PARADIGM pathway analysis of mRNA expression and copy number 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 38 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 24
TCGA08_retinoblastoma 24
Signaling events mediated by the Hedgehog family 20
IL4-mediated signaling events 18
Osteopontin-mediated events 17
IL23-mediated signaling events 17
Fc-epsilon receptor I signaling in mast cells 16
Signaling mediated by p38-alpha and p38-beta 16
Glucocorticoid receptor regulatory network 15
Endothelins 15
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 24 1858 76 -0.282 0.035 1000 -1000 -0.041 -1000
TCGA08_retinoblastoma 24 197 8 -0.071 0.089 1000 -1000 -0.002 -1000
Signaling events mediated by the Hedgehog family 20 1043 52 -0.25 0.047 1000 -1000 -0.027 -1000
IL4-mediated signaling events 18 1690 91 -0.54 0.488 1000 -1000 -0.067 -1000
Osteopontin-mediated events 17 674 38 -0.161 0.033 1000 -1000 -0.034 -1000
IL23-mediated signaling events 17 1071 60 -0.482 0.032 1000 -1000 -0.071 -1000
Fc-epsilon receptor I signaling in mast cells 16 1598 97 -0.115 0.043 1000 -1000 -0.055 -1000
Signaling mediated by p38-alpha and p38-beta 16 747 44 -0.169 0.033 1000 -1000 -0.023 -1000
Glucocorticoid receptor regulatory network 15 1771 114 -0.451 0.274 1000 -1000 -0.046 -1000
Endothelins 15 1473 96 -0.207 0.032 1000 -1000 -0.044 -1000
Wnt signaling 15 106 7 -0.121 0.029 1000 -1000 -0.019 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 15 1067 68 -0.389 0.158 1000 -1000 -0.045 -1000
Noncanonical Wnt signaling pathway 14 375 26 -0.124 0.032 1000 -1000 -0.048 -1000
Thromboxane A2 receptor signaling 13 1443 105 -0.163 0.055 1000 -1000 -0.036 -1000
BCR signaling pathway 13 1352 99 -0.201 0.044 1000 -1000 -0.042 -1000
IGF1 pathway 13 754 57 -0.072 0.056 1000 -1000 -0.038 -1000
FOXM1 transcription factor network 13 687 51 -0.254 0.041 1000 -1000 -0.079 -1000
Syndecan-1-mediated signaling events 12 435 34 -0.121 0.037 1000 -1000 -0.031 -1000
Ephrin B reverse signaling 12 609 48 -0.093 0.041 1000 -1000 -0.032 -1000
EPHB forward signaling 12 1091 85 -0.104 0.073 1000 -1000 -0.066 -1000
Nectin adhesion pathway 11 755 63 -0.103 0.051 1000 -1000 -0.044 -1000
TCR signaling in naïve CD8+ T cells 11 1089 93 -0.094 0.045 1000 -1000 -0.037 -1000
Calcium signaling in the CD4+ TCR pathway 11 353 31 -0.198 0.037 1000 -1000 -0.029 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 11 885 78 -0.149 0.066 1000 -1000 -0.055 -1000
IL12-mediated signaling events 10 931 87 -0.2 0.035 1000 -1000 -0.05 -1000
TCGA08_p53 10 71 7 -0.041 0.033 1000 -1000 -0.006 -1000
BMP receptor signaling 9 750 81 -0.159 0.055 1000 -1000 -0.031 -1000
Glypican 1 network 9 461 48 -0.047 0.033 1000 -1000 -0.023 -1000
IL1-mediated signaling events 9 599 62 -0.147 0.069 1000 -1000 -0.037 -1000
S1P1 pathway 9 344 36 -0.19 0.032 1000 -1000 -0.029 -1000
FAS signaling pathway (CD95) 9 447 47 -0.162 0.073 1000 -1000 -0.036 -1000
IL27-mediated signaling events 9 498 51 -0.185 0.114 1000 -1000 -0.043 -1000
LPA receptor mediated events 9 955 102 -0.195 0.033 1000 -1000 -0.067 -1000
EGFR-dependent Endothelin signaling events 9 209 21 -0.069 0.045 1000 -1000 -0.025 -1000
Syndecan-2-mediated signaling events 8 555 69 -0.122 0.035 1000 -1000 -0.029 -1000
IFN-gamma pathway 8 593 68 -0.101 0.043 1000 -1000 -0.042 -1000
amb2 Integrin signaling 8 666 82 -0.111 0.035 1000 -1000 -0.033 -1000
Syndecan-4-mediated signaling events 8 602 67 -0.075 0.032 1000 -1000 -0.037 -1000
HIF-2-alpha transcription factor network 7 324 43 -0.063 0.051 1000 -1000 -0.042 -1000
Stabilization and expansion of the E-cadherin adherens junction 7 559 74 -0.092 0.052 1000 -1000 -0.058 -1000
Caspase cascade in apoptosis 6 506 74 -0.059 0.045 1000 -1000 -0.034 -1000
Arf6 signaling events 6 421 62 -0.07 0.068 1000 -1000 -0.015 -1000
Canonical Wnt signaling pathway 6 308 51 -0.128 0.064 1000 -1000 -0.046 -1000
Glypican 2 network 6 26 4 -0.003 0 1000 -1000 0 -1000
IL6-mediated signaling events 6 522 75 -0.084 0.053 1000 -1000 -0.048 -1000
Plasma membrane estrogen receptor signaling 6 550 86 -0.074 0.047 1000 -1000 -0.05 -1000
E-cadherin signaling in keratinocytes 6 294 43 -0.033 0.045 1000 -1000 -0.031 -1000
E-cadherin signaling events 6 34 5 0.002 0.028 1000 -1000 0.014 -1000
Regulation of nuclear SMAD2/3 signaling 5 721 136 -0.405 0.083 1000 -1000 -0.028 -1000
Coregulation of Androgen receptor activity 5 388 76 -0.182 0.054 1000 -1000 -0.022 -1000
Signaling events mediated by PTP1B 5 435 76 -0.081 0.063 1000 -1000 -0.032 -1000
Hedgehog signaling events mediated by Gli proteins 5 387 65 -0.137 0.074 1000 -1000 -0.044 -1000
Arf6 downstream pathway 5 254 43 -0.051 0.052 1000 -1000 -0.02 -1000
PDGFR-alpha signaling pathway 5 229 44 -0.114 0.05 1000 -1000 -0.035 -1000
Reelin signaling pathway 5 322 56 -0.081 0.083 1000 -1000 -0.035 -1000
TRAIL signaling pathway 5 284 48 -0.029 0.051 1000 -1000 -0.032 -1000
Signaling mediated by p38-gamma and p38-delta 5 81 15 -0.032 0.032 1000 -1000 -0.032 -1000
Syndecan-3-mediated signaling events 5 178 35 -0.139 0.062 1000 -1000 -0.037 -1000
Integrins in angiogenesis 5 465 84 -0.113 0.068 1000 -1000 -0.035 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 5 247 45 -0.056 0.046 1000 -1000 -0.044 -1000
E-cadherin signaling in the nascent adherens junction 5 397 76 -0.064 0.058 1000 -1000 -0.054 -1000
ErbB2/ErbB3 signaling events 4 260 65 -0.032 0.045 1000 -1000 -0.044 -1000
Sphingosine 1-phosphate (S1P) pathway 4 126 28 -0.023 0.042 1000 -1000 -0.014 -1000
PLK2 and PLK4 events 4 14 3 -0.008 0.03 1000 -1000 -0.003 -1000
Visual signal transduction: Cones 4 162 38 -0.019 0.048 1000 -1000 0 -1000
Presenilin action in Notch and Wnt signaling 4 294 61 -0.128 0.062 1000 -1000 -0.051 -1000
p75(NTR)-mediated signaling 4 538 125 -0.118 0.074 1000 -1000 -0.038 -1000
mTOR signaling pathway 4 221 53 -0.014 0.087 1000 -1000 -0.033 -1000
Ceramide signaling pathway 4 360 76 -0.054 0.06 1000 -1000 -0.035 -1000
Nongenotropic Androgen signaling 4 226 52 -0.071 0.06 1000 -1000 -0.03 -1000
Signaling events mediated by VEGFR1 and VEGFR2 4 579 125 -0.037 0.039 1000 -1000 -0.043 -1000
IL2 signaling events mediated by STAT5 4 93 22 -0.074 0.033 1000 -1000 -0.031 -1000
Class I PI3K signaling events 4 301 73 -0.034 0.037 1000 -1000 -0.033 -1000
VEGFR1 specific signals 4 265 56 -0.042 0.039 1000 -1000 -0.046 -1000
S1P3 pathway 4 191 42 -0.049 0.042 1000 -1000 -0.031 -1000
Neurotrophic factor-mediated Trk receptor signaling 4 529 120 -0.141 0.082 1000 -1000 -0.042 -1000
Visual signal transduction: Rods 4 237 52 -0.075 0.047 1000 -1000 -0.029 -1000
S1P4 pathway 4 108 25 -0.019 0.042 1000 -1000 -0.021 -1000
Ras signaling in the CD4+ TCR pathway 4 70 17 -0.011 0.033 1000 -1000 -0.017 -1000
ErbB4 signaling events 3 263 69 -0.08 0.046 1000 -1000 -0.031 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 3 201 54 -0.057 0.047 1000 -1000 -0.042 -1000
a4b1 and a4b7 Integrin signaling 3 18 5 0.012 0.033 1000 -1000 0.014 -1000
Cellular roles of Anthrax toxin 3 146 39 -0.051 0.032 1000 -1000 -0.022 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 3 339 85 -0.097 0.088 1000 -1000 -0.04 -1000
FOXA2 and FOXA3 transcription factor networks 3 170 46 -0.071 0.071 1000 -1000 -0.075 -1000
PLK1 signaling events 3 257 85 -0.023 0.1 1000 -1000 -0.024 -1000
Paxillin-independent events mediated by a4b1 and a4b7 3 113 37 -0.04 0.061 1000 -1000 -0.034 -1000
Signaling events mediated by HDAC Class III 3 156 40 -0.061 0.061 1000 -1000 -0.028 -1000
S1P5 pathway 3 61 17 -0.013 0.032 1000 -1000 -0.012 -1000
RXR and RAR heterodimerization with other nuclear receptor 3 204 52 -0.026 0.077 1000 -1000 -0.027 -1000
FoxO family signaling 3 199 64 -0.111 0.066 1000 -1000 -0.033 -1000
Retinoic acid receptors-mediated signaling 3 212 58 -0.061 0.061 1000 -1000 -0.028 -1000
Atypical NF-kappaB pathway 3 95 31 -0.007 0.033 1000 -1000 -0.016 -1000
IL2 signaling events mediated by PI3K 3 227 58 -0.094 0.033 1000 -1000 -0.039 -1000
TCGA08_rtk_signaling 3 78 26 -0.063 0.063 1000 -1000 -0.007 -1000
Insulin Pathway 3 233 74 -0.048 0.081 1000 -1000 -0.035 -1000
Angiopoietin receptor Tie2-mediated signaling 3 339 88 -0.048 0.035 1000 -1000 -0.063 -1000
PDGFR-beta signaling pathway 3 341 97 -0.06 0.076 1000 -1000 -0.051 -1000
Regulation of Androgen receptor activity 3 266 70 -0.215 0.053 1000 -1000 -0.039 -1000
Aurora B signaling 3 253 67 -0.093 0.057 1000 -1000 -0.035 -1000
JNK signaling in the CD4+ TCR pathway 2 48 17 -0.013 0.047 1000 -1000 -0.033 -1000
Aurora A signaling 2 124 60 -0.005 0.056 1000 -1000 -0.02 -1000
EPO signaling pathway 2 161 55 -0.014 0.057 1000 -1000 -0.032 -1000
ceramide signaling pathway 2 143 49 -0.027 0.043 1000 -1000 -0.035 -1000
Paxillin-dependent events mediated by a4b1 2 104 36 -0.048 0.062 1000 -1000 -0.036 -1000
Regulation of Telomerase 2 292 102 -0.095 0.08 1000 -1000 -0.039 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 2 92 33 -0.053 0.074 1000 -1000 -0.026 -1000
LPA4-mediated signaling events 1 21 12 -0.015 0.041 1000 -1000 -0.025 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 1 28 23 0.012 0.06 1000 -1000 -0.017 -1000
Nephrin/Neph1 signaling in the kidney podocyte 1 39 34 -0.04 0.064 1000 -1000 -0.023 -1000
BARD1 signaling events 1 64 57 -0.047 0.073 1000 -1000 -0.031 -1000
Circadian rhythm pathway 1 28 22 -0.01 0.048 1000 -1000 -0.037 -1000
Ephrin A reverse signaling 1 8 7 0 0.032 1000 -1000 0 -1000
Insulin-mediated glucose transport 1 58 32 -0.025 0.042 1000 -1000 -0.022 -1000
Class I PI3K signaling events mediated by Akt 1 116 68 -0.044 0.065 1000 -1000 -0.033 -1000
Signaling events regulated by Ret tyrosine kinase 1 158 82 -0.029 0.054 1000 -1000 -0.056 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 1 130 83 -0.025 0.059 1000 -1000 -0.037 -1000
Signaling events mediated by HDAC Class I 1 162 104 -0.042 0.076 1000 -1000 -0.033 -1000
Regulation of p38-alpha and p38-beta 1 101 54 -0.007 0.075 1000 -1000 -0.034 -1000
Arf6 trafficking events 1 79 71 -0.035 0.043 1000 -1000 -0.025 -1000
Rapid glucocorticoid signaling 1 20 20 0 0.042 1000 -1000 -0.003 -1000
Signaling events mediated by PRL 1 55 34 -0.031 0.046 1000 -1000 -0.043 -1000
Class IB PI3K non-lipid kinase events 1 3 3 -0.026 0.026 1000 -1000 -0.018 -1000
p38 MAPK signaling pathway 1 57 44 -0.017 0.06 1000 -1000 -0.026 -1000
Alternative NF-kappaB pathway 1 16 13 0 0.074 1000 -1000 0 -1000
Canonical NF-kappaB pathway 0 20 39 0 0.067 1000 -1000 -0.019 -1000
Signaling events mediated by HDAC Class II 0 68 75 -0.04 0.057 1000 -1000 -0.033 -1000
Aurora C signaling 0 1 7 0 0.057 1000 -1000 -0.013 -1000
Effects of Botulinum toxin 0 20 26 -0.01 0.054 1000 -1000 -0.003 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 6 27 0 0.063 1000 -1000 -0.028 -1000
Arf1 pathway 0 24 54 -0.002 0.043 1000 -1000 -0.019 -1000
Total 776 49727 7203 -11.7497232648 7.61708459751 131000 -131000 -4.26448613509 -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 -0.228 0.498 -9999 0 -0.913 37 37
HDAC7 -0.001 0.008 -9999 0 -9999 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.173 0.426 -9999 0 -0.803 30 30
SMAD4 0.024 0.067 -9999 0 -0.517 2 2
ID2 -0.236 0.511 -9999 0 -0.941 37 37
AP1 -0.034 0.159 -9999 0 -0.446 15 15
ABCG2 -0.242 0.493 -9999 0 -0.931 36 36
HIF1A -0.032 0.122 -9999 0 -0.384 5 5
TFF3 -0.266 0.523 -9999 0 -0.949 40 40
GATA2 0.014 0.053 -9999 0 -0.517 1 1
AKT1 -0.025 0.1 -9999 0 -0.226 2 2
response to hypoxia -0.038 0.083 -9999 0 -0.172 16 16
MCL1 -0.235 0.486 -9999 0 -0.931 35 35
NDRG1 -0.253 0.509 -9999 0 -0.932 39 39
SERPINE1 -0.245 0.511 -9999 0 -0.961 36 36
FECH -0.238 0.499 -9999 0 -0.924 37 37
FURIN -0.23 0.498 -9999 0 -0.904 38 38
NCOA2 0.025 0.067 -9999 0 -0.517 2 2
EP300 -0.039 0.147 -9999 0 -0.413 10 10
HMOX1 -0.233 0.503 -9999 0 -0.934 36 36
BHLHE40 -0.246 0.483 -9999 0 -0.913 37 37
BHLHE41 -0.246 0.483 -9999 0 -0.913 37 37
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.002 0.172 -9999 0 -0.408 8 8
ENG -0.021 0.145 0.294 1 -0.409 6 7
JUN -0.009 0.124 -9999 0 -0.522 7 7
RORA -0.271 0.527 -9999 0 -0.993 37 37
ABCB1 -0.039 0.124 -9999 0 -0.952 1 1
TFRC -0.274 0.457 -9999 0 -0.944 34 34
CXCR4 -0.256 0.53 -9999 0 -0.967 39 39
TF -0.236 0.476 -9999 0 -0.903 36 36
CITED2 -0.23 0.496 -9999 0 -0.935 35 35
HIF1A/ARNT -0.257 0.611 -9999 0 -1.14 32 32
LDHA -0.047 0.253 -9999 0 -1.059 7 7
ETS1 -0.24 0.492 -9999 0 -0.957 34 34
PGK1 -0.229 0.502 -9999 0 -0.92 37 37
NOS2 -0.246 0.483 -9999 0 -0.913 37 37
ITGB2 -0.242 0.518 -9999 0 -0.945 38 38
ALDOA -0.23 0.497 -9999 0 -0.924 36 36
Cbp/p300/CITED2 -0.242 0.512 -9999 0 -1.023 31 31
FOS -0.035 0.15 -9999 0 -0.522 11 11
HK2 -0.226 0.505 -9999 0 -0.948 35 35
SP1 0.035 0.049 -9999 0 -0.516 1 1
GCK -0.037 0.205 -9999 0 -1.545 1 1
HK1 -0.228 0.496 -9999 0 -0.935 35 35
NPM1 -0.228 0.497 -9999 0 -0.947 34 34
EGLN1 -0.23 0.502 -9999 0 -0.927 37 37
CREB1 0.032 0.051 -9999 0 -0.517 1 1
PGM1 -0.231 0.494 -9999 0 -0.934 35 35
SMAD3 0.016 0.093 -9999 0 -0.516 4 4
EDN1 -0.187 0.465 -9999 0 -1.295 19 19
IGFBP1 -0.229 0.499 -9999 0 -0.916 37 37
VEGFA -0.176 0.35 -9999 0 -0.677 33 33
HIF1A/JAB1 -0.005 0.098 -9999 0 -0.473 2 2
CP -0.282 0.472 -9999 0 -0.943 37 37
CXCL12 -0.256 0.526 -9999 0 -0.961 39 39
COPS5 0.033 0.006 -9999 0 -9999 0 0
SMAD3/SMAD4 0.025 0.09 -9999 0 -0.377 6 6
BNIP3 -0.248 0.513 -9999 0 -0.929 39 39
EGLN3 -0.268 0.519 -9999 0 -0.959 39 39
CA9 -0.266 0.512 -9999 0 -0.97 38 38
TERT -0.221 0.487 -9999 0 -0.906 36 36
ENO1 -0.232 0.495 -9999 0 -0.936 35 35
PFKL -0.231 0.499 -9999 0 -0.92 37 37
NCOA1 0.032 0.006 -9999 0 -9999 0 0
ADM -0.264 0.511 -9999 0 -0.925 40 40
ARNT -0.021 0.091 -9999 0 -0.228 1 1
HNF4A 0.033 0.018 -9999 0 -9999 0 0
ADFP -0.247 0.522 -9999 0 -0.967 37 37
SLC2A1 -0.186 0.385 -9999 0 -0.732 33 33
LEP -0.24 0.493 -9999 0 -0.967 33 33
HIF1A/ARNT/Cbp/p300 -0.182 0.438 -9999 0 -0.829 30 30
EPO -0.089 0.299 -9999 0 -0.845 5 5
CREBBP -0.015 0.106 -9999 0 -0.29 2 2
HIF1A/ARNT/Cbp/p300/HDAC7 -0.186 0.435 -9999 0 -0.817 31 31
PFKFB3 -0.231 0.499 -9999 0 -0.955 34 34
NT5E -0.244 0.506 -9999 0 -0.94 37 37
TCGA08_retinoblastoma

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
CDKN2B 0.004 0.054 -9999 0 -0.476 1 1
CDKN2C 0.028 0.027 -9999 0 -9999 0 0
CDKN2A -0.044 0.158 -9999 0 -0.498 14 14
CCND2 0.043 0.099 0.222 28 -0.119 4 32
RB1 -0.071 0.136 0.361 2 -0.261 38 40
CDK4 0.06 0.115 0.26 31 -9999 0 31
CDK6 0.05 0.132 0.27 28 -0.411 2 30
G1/S progression 0.089 0.149 0.271 46 -0.33 3 49
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.132 0.271 -9999 0 -0.57 36 36
IHH -0.011 0.089 -9999 0 -0.276 4 4
SHH Np/Cholesterol/GAS1 -0.046 0.139 -9999 0 -0.314 27 27
LRPAP1 0.03 0.01 -9999 0 -9999 0 0
dorsoventral neural tube patterning 0.046 0.138 0.312 27 -9999 0 27
SMO/beta Arrestin2 -0.116 0.227 -9999 0 -0.392 45 45
SMO -0.131 0.23 -9999 0 -0.399 49 49
AKT1 -0.086 0.195 -9999 0 -0.637 12 12
ARRB2 0.031 0.007 -9999 0 -9999 0 0
BOC 0.021 0.029 -9999 0 -9999 0 0
ADRBK1 0.032 0.005 -9999 0 -9999 0 0
heart looping -0.129 0.226 -9999 0 -0.393 49 49
STIL -0.074 0.144 -9999 0 -0.277 41 41
DHH N/PTCH2 0.047 0.009 -9999 0 -9999 0 0
DHH N/PTCH1 -0.053 0.145 -9999 0 -0.288 36 36
PIK3CA 0.011 0.048 -9999 0 -0.518 1 1
DHH 0.033 0 -9999 0 -9999 0 0
PTHLH -0.25 0.45 -9999 0 -0.987 36 36
determination of left/right symmetry -0.129 0.226 -9999 0 -0.393 49 49
PIK3R1 0.004 0.097 -9999 0 -0.518 4 4
skeletal system development -0.246 0.443 -9999 0 -0.972 36 36
IHH N/Hhip -0.059 0.163 -9999 0 -0.428 20 20
DHH N/Hhip -0.031 0.145 -9999 0 -0.378 19 19
mol:Cholesterol 0 0 -9999 0 -9999 0 0
heart development -0.129 0.226 -9999 0 -0.393 49 49
pancreas development -0.065 0.187 -9999 0 -0.517 19 19
HHAT -0.003 0.137 -9999 0 -0.518 9 9
PI3K 0.005 0.067 -9999 0 -0.378 3 3
EntrezGene:84976 0 0 -9999 0 -9999 0 0
GAS1 -0.058 0.189 -9999 0 -0.518 19 19
somite specification -0.129 0.226 -9999 0 -0.393 49 49
SHH Np/Cholesterol/PTCH1 -0.073 0.151 -9999 0 -0.287 41 41
SHH Np/Cholesterol/PTCH2 0.008 0.085 -9999 0 -0.294 10 10
SHH Np/Cholesterol/Megalin 0.001 0.092 -9999 0 -0.303 11 11
SHH -0.013 0.103 -9999 0 -0.379 10 10
catabolic process -0.075 0.152 -9999 0 -0.323 36 36
SMO/Vitamin D3 -0.108 0.19 -9999 0 -0.36 41 41
SHH Np/Cholesterol/Hhip -0.048 0.137 -9999 0 -0.315 26 26
LRP2 0.019 0.056 -9999 0 -0.518 1 1
receptor-mediated endocytosis -0.104 0.183 -9999 0 -0.36 38 38
SHH Np/Cholesterol/BOC -0.001 0.085 -9999 0 -0.294 10 10
SHH Np/Cholesterol/CDO 0.006 0.086 -9999 0 -0.296 10 10
mesenchymal cell differentiation 0.047 0.136 0.313 26 -9999 0 26
mol:Vitamin D3 -0.073 0.151 -9999 0 -0.287 41 41
IHH N/PTCH2 0.018 0.06 -9999 0 -0.334 1 1
CDON 0.028 0.023 -9999 0 -9999 0 0
IHH N/PTCH1 -0.06 0.162 -9999 0 -0.325 36 36
Megalin/LRPAP1 0.032 0.047 -9999 0 -0.378 1 1
PTCH2 0.032 0.006 -9999 0 -9999 0 0
SHH Np/Cholesterol -0.003 0.081 -9999 0 -0.292 10 10
PTCH1 -0.075 0.152 -9999 0 -0.324 36 36
HHIP -0.065 0.187 -9999 0 -0.518 19 19
IL4-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
BCL2L1 -0.411 0.588 -9999 0 -1.317 32 32
STAT6 (cleaved dimer) -0.452 0.602 -9999 0 -1.288 39 39
IGHG1 -0.124 0.219 -9999 0 -0.646 5 5
IGHG3 -0.411 0.564 -9999 0 -1.18 40 40
AKT1 -0.199 0.325 -9999 0 -0.891 15 15
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.129 0.289 -9999 0 -0.875 11 11
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.194 0.339 -9999 0 -0.87 16 16
THY1 -0.433 0.6 -9999 0 -1.318 35 35
MYB -0.031 0.151 -9999 0 -0.518 11 11
HMGA1 0.029 0.047 -9999 0 -0.518 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.233 0.368 -9999 0 -0.781 27 27
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.187 0.334 -9999 0 -0.92 13 13
SP1 0.018 0.062 -9999 0 -0.517 1 1
INPP5D 0 0 -9999 0 -9999 0 0
SOCS5 0.03 0.032 -9999 0 -9999 0 0
STAT6 (dimer)/ETS1 -0.433 0.603 -9999 0 -1.283 38 38
SOCS1 -0.265 0.355 -9999 0 -0.765 35 35
SOCS3 -0.198 0.333 -9999 0 -1.005 10 10
FCER2 -0.374 0.489 -9999 0 -1.066 35 35
PARP14 0.025 0.022 -9999 0 -9999 0 0
CCL17 -0.484 0.651 -9999 0 -1.384 40 40
GRB2 0.032 0.006 -9999 0 -9999 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.145 0.264 -9999 0 -0.694 14 14
T cell proliferation -0.444 0.614 -9999 0 -1.33 37 37
IL4R/JAK1 -0.439 0.605 -9999 0 -1.298 38 38
EGR2 -0.499 0.656 -9999 0 -1.383 41 41
JAK2 -0.014 0.053 -9999 0 -9999 0 0
JAK3 0.034 0.015 -9999 0 -9999 0 0
PIK3R1 0.004 0.097 -9999 0 -0.518 4 4
JAK1 0.011 0.054 -9999 0 -0.512 1 1
COL1A2 -0.208 0.458 -9999 0 -1.588 12 12
CCL26 -0.522 0.664 -9999 0 -1.365 45 45
IL4R -0.467 0.651 -9999 0 -1.404 37 37
PTPN6 0.03 0.052 -9999 0 -0.504 1 1
IL13RA2 -0.54 0.708 -9999 0 -1.518 41 41
IL13RA1 -0.016 0.055 -9999 0 -9999 0 0
IRF4 -0.071 0.253 -9999 0 -1.311 4 4
ARG1 -0.144 0.321 -9999 0 -1.185 9 9
CBL -0.223 0.342 -9999 0 -0.735 27 27
GTF3A 0.012 0.051 -9999 0 -9999 0 0
PIK3CA 0.011 0.048 -9999 0 -0.518 1 1
IL13RA1/JAK2 -0.015 0.078 -9999 0 -9999 0 0
IRF4/BCL6 -0.06 0.224 -9999 0 -1.139 4 4
CD40LG 0.031 0.052 -9999 0 -0.517 1 1
MAPK14 -0.221 0.359 -9999 0 -0.766 26 26
mitosis -0.188 0.303 -9999 0 -0.821 15 15
STAT6 -0.521 0.761 -9999 0 -1.565 38 38
SPI1 0.007 0.091 -9999 0 -0.442 4 4
RPS6KB1 -0.177 0.292 -9999 0 -0.801 14 14
STAT6 (dimer) -0.519 0.763 -9999 0 -1.565 38 38
STAT6 (dimer)/PARP14 -0.452 0.655 -9999 0 -1.399 36 36
mast cell activation 0.008 0.015 -9999 0 -9999 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.212 0.371 -9999 0 -0.867 22 22
FRAP1 -0.2 0.325 -9999 0 -0.892 15 15
LTA -0.425 0.59 -9999 0 -1.294 35 35
FES 0.018 0.082 -9999 0 -0.518 3 3
T-helper 1 cell differentiation 0.488 0.702 1.465 38 -9999 0 38
CCL11 -0.527 0.679 -9999 0 -1.436 43 43
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.183 0.339 -9999 0 -0.967 13 13
IL2RG 0.023 0.071 -9999 0 -0.51 2 2
IL10 -0.426 0.589 -9999 0 -1.295 35 35
IRS1 0.008 0.105 -9999 0 -0.518 5 5
IRS2 0.001 0.122 -9999 0 -0.518 7 7
IL4 -0.107 0.281 -9999 0 -1.26 6 6
IL5 -0.427 0.588 -9999 0 -1.279 36 36
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.333 0.493 -9999 0 -0.996 37 37
COL1A1 -0.326 0.601 -9999 0 -1.508 25 25
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -9999 0 0
IL4/IL4R/JAK1 -0.455 0.636 -9999 0 -1.39 36 36
IL2R gamma/JAK3 0.038 0.059 -9999 0 -0.374 2 2
TFF3 -0.514 0.662 -9999 0 -1.407 41 41
ALOX15 -0.439 0.591 -9999 0 -1.283 37 37
MYBL1 0.031 0.012 -9999 0 -9999 0 0
T-helper 2 cell differentiation -0.482 0.541 -9999 0 -1.157 43 43
SHC1 0.03 0.009 -9999 0 -9999 0 0
CEBPB 0.016 0.061 -9999 0 -0.292 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.195 0.333 -9999 0 -0.902 15 15
mol:PI-3-4-5-P3 -0.2 0.325 -9999 0 -0.89 15 15
PI3K -0.215 0.356 -9999 0 -0.986 15 15
DOK2 -0.024 0.161 -9999 0 -0.518 13 13
ETS1 0.023 0.069 -9999 0 -0.489 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.126 0.234 -9999 0 -0.639 11 11
ITGB3 -0.429 0.595 -9999 0 -1.302 35 35
PIGR -0.536 0.691 -9999 0 -1.422 45 45
IGHE 0.031 0.067 0.228 2 -0.263 1 3
MAPKKK cascade -0.123 0.23 -9999 0 -0.626 11 11
BCL6 -0.003 0.102 -9999 0 -0.519 5 5
OPRM1 -0.428 0.596 -9999 0 -1.281 37 37
RETNLB -0.4 0.596 -9999 0 -1.337 31 31
SELP -0.51 0.706 -9999 0 -1.48 41 41
AICDA -0.41 0.576 -9999 0 -1.261 35 35
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.069 0.166 -9999 0 -0.331 32 32
NF kappa B1 p50/RelA/I kappa B alpha -0.054 0.174 -9999 0 -0.484 9 9
alphaV/beta3 Integrin/Osteopontin/Src -0.078 0.189 -9999 0 -0.407 31 31
AP1 -0.12 0.222 -9999 0 -0.532 21 21
ILK -0.076 0.151 -9999 0 -0.328 32 32
bone resorption -0.081 0.153 -9999 0 -0.344 22 22
PTK2B 0.028 0.017 -9999 0 -9999 0 0
PYK2/p130Cas -0.05 0.171 -9999 0 -0.31 35 35
ITGAV 0.015 0.085 -9999 0 -0.526 3 3
mol:GTP 0 0 -9999 0 -9999 0 0
CD44/Rho Family GTPase/ROCK2 0.031 0.081 -9999 0 -0.378 5 5
alphaV/beta3 Integrin/Osteopontin -0.059 0.179 -9999 0 -0.357 32 32
MAP3K1 -0.086 0.159 -9999 0 -0.336 35 35
JUN -0.002 0.123 -9999 0 -0.519 7 7
MAPK3 -0.089 0.158 -9999 0 -0.334 33 33
MAPK1 -0.081 0.151 -9999 0 -0.331 30 30
Rac1/GDP 0.024 0.004 -9999 0 -9999 0 0
NFKB1 0.031 0.008 -9999 0 -9999 0 0
MAPK8 -0.087 0.149 -9999 0 -0.324 34 34
ITGB3 0.021 0.055 -9999 0 -0.524 1 1
NFKBIA -0.087 0.165 -9999 0 -0.396 20 20
FOS -0.028 0.15 -9999 0 -0.517 11 11
CD44 0.012 0.104 -9999 0 -0.518 5 5
CHUK 0.028 0.047 -9999 0 -0.518 1 1
PLAU -0.161 0.348 -9999 0 -1.049 15 15
NF kappa B1 p50/RelA -0.046 0.191 -9999 0 -0.403 18 18
BCAR1 0.032 0.005 -9999 0 -9999 0 0
RELA 0.033 0 -9999 0 -9999 0 0
alphaV beta3 Integrin 0.026 0.082 -9999 0 -0.39 4 4
mol:GDP 0 0 -9999 0 -9999 0 0
SYK -0.088 0.161 -9999 0 -0.336 36 36
VAV3 -0.149 0.17 -9999 0 -0.327 58 58
MAP3K14 -0.082 0.16 -9999 0 -0.339 33 33
ROCK2 0.032 0.006 -9999 0 -9999 0 0
SPP1 -0.114 0.225 -9999 0 -0.521 31 31
RAC1 0.032 0.005 -9999 0 -9999 0 0
Rac1/GTP -0.133 0.162 -9999 0 -0.305 57 57
MMP2 -0.139 0.213 -9999 0 -0.54 23 23
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.372 0.513 -9999 0 -1.318 23 23
IL23A -0.462 0.574 -9999 0 -1.252 40 40
NF kappa B1 p50/RelA/I kappa B alpha -0.355 0.499 -9999 0 -1.129 29 29
positive regulation of T cell mediated cytotoxicity -0.398 0.563 -9999 0 -1.315 28 28
ITGA3 -0.392 0.501 -9999 0 -1.224 27 27
IL17F -0.186 0.322 0.484 1 -0.729 22 23
IL12B -0.017 0.093 -9999 0 -0.548 3 3
STAT1 (dimer) -0.391 0.543 -9999 0 -1.279 28 28
CD4 -0.33 0.467 -9999 0 -1.208 20 20
IL23 -0.444 0.553 -9999 0 -1.2 40 40
IL23R -0.058 0.217 -9999 0 -1.08 5 5
IL1B -0.463 0.6 -9999 0 -1.402 32 32
T-helper cell lineage commitment 0 0 -9999 0 -9999 0 0
IL24 -0.343 0.463 -9999 0 -1.132 25 25
TYK2 -0.007 0.04 -9999 0 -9999 0 0
STAT4 0.014 0.094 -9999 0 -0.518 4 4
STAT3 0.032 0.006 -9999 0 -9999 0 0
IL18RAP -0.051 0.184 -9999 0 -0.53 17 17
IL12RB1 -0.006 0.039 -9999 0 -9999 0 0
PIK3CA 0.011 0.048 -9999 0 -0.518 1 1
IL12Rbeta1/TYK2 -0.004 0.051 -9999 0 -9999 0 0
IL23R/JAK2 -0.053 0.205 -9999 0 -0.946 5 5
positive regulation of chronic inflammatory response -0.398 0.563 -9999 0 -1.315 28 28
natural killer cell activation 0.005 0.01 0.083 1 -9999 0 1
JAK2 -0.004 0.047 -9999 0 -9999 0 0
PIK3R1 0.004 0.097 -9999 0 -0.517 4 4
NFKB1 0.029 0.009 -9999 0 -9999 0 0
RELA 0.031 0.004 -9999 0 -9999 0 0
positive regulation of dendritic cell antigen processing and presentation -0.417 0.517 -9999 0 -1.119 40 40
ALOX12B -0.343 0.463 -9999 0 -1.197 21 21
CXCL1 -0.473 0.581 -9999 0 -1.334 35 35
T cell proliferation -0.398 0.563 -9999 0 -1.315 28 28
NFKBIA 0.025 0.048 -9999 0 -0.526 1 1
IL17A -0.165 0.251 -9999 0 -0.555 22 22
PI3K -0.335 0.478 -9999 0 -1.233 23 23
IFNG -0.041 0.062 0.148 1 -0.131 35 36
STAT3 (dimer) -0.313 0.452 -9999 0 -1.156 23 23
IL18R1 0 0.106 -9999 0 -0.522 5 5
IL23/IL23R/JAK2/TYK2/SOCS3 -0.204 0.331 -9999 0 -0.832 16 16
IL18/IL18R -0.06 0.186 -9999 0 -0.386 28 28
macrophage activation -0.021 0.022 -9999 0 -0.049 35 35
TNF -0.399 0.509 -9999 0 -1.201 28 28
STAT3/STAT4 -0.363 0.518 -9999 0 -1.222 27 27
STAT4 (dimer) -0.385 0.542 -9999 0 -1.287 27 27
IL18 -0.02 0.144 -9999 0 -0.521 10 10
IL19 -0.357 0.468 -9999 0 -1.198 22 22
STAT5A (dimer) -0.381 0.537 -9999 0 -1.256 28 28
STAT1 0.007 0.114 -9999 0 -0.518 6 6
SOCS3 0.018 0.082 -9999 0 -0.518 3 3
CXCL9 -0.482 0.615 -9999 0 -1.347 40 40
MPO -0.343 0.468 -9999 0 -1.212 21 21
positive regulation of humoral immune response -0.398 0.563 -9999 0 -1.315 28 28
IL23/IL23R/JAK2/TYK2 -0.43 0.645 -9999 0 -1.46 28 28
IL6 -0.413 0.539 -9999 0 -1.287 29 29
STAT5A 0.031 0.012 -9999 0 -9999 0 0
IL2 0.018 0.029 -9999 0 -9999 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.005 0.01 0.083 1 -9999 0 1
CD3E -0.342 0.463 -9999 0 -1.195 21 21
keratinocyte proliferation -0.398 0.563 -9999 0 -1.315 28 28
NOS2 -0.342 0.464 -9999 0 -1.091 28 28
Fc-epsilon receptor I signaling in mast cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A 0.02 0.068 -9999 0 -0.518 2 2
LAT2 -0.072 0.183 -9999 0 -0.426 23 23
AP1 -0.065 0.251 -9999 0 -0.553 22 22
mol:PIP3 -0.087 0.231 0.328 1 -0.489 27 28
IKBKB -0.027 0.138 0.202 10 -0.272 21 31
AKT1 -0.008 0.196 0.461 6 -0.427 11 17
IKBKG -0.042 0.127 0.204 4 -0.271 22 26
MS4A2 -0.048 0.188 -9999 0 -0.523 18 18
mol:Sphingosine-1-phosphate 0 0 -9999 0 -9999 0 0
PIK3CA 0.011 0.049 -9999 0 -0.521 1 1
MAP3K1 0.012 0.224 0.306 13 -0.444 17 30
mol:Ca2+ -0.06 0.174 0.238 4 -0.358 27 31
LYN 0.025 0.051 -9999 0 -0.53 1 1
CBLB -0.062 0.169 0.204 1 -0.402 22 23
SHC1 0.03 0.009 -9999 0 -9999 0 0
RasGAP/p62DOK 0.043 0.051 -9999 0 -0.288 2 2
positive regulation of cell migration -0.011 0.079 -9999 0 -0.375 6 6
INPP5D 0 0 -9999 0 -9999 0 0
PLD2 -0.094 0.173 0.333 4 -0.343 36 40
PTPN13 -0.066 0.213 -9999 0 -0.577 14 14
PTPN11 0.02 0.054 -9999 0 -0.533 1 1
GO:0007205 0 0 -9999 0 -9999 0 0
regulation of mast cell degranulation 0.006 0.172 0.338 8 -0.358 11 19
SYK 0.011 0.107 -9999 0 -0.533 5 5
GRB2 0.032 0.006 -9999 0 -9999 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.102 0.225 -9999 0 -0.483 30 30
LAT -0.069 0.174 -9999 0 -0.412 23 23
PAK2 0.018 0.242 0.263 38 -0.499 16 54
NFATC2 -0.022 0.056 -9999 0 -0.155 8 8
HRAS -0.067 0.228 0.246 3 -0.488 24 27
GAB2 0.031 0.015 -9999 0 -9999 0 0
PLA2G1B -0.022 0.213 -9999 0 -0.864 8 8
Fc epsilon R1 -0.077 0.211 -9999 0 -0.411 35 35
Antigen/IgE/Fc epsilon R1 -0.068 0.193 -9999 0 -0.372 35 35
mol:GDP -0.077 0.244 0.28 1 -0.542 23 24
JUN -0.002 0.123 -9999 0 -0.518 7 7
mol:Ca++ 0 0 -9999 0 -9999 0 0
PIK3R1 0.004 0.097 -9999 0 -0.52 4 4
FOS -0.027 0.151 -9999 0 -0.518 11 11
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.066 0.185 -9999 0 -0.412 25 25
CHUK -0.043 0.129 0.204 4 -0.277 22 26
KLRG1 -0.068 0.168 -9999 0 -0.371 26 26
VAV1 -0.078 0.186 -9999 0 -0.413 27 27
calcium-dependent protein kinase C activity 0 0 -9999 0 -9999 0 0
CBL -0.068 0.175 -9999 0 -0.411 23 23
negative regulation of mast cell degranulation -0.064 0.157 -9999 0 -0.346 26 26
BTK -0.087 0.265 -9999 0 -0.596 23 23
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.115 0.23 -9999 0 -0.409 40 40
GAB2/PI3K/SHP2 -0.08 0.136 -9999 0 -0.414 15 15
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.079 0.175 -9999 0 -0.34 35 35
RAF1 -0.017 0.231 -9999 0 -0.933 8 8
Fc epsilon R1/FcgammaRIIB/SHIP -0.086 0.226 -9999 0 -0.391 41 41
FCER1G 0.022 0.068 -9999 0 -0.521 2 2
FCER1A -0.092 0.216 -9999 0 -0.529 26 26
Antigen/IgE/Fc epsilon R1/Fyn -0.057 0.193 -9999 0 -0.352 36 36
MAPK3 -0.018 0.211 -9999 0 -0.851 8 8
MAPK1 -0.019 0.218 -9999 0 -0.884 8 8
NFKB1 0.031 0.008 -9999 0 -9999 0 0
MAPK8 -0.002 0.188 -9999 0 -0.755 5 5
DUSP1 0.016 0.071 -9999 0 -0.518 2 2
NF-kappa-B/RelA -0.012 0.088 0.169 1 -0.177 17 18
actin cytoskeleton reorganization -0.05 0.206 -9999 0 -0.555 14 14
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -9999 0 0
PI3K -0.075 0.19 -9999 0 -0.524 17 17
FER -0.069 0.173 -9999 0 -0.411 23 23
RELA 0.033 0 -9999 0 -9999 0 0
ITK -0.031 0.103 -9999 0 -0.341 10 10
SOS1 0.032 0.007 -9999 0 -9999 0 0
PLCG1 -0.071 0.25 0.296 2 -0.522 25 27
cytokine secretion -0.017 0.056 -9999 0 -9999 0 0
SPHK1 -0.085 0.195 -9999 0 -0.42 28 28
PTK2 -0.053 0.217 -9999 0 -0.586 14 14
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.103 0.236 -9999 0 -0.501 30 30
EDG1 -0.011 0.079 -9999 0 -0.376 6 6
mol:DAG -0.087 0.23 0.282 3 -0.474 29 32
MAP2K2 -0.021 0.214 -9999 0 -0.871 8 8
MAP2K1 -0.022 0.214 -9999 0 -0.871 8 8
MAP2K7 0.031 0.012 -9999 0 -9999 0 0
KLRG1/SHP2 -0.05 0.168 0.202 2 -0.426 17 19
MAP2K4 -0.009 0.221 -9999 0 -0.827 9 9
Fc epsilon R1/FcgammaRIIB -0.091 0.239 -9999 0 -0.416 41 41
mol:Choline -0.093 0.17 0.331 4 -0.338 36 40
SHC/Grb2/SOS1 -0.029 0.179 -9999 0 -0.394 20 20
FYN 0.023 0.067 -9999 0 -0.518 2 2
DOK1 0.032 0.006 -9999 0 -9999 0 0
PXN -0.049 0.198 -9999 0 -0.55 13 13
HCLS1 -0.074 0.187 0.204 1 -0.402 27 28
PRKCB -0.061 0.171 0.235 4 -0.347 29 33
FCGR2B -0.026 0.167 -9999 0 -0.518 14 14
IGHE -0.002 0.009 -9999 0 -9999 0 0
KLRG1/SHIP -0.065 0.16 -9999 0 -0.36 25 25
LCP2 -0.014 0.15 -9999 0 -0.52 11 11
PLA2G4A -0.105 0.202 -9999 0 -0.395 36 36
RASA1 0.029 0.01 -9999 0 -9999 0 0
mol:Phosphatidic acid -0.093 0.17 0.331 4 -0.338 36 40
IKK complex -0.019 0.11 0.193 7 -0.219 17 24
WIPF1 0 0 -9999 0 -9999 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.169 0.407 -9999 0 -1.138 20 20
MKNK1 0.032 0.006 -9999 0 -9999 0 0
MAPK14 -0.035 0.128 -9999 0 -0.329 19 19
ATF2/c-Jun -0.056 0.197 -9999 0 -0.816 7 7
MAPK11 -0.036 0.127 -9999 0 -0.327 19 19
MITF -0.051 0.159 -9999 0 -0.431 19 19
MAPKAPK5 -0.043 0.141 -9999 0 -0.379 19 19
KRT8 -0.06 0.164 -9999 0 -0.392 24 24
MAPKAPK3 0.029 0.014 -9999 0 -9999 0 0
MAPKAPK2 0.033 0 -9999 0 -9999 0 0
p38alpha-beta/CK2 -0.055 0.187 -9999 0 -0.475 20 20
CEBPB -0.049 0.156 -9999 0 -0.402 20 20
SLC9A1 -0.045 0.145 -9999 0 -0.391 19 19
mol:GDP 0 0 -9999 0 -9999 0 0
ATF2 -0.049 0.153 -9999 0 -0.392 20 20
p38alpha-beta/MNK1 -0.029 0.161 -9999 0 -0.394 19 19
JUN -0.056 0.194 -9999 0 -0.808 7 7
PPARGC1A -0.062 0.167 -9999 0 -0.401 23 23
USF1 -0.059 0.177 -9999 0 -0.438 21 21
RAB5/GDP/GDI1 -0.029 0.123 -9999 0 -0.299 19 19
NOS2 -0.052 0.143 -9999 0 -0.384 20 20
DDIT3 -0.054 0.151 -9999 0 -0.377 23 23
RAB5A 0.03 0.01 -9999 0 -9999 0 0
HSPB1 -0.049 0.125 -9999 0 -0.329 21 21
p38alpha-beta/HBP1 -0.034 0.161 -9999 0 -0.383 20 20
CREB1 -0.058 0.178 -9999 0 -0.439 21 21
RAB5/GDP 0.021 0.014 -9999 0 -9999 0 0
EIF4E -0.044 0.131 -9999 0 -0.359 18 18
RPS6KA4 -0.049 0.149 -9999 0 -0.385 21 21
PLA2G4A -0.092 0.194 -9999 0 -0.457 26 26
GDI1 -0.049 0.159 -9999 0 -0.402 20 20
TP53 -0.075 0.179 -9999 0 -0.49 20 20
RPS6KA5 -0.06 0.173 -9999 0 -0.419 22 22
ESR1 -0.065 0.169 -9999 0 -0.411 23 23
HBP1 0.019 0.081 -9999 0 -0.518 3 3
MEF2C -0.064 0.189 -9999 0 -0.467 21 21
MEF2A -0.046 0.143 -9999 0 -0.378 20 20
EIF4EBP1 -0.058 0.164 -9999 0 -0.42 21 21
KRT19 -0.087 0.19 -9999 0 -0.395 33 33
ELK4 -0.056 0.163 -9999 0 -0.397 23 23
ATF6 -0.043 0.141 -9999 0 -0.379 19 19
ATF1 -0.055 0.165 -9999 0 -0.42 21 21
p38alpha-beta/MAPKAPK2 -0.028 0.162 -9999 0 -0.404 18 18
p38alpha-beta/MAPKAPK3 -0.028 0.16 -9999 0 -0.401 18 18
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.093 0.097 0.36 1 -9999 0 1
SMARCC2 0.033 0 -9999 0 -9999 0 0
SMARCC1 0.022 0.067 -9999 0 -0.518 2 2
TBX21 -0.193 0.304 0.374 1 -0.665 33 34
SUMO2 0.032 0.017 -9999 0 -9999 0 0
STAT1 (dimer) 0.002 0.139 -9999 0 -0.514 8 8
FKBP4 0.027 0.048 -9999 0 -0.518 1 1
FKBP5 0.02 0.069 -9999 0 -0.518 2 2
GR alpha/HSP90/FKBP51/HSP90 0.113 0.112 0.278 30 -9999 0 30
PRL -0.075 0.13 -9999 0 -9999 0 0
cortisol/GR alpha (dimer)/TIF2 0.222 0.256 0.582 36 -9999 0 36
RELA -0.07 0.105 -9999 0 -0.261 11 11
FGG 0.162 0.239 0.511 27 -0.574 3 30
GR beta/TIF2 0.123 0.133 0.336 26 -9999 0 26
IFNG -0.451 0.528 -9999 0 -1.066 50 50
apoptosis 0.056 0.201 0.515 11 -0.51 3 14
CREB1 0.034 0.049 -9999 0 -0.512 1 1
histone acetylation -0.066 0.164 0.272 3 -0.377 20 23
BGLAP -0.108 0.154 -9999 0 -0.551 5 5
GR/PKAc 0.146 0.115 0.339 20 -9999 0 20
NF kappa B1 p50/RelA -0.127 0.182 -9999 0 -0.364 37 37
SMARCD1 0.033 0 -9999 0 -9999 0 0
MDM2 0.098 0.112 0.254 36 -9999 0 36
GATA3 0.034 0.031 -9999 0 -9999 0 0
AKT1 0.026 0.008 -9999 0 -9999 0 0
CSF2 -0.178 0.376 -9999 0 -1.344 11 11
GSK3B 0.026 0.022 -9999 0 -9999 0 0
NR1I3 0.071 0.206 0.541 9 -0.662 2 11
CSN2 0.159 0.174 0.399 35 -9999 0 35
BRG1/BAF155/BAF170/BAF60A 0.067 0.054 -9999 0 -0.298 2 2
NFATC1 0.021 0.094 -9999 0 -0.513 4 4
POU2F1 0.036 0.015 -9999 0 -9999 0 0
CDKN1A -0.031 0.23 -9999 0 -1.506 3 3
response to stress 0 0 -9999 0 -9999 0 0
response to UV 0.002 0.011 -9999 0 -9999 0 0
SFN -0.025 0.167 -9999 0 -0.518 14 14
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.09 0.139 0.292 22 -0.331 3 25
prolactin receptor activity 0 0 -9999 0 -9999 0 0
EGR1 0.017 0.285 0.502 9 -0.788 11 20
JUN -0.189 0.248 0.368 1 -0.522 36 37
IL4 -0.113 0.195 -9999 0 -0.607 12 12
CDK5R1 0.031 0.019 -9999 0 -9999 0 0
PRKACA 0.032 0.007 -9999 0 -9999 0 0
cortisol/GR alpha (monomer)/AP-1 -0.122 0.216 0.221 8 -0.459 31 39
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.117 0.11 0.286 25 -9999 0 25
cortisol/GR alpha (monomer) 0.274 0.326 0.686 42 -9999 0 42
NCOA2 0.023 0.066 -9999 0 -0.518 2 2
response to hypoxia 0 0 -9999 0 -9999 0 0
FOS -0.09 0.162 -9999 0 -0.42 19 19
AP-1/NFAT1-c-4 -0.315 0.37 -9999 0 -0.72 50 50
AFP -0.139 0.216 -9999 0 -1.17 2 2
SUV420H1 0.032 0.005 -9999 0 -9999 0 0
IRF1 0.111 0.242 0.479 14 -0.91 4 18
TP53 0.019 0.116 -9999 0 -0.508 6 6
PPP5C 0.028 0.047 -9999 0 -0.518 1 1
KRT17 -0.387 0.519 -9999 0 -1.122 37 37
KRT14 -0.339 0.524 -9999 0 -1.334 27 27
TBP 0.039 0.012 -9999 0 -9999 0 0
CREBBP 0.089 0.102 0.305 21 -9999 0 21
HDAC1 0.027 0.012 -9999 0 -9999 0 0
HDAC2 0.039 0.023 -9999 0 -9999 0 0
AP-1 -0.317 0.374 -9999 0 -0.72 51 51
MAPK14 0.033 0.014 -9999 0 -9999 0 0
MAPK10 0 0.097 -9999 0 -0.504 4 4
MAPK11 0.032 0.017 -9999 0 -9999 0 0
KRT5 -0.391 0.533 -9999 0 -1.112 39 39
interleukin-1 receptor activity 0.008 0.024 -9999 0 -9999 0 0
NCOA1 0.034 0.01 -9999 0 -9999 0 0
STAT1 0.002 0.139 -9999 0 -0.514 8 8
CGA -0.108 0.164 -9999 0 -0.536 9 9
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.122 0.218 0.484 26 -9999 0 26
MAPK3 0.033 0.016 -9999 0 -9999 0 0
MAPK1 0.031 0.016 -9999 0 -9999 0 0
ICAM1 -0.247 0.337 -9999 0 -0.763 28 28
NFKB1 -0.069 0.102 -9999 0 -0.26 11 11
MAPK8 -0.145 0.211 0.43 1 -0.43 36 37
MAPK9 0.031 0.015 -9999 0 -9999 0 0
cortisol/GR alpha (dimer) 0.055 0.206 0.519 11 -0.533 3 14
BAX -0.004 0.09 -9999 0 -9999 0 0
POMC -0.258 0.508 -9999 0 -1.76 13 13
EP300 0.053 0.155 0.288 18 -0.438 8 26
cortisol/GR alpha (dimer)/p53 0.22 0.254 0.571 36 -9999 0 36
proteasomal ubiquitin-dependent protein catabolic process 0.063 0.095 0.245 19 -9999 0 19
SGK1 0.088 0.134 0.323 24 -0.321 2 26
IL13 -0.21 0.26 -9999 0 -0.694 20 20
IL6 -0.295 0.409 -9999 0 -0.931 30 30
PRKACG 0.032 0.006 -9999 0 -9999 0 0
IL5 -0.186 0.223 -9999 0 -0.653 15 15
IL2 -0.276 0.345 -9999 0 -0.78 32 32
CDK5 0.033 0.007 -9999 0 -9999 0 0
PRKACB 0.026 0.049 -9999 0 -0.518 1 1
HSP90AA1 0 0 -9999 0 -9999 0 0
IL8 -0.414 0.498 -9999 0 -1.086 43 43
CDK5R1/CDK5 0.047 0.022 -9999 0 -9999 0 0
NF kappa B1 p50/RelA/PKAc -0.064 0.168 -9999 0 -0.42 9 9
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.215 0.244 0.548 39 -9999 0 39
SMARCA4 0.03 0.013 -9999 0 -9999 0 0
chromatin remodeling 0.143 0.165 0.367 37 -9999 0 37
NF kappa B1 p50/RelA/Cbp -0.057 0.194 0.382 2 -0.426 15 17
JUN (dimer) -0.188 0.247 0.368 1 -0.526 35 36
YWHAH 0.031 0.008 -9999 0 -9999 0 0
VIPR1 -0.123 0.203 -9999 0 -0.634 13 13
NR3C1 0.179 0.215 0.47 37 -9999 0 37
NR4A1 -0.013 0.143 -9999 0 -0.44 13 13
TIF2/SUV420H1 0.04 0.052 -9999 0 -0.378 2 2
MAPKKK cascade 0.056 0.201 0.515 11 -0.51 3 14
cortisol/GR alpha (dimer)/Src-1 0.242 0.262 0.591 39 -9999 0 39
PBX1 0.018 0.095 -9999 0 -0.513 4 4
POU1F1 0.031 0.019 -9999 0 -9999 0 0
SELE -0.392 0.496 -9999 0 -1.017 44 44
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.143 0.166 0.367 37 -9999 0 37
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.215 0.244 0.548 39 -9999 0 39
mol:cortisol 0.162 0.208 0.411 44 -9999 0 44
MMP1 -0.333 0.534 -9999 0 -1.339 29 29
Endothelins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.017 0.187 0.275 12 -0.384 20 32
PTK2B 0.028 0.017 -9999 0 -9999 0 0
mol:Ca2+ -0.08 0.266 -9999 0 -0.813 11 11
EDN1 -0.029 0.21 0.24 10 -0.499 19 29
EDN3 0.013 0.074 -9999 0 -0.518 2 2
EDN2 -0.154 0.235 -9999 0 -0.518 39 39
HRAS/GDP -0.058 0.19 0.278 1 -0.45 16 17
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.037 0.159 0.21 1 -0.357 19 20
ADCY4 -0.029 0.168 0.348 1 -0.364 18 19
ADCY5 -0.034 0.144 0.272 1 -0.353 16 17
ADCY6 -0.026 0.164 0.31 2 -0.351 18 20
ADCY7 -0.026 0.164 0.31 2 -0.345 19 21
ADCY1 -0.028 0.162 0.31 2 -0.419 11 13
ADCY2 -0.033 0.154 0.31 2 -0.434 10 12
ADCY3 -0.03 0.165 0.31 2 -0.341 21 23
ADCY8 -0.033 0.149 0.348 1 -0.358 16 17
ADCY9 -0.027 0.165 0.31 2 -0.384 14 16
arachidonic acid secretion -0.109 0.221 -9999 0 -0.499 24 24
ETB receptor/Endothelin-1/Gq/GTP -0.051 0.145 -9999 0 -0.327 22 22
GNAO1 0.032 0.007 -9999 0 -9999 0 0
HRAS 0.027 0.048 -9999 0 -0.518 1 1
ETA receptor/Endothelin-1/G12/GTP 0.023 0.201 0.378 13 -0.373 17 30
ETA receptor/Endothelin-1/Gs/GTP 0.002 0.196 0.346 12 -0.348 21 33
mol:GTP -0.001 0.006 -9999 0 -9999 0 0
COL3A1 -0.037 0.237 0.276 12 -0.513 20 32
EDNRB -0.002 0.102 -9999 0 -0.409 6 6
response to oxidative stress 0 0 -9999 0 -9999 0 0
CYSLTR2 -0.014 0.184 0.276 12 -0.434 13 25
CYSLTR1 -0.02 0.202 0.311 2 -0.532 10 12
SLC9A1 -0.004 0.118 0.198 12 -0.294 9 21
mol:GDP -0.069 0.189 0.273 1 -0.454 17 18
SLC9A3 -0.113 0.324 -9999 0 -0.722 24 24
RAF1 -0.074 0.187 -9999 0 -0.443 18 18
JUN -0.093 0.306 -9999 0 -0.963 11 11
JAK2 -0.016 0.184 0.281 11 -0.388 19 30
mol:IP3 -0.044 0.157 -9999 0 -0.379 17 17
ETA receptor/Endothelin-1 0.006 0.241 0.436 13 -0.429 22 35
PLCB1 0.01 0.104 -9999 0 -0.519 5 5
PLCB2 0.03 0.013 -9999 0 -9999 0 0
ETA receptor/Endothelin-3 0.024 0.122 -9999 0 -0.423 6 6
FOS -0.111 0.294 -9999 0 -0.905 14 14
Gai/GDP -0.063 0.266 -9999 0 -0.756 15 15
CRK 0.031 0.007 -9999 0 -9999 0 0
mol:Ca ++ -0.065 0.226 0.245 1 -0.535 20 21
BCAR1 0.032 0.005 -9999 0 -9999 0 0
PRKCB1 -0.064 0.163 -9999 0 -0.377 21 21
GNAQ -0.002 0.006 -9999 0 -9999 0 0
GNAZ 0 0.122 -9999 0 -0.518 7 7
GNAL 0.007 0.105 -9999 0 -0.518 5 5
Gs family/GDP -0.068 0.181 0.261 1 -0.425 17 18
ETA receptor/Endothelin-1/Gq/GTP -0.038 0.165 0.208 7 -0.345 22 29
MAPK14 -0.046 0.14 -9999 0 -0.364 15 15
TRPC6 -0.086 0.285 -9999 0 -0.878 11 11
GNAI2 0.027 0.02 -9999 0 -9999 0 0
GNAI3 0.032 0.006 -9999 0 -9999 0 0
GNAI1 -0.001 0.13 -9999 0 -0.518 8 8
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.049 0.15 -9999 0 -0.338 21 21
ETB receptor/Endothelin-2 -0.121 0.192 -9999 0 -0.393 42 42
ETB receptor/Endothelin-3 0.006 0.096 -9999 0 -0.383 6 6
ETB receptor/Endothelin-1 -0.025 0.18 -9999 0 -0.379 23 23
MAPK3 -0.105 0.273 -9999 0 -0.8 14 14
MAPK1 -0.108 0.276 -9999 0 -0.833 14 14
Rac1/GDP -0.053 0.182 0.277 1 -0.427 16 17
cAMP biosynthetic process -0.007 0.152 0.317 4 -0.446 7 11
MAPK8 -0.073 0.255 -9999 0 -0.696 13 13
SRC 0.03 0.013 -9999 0 -9999 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.048 0.157 -9999 0 -0.366 18 18
p130Cas/CRK/Src/PYK2 -0.074 0.198 -9999 0 -0.504 16 16
mol:K + 0 0 -9999 0 -9999 0 0
G12/GDP -0.052 0.182 0.277 1 -0.427 16 17
COL1A2 -0.066 0.274 -9999 0 -0.606 20 20
EntrezGene:2778 0 0 -9999 0 -9999 0 0
ETA receptor/Endothelin-2 -0.105 0.201 -9999 0 -0.381 42 42
mol:DAG -0.044 0.157 -9999 0 -0.38 17 17
MAP2K2 -0.089 0.215 -9999 0 -0.544 18 18
MAP2K1 -0.089 0.216 -9999 0 -0.558 17 17
EDNRA 0.024 0.135 0.237 13 -0.51 5 18
positive regulation of muscle contraction -0.016 0.162 0.229 13 -0.362 16 29
Gq family/GDP -0.064 0.171 -9999 0 -0.418 17 17
HRAS/GTP -0.063 0.17 -9999 0 -0.385 20 20
PRKCH -0.049 0.158 -9999 0 -0.398 16 16
RAC1 0.032 0.005 -9999 0 -9999 0 0
PRKCA -0.045 0.156 0.329 1 -0.392 15 16
PRKCB -0.048 0.153 -9999 0 -0.373 17 17
PRKCE -0.034 0.142 0.221 3 -0.361 14 17
PRKCD -0.049 0.15 -9999 0 -0.389 15 15
PRKCG -0.048 0.15 -9999 0 -0.367 16 16
regulation of vascular smooth muscle contraction -0.135 0.346 -9999 0 -1.122 13 13
PRKCQ -0.061 0.172 -9999 0 -0.418 18 18
PLA2G4A -0.119 0.244 -9999 0 -0.547 24 24
GNA14 0.006 0.086 -9999 0 -0.519 3 3
GNA15 0.002 0.114 -9999 0 -0.518 6 6
GNA12 0.032 0.007 -9999 0 -9999 0 0
GNA11 0.024 0.049 -9999 0 -0.518 1 1
Rac1/GTP 0.023 0.201 0.378 13 -0.373 17 30
MMP1 -0.207 0.379 -9999 0 -0.915 29 29
Wnt signaling

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
Noncanonical Wnts/FZD -0.121 0.187 -9999 0 -0.345 47 47
FZD6 0.018 0.081 -9999 0 -0.518 3 3
WNT6 0.029 0.018 -9999 0 -9999 0 0
WNT4 -0.065 0.201 -9999 0 -0.518 22 22
FZD3 -0.007 0.13 -9999 0 -0.518 8 8
WNT5A -0.076 0.198 -9999 0 -0.518 22 22
WNT11 0.001 0.099 -9999 0 -0.518 4 4
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.028 0.056 -9999 0 -0.373 2 2
NFATC2 -0.081 0.228 -9999 0 -0.608 13 13
NFATC3 -0.034 0.107 -9999 0 -0.268 12 12
CD40LG -0.313 0.4 -9999 0 -0.892 35 35
ITCH -0.03 0.104 -9999 0 -9999 0 0
CBLB -0.023 0.096 -9999 0 -9999 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.213 0.369 -9999 0 -0.928 22 22
JUNB 0.014 0.084 -9999 0 -0.518 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.035 0.131 -9999 0 -0.283 28 28
T cell anergy -0.068 0.17 0.268 1 -0.396 24 25
TLE4 -0.064 0.199 -9999 0 -0.598 10 10
Jun/NFAT1-c-4/p21SNFT -0.235 0.398 -9999 0 -0.94 26 26
AP-1/NFAT1-c-4 -0.348 0.504 -9999 0 -1.069 34 34
IKZF1 -0.058 0.156 -9999 0 -0.433 13 13
T-helper 2 cell differentiation -0.08 0.208 -9999 0 -0.682 7 7
AP-1/NFAT1 -0.115 0.213 -9999 0 -0.515 20 20
CALM1 -0.013 0.085 -9999 0 -9999 0 0
EGR2 -0.235 0.502 -9999 0 -1.344 20 20
EGR3 -0.203 0.43 -9999 0 -1.037 22 22
NFAT1/FOXP3 -0.041 0.186 -9999 0 -0.496 12 12
EGR1 -0.013 0.138 -9999 0 -0.519 9 9
JUN -0.031 0.127 -9999 0 -0.54 7 7
EGR4 0.001 0.001 -9999 0 -9999 0 0
mol:Ca2+ -0.03 0.069 -9999 0 -0.164 28 28
GBP3 -0.137 0.31 -9999 0 -0.795 23 23
FOSL1 0.025 0.03 -9999 0 -9999 0 0
NFAT1-c-4/MAF/IRF4 -0.193 0.407 -9999 0 -0.929 25 25
DGKA -0.078 0.222 -9999 0 -0.613 14 14
CREM 0.031 0.006 -9999 0 -9999 0 0
NFAT1-c-4/PPARG -0.214 0.401 -9999 0 -0.935 25 25
CTLA4 -0.049 0.167 -9999 0 -0.514 10 10
NFAT1-c-4 (dimer)/EGR1 -0.202 0.414 -9999 0 -0.953 25 25
NFAT1-c-4 (dimer)/EGR4 -0.187 0.391 -9999 0 -0.911 25 25
FOS -0.057 0.151 -9999 0 -0.535 11 11
IFNG -0.389 0.598 -9999 0 -1.329 36 36
T cell activation -0.132 0.226 -9999 0 -0.771 6 6
MAF -0.028 0.167 -9999 0 -0.517 14 14
T-helper 2 cell lineage commitment 0 0 -9999 0 -9999 0 0
activation-induced cell death of T cells 0.158 0.345 0.815 22 -9999 0 22
TNF -0.189 0.352 -9999 0 -0.839 25 25
FASLG -0.344 0.625 -9999 0 -1.403 32 32
TBX21 -0.08 0.202 -9999 0 -0.375 34 34
BATF3 0 0 -9999 0 -9999 0 0
PRKCQ -0.005 0.118 -9999 0 -0.527 6 6
PTPN1 -0.053 0.158 -9999 0 -0.519 8 8
NFAT1-c-4/ICER1 -0.183 0.395 -9999 0 -0.912 25 25
GATA3 0.027 0.029 -9999 0 -9999 0 0
T-helper 1 cell differentiation -0.37 0.567 -9999 0 -1.265 36 36
IL2RA -0.205 0.367 -9999 0 -0.876 24 24
T-helper 1 cell lineage commitment 0 0 -9999 0 -9999 0 0
CASP3 -0.047 0.157 -9999 0 -0.484 10 10
E2F1 0.036 0.011 -9999 0 -9999 0 0
PPARG -0.022 0.156 -9999 0 -0.517 12 12
SLC3A2 -0.06 0.171 -9999 0 -0.546 9 9
IRF4 0.024 0.052 -9999 0 -0.518 1 1
PTGS2 -0.353 0.428 -9999 0 -0.932 39 39
CSF2 -0.331 0.418 -9999 0 -0.912 37 37
JunB/Fra1/NFAT1-c-4 -0.174 0.389 -9999 0 -0.888 25 25
IL4 -0.082 0.215 -9999 0 -0.71 7 7
IL5 -0.31 0.399 -9999 0 -0.895 34 34
IL2 -0.134 0.229 -9999 0 -0.786 6 6
IL3 -0.054 0.175 -9999 0 -0.728 7 7
RNF128 -0.117 0.254 -9999 0 -0.609 28 28
NFATC1 -0.159 0.349 -9999 0 -0.821 22 22
CDK4 0.108 0.191 0.596 8 -9999 0 8
PTPRK -0.068 0.201 -9999 0 -0.708 9 9
IL8 -0.377 0.424 -9999 0 -0.93 39 39
POU2F1 0.037 0.009 -9999 0 -9999 0 0
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.032 0.006 -9999 0 -9999 0 0
GNB1/GNG2 -0.094 0.188 -9999 0 -0.41 22 22
mol:DAG -0.101 0.158 -9999 0 -0.388 20 20
PLCG1 -0.104 0.163 -9999 0 -0.401 20 20
YES1 -0.114 0.172 -9999 0 -0.392 27 27
FZD3 -0.007 0.13 -9999 0 -0.518 8 8
FZD6 0.018 0.081 -9999 0 -0.518 3 3
G protein -0.097 0.18 -9999 0 -0.427 18 18
MAP3K7 -0.09 0.131 -9999 0 -0.359 16 16
mol:Ca2+ -0.098 0.153 -9999 0 -0.377 20 20
mol:IP3 -0.101 0.158 -9999 0 -0.388 20 20
NLK 0.001 0.164 -9999 0 -0.832 5 5
GNB1 0.032 0.006 -9999 0 -9999 0 0
CAMK2A -0.094 0.143 -9999 0 -0.383 16 16
MAP3K7IP1 0.031 0.009 -9999 0 -9999 0 0
Noncanonical Wnts/FZD -0.121 0.187 -9999 0 -0.345 47 47
CSNK1A1 0.031 0.007 -9999 0 -9999 0 0
GNAS -0.124 0.175 -9999 0 -0.386 31 31
GO:0007205 -0.101 0.151 -9999 0 -0.409 16 16
WNT6 0.029 0.018 -9999 0 -9999 0 0
WNT4 -0.065 0.201 -9999 0 -0.518 22 22
NFAT1/CK1 alpha -0.082 0.181 -9999 0 -0.444 15 15
GNG2 0.032 0.005 -9999 0 -9999 0 0
WNT5A -0.076 0.198 -9999 0 -0.518 22 22
WNT11 0.001 0.099 -9999 0 -0.518 4 4
CDC42 -0.105 0.169 -9999 0 -0.398 23 23
Thromboxane A2 receptor signaling

