 0.064 -9999 0 -0.523 1 1
PAK1 0.012 0.064 -9999 0 -0.523 1 1
Tie2/Ang1/alpha5/beta1 Integrin -0.17 0.393 -9999 0 -1.169 9 9
CDKN1A -0.064 0.329 -9999 0 -0.722 13 13
ITGA5 -0.031 0.185 -9999 0 -0.708 5 5
mol:GTP 0 0 -9999 0 -9999 0 0
RasGAP/Dok-R -0.077 0.412 -9999 0 -1.078 9 9
CRK 0 0.12 -9999 0 -0.708 2 2
mol:NO -0.031 0.314 -9999 0 -0.676 12 12
PLG -0.133 0.397 -9999 0 -1.217 7 7
mol:GDP 0 0 -9999 0 -9999 0 0
chemokinesis -0.063 0.364 -9999 0 -0.916 9 9
GRB2 0.01 0.085 -9999 0 -0.708 1 1
PIK3R1 -0.038 0.195 -9999 0 -0.681 6 6
ANGPT2 -0.178 0.424 -9999 0 -1.01 12 12
BMX -0.097 0.398 -9999 0 -1.201 7 7
ANGPT1 -0.014 0.194 -9999 0 -0.675 3 3
tube development -0.111 0.377 -9999 0 -0.808 15 15
ANGPT4 -0.008 0.135 -9999 0 -0.648 3 3
response to hypoxia -0.005 0.026 -9999 0 -9999 0 0
Tie2/Ang1/GRB14 -0.144 0.447 -9999 0 -1.129 10 10
alpha5/beta1 Integrin -0.015 0.17 -9999 0 -0.613 5 5
FGF2 -0.079 0.245 -9999 0 -0.688 10 10
STAT5A (dimer) -0.098 0.412 -9999 0 -0.955 12 12
mol:L-citrulline -0.031 0.314 -9999 0 -0.676 12 12
AGTR1 -0.322 0.314 -9999 0 -0.596 40 40
MAPK14 -0.09 0.441 -9999 0 -1.326 7 7
Tie2/SHP2 -0.125 0.355 -9999 0 -1.202 7 7
TEK -0.076 0.42 -9999 0 -1.338 7 7
RPS6KB1 -0.062 0.381 -9999 0 -0.917 10 10
Angiotensin II/AT1 -0.239 0.236 -9999 0 -0.442 40 40
Tie2/Ang1/GRB2 -0.07 0.405 -9999 0 -1.149 8 8
MAPK3 -0.053 0.388 -9999 0 -1.081 8 8
MAPK1 -0.053 0.388 -9999 0 -1.081 8 8
Tie2/Ang1/GRB7 -0.068 0.406 -9999 0 -1.213 7 7
NFKB1 0.02 0 -9999 0 -9999 0 0
MAPK8 -0.061 0.39 -9999 0 -1.156 7 7
PI3K -0.101 0.458 -9999 0 -1.14 10 10
FES -0.096 0.444 -9999 0 -1.238 8 8
Crk/Dok-R -0.087 0.423 -9999 0 -1.114 9 9
Tie2/Ang1/ABIN2 -0.08 0.404 -9999 0 -1.214 7 7
blood circulation 0 0 -9999 0 -9999 0 0
negative regulation of caspase activity -0.057 0.367 -9999 0 -0.818 12 12
STAT5A 0.013 0.064 -9999 0 -0.523 1 1
mol:ROS 0 0 -9999 0 -9999 0 0
PTK2 -0.062 0.381 -9999 0 -0.917 10 10
Tie2/Ang2 -0.153 0.505 -9999 0 -1.228 12 12
Tie2/Ang1 -0.077 0.417 -9999 0 -1.251 7 7
FOXO1 -0.072 0.405 -9999 0 -0.889 13 13
ELF1 0.023 0.033 -9999 0 -9999 0 0
ELF2 -0.068 0.396 -9999 0 -1.181 7 7
mol:Choline -0.067 0.402 -9999 0 -1.13 8 8
cell migration -0.049 0.093 -9999 0 -9999 0 0
FYN -0.142 0.442 -9999 0 -0.961 15 15
DOK2 -0.038 0.194 -9999 0 -0.677 6 6
negative regulation of cell cycle -0.051 0.298 -9999 0 -0.644 13 13
ETS1 -0.049 0.231 -9999 0 -0.746 7 7
PXN -0.029 0.319 -9999 0 -0.735 10 10
ITGB1 0.01 0.085 -9999 0 -0.708 1 1
NOS3 -0.047 0.355 -9999 0 -0.78 12 12
RAC1 0.02 0 -9999 0 -9999 0 0
TNF 0.005 0.12 -9999 0 -0.656 2 2
MAPKKK cascade -0.067 0.402 -9999 0 -1.13 8 8
RASA1 0.02 0 -9999 0 -9999 0 0
Tie2/Ang1/Shc -0.066 0.399 -9999 0 -1.188 7 7
NCK1 0.01 0.085 -9999 0 -0.708 1 1
vasculogenesis -0.019 0.285 -9999 0 -0.6 12 12
mol:Phosphatidic acid -0.067 0.402 -9999 0 -1.13 8 8
mol:Angiotensin II -0.001 0.009 -9999 0 -9999 0 0
mol:NADP -0.031 0.314 -9999 0 -0.676 12 12
Rac1/GTP -0.149 0.305 -9999 0 -0.845 10 10
MMP2 -0.073 0.391 -9999 0 -1.156 7 7
Visual signal transduction: Rods

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
mol:K + -0.008 0.134 -9999 0 -0.645 3 3
GNAT1/GTP 0.009 0.046 -9999 0 -0.38 1 1
Metarhodopsin II/Arrestin 0.011 0.078 -9999 0 -0.359 3 3
PDE6G/GNAT1/GTP 0.004 0.086 -9999 0 -0.311 5 5
mol:GTP 0 0 -9999 0 -9999 0 0
absorption of light 0 0 -9999 0 -9999 0 0
GNAT1 0.012 0.064 -9999 0 -0.523 1 1
GRK1 0 0 -9999 0 -9999 0 0
CNG Channel -0.127 0.21 -9999 0 -0.724 5 5
mol:Na + -0.076 0.121 -9999 0 -0.442 1 1
mol:ADP 0 0 -9999 0 -9999 0 0
RGS9-1/Gbeta5/R9AP -0.12 0.228 -9999 0 -0.494 14 14
mol:GDP 0 0 -9999 0 -9999 0 0
cGMP/CNG Channel -0.077 0.124 -9999 0 -0.455 1 1
CNGB1 0.005 0.089 -9999 0 -0.523 2 2
RDH5 -0.099 0.266 -9999 0 -0.693 12 12
SAG -0.005 0.122 -9999 0 -0.585 3 3
mol:Ca2+ -0.028 0.177 -9999 0 -0.55 2 2
Na + (4 Units) -0.083 0.14 -9999 0 -0.507 3 3
RGS9 -0.139 0.289 -9999 0 -0.654 17 17
GNB1/GNGT1 -0.306 0.239 -9999 0 -0.464 49 49
GNAT1/GDP -0.096 0.199 -9999 0 -0.419 14 14
GUCY2D 0.02 0 -9999 0 -9999 0 0
GNGT1 -0.417 0.317 -9999 0 -0.635 48 48
GUCY2F 0.012 0.064 -9999 0 -0.523 1 1
GNB5 0.012 0.064 -9999 0 -0.523 1 1
mol:GMP (4 units) -0.03 0.178 -9999 0 -0.473 8 8
mol:11-cis-retinal -0.099 0.266 -9999 0 -0.691 12 12
mol:cGMP 0.038 0.082 -9999 0 -9999 0 0
GNB1 0.01 0.085 -9999 0 -0.708 1 1
Rhodopsin -0.06 0.202 -9999 0 -0.511 12 12
SLC24A1 -0.008 0.134 -9999 0 -0.646 3 3
CNGA1 -0.119 0.263 -9999 0 -0.604 16 16
Metarhodopsin II 0.013 0 -9999 0 -9999 0 0
mol:Ca ++ 0 0 -9999 0 -9999 0 0
GC1/GCAP Family 0.032 0.08 -9999 0 -0.396 1 1
RGS9BP -0.063 0.209 -9999 0 -0.579 10 10
Metarhodopsin II/Transducin -0.155 0.141 -9999 0 -0.298 30 30
GCAP Family/Ca ++ 0.019 0.08 -9999 0 -0.407 1 1
PDE6A/B -0.048 0.186 -9999 0 -0.482 11 11
mol:Pi -0.119 0.227 -9999 0 -0.492 14 14
mol:all-trans-retinal 0 0 -9999 0 -9999 0 0
Transducin -0.233 0.189 -9999 0 -0.407 30 30
PDE6B -0.076 0.241 -9999 0 -0.671 10 10
PDE6A 0.012 0.064 -9999 0 -0.523 1 1
PDE6G -0.01 0.124 -9999 0 -0.523 4 4
RHO 0.02 0 -9999 0 -9999 0 0
PDE6 -0.176 0.275 -9999 0 -0.73 12 12
GUCA1A 0.002 0.106 -9999 0 -0.616 2 2
GC2/GCAP Family 0.028 0.087 -9999 0 -0.396 1 1
GUCA1C 0.004 0.089 -9999 0 -0.523 2 2
GUCA1B 0.02 0 -9999 0 -9999 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.049 0.199 -9999 0 -0.457 10 10
CRKL -0.06 0.209 -9999 0 -0.462 13 13
HRAS -0.027 0.21 -9999 0 -0.546 5 5
mol:PIP3 -0.083 0.219 -9999 0 -0.485 15 15
SPRED1 -0.01 0.145 -9999 0 -0.708 3 3
SPRED2 0 0.12 -9999 0 -0.708 2 2
GAB1 -0.074 0.219 -9999 0 -0.485 14 14
FOXO3 -0.058 0.21 -9999 0 -0.476 12 12
AKT1 -0.075 0.227 -9999 0 -0.512 13 13
BAD -0.058 0.21 -9999 0 -0.476 12 12
megakaryocyte differentiation -0.099 0.258 -9999 0 -0.548 16 16
GSK3B -0.058 0.21 -9999 0 -0.476 12 12
RAF1 -0.006 0.175 -9999 0 -0.464 3 3
SHC1 0.02 0 -9999 0 -9999 0 0
STAT3 -0.057 0.196 -9999 0 -0.456 12 12
STAT1 -0.131 0.382 -9999 0 -0.96 10 10
HRAS/SPRED1 -0.021 0.19 -9999 0 -0.506 4 4
cell proliferation -0.051 0.181 -9999 0 -0.429 11 11
PIK3CA 0.02 0.001 -9999 0 -9999 0 0
TEC 0.02 0 -9999 0 -9999 0 0
RPS6KB1 -0.061 0.198 -9999 0 -0.447 13 13
HRAS/SPRED2 -0.018 0.176 -9999 0 -0.464 3 3
LYN/TEC/p62DOK -0.029 0.175 -9999 0 -0.428 7 7
MAPK3 0.017 0.131 -9999 0 -0.359 1 1
STAP1 -0.103 0.25 -9999 0 -0.54 16 16
GRAP2 0 0.12 -9999 0 -0.708 2 2
JAK2 -0.144 0.271 -9999 0 -0.753 9 9
STAT1 (dimer) -0.127 0.374 -9999 0 -0.936 10 10
mol:Gleevec 0 0.007 -9999 0 -9999 0 0
GRB2/SOCS1/VAV1 -0.075 0.259 -9999 0 -0.555 14 14
actin filament polymerization -0.061 0.18 -9999 0 -0.426 12 12
LYN 0.02 0 -9999 0 -9999 0 0
STAP1/STAT5A (dimer) -0.104 0.288 -9999 0 -0.605 16 16
PIK3R1 -0.038 0.194 -9999 0 -0.679 6 6
CBL/CRKL/GRB2 -0.038 0.206 -9999 0 -0.535 6 6
PI3K -0.067 0.246 -9999 0 -0.548 13 13
PTEN 0.02 0 -9999 0 -9999 0 0
SCF/KIT/EPO/EPOR -0.161 0.392 -9999 0 -1.06 8 8
MAPK8 -0.052 0.184 -9999 0 -0.437 11 11
STAT3 (dimer) -0.056 0.192 -9999 0 -0.447 12 12
positive regulation of transcription 0.021 0.112 -9999 0 -0.286 1 1
mol:GDP -0.043 0.229 -9999 0 -0.62 5 5
PIK3C2B -0.094 0.265 -9999 0 -0.584 15 15
CBL/CRKL -0.045 0.198 -9999 0 -0.457 10 10
FER -0.052 0.184 -9999 0 -0.437 11 11
SH2B3 -0.073 0.23 -9999 0 -0.518 13 13
PDPK1 -0.071 0.214 -9999 0 -0.485 13 13
SNAI2 -0.099 0.257 -9999 0 -0.538 16 16
positive regulation of cell proliferation -0.086 0.281 -9999 0 -0.628 13 13
KITLG -0.052 0.195 -9999 0 -0.564 9 9
cell motility -0.086 0.281 -9999 0 -0.628 13 13
PTPN6 0.021 0.01 -9999 0 -9999 0 0
EPOR 0.005 0.125 -9999 0 -9999 0 0
STAT5A (dimer) -0.065 0.233 -9999 0 -0.539 11 11
SOCS1 0.002 0.106 -9999 0 -0.616 2 2
cell migration 0.058 0.186 0.432 12 -9999 0 12
SOS1 0.02 0 -9999 0 -9999 0 0
EPO -0.139 0.245 -9999 0 -0.521 21 21
VAV1 -0.048 0.209 -9999 0 -0.682 7 7
GRB10 -0.095 0.255 -9999 0 -0.556 14 14
PTPN11 0.021 0.007 -9999 0 -9999 0 0
SCF/KIT -0.066 0.193 -9999 0 -0.455 12 12
GO:0007205 0.001 0.01 -9999 0 -9999 0 0
MAP2K1 0.011 0.142 -9999 0 -0.405 1 1
CBL 0.02 0 -9999 0 -9999 0 0
KIT -0.086 0.333 -9999 0 -1.124 4 4
MAP2K2 0.011 0.142 -9999 0 -0.405 1 1
SHC/Grb2/SOS1 -0.034 0.186 -9999 0 -0.45 8 8
STAT5A -0.067 0.239 -9999 0 -0.554 11 11
GRB2 0.01 0.085 -9999 0 -0.708 1 1
response to radiation -0.096 0.251 -9999 0 -0.525 16 16
SHC/GRAP2 0.014 0.091 -9999 0 -0.526 2 2
PTPRO -0.102 0.264 -9999 0 -0.562 16 16
SH2B2 -0.063 0.183 -9999 0 -0.434 12 12
DOK1 0.02 0 -9999 0 -9999 0 0
MATK -0.06 0.19 -9999 0 -0.44 12 12
CREBBP 0.043 0.024 -9999 0 -9999 0 0
BCL2 -0.096 0.44 -9999 0 -1.527 6 6
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.039 0.168 -9999 0 -0.457 10 10
ADCY5 -0.03 0.156 -9999 0 -0.44 9 9
ADCY6 0.029 0 -9999 0 -9999 0 0
ADCY7 -0.001 0.11 -9999 0 -0.398 5 5
ADCY1 0.029 0 -9999 0 -9999 0 0
ADCY2 -0.088 0.173 -9999 0 -0.336 23 23
ADCY3 -0.003 0.117 -9999 0 -0.427 5 5
ADCY8 -0.056 0.147 -9999 0 -0.311 18 18
PRKCE 0.017 0 -9999 0 -9999 0 0
ADCY9 0.017 0.069 -9999 0 -0.384 2 2
mol:DAG 0 0 -9999 0 -9999 0 0
cAMP biosynthetic process -0.083 0.147 -9999 0 -0.404 7 7
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.01 0.085 -9999 0 -0.708 1 1
ITGB7 0.02 0 -9999 0 -9999 0 0
ITGA4 -0.081 0.252 -9999 0 -0.708 10 10
alpha4/beta7 Integrin -0.047 0.192 -9999 0 -0.526 10 10
alpha4/beta1 Integrin -0.055 0.2 -9999 0 -0.526 11 11
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.043 0.184 -9999 0 -0.476 9 9
fibroblast growth factor receptor signaling pathway -0.043 0.183 -9999 0 -0.474 9 9
LAMA1 -0.01 0.145 -9999 0 -0.708 3 3
PRNP 0.02 0 -9999 0 -9999 0 0
GPC1/SLIT2 -0.101 0.208 -9999 0 -0.419 21 21
SMAD2 0.013 0.14 -9999 0 -0.531 4 4
GPC1/PrPc/Cu2+ 0.013 0.067 -9999 0 -0.311 3 3
GPC1/Laminin alpha1 -0.01 0.133 -9999 0 -0.446 6 6
TDGF1 -0.033 0.161 -9999 0 -0.523 7 7
CRIPTO/GPC1 -0.025 0.137 -9999 0 -0.366 10 10
APP/GPC1 -0.047 0.197 -9999 0 -0.524 10 10
mol:NO 0 0 -9999 0 -9999 0 0
YES1 -0.006 0.117 -9999 0 -9999 0 0
FLT1 -0.132 0.296 -9999 0 -0.708 15 15
GPC1/TGFB/TGFBR1/TGFBR2 0.001 0.152 -9999 0 -0.587 4 4
SERPINC1 0.005 0.089 -9999 0 -0.523 2 2
FYN -0.083 0.238 -9999 0 -0.564 12 12
FGR -0.006 0.117 -9999 0 -9999 0 0
positive regulation of MAPKKK cascade -0.045 0.221 -9999 0 -0.58 8 8
SLIT2 -0.134 0.27 -9999 0 -0.595 18 18
GPC1/NRG -0.036 0.167 -9999 0 -0.446 10 10
NRG1 -0.046 0.202 -9999 0 -0.655 7 7
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.163 0.354 -9999 0 -0.753 18 18
LYN -0.006 0.117 -9999 0 -9999 0 0
mol:Spermine 0 0.079 -9999 0 -0.38 3 3
cell growth -0.043 0.183 -9999 0 -0.474 9 9
BMP signaling pathway 0.003 0.108 0.523 3 -9999 0 3
SRC -0.006 0.117 -9999 0 -9999 0 0
TGFBR1 -0.01 0.145 -9999 0 -0.708 3 3
mol:Cu2+ 0 0 -9999 0 -9999 0 0
PLA2G2A -0.046 0.187 -9999 0 -0.57 8 8
GPC1 -0.003 0.109 -9999 0 -0.523 3 3
TGFBR1 (dimer) -0.01 0.145 -9999 0 -0.707 3 3
VEGFA -0.132 0.296 -9999 0 -0.708 15 15
BLK -0.015 0.126 -9999 0 -9999 0 0
HCK -0.019 0.149 -9999 0 -0.588 2 2
FGF2 -0.079 0.246 -9999 0 -0.689 10 10
FGFR1 0.012 0.064 -9999 0 -0.523 1 1
VEGFR1 homodimer -0.131 0.295 -9999 0 -0.707 15 15
TGFBR2 0.01 0.085 -9999 0 -0.708 1 1
cell death -0.047 0.196 -9999 0 -0.523 10 10
ATIII/GPC1 0.002 0.101 -9999 0 -0.366 5 5
PLA2G2A/GPC1 -0.034 0.164 -9999 0 -0.43 10 10
LCK -0.082 0.233 -9999 0 -0.642 8 8
neuron differentiation -0.036 0.167 -9999 0 -0.445 10 10
PrPc/Cu2+ 0.015 0 -9999 0 -9999 0 0
APP -0.061 0.229 -9999 0 -0.708 8 8
TGFBR2 (dimer) 0.01 0.085 -9999 0 -0.707 1 1
Syndecan-3-mediated signaling events

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
CTTN 0.02 0 -9999 0 -9999 0 0
Syndecan-3/Src/Cortactin -0.12 0.214 -9999 0 -0.802 3 3
Syndecan-3/Neurocan -0.048 0.151 -9999 0 -0.637 4 4
POMC -0.028 0.16 -9999 0 -0.554 6 6
EGFR -0.106 0.26 -9999 0 -0.629 14 14
Syndecan-3/EGFR -0.103 0.185 -9999 0 -0.478 11 11
AGRP -0.003 0.109 -9999 0 -0.523 3 3
NCSTN 0.02 0 -9999 0 -9999 0 0
PSENEN 0.02 0 -9999 0 -9999 0 0
RP11-540L11.1 0 0 -9999 0 -9999 0 0
APH1B 0.01 0.085 -9999 0 -0.708 1 1
APH1A -0.02 0.167 -9999 0 -0.708 4 4
NCAN 0.005 0.089 -9999 0 -0.523 2 2
long-term memory -0.058 0.229 -9999 0 -0.492 12 12
Syndecan-3/IL8 -0.125 0.187 -9999 0 -0.487 11 11
PSEN1 0.01 0.085 -9999 0 -0.708 1 1
Src/Cortactin 0.03 0 -9999 0 -9999 0 0
FYN -0.101 0.271 -9999 0 -0.708 12 12
limb bud formation -0.044 0.147 -9999 0 -0.537 5 5
MC4R 0 0.12 -9999 0 -0.708 2 2
SRC 0.02 0 -9999 0 -9999 0 0
PTN -0.247 0.313 -9999 0 -0.601 31 31
FGFR/FGF/Syndecan-3 -0.045 0.149 -9999 0 -0.543 5 5
neuron projection morphogenesis -0.114 0.21 -9999 0 -0.69 4 4
Syndecan-3/AgRP -0.052 0.153 -9999 0 -0.637 4 4
Syndecan-3/AgRP/MC4R -0.017 0.201 -9999 0 -0.788 4 4
Fyn/Cortactin -0.063 0.207 -9999 0 -0.526 12 12
SDC3 -0.045 0.151 -9999 0 -0.55 5 5
GO:0007205 0 0 -9999 0 -9999 0 0
positive regulation of leukocyte migration -0.123 0.184 -9999 0 -0.479 11 11
IL8 -0.156 0.279 -9999 0 -0.585 21 21
Syndecan-3/Fyn/Cortactin -0.06 0.238 -9999 0 -0.509 12 12
Syndecan-3/CASK -0.043 0.143 -9999 0 -0.522 5 5
alpha-MSH/MC4R -0.02 0.158 -9999 0 -0.478 7 7
Gamma Secretase 0.024 0.117 -9999 0 -9999 0 0
Integrins in angiogenesis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.15 0.34 -9999 0 -0.732 17 17
alphaV beta3 Integrin -0.069 0.207 -9999 0 -0.479 12 12
PTK2 -0.144 0.369 -9999 0 -0.758 18 18
IGF1R 0.01 0.085 -9999 0 -0.708 1 1
PI4KB 0.02 0 -9999 0 -9999 0 0
MFGE8 0.02 0 -9999 0 -9999 0 0
SRC 0.02 0 -9999 0 -9999 0 0
CDKN1B -0.007 0.101 -9999 0 -0.532 1 1
VEGFA -0.132 0.296 -9999 0 -0.708 15 15
ILK 0.001 0.08 -9999 0 -9999 0 0
ROCK1 0.02 0 -9999 0 -9999 0 0
AKT1 0.014 0.074 -9999 0 -9999 0 0
PTK2B -0.12 0.329 -9999 0 -0.796 12 12
alphaV/beta3 Integrin/JAM-A -0.047 0.197 -9999 0 -0.41 14 14
CBL 0.02 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
alphaV beta3 Integrin/ANGPTL3 -0.17 0.243 -9999 0 -0.552 13 13
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.034 0.184 -9999 0 -0.485 8 8
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.07 0.247 -9999 0 -0.524 15 15
alphaV/beta3 Integrin/Syndecan-1 -0.042 0.165 -9999 0 -0.444 6 6
PI4KA 0.02 0 -9999 0 -9999 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.153 0.265 -9999 0 -0.712 11 11
PI4 Kinase 0.03 0 -9999 0 -9999 0 0
PIK3CA 0.02 0 -9999 0 -9999 0 0
alphaV/beta3 Integrin/Osteopontin -0.084 0.237 -9999 0 -0.565 12 12
RPS6KB1 -0.085 0.275 -9999 0 -0.704 9 9
TLN1 0.02 0 -9999 0 -9999 0 0
MAPK3 -0.102 0.323 -9999 0 -0.718 14 14
GPR124 -0.041 0.201 -9999 0 -0.708 6 6
MAPK1 -0.102 0.323 -9999 0 -0.718 14 14
PXN 0.02 0 -9999 0 -9999 0 0
PIK3R1 -0.038 0.194 -9999 0 -0.677 6 6
alphaV/beta3 Integrin/Tumstatin -0.056 0.2 -9999 0 -0.507 9 9
cell adhesion -0.145 0.187 -9999 0 -0.65 5 5
ANGPTL3 -0.242 0.307 -9999 0 -0.589 31 31
VEGFR2 homodimer/VEGFA homodimer/Src -0.12 0.306 -9999 0 -0.64 17 17
IGF-1R heterotetramer 0.01 0.085 -9999 0 -0.707 1 1
Rac1/GDP 0.015 0 -9999 0 -9999 0 0
TGFBR2 0.01 0.085 -9999 0 -0.708 1 1
ITGB3 -0.03 0.169 -9999 0 -0.585 6 6
IGF1 -0.081 0.228 -9999 0 -0.585 12 12
RAC1 0.02 0 -9999 0 -9999 0 0
regulation of cell-matrix adhesion -0.042 0.219 -9999 0 -0.616 8 8
apoptosis 0 0.119 -9999 0 -0.705 2 2
CD47 0.02 0 -9999 0 -9999 0 0
alphaV/beta3 Integrin/CD47 -0.005 0.132 -9999 0 -0.444 4 4
VCL 0.02 0 -9999 0 -9999 0 0
alphaV/beta3 Integrin/Del1 -0.14 0.259 -9999 0 -0.442 27 27
CSF1 0.01 0.085 -9999 0 -0.708 1 1
PIK3C2A -0.011 0.104 -9999 0 -0.532 1 1
PI4 Kinase/Pyk2 -0.177 0.289 -9999 0 -0.672 17 17
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.136 0.348 -9999 0 -0.7 18 18
FAK1/Vinculin -0.088 0.277 -9999 0 -0.558 17 17
alphaV beta3/Integrin/ppsTEM5 -0.042 0.22 -9999 0 -0.62 8 8
RHOA 0.01 0.085 -9999 0 -0.708 1 1
VTN 0.02 0 -9999 0 -9999 0 0
BCAR1 0.02 0 -9999 0 -9999 0 0
FGF2 -0.079 0.246 -9999 0 -0.689 10 10
F11R -0.057 0.204 -9999 0 -0.512 12 12
alphaV/beta3 Integrin/Lactadherin -0.005 0.132 -9999 0 -0.444 4 4
alphaV/beta3 Integrin/TGFBR2 -0.012 0.141 -9999 0 -0.444 5 5
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.033 0.09 -9999 0 -0.396 3 3
HSP90AA1 0.005 0.089 -9999 0 -0.523 2 2
alphaV/beta3 Integrin/Talin -0.003 0.121 -9999 0 -0.407 4 4
mol:GDP 0 0 -9999 0 -9999 0 0
FN1 -0.013 0.136 -9999 0 -0.57 4 4
alphaV/beta3 Integrin/Pyk2 -0.119 0.331 -9999 0 -0.799 12 12
SDC1 -0.038 0.179 -9999 0 -0.576 7 7
VAV3 0.019 0.151 -9999 0 -0.754 2 2
PTPN11 0.02 0 -9999 0 -9999 0 0
IRS1 -0.018 0.138 -9999 0 -0.523 5 5
FAK1/Paxillin -0.088 0.277 -9999 0 -0.558 17 17
cell migration -0.064 0.252 -9999 0 -0.491 17 17
ITGAV 0 0.12 -9999 0 -0.708 2 2
PI3K -0.109 0.198 -9999 0 -0.646 6 6
SPP1 -0.109 0.254 -9999 0 -0.597 15 15
KDR -0.081 0.252 -9999 0 -0.708 10 10
mol:PI-4-5-P2 0 0 -9999 0 -9999 0 0
alphaV/beta3 Integrin/Caspase 8 0 0.119 -9999 0 -0.707 2 2
COL4A3 -0.061 0.216 -9999 0 -0.626 9 9
angiogenesis -0.091 0.317 -9999 0 -0.719 13 13
Rac1/GTP 0.028 0.14 -9999 0 -0.687 2 2
EDIL3 -0.197 0.302 -9999 0 -0.605 25 25
cell proliferation -0.012 0.141 -9999 0 -0.442 5 5
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.02 0 -9999 0 -9999 0 0
Caspase 8 (4 units) -0.108 0.199 -9999 0 -0.58 9 9
NEF -0.035 0.066 -9999 0 -9999 0 0
NFKBIA -0.037 0.165 -9999 0 -0.788 3 3
BIRC3 -0.142 0.347 -9999 0 -0.699 19 19
CYCS -0.109 0.301 -9999 0 -0.719 12 12
RIPK1 0.02 0 -9999 0 -9999 0 0
CD247 -0.19 0.341 -9999 0 -0.788 17 17
MAP2K7 -0.074 0.251 -9999 0 -0.589 11 11
protein ubiquitination -0.025 0.233 -9999 0 -0.543 11 11
CRADD 0.012 0.064 -9999 0 -0.523 1 1
DAXX 0.02 0 -9999 0 -9999 0 0
FAS -0.061 0.229 -9999 0 -0.708 8 8
BID -0.087 0.247 -9999 0 -0.618 10 10
NF-kappa-B/RelA/I kappa B alpha -0.095 0.172 -9999 0 -0.658 3 3
TRADD 0.01 0.085 -9999 0 -0.708 1 1
MAP3K5 0 0.12 -9999 0 -0.708 2 2
CFLAR -0.01 0.145 -9999 0 -0.708 3 3
FADD 0.02 0 -9999 0 -9999 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.095 0.173 -9999 0 -0.661 3 3
MAPK8 -0.057 0.232 -9999 0 -0.554 10 10
APAF1 0.02 0 -9999 0 -9999 0 0
TRAF1 -0.038 0.194 -9999 0 -0.677 6 6
TRAF2 0.005 0.089 -9999 0 -0.523 2 2
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.081 0.207 -9999 0 -0.546 9 9
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.022 0.214 -9999 0 -0.651 5 5
CHUK -0.034 0.259 -9999 0 -0.612 11 11
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.001 0.147 -9999 0 -9999 0 0
TCRz/NEF -0.211 0.309 -9999 0 -0.684 19 19
TNF 0.002 0.106 -9999 0 -0.616 2 2
FASLG -0.266 0.428 -9999 0 -0.752 28 28
NFKB1 -0.004 0.05 -9999 0 -9999 0 0
TNFR1A/BAG4/TNF-alpha -0.024 0.178 -9999 0 -0.496 8 8
CASP6 -0.08 0.181 -9999 0 -0.797 3 3
CASP7 -0.106 0.327 -9999 0 -0.693 15 15
RELA -0.004 0.05 -9999 0 -9999 0 0
CASP2 0.02 0 -9999 0 -9999 0 0
CASP3 -0.108 0.329 -9999 0 -0.68 16 16
TNFRSF1A -0.061 0.229 -9999 0 -0.708 8 8
TNFR1A/BAG4 -0.032 0.175 -9999 0 -0.526 8 8
CASP8 0.02 0 -9999 0 -9999 0 0
CASP9 0.02 0 -9999 0 -9999 0 0
MAP3K14 -0.057 0.298 -9999 0 -0.72 11 11
APAF-1/Caspase 9 -0.164 0.255 -9999 0 -0.595 17 17
BCL2 -0.07 0.234 -9999 0 -0.571 9 9
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.026 0.137 -9999 0 -0.461 6 6
NFATC2 0.008 0.068 -9999 0 -0.464 1 1
NFATC3 0.014 0.039 -9999 0 -9999 0 0
CD40LG -0.224 0.374 -9999 0 -0.812 14 14
PTGS2 -0.253 0.398 -9999 0 -0.835 17 17
JUNB 0.002 0.106 -9999 0 -0.616 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.005 0.015 -9999 0 -9999 0 0
CaM/Ca2+ -0.004 0.015 -9999 0 -9999 0 0
CALM1 0.017 0.01 -9999 0 -9999 0 0
JUN -0.097 0.259 -9999 0 -0.671 12 12
mol:Ca2+ -0.009 0.016 -9999 0 -9999 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.004 0.006 -9999 0 -9999 0 0
FOSL1 0.02 0 -9999 0 -9999 0 0
CREM 0.012 0.064 -9999 0 -0.524 1 1
Jun/NFAT1-c-4/p21SNFT -0.163 0.243 -9999 0 -0.672 10 10
FOS -0.158 0.286 -9999 0 -0.612 20 20
IFNG -0.319 0.43 -9999 0 -0.787 26 26
AP-1/NFAT1-c-4 -0.298 0.551 -9999 0 -1.106 16 16
FASLG -0.295 0.45 -9999 0 -0.821 25 25
NFAT1-c-4/ICER1 -0.063 0.137 -9999 0 -0.478 5 5
IL2RA -0.258 0.418 -9999 0 -0.861 18 18
FKBP12/FK506 0.015 0 -9999 0 -9999 0 0
CSF2 -0.216 0.367 -9999 0 -0.801 14 14
JunB/Fra1/NFAT1-c-4 -0.057 0.129 -9999 0 -0.461 4 4
IL4 -0.216 0.367 -9999 0 -0.801 14 14
IL2 -0.03 0.257 -9999 0 -1.55 2 2
IL3 0.008 0.024 -9999 0 -9999 0 0
FKBP1A 0.02 0 -9999 0 -9999 0 0
BATF3 0 0 -9999 0 -9999 0 0
mol:FK506 0 0 -9999 0 -9999 0 0
POU2F1 0.032 0 -9999 0 -9999 0 0
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 0.027 0.054 -9999 0 -0.425 1 1
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -9999 0 -9999 0 0
cytokine production during immune response 0.14 0.283 0.802 9 -9999 0 9
IL27/IL27R/JAK1 -0.236 0.445 -9999 0 -1.256 10 10
TBX21 -0.215 0.359 -9999 0 -0.832 15 15
IL12B -0.005 0.106 -9999 0 -0.621 2 2
IL12A 0.013 0.006 -9999 0 -9999 0 0
IL6ST -0.04 0.186 -9999 0 -0.72 5 5
IL27RA/JAK1 -0.156 0.438 -9999 0 -1.344 8 8
IL27 -0.068 0.211 -9999 0 -0.62 9 9
TYK2 0.012 0.012 -9999 0 -9999 0 0
T-helper cell lineage commitment -0.036 0.221 -9999 0 -1.566 1 1
T-helper 2 cell differentiation 0.14 0.283 0.802 9 -9999 0 9
T cell proliferation during immune response 0.14 0.283 0.802 9 -9999 0 9
MAPKKK cascade -0.14 0.283 -9999 0 -0.802 9 9
STAT3 0.01 0.085 -9999 0 -0.708 1 1
STAT2 0.01 0.085 -9999 0 -0.708 1 1
STAT1 -0.057 0.216 -9999 0 -0.663 8 8
IL12RB1 0.017 0.005 -9999 0 -9999 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -9999 0 -9999 0 0
IL12RB2 -0.229 0.333 -9999 0 -0.703 20 20
IL27/IL27R/JAK2/TYK2 -0.142 0.29 -9999 0 -0.82 9 9
positive regulation of T cell mediated cytotoxicity -0.14 0.283 -9999 0 -0.802 9 9
STAT1 (dimer) -0.331 0.502 -9999 0 -1.346 12 12
JAK2 0.011 0.01 -9999 0 -9999 0 0
JAK1 -0.022 0.167 -9999 0 -0.712 4 4
STAT2 (dimer) -0.129 0.28 -9999 0 -0.756 10 10
T cell proliferation -0.204 0.295 -9999 0 -0.814 10 10
IL12/IL12R/TYK2/JAK2 -0.052 0.181 -9999 0 -1.268 1 1
IL17A -0.047 0.219 -9999 0 -1.576 1 1
mast cell activation 0.14 0.283 0.802 9 -9999 0 9
IFNG -0.038 0.054 -9999 0 -0.122 8 8
T cell differentiation -0.011 0.01 -9999 0 -0.025 20 20
STAT3 (dimer) -0.129 0.28 -9999 0 -0.756 10 10
STAT5A (dimer) -0.128 0.275 -9999 0 -0.766 9 9
STAT4 (dimer) -0.163 0.36 -9999 0 -0.922 11 11
STAT4 -0.061 0.229 -9999 0 -0.708 8 8
T cell activation 0.001 0.04 0.121 7 -9999 0 7
IL27R/JAK2/TYK2 -0.151 0.428 -9999 0 -1.414 7 7
GATA3 0.016 0.093 -9999 0 -9999 0 0
IL18 -0.054 0.166 -9999 0 -0.439 11 11
positive regulation of mast cell cytokine production -0.126 0.272 -9999 0 -0.733 10 10
IL27/EBI3 -0.052 0.168 -9999 0 -0.462 10 10
IL27RA -0.155 0.44 -9999 0 -1.471 7 7
IL6 -0.147 0.275 -9999 0 -0.555 22 22
STAT5A 0.012 0.064 -9999 0 -0.523 1 1
monocyte differentiation -0.002 0.003 -9999 0 -9999 0 0
IL2 0.023 0.246 0.514 6 -1.133 2 8
IL1B -0.087 0.203 -9999 0 -0.477 15 15
EBI3 0 0.086 -9999 0 -0.717 1 1
TNF 0.002 0.079 -9999 0 -0.46 2 2
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.01 0.111 -9999 0 -0.548 2 2
Syndecan-4/Syndesmos -0.129 0.217 -9999 0 -0.603 7 7
positive regulation of JNK cascade -0.223 0.308 -9999 0 -0.709 15 15
Syndecan-4/ADAM12 -0.145 0.23 -9999 0 -0.613 8 8
CCL5 -0.096 0.25 -9999 0 -0.623 13 13
Rac1/GDP 0.015 0 -9999 0 -9999 0 0
DNM2 0.012 0.064 -9999 0 -0.523 1 1
ITGA5 -0.031 0.185 -9999 0 -0.708 5 5
SDCBP 0.002 0.106 -9999 0 -0.616 2 2
PLG -0.123 0.244 -9999 0 -0.53 19 19
ADAM12 -0.028 0.16 -9999 0 -0.554 6 6
mol:GTP 0 0 -9999 0 -9999 0 0
NUDT16L1 0.005 0.089 -9999 0 -0.523 2 2
mol:PI-4-5-P2 0 0 -9999 0 -9999 0 0
Syndecan-4/PKC alpha -0.053 0.047 -9999 0 -9999 0 0
Syndecan-4/Laminin alpha1 -0.137 0.237 -9999 0 -0.662 7 7
Syndecan-4/CXCL12/CXCR4 -0.24 0.341 -9999 0 -0.778 15 15
Syndecan-4/Laminin alpha3 -0.133 0.212 -9999 0 -0.627 5 5
MDK -0.071 0.203 -9999 0 -0.523 12 12
Syndecan-4/FZD7 -0.154 0.235 -9999 0 -0.678 7 7
Syndecan-4/Midkine -0.165 0.227 -9999 0 -0.623 7 7
FZD7 -0.046 0.187 -9999 0 -0.57 8 8
Syndecan-4/FGFR1/FGF -0.19 0.22 -9999 0 -0.603 11 11
THBS1 -0.031 0.185 -9999 0 -0.708 5 5
integrin-mediated signaling pathway -0.124 0.211 -9999 0 -0.596 7 7
positive regulation of MAPKKK cascade -0.223 0.308 -9999 0 -0.709 15 15
Syndecan-4/TACI -0.122 0.208 -9999 0 -0.627 5 5
CXCR4 -0.119 0.284 -9999 0 -0.695 14 14
cell adhesion 0.015 0.116 -9999 0 -0.755 1 1
Syndecan-4/Dynamin -0.126 0.21 -9999 0 -0.627 5 5
Syndecan-4/TSP1 -0.146 0.259 -9999 0 -0.756 7 7
Syndecan-4/GIPC -0.122 0.208 -9999 0 -0.627 5 5
Syndecan-4/RANTES -0.178 0.276 -9999 0 -0.725 10 10
ITGB1 0.01 0.085 -9999 0 -0.708 1 1
LAMA1 -0.01 0.145 -9999 0 -0.708 3 3
LAMA3 -0.003 0.109 -9999 0 -0.523 3 3
RAC1 0.02 0 -9999 0 -9999 0 0
PRKCA 0.054 0.046 -9999 0 -9999 0 0
Syndecan-4/alpha-Actinin -0.159 0.268 -9999 0 -0.749 8 8
TFPI -0.18 0.323 -9999 0 -0.699 20 20
F2 -0.03 0.154 -9999 0 -0.54 6 6
alpha5/beta1 Integrin -0.015 0.17 -9999 0 -0.613 5 5
positive regulation of cell adhesion -0.133 0.233 -9999 0 -0.629 7 7
ACTN1 -0.056 0.216 -9999 0 -0.662 8 8
TNC 0.005 0.089 -9999 0 -0.523 2 2
Syndecan-4/CXCL12 -0.194 0.285 -9999 0 -0.724 11 11
FGF6 -0.011 0.145 -9999 0 -0.708 3 3
RHOA 0.01 0.085 -9999 0 -0.708 1 1
CXCL12 -0.126 0.277 -9999 0 -0.639 16 16
TNFRSF13B 0.02 0 -9999 0 -9999 0 0
FGF2 -0.079 0.246 -9999 0 -0.689 10 10
FGFR1 0.012 0.064 -9999 0 -0.523 1 1
Syndecan-4/PI-4-5-P2 -0.133 0.206 -9999 0 -0.636 5 5
mol:GDP 0 0 -9999 0 -9999 0 0
FN1 -0.014 0.135 -9999 0 -0.563 4 4
cell migration -0.018 0.017 -9999 0 -9999 0 0
PRKCD -0.027 0.149 -9999 0 -0.519 6 6
vasculogenesis -0.14 0.245 -9999 0 -0.713 7 7
SDC4 -0.14 0.219 -9999 0 -0.677 5 5
Syndecan-4/Tenascin C -0.129 0.219 -9999 0 -0.623 7 7
Syndecan-4/PI-4-5-P2/PKC alpha -0.042 0.037 -9999 0 -9999 0 0
Syndecan-4/Syntenin -0.131 0.212 -9999 0 -0.612 6 6
MMP9 -0.148 0.268 -9999 0 -0.561 21 21
Rac1/GTP 0.003 0.118 -9999 0 -0.79 1 1
cytoskeleton organization -0.125 0.209 -9999 0 -0.577 7 7
GIPC1 0.02 0 -9999 0 -9999 0 0
Syndecan-4/TFPI -0.222 0.31 -9999 0 -0.689 17 17
E-cadherin 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
E-cadherin/beta catenin-gamma catenin -0.04 0.184 -9999 0 -0.503 7 7
E-cadherin/beta catenin -0.057 0.188 -9999 0 -0.452 13 13
CTNNB1 0.02 0 -9999 0 -9999 0 0
JUP 0.01 0.085 -9999 0 -0.708 1 1
CDH1 -0.096 0.25 -9999 0 -0.623 13 13
Ephrin A reverse signaling

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
MAPKKK cascade -0.005 0.108 -9999 0 -0.357 6 6
EFNA5 -0.023 0.159 -9999 0 -0.597 5 5
FYN -0.066 0.182 -9999 0 -0.408 14 14
neuron projection morphogenesis -0.005 0.108 -9999 0 -0.357 6 6
cell-cell signaling 0 0 -9999 0 -9999 0 0
Ephrin A5/EPHA5 -0.005 0.108 -9999 0 -0.359 6 6
EPHA5 0.012 0.064 -9999 0 -0.523 1 1
Signaling events mediated by PTP1B

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
PDGFRB 0 0.12 -9999 0 -0.708 2 2
Jak2/Leptin Receptor -0.046 0.127 -9999 0 -0.462 4 4
PTP1B/AKT1 -0.057 0.154 -9999 0 -0.472 6 6
FYN -0.101 0.271 -9999 0 -0.708 12 12
p210 bcr-abl/PTP1B -0.072 0.159 -9999 0 -0.497 6 6
EGFR -0.113 0.262 -9999 0 -0.638 14 14
EGF/EGFR -0.23 0.249 -9999 0 -0.529 22 22
CSF1 0.01 0.085 -9999 0 -0.708 1 1
AKT1 0.019 0.003 -9999 0 -9999 0 0
INSR -0.071 0.242 -9999 0 -0.712 9 9
PTP1B/N-cadherin -0.13 0.243 -9999 0 -0.521 16 16
Insulin Receptor/Insulin -0.083 0.201 -9999 0 -0.576 9 9
HCK 0 0.12 -9999 0 -0.708 2 2
CRK 0 0.12 -9999 0 -0.708 2 2
TYK2 -0.058 0.153 -9999 0 -0.5 5 5
EGF -0.251 0.306 -9999 0 -0.587 32 32
YES1 0.02 0 -9999 0 -9999 0 0
CAV1 -0.125 0.256 -9999 0 -0.686 9 9
TXN 0.007 0.065 -9999 0 -0.538 1 1
PTP1B/IRS1/GRB2 -0.068 0.184 -9999 0 -0.579 6 6
cell migration 0.072 0.159 0.497 6 -9999 0 6
STAT3 0.009 0.086 -9999 0 -0.713 1 1
PRLR -0.048 0.187 -9999 0 -0.513 10 10
ITGA2B 0.018 0.002 -9999 0 -9999 0 0
CSF1R 0.02 0 -9999 0 -9999 0 0
Prolactin Receptor/Prolactin -0.009 0.137 -9999 0 -0.351 10 10
FGR 0.02 0 -9999 0 -9999 0 0
PTP1B/p130 Cas -0.058 0.153 -9999 0 -0.468 6 6
Crk/p130 Cas -0.055 0.169 -9999 0 -0.525 6 6
DOK1 -0.058 0.18 -9999 0 -0.554 6 6
JAK2 -0.024 0.103 -9999 0 -0.468 1 1
Jak2/Leptin Receptor/Leptin -0.105 0.182 -9999 0 -0.523 9 9
PIK3R1 -0.038 0.194 -9999 0 -0.677 6 6
PTPN1 -0.073 0.161 -9999 0 -0.503 6 6
LYN 0.02 0 -9999 0 -9999 0 0
CDH2 -0.111 0.28 -9999 0 -0.708 13 13
SRC -0.004 0.056 -9999 0 -9999 0 0
ITGB3 -0.032 0.17 -9999 0 -0.59 6 6
CAT1/PTP1B -0.083 0.225 -9999 0 -0.532 11 11
CAPN1 0.016 0.006 -9999 0 -9999 0 0
CSK 0.012 0.064 -9999 0 -0.523 1 1
PI3K -0.095 0.215 -9999 0 -0.611 8 8
mol:H2O2 -0.003 0.006 -9999 0 -9999 0 0
STAT3 (dimer) -0.096 0.192 -9999 0 -0.545 8 8
negative regulation of transcription -0.023 0.102 -9999 0 -0.461 1 1
FCGR2A -0.031 0.185 -9999 0 -0.708 5 5
FER 0.014 0.006 -9999 0 -9999 0 0
alphaIIb/beta3 Integrin -0.025 0.124 -9999 0 -0.427 6 6
BLK 0.005 0.089 -9999 0 -0.523 2 2
Insulin Receptor/Insulin/Shc -0.02 0.161 -9999 0 -0.446 9 9
RHOA 0.006 0.086 -9999 0 -0.715 1 1
LEPR -0.01 0.145 -9999 0 -0.707 3 3
BCAR1 0.02 0 -9999 0 -9999 0 0
p210 bcr-abl/Grb2 0.01 0.085 -9999 0 -0.707 1 1
mol:NADPH -0.004 0.005 -9999 0 -9999 0 0
TRPV6 -0.058 0.238 -9999 0 -0.627 9 9
PRL 0.027 0.004 -9999 0 -9999 0 0
SOCS3 -0.069 0.355 -9999 0 -1.514 4 4
SPRY2 -0.022 0.158 -9999 0 -0.67 4 4
Insulin Receptor/Insulin/IRS1 -0.043 0.185 -9999 0 -0.478 9 9
CSF1/CSF1R -0.05 0.159 -9999 0 -0.518 5 5
Ras protein signal transduction 0.033 0.083 -9999 0 -0.577 1 1
IRS1 -0.018 0.138 -9999 0 -0.523 5 5
INS 0.019 0.003 -9999 0 -9999 0 0
LEP -0.041 0.171 -9999 0 -0.524 8 8
STAT5B -0.047 0.134 -9999 0 -0.401 6 6
STAT5A -0.047 0.133 -9999 0 -0.401 6 6
GRB2 0.01 0.085 -9999 0 -0.708 1 1
PDGFB-D/PDGFRB -0.069 0.171 -9999 0 -0.482 8 8
CSN2 0.039 0.05 -9999 0 -9999 0 0
PIK3CA 0.02 0 -9999 0 -9999 0 0
LAT -0.078 0.252 -9999 0 -0.819 6 6
YBX1 0.009 0.12 -9999 0 -0.699 2 2
LCK -0.104 0.255 -9999 0 -0.616 14 14
SHC1 0.02 0 -9999 0 -9999 0 0
NOX4 -0.111 0.261 -9999 0 -0.635 14 14
BMP receptor 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
BMP7/BMPR2/BMPR1A-1B/FS -0.002 0.153 -9999 0 -0.636 2 2
SMAD6-7/SMURF1 0.002 0.121 -9999 0 -0.444 3 3
NOG -0.016 0.147 -9999 0 -0.616 4 4
SMAD9 -0.118 0.286 -9999 0 -0.695 13 13
SMAD4 0.01 0.085 -9999 0 -0.708 1 1
SMAD5 -0.017 0.131 -9999 0 -0.451 2 2
BMP7/USAG1 -0.131 0.218 -9999 0 -0.415 26 26
SMAD5/SKI -0.005 0.125 -9999 0 -0.421 2 2
SMAD1 0.033 0.101 -9999 0 -0.559 1 1
BMP2 -0.114 0.274 -9999 0 -0.668 14 14
SMAD1/SMAD1/SMAD4 -0.038 0.105 -9999 0 -0.685 1 1
BMPR1A 0.02 0 -9999 0 -9999 0 0
BMPR1B -0.028 0.16 -9999 0 -0.554 6 6
BMPR1A-1B/BAMBI -0.085 0.219 -9999 0 -0.485 14 14
AHSG -0.005 0.122 -9999 0 -0.585 3 3
CER1 0.01 0.085 -9999 0 -0.708 1 1
BMP2-4/CER1 -0.105 0.213 -9999 0 -0.464 14 14
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.016 0.138 -9999 0 -0.462 1 1
BMP2-4 (homodimer) -0.13 0.241 -9999 0 -0.47 23 23
RGMB 0.02 0 -9999 0 -9999 0 0
BMP6/BMPR2/BMPR1A-1B -0.014 0.137 -9999 0 -0.396 3 3
RGMA 0.012 0.064 -9999 0 -0.523 1 1
SMURF1 0.005 0.089 -9999 0 -0.523 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.032 0.128 -9999 0 -0.349 5 5
BMP2-4/USAG1 -0.209 0.252 -9999 0 -0.495 26 26
SMAD6/SMURF1/SMAD5 -0.013 0.137 -9999 0 -0.421 2 2
SOSTDC1 -0.159 0.283 -9999 0 -0.594 21 21
BMP7/BMPR2/BMPR1A-1B 0.003 0.127 -9999 0 -0.469 2 2
SKI 0.02 0 -9999 0 -9999 0 0
BMP6 (homodimer) -0.045 0.187 -9999 0 -0.569 8 8
HFE2 -0.008 0.134 -9999 0 -0.646 3 3
ZFYVE16 0.02 0 -9999 0 -9999 0 0
MAP3K7 0.02 0 -9999 0 -9999 0 0
BMP2-4/CHRD -0.107 0.211 -9999 0 -0.466 13 13
SMAD5/SMAD5/SMAD4 -0.011 0.133 -9999 0 -0.412 3 3
MAPK1 0.02 0 -9999 0 -9999 0 0
TAK1/TAB family -0.053 0.092 -9999 0 -9999 0 0
BMP7 (homodimer) -0.018 0.138 -9999 0 -0.523 5 5
NUP214 0.02 0 -9999 0 -9999 0 0
BMP6/FETUA -0.037 0.161 -9999 0 -0.41 11 11
SMAD1/SKI 0.043 0.097 -9999 0 -0.522 1 1
SMAD6 -0.005 0.122 -9999 0 -0.585 3 3
CTDSP2 0.01 0.085 -9999 0 -0.708 1 1
BMP2-4/FETUA -0.114 0.214 -9999 0 -0.464 14 14
MAP3K7IP1 0.01 0.085 -9999 0 -0.708 1 1
GREM1 -0.018 0.138 -9999 0 -0.523 5 5
BMPR2 (homodimer) 0.02 0 -9999 0 -9999 0 0
GADD34/PP1CA 0.031 0.056 -9999 0 -9999 0 0
BMPR1A-1B (homodimer) -0.005 0.118 -9999 0 -0.393 6 6
CHRDL1 -0.043 0.179 -9999 0 -0.547 8 8
ENDOFIN/SMAD1 0.043 0.097 -9999 0 -0.522 1 1
SMAD6-7/SMURF1/SMAD1 -0.037 0.121 -9999 0 -0.795 1 1
SMAD6/SMURF1 0.005 0.089 -9999 0 -0.523 2 2
BAMBI -0.127 0.287 -9999 0 -0.683 15 15
SMURF2 0.01 0.085 -9999 0 -0.708 1 1
BMP2-4/CHRDL1 -0.138 0.215 -9999 0 -0.464 14 14
BMP2-4/GREM1 -0.12 0.227 -9999 0 -0.496 14 14
SMAD7 0 0.12 -9999 0 -0.708 2 2
SMAD8A/SMAD8A/SMAD4 -0.106 0.276 -9999 0 -0.642 14 14
SMAD1/SMAD6 0.036 0.111 -9999 0 -0.464 2 2
TAK1/SMAD6 0.019 0.065 -9999 0 -0.366 2 2
BMP7 -0.018 0.138 -9999 0 -0.523 5 5
BMP6 -0.046 0.187 -9999 0 -0.57 8 8
MAP3K7IP2 0.02 0 -9999 0 -9999 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.025 0.135 -9999 0 -0.448 2 2
PPM1A -0.003 0.109 -9999 0 -0.523 3 3
SMAD1/SMURF2 0.038 0.115 -9999 0 -0.524 2 2
SMAD7/SMURF1 0.003 0.111 -9999 0 -0.446 4 4
CTDSPL -0.005 0.122 -9999 0 -0.585 3 3
PPP1CA 0.02 0 -9999 0 -9999 0 0
XIAP 0 0 -9999 0 -9999 0 0
CTDSP1 0.02 0 -9999 0 -9999 0 0
PPP1R15A 0.005 0.089 -9999 0 -0.523 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.034 0.136 -9999 0 -0.349 6 6
CHRD 0.005 0.089 -9999 0 -0.523 2 2
BMPR2 0.02 0 -9999 0 -9999 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.035 0.139 -9999 0 -0.381 5 5
BMP4 -0.061 0.203 -9999 0 -0.56 10 10
FST -0.01 0.124 -9999 0 -0.523 4 4
BMP2-4/NOG -0.12 0.225 -9999 0 -0.483 15 15
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.006 0.148 -9999 0 -0.636 2 2
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.1 0.192 -9999 0 -0.5 8 8
positive regulation of NF-kappaB transcription factor activity 0 0.001 -9999 0 -9999 0 0
CRKL 0.02 0 -9999 0 -9999 0 0
STAT1 (dimer)/Cbp/p300 -0.134 0.304 -9999 0 -0.71 12 12
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.037 0.111 -9999 0 -0.489 4 4
antigen processing and presentation of peptide antigen via MHC class I -0.089 0.176 -9999 0 -0.456 12 12
CaM/Ca2+ -0.117 0.154 -9999 0 -0.522 4 4
RAP1A 0.01 0.085 -9999 0 -0.708 1 1
STAT1 (dimer)/SHP2 -0.133 0.245 -9999 0 -0.552 13 13
AKT1 -0.083 0.212 -9999 0 -0.683 4 4
MAP2K1 -0.074 0.197 -9999 0 -0.595 4 4
MAP3K11 -0.089 0.183 -9999 0 -0.535 4 4
IFNGR1 0.011 0.015 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
CaM/Ca2+/CAMKII -0.058 0.127 -9999 0 -0.885 1 1
Rap1/GTP -0.09 0.135 -9999 0 -0.639 2 2
CRKL/C3G 0.022 0.065 -9999 0 -0.526 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.099 0.189 -9999 0 -0.687 2 2
CEBPB -0.06 0.26 -9999 0 -0.772 5 5
STAT3 0.01 0.085 -9999 0 -0.708 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.097 0.225 -9999 0 -0.829 3 3
STAT1 -0.134 0.246 -9999 0 -0.555 13 13
CALM1 0.02 0 -9999 0 -9999 0 0
IFN-gamma (dimer) -0.228 0.291 -9999 0 -0.557 31 31
PIK3CA 0.02 0 -9999 0 -9999 0 0
STAT1 (dimer)/PIAS1 -0.116 0.233 -9999 0 -0.534 11 11
CEBPB/PTGES2/Cbp/p300 -0.089 0.19 -9999 0 -0.571 8 8
mol:Ca2+ -0.101 0.188 -9999 0 -0.493 8 8
MAPK3 -0.052 0.191 -9999 0 -0.927 1 1
STAT1 (dimer) -0.135 0.284 -9999 0 -0.73 12 12
MAPK1 -0.052 0.191 -9999 0 -0.641 3 3
JAK2 0.011 0.015 -9999 0 -9999 0 0
PIK3R1 -0.038 0.194 -9999 0 -0.677 6 6
JAK1 -0.028 0.17 -9999 0 -0.728 4 4
CAMK2D 0.013 0.064 -9999 0 -0.524 1 1
DAPK1 -0.042 0.23 -9999 0 -0.666 7 7
SMAD7 -0.003 0.12 -9999 0 -0.275 5 5
CBL/CRKL/C3G -0.065 0.187 -9999 0 -0.723 2 2
PI3K -0.139 0.202 -9999 0 -0.765 4 4
IFNG -0.229 0.292 -9999 0 -0.558 31 31
apoptosis -0.039 0.177 -9999 0 -0.492 7 7
CAMK2G 0.01 0.085 -9999 0 -0.708 1 1
STAT3 (dimer) 0.01 0.085 -9999 0 -0.707 1 1
CAMK2A 0.02 0 -9999 0 -9999 0 0
CAMK2B -0.055 0.188 -9999 0 -0.524 10 10
FRAP1 -0.066 0.196 -9999 0 -0.609 4 4
PRKCD -0.104 0.252 -9999 0 -0.729 7 7
RAP1B 0.01 0.085 -9999 0 -0.708 1 1
negative regulation of cell growth -0.089 0.176 -9999 0 -0.456 12 12
PTPN2 0.02 0 -9999 0 -9999 0 0
EP300 0.01 0.085 -9999 0 -0.707 1 1
IRF1 -0.128 0.311 -9999 0 -0.685 15 15
STAT1 (dimer)/PIASy -0.122 0.246 -9999 0 -0.556 11 11
SOCS1 -0.007 0.193 -9999 0 -1.554 1 1
mol:GDP -0.1 0.149 -9999 0 -0.671 2 2
CASP1 -0.026 0.165 -9999 0 -0.381 11 11
PTGES2 0.012 0.064 -9999 0 -0.523 1 1
IRF9 0.008 0.124 -9999 0 -0.401 4 4
mol:PI-3-4-5-P3 -0.135 0.193 -9999 0 -0.666 5 5
RAP1/GDP -0.091 0.138 -9999 0 -0.661 2 2
CBL -0.085 0.183 -9999 0 -0.53 4 4
MAP3K1 -0.09 0.205 -9999 0 -0.63 4 4
PIAS1 0.02 0 -9999 0 -9999 0 0
PIAS4 0.012 0.064 -9999 0 -0.524 1 1
antigen processing and presentation of peptide antigen via MHC class II -0.089 0.176 -9999 0 -0.456 12 12
PTPN11 -0.1 0.19 -9999 0 -0.495 8 8
CREBBP 0.02 0.002 -9999 0 -9999 0 0
RAPGEF1 0.01 0.085 -9999 0 -0.708 1 1
Nectin adhesion pathway

