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 47 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
IL23-mediated signaling events 43
TCGA08_p53 34
HIF-1-alpha transcription factor network 32
Ephrin B reverse signaling 32
Wnt signaling 31
IL4-mediated signaling events 29
Fc-epsilon receptor I signaling in mast cells 26
Endothelins 25
Signaling mediated by p38-alpha and p38-beta 25
Syndecan-1-mediated signaling events 24
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
IL23-mediated signaling events 43 2602 60 -0.62 0.035 1000 -1000 -0.066 -1000
TCGA08_p53 34 238 7 -0.082 0.029 1000 -1000 -0.007 -1000
HIF-1-alpha transcription factor network 32 2507 76 -0.293 0.041 1000 -1000 -0.033 -1000
Ephrin B reverse signaling 32 1565 48 -0.246 0.05 1000 -1000 -0.024 -1000
Wnt signaling 31 220 7 -0.118 0.031 1000 -1000 -0.017 -1000
IL4-mediated signaling events 29 2671 91 -0.612 0.487 1000 -1000 -0.087 -1000
Fc-epsilon receptor I signaling in mast cells 26 2561 97 -0.182 0.036 1000 -1000 -0.053 -1000
Endothelins 25 2438 96 -0.226 0.041 1000 -1000 -0.039 -1000
Signaling mediated by p38-alpha and p38-beta 25 1100 44 -0.155 0.035 1000 -1000 -0.022 -1000
Syndecan-1-mediated signaling events 24 843 34 -0.134 0.042 1000 -1000 -0.031 -1000
TCGA08_retinoblastoma 23 189 8 -0.03 0.036 1000 -1000 -0.003 -1000
EGFR-dependent Endothelin signaling events 22 471 21 -0.088 0.051 1000 -1000 -0.007 -1000
Noncanonical Wnt signaling pathway 21 554 26 -0.118 0.035 1000 -1000 -0.052 -1000
Glypican 1 network 21 1010 48 -0.129 0.044 1000 -1000 -0.025 -1000
IL12-mediated signaling events 20 1798 87 -0.327 0.039 1000 -1000 -0.052 -1000
Osteopontin-mediated events 20 782 38 -0.172 0.04 1000 -1000 -0.046 -1000
Thromboxane A2 receptor signaling 20 2197 105 -0.171 0.051 1000 -1000 -0.041 -1000
IL27-mediated signaling events 20 1069 51 -0.188 0.125 1000 -1000 -0.048 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 20 1409 68 -0.378 0.174 1000 -1000 -0.082 -1000
IL1-mediated signaling events 19 1178 62 -0.153 0.082 1000 -1000 -0.03 -1000
FOXA2 and FOXA3 transcription factor networks 18 857 46 -0.248 0.04 1000 -1000 -0.067 -1000
Glucocorticoid receptor regulatory network 18 2057 114 -0.389 0.212 1000 -1000 -0.054 -1000
Glypican 2 network 18 75 4 -0.01 0 1000 -1000 0 -1000
Calcium signaling in the CD4+ TCR pathway 18 570 31 -0.199 0.032 1000 -1000 -0.032 -1000
FAS signaling pathway (CD95) 17 806 47 -0.311 0.057 1000 -1000 -0.044 -1000
TCR signaling in naïve CD8+ T cells 17 1604 93 -0.084 0.051 1000 -1000 -0.035 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 17 1330 78 -0.238 0.052 1000 -1000 -0.057 -1000
Presenilin action in Notch and Wnt signaling 16 984 61 -0.144 0.1 1000 -1000 -0.044 -1000
BMP receptor signaling 16 1369 81 -0.155 0.064 1000 -1000 -0.034 -1000
amb2 Integrin signaling 16 1388 82 -0.163 0.045 1000 -1000 -0.03 -1000
Signaling events mediated by the Hedgehog family 15 794 52 -0.118 0.071 1000 -1000 -0.026 -1000
Canonical Wnt signaling pathway 15 784 51 -0.263 0.112 1000 -1000 -0.048 -1000
Visual signal transduction: Rods 15 830 52 -0.17 0.052 1000 -1000 -0.031 -1000
PLK2 and PLK4 events 14 44 3 -0.016 0.029 1000 -1000 -0.009 -1000
Syndecan-2-mediated signaling events 14 987 69 -0.135 0.043 1000 -1000 -0.03 -1000
Arf6 signaling events 14 881 62 -0.088 0.083 1000 -1000 -0.015 -1000
IFN-gamma pathway 14 952 68 -0.108 0.046 1000 -1000 -0.04 -1000
EPHB forward signaling 14 1234 85 -0.078 0.095 1000 -1000 -0.063 -1000
FOXM1 transcription factor network 14 727 51 -0.24 0.033 1000 -1000 -0.1 -1000
Ras signaling in the CD4+ TCR pathway 14 240 17 -0.028 0.046 1000 -1000 -0.015 -1000
Cellular roles of Anthrax toxin 13 528 39 -0.062 0.032 1000 -1000 -0.022 -1000
S1P1 pathway 13 483 36 -0.149 0.035 1000 -1000 -0.03 -1000
IL6-mediated signaling events 13 999 75 -0.119 0.047 1000 -1000 -0.036 -1000
Caspase cascade in apoptosis 12 892 74 -0.125 0.063 1000 -1000 -0.034 -1000
Nectin adhesion pathway 12 799 63 -0.052 0.054 1000 -1000 -0.043 -1000
Syndecan-3-mediated signaling events 12 424 35 -0.135 0.05 1000 -1000 -0.033 -1000
BCR signaling pathway 12 1264 99 -0.187 0.04 1000 -1000 -0.05 -1000
a4b1 and a4b7 Integrin signaling 11 58 5 0 0.033 1000 -1000 0.01 -1000
LPA receptor mediated events 11 1186 102 -0.141 0.035 1000 -1000 -0.077 -1000
Stabilization and expansion of the E-cadherin adherens junction 11 842 74 -0.088 0.048 1000 -1000 -0.063 -1000
Syndecan-4-mediated signaling events 11 737 67 -0.058 0.065 1000 -1000 -0.035 -1000
E-cadherin signaling events 11 56 5 0.011 0.033 1000 -1000 0.011 -1000
Sphingosine 1-phosphate (S1P) pathway 10 296 28 -0.039 0.046 1000 -1000 -0.007 -1000
Ceramide signaling pathway 10 775 76 -0.088 0.069 1000 -1000 -0.038 -1000
Reelin signaling pathway 10 614 56 -0.084 0.092 1000 -1000 -0.033 -1000
IL2 signaling events mediated by STAT5 10 227 22 -0.088 0.036 1000 -1000 -0.021 -1000
Signaling events mediated by PRL 10 346 34 -0.051 0.054 1000 -1000 -0.035 -1000
Aurora B signaling 10 697 67 -0.141 0.054 1000 -1000 -0.04 -1000
JNK signaling in the CD4+ TCR pathway 9 161 17 -0.035 0.034 1000 -1000 -0.027 -1000
Signaling events mediated by PTP1B 9 694 76 -0.087 0.059 1000 -1000 -0.042 -1000
p75(NTR)-mediated signaling 9 1146 125 -0.139 0.077 1000 -1000 -0.044 -1000
IL2 signaling events mediated by PI3K 9 553 58 -0.066 0.051 1000 -1000 -0.041 -1000
Nongenotropic Androgen signaling 9 519 52 -0.093 0.061 1000 -1000 -0.026 -1000
Visual signal transduction: Cones 8 327 38 -0.004 0.043 1000 -1000 -0.002 -1000
Hedgehog signaling events mediated by Gli proteins 8 522 65 -0.112 0.058 1000 -1000 -0.035 -1000
Arf6 downstream pathway 8 350 43 -0.034 0.041 1000 -1000 -0.023 -1000
PDGFR-alpha signaling pathway 8 371 44 -0.13 0.068 1000 -1000 -0.033 -1000
Integrins in angiogenesis 8 739 84 -0.172 0.073 1000 -1000 -0.035 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 8 384 45 -0.053 0.05 1000 -1000 -0.041 -1000
E-cadherin signaling in the nascent adherens junction 8 676 76 -0.047 0.075 1000 -1000 -0.052 -1000
Plasma membrane estrogen receptor signaling 8 692 86 -0.051 0.098 1000 -1000 -0.047 -1000
VEGFR1 specific signals 8 469 56 -0.007 0.09 1000 -1000 -0.036 -1000
mTOR signaling pathway 7 384 53 -0.052 0.039 1000 -1000 -0.034 -1000
RXR and RAR heterodimerization with other nuclear receptor 7 377 52 -0.07 0.092 1000 -1000 -0.033 -1000
Signaling mediated by p38-gamma and p38-delta 7 116 15 -0.022 0.03 1000 -1000 -0.028 -1000
Regulation of p38-alpha and p38-beta 7 414 54 -0.031 0.067 1000 -1000 -0.03 -1000
Class I PI3K signaling events 7 558 73 -0.061 0.049 1000 -1000 -0.029 -1000
Regulation of Telomerase 7 747 102 -0.2 0.077 1000 -1000 -0.037 -1000
Insulin Pathway 7 539 74 -0.167 0.104 1000 -1000 -0.037 -1000
S1P3 pathway 7 319 42 -0.033 0.046 1000 -1000 -0.024 -1000
Regulation of Androgen receptor activity 7 538 70 -0.104 0.083 1000 -1000 -0.048 -1000
Regulation of nuclear SMAD2/3 signaling 6 911 136 -0.073 0.05 1000 -1000 -0.047 -1000
ErbB4 signaling events 6 453 69 -0.179 0.064 1000 -1000 -0.036 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 6 352 54 -0.084 0.047 1000 -1000 -0.039 -1000
Paxillin-independent events mediated by a4b1 and a4b7 6 239 37 -0.017 0.068 1000 -1000 -0.029 -1000
HIF-2-alpha transcription factor network 6 276 43 -0.038 0.053 1000 -1000 -0.042 -1000
Effects of Botulinum toxin 6 158 26 -0.094 0.06 1000 -1000 -0.003 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 6 218 33 -0.048 0.075 1000 -1000 -0.035 -1000
PDGFR-beta signaling pathway 6 642 97 -0.05 0.096 1000 -1000 -0.047 -1000
S1P4 pathway 6 152 25 -0.016 0.046 1000 -1000 -0.017 -1000
EPO signaling pathway 5 284 55 -0.019 0.055 1000 -1000 -0.031 -1000
Signaling events mediated by HDAC Class III 5 235 40 -0.056 0.061 1000 -1000 -0.025 -1000
TRAIL signaling pathway 5 274 48 -0.02 0.061 1000 -1000 -0.027 -1000
Signaling events regulated by Ret tyrosine kinase 5 445 82 -0.026 0.063 1000 -1000 -0.057 -1000
S1P5 pathway 5 100 17 -0.013 0.036 1000 -1000 -0.005 -1000
FoxO family signaling 5 335 64 -0.081 0.05 1000 -1000 -0.04 -1000
Retinoic acid receptors-mediated signaling 5 310 58 -0.107 0.067 1000 -1000 -0.032 -1000
Paxillin-dependent events mediated by a4b1 5 206 36 -0.06 0.063 1000 -1000 -0.032 -1000
Signaling events mediated by VEGFR1 and VEGFR2 5 733 125 -0.05 0.095 1000 -1000 -0.042 -1000
Arf6 trafficking events 5 421 71 -0.049 0.037 1000 -1000 -0.027 -1000
Class IB PI3K non-lipid kinase events 5 15 3 -0.025 0.025 1000 -1000 -0.016 -1000
LPA4-mediated signaling events 4 50 12 -0.023 0.017 1000 -1000 -0.024 -1000
ErbB2/ErbB3 signaling events 4 295 65 -0.087 0.05 1000 -1000 -0.067 -1000
Coregulation of Androgen receptor activity 4 307 76 -0.076 0.056 1000 -1000 -0.023 -1000
BARD1 signaling events 4 250 57 -0.048 0.073 1000 -1000 -0.039 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 4 423 85 -0.18 0.075 1000 -1000 -0.041 -1000
Aurora A signaling 4 248 60 -0.055 0.054 1000 -1000 -0.014 -1000
Aurora C signaling 4 30 7 0 0.036 1000 -1000 -0.013 -1000
PLK1 signaling events 4 402 85 -0.026 0.055 1000 -1000 -0.026 -1000
Class I PI3K signaling events mediated by Akt 4 302 68 -0.054 0.071 1000 -1000 -0.028 -1000
ceramide signaling pathway 4 208 49 -0.011 0.05 1000 -1000 -0.039 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 4 351 83 -0.04 0.07 1000 -1000 -0.021 -1000
IGF1 pathway 4 235 57 -0.025 0.083 1000 -1000 -0.037 -1000
Angiopoietin receptor Tie2-mediated signaling 4 355 88 -0.167 0.099 1000 -1000 -0.063 -1000
Neurotrophic factor-mediated Trk receptor signaling 4 481 120 -0.016 0.092 1000 -1000 -0.043 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 3 80 23 0.003 0.038 1000 -1000 -0.022 -1000
Ephrin A reverse signaling 3 26 7 -0.002 0.037 1000 -1000 0 -1000
TCGA08_rtk_signaling 3 100 26 -0.027 0.058 1000 -1000 -0.011 -1000
E-cadherin signaling in keratinocytes 3 157 43 -0.044 0.091 1000 -1000 -0.03 -1000
p38 MAPK signaling pathway 3 140 44 0 0.059 1000 -1000 -0.018 -1000
Signaling events mediated by HDAC Class II 2 170 75 -0.017 0.066 1000 -1000 -0.018 -1000
Insulin-mediated glucose transport 2 79 32 -0.013 0.044 1000 -1000 -0.022 -1000
Signaling events mediated by HDAC Class I 2 236 104 -0.047 0.079 1000 -1000 -0.032 -1000
Atypical NF-kappaB pathway 2 78 31 -0.015 0.045 1000 -1000 -0.019 -1000
Nephrin/Neph1 signaling in the kidney podocyte 1 55 34 -0.043 0.085 1000 -1000 -0.029 -1000
Canonical NF-kappaB pathway 1 43 39 0 0.076 1000 -1000 -0.021 -1000
Circadian rhythm pathway 1 26 22 -0.012 0.073 1000 -1000 -0.037 -1000
Alternative NF-kappaB pathway 1 15 13 0 0.09 1000 -1000 0 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 25 27 0 0.049 1000 -1000 -0.03 -1000
Rapid glucocorticoid signaling 0 16 20 0 0.041 1000 -1000 -0.002 -1000
Arf1 pathway 0 49 54 -0.001 0.065 1000 -1000 -0.018 -1000
Total 1395 80724 7203 -13.1030857657 8.16805939539 131000 -131000 -4.31963884719 -131000
IL23-mediated signaling events

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
CCL2 -0.509 0.611 -9999 0 -1.299 67 67
IL23A -0.564 0.626 -9999 0 -1.305 76 76
NF kappa B1 p50/RelA/I kappa B alpha -0.483 0.587 -9999 0 -1.178 73 73
positive regulation of T cell mediated cytotoxicity -0.526 0.652 -9999 0 -1.33 69 69
ITGA3 -0.485 0.568 -9999 0 -1.217 65 65
IL17F -0.303 0.353 -9999 0 -0.746 62 62
IL12B -0.018 0.074 -9999 0 -0.371 4 4
STAT1 (dimer) -0.505 0.623 -9999 0 -1.276 69 69
CD4 -0.442 0.529 -9999 0 -1.155 59 59
IL23 -0.542 0.594 -9999 0 -1.242 76 76
IL23R -0.123 0.362 -9999 0 -1.404 14 14
IL1B -0.555 0.64 -9999 0 -1.338 71 71
T-helper cell lineage commitment 0 0 -9999 0 -9999 0 0
IL24 -0.451 0.535 -9999 0 -1.178 58 58
TYK2 -0.009 0.041 -9999 0 -9999 0 0
STAT4 0.02 0.079 -9999 0 -0.328 9 9
STAT3 0.034 0.007 -9999 0 -9999 0 0
IL18RAP -0.067 0.186 -9999 0 -0.373 50 50
IL12RB1 -0.011 0.044 -9999 0 -0.242 1 1
PIK3CA 0.035 0.006 -9999 0 -9999 0 0
IL12Rbeta1/TYK2 -0.008 0.055 -9999 0 -9999 0 0
IL23R/JAK2 -0.133 0.349 -9999 0 -1.384 13 13
positive regulation of chronic inflammatory response -0.526 0.652 -9999 0 -1.33 69 69
natural killer cell activation 0.01 0.019 0.081 11 -9999 0 11
JAK2 -0.026 0.089 -9999 0 -0.301 12 12
PIK3R1 0.028 0.062 -9999 0 -0.483 3 3
NFKB1 0.032 0.007 -9999 0 -9999 0 0
RELA 0.033 0.005 -9999 0 -9999 0 0
positive regulation of dendritic cell antigen processing and presentation -0.507 0.551 -9999 0 -1.154 76 76
ALOX12B -0.446 0.534 -9999 0 -1.163 60 60
CXCL1 -0.545 0.616 -9999 0 -1.277 75 75
T cell proliferation -0.526 0.652 -9999 0 -1.33 69 69
NFKBIA 0.025 0.044 -9999 0 -0.306 3 3
IL17A -0.236 0.275 -9999 0 -0.562 64 64
PI3K -0.472 0.597 -9999 0 -1.22 68 68
IFNG -0.03 0.06 0.13 7 -0.13 37 44
STAT3 (dimer) -0.441 0.566 -9999 0 -1.181 63 63
IL18R1 0.003 0.097 -9999 0 -0.284 18 18
IL23/IL23R/JAK2/TYK2/SOCS3 -0.244 0.325 -9999 0 -0.741 38 38
IL18/IL18R -0.072 0.189 -9999 0 -0.357 51 51
macrophage activation -0.024 0.022 -9999 0 -0.047 72 72
TNF -0.511 0.58 -9999 0 -1.221 70 70
STAT3/STAT4 -0.472 0.597 -9999 0 -1.218 68 68
STAT4 (dimer) -0.504 0.627 -9999 0 -1.282 69 69
IL18 -0.027 0.156 -9999 0 -0.422 26 26
IL19 -0.446 0.529 -9999 0 -1.17 57 57
STAT5A (dimer) -0.498 0.623 -9999 0 -1.268 69 69
STAT1 0.015 0.067 -9999 0 -0.204 18 18
SOCS3 0.013 0.091 -9999 0 -0.311 13 13
CXCL9 -0.62 0.662 -9999 0 -1.319 91 91
MPO -0.444 0.533 -9999 0 -1.155 60 60
positive regulation of humoral immune response -0.526 0.652 -9999 0 -1.33 69 69
IL23/IL23R/JAK2/TYK2 -0.572 0.742 -9999 0 -1.465 69 69
IL6 -0.56 0.638 -9999 0 -1.32 75 75
STAT5A 0.027 0.049 -9999 0 -0.259 5 5
IL2 0.026 0.028 -9999 0 -9999 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.01 0.019 0.081 11 -9999 0 11
CD3E -0.445 0.53 -9999 0 -1.143 62 62
keratinocyte proliferation -0.526 0.652 -9999 0 -1.33 69 69
NOS2 -0.445 0.532 -9999 0 -1.104 69 69
TCGA08_p53

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
CDKN2A -0.036 0.103 -9999 0 -0.222 41 41
TP53 -0.061 0.127 0.257 2 -0.302 41 43
Senescence -0.082 0.131 0.257 2 -0.26 64 66
Apoptosis -0.082 0.131 0.257 2 -0.26 64 66
Activated_Oncogenes 0 0 -9999 0 -9999 0 0
MDM2 0.022 0.076 0.242 19 -9999 0 19
MDM4 0.029 0.053 -9999 0 -0.39 3 3
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.214 0.445 -9999 0 -0.909 45 45
HDAC7 -0.001 0.006 -9999 0 -9999 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.151 0.392 -9999 0 -0.764 38 38
SMAD4 0.017 0.063 -9999 0 -0.481 3 3
ID2 -0.219 0.457 -9999 0 -0.933 45 45
AP1 -0.08 0.161 -9999 0 -0.344 47 47
ABCG2 -0.229 0.458 -9999 0 -0.928 47 47
HIF1A -0.02 0.102 -9999 0 -0.32 7 7
TFF3 -0.222 0.464 -9999 0 -0.939 46 46
GATA2 0.018 0.06 -9999 0 -0.391 3 3
AKT1 -0.021 0.095 -9999 0 -0.309 3 3
response to hypoxia -0.036 0.073 -9999 0 -0.18 3 3
MCL1 -0.212 0.446 -9999 0 -0.913 45 45
NDRG1 -0.217 0.439 -9999 0 -0.919 44 44
SERPINE1 -0.22 0.442 -9999 0 -0.897 47 47
FECH -0.238 0.433 -9999 0 -0.916 46 46
FURIN -0.212 0.444 -9999 0 -0.897 46 46
NCOA2 0.026 0.052 -9999 0 -0.483 2 2
EP300 -0.038 0.125 -9999 0 -0.302 20 20
HMOX1 -0.225 0.454 -9999 0 -0.926 46 46
BHLHE40 -0.226 0.43 -9999 0 -0.887 47 47
BHLHE41 -0.226 0.43 -9999 0 -0.887 47 47
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.017 0.149 -9999 0 -0.348 8 8
ENG -0.031 0.122 0.302 1 -0.403 3 4
JUN -0.025 0.149 -9999 0 -0.407 25 25
RORA -0.226 0.455 -9999 0 -0.928 46 46
ABCB1 -0.293 0.493 -9999 0 -1.14 49 49
TFRC -0.215 0.447 -9999 0 -0.891 47 47
CXCR4 -0.233 0.471 -9999 0 -0.938 49 49
TF -0.212 0.45 -9999 0 -0.904 46 46
CITED2 -0.212 0.444 -9999 0 -0.905 45 45
HIF1A/ARNT -0.207 0.538 -9999 0 -1.023 45 45
LDHA -0.001 0.118 -9999 0 -0.949 2 2
ETS1 -0.215 0.445 -9999 0 -0.912 45 45
PGK1 -0.211 0.449 -9999 0 -0.914 45 45
NOS2 -0.226 0.43 -9999 0 -0.887 47 47
ITGB2 -0.229 0.465 -9999 0 -0.926 48 48
ALDOA -0.21 0.442 -9999 0 -0.902 45 45
Cbp/p300/CITED2 -0.223 0.449 -9999 0 -0.924 44 44
FOS -0.07 0.171 -9999 0 -0.323 56 56
HK2 -0.21 0.449 -9999 0 -0.902 46 46
SP1 -0.007 0.069 -9999 0 -0.201 2 2
GCK -0.031 0.206 -9999 0 -1.402 2 2
HK1 -0.21 0.441 -9999 0 -0.898 45 45
NPM1 -0.21 0.447 -9999 0 -0.907 45 45
EGLN1 -0.214 0.439 -9999 0 -0.911 44 44
CREB1 0.041 0.019 -9999 0 -9999 0 0
PGM1 -0.219 0.461 -9999 0 -0.917 48 48
SMAD3 0.029 0.054 -9999 0 -0.389 3 3
EDN1 -0.235 0.426 -9999 0 -1.208 30 30
IGFBP1 -0.221 0.445 -9999 0 -0.908 46 46
VEGFA -0.164 0.311 -9999 0 -0.637 43 43
HIF1A/JAB1 0.004 0.083 -9999 0 -0.232 9 9
CP -0.215 0.451 -9999 0 -0.912 46 46
CXCL12 -0.228 0.466 -9999 0 -0.955 46 46
COPS5 0.029 0.038 -9999 0 -0.482 1 1
SMAD3/SMAD4 0.026 0.065 -9999 0 -0.347 5 5
BNIP3 -0.255 0.467 -9999 0 -0.911 54 54
EGLN3 -0.242 0.469 -9999 0 -0.94 49 49
CA9 -0.269 0.478 -9999 0 -0.953 52 52
TERT -0.212 0.445 -9999 0 -0.896 46 46
ENO1 -0.21 0.444 -9999 0 -0.905 45 45
PFKL -0.212 0.443 -9999 0 -0.894 46 46
NCOA1 0.026 0.071 -9999 0 -0.483 4 4
ADM -0.221 0.462 -9999 0 -0.92 48 48
ARNT -0.019 0.096 -9999 0 -0.545 1 1
HNF4A 0.009 0.072 -9999 0 -0.482 4 4
ADFP -0.23 0.457 -9999 0 -0.918 47 47
SLC2A1 -0.168 0.336 -9999 0 -0.678 41 41
LEP -0.218 0.443 -9999 0 -0.911 45 45
HIF1A/ARNT/Cbp/p300 -0.16 0.392 -9999 0 -0.754 42 42
EPO -0.1 0.277 -9999 0 -0.916 7 7
CREBBP -0.021 0.106 -9999 0 -0.277 10 10
HIF1A/ARNT/Cbp/p300/HDAC7 -0.162 0.383 -9999 0 -0.758 39 39
PFKFB3 -0.21 0.445 -9999 0 -0.907 45 45
NT5E -0.248 0.47 -9999 0 -0.946 48 48
Ephrin B reverse signaling

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
EFNB2 -0.004 0.121 -9999 0 -0.462 13 13
EPHB2 0.005 0.122 -9999 0 -0.484 12 12
EFNB1 0.012 0.047 -9999 0 -0.355 2 2
mol:GTP 0 0 -9999 0 -9999 0 0
Rac1/GDP -0.007 0.131 -9999 0 -0.297 19 19
Ephrin B2/EPHB1-2 -0.038 0.132 -9999 0 -0.305 32 32
neuron projection morphogenesis -0.022 0.116 -9999 0 -0.279 21 21
Ephrin B1/EPHB1-2/Tiam1 -0.016 0.135 -9999 0 -0.293 26 26
DNM1 0.031 0.036 -9999 0 -0.197 5 5
cell-cell signaling 0.001 0.004 -9999 0 -9999 0 0
MAP2K4 -0.162 0.25 -9999 0 -0.532 62 62
YES1 -0.239 0.366 -9999 0 -0.778 64 64
Ephrin B1/EPHB1-2/NCK2 -0.011 0.134 -9999 0 -0.297 24 24
PI3K -0.141 0.274 -9999 0 -0.516 68 68
mol:GDP -0.017 0.133 -9999 0 -0.29 26 26
ITGA2B 0.035 0.006 -9999 0 -9999 0 0
endothelial cell proliferation 0.01 0.084 -9999 0 -0.294 13 13
FYN -0.239 0.37 -9999 0 -0.779 65 65
MAP3K7 -0.175 0.264 -9999 0 -0.558 64 64
FGR -0.237 0.362 -9999 0 -0.766 65 65
TIAM1 0.028 0.054 -9999 0 -0.39 3 3
PIK3R1 0.028 0.062 -9999 0 -0.483 3 3
RGS3 0.035 0.005 -9999 0 -9999 0 0
cell adhesion -0.135 0.247 -9999 0 -0.494 62 62
LYN -0.223 0.362 -9999 0 -0.763 63 63
Ephrin B1/EPHB1-2/Src Family Kinases -0.216 0.327 -9999 0 -0.69 65 65
Ephrin B1/EPHB1-2 -0.181 0.282 -9999 0 -0.609 61 61
SRC -0.221 0.347 -9999 0 -0.736 63 63
ITGB3 0.033 0.018 -9999 0 -0.204 1 1
EPHB1 -0.061 0.157 -9999 0 -0.264 68 68
EPHB4 0.022 0.07 -9999 0 -0.323 7 7
RAC1 0.033 0.011 -9999 0 -9999 0 0
Ephrin B2/EPHB4 0.01 0.085 -9999 0 -0.295 13 13
alphaIIb/beta3 Integrin 0.05 0.018 -9999 0 -9999 0 0
BLK -0.245 0.366 -9999 0 -0.778 65 65
HCK -0.23 0.349 -9999 0 -0.746 63 63
regulation of stress fiber formation 0.012 0.132 0.295 24 -9999 0 24
MAPK8 -0.16 0.238 -9999 0 -0.501 64 64
Ephrin B1/EPHB1-2/RGS3 -0.011 0.134 -9999 0 -0.291 26 26
endothelial cell migration -0.11 0.228 0.337 1 -0.466 52 53
NCK2 0.035 0.017 -9999 0 -0.204 1 1
PTPN13 -0.19 0.271 -9999 0 -0.493 82 82
regulation of focal adhesion formation 0.012 0.132 0.295 24 -9999 0 24
chemotaxis 0.012 0.131 0.289 26 -9999 0 26
PIK3CA 0.035 0.006 -9999 0 -9999 0 0
Rac1/GTP -0.012 0.124 -9999 0 -0.291 19 19
angiogenesis -0.184 0.281 -9999 0 -0.6 63 63
LCK -0.246 0.369 -9999 0 -0.782 65 65
Wnt signaling