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
TGM2 0.001 0.114 -9999 0 -0.52 6 6
GNB1/GNG2 -0.064 0.081 -9999 0 -0.189 35 35
AKT1 -0.041 0.113 -9999 0 -0.219 10 10
EGF -0.032 0.15 -9999 0 -0.518 11 11
mol:TXA2 0 0.001 -9999 0 -9999 0 0
FGR 0.011 0.061 0.235 2 -9999 0 2
mol:Ca2+ -0.072 0.163 -9999 0 -0.302 41 41
LYN 0.007 0.06 0.208 1 -0.244 1 2
RhoA/GTP -0.032 0.07 -9999 0 -0.134 28 28
mol:PGI2 0 0 -9999 0 -9999 0 0
SYK -0.091 0.183 -9999 0 -0.352 38 38
GNG2 0.032 0.005 -9999 0 -9999 0 0
ARRB2 0.031 0.007 -9999 0 -9999 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.019 0.155 -9999 0 -0.476 11 11
G beta5/gamma2 -0.075 0.114 -9999 0 -0.249 35 35
PRKCH -0.09 0.187 -9999 0 -0.359 39 39
DNM1 0.027 0.049 -9999 0 -0.518 1 1
TXA2/TP beta/beta Arrestin3 0.026 0.03 -9999 0 -9999 0 0
mol:GTP 0 0.001 -9999 0 -9999 0 0
PTGDR 0.027 0.025 -9999 0 -9999 0 0
G12 family/GTP -0.08 0.155 -9999 0 -0.307 37 37
ADRBK1 0.032 0.005 -9999 0 -9999 0 0
ADRBK2 0.021 0.068 -9999 0 -0.518 2 2
RhoA/GTP/ROCK1 0.039 0.015 -9999 0 -9999 0 0
mol:GDP 0.032 0.118 0.4 5 -9999 0 5
mol:NADP 0.027 0.025 -9999 0 -9999 0 0
RAB11A 0.032 0.005 -9999 0 -9999 0 0
PRKG1 0.029 0.019 -9999 0 -9999 0 0
mol:IP3 -0.095 0.2 -9999 0 -0.379 41 41
cell morphogenesis 0.038 0.014 -9999 0 -9999 0 0
PLCB2 -0.139 0.264 -9999 0 -0.516 41 41
mol:cGMP 0 0.001 -9999 0 -9999 0 0
BLK 0.002 0.067 0.261 1 -0.244 1 2
mol:PDG2 0 0 -9999 0 -9999 0 0
HCK -0.003 0.079 0.261 1 -0.279 2 3
RHOA 0.03 0.01 -9999 0 -9999 0 0
PTGIR 0.024 0.066 -9999 0 -0.518 2 2
PRKCB1 -0.103 0.204 -9999 0 -0.396 39 39
GNAQ 0 0 -9999 0 -9999 0 0
mol:L-citrulline 0.027 0.025 -9999 0 -9999 0 0
TXA2/TXA2-R family -0.139 0.266 -9999 0 -0.529 39 39
LCK -0.003 0.076 0.261 1 -0.243 2 3
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.039 0.046 -9999 0 -9999 0 0
TXA2-R family/G12 family/GDP/G beta/gamma 0.018 0.092 -9999 0 -0.392 6 6
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.038 0.047 -9999 0 -9999 0 0
MAPK14 -0.058 0.124 -9999 0 -0.235 36 36
TGM2/GTP -0.114 0.221 -9999 0 -0.428 41 41
MAPK11 -0.056 0.125 -9999 0 -0.235 36 36
ARHGEF1 -0.045 0.094 -9999 0 -0.182 35 35
GNAI2 0.027 0.02 -9999 0 -9999 0 0
JNK cascade -0.096 0.2 -9999 0 -0.387 39 39
RAB11/GDP 0.032 0.005 -9999 0 -9999 0 0
ICAM1 -0.072 0.16 -9999 0 -0.302 38 38
cAMP biosynthetic process -0.09 0.184 -9999 0 -0.349 42 42
Gq family/GTP/EBP50 -0.029 0.11 -9999 0 -0.265 21 21
actin cytoskeleton reorganization 0.038 0.014 -9999 0 -9999 0 0
SRC 0.008 0.06 0.261 1 -9999 0 1
GNB5 0.02 0.081 -9999 0 -0.518 3 3
GNB1 0.032 0.006 -9999 0 -9999 0 0
EGF/EGFR -0.017 0.099 0.191 2 -0.299 7 9
VCAM1 -0.077 0.165 -9999 0 -0.316 38 38
TP beta/Gq family/GDP/G beta5/gamma2 -0.019 0.155 -9999 0 -0.476 11 11
platelet activation -0.074 0.162 -9999 0 -0.303 38 38
PGI2/IP 0.018 0.048 -9999 0 -0.376 2 2
PRKACA 0.014 0.036 -9999 0 -0.258 2 2
Gq family/GDP/G beta5/gamma2 -0.01 0.123 -9999 0 -0.393 10 10
TXA2/TP beta/beta Arrestin2 0.012 0.058 -9999 0 -0.526 1 1
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -9999 0 0
TBXA2R 0.005 0.033 -9999 0 -0.246 2 2
mol:DAG -0.109 0.221 -9999 0 -0.427 40 40
EGFR -0.014 0.144 -9999 0 -0.518 10 10
TXA2/TP alpha -0.125 0.247 -9999 0 -0.475 42 42
Gq family/GTP -0.013 0.073 -9999 0 -0.247 11 11
YES1 0.01 0.057 0.261 1 -9999 0 1
GNAI2/GTP 0.015 0.047 -9999 0 -0.239 1 1
PGD2/DP 0.02 0.016 -9999 0 -9999 0 0
SLC9A3R1 -0.024 0.162 -9999 0 -0.518 13 13
FYN 0.006 0.071 0.261 1 -0.412 1 2
mol:NO 0.027 0.025 -9999 0 -9999 0 0
GNA15 0.007 0.114 -9999 0 -0.518 6 6
PGK/cGMP 0.036 0.024 -9999 0 -9999 0 0
RhoA/GDP 0.03 0.01 -9999 0 -9999 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.04 0.082 -9999 0 -0.388 2 2
NOS3 0.027 0.025 -9999 0 -9999 0 0
RAC1 0.032 0.005 -9999 0 -9999 0 0
PRKCA -0.088 0.187 -9999 0 -0.355 40 40
PRKCB -0.09 0.187 -9999 0 -0.361 39 39
PRKCE -0.082 0.185 -9999 0 -0.357 35 35
PRKCD -0.104 0.194 -9999 0 -0.388 39 39
PRKCG -0.099 0.203 -9999 0 -0.392 39 39
muscle contraction -0.129 0.248 -9999 0 -0.491 39 39
PRKCZ -0.085 0.178 -9999 0 -0.342 39 39
ARR3 0.033 0 -9999 0 -9999 0 0
TXA2/TP beta 0.031 0.056 -9999 0 -0.254 1 1
PRKCQ -0.101 0.19 -9999 0 -0.374 39 39
MAPKKK cascade -0.118 0.232 -9999 0 -0.453 40 40
SELE -0.097 0.193 -9999 0 -0.387 38 38
TP beta/GNAI2/GDP/G beta/gamma 0.055 0.05 -9999 0 -9999 0 0
ROCK1 0.032 0.006 -9999 0 -9999 0 0
GNA14 0.011 0.085 -9999 0 -0.518 3 3
chemotaxis -0.163 0.303 -9999 0 -0.62 38 38
GNA12 0.032 0.007 -9999 0 -9999 0 0
GNA13 0.027 0.048 -9999 0 -0.518 1 1
GNA11 0.029 0.047 -9999 0 -0.518 1 1
Rac1/GTP 0.023 0.004 -9999 0 -9999 0 0
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.102 0.2 -9999 0 -0.454 26 26
IKBKB 0 0.11 -9999 0 -0.272 9 9
AKT1 -0.003 0.141 0.249 11 -0.254 17 28
IKBKG -0.003 0.104 0.207 1 -0.284 7 8
CALM1 -0.061 0.228 0.323 1 -0.573 18 19
PIK3CA 0.011 0.048 -9999 0 -0.517 1 1
MAP3K1 -0.131 0.283 -9999 0 -0.629 28 28
MAP3K7 0.031 0.011 -9999 0 -9999 0 0
mol:Ca2+ -0.064 0.247 0.342 1 -0.614 18 19
DOK1 0.032 0.006 -9999 0 -9999 0 0
AP-1 -0.054 0.117 -9999 0 -0.27 22 22
LYN 0.028 0.047 -9999 0 -0.517 1 1
BLNK 0.019 0.081 -9999 0 -0.517 3 3
SHC1 0.03 0.009 -9999 0 -9999 0 0
BCR complex -0.046 0.198 -9999 0 -0.47 21 21
CD22 -0.11 0.308 -9999 0 -0.751 21 21
CAMK2G -0.056 0.209 0.308 1 -0.584 15 16
CSNK2A1 0.031 0.008 -9999 0 -9999 0 0
INPP5D 0 0 -9999 0 -9999 0 0
SHC/GRB2/SOS1 -0.046 0.162 -9999 0 -0.383 22 22
GO:0007205 -0.067 0.255 0.342 1 -0.633 18 19
SYK 0.012 0.104 -9999 0 -0.517 5 5
ELK1 -0.063 0.235 0.324 1 -0.588 18 19
NFATC1 -0.12 0.266 0.255 2 -0.538 31 33
B-cell antigen/BCR complex -0.046 0.198 -9999 0 -0.47 21 21
PAG1/CSK 0.032 0.073 -9999 0 -0.379 4 4
NFKBIB 0.015 0.054 0.124 1 -0.125 7 8
HRAS -0.054 0.206 0.265 2 -0.518 18 20
NFKBIA 0.015 0.053 0.124 1 -0.122 8 9
NF-kappa-B/RelA/I kappa B beta 0.022 0.047 0.126 1 -9999 0 1
RasGAP/Csk -0.035 0.217 -9999 0 -0.442 25 25
mol:GDP -0.061 0.239 0.333 1 -0.594 18 19
PTEN 0.023 0.067 -9999 0 -0.518 2 2
CD79B -0.043 0.181 -9999 0 -0.517 17 17
NF-kappa-B/RelA/I kappa B alpha 0.022 0.046 0.126 1 -9999 0 1
GRB2 0.032 0.006 -9999 0 -9999 0 0
PI3K/BCAP/CD19 -0.118 0.255 -9999 0 -0.595 25 25
PIK3R1 0.004 0.097 -9999 0 -0.518 4 4
mol:IP3 -0.069 0.259 0.344 1 -0.643 18 19
CSK 0.033 0.004 -9999 0 -9999 0 0
FOS -0.08 0.223 0.309 1 -0.557 19 20
CHUK -0.011 0.118 0.207 1 -0.309 10 11
IBTK 0.029 0.047 -9999 0 -0.518 1 1
CARD11/BCL10/MALT1/TAK1 -0.03 0.203 0.302 1 -0.535 15 16
PTPN6 -0.106 0.278 -9999 0 -0.783 17 17
RELA 0.033 0 -9999 0 -9999 0 0
BCL2A1 0.008 0.043 -9999 0 -0.123 2 2
VAV2 -0.171 0.363 -9999 0 -0.78 29 29
ubiquitin-dependent protein catabolic process 0.018 0.053 0.126 1 -0.119 7 8
BTK -0.073 0.322 -9999 0 -1.215 10 10
CD19 -0.153 0.363 -9999 0 -0.862 23 23
MAP4K1 0.028 0.011 -9999 0 -9999 0 0
CD72 -0.041 0.181 -9999 0 -0.518 17 17
PAG1 0.014 0.094 -9999 0 -0.518 4 4
MAPK14 -0.107 0.23 -9999 0 -0.528 26 26
SH3BP5 0.025 0.049 -9999 0 -0.518 1 1
PIK3AP1 -0.083 0.266 -9999 0 -0.664 19 19
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.109 0.348 -9999 0 -0.797 22 22
RAF1 -0.051 0.193 0.253 2 -0.485 18 20
RasGAP/p62DOK/SHIP -0.039 0.198 -9999 0 -0.414 25 25
CD79A -0.026 0.156 -9999 0 -0.517 12 12
re-entry into mitotic cell cycle -0.054 0.117 0.195 1 -0.27 22 23
RASA1 0.029 0.01 -9999 0 -9999 0 0
MAPK3 -0.044 0.159 0.227 2 -0.439 15 17
MAPK1 -0.033 0.158 0.293 4 -0.417 14 18
CD72/SHP1 -0.087 0.314 0.325 3 -0.739 21 24
NFKB1 0.031 0.008 -9999 0 -9999 0 0
MAPK8 -0.106 0.23 -9999 0 -0.549 24 24
actin cytoskeleton organization -0.135 0.285 -9999 0 -0.621 29 29
NF-kappa-B/RelA 0.044 0.092 0.235 1 -0.248 1 2
Calcineurin -0.026 0.204 0.305 1 -0.541 15 16
PI3K -0.105 0.212 -9999 0 -0.55 21 21
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.076 0.27 0.376 1 -0.658 19 20
SOS1 0.032 0.007 -9999 0 -9999 0 0
Bam32/HPK1 -0.16 0.37 -9999 0 -0.849 28 28
DAPP1 -0.201 0.438 -9999 0 -0.995 29 29
cytokine secretion -0.109 0.24 0.251 2 -0.489 31 33
mol:DAG -0.069 0.259 0.344 1 -0.643 18 19
PLCG2 0.011 0.104 -9999 0 -0.517 5 5
MAP2K1 -0.049 0.177 0.24 2 -0.49 15 17
B-cell antigen/BCR complex/FcgammaRIIB -0.059 0.233 -9999 0 -0.502 25 25
mol:PI-3-4-5-P3 -0.042 0.161 0.243 5 -0.356 19 24
ETS1 -0.044 0.193 0.253 3 -0.504 16 19
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.021 0.203 -9999 0 -0.427 23 23
B-cell antigen/BCR complex/LYN -0.116 0.331 -9999 0 -0.805 21 21
MALT1 0.03 0.013 -9999 0 -9999 0 0
TRAF6 0.028 0.047 -9999 0 -0.517 1 1
RAC1 -0.152 0.314 -9999 0 -0.686 29 29
B-cell antigen/BCR complex/LYN/SYK -0.067 0.303 0.386 1 -0.692 21 22
CARD11 -0.064 0.238 0.324 1 -0.594 18 19
FCGR2B -0.026 0.167 -9999 0 -0.518 14 14
PPP3CA 0.031 0.008 -9999 0 -9999 0 0
BCL10 0.028 0.047 -9999 0 -0.518 1 1
IKK complex 0.015 0.057 0.135 4 -0.118 1 5
PTPRC -0.022 0.162 -9999 0 -0.518 13 13
PDPK1 -0.008 0.133 0.23 12 -0.247 16 28
PPP3CB 0.032 0.007 -9999 0 -9999 0 0
PPP3CC 0.026 0.048 -9999 0 -0.518 1 1
POU2F2 0.02 0.037 0.125 4 -9999 0 4
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.033 0.003 -9999 0 -9999 0 0
PTK2 0.027 0.048 -9999 0 -0.518 1 1
CRKL -0.051 0.124 -9999 0 -0.288 26 26
GRB2/SOS1/SHC 0.056 0.025 -9999 0 -9999 0 0
HRAS 0.027 0.048 -9999 0 -0.518 1 1
IRS1/Crk -0.049 0.133 -9999 0 -0.287 29 29
IGF-1R heterotetramer/IGF1/PTP1B -0.029 0.15 -9999 0 -0.326 25 25
AKT1 0.012 0.163 0.193 5 -0.351 13 18
BAD 0.009 0.154 0.203 2 -0.418 7 9
mol:GTP 0 0 -9999 0 -9999 0 0
CRK -0.057 0.128 -9999 0 -0.287 29 29
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.047 0.136 -9999 0 -0.289 29 29
RAF1 0.017 0.166 -9999 0 -0.43 8 8
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.018 0.144 -9999 0 -0.294 24 24
YWHAZ 0.031 0.008 -9999 0 -9999 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.049 0.146 -9999 0 -0.309 29 29
PIK3CA 0.011 0.048 -9999 0 -0.518 1 1
RPS6KB1 0.013 0.163 0.236 3 -0.441 7 10
GNB2L1 0.03 0.009 -9999 0 -9999 0 0
positive regulation of MAPKKK cascade 0.017 0.146 0.321 1 -0.376 7 8
PXN 0.033 0.003 -9999 0 -9999 0 0
PIK3R1 0.004 0.097 -9999 0 -0.518 4 4
cell adhesion 0 0 -9999 0 -9999 0 0
GRB2/SOS1 0.045 0.013 -9999 0 -9999 0 0
HRAS/GTP -0.038 0.125 -9999 0 -0.285 23 23
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.001 0.139 -9999 0 -0.275 23 23
IGF-1R heterotetramer -0.027 0.152 -9999 0 -0.546 10 10
IGF-1R heterotetramer/IGF1/IRS/Nck -0.031 0.146 -9999 0 -0.289 29 29
Crk/p130 Cas/Paxillin -0.019 0.141 -9999 0 -0.284 25 25
IGF1R -0.027 0.152 -9999 0 -0.546 10 10
IGF1 -0.067 0.192 -9999 0 -0.541 18 18
IRS2/Crk -0.063 0.146 -9999 0 -0.31 30 30
PI3K -0.04 0.131 -9999 0 -0.374 13 13
apoptosis -0.021 0.144 0.387 6 -0.205 2 8
HRAS/GDP 0.02 0.035 -9999 0 -0.375 1 1
PRKCD -0.06 0.157 -9999 0 -0.366 25 25
RAF1/14-3-3 E 0.024 0.164 -9999 0 -0.383 8 8
BAD/14-3-3 0.021 0.152 0.212 2 -0.413 6 8
PRKCZ 0.013 0.162 0.231 3 -0.34 14 17
Crk/p130 Cas/Paxillin/FAK1 0.014 0.146 -9999 0 -0.453 6 6
PTPN1 0.032 0.007 -9999 0 -9999 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.066 0.163 -9999 0 -0.382 25 25
BCAR1 0.032 0.005 -9999 0 -9999 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.032 0.168 -9999 0 -0.337 27 27
mol:GDP 0 0 -9999 0 -9999 0 0
SOS1 0.032 0.007 -9999 0 -9999 0 0
IRS1/NCK2 -0.045 0.136 -9999 0 -0.287 29 29
GRB10 -0.004 0.13 -9999 0 -0.518 8 8
PTPN11 -0.058 0.128 -9999 0 -0.288 29 29
IRS1 -0.061 0.138 -9999 0 -0.309 29 29
IRS2 -0.072 0.15 -9999 0 -0.316 33 33
IGF-1R heterotetramer/IGF1 -0.061 0.184 -9999 0 -0.427 25 25
GRB2 0.032 0.006 -9999 0 -9999 0 0
PDPK1 0.021 0.171 0.243 3 -0.357 14 17
YWHAE 0.031 0.007 -9999 0 -9999 0 0
PRKD1 -0.071 0.188 -9999 0 -0.415 27 27
SHC1 0.03 0.009 -9999 0 -9999 0 0
FOXM1 transcription factor network

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
NFATC3 -0.128 0.494 -9999 0 -1.137 17 17
PLK1 0.041 0.127 -9999 0 -1.277 1 1
BIRC5 -0.049 0.389 -9999 0 -1.493 9 9
HSPA1B -0.13 0.494 -9999 0 -1.119 18 18
MAP2K1 0.02 0.058 -9999 0 -9999 0 0
BRCA2 -0.165 0.533 -9999 0 -1.173 21 21
FOXM1 -0.228 0.804 -9999 0 -1.833 18 18
XRCC1 -0.122 0.5 -9999 0 -1.137 17 17
FOXM1B/p19 -0.254 0.51 -9999 0 -1.225 22 22
Cyclin D1/CDK4 -0.15 0.497 -9999 0 -1.102 20 20
CDC2 -0.144 0.531 -9999 0 -1.252 17 17
TGFA -0.159 0.476 -9999 0 -1.006 22 22
SKP2 -0.126 0.541 -9999 0 -1.22 18 18
CCNE1 0.02 0.052 -9999 0 -0.513 1 1
CKS1B -0.119 0.504 -9999 0 -1.144 17 17
RB1 -0.083 0.327 -9999 0 -0.953 11 11
FOXM1C/SP1 -0.164 0.593 -9999 0 -1.396 18 18
AURKB 0.01 0.196 -9999 0 -0.879 5 5
CENPF -0.161 0.535 -9999 0 -1.185 21 21
CDK4 0.021 0.034 -9999 0 -9999 0 0
MYC -0.123 0.442 -9999 0 -1 18 18
CHEK2 0.019 0.057 -9999 0 -9999 0 0
ONECUT1 -0.153 0.499 -9999 0 -1.128 19 19
CDKN2A -0.05 0.162 -9999 0 -0.514 14 14
LAMA4 -0.14 0.513 -9999 0 -1.239 16 16
FOXM1B/HNF6 -0.21 0.613 -9999 0 -1.468 19 19
FOS -0.198 0.566 -9999 0 -1.19 26 26
SP1 0.03 0.047 -9999 0 -0.518 1 1
CDC25B -0.124 0.507 -9999 0 -1.151 17 17
response to radiation 0.004 0.033 -9999 0 -9999 0 0
CENPB -0.127 0.511 -9999 0 -1.164 17 17
CENPA -0.136 0.516 -9999 0 -1.205 17 17
NEK2 -0.176 0.555 -9999 0 -1.203 23 23
HIST1H2BA -0.141 0.505 -9999 0 -1.186 17 17
CCNA2 0.02 0.07 -9999 0 -0.532 2 2
EP300 -0.001 0.129 -9999 0 -0.518 8 8
CCNB1/CDK1 -0.175 0.596 -9999 0 -1.527 15 15
CCNB2 -0.132 0.497 -9999 0 -1.17 16 16
CCNB1 -0.141 0.526 -9999 0 -1.229 17 17
ETV5 -0.094 0.607 -9999 0 -1.253 22 22
ESR1 -0.159 0.532 -9999 0 -1.267 16 16
CCND1 -0.167 0.501 -9999 0 -1.138 20 20
GSK3A 0.019 0.05 -9999 0 -9999 0 0
Cyclin A-E1/CDK1-2 0.034 0.083 -9999 0 -0.342 3 3
CDK2 0.03 0.019 -9999 0 -9999 0 0
G2/M transition of mitotic cell cycle 0.004 0.039 -9999 0 -9999 0 0
FOXM1B/Cbp/p300 -0.159 0.548 -9999 0 -1.29 17 17
GAS1 -0.219 0.606 -9999 0 -1.249 29 29
MMP2 -0.188 0.573 -9999 0 -1.231 25 25
RB1/FOXM1C -0.172 0.507 -9999 0 -1.156 20 20
CREBBP 0.032 0.006 -9999 0 -9999 0 0
Syndecan-1-mediated signaling events

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
TGFB1 0.031 0.008 -9999 0 -9999 0 0
CCL5 -0.018 0.156 -9999 0 -0.518 12 12
SDCBP 0.027 0.047 -9999 0 -0.518 1 1
FGFR/FGF2/Syndecan-1 -0.114 0.234 -9999 0 -0.572 21 21
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 -0.106 0.236 -9999 0 -0.559 22 22
Syndecan-1/Syntenin -0.099 0.235 -9999 0 -0.593 19 19
MAPK3 -0.098 0.213 -9999 0 -0.528 20 20
HGF/MET 0.037 0.055 -9999 0 -0.378 2 2
TGFB1/TGF beta receptor Type II 0.031 0.008 -9999 0 -9999 0 0
BSG 0.032 0.005 -9999 0 -9999 0 0
keratinocyte migration -0.104 0.232 -9999 0 -0.548 22 22
Syndecan-1/RANTES -0.121 0.272 -9999 0 -0.609 24 24
Syndecan-1/CD147 -0.083 0.236 -9999 0 -0.545 21 21
Syndecan-1/Syntenin/PIP2 -0.097 0.227 -9999 0 -0.574 19 19
LAMA5 0.015 0.093 -9999 0 -0.518 4 4
positive regulation of cell-cell adhesion -0.094 0.22 -9999 0 -0.557 19 19
MMP7 -0.045 0.191 -9999 0 -0.518 19 19
HGF 0.029 0.021 -9999 0 -9999 0 0
Syndecan-1/CASK -0.112 0.222 -9999 0 -0.549 21 21
Syndecan-1/HGF/MET -0.082 0.232 -9999 0 -0.545 20 20
regulation of cell adhesion -0.093 0.193 -9999 0 -0.515 17 17
HPSE 0.008 0.104 -9999 0 -0.518 5 5
positive regulation of cell migration -0.114 0.234 -9999 0 -0.572 21 21
SDC1 -0.116 0.237 -9999 0 -0.579 21 21
Syndecan-1/Collagen -0.114 0.234 -9999 0 -0.572 21 21
PPIB 0.027 0.048 -9999 0 -0.518 1 1
MET 0.022 0.068 -9999 0 -0.518 2 2
PRKACA 0.032 0.007 -9999 0 -9999 0 0
MMP9 -0.017 0.156 -9999 0 -0.518 12 12
MAPK1 -0.089 0.202 -9999 0 -0.502 19 19
homophilic cell adhesion -0.112 0.23 -9999 0 -0.564 21 21
MMP1 -0.106 0.219 -9999 0 -0.518 29 29
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.009 0.096 -9999 0 -0.518 4 4
EPHB2 -0.026 0.162 -9999 0 -0.518 13 13
EFNB1 -0.025 0.115 -9999 0 -0.375 13 13
mol:GTP 0 0 -9999 0 -9999 0 0
Rac1/GDP -0.024 0.143 -9999 0 -0.302 24 24
Ephrin B2/EPHB1-2 -0.022 0.121 -9999 0 -0.305 18 18
neuron projection morphogenesis -0.033 0.13 -9999 0 -0.289 24 24
Ephrin B1/EPHB1-2/Tiam1 -0.033 0.148 -9999 0 -0.317 25 25
DNM1 0.027 0.049 -9999 0 -0.516 1 1
cell-cell signaling 0 0.004 -9999 0 -9999 0 0
MAP2K4 -0.062 0.191 -9999 0 -0.567 16 16
YES1 -0.085 0.276 -9999 0 -0.805 17 17
Ephrin B1/EPHB1-2/NCK2 -0.033 0.148 -9999 0 -0.319 25 25
PI3K -0.05 0.201 -9999 0 -0.621 13 13
mol:GDP -0.034 0.145 -9999 0 -0.314 25 25
ITGA2B 0.033 0.003 -9999 0 -9999 0 0
endothelial cell proliferation 0.019 0.088 -9999 0 -0.398 5 5
FYN -0.088 0.277 -9999 0 -0.805 17 17
MAP3K7 -0.07 0.202 -9999 0 -0.591 17 17
FGR -0.082 0.272 -9999 0 -0.789 17 17
TIAM1 0.032 0.006 -9999 0 -9999 0 0
PIK3R1 0.004 0.097 -9999 0 -0.518 4 4
RGS3 0.032 0.005 -9999 0 -9999 0 0
cell adhesion -0.054 0.185 -9999 0 -0.603 12 12
LYN -0.087 0.275 -9999 0 -0.802 17 17
Ephrin B1/EPHB1-2/Src Family Kinases -0.087 0.255 -9999 0 -0.75 17 17
Ephrin B1/EPHB1-2 -0.075 0.217 -9999 0 -0.633 17 17
SRC -0.081 0.272 -9999 0 -0.789 17 17
ITGB3 0.024 0.052 -9999 0 -0.518 1 1
EPHB1 -0.014 0.108 -9999 0 -0.518 5 5
EPHB4 0.017 0.082 -9999 0 -0.518 3 3
RAC1 0.032 0.005 -9999 0 -9999 0 0
Ephrin B2/EPHB4 0.019 0.088 -9999 0 -0.4 5 5
alphaIIb/beta3 Integrin 0.041 0.042 -9999 0 -0.378 1 1
BLK -0.093 0.273 -9999 0 -0.798 17 17
HCK -0.09 0.274 -9999 0 -0.798 17 17
regulation of stress fiber formation 0.034 0.146 0.315 25 -9999 0 25
MAPK8 -0.057 0.182 -9999 0 -0.551 15 15
Ephrin B1/EPHB1-2/RGS3 -0.033 0.148 -9999 0 -0.319 25 25
endothelial cell migration -0.07 0.189 -9999 0 -0.503 19 19
NCK2 0.033 0.003 -9999 0 -9999 0 0
PTPN13 -0.016 0.167 -9999 0 -0.638 9 9
regulation of focal adhesion formation 0.034 0.146 0.315 25 -9999 0 25
chemotaxis 0.034 0.146 0.315 25 -9999 0 25
PIK3CA 0.011 0.048 -9999 0 -0.518 1 1
Rac1/GTP -0.028 0.137 -9999 0 -0.295 24 24
angiogenesis -0.074 0.215 -9999 0 -0.63 17 17
LCK -0.091 0.277 -9999 0 -0.806 17 17
EPHB forward 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
Ephrin A5/EPHB2 0.002 0.107 -9999 0 -0.321 13 13
cell-cell adhesion 0.073 0.114 0.295 24 -9999 0 24
Ephrin B/EPHB2/RasGAP -0.004 0.162 -9999 0 -0.315 26 26
ITSN1 0.033 0.004 -9999 0 -9999 0 0
PIK3CA 0.011 0.048 -9999 0 -0.518 1 1
SHC1 0.03 0.009 -9999 0 -9999 0 0
Ephrin B1/EPHB3 -0.029 0.127 -9999 0 -0.356 16 16
Ephrin B1/EPHB1 -0.021 0.122 -9999 0 -0.346 15 15
HRAS/GDP -0.096 0.152 -9999 0 -0.388 17 17
Ephrin B/EPHB1/GRB7 -0.001 0.135 -9999 0 -0.31 18 18
Endophilin/SYNJ1 -0.068 0.12 -9999 0 -0.298 26 26
KRAS 0.014 0.093 -9999 0 -0.518 4 4
Ephrin B/EPHB1/Src 0.002 0.129 -9999 0 -0.31 15 15
endothelial cell migration 0.001 0.08 -9999 0 -0.314 6 6
GRB2 0.032 0.006 -9999 0 -9999 0 0
GRB7 0.031 0.007 -9999 0 -9999 0 0
PAK1 -0.041 0.138 -9999 0 -0.307 21 21
HRAS 0.027 0.048 -9999 0 -0.518 1 1
RRAS -0.072 0.122 -9999 0 -0.301 27 27
DNM1 0.027 0.049 -9999 0 -0.518 1 1
cell-cell signaling 0 0 -9999 0 -9999 0 0
CRK -0.024 0.13 -9999 0 -0.294 18 18
lamellipodium assembly -0.073 0.114 -9999 0 -0.295 24 24
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.014 0.094 -9999 0 -0.34 4 4
PIK3R1 0.004 0.097 -9999 0 -0.518 4 4
EPHB2 -0.026 0.162 -9999 0 -0.518 13 13
EPHB3 -0.021 0.133 -9999 0 -0.518 9 9
EPHB1 -0.014 0.108 -9999 0 -0.518 5 5
EPHB4 0.017 0.082 -9999 0 -0.518 3 3
mol:GDP -0.094 0.148 -9999 0 -0.397 16 16
Ephrin B/EPHB2 -0.012 0.155 -9999 0 -0.314 26 26
Ephrin B/EPHB3 -0.021 0.126 -9999 0 -0.316 18 18
JNK cascade -0.01 0.207 0.358 19 -0.325 27 46
Ephrin B/EPHB1 -0.009 0.128 -9999 0 -0.307 18 18
RAP1/GDP -0.079 0.154 -9999 0 -0.4 13 13
EFNB2 0.009 0.096 -9999 0 -0.518 4 4
EFNB3 0.031 0.007 -9999 0 -9999 0 0
EFNB1 -0.016 0.156 -9999 0 -0.518 12 12
Ephrin B2/EPHB1-2 -0.022 0.121 -9999 0 -0.306 18 18
RAP1B 0.031 0.007 -9999 0 -9999 0 0
RAP1A 0.023 0.066 -9999 0 -0.518 2 2
CDC42/GTP -0.045 0.16 -9999 0 -0.35 24 24
Rap1/GTP -0.053 0.127 -9999 0 -0.344 11 11
axon guidance 0.001 0.107 -9999 0 -0.32 13 13
MAPK3 -0.019 0.082 -9999 0 -0.376 2 2
MAPK1 -0.009 0.078 -9999 0 -0.406 1 1
Rac1/GDP -0.087 0.147 -9999 0 -0.37 16 16
actin cytoskeleton reorganization -0.094 0.119 -9999 0 -0.357 15 15
CDC42/GDP -0.088 0.147 -9999 0 -0.371 16 16
PI3K 0.003 0.083 -9999 0 -0.317 6 6
EFNA5 0.03 0.009 -9999 0 -9999 0 0
Ephrin B2/EPHB4 0.019 0.088 -9999 0 -0.4 5 5
Ephrin B/EPHB2/Intersectin/N-WASP -0.045 0.144 -9999 0 -0.302 28 28
CDC42 0.032 0.005 -9999 0 -9999 0 0
RAS family/GTP -0.061 0.136 -9999 0 -0.369 13 13
PTK2 0.044 0.161 0.611 9 -0.502 1 10
MAP4K4 -0.01 0.209 0.359 19 -0.329 27 46
SRC 0.03 0.013 -9999 0 -9999 0 0
KALRN 0.026 0.016 -9999 0 -9999 0 0
Intersectin/N-WASP 0.035 0.073 -9999 0 -0.378 4 4
neuron projection morphogenesis -0.025 0.161 0.288 13 -0.426 5 18
MAP2K1 -0.016 0.087 -9999 0 -0.35 3 3
WASL 0.016 0.093 -9999 0 -0.518 4 4
Ephrin B1/EPHB1-2/NCK1 -0.032 0.162 -9999 0 -0.34 26 26
cell migration -0.016 0.116 0.295 1 -0.338 5 6
NRAS 0.026 0.049 -9999 0 -0.518 1 1
SYNJ1 -0.069 0.121 -9999 0 -0.302 26 26
PXN 0.033 0.003 -9999 0 -9999 0 0
TF -0.063 0.109 -9999 0 -0.292 22 22
HRAS/GTP -0.04 0.143 -9999 0 -0.303 26 26
Ephrin B1/EPHB1-2 -0.038 0.151 -9999 0 -0.339 24 24
cell adhesion mediated by integrin 0.011 0.116 0.306 12 -0.186 1 13
RAC1 0.032 0.005 -9999 0 -9999 0 0
mol:GTP -0.039 0.145 -9999 0 -0.305 27 27
RAC1-CDC42/GTP -0.059 0.124 -9999 0 -0.389 8 8
RASA1 0.029 0.01 -9999 0 -9999 0 0
RAC1-CDC42/GDP -0.077 0.149 -9999 0 -0.385 12 12
ruffle organization -0.048 0.149 0.327 2 -0.473 5 7
NCK1 0.019 0.067 -9999 0 -0.518 2 2
receptor internalization -0.071 0.121 -9999 0 -0.301 26 26
Ephrin B/EPHB2/KALRN -0.007 0.152 -9999 0 -0.314 23 23
ROCK1 0.057 0.162 0.188 65 -0.315 16 81
RAS family/GDP -0.104 0.118 -9999 0 -0.374 14 14
Rac1/GTP -0.057 0.132 -9999 0 -0.311 24 24
Ephrin B/EPHB1/Src/Paxillin -0.027 0.107 -9999 0 -0.402 4 4
Nectin adhesion pathway

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
PDGFRB 0.03 0.012 -9999 0 -9999 0 0
alphaV beta3 Integrin 0.031 0.075 -9999 0 -0.378 4 4
PTK2 -0.078 0.196 -9999 0 -0.439 25 25
positive regulation of JNK cascade -0.041 0.153 -9999 0 -0.329 23 23
CDC42/GDP -0.052 0.212 -9999 0 -0.441 26 26
Rac1/GDP -0.051 0.21 -9999 0 -0.437 26 26
RAP1B 0.031 0.007 -9999 0 -9999 0 0
RAP1A 0.023 0.066 -9999 0 -0.518 2 2
CTNNB1 0.028 0.017 -9999 0 -9999 0 0
CDC42/GTP -0.045 0.191 -9999 0 -0.407 23 23
nectin-3/I-afadin -0.05 0.163 -9999 0 -0.378 26 26
RAPGEF1 -0.071 0.213 -9999 0 -0.465 27 27
mol:GTP 0 0 -9999 0 -9999 0 0
CRK -0.083 0.236 -9999 0 -0.527 27 27
PDGFB-D/PDGFRB 0.03 0.012 -9999 0 -9999 0 0
TLN1 -0.032 0.08 -9999 0 -0.451 2 2
Rap1/GTP -0.053 0.158 -9999 0 -0.346 25 25
IQGAP1 0.032 0.005 -9999 0 -9999 0 0
Rap1/GTP/I-afadin 0.051 0.047 -9999 0 -0.295 2 2
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.05 0.163 -9999 0 -0.378 26 26
PVR 0.023 0.067 -9999 0 -0.518 2 2
Necl-5(dimer) 0.023 0.066 -9999 0 -0.517 2 2
mol:GDP -0.082 0.248 -9999 0 -0.538 27 27
MLLT4 0.032 0.006 -9999 0 -9999 0 0
PIK3CA 0.011 0.048 -9999 0 -0.518 1 1
PI3K -0.014 0.113 -9999 0 -0.306 12 12
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.023 0.096 -9999 0 -0.378 7 7
positive regulation of lamellipodium assembly -0.054 0.168 -9999 0 -0.349 25 25
PVRL1 0.004 0.122 -9999 0 -0.518 7 7
PVRL3 -0.086 0.212 -9999 0 -0.518 26 26
PVRL2 0.03 0.013 -9999 0 -9999 0 0
PIK3R1 0.004 0.097 -9999 0 -0.518 4 4
CDH1 0.002 0.122 -9999 0 -0.518 7 7
CLDN1 -0.074 0.191 -9999 0 -0.518 21 21
JAM-A/CLDN1 -0.069 0.165 -9999 0 -0.354 28 28
SRC -0.103 0.256 -9999 0 -0.582 27 27
ITGB3 0.024 0.052 -9999 0 -0.518 1 1
nectin-1(dimer)/I-afadin/I-afadin 0.023 0.096 -9999 0 -0.378 7 7
FARP2 -0.071 0.249 -9999 0 -0.55 22 22
RAC1 0.032 0.005 -9999 0 -9999 0 0
CTNNA1 0.031 0.008 -9999 0 -9999 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.033 0.153 -9999 0 -0.334 26 26
nectin-1/I-afadin 0.023 0.096 -9999 0 -0.378 7 7
nectin-2/I-afadin 0.044 0.017 -9999 0 -9999 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.043 0.009 -9999 0 -9999 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.048 0.166 -9999 0 -0.337 32 32
CDC42/GTP/IQGAP1/filamentous actin 0.043 0.009 -9999 0 -9999 0 0
F11R 0.027 0.047 -9999 0 -0.518 1 1
positive regulation of filopodium formation -0.041 0.153 -9999 0 -0.329 23 23
alphaV/beta3 Integrin/Talin 0.009 0.129 0.323 3 -0.438 4 7
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.044 0.017 -9999 0 -9999 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.044 0.017 -9999 0 -9999 0 0
PIP5K1C -0.037 0.097 -9999 0 -0.564 2 2
VAV2 -0.101 0.269 -9999 0 -0.572 25 25
RAP1/GDP -0.05 0.199 -9999 0 -0.412 26 26
ITGAV 0.019 0.082 -9999 0 -0.518 3 3
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.028 0.146 -9999 0 -0.324 25 25
nectin-3(dimer)/I-afadin/I-afadin -0.05 0.163 -9999 0 -0.378 26 26
Rac1/GTP -0.064 0.207 -9999 0 -0.429 25 25
PTPRM -0.033 0.101 -9999 0 -0.221 25 25
E-cadherin/beta catenin/alpha catenin 0.042 0.116 -9999 0 -0.293 12 12
adherens junction assembly 0 0 -9999 0 -9999 0 0
CDC42 0.032 0.005 -9999 0 -9999 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.014 0.184 0.292 1 -0.451 15 16
FYN -0.056 0.242 0.238 2 -0.578 19 21
LAT/GRAP2/SLP76 -0.038 0.204 -9999 0 -0.532 16 16
IKBKB 0.029 0.01 -9999 0 -9999 0 0
AKT1 -0.041 0.168 0.195 2 -0.398 20 22
B2M 0.006 0.115 -9999 0 -0.525 6 6
IKBKG -0.009 0.054 0.109 2 -0.139 10 12
MAP3K8 -0.01 0.144 -9999 0 -0.518 10 10
mol:Ca2+ -0.014 0.014 -9999 0 -0.052 9 9
integrin-mediated signaling pathway 0.033 0.055 -9999 0 -0.32 3 3
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.067 0.243 0.231 1 -0.601 19 20
TRPV6 -0.001 0.104 1.186 1 -9999 0 1
CD28 -0.015 0.152 -9999 0 -0.523 11 11
SHC1 -0.048 0.215 0.198 2 -0.482 21 23
receptor internalization -0.068 0.226 -9999 0 -0.481 26 26
PRF1 -0.094 0.334 -9999 0 -1.018 13 13
KRAS 0.014 0.093 -9999 0 -0.518 4 4
GRB2 0.032 0.006 -9999 0 -9999 0 0
COT/AKT1 -0.033 0.16 0.197 1 -0.356 22 23
LAT -0.057 0.214 -9999 0 -0.494 21 21
EntrezGene:6955 0 0.004 -9999 0 -0.015 7 7
CD3D -0.007 0.14 -9999 0 -0.527 9 9
CD3E 0.03 0.014 -9999 0 -9999 0 0
CD3G -0.059 0.204 -9999 0 -0.523 22 22
RASGRP2 0.004 0.025 -9999 0 -0.192 1 1
RASGRP1 -0.039 0.166 0.268 1 -0.389 20 21
HLA-A 0.021 0.069 -9999 0 -0.532 2 2
RASSF5 0.027 0.049 -9999 0 -0.518 1 1
RAP1A/GTP/RAPL 0.033 0.055 -9999 0 -0.321 3 3
mol:GTP 0 0 -9999 0 -9999 0 0
mol:GDP 0.012 0.058 0.141 4 -0.114 7 11
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.031 0.078 -9999 0 -0.222 14 14
PRKCA -0.019 0.104 0.176 2 -0.252 17 19
GRAP2 0.031 0.008 -9999 0 -9999 0 0
mol:IP3 -0.048 0.149 -9999 0 -0.391 18 18
EntrezGene:6957 0 0.005 0.008 1 -0.016 9 10
TCR/CD3/MHC I/CD8 -0.059 0.207 -9999 0 -0.413 24 24
ORAI1 -0.004 0.087 -9999 0 -1.003 1 1
CSK -0.052 0.213 0.198 1 -0.498 20 21
B7 family/CD28 -0.065 0.273 -9999 0 -0.619 21 21
CHUK 0.028 0.047 -9999 0 -0.518 1 1
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.077 0.238 -9999 0 -0.559 21 21
PTPN6 -0.056 0.222 0.189 1 -0.495 22 23
VAV1 -0.065 0.232 0.198 1 -0.554 20 21
Monovalent TCR/CD3 -0.054 0.181 -9999 0 -0.399 24 24
CBL 0.032 0.005 -9999 0 -9999 0 0
LCK -0.059 0.248 0.233 2 -0.566 20 22
PAG1 -0.053 0.221 0.198 1 -0.515 20 21
RAP1A 0.023 0.066 -9999 0 -0.518 2 2
TCR/CD3/MHC I/CD8/LCK -0.078 0.246 0.222 1 -0.561 22 23
CD80 0.025 0.021 -9999 0 -9999 0 0
CD86 -0.01 0.137 -9999 0 -0.522 9 9
PDK1/CARD11/BCL10/MALT1 -0.027 0.096 -9999 0 -0.268 13 13
HRAS 0.027 0.048 -9999 0 -0.518 1 1
GO:0035030 -0.074 0.209 -9999 0 -0.506 21 21
CD8A 0 0.005 0.008 1 -0.015 9 10
CD8B -0.001 0.005 -9999 0 -0.014 13 13
PTPRC -0.022 0.164 -9999 0 -0.523 13 13
PDK1/PKC theta -0.058 0.2 -9999 0 -0.478 21 21
CSK/PAG1 -0.049 0.209 -9999 0 -0.551 16 16
SOS1 0.032 0.007 -9999 0 -9999 0 0
peptide-MHC class I 0.017 0.116 -9999 0 -0.46 7 7
GRAP2/SLP76 -0.042 0.237 -9999 0 -0.561 19 19
STIM1 -0.006 0.019 -9999 0 -9999 0 0
RAS family/GTP 0.003 0.083 0.163 3 -0.171 12 15
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.073 0.24 -9999 0 -0.509 26 26
mol:DAG -0.055 0.128 -9999 0 -0.352 18 18
RAP1A/GDP 0.008 0.032 0.078 2 -0.12 2 4
PLCG1 0.031 0.008 -9999 0 -9999 0 0
CD247 0 0.004 -9999 0 -0.015 7 7
cytotoxic T cell degranulation -0.087 0.311 -9999 0 -0.908 14 14
RAP1A/GTP 0.001 0.015 -9999 0 -0.086 3 3
mol:PI-3-4-5-P3 -0.05 0.2 0.213 2 -0.487 19 21
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.05 0.199 -9999 0 -0.505 18 18
NRAS 0.026 0.049 -9999 0 -0.518 1 1
ZAP70 0.03 0.015 -9999 0 -9999 0 0
GRB2/SOS1 0.045 0.013 -9999 0 -9999 0 0
LAT/GRAP2/SLP76/VAV1 -0.05 0.202 -9999 0 -0.513 18 18
MALT1 0.03 0.013 -9999 0 -9999 0 0
TRAF6 0.028 0.047 -9999 0 -0.518 1 1
CD8 heterodimer 0 0.007 0.013 2 -0.018 13 15
CARD11 0.02 0.035 -9999 0 -9999 0 0
PRKCB -0.043 0.087 -9999 0 -0.246 18 18
PRKCE -0.02 0.1 0.193 1 -0.25 15 16
PRKCQ -0.066 0.228 -9999 0 -0.557 20 20
LCP2 -0.013 0.15 -9999 0 -0.518 11 11
BCL10 0.028 0.047 -9999 0 -0.518 1 1
regulation of survival gene product expression -0.032 0.145 0.186 2 -0.337 20 22
IKK complex 0.008 0.056 0.139 7 -0.105 7 14
RAS family/GDP -0.004 0.016 -9999 0 -0.059 6 6
MAP3K14 -0.028 0.124 0.164 1 -0.287 20 21
PDPK1 -0.04 0.16 0.2 1 -0.388 19 20
TCR/CD3/MHC I/CD8/Fyn -0.064 0.229 -9999 0 -0.604 16 16
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.018 0.07 -9999 0 -0.356 4 4
NFATC2 -0.009 0.039 -9999 0 -9999 0 0
NFATC3 -0.008 0.038 -9999 0 -9999 0 0
CD40LG -0.145 0.259 -9999 0 -0.549 31 31
PTGS2 -0.185 0.302 -9999 0 -0.632 36 36
JUNB 0.014 0.084 -9999 0 -0.518 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 0.003 0.031 -9999 0 -9999 0 0
CaM/Ca2+ 0.003 0.031 -9999 0 -9999 0 0
CALM1 0.017 0.028 -9999 0 -9999 0 0
JUN -0.015 0.124 -9999 0 -0.526 7 7
mol:Ca2+ -0.007 0.011 -9999 0 -9999 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.016 0.014 -9999 0 -9999 0 0
FOSL1 0.025 0.03 -9999 0 -9999 0 0
CREM 0.031 0.006 -9999 0 -9999 0 0
Jun/NFAT1-c-4/p21SNFT -0.065 0.159 -9999 0 -0.338 24 24
FOS -0.04 0.151 -9999 0 -0.528 11 11
IFNG -0.198 0.309 -9999 0 -0.603 43 43
AP-1/NFAT1-c-4 -0.152 0.333 -9999 0 -0.658 31 31
FASLG -0.165 0.295 -9999 0 -0.61 33 33
NFAT1-c-4/ICER1 -0.032 0.105 -9999 0 -0.308 7 7
IL2RA -0.157 0.284 -9999 0 -0.581 33 33
FKBP12/FK506 0.023 0.005 -9999 0 -9999 0 0
CSF2 -0.164 0.283 -9999 0 -0.593 33 33
JunB/Fra1/NFAT1-c-4 -0.016 0.129 -9999 0 -0.338 9 9
IL4 -0.142 0.258 -9999 0 -0.551 30 30
IL2 -0.04 0.253 -9999 0 -0.984 9 9
IL3 -0.017 0.191 -9999 0 -0.721 9 9
FKBP1A 0.032 0.007 -9999 0 -9999 0 0
BATF3 0 0 -9999 0 -9999 0 0
mol:FK506 0 0 -9999 0 -9999 0 0
POU2F1 0.037 0.009 -9999 0 -9999 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.043 0.154 -9999 0 -0.403 13 13
CRKL -0.054 0.152 -9999 0 -0.415 14 14
HRAS -0.041 0.159 -9999 0 -0.41 14 14
mol:PIP3 -0.036 0.164 -9999 0 -0.428 13 13
SPRED1 0.023 0.067 -9999 0 -0.518 2 2
SPRED2 0.03 0.013 -9999 0 -9999 0 0
GAB1 -0.066 0.165 -9999 0 -0.422 20 20
FOXO3 -0.058 0.165 -9999 0 -0.401 18 18
AKT1 -0.063 0.177 -9999 0 -0.432 18 18
BAD -0.06 0.165 -9999 0 -0.431 14 14
megakaryocyte differentiation -0.077 0.169 -9999 0 -0.452 17 17
GSK3B -0.036 0.178 0.379 1 -0.437 13 14
RAF1 -0.028 0.136 0.256 1 -0.34 13 14
SHC1 0.03 0.009 -9999 0 -9999 0 0
STAT3 -0.068 0.165 -9999 0 -0.436 18 18
STAT1 -0.149 0.364 -9999 0 -0.969 18 18
HRAS/SPRED1 -0.024 0.145 -9999 0 -0.345 14 14
cell proliferation -0.062 0.163 0.273 1 -0.433 17 18
PIK3CA 0.011 0.048 -9999 0 -0.518 1 1
TEC 0.03 0.016 -9999 0 -9999 0 0
RPS6KB1 -0.061 0.171 -9999 0 -0.429 18 18
HRAS/SPRED2 -0.019 0.138 -9999 0 -0.339 12 12
LYN/TEC/p62DOK -0.035 0.178 -9999 0 -0.435 17 17
MAPK3 -0.019 0.105 0.228 1 -0.296 6 7
STAP1 -0.065 0.164 -9999 0 -0.43 18 18
GRAP2 0.031 0.008 -9999 0 -9999 0 0
JAK2 -0.119 0.292 -9999 0 -0.801 16 16
STAT1 (dimer) -0.147 0.354 -9999 0 -0.945 18 18
mol:Gleevec 0.002 0.006 -9999 0 -9999 0 0
GRB2/SOCS1/VAV1 -0.051 0.197 -9999 0 -0.462 19 19
actin filament polymerization -0.063 0.161 -9999 0 -0.421 18 18
LYN 0.028 0.047 -9999 0 -0.518 1 1
STAP1/STAT5A (dimer) -0.089 0.215 -9999 0 -0.565 18 18
PIK3R1 0.004 0.097 -9999 0 -0.518 4 4
CBL/CRKL/GRB2 -0.034 0.158 -9999 0 -0.401 12 12
PI3K -0.051 0.153 -9999 0 -0.479 9 9
PTEN 0.023 0.067 -9999 0 -0.518 2 2
SCF/KIT/EPO/EPOR -0.141 0.417 -9999 0 -1.305 13 13
MAPK8 -0.063 0.166 0.274 1 -0.442 17 18
STAT3 (dimer) -0.068 0.162 -9999 0 -0.427 18 18
positive regulation of transcription -0.013 0.089 0.213 1 -0.247 5 6
mol:GDP -0.043 0.161 -9999 0 -0.413 15 15
PIK3C2B -0.068 0.171 -9999 0 -0.459 17 17
CBL/CRKL -0.043 0.156 -9999 0 -0.403 13 13
FER -0.065 0.163 -9999 0 -0.442 17 17
SH2B3 -0.065 0.164 -9999 0 -0.43 18 18
PDPK1 -0.032 0.158 -9999 0 -0.421 12 12
SNAI2 -0.093 0.183 -9999 0 -0.419 25 25
positive regulation of cell proliferation -0.11 0.263 -9999 0 -0.691 18 18
KITLG -0.022 0.154 -9999 0 -0.534 11 11
cell motility -0.11 0.263 -9999 0 -0.691 18 18
PTPN6 0.029 0.048 -9999 0 -0.512 1 1
EPOR -0.022 0.149 -9999 0 -0.721 1 1
STAT5A (dimer) -0.089 0.22 -9999 0 -0.573 18 18
SOCS1 0.026 0.049 -9999 0 -0.518 1 1
cell migration 0.066 0.162 0.428 18 -9999 0 18
SOS1 0.032 0.007 -9999 0 -9999 0 0
EPO 0.021 0.027 -9999 0 -9999 0 0
VAV1 0.003 0.122 -9999 0 -0.518 7 7
GRB10 -0.081 0.179 -9999 0 -0.453 20 20
PTPN11 0.03 0.047 -9999 0 -0.514 1 1
SCF/KIT -0.066 0.173 -9999 0 -0.451 18 18
GO:0007205 0.003 0.008 -9999 0 -9999 0 0
MAP2K1 -0.021 0.111 0.237 1 -0.302 7 8
CBL 0.032 0.005 -9999 0 -9999 0 0
KIT -0.138 0.413 -9999 0 -1.345 13 13
MAP2K2 -0.021 0.111 0.237 1 -0.302 7 8
SHC/Grb2/SOS1 -0.034 0.171 -9999 0 -0.425 16 16
STAT5A -0.092 0.226 -9999 0 -0.591 18 18
GRB2 0.032 0.006 -9999 0 -9999 0 0
response to radiation -0.092 0.179 -9999 0 -0.411 25 25
SHC/GRAP2 0.043 0.017 -9999 0 -9999 0 0
PTPRO -0.078 0.173 -9999 0 -0.462 17 17
SH2B2 -0.065 0.164 -9999 0 -0.43 18 18
DOK1 0.032 0.006 -9999 0 -9999 0 0
MATK -0.067 0.165 -9999 0 -0.436 18 18
CREBBP 0.013 0.061 -9999 0 -0.18 1 1
BCL2 -0.11 0.382 -9999 0 -1.372 10 10
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.008 0.16 -9999 0 -0.431 11 11
TBX21 -0.2 0.545 -9999 0 -1.347 23 23
B2M 0.006 0.113 -9999 0 -0.517 6 6
TYK2 0.023 0.034 -9999 0 -9999 0 0
IL12RB1 0.023 0.033 -9999 0 -9999 0 0
GADD45B -0.11 0.385 -9999 0 -1.007 17 17
IL12RB2 -0.053 0.175 -9999 0 -0.53 15 15
GADD45G -0.111 0.38 -9999 0 -0.991 17 17
natural killer cell activation 0.001 0.018 -9999 0 -0.038 15 15
RELB 0.022 0.068 -9999 0 -0.518 2 2
RELA 0.033 0 -9999 0 -9999 0 0
IL18 -0.01 0.145 -9999 0 -0.521 10 10
IL2RA -0.005 0.137 -9999 0 -0.518 9 9
IFNG -0.099 0.217 -9999 0 -0.518 28 28
STAT3 (dimer) -0.08 0.331 -9999 0 -0.787 20 20
HLA-DRB5 -0.004 0.102 -9999 0 -0.518 5 5
FASLG -0.159 0.503 -9999 0 -1.316 19 19
NF kappa B2 p52/RelB -0.113 0.418 -9999 0 -0.986 21 21
CD4 0.025 0.021 -9999 0 -9999 0 0
SOCS1 0.026 0.049 -9999 0 -0.518 1 1
EntrezGene:6955 -0.002 0.011 -9999 0 -0.031 13 13
CD3D -0.012 0.138 -9999 0 -0.521 9 9
CD3E 0.027 0.022 -9999 0 -9999 0 0
CD3G -0.064 0.203 -9999 0 -0.521 22 22
IL12Rbeta2/JAK2 -0.027 0.142 -9999 0 -0.404 14 14
CCL3 -0.127 0.424 -9999 0 -1.162 16 16
CCL4 -0.127 0.43 -9999 0 -1.106 18 18
HLA-A 0.022 0.07 -9999 0 -0.53 2 2
IL18/IL18R -0.028 0.19 -9999 0 -0.373 28 28
NOS2 -0.119 0.393 -9999 0 -0.958 20 20
IL12/IL12R/TYK2/JAK2/SPHK2 -0.006 0.149 -9999 0 -0.394 11 11
IL1R1 -0.146 0.457 -9999 0 -1.214 18 18
IL4 0.021 0.03 -9999 0 -9999 0 0
JAK2 0.021 0.033 -9999 0 -9999 0 0
EntrezGene:6957 -0.002 0.011 -9999 0 -0.03 13 13
TCR/CD3/MHC I/CD8 -0.084 0.289 -9999 0 -0.814 14 14
RAB7A -0.08 0.302 -9999 0 -0.752 18 18
lysosomal transport -0.073 0.285 -9999 0 -0.707 18 18
FOS -0.187 0.472 -9999 0 -1.262 20 20
STAT4 (dimer) -0.107 0.385 -9999 0 -0.938 20 20
STAT5A (dimer) -0.167 0.42 -9999 0 -0.984 23 23
GZMA -0.118 0.396 -9999 0 -0.973 20 20
GZMB -0.125 0.432 -9999 0 -1.209 15 15
HLX 0 0 -9999 0 -9999 0 0
LCK -0.155 0.469 -9999 0 -1.087 22 22
TCR/CD3/MHC II/CD4 -0.092 0.27 -9999 0 -0.662 18 18
IL2/IL2R 0.035 0.111 -9999 0 -0.327 9 9
MAPK14 -0.111 0.387 -9999 0 -0.978 18 18
CCR5 -0.116 0.366 -9999 0 -0.787 25 25
IL1B -0.076 0.209 -9999 0 -0.531 23 23
STAT6 -0.021 0.156 -9999 0 -0.426 8 8
STAT4 0.014 0.094 -9999 0 -0.518 4 4
STAT3 0.032 0.006 -9999 0 -9999 0 0
STAT1 0.007 0.114 -9999 0 -0.518 6 6
NFKB1 0.031 0.008 -9999 0 -9999 0 0
NFKB2 0.031 0.012 -9999 0 -9999 0 0
IL12B 0.01 0.087 -9999 0 -0.517 3 3
CD8A 0 0.007 -9999 0 -0.037 4 4
CD8B 0 0.008 -9999 0 -0.043 4 4
T-helper 1 cell differentiation 0 0 -9999 0 -9999 0 0
natural killer cell mediated cytotoxicity 0.008 0.159 0.427 11 -9999 0 11
IL2RB 0.021 0.068 -9999 0 -0.518 2 2
proteasomal ubiquitin-dependent protein catabolic process -0.092 0.341 -9999 0 -0.828 20 20
IL2RG 0.02 0.07 -9999 0 -0.518 2 2
IL12 0.006 0.08 -9999 0 -0.331 5 5
STAT5A 0.031 0.012 -9999 0 -9999 0 0
CD247 -0.002 0.01 -9999 0 -0.028 13 13
IL2 0.031 0.008 -9999 0 -9999 0 0
SPHK2 0.032 0.005 -9999 0 -9999 0 0
FRAP1 0.032 0.005 -9999 0 -9999 0 0
IL12A 0.004 0.073 -9999 0 -0.529 2 2
IL12/IL12R/TYK2/JAK2 -0.166 0.538 -9999 0 -1.269 20 20
MAP2K3 -0.119 0.397 -9999 0 -0.979 19 19
RIPK2 0.029 0.016 -9999 0 -9999 0 0
MAP2K6 -0.116 0.396 -9999 0 -1.001 18 18
regulation of dendritic cell antigen processing and presentation 0 0 -9999 0 -9999 0 0
HLA-DRA -0.005 0.129 -9999 0 -0.518 8 8
IL18RAP -0.041 0.185 -9999 0 -0.524 17 17
IL12Rbeta1/TYK2 0.034 0.045 -9999 0 -9999 0 0
EOMES -0.076 0.279 -9999 0 -0.942 10 10
STAT1 (dimer) -0.163 0.375 -9999 0 -0.874 24 24
T cell proliferation -0.062 0.269 -9999 0 -0.618 21 21
T-helper 1 cell lineage commitment 0 0 -9999 0 -9999 0 0
IL18R1 0.01 0.106 -9999 0 -0.52 5 5
CD8-positive alpha-beta T cell lineage commitment 0 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelA -0.089 0.303 -9999 0 -0.712 21 21
ATF2 -0.099 0.348 -9999 0 -0.878 18 18
TCGA08_p53