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
PDGFRB 0 0.12 -9999 0 -0.708 2 2
alphaV beta3 Integrin -0.023 0.152 -9999 0 -0.446 8 8
PTK2 -0.097 0.189 -9999 0 -0.523 9 9
positive regulation of JNK cascade -0.048 0.107 -9999 0 -0.322 9 9
CDC42/GDP -0.002 0.177 -9999 0 -0.435 9 9
Rac1/GDP 0 0.176 -9999 0 -0.429 9 9
RAP1B 0.01 0.085 -9999 0 -0.708 1 1
RAP1A 0.01 0.085 -9999 0 -0.708 1 1
CTNNB1 0.02 0 -9999 0 -9999 0 0
CDC42/GTP -0.058 0.133 -9999 0 -0.397 9 9
nectin-3/I-afadin -0.051 0.191 -9999 0 -0.497 11 11
RAPGEF1 -0.027 0.21 -9999 0 -0.508 10 10
mol:GTP 0 0 -9999 0 -9999 0 0
CRK -0.042 0.227 -9999 0 -0.577 9 9
PDGFB-D/PDGFRB 0 0.119 -9999 0 -0.707 2 2
TLN1 -0.062 0.199 -9999 0 -0.456 12 12
Rap1/GTP -0.065 0.133 -9999 0 -0.361 11 11
IQGAP1 0.02 0 -9999 0 -9999 0 0
Rap1/GTP/I-afadin 0.021 0.111 -9999 0 -0.608 2 2
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.051 0.191 -9999 0 -0.497 11 11
PVR 0.005 0.089 -9999 0 -0.523 2 2
Necl-5(dimer) 0.005 0.089 -9999 0 -0.523 2 2
mol:GDP -0.019 0.214 -9999 0 -0.543 9 9
MLLT4 0.01 0.085 -9999 0 -0.708 1 1
PIK3CA 0.02 0 -9999 0 -9999 0 0
PI3K -0.045 0.223 -9999 0 -0.68 5 5
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.022 0.065 -9999 0 -0.526 1 1
positive regulation of lamellipodium assembly -0.049 0.113 -9999 0 -0.338 9 9
PVRL1 0.02 0 -9999 0 -9999 0 0
PVRL3 -0.076 0.241 -9999 0 -0.671 10 10
PVRL2 0.02 0 -9999 0 -9999 0 0
PIK3R1 -0.038 0.194 -9999 0 -0.677 6 6
CDH1 -0.096 0.25 -9999 0 -0.623 13 13
CLDN1 -0.146 0.282 -9999 0 -0.611 19 19
JAM-A/CLDN1 -0.123 0.221 -9999 0 -0.431 19 19
SRC -0.098 0.221 -9999 0 -0.655 9 9
ITGB3 -0.03 0.169 -9999 0 -0.585 6 6
nectin-1(dimer)/I-afadin/I-afadin 0.022 0.065 -9999 0 -0.526 1 1
FARP2 -0.022 0.206 -9999 0 -0.536 9 9
RAC1 0.02 0 -9999 0 -9999 0 0
CTNNA1 0.02 0 -9999 0 -9999 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.039 0.172 -9999 0 -0.444 9 9
nectin-1/I-afadin 0.022 0.065 -9999 0 -0.526 1 1
nectin-2/I-afadin 0.022 0.065 -9999 0 -0.526 1 1
RAC1/GTP/IQGAP1/filamentous actin 0.027 0 -9999 0 -9999 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.029 0.166 -9999 0 -0.444 9 9
CDC42/GTP/IQGAP1/filamentous actin 0.027 0 -9999 0 -9999 0 0
F11R 0 0.12 -9999 0 -0.708 2 2
positive regulation of filopodium formation -0.048 0.107 -9999 0 -0.322 9 9
alphaV/beta3 Integrin/Talin -0.071 0.236 -9999 0 -0.636 7 7
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.022 0.065 -9999 0 -0.526 1 1
nectin-2(dimer)/I-afadin/I-afadin 0.022 0.065 -9999 0 -0.526 1 1
PIP5K1C -0.078 0.211 -9999 0 -0.494 12 12
VAV2 -0.023 0.209 -9999 0 -0.546 9 9
RAP1/GDP -0.067 0.146 -9999 0 -0.413 10 10
ITGAV 0 0.12 -9999 0 -0.708 2 2
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.029 0.166 -9999 0 -0.444 9 9
nectin-3(dimer)/I-afadin/I-afadin -0.051 0.191 -9999 0 -0.497 11 11
Rac1/GTP -0.059 0.138 -9999 0 -0.413 9 9
PTPRM -0.098 0.227 -9999 0 -0.428 20 20
E-cadherin/beta catenin/alpha catenin -0.056 0.132 -9999 0 -0.721 1 1
adherens junction assembly 0 0 -9999 0 -9999 0 0
CDC42 0.02 0 -9999 0 -9999 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.032 0.186 -9999 0 -0.48 10 10
CRKL 0.02 0 -9999 0 -9999 0 0
Rac1/GDP 0.015 0 -9999 0 -9999 0 0
DOCK1 0 0.12 -9999 0 -0.708 2 2
ITGA4 -0.081 0.252 -9999 0 -0.708 10 10
alpha4/beta7 Integrin/MAdCAM1 -0.016 0.175 -9999 0 -0.437 10 10
EPO -0.139 0.247 -9999 0 -0.523 21 21
alpha4/beta7 Integrin -0.047 0.192 -9999 0 -0.526 10 10
mol:GTP 0 0 -9999 0 -9999 0 0
CRK 0 0.12 -9999 0 -0.708 2 2
alpha4/beta1 Integrin -0.055 0.2 -9999 0 -0.526 11 11
EPO/EPOR (dimer) -0.086 0.18 -9999 0 -0.366 21 21
lamellipodium assembly -0.022 0.105 -9999 0 -0.391 5 5
PIK3CA 0.02 0 -9999 0 -9999 0 0
PI3K -0.014 0.147 -9999 0 -0.499 6 6
ARF6 0.02 0 -9999 0 -9999 0 0
JAK2 -0.066 0.139 -9999 0 -9999 0 0
PXN 0.02 0 -9999 0 -9999 0 0
PIK3R1 -0.038 0.194 -9999 0 -0.677 6 6
MADCAM1 0.02 0 -9999 0 -9999 0 0
cell adhesion -0.017 0.173 -9999 0 -0.433 10 10
CRKL/CBL 0.03 0 -9999 0 -9999 0 0
ITGB1 0.01 0.085 -9999 0 -0.708 1 1
SRC -0.093 0.291 -9999 0 -0.633 15 15
ITGB7 0.02 0 -9999 0 -9999 0 0
RAC1 0.02 0 -9999 0 -9999 0 0
alpha4/beta1 Integrin/VCAM1 -0.112 0.313 -9999 0 -0.694 15 15
p130Cas/Crk/Dock1 -0.069 0.293 -9999 0 -0.736 10 10
VCAM1 -0.111 0.28 -9999 0 -0.708 13 13
RHOA 0.01 0.085 -9999 0 -0.708 1 1
alpha4/beta1 Integrin/Paxillin/GIT1 -0.023 0.167 -9999 0 -0.396 12 12
BCAR1 -0.076 0.276 -9999 0 -0.74 9 9
EPOR 0.02 0 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
CBL 0.02 0 -9999 0 -9999 0 0
GIT1 0.01 0.085 -9999 0 -0.708 1 1
Rac1/GTP -0.023 0.108 -9999 0 -0.403 5 5
TRAIL signaling pathway

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
TNFSF10 -0.091 0.262 -9999 0 -0.708 11 11
positive regulation of NF-kappaB transcription factor activity -0.061 0.219 -9999 0 -0.564 11 11
MAP2K4 -0.003 0.185 -9999 0 -0.801 2 2
IKBKB 0.02 0 -9999 0 -9999 0 0
TNFRSF10B 0.02 0 -9999 0 -9999 0 0
TNFRSF10A -0.02 0.167 -9999 0 -0.708 4 4
SMPD1 -0.013 0.101 -9999 0 -0.252 11 11
IKBKG 0.02 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
TNFRSF10D 0.01 0.085 -9999 0 -0.708 1 1
TRAIL/TRAILR2 -0.055 0.2 -9999 0 -0.526 11 11
TRAIL/TRAILR3 -0.083 0.264 -9999 0 -0.65 12 12
TRAIL/TRAILR1 -0.083 0.249 -9999 0 -0.593 13 13
TRAIL/TRAILR4 -0.061 0.22 -9999 0 -0.565 11 11
TRAIL/TRAILR1/DAP3/GTP -0.053 0.205 -9999 0 -0.469 13 13
IKK complex -0.027 0.063 -9999 0 -9999 0 0
RIPK1 0.02 0 -9999 0 -9999 0 0
response to oxidative stress 0 0 -9999 0 -9999 0 0
DAP3/GTP 0.015 0 -9999 0 -9999 0 0
MAPK3 -0.052 0.201 -9999 0 -0.524 11 11
MAP3K1 -0.015 0.197 -9999 0 -0.867 2 2
TRAILR4 (trimer) 0.01 0.085 -9999 0 -0.707 1 1
TRADD 0.01 0.085 -9999 0 -0.708 1 1
TRAILR1 (trimer) -0.02 0.166 -9999 0 -0.707 4 4
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.026 0.19 -9999 0 -0.853 2 2
CFLAR -0.01 0.145 -9999 0 -0.708 3 3
MAPK1 -0.052 0.201 -9999 0 -0.524 11 11
TRAIL/TRAILR1/FADD/TRADD/RIP -0.033 0.218 -9999 0 -0.939 2 2
mol:ceramide -0.013 0.101 -9999 0 -0.251 11 11
FADD 0.02 0 -9999 0 -9999 0 0
MAPK8 0.008 0.173 -9999 0 -0.733 2 2
TRAF2 0.005 0.089 -9999 0 -0.523 2 2
TRAILR3 (trimer) -0.028 0.16 -9999 0 -0.553 6 6
CHUK 0.02 0 -9999 0 -9999 0 0
TRAIL/TRAILR1/FADD -0.058 0.221 -9999 0 -0.508 13 13
DAP3 0.02 0 -9999 0 -9999 0 0
CASP10 -0.083 0.206 -9999 0 -0.533 10 10
JNK cascade -0.061 0.219 -9999 0 -0.564 11 11
TRAIL (trimer) -0.091 0.261 -9999 0 -0.707 11 11
TNFRSF10C -0.028 0.16 -9999 0 -0.554 6 6
TRAIL/TRAILR1/DAP3/GTP/FADD -0.039 0.195 -9999 0 -0.435 13 13
TRAIL/TRAILR2/FADD -0.033 0.174 -9999 0 -0.444 11 11
cell death -0.013 0.1 -9999 0 -0.25 11 11
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.005 0.136 -9999 0 -0.586 1 1
TRAILR2 (trimer) 0.02 0 -9999 0 -9999 0 0
CASP8 0.007 0.074 -9999 0 -9999 0 0
negative regulation of caspase activity 0 0 -9999 0 -9999 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.01 0.171 -9999 0 -0.755 1 1
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer -0.182 0.421 -9999 0 -0.883 17 17
PDGFRB 0 0.122 -9999 0 -0.719 2 2
SPHK1 -0.061 0.184 -9999 0 -0.793 3 3
mol:S1P -0.064 0.179 -9999 0 -0.612 5 5
S1P1/S1P/Gi -0.057 0.283 -9999 0 -0.683 8 8
GNAO1 0.02 0.006 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/PLCgamma1 -0.03 0.251 -9999 0 -0.97 3 3
PLCG1 -0.04 0.255 -9999 0 -0.688 6 6
mol:GTP 0 0 -9999 0 -9999 0 0
PDGFB-D/PDGFRB 0 0.121 -9999 0 -0.718 2 2
GNAI2 0.01 0.086 -9999 0 -0.714 1 1
GNAI3 0.019 0.006 -9999 0 -9999 0 0
GNAI1 -0.001 0.12 -9999 0 -0.713 2 2
mol:GDP 0 0 -9999 0 -9999 0 0
EDG1 -0.194 0.481 -9999 0 -1.003 16 16
S1P1/S1P -0.153 0.407 -9999 0 -0.949 13 13
negative regulation of cAMP metabolic process -0.053 0.269 -9999 0 -0.649 8 8
MAPK3 -0.052 0.282 -9999 0 -0.751 6 6
calcium-dependent phospholipase C activity -0.001 0.003 -9999 0 -9999 0 0
Rac1/GDP 0.015 0 -9999 0 -9999 0 0
RhoA/GDP 0.007 0.065 -9999 0 -0.538 1 1
KDR -0.089 0.281 -9999 0 -0.784 10 10
PLCB2 -0.11 0.334 -9999 0 -0.762 13 13
RAC1 0.02 0 -9999 0 -9999 0 0
RhoA/GTP -0.159 0.28 -9999 0 -0.718 13 13
receptor internalization -0.182 0.321 -9999 0 -0.819 13 13
PTGS2 -0.065 0.311 -9999 0 -0.914 5 5
Rac1/GTP -0.156 0.275 -9999 0 -0.702 13 13
RHOA 0.01 0.085 -9999 0 -0.708 1 1
VEGFA -0.137 0.312 -9999 0 -0.741 15 15
negative regulation of T cell proliferation -0.053 0.269 -9999 0 -0.649 8 8
GO:0007205 0 0 -9999 0 -9999 0 0
GNAZ 0.012 0.064 -9999 0 -0.525 1 1
MAPK1 -0.052 0.282 -9999 0 -0.705 7 7
S1P1/S1P/PDGFB-D/PDGFRB -0.149 0.428 -9999 0 -0.982 13 13
ABCC1 0.002 0.107 -9999 0 -0.622 2 2
FAS signaling pathway (CD95)

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
SPTAN1 0.017 0.088 0.277 6 -0.299 1 7
RFC1 0.014 0.079 0.276 5 -9999 0 5
PRKDC 0.021 0.08 0.277 6 -9999 0 6
RIPK1 0.022 0.004 -9999 0 -9999 0 0
CASP7 -0.029 0.046 -9999 0 -9999 0 0
FASLG/FAS/FADD/FAF1 -0.113 0.19 0.254 1 -0.499 11 12
MAP2K4 -0.082 0.221 -9999 0 -0.552 9 9
mol:ceramide -0.123 0.299 -9999 0 -0.831 8 8
GSN -0.006 0.093 0.279 3 -0.446 1 4
FASLG/FAS/FADD/FAF1/Caspase 8 -0.112 0.261 -9999 0 -0.666 10 10
FAS -0.065 0.228 -9999 0 -0.71 8 8
BID -0.026 0.106 -9999 0 -0.464 4 4
MAP3K1 -0.033 0.136 -9999 0 -0.545 2 2
MAP3K7 0.018 0.003 -9999 0 -9999 0 0
RB1 0.021 0.08 0.277 6 -9999 0 6
CFLAR -0.009 0.144 -9999 0 -0.699 3 3
HGF/MET -0.016 0.153 -9999 0 -0.469 6 6
ARHGDIB -0.016 0.151 0.277 6 -0.44 6 12
FADD 0.015 0.01 -9999 0 -9999 0 0
actin filament polymerization 0.006 0.092 0.443 1 -0.278 3 4
NFKB1 -0.056 0.074 -9999 0 -9999 0 0
MAPK8 -0.095 0.236 -9999 0 -0.519 12 12
DFFA 0.021 0.08 0.277 6 -9999 0 6
DNA fragmentation during apoptosis 0.021 0.079 0.277 6 -9999 0 6
FAS/FADD/MET -0.039 0.165 -9999 0 -0.447 9 9
CFLAR/RIP1 -0.002 0.107 -9999 0 -0.513 3 3
FAIM3 0.021 0.002 -9999 0 -9999 0 0
FAF1 0.016 0.01 -9999 0 -9999 0 0
PARP1 0.017 0.088 0.277 6 -9999 0 6
DFFB 0.021 0.08 0.277 6 -9999 0 6
CHUK -0.044 0.064 -9999 0 -9999 0 0
FASLG -0.191 0.296 -9999 0 -0.603 24 24
FAS/FADD -0.039 0.174 -9999 0 -0.529 8 8
HGF -0.023 0.159 -9999 0 -0.597 5 5
LMNA -0.021 0.126 0.254 4 -0.402 5 9
CASP6 0.021 0.08 0.277 6 -9999 0 6
CASP10 0.005 0.085 -9999 0 -0.708 1 1
CASP3 0.025 0.095 0.328 6 -9999 0 6
PTPN13 0 0.12 -9999 0 -0.708 2 2
CASP8 0 0 -9999 0 -9999 0 0
IL6 -0.19 0.412 -9999 0 -1.402 6 6
MET -0.005 0.122 -9999 0 -0.585 3 3
ICAD/CAD 0.02 0.074 0.263 2 -9999 0 2
FASLG/FAS/FADD/FAF1/Caspase 10 -0.127 0.31 -9999 0 -0.86 8 8
activation of caspase activity by cytochrome c -0.026 0.106 -9999 0 -0.462 4 4
PAK2 0.021 0.079 0.275 6 -9999 0 6
BCL2 -0.04 0.201 -9999 0 -0.707 6 6
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.041 0.188 -9999 0 -0.496 8 8
SNTA1 -0.005 0.122 -9999 0 -0.585 3 3
response to hypoxia 0 0 -9999 0 -9999 0 0
STMN1 -0.028 0.161 -9999 0 -0.443 7 7
MAPK12 -0.015 0.138 -9999 0 -0.416 4 4
CCND1 -0.105 0.232 -9999 0 -0.508 16 16
p38 gamma/SNTA1 -0.018 0.141 -9999 0 -0.406 4 4
MAP2K3 0 0.12 -9999 0 -0.708 2 2
PKN1 0.02 0 -9999 0 -9999 0 0
G2/M transition checkpoint -0.015 0.137 -9999 0 -0.412 4 4
MAP2K6 0.021 0.088 -9999 0 -0.482 2 2
MAPT -0.035 0.141 -9999 0 -0.33 11 11
MAPK13 -0.049 0.187 -9999 0 -0.46 12 12
hyperosmotic response 0 0 -9999 0 -9999 0 0
ZAK 0.014 0.07 -9999 0 -0.402 2 2
Nongenotropic Androgen signaling

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
PTK2 0.017 0.001 -9999 0 -9999 0 0
GNB1/GNG2 -0.042 0.185 -9999 0 -0.442 12 12
regulation of S phase of mitotic cell cycle -0.036 0.164 -9999 0 -0.548 3 3
GNAO1 0.02 0 -9999 0 -9999 0 0
HRAS 0.019 0.002 -9999 0 -9999 0 0
SHBG/T-DHT -0.002 0.078 -9999 0 -0.371 3 3
PELP1 0.019 0.002 -9999 0 -9999 0 0
AKT1 0.017 0.001 -9999 0 -9999 0 0
MAP2K1 -0.021 0.152 -9999 0 -0.422 4 4
T-DHT/AR -0.078 0.207 -9999 0 -0.541 12 12
G-protein coupled receptor activity 0 0 -9999 0 -9999 0 0
mol:GTP -0.001 0.003 -9999 0 -0.006 19 19
GNAI2 0.01 0.085 -9999 0 -0.708 1 1
GNAI3 0.02 0 -9999 0 -9999 0 0
GNAI1 0 0.12 -9999 0 -0.708 2 2
mol:GDP -0.112 0.238 -9999 0 -0.615 12 12
cell proliferation -0.047 0.213 -9999 0 -0.633 4 4
PIK3CA 0.02 0 -9999 0 -9999 0 0
FOS -0.124 0.337 -9999 0 -0.873 10 10
mol:Ca2+ -0.011 0.024 -9999 0 -0.11 2 2
MAPK3 -0.032 0.181 -9999 0 -0.536 4 4
MAPK1 -0.015 0.104 -9999 0 -0.286 3 3
PIK3R1 -0.038 0.194 -9999 0 -0.677 6 6
mol:IP3 -0.001 0.002 -9999 0 -0.004 19 19
cAMP biosynthetic process -0.004 0.075 -9999 0 -0.34 3 3
GNG2 0.02 0 -9999 0 -9999 0 0
potassium channel inhibitor activity -0.001 0.002 -9999 0 -0.004 19 19
HRAS/GTP -0.064 0.139 -9999 0 -0.374 12 12
actin cytoskeleton reorganization -0.028 0.093 -9999 0 -0.354 5 5
SRC 0.019 0.002 -9999 0 -9999 0 0
voltage-gated calcium channel activity -0.001 0.002 -9999 0 -0.004 19 19
PI3K -0.011 0.128 -9999 0 -0.432 6 6
apoptosis 0.052 0.209 0.477 10 -9999 0 10
T-DHT/AR/PELP1 -0.055 0.181 -9999 0 -0.46 12 12
HRAS/GDP -0.103 0.224 -9999 0 -0.577 12 12
CREB1 -0.059 0.226 -9999 0 -0.518 10 10
RAC1-CDC42/GTP -0.028 0.095 -9999 0 -0.36 5 5
AR -0.102 0.272 -9999 0 -0.71 12 12
GNB1 0.01 0.085 -9999 0 -0.708 1 1
RAF1 -0.026 0.153 -9999 0 -0.418 4 4
RAC1-CDC42/GDP -0.096 0.214 -9999 0 -0.548 12 12
T-DHT/AR/PELP1/Src -0.039 0.168 -9999 0 -0.414 12 12
MAP2K2 -0.021 0.152 -9999 0 -0.422 4 4
T-DHT/AR/PELP1/Src/PI3K -0.036 0.165 -9999 0 -0.554 3 3
GNAZ 0.012 0.064 -9999 0 -0.523 1 1
SHBG -0.005 0.122 -9999 0 -0.585 3 3
Gi family/GNB1/GNG2/GDP 0.02 0.178 -9999 0 -1.362 1 1
mol:T-DHT -0.001 0.001 -9999 0 -0.003 16 16
RAC1 0.02 0 -9999 0 -9999 0 0
GNRH1 -0.03 0.154 -9999 0 -0.539 6 6
Gi family/GTP -0.006 0.114 -9999 0 -0.5 2 2
CDC42 0.02 0 -9999 0 -9999 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.036 0.162 -9999 0 -0.353 13 13
epithelial cell differentiation -0.077 0.155 -9999 0 -0.409 10 10
CYFIP2 0.01 0.085 -9999 0 -0.708 1 1
ENAH -0.026 0.199 -9999 0 -0.461 8 8
EGFR -0.106 0.26 -9999 0 -0.629 14 14
EPHA2 -0.018 0.157 -9999 0 -0.662 4 4
MYO6 -0.034 0.182 -9999 0 -0.723 2 2
CTNNB1 0.02 0 -9999 0 -9999 0 0
ABI1/Sra1/Nap1 0.025 0.079 -9999 0 -0.444 1 1
AQP5 -0.086 0.203 -9999 0 -0.93 3 3
CTNND1 -0.02 0.167 -9999 0 -0.708 4 4
mol:PI-4-5-P2 -0.028 0.164 -9999 0 -0.377 10 10
regulation of calcium-dependent cell-cell adhesion -0.132 0.267 -9999 0 -0.673 10 10
EGF -0.247 0.304 -9999 0 -0.581 32 32
NCKAP1 0.005 0.089 -9999 0 -0.523 2 2
AQP3 -0.142 0.281 -9999 0 -0.823 9 9
cortical microtubule organization -0.077 0.155 -9999 0 -0.409 10 10
GO:0000145 -0.027 0.156 -9999 0 -0.36 10 10
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.041 0.175 -9999 0 -0.414 10 10
MLLT4 0.01 0.085 -9999 0 -0.708 1 1
ARF6/GDP -0.126 0.238 -9999 0 -0.657 10 10
ARF6 0.02 0 -9999 0 -9999 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.053 0.25 -9999 0 -0.577 11 11
mol:Ca2+ 0 0 -9999 0 -9999 0 0
VASP -0.041 0.199 -9999 0 -0.567 5 5
PVRL2 0.02 0 -9999 0 -9999 0 0
ZYX -0.036 0.169 -9999 0 -0.718 1 1
ARF6/GTP -0.087 0.213 -9999 0 -0.822 4 4
CDH1 -0.096 0.25 -9999 0 -0.623 13 13
EGFR/EGFR/EGF/EGF -0.24 0.268 -9999 0 -0.668 14 14
RhoA/GDP -0.076 0.147 -9999 0 -0.705 1 1
actin cytoskeleton organization -0.022 0.173 -9999 0 -0.668 2 2
IGF-1R heterotetramer 0.01 0.085 -9999 0 -0.707 1 1
GIT1 0.01 0.085 -9999 0 -0.708 1 1
IGF1R 0.01 0.085 -9999 0 -0.708 1 1
IGF1 -0.081 0.228 -9999 0 -0.585 12 12
DIAPH1 -0.012 0.08 -9999 0 -0.631 1 1
Wnt receptor signaling pathway 0.077 0.155 0.409 10 -9999 0 10
RHOA 0.01 0.085 -9999 0 -0.708 1 1
RhoA/GTP -0.13 0.238 -9999 0 -0.655 10 10
CTNNA1 0.02 0 -9999 0 -9999 0 0
VCL -0.023 0.178 -9999 0 -0.693 2 2
EFNA1 -0.099 0.266 -9999 0 -0.693 12 12
LPP -0.063 0.246 -9999 0 -0.758 5 5
Ephrin A1/EPHA2 -0.143 0.259 -9999 0 -0.72 10 10
SEC6/SEC8 -0.071 0.158 -9999 0 -0.782 2 2
MGAT3 -0.135 0.274 -9999 0 -0.691 10 10
HGF/MET -0.097 0.161 -9999 0 -0.578 3 3
HGF -0.023 0.159 -9999 0 -0.597 5 5
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.037 0.163 -9999 0 -0.356 13 13
actin cable formation -0.002 0.182 -9999 0 -0.411 7 7
KIAA1543 -0.025 0.164 -9999 0 -0.67 1 1
KIFC3 -0.029 0.167 -9999 0 -0.384 10 10
NCK1 0.01 0.085 -9999 0 -0.708 1 1
EXOC3 0.002 0.106 -9999 0 -0.616 2 2
ACTN1 -0.068 0.237 -9999 0 -0.502 13 13
NCK1/GIT1 0.016 0.116 -9999 0 -0.964 1 1
mol:GDP -0.077 0.155 -9999 0 -0.409 10 10
EXOC4 0.02 0 -9999 0 -9999 0 0
STX4 -0.039 0.196 -9999 0 -0.725 3 3
PIP5K1C -0.029 0.167 -9999 0 -0.384 10 10
LIMA1 -0.028 0.16 -9999 0 -0.554 6 6
ABI1 0.02 0 -9999 0 -9999 0 0
ROCK1 -0.045 0.23 -9999 0 -0.538 10 10
adherens junction assembly -0.001 0.158 -9999 0 -0.615 1 1
IGF-1R heterotetramer/IGF1 -0.117 0.193 -9999 0 -0.578 7 7
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.022 0.065 -9999 0 -0.526 1 1
MET -0.005 0.122 -9999 0 -0.585 3 3
PLEKHA7 -0.029 0.167 -9999 0 -0.718 1 1
mol:GTP -0.053 0.246 -9999 0 -0.571 11 11
establishment of epithelial cell apical/basal polarity -0.006 0.204 -9999 0 -0.778 3 3
cortical actin cytoskeleton stabilization -0.036 0.162 -9999 0 -0.353 13 13
regulation of cell-cell adhesion -0.022 0.173 -9999 0 -0.668 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.037 0.163 -9999 0 -0.356 13 13
Caspase cascade in apoptosis

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
TOP1 0.027 0.14 0.266 1 -0.407 2 3
ACTA1 0.011 0.164 0.297 7 -0.439 2 9
NUMA1 0.026 0.14 0.254 4 -0.407 2 6
SPTAN1 0.02 0.165 0.31 4 -0.436 2 6
LIMK1 0.003 0.193 0.31 4 -0.518 4 8
BIRC3 -0.162 0.306 -9999 0 -0.669 19 19
BIRC2 0.02 0 -9999 0 -9999 0 0
BAX 0.02 0 -9999 0 -9999 0 0
CASP10 -0.041 0.185 -9999 0 -0.557 5 5
CRMA 0 0 -9999 0 -9999 0 0
XIAP 0 0 -9999 0 -9999 0 0
PTK2 0.027 0.14 0.266 1 -0.407 2 3
DIABLO 0.02 0 -9999 0 -9999 0 0
apoptotic nuclear changes 0.021 0.164 0.309 4 -0.429 2 6
response to UV 0 0 -9999 0 -9999 0 0
CRADD 0.012 0.064 -9999 0 -0.524 1 1
GSN 0.001 0.177 0.312 4 -0.405 4 8
MADD 0.02 0 -9999 0 -9999 0 0
TFAP2A 0.004 0.157 -9999 0 -1.227 1 1
BID -0.026 0.142 -9999 0 -0.382 7 7
MAP3K1 0.015 0.127 -9999 0 -0.868 1 1
TRADD 0.01 0.085 -9999 0 -0.708 1 1
mol:Ca2+ 0 0 -9999 0 -9999 0 0
APAF-1/Pro-Caspase 9 0.03 0.001 -9999 0 -9999 0 0
mol:Activated DNA 0 0 -9999 0 -9999 0 0
ARHGDIB -0.01 0.191 0.31 3 -0.616 3 6
CASP9 0.02 0.001 -9999 0 -9999 0 0
DNA repair -0.051 0.097 0.22 1 -0.242 11 12
neuron apoptosis -0.044 0.217 -9999 0 -0.65 8 8
mol:NAD 0 0 -9999 0 -9999 0 0
DNA fragmentation during apoptosis 0.032 0.154 0.293 4 -0.417 2 6
APAF1 0.02 0 -9999 0 -9999 0 0
CASP6 0.024 0.109 -9999 0 -0.587 1 1
TRAF2 0.005 0.089 -9999 0 -0.523 2 2
ICAD/CAD 0.033 0.156 -9999 0 -0.413 2 2
CASP7 0.084 0.141 0.332 16 -9999 0 16
KRT18 -0.011 0.146 -9999 0 -0.594 4 4
apoptosis -0.001 0.144 -9999 0 -0.44 3 3
DFFA 0.024 0.162 0.31 4 -0.436 2 6
DFFB 0.024 0.162 0.31 4 -0.436 2 6
PARP1 0.051 0.097 0.242 11 -0.221 1 12
actin filament polymerization 0.01 0.188 0.585 3 -0.303 1 4
TNF 0.002 0.106 -9999 0 -0.616 2 2
CYCS -0.035 0.123 -9999 0 -0.277 10 10
SATB1 0.001 0.141 -9999 0 -0.554 2 2
SLK 0.024 0.162 0.31 4 -0.436 2 6
p15 BID/BAX -0.013 0.13 -9999 0 -0.441 4 4
CASP2 -0.031 0.204 -9999 0 -0.561 7 7
JNK cascade -0.015 0.126 0.857 1 -9999 0 1
CASP3 0.015 0.173 0.308 7 -0.47 2 9
LMNB2 0.009 0.131 -9999 0 -0.592 2 2
RIPK1 0.02 0 -9999 0 -9999 0 0
CASP4 -0.041 0.201 -9999 0 -0.708 6 6
Mammalian IAPs/DIABLO -0.071 0.186 -9999 0 -0.408 15 15
negative regulation of DNA binding 0.004 0.154 -9999 0 -1.193 1 1
stress fiber formation 0.024 0.161 0.309 4 -0.429 2 6
GZMB -0.057 0.191 -9999 0 -0.435 14 14
CASP1 -0.091 0.3 -9999 0 -0.738 11 11
LMNB1 -0.02 0.188 -9999 0 -0.643 5 5
APP -0.045 0.22 -9999 0 -0.659 8 8
TNFRSF1A -0.061 0.229 -9999 0 -0.708 8 8
response to stress 0 0 -9999 0 -9999 0 0
CASP8 0.017 0 -9999 0 -9999 0 0
VIM -0.009 0.145 -9999 0 -0.431 4 4
LMNA -0.032 0.232 -9999 0 -0.618 8 8
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.044 0.216 -9999 0 -0.603 7 7
LRDD 0.012 0.064 -9999 0 -0.523 1 1
SREBF1 0.016 0.162 0.312 3 -0.436 2 5
APAF-1/Caspase 9 0.023 0.057 -9999 0 -9999 0 0
nuclear fragmentation during apoptosis 0.026 0.139 0.253 4 -0.401 2 6
CFL2 -0.011 0.193 0.305 1 -0.607 3 4
GAS2 -0.091 0.211 -9999 0 -0.48 11 11
positive regulation of apoptosis -0.018 0.191 -9999 0 -0.495 8 8
PRF1 -0.048 0.18 -9999 0 -0.523 9 9
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.064 0.171 0.414 13 -9999 0 13
KIRREL -0.015 0.125 -9999 0 -0.739 2 2
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.064 0.172 -9999 0 -0.415 13 13
PLCG1 0.02 0 -9999 0 -9999 0 0
ARRB2 0.02 0 -9999 0 -9999 0 0
WASL 0.012 0.064 -9999 0 -0.523 1 1
Nephrin/NEPH1/podocin/CD2AP -0.052 0.166 -9999 0 -0.439 6 6
ChemicalAbstracts:57-88-5 0 0 -9999 0 -9999 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.017 0.131 -9999 0 -0.661 1 1
FYN -0.093 0.2 -9999 0 -0.416 16 16
mol:Ca2+ -0.08 0.141 -9999 0 -0.45 5 5
mol:DAG -0.08 0.142 -9999 0 -0.452 5 5
NPHS2 -0.039 0.16 -9999 0 -0.566 6 6
mol:IP3 -0.08 0.142 -9999 0 -0.452 5 5
regulation of endocytosis -0.075 0.19 -9999 0 -0.52 6 6
Nephrin/NEPH1/podocin/Cholesterol -0.061 0.161 -9999 0 -0.424 8 8
establishment of cell polarity -0.064 0.171 -9999 0 -0.414 13 13
Nephrin/NEPH1/podocin/NCK1-2 -0.036 0.17 -9999 0 -0.588 3 3
Nephrin/NEPH1/beta Arrestin2 -0.075 0.193 -9999 0 -0.528 6 6
NPHS1 -0.075 0.201 -9999 0 -0.542 11 11
Nephrin/NEPH1/podocin -0.092 0.202 -9999 0 -0.416 16 16
TJP1 0.02 0 -9999 0 -9999 0 0
NCK1 0.01 0.085 -9999 0 -0.708 1 1
NCK2 0.02 0 -9999 0 -9999 0 0
heterophilic cell adhesion 0 0 -9999 0 -9999 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.048 0.162 -9999 0 -0.454 5 5
CD2AP 0.012 0.064 -9999 0 -0.523 1 1
Nephrin/NEPH1/podocin/GRB2 -0.053 0.183 -9999 0 -0.536 5 5
GRB2 0.01 0.085 -9999 0 -0.708 1 1
homophilic cell adhesion 0 0 -9999 0 -9999 0 0
TRPC6 -0.096 0.203 -9999 0 -0.481 10 10
cytoskeleton organization -0.028 0.182 -9999 0 -1.076 1 1
Nephrin/NEPH1 -0.042 0.124 -9999 0 -0.367 5 5
Nephrin/NEPH1/ZO-1 -0.035 0.14 -9999 0 -0.445 3 3
ErbB4 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
ErbB4/ErbB4/HBEGF/HBEGF -0.012 0.182 -9999 0 -0.884 2 2
epithelial cell differentiation -0.07 0.152 -9999 0 -0.584 3 3
ITCH 0.026 0.024 -9999 0 -9999 0 0
WWP1 -0.009 0.207 -9999 0 -1.507 1 1
FYN -0.101 0.271 -9999 0 -0.708 12 12
EGFR -0.106 0.26 -9999 0 -0.629 14 14
PRL 0.02 0 -9999 0 -9999 0 0
neuron projection morphogenesis 0.026 0.151 -9999 0 -0.464 3 3
PTPRZ1 -0.01 0.124 -9999 0 -0.523 4 4
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.005 0.162 -9999 0 -0.526 3 3
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.025 0.17 -9999 0 -0.49 6 6
ADAM17 0.026 0.024 -9999 0 -9999 0 0
ErbB4/ErbB4 -0.003 0.149 -9999 0 -0.55 2 2
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.034 0.198 -9999 0 -0.543 8 8
NCOR1 0.02 0 -9999 0 -9999 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.081 0.267 -9999 0 -0.597 13 13
GRIN2B -0.084 0.285 -9999 0 -0.613 13 13
ErbB4/ErbB2/betacellulin -0.038 0.194 -9999 0 -0.525 6 6
STAT1 -0.056 0.216 -9999 0 -0.662 8 8
HBEGF -0.008 0.134 -9999 0 -0.646 3 3
PRLR -0.055 0.188 -9999 0 -0.523 10 10
E4ICDs/ETO2 -0.003 0.151 -9999 0 -0.689 2 2
axon guidance -0.002 0.131 -9999 0 -0.48 3 3
NEDD4 -0.05 0.212 -9999 0 -0.695 7 7
Prolactin receptor/Prolactin receptor/Prolactin -0.025 0.137 -9999 0 -0.366 10 10
CBFA2T3 0.01 0.085 -9999 0 -0.708 1 1
ErbB4/ErbB2/HBEGF -0.003 0.168 -9999 0 -0.77 2 2
MAPK3 0.016 0.155 -9999 0 -0.487 3 3
STAT1 (dimer) -0.042 0.207 -9999 0 -0.592 7 7
MAPK1 0.016 0.155 -9999 0 -0.487 3 3
JAK2 0.02 0 -9999 0 -9999 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.025 0.169 -9999 0 -0.504 4 4
NRG1 -0.014 0.156 -9999 0 -0.483 7 7
NRG3 -0.043 0.194 -9999 0 -0.629 7 7
NRG2 -0.04 0.171 -9999 0 -0.523 8 8
NRG4 -0.05 0.188 -9999 0 -0.544 9 9
heart development -0.002 0.131 -9999 0 -0.48 3 3
neural crest cell migration -0.025 0.168 -9999 0 -0.498 4 4
ERBB2 0.021 0.095 -9999 0 -0.533 2 2
WWOX/E4ICDs 0.003 0.131 -9999 0 -0.692 1 1
SHC1 0.02 0 -9999 0 -9999 0 0
ErbB4/EGFR/neuregulin 4 -0.093 0.248 -9999 0 -0.537 13 13
apoptosis 0.065 0.143 0.428 8 -9999 0 8
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.03 0.193 -9999 0 -0.522 8 8
ErbB4/ErbB2/epiregulin -0.008 0.147 -9999 0 -0.601 2 2
ErbB4/ErbB4/betacellulin/betacellulin -0.052 0.203 -9999 0 -0.477 11 11
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.015 0.206 -9999 0 -0.54 7 7
MDM2 0.008 0.133 -9999 0 -0.692 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.058 0.134 -9999 0 -0.449 6 6
STAT5A 0.005 0.127 -9999 0 -0.633 1 1
ErbB4/EGFR/neuregulin 1 beta -0.082 0.239 -9999 0 -0.625 8 8
DLG4 0.02 0 -9999 0 -9999 0 0
GRB2/SHC 0.022 0.065 -9999 0 -0.526 1 1
E4ICDs/TAB2/NCoR1 0.015 0.122 -9999 0 -0.644 1 1
STAT5A (dimer) -0.075 0.167 -9999 0 -0.647 3 3
MAP3K7IP2 0.02 0 -9999 0 -9999 0 0
STAT5B (dimer) 0.008 0.124 -9999 0 -0.633 1 1
LRIG1 0 0.12 -9999 0 -0.708 2 2
EREG -0.018 0.138 -9999 0 -0.523 5 5
BTC -0.073 0.222 -9999 0 -0.591 11 11
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.002 0.132 -9999 0 -0.484 3 3
ERBB4 -0.004 0.15 -9999 0 -0.552 2 2
STAT5B 0.02 0 -9999 0 -9999 0 0
YAP1 -0.011 0.028 -9999 0 -9999 0 0
GRB2 0.01 0.085 -9999 0 -0.708 1 1
ErbB4/ErbB2/neuregulin 4 -0.025 0.175 -9999 0 -0.48 5 5
glial cell differentiation -0.015 0.121 0.636 1 -9999 0 1
WWOX 0.02 0 -9999 0 -9999 0 0
cell proliferation -0.055 0.237 -9999 0 -0.656 7 7
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.008 0.101 -9999 0 -0.385 4 4
RGS9BP -0.063 0.209 -9999 0 -0.579 10 10
mol:GTP 0 0 -9999 0 -9999 0 0
GRK1 0 0 -9999 0 -9999 0 0
mol:Na + -0.019 0.131 -9999 0 -0.383 8 8
mol:ADP 0.011 0.046 -9999 0 -0.38 1 1
GNAT2 0 0.12 -9999 0 -0.708 2 2
RGS9-1/Gbeta5/R9AP -0.12 0.228 -9999 0 -0.494 14 14
mol:GDP 0 0 -9999 0 -9999 0 0
PDE6H/GNAT2/GTP 0.002 0.103 -9999 0 -0.419 4 4
GRK7 0.012 0.064 -9999 0 -0.523 1 1
CNGB3 -0.033 0.178 -9999 0 -0.616 6 6
Cone Metarhodopsin II/X-Arrestin 0.015 0 -9999 0 -9999 0 0
mol:Ca2+ -0.014 0.151 -9999 0 -0.476 6 6
Cone PDE6 -0.105 0.219 -9999 0 -0.659 4 4
Cone Metarhodopsin II 0.009 0.036 -9999 0 -0.293 1 1
Na + (4 Units) -0.013 0.151 -9999 0 -0.474 6 6
GNAT2/GDP -0.103 0.203 -9999 0 -0.414 16 16
GNB5 0.012 0.064 -9999 0 -0.523 1 1
mol:GMP (4 units) -0.002 0.121 -9999 0 -0.406 5 5
Cone Transducin 0.01 0.107 -9999 0 -0.407 4 4
SLC24A2 0.002 0.106 -9999 0 -0.616 2 2
GNB3/GNGT2 0.009 0.102 -9999 0 -0.473 3 3
GNB3 0.02 0 -9999 0 -9999 0 0
GNAT2/GTP -0.001 0.091 -9999 0 -0.538 2 2
CNGA3 0.002 0.106 -9999 0 -0.616 2 2
ARR3 0.02 0 -9999 0 -9999 0 0
absorption of light 0 0 -9999 0 -9999 0 0
cGMP/Cone CNG Channel -0.019 0.131 -9999 0 -0.384 8 8
mol:Pi -0.119 0.227 -9999 0 -0.492 14 14
Cone CNG Channel -0.064 0.149 -9999 0 -0.532 3 3
mol:all-trans-retinal 0 0 -9999 0 -9999 0 0
mol:K + 0.002 0.105 -9999 0 -0.615 2 2
RGS9 -0.139 0.289 -9999 0 -0.654 17 17
PDE6C -0.008 0.134 -9999 0 -0.646 3 3
GNGT2 -0.008 0.134 -9999 0 -0.646 3 3
mol:cGMP (4 units) 0 0 -9999 0 -9999 0 0
PDE6H 0.002 0.106 -9999 0 -0.616 2 2
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.178 0.239 -9999 0 -0.752 1 1
IHH -0.14 0.232 -9999 0 -0.529 18 18
SHH Np/Cholesterol/GAS1 0.007 0.099 -9999 0 -0.407 2 2
LRPAP1 0.02 0 -9999 0 -9999 0 0
dorsoventral neural tube patterning -0.007 0.098 0.404 2 -9999 0 2
SMO/beta Arrestin2 -0.102 0.174 -9999 0 -0.575 3 3
SMO -0.118 0.182 -9999 0 -0.614 3 3
AKT1 -0.063 0.176 -9999 0 -0.618 5 5
ARRB2 0.02 0 -9999 0 -9999 0 0
BOC 0 0.12 -9999 0 -0.708 2 2
ADRBK1 0.02 0 -9999 0 -9999 0 0
heart looping -0.117 0.18 -9999 0 -0.567 4 4
STIL -0.065 0.133 -9999 0 -0.472 1 1
DHH N/PTCH2 0.014 0.091 -9999 0 -0.526 2 2
DHH N/PTCH1 -0.106 0.16 -9999 0 -0.584 2 2
PIK3CA 0.02 0 -9999 0 -9999 0 0
DHH 0 0.12 -9999 0 -0.708 2 2
PTHLH -0.31 0.428 -9999 0 -1.123 12 12
determination of left/right symmetry -0.117 0.18 -9999 0 -0.567 4 4
PIK3R1 -0.038 0.194 -9999 0 -0.677 6 6
skeletal system development -0.306 0.421 -9999 0 -1.103 12 12
IHH N/Hhip -0.131 0.219 -9999 0 -0.486 16 16
DHH N/Hhip -0.048 0.199 -9999 0 -0.477 11 11
mol:Cholesterol 0 0 -9999 0 -9999 0 0
heart development -0.117 0.18 -9999 0 -0.567 4 4
pancreas development -0.068 0.209 -9999 0 -0.556 11 11
HHAT 0.002 0.106 -9999 0 -0.616 2 2
PI3K -0.014 0.147 -9999 0 -0.499 6 6
EntrezGene:84976 0 0 -9999 0 -9999 0 0
GAS1 -0.013 0.136 -9999 0 -0.57 4 4
somite specification -0.117 0.18 -9999 0 -0.567 4 4
SHH Np/Cholesterol/PTCH1 -0.079 0.14 -9999 0 -0.486 2 2
SHH Np/Cholesterol/PTCH2 0.026 0.063 -9999 0 -0.406 1 1
SHH Np/Cholesterol/Megalin -0.065 0.206 -9999 0 -0.452 15 15
SHH 0.02 0.08 -9999 0 -0.446 2 2
catabolic process -0.12 0.165 -9999 0 -0.637 1 1
SMO/Vitamin D3 -0.094 0.157 -9999 0 -0.5 3 3
SHH Np/Cholesterol/Hhip -0.025 0.132 -9999 0 -0.407 3 3
LRP2 -0.132 0.296 -9999 0 -0.708 15 15
receptor-mediated endocytosis -0.136 0.231 -9999 0 -0.601 9 9
SHH Np/Cholesterol/BOC 0.014 0.095 -9999 0 -0.407 3 3
SHH Np/Cholesterol/CDO -0.033 0.181 -9999 0 -0.482 9 9
mesenchymal cell differentiation 0.025 0.132 0.404 3 -9999 0 3
mol:Vitamin D3 -0.078 0.142 -9999 0 -0.489 2 2
IHH N/PTCH2 -0.064 0.143 -9999 0 -0.375 6 6
CDON -0.079 0.246 -9999 0 -0.689 10 10
IHH N/PTCH1 -0.12 0.167 -9999 0 -0.647 1 1
Megalin/LRPAP1 -0.086 0.226 -9999 0 -0.526 15 15
PTCH2 0.02 0 -9999 0 -9999 0 0
SHH Np/Cholesterol -0.01 0.059 -9999 0 -0.418 1 1
PTCH1 -0.12 0.166 -9999 0 -0.64 1 1
HHIP -0.068 0.209 -9999 0 -0.557 11 11
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 -0.052 0.226 -9999 0 -0.521 12 12
MAP4K1 0.012 0.064 -9999 0 -0.523 1 1
MAP3K8 -0.089 0.257 -9999 0 -0.691 11 11
PRKCB 0 0 -9999 0 -9999 0 0
DBNL 0.02 0 -9999 0 -9999 0 0
CRKL 0.02 0 -9999 0 -9999 0 0
MAP3K1 -0.016 0.217 -9999 0 -0.765 4 4
JUN -0.038 0.167 -9999 0 -0.445 9 9
MAP3K7 -0.011 0.193 -9999 0 -0.677 4 4
GRAP2 0 0.12 -9999 0 -0.708 2 2
CRK 0 0.12 -9999 0 -0.708 2 2
MAP2K4 -0.028 0.246 -9999 0 -0.661 7 7
LAT -0.041 0.187 -9999 0 -0.603 7 7
LCP2 -0.068 0.235 -9999 0 -0.687 9 9
MAPK8 0.015 0.049 -9999 0 -9999 0 0
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.024 0.203 -9999 0 -0.724 4 4
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.039 0.216 -9999 0 -0.655 5 5
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.009 0.123 -9999 0 -0.33 9 9
EPHB2 0.02 0 -9999 0 -9999 0 0
Syndecan-2/TACI 0.012 0.093 -9999 0 -0.325 5 5
LAMA1 -0.01 0.145 -9999 0 -0.708 3 3
Syndecan-2/alpha2 ITGB1 0.007 0.146 -9999 0 -0.498 4 4
HRAS 0.02 0 -9999 0 -9999 0 0
Syndecan-2/CASK -0.003 0.093 -9999 0 -0.337 5 5
ITGA5 -0.031 0.185 -9999 0 -0.708 5 5
BAX 0.036 0.085 -9999 0 -9999 0 0
EPB41 0.005 0.089 -9999 0 -0.523 2 2
positive regulation of cell-cell adhesion 0.001 0.122 -9999 0 -0.356 6 6
LAMA3 -0.003 0.109 -9999 0 -0.523 3 3
EZR 0 0 -9999 0 -9999 0 0
mol:PI-4-5-P2 0 0 -9999 0 -9999 0 0
CAV2 -0.031 0.185 -9999 0 -0.708 5 5
Syndecan-2/MMP2 -0.002 0.112 -9999 0 -0.316 8 8
RP11-540L11.1 0 0 -9999 0 -9999 0 0
alpha2 ITGB1 0.007 0.111 -9999 0 -0.526 3 3
dendrite morphogenesis 0.012 0.093 -9999 0 -0.324 5 5
Syndecan-2/GM-CSF 0.012 0.093 -9999 0 -0.325 5 5
determination of left/right symmetry 0 0.109 -9999 0 -0.396 5 5
Syndecan-2/PKC delta -0.014 0.153 -9999 0 -0.428 8 8
GNB2L1 0.01 0.085 -9999 0 -0.708 1 1
MAPK3 0.025 0.085 -9999 0 -0.391 1 1
MAPK1 0.025 0.085 -9999 0 -0.391 1 1
Syndecan-2/RACK1 0.018 0.093 -9999 0 -0.374 2 2
NF1 0.02 0 -9999 0 -9999 0 0
FGFR/FGF/Syndecan-2 0 0.109 -9999 0 -0.396 5 5
ITGA2 0 0.12 -9999 0 -0.708 2 2
MAPK8 0.025 0.095 -9999 0 -0.432 1 1
Syndecan-2/alpha2/beta1 Integrin 0.002 0.157 -9999 0 -0.441 7 7
Syndecan-2/Kininogen -0.028 0.17 -9999 0 -0.432 10 10
ITGB1 0.01 0.085 -9999 0 -0.708 1 1
SRC 0.028 0.089 -9999 0 -0.346 2 2
Syndecan-2/CASK/Protein 4.1 0.003 0.097 -9999 0 -0.289 7 7
extracellular matrix organization 0.012 0.093 -9999 0 -0.324 5 5
actin cytoskeleton reorganization -0.009 0.123 -9999 0 -0.329 9 9
Syndecan-2/Caveolin-2/Ras -0.006 0.137 -9999 0 -0.397 6 6
Syndecan-2/Laminin alpha3 -0.001 0.126 -9999 0 -0.359 7 7
Syndecan-2/RasGAP 0.027 0.089 -9999 0 -0.349 2 2
alpha5/beta1 Integrin -0.015 0.17 -9999 0 -0.613 5 5
PRKCD -0.025 0.15 -9999 0 -0.523 6 6
Syndecan-2 dimer 0.012 0.093 -9999 0 -0.325 5 5
GO:0007205 0.005 0.001 -9999 0 -9999 0 0
DNA mediated transformation 0 0 -9999 0 -9999 0 0
Syndecan-2/RasGAP/Src 0.039 0.087 -9999 0 -9999 0 0
RHOA 0.01 0.085 -9999 0 -0.708 1 1
SDCBP 0.002 0.106 -9999 0 -0.616 2 2
TNFRSF13B 0.02 0 -9999 0 -9999 0 0
RASA1 0.02 0 -9999 0 -9999 0 0
alpha2/beta1 Integrin 0.007 0.111 -9999 0 -0.526 3 3
Syndecan-2/Synbindin 0.012 0.093 -9999 0 -0.325 5 5
TGFB1 0.02 0 -9999 0 -9999 0 0
CASP3 -0.004 0.144 -9999 0 -0.501 4 4
FN1 -0.013 0.136 -9999 0 -0.57 4 4
Syndecan-2/IL8 -0.101 0.188 -9999 0 -0.344 26 26
SDC2 0 0.11 -9999 0 -0.397 5 5
KNG1 -0.048 0.18 -9999 0 -0.523 9 9
Syndecan-2/Neurofibromin 0.012 0.093 -9999 0 -0.325 5 5
TRAPPC4 0.02 0 -9999 0 -9999 0 0
CSF2 0.02 0 -9999 0 -9999 0 0
Syndecan-2/TGFB1 0.012 0.093 -9999 0 -0.325 5 5
Syndecan-2/Syntenin/PI-4-5-P2 0.001 0.123 -9999 0 -0.359 6 6
Syndecan-2/Ezrin 0.005 0.119 -9999 0 -0.376 5 5
PRKACA 0.025 0.085 -9999 0 -0.391 1 1
angiogenesis -0.1 0.187 -9999 0 -0.343 26 26
MMP2 -0.003 0.109 -9999 0 -0.523 3 3
IL8 -0.156 0.279 -9999 0 -0.585 21 21
calcineurin-NFAT signaling pathway 0.012 0.093 -9999 0 -0.324 5 5
Cellular roles of Anthrax toxin