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
Noncanonical Wnts/FZD -0.118 0.207 -9999 0 -0.369 64 64
FZD6 0.021 0.065 -9999 0 -0.413 4 4
WNT6 0.031 0.033 -9999 0 -0.204 4 4
WNT4 -0.037 0.165 -9999 0 -0.374 36 36
FZD3 -0.038 0.159 -9999 0 -0.382 33 33
WNT5A -0.011 0.139 -9999 0 -0.386 23 23
WNT11 -0.068 0.185 -9999 0 -0.348 56 56
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.343 0.641 -9999 0 -1.377 43 43
STAT6 (cleaved dimer) -0.445 0.63 -9999 0 -1.348 56 56
IGHG1 -0.111 0.236 -9999 0 -0.517 12 12
IGHG3 -0.409 0.584 -9999 0 -1.24 56 56
AKT1 -0.187 0.361 -9999 0 -0.882 29 29
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.162 0.367 -9999 0 -1.071 21 21
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.216 0.412 -9999 0 -1.112 24 24
THY1 -0.43 0.624 -9999 0 -1.418 45 45
MYB 0 0.13 -9999 0 -0.483 14 14
HMGA1 0.036 0.004 -9999 0 -9999 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.239 0.4 -9999 0 -0.863 42 42
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.214 0.401 -9999 0 -0.998 28 28
SP1 0.023 0.048 -9999 0 -0.191 2 2
INPP5D 0 0 -9999 0 -9999 0 0
SOCS5 0.035 0.034 -9999 0 -9999 0 0
STAT6 (dimer)/ETS1 -0.426 0.642 -9999 0 -1.339 56 56
SOCS1 -0.251 0.387 -9999 0 -0.805 47 47
SOCS3 -0.224 0.385 -9999 0 -1.002 27 27
FCER2 -0.303 0.478 -9999 0 -1.075 35 35
PARP14 0.031 0.037 -9999 0 -0.203 5 5
CCL17 -0.462 0.655 -9999 0 -1.408 55 55
GRB2 0.034 0.008 -9999 0 -9999 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.15 0.281 -9999 0 -0.757 20 20
T cell proliferation -0.43 0.634 -9999 0 -1.365 53 53
IL4R/JAK1 -0.426 0.616 -9999 0 -1.328 53 53
EGR2 -0.502 0.695 -9999 0 -1.451 61 61
JAK2 -0.026 0.095 -9999 0 -0.317 11 11
JAK3 0.037 0.016 -9999 0 -9999 0 0
PIK3R1 0.028 0.062 -9999 0 -0.483 3 3
JAK1 0.014 0.047 -9999 0 -0.488 1 1
COL1A2 -0.189 0.438 -9999 0 -1.483 18 18
CCL26 -0.488 0.674 -9999 0 -1.406 62 62
IL4R -0.452 0.664 -9999 0 -1.423 53 53
PTPN6 0.037 0.026 -9999 0 -9999 0 0
IL13RA2 -0.54 0.714 -9999 0 -1.484 65 65
IL13RA1 -0.02 0.08 -9999 0 -0.329 5 5
IRF4 -0.098 0.332 -9999 0 -1.236 13 13
ARG1 -0.085 0.333 -9999 0 -1.327 10 10
CBL -0.229 0.375 -9999 0 -0.817 42 42
GTF3A -0.013 0.118 -9999 0 -0.405 14 14
PIK3CA 0.035 0.006 -9999 0 -9999 0 0
IL13RA1/JAK2 -0.025 0.106 -9999 0 -0.321 8 8
IRF4/BCL6 -0.098 0.315 -9999 0 -1.156 13 13
CD40LG 0.023 0.077 -9999 0 -0.329 7 7
MAPK14 -0.235 0.395 -9999 0 -0.926 35 35
mitosis -0.174 0.338 -9999 0 -0.815 29 29
STAT6 -0.522 0.815 -9999 0 -1.661 55 55
SPI1 0.016 0.075 -9999 0 -0.235 12 12
RPS6KB1 -0.162 0.328 -9999 0 -0.8 27 27
STAT6 (dimer) -0.523 0.818 -9999 0 -1.665 55 55
STAT6 (dimer)/PARP14 -0.466 0.692 -9999 0 -1.458 55 55
mast cell activation 0.007 0.016 -9999 0 -9999 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.238 0.408 -9999 0 -1.038 29 29
FRAP1 -0.187 0.362 -9999 0 -0.884 29 29
LTA -0.432 0.616 -9999 0 -1.314 55 55
FES 0.017 0.081 -9999 0 -0.315 10 10
T-helper 1 cell differentiation 0.487 0.733 1.53 55 -9999 0 55
CCL11 -0.497 0.686 -9999 0 -1.461 60 60
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.209 0.4 -9999 0 -0.983 30 30
IL2RG -0.019 0.156 -9999 0 -0.431 25 25
IL10 -0.419 0.614 -9999 0 -1.315 53 53
IRS1 0.013 0.098 -9999 0 -0.382 11 11
IRS2 -0.008 0.126 -9999 0 -0.446 15 15
IL4 -0.063 0.203 -9999 0 -1.19 3 3
IL5 -0.426 0.612 -9999 0 -1.343 50 50
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.302 0.471 -9999 0 -0.958 49 49
COL1A1 -0.287 0.557 -9999 0 -1.53 30 30
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -9999 0 0
IL4/IL4R/JAK1 -0.442 0.646 -9999 0 -1.466 46 46
IL2R gamma/JAK3 0.009 0.123 -9999 0 -0.343 21 21
TFF3 -0.453 0.651 -9999 0 -1.374 57 57
ALOX15 -0.428 0.62 -9999 0 -1.321 55 55
MYBL1 0.025 0.044 -9999 0 -0.297 3 3
T-helper 2 cell differentiation -0.333 0.52 -9999 0 -1.096 49 49
SHC1 0.035 0.007 -9999 0 -9999 0 0
CEBPB 0.013 0.045 -9999 0 -0.5 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.204 0.4 -9999 0 -1.044 25 25
mol:PI-3-4-5-P3 -0.186 0.362 -9999 0 -0.881 29 29
PI3K -0.203 0.396 -9999 0 -0.975 29 29
DOK2 0.011 0.066 -9999 0 -0.225 13 13
ETS1 0.027 0.057 -9999 0 -0.276 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.14 0.271 -9999 0 -0.721 21 21
ITGB3 -0.419 0.613 -9999 0 -1.315 53 53
PIGR -0.476 0.69 -9999 0 -1.471 57 57
IGHE 0.062 0.087 0.175 41 -0.324 1 42
MAPKKK cascade -0.137 0.267 -9999 0 -0.705 21 21
BCL6 0.007 0.104 -9999 0 -0.327 16 16
OPRM1 -0.43 0.62 -9999 0 -1.329 54 54
RETNLB -0.612 0.744 -9999 0 -1.455 82 82
SELP -0.496 0.708 -9999 0 -1.506 58 58
AICDA -0.421 0.6 -9999 0 -1.291 55 55
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 0.029 0.056 -9999 0 -0.343 4 4
LAT2 -0.08 0.163 -9999 0 -0.4 33 33
AP1 -0.129 0.244 0.328 1 -0.553 37 38
mol:PIP3 -0.111 0.238 0.438 3 -0.537 37 40
IKBKB -0.036 0.14 0.261 11 -0.276 31 42
AKT1 -0.111 0.171 0.309 7 -0.429 29 36
IKBKG -0.053 0.131 0.337 3 -0.277 35 38
MS4A2 -0.069 0.191 -9999 0 -0.376 52 52
mol:Sphingosine-1-phosphate 0 0 -9999 0 -9999 0 0
PIK3CA 0.035 0.006 -9999 0 -9999 0 0
MAP3K1 -0.076 0.184 0.33 2 -0.437 32 34
mol:Ca2+ -0.078 0.179 0.404 3 -0.392 36 39
LYN 0.028 0.015 -9999 0 -9999 0 0
CBLB -0.078 0.167 -9999 0 -0.4 34 34
SHC1 0.035 0.007 -9999 0 -9999 0 0
RasGAP/p62DOK 0.033 0.086 -9999 0 -0.262 11 11
positive regulation of cell migration -0.011 0.079 -9999 0 -0.346 10 10
INPP5D 0 0 -9999 0 -9999 0 0
PLD2 -0.113 0.186 0.323 6 -0.368 54 60
PTPN13 -0.139 0.216 -9999 0 -0.639 18 18
PTPN11 0.016 0.062 -9999 0 -0.417 3 3
GO:0007205 0 0 -9999 0 -9999 0 0
regulation of mast cell degranulation -0.07 0.144 0.317 4 -0.353 24 28
SYK 0.027 0.056 -9999 0 -0.405 3 3
GRB2 0.034 0.008 -9999 0 -9999 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.098 0.246 -9999 0 -0.531 40 40
LAT -0.081 0.171 0.192 1 -0.405 35 36
PAK2 -0.082 0.205 0.345 2 -0.48 33 35
NFATC2 -0.02 0.048 -9999 0 -9999 0 0
HRAS -0.093 0.222 0.36 2 -0.504 37 39
GAB2 0.036 0.004 -9999 0 -9999 0 0
PLA2G1B 0.029 0.122 -9999 0 -0.81 4 4
Fc epsilon R1 -0.107 0.214 -9999 0 -0.367 73 73
Antigen/IgE/Fc epsilon R1 -0.096 0.196 -9999 0 -0.334 73 73
mol:GDP -0.103 0.239 0.414 1 -0.543 38 39
JUN -0.017 0.15 -9999 0 -0.405 25 25
mol:Ca++ 0 0 -9999 0 -9999 0 0
PIK3R1 0.027 0.062 -9999 0 -0.487 3 3
FOS -0.063 0.171 -9999 0 -0.318 56 56
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.077 0.172 -9999 0 -0.404 35 35
CHUK -0.055 0.133 0.271 5 -0.277 37 42
KLRG1 -0.074 0.153 -9999 0 -0.392 28 28
VAV1 -0.097 0.188 -9999 0 -0.426 41 41
calcium-dependent protein kinase C activity 0 0 -9999 0 -9999 0 0
CBL -0.078 0.162 -9999 0 -0.391 34 34
negative regulation of mast cell degranulation -0.072 0.143 -9999 0 -0.362 29 29
BTK -0.103 0.252 -9999 0 -0.628 31 31
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.16 0.265 -9999 0 -0.519 59 59
GAB2/PI3K/SHP2 -0.122 0.17 -9999 0 -0.368 53 53
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.084 0.161 -9999 0 -0.328 51 51
RAF1 0.029 0.139 -9999 0 -0.931 4 4
Fc epsilon R1/FcgammaRIIB/SHIP -0.14 0.24 -9999 0 -0.398 79 79
FCER1G 0.027 0.06 -9999 0 -0.323 5 5
FCER1A -0.127 0.226 -9999 0 -0.404 76 76
Antigen/IgE/Fc epsilon R1/Fyn -0.095 0.209 -9999 0 -0.34 74 74
MAPK3 0.028 0.124 -9999 0 -0.823 4 4
MAPK1 0.025 0.126 -9999 0 -0.823 4 4
NFKB1 0.035 0.006 -9999 0 -9999 0 0
MAPK8 -0.106 0.272 -9999 0 -0.669 29 29
DUSP1 0 0.104 -9999 0 -0.259 25 25
NF-kappa-B/RelA -0.02 0.087 0.156 6 -0.18 23 29
actin cytoskeleton reorganization -0.062 0.189 -9999 0 -0.718 5 5
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -9999 0 0
PI3K -0.074 0.214 0.357 2 -0.48 34 36
FER -0.082 0.162 -9999 0 -0.398 34 34
RELA 0.035 0.004 -9999 0 -9999 0 0
ITK -0.023 0.088 -9999 0 -0.427 7 7
SOS1 0.036 0.002 -9999 0 -9999 0 0
PLCG1 -0.045 0.246 0.366 4 -0.515 33 37
cytokine secretion -0.022 0.054 -9999 0 -0.152 1 1
SPHK1 -0.103 0.194 -9999 0 -0.451 38 38
PTK2 -0.065 0.198 -9999 0 -0.77 5 5
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.1 0.261 -9999 0 -0.536 43 43
EDG1 -0.011 0.079 -9999 0 -0.347 10 10
mol:DAG -0.102 0.234 0.408 3 -0.525 37 40
MAP2K2 0.025 0.125 -9999 0 -0.83 4 4
MAP2K1 0.02 0.128 -9999 0 -0.868 4 4
MAP2K7 0.03 0.043 -9999 0 -0.297 3 3
KLRG1/SHP2 -0.063 0.148 -9999 0 -0.359 28 28
MAP2K4 -0.182 0.413 -9999 0 -0.9 50 50
Fc epsilon R1/FcgammaRIIB -0.148 0.254 -9999 0 -0.414 82 82
mol:Choline -0.112 0.183 0.321 6 -0.363 54 60
SHC/Grb2/SOS1 -0.035 0.179 -9999 0 -0.425 24 24
FYN 0.006 0.108 -9999 0 -0.343 16 16
DOK1 0.032 0.039 -9999 0 -0.343 2 2
PXN -0.06 0.185 -9999 0 -0.692 5 5
HCLS1 -0.085 0.181 -9999 0 -0.425 35 35
PRKCB -0.075 0.176 0.381 3 -0.387 36 39
FCGR2B -0.085 0.198 -9999 0 -0.369 61 61
IGHE -0.004 0.007 -9999 0 -9999 0 0
KLRG1/SHIP -0.073 0.145 -9999 0 -0.369 29 29
LCP2 -0.028 0.156 -9999 0 -0.371 32 32
PLA2G4A -0.16 0.199 -9999 0 -0.433 57 57
RASA1 0.024 0.073 -9999 0 -0.427 5 5
mol:Phosphatidic acid -0.112 0.183 0.321 6 -0.363 54 60
IKK complex -0.026 0.112 0.249 9 -0.222 22 31
WIPF1 0 0 -9999 0 -9999 0 0
Endothelins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.019 0.178 0.274 20 -0.413 13 33
PTK2B 0.028 0.015 -9999 0 -9999 0 0
mol:Ca2+ -0.062 0.242 -9999 0 -0.693 15 15
EDN1 -0.03 0.218 0.243 18 -0.447 35 53
EDN3 -0.098 0.197 -9999 0 -0.407 55 55
EDN2 -0.089 0.195 -9999 0 -0.343 68 68
HRAS/GDP -0.074 0.209 0.294 3 -0.452 30 33
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.055 0.162 0.265 1 -0.35 32 33
ADCY4 -0.036 0.154 0.352 1 -0.389 16 17
ADCY5 -0.022 0.14 0.352 1 -0.339 13 14
ADCY6 -0.02 0.139 0.352 1 -0.346 12 13
ADCY7 -0.025 0.143 0.352 1 -0.356 14 15
ADCY1 -0.018 0.135 0.352 1 -0.356 10 11
ADCY2 -0.021 0.139 0.352 1 -0.339 13 14
ADCY3 -0.033 0.153 0.352 1 -0.37 15 16
ADCY8 -0.024 0.126 -9999 0 -0.341 12 12
ADCY9 -0.024 0.142 0.352 1 -0.361 12 13
arachidonic acid secretion -0.169 0.267 -9999 0 -0.582 47 47
ETB receptor/Endothelin-1/Gq/GTP -0.053 0.151 -9999 0 -0.333 33 33
GNAO1 0.036 0.002 -9999 0 -9999 0 0
HRAS 0.031 0.04 -9999 0 -0.343 2 2
ETA receptor/Endothelin-1/G12/GTP 0.041 0.202 0.374 28 -0.389 11 39
ETA receptor/Endothelin-1/Gs/GTP 0.013 0.182 0.343 22 -0.354 13 35
mol:GTP -0.002 0.006 -9999 0 -9999 0 0
COL3A1 -0.033 0.218 -9999 0 -0.565 16 16
EDNRB -0.017 0.129 -9999 0 -0.429 16 16
response to oxidative stress 0 0 -9999 0 -9999 0 0
CYSLTR2 -0.003 0.174 0.377 8 -0.453 6 14
CYSLTR1 -0.025 0.202 -9999 0 -0.523 13 13
SLC9A1 -0.006 0.138 0.201 18 -0.402 9 27
mol:GDP -0.086 0.211 0.289 3 -0.451 34 37
SLC9A3 -0.099 0.317 -9999 0 -0.702 35 35
RAF1 -0.105 0.221 0.273 1 -0.51 32 33
JUN -0.113 0.346 -9999 0 -0.958 24 24
JAK2 -0.023 0.189 0.287 21 -0.418 18 39
mol:IP3 -0.064 0.177 0.277 2 -0.375 36 38
ETA receptor/Endothelin-1 0.026 0.251 0.429 30 -0.386 31 61
PLCB1 -0.037 0.161 -9999 0 -0.41 30 30
PLCB2 0.03 0.02 -9999 0 -0.211 1 1
ETA receptor/Endothelin-3 -0.062 0.165 -9999 0 -0.358 43 43
FOS -0.184 0.364 -9999 0 -0.939 35 35
Gai/GDP -0.007 0.195 -9999 0 -0.898 8 8
CRK 0.03 0.014 -9999 0 -9999 0 0
mol:Ca ++ -0.079 0.218 0.361 2 -0.462 34 36
BCAR1 0.034 0.017 -9999 0 -0.203 1 1
PRKCB1 -0.065 0.182 0.252 4 -0.391 33 37
GNAQ -0.002 0.008 -9999 0 -9999 0 0
GNAZ 0.022 0.064 -9999 0 -0.273 8 8
GNAL 0.022 0.035 -9999 0 -0.204 4 4
Gs family/GDP -0.077 0.192 0.267 2 -0.421 31 33
ETA receptor/Endothelin-1/Gq/GTP -0.038 0.155 0.215 6 -0.334 25 31
MAPK14 -0.067 0.153 -9999 0 -0.391 26 26
TRPC6 -0.067 0.255 -9999 0 -0.757 14 14
GNAI2 0.024 0.073 -9999 0 -0.427 5 5
GNAI3 0.03 0.051 -9999 0 -0.483 2 2
GNAI1 -0.013 0.142 -9999 0 -0.398 23 23
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.071 0.161 -9999 0 -0.349 38 38
ETB receptor/Endothelin-2 -0.064 0.165 -9999 0 -0.416 30 30
ETB receptor/Endothelin-3 -0.078 0.169 -9999 0 -0.398 39 39
ETB receptor/Endothelin-1 -0.035 0.187 -9999 0 -0.384 37 37
MAPK3 -0.161 0.323 0.337 1 -0.766 38 39
MAPK1 -0.165 0.326 0.337 1 -0.785 37 38
Rac1/GDP -0.074 0.201 0.294 3 -0.439 31 34
cAMP biosynthetic process -0.015 0.144 0.278 5 -0.366 12 17
MAPK8 -0.062 0.231 -9999 0 -0.543 24 24
SRC 0.011 0.063 -9999 0 -0.485 3 3
ETB receptor/Endothelin-1/Gi/GTP -0.035 0.144 0.182 2 -0.357 24 26
p130Cas/CRK/Src/PYK2 -0.065 0.238 0.35 5 -0.506 28 33
mol:K + 0 0 -9999 0 -9999 0 0
G12/GDP -0.072 0.202 0.294 3 -0.442 30 33
COL1A2 -0.033 0.278 0.381 8 -0.637 24 32
EntrezGene:2778 0 0 -9999 0 -9999 0 0
ETA receptor/Endothelin-2 -0.039 0.179 -9999 0 -0.361 38 38
mol:DAG -0.065 0.178 0.277 2 -0.376 36 38
MAP2K2 -0.127 0.257 0.393 1 -0.57 40 41
MAP2K1 -0.135 0.266 -9999 0 -0.586 41 41
EDNRA 0.035 0.129 0.242 18 -0.313 11 29
positive regulation of muscle contraction -0.001 0.16 0.248 23 -0.379 10 33
Gq family/GDP -0.079 0.19 -9999 0 -0.434 31 31
HRAS/GTP -0.083 0.198 0.25 4 -0.431 33 37
PRKCH -0.066 0.183 0.313 2 -0.384 36 38
RAC1 0.033 0.011 -9999 0 -9999 0 0
PRKCA -0.058 0.179 0.254 3 -0.395 30 33
PRKCB -0.06 0.176 0.243 3 -0.362 37 40
PRKCE -0.061 0.176 0.259 2 -0.387 31 33
PRKCD -0.059 0.175 0.259 2 -0.386 30 32
PRKCG -0.065 0.179 0.262 2 -0.39 32 34
regulation of vascular smooth muscle contraction -0.218 0.429 -9999 0 -1.114 35 35
PRKCQ -0.08 0.188 0.259 2 -0.384 40 42
PLA2G4A -0.186 0.296 -9999 0 -0.637 48 48
GNA14 -0.027 0.149 -9999 0 -0.371 29 29
GNA15 0.015 0.069 -9999 0 -0.264 10 10
GNA12 0.033 0.01 -9999 0 -9999 0 0
GNA11 0.023 0.056 -9999 0 -0.395 3 3
Rac1/GTP 0.039 0.202 0.374 28 -0.388 11 39
MMP1 -0.226 0.382 0.437 1 -0.883 49 50
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.155 0.375 -9999 0 -1.084 28 28
MKNK1 0.035 0.005 -9999 0 -9999 0 0
MAPK14 -0.035 0.122 -9999 0 -0.306 27 27
ATF2/c-Jun -0.08 0.197 -9999 0 -0.612 20 20
MAPK11 -0.034 0.12 -9999 0 -0.31 26 26
MITF -0.052 0.151 -9999 0 -0.374 31 31
MAPKAPK5 -0.041 0.132 -9999 0 -0.351 28 28
KRT8 -0.047 0.142 -9999 0 -0.362 30 30
MAPKAPK3 0.035 0.005 -9999 0 -9999 0 0
MAPKAPK2 0.035 0.006 -9999 0 -9999 0 0
p38alpha-beta/CK2 -0.051 0.173 -9999 0 -0.437 28 28
CEBPB -0.025 0.094 -9999 0 -0.346 13 13
SLC9A1 -0.042 0.135 -9999 0 -0.365 27 27
mol:GDP 0 0 -9999 0 -9999 0 0
ATF2 -0.048 0.141 -9999 0 -0.346 29 29
p38alpha-beta/MNK1 -0.023 0.15 -9999 0 -0.358 27 27
JUN -0.082 0.194 -9999 0 -0.608 20 20
PPARGC1A -0.083 0.176 -9999 0 -0.389 45 45
USF1 -0.062 0.154 -9999 0 -0.374 32 32
RAB5/GDP/GDI1 -0.027 0.105 -9999 0 -0.259 28 28
NOS2 -0.048 0.131 -9999 0 -0.358 28 28
DDIT3 -0.05 0.137 -9999 0 -0.35 31 31
RAB5A 0.035 0.005 -9999 0 -9999 0 0
HSPB1 -0.033 0.126 0.286 8 -0.29 30 38
p38alpha-beta/HBP1 -0.028 0.15 -9999 0 -0.355 28 28
CREB1 -0.046 0.14 -9999 0 -0.373 28 28
RAB5/GDP 0.026 0.004 -9999 0 -9999 0 0
EIF4E -0.044 0.117 -9999 0 -0.326 25 25
RPS6KA4 -0.041 0.132 -9999 0 -0.351 28 28
PLA2G4A -0.153 0.17 -9999 0 -0.353 72 72
GDI1 -0.041 0.132 -9999 0 -0.351 28 28
TP53 -0.1 0.169 -9999 0 -0.459 30 30
RPS6KA5 -0.053 0.142 -9999 0 -0.363 32 32
ESR1 -0.049 0.153 -9999 0 -0.384 30 30
HBP1 0.03 0.051 -9999 0 -0.483 2 2
MEF2C -0.064 0.154 -9999 0 -0.359 38 38
MEF2A -0.042 0.137 -9999 0 -0.374 26 26
EIF4EBP1 -0.055 0.151 -9999 0 -0.401 28 28
KRT19 -0.055 0.138 -9999 0 -0.339 35 35
ELK4 -0.044 0.132 -9999 0 -0.348 29 29
ATF6 -0.04 0.13 -9999 0 -0.352 27 27
ATF1 -0.047 0.14 -9999 0 -0.373 28 28
p38alpha-beta/MAPKAPK2 -0.024 0.149 -9999 0 -0.368 25 25
p38alpha-beta/MAPKAPK3 -0.024 0.15 -9999 0 -0.368 25 25
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.034 0.017 -9999 0 -0.204 1 1
CCL5 -0.04 0.163 -9999 0 -0.35 40 40
SDCBP 0.03 0.02 -9999 0 -0.204 1 1
FGFR/FGF2/Syndecan-1 -0.08 0.175 0.25 5 -0.355 36 41
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 -0.082 0.134 -9999 0 -0.39 19 19
Syndecan-1/Syntenin -0.068 0.163 0.342 1 -0.347 31 32
MAPK3 -0.077 0.161 0.321 1 -0.353 28 29
HGF/MET 0.042 0.057 -9999 0 -0.383 3 3
TGFB1/TGF beta receptor Type II 0.034 0.017 -9999 0 -0.203 1 1
BSG 0.035 0.007 -9999 0 -9999 0 0
keratinocyte migration -0.081 0.132 -9999 0 -0.384 19 19
Syndecan-1/RANTES -0.104 0.198 0.342 1 -0.384 47 48
Syndecan-1/CD147 -0.065 0.176 0.344 1 -0.346 33 34
Syndecan-1/Syntenin/PIP2 -0.067 0.157 0.32 1 -0.339 30 31
LAMA5 0.013 0.047 -9999 0 -0.273 4 4
positive regulation of cell-cell adhesion -0.066 0.154 0.314 1 -0.329 31 32
MMP7 -0.122 0.22 -9999 0 -0.389 77 77
HGF 0.03 0.043 -9999 0 -0.297 3 3
Syndecan-1/CASK -0.088 0.157 -9999 0 -0.329 40 40
Syndecan-1/HGF/MET -0.064 0.179 0.344 1 -0.354 32 33
regulation of cell adhesion -0.073 0.161 0.336 4 -0.389 18 22
HPSE -0.016 0.134 -9999 0 -0.315 30 30
positive regulation of cell migration -0.08 0.175 0.25 5 -0.355 36 41
SDC1 -0.074 0.17 -9999 0 -0.349 39 39
Syndecan-1/Collagen -0.08 0.175 0.25 5 -0.355 36 41
PPIB 0.028 0.046 -9999 0 -0.273 4 4
MET 0.027 0.056 -9999 0 -0.343 4 4
PRKACA 0.035 0.006 -9999 0 -9999 0 0
MMP9 -0.006 0.09 -9999 0 -0.297 15 15
MAPK1 -0.073 0.159 0.321 1 -0.351 26 27
homophilic cell adhesion -0.081 0.174 0.25 5 -0.358 35 40
MMP1 -0.134 0.211 -9999 0 -0.346 92 92
TCGA08_retinoblastoma

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
CDKN2B 0.004 0.084 -9999 0 -0.26 15 15
CDKN2C 0.036 0.055 -9999 0 -0.366 3 3
CDKN2A -0.03 0.15 -9999 0 -0.309 41 41
CCND2 0.003 0.08 0.177 20 -0.136 20 40
RB1 0.004 0.079 0.177 7 -0.2 15 22
CDK4 0.015 0.072 0.205 21 -9999 0 21
CDK6 0.012 0.074 0.202 20 -0.172 2 22
G1/S progression -0.005 0.089 0.197 17 -0.223 8 25
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.032 0.04 -9999 0 -0.343 2 2
EGFR 0.016 0.09 -9999 0 -0.413 8 8
EGF/EGFR -0.082 0.149 -9999 0 -0.286 57 57
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.002 0.135 -9999 0 -0.258 32 32
mol:GTP 0 0 -9999 0 -9999 0 0
EDNRA 0.009 0.091 -9999 0 -0.266 18 18
response to oxidative stress 0 0 -9999 0 -9999 0 0
EGF -0.088 0.187 -9999 0 -0.32 72 72
EGF/EGFR dimer/SHC -0.029 0.136 -9999 0 -0.295 33 33
mol:GDP -0.007 0.13 -9999 0 -0.255 32 32
mol:Ca2+ 0 0 -9999 0 -9999 0 0
EDN1 -0.061 0.183 -9999 0 -0.357 51 51
GRB2/SOS1 0.051 0.012 -9999 0 -9999 0 0
HRAS/GTP -0.02 0.114 -9999 0 -0.239 33 33
SHC1 0.035 0.007 -9999 0 -9999 0 0
HRAS/GDP -0.008 0.126 -9999 0 -0.245 33 33
FRAP1 -0.03 0.12 0.299 3 -0.254 30 33
EGF/EGFR dimer -0.054 0.148 -9999 0 -0.346 34 34
SOS1 0.036 0.002 -9999 0 -9999 0 0
GRB2 0.034 0.008 -9999 0 -9999 0 0
ETA receptor/Endothelin-1 -0.043 0.149 -9999 0 -0.346 33 33
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 0.018 0.018 -9999 0 -9999 0 0
GNB1/GNG2 -0.091 0.207 -9999 0 -0.475 31 31
mol:DAG -0.079 0.163 -9999 0 -0.467 23 23
PLCG1 -0.082 0.17 -9999 0 -0.485 23 23
YES1 -0.104 0.196 -9999 0 -0.476 32 32
FZD3 -0.038 0.159 -9999 0 -0.382 33 33
FZD6 0.021 0.065 -9999 0 -0.413 4 4
G protein -0.032 0.216 0.287 5 -0.488 24 29
MAP3K7 -0.074 0.138 0.232 1 -0.435 18 19
mol:Ca2+ -0.077 0.158 -9999 0 -0.451 23 23
mol:IP3 -0.079 0.163 -9999 0 -0.467 23 23
NLK -0.012 0.203 -9999 0 -0.789 13 13
GNB1 0.034 0.008 -9999 0 -9999 0 0
CAMK2A -0.075 0.148 -9999 0 -0.451 20 20
MAP3K7IP1 0.034 0.009 -9999 0 -9999 0 0
Noncanonical Wnts/FZD -0.118 0.207 -9999 0 -0.369 64 64
CSNK1A1 0.035 0.006 -9999 0 -9999 0 0
GNAS -0.082 0.192 -9999 0 -0.488 28 28
GO:0007205 -0.08 0.161 -9999 0 -0.474 22 22
WNT6 0.031 0.033 -9999 0 -0.204 4 4
WNT4 -0.037 0.165 -9999 0 -0.374 36 36
NFAT1/CK1 alpha -0.076 0.174 -9999 0 -0.516 20 20
GNG2 0.033 0.01 -9999 0 -9999 0 0
WNT5A -0.011 0.139 -9999 0 -0.386 23 23
WNT11 -0.068 0.185 -9999 0 -0.348 56 56
CDC42 -0.1 0.187 -9999 0 -0.488 28 28
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.012 0.124 -9999 0 -0.33 18 18
fibroblast growth factor receptor signaling pathway 0.011 0.123 -9999 0 -0.329 18 18
LAMA1 0.026 0.016 -9999 0 -9999 0 0
PRNP 0.014 0.081 -9999 0 -0.437 6 6
GPC1/SLIT2 -0.04 0.165 -9999 0 -0.384 32 32
SMAD2 -0.002 0.065 -9999 0 -0.265 10 10
GPC1/PrPc/Cu2+ 0.014 0.078 -9999 0 -0.292 10 10
GPC1/Laminin alpha1 0.018 0.078 -9999 0 -0.34 7 7
TDGF1 -0.065 0.203 -9999 0 -0.463 42 42
CRIPTO/GPC1 -0.048 0.168 -9999 0 -0.353 46 46
APP/GPC1 0.011 0.105 -9999 0 -0.349 13 13
mol:NO 0 0 -9999 0 -9999 0 0
YES1 -0.059 0.131 -9999 0 -0.296 47 47
FLT1 0.009 0.076 -9999 0 -0.28 11 11
GPC1/TGFB/TGFBR1/TGFBR2 0.044 0.084 -9999 0 -0.296 9 9
SERPINC1 0.025 0.06 -9999 0 -0.297 6 6
FYN -0.072 0.148 -9999 0 -0.313 53 53
FGR -0.059 0.139 -9999 0 -0.312 46 46
positive regulation of MAPKKK cascade -0.042 0.213 0.274 7 -0.406 39 46
SLIT2 -0.059 0.18 -9999 0 -0.355 50 50
GPC1/NRG 0.016 0.088 -9999 0 -0.344 9 9
NRG1 0.023 0.054 -9999 0 -0.39 3 3
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.014 0.073 -9999 0 -0.324 6 6
LYN -0.05 0.129 -9999 0 -0.301 42 42
mol:Spermine -0.008 0.069 -9999 0 -0.347 7 7
cell growth 0.011 0.123 -9999 0 -0.329 18 18
BMP signaling pathway -0.008 0.103 0.334 15 -9999 0 15
SRC -0.052 0.126 -9999 0 -0.313 37 37
TGFBR1 0.031 0.04 -9999 0 -0.343 2 2
mol:Cu2+ 0 0 -9999 0 -9999 0 0
PLA2G2A -0.129 0.222 -9999 0 -0.397 78 78
GPC1 0.008 0.103 -9999 0 -0.334 15 15
TGFBR1 (dimer) 0.031 0.04 -9999 0 -0.343 2 2
VEGFA 0 0 -9999 0 -9999 0 0
BLK -0.069 0.141 -9999 0 -0.309 50 50
HCK -0.066 0.139 -9999 0 -0.32 45 45
FGF2 -0.003 0.115 -9999 0 -0.297 24 24
FGFR1 0.022 0.06 -9999 0 -0.297 6 6
VEGFR1 homodimer 0.009 0.076 -9999 0 -0.279 11 11
TGFBR2 0.03 0.051 -9999 0 -0.483 2 2
cell death 0.011 0.105 -9999 0 -0.349 13 13
ATIII/GPC1 0.022 0.091 -9999 0 -0.349 9 9
PLA2G2A/GPC1 -0.099 0.183 -9999 0 -0.361 61 61
LCK -0.082 0.154 -9999 0 -0.319 57 57
neuron differentiation 0.016 0.088 -9999 0 -0.343 9 9
PrPc/Cu2+ 0.011 0.058 -9999 0 -0.311 6 6
APP 0.013 0.093 -9999 0 -0.356 11 11
TGFBR2 (dimer) 0.03 0.051 -9999 0 -0.482 2 2
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.025 0.121 -9999 0 -0.368 12 12
TBX21 -0.265 0.509 -9999 0 -1.296 35 35
B2M 0.016 0.087 -9999 0 -0.345 10 10
TYK2 0.012 0.038 -9999 0 -9999 0 0
IL12RB1 0.011 0.042 -9999 0 -0.226 1 1
GADD45B -0.177 0.376 -9999 0 -1.093 22 22
IL12RB2 -0.005 0.087 -9999 0 -0.275 14 14
GADD45G -0.185 0.38 -9999 0 -1.05 25 25
natural killer cell activation -0.008 0.02 -9999 0 -0.044 26 26
RELB 0.033 0.036 -9999 0 -0.483 1 1
RELA 0.035 0.004 -9999 0 -9999 0 0
IL18 -0.023 0.157 -9999 0 -0.422 26 26
IL2RA -0.039 0.164 -9999 0 -0.35 40 40
IFNG -0.107 0.199 -9999 0 -0.333 80 80
STAT3 (dimer) -0.165 0.339 -9999 0 -0.79 37 37
HLA-DRB5 -0.034 0.15 -9999 0 -0.461 22 22
FASLG -0.226 0.456 -9999 0 -1.233 28 28
NF kappa B2 p52/RelB -0.182 0.39 -9999 0 -0.888 38 38
CD4 0.028 0.018 -9999 0 -9999 0 0
SOCS1 0.027 0.064 -9999 0 -0.413 4 4
EntrezGene:6955 -0.003 0.008 -9999 0 -0.026 16 16
CD3D -0.009 0.128 -9999 0 -0.387 19 19
CD3E 0.028 0.026 -9999 0 -0.214 1 1
CD3G -0.032 0.152 -9999 0 -0.354 33 33
IL12Rbeta2/JAK2 -0.003 0.101 -9999 0 -0.37 8 8
CCL3 -0.213 0.43 -9999 0 -1.086 32 32
CCL4 -0.223 0.45 -9999 0 -1.121 33 33
HLA-A 0 0.122 -9999 0 -0.386 17 17
IL18/IL18R -0.051 0.194 -9999 0 -0.351 51 51
NOS2 -0.19 0.373 -9999 0 -0.846 39 39
IL12/IL12R/TYK2/JAK2/SPHK2 -0.028 0.119 -9999 0 -0.365 11 11
IL1R1 -0.2 0.394 -9999 0 -1.034 29 29
IL4 0.039 0.046 -9999 0 -0.335 2 2
JAK2 -0.004 0.085 -9999 0 -0.291 12 12
EntrezGene:6957 -0.002 0.008 -9999 0 -0.025 15 15
TCR/CD3/MHC I/CD8 -0.054 0.203 -9999 0 -0.65 15 15
RAB7A -0.153 0.304 -9999 0 -0.737 32 32
lysosomal transport -0.145 0.288 -9999 0 -0.686 33 33
FOS -0.327 0.556 -9999 0 -1.285 47 47
STAT4 (dimer) -0.17 0.368 -9999 0 -0.873 33 33
STAT5A (dimer) -0.23 0.412 -9999 0 -0.873 47 47
GZMA -0.192 0.375 -9999 0 -0.856 40 40
GZMB -0.276 0.514 -9999 0 -1.234 41 41
HLX 0 0 -9999 0 -9999 0 0
LCK -0.227 0.436 -9999 0 -0.986 40 40
TCR/CD3/MHC II/CD4 -0.089 0.228 -9999 0 -0.503 36 36
IL2/IL2R -0.012 0.176 -9999 0 -0.356 35 35
MAPK14 -0.194 0.391 -9999 0 -0.983 30 30
CCR5 -0.176 0.348 -9999 0 -0.782 39 39
IL1B -0.077 0.189 -9999 0 -0.399 47 47
STAT6 -0.053 0.172 -9999 0 -0.737 7 7
STAT4 0.02 0.079 -9999 0 -0.328 9 9
STAT3 0.034 0.007 -9999 0 -9999 0 0
STAT1 0.015 0.067 -9999 0 -0.204 18 18
NFKB1 0.035 0.006 -9999 0 -9999 0 0
NFKB2 0.033 0.018 -9999 0 -0.204 1 1
IL12B 0.006 0.068 -9999 0 -0.325 5 5
CD8A 0.001 0.004 -9999 0 -0.025 2 2
CD8B 0 0.005 -9999 0 -0.039 2 2
T-helper 1 cell differentiation 0 0 -9999 0 -9999 0 0
natural killer cell mediated cytotoxicity 0.024 0.12 0.365 12 -9999 0 12
IL2RB 0.018 0.084 -9999 0 -0.378 8 8
proteasomal ubiquitin-dependent protein catabolic process -0.153 0.331 -9999 0 -0.78 33 33
IL2RG -0.021 0.158 -9999 0 -0.438 25 25
IL12 -0.02 0.117 -9999 0 -0.337 17 17
STAT5A 0.027 0.049 -9999 0 -0.259 5 5
CD247 -0.002 0.008 -9999 0 -0.023 15 15
IL2 0.035 0.005 -9999 0 -9999 0 0
SPHK2 0.021 0.081 -9999 0 -0.437 6 6
FRAP1 0.031 0.037 -9999 0 -0.483 1 1
IL12A -0.033 0.134 -9999 0 -0.341 27 27
IL12/IL12R/TYK2/JAK2 -0.227 0.469 -9999 0 -1.029 40 40
MAP2K3 -0.211 0.411 -9999 0 -1.005 32 32
RIPK2 0.022 0.063 -9999 0 -0.483 3 3
MAP2K6 -0.196 0.402 -9999 0 -0.994 31 31
regulation of dendritic cell antigen processing and presentation 0 0 -9999 0 -9999 0 0
HLA-DRA -0.036 0.16 -9999 0 -0.389 32 32
IL18RAP -0.063 0.187 -9999 0 -0.372 50 50
IL12Rbeta1/TYK2 0.021 0.054 -9999 0 -9999 0 0
EOMES -0.001 0.181 -9999 0 -1.272 3 3
STAT1 (dimer) -0.221 0.377 -9999 0 -0.844 44 44
T cell proliferation -0.135 0.268 -9999 0 -0.602 37 37
T-helper 1 cell lineage commitment 0 0 -9999 0 -9999 0 0
IL18R1 0.007 0.098 -9999 0 -0.286 18 18
CD8-positive alpha-beta T cell lineage commitment 0 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelA -0.147 0.305 -9999 0 -0.709 31 31
ATF2 -0.177 0.351 -9999 0 -0.881 30 30
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.083 0.143 -9999 0 -0.386 12 12
NF kappa B1 p50/RelA/I kappa B alpha -0.084 0.151 0.33 2 -0.417 12 14
alphaV/beta3 Integrin/Osteopontin/Src -0.117 0.179 -9999 0 -0.356 64 64
AP1 -0.149 0.18 -9999 0 -0.444 28 28
ILK -0.092 0.136 -9999 0 -0.371 9 9
bone resorption -0.093 0.134 -9999 0 -0.353 13 13
PTK2B 0.028 0.015 -9999 0 -9999 0 0
PYK2/p130Cas -0.067 0.149 -9999 0 -0.344 11 11
ITGAV 0.02 0.083 -9999 0 -0.403 7 7
mol:GTP 0 0 -9999 0 -9999 0 0
CD44/Rho Family GTPase/ROCK2 0.026 0.098 -9999 0 -0.349 13 13
alphaV/beta3 Integrin/Osteopontin -0.087 0.164 -9999 0 -0.299 64 64
MAP3K1 -0.095 0.138 -9999 0 -0.278 60 60
JUN -0.017 0.15 -9999 0 -0.405 25 25
MAPK3 -0.101 0.133 -9999 0 -0.41 10 10
MAPK1 -0.096 0.132 -9999 0 -0.396 11 11
Rac1/GDP 0.024 0.008 -9999 0 -9999 0 0
NFKB1 0.035 0.006 -9999 0 -9999 0 0
MAPK8 -0.094 0.126 -9999 0 -0.348 12 12
ITGB3 0.032 0.024 -9999 0 -0.212 1 1
NFKBIA -0.101 0.143 0.339 1 -0.392 18 19
FOS -0.063 0.171 -9999 0 -0.319 56 56
CD44 0.03 0.051 -9999 0 -0.483 2 2
CHUK 0.027 0.062 -9999 0 -0.483 3 3
PLAU -0.153 0.303 -9999 0 -1.142 15 15
NF kappa B1 p50/RelA -0.084 0.163 -9999 0 -0.437 15 15
BCAR1 0.034 0.017 -9999 0 -0.204 1 1
RELA 0.035 0.004 -9999 0 -9999 0 0
alphaV beta3 Integrin 0.04 0.064 -9999 0 -0.344 4 4
mol:GDP 0 0 -9999 0 -9999 0 0
SYK -0.095 0.139 -9999 0 -0.277 64 64
VAV3 -0.145 0.155 -9999 0 -0.363 41 41
MAP3K14 -0.093 0.136 -9999 0 -0.277 57 57
ROCK2 0.007 0.117 -9999 0 -0.46 12 12
SPP1 -0.172 0.219 -9999 0 -0.43 75 75
RAC1 0.033 0.011 -9999 0 -9999 0 0
Rac1/GTP -0.124 0.145 -9999 0 -0.344 35 35
MMP2 -0.147 0.161 -9999 0 -0.424 29 29
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 -0.015 0.117 -9999 0 -0.397 16 16
GNB1/GNG2 -0.064 0.079 -9999 0 -0.182 55 55
AKT1 -0.06 0.135 0.284 3 -0.304 18 21
EGF -0.088 0.187 -9999 0 -0.32 72 72
mol:TXA2 0 0.001 -9999 0 -9999 0 0
FGR -0.019 0.081 0.304 3 -0.24 2 5
mol:Ca2+ -0.081 0.164 0.282 3 -0.315 41 44
LYN -0.016 0.072 0.324 2 -0.24 2 4
RhoA/GTP -0.034 0.068 -9999 0 -0.146 6 6
mol:PGI2 0 0 -9999 0 -9999 0 0
SYK -0.094 0.179 0.29 2 -0.348 52 54
GNG2 0.033 0.01 -9999 0 -9999 0 0
ARRB2 0.027 0.038 -9999 0 -0.483 1 1
TP alpha/Gq family/GDP/G beta5/gamma2 -0.052 0.163 -9999 0 -0.462 22 22
G beta5/gamma2 -0.082 0.104 -9999 0 -0.246 45 45
PRKCH -0.098 0.187 0.295 1 -0.367 53 54
DNM1 0.029 0.037 -9999 0 -0.204 5 5
TXA2/TP beta/beta Arrestin3 0.019 0.023 -9999 0 -9999 0 0
mol:GTP 0 0.001 -9999 0 -9999 0 0
PTGDR -0.057 0.16 -9999 0 -0.292 57 57
G12 family/GTP -0.089 0.148 -9999 0 -0.307 50 50
ADRBK1 0.036 0.004 -9999 0 -9999 0 0
ADRBK2 0.029 0.043 -9999 0 -0.297 3 3
RhoA/GTP/ROCK1 0.036 0.021 -9999 0 -9999 0 0
mol:GDP 0.051 0.132 0.337 17 -0.289 2 19
mol:NADP 0.029 0.053 -9999 0 -0.39 3 3
RAB11A 0.03 0.04 -9999 0 -0.343 2 2
PRKG1 0.034 0.007 -9999 0 -9999 0 0
mol:IP3 -0.105 0.2 0.319 1 -0.394 43 44
cell morphogenesis 0.036 0.02 -9999 0 -9999 0 0
PLCB2 -0.155 0.259 -9999 0 -0.524 54 54
mol:cGMP 0 0.001 -9999 0 -9999 0 0
BLK -0.025 0.086 0.279 4 -0.256 4 8
mol:PDG2 0 0 -9999 0 -9999 0 0
HCK -0.023 0.077 0.263 1 -0.29 9 10
RHOA 0.035 0.004 -9999 0 -9999 0 0
PTGIR 0.034 0.017 -9999 0 -0.204 1 1
PRKCB1 -0.108 0.2 0.335 1 -0.39 54 55
GNAQ 0 0 -9999 0 -9999 0 0
mol:L-citrulline 0.029 0.053 -9999 0 -0.39 3 3
TXA2/TXA2-R family -0.149 0.262 -9999 0 -0.532 55 55
LCK -0.038 0.098 0.284 3 -0.27 13 16
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.002 0.083 -9999 0 -0.289 1 1
TXA2-R family/G12 family/GDP/G beta/gamma 0 0.115 -9999 0 -0.449 11 11
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.005 0.081 -9999 0 -0.277 1 1
MAPK14 -0.06 0.125 0.231 3 -0.241 28 31
TGM2/GTP -0.128 0.204 -9999 0 -0.475 23 23
MAPK11 -0.061 0.123 0.229 3 -0.238 32 35
ARHGEF1 -0.042 0.101 0.213 5 -0.192 20 25
GNAI2 0.024 0.073 -9999 0 -0.427 5 5
JNK cascade -0.105 0.199 0.312 2 -0.39 54 56
RAB11/GDP 0.031 0.04 -9999 0 -0.338 2 2
ICAM1 -0.076 0.153 0.262 2 -0.291 51 53
cAMP biosynthetic process -0.1 0.186 0.31 2 -0.376 34 36
Gq family/GTP/EBP50 -0.007 0.073 -9999 0 -0.214 20 20
actin cytoskeleton reorganization 0.036 0.02 -9999 0 -9999 0 0
SRC -0.013 0.055 0.263 1 -0.247 1 2
GNB5 -0.004 0.126 -9999 0 -0.38 19 19
GNB1 0.034 0.008 -9999 0 -9999 0 0
EGF/EGFR -0.023 0.127 0.38 4 -0.288 14 18
VCAM1 -0.079 0.158 0.277 1 -0.304 53 54
TP beta/Gq family/GDP/G beta5/gamma2 -0.052 0.163 -9999 0 -0.462 22 22
platelet activation -0.079 0.166 0.317 3 -0.311 39 42
PGI2/IP 0.025 0.012 -9999 0 -0.134 1 1
PRKACA -0.016 0.078 -9999 0 -0.25 17 17
Gq family/GDP/G beta5/gamma2 -0.049 0.151 -9999 0 -0.416 23 23
TXA2/TP beta/beta Arrestin2 -0.009 0.063 -9999 0 -0.326 2 2
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -9999 0 0
TBXA2R -0.022 0.068 -9999 0 -0.229 16 16
mol:DAG -0.117 0.218 -9999 0 -0.429 54 54
EGFR 0.016 0.09 -9999 0 -0.413 8 8
TXA2/TP alpha -0.138 0.249 -9999 0 -0.51 39 39
Gq family/GTP -0.019 0.081 -9999 0 -0.24 22 22
YES1 -0.015 0.075 0.283 3 -0.24 2 5
GNAI2/GTP -0.016 0.079 -9999 0 -0.218 15 15
PGD2/DP -0.039 0.113 -9999 0 -0.2 58 58
SLC9A3R1 0.025 0.064 -9999 0 -0.413 4 4
FYN -0.029 0.096 0.279 4 -0.305 8 12
mol:NO 0.029 0.053 -9999 0 -0.39 3 3
GNA15 0.02 0.068 -9999 0 -0.259 10 10
PGK/cGMP 0.041 0.037 -9999 0 -0.296 2 2
RhoA/GDP 0.036 0.005 -9999 0 -9999 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.008 0.087 0.286 1 -0.306 4 5
NOS3 0.029 0.053 -9999 0 -0.391 3 3
RAC1 0.033 0.011 -9999 0 -9999 0 0
PRKCA -0.092 0.186 0.325 2 -0.357 53 55
PRKCB -0.095 0.185 0.285 1 -0.357 56 57
PRKCE -0.096 0.186 0.286 1 -0.361 53 54
PRKCD -0.104 0.194 0.296 1 -0.382 56 57
PRKCG -0.106 0.2 0.306 3 -0.391 54 57
muscle contraction -0.139 0.245 -9999 0 -0.494 54 54
PRKCZ -0.092 0.178 0.291 2 -0.345 54 56
ARR3 0.036 0 -9999 0 -9999 0 0
TXA2/TP beta -0.002 0.085 -9999 0 -0.225 12 12
PRKCQ -0.109 0.191 0.376 1 -0.37 57 58
MAPKKK cascade -0.129 0.233 -9999 0 -0.462 54 54
SELE -0.105 0.19 0.277 1 -0.386 55 56
TP beta/GNAI2/GDP/G beta/gamma 0.01 0.097 0.286 1 -0.279 2 3
ROCK1 0.028 0.015 -9999 0 -9999 0 0
GNA14 -0.021 0.149 -9999 0 -0.367 29 29
chemotaxis -0.171 0.294 -9999 0 -0.618 53 53
GNA12 0.033 0.01 -9999 0 -9999 0 0
GNA13 0.034 0.009 -9999 0 -9999 0 0
GNA11 0.028 0.054 -9999 0 -0.39 3 3
Rac1/GTP 0.023 0.008 -9999 0 -9999 0 0
IL27-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 0.034 0.017 -9999 0 -0.204 1 1
CD4-positive alpha-beta T cell lineage commitment 0 0 -9999 0 -9999 0 0
cytokine production during immune response 0.125 0.211 0.609 22 -9999 0 22
IL27/IL27R/JAK1 -0.144 0.33 -9999 0 -1.144 16 16
TBX21 -0.188 0.249 0.378 1 -0.57 48 49
IL12B 0.018 0.06 -9999 0 -0.317 5 5
IL12A -0.027 0.088 -9999 0 -0.231 27 27
IL6ST 0.017 0.028 -9999 0 -9999 0 0
IL27RA/JAK1 -0.098 0.339 -9999 0 -1.296 15 15
IL27 -0.098 0.201 -9999 0 -0.411 55 55
TYK2 0.013 0.031 -9999 0 -9999 0 0
T-helper cell lineage commitment -0.041 0.125 0.198 15 -0.268 39 54
T-helper 2 cell differentiation 0.125 0.211 0.609 22 -9999 0 22
T cell proliferation during immune response 0.125 0.211 0.609 22 -9999 0 22
MAPKKK cascade -0.125 0.211 -9999 0 -0.609 22 22
STAT3 0.034 0.007 -9999 0 -9999 0 0
STAT2 0.032 0.04 -9999 0 -0.343 2 2
STAT1 0.014 0.068 -9999 0 -0.207 18 18
IL12RB1 0.032 0.018 -9999 0 -0.206 1 1
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -9999 0 -9999 0 0
IL12RB2 -0.17 0.232 0.344 2 -0.563 37 39
IL27/IL27R/JAK2/TYK2 -0.126 0.214 -9999 0 -0.619 22 22
positive regulation of T cell mediated cytotoxicity -0.125 0.211 -9999 0 -0.609 22 22
STAT1 (dimer) -0.186 0.348 0.518 1 -0.792 35 36
JAK2 -0.002 0.081 -9999 0 -0.285 12 12
JAK1 0.032 0.036 -9999 0 -0.482 1 1
STAT2 (dimer) -0.114 0.212 -9999 0 -0.593 22 22
T cell proliferation -0.177 0.227 -9999 0 -0.552 38 38
IL12/IL12R/TYK2/JAK2 -0.061 0.199 -9999 0 -0.864 7 7
IL17A -0.042 0.124 0.199 14 -0.268 39 53
mast cell activation 0.125 0.211 0.609 22 -9999 0 22
IFNG -0.033 0.056 -9999 0 -0.126 42 42
T cell differentiation -0.01 0.01 -9999 0 -0.024 56 56
STAT3 (dimer) -0.107 0.21 -9999 0 -0.588 21 21
STAT5A (dimer) -0.11 0.213 -9999 0 -0.602 21 21
STAT4 (dimer) -0.118 0.219 -9999 0 -0.608 23 23
STAT4 0.02 0.079 -9999 0 -0.328 9 9
T cell activation 0.001 0.034 0.121 15 -9999 0 15
IL27R/JAK2/TYK2 -0.1 0.33 -9999 0 -1.178 16 16
GATA3 0.015 0.151 0.565 1 -1.393 2 3
IL18 -0.031 0.106 -9999 0 -0.299 26 26
positive regulation of mast cell cytokine production -0.105 0.205 -9999 0 -0.574 21 21
IL27/EBI3 -0.062 0.152 -9999 0 -0.359 38 38
IL27RA -0.113 0.356 -9999 0 -1.38 15 15
IL6 -0.117 0.203 -9999 0 -0.343 82 82
STAT5A 0.027 0.049 -9999 0 -0.259 5 5
monocyte differentiation -0.002 0.003 -9999 0 -9999 0 0
IL2 0.036 0.122 0.465 15 -9999 0 15
IL1B -0.055 0.126 -9999 0 -0.271 47 47
EBI3 0.017 0.027 -9999 0 -9999 0 0
TNF -0.001 0.043 -9999 0 -0.182 9 9
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.031 0.034 -9999 0 -0.222 2 2
NFATC2 -0.046 0.17 -9999 0 -0.529 14 14
NFATC3 -0.048 0.113 -9999 0 -0.333 13 13
CD40LG -0.315 0.39 -9999 0 -0.842 53 53
ITCH 0.006 0.059 -9999 0 -9999 0 0
CBLB 0.017 0.082 -9999 0 -0.511 2 2
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.252 0.373 -9999 0 -1.073 27 27
JUNB 0.015 0.081 -9999 0 -0.263 14 14
CaM/Ca2+/Calcineurin A alpha-beta B1 0.025 0.083 -9999 0 -0.269 13 13
T cell anergy 0.019 0.115 -9999 0 -0.382 10 10
TLE4 -0.037 0.143 -9999 0 -0.557 9 9
Jun/NFAT1-c-4/p21SNFT -0.22 0.318 -9999 0 -0.843 28 28
AP-1/NFAT1-c-4 -0.365 0.436 -9999 0 -0.975 51 51
IKZF1 -0.033 0.113 -9999 0 -0.365 14 14
T-helper 2 cell differentiation -0.086 0.196 -9999 0 -0.687 8 8
AP-1/NFAT1 -0.098 0.181 -9999 0 -0.446 29 29
CALM1 0.028 0.055 -9999 0 -9999 0 0
EGR2 -0.239 0.487 -9999 0 -1.361 29 29
EGR3 -0.228 0.44 -9999 0 -1.205 29 29
NFAT1/FOXP3 -0.023 0.129 -9999 0 -0.447 8 8
EGR1 -0.053 0.167 -9999 0 -0.313 53 53
JUN -0.052 0.153 -9999 0 -0.428 25 25
EGR4 0.001 0.002 -9999 0 -9999 0 0
mol:Ca2+ 0 0.044 -9999 0 -9999 0 0
GBP3 -0.077 0.231 -9999 0 -0.738 20 20
FOSL1 0.029 0.04 -9999 0 -0.203 6 6
NFAT1-c-4/MAF/IRF4 -0.179 0.325 -9999 0 -0.891 25 25
DGKA -0.035 0.13 -9999 0 -0.488 8 8
CREM 0.031 0.04 -9999 0 -0.344 2 2
NFAT1-c-4/PPARG -0.193 0.32 -9999 0 -0.866 26 26
CTLA4 -0.002 0.135 -9999 0 -0.416 8 8
NFAT1-c-4 (dimer)/EGR1 -0.202 0.33 -9999 0 -0.865 29 29
NFAT1-c-4 (dimer)/EGR4 -0.175 0.304 -9999 0 -0.874 23 23
FOS -0.096 0.168 -9999 0 -0.337 56 56
IFNG -0.336 0.536 -9999 0 -1.21 50 50
T cell activation -0.1 0.216 -9999 0 -0.664 9 9
MAF -0.004 0.125 -9999 0 -0.343 22 22
T-helper 2 cell lineage commitment 0 0 -9999 0 -9999 0 0
activation-induced cell death of T cells 0.174 0.285 0.735 34 -9999 0 34
TNF -0.18 0.312 -9999 0 -0.808 28 28
FASLG -0.355 0.613 -9999 0 -1.456 42 42
TBX21 -0.082 0.18 -9999 0 -0.354 52 52
BATF3 0 0 -9999 0 -9999 0 0
PRKCQ -0.022 0.14 -9999 0 -0.377 24 24
PTPN1 -0.033 0.126 -9999 0 -0.483 8 8
NFAT1-c-4/ICER1 -0.174 0.309 -9999 0 -0.883 23 23
GATA3 0.031 0.054 -9999 0 -0.389 3 3
T-helper 1 cell differentiation -0.323 0.51 -9999 0 -1.144 51 51
IL2RA -0.258 0.376 -9999 0 -0.998 32 32
T-helper 1 cell lineage commitment 0 0 -9999 0 -9999 0 0
CASP3 -0.034 0.128 -9999 0 -0.496 8 8
E2F1 0.017 0.053 -9999 0 -0.479 2 2
PPARG -0.021 0.158 -9999 0 -0.448 24 24
SLC3A2 -0.034 0.128 -9999 0 -0.546 6 6
IRF4 0.006 0.108 -9999 0 -0.343 16 16
PTGS2 -0.351 0.415 -9999 0 -0.868 60 60
CSF2 -0.348 0.418 -9999 0 -0.877 60 60
JunB/Fra1/NFAT1-c-4 -0.167 0.301 -9999 0 -0.859 22 22
IL4 -0.09 0.203 -9999 0 -0.718 8 8
IL5 -0.316 0.387 -9999 0 -0.848 51 51
IL2 -0.101 0.219 -9999 0 -0.675 9 9
IL3 -0.044 0.15 -9999 0 -0.765 7 7
RNF128 -0.005 0.147 -9999 0 -0.576 12 12
NFATC1 -0.174 0.286 -9999 0 -0.744 33 33
CDK4 0.09 0.172 0.605 4 -9999 0 4
PTPRK -0.039 0.144 -9999 0 -0.593 8 8
IL8 -0.378 0.429 -9999 0 -0.905 62 62
POU2F1 0.032 0.067 -9999 0 -0.369 5 5
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.026 0.004 -9999 0 -9999 0 0
PRKCZ 0 0 -9999 0 -9999 0 0
MAP3K7IP2 0.035 0.006 -9999 0 -9999 0 0
ERC1 0 0 -9999 0 -9999 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.033 0.092 -9999 0 -0.252 12 12
IRAK/TOLLIP 0.04 0.018 -9999 0 -0.166 1 1
IKBKB 0.031 0.012 -9999 0 -9999 0 0
IKBKG 0.035 0.017 -9999 0 -0.204 1 1
IL1 alpha/IL1R2 -0.118 0.19 -9999 0 -0.368 64 64
IL1A -0.08 0.184 -9999 0 -0.319 68 68
IL1B -0.122 0.185 -9999 0 -0.385 61 61
IRAK/TRAF6/p62/Atypical PKCs 0.063 0.043 -9999 0 -0.239 2 2
IL1R2 -0.079 0.193 -9999 0 -0.355 61 61
IL1R1 0.016 0.081 -9999 0 -0.263 14 14
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.02 0.087 -9999 0 -0.306 2 2
TOLLIP 0.036 0.002 -9999 0 -9999 0 0
TICAM2 0 0 -9999 0 -9999 0 0
MAP3K3 0.034 0.009 -9999 0 -9999 0 0
TAK1/TAB1/TAB2 0.066 0.032 -9999 0 -0.298 1 1
IKK complex/ELKS 0.023 0.066 -9999 0 -0.354 2 2
JUN -0.044 0.079 -9999 0 -0.432 2 2
MAP3K7 0.033 0.036 -9999 0 -0.483 1 1
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.06 0.179 -9999 0 -0.299 63 63
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.006 0.143 -9999 0 -0.27 36 36
PIK3R1 0.028 0.062 -9999 0 -0.483 3 3
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.004 0.145 -9999 0 -0.265 33 33
IL1 beta fragment/IL1R1/IL1RAP -0.084 0.178 -9999 0 -0.321 65 65
NFKB1 0.035 0.006 -9999 0 -9999 0 0
MAPK8 -0.022 0.049 -9999 0 -9999 0 0
IRAK1 0.018 0.017 -9999 0 -0.183 1 1
IL1RN/IL1R1 -0.02 0.141 -9999 0 -0.345 26 26
IRAK4 0.033 0.036 -9999 0 -0.483 1 1
PRKCI 0.028 0.056 -9999 0 -0.343 4 4
TRAF6 0.036 0.004 -9999 0 -9999 0 0
PI3K 0.045 0.049 -9999 0 -0.349 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.039 0.105 -9999 0 -0.305 12 12
CHUK 0.027 0.062 -9999 0 -0.483 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.084 0.178 -9999 0 -0.321 65 65
IL1 beta/IL1R2 -0.153 0.216 -9999 0 -0.373 87 87
IRAK/TRAF6/TAK1/TAB1/TAB2 0.082 0.039 -9999 0 -0.241 1 1
NF kappa B1 p50/RelA -0.064 0.162 -9999 0 -0.377 21 21
IRAK3 -0.012 0.129 -9999 0 -0.313 28 28
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.069 0.17 -9999 0 -0.299 62 62
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.016 0.101 -9999 0 -0.238 30 30
IL1 alpha/IL1R1/IL1RAP -0.025 0.144 -9999 0 -0.296 36 36
RELA 0.035 0.004 -9999 0 -9999 0 0
MAP3K7IP1 0.034 0.009 -9999 0 -9999 0 0
SQSTM1 0.034 0.017 -9999 0 -0.204 1 1
MYD88 0.036 0.004 -9999 0 -9999 0 0
IRAK/TRAF6/MEKK3 0.057 0.025 -9999 0 -9999 0 0
IL1RAP 0.031 0.033 -9999 0 -0.204 4 4
UBE2N 0.035 0.005 -9999 0 -9999 0 0
IRAK/TRAF6 -0.075 0.142 -9999 0 -0.27 59 59
CASP1 -0.085 0.198 -9999 0 -0.366 62 62
IL1RN/IL1R2 -0.086 0.196 -9999 0 -0.374 56 56
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.068 0.178 -9999 0 -0.312 61 61
TMEM189-UBE2V1 0 0 -9999 0 -9999 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.002 0.093 -9999 0 -0.373 5 5
PIK3CA 0.035 0.006 -9999 0 -9999 0 0
IL1RN -0.042 0.159 -9999 0 -0.311 47 47
TRAF6/TAK1/TAB1/TAB2 0.08 0.035 -9999 0 -0.247 1 1
MAP2K6 0.001 0.057 -9999 0 -0.241 10 10
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.119 0.365 -9999 0 -0.99 20 20
PCK1 -0.248 0.549 -9999 0 -1.361 37 37
HNF4A -0.083 0.427 0.583 7 -1.179 18 25
KCNJ11 -0.096 0.363 -9999 0 -0.939 20 20
AKT1 -0.045 0.215 -9999 0 -0.518 19 19
response to starvation -0.006 0.036 -9999 0 -0.148 9 9
DLK1 -0.105 0.403 -9999 0 -1.05 22 22
NKX2-1 0.04 0.205 0.424 26 -0.4 7 33
ACADM -0.119 0.383 0.581 1 -0.977 23 24
TAT -0.076 0.243 -9999 0 -0.707 13 13
CEBPB 0.013 0.041 -9999 0 -0.478 1 1
CEBPA 0.007 0.096 -9999 0 -0.379 10 10
TTR -0.205 0.495 0.586 2 -1.171 35 37
PKLR -0.125 0.386 -9999 0 -1.035 22 22
APOA1 -0.125 0.543 -9999 0 -1.341 26 26
CPT1C -0.124 0.385 -9999 0 -0.998 23 23
ALAS1 -0.03 0.185 -9999 0 -0.774 1 1
TFRC -0.119 0.383 -9999 0 -0.954 24 24
FOXF1 0 0.128 -9999 0 -0.431 16 16
NF1 0.04 0.011 -9999 0 -9999 0 0
HNF1A (dimer) 0.002 0.033 -9999 0 -0.152 7 7
CPT1A -0.12 0.375 -9999 0 -0.936 25 25
HMGCS1 -0.124 0.38 0.581 1 -0.968 23 24
NR3C1 0.02 0.094 -9999 0 -0.404 8 8
CPT1B -0.116 0.363 -9999 0 -0.958 21 21
chromatin remodeling 0 0 -9999 0 -9999 0 0
SP1 0.034 0.017 -9999 0 -0.204 1 1
GCK -0.108 0.376 -9999 0 -0.961 22 22
CREB1 -0.008 0.09 -9999 0 -0.219 23 23
IGFBP1 -0.064 0.256 -9999 0 -0.817 11 11
PDX1 -0.03 0.181 -9999 0 -0.383 18 18
UCP2 -0.139 0.391 -9999 0 -0.968 26 26
ALDOB -0.209 0.489 -9999 0 -1.025 45 45
AFP -0.141 0.274 -9999 0 -0.907 18 18
BDH1 -0.127 0.4 -9999 0 -1.011 25 25
HADH -0.094 0.356 -9999 0 -0.882 22 22
F2 -0.083 0.47 -9999 0 -1.3 16 16
HNF1A 0.002 0.033 -9999 0 -0.151 7 7
G6PC 0.005 0.191 -9999 0 -0.938 4 4
SLC2A2 -0.07 0.31 -9999 0 -1.134 9 9
INS 0.025 0.029 0.219 1 -9999 0 1
FOXA1 -0.12 0.228 -9999 0 -0.458 60 60
FOXA3 -0.049 0.178 -9999 0 -0.42 27 27
FOXA2 -0.1 0.414 -9999 0 -1 22 22
ABCC8 -0.103 0.363 -9999 0 -0.955 19 19
ALB -0.116 0.209 -9999 0 -0.696 14 14
Glucocorticoid receptor regulatory network