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
CDKN2A -0.041 0.115 -9999 0 -0.376 14 14
TP53 -0.028 0.086 0.191 1 -0.305 9 10
Senescence -0.033 0.09 0.191 1 -0.267 13 14
Apoptosis -0.033 0.09 0.191 1 -0.267 13 14
Activated_Oncogenes 0 0 -9999 0 -9999 0 0
MDM2 0.033 0.105 0.268 18 -0.379 1 19
MDM4 0.033 0.003 -9999 0 -9999 0 0
BMP receptor 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
BMP7/BMPR2/BMPR1A-1B/FS -0.065 0.207 -9999 0 -0.365 39 39
SMAD6-7/SMURF1 0.048 0.062 -9999 0 -0.324 3 3
NOG 0.032 0.011 -9999 0 -9999 0 0
SMAD9 -0.044 0.194 -9999 0 -0.651 11 11
SMAD4 0.023 0.067 -9999 0 -0.518 2 2
SMAD5 -0.053 0.152 -9999 0 -0.455 11 11
BMP7/USAG1 -0.159 0.244 -9999 0 -0.47 47 47
SMAD5/SKI -0.043 0.154 -9999 0 -0.428 12 12
SMAD1 0.004 0.105 -9999 0 -0.473 4 4
BMP2 -0.06 0.193 -9999 0 -0.518 20 20
SMAD1/SMAD1/SMAD4 0.012 0.111 -9999 0 -0.448 4 4
BMPR1A 0.019 0.081 -9999 0 -0.518 3 3
BMPR1B 0.025 0.025 -9999 0 -9999 0 0
BMPR1A-1B/BAMBI 0.023 0.112 -9999 0 -0.349 10 10
AHSG 0.017 0.017 -9999 0 -9999 0 0
CER1 0.03 0.01 -9999 0 -9999 0 0
BMP2-4/CER1 -0.014 0.14 -9999 0 -0.341 19 19
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.063 0.162 -9999 0 -0.445 12 12
BMP2-4 (homodimer) -0.033 0.157 -9999 0 -0.396 20 20
RGMB 0.03 0.009 -9999 0 -9999 0 0
BMP6/BMPR2/BMPR1A-1B 0.032 0.109 -9999 0 -0.327 9 9
RGMA -0.055 0.194 -9999 0 -0.518 20 20
SMURF1 0.023 0.066 -9999 0 -0.518 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.056 0.151 -9999 0 -0.429 13 13
BMP2-4/USAG1 -0.127 0.204 -9999 0 -0.381 48 48
SMAD6/SMURF1/SMAD5 -0.046 0.153 -9999 0 -0.423 11 11
SOSTDC1 -0.149 0.238 -9999 0 -0.518 39 39
BMP7/BMPR2/BMPR1A-1B -0.018 0.157 -9999 0 -0.306 29 29
SKI 0.032 0.006 -9999 0 -9999 0 0
BMP6 (homodimer) 0.002 0.107 -9999 0 -0.517 5 5
HFE2 0.023 0.066 -9999 0 -0.518 2 2
ZFYVE16 0.03 0.01 -9999 0 -9999 0 0
MAP3K7 0.031 0.011 -9999 0 -9999 0 0
BMP2-4/CHRD -0.019 0.106 -9999 0 -0.337 11 11
SMAD5/SMAD5/SMAD4 -0.047 0.164 -9999 0 -0.438 13 13
MAPK1 0.03 0.01 -9999 0 -9999 0 0
TAK1/TAB family -0.02 0.155 -9999 0 -0.417 10 10
BMP7 (homodimer) -0.075 0.211 -9999 0 -0.517 25 25
NUP214 0.033 0.004 -9999 0 -9999 0 0
BMP6/FETUA 0.006 0.08 -9999 0 -0.378 5 5
SMAD1/SKI 0.019 0.117 -9999 0 -0.466 5 5
SMAD6 0.031 0.011 -9999 0 -9999 0 0
CTDSP2 0.033 0.003 -9999 0 -9999 0 0
BMP2-4/FETUA -0.018 0.107 -9999 0 -0.337 11 11
MAP3K7IP1 0.031 0.009 -9999 0 -9999 0 0
GREM1 -0.027 0.162 -9999 0 -0.518 13 13
BMPR2 (homodimer) 0.023 0.067 -9999 0 -0.517 2 2
GADD34/PP1CA 0.055 0.041 -9999 0 -0.324 1 1
BMPR1A-1B (homodimer) 0.03 0.066 -9999 0 -0.373 3 3
CHRDL1 0.025 0.052 -9999 0 -0.518 1 1
ENDOFIN/SMAD1 0.017 0.115 -9999 0 -0.464 5 5
SMAD6-7/SMURF1/SMAD1 0.033 0.119 -9999 0 -0.412 5 5
SMAD6/SMURF1 0.023 0.066 -9999 0 -0.517 2 2
BAMBI -0.003 0.13 -9999 0 -0.518 8 8
SMURF2 0.028 0.047 -9999 0 -0.518 1 1
BMP2-4/CHRDL1 -0.017 0.15 -9999 0 -0.355 20 20
BMP2-4/GREM1 -0.048 0.177 -9999 0 -0.377 27 27
SMAD7 0.026 0.049 -9999 0 -0.518 1 1
SMAD8A/SMAD8A/SMAD4 -0.04 0.196 -9999 0 -0.561 14 14
SMAD1/SMAD6 0.015 0.119 -9999 0 -0.469 5 5
TAK1/SMAD6 0.039 0.053 -9999 0 -0.378 2 2
BMP7 -0.075 0.212 -9999 0 -0.518 25 25
BMP6 0.002 0.107 -9999 0 -0.518 5 5
MAP3K7IP2 0.032 0.006 -9999 0 -9999 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.06 0.153 -9999 0 -0.422 14 14
PPM1A 0.032 0.005 -9999 0 -9999 0 0
SMAD1/SMURF2 0.017 0.121 -9999 0 -0.482 5 5
SMAD7/SMURF1 0.033 0.064 -9999 0 -0.378 3 3
CTDSPL 0.024 0.048 -9999 0 -0.518 1 1
PPP1CA 0.032 0.005 -9999 0 -9999 0 0
XIAP 0 0 -9999 0 -9999 0 0
CTDSP1 0.032 0.006 -9999 0 -9999 0 0
PPP1R15A 0.027 0.048 -9999 0 -0.518 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.111 0.219 -9999 0 -0.513 25 25
CHRD 0.016 0.017 -9999 0 -9999 0 0
BMPR2 0.023 0.067 -9999 0 -0.518 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.071 0.171 -9999 0 -0.489 13 13
BMP4 0.023 0.053 -9999 0 -0.518 1 1
FST -0.065 0.201 -9999 0 -0.518 22 22
BMP2-4/NOG -0.013 0.144 -9999 0 -0.342 20 20
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.011 0.159 -9999 0 -0.301 28 28
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 -0.002 0.122 -9999 0 -0.364 11 11
fibroblast growth factor receptor signaling pathway -0.002 0.122 -9999 0 -0.363 11 11
LAMA1 0.023 0.031 -9999 0 -9999 0 0
PRNP 0.018 0.081 -9999 0 -0.518 3 3
GPC1/SLIT2 -0.047 0.173 -9999 0 -0.405 24 24
SMAD2 -0.018 0.094 -9999 0 -0.295 13 13
GPC1/PrPc/Cu2+ -0.004 0.119 -9999 0 -0.341 14 14
GPC1/Laminin alpha1 -0.003 0.123 -9999 0 -0.382 12 12
TDGF1 0.029 0.014 -9999 0 -9999 0 0
CRIPTO/GPC1 0.001 0.12 -9999 0 -0.376 12 12
APP/GPC1 -0.016 0.149 -9999 0 -0.396 17 17
mol:NO 0 0 -9999 0 -9999 0 0
YES1 -0.017 0.096 -9999 0 -0.321 12 12
FLT1 0.011 0.104 -9999 0 -0.518 5 5
GPC1/TGFB/TGFBR1/TGFBR2 0.015 0.116 -9999 0 -0.325 13 13
SERPINC1 0.03 0.016 -9999 0 -9999 0 0
FYN -0.021 0.104 -9999 0 -0.324 14 14
FGR -0.016 0.096 -9999 0 -0.321 12 12
positive regulation of MAPKKK cascade -0.045 0.162 -9999 0 -0.383 18 18
SLIT2 -0.032 0.167 -9999 0 -0.518 14 14
GPC1/NRG -0.03 0.181 -9999 0 -0.496 16 16
NRG1 -0.015 0.144 -9999 0 -0.518 10 10
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.008 0.121 -9999 0 -0.321 17 17
LYN -0.017 0.097 -9999 0 -0.322 12 12
mol:Spermine -0.029 0.109 -9999 0 -0.375 12 12
cell growth -0.002 0.122 -9999 0 -0.363 11 11
BMP signaling pathway 0.022 0.156 0.517 12 -9999 0 12
SRC -0.018 0.096 -9999 0 -0.321 12 12
TGFBR1 0.033 0.004 -9999 0 -9999 0 0
mol:Cu2+ 0 0 -9999 0 -9999 0 0
PLA2G2A 0.001 0.115 -9999 0 -0.518 6 6
GPC1 -0.022 0.156 -9999 0 -0.518 12 12
TGFBR1 (dimer) 0.033 0.004 -9999 0 -9999 0 0
VEGFA 0 0 -9999 0 -9999 0 0
BLK -0.028 0.104 -9999 0 -0.325 14 14
HCK -0.032 0.114 -9999 0 -0.322 18 18
FGF2 0.014 0.083 -9999 0 -0.518 3 3
FGFR1 0.016 0.067 -9999 0 -0.518 2 2
VEGFR1 homodimer 0.011 0.103 -9999 0 -0.517 5 5
TGFBR2 0.024 0.05 -9999 0 -0.518 1 1
cell death -0.016 0.148 -9999 0 -0.395 17 17
ATIII/GPC1 0.002 0.121 -9999 0 -0.378 12 12
PLA2G2A/GPC1 -0.02 0.15 -9999 0 -0.4 17 17
LCK -0.039 0.124 -9999 0 -0.326 21 21
neuron differentiation -0.03 0.18 -9999 0 -0.495 16 16
PrPc/Cu2+ 0.013 0.059 -9999 0 -0.375 3 3
APP 0.006 0.114 -9999 0 -0.518 6 6
TGFBR2 (dimer) 0.024 0.05 -9999 0 -0.517 1 1
IL1-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
UBC13/UEV1A 0.024 0 -9999 0 -9999 0 0
PRKCZ 0 0 -9999 0 -9999 0 0
MAP3K7IP2 0.032 0.006 -9999 0 -9999 0 0
ERC1 0 0 -9999 0 -9999 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.077 0.207 -9999 0 -0.501 20 20
IRAK/TOLLIP 0.037 0.007 -9999 0 -9999 0 0
IKBKB 0.029 0.01 -9999 0 -9999 0 0
IKBKG 0.032 0.01 -9999 0 -9999 0 0
IL1 alpha/IL1R2 -0.135 0.213 -9999 0 -0.424 44 44
IL1A -0.147 0.235 -9999 0 -0.518 38 38
IL1B -0.074 0.179 -9999 0 -0.427 26 26
IRAK/TRAF6/p62/Atypical PKCs 0.014 0.068 -9999 0 -0.263 6 6
IL1R2 -0.034 0.162 -9999 0 -0.518 13 13
IL1R1 0.002 0.122 -9999 0 -0.518 7 7
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.029 0.188 0.258 4 -0.486 14 18
TOLLIP 0.032 0.006 -9999 0 -9999 0 0
TICAM2 0 0 -9999 0 -9999 0 0
MAP3K3 0.031 0.011 -9999 0 -9999 0 0
TAK1/TAB1/TAB2 0.058 0.024 -9999 0 -9999 0 0
IKK complex/ELKS 0.039 0.058 -9999 0 -9999 0 0
JUN -0.029 0.089 -9999 0 -0.472 1 1
MAP3K7 0.031 0.011 -9999 0 -9999 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.054 0.201 -9999 0 -0.506 17 17
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.084 0.188 -9999 0 -0.454 23 23
PIK3R1 0.004 0.097 -9999 0 -0.518 4 4
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.084 0.185 -9999 0 -0.42 26 26
IL1 beta fragment/IL1R1/IL1RAP -0.065 0.204 -9999 0 -0.503 19 19
NFKB1 0.031 0.008 -9999 0 -9999 0 0
MAPK8 -0.013 0.07 -9999 0 -0.256 5 5
IRAK1 0.017 0 -9999 0 -9999 0 0
IL1RN/IL1R1 -0.038 0.17 -9999 0 -0.409 22 22
IRAK4 0.02 0.081 -9999 0 -0.518 3 3
PRKCI -0.009 0.11 -9999 0 -0.518 6 6
TRAF6 0.028 0.047 -9999 0 -0.518 1 1
PI3K 0.005 0.067 -9999 0 -0.378 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.067 0.227 -9999 0 -0.492 23 23
CHUK 0.028 0.047 -9999 0 -0.518 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.065 0.204 -9999 0 -0.503 19 19
IL1 beta/IL1R2 -0.081 0.199 -9999 0 -0.416 32 32
IRAK/TRAF6/TAK1/TAB1/TAB2 0.069 0.043 -9999 0 -0.266 1 1
NF kappa B1 p50/RelA -0.053 0.183 -9999 0 -0.581 11 11
IRAK3 -0.022 0.156 -9999 0 -0.518 12 12
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.06 0.2 -9999 0 -0.501 19 19
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.099 0.197 -9999 0 -0.429 28 28
IL1 alpha/IL1R1/IL1RAP -0.095 0.2 -9999 0 -0.49 23 23
RELA 0.033 0 -9999 0 -9999 0 0
MAP3K7IP1 0.031 0.009 -9999 0 -9999 0 0
SQSTM1 0.027 0.021 -9999 0 -9999 0 0
MYD88 0.03 0.01 -9999 0 -9999 0 0
IRAK/TRAF6/MEKK3 0.052 0.032 -9999 0 -0.28 1 1
IL1RAP -0.032 0.146 -9999 0 -0.518 11 11
UBE2N 0.033 0 -9999 0 -9999 0 0
IRAK/TRAF6 -0.062 0.172 -9999 0 -0.447 19 19
CASP1 0.004 0.122 -9999 0 -0.518 7 7
IL1RN/IL1R2 -0.062 0.183 -9999 0 -0.415 26 26
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.057 0.198 -9999 0 -0.496 18 18
TMEM189-UBE2V1 0 0 -9999 0 -9999 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.072 0.207 -9999 0 -0.503 20 20
PIK3CA 0.011 0.048 -9999 0 -0.518 1 1
IL1RN -0.051 0.185 -9999 0 -0.518 18 18
TRAF6/TAK1/TAB1/TAB2 0.067 0.042 -9999 0 -0.271 1 1
MAP2K6 -0.01 0.076 -9999 0 -0.265 6 6
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.003 0.1 -9999 0 -0.421 6 6
PDGFRB 0.029 0.013 -9999 0 -9999 0 0
SPHK1 -0.052 0.218 -9999 0 -0.896 8 8
mol:S1P -0.067 0.203 -9999 0 -0.758 9 9
S1P1/S1P/Gi -0.108 0.253 -9999 0 -0.565 24 24
GNAO1 0.025 0.018 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/PLCgamma1 -0.087 0.222 -9999 0 -0.486 24 24
PLCG1 -0.109 0.227 -9999 0 -0.523 24 24
mol:GTP 0 0 -9999 0 -9999 0 0
PDGFB-D/PDGFRB 0.029 0.013 -9999 0 -9999 0 0
GNAI2 0.021 0.025 -9999 0 -9999 0 0
GNAI3 0.026 0.017 -9999 0 -9999 0 0
GNAI1 -0.007 0.13 -9999 0 -0.522 8 8
mol:GDP 0 0 -9999 0 -9999 0 0
EDG1 -0.018 0.151 -9999 0 -0.705 6 6
S1P1/S1P -0.07 0.21 -9999 0 -0.599 15 15
negative regulation of cAMP metabolic process -0.104 0.242 -9999 0 -0.544 24 24
MAPK3 -0.141 0.296 -9999 0 -0.671 26 26
calcium-dependent phospholipase C activity -0.002 0.003 -9999 0 -9999 0 0
Rac1/GDP 0.024 0.004 -9999 0 -9999 0 0
RhoA/GDP 0.022 0.007 -9999 0 -9999 0 0
KDR 0.012 0.094 -9999 0 -0.35 6 6
PLCB2 -0.06 0.183 -9999 0 -0.539 14 14
RAC1 0.032 0.005 -9999 0 -9999 0 0
RhoA/GTP -0.058 0.169 -9999 0 -0.487 15 15
receptor internalization -0.064 0.19 -9999 0 -0.544 15 15
PTGS2 -0.19 0.399 -9999 0 -1.053 22 22
Rac1/GTP -0.059 0.17 -9999 0 -0.488 15 15
RHOA 0.03 0.01 -9999 0 -9999 0 0
VEGFA -0.005 0.033 -9999 0 -0.146 6 6
negative regulation of T cell proliferation -0.104 0.242 -9999 0 -0.544 24 24
GO:0007205 0 0 -9999 0 -9999 0 0
GNAZ -0.006 0.123 -9999 0 -0.522 7 7
MAPK1 -0.126 0.273 0.305 1 -0.663 23 24
S1P1/S1P/PDGFB-D/PDGFRB -0.061 0.219 -9999 0 -0.595 15 15
ABCC1 -0.011 0.125 -9999 0 -0.522 7 7
FAS signaling pathway (CD95)

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
SPTAN1 -0.013 0.069 0.207 4 -0.208 2 6
RFC1 -0.011 0.075 0.207 4 -0.224 9 13
PRKDC -0.003 0.092 0.224 10 -0.345 2 12
RIPK1 0.033 0.006 -9999 0 -9999 0 0
CASP7 -0.03 0.143 -9999 0 -0.577 7 7
FASLG/FAS/FADD/FAF1 -0.028 0.121 0.211 5 -0.312 16 21
MAP2K4 -0.042 0.189 0.268 1 -0.546 10 11
mol:ceramide -0.056 0.169 -9999 0 -0.383 21 21
GSN -0.024 0.091 0.207 4 -0.284 8 12
FASLG/FAS/FADD/FAF1/Caspase 8 -0.038 0.158 -9999 0 -0.37 19 19
FAS -0.023 0.15 -9999 0 -0.519 11 11
BID -0.028 0.047 -9999 0 -0.335 3 3
MAP3K1 0.002 0.161 0.282 3 -0.55 6 9
MAP3K7 0.03 0.012 -9999 0 -9999 0 0
RB1 -0.01 0.077 0.211 6 -0.236 4 10
CFLAR 0.017 0.093 -9999 0 -0.518 4 4
HGF/MET 0.022 0.11 -9999 0 -0.33 11 11
ARHGDIB -0.011 0.101 0.214 9 -0.303 7 16
FADD 0.025 0.018 -9999 0 -9999 0 0
actin filament polymerization 0.023 0.091 0.282 8 -0.207 4 12
NFKB1 -0.044 0.185 -9999 0 -0.753 7 7
MAPK8 -0.06 0.212 -9999 0 -0.498 19 19
DFFA -0.012 0.069 0.207 4 -0.197 6 10
DNA fragmentation during apoptosis -0.012 0.069 0.207 4 -0.207 2 6
FAS/FADD/MET 0.015 0.103 -9999 0 -0.325 9 9
CFLAR/RIP1 0.035 0.073 -9999 0 -0.379 4 4
FAIM3 0.033 0.01 -9999 0 -9999 0 0
FAF1 0.026 0.019 -9999 0 -9999 0 0
PARP1 -0.012 0.073 0.21 5 -0.208 2 7
DFFB -0.012 0.069 0.207 4 -0.208 2 6
CHUK -0.051 0.178 -9999 0 -0.644 9 9
FASLG -0.034 0.161 -9999 0 -0.521 13 13
FAS/FADD 0.002 0.105 -9999 0 -0.379 8 8
HGF 0.029 0.021 -9999 0 -9999 0 0
LMNA -0.009 0.077 0.191 8 -0.266 2 10
CASP6 -0.007 0.061 0.207 4 -0.208 2 6
CASP10 0.018 0.069 -9999 0 -0.522 2 2
CASP3 -0.009 0.08 0.239 5 -0.216 12 17
PTPN13 -0.008 0.137 -9999 0 -0.518 9 9
CASP8 -0.029 0.045 -9999 0 -0.391 2 2
IL6 -0.162 0.432 -9999 0 -1.245 17 17
MET 0.022 0.068 -9999 0 -0.518 2 2
ICAD/CAD -0.014 0.063 0.183 4 -9999 0 4
FASLG/FAS/FADD/FAF1/Caspase 10 -0.057 0.172 -9999 0 -0.389 21 21
activation of caspase activity by cytochrome c -0.027 0.047 -9999 0 -0.334 3 3
PAK2 0.073 0.127 0.227 49 -0.239 3 52
BCL2 -0.007 0.116 -9999 0 -0.517 6 6
IL27-mediated signaling events

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
TGFB1 0.031 0.008 -9999 0 -9999 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -9999 0 -9999 0 0
cytokine production during immune response 0.114 0.212 0.63 12 -9999 0 12
IL27/IL27R/JAK1 -0.106 0.264 -9999 0 -1.048 6 6
TBX21 -0.176 0.255 -9999 0 -0.666 23 23
IL12B 0.006 0.083 -9999 0 -0.518 3 3
IL12A -0.005 0.047 -9999 0 -0.376 2 2
IL6ST 0.004 0.072 -9999 0 -0.53 2 2
IL27RA/JAK1 -0.049 0.238 -9999 0 -1.37 4 4
IL27 -0.076 0.192 -9999 0 -0.529 20 20
TYK2 0.01 0.033 -9999 0 -9999 0 0
T-helper cell lineage commitment -0.011 0.113 0.193 12 -0.293 14 26
T-helper 2 cell differentiation 0.114 0.212 0.63 12 -9999 0 12
T cell proliferation during immune response 0.114 0.212 0.63 12 -9999 0 12
MAPKKK cascade -0.114 0.212 -9999 0 -0.63 12 12
STAT3 0.032 0.006 -9999 0 -9999 0 0
STAT2 0.033 0 -9999 0 -9999 0 0
STAT1 0.005 0.115 -9999 0 -0.527 6 6
IL12RB1 0.029 0.008 -9999 0 -9999 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -9999 0 -9999 0 0
IL12RB2 -0.185 0.255 -9999 0 -0.611 28 28
IL27/IL27R/JAK2/TYK2 -0.116 0.217 -9999 0 -0.643 12 12
positive regulation of T cell mediated cytotoxicity -0.114 0.212 -9999 0 -0.63 12 12
STAT1 (dimer) -0.184 0.349 -9999 0 -0.894 18 18
JAK2 0.012 0.029 -9999 0 -9999 0 0
JAK1 0.027 0.048 -9999 0 -0.519 1 1
STAT2 (dimer) -0.106 0.211 -9999 0 -0.61 12 12
T cell proliferation -0.144 0.224 -9999 0 -0.619 15 15
IL12/IL12R/TYK2/JAK2 -0.105 0.289 -9999 0 -0.912 13 13
IL17A -0.011 0.113 0.193 12 -0.293 14 26
mast cell activation 0.114 0.212 0.63 12 -9999 0 12
IFNG -0.034 0.059 -9999 0 -0.127 34 34
T cell differentiation -0.01 0.011 -9999 0 -0.026 36 36
STAT3 (dimer) -0.106 0.212 -9999 0 -0.614 12 12
STAT5A (dimer) -0.106 0.21 -9999 0 -0.586 13 13
STAT4 (dimer) -0.115 0.218 -9999 0 -0.607 14 14
STAT4 0.014 0.094 -9999 0 -0.518 4 4
T cell activation -0.004 0.023 0.123 4 -9999 0 4
IL27R/JAK2/TYK2 -0.061 0.243 -9999 0 -1.338 4 4
GATA3 0.015 0.047 -9999 0 -9999 0 0
IL18 -0.025 0.1 -9999 0 -0.377 10 10
positive regulation of mast cell cytokine production -0.104 0.205 -9999 0 -0.597 12 12
IL27/EBI3 -0.049 0.148 -9999 0 -0.392 20 20
IL27RA -0.061 0.247 -9999 0 -1.455 4 4
IL6 -0.048 0.165 -9999 0 -0.518 14 14
STAT5A 0.031 0.012 -9999 0 -9999 0 0
monocyte differentiation -0.002 0.004 -9999 0 -9999 0 0
IL2 0.017 0.085 0.484 4 -9999 0 4
IL1B -0.064 0.142 -9999 0 -0.376 23 23
EBI3 0.014 0.029 -9999 0 -9999 0 0
TNF 0 0.035 -9999 0 -0.379 1 1
LPA receptor mediated 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
GNB1/GNG2 0.017 0.079 -9999 0 -0.23 11 11
NF kappa B1 p50/RelA/I kappa B alpha 0.005 0.074 -9999 0 -0.27 3 3
AP1 -0.052 0.119 -9999 0 -0.273 26 26
mol:PIP3 -0.042 0.093 -9999 0 -0.254 19 19
AKT1 -0.002 0.116 0.239 2 -0.327 5 7
PTK2B -0.033 0.086 -9999 0 -0.197 26 26
RHOA -0.026 0.089 -9999 0 -0.288 10 10
PIK3CB 0.02 0.05 -9999 0 -0.516 1 1
mol:Ca2+ -0.018 0.052 -9999 0 -0.247 4 4
MAGI3 0.02 0.068 -9999 0 -0.518 2 2
RELA 0.033 0 -9999 0 -9999 0 0
apoptosis -0.009 0.071 -9999 0 -0.231 12 12
HRAS/GDP 0.02 0.035 -9999 0 -0.375 1 1
positive regulation of microtubule depolymerization -0.008 0.096 0.178 15 -0.221 3 18
NF kappa B1 p50/RelA -0.032 0.074 -9999 0 -0.246 8 8
endothelial cell migration -0.044 0.181 -9999 0 -0.589 13 13
ADCY4 -0.025 0.096 -9999 0 -0.27 13 13
ADCY5 -0.026 0.087 -9999 0 -0.247 13 13
ADCY6 -0.021 0.089 -9999 0 -0.243 13 13
ADCY7 -0.024 0.093 -9999 0 -0.269 12 12
ADCY1 -0.022 0.089 -9999 0 -0.247 13 13
ADCY2 -0.029 0.093 -9999 0 -0.252 14 14
ADCY3 -0.027 0.096 -9999 0 -0.258 15 15
ADCY8 -0.027 0.087 -9999 0 -0.25 13 13
ADCY9 -0.023 0.091 -9999 0 -0.259 12 12
GSK3B -0.006 0.102 0.187 17 -0.203 8 25
arachidonic acid secretion -0.033 0.099 -9999 0 -0.272 14 14
GNG2 0.032 0.005 -9999 0 -9999 0 0
TRIP6 0.007 0.065 -9999 0 -0.349 4 4
GNAO1 -0.008 0.078 -9999 0 -0.253 12 12
HRAS 0.027 0.048 -9999 0 -0.518 1 1
NFKBIA -0.017 0.066 -9999 0 -0.268 4 4
GAB1 0.021 0.068 -9999 0 -0.518 2 2
mol:GTP 0 0 -9999 0 -9999 0 0
lamellipodium assembly 0.029 0.153 -9999 0 -0.847 4 4
JUN -0.002 0.123 -9999 0 -0.518 7 7
LPA/LPA2/NHERF2 0.003 0.053 -9999 0 -0.151 8 8
TIAM1 0.006 0.173 -9999 0 -0.981 4 4
PIK3R1 0.004 0.096 -9999 0 -0.517 4 4
mol:IP3 -0.017 0.052 -9999 0 -0.251 4 4
PLCB3 0.002 0.049 -9999 0 -0.29 2 2
FOS -0.028 0.151 -9999 0 -0.518 11 11
positive regulation of mitosis -0.033 0.099 -9999 0 -0.272 14 14
LPA/LPA1-2-3 -0.019 0.066 -9999 0 -0.22 13 13
mol:Ca ++ 0 0 -9999 0 -9999 0 0
JNK cascade 0 0.001 -9999 0 -9999 0 0
BCAR1 0.032 0.005 -9999 0 -9999 0 0
stress fiber formation -0.009 0.071 -9999 0 -0.268 3 3
GNAZ -0.026 0.107 -9999 0 -0.29 18 18
EGFR/PI3K-beta/Gab1 -0.038 0.1 -9999 0 -0.263 19 19
positive regulation of dendritic cell cytokine production -0.019 0.066 -9999 0 -0.219 13 13
LPA/LPA2/MAGI-3 0.003 0.052 -9999 0 -0.134 11 11
ARHGEF1 -0.002 0.08 0.193 5 -0.221 12 17
GNAI2 -0.01 0.078 -9999 0 -0.253 12 12
GNAI3 -0.009 0.079 -9999 0 -0.245 13 13
GNAI1 -0.026 0.108 -9999 0 -0.287 19 19
LPA/LPA3 -0.01 0.033 -9999 0 -0.11 13 13
LPA/LPA2 -0.01 0.033 -9999 0 -0.109 13 13
LPA/LPA1 -0.024 0.088 -9999 0 -0.29 13 13
HB-EGF/EGFR -0.059 0.173 -9999 0 -0.388 27 27
HBEGF -0.054 0.143 -9999 0 -0.379 22 22
mol:DAG -0.017 0.052 -9999 0 -0.251 4 4
cAMP biosynthetic process -0.031 0.106 0.189 2 -0.278 14 16
NFKB1 0.031 0.008 -9999 0 -9999 0 0
SRC 0.03 0.013 -9999 0 -9999 0 0
GNB1 0.032 0.006 -9999 0 -9999 0 0
LYN -0.018 0.063 -9999 0 -0.249 4 4
GNAQ -0.008 0.026 -9999 0 -0.086 13 13
LPAR2 -0.001 0.001 -9999 0 -9999 0 0
LPAR3 0 0.001 -9999 0 -9999 0 0
LPAR1 -0.015 0.051 -9999 0 -0.169 13 13
IL8 -0.195 0.224 -9999 0 -0.482 46 46
PTK2 -0.006 0.072 -9999 0 -0.212 14 14
Rac1/GDP 0.024 0.004 -9999 0 -9999 0 0
CASP3 -0.009 0.071 -9999 0 -0.232 12 12
EGFR -0.015 0.144 -9999 0 -0.518 10 10
PLCG1 -0.006 0.045 -9999 0 -0.156 8 8
PLD2 -0.007 0.076 -9999 0 -0.218 15 15
G12/G13 0.011 0.086 -9999 0 -0.229 14 14
PI3K-beta -0.035 0.099 -9999 0 -0.336 7 7
cell migration 0.017 0.062 -9999 0 -0.247 4 4
SLC9A3R2 0.02 0.069 -9999 0 -0.518 2 2
PXN -0.009 0.072 -9999 0 -0.272 3 3
HRAS/GTP -0.033 0.101 -9999 0 -0.278 14 14
RAC1 0.032 0.005 -9999 0 -9999 0 0
MMP9 -0.018 0.156 -9999 0 -0.518 12 12
PRKCE 0.03 0.01 -9999 0 -9999 0 0
PRKCD -0.018 0.049 -9999 0 -0.262 3 3
Gi(beta/gamma) -0.026 0.102 -9999 0 -0.28 13 13
mol:LPA -0.015 0.051 -9999 0 -0.169 13 13
TRIP6/p130 Cas/FAK1/Paxillin 0.014 0.084 -9999 0 -0.297 2 2
MAPKKK cascade -0.033 0.099 -9999 0 -0.272 14 14
contractile ring contraction involved in cytokinesis -0.028 0.09 -9999 0 -0.278 11 11
mol:GDP 0 0 -9999 0 -9999 0 0
GNA14 -0.006 0.055 -9999 0 -0.14 13 13
GNA15 -0.01 0.069 -9999 0 -0.215 10 10
GNA12 0.031 0.007 -9999 0 -9999 0 0
GNA13 0.027 0.048 -9999 0 -0.518 1 1
MAPT -0.008 0.097 0.18 15 -0.226 3 18
GNA11 0.001 0.038 -9999 0 -0.139 4 4
Rac1/GTP 0.029 0.162 -9999 0 -0.897 4 4
MMP2 -0.044 0.182 -9999 0 -0.592 13 13
EGFR-dependent Endothelin 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
HRAS 0.027 0.048 -9999 0 -0.518 1 1
EGFR -0.014 0.144 -9999 0 -0.518 10 10
EGF/EGFR -0.069 0.171 -9999 0 -0.34 33 33
EGF/EGFR dimer/SHC/GRB2/SOS1 0.005 0.134 -9999 0 -0.323 15 15
mol:GTP 0 0 -9999 0 -9999 0 0
EDNRA 0.002 0.106 -9999 0 -0.518 5 5
response to oxidative stress 0 0 -9999 0 -9999 0 0
EGF -0.032 0.15 -9999 0 -0.518 11 11
EGF/EGFR dimer/SHC -0.017 0.141 -9999 0 -0.365 16 16
mol:GDP 0.001 0.13 -9999 0 -0.319 15 15
mol:Ca2+ 0 0 -9999 0 -9999 0 0
EDN1 -0.046 0.181 -9999 0 -0.518 17 17
GRB2/SOS1 0.045 0.013 -9999 0 -9999 0 0
HRAS/GTP -0.012 0.118 -9999 0 -0.302 16 16
SHC1 0.03 0.009 -9999 0 -9999 0 0
HRAS/GDP -0.001 0.129 -9999 0 -0.308 16 16
FRAP1 -0.029 0.124 -9999 0 -0.309 15 15
EGF/EGFR dimer -0.038 0.16 -9999 0 -0.42 18 18
SOS1 0.032 0.007 -9999 0 -9999 0 0
GRB2 0.032 0.006 -9999 0 -9999 0 0
ETA receptor/Endothelin-1 -0.039 0.159 -9999 0 -0.394 21 21
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.012 0.115 -9999 0 -0.349 13 13
EPHB2 -0.026 0.162 -9999 0 -0.518 13 13
Syndecan-2/TACI 0.009 0.078 -9999 0 -0.314 7 7
LAMA1 0.023 0.031 -9999 0 -9999 0 0
Syndecan-2/alpha2 ITGB1 -0.013 0.151 -9999 0 -0.338 21 21
HRAS 0.027 0.048 -9999 0 -0.518 1 1
Syndecan-2/CASK -0.006 0.066 -9999 0 -0.311 6 6
ITGA5 0.022 0.068 -9999 0 -0.518 2 2
BAX -0.004 0.054 -9999 0 -9999 0 0
EPB41 0.032 0.006 -9999 0 -9999 0 0
positive regulation of cell-cell adhesion 0.011 0.07 -9999 0 -0.281 7 7
LAMA3 -0.014 0.144 -9999 0 -0.518 10 10
EZR 0 0 -9999 0 -9999 0 0
mol:PI-4-5-P2 0 0 -9999 0 -9999 0 0
CAV2 -0.037 0.182 -9999 0 -0.518 17 17
Syndecan-2/MMP2 -0.02 0.131 -9999 0 -0.371 15 15
RP11-540L11.1 0 0 -9999 0 -9999 0 0
alpha2 ITGB1 -0.003 0.136 -9999 0 -0.402 13 13
dendrite morphogenesis -0.019 0.126 -9999 0 -0.349 16 16
Syndecan-2/GM-CSF -0.021 0.118 -9999 0 -0.358 13 13
determination of left/right symmetry -0.005 0.079 -9999 0 -0.367 6 6
Syndecan-2/PKC delta 0.012 0.073 -9999 0 -0.314 6 6
GNB2L1 0.03 0.009 -9999 0 -9999 0 0
MAPK3 -0.02 0.113 0.197 5 -0.328 13 18
MAPK1 -0.021 0.108 0.197 4 -0.331 12 16
Syndecan-2/RACK1 0.024 0.073 -9999 0 -0.269 7 7
NF1 0.028 0.047 -9999 0 -0.518 1 1
FGFR/FGF/Syndecan-2 -0.005 0.079 -9999 0 -0.367 6 6
ITGA2 -0.019 0.156 -9999 0 -0.518 12 12
MAPK8 -0.003 0.066 -9999 0 -0.309 6 6
Syndecan-2/alpha2/beta1 Integrin 0.002 0.126 -9999 0 -0.308 16 16
Syndecan-2/Kininogen 0.007 0.048 -9999 0 -0.314 2 2
ITGB1 0.023 0.067 -9999 0 -0.518 2 2
SRC 0.011 0.067 -9999 0 -0.266 5 5
Syndecan-2/CASK/Protein 4.1 0.013 0.066 -9999 0 -0.285 6 6
extracellular matrix organization 0.015 0.068 -9999 0 -0.313 5 5
actin cytoskeleton reorganization -0.012 0.115 -9999 0 -0.348 13 13
Syndecan-2/Caveolin-2/Ras -0.012 0.13 -9999 0 -0.302 21 21
Syndecan-2/Laminin alpha3 -0.005 0.099 -9999 0 -0.315 12 12
Syndecan-2/RasGAP 0.035 0.076 -9999 0 -0.26 7 7
alpha5/beta1 Integrin 0.032 0.074 -9999 0 -0.378 4 4
PRKCD 0.029 0.014 -9999 0 -9999 0 0
Syndecan-2 dimer -0.019 0.127 -9999 0 -0.35 16 16
GO:0007205 0.003 0 -9999 0 -9999 0 0
DNA mediated transformation 0 0 -9999 0 -9999 0 0
Syndecan-2/RasGAP/Src 0.021 0.062 -9999 0 -0.262 5 5
RHOA 0.03 0.01 -9999 0 -9999 0 0
SDCBP 0.027 0.047 -9999 0 -0.518 1 1
TNFRSF13B 0.026 0.049 -9999 0 -0.518 1 1
RASA1 0.029 0.01 -9999 0 -9999 0 0
alpha2/beta1 Integrin -0.003 0.136 -9999 0 -0.402 13 13
Syndecan-2/Synbindin 0.014 0.073 -9999 0 -0.314 6 6
TGFB1 0.031 0.008 -9999 0 -9999 0 0
CASP3 0.003 0.069 0.197 3 -0.284 6 9
FN1 -0.009 0.131 -9999 0 -0.518 8 8
Syndecan-2/IL8 -0.076 0.162 -9999 0 -0.344 34 34
SDC2 -0.005 0.079 -9999 0 -0.367 6 6
KNG1 0.017 0.017 -9999 0 -9999 0 0
Syndecan-2/Neurofibromin 0.011 0.078 -9999 0 -0.314 7 7
TRAPPC4 0.033 0.004 -9999 0 -9999 0 0
CSF2 -0.024 0.138 -9999 0 -0.518 9 9
Syndecan-2/TGFB1 0.015 0.068 -9999 0 -0.314 5 5
Syndecan-2/Syntenin/PI-4-5-P2 0.011 0.07 -9999 0 -0.283 7 7
Syndecan-2/Ezrin 0.011 0.066 -9999 0 -0.285 6 6
PRKACA 0.007 0.073 0.197 5 -0.287 6 11
angiogenesis -0.076 0.161 -9999 0 -0.343 34 34
MMP2 -0.024 0.156 -9999 0 -0.518 12 12
IL8 -0.122 0.228 -9999 0 -0.518 33 33
calcineurin-NFAT signaling pathway 0.009 0.078 -9999 0 -0.313 7 7
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.033 0.144 -9999 0 -0.28 30 30
positive regulation of NF-kappaB transcription factor activity 0 0.001 -9999 0 -9999 0 0
CRKL 0.029 0.011 -9999 0 -9999 0 0
STAT1 (dimer)/Cbp/p300 -0.045 0.189 0.303 1 -0.477 12 13
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.009 0.1 -9999 0 -0.346 7 7
antigen processing and presentation of peptide antigen via MHC class I -0.032 0.087 -9999 0 -0.299 7 7
CaM/Ca2+ -0.03 0.139 -9999 0 -0.268 29 29
RAP1A 0.023 0.066 -9999 0 -0.518 2 2
STAT1 (dimer)/SHP2 -0.054 0.169 0.277 1 -0.33 29 30
AKT1 0.019 0.146 0.323 4 -0.386 3 7
MAP2K1 -0.069 0.127 0.281 1 -0.353 9 10
MAP3K11 -0.052 0.129 0.284 1 -0.271 29 30
IFNGR1 -0.006 0.116 -9999 0 -0.523 6 6
mol:GTP 0 0 -9999 0 -9999 0 0
CaM/Ca2+/CAMKII -0.017 0.119 -9999 0 -0.459 5 5
Rap1/GTP -0.044 0.099 -9999 0 -0.365 3 3
CRKL/C3G 0.043 0.016 -9999 0 -9999 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.027 0.153 -9999 0 -0.29 30 30
CEBPB -0.058 0.175 -9999 0 -0.509 9 9
STAT3 0.032 0.006 -9999 0 -9999 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.028 0.195 -9999 0 -0.906 3 3
STAT1 -0.064 0.164 0.284 1 -0.33 29 30
CALM1 0.032 0.006 -9999 0 -9999 0 0
IFN-gamma (dimer) -0.101 0.218 -9999 0 -0.52 28 28
PIK3CA 0.011 0.048 -9999 0 -0.518 1 1
STAT1 (dimer)/PIAS1 -0.048 0.162 0.288 1 -0.499 8 9
CEBPB/PTGES2/Cbp/p300 -0.043 0.127 -9999 0 -0.35 10 10
mol:Ca2+ -0.035 0.141 -9999 0 -0.277 30 30
MAPK3 -0.064 0.174 -9999 0 -0.585 7 7
STAT1 (dimer) -0.005 0.147 -9999 0 -0.425 7 7
MAPK1 -0.067 0.179 -9999 0 -0.606 7 7
JAK2 0.013 0.032 -9999 0 -9999 0 0
PIK3R1 0.004 0.097 -9999 0 -0.518 4 4
JAK1 0.013 0.057 -9999 0 -0.533 1 1
CAMK2D 0.022 0.067 -9999 0 -0.518 2 2
DAPK1 -0.04 0.147 -9999 0 -0.564 5 5
SMAD7 0.011 0.074 0.222 1 -0.229 3 4
CBL/CRKL/C3G -0.022 0.126 0.29 1 -0.351 3 4
PI3K -0.032 0.105 -9999 0 -0.337 6 6
IFNG -0.101 0.218 -9999 0 -0.521 28 28
apoptosis -0.026 0.121 -9999 0 -0.432 5 5
CAMK2G 0.031 0.012 -9999 0 -9999 0 0
STAT3 (dimer) 0.032 0.006 -9999 0 -9999 0 0
CAMK2A 0.031 0.007 -9999 0 -9999 0 0
CAMK2B 0.019 0.056 -9999 0 -0.518 1 1
FRAP1 0.009 0.136 0.324 3 -0.362 3 6
PRKCD 0.02 0.148 0.31 5 -0.39 3 8
RAP1B 0.031 0.007 -9999 0 -9999 0 0
negative regulation of cell growth -0.032 0.087 -9999 0 -0.299 7 7
PTPN2 0.032 0.005 -9999 0 -9999 0 0
EP300 -0.001 0.129 -9999 0 -0.518 8 8
IRF1 -0.068 0.159 0.268 2 -0.519 9 11
STAT1 (dimer)/PIASy -0.053 0.164 0.285 1 -0.481 9 10
SOCS1 0.006 0.183 -9999 0 -1.188 3 3
mol:GDP -0.023 0.12 0.272 1 -0.337 3 4
CASP1 0.007 0.093 0.189 2 -0.267 8 10
PTGES2 0.033 0.004 -9999 0 -9999 0 0
IRF9 -0.018 0.057 0.144 1 -9999 0 1
mol:PI-3-4-5-P3 -0.035 0.099 -9999 0 -0.285 12 12
RAP1/GDP -0.03 0.112 -9999 0 -0.372 3 3
CBL -0.053 0.128 0.283 1 -0.271 29 30
MAP3K1 -0.06 0.138 0.284 1 -0.285 31 32
PIAS1 0.032 0.006 -9999 0 -9999 0 0
PIAS4 0.032 0.004 -9999 0 -9999 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.032 0.087 -9999 0 -0.299 7 7
PTPN11 -0.05 0.135 0.304 1 -0.278 30 31
CREBBP 0.032 0.006 -9999 0 -9999 0 0
RAPGEF1 0.033 0.004 -9999 0 -9999 0 0
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.017 0.171 -9999 0 -0.418 18 18
alphaM/beta2 Integrin/GPIbA 0.015 0.118 -9999 0 -0.382 9 9
alphaM/beta2 Integrin/proMMP-9 -0.012 0.164 -9999 0 -0.4 18 18
PLAUR -0.002 0.129 -9999 0 -0.518 8 8
HMGB1 0.024 0.025 -9999 0 -9999 0 0
alphaM/beta2 Integrin/Talin 0.021 0.11 -9999 0 -0.395 7 7
AGER -0.013 0.111 -9999 0 -0.46 6 6
RAP1A 0.023 0.066 -9999 0 -0.518 2 2
SELPLG 0.02 0.081 -9999 0 -0.518 3 3
mol:LDL 0 0 -9999 0 -9999 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.012 0.156 -9999 0 -0.316 22 22
mol:GTP 0 0 -9999 0 -9999 0 0
MMP9 -0.017 0.156 -9999 0 -0.518 12 12
CYR61 -0.012 0.138 -9999 0 -0.518 9 9
TLN1 0.029 0.01 -9999 0 -9999 0 0
Rap1/GTP 0.02 0.141 -9999 0 -0.466 7 7
RHOA 0.03 0.01 -9999 0 -9999 0 0
P-selectin oligomer -0.063 0.201 -9999 0 -0.517 22 22
MYH2 0.002 0.137 -9999 0 -0.49 6 6
MST1R -0.017 0.144 -9999 0 -0.518 10 10
leukocyte activation during inflammatory response 0.017 0.105 -9999 0 -0.332 9 9
APOB 0.027 0.047 -9999 0 -0.518 1 1
mol:GDP 0 0 -9999 0 -9999 0 0
complement component iC3b receptor activity 0 0 -9999 0 -9999 0 0
MMP2 -0.024 0.156 -9999 0 -0.518 12 12
JAM3 0.016 0.072 -9999 0 -0.518 2 2
GP1BA 0.025 0.027 -9999 0 -9999 0 0
alphaM/beta2 Integrin/CTGF 0.011 0.143 -9999 0 -0.42 11 11
alphaM/beta2 Integrin 0 0.145 -9999 0 -0.453 9 9
JAM3 homodimer 0.016 0.072 -9999 0 -0.517 2 2
ICAM2 0.026 0.049 -9999 0 -0.518 1 1
ICAM1 0.004 0.106 -9999 0 -0.518 5 5
phagocytosis triggered by activation of immune response cell surface activating receptor 0.002 0.144 -9999 0 -0.448 9 9
cell adhesion 0.014 0.117 -9999 0 -0.38 9 9
NFKB1 -0.063 0.171 -9999 0 -0.436 17 17
THY1 0.016 0.083 -9999 0 -0.518 3 3
RhoA/GDP 0.022 0.007 -9999 0 -9999 0 0
Lipoprotein(a) 0.032 0.036 -9999 0 -0.321 1 1
alphaM/beta2 Integrin/LRP/tPA -0.011 0.15 -9999 0 -0.355 18 18
IL6 -0.111 0.257 -9999 0 -0.782 15 15
ITGB2 -0.01 0.134 -9999 0 -0.533 8 8
elevation of cytosolic calcium ion concentration -0.021 0.193 -9999 0 -0.441 19 19
alphaM/beta2 Integrin/JAM2/JAM3 0.007 0.155 -9999 0 -0.4 14 14
JAM2 0.005 0.114 -9999 0 -0.518 6 6
alphaM/beta2 Integrin/ICAM1 -0.007 0.175 -9999 0 -0.398 18 18
alphaM/beta2 Integrin/uPA/Plg -0.003 0.154 -9999 0 -0.365 17 17
RhoA/GTP -0.03 0.13 -9999 0 -0.497 7 7
positive regulation of phagocytosis -0.001 0.173 -9999 0 -0.644 7 7
Ron/MSP 0.007 0.112 -9999 0 -0.378 10 10
alphaM/beta2 Integrin/uPAR/uPA -0.02 0.196 -9999 0 -0.445 19 19
alphaM/beta2 Integrin/uPAR 0.004 0.166 -9999 0 -0.511 11 11
PLAU -0.023 0.151 -9999 0 -0.518 11 11
PLAT -0.031 0.15 -9999 0 -0.518 11 11
actin filament polymerization 0.004 0.132 -9999 0 -0.466 6 6
MST1 0.03 0.01 -9999 0 -9999 0 0
alphaM/beta2 Integrin/lipoprotein(a) 0.022 0.109 -9999 0 -0.335 9 9
TNF -0.069 0.165 -9999 0 -0.454 13 13
RAP1B 0.031 0.007 -9999 0 -9999 0 0
alphaM/beta2 Integrin/uPA -0.019 0.16 -9999 0 -0.392 18 18
fibrinolysis -0.004 0.152 -9999 0 -0.363 17 17
HCK 0.006 0.113 -9999 0 -0.518 6 6
dendritic cell antigen processing and presentation 0.002 0.144 -9999 0 -0.448 9 9
VTN 0.032 0.006 -9999 0 -9999 0 0
alphaM/beta2 Integrin/CYR61 -0.004 0.163 -9999 0 -0.469 12 12
LPA 0.027 0.018 -9999 0 -9999 0 0
LRP1 0.033 0 -9999 0 -9999 0 0
cell migration -0.047 0.183 -9999 0 -0.405 24 24
FN1 -0.009 0.131 -9999 0 -0.518 8 8
alphaM/beta2 Integrin/Thy1 0.009 0.133 -9999 0 -0.395 11 11
MPO 0.027 0.049 -9999 0 -0.518 1 1
KNG1 0.017 0.017 -9999 0 -9999 0 0
RAP1/GDP 0.035 0.045 -9999 0 -0.321 2 2
ROCK1 0.003 0.14 -9999 0 -0.467 7 7
ELA2 0.031 0.011 -9999 0 -9999 0 0
PLG 0.032 0.006 -9999 0 -9999 0 0
CTGF 0.016 0.093 -9999 0 -0.518 4 4
alphaM/beta2 Integrin/Hck 0.006 0.153 -9999 0 -0.492 10 10
ITGAM 0.015 0.073 -9999 0 -0.54 2 2
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.031 0.204 -9999 0 -0.419 24 24
HP 0.008 0.096 -9999 0 -0.518 4 4
leukocyte adhesion -0.039 0.182 -9999 0 -0.451 16 16
SELP -0.063 0.201 -9999 0 -0.518 22 22
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.037 0.153 -9999 0 -0.413 15 15
Syndecan-4/Syndesmos -0.029 0.173 -9999 0 -0.479 14 14
positive regulation of JNK cascade -0.07 0.231 -9999 0 -0.521 24 24
Syndecan-4/ADAM12 -0.047 0.203 -9999 0 -0.513 17 17
CCL5 -0.018 0.156 -9999 0 -0.518 12 12
Rac1/GDP 0.024 0.004 -9999 0 -9999 0 0
DNM2 0.031 0.007 -9999 0 -9999 0 0
ITGA5 0.022 0.068 -9999 0 -0.518 2 2
SDCBP 0.027 0.047 -9999 0 -0.518 1 1
PLG 0.03 0.018 -9999 0 -9999 0 0
ADAM12 -0.007 0.137 -9999 0 -0.518 9 9
mol:GTP 0 0 -9999 0 -9999 0 0
NUDT16L1 0.032 0.006 -9999 0 -9999 0 0
mol:PI-4-5-P2 0 0 -9999 0 -9999 0 0
Syndecan-4/PKC alpha -0.034 0.018 -9999 0 -9999 0 0
Syndecan-4/Laminin alpha1 -0.032 0.171 -9999 0 -0.485 13 13
Syndecan-4/CXCL12/CXCR4 -0.075 0.247 -9999 0 -0.555 24 24
Syndecan-4/Laminin alpha3 -0.051 0.181 -9999 0 -0.503 12 12
MDK -0.003 0.13 -9999 0 -0.518 8 8
Syndecan-4/FZD7 -0.061 0.185 -9999 0 -0.496 14 14
Syndecan-4/Midkine -0.05 0.18 -9999 0 -0.471 16 16
FZD7 -0.038 0.177 -9999 0 -0.518 16 16
Syndecan-4/FGFR1/FGF -0.038 0.176 -9999 0 -0.498 11 11
THBS1 0.023 0.067 -9999 0 -0.518 2 2
integrin-mediated signaling pathway -0.052 0.184 -9999 0 -0.483 15 15
positive regulation of MAPKKK cascade -0.07 0.231 -9999 0 -0.521 24 24
Syndecan-4/TACI -0.032 0.176 -9999 0 -0.476 15 15
CXCR4 -0.037 0.177 -9999 0 -0.518 16 16
cell adhesion -0.01 0.104 0.206 2 -0.34 10 12
Syndecan-4/Dynamin -0.028 0.173 -9999 0 -0.479 14 14
Syndecan-4/TSP1 -0.036 0.179 -9999 0 -0.476 15 15
Syndecan-4/GIPC -0.031 0.175 -9999 0 -0.471 15 15
Syndecan-4/RANTES -0.052 0.214 -9999 0 -0.553 17 17
ITGB1 0.023 0.067 -9999 0 -0.518 2 2
LAMA1 0.023 0.031 -9999 0 -9999 0 0
LAMA3 -0.014 0.144 -9999 0 -0.518 10 10
RAC1 0.032 0.005 -9999 0 -9999 0 0
PRKCA 0.029 0.176 0.888 5 -0.489 1 6
Syndecan-4/alpha-Actinin -0.032 0.176 -9999 0 -0.476 15 15
TFPI -0.004 0.124 -9999 0 -0.518 7 7
F2 0.026 0.024 -9999 0 -9999 0 0
alpha5/beta1 Integrin 0.032 0.074 -9999 0 -0.378 4 4
positive regulation of cell adhesion -0.053 0.171 -9999 0 -0.495 12 12
ACTN1 0.029 0.018 -9999 0 -9999 0 0
TNC -0.022 0.145 -9999 0 -0.518 10 10
Syndecan-4/CXCL12 -0.058 0.206 -9999 0 -0.509 19 19
FGF6 0.01 0.104 -9999 0 -0.518 5 5
RHOA 0.03 0.01 -9999 0 -9999 0 0
CXCL12 -0.029 0.162 -9999 0 -0.518 13 13
TNFRSF13B 0.026 0.049 -9999 0 -0.518 1 1
FGF2 0.014 0.083 -9999 0 -0.518 3 3
FGFR1 0.016 0.067 -9999 0 -0.518 2 2
Syndecan-4/PI-4-5-P2 -0.048 0.165 -9999 0 -0.474 15 15
mol:GDP 0 0 -9999 0 -9999 0 0
FN1 -0.011 0.13 -9999 0 -0.512 8 8
cell migration -0.016 0.013 -9999 0 -9999 0 0
PRKCD 0.027 0.02 -9999 0 -9999 0 0
vasculogenesis -0.034 0.173 -9999 0 -0.46 15 15
SDC4 -0.044 0.173 -9999 0 -0.499 15 15
Syndecan-4/Tenascin C -0.054 0.19 -9999 0 -0.502 15 15
Syndecan-4/PI-4-5-P2/PKC alpha -0.027 0.014 -9999 0 -9999 0 0
Syndecan-4/Syntenin -0.032 0.179 -9999 0 -0.474 16 16
MMP9 -0.018 0.156 -9999 0 -0.515 12 12
Rac1/GTP -0.011 0.106 0.208 2 -0.349 10 12
cytoskeleton organization -0.027 0.168 -9999 0 -0.462 14 14
GIPC1 0.028 0.047 -9999 0 -0.518 1 1
Syndecan-4/TFPI -0.049 0.185 -9999 0 -0.477 17 17
HIF-2-alpha transcription factor network

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
MMP14 0.019 0.179 -9999 0 -1.134 3 3
oxygen homeostasis 0.002 0.011 -9999 0 -9999 0 0
TCEB2 0.032 0.005 -9999 0 -9999 0 0
TCEB1 0.032 0.006 -9999 0 -9999 0 0
VHL/Elongin B/Elongin C/HIF2A 0.003 0.167 -9999 0 -0.387 13 13
EPO 0.001 0.211 -9999 0 -0.52 8 8
FIH (dimer) 0.028 0.025 -9999 0 -9999 0 0
APEX1 0.025 0.03 -9999 0 -9999 0 0
SERPINE1 -0.026 0.272 0.454 1 -0.582 18 19
FLT1 -0.063 0.319 -9999 0 -0.98 13 13
ADORA2A -0.006 0.227 0.452 1 -0.542 10 11
germ cell development 0.002 0.233 0.449 1 -0.516 12 13
SLC11A2 0 0.242 0.454 1 -0.571 10 11
BHLHE40 -0.021 0.224 -9999 0 -0.523 14 14
HIF1AN 0.028 0.025 -9999 0 -9999 0 0
HIF2A/ARNT/SIRT1 0.013 0.184 -9999 0 -0.427 11 11
ETS1 0.024 0.076 -9999 0 -0.406 3 3
CITED2 0.04 0.041 -9999 0 -9999 0 0
KDR -0.034 0.246 -9999 0 -0.856 9 9
PGK1 -0.002 0.248 0.454 1 -0.569 12 13
SIRT1 0.032 0.006 -9999 0 -9999 0 0
response to hypoxia 0 0 -9999 0 -9999 0 0
HIF2A/ARNT 0.007 0.277 -9999 0 -0.626 12 12
EPAS1 -0.02 0.157 -9999 0 -0.406 13 13
SP1 0.034 0.049 -9999 0 -0.517 1 1
ABCG2 -0.019 0.238 -9999 0 -0.572 12 12
EFNA1 -0.011 0.244 -9999 0 -0.616 10 10
FXN -0.006 0.228 0.395 3 -0.552 10 13
POU5F1 0 0.239 0.454 1 -0.535 12 13
neuron apoptosis -0.007 0.27 0.608 12 -9999 0 12
EP300 -0.001 0.129 -9999 0 -0.518 8 8
EGLN3 -0.055 0.182 -9999 0 -0.523 17 17
EGLN2 0.021 0.053 -9999 0 -0.529 1 1
EGLN1 0.019 0.072 -9999 0 -0.52 2 2
VHL/Elongin B/Elongin C 0.051 0.054 -9999 0 -0.324 2 2
VHL 0.02 0.068 -9999 0 -0.518 2 2
ARNT 0.023 0.03 -9999 0 -9999 0 0
SLC2A1 -0.039 0.27 -9999 0 -0.585 18 18
TWIST1 -0.042 0.286 0.452 1 -0.644 18 19
ELK1 0.039 0.006 -9999 0 -9999 0 0
HIF2A/ARNT/Cbp/p300 0 0.207 -9999 0 -0.433 14 14
VEGFA -0.021 0.224 -9999 0 -0.523 14 14
CREBBP 0.032 0.006 -9999 0 -9999 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.002 0.072 -9999 0 -0.262 9 9
epithelial cell differentiation 0.037 0.088 -9999 0 -0.276 9 9
CYFIP2 0.025 0.049 -9999 0 -0.518 1 1
ENAH -0.01 0.107 0.268 3 -0.336 2 5
EGFR -0.014 0.144 -9999 0 -0.518 10 10
EPHA2 -0.006 0.13 -9999 0 -0.518 8 8
MYO6 -0.031 0.073 -9999 0 -0.267 11 11
CTNNB1 0.028 0.017 -9999 0 -9999 0 0
ABI1/Sra1/Nap1 0.052 0.045 -9999 0 -0.324 1 1
AQP5 -0.077 0.18 -9999 0 -0.51 18 18
CTNND1 0.025 0.066 -9999 0 -0.518 2 2
mol:PI-4-5-P2 -0.029 0.069 -9999 0 -0.264 10 10
regulation of calcium-dependent cell-cell adhesion -0.041 0.089 -9999 0 -0.281 15 15
EGF -0.032 0.15 -9999 0 -0.518 11 11
NCKAP1 0.028 0.023 -9999 0 -9999 0 0
AQP3 -0.092 0.173 -9999 0 -0.458 22 22
cortical microtubule organization 0.037 0.088 -9999 0 -0.276 9 9
GO:0000145 -0.028 0.066 -9999 0 -0.252 10 10
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.043 0.091 -9999 0 -0.278 9 9
MLLT4 0.032 0.006 -9999 0 -9999 0 0
ARF6/GDP -0.052 0.092 -9999 0 -0.28 17 17
ARF6 0.031 0.012 -9999 0 -9999 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.023 0.113 -9999 0 -0.332 10 10
mol:Ca2+ 0 0 -9999 0 -9999 0 0
VASP -0.011 0.052 -9999 0 -9999 0 0
PVRL2 0.03 0.013 -9999 0 -9999 0 0
ZYX -0.03 0.07 -9999 0 -0.266 10 10
ARF6/GTP 0.027 0.111 -9999 0 -0.311 10 10
CDH1 0.002 0.122 -9999 0 -0.518 7 7
EGFR/EGFR/EGF/EGF -0.031 0.139 -9999 0 -0.298 25 25
RhoA/GDP 0.039 0.086 -9999 0 -0.262 9 9
actin cytoskeleton organization -0.032 0.076 -9999 0 -0.285 10 10
IGF-1R heterotetramer -0.01 0.143 -9999 0 -0.517 10 10
GIT1 0.024 0.067 -9999 0 -0.518 2 2
IGF1R -0.01 0.144 -9999 0 -0.518 10 10
IGF1 -0.054 0.185 -9999 0 -0.518 18 18
DIAPH1 0.021 0.161 -9999 0 -0.661 2 2
Wnt receptor signaling pathway -0.037 0.088 0.276 9 -9999 0 9
RHOA 0.03 0.01 -9999 0 -9999 0 0
RhoA/GTP -0.052 0.091 -9999 0 -0.279 16 16
CTNNA1 0.031 0.008 -9999 0 -9999 0 0
VCL -0.033 0.078 -9999 0 -0.291 10 10
EFNA1 0.022 0.067 -9999 0 -0.518 2 2
LPP -0.02 0.051 -9999 0 -0.265 5 5
Ephrin A1/EPHA2 0.006 0.112 -9999 0 -0.278 16 16
SEC6/SEC8 -0.029 0.056 -9999 0 -0.262 7 7
MGAT3 -0.042 0.091 -9999 0 -0.286 15 15
HGF/MET 0.026 0.089 -9999 0 -0.264 10 10
HGF 0.029 0.021 -9999 0 -9999 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.002 0.073 -9999 0 -0.264 9 9
actin cable formation 0.035 0.119 0.286 6 -0.28 1 7
KIAA1543 -0.033 0.071 -9999 0 -0.262 11 11
KIFC3 -0.026 0.064 -9999 0 -0.267 8 8
NCK1 0.019 0.067 -9999 0 -0.518 2 2
EXOC3 0.026 0.013 -9999 0 -9999 0 0
ACTN1 -0.028 0.068 -9999 0 -0.271 9 9
NCK1/GIT1 0.026 0.074 -9999 0 -0.378 4 4
mol:GDP 0.037 0.088 -9999 0 -0.276 9 9
EXOC4 0.033 0.004 -9999 0 -9999 0 0
STX4 -0.028 0.063 -9999 0 -0.265 9 9
PIP5K1C -0.029 0.07 -9999 0 -0.268 10 10
LIMA1 0 0 -9999 0 -9999 0 0
ABI1 0.032 0.006 -9999 0 -9999 0 0
ROCK1 -0.01 0.122 0.306 3 -0.355 3 6
adherens junction assembly -0.022 0.104 -9999 0 -0.571 2 2
IGF-1R heterotetramer/IGF1 -0.043 0.151 -9999 0 -0.294 32 32
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.044 0.017 -9999 0 -9999 0 0
MET 0.022 0.068 -9999 0 -0.518 2 2
PLEKHA7 -0.027 0.067 -9999 0 -0.267 9 9
mol:GTP 0.021 0.111 -9999 0 -0.33 10 10
establishment of epithelial cell apical/basal polarity -0.002 0.088 0.307 1 -0.298 1 2
cortical actin cytoskeleton stabilization 0.002 0.072 -9999 0 -0.262 9 9
regulation of cell-cell adhesion -0.032 0.076 -9999 0 -0.285 10 10
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.002 0.073 -9999 0 -0.264 9 9
Caspase cascade in apoptosis