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
ANTXR1 0.002 0.106 -9999 0 -0.616 2 2
ANTXR2 -0.041 0.201 -9999 0 -0.708 6 6
negative regulation of myeloid dendritic cell antigen processing and presentation -0.009 0.028 -9999 0 -0.092 7 7
monocyte activation -0.076 0.22 -9999 0 -0.516 13 13
MAP2K2 -0.003 0.01 -9999 0 -9999 0 0
MAP2K1 -0.007 0.023 -9999 0 -9999 0 0
MAP2K7 -0.024 0.082 -9999 0 -0.403 3 3
MAP2K6 -0.011 0.046 -9999 0 -0.355 1 1
CYAA -0.022 0.141 -9999 0 -0.429 7 7
MAP2K4 -0.007 0.023 -9999 0 -9999 0 0
IL1B -0.094 0.207 -9999 0 -0.417 18 18
Channel -0.021 0.151 -9999 0 -0.456 7 7
NLRP1 -0.035 0.112 -9999 0 -0.436 5 5
CALM1 0.02 0 -9999 0 -9999 0 0
negative regulation of phagocytosis -0.01 0.031 -9999 0 -9999 0 0
mol:Ca2+ 0 0 -9999 0 -9999 0 0
regulation of endothelial cell proliferation 0.009 0.028 0.092 7 -9999 0 7
MAPK3 -0.007 0.023 -9999 0 -9999 0 0
MAPK1 -0.007 0.023 -9999 0 -9999 0 0
PGR -0.034 0.097 -9999 0 -0.324 7 7
PA/Cellular Receptors -0.024 0.162 -9999 0 -0.494 7 7
apoptosis -0.009 0.028 -9999 0 -0.092 7 7
LOC728358 0 0 -9999 0 -9999 0 0
Lethal toxin (unfolded) -0.019 0.141 -9999 0 -0.426 7 7
macrophage activation 0.02 0.026 -9999 0 -9999 0 0
TNF 0.002 0.106 -9999 0 -0.616 2 2
VCAM1 -0.076 0.222 -9999 0 -0.52 13 13
platelet activation -0.01 0.031 -9999 0 -9999 0 0
MAPKKK cascade -0.009 0.037 0.127 2 -9999 0 2
IL18 -0.069 0.201 -9999 0 -0.475 13 13
negative regulation of macrophage activation -0.009 0.028 -9999 0 -0.092 7 7
LEF -0.009 0.028 -9999 0 -0.092 7 7
CASP1 -0.045 0.128 -9999 0 -0.402 7 7
mol:cAMP -0.01 0.031 -9999 0 -9999 0 0
necrosis -0.009 0.028 -9999 0 -0.092 7 7
intracellular pH reduction 0 0 -9999 0 -9999 0 0
PAGA 0 0 -9999 0 -9999 0 0
Edema toxin (unfolded) -0.019 0.144 -9999 0 -0.433 7 7
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -9999 0 -9999 0 0
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.03 0 -9999 0 -9999 0 0
Necdin/E2F1 -0.102 0.231 -9999 0 -0.499 18 18
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.038 0.06 -9999 0 -0.375 1 1
NGF (dimer)/p75(NTR)/BEX1 -0.024 0.131 -9999 0 -0.34 10 10
NT-4/5 (dimer)/p75(NTR) 0.009 0.046 -9999 0 -0.38 1 1
IKBKB 0.02 0 -9999 0 -9999 0 0
AKT1 0.01 0.126 -9999 0 -0.425 5 5
IKBKG 0.02 0 -9999 0 -9999 0 0
BDNF -0.253 0.328 -9999 0 -0.634 30 30
MGDIs/NGR/p75(NTR)/LINGO1 -0.009 0.145 -9999 0 -0.474 5 5
FURIN 0.02 0 -9999 0 -9999 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.141 0.223 -9999 0 -0.46 18 18
LINGO1 -0.02 0.167 -9999 0 -0.708 4 4
Sortilin/TRAF6/NRIF -0.029 0.089 -9999 0 -9999 0 0
proBDNF (dimer) -0.252 0.327 -9999 0 -0.633 30 30
NTRK1 0.005 0.089 -9999 0 -0.523 2 2
RTN4R -0.01 0.124 -9999 0 -0.523 4 4
neuron apoptosis -0.079 0.186 -9999 0 -0.521 3 3
IRAK1 0.02 0 -9999 0 -9999 0 0
SHC1 0.023 0.04 -9999 0 -0.31 1 1
ARHGDIA 0.02 0 -9999 0 -9999 0 0
RhoA/GTP 0.007 0.065 -9999 0 -0.538 1 1
Gamma Secretase 0.024 0.117 -9999 0 -9999 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.016 0.095 -9999 0 -0.407 3 3
MAGEH1 -0.01 0.145 -9999 0 -0.708 3 3
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.067 0.194 -9999 0 -0.426 15 15
Mammalian IAPs/DIABLO -0.071 0.186 -9999 0 -0.407 15 15
proNGF (dimer) 0 0 -9999 0 -9999 0 0
MAGED1 0.012 0.064 -9999 0 -0.523 1 1
APP -0.061 0.229 -9999 0 -0.708 8 8
NT-4/5 (dimer) 0 0 -9999 0 -9999 0 0
ZNF274 0.01 0.085 -9999 0 -0.708 1 1
RhoA/GDP/RHOGDI 0.027 0.06 -9999 0 -0.386 1 1
NGF 0 0 -9999 0 -9999 0 0
cell cycle arrest 0.01 0.079 -9999 0 -0.531 1 1
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.041 0.031 -9999 0 -9999 0 0
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.022 0.04 -9999 0 -0.311 1 1
NCSTN 0.02 0 -9999 0 -9999 0 0
mol:GTP -0.003 0.101 -9999 0 -0.333 6 6
PSENEN 0.02 0 -9999 0 -9999 0 0
mol:ceramide 0.025 0.061 -9999 0 -9999 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.044 0.026 -9999 0 -9999 0 0
p75(NTR)/beta APP -0.037 0.179 -9999 0 -0.508 9 9
BEX1 -0.055 0.188 -9999 0 -0.523 10 10
mol:GDP 0.008 0.039 -9999 0 -0.322 1 1
NGF (dimer) -0.159 0.227 -9999 0 -0.516 14 14
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.006 0.134 -9999 0 -0.426 5 5
PIK3R1 -0.038 0.194 -9999 0 -0.677 6 6
RAC1/GTP 0.02 0.034 -9999 0 -0.264 1 1
MYD88 0.02 0 -9999 0 -9999 0 0
CHUK 0.02 0 -9999 0 -9999 0 0
NGF (dimer)/p75(NTR)/PKA -0.003 0.101 -9999 0 -0.335 6 6
RHOB -0.109 0.265 -9999 0 -0.642 14 14
RHOA 0.01 0.085 -9999 0 -0.708 1 1
MAGE-G1/E2F1 0.024 0.046 -9999 0 -0.366 1 1
NT3 (dimer) -0.028 0.176 -9999 0 -0.67 5 5
TP53 -0.095 0.188 -9999 0 -0.591 1 1
PRDM4 0.029 0.069 -9999 0 -0.552 1 1
BDNF (dimer) -0.329 0.317 -9999 0 -0.599 35 35
PIK3CA 0.02 0 -9999 0 -9999 0 0
SORT1 0.02 0 -9999 0 -9999 0 0
activation of caspase activity -0.009 0.051 -9999 0 -0.371 1 1
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.034 0.036 -9999 0 -9999 0 0
RHOC 0.02 0 -9999 0 -9999 0 0
XIAP 0 0 -9999 0 -9999 0 0
MAPK10 -0.095 0.183 -9999 0 -0.596 3 3
DIABLO 0.02 0 -9999 0 -9999 0 0
SMPD2 0.025 0.062 -9999 0 -9999 0 0
APH1B 0.01 0.085 -9999 0 -0.708 1 1
APH1A -0.02 0.167 -9999 0 -0.708 4 4
proNGF (dimer)/p75(NTR)/Sortilin 0.022 0.04 -9999 0 -0.311 1 1
PSEN1 0.01 0.085 -9999 0 -0.708 1 1
APAF-1/Pro-Caspase 9 0.03 0 -9999 0 -9999 0 0
NT3 (dimer)/p75(NTR) -0.012 0.14 -9999 0 -0.473 6 6
MAPK8 -0.061 0.164 -9999 0 -9999 0 0
MAPK9 -0.069 0.171 -9999 0 -0.43 6 6
APAF1 0.02 0 -9999 0 -9999 0 0
NTF3 -0.028 0.177 -9999 0 -0.671 5 5
NTF4 0 0 -9999 0 -9999 0 0
NDN -0.147 0.301 -9999 0 -0.686 17 17
RAC1/GDP 0.015 0 -9999 0 -9999 0 0
RhoA-B-C/GDP -0.084 0.177 -9999 0 -0.616 5 5
p75 CTF/Sortilin/TRAF6/NRIF 0.045 0.052 -9999 0 -0.396 1 1
RhoA-B-C/GTP -0.003 0.1 -9999 0 -0.332 6 6
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.105 0.197 -9999 0 -0.631 1 1
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.116 0.207 -9999 0 -0.412 18 18
PRKACB -0.02 0.149 -9999 0 -0.56 5 5
proBDNF (dimer)/p75 ECD -0.175 0.248 -9999 0 -0.462 30 30
ChemicalAbstracts:86-01-1 0 0 -9999 0 -9999 0 0
BIRC3 -0.162 0.306 -9999 0 -0.669 19 19
BIRC2 0.02 0 -9999 0 -9999 0 0
neuron projection morphogenesis -0.049 0.131 -9999 0 -0.392 5 5
BAD -0.071 0.172 -9999 0 -0.466 5 5
RIPK2 0.012 0.064 -9999 0 -0.523 1 1
NGFR 0.012 0.064 -9999 0 -0.523 1 1
CYCS -0.006 0.121 -9999 0 -0.515 1 1
ADAM17 0.02 0 -9999 0 -9999 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.03 0.051 -9999 0 -9999 0 0
BCL2L11 -0.071 0.172 -9999 0 -0.466 5 5
BDNF (dimer)/p75(NTR) -0.179 0.256 -9999 0 -0.472 30 30
PI3K 0 0.134 -9999 0 -0.462 5 5
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.034 0.036 -9999 0 -9999 0 0
NDNL2 0.02 0 -9999 0 -9999 0 0
YWHAE 0.02 0 -9999 0 -9999 0 0
PRKCI 0.02 0 -9999 0 -9999 0 0
NGF (dimer)/p75(NTR) 0.009 0.046 -9999 0 -0.38 1 1
ChemicalAbstracts:146-91-8 0 0 -9999 0 -9999 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.03 0.051 -9999 0 -9999 0 0
TRAF6 0.02 0 -9999 0 -9999 0 0
RAC1 0.02 0 -9999 0 -9999 0 0
PRKCZ 0 0 -9999 0 -9999 0 0
PLG -0.123 0.24 -9999 0 -0.523 19 19
oligodendrocyte cell fate commitment 0 0 -9999 0 -9999 0 0
CASP6 -0.098 0.18 -9999 0 -0.36 18 18
SQSTM1 0.02 0 -9999 0 -9999 0 0
NGFRAP1 0.01 0.085 -9999 0 -0.708 1 1
CASP3 -0.063 0.16 -9999 0 -0.427 5 5
E2F1 0.012 0.064 -9999 0 -0.523 1 1
CASP9 0.02 0 -9999 0 -9999 0 0
IKK complex -0.006 0.03 -9999 0 -9999 0 0
NGF (dimer)/TRKA 0.004 0.065 -9999 0 -0.38 2 2
MMP7 -0.179 0.305 -9999 0 -0.632 22 22
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.038 0.06 -9999 0 -0.375 1 1
MMP3 -0.03 0.169 -9999 0 -0.585 6 6
APAF-1/Caspase 9 -0.099 0.176 -9999 0 -0.492 10 10
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.032 0.151 -9999 0 -0.531 6 6
PDGF/PDGFRA/CRKL -0.007 0.107 -9999 0 -0.36 6 6
positive regulation of JUN kinase activity 0.016 0.096 -9999 0 -0.413 1 1
CRKL 0.02 0 -9999 0 -9999 0 0
PDGF/PDGFRA/Caveolin-3 -0.007 0.107 -9999 0 -0.36 6 6
AP1 -0.268 0.418 -9999 0 -1.051 14 14
mol:IP3 -0.013 0.113 -9999 0 -0.377 6 6
PLCG1 -0.013 0.114 -9999 0 -0.377 6 6
PDGF/PDGFRA/alphaV Integrin -0.022 0.137 -9999 0 -0.403 8 8
RAPGEF1 0.01 0.085 -9999 0 -0.708 1 1
CRK 0 0.12 -9999 0 -0.708 2 2
mol:Ca2+ -0.013 0.113 -9999 0 -0.376 6 6
CAV3 0.02 0 -9999 0 -9999 0 0
CAV1 -0.031 0.185 -9999 0 -0.708 5 5
SHC/Grb2/SOS1 0.017 0.097 -9999 0 -0.415 1 1
PDGF/PDGFRA/Shf -0.011 0.128 -9999 0 -0.414 6 6
FOS -0.221 0.431 -9999 0 -1.017 14 14
JUN -0.1 0.201 -9999 0 -0.544 12 12
oligodendrocyte development -0.022 0.137 -9999 0 -0.403 8 8
GRB2 0.01 0.085 -9999 0 -0.708 1 1
PIK3R1 -0.038 0.194 -9999 0 -0.677 6 6
mol:DAG -0.013 0.113 -9999 0 -0.377 6 6
PDGF/PDGFRA -0.032 0.151 -9999 0 -0.53 6 6
actin cytoskeleton reorganization -0.007 0.107 -9999 0 -0.359 6 6
SRF 0.038 0.011 -9999 0 -9999 0 0
SHC1 0.02 0 -9999 0 -9999 0 0
PI3K -0.029 0.152 -9999 0 -0.459 5 5
PDGF/PDGFRA/Crk/C3G -0.01 0.148 -9999 0 -0.665 2 2
JAK1 -0.035 0.165 -9999 0 -0.435 10 10
ELK1/SRF 0.029 0.077 -9999 0 -9999 0 0
SHB 0.02 0 -9999 0 -9999 0 0
SHF 0.012 0.064 -9999 0 -0.523 1 1
CSNK2A1 0.021 0.028 -9999 0 -9999 0 0
GO:0007205 -0.012 0.108 -9999 0 -0.354 6 6
SOS1 0.02 0 -9999 0 -9999 0 0
Ras protein signal transduction 0.016 0.096 -9999 0 -0.413 1 1
PDGF/PDGFRA/SHB -0.007 0.107 -9999 0 -0.36 6 6
PDGF/PDGFRA/Caveolin-1 -0.046 0.173 -9999 0 -0.445 11 11
ITGAV 0 0.12 -9999 0 -0.708 2 2
ELK1 -0.008 0.1 -9999 0 -0.362 2 2
PIK3CA 0.02 0 -9999 0 -9999 0 0
PDGF/PDGFRA/Crk -0.022 0.139 -9999 0 -0.406 8 8
JAK-STAT cascade -0.035 0.164 -9999 0 -0.434 10 10
cell proliferation -0.011 0.127 -9999 0 -0.413 6 6
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.042 0.189 -9999 0 -0.51 10 10
MAP4K4 -0.055 0.244 -9999 0 -0.572 10 10
BAG4 0.02 0 -9999 0 -9999 0 0
PKC zeta/ceramide -0.023 0.065 -9999 0 -9999 0 0
NFKBIA -0.01 0.145 -9999 0 -0.708 3 3
BIRC3 -0.162 0.306 -9999 0 -0.669 19 19
BAX 0.001 0.034 -9999 0 -9999 0 0
RIPK1 0.02 0 -9999 0 -9999 0 0
AKT1 0.03 0.015 -9999 0 -9999 0 0
BAD -0.01 0.067 -9999 0 -9999 0 0
SMPD1 -0.009 0.107 -9999 0 -0.295 7 7
RB1 -0.01 0.067 -9999 0 -9999 0 0
FADD/Caspase 8 -0.02 0.21 -9999 0 -0.527 7 7
MAP2K4 -0.005 0.069 -9999 0 -0.274 1 1
NSMAF 0.002 0.106 -9999 0 -0.616 2 2
response to UV 0 0 -9999 0 -9999 0 0
RAF1 -0.01 0.093 -9999 0 -0.414 2 2
EGF -0.247 0.304 -9999 0 -0.581 32 32
mol:ceramide -0.024 0.072 0.151 1 -9999 0 1
MADD 0.02 0 -9999 0 -9999 0 0
response to oxidative stress 0 0 -9999 0 -9999 0 0
mol:Free Fatty acid -0.068 0.21 -9999 0 -0.491 14 14
ASAH1 -0.015 0.147 -9999 0 -0.616 4 4
negative regulation of cell cycle -0.011 0.067 -9999 0 -9999 0 0
cell proliferation -0.049 0.133 -9999 0 -0.369 5 5
BID -0.062 0.271 -9999 0 -1.099 4 4
MAP3K1 -0.016 0.073 -9999 0 -0.298 1 1
EIF2A -0.016 0.111 -9999 0 -0.362 3 3
TRADD 0.01 0.085 -9999 0 -0.708 1 1
CRADD 0.012 0.064 -9999 0 -0.523 1 1
MAPK3 0.007 0.088 -9999 0 -0.373 2 2
response to heat 0 0 -9999 0 -9999 0 0
MAPK1 0.007 0.088 -9999 0 -0.373 2 2
Cathepsin D/ceramide -0.01 0.066 -9999 0 -9999 0 0
FADD -0.039 0.22 -9999 0 -0.566 7 7
KSR1 -0.022 0.098 -9999 0 -0.444 2 2
MAPK8 -0.002 0.062 -9999 0 -9999 0 0
PRKRA -0.01 0.067 -9999 0 -9999 0 0
PDGFA -0.079 0.246 -9999 0 -0.689 10 10
TRAF2 0.005 0.089 -9999 0 -0.523 2 2
IGF1 -0.081 0.228 -9999 0 -0.585 12 12
mol:GD3 0 0 -9999 0 -9999 0 0
ganglioside biosynthetic process -0.023 0.072 0.15 1 -9999 0 1
CTSD 0.02 0 -9999 0 -9999 0 0
regulation of nitric oxide biosynthetic process 0.03 0 -9999 0 -9999 0 0
response to radiation 0 0 -9999 0 -9999 0 0
ERK1/PKC delta -0.051 0.144 -9999 0 -0.398 5 5
PRKCD -0.025 0.15 -9999 0 -0.523 6 6
PRKCZ 0 0 -9999 0 -9999 0 0
mol:GW4869 0 0 -9999 0 -9999 0 0
mol:sphingosine -0.068 0.21 -9999 0 -0.491 14 14
RelA/NF kappa B1 0.03 0 -9999 0 -9999 0 0
mol:glutathione 0 0 -9999 0 -9999 0 0
PAWR 0.01 0.085 -9999 0 -0.708 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.053 0.234 -9999 0 -0.612 7 7
TNFR1A/BAG4/TNF-alpha -0.024 0.178 -9999 0 -0.496 8 8
mol:Sphingosine-1-phosphate -0.042 0.188 -9999 0 -0.508 10 10
MAP2K1 0.001 0.089 -9999 0 -0.385 2 2
mol:C11AG 0 0 -9999 0 -9999 0 0
RELA 0.02 0 -9999 0 -9999 0 0
CYCS -0.01 0.069 0.2 3 -0.19 2 5
TNFRSF1A -0.061 0.229 -9999 0 -0.708 8 8
NFKB1 0.02 0 -9999 0 -9999 0 0
TNFR1A/BAG4 -0.032 0.175 -9999 0 -0.526 8 8
EIF2AK2 -0.02 0.106 -9999 0 -0.325 5 5
TNF-alpha/TNFR1A/FAN -0.034 0.209 -9999 0 -0.544 8 8
response to hydrogen peroxide 0 0 -9999 0 -9999 0 0
CASP8 0.005 0.106 -9999 0 -0.431 1 1
MAP2K2 0.001 0.089 -9999 0 -0.385 2 2
SMPD3 -0.017 0.127 -9999 0 -0.334 8 8
TNF 0.002 0.106 -9999 0 -0.616 2 2
PKC zeta/PAR4 0.007 0.065 -9999 0 -0.538 1 1
mol:PHOSPHOCHOLINE 0.093 0.133 0.239 30 -9999 0 30
NF kappa B1/RelA/I kappa B alpha 0.024 0.097 -9999 0 -0.375 4 4
AIFM1 0.012 0.07 0.215 4 -9999 0 4
BCL2 -0.041 0.201 -9999 0 -0.708 6 6
IL1-mediated signaling events

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
UBC13/UEV1A 0.015 0 -9999 0 -9999 0 0
PRKCZ 0 0 -9999 0 -9999 0 0
MAP3K7IP2 0.02 0 -9999 0 -9999 0 0
ERC1 0.01 0.085 -9999 0 -0.708 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.092 0.166 -9999 0 -0.457 9 9
IRAK/TOLLIP 0.038 0 -9999 0 -9999 0 0
IKBKB 0.02 0 -9999 0 -9999 0 0
IKBKG 0.02 0 -9999 0 -9999 0 0
IL1 alpha/IL1R2 -0.121 0.211 -9999 0 -0.405 25 25
IL1A -0.003 0.109 -9999 0 -0.523 3 3
IL1B -0.148 0.296 -9999 0 -0.562 22 22
IRAK/TRAF6/p62/Atypical PKCs 0 0 -9999 0 -9999 0 0
IL1R2 -0.161 0.277 -9999 0 -0.574 22 22
IL1R1 -0.025 0.168 -9999 0 -0.634 5 5
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.038 0.172 -9999 0 -0.441 8 8
TOLLIP 0.02 0 -9999 0 -9999 0 0
TICAM2 0 0 -9999 0 -9999 0 0
MAP3K3 0.02 0 -9999 0 -9999 0 0
TAK1/TAB1/TAB2 0.034 0.057 -9999 0 -0.444 1 1
IKK complex/ELKS 0.088 0.056 -9999 0 -9999 0 0
JUN 0.014 0.145 -9999 0 -0.527 1 1
MAP3K7 0.02 0 -9999 0 -9999 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.127 0.34 -9999 0 -0.931 8 8
IL1 alpha/IL1R1/IL1RAP/MYD88 0.002 0.156 -9999 0 -0.622 3 3
PIK3R1 -0.038 0.194 -9999 0 -0.677 6 6
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.011 0.171 -9999 0 -0.673 3 3
IL1 beta fragment/IL1R1/IL1RAP -0.131 0.306 -9999 0 -0.606 17 17
NFKB1 0.02 0 -9999 0 -9999 0 0
MAPK8 0.064 0.053 -9999 0 -9999 0 0
IRAK1 0.028 0 -9999 0 -9999 0 0
IL1RN/IL1R1 -0.032 0.156 -9999 0 -0.414 10 10
IRAK4 -0.025 0.15 -9999 0 -0.523 6 6
PRKCI 0.02 0 -9999 0 -9999 0 0
TRAF6 0.02 0 -9999 0 -9999 0 0
PI3K -0.014 0.147 -9999 0 -0.499 6 6
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.063 0.216 -9999 0 -0.513 10 10
CHUK 0.02 0 -9999 0 -9999 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.131 0.306 -9999 0 -0.606 17 17
IL1 beta/IL1R2 -0.229 0.317 -9999 0 -0.657 18 18
IRAK/TRAF6/TAK1/TAB1/TAB2 0.058 0.046 -9999 0 -9999 0 0
NF kappa B1 p50/RelA -0.148 0.272 -9999 0 -0.809 8 8
IRAK3 -0.008 0.134 -9999 0 -0.646 3 3
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.131 0.312 -9999 0 -0.772 11 11
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.005 0.128 -9999 0 -0.518 3 3
IL1 alpha/IL1R1/IL1RAP -0.013 0.167 -9999 0 -0.678 3 3
RELA 0.02 0 -9999 0 -9999 0 0
MAP3K7IP1 0.01 0.085 -9999 0 -0.708 1 1
SQSTM1 0.02 0 -9999 0 -9999 0 0
MYD88 0.02 0 -9999 0 -9999 0 0
IRAK/TRAF6/MEKK3 0.049 0 -9999 0 -9999 0 0
IL1RAP 0.002 0.106 -9999 0 -0.616 2 2
UBE2N 0.02 0 -9999 0 -9999 0 0
IRAK/TRAF6 -0.134 0.231 -9999 0 -0.642 10 10
CASP1 -0.091 0.262 -9999 0 -0.708 11 11
IL1RN/IL1R2 -0.128 0.243 -9999 0 -0.463 23 23
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.112 0.294 -9999 0 -0.568 17 17
TMEM189-UBE2V1 0 0 -9999 0 -9999 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.018 0.122 -9999 0 -0.509 3 3
PIK3CA 0.02 0 -9999 0 -9999 0 0
IL1RN -0.018 0.138 -9999 0 -0.523 5 5
TRAF6/TAK1/TAB1/TAB2 -0.005 0.041 -9999 0 -9999 0 0
MAP2K6 0.055 0.055 -9999 0 -9999 0 0
ceramide signaling pathway

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
MAP4K4 -0.084 0.3 -9999 0 -0.765 10 10
BAG4 0.02 0 -9999 0 -9999 0 0
BAD 0.007 0.075 -9999 0 -0.223 2 2
NFKBIA -0.01 0.145 -9999 0 -0.708 3 3
BIRC3 -0.162 0.306 -9999 0 -0.669 19 19
BAX 0.007 0.075 -9999 0 -0.223 2 2
EnzymeConsortium:3.1.4.12 -0.006 0.054 -9999 0 -0.139 7 7
IKBKB -0.066 0.277 -9999 0 -0.697 10 10
MAP2K2 0.019 0.099 -9999 0 -0.392 2 2
MAP2K1 0.019 0.099 -9999 0 -0.392 2 2
SMPD1 0.002 0.054 -9999 0 -0.158 2 2
GO:0005551 0 0 -9999 0 -9999 0 0
FADD/Caspase 8 -0.054 0.27 -9999 0 -0.779 7 7
MAP2K4 0.013 0.097 -9999 0 -0.579 1 1
protein ubiquitination -0.066 0.283 -9999 0 -0.711 10 10
EnzymeConsortium:2.7.1.37 0.023 0.109 -9999 0 -0.41 3 3
response to UV 0 0.001 -9999 0 -0.003 3 3
RAF1 0.01 0.103 -9999 0 -0.38 3 3
CRADD 0.013 0.064 -9999 0 -0.523 1 1
mol:ceramide -0.003 0.078 -9999 0 -0.197 7 7
I-kappa-B-alpha/RELA/p50/ubiquitin 0.007 0.096 -9999 0 -0.455 3 3
MADD 0.02 0.001 -9999 0 -9999 0 0
MAP3K1 0.002 0.101 -9999 0 -0.414 2 2
TRADD 0.01 0.086 -9999 0 -0.711 1 1
RELA/p50 0.02 0 -9999 0 -9999 0 0
MAPK3 0.023 0.097 -9999 0 -0.347 3 3
MAPK1 0.023 0.097 -9999 0 -0.347 3 3
p50/RELA/I-kappa-B-alpha 0.007 0.111 -9999 0 -0.526 3 3
FADD -0.068 0.28 -9999 0 -0.82 7 7
KSR1 -0.001 0.106 -9999 0 -0.398 3 3
MAPK8 0.023 0.09 -9999 0 -0.515 1 1
TRAF2 0.005 0.089 -9999 0 -0.523 2 2
response to radiation 0 0.001 -9999 0 -0.003 1 1
CHUK -0.066 0.277 -9999 0 -0.697 10 10
TNF R/SODD -0.032 0.174 -9999 0 -0.525 8 8
TNF 0.003 0.106 -9999 0 -0.617 2 2
CYCS 0.005 0.103 0.166 3 -0.27 6 9
IKBKG -0.066 0.277 -9999 0 -0.697 10 10
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.085 0.301 -9999 0 -0.892 7 7
RELA 0.02 0 -9999 0 -9999 0 0
RIPK1 0.021 0.001 -9999 0 -9999 0 0
AIFM1 0.019 0.076 0.166 3 -0.215 2 5
TNF/TNF R/SODD -0.023 0.178 -9999 0 -0.496 8 8
TNFRSF1A -0.061 0.229 -9999 0 -0.707 8 8
response to heat 0 0.001 -9999 0 -0.003 1 1
CASP8 0.015 0.055 -9999 0 -9999 0 0
NSMAF -0.072 0.292 -9999 0 -0.793 8 8
response to hydrogen peroxide 0 0.001 -9999 0 -0.003 3 3
BCL2 -0.041 0.201 -9999 0 -0.708 6 6
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.045 0.306 -9999 0 -0.869 7 7
UGCG 0.016 0.053 -9999 0 -9999 0 0
AKT1/mTOR/p70S6K/Hsp90/TERT 0.001 0.237 -9999 0 -0.543 8 8
mol:GTP 0 0.001 -9999 0 -9999 0 0
mol:glucosylceramide 0.016 0.053 -9999 0 -9999 0 0
mol:DAG -0.022 0.124 -9999 0 -1.019 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.124 0.242 -9999 0 -0.666 10 10
FRAP1 -0.05 0.36 -9999 0 -0.833 10 10
FOXO3 -0.041 0.333 -9999 0 -0.755 11 11
AKT1 -0.064 0.371 -9999 0 -0.858 11 11
GAB2 0.02 0.004 -9999 0 -9999 0 0
SMPD1 0.016 0.053 -9999 0 -9999 0 0
SGMS1 0.001 0.103 -9999 0 -0.414 3 3
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 -0.009 0.129 -9999 0 -0.434 6 6
CALM1 0.02 0 -9999 0 -9999 0 0
cell proliferation 0.003 0.142 -9999 0 -0.459 2 2
EIF3A 0.02 0 -9999 0 -9999 0 0
PI3K -0.01 0.15 -9999 0 -0.502 6 6
RPS6KB1 0.024 0.052 -9999 0 -9999 0 0
mol:sphingomyelin -0.022 0.124 -9999 0 -1.019 1 1
natural killer cell activation 0 0.003 -9999 0 -9999 0 0
JAK3 0.023 0.004 -9999 0 -9999 0 0
PIK3R1 -0.035 0.195 -9999 0 -0.679 6 6
JAK1 -0.017 0.168 -9999 0 -0.708 4 4
NFKB1 0.02 0 -9999 0 -9999 0 0
MYC -0.076 0.41 -9999 0 -1.047 10 10
MYB 0.015 0.182 -9999 0 -1.364 1 1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.053 0.332 -9999 0 -0.776 10 10
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.041 0.06 -9999 0 -9999 0 0
mol:PI-3-4-5-P3 -0.048 0.316 -9999 0 -0.739 10 10
Rac1/GDP 0.003 0.119 -9999 0 -0.407 5 5
T cell proliferation -0.041 0.287 -9999 0 -0.669 10 10
SHC1 0.02 0.004 -9999 0 -9999 0 0
RAC1 0.02 0.001 -9999 0 -9999 0 0
positive regulation of cyclin-dependent protein kinase activity 0.006 0.012 -9999 0 -0.051 3 3
PRKCZ -0.046 0.305 -9999 0 -0.713 10 10
NF kappa B1 p50/RelA -0.118 0.242 -9999 0 -0.659 10 10
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.067 0.335 -9999 0 -0.9 8 8
HSP90AA1 0.005 0.089 -9999 0 -0.523 2 2
RELA 0.02 0 -9999 0 -9999 0 0
IL2RA -0.091 0.251 -9999 0 -0.647 12 12
IL2RB -0.047 0.217 -9999 0 -0.71 7 7
TERT 0.002 0.106 -9999 0 -0.616 2 2
E2F1 0.025 0.077 -9999 0 -0.463 1 1
SOS1 0.02 0.004 -9999 0 -9999 0 0
RPS6 0.012 0.064 -9999 0 -0.523 1 1
mol:cAMP -0.003 0.006 0.024 3 -9999 0 3
PTPN11 0.02 0.005 -9999 0 -9999 0 0
IL2RG 0 0.109 -9999 0 -0.519 3 3
actin cytoskeleton organization -0.041 0.287 -9999 0 -0.669 10 10
GRB2 0.01 0.085 -9999 0 -0.708 1 1
IL2 0.003 0.12 -9999 0 -0.708 2 2
PIK3CA 0.023 0.005 -9999 0 -9999 0 0
Rac1/GTP 0.014 0.117 -9999 0 -0.387 5 5
LCK -0.1 0.257 -9999 0 -0.615 14 14
BCL2 -0.049 0.354 -9999 0 -0.805 11 11
IL2 signaling events mediated by STAT5

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
GAB2 0.021 0 -9999 0 -9999 0 0
ELF1 -0.025 0.133 -9999 0 -0.361 8 8
CCNA2 0.02 0 -9999 0 -9999 0 0
PIK3CA 0.021 0 -9999 0 -9999 0 0
JAK3 0.021 0 -9999 0 -9999 0 0
PIK3R1 -0.037 0.194 -9999 0 -0.677 6 6
JAK1 -0.019 0.167 -9999 0 -0.708 4 4
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.024 0.28 -9999 0 -0.82 6 6
SHC1 0.021 0 -9999 0 -9999 0 0
SP1 -0.004 0.112 -9999 0 -0.361 6 6
IL2RA -0.091 0.322 -9999 0 -0.782 12 12
IL2RB -0.05 0.216 -9999 0 -0.708 7 7
SOS1 0.021 0 -9999 0 -9999 0 0
IL2RG -0.001 0.109 -9999 0 -0.522 3 3
G1/S transition of mitotic cell cycle -0.048 0.325 -9999 0 -0.978 7 7
PTPN11 0.021 0 -9999 0 -9999 0 0
CCND2 -0.043 0.277 -9999 0 -0.872 7 7
LCK -0.102 0.255 -9999 0 -0.615 14 14
GRB2 0.011 0.085 -9999 0 -0.708 1 1
IL2 0.001 0.12 -9999 0 -0.707 2 2
CDK6 -0.01 0.145 -9999 0 -0.708 3 3
CCND3 0.001 0.228 -9999 0 -0.728 4 4
Regulation of Telomerase

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
Telomerase catalytic core complex -0.153 0.354 -9999 0 -0.855 11 11
RAD9A 0.02 0 -9999 0 -9999 0 0
AP1 -0.178 0.319 -9999 0 -0.593 24 24
IFNAR2 0.001 0.106 -9999 0 -0.615 2 2
AKT1 0.011 0.095 -9999 0 -0.4 3 3
ER alpha/Oestrogen -0.002 0.091 -9999 0 -0.541 2 2
NFX1/SIN3/HDAC complex 0.034 0.145 -9999 0 -1.035 1 1
EGF -0.247 0.305 -9999 0 -0.582 32 32
SMG5 0.012 0.064 -9999 0 -0.523 1 1
SMG6 0.02 0 -9999 0 -9999 0 0
SP3/HDAC2 0.028 0.015 -9999 0 -9999 0 0
TERT/c-Abl -0.145 0.319 -9999 0 -0.785 11 11
SAP18 0.02 0.001 -9999 0 -9999 0 0
MRN complex 0.034 0.057 -9999 0 -0.444 1 1
WT1 -0.17 0.267 -9999 0 -0.544 24 24
WRN 0.02 0 -9999 0 -9999 0 0
SP1 0.02 0.01 -9999 0 -9999 0 0
SP3 0.02 0.004 -9999 0 -9999 0 0
TERF2IP 0.02 0 -9999 0 -9999 0 0
Telomerase/Nucleolin -0.155 0.292 -9999 0 -0.787 10 10
Mad/Max 0.027 0.014 -9999 0 -9999 0 0
TERT -0.161 0.378 -9999 0 -0.905 11 11
CCND1 -0.271 0.553 -9999 0 -1.294 16 16
MAX 0.02 0.005 -9999 0 -9999 0 0
RBBP7 0.02 0.002 -9999 0 -9999 0 0
RBBP4 0.02 0.001 -9999 0 -9999 0 0
TERF2 0.001 0.111 -9999 0 -0.653 2 2
PTGES3 0.02 0 -9999 0 -9999 0 0
SIN3A 0.01 0.085 -9999 0 -0.709 1 1
Telomerase/911 0.028 0.084 -9999 0 -0.422 1 1
CDKN1B -0.181 0.308 -9999 0 -0.818 9 9
RAD1 0.02 0 -9999 0 -9999 0 0
XRCC5 0.02 0 -9999 0 -9999 0 0
XRCC6 0.02 0 -9999 0 -9999 0 0
SAP30 -0.02 0.167 -9999 0 -0.709 4 4
TRF2/PARP2 -0.013 0.086 -9999 0 -0.52 2 2
UBE3A 0.02 0.003 -9999 0 -9999 0 0
JUN -0.094 0.257 -9999 0 -0.664 12 12
E6 0 0.004 -9999 0 -9999 0 0
HPV-16 E6/E6AP 0.014 0.008 -9999 0 -9999 0 0
FOS -0.157 0.289 -9999 0 -0.616 20 20
IFN-gamma/IRF1 -0.224 0.326 -9999 0 -0.747 14 14
PARP2 0.02 0 -9999 0 -9999 0 0
BLM 0.005 0.089 -9999 0 -0.523 2 2
Telomerase 0.044 0.078 -9999 0 -9999 0 0
IRF1 -0.098 0.268 -9999 0 -0.665 13 13
ESR1 0 0.12 -9999 0 -0.71 2 2
KU/TER 0.03 0 -9999 0 -9999 0 0
ATM/TRF2 0.006 0.126 -9999 0 -0.57 3 3
ubiquitin-dependent protein catabolic process 0.042 0.147 -9999 0 -1.069 1 1
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.04 0.155 -9999 0 -1.142 1 1
HDAC1 0.01 0.085 -9999 0 -0.709 1 1
HDAC2 0.019 0.01 -9999 0 -9999 0 0
ATM -0.008 0.076 0.25 1 -0.415 2 3
SMAD3 0.026 0.065 -9999 0 -0.524 1 1
ABL1 0.02 0 -9999 0 -9999 0 0
MXD1 0.02 0.005 -9999 0 -9999 0 0
MRE11A 0.02 0 -9999 0 -9999 0 0
HUS1 -0.003 0.109 -9999 0 -0.523 3 3
RPS6KB1 0.02 0 -9999 0 -9999 0 0
TERT/NF kappa B1/14-3-3 -0.105 0.3 -9999 0 -0.926 5 5
NR2F2 -0.02 0.165 -9999 0 -0.701 4 4
MAPK3 0.017 0.092 -9999 0 -0.525 2 2
MAPK1 0.017 0.092 -9999 0 -0.525 2 2
TGFB1/TGF beta receptor Type II 0.02 0.002 -9999 0 -9999 0 0
NFKB1 0.02 0 -9999 0 -9999 0 0
HNRNPC 0.02 0 -9999 0 -9999 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.008 0.076 0.25 1 -0.414 2 3
NBN 0.02 0 -9999 0 -9999 0 0
EGFR -0.106 0.261 -9999 0 -0.632 14 14
mol:Oestrogen 0 0.003 -9999 0 -9999 0 0
EGF/EGFR -0.254 0.292 -9999 0 -0.497 39 39
MYC -0.062 0.23 -9999 0 -0.711 8 8
IL2 0 0.12 -9999 0 -0.708 2 2
KU 0.03 0 -9999 0 -9999 0 0
RAD50 0.01 0.085 -9999 0 -0.708 1 1
HSP90AA1 0.005 0.089 -9999 0 -0.523 2 2
TGFB1 0.02 0.002 -9999 0 -9999 0 0
TRF2/BLM -0.022 0.101 -9999 0 -0.429 4 4
FRAP1 0.02 0 -9999 0 -9999 0 0
KU/TERT -0.122 0.327 -9999 0 -0.774 11 11
SP1/HDAC2 0.031 0.017 -9999 0 -9999 0 0
PINX1 0.02 0 -9999 0 -9999 0 0
Telomerase/EST1A -0.144 0.271 -9999 0 -0.8 7 7
Smad3/Myc -0.02 0.174 -9999 0 -0.495 8 8
911 complex 0.027 0.068 -9999 0 -9999 0 0
IFNG -0.221 0.29 -9999 0 -0.549 31 31
Telomerase/PinX1 -0.144 0.271 -9999 0 -0.8 7 7
Telomerase/AKT1/mTOR/p70S6K 0.013 0.13 -9999 0 -0.572 2 2
SIN3B 0.02 0.002 -9999 0 -9999 0 0
YWHAE 0.02 0 -9999 0 -9999 0 0
Telomerase/EST1B -0.148 0.271 -9999 0 -0.8 7 7
response to DNA damage stimulus 0.003 0.02 -9999 0 -9999 0 0
MRN complex/TRF2/Rap1 -0.014 0.076 -9999 0 -0.386 1 1
TRF2/WRN -0.013 0.086 -9999 0 -0.52 2 2
Telomerase/hnRNP C1/C2 -0.144 0.271 -9999 0 -0.8 7 7
E2F1 0.011 0.064 -9999 0 -0.521 1 1
ZNFX1 0.01 0.085 -9999 0 -0.709 1 1
PIF1 0.012 0.064 -9999 0 -0.523 1 1
NCL -0.01 0.145 -9999 0 -0.708 3 3
DKC1 0.02 0 -9999 0 -9999 0 0
telomeric DNA binding 0 0 -9999 0 -9999 0 0
BCR signaling pathway