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
PCK2 0.062 0.117 -9999 0 -0.738 2 2
SMARCC2 0.035 0.004 -9999 0 -9999 0 0
SMARCC1 0.035 0.005 -9999 0 -9999 0 0
TBX21 -0.153 0.259 -9999 0 -0.76 26 26
SUMO2 0.031 0.017 -9999 0 -9999 0 0
STAT1 (dimer) 0.005 0.101 -9999 0 -0.261 25 25
FKBP4 0.032 0.037 -9999 0 -0.483 1 1
FKBP5 0.026 0.066 -9999 0 -0.371 5 5
GR alpha/HSP90/FKBP51/HSP90 0.098 0.104 0.274 27 -0.226 2 29
PRL -0.05 0.101 -9999 0 -9999 0 0
cortisol/GR alpha (dimer)/TIF2 0.17 0.223 0.531 40 -9999 0 40
RELA -0.084 0.115 -9999 0 -0.266 34 34
FGG 0.14 0.197 0.462 33 -0.515 2 35
GR beta/TIF2 0.093 0.116 0.31 23 -0.34 1 24
IFNG -0.348 0.445 -9999 0 -1.101 47 47
apoptosis -0.015 0.233 0.622 4 -0.576 16 20
CREB1 0.041 0.042 -9999 0 -0.381 2 2
histone acetylation -0.076 0.122 -9999 0 -0.348 18 18
BGLAP -0.064 0.118 -9999 0 -9999 0 0
GR/PKAc 0.091 0.148 0.327 15 -0.259 13 28
NF kappa B1 p50/RelA -0.155 0.219 -9999 0 -0.43 60 60
SMARCD1 0.035 0.005 -9999 0 -9999 0 0
MDM2 0.078 0.086 0.225 36 -9999 0 36
GATA3 0.036 0.058 -9999 0 -0.382 3 3
AKT1 0.025 0.035 0.235 2 -0.211 2 4
CSF2 -0.234 0.427 -9999 0 -1.304 27 27
GSK3B 0.03 0.039 -9999 0 -0.483 1 1
NR1I3 -0.002 0.21 0.632 4 -0.555 8 12
CSN2 0.119 0.155 0.377 32 -9999 0 32
BRG1/BAF155/BAF170/BAF60A 0.083 0.039 -9999 0 -0.272 1 1
NFATC1 0.007 0.067 -9999 0 -0.33 1 1
POU2F1 0.031 0.068 -9999 0 -0.377 5 5
CDKN1A -0.097 0.281 -9999 0 -1.672 5 5
response to stress 0 0 -9999 0 -9999 0 0
response to UV -0.001 0.007 -9999 0 -9999 0 0
SFN 0.02 0.071 -9999 0 -0.308 8 8
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.103 0.105 0.291 21 -0.228 3 24
prolactin receptor activity 0 0 -9999 0 -9999 0 0
EGR1 -0.072 0.315 0.565 4 -0.776 28 32
JUN -0.157 0.195 -9999 0 -0.473 40 40
IL4 -0.065 0.141 -9999 0 -0.658 5 5
CDK5R1 0.034 0.008 -9999 0 -9999 0 0
PRKACA 0.035 0.006 -9999 0 -9999 0 0
cortisol/GR alpha (monomer)/AP-1 -0.072 0.178 0.205 33 -0.337 42 75
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.116 0.099 0.288 24 -0.215 1 25
cortisol/GR alpha (monomer) 0.212 0.262 0.633 41 -9999 0 41
NCOA2 0.025 0.052 -9999 0 -0.483 2 2
response to hypoxia 0 0 -9999 0 -9999 0 0
FOS -0.102 0.175 -9999 0 -0.37 52 52
AP-1/NFAT1-c-4 -0.246 0.261 -9999 0 -0.591 54 54
AFP -0.191 0.382 -9999 0 -1.575 13 13
SUV420H1 0.036 0.004 -9999 0 -9999 0 0
IRF1 0.079 0.209 0.454 7 -0.728 7 14
TP53 -0.046 0.195 -9999 0 -0.496 31 31
PPP5C 0.034 0.017 -9999 0 -0.204 1 1
KRT17 -0.207 0.269 -9999 0 -0.761 23 23
KRT14 -0.069 0.128 -9999 0 -9999 0 0
TBP 0.042 0.018 -9999 0 -9999 0 0
CREBBP 0.036 0.043 -9999 0 -0.442 1 1
HDAC1 0.032 0.014 -9999 0 -9999 0 0
HDAC2 0.042 0.045 -9999 0 -0.484 1 1
AP-1 -0.248 0.263 -9999 0 -0.595 54 54
MAPK14 0.034 0.01 -9999 0 -9999 0 0
MAPK10 0.009 0.101 -9999 0 -0.356 13 13
MAPK11 0.028 0.024 -9999 0 -0.203 1 1
KRT5 -0.209 0.276 -9999 0 -0.81 22 22
interleukin-1 receptor activity 0.01 0.025 -9999 0 -9999 0 0
NCOA1 0.027 0.073 -9999 0 -0.479 4 4
STAT1 0.005 0.101 -9999 0 -0.261 25 25
CGA -0.077 0.158 -9999 0 -1.141 2 2
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.084 0.185 0.479 27 -0.389 1 28
MAPK3 0.022 0.074 -9999 0 -0.433 5 5
MAPK1 0.033 0.012 -9999 0 -9999 0 0
ICAM1 -0.215 0.285 -9999 0 -0.699 36 36
NFKB1 -0.082 0.116 -9999 0 -0.275 29 29
MAPK8 -0.11 0.152 -9999 0 -0.382 33 33
MAPK9 0.031 0.038 -9999 0 -0.493 1 1
cortisol/GR alpha (dimer) -0.016 0.24 0.626 4 -0.606 16 20
BAX -0.068 0.184 -9999 0 -1.806 1 1
POMC -0.111 0.229 -9999 0 -1.649 3 3
EP300 0.023 0.096 -9999 0 -0.445 7 7
cortisol/GR alpha (dimer)/p53 0.112 0.252 0.566 28 -0.468 1 29
proteasomal ubiquitin-dependent protein catabolic process 0.049 0.085 0.269 13 -9999 0 13
SGK1 0.035 0.089 0.234 5 -0.243 8 13
IL13 -0.151 0.189 -9999 0 -0.657 10 10
IL6 -0.351 0.479 -9999 0 -1.099 53 53
PRKACG 0.035 0.006 -9999 0 -9999 0 0
IL5 -0.134 0.162 -9999 0 -0.806 1 1
IL2 -0.192 0.226 -9999 0 -0.628 28 28
CDK5 0.034 0.006 -9999 0 -9999 0 0
PRKACB -0.032 0.166 -9999 0 -0.411 31 31
HSP90AA1 0 0 -9999 0 -9999 0 0
IL8 -0.389 0.499 -9999 0 -1.085 62 62
CDK5R1/CDK5 0.049 0.014 -9999 0 -9999 0 0
NF kappa B1 p50/RelA/PKAc -0.115 0.209 -9999 0 -0.411 46 46
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.18 0.209 0.514 40 -9999 0 40
SMARCA4 0.03 0.043 -9999 0 -0.297 3 3
chromatin remodeling 0.124 0.133 0.347 37 -9999 0 37
NF kappa B1 p50/RelA/Cbp -0.108 0.189 0.331 1 -0.428 32 33
JUN (dimer) -0.157 0.194 -9999 0 -0.472 40 40
YWHAH 0.031 0.037 -9999 0 -0.483 1 1
VIPR1 -0.131 0.243 -9999 0 -0.764 22 22
NR3C1 0.133 0.164 0.411 36 -9999 0 36
NR4A1 0.014 0.087 -9999 0 -0.417 4 4
TIF2/SUV420H1 0.04 0.044 -9999 0 -0.349 2 2
MAPKKK cascade -0.015 0.233 0.622 4 -0.576 16 20
cortisol/GR alpha (dimer)/Src-1 0.199 0.228 0.555 40 -9999 0 40
PBX1 0.021 0.097 -9999 0 -0.416 9 9
POU1F1 0.039 0.037 -9999 0 -0.478 1 1
SELE -0.375 0.483 -9999 0 -1.065 59 59
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.124 0.134 0.348 37 -9999 0 37
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.18 0.209 0.514 40 -9999 0 40
mol:cortisol 0.118 0.157 0.357 47 -9999 0 47
MMP1 -0.349 0.512 -9999 0 -1.225 51 51
Glypican 2 network

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
MDK -0.01 0.131 -9999 0 -0.338 25 25
GPC2 0 0 -9999 0 -9999 0 0
GPC2/Midkine -0.005 0.093 -9999 0 -0.236 25 25
neuron projection morphogenesis -0.005 0.093 -9999 0 -0.235 25 25
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.021 0.047 -9999 0 -0.159 2 2
NFATC2 -0.008 0.028 -9999 0 -9999 0 0
NFATC3 -0.021 0.051 -9999 0 -0.35 1 1
CD40LG -0.151 0.27 -9999 0 -0.547 48 48
PTGS2 -0.189 0.298 -9999 0 -0.572 61 61
JUNB 0.015 0.081 -9999 0 -0.263 14 14
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.005 0.035 -9999 0 -9999 0 0
CaM/Ca2+ -0.005 0.035 -9999 0 -9999 0 0
CALM1 0.013 0.031 -9999 0 -9999 0 0
JUN -0.037 0.149 -9999 0 -0.414 25 25
mol:Ca2+ -0.011 0.014 -9999 0 -9999 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.012 0.026 -9999 0 -0.288 1 1
FOSL1 0.029 0.04 -9999 0 -0.204 6 6
CREM 0.031 0.04 -9999 0 -0.344 2 2
Jun/NFAT1-c-4/p21SNFT -0.069 0.143 -9999 0 -0.374 23 23
FOS -0.08 0.169 -9999 0 -0.327 56 56
IFNG -0.199 0.314 -9999 0 -0.619 59 59
AP-1/NFAT1-c-4 -0.177 0.313 -9999 0 -0.631 49 49
FASLG -0.168 0.29 -9999 0 -0.601 48 48
NFAT1-c-4/ICER1 -0.025 0.083 -9999 0 -0.379 1 1
IL2RA -0.173 0.304 -9999 0 -0.605 53 53
FKBP12/FK506 0.019 0.028 -9999 0 -0.347 1 1
CSF2 -0.185 0.3 -9999 0 -0.603 53 53
JunB/Fra1/NFAT1-c-4 -0.004 0.114 -9999 0 -0.368 2 2
IL4 -0.149 0.264 -9999 0 -0.538 47 47
IL2 0 0.136 -9999 0 -0.956 4 4
IL3 0 0.156 -9999 0 -0.76 8 8
FKBP1A 0.026 0.038 -9999 0 -0.483 1 1
BATF3 0 0 -9999 0 -9999 0 0
mol:FK506 0 0 -9999 0 -9999 0 0
POU2F1 0.032 0.067 -9999 0 -0.369 5 5
FAS signaling pathway (CD95)