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
TOP1 -0.012 0.161 -9999 0 -0.492 11 11
ACTA1 -0.031 0.158 0.245 2 -0.545 9 11
NUMA1 -0.016 0.176 -9999 0 -0.541 11 11
SPTAN1 -0.029 0.155 0.25 2 -0.568 8 10
LIMK1 -0.033 0.166 0.25 2 -0.561 9 11
BIRC3 -0.027 0.156 -9999 0 -0.518 12 12
BIRC2 0.032 0.005 -9999 0 -9999 0 0
BAX 0.032 0.005 -9999 0 -9999 0 0
CASP10 -0.04 0.111 -9999 0 -0.436 9 9
CRMA 0 0 -9999 0 -9999 0 0
XIAP 0 0 -9999 0 -9999 0 0
PTK2 -0.014 0.158 -9999 0 -0.485 11 11
DIABLO 0.033 0 -9999 0 -9999 0 0
apoptotic nuclear changes -0.028 0.152 0.249 2 -0.557 8 10
response to UV 0 0 -9999 0 -9999 0 0
CRADD 0.025 0.066 -9999 0 -0.518 2 2
GSN -0.039 0.165 0.25 2 -0.488 12 14
MADD 0.032 0.005 -9999 0 -9999 0 0
TFAP2A -0.01 0.156 -9999 0 -0.545 9 9
BID -0.015 0.082 -9999 0 -0.306 9 9
MAP3K1 -0.043 0.177 -9999 0 -0.5 15 15
TRADD 0.028 0.047 -9999 0 -0.518 1 1
mol:Ca2+ 0 0 -9999 0 -9999 0 0
APAF-1/Pro-Caspase 9 0.045 0.037 -9999 0 -0.378 1 1
mol:Activated DNA 0 0 -9999 0 -9999 0 0
ARHGDIB -0.029 0.185 0.25 2 -0.631 9 11
CASP9 0.032 0.006 -9999 0 -9999 0 0
DNA repair -0.015 0.06 0.206 1 -0.186 8 9
neuron apoptosis -0.019 0.19 -9999 0 -0.796 7 7
mol:NAD 0 0 -9999 0 -9999 0 0
DNA fragmentation during apoptosis -0.025 0.18 -9999 0 -0.665 8 8
APAF1 0.029 0.047 -9999 0 -0.517 1 1
CASP6 -0.03 0.244 -9999 0 -1.002 7 7
TRAF2 0.031 0.012 -9999 0 -9999 0 0
ICAD/CAD -0.03 0.15 0.255 1 -0.555 8 9
CASP7 0.025 0.094 0.285 11 -0.247 2 13
KRT18 -0.013 0.129 -9999 0 -0.576 6 6
apoptosis -0.035 0.171 0.25 1 -0.544 11 12
DFFA -0.028 0.155 0.25 2 -0.57 8 10
DFFB -0.028 0.155 0.25 2 -0.57 8 10
PARP1 0.015 0.06 0.186 8 -0.208 1 9
actin filament polymerization 0.029 0.158 0.535 8 -0.305 4 12
TNF 0.025 0.051 -9999 0 -0.518 1 1
CYCS -0.001 0.065 0.155 1 -0.215 8 9
SATB1 -0.037 0.226 -9999 0 -0.862 8 8
SLK -0.028 0.155 0.25 2 -0.566 8 10
p15 BID/BAX 0.003 0.094 0.202 1 -0.328 7 8
CASP2 0.002 0.09 0.22 1 -0.334 5 6
JNK cascade 0.043 0.175 0.496 15 -9999 0 15
CASP3 -0.026 0.164 0.274 2 -0.596 8 10
LMNB2 -0.001 0.152 -9999 0 -0.522 6 6
RIPK1 0.032 0.005 -9999 0 -9999 0 0
CASP4 0.029 0.047 -9999 0 -0.518 1 1
Mammalian IAPs/DIABLO 0.021 0.104 -9999 0 -0.295 12 12
negative regulation of DNA binding -0.01 0.155 -9999 0 -0.539 9 9
stress fiber formation -0.027 0.152 0.249 2 -0.555 8 10
GZMB -0.017 0.132 -9999 0 -0.564 7 7
CASP1 -0.003 0.097 -9999 0 -0.392 7 7
LMNB1 -0.035 0.209 -9999 0 -0.555 12 12
APP -0.019 0.193 -9999 0 -0.81 7 7
TNFRSF1A 0.026 0.048 -9999 0 -0.518 1 1
response to stress 0 0 -9999 0 -9999 0 0
CASP8 0.003 0.046 -9999 0 -0.376 2 2
VIM -0.032 0.174 0.261 1 -0.508 13 14
LMNA 0.004 0.118 -9999 0 -0.4 7 7
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.005 0.094 -9999 0 -0.35 5 5
LRDD 0.032 0.006 -9999 0 -9999 0 0
SREBF1 -0.03 0.156 0.25 2 -0.534 9 11
APAF-1/Caspase 9 0.024 0.108 -9999 0 -0.618 3 3
nuclear fragmentation during apoptosis -0.015 0.172 -9999 0 -0.529 11 11
CFL2 -0.03 0.162 0.306 4 -0.551 8 12
GAS2 -0.059 0.166 0.238 1 -0.42 17 18
positive regulation of apoptosis -0.012 0.17 -9999 0 -0.571 7 7
PRF1 0.003 0.114 -9999 0 -0.518 6 6
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.02 0.008 -9999 0 -9999 0 0
ARNO/beta Arrestin1-2 -0.005 0.091 -9999 0 -0.245 14 14
EGFR -0.014 0.144 -9999 0 -0.518 10 10
EPHA2 -0.006 0.13 -9999 0 -0.518 8 8
USP6 0.031 0.007 -9999 0 -9999 0 0
IQSEC1 0.03 0.009 -9999 0 -9999 0 0
EGFR/EGFR/EGF/EGF -0.038 0.16 -9999 0 -0.42 18 18
ARRB2 0.007 0.051 -9999 0 -0.328 3 3
mol:GTP 0.002 0.026 -9999 0 -0.177 2 2
ARRB1 0.027 0.025 -9999 0 -9999 0 0
FBXO8 0.029 0.014 -9999 0 -9999 0 0
TSHR 0.023 0.067 -9999 0 -0.518 2 2
EGF -0.032 0.15 -9999 0 -0.518 11 11
somatostatin receptor activity 0 0 -9999 0 -0.001 9 9
ARAP2 0 0 0 5 0 11 16
mol:GDP -0.003 0.082 -9999 0 -0.256 7 7
mol:PI-3-4-5-P3 0 0 0 3 0 9 12
ITGA2B 0.033 0.003 -9999 0 -9999 0 0
ARF6 0.031 0.012 -9999 0 -9999 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.023 0.113 -9999 0 -0.333 10 10
ADAP1 0 0 0 1 0 6 7
KIF13B 0.029 0.014 -9999 0 -9999 0 0
HGF/MET 0.037 0.055 -9999 0 -0.379 2 2
PXN 0.033 0.003 -9999 0 -9999 0 0
ARF6/GTP -0.005 0.09 0.167 3 -0.233 9 12
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.019 0.146 -9999 0 -0.362 18 18
ADRB2 -0.039 0.172 -9999 0 -0.518 15 15
receptor agonist activity 0 0 0 4 0 7 11
actin filament binding 0 0 -9999 0 0 9 9
SRC 0.03 0.013 -9999 0 -9999 0 0
ITGB3 0.024 0.052 -9999 0 -0.518 1 1
GNAQ 0 0 0.001 3 -0.001 8 11
EFA6/PI-4-5-P2 0 0 0.001 2 -0.001 8 10
ARF6/GDP 0.015 0.089 0.192 2 -0.308 4 6
ARF6/GDP/GULP/ACAP1 -0.029 0.136 -9999 0 -0.267 25 25
alphaIIb/beta3 Integrin/paxillin/GIT1 0.068 0.063 -9999 0 -0.298 3 3
ACAP1 0 0 -9999 0 -9999 0 0
ACAP2 0 0 0 5 0 8 13
LHCGR/beta Arrestin2 0.015 0.073 -9999 0 -0.453 3 3
EFNA1 0.022 0.067 -9999 0 -0.518 2 2
HGF 0.029 0.021 -9999 0 -9999 0 0
CYTH3 0 0 0.001 3 -0.001 7 10
CYTH2 0 0.001 -9999 0 -0.004 10 10
NCK1 0.019 0.067 -9999 0 -0.518 2 2
fibronectin binding 0 0 0 3 0 9 12
endosomal lumen acidification 0 0 0 7 0 5 12
microtubule-based process 0 0 -9999 0 -9999 0 0
GULP1 -0.07 0.2 -9999 0 -0.518 22 22
GNAQ/ARNO 0 0.003 0.008 3 -0.006 8 11
mol:Phosphatidic acid 0 0 0 5 0 8 13
PIP3-E 0.018 0.07 -9999 0 -0.518 2 2
MET 0.022 0.068 -9999 0 -0.518 2 2
GNA14 0.011 0.085 -9999 0 -0.518 3 3
GNA15 0.007 0.114 -9999 0 -0.518 6 6
GIT1 0.024 0.067 -9999 0 -0.518 2 2
mol:PI-4-5-P2 0 0 0.001 4 -0.001 9 13
GNA11 0.029 0.047 -9999 0 -0.518 1 1
LHCGR 0.016 0.082 -9999 0 -0.518 3 3
AGTR1 0.004 0.082 -9999 0 -0.518 3 3
desensitization of G-protein coupled receptor protein signaling pathway 0.015 0.073 -9999 0 -0.452 3 3
IPCEF1/ARNO -0.016 0.119 -9999 0 -0.278 20 20
alphaIIb/beta3 Integrin 0.041 0.042 -9999 0 -0.379 1 1
Canonical Wnt signaling 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
HDAC1 0.039 0.044 0.452 1 -9999 0 1
AES 0.036 0.02 -9999 0 -9999 0 0
FBXW11 0.031 0.008 -9999 0 -9999 0 0
mol:GTP 0 0.001 -9999 0 -9999 0 0
LRP6/FZD1 0.036 0.056 -9999 0 -0.381 2 2
SMAD4 0.023 0.067 -9999 0 -0.518 2 2
DKK2 0.008 0.096 -9999 0 -0.517 4 4
TLE1 0.033 0.053 0.314 1 -0.471 1 2
MACF1 0.023 0.067 -9999 0 -0.519 2 2
CTNNB1 0.011 0.124 0.328 2 -0.403 4 6
WIF1 -0.064 0.187 -9999 0 -0.517 19 19
beta catenin/RanBP3 0.02 0.155 0.384 13 -0.376 3 16
KREMEN2 -0.103 0.212 -9999 0 -0.518 27 27
DKK1 -0.1 0.213 -9999 0 -0.517 27 27
beta catenin/beta TrCP1 0.027 0.123 0.329 2 -0.393 3 5
FZD1 0.026 0.05 -9999 0 -0.519 1 1
AXIN2 -0.027 0.266 0.639 4 -1.352 4 8
AXIN1 0.032 0.012 -9999 0 -9999 0 0
RAN 0.033 0.003 -9999 0 -9999 0 0
Axin1/APC/GSK3/beta catenin 0.016 0.109 -9999 0 -0.609 3 3
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.025 0.122 -9999 0 -0.495 4 4
Axin1/APC/GSK3 0.029 0.071 0.241 1 -0.355 2 3
Axin1/APC/GSK3/beta catenin/Macf1 0.025 0.106 -9999 0 -0.376 4 4
HNF1A 0.006 0.031 0.283 1 -9999 0 1
CTBP1 0.035 0.033 0.322 1 -9999 0 1
MYC 0.013 0.311 0.626 12 -1.385 4 16
RANBP3 0.033 0.005 -9999 0 -9999 0 0
DKK2/LRP6/Kremen 2 -0.061 0.155 -9999 0 -0.326 32 32
NKD1 0.028 0.021 -9999 0 -9999 0 0
TCF4 0.006 0.117 -9999 0 -0.485 7 7
TCF3 0.035 0.02 -9999 0 -9999 0 0
WNT1/LRP6/FZD1/Axin1 0.064 0.058 -9999 0 -0.303 2 2
Ran/GTP 0.025 0.004 -9999 0 -9999 0 0
CtBP/CBP/TCF/TLE1/AES 0.017 0.169 0.512 8 -0.464 1 9
LEF1 0.02 0.101 0.439 1 -0.506 4 5
DVL1 0.036 0.068 0.264 1 -0.505 1 2
CSNK2A1 0.031 0.008 -9999 0 -9999 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.006 0.16 -9999 0 -0.531 7 7
DKK1/LRP6/Kremen 2 -0.128 0.192 -9999 0 -0.363 49 49
LRP6 0.026 0.049 -9999 0 -0.52 1 1
CSNK1A1 0.038 0.043 0.46 1 -9999 0 1
NLK 0.03 0.012 -9999 0 -9999 0 0
CCND1 -0.063 0.449 0.602 6 -1.548 10 16
WNT1 0.033 0.003 -9999 0 -9999 0 0
GSK3A 0.031 0.008 -9999 0 -9999 0 0
GSK3B 0.027 0.016 -9999 0 -9999 0 0
FRAT1 0.031 0.012 -9999 0 -9999 0 0
PPP2R5D 0.029 0.086 -9999 0 -0.534 2 2
APC 0.021 0.07 -9999 0 -0.286 2 2
WNT1/LRP6/FZD1 0.051 0.085 0.236 16 -0.272 2 18
CREBBP 0.037 0.032 0.323 1 -9999 0 1
Glypican 2 network

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
MDK -0.003 0.13 -9999 0 -0.518 8 8
GPC2 0 0 -9999 0 -9999 0 0
GPC2/Midkine -0.003 0.095 -9999 0 -0.347 9 9
neuron projection morphogenesis -0.003 0.094 -9999 0 -0.346 9 9
IL6-mediated signaling events

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
BCL2L1 -0.036 0.24 -9999 0 -0.705 6 6
CRP -0.043 0.237 -9999 0 -0.73 5 5
cell cycle arrest -0.061 0.269 -9999 0 -0.709 12 12
TIMP1 -0.052 0.273 -9999 0 -0.924 7 7
IL6ST 0.021 0.069 -9999 0 -0.513 2 2
Rac1/GDP -0.034 0.181 0.326 1 -0.496 10 11
AP1 0.023 0.148 -9999 0 -0.531 2 2
GAB2 0.033 0.016 -9999 0 -9999 0 0
TNFSF11 -0.084 0.306 -9999 0 -1.038 8 8
HSP90B1 0.008 0.106 -9999 0 -1.102 1 1
GAB1 0.022 0.068 -9999 0 -0.514 2 2
MAPK14 -0.039 0.17 0.29 1 -0.882 3 4
AKT1 0.039 0.072 0.278 1 -9999 0 1
FOXO1 0.046 0.074 -9999 0 -9999 0 0
MAP2K6 -0.042 0.167 0.276 2 -0.476 9 11
mol:GTP 0 0.002 -9999 0 -9999 0 0
MAP2K4 -0.04 0.184 0.325 1 -0.519 10 11
MITF -0.031 0.156 0.286 2 -0.42 11 13
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -9999 0 0
TYK2 0.03 0.012 -9999 0 -9999 0 0
A2M -0.032 0.252 -9999 0 -1.456 4 4
CEBPB 0.028 0.047 -9999 0 -0.518 1 1
GRB2/SOS1/GAB family/SHP2 0.022 0.105 -9999 0 -0.601 1 1
STAT3 -0.065 0.284 -9999 0 -0.763 12 12
STAT1 -0.019 0.193 -9999 0 -0.894 6 6
CEBPD -0.057 0.273 -9999 0 -0.921 6 6
PIK3CA 0.012 0.049 -9999 0 -0.517 1 1
PI3K 0.006 0.068 -9999 0 -0.378 3 3
JUN -0.001 0.123 -9999 0 -0.518 7 7
PIAS3/MITF -0.024 0.154 -9999 0 -0.437 9 9
MAPK11 -0.04 0.175 0.29 1 -0.767 4 5
STAT3 (dimer)/FOXO1 -0.024 0.25 0.389 1 -0.621 10 11
GRB2/SOS1/GAB family 0.005 0.186 -9999 0 -0.58 7 7
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.048 0.185 -9999 0 -0.447 15 15
GRB2 0.033 0.007 -9999 0 -9999 0 0
JAK2 0.029 0.014 -9999 0 -9999 0 0
LBP -0.016 0.203 -9999 0 -0.644 4 4
PIK3R1 0.005 0.097 -9999 0 -0.517 4 4
JAK1 0.028 0.05 -9999 0 -0.531 1 1
MYC -0.051 0.279 -9999 0 -0.837 9 9
FGG -0.083 0.285 -9999 0 -0.848 10 10
macrophage differentiation -0.061 0.269 -9999 0 -0.709 12 12
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.012 0.161 -9999 0 -0.325 22 22
JUNB -0.062 0.268 -9999 0 -0.849 8 8
FOS -0.027 0.151 -9999 0 -0.518 11 11
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.035 0.167 0.315 2 -0.401 14 16
STAT1/PIAS1 -0.024 0.179 0.336 2 -0.441 12 14
GRB2/SOS1/GAB family/SHP2/PI3K 0.04 0.072 -9999 0 -0.327 2 2
STAT3 (dimer) -0.067 0.283 -9999 0 -0.75 12 12
PRKCD -0.041 0.199 0.33 3 -0.561 10 13
IL6R 0.014 0.096 -9999 0 -0.526 4 4
SOCS3 -0.047 0.213 -9999 0 -1.227 3 3
gp130 (dimer)/JAK1/JAK1/LMO4 0.021 0.12 -9999 0 -0.322 13 13
Rac1/GTP -0.036 0.185 0.32 1 -0.514 10 11
HCK 0.006 0.113 -9999 0 -0.517 6 6
MAPKKK cascade 0.044 0.102 -9999 0 -0.49 2 2
bone resorption -0.076 0.286 -9999 0 -0.948 8 8
IRF1 -0.074 0.294 -9999 0 -1.04 7 7
mol:GDP -0.047 0.178 0.289 2 -0.436 14 16
SOS1 0.033 0.008 -9999 0 -9999 0 0
VAV1 -0.048 0.182 0.29 2 -0.444 14 16
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.041 0.202 -9999 0 -0.729 6 6
PTPN11 0.017 0.087 -9999 0 -0.939 1 1
IL6/IL6RA -0.027 0.148 -9999 0 -0.392 17 17
gp130 (dimer)/TYK2/TYK2/LMO4 0.022 0.113 -9999 0 -0.321 12 12
gp130 (dimer)/JAK2/JAK2/LMO4 0.02 0.11 -9999 0 -0.322 11 11
IL6 -0.048 0.167 -9999 0 -0.52 14 14
PIAS3 0.032 0.007 -9999 0 -9999 0 0
PTPRE -0.001 0.114 -9999 0 -0.52 6 6
PIAS1 0.032 0.006 -9999 0 -9999 0 0
RAC1 0.032 0.005 -9999 0 -9999 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.038 0.143 0.284 2 -0.3 23 25
LMO4 -0.013 0.145 -9999 0 -0.516 10 10
STAT3 (dimer)/PIAS3 -0.06 0.268 -9999 0 -0.702 12 12
MCL1 0.053 0.082 -9999 0 -9999 0 0
Plasma membrane estrogen receptor 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
GNB1/GNG2 0.043 0.084 -9999 0 -0.28 7 7
ER alpha/Gai/GDP/Gbeta gamma -0.042 0.191 -9999 0 -0.516 14 14
AKT1 -0.05 0.229 -9999 0 -0.816 10 10
PIK3CA 0.011 0.048 -9999 0 -0.518 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.049 0.234 -9999 0 -0.833 10 10
mol:Ca2+ -0.022 0.098 -9999 0 -0.302 9 9
IGF1R -0.01 0.144 -9999 0 -0.518 10 10
E2/ER alpha (dimer)/Striatin 0.006 0.096 -9999 0 -0.32 10 10
SHC1 0.03 0.009 -9999 0 -9999 0 0
apoptosis 0.047 0.216 0.771 10 -9999 0 10
RhoA/GTP -0.009 0.085 -9999 0 -0.256 13 13
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.014 0.176 -9999 0 -0.487 11 11
regulation of stress fiber formation 0.03 0.1 0.408 2 -9999 0 2
E2/ERA-ERB (dimer) 0.015 0.083 -9999 0 -0.321 7 7
KRAS 0.014 0.093 -9999 0 -0.518 4 4
G13/GTP 0.013 0.08 -9999 0 -0.291 8 8
pseudopodium formation -0.03 0.1 -9999 0 -0.408 2 2
E2/ER alpha (dimer)/PELP1 0.015 0.083 -9999 0 -0.321 7 7
GRB2 0.032 0.006 -9999 0 -9999 0 0
GNG2 0.032 0.005 -9999 0 -9999 0 0
GNAO1 0.032 0.007 -9999 0 -9999 0 0
HRAS 0.027 0.048 -9999 0 -0.518 1 1
mol:GTP 0 0 -9999 0 -9999 0 0
mol:NO -0.034 0.175 -9999 0 -0.539 11 11
E2/ER beta (dimer) 0.024 0.004 -9999 0 -9999 0 0
mol:GDP -0.016 0.101 -9999 0 -0.385 7 7
mol:NADP -0.034 0.175 -9999 0 -0.539 11 11
PIK3R1 0.004 0.097 -9999 0 -0.518 4 4
mol:IP3 -0.027 0.096 -9999 0 -0.297 11 11
IGF-1R heterotetramer -0.01 0.143 -9999 0 -0.517 10 10
PLCB1 -0.023 0.101 -9999 0 -0.294 13 13
PLCB2 -0.017 0.098 -9999 0 -0.336 9 9
IGF1 -0.054 0.185 -9999 0 -0.518 18 18
mol:L-citrulline -0.034 0.175 -9999 0 -0.539 11 11
RHOA 0.03 0.01 -9999 0 -9999 0 0
Gai/GDP -0.052 0.244 -9999 0 -0.7 15 15
JNK cascade 0.024 0.004 -9999 0 -9999 0 0
BCAR1 0.032 0.005 -9999 0 -9999 0 0
ESR2 0.032 0.006 -9999 0 -9999 0 0
GNAQ 0 0 -9999 0 -9999 0 0
ESR1 -0.006 0.123 -9999 0 -0.518 7 7
Gq family/GDP/Gbeta gamma -0.015 0.163 -9999 0 -0.563 9 9
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.015 0.092 -9999 0 -0.464 2 2
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.012 0.166 -9999 0 -0.474 10 10
GNAZ 0 0.122 -9999 0 -0.518 7 7
E2/ER alpha (dimer) -0.003 0.089 -9999 0 -0.375 7 7
STRN 0.018 0.082 -9999 0 -0.518 3 3
GNAL 0.007 0.105 -9999 0 -0.518 5 5
PELP1 0.031 0.007 -9999 0 -9999 0 0
MAPK11 0.016 0.005 -9999 0 -9999 0 0
GNAI2 0.027 0.02 -9999 0 -9999 0 0
GNAI3 0.032 0.006 -9999 0 -9999 0 0
GNAI1 -0.001 0.13 -9999 0 -0.518 8 8
HBEGF -0.066 0.211 0.36 3 -0.576 14 17
cAMP biosynthetic process 0 0.087 -9999 0 -0.266 12 12
SRC -0.033 0.188 0.274 2 -0.566 10 12
PI3K 0.005 0.067 -9999 0 -0.378 3 3
GNB1 0.032 0.006 -9999 0 -9999 0 0
G13/GDP/Gbeta gamma 0.014 0.108 -9999 0 -0.352 7 7
SOS1 0.032 0.007 -9999 0 -9999 0 0
IGF-1R heterotetramer/IGF1 -0.074 0.148 -9999 0 -0.386 17 17
Gs family/GTP 0.006 0.091 -9999 0 -0.27 12 12
EntrezGene:2778 0 0 -9999 0 -9999 0 0
RAS family/GTP 0.036 0.077 -9999 0 -0.295 6 6
vasodilation -0.031 0.166 -9999 0 -0.511 11 11
mol:DAG -0.027 0.096 -9999 0 -0.297 11 11
Gs family/GDP/Gbeta gamma -0.016 0.105 -9999 0 -0.343 8 8
MSN -0.033 0.106 -9999 0 -0.38 3 3
Gq family/GTP -0.016 0.106 -9999 0 -0.346 10 10
mol:PI-3-4-5-P3 -0.046 0.223 -9999 0 -0.794 10 10
NRAS 0.026 0.049 -9999 0 -0.518 1 1
mol:E2 0 0 -9999 0 -9999 0 0
cell adhesion 0.031 0.166 0.511 11 -9999 0 11
GRB2/SOS1 0.045 0.013 -9999 0 -9999 0 0
RhoA/GDP -0.001 0.104 -9999 0 -0.386 6 6
NOS3 -0.037 0.184 -9999 0 -0.571 11 11
GNA11 0.029 0.047 -9999 0 -0.518 1 1
MAPKKK cascade -0.02 0.194 0.335 1 -0.592 11 12
E2/ER alpha (dimer)/PELP1/Src -0.02 0.181 -9999 0 -0.494 12 12
ruffle organization -0.03 0.1 -9999 0 -0.408 2 2
ROCK2 -0.018 0.094 -9999 0 -0.271 1 1
GNA14 0.011 0.085 -9999 0 -0.518 3 3
GNA15 0.007 0.114 -9999 0 -0.518 6 6
GNA13 0.027 0.048 -9999 0 -0.518 1 1
MMP9 -0.05 0.202 0.402 3 -0.569 12 15
MMP2 -0.051 0.188 0.351 2 -0.506 13 15
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.029 0.125 0.208 2 -0.376 7 9
adherens junction organization -0.005 0.146 -9999 0 -0.38 12 12
mol:GTP 0 0 -9999 0 -9999 0 0
Rac1/GDP 0.032 0.143 0.229 1 -0.411 5 6
FMN1 0.009 0.127 -9999 0 -0.34 11 11
mol:IP3 -0.011 0.087 -9999 0 -0.348 6 6
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.012 0.135 -9999 0 -0.356 11 11
CTNNB1 0.03 0.018 -9999 0 -9999 0 0
AKT1 -0.017 0.092 -9999 0 -0.365 6 6
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.011 0.178 -9999 0 -0.534 9 9
CTNND1 0.028 0.068 -9999 0 -0.528 2 2
mol:PI-4-5-P2 0.005 0.123 -9999 0 -0.335 11 11
VASP 0.003 0.14 -9999 0 -0.386 11 11
ZYX 0.004 0.13 -9999 0 -0.34 12 12
JUB -0.011 0.141 -9999 0 -0.321 17 17
EGFR(dimer) -0.004 0.154 -9999 0 -0.421 9 9
E-cadherin/beta catenin-gamma catenin 0.014 0.114 -9999 0 -0.318 13 13
mol:PI-3-4-5-P3 -0.008 0.101 -9999 0 -0.362 7 7
PIK3CA 0.011 0.049 -9999 0 -0.519 1 1
PI3K -0.008 0.104 -9999 0 -0.369 7 7
FYN 0.024 0.111 0.213 2 -0.366 4 6
mol:Ca2+ -0.011 0.085 -9999 0 -0.341 6 6
JUP 0.005 0.121 -9999 0 -0.511 7 7
PIK3R1 0.007 0.097 -9999 0 -0.521 4 4
mol:DAG -0.013 0.085 -9999 0 -0.348 6 6
CDH1 0.004 0.122 -9999 0 -0.516 7 7
RhoA/GDP 0.034 0.142 0.229 1 -0.408 5 6
establishment of polarity of embryonic epithelium 0.003 0.137 -9999 0 -0.377 11 11
SRC 0.03 0.013 -9999 0 -9999 0 0
RAC1 0.032 0.005 -9999 0 -9999 0 0
RHOA 0.03 0.01 -9999 0 -9999 0 0
EGFR -0.014 0.144 -9999 0 -0.518 10 10
CASR 0.024 0.109 0.213 2 -0.344 5 7
RhoA/GTP 0.045 0.111 -9999 0 -0.332 5 5
AKT2 -0.018 0.09 -9999 0 -0.39 5 5
actin cable formation 0.001 0.136 -9999 0 -0.375 11 11
apoptosis -0.033 0.127 0.367 7 -0.219 3 10
CTNNA1 0.035 0.01 -9999 0 -9999 0 0
mol:GDP 0.015 0.14 -9999 0 -0.389 7 7
PIP5K1A 0.004 0.126 -9999 0 -0.342 11 11
PLCG1 -0.013 0.087 -9999 0 -0.356 6 6
Rac1/GTP 0.004 0.148 -9999 0 -0.39 9 9
homophilic cell adhesion 0.003 0.005 -9999 0 -9999 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.015 0.123 -9999 0 -0.343 13 13
E-cadherin/beta catenin 0.019 0.095 -9999 0 -0.376 7 7
CTNNB1 0.028 0.017 -9999 0 -9999 0 0
JUP 0.003 0.122 -9999 0 -0.518 7 7
CDH1 0.002 0.122 -9999 0 -0.518 7 7
Regulation of nuclear SMAD2/3 signaling

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
EP300 -0.003 0.131 -9999 0 -0.518 8 8
HSPA8 0.028 0.048 -9999 0 -0.519 1 1
SMAD3/SMAD4/ER alpha 0.002 0.143 0.26 1 -0.363 12 13
AKT1 0.003 0.052 -9999 0 -9999 0 0
GSC -0.023 0.194 -9999 0 -1.47 2 2
NKX2-5 -0.018 0.135 -9999 0 -0.487 9 9
muscle cell differentiation 0.043 0.172 0.426 17 -9999 0 17
SMAD2-3/SMAD4/SP1 0.006 0.158 -9999 0 -0.389 9 9
SMAD4 -0.005 0.1 -9999 0 -0.423 4 4
CBFB 0.032 0.007 -9999 0 -9999 0 0
SAP18 0.031 0.007 -9999 0 -9999 0 0
Cbp/p300/MSG1 0.036 0.098 -9999 0 -0.326 8 8
SMAD3/SMAD4/VDR 0.021 0.154 -9999 0 -0.348 13 13
MYC 0.025 0.083 -9999 0 -0.504 3 3
CDKN2B -0.405 0.703 -9999 0 -1.692 30 30
AP1 -0.033 0.19 -9999 0 -0.589 10 10
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.041 0.087 -9999 0 -0.337 3 3
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.067 0.153 -9999 0 -0.336 29 29
SP3 0.033 0.011 -9999 0 -9999 0 0
CREB1 0.028 0.047 -9999 0 -0.518 1 1
FOXH1 0.02 0.032 -9999 0 -9999 0 0
SMAD3/SMAD4/GR 0.019 0.113 -9999 0 -0.349 6 6
GATA3 0.029 0.029 -9999 0 -9999 0 0
SKI/SIN3/HDAC complex/NCoR1 0.013 0.086 -9999 0 -0.31 7 7
MEF2C/TIF2 -0.03 0.167 0.323 2 -0.497 10 12
endothelial cell migration 0.083 0.377 1.403 10 -9999 0 10
MAX 0.034 0.014 -9999 0 -9999 0 0
RBBP7 0.03 0.018 -9999 0 -9999 0 0
RBBP4 0.028 0.047 -9999 0 -0.518 1 1
RUNX2 0.025 0.066 -9999 0 -0.518 2 2
RUNX3 0.003 0.122 -9999 0 -0.518 7 7
RUNX1 0.023 0.067 -9999 0 -0.518 2 2
CTBP1 0.029 0.01 -9999 0 -9999 0 0
NR3C1 0.032 0.017 -9999 0 -9999 0 0
VDR 0.001 0.122 -9999 0 -0.518 7 7
CDKN1A -0.044 0.234 -9999 0 -1.102 5 5
KAT2B 0 0.005 -9999 0 -9999 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.013 0.092 -9999 0 -0.267 5 5
DCP1A 0.03 0.009 -9999 0 -9999 0 0
SKI 0.032 0.006 -9999 0 -9999 0 0
SERPINE1 -0.085 0.384 -9999 0 -1.43 10 10
SMAD3/SMAD4/ATF2 0.017 0.113 -9999 0 -0.334 7 7
SMAD3/SMAD4/ATF3 -0.004 0.142 -9999 0 -0.36 13 13
SAP30 0.03 0.01 -9999 0 -9999 0 0
Cbp/p300/PIAS3 0.039 0.096 -9999 0 -0.326 7 7
JUN -0.045 0.183 -9999 0 -0.587 10 10
SMAD3/SMAD4/IRF7 0.017 0.123 -9999 0 -0.346 9 9
TFE3 0.025 0.038 -9999 0 -9999 0 0
COL1A2 -0.061 0.254 -9999 0 -0.892 11 11
mesenchymal cell differentiation -0.013 0.128 0.352 9 -9999 0 9
DLX1 0.026 0.026 -9999 0 -9999 0 0
TCF3 0.032 0.006 -9999 0 -9999 0 0
FOS -0.035 0.158 -9999 0 -0.541 11 11
SMAD3/SMAD4/Max 0.021 0.114 -9999 0 -0.349 6 6
Cbp/p300/SNIP1 0.035 0.095 -9999 0 -0.325 8 8
ZBTB17 0.033 0.015 -9999 0 -9999 0 0
LAMC1 -0.022 0.149 -9999 0 -0.561 7 7
TGIF2/HDAC complex/SMAD3/SMAD4 0.016 0.111 -9999 0 -0.334 7 7
IRF7 0.028 0.051 -9999 0 -0.513 1 1
ESR1 0 0.118 -9999 0 -0.476 7 7
HNF4A 0.031 0.012 -9999 0 -9999 0 0
MEF2C -0.033 0.169 0.33 2 -0.505 10 12
SMAD2-3/SMAD4 0.005 0.12 -9999 0 -0.303 8 8
Cbp/p300/Src-1 0.036 0.097 -9999 0 -0.325 8 8
IGHV3OR16-13 -0.008 0.097 -9999 0 -0.583 3 3
TGIF2/HDAC complex 0.03 0.013 -9999 0 -9999 0 0
CREBBP 0.03 0.018 -9999 0 -9999 0 0
SKIL 0.007 0.066 -9999 0 -0.518 2 2
HDAC1 0.031 0.011 -9999 0 -9999 0 0
HDAC2 0.032 0.011 -9999 0 -9999 0 0
SNIP1 0.031 0.007 -9999 0 -9999 0 0
GCN5L2 0.031 0.017 -9999 0 -9999 0 0
SMAD3/SMAD4/TFE3 0.016 0.135 -9999 0 -0.358 10 10
MSG1/HSC70 0.043 0.04 -9999 0 -0.38 1 1
SMAD2 0.006 0.052 -9999 0 -0.213 1 1
SMAD3 -0.008 0.107 -9999 0 -0.418 6 6
SMAD3/E2F4-5/DP1/p107/SMAD4 -0.002 0.087 -9999 0 -0.275 8 8
SMAD2/SMAD2/SMAD4 -0.013 0.076 0.158 3 -0.298 5 8
NCOR1 0.032 0.006 -9999 0 -9999 0 0
NCOA2 0.023 0.066 -9999 0 -0.518 2 2
NCOA1 0.032 0.006 -9999 0 -9999 0 0
MYOD/E2A 0.024 0.095 -9999 0 -0.378 7 7
SMAD2-3/SMAD4/SP1/MIZ-1 0.011 0.164 -9999 0 -0.401 8 8
IFNB1 -0.011 0.114 -9999 0 -0.391 8 8
SMAD3/SMAD4/MEF2C -0.03 0.18 -9999 0 -0.533 9 9
CITED1 0.031 0.014 -9999 0 -9999 0 0
SMAD2-3/SMAD4/ARC105 0.009 0.107 -9999 0 -0.277 7 7
RBL1 0.031 0.007 -9999 0 -9999 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.106 0.238 -9999 0 -0.532 30 30
RUNX1-3/PEBPB2 0.035 0.103 -9999 0 -0.357 8 8
SMAD7 -0.048 0.197 -9999 0 -0.663 8 8
MYC/MIZ-1 0.044 0.072 -9999 0 -0.365 3 3
SMAD3/SMAD4 -0.02 0.179 0.317 1 -0.49 13 14
IL10 -0.003 0.09 -9999 0 -0.41 2 2
PIASy/HDAC complex 0.03 0.015 -9999 0 -9999 0 0
PIAS3 0.03 0.014 -9999 0 -9999 0 0
CDK2 0.03 0.017 -9999 0 -9999 0 0
IL5 -0.004 0.09 -9999 0 -0.34 4 4
CDK4 0.031 0.018 -9999 0 -9999 0 0
PIAS4 0.03 0.015 -9999 0 -9999 0 0
ATF3 0.001 0.115 -9999 0 -0.518 6 6
SMAD3/SMAD4/SP1 -0.001 0.153 -9999 0 -0.378 11 11
FOXG1 -0.001 0.003 -9999 0 -9999 0 0
FOXO3 -0.016 0.049 -9999 0 -0.148 2 2
FOXO1 -0.016 0.049 -9999 0 -0.145 2 2
FOXO4 -0.016 0.049 -9999 0 -0.145 2 2
heart looping -0.032 0.167 0.329 2 -0.499 10 12
CEBPB 0.01 0.058 -9999 0 -0.517 1 1
SMAD3/SMAD4/DLX1 0.014 0.114 -9999 0 -0.339 7 7
MYOD1 0.003 0.122 -9999 0 -0.518 7 7
SMAD3/SMAD4/HNF4 0.018 0.112 -9999 0 -0.334 7 7
SMAD3/SMAD4/GATA3 0.022 0.115 -9999 0 -0.348 6 6
SnoN/SIN3/HDAC complex/NCoR1 0.007 0.066 -9999 0 -0.517 2 2
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.025 0.148 -9999 0 -0.398 9 9
SMAD3/SMAD4/SP1-3 0.018 0.152 -9999 0 -0.437 6 6
MED15 0 0 -9999 0 -9999 0 0
SP1 0.002 0.075 -9999 0 -0.365 2 2
SIN3B 0.032 0.006 -9999 0 -9999 0 0
SIN3A 0.032 0.004 -9999 0 -9999 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.007 0.143 -9999 0 -0.346 14 14
ITGB5 -0.022 0.123 -9999 0 -0.52 4 4
TGIF/SIN3/HDAC complex/CtBP 0.01 0.079 -9999 0 -0.387 4 4
SMAD3/SMAD4/AR 0.005 0.124 -9999 0 -0.357 9 9
AR 0.014 0.074 -9999 0 -0.518 2 2
negative regulation of cell growth -0.018 0.113 -9999 0 -0.332 9 9
SMAD3/SMAD4/MYOD -0.003 0.145 -9999 0 -0.353 14 14
E2F5 0.011 0.095 -9999 0 -0.518 4 4
E2F4 0.032 0.007 -9999 0 -9999 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.029 0.121 -9999 0 -0.322 9 9
SMAD2-3/SMAD4/FOXO1-3a-4 -0.062 0.168 -9999 0 -0.378 27 27
TFDP1 0.031 0.009 -9999 0 -9999 0 0
SMAD3/SMAD4/AP1 -0.02 0.201 -9999 0 -0.599 10 10
SMAD3/SMAD4/RUNX2 0.013 0.129 -9999 0 -0.354 9 9
TGIF2 0.03 0.013 -9999 0 -9999 0 0
TGIF1 0 0 -9999 0 -9999 0 0
ATF2 0.033 0.003 -9999 0 -9999 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.016 0.093 -9999 0 -0.517 4 4
SVIL 0.024 0.067 -9999 0 -0.517 2 2
ZNF318 0.029 0.01 -9999 0 -9999 0 0
JMJD2C 0.031 0.049 -9999 0 -0.515 1 1
T-DHT/AR/Ubc9 -0.008 0.087 -9999 0 -0.308 4 4
CARM1 0.032 0.007 -9999 0 -9999 0 0
PRDX1 0.015 0.072 -9999 0 -0.518 2 2
PELP1 0.031 0.007 -9999 0 -9999 0 0
CTNNB1 0.029 0.017 -9999 0 -9999 0 0
AKT1 0.031 0.007 -9999 0 -9999 0 0
PTK2B 0.028 0.017 -9999 0 -9999 0 0
MED1 -0.001 0 -9999 0 -9999 0 0
MAK 0.028 0.011 -9999 0 -9999 0 0
response to oxidative stress 0 0 -9999 0 -9999 0 0
HIP1 0.033 0.011 -9999 0 -9999 0 0
GSN 0.011 0.105 -9999 0 -0.517 5 5
NCOA2 0.024 0.066 -9999 0 -0.517 2 2
NCOA6 0.024 0.067 -9999 0 -0.517 2 2
DNA-PK 0.054 0.039 -9999 0 -0.326 1 1
NCOA4 0.031 0.007 -9999 0 -9999 0 0
PIAS3 0.033 0.007 -9999 0 -9999 0 0
cell proliferation -0.001 0.044 -9999 0 -0.369 1 1
XRCC5 0.031 0.005 -9999 0 -9999 0 0
UBE3A 0.034 0.004 -9999 0 -9999 0 0
T-DHT/AR/SNURF -0.024 0.076 -9999 0 -0.194 11 11
FHL2 -0.126 0.342 -9999 0 -0.986 18 18
RANBP9 0.034 0.006 -9999 0 -9999 0 0
JMJD1A -0.004 0.072 -9999 0 -0.155 17 17
CDK6 0.011 0.104 -9999 0 -0.518 5 5
TGFB1I1 0.029 0.048 -9999 0 -0.517 1 1
T-DHT/AR/CyclinD1 -0.033 0.122 -9999 0 -0.367 12 12
XRCC6 0.031 0.006 -9999 0 -9999 0 0
T-DHT/AR -0.045 0.121 -9999 0 -0.203 42 42
CTDSP1 0.032 0.006 -9999 0 -9999 0 0
CTDSP2 0.031 0.003 -9999 0 -9999 0 0
BRCA1 0.029 0.047 -9999 0 -0.517 1 1
TCF4 -0.002 0.129 -9999 0 -0.519 8 8
CDKN2A -0.049 0.163 -9999 0 -0.519 14 14
SRF 0.007 0.066 -9999 0 -0.158 14 14
NKX3-1 -0.039 0.098 -9999 0 -0.236 24 24
KLK3 0.03 0.047 -9999 0 -9999 0 0
TMF1 0.025 0.048 -9999 0 -0.517 1 1
HNRNPA1 -0.001 0 -9999 0 -9999 0 0
AOF2 0.034 0.006 -9999 0 -9999 0 0
APPL1 0.005 0.004 -9999 0 -9999 0 0
T-DHT/AR/Caspase 8 -0.014 0.096 -9999 0 -0.326 6 6
AR -0.018 0.093 -9999 0 -0.597 2 2
UBA3 0 0 -9999 0 -9999 0 0
PATZ1 -0.001 0 -9999 0 -9999 0 0
PAWR 0.021 0.081 -9999 0 -0.517 3 3
PRKDC 0.026 0.048 -9999 0 -0.518 1 1
PA2G4 0.032 0 -9999 0 -9999 0 0
UBE2I 0.032 0.005 -9999 0 -9999 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.008 0.08 -9999 0 -0.241 6 6
RPS6KA3 0.03 0.048 -9999 0 -0.517 1 1
T-DHT/AR/ARA70 -0.009 0.086 -9999 0 -0.308 4 4
LATS2 0.022 0.066 -9999 0 -0.518 2 2
T-DHT/AR/PRX1 -0.016 0.09 -9999 0 -0.311 6 6
Cyclin D3/CDK11 p58 0.023 0.01 -9999 0 -9999 0 0
VAV3 -0.088 0.216 -9999 0 -0.517 27 27
KLK2 -0.004 0.079 -9999 0 -0.402 2 2
CASP8 0.023 0.066 -9999 0 -0.518 2 2
T-DHT/AR/TIF2/CARM1 0.003 0.096 -9999 0 -0.337 5 5
TMPRSS2 -0.182 0.392 -9999 0 -0.957 27 27
CCND1 -0.013 0.143 -9999 0 -0.517 10 10
PIAS1 0.034 0.007 -9999 0 -9999 0 0
mol:T-DHT -0.02 0.034 -9999 0 -0.068 41 41
CDC2L1 0 0 -9999 0 -9999 0 0
PIAS4 0.035 0.004 -9999 0 -9999 0 0
T-DHT/AR/CDK6 -0.017 0.105 -9999 0 -0.319 9 9
CMTM2 0.025 0.028 -9999 0 -9999 0 0
SNURF 0 0 -9999 0 -9999 0 0
ZMIZ1 -0.02 0.034 -9999 0 -0.068 41 41
CCND3 0.031 0.015 -9999 0 -9999 0 0
TGIF1 -0.001 0 -9999 0 -9999 0 0
FKBP4 0.028 0.048 -9999 0 -0.517 1 1
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.03 0.012 -9999 0 -9999 0 0
Jak2/Leptin Receptor -0.015 0.138 -9999 0 -0.458 8 8
PTP1B/AKT1 -0.044 0.124 -9999 0 -0.312 13 13
FYN 0.023 0.067 -9999 0 -0.518 2 2
p210 bcr-abl/PTP1B -0.063 0.127 -9999 0 -0.319 16 16
EGFR -0.02 0.146 -9999 0 -0.528 10 10
EGF/EGFR -0.081 0.17 -9999 0 -0.388 24 24
CSF1 0.03 0.012 -9999 0 -9999 0 0
AKT1 0.032 0.007 -9999 0 -9999 0 0
INSR 0.028 0.048 -9999 0 -0.52 1 1
PTP1B/N-cadherin -0.053 0.139 -9999 0 -0.337 17 17
Insulin Receptor/Insulin -0.018 0.12 -9999 0 -0.345 6 6
HCK 0.006 0.113 -9999 0 -0.518 6 6
CRK 0.031 0.007 -9999 0 -9999 0 0
TYK2 -0.058 0.127 0.214 3 -0.32 14 17
EGF -0.035 0.153 -9999 0 -0.528 11 11
YES1 0.031 0.008 -9999 0 -9999 0 0
CAV1 -0.076 0.151 -9999 0 -0.341 23 23
TXN 0.027 0.02 -9999 0 -9999 0 0
PTP1B/IRS1/GRB2 -0.048 0.141 -9999 0 -0.325 16 16
cell migration 0.063 0.127 0.319 16 -9999 0 16
STAT3 0.032 0.006 -9999 0 -9999 0 0
PRLR 0.02 0.054 -9999 0 -0.515 1 1
ITGA2B 0.032 0.003 -9999 0 -9999 0 0
CSF1R 0.031 0.007 -9999 0 -9999 0 0
Prolactin Receptor/Prolactin 0.036 0.049 -9999 0 -0.375 1 1
FGR 0.032 0.006 -9999 0 -9999 0 0
PTP1B/p130 Cas -0.05 0.13 -9999 0 -0.314 15 15
Crk/p130 Cas -0.036 0.134 -9999 0 -0.343 10 10
DOK1 -0.049 0.12 -9999 0 -0.342 10 10
JAK2 -0.027 0.139 -9999 0 -0.481 8 8
Jak2/Leptin Receptor/Leptin -0.024 0.155 -9999 0 -0.496 7 7
PIK3R1 0.004 0.097 -9999 0 -0.518 4 4
PTPN1 -0.064 0.128 -9999 0 -0.322 16 16
LYN 0.028 0.047 -9999 0 -0.518 1 1
CDH2 0.009 0.074 -9999 0 -0.518 2 2
SRC 0.001 0.08 -9999 0 -0.537 2 2
ITGB3 0.024 0.052 -9999 0 -0.521 1 1
CAT1/PTP1B -0.057 0.176 -9999 0 -0.472 12 12
CAPN1 0.026 0.05 -9999 0 -0.526 1 1
CSK 0.033 0.004 -9999 0 -9999 0 0
PI3K -0.019 0.106 -9999 0 -0.39 5 5
mol:H2O2 -0.001 0.004 -9999 0 -9999 0 0
STAT3 (dimer) -0.02 0.154 -9999 0 -0.495 7 7
negative regulation of transcription -0.026 0.137 -9999 0 -0.473 8 8
FCGR2A -0.017 0.156 -9999 0 -0.518 12 12
FER 0.026 0.019 -9999 0 -9999 0 0
alphaIIb/beta3 Integrin 0.039 0.042 -9999 0 -0.384 1 1
BLK 0.01 0.073 -9999 0 -0.518 2 2
Insulin Receptor/Insulin/Shc 0.055 0.04 -9999 0 -0.324 1 1
RHOA 0.028 0.01 -9999 0 -9999 0 0
LEPR 0.023 0.068 -9999 0 -0.517 2 2
BCAR1 0.032 0.005 -9999 0 -9999 0 0
p210 bcr-abl/Grb2 0.032 0.006 -9999 0 -9999 0 0
mol:NADPH -0.002 0.003 -9999 0 -9999 0 0
TRPV6 -0.021 0.176 -9999 0 -0.558 8 8
PRL 0.033 0.018 -9999 0 -9999 0 0
SOCS3 -0.001 0.214 -9999 0 -1.42 3 3
SPRY2 -0.016 0.139 -9999 0 -0.524 9 9
Insulin Receptor/Insulin/IRS1 0.04 0.083 -9999 0 -0.325 6 6
CSF1/CSF1R -0.037 0.133 -9999 0 -0.366 8 8
Ras protein signal transduction 0.033 0.122 0.629 5 -9999 0 5
IRS1 0.008 0.105 -9999 0 -0.518 5 5
INS 0.032 0.006 -9999 0 -9999 0 0
LEP 0.012 0.061 -9999 0 -0.52 1 1
STAT5B -0.042 0.137 -9999 0 -0.405 9 9
STAT5A -0.042 0.137 -9999 0 -0.405 9 9
GRB2 0.032 0.006 -9999 0 -9999 0 0
PDGFB-D/PDGFRB -0.05 0.129 -9999 0 -0.312 15 15
CSN2 0.042 0.062 -9999 0 -9999 0 0
PIK3CA 0.011 0.048 -9999 0 -0.518 1 1
LAT -0.05 0.199 -9999 0 -0.633 13 13
YBX1 0.034 0.049 -9999 0 -0.514 1 1
LCK -0.007 0.137 -9999 0 -0.518 9 9
SHC1 0.03 0.009 -9999 0 -9999 0 0
NOX4 -0.05 0.187 -9999 0 -0.523 18 18
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.032 0.011 -9999 0 -9999 0 0
HDAC2 0.032 0.011 -9999 0 -9999 0 0
GNB1/GNG2 -0.001 0.141 -9999 0 -0.325 21 21
forebrain development -0.083 0.217 -9999 0 -0.6 14 14
GNAO1 0.031 0.007 -9999 0 -9999 0 0
SMO/beta Arrestin2 -0.028 0.155 -9999 0 -0.378 22 22
SMO -0.062 0.202 -9999 0 -0.518 22 22
ARRB2 0.031 0.008 -9999 0 -9999 0 0
GLI3/SPOP 0.01 0.161 0.278 1 -0.452 7 8
mol:GTP 0 0.002 -9999 0 -9999 0 0
GSK3B 0.027 0.016 -9999 0 -9999 0 0
GNAI2 0.027 0.02 -9999 0 -9999 0 0
SIN3/HDAC complex 0.074 0.03 -9999 0 -9999 0 0
GNAI1 -0.001 0.13 -9999 0 -0.518 8 8
XPO1 0.025 0.018 -9999 0 -9999 0 0
GLI1/Su(fu) -0.093 0.231 -9999 0 -0.648 13 13
SAP30 0.03 0.01 -9999 0 -9999 0 0
mol:GDP -0.062 0.201 -9999 0 -0.517 22 22
MIM/GLI2A -0.019 0.134 -9999 0 -0.48 9 9
IFT88 0.027 0.048 -9999 0 -0.518 1 1
GNAI3 0.031 0.006 -9999 0 -9999 0 0
GLI2 -0.012 0.113 -9999 0 -0.369 5 5
GLI3 -0.003 0.162 0.266 2 -0.471 7 9
CSNK1D 0.031 0.007 -9999 0 -9999 0 0
CSNK1E 0.027 0.048 -9999 0 -0.518 1 1
SAP18 0.032 0.007 -9999 0 -9999 0 0
embryonic digit morphogenesis 0.027 0.047 -9999 0 -0.517 1 1
GNG2 0.032 0.005 -9999 0 -9999 0 0
Gi family/GTP -0.056 0.161 -9999 0 -0.333 29 29
SIN3B 0.032 0.006 -9999 0 -9999 0 0
SIN3A 0.033 0.004 -9999 0 -9999 0 0
GLI3/Su(fu) -0.005 0.152 -9999 0 -0.473 8 8
GLI2/Su(fu) -0.03 0.148 -9999 0 -0.342 16 16
FOXA2 -0.137 0.373 -9999 0 -0.98 21 21
neural tube patterning -0.083 0.217 -9999 0 -0.6 14 14
SPOP 0.033 0 -9999 0 -9999 0 0
Su(fu)/PIAS1 -0.007 0.104 -9999 0 -0.675 1 1
GNB1 0.032 0.006 -9999 0 -9999 0 0
CSNK1G2 0.032 0.005 -9999 0 -9999 0 0
CSNK1G3 0.031 0.008 -9999 0 -9999 0 0
MTSS1 -0.019 0.134 -9999 0 -0.481 9 9
embryonic limb morphogenesis -0.083 0.217 -9999 0 -0.6 14 14
SUFU -0.015 0.099 -9999 0 -0.722 1 1
LGALS3 0.023 0.067 -9999 0 -0.518 2 2
catabolic process -0.011 0.179 -9999 0 -0.531 8 8
GLI3A/CBP -0.001 0.1 -9999 0 -0.352 9 9
KIF3A 0.023 0.067 -9999 0 -0.518 2 2
GLI1 -0.085 0.224 -9999 0 -0.619 14 14
RAB23 0.031 0.012 -9999 0 -9999 0 0
CSNK1A1 0.031 0.007 -9999 0 -9999 0 0
IFT172 0.03 0.015 -9999 0 -9999 0 0
RBBP7 0.031 0.018 -9999 0 -9999 0 0
Su(fu)/Galectin3 -0.01 0.113 -9999 0 -0.424 4 4
GNAZ -0.001 0.122 -9999 0 -0.518 7 7
RBBP4 0.028 0.047 -9999 0 -0.518 1 1
CSNK1G1 0.032 0.005 -9999 0 -9999 0 0
PIAS1 0.032 0.006 -9999 0 -9999 0 0
PRKACA 0.032 0.007 -9999 0 -9999 0 0
GLI2/SPOP 0.001 0.117 -9999 0 -0.358 5 5
STK36 0.023 0.049 -9999 0 -0.518 1 1
Gi family/GNB1/GNG2/GDP -0.047 0.156 -9999 0 -0.46 12 12
PTCH1 -0.074 0.194 -9999 0 -0.536 14 14
MIM/GLI1 -0.102 0.256 -9999 0 -0.581 24 24
CREBBP 0 0.1 -9999 0 -0.352 9 9
Su(fu)/SIN3/HDAC complex 0.01 0.085 -9999 0 -0.332 6 6
Arf6 downstream 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
PLAUR -0.038 0.261 -9999 0 -1.075 8 8
regulation of axonogenesis 0.005 0.051 0.288 2 -9999 0 2
myoblast fusion -0.02 0.109 0.39 8 -9999 0 8
mol:GTP 0.011 0.069 -9999 0 -0.223 10 10
regulation of calcium-dependent cell-cell adhesion -0.051 0.08 0.237 8 -9999 0 8
ARF1/GTP 0.031 0.06 -9999 0 -0.187 7 7
mol:GM1 0.002 0.05 -9999 0 -0.183 7 7
mol:Choline -0.01 0.072 -9999 0 -0.337 5 5
lamellipodium assembly -0.007 0.116 -9999 0 -0.434 9 9
MAPK3 0.006 0.096 -9999 0 -0.361 8 8
ARF6/GTP/NME1/Tiam1 0.052 0.081 -9999 0 -0.238 8 8
ARF1 0.033 0.003 -9999 0 -9999 0 0
ARF6/GDP 0.02 0.109 -9999 0 -0.392 8 8
ARF1/GDP 0.023 0.108 -9999 0 -0.342 10 10
ARF6 0.032 0.048 -9999 0 -0.188 1 1
RAB11A 0.032 0.005 -9999 0 -9999 0 0
TIAM1 0.03 0.018 -9999 0 -9999 0 0
fibronectin binding 0 0 -9999 0 -9999 0 0
MAPK1 0.011 0.083 -9999 0 -0.308 8 8
actin filament bundle formation -0.017 0.105 0.339 10 -9999 0 10
KALRN -0.004 0.074 -9999 0 -0.308 7 7
RAB11FIP3/RAB11A 0.045 0.017 -9999 0 -9999 0 0
RhoA/GDP 0.017 0.106 -9999 0 -0.341 10 10
NME1 0.031 0.018 -9999 0 -9999 0 0
Rac1/GDP 0.022 0.107 -9999 0 -0.343 10 10
substrate adhesion-dependent cell spreading 0.011 0.068 -9999 0 -0.223 10 10
cortical actin cytoskeleton organization -0.009 0.116 -9999 0 -0.437 9 9
RAC1 0.032 0.005 -9999 0 -9999 0 0
liver development 0.011 0.068 -9999 0 -0.223 10 10
ARF6/GTP 0.011 0.069 -9999 0 -0.223 10 10
RhoA/GTP 0.028 0.059 -9999 0 -0.187 7 7
mol:GDP -0.014 0.102 -9999 0 -0.369 10 10
ARF6/GTP/RAB11FIP3/RAB11A 0.047 0.059 -9999 0 -0.216 1 1
RHOA 0.03 0.01 -9999 0 -9999 0 0
PLD1 -0.007 0.068 -9999 0 -0.278 7 7
RAB11FIP3 0.03 0.015 -9999 0 -9999 0 0
tube morphogenesis -0.007 0.116 -9999 0 -0.434 9 9
ruffle organization -0.005 0.051 -9999 0 -0.288 2 2
regulation of epithelial cell migration 0.011 0.068 -9999 0 -0.223 10 10
PLD2 0.008 0.068 -9999 0 -0.22 9 9
PIP5K1A -0.006 0.051 -9999 0 -0.29 2 2
mol:Phosphatidic acid -0.01 0.072 -9999 0 -0.337 5 5
Rac1/GTP -0.009 0.117 -9999 0 -0.439 9 9
PDGFR-alpha signaling pathway

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
PDGFRA -0.006 0.122 -9999 0 -0.516 7 7
PDGF/PDGFRA/CRKL 0.018 0.081 -9999 0 -0.365 5 5
positive regulation of JUN kinase activity 0.048 0.074 -9999 0 -0.28 5 5
CRKL 0.029 0.011 -9999 0 -9999 0 0
PDGF/PDGFRA/Caveolin-3 0.016 0.091 -9999 0 -0.358 7 7
AP1 -0.099 0.284 -9999 0 -0.964 12 12
mol:IP3 -0.013 0.077 -9999 0 -0.381 5 5
PLCG1 -0.013 0.077 -9999 0 -0.381 5 5
PDGF/PDGFRA/alphaV Integrin 0.006 0.115 -9999 0 -0.404 9 9
RAPGEF1 0.033 0.004 -9999 0 -9999 0 0
CRK 0.031 0.007 -9999 0 -9999 0 0
mol:Ca2+ -0.013 0.077 -9999 0 -0.38 5 5
CAV3 0.03 0.009 -9999 0 -9999 0 0
CAV1 -0.022 0.151 -9999 0 -0.518 11 11
SHC/Grb2/SOS1 0.05 0.076 -9999 0 -0.281 5 5
PDGF/PDGFRA/Shf 0.008 0.104 -9999 0 -0.369 9 9
FOS -0.114 0.269 -9999 0 -0.945 12 12
JUN -0.044 0.085 -9999 0 -0.417 6 6
oligodendrocyte development 0.005 0.115 -9999 0 -0.403 9 9
GRB2 0.032 0.006 -9999 0 -9999 0 0
PIK3R1 0.004 0.097 -9999 0 -0.518 4 4
mol:DAG -0.013 0.077 -9999 0 -0.381 5 5
PDGF/PDGFRA -0.006 0.121 -9999 0 -0.515 7 7
actin cytoskeleton reorganization 0.007 0.099 -9999 0 -0.363 8 8
SRF 0.016 0.013 -9999 0 -9999 0 0
SHC1 0.03 0.009 -9999 0 -9999 0 0
PI3K -0.002 0.084 -9999 0 -0.316 7 7
PDGF/PDGFRA/Crk/C3G 0.038 0.083 -9999 0 -0.305 7 7
JAK1 -0.013 0.085 -9999 0 -0.371 7 7
ELK1/SRF -0.015 0.078 -9999 0 -0.298 5 5
SHB 0.019 0.068 -9999 0 -0.518 2 2
SHF 0.022 0.068 -9999 0 -0.518 2 2
CSNK2A1 0.033 0.023 -9999 0 -9999 0 0
GO:0007205 -0.018 0.078 -9999 0 -0.4 5 5
SOS1 0.032 0.007 -9999 0 -9999 0 0
Ras protein signal transduction 0.048 0.074 -9999 0 -0.28 5 5
PDGF/PDGFRA/SHB 0.007 0.099 -9999 0 -0.364 8 8
PDGF/PDGFRA/Caveolin-1 -0.021 0.157 -9999 0 -0.473 13 13
ITGAV 0.019 0.082 -9999 0 -0.518 3 3
ELK1 -0.028 0.069 -9999 0 -0.348 5 5
PIK3CA 0.011 0.048 -9999 0 -0.518 1 1
PDGF/PDGFRA/Crk 0.015 0.092 -9999 0 -0.363 7 7
JAK-STAT cascade -0.013 0.085 -9999 0 -0.37 7 7
cell proliferation 0.008 0.104 -9999 0 -0.368 9 9
Reelin signaling pathway

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
CDK5R1/CDK5 0.045 0.018 -9999 0 -9999 0 0
VLDLR -0.015 0.137 -9999 0 -0.518 9 9
CRKL 0.029 0.011 -9999 0 -9999 0 0
LRPAP1 0.03 0.01 -9999 0 -9999 0 0
FYN 0.023 0.067 -9999 0 -0.518 2 2
ITGA3 0.002 0.099 -9999 0 -0.518 4 4
RELN/VLDLR/Fyn 0.011 0.11 -9999 0 -0.324 11 11
MAPK8IP1/MKK7/MAP3K11/JNK1 0.083 0.038 -9999 0 -9999 0 0
AKT1 -0.023 0.088 -9999 0 -0.331 7 7
MAP2K7 0.031 0.012 -9999 0 -9999 0 0
RAPGEF1 0.033 0.004 -9999 0 -9999 0 0
DAB1 0.031 0.012 -9999 0 -9999 0 0
RELN/LRP8/DAB1 0.027 0.095 -9999 0 -0.295 10 10
LRPAP1/LRP8 0.009 0.111 -9999 0 -0.377 10 10
RELN/LRP8/DAB1/Fyn 0.034 0.108 -9999 0 -0.303 11 11
DAB1/alpha3/beta1 Integrin -0.025 0.137 -9999 0 -0.299 22 22
long-term memory 0.042 0.12 -9999 0 -0.319 11 11
DAB1/LIS1 0.011 0.132 -9999 0 -0.289 18 18
DAB1/CRLK/C3G -0.001 0.118 -9999 0 -0.287 16 16
PIK3CA 0.011 0.048 -9999 0 -0.518 1 1
DAB1/NCK2 0.011 0.133 -9999 0 -0.291 18 18
ARHGEF2 0.031 0.007 -9999 0 -9999 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -9999 0 0
GRIN2A 0.032 0.006 -9999 0 -9999 0 0
CDK5R1 0.03 0.018 -9999 0 -9999 0 0
RELN 0.03 0.012 -9999 0 -9999 0 0
PIK3R1 0.004 0.097 -9999 0 -0.518 4 4
RELN/LRP8/Fyn 0.022 0.116 -9999 0 -0.35 11 11
GRIN2A/RELN/LRP8/DAB1/Fyn 0.047 0.115 -9999 0 -0.306 11 11
MAPK8 0.032 0.007 -9999 0 -9999 0 0
RELN/VLDLR/DAB1 0.018 0.094 -9999 0 -0.295 9 9
ITGB1 0.023 0.067 -9999 0 -0.518 2 2
MAP1B -0.081 0.159 -9999 0 -0.321 36 36
RELN/LRP8 0.023 0.102 -9999 0 -0.323 10 10
GRIN2B/RELN/LRP8/DAB1/Fyn 0.042 0.122 -9999 0 -0.329 11 11
PI3K 0.005 0.067 -9999 0 -0.378 3 3
mol:PP2 0 0 -9999 0 -9999 0 0
alpha3/beta1 Integrin 0.015 0.092 -9999 0 -0.378 6 6
RAP1A -0.028 0.128 0.531 1 -0.393 4 5
PAFAH1B1 0.031 0.007 -9999 0 -9999 0 0
MAPK8IP1 0.031 0.012 -9999 0 -9999 0 0
CRLK/C3G 0.043 0.016 -9999 0 -9999 0 0
GRIN2B 0.026 0.048 -9999 0 -0.518 1 1
NCK2 0.033 0.003 -9999 0 -9999 0 0
neuron differentiation 0.017 0.073 -9999 0 -0.369 1 1
neuron adhesion -0.046 0.136 0.522 1 -0.406 5 6
LRP8 -0.013 0.144 -9999 0 -0.518 10 10
GSK3B 0 0.098 -9999 0 -0.446 3 3
RELN/VLDLR/DAB1/Fyn 0.023 0.103 -9999 0 -0.28 11 11
MAP3K11 0.033 0 -9999 0 -9999 0 0
RELN/VLDLR/DAB1/P13K -0.023 0.097 -9999 0 -0.326 9 9
CDK5 0.032 0.005 -9999 0 -9999 0 0
MAPT 0.005 0.058 0.67 1 -9999 0 1
neuron migration -0.007 0.122 -9999 0 -0.434 3 3
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.017 0.073 -9999 0 -0.372 1 1
RELN/VLDLR 0.001 0.136 -9999 0 -0.315 18 18
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.029 0.146 -9999 0 -0.518 11 11
positive regulation of NF-kappaB transcription factor activity -0.016 0.11 -9999 0 -0.373 11 11
MAP2K4 0.027 0.1 0.216 1 -0.297 4 5
IKBKB 0.029 0.01 -9999 0 -9999 0 0
TNFRSF10B 0.022 0.067 -9999 0 -0.518 2 2
TNFRSF10A 0.024 0.05 -9999 0 -0.518 1 1
SMPD1 -0.012 0.062 -9999 0 -0.208 12 12
IKBKG 0.032 0.01 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
TNFRSF10D 0.02 0.067 -9999 0 -0.518 2 2
TRAIL/TRAILR2 -0.019 0.124 -9999 0 -0.401 12 12
TRAIL/TRAILR3 -0.021 0.114 -9999 0 -0.387 11 11
TRAIL/TRAILR1 -0.016 0.111 -9999 0 -0.359 12 12
TRAIL/TRAILR4 -0.016 0.11 -9999 0 -0.374 11 11
TRAIL/TRAILR1/DAP3/GTP -0.004 0.092 -9999 0 -0.294 11 11
IKK complex 0.04 0.08 -9999 0 -0.457 1 1
RIPK1 0.032 0.005 -9999 0 -9999 0 0
response to oxidative stress 0 0 -9999 0 -9999 0 0
DAP3/GTP 0.023 0.006 -9999 0 -9999 0 0
MAPK3 -0.022 0.101 -9999 0 -0.378 10 10
MAP3K1 -0.016 0.105 -9999 0 -0.379 6 6
TRAILR4 (trimer) 0.02 0.067 -9999 0 -0.517 2 2
TRADD 0.028 0.047 -9999 0 -0.518 1 1
TRAILR1 (trimer) 0.024 0.05 -9999 0 -0.517 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.015 0.09 -9999 0 -0.287 11 11
CFLAR 0.016 0.093 -9999 0 -0.518 4 4
MAPK1 -0.016 0.091 -9999 0 -0.378 8 8
TRAIL/TRAILR1/FADD/TRADD/RIP 0.004 0.096 -9999 0 -0.286 10 10
mol:ceramide -0.012 0.062 -9999 0 -0.208 12 12
FADD 0.03 0.01 -9999 0 -9999 0 0
MAPK8 0.029 0.102 0.268 1 -0.302 2 3
TRAF2 0.031 0.012 -9999 0 -9999 0 0
TRAILR3 (trimer) 0.011 0.084 -9999 0 -0.517 3 3
CHUK 0.028 0.047 -9999 0 -0.518 1 1
TRAIL/TRAILR1/FADD -0.006 0.096 -9999 0 -0.323 10 10
DAP3 0.031 0.008 -9999 0 -9999 0 0
CASP10 0.051 0.155 0.368 4 -0.423 7 11
JNK cascade -0.016 0.11 -9999 0 -0.373 11 11
TRAIL (trimer) -0.029 0.145 -9999 0 -0.517 11 11
TNFRSF10C 0.011 0.084 -9999 0 -0.518 3 3
TRAIL/TRAILR1/DAP3/GTP/FADD 0.001 0.088 -9999 0 -0.279 10 10
TRAIL/TRAILR2/FADD -0.009 0.108 -9999 0 -0.347 11 11
cell death -0.012 0.062 -9999 0 -0.207 12 12
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.017 0.094 -9999 0 -0.295 12 12
TRAILR2 (trimer) 0.022 0.067 -9999 0 -0.517 2 2
CASP8 -0.015 0.141 -9999 0 -0.684 5 5
negative regulation of caspase activity 0 0 -9999 0 -9999 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.002 0.103 -9999 0 -0.293 12 12
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.017 0.046 -9999 0 -0.324 3 3
SNTA1 0.026 0.048 -9999 0 -0.518 1 1
response to hypoxia 0 0 -9999 0 -9999 0 0
STMN1 -0.022 0.059 -9999 0 -0.325 5 5
MAPK12 -0.021 0.104 0.211 4 -0.322 12 16
CCND1 -0.032 0.136 -9999 0 -0.472 10 10
p38 gamma/SNTA1 -0.002 0.107 -9999 0 -0.306 12 12
MAP2K3 0.031 0.008 -9999 0 -9999 0 0
PKN1 0.032 0.007 -9999 0 -9999 0 0
G2/M transition checkpoint -0.019 0.105 0.21 5 -0.32 12 17
MAP2K6 -0.004 0.074 0.243 2 -0.299 7 9
MAPT -0.002 0.058 -9999 0 -0.241 3 3
MAPK13 0.006 0.058 -9999 0 -0.379 3 3
hyperosmotic response 0 0 -9999 0 -9999 0 0
ZAK 0.012 0.042 -9999 0 -0.329 2 2
Syndecan-3-mediated signaling events