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
JUN -0.031 0.217 -9999 0 -0.527 9 9
IKBKB 0.015 0.098 -9999 0 -0.288 1 1
AKT1 0.005 0.114 -9999 0 -0.287 5 5
IKBKG 0.011 0.104 -9999 0 -0.309 1 1
CALM1 -0.01 0.128 -9999 0 -0.429 4 4
PIK3CA 0.02 0 -9999 0 -9999 0 0
MAP3K1 -0.025 0.232 -9999 0 -0.62 7 7
MAP3K7 0.02 0 -9999 0 -9999 0 0
mol:Ca2+ -0.022 0.134 0.248 1 -0.424 5 6
DOK1 0.02 0 -9999 0 -9999 0 0
AP-1 -0.025 0.135 0.219 1 -0.308 6 7
LYN 0.02 0 -9999 0 -9999 0 0
BLNK -0.041 0.187 -9999 0 -0.602 7 7
SHC1 0.02 0 -9999 0 -9999 0 0
BCR complex -0.028 0.163 -9999 0 -0.485 8 8
CD22 -0.091 0.237 -9999 0 -0.728 7 7
CAMK2G -0.003 0.136 -9999 0 -0.457 4 4
CSNK2A1 0.02 0 -9999 0 -9999 0 0
INPP5D 0 0 -9999 0 -9999 0 0
SHC/GRB2/SOS1 -0.068 0.144 -9999 0 -0.579 3 3
GO:0007205 -0.022 0.136 0.248 1 -0.43 5 6
SYK -0.005 0.122 -9999 0 -0.585 3 3
ELK1 -0.01 0.13 -9999 0 -0.435 4 4
NFATC1 -0.043 0.23 -9999 0 -0.531 10 10
B-cell antigen/BCR complex -0.028 0.163 -9999 0 -0.485 8 8
PAG1/CSK -0.053 0.195 -9999 0 -0.511 11 11
NFKBIB 0.02 0.039 0.105 1 -9999 0 1
HRAS -0.005 0.131 -9999 0 -0.452 3 3
NFKBIA 0.02 0.039 0.105 1 -9999 0 1
NF-kappa-B/RelA/I kappa B beta 0.028 0.033 -9999 0 -9999 0 0
RasGAP/Csk -0.063 0.22 -9999 0 -0.449 15 15
mol:GDP -0.02 0.129 0.236 1 -0.444 4 5
PTEN 0.02 0 -9999 0 -9999 0 0
CD79B -0.041 0.201 -9999 0 -0.708 6 6
NF-kappa-B/RelA/I kappa B alpha 0.027 0.033 -9999 0 -9999 0 0
GRB2 0.01 0.085 -9999 0 -0.708 1 1
PI3K/BCAP/CD19 -0.044 0.222 -9999 0 -0.592 7 7
PIK3R1 -0.038 0.194 -9999 0 -0.677 6 6
mol:IP3 -0.023 0.138 0.25 1 -0.436 5 6
CSK 0.012 0.064 -9999 0 -0.523 1 1
FOS -0.085 0.207 -9999 0 -0.483 10 10
CHUK 0.011 0.104 -9999 0 -0.309 1 1
IBTK 0.01 0.085 -9999 0 -0.708 1 1
CARD11/BCL10/MALT1/TAK1 -0.084 0.163 -9999 0 -0.544 5 5
PTPN6 -0.041 0.235 -9999 0 -0.673 7 7
RELA 0.02 0 -9999 0 -9999 0 0
BCL2A1 0.014 0.046 -9999 0 -0.119 3 3
VAV2 -0.053 0.249 -9999 0 -0.709 7 7
ubiquitin-dependent protein catabolic process 0.025 0.04 0.11 1 -9999 0 1
BTK -0.082 0.313 -9999 0 -1.228 5 5
CD19 -0.101 0.247 -9999 0 -0.674 9 9
MAP4K1 0.012 0.064 -9999 0 -0.523 1 1
CD72 -0.157 0.289 -9999 0 -0.616 20 20
PAG1 -0.081 0.252 -9999 0 -0.708 10 10
MAPK14 -0.005 0.195 -9999 0 -0.529 6 6
SH3BP5 -0.068 0.235 -9999 0 -0.688 9 9
PIK3AP1 -0.05 0.196 -9999 0 -0.482 9 9
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.094 0.263 -9999 0 -0.591 13 13
RAF1 0.007 0.124 -9999 0 -0.416 3 3
RasGAP/p62DOK/SHIP -0.099 0.185 -9999 0 -0.429 14 14
CD79A 0.005 0.089 -9999 0 -0.523 2 2
re-entry into mitotic cell cycle -0.025 0.134 0.22 1 -0.305 6 7
RASA1 0.02 0 -9999 0 -9999 0 0
MAPK3 0.028 0.108 -9999 0 -0.411 1 1
MAPK1 0.028 0.108 -9999 0 -0.411 1 1
CD72/SHP1 -0.111 0.299 -9999 0 -0.684 12 12
NFKB1 0.02 0 -9999 0 -9999 0 0
MAPK8 -0.005 0.195 -9999 0 -0.529 6 6
actin cytoskeleton organization -0.03 0.209 -9999 0 -0.579 7 7
NF-kappa-B/RelA 0.048 0.089 -9999 0 -0.285 2 2
Calcineurin -0.034 0.087 -9999 0 -0.468 1 1
PI3K -0.087 0.178 -9999 0 -0.526 8 8
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.024 0.147 0.278 1 -0.466 5 6
SOS1 0.02 0 -9999 0 -9999 0 0
Bam32/HPK1 -0.084 0.318 -9999 0 -0.798 11 11
DAPP1 -0.143 0.353 -9999 0 -0.967 10 10
cytokine secretion -0.036 0.208 -9999 0 -0.483 10 10
mol:DAG -0.023 0.138 0.25 1 -0.436 5 6
PLCG2 -0.056 0.188 -9999 0 -0.523 10 10
MAP2K1 0.017 0.117 -9999 0 -0.409 2 2
B-cell antigen/BCR complex/FcgammaRIIB -0.095 0.244 -9999 0 -0.533 14 14
mol:PI-3-4-5-P3 -0.062 0.121 -9999 0 -0.405 5 5
ETS1 -0.026 0.175 -9999 0 -0.531 4 4
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.031 0.179 -9999 0 -0.63 2 2
B-cell antigen/BCR complex/LYN -0.095 0.255 -9999 0 -0.782 7 7
MALT1 -0.031 0.185 -9999 0 -0.708 5 5
TRAF6 0.02 0 -9999 0 -9999 0 0
RAC1 -0.036 0.226 -9999 0 -0.63 7 7
B-cell antigen/BCR complex/LYN/SYK -0.082 0.227 -9999 0 -0.706 7 7
CARD11 -0.045 0.17 -9999 0 -0.454 7 7
FCGR2B -0.114 0.274 -9999 0 -0.668 14 14
PPP3CA 0.02 0 -9999 0 -9999 0 0
BCL10 0.01 0.085 -9999 0 -0.708 1 1
IKK complex 0.023 0.048 -9999 0 -9999 0 0
PTPRC -0.068 0.235 -9999 0 -0.687 9 9
PDPK1 0.001 0.112 -9999 0 -0.31 4 4
PPP3CB 0.02 0 -9999 0 -9999 0 0
PPP3CC 0.02 0 -9999 0 -9999 0 0
POU2F2 0.024 0.033 -9999 0 -9999 0 0
IGF1 pathway

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
NCK2 0.02 0 -9999 0 -9999 0 0
PTK2 0.02 0 -9999 0 -9999 0 0
CRKL -0.031 0.154 -9999 0 -0.42 8 8
GRB2/SOS1/SHC 0.034 0.057 -9999 0 -0.444 1 1
HRAS 0.02 0 -9999 0 -9999 0 0
IRS1/Crk -0.042 0.173 -9999 0 -0.437 10 10
IGF-1R heterotetramer/IGF1/PTP1B -0.063 0.137 -9999 0 -0.432 5 5
AKT1 -0.028 0.207 -9999 0 -0.645 5 5
BAD -0.015 0.194 -9999 0 -0.59 5 5
mol:GTP 0 0 -9999 0 -9999 0 0
CRK -0.042 0.172 -9999 0 -0.436 10 10
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.031 0.155 -9999 0 -0.422 8 8
RAF1 -0.005 0.187 -9999 0 -0.652 3 3
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.022 0.162 -9999 0 -0.478 5 5
YWHAZ 0.01 0.085 -9999 0 -0.708 1 1
IGF-1R heterotetramer/IGF1/IRS1 -0.046 0.166 -9999 0 -0.464 8 8
PIK3CA 0.02 0 -9999 0 -9999 0 0
RPS6KB1 -0.028 0.207 -9999 0 -0.645 5 5
GNB2L1 0.01 0.085 -9999 0 -0.708 1 1
positive regulation of MAPKKK cascade -0.005 0.159 -9999 0 -0.534 3 3
PXN 0.02 0 -9999 0 -9999 0 0
PIK3R1 -0.038 0.194 -9999 0 -0.677 6 6
cell adhesion 0 0 -9999 0 -9999 0 0
GRB2/SOS1 0.022 0.065 -9999 0 -0.526 1 1
HRAS/GTP -0.054 0.124 -9999 0 -0.504 2 2
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.004 0.141 -9999 0 -0.595 1 1
IGF-1R heterotetramer -0.004 0.097 -9999 0 -0.783 1 1
IGF-1R heterotetramer/IGF1/IRS/Nck -0.03 0.156 -9999 0 -0.422 8 8
Crk/p130 Cas/Paxillin -0.017 0.16 -9999 0 -0.45 5 5
IGF1R -0.004 0.097 -9999 0 -0.784 1 1
IGF1 -0.085 0.234 -9999 0 -0.6 12 12
IRS2/Crk -0.06 0.192 -9999 0 -0.488 8 8
PI3K -0.048 0.213 -9999 0 -0.565 8 8
apoptosis 0.004 0.171 0.49 5 -9999 0 5
HRAS/GDP 0.015 0 -9999 0 -9999 0 0
PRKCD -0.03 0.178 -9999 0 -0.439 9 9
RAF1/14-3-3 E 0.01 0.162 -9999 0 -0.534 3 3
BAD/14-3-3 -0.006 0.182 -9999 0 -0.529 5 5
PRKCZ -0.039 0.206 -9999 0 -0.655 5 5
Crk/p130 Cas/Paxillin/FAK1 -0.07 0.161 -9999 0 -0.668 3 3
PTPN1 0.02 0 -9999 0 -9999 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.019 0.154 -9999 0 -0.44 6 6
BCAR1 0.02 0 -9999 0 -9999 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.064 0.198 -9999 0 -0.529 6 6
mol:GDP 0 0 -9999 0 -9999 0 0
SOS1 0.02 0 -9999 0 -9999 0 0
IRS1/NCK2 -0.03 0.154 -9999 0 -0.419 8 8
GRB10 -0.063 0.223 -9999 0 -0.646 9 9
PTPN11 -0.031 0.154 -9999 0 -0.42 8 8
IRS1 -0.046 0.165 -9999 0 -0.463 8 8
IRS2 -0.063 0.187 -9999 0 -0.459 10 10
IGF-1R heterotetramer/IGF1 -0.061 0.191 -9999 0 -0.52 8 8
GRB2 0.01 0.085 -9999 0 -0.708 1 1
PDPK1 -0.041 0.219 -9999 0 -0.696 5 5
YWHAE 0.02 0 -9999 0 -9999 0 0
PRKD1 -0.029 0.19 -9999 0 -0.535 6 6
SHC1 0.02 0 -9999 0 -9999 0 0
Insulin 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
CBL/APS/CAP -0.08 0.161 -9999 0 -0.641 3 3
TC10/GTP -0.039 0.12 -9999 0 -0.697 1 1
Insulin Receptor/Insulin/IRS1/Shp2 -0.019 0.164 -9999 0 -0.398 9 9
HRAS 0.02 0 -9999 0 -9999 0 0
APS homodimer 0 0 -9999 0 -9999 0 0
GRB14 -0.139 0.269 -9999 0 -0.582 19 19
FOXO3 -0.021 0.033 -9999 0 -9999 0 0
AKT1 -0.079 0.254 -9999 0 -0.599 9 9
INSR -0.067 0.24 -9999 0 -0.701 9 9
Insulin Receptor/Insulin 0.016 0.131 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
GRB10 -0.063 0.223 -9999 0 -0.646 9 9
SORBS1 -0.036 0.186 -9999 0 -0.646 6 6
CRK 0 0.12 -9999 0 -0.708 2 2
PTPN1 0.012 0.127 -9999 0 -9999 0 0
CAV1 -0.047 0.217 -9999 0 -0.531 10 10
CBL/APS/CAP/Crk-II/C3G -0.001 0.147 -9999 0 -0.44 6 6
Insulin Receptor/Insulin/IRS1/NCK2 -0.019 0.164 -9999 0 -0.398 9 9
mol:GDP 0 0 -9999 0 -9999 0 0
mol:PI-3-4-5-P3 -0.083 0.175 -9999 0 -0.524 6 6
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.029 0.231 -9999 0 -0.62 9 9
RPS6KB1 -0.06 0.231 -9999 0 -0.529 9 9
PARD6A -0.018 0.138 -9999 0 -0.523 5 5
CBL 0.02 0 -9999 0 -9999 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -9999 0 0
DOK1 0.013 0.03 -9999 0 -9999 0 0
PIK3R1 -0.038 0.194 -9999 0 -0.677 6 6
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.121 0.205 -9999 0 -0.552 9 9
HRAS/GTP -0.051 0.12 -9999 0 -0.548 2 2
Insulin Receptor -0.067 0.239 -9999 0 -0.7 9 9
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.012 0.172 -9999 0 -0.667 2 2
PRKCI -0.088 0.228 -9999 0 -0.831 6 6
Insulin Receptor/Insulin/GRB14/PDK1 -0.148 0.245 -9999 0 -0.608 12 12
SHC1 0.02 0 -9999 0 -9999 0 0
negative regulation of MAPKKK cascade 0.007 0.056 -9999 0 -0.395 1 1
PI3K -0.085 0.178 -9999 0 -0.535 6 6
NCK2 0.02 0 -9999 0 -9999 0 0
RHOQ 0.02 0 -9999 0 -9999 0 0
mol:H2O2 -0.005 0.014 -9999 0 -9999 0 0
HRAS/GDP 0.015 0 -9999 0 -9999 0 0
AKT2 -0.079 0.254 -9999 0 -0.599 9 9
PRKCZ -0.092 0.23 -9999 0 -0.839 6 6
SH2B2 0 0 -9999 0 -9999 0 0
SHC/SHIP -0.019 0.144 -9999 0 -0.352 9 9
F2RL2 0.02 0 -9999 0 -9999 0 0
TRIP10 -0.041 0.201 -9999 0 -0.708 6 6
Insulin Receptor/Insulin/Shc -0.01 0.139 -9999 0 -0.378 9 9
TC10/GTP/CIP4/Exocyst -0.013 0.133 -9999 0 -0.455 6 6
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.009 0.152 -9999 0 -0.729 1 1
RAPGEF1 0.01 0.085 -9999 0 -0.708 1 1
RASA1 0.02 0 -9999 0 -9999 0 0
NCK1 0.01 0.085 -9999 0 -0.708 1 1
CBL/APS/CAP/Crk-II -0.007 0.131 -9999 0 -0.407 6 6
TC10/GDP 0.015 0 -9999 0 -9999 0 0
Insulin Receptor/Insulin/SHC/GRB10 -0.045 0.244 -9999 0 -0.777 6 6
INPP5D -0.033 0.151 -9999 0 -0.382 9 9
SOS1 0.02 0 -9999 0 -9999 0 0
SGK1 -0.012 0.018 -9999 0 -9999 0 0
mol:cAMP 0 0 -9999 0 -9999 0 0
PTPN11 0.02 0 -9999 0 -9999 0 0
IRS1 -0.018 0.138 -9999 0 -0.523 5 5
p62DOK/RasGAP 0.007 0.057 -9999 0 -0.398 1 1
INS 0.019 0.011 -9999 0 -9999 0 0
mol:PI-3-4-P2 -0.032 0.149 -9999 0 -0.378 9 9
GRB2 0.01 0.085 -9999 0 -0.708 1 1
EIF4EBP1 -0.098 0.296 -9999 0 -0.654 13 13
PTPRA 0.019 0.011 -9999 0 -9999 0 0
PIK3CA 0.02 0 -9999 0 -9999 0 0
TC10/GTP/CIP4 -0.013 0.133 -9999 0 -0.455 6 6
PDPK1 0.01 0.085 -9999 0 -0.708 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.004 0.153 -9999 0 -0.632 2 2
Insulin Receptor/Insulin/IRS1 -0.032 0.163 -9999 0 -0.409 9 9
Insulin Receptor/Insulin/IRS3 -0.035 0.183 -9999 0 -0.519 9 9
Par3/Par6 -0.007 0.153 -9999 0 -0.462 6 6
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.006 0.172 -9999 0 -0.5 6 6
adherens junction organization -0.041 0.195 -9999 0 -0.511 7 7
mol:GTP 0 0 -9999 0 -9999 0 0
Rac1/GDP -0.052 0.214 -9999 0 -0.622 5 5
FMN1 -0.025 0.166 -9999 0 -0.59 3 3
mol:IP3 -0.015 0.166 -9999 0 -0.488 6 6
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.026 0.175 -9999 0 -0.623 3 3
CTNNB1 0.021 0.004 -9999 0 -9999 0 0
AKT1 -0.009 0.171 -9999 0 -0.493 6 6
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.041 0.206 -9999 0 -0.57 7 7
CTNND1 -0.021 0.168 -9999 0 -0.715 4 4
mol:PI-4-5-P2 -0.013 0.163 -9999 0 -0.563 3 3
VASP -0.018 0.168 -9999 0 -0.581 3 3
ZYX -0.021 0.169 -9999 0 -0.581 3 3
JUB -0.08 0.258 -9999 0 -0.644 10 10
EGFR(dimer) -0.079 0.234 -9999 0 -0.701 6 6
E-cadherin/beta catenin-gamma catenin -0.07 0.167 -9999 0 -0.487 7 7
mol:PI-3-4-5-P3 -0.022 0.179 -9999 0 -0.53 6 6
PIK3CA 0.019 0.004 -9999 0 -9999 0 0
PI3K -0.023 0.184 -9999 0 -0.545 6 6
FYN -0.099 0.268 -9999 0 -0.655 11 11
mol:Ca2+ -0.014 0.162 -9999 0 -0.475 6 6
JUP 0.011 0.086 -9999 0 -0.71 1 1
PIK3R1 -0.038 0.196 -9999 0 -0.684 6 6
mol:DAG -0.015 0.166 -9999 0 -0.488 6 6
CDH1 -0.097 0.25 -9999 0 -0.624 13 13
RhoA/GDP -0.057 0.216 -9999 0 -0.622 5 5
establishment of polarity of embryonic epithelium -0.016 0.164 -9999 0 -0.563 3 3
SRC 0.02 0 -9999 0 -9999 0 0
RAC1 0.02 0 -9999 0 -9999 0 0
RHOA 0.01 0.085 -9999 0 -0.708 1 1
EGFR -0.106 0.26 -9999 0 -0.629 14 14
CASR -0.058 0.187 -9999 0 -0.523 6 6
RhoA/GTP -0.058 0.13 -9999 0 -0.444 5 5
AKT2 -0.009 0.171 -9999 0 -0.493 6 6
actin cable formation -0.017 0.163 -9999 0 -0.564 3 3
apoptosis 0.011 0.17 0.494 6 -9999 0 6
CTNNA1 0.019 0.006 -9999 0 -9999 0 0
mol:GDP -0.068 0.23 -9999 0 -0.571 9 9
PIP5K1A -0.014 0.167 -9999 0 -0.581 3 3
PLCG1 -0.016 0.17 -9999 0 -0.501 6 6
Rac1/GTP -0.108 0.187 -9999 0 -0.628 6 6
homophilic cell adhesion 0 0.005 -9999 0 -9999 0 0
FOXM1 transcription factor 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
NFATC3 0.18 0.509 -9999 0 -1.119 4 4
PLK1 0.096 0.075 -9999 0 -9999 0 0
BIRC5 0.07 0.152 -9999 0 -0.515 1 1
HSPA1B 0.167 0.507 -9999 0 -1.008 6 6
MAP2K1 0.074 0.055 -9999 0 -9999 0 0
BRCA2 0.173 0.528 -9999 0 -1.241 4 4
FOXM1 0.161 0.597 -9999 0 -1.484 4 4
XRCC1 0.174 0.525 -9999 0 -1.227 4 4
FOXM1B/p19 -0.189 0.373 -9999 0 -1.099 8 8
Cyclin D1/CDK4 0.023 0.668 -9999 0 -1.098 14 14
CDC2 0.181 0.534 -9999 0 -1.193 4 4
TGFA 0.036 0.677 -9999 0 -1.124 15 15
SKP2 0.18 0.509 -9999 0 -1.119 4 4
CCNE1 0.031 0.013 -9999 0 -9999 0 0
CKS1B 0.18 0.509 -9999 0 -1.119 4 4
RB1 -0.092 0.141 -9999 0 -9999 0 0
FOXM1C/SP1 0.131 0.57 -9999 0 -1.425 4 4
AURKB 0.096 0.075 -9999 0 -9999 0 0
CENPF 0.148 0.561 -9999 0 -1.223 6 6
CDK4 0.037 0.028 -9999 0 -9999 0 0
MYC 0.125 0.557 -9999 0 -1.055 8 8
CHEK2 0.056 0.134 -9999 0 -0.666 2 2
ONECUT1 0.081 0.609 -9999 0 -1.066 10 10
CDKN2A -0.051 0.191 -9999 0 -0.681 6 6
LAMA4 0.166 0.544 -9999 0 -1.235 5 5
FOXM1B/HNF6 0.04 0.703 -9999 0 -1.347 10 10
FOS 0.035 0.672 -9999 0 -1.21 13 13
SP1 0.021 0.006 -9999 0 -9999 0 0
CDC25B 0.18 0.509 -9999 0 -1.119 4 4
response to radiation 0.044 0.054 -9999 0 -9999 0 0
CENPB 0.18 0.509 -9999 0 -1.119 4 4
CENPA 0.165 0.528 -9999 0 -1.121 5 5
NEK2 0.151 0.555 -9999 0 -1.155 6 6
HIST1H2BA 0.176 0.508 -9999 0 -1.119 4 4
CCNA2 0.031 0.013 -9999 0 -9999 0 0
EP300 0.01 0.085 -9999 0 -0.708 1 1
CCNB1/CDK1 0.165 0.562 -9999 0 -1.358 4 4
CCNB2 0.158 0.557 -9999 0 -1.22 6 6
CCNB1 0.179 0.538 -9999 0 -1.215 4 4
ETV5 0.177 0.512 -9999 0 -1.119 4 4
ESR1 0.166 0.543 -9999 0 -1.233 5 5
CCND1 0.021 0.704 -9999 0 -1.164 14 14
GSK3A 0.056 0.107 -9999 0 -0.746 1 1
Cyclin A-E1/CDK1-2 0.084 0.06 -9999 0 -9999 0 0
CDK2 0.031 0.013 -9999 0 -9999 0 0
G2/M transition of mitotic cell cycle 0.053 0.061 -9999 0 -9999 0 0
FOXM1B/Cbp/p300 -0.152 0.348 -9999 0 -1.113 6 6
GAS1 0.156 0.537 -9999 0 -1.063 6 6
MMP2 0.171 0.517 -9999 0 -1.158 4 4
RB1/FOXM1C 0.073 0.618 -9999 0 -1.07 10 10
CREBBP 0.02 0 -9999 0 -9999 0 0
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.005 0.086 -9999 0 -0.717 1 1
HSPA8 0.022 0.003 -9999 0 -9999 0 0
SMAD3/SMAD4/ER alpha -0.001 0.17 -9999 0 -0.583 4 4
AKT1 0.023 0.013 -9999 0 -9999 0 0
GSC 0.041 0.059 -9999 0 -9999 0 0
NKX2-5 0.013 0.027 -9999 0 -9999 0 0
muscle cell differentiation 0.071 0.207 0.723 4 -9999 0 4
SMAD2-3/SMAD4/SP1 0.037 0.183 -9999 0 -0.667 3 3
SMAD4 0.006 0.111 -9999 0 -0.431 3 3
CBFB 0.02 0 -9999 0 -9999 0 0
SAP18 0.021 0.001 -9999 0 -9999 0 0
Cbp/p300/MSG1 0.013 0.092 -9999 0 -0.471 2 2
SMAD3/SMAD4/VDR -0.092 0.19 -9999 0 -0.548 5 5
MYC -0.062 0.219 -9999 0 -0.679 8 8
CDKN2B 0.025 0.248 -9999 0 -1.412 2 2
AP1 -0.128 0.389 -9999 0 -0.916 12 12
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.062 0.141 -9999 0 -0.917 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.04 0.131 -9999 0 -0.531 2 2
SP3 0.024 0.001 -9999 0 -9999 0 0
CREB1 0.01 0.085 -9999 0 -0.708 1 1
FOXH1 0.017 0.027 -9999 0 -9999 0 0
SMAD3/SMAD4/GR -0.01 0.126 -9999 0 -0.518 3 3
GATA3 0.001 0.124 -9999 0 -0.508 4 4
SKI/SIN3/HDAC complex/NCoR1 0.056 0.076 -9999 0 -0.387 1 1
MEF2C/TIF2 -0.013 0.265 -9999 0 -0.66 10 10
endothelial cell migration 0.197 0.454 1.498 7 -9999 0 7
MAX 0.025 0.017 -9999 0 -9999 0 0
RBBP7 0.021 0.001 -9999 0 -9999 0 0
RBBP4 0.021 0.001 -9999 0 -9999 0 0
RUNX2 0.02 0 -9999 0 -9999 0 0
RUNX3 -0.142 0.293 -9999 0 -0.665 17 17
RUNX1 -0.111 0.259 -9999 0 -0.61 15 15
CTBP1 0.02 0 -9999 0 -9999 0 0
NR3C1 0.025 0.017 -9999 0 -9999 0 0
VDR -0.139 0.279 -9999 0 -0.616 18 18
CDKN1A 0.005 0.269 -9999 0 -1.14 3 3
KAT2B -0.003 0.006 -9999 0 -9999 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.032 0.109 -9999 0 -9999 0 0
DCP1A 0.02 0 -9999 0 -9999 0 0
SKI 0.021 0.001 -9999 0 -9999 0 0
SERPINE1 -0.202 0.463 -9999 0 -1.532 7 7
SMAD3/SMAD4/ATF2 -0.013 0.127 -9999 0 -0.529 3 3
SMAD3/SMAD4/ATF3 -0.051 0.161 -9999 0 -0.439 7 7
SAP30 -0.02 0.167 -9999 0 -0.707 4 4
Cbp/p300/PIAS3 0.022 0.06 -9999 0 -0.459 1 1
JUN -0.127 0.384 -9999 0 -0.908 12 12
SMAD3/SMAD4/IRF7 -0.015 0.125 -9999 0 -0.521 3 3
TFE3 0.013 0.039 -9999 0 -9999 0 0
COL1A2 -0.16 0.332 -9999 0 -0.7 15 15
mesenchymal cell differentiation 0.017 0.125 0.527 3 -9999 0 3
DLX1 0.012 0.064 -9999 0 -0.523 1 1
TCF3 0.01 0.085 -9999 0 -0.708 1 1
FOS -0.161 0.303 -9999 0 -0.637 20 20
SMAD3/SMAD4/Max -0.01 0.126 -9999 0 -0.518 3 3
Cbp/p300/SNIP1 0.025 0.059 -9999 0 -0.454 1 1
ZBTB17 0.017 0.003 -9999 0 -9999 0 0
LAMC1 -0.01 0.277 -9999 0 -0.894 6 6
TGIF2/HDAC complex/SMAD3/SMAD4 -0.013 0.127 -9999 0 -0.529 3 3
IRF7 0.026 0.001 -9999 0 -9999 0 0
ESR1 0.007 0.118 -9999 0 -0.683 2 2
HNF4A 0.01 0.085 -9999 0 -0.708 1 1
MEF2C -0.021 0.278 -9999 0 -0.704 10 10
SMAD2-3/SMAD4 -0.019 0.144 -9999 0 -0.596 3 3
Cbp/p300/Src-1 0.024 0.059 -9999 0 -0.456 1 1
IGHV3OR16-13 -0.046 0.138 -9999 0 -1.139 1 1
TGIF2/HDAC complex 0.02 0 -9999 0 -9999 0 0
CREBBP 0.015 0.008 -9999 0 -9999 0 0
SKIL 0.01 0.085 -9999 0 -0.708 1 1
HDAC1 0.011 0.085 -9999 0 -0.708 1 1
HDAC2 0.021 0.001 -9999 0 -9999 0 0
SNIP1 0.021 0.002 -9999 0 -9999 0 0
GCN5L2 -0.015 0.145 -9999 0 -0.708 3 3
SMAD3/SMAD4/TFE3 0.014 0.189 -9999 0 -0.622 4 4
MSG1/HSC70 0.019 0.079 -9999 0 -0.444 2 2
SMAD2 0.019 0.033 -9999 0 -9999 0 0
SMAD3 0.01 0.128 -9999 0 -0.612 2 2
SMAD3/E2F4-5/DP1/p107/SMAD4 0.037 0.109 -9999 0 -0.406 2 2
SMAD2/SMAD2/SMAD4 -0.005 0.062 -9999 0 -0.377 1 1
NCOR1 0.021 0.001 -9999 0 -9999 0 0
NCOA2 0.012 0.064 -9999 0 -0.523 1 1
NCOA1 0.02 0 -9999 0 -9999 0 0
MYOD/E2A 0.007 0.111 -9999 0 -0.526 3 3
SMAD2-3/SMAD4/SP1/MIZ-1 0.052 0.182 -9999 0 -0.646 3 3
IFNB1 0.047 0.124 -9999 0 -0.654 1 1
SMAD3/SMAD4/MEF2C -0.02 0.319 -9999 0 -0.776 10 10
CITED1 0.003 0.106 -9999 0 -0.617 2 2
SMAD2-3/SMAD4/ARC105 0.04 0.147 -9999 0 -0.621 2 2
RBL1 0.02 0 -9999 0 -9999 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.04 0.187 -9999 0 -0.931 2 2
RUNX1-3/PEBPB2 -0.144 0.285 -9999 0 -0.621 15 15
SMAD7 -0.066 0.339 -9999 0 -0.867 8 8
MYC/MIZ-1 -0.048 0.158 -9999 0 -0.535 6 6
SMAD3/SMAD4 -0.091 0.216 -9999 0 -0.61 7 7
IL10 0.03 0.197 -9999 0 -0.94 2 2
PIASy/HDAC complex 0.017 0.065 -9999 0 -0.522 1 1
PIAS3 0.018 0.004 -9999 0 -9999 0 0
CDK2 0.015 0.008 -9999 0 -9999 0 0
IL5 0.036 0.171 -9999 0 -0.62 3 3
CDK4 0.015 0.008 -9999 0 -9999 0 0
PIAS4 0.017 0.065 -9999 0 -0.523 1 1
ATF3 -0.04 0.171 -9999 0 -0.523 8 8
SMAD3/SMAD4/SP1 0.011 0.174 -9999 0 -0.664 3 3
FOXG1 -0.006 0.123 -9999 0 -0.587 3 3
FOXO3 0.038 0.018 -9999 0 -9999 0 0
FOXO1 0.004 0.112 -9999 0 -0.361 6 6
FOXO4 0.037 0.019 -9999 0 -9999 0 0
heart looping -0.02 0.274 -9999 0 -0.694 10 10
CEBPB 0.006 0.089 -9999 0 -0.521 2 2
SMAD3/SMAD4/DLX1 -0.017 0.145 -9999 0 -0.626 3 3
MYOD1 0 0.12 -9999 0 -0.708 2 2
SMAD3/SMAD4/HNF4 -0.021 0.136 -9999 0 -0.51 4 4
SMAD3/SMAD4/GATA3 -0.032 0.174 -9999 0 -0.573 5 5
SnoN/SIN3/HDAC complex/NCoR1 0.01 0.085 -9999 0 -0.707 1 1
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.118 0.329 -9999 0 -0.708 13 13
SMAD3/SMAD4/SP1-3 0.035 0.159 -9999 0 -0.586 3 3
MED15 0.02 0 -9999 0 -9999 0 0
SP1 0.006 0.05 -9999 0 -9999 0 0
SIN3B 0.021 0.001 -9999 0 -9999 0 0
SIN3A 0.01 0.085 -9999 0 -0.708 1 1
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.028 0.153 -9999 0 -0.404 3 3
ITGB5 0.044 0.144 -9999 0 -0.594 2 2
TGIF/SIN3/HDAC complex/CtBP 0.041 0.143 -9999 0 -0.694 2 2
SMAD3/SMAD4/AR -0.091 0.255 -9999 0 -0.613 12 12
AR -0.101 0.271 -9999 0 -0.708 12 12
negative regulation of cell growth 0.029 0.131 -9999 0 -0.474 2 2
SMAD3/SMAD4/MYOD -0.027 0.144 -9999 0 -0.493 5 5
E2F5 -0.013 0.136 -9999 0 -0.57 4 4
E2F4 0.02 0 -9999 0 -9999 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.039 0.118 -9999 0 -0.603 1 1
SMAD2-3/SMAD4/FOXO1-3a-4 0.043 0.141 -9999 0 -0.6 2 2
TFDP1 0.02 0 -9999 0 -9999 0 0
SMAD3/SMAD4/AP1 -0.128 0.401 -9999 0 -0.937 12 12
SMAD3/SMAD4/RUNX2 -0.013 0.127 -9999 0 -0.529 3 3
TGIF2 0.02 0 -9999 0 -9999 0 0
TGIF1 0 0.12 -9999 0 -0.708 2 2
ATF2 0.02 0 -9999 0 -9999 0 0
Coregulation of Androgen receptor activity

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
NRIP1 -0.05 0.217 -9999 0 -0.711 7 7
SVIL 0.001 0.121 -9999 0 -0.716 2 2
ZNF318 0.011 0.089 -9999 0 -0.712 1 1
JMJD2C 0.02 0.086 -9999 0 -0.706 1 1
T-DHT/AR/Ubc9 -0.088 0.214 -9999 0 -0.547 12 12
CARM1 0.02 0.001 -9999 0 -9999 0 0
PRDX1 0.02 0.001 -9999 0 -9999 0 0
PELP1 0.02 0.003 -9999 0 -9999 0 0
CTNNB1 0.02 0.005 -9999 0 -9999 0 0
AKT1 0.02 0.006 -9999 0 -9999 0 0
PTK2B 0.021 0.002 -9999 0 -9999 0 0
MED1 0.009 0.085 -9999 0 -0.709 1 1
MAK 0.021 0.023 -9999 0 -9999 0 0
response to oxidative stress 0 0.001 -9999 0 -9999 0 0
HIP1 0.001 0.123 -9999 0 -0.728 2 2
GSN -0.02 0.167 -9999 0 -0.706 4 4
NCOA2 0.013 0.064 -9999 0 -0.523 1 1
NCOA6 0.011 0.085 -9999 0 -0.707 1 1
DNA-PK 0.008 0.031 -9999 0 -9999 0 0
NCOA4 0 0.12 -9999 0 -0.708 2 2
PIAS3 0.02 0.005 -9999 0 -9999 0 0
cell proliferation -0.018 0.031 -9999 0 -9999 0 0
XRCC5 0.02 0.005 -9999 0 -9999 0 0
UBE3A 0.021 0.01 -9999 0 -9999 0 0
T-DHT/AR/SNURF -0.102 0.213 -9999 0 -0.558 12 12
FHL2 -0.234 0.47 -9999 0 -0.898 20 20
RANBP9 0.021 0.006 -9999 0 -9999 0 0
JMJD1A -0.009 0.101 -9999 0 -0.741 1 1
CDK6 -0.01 0.145 -9999 0 -0.707 3 3
TGFB1I1 -0.01 0.145 -9999 0 -0.706 3 3
T-DHT/AR/CyclinD1 -0.189 0.332 -9999 0 -0.643 22 22
XRCC6 0.02 0.005 -9999 0 -9999 0 0
T-DHT/AR -0.118 0.258 -9999 0 -0.559 15 15
CTDSP1 0.02 0.003 -9999 0 -9999 0 0
CTDSP2 0.01 0.086 -9999 0 -0.71 1 1
BRCA1 0.021 0.006 -9999 0 -9999 0 0
TCF4 -0.089 0.255 -9999 0 -0.688 11 11
CDKN2A -0.038 0.193 -9999 0 -0.674 6 6
SRF 0.004 0.049 -9999 0 -9999 0 0
NKX3-1 -0.099 0.164 -9999 0 -0.424 8 8
KLK3 0.007 0.126 -9999 0 -9999 0 0
TMF1 0.01 0.085 -9999 0 -0.708 1 1
HNRNPA1 0.021 0.009 -9999 0 -9999 0 0
AOF2 0.021 0.006 -9999 0 -9999 0 0
APPL1 0.034 0.012 -9999 0 -9999 0 0
T-DHT/AR/Caspase 8 -0.089 0.213 -9999 0 -0.546 12 12
AR -0.126 0.29 -9999 0 -0.768 12 12
UBA3 0 0.003 -9999 0 -9999 0 0
PATZ1 0.021 0.009 -9999 0 -9999 0 0
PAWR 0.01 0.085 -9999 0 -0.708 1 1
PRKDC 0.02 0.005 -9999 0 -9999 0 0
PA2G4 0.02 0.008 -9999 0 -9999 0 0
UBE2I 0.02 0 -9999 0 -9999 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.081 0.198 -9999 0 -0.505 12 12
RPS6KA3 0.021 0.006 -9999 0 -9999 0 0
T-DHT/AR/ARA70 -0.101 0.224 -9999 0 -0.538 14 14
LATS2 0.01 0.086 -9999 0 -0.709 1 1
T-DHT/AR/PRX1 -0.082 0.197 -9999 0 -0.505 12 12
Cyclin D3/CDK11 p58 0.015 0.001 -9999 0 -9999 0 0
VAV3 -0.017 0.157 -9999 0 -0.661 4 4
KLK2 -0.028 0.186 -9999 0 -0.822 3 3
CASP8 0.02 0.002 -9999 0 -9999 0 0
T-DHT/AR/TIF2/CARM1 -0.072 0.203 -9999 0 -0.483 13 13
TMPRSS2 -0.215 0.393 -9999 0 -0.832 17 17
CCND1 -0.142 0.304 -9999 0 -0.71 16 16
PIAS1 0.021 0.01 -9999 0 -9999 0 0
mol:T-DHT -0.023 0.038 -9999 0 -0.08 14 14
CDC2L1 0 0 -9999 0 -9999 0 0
PIAS4 0.012 0.066 -9999 0 -0.518 1 1
T-DHT/AR/CDK6 -0.107 0.241 -9999 0 -0.57 14 14
CMTM2 0.02 0 -9999 0 -9999 0 0
SNURF 0 0 -9999 0 -9999 0 0
ZMIZ1 0.002 0.033 -9999 0 -9999 0 0
CCND3 0.02 0 -9999 0 -9999 0 0
TGIF1 0 0.118 -9999 0 -0.695 2 2
FKBP4 0.021 0.006 -9999 0 -9999 0 0
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) -0.099 0.259 -9999 0 -0.744 9 9
HDAC1 0.015 0.085 -9999 0 -0.673 1 1
AES 0.023 0.012 -9999 0 -9999 0 0
FBXW11 0.02 0 -9999 0 -9999 0 0
DTX1 0.02 0 -9999 0 -9999 0 0
LRP6/FZD1 -0.055 0.2 -9999 0 -0.527 11 11
TLE1 0.005 0.103 -9999 0 -0.6 2 2
AP1 -0.066 0.166 -9999 0 -0.376 12 12
NCSTN 0.02 0 -9999 0 -9999 0 0
ADAM10 0.002 0.105 -9999 0 -0.615 2 2
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.032 0.194 -9999 0 -0.633 4 4
NICD/RBPSUH -0.059 0.268 -9999 0 -0.745 9 9
WIF1 0.005 0.089 -9999 0 -0.524 2 2
NOTCH1 -0.102 0.252 -9999 0 -0.752 9 9
PSENEN 0.02 0 -9999 0 -9999 0 0
KREMEN2 -0.013 0.136 -9999 0 -0.57 4 4
DKK1 -0.043 0.179 -9999 0 -0.547 8 8
beta catenin/beta TrCP1 0.028 0.057 -9999 0 -9999 0 0
APH1B 0.01 0.085 -9999 0 -0.708 1 1
APH1A -0.021 0.167 -9999 0 -0.708 4 4
AXIN1 -0.015 0.08 -9999 0 -0.267 1 1
CtBP/CBP/TCF1/TLE1/AES 0.05 0.095 0.306 4 -9999 0 4
PSEN1 0.01 0.085 -9999 0 -0.709 1 1
FOS -0.157 0.289 -9999 0 -0.616 20 20
JUN -0.094 0.256 -9999 0 -0.662 12 12
MAP3K7 0.022 0.009 -9999 0 -9999 0 0
CTNNB1 0.016 0.06 -9999 0 -9999 0 0
MAPK3 0.02 0 -9999 0 -9999 0 0
DKK2/LRP6/Kremen 2 0.015 0.095 -9999 0 -0.444 1 1
HNF1A -0.015 0.153 -9999 0 -0.642 4 4
CTBP1 0.023 0.012 -9999 0 -9999 0 0
MYC -0.157 0.515 -9999 0 -1.611 8 8
NKD1 0.013 0.064 -9999 0 -0.525 1 1
FZD1 -0.091 0.262 -9999 0 -0.709 11 11
NOTCH1 precursor/Deltex homolog 1 -0.054 0.253 -9999 0 -0.704 9 9
apoptosis -0.066 0.165 -9999 0 -0.374 12 12
Delta 1/NOTCHprecursor -0.059 0.273 -9999 0 -0.741 9 9
DLL1 0.01 0.085 -9999 0 -0.708 1 1
PPARD 0.013 0.048 -9999 0 -9999 0 0
Gamma Secretase 0.017 0.117 -9999 0 -9999 0 0
APC -0.037 0.181 0.23 1 -0.929 2 3
DVL1 -0.01 0.023 -9999 0 -9999 0 0
CSNK2A1 0.019 0.003 -9999 0 -9999 0 0
MAP3K7IP1 0.012 0.086 -9999 0 -0.711 1 1
DKK1/LRP6/Kremen 2 -0.02 0.137 -9999 0 -0.444 2 2
LRP6 0.02 0 -9999 0 -9999 0 0
CSNK1A1 0.019 0.003 -9999 0 -9999 0 0
NLK 0.037 0.056 -9999 0 -0.395 1 1
CCND1 -0.323 0.671 -9999 0 -1.578 16 16
WNT1 0.02 0 -9999 0 -9999 0 0
Axin1/APC/beta catenin 0.005 0.146 -9999 0 -0.802 1 1
DKK2 0.012 0.064 -9999 0 -0.523 1 1
NOTCH1 precursor/DVL1 -0.088 0.228 -9999 0 -0.676 9 9
GSK3B 0.02 0.002 -9999 0 -9999 0 0
FRAT1 0.006 0.089 -9999 0 -0.518 2 2
NOTCH/Deltex homolog 1 -0.094 0.238 -9999 0 -0.708 9 9
PPP2R5D -0.006 0.042 0.27 1 -9999 0 1
MAPK1 0.02 0 -9999 0 -9999 0 0
WNT1/LRP6/FZD1 -0.029 0.166 -9999 0 -0.4 11 11
RBPJ 0.01 0.085 -9999 0 -0.708 1 1
CREBBP 0.02 0.011 -9999 0 -9999 0 0
Glucocorticoid receptor regulatory network

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
PCK2 -0.013 0.131 -9999 0 -0.698 2 2
SMARCC2 0.02 0 -9999 0 -9999 0 0
SMARCC1 0.02 0 -9999 0 -9999 0 0
TBX21 -0.148 0.36 -9999 0 -0.782 16 16
SUMO2 0.018 0.01 -9999 0 -9999 0 0
STAT1 (dimer) -0.09 0.257 -9999 0 -0.607 12 12
FKBP4 0.02 0 -9999 0 -9999 0 0
FKBP5 -0.116 0.258 -9999 0 -0.593 16 16
GR alpha/HSP90/FKBP51/HSP90 -0.057 0.176 0.301 1 -0.435 6 7
PRL 0.021 0.094 -9999 0 -9999 0 0
cortisol/GR alpha (dimer)/TIF2 0.07 0.202 0.538 6 -9999 0 6
RELA -0.075 0.108 -9999 0 -9999 0 0
FGG 0.017 0.234 0.477 4 -0.583 1 5
GR beta/TIF2 0.036 0.096 0.315 2 -9999 0 2
IFNG -0.326 0.474 -9999 0 -1.215 11 11
apoptosis -0.05 0.209 0.505 3 -0.651 2 5
CREB1 0.014 0.109 -9999 0 -0.837 1 1
histone acetylation -0.013 0.111 -9999 0 -0.422 3 3
BGLAP 0.012 0.089 -9999 0 -9999 0 0
GR/PKAc 0.025 0.103 0.298 1 -9999 0 1
NF kappa B1 p50/RelA -0.134 0.202 -9999 0 -0.482 8 8
SMARCD1 0.01 0.085 -9999 0 -0.708 1 1
MDM2 0.033 0.073 0.245 3 -9999 0 3
GATA3 0.013 0.125 -9999 0 -0.502 4 4
AKT1 0.009 0.031 0.248 1 -9999 0 1
CSF2 -0.006 0.092 -9999 0 -9999 0 0
GSK3B 0.018 0.01 -9999 0 -9999 0 0
NR1I3 -0.002 0.204 -9999 0 -0.624 1 1
CSN2 0.061 0.142 0.397 3 -9999 0 3
BRG1/BAF155/BAF170/BAF60A 0.041 0.063 -9999 0 -0.396 1 1
NFATC1 -0.026 0.201 -9999 0 -0.695 6 6
POU2F1 0.031 0 -9999 0 -9999 0 0
CDKN1A 0.004 0.277 -9999 0 -1.6 2 2
response to stress 0 0 -9999 0 -9999 0 0
response to UV -0.001 0.01 -9999 0 -9999 0 0
SFN -0.025 0.15 -9999 0 -0.523 6 6
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.066 0.163 -9999 0 -0.414 4 4
prolactin receptor activity 0 0 -9999 0 -9999 0 0
EGR1 -0.098 0.341 -9999 0 -0.892 7 7
JUN -0.118 0.246 -9999 0 -0.677 8 8
IL4 -0.029 0.175 -9999 0 -0.691 2 2
CDK5R1 0.019 0.005 -9999 0 -9999 0 0
PRKACA 0.02 0 -9999 0 -9999 0 0
cortisol/GR alpha (monomer)/AP-1 -0.175 0.275 -9999 0 -0.628 14 14
GR alpha/HSP90/FKBP51/HSP90/PP5C -0.048 0.172 -9999 0 -0.443 5 5
cortisol/GR alpha (monomer) 0.072 0.237 0.628 6 -9999 0 6
NCOA2 0.012 0.064 -9999 0 -0.523 1 1
response to hypoxia 0 0 -9999 0 -9999 0 0
FOS -0.177 0.279 -9999 0 -0.609 20 20
AP-1/NFAT1-c-4 -0.25 0.374 -9999 0 -0.892 13 13
AFP -0.077 0.251 -9999 0 -0.766 5 5
SUV420H1 0.02 0 -9999 0 -9999 0 0
IRF1 -0.138 0.382 -9999 0 -0.96 11 11
TP53 0.028 0.119 -9999 0 -0.535 3 3
PPP5C 0.01 0.085 -9999 0 -0.708 1 1
KRT17 -0.135 0.239 -9999 0 -0.81 5 5
KRT14 -0.003 0.077 -9999 0 -9999 0 0
TBP 0.034 0.001 -9999 0 -9999 0 0
CREBBP 0 0 -9999 0 -9999 0 0
HDAC1 -0.005 0.084 -9999 0 -0.715 1 1
HDAC2 0.017 0 -9999 0 -9999 0 0
AP-1 -0.251 0.377 -9999 0 -0.899 13 13
MAPK14 0.018 0.01 -9999 0 -9999 0 0
MAPK10 -0.09 0.226 -9999 0 -0.565 13 13
MAPK11 0.018 0.01 -9999 0 -9999 0 0
KRT5 -0.13 0.223 -9999 0 -0.777 4 4
interleukin-1 receptor activity -0.003 0 -9999 0 -9999 0 0
NCOA1 0.021 0.02 -9999 0 -9999 0 0
STAT1 -0.09 0.257 -9999 0 -0.607 12 12
CGA -0.018 0.199 -9999 0 -0.814 3 3
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.01 0.083 -9999 0 -9999 0 0
MAPK3 0.016 0.013 -9999 0 -9999 0 0
MAPK1 0.018 0.01 -9999 0 -9999 0 0
ICAM1 -0.248 0.47 -9999 0 -1.207 12 12
NFKB1 -0.075 0.108 -9999 0 -9999 0 0
MAPK8 -0.019 0.118 -9999 0 -0.374 2 2
MAPK9 -0.002 0.119 -9999 0 -0.705 2 2
cortisol/GR alpha (dimer) -0.057 0.213 0.508 3 -0.689 2 5
BAX 0.038 0.088 -9999 0 -9999 0 0
POMC -0.073 0.258 -9999 0 -0.912 4 4
EP300 -0.01 0.084 -9999 0 -0.719 1 1
cortisol/GR alpha (dimer)/p53 0.07 0.202 0.542 5 -9999 0 5
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.056 -9999 0 -9999 0 0
SGK1 0.023 0.046 -9999 0 -0.246 1 1
IL13 -0.078 0.179 -9999 0 -0.608 1 1
IL6 -0.267 0.413 -9999 0 -0.997 12 12
PRKACG 0.02 0 -9999 0 -9999 0 0
IL5 -0.065 0.143 -9999 0 -9999 0 0
IL2 -0.159 0.318 -9999 0 -1.097 5 5
CDK5 0.012 0.064 -9999 0 -0.523 1 1
PRKACB -0.02 0.149 -9999 0 -0.56 5 5
HSP90AA1 0.005 0.089 -9999 0 -0.523 2 2
IL8 -0.275 0.426 -9999 0 -0.972 15 15
CDK5R1/CDK5 0.017 0.049 -9999 0 -0.366 1 1
NF kappa B1 p50/RelA/PKAc -0.079 0.186 -9999 0 -0.522 4 4
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.073 0.184 0.511 5 -9999 0 5
SMARCA4 0.012 0.064 -9999 0 -0.523 1 1
chromatin remodeling 0.063 0.113 0.366 3 -9999 0 3
NF kappa B1 p50/RelA/Cbp -0.097 0.166 -9999 0 -0.477 3 3
JUN (dimer) -0.117 0.245 -9999 0 -0.674 8 8
YWHAH 0.02 0 -9999 0 -9999 0 0
VIPR1 0.002 0.095 -9999 0 -0.356 2 2
NR3C1 0.052 0.131 0.447 3 -9999 0 3
NR4A1 -0.046 0.181 -9999 0 -0.535 8 8
TIF2/SUV420H1 0.024 0.046 -9999 0 -0.366 1 1
MAPKKK cascade -0.05 0.209 0.505 3 -0.651 2 5
cortisol/GR alpha (dimer)/Src-1 0.078 0.197 0.541 5 -9999 0 5
PBX1 0.024 0.064 -9999 0 -0.512 1 1
POU1F1 0.014 0.106 -9999 0 -0.605 2 2
SELE -0.244 0.445 -9999 0 -1.302 9 9
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.061 0.113 0.366 3 -9999 0 3
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.073 0.184 0.511 5 -9999 0 5
mol:cortisol 0.031 0.137 0.338 7 -9999 0 7
MMP1 -0.27 0.496 -9999 0 -1.175 14 14
Reelin signaling 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
CDK5R1/CDK5 0.024 0.046 -9999 0 -0.366 1 1
VLDLR -0.033 0.161 -9999 0 -0.523 7 7
CRKL 0.02 0 -9999 0 -9999 0 0
LRPAP1 0.02 0 -9999 0 -9999 0 0
FYN -0.101 0.271 -9999 0 -0.708 12 12
ITGA3 -0.119 0.263 -9999 0 -0.604 16 16
RELN/VLDLR/Fyn -0.082 0.253 -9999 0 -0.611 12 12
MAPK8IP1/MKK7/MAP3K11/JNK1 0.034 0.11 -9999 0 -0.631 1 1
AKT1 0.004 0.13 -9999 0 -0.488 3 3
MAP2K7 -0.01 0.145 -9999 0 -0.708 3 3
RAPGEF1 0.01 0.085 -9999 0 -0.708 1 1
DAB1 0.02 0 -9999 0 -9999 0 0
RELN/LRP8/DAB1 0.001 0.122 -9999 0 -0.553 2 2
LRPAP1/LRP8 -0.003 0.11 -9999 0 -0.366 6 6
RELN/LRP8/DAB1/Fyn -0.058 0.19 -9999 0 -0.414 14 14
DAB1/alpha3/beta1 Integrin -0.112 0.201 -9999 0 -0.575 9 9
long-term memory -0.062 0.222 -9999 0 -0.65 5 5
DAB1/LIS1 -0.048 0.106 -9999 0 -0.473 2 2
DAB1/CRLK/C3G -0.05 0.105 -9999 0 -0.454 2 2
PIK3CA 0.02 0 -9999 0 -9999 0 0
DAB1/NCK2 -0.049 0.107 -9999 0 -0.478 2 2
ARHGEF2 0.012 0.064 -9999 0 -0.523 1 1
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -9999 0 0
GRIN2A 0.005 0.089 -9999 0 -0.523 2 2
CDK5R1 0.02 0 -9999 0 -9999 0 0
RELN -0.003 0.109 -9999 0 -0.523 3 3
PIK3R1 -0.038 0.194 -9999 0 -0.677 6 6
RELN/LRP8/Fyn -0.081 0.217 -9999 0 -0.486 14 14
GRIN2A/RELN/LRP8/DAB1/Fyn -0.054 0.202 -9999 0 -0.635 3 3
MAPK8 0.02 0 -9999 0 -9999 0 0
RELN/VLDLR/DAB1 -0.004 0.107 -9999 0 -9999 0 0
ITGB1 0.01 0.085 -9999 0 -0.708 1 1
MAP1B -0.041 0.188 -9999 0 -0.587 5 5
RELN/LRP8 0 0.133 -9999 0 -0.596 2 2
GRIN2B/RELN/LRP8/DAB1/Fyn -0.067 0.221 -9999 0 -0.631 5 5
PI3K -0.014 0.147 -9999 0 -0.499 6 6
mol:PP2 0 0 -9999 0 -9999 0 0
alpha3/beta1 Integrin -0.08 0.217 -9999 0 -0.463 16 16
RAP1A 0.015 0.133 -9999 0 -9999 0 0
PAFAH1B1 0.02 0 -9999 0 -9999 0 0
MAPK8IP1 0.02 0 -9999 0 -9999 0 0
CRLK/C3G 0.022 0.065 -9999 0 -0.526 1 1
GRIN2B -0.018 0.157 -9999 0 -0.662 4 4
NCK2 0.02 0 -9999 0 -9999 0 0
neuron differentiation -0.004 0.115 -9999 0 -0.33 1 1
neuron adhesion -0.034 0.225 -9999 0 -0.566 7 7
LRP8 -0.025 0.15 -9999 0 -0.523 6 6
GSK3B 0.015 0.124 -9999 0 -0.455 3 3
RELN/VLDLR/DAB1/Fyn -0.061 0.224 -9999 0 -0.53 12 12
MAP3K11 0.012 0.064 -9999 0 -0.523 1 1
RELN/VLDLR/DAB1/P13K -0.008 0.137 -9999 0 -0.475 4 4
CDK5 0.012 0.064 -9999 0 -0.523 1 1
MAPT -0.018 0.136 -9999 0 -0.66 3 3
neuron migration -0.01 0.203 -9999 0 -0.481 7 7
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.004 0.116 -9999 0 -0.333 1 1
RELN/VLDLR -0.017 0.146 -9999 0 -0.541 2 2
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.009 0.023 -9999 0 -9999 0 0
VDR -0.139 0.279 -9999 0 -0.616 18 18
FAM120B 0.02 0 -9999 0 -9999 0 0
RXRs/LXRs/DNA/9cRA 0.05 0.132 -9999 0 -0.453 3 3
RXRs/LXRs/DNA/Oxysterols 0.05 0.174 -9999 0 -0.629 3 3
MED1 0.01 0.085 -9999 0 -0.708 1 1
mol:9cRA 0.006 0.017 -9999 0 -9999 0 0
RARs/THRs/DNA/Src-1 0.024 0.088 -9999 0 -9999 0 0
RXRs/NUR77 0.009 0.162 -9999 0 -0.564 3 3
RXRs/PPAR 0.025 0.107 -9999 0 -9999 0 0
NCOR2 -0.02 0.167 -9999 0 -0.708 4 4
VDR/VDR/Vit D3 -0.104 0.209 -9999 0 -0.459 18 18
RARs/VDR/DNA/Vit D3 -0.053 0.166 -9999 0 -0.375 11 11
RARA 0.02 0 -9999 0 -9999 0 0
NCOA1 0.02 0 -9999 0 -9999 0 0
VDR/VDR/DNA -0.139 0.279 -9999 0 -0.615 18 18
RARs/RARs/DNA/9cRA 0.026 0.07 -9999 0 -0.381 2 2
RARG 0.02 0 -9999 0 -9999 0 0
RPS6KB1 0.012 0.033 -9999 0 -9999 0 0
RARs/THRs/DNA/SMRT 0.005 0.111 -9999 0 -9999 0 0
THRA 0 0.12 -9999 0 -0.708 2 2
mol:Bile acids 0 0 -9999 0 -9999 0 0
VDR/Vit D3/DNA -0.104 0.209 -9999 0 -0.459 18 18
RXRs/PPAR/9cRA/PGJ2/DNA 0.032 0.123 -9999 0 -0.44 4 4
NR1H4 -0.089 0.257 -9999 0 -0.691 11 11
RXRs/LXRs/DNA 0.063 0.13 -9999 0 -0.49 2 2
NR1H2 0.027 0.013 -9999 0 -9999 0 0
NR1H3 0.027 0.014 -9999 0 -9999 0 0
RXRs/VDR/DNA/Vit D3 -0.053 0.185 -9999 0 -0.37 14 14
NR4A1 -0.035 0.17 -9999 0 -0.55 7 7
mol:ATRA 0 0 -9999 0 -9999 0 0
RXRs/FXR/9cRA/MED1 -0.019 0.171 -9999 0 -0.36 12 12
RXRG 0.006 0.122 -9999 0 -0.714 2 2
RXR alpha/CCPG 0.018 0.094 -9999 0 -0.536 2 2
RXRA 0.006 0.123 -9999 0 -0.72 2 2
RXRB 0.026 0.014 -9999 0 -9999 0 0
THRB -0.018 0.138 -9999 0 -0.523 5 5
PPARG -0.03 0.169 -9999 0 -0.585 6 6
PPARD 0.02 0 -9999 0 -9999 0 0
TNF 0.047 0.222 -9999 0 -1.41 1 1
mol:Oxysterols 0.006 0.015 -9999 0 -9999 0 0
cholesterol transport 0.05 0.172 -9999 0 -0.621 3 3
PPARA 0.02 0 -9999 0 -9999 0 0
mol:Vit D3 0 0 -9999 0 -9999 0 0
RARB 0 0.12 -9999 0 -0.708 2 2
RXRs/NUR77/BCL2 -0.019 0.166 -9999 0 -0.605 3 3
SREBF1 0.053 0.177 -9999 0 -0.726 1 1
RXRs/RXRs/DNA/9cRA 0.032 0.123 -9999 0 -0.44 4 4
ABCA1 0.016 0.322 -9999 0 -1.264 4 4
RARs/THRs 0.016 0.118 -9999 0 -9999 0 0
RXRs/FXR -0.025 0.197 -9999 0 -0.417 14 14
BCL2 -0.041 0.201 -9999 0 -0.708 6 6
Ephrin B reverse 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
EFNB2 -0.066 0.229 -9999 0 -0.667 9 9
EPHB2 0.019 0.002 -9999 0 -9999 0 0
EFNB1 -0.056 0.203 -9999 0 -0.463 13 13
mol:GTP 0 0 -9999 0 -9999 0 0
Rac1/GDP -0.081 0.162 -9999 0 -0.52 4 4
Ephrin B2/EPHB1-2 -0.047 0.184 -9999 0 -0.497 8 8
neuron projection morphogenesis -0.086 0.149 -9999 0 -0.497 4 4
Ephrin B1/EPHB1-2/Tiam1 -0.056 0.196 -9999 0 -0.564 4 4
DNM1 -0.053 0.195 -9999 0 -0.565 9 9
cell-cell signaling -0.001 0.002 -9999 0 -9999 0 0
MAP2K4 0.006 0.156 -9999 0 -0.909 2 2
YES1 -0.027 0.187 -9999 0 -1.133 2 2
Ephrin B1/EPHB1-2/NCK2 -0.039 0.185 -9999 0 -0.564 4 4
PI3K -0.023 0.232 -9999 0 -0.755 5 5
mol:GDP -0.057 0.193 -9999 0 -0.557 4 4
ITGA2B 0.02 0 -9999 0 -9999 0 0
endothelial cell proliferation -0.03 0.15 -9999 0 -0.423 9 9
FYN -0.057 0.221 -9999 0 -1.311 2 2
MAP3K7 -0.024 0.161 -9999 0 -0.971 2 2
FGR -0.027 0.187 -9999 0 -1.129 2 2
TIAM1 -0.01 0.145 -9999 0 -0.708 3 3
PIK3R1 -0.038 0.194 -9999 0 -0.677 6 6
RGS3 0.02 0 -9999 0 -9999 0 0
cell adhesion -0.025 0.228 -9999 0 -0.943 3 3
LYN -0.027 0.187 -9999 0 -1.133 2 2
Ephrin B1/EPHB1-2/Src Family Kinases -0.03 0.184 -9999 0 -1.114 2 2
Ephrin B1/EPHB1-2 -0.031 0.172 -9999 0 -1.045 2 2
SRC -0.027 0.187 -9999 0 -1.129 2 2
ITGB3 -0.03 0.169 -9999 0 -0.585 6 6
EPHB1 -0.041 0.171 -9999 0 -0.523 8 8
EPHB4 0.02 0 -9999 0 -9999 0 0
RAC1 0.02 0 -9999 0 -9999 0 0
Ephrin B2/EPHB4 -0.03 0.151 -9999 0 -0.425 9 9
alphaIIb/beta3 Integrin -0.008 0.126 -9999 0 -0.419 6 6
BLK -0.03 0.189 -9999 0 -1.144 2 2
HCK -0.033 0.191 -9999 0 -1.144 2 2
regulation of stress fiber formation 0.039 0.183 0.557 4 -9999 0 4
MAPK8 0.016 0.147 -9999 0 -0.851 2 2
Ephrin B1/EPHB1-2/RGS3 -0.039 0.185 -9999 0 -0.564 4 4
endothelial cell migration -0.063 0.201 -9999 0 -0.547 8 8
NCK2 0.02 0 -9999 0 -9999 0 0
PTPN13 -0.012 0.143 -9999 0 -0.854 2 2
regulation of focal adhesion formation 0.039 0.183 0.557 4 -9999 0 4
chemotaxis 0.039 0.183 0.557 4 -9999 0 4
PIK3CA 0.02 0 -9999 0 -9999 0 0
Rac1/GTP -0.088 0.153 -9999 0 -0.512 4 4
angiogenesis -0.031 0.17 -9999 0 -1.034 2 2
LCK -0.051 0.212 -9999 0 -1.27 2 2
TCGA08_p53