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
SPTAN1 0.004 0.066 0.225 8 -0.282 2 10
RFC1 0.003 0.064 0.226 7 -0.282 2 9
PRKDC 0.018 0.079 0.218 20 -0.282 2 22
RIPK1 0.038 0.006 -9999 0 -9999 0 0
CASP7 -0.038 0.152 -9999 0 -0.615 11 11
FASLG/FAS/FADD/FAF1 0.01 0.137 0.21 33 -0.291 19 52
MAP2K4 -0.107 0.189 -9999 0 -0.45 33 33
mol:ceramide -0.076 0.159 -9999 0 -0.436 24 24
GSN -0.002 0.077 0.224 9 -0.267 5 14
FASLG/FAS/FADD/FAF1/Caspase 8 -0.008 0.142 -9999 0 -0.389 13 13
FAS -0.048 0.167 -9999 0 -0.405 34 34
BID -0.024 0.049 0.268 2 -0.343 3 5
MAP3K1 -0.048 0.14 0.252 2 -0.473 10 12
MAP3K7 0.03 0.036 -9999 0 -0.483 1 1
RB1 0.035 0.108 0.26 31 -0.31 1 32
CFLAR 0.038 0.007 -9999 0 -9999 0 0
HGF/MET -0.075 0.164 -9999 0 -0.302 63 63
ARHGDIB -0.006 0.071 0.222 6 -0.269 6 12
FADD 0.023 0.025 -9999 0 -9999 0 0
actin filament polymerization 0.002 0.077 0.282 4 -0.224 9 13
NFKB1 -0.055 0.154 -9999 0 -0.743 6 6
MAPK8 -0.148 0.236 -9999 0 -0.517 51 51
DFFA 0.004 0.065 0.226 7 -0.255 3 10
DNA fragmentation during apoptosis 0.003 0.063 0.23 6 -0.281 2 8
FAS/FADD/MET 0.005 0.125 -9999 0 -0.314 23 23
CFLAR/RIP1 0.057 0.012 -9999 0 -9999 0 0
FAIM3 0.028 0.058 -9999 0 -0.315 5 5
FAF1 0.021 0.027 -9999 0 -9999 0 0
PARP1 0.001 0.062 0.231 6 -0.255 3 9
DFFB 0.003 0.064 0.231 6 -0.282 2 8
CHUK -0.054 0.144 -9999 0 -0.697 6 6
FASLG -0.041 0.145 -9999 0 -0.321 37 37
FAS/FADD -0.021 0.131 -9999 0 -0.356 24 24
HGF 0.03 0.043 -9999 0 -0.297 3 3
LMNA -0.003 0.068 0.248 2 -0.261 5 7
CASP6 0.001 0.07 0.226 7 -0.279 4 11
CASP10 0.013 0.064 -9999 0 -0.305 6 6
CASP3 0.005 0.072 0.257 9 -0.247 6 15
PTPN13 -0.16 0.229 -9999 0 -0.387 96 96
CASP8 -0.026 0.057 0.355 2 -0.367 3 5
IL6 -0.311 0.553 -9999 0 -1.305 48 48
MET 0.027 0.056 -9999 0 -0.343 4 4
ICAD/CAD -0.003 0.053 0.199 5 -0.265 2 7
FASLG/FAS/FADD/FAF1/Caspase 10 -0.077 0.161 -9999 0 -0.442 24 24
activation of caspase activity by cytochrome c -0.023 0.049 0.268 2 -0.342 3 5
PAK2 0.006 0.071 0.229 10 -0.285 2 12
BCL2 -0.002 0.098 -9999 0 -0.308 16 16
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.024 0.153 0.243 3 -0.42 17 20
FYN -0.064 0.192 0.379 1 -0.526 21 22
LAT/GRAP2/SLP76 -0.056 0.184 -9999 0 -0.43 28 28
IKBKB 0.031 0.012 -9999 0 -9999 0 0
AKT1 -0.062 0.148 0.241 3 -0.37 28 31
B2M 0.014 0.088 -9999 0 -0.349 10 10
IKBKG -0.019 0.05 0.132 2 -0.142 7 9
MAP3K8 0.005 0.106 -9999 0 -0.312 18 18
mol:Ca2+ -0.011 0.021 0.09 3 -0.058 13 16
integrin-mediated signaling pathway 0.036 0.048 -9999 0 -0.294 3 3
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.084 0.209 0.385 1 -0.52 28 29
TRPV6 0.024 0.22 1.177 7 -9999 0 7
CD28 -0.001 0.121 -9999 0 -0.346 20 20
SHC1 -0.052 0.173 0.242 3 -0.442 24 27
receptor internalization -0.053 0.181 0.177 1 -0.505 22 23
PRF1 -0.065 0.225 -9999 0 -0.783 13 13
KRAS 0.033 0.018 -9999 0 -0.204 1 1
GRB2 0.034 0.008 -9999 0 -9999 0 0
COT/AKT1 -0.051 0.132 0.234 3 -0.308 29 32
LAT -0.059 0.178 0.241 1 -0.442 26 27
EntrezGene:6955 -0.001 0.003 -9999 0 -0.012 5 5
CD3D -0.004 0.128 -9999 0 -0.385 19 19
CD3E 0.033 0.019 -9999 0 -0.21 1 1
CD3G -0.026 0.152 -9999 0 -0.351 33 33
RASGRP2 0.002 0.033 -9999 0 -0.174 5 5
RASGRP1 -0.037 0.157 0.295 3 -0.396 21 24
HLA-A -0.001 0.122 -9999 0 -0.389 17 17
RASSF5 0.022 0.071 -9999 0 -0.308 8 8
RAP1A/GTP/RAPL 0.036 0.048 -9999 0 -0.295 3 3
mol:GTP 0 0 -9999 0 -9999 0 0
mol:GDP 0.01 0.062 0.191 4 -0.125 11 15
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.042 0.07 -9999 0 -0.193 25 25
PRKCA 0 0.113 0.192 7 -0.259 16 23
GRAP2 0.019 0.083 -9999 0 -0.403 7 7
mol:IP3 -0.052 0.127 -9999 0 -0.367 21 21
EntrezGene:6957 -0.001 0.004 0.01 1 -0.01 12 13
TCR/CD3/MHC I/CD8 -0.044 0.157 -9999 0 -0.359 29 29
ORAI1 -0.022 0.188 0.361 3 -0.992 7 10
CSK -0.053 0.171 0.248 1 -0.438 24 25
B7 family/CD28 -0.062 0.228 -9999 0 -0.53 26 26
CHUK 0.027 0.062 -9999 0 -0.483 3 3
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.064 0.196 -9999 0 -0.474 27 27
PTPN6 -0.062 0.175 -9999 0 -0.441 25 25
VAV1 -0.07 0.199 0.301 3 -0.476 29 32
Monovalent TCR/CD3 -0.033 0.152 -9999 0 -0.455 20 20
CBL 0.035 0.005 -9999 0 -9999 0 0
LCK -0.07 0.206 0.356 1 -0.512 26 27
PAG1 -0.047 0.175 -9999 0 -0.428 26 26
RAP1A 0.034 0.008 -9999 0 -9999 0 0
TCR/CD3/MHC I/CD8/LCK -0.064 0.199 0.258 1 -0.468 28 29
CD80 0.026 0.047 -9999 0 -0.206 8 8
CD86 -0.048 0.177 -9999 0 -0.379 42 42
PDK1/CARD11/BCL10/MALT1 -0.044 0.088 -9999 0 -0.232 25 25
HRAS 0.032 0.04 -9999 0 -0.343 2 2
GO:0035030 -0.078 0.173 -9999 0 -0.442 26 26
CD8A -0.001 0.004 0.01 1 -0.009 17 18
CD8B -0.001 0.004 0.012 1 -0.01 21 22
PTPRC -0.026 0.154 -9999 0 -0.369 31 31
PDK1/PKC theta -0.068 0.175 0.305 2 -0.44 26 28
CSK/PAG1 -0.044 0.168 -9999 0 -0.427 23 23
SOS1 0.036 0.002 -9999 0 -9999 0 0
peptide-MHC class I 0.007 0.119 -9999 0 -0.371 16 16
GRAP2/SLP76 -0.059 0.208 -9999 0 -0.445 33 33
STIM1 0.012 0.145 1.181 3 -9999 0 3
RAS family/GTP 0.006 0.076 0.211 3 -0.177 7 10
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.055 0.192 0.179 1 -0.534 22 23
mol:DAG -0.054 0.11 -9999 0 -0.312 24 24
RAP1A/GDP 0.008 0.031 0.106 3 -0.064 4 7
PLCG1 0.019 0.018 -9999 0 -9999 0 0
CD247 -0.001 0.003 -9999 0 -0.012 5 5
cytotoxic T cell degranulation -0.062 0.214 -9999 0 -0.721 14 14
RAP1A/GTP 0.002 0.013 -9999 0 -0.065 5 5
mol:PI-3-4-5-P3 -0.069 0.173 0.262 3 -0.427 28 31
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.064 0.164 -9999 0 -0.481 20 20
NRAS 0.019 0.079 -9999 0 -0.328 9 9
ZAP70 0.03 0.053 -9999 0 -0.391 3 3
GRB2/SOS1 0.051 0.012 -9999 0 -9999 0 0
LAT/GRAP2/SLP76/VAV1 -0.066 0.186 0.234 2 -0.456 27 29
MALT1 0.021 0.039 -9999 0 -0.483 1 1
TRAF6 0.036 0.004 -9999 0 -9999 0 0
CD8 heterodimer -0.001 0.006 0.021 1 -0.014 16 17
CARD11 -0.013 0.1 -9999 0 -0.219 37 37
PRKCB -0.041 0.076 -9999 0 -0.213 26 26
PRKCE 0.003 0.114 0.196 9 -0.257 16 25
PRKCQ -0.074 0.199 0.287 3 -0.496 27 30
LCP2 -0.027 0.156 -9999 0 -0.37 32 32
BCL10 0.033 0.036 -9999 0 -0.483 1 1
regulation of survival gene product expression -0.052 0.129 0.232 3 -0.315 28 31
IKK complex 0.019 0.068 0.147 19 -0.107 8 27
RAS family/GDP -0.005 0.014 -9999 0 -0.056 6 6
MAP3K14 -0.041 0.1 0.197 3 -0.24 26 29
PDPK1 -0.056 0.139 0.238 3 -0.35 26 29
TCR/CD3/MHC I/CD8/Fyn -0.055 0.18 -9999 0 -0.486 22 22
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.05 0.148 -9999 0 -0.417 22 22
CRKL -0.053 0.154 -9999 0 -0.432 24 24
HRAS -0.035 0.155 -9999 0 -0.404 22 22
mol:PIP3 -0.049 0.153 -9999 0 -0.399 25 25
SPRED1 0.014 0.1 -9999 0 -0.483 8 8
SPRED2 0.031 0.051 -9999 0 -0.483 2 2
GAB1 -0.055 0.16 -9999 0 -0.451 24 24
FOXO3 -0.071 0.189 -9999 0 -0.439 33 33
AKT1 -0.078 0.204 -9999 0 -0.476 33 33
BAD -0.074 0.189 -9999 0 -0.46 29 29
megakaryocyte differentiation -0.099 0.181 -9999 0 -0.457 31 31
GSK3B -0.073 0.186 -9999 0 -0.462 27 27
RAF1 -0.029 0.128 0.249 1 -0.333 21 22
SHC1 0.035 0.007 -9999 0 -9999 0 0
STAT3 -0.05 0.152 -9999 0 -0.443 21 21
STAT1 -0.139 0.374 -9999 0 -1.067 25 25
HRAS/SPRED1 -0.026 0.145 -9999 0 -0.355 22 22
cell proliferation -0.049 0.152 -9999 0 -0.436 23 23
PIK3CA 0.035 0.006 -9999 0 -9999 0 0
TEC 0.035 0.006 -9999 0 -9999 0 0
RPS6KB1 -0.056 0.174 -9999 0 -0.446 28 28
HRAS/SPRED2 -0.02 0.14 -9999 0 -0.363 16 16
LYN/TEC/p62DOK -0.018 0.166 -9999 0 -0.419 22 22
MAPK3 -0.018 0.102 0.266 2 -0.289 12 14
STAP1 -0.051 0.158 -9999 0 -0.446 24 24
GRAP2 0.019 0.083 -9999 0 -0.403 7 7
JAK2 -0.105 0.307 -9999 0 -0.878 24 24
STAT1 (dimer) -0.133 0.367 -9999 0 -1.039 25 25
mol:Gleevec 0.002 0.007 -9999 0 -9999 0 0
GRB2/SOCS1/VAV1 -0.033 0.191 -9999 0 -0.487 23 23
actin filament polymerization -0.05 0.155 -9999 0 -0.437 24 24
LYN 0.03 0.013 -9999 0 -9999 0 0
STAP1/STAT5A (dimer) -0.074 0.222 -9999 0 -0.621 25 25
PIK3R1 0.028 0.062 -9999 0 -0.484 3 3
CBL/CRKL/GRB2 -0.024 0.157 -9999 0 -0.408 21 21
PI3K -0.031 0.178 -9999 0 -0.425 25 25
PTEN 0.026 0.062 -9999 0 -0.483 3 3
SCF/KIT/EPO/EPOR -0.132 0.444 -9999 0 -1.326 23 23
MAPK8 -0.05 0.155 -9999 0 -0.445 23 23
STAT3 (dimer) -0.049 0.149 -9999 0 -0.434 21 21
positive regulation of transcription -0.013 0.086 0.249 2 -0.241 10 12
mol:GDP -0.037 0.166 -9999 0 -0.438 21 21
PIK3C2B -0.054 0.16 -9999 0 -0.45 24 24
CBL/CRKL -0.038 0.157 -9999 0 -0.416 23 23
FER -0.058 0.159 -9999 0 -0.453 24 24
SH2B3 -0.051 0.158 -9999 0 -0.446 24 24
PDPK1 -0.045 0.141 -9999 0 -0.364 25 25
SNAI2 -0.062 0.166 -9999 0 -0.46 25 25
positive regulation of cell proliferation -0.091 0.269 -9999 0 -0.749 25 25
KITLG 0.009 0.084 -9999 0 -0.293 11 11
cell motility -0.091 0.269 -9999 0 -0.749 25 25
PTPN6 0.037 0.012 -9999 0 -9999 0 0
EPOR -0.005 0.133 -9999 0 -0.671 1 1
STAT5A (dimer) -0.073 0.227 -9999 0 -0.639 24 24
SOCS1 0.027 0.064 -9999 0 -0.413 4 4
cell migration 0.052 0.154 0.446 22 -9999 0 22
SOS1 0.036 0.002 -9999 0 -9999 0 0
EPO 0.025 0.032 -9999 0 -0.209 2 2
VAV1 -0.004 0.133 -9999 0 -0.421 18 18
GRB10 -0.066 0.161 -9999 0 -0.429 26 26
PTPN11 0.031 0.053 -9999 0 -0.382 3 3
SCF/KIT -0.052 0.167 -9999 0 -0.468 24 24
GO:0007205 0.003 0.009 -9999 0 -9999 0 0
MAP2K1 -0.024 0.102 0.23 1 -0.306 9 10
CBL 0.035 0.005 -9999 0 -9999 0 0
KIT -0.142 0.454 -9999 0 -1.362 24 24
MAP2K2 -0.022 0.106 0.289 3 -0.31 8 11
SHC/Grb2/SOS1 -0.01 0.167 -9999 0 -0.44 19 19
STAT5A -0.078 0.233 -9999 0 -0.659 24 24
GRB2 0.034 0.008 -9999 0 -9999 0 0
response to radiation -0.06 0.164 -9999 0 -0.458 24 24
SHC/GRAP2 0.038 0.064 -9999 0 -0.349 5 5
PTPRO -0.1 0.185 -9999 0 -0.467 31 31
SH2B2 -0.051 0.158 -9999 0 -0.446 24 24
DOK1 0.032 0.039 -9999 0 -0.343 2 2
MATK -0.053 0.156 -9999 0 -0.456 22 22
CREBBP 0.016 0.07 -9999 0 -0.486 1 1
BCL2 -0.238 0.469 -9999 0 -1.315 26 26
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.001 0.18 -9999 0 -0.494 21 21
HDAC1 0.033 0.013 -9999 0 -9999 0 0
AES 0.031 0.037 -9999 0 -0.485 1 1
FBXW11 0.036 0.004 -9999 0 -9999 0 0
DTX1 0.036 0.004 -9999 0 -9999 0 0
LRP6/FZD1 0.049 0.019 -9999 0 -9999 0 0
TLE1 0.005 0.121 -9999 0 -0.484 12 12
AP1 -0.126 0.173 -9999 0 -0.33 71 71
NCSTN 0.034 0.007 -9999 0 -9999 0 0
ADAM10 0.024 0.066 -9999 0 -0.371 5 5
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.016 0.112 -9999 0 -0.501 4 4
NICD/RBPSUH -0.029 0.165 -9999 0 -0.475 22 22
WIF1 -0.023 0.103 -9999 0 -0.204 51 51
NOTCH1 -0.029 0.175 -9999 0 -0.5 22 22
PSENEN 0.031 0.04 -9999 0 -0.344 2 2
KREMEN2 -0.071 0.175 -9999 0 -0.308 64 64
DKK1 -0.099 0.19 -9999 0 -0.317 79 79
beta catenin/beta TrCP1 0.07 0.11 0.358 1 -0.324 3 4
APH1B 0.02 0.073 -9999 0 -0.297 9 9
APH1A 0.003 0.107 -9999 0 -0.306 19 19
AXIN1 -0.028 0.106 -9999 0 -0.63 4 4
CtBP/CBP/TCF1/TLE1/AES 0.006 0.077 0.201 2 -0.257 10 12
PSEN1 0.032 0.019 -9999 0 -0.203 1 1
FOS -0.063 0.171 -9999 0 -0.318 56 56
JUN -0.017 0.15 -9999 0 -0.405 25 25
MAP3K7 0.032 0.037 -9999 0 -0.485 1 1
CTNNB1 0.056 0.109 0.306 3 -0.337 3 6
MAPK3 0.024 0.073 -9999 0 -0.427 5 5
DKK2/LRP6/Kremen 2 -0.053 0.154 -9999 0 -0.308 44 44
HNF1A 0 0.003 -9999 0 -9999 0 0
CTBP1 0.034 0.008 -9999 0 -9999 0 0
MYC -0.039 0.312 -9999 0 -1.418 10 10
NKD1 -0.144 0.215 -9999 0 -0.351 97 97
FZD1 0.035 0.006 -9999 0 -9999 0 0
NOTCH1 precursor/Deltex homolog 1 -0.003 0.176 -9999 0 -0.534 14 14
apoptosis -0.126 0.172 -9999 0 -0.328 71 71
Delta 1/NOTCHprecursor -0.005 0.179 -9999 0 -0.492 21 21
DLL1 0.031 0.04 -9999 0 -0.343 2 2
PPARD 0.032 0.06 -9999 0 -0.743 1 1
Gamma Secretase 0.05 0.099 -9999 0 -0.262 10 10
APC -0.058 0.146 -9999 0 -0.449 20 20
DVL1 0.002 0.103 -9999 0 -0.586 5 5
CSNK2A1 0.028 0.015 -9999 0 -9999 0 0
MAP3K7IP1 0.033 0.01 -9999 0 -9999 0 0
DKK1/LRP6/Kremen 2 -0.094 0.174 -9999 0 -0.332 57 57
LRP6 0.033 0.018 -9999 0 -0.203 1 1
CSNK1A1 0.035 0.006 -9999 0 -9999 0 0
NLK 0.025 0.028 -9999 0 -0.309 1 1
CCND1 0.006 0.207 -9999 0 -1.384 4 4
WNT1 0.035 0.005 -9999 0 -9999 0 0
Axin1/APC/beta catenin 0.01 0.142 0.355 2 -0.438 7 9
DKK2 -0.031 0.148 -9999 0 -0.308 40 40
NOTCH1 precursor/DVL1 -0.02 0.197 -9999 0 -0.595 16 16
GSK3B 0.033 0.036 -9999 0 -0.483 1 1
FRAT1 0.029 0.051 -9999 0 -0.481 2 2
NOTCH/Deltex homolog 1 0 0.177 -9999 0 -0.55 13 13
PPP2R5D 0.1 0.112 0.28 48 -9999 0 48
MAPK1 0.034 0.008 -9999 0 -9999 0 0
WNT1/LRP6/FZD1 0.038 0.083 -9999 0 -9999 0 0
RBPJ 0 0 -9999 0 -9999 0 0
CREBBP 0.033 0.038 -9999 0 -0.486 1 1
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.035 0.115 -9999 0 -0.264 31 31
SMAD6-7/SMURF1 0.044 0.046 -9999 0 -0.298 1 1
NOG 0.029 0.051 -9999 0 -0.483 2 2
SMAD9 -0.077 0.2 -9999 0 -0.517 32 32
SMAD4 0.017 0.063 -9999 0 -0.483 3 3
SMAD5 -0.038 0.122 -9999 0 -0.382 14 14
BMP7/USAG1 -0.142 0.198 -9999 0 -0.426 59 59
SMAD5/SKI -0.035 0.137 -9999 0 -0.425 12 12
SMAD1 0.007 0.107 -9999 0 -0.504 6 6
BMP2 -0.023 0.149 -9999 0 -0.445 22 22
SMAD1/SMAD1/SMAD4 0.012 0.097 -9999 0 -0.463 4 4
BMPR1A 0.032 0.037 -9999 0 -0.483 1 1
BMPR1B 0.032 0.029 -9999 0 -0.204 3 3
BMPR1A-1B/BAMBI -0.012 0.134 -9999 0 -0.297 30 30
AHSG 0.011 0.111 -9999 0 -0.483 10 10
CER1 0.031 0.04 -9999 0 -0.343 2 2
BMP2-4/CER1 -0.035 0.144 -9999 0 -0.313 38 38
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.037 0.133 -9999 0 -0.365 16 16
BMP2-4 (homodimer) -0.052 0.158 -9999 0 -0.367 37 37
RGMB -0.014 0.119 -9999 0 -0.261 34 34
BMP6/BMPR2/BMPR1A-1B 0.064 0.078 -9999 0 -0.272 7 7
RGMA 0.017 0.084 -9999 0 -0.378 8 8
SMURF1 0.034 0.008 -9999 0 -9999 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.055 0.133 -9999 0 -0.335 24 24
BMP2-4/USAG1 -0.135 0.19 -9999 0 -0.358 72 72
SMAD6/SMURF1/SMAD5 -0.033 0.136 -9999 0 -0.428 11 11
SOSTDC1 -0.155 0.225 -9999 0 -0.384 93 93
BMP7/BMPR2/BMPR1A-1B -0.036 0.112 -9999 0 -0.27 29 29
SKI 0.034 0.009 -9999 0 -9999 0 0
BMP6 (homodimer) 0.013 0.096 -9999 0 -0.332 13 13
HFE2 0.029 0.053 -9999 0 -0.39 3 3
ZFYVE16 0.035 0.006 -9999 0 -9999 0 0
MAP3K7 0.033 0.036 -9999 0 -0.483 1 1
BMP2-4/CHRD -0.03 0.143 -9999 0 -0.314 36 36
SMAD5/SMAD5/SMAD4 -0.037 0.135 -9999 0 -0.4 14 14
MAPK1 0.034 0.008 -9999 0 -9999 0 0
TAK1/TAB family -0.008 0.145 -9999 0 -0.34 14 14
BMP7 (homodimer) -0.091 0.176 -9999 0 -0.334 62 62
NUP214 0.034 0.017 -9999 0 -0.204 1 1
BMP6/FETUA 0.016 0.114 -9999 0 -0.368 15 15
SMAD1/SKI 0.017 0.111 -9999 0 -0.478 6 6
SMAD6 0.03 0.03 -9999 0 -0.204 3 3
CTDSP2 0.025 0.066 -9999 0 -0.371 5 5
BMP2-4/FETUA -0.044 0.159 -9999 0 -0.331 42 42
MAP3K7IP1 0.034 0.009 -9999 0 -9999 0 0
GREM1 -0.055 0.182 -9999 0 -0.392 43 43
BMPR2 (homodimer) 0.035 0.004 -9999 0 -9999 0 0
GADD34/PP1CA 0.062 0.039 -9999 0 -9999 0 0
BMPR1A-1B (homodimer) 0.045 0.039 -9999 0 -0.349 1 1
CHRDL1 0.022 0.073 -9999 0 -0.297 9 9
ENDOFIN/SMAD1 0.018 0.113 -9999 0 -0.48 6 6
SMAD6-7/SMURF1/SMAD1 0.03 0.114 -9999 0 -0.476 5 5
SMAD6/SMURF1 0.034 0.008 -9999 0 -9999 0 0
BAMBI -0.068 0.185 -9999 0 -0.348 56 56
SMURF2 0.021 0.066 -9999 0 -0.266 9 9
BMP2-4/CHRDL1 -0.04 0.152 -9999 0 -0.326 39 39
BMP2-4/GREM1 -0.087 0.172 -9999 0 -0.324 63 63
SMAD7 0.022 0.039 -9999 0 -0.483 1 1
SMAD8A/SMAD8A/SMAD4 -0.078 0.203 -9999 0 -0.482 35 35
SMAD1/SMAD6 0.018 0.112 -9999 0 -0.48 6 6
TAK1/SMAD6 0.047 0.031 -9999 0 -0.349 1 1
BMP7 -0.091 0.176 -9999 0 -0.334 62 62
BMP6 0.013 0.096 -9999 0 -0.333 13 13
MAP3K7IP2 0.035 0.006 -9999 0 -9999 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.054 0.141 -9999 0 -0.379 22 22
PPM1A 0.032 0.011 -9999 0 -9999 0 0
SMAD1/SMURF2 0.013 0.114 -9999 0 -0.489 6 6
SMAD7/SMURF1 0.033 0.037 -9999 0 -0.349 1 1
CTDSPL 0.016 0.091 -9999 0 -0.39 9 9
PPP1CA 0.03 0.037 -9999 0 -0.204 5 5
XIAP 0 0 -9999 0 -9999 0 0
CTDSP1 0.036 0.002 -9999 0 -9999 0 0
PPP1R15A 0.032 0.029 -9999 0 -0.204 3 3
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.056 0.141 -9999 0 -0.37 22 22
CHRD 0.036 0.004 -9999 0 -9999 0 0
BMPR2 0.035 0.004 -9999 0 -9999 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.049 0.137 -9999 0 -0.359 21 21
BMP4 -0.047 0.172 -9999 0 -0.378 40 40
FST 0.016 0.096 -9999 0 -0.421 9 9
BMP2-4/NOG -0.034 0.145 -9999 0 -0.313 38 38
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.029 0.109 -9999 0 -0.256 28 28
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.036 0.16 -9999 0 -0.367 29 29
alphaM/beta2 Integrin/GPIbA -0.024 0.136 -9999 0 -0.337 23 23
alphaM/beta2 Integrin/proMMP-9 -0.031 0.124 -9999 0 -0.351 20 20
PLAUR 0.013 0.095 -9999 0 -0.343 12 12
HMGB1 0.008 0.049 -9999 0 -0.499 1 1
alphaM/beta2 Integrin/Talin -0.019 0.138 -9999 0 -0.336 23 23
AGER 0.01 0.042 -9999 0 -9999 0 0
RAP1A 0.034 0.008 -9999 0 -9999 0 0
SELPLG 0.013 0.096 -9999 0 -0.333 13 13
mol:LDL 0 0 -9999 0 -9999 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.04 0.151 -9999 0 -0.364 20 20
mol:GTP 0 0 -9999 0 -9999 0 0
MMP9 -0.006 0.09 -9999 0 -0.297 15 15
CYR61 -0.008 0.124 -9999 0 -0.311 26 26
TLN1 0.035 0.006 -9999 0 -9999 0 0
Rap1/GTP -0.011 0.139 -9999 0 -0.461 11 11
RHOA 0.035 0.004 -9999 0 -9999 0 0
P-selectin oligomer -0.057 0.183 -9999 0 -0.379 46 46
MYH2 -0.034 0.147 -9999 0 -0.546 12 12
MST1R 0.028 0.062 -9999 0 -0.483 3 3
leukocyte activation during inflammatory response -0.028 0.137 -9999 0 -0.305 30 30
APOB 0.002 0.126 -9999 0 -0.463 14 14
mol:GDP 0 0 -9999 0 -9999 0 0
complement component iC3b receptor activity 0 0 -9999 0 -9999 0 0
MMP2 0.005 0.107 -9999 0 -0.307 19 19
JAM3 0.027 0.043 -9999 0 -0.204 7 7
GP1BA 0.027 0.027 -9999 0 -0.204 2 2
alphaM/beta2 Integrin/CTGF -0.022 0.142 -9999 0 -0.348 23 23
alphaM/beta2 Integrin -0.035 0.148 -9999 0 -0.465 15 15
JAM3 homodimer 0.027 0.043 -9999 0 -0.203 7 7
ICAM2 0.011 0.099 -9999 0 -0.367 12 12
ICAM1 0.007 0.094 -9999 0 -0.259 20 20
phagocytosis triggered by activation of immune response cell surface activating receptor -0.035 0.146 -9999 0 -0.46 15 15
cell adhesion -0.024 0.135 -9999 0 -0.335 23 23
NFKB1 -0.071 0.217 0.303 1 -0.421 42 43
THY1 0.012 0.1 -9999 0 -0.367 12 12
RhoA/GDP 0.026 0.003 -9999 0 -9999 0 0
Lipoprotein(a) 0.02 0.081 -9999 0 -0.295 12 12
alphaM/beta2 Integrin/LRP/tPA -0.018 0.15 -9999 0 -0.327 27 27
IL6 -0.163 0.319 -9999 0 -0.679 50 50
ITGB2 -0.039 0.137 -9999 0 -0.338 29 29
elevation of cytosolic calcium ion concentration -0.037 0.177 -9999 0 -0.364 36 36
alphaM/beta2 Integrin/JAM2/JAM3 -0.033 0.179 -9999 0 -0.393 29 29
JAM2 -0.013 0.139 -9999 0 -0.386 23 23
alphaM/beta2 Integrin/ICAM1 -0.011 0.161 -9999 0 -0.329 31 31
alphaM/beta2 Integrin/uPA/Plg -0.031 0.174 -9999 0 -0.373 31 31
RhoA/GTP -0.026 0.151 -9999 0 -0.626 9 9
positive regulation of phagocytosis -0.042 0.142 -9999 0 -0.429 18 18
Ron/MSP 0.031 0.075 -9999 0 -0.349 5 5
alphaM/beta2 Integrin/uPAR/uPA -0.036 0.18 -9999 0 -0.366 36 36
alphaM/beta2 Integrin/uPAR -0.028 0.146 -9999 0 -0.325 31 31
PLAU -0.014 0.138 -9999 0 -0.354 26 26
PLAT 0.008 0.103 -9999 0 -0.407 11 11
actin filament polymerization -0.032 0.14 -9999 0 -0.518 12 12
MST1 0.015 0.076 -9999 0 -0.241 15 15
alphaM/beta2 Integrin/lipoprotein(a) -0.025 0.141 -9999 0 -0.308 30 30
TNF -0.074 0.213 0.289 1 -0.529 19 20
RAP1B 0.035 0.004 -9999 0 -9999 0 0
alphaM/beta2 Integrin/uPA -0.045 0.178 -9999 0 -0.387 33 33
fibrinolysis -0.032 0.172 -9999 0 -0.371 31 31
HCK -0.013 0.11 -9999 0 -0.352 17 17
dendritic cell antigen processing and presentation -0.035 0.146 -9999 0 -0.46 15 15
VTN 0.034 0.008 -9999 0 -9999 0 0
alphaM/beta2 Integrin/CYR61 -0.044 0.163 -9999 0 -0.357 33 33
LPA 0.031 0.013 -9999 0 -9999 0 0
LRP1 0.035 0.005 -9999 0 -9999 0 0
cell migration -0.041 0.128 -9999 0 -0.334 26 26
FN1 -0.016 0.132 -9999 0 -0.3 32 32
alphaM/beta2 Integrin/Thy1 -0.031 0.165 -9999 0 -0.392 25 25
MPO 0.021 0.056 -9999 0 -0.204 12 12
KNG1 0.003 0.108 -9999 0 -0.301 20 20
RAP1/GDP 0.045 0.014 -9999 0 -9999 0 0
ROCK1 -0.024 0.143 0.338 1 -0.584 9 10
ELA2 0.031 0.04 -9999 0 -0.343 2 2
PLG 0.032 0.036 -9999 0 -0.483 1 1
CTGF 0.029 0.037 -9999 0 -0.204 5 5
alphaM/beta2 Integrin/Hck -0.034 0.135 -9999 0 -0.361 23 23
ITGAM -0.016 0.108 -9999 0 -0.332 16 16
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.063 0.192 -9999 0 -0.363 46 46
HP 0.03 0.051 -9999 0 -0.483 2 2
leukocyte adhesion -0.043 0.2 -9999 0 -0.584 16 16
SELP -0.057 0.183 -9999 0 -0.38 46 46
Signaling events mediated by the Hedgehog family

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
TGFB2 0.015 0.116 -9999 0 -0.485 8 8
IHH 0.025 0.095 -9999 0 -0.528 5 5
SHH Np/Cholesterol/GAS1 -0.071 0.139 -9999 0 -0.303 45 45
LRPAP1 0.035 0.007 -9999 0 -9999 0 0
dorsoventral neural tube patterning 0.071 0.138 0.301 45 -9999 0 45
SMO/beta Arrestin2 0.003 0.123 -9999 0 -0.373 12 12
SMO -0.007 0.117 -9999 0 -0.338 20 20
AKT1 -0.013 0.151 -9999 0 -0.402 21 21
ARRB2 0.027 0.038 -9999 0 -0.483 1 1
BOC 0.026 0.054 -9999 0 -0.244 7 7
ADRBK1 0.036 0.004 -9999 0 -9999 0 0
heart looping -0.008 0.119 -9999 0 -0.335 21 21
STIL -0.003 0.102 0.198 2 -0.243 26 28
DHH N/PTCH2 0.051 0.01 -9999 0 -9999 0 0
DHH N/PTCH1 0.028 0.076 -9999 0 -0.296 9 9
PIK3CA 0.035 0.006 -9999 0 -9999 0 0
DHH 0.035 0.005 -9999 0 -9999 0 0
PTHLH 0.004 0.167 -9999 0 -0.864 6 6
determination of left/right symmetry -0.008 0.119 -9999 0 -0.335 21 21
PIK3R1 0.028 0.062 -9999 0 -0.483 3 3
skeletal system development 0.004 0.165 -9999 0 -0.852 6 6
IHH N/Hhip -0.017 0.161 -9999 0 -0.402 28 28
DHH N/Hhip -0.008 0.134 -9999 0 -0.349 25 25
mol:Cholesterol 0 0 -9999 0 -9999 0 0
heart development -0.008 0.119 -9999 0 -0.335 21 21
pancreas development -0.039 0.172 -9999 0 -0.403 35 35
HHAT -0.001 0.125 -9999 0 -0.401 17 17
PI3K 0.045 0.049 -9999 0 -0.349 3 3
EntrezGene:84976 0 0 -9999 0 -9999 0 0
GAS1 -0.118 0.201 -9999 0 -0.329 87 87
somite specification -0.008 0.119 -9999 0 -0.335 21 21
SHH Np/Cholesterol/PTCH1 -0.004 0.091 -9999 0 -0.249 22 22
SHH Np/Cholesterol/PTCH2 0.01 0.079 -9999 0 -0.275 13 13
SHH Np/Cholesterol/Megalin 0.009 0.08 -9999 0 -0.276 13 13
SHH -0.01 0.094 -9999 0 -0.357 13 13
catabolic process 0.008 0.079 -9999 0 -0.332 9 9
SMO/Vitamin D3 -0.012 0.112 0.204 3 -0.333 13 16
SHH Np/Cholesterol/Hhip -0.032 0.131 -9999 0 -0.308 33 33
LRP2 0.033 0.024 -9999 0 -0.204 2 2
receptor-mediated endocytosis -0.011 0.108 -9999 0 -0.321 13 13
SHH Np/Cholesterol/BOC 0.005 0.081 -9999 0 -0.276 13 13
SHH Np/Cholesterol/CDO 0.008 0.079 -9999 0 -0.276 13 13
mesenchymal cell differentiation 0.032 0.13 0.307 33 -9999 0 33
mol:Vitamin D3 0.005 0.101 0.201 9 -0.249 22 31
IHH N/PTCH2 0.044 0.063 -9999 0 -0.318 5 5
CDON 0.033 0.024 -9999 0 -0.204 2 2
IHH N/PTCH1 0.027 0.084 -9999 0 -0.304 11 11
Megalin/LRPAP1 0.049 0.022 -9999 0 -9999 0 0
PTCH2 0.035 0.005 -9999 0 -9999 0 0
SHH Np/Cholesterol -0.003 0.074 -9999 0 -0.274 13 13
PTCH1 0.008 0.079 -9999 0 -0.333 9 9
HHIP -0.039 0.172 -9999 0 -0.403 35 35
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.05 0.041 0.213 5 -9999 0 5
AES 0.044 0.051 0.2 1 -0.487 1 2
FBXW11 0.036 0.004 -9999 0 -9999 0 0
mol:GTP 0.001 0.001 -9999 0 -9999 0 0
LRP6/FZD1 0.049 0.019 -9999 0 -9999 0 0
SMAD4 0.017 0.063 -9999 0 -0.483 3 3
DKK2 -0.031 0.148 -9999 0 -0.308 40 40
TLE1 0.019 0.126 0.198 2 -0.471 12 14
MACF1 0.036 0.004 -9999 0 -9999 0 0
CTNNB1 0.038 0.093 0.358 2 -9999 0 2
WIF1 -0.023 0.103 -9999 0 -0.204 51 51
beta catenin/RanBP3 0.086 0.184 0.417 42 -9999 0 42
KREMEN2 -0.071 0.175 -9999 0 -0.308 64 64
DKK1 -0.099 0.19 -9999 0 -0.317 79 79
beta catenin/beta TrCP1 0.054 0.094 0.359 2 -9999 0 2
FZD1 0.035 0.007 -9999 0 -9999 0 0
AXIN2 -0.263 0.63 0.644 8 -1.521 40 48
AXIN1 0.031 0.051 -9999 0 -0.481 2 2
RAN 0.036 0.004 -9999 0 -9999 0 0
Axin1/APC/GSK3/beta catenin 0.04 0.088 -9999 0 -0.618 2 2
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.053 0.191 0.289 1 -0.558 12 13
Axin1/APC/GSK3 0.062 0.08 0.268 2 -0.37 1 3
Axin1/APC/GSK3/beta catenin/Macf1 0.025 0.088 -9999 0 -0.385 2 2
HNF1A 0.014 0.036 0.16 6 -9999 0 6
CTBP1 0.048 0.037 0.216 2 -9999 0 2
MYC 0.012 0.437 0.626 29 -1.595 10 39
RANBP3 0.033 0.036 -9999 0 -0.473 1 1
DKK2/LRP6/Kremen 2 -0.052 0.154 -9999 0 -0.308 44 44
NKD1 -0.144 0.215 -9999 0 -0.351 97 97
TCF4 0.033 0.048 0.197 4 -0.194 2 6
TCF3 0.04 0.069 0.213 1 -0.442 3 4
WNT1/LRP6/FZD1/Axin1 0.08 0.047 -9999 0 -0.267 2 2
Ran/GTP 0.028 0.004 -9999 0 -9999 0 0
CtBP/CBP/TCF/TLE1/AES 0.048 0.245 0.478 41 -0.51 3 44
LEF1 0.016 0.115 0.196 4 -0.305 19 23
DVL1 0.029 0.08 -9999 0 -0.518 2 2
CSNK2A1 0.028 0.015 -9999 0 -9999 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.04 0.152 0.306 1 -0.567 7 8
DKK1/LRP6/Kremen 2 -0.093 0.174 -9999 0 -0.333 57 57
LRP6 0.034 0.018 -9999 0 -0.203 1 1
CSNK1A1 0.051 0.04 0.21 5 -9999 0 5
NLK 0.029 0.021 -9999 0 -0.203 1 1
CCND1 -0.057 0.214 -9999 0 -1.31 4 4
WNT1 0.035 0.005 -9999 0 -9999 0 0
GSK3A 0.035 0.005 -9999 0 -9999 0 0
GSK3B 0.033 0.036 -9999 0 -0.483 1 1
FRAT1 0.029 0.051 -9999 0 -0.483 2 2
PPP2R5D 0.112 0.114 0.291 48 -9999 0 48
APC 0.016 0.081 0.544 1 -0.261 9 10
WNT1/LRP6/FZD1 0.045 0.041 -9999 0 -9999 0 0
CREBBP 0.046 0.053 0.213 2 -0.486 1 3
Visual signal transduction: Rods

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
mol:K + 0.03 0.04 -9999 0 -0.343 2 2
GNAT1/GTP 0.022 0.025 -9999 0 -0.133 5 5
Metarhodopsin II/Arrestin 0.039 0.044 -9999 0 -0.295 2 2
PDE6G/GNAT1/GTP 0.042 0.028 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
absorption of light 0 0 -9999 0 -9999 0 0
GNAT1 0.03 0.037 -9999 0 -0.204 5 5
GRK1 0 0 -9999 0 -9999 0 0
CNG Channel -0.054 0.147 -9999 0 -0.271 52 52
mol:Na + -0.036 0.147 -9999 0 -0.375 13 13
mol:ADP 0 0 -9999 0 -9999 0 0
RGS9-1/Gbeta5/R9AP 0.01 0.116 -9999 0 -0.302 20 20
mol:GDP 0 0 -9999 0 -9999 0 0
cGMP/CNG Channel -0.029 0.157 -9999 0 -0.385 13 13
CNGB1 0.036 0.002 -9999 0 -9999 0 0
RDH5 0.017 0.091 -9999 0 -0.39 9 9
SAG 0.021 0.068 -9999 0 -0.259 10 10
mol:Ca2+ -0.071 0.131 0.332 5 -0.372 13 18
Na + (4 Units) -0.04 0.138 -9999 0 -0.363 13 13
RGS9 0.025 0.051 -9999 0 -0.25 6 6
GNB1/GNGT1 -0.108 0.174 -9999 0 -0.348 64 64
GNAT1/GDP 0.019 0.109 -9999 0 -0.257 20 20
GUCY2D 0.028 0.021 -9999 0 -0.204 1 1
GNGT1 -0.17 0.226 -9999 0 -0.377 103 103
GUCY2F 0.015 0.101 -9999 0 -0.452 9 9
GNB5 -0.004 0.126 -9999 0 -0.38 19 19
mol:GMP (4 units) -0.012 0.099 -9999 0 -0.262 23 23
mol:11-cis-retinal 0.017 0.091 -9999 0 -0.389 9 9
mol:cGMP 0.031 0.101 -9999 0 -0.275 17 17
GNB1 0.034 0.008 -9999 0 -9999 0 0
Rhodopsin 0.037 0.071 -9999 0 -0.349 6 6
SLC24A1 0.03 0.04 -9999 0 -0.343 2 2
CNGA1 -0.085 0.198 -9999 0 -0.366 62 62
Metarhodopsin II 0.023 0.002 -9999 0 -9999 0 0
mol:Ca ++ 0 0 -9999 0 -9999 0 0
GC1/GCAP Family 0.05 0.087 -9999 0 -0.28 9 9
RGS9BP 0.007 0.1 -9999 0 -0.302 17 17
Metarhodopsin II/Transducin -0.072 0.12 -9999 0 -0.242 64 64
GCAP Family/Ca ++ 0.045 0.077 -9999 0 -0.279 9 9
PDE6A/B -0.014 0.131 -9999 0 -0.345 23 23
mol:Pi 0.009 0.116 -9999 0 -0.301 20 20
mol:all-trans-retinal 0 0 -9999 0 -9999 0 0
Transducin -0.073 0.148 -9999 0 -0.272 65 65
PDE6B 0.019 0.075 -9999 0 -0.287 10 10
PDE6A -0.031 0.157 -9999 0 -0.355 35 35
PDE6G 0.034 0.018 -9999 0 -0.204 1 1
RHO 0.036 0.004 -9999 0 -9999 0 0
PDE6 -0.016 0.146 -9999 0 -0.267 39 39
GUCA1A 0.033 0.024 -9999 0 -0.204 2 2
GC2/GCAP Family 0.052 0.109 -9999 0 -0.292 17 17
GUCA1C 0.011 0.104 -9999 0 -0.39 12 12
GUCA1B 0.029 0.046 -9999 0 -0.273 4 4
PLK2 and PLK4 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
PLK2 -0.013 0.135 -9999 0 -0.338 27 27
PLK4 0.029 0.053 -9999 0 -0.39 3 3
regulation of centriole replication -0.016 0.099 -9999 0 -0.357 14 14
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 -0.013 0.116 -9999 0 -0.374 15 15
EPHB2 0.004 0.121 -9999 0 -0.483 12 12
Syndecan-2/TACI 0.008 0.07 -9999 0 -0.275 10 10
LAMA1 0.026 0.016 -9999 0 -9999 0 0
Syndecan-2/alpha2 ITGB1 0.007 0.1 -9999 0 -0.26 18 18
HRAS 0.032 0.04 -9999 0 -0.343 2 2
Syndecan-2/CASK -0.006 0.063 -9999 0 -0.276 10 10
ITGA5 0.025 0.049 -9999 0 -0.204 9 9
BAX -0.011 0.097 -9999 0 -1.14 1 1
EPB41 0.028 0.046 -9999 0 -0.273 4 4
positive regulation of cell-cell adhesion 0.012 0.064 -9999 0 -0.25 10 10
LAMA3 0.004 0.087 -9999 0 -0.278 15 15
EZR 0 0 -9999 0 -9999 0 0
mol:PI-4-5-P2 0 0 -9999 0 -9999 0 0
CAV2 -0.01 0.128 -9999 0 -0.322 26 26
Syndecan-2/MMP2 0.001 0.101 -9999 0 -0.322 15 15
RP11-540L11.1 0 0 -9999 0 -9999 0 0
alpha2 ITGB1 0.034 0.078 -9999 0 -0.349 7 7
dendrite morphogenesis -0.005 0.096 -9999 0 -0.282 21 21
Syndecan-2/GM-CSF -0.04 0.127 -9999 0 -0.302 32 32
determination of left/right symmetry -0.006 0.076 -9999 0 -0.327 10 10
Syndecan-2/PKC delta 0.014 0.071 -9999 0 -0.278 10 10
GNB2L1 0.035 0.006 -9999 0 -9999 0 0
MAPK3 -0.026 0.14 0.198 24 -0.288 32 56
MAPK1 -0.02 0.134 0.198 23 -0.292 27 50
Syndecan-2/RACK1 0.026 0.074 -9999 0 -0.273 9 9
NF1 0.034 0.008 -9999 0 -9999 0 0
FGFR/FGF/Syndecan-2 -0.006 0.076 -9999 0 -0.327 10 10
ITGA2 0.012 0.103 -9999 0 -0.407 11 11
MAPK8 -0.005 0.07 -9999 0 -0.296 10 10
Syndecan-2/alpha2/beta1 Integrin 0.021 0.089 -9999 0 -0.251 15 15
Syndecan-2/Kininogen -0.003 0.091 -9999 0 -0.288 16 16
ITGB1 0.034 0.017 -9999 0 -0.204 1 1
SRC 0.009 0.063 -9999 0 -0.261 6 6
Syndecan-2/CASK/Protein 4.1 0.009 0.067 -9999 0 -0.251 11 11
extracellular matrix organization 0.013 0.07 -9999 0 -0.277 10 10
actin cytoskeleton reorganization -0.012 0.116 -9999 0 -0.372 15 15
Syndecan-2/Caveolin-2/Ras 0.004 0.114 -9999 0 -0.333 15 15
Syndecan-2/Laminin alpha3 -0.005 0.082 -9999 0 -0.284 13 13
Syndecan-2/RasGAP 0.034 0.083 -9999 0 -0.259 11 11
alpha5/beta1 Integrin 0.043 0.041 -9999 0 -9999 0 0
PRKCD 0.035 0.004 -9999 0 -9999 0 0
Syndecan-2 dimer -0.005 0.097 -9999 0 -0.283 21 21
GO:0007205 0.002 0.012 -9999 0 -9999 0 0
DNA mediated transformation 0 0 -9999 0 -9999 0 0
Syndecan-2/RasGAP/Src 0.01 0.058 -9999 0 -0.255 6 6
RHOA 0.035 0.004 -9999 0 -9999 0 0
SDCBP 0.03 0.02 -9999 0 -0.204 1 1
TNFRSF13B 0.028 0.022 -9999 0 -0.204 1 1
RASA1 0.024 0.073 -9999 0 -0.427 5 5
alpha2/beta1 Integrin 0.034 0.078 -9999 0 -0.349 7 7
Syndecan-2/Synbindin 0.013 0.07 -9999 0 -0.278 10 10
TGFB1 0.034 0.017 -9999 0 -0.204 1 1
CASP3 0.024 0.09 0.198 25 -0.262 10 35
FN1 -0.016 0.132 -9999 0 -0.3 32 32
Syndecan-2/IL8 -0.073 0.151 -9999 0 -0.321 47 47
SDC2 -0.006 0.076 -9999 0 -0.328 10 10
KNG1 0.003 0.108 -9999 0 -0.301 20 20
Syndecan-2/Neurofibromin 0.014 0.067 -9999 0 -0.277 9 9
TRAPPC4 0.035 0.005 -9999 0 -9999 0 0
CSF2 -0.068 0.177 -9999 0 -0.32 60 60
Syndecan-2/TGFB1 0.013 0.071 -9999 0 -0.278 10 10
Syndecan-2/Syntenin/PI-4-5-P2 0.012 0.064 -9999 0 -0.252 10 10
Syndecan-2/Ezrin 0.013 0.064 -9999 0 -0.252 10 10
PRKACA 0.032 0.091 0.199 31 -0.252 9 40
angiogenesis -0.073 0.15 -9999 0 -0.32 47 47
MMP2 0.005 0.107 -9999 0 -0.307 19 19
IL8 -0.135 0.216 -9999 0 -0.359 90 90
calcineurin-NFAT signaling pathway 0.008 0.069 -9999 0 -0.274 10 10
Arf6 signaling events