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
CTTN 0.03 0.01 -9999 0 -9999 0 0
Syndecan-3/Src/Cortactin -0.047 0.157 -9999 0 -0.541 4 4
Syndecan-3/Neurocan -0.005 0.09 -9999 0 -0.5 4 4
POMC -0.026 0.162 -9999 0 -0.518 13 13
EGFR -0.014 0.144 -9999 0 -0.518 10 10
Syndecan-3/EGFR 0.003 0.117 -9999 0 -0.54 3 3
AGRP 0.028 0.021 -9999 0 -9999 0 0
NCSTN 0.031 0.007 -9999 0 -9999 0 0
PSENEN 0.029 0.011 -9999 0 -9999 0 0
RP11-540L11.1 0 0 -9999 0 -9999 0 0
APH1B 0.028 0.047 -9999 0 -0.518 1 1
APH1A 0.014 0.093 -9999 0 -0.518 4 4
NCAN 0 0 -9999 0 -9999 0 0
long-term memory 0.035 0.101 -9999 0 -0.478 4 4
Syndecan-3/IL8 -0.055 0.153 -9999 0 -0.578 4 4
PSEN1 0.028 0.047 -9999 0 -0.518 1 1
Src/Cortactin 0.04 0.02 -9999 0 -9999 0 0
FYN 0.023 0.067 -9999 0 -0.518 2 2
limb bud formation -0.004 0.093 -9999 0 -0.515 4 4
MC4R 0.022 0.067 -9999 0 -0.518 2 2
SRC 0.03 0.013 -9999 0 -9999 0 0
PTN -0.139 0.236 -9999 0 -0.518 37 37
FGFR/FGF/Syndecan-3 -0.004 0.094 -9999 0 -0.521 4 4
neuron projection morphogenesis -0.069 0.134 -9999 0 -0.524 4 4
Syndecan-3/AgRP 0.024 0.099 -9999 0 -0.503 4 4
Syndecan-3/AgRP/MC4R 0.032 0.107 -9999 0 -0.49 4 4
Fyn/Cortactin 0.038 0.043 -9999 0 -0.378 1 1
SDC3 -0.004 0.095 -9999 0 -0.527 4 4
GO:0007205 0 0 -9999 0 -9999 0 0
positive regulation of leukocyte migration -0.054 0.151 -9999 0 -0.568 4 4
IL8 -0.122 0.228 -9999 0 -0.518 33 33
Syndecan-3/Fyn/Cortactin 0.036 0.104 -9999 0 -0.49 4 4
Syndecan-3/CASK -0.005 0.09 -9999 0 -0.5 4 4
alpha-MSH/MC4R -0.007 0.133 -9999 0 -0.377 15 15
Gamma Secretase 0.062 0.085 -9999 0 -0.346 4 4
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.015 0.049 -9999 0 -0.375 2 2
alphaV beta3 Integrin 0.033 0.093 -9999 0 -0.332 7 7
PTK2 -0.007 0.123 -9999 0 -0.489 5 5
IGF1R -0.01 0.144 -9999 0 -0.518 10 10
PI4KB 0 0 -9999 0 -9999 0 0
MFGE8 0.028 0.048 -9999 0 -0.518 1 1
SRC 0.03 0.013 -9999 0 -9999 0 0
CDKN1B 0.017 0.035 -9999 0 -9999 0 0
VEGFA 0 0 -9999 0 -9999 0 0
ILK 0.018 0.035 -9999 0 -9999 0 0
ROCK1 0.032 0.006 -9999 0 -9999 0 0
AKT1 0.01 0.031 -9999 0 -9999 0 0
PTK2B 0.007 0.085 -9999 0 -0.404 4 4
alphaV/beta3 Integrin/JAM-A 0.039 0.092 -9999 0 -0.288 8 8
CBL 0.032 0.005 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
alphaV beta3 Integrin/ANGPTL3 0.047 0.066 -9999 0 -0.324 3 3
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.031 0.167 -9999 0 -0.326 29 29
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.003 0.079 -9999 0 -0.385 4 4
alphaV/beta3 Integrin/Syndecan-1 0.03 0.105 -9999 0 -0.359 8 8
PI4KA 0 0 -9999 0 -9999 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.07 0.194 -9999 0 -0.361 35 35
PI4 Kinase 0 0 -9999 0 -9999 0 0
PIK3CA 0.011 0.048 -9999 0 -0.518 1 1
alphaV/beta3 Integrin/Osteopontin -0.059 0.17 -9999 0 -0.346 32 32
RPS6KB1 -0.104 0.156 -9999 0 -0.5 12 12
TLN1 0.029 0.01 -9999 0 -9999 0 0
MAPK3 -0.057 0.174 -9999 0 -0.612 10 10
GPR124 0.026 0.018 -9999 0 -9999 0 0
MAPK1 -0.054 0.173 -9999 0 -0.611 10 10
PXN 0.033 0.003 -9999 0 -9999 0 0
PIK3R1 0.004 0.097 -9999 0 -0.518 4 4
alphaV/beta3 Integrin/Tumstatin 0.045 0.078 -9999 0 -0.324 5 5
cell adhesion 0.019 0.082 -9999 0 -0.283 7 7
ANGPTL3 0.03 0.016 -9999 0 -9999 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.03 0.047 -9999 0 -0.321 2 2
IGF-1R heterotetramer -0.01 0.143 -9999 0 -0.517 10 10
Rac1/GDP 0.024 0.004 -9999 0 -9999 0 0
TGFBR2 0.024 0.05 -9999 0 -0.518 1 1
ITGB3 0.024 0.052 -9999 0 -0.518 1 1
IGF1 -0.054 0.185 -9999 0 -0.518 18 18
RAC1 0.032 0.005 -9999 0 -9999 0 0
regulation of cell-matrix adhesion 0.039 0.066 -9999 0 -0.323 3 3
apoptosis 0.019 0.082 -9999 0 -0.516 3 3
CD47 0.01 0.093 -9999 0 -0.518 4 4
alphaV/beta3 Integrin/CD47 0.027 0.09 -9999 0 -0.324 7 7
VCL 0.028 0.047 -9999 0 -0.518 1 1
alphaV/beta3 Integrin/Del1 -0.005 0.132 -9999 0 -0.371 13 13
CSF1 0.03 0.012 -9999 0 -9999 0 0
PIK3C2A 0.011 0.07 -9999 0 -0.481 2 2
PI4 Kinase/Pyk2 0.003 0.084 -9999 0 -0.325 7 7
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.037 0.089 -9999 0 -0.427 4 4
FAK1/Vinculin 0.013 0.107 -9999 0 -0.386 5 5
alphaV beta3/Integrin/ppsTEM5 0.039 0.067 -9999 0 -0.324 3 3
RHOA 0.03 0.01 -9999 0 -9999 0 0
VTN 0.032 0.006 -9999 0 -9999 0 0
BCAR1 0.032 0.005 -9999 0 -9999 0 0
FGF2 0.014 0.083 -9999 0 -0.518 3 3
F11R 0 0.068 -9999 0 -0.379 4 4
alphaV/beta3 Integrin/Lactadherin 0.045 0.078 -9999 0 -0.324 5 5
alphaV/beta3 Integrin/TGFBR2 0.041 0.086 -9999 0 -0.39 4 4
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.068 0.061 -9999 0 -0.293 3 3
HSP90AA1 0 0 -9999 0 -9999 0 0
alphaV/beta3 Integrin/Talin 0.041 0.065 -9999 0 -0.291 4 4
mol:GDP 0 0 -9999 0 -9999 0 0
FN1 -0.009 0.131 -9999 0 -0.518 8 8
alphaV/beta3 Integrin/Pyk2 0.035 0.091 -9999 0 -0.406 4 4
SDC1 0.01 0.104 -9999 0 -0.518 5 5
VAV3 -0.054 0.125 -9999 0 -0.291 28 28
PTPN11 0.029 0.047 -9999 0 -0.518 1 1
IRS1 0.008 0.105 -9999 0 -0.518 5 5
FAK1/Paxillin 0.014 0.109 -9999 0 -0.386 5 5
cell migration 0.006 0.098 -9999 0 -0.351 5 5
ITGAV 0.019 0.082 -9999 0 -0.518 3 3
PI3K 0.001 0.085 -9999 0 -0.274 7 7
SPP1 -0.113 0.224 -9999 0 -0.518 31 31
KDR 0.02 0.067 -9999 0 -0.518 2 2
mol:PI-4-5-P2 0 0 -9999 0 -9999 0 0
alphaV/beta3 Integrin/Caspase 8 0.019 0.082 -9999 0 -0.517 3 3
COL4A3 0.027 0.048 -9999 0 -0.518 1 1
angiogenesis -0.046 0.178 -9999 0 -0.615 10 10
Rac1/GTP -0.04 0.123 -9999 0 -0.271 28 28
EDIL3 -0.033 0.15 -9999 0 -0.518 11 11
cell proliferation 0.04 0.085 -9999 0 -0.388 4 4
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.027 0.013 -9999 0 -9999 0 0
Caspase 8 (4 units) 0 0.154 -9999 0 -0.473 8 8
NEF -0.015 0.052 -9999 0 -0.174 13 13
NFKBIA 0.011 0.068 -9999 0 -0.613 1 1
BIRC3 -0.03 0.175 -9999 0 -0.583 11 11
CYCS -0.018 0.123 0.19 4 -0.353 10 14
RIPK1 0.032 0.005 -9999 0 -9999 0 0
CD247 -0.015 0.052 -9999 0 -0.174 13 13
MAP2K7 -0.006 0.16 -9999 0 -0.717 4 4
protein ubiquitination 0.015 0.085 -9999 0 -0.41 2 2
CRADD 0.025 0.066 -9999 0 -0.518 2 2
DAXX 0.032 0.005 -9999 0 -9999 0 0
FAS -0.017 0.15 -9999 0 -0.518 11 11
BID -0.022 0.128 -9999 0 -0.372 11 11
NF-kappa-B/RelA/I kappa B alpha 0.023 0.113 -9999 0 -0.313 11 11
TRADD 0.028 0.047 -9999 0 -0.518 1 1
MAP3K5 0.032 0.011 -9999 0 -9999 0 0
CFLAR 0.016 0.093 -9999 0 -0.518 4 4
FADD 0.03 0.01 -9999 0 -9999 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.023 0.113 -9999 0 -0.314 11 11
MAPK8 -0.004 0.149 -9999 0 -0.654 4 4
APAF1 0.029 0.047 -9999 0 -0.518 1 1
TRAF1 0.023 0.068 -9999 0 -0.518 2 2
TRAF2 0.031 0.012 -9999 0 -9999 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.021 0.14 -9999 0 -0.334 18 18
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.024 0.098 -9999 0 -0.388 3 3
CHUK 0.015 0.09 -9999 0 -0.392 3 3
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.046 0.105 -9999 0 -0.291 9 9
TCRz/NEF -0.023 0.09 -9999 0 -0.297 13 13
TNF 0.025 0.051 -9999 0 -0.518 1 1
FASLG -0.045 0.187 -9999 0 -0.614 13 13
NFKB1 0.017 0.04 -9999 0 -9999 0 0
TNFR1A/BAG4/TNF-alpha 0.042 0.048 -9999 0 -0.324 1 1
CASP6 -0.019 0.21 -9999 0 -0.69 9 9
CASP7 -0.046 0.209 -9999 0 -0.598 14 14
RELA 0.016 0.044 -9999 0 -9999 0 0
CASP2 0.033 0.004 -9999 0 -9999 0 0
CASP3 -0.056 0.214 -9999 0 -0.605 14 14
TNFRSF1A 0.026 0.048 -9999 0 -0.518 1 1
TNFR1A/BAG4 0.033 0.041 -9999 0 -0.378 1 1
CASP8 0.024 0.066 -9999 0 -0.518 2 2
CASP9 0.032 0.006 -9999 0 -9999 0 0
MAP3K14 0.019 0.101 -9999 0 -0.437 3 3
APAF-1/Caspase 9 -0.036 0.154 -9999 0 -0.436 13 13
BCL2 -0.016 0.145 -9999 0 -0.546 5 5
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.029 0.142 -9999 0 -0.405 13 13
KLHL20 -0.01 0.109 0.201 1 -0.311 8 9
CYFIP2 0.025 0.049 -9999 0 -0.518 1 1
Rac1/GDP -0.001 0.109 0.342 1 -0.284 7 8
ENAH -0.03 0.147 -9999 0 -0.412 14 14
AP1M1 0.032 0.006 -9999 0 -9999 0 0
RAP1B 0.031 0.007 -9999 0 -9999 0 0
RAP1A 0.023 0.066 -9999 0 -0.518 2 2
CTNNB1 0.028 0.017 -9999 0 -9999 0 0
CDC42/GTP 0.01 0.079 -9999 0 -9999 0 0
ABI1/Sra1/Nap1 -0.032 0.059 -9999 0 -0.202 9 9
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.052 0.088 -9999 0 -0.296 7 7
RAPGEF1 -0.021 0.135 0.343 1 -0.398 9 10
CTNND1 0.025 0.066 -9999 0 -0.518 2 2
regulation of calcium-dependent cell-cell adhesion -0.025 0.153 -9999 0 -0.421 14 14
CRK -0.016 0.137 -9999 0 -0.399 12 12
E-cadherin/gamma catenin/alpha catenin 0.02 0.124 -9999 0 -0.345 13 13
alphaE/beta7 Integrin 0.047 0.01 -9999 0 -9999 0 0
IQGAP1 0.032 0.005 -9999 0 -9999 0 0
NCKAP1 0.028 0.023 -9999 0 -9999 0 0
Rap1/GTP/I-afadin 0.05 0.047 -9999 0 -0.295 2 2
DLG1 -0.017 0.109 -9999 0 -0.376 9 9
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -9999 0 0
mol:PI-3-4-5-P3 -0.01 0.044 -9999 0 -0.258 2 2
MLLT4 0.032 0.006 -9999 0 -9999 0 0
ARF6/GTP/NME1/Tiam1 0.058 0.021 -9999 0 -9999 0 0
PI3K -0.011 0.057 -9999 0 -0.34 2 2
ARF6 0.031 0.012 -9999 0 -9999 0 0
mol:Ca2+ 0 0 -9999 0 -9999 0 0
E-cadherin/gamma catenin 0.001 0.135 -9999 0 -0.402 13 13
TIAM1 0.032 0.006 -9999 0 -9999 0 0
E-cadherin(dimer)/Ca2+ 0.043 0.091 -9999 0 -0.278 9 9
AKT1 -0.001 0.044 -9999 0 -0.191 2 2
PIK3R1 0.004 0.097 -9999 0 -0.518 4 4
CDH1 0.002 0.122 -9999 0 -0.518 7 7
RhoA/GDP 0.005 0.107 0.342 1 -0.284 6 7
actin cytoskeleton organization -0.004 0.081 0.152 2 -0.229 7 9
CDC42/GDP 0.002 0.11 0.342 1 -0.284 7 8
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.011 0.097 -9999 0 -0.274 15 15
ITGB7 0.033 0 -9999 0 -9999 0 0
RAC1 0.032 0.005 -9999 0 -9999 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.047 0.097 -9999 0 -0.296 9 9
E-cadherin/Ca2+/beta catenin/alpha catenin 0.032 0.076 -9999 0 -0.275 7 7
mol:GDP -0.016 0.115 0.349 1 -0.326 7 8
CDC42/GTP/IQGAP1 0.043 0.009 -9999 0 -9999 0 0
JUP 0.003 0.122 -9999 0 -0.518 7 7
p120 catenin/RhoA/GDP 0.01 0.115 0.347 1 -0.289 8 9
RAC1/GTP/IQGAP1 0.043 0.009 -9999 0 -9999 0 0
PIP5K1C/AP1M1 0.043 0.039 -9999 0 -0.378 1 1
RHOA 0.03 0.01 -9999 0 -9999 0 0
CDC42 0.032 0.005 -9999 0 -9999 0 0
CTNNA1 0.031 0.008 -9999 0 -9999 0 0
positive regulation of S phase of mitotic cell cycle -0.007 0.076 0.127 1 -0.232 10 11
NME1 0.033 0 -9999 0 -9999 0 0
clathrin coat assembly 0 0 -9999 0 -9999 0 0
TJP1 -0.034 0.149 -9999 0 -0.407 15 15
regulation of cell-cell adhesion -0.004 0.062 -9999 0 -9999 0 0
WASF2 -0.003 0.043 -9999 0 -0.124 5 5
Rap1/GTP 0.012 0.092 0.317 1 -9999 0 1
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.048 0.121 -9999 0 -0.301 13 13
CCND1 -0.01 0.094 0.146 1 -0.292 10 11
VAV2 -0.043 0.228 -9999 0 -0.627 13 13
RAP1/GDP 0.013 0.099 0.349 1 -9999 0 1
adherens junction assembly -0.032 0.145 -9999 0 -0.394 15 15
homophilic cell adhesion 0 0 -9999 0 -9999 0 0
ABI1 0.032 0.006 -9999 0 -9999 0 0
PIP5K1C 0.027 0.049 -9999 0 -0.518 1 1
regulation of heterotypic cell-cell adhesion 0.027 0.111 -9999 0 -0.293 12 12
E-cadherin/beta catenin -0.007 0.087 -9999 0 -0.346 8 8
mol:GTP 0 0 -9999 0 -9999 0 0
SRC -0.031 0.145 -9999 0 -0.417 13 13
PIK3CA 0.011 0.048 -9999 0 -0.518 1 1
Rac1/GTP -0.064 0.156 -9999 0 -0.477 12 12
E-cadherin/beta catenin/alpha catenin 0.036 0.088 -9999 0 -0.322 7 7
ITGAE 0.032 0.007 -9999 0 -9999 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.026 0.156 -9999 0 -0.43 14 14
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.006 0.008 -9999 0 -9999 0 0
RAS family/GTP 0.018 0.108 -9999 0 -0.288 3 3
NFATC4 -0.017 0.082 0.227 1 -0.283 3 4
ERBB2IP 0.03 0.01 -9999 0 -9999 0 0
HSP90 (dimer) 0 0 -9999 0 -9999 0 0
mammary gland morphogenesis -0.002 0.096 -9999 0 -0.305 9 9
JUN 0.017 0.067 -9999 0 -9999 0 0
HRAS 0.027 0.049 -9999 0 -0.521 1 1
DOCK7 -0.024 0.091 -9999 0 -0.295 9 9
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.024 0.107 -9999 0 -0.328 9 9
AKT1 0.006 0.007 -9999 0 -9999 0 0
BAD -0.006 0.006 -9999 0 -9999 0 0
MAPK10 -0.021 0.063 0.179 1 -0.214 4 5
mol:GTP 0 0.002 -9999 0 -9999 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.002 0.103 -9999 0 -0.327 9 9
RAF1 0.003 0.103 0.229 1 -0.302 3 4
ErbB2/ErbB3/neuregulin 2 0.025 0.05 -9999 0 -0.313 2 2
STAT3 0.01 0.161 -9999 0 -0.896 4 4
cell migration -0.013 0.061 0.188 1 -0.217 1 2
mol:PI-3-4-5-P3 -0.001 0.002 -9999 0 -9999 0 0
cell proliferation -0.032 0.216 -9999 0 -0.637 11 11
FOS -0.032 0.182 -9999 0 -0.448 18 18
NRAS 0.025 0.049 -9999 0 -0.517 1 1
mol:Ca2+ -0.002 0.096 -9999 0 -0.305 9 9
MAPK3 -0.022 0.185 -9999 0 -0.579 8 8
MAPK1 -0.023 0.186 -9999 0 -0.574 9 9
JAK2 -0.024 0.09 -9999 0 -0.306 8 8
NF2 0.006 0.065 -9999 0 -0.729 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.006 0.082 -9999 0 -0.279 8 8
NRG1 -0.015 0.144 -9999 0 -0.519 10 10
GRB2/SOS1 0.045 0.013 -9999 0 -9999 0 0
MAPK8 -0.004 0.1 -9999 0 -0.295 9 9
MAPK9 -0.012 0.059 0.179 1 -0.231 1 2
ERBB2 -0.025 0.034 -9999 0 -0.398 1 1
ERBB3 0.028 0.048 -9999 0 -0.519 1 1
SHC1 0.03 0.009 -9999 0 -9999 0 0
RAC1 0.032 0.005 -9999 0 -9999 0 0
apoptosis 0.002 0.006 -9999 0 -9999 0 0
STAT3 (dimer) 0.011 0.157 -9999 0 -0.873 4 4
RNF41 -0.009 0.009 -9999 0 -9999 0 0
FRAP1 -0.006 0.006 -9999 0 -9999 0 0
RAC1-CDC42/GTP -0.016 0.063 -9999 0 -0.223 9 9
ErbB2/ErbB2/HSP90 (dimer) -0.02 0.029 -9999 0 -0.337 1 1
CHRNA1 -0.004 0.146 -9999 0 -0.404 10 10
myelination -0.012 0.087 0.235 2 -0.358 1 3
PPP3CB -0.023 0.086 -9999 0 -0.278 9 9
KRAS 0.014 0.093 -9999 0 -0.519 4 4
RAC1-CDC42/GDP 0.034 0.094 -9999 0 -0.25 8 8
NRG2 0.029 0.016 -9999 0 -9999 0 0
mol:GDP 0.006 0.082 -9999 0 -0.277 8 8
SOS1 0.032 0.007 -9999 0 -9999 0 0
MAP2K2 -0.004 0.1 0.224 2 -0.35 2 4
SRC 0.03 0.013 -9999 0 -9999 0 0
mol:cAMP -0.001 0.001 -9999 0 -9999 0 0
PTPN11 -0.026 0.093 -9999 0 -0.296 9 9
MAP2K1 -0.024 0.181 -9999 0 -0.518 9 9
heart morphogenesis -0.002 0.096 -9999 0 -0.305 9 9
RAS family/GDP 0.025 0.112 -9999 0 -0.267 5 5
GRB2 0.032 0.006 -9999 0 -9999 0 0
PRKACA 0.005 0.084 -9999 0 -0.675 2 2
CHRNE 0.011 0.017 -9999 0 -9999 0 0
HSP90AA1 0 0 -9999 0 -9999 0 0
activation of caspase activity -0.006 0.007 -9999 0 -9999 0 0
nervous system development -0.002 0.096 -9999 0 -0.305 9 9
CDC42 0.032 0.005 -9999 0 -9999 0 0
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.032 0.005 -9999 0 -9999 0 0
SPHK1 -0.004 0.13 -9999 0 -0.518 8 8
GNAI2 0.027 0.02 -9999 0 -9999 0 0
mol:S1P -0.015 0.092 -9999 0 -0.308 11 11
GNAO1 0.032 0.007 -9999 0 -9999 0 0
mol:Sphinganine-1-P -0.007 0.087 -9999 0 -0.378 7 7
growth factor activity 0 0 -9999 0 -9999 0 0
S1P/S1P2/G12/G13 0.013 0.089 -9999 0 -0.239 12 12
GNAI3 0.032 0.006 -9999 0 -9999 0 0
G12/G13 0.042 0.039 -9999 0 -0.378 1 1
S1PR3 0 0 -9999 0 -9999 0 0
S1PR2 0 0 -9999 0 -9999 0 0
EDG1 0.003 0.114 -9999 0 -0.518 6 6
S1P1/S1P -0.015 0.116 -9999 0 -0.302 16 16
S1PR5 0 0 -9999 0 -9999 0 0
S1PR4 0 0 -9999 0 -9999 0 0
GNAI1 -0.001 0.13 -9999 0 -0.518 8 8
S1P/S1P5/G12 0.001 0.084 -9999 0 -0.247 11 11
S1P/S1P3/Gq -0.018 0.115 -9999 0 -0.37 10 10
S1P/S1P4/Gi -0.023 0.123 -9999 0 -0.351 11 11
GNAQ 0 0 -9999 0 -9999 0 0
GNAZ 0 0.122 -9999 0 -0.518 7 7
GNA14 0.011 0.085 -9999 0 -0.518 3 3
GNA15 0.007 0.114 -9999 0 -0.518 6 6
GNA12 0.032 0.007 -9999 0 -9999 0 0
GNA13 0.027 0.048 -9999 0 -0.518 1 1
GNA11 0.029 0.047 -9999 0 -0.518 1 1
ABCC1 -0.01 0.124 -9999 0 -0.518 7 7
PLK2 and PLK4 events

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
PLK2 -0.002 0.122 -9999 0 -0.518 7 7
PLK4 0.03 0.013 -9999 0 -9999 0 0
regulation of centriole replication -0.008 0.087 -9999 0 -0.378 7 7
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.044 0.052 -9999 0 -0.277 3 3
RGS9BP 0 0.107 -9999 0 -0.518 5 5
mol:GTP 0 0 -9999 0 -9999 0 0
GRK1 0 0 -9999 0 -9999 0 0
mol:Na + -0.004 0.105 -9999 0 -0.326 12 12
mol:ADP 0.003 0.033 -9999 0 -0.375 1 1
GNAT2 0.03 0.013 -9999 0 -9999 0 0
RGS9-1/Gbeta5/R9AP 0.015 0.11 -9999 0 -0.327 11 11
mol:GDP 0 0 -9999 0 -9999 0 0
PDE6H/GNAT2/GTP 0.04 0.015 -9999 0 -9999 0 0
GRK7 0.019 0.05 -9999 0 -0.518 1 1
CNGB3 -0.019 0.138 -9999 0 -0.518 9 9
Cone Metarhodopsin II/X-Arrestin 0.024 0 -9999 0 -9999 0 0
mol:Ca2+ -0.013 0.096 0.186 4 -0.297 12 16
Cone PDE6 0.029 0.116 -9999 0 -0.286 13 13
Cone Metarhodopsin II 0.012 0.028 -9999 0 -0.289 1 1
Na + (4 Units) 0.009 0.102 -9999 0 -0.296 12 12
GNAT2/GDP 0.025 0.101 -9999 0 -0.282 11 11
GNB5 0.02 0.081 -9999 0 -0.518 3 3
mol:GMP (4 units) 0.02 0.055 0.188 7 -0.295 2 9
Cone Transducin 0.048 0.056 -9999 0 -0.295 3 3
SLC24A2 0.029 0.014 -9999 0 -9999 0 0
GNB3/GNGT2 0.036 0.064 -9999 0 -0.378 3 3
GNB3 0.03 0.009 -9999 0 -9999 0 0
GNAT2/GTP 0.023 0.008 -9999 0 -9999 0 0
CNGA3 0.015 0.084 -9999 0 -0.518 3 3
ARR3 0.033 0 -9999 0 -9999 0 0
absorption of light 0 0 -9999 0 -9999 0 0
cGMP/Cone CNG Channel -0.004 0.106 -9999 0 -0.327 12 12
mol:Pi 0.015 0.109 -9999 0 -0.326 11 11
Cone CNG Channel 0.016 0.11 -9999 0 -0.278 14 14
mol:all-trans-retinal 0 0 -9999 0 -9999 0 0
mol:K + 0.029 0.014 -9999 0 -9999 0 0
RGS9 0.013 0.094 -9999 0 -0.518 4 4
PDE6C 0.023 0.067 -9999 0 -0.518 2 2
GNGT2 0.021 0.081 -9999 0 -0.518 3 3
mol:cGMP (4 units) 0 0 -9999 0 -9999 0 0
PDE6H 0.031 0.008 -9999 0 -9999 0 0
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.021 0.118 -9999 0 -0.451 2 2
HDAC1 0.033 0.016 -9999 0 -9999 0 0
AES 0.032 0.005 -9999 0 -9999 0 0
FBXW11 0.031 0.008 -9999 0 -9999 0 0
DTX1 0.029 0.047 -9999 0 -0.518 1 1
LRP6/FZD1 0.035 0.055 -9999 0 -0.378 2 2
TLE1 0.028 0.046 -9999 0 -0.507 1 1
AP1 -0.02 0.107 -9999 0 -0.299 14 14
NCSTN 0.031 0.007 -9999 0 -9999 0 0
ADAM10 0.031 0.011 -9999 0 -9999 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.003 0.142 -9999 0 -0.656 4 4
NICD/RBPSUH -0.001 0.101 -9999 0 -0.486 1 1
WIF1 -0.064 0.188 -9999 0 -0.518 19 19
NOTCH1 0 0.107 -9999 0 -0.511 1 1
PSENEN 0.029 0.011 -9999 0 -9999 0 0
KREMEN2 -0.103 0.212 -9999 0 -0.518 27 27
DKK1 -0.1 0.213 -9999 0 -0.518 27 27
beta catenin/beta TrCP1 0.011 0.094 -9999 0 -0.391 2 2
APH1B 0.028 0.047 -9999 0 -0.518 1 1
APH1A 0.014 0.093 -9999 0 -0.518 4 4
AXIN1 0.009 0.078 -9999 0 -0.455 2 2
CtBP/CBP/TCF1/TLE1/AES 0.02 0.046 0.192 1 -9999 0 1
PSEN1 0.028 0.047 -9999 0 -0.518 1 1
FOS -0.027 0.151 -9999 0 -0.518 11 11
JUN -0.002 0.123 -9999 0 -0.518 7 7
MAP3K7 0.032 0.013 -9999 0 -9999 0 0
CTNNB1 -0.004 0.093 -9999 0 -0.341 5 5
MAPK3 0.032 0.005 -9999 0 -9999 0 0
DKK2/LRP6/Kremen 2 -0.062 0.154 -9999 0 -0.327 32 32
HNF1A 0 0.006 -9999 0 -9999 0 0
CTBP1 0.029 0.011 -9999 0 -9999 0 0
MYC -0.02 0.256 -9999 0 -1.482 4 4
NKD1 0.029 0.02 -9999 0 -9999 0 0
FZD1 0.026 0.049 -9999 0 -0.518 1 1
NOTCH1 precursor/Deltex homolog 1 0.029 0.114 -9999 0 -0.488 1 1
apoptosis -0.02 0.106 -9999 0 -0.297 14 14
Delta 1/NOTCHprecursor 0.022 0.12 -9999 0 -0.45 2 2
DLL1 0.018 0.082 -9999 0 -0.518 3 3
PPARD 0.019 0.081 -9999 0 -0.869 1 1
Gamma Secretase 0.062 0.085 -9999 0 -0.346 4 4
APC -0.004 0.11 -9999 0 -0.424 6 6
DVL1 0.015 0.052 -9999 0 -0.274 2 2
CSNK2A1 0.031 0.008 -9999 0 -9999 0 0
MAP3K7IP1 0.031 0.01 -9999 0 -9999 0 0
DKK1/LRP6/Kremen 2 -0.128 0.192 -9999 0 -0.364 49 49
LRP6 0.026 0.049 -9999 0 -0.517 1 1
CSNK1A1 0.031 0.007 -9999 0 -9999 0 0
NLK 0.023 0.015 -9999 0 -9999 0 0
CCND1 -0.093 0.389 -9999 0 -1.461 10 10
WNT1 0.033 0.003 -9999 0 -9999 0 0
Axin1/APC/beta catenin 0.012 0.119 -9999 0 -0.486 3 3
DKK2 0.008 0.096 -9999 0 -0.518 4 4
NOTCH1 precursor/DVL1 0.009 0.127 -9999 0 -0.573 2 2
GSK3B 0.027 0.016 -9999 0 -9999 0 0
FRAT1 0.031 0.012 -9999 0 -9999 0 0
NOTCH/Deltex homolog 1 0.027 0.112 -9999 0 -0.489 1 1
PPP2R5D 0.017 0.051 -9999 0 -0.344 2 2
MAPK1 0.03 0.01 -9999 0 -9999 0 0
WNT1/LRP6/FZD1 -0.002 0.13 -9999 0 -0.297 19 19
RBPJ 0 0 -9999 0 -9999 0 0
CREBBP 0.032 0.011 -9999 0 -9999 0 0
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.036 0.064 -9999 0 -0.378 3 3
Necdin/E2F1 -0.001 0.122 -9999 0 -0.378 12 12
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.036 0.093 -9999 0 -0.277 9 9
NGF (dimer)/p75(NTR)/BEX1 0.019 0.05 -9999 0 -0.321 1 1
NT-4/5 (dimer)/p75(NTR) 0.016 0.024 -9999 0 -9999 0 0
IKBKB 0.029 0.01 -9999 0 -9999 0 0
AKT1 0.074 0.107 -9999 0 -0.278 3 3
IKBKG 0.032 0.01 -9999 0 -9999 0 0
BDNF -0.029 0.156 -9999 0 -0.518 12 12
MGDIs/NGR/p75(NTR)/LINGO1 0.01 0.088 -9999 0 -0.321 8 8
FURIN 0.022 0.068 -9999 0 -0.518 2 2
proBDNF (dimer)/p75(NTR)/Sortilin 0.002 0.122 -9999 0 -0.332 14 14
LINGO1 0 0 -9999 0 -9999 0 0
Sortilin/TRAF6/NRIF 0.015 0.079 -9999 0 -0.491 1 1
proBDNF (dimer) -0.029 0.156 -9999 0 -0.517 12 12
NTRK1 0.031 0.012 -9999 0 -9999 0 0
RTN4R -0.003 0.129 -9999 0 -0.518 8 8
neuron apoptosis -0.037 0.139 -9999 0 -0.553 5 5
IRAK1 0.033 0 -9999 0 -9999 0 0
SHC1 0.009 0.019 -9999 0 -9999 0 0
ARHGDIA 0.031 0.007 -9999 0 -9999 0 0
RhoA/GTP 0.022 0.007 -9999 0 -9999 0 0
Gamma Secretase 0.062 0.085 -9999 0 -0.346 4 4
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.034 0.081 -9999 0 -0.361 4 4
MAGEH1 0.017 0.083 -9999 0 -0.518 3 3
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.003 0.117 -9999 0 -0.313 14 14
Mammalian IAPs/DIABLO 0.021 0.104 -9999 0 -0.295 12 12
proNGF (dimer) 0 0 -9999 0 -9999 0 0
MAGED1 0.015 0.094 -9999 0 -0.518 4 4
APP 0.006 0.114 -9999 0 -0.518 6 6
NT-4/5 (dimer) 0 0 -9999 0 -9999 0 0
ZNF274 0.028 0.047 -9999 0 -0.518 1 1
RhoA/GDP/RHOGDI 0.031 0.029 -9999 0 -9999 0 0
NGF 0 0 -9999 0 -9999 0 0
cell cycle arrest -0.016 0.035 -9999 0 -0.27 2 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.019 0.034 -9999 0 -0.294 1 1
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.032 0.043 -9999 0 -0.354 1 1
NCSTN 0.031 0.007 -9999 0 -9999 0 0
mol:GTP 0.03 0.042 -9999 0 -0.32 1 1
PSENEN 0.029 0.011 -9999 0 -9999 0 0
mol:ceramide 0.004 0.05 -9999 0 -0.303 3 3
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.001 0.045 -9999 0 -0.209 5 5
p75(NTR)/beta APP 0.017 0.093 -9999 0 -0.385 6 6
BEX1 0.01 0.063 -9999 0 -0.518 1 1
mol:GDP -0.008 0.012 -9999 0 -9999 0 0
NGF (dimer) 0.005 0.126 -9999 0 -0.294 20 20
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.024 0.087 -9999 0 -0.295 8 8
PIK3R1 0.004 0.097 -9999 0 -0.518 4 4
RAC1/GTP 0.03 0.024 -9999 0 -9999 0 0
MYD88 0.03 0.01 -9999 0 -9999 0 0
CHUK 0.028 0.047 -9999 0 -0.518 1 1
NGF (dimer)/p75(NTR)/PKA 0.03 0.042 -9999 0 -0.321 1 1
RHOB 0.014 0.084 -9999 0 -0.518 3 3
RHOA 0.03 0.01 -9999 0 -9999 0 0
MAGE-G1/E2F1 0.044 0.019 -9999 0 -9999 0 0
NT3 (dimer) -0.008 0.116 -9999 0 -0.517 6 6
TP53 -0.053 0.102 -9999 0 -0.296 16 16
PRDM4 0.006 0.042 -9999 0 -0.294 2 2
BDNF (dimer) -0.117 0.196 -9999 0 -0.346 52 52
PIK3CA 0.011 0.048 -9999 0 -0.518 1 1
SORT1 0.023 0.067 -9999 0 -0.518 2 2
activation of caspase activity 0.031 0.09 -9999 0 -0.274 9 9
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.041 0.063 -9999 0 -0.305 3 3
RHOC 0.031 0.008 -9999 0 -9999 0 0
XIAP 0 0 -9999 0 -9999 0 0
MAPK10 -0.041 0.105 -9999 0 -0.369 5 5
DIABLO 0.033 0 -9999 0 -9999 0 0
SMPD2 0.004 0.05 -9999 0 -0.304 3 3
APH1B 0.028 0.047 -9999 0 -0.518 1 1
APH1A 0.014 0.093 -9999 0 -0.518 4 4
proNGF (dimer)/p75(NTR)/Sortilin 0.028 0.052 -9999 0 -0.321 2 2
PSEN1 0.028 0.047 -9999 0 -0.518 1 1
APAF-1/Pro-Caspase 9 0.044 0.037 -9999 0 -0.378 1 1
NT3 (dimer)/p75(NTR) 0.004 0.093 -9999 0 -0.378 6 6
MAPK8 -0.03 0.099 -9999 0 -0.389 3 3
MAPK9 -0.032 0.101 -9999 0 -0.373 4 4
APAF1 0.029 0.047 -9999 0 -0.518 1 1
NTF3 -0.008 0.116 -9999 0 -0.518 6 6
NTF4 0 0 -9999 0 -9999 0 0
NDN -0.029 0.162 -9999 0 -0.518 13 13
RAC1/GDP 0.024 0.004 -9999 0 -9999 0 0
RhoA-B-C/GDP 0.035 0.068 -9999 0 -0.26 4 4
p75 CTF/Sortilin/TRAF6/NRIF 0.062 0.071 -9999 0 -0.305 4 4
RhoA-B-C/GTP 0.029 0.042 -9999 0 -0.319 1 1
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.019 0.127 -9999 0 -0.292 16 16
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.013 0.124 -9999 0 -0.306 15 15
PRKACB 0.026 0.049 -9999 0 -0.518 1 1
proBDNF (dimer)/p75 ECD -0.003 0.122 -9999 0 -0.378 12 12
ChemicalAbstracts:86-01-1 0 0 -9999 0 -9999 0 0
BIRC3 -0.027 0.156 -9999 0 -0.518 12 12
BIRC2 0.032 0.005 -9999 0 -9999 0 0
neuron projection morphogenesis -0.031 0.066 -9999 0 -0.289 3 3
BAD -0.039 0.101 -9999 0 -0.396 3 3
RIPK2 0.029 0.016 -9999 0 -9999 0 0
NGFR 0.021 0.036 -9999 0 -9999 0 0
CYCS -0.005 0.069 -9999 0 -0.329 5 5
ADAM17 0.03 0.015 -9999 0 -9999 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.045 0.047 -9999 0 -0.326 1 1
BCL2L11 -0.039 0.101 -9999 0 -0.396 3 3
BDNF (dimer)/p75(NTR) -0.01 0.125 -9999 0 -0.388 12 12
PI3K 0.007 0.06 -9999 0 -0.295 3 3
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.043 0.056 -9999 0 -0.295 2 2
NDNL2 0.032 0.005 -9999 0 -9999 0 0
YWHAE 0.031 0.007 -9999 0 -9999 0 0
PRKCI -0.009 0.11 -9999 0 -0.518 6 6
NGF (dimer)/p75(NTR) 0.016 0.024 -9999 0 -9999 0 0
ChemicalAbstracts:146-91-8 0 0 -9999 0 -9999 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.033 0.085 -9999 0 -0.347 5 5
TRAF6 0.028 0.047 -9999 0 -0.518 1 1
RAC1 0.032 0.005 -9999 0 -9999 0 0
PRKCZ 0 0 -9999 0 -9999 0 0
PLG 0.032 0.006 -9999 0 -9999 0 0
oligodendrocyte cell fate commitment 0 0 -9999 0 -9999 0 0
CASP6 -0.02 0.094 -9999 0 -0.285 14 14
SQSTM1 0.027 0.021 -9999 0 -9999 0 0
NGFRAP1 0.004 0.122 -9999 0 -0.518 7 7
CASP3 -0.042 0.1 -9999 0 -0.365 4 4
E2F1 0.031 0.008 -9999 0 -9999 0 0
CASP9 0.032 0.006 -9999 0 -9999 0 0
IKK complex 0.061 0.064 -9999 0 -9999 0 0
NGF (dimer)/TRKA 0.023 0.008 -9999 0 -9999 0 0
MMP7 -0.045 0.191 -9999 0 -0.518 19 19
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.048 0.072 -9999 0 -0.287 4 4
MMP3 -0.118 0.218 -9999 0 -0.518 30 30
APAF-1/Caspase 9 -0.029 0.093 -9999 0 -0.266 15 15
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0.032 0.005 -9999 0 -9999 0 0
MKNK1 0.032 0.006 -9999 0 -9999 0 0
mol:PIP3 -0.013 0.085 0.382 2 -0.286 8 10
FRAP1 0.053 0.084 -9999 0 -0.447 1 1
AKT1 0.063 0.124 0.254 10 -0.264 8 18
INSR 0.028 0.047 -9999 0 -0.518 1 1
Insulin Receptor/Insulin 0.039 0.033 -9999 0 -0.321 1 1
mol:GTP 0.08 0.122 0.313 7 -0.34 2 9
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.002 0.031 -9999 0 -9999 0 0
TSC2 0.027 0.048 -9999 0 -0.516 1 1
RHEB/GDP 0 0.066 -9999 0 -0.309 2 2
TSC1 0.029 0.047 -9999 0 -0.519 1 1
Insulin Receptor/IRS1 0.01 0.083 -9999 0 -0.286 9 9
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.007 0.043 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
EIF3A 0 0 -9999 0 -9999 0 0
RPS6KB1 0.075 0.095 0.276 8 -9999 0 8
MAP3K5 0.002 0.023 -9999 0 -0.18 2 2
PIK3R1 0.005 0.097 -9999 0 -0.517 4 4
apoptosis 0.002 0.023 -9999 0 -0.18 2 2
mol:LY294002 0 0 -9999 0 -0.001 9 9
EIF4B 0.069 0.089 0.26 8 -9999 0 8
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.07 0.083 0.245 8 -9999 0 8
eIF4E/eIF4G1/eIF4A1 0.003 0.041 -9999 0 -0.278 1 1
KIAA1303 0 0 -9999 0 -9999 0 0
PI3K -0.005 0.079 -9999 0 -0.295 8 8
mTOR/RHEB/GTP/Raptor/GBL 0.065 0.086 0.233 11 -0.222 2 13
FKBP1A 0.033 0.007 -9999 0 -9999 0 0
RHEB/GTP 0.078 0.111 0.286 7 -0.385 1 8
mol:Amino Acids 0 0 -9999 0 -0.001 9 9
FKBP12/Rapamycin 0.026 0.007 -9999 0 -9999 0 0
PDPK1 0.033 0.116 0.22 7 -0.267 8 15
EIF4E 0.031 0.008 -9999 0 -9999 0 0
ASK1/PP5C 0.065 0.107 -9999 0 -0.537 3 3
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.007 0.097 -9999 0 -0.891 1 1
TSC1/TSC2 0.087 0.131 0.337 7 -0.368 2 9
tumor necrosis factor receptor activity 0 0 0.001 9 -9999 0 9
RPS6 0.03 0.013 -9999 0 -9999 0 0
PPP5C 0.028 0.047 -9999 0 -0.518 1 1
EIF4G1 0.007 0.066 -9999 0 -0.518 2 2
IRS1 -0.007 0.078 -9999 0 -0.305 8 8
INS 0.032 0.006 -9999 0 -9999 0 0
PTEN 0.022 0.066 -9999 0 -0.516 2 2
PDK2 0.034 0.116 0.213 8 -0.269 8 16
EIF4EBP1 -0.014 0.187 -9999 0 -1.202 3 3
PIK3CA 0.011 0.048 -9999 0 -0.518 1 1
PPP2R5D 0.048 0.082 -9999 0 -0.405 1 1
peptide biosynthetic process 0.016 0.031 0.187 1 -0.292 1 2
RHEB 0.033 0.005 -9999 0 -9999 0 0
EIF4A1 0.031 0.007 -9999 0 -9999 0 0
mol:Rapamycin 0.001 0.002 0.005 10 -9999 0 10
EEF2 0.016 0.031 0.188 1 -0.293 1 2
eIF4E/4E-BP1 0 0.178 -9999 0 -1.12 3 3
Ceramide signaling pathway

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
SPHK2 -0.005 0.075 -9999 0 -0.378 5 5
MAP4K4 -0.006 0.104 -9999 0 -0.415 4 4
BAG4 0.027 0.013 -9999 0 -9999 0 0
PKC zeta/ceramide -0.007 0.054 0.14 2 -0.212 6 8
NFKBIA 0.027 0.048 -9999 0 -0.518 1 1
BIRC3 -0.027 0.156 -9999 0 -0.518 12 12
BAX 0.009 0.041 -9999 0 -0.351 1 1
RIPK1 0.032 0.005 -9999 0 -9999 0 0
AKT1 0.009 0.087 0.586 3 -9999 0 3
BAD -0.01 0.054 0.158 1 -0.215 6 7
SMPD1 0.011 0.058 0.213 1 -0.212 2 3
RB1 -0.01 0.07 0.184 4 -0.236 8 12
FADD/Caspase 8 0.019 0.123 0.28 3 -0.432 4 7
MAP2K4 -0.017 0.069 0.202 1 -0.247 7 8
NSMAF 0.027 0.047 -9999 0 -0.518 1 1
response to UV 0 0 -9999 0 -9999 0 0
RAF1 -0.011 0.055 0.169 1 -0.24 4 5
EGF -0.032 0.15 -9999 0 -0.518 11 11
mol:ceramide -0.007 0.058 0.147 4 -0.225 6 10
MADD 0.032 0.005 -9999 0 -9999 0 0
response to oxidative stress 0 0 -9999 0 -9999 0 0
mol:Free Fatty acid -0.009 0.082 -9999 0 -0.378 6 6
ASAH1 0.022 0.067 -9999 0 -0.518 2 2
negative regulation of cell cycle -0.01 0.069 0.184 4 -0.234 8 12
cell proliferation -0.022 0.108 -9999 0 -0.27 16 16
BID -0.021 0.187 -9999 0 -0.665 9 9
MAP3K1 -0.017 0.07 0.173 1 -0.235 10 11
EIF2A 0.058 0.117 0.287 11 -0.247 3 14
TRADD 0.028 0.047 -9999 0 -0.518 1 1
CRADD 0.025 0.066 -9999 0 -0.518 2 2
MAPK3 -0.01 0.056 -9999 0 -0.276 3 3
response to heat 0 0 -9999 0 -9999 0 0
MAPK1 -0.011 0.054 -9999 0 -0.239 3 3
Cathepsin D/ceramide 0.011 0.059 0.173 1 -0.215 6 7
FADD 0.003 0.1 0.214 3 -0.415 4 7
KSR1 -0.011 0.06 0.17 2 -0.22 7 9
MAPK8 -0.01 0.058 -9999 0 -0.221 4 4
PRKRA -0.002 0.062 0.188 5 -0.218 5 10
PDGFA 0.002 0.106 -9999 0 -0.518 5 5
TRAF2 0.031 0.012 -9999 0 -9999 0 0
IGF1 -0.054 0.185 -9999 0 -0.518 18 18
mol:GD3 0 0 -9999 0 -9999 0 0
ganglioside biosynthetic process -0.007 0.058 0.147 4 -0.224 6 10
CTSD 0.032 0.006 -9999 0 -9999 0 0
regulation of nitric oxide biosynthetic process 0.046 0.012 -9999 0 -9999 0 0
response to radiation 0 0 -9999 0 -9999 0 0
ERK1/PKC delta -0.023 0.115 -9999 0 -0.289 16 16
PRKCD 0.029 0.014 -9999 0 -9999 0 0
PRKCZ 0 0 -9999 0 -9999 0 0
mol:GW4869 0 0 -9999 0 -9999 0 0
mol:sphingosine -0.009 0.082 -9999 0 -0.378 6 6
RelA/NF kappa B1 0.046 0.012 -9999 0 -9999 0 0
mol:glutathione 0 0 -9999 0 -9999 0 0
PAWR 0.021 0.081 -9999 0 -0.518 3 3
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.003 0.106 -9999 0 -0.435 4 4
TNFR1A/BAG4/TNF-alpha 0.042 0.048 -9999 0 -0.324 1 1
mol:Sphingosine-1-phosphate -0.005 0.075 -9999 0 -0.378 5 5
MAP2K1 -0.013 0.053 -9999 0 -0.243 3 3
mol:C11AG 0 0 -9999 0 -9999 0 0
RELA 0.033 0 -9999 0 -9999 0 0
CYCS 0.013 0.059 0.178 5 -0.195 3 8
TNFRSF1A 0.026 0.048 -9999 0 -0.518 1 1
NFKB1 0.031 0.008 -9999 0 -9999 0 0
TNFR1A/BAG4 0.033 0.041 -9999 0 -0.378 1 1
EIF2AK2 -0.005 0.081 0.213 7 -0.246 6 13
TNF-alpha/TNFR1A/FAN 0.047 0.056 -9999 0 -0.324 2 2
response to hydrogen peroxide 0 0 -9999 0 -9999 0 0
CASP8 0.004 0.121 -9999 0 -0.45 6 6
MAP2K2 -0.013 0.053 -9999 0 -0.243 3 3
SMPD3 0.016 0.068 0.193 1 -0.314 3 4
TNF 0.025 0.051 -9999 0 -0.518 1 1
PKC zeta/PAR4 0.016 0.059 -9999 0 -0.375 3 3
mol:PHOSPHOCHOLINE 0.033 0.067 0.203 14 -9999 0 14
NF kappa B1/RelA/I kappa B alpha 0.06 0.063 -9999 0 -0.276 4 4
AIFM1 0.01 0.055 0.168 6 -0.163 3 9
BCL2 -0.007 0.116 -9999 0 -0.518 6 6
Nongenotropic Androgen signaling

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
PTK2 0.005 0.033 -9999 0 -0.378 1 1
GNB1/GNG2 0.047 0.046 -9999 0 -0.294 1 1
regulation of S phase of mitotic cell cycle -0.002 0.049 -9999 0 -0.242 3 3
GNAO1 0.032 0.007 -9999 0 -9999 0 0
HRAS 0.027 0.049 -9999 0 -0.524 1 1
SHBG/T-DHT 0.021 0.005 -9999 0 -9999 0 0
PELP1 0.031 0.007 -9999 0 -9999 0 0
AKT1 0.008 0.002 -9999 0 -9999 0 0
MAP2K1 -0.017 0.07 0.182 2 -0.306 2 4
T-DHT/AR 0.011 0.052 -9999 0 -0.375 2 2
G-protein coupled receptor activity 0 0 -9999 0 -9999 0 0
mol:GTP -0.001 0.002 -9999 0 -0.006 13 13
GNAI2 0.027 0.02 -9999 0 -9999 0 0
GNAI3 0.032 0.006 -9999 0 -9999 0 0
GNAI1 -0.001 0.13 -9999 0 -0.518 8 8
mol:GDP -0.012 0.047 -9999 0 -0.291 2 2
cell proliferation -0.041 0.15 -9999 0 -0.442 13 13
PIK3CA 0.011 0.048 -9999 0 -0.518 1 1
FOS -0.071 0.247 -9999 0 -0.836 12 12
mol:Ca2+ -0.006 0.024 -9999 0 -0.069 14 14
MAPK3 -0.033 0.11 -9999 0 -0.424 4 4
MAPK1 -0.018 0.119 -9999 0 -0.51 5 5
PIK3R1 0.004 0.097 -9999 0 -0.518 4 4
mol:IP3 0 0.001 -9999 0 -0.004 12 12
cAMP biosynthetic process -0.001 0.016 -9999 0 -9999 0 0
GNG2 0.032 0.005 -9999 0 -9999 0 0
potassium channel inhibitor activity 0 0.001 -9999 0 -0.004 12 12
HRAS/GTP 0.031 0.066 -9999 0 -0.284 3 3
actin cytoskeleton reorganization 0.01 0.051 -9999 0 -0.264 3 3
SRC 0.03 0.013 -9999 0 -9999 0 0
voltage-gated calcium channel activity 0 0.001 -9999 0 -0.004 12 12
PI3K 0.006 0.058 -9999 0 -0.321 3 3
apoptosis 0.036 0.155 0.458 14 -9999 0 14
T-DHT/AR/PELP1 0.028 0.051 -9999 0 -0.321 2 2
HRAS/GDP 0.032 0.08 -9999 0 -0.281 3 3
CREB1 -0.04 0.167 -9999 0 -0.494 14 14
RAC1-CDC42/GTP 0.014 0.056 -9999 0 -0.267 3 3
AR 0.013 0.074 -9999 0 -0.517 2 2
GNB1 0.032 0.006 -9999 0 -9999 0 0
RAF1 0.003 0.069 -9999 0 -0.3 2 2
RAC1-CDC42/GDP 0.06 0.078 -9999 0 -0.272 2 2
T-DHT/AR/PELP1/Src 0.04 0.054 -9999 0 -0.294 2 2
MAP2K2 -0.017 0.07 -9999 0 -0.368 1 1
T-DHT/AR/PELP1/Src/PI3K -0.002 0.048 -9999 0 -0.243 3 3
GNAZ 0 0.122 -9999 0 -0.518 7 7
SHBG 0.031 0.007 -9999 0 -9999 0 0
Gi family/GNB1/GNG2/GDP -0.007 0.157 -9999 0 -0.562 7 7
mol:T-DHT 0 0.001 -9999 0 -0.003 9 9
RAC1 0.032 0.005 -9999 0 -9999 0 0
GNRH1 -0.016 0.09 -9999 0 -0.376 8 8
Gi family/GTP -0.019 0.092 -9999 0 -0.263 14 14
CDC42 0.032 0.005 -9999 0 -9999 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.031 0.075 -9999 0 -0.378 4 4
AKT1 0.014 0.183 0.329 3 -0.569 7 10
PTK2B -0.004 0.15 -9999 0 -0.676 4 4
VEGFR2 homodimer/Frs2 0.002 0.124 -9999 0 -0.505 6 6
CAV1 -0.022 0.151 -9999 0 -0.518 11 11
CALM1 0.032 0.006 -9999 0 -9999 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.003 0.13 -9999 0 -0.447 8 8
endothelial cell proliferation 0.038 0.177 0.349 7 -0.483 8 15
mol:Ca2+ -0.002 0.166 -9999 0 -0.627 6 6
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.013 0.13 -9999 0 -0.531 5 5
RP11-342D11.1 -0.012 0.162 -9999 0 -0.576 7 7
CDH5 0.024 0.066 -9999 0 -0.518 2 2
VEGFA homodimer 0.038 0.064 -9999 0 -0.298 3 3
SHC1 0.03 0.009 -9999 0 -9999 0 0
SHC2 0.026 0.027 -9999 0 -9999 0 0
HRAS/GDP -0.004 0.134 -9999 0 -0.512 6 6
SH2D2A 0.018 0.082 -9999 0 -0.518 3 3
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.008 0.148 -9999 0 -0.491 7 7
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.01 0.136 -9999 0 -0.432 9 9
VEGFR1 homodimer 0.011 0.103 -9999 0 -0.517 5 5
SHC/GRB2/SOS1 0.026 0.159 -9999 0 -0.56 6 6
GRB10 -0.018 0.21 -9999 0 -0.652 11 11
PTPN11 0.029 0.047 -9999 0 -0.518 1 1
GRB2 0.032 0.006 -9999 0 -9999 0 0
PAK1 0.03 0.018 -9999 0 -9999 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.034 0.152 -9999 0 -0.585 5 5
HRAS 0.027 0.048 -9999 0 -0.518 1 1
VEGF/Rho/ROCK1/Integrin Complex -0.008 0.139 -9999 0 -0.802 3 3
HIF1A 0.023 0.067 -9999 0 -0.518 2 2
FRS2 0.031 0.008 -9999 0 -9999 0 0
oxygen and reactive oxygen species metabolic process 0.012 0.128 -9999 0 -0.524 5 5
mol:GTP 0 0 -9999 0 -9999 0 0
FLT4 0.031 0.008 -9999 0 -9999 0 0
Nck/Pak 0.031 0.055 -9999 0 -0.378 2 2
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.006 0.145 -9999 0 -0.51 7 7
mol:GDP 0.004 0.145 -9999 0 -0.541 6 6
mol:NADP 0.027 0.141 0.346 2 -0.444 5 7
eNOS/Hsp90 0.025 0.133 0.325 2 -0.419 5 7
PIK3R1 0.004 0.097 -9999 0 -0.518 4 4
mol:IP3 -0.002 0.169 -9999 0 -0.637 6 6
HIF1A/ARNT 0.039 0.045 -9999 0 -0.378 1 1
SHB 0.019 0.068 -9999 0 -0.518 2 2
VEGFA -0.003 0.021 -9999 0 -9999 0 0
VEGFC 0.005 0.105 -9999 0 -0.518 5 5
FAK1/Vinculin 0.018 0.16 -9999 0 -0.707 4 4
mol:Ca ++ 0 0 -9999 0 -9999 0 0
RHOA 0.03 0.01 -9999 0 -9999 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.004 0.155 -9999 0 -0.626 5 5
PTPN6 0.026 0.048 -9999 0 -0.518 1 1
EPAS1 0.007 0.113 -9999 0 -0.486 6 6
mol:L-citrulline 0.027 0.141 0.346 2 -0.444 5 7
ITGAV 0.019 0.082 -9999 0 -0.518 3 3
PIK3CA 0.011 0.048 -9999 0 -0.518 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.011 0.129 -9999 0 -0.531 5 5
VEGFR2 homodimer/VEGFA homodimer -0.011 0.17 -9999 0 -0.629 7 7
VEGFR2/3 heterodimer 0.003 0.124 -9999 0 -0.505 6 6
VEGFB 0.033 0 -9999 0 -9999 0 0
MAPK11 -0.014 0.16 0.285 3 -0.558 7 10
VEGFR2 homodimer -0.01 0.131 -9999 0 -0.613 5 5
FLT1 0.011 0.104 -9999 0 -0.518 5 5
NEDD4 0.023 0.055 -9999 0 -0.512 1 1
MAPK3 -0.003 0.165 0.319 3 -0.593 6 9
MAPK1 -0.002 0.161 0.3 5 -0.566 6 11
VEGFA145/NRP2 0.014 0.055 -9999 0 -0.307 3 3
VEGFR1/2 heterodimer -0.006 0.152 -9999 0 -0.549 7 7
KDR -0.01 0.132 -9999 0 -0.615 5 5
VEGFA165/NRP1/VEGFR2 homodimer -0.011 0.164 -9999 0 -0.618 7 7
SRC 0.03 0.013 -9999 0 -9999 0 0
platelet activating factor biosynthetic process 0.009 0.168 0.354 2 -0.586 6 8
PI3K -0.028 0.162 -9999 0 -0.615 7 7
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.009 0.127 -9999 0 -0.437 8 8
FES -0.004 0.172 -9999 0 -0.652 6 6
GAB1 -0.017 0.176 -9999 0 -0.519 9 9
VEGFR2 homodimer/VEGFA homodimer/Src -0.005 0.13 -9999 0 -0.508 6 6
CTNNB1 0.028 0.017 -9999 0 -9999 0 0
SOS1 0.032 0.007 -9999 0 -9999 0 0
ARNT 0.031 0.009 -9999 0 -9999 0 0
eNOS/Caveolin-1 0.016 0.15 0.372 1 -0.411 6 7
VEGFR2 homodimer/VEGFA homodimer/Yes -0.003 0.127 -9999 0 -0.523 5 5
PI3K/GAB1 0 0.168 0.283 2 -0.568 6 8
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.026 0.128 -9999 0 -0.524 4 4
PRKACA 0.032 0.007 -9999 0 -9999 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0 0.145 -9999 0 -0.479 8 8
HSP90AA1 0 0 -9999 0 -9999 0 0
CDC42 0.001 0.173 -9999 0 -0.647 6 6
actin cytoskeleton reorganization -0.01 0.135 -9999 0 -0.428 9 9
PTK2 -0.007 0.166 0.271 1 -0.703 5 6
EDG1 -0.013 0.212 -9999 0 -0.746 8 8
mol:DAG -0.002 0.169 -9999 0 -0.637 6 6
CaM/Ca2+ 0.012 0.159 -9999 0 -0.591 6 6
MAP2K3 -0.021 0.122 -9999 0 -0.487 6 6
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.026 0.208 -9999 0 -0.667 11 11
PLCG1 -0.003 0.171 -9999 0 -0.647 6 6
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.004 0.128 -9999 0 -0.654 3 3
IQGAP1 0.032 0.005 -9999 0 -9999 0 0
YES1 0.031 0.008 -9999 0 -9999 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.002 0.129 -9999 0 -0.482 6 6
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.007 0.136 -9999 0 -0.552 6 6
cell migration 0.021 0.144 -9999 0 -0.671 3 3
mol:PI-3-4-5-P3 -0.025 0.148 -9999 0 -0.56 7 7
FYN 0.023 0.067 -9999 0 -0.518 2 2
VEGFB/NRP1 0.007 0.161 -9999 0 -0.597 6 6
mol:NO 0.027 0.141 0.346 2 -0.444 5 7
PXN 0.033 0.003 -9999 0 -9999 0 0
HRAS/GTP -0.018 0.127 -9999 0 -0.511 6 6
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.037 0.202 -9999 0 -0.666 11 11
VHL 0.02 0.068 -9999 0 -0.518 2 2
ITGB3 0.024 0.052 -9999 0 -0.518 1 1
NOS3 0.025 0.153 0.354 2 -0.532 4 6
VEGFR2 homodimer/VEGFA homodimer/Sck -0.004 0.131 -9999 0 -0.513 6 6
RAC1 0.032 0.005 -9999 0 -9999 0 0
PRKCA -0.011 0.164 -9999 0 -0.639 6 6
PRKCB -0.011 0.156 -9999 0 -0.596 6 6
VCL 0.028 0.047 -9999 0 -0.518 1 1
VEGFA165/NRP1 -0.029 0.148 -9999 0 -0.577 7 7
VEGFR1/2 heterodimer/VEGFA homodimer -0.013 0.156 -9999 0 -0.545 7 7
VEGFA165/NRP2 0.014 0.055 -9999 0 -0.307 3 3
MAPKKK cascade -0.027 0.167 -9999 0 -0.567 10 10
NRP2 0.022 0.068 -9999 0 -0.518 2 2
VEGFC homodimer 0.005 0.105 -9999 0 -0.517 5 5
NCK1 0.019 0.067 -9999 0 -0.518 2 2
ROCK1 0.032 0.006 -9999 0 -9999 0 0
FAK1/Paxillin 0.02 0.163 -9999 0 -0.646 5 5
MAP3K13 -0.017 0.129 -9999 0 -0.509 6 6
PDPK1 -0.027 0.136 -9999 0 -0.527 7 7
IL2 signaling events mediated by STAT5

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
GAB2 0.031 0.015 -9999 0 -9999 0 0
ELF1 0.012 0.098 -9999 0 -0.352 9 9
CCNA2 0.023 0.067 -9999 0 -0.518 2 2
PIK3CA 0.012 0.048 -9999 0 -0.517 1 1
JAK3 0.032 0.007 -9999 0 -9999 0 0
PIK3R1 0.005 0.097 -9999 0 -0.517 4 4
JAK1 0.029 0.047 -9999 0 -0.517 1 1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.033 0.114 -9999 0 -0.377 3 3
SHC1 0.031 0.009 -9999 0 -9999 0 0
SP1 -0.016 0.125 -9999 0 -0.363 14 14
IL2RA -0.032 0.203 -9999 0 -0.794 9 9
IL2RB 0.022 0.068 -9999 0 -0.517 2 2
SOS1 0.032 0.007 -9999 0 -9999 0 0
IL2RG 0.02 0.07 -9999 0 -0.517 2 2
G1/S transition of mitotic cell cycle -0.07 0.294 -9999 0 -0.764 17 17
PTPN11 0.029 0.047 -9999 0 -0.517 1 1
CCND2 -0.074 0.24 -9999 0 -0.764 14 14
LCK -0.006 0.137 -9999 0 -0.518 9 9
GRB2 0.032 0.006 -9999 0 -9999 0 0
IL2 0.031 0.008 -9999 0 -9999 0 0
CDK6 0.011 0.104 -9999 0 -0.518 5 5
CCND3 0.027 0.11 -9999 0 -9999 0 0
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.02 0.076 0.352 1 -0.257 7 8
DAPP1 -0.027 0.169 -9999 0 -0.488 10 10
Src family/SYK family/BLNK-LAT/BTK-ITK -0.031 0.211 -9999 0 -0.644 10 10
mol:DAG -0.003 0.089 0.168 3 -0.254 7 10
HRAS 0.026 0.05 -9999 0 -0.521 1 1
RAP1A 0.023 0.067 -9999 0 -0.508 2 2
ARF5/GDP 0.01 0.096 -9999 0 -0.337 4 4
PLCG2 0.011 0.104 -9999 0 -0.518 5 5
PLCG1 0.031 0.008 -9999 0 -9999 0 0
ARF5 0.029 0.047 -9999 0 -0.518 1 1
mol:GTP -0.018 0.073 0.343 1 -0.266 6 7
ARF1/GTP -0.01 0.069 0.33 1 -0.248 6 7
RHOA 0.03 0.01 -9999 0 -9999 0 0
YES1 0.031 0.008 -9999 0 -9999 0 0
RAP1A/GTP -0.012 0.081 0.244 4 -0.264 6 10
ADAP1 -0.019 0.068 0.324 1 -0.254 6 7
ARAP3 -0.018 0.072 0.34 1 -0.262 6 7
INPPL1 0.026 0.049 -9999 0 -0.518 1 1
PREX1 -0.009 0.137 -9999 0 -0.518 9 9
ARHGEF6 0.02 0.081 -9999 0 -0.518 3 3
ARHGEF7 0.031 0.008 -9999 0 -9999 0 0
ARF1 0.033 0.003 -9999 0 -9999 0 0
NRAS 0.024 0.05 -9999 0 -0.498 1 1
FYN 0.023 0.067 -9999 0 -0.518 2 2
ARF6 0.031 0.012 -9999 0 -9999 0 0
FGR 0.032 0.006 -9999 0 -9999 0 0
mol:Ca2+ 0 0.054 0.149 3 -0.155 3 6
mol:IP4 0 0 -9999 0 -9999 0 0
TIAM1 0.032 0.006 -9999 0 -9999 0 0
ZAP70 0.03 0.015 -9999 0 -9999 0 0
mol:IP3 -0.004 0.072 0.179 3 -0.191 8 11
LYN 0.028 0.047 -9999 0 -0.518 1 1
ARF1/GDP 0.01 0.095 -9999 0 -0.375 3 3
RhoA/GDP 0.015 0.09 0.381 1 -0.238 7 8
PDK1/Src/Hsp90 0.037 0.034 -9999 0 -0.321 1 1
BLNK 0.019 0.081 -9999 0 -0.518 3 3
actin cytoskeleton reorganization -0.016 0.113 0.37 1 -0.501 2 3
SRC 0.03 0.013 -9999 0 -9999 0 0
PLEKHA2 -0.011 0.038 -9999 0 -0.321 2 2
RAC1 0.032 0.005 -9999 0 -9999 0 0
PTEN 0.022 0.065 -9999 0 -0.493 2 2
HSP90AA1 0 0 -9999 0 -9999 0 0
ARF6/GTP -0.018 0.073 0.352 1 -0.256 6 7
RhoA/GTP -0.012 0.08 0.315 2 -0.257 6 8
Src family/SYK family/BLNK-LAT -0.015 0.165 -9999 0 -0.507 9 9
BLK 0.01 0.073 -9999 0 -0.518 2 2
PDPK1 0.028 0.047 -9999 0 -0.518 1 1
CYTH1 -0.019 0.068 0.324 1 -0.254 6 7
HCK 0.006 0.113 -9999 0 -0.518 6 6
CYTH3 -0.019 0.068 0.324 1 -0.254 6 7
CYTH2 -0.019 0.068 0.324 1 -0.254 6 7
KRAS 0.014 0.094 -9999 0 -0.521 4 4
GO:0030676 0 0 -9999 0 -9999 0 0
FOXO3 0.001 0.059 0.246 1 -0.438 1 2
SGK1 0.001 0.061 0.259 1 -0.47 1 2
INPP5D 0 0 -9999 0 -9999 0 0
mol:GDP -0.005 0.091 -9999 0 -0.39 3 3
SOS1 0.032 0.007 -9999 0 -9999 0 0
SYK 0.012 0.104 -9999 0 -0.518 5 5
ARF6/GDP 0.001 0.086 0.371 1 -0.239 6 7
mol:PI-3-4-5-P3 -0.02 0.071 0.383 1 -0.266 6 7
ARAP3/RAP1A/GTP -0.015 0.077 0.226 3 -0.266 6 9
VAV1 0.003 0.122 -9999 0 -0.518 7 7
mol:PI-3-4-P2 0.005 0.034 -9999 0 -0.375 1 1
RAS family/GTP/PI3K Class I 0.032 0.079 -9999 0 -0.27 6 6
PLEKHA1 -0.017 0.053 -9999 0 -0.322 4 4
Rac1/GDP 0.011 0.095 -9999 0 -0.375 3 3
LAT 0.031 0.015 -9999 0 -9999 0 0
Rac1/GTP -0.005 0.112 -9999 0 -0.399 7 7
ITK -0.025 0.066 -9999 0 -0.259 7 7
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.011 0.118 -9999 0 -0.366 7 7
LCK -0.007 0.137 -9999 0 -0.518 9 9
BTK -0.034 0.083 -9999 0 -0.271 12 12
VEGFR1 specific signals