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
CDKN2A -0.027 0.147 -9999 0 -0.513 6 6
TP53 -0.01 0.087 0.342 2 -0.381 1 3
Senescence -0.01 0.087 0.342 2 -0.38 1 3
Apoptosis -0.01 0.087 0.342 2 -0.38 1 3
Activated_Oncogenes 0 0 -9999 0 -9999 0 0
MDM2 0.025 0.082 0.311 5 -9999 0 5
MDM4 0 0.12 -9999 0 -0.708 2 2
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.054 0.267 -9999 0 -0.824 5 5
MKNK1 0.02 0 -9999 0 -9999 0 0
MAPK14 -0.012 0.09 -9999 0 -9999 0 0
ATF2/c-Jun -0.096 0.309 -9999 0 -0.762 12 12
MAPK11 -0.012 0.09 -9999 0 -9999 0 0
MITF 0.003 0.105 -9999 0 -0.337 2 2
MAPKAPK5 0.003 0.105 -9999 0 -0.337 2 2
KRT8 -0.008 0.122 -9999 0 -0.352 4 4
MAPKAPK3 0.012 0.064 -9999 0 -0.523 1 1
MAPKAPK2 0.02 0 -9999 0 -9999 0 0
p38alpha-beta/CK2 -0.017 0.129 -9999 0 -0.4 4 4
CEBPB -0.004 0.123 -9999 0 -0.374 4 4
SLC9A1 0.003 0.105 -9999 0 -0.337 2 2
mol:GDP 0 0 -9999 0 -9999 0 0
ATF2 -0.009 0.132 -9999 0 -0.357 5 5
p38alpha-beta/MNK1 0.005 0.103 -9999 0 -9999 0 0
JUN -0.095 0.307 -9999 0 -0.757 12 12
PPARGC1A -0.052 0.177 -9999 0 -0.377 14 14
USF1 -0.025 0.127 -9999 0 -0.331 4 4
RAB5/GDP/GDI1 -0.029 0.066 -9999 0 -0.334 1 1
NOS2 -0.01 0.105 -9999 0 -0.31 5 5
DDIT3 -0.033 0.157 -9999 0 -0.381 9 9
RAB5A 0.012 0.064 -9999 0 -0.523 1 1
HSPB1 0.017 0.085 -9999 0 -9999 0 0
p38alpha-beta/HBP1 -0.002 0.116 -9999 0 -0.463 1 1
CREB1 -0.004 0.136 -9999 0 -0.455 3 3
RAB5/GDP 0.009 0.046 -9999 0 -0.38 1 1
EIF4E 0.016 0.089 -9999 0 -9999 0 0
RPS6KA4 -0.001 0.123 -9999 0 -0.489 2 2
PLA2G4A -0.053 0.182 -9999 0 -0.424 8 8
GDI1 0.003 0.105 -9999 0 -0.337 2 2
TP53 -0.008 0.151 -9999 0 -0.634 2 2
RPS6KA5 -0.015 0.155 -9999 0 -0.479 5 5
ESR1 -0.009 0.145 -9999 0 -0.477 4 4
HBP1 0.01 0.085 -9999 0 -0.708 1 1
MEF2C -0.057 0.202 -9999 0 -0.462 12 12
MEF2A 0.003 0.105 -9999 0 -0.337 2 2
EIF4EBP1 -0.023 0.161 -9999 0 -0.425 7 7
KRT19 -0.095 0.178 -9999 0 -0.428 10 10
ELK4 -0.008 0.12 -9999 0 -0.349 4 4
ATF6 0.003 0.105 -9999 0 -0.337 2 2
ATF1 -0.001 0.133 -9999 0 -0.455 3 3
p38alpha-beta/MAPKAPK2 0.005 0.103 -9999 0 -9999 0 0
p38alpha-beta/MAPKAPK3 0 0.113 -9999 0 -0.399 1 1
Canonical Wnt signaling 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
HDAC1 0.029 0.101 -9999 0 -0.676 1 1
AES 0.038 0.052 -9999 0 -9999 0 0
FBXW11 0.02 0 -9999 0 -9999 0 0
mol:GTP 0.001 0.003 -9999 0 -9999 0 0
LRP6/FZD1 -0.055 0.199 -9999 0 -0.524 11 11
SMAD4 0.01 0.085 -9999 0 -0.708 1 1
DKK2 0.013 0.064 -9999 0 -0.524 1 1
TLE1 0.017 0.105 -9999 0 -0.539 2 2
MACF1 0 0.119 -9999 0 -0.706 2 2
CTNNB1 0.031 0.121 0.388 2 -0.559 1 3
WIF1 0.004 0.09 -9999 0 -0.527 2 2
beta catenin/RanBP3 0.086 0.217 0.512 12 -9999 0 12
KREMEN2 -0.012 0.136 -9999 0 -0.57 4 4
DKK1 -0.043 0.179 -9999 0 -0.546 8 8
beta catenin/beta TrCP1 0.038 0.116 0.377 2 -0.497 1 3
FZD1 -0.09 0.262 -9999 0 -0.707 11 11
AXIN2 -0.024 0.147 -9999 0 -0.629 2 2
AXIN1 0.02 0.001 -9999 0 -9999 0 0
RAN 0.021 0.002 -9999 0 -9999 0 0
Axin1/APC/GSK3/beta catenin 0.01 0.083 -9999 0 -0.584 1 1
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.011 0.185 -9999 0 -0.532 4 4
Axin1/APC/GSK3 -0.002 0.082 0.317 1 -0.516 1 2
Axin1/APC/GSK3/beta catenin/Macf1 0.009 0.172 -9999 0 -0.908 1 1
HNF1A -0.004 0.149 -9999 0 -0.596 4 4
CTBP1 0.035 0.048 -9999 0 -9999 0 0
MYC -0.171 0.54 -9999 0 -1.686 8 8
RANBP3 0.011 0.085 -9999 0 -0.707 1 1
DKK2/LRP6/Kremen 2 0.017 0.095 -9999 0 -0.444 1 1
NKD1 0.012 0.064 -9999 0 -0.523 1 1
TCF4 -0.073 0.246 -9999 0 -0.641 11 11
TCF3 0.025 0.096 -9999 0 -0.675 1 1
WNT1/LRP6/FZD1/Axin1 -0.017 0.16 -9999 0 -0.394 11 11
Ran/GTP 0.016 0.006 -9999 0 -9999 0 0
CtBP/CBP/TCF/TLE1/AES 0.066 0.242 0.613 9 -9999 0 9
LEF1 -0.085 0.216 -9999 0 -0.477 16 16
DVL1 0.042 0.042 -9999 0 -9999 0 0
CSNK2A1 0.02 0.001 -9999 0 -9999 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.073 0.307 -9999 0 -0.745 10 10
DKK1/LRP6/Kremen 2 -0.019 0.138 -9999 0 -0.443 2 2
LRP6 0.02 0.002 -9999 0 -9999 0 0
CSNK1A1 0.039 0.057 -9999 0 -9999 0 0
NLK 0.018 0.007 -9999 0 -9999 0 0
CCND1 -0.336 0.69 -9999 0 -1.623 16 16
WNT1 0.02 0.001 -9999 0 -9999 0 0
GSK3A 0.01 0.086 -9999 0 -0.711 1 1
GSK3B 0.02 0.002 -9999 0 -9999 0 0
FRAT1 0.004 0.09 -9999 0 -0.529 2 2
PPP2R5D 0.022 0.039 0.251 1 -9999 0 1
APC -0.016 0.173 -9999 0 -0.761 1 1
WNT1/LRP6/FZD1 -0.034 0.125 0.274 1 -0.427 2 3
CREBBP 0.035 0.048 -9999 0 -9999 0 0
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0 0.102 -9999 0 -0.368 5 5
cell-cell adhesion 0.072 0.145 0.52 4 -9999 0 4
Ephrin B/EPHB2/RasGAP -0.016 0.18 -9999 0 -0.693 2 2
ITSN1 0.01 0.085 -9999 0 -0.708 1 1
PIK3CA 0.02 0 -9999 0 -9999 0 0
SHC1 0.02 0 -9999 0 -9999 0 0
Ephrin B1/EPHB3 -0.009 0.122 -9999 0 -0.407 6 6
Ephrin B1/EPHB1 -0.042 0.15 -9999 0 -0.355 13 13
HRAS/GDP -0.086 0.174 -9999 0 -0.638 4 4
Ephrin B/EPHB1/GRB7 -0.052 0.211 -9999 0 -0.631 5 5
Endophilin/SYNJ1 -0.016 0.168 -9999 0 -0.644 2 2
KRAS 0.02 0 -9999 0 -9999 0 0
Ephrin B/EPHB1/Src -0.048 0.21 -9999 0 -0.631 5 5
endothelial cell migration -0.072 0.176 -9999 0 -0.472 10 10
GRB2 0.01 0.085 -9999 0 -0.708 1 1
GRB7 0.012 0.064 -9999 0 -0.523 1 1
PAK1 -0.025 0.196 -9999 0 -0.62 4 4
HRAS 0.02 0 -9999 0 -9999 0 0
RRAS -0.028 0.19 -9999 0 -0.682 3 3
DNM1 -0.053 0.195 -9999 0 -0.564 9 9
cell-cell signaling 0 0 -9999 0 -9999 0 0
CRK -0.057 0.22 -9999 0 -0.674 5 5
lamellipodium assembly -0.072 0.145 -9999 0 -0.52 4 4
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.021 0.156 -9999 0 -0.492 4 4
PIK3R1 -0.038 0.194 -9999 0 -0.677 6 6
EPHB2 0.02 0 -9999 0 -9999 0 0
EPHB3 0.012 0.064 -9999 0 -0.523 1 1
EPHB1 -0.04 0.171 -9999 0 -0.523 8 8
EPHB4 0.02 0 -9999 0 -9999 0 0
mol:GDP -0.042 0.207 -9999 0 -0.688 4 4
Ephrin B/EPHB2 -0.028 0.179 -9999 0 -0.441 10 10
Ephrin B/EPHB3 -0.032 0.189 -9999 0 -0.467 10 10
JNK cascade -0.024 0.164 -9999 0 -0.741 1 1
Ephrin B/EPHB1 -0.06 0.209 -9999 0 -0.496 11 11
RAP1/GDP -0.026 0.194 -9999 0 -0.577 5 5
EFNB2 -0.066 0.229 -9999 0 -0.667 9 9
EFNB3 0.02 0 -9999 0 -9999 0 0
EFNB1 -0.028 0.177 -9999 0 -0.671 5 5
Ephrin B2/EPHB1-2 -0.046 0.184 -9999 0 -0.494 8 8
RAP1B 0.01 0.085 -9999 0 -0.708 1 1
RAP1A 0.01 0.085 -9999 0 -0.708 1 1
CDC42/GTP -0.082 0.162 -9999 0 -0.586 4 4
Rap1/GTP -0.087 0.173 -9999 0 -0.601 5 5
axon guidance -0.001 0.102 -9999 0 -0.367 5 5
MAPK3 0.003 0.141 -9999 0 -0.449 3 3
MAPK1 0.003 0.141 -9999 0 -0.449 3 3
Rac1/GDP -0.026 0.19 -9999 0 -0.609 4 4
actin cytoskeleton reorganization -0.064 0.131 -9999 0 -0.459 5 5
CDC42/GDP -0.026 0.19 -9999 0 -0.609 4 4
PI3K -0.034 0.194 -9999 0 -0.478 10 10
EFNA5 -0.023 0.159 -9999 0 -0.597 5 5
Ephrin B2/EPHB4 -0.029 0.15 -9999 0 -0.423 9 9
Ephrin B/EPHB2/Intersectin/N-WASP -0.01 0.143 -9999 0 -0.519 2 2
CDC42 0.02 0 -9999 0 -9999 0 0
RAS family/GTP -0.075 0.158 -9999 0 -0.549 5 5
PTK2 0.016 0.034 -9999 0 -9999 0 0
MAP4K4 -0.025 0.166 -9999 0 -0.754 1 1
SRC 0.02 0 -9999 0 -9999 0 0
KALRN -0.008 0.134 -9999 0 -0.646 3 3
Intersectin/N-WASP 0.016 0.079 -9999 0 -0.446 2 2
neuron projection morphogenesis 0.009 0.173 -9999 0 -0.477 2 2
MAP2K1 -0.008 0.148 -9999 0 -0.481 3 3
WASL 0.012 0.064 -9999 0 -0.523 1 1
Ephrin B1/EPHB1-2/NCK1 -0.018 0.145 -9999 0 -0.396 5 5
cell migration -0.002 0.154 -9999 0 -0.486 3 3
NRAS 0.005 0.089 -9999 0 -0.523 2 2
SYNJ1 -0.017 0.171 -9999 0 -0.659 2 2
PXN 0.02 0 -9999 0 -9999 0 0
TF -0.02 0.176 -9999 0 -0.603 3 3
HRAS/GTP -0.078 0.158 -9999 0 -0.539 5 5
Ephrin B1/EPHB1-2 -0.025 0.138 -9999 0 -0.407 4 4
cell adhesion mediated by integrin 0.061 0.167 0.47 8 -9999 0 8
RAC1 0.02 0 -9999 0 -9999 0 0
mol:GTP -0.036 0.196 -9999 0 -0.583 5 5
RAC1-CDC42/GTP -0.073 0.154 -9999 0 -0.574 4 4
RASA1 0.02 0 -9999 0 -9999 0 0
RAC1-CDC42/GDP -0.016 0.182 -9999 0 -0.572 4 4
ruffle organization -0.012 0.196 -9999 0 -0.601 4 4
NCK1 0.01 0.085 -9999 0 -0.708 1 1
receptor internalization -0.042 0.195 -9999 0 -0.625 4 4
Ephrin B/EPHB2/KALRN -0.032 0.206 -9999 0 -0.662 4 4
ROCK1 0.004 0.111 -9999 0 -0.405 4 4
RAS family/GDP -0.064 0.134 -9999 0 -0.474 5 5
Rac1/GTP -0.076 0.155 -9999 0 -0.559 4 4
Ephrin B/EPHB1/Src/Paxillin -0.025 0.161 -9999 0 -0.518 4 4
Wnt signaling

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
Noncanonical Wnts/FZD -0.029 0.149 -9999 0 -0.837 1 1
FZD6 -0.018 0.157 -9999 0 -0.662 4 4
WNT6 0.02 0 -9999 0 -9999 0 0
WNT4 -0.013 0.136 -9999 0 -0.57 4 4
FZD3 -0.038 0.194 -9999 0 -0.677 6 6
WNT5A -0.025 0.15 -9999 0 -0.523 6 6
WNT11 -0.01 0.124 -9999 0 -0.523 4 4
LPA receptor mediated events

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
GNB1/GNG2 0.022 0.066 -9999 0 -0.397 1 1
NF kappa B1 p50/RelA/I kappa B alpha -0.008 0.126 -9999 0 -0.419 4 4
AP1 -0.146 0.226 -9999 0 -0.497 18 18
mol:PIP3 -0.104 0.203 -9999 0 -0.484 12 12
AKT1 0.018 0.134 -9999 0 -0.496 2 2
PTK2B 0.011 0.039 -9999 0 -9999 0 0
RHOA 0.003 0.101 -9999 0 -0.732 1 1
PIK3CB 0.01 0.085 -9999 0 -0.709 1 1
mol:Ca2+ -0.01 0.1 -9999 0 -0.335 3 3
MAGI3 -0.043 0.179 -9999 0 -0.546 8 8
RELA 0.02 0 -9999 0 -9999 0 0
apoptosis 0.012 0.048 -9999 0 -0.222 1 1
HRAS/GDP 0.015 0 -9999 0 -9999 0 0
positive regulation of microtubule depolymerization 0.015 0.084 -9999 0 -0.35 3 3
NF kappa B1 p50/RelA -0.044 0.097 -9999 0 -0.556 1 1
endothelial cell migration 0.007 0.106 -9999 0 -0.501 3 3
ADCY4 0.004 0.128 -9999 0 -0.495 3 3
ADCY5 0.008 0.115 -9999 0 -0.475 2 2
ADCY6 0.036 0.068 -9999 0 -0.342 1 1
ADCY7 0.024 0.086 -9999 0 -0.346 2 2
ADCY1 0.036 0.068 -9999 0 -0.342 1 1
ADCY2 -0.006 0.089 -9999 0 -0.342 1 1
ADCY3 0.023 0.098 -9999 0 -0.438 2 2
ADCY8 0.008 0.081 -9999 0 -0.342 1 1
ADCY9 0.032 0.08 -9999 0 -0.346 2 2
GSK3B 0.021 0.037 -9999 0 -9999 0 0
arachidonic acid secretion 0.041 0.081 -9999 0 -0.371 2 2
GNG2 0.02 0.001 -9999 0 -9999 0 0
TRIP6 0.021 0.059 -9999 0 -0.469 1 1
GNAO1 0.019 0.048 -9999 0 -9999 0 0
HRAS 0.02 0 -9999 0 -9999 0 0
NFKBIA -0.021 0.143 -9999 0 -0.495 4 4
GAB1 -0.02 0.167 -9999 0 -0.708 4 4
mol:GTP 0 0 -9999 0 -9999 0 0
lamellipodium assembly -0.014 0.206 -9999 0 -0.999 3 3
JUN -0.094 0.256 -9999 0 -0.662 12 12
LPA/LPA2/NHERF2 -0.038 0.108 -9999 0 -0.359 7 7
TIAM1 -0.046 0.244 -9999 0 -1.213 3 3
PIK3R1 -0.038 0.193 -9999 0 -0.676 6 6
mol:IP3 -0.011 0.102 -9999 0 -0.394 2 2
PLCB3 -0.006 0.104 -9999 0 -0.315 7 7
FOS -0.157 0.289 -9999 0 -0.616 20 20
positive regulation of mitosis 0.041 0.081 -9999 0 -0.371 2 2
LPA/LPA1-2-3 -0.008 0.04 -9999 0 -0.2 3 3
mol:Ca ++ 0 0 -9999 0 -9999 0 0
JNK cascade 0 0.001 -9999 0 -9999 0 0
BCAR1 0.02 0 -9999 0 -9999 0 0
stress fiber formation 0.023 0.036 -9999 0 -9999 0 0
GNAZ 0.014 0.061 -9999 0 -0.305 1 1
EGFR/PI3K-beta/Gab1 -0.11 0.218 -9999 0 -0.514 12 12
positive regulation of dendritic cell cytokine production -0.008 0.04 -9999 0 -0.199 3 3
LPA/LPA2/MAGI-3 -0.039 0.106 -9999 0 -0.333 8 8
ARHGEF1 0.029 0.07 -9999 0 -0.369 1 1
GNAI2 0.012 0.073 -9999 0 -0.45 1 1
GNAI3 0.019 0.048 -9999 0 -9999 0 0
GNAI1 0.006 0.103 -9999 0 -0.55 2 2
LPA/LPA3 -0.004 0.02 -9999 0 -0.101 3 3
LPA/LPA2 -0.004 0.02 -9999 0 -0.101 3 3
LPA/LPA1 -0.011 0.053 -9999 0 -0.267 3 3
HB-EGF/EGFR -0.164 0.277 -9999 0 -0.656 11 11
HBEGF -0.109 0.24 -9999 0 -0.456 21 21
mol:DAG -0.011 0.102 -9999 0 -0.394 2 2
cAMP biosynthetic process 0.018 0.089 -9999 0 -0.395 2 2
NFKB1 0.02 0 -9999 0 -9999 0 0
SRC 0.02 0 -9999 0 -9999 0 0
GNB1 0.01 0.085 -9999 0 -0.705 1 1
LYN -0.004 0.102 -9999 0 -0.45 1 1
GNAQ 0.002 0.016 -9999 0 -0.075 3 3
LPAR2 0 0.001 -9999 0 -9999 0 0
LPAR3 0 0.001 -9999 0 -9999 0 0
LPAR1 0 0.033 -9999 0 -0.157 3 3
IL8 -0.186 0.237 -9999 0 -0.481 24 24
PTK2 0.017 0.04 -9999 0 -9999 0 0
Rac1/GDP 0.015 0 -9999 0 -9999 0 0
CASP3 0.012 0.048 -9999 0 -0.223 1 1
EGFR -0.107 0.26 -9999 0 -0.629 14 14
PLCG1 -0.002 0.054 -9999 0 -0.138 8 8
PLD2 -0.001 0.091 -9999 0 -0.392 3 3
G12/G13 0.021 0.067 -9999 0 -0.404 1 1
PI3K-beta -0.048 0.13 -9999 0 -0.474 5 5
cell migration -0.002 0.062 -9999 0 -0.278 3 3
SLC9A3R2 -0.038 0.179 -9999 0 -0.576 7 7
PXN 0.023 0.037 -9999 0 -9999 0 0
HRAS/GTP 0.041 0.082 -9999 0 -0.38 2 2
RAC1 0.02 0 -9999 0 -9999 0 0
MMP9 -0.149 0.266 -9999 0 -0.559 21 21
PRKCE 0.02 0 -9999 0 -9999 0 0
PRKCD -0.022 0.129 -9999 0 -0.423 3 3
Gi(beta/gamma) 0.036 0.098 -9999 0 -0.47 2 2
mol:LPA 0 0.033 -9999 0 -0.157 3 3
TRIP6/p130 Cas/FAK1/Paxillin 0.002 0.04 -9999 0 -9999 0 0
MAPKKK cascade 0.041 0.081 -9999 0 -0.371 2 2
contractile ring contraction involved in cytokinesis 0.003 0.099 -9999 0 -0.721 1 1
mol:GDP 0 0 -9999 0 -9999 0 0
GNA14 -0.029 0.124 -9999 0 -0.372 8 8
GNA15 0.008 0.049 -9999 0 -0.379 1 1
GNA12 0.02 0 -9999 0 -9999 0 0
GNA13 0.01 0.085 -9999 0 -0.708 1 1
MAPT 0.015 0.086 -9999 0 -0.36 3 3
GNA11 0 0.058 -9999 0 -0.231 4 4
Rac1/GTP -0.007 0.223 -9999 0 -1.076 3 3
MMP2 0.007 0.106 -9999 0 -0.503 3 3
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.035 0.208 -9999 0 -0.589 7 7
KLHL20 -0.069 0.118 -9999 0 -0.317 10 10
CYFIP2 0.01 0.085 -9999 0 -0.708 1 1
Rac1/GDP 0.004 0.163 -9999 0 -0.595 2 2
ENAH -0.041 0.216 -9999 0 -0.583 8 8
AP1M1 0.02 0 -9999 0 -9999 0 0
RAP1B 0.01 0.085 -9999 0 -0.708 1 1
RAP1A 0.01 0.085 -9999 0 -0.708 1 1
CTNNB1 0.02 0 -9999 0 -9999 0 0
CDC42/GTP -0.058 0.125 -9999 0 -0.545 3 3
ABI1/Sra1/Nap1 -0.046 0.073 -9999 0 -0.214 6 6
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.022 0.163 -9999 0 -0.436 7 7
RAPGEF1 -0.022 0.204 -9999 0 -0.527 8 8
CTNND1 -0.021 0.167 -9999 0 -0.708 4 4
regulation of calcium-dependent cell-cell adhesion -0.052 0.212 -9999 0 -0.617 7 7
CRK -0.032 0.207 -9999 0 -0.545 8 8
E-cadherin/gamma catenin/alpha catenin -0.041 0.184 -9999 0 -0.504 7 7
alphaE/beta7 Integrin 0.024 0.046 -9999 0 -0.366 1 1
IQGAP1 0.02 0 -9999 0 -9999 0 0
NCKAP1 0.005 0.089 -9999 0 -0.523 2 2
Rap1/GTP/I-afadin 0.02 0.111 -9999 0 -0.608 2 2
DLG1 -0.035 0.208 -9999 0 -0.589 7 7
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -9999 0 0
mol:PI-3-4-5-P3 -0.053 0.101 -9999 0 -0.317 6 6
MLLT4 0.01 0.085 -9999 0 -0.708 1 1
ARF6/GTP/NME1/Tiam1 0.02 0.089 -9999 0 -0.408 3 3
PI3K -0.07 0.137 -9999 0 -0.434 6 6
ARF6 0.02 0 -9999 0 -9999 0 0
mol:Ca2+ 0 0 -9999 0 -9999 0 0
E-cadherin/gamma catenin -0.063 0.209 -9999 0 -0.486 13 13
TIAM1 -0.01 0.145 -9999 0 -0.708 3 3
E-cadherin(dimer)/Ca2+ -0.045 0.175 -9999 0 -0.415 10 10
AKT1 -0.037 0.07 -9999 0 -0.272 2 2
PIK3R1 -0.038 0.194 -9999 0 -0.677 6 6
CDH1 -0.096 0.25 -9999 0 -0.623 13 13
RhoA/GDP 0.001 0.171 -9999 0 -0.566 3 3
actin cytoskeleton organization -0.001 0.113 -9999 0 -0.25 6 6
CDC42/GDP 0.005 0.162 -9999 0 -0.592 2 2
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.037 0.164 -9999 0 -0.385 10 10
ITGB7 0.02 0 -9999 0 -9999 0 0
RAC1 0.02 0 -9999 0 -9999 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.046 0.185 -9999 0 -0.437 10 10
E-cadherin/Ca2+/beta catenin/alpha catenin -0.033 0.14 -9999 0 -0.386 7 7
mol:GDP -0.012 0.19 -9999 0 -0.757 2 2
CDC42/GTP/IQGAP1 0.027 0 -9999 0 -9999 0 0
JUP 0.01 0.085 -9999 0 -0.708 1 1
p120 catenin/RhoA/GDP -0.07 0.162 -9999 0 -0.661 3 3
RAC1/GTP/IQGAP1 0.027 0 -9999 0 -9999 0 0
PIP5K1C/AP1M1 0.03 0 -9999 0 -9999 0 0
RHOA 0.01 0.085 -9999 0 -0.708 1 1
CDC42 0.02 0 -9999 0 -9999 0 0
CTNNA1 0.02 0 -9999 0 -9999 0 0
positive regulation of S phase of mitotic cell cycle -0.025 0.131 -9999 0 -0.262 16 16
NME1 0.02 0 -9999 0 -9999 0 0
clathrin coat assembly 0 0 -9999 0 -9999 0 0
TJP1 -0.035 0.208 -9999 0 -0.589 7 7
regulation of cell-cell adhesion -0.051 0.107 -9999 0 -0.457 3 3
WASF2 -0.023 0.037 -9999 0 -9999 0 0
Rap1/GTP -0.069 0.15 -9999 0 -0.659 3 3
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.015 0.173 -9999 0 -0.693 2 2
CCND1 -0.036 0.164 -9999 0 -0.333 16 16
VAV2 -0.02 0.194 -9999 0 -0.583 4 4
RAP1/GDP -0.006 0.176 -9999 0 -0.628 3 3
adherens junction assembly -0.033 0.199 -9999 0 -0.564 7 7
homophilic cell adhesion 0 0 -9999 0 -9999 0 0
ABI1 0.02 0 -9999 0 -9999 0 0
PIP5K1C 0.02 0 -9999 0 -9999 0 0
regulation of heterotypic cell-cell adhesion -0.004 0.167 -9999 0 -0.66 2 2
E-cadherin/beta catenin -0.062 0.139 -9999 0 -0.444 7 7
mol:GTP 0 0 -9999 0 -9999 0 0
SRC -0.04 0.207 -9999 0 -0.591 7 7
PIK3CA 0.02 0 -9999 0 -9999 0 0
Rac1/GTP -0.115 0.2 -9999 0 -0.541 10 10
E-cadherin/beta catenin/alpha catenin -0.039 0.162 -9999 0 -0.444 7 7
ITGAE 0.012 0.064 -9999 0 -0.523 1 1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.09 0.203 -9999 0 -0.637 7 7
S1P3 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
PDGFRB 0 0.12 -9999 0 -0.708 2 2
mol:S1P 0.002 0.002 -9999 0 -0.017 1 1
S1P1/S1P/Gi 0.006 0.145 -9999 0 -0.485 4 4
GNAO1 0.022 0.003 -9999 0 -9999 0 0
S1P/S1P3/G12/G13 0.024 0.052 -9999 0 -0.417 1 1
AKT1 0.026 0.126 -9999 0 -0.707 2 2
AKT3 -0.033 0.246 -9999 0 -1.095 2 2
mol:GTP 0 0 -9999 0 -9999 0 0
PDGFB-D/PDGFRB 0 0.119 -9999 0 -0.707 2 2
GNAI2 0.012 0.085 -9999 0 -0.707 1 1
GNAI3 0.022 0.003 -9999 0 -9999 0 0
GNAI1 0.002 0.121 -9999 0 -0.715 2 2
mol:GDP 0 0 -9999 0 -9999 0 0
S1PR3 0.003 0.002 -9999 0 -0.014 1 1
S1PR2 0 0 -9999 0 -9999 0 0
EDG1 -0.071 0.241 -9999 0 -0.708 9 9
mol:Ca2+ 0.041 0.075 -9999 0 -0.396 1 1
MAPK3 0.05 0.071 -9999 0 -0.368 1 1
MAPK1 0.05 0.071 -9999 0 -0.368 1 1
JAK2 0.015 0.133 -9999 0 -0.477 3 3
CXCR4 -0.028 0.202 -9999 0 -0.435 13 13
FLT1 -0.128 0.297 -9999 0 -0.707 15 15
RhoA/GDP 0.007 0.065 -9999 0 -0.538 1 1
Rac1/GDP 0.015 0 -9999 0 -9999 0 0
SRC 0.05 0.071 -9999 0 -0.368 1 1
S1P/S1P3/Gi 0.041 0.075 -9999 0 -0.399 1 1
RAC1 0.02 0 -9999 0 -9999 0 0
RhoA/GTP 0.041 0.09 -9999 0 -0.413 2 2
VEGFA -0.128 0.297 -9999 0 -0.707 15 15
S1P/S1P2/Gi 0.036 0.07 -9999 0 -0.34 1 1
VEGFR1 homodimer/VEGFA homodimer -0.172 0.386 -9999 0 -0.816 18 18
RHOA 0.01 0.085 -9999 0 -0.708 1 1
S1P/S1P3/Gq -0.021 0.113 -9999 0 -0.31 8 8
GNAQ 0 0 -9999 0 -9999 0 0
GNAZ 0.014 0.064 -9999 0 -0.521 1 1
G12/G13 0.022 0.065 -9999 0 -0.526 1 1
GNA14 -0.058 0.222 -9999 0 -0.685 8 8
GNA15 0.01 0.085 -9999 0 -0.708 1 1
GNA12 0.02 0 -9999 0 -9999 0 0
GNA13 0.01 0.085 -9999 0 -0.708 1 1
GNA11 -0.01 0.124 -9999 0 -0.523 4 4
Rac1/GTP 0.047 0.069 -9999 0 -0.355 1 1
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.02 0 -9999 0 -9999 0 0
RAS family/GTP/Tiam1 0.013 0.107 -9999 0 -0.49 2 2
NT3 (dimer)/TRKC -0.018 0.146 -9999 0 -0.457 7 7
NT3 (dimer)/TRKB -0.051 0.175 -9999 0 -0.444 8 8
SHC/Grb2/SOS1/GAB1/PI3K 0.005 0.182 -9999 0 -0.764 3 3
RAPGEF1 0.01 0.085 -9999 0 -0.708 1 1
BDNF -0.253 0.328 -9999 0 -0.634 30 30
PIK3CA 0.02 0 -9999 0 -9999 0 0
DYNLT1 0.02 0 -9999 0 -9999 0 0
NTRK1 0.005 0.089 -9999 0 -0.523 2 2
NTRK2 -0.066 0.216 -9999 0 -0.597 10 10
NTRK3 0.005 0.089 -9999 0 -0.523 2 2
NT-4/5 (dimer)/TRKB -0.032 0.143 -9999 0 -0.363 11 11
neuron apoptosis 0.102 0.214 0.686 6 -9999 0 6
SHC 2-3/Grb2 -0.113 0.241 -9999 0 -0.781 6 6
SHC1 0.02 0 -9999 0 -9999 0 0
SHC2 -0.142 0.258 -9999 0 -0.71 10 10
SHC3 -0.075 0.097 -9999 0 -0.459 2 2
STAT3 (dimer) -0.065 0.197 -9999 0 -0.404 16 16
NT3 (dimer)/TRKA -0.005 0.132 -9999 0 -0.444 4 4
RIN/GDP 0.053 0.079 -9999 0 -0.34 1 1
GIPC1 0.02 0 -9999 0 -9999 0 0
KRAS 0.02 0 -9999 0 -9999 0 0
DNAJA3 -0.02 0.075 -9999 0 -0.39 2 2
RIN/GTP 0.015 0 -9999 0 -9999 0 0
CCND1 -0.177 0.419 -9999 0 -0.958 16 16
MAGED1 0.012 0.064 -9999 0 -0.523 1 1
PTPN11 0.02 0 -9999 0 -9999 0 0
RICS 0.02 0 -9999 0 -9999 0 0
NT-4/5 (dimer) 0 0 -9999 0 -9999 0 0
SHC/GRB2/SOS1 0.034 0.057 -9999 0 -0.444 1 1
GRB2 0.01 0.085 -9999 0 -0.708 1 1
NGF (dimer)/TRKA/MATK 0.008 0.077 -9999 0 -0.311 4 4
TRKA/NEDD4-2 -0.035 0.157 -9999 0 -0.396 11 11
ELMO1 0.01 0.085 -9999 0 -0.708 1 1
RhoG/GTP/ELMO1/DOCK1 0.007 0.096 -9999 0 -0.455 3 3
NGF 0 0 -9999 0 -9999 0 0
HRAS 0.02 0 -9999 0 -9999 0 0
DOCK1 0 0.12 -9999 0 -0.708 2 2
GAB2 0.02 0 -9999 0 -9999 0 0
RIT2 0.02 0 -9999 0 -9999 0 0
RIT1 -0.061 0.229 -9999 0 -0.708 8 8
FRS2 0.02 0 -9999 0 -9999 0 0
DNM1 -0.053 0.195 -9999 0 -0.564 9 9
mol:GTP 0 0 -9999 0 -9999 0 0
CRK 0 0.12 -9999 0 -0.708 2 2
SH2B1 (homopentamer) 0 0 -9999 0 -9999 0 0
RhoG/GTP -0.025 0.083 -9999 0 -0.372 3 3
mol:GDP 0.056 0.113 -9999 0 -0.568 1 1
NGF (dimer) 0 0 -9999 0 -9999 0 0
RhoG/GDP 0.007 0.065 -9999 0 -0.538 1 1
RIT1/GDP 0.026 0.122 -9999 0 -0.437 2 2
TIAM1 -0.01 0.145 -9999 0 -0.708 3 3
PIK3R1 -0.038 0.194 -9999 0 -0.677 6 6
BDNF (dimer)/TRKB -0.19 0.246 -9999 0 -0.5 20 20
KIDINS220/CRKL/C3G 0.022 0.065 -9999 0 -0.526 1 1
SHC/RasGAP 0.03 0 -9999 0 -9999 0 0
FRS2 family/SHP2 0.036 0.04 -9999 0 -9999 0 0
SHC/GRB2/SOS1/GAB1 0.021 0.132 -9999 0 -0.497 4 4
RIT1/GTP -0.047 0.174 -9999 0 -0.538 8 8
NT3 (dimer) -0.028 0.176 -9999 0 -0.67 5 5
RAP1/GDP -0.017 0.059 -9999 0 -0.323 2 2
KIDINS220/CRKL 0.02 0 -9999 0 -9999 0 0
BDNF (dimer) -0.252 0.327 -9999 0 -0.633 30 30
ubiquitin-dependent protein catabolic process -0.029 0.135 -9999 0 -0.336 11 11
Schwann cell development -0.027 0.028 -9999 0 -9999 0 0
EHD4 0.02 0 -9999 0 -9999 0 0
FRS2 family/GRB2/SOS1 0.041 0.063 -9999 0 -9999 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.044 0.092 -9999 0 -0.654 1 1
RAP1B 0.01 0.085 -9999 0 -0.708 1 1
RAP1A 0.01 0.085 -9999 0 -0.708 1 1
CDC42/GTP -0.176 0.192 -9999 0 -0.619 7 7
ABL1 0.02 0 -9999 0 -9999 0 0
SH2B family/GRB2/SOS1 0.022 0.065 -9999 0 -0.526 1 1
Rap1/GTP -0.077 0.137 -9999 0 -0.754 2 2
STAT3 -0.065 0.197 -9999 0 -0.403 16 16
axon guidance -0.17 0.183 -9999 0 -0.587 7 7
MAPK3 0.02 0.07 -9999 0 -9999 0 0
MAPK1 0.02 0.07 -9999 0 -9999 0 0
CDC42/GDP 0.053 0.079 -9999 0 -0.34 1 1
NTF3 -0.028 0.177 -9999 0 -0.671 5 5
NTF4 0 0 -9999 0 -9999 0 0
NGF (dimer)/TRKA/FAIM 0.007 0.105 -9999 0 -0.454 3 3
PI3K -0.014 0.147 -9999 0 -0.499 6 6
FRS3 0.012 0.064 -9999 0 -0.523 1 1
FAIM 0.002 0.106 -9999 0 -0.616 2 2
GAB1 -0.02 0.167 -9999 0 -0.708 4 4
RASGRF1 -0.02 0.075 -9999 0 -0.39 2 2
SOS1 0.02 0 -9999 0 -9999 0 0
MCF2L -0.007 0.137 -9999 0 -0.443 5 5
RGS19 0.02 0 -9999 0 -9999 0 0
CDC42 0.02 0 -9999 0 -9999 0 0
RAS family/GTP 0.067 0.09 -9999 0 -0.628 1 1
Rac1/GDP 0.053 0.079 -9999 0 -0.34 1 1
NGF (dimer)/TRKA/GRIT 0.018 0.055 -9999 0 -0.311 2 2
neuron projection morphogenesis -0.029 0.196 -9999 0 -0.906 2 2
NGF (dimer)/TRKA/NEDD4-2 -0.029 0.135 -9999 0 -0.338 11 11
MAP2K1 0.029 0.124 -9999 0 -0.746 1 1
NGFR 0.012 0.064 -9999 0 -0.523 1 1
NGF (dimer)/TRKA/GIPC/GAIP 0.014 0.08 -9999 0 -0.286 2 2
RAS family/GTP/PI3K 0.015 0.091 -9999 0 -9999 0 0
FRS2 family/SHP2/GRB2/SOS1 0.05 0.06 -9999 0 -9999 0 0
NRAS 0.005 0.089 -9999 0 -0.523 2 2
GRB2/SOS1 0.022 0.065 -9999 0 -0.526 1 1
PRKCI 0.02 0 -9999 0 -9999 0 0
ChemicalAbstracts:146-91-8 0 0 -9999 0 -9999 0 0
RAC1 0.02 0 -9999 0 -9999 0 0
PRKCZ 0 0 -9999 0 -9999 0 0
MAPKKK cascade -0.037 0.135 -9999 0 -1.077 1 1
RASA1 0.02 0 -9999 0 -9999 0 0
TRKA/c-Abl 0.019 0.065 -9999 0 -0.366 2 2
SQSTM1 0.02 0 -9999 0 -9999 0 0
BDNF (dimer)/TRKB/GIPC -0.161 0.229 -9999 0 -0.45 20 20
NGF (dimer)/TRKA/p62/Atypical PKCs 0.028 0.048 -9999 0 -9999 0 0
MATK 0.005 0.089 -9999 0 -0.523 2 2
NEDD4L -0.055 0.188 -9999 0 -0.523 10 10
RAS family/GDP -0.013 0.041 -9999 0 -9999 0 0
NGF (dimer)/TRKA -0.022 0.081 -9999 0 -0.42 2 2
Rac1/GTP -0.028 0.077 -9999 0 -0.373 2 2
FRS2 family/SHP2/CRK family 0.044 0.077 -9999 0 -9999 0 0
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.039 0.186 -9999 0 -0.489 5 5
MAP3K8 -0.09 0.258 -9999 0 -0.695 11 11
FOS -0.016 0.127 -9999 0 -0.363 3 3
PRKCA 0.016 0.01 -9999 0 -9999 0 0
PTPN7 0.002 0.089 -9999 0 -0.521 2 2
HRAS 0.019 0.001 -9999 0 -9999 0 0
PRKCB -0.003 0.008 -9999 0 -0.016 20 20
NRAS 0.004 0.09 -9999 0 -0.529 2 2
RAS family/GTP 0.022 0.056 -9999 0 -9999 0 0
MAPK3 0.002 0.075 -9999 0 -9999 0 0
MAP2K1 -0.013 0.118 -9999 0 -0.37 4 4
ELK1 0.017 0.008 -9999 0 -9999 0 0
BRAF -0.019 0.057 -9999 0 -9999 0 0
mol:GTP -0.001 0.002 -9999 0 -0.005 20 20
MAPK1 0.002 0.075 -9999 0 -9999 0 0
RAF1 -0.004 0.015 -9999 0 -9999 0 0
KRAS 0.019 0.001 -9999 0 -9999 0 0
ErbB2/ErbB3 signaling events