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
CENTA1/KIF3B 0.018 0.024 -9999 0 -0.293 1 1
ARNO/beta Arrestin1-2 -0.001 0.09 -9999 0 -0.239 21 21
EGFR 0.016 0.09 -9999 0 -0.413 8 8
EPHA2 0.011 0.088 -9999 0 -0.278 15 15
USP6 0.03 0.014 -9999 0 -9999 0 0
IQSEC1 0.034 0.017 -9999 0 -0.204 1 1
EGFR/EGFR/EGF/EGF -0.054 0.149 -9999 0 -0.347 34 34
ARRB2 0.009 0.049 -9999 0 -0.365 3 3
mol:GTP 0.006 0.022 0.11 6 -9999 0 6
ARRB1 0.015 0.101 -9999 0 -0.452 9 9
FBXO8 0.034 0.008 -9999 0 -9999 0 0
TSHR 0.03 0.037 -9999 0 -0.483 1 1
EGF -0.088 0.187 -9999 0 -0.32 72 72
somatostatin receptor activity 0 0 0.001 10 -0.001 19 29
ARAP2 0 0 0 11 0 15 26
mol:GDP 0.001 0.076 0.147 3 -0.246 10 13
mol:PI-3-4-5-P3 0 0 0 9 0 17 26
ITGA2B 0.035 0.006 -9999 0 -9999 0 0
ARF6 0.028 0.051 -9999 0 -0.483 2 2
Ephrin A1/EPHA2/NCK1/GIT1 0.047 0.097 -9999 0 -0.287 11 11
ADAP1 0 0 0 6 0 5 11
KIF13B 0.026 0.038 -9999 0 -0.483 1 1
HGF/MET 0.042 0.057 -9999 0 -0.383 3 3
PXN 0.036 0.004 -9999 0 -9999 0 0
ARF6/GTP -0.003 0.1 0.196 7 -0.222 19 26
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.031 0.138 -9999 0 -0.298 34 34
ADRB2 -0.002 0.126 -9999 0 -0.39 18 18
receptor agonist activity 0 0 0 7 0 8 15
actin filament binding 0 0 0 10 0 18 28
SRC 0.011 0.062 -9999 0 -0.484 3 3
ITGB3 0.033 0.018 -9999 0 -0.204 1 1
GNAQ 0 0 0.001 12 -0.001 10 22
EFA6/PI-4-5-P2 0 0 0.001 13 -0.001 8 21
ARF6/GDP -0.018 0.107 0.199 1 -0.281 23 24
ARF6/GDP/GULP/ACAP1 -0.013 0.117 -9999 0 -0.277 18 18
alphaIIb/beta3 Integrin/paxillin/GIT1 0.083 0.031 -9999 0 -9999 0 0
ACAP1 0 0 0 1 -9999 0 1
ACAP2 0 0 0 10 0 14 24
LHCGR/beta Arrestin2 0.011 0.06 -9999 0 -0.365 3 3
EFNA1 0.021 0.076 -9999 0 -0.363 7 7
HGF 0.03 0.043 -9999 0 -0.297 3 3
CYTH3 0 0 0.001 11 -0.001 13 24
CYTH2 -0.001 0.001 -9999 0 -0.004 21 21
NCK1 0.026 0.071 -9999 0 -0.483 4 4
fibronectin binding 0 0 0 7 0 16 23
endosomal lumen acidification 0 0 0 14 0 14 28
microtubule-based process 0 0 -9999 0 -9999 0 0
GULP1 -0.046 0.168 -9999 0 -0.34 45 45
GNAQ/ARNO 0 0.003 0.008 12 -0.006 8 20
mol:Phosphatidic acid 0 0 0 10 0 14 24
PIP3-E 0.011 0.107 -9999 0 -0.455 10 10
MET 0.027 0.056 -9999 0 -0.343 4 4
GNA14 -0.021 0.149 -9999 0 -0.368 29 29
GNA15 0.02 0.068 -9999 0 -0.26 10 10
GIT1 0.033 0.018 -9999 0 -0.204 1 1
mol:PI-4-5-P2 0 0 0.001 12 -0.001 11 23
GNA11 0.028 0.054 -9999 0 -0.39 3 3
LHCGR 0.025 0.062 -9999 0 -0.284 7 7
AGTR1 0.013 0.071 -9999 0 -0.204 20 20
desensitization of G-protein coupled receptor protein signaling pathway 0.011 0.059 -9999 0 -0.364 3 3
IPCEF1/ARNO -0.03 0.117 -9999 0 -0.233 41 41
alphaIIb/beta3 Integrin 0.05 0.018 -9999 0 -9999 0 0
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.026 0.139 -9999 0 -0.252 41 41
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -9999 0 0
CRKL 0.029 0.051 -9999 0 -0.483 2 2
STAT1 (dimer)/Cbp/p300 -0.049 0.16 -9999 0 -0.379 21 21
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.021 0.082 -9999 0 -0.311 4 4
antigen processing and presentation of peptide antigen via MHC class I -0.066 0.115 -9999 0 -0.297 21 21
CaM/Ca2+ -0.026 0.131 -9999 0 -0.241 39 39
RAP1A 0.034 0.008 -9999 0 -9999 0 0
STAT1 (dimer)/SHP2 -0.049 0.132 -9999 0 -0.256 46 46
AKT1 -0.054 0.108 -9999 0 -0.357 6 6
MAP2K1 -0.06 0.105 -9999 0 -0.282 9 9
MAP3K11 -0.051 0.115 -9999 0 -0.244 38 38
IFNGR1 0.016 0.046 -9999 0 -0.454 1 1
mol:GTP 0 0 -9999 0 -9999 0 0
CaM/Ca2+/CAMKII -0.009 0.107 -9999 0 -0.416 6 6
Rap1/GTP -0.043 0.096 -9999 0 -0.316 4 4
CRKL/C3G 0.046 0.041 -9999 0 -0.349 2 2
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.028 0.14 -9999 0 -0.258 38 38
CEBPB -0.016 0.165 -9999 0 -0.518 7 7
STAT3 0.034 0.007 -9999 0 -9999 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.007 0.224 -9999 0 -1.162 5 5
STAT1 -0.06 0.124 -9999 0 -0.256 45 45
CALM1 0.032 0.011 -9999 0 -9999 0 0
IFN-gamma (dimer) -0.107 0.2 -9999 0 -0.335 80 80
PIK3CA 0.035 0.006 -9999 0 -9999 0 0
STAT1 (dimer)/PIAS1 -0.048 0.127 -9999 0 -0.298 14 14
CEBPB/PTGES2/Cbp/p300 -0.012 0.122 -9999 0 -0.347 7 7
mol:Ca2+ -0.027 0.135 -9999 0 -0.25 41 41
MAPK3 -0.054 0.16 -9999 0 -0.805 5 5
STAT1 (dimer) -0.084 0.162 -9999 0 -0.416 21 21
MAPK1 -0.069 0.19 -9999 0 -0.77 10 10
JAK2 0.001 0.083 -9999 0 -0.289 12 12
PIK3R1 0.028 0.062 -9999 0 -0.483 3 3
JAK1 0.016 0.047 -9999 0 -0.482 1 1
CAMK2D 0.033 0.036 -9999 0 -0.483 1 1
DAPK1 -0.01 0.139 -9999 0 -0.539 5 5
SMAD7 -0.03 0.063 0.138 1 -0.183 7 8
CBL/CRKL/C3G -0.025 0.127 -9999 0 -0.364 4 4
PI3K -0.023 0.136 -9999 0 -0.283 18 18
IFNG -0.108 0.201 -9999 0 -0.336 80 80
apoptosis -0.029 0.135 -9999 0 -0.418 12 12
CAMK2G 0.035 0.007 -9999 0 -9999 0 0
STAT3 (dimer) 0.034 0.007 -9999 0 -9999 0 0
CAMK2A 0.034 0.017 -9999 0 -0.203 1 1
CAMK2B 0.026 0.049 -9999 0 -0.26 5 5
FRAP1 -0.056 0.101 -9999 0 -0.346 7 7
PRKCD -0.054 0.111 -9999 0 -0.361 6 6
RAP1B 0.035 0.004 -9999 0 -9999 0 0
negative regulation of cell growth -0.066 0.115 -9999 0 -0.297 21 21
PTPN2 0.027 0.015 -9999 0 -9999 0 0
EP300 0.018 0.088 -9999 0 -0.443 7 7
IRF1 -0.073 0.167 0.275 1 -0.48 18 19
STAT1 (dimer)/PIASy -0.05 0.127 -9999 0 -0.305 13 13
SOCS1 0.007 0.205 -9999 0 -1.284 5 5
mol:GDP -0.026 0.121 -9999 0 -0.35 4 4
CASP1 -0.068 0.112 -9999 0 -0.26 43 43
PTGES2 0.035 0.005 -9999 0 -9999 0 0
IRF9 -0.003 0.057 -9999 0 -0.182 1 1
mol:PI-3-4-5-P3 -0.034 0.124 -9999 0 -0.268 21 21
RAP1/GDP -0.024 0.112 -9999 0 -0.319 4 4
CBL -0.05 0.115 -9999 0 -0.244 38 38
MAP3K1 -0.053 0.114 -9999 0 -0.246 35 35
PIAS1 0.034 0.009 -9999 0 -9999 0 0
PIAS4 0.031 0.04 -9999 0 -0.344 2 2
antigen processing and presentation of peptide antigen via MHC class II -0.066 0.115 -9999 0 -0.297 21 21
PTPN11 -0.053 0.118 -9999 0 -0.251 41 41
CREBBP 0.032 0.036 -9999 0 -0.483 1 1
RAPGEF1 0.035 0.004 -9999 0 -9999 0 0
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.019 0.088 -9999 0 -0.302 14 14
cell-cell adhesion 0.054 0.11 0.389 12 -9999 0 12
Ephrin B/EPHB2/RasGAP 0.014 0.132 -9999 0 -0.294 26 26
ITSN1 0.034 0.008 -9999 0 -9999 0 0
PIK3CA 0.035 0.006 -9999 0 -9999 0 0
SHC1 0.035 0.007 -9999 0 -9999 0 0
Ephrin B1/EPHB3 -0.007 0.131 -9999 0 -0.315 30 30
Ephrin B1/EPHB1 -0.022 0.113 -9999 0 -0.31 18 18
HRAS/GDP -0.031 0.127 -9999 0 -0.356 15 15
Ephrin B/EPHB1/GRB7 -0.011 0.124 -9999 0 -0.272 26 26
Endophilin/SYNJ1 0.02 0.124 -9999 0 -0.257 24 24
KRAS 0.033 0.018 -9999 0 -0.204 1 1
Ephrin B/EPHB1/Src -0.011 0.112 -9999 0 -0.308 16 16
endothelial cell migration 0.025 0.093 -9999 0 -0.268 15 15
GRB2 0.034 0.008 -9999 0 -9999 0 0
GRB7 0.028 0.051 -9999 0 -0.483 2 2
PAK1 0.023 0.132 0.363 1 -0.47 2 3
HRAS 0.032 0.04 -9999 0 -0.343 2 2
RRAS 0.023 0.127 -9999 0 -0.261 24 24
DNM1 0.029 0.037 -9999 0 -0.204 5 5
cell-cell signaling 0 0 -9999 0 -9999 0 0
CRK -0.013 0.119 -9999 0 -0.272 22 22
lamellipodium assembly -0.054 0.11 -9999 0 -0.389 12 12
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.004 0.111 -9999 0 -0.503 4 4
PIK3R1 0.028 0.062 -9999 0 -0.483 3 3
EPHB2 0.004 0.121 -9999 0 -0.483 12 12
EPHB3 -0.043 0.183 -9999 0 -0.458 33 33
EPHB1 -0.064 0.158 -9999 0 -0.269 68 68
EPHB4 0.022 0.07 -9999 0 -0.323 7 7
mol:GDP -0.012 0.132 0.26 7 -0.377 15 22
Ephrin B/EPHB2 0.011 0.113 -9999 0 -0.273 24 24
Ephrin B/EPHB3 -0.008 0.127 -9999 0 -0.267 34 34
JNK cascade -0.056 0.129 0.312 2 -0.309 32 34
Ephrin B/EPHB1 -0.016 0.118 -9999 0 -0.279 24 24
RAP1/GDP -0.002 0.144 0.308 6 -0.346 14 20
EFNB2 -0.004 0.121 -9999 0 -0.462 13 13
EFNB3 0.029 0.014 -9999 0 -9999 0 0
EFNB1 0.028 0.058 -9999 0 -0.315 5 5
Ephrin B2/EPHB1-2 -0.04 0.133 -9999 0 -0.308 32 32
RAP1B 0.035 0.004 -9999 0 -9999 0 0
RAP1A 0.034 0.008 -9999 0 -9999 0 0
CDC42/GTP -0.042 0.144 -9999 0 -0.436 13 13
Rap1/GTP -0.047 0.12 -9999 0 -0.398 12 12
axon guidance 0.019 0.088 -9999 0 -0.301 14 14
MAPK3 -0.001 0.108 -9999 0 -0.444 5 5
MAPK1 0.003 0.104 -9999 0 -0.459 4 4
Rac1/GDP -0.015 0.134 0.278 5 -0.362 13 18
actin cytoskeleton reorganization -0.056 0.099 -9999 0 -0.341 12 12
CDC42/GDP -0.008 0.145 0.311 8 -0.358 14 22
PI3K 0.029 0.096 -9999 0 -0.27 15 15
EFNA5 0.028 0.054 -9999 0 -0.39 3 3
Ephrin B2/EPHB4 0.01 0.085 -9999 0 -0.295 13 13
Ephrin B/EPHB2/Intersectin/N-WASP -0.014 0.106 -9999 0 -0.42 6 6
CDC42 0.032 0.019 -9999 0 -0.204 1 1
RAS family/GTP -0.055 0.119 -9999 0 -0.382 14 14
PTK2 0.095 0.21 0.588 31 -9999 0 31
MAP4K4 -0.057 0.13 0.313 2 -0.312 32 34
SRC 0.011 0.062 -9999 0 -0.483 3 3
KALRN 0.035 0.004 -9999 0 -9999 0 0
Intersectin/N-WASP 0.047 0.031 -9999 0 -0.349 1 1
neuron projection morphogenesis -0.02 0.148 0.389 7 -0.404 8 15
MAP2K1 -0.005 0.103 -9999 0 -0.479 4 4
WASL 0.032 0.036 -9999 0 -0.483 1 1
Ephrin B1/EPHB1-2/NCK1 -0.02 0.148 -9999 0 -0.31 30 30
cell migration 0.022 0.14 0.263 8 -0.586 3 11
NRAS 0.019 0.079 -9999 0 -0.328 9 9
SYNJ1 0.02 0.125 -9999 0 -0.261 24 24
PXN 0.036 0.004 -9999 0 -9999 0 0
TF 0.001 0.125 0.184 14 -0.448 3 17
HRAS/GTP -0.037 0.133 -9999 0 -0.414 12 12
Ephrin B1/EPHB1-2 -0.025 0.134 -9999 0 -0.309 27 27
cell adhesion mediated by integrin -0.011 0.12 0.263 13 -0.198 40 53
RAC1 0.033 0.011 -9999 0 -9999 0 0
mol:GTP -0.037 0.139 -9999 0 -0.313 31 31
RAC1-CDC42/GTP -0.078 0.144 -9999 0 -0.396 25 25
RASA1 0.024 0.073 -9999 0 -0.427 5 5
RAC1-CDC42/GDP -0.008 0.134 0.281 5 -0.357 12 17
ruffle organization -0.025 0.157 0.334 11 -0.459 8 19
NCK1 0.026 0.071 -9999 0 -0.483 4 4
receptor internalization 0.002 0.12 0.184 13 -0.443 2 15
Ephrin B/EPHB2/KALRN 0.022 0.121 -9999 0 -0.275 24 24
ROCK1 -0.028 0.11 -9999 0 -0.286 30 30
RAS family/GDP -0.056 0.099 -9999 0 -0.366 10 10
Rac1/GTP -0.053 0.12 -9999 0 -0.413 12 12
Ephrin B/EPHB1/Src/Paxillin -0.018 0.105 -9999 0 -0.312 16 16
FOXM1 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
NFATC3 -0.084 0.421 -9999 0 -1.236 12 12
PLK1 0.027 0.164 -9999 0 -1.273 3 3
BIRC5 -0.012 0.269 -9999 0 -1.208 9 9
HSPA1B -0.083 0.418 -9999 0 -1.088 19 19
MAP2K1 0.028 0.049 -9999 0 -9999 0 0
BRCA2 -0.057 0.45 -9999 0 -1.211 15 15
FOXM1 -0.138 0.598 -9999 0 -1.651 18 18
XRCC1 -0.078 0.419 -9999 0 -1.192 13 13
FOXM1B/p19 -0.136 0.456 -9999 0 -1.253 19 19
Cyclin D1/CDK4 -0.084 0.409 -9999 0 -1.012 18 18
CDC2 -0.091 0.445 -9999 0 -1.276 14 14
TGFA -0.114 0.407 -9999 0 -0.994 20 20
SKP2 -0.087 0.433 -9999 0 -1.219 14 14
CCNE1 0.027 0.059 -9999 0 -0.317 5 5
CKS1B -0.077 0.418 -9999 0 -1.168 14 14
RB1 -0.029 0.227 -9999 0 -1.086 4 4
FOXM1C/SP1 -0.105 0.484 -9999 0 -1.3 19 19
AURKB -0.143 0.411 -9999 0 -0.989 36 36
CENPF -0.088 0.436 -9999 0 -1.202 16 16
CDK4 0.029 0.029 -9999 0 -9999 0 0
MYC -0.095 0.378 -9999 0 -1.027 14 14
CHEK2 0.026 0.063 -9999 0 -0.533 1 1
ONECUT1 -0.099 0.416 -9999 0 -1.088 17 17
CDKN2A -0.039 0.154 -9999 0 -0.323 41 41
LAMA4 -0.084 0.423 -9999 0 -1.198 14 14
FOXM1B/HNF6 -0.126 0.485 -9999 0 -1.304 19 19
FOS -0.207 0.565 -9999 0 -1.215 42 42
SP1 0.033 0.022 -9999 0 -0.203 1 1
CDC25B -0.111 0.509 -9999 0 -1.238 25 25
response to radiation 0.004 0.029 -9999 0 -9999 0 0
CENPB -0.059 0.426 -9999 0 -1.173 13 13
CENPA -0.085 0.426 -9999 0 -1.211 14 14
NEK2 -0.084 0.433 -9999 0 -1.22 15 15
HIST1H2BA -0.084 0.418 -9999 0 -1.173 14 14
CCNA2 0.019 0.095 -9999 0 -0.489 7 7
EP300 0.018 0.088 -9999 0 -0.443 7 7
CCNB1/CDK1 -0.116 0.508 -9999 0 -1.564 14 14
CCNB2 -0.091 0.439 -9999 0 -1.247 15 15
CCNB1 -0.096 0.461 -9999 0 -1.358 14 14
ETV5 -0.112 0.458 -9999 0 -1.294 17 17
ESR1 -0.092 0.441 -9999 0 -1.243 16 16
CCND1 -0.1 0.407 -9999 0 -1.025 19 19
GSK3A 0.027 0.045 -9999 0 -9999 0 0
Cyclin A-E1/CDK1-2 0.031 0.105 -9999 0 -0.294 13 13
CDK2 0.021 0.075 -9999 0 -0.285 10 10
G2/M transition of mitotic cell cycle 0.005 0.034 -9999 0 -9999 0 0
FOXM1B/Cbp/p300 -0.097 0.459 -9999 0 -1.252 17 17
GAS1 -0.24 0.591 -9999 0 -1.228 48 48
MMP2 -0.105 0.455 -9999 0 -1.256 18 18
RB1/FOXM1C -0.113 0.394 -9999 0 -1.137 13 13
CREBBP 0.032 0.036 -9999 0 -0.483 1 1
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.028 0.158 -9999 0 -0.397 16 16
MAP3K8 0.003 0.106 -9999 0 -0.315 18 18
FOS -0.014 0.11 -9999 0 -0.361 8 8
PRKCA 0.023 0.044 -9999 0 -0.352 2 2
PTPN7 -0.002 0.076 -9999 0 -0.206 23 23
HRAS 0.031 0.04 -9999 0 -0.343 2 2
PRKCB -0.003 0.006 -9999 0 -0.011 66 66
NRAS 0.018 0.08 -9999 0 -0.329 9 9
RAS family/GTP 0.046 0.06 -9999 0 -0.258 5 5
MAPK3 0.005 0.089 -9999 0 -0.464 5 5
MAP2K1 -0.005 0.074 -9999 0 -0.281 7 7
ELK1 0.022 0.038 -9999 0 -0.217 3 3
BRAF 0.004 0.043 -9999 0 -0.293 3 3
mol:GTP -0.001 0.002 -9999 0 -0.003 60 60
MAPK1 -0.004 0.111 -9999 0 -0.464 9 9
RAF1 0.005 0.043 -9999 0 -0.293 3 3
KRAS 0.033 0.018 -9999 0 -0.205 1 1
Cellular roles of Anthrax toxin

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
ANTXR1 -0.016 0.142 -9999 0 -0.353 28 28
ANTXR2 0.014 0.086 -9999 0 -0.283 14 14
negative regulation of myeloid dendritic cell antigen processing and presentation -0.009 0.02 -9999 0 -0.067 18 18
monocyte activation -0.006 0.118 -9999 0 -0.405 15 15
MAP2K2 0.003 0.094 -9999 0 -0.593 5 5
MAP2K1 -0.009 0.017 -9999 0 -0.097 1 1
MAP2K7 -0.012 0.027 -9999 0 -0.16 3 3
MAP2K6 -0.021 0.056 0.129 1 -0.235 11 12
CYAA -0.036 0.076 -9999 0 -0.263 18 18
MAP2K4 -0.01 0.028 -9999 0 -0.2 3 3
IL1B -0.062 0.094 -9999 0 -0.242 38 38
Channel 0.001 0.099 -9999 0 -0.281 18 18
NLRP1 -0.008 0.018 -9999 0 -0.062 18 18
CALM1 0.032 0.011 -9999 0 -9999 0 0
negative regulation of phagocytosis -0.038 0.136 -9999 0 -0.421 22 22
mol:Ca2+ 0 0 -9999 0 -9999 0 0
regulation of endothelial cell proliferation 0.009 0.02 0.067 18 -9999 0 18
MAPK3 -0.015 0.041 0.129 1 -0.231 5 6
MAPK1 -0.01 0.019 -9999 0 -0.126 1 1
PGR -0.012 0.026 -9999 0 -0.181 2 2
PA/Cellular Receptors -0.001 0.109 -9999 0 -0.31 18 18
apoptosis -0.009 0.02 -9999 0 -0.067 18 18
LOC728358 0 0 -9999 0 -9999 0 0
Lethal toxin (unfolded) 0.003 0.093 -9999 0 -0.266 18 18
macrophage activation -0.012 0.047 0.164 5 -0.255 4 9
TNF 0.023 0.066 -9999 0 -0.266 9 9
VCAM1 -0.007 0.119 -9999 0 -0.407 15 15
platelet activation -0.038 0.136 -9999 0 -0.421 22 22
MAPKKK cascade 0.01 0.03 0.092 8 -0.128 1 9
IL18 -0.045 0.081 -9999 0 -0.234 26 26
negative regulation of macrophage activation -0.009 0.02 -9999 0 -0.067 18 18
LEF -0.009 0.02 -9999 0 -0.068 18 18
CASP1 -0.019 0.034 -9999 0 -0.077 50 50
mol:cAMP -0.038 0.137 -9999 0 -0.425 22 22
necrosis -0.009 0.02 -9999 0 -0.067 18 18
intracellular pH reduction 0 0 -9999 0 -9999 0 0
PAGA 0 0 -9999 0 -9999 0 0
Edema toxin (unfolded) 0.002 0.094 -9999 0 -0.264 18 18
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -9999 0 -9999 0 0
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.011 0.079 -9999 0 -0.293 12 12
PDGFRB 0.034 0.037 -9999 0 -0.485 1 1
SPHK1 -0.09 0.246 -9999 0 -0.735 25 25
mol:S1P -0.065 0.222 -9999 0 -0.631 25 25
S1P1/S1P/Gi -0.058 0.199 -9999 0 -0.468 27 27
GNAO1 0.031 0.018 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/PLCgamma1 -0.002 0.191 0.28 3 -0.42 20 23
PLCG1 -0.018 0.187 -9999 0 -0.457 18 18
mol:GTP 0 0 -9999 0 -9999 0 0
PDGFB-D/PDGFRB 0.034 0.037 -9999 0 -0.484 1 1
GNAI2 0.019 0.075 -9999 0 -0.435 5 5
GNAI3 0.027 0.053 -9999 0 -0.483 2 2
GNAI1 -0.017 0.143 -9999 0 -0.402 23 23
mol:GDP 0 0 -9999 0 -9999 0 0
EDG1 -0.016 0.138 -9999 0 -0.542 12 12
S1P1/S1P -0.057 0.217 -9999 0 -0.578 23 23
negative regulation of cAMP metabolic process -0.056 0.193 -9999 0 -0.454 27 27
MAPK3 -0.094 0.249 -9999 0 -0.621 30 30
calcium-dependent phospholipase C activity -0.001 0.004 -9999 0 -9999 0 0
Rac1/GDP 0.024 0.008 -9999 0 -9999 0 0
RhoA/GDP 0.026 0.003 -9999 0 -9999 0 0
KDR 0.022 0.063 -9999 0 -0.372 2 2
PLCB2 -0.05 0.189 -9999 0 -0.504 23 23
RAC1 0.033 0.011 -9999 0 -9999 0 0
RhoA/GTP -0.05 0.176 -9999 0 -0.476 23 23
receptor internalization -0.052 0.198 0.245 1 -0.518 24 25
PTGS2 -0.149 0.381 -9999 0 -1.048 29 29
Rac1/GTP -0.051 0.173 -9999 0 -0.471 23 23
RHOA 0.035 0.004 -9999 0 -9999 0 0
VEGFA -0.007 0.039 -9999 0 -0.137 15 15
negative regulation of T cell proliferation -0.056 0.193 -9999 0 -0.454 27 27
GO:0007205 0 0 -9999 0 -9999 0 0
GNAZ 0.018 0.067 -9999 0 -0.28 8 8
MAPK1 -0.082 0.235 -9999 0 -0.61 27 27
S1P1/S1P/PDGFB-D/PDGFRB -0.035 0.22 0.307 2 -0.554 22 24
ABCC1 0.031 0.043 -9999 0 -0.298 3 3
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.002 0.278 -9999 0 -0.778 11 11
CRP -0.057 0.255 -9999 0 -0.786 12 12
cell cycle arrest -0.08 0.29 -9999 0 -0.833 17 17
TIMP1 -0.046 0.241 -9999 0 -0.721 13 13
IL6ST 0.032 0.024 -9999 0 -9999 0 0
Rac1/GDP -0.063 0.183 -9999 0 -0.537 16 16
AP1 0.009 0.149 -9999 0 -0.478 4 4
GAB2 0.037 0.007 -9999 0 -9999 0 0
TNFSF11 -0.108 0.41 -9999 0 -1.013 30 30
HSP90B1 -0.001 0.087 -9999 0 -1.041 1 1
GAB1 0.029 0.054 -9999 0 -0.398 3 3
MAPK14 -0.07 0.19 -9999 0 -0.66 12 12
AKT1 0.029 0.081 -9999 0 -0.421 4 4
FOXO1 0.031 0.079 -9999 0 -0.401 4 4
MAP2K6 -0.067 0.178 -9999 0 -0.516 16 16
mol:GTP 0 0.002 -9999 0 -9999 0 0
MAP2K4 -0.078 0.187 -9999 0 -0.548 17 17
MITF -0.06 0.167 -9999 0 -0.443 19 19
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -9999 0 0
TYK2 0.035 0.006 -9999 0 -9999 0 0
A2M -0.029 0.28 -9999 0 -1.33 9 9
CEBPB 0.016 0.039 -9999 0 -0.483 1 1
GRB2/SOS1/GAB family/SHP2 0.018 0.101 -9999 0 -0.411 4 4
STAT3 -0.087 0.31 -9999 0 -0.904 17 17
STAT1 0.016 0.03 -9999 0 -9999 0 0
CEBPD -0.047 0.255 -9999 0 -0.783 11 11
PIK3CA 0.036 0.008 -9999 0 -9999 0 0
PI3K 0.047 0.05 -9999 0 -0.349 3 3
JUN -0.017 0.15 -9999 0 -0.405 25 25
PIAS3/MITF -0.049 0.169 -9999 0 -0.464 16 16
MAPK11 -0.068 0.187 -9999 0 -0.647 12 12
STAT3 (dimer)/FOXO1 -0.04 0.24 -9999 0 -0.671 14 14
GRB2/SOS1/GAB family 0.004 0.173 -9999 0 -0.447 13 13
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.067 0.145 -9999 0 -0.449 16 16
GRB2 0.035 0.009 -9999 0 -9999 0 0
JAK2 0.015 0.078 -9999 0 -0.273 12 12
LBP 0.042 0.23 -9999 0 -0.566 10 10
PIK3R1 0.029 0.062 -9999 0 -0.483 3 3
JAK1 0.031 0.038 -9999 0 -0.47 1 1
MYC -0.068 0.33 -9999 0 -0.96 18 18
FGG -0.073 0.267 -9999 0 -0.833 14 14
macrophage differentiation -0.08 0.29 -9999 0 -0.833 17 17
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.048 0.172 -9999 0 -0.288 55 55
JUNB -0.07 0.263 -9999 0 -0.795 15 15
FOS -0.063 0.171 -9999 0 -0.318 56 56
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.061 0.164 -9999 0 -0.483 15 15
STAT1/PIAS1 -0.033 0.166 -9999 0 -0.472 11 11
GRB2/SOS1/GAB family/SHP2/PI3K 0.038 0.075 -9999 0 -0.387 3 3
STAT3 (dimer) -0.084 0.307 -9999 0 -0.89 17 17
PRKCD -0.07 0.229 0.363 9 -0.609 18 27
IL6R 0.019 0.08 -9999 0 -0.345 8 8
SOCS3 -0.078 0.256 -9999 0 -1.094 9 9
gp130 (dimer)/JAK1/JAK1/LMO4 0.03 0.106 -9999 0 -0.291 13 13
Rac1/GTP -0.064 0.191 -9999 0 -0.554 16 16
HCK -0.013 0.11 -9999 0 -0.352 17 17
MAPKKK cascade 0.043 0.11 -9999 0 -0.479 5 5
bone resorption -0.094 0.382 -9999 0 -0.928 30 30
IRF1 -0.088 0.302 -9999 0 -0.957 15 15
mol:GDP -0.071 0.185 -9999 0 -0.51 19 19
SOS1 0.037 0.007 -9999 0 -9999 0 0
VAV1 -0.073 0.187 -9999 0 -0.519 19 19
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.069 0.209 -9999 0 -0.724 13 13
PTPN11 0.009 0.116 -9999 0 -0.92 3 3
IL6/IL6RA -0.077 0.166 -9999 0 -0.34 49 49
gp130 (dimer)/TYK2/TYK2/LMO4 0.035 0.098 -9999 0 -0.294 12 12
gp130 (dimer)/JAK2/JAK2/LMO4 0.023 0.109 -9999 0 -0.274 19 19
IL6 -0.119 0.203 -9999 0 -0.345 82 82
PIAS3 0.033 0.024 -9999 0 -0.204 2 2
PTPRE 0.019 0.069 -9999 0 -0.336 6 6
PIAS1 0.034 0.009 -9999 0 -9999 0 0
RAC1 0.033 0.011 -9999 0 -9999 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.057 0.133 -9999 0 -0.328 22 22
LMO4 -0.017 0.133 -9999 0 -0.323 28 28
STAT3 (dimer)/PIAS3 -0.077 0.293 -9999 0 -0.853 16 16
MCL1 0.034 0.136 -9999 0 -1.127 2 2
Caspase cascade in apoptosis