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR1 homodimer/VEGFB homodimer 0.004 0.152 -9999 0 -0.625 7 7
VEGFR1 homodimer/NRP1 -0.017 0.147 -9999 0 -0.622 7 7
mol:DAG -0.022 0.137 -9999 0 -0.625 6 6
VEGFR1 homodimer/NRP1/VEGFR 121 -0.016 0.136 -9999 0 -0.579 7 7
CaM/Ca2+ -0.005 0.137 -9999 0 -0.599 6 6
HIF1A 0.016 0.11 -9999 0 -0.427 7 7
GAB1 0.021 0.068 -9999 0 -0.518 2 2
AKT1 0.027 0.152 -9999 0 -0.504 6 6
PLCG1 -0.022 0.139 -9999 0 -0.631 6 6
NOS3 0.017 0.13 -9999 0 -0.527 5 5
CBL 0.032 0.005 -9999 0 -9999 0 0
mol:NO 0.025 0.132 0.395 1 -0.506 5 6
FLT1 -0.013 0.163 -9999 0 -0.763 6 6
PGF 0.018 0.057 -9999 0 -0.518 1 1
VEGFR1 homodimer/NRP2/VEGFR121 -0.004 0.146 -9999 0 -0.517 9 9
CALM1 0.032 0.006 -9999 0 -9999 0 0
PIK3CA 0.011 0.048 -9999 0 -0.518 1 1
eNOS/Hsp90 0.012 0.124 -9999 0 -0.492 5 5
endothelial cell proliferation -0.01 0.142 -9999 0 -0.589 6 6
mol:Ca2+ -0.022 0.136 -9999 0 -0.62 6 6
MAPK3 -0.042 0.12 -9999 0 -0.562 6 6
MAPK1 -0.039 0.118 -9999 0 -0.562 6 6
PIK3R1 0.004 0.097 -9999 0 -0.518 4 4
PLGF homodimer 0.018 0.057 -9999 0 -0.517 1 1
PRKACA 0.032 0.007 -9999 0 -9999 0 0
RP11-342D11.1 0 0 -9999 0 -9999 0 0
CAV1 -0.022 0.151 -9999 0 -0.518 11 11
VEGFA homodimer 0 0 -9999 0 -9999 0 0
VEGFR1 homodimer/VEGFA homodimer -0.017 0.147 -9999 0 -0.622 7 7
platelet activating factor biosynthetic process -0.025 0.129 -9999 0 -0.549 6 6
PI3K -0.014 0.126 -9999 0 -0.514 6 6
PRKCA -0.042 0.126 -9999 0 -0.588 6 6
PRKCB -0.038 0.124 -9999 0 -0.585 6 6
VEGFR1 homodimer/PLGF homodimer -0.006 0.155 -9999 0 -0.587 8 8
VEGFA 0 0 -9999 0 -9999 0 0
VEGFB 0.033 0 -9999 0 -9999 0 0
mol:IP3 -0.022 0.137 -9999 0 -0.625 6 6
RASA1 -0.015 0.138 -9999 0 -0.631 6 6
NRP2 0.022 0.068 -9999 0 -0.518 2 2
VEGFR1 homodimer -0.013 0.163 -9999 0 -0.76 6 6
VEGFB homodimer 0.033 0 -9999 0 -9999 0 0
NCK1 0.019 0.067 -9999 0 -0.518 2 2
eNOS/Caveolin-1 0.01 0.155 0.393 1 -0.492 6 7
PTPN11 0.029 0.047 -9999 0 -0.518 1 1
mol:PI-3-4-5-P3 -0.015 0.124 -9999 0 -0.508 6 6
mol:L-citrulline 0.025 0.132 0.395 1 -0.506 5 6
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.019 0.141 -9999 0 -0.606 6 6
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.006 0.134 -9999 0 -0.478 9 9
CD2AP 0.032 0.006 -9999 0 -9999 0 0
PI3K/GAB1 -0.012 0.129 -9999 0 -0.478 7 7
PDPK1 0.039 0.152 -9999 0 -0.486 6 6
VEGFR1 homodimer/VEGFA homodimer/SHP2 0 0.144 -9999 0 -0.545 8 8
mol:NADP 0.025 0.132 0.395 1 -0.506 5 6
HSP90AA1 0 0 -9999 0 -9999 0 0
ubiquitin-dependent protein catabolic process 0.018 0.138 -9999 0 -0.598 6 6
VEGFR1 homodimer/NRP2 -0.004 0.157 -9999 0 -0.557 9 9
S1P3 pathway

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
PDGFRB 0.03 0.012 -9999 0 -9999 0 0
mol:S1P 0 0.005 -9999 0 -0.034 2 2
S1P1/S1P/Gi -0.029 0.132 -9999 0 -0.319 18 18
GNAO1 0.031 0.012 -9999 0 -9999 0 0
S1P/S1P3/G12/G13 0.037 0.033 -9999 0 -0.291 1 1
AKT1 -0.01 0.152 -9999 0 -0.542 9 9
AKT3 -0.026 0.18 -9999 0 -1.036 3 3
mol:GTP 0 0 -9999 0 -9999 0 0
PDGFB-D/PDGFRB 0.03 0.012 -9999 0 -9999 0 0
GNAI2 0.027 0.022 -9999 0 -9999 0 0
GNAI3 0.032 0.011 -9999 0 -9999 0 0
GNAI1 -0.001 0.13 -9999 0 -0.517 8 8
mol:GDP 0 0 -9999 0 -9999 0 0
S1PR3 0 0.005 -9999 0 -0.039 2 2
S1PR2 0 0 -9999 0 -9999 0 0
EDG1 0.003 0.114 -9999 0 -0.518 6 6
mol:Ca2+ -0.012 0.104 -9999 0 -0.315 9 9
MAPK3 -0.016 0.098 -9999 0 -0.316 8 8
MAPK1 -0.008 0.079 -9999 0 -0.275 5 5
JAK2 -0.037 0.141 -9999 0 -0.4 11 11
CXCR4 -0.049 0.136 -9999 0 -0.32 20 20
FLT1 0.01 0.104 -9999 0 -0.517 5 5
RhoA/GDP 0.022 0.007 -9999 0 -9999 0 0
Rac1/GDP 0.024 0.004 -9999 0 -9999 0 0
SRC -0.018 0.099 -9999 0 -0.32 8 8
S1P/S1P3/Gi -0.012 0.105 -9999 0 -0.318 9 9
RAC1 0.032 0.005 -9999 0 -9999 0 0
RhoA/GTP 0.001 0.105 -9999 0 -0.309 7 7
VEGFA 0.001 0.006 -9999 0 -0.047 2 2
S1P/S1P2/Gi -0.012 0.103 -9999 0 -0.266 16 16
VEGFR1 homodimer/VEGFA homodimer 0.01 0.078 -9999 0 -0.374 5 5
RHOA 0.03 0.01 -9999 0 -9999 0 0
S1P/S1P3/Gq -0.007 0.082 -9999 0 -0.284 10 10
GNAQ 0 0 -9999 0 -9999 0 0
GNAZ 0 0.122 -9999 0 -0.517 7 7
G12/G13 0.042 0.039 -9999 0 -0.378 1 1
GNA14 0.011 0.085 -9999 0 -0.518 3 3
GNA15 0.007 0.114 -9999 0 -0.518 6 6
GNA12 0.032 0.007 -9999 0 -9999 0 0
GNA13 0.027 0.048 -9999 0 -0.518 1 1
GNA11 0.029 0.047 -9999 0 -0.518 1 1
Rac1/GTP -0.001 0.107 -9999 0 -0.304 8 8
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.029 0.011 -9999 0 -9999 0 0
RAS family/GTP/Tiam1 -0.008 0.08 -9999 0 -0.289 7 7
NT3 (dimer)/TRKC 0.011 0.091 -9999 0 -0.376 6 6
NT3 (dimer)/TRKB -0.094 0.179 -9999 0 -0.35 41 41
SHC/Grb2/SOS1/GAB1/PI3K 0.002 0.056 -9999 0 -0.277 4 4
RAPGEF1 0.033 0.004 -9999 0 -9999 0 0
BDNF -0.029 0.156 -9999 0 -0.518 12 12
PIK3CA 0.011 0.048 -9999 0 -0.518 1 1
DYNLT1 0.032 0.006 -9999 0 -9999 0 0
NTRK1 0.031 0.012 -9999 0 -9999 0 0
NTRK2 -0.141 0.246 -9999 0 -0.518 40 40
NTRK3 0.031 0.015 -9999 0 -9999 0 0
NT-4/5 (dimer)/TRKB -0.08 0.16 -9999 0 -0.323 40 40
neuron apoptosis 0.026 0.144 0.409 4 -9999 0 4
SHC 2-3/Grb2 -0.029 0.154 -9999 0 -0.447 4 4
SHC1 0.03 0.009 -9999 0 -9999 0 0
SHC2 -0.02 0.128 0.243 1 -0.598 2 3
SHC3 -0.037 0.143 -9999 0 -0.484 6 6
STAT3 (dimer) 0 0.108 -9999 0 -0.362 10 10
NT3 (dimer)/TRKA 0.018 0.088 -9999 0 -0.324 6 6
RIN/GDP 0.05 0.074 0.226 3 -9999 0 3
GIPC1 0.028 0.047 -9999 0 -0.518 1 1
KRAS 0.014 0.093 -9999 0 -0.518 4 4
DNAJA3 0.033 0.059 0.245 2 -9999 0 2
RIN/GTP 0.02 0.035 -9999 0 -0.375 1 1
CCND1 -0.041 0.209 -9999 0 -0.778 10 10
MAGED1 0.015 0.094 -9999 0 -0.518 4 4
PTPN11 0.029 0.047 -9999 0 -0.518 1 1
RICS 0.022 0.068 -9999 0 -0.518 2 2
NT-4/5 (dimer) 0 0 -9999 0 -9999 0 0
SHC/GRB2/SOS1 0.056 0.025 -9999 0 -9999 0 0
GRB2 0.032 0.006 -9999 0 -9999 0 0
NGF (dimer)/TRKA/MATK 0.037 0.036 -9999 0 -0.321 1 1
TRKA/NEDD4-2 0.041 0.039 -9999 0 -0.378 1 1
ELMO1 0.027 0.048 -9999 0 -0.518 1 1
RhoG/GTP/ELMO1/DOCK1 0.039 0.033 -9999 0 -0.321 1 1
NGF 0 0 -9999 0 -9999 0 0
HRAS 0.027 0.048 -9999 0 -0.518 1 1
DOCK1 0.032 0.006 -9999 0 -9999 0 0
GAB2 0.031 0.015 -9999 0 -9999 0 0
RIT2 0.026 0.048 -9999 0 -0.518 1 1
RIT1 0.021 0.068 -9999 0 -0.518 2 2
FRS2 0.031 0.008 -9999 0 -9999 0 0
DNM1 0.027 0.049 -9999 0 -0.518 1 1
mol:GTP 0 0 -9999 0 -9999 0 0
CRK 0.031 0.007 -9999 0 -9999 0 0
SH2B1 (homopentamer) 0 0 -9999 0 -9999 0 0
RhoG/GTP 0.044 0.062 0.25 2 -9999 0 2
mol:GDP 0.057 0.092 0.295 3 -9999 0 3
NGF (dimer) 0 0 -9999 0 -9999 0 0
RhoG/GDP 0.02 0.035 -9999 0 -0.375 1 1
RIT1/GDP 0.047 0.077 0.242 2 -0.284 1 3
TIAM1 0.032 0.006 -9999 0 -9999 0 0
PIK3R1 0.004 0.097 -9999 0 -0.518 4 4
BDNF (dimer)/TRKB -0.097 0.206 -9999 0 -0.374 44 44
KIDINS220/CRKL/C3G 0.043 0.016 -9999 0 -9999 0 0
SHC/RasGAP 0.04 0.019 -9999 0 -9999 0 0
FRS2 family/SHP2 0.061 0.023 -9999 0 -9999 0 0
SHC/GRB2/SOS1/GAB1 0.061 0.057 -9999 0 -0.298 2 2
RIT1/GTP 0.016 0.049 -9999 0 -0.375 2 2
NT3 (dimer) -0.008 0.116 -9999 0 -0.517 6 6
RAP1/GDP 0.035 0.055 -9999 0 -9999 0 0
KIDINS220/CRKL 0.029 0.011 -9999 0 -9999 0 0
BDNF (dimer) -0.029 0.156 -9999 0 -0.517 12 12
ubiquitin-dependent protein catabolic process 0.037 0.034 -9999 0 -0.32 1 1
Schwann cell development -0.021 0.026 -9999 0 -9999 0 0
EHD4 0.031 0.012 -9999 0 -9999 0 0
FRS2 family/GRB2/SOS1 0.073 0.03 -9999 0 -9999 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.027 0.045 -9999 0 -9999 0 0
RAP1B 0.031 0.007 -9999 0 -9999 0 0
RAP1A 0.023 0.066 -9999 0 -0.518 2 2
CDC42/GTP -0.086 0.175 -9999 0 -0.308 45 45
ABL1 0.033 0.004 -9999 0 -9999 0 0
SH2B family/GRB2/SOS1 0.045 0.013 -9999 0 -9999 0 0
Rap1/GTP -0.033 0.115 -9999 0 -0.495 3 3
STAT3 0 0.108 -9999 0 -0.361 10 10
axon guidance -0.094 0.158 -9999 0 -0.297 45 45
MAPK3 0.02 0.044 0.188 5 -0.294 1 6
MAPK1 0.02 0.031 0.188 4 -9999 0 4
CDC42/GDP 0.057 0.075 0.235 4 -9999 0 4
NTF3 -0.008 0.116 -9999 0 -0.518 6 6
NTF4 0 0 -9999 0 -9999 0 0
NGF (dimer)/TRKA/FAIM 0.03 0.037 -9999 0 -0.321 1 1
PI3K 0.005 0.067 -9999 0 -0.378 3 3
FRS3 0.033 0.003 -9999 0 -9999 0 0
FAIM 0.022 0.048 -9999 0 -0.518 1 1
GAB1 0.021 0.068 -9999 0 -0.518 2 2
RASGRF1 0.025 0.065 0.245 2 -0.255 1 3
SOS1 0.032 0.007 -9999 0 -9999 0 0
MCF2L -0.007 0.071 -9999 0 -0.321 6 6
RGS19 0.029 0.047 -9999 0 -0.518 1 1
CDC42 0.032 0.005 -9999 0 -9999 0 0
RAS family/GTP 0.055 0.095 0.285 1 -0.354 1 2
Rac1/GDP 0.056 0.074 0.235 4 -9999 0 4
NGF (dimer)/TRKA/GRIT 0.034 0.047 -9999 0 -0.321 2 2
neuron projection morphogenesis 0.022 0.176 -9999 0 -0.847 4 4
NGF (dimer)/TRKA/NEDD4-2 0.037 0.034 -9999 0 -0.321 1 1
MAP2K1 0.033 0.07 -9999 0 -0.274 2 2
NGFR 0.021 0.036 -9999 0 -9999 0 0
NGF (dimer)/TRKA/GIPC/GAIP 0.021 0.046 -9999 0 -0.272 3 3
RAS family/GTP/PI3K -0.009 0.065 -9999 0 -0.259 6 6
FRS2 family/SHP2/GRB2/SOS1 0.082 0.039 -9999 0 -9999 0 0
NRAS 0.026 0.049 -9999 0 -0.518 1 1
GRB2/SOS1 0.045 0.013 -9999 0 -9999 0 0
PRKCI -0.009 0.11 -9999 0 -0.518 6 6
ChemicalAbstracts:146-91-8 0 0 -9999 0 -9999 0 0
RAC1 0.032 0.005 -9999 0 -9999 0 0
PRKCZ 0 0 -9999 0 -9999 0 0
MAPKKK cascade 0.003 0.051 -9999 0 -0.398 1 1
RASA1 0.029 0.01 -9999 0 -9999 0 0
TRKA/c-Abl 0.045 0.015 -9999 0 -9999 0 0
SQSTM1 0.027 0.021 -9999 0 -9999 0 0
BDNF (dimer)/TRKB/GIPC -0.079 0.197 -9999 0 -0.349 42 42
NGF (dimer)/TRKA/p62/Atypical PKCs 0.01 0.068 -9999 0 -0.277 6 6
MATK 0.026 0.05 -9999 0 -0.518 1 1
NEDD4L 0.026 0.049 -9999 0 -0.518 1 1
RAS family/GDP -0.01 0.033 -9999 0 -9999 0 0
NGF (dimer)/TRKA 0.002 0.043 0.267 2 -9999 0 2
Rac1/GTP -0.014 0.05 -9999 0 -0.25 2 2
FRS2 family/SHP2/CRK family 0.077 0.043 -9999 0 -9999 0 0
Visual signal transduction: Rods

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
mol:K + 0.032 0.005 -9999 0 -9999 0 0
GNAT1/GTP 0.018 0.035 -9999 0 -0.375 1 1
Metarhodopsin II/Arrestin 0.035 0.022 -9999 0 -9999 0 0
PDE6G/GNAT1/GTP 0.035 0.036 -9999 0 -0.321 1 1
mol:GTP 0 0 -9999 0 -9999 0 0
absorption of light 0 0 -9999 0 -9999 0 0
GNAT1 0.025 0.049 -9999 0 -0.518 1 1
GRK1 0 0 -9999 0 -9999 0 0
CNG Channel 0.019 0.085 -9999 0 -0.269 8 8
mol:Na + 0.022 0.097 -9999 0 -0.344 6 6
mol:ADP 0 0 -9999 0 -9999 0 0
RGS9-1/Gbeta5/R9AP 0.015 0.11 -9999 0 -0.327 11 11
mol:GDP 0 0 -9999 0 -9999 0 0
cGMP/CNG Channel 0.032 0.104 -9999 0 -0.354 6 6
CNGB1 0.032 0.006 -9999 0 -9999 0 0
RDH5 0.032 0.01 -9999 0 -9999 0 0
SAG 0.031 0.012 -9999 0 -9999 0 0
mol:Ca2+ -0.002 0.114 0.329 3 -0.685 1 4
Na + (4 Units) 0.015 0.09 -9999 0 -0.328 6 6
RGS9 0.013 0.094 -9999 0 -0.518 4 4
GNB1/GNGT1 -0.037 0.16 -9999 0 -0.378 24 24
GNAT1/GDP 0.019 0.104 -9999 0 -0.284 12 12
GUCY2D 0.027 0.047 -9999 0 -0.518 1 1
GNGT1 -0.075 0.207 -9999 0 -0.518 24 24
GUCY2F 0.023 0.068 -9999 0 -0.518 2 2
GNB5 0.02 0.081 -9999 0 -0.518 3 3
mol:GMP (4 units) 0.005 0.068 -9999 0 -0.279 6 6
mol:11-cis-retinal 0.032 0.01 -9999 0 -9999 0 0
mol:cGMP 0.034 0.09 -9999 0 -0.336 6 6
GNB1 0.032 0.006 -9999 0 -9999 0 0
Rhodopsin 0.04 0.02 -9999 0 -9999 0 0
SLC24A1 0.032 0.005 -9999 0 -9999 0 0
CNGA1 0.013 0.073 -9999 0 -0.518 2 2
Metarhodopsin II 0.018 0.008 -9999 0 -9999 0 0
mol:Ca ++ 0 0 -9999 0 -9999 0 0
GC1/GCAP Family 0.045 0.085 -9999 0 -0.304 6 6
RGS9BP 0 0.107 -9999 0 -0.518 5 5
Metarhodopsin II/Transducin -0.035 0.113 -9999 0 -0.275 22 22
GCAP Family/Ca ++ 0.036 0.072 -9999 0 -0.302 5 5
PDE6A/B 0.017 0.086 -9999 0 -0.378 5 5
mol:Pi 0.015 0.109 -9999 0 -0.326 11 11
mol:all-trans-retinal 0 0 -9999 0 -9999 0 0
Transducin -0.018 0.138 -9999 0 -0.304 24 24
PDE6B 0.009 0.085 -9999 0 -0.518 3 3
PDE6A 0.022 0.067 -9999 0 -0.518 2 2
PDE6G 0.03 0.016 -9999 0 -9999 0 0
RHO 0.028 0.012 -9999 0 -9999 0 0
PDE6 0.014 0.128 -9999 0 -0.301 15 15
GUCA1A 0.019 0.082 -9999 0 -0.518 3 3
GC2/GCAP Family 0.047 0.087 -9999 0 -0.309 6 6
GUCA1C 0.017 0.067 -9999 0 -0.518 2 2
GUCA1B 0.031 0.015 -9999 0 -9999 0 0
S1P4 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
mol:S1P 0 0 -9999 0 -9999 0 0
GNAO1 0.032 0.007 -9999 0 -9999 0 0
CDC42/GTP -0.002 0.104 -9999 0 -0.306 8 8
PLCG1 -0.019 0.097 -9999 0 -0.259 16 16
mol:GTP 0 0 -9999 0 -9999 0 0
GNAI2 0.027 0.02 -9999 0 -9999 0 0
GNAI3 0.032 0.006 -9999 0 -9999 0 0
G12/G13 0.042 0.039 -9999 0 -0.378 1 1
cell migration -0.002 0.102 -9999 0 -0.3 8 8
S1PR5 0 0 -9999 0 -9999 0 0
S1PR4 0 0 -9999 0 -9999 0 0
MAPK3 -0.016 0.096 -9999 0 -0.334 7 7
MAPK1 -0.01 0.077 -9999 0 -0.228 13 13
S1P/S1P5/Gi -0.013 0.102 -9999 0 -0.271 16 16
GNAI1 -0.001 0.13 -9999 0 -0.518 8 8
CDC42/GDP 0.024 0.004 -9999 0 -9999 0 0
S1P/S1P5/G12 0.021 0.005 -9999 0 -9999 0 0
RHOA 0.02 0.041 0.187 5 -0.276 1 6
S1P/S1P4/Gi -0.013 0.102 -9999 0 -0.271 16 16
mol:GDP 0 0 -9999 0 -9999 0 0
GNAZ 0 0.122 -9999 0 -0.518 7 7
S1P/S1P4/G12/G13 0.037 0.031 -9999 0 -0.292 1 1
GNA12 0.032 0.007 -9999 0 -9999 0 0
GNA13 0.027 0.048 -9999 0 -0.518 1 1
CDC42 0.032 0.005 -9999 0 -9999 0 0
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 0.002 0.137 -9999 0 -0.471 5 5
MAP3K8 -0.011 0.144 -9999 0 -0.519 10 10
FOS 0.001 0.096 -9999 0 -0.406 3 3
PRKCA 0.024 0.05 -9999 0 -0.528 1 1
PTPN7 0.025 0.025 -9999 0 -9999 0 0
HRAS 0.027 0.049 -9999 0 -0.522 1 1
PRKCB -0.001 0.005 -9999 0 -0.015 12 12
NRAS 0.025 0.049 -9999 0 -0.517 1 1
RAS family/GTP 0.033 0.077 -9999 0 -0.299 6 6
MAPK3 0.011 0.079 -9999 0 -0.418 3 3
MAP2K1 -0.006 0.082 -9999 0 -0.392 3 3
ELK1 0.027 0.019 -9999 0 -9999 0 0
BRAF 0.001 0.069 -9999 0 -0.426 3 3
mol:GTP 0 0.001 -9999 0 -0.004 13 13
MAPK1 0.011 0.084 -9999 0 -0.454 3 3
RAF1 0.003 0.059 -9999 0 -0.421 2 2
KRAS 0.014 0.093 -9999 0 -0.518 4 4
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.003 0.118 -9999 0 -0.336 11 11
epithelial cell differentiation 0.013 0.103 -9999 0 -0.495 2 2
ITCH 0.032 0.018 -9999 0 -9999 0 0
WWP1 0.009 0.131 -9999 0 -1.449 1 1
FYN 0.023 0.067 -9999 0 -0.518 2 2
EGFR -0.014 0.144 -9999 0 -0.518 10 10
PRL 0.03 0.015 -9999 0 -9999 0 0
neuron projection morphogenesis 0.004 0.085 -9999 0 -0.375 2 2
PTPRZ1 -0.08 0.219 -9999 0 -0.518 27 27
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.04 0.098 -9999 0 -0.401 2 2
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.004 0.1 -9999 0 -0.344 8 8
ADAM17 0.031 0.025 -9999 0 -0.185 1 1
ErbB4/ErbB4 0.017 0.078 -9999 0 -0.801 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.023 0.093 -9999 0 -0.414 4 4
NCOR1 0.032 0.006 -9999 0 -9999 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.002 0.122 -9999 0 -0.474 5 5
GRIN2B -0.01 0.116 -9999 0 -0.496 4 4
ErbB4/ErbB2/betacellulin 0.007 0.104 -9999 0 -0.441 3 3
STAT1 0.007 0.114 -9999 0 -0.518 6 6
HBEGF -0.016 0.15 -9999 0 -0.518 11 11
PRLR 0.018 0.053 -9999 0 -0.518 1 1
E4ICDs/ETO2 0.022 0.09 -9999 0 -0.546 2 2
axon guidance 0.016 0.095 -9999 0 -0.679 1 1
NEDD4 0.028 0.05 -9999 0 -0.518 1 1
Prolactin receptor/Prolactin receptor/Prolactin 0.03 0.046 -9999 0 -0.378 1 1
CBFA2T3 0.015 0.072 -9999 0 -0.518 2 2
ErbB4/ErbB2/HBEGF 0.008 0.109 -9999 0 -0.365 6 6
MAPK3 0.009 0.089 -9999 0 -0.383 2 2
STAT1 (dimer) 0.018 0.116 -9999 0 -0.414 6 6
MAPK1 0.013 0.088 -9999 0 -0.383 2 2
JAK2 0.029 0.014 -9999 0 -9999 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.006 0.109 0.269 1 -0.431 5 6
NRG1 -0.02 0.103 -9999 0 -0.379 10 10
NRG3 0.019 0.081 -9999 0 -0.518 3 3
NRG2 0.029 0.016 -9999 0 -9999 0 0
NRG4 -0.028 0.151 -9999 0 -0.518 11 11
heart development 0.016 0.095 -9999 0 -0.679 1 1
neural crest cell migration -0.006 0.108 0.268 1 -0.425 5 6
ERBB2 0.008 0.038 -9999 0 -0.37 1 1
WWOX/E4ICDs 0.02 0.077 -9999 0 -0.738 1 1
SHC1 0.03 0.009 -9999 0 -9999 0 0
ErbB4/EGFR/neuregulin 4 -0.014 0.142 -9999 0 -0.457 6 6
apoptosis -0.01 0.102 0.453 5 -9999 0 5
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.03 0.079 -9999 0 -0.738 1 1
ErbB4/ErbB2/epiregulin 0.01 0.091 -9999 0 -0.436 3 3
ErbB4/ErbB4/betacellulin/betacellulin 0 0.117 -9999 0 -0.33 11 11
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.027 0.115 -9999 0 -0.485 2 2
MDM2 0.021 0.093 0.262 7 -0.51 2 9
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.006 0.098 -9999 0 -0.323 8 8
STAT5A 0.013 0.088 -9999 0 -0.654 1 1
ErbB4/EGFR/neuregulin 1 beta -0.019 0.139 -9999 0 -0.453 8 8
DLG4 0.031 0.007 -9999 0 -9999 0 0
GRB2/SHC 0.043 0.016 -9999 0 -9999 0 0
E4ICDs/TAB2/NCoR1 0.046 0.08 -9999 0 -0.701 1 1
STAT5A (dimer) 0.021 0.115 -9999 0 -0.54 2 2
MAP3K7IP2 0.032 0.006 -9999 0 -9999 0 0
STAT5B (dimer) 0.033 0.095 -9999 0 -0.654 1 1
LRIG1 -0.013 0.143 -9999 0 -0.518 10 10
EREG -0.007 0.1 -9999 0 -0.518 4 4
BTC -0.024 0.156 -9999 0 -0.518 12 12
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.014 0.094 -9999 0 -0.687 1 1
ERBB4 0.017 0.078 -9999 0 -0.805 1 1
STAT5B 0.032 0.006 -9999 0 -9999 0 0
YAP1 -0.008 0.106 -9999 0 -0.664 3 3
GRB2 0.032 0.006 -9999 0 -9999 0 0
ErbB4/ErbB2/neuregulin 4 0.001 0.112 -9999 0 -0.634 2 2
glial cell differentiation -0.046 0.079 0.692 1 -9999 0 1
WWOX 0.023 0.015 -9999 0 -9999 0 0
cell proliferation -0.05 0.153 -9999 0 -0.477 8 8
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.031 0.012 -9999 0 -9999 0 0
VLDLR -0.015 0.137 -9999 0 -0.518 9 9
LRPAP1 0.03 0.01 -9999 0 -9999 0 0
NUDC 0.032 0.006 -9999 0 -9999 0 0
RELN/LRP8 0.023 0.102 -9999 0 -0.323 10 10
CaM/Ca2+ 0.024 0.004 -9999 0 -9999 0 0
KATNA1 0.032 0.006 -9999 0 -9999 0 0
GO:0030286 0 0 -9999 0 -9999 0 0
ABL1 -0.002 0.091 -9999 0 -0.295 10 10
IQGAP1/CaM 0.047 0.011 -9999 0 -9999 0 0
DAB1 0.031 0.012 -9999 0 -9999 0 0
IQGAP1 0.032 0.005 -9999 0 -9999 0 0
PLA2G7 -0.054 0.194 -9999 0 -0.518 20 20
CALM1 0.032 0.006 -9999 0 -9999 0 0
DYNLT1 0.032 0.006 -9999 0 -9999 0 0
mol:Ca2+ 0 0 -9999 0 -9999 0 0
LRPAP1/LRP8 0.009 0.111 -9999 0 -0.377 10 10
UniProt:Q4QZ09 0 0 -9999 0 -9999 0 0
CLIP1 0 0 -9999 0 -9999 0 0
CDK5R1 0.03 0.018 -9999 0 -9999 0 0
LIS1/Poliovirus Protein 3A 0.011 0.004 -9999 0 -9999 0 0
CDK5R2 0.032 0.006 -9999 0 -9999 0 0
mol:PP1 0 0 -9999 0 -9999 0 0
RELN/VLDLR/DAB1 0.018 0.102 -9999 0 -0.324 9 9
YWHAE 0.031 0.007 -9999 0 -9999 0 0
NDEL1/14-3-3 E 0.015 0.085 -9999 0 -9999 0 0
MAP1B -0.057 0.117 -9999 0 -0.276 29 29
RAC1 0.015 0.006 -9999 0 -9999 0 0
p35/CDK5 0.005 0.086 -9999 0 -0.267 10 10
RELN 0.03 0.012 -9999 0 -9999 0 0
PAFAH/LIS1 -0.022 0.123 -9999 0 -0.324 19 19
LIS1/CLIP170 0.011 0.004 -9999 0 -9999 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain 0.019 0.071 -9999 0 -9999 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.003 0.092 -9999 0 -0.269 9 9
GO:0005869 0 0 -9999 0 -9999 0 0
NDEL1 -0.001 0.081 -9999 0 -9999 0 0
LIS1/IQGAP1 0.032 0.012 -9999 0 -9999 0 0
RHOA 0.015 0.007 -9999 0 -9999 0 0
PAFAH1B1 0.014 0.005 -9999 0 -9999 0 0
PAFAH1B3 0.031 0.008 -9999 0 -9999 0 0
PAFAH1B2 0.031 0.012 -9999 0 -9999 0 0
MAP1B/LIS1/Dynein heavy chain -0.024 0.092 -9999 0 -0.306 2 2
NDEL1/Katanin 60/Dynein heavy chain 0.023 0.089 -9999 0 -9999 0 0
LRP8 -0.013 0.144 -9999 0 -0.518 10 10
NDEL1/Katanin 60 0.011 0.087 -9999 0 -9999 0 0
P39/CDK5 0.007 0.086 -9999 0 -0.267 10 10
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.032 0.012 -9999 0 -9999 0 0
CDK5 -0.025 0.083 0.184 6 -0.279 10 16
PPP2R5D 0.029 0.047 -9999 0 -0.518 1 1
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.009 0.003 -9999 0 -9999 0 0
CSNK2A1 0.031 0.008 -9999 0 -9999 0 0
RELN/VLDLR/DAB1/LIS1 0.029 0.098 -9999 0 -0.283 9 9
RELN/VLDLR 0.001 0.136 -9999 0 -0.315 18 18
CDC42 0.015 0.006 -9999 0 -9999 0 0
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.023 0.067 -9999 0 -0.518 2 2
ITGB7 0.033 0 -9999 0 -9999 0 0
ITGA4 0.012 0.104 -9999 0 -0.518 5 5
alpha4/beta7 Integrin 0.032 0.081 -9999 0 -0.378 5 5
alpha4/beta1 Integrin 0.025 0.101 -9999 0 -0.426 6 6
Cellular roles of Anthrax toxin

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
ANTXR1 0.019 0.07 -9999 0 -0.518 2 2
ANTXR2 0.021 0.068 -9999 0 -0.518 2 2
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.012 -9999 0 -0.07 4 4
monocyte activation -0.022 0.139 -9999 0 -0.421 13 13
MAP2K2 0.005 0.086 -9999 0 -0.561 3 3
MAP2K1 -0.005 0.01 -9999 0 -9999 0 0
MAP2K7 -0.006 0.011 -9999 0 -9999 0 0
MAP2K6 -0.016 0.052 -9999 0 -0.274 5 5
CYAA -0.015 0.046 -9999 0 -0.273 4 4
MAP2K4 -0.006 0.011 -9999 0 -9999 0 0
IL1B -0.051 0.105 -9999 0 -0.269 24 24
Channel 0.024 0.059 -9999 0 -0.292 4 4
NLRP1 -0.003 0.011 -9999 0 -0.065 4 4
CALM1 0.032 0.006 -9999 0 -9999 0 0
negative regulation of phagocytosis 0.003 0.061 -9999 0 -0.391 3 3
mol:Ca2+ 0 0 -9999 0 -9999 0 0
regulation of endothelial cell proliferation 0.003 0.012 0.07 4 -9999 0 4
MAPK3 -0.006 0.011 -9999 0 -9999 0 0
MAPK1 -0.004 0.015 0.127 1 -9999 0 1
PGR -0.01 0.034 -9999 0 -0.274 2 2
PA/Cellular Receptors 0.025 0.065 -9999 0 -0.321 4 4
apoptosis -0.003 0.012 -9999 0 -0.07 4 4
LOC728358 0 0 -9999 0 -9999 0 0
Lethal toxin (unfolded) 0.024 0.056 -9999 0 -0.275 4 4
macrophage activation -0.006 0.014 0.116 1 -9999 0 1
TNF 0.025 0.051 -9999 0 -0.518 1 1
VCAM1 -0.024 0.14 -9999 0 -0.424 13 13
platelet activation 0.003 0.061 -9999 0 -0.391 3 3
MAPKKK cascade 0.002 0.027 -9999 0 -0.132 1 1
IL18 -0.025 0.076 -9999 0 -0.267 11 11
negative regulation of macrophage activation -0.003 0.012 -9999 0 -0.07 4 4
LEF -0.003 0.012 -9999 0 -0.07 4 4
CASP1 -0.004 0.022 -9999 0 -0.079 10 10
mol:cAMP 0.003 0.061 -9999 0 -0.394 3 3
necrosis -0.003 0.012 -9999 0 -0.07 4 4
intracellular pH reduction 0 0 -9999 0 -9999 0 0
PAGA 0 0 -9999 0 -9999 0 0
Edema toxin (unfolded) 0.024 0.056 -9999 0 -0.274 4 4
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -9999 0 -9999 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

Figure 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
MET/RANBP9 0.038 0.054 -9999 0 -0.378 2 2
CRKL 0.003 0.149 0.26 4 -0.424 11 15
mol:PIP3 0.007 0.117 0.461 2 -0.799 2 4
AKT1 0.003 0.113 0.406 3 -0.703 2 5
PTK2B 0.028 0.017 -9999 0 -9999 0 0
RAPGEF1 0.001 0.142 0.254 2 -0.419 10 12
RANBP10 0.028 0.047 -9999 0 -0.518 1 1
PIK3CA 0.011 0.048 -9999 0 -0.518 1 1
HGF/MET/SHIP2 0.048 0.063 -9999 0 -0.324 3 3
MAP3K5 0.009 0.135 -9999 0 -0.429 8 8
HGF/MET/CIN85/CBL/ENDOPHILINS 0.056 0.08 -9999 0 -0.298 5 5
AP1 -0.025 0.14 -9999 0 -0.387 15 15
mol:SU11274 0 0 -9999 0 -9999 0 0
SHC1 0.03 0.009 -9999 0 -9999 0 0
apoptosis -0.097 0.3 -9999 0 -0.792 20 20
STAT3 (dimer) 0.012 0.059 -9999 0 -0.288 1 1
GAB1/CRKL/SHP2/PI3K -0.003 0.115 -9999 0 -0.43 3 3
INPP5D 0 0 -9999 0 -9999 0 0
CBL/CRK 0.006 0.138 -9999 0 -0.429 11 11
PTPN11 0.029 0.047 -9999 0 -0.518 1 1
GO:0007205 0 0 -9999 0 -9999 0 0
PLCG1 0.031 0.008 -9999 0 -9999 0 0
PTEN 0.023 0.067 -9999 0 -0.518 2 2
ELK1 0.002 0.082 0.262 10 -9999 0 10
mol:SU5416 0 0 -9999 0 -9999 0 0
SHP2/GRB2/SOS1GAB1 0.009 0.054 -9999 0 -0.222 3 3
PAK1 0.001 0.107 0.365 3 -0.671 2 5
HGF/MET/RANBP10 0.05 0.063 -9999 0 -0.335 3 3
HRAS 0.011 0.1 -9999 0 -0.571 3 3
DOCK1 0.002 0.142 0.254 2 -0.417 10 12
GAB1 -0.014 0.147 -9999 0 -0.461 12 12
CRK -0.013 0.138 -9999 0 -0.452 11 11
mol:PHA665752 0 0 -9999 0 -9999 0 0
mol:GDP 0.018 0.091 -9999 0 -0.511 3 3
JUN -0.002 0.123 -9999 0 -0.518 7 7
EntrezGene:200958 0 0 -9999 0 -9999 0 0
HGF/MET 0.006 0.043 -9999 0 -0.262 3 3
PIK3R1 0.004 0.097 -9999 0 -0.518 4 4
cell morphogenesis 0.088 0.147 0.343 15 -9999 0 15
GRB2/SHC 0.041 0.048 -9999 0 -0.239 2 2
FOS -0.027 0.151 -9999 0 -0.518 11 11
GLMN 0.004 0.001 -9999 0 -9999 0 0
cell motility 0.002 0.081 0.261 10 -9999 0 10
HGF/MET/MUC20 0.034 0.047 -9999 0 -0.321 2 2
cell migration 0.04 0.048 -9999 0 -0.236 2 2
GRB2 0.032 0.006 -9999 0 -9999 0 0
CBL 0.032 0.005 -9999 0 -9999 0 0
MET/RANBP10 0.035 0.066 -9999 0 -0.391 3 3
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.02 0.045 -9999 0 -0.239 3 3
MET/MUC20 0.017 0.049 -9999 0 -0.375 2 2
RAP1B 0.008 0.142 0.403 1 -0.424 8 9
RAP1A -0.005 0.136 -9999 0 -0.422 8 8
HGF/MET/RANBP9 0.053 0.053 -9999 0 -0.324 2 2
RAF1 0.014 0.088 -9999 0 -0.489 3 3
STAT3 0.012 0.059 -9999 0 -0.291 1 1
cell proliferation 0.025 0.083 0.263 2 -0.422 1 3
RPS6KB1 0.014 0.02 -9999 0 -9999 0 0
MAPK3 -0.005 0.118 0.675 3 -9999 0 3
MAPK1 0.001 0.137 0.825 3 -9999 0 3
RANBP9 0.032 0.006 -9999 0 -9999 0 0
MAPK8 0.026 0.137 0.282 1 -0.424 6 7
SRC 0.001 0.048 -9999 0 -9999 0 0
PI3K 0.005 0.061 -9999 0 -0.25 5 5
MET/Glomulin 0.015 0.05 -9999 0 -0.327 2 2
SOS1 0.032 0.007 -9999 0 -9999 0 0
MAP2K1 0.013 0.083 -9999 0 -0.458 3 3
MET 0.022 0.068 -9999 0 -0.518 2 2
MAP4K1 0.011 0.143 0.268 1 -0.46 8 9
PTK2 0.027 0.048 -9999 0 -0.518 1 1
MAP2K2 0.012 0.083 -9999 0 -0.458 3 3
BAD 0.001 0.106 0.365 3 -0.671 2 5
MAP2K4 0.01 0.121 -9999 0 -0.401 7 7
SHP2/GRB2/SOS1/GAB1 0.018 0.129 -9999 0 -0.424 8 8
INPPL1 0.026 0.049 -9999 0 -0.518 1 1
PXN 0.033 0.003 -9999 0 -9999 0 0
SH3KBP1 0.015 0.084 -9999 0 -0.518 3 3
HGS 0.002 0.034 -9999 0 -0.247 2 2
PLCgamma1/PKC 0.023 0.006 -9999 0 -9999 0 0
HGF 0.029 0.021 -9999 0 -9999 0 0
RASA1 0.029 0.01 -9999 0 -9999 0 0
NCK1 0.019 0.067 -9999 0 -0.518 2 2
PTPRJ 0.029 0.047 -9999 0 -0.518 1 1
NCK/PLCgamma1 0.028 0.067 -9999 0 -0.266 5 5
PDPK1 0.003 0.11 0.356 2 -0.742 2 4
HGF/MET/SHIP 0.034 0.047 -9999 0 -0.321 2 2
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.017 0.213 -9999 0 -0.693 3 3
PCK1 0.021 0.166 -9999 0 -9999 0 0
HNF4A 0.034 0.215 -9999 0 -0.732 1 1
KCNJ11 0.013 0.259 -9999 0 -0.85 4 4
AKT1 0.043 0.134 -9999 0 -9999 0 0
response to starvation 0.005 0.003 -9999 0 -9999 0 0
DLK1 0.019 0.244 0.64 1 -0.748 3 4
NKX2-1 0.058 0.17 0.375 14 -0.377 2 16
ACADM 0.018 0.227 -9999 0 -0.731 4 4
TAT 0.023 0.164 -9999 0 -0.571 2 2
CEBPB 0.032 0.048 -9999 0 -0.514 1 1
CEBPA 0.019 0.094 -9999 0 -0.516 4 4
TTR -0.037 0.254 -9999 0 -0.834 6 6
PKLR 0.035 0.212 -9999 0 -0.721 2 2
APOA1 0.034 0.255 -9999 0 -0.84 2 2
CPT1C -0.05 0.322 -9999 0 -0.838 14 14
ALAS1 0.029 0.148 -9999 0 -9999 0 0
TFRC -0.071 0.443 -9999 0 -1.293 14 14
FOXF1 0.018 0.071 -9999 0 -0.518 2 2
NF1 0.035 0.047 -9999 0 -0.512 1 1
HNF1A (dimer) 0.01 0.004 -9999 0 -9999 0 0
CPT1A 0.022 0.219 -9999 0 -0.733 4 4
HMGCS1 0.027 0.256 -9999 0 -0.828 5 5
NR3C1 0.04 0.021 -9999 0 -9999 0 0
CPT1B 0.013 0.227 -9999 0 -0.735 4 4
chromatin remodeling 0 0 -9999 0 -9999 0 0
SP1 0.029 0.047 -9999 0 -0.518 1 1
GCK 0.018 0.225 -9999 0 -0.757 4 4
CREB1 0.035 0.049 -9999 0 -0.511 1 1
IGFBP1 0.033 0.128 -9999 0 -9999 0 0
PDX1 0.03 0.137 -9999 0 -0.345 2 2
UCP2 -0.011 0.29 -9999 0 -0.878 9 9
ALDOB 0.025 0.242 -9999 0 -0.748 3 3
AFP -0.052 0.153 -9999 0 -0.578 4 4
BDH1 0.071 0.31 -9999 0 -0.985 5 5
HADH 0.021 0.237 -9999 0 -0.669 5 5
F2 0.031 0.254 -9999 0 -0.84 2 2
HNF1A 0.01 0.004 -9999 0 -9999 0 0
G6PC 0.021 0.104 -9999 0 -0.592 1 1
SLC2A2 -0.005 0.138 -9999 0 -9999 0 0
INS -0.005 0.023 -9999 0 -9999 0 0
FOXA1 -0.065 0.204 -9999 0 -0.505 23 23
FOXA3 0.006 0.124 -9999 0 -0.438 6 6
FOXA2 0.04 0.287 -9999 0 -0.848 3 3
ABCC8 0.012 0.257 -9999 0 -0.85 4 4
ALB -0.051 0.156 -9999 0 -0.585 4 4
PLK1 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
regulation of centriole-centriole cohesion 0.009 0.049 0.153 13 -9999 0 13
BUB1B -0.006 0.076 -9999 0 -0.321 6 6
PLK1 0.006 0.018 -9999 0 -9999 0 0
PLK1S1 0.003 0.01 -9999 0 -9999 0 0
KIF2A 0.006 0.016 -9999 0 -9999 0 0
regulation of mitotic centrosome separation 0.006 0.018 -9999 0 -9999 0 0
GOLGA2 0.024 0.066 -9999 0 -0.518 2 2
Hec1/SPC24 -0.003 0.009 -9999 0 -9999 0 0
WEE1 0.007 0.064 -9999 0 -0.315 4 4
cytokinesis 0.003 0.06 -9999 0 -0.329 1 1
PP2A-alpha B56 0.047 0.151 -9999 0 -0.797 4 4
AURKA 0.003 0.012 -9999 0 -9999 0 0
PICH/PLK1 -0.001 0.055 -9999 0 -0.303 4 4
CENPE -0.002 0.039 -9999 0 -0.303 2 2
RhoA/GTP 0.022 0.007 -9999 0 -9999 0 0
positive regulation of microtubule depolymerization 0.006 0.016 -9999 0 -9999 0 0
PPP2CA 0.031 0.008 -9999 0 -9999 0 0
FZR1 0.033 0.004 -9999 0 -9999 0 0
TPX2 0.011 0.041 -9999 0 -0.306 2 2
PAK1 0.03 0.018 -9999 0 -9999 0 0
SPC24 0 0 -9999 0 -9999 0 0
FBXW11 0.031 0.008 -9999 0 -9999 0 0
CLSPN 0.006 0.044 -9999 0 -0.238 4 4
GORASP1 0.03 0.01 -9999 0 -9999 0 0
metaphase 0 0.001 0.012 1 -9999 0 1
mol:GTP 0 0 -9999 0 -9999 0 0
NLP 0.003 0.01 -9999 0 -9999 0 0
G2 phase of mitotic cell cycle -0.001 0.002 0.009 2 -9999 0 2
STAG2 0.025 0.066 -9999 0 -0.518 2 2
GRASP65/GM130/RAB1/GTP -0.023 0.156 -9999 0 -0.512 12 12
spindle elongation 0.006 0.018 -9999 0 -9999 0 0
ODF2 0.033 0.004 -9999 0 -9999 0 0
BUB1 0.01 0.155 -9999 0 -0.862 4 4
TPT1 0 0.049 -9999 0 -0.191 8 8
CDC25C -0.002 0.071 -9999 0 -0.282 8 8
CDC25B 0.026 0.049 -9999 0 -0.526 1 1
SGOL1 -0.009 0.049 -9999 0 -0.153 13 13
RHOA 0.03 0.01 -9999 0 -9999 0 0
CCNB1/CDK1 0.041 0.087 -9999 0 -0.372 4 4
CDC14B 0.007 0.002 -9999 0 -9999 0 0
CDC20 0.023 0.067 -9999 0 -0.518 2 2
PLK1/PBIP1 -0.002 0.051 -9999 0 -0.285 4 4
mitosis -0.001 0.002 0.009 1 -9999 0 1
FBXO5 0.006 0.027 0.13 1 -9999 0 1
CDC2 0.023 0.068 -9999 0 -0.529 2 2
NDC80 0 0 -9999 0 -9999 0 0
metaphase plate congression 0.007 0.044 -9999 0 -0.237 4 4
ERCC6L 0.003 0.07 -9999 0 -0.354 4 4
NLP/gamma Tubulin 0.005 0.018 -9999 0 -0.091 2 2
microtubule cytoskeleton organization 0 0.049 -9999 0 -0.19 8 8
G2/M transition DNA damage checkpoint -0.001 0.001 -9999 0 -9999 0 0
PPP1R12A 0.029 0.047 -9999 0 -0.521 1 1
interphase -0.001 0.001 -9999 0 -9999 0 0
PLK1/PRC1-2 0.04 0.039 -9999 0 -0.318 1 1
GRASP65/GM130/RAB1/GTP/PLK1 0.047 0.045 -9999 0 -0.25 2 2
RAB1A 0.031 0.008 -9999 0 -9999 0 0
prophase 0 0 -9999 0 -9999 0 0
Aurora A/BORA 0.003 0.014 -9999 0 -9999 0 0
mitotic prometaphase -0.001 0.003 0.018 4 -9999 0 4
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.058 -9999 0 -0.478 1 1
microtubule-based process 0.025 0.021 -9999 0 -9999 0 0
Golgi organization 0.006 0.018 -9999 0 -9999 0 0
Cohesin/SA2 0.02 0.044 -9999 0 -0.308 2 2
PPP1CB/MYPT1 0.041 0.053 -9999 0 -0.383 2 2
KIF20A 0.031 0.008 -9999 0 -9999 0 0
APC/C/CDC20 0.021 0.047 -9999 0 -0.331 2 2
PPP2R1A 0.032 0.007 -9999 0 -9999 0 0
chromosome segregation -0.002 0.05 -9999 0 -0.281 4 4
PRC1 0.027 0.048 -9999 0 -0.518 1 1
ECT2 0.1 0.148 0.218 74 -0.295 9 83
C13orf34 0.004 0.015 -9999 0 -9999 0 0
NUDC 0.007 0.044 -9999 0 -0.237 4 4
regulation of attachment of spindle microtubules to kinetochore -0.006 0.075 -9999 0 -0.317 6 6
spindle assembly 0.005 0.017 0.085 1 -9999 0 1
spindle stabilization 0.003 0.01 -9999 0 -9999 0 0
APC/C/HCDH1 0.03 0.004 -9999 0 -9999 0 0
MKLP2/PLK1 0.026 0.021 -9999 0 -9999 0 0
CCNB1 0.026 0.05 -9999 0 -0.529 1 1
PPP1CB 0.028 0.048 -9999 0 -0.521 1 1
BTRC 0.032 0.006 -9999 0 -9999 0 0
ROCK2 0.003 0.058 -9999 0 -0.271 3 3
TUBG1 0.006 0.035 -9999 0 -0.185 4 4
G2/M transition of mitotic cell cycle -0.002 0.068 -9999 0 -0.365 4 4
MLF1IP -0.005 0.066 -9999 0 -0.381 4 4
INCENP 0.029 0.048 -9999 0 -0.523 1 1
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.004 0.105 -9999 0 -0.466 6 6
CRKL 0.029 0.011 -9999 0 -9999 0 0
Rac1/GDP 0.024 0.004 -9999 0 -9999 0 0
DOCK1 0.032 0.006 -9999 0 -9999 0 0
ITGA4 0.012 0.104 -9999 0 -0.518 5 5
alpha4/beta7 Integrin/MAdCAM1 0.061 0.074 -9999 0 -0.289 5 5
EPO 0.03 0.016 -9999 0 -9999 0 0
alpha4/beta7 Integrin 0.032 0.081 -9999 0 -0.378 5 5
mol:GTP 0 0 -9999 0 -9999 0 0
CRK 0.031 0.007 -9999 0 -9999 0 0
alpha4/beta1 Integrin 0.025 0.101 -9999 0 -0.426 6 6
EPO/EPOR (dimer) 0.044 0.018 -9999 0 -9999 0 0
lamellipodium assembly 0.052 0.118 -9999 0 -0.497 3 3
PIK3CA 0.011 0.048 -9999 0 -0.518 1 1
PI3K 0.005 0.067 -9999 0 -0.378 3 3
ARF6 0.031 0.012 -9999 0 -9999 0 0
JAK2 0.007 0.08 -9999 0 -0.325 6 6
PXN 0.033 0.003 -9999 0 -9999 0 0
PIK3R1 0.004 0.097 -9999 0 -0.518 4 4
MADCAM1 0.031 0.011 -9999 0 -9999 0 0
cell adhesion 0.059 0.073 -9999 0 -0.287 5 5
CRKL/CBL 0.043 0.016 -9999 0 -9999 0 0
ITGB1 0.023 0.067 -9999 0 -0.518 2 2
SRC -0.016 0.113 -9999 0 -0.375 10 10
ITGB7 0.033 0 -9999 0 -9999 0 0
RAC1 0.032 0.005 -9999 0 -9999 0 0
alpha4/beta1 Integrin/VCAM1 0.014 0.139 -9999 0 -0.391 12 12
p130Cas/Crk/Dock1 0.016 0.113 -9999 0 -0.338 9 9
VCAM1 -0.008 0.131 -9999 0 -0.518 8 8
RHOA 0.03 0.01 -9999 0 -9999 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.054 0.106 -9999 0 -0.371 7 7
BCAR1 -0.04 0.1 0.184 1 -0.354 10 11
EPOR 0.032 0.006 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
CBL 0.032 0.005 -9999 0 -9999 0 0
GIT1 0.024 0.067 -9999 0 -0.518 2 2
Rac1/GTP 0.053 0.121 -9999 0 -0.517 3 3
Signaling events mediated by HDAC Class III

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
EP300 -0.001 0.129 -9999 0 -0.518 8 8
HDAC4 0.033 0.004 -9999 0 -9999 0 0
induction of apoptosis 0 0 -9999 0 -9999 0 0
regulation of S phase of mitotic cell cycle 0.003 0.02 -9999 0 -0.129 3 3
CDKN1A -0.018 0.118 0.414 1 -0.755 3 4
KAT2B 0 0 -9999 0 -9999 0 0
BAX 0.032 0.005 -9999 0 -9999 0 0
FOXO3 0.016 0.096 0.399 8 -9999 0 8
FOXO1 0 0 -9999 0 -9999 0 0
FOXO4 -0.005 0.07 -9999 0 -0.284 8 8
response to UV 0 0 -9999 0 -9999 0 0
XRCC6 0.032 0.006 -9999 0 -9999 0 0
TAT 0.031 0.011 -9999 0 -9999 0 0
mol:Lysophosphatidic acid 0 0 -9999 0 -9999 0 0
MYOD1 -0.012 0.085 -9999 0 -0.376 7 7
PPARGC1A 0.007 0.096 -9999 0 -0.518 4 4
FHL2 -0.046 0.181 -9999 0 -0.518 17 17
response to nutrient levels 0 0 -9999 0 -9999 0 0
KU70/SIRT1 0.046 0.023 -9999 0 -9999 0 0
HIST2H4A -0.003 0.02 0.129 3 -9999 0 3
SIRT1/FOXO3a 0.031 0.076 0.31 7 -0.182 3 10
SIRT1 0.032 0.028 0.216 3 -9999 0 3
response to hypoxia 0 0 -9999 0 -9999 0 0
SIRT1/MEF2D/HDAC4 0.061 0.026 -9999 0 -9999 0 0
SIRT1/Histone H1b 0.013 0.08 -9999 0 -0.239 10 10
apoptosis -0.061 0.025 -9999 0 -9999 0 0
SIRT1/PGC1A 0.023 0.068 -9999 0 -0.323 4 4
p53/SIRT1 0.028 0.088 0.414 3 -0.384 3 6
SIRT1/FOXO4 0.017 0.067 -9999 0 -0.234 8 8
FOXO1/FHL2/SIRT1 -0.008 0.11 -9999 0 -0.289 17 17
HIST1H1E -0.008 0.082 -9999 0 -0.282 11 11
SIRT1/p300 0.022 0.095 -9999 0 -0.369 7 7
muscle cell differentiation -0.003 0.073 0.322 6 -9999 0 6
TP53 0.014 0.089 0.216 3 -0.521 3 6
KU70/SIRT1/BAX 0.061 0.026 -9999 0 -9999 0 0
CREBBP 0.032 0.006 -9999 0 -9999 0 0
MEF2D 0.032 0.007 -9999 0 -9999 0 0
HIV-1 Tat/SIRT1 0.046 0.023 -9999 0 -9999 0 0
ACSS2 0.014 0.016 -9999 0 -9999 0 0
SIRT1/PCAF/MYOD 0.003 0.074 -9999 0 -0.323 6 6
S1P5 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
mol:S1P 0 0 -9999 0 -9999 0 0
telencephalon oligodendrocyte cell migration 0.002 0.1 0.308 7 -9999 0 7
GNAI2 0.027 0.02 -9999 0 -9999 0 0
S1P/S1P5/G12 0.021 0.005 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
GNAO1 0.032 0.007 -9999 0 -9999 0 0
RhoA/GTP -0.001 0.102 -9999 0 -0.314 7 7
negative regulation of cAMP metabolic process -0.013 0.102 -9999 0 -0.269 16 16
GNAZ 0 0.122 -9999 0 -0.518 7 7
GNAI3 0.032 0.006 -9999 0 -9999 0 0
GNA12 0.032 0.007 -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 -0.013 0.102 -9999 0 -0.271 16 16
RhoA/GDP 0.022 0.007 -9999 0 -9999 0 0
RHOA 0.03 0.01 -9999 0 -9999 0 0
GNAI1 -0.001 0.13 -9999 0 -0.518 8 8
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.031 0.087 -9999 0 -9999 0 0
VDR 0.001 0.122 -9999 0 -0.518 7 7
FAM120B 0 0 -9999 0 -9999 0 0
RXRs/LXRs/DNA/9cRA 0.023 0.081 -9999 0 -0.259 6 6
RXRs/LXRs/DNA/Oxysterols 0.027 0.109 -9999 0 -0.389 6 6
MED1 0 0 -9999 0 -9999 0 0
mol:9cRA 0.002 0.013 -9999 0 -9999 0 0
RARs/THRs/DNA/Src-1 -0.018 0.106 -9999 0 -0.264 15 15
RXRs/NUR77 0.07 0.061 -9999 0 -0.29 1 1
RXRs/PPAR 0.004 0.081 -9999 0 -0.251 2 2
NCOR2 0.025 0.066 -9999 0 -0.518 2 2
VDR/VDR/Vit D3 0.001 0.089 -9999 0 -0.375 7 7
RARs/VDR/DNA/Vit D3 0.008 0.14 -9999 0 -0.327 18 18
RARA 0.032 0.006 -9999 0 -9999 0 0
NCOA1 0.032 0.006 -9999 0 -9999 0 0
VDR/VDR/DNA 0.001 0.122 -9999 0 -0.517 7 7
RARs/RARs/DNA/9cRA 0.013 0.108 -9999 0 -0.298 13 13
RARG 0.025 0.066 -9999 0 -0.518 2 2
RPS6KB1 0.03 0.1 0.541 5 -9999 0 5
RARs/THRs/DNA/SMRT -0.021 0.109 -9999 0 -0.261 17 17
THRA 0.022 0.068 -9999 0 -0.518 2 2
mol:Bile acids 0 0 -9999 0 -9999 0 0
VDR/Vit D3/DNA 0.001 0.089 -9999 0 -0.375 7 7
RXRs/PPAR/9cRA/PGJ2/DNA 0.055 0.062 -9999 0 -0.283 1 1
NR1H4 0.025 0.052 -9999 0 -0.518 1 1
RXRs/LXRs/DNA 0.077 0.096 -9999 0 -0.265 4 4
NR1H2 0.032 0.021 -9999 0 -9999 0 0
NR1H3 0.02 0.084 -9999 0 -0.513 3 3
RXRs/VDR/DNA/Vit D3 0.05 0.089 -9999 0 -0.286 6 6
NR4A1 0.03 0.017 -9999 0 -9999 0 0
mol:ATRA 0 0 -9999 0 -9999 0 0
RXRs/FXR/9cRA/MED1 0.019 0.048 -9999 0 -0.237 2 2
RXRG 0.03 0.023 -9999 0 -9999 0 0
RXR alpha/CCPG 0.02 0.037 -9999 0 -0.372 1 1
RXRA 0.026 0.052 -9999 0 -0.514 1 1
RXRB 0.033 0.021 -9999 0 -9999 0 0
THRB 0.029 0.014 -9999 0 -9999 0 0
PPARG -0.022 0.156 -9999 0 -0.518 12 12
PPARD 0.032 0.005 -9999 0 -9999 0 0
TNF 0.016 0.133 -9999 0 -0.758 2 2
mol:Oxysterols 0.003 0.011 -9999 0 -9999 0 0
cholesterol transport 0.027 0.108 -9999 0 -0.386 6 6
PPARA 0.031 0.008 -9999 0 -9999 0 0
mol:Vit D3 0 0 -9999 0 -9999 0 0
RARB -0.026 0.156 -9999 0 -0.518 12 12
RXRs/NUR77/BCL2 0.002 0.068 -9999 0 -0.245 7 7
SREBF1 0.016 0.133 -9999 0 -1.096 1 1
RXRs/RXRs/DNA/9cRA 0.055 0.062 -9999 0 -0.283 1 1
ABCA1 -0.003 0.212 -9999 0 -1.029 5 5
RARs/THRs 0.034 0.126 -9999 0 -0.302 14 14
RXRs/FXR 0.067 0.069 -9999 0 -0.305 2 2
BCL2 -0.007 0.116 -9999 0 -0.518 6 6
FoxO family signaling