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
USP8 0.027 0.006 -9999 0 -9999 0 0
RAS family/GTP -0.019 0.161 -9999 0 -0.548 2 2
NFATC4 -0.014 0.145 -9999 0 -0.48 2 2
ERBB2IP 0.02 0.003 -9999 0 -9999 0 0
HSP90 (dimer) 0.005 0.089 -9999 0 -0.523 2 2
mammary gland morphogenesis -0.038 0.164 -9999 0 -0.599 1 1
JUN 0.038 0.097 -9999 0 -9999 0 0
HRAS 0.02 0.001 -9999 0 -9999 0 0
DOCK7 -0.033 0.161 -9999 0 -0.561 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.067 0.188 -9999 0 -0.411 15 15
AKT1 0.016 0.004 -9999 0 -9999 0 0
BAD 0.028 0.003 -9999 0 -9999 0 0
MAPK10 -0.026 0.125 -9999 0 -0.315 5 5
mol:GTP 0 0.002 -9999 0 -9999 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.041 0.177 -9999 0 -0.666 1 1
RAF1 -0.005 0.167 -9999 0 -0.634 1 1
ErbB2/ErbB3/neuregulin 2 -0.078 0.198 -9999 0 -0.491 11 11
STAT3 -0.011 0.122 -9999 0 -1.039 1 1
cell migration -0.001 0.117 -9999 0 -0.3 4 4
mol:PI-3-4-5-P3 -0.001 0.003 -9999 0 -9999 0 0
cell proliferation -0.054 0.31 -9999 0 -0.672 11 11
FOS -0.056 0.268 -9999 0 -0.49 15 15
NRAS 0.005 0.09 -9999 0 -0.527 2 2
mol:Ca2+ -0.038 0.164 -9999 0 -0.599 1 1
MAPK3 -0.031 0.256 -9999 0 -0.57 9 9
MAPK1 -0.031 0.256 -9999 0 -0.557 10 10
JAK2 -0.029 0.158 -9999 0 -0.561 1 1
NF2 -0.001 0.003 -9999 0 -9999 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.04 0.169 -9999 0 -0.354 13 13
NRG1 -0.046 0.202 -9999 0 -0.657 7 7
GRB2/SOS1 0.022 0.065 -9999 0 -0.529 1 1
MAPK8 -0.019 0.147 -9999 0 -0.425 1 1
MAPK9 0.005 0.11 -9999 0 -0.335 3 3
ERBB2 -0.015 0.09 -9999 0 -0.547 2 2
ERBB3 -0.071 0.241 -9999 0 -0.71 9 9
SHC1 0.02 0.001 -9999 0 -9999 0 0
RAC1 0.02 0 -9999 0 -9999 0 0
apoptosis 0.003 0.011 -9999 0 -9999 0 0
STAT3 (dimer) 0.014 0.122 -9999 0 -1.008 1 1
RNF41 0.035 0.009 -9999 0 -9999 0 0
FRAP1 0.028 0.003 -9999 0 -9999 0 0
RAC1-CDC42/GTP -0.053 0.094 -9999 0 -0.373 1 1
ErbB2/ErbB2/HSP90 (dimer) -0.022 0.091 -9999 0 -0.391 4 4
CHRNA1 0.001 0.196 -9999 0 -0.413 6 6
myelination 0.001 0.142 -9999 0 -0.435 2 2
PPP3CB -0.026 0.148 -9999 0 -0.513 1 1
KRAS 0.02 0.001 -9999 0 -9999 0 0
RAC1-CDC42/GDP -0.013 0.15 -9999 0 -0.767 1 1
NRG2 -0.04 0.171 -9999 0 -0.523 8 8
mol:GDP -0.039 0.168 -9999 0 -0.352 13 13
SOS1 0.02 0.001 -9999 0 -9999 0 0
MAP2K2 0.002 0.17 -9999 0 -0.554 1 1
SRC 0.02 0 -9999 0 -9999 0 0
mol:cAMP -0.001 0.002 -9999 0 -9999 0 0
PTPN11 -0.03 0.157 -9999 0 -0.562 1 1
MAP2K1 -0.041 0.244 -9999 0 -0.543 9 9
heart morphogenesis -0.038 0.164 -9999 0 -0.599 1 1
RAS family/GDP -0.015 0.159 -9999 0 -0.557 2 2
GRB2 0.01 0.085 -9999 0 -0.71 1 1
PRKACA -0.004 0.008 -9999 0 -9999 0 0
CHRNE 0.026 0.025 -9999 0 -9999 0 0
HSP90AA1 0.005 0.089 -9999 0 -0.523 2 2
activation of caspase activity -0.016 0.004 -9999 0 -9999 0 0
nervous system development -0.038 0.164 -9999 0 -0.599 1 1
CDC42 0.02 0 -9999 0 -9999 0 0
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.02 0.024 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.061 0.131 -9999 0 -0.387 2 2
ERC1 0.01 0.085 -9999 0 -0.708 1 1
RIP2/NOD2 -0.1 0.229 -9999 0 -0.49 18 18
NFKBIA 0.035 0.156 -9999 0 -0.713 3 3
BIRC2 0.02 0 -9999 0 -9999 0 0
IKBKB 0.02 0 -9999 0 -9999 0 0
RIPK2 0.012 0.064 -9999 0 -0.523 1 1
IKBKG -0.02 0.194 -9999 0 -0.541 6 6
IKK complex/A20 -0.099 0.241 -9999 0 -0.718 8 8
NEMO/A20/RIP2 0.012 0.064 -9999 0 -0.523 1 1
XPO1 0.02 0 -9999 0 -9999 0 0
NEMO/ATM -0.018 0.213 -9999 0 -0.626 6 6
tumor necrosis factor receptor activity 0 0 -9999 0 -9999 0 0
RAN 0.02 0 -9999 0 -9999 0 0
Exportin 1/RanGTP 0.027 0 -9999 0 -9999 0 0
IKK complex/ELKS -0.059 0.151 -9999 0 -0.779 2 2
BCL10/MALT1/TRAF6 0 0.134 -9999 0 -0.444 6 6
NOD2 -0.147 0.292 -9999 0 -0.646 18 18
NFKB1 0.02 0.025 -9999 0 -9999 0 0
RELA 0.02 0.025 -9999 0 -9999 0 0
MALT1 -0.031 0.185 -9999 0 -0.708 5 5
cIAP1/UbcH5C 0.03 0 -9999 0 -9999 0 0
ATM 0 0.12 -9999 0 -0.708 2 2
TNF/TNFR1A -0.044 0.201 -9999 0 -0.557 9 9
TRAF6 0.02 0 -9999 0 -9999 0 0
PRKCA 0.02 0 -9999 0 -9999 0 0
CHUK 0.02 0 -9999 0 -9999 0 0
UBE2D3 0.02 0 -9999 0 -9999 0 0
TNF 0.002 0.106 -9999 0 -0.616 2 2
NF kappa B1 p50/RelA -0.013 0.061 -9999 0 -9999 0 0
BCL10 0.01 0.085 -9999 0 -0.708 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.035 0.154 -9999 0 -0.705 3 3
beta TrCP1/SCF ubiquitin ligase complex 0.02 0.025 -9999 0 -9999 0 0
TNFRSF1A -0.061 0.229 -9999 0 -0.708 8 8
IKK complex 0.003 0.179 -9999 0 -0.978 1 1
CYLD 0.01 0.085 -9999 0 -0.708 1 1
IKK complex/PKC alpha -0.057 0.143 -9999 0 -0.93 1 1
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.02 0 -9999 0 -9999 0 0
SPHK1 -0.068 0.209 -9999 0 -0.557 11 11
GNAI2 0.01 0.085 -9999 0 -0.708 1 1
mol:S1P -0.01 0.103 -9999 0 -0.339 4 4
GNAO1 0.02 0 -9999 0 -9999 0 0
mol:Sphinganine-1-P -0.032 0.156 -9999 0 -0.395 11 11
growth factor activity 0 0 -9999 0 -9999 0 0
S1P/S1P2/G12/G13 0.008 0.097 -9999 0 -0.507 1 1
GNAI3 0.02 0 -9999 0 -9999 0 0
G12/G13 0.022 0.065 -9999 0 -0.526 1 1
S1PR3 0 0 -9999 0 -9999 0 0
S1PR2 0 0 -9999 0 -9999 0 0
EDG1 -0.071 0.241 -9999 0 -0.708 9 9
S1P1/S1P -0.054 0.204 -9999 0 -0.531 10 10
S1PR5 0 0 -9999 0 -9999 0 0
S1PR4 0 0 -9999 0 -9999 0 0
GNAI1 0 0.12 -9999 0 -0.708 2 2
S1P/S1P5/G12 0.001 0.08 -9999 0 -0.258 4 4
S1P/S1P3/Gq -0.026 0.127 -9999 0 -0.322 9 9
S1P/S1P4/Gi 0.023 0.09 -9999 0 -0.411 2 2
GNAQ 0 0 -9999 0 -9999 0 0
GNAZ 0.012 0.064 -9999 0 -0.523 1 1
GNA14 -0.058 0.222 -9999 0 -0.685 8 8
GNA15 0.01 0.085 -9999 0 -0.708 1 1
GNA12 0.02 0 -9999 0 -9999 0 0
GNA13 0.01 0.085 -9999 0 -0.708 1 1
GNA11 -0.01 0.124 -9999 0 -0.523 4 4
ABCC1 0.002 0.106 -9999 0 -0.616 2 2
Noncanonical Wnt signaling 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
NFATC2 0.01 0.085 -9999 0 -0.708 1 1
GNB1/GNG2 -0.009 0.152 -9999 0 -0.683 2 2
mol:DAG 0.003 0.14 -9999 0 -0.609 2 2
PLCG1 0.002 0.145 -9999 0 -0.635 2 2
YES1 -0.015 0.141 -9999 0 -0.785 1 1
FZD3 -0.038 0.194 -9999 0 -0.677 6 6
FZD6 -0.018 0.157 -9999 0 -0.662 4 4
G protein 0.002 0.147 -9999 0 -0.645 2 2
MAP3K7 0.024 0.121 -9999 0 -0.487 2 2
mol:Ca2+ 0.003 0.136 -9999 0 -0.586 2 2
mol:IP3 0.003 0.14 -9999 0 -0.609 2 2
NLK 0.016 0.14 -9999 0 -1.156 1 1
GNB1 0.01 0.085 -9999 0 -0.708 1 1
CAMK2A 0.014 0.129 -9999 0 -0.539 2 2
MAP3K7IP1 0.01 0.085 -9999 0 -0.708 1 1
Noncanonical Wnts/FZD -0.029 0.149 -9999 0 -0.837 1 1
CSNK1A1 0.02 0 -9999 0 -9999 0 0
GNAS -0.015 0.141 -9999 0 -0.785 1 1
GO:0007205 0.003 0.138 -9999 0 -0.602 2 2
WNT6 0.02 0 -9999 0 -9999 0 0
WNT4 -0.013 0.136 -9999 0 -0.57 4 4
NFAT1/CK1 alpha 0.011 0.144 -9999 0 -0.626 2 2
GNG2 0.02 0 -9999 0 -9999 0 0
WNT5A -0.025 0.15 -9999 0 -0.523 6 6
WNT11 -0.01 0.124 -9999 0 -0.523 4 4
CDC42 -0.004 0.135 -9999 0 -0.735 1 1
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.011 0.091 -9999 0 -0.419 3 3
CRKL 0.002 0.183 -9999 0 -0.681 4 4
mol:PIP3 -0.03 0.01 -9999 0 -9999 0 0
AKT1 -0.005 0.048 -9999 0 -0.407 1 1
PTK2B 0.02 0 -9999 0 -9999 0 0
RAPGEF1 0.008 0.188 -9999 0 -0.719 4 4
RANBP10 0.02 0 -9999 0 -9999 0 0
PIK3CA 0.02 0 -9999 0 -9999 0 0
HGF/MET/SHIP2 -0.006 0.152 -9999 0 -0.554 4 4
MAP3K5 0.014 0.179 -9999 0 -0.616 4 4
HGF/MET/CIN85/CBL/ENDOPHILINS -0.012 0.17 -9999 0 -0.475 7 7
AP1 -0.161 0.286 -9999 0 -0.528 24 24
mol:SU11274 0 0 -9999 0 -9999 0 0
SHC1 0.02 0 -9999 0 -9999 0 0
apoptosis -0.174 0.357 -9999 0 -0.864 14 14
STAT3 (dimer) 0.037 0.081 -9999 0 -9999 0 0
GAB1/CRKL/SHP2/PI3K -0.065 0.196 -9999 0 -0.808 4 4
INPP5D 0 0 -9999 0 -9999 0 0
CBL/CRK 0.005 0.205 -9999 0 -0.783 4 4
PTPN11 0.02 0 -9999 0 -9999 0 0
GO:0007205 0 0 -9999 0 -9999 0 0
PLCG1 0.02 0 -9999 0 -9999 0 0
PTEN 0.02 0 -9999 0 -9999 0 0
ELK1 -0.005 0.045 -9999 0 -0.213 3 3
mol:SU5416 0 0 -9999 0 -9999 0 0
SHP2/GRB2/SOS1GAB1 -0.029 0.083 -9999 0 -0.36 3 3
PAK1 0.001 0.055 -9999 0 -0.376 1 1
HGF/MET/RANBP10 -0.002 0.135 -9999 0 -0.403 7 7
HRAS 0.015 0.137 -9999 0 -0.631 2 2
DOCK1 0.003 0.202 -9999 0 -0.647 5 5
GAB1 -0.01 0.193 -9999 0 -0.73 4 4
CRK -0.008 0.221 -9999 0 -0.857 4 4
mol:PHA665752 0 0 -9999 0 -9999 0 0
mol:GDP -0.042 0.144 -9999 0 -0.672 3 3
JUN -0.094 0.256 -9999 0 -0.662 12 12
EntrezGene:200958 0 0 -9999 0 -9999 0 0
HGF/MET -0.011 0.091 -9999 0 -0.319 4 4
PIK3R1 -0.038 0.194 -9999 0 -0.677 6 6
cell morphogenesis 0.035 0.179 -9999 0 -0.589 4 4
GRB2/SHC 0.009 0.094 -9999 0 -0.357 2 2
FOS -0.157 0.289 -9999 0 -0.616 20 20
GLMN 0 0 -9999 0 -9999 0 0
cell motility -0.005 0.045 -9999 0 -0.213 3 3
HGF/MET/MUC20 -0.016 0.135 -9999 0 -0.415 7 7
cell migration 0.008 0.092 -9999 0 -0.351 2 2
GRB2 0.01 0.085 -9999 0 -0.708 1 1
CBL 0.02 0 -9999 0 -9999 0 0
MET/RANBP10 0.011 0.091 -9999 0 -0.419 3 3
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.029 0.085 -9999 0 -9999 0 0
MET/MUC20 -0.004 0.091 -9999 0 -0.433 3 3
RAP1B 0.015 0.185 -9999 0 -0.631 5 5
RAP1A 0.015 0.185 -9999 0 -0.631 5 5
HGF/MET/RANBP9 -0.002 0.135 -9999 0 -0.403 7 7
RAF1 0.026 0.13 -9999 0 -0.582 2 2
STAT3 0.037 0.082 -9999 0 -9999 0 0
cell proliferation 0.036 0.125 -9999 0 -0.487 1 1
RPS6KB1 0.009 0.034 -9999 0 -9999 0 0
MAPK3 -0.012 0.042 -9999 0 -9999 0 0
MAPK1 -0.012 0.042 -9999 0 -9999 0 0
RANBP9 0.02 0 -9999 0 -9999 0 0
MAPK8 0.039 0.153 -9999 0 -0.507 4 4
SRC 0.039 0.081 -9999 0 -9999 0 0
PI3K -0.017 0.161 -9999 0 -0.535 5 5
MET/Glomulin 0.002 0.081 -9999 0 -0.38 3 3
SOS1 0.02 0 -9999 0 -9999 0 0
MAP2K1 0.036 0.121 -9999 0 -0.653 1 1
MET -0.005 0.122 -9999 0 -0.585 3 3
MAP4K1 0.013 0.187 -9999 0 -0.616 5 5
PTK2 0.02 0 -9999 0 -9999 0 0
MAP2K2 0.036 0.121 -9999 0 -0.653 1 1
BAD 0.005 0.046 -9999 0 -0.376 1 1
MAP2K4 0.026 0.163 -9999 0 -0.541 4 4
SHP2/GRB2/SOS1/GAB1 -0.048 0.161 -9999 0 -0.67 4 4
INPPL1 0.012 0.064 -9999 0 -0.523 1 1
PXN 0.02 0 -9999 0 -9999 0 0
SH3KBP1 -0.02 0.167 -9999 0 -0.708 4 4
HGS 0.002 0.085 -9999 0 -0.315 3 3
PLCgamma1/PKC 0.015 0 -9999 0 -9999 0 0
HGF -0.023 0.159 -9999 0 -0.597 5 5
RASA1 0.02 0 -9999 0 -9999 0 0
NCK1 0.01 0.085 -9999 0 -0.708 1 1
PTPRJ -0.01 0.124 -9999 0 -0.523 4 4
NCK/PLCgamma1 0.011 0.096 -9999 0 -0.365 2 2
PDPK1 -0.02 0.051 -9999 0 -0.446 1 1
HGF/MET/SHIP -0.016 0.135 -9999 0 -0.415 7 7
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.01 0.085 -9999 0 -0.708 1 1
HDAC2 0.02 0.001 -9999 0 -9999 0 0
GNB1/GNG2 -0.014 0.146 -9999 0 -0.443 6 6
forebrain development -0.04 0.222 -9999 0 -0.693 5 5
GNAO1 0.021 0.002 -9999 0 -9999 0 0
SMO/beta Arrestin2 -0.022 0.159 -9999 0 -0.464 8 8
SMO -0.052 0.209 -9999 0 -0.637 8 8
ARRB2 0.021 0.003 -9999 0 -9999 0 0
GLI3/SPOP 0.015 0.123 -9999 0 -0.358 1 1
mol:GTP 0.001 0.002 -9999 0 -9999 0 0
GSK3B 0.02 0 -9999 0 -9999 0 0
GNAI2 0.011 0.086 -9999 0 -0.711 1 1
SIN3/HDAC complex 0.019 0.114 -9999 0 -0.397 5 5
GNAI1 0.001 0.12 -9999 0 -0.707 2 2
XPO1 0.023 0.006 -9999 0 -9999 0 0
GLI1/Su(fu) -0.102 0.244 -9999 0 -0.926 5 5
SAP30 -0.021 0.167 -9999 0 -0.708 4 4
mol:GDP -0.052 0.209 -9999 0 -0.636 8 8
MIM/GLI2A -0.021 0.172 -9999 0 -0.583 6 6
IFT88 -0.061 0.229 -9999 0 -0.708 8 8
GNAI3 0.021 0.001 -9999 0 -9999 0 0
GLI2 0.046 0.064 -9999 0 -9999 0 0
GLI3 0.004 0.128 -9999 0 -0.358 3 3
CSNK1D 0.02 0 -9999 0 -9999 0 0
CSNK1E 0.01 0.085 -9999 0 -0.708 1 1
SAP18 0.02 0 -9999 0 -9999 0 0
embryonic digit morphogenesis -0.061 0.228 -9999 0 -0.707 8 8
GNG2 0.02 0 -9999 0 -9999 0 0
Gi family/GTP 0.011 0.107 -9999 0 -9999 0 0
SIN3B 0.02 0.001 -9999 0 -9999 0 0
SIN3A 0.01 0.085 -9999 0 -0.708 1 1
GLI3/Su(fu) -0.012 0.249 -9999 0 -0.824 5 5
GLI2/Su(fu) 0.015 0.178 -9999 0 -0.738 3 3
FOXA2 -0.069 0.208 -9999 0 -1.007 2 2
neural tube patterning -0.04 0.222 -9999 0 -0.693 5 5
SPOP 0.02 0 -9999 0 -9999 0 0
Su(fu)/PIAS1 -0.011 0.197 -9999 0 -0.758 4 4
GNB1 0.01 0.085 -9999 0 -0.708 1 1
CSNK1G2 0.02 0 -9999 0 -9999 0 0
CSNK1G3 0.02 0 -9999 0 -9999 0 0
MTSS1 -0.021 0.172 -9999 0 -0.584 6 6
embryonic limb morphogenesis -0.04 0.222 -9999 0 -0.693 5 5
SUFU -0.023 0.211 -9999 0 -0.822 4 4
LGALS3 -0.063 0.196 -9999 0 -0.523 11 11
catabolic process 0.047 0.123 -9999 0 -9999 0 0
GLI3A/CBP -0.037 0.125 -9999 0 -0.36 3 3
KIF3A 0.01 0.085 -9999 0 -0.708 1 1
GLI1 -0.042 0.228 -9999 0 -0.715 5 5
RAB23 0.012 0.064 -9999 0 -0.523 1 1
CSNK1A1 0.02 0 -9999 0 -9999 0 0
IFT172 0.02 0 -9999 0 -9999 0 0
RBBP7 0.02 0.001 -9999 0 -9999 0 0
Su(fu)/Galectin3 -0.054 0.27 -9999 0 -0.79 7 7
GNAZ 0.013 0.064 -9999 0 -0.522 1 1
RBBP4 0.02 0 -9999 0 -9999 0 0
CSNK1G1 0.02 0 -9999 0 -9999 0 0
PIAS1 0.02 0 -9999 0 -9999 0 0
PRKACA 0.02 0 -9999 0 -9999 0 0
GLI2/SPOP 0.053 0.06 -9999 0 -9999 0 0
STK36 -0.017 0.168 -9999 0 -0.708 4 4
Gi family/GNB1/GNG2/GDP 0.022 0.12 -9999 0 -0.667 1 1
PTCH1 -0.023 0.2 -9999 0 -0.649 4 4
MIM/GLI1 -0.055 0.267 -9999 0 -0.779 6 6
CREBBP -0.037 0.125 -9999 0 -0.36 3 3
Su(fu)/SIN3/HDAC complex 0.029 0.162 -9999 0 -0.753 2 2
Aurora A signaling

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
Aurora A/GADD45A 0.006 0.11 -9999 0 -0.443 2 2
BIRC5 -0.01 0.124 -9999 0 -0.523 4 4
NFKBIA 0.023 0.1 -9999 0 -0.444 3 3
CPEB1 -0.131 0.243 -9999 0 -0.523 20 20
AKT1 0.043 0.022 -9999 0 -9999 0 0
NDEL1 0.01 0.085 -9999 0 -0.708 1 1
Aurora A/BRCA1 0.002 0.02 -9999 0 -9999 0 0
NDEL1/TACC3 0.02 0.089 -9999 0 -0.374 1 1
GADD45A -0.03 0.169 -9999 0 -0.585 6 6
GSK3B 0.02 0.006 -9999 0 -9999 0 0
PAK1/Aurora A 0.034 0.045 -9999 0 -0.298 1 1
MDM2 0.02 0 -9999 0 -9999 0 0
JUB -0.106 0.271 -9999 0 -0.68 13 13
TPX2 0.006 0.102 -9999 0 -0.367 5 5
TP53 0.038 0.047 -9999 0 -0.333 1 1
DLG7 0.031 0.073 -9999 0 -0.444 1 1
AURKAIP1 0.02 0 -9999 0 -9999 0 0
ARHGEF7 0.02 0 -9999 0 -9999 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -9999 0 0
Aurora A/NDEL1/TACC3 0.021 0.094 -9999 0 -0.396 1 1
G2/M transition of mitotic cell cycle 0.002 0.02 -9999 0 -9999 0 0
AURKA 0.035 0.027 -9999 0 -9999 0 0
AURKB 0.018 0.02 -9999 0 -9999 0 0
CDC25B 0.016 0.061 -9999 0 -9999 0 0
G2/M transition checkpoint -0.067 0.151 -9999 0 -0.404 11 11
mRNA polyadenylation -0.075 0.124 -9999 0 -0.277 17 17
Aurora A/CPEB -0.075 0.124 -9999 0 -0.278 17 17
Aurora A/TACC1/TRAP/chTOG 0.053 0.05 -9999 0 -0.341 1 1
BRCA1 0.02 0 -9999 0 -9999 0 0
centrosome duplication 0.034 0.045 -9999 0 -0.297 1 1
regulation of centrosome cycle -0.019 0.077 -9999 0 -0.371 1 1
spindle assembly 0.051 0.049 -9999 0 -0.338 1 1
TDRD7 0.02 0 -9999 0 -9999 0 0
Aurora A/RasGAP/Survivin 0.039 0.07 -9999 0 -0.352 1 1
CENPA 0.02 0.033 -9999 0 -0.178 1 1
Aurora A/PP2A 0.034 0.045 -9999 0 -9999 0 0
meiosis 0 0 -9999 0 -9999 0 0
protein catabolic process 0.05 0.059 -9999 0 -0.304 1 1
negative regulation of DNA binding 0.038 0.046 -9999 0 -0.332 1 1
prophase 0 0 -9999 0 -9999 0 0
GIT1/beta-PIX 0.022 0.065 -9999 0 -0.526 1 1
RASA1 0.02 0 -9999 0 -9999 0 0
Ajuba/Aurora A -0.068 0.152 -9999 0 -0.407 11 11
mitotic prometaphase 0 0.002 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.035 0.027 -9999 0 -9999 0 0
TACC1 0.01 0.085 -9999 0 -0.708 1 1
TACC3 -0.018 0.138 -9999 0 -0.523 5 5
Aurora A/Antizyme1 0.048 0.019 -9999 0 -9999 0 0
Aurora A/RasGAP 0.038 0.021 -9999 0 -9999 0 0
OAZ1 0.02 0 -9999 0 -9999 0 0
RAN 0.02 0 -9999 0 -9999 0 0
mitosis 0 0 -9999 0 -9999 0 0
PRKACA 0.02 0.006 -9999 0 -9999 0 0
GIT1 0.01 0.085 -9999 0 -0.708 1 1
GIT1/beta-PIX/PAK1 0.029 0.069 -9999 0 -0.444 1 1
Importin alpha/Importin beta/TPX2 0.006 0.102 -9999 0 -0.366 5 5
PPP2R5D 0.012 0.064 -9999 0 -0.523 1 1
Aurora A/TPX2 0.028 0.085 -9999 0 -0.398 1 1
PAK1 0.012 0.064 -9999 0 -0.523 1 1
CKAP5 0.02 0 -9999 0 -9999 0 0
EPO signaling pathway

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
BCL2L1 -0.018 0.191 -9999 0 -0.637 2 2
CRKL -0.027 0.14 -9999 0 -9999 0 0
mol:DAG -0.011 0.129 -9999 0 -9999 0 0
HRAS -0.008 0.165 -9999 0 -0.565 3 3
MAPK8 -0.031 0.131 -9999 0 -9999 0 0
RAP1A -0.033 0.144 -9999 0 -9999 0 0
GAB1 -0.049 0.179 -9999 0 -0.718 2 2
MAPK14 -0.031 0.131 -9999 0 -9999 0 0
EPO -0.135 0.244 -9999 0 -0.516 21 21
PLCG1 -0.012 0.131 -9999 0 -9999 0 0
EPOR/TRPC2/IP3 Receptors 0.016 0.013 -9999 0 -9999 0 0
RAPGEF1 0.01 0.085 -9999 0 -0.708 1 1
EPO/EPOR (dimer)/SOCS3 -0.083 0.182 -9999 0 -0.494 5 5
GAB1/SHC/GRB2/SOS1 -0.078 0.137 -9999 0 -0.613 3 3
EPO/EPOR (dimer) -0.081 0.179 -9999 0 -0.359 21 21
IRS2 -0.058 0.161 -9999 0 -0.534 2 2
STAT1 -0.052 0.202 -9999 0 -0.902 1 1
STAT5B -0.01 0.141 -9999 0 -9999 0 0
cell proliferation -0.018 0.122 -9999 0 -9999 0 0
GAB1/SHIP/PIK3R1/SHP2/SHC -0.093 0.17 -9999 0 -0.685 4 4
TEC -0.027 0.14 -9999 0 -9999 0 0
SOCS3 -0.028 0.177 -9999 0 -0.671 5 5
STAT1 (dimer) -0.05 0.198 -9999 0 -0.87 1 1
JAK2 0.016 0.012 -9999 0 -9999 0 0
PIK3R1 -0.038 0.194 -9999 0 -0.677 6 6
EPO/EPOR (dimer)/JAK2 -0.026 0.157 -9999 0 -0.393 2 2
EPO/EPOR -0.081 0.179 -9999 0 -0.359 21 21
LYN 0.021 0.006 -9999 0 -9999 0 0
TEC/VAV2 -0.014 0.138 -9999 0 -9999 0 0
elevation of cytosolic calcium ion concentration 0.016 0.013 -9999 0 -9999 0 0
SHC1 0.02 0 -9999 0 -9999 0 0
EPO/EPOR (dimer)/LYN -0.044 0.152 -9999 0 -9999 0 0
mol:IP3 -0.011 0.129 -9999 0 -9999 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.074 0.197 -9999 0 -0.596 5 5
SH2B3 -0.023 0.166 -9999 0 -0.706 4 4
NFKB1 -0.031 0.131 -9999 0 -9999 0 0
EPO/EPOR (dimer)/JAK2/SOCS3 -0.048 0.117 0.314 3 -0.308 1 4
PTPN6 -0.04 0.146 -9999 0 -0.389 2 2
TEC/VAV2/GRB2 -0.01 0.138 -9999 0 -9999 0 0
EPOR 0.016 0.013 -9999 0 -9999 0 0
INPP5D 0 0 -9999 0 -9999 0 0
mol:GDP -0.079 0.14 -9999 0 -0.624 3 3
SOS1 0.02 0 -9999 0 -9999 0 0
PLCG2 -0.055 0.188 -9999 0 -0.523 10 10
CRKL/CBL/C3G -0.01 0.138 -9999 0 -9999 0 0
VAV2 -0.027 0.14 -9999 0 -9999 0 0
CBL -0.027 0.14 -9999 0 -9999 0 0
SHC/Grb2/SOS1 -0.067 0.097 -9999 0 -9999 0 0
STAT5A -0.013 0.147 -9999 0 -9999 0 0
GRB2 0.01 0.085 -9999 0 -0.708 1 1
STAT5 (dimer) 0 0.175 -9999 0 -0.476 3 3
LYN/PLCgamma2 -0.025 0.137 -9999 0 -0.367 10 10
PTPN11 0.02 0 -9999 0 -9999 0 0
BTK -0.054 0.195 -9999 0 -0.639 4 4
BCL2 -0.064 0.315 -9999 0 -1.017 6 6
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0.02 0 -9999 0 -9999 0 0
MKNK1 0.02 0 -9999 0 -9999 0 0
mol:PIP3 -0.038 0.111 -9999 0 -0.393 6 6
FRAP1 0.018 0.045 -9999 0 -9999 0 0
AKT1 0.001 0.125 -9999 0 -0.393 6 6
INSR -0.071 0.241 -9999 0 -0.708 9 9
Insulin Receptor/Insulin -0.033 0.16 -9999 0 -0.455 9 9
mol:GTP -0.032 0.107 -9999 0 -0.524 2 2
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.018 0.063 -9999 0 -0.441 1 1
TSC2 0.02 0 -9999 0 -9999 0 0
RHEB/GDP -0.028 0.096 -9999 0 -0.467 2 2
TSC1 0.01 0.085 -9999 0 -0.709 1 1
Insulin Receptor/IRS1 -0.04 0.15 -9999 0 -0.416 9 9
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.021 0.076 -9999 0 -0.534 1 1
mol:GDP 0 0 -9999 0 -9999 0 0
EIF3A 0.02 0 -9999 0 -9999 0 0
RPS6KB1 0.021 0.077 -9999 0 -0.296 1 1
MAP3K5 0.003 0.072 -9999 0 -0.425 2 2
PIK3R1 -0.038 0.194 -9999 0 -0.677 6 6
apoptosis 0.003 0.072 -9999 0 -0.425 2 2
mol:LY294002 0 0 0.001 1 -0.001 3 4
EIF4B 0.031 0.07 -9999 0 -9999 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.016 0.053 -9999 0 -9999 0 0
eIF4E/eIF4G1/eIF4A1 -0.017 0.068 -9999 0 -0.486 1 1
KIAA1303 0.005 0.089 -9999 0 -0.523 2 2
PI3K -0.006 0.126 -9999 0 -0.405 6 6
mTOR/RHEB/GTP/Raptor/GBL 0.044 0.071 -9999 0 -0.305 1 1
FKBP1A 0.02 0.001 -9999 0 -9999 0 0
RHEB/GTP -0.028 0.094 -9999 0 -0.458 2 2
mol:Amino Acids 0 0 0.001 1 -0.001 3 4
FKBP12/Rapamycin 0.014 0.004 -9999 0 -9999 0 0
PDPK1 -0.04 0.124 -9999 0 -0.424 6 6
EIF4E 0.02 0 -9999 0 -9999 0 0
ASK1/PP5C 0.01 0.117 -9999 0 -0.629 2 2
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.045 0.032 -9999 0 -9999 0 0
TSC1/TSC2 0.019 0.135 -9999 0 -0.585 2 2
tumor necrosis factor receptor activity 0 0 0.001 3 -0.001 1 4
RPS6 0.012 0.064 -9999 0 -0.523 1 1
PPP5C 0.01 0.085 -9999 0 -0.708 1 1
EIF4G1 -0.01 0.145 -9999 0 -0.708 3 3
IRS1 -0.001 0.051 -9999 0 -0.186 5 5
INS 0.02 0 -9999 0 -9999 0 0
PTEN 0.019 0.001 -9999 0 -9999 0 0
PDK2 -0.035 0.103 -9999 0 -0.366 6 6
EIF4EBP1 -0.123 0.391 -9999 0 -1.225 8 8
PIK3CA 0.02 0.001 -9999 0 -9999 0 0
PPP2R5D 0.024 0.05 -9999 0 -9999 0 0
peptide biosynthetic process -0.023 0.166 -9999 0 -0.447 9 9
RHEB 0.02 0 -9999 0 -9999 0 0
EIF4A1 0.01 0.085 -9999 0 -0.708 1 1
mol:Rapamycin 0 0.001 -9999 0 -0.004 1 1
EEF2 -0.023 0.167 -9999 0 -0.45 9 9
eIF4E/4E-BP1 -0.103 0.365 -9999 0 -1.131 8 8
Signaling events mediated by HDAC Class III

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
EP300 0.01 0.085 -9999 0 -0.708 1 1
HDAC4 0.02 0 -9999 0 -9999 0 0
induction of apoptosis 0 0 -9999 0 -9999 0 0
regulation of S phase of mitotic cell cycle -0.008 0.068 0.538 1 -9999 0 1
CDKN1A -0.021 0.148 -9999 0 -0.89 2 2
KAT2B 0 0 -9999 0 -9999 0 0
BAX 0.02 0 -9999 0 -9999 0 0
FOXO3 0.009 0.063 0.518 1 -9999 0 1
FOXO1 -0.025 0.15 -9999 0 -0.523 6 6
FOXO4 0.029 0.042 -9999 0 -0.327 1 1
response to UV 0 0 -9999 0 -9999 0 0
XRCC6 0.02 0 -9999 0 -9999 0 0
TAT 0.012 0.064 -9999 0 -0.523 1 1
mol:Lysophosphatidic acid 0 0 -9999 0 -9999 0 0
MYOD1 0.001 0.091 -9999 0 -0.539 2 2
PPARGC1A -0.088 0.234 -9999 0 -0.58 13 13
FHL2 -0.159 0.293 -9999 0 -0.625 20 20
response to nutrient levels 0 0 -9999 0 -9999 0 0
KU70/SIRT1 -0.002 0.068 -9999 0 -0.527 1 1
HIST2H4A 0.008 0.068 -9999 0 -0.54 1 1
SIRT1/FOXO3a 0.002 0.071 0.323 1 -0.461 1 2
SIRT1 -0.004 0.091 -9999 0 -0.71 1 1
response to hypoxia 0 0 -9999 0 -9999 0 0
SIRT1/MEF2D/HDAC4 -0.001 0.059 -9999 0 -0.446 1 1
SIRT1/Histone H1b -0.018 0.081 -9999 0 -0.432 1 1
apoptosis 0.001 0.059 0.444 1 -9999 0 1
SIRT1/PGC1A -0.066 0.152 -9999 0 -0.364 14 14
p53/SIRT1 -0.003 0.114 0.434 2 -0.528 2 4
SIRT1/FOXO4 -0.004 0.067 -9999 0 -0.432 1 1
FOXO1/FHL2/SIRT1 -0.122 0.21 -9999 0 -0.523 12 12
HIST1H1E 0.009 0.078 -9999 0 -0.327 2 2
SIRT1/p300 -0.01 0.092 -9999 0 -0.527 2 2
muscle cell differentiation 0.014 0.095 0.455 3 -9999 0 3
TP53 -0.004 0.091 -9999 0 -0.71 1 1
KU70/SIRT1/BAX -0.001 0.059 -9999 0 -0.446 1 1
CREBBP 0.02 0 -9999 0 -9999 0 0
MEF2D 0.02 0 -9999 0 -9999 0 0
HIV-1 Tat/SIRT1 -0.007 0.08 -9999 0 -0.448 2 2
ACSS2 0.025 0.069 -9999 0 -0.527 1 1
SIRT1/PCAF/MYOD -0.014 0.096 -9999 0 -0.457 3 3
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.022 0.074 -9999 0 -0.614 1 1
Crk/p130 Cas/Paxillin -0.064 0.118 -9999 0 -0.516 3 3
JUN -0.034 0.174 -9999 0 -0.558 3 3
HRAS 0.02 0 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.071 0.187 -9999 0 -0.488 6 6
RAP1A 0.01 0.085 -9999 0 -0.708 1 1
FRS2 0.02 0 -9999 0 -9999 0 0
RAP1A/GDP 0.007 0.065 -9999 0 -0.538 1 1
RET51/GFRalpha1/GDNF/DOK1 -0.022 0.132 -9999 0 -9999 0 0
EntrezGene:5979 0 0 -9999 0 -9999 0 0
PTPN11 0.02 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
CRK 0 0.12 -9999 0 -0.708 2 2
RET9/GFRalpha1/GDNF/Enigma -0.026 0.126 -9999 0 -9999 0 0
RHOA 0.01 0.085 -9999 0 -0.708 1 1
RAP1A/GTP -0.102 0.153 -9999 0 -0.604 2 2
GRB7 0.012 0.064 -9999 0 -0.523 1 1
RET51/GFRalpha1/GDNF -0.022 0.132 -9999 0 -9999 0 0
MAPKKK cascade -0.059 0.109 -9999 0 -0.637 1 1
BCAR1 0.02 0 -9999 0 -9999 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.047 0.138 -9999 0 -9999 0 0
lamellipodium assembly -0.063 0.106 -9999 0 -0.421 4 4
RET51/GFRalpha1/GDNF/SHC -0.022 0.132 -9999 0 -9999 0 0
PIK3CA 0.02 0 -9999 0 -9999 0 0
RET9/GFRalpha1/GDNF/SHC -0.026 0.126 -9999 0 -9999 0 0
RET9/GFRalpha1/GDNF/Shank3 -0.05 0.152 -9999 0 -0.407 4 4
MAPK3 -0.052 0.17 -9999 0 -0.565 2 2
DOK1 0.02 0 -9999 0 -9999 0 0
DOK6 -0.169 0.299 -9999 0 -0.629 21 21
PXN 0.02 0 -9999 0 -9999 0 0
neurite development -0.07 0.188 -9999 0 -0.482 8 8
DOK5 -0.053 0.195 -9999 0 -0.564 9 9
GFRA1 -0.093 0.221 -9999 0 -0.523 15 15
MAPK8 0.017 0.095 -9999 0 -0.48 1 1
HRAS/GTP -0.048 0.089 -9999 0 -0.386 1 1
tube development -0.043 0.148 -9999 0 -0.375 5 5
MAPK1 -0.052 0.17 -9999 0 -0.565 2 2
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.002 0.084 -9999 0 -9999 0 0
Rac1/GDP 0.015 0 -9999 0 -9999 0 0
SRC 0.02 0 -9999 0 -9999 0 0
PDLIM7 0.02 0 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.116 0.187 -9999 0 -0.568 2 2
SHC1 0.02 0 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.077 0.194 -9999 0 -0.458 9 9
RET51/GFRalpha1/GDNF/Dok5 -0.064 0.17 -9999 0 -0.469 4 4
PRKCA 0.02 0 -9999 0 -9999 0 0
HRAS/GDP 0.015 0 -9999 0 -9999 0 0
CREB1 0.009 0.105 -9999 0 -0.602 1 1
PIK3R1 -0.038 0.194 -9999 0 -0.677 6 6
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.016 0.118 -9999 0 -0.597 1 1
RET51/GFRalpha1/GDNF/Grb7 -0.026 0.135 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
RET 0.005 0.089 -9999 0 -0.523 2 2
DOK4 -0.071 0.241 -9999 0 -0.708 9 9
JNK cascade -0.033 0.171 -9999 0 -0.543 3 3
RET9/GFRalpha1/GDNF/FRS2 -0.026 0.126 -9999 0 -9999 0 0
SHANK3 -0.02 0.167 -9999 0 -0.708 4 4
RASA1 0.02 0 -9999 0 -9999 0 0
NCK1 0.01 0.085 -9999 0 -0.708 1 1
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.002 0.084 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.006 0.1 -9999 0 -0.517 1 1
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.006 0.1 -9999 0 -0.517 1 1
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.006 0.096 -9999 0 -0.452 1 1
PI3K -0.042 0.208 -9999 0 -0.655 5 5
SOS1 0.02 0 -9999 0 -9999 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.042 0.148 -9999 0 -0.375 5 5
GRB10 -0.063 0.223 -9999 0 -0.646 9 9
activation of MAPKK activity 0.006 0.104 -9999 0 -0.608 1 1
RET51/GFRalpha1/GDNF/FRS2 -0.022 0.132 -9999 0 -9999 0 0
GAB1 -0.02 0.167 -9999 0 -0.708 4 4
IRS1 -0.018 0.138 -9999 0 -0.523 5 5
IRS2 -0.04 0.171 -9999 0 -0.523 8 8
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.013 0.145 -9999 0 -0.665 2 2
RET51/GFRalpha1/GDNF/PKC alpha -0.022 0.132 -9999 0 -9999 0 0
GRB2 0.01 0.085 -9999 0 -0.708 1 1
PRKACA 0.02 0 -9999 0 -9999 0 0
GDNF 0.02 0 -9999 0 -9999 0 0
RAC1 0.02 0 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.043 0.143 -9999 0 -9999 0 0
Rac1/GTP -0.074 0.129 -9999 0 -0.484 5 5
RET9/GFRalpha1/GDNF -0.043 0.137 -9999 0 -0.311 15 15
GFRalpha1/GDNF -0.053 0.161 -9999 0 -0.366 15 15
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC -0.122 0.317 -9999 0 -1.514 2 2
PLK1 0.008 0.256 -9999 0 -1.121 1 1
CDKN1B 0.046 0.19 -9999 0 -0.565 1 1
FOXO3 -0.006 0.285 -9999 0 -0.71 7 7
KAT2B 0.004 0.025 -9999 0 -0.063 3 3
FOXO1/SIRT1 -0.052 0.134 -9999 0 -0.442 3 3
CAT -0.006 0.312 -9999 0 -1.138 3 3
CTNNB1 0.02 0 -9999 0 -9999 0 0
AKT1 0.018 0.025 -9999 0 -9999 0 0
FOXO1 -0.043 0.151 -9999 0 -0.53 2 2
MAPK10 -0.051 0.183 -9999 0 -0.41 10 10
mol:GTP 0.001 0.004 -9999 0 -9999 0 0
FOXO4 0.016 0.218 -9999 0 -0.838 2 2
response to oxidative stress -0.004 0.03 -9999 0 -0.062 7 7
FOXO3A/SIRT1 -0.001 0.226 -9999 0 -0.587 6 6
XPO1 0.02 0.001 -9999 0 -9999 0 0
EP300 0.004 0.086 -9999 0 -0.708 1 1
BCL2L11 0.031 0.043 -9999 0 -9999 0 0
FOXO1/SKP2 -0.03 0.137 -9999 0 -0.483 2 2
mol:GDP -0.004 0.03 -9999 0 -0.062 7 7
RAN 0.021 0.003 -9999 0 -9999 0 0
GADD45A 0.029 0.273 -9999 0 -0.893 4 4
YWHAQ 0.02 0 -9999 0 -9999 0 0
FOXO1/14-3-3 family 0.071 0.056 -9999 0 -9999 0 0
MST1 -0.063 0.214 -9999 0 -0.557 11 11
CSNK1D 0.02 0 -9999 0 -9999 0 0
CSNK1E 0.01 0.085 -9999 0 -0.708 1 1
FOXO4/14-3-3 family 0.059 0.067 -9999 0 -9999 0 0
YWHAB 0.02 0 -9999 0 -9999 0 0
MAPK8 0.007 0.125 -9999 0 -0.466 3 3
MAPK9 -0.004 0.157 -9999 0 -0.432 7 7
YWHAG 0.02 0 -9999 0 -9999 0 0
YWHAE 0.02 0 -9999 0 -9999 0 0
YWHAZ 0.01 0.085 -9999 0 -0.708 1 1
SIRT1 0.014 0.088 -9999 0 -0.693 1 1
SOD2 -0.099 0.44 -9999 0 -0.985 13 13
RBL2 0.026 0.232 -9999 0 -1.004 1 1
RAL/GDP -0.008 0.137 -9999 0 -0.431 6 6
CHUK 0.026 0.021 -9999 0 -9999 0 0
Ran/GTP 0.015 0.01 -9999 0 -9999 0 0
CSNK1G2 0.02 0 -9999 0 -9999 0 0
RAL/GTP 0 0.132 -9999 0 -0.401 6 6
CSNK1G1 0.02 0 -9999 0 -9999 0 0
FASLG -0.269 0.565 -9999 0 -1.592 10 10
SKP2 0.02 0 -9999 0 -9999 0 0
USP7 0.021 0.003 -9999 0 -9999 0 0
IKBKB 0.026 0.021 -9999 0 -9999 0 0
CCNB1 0.002 0.265 -9999 0 -0.759 4 4
FOXO1-3a-4/beta catenin 0.014 0.247 -9999 0 -0.432 9 9
proteasomal ubiquitin-dependent protein catabolic process -0.03 0.136 -9999 0 -0.478 2 2
CSNK1A1 0.02 0 -9999 0 -9999 0 0
SGK1 0.004 0.025 -9999 0 -0.063 3 3
CSNK1G3 0.02 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0.026 0.018 -9999 0 -9999 0 0
ZFAND5 0.027 0.198 -9999 0 -0.63 3 3
SFN -0.025 0.15 -9999 0 -0.523 6 6
CDK2 0.007 0.027 -9999 0 -9999 0 0
FOXO3A/14-3-3 0.06 0.087 -9999 0 -0.404 1 1
CREBBP 0.007 0.027 -9999 0 -9999 0 0
FBXO32 -0.016 0.305 -9999 0 -0.845 5 5
BCL6 -0.066 0.458 -9999 0 -1.272 8 8
RALB 0 0.12 -9999 0 -0.711 2 2
RALA -0.017 0.139 -9999 0 -0.526 5 5
YWHAH 0.02 0 -9999 0 -9999 0 0
Retinoic acid receptors-mediated signaling

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
HDAC1 0.01 0.085 -9999 0 -0.708 1 1
HDAC3 0.02 0 -9999 0 -9999 0 0
VDR -0.139 0.279 -9999 0 -0.616 18 18
Cbp/p300/PCAF 0.02 0.056 -9999 0 -0.455 1 1
EP300 0.01 0.085 -9999 0 -0.708 1 1
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.048 0.058 -9999 0 -0.288 1 1
KAT2B 0 0 -9999 0 -9999 0 0
MAPK14 0.02 0 -9999 0 -9999 0 0
AKT1 0.039 0.076 0.25 2 -0.292 2 4
RAR alpha/9cRA/Cyclin H -0.023 0.068 -9999 0 -0.407 1 1
mol:9cRA 0 0 -9999 0 -9999 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.042 0.062 -9999 0 -0.29 1 1
CDC2 0.019 0.006 -9999 0 -9999 0 0
response to UV -0.001 0.009 -9999 0 -9999 0 0
RAR alpha/Jnk1 0.03 0.025 -9999 0 -9999 0 0
NCOR2 -0.02 0.167 -9999 0 -0.708 4 4
VDR/VDR/Vit D3 -0.104 0.209 -9999 0 -0.459 18 18
RXRs/RARs/NRIP1/9cRA 0.03 0.186 -9999 0 -0.512 7 7
NCOA2 0.012 0.064 -9999 0 -0.523 1 1
NCOA3 0.02 0 -9999 0 -9999 0 0
NCOA1 0.02 0 -9999 0 -9999 0 0
VDR/VDR/DNA -0.139 0.279 -9999 0 -0.615 18 18
RARG 0.02 0.006 -9999 0 -9999 0 0
RAR gamma1/9cRA 0.026 0.008 -9999 0 -9999 0 0
MAPK3 0.019 0.006 -9999 0 -9999 0 0
MAPK1 0.02 0 -9999 0 -9999 0 0
MAPK8 0.02 0.007 -9999 0 -9999 0 0
mol:Vit D3 0 0 -9999 0 -9999 0 0
RXRs/VDR/DNA/Vit D3 -0.096 0.157 -9999 0 -0.513 5 5
RARA 0.037 0.031 -9999 0 -9999 0 0
negative regulation of phosphoinositide 3-kinase cascade 0 0 -9999 0 -9999 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.04 0.066 -9999 0 -0.29 1 1
PRKCA 0.021 0.016 -9999 0 -9999 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 0.01 0.213 -9999 0 -0.618 7 7
RXRG 0.025 0.074 -9999 0 -0.378 2 2
RXRA 0.036 0.091 -9999 0 -0.495 1 1
RXRB 0.037 0.028 -9999 0 -9999 0 0
VDR/Vit D3/DNA -0.104 0.209 -9999 0 -0.459 18 18
RBP1 -0.038 0.179 -9999 0 -0.576 7 7
CRBP1/9-cic-RA -0.028 0.132 -9999 0 -0.425 7 7
RARB 0.001 0.12 -9999 0 -0.708 2 2
PRKCG 0.021 0.015 -9999 0 -9999 0 0
MNAT1 0.02 0 -9999 0 -9999 0 0
RAR alpha/RXRs 0.046 0.144 -9999 0 -0.525 1 1
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.046 0.129 -9999 0 -0.443 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.051 0.056 -9999 0 -9999 0 0
RXRs/RARs/NRIP1/9cRA/HDAC3 0.012 0.208 -9999 0 -0.601 7 7
positive regulation of DNA binding -0.022 0.065 -9999 0 -0.384 1 1
NRIP1 -0.06 0.419 -9999 0 -1.329 7 7
RXRs/RARs 0.023 0.151 -9999 0 -0.413 7 7
RXRs/RXRs/DNA/9cRA -0.033 0.101 -9999 0 -0.537 1 1
PRKACA 0.02 0 -9999 0 -9999 0 0
CDK7 0.01 0.085 -9999 0 -0.708 1 1
TFIIH 0.034 0.057 -9999 0 -0.444 1 1
RAR alpha/9cRA -0.003 0.038 -9999 0 -9999 0 0
CCNH 0.02 0 -9999 0 -9999 0 0
CREBBP 0.02 0 -9999 0 -9999 0 0
RAR gamma2/9cRA -0.005 0.038 -9999 0 -9999 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.02 0 -9999 0 -9999 0 0
Rac1/GDP 0.011 0.025 -9999 0 -9999 0 0
DOCK1 0 0.12 -9999 0 -0.708 2 2
ITGA4 -0.081 0.252 -9999 0 -0.708 10 10
RAC1 0.02 0 -9999 0 -9999 0 0
alpha4/beta7 Integrin -0.047 0.192 -9999 0 -0.526 10 10
mol:GTP 0 0 -9999 0 -9999 0 0
CRK 0 0.12 -9999 0 -0.708 2 2
alpha4/beta1 Integrin -0.033 0.174 -9999 0 -0.444 11 11
alpha4/beta7 Integrin/Paxillin -0.012 0.154 -9999 0 -0.396 10 10
lamellipodium assembly -0.042 0.172 -9999 0 -0.631 5 5
PIK3CA 0.02 0 -9999 0 -9999 0 0
PI3K -0.014 0.147 -9999 0 -0.499 6 6
ARF6 0.02 0 -9999 0 -9999 0 0
TLN1 0.02 0 -9999 0 -9999 0 0
PXN 0.034 0 -9999 0 -9999 0 0
PIK3R1 -0.038 0.194 -9999 0 -0.677 6 6
ARF6/GTP -0.054 0.122 -9999 0 -9999 0 0
cell adhesion -0.006 0.151 -9999 0 -9999 0 0
CRKL/CBL 0.03 0 -9999 0 -9999 0 0
alpha4/beta1 Integrin/Paxillin -0.018 0.161 -9999 0 -0.396 11 11
ITGB1 0.01 0.085 -9999 0 -0.708 1 1
ITGB7 0.02 0 -9999 0 -9999 0 0
ARF6/GDP 0.011 0.025 -9999 0 -9999 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.077 0.282 -9999 0 -0.755 9 9
p130Cas/Crk/Dock1 0.014 0.111 -9999 0 -0.444 4 4
VCAM1 -0.111 0.28 -9999 0 -0.708 13 13
alpha4/beta1 Integrin/Paxillin/Talin -0.004 0.153 -9999 0 -9999 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.01 0.158 -9999 0 -9999 0 0
BCAR1 0.02 0 -9999 0 -9999 0 0
mol:GDP 0.011 0.156 -9999 0 -9999 0 0
CBL 0.02 0 -9999 0 -9999 0 0
PRKACA 0.02 0 -9999 0 -9999 0 0
GIT1 0.01 0.085 -9999 0 -0.708 1 1
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.004 0.153 -9999 0 -9999 0 0
Rac1/GTP -0.049 0.202 -9999 0 -0.742 5 5
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA -0.04 0.184 -9999 0 -0.526 9 9
FBXW11 0.02 0 -9999 0 -9999 0 0
NF kappa B1 p50/c-Rel 0.026 0.08 -9999 0 -0.444 2 2
NF kappa B1 p50/RelA/I kappa B alpha 0.011 0.137 -9999 0 -0.505 3 3
NFKBIA -0.024 0.152 -9999 0 -0.517 4 4
MAPK14 0.02 0 -9999 0 -9999 0 0
NF kappa B1 p105/p50 0.04 0 -9999 0 -9999 0 0
ARRB2 0.026 0 -9999 0 -9999 0 0
REL 0 0.12 -9999 0 -0.708 2 2
response to oxidative stress 0 0 -9999 0 -9999 0 0
BCL3/NF kappa B1 p50 -0.021 0.16 -9999 0 -0.444 9 9
response to UV 0 0 -9999 0 -9999 0 0
NF kappa B1 p105/RelA 0.04 0 -9999 0 -9999 0 0
PIK3CA 0.02 0 -9999 0 -9999 0 0
NF kappa B1 p50 dimer 0.03 0 -9999 0 -9999 0 0
PIK3R1 -0.038 0.194 -9999 0 -0.677 6 6
NFKB1 0.034 0 -9999 0 -9999 0 0
RELA 0.02 0 -9999 0 -9999 0 0
positive regulation of anti-apoptosis 0.003 0.104 -9999 0 -0.371 1 1
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.017 0.134 -9999 0 -0.558 2 2
SRC 0.02 0 -9999 0 -9999 0 0
PI3K -0.014 0.147 -9999 0 -0.499 6 6
NF kappa B1 p50/RelA 0.003 0.105 -9999 0 -0.375 1 1
IKBKB 0.02 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0 -9999 0 -9999 0 0
SYK -0.005 0.122 -9999 0 -0.585 3 3
I kappa B alpha/PIK3R1 -0.043 0.206 -9999 0 -0.625 6 6
cell death 0.016 0.128 -9999 0 -0.528 2 2
NF kappa B1 p105/c-Rel 0.026 0.08 -9999 0 -0.444 2 2
LCK -0.104 0.255 -9999 0 -0.616 14 14
BCL3 -0.071 0.241 -9999 0 -0.708 9 9
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.027 0 -9999 0 -9999 0 0
response to insulin stimulus 0 0 -9999 0 -9999 0 0
RIPK1 0.02 0 -9999 0 -9999 0 0
response to stress 0 0 -9999 0 -9999 0 0
MAP2K6 0.012 0.064 -9999 0 -0.523 1 1
mol:GTP 0 0 -9999 0 -9999 0 0
MAP2K4 0.02 0 -9999 0 -9999 0 0
RAC1-CDC42/GTP/PAK family -0.003 0.09 -9999 0 -0.249 6 6
response to UV 0 0 -9999 0 -9999 0 0
YES1 0.02 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 0.02 0 -9999 0 -9999 0 0
FYN -0.101 0.271 -9999 0 -0.708 12 12
MAP3K12 0.02 0 -9999 0 -9999 0 0
FGR 0.02 0 -9999 0 -9999 0 0
p38 alpha/TAB1 -0.049 0.14 -9999 0 -0.412 8 8
PRKG1 0.02 0 -9999 0 -9999 0 0
DUSP8 -0.01 0.124 -9999 0 -0.523 4 4
PGK/cGMP/p38 alpha -0.05 0.124 -9999 0 -0.398 7 7
apoptosis -0.054 0.129 -9999 0 -0.394 8 8
RAL/GTP -0.009 0.128 -9999 0 -0.406 6 6
LYN 0.02 0 -9999 0 -9999 0 0
DUSP1 -0.051 0.216 -9999 0 -0.708 7 7
PAK1 0.012 0.064 -9999 0 -0.523 1 1
SRC 0.02 0 -9999 0 -9999 0 0
RAC1/OSM/MEKK3/MKK3 0.039 0.074 -9999 0 -0.396 2 2
TRAF6 0.02 0 -9999 0 -9999 0 0
RAC1 0.02 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 0.02 0 -9999 0 -9999 0 0
RAC1-CDC42/GTP 0.027 0 -9999 0 -9999 0 0
MAPK11 -0.009 0.19 -9999 0 -0.486 8 8
BLK 0.005 0.089 -9999 0 -0.523 2 2
HCK 0 0.12 -9999 0 -0.708 2 2
MAP2K3 0 0.12 -9999 0 -0.708 2 2
DUSP16 0.02 0 -9999 0 -9999 0 0
DUSP10 -0.018 0.157 -9999 0 -0.662 4 4
TRAF6/MEKK3 0.026 0 -9999 0 -9999 0 0
MAP3K7IP1 0.01 0.085 -9999 0 -0.708 1 1
MAPK14 0.001 0.169 -9999 0 -0.432 8 8
positive regulation of innate immune response -0.004 0.212 -9999 0 -0.54 8 8
LCK -0.104 0.255 -9999 0 -0.616 14 14
p38alpha-beta/MKP7 0.007 0.203 -9999 0 -0.505 8 8
p38alpha-beta/MKP5 -0.008 0.233 -9999 0 -0.559 9 9
PGK/cGMP 0.015 0 -9999 0 -9999 0 0
PAK2 0.02 0 -9999 0 -9999 0 0
p38alpha-beta/MKP1 -0.024 0.242 -9999 0 -0.552 10 10
CDC42 0.02 0 -9999 0 -9999 0 0
RALB 0 0.12 -9999 0 -0.708 2 2
RALA -0.018 0.138 -9999 0 -0.523 5 5
PAK3 -0.106 0.249 -9999 0 -0.585 15 15
TCGA08_rtk_signaling