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
TOP1 -0.032 0.143 -9999 0 -0.496 11 11
ACTA1 -0.047 0.149 0.283 3 -0.386 22 25
NUMA1 -0.022 0.157 -9999 0 -0.496 11 11
SPTAN1 -0.046 0.148 0.42 1 -0.4 21 22
LIMK1 -0.058 0.17 0.26 4 -0.402 25 29
BIRC3 -0.011 0.126 -9999 0 -0.303 28 28
BIRC2 0.034 0.018 -9999 0 -0.204 1 1
BAX 0.029 0.046 -9999 0 -0.274 4 4
CASP10 -0.056 0.104 -9999 0 -0.307 26 26
CRMA 0 0 -9999 0 -9999 0 0
XIAP 0 0 -9999 0 -9999 0 0
PTK2 -0.023 0.141 -9999 0 -0.478 11 11
DIABLO 0.036 0.004 -9999 0 -9999 0 0
apoptotic nuclear changes -0.045 0.146 0.419 1 -0.393 21 22
response to UV 0 0 -9999 0 -9999 0 0
CRADD 0.025 0.071 -9999 0 -0.483 4 4
GSN -0.054 0.152 0.424 1 -0.39 23 24
MADD 0.036 0.002 -9999 0 -9999 0 0
TFAP2A 0.023 0.106 -9999 0 -0.674 4 4
BID -0.024 0.071 0.133 1 -0.192 28 29
MAP3K1 -0.006 0.079 -9999 0 -0.585 2 2
TRADD 0.036 0.004 -9999 0 -9999 0 0
mol:Ca2+ 0 0 -9999 0 -9999 0 0
APAF-1/Pro-Caspase 9 0.027 0.085 -9999 0 -0.335 9 9
mol:Activated DNA 0 0 -9999 0 -9999 0 0
ARHGDIB -0.057 0.161 0.317 3 -0.401 26 29
CASP9 0.033 0.009 -9999 0 -9999 0 0
DNA repair -0.004 0.065 0.287 3 -0.19 6 9
neuron apoptosis -0.037 0.225 -9999 0 -0.735 18 18
mol:NAD 0 0 -9999 0 -9999 0 0
DNA fragmentation during apoptosis -0.035 0.163 -9999 0 -0.426 18 18
APAF1 0.008 0.107 -9999 0 -0.352 15 15
CASP6 -0.013 0.18 -9999 0 -0.877 7 7
TRAF2 0.033 0.024 -9999 0 -0.204 2 2
ICAD/CAD -0.048 0.138 -9999 0 -0.394 19 19
CASP7 0.019 0.089 0.276 10 -0.357 3 13
KRT18 0.013 0.065 -9999 0 -0.427 3 3
apoptosis -0.046 0.151 0.296 1 -0.45 16 17
DFFA -0.046 0.142 0.219 1 -0.399 20 21
DFFB -0.048 0.143 -9999 0 -0.399 20 20
PARP1 0.003 0.065 0.19 6 -0.29 3 9
actin filament polymerization 0.063 0.165 0.404 25 -0.348 2 27
TNF 0.023 0.066 -9999 0 -0.266 9 9
CYCS -0.01 0.068 0.201 2 -0.264 5 7
SATB1 -0.062 0.187 -9999 0 -0.836 7 7
SLK -0.047 0.143 0.219 1 -0.399 20 21
p15 BID/BAX -0.017 0.086 -9999 0 -0.249 11 11
CASP2 0.019 0.067 0.224 5 -0.319 2 7
JNK cascade 0.006 0.079 0.58 2 -9999 0 2
CASP3 -0.047 0.151 0.227 2 -0.403 22 24
LMNB2 0.014 0.121 0.288 1 -0.486 6 7
RIPK1 0.036 0.004 -9999 0 -9999 0 0
CASP4 0.019 0.08 -9999 0 -0.328 9 9
Mammalian IAPs/DIABLO 0.035 0.085 -9999 0 -0.263 11 11
negative regulation of DNA binding 0.023 0.105 -9999 0 -0.665 4 4
stress fiber formation -0.047 0.14 0.218 1 -0.392 20 21
GZMB -0.042 0.121 -9999 0 -0.364 21 21
CASP1 -0.058 0.141 -9999 0 -0.337 38 38
LMNB1 -0.015 0.152 0.288 1 -0.634 6 7
APP -0.038 0.229 -9999 0 -0.747 18 18
TNFRSF1A 0.035 0.007 -9999 0 -9999 0 0
response to stress 0 0 -9999 0 -9999 0 0
CASP8 0.005 0.043 -9999 0 -0.347 3 3
VIM -0.043 0.153 0.281 2 -0.458 16 18
LMNA 0.022 0.088 0.288 1 -0.364 5 6
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.019 0.064 -9999 0 -0.334 2 2
LRDD 0.035 0.017 -9999 0 -0.204 1 1
SREBF1 -0.048 0.142 0.219 1 -0.398 20 21
APAF-1/Caspase 9 -0.028 0.178 -9999 0 -0.626 15 15
nuclear fragmentation during apoptosis -0.021 0.151 -9999 0 -0.482 11 11
CFL2 -0.065 0.17 0.35 2 -0.415 25 27
GAS2 -0.125 0.168 -9999 0 -0.376 43 43
positive regulation of apoptosis 0.009 0.117 0.3 1 -0.51 6 7
PRF1 0.003 0.089 -9999 0 -0.226 25 25
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.033 0.036 -9999 0 -0.483 1 1
alphaV beta3 Integrin 0.039 0.061 -9999 0 -0.349 4 4
PTK2 -0.023 0.148 -9999 0 -0.401 23 23
positive regulation of JNK cascade -0.001 0.126 -9999 0 -0.314 16 16
CDC42/GDP 0.01 0.184 -9999 0 -0.435 20 20
Rac1/GDP 0.003 0.18 -9999 0 -0.432 20 20
RAP1B 0.035 0.004 -9999 0 -9999 0 0
RAP1A 0.034 0.008 -9999 0 -9999 0 0
CTNNB1 0.011 0.093 -9999 0 -0.297 15 15
CDC42/GTP 0.012 0.16 -9999 0 -0.389 15 15
nectin-3/I-afadin -0.008 0.14 -9999 0 -0.359 26 26
RAPGEF1 -0.014 0.172 -9999 0 -0.437 24 24
mol:GTP 0 0 -9999 0 -9999 0 0
CRK -0.031 0.186 -9999 0 -0.5 24 24
PDGFB-D/PDGFRB 0.033 0.036 -9999 0 -0.482 1 1
TLN1 -0.018 0.071 0.195 2 -0.266 7 9
Rap1/GTP -0.005 0.128 -9999 0 -0.333 17 17
IQGAP1 0.034 0.008 -9999 0 -9999 0 0
Rap1/GTP/I-afadin 0.054 0.06 -9999 0 -0.27 6 6
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.008 0.14 -9999 0 -0.359 26 26
PVR 0.033 0.036 -9999 0 -0.483 1 1
Necl-5(dimer) 0.033 0.036 -9999 0 -0.482 1 1
mol:GDP -0.012 0.212 -9999 0 -0.53 21 21
MLLT4 0.02 0.087 -9999 0 -0.483 6 6
PIK3CA 0.035 0.006 -9999 0 -9999 0 0
PI3K 0.04 0.134 -9999 0 -0.273 28 28
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.038 0.07 -9999 0 -0.349 6 6
positive regulation of lamellipodium assembly -0.018 0.154 -9999 0 -0.358 22 22
PVRL1 0.034 0.017 -9999 0 -0.204 1 1
PVRL3 -0.027 0.16 -9999 0 -0.399 30 30
PVRL2 0.03 0.043 -9999 0 -0.297 3 3
PIK3R1 0.028 0.062 -9999 0 -0.483 3 3
CDH1 0.011 0.111 -9999 0 -0.483 10 10
CLDN1 -0.031 0.164 -9999 0 -0.396 32 32
JAM-A/CLDN1 -0.015 0.165 -9999 0 -0.3 47 47
SRC -0.052 0.199 -9999 0 -0.546 25 25
ITGB3 0.033 0.018 -9999 0 -0.204 1 1
nectin-1(dimer)/I-afadin/I-afadin 0.038 0.07 -9999 0 -0.349 6 6
FARP2 0.003 0.202 -9999 0 -0.564 8 8
RAC1 0.033 0.011 -9999 0 -9999 0 0
CTNNA1 0.035 0.006 -9999 0 -9999 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.015 0.13 -9999 0 -0.318 24 24
nectin-1/I-afadin 0.038 0.07 -9999 0 -0.349 6 6
nectin-2/I-afadin 0.035 0.076 -9999 0 -0.349 7 7
RAC1/GTP/IQGAP1/filamentous actin 0.042 0.017 -9999 0 -9999 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.014 0.129 -9999 0 -0.306 26 26
CDC42/GTP/IQGAP1/filamentous actin 0.042 0.019 -9999 0 -9999 0 0
F11R 0.022 0.08 -9999 0 -0.483 5 5
positive regulation of filopodium formation -0.001 0.126 -9999 0 -0.314 16 16
alphaV/beta3 Integrin/Talin -0.023 0.107 -9999 0 -0.311 7 7
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.035 0.076 -9999 0 -0.349 7 7
nectin-2(dimer)/I-afadin/I-afadin 0.035 0.076 -9999 0 -0.349 7 7
PIP5K1C -0.019 0.074 -9999 0 -0.199 27 27
VAV2 -0.04 0.256 -9999 0 -0.599 23 23
RAP1/GDP 0.017 0.172 -9999 0 -0.398 20 20
ITGAV 0.021 0.083 -9999 0 -0.403 7 7
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.012 0.128 -9999 0 -0.307 25 25
nectin-3(dimer)/I-afadin/I-afadin -0.008 0.14 -9999 0 -0.359 26 26
Rac1/GTP -0.019 0.189 -9999 0 -0.442 22 22
PTPRM -0.02 0.084 -9999 0 -0.218 29 29
E-cadherin/beta catenin/alpha catenin 0.051 0.128 -9999 0 -0.33 16 16
adherens junction assembly 0 0 -9999 0 -9999 0 0
CDC42 0.032 0.019 -9999 0 -0.204 1 1
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.034 0.017 -9999 0 -0.204 1 1
Syndecan-3/Src/Cortactin -0.013 0.145 -9999 0 -0.471 13 13
Syndecan-3/Neurocan -0.025 0.127 -9999 0 -0.461 15 15
POMC 0.02 0.075 -9999 0 -0.287 10 10
EGFR 0.016 0.09 -9999 0 -0.413 8 8
Syndecan-3/EGFR -0.012 0.142 -9999 0 -0.441 17 17
AGRP 0.033 0.023 -9999 0 -0.204 2 2
NCSTN 0.034 0.007 -9999 0 -9999 0 0
PSENEN 0.031 0.04 -9999 0 -0.343 2 2
RP11-540L11.1 0 0 -9999 0 -9999 0 0
APH1B 0.02 0.073 -9999 0 -0.297 9 9
APH1A 0.003 0.107 -9999 0 -0.307 19 19
NCAN 0 0 -9999 0 -9999 0 0
long-term memory 0.003 0.15 -9999 0 -0.47 15 15
Syndecan-3/IL8 -0.082 0.179 -9999 0 -0.477 22 22
PSEN1 0.032 0.019 -9999 0 -0.204 1 1
Src/Cortactin 0.021 0.052 -9999 0 -0.349 3 3
FYN 0.006 0.108 -9999 0 -0.343 16 16
limb bud formation -0.023 0.13 -9999 0 -0.492 14 14
MC4R 0.024 0.017 -9999 0 -9999 0 0
SRC 0.011 0.062 -9999 0 -0.483 3 3
PTN -0.013 0.142 -9999 0 -0.407 22 22
FGFR/FGF/Syndecan-3 -0.024 0.132 -9999 0 -0.497 14 14
neuron projection morphogenesis -0.032 0.13 -9999 0 -0.457 13 13
Syndecan-3/AgRP -0.001 0.137 -9999 0 -0.479 14 14
Syndecan-3/AgRP/MC4R 0.004 0.135 -9999 0 -0.457 14 14
Fyn/Cortactin 0.028 0.085 -9999 0 -0.349 8 8
SDC3 -0.024 0.133 -9999 0 -0.502 14 14
GO:0007205 0 0 -9999 0 -9999 0 0
positive regulation of leukocyte migration -0.081 0.176 -9999 0 -0.469 22 22
IL8 -0.135 0.216 -9999 0 -0.359 90 90
Syndecan-3/Fyn/Cortactin 0.003 0.154 -9999 0 -0.482 15 15
Syndecan-3/CASK -0.025 0.127 -9999 0 -0.461 15 15
alpha-MSH/MC4R 0.024 0.059 -9999 0 -0.338 3 3
Gamma Secretase 0.05 0.099 -9999 0 -0.262 10 10
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.083 0.157 -9999 0 -0.395 26 26
IKBKB 0.003 0.089 0.25 2 -0.267 4 6
AKT1 -0.032 0.09 0.276 5 -0.249 10 15
IKBKG 0.003 0.076 0.253 2 -0.25 1 3
CALM1 -0.015 0.12 0.221 1 -0.405 11 12
PIK3CA 0.035 0.006 -9999 0 -9999 0 0
MAP3K1 -0.067 0.186 0.471 1 -0.535 18 19
MAP3K7 0.033 0.036 -9999 0 -0.483 1 1
mol:Ca2+ -0.014 0.129 0.233 1 -0.389 14 15
DOK1 0.032 0.039 -9999 0 -0.343 2 2
AP-1 -0.064 0.1 -9999 0 -0.243 23 23
LYN 0.03 0.013 -9999 0 -9999 0 0
BLNK 0.004 0.118 -9999 0 -0.44 13 13
SHC1 0.035 0.007 -9999 0 -9999 0 0
BCR complex 0.011 0.107 -9999 0 -0.319 17 17
CD22 -0.052 0.158 -9999 0 -0.626 11 11
CAMK2G -0.014 0.112 -9999 0 -0.393 9 9
CSNK2A1 0.028 0.015 -9999 0 -9999 0 0
INPP5D 0 0 -9999 0 -9999 0 0
SHC/GRB2/SOS1 0.002 0.089 -9999 0 -0.448 2 2
GO:0007205 -0.015 0.131 0.233 1 -0.395 14 15
SYK 0.029 0.053 -9999 0 -0.39 3 3
ELK1 -0.016 0.124 0.221 1 -0.413 11 12
NFATC1 -0.084 0.175 0.324 2 -0.441 27 29
B-cell antigen/BCR complex 0.011 0.107 -9999 0 -0.319 17 17
PAG1/CSK 0.031 0.066 -9999 0 -0.349 5 5
NFKBIB 0.014 0.043 0.152 1 -0.126 7 8
HRAS -0.003 0.108 0.237 3 -0.405 6 9
NFKBIA 0.014 0.042 0.152 1 -0.122 6 7
NF-kappa-B/RelA/I kappa B beta 0.02 0.038 0.153 1 -9999 0 1
RasGAP/Csk -0.03 0.165 -9999 0 -0.302 41 41
mol:GDP -0.011 0.127 0.22 3 -0.403 12 15
PTEN 0.026 0.062 -9999 0 -0.483 3 3
CD79B 0.001 0.111 -9999 0 -0.321 19 19
NF-kappa-B/RelA/I kappa B alpha 0.021 0.038 0.153 1 -9999 0 1
GRB2 0.034 0.008 -9999 0 -9999 0 0
PI3K/BCAP/CD19 -0.057 0.169 -9999 0 -0.552 14 14
PIK3R1 0.028 0.062 -9999 0 -0.483 3 3
mol:IP3 -0.015 0.132 0.234 1 -0.4 14 15
CSK 0.033 0.01 -9999 0 -9999 0 0
FOS -0.056 0.141 -9999 0 -0.38 22 22
CHUK -0.014 0.106 0.253 2 -0.331 11 13
IBTK 0.029 0.046 -9999 0 -0.274 4 4
CARD11/BCL10/MALT1/TAK1 -0.013 0.127 0.27 3 -0.391 9 12
PTPN6 -0.05 0.15 -9999 0 -0.609 10 10
RELA 0.035 0.004 -9999 0 -9999 0 0
BCL2A1 0.003 0.038 -9999 0 -9999 0 0
VAV2 -0.093 0.213 -9999 0 -0.571 27 27
ubiquitin-dependent protein catabolic process 0.018 0.042 0.154 1 -0.122 6 7
BTK -0.058 0.299 -9999 0 -1.169 14 14
CD19 -0.066 0.17 -9999 0 -0.624 12 12
MAP4K1 0.034 0.018 -9999 0 -0.204 1 1
CD72 -0.028 0.154 -9999 0 -0.352 34 34
PAG1 0.015 0.083 -9999 0 -0.403 7 7
MAPK14 -0.057 0.16 0.447 1 -0.48 15 16
SH3BP5 0.018 0.094 -9999 0 -0.483 7 7
PIK3AP1 -0.033 0.139 0.231 1 -0.431 14 15
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.033 0.178 -9999 0 -0.531 16 16
RAF1 -0.003 0.103 0.23 3 -0.385 6 9
RasGAP/p62DOK/SHIP -0.034 0.159 -9999 0 -0.296 41 41
CD79A 0.016 0.079 -9999 0 -0.268 13 13
re-entry into mitotic cell cycle -0.063 0.099 -9999 0 -0.246 20 20
RASA1 0.024 0.073 -9999 0 -0.427 5 5
MAPK3 -0.005 0.1 0.224 2 -0.359 7 9
MAPK1 -0.003 0.089 0.228 1 -0.327 6 7
CD72/SHP1 -0.053 0.18 -9999 0 -0.581 15 15
NFKB1 0.035 0.006 -9999 0 -9999 0 0
MAPK8 -0.056 0.159 0.447 1 -0.471 15 16
actin cytoskeleton organization -0.063 0.192 0.46 2 -0.47 27 29
NF-kappa-B/RelA 0.04 0.073 0.28 1 -9999 0 1
Calcineurin 0.003 0.122 -9999 0 -0.392 9 9
PI3K -0.063 0.142 -9999 0 -0.441 16 16
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.015 0.137 0.236 4 -0.438 13 17
SOS1 0.036 0.002 -9999 0 -9999 0 0
Bam32/HPK1 -0.147 0.349 -9999 0 -0.806 43 43
DAPP1 -0.187 0.398 -9999 0 -0.936 43 43
cytokine secretion -0.078 0.163 0.32 2 -0.408 27 29
mol:DAG -0.015 0.132 0.234 1 -0.4 14 15
PLCG2 -0.012 0.132 -9999 0 -0.328 27 27
MAP2K1 -0.003 0.097 0.24 1 -0.36 6 7
B-cell antigen/BCR complex/FcgammaRIIB -0.049 0.166 -9999 0 -0.313 49 49
mol:PI-3-4-5-P3 -0.057 0.1 0.206 1 -0.308 16 17
ETS1 -0.015 0.109 -9999 0 -0.359 11 11
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.034 0.118 -9999 0 -0.291 15 15
B-cell antigen/BCR complex/LYN -0.046 0.172 -9999 0 -0.587 14 14
MALT1 0.021 0.039 -9999 0 -0.483 1 1
TRAF6 0.036 0.004 -9999 0 -9999 0 0
RAC1 -0.077 0.196 -9999 0 -0.506 27 27
B-cell antigen/BCR complex/LYN/SYK -0.013 0.159 -9999 0 -0.569 10 10
CARD11 -0.016 0.136 0.263 5 -0.404 11 16
FCGR2B -0.085 0.198 -9999 0 -0.369 61 61
PPP3CA 0.034 0.018 -9999 0 -0.204 1 1
BCL10 0.033 0.036 -9999 0 -0.483 1 1
IKK complex 0.004 0.045 0.157 4 -0.12 2 6
PTPRC -0.025 0.152 -9999 0 -0.366 31 31
PDPK1 -0.032 0.088 0.261 6 -0.22 13 19
PPP3CB 0.035 0.007 -9999 0 -9999 0 0
PPP3CC 0.016 0.073 -9999 0 -0.427 5 5
POU2F2 0.017 0.028 0.14 1 -9999 0 1
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.034 0.017 -9999 0 -0.204 1 1
ITGB7 0 0.13 -9999 0 -0.483 14 14
ITGA4 0.01 0.112 -9999 0 -0.458 11 11
alpha4/beta7 Integrin 0.005 0.131 -9999 0 -0.361 23 23
alpha4/beta1 Integrin 0.033 0.084 -9999 0 -0.349 9 9
LPA receptor mediated events

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
GNB1/GNG2 0.03 0.057 -9999 0 -0.217 7 7
NF kappa B1 p50/RelA/I kappa B alpha -0.002 0.091 -9999 0 -0.27 7 7
AP1 -0.069 0.108 -9999 0 -0.227 57 57
mol:PIP3 -0.016 0.069 -9999 0 -0.223 18 18
AKT1 0.02 0.065 0.268 1 -0.358 1 2
PTK2B -0.038 0.091 -9999 0 -0.196 46 46
RHOA 0.015 0.057 0.265 2 -0.259 3 5
PIK3CB 0.033 0.036 -9999 0 -0.481 1 1
mol:Ca2+ -0.02 0.078 0.212 1 -0.247 17 18
MAGI3 0.032 0.036 -9999 0 -0.483 1 1
RELA 0.035 0.004 -9999 0 -9999 0 0
apoptosis 0.004 0.049 -9999 0 -0.219 8 8
HRAS/GDP 0.024 0.028 -9999 0 -0.24 2 2
positive regulation of microtubule depolymerization -0.034 0.087 0.191 1 -0.254 9 10
NF kappa B1 p50/RelA -0.034 0.078 -9999 0 -0.25 14 14
endothelial cell migration -0.007 0.117 -9999 0 -0.328 19 19
ADCY4 -0.031 0.107 -9999 0 -0.319 17 17
ADCY5 -0.012 0.084 -9999 0 -0.296 11 11
ADCY6 -0.013 0.085 -9999 0 -0.296 11 11
ADCY7 -0.015 0.087 -9999 0 -0.296 11 11
ADCY1 -0.014 0.084 -9999 0 -0.282 12 12
ADCY2 -0.014 0.085 -9999 0 -0.274 13 13
ADCY3 -0.022 0.094 -9999 0 -0.29 14 14
ADCY8 -0.014 0.082 -9999 0 -0.285 11 11
ADCY9 -0.016 0.088 -9999 0 -0.266 15 15
GSK3B -0.038 0.09 0.168 2 -0.224 21 23
arachidonic acid secretion -0.015 0.091 -9999 0 -0.28 15 15
GNG2 0.033 0.01 -9999 0 -9999 0 0
TRIP6 -0.014 0.108 -9999 0 -0.43 12 12
GNAO1 0.009 0.054 -9999 0 -0.243 7 7
HRAS 0.032 0.04 -9999 0 -0.343 2 2
NFKBIA -0.026 0.082 -9999 0 -0.277 9 9
GAB1 0.028 0.054 -9999 0 -0.39 3 3
mol:GTP 0 0 -9999 0 -9999 0 0
lamellipodium assembly -0.004 0.232 -9999 0 -0.845 14 14
JUN -0.018 0.15 -9999 0 -0.405 25 25
LPA/LPA2/NHERF2 0.002 0.07 -9999 0 -0.278 10 10
TIAM1 -0.027 0.265 -9999 0 -0.973 15 15
PIK3R1 0.028 0.062 -9999 0 -0.482 3 3
mol:IP3 -0.027 0.075 0.213 1 -0.251 17 18
PLCB3 -0.008 0.085 0.192 4 -0.263 16 20
FOS -0.063 0.171 -9999 0 -0.319 56 56
positive regulation of mitosis -0.015 0.091 -9999 0 -0.28 15 15
LPA/LPA1-2-3 -0.007 0.044 -9999 0 -0.129 19 19
mol:Ca ++ 0 0 -9999 0 -9999 0 0
JNK cascade 0 0.001 -9999 0 -9999 0 0
BCAR1 0.034 0.017 -9999 0 -0.204 1 1
stress fiber formation -0.002 0.063 -9999 0 -0.282 3 3
GNAZ 0.001 0.07 -9999 0 -0.301 8 8
EGFR/PI3K-beta/Gab1 -0.007 0.075 -9999 0 -0.23 18 18
positive regulation of dendritic cell cytokine production -0.007 0.044 -9999 0 -0.128 19 19
LPA/LPA2/MAGI-3 0.017 0.033 -9999 0 -0.289 1 1
ARHGEF1 0.032 0.077 0.204 22 -0.208 7 29
GNAI2 0.002 0.071 -9999 0 -0.282 10 10
GNAI3 0.005 0.061 -9999 0 -0.252 9 9
GNAI1 -0.02 0.099 -9999 0 -0.288 22 22
LPA/LPA3 -0.006 0.022 -9999 0 -0.067 19 19
LPA/LPA2 -0.005 0.022 -9999 0 -0.066 19 19
LPA/LPA1 -0.008 0.059 -9999 0 -0.172 19 19
HB-EGF/EGFR -0.018 0.097 -9999 0 -0.336 14 14
HBEGF -0.022 0.087 -9999 0 -0.351 11 11
mol:DAG -0.027 0.075 0.213 1 -0.251 17 18
cAMP biosynthetic process -0.019 0.091 -9999 0 -0.294 13 13
NFKB1 0.035 0.006 -9999 0 -9999 0 0
SRC 0.011 0.062 -9999 0 -0.483 3 3
GNB1 0.034 0.008 -9999 0 -9999 0 0
LYN 0.001 0.077 0.195 2 -0.255 4 6
GNAQ -0.003 0.018 -9999 0 -0.087 7 7
LPAR2 0 0.001 -9999 0 -9999 0 0
LPAR3 -0.001 0.001 -9999 0 -9999 0 0
LPAR1 -0.006 0.034 -9999 0 -0.104 19 19
IL8 -0.141 0.232 -9999 0 -0.478 58 58
PTK2 0.01 0.045 -9999 0 -0.207 6 6
Rac1/GDP 0.024 0.008 -9999 0 -9999 0 0
CASP3 0.004 0.05 -9999 0 -0.22 8 8
EGFR 0.015 0.089 -9999 0 -0.414 8 8
PLCG1 -0.002 0.031 -9999 0 -0.128 9 9
PLD2 0.01 0.046 -9999 0 -0.203 7 7
G12/G13 0.031 0.058 -9999 0 -0.221 7 7
PI3K-beta 0.006 0.057 -9999 0 -0.404 1 1
cell migration 0.015 0.085 -9999 0 -0.237 13 13
SLC9A3R2 0.008 0.11 -9999 0 -0.397 13 13
PXN -0.002 0.064 -9999 0 -0.287 3 3
HRAS/GTP -0.016 0.093 -9999 0 -0.286 15 15
RAC1 0.033 0.011 -9999 0 -9999 0 0
MMP9 -0.006 0.09 -9999 0 -0.297 15 15
PRKCE 0.033 0.036 -9999 0 -0.484 1 1
PRKCD -0.02 0.078 0.203 1 -0.251 15 16
Gi(beta/gamma) -0.015 0.097 -9999 0 -0.287 17 17
mol:LPA -0.006 0.034 -9999 0 -0.104 19 19
TRIP6/p130 Cas/FAK1/Paxillin 0.029 0.099 -9999 0 -0.405 4 4
MAPKKK cascade -0.015 0.091 -9999 0 -0.28 15 15
contractile ring contraction involved in cytokinesis 0.016 0.057 0.264 2 -0.257 3 5
mol:GDP 0 0 -9999 0 -9999 0 0
GNA14 -0.018 0.081 -9999 0 -0.202 27 27
GNA15 0.003 0.038 -9999 0 -0.216 3 3
GNA12 0.033 0.01 -9999 0 -9999 0 0
GNA13 0.034 0.009 -9999 0 -9999 0 0
MAPT -0.035 0.088 0.193 1 -0.26 9 10
GNA11 0.006 0.034 -9999 0 -0.126 9 9
Rac1/GTP -0.006 0.245 -9999 0 -0.896 14 14
MMP2 -0.008 0.117 -9999 0 -0.329 19 19
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.005 0.07 -9999 0 -0.236 15 15
epithelial cell differentiation 0.041 0.093 -9999 0 -0.259 15 15
CYFIP2 0.009 0.112 -9999 0 -0.458 11 11
ENAH -0.042 0.089 0.279 1 -0.358 5 6
EGFR 0.016 0.09 -9999 0 -0.413 8 8
EPHA2 0.011 0.088 -9999 0 -0.278 15 15
MYO6 -0.009 0.083 -9999 0 -0.249 19 19
CTNNB1 0.011 0.093 -9999 0 -0.297 15 15
ABI1/Sra1/Nap1 0.044 0.089 -9999 0 -0.307 10 10
AQP5 -0.023 0.093 -9999 0 -0.471 4 4
CTNND1 0.036 0.004 -9999 0 -9999 0 0
mol:PI-4-5-P2 -0.005 0.074 -9999 0 -0.246 15 15
regulation of calcium-dependent cell-cell adhesion -0.039 0.101 -9999 0 -0.247 33 33
EGF -0.088 0.187 -9999 0 -0.32 72 72
NCKAP1 0.021 0.068 -9999 0 -0.259 10 10
AQP3 -0.038 0.109 -9999 0 -0.37 15 15
cortical microtubule organization 0.041 0.093 -9999 0 -0.259 15 15
GO:0000145 -0.026 0.064 -9999 0 -0.235 15 15
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.048 0.096 -9999 0 -0.261 15 15
MLLT4 0.02 0.087 -9999 0 -0.483 6 6
ARF6/GDP -0.051 0.089 -9999 0 -0.383 7 7
ARF6 0.028 0.051 -9999 0 -0.483 2 2
Ephrin A1/EPHA2/NCK1/GIT1 0.047 0.097 -9999 0 -0.287 11 11
mol:Ca2+ 0 0 -9999 0 -9999 0 0
VASP -0.015 0.076 -9999 0 -0.27 5 5
PVRL2 0.03 0.043 -9999 0 -0.297 3 3
ZYX -0.006 0.08 -9999 0 -0.249 17 17
ARF6/GTP 0.046 0.103 -9999 0 -0.272 13 13
CDH1 0.011 0.111 -9999 0 -0.483 10 10
EGFR/EGFR/EGF/EGF -0.043 0.139 -9999 0 -0.271 44 44
RhoA/GDP 0.044 0.091 -9999 0 -0.248 15 15
actin cytoskeleton organization -0.016 0.078 -9999 0 -0.246 15 15
IGF-1R heterotetramer 0.03 0.04 -9999 0 -0.343 2 2
GIT1 0.033 0.018 -9999 0 -0.204 1 1
IGF1R 0.03 0.04 -9999 0 -0.343 2 2
IGF1 0.015 0.081 -9999 0 -0.263 14 14
DIAPH1 0.021 0.185 -9999 0 -0.64 10 10
Wnt receptor signaling pathway -0.041 0.093 0.259 15 -9999 0 15
RHOA 0.035 0.004 -9999 0 -9999 0 0
RhoA/GTP -0.05 0.087 -9999 0 -0.401 6 6
CTNNA1 0.035 0.006 -9999 0 -9999 0 0
VCL -0.016 0.079 -9999 0 -0.251 15 15
EFNA1 0.021 0.076 -9999 0 -0.363 7 7
LPP -0.026 0.067 -9999 0 -0.31 1 1
Ephrin A1/EPHA2 0.014 0.118 -9999 0 -0.299 20 20
SEC6/SEC8 -0.014 0.093 -9999 0 -0.4 7 7
MGAT3 -0.04 0.102 -9999 0 -0.251 33 33
HGF/MET 0.028 0.098 -9999 0 -0.261 17 17
HGF 0.03 0.043 -9999 0 -0.297 3 3
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.005 0.07 -9999 0 -0.238 15 15
actin cable formation -0.02 0.101 0.239 7 -0.299 8 15
KIAA1543 -0.035 0.08 -9999 0 -0.409 3 3
KIFC3 -0.007 0.08 -9999 0 -0.25 16 16
NCK1 0.026 0.071 -9999 0 -0.483 4 4
EXOC3 0.035 0.006 -9999 0 -9999 0 0
ACTN1 -0.004 0.076 -9999 0 -0.25 15 15
NCK1/GIT1 0.042 0.058 -9999 0 -0.349 4 4
mol:GDP 0.041 0.093 -9999 0 -0.259 15 15
EXOC4 0.034 0.007 -9999 0 -9999 0 0
STX4 -0.029 0.064 -9999 0 -0.248 15 15
PIP5K1C -0.005 0.075 -9999 0 -0.25 15 15
LIMA1 0 0 -9999 0 -9999 0 0
ABI1 0.035 0.004 -9999 0 -9999 0 0
ROCK1 -0.033 0.093 0.3 1 -0.399 4 5
adherens junction assembly -0.013 0.095 0.38 1 -0.469 2 3
IGF-1R heterotetramer/IGF1 0.019 0.099 -9999 0 -0.252 19 19
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.035 0.076 -9999 0 -0.349 7 7
MET 0.027 0.056 -9999 0 -0.343 4 4
PLEKHA7 -0.003 0.076 -9999 0 -0.25 15 15
mol:GTP 0.045 0.096 -9999 0 -0.286 11 11
establishment of epithelial cell apical/basal polarity -0.026 0.096 -9999 0 -0.385 7 7
cortical actin cytoskeleton stabilization 0.005 0.07 -9999 0 -0.236 15 15
regulation of cell-cell adhesion -0.016 0.078 -9999 0 -0.246 15 15
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.005 0.07 -9999 0 -0.238 15 15
Syndecan-4-mediated signaling events