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
G6PC 0.015 0.052 -9999 0 -9999 0 0
PLK1 0.016 0.16 -9999 0 -0.664 2 2
CDKN1B 0.066 0.136 -9999 0 -0.389 2 2
FOXO3 0.019 0.17 -9999 0 -0.527 7 7
KAT2B 0.003 0.017 -9999 0 -0.045 8 8
FOXO1/SIRT1 0.035 0.056 -9999 0 -9999 0 0
CAT -0.001 0.248 -9999 0 -1.388 3 3
CTNNB1 0.028 0.017 -9999 0 -9999 0 0
AKT1 0.031 0.032 -9999 0 -9999 0 0
FOXO1 0.016 0.054 -9999 0 -0.231 1 1
MAPK10 -0.003 0.083 0.193 3 -0.284 9 12
mol:GTP 0.001 0.002 -9999 0 -9999 0 0
FOXO4 0.012 0.109 -9999 0 -0.457 3 3
response to oxidative stress 0.006 0.017 -9999 0 -0.047 5 5
FOXO3A/SIRT1 0.048 0.147 -9999 0 -0.485 4 4
XPO1 0.029 0.011 -9999 0 -9999 0 0
EP300 0.002 0.13 -9999 0 -0.516 8 8
BCL2L11 0.033 0.034 -9999 0 -9999 0 0
FOXO1/SKP2 0.013 0.077 -9999 0 -0.257 6 6
mol:GDP 0.006 0.017 -9999 0 -0.047 5 5
RAN 0.033 0.003 -9999 0 -9999 0 0
GADD45A 0.027 0.19 -9999 0 -0.708 6 6
YWHAQ 0.032 0.006 -9999 0 -9999 0 0
FOXO1/14-3-3 family 0.026 0.124 -9999 0 -0.508 4 4
MST1 0.027 0.031 -9999 0 -9999 0 0
CSNK1D 0.031 0.007 -9999 0 -9999 0 0
CSNK1E 0.027 0.048 -9999 0 -0.518 1 1
FOXO4/14-3-3 family 0.008 0.143 -9999 0 -0.801 2 2
YWHAB 0.032 0.006 -9999 0 -9999 0 0
MAPK8 0.011 0.072 0.195 4 -0.276 6 10
MAPK9 0.011 0.071 0.194 4 -0.276 6 10
YWHAG 0.033 0.004 -9999 0 -9999 0 0
YWHAE 0.031 0.007 -9999 0 -9999 0 0
YWHAZ 0.031 0.008 -9999 0 -9999 0 0
SIRT1 0.033 0.021 -9999 0 -9999 0 0
SOD2 0.024 0.201 -9999 0 -0.834 5 5
RBL2 0.015 0.208 -9999 0 -0.83 5 5
RAL/GDP 0.029 0.079 -9999 0 -0.32 6 6
CHUK 0.025 0.056 -9999 0 -0.514 1 1
Ran/GTP 0.025 0.008 -9999 0 -9999 0 0
CSNK1G2 0.032 0.005 -9999 0 -9999 0 0
RAL/GTP 0.031 0.075 -9999 0 -0.292 6 6
CSNK1G1 0.032 0.005 -9999 0 -9999 0 0
FASLG -0.111 0.445 -9999 0 -1.474 13 13
SKP2 0.002 0.113 -9999 0 -0.518 6 6
USP7 0.033 0.006 -9999 0 -9999 0 0
IKBKB 0.025 0.032 -9999 0 -9999 0 0
CCNB1 0.01 0.192 -9999 0 -0.874 3 3
FOXO1-3a-4/beta catenin 0.035 0.15 -9999 0 -0.422 6 6
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.076 -9999 0 -0.256 6 6
CSNK1A1 0.031 0.007 -9999 0 -9999 0 0
SGK1 0.003 0.017 -9999 0 -0.045 8 8
CSNK1G3 0.031 0.008 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0.04 0.019 -9999 0 -9999 0 0
ZFAND5 0.013 0.093 -9999 0 -0.367 3 3
SFN -0.025 0.167 -9999 0 -0.518 14 14
CDK2 0.036 0.002 -9999 0 -9999 0 0
FOXO3A/14-3-3 0.016 0.124 -9999 0 -0.732 2 2
CREBBP 0.035 0.006 -9999 0 -9999 0 0
FBXO32 0.005 0.276 -9999 0 -1.18 5 5
BCL6 -0.017 0.266 -9999 0 -1.243 5 5
RALB 0.012 0.104 -9999 0 -0.518 5 5
RALA 0.028 0.047 -9999 0 -0.516 1 1
YWHAH 0.031 0.008 -9999 0 -9999 0 0
Retinoic acid receptors-mediated 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
HDAC1 0.031 0.011 -9999 0 -9999 0 0
HDAC3 0.031 0.008 -9999 0 -9999 0 0
VDR 0.001 0.122 -9999 0 -0.518 7 7
Cbp/p300/PCAF 0.021 0.086 -9999 0 -0.321 8 8
EP300 -0.001 0.129 -9999 0 -0.518 8 8
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.01 0.101 -9999 0 -0.371 6 6
KAT2B 0 0 -9999 0 -9999 0 0
MAPK14 0.033 0.004 -9999 0 -9999 0 0
AKT1 -0.003 0.101 0.209 11 -0.282 6 17
RAR alpha/9cRA/Cyclin H 0.041 0.088 -9999 0 -0.583 1 1
mol:9cRA 0 0 -9999 0 -9999 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.012 0.102 -9999 0 -0.347 6 6
CDC2 0.023 0.067 -9999 0 -0.517 2 2
response to UV 0 0.004 -9999 0 -9999 0 0
RAR alpha/Jnk1 0.03 0.039 -9999 0 -0.247 1 1
NCOR2 0.025 0.066 -9999 0 -0.518 2 2
VDR/VDR/Vit D3 0.001 0.089 -9999 0 -0.375 7 7
RXRs/RARs/NRIP1/9cRA -0.006 0.143 -9999 0 -0.493 7 7
NCOA2 0.023 0.066 -9999 0 -0.518 2 2
NCOA3 0.024 0.066 -9999 0 -0.518 2 2
NCOA1 0.032 0.006 -9999 0 -9999 0 0
VDR/VDR/DNA 0.001 0.122 -9999 0 -0.517 7 7
RARG 0.024 0.067 -9999 0 -0.518 2 2
RAR gamma1/9cRA 0.037 0.045 -9999 0 -0.321 2 2
MAPK3 0.031 0.01 -9999 0 -9999 0 0
MAPK1 0.03 0.01 -9999 0 -9999 0 0
MAPK8 0.03 0.013 -9999 0 -9999 0 0
mol:Vit D3 0 0 -9999 0 -9999 0 0
RXRs/VDR/DNA/Vit D3 0.021 0.119 -9999 0 -0.403 6 6
RARA 0.019 0.028 -9999 0 -0.235 1 1
negative regulation of phosphoinositide 3-kinase cascade 0 0 -9999 0 -9999 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.017 0.117 -9999 0 -0.453 6 6
PRKCA 0.026 0.051 -9999 0 -0.517 1 1
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.015 0.157 -9999 0 -0.61 6 6
RXRG 0.021 0.036 -9999 0 -0.319 1 1
RXRA 0.013 0.076 -9999 0 -0.448 2 2
RXRB 0.022 0.035 -9999 0 -0.319 1 1
VDR/Vit D3/DNA 0.001 0.089 -9999 0 -0.375 7 7
RBP1 -0.061 0.196 -9999 0 -0.518 21 21
CRBP1/9-cic-RA -0.044 0.142 -9999 0 -0.375 21 21
RARB -0.027 0.156 -9999 0 -0.518 12 12
PRKCG 0.031 0.018 -9999 0 -9999 0 0
MNAT1 0.032 0.005 -9999 0 -9999 0 0
RAR alpha/RXRs -0.001 0.13 -9999 0 -0.512 4 4
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.004 0.106 -9999 0 -0.383 4 4
proteasomal ubiquitin-dependent protein catabolic process -0.009 0.095 -9999 0 -0.306 7 7
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.016 0.158 -9999 0 -0.61 6 6
positive regulation of DNA binding 0.03 0.079 -9999 0 -0.542 1 1
NRIP1 -0.029 0.245 -9999 0 -1.301 4 4
RXRs/RARs -0.013 0.14 -9999 0 -0.436 8 8
RXRs/RXRs/DNA/9cRA 0.012 0.101 -9999 0 -0.43 5 5
PRKACA 0.032 0.007 -9999 0 -9999 0 0
CDK7 0.03 0.01 -9999 0 -9999 0 0
TFIIH 0.059 0.022 -9999 0 -9999 0 0
RAR alpha/9cRA 0.061 0.05 -9999 0 -9999 0 0
CCNH 0.029 0.01 -9999 0 -9999 0 0
CREBBP 0.032 0.006 -9999 0 -9999 0 0
RAR gamma2/9cRA 0.053 0.039 -9999 0 -0.266 1 1
Atypical NF-kappaB 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
BCL3/RelA 0.032 0.073 -9999 0 -0.378 4 4
FBXW11 0.031 0.008 -9999 0 -9999 0 0
NF kappa B1 p50/c-Rel 0.013 0.068 -9999 0 -0.321 5 5
NF kappa B1 p50/RelA/I kappa B alpha 0.015 0.09 -9999 0 -0.405 2 2
NFKBIA 0.002 0.089 -9999 0 -0.251 12 12
MAPK14 0.033 0.004 -9999 0 -9999 0 0
NF kappa B1 p105/p50 0.029 0.015 -9999 0 -9999 0 0
ARRB2 0.017 0.004 -9999 0 -9999 0 0
REL -0.001 0.121 -9999 0 -0.518 7 7
response to oxidative stress 0 0 -9999 0 -9999 0 0
BCL3/NF kappa B1 p50 0.018 0.061 -9999 0 -0.321 4 4
response to UV 0 0 -9999 0 -9999 0 0
NF kappa B1 p105/RelA 0.03 0.014 -9999 0 -9999 0 0
PIK3CA 0.011 0.048 -9999 0 -0.518 1 1
NF kappa B1 p50 dimer 0.023 0.009 -9999 0 -9999 0 0
PIK3R1 0.004 0.097 -9999 0 -0.518 4 4
NFKB1 0.013 0.006 -9999 0 -9999 0 0
RELA 0.033 0 -9999 0 -9999 0 0
positive regulation of anti-apoptosis 0.005 0.089 -9999 0 -0.247 9 9
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.016 0.091 -9999 0 -0.396 2 2
SRC 0.03 0.013 -9999 0 -9999 0 0
PI3K 0.005 0.067 -9999 0 -0.378 3 3
NF kappa B1 p50/RelA 0.005 0.09 -9999 0 -0.25 9 9
IKBKB 0.029 0.01 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.031 0.008 -9999 0 -9999 0 0
SYK 0.012 0.104 -9999 0 -0.518 5 5
I kappa B alpha/PIK3R1 0.002 0.1 -9999 0 -0.289 8 8
cell death 0.015 0.087 -9999 0 -0.379 2 2
NF kappa B1 p105/c-Rel 0.013 0.068 -9999 0 -0.321 5 5
LCK -0.007 0.137 -9999 0 -0.518 9 9
BCL3 0.014 0.093 -9999 0 -0.518 4 4
IL2 signaling events mediated by PI3K

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
BCL2L1 0.033 0.098 -9999 0 -9999 0 0
UGCG 0.002 0.137 -9999 0 -0.751 4 4
AKT1/mTOR/p70S6K/Hsp90/TERT 0.005 0.161 -9999 0 -0.455 9 9
mol:GTP 0 0 -9999 0 -9999 0 0
mol:glucosylceramide 0.003 0.135 -9999 0 -0.739 4 4
mol:DAG -0.002 0.031 0.174 4 -9999 0 4
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.19 -9999 0 -0.553 9 9
FRAP1 -0.013 0.219 -9999 0 -0.667 9 9
FOXO3 0.005 0.187 -9999 0 -0.609 7 7
AKT1 0.003 0.208 -9999 0 -0.683 7 7
GAB2 0.03 0.016 -9999 0 -9999 0 0
SMPD1 0.006 0.117 -9999 0 -0.634 4 4
SGMS1 0.007 0.029 -9999 0 -0.08 7 7
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 0.051 -9999 0 -0.326 3 3
CALM1 0.032 0.006 -9999 0 -9999 0 0
cell proliferation 0.012 0.135 -9999 0 -0.451 6 6
EIF3A 0 0 -9999 0 -9999 0 0
PI3K 0.006 0.069 -9999 0 -0.382 3 3
RPS6KB1 0.005 0.067 -9999 0 -9999 0 0
mol:sphingomyelin -0.002 0.031 0.174 4 -9999 0 4
natural killer cell activation 0 0.003 -9999 0 -0.015 1 1
JAK3 0.033 0.008 -9999 0 -9999 0 0
PIK3R1 0.005 0.097 -9999 0 -0.518 4 4
JAK1 0.03 0.047 -9999 0 -0.516 1 1
NFKB1 0.031 0.008 -9999 0 -9999 0 0
MYC 0.012 0.219 -9999 0 -0.933 5 5
MYB -0.094 0.358 -9999 0 -1.288 11 11
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.017 0.142 -9999 0 -0.425 8 8
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.018 0.068 -9999 0 -9999 0 0
mol:PI-3-4-5-P3 0.017 0.14 -9999 0 -0.415 8 8
Rac1/GDP 0 0.051 -9999 0 -0.299 3 3
T cell proliferation 0.016 0.134 -9999 0 -0.388 8 8
SHC1 0.03 0.011 -9999 0 -9999 0 0
RAC1 0.032 0.005 -9999 0 -9999 0 0
positive regulation of cyclin-dependent protein kinase activity -0.004 0.02 -9999 0 -0.067 11 11
PRKCZ 0.016 0.136 -9999 0 -0.403 8 8
NF kappa B1 p50/RelA 0.01 0.197 -9999 0 -0.582 8 8
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.028 0.096 -9999 0 -0.331 3 3
HSP90AA1 0 0 -9999 0 -9999 0 0
RELA 0.033 0 -9999 0 -9999 0 0
IL2RA -0.006 0.137 -9999 0 -0.518 9 9
IL2RB 0.023 0.068 -9999 0 -0.516 2 2
TERT 0.023 0.049 -9999 0 -0.518 1 1
E2F1 -0.014 0.124 -9999 0 -0.417 11 11
SOS1 0.031 0.008 -9999 0 -9999 0 0
RPS6 0.03 0.013 -9999 0 -9999 0 0
mol:cAMP 0.002 0.01 0.032 11 -9999 0 11
PTPN11 0.028 0.047 -9999 0 -0.517 1 1
IL2RG 0.021 0.071 -9999 0 -0.519 2 2
actin cytoskeleton organization 0.016 0.134 -9999 0 -0.388 8 8
GRB2 0.031 0.009 -9999 0 -9999 0 0
IL2 0.032 0.01 -9999 0 -9999 0 0
PIK3CA 0.012 0.049 -9999 0 -0.516 1 1
Rac1/GTP 0.012 0.058 -9999 0 -0.283 3 3
LCK -0.005 0.137 -9999 0 -0.516 9 9
BCL2 -0.033 0.257 -9999 0 -0.851 10 10
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.002 0.121 -9999 0 -0.518 7 7
HRAS 0.027 0.048 -9999 0 -0.518 1 1
EGFR -0.014 0.144 -9999 0 -0.518 10 10
AKT 0.054 0.097 0.257 2 -0.377 2 4
FOXO3 0 0 -9999 0 -9999 0 0
AKT1 0.032 0.007 -9999 0 -9999 0 0
FOXO1 0 0 -9999 0 -9999 0 0
AKT3 0.019 0.07 -9999 0 -0.518 2 2
FOXO4 0 0 -9999 0 -9999 0 0
MET 0.022 0.068 -9999 0 -0.518 2 2
PIK3CA 0.011 0.048 -9999 0 -0.518 1 1
PIK3CB 0.02 0.05 -9999 0 -0.518 1 1
NRAS 0.026 0.049 -9999 0 -0.518 1 1
PIK3CG 0.023 0.067 -9999 0 -0.518 2 2
PIK3R3 0.014 0.084 -9999 0 -0.518 3 3
PIK3R2 0.031 0.007 -9999 0 -9999 0 0
NF1 0.028 0.047 -9999 0 -0.518 1 1
RAS -0.001 0.081 -9999 0 -0.285 5 5
ERBB2 0.025 0.049 -9999 0 -0.518 1 1
proliferation/survival/translation -0.063 0.084 0.197 1 -0.221 14 15
PI3K 0.024 0.089 0.209 4 -0.256 5 9
PIK3R1 0.004 0.097 -9999 0 -0.518 4 4
KRAS 0.014 0.093 -9999 0 -0.518 4 4
FOXO 0.063 0.058 0.219 3 -9999 0 3
AKT2 0.029 0.011 -9999 0 -9999 0 0
PTEN 0.023 0.067 -9999 0 -0.518 2 2
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.036 0.069 -9999 0 -0.253 6 6
TC10/GTP 0.036 0.051 -9999 0 -0.263 3 3
Insulin Receptor/Insulin/IRS1/Shp2 0.057 0.09 -9999 0 -0.3 7 7
HRAS 0.027 0.048 -9999 0 -0.518 1 1
APS homodimer 0 0 -9999 0 -9999 0 0
GRB14 -0.048 0.186 -9999 0 -0.518 18 18
FOXO3 -0.011 0.021 -9999 0 -9999 0 0
AKT1 0.03 0.155 0.328 1 -0.322 8 9
INSR 0.031 0.048 -9999 0 -0.519 1 1
Insulin Receptor/Insulin 0.07 0.048 -9999 0 -0.255 1 1
mol:GTP 0 0 -9999 0 -9999 0 0
GRB10 -0.004 0.13 -9999 0 -0.518 8 8
SORBS1 0.029 0.021 -9999 0 -9999 0 0
CRK 0.031 0.007 -9999 0 -9999 0 0
PTPN1 0.016 0.042 -9999 0 -0.25 1 1
CAV1 -0.023 0.114 -9999 0 -0.338 14 14
CBL/APS/CAP/Crk-II/C3G 0.069 0.029 -9999 0 -9999 0 0
Insulin Receptor/Insulin/IRS1/NCK2 0.06 0.085 -9999 0 -0.299 6 6
mol:GDP 0 0 -9999 0 -9999 0 0
mol:PI-3-4-5-P3 0 0.081 -9999 0 -0.263 9 9
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.024 0.085 -9999 0 -0.413 2 2
RPS6KB1 0.024 0.142 0.312 1 -0.423 2 3
PARD6A 0.024 0.03 -9999 0 -9999 0 0
CBL 0.032 0.005 -9999 0 -9999 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -9999 0 0
DOK1 0.027 0.019 -9999 0 -9999 0 0
PIK3R1 0.004 0.097 -9999 0 -0.518 4 4
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.03 0.14 -9999 0 -0.437 2 2
HRAS/GTP 0.005 0.057 -9999 0 -0.244 6 6
Insulin Receptor 0.031 0.048 -9999 0 -0.519 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.066 0.083 -9999 0 -0.282 5 5
PRKCI -0.036 0.164 -9999 0 -0.603 10 10
Insulin Receptor/Insulin/GRB14/PDK1 -0.037 0.111 -9999 0 -0.295 18 18
SHC1 0.03 0.009 -9999 0 -9999 0 0
negative regulation of MAPKKK cascade 0.041 0.049 -9999 0 -9999 0 0
PI3K 0.005 0.086 -9999 0 -0.266 9 9
NCK2 0.033 0.003 -9999 0 -9999 0 0
RHOQ 0.018 0.081 -9999 0 -0.518 3 3
mol:H2O2 0.001 0.005 -9999 0 -9999 0 0
HRAS/GDP 0.02 0.035 -9999 0 -0.375 1 1
AKT2 0.019 0.152 0.328 1 -0.316 9 10
PRKCZ -0.019 0.116 -9999 0 -0.653 4 4
SH2B2 0 0 -9999 0 -9999 0 0
SHC/SHIP 0.006 0.06 -9999 0 -0.262 6 6
F2RL2 0.003 0.077 -9999 0 -0.518 2 2
TRIP10 0.03 0.018 -9999 0 -9999 0 0
Insulin Receptor/Insulin/Shc 0.056 0.038 -9999 0 -0.278 1 1
TC10/GTP/CIP4/Exocyst 0.03 0.056 -9999 0 -0.321 3 3
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.081 0.051 -9999 0 -0.264 1 1
RAPGEF1 0.033 0.004 -9999 0 -9999 0 0
RASA1 0.029 0.01 -9999 0 -9999 0 0
NCK1 0.019 0.067 -9999 0 -0.518 2 2
CBL/APS/CAP/Crk-II 0.055 0.025 -9999 0 -9999 0 0
TC10/GDP 0.013 0.059 -9999 0 -0.375 3 3
Insulin Receptor/Insulin/SHC/GRB10 0.048 0.096 -9999 0 -0.297 8 8
INPP5D -0.017 0.056 -9999 0 -0.274 6 6
SOS1 0.032 0.007 -9999 0 -9999 0 0
SGK1 -0.006 0.01 -9999 0 -9999 0 0
mol:cAMP 0 0 -9999 0 -9999 0 0
PTPN11 0.029 0.047 -9999 0 -0.518 1 1
IRS1 0.008 0.105 -9999 0 -0.518 5 5
p62DOK/RasGAP 0.042 0.05 -9999 0 -9999 0 0
INS 0.035 0.011 -9999 0 -9999 0 0
mol:PI-3-4-P2 -0.017 0.056 -9999 0 -0.272 6 6
GRB2 0.032 0.006 -9999 0 -9999 0 0
EIF4EBP1 0.02 0.139 0.312 1 -0.382 3 4
PTPRA 0.033 0.011 -9999 0 -9999 0 0
PIK3CA 0.011 0.048 -9999 0 -0.518 1 1
TC10/GTP/CIP4 0.03 0.056 -9999 0 -0.321 3 3
PDPK1 0.028 0.047 -9999 0 -0.518 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.018 0.06 -9999 0 -0.246 6 6
Insulin Receptor/Insulin/IRS1 0.043 0.078 -9999 0 -0.296 6 6
Insulin Receptor/Insulin/IRS3 0.048 0.04 -9999 0 -0.381 1 1
Par3/Par6 0.027 0.079 -9999 0 -0.285 5 5
Angiopoietin receptor Tie2-mediated 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
AKT1 0.004 0.171 -9999 0 -0.651 6 6
NCK1/PAK1/Dok-R -0.041 0.092 -9999 0 -0.376 7 7
NCK1/Dok-R -0.015 0.196 -9999 0 -0.824 6 6
PIK3CA 0.011 0.048 -9999 0 -0.516 1 1
mol:beta2-estradiol -0.007 0.012 -9999 0 -9999 0 0
RELA 0.033 0 -9999 0 -9999 0 0
SHC1 0.031 0.009 -9999 0 -9999 0 0
Rac/GDP 0.024 0.004 -9999 0 -9999 0 0
F2 0.01 0.027 -9999 0 -9999 0 0
TNIP2 0.025 0.049 -9999 0 -0.518 1 1
NF kappa B/RelA 0.032 0.171 -9999 0 -0.705 6 6
FN1 -0.009 0.131 -9999 0 -0.518 8 8
PLD2 -0.008 0.184 -9999 0 -0.835 6 6
PTPN11 0.029 0.047 -9999 0 -0.518 1 1
GRB14 -0.048 0.186 -9999 0 -0.518 18 18
ELK1 0.005 0.175 -9999 0 -0.764 6 6
GRB7 0.031 0.007 -9999 0 -9999 0 0
PAK1 0.03 0.018 -9999 0 -9999 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0.008 0.195 -9999 0 -0.758 6 6
CDKN1A 0.014 0.189 -9999 0 -0.778 4 4
ITGA5 0.022 0.068 -9999 0 -0.518 2 2
mol:GTP 0 0 -9999 0 -9999 0 0
RasGAP/Dok-R -0.005 0.199 -9999 0 -0.812 6 6
CRK 0.031 0.007 -9999 0 -9999 0 0
mol:NO 0.011 0.143 -9999 0 -0.519 6 6
PLG -0.004 0.167 -9999 0 -0.759 6 6
mol:GDP 0 0 -9999 0 -9999 0 0
chemokinesis 0.005 0.162 -9999 0 -0.629 6 6
GRB2 0.032 0.006 -9999 0 -9999 0 0
PIK3R1 0.005 0.097 -9999 0 -0.517 4 4
ANGPT2 0.01 0.174 -9999 0 -1.325 1 1
BMX -0.008 0.168 -9999 0 -0.759 6 6
ANGPT1 0.015 0.054 -9999 0 -9999 0 0
tube development 0.01 0.157 -9999 0 -0.665 2 2
ANGPT4 0.02 0.081 -9999 0 -0.517 3 3
response to hypoxia -0.002 0.018 -9999 0 -9999 0 0
Tie2/Ang1/GRB14 -0.026 0.192 -9999 0 -0.768 6 6
alpha5/beta1 Integrin 0.032 0.074 -9999 0 -0.378 4 4
FGF2 0.014 0.083 -9999 0 -0.517 3 3
STAT5A (dimer) 0.023 0.192 -9999 0 -0.667 4 4
mol:L-citrulline 0.011 0.143 -9999 0 -0.519 6 6
AGTR1 0.005 0.082 -9999 0 -0.516 3 3
MAPK14 0.01 0.177 -9999 0 -0.759 6 6
Tie2/SHP2 0.01 0.112 -9999 0 -0.52 1 1
TEK 0.023 0.077 -9999 0 -9999 0 0
RPS6KB1 0.007 0.167 -9999 0 -0.633 6 6
Angiotensin II/AT1 0.005 0.06 -9999 0 -0.372 3 3
Tie2/Ang1/GRB2 0.013 0.175 -9999 0 -0.763 6 6
MAPK3 -0.011 0.173 -9999 0 -0.789 6 6
MAPK1 -0.002 0.174 -9999 0 -0.802 5 5
Tie2/Ang1/GRB7 0.013 0.175 -9999 0 -0.763 6 6
NFKB1 0.031 0.008 -9999 0 -9999 0 0
MAPK8 -0.004 0.167 -9999 0 -0.759 6 6
PI3K -0.028 0.17 -9999 0 -0.71 6 6
FES 0.002 0.187 -9999 0 -0.741 7 7
Crk/Dok-R -0.004 0.2 -9999 0 -0.812 6 6
Tie2/Ang1/ABIN2 0.008 0.175 -9999 0 -0.763 6 6
blood circulation 0 0 -9999 0 -9999 0 0
negative regulation of caspase activity 0.009 0.161 -9999 0 -0.598 6 6
STAT5A 0.031 0.012 -9999 0 -9999 0 0
mol:ROS 0 0 -9999 0 -9999 0 0
PTK2 0.011 0.17 -9999 0 -0.668 5 5
Tie2/Ang2 0.003 0.19 -9999 0 -0.913 2 2
Tie2/Ang1 -0.001 0.176 -9999 0 -0.796 6 6
FOXO1 0.011 0.166 -9999 0 -0.609 7 7
ELF1 0.035 0.024 -9999 0 -9999 0 0
ELF2 -0.016 0.23 -9999 0 -1.067 6 6
mol:Choline -0.007 0.178 -9999 0 -0.81 6 6
cell migration -0.024 0.061 -9999 0 -0.21 7 7
FYN 0.004 0.169 -9999 0 -0.762 2 2
DOK2 -0.024 0.161 -9999 0 -0.518 13 13
negative regulation of cell cycle 0.018 0.173 -9999 0 -0.641 5 5
ETS1 0.023 0.071 -9999 0 -0.523 2 2
PXN 0.013 0.154 -9999 0 -0.574 5 5
ITGB1 0.023 0.067 -9999 0 -0.518 2 2
NOS3 0.01 0.154 -9999 0 -0.578 6 6
RAC1 0.032 0.005 -9999 0 -9999 0 0
TNF 0.029 0.056 -9999 0 -0.523 1 1
MAPKKK cascade -0.007 0.178 -9999 0 -0.81 6 6
RASA1 0.029 0.01 -9999 0 -9999 0 0
Tie2/Ang1/Shc 0.013 0.171 -9999 0 -0.771 5 5
NCK1 0.019 0.067 -9999 0 -0.518 2 2
vasculogenesis 0.013 0.132 -9999 0 -0.463 7 7
mol:Phosphatidic acid -0.007 0.178 -9999 0 -0.81 6 6
mol:Angiotensin II 0.001 0.002 -9999 0 -9999 0 0
mol:NADP 0.011 0.143 -9999 0 -0.519 6 6
Rac1/GTP 0.01 0.164 -9999 0 -0.599 6 6
MMP2 -0.025 0.181 -9999 0 -0.763 6 6
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.008 0.156 0.286 1 -0.393 12 13
PDGFB-D/PDGFRB/SLAP 0.02 0.096 -9999 0 -0.384 7 7
PDGFB-D/PDGFRB/APS/CBL 0.042 0.013 -9999 0 -9999 0 0
AKT1 0.05 0.144 0.301 5 -0.382 2 7
mol:PI-4-5-P2 0 0.001 -9999 0 -9999 0 0
mol:Sphingosine-1-phosphate 0.005 0.143 -9999 0 -0.441 8 8
PIK3CA 0.011 0.048 -9999 0 -0.518 1 1
FGR -0.006 0.12 -9999 0 -0.542 5 5
mol:Ca2+ 0.006 0.124 -9999 0 -0.487 5 5
MYC 0.007 0.181 -9999 0 -0.677 6 6
SHC1 0.03 0.009 -9999 0 -9999 0 0
HRAS/GDP 0.032 0.044 -9999 0 -0.27 1 1
LRP1/PDGFRB/PDGFB 0.059 0.024 -9999 0 -9999 0 0
GRB10 -0.004 0.13 -9999 0 -0.518 8 8
PTPN11 0.029 0.047 -9999 0 -0.518 1 1
GO:0007205 0.006 0.126 -9999 0 -0.496 5 5
PTEN 0.023 0.067 -9999 0 -0.518 2 2
GRB2 0.032 0.006 -9999 0 -9999 0 0
GRB7 0.031 0.007 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/SHP2 0.042 0.04 -9999 0 -0.381 1 1
PDGFB-D/PDGFRB/GRB10 0.016 0.102 -9999 0 -0.381 8 8
cell cycle arrest 0.019 0.096 -9999 0 -0.383 7 7
HRAS 0.027 0.048 -9999 0 -0.518 1 1
HIF1A 0.04 0.136 0.283 5 -0.372 3 8
GAB1 -0.001 0.143 -9999 0 -0.508 6 6
mol:GTP 0 0 -9999 0 -9999 0 0
DNM2 -0.002 0.138 0.308 2 -0.476 5 7
PDGFB-D/PDGFRB 0.058 0.028 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.045 0.015 -9999 0 -9999 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.001 0.156 0.316 1 -0.427 11 12
positive regulation of MAPKKK cascade 0.042 0.039 -9999 0 -0.38 1 1
PIK3R1 0.004 0.097 -9999 0 -0.518 4 4
mol:IP3 0.006 0.127 -9999 0 -0.5 5 5
E5 -0.001 0.002 -9999 0 -9999 0 0
CSK 0.032 0.007 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/GRB7 0.045 0.016 -9999 0 -9999 0 0
SHB 0.019 0.068 -9999 0 -0.518 2 2
BLK -0.06 0.19 -9999 0 -0.599 11 11
PTPN2 0.032 0.01 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/SNX15 0.046 0.014 -9999 0 -9999 0 0
BCAR1 0.032 0.005 -9999 0 -9999 0 0
VAV2 -0.006 0.159 -9999 0 -0.515 7 7
CBL 0.032 0.005 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/DEP1 0.042 0.04 -9999 0 -0.386 1 1
LCK -0.042 0.192 -9999 0 -0.598 13 13
PDGFRB 0.03 0.015 -9999 0 -9999 0 0
ACP1 0.032 0.005 -9999 0 -9999 0 0
HCK -0.02 0.167 -9999 0 -0.738 6 6
ABL1 -0.001 0.131 -9999 0 -0.484 6 6
PDGFB-D/PDGFRB/CBL -0.001 0.158 -9999 0 -0.578 6 6
PTPN1 0.031 0.011 -9999 0 -9999 0 0
SNX15 0.033 0 -9999 0 -9999 0 0
STAT3 0.032 0.006 -9999 0 -9999 0 0
STAT1 0.007 0.114 -9999 0 -0.518 6 6
cell proliferation 0.011 0.164 -9999 0 -0.596 6 6
SLA 0.001 0.122 -9999 0 -0.518 7 7
actin cytoskeleton reorganization 0.048 0.092 0.351 2 -0.266 3 5
SRC 0.007 0.054 -9999 0 -0.334 1 1
PI3K -0.033 0.092 -9999 0 -0.327 6 6
PDGFB-D/PDGFRB/GRB7/SHC 0.056 0.026 -9999 0 -9999 0 0
SH2B2 0 0 -9999 0 -9999 0 0
PLCgamma1/SPHK1 0.005 0.148 -9999 0 -0.457 8 8
LYN 0 0.086 -9999 0 -0.456 3 3
LRP1 0.033 0 -9999 0 -9999 0 0
SOS1 0.032 0.007 -9999 0 -9999 0 0
STAT5B 0.032 0.006 -9999 0 -9999 0 0
STAT5A 0.031 0.012 -9999 0 -9999 0 0
NCK1-2/p130 Cas 0.065 0.065 -9999 0 -0.274 2 2
SPHK1 -0.004 0.131 -9999 0 -0.521 8 8
EDG1 0.004 0.115 -9999 0 -0.522 6 6
mol:DAG 0.006 0.127 -9999 0 -0.5 5 5
PLCG1 0.005 0.13 -9999 0 -0.515 5 5
NHERF/PDGFRB 0.013 0.122 -9999 0 -0.334 14 14
YES1 0.008 0.057 -9999 0 -0.333 1 1
cell migration 0.013 0.122 -9999 0 -0.332 14 14
SHC/Grb2/SOS1 0.076 0.047 -9999 0 -9999 0 0
SLC9A3R2 0.02 0.069 -9999 0 -0.518 2 2
SLC9A3R1 -0.024 0.162 -9999 0 -0.518 13 13
NHERF1-2/PDGFRB/PTEN 0.017 0.127 -9999 0 -0.305 16 16
FYN -0.011 0.135 -9999 0 -0.657 5 5
DOK1 0.02 0.035 -9999 0 -9999 0 0
HRAS/GTP 0.02 0.035 -9999 0 -0.375 1 1
PDGFB 0.03 0.013 -9999 0 -9999 0 0
RAC1 -0.01 0.189 -9999 0 -0.576 9 9
PRKCD 0.021 0.042 -9999 0 -9999 0 0
FER 0.02 0.043 -9999 0 -9999 0 0
MAPKKK cascade 0.014 0.071 0.35 1 -9999 0 1
RASA1 0.021 0.042 -9999 0 -9999 0 0
NCK1 0.019 0.067 -9999 0 -0.518 2 2
NCK2 0.033 0.003 -9999 0 -9999 0 0
p62DOK/Csk 0.041 0.033 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/SHB 0.034 0.056 -9999 0 -0.381 2 2
chemotaxis 0 0.128 -9999 0 -0.47 6 6
STAT1-3-5/STAT1-3-5 0.054 0.075 -9999 0 -0.269 5 5
Bovine Papilomavirus E5/PDGFRB 0.021 0.013 -9999 0 -9999 0 0
PTPRJ 0.029 0.047 -9999 0 -0.518 1 1
Regulation of Androgen receptor activity

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
HDAC1 0.016 0.007 -9999 0 -9999 0 0
SMARCC1 -0.003 0.169 -9999 0 -1.383 2 2
REL -0.001 0.121 -9999 0 -0.518 7 7
HDAC7 -0.034 0.112 0.225 1 -0.353 5 6
JUN -0.001 0.123 -9999 0 -0.518 7 7
EP300 -0.001 0.129 -9999 0 -0.518 8 8
KAT2B 0 0 -9999 0 -9999 0 0
KAT5 0 0 -9999 0 -9999 0 0
MAPK14 -0.011 0.077 -9999 0 -0.381 5 5
FOXO1 0 0 -9999 0 -9999 0 0
T-DHT/AR -0.008 0.134 -9999 0 -0.37 5 5
MAP2K6 0 0.105 -9999 0 -0.52 5 5
BRM/BAF57 0.039 0.033 -9999 0 -9999 0 0
MAP2K4 0.021 0.025 -9999 0 -9999 0 0
SMARCA2 0.027 0.022 -9999 0 -9999 0 0
PDE9A -0.041 0.213 -9999 0 -1.045 5 5
NCOA2 0.024 0.067 -9999 0 -0.517 2 2
CEBPA 0.014 0.093 -9999 0 -0.518 4 4
EHMT2 0.032 0.011 -9999 0 -9999 0 0
cell proliferation -0.003 0.143 0.292 4 -0.372 6 10
NR0B1 -0.215 0.235 -9999 0 -0.518 50 50
EGR1 -0.013 0.138 -9999 0 -0.517 9 9
RXRs/9cRA 0.053 0.039 -9999 0 -0.293 1 1
AR/RACK1/Src 0.008 0.093 -9999 0 -0.364 1 1
AR/GR 0.014 0.082 -9999 0 -0.363 3 3
GNB2L1 0.031 0.009 -9999 0 -9999 0 0
PKN1 0.032 0.007 -9999 0 -9999 0 0
RCHY1 0.022 0.067 -9999 0 -0.518 2 2
epidermal growth factor receptor activity 0 0 -9999 0 -9999 0 0
MAPK8 0.002 0.024 -9999 0 -9999 0 0
T-DHT/AR/TIF2/CARM1 0.017 0.106 -9999 0 -0.357 5 5
SRC -0.021 0.076 0.2 2 -0.282 5 7
NR3C1 0.03 0.012 -9999 0 -9999 0 0
KLK3 -0.014 0.129 0.4 1 -9999 0 1
APPBP2 0.02 0.026 -9999 0 -9999 0 0
TRIM24 0.02 0.081 -9999 0 -0.517 3 3
T-DHT/AR/TIP60 -0.028 0.07 -9999 0 -0.302 5 5
TMPRSS2 -0.209 0.438 -9999 0 -1.052 28 28
RXRG 0.031 0.012 -9999 0 -9999 0 0
mol:9cRA 0 0 -9999 0 -9999 0 0
RXRA 0.026 0.049 -9999 0 -0.517 1 1
RXRB 0.032 0.006 -9999 0 -9999 0 0
CARM1 0.032 0.007 -9999 0 -9999 0 0
NR2C2 0.027 0.048 -9999 0 -0.517 1 1
KLK2 0.013 0.088 -9999 0 -0.408 1 1
AR -0.011 0.074 -9999 0 -0.395 3 3
SENP1 0.033 0.003 -9999 0 -9999 0 0
HSP90AA1 0 0 -9999 0 -9999 0 0
MDM2 0.026 0.047 -9999 0 -0.519 1 1
SRY 0.029 0.017 -9999 0 -9999 0 0
GATA2 0.024 0.048 -9999 0 -0.518 1 1
MYST2 0.029 0.047 -9999 0 -0.518 1 1
HOXB13 -0.104 0.227 -9999 0 -0.517 31 31
T-DHT/AR/RACK1/Src 0.005 0.094 0.252 1 -0.377 1 2
positive regulation of transcription 0.024 0.048 -9999 0 -0.517 1 1
DNAJA1 0.02 0.024 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.052 -9999 0 -0.327 3 3
NCOA1 0.038 0.032 -9999 0 -0.175 2 2
SPDEF 0.024 0.033 -9999 0 -9999 0 0
T-DHT/AR/TIF2 0.003 0.087 -9999 0 -0.42 2 2
T-DHT/AR/Hsp90 -0.023 0.073 -9999 0 -0.302 5 5
GSK3B 0.026 0.016 -9999 0 -9999 0 0
NR2C1 0.033 0 -9999 0 -9999 0 0
mol:T-DHT -0.029 0.066 0.223 1 -0.3 5 6
SIRT1 0.032 0.006 -9999 0 -9999 0 0
ZMIZ2 -0.001 0 -9999 0 -9999 0 0
POU2F1 0.003 0.063 -9999 0 -0.181 1 1
T-DHT/AR/DAX-1 -0.123 0.14 -9999 0 -0.327 23 23
CREBBP 0.032 0.006 -9999 0 -9999 0 0
SMARCE1 0.033 0.006 -9999 0 -9999 0 0
Aurora B signaling

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
Condensin I complex 0 0.021 -9999 0 -0.091 7 7
STMN1 0.007 0.05 -9999 0 -0.389 2 2
Aurora B/RasGAP/Survivin 0.029 0.099 -9999 0 -0.33 9 9
Chromosomal passenger complex/Cul3 protein complex -0.071 0.144 -9999 0 -0.265 34 34
BIRC5 -0.006 0.14 -9999 0 -0.531 9 9
DES -0.018 0.188 -9999 0 -0.613 12 12
Aurora C/Aurora B/INCENP 0.057 0.023 -9999 0 -9999 0 0
Aurora B/TACC1 0.035 0.018 -9999 0 -9999 0 0
Aurora B/PP2A 0.043 0.039 -9999 0 -0.384 1 1
mol:GTP 0 0 -9999 0 -9999 0 0
CBX5 0.01 0.025 -9999 0 -0.277 1 1
mitotic metaphase/anaphase transition 0 0.004 0.019 3 -9999 0 3
NDC80 0.007 0.006 -9999 0 -9999 0 0
Cul3 protein complex -0.051 0.159 -9999 0 -0.328 31 31
KIF2C -0.014 0.122 -9999 0 -0.499 7 7
PEBP1 -0.001 0.002 -9999 0 -0.016 1 1
KIF20A 0.031 0.008 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
Aurora B/RasGAP 0.042 0.017 -9999 0 -9999 0 0
SEPT1 0.027 0.049 -9999 0 -0.518 1 1
SMC2 0 0 -9999 0 -9999 0 0
SMC4 0 0 -9999 0 -9999 0 0
NSUN2/NPM1/Nucleolin 0 0.145 -9999 0 -0.574 7 7
PSMA3 0.032 0.005 -9999 0 -9999 0 0
G2/M transition of mitotic cell cycle 0 0.003 0.009 9 -9999 0 9
H3F3B 0.016 0.005 -9999 0 -9999 0 0
AURKB 0.031 0.011 -9999 0 -9999 0 0
AURKC 0.032 0.006 -9999 0 -9999 0 0
CDCA8 0.028 0.05 -9999 0 -0.542 1 1
cytokinesis -0.004 0.128 -9999 0 -0.641 3 3
Aurora B/Septin1 0.015 0.135 -9999 0 -0.591 3 3
AURKA 0 0.003 0.009 9 -9999 0 9
INCENP 0.028 0.049 -9999 0 -0.534 1 1
KLHL13 -0.093 0.219 -9999 0 -0.518 28 28
BUB1 0.021 0.082 -9999 0 -0.526 3 3
hSgo1/Aurora B/Survivin 0.027 0.109 -9999 0 -0.358 9 9
EVI5 0.032 0.006 -9999 0 -9999 0 0
RhoA/GTP 0.029 0.114 -9999 0 -0.52 3 3
SGOL1 0.022 0.067 -9999 0 -0.518 2 2
CENPA -0.002 0.08 -9999 0 -0.332 6 6
NCAPG 0 0 -9999 0 -9999 0 0
Aurora B/HC8 Proteasome 0.046 0.013 -9999 0 -9999 0 0
NCAPD2 0 0 -9999 0 -9999 0 0
Aurora B/PP1-gamma 0.047 0.011 -9999 0 -9999 0 0
RHOA 0.03 0.01 -9999 0 -9999 0 0
NCAPH 0 0 -9999 0 -9999 0 0
NPM1 -0.016 0.147 -9999 0 -0.649 5 5
RASA1 0.029 0.01 -9999 0 -9999 0 0
KLHL9 0.015 0.081 -9999 0 -0.518 3 3
mitotic prometaphase -0.001 0.002 -9999 0 -0.016 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.046 0.012 -9999 0 -9999 0 0
PPP1CC 0.033 0 -9999 0 -9999 0 0
Centraspindlin 0.02 0.119 -9999 0 -0.561 3 3
RhoA/GDP 0.022 0.007 -9999 0 -9999 0 0
NSUN2 0.006 0.109 -9999 0 -0.474 4 4
MYLK 0.009 0.042 -9999 0 -0.329 2 2
KIF23 0.025 0.068 -9999 0 -0.53 2 2
VIM -0.015 0.09 -9999 0 -0.385 7 7
RACGAP1 0.033 0.005 -9999 0 -9999 0 0
mitosis 0 0 -9999 0 -9999 0 0
NCL 0.005 0.066 -9999 0 -0.276 6 6
Chromosomal passenger complex -0.01 0.093 -9999 0 -0.295 8 8
Chromosomal passenger complex/EVI5 0.055 0.111 -9999 0 -0.327 9 9
TACC1 0.027 0.012 -9999 0 -9999 0 0
PPP2R5D 0.029 0.047 -9999 0 -0.518 1 1
CUL3 0.032 0.006 -9999 0 -9999 0 0
response to DNA damage stimulus 0 0 -9999 0 -9999 0 0
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.038 0.092 -9999 0 -0.298 7 7
MAP4K1 0.028 0.011 -9999 0 -9999 0 0
MAP3K8 -0.01 0.144 -9999 0 -0.518 10 10
PRKCB 0 0 -9999 0 -9999 0 0
DBNL 0.028 0.047 -9999 0 -0.518 1 1
CRKL 0.029 0.011 -9999 0 -9999 0 0
MAP3K1 0.005 0.072 -9999 0 -9999 0 0
JUN -0.013 0.112 -9999 0 -0.599 3 3
MAP3K7 0.01 0.066 -9999 0 -9999 0 0
GRAP2 0.031 0.008 -9999 0 -9999 0 0
CRK 0.031 0.007 -9999 0 -9999 0 0
MAP2K4 0.003 0.096 0.236 1 -0.356 4 5
LAT 0.031 0.015 -9999 0 -9999 0 0
LCP2 -0.013 0.15 -9999 0 -0.518 11 11
MAPK8 0.001 0.119 -9999 0 -0.636 4 4
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.015 0.073 -9999 0 -9999 0 0
LAT/GRAP2/SLP76/HPK1/HIP-55 0.047 0.095 -9999 0 -0.283 7 7
Aurora A 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
Aurora A/GADD45A 0.02 0.05 -9999 0 -0.266 2 2
BIRC5 -0.005 0.137 -9999 0 -0.518 9 9
NFKBIA 0.012 0.059 0.246 5 -0.317 1 6
CPEB1 0.005 0.106 -9999 0 -0.518 5 5
AKT1 0.009 0.039 0.246 2 -9999 0 2
NDEL1 0.031 0.007 -9999 0 -9999 0 0
Aurora A/BRCA1 0.021 0.036 -9999 0 -0.217 1 1
NDEL1/TACC3 0.049 0.041 -9999 0 -9999 0 0
GADD45A 0.021 0.068 -9999 0 -0.518 2 2
GSK3B 0.027 0.02 -9999 0 -9999 0 0
PAK1/Aurora A 0.025 0.036 -9999 0 -9999 0 0
MDM2 0.027 0.048 -9999 0 -0.518 1 1
JUB -0.005 0.137 -9999 0 -0.518 9 9
TPX2 0.009 0.048 -9999 0 -0.379 2 2
TP53 0.005 0.07 -9999 0 -0.334 5 5
DLG7 0 0.047 0.246 1 -0.241 3 4
AURKAIP1 0 0 -9999 0 -9999 0 0
ARHGEF7 0.031 0.008 -9999 0 -9999 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -9999 0 0
Aurora A/NDEL1/TACC3 0.052 0.044 -9999 0 -9999 0 0
G2/M transition of mitotic cell cycle 0.021 0.035 -9999 0 -0.216 1 1
AURKA 0.015 0.027 -9999 0 -9999 0 0
AURKB 0.008 0.03 -9999 0 -0.142 5 5
CDC25B 0.005 0.049 -9999 0 -0.24 3 3
G2/M transition checkpoint 0.005 0.076 -9999 0 -0.252 9 9
mRNA polyadenylation 0.009 0.068 -9999 0 -0.3 5 5
Aurora A/CPEB 0.009 0.068 -9999 0 -0.302 5 5
Aurora A/TACC1/TRAP/chTOG 0.056 0.072 -9999 0 -0.276 3 3
BRCA1 0.028 0.047 -9999 0 -0.518 1 1
centrosome duplication 0.025 0.036 -9999 0 -9999 0 0
regulation of centrosome cycle 0.048 0.04 -9999 0 -9999 0 0
spindle assembly 0.054 0.071 -9999 0 -0.273 3 3
TDRD7 0.017 0.093 -9999 0 -0.518 4 4
Aurora A/RasGAP/Survivin 0.04 0.091 -9999 0 -0.301 5 5
CENPA 0.005 0.053 -9999 0 -0.263 5 5
Aurora A/PP2A 0.023 0.046 -9999 0 -0.316 1 1
meiosis 0 0 -9999 0 -9999 0 0
protein catabolic process 0.01 0.056 -9999 0 -0.317 1 1
negative regulation of DNA binding 0 0.078 -9999 0 -0.333 5 5
prophase 0 0 -9999 0 -9999 0 0
GIT1/beta-PIX 0.038 0.053 -9999 0 -0.378 2 2
RASA1 0.029 0.01 -9999 0 -9999 0 0
Ajuba/Aurora A 0.005 0.077 -9999 0 -0.254 9 9
mitotic prometaphase 0 0.016 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.027 -9999 0 -9999 0 0
TACC1 0.027 0.012 -9999 0 -9999 0 0
TACC3 0.027 0.02 -9999 0 -9999 0 0
Aurora A/Antizyme1 0.024 0.03 -9999 0 -9999 0 0
Aurora A/RasGAP 0.024 0.031 -9999 0 -9999 0 0
OAZ1 0.033 0.004 -9999 0 -9999 0 0
RAN 0.033 0.003 -9999 0 -9999 0 0
mitosis 0 0 -9999 0 -9999 0 0
PRKACA 0.032 0.013 -9999 0 -9999 0 0
GIT1 0.024 0.067 -9999 0 -0.518 2 2
GIT1/beta-PIX/PAK1 0.052 0.053 -9999 0 -0.324 2 2
Importin alpha/Importin beta/TPX2 0.009 0.048 -9999 0 -0.378 2 2
PPP2R5D 0.029 0.047 -9999 0 -0.518 1 1
Aurora A/TPX2 0.01 0.04 -9999 0 -0.22 2 2
PAK1 0.03 0.018 -9999 0 -9999 0 0
CKAP5 0.032 0.006 -9999 0 -9999 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.021 0.107 -9999 0 -0.559 1 1
CRKL 0.029 0.069 0.279 1 -0.219 1 2
mol:DAG 0.03 0.069 -9999 0 -0.434 1 1
HRAS 0.035 0.09 0.27 6 -9999 0 6
MAPK8 0.023 0.053 0.194 2 -0.331 1 3
RAP1A 0.027 0.078 0.299 1 -0.248 3 4
GAB1 0.028 0.077 0.289 2 -0.248 2 4
MAPK14 0.025 0.056 0.194 3 -0.331 1 4
EPO 0.031 0.021 -9999 0 -9999 0 0
PLCG1 0.03 0.07 -9999 0 -0.445 1 1
EPOR/TRPC2/IP3 Receptors 0.033 0.017 -9999 0 -9999 0 0
RAPGEF1 0.033 0.004 -9999 0 -9999 0 0
EPO/EPOR (dimer)/SOCS3 0.049 0.067 -9999 0 -0.338 3 3
GAB1/SHC/GRB2/SOS1 0.053 0.076 0.278 2 -0.269 1 3
EPO/EPOR (dimer) 0.045 0.028 -9999 0 -9999 0 0
IRS2 0.014 0.092 0.289 2 -0.267 7 9
STAT1 0.021 0.098 -9999 0 -0.381 3 3
STAT5B 0.03 0.08 -9999 0 -0.493 1 1
cell proliferation 0.002 0.057 0.186 5 -0.312 1 6
GAB1/SHIP/PIK3R1/SHP2/SHC 0.012 0.079 -9999 0 -0.286 4 4
TEC 0.033 0.073 0.289 2 -9999 0 2
SOCS3 0.018 0.082 -9999 0 -0.518 3 3
STAT1 (dimer) 0.021 0.097 -9999 0 -0.346 4 4
JAK2 0.029 0.02 -9999 0 -9999 0 0
PIK3R1 0.004 0.097 -9999 0 -0.518 4 4
EPO/EPOR (dimer)/JAK2 0.05 0.069 -9999 0 -0.228 1 1
EPO/EPOR 0.045 0.028 -9999 0 -9999 0 0
LYN 0.025 0.05 -9999 0 -0.532 1 1
TEC/VAV2 0.023 0.099 0.276 2 -0.257 7 9
elevation of cytosolic calcium ion concentration 0.033 0.017 -9999 0 -9999 0 0
SHC1 0.03 0.009 -9999 0 -9999 0 0
EPO/EPOR (dimer)/LYN 0.057 0.052 -9999 0 -0.368 1 1
mol:IP3 0.03 0.069 -9999 0 -0.434 1 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.005 0.099 0.284 1 -0.276 8 9
SH2B3 0 0.008 -9999 0 -9999 0 0
NFKB1 0.025 0.056 0.194 3 -0.331 1 4
EPO/EPOR (dimer)/JAK2/SOCS3 0.011 0.059 -9999 0 -0.318 3 3
PTPN6 0.021 0.059 -9999 0 -0.228 1 1
TEC/VAV2/GRB2 0.033 0.099 0.281 2 -0.254 6 8
EPOR 0.033 0.017 -9999 0 -9999 0 0
INPP5D 0 0 -9999 0 -9999 0 0
mol:GDP 0.052 0.076 0.279 2 -0.273 1 3
SOS1 0.032 0.007 -9999 0 -9999 0 0
PLCG2 0.011 0.104 -9999 0 -0.518 5 5
CRKL/CBL/C3G 0.051 0.072 0.271 1 -9999 0 1
VAV2 0.015 0.097 0.289 2 -0.257 8 10
CBL 0.032 0.072 0.289 2 -0.219 1 3
SHC/Grb2/SOS1 0.022 0.048 -9999 0 -9999 0 0
STAT5A 0.029 0.08 -9999 0 -0.493 1 1
GRB2 0.032 0.006 -9999 0 -9999 0 0
STAT5 (dimer) 0.036 0.108 -9999 0 -0.359 6 6
LYN/PLCgamma2 0.028 0.083 -9999 0 -0.381 5 5
PTPN11 0.029 0.047 -9999 0 -0.518 1 1
BTK 0.013 0.104 0.289 2 -0.266 10 12
BCL2 -0.014 0.227 -9999 0 -0.874 8 8
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.01 0.126 -9999 0 -0.485 5 5
BAG4 0.027 0.013 -9999 0 -9999 0 0
BAD 0 0.041 -9999 0 -0.158 1 1
NFKBIA 0.027 0.048 -9999 0 -0.518 1 1
BIRC3 -0.027 0.156 -9999 0 -0.518 12 12
BAX 0.002 0.044 0.213 1 -0.147 4 5
EnzymeConsortium:3.1.4.12 0.002 0.03 -9999 0 -0.103 5 5
IKBKB 0.004 0.133 -9999 0 -0.46 5 5
MAP2K2 -0.004 0.045 0.171 1 -0.215 1 2
MAP2K1 -0.005 0.044 0.171 1 -0.215 1 2
SMPD1 0.002 0.033 -9999 0 -0.121 2 2
GO:0005551 0 0 -9999 0 -9999 0 0
FADD/Caspase 8 0.015 0.134 0.275 2 -0.447 6 8
MAP2K4 -0.006 0.052 -9999 0 -0.217 4 4
protein ubiquitination -0.004 0.126 -9999 0 -0.468 5 5
EnzymeConsortium:2.7.1.37 -0.005 0.048 0.169 1 -0.222 1 2
response to UV 0 0 0.002 1 -9999 0 1
RAF1 -0.002 0.047 0.178 1 -0.225 1 2
CRADD 0.025 0.066 -9999 0 -0.519 2 2
mol:ceramide 0.003 0.043 -9999 0 -0.146 5 5
I-kappa-B-alpha/RELA/p50/ubiquitin 0.039 0.033 -9999 0 -0.321 1 1
MADD 0.032 0.005 -9999 0 -9999 0 0
MAP3K1 -0.007 0.055 -9999 0 -0.225 4 4
TRADD 0.027 0.048 -9999 0 -0.519 1 1
RELA/p50 0.033 0 -9999 0 -9999 0 0
MAPK3 0 0.048 0.172 1 -0.208 1 2
MAPK1 -0.001 0.049 0.172 1 -0.226 2 3
p50/RELA/I-kappa-B-alpha 0.043 0.038 -9999 0 -0.378 1 1
FADD 0.009 0.132 0.269 1 -0.485 5 6
KSR1 -0.001 0.047 0.123 1 -0.172 4 5
MAPK8 -0.006 0.051 0.185 1 -0.21 3 4
TRAF2 0.031 0.012 -9999 0 -9999 0 0
response to radiation 0 0 -9999 0 -9999 0 0
CHUK -0.01 0.12 -9999 0 -0.457 5 5
TNF R/SODD 0.033 0.041 -9999 0 -0.377 1 1
TNF 0.025 0.051 -9999 0 -0.519 1 1
CYCS 0.01 0.049 0.146 2 -0.147 3 5
IKBKG -0.01 0.12 -9999 0 -0.46 5 5
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.003 0.13 -9999 0 -0.506 5 5
RELA 0.033 0 -9999 0 -9999 0 0
RIPK1 0.032 0.005 -9999 0 -9999 0 0
AIFM1 0.008 0.048 0.138 3 -0.148 3 6
TNF/TNF R/SODD 0.042 0.048 -9999 0 -0.324 1 1
TNFRSF1A 0.026 0.048 -9999 0 -0.516 1 1
response to heat 0 0 -9999 0 -9999 0 0
CASP8 0.019 0.114 -9999 0 -0.593 4 4
NSMAF -0.001 0.127 0.27 1 -0.473 5 6
response to hydrogen peroxide 0 0 0.002 1 -9999 0 1
BCL2 -0.007 0.116 -9999 0 -0.518 6 6
Paxillin-dependent events mediated by a4b1

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
CRKL 0.029 0.011 -9999 0 -9999 0 0
Rac1/GDP 0.033 0.015 -9999 0 -9999 0 0
DOCK1 0.032 0.006 -9999 0 -9999 0 0
ITGA4 0.012 0.104 -9999 0 -0.518 5 5
RAC1 0.032 0.005 -9999 0 -9999 0 0
alpha4/beta7 Integrin 0.032 0.081 -9999 0 -0.378 5 5
mol:GTP 0 0 -9999 0 -9999 0 0
CRK 0.031 0.007 -9999 0 -9999 0 0
alpha4/beta1 Integrin 0.042 0.093 -9999 0 -0.366 6 6
alpha4/beta7 Integrin/Paxillin 0.039 0.067 -9999 0 -0.295 5 5
lamellipodium assembly 0.012 0.119 -9999 0 -0.407 6 6
PIK3CA 0.011 0.048 -9999 0 -0.518 1 1
PI3K 0.005 0.067 -9999 0 -0.378 3 3
ARF6 0.031 0.012 -9999 0 -9999 0 0
TLN1 0.029 0.01 -9999 0 -9999 0 0
PXN 0.015 0.004 -9999 0 -9999 0 0
PIK3R1 0.004 0.097 -9999 0 -0.518 4 4
ARF6/GTP 0.042 0.093 -9999 0 -0.327 7 7
cell adhesion 0.052 0.079 -9999 0 -0.329 4 4
CRKL/CBL 0.043 0.016 -9999 0 -9999 0 0
alpha4/beta1 Integrin/Paxillin 0.033 0.084 -9999 0 -0.337 6 6
ITGB1 0.023 0.067 -9999 0 -0.518 2 2
ITGB7 0.033 0 -9999 0 -9999 0 0
ARF6/GDP 0.032 0.018 -9999 0 -9999 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.027 0.13 -9999 0 -0.343 12 12
p130Cas/Crk/Dock1 0.062 0.018 -9999 0 -9999 0 0
VCAM1 -0.008 0.131 -9999 0 -0.518 8 8
alpha4/beta1 Integrin/Paxillin/Talin 0.054 0.081 -9999 0 -0.333 4 4
alpha4/beta1 Integrin/Paxillin/GIT1 0.05 0.102 -9999 0 -0.351 7 7
BCAR1 0.032 0.005 -9999 0 -9999 0 0
mol:GDP -0.048 0.101 0.348 7 -9999 0 7
CBL 0.032 0.005 -9999 0 -9999 0 0
PRKACA 0.032 0.007 -9999 0 -9999 0 0
GIT1 0.024 0.067 -9999 0 -0.518 2 2
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.054 0.081 -9999 0 -0.333 4 4
Rac1/GTP 0.011 0.13 -9999 0 -0.452 6 6
Regulation of Telomerase

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
Telomerase catalytic core complex -0.046 0.208 -9999 0 -0.812 5 5
RAD9A 0.032 0.005 -9999 0 -9999 0 0
AP1 -0.024 0.158 -9999 0 -0.441 15 15
IFNAR2 0.021 0.068 -9999 0 -0.517 2 2
AKT1 0.01 0.051 -9999 0 -0.236 3 3
ER alpha/Oestrogen -0.005 0.09 -9999 0 -0.379 7 7
NFX1/SIN3/HDAC complex 0.015 0.068 -9999 0 -0.319 4 4
EGF -0.032 0.15 -9999 0 -0.518 11 11
SMG5 0 0 -9999 0 -9999 0 0
SMG6 0 0 -9999 0 -9999 0 0
SP3/HDAC2 0.044 0.024 -9999 0 -9999 0 0
TERT/c-Abl -0.033 0.199 -9999 0 -0.745 5 5
SAP18 0.032 0.007 -9999 0 -9999 0 0
MRN complex 0.059 0.022 -9999 0 -9999 0 0
WT1 -0.02 0.144 -9999 0 -0.517 10 10
WRN 0.03 0.009 -9999 0 -9999 0 0
SP1 0.026 0.051 -9999 0 -0.528 1 1
SP3 0.032 0.006 -9999 0 -9999 0 0
TERF2IP 0.032 0.006 -9999 0 -9999 0 0
Telomerase/Nucleolin -0.024 0.184 -9999 0 -0.673 5 5
Mad/Max 0.039 0.043 -9999 0 -0.377 1 1
TERT -0.049 0.22 -9999 0 -0.862 5 5
CCND1 -0.078 0.331 -9999 0 -1.199 10 10
MAX 0.032 0.008 -9999 0 -9999 0 0
RBBP7 0.03 0.018 -9999 0 -9999 0 0
RBBP4 0.028 0.047 -9999 0 -0.517 1 1
TERF2 0.027 0.017 -9999 0 -9999 0 0
PTGES3 0.033 0 -9999 0 -9999 0 0
SIN3A 0.033 0.004 -9999 0 -9999 0 0
Telomerase/911 0.035 0.072 -9999 0 -0.354 2 2
CDKN1B -0.061 0.145 -9999 0 -0.34 27 27
RAD1 0.027 0.013 -9999 0 -9999 0 0
XRCC5 0.032 0.006 -9999 0 -9999 0 0
XRCC6 0.032 0.006 -9999 0 -9999 0 0
SAP30 0.03 0.01 -9999 0 -9999 0 0
TRF2/PARP2 0.043 0.019 -9999 0 -9999 0 0
UBE3A 0.032 0.005 -9999 0 -9999 0 0
JUN -0.001 0.123 -9999 0 -0.519 7 7
E6 0 0.003 -9999 0 -9999 0 0
HPV-16 E6/E6AP 0.023 0.011 -9999 0 -9999 0 0
FOS -0.027 0.151 -9999 0 -0.518 11 11
IFN-gamma/IRF1 -0.065 0.186 -9999 0 -0.404 29 29
PARP2 0.032 0.007 -9999 0 -9999 0 0
BLM 0.024 0.066 -9999 0 -0.518 2 2
Telomerase 0.027 0.044 -9999 0 -9999 0 0
IRF1 0.013 0.095 -9999 0 -0.514 4 4
ESR1 -0.006 0.124 -9999 0 -0.52 7 7
KU/TER 0.046 0.012 -9999 0 -9999 0 0
ATM/TRF2 0.043 0.038 -9999 0 -0.351 1 1
ubiquitin-dependent protein catabolic process 0.02 0.063 -9999 0 -0.254 4 4
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.02 0.064 -9999 0 -0.259 4 4
HDAC1 0.031 0.011 -9999 0 -9999 0 0
HDAC2 0.029 0.02 -9999 0 -9999 0 0
ATM 0.012 0.038 -9999 0 -0.406 1 1
SMAD3 0.003 0.067 -9999 0 -0.38 4 4
ABL1 0.033 0.004 -9999 0 -9999 0 0
MXD1 0.025 0.05 -9999 0 -0.517 1 1
MRE11A 0.033 0.004 -9999 0 -9999 0 0
HUS1 0.028 0.047 -9999 0 -0.518 1 1
RPS6KB1 0.032 0.006 -9999 0 -9999 0 0
TERT/NF kappa B1/14-3-3 -0.012 0.205 -9999 0 -0.741 5 5
NR2F2 0.027 0.048 -9999 0 -0.515 1 1
MAPK3 0.012 0.013 -9999 0 -9999 0 0
MAPK1 0.011 0.013 -9999 0 -9999 0 0
TGFB1/TGF beta receptor Type II 0.031 0.008 -9999 0 -9999 0 0
NFKB1 0.031 0.008 -9999 0 -9999 0 0
HNRNPC 0 0 -9999 0 -9999 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.012 0.037 -9999 0 -0.405 1 1
NBN 0.031 0.008 -9999 0 -9999 0 0
EGFR -0.014 0.144 -9999 0 -0.517 10 10
mol:Oestrogen 0 0.002 -9999 0 -9999 0 0
EGF/EGFR -0.038 0.16 -9999 0 -0.42 18 18
MYC 0.017 0.081 -9999 0 -0.518 3 3
IL2 0.029 0.018 -9999 0 -9999 0 0
KU 0.046 0.012 -9999 0 -9999 0 0
RAD50 0.031 0.008 -9999 0 -9999 0 0
HSP90AA1 0 0 -9999 0 -9999 0 0
TGFB1 0.031 0.008 -9999 0 -9999 0 0
TRF2/BLM 0.038 0.051 -9999 0 -0.357 2 2
FRAP1 0.032 0.005 -9999 0 -9999 0 0
KU/TERT -0.022 0.203 -9999 0 -0.822 4 4
SP1/HDAC2 0.042 0.046 -9999 0 -0.393 1 1
PINX1 0.028 0.012 -9999 0 -9999 0 0
Telomerase/EST1A -0.032 0.178 -9999 0 -0.672 5 5
Smad3/Myc 0.014 0.074 -9999 0 -0.325 6 6
911 complex 0.047 0.045 -9999 0 -0.324 1 1
IFNG -0.095 0.216 -9999 0 -0.513 28 28
Telomerase/PinX1 -0.029 0.181 -9999 0 -0.669 5 5
Telomerase/AKT1/mTOR/p70S6K 0.01 0.078 -9999 0 -0.318 1 1
SIN3B 0.032 0.006 -9999 0 -9999 0 0
YWHAE 0.031 0.007 -9999 0 -9999 0 0
Telomerase/EST1B -0.032 0.178 -9999 0 -0.672 5 5
response to DNA damage stimulus 0.004 0.018 -9999 0 -0.132 1 1
MRN complex/TRF2/Rap1 0.08 0.036 -9999 0 -9999 0 0
TRF2/WRN 0.041 0.024 -9999 0 -9999 0 0
Telomerase/hnRNP C1/C2 -0.032 0.178 -9999 0 -0.672 5 5
E2F1 0.03 0.014 -9999 0 -9999 0 0
ZNFX1 0 0.001 -9999 0 -9999 0 0
PIF1 0 0 -9999 0 -9999 0 0
NCL 0.032 0.005 -9999 0 -9999 0 0
DKC1 0.032 0.01 -9999 0 -9999 0 0
telomeric DNA binding 0 0 -9999 0 -9999 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.03 0.015 -9999 0 -9999 0 0
oxygen homeostasis 0 0 -9999 0 -9999 0 0
TCEB2 0.032 0.005 -9999 0 -9999 0 0
TCEB1 0.032 0.006 -9999 0 -9999 0 0
HIF1A/p53 0.006 0.087 -9999 0 -0.362 4 4
HIF1A 0.002 0.059 -9999 0 -0.301 2 2
COPS5 0.032 0.006 -9999 0 -9999 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.074 0.061 -9999 0 -0.283 2 2
FIH (dimer) 0.032 0.006 -9999 0 -9999 0 0
CDKN2A -0.048 0.163 -9999 0 -0.518 14 14
ARNT/IPAS 0.042 0.019 -9999 0 -9999 0 0
HIF1AN 0.032 0.006 -9999 0 -9999 0 0
GNB2L1 0.03 0.009 -9999 0 -9999 0 0
HIF1A/ARNT 0.016 0.065 -9999 0 -0.313 2 2
CUL2 0.031 0.012 -9999 0 -9999 0 0
OS9 0.032 0.01 -9999 0 -9999 0 0
RACK1/Elongin B/Elongin C 0.059 0.022 -9999 0 -9999 0 0
response to hypoxia 0 0 -9999 0 -9999 0 0
HIF1A/Hsp90 -0.003 0.065 -9999 0 -0.301 3 3
PHD1-3/OS9 0.001 0.132 -9999 0 -0.312 17 17
HIF1A/RACK1/Elongin B/Elongin C 0.038 0.077 -9999 0 -0.289 2 2
VHL 0.02 0.068 -9999 0 -0.518 2 2
HSP90AA1 0 0 -9999 0 -9999 0 0
HIF1A/JAB1 0.016 0.072 -9999 0 -0.304 3 3
EGLN3 -0.053 0.18 -9999 0 -0.518 17 17
EGLN2 0.025 0.048 -9999 0 -0.518 1 1
EGLN1 0.023 0.068 -9999 0 -0.518 2 2
TP53 0.014 0.084 -9999 0 -0.518 3 3
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A -0.005 0.166 -9999 0 -0.513 12 12
ARNT 0.031 0.009 -9999 0 -9999 0 0
ARD1A 0.033 0 -9999 0 -9999 0 0
RBX1 0.031 0.012 -9999 0 -9999 0 0
HIF1A/p19ARF -0.03 0.101 -9999 0 -0.314 6 6
LPA4-mediated signaling events