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
PDGFRA -0.025 0.15 -9999 0 -0.523 6 6
HRAS 0.02 0 -9999 0 -9999 0 0
EGFR -0.106 0.26 -9999 0 -0.629 14 14
AKT 0.036 0.07 -9999 0 -0.479 1 1
FOXO3 0.02 0 -9999 0 -9999 0 0
AKT1 0.02 0 -9999 0 -9999 0 0
FOXO1 -0.025 0.15 -9999 0 -0.523 6 6
AKT3 0.01 0.085 -9999 0 -0.708 1 1
FOXO4 0.02 0 -9999 0 -9999 0 0
MET -0.005 0.122 -9999 0 -0.585 3 3
PIK3CA 0.02 0 -9999 0 -9999 0 0
PIK3CB 0.01 0.085 -9999 0 -0.708 1 1
NRAS 0.005 0.089 -9999 0 -0.523 2 2
PIK3CG -0.038 0.194 -9999 0 -0.677 6 6
PIK3R3 -0.041 0.201 -9999 0 -0.708 6 6
PIK3R2 0.02 0 -9999 0 -9999 0 0
NF1 0.02 0 -9999 0 -9999 0 0
RAS -0.013 0.092 -9999 0 -0.256 5 5
ERBB2 0 0.12 -9999 0 -0.708 2 2
proliferation/survival/translation -0.019 0.074 0.231 3 -9999 0 3
PI3K -0.026 0.124 -9999 0 -0.296 9 9
PIK3R1 -0.038 0.194 -9999 0 -0.677 6 6
KRAS 0.02 0 -9999 0 -9999 0 0
FOXO 0.046 0.049 -9999 0 -9999 0 0
AKT2 0.02 0 -9999 0 -9999 0 0
PTEN 0.02 0 -9999 0 -9999 0 0
Class I PI3K signaling events

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
ARF5/GTP -0.01 0.048 -9999 0 -9999 0 0
DAPP1 -0.061 0.276 -9999 0 -0.744 8 8
Src family/SYK family/BLNK-LAT/BTK-ITK -0.061 0.284 -9999 0 -0.658 11 11
mol:DAG 0.004 0.141 -9999 0 -0.298 9 9
HRAS 0.02 0.003 -9999 0 -9999 0 0
RAP1A 0.01 0.085 -9999 0 -0.705 1 1
ARF5/GDP 0.002 0.14 -9999 0 -0.392 6 6
PLCG2 -0.055 0.188 -9999 0 -0.523 10 10
PLCG1 0.02 0 -9999 0 -9999 0 0
ARF5 0.02 0 -9999 0 -9999 0 0
mol:GTP -0.011 0.053 -9999 0 -0.344 1 1
ARF1/GTP -0.01 0.049 -9999 0 -0.317 1 1
RHOA 0.01 0.085 -9999 0 -0.708 1 1
YES1 0.02 0 -9999 0 -9999 0 0
RAP1A/GTP -0.011 0.053 -9999 0 -0.345 1 1
ADAP1 -0.01 0.05 -9999 0 -0.324 1 1
ARAP3 -0.011 0.052 -9999 0 -0.337 1 1
INPPL1 0.012 0.064 -9999 0 -0.523 1 1
PREX1 -0.061 0.229 -9999 0 -0.708 8 8
ARHGEF6 0.01 0.085 -9999 0 -0.708 1 1
ARHGEF7 0.02 0 -9999 0 -9999 0 0
ARF1 0.02 0 -9999 0 -9999 0 0
NRAS 0.005 0.089 -9999 0 -0.52 2 2
FYN -0.101 0.271 -9999 0 -0.708 12 12
ARF6 0.02 0 -9999 0 -9999 0 0
FGR 0.02 0 -9999 0 -9999 0 0
mol:Ca2+ 0.019 0.075 -9999 0 -9999 0 0
mol:IP4 0 0 -9999 0 -9999 0 0
TIAM1 -0.01 0.145 -9999 0 -0.708 3 3
ZAP70 -0.005 0.122 -9999 0 -0.585 3 3
mol:IP3 0.018 0.101 -9999 0 -0.227 1 1
LYN 0.02 0 -9999 0 -9999 0 0
ARF1/GDP 0.002 0.14 -9999 0 -0.392 6 6
RhoA/GDP -0.034 0.102 -9999 0 -0.5 2 2
PDK1/Src/Hsp90 0.025 0.079 -9999 0 -0.444 1 1
BLNK -0.041 0.187 -9999 0 -0.603 7 7
actin cytoskeleton reorganization 0.013 0.158 -9999 0 -0.466 5 5
SRC 0.02 0 -9999 0 -9999 0 0
PLEKHA2 0.01 0.088 -9999 0 -0.408 3 3
RAC1 0.02 0 -9999 0 -9999 0 0
PTEN 0.016 0.006 -9999 0 -9999 0 0
HSP90AA1 0.005 0.089 -9999 0 -0.523 2 2
ARF6/GTP -0.01 0.048 -9999 0 -9999 0 0
RhoA/GTP -0.015 0.086 -9999 0 -0.689 1 1
Src family/SYK family/BLNK-LAT -0.071 0.28 -9999 0 -0.677 10 10
BLK 0.005 0.089 -9999 0 -0.523 2 2
PDPK1 0.01 0.085 -9999 0 -0.708 1 1
CYTH1 -0.01 0.05 -9999 0 -0.324 1 1
HCK 0 0.12 -9999 0 -0.708 2 2
CYTH3 -0.01 0.05 -9999 0 -0.324 1 1
CYTH2 -0.01 0.05 -9999 0 -0.324 1 1
KRAS 0.02 0.003 -9999 0 -9999 0 0
GO:0030676 0 0 -9999 0 -9999 0 0
FOXO3 -0.01 0.041 -9999 0 -9999 0 0
SGK1 -0.012 0.046 -9999 0 -9999 0 0
INPP5D 0 0 -9999 0 -9999 0 0
mol:GDP -0.01 0.146 -9999 0 -0.402 7 7
SOS1 0.02 0 -9999 0 -9999 0 0
SYK -0.005 0.122 -9999 0 -0.585 3 3
ARF6/GDP -0.029 0.079 -9999 0 -0.372 1 1
mol:PI-3-4-5-P3 -0.011 0.053 -9999 0 -0.339 1 1
ARAP3/RAP1A/GTP -0.011 0.053 -9999 0 -0.344 1 1
VAV1 -0.048 0.209 -9999 0 -0.682 7 7
mol:PI-3-4-P2 0.011 0.046 -9999 0 -0.38 1 1
RAS family/GTP/PI3K Class I 0.026 0.061 -9999 0 -0.342 1 1
PLEKHA1 -0.01 0.128 -9999 0 -0.457 5 5
Rac1/GDP 0.002 0.14 -9999 0 -0.392 6 6
LAT -0.041 0.187 -9999 0 -0.603 7 7
Rac1/GTP -0.02 0.207 -9999 0 -0.647 6 6
ITK -0.049 0.121 -9999 0 -0.387 6 6
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.011 0.193 -9999 0 -0.44 9 9
LCK -0.104 0.255 -9999 0 -0.616 14 14
BTK -0.035 0.11 -9999 0 -0.395 5 5
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.026 0.09 -9999 0 -0.375 3 3
ER alpha/Gai/GDP/Gbeta gamma 0.037 0.127 -9999 0 -0.571 2 2
AKT1 0.008 0.165 -9999 0 -0.807 2 2
PIK3CA 0.02 0 -9999 0 -9999 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K 0.006 0.164 -9999 0 -0.817 2 2
mol:Ca2+ -0.082 0.257 -9999 0 -0.593 12 12
IGF1R 0.01 0.085 -9999 0 -0.708 1 1
E2/ER alpha (dimer)/Striatin -0.006 0.123 -9999 0 -0.455 5 5
SHC1 0.02 0 -9999 0 -9999 0 0
apoptosis -0.01 0.158 0.766 2 -9999 0 2
RhoA/GTP -0.024 0.11 -9999 0 -0.621 2 2
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.025 0.097 -9999 0 -0.477 3 3
regulation of stress fiber formation -0.026 0.147 0.5 4 -9999 0 4
E2/ERA-ERB (dimer) 0.009 0.088 -9999 0 -0.407 3 3
KRAS 0.02 0 -9999 0 -9999 0 0
G13/GTP 0.007 0.089 -9999 0 -0.417 3 3
pseudopodium formation 0.026 0.147 -9999 0 -0.5 4 4
E2/ER alpha (dimer)/PELP1 0.014 0.079 -9999 0 -0.455 2 2
GRB2 0.01 0.085 -9999 0 -0.708 1 1
GNG2 0.02 0 -9999 0 -9999 0 0
GNAO1 0.02 0 -9999 0 -9999 0 0
HRAS 0.02 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
mol:NO 0.038 0.13 -9999 0 -0.515 3 3
E2/ER beta (dimer) 0.009 0.046 -9999 0 -0.38 1 1
mol:GDP -0.024 0.105 -9999 0 -0.586 2 2
mol:NADP 0.038 0.13 -9999 0 -0.515 3 3
PIK3R1 -0.038 0.194 -9999 0 -0.677 6 6
mol:IP3 -0.088 0.272 -9999 0 -0.628 12 12
IGF-1R heterotetramer 0.01 0.085 -9999 0 -0.707 1 1
PLCB1 -0.102 0.28 -9999 0 -0.58 16 16
PLCB2 -0.025 0.17 -9999 0 -0.496 7 7
IGF1 -0.081 0.228 -9999 0 -0.585 12 12
mol:L-citrulline 0.038 0.13 -9999 0 -0.515 3 3
RHOA 0.01 0.085 -9999 0 -0.708 1 1
Gai/GDP 0.034 0.1 -9999 0 -0.669 1 1
JNK cascade 0.009 0.046 -9999 0 -0.379 1 1
BCAR1 0.02 0 -9999 0 -9999 0 0
ESR2 0.012 0.064 -9999 0 -0.523 1 1
GNAQ 0 0 -9999 0 -9999 0 0
ESR1 0 0.12 -9999 0 -0.708 2 2
Gq family/GDP/Gbeta gamma -0.005 0.163 -9999 0 -1.066 1 1
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.038 0.131 -9999 0 -0.958 1 1
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.025 0.097 -9999 0 -0.477 3 3
GNAZ 0.012 0.064 -9999 0 -0.523 1 1
E2/ER alpha (dimer) -0.001 0.091 -9999 0 -0.538 2 2
STRN -0.01 0.145 -9999 0 -0.708 3 3
GNAL 0.01 0.085 -9999 0 -0.708 1 1
PELP1 0.02 0 -9999 0 -9999 0 0
MAPK11 0.023 0.04 -9999 0 -0.31 1 1
GNAI2 0.01 0.085 -9999 0 -0.708 1 1
GNAI3 0.02 0 -9999 0 -9999 0 0
GNAI1 0 0.12 -9999 0 -0.708 2 2
HBEGF 0.003 0.179 -9999 0 -0.678 3 3
cAMP biosynthetic process -0.018 0.077 -9999 0 -0.364 3 3
SRC 0.047 0.121 -9999 0 -0.704 1 1
PI3K -0.014 0.147 -9999 0 -0.499 6 6
GNB1 0.01 0.085 -9999 0 -0.708 1 1
G13/GDP/Gbeta gamma -0.026 0.099 -9999 0 -0.503 2 2
SOS1 0.02 0 -9999 0 -9999 0 0
IGF-1R heterotetramer/IGF1 -0.052 0.119 -9999 0 -0.555 2 2
Gs family/GTP -0.019 0.078 -9999 0 -0.37 3 3
EntrezGene:2778 0 0 -9999 0 -9999 0 0
RAS family/GTP 0.03 0.051 -9999 0 -9999 0 0
vasodilation 0.039 0.125 -9999 0 -0.492 3 3
mol:DAG -0.088 0.272 -9999 0 -0.628 12 12
Gs family/GDP/Gbeta gamma -0.026 0.092 -9999 0 -0.547 1 1
MSN 0.024 0.159 -9999 0 -0.551 4 4
Gq family/GTP -0.038 0.178 -9999 0 -0.532 7 7
mol:PI-3-4-5-P3 0.007 0.158 -9999 0 -0.782 2 2
NRAS 0.005 0.089 -9999 0 -0.523 2 2
mol:E2 0 0 -9999 0 -9999 0 0
cell adhesion -0.039 0.125 0.492 3 -9999 0 3
GRB2/SOS1 0.022 0.065 -9999 0 -0.526 1 1
RhoA/GDP -0.027 0.116 -9999 0 -0.568 3 3
NOS3 0.038 0.135 -9999 0 -0.542 3 3
GNA11 -0.01 0.124 -9999 0 -0.523 4 4
MAPKKK cascade 0.042 0.171 -9999 0 -0.684 3 3
E2/ER alpha (dimer)/PELP1/Src -0.026 0.104 -9999 0 -0.506 3 3
ruffle organization 0.026 0.147 -9999 0 -0.5 4 4
ROCK2 0.034 0.128 -9999 0 -0.562 2 2
GNA14 -0.058 0.222 -9999 0 -0.685 8 8
GNA15 0.01 0.085 -9999 0 -0.708 1 1
GNA13 0.01 0.085 -9999 0 -0.708 1 1
MMP9 -0.026 0.202 -9999 0 -0.779 3 3
MMP2 0.045 0.13 -9999 0 -0.647 1 1
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.058 0.275 -9999 0 -0.787 7 7
PDGFB-D/PDGFRB/SLAP -0.025 0.176 -9999 0 -0.579 6 6
PDGFB-D/PDGFRB/APS/CBL 0.008 0.08 -9999 0 -0.461 2 2
AKT1 0.018 0.162 -9999 0 -0.582 3 3
mol:PI-4-5-P2 0 0.001 -9999 0 -9999 0 0
mol:Sphingosine-1-phosphate -0.031 0.215 -9999 0 -0.749 4 4
PIK3CA 0.02 0 -9999 0 -9999 0 0
FGR -0.017 0.09 -9999 0 -0.523 2 2
mol:Ca2+ -0.002 0.169 -9999 0 -0.917 2 2
MYC -0.046 0.313 -9999 0 -0.853 9 9
SHC1 0.02 0 -9999 0 -9999 0 0
HRAS/GDP 0.04 0.07 -9999 0 -9999 0 0
LRP1/PDGFRB/PDGFB -0.004 0.152 -9999 0 -0.534 5 5
GRB10 -0.063 0.223 -9999 0 -0.646 9 9
PTPN11 0.02 0 -9999 0 -9999 0 0
GO:0007205 -0.003 0.173 -9999 0 -0.945 2 2
PTEN 0.02 0 -9999 0 -9999 0 0
GRB2 0.01 0.085 -9999 0 -0.708 1 1
GRB7 0.012 0.064 -9999 0 -0.523 1 1
PDGFB-D/PDGFRB/SHP2 0.01 0.093 -9999 0 -0.534 2 2
PDGFB-D/PDGFRB/GRB10 -0.05 0.201 -9999 0 -0.527 10 10
cell cycle arrest -0.024 0.175 -9999 0 -0.578 6 6
HRAS 0.02 0 -9999 0 -9999 0 0
HIF1A 0.009 0.173 -9999 0 -0.625 3 3
GAB1 -0.036 0.244 -9999 0 -0.854 4 4
mol:GTP 0 0 -9999 0 -9999 0 0
DNM2 -0.034 0.234 -9999 0 -0.722 5 5
PDGFB-D/PDGFRB 0.021 0.086 -9999 0 -0.475 2 2
mol:GDP 0 0 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.01 0.093 -9999 0 -0.534 2 2
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.121 0.271 -9999 0 -0.856 7 7
positive regulation of MAPKKK cascade 0.01 0.092 -9999 0 -0.532 2 2
PIK3R1 -0.038 0.194 -9999 0 -0.677 6 6
mol:IP3 -0.003 0.176 -9999 0 -0.96 2 2
E5 -0.001 0.002 -9999 0 -9999 0 0
CSK 0.012 0.064 -9999 0 -0.523 1 1
PDGFB-D/PDGFRB/GRB7 0.005 0.103 -9999 0 -0.481 3 3
SHB 0.02 0 -9999 0 -9999 0 0
BLK -0.022 0.092 -9999 0 -0.516 2 2
PTPN2 0.02 0.004 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/SNX15 0.002 0.112 -9999 0 -0.534 3 3
BCAR1 0.02 0 -9999 0 -9999 0 0
VAV2 -0.034 0.254 -9999 0 -0.805 5 5
CBL 0.02 0 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/DEP1 -0.01 0.142 -9999 0 -0.499 5 5
LCK -0.107 0.267 -9999 0 -0.8 8 8
PDGFRB -0.003 0.122 -9999 0 -0.724 2 2
ACP1 0.02 0 -9999 0 -9999 0 0
HCK -0.041 0.212 -9999 0 -0.973 3 3
ABL1 -0.019 0.192 -9999 0 -0.79 3 3
PDGFB-D/PDGFRB/CBL -0.036 0.245 -9999 0 -1.014 3 3
PTPN1 0.02 0.004 -9999 0 -9999 0 0
SNX15 0.01 0.085 -9999 0 -0.708 1 1
STAT3 0.01 0.085 -9999 0 -0.708 1 1
STAT1 -0.056 0.216 -9999 0 -0.662 8 8
cell proliferation -0.033 0.274 -9999 0 -0.737 9 9
SLA -0.028 0.177 -9999 0 -0.671 5 5
actin cytoskeleton reorganization 0.046 0.106 -9999 0 -0.709 1 1
SRC -0.016 0.089 -9999 0 -0.518 2 2
PI3K -0.06 0.151 -9999 0 -0.662 3 3
PDGFB-D/PDGFRB/GRB7/SHC 0.016 0.09 -9999 0 -0.45 2 2
SH2B2 0 0 -9999 0 -9999 0 0
PLCgamma1/SPHK1 -0.033 0.228 -9999 0 -0.797 4 4
LYN -0.016 0.09 -9999 0 -0.52 2 2
LRP1 0.02 0 -9999 0 -9999 0 0
SOS1 0.02 0 -9999 0 -9999 0 0
STAT5B 0.02 0 -9999 0 -9999 0 0
STAT5A 0.012 0.064 -9999 0 -0.523 1 1
NCK1-2/p130 Cas -0.007 0.1 -9999 0 -0.741 1 1
SPHK1 -0.068 0.211 -9999 0 -0.561 11 11
EDG1 -0.071 0.243 -9999 0 -0.714 9 9
mol:DAG -0.003 0.176 -9999 0 -0.96 2 2
PLCG1 -0.004 0.184 -9999 0 -1.01 2 2
NHERF/PDGFRB -0.022 0.145 -9999 0 -0.449 5 5
YES1 -0.017 0.091 -9999 0 -0.526 2 2
cell migration -0.023 0.144 -9999 0 -0.448 5 5
SHC/Grb2/SOS1 -0.007 0.1 -9999 0 -0.741 1 1
SLC9A3R2 -0.038 0.179 -9999 0 -0.576 7 7
SLC9A3R1 0.01 0.085 -9999 0 -0.708 1 1
NHERF1-2/PDGFRB/PTEN -0.005 0.134 -9999 0 -0.401 5 5
FYN -0.141 0.345 -9999 0 -0.858 12 12
DOK1 0.035 0.076 -9999 0 -0.412 2 2
HRAS/GTP 0.015 0 -9999 0 -9999 0 0
PDGFB -0.02 0.167 -9999 0 -0.708 4 4
RAC1 -0.035 0.28 -9999 0 -0.745 8 8
PRKCD 0.008 0.129 -9999 0 -0.559 2 2
FER 0.033 0.078 -9999 0 -0.421 2 2
MAPKKK cascade -0.015 0.093 -9999 0 -0.719 1 1
RASA1 0.033 0.078 -9999 0 -0.421 2 2
NCK1 0.01 0.085 -9999 0 -0.708 1 1
NCK2 0.02 0 -9999 0 -9999 0 0
p62DOK/Csk 0.042 0.077 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/SHB 0.01 0.093 -9999 0 -0.534 2 2
chemotaxis -0.017 0.184 -9999 0 -0.752 3 3
STAT1-3-5/STAT1-3-5 -0.052 0.16 -9999 0 -0.756 2 2
Bovine Papilomavirus E5/PDGFRB -0.003 0.093 -9999 0 -0.552 2 2
PTPRJ -0.01 0.124 -9999 0 -0.523 4 4
Signaling events mediated by PRL

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
CCNE1 0.02 0 -9999 0 -9999 0 0
mol:Halofuginone 0.004 0.029 -9999 0 -0.24 1 1
ITGA1 -0.01 0.145 -9999 0 -0.708 3 3
CDKN1A -0.015 0.102 -9999 0 -0.406 2 2
PRL-3/alpha Tubulin 0.017 0.079 -9999 0 -0.446 2 2
mol:Ca2+ -0.132 0.236 0.442 1 -0.499 20 21
AGT -0.167 0.305 -9999 0 -0.653 20 20
CCNA2 -0.054 0.188 -9999 0 -1.002 1 1
TUBA1B 0.012 0.064 -9999 0 -0.523 1 1
EGR1 -0.109 0.209 -9999 0 -0.4 24 24
CDK2/Cyclin E1 0.008 0.091 -9999 0 -9999 0 0
MAPK3 0.026 0.065 -9999 0 -0.526 1 1
PRL-2 /Rab GGTase beta 0.022 0.065 -9999 0 -0.526 1 1
MAPK1 0.026 0.065 -9999 0 -0.526 1 1
PTP4A1 -0.069 0.2 -9999 0 -1.07 1 1
PTP4A3 0.01 0.085 -9999 0 -0.708 1 1
PTP4A2 0.02 0 -9999 0 -9999 0 0
ITGB1 0.018 0.092 -9999 0 -0.526 2 2
SRC 0.02 0 -9999 0 -9999 0 0
RAC1 -0.009 0.091 -9999 0 -0.405 1 1
Rab GGTase beta/Rab GGTase alpha 0.022 0.065 -9999 0 -0.526 1 1
PRL-1/ATF-5 -0.061 0.19 -9999 0 -1.002 1 1
RABGGTA 0.02 0 -9999 0 -9999 0 0
BCAR1 0.006 0.052 0.442 1 -9999 0 1
RHOC -0.009 0.091 -9999 0 -0.405 1 1
RHOA -0.015 0.102 -9999 0 -0.406 2 2
cell motility -0.008 0.097 -9999 0 -0.404 1 1
PRL-1/alpha Tubulin -0.059 0.188 -9999 0 -1.002 1 1
PRL-3/alpha1 Integrin -0.001 0.127 -9999 0 -0.526 4 4
ROCK1 -0.008 0.098 -9999 0 -0.407 1 1
RABGGTB 0.01 0.085 -9999 0 -0.708 1 1
CDK2 0.02 0 -9999 0 -9999 0 0
mitosis -0.069 0.198 -9999 0 -1.052 1 1
ATF5 0.01 0.085 -9999 0 -0.708 1 1
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.005 0.089 0.522 2 -9999 0 2
PI3K Class IB/PDE3B 0.005 0.089 -9999 0 -0.523 2 2
PDE3B 0.005 0.089 -9999 0 -0.523 2 2
p38 MAPK signaling 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
TRAF6/ASK1 0.017 0.068 -9999 0 -0.386 2 2
TRAF2/ASK1 0.004 0.095 -9999 0 -0.383 4 4
ATM 0 0.12 -9999 0 -0.708 2 2
MAP2K3 0.012 0.147 -9999 0 -0.591 3 3
response to stress 0 0 -9999 0 -9999 0 0
MAP2K6 0.015 0.13 -9999 0 -0.413 5 5
hyperosmotic response 0 0 -9999 0 -9999 0 0
response to oxidative stress 0 0 -9999 0 -9999 0 0
GADD45G -0.078 0.209 -9999 0 -0.523 13 13
TXN 0.009 0.029 -9999 0 -0.238 1 1
CALM1 0.02 0 -9999 0 -9999 0 0
GADD45A -0.03 0.169 -9999 0 -0.585 6 6
GADD45B -0.013 0.136 -9999 0 -0.57 4 4
MAP3K1 0.01 0.085 -9999 0 -0.708 1 1
MAP3K6 0.02 0 -9999 0 -9999 0 0
MAP3K7 0.02 0 -9999 0 -9999 0 0
MAP3K4 0.02 0 -9999 0 -9999 0 0
mol:Ca2+ 0 0 -9999 0 -9999 0 0
ASK1/ASK2 0.014 0.091 -9999 0 -0.526 2 2
TAK1/TAB family -0.004 0.033 -9999 0 -9999 0 0
RAC1/OSM/MEKK3 0.039 0 -9999 0 -9999 0 0
TRAF2 0.005 0.089 -9999 0 -0.523 2 2
RAC1/OSM/MEKK3/MKK3 -0.027 0.09 -9999 0 -0.471 2 2
TRAF6 0.026 0 -9999 0 -9999 0 0
RAC1 0.02 0 -9999 0 -9999 0 0
mol:LPS 0 0 -9999 0 -9999 0 0
CAMK2B -0.055 0.188 -9999 0 -0.523 10 10
CCM2 0.02 0 -9999 0 -9999 0 0
CaM/Ca2+/CAMKIIB -0.02 0.117 -9999 0 -0.311 10 10
MAPK11 0.02 0 -9999 0 -9999 0 0
response to DNA damage stimulus 0 0 -9999 0 -9999 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.017 0.125 -9999 0 -0.407 2 2
OSM/MEKK3 0.03 0 -9999 0 -9999 0 0
TAOK1 -0.002 0.101 -9999 0 -0.366 5 5
TAOK2 0.007 0.08 -9999 0 -0.401 2 2
TAOK3 0.002 0.098 -9999 0 -0.401 4 4
MAP3K7IP1 0.01 0.085 -9999 0 -0.708 1 1
MAPK14 0.02 0 -9999 0 -9999 0 0
MAP3K7IP2 0.02 0 -9999 0 -9999 0 0
MAP3K5 0 0.12 -9999 0 -0.708 2 2
MAP3K10 -0.008 0.134 -9999 0 -0.646 3 3
MAP3K3 0.02 0 -9999 0 -9999 0 0
TRX/ASK1 0.008 0.081 -9999 0 -0.448 2 2
GADD45/MTK1/MTK1 -0.049 0.183 -9999 0 -0.493 7 7
Alternative NF-kappaB 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
IKK alpha homodimer -0.055 0.2 -9999 0 -0.526 11 11
FBXW11 0.02 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 0.02 0 -9999 0 -9999 0 0
CHUK 0.02 0 -9999 0 -9999 0 0
NF kappa B2 p100/RelB -0.026 0.193 -9999 0 -0.755 2 2
NFKB1 0.02 0 -9999 0 -9999 0 0
MAP3K14 -0.091 0.262 -9999 0 -0.708 11 11
NF kappa B1 p50/RelB 0.014 0.091 -9999 0 -0.526 2 2
RELB 0 0.12 -9999 0 -0.708 2 2
NFKB2 0.002 0.106 -9999 0 -0.616 2 2
NF kappa B2 p52/RelB 0.002 0.103 -9999 0 -0.419 4 4
regulation of B cell activation 0.002 0.103 -9999 0 -0.417 4 4
Regulation of Androgen receptor activity

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
HDAC1 0.026 0.066 -9999 0 -0.526 1 1
SMARCC1 0.014 0.018 -9999 0 -9999 0 0
REL -0.001 0.12 -9999 0 -0.709 2 2
HDAC7 0.022 0.12 -9999 0 -0.409 1 1
JUN -0.093 0.256 -9999 0 -0.662 12 12
EP300 0.01 0.085 -9999 0 -0.708 1 1
KAT2B 0 0 -9999 0 -9999 0 0
KAT5 0 0 -9999 0 -9999 0 0
MAPK14 0.027 0.051 -9999 0 -0.385 1 1
FOXO1 -0.025 0.151 -9999 0 -0.525 6 6
T-DHT/AR 0.032 0.131 -9999 0 -0.429 1 1
MAP2K6 0.012 0.065 -9999 0 -0.536 1 1
BRM/BAF57 0.03 0.008 -9999 0 -9999 0 0
MAP2K4 0.019 0.007 -9999 0 -9999 0 0
SMARCA2 0.02 0.003 -9999 0 -9999 0 0
PDE9A -0.052 0.173 -9999 0 -1.346 1 1
NCOA2 0.013 0.064 -9999 0 -0.522 1 1
CEBPA -0.005 0.122 -9999 0 -0.584 3 3
EHMT2 0.02 0.003 -9999 0 -9999 0 0
cell proliferation 0.063 0.152 -9999 0 -0.486 2 2
NR0B1 -0.035 0.17 -9999 0 -0.55 7 7
EGR1 -0.169 0.279 -9999 0 -0.57 23 23
RXRs/9cRA 0.014 0.102 -9999 0 -0.405 4 4
AR/RACK1/Src 0.046 0.102 -9999 0 -9999 0 0
AR/GR 0 0.134 -9999 0 -0.364 4 4
GNB2L1 0.01 0.085 -9999 0 -0.707 1 1
PKN1 0.02 0 -9999 0 -9999 0 0
RCHY1 0 0.12 -9999 0 -0.708 2 2
epidermal growth factor receptor activity 0.001 0.001 -9999 0 -0.007 2 2
MAPK8 0.032 0.016 -9999 0 -9999 0 0
T-DHT/AR/TIF2/CARM1 0.049 0.094 -9999 0 -9999 0 0
SRC 0.051 0.05 -9999 0 -9999 0 0
NR3C1 0.02 0 -9999 0 -9999 0 0
KLK3 -0.018 0.174 -9999 0 -0.677 3 3
APPBP2 0.018 0.008 -9999 0 -9999 0 0
TRIM24 0.02 0.006 -9999 0 -9999 0 0
T-DHT/AR/TIP60 -0.024 0.061 -9999 0 -0.386 1 1
TMPRSS2 -0.211 0.359 -9999 0 -0.935 11 11
RXRG 0 0.12 -9999 0 -0.707 2 2
mol:9cRA 0 0.001 -9999 0 -0.005 5 5
RXRA 0 0.12 -9999 0 -0.707 2 2
RXRB 0.02 0.001 -9999 0 -9999 0 0
CARM1 0.021 0.001 -9999 0 -9999 0 0
NR2C2 0.01 0.085 -9999 0 -0.708 1 1
KLK2 0.061 0.119 -9999 0 -0.486 2 2
AR -0.009 0.15 -9999 0 -0.334 12 12
SENP1 0.02 0.001 -9999 0 -9999 0 0
HSP90AA1 0.005 0.089 -9999 0 -0.523 2 2
MDM2 0.019 0.006 -9999 0 -9999 0 0
SRY -0.016 0.148 -9999 0 -0.618 4 4
GATA2 -0.01 0.124 -9999 0 -0.523 4 4
MYST2 0.01 0.085 -9999 0 -0.708 1 1
HOXB13 -0.024 0.15 -9999 0 -0.521 6 6
T-DHT/AR/RACK1/Src 0.041 0.1 -9999 0 -0.397 1 1
positive regulation of transcription -0.01 0.124 -9999 0 -0.523 4 4
DNAJA1 0.018 0.008 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.028 0.075 -9999 0 -0.354 2 2
NCOA1 0.026 0.004 -9999 0 -9999 0 0
SPDEF -0.007 0.135 -9999 0 -0.646 3 3
T-DHT/AR/TIF2 0.042 0.099 -9999 0 -0.453 2 2
T-DHT/AR/Hsp90 0.025 0.103 -9999 0 -0.38 2 2
GSK3B 0.02 0.004 -9999 0 -9999 0 0
NR2C1 0.01 0.085 -9999 0 -0.708 1 1
mol:T-DHT 0.04 0.055 -9999 0 -9999 0 0
SIRT1 0.01 0.085 -9999 0 -0.708 1 1
ZMIZ2 0.012 0.064 -9999 0 -0.526 1 1
POU2F1 0.028 0.02 -9999 0 -9999 0 0
T-DHT/AR/DAX-1 0.004 0.131 -9999 0 -0.401 3 3
CREBBP 0.02 0 -9999 0 -9999 0 0
SMARCE1 0.02 0.003 -9999 0 -9999 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.01 0.085 -9999 0 -0.708 1 1
SMAD2 0.008 0.063 0.273 1 -0.278 1 2
SMAD3 0.036 0.073 -9999 0 -9999 0 0
SMAD3/SMAD4 0.029 0.145 -9999 0 -0.513 4 4
SMAD4/Ubc9/PIASy 0.029 0.069 -9999 0 -0.444 1 1
SMAD2/SMAD2/SMAD4 0.032 0.079 -9999 0 -9999 0 0
PPM1A -0.003 0.109 -9999 0 -0.523 3 3
CALM1 0.02 0 -9999 0 -9999 0 0
SMAD2/SMAD4 0.013 0.074 -9999 0 -0.4 1 1
MAP3K1 0.01 0.085 -9999 0 -0.708 1 1
TRAP-1/SMAD4 0.014 0.091 -9999 0 -0.526 2 2
MAPK3 0.02 0 -9999 0 -9999 0 0
MAPK1 0.02 0 -9999 0 -9999 0 0
NUP214 0.02 0 -9999 0 -9999 0 0
CTDSP1 0.02 0 -9999 0 -9999 0 0
CTDSP2 0.01 0.085 -9999 0 -0.708 1 1
CTDSPL -0.005 0.122 -9999 0 -0.585 3 3
KPNB1 -0.015 0.147 -9999 0 -0.616 4 4
TGFBRAP1 0.01 0.085 -9999 0 -0.708 1 1
UBE2I 0.02 0 -9999 0 -9999 0 0
NUP153 0.01 0.085 -9999 0 -0.708 1 1
KPNA2 0.01 0.085 -9999 0 -0.708 1 1
PIAS4 0.012 0.064 -9999 0 -0.523 1 1
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.045 0.052 -9999 0 -0.396 1 1
HDAC3 0.02 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 -0.005 0.038 -9999 0 -0.327 1 1
GATA1/HDAC4 0.008 0.091 -9999 0 -0.366 4 4
GATA1/HDAC5 0.008 0.091 -9999 0 -0.366 4 4
GATA2/HDAC5 0.008 0.091 -9999 0 -0.366 4 4
HDAC5/BCL6/BCoR -0.011 0.147 -9999 0 -0.444 7 7
HDAC9 0.02 0 -9999 0 -9999 0 0
Glucocorticoid receptor/Hsp90/HDAC6 0.031 0.056 -9999 0 -9999 0 0
HDAC4/ANKRA2 0.03 0 -9999 0 -9999 0 0
HDAC5/YWHAB 0.03 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.028 0.033 -9999 0 -0.25 1 1
GATA2 -0.01 0.124 -9999 0 -0.523 4 4
HDAC4/RFXANK 0.03 0 -9999 0 -9999 0 0
BCOR 0.02 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
HDAC10 0.02 0 -9999 0 -9999 0 0
HDAC5 0.02 0 -9999 0 -9999 0 0
GNB1/GNG2 0.022 0.065 -9999 0 -0.526 1 1
Histones 0.04 0.043 -9999 0 -9999 0 0
ADRBK1 0.02 0 -9999 0 -9999 0 0
HDAC4 0.02 0 -9999 0 -9999 0 0
XPO1 0.02 0 -9999 0 -9999 0 0
HDAC5/ANKRA2 0.03 0 -9999 0 -9999 0 0
HDAC4/Ubc9 0.03 0 -9999 0 -9999 0 0
HDAC7 0 0 -9999 0 -9999 0 0
HDAC5/14-3-3 E 0.03 0 -9999 0 -9999 0 0
TUBA1B 0.012 0.064 -9999 0 -0.523 1 1
HDAC6 0.02 0 -9999 0 -9999 0 0
HDAC5/RFXANK 0.03 0 -9999 0 -9999 0 0
CAMK4 0.02 0 -9999 0 -9999 0 0
Tubulin/HDAC6 0.017 0.086 -9999 0 -9999 0 0
SUMO1 0.02 0 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 0 0
YWHAB 0.02 0 -9999 0 -9999 0 0
GATA1 -0.01 0.124 -9999 0 -0.523 4 4
EntrezGene:8021 0 0 -9999 0 -9999 0 0
YWHAE 0.02 0 -9999 0 -9999 0 0
NR3C1 0.02 0 -9999 0 -9999 0 0
SUMO1/HDAC4 0.043 0.027 -9999 0 -9999 0 0
SRF 0.02 0 -9999 0 -9999 0 0
HDAC4/YWHAB 0.03 0 -9999 0 -9999 0 0
Tubulin 0.002 0.101 -9999 0 -0.366 5 5
HDAC4/14-3-3 E 0.03 0 -9999 0 -9999 0 0
GNB1 0.01 0.085 -9999 0 -0.708 1 1
RANGAP1 0.02 0 -9999 0 -9999 0 0
BCL6/BCoR -0.03 0.169 -9999 0 -0.506 8 8
HDAC4/HDAC3/SMRT (N-CoR2) 0.014 0.111 -9999 0 -0.444 4 4
HDAC4/SRF 0.041 0 -9999 0 -9999 0 0
HDAC4/ER alpha 0.014 0.091 -9999 0 -0.526 2 2
EntrezGene:23225 0 0 -9999 0 -9999 0 0
positive regulation of chromatin silencing 0.04 0.043 -9999 0 -9999 0 0
cell motility 0.017 0.086 -9999 0 -9999 0 0
EntrezGene:23636 0 0 -9999 0 -9999 0 0
UBE2I 0.02 0 -9999 0 -9999 0 0
HDAC7/HDAC3 0.015 0 -9999 0 -9999 0 0
BCL6 -0.058 0.222 -9999 0 -0.685 8 8
HDAC4/CaMK II delta B 0.02 0 -9999 0 -9999 0 0
Hsp90/HDAC6 0.019 0.065 -9999 0 -0.366 2 2
ESR1 0 0.12 -9999 0 -0.708 2 2
HDAC6/HDAC11 0.008 0.091 -9999 0 -0.366 4 4
Ran/GTP/Exportin 1 0.046 0.029 -9999 0 -9999 0 0
NPC 0.006 0.049 -9999 0 -0.406 1 1
MEF2C -0.081 0.252 -9999 0 -0.708 10 10
RAN 0.02 0 -9999 0 -9999 0 0
HDAC4/MEF2C -0.021 0.213 -9999 0 -0.52 10 10
GNG2 0.02 0 -9999 0 -9999 0 0
NCOR2 -0.02 0.167 -9999 0 -0.708 4 4
TUBB2A -0.01 0.124 -9999 0 -0.523 4 4
HDAC11 -0.01 0.124 -9999 0 -0.523 4 4
HSP90AA1 0.005 0.089 -9999 0 -0.523 2 2
RANBP2 0.01 0.085 -9999 0 -0.708 1 1
ANKRA2 0.02 0 -9999 0 -9999 0 0
RFXANK 0.02 0 -9999 0 -9999 0 0
nuclear import -0.044 0 -9999 0 -9999 0 0
BARD1 signaling events