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
PTK2 0.009 0.117 -9999 0 -0.451 11 11
Syndecan-4/Syndesmos 0.065 0.167 -9999 0 -0.488 10 10
positive regulation of JNK cascade 0.031 0.203 -9999 0 -0.502 17 17
Syndecan-4/ADAM12 0.037 0.192 -9999 0 -0.505 15 15
CCL5 -0.04 0.163 -9999 0 -0.35 40 40
Rac1/GDP 0.024 0.008 -9999 0 -9999 0 0
DNM2 0.035 0.006 -9999 0 -9999 0 0
ITGA5 0.025 0.049 -9999 0 -0.204 9 9
SDCBP 0.03 0.02 -9999 0 -0.204 1 1
PLG 0.002 0.047 -9999 0 -0.461 1 1
ADAM12 -0.025 0.14 -9999 0 -0.305 36 36
mol:GTP 0 0 -9999 0 -9999 0 0
NUDT16L1 0.035 0.005 -9999 0 -9999 0 0
mol:PI-4-5-P2 0 0 -9999 0 -9999 0 0
Syndecan-4/PKC alpha -0.021 0.026 -9999 0 -9999 0 0
Syndecan-4/Laminin alpha1 0.034 0.159 -9999 0 -0.481 11 11
Syndecan-4/CXCL12/CXCR4 0.033 0.214 -9999 0 -0.533 17 17
Syndecan-4/Laminin alpha3 0.027 0.171 -9999 0 -0.506 11 11
MDK -0.01 0.131 -9999 0 -0.338 25 25
Syndecan-4/FZD7 0.023 0.197 -9999 0 -0.514 14 14
Syndecan-4/Midkine 0.043 0.184 -9999 0 -0.527 11 11
FZD7 -0.058 0.18 -9999 0 -0.355 50 50
Syndecan-4/FGFR1/FGF 0.045 0.188 -9999 0 -0.506 12 12
THBS1 0.016 0.085 -9999 0 -0.359 9 9
integrin-mediated signaling pathway 0.049 0.177 -9999 0 -0.488 13 13
positive regulation of MAPKKK cascade 0.031 0.203 -9999 0 -0.502 17 17
Syndecan-4/TACI 0.044 0.165 -9999 0 -0.48 11 11
CXCR4 -0.028 0.15 -9999 0 -0.324 37 37
cell adhesion -0.005 0.075 0.188 5 -0.302 9 14
Syndecan-4/Dynamin 0.059 0.171 -9999 0 -0.482 11 11
Syndecan-4/TSP1 0.05 0.18 -9999 0 -0.508 12 12
Syndecan-4/GIPC 0.057 0.173 -9999 0 -0.482 11 11
Syndecan-4/RANTES 0.026 0.192 -9999 0 -0.533 12 12
ITGB1 0.034 0.017 -9999 0 -0.204 1 1
LAMA1 0.026 0.016 -9999 0 -9999 0 0
LAMA3 0.004 0.087 -9999 0 -0.278 15 15
RAC1 0.033 0.011 -9999 0 -9999 0 0
PRKCA 0.022 0.136 0.67 8 -0.419 1 9
Syndecan-4/alpha-Actinin 0.052 0.167 -9999 0 -0.482 11 11
TFPI 0.024 0.058 -9999 0 -0.235 9 9
F2 0.036 0.083 -9999 0 -0.396 6 6
alpha5/beta1 Integrin 0.043 0.041 -9999 0 -9999 0 0
positive regulation of cell adhesion 0.017 0.161 -9999 0 -0.503 10 10
ACTN1 0.033 0.01 -9999 0 -9999 0 0
TNC 0.011 0.086 -9999 0 -0.25 18 18
Syndecan-4/CXCL12 0.042 0.192 -9999 0 -0.5 14 14
FGF6 0.027 0.056 -9999 0 -0.343 4 4
RHOA 0.035 0.004 -9999 0 -9999 0 0
CXCL12 -0.014 0.133 -9999 0 -0.319 29 29
TNFRSF13B 0.028 0.022 -9999 0 -0.204 1 1
FGF2 -0.003 0.115 -9999 0 -0.297 24 24
FGFR1 0.022 0.06 -9999 0 -0.297 6 6
Syndecan-4/PI-4-5-P2 -0.026 0.123 -9999 0 -0.48 11 11
mol:GDP 0 0 -9999 0 -9999 0 0
FN1 -0.044 0.125 -9999 0 -0.302 32 32
cell migration -0.011 0.015 -9999 0 -9999 0 0
PRKCD 0.006 0.034 -9999 0 -9999 0 0
vasculogenesis 0.05 0.175 -9999 0 -0.489 12 12
SDC4 -0.016 0.124 -9999 0 -0.506 11 11
Syndecan-4/Tenascin C 0.049 0.182 -9999 0 -0.506 13 13
Syndecan-4/PI-4-5-P2/PKC alpha -0.017 0.02 -9999 0 -9999 0 0
Syndecan-4/Syntenin 0.047 0.163 -9999 0 -0.488 10 10
MMP9 -0.005 0.09 -9999 0 -0.296 15 15
Rac1/GTP -0.005 0.077 0.189 5 -0.31 9 14
cytoskeleton organization 0.064 0.163 -9999 0 -0.471 10 10
GIPC1 0.029 0.053 -9999 0 -0.39 3 3
Syndecan-4/TFPI 0.058 0.175 -9999 0 -0.495 11 11
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.032 0.103 -9999 0 -0.304 15 15
E-cadherin/beta catenin 0.014 0.111 -9999 0 -0.356 15 15
CTNNB1 0.011 0.093 -9999 0 -0.297 15 15
JUP 0.033 0.018 -9999 0 -0.204 1 1
CDH1 0.011 0.111 -9999 0 -0.483 10 10
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.021 0.081 -9999 0 -0.437 6 6
SPHK1 -0.038 0.156 -9999 0 -0.323 42 42
GNAI2 0.024 0.073 -9999 0 -0.427 5 5
mol:S1P -0.02 0.099 -9999 0 -0.292 22 22
GNAO1 0.036 0.002 -9999 0 -9999 0 0
mol:Sphinganine-1-P -0.039 0.123 -9999 0 -0.368 22 22
growth factor activity 0 0 -9999 0 -9999 0 0
S1P/S1P2/G12/G13 0.011 0.09 -9999 0 -0.223 21 21
GNAI3 0.03 0.051 -9999 0 -0.483 2 2
G12/G13 0.046 0.018 -9999 0 -9999 0 0
S1PR3 0 0 -9999 0 -9999 0 0
S1PR2 0 0 -9999 0 -9999 0 0
EDG1 0.003 0.116 -9999 0 -0.378 16 16
S1P1/S1P -0.017 0.127 -9999 0 -0.308 27 27
S1PR5 0 0 -9999 0 -9999 0 0
S1PR4 0 0 -9999 0 -9999 0 0
GNAI1 -0.013 0.142 -9999 0 -0.398 23 23
S1P/S1P5/G12 -0.003 0.087 -9999 0 -0.234 21 21
S1P/S1P3/Gq -0.022 0.109 -9999 0 -0.293 21 21
S1P/S1P4/Gi -0.018 0.118 -9999 0 -0.358 15 15
GNAQ 0 0 -9999 0 -9999 0 0
GNAZ 0.022 0.064 -9999 0 -0.273 8 8
GNA14 -0.021 0.149 -9999 0 -0.367 29 29
GNA15 0.02 0.068 -9999 0 -0.259 10 10
GNA12 0.033 0.01 -9999 0 -9999 0 0
GNA13 0.034 0.009 -9999 0 -9999 0 0
GNA11 0.028 0.054 -9999 0 -0.39 3 3
ABCC1 0.031 0.043 -9999 0 -0.297 3 3
Ceramide 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
SPHK2 -0.014 0.092 -9999 0 -0.342 13 13
MAP4K4 0.002 0.08 -9999 0 -0.413 3 3
BAG4 0.027 0.051 -9999 0 -0.483 2 2
PKC zeta/ceramide -0.024 0.093 0.142 2 -0.24 21 23
NFKBIA 0.028 0.044 -9999 0 -0.297 3 3
BIRC3 -0.011 0.126 -9999 0 -0.303 28 28
BAX 0.004 0.052 -9999 0 -0.302 3 3
RIPK1 0.036 0.004 -9999 0 -9999 0 0
AKT1 -0.001 0.025 -9999 0 -9999 0 0
BAD -0.026 0.094 0.153 1 -0.242 21 22
SMPD1 0.022 0.049 0.183 2 -0.236 2 4
RB1 0.029 0.119 0.2 42 -0.27 11 53
FADD/Caspase 8 0.014 0.082 -9999 0 -0.429 4 4
MAP2K4 -0.029 0.094 -9999 0 -0.276 16 16
NSMAF 0.027 0.041 -9999 0 -0.343 2 2
response to UV 0 0 -9999 0 -9999 0 0
RAF1 -0.018 0.094 0.175 6 -0.247 16 22
EGF -0.088 0.187 -9999 0 -0.32 72 72
mol:ceramide -0.024 0.1 0.146 9 -0.255 21 30
MADD 0.036 0.002 -9999 0 -9999 0 0
response to oxidative stress 0 0 -9999 0 -9999 0 0
mol:Free Fatty acid -0.003 0.065 -9999 0 -0.328 6 6
ASAH1 0.028 0.015 -9999 0 -9999 0 0
negative regulation of cell cycle 0.028 0.119 0.199 42 -0.266 11 53
cell proliferation 0.007 0.096 0.206 1 -0.275 8 9
BID -0.001 0.15 -9999 0 -0.603 10 10
MAP3K1 -0.027 0.096 0.153 1 -0.25 21 22
EIF2A -0.028 0.083 -9999 0 -0.344 5 5
TRADD 0.036 0.004 -9999 0 -9999 0 0
CRADD 0.025 0.071 -9999 0 -0.483 4 4
MAPK3 -0.014 0.085 0.179 4 -0.32 5 9
response to heat 0 0 -9999 0 -9999 0 0
MAPK1 -0.017 0.085 0.18 3 -0.309 6 9
Cathepsin D/ceramide -0.01 0.105 0.17 1 -0.253 21 22
FADD 0.008 0.066 -9999 0 -0.464 1 1
KSR1 -0.019 0.097 0.174 6 -0.244 19 25
MAPK8 -0.023 0.097 -9999 0 -0.244 20 20
PRKRA -0.024 0.09 0.153 1 -0.234 21 22
PDGFA 0 0.107 -9999 0 -0.301 20 20
TRAF2 0.033 0.024 -9999 0 -0.204 2 2
IGF1 0.015 0.081 -9999 0 -0.263 14 14
mol:GD3 0 0 -9999 0 -9999 0 0
ganglioside biosynthetic process -0.024 0.1 0.146 9 -0.253 21 30
CTSD 0.031 0.043 -9999 0 -0.297 3 3
regulation of nitric oxide biosynthetic process 0.051 0.01 -9999 0 -9999 0 0
response to radiation 0 0 -9999 0 -9999 0 0
ERK1/PKC delta 0.009 0.103 0.221 1 -0.294 8 9
PRKCD 0.035 0.004 -9999 0 -9999 0 0
PRKCZ 0 0 -9999 0 -9999 0 0
mol:GW4869 0 0 -9999 0 -9999 0 0
mol:sphingosine -0.003 0.065 -9999 0 -0.328 6 6
RelA/NF kappa B1 0.051 0.01 -9999 0 -9999 0 0
mol:glutathione 0 0 -9999 0 -9999 0 0
PAWR 0.033 0.036 -9999 0 -0.483 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.016 0.07 -9999 0 -0.338 3 3
TNFR1A/BAG4/TNF-alpha 0.05 0.063 -9999 0 -0.294 4 4
mol:Sphingosine-1-phosphate -0.014 0.092 -9999 0 -0.341 13 13
MAP2K1 -0.019 0.089 0.178 3 -0.289 9 12
mol:C11AG 0 0 -9999 0 -9999 0 0
RELA 0.035 0.004 -9999 0 -9999 0 0
CYCS 0.032 0.072 0.172 7 -0.252 3 10
TNFRSF1A 0.035 0.007 -9999 0 -9999 0 0
NFKB1 0.035 0.006 -9999 0 -9999 0 0
TNFR1A/BAG4 0.042 0.044 -9999 0 -0.349 2 2
EIF2AK2 -0.026 0.085 -9999 0 -0.239 17 17
TNF-alpha/TNFR1A/FAN 0.05 0.056 -9999 0 -0.298 2 2
response to hydrogen peroxide 0 0 -9999 0 -9999 0 0
CASP8 0.025 0.091 -9999 0 -0.516 4 4
MAP2K2 -0.018 0.081 0.175 5 -0.254 9 14
SMPD3 -0.002 0.102 -9999 0 -0.316 17 17
TNF 0.023 0.066 -9999 0 -0.266 9 9
PKC zeta/PAR4 0.024 0.026 -9999 0 -0.347 1 1
mol:PHOSPHOCHOLINE 0.039 0.097 0.224 30 -0.301 2 32
NF kappa B1/RelA/I kappa B alpha 0.069 0.047 -9999 0 -0.255 2 2
AIFM1 0.023 0.08 0.164 12 -0.317 3 15
BCL2 -0.002 0.098 -9999 0 -0.308 16 16
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 0.05 0.012 -9999 0 -9999 0 0
VLDLR -0.084 0.198 -9999 0 -0.369 61 61
CRKL 0.029 0.051 -9999 0 -0.483 2 2
LRPAP1 0.035 0.007 -9999 0 -9999 0 0
FYN 0.006 0.108 -9999 0 -0.343 16 16
ITGA3 0.018 0.084 -9999 0 -0.378 8 8
RELN/VLDLR/Fyn -0.033 0.152 -9999 0 -0.316 38 38
MAPK8IP1/MKK7/MAP3K11/JNK1 0.092 0.047 -9999 0 -0.258 1 1
AKT1 -0.031 0.094 -9999 0 -0.225 32 32
MAP2K7 0.03 0.043 -9999 0 -0.297 3 3
RAPGEF1 0.035 0.004 -9999 0 -9999 0 0
DAB1 0.035 0.005 -9999 0 -9999 0 0
RELN/LRP8/DAB1 0.047 0.073 -9999 0 -0.27 9 9
LRPAP1/LRP8 0.031 0.084 -9999 0 -0.349 9 9
RELN/LRP8/DAB1/Fyn 0.042 0.099 -9999 0 -0.259 16 16
DAB1/alpha3/beta1 Integrin -0.023 0.137 -9999 0 -0.344 6 6
long-term memory 0.039 0.11 -9999 0 -0.263 17 17
DAB1/LIS1 -0.011 0.137 -9999 0 -0.248 41 41
DAB1/CRLK/C3G -0.017 0.133 -9999 0 -0.368 3 3
PIK3CA 0.035 0.006 -9999 0 -9999 0 0
DAB1/NCK2 -0.002 0.143 -9999 0 -0.252 40 40
ARHGEF2 0.033 0.018 -9999 0 -0.204 1 1
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -9999 0 0
GRIN2A 0.035 0.005 -9999 0 -9999 0 0
CDK5R1 0.035 0.007 -9999 0 -9999 0 0
RELN 0.033 0.018 -9999 0 -0.204 1 1
PIK3R1 0.028 0.062 -9999 0 -0.483 3 3
RELN/LRP8/Fyn 0.028 0.106 -9999 0 -0.302 16 16
GRIN2A/RELN/LRP8/DAB1/Fyn 0.057 0.107 -9999 0 -0.261 16 16
MAPK8 0.035 0.007 -9999 0 -9999 0 0
RELN/VLDLR/DAB1 -0.011 0.125 -9999 0 -0.27 32 32
ITGB1 0.034 0.017 -9999 0 -0.204 1 1
MAP1B -0.045 0.11 -9999 0 -0.243 41 41
RELN/LRP8 0.047 0.08 -9999 0 -0.298 9 9
GRIN2B/RELN/LRP8/DAB1/Fyn 0.046 0.116 -9999 0 -0.27 18 18
PI3K 0.045 0.049 -9999 0 -0.349 3 3
mol:PP2 0 0 -9999 0 -9999 0 0
alpha3/beta1 Integrin 0.035 0.068 -9999 0 -0.349 5 5
RAP1A -0.061 0.104 0.347 1 -0.351 3 4
PAFAH1B1 0.03 0.013 -9999 0 -9999 0 0
MAPK8IP1 0.033 0.023 -9999 0 -0.204 2 2
CRLK/C3G 0.046 0.041 -9999 0 -0.349 2 2
GRIN2B 0.018 0.071 -9999 0 -0.25 12 12
NCK2 0.035 0.017 -9999 0 -0.204 1 1
neuron differentiation 0.02 0.073 -9999 0 -0.286 3 3
neuron adhesion -0.062 0.114 0.329 2 -0.46 2 4
LRP8 0.009 0.109 -9999 0 -0.413 12 12
GSK3B -0.031 0.095 -9999 0 -0.49 2 2
RELN/VLDLR/DAB1/Fyn -0.015 0.14 -9999 0 -0.272 38 38
MAP3K11 0.036 0.004 -9999 0 -9999 0 0
RELN/VLDLR/DAB1/P13K -0.023 0.103 -9999 0 -0.238 32 32
CDK5 0.035 0.006 -9999 0 -9999 0 0
MAPT 0.017 0.13 0.816 5 -0.447 1 6
neuron migration -0.048 0.121 -9999 0 -0.394 4 4
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.02 0.073 -9999 0 -0.288 3 3
RELN/VLDLR -0.017 0.145 -9999 0 -0.273 41 41
IL2 signaling events mediated by STAT5

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
GAB2 0.036 0.004 -9999 0 -9999 0 0
ELF1 -0.009 0.107 -9999 0 -0.359 15 15
CCNA2 0.018 0.094 -9999 0 -0.483 7 7
PIK3CA 0.036 0.006 -9999 0 -9999 0 0
JAK3 0.036 0.005 -9999 0 -9999 0 0
PIK3R1 0.028 0.062 -9999 0 -0.483 3 3
JAK1 0.034 0.036 -9999 0 -0.483 1 1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.005 0.167 0.255 1 -0.475 15 16
SHC1 0.035 0.007 -9999 0 -9999 0 0
SP1 -0.017 0.134 -9999 0 -0.338 29 29
IL2RA -0.05 0.194 -9999 0 -0.704 15 15
IL2RB 0.018 0.084 -9999 0 -0.378 8 8
SOS1 0.036 0.003 -9999 0 -9999 0 0
IL2RG -0.02 0.158 -9999 0 -0.438 25 25
G1/S transition of mitotic cell cycle -0.08 0.268 0.34 1 -0.62 37 38
PTPN11 0.03 0.053 -9999 0 -0.39 3 3
CCND2 -0.088 0.265 -9999 0 -0.734 29 29
LCK -0.014 0.138 -9999 0 -0.354 26 26
GRB2 0.035 0.008 -9999 0 -9999 0 0
IL2 0.036 0.005 -9999 0 -9999 0 0
CDK6 0.025 0.066 -9999 0 -0.371 5 5
CCND3 0.009 0.146 -9999 0 -0.537 7 7
Signaling events mediated by PRL

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
CCNE1 0.026 0.058 -9999 0 -0.315 5 5
mol:Halofuginone 0.002 0.021 -9999 0 -0.207 2 2
ITGA1 0.02 0.088 -9999 0 -0.443 7 7
CDKN1A 0.039 0.106 -9999 0 -0.413 5 5
PRL-3/alpha Tubulin -0.009 0.098 -9999 0 -0.293 20 20
mol:Ca2+ -0.039 0.133 0.346 11 -0.363 15 26
AGT -0.051 0.166 -9999 0 -0.321 50 50
CCNA2 0.039 0.145 -9999 0 -0.61 3 3
TUBA1B 0 0 -9999 0 -9999 0 0
EGR1 -0.041 0.118 -9999 0 -0.336 24 24
CDK2/Cyclin E1 0.048 0.123 -9999 0 -0.414 4 4
MAPK3 -0.022 0.11 -9999 0 -0.365 18 18
PRL-2 /Rab GGTase beta 0.05 0.013 -9999 0 -9999 0 0
MAPK1 -0.013 0.093 -9999 0 -0.349 14 14
PTP4A1 -0.021 0.092 -9999 0 -0.711 2 2
PTP4A3 -0.013 0.136 -9999 0 -0.413 20 20
PTP4A2 0.034 0.008 -9999 0 -9999 0 0
ITGB1 -0.015 0.098 -9999 0 -0.356 15 15
SRC 0.011 0.062 -9999 0 -0.483 3 3
RAC1 0.006 0.141 -9999 0 -0.474 12 12
Rab GGTase beta/Rab GGTase alpha 0.047 0.017 -9999 0 -9999 0 0
PRL-1/ATF-5 0.054 0.143 -9999 0 -0.61 3 3
RABGGTA 0.033 0.01 -9999 0 -9999 0 0
BCAR1 0.009 0.099 0.358 15 -9999 0 15
RHOC 0.006 0.149 -9999 0 -0.445 15 15
RHOA 0.011 0.147 -9999 0 -0.472 13 13
cell motility -0.004 0.169 -9999 0 -0.452 17 17
PRL-1/alpha Tubulin -0.026 0.093 -9999 0 -0.608 3 3
PRL-3/alpha1 Integrin 0.003 0.115 -9999 0 -0.348 18 18
ROCK1 -0.001 0.167 -9999 0 -0.461 16 16
RABGGTB 0.035 0.006 -9999 0 -9999 0 0
CDK2 0.02 0.075 -9999 0 -0.287 10 10
mitosis -0.024 0.097 -9999 0 -0.637 3 3
ATF5 0.03 0.043 -9999 0 -0.297 3 3
Aurora B signaling

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
Condensin I complex -0.015 0.045 -9999 0 -0.1 41 41
STMN1 0.006 0.064 -9999 0 -0.426 4 4
Aurora B/RasGAP/Survivin 0.039 0.095 -9999 0 -0.364 9 9
Chromosomal passenger complex/Cul3 protein complex -0.042 0.119 -9999 0 -0.334 19 19
BIRC5 0.023 0.077 -9999 0 -0.449 5 5
DES -0.141 0.321 -9999 0 -0.675 53 53
Aurora C/Aurora B/INCENP 0.036 0.079 -9999 0 -0.267 11 11
Aurora B/TACC1 0.016 0.077 -9999 0 -0.304 9 9
Aurora B/PP2A 0.038 0.047 -9999 0 -0.352 2 2
mol:GTP 0 0 -9999 0 -9999 0 0
CBX5 0.005 0.036 -9999 0 -0.19 6 6
mitotic metaphase/anaphase transition 0.001 0.004 0.01 26 -0.009 2 28
NDC80 0.003 0.043 -9999 0 -0.353 3 3
Cul3 protein complex -0.031 0.135 -9999 0 -0.304 28 28
KIF2C -0.009 0.121 -9999 0 -0.628 6 6
PEBP1 -0.001 0.003 -9999 0 -0.018 4 4
KIF20A 0.026 0.072 -9999 0 -0.488 4 4
mol:GDP 0 0 -9999 0 -9999 0 0
Aurora B/RasGAP 0.029 0.076 -9999 0 -0.354 7 7
SEPT1 0.034 0.018 -9999 0 -0.204 1 1
SMC2 0 0 -9999 0 -9999 0 0
SMC4 0 0 -9999 0 -9999 0 0
NSUN2/NPM1/Nucleolin -0.082 0.236 -9999 0 -0.524 41 41
PSMA3 0.029 0.041 -9999 0 -0.343 2 2
G2/M transition of mitotic cell cycle 0.001 0.004 0.009 27 -0.008 1 28
H3F3B 0.008 0.058 -9999 0 -0.349 5 5
AURKB 0.022 0.065 -9999 0 -0.501 3 3
AURKC 0.033 0.024 -9999 0 -0.204 2 2
CDCA8 0.032 0.039 -9999 0 -0.518 1 1
cytokinesis -0.02 0.163 -9999 0 -0.477 15 15
Aurora B/Septin1 -0.012 0.171 -9999 0 -0.548 9 9
AURKA 0.001 0.004 0.009 27 -0.008 1 28
INCENP 0.013 0.1 -9999 0 -0.408 10 10
KLHL13 -0.098 0.182 -9999 0 -0.292 85 85
BUB1 0.024 0.081 -9999 0 -0.489 5 5
hSgo1/Aurora B/Survivin 0.036 0.087 -9999 0 -0.345 8 8
EVI5 0.031 0.04 -9999 0 -0.342 2 2
RhoA/GTP 0.016 0.151 -9999 0 -0.526 8 8
SGOL1 0.023 0.07 -9999 0 -0.323 7 7
CENPA -0.027 0.129 -9999 0 -0.36 14 14
NCAPG 0 0 -9999 0 -9999 0 0
Aurora B/HC8 Proteasome 0.035 0.06 -9999 0 -0.355 4 4
NCAPD2 0 0 -9999 0 -9999 0 0
Aurora B/PP1-gamma 0.038 0.052 -9999 0 -0.356 3 3
RHOA 0.035 0.004 -9999 0 -9999 0 0
NCAPH 0 0 -9999 0 -9999 0 0
NPM1 -0.051 0.182 -9999 0 -0.717 7 7
RASA1 0.024 0.073 -9999 0 -0.427 5 5
KLHL9 0.032 0.036 -9999 0 -0.483 1 1
mitotic prometaphase -0.001 0.003 -9999 0 -0.018 4 4
proteasomal ubiquitin-dependent protein catabolic process 0.035 0.06 -9999 0 -0.355 4 4
PPP1CC 0.036 0.004 -9999 0 -9999 0 0
Centraspindlin 0.005 0.164 -9999 0 -0.548 9 9
RhoA/GDP 0.026 0.003 -9999 0 -9999 0 0
NSUN2 -0.038 0.136 -9999 0 -0.297 40 40
MYLK 0.007 0.053 -9999 0 -0.314 5 5
KIF23 0.029 0.053 -9999 0 -0.499 2 2
VIM -0.018 0.103 -9999 0 -0.385 13 13
RACGAP1 0.032 0.038 -9999 0 -0.499 1 1
mitosis 0 0 -9999 0 -9999 0 0
NCL -0.052 0.165 -9999 0 -0.336 42 42
Chromosomal passenger complex -0.025 0.143 -9999 0 -0.408 14 14
Chromosomal passenger complex/EVI5 0.054 0.119 -9999 0 -0.335 13 13
TACC1 0.009 0.095 -9999 0 -0.333 13 13
PPP2R5D 0.034 0.017 -9999 0 -0.204 1 1
CUL3 0.032 0.029 -9999 0 -0.204 3 3
response to DNA damage stimulus 0 0 -9999 0 -9999 0 0
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.024 0.131 -9999 0 -0.3 22 22
MAP4K1 0.034 0.018 -9999 0 -0.204 1 1
MAP3K8 0.005 0.106 -9999 0 -0.312 18 18
PRKCB 0 0 -9999 0 -9999 0 0
DBNL 0.029 0.034 -9999 0 -0.204 4 4
CRKL 0.029 0.051 -9999 0 -0.483 2 2
MAP3K1 -0.015 0.11 -9999 0 -0.448 7 7
JUN -0.035 0.133 -9999 0 -0.503 10 10
MAP3K7 -0.014 0.111 -9999 0 -0.429 8 8
GRAP2 0.019 0.083 -9999 0 -0.403 7 7
CRK 0.03 0.013 -9999 0 -9999 0 0
MAP2K4 -0.032 0.134 -9999 0 -0.484 10 10
LAT 0.023 0.064 -9999 0 -0.273 8 8
LCP2 -0.027 0.156 -9999 0 -0.37 32 32
MAPK8 -0.009 0.123 -9999 0 -0.622 7 7
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.006 0.114 -9999 0 -0.475 6 6
LAT/GRAP2/SLP76/HPK1/HIP-55 0.032 0.127 -9999 0 -0.289 19 19
Signaling events mediated by PTP1B

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
PDGFRB 0.033 0.036 -9999 0 -0.483 1 1
Jak2/Leptin Receptor 0.029 0.127 0.275 2 -0.402 7 9
PTP1B/AKT1 0.023 0.098 0.203 1 -0.282 5 6
FYN 0.006 0.108 -9999 0 -0.343 16 16
p210 bcr-abl/PTP1B 0.017 0.105 0.202 5 -0.29 7 12
EGFR 0.011 0.091 -9999 0 -0.418 8 8
EGF/EGFR -0.013 0.145 -9999 0 -0.306 24 24
CSF1 0.034 0.018 -9999 0 -0.204 1 1
AKT1 0.03 0.03 -9999 0 -0.203 3 3
INSR 0.023 0.075 -9999 0 -0.391 6 6
PTP1B/N-cadherin 0.002 0.106 0.241 1 -0.297 10 11
Insulin Receptor/Insulin 0.04 0.098 -9999 0 -0.36 2 2
HCK -0.013 0.11 -9999 0 -0.352 17 17
CRK 0.03 0.013 -9999 0 -9999 0 0
TYK2 0.018 0.107 0.303 5 -0.279 7 12
EGF -0.087 0.189 -9999 0 -0.319 72 72
YES1 0.028 0.015 -9999 0 -9999 0 0
CAV1 0.026 0.126 0.237 10 -0.343 7 17
TXN 0.034 0.006 -9999 0 -9999 0 0
PTP1B/IRS1/GRB2 0.031 0.12 -9999 0 -0.288 9 9
cell migration -0.017 0.105 0.29 7 -0.202 5 12
STAT3 0.035 0.007 -9999 0 -9999 0 0
PRLR 0.009 0.118 -9999 0 -0.437 13 13
ITGA2B 0.034 0.006 -9999 0 -9999 0 0
CSF1R 0.018 0.09 -9999 0 -0.413 8 8
Prolactin Receptor/Prolactin 0.037 0.096 -9999 0 -0.354 11 11
FGR 0.025 0.044 -9999 0 -0.204 7 7
PTP1B/p130 Cas 0.028 0.107 0.241 1 -0.279 7 8
Crk/p130 Cas 0.029 0.105 -9999 0 -0.282 5 5
DOK1 0.02 0.1 0.221 3 -0.293 5 8
JAK2 0.022 0.122 -9999 0 -0.41 7 7
Jak2/Leptin Receptor/Leptin 0.02 0.133 -9999 0 -0.343 3 3
PIK3R1 0.028 0.062 -9999 0 -0.483 3 3
PTPN1 0.017 0.106 0.207 4 -0.293 7 11
LYN 0.03 0.013 -9999 0 -9999 0 0
CDH2 -0.003 0.095 -9999 0 -0.281 18 18
SRC 0.016 0.125 -9999 0 -0.511 7 7
ITGB3 0.032 0.018 -9999 0 -0.204 1 1
CAT1/PTP1B 0.018 0.185 0.267 24 -0.423 14 38
CAPN1 0.017 0.082 -9999 0 -0.319 10 10
CSK 0.033 0.01 -9999 0 -9999 0 0
PI3K 0.049 0.106 -9999 0 -0.407 3 3
mol:H2O2 -0.001 0.005 -9999 0 -9999 0 0
STAT3 (dimer) 0.019 0.127 -9999 0 -0.346 4 4
negative regulation of transcription 0.022 0.12 -9999 0 -0.404 7 7
FCGR2A -0.028 0.153 -9999 0 -0.356 33 33
FER 0.022 0.051 -9999 0 -0.204 10 10
alphaIIb/beta3 Integrin 0.047 0.017 -9999 0 -9999 0 0
BLK 0.007 0.089 -9999 0 -0.32 12 12
Insulin Receptor/Insulin/Shc 0.059 0.052 -9999 0 -0.298 3 3
RHOA 0.034 0.005 -9999 0 -9999 0 0
LEPR 0.024 0.062 -9999 0 -0.284 7 7
BCAR1 0.034 0.017 -9999 0 -0.204 1 1
p210 bcr-abl/Grb2 0.034 0.008 -9999 0 -9999 0 0
mol:NADPH -0.001 0.003 -9999 0 -9999 0 0
TRPV6 -0.051 0.221 0.235 2 -0.54 22 24
PRL 0.038 0.024 -9999 0 -0.201 2 2
SOCS3 -0.05 0.308 -9999 0 -1.274 12 12
SPRY2 -0.002 0.113 -9999 0 -0.442 12 12
Insulin Receptor/Insulin/IRS1 0.045 0.092 -9999 0 -0.364 8 8
CSF1/CSF1R 0.033 0.123 0.25 1 -0.31 9 10
Ras protein signal transduction -0.002 0.082 0.472 5 -9999 0 5
IRS1 0.013 0.098 -9999 0 -0.382 11 11
INS 0.035 0.008 -9999 0 -9999 0 0
LEP 0.022 0.066 -9999 0 -0.267 9 9
STAT5B 0.027 0.103 0.208 4 -0.268 6 10
STAT5A 0.025 0.107 0.208 4 -0.283 8 12
GRB2 0.034 0.008 -9999 0 -9999 0 0
PDGFB-D/PDGFRB 0.029 0.108 0.241 1 -0.286 8 9
CSN2 0.012 0.05 -9999 0 -9999 0 0
PIK3CA 0.035 0.006 -9999 0 -9999 0 0
LAT -0.011 0.173 -9999 0 -0.498 20 20
YBX1 0.046 0.029 -9999 0 -0.356 1 1
LCK -0.015 0.138 -9999 0 -0.354 26 26
SHC1 0.035 0.007 -9999 0 -9999 0 0
NOX4 -0.043 0.156 -9999 0 -0.306 47 47
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.049 0.032 -9999 0 -0.349 1 1
Necdin/E2F1 -0.004 0.091 -9999 0 -0.349 10 10
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.009 0.126 -9999 0 -0.25 36 36
NGF (dimer)/p75(NTR)/BEX1 0.045 0.019 -9999 0 -9999 0 0
NT-4/5 (dimer)/p75(NTR) 0.024 0.012 -9999 0 -0.133 1 1
IKBKB 0.031 0.012 -9999 0 -9999 0 0
AKT1 0.017 0.047 0.187 3 -0.254 3 6
IKBKG 0.035 0.017 -9999 0 -0.204 1 1
BDNF 0.017 0.084 -9999 0 -0.297 12 12
MGDIs/NGR/p75(NTR)/LINGO1 0.032 0.052 -9999 0 -0.295 3 3
FURIN 0.027 0.049 -9999 0 -0.259 5 5
proBDNF (dimer)/p75(NTR)/Sortilin 0.051 0.074 -9999 0 -0.332 5 5
LINGO1 0 0 -9999 0 -9999 0 0
Sortilin/TRAF6/NRIF 0.006 0.084 -9999 0 -0.241 15 15
proBDNF (dimer) 0.017 0.084 -9999 0 -0.296 12 12
NTRK1 0.033 0.018 -9999 0 -0.204 1 1
RTN4R 0.02 0.073 -9999 0 -0.297 9 9
neuron apoptosis -0.031 0.13 -9999 0 -0.485 7 7
IRAK1 0.034 0.023 -9999 0 -0.204 2 2
SHC1 0.018 0.01 -9999 0 -9999 0 0
ARHGDIA 0.035 0.006 -9999 0 -9999 0 0
RhoA/GTP 0.026 0.003 -9999 0 -9999 0 0
Gamma Secretase 0.05 0.099 -9999 0 -0.262 10 10
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.022 0.1 -9999 0 -0.264 18 18
MAGEH1 -0.026 0.151 -9999 0 -0.343 34 34
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.02 0.104 -9999 0 -0.279 18 18
Mammalian IAPs/DIABLO 0.035 0.085 -9999 0 -0.262 11 11
proNGF (dimer) 0 0 -9999 0 -9999 0 0
MAGED1 0.024 0.075 -9999 0 -0.39 6 6
APP 0.013 0.093 -9999 0 -0.356 11 11
NT-4/5 (dimer) 0 0 -9999 0 -9999 0 0
ZNF274 0.023 0.075 -9999 0 -0.39 6 6
RhoA/GDP/RHOGDI 0.05 0.023 -9999 0 -9999 0 0
NGF 0 0 -9999 0 -9999 0 0
cell cycle arrest -0.009 0.04 0.205 5 -0.232 2 7
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.025 0.04 -9999 0 -0.275 3 3
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.045 0.016 -9999 0 -9999 0 0
NCSTN 0.034 0.007 -9999 0 -9999 0 0
mol:GTP -0.001 0.11 -9999 0 -0.298 23 23
PSENEN 0.031 0.04 -9999 0 -0.343 2 2
mol:ceramide 0.022 0.036 0.189 5 -0.228 2 7
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.02 0.037 -9999 0 -0.222 4 4
p75(NTR)/beta APP 0.032 0.071 -9999 0 -0.349 5 5
BEX1 0.035 0.017 -9999 0 -0.204 1 1
mol:GDP 0.003 0.008 -9999 0 -9999 0 0
NGF (dimer) -0.046 0.144 -9999 0 -0.275 51 51
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.051 0.055 -9999 0 -0.27 3 3
PIK3R1 0.028 0.062 -9999 0 -0.483 3 3
RAC1/GTP 0.036 0.017 -9999 0 -9999 0 0
MYD88 0.036 0.004 -9999 0 -9999 0 0
CHUK 0.027 0.062 -9999 0 -0.483 3 3
NGF (dimer)/p75(NTR)/PKA 0 0.111 -9999 0 -0.299 23 23
RHOB 0.019 0.081 -9999 0 -0.315 10 10
RHOA 0.035 0.004 -9999 0 -9999 0 0
MAGE-G1/E2F1 0.021 0.047 -9999 0 -0.349 2 2
NT3 (dimer) 0.01 0.097 -9999 0 -0.323 14 14
TP53 -0.04 0.113 -9999 0 -0.267 37 37
PRDM4 0.022 0.036 0.189 5 -0.229 2 7
BDNF (dimer) -0.139 0.209 -9999 0 -0.338 94 94
PIK3CA 0.035 0.006 -9999 0 -9999 0 0
SORT1 0.032 0.04 -9999 0 -0.343 2 2
activation of caspase activity 0.004 0.122 -9999 0 -0.248 36 36
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.061 0.034 -9999 0 -0.23 2 2
RHOC 0.035 0.006 -9999 0 -9999 0 0
XIAP 0 0 -9999 0 -9999 0 0
MAPK10 -0.004 0.093 0.255 3 -0.348 3 6
DIABLO 0.036 0.004 -9999 0 -9999 0 0
SMPD2 0.022 0.036 0.189 5 -0.229 2 7
APH1B 0.02 0.073 -9999 0 -0.297 9 9
APH1A 0.003 0.107 -9999 0 -0.307 19 19
proNGF (dimer)/p75(NTR)/Sortilin 0.042 0.032 -9999 0 -0.252 2 2
PSEN1 0.032 0.019 -9999 0 -0.204 1 1
APAF-1/Pro-Caspase 9 0.027 0.085 -9999 0 -0.335 9 9
NT3 (dimer)/p75(NTR) 0.029 0.077 -9999 0 -0.335 7 7
MAPK8 0.006 0.084 0.255 3 -0.337 3 6
MAPK9 0.005 0.082 0.267 2 -0.344 2 4
APAF1 0.008 0.107 -9999 0 -0.353 15 15
NTF3 0.01 0.097 -9999 0 -0.323 14 14
NTF4 0 0 -9999 0 -9999 0 0
NDN -0.023 0.148 -9999 0 -0.367 29 29
RAC1/GDP 0.024 0.008 -9999 0 -9999 0 0
RhoA-B-C/GDP 0.019 0.11 -9999 0 -0.244 26 26
p75 CTF/Sortilin/TRAF6/NRIF 0.077 0.063 -9999 0 -0.272 5 5
RhoA-B-C/GTP -0.001 0.11 -9999 0 -0.297 23 23
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.072 0.091 -9999 0 -0.287 8 8
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.068 0.075 -9999 0 -0.305 5 5
PRKACB -0.032 0.166 -9999 0 -0.411 31 31
proBDNF (dimer)/p75 ECD 0.037 0.066 -9999 0 -0.349 4 4
ChemicalAbstracts:86-01-1 0 0 -9999 0 -9999 0 0
BIRC3 -0.011 0.126 -9999 0 -0.303 28 28
BIRC2 0.034 0.018 -9999 0 -0.204 1 1
neuron projection morphogenesis -0.063 0.102 -9999 0 -0.26 33 33
BAD -0.003 0.088 0.304 1 -0.328 3 4
RIPK2 0.022 0.063 -9999 0 -0.483 3 3
NGFR 0.033 0.018 -9999 0 -0.204 1 1
CYCS 0.009 0.057 0.187 3 -0.253 7 10
ADAM17 0.036 0.002 -9999 0 -9999 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.049 0.05 -9999 0 -0.293 3 3
BCL2L11 -0.003 0.087 0.304 1 -0.328 3 4
BDNF (dimer)/p75(NTR) 0.035 0.067 -9999 0 -0.349 4 4
PI3K 0.057 0.046 -9999 0 -0.27 3 3
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.056 0.039 -9999 0 -0.23 2 2
NDNL2 0.032 0.019 -9999 0 -0.204 1 1
YWHAE 0.03 0.013 -9999 0 -9999 0 0
PRKCI 0.028 0.056 -9999 0 -0.343 4 4
NGF (dimer)/p75(NTR) 0.024 0.012 -9999 0 -0.133 1 1
ChemicalAbstracts:146-91-8 0 0 -9999 0 -9999 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.053 0.059 -9999 0 -0.256 6 6
TRAF6 0.036 0.004 -9999 0 -9999 0 0
RAC1 0.033 0.011 -9999 0 -9999 0 0
PRKCZ 0 0 -9999 0 -9999 0 0
PLG 0.032 0.036 -9999 0 -0.483 1 1
oligodendrocyte cell fate commitment 0 0 -9999 0 -9999 0 0
CASP6 0.014 0.063 -9999 0 -0.307 6 6
SQSTM1 0.034 0.017 -9999 0 -0.204 1 1
NGFRAP1 -0.063 0.199 -9999 0 -0.444 43 43
CASP3 -0.004 0.083 0.242 1 -0.329 2 3
E2F1 0.014 0.052 -9999 0 -0.483 2 2
CASP9 0.033 0.009 -9999 0 -9999 0 0
IKK complex 0.057 0.059 -9999 0 -0.427 1 1
NGF (dimer)/TRKA 0.025 0.012 -9999 0 -0.133 1 1
MMP7 -0.122 0.22 -9999 0 -0.389 77 77
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.067 0.061 -9999 0 -0.243 6 6
MMP3 -0.133 0.221 -9999 0 -0.38 84 84
APAF-1/Caspase 9 -0.021 0.086 -9999 0 -0.369 4 4
IL2 signaling events mediated by PI3K

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
BCL2L1 0.063 0.143 -9999 0 -0.606 1 1
UGCG 0.009 0.093 -9999 0 -0.696 3 3
AKT1/mTOR/p70S6K/Hsp90/TERT -0.022 0.165 -9999 0 -0.438 17 17
mol:GTP 0 0 -9999 0 -9999 0 0
mol:glucosylceramide 0.008 0.092 -9999 0 -0.686 3 3
mol:DAG -0.011 0.015 0.174 1 -9999 0 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.036 0.211 -9999 0 -0.491 27 27
FRAP1 -0.056 0.247 -9999 0 -0.562 30 30
FOXO3 -0.038 0.197 -9999 0 -0.455 28 28
AKT1 -0.042 0.213 -9999 0 -0.493 28 28
GAB2 0.035 0.005 -9999 0 -9999 0 0
SMPD1 0.015 0.069 -9999 0 -0.844 1 1
SGMS1 -0.002 0.036 -9999 0 -0.082 22 22
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 0.004 0.038 -9999 0 -0.294 3 3
CALM1 0.032 0.011 -9999 0 -9999 0 0
cell proliferation 0.004 0.106 -9999 0 -0.284 14 14
EIF3A 0 0 -9999 0 -9999 0 0
PI3K 0.048 0.05 -9999 0 -0.349 3 3
RPS6KB1 -0.004 0.131 -9999 0 -0.804 4 4
mol:sphingomyelin -0.011 0.015 0.174 1 -9999 0 1
natural killer cell activation 0 0.003 -9999 0 -0.015 3 3
JAK3 0.037 0.007 -9999 0 -9999 0 0
PIK3R1 0.029 0.062 -9999 0 -0.483 3 3
JAK1 0.035 0.037 -9999 0 -0.485 1 1
NFKB1 0.035 0.006 -9999 0 -9999 0 0
MYC -0.027 0.27 -9999 0 -0.819 16 16
MYB -0.066 0.339 -9999 0 -1.267 15 15
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.025 0.179 -9999 0 -0.438 22 22
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.014 0.127 -9999 0 -0.742 4 4
mol:PI-3-4-5-P3 -0.024 0.174 -9999 0 -0.426 22 22
Rac1/GDP 0.023 0.04 -9999 0 -0.268 3 3
T cell proliferation -0.024 0.162 -9999 0 -0.398 22 22
SHC1 0.034 0.007 -9999 0 -9999 0 0
RAC1 0.032 0.011 -9999 0 -9999 0 0
positive regulation of cyclin-dependent protein kinase activity -0.001 0.018 -9999 0 -0.066 15 15
PRKCZ -0.026 0.168 -9999 0 -0.414 22 22
NF kappa B1 p50/RelA -0.023 0.22 -9999 0 -0.534 22 22
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.004 0.131 -9999 0 -0.441 11 11
HSP90AA1 0 0 -9999 0 -9999 0 0
RELA 0.035 0.004 -9999 0 -9999 0 0
IL2RA -0.039 0.164 -9999 0 -0.351 40 40
IL2RB 0.019 0.084 -9999 0 -0.377 8 8
TERT 0.025 0.066 -9999 0 -0.371 5 5
E2F1 -0.02 0.126 -9999 0 -0.426 17 17
SOS1 0.036 0.004 -9999 0 -9999 0 0
RPS6 0.033 0.024 -9999 0 -0.204 2 2
mol:cAMP 0 0.009 0.032 15 -9999 0 15
PTPN11 0.029 0.054 -9999 0 -0.391 3 3
IL2RG -0.019 0.159 -9999 0 -0.437 25 25
actin cytoskeleton organization -0.024 0.162 -9999 0 -0.398 22 22
GRB2 0.034 0.008 -9999 0 -9999 0 0
IL2 0.037 0.008 -9999 0 -9999 0 0
PIK3CA 0.037 0.008 -9999 0 -9999 0 0
Rac1/GTP 0.051 0.051 -9999 0 -0.253 3 3
LCK -0.013 0.138 -9999 0 -0.353 26 26
BCL2 -0.066 0.273 -9999 0 -0.805 20 20
Nongenotropic Androgen signaling