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
ADCY4 -0.011 0.038 -9999 0 -0.322 2 2
ADCY5 -0.007 0.009 -9999 0 -9999 0 0
ADCY6 -0.007 0.002 -9999 0 -9999 0 0
ADCY7 -0.009 0.027 -9999 0 -0.322 1 1
ADCY1 -0.006 0.002 -9999 0 -9999 0 0
ADCY2 -0.013 0.039 -9999 0 -0.322 2 2
ADCY3 -0.012 0.038 -9999 0 -0.322 2 2
ADCY8 -0.015 0.031 -9999 0 -0.322 1 1
PRKCE 0.008 0.003 -9999 0 -9999 0 0
ADCY9 -0.009 0.027 -9999 0 -0.322 1 1
mol:DAG 0 0 -9999 0 -9999 0 0
cAMP biosynthetic process 0.041 0.096 0.266 11 -0.305 1 12
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.023 0.067 -9999 0 -0.518 2 2
SMAD2 0.012 0.055 -9999 0 -0.247 2 2
SMAD3 0.018 0.059 -9999 0 -9999 0 0
SMAD3/SMAD4 0.031 0.076 -9999 0 -0.376 3 3
SMAD4/Ubc9/PIASy 0.054 0.052 -9999 0 -0.324 2 2
SMAD2/SMAD2/SMAD4 0.06 0.078 -9999 0 -0.252 3 3
PPM1A 0.032 0.005 -9999 0 -9999 0 0
CALM1 0.032 0.006 -9999 0 -9999 0 0
SMAD2/SMAD4 0.023 0.069 -9999 0 -0.253 4 4
MAP3K1 0.013 0.093 -9999 0 -0.518 4 4
TRAP-1/SMAD4 0.035 0.065 -9999 0 -0.378 3 3
MAPK3 0.032 0.005 -9999 0 -9999 0 0
MAPK1 0.03 0.01 -9999 0 -9999 0 0
NUP214 0.033 0.004 -9999 0 -9999 0 0
CTDSP1 0.032 0.006 -9999 0 -9999 0 0
CTDSP2 0.033 0.003 -9999 0 -9999 0 0
CTDSPL 0.024 0.048 -9999 0 -0.518 1 1
KPNB1 0.029 0.047 -9999 0 -0.518 1 1
TGFBRAP1 0.029 0.047 -9999 0 -0.518 1 1
UBE2I 0.032 0.005 -9999 0 -9999 0 0
NUP153 0.032 0.006 -9999 0 -9999 0 0
KPNA2 0.024 0.066 -9999 0 -0.518 2 2
PIAS4 0.033 0.004 -9999 0 -9999 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.04 0.025 -9999 0 -9999 0 0
KIRREL 0.034 0.014 -9999 0 -9999 0 0
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.04 0.025 -9999 0 -9999 0 0
PLCG1 0.031 0.008 -9999 0 -9999 0 0
ARRB2 0.031 0.007 -9999 0 -9999 0 0
WASL 0.016 0.093 -9999 0 -0.518 4 4
Nephrin/NEPH1/podocin/CD2AP 0.064 0.039 -9999 0 -9999 0 0
ChemicalAbstracts:57-88-5 0 0 -9999 0 -9999 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.008 0.08 -9999 0 -0.35 5 5
FYN 0.035 0.064 0.278 3 -0.223 2 5
mol:Ca2+ 0.06 0.039 -9999 0 -9999 0 0
mol:DAG 0.061 0.039 -9999 0 -9999 0 0
NPHS2 0.035 0.015 -9999 0 -9999 0 0
mol:IP3 0.061 0.039 -9999 0 -9999 0 0
regulation of endocytosis 0.051 0.046 -9999 0 -0.211 2 2
Nephrin/NEPH1/podocin/Cholesterol 0.048 0.03 -9999 0 -9999 0 0
establishment of cell polarity 0.04 0.025 -9999 0 -9999 0 0
Nephrin/NEPH1/podocin/NCK1-2 0.06 0.065 -9999 0 -0.296 2 2
Nephrin/NEPH1/beta Arrestin2 0.054 0.047 -9999 0 -0.213 2 2
NPHS1 0.03 0.02 -9999 0 -9999 0 0
Nephrin/NEPH1/podocin 0.049 0.044 -9999 0 -0.222 2 2
TJP1 0.028 0.047 -9999 0 -0.518 1 1
NCK1 0.019 0.067 -9999 0 -0.518 2 2
NCK2 0.033 0.003 -9999 0 -9999 0 0
heterophilic cell adhesion 0 0 -9999 0 -9999 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.063 0.04 -9999 0 -9999 0 0
CD2AP 0.032 0.006 -9999 0 -9999 0 0
Nephrin/NEPH1/podocin/GRB2 0.064 0.039 -9999 0 -9999 0 0
GRB2 0.032 0.006 -9999 0 -9999 0 0
homophilic cell adhesion 0 0 -9999 0 -9999 0 0
TRPC6 0.019 0.081 0.289 3 -0.293 4 7
cytoskeleton organization 0.007 0.082 0.254 4 -0.466 2 6
Nephrin/NEPH1 0.034 0.02 -9999 0 -9999 0 0
Nephrin/NEPH1/ZO-1 0.049 0.048 -9999 0 -0.346 1 1
BARD1 signaling events

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
BARD1/CSTF1 0.047 0.009 -9999 0 -9999 0 0
ATM 0.029 0.047 -9999 0 -0.518 1 1
UBE2D3 0.031 0.008 -9999 0 -9999 0 0
PRKDC 0.027 0.048 -9999 0 -0.518 1 1
ATR 0.024 0.015 -9999 0 -9999 0 0
UBE2L3 0.03 0.01 -9999 0 -9999 0 0
FANCD2 0.016 0.032 -9999 0 -0.321 1 1
protein ubiquitination 0.066 0.063 -9999 0 -0.28 3 3
XRCC5 0.032 0.006 -9999 0 -9999 0 0
XRCC6 0.032 0.006 -9999 0 -9999 0 0
M/R/N Complex 0.059 0.022 -9999 0 -9999 0 0
MRE11A 0.033 0.004 -9999 0 -9999 0 0
DNA-PK 0.056 0.039 -9999 0 -0.324 1 1
FA complex/FANCD2/Ubiquitin 0.018 0.107 -9999 0 -0.391 6 6
FANCF 0.016 0.093 -9999 0 -0.518 4 4
BRCA1 0.028 0.047 -9999 0 -0.518 1 1
CCNE1 0.023 0.05 -9999 0 -0.518 1 1
CDK2/Cyclin E1 0.039 0.042 -9999 0 -0.378 1 1
FANCG 0.03 0.01 -9999 0 -9999 0 0
BRCA1/BACH1/BARD1 0.044 0.038 -9999 0 -0.378 1 1
FANCE 0.011 0.104 -9999 0 -0.518 5 5
FANCC 0.033 0.003 -9999 0 -9999 0 0
NBN 0.031 0.008 -9999 0 -9999 0 0
FANCA 0.025 0.05 -9999 0 -0.518 1 1
DNA repair 0.024 0.09 -9999 0 -0.336 2 2
BRCA1/BARD1/ubiquitin 0.044 0.038 -9999 0 -0.378 1 1
BARD1/DNA-PK 0.072 0.042 -9999 0 -0.298 1 1
FANCL 0.03 0.01 -9999 0 -9999 0 0
mRNA polyadenylation -0.047 0.009 -9999 0 -9999 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.029 0.048 -9999 0 -0.386 1 1
BRCA1/BACH1/BARD1/TopBP1 0.049 0.043 -9999 0 -0.324 1 1
BRCA1/BARD1/P53 0.042 0.069 -9999 0 -0.288 3 3
BARD1/CSTF1/BRCA1 0.061 0.036 -9999 0 -0.324 1 1
BRCA1/BACH1 0.028 0.047 -9999 0 -0.517 1 1
BARD1 0.032 0.006 -9999 0 -9999 0 0
PCNA 0.031 0.008 -9999 0 -9999 0 0
BRCA1/BARD1/UbcH5C 0.058 0.038 -9999 0 -0.324 1 1
BRCA1/BARD1/UbcH7 0.055 0.04 -9999 0 -0.324 1 1
BRCA1/BARD1/RAD51/PCNA 0.069 0.046 -9999 0 -0.298 1 1
BARD1/DNA-PK/P53 0.068 0.07 -9999 0 -0.274 3 3
BRCA1/BARD1/Ubiquitin 0.044 0.038 -9999 0 -0.378 1 1
BRCA1/BARD1/CTIP 0.043 0.047 -9999 0 -0.297 2 2
FA complex 0.027 0.076 -9999 0 -0.234 6 6
BARD1/EWS 0.045 0.014 -9999 0 -9999 0 0
RBBP8 0.012 0.034 -9999 0 -0.378 1 1
TP53 0.014 0.084 -9999 0 -0.518 3 3
TOPBP1 0.027 0.013 -9999 0 -9999 0 0
G1/S transition of mitotic cell cycle -0.04 0.067 0.286 3 -9999 0 3
BRCA1/BARD1 0.073 0.066 -9999 0 -0.283 3 3
CSTF1 0.033 0.003 -9999 0 -9999 0 0
BARD1/EWS-Fli1 0.024 0.004 -9999 0 -9999 0 0
CDK2 0.033 0 -9999 0 -9999 0 0
UniProt:Q9BZD1 0 0 -9999 0 -9999 0 0
RAD51 0.031 0.012 -9999 0 -9999 0 0
RAD50 0.031 0.008 -9999 0 -9999 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.044 0.038 -9999 0 -0.378 1 1
EWSR1 0.031 0.008 -9999 0 -9999 0 0
Circadian rhythm pathway

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
chromatin modification 0.028 0.12 -9999 0 -1.192 1 1
CLOCK 0.031 0.014 -9999 0 -9999 0 0
TIMELESS/CRY2 0.035 0.117 -9999 0 -1.287 1 1
DEC1/BMAL1 0.041 0.053 -9999 0 -0.376 2 2
ATR 0.024 0.015 -9999 0 -9999 0 0
NR1D1 0.017 0.046 -9999 0 -9999 0 0
ARNTL 0.026 0.067 -9999 0 -0.514 2 2
TIMELESS 0.013 0.121 -9999 0 -1.37 1 1
NPAS2 0.012 0.105 -9999 0 -0.514 5 5
CRY2 0.032 0.006 -9999 0 -9999 0 0
mol:CO -0.01 0.013 0.138 1 -9999 0 1
CHEK1 0.02 0.081 -9999 0 -0.518 3 3
mol:HEME 0.01 0.013 -9999 0 -0.138 1 1
PER1 0.031 0.007 -9999 0 -9999 0 0
BMAL/CLOCK/NPAS2 0.048 0.087 -9999 0 -0.314 6 6
BMAL1/CLOCK 0.027 0.09 -9999 0 -0.552 1 1
S phase of mitotic cell cycle 0.028 0.12 -9999 0 -1.192 1 1
TIMELESS/CHEK1/ATR 0.028 0.124 -9999 0 -1.243 1 1
mol:NADPH 0.01 0.013 -9999 0 -0.138 1 1
PER1/TIMELESS 0.035 0.117 -9999 0 -1.287 1 1
PER1-2 / CRY1-2 0 0 -9999 0 -9999 0 0
DEC1 0.031 0.011 -9999 0 -9999 0 0
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0.032 0.038 -9999 0 -0.32 1 1
EFNA5 0.03 0.009 -9999 0 -9999 0 0
FYN 0.007 0.05 0.188 1 -0.295 3 4
neuron projection morphogenesis 0.032 0.038 -9999 0 -0.32 1 1
cell-cell signaling 0 0 -9999 0 -9999 0 0
Ephrin A5/EPHA5 0.032 0.038 -9999 0 -0.321 1 1
EPHA5 0.022 0.053 -9999 0 -0.518 1 1
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.055 0.095 -9999 0 -0.24 3 3
CaM/Ca2+ 0.024 0.004 -9999 0 -9999 0 0
AKT1 0.032 0.007 -9999 0 -9999 0 0
AKT2 0.029 0.011 -9999 0 -9999 0 0
STXBP4 0.033 0.003 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
mol:glucose 0.042 0.095 0.177 4 -0.22 9 13
YWHAZ 0.031 0.008 -9999 0 -9999 0 0
CALM1 0.032 0.006 -9999 0 -9999 0 0
YWHAQ 0.032 0.006 -9999 0 -9999 0 0
TBC1D4 0.012 0.034 -9999 0 -0.379 1 1
mol:Ca2+ 0 0 -9999 0 -9999 0 0
YWHAH 0.031 0.008 -9999 0 -9999 0 0
YWHAB 0.032 0.006 -9999 0 -9999 0 0
SNARE/Synip 0.041 0.013 -9999 0 -9999 0 0
YWHAG 0.033 0.004 -9999 0 -9999 0 0
ASIP 0 0 -9999 0 -9999 0 0
PRKCI -0.009 0.11 -9999 0 -0.518 6 6
AS160/CaM/Ca2+ 0.024 0.004 -9999 0 -9999 0 0
RHOQ 0.018 0.081 -9999 0 -0.518 3 3
GYS1 0.009 0.017 -9999 0 -9999 0 0
PRKCZ 0 0 -9999 0 -9999 0 0
TRIP10 0.03 0.018 -9999 0 -9999 0 0
TC10/GTP/CIP4/Exocyst 0.03 0.056 -9999 0 -0.321 3 3
AS160/14-3-3 0.004 0.082 -9999 0 -0.393 2 2
VAMP2 0.03 0.012 -9999 0 -9999 0 0
SLC2A4 0.042 0.1 0.185 3 -0.239 9 12
STX4 0 0 -9999 0 -9999 0 0
GSK3B 0.017 0.023 -9999 0 -0.201 1 1
SFN -0.025 0.167 -9999 0 -0.518 14 14
LNPEP 0.029 0.014 -9999 0 -9999 0 0
YWHAE 0.031 0.007 -9999 0 -9999 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.014 0.006 -9999 0 -9999 0 0
BAD/BCL-XL/YWHAZ 0.046 0.022 -9999 0 -9999 0 0
CDKN1B 0.025 0.089 0.272 1 -0.54 2 3
CDKN1A 0.015 0.085 -9999 0 -0.54 2 2
FRAP1 0.032 0.005 -9999 0 -9999 0 0
PRKDC 0.027 0.048 -9999 0 -0.518 1 1
FOXO3 0.019 0.078 -9999 0 -0.445 3 3
AKT1 0.021 0.082 -9999 0 -0.468 3 3
BAD 0.033 0 -9999 0 -9999 0 0
AKT3 0.007 0.052 -9999 0 -0.328 3 3
mol:GTP 0 0 -9999 0 -9999 0 0
FOXO4 0.019 0.078 -9999 0 -0.445 3 3
AKT1/ASK1 0.044 0.084 -9999 0 -0.525 2 2
BAD/YWHAZ 0.061 0.019 -9999 0 -9999 0 0
RICTOR 0.026 0.013 -9999 0 -9999 0 0
RAF1 0.031 0.008 -9999 0 -9999 0 0
JNK cascade -0.043 0.081 0.506 2 -9999 0 2
TSC1 0.015 0.081 -9999 0 -0.54 2 2
YWHAZ 0.031 0.008 -9999 0 -9999 0 0
AKT1/RAF1 0.044 0.086 -9999 0 -0.534 2 2
EP300 -0.001 0.129 -9999 0 -0.518 8 8
mol:GDP 0.021 0.081 -9999 0 -0.46 3 3
mol:PI-3-4-5-P3 0 0 -9999 0 -9999 0 0
TSC2 0.02 0.055 -9999 0 -0.425 1 1
YWHAQ 0.032 0.006 -9999 0 -9999 0 0
TBC1D4 0.003 0.037 -9999 0 -0.295 2 2
MAP3K5 0.032 0.011 -9999 0 -9999 0 0
MAPKAP1 0.033 0.004 -9999 0 -9999 0 0
negative regulation of cell cycle -0.019 0.091 0.513 2 -9999 0 2
YWHAH 0.031 0.008 -9999 0 -9999 0 0
AKT1S1 0.017 0.085 0.272 1 -0.54 2 3
CASP9 0.019 0.074 -9999 0 -0.54 2 2
YWHAB 0.032 0.006 -9999 0 -9999 0 0
p27Kip1/KPNA1 0.04 0.09 0.272 1 -0.515 2 3
GBL 0.032 0.005 -9999 0 -9999 0 0
PDK1/Src/Hsp90 0.037 0.034 -9999 0 -0.321 1 1
YWHAE 0.031 0.007 -9999 0 -9999 0 0
SRC 0.03 0.013 -9999 0 -9999 0 0
AKT2/p21CIP1 0.013 0.082 -9999 0 -0.512 2 2
KIAA1303 0 0 -9999 0 -9999 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.035 0.088 -9999 0 -0.6 2 2
CHUK 0.02 0.057 -9999 0 -0.425 1 1
BAD/BCL-XL 0.041 0.083 -9999 0 -0.515 2 2
mTORC2 0.065 0.036 -9999 0 -9999 0 0
AKT2 0.013 0.03 -9999 0 -0.328 1 1
FOXO1-3a-4/14-3-3 family 0.029 0.118 -9999 0 -0.683 2 2
PDPK1 0.028 0.047 -9999 0 -0.518 1 1
MDM2 0.019 0.083 -9999 0 -0.502 2 2
MAPKKK cascade -0.044 0.084 0.521 2 -9999 0 2
MDM2/Cbp/p300 0.048 0.122 -9999 0 -0.539 3 3
TSC1/TSC2 0.01 0.08 -9999 0 -0.522 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.046 0.116 -9999 0 -0.511 3 3
glucose import -0.002 0.033 -9999 0 -0.27 2 2
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.035 0.09 -9999 0 -0.554 2 2
response to stress 0 0 -9999 0 -9999 0 0
SLC2A4 -0.002 0.033 -9999 0 -0.271 2 2
GSK3A 0.026 0.083 0.272 1 -0.54 2 3
FOXO1 0.019 0.078 -9999 0 -0.445 3 3
GSK3B 0.036 0.1 0.272 2 -0.54 2 4
SFN -0.025 0.167 -9999 0 -0.518 14 14
G1/S transition of mitotic cell cycle 0.055 0.113 0.289 9 -0.528 2 11
p27Kip1/14-3-3 family 0.02 0.083 -9999 0 -0.537 1 1
PRKACA 0.032 0.007 -9999 0 -9999 0 0
KPNA1 0.027 0.012 -9999 0 -9999 0 0
HSP90AA1 0 0 -9999 0 -9999 0 0
YWHAG 0.033 0.004 -9999 0 -9999 0 0
RHEB 0.032 0.005 -9999 0 -9999 0 0
CREBBP 0.032 0.006 -9999 0 -9999 0 0
Signaling events regulated by Ret tyrosine kinase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.006 0.081 -9999 0 -0.354 6 6
Crk/p130 Cas/Paxillin -0.024 0.069 -9999 0 -9999 0 0
JUN 0.007 0.076 -9999 0 -0.295 2 2
HRAS 0.027 0.048 -9999 0 -0.518 1 1
RET51/GFRalpha1/GDNF/GRB10 0.031 0.089 -9999 0 -0.298 6 6
RAP1A 0.023 0.066 -9999 0 -0.518 2 2
FRS2 0.031 0.008 -9999 0 -9999 0 0
RAP1A/GDP 0.017 0.048 -9999 0 -0.375 2 2
RET51/GFRalpha1/GDNF/DOK1 0.051 0.056 -9999 0 -0.298 1 1
EntrezGene:5979 0 0 -9999 0 -9999 0 0
PTPN11 0.029 0.047 -9999 0 -0.518 1 1
mol:GTP 0 0 -9999 0 -9999 0 0
CRK 0.031 0.007 -9999 0 -9999 0 0
RET9/GFRalpha1/GDNF/Enigma 0.045 0.041 -9999 0 -0.295 1 1
RHOA 0.03 0.01 -9999 0 -9999 0 0
RAP1A/GTP 0.037 0.076 -9999 0 -0.279 5 5
GRB7 0.031 0.007 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF 0.051 0.056 -9999 0 -0.298 1 1
MAPKKK cascade 0.021 0.05 -9999 0 -0.282 1 1
BCAR1 0.032 0.005 -9999 0 -9999 0 0
RET9/GFRalpha1/GDNF/IRS1 0.031 0.072 -9999 0 -0.292 5 5
lamellipodium assembly 0 0.082 -9999 0 -0.249 2 2
RET51/GFRalpha1/GDNF/SHC 0.049 0.056 -9999 0 -0.298 1 1
PIK3CA 0.011 0.048 -9999 0 -0.518 1 1
RET9/GFRalpha1/GDNF/SHC 0.042 0.042 -9999 0 -0.295 1 1
RET9/GFRalpha1/GDNF/Shank3 0.045 0.041 -9999 0 -0.295 1 1
MAPK3 0.013 0.099 0.344 2 -0.269 5 7
DOK1 0.032 0.006 -9999 0 -9999 0 0
DOK6 -0.029 0.144 -9999 0 -0.518 10 10
PXN 0.033 0.003 -9999 0 -9999 0 0
neurite development 0.008 0.094 0.324 3 -0.349 1 4
DOK5 0.006 0.114 -9999 0 -0.518 6 6
GFRA1 0.029 0.018 -9999 0 -9999 0 0
MAPK8 0.006 0.039 -9999 0 -0.277 1 1
HRAS/GTP 0.036 0.063 -9999 0 -0.278 2 2
tube development 0.044 0.047 -9999 0 -0.28 1 1
MAPK1 0.01 0.096 0.3 3 -0.269 5 8
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.019 0.034 -9999 0 -0.245 1 1
Rac1/GDP 0.024 0.004 -9999 0 -9999 0 0
SRC 0.03 0.013 -9999 0 -9999 0 0
PDLIM7 0.031 0.008 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF/Dok6 0.016 0.106 -9999 0 -0.315 8 8
SHC1 0.03 0.009 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF/Dok4 0.047 0.072 -9999 0 -0.318 3 3
RET51/GFRalpha1/GDNF/Dok5 0.041 0.084 -9999 0 -0.304 5 5
PRKCA 0.028 0.047 -9999 0 -0.518 1 1
HRAS/GDP 0.02 0.035 -9999 0 -0.375 1 1
CREB1 0.017 0.04 -9999 0 -9999 0 0
PIK3R1 0.004 0.097 -9999 0 -0.518 4 4
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.014 0.044 -9999 0 -0.261 2 2
RET51/GFRalpha1/GDNF/Grb7 0.051 0.056 -9999 0 -0.298 1 1
mol:GDP 0 0 -9999 0 -9999 0 0
RET 0.02 0.036 -9999 0 -9999 0 0
DOK4 0.024 0.066 -9999 0 -0.518 2 2
JNK cascade 0.007 0.075 -9999 0 -0.29 2 2
RET9/GFRalpha1/GDNF/FRS2 0.045 0.041 -9999 0 -0.295 1 1
SHANK3 0.031 0.008 -9999 0 -9999 0 0
RASA1 0.029 0.01 -9999 0 -9999 0 0
NCK1 0.019 0.067 -9999 0 -0.518 2 2
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.019 0.028 -9999 0 -0.242 1 1
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.02 0.034 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.016 0.04 -9999 0 -0.265 2 2
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.02 0.031 -9999 0 -0.239 1 1
PI3K 0.005 0.117 -9999 0 -0.348 3 3
SOS1 0.032 0.007 -9999 0 -9999 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.054 0.046 -9999 0 -0.28 1 1
GRB10 -0.004 0.13 -9999 0 -0.518 8 8
activation of MAPKK activity 0.034 0.047 -9999 0 -0.32 1 1
RET51/GFRalpha1/GDNF/FRS2 0.05 0.056 -9999 0 -0.298 1 1
GAB1 0.021 0.068 -9999 0 -0.518 2 2
IRS1 0.008 0.105 -9999 0 -0.518 5 5
IRS2 0.001 0.122 -9999 0 -0.518 7 7
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.014 0.047 -9999 0 -0.256 2 2
RET51/GFRalpha1/GDNF/PKC alpha 0.049 0.064 -9999 0 -0.298 2 2
GRB2 0.032 0.006 -9999 0 -9999 0 0
PRKACA 0.032 0.007 -9999 0 -9999 0 0
GDNF 0.023 0.048 -9999 0 -0.518 1 1
RAC1 0.032 0.005 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF/IRS1 0.037 0.084 -9999 0 -0.298 5 5
Rac1/GTP 0.01 0.102 -9999 0 -0.292 2 2
RET9/GFRalpha1/GDNF 0.031 0.037 -9999 0 -0.321 1 1
GFRalpha1/GDNF 0.034 0.042 -9999 0 -0.378 1 1
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.03 0.01 -9999 0 -9999 0 0
NFATC1 0.032 0.101 -9999 0 -0.461 2 2
NFATC2 0.01 0.073 0.172 1 -0.291 4 5
NFATC3 0.014 0.006 -9999 0 -9999 0 0
YWHAE 0.031 0.007 -9999 0 -9999 0 0
Calcineurin A alpha-beta B1/CABIN1 0.004 0.079 -9999 0 -0.341 2 2
Exportin 1/Ran/NUP214 0.059 0.023 -9999 0 -9999 0 0
mol:DAG 0 0 -9999 0 -9999 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.033 0.092 -9999 0 -0.334 1 1
BCL2/BAX 0.013 0.093 -9999 0 -0.378 6 6
CaM/Ca2+/Calcineurin A alpha-beta B1 0.025 0.004 -9999 0 -9999 0 0
CaM/Ca2+ 0.025 0.004 -9999 0 -9999 0 0
BAX 0.032 0.005 -9999 0 -9999 0 0
MAPK14 0.033 0.004 -9999 0 -9999 0 0
BAD 0.033 0 -9999 0 -9999 0 0
CABIN1/MEF2D 0.016 0.087 -9999 0 -0.313 3 3
Calcineurin A alpha-beta B1/BCL2 -0.007 0.116 -9999 0 -0.517 6 6
FKBP8 0.031 0.007 -9999 0 -9999 0 0
activation-induced cell death of T cells -0.016 0.086 0.309 3 -9999 0 3
KPNB1 0.029 0.047 -9999 0 -0.518 1 1
KPNA2 0.024 0.066 -9999 0 -0.518 2 2
XPO1 0.029 0.011 -9999 0 -9999 0 0
SFN -0.025 0.167 -9999 0 -0.518 14 14
MAP3K8 -0.01 0.144 -9999 0 -0.517 10 10
NFAT4/CK1 alpha 0.025 0.053 -9999 0 -0.266 4 4
MEF2D/NFAT1/Cbp/p300 0.043 0.104 -9999 0 -0.285 2 2
CABIN1 0.004 0.08 -9999 0 -0.344 2 2
CALM1 0.032 0.006 -9999 0 -9999 0 0
RAN 0.033 0.003 -9999 0 -9999 0 0
MAP3K1 0.013 0.093 -9999 0 -0.518 4 4
CAMK4 0.026 0.049 -9999 0 -0.518 1 1
mol:Ca2+ 0.001 0.001 -9999 0 -9999 0 0
MAPK3 0.032 0.005 -9999 0 -9999 0 0
YWHAH 0.031 0.008 -9999 0 -9999 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.04 0.041 -9999 0 -0.378 1 1
YWHAB 0.032 0.006 -9999 0 -9999 0 0
MAPK8 0.032 0.007 -9999 0 -9999 0 0
MAPK9 0.031 0.008 -9999 0 -9999 0 0
YWHAG 0.033 0.004 -9999 0 -9999 0 0
FKBP1A 0.032 0.007 -9999 0 -9999 0 0
NFAT1-c-4/YWHAQ 0.043 0.1 -9999 0 -0.454 1 1
PRKCH 0.028 0.047 -9999 0 -0.518 1 1
CABIN1/Cbp/p300 0.022 0.1 -9999 0 -0.377 8 8
CASP3 0.029 0.011 -9999 0 -9999 0 0
PIM1 0.031 0.011 -9999 0 -9999 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.022 0.005 -9999 0 -9999 0 0
apoptosis 0.014 0.029 -9999 0 -9999 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.011 0.084 -9999 0 -0.363 3 3
PRKCB 0 0 -9999 0 -9999 0 0
PRKCE 0.03 0.01 -9999 0 -9999 0 0
JNK2/NFAT4 0.031 0.022 -9999 0 -9999 0 0
BAD/BCL-XL 0.044 0.015 -9999 0 -9999 0 0
PRKCD 0.029 0.014 -9999 0 -9999 0 0
NUP214 0.033 0.004 -9999 0 -9999 0 0
PRKCZ 0 0 -9999 0 -9999 0 0
PRKCA 0.028 0.047 -9999 0 -0.518 1 1
PRKCG 0.032 0.006 -9999 0 -9999 0 0
PRKCQ 0.003 0.114 -9999 0 -0.518 6 6
FKBP38/BCL2 0.012 0.092 -9999 0 -0.378 6 6
EP300 0 0.129 -9999 0 -0.517 8 8
PRKCB1 0.001 0.122 -9999 0 -0.518 7 7
CSNK2A1 0.031 0.008 -9999 0 -9999 0 0
NFATc/JNK1 0.047 0.101 -9999 0 -0.436 2 2
CaM/Ca2+/FKBP38 0.042 0.012 -9999 0 -9999 0 0
FKBP12/FK506 0.023 0.005 -9999 0 -9999 0 0
CSNK1A1 0.017 0.005 -9999 0 -9999 0 0
CaM/Ca2+/CAMK IV 0.038 0.034 -9999 0 -0.321 1 1
NFATc/ERK1 0.047 0.102 -9999 0 -0.437 2 2
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.033 0.091 -9999 0 -0.335 1 1
NR4A1 0.02 0.091 -9999 0 -9999 0 0
GSK3B 0.027 0.016 -9999 0 -9999 0 0
positive T cell selection 0.014 0.006 -9999 0 -9999 0 0
NFAT1/CK1 alpha 0.014 0.056 -9999 0 -0.245 3 3
RCH1/ KPNB1 0.04 0.054 -9999 0 -0.378 2 2
YWHAQ 0.032 0.006 -9999 0 -9999 0 0
PRKACA 0.032 0.007 -9999 0 -9999 0 0
AKAP5 0.025 0.05 -9999 0 -0.518 1 1
MEF2D 0.032 0.007 -9999 0 -9999 0 0
mol:FK506 0 0 -9999 0 -9999 0 0
YWHAZ 0.031 0.008 -9999 0 -9999 0 0
NFATc/p38 alpha 0.05 0.1 -9999 0 -0.437 2 2
CREBBP 0.032 0.006 -9999 0 -9999 0 0
BCL2 -0.007 0.116 -9999 0 -0.518 6 6
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.045 0.075 -9999 0 -0.332 1 1
Ran/GTP/Exportin 1/HDAC1 -0.009 0.004 -9999 0 -9999 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.031 0.088 -9999 0 -0.355 3 3
SUMO1 0.032 0.006 -9999 0 -9999 0 0
ZFPM1 0.023 0.067 -9999 0 -0.518 2 2
NPC/RanGAP1/SUMO1/Ubc9 0.017 0.005 -9999 0 -9999 0 0
FKBP3 0.032 0.007 -9999 0 -9999 0 0
Histones 0.071 0.065 -9999 0 -9999 0 0
YY1/LSF 0.016 0.091 -9999 0 -0.28 10 10
SMG5 0 0 -9999 0 -9999 0 0
RAN 0.033 0.003 -9999 0 -9999 0 0
I kappa B alpha/HDAC3 0.02 0.053 -9999 0 -0.373 2 2
I kappa B alpha/HDAC1 0.035 0.069 -9999 0 -0.522 1 1
SAP18 0.032 0.007 -9999 0 -9999 0 0
RELA 0.02 0.072 -9999 0 -0.214 9 9
HDAC1/Smad7 0.048 0.062 -9999 0 -0.324 3 3
RANGAP1 0.032 0.006 -9999 0 -9999 0 0
HDAC3/TR2 0.038 0.058 -9999 0 -9999 0 0
NuRD/MBD3 Complex 0.041 0.033 -9999 0 -9999 0 0
NF kappa B1 p50/RelA 0.027 0.084 -9999 0 -0.348 1 1
EntrezGene:23225 0 0 -9999 0 -9999 0 0
GATA2 0.024 0.048 -9999 0 -0.518 1 1
GATA1 0.033 0 -9999 0 -9999 0 0
Mad/Max 0.04 0.041 -9999 0 -0.378 1 1
NuRD/MBD3 Complex/GATA1/Fog1 0.041 0.052 -9999 0 -9999 0 0
RBBP7 0.03 0.017 -9999 0 -9999 0 0
NPC 0.019 0.002 -9999 0 -9999 0 0
RBBP4 0.028 0.047 -9999 0 -0.518 1 1
MAX 0.032 0.006 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 0 0
FBXW11 0.031 0.008 -9999 0 -9999 0 0
NFKBIA 0.017 0.055 -9999 0 -0.563 1 1
KAT2B 0 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
SIN3/HDAC complex 0.02 0.058 -9999 0 -0.354 2 2
SIN3 complex 0.073 0.03 -9999 0 -9999 0 0
SMURF1 0.023 0.066 -9999 0 -0.518 2 2
CHD3 0.03 0.012 -9999 0 -9999 0 0
SAP30 0.03 0.01 -9999 0 -9999 0 0
EntrezGene:23636 0 0 -9999 0 -9999 0 0
NCOR1 0.032 0.006 -9999 0 -9999 0 0
YY1/HDAC3 0.01 0.086 -9999 0 -0.407 3 3
YY1/HDAC2 0.017 0.091 -9999 0 -0.28 10 10
YY1/HDAC1 0.016 0.091 -9999 0 -0.283 10 10
NuRD/MBD2 Complex (MeCP1) 0.036 0.037 -9999 0 -9999 0 0
PPARG -0.002 0.113 -9999 0 -0.32 12 12
HDAC8/hEST1B 0.043 0.009 -9999 0 -9999 0 0
UBE2I 0.032 0.005 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.031 0.008 -9999 0 -9999 0 0
TNFRSF1A 0.026 0.048 -9999 0 -0.518 1 1
HDAC3/SMRT (N-CoR2) 0.033 0.069 -9999 0 -0.275 2 2
MBD3L2 0.015 0.093 -9999 0 -0.518 4 4
ubiquitin-dependent protein catabolic process 0.047 0.061 -9999 0 -0.323 3 3
CREBBP 0.032 0.006 -9999 0 -9999 0 0
NuRD/MBD3/MBD3L2 Complex 0.036 0.064 -9999 0 -0.288 1 1
HDAC1 0.031 0.011 -9999 0 -9999 0 0
HDAC3 0.021 0.024 -9999 0 -9999 0 0
HDAC2 0.032 0.011 -9999 0 -9999 0 0
YY1 -0.003 0.086 -9999 0 -0.324 8 8
HDAC8 0.033 0 -9999 0 -9999 0 0
SMAD7 0.026 0.049 -9999 0 -0.518 1 1
NCOR2 0.025 0.066 -9999 0 -0.518 2 2
MXD1 0.025 0.05 -9999 0 -0.518 1 1
STAT3 0.004 0.082 -9999 0 -0.321 8 8
NFKB1 0.031 0.008 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.033 0.004 -9999 0 -9999 0 0
YY1/LSF/HDAC1 0.034 0.091 -9999 0 -0.263 10 10
YY1/SAP30/HDAC1 0.029 0.089 -9999 0 -0.261 10 10
EP300 -0.001 0.129 -9999 0 -0.518 8 8
STAT3 (dimer non-phopshorylated) 0.004 0.081 -9999 0 -0.321 8 8
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.054 -9999 0 -0.56 1 1
histone deacetylation 0.036 0.037 -9999 0 -9999 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.022 0.075 -9999 0 -9999 0 0
nuclear export -0.042 0.009 -9999 0 -9999 0 0
PRKACA 0.032 0.007 -9999 0 -9999 0 0
GATAD2B 0.031 0.008 -9999 0 -9999 0 0
GATAD2A 0.031 0.007 -9999 0 -9999 0 0
GATA2/HDAC3 0.028 0.066 -9999 0 -0.436 1 1
GATA1/HDAC1 0.047 0.012 -9999 0 -9999 0 0
GATA1/HDAC3 0.038 0.058 -9999 0 -9999 0 0
CHD4 0.03 0.009 -9999 0 -9999 0 0
TNF-alpha/TNFR1A 0.037 0.045 -9999 0 -0.378 1 1
SIN3/HDAC complex/Mad/Max 0.02 0.072 -9999 0 -0.319 4 4
NuRD Complex 0.041 0.048 -9999 0 -9999 0 0
positive regulation of chromatin silencing 0.067 0.063 -9999 0 -9999 0 0
SIN3B 0.032 0.006 -9999 0 -9999 0 0
MTA2 0.033 0 -9999 0 -9999 0 0
SIN3A 0.033 0.004 -9999 0 -9999 0 0
XPO1 0.029 0.011 -9999 0 -9999 0 0
SUMO1/HDAC1 0.049 0.031 -9999 0 -9999 0 0
HDAC complex 0.076 0.041 -9999 0 -0.298 1 1
GATA1/Fog1 0.041 0.053 -9999 0 -0.378 2 2
FKBP25/HDAC1/HDAC2 0.06 0.026 -9999 0 -9999 0 0
TNF 0.025 0.051 -9999 0 -0.518 1 1
negative regulation of cell growth 0.02 0.071 -9999 0 -0.317 4 4
NuRD/MBD2/PRMT5 Complex 0.036 0.037 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0.048 0.034 -9999 0 -9999 0 0
NF kappa B/RelA/I kappa B alpha 0.009 0.072 -9999 0 -0.371 3 3
SIN3/HDAC complex/NCoR1 0.016 0.07 -9999 0 -0.41 2 2
TFCP2 0.033 0 -9999 0 -9999 0 0
NR2C1 0.033 0 -9999 0 -9999 0 0
MBD3 0.033 0.004 -9999 0 -9999 0 0
MBD2 0.031 0.008 -9999 0 -9999 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.042 0.012 -9999 0 -9999 0 0
response to insulin stimulus 0 0 -9999 0 -9999 0 0
RIPK1 0.032 0.005 -9999 0 -9999 0 0
response to stress 0 0 -9999 0 -9999 0 0
MAP2K6 0.011 0.104 -9999 0 -0.518 5 5
mol:GTP 0 0 -9999 0 -9999 0 0
MAP2K4 0.031 0.008 -9999 0 -9999 0 0
RAC1-CDC42/GTP/PAK family 0.007 0.024 -9999 0 -0.206 1 1
response to UV 0 0 -9999 0 -9999 0 0
YES1 0.031 0.008 -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 0.031 0.011 -9999 0 -9999 0 0
FYN 0.023 0.067 -9999 0 -0.518 2 2
MAP3K12 0.033 0 -9999 0 -9999 0 0
FGR 0.032 0.006 -9999 0 -9999 0 0
p38 alpha/TAB1 0.02 0.124 -9999 0 -0.456 5 5
PRKG1 0.029 0.019 -9999 0 -9999 0 0
DUSP8 0.021 0.068 -9999 0 -0.518 2 2
PGK/cGMP/p38 alpha 0.013 0.119 -9999 0 -0.407 6 6
apoptosis 0.019 0.118 -9999 0 -0.433 5 5
RAL/GTP 0.026 0.076 -9999 0 -0.321 6 6
LYN 0.028 0.047 -9999 0 -0.518 1 1
DUSP1 0.016 0.071 -9999 0 -0.518 2 2
PAK1 0.03 0.018 -9999 0 -9999 0 0
SRC 0.03 0.013 -9999 0 -9999 0 0
RAC1/OSM/MEKK3/MKK3 0.075 0.031 -9999 0 -9999 0 0
TRAF6 0.028 0.047 -9999 0 -0.518 1 1
RAC1 0.032 0.005 -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 0.032 0.005 -9999 0 -9999 0 0
RAC1-CDC42/GTP 0.043 0.009 -9999 0 -9999 0 0
MAPK11 0.009 0.131 -9999 0 -0.418 6 6
BLK 0.01 0.073 -9999 0 -0.518 2 2
HCK 0.006 0.113 -9999 0 -0.518 6 6
MAP2K3 0.031 0.008 -9999 0 -9999 0 0
DUSP16 0.025 0.049 -9999 0 -0.518 1 1
DUSP10 0.013 0.095 -9999 0 -0.518 4 4
TRAF6/MEKK3 0.038 0.03 -9999 0 -0.292 1 1
MAP3K7IP1 0.031 0.009 -9999 0 -9999 0 0
MAPK14 0.007 0.13 -9999 0 -0.454 6 6
positive regulation of innate immune response 0.01 0.148 -9999 0 -0.465 7 7
LCK -0.007 0.137 -9999 0 -0.518 9 9
p38alpha-beta/MKP7 0.019 0.145 -9999 0 -0.486 5 5
p38alpha-beta/MKP5 0.016 0.153 -9999 0 -0.465 6 6
PGK/cGMP 0.022 0.012 -9999 0 -9999 0 0
PAK2 0.013 0.049 -9999 0 -0.518 1 1
p38alpha-beta/MKP1 0.015 0.147 -9999 0 -0.494 5 5
CDC42 0.032 0.005 -9999 0 -9999 0 0
RALB 0.011 0.104 -9999 0 -0.518 5 5
RALA 0.028 0.047 -9999 0 -0.518 1 1
PAK3 0.025 0.03 -9999 0 -9999 0 0
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 0.03 0.012 -9999 0 -9999 0 0
CLTC 0.03 0.059 -9999 0 -0.391 2 2
calcium ion-dependent exocytosis 0.003 0.038 -9999 0 -0.199 2 2
Dynamin 2/GTP 0.029 0.015 -9999 0 -9999 0 0
EXOC4 0.033 0.004 -9999 0 -9999 0 0
CD59 0.001 0.042 -9999 0 -0.337 1 1
CPE -0.005 0.071 -9999 0 -0.322 6 6
CTNNB1 0.028 0.017 -9999 0 -9999 0 0
membrane fusion 0.002 0.039 -9999 0 -0.208 2 2
CTNND1 0.01 0.044 0.184 2 -0.295 2 4
DNM2 0.031 0.007 -9999 0 -9999 0 0
mol:PI-4-5-P2 0.029 0.053 -9999 0 -9999 0 0
TSHR 0.01 0.043 -9999 0 -0.322 2 2
INS 0.011 0.096 -9999 0 -0.468 5 5
BIN1 0.028 0.048 -9999 0 -0.518 1 1
mol:Choline 0.002 0.039 -9999 0 -0.208 2 2
growth hormone secretagogue receptor activity 0 0 -9999 0 -9999 0 0
mol:GDP 0.016 0.012 -9999 0 -9999 0 0
membrane depolarization 0 0 -9999 0 -9999 0 0
ARF6 0.031 0.012 -9999 0 -9999 0 0
mol:Ca2+ 0.029 0.015 -9999 0 -9999 0 0
JUP -0.004 0.049 -9999 0 -0.337 1 1
ASAP2/amphiphysin II 0.037 0.033 -9999 0 -0.292 1 1
ARF6/GTP 0.022 0.015 -9999 0 -0.122 1 1
CDH1 -0.005 0.052 -9999 0 -0.337 1 1
clathrin-independent pinocytosis 0.022 0.015 -9999 0 -0.122 1 1
MAPK8IP3 0.027 0.048 -9999 0 -0.518 1 1
positive regulation of endocytosis 0.022 0.015 -9999 0 -0.122 1 1
EXOC2 0.028 0.047 -9999 0 -0.518 1 1
substrate adhesion-dependent cell spreading 0.034 0.059 -9999 0 -9999 0 0
insulin receptor binding 0 0 -9999 0 -9999 0 0
SPAG9 0.033 0 -9999 0 -9999 0 0
regulation of calcium-dependent cell-cell adhesion -0.033 0.064 0.328 1 -9999 0 1
positive regulation of phagocytosis 0.015 0.012 -9999 0 -9999 0 0
ARF6/GTP/JIP3 0.038 0.036 -9999 0 -0.321 1 1
ACAP1 0.002 0.039 -9999 0 -0.212 2 2
mol:GTP 0 0 -9999 0 -9999 0 0
CHRM2 -0.024 0.09 -9999 0 -0.35 5 5
clathrin heavy chain/ACAP1 0.031 0.06 -9999 0 -0.303 2 2
JIP4/KLC1 0.04 0.015 -9999 0 -9999 0 0
EXOC1 0.026 0.048 -9999 0 -0.518 1 1
exocyst 0.034 0.059 -9999 0 -9999 0 0
RALA/GTP 0.021 0.034 -9999 0 -0.375 1 1
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.042 0.016 -9999 0 -9999 0 0
receptor recycling 0.022 0.015 -9999 0 -0.122 1 1
CTNNA1 0.013 0.023 0.184 2 -9999 0 2
NME1 0.016 0.012 -9999 0 -9999 0 0
clathrin coat assembly 0.032 0.059 -9999 0 -0.386 2 2
IL2RA -0.009 0.073 -9999 0 -0.677 1 1
VAMP3 0.015 0.012 -9999 0 -9999 0 0
GLUT4/clathrin heavy chain/ACAP1 0.043 0.059 -9999 0 -0.284 2 2
EXOC6 0.028 0.047 -9999 0 -0.518 1 1
PLD1 -0.002 0.05 -9999 0 -0.25 5 5
PLD2 0.011 0.039 -9999 0 -0.235 3 3
EXOC5 0.032 0.005 -9999 0 -9999 0 0
PIP5K1C 0.002 0.037 -9999 0 -9999 0 0
SDC1 -0.006 0.071 -9999 0 -0.406 3 3
ARF6/GDP 0.029 0.008 -9999 0 -9999 0 0
EXOC7 0.032 0.006 -9999 0 -9999 0 0
E-cadherin/beta catenin 0.036 0.066 -9999 0 -0.338 1 1
mol:Phosphatidic acid 0.002 0.039 -9999 0 -0.208 2 2
endocytosis -0.035 0.032 0.29 1 -9999 0 1
SCAMP2 0.033 0.004 -9999 0 -9999 0 0
ADRB2 -0.004 0.103 -9999 0 -0.464 3 3
EXOC3 0.026 0.013 -9999 0 -9999 0 0
ASAP2 0 0 -9999 0 -9999 0 0
Dynamin 2/GDP 0.034 0.016 -9999 0 -9999 0 0
KLC1 0 0 -9999 0 -9999 0 0
AVPR2 0.028 0.056 -9999 0 -0.371 2 2
RALA 0.028 0.047 -9999 0 -0.518 1 1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.025 0.07 -9999 0 -0.324 1 1
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.038 0.066 -9999 0 -0.277 5 5
MAPK9 0.008 0.002 -9999 0 -9999 0 0
adrenocorticotropin secretion 0.008 0.005 -9999 0 -9999 0 0
GNB1/GNG2 0.042 0.01 -9999 0 -9999 0 0
GNB1 0.032 0.006 -9999 0 -9999 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
MAPK14 0.009 0.001 -9999 0 -9999 0 0
Gs family/GTP 0.007 0.059 -9999 0 -0.289 5 5
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 0.004 0.014 0.077 5 -9999 0 5
GNAL 0.007 0.105 -9999 0 -0.518 5 5
GNG2 0.032 0.005 -9999 0 -9999 0 0
CRH 0.031 0.012 -9999 0 -9999 0 0
mol:cortisol 0 0 -9999 0 -9999 0 0
MAPK8 0.009 0.002 -9999 0 -9999 0 0
MAPK11 0.008 0.002 -9999 0 -9999 0 0
Signaling events mediated by PRL

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
CCNE1 0.023 0.05 -9999 0 -0.518 1 1
mol:Halofuginone 0.002 0.027 -9999 0 -0.216 2 2
ITGA1 0.021 0.068 -9999 0 -0.518 2 2
CDKN1A 0.005 0.101 -9999 0 -0.577 3 3
PRL-3/alpha Tubulin 0.021 0.013 -9999 0 -9999 0 0
mol:Ca2+ -0.023 0.017 -9999 0 -9999 0 0
AGT 0.027 0.026 -9999 0 -9999 0 0
CCNA2 -0.031 0.137 -9999 0 -0.786 3 3
TUBA1B 0 0 -9999 0 -9999 0 0
EGR1 -0.017 0.106 -9999 0 -0.37 11 11
CDK2/Cyclin E1 0.03 0.114 -9999 0 -0.442 5 5
MAPK3 0.013 0.012 -9999 0 -9999 0 0
PRL-2 /Rab GGTase beta 0.046 0.012 -9999 0 -9999 0 0
MAPK1 0.013 0.01 -9999 0 -9999 0 0
PTP4A1 -0.029 0.132 -9999 0 -0.953 2 2
PTP4A3 0.028 0.019 -9999 0 -9999 0 0
PTP4A2 0.032 0.005 -9999 0 -9999 0 0
ITGB1 0.007 0.049 -9999 0 -0.379 2 2
SRC 0.03 0.013 -9999 0 -9999 0 0
RAC1 0.012 0.062 -9999 0 -0.388 1 1
Rab GGTase beta/Rab GGTase alpha 0.045 0.013 -9999 0 -9999 0 0
PRL-1/ATF-5 -0.011 0.152 -9999 0 -0.777 3 3
RABGGTA 0.032 0.005 -9999 0 -9999 0 0
BCAR1 -0.02 0.015 -9999 0 -9999 0 0
RHOC 0.004 0.074 -9999 0 -0.311 4 4
RHOA -0.001 0.088 -9999 0 -0.337 6 6
cell motility 0.013 0.082 -9999 0 -9999 0 0
PRL-1/alpha Tubulin -0.029 0.125 -9999 0 -0.902 2 2
PRL-3/alpha1 Integrin 0.032 0.056 -9999 0 -0.378 2 2
ROCK1 0.015 0.077 -9999 0 -9999 0 0
RABGGTB 0.031 0.008 -9999 0 -9999 0 0
CDK2 0.033 0 -9999 0 -9999 0 0
mitosis -0.028 0.131 -9999 0 -0.939 2 2
ATF5 0.007 0.097 -9999 0 -0.518 4 4
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.026 0.049 0.516 1 -9999 0 1
PI3K Class IB/PDE3B 0.026 0.049 -9999 0 -0.517 1 1
PDE3B 0.026 0.049 -9999 0 -0.518 1 1
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.024 0.033 -9999 0 -0.246 1 1
TRAF2/ASK1 0.041 0.014 -9999 0 -9999 0 0
ATM 0.029 0.047 -9999 0 -0.518 1 1
MAP2K3 -0.011 0.125 -9999 0 -0.409 7 7
response to stress 0 0 -9999 0 -9999 0 0
MAP2K6 -0.017 0.103 -9999 0 -0.349 6 6
hyperosmotic response 0 0 -9999 0 -9999 0 0
response to oxidative stress 0 0 -9999 0 -9999 0 0
GADD45G 0.02 0.055 -9999 0 -0.518 1 1
TXN 0.007 0.01 -9999 0 -9999 0 0
CALM1 0.032 0.006 -9999 0 -9999 0 0
GADD45A 0.021 0.068 -9999 0 -0.518 2 2
GADD45B 0.023 0.068 -9999 0 -0.518 2 2
MAP3K1 0.013 0.093 -9999 0 -0.518 4 4
MAP3K6 0.023 0.067 -9999 0 -0.518 2 2
MAP3K7 0.031 0.011 -9999 0 -9999 0 0
MAP3K4 0.028 0.047 -9999 0 -0.518 1 1
mol:Ca2+ 0 0 -9999 0 -9999 0 0
ASK1/ASK2 0.039 0.053 -9999 0 -0.378 2 2
TAK1/TAB family 0.018 0.021 -9999 0 -9999 0 0
RAC1/OSM/MEKK3 0.06 0.017 -9999 0 -9999 0 0
TRAF2 0.031 0.012 -9999 0 -9999 0 0
RAC1/OSM/MEKK3/MKK3 0.016 0.109 -9999 0 -0.375 4 4
TRAF6 0.014 0.03 -9999 0 -0.329 1 1
RAC1 0.032 0.005 -9999 0 -9999 0 0
mol:LPS 0 0 -9999 0 -9999 0 0
CAMK2B 0.019 0.056 -9999 0 -0.518 1 1
CCM2 0.032 0.005 -9999 0 -9999 0 0
CaM/Ca2+/CAMKIIB 0.033 0.04 -9999 0 -0.321 1 1
MAPK11 0.031 0.008 -9999 0 -9999 0 0
response to DNA damage stimulus 0 0 -9999 0 -9999 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.048 0.044 -9999 0 -0.295 1 1
OSM/MEKK3 0.046 0.013 -9999 0 -9999 0 0
TAOK1 -0.004 0.082 -9999 0 -0.329 8 8
TAOK2 0.015 0.03 -9999 0 -0.328 1 1
TAOK3 0.012 0.042 -9999 0 -0.328 2 2
MAP3K7IP1 0.031 0.009 -9999 0 -9999 0 0
MAPK14 0.033 0.004 -9999 0 -9999 0 0
MAP3K7IP2 0.032 0.006 -9999 0 -9999 0 0
MAP3K5 0.032 0.011 -9999 0 -9999 0 0
MAP3K10 0.02 0.067 -9999 0 -0.518 2 2
MAP3K3 0.031 0.011 -9999 0 -9999 0 0
TRX/ASK1 0.027 0.023 -9999 0 -0.177 1 1
GADD45/MTK1/MTK1 0.046 0.08 -9999 0 -0.28 6 6
Alternative NF-kappaB pathway

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
IKK alpha homodimer 0.041 0.052 -9999 0 -0.378 2 2
FBXW11 0.031 0.008 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.031 0.008 -9999 0 -9999 0 0
CHUK 0.028 0.047 -9999 0 -0.518 1 1
NF kappa B2 p100/RelB 0.074 0.072 -9999 0 -0.283 4 4
NFKB1 0.031 0.008 -9999 0 -9999 0 0
MAP3K14 0.029 0.047 -9999 0 -0.518 1 1
NF kappa B1 p50/RelB 0.037 0.053 -9999 0 -0.37 2 2
RELB 0.022 0.068 -9999 0 -0.518 2 2
NFKB2 0.031 0.012 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.034 0.047 -9999 0 -0.321 2 2
regulation of B cell activation 0.034 0.047 -9999 0 -0.32 2 2
Canonical NF-kappaB 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
FBXW11 0.032 0.015 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.057 0.072 0.228 1 -0.262 1 2
ERC1 0 0 -9999 0 -9999 0 0
RIP2/NOD2 0.022 0.011 -9999 0 -9999 0 0
NFKBIA 0.009 0.05 -9999 0 -0.572 1 1
BIRC2 0.032 0.005 -9999 0 -9999 0 0
IKBKB 0.029 0.01 -9999 0 -9999 0 0
RIPK2 0.029 0.016 -9999 0 -9999 0 0
IKBKG 0.028 0.034 -9999 0 -9999 0 0
IKK complex/A20 0.051 0.07 -9999 0 -0.298 1 1
NEMO/A20/RIP2 0.029 0.016 -9999 0 -9999 0 0
XPO1 0.029 0.011 -9999 0 -9999 0 0
NEMO/ATM 0.039 0.061 -9999 0 -0.309 1 1
tumor necrosis factor receptor activity 0 0 -9999 0 -9999 0 0
RAN 0.033 0.003 -9999 0 -9999 0 0
Exportin 1/RanGTP 0.039 0.015 -9999 0 -9999 0 0
IKK complex/ELKS 0.036 0.056 -9999 0 -0.275 1 1
BCL10/MALT1/TRAF6 0.053 0.053 -9999 0 -0.324 2 2
NOD2 0 0 -9999 0 -9999 0 0
NFKB1 0.032 0.015 -9999 0 -9999 0 0
RELA 0.034 0.012 -9999 0 -9999 0 0
MALT1 0.03 0.013 -9999 0 -9999 0 0
cIAP1/UbcH5C 0.045 0.013 -9999 0 -9999 0 0
ATM 0.029 0.047 -9999 0 -0.518 1 1
TNF/TNFR1A 0.037 0.045 -9999 0 -0.378 1 1
TRAF6 0.028 0.047 -9999 0 -0.518 1 1
PRKCA 0.028 0.047 -9999 0 -0.518 1 1
CHUK 0.028 0.047 -9999 0 -0.518 1 1
UBE2D3 0.031 0.008 -9999 0 -9999 0 0
TNF 0.025 0.051 -9999 0 -0.518 1 1
NF kappa B1 p50/RelA 0.067 0.039 -9999 0 -0.291 1 1
BCL10 0.028 0.047 -9999 0 -0.518 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.009 0.05 -9999 0 -0.567 1 1
beta TrCP1/SCF ubiquitin ligase complex 0.032 0.015 -9999 0 -9999 0 0
TNFRSF1A 0.026 0.048 -9999 0 -0.518 1 1
IKK complex 0.05 0.065 -9999 0 -0.291 1 1
CYLD 0.032 0.006 -9999 0 -9999 0 0
IKK complex/PKC alpha 0.06 0.068 -9999 0 -0.324 1 1
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.079 0.022 -9999 0 -9999 0 0
HDAC3 0.031 0.008 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 -0.009 0.004 -9999 0 -9999 0 0
GATA1/HDAC4 0.048 0.006 -9999 0 -9999 0 0
GATA1/HDAC5 0.049 0.004 -9999 0 -9999 0 0
GATA2/HDAC5 0.038 0.04 -9999 0 -0.378 1 1
HDAC5/BCL6/BCoR 0.021 0.075 -9999 0 -0.324 5 5
HDAC9 0.025 0.05 -9999 0 -0.518 1 1
Glucocorticoid receptor/Hsp90/HDAC6 0.042 0.012 -9999 0 -9999 0 0
HDAC4/ANKRA2 0.044 0.015 -9999 0 -9999 0 0
HDAC5/YWHAB 0.047 0.009 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.017 0.005 -9999 0 -9999 0 0
GATA2 0.024 0.048 -9999 0 -0.518 1 1
HDAC4/RFXANK 0.046 0.012 -9999 0 -9999 0 0
BCOR 0.033 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
HDAC10 0.03 0.013 -9999 0 -9999 0 0
HDAC5 0.033 0.003 -9999 0 -9999 0 0
GNB1/GNG2 0.047 0.011 -9999 0 -9999 0 0
Histones 0.024 0.051 -9999 0 -0.342 2 2
ADRBK1 0.032 0.005 -9999 0 -9999 0 0
HDAC4 0.033 0.004 -9999 0 -9999 0 0
XPO1 0.029 0.011 -9999 0 -9999 0 0
HDAC5/ANKRA2 0.044 0.014 -9999 0 -9999 0 0
HDAC4/Ubc9 0.047 0.009 -9999 0 -9999 0 0
HDAC7 0 0 -9999 0 -9999 0 0
HDAC5/14-3-3 E 0.046 0.012 -9999 0 -9999 0 0
TUBA1B 0 0 -9999 0 -9999 0 0
HDAC6 0.033 0 -9999 0 -9999 0 0
HDAC5/RFXANK 0.047 0.011 -9999 0 -9999 0 0
CAMK4 0.026 0.049 -9999 0 -0.518 1 1
Tubulin/HDAC6 0.032 0.056 -9999 0 -0.321 3 3
SUMO1 0.032 0.006 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 0 0
YWHAB 0.032 0.006 -9999 0 -9999 0 0
GATA1 0.033 0 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
YWHAE 0.031 0.007 -9999 0 -9999 0 0
NR3C1 0.03 0.012 -9999 0 -9999 0 0
SUMO1/HDAC4 0.05 0.029 -9999 0 -9999 0 0
SRF 0.033 0.003 -9999 0 -9999 0 0
HDAC4/YWHAB 0.047 0.01 -9999 0 -9999 0 0
Tubulin 0.012 0.06 -9999 0 -0.375 3 3
HDAC4/14-3-3 E 0.046 0.012 -9999 0 -9999 0 0
GNB1 0.032 0.006 -9999 0 -9999 0 0
RANGAP1 0.032 0.006 -9999 0 -9999 0 0
BCL6/BCoR 0.01 0.08 -9999 0 -0.378 5 5
HDAC4/HDAC3/SMRT (N-CoR2) 0.056 0.05 -9999 0 -0.324 2 2
HDAC4/SRF 0.057 0.039 -9999 0 -0.324 1 1
HDAC4/ER alpha 0.016 0.097 -9999 0 -0.378 7 7
EntrezGene:23225 0 0 -9999 0 -9999 0 0
positive regulation of chromatin silencing 0.024 0.051 -9999 0 -0.339 2 2
cell motility 0.032 0.056 -9999 0 -0.32 3 3
EntrezGene:23636 0 0 -9999 0 -9999 0 0
UBE2I 0.032 0.005 -9999 0 -9999 0 0
HDAC7/HDAC3 0.023 0.006 -9999 0 -9999 0 0
BCL6 -0.003 0.102 -9999 0 -0.518 5 5
HDAC4/CaMK II delta B 0.033 0.004 -9999 0 -9999 0 0
Hsp90/HDAC6 0.024 0 -9999 0 -9999 0 0
ESR1 -0.006 0.123 -9999 0 -0.518 7 7
HDAC6/HDAC11 0.045 0.013 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0.048 0.034 -9999 0 -9999 0 0
NPC 0.019 0.002 -9999 0 -9999 0 0
MEF2C 0 0.114 -9999 0 -0.518 6 6
RAN 0.033 0.003 -9999 0 -9999 0 0
HDAC4/MEF2C 0.057 0.095 -9999 0 -0.283 8 8
GNG2 0.032 0.005 -9999 0 -9999 0 0
NCOR2 0.025 0.066 -9999 0 -0.518 2 2
TUBB2A 0.016 0.083 -9999 0 -0.518 3 3
HDAC11 0.031 0.009 -9999 0 -9999 0 0
HSP90AA1 0 0 -9999 0 -9999 0 0
RANBP2 0.033 0.004 -9999 0 -9999 0 0
ANKRA2 0.03 0.01 -9999 0 -9999 0 0
RFXANK 0.031 0.007 -9999 0 -9999 0 0
nuclear import -0.04 0.013 -9999 0 -9999 0 0
Aurora C signaling

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
INCENP 0.029 0.047 -9999 0 -0.518 1 1
Aurora C/Aurora B/INCENP 0.057 0.022 -9999 0 -9999 0 0
metaphase 0 0 -9999 0 -9999 0 0
mitosis 0 0 -9999 0 -9999 0 0
H3F3B 0.015 0.006 -9999 0 -9999 0 0
AURKB 0.031 0.007 -9999 0 -9999 0 0
AURKC 0.032 0.006 -9999 0 -9999 0 0
Effects of Botulinum toxin

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
STX1A 0.007 0.008 -9999 0 -9999 0 0
UniProt:P19321 0 0 -9999 0 -9999 0 0
RIMS1/UNC13B 0.038 0.026 -9999 0 -9999 0 0
STXBP1 0.033 0.004 -9999 0 -9999 0 0
ACh/CHRNA1 0.021 0.038 -9999 0 -0.335 1 1
RAB3GAP2/RIMS1/UNC13B 0.054 0.031 -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 0.029 0.021 -9999 0 -9999 0 0
mol:ACh 0.003 0.021 0.088 1 -9999 0 1
RAB3GAP2 0.033 0 -9999 0 -9999 0 0
STX1A/SNAP25/VAMP2 0.043 0.043 -9999 0 -9999 0 0
UniProt:P10844 0 0 -9999 0 -9999 0 0
muscle contraction 0.021 0.038 -9999 0 -0.334 1 1
UNC13B 0.028 0.017 -9999 0 -9999 0 0
CHRNA1 0.028 0.048 -9999 0 -0.518 1 1
UniProt:P10845 0 0 -9999 0 -9999 0 0
ACh/Synaptotagmin 1 -0.004 0.087 -9999 0 -0.335 8 8
SNAP25 0.004 0.011 -9999 0 -9999 0 0
VAMP2 0.005 0.004 -9999 0 -9999 0 0
SYT1 -0.01 0.131 -9999 0 -0.518 8 8
UniProt:Q00496 0 0 -9999 0 -9999 0 0
STXIA/STXBP1 0.029 0.011 -9999 0 -9999 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.043 0.043 -9999 0 -9999 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.031 0.011 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0.007 0.008 -9999 0 -9999 0 0
MDM2/SUMO1 0.046 0.038 -9999 0 -0.25 1 1
HDAC4 0.033 0.004 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 0.007 0.009 -9999 0 -9999 0 0
SUMO1 0.032 0.006 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1 0.014 0.009 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
XPO1 0.01 0.012 -9999 0 -9999 0 0
EntrezGene:23636 0 0 -9999 0 -9999 0 0
RAN 0.033 0.003 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.033 0.004 -9999 0 -9999 0 0
SUMO1/HDAC4 0.05 0.029 -9999 0 -9999 0 0
SUMO1/HDAC1 0.049 0.031 -9999 0 -9999 0 0
RANGAP1 0.032 0.006 -9999 0 -9999 0 0
MDM2/SUMO1/SUMO1 0.063 0.058 -9999 0 -0.298 2 2
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.017 0.005 -9999 0 -9999 0 0
Ran/GTP 0.035 0.026 -9999 0 -9999 0 0
EntrezGene:23225 0 0 -9999 0 -9999 0 0
MDM2 0.027 0.048 -9999 0 -0.518 1 1
UBE2I 0.032 0.005 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0.05 0.058 -9999 0 -9999 0 0
NPC 0.019 0.002 -9999 0 -9999 0 0
PIAS2 0.023 0.067 -9999 0 -0.518 2 2
PIAS1 0.032 0.006 -9999 0 -9999 0 0
EntrezGene:9972 0 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 0.009 0.015 -9999 0 -9999 0 0
EntrezGene:79658 0 0 -9999 0 -9999 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.015 0.025 -9999 0 -9999 0 0
AP2 0.02 0.042 -9999 0 -0.378 1 1
mol:DAG 0 0 -9999 0 -9999 0 0
Arfaptin 2/Rac/GTP 0.043 0.01 -9999 0 -9999 0 0
CLTB 0.03 0.016 -9999 0 -9999 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.02 0.011 -9999 0 -9999 0 0
CD4 0.03 0.013 -9999 0 -9999 0 0
CLTA 0.03 0.01 -9999 0 -9999 0 0
mol:GTP -0.002 0.002 -9999 0 -9999 0 0
ARFGAP1 0.008 0.001 -9999 0 -9999 0 0
mol:PI-4-5-P2 0.004 0.024 -9999 0 -0.185 2 2
ARF1/GTP 0.016 0.016 -9999 0 -0.099 2 2
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.012 0.006 -9999 0 -9999 0 0
mol:Choline 0.004 0.025 -9999 0 -0.193 2 2
mol:GDP 0 0 -9999 0 -9999 0 0
ARF1 0.034 0.004 -9999 0 -9999 0 0
DDEF1 0.004 0.018 -9999 0 -0.193 1 1
ARF1/GDP 0.006 0.021 -9999 0 -9999 0 0
AP2M1 0.012 0.048 -9999 0 -0.518 1 1
EntrezGene:1313 0 0 -9999 0 -9999 0 0
actin filament polymerization 0.015 0.006 -9999 0 -9999 0 0
Rac/GTP 0.025 0.004 -9999 0 -9999 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.043 0.03 -9999 0 -0.283 1 1
ARFIP2 0.028 0.013 -9999 0 -9999 0 0
COPA 0.031 0.007 -9999 0 -9999 0 0
RAC1 0.032 0.005 -9999 0 -9999 0 0
ARF1/GTP/coatomer protein complex 0.023 0.039 -9999 0 -9999 0 0
ARF1/GTP/ARHGAP10 0.022 0.004 -9999 0 -9999 0 0
GGA3 0.028 0.047 -9999 0 -0.518 1 1
ARF1/GTP/Membrin 0.026 0.015 -9999 0 -9999 0 0
AP2A1 0.031 0.015 -9999 0 -9999 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.012 0.032 -9999 0 -0.219 1 1
ARF1/GDP/Membrin 0.033 0.017 -9999 0 -9999 0 0
Arfaptin 2/Rac/GDP 0.042 0.012 -9999 0 -9999 0 0
CYTH2 -0.002 0.002 -9999 0 -9999 0 0
ARF1/GTP/GGA3 0.04 0.034 -9999 0 -0.336 1 1
mol:ATP 0 0 -9999 0 -9999 0 0
Rac/GDP 0.024 0.004 -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 0.008 0.028 -9999 0 -9999 0 0
PLD2 0.004 0.025 -9999 0 -0.194 2 2
ARF-GAP1/v-SNARE 0.008 0.001 -9999 0 -9999 0 0
PIP5K1A 0.004 0.024 -9999 0 -0.186 2 2
ARF1/GTP/Membrin/GBF1/p115 0.019 0.021 -9999 0 -9999 0 0
mol:Phosphatic acid 0 0 -9999 0 -9999 0 0
mol:Phosphatidic acid 0.004 0.025 -9999 0 -0.193 2 2
KDEL Receptor/Ligand/ARF-GAP1 0.008 0.001 -9999 0 -9999 0 0
GOSR2 0.013 0.012 -9999 0 -9999 0 0
USO1 0.001 0.011 -9999 0 -0.088 2 2
GBF1 0.009 0.042 -9999 0 -0.318 2 2
ARF1/GTP/Arfaptin 2 0.041 0.014 -9999 0 -9999 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.026 0.045 -9999 0 -0.324 1 1
Methods & Data
Input

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

  • Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/LUSC/760634/1.GDAC_MergeDataFiles.Finished/LUSC.transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/writeReducedSegments/LUSC/718115/1.GetReducedSegments.Finished/LUSC.RS.tsv

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

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)