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
BARD1/CSTF1 0.014 0.091 -9999 0 -0.526 2 2
ATM 0 0.12 -9999 0 -0.708 2 2
UBE2D3 0.02 0 -9999 0 -9999 0 0
PRKDC 0.02 0 -9999 0 -9999 0 0
ATR 0.02 0 -9999 0 -9999 0 0
UBE2L3 0.02 0 -9999 0 -9999 0 0
FANCD2 0.027 0.07 -9999 0 -0.387 2 2
protein ubiquitination -0.02 0.104 -9999 0 -0.742 1 1
XRCC5 0.02 0 -9999 0 -9999 0 0
XRCC6 0.02 0 -9999 0 -9999 0 0
M/R/N Complex 0.034 0.057 -9999 0 -0.444 1 1
MRE11A 0.02 0 -9999 0 -9999 0 0
DNA-PK 0.041 0 -9999 0 -9999 0 0
FA complex/FANCD2/Ubiquitin 0.027 0.15 -9999 0 -0.626 2 2
FANCF 0.02 0 -9999 0 -9999 0 0
BRCA1 0.02 0 -9999 0 -9999 0 0
CCNE1 0.02 0 -9999 0 -9999 0 0
CDK2/Cyclin E1 0.03 0 -9999 0 -9999 0 0
FANCG 0.02 0 -9999 0 -9999 0 0
BRCA1/BACH1/BARD1 0.014 0.091 -9999 0 -0.526 2 2
FANCE 0.012 0.064 -9999 0 -0.523 1 1
FANCC -0.02 0.167 -9999 0 -0.708 4 4
NBN 0.02 0 -9999 0 -9999 0 0
FANCA -0.023 0.159 -9999 0 -0.597 5 5
DNA repair 0.054 0.141 -9999 0 -9999 0 0
BRCA1/BARD1/ubiquitin 0.014 0.091 -9999 0 -0.526 2 2
BARD1/DNA-PK 0.039 0.074 -9999 0 -0.396 2 2
FANCL 0.01 0.085 -9999 0 -0.708 1 1
mRNA polyadenylation -0.014 0.091 0.524 2 -9999 0 2
BRCA1/BARD1/CTIP/M/R/N Complex 0.021 0.148 -9999 0 -0.608 3 3
BRCA1/BACH1/BARD1/TopBP1 0.027 0.08 -9999 0 -0.444 2 2
BRCA1/BARD1/P53 0.033 0.09 -9999 0 -0.396 3 3
BARD1/CSTF1/BRCA1 0.027 0.08 -9999 0 -0.444 2 2
BRCA1/BACH1 0.02 0 -9999 0 -9999 0 0
BARD1 0 0.12 -9999 0 -0.708 2 2
PCNA 0.02 0 -9999 0 -9999 0 0
BRCA1/BARD1/UbcH5C 0.027 0.08 -9999 0 -0.444 2 2
BRCA1/BARD1/UbcH7 0.027 0.08 -9999 0 -0.444 2 2
BRCA1/BARD1/RAD51/PCNA 0.035 0.081 -9999 0 -0.396 2 2
BARD1/DNA-PK/P53 0.042 0.085 -9999 0 -9999 0 0
BRCA1/BARD1/Ubiquitin 0.014 0.091 -9999 0 -0.526 2 2
BRCA1/BARD1/CTIP 0.006 0.17 -9999 0 -0.707 3 3
FA complex 0.019 0.126 -9999 0 -0.592 2 2
BARD1/EWS 0.014 0.091 -9999 0 -0.526 2 2
RBBP8 -0.008 0.148 -9999 0 -0.47 6 6
TP53 0.01 0.085 -9999 0 -0.708 1 1
TOPBP1 0.02 0 -9999 0 -9999 0 0
G1/S transition of mitotic cell cycle -0.031 0.089 0.394 3 -9999 0 3
BRCA1/BARD1 0.037 0.117 -9999 0 -0.755 1 1
CSTF1 0.02 0 -9999 0 -9999 0 0
BARD1/EWS-Fli1 -0.001 0.091 -9999 0 -0.538 2 2
CDK2 0.02 0 -9999 0 -9999 0 0
UniProt:Q9BZD1 0 0 -9999 0 -9999 0 0
RAD51 0.012 0.064 -9999 0 -0.523 1 1
RAD50 0.01 0.085 -9999 0 -0.708 1 1
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.014 0.091 -9999 0 -0.526 2 2
EWSR1 0.02 0 -9999 0 -9999 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.02 0 -9999 0 -9999 0 0
VLDLR -0.033 0.161 -9999 0 -0.523 7 7
LRPAP1 0.02 0 -9999 0 -9999 0 0
NUDC 0.02 0 -9999 0 -9999 0 0
RELN/LRP8 0 0.133 -9999 0 -0.596 2 2
CaM/Ca2+ 0.015 0 -9999 0 -9999 0 0
KATNA1 0.02 0 -9999 0 -9999 0 0
GO:0030286 0 0 -9999 0 -9999 0 0
ABL1 0.012 0.121 -9999 0 -0.539 2 2
IQGAP1/CaM 0.03 0 -9999 0 -9999 0 0
DAB1 0.02 0 -9999 0 -9999 0 0
IQGAP1 0.02 0 -9999 0 -9999 0 0
PLA2G7 -0.141 0.283 -9999 0 -0.626 18 18
CALM1 0.02 0 -9999 0 -9999 0 0
DYNLT1 0.02 0 -9999 0 -9999 0 0
mol:Ca2+ 0 0 -9999 0 -9999 0 0
LRPAP1/LRP8 -0.003 0.11 -9999 0 -0.366 6 6
UniProt:Q4QZ09 0 0 -9999 0 -9999 0 0
CLIP1 0.012 0.064 -9999 0 -0.523 1 1
CDK5R1 0.02 0 -9999 0 -9999 0 0
LIS1/Poliovirus Protein 3A 0.025 0 -9999 0 -9999 0 0
CDK5R2 0.02 0 -9999 0 -9999 0 0
mol:PP1 0 0 -9999 0 -9999 0 0
RELN/VLDLR/DAB1 -0.006 0.117 -9999 0 -9999 0 0
YWHAE 0.02 0 -9999 0 -9999 0 0
NDEL1/14-3-3 E 0.048 0.114 -9999 0 -9999 0 0
MAP1B -0.03 0.1 0.203 1 -0.353 5 6
RAC1 0 0 -9999 0 -9999 0 0
p35/CDK5 0.029 0.121 -9999 0 -0.466 3 3
RELN -0.003 0.109 -9999 0 -0.523 3 3
PAFAH/LIS1 -0.065 0.185 -9999 0 -0.379 18 18
LIS1/CLIP170 0.035 0.04 -9999 0 -9999 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.02 0.065 -9999 0 -9999 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 0.028 0.073 -9999 0 -9999 0 0
GO:0005869 0 0 -9999 0 -9999 0 0
NDEL1 0.038 0.119 -9999 0 -0.427 3 3
LIS1/IQGAP1 0.04 0 -9999 0 -9999 0 0
RHOA -0.007 0.055 -9999 0 -0.473 1 1
PAFAH1B1 0.034 0 -9999 0 -9999 0 0
PAFAH1B3 0.012 0.064 -9999 0 -0.523 1 1
PAFAH1B2 -0.003 0.109 -9999 0 -0.523 3 3
MAP1B/LIS1/Dynein heavy chain 0.016 0.07 -9999 0 -9999 0 0
NDEL1/Katanin 60/Dynein heavy chain 0.056 0.11 -9999 0 -9999 0 0
LRP8 -0.025 0.15 -9999 0 -0.523 6 6
NDEL1/Katanin 60 0.048 0.114 -9999 0 -9999 0 0
P39/CDK5 0.029 0.121 -9999 0 -0.466 3 3
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.04 0 -9999 0 -9999 0 0
CDK5 0.019 0.127 -9999 0 -0.5 3 3
PPP2R5D 0.012 0.064 -9999 0 -0.523 1 1
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.031 0.034 -9999 0 -9999 0 0
CSNK2A1 0.02 0 -9999 0 -9999 0 0
RELN/VLDLR/DAB1/LIS1 0.02 0.101 -9999 0 -9999 0 0
RELN/VLDLR -0.017 0.146 -9999 0 -0.541 2 2
CDC42 0 0 -9999 0 -9999 0 0
Arf6 downstream 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
PLAUR 0.023 0.178 -9999 0 -1.224 1 1
regulation of axonogenesis -0.023 0.066 0.255 3 -9999 0 3
myoblast fusion -0.007 0.076 0.424 1 -9999 0 1
mol:GTP -0.011 0.04 -9999 0 -0.239 1 1
regulation of calcium-dependent cell-cell adhesion -0.022 0.102 0.419 3 -9999 0 3
ARF1/GTP -0.006 0.026 -9999 0 -9999 0 0
mol:GM1 0.007 0.034 -9999 0 -0.179 1 1
mol:Choline 0.015 0.096 -9999 0 -0.424 3 3
lamellipodium assembly -0.015 0.078 -9999 0 -0.462 1 1
MAPK3 0.027 0.065 -9999 0 -0.344 1 1
ARF6/GTP/NME1/Tiam1 0.022 0.103 -9999 0 -0.421 3 3
ARF1 0.02 0 -9999 0 -9999 0 0
ARF6/GDP 0.007 0.076 -9999 0 -0.426 1 1
ARF1/GDP 0.024 0.073 -9999 0 -0.384 1 1
ARF6 0.013 0.023 -9999 0 -9999 0 0
RAB11A 0.01 0.085 -9999 0 -0.708 1 1
TIAM1 -0.009 0.145 -9999 0 -0.706 3 3
fibronectin binding 0 0 -9999 0 -9999 0 0
MAPK1 0.027 0.065 -9999 0 -0.344 1 1
actin filament bundle formation -0.012 0.085 0.388 2 -9999 0 2
KALRN -0.022 0.089 -9999 0 -0.377 3 3
RAB11FIP3/RAB11A -0.032 0.175 -9999 0 -0.526 8 8
RhoA/GDP 0.013 0.086 -9999 0 -0.39 2 2
NME1 0.022 0.005 -9999 0 -9999 0 0
Rac1/GDP 0.019 0.071 -9999 0 -0.386 1 1
substrate adhesion-dependent cell spreading -0.011 0.04 -9999 0 -0.239 1 1
cortical actin cytoskeleton organization -0.015 0.078 -9999 0 -0.465 1 1
RAC1 0.02 0 -9999 0 -9999 0 0
liver development -0.011 0.04 -9999 0 -0.239 1 1
ARF6/GTP -0.011 0.04 -9999 0 -0.239 1 1
RhoA/GTP -0.013 0.062 -9999 0 -0.488 1 1
mol:GDP -0.014 0.074 -9999 0 -0.428 1 1
ARF6/GTP/RAB11FIP3/RAB11A -0.052 0.136 -9999 0 -0.432 8 8
RHOA 0.01 0.085 -9999 0 -0.708 1 1
PLD1 0.023 0.034 -9999 0 -9999 0 0
RAB11FIP3 -0.051 0.216 -9999 0 -0.708 7 7
tube morphogenesis -0.015 0.078 -9999 0 -0.462 1 1
ruffle organization 0.023 0.066 -9999 0 -0.255 3 3
regulation of epithelial cell migration -0.011 0.04 -9999 0 -0.239 1 1
PLD2 0.001 0.108 -9999 0 -0.489 3 3
PIP5K1A 0.023 0.066 -9999 0 -0.256 3 3
mol:Phosphatidic acid 0.015 0.096 -9999 0 -0.424 3 3
Rac1/GTP -0.015 0.078 -9999 0 -0.467 1 1
PLK1 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
regulation of centriole-centriole cohesion -0.017 0.007 -9999 0 -9999 0 0
BUB1B 0.029 0.041 -9999 0 -0.254 1 1
PLK1 0.024 0.022 -9999 0 -9999 0 0
PLK1S1 0.013 0.011 -9999 0 -9999 0 0
KIF2A 0.017 0.074 -9999 0 -0.278 4 4
regulation of mitotic centrosome separation 0.024 0.022 -9999 0 -9999 0 0
GOLGA2 -0.01 0.145 -9999 0 -0.708 3 3
Hec1/SPC24 0.021 0.064 -9999 0 -0.337 2 2
WEE1 0.018 0.1 -9999 0 -0.539 2 2
cytokinesis 0.021 0.085 -9999 0 -0.321 1 1
PP2A-alpha B56 0.028 0.109 -9999 0 -0.682 1 1
AURKA 0.021 0.022 -9999 0 -0.134 1 1
PICH/PLK1 0.041 0.078 -9999 0 -9999 0 0
CENPE 0.021 0.068 -9999 0 -0.293 3 3
RhoA/GTP 0.007 0.065 -9999 0 -0.538 1 1
positive regulation of microtubule depolymerization 0.017 0.074 -9999 0 -0.276 4 4
PPP2CA 0.02 0 -9999 0 -9999 0 0
FZR1 0.02 0 -9999 0 -9999 0 0
TPX2 0.013 0.04 -9999 0 -0.131 5 5
PAK1 0.012 0.063 -9999 0 -0.521 1 1
SPC24 0 0 -9999 0 -9999 0 0
FBXW11 0.02 0 -9999 0 -9999 0 0
CLSPN 0.023 0.012 -9999 0 -9999 0 0
GORASP1 0.012 0.064 -9999 0 -0.523 1 1
metaphase 0.001 0.001 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
NLP 0.013 0.011 -9999 0 -9999 0 0
G2 phase of mitotic cell cycle 0 0.002 0.016 1 -9999 0 1
STAG2 0 0.12 -9999 0 -0.708 2 2
GRASP65/GM130/RAB1/GTP -0.019 0.104 -9999 0 -0.795 1 1
spindle elongation 0.024 0.022 -9999 0 -9999 0 0
ODF2 0.009 0.086 -9999 0 -0.717 1 1
BUB1 -0.027 0.109 -9999 0 -0.76 1 1
TPT1 0.018 0.039 -9999 0 -0.298 1 1
CDC25C 0.012 0.05 -9999 0 -0.172 4 4
CDC25B 0.021 0.002 -9999 0 -9999 0 0
SGOL1 0.017 0.007 -9999 0 -9999 0 0
RHOA 0.01 0.085 -9999 0 -0.708 1 1
CCNB1/CDK1 -0.014 0.064 -9999 0 -9999 0 0
CDC14B 0.017 0.001 -9999 0 -9999 0 0
CDC20 -0.003 0.109 -9999 0 -0.523 3 3
PLK1/PBIP1 -0.012 0.064 -9999 0 -0.311 3 3
mitosis 0 0.003 0.024 1 -9999 0 1
FBXO5 0.03 0.021 -9999 0 -9999 0 0
CDC2 0.021 0.002 -9999 0 -9999 0 0
NDC80 0.002 0.106 -9999 0 -0.616 2 2
metaphase plate congression 0.023 0.012 -9999 0 -9999 0 0
ERCC6L 0.039 0.08 -9999 0 -9999 0 0
NLP/gamma Tubulin 0.019 0.013 -9999 0 -9999 0 0
microtubule cytoskeleton organization 0.018 0.039 -9999 0 -0.297 1 1
G2/M transition DNA damage checkpoint 0 0.001 -9999 0 -9999 0 0
PPP1R12A 0.02 0.001 -9999 0 -9999 0 0
interphase 0 0.001 -9999 0 -9999 0 0
PLK1/PRC1-2 0.024 0.08 -9999 0 -0.277 2 2
GRASP65/GM130/RAB1/GTP/PLK1 0.025 0.12 -9999 0 -0.482 3 3
RAB1A 0.01 0.085 -9999 0 -0.708 1 1
prophase 0 0 -9999 0 -9999 0 0
Aurora A/BORA 0.027 0.02 -9999 0 -9999 0 0
mitotic prometaphase 0 0.001 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.041 0.063 -9999 0 -0.453 1 1
microtubule-based process 0.012 0.083 -9999 0 -0.285 5 5
Golgi organization 0.024 0.022 -9999 0 -9999 0 0
Cohesin/SA2 -0.012 0.063 -9999 0 -0.382 2 2
PPP1CB/MYPT1 0.021 0.065 -9999 0 -0.528 1 1
KIF20A -0.018 0.138 -9999 0 -0.523 5 5
APC/C/CDC20 0.02 0.065 -9999 0 -0.279 3 3
PPP2R1A 0.02 0 -9999 0 -9999 0 0
chromosome segregation -0.012 0.063 -9999 0 -0.307 3 3
PRC1 0.02 0 -9999 0 -9999 0 0
ECT2 0.021 0.066 -9999 0 -0.282 3 3
C13orf34 0.028 0.019 -9999 0 -9999 0 0
NUDC 0.023 0.012 -9999 0 -9999 0 0
regulation of attachment of spindle microtubules to kinetochore 0.029 0.041 -9999 0 -0.252 1 1
spindle assembly 0.024 0.018 -9999 0 -9999 0 0
spindle stabilization 0.013 0.011 -9999 0 -9999 0 0
APC/C/HCDH1 0.027 0.001 -9999 0 -9999 0 0
MKLP2/PLK1 0.012 0.084 -9999 0 -0.287 5 5
CCNB1 0.006 0.09 -9999 0 -0.523 2 2
PPP1CB 0.01 0.085 -9999 0 -0.709 1 1
BTRC 0.01 0.085 -9999 0 -0.708 1 1
ROCK2 0.017 0.091 -9999 0 -0.396 3 3
TUBG1 0.022 0.012 -9999 0 -9999 0 0
G2/M transition of mitotic cell cycle -0.012 0.065 -9999 0 -9999 0 0
MLF1IP -0.002 0.093 -9999 0 -0.44 3 3
INCENP 0.012 0.064 -9999 0 -0.527 1 1
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.026 0.077 -9999 0 -0.296 1 1
CaM/Ca2+ 0.015 0 -9999 0 -9999 0 0
AKT1 0.02 0 -9999 0 -9999 0 0
AKT2 0.02 0 -9999 0 -9999 0 0
STXBP4 0.02 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
mol:glucose 0.02 0.106 -9999 0 -0.299 2 2
YWHAZ 0.01 0.085 -9999 0 -0.708 1 1
CALM1 0.02 0 -9999 0 -9999 0 0
YWHAQ 0.02 0 -9999 0 -9999 0 0
TBC1D4 -0.019 0.14 -9999 0 -0.385 9 9
mol:Ca2+ 0 0 -9999 0 -9999 0 0
YWHAH 0.02 0 -9999 0 -9999 0 0
YWHAB 0.02 0 -9999 0 -9999 0 0
SNARE/Synip 0.027 0.08 -9999 0 -0.444 2 2
YWHAG 0.02 0 -9999 0 -9999 0 0
ASIP 0 0 -9999 0 -9999 0 0
PRKCI 0.02 0 -9999 0 -9999 0 0
AS160/CaM/Ca2+ 0.015 0 -9999 0 -9999 0 0
RHOQ 0.02 0 -9999 0 -9999 0 0
GYS1 0.035 0.068 -9999 0 -0.359 2 2
PRKCZ 0 0 -9999 0 -9999 0 0
TRIP10 -0.041 0.201 -9999 0 -0.708 6 6
TC10/GTP/CIP4/Exocyst -0.013 0.133 -9999 0 -0.455 6 6
AS160/14-3-3 0.034 0.072 -9999 0 -9999 0 0
VAMP2 0.02 0 -9999 0 -9999 0 0
SLC2A4 0.018 0.114 -9999 0 -0.329 2 2
STX4 0 0.12 -9999 0 -0.708 2 2
GSK3B 0.039 0 -9999 0 -9999 0 0
SFN -0.025 0.15 -9999 0 -0.523 6 6
LNPEP 0.02 0 -9999 0 -9999 0 0
YWHAE 0.02 0 -9999 0 -9999 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.028 0.047 -9999 0 -0.367 1 1
BAD/BCL-XL/YWHAZ 0.04 0.063 -9999 0 -0.396 1 1
CDKN1B 0.048 0.067 -9999 0 -0.489 1 1
CDKN1A 0.043 0.07 -9999 0 -0.34 2 2
FRAP1 0.02 0 -9999 0 -9999 0 0
PRKDC 0.02 0 -9999 0 -9999 0 0
FOXO3 0.054 0.028 -9999 0 -9999 0 0
AKT1 -0.004 0.016 -9999 0 -9999 0 0
BAD 0.02 0 -9999 0 -9999 0 0
AKT3 0.014 0.07 -9999 0 -0.401 2 2
mol:GTP 0 0 -9999 0 -9999 0 0
FOXO4 0.054 0.028 -9999 0 -9999 0 0
AKT1/ASK1 0.04 0.068 -9999 0 -0.33 2 2
BAD/YWHAZ 0.034 0.057 -9999 0 -0.444 1 1
RICTOR 0.02 0 -9999 0 -9999 0 0
RAF1 0.02 0 -9999 0 -9999 0 0
JNK cascade 0.012 0.054 0.321 2 -9999 0 2
TSC1 0.048 0.067 -9999 0 -0.489 1 1
YWHAZ 0.01 0.085 -9999 0 -0.708 1 1
AKT1/RAF1 0.054 0.028 -9999 0 -9999 0 0
EP300 0.01 0.085 -9999 0 -0.708 1 1
mol:GDP -0.004 0.016 -9999 0 -9999 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -9999 0 0
TSC2 0.054 0.028 -9999 0 -9999 0 0
YWHAQ 0.02 0 -9999 0 -9999 0 0
TBC1D4 -0.013 0.133 -9999 0 -0.349 9 9
MAP3K5 0 0.12 -9999 0 -0.708 2 2
MAPKAP1 -0.003 0.109 -9999 0 -0.523 3 3
negative regulation of cell cycle -0.054 0.037 -9999 0 -9999 0 0
YWHAH 0.02 0 -9999 0 -9999 0 0
AKT1S1 0.048 0.067 -9999 0 -0.489 1 1
CASP9 0.054 0.028 -9999 0 -9999 0 0
YWHAB 0.02 0 -9999 0 -9999 0 0
p27Kip1/KPNA1 0.058 0.064 -9999 0 -0.455 1 1
GBL 0.02 0 -9999 0 -9999 0 0
PDK1/Src/Hsp90 0.025 0.079 -9999 0 -0.444 1 1
YWHAE 0.02 0 -9999 0 -9999 0 0
SRC 0.02 0 -9999 0 -9999 0 0
AKT2/p21CIP1 -0.013 0.061 -9999 0 -9999 0 0
KIAA1303 0.005 0.089 -9999 0 -0.523 2 2
mTOR/RHEB/GTP/Raptor/GBL 0.048 0.033 -9999 0 -9999 0 0
CHUK 0.054 0.028 -9999 0 -9999 0 0
BAD/BCL-XL 0.069 0.047 -9999 0 -9999 0 0
mTORC2 0.039 0.062 -9999 0 -9999 0 0
AKT2 0.02 0.05 -9999 0 -0.401 1 1
FOXO1-3a-4/14-3-3 family 0.069 0.056 -9999 0 -9999 0 0
PDPK1 0.01 0.085 -9999 0 -0.708 1 1
MDM2 0.054 0.028 -9999 0 -9999 0 0
MAPKKK cascade -0.053 0.027 -9999 0 -9999 0 0
MDM2/Cbp/p300 0.067 0.051 -9999 0 -9999 0 0
TSC1/TSC2 0.057 0.065 -9999 0 -0.465 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.064 0.049 -9999 0 -9999 0 0
glucose import -0.052 0.194 -9999 0 -0.474 11 11
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.061 0.043 -9999 0 -9999 0 0
response to stress 0 0 -9999 0 -9999 0 0
SLC2A4 -0.052 0.196 -9999 0 -0.478 11 11
GSK3A 0.048 0.067 -9999 0 -0.489 1 1
FOXO1 0.031 0.093 -9999 0 -9999 0 0
GSK3B 0.054 0.028 -9999 0 -9999 0 0
SFN -0.025 0.15 -9999 0 -0.523 6 6
G1/S transition of mitotic cell cycle 0.057 0.065 -9999 0 -0.465 1 1
p27Kip1/14-3-3 family 0.056 0.052 -9999 0 -9999 0 0
PRKACA 0.02 0 -9999 0 -9999 0 0
KPNA1 0.02 0 -9999 0 -9999 0 0
HSP90AA1 0.005 0.089 -9999 0 -0.523 2 2
YWHAG 0.02 0 -9999 0 -9999 0 0
RHEB 0.02 0 -9999 0 -9999 0 0
CREBBP 0.02 0 -9999 0 -9999 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.012 0.064 -9999 0 -0.523 1 1
NFATC1 0.029 0.129 -9999 0 -0.478 2 2
NFATC2 0.023 0.07 -9999 0 -0.286 1 1
NFATC3 0.021 0.007 -9999 0 -9999 0 0
YWHAE 0.02 0 -9999 0 -9999 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.02 0.192 -9999 0 -0.487 8 8
Exportin 1/Ran/NUP214 0.038 0.012 -9999 0 -9999 0 0
mol:DAG 0 0.002 -9999 0 -9999 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.055 0.144 -9999 0 -0.628 3 3
BCL2/BAX -0.017 0.153 -9999 0 -0.526 6 6
CaM/Ca2+/Calcineurin A alpha-beta B1 0.016 0.006 -9999 0 -9999 0 0
CaM/Ca2+ 0.016 0.006 -9999 0 -9999 0 0
BAX 0.02 0 -9999 0 -9999 0 0
MAPK14 0.02 0.003 -9999 0 -9999 0 0
BAD 0.02 0 -9999 0 -9999 0 0
CABIN1/MEF2D -0.01 0.185 -9999 0 -0.608 4 4
Calcineurin A alpha-beta B1/BCL2 -0.041 0.201 -9999 0 -0.707 6 6
FKBP8 0.02 0 -9999 0 -9999 0 0
activation-induced cell death of T cells 0.01 0.181 0.595 4 -9999 0 4
KPNB1 -0.015 0.147 -9999 0 -0.616 4 4
KPNA2 0.01 0.085 -9999 0 -0.708 1 1
XPO1 0.02 0.001 -9999 0 -9999 0 0
SFN -0.025 0.15 -9999 0 -0.523 6 6
MAP3K8 -0.089 0.256 -9999 0 -0.691 11 11
NFAT4/CK1 alpha 0.036 0.049 -9999 0 -0.364 1 1
MEF2D/NFAT1/Cbp/p300 0.039 0.109 -9999 0 -9999 0 0
CABIN1 -0.021 0.195 -9999 0 -0.493 8 8
CALM1 0.02 0.003 -9999 0 -9999 0 0
RAN 0.02 0.001 -9999 0 -9999 0 0
MAP3K1 0.01 0.085 -9999 0 -0.708 1 1
CAMK4 0.02 0 -9999 0 -9999 0 0
mol:Ca2+ 0 0.006 -9999 0 -9999 0 0
MAPK3 0.02 0 -9999 0 -9999 0 0
YWHAH 0.02 0 -9999 0 -9999 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.022 0.152 -9999 0 -0.48 7 7
YWHAB 0.02 0 -9999 0 -9999 0 0
MAPK8 0.019 0.006 -9999 0 -9999 0 0
MAPK9 0 0.12 -9999 0 -0.708 2 2
YWHAG 0.02 0 -9999 0 -9999 0 0
FKBP1A 0.02 0 -9999 0 -9999 0 0
NFAT1-c-4/YWHAQ 0.051 0.118 -9999 0 -0.557 1 1
PRKCH -0.041 0.201 -9999 0 -0.708 6 6
CABIN1/Cbp/p300 0.022 0.065 -9999 0 -0.522 1 1
CASP3 0.012 0.064 -9999 0 -0.523 1 1
PIM1 0.02 0 -9999 0 -9999 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.013 0.004 -9999 0 -9999 0 0
apoptosis -0.016 0.048 -9999 0 -9999 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.05 0.044 -9999 0 -9999 0 0
PRKCB 0 0 -9999 0 -9999 0 0
PRKCE 0.02 0 -9999 0 -9999 0 0
JNK2/NFAT4 0.019 0.072 -9999 0 -0.408 2 2
BAD/BCL-XL 0.024 0.046 -9999 0 -0.366 1 1
PRKCD -0.025 0.15 -9999 0 -0.523 6 6
NUP214 0.02 0.001 -9999 0 -9999 0 0
PRKCZ 0 0.003 -9999 0 -9999 0 0
PRKCA 0.02 0 -9999 0 -9999 0 0
PRKCG 0.02 0 -9999 0 -9999 0 0
PRKCQ -0.015 0.147 -9999 0 -0.616 4 4
FKBP38/BCL2 -0.017 0.153 -9999 0 -0.526 6 6
EP300 0.01 0.085 -9999 0 -0.706 1 1
PRKCB1 -0.058 0.222 -9999 0 -0.685 8 8
CSNK2A1 0.02 0 -9999 0 -9999 0 0
NFATc/JNK1 0.035 0.123 -9999 0 -0.573 1 1
CaM/Ca2+/FKBP38 0.027 0.009 -9999 0 -9999 0 0
FKBP12/FK506 0.015 0 -9999 0 -9999 0 0
CSNK1A1 0.028 0.009 -9999 0 -9999 0 0
CaM/Ca2+/CAMK IV 0.027 0.009 -9999 0 -9999 0 0
NFATc/ERK1 0.04 0.123 -9999 0 -0.574 1 1
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.054 0.143 -9999 0 -0.625 3 3
NR4A1 0.021 0.167 -9999 0 -0.621 1 1
GSK3B 0.019 0.006 -9999 0 -9999 0 0
positive T cell selection 0.021 0.007 -9999 0 -9999 0 0
NFAT1/CK1 alpha -0.016 0.04 -9999 0 -9999 0 0
RCH1/ KPNB1 -0.004 0.127 -9999 0 -0.462 5 5
YWHAQ 0.02 0 -9999 0 -9999 0 0
PRKACA 0.02 0.003 -9999 0 -9999 0 0
AKAP5 -0.046 0.202 -9999 0 -0.655 7 7
MEF2D 0.02 0.003 -9999 0 -9999 0 0
mol:FK506 0 0 -9999 0 -9999 0 0
YWHAZ 0.01 0.085 -9999 0 -0.708 1 1
NFATc/p38 alpha 0.035 0.123 -9999 0 -0.573 1 1
CREBBP 0.02 0.003 -9999 0 -9999 0 0
BCL2 -0.041 0.201 -9999 0 -0.708 6 6
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.055 0.15 -9999 0 -0.792 1 1
Ran/GTP/Exportin 1/HDAC1 -0.009 0.054 -9999 0 -0.33 2 2
NF kappa B1 p50/RelA/I kappa B alpha 0.001 0.173 -9999 0 -0.692 2 2
SUMO1 0.02 0 -9999 0 -9999 0 0
ZFPM1 0.01 0.085 -9999 0 -0.708 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.028 0.033 -9999 0 -0.25 1 1
FKBP3 0.02 0 -9999 0 -9999 0 0
Histones 0.034 0.107 -9999 0 -0.655 1 1
YY1/LSF 0.035 0.036 -9999 0 -0.27 1 1
SMG5 0.012 0.064 -9999 0 -0.523 1 1
RAN 0.02 0 -9999 0 -9999 0 0
I kappa B alpha/HDAC3 -0.012 0.163 -9999 0 -0.675 2 2
I kappa B alpha/HDAC1 -0.01 0.167 -9999 0 -0.6 4 4
SAP18 0.02 0 -9999 0 -9999 0 0
RELA 0.012 0.114 -9999 0 -0.405 1 1
HDAC1/Smad7 0.011 0.11 -9999 0 -0.444 3 3
RANGAP1 0.02 0 -9999 0 -9999 0 0
HDAC3/TR2 0.012 0.116 -9999 0 -0.727 1 1
NuRD/MBD3 Complex 0.057 0.063 -9999 0 -0.331 1 1
NF kappa B1 p50/RelA 0.02 0.104 -9999 0 -0.367 1 1
EntrezGene:23225 0 0 -9999 0 -9999 0 0
GATA2 -0.01 0.124 -9999 0 -0.523 4 4
GATA1 -0.01 0.124 -9999 0 -0.523 4 4
Mad/Max 0.03 0 -9999 0 -9999 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.06 0.093 -9999 0 -0.448 1 1
RBBP7 0.02 0 -9999 0 -9999 0 0
NPC 0.006 0.049 -9999 0 -0.406 1 1
RBBP4 0.02 0 -9999 0 -9999 0 0
MAX 0.02 0 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 0 0
FBXW11 0.02 0 -9999 0 -9999 0 0
NFKBIA -0.016 0.161 -9999 0 -0.551 4 4
KAT2B 0 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
SIN3/HDAC complex 0.039 0.103 -9999 0 -0.648 1 1
SIN3 complex 0.021 0.114 -9999 0 -0.396 5 5
SMURF1 0.005 0.089 -9999 0 -0.523 2 2
CHD3 0.012 0.064 -9999 0 -0.523 1 1
SAP30 -0.02 0.167 -9999 0 -0.708 4 4
EntrezGene:23636 0 0 -9999 0 -9999 0 0
NCOR1 0.02 0 -9999 0 -9999 0 0
YY1/HDAC3 0.025 0.085 -9999 0 -9999 0 0
YY1/HDAC2 0.035 0.036 -9999 0 -9999 0 0
YY1/HDAC1 0.028 0.065 -9999 0 -0.351 2 2
NuRD/MBD2 Complex (MeCP1) 0.057 0.063 -9999 0 -0.331 1 1
PPARG -0.032 0.218 -9999 0 -0.558 8 8
HDAC8/hEST1B 0.036 0.04 -9999 0 -9999 0 0
UBE2I 0.02 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0 -9999 0 -9999 0 0
TNFRSF1A -0.061 0.229 -9999 0 -0.708 8 8
HDAC3/SMRT (N-CoR2) -0.006 0.15 -9999 0 -0.532 4 4
MBD3L2 0.002 0.106 -9999 0 -0.616 2 2
ubiquitin-dependent protein catabolic process 0.011 0.11 -9999 0 -0.442 3 3
CREBBP 0.02 0 -9999 0 -9999 0 0
NuRD/MBD3/MBD3L2 Complex 0.062 0.073 -9999 0 -9999 0 0
HDAC1 0.01 0.085 -9999 0 -0.708 1 1
HDAC3 0.007 0.096 -9999 0 -0.364 1 1
HDAC2 0.02 0 -9999 0 -9999 0 0
YY1 0.029 0.042 -9999 0 -0.327 1 1
HDAC8 0.02 0 -9999 0 -9999 0 0
SMAD7 0 0.12 -9999 0 -0.708 2 2
NCOR2 -0.02 0.167 -9999 0 -0.708 4 4
MXD1 0.02 0 -9999 0 -9999 0 0
STAT3 0.027 0.07 -9999 0 -0.387 2 2
NFKB1 0.02 0 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.01 0.085 -9999 0 -0.708 1 1
YY1/LSF/HDAC1 0.039 0.061 -9999 0 -0.389 1 1
YY1/SAP30/HDAC1 0.014 0.115 -9999 0 -0.389 5 5
EP300 0.01 0.085 -9999 0 -0.708 1 1
STAT3 (dimer non-phopshorylated) 0.027 0.07 -9999 0 -0.386 2 2
proteasomal ubiquitin-dependent protein catabolic process -0.016 0.16 -9999 0 -0.548 4 4
histone deacetylation 0.057 0.062 -9999 0 -0.328 1 1
STAT3 (dimer non-phopshorylated)/HDAC3 0.023 0.107 -9999 0 -0.585 1 1
nuclear export -0.036 0.04 -9999 0 -9999 0 0
PRKACA 0.02 0 -9999 0 -9999 0 0
GATAD2B 0.01 0.085 -9999 0 -0.708 1 1
GATAD2A 0.02 0 -9999 0 -9999 0 0
GATA2/HDAC3 0.001 0.122 -9999 0 -0.488 2 2
GATA1/HDAC1 0.001 0.126 -9999 0 -0.482 4 4
GATA1/HDAC3 0.001 0.118 -9999 0 -0.599 1 1
CHD4 0.005 0.089 -9999 0 -0.523 2 2
TNF-alpha/TNFR1A -0.044 0.201 -9999 0 -0.557 9 9
SIN3/HDAC complex/Mad/Max 0.05 0.086 -9999 0 -0.508 1 1
NuRD Complex 0.068 0.066 -9999 0 -9999 0 0
positive regulation of chromatin silencing 0.032 0.105 -9999 0 -0.639 1 1
SIN3B 0.02 0 -9999 0 -9999 0 0
MTA2 0.012 0.064 -9999 0 -0.523 1 1
SIN3A 0.01 0.085 -9999 0 -0.708 1 1
XPO1 0.02 0 -9999 0 -9999 0 0
SUMO1/HDAC1 0.037 0.054 -9999 0 -0.361 1 1
HDAC complex 0.045 0.052 -9999 0 -0.396 1 1
GATA1/Fog1 0 0.11 -9999 0 -0.398 5 5
FKBP25/HDAC1/HDAC2 0.034 0.057 -9999 0 -0.444 1 1
TNF 0.002 0.106 -9999 0 -0.616 2 2
negative regulation of cell growth 0.05 0.085 -9999 0 -0.503 1 1
NuRD/MBD2/PRMT5 Complex 0.057 0.063 -9999 0 -0.331 1 1
Ran/GTP/Exportin 1 0.046 0.029 -9999 0 -9999 0 0
NF kappa B/RelA/I kappa B alpha -0.009 0.179 -9999 0 -0.459 8 8
SIN3/HDAC complex/NCoR1 0.048 0.078 -9999 0 -0.431 1 1
TFCP2 0.02 0 -9999 0 -9999 0 0
NR2C1 0.01 0.085 -9999 0 -0.708 1 1
MBD3 0.02 0 -9999 0 -9999 0 0
MBD2 0.02 0 -9999 0 -9999 0 0
Effects of Botulinum toxin

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
STX1A 0.017 0 -9999 0 -9999 0 0
UniProt:P19321 0 0 -9999 0 -9999 0 0
RIMS1/UNC13B 0.013 0.079 -9999 0 -0.366 3 3
STXBP1 0.005 0.089 -9999 0 -0.523 2 2
ACh/CHRNA1 0.007 0.04 -9999 0 -9999 0 0
RAB3GAP2/RIMS1/UNC13B 0.027 0.068 -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 -0.003 0.109 -9999 0 -0.523 3 3
mol:ACh -0.008 0.053 -9999 0 -0.138 10 10
RAB3GAP2 0.02 0 -9999 0 -9999 0 0
STX1A/SNAP25/VAMP2 -0.036 0.089 -9999 0 -0.383 3 3
UniProt:P10844 0 0 -9999 0 -9999 0 0
muscle contraction 0.007 0.04 -9999 0 -9999 0 0
UNC13B 0.02 0 -9999 0 -9999 0 0
CHRNA1 0.02 0 -9999 0 -9999 0 0
UniProt:P10845 0 0 -9999 0 -9999 0 0
ACh/Synaptotagmin 1 -0.01 0.089 -9999 0 -0.384 3 3
SNAP25 -0.042 0.127 -9999 0 -0.338 11 11
VAMP2 0.01 0 -9999 0 -9999 0 0
SYT1 -0.005 0.122 -9999 0 -0.585 3 3
UniProt:Q00496 0 0 -9999 0 -9999 0 0
STXIA/STXBP1 0.018 0.056 -9999 0 -0.311 2 2
STX1A/SNAP25 fragment 1/VAMP2 -0.036 0.089 -9999 0 -0.383 3 3
Arf6 trafficking events

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
SLC2A4 -0.073 0.222 -9999 0 -0.591 11 11
CLTC 0.041 0.022 -9999 0 -9999 0 0
calcium ion-dependent exocytosis 0.021 0.062 -9999 0 -0.33 1 1
Dynamin 2/GTP 0.032 0.036 -9999 0 -9999 0 0
EXOC4 0.02 0 -9999 0 -9999 0 0
CD59 0.027 0.055 -9999 0 -0.298 1 1
CPE -0.077 0.185 -9999 0 -0.392 18 18
CTNNB1 0.02 0 -9999 0 -9999 0 0
membrane fusion 0.019 0.067 -9999 0 -0.359 1 1
CTNND1 0.019 0.102 -9999 0 -0.376 4 4
DNM2 0.012 0.064 -9999 0 -0.523 1 1
mol:PI-4-5-P2 0.036 0.038 -9999 0 -9999 0 0
TSHR 0.014 0.068 -9999 0 -0.311 3 3
INS 0.026 0.013 -9999 0 -9999 0 0
BIN1 0.002 0.106 -9999 0 -0.616 2 2
mol:Choline 0.019 0.067 -9999 0 -0.359 1 1
growth hormone secretagogue receptor activity 0 0 -9999 0 -9999 0 0
mol:GDP 0.028 0 -9999 0 -9999 0 0
membrane depolarization 0 0 -9999 0 -9999 0 0
ARF6 0.02 0 -9999 0 -9999 0 0
mol:Ca2+ 0.032 0.036 -9999 0 -9999 0 0
JUP 0.03 0.042 -9999 0 -9999 0 0
ASAP2/amphiphysin II 0.015 0.063 -9999 0 -0.35 2 2
ARF6/GTP 0.015 0 -9999 0 -9999 0 0
CDH1 -0.007 0.098 -9999 0 -0.298 1 1
clathrin-independent pinocytosis 0.015 0 -9999 0 -9999 0 0
MAPK8IP3 0.01 0.085 -9999 0 -0.708 1 1
positive regulation of endocytosis 0.015 0 -9999 0 -9999 0 0
EXOC2 0.02 0 -9999 0 -9999 0 0
substrate adhesion-dependent cell spreading 0.052 0.081 -9999 0 -0.615 1 1
insulin receptor binding 0 0 -9999 0 -9999 0 0
SPAG9 0.01 0.085 -9999 0 -0.708 1 1
regulation of calcium-dependent cell-cell adhesion 0.025 0.057 -9999 0 -9999 0 0
positive regulation of phagocytosis 0.021 0.056 -9999 0 -0.455 1 1
ARF6/GTP/JIP3 0.02 0.056 -9999 0 -0.455 1 1
ACAP1 0.018 0.055 -9999 0 -0.285 1 1
mol:GTP 0 0 -9999 0 -9999 0 0
CHRM2 0.017 0.068 -9999 0 -0.329 1 1
clathrin heavy chain/ACAP1 0.04 0.046 -9999 0 -9999 0 0
JIP4/KLC1 0.032 0.052 -9999 0 -0.407 1 1
EXOC1 0.02 0 -9999 0 -9999 0 0
exocyst 0.053 0.082 -9999 0 -0.626 1 1
RALA/GTP -0.013 0.1 -9999 0 -0.38 5 5
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.02 0.056 -9999 0 -0.455 1 1
receptor recycling 0.015 0 -9999 0 -9999 0 0
CTNNA1 0.043 0.034 -9999 0 -9999 0 0
NME1 0.028 0 -9999 0 -9999 0 0
clathrin coat assembly 0.04 0.022 -9999 0 -9999 0 0
IL2RA -0.006 0.103 -9999 0 -0.326 3 3
VAMP3 0.021 0.057 -9999 0 -0.457 1 1
GLUT4/clathrin heavy chain/ACAP1 -0.047 0.111 -9999 0 -0.325 9 9
EXOC6 0.02 0 -9999 0 -9999 0 0
PLD1 0.024 0.035 -9999 0 -9999 0 0
PLD2 0.009 0.087 -9999 0 -0.37 3 3
EXOC5 0.02 0 -9999 0 -9999 0 0
PIP5K1C 0.036 0.038 -9999 0 -9999 0 0
SDC1 0.015 0.064 -9999 0 -9999 0 0
ARF6/GDP 0.027 0 -9999 0 -9999 0 0
EXOC7 0.01 0.085 -9999 0 -0.708 1 1
E-cadherin/beta catenin -0.025 0.059 -9999 0 -9999 0 0
mol:Phosphatidic acid 0.019 0.067 -9999 0 -0.359 1 1
endocytosis -0.014 0.062 0.348 2 -9999 0 2
SCAMP2 0.02 0 -9999 0 -9999 0 0
ADRB2 0.031 0.09 -9999 0 -0.354 3 3
EXOC3 0.002 0.106 -9999 0 -0.616 2 2
ASAP2 0 0 -9999 0 -9999 0 0
Dynamin 2/GDP 0.034 0.036 -9999 0 -9999 0 0
KLC1 0.02 0 -9999 0 -9999 0 0
AVPR2 0.038 0.06 -9999 0 -9999 0 0
RALA -0.018 0.138 -9999 0 -0.523 5 5
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.039 0.094 -9999 0 -0.474 1 1
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.02 0 -9999 0 -9999 0 0
oxygen homeostasis 0 0 -9999 0 -9999 0 0
TCEB2 0.02 0 -9999 0 -9999 0 0
TCEB1 0.02 0 -9999 0 -9999 0 0
HIF1A/p53 -0.002 0.141 -9999 0 -0.628 2 2
HIF1A -0.009 0.145 -9999 0 -1.008 1 1
COPS5 0.02 0 -9999 0 -9999 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.06 0 -9999 0 -9999 0 0
FIH (dimer) 0.01 0.085 -9999 0 -0.707 1 1
CDKN2A -0.038 0.194 -9999 0 -0.677 6 6
ARNT/IPAS 0.03 0 -9999 0 -9999 0 0
HIF1AN 0.01 0.085 -9999 0 -0.708 1 1
GNB2L1 0.01 0.085 -9999 0 -0.708 1 1
HIF1A/ARNT 0.003 0.136 -9999 0 -0.922 1 1
CUL2 0.02 0 -9999 0 -9999 0 0
OS9 0.02 0 -9999 0 -9999 0 0
RACK1/Elongin B/Elongin C 0.034 0.057 -9999 0 -0.444 1 1
response to hypoxia 0 0 -9999 0 -9999 0 0
HIF1A/Hsp90 -0.004 0.146 -9999 0 -0.526 3 3
PHD1-3/OS9 -0.05 0.185 -9999 0 -0.396 15 15
HIF1A/RACK1/Elongin B/Elongin C -0.036 0.112 -9999 0 -0.829 1 1
VHL 0.02 0 -9999 0 -9999 0 0
HSP90AA1 0.005 0.089 -9999 0 -0.523 2 2
HIF1A/JAB1 0.003 0.136 -9999 0 -0.922 1 1
EGLN3 -0.147 0.301 -9999 0 -0.686 17 17
EGLN2 0.02 0 -9999 0 -9999 0 0
EGLN1 0.02 0 -9999 0 -9999 0 0
TP53 0.01 0.085 -9999 0 -0.708 1 1
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.049 0.024 -9999 0 -9999 0 0
ARNT 0.02 0 -9999 0 -9999 0 0
ARD1A 0.02 0 -9999 0 -9999 0 0
RBX1 0.02 0 -9999 0 -9999 0 0
HIF1A/p19ARF -0.027 0.18 -9999 0 -0.536 6 6
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.024 0.069 -9999 0 -0.385 2 2
MAPK9 0.001 0.07 -9999 0 -0.416 2 2
adrenocorticotropin secretion -0.021 0.126 -9999 0 -0.433 6 6
GNB1/GNG2 0.02 0.056 -9999 0 -0.455 1 1
GNB1 0.01 0.085 -9999 0 -0.708 1 1
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 0.013 0 -9999 0 -9999 0 0
Gs family/GTP 0.007 0.052 -9999 0 -0.429 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 0.012 0.103 1 -9999 0 1
GNAL 0.01 0.085 -9999 0 -0.708 1 1
GNG2 0.02 0 -9999 0 -9999 0 0
CRH -0.03 0.169 -9999 0 -0.585 6 6
mol:cortisol 0 0 -9999 0 -9999 0 0
MAPK8 0.013 0 -9999 0 -9999 0 0
MAPK11 0.013 0 -9999 0 -9999 0 0
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.04 0.032 -9999 0 -9999 0 0
STMN1 0.034 0.002 -9999 0 -9999 0 0
Aurora B/RasGAP/Survivin -0.01 0.072 -9999 0 -9999 0 0
Chromosomal passenger complex/Cul3 protein complex 0.008 0.123 -9999 0 -0.578 2 2
BIRC5 -0.01 0.127 -9999 0 -0.532 4 4
DES -0.021 0.075 -9999 0 -0.558 1 1
Aurora C/Aurora B/INCENP 0.03 0.053 -9999 0 -9999 0 0
Aurora B/TACC1 -0.001 0.057 -9999 0 -0.465 1 1
Aurora B/PP2A 0.024 0.047 -9999 0 -0.372 1 1
mol:GTP 0 0 -9999 0 -9999 0 0
CBX5 0.012 0.047 -9999 0 -0.183 4 4
mitotic metaphase/anaphase transition 0 0.003 -9999 0 -9999 0 0
NDC80 0.02 0.081 -9999 0 -0.454 2 2
Cul3 protein complex -0.015 0.161 -9999 0 -0.548 4 4
KIF2C 0.01 0.088 -9999 0 -0.323 4 4
PEBP1 0.01 0.086 -9999 0 -0.717 1 1
KIF20A -0.018 0.139 -9999 0 -0.526 5 5
mol:GDP 0 0 -9999 0 -9999 0 0
Aurora B/RasGAP 0.03 0.003 -9999 0 -9999 0 0
SEPT1 0.005 0.089 -9999 0 -0.523 2 2
SMC2 0.01 0.085 -9999 0 -0.708 1 1
SMC4 0.02 0 -9999 0 -9999 0 0
NSUN2/NPM1/Nucleolin 0.033 0.069 -9999 0 -9999 0 0
PSMA3 0.02 0 -9999 0 -9999 0 0
G2/M transition of mitotic cell cycle 0 0.002 -9999 0 -9999 0 0
H3F3B 0.002 0.097 -9999 0 -0.4 4 4
AURKB 0.02 0.004 -9999 0 -9999 0 0
AURKC 0.012 0.064 -9999 0 -0.523 1 1
CDCA8 -0.002 0.112 -9999 0 -0.539 3 3
cytokinesis -0.032 0.11 -9999 0 -0.519 3 3
Aurora B/Septin1 -0.029 0.113 -9999 0 -0.525 2 2
AURKA 0.012 0.063 -9999 0 -0.522 1 1
INCENP 0.013 0.066 -9999 0 -0.54 1 1
KLHL13 -0.038 0.179 -9999 0 -0.576 7 7
BUB1 -0.028 0.161 -9999 0 -0.558 6 6
hSgo1/Aurora B/Survivin -0.009 0.066 -9999 0 -9999 0 0
EVI5 0.02 0.001 -9999 0 -9999 0 0
RhoA/GTP -0.04 0.121 -9999 0 -0.492 4 4
SGOL1 0.02 0 -9999 0 -9999 0 0
CENPA 0.02 0.083 -9999 0 -0.296 4 4
NCAPG 0 0 -9999 0 -9999 0 0
Aurora B/HC8 Proteasome 0.03 0.003 -9999 0 -9999 0 0
NCAPD2 0.02 0 -9999 0 -9999 0 0
Aurora B/PP1-gamma 0.03 0.003 -9999 0 -9999 0 0
RHOA 0.01 0.085 -9999 0 -0.708 1 1
NCAPH 0.02 0 -9999 0 -9999 0 0
NPM1 0.03 0.013 -9999 0 -9999 0 0
RASA1 0.02 0 -9999 0 -9999 0 0
KLHL9 0 0.12 -9999 0 -0.708 2 2
mitotic prometaphase 0 0.004 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.03 0.003 -9999 0 -9999 0 0
PPP1CC 0.02 0 -9999 0 -9999 0 0
Centraspindlin -0.039 0.125 -9999 0 -0.578 3 3
RhoA/GDP 0.007 0.065 -9999 0 -0.538 1 1
NSUN2 0.023 0.063 -9999 0 -0.493 1 1
MYLK -0.01 0.118 -9999 0 -0.402 6 6
KIF23 -0.002 0.11 -9999 0 -0.53 3 3
VIM -0.076 0.225 -9999 0 -0.533 14 14
RACGAP1 0.013 0.063 -9999 0 -0.52 1 1
mitosis 0 0 -9999 0 -9999 0 0
NCL 0.008 0.107 -9999 0 -0.502 3 3
Chromosomal passenger complex 0.017 0.117 -9999 0 -0.42 4 4
Chromosomal passenger complex/EVI5 -0.016 0.117 -9999 0 -0.521 3 3
TACC1 0.01 0.085 -9999 0 -0.708 1 1
PPP2R5D 0.012 0.064 -9999 0 -0.523 1 1
CUL3 0.01 0.085 -9999 0 -0.708 1 1
response to DNA damage stimulus 0 0 -9999 0 -9999 0 0
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.061 0.043 -9999 0 -9999 0 0
CLOCK 0.015 0.085 -9999 0 -0.705 1 1
TIMELESS/CRY2 0.05 0.058 -9999 0 -9999 0 0
DEC1/BMAL1 0.02 0.079 -9999 0 -0.443 2 2
ATR 0.02 0 -9999 0 -9999 0 0
NR1D1 0.053 0.035 -9999 0 -9999 0 0
ARNTL 0.015 0.085 -9999 0 -0.705 1 1
TIMELESS 0.053 0.035 -9999 0 -9999 0 0
NPAS2 -0.033 0.193 -9999 0 -0.67 6 6
CRY2 0.01 0.085 -9999 0 -0.708 1 1
mol:CO -0.021 0 -9999 0 -9999 0 0
CHEK1 0.012 0.064 -9999 0 -0.523 1 1
mol:HEME 0.021 0 -9999 0 -9999 0 0
PER1 0.01 0.085 -9999 0 -0.708 1 1
BMAL/CLOCK/NPAS2 0.014 0.166 -9999 0 -0.499 6 6
BMAL1/CLOCK 0.055 0.113 -9999 0 -0.803 1 1
S phase of mitotic cell cycle 0.061 0.043 -9999 0 -9999 0 0
TIMELESS/CHEK1/ATR 0.062 0.043 -9999 0 -9999 0 0
mol:NADPH 0.021 0 -9999 0 -9999 0 0
PER1/TIMELESS 0.05 0.058 -9999 0 -9999 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -9999 0 0
DEC1 0.012 0.064 -9999 0 -0.523 1 1
Aurora C signaling

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
INCENP 0.012 0.064 -9999 0 -0.523 1 1
Aurora C/Aurora B/INCENP 0.03 0.051 -9999 0 -9999 0 0
metaphase 0 0 -9999 0 -9999 0 0
mitosis 0 0 -9999 0 -9999 0 0
H3F3B -0.037 0.146 -9999 0 -0.636 4 4
AURKB 0.02 0 -9999 0 -9999 0 0
AURKC 0.012 0.064 -9999 0 -0.523 1 1
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -9999 0 0
telencephalon oligodendrocyte cell migration -0.029 0.08 0.47 1 -9999 0 1
GNAI2 0.01 0.085 -9999 0 -0.708 1 1
S1P/S1P5/G12 0.014 0 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
GNAO1 0.02 0 -9999 0 -9999 0 0
RhoA/GTP 0.03 0.082 -9999 0 -0.481 1 1
negative regulation of cAMP metabolic process 0.028 0.062 -9999 0 -0.289 1 1
GNAZ 0.012 0.064 -9999 0 -0.523 1 1
GNAI3 0.02 0 -9999 0 -9999 0 0
GNA12 0.02 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 0.028 0.062 -9999 0 -0.291 1 1
RhoA/GDP 0.007 0.065 -9999 0 -0.538 1 1
RHOA 0.01 0.085 -9999 0 -0.708 1 1
GNAI1 0 0.12 -9999 0 -0.708 2 2
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.01 0.085 -9999 0 -0.708 1 1
Ran/GTP/Exportin 1/HDAC4 -0.005 0.039 -9999 0 -0.334 1 1
MDM2/SUMO1 0.043 0.027 -9999 0 -9999 0 0
HDAC4 0.02 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 -0.009 0.052 -9999 0 -0.318 2 2
SUMO1 0.02 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1 0.021 0.033 -9999 0 -0.257 1 1
mol:GTP 0 0 -9999 0 -9999 0 0
XPO1 0.038 0.031 -9999 0 -9999 0 0
EntrezGene:23636 0 0 -9999 0 -9999 0 0
RAN 0.02 0 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.01 0.085 -9999 0 -0.708 1 1
SUMO1/HDAC4 0.043 0.027 -9999 0 -9999 0 0
SUMO1/HDAC1 0.037 0.054 -9999 0 -0.361 1 1
RANGAP1 0.02 0 -9999 0 -9999 0 0
MDM2/SUMO1/SUMO1 0.039 0.062 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.028 0.033 -9999 0 -0.25 1 1
Ran/GTP 0.037 0.03 -9999 0 -9999 0 0
EntrezGene:23225 0 0 -9999 0 -9999 0 0
MDM2 0.02 0 -9999 0 -9999 0 0
UBE2I 0.02 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0.046 0.029 -9999 0 -9999 0 0
NPC 0.006 0.049 -9999 0 -0.406 1 1
PIAS2 -0.003 0.109 -9999 0 -0.523 3 3
PIAS1 0.02 0 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 0 0
S1P4 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
mol:S1P 0 0 -9999 0 -9999 0 0
GNAO1 0.02 0 -9999 0 -9999 0 0
CDC42/GTP 0.036 0.056 -9999 0 -9999 0 0
PLCG1 0.038 0.059 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
GNAI2 0.01 0.085 -9999 0 -0.708 1 1
GNAI3 0.02 0 -9999 0 -9999 0 0
G12/G13 0.022 0.065 -9999 0 -0.526 1 1
cell migration 0.035 0.055 -9999 0 -9999 0 0
S1PR5 0 0 -9999 0 -9999 0 0
S1PR4 0 0 -9999 0 -9999 0 0
MAPK3 0.038 0.059 -9999 0 -9999 0 0
MAPK1 0.038 0.059 -9999 0 -9999 0 0
S1P/S1P5/Gi 0.028 0.062 -9999 0 -0.291 1 1
GNAI1 0 0.12 -9999 0 -0.708 2 2
CDC42/GDP 0.015 0 -9999 0 -9999 0 0
S1P/S1P5/G12 0.014 0 -9999 0 -9999 0 0
RHOA 0.024 0.095 -9999 0 -0.773 1 1
S1P/S1P4/Gi 0.028 0.062 -9999 0 -0.291 1 1
mol:GDP 0 0 -9999 0 -9999 0 0
GNAZ 0.012 0.064 -9999 0 -0.523 1 1
S1P/S1P4/G12/G13 0.02 0.052 -9999 0 -0.418 1 1
GNA12 0.02 0 -9999 0 -9999 0 0
GNA13 0.01 0.085 -9999 0 -0.708 1 1
CDC42 0.02 0 -9999 0 -9999 0 0
Arf1 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
coatomer protein complex 0.001 0.011 -9999 0 -9999 0 0
EntrezGene:79658 0 0 -9999 0 -9999 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.021 0.027 -9999 0 -9999 0 0
AP2 0.03 0 -9999 0 -9999 0 0
mol:DAG 0 0 -9999 0 -9999 0 0
Arfaptin 2/Rac/GTP 0.001 0.005 -9999 0 -9999 0 0
CLTB 0.02 0 -9999 0 -9999 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.037 0 -9999 0 -9999 0 0
CD4 0.02 0 -9999 0 -9999 0 0
CLTA 0.02 0 -9999 0 -9999 0 0
mol:GTP 0.001 0.001 -9999 0 -9999 0 0
ARFGAP1 0.017 0 -9999 0 -9999 0 0
mol:PI-4-5-P2 -0.01 0.046 -9999 0 -0.229 3 3
ARF1/GTP -0.005 0.022 -9999 0 -9999 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.039 0.001 -9999 0 -9999 0 0
mol:Choline -0.01 0.048 -9999 0 -0.239 3 3
mol:GDP 0 0 -9999 0 -9999 0 0
ARF1 0.019 0 -9999 0 -9999 0 0
DDEF1 -0.01 0.048 -9999 0 -0.238 3 3
ARF1/GDP -0.003 0.013 -9999 0 -9999 0 0
AP2M1 0.02 0 -9999 0 -9999 0 0
EntrezGene:1313 0 0 -9999 0 -9999 0 0
actin filament polymerization 0.023 0 -9999 0 -9999 0 0
Rac/GTP 0.016 0 -9999 0 -9999 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.03 0.05 -9999 0 -0.391 1 1
ARFIP2 0.018 0.003 -9999 0 -9999 0 0
COPA 0.02 0 -9999 0 -9999 0 0
RAC1 0.02 0 -9999 0 -9999 0 0
ARF1/GTP/coatomer protein complex 0.032 0.014 -9999 0 -9999 0 0
ARF1/GTP/ARHGAP10 0.001 0.003 -9999 0 -9999 0 0
GGA3 0.01 0.085 -9999 0 -0.708 1 1
ARF1/GTP/Membrin -0.003 0.013 -9999 0 -9999 0 0
AP2A1 0.02 0 -9999 0 -9999 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.04 0.001 -9999 0 -9999 0 0
ARF1/GDP/Membrin 0.02 0.019 -9999 0 -9999 0 0
Arfaptin 2/Rac/GDP 0.002 0.007 -9999 0 -9999 0 0
CYTH2 0.001 0.001 -9999 0 -9999 0 0
ARF1/GTP/GGA3 -0.005 0.056 -9999 0 -0.472 1 1
mol:ATP 0 0 -9999 0 -9999 0 0
Rac/GDP 0.015 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 0.052 0 -9999 0 -9999 0 0
PLD2 -0.01 0.048 -9999 0 -0.24 3 3
ARF-GAP1/v-SNARE 0.017 0 -9999 0 -9999 0 0
PIP5K1A -0.01 0.046 -9999 0 -0.23 3 3
ARF1/GTP/Membrin/GBF1/p115 -0.004 0.021 -9999 0 -9999 0 0
mol:Phosphatic acid 0 0 -9999 0 -9999 0 0
mol:Phosphatidic acid -0.01 0.048 -9999 0 -0.238 3 3
KDEL Receptor/Ligand/ARF-GAP1 0.017 0 -9999 0 -9999 0 0
GOSR2 -0.004 0.019 -9999 0 -9999 0 0
USO1 -0.004 0.019 -9999 0 -9999 0 0
GBF1 -0.004 0.019 -9999 0 -9999 0 0
ARF1/GTP/Arfaptin 2 0 0.002 -9999 0 -9999 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.041 0 -9999 0 -9999 0 0
Methods & Data
Input

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

  • Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/KIRC/349792/1.GDAC_MergeDataFiles.Finished/KIRC.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)