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
PTK2 0.008 0.004 -9999 0 -9999 0 0
GNB1/GNG2 0.049 0.05 -9999 0 -0.26 2 2
regulation of S phase of mitotic cell cycle 0.006 0.053 -9999 0 -0.27 6 6
GNAO1 0.036 0.002 -9999 0 -9999 0 0
HRAS 0.031 0.04 -9999 0 -0.343 2 2
SHBG/T-DHT 0.02 0.009 -9999 0 -9999 0 0
PELP1 0.029 0.014 -9999 0 -9999 0 0
AKT1 0.007 0.017 -9999 0 -0.133 3 3
MAP2K1 0.044 0.104 0.274 1 -0.292 1 2
T-DHT/AR 0.015 0.049 -9999 0 -0.174 11 11
G-protein coupled receptor activity 0 0 -9999 0 -9999 0 0
mol:GTP -0.002 0.003 -9999 0 -0.008 43 43
GNAI2 0.024 0.073 -9999 0 -0.427 5 5
GNAI3 0.03 0.051 -9999 0 -0.483 2 2
GNAI1 -0.013 0.142 -9999 0 -0.398 23 23
mol:GDP -0.005 0.041 -9999 0 -0.277 3 3
cell proliferation -0.004 0.175 0.274 2 -0.395 19 21
PIK3CA 0.035 0.006 -9999 0 -9999 0 0
FOS -0.093 0.318 -9999 0 -0.797 33 33
mol:Ca2+ -0.007 0.026 -9999 0 -0.072 22 22
MAPK3 0.019 0.141 0.268 4 -0.309 14 18
MAPK1 0 0.118 -9999 0 -0.406 6 6
PIK3R1 0.028 0.062 -9999 0 -0.483 3 3
mol:IP3 -0.001 0.002 -9999 0 -0.004 43 43
cAMP biosynthetic process 0.003 0.021 -9999 0 -9999 0 0
GNG2 0.033 0.01 -9999 0 -9999 0 0
potassium channel inhibitor activity -0.001 0.002 -9999 0 -0.004 43 43
HRAS/GTP 0.014 0.057 -9999 0 -0.267 3 3
actin cytoskeleton reorganization 0.041 0.041 -9999 0 -0.241 3 3
SRC 0.011 0.062 -9999 0 -0.483 3 3
voltage-gated calcium channel activity -0.001 0.002 -9999 0 -0.004 43 43
PI3K 0.041 0.042 -9999 0 -0.295 3 3
apoptosis 0.009 0.17 0.357 31 -0.237 1 32
T-DHT/AR/PELP1 0.029 0.048 -9999 0 -0.289 2 2
HRAS/GDP 0.043 0.069 -9999 0 -0.293 3 3
CREB1 -0.012 0.179 0.241 1 -0.38 31 32
RAC1-CDC42/GTP 0.052 0.046 -9999 0 -0.245 3 3
AR 0.02 0.07 -9999 0 -0.256 11 11
GNB1 0.034 0.008 -9999 0 -9999 0 0
RAF1 0.059 0.105 0.283 1 -0.256 3 4
RAC1-CDC42/GDP 0.061 0.07 -9999 0 -0.277 2 2
T-DHT/AR/PELP1/Src 0.02 0.054 -9999 0 -0.269 3 3
MAP2K2 0.044 0.103 -9999 0 -0.292 1 1
T-DHT/AR/PELP1/Src/PI3K 0.006 0.054 -9999 0 -0.272 6 6
GNAZ 0.022 0.064 -9999 0 -0.274 8 8
SHBG 0.029 0.014 -9999 0 -9999 0 0
Gi family/GNB1/GNG2/GDP 0.002 0.116 -9999 0 -0.445 8 8
mol:T-DHT -0.001 0.002 0.002 1 -0.004 29 30
RAC1 0.033 0.011 -9999 0 -9999 0 0
GNRH1 0.002 0.039 -9999 0 -0.22 5 5
Gi family/GTP -0.015 0.094 -9999 0 -0.256 22 22
CDC42 0.032 0.019 -9999 0 -0.204 1 1
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.04 0.067 -9999 0 -0.253 8 8
RGS9BP 0.007 0.1 -9999 0 -0.302 17 17
mol:GTP 0 0 -9999 0 -9999 0 0
GRK1 0 0 -9999 0 -9999 0 0
mol:Na + 0.012 0.08 -9999 0 -0.319 7 7
mol:ADP 0.009 0.01 -9999 0 -0.133 1 1
GNAT2 0.014 0.097 -9999 0 -0.399 10 10
RGS9-1/Gbeta5/R9AP 0.01 0.116 -9999 0 -0.302 20 20
mol:GDP 0 0 -9999 0 -9999 0 0
PDE6H/GNAT2/GTP 0.025 0.085 -9999 0 -0.317 11 11
GRK7 0.034 0.017 -9999 0 -0.204 1 1
CNGB3 0 0.094 -9999 0 -0.257 21 21
Cone Metarhodopsin II/X-Arrestin 0.027 0 -9999 0 -9999 0 0
mol:Ca2+ 0.023 0.1 0.188 30 -0.288 9 39
Cone PDE6 0.02 0.128 -9999 0 -0.276 23 23
Cone Metarhodopsin II 0.022 0.009 -9999 0 -9999 0 0
Na + (4 Units) 0.025 0.085 -9999 0 -0.287 9 9
GNAT2/GDP 0.012 0.121 -9999 0 -0.278 23 23
GNB5 -0.004 0.126 -9999 0 -0.38 19 19
mol:GMP (4 units) 0 0.08 0.189 3 -0.288 12 15
Cone Transducin 0.043 0.072 -9999 0 -0.27 8 8
SLC24A2 0.029 0.046 -9999 0 -0.273 4 4
GNB3/GNGT2 0.043 0.04 -9999 0 -0.349 1 1
GNB3 0.033 0.018 -9999 0 -0.204 1 1
GNAT2/GTP 0.011 0.07 -9999 0 -0.283 10 10
CNGA3 0.019 0.076 -9999 0 -0.28 11 11
ARR3 0.036 0 -9999 0 -9999 0 0
absorption of light 0 0 -9999 0 -9999 0 0
cGMP/Cone CNG Channel 0.012 0.08 -9999 0 -0.32 7 7
mol:Pi 0.009 0.116 -9999 0 -0.301 20 20
Cone CNG Channel 0.017 0.109 -9999 0 -0.286 15 15
mol:all-trans-retinal 0 0 -9999 0 -9999 0 0
mol:K + 0.029 0.046 -9999 0 -0.273 4 4
RGS9 0.025 0.051 -9999 0 -0.25 6 6
PDE6C 0.025 0.054 -9999 0 -0.244 7 7
GNGT2 0.028 0.046 -9999 0 -0.273 4 4
mol:cGMP (4 units) 0 0 -9999 0 -9999 0 0
PDE6H 0.022 0.08 -9999 0 -0.483 5 5
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.034 0.008 -9999 0 -9999 0 0
HDAC2 0.032 0.036 -9999 0 -0.483 1 1
GNB1/GNG2 0.022 0.097 -9999 0 -0.293 12 12
forebrain development -0.053 0.24 -9999 0 -0.7 19 19
GNAO1 0.036 0.003 -9999 0 -9999 0 0
SMO/beta Arrestin2 -0.001 0.105 -9999 0 -0.345 13 13
SMO -0.02 0.135 -9999 0 -0.305 33 33
ARRB2 0.027 0.038 -9999 0 -0.483 1 1
GLI3/SPOP 0.033 0.13 0.279 1 -0.405 6 7
mol:GTP 0 0.002 -9999 0 -9999 0 0
GSK3B 0.033 0.036 -9999 0 -0.483 1 1
GNAI2 0.024 0.073 -9999 0 -0.427 5 5
SIN3/HDAC complex 0.058 0.051 -9999 0 -0.272 1 1
GNAI1 -0.013 0.142 -9999 0 -0.398 23 23
XPO1 0.034 0.013 -9999 0 -9999 0 0
GLI1/Su(fu) -0.054 0.229 -9999 0 -0.808 13 13
SAP30 0.031 0.037 -9999 0 -0.483 1 1
mol:GDP -0.02 0.135 -9999 0 -0.305 33 33
MIM/GLI2A -0.012 0.131 -9999 0 -0.418 17 17
IFT88 0.004 0.105 -9999 0 -0.483 9 9
GNAI3 0.03 0.051 -9999 0 -0.485 2 2
GLI2 0.011 0.085 -9999 0 -0.407 4 4
GLI3 0.021 0.132 0.312 2 -0.422 6 8
CSNK1D 0.035 0.007 -9999 0 -9999 0 0
CSNK1E 0.025 0.064 -9999 0 -0.413 4 4
SAP18 0.026 0.016 -9999 0 -9999 0 0
embryonic digit morphogenesis 0.004 0.105 -9999 0 -0.482 9 9
GNG2 0.033 0.01 -9999 0 -9999 0 0
Gi family/GTP -0.026 0.13 -9999 0 -0.325 22 22
SIN3B 0.035 0.006 -9999 0 -9999 0 0
SIN3A 0.032 0.019 -9999 0 -0.204 1 1
GLI3/Su(fu) 0.025 0.127 0.314 1 -0.41 6 7
GLI2/Su(fu) 0.003 0.107 -9999 0 -0.474 5 5
FOXA2 -0.112 0.354 -9999 0 -0.951 29 29
neural tube patterning -0.053 0.24 -9999 0 -0.7 19 19
SPOP 0.034 0.008 -9999 0 -9999 0 0
Su(fu)/PIAS1 0.01 0.081 -9999 0 -0.635 1 1
GNB1 0.034 0.008 -9999 0 -9999 0 0
CSNK1G2 0.034 0.007 -9999 0 -9999 0 0
CSNK1G3 0.035 0.006 -9999 0 -9999 0 0
MTSS1 -0.012 0.131 -9999 0 -0.418 17 17
embryonic limb morphogenesis -0.053 0.24 -9999 0 -0.7 19 19
SUFU 0.002 0.072 -9999 0 -0.458 2 2
LGALS3 0.021 0.075 -9999 0 -0.39 6 6
catabolic process 0.033 0.14 -9999 0 -0.407 7 7
GLI3A/CBP 0.007 0.114 -9999 0 -0.367 16 16
KIF3A 0.03 0.051 -9999 0 -0.483 2 2
GLI1 -0.056 0.251 -9999 0 -0.731 19 19
RAB23 0.022 0.071 -9999 0 -0.308 8 8
CSNK1A1 0.035 0.006 -9999 0 -9999 0 0
IFT172 0.004 0.126 -9999 0 -0.483 13 13
RBBP7 0.034 0.023 -9999 0 -0.204 2 2
Su(fu)/Galectin3 0.006 0.094 -9999 0 -0.343 6 6
GNAZ 0.022 0.064 -9999 0 -0.274 8 8
RBBP4 0.031 0.029 -9999 0 -0.204 3 3
CSNK1G1 0.034 0.008 -9999 0 -9999 0 0
PIAS1 0.034 0.009 -9999 0 -9999 0 0
PRKACA 0.035 0.006 -9999 0 -9999 0 0
GLI2/SPOP 0.026 0.09 -9999 0 -0.386 5 5
STK36 0.029 0.045 -9999 0 -0.296 3 3
Gi family/GNB1/GNG2/GDP -0.022 0.13 -9999 0 -0.397 15 15
PTCH1 -0.045 0.208 -9999 0 -0.596 20 20
MIM/GLI1 -0.069 0.271 -9999 0 -0.654 28 28
CREBBP 0.007 0.114 -9999 0 -0.366 16 16
Su(fu)/SIN3/HDAC complex 0.022 0.1 -9999 0 -0.369 7 7
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR -0.02 0.192 -9999 0 -1.076 6 6
regulation of axonogenesis 0 0.064 0.336 5 -9999 0 5
myoblast fusion -0.012 0.081 0.369 8 -9999 0 8
mol:GTP 0.001 0.077 -9999 0 -0.258 10 10
regulation of calcium-dependent cell-cell adhesion -0.034 0.086 0.261 10 -9999 0 10
ARF1/GTP 0.023 0.068 -9999 0 -0.205 9 9
mol:GM1 -0.005 0.055 -9999 0 -0.229 5 5
mol:Choline 0.001 0.052 -9999 0 -0.271 5 5
lamellipodium assembly -0.021 0.126 -9999 0 -0.377 22 22
MAPK3 0 0.088 -9999 0 -0.311 12 12
ARF6/GTP/NME1/Tiam1 0.035 0.086 -9999 0 -0.262 10 10
ARF1 0.035 0.006 -9999 0 -9999 0 0
ARF6/GDP 0.012 0.081 -9999 0 -0.371 8 8
ARF1/GDP 0.005 0.1 -9999 0 -0.304 14 14
ARF6 0.027 0.069 -9999 0 -0.583 2 2
RAB11A 0.03 0.04 -9999 0 -0.343 2 2
TIAM1 0.027 0.055 -9999 0 -0.387 3 3
fibronectin binding 0 0 -9999 0 -9999 0 0
MAPK1 0.008 0.077 -9999 0 -0.323 8 8
actin filament bundle formation -0.009 0.103 0.299 15 -9999 0 15
KALRN 0.007 0.063 -9999 0 -0.307 7 7
RAB11FIP3/RAB11A 0.041 0.061 -9999 0 -0.375 4 4
RhoA/GDP 0.009 0.104 -9999 0 -0.301 15 15
NME1 0.03 0.039 -9999 0 -0.483 1 1
Rac1/GDP 0.008 0.1 -9999 0 -0.301 13 13
substrate adhesion-dependent cell spreading 0.001 0.076 -9999 0 -0.258 10 10
cortical actin cytoskeleton organization -0.021 0.127 -9999 0 -0.38 22 22
RAC1 0.033 0.011 -9999 0 -9999 0 0
liver development 0.001 0.076 -9999 0 -0.258 10 10
ARF6/GTP 0.001 0.077 -9999 0 -0.259 10 10
RhoA/GTP 0.023 0.068 -9999 0 -0.231 5 5
mol:GDP -0.014 0.099 -9999 0 -0.329 14 14
ARF6/GTP/RAB11FIP3/RAB11A 0.035 0.086 -9999 0 -0.321 6 6
RHOA 0.035 0.004 -9999 0 -9999 0 0
PLD1 0 0.072 -9999 0 -0.308 5 5
RAB11FIP3 0.028 0.062 -9999 0 -0.483 3 3
tube morphogenesis -0.021 0.126 -9999 0 -0.377 22 22
ruffle organization 0 0.064 -9999 0 -0.336 5 5
regulation of epithelial cell migration 0.001 0.076 -9999 0 -0.258 10 10
PLD2 0.013 0.047 -9999 0 -0.303 2 2
PIP5K1A 0 0.065 -9999 0 -0.337 5 5
mol:Phosphatidic acid 0.001 0.052 -9999 0 -0.271 5 5
Rac1/GTP -0.021 0.127 -9999 0 -0.381 22 22
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.004 0.101 -9999 0 -0.427 9 9
PDGF/PDGFRA/CRKL 0.031 0.08 -9999 0 -0.348 8 8
positive regulation of JUN kinase activity 0.066 0.07 -9999 0 -0.26 7 7
CRKL 0.029 0.051 -9999 0 -0.483 2 2
PDGF/PDGFRA/Caveolin-3 0.034 0.075 -9999 0 -0.34 7 7
AP1 -0.114 0.288 -9999 0 -0.75 28 28
mol:IP3 -0.01 0.051 -9999 0 -0.361 3 3
PLCG1 -0.01 0.051 -9999 0 -0.362 3 3
PDGF/PDGFRA/alphaV Integrin 0.024 0.1 -9999 0 -0.374 11 11
RAPGEF1 0.035 0.004 -9999 0 -9999 0 0
CRK 0.03 0.013 -9999 0 -9999 0 0
mol:Ca2+ -0.01 0.05 -9999 0 -0.361 3 3
CAV3 0.034 0.018 -9999 0 -0.204 1 1
CAV1 0.023 0.064 -9999 0 -0.273 8 8
SHC/Grb2/SOS1 0.068 0.071 -9999 0 -0.262 7 7
PDGF/PDGFRA/Shf -0.033 0.141 -9999 0 -0.357 26 26
FOS -0.13 0.267 0.316 4 -0.752 27 31
JUN -0.046 0.096 -9999 0 -0.359 15 15
oligodendrocyte development 0.024 0.1 -9999 0 -0.373 11 11
GRB2 0.034 0.008 -9999 0 -9999 0 0
PIK3R1 0.028 0.062 -9999 0 -0.483 3 3
mol:DAG -0.01 0.051 -9999 0 -0.361 3 3
PDGF/PDGFRA 0.004 0.1 -9999 0 -0.426 9 9
actin cytoskeleton reorganization 0.031 0.078 -9999 0 -0.342 7 7
SRF 0.011 0.03 -9999 0 -0.347 1 1
SHC1 0.035 0.007 -9999 0 -9999 0 0
PI3K 0.05 0.075 -9999 0 -0.291 8 8
PDGF/PDGFRA/Crk/C3G 0.044 0.07 -9999 0 -0.284 7 7
JAK1 -0.005 0.073 -9999 0 -0.345 8 8
ELK1/SRF 0.032 0.091 0.293 2 -0.278 4 6
SHB 0.032 0.029 -9999 0 -0.204 3 3
SHF -0.052 0.161 -9999 0 -0.306 52 52
CSNK2A1 0.025 0.031 -9999 0 -9999 0 0
GO:0007205 -0.007 0.061 0.233 4 -0.384 3 7
SOS1 0.036 0.002 -9999 0 -9999 0 0
Ras protein signal transduction 0.066 0.07 -9999 0 -0.26 7 7
PDGF/PDGFRA/SHB 0.032 0.078 -9999 0 -0.342 7 7
PDGF/PDGFRA/Caveolin-1 0.025 0.092 -9999 0 -0.38 8 8
ITGAV 0.021 0.083 -9999 0 -0.403 7 7
ELK1 -0.013 0.059 0.203 4 -0.339 3 7
PIK3CA 0.035 0.006 -9999 0 -9999 0 0
PDGF/PDGFRA/Crk 0.028 0.074 -9999 0 -0.337 7 7
JAK-STAT cascade -0.005 0.073 -9999 0 -0.344 8 8
cell proliferation -0.034 0.141 -9999 0 -0.356 26 26
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.024 0.028 -9999 0 -0.347 1 1
alphaV beta3 Integrin 0.032 0.094 -9999 0 -0.288 11 11
PTK2 0.038 0.106 0.355 3 -0.376 2 5
IGF1R 0.03 0.04 -9999 0 -0.343 2 2
PI4KB 0 0 -9999 0 -9999 0 0
MFGE8 0.017 0.085 -9999 0 -0.359 9 9
SRC 0.011 0.062 -9999 0 -0.483 3 3
CDKN1B 0.014 0.061 -9999 0 -0.393 3 3
VEGFA 0 0 -9999 0 -9999 0 0
ILK 0.021 0.034 -9999 0 -9999 0 0
ROCK1 0.028 0.015 -9999 0 -9999 0 0
AKT1 0.012 0.031 -9999 0 -9999 0 0
PTK2B 0.01 0.049 -9999 0 -0.249 5 5
alphaV/beta3 Integrin/JAM-A 0.038 0.1 -9999 0 -0.268 14 14
CBL 0.035 0.005 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
alphaV beta3 Integrin/ANGPTL3 0.048 0.08 -9999 0 -0.309 8 8
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.046 0.103 -9999 0 -0.292 12 12
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.017 0.043 -9999 0 -0.33 2 2
alphaV/beta3 Integrin/Syndecan-1 0.057 0.065 -9999 0 -0.316 5 5
PI4KA 0 0 -9999 0 -9999 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.012 0.141 -9999 0 -0.298 29 29
PI4 Kinase 0 0 -9999 0 -9999 0 0
PIK3CA 0.035 0.006 -9999 0 -9999 0 0
alphaV/beta3 Integrin/Osteopontin -0.091 0.162 -9999 0 -0.303 65 65
RPS6KB1 -0.063 0.103 -9999 0 -0.424 8 8
TLN1 0.035 0.006 -9999 0 -9999 0 0
MAPK3 -0.026 0.143 -9999 0 -0.491 13 13
GPR124 0.02 0.064 -9999 0 -0.273 8 8
MAPK1 -0.024 0.145 -9999 0 -0.491 14 14
PXN 0.036 0.004 -9999 0 -9999 0 0
PIK3R1 0.028 0.062 -9999 0 -0.483 3 3
alphaV/beta3 Integrin/Tumstatin 0.055 0.062 -9999 0 -0.298 4 4
cell adhesion 0.024 0.103 -9999 0 -0.283 17 17
ANGPTL3 0.022 0.076 -9999 0 -0.363 7 7
VEGFR2 homodimer/VEGFA homodimer/Src 0.02 0.046 -9999 0 -0.295 3 3
IGF-1R heterotetramer 0.03 0.04 -9999 0 -0.343 2 2
Rac1/GDP 0.024 0.008 -9999 0 -9999 0 0
TGFBR2 0.03 0.051 -9999 0 -0.483 2 2
ITGB3 0.033 0.018 -9999 0 -0.204 1 1
IGF1 0.015 0.081 -9999 0 -0.263 14 14
RAC1 0.033 0.011 -9999 0 -9999 0 0
regulation of cell-matrix adhesion 0.042 0.075 -9999 0 -0.309 6 6
apoptosis 0.021 0.082 -9999 0 -0.402 7 7
CD47 0.022 0.081 -9999 0 -0.437 6 6
alphaV/beta3 Integrin/CD47 0.049 0.084 -9999 0 -0.33 8 8
VCL 0.032 0.036 -9999 0 -0.483 1 1
alphaV/beta3 Integrin/Del1 0.008 0.133 -9999 0 -0.31 27 27
CSF1 0.034 0.018 -9999 0 -0.204 1 1
PIK3C2A 0.014 0.067 -9999 0 -0.465 3 3
PI4 Kinase/Pyk2 0.006 0.065 -9999 0 -0.223 9 9
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.053 0.059 -9999 0 -0.27 5 5
FAK1/Vinculin 0.055 0.103 0.313 2 -0.308 2 4
alphaV beta3/Integrin/ppsTEM5 0.042 0.075 -9999 0 -0.31 6 6
RHOA 0.035 0.004 -9999 0 -9999 0 0
VTN 0.034 0.008 -9999 0 -9999 0 0
BCAR1 0.034 0.017 -9999 0 -0.204 1 1
FGF2 -0.003 0.115 -9999 0 -0.297 24 24
F11R -0.013 0.091 -9999 0 -0.359 11 11
alphaV/beta3 Integrin/Lactadherin 0.043 0.083 -9999 0 -0.289 10 10
alphaV/beta3 Integrin/TGFBR2 0.054 0.068 -9999 0 -0.298 6 6
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.073 0.065 -9999 0 -0.272 5 5
HSP90AA1 0 0 -9999 0 -9999 0 0
alphaV/beta3 Integrin/Talin 0.054 0.054 -9999 0 -0.27 4 4
mol:GDP 0 0 -9999 0 -9999 0 0
FN1 -0.016 0.132 -9999 0 -0.3 32 32
alphaV/beta3 Integrin/Pyk2 0.038 0.056 -9999 0 -0.25 5 5
SDC1 0.033 0.036 -9999 0 -0.483 1 1
VAV3 -0.047 0.115 -9999 0 -0.265 43 43
PTPN11 0.029 0.053 -9999 0 -0.39 3 3
IRS1 0.013 0.098 -9999 0 -0.382 11 11
FAK1/Paxillin 0.058 0.102 0.313 2 -0.308 2 4
cell migration 0.049 0.097 0.263 4 -0.283 2 6
ITGAV 0.021 0.083 -9999 0 -0.403 7 7
PI3K 0.045 0.106 -9999 0 -0.318 2 2
SPP1 -0.172 0.221 -9999 0 -0.36 109 109
KDR 0.032 0.04 -9999 0 -0.343 2 2
mol:PI-4-5-P2 0 0 -9999 0 -9999 0 0
alphaV/beta3 Integrin/Caspase 8 0.021 0.082 -9999 0 -0.403 7 7
COL4A3 0.031 0.033 -9999 0 -0.204 4 4
angiogenesis -0.022 0.148 -9999 0 -0.529 12 12
Rac1/GTP -0.029 0.112 -9999 0 -0.248 37 37
EDIL3 -0.035 0.167 -9999 0 -0.393 34 34
cell proliferation 0.053 0.067 -9999 0 -0.297 6 6
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.027 0.051 -9999 0 -0.483 2 2
Caspase 8 (4 units) -0.019 0.16 -9999 0 -0.445 17 17
NEF -0.015 0.048 -9999 0 -0.168 15 15
NFKBIA 0.017 0.056 -9999 0 -0.308 3 3
BIRC3 -0.02 0.13 -9999 0 -0.471 12 12
CYCS -0.036 0.15 -9999 0 -0.49 13 13
RIPK1 0.036 0.004 -9999 0 -9999 0 0
CD247 -0.015 0.048 -9999 0 -0.168 15 15
MAP2K7 -0.014 0.158 -9999 0 -0.608 8 8
protein ubiquitination 0.015 0.068 0.249 1 -0.333 1 2
CRADD 0.025 0.071 -9999 0 -0.483 4 4
DAXX 0.036 0.004 -9999 0 -9999 0 0
FAS -0.037 0.169 -9999 0 -0.401 34 34
BID -0.046 0.152 -9999 0 -0.413 22 22
NF-kappa-B/RelA/I kappa B alpha 0.038 0.094 -9999 0 -0.271 11 11
TRADD 0.036 0.004 -9999 0 -9999 0 0
MAP3K5 0.011 0.101 -9999 0 -0.354 13 13
CFLAR 0.035 0.004 -9999 0 -9999 0 0
FADD 0.036 0.004 -9999 0 -9999 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.038 0.094 -9999 0 -0.272 11 11
MAPK8 -0.012 0.143 -9999 0 -0.556 8 8
APAF1 0.008 0.107 -9999 0 -0.353 15 15
TRAF1 0.034 0.017 -9999 0 -0.204 1 1
TRAF2 0.033 0.024 -9999 0 -0.204 2 2
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.042 0.16 -9999 0 -0.437 21 21
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.025 0.072 -9999 0 -0.389 1 1
CHUK 0.015 0.072 0.254 1 -0.337 2 3
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.027 0.15 -9999 0 -0.306 29 29
TCRz/NEF -0.024 0.081 -9999 0 -0.285 15 15
TNF 0.023 0.066 -9999 0 -0.266 9 9
FASLG -0.041 0.163 -9999 0 -0.58 15 15
NFKB1 0.023 0.039 -9999 0 -9999 0 0
TNFR1A/BAG4/TNF-alpha 0.05 0.063 -9999 0 -0.294 4 4
CASP6 -0.01 0.17 -9999 0 -0.59 10 10
CASP7 -0.051 0.171 -9999 0 -0.515 16 16
RELA 0.023 0.039 -9999 0 -9999 0 0
CASP2 0.035 0.007 -9999 0 -9999 0 0
CASP3 -0.053 0.174 -9999 0 -0.529 17 17
TNFRSF1A 0.035 0.007 -9999 0 -9999 0 0
TNFR1A/BAG4 0.042 0.044 -9999 0 -0.349 2 2
CASP8 0.028 0.062 -9999 0 -0.483 3 3
CASP9 0.033 0.009 -9999 0 -9999 0 0
MAP3K14 0.021 0.071 -9999 0 -0.353 1 1
APAF-1/Caspase 9 -0.046 0.155 -9999 0 -0.407 21 21
BCL2 -0.027 0.14 -9999 0 -0.536 9 9
E-cadherin signaling in the nascent adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN -0.01 0.15 -9999 0 -0.51 16 16
KLHL20 0.027 0.119 0.217 9 -0.26 15 24
CYFIP2 0.009 0.112 -9999 0 -0.458 11 11
Rac1/GDP 0.051 0.139 0.281 3 -0.398 8 11
ENAH -0.022 0.157 -9999 0 -0.523 16 16
AP1M1 0.033 0.036 -9999 0 -0.483 1 1
RAP1B 0.035 0.004 -9999 0 -9999 0 0
RAP1A 0.034 0.008 -9999 0 -9999 0 0
CTNNB1 0.011 0.093 -9999 0 -0.297 15 15
CDC42/GTP 0.039 0.103 -9999 0 -0.363 6 6
ABI1/Sra1/Nap1 -0.029 0.058 -9999 0 -0.182 19 19
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.015 0.126 -9999 0 -0.273 28 28
RAPGEF1 0.037 0.158 0.305 2 -0.487 11 13
CTNND1 0.036 0.004 -9999 0 -9999 0 0
regulation of calcium-dependent cell-cell adhesion -0.004 0.155 -9999 0 -0.522 16 16
CRK 0.033 0.168 -9999 0 -0.546 11 11
E-cadherin/gamma catenin/alpha catenin 0.049 0.081 -9999 0 -0.298 10 10
alphaE/beta7 Integrin 0.014 0.101 -9999 0 -0.346 14 14
IQGAP1 0.034 0.008 -9999 0 -9999 0 0
NCKAP1 0.021 0.068 -9999 0 -0.259 10 10
Rap1/GTP/I-afadin 0.054 0.06 -9999 0 -0.27 6 6
DLG1 -0.01 0.147 -9999 0 -0.5 16 16
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -9999 0 0
mol:PI-3-4-5-P3 -0.011 0.055 -9999 0 -0.281 5 5
MLLT4 0.02 0.087 -9999 0 -0.483 6 6
ARF6/GTP/NME1/Tiam1 0.048 0.06 -9999 0 -0.282 5 5
PI3K -0.011 0.074 -9999 0 -0.377 5 5
ARF6 0.028 0.051 -9999 0 -0.483 2 2
mol:Ca2+ 0 0 -9999 0 -9999 0 0
E-cadherin/gamma catenin 0.03 0.087 -9999 0 -0.349 10 10
TIAM1 0.028 0.054 -9999 0 -0.39 3 3
E-cadherin(dimer)/Ca2+ 0.048 0.096 -9999 0 -0.261 15 15
AKT1 0.031 0.068 0.177 3 -0.206 5 8
PIK3R1 0.028 0.062 -9999 0 -0.483 3 3
CDH1 0.011 0.111 -9999 0 -0.483 10 10
RhoA/GDP 0.062 0.142 0.273 4 -0.396 8 12
actin cytoskeleton organization 0.026 0.092 0.182 10 -0.187 15 25
CDC42/GDP 0.057 0.142 0.273 4 -0.396 8 12
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.015 0.056 -9999 0 -0.233 10 10
ITGB7 0 0.13 -9999 0 -0.483 14 14
RAC1 0.033 0.011 -9999 0 -9999 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.052 0.103 -9999 0 -0.278 15 15
E-cadherin/Ca2+/beta catenin/alpha catenin 0.031 0.088 -9999 0 -0.259 15 15
mol:GDP 0.047 0.155 0.274 4 -0.426 11 15
CDC42/GTP/IQGAP1 0.042 0.019 -9999 0 -9999 0 0
JUP 0.033 0.018 -9999 0 -0.204 1 1
p120 catenin/RhoA/GDP 0.071 0.147 0.286 3 -0.407 8 11
RAC1/GTP/IQGAP1 0.042 0.017 -9999 0 -9999 0 0
PIP5K1C/AP1M1 0.049 0.03 -9999 0 -0.349 1 1
RHOA 0.035 0.004 -9999 0 -9999 0 0
CDC42 0.032 0.019 -9999 0 -0.204 1 1
CTNNA1 0.035 0.006 -9999 0 -9999 0 0
positive regulation of S phase of mitotic cell cycle 0.025 0.074 0.156 13 -0.195 5 18
NME1 0.031 0.037 -9999 0 -0.483 1 1
clathrin coat assembly 0 0 -9999 0 -9999 0 0
TJP1 -0.011 0.149 -9999 0 -0.51 16 16
regulation of cell-cell adhesion -0.002 0.069 -9999 0 -0.314 6 6
WASF2 0.01 0.053 0.107 9 -0.15 3 12
Rap1/GTP 0.073 0.127 0.287 2 -0.413 6 8
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.039 0.117 -9999 0 -0.255 24 24
CCND1 0.028 0.088 0.181 12 -0.244 5 17
VAV2 0 0.288 -9999 0 -0.691 24 24
RAP1/GDP 0.075 0.136 0.297 2 -0.427 6 8
adherens junction assembly -0.011 0.144 -9999 0 -0.491 16 16
homophilic cell adhesion 0 0 -9999 0 -9999 0 0
ABI1 0.035 0.004 -9999 0 -9999 0 0
PIP5K1C 0.034 0.007 -9999 0 -9999 0 0
regulation of heterotypic cell-cell adhesion 0.014 0.117 -9999 0 -0.328 1 1
E-cadherin/beta catenin -0.004 0.081 -9999 0 -0.336 11 11
mol:GTP 0 0 -9999 0 -9999 0 0
SRC -0.022 0.145 -9999 0 -0.584 11 11
PIK3CA 0.035 0.006 -9999 0 -9999 0 0
Rac1/GTP -0.047 0.137 -9999 0 -0.397 22 22
E-cadherin/beta catenin/alpha catenin 0.034 0.103 -9999 0 -0.304 15 15
ITGAE 0.026 0.031 -9999 0 -0.204 3 3
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.004 0.159 -9999 0 -0.535 16 16
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.064 0.056 -9999 0 -0.255 4 4
ER alpha/Gai/GDP/Gbeta gamma -0.013 0.143 -9999 0 -0.424 17 17
AKT1 0.017 0.164 -9999 0 -0.716 9 9
PIK3CA 0.035 0.006 -9999 0 -9999 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K 0.022 0.165 -9999 0 -0.716 9 9
mol:Ca2+ -0.036 0.135 -9999 0 -0.374 18 18
IGF1R 0.03 0.04 -9999 0 -0.343 2 2
E2/ER alpha (dimer)/Striatin 0.037 0.055 -9999 0 -0.295 5 5
SHC1 0.035 0.007 -9999 0 -9999 0 0
apoptosis -0.018 0.158 0.684 9 -9999 0 9
RhoA/GTP 0.017 0.057 -9999 0 -0.234 8 8
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.063 0.138 -9999 0 -0.39 6 6
regulation of stress fiber formation 0.025 0.079 0.296 3 -9999 0 3
E2/ERA-ERB (dimer) 0.036 0.05 -9999 0 -0.295 4 4
KRAS 0.033 0.018 -9999 0 -0.204 1 1
G13/GTP 0.036 0.044 -9999 0 -0.267 4 4
pseudopodium formation -0.025 0.079 -9999 0 -0.296 3 3
E2/ER alpha (dimer)/PELP1 0.033 0.049 -9999 0 -0.291 4 4
GRB2 0.034 0.008 -9999 0 -9999 0 0
GNG2 0.033 0.01 -9999 0 -9999 0 0
GNAO1 0.036 0.002 -9999 0 -9999 0 0
HRAS 0.032 0.04 -9999 0 -0.343 2 2
mol:GTP 0 0 -9999 0 -9999 0 0
mol:NO 0.005 0.139 -9999 0 -0.419 14 14
E2/ER beta (dimer) 0.024 0.013 -9999 0 -0.133 1 1
mol:GDP 0.006 0.071 -9999 0 -0.387 4 4
mol:NADP 0.005 0.139 -9999 0 -0.419 14 14
PIK3R1 0.028 0.062 -9999 0 -0.483 3 3
mol:IP3 -0.047 0.126 0.172 1 -0.302 33 34
IGF-1R heterotetramer 0.03 0.04 -9999 0 -0.343 2 2
PLCB1 -0.051 0.133 -9999 0 -0.313 36 36
PLCB2 -0.028 0.121 -9999 0 -0.39 19 19
IGF1 0.015 0.081 -9999 0 -0.263 14 14
mol:L-citrulline 0.005 0.139 -9999 0 -0.419 14 14
RHOA 0.035 0.004 -9999 0 -9999 0 0
Gai/GDP 0.006 0.164 -9999 0 -0.733 8 8
JNK cascade 0.023 0.013 -9999 0 -0.133 1 1
BCAR1 0.034 0.017 -9999 0 -0.204 1 1
ESR2 0.032 0.019 -9999 0 -0.204 1 1
GNAQ 0 0 -9999 0 -9999 0 0
ESR1 0.025 0.071 -9999 0 -0.483 4 4
Gq family/GDP/Gbeta gamma -0.02 0.157 -9999 0 -0.561 12 12
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.044 0.101 -9999 0 -0.541 3 3
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.063 0.135 0.266 2 -0.4 5 7
GNAZ 0.022 0.064 -9999 0 -0.273 8 8
E2/ER alpha (dimer) 0.019 0.051 -9999 0 -0.347 4 4
STRN 0.031 0.043 -9999 0 -0.297 3 3
GNAL 0.022 0.035 -9999 0 -0.204 4 4
PELP1 0.03 0.014 -9999 0 -9999 0 0
MAPK11 0.015 0.015 -9999 0 -9999 0 0
GNAI2 0.024 0.073 -9999 0 -0.427 5 5
GNAI3 0.03 0.051 -9999 0 -0.483 2 2
GNAI1 -0.013 0.142 -9999 0 -0.398 23 23
HBEGF 0.092 0.183 0.327 55 -0.449 5 60
cAMP biosynthetic process 0.023 0.044 -9999 0 -0.232 4 4
SRC 0.056 0.138 -9999 0 -0.401 6 6
PI3K 0.045 0.049 -9999 0 -0.349 3 3
GNB1 0.034 0.008 -9999 0 -9999 0 0
G13/GDP/Gbeta gamma 0.042 0.078 -9999 0 -0.347 4 4
SOS1 0.036 0.002 -9999 0 -9999 0 0
IGF-1R heterotetramer/IGF1 -0.013 0.08 -9999 0 -0.361 5 5
Gs family/GTP 0.03 0.048 -9999 0 -0.235 4 4
EntrezGene:2778 0 0 -9999 0 -9999 0 0
RAS family/GTP 0.051 0.059 -9999 0 -0.254 5 5
vasodilation 0.006 0.134 -9999 0 -0.401 14 14
mol:DAG -0.047 0.126 0.172 1 -0.302 33 34
Gs family/GDP/Gbeta gamma 0.012 0.065 -9999 0 -0.33 4 4
MSN -0.027 0.083 -9999 0 -0.318 3 3
Gq family/GTP -0.022 0.127 -9999 0 -0.405 19 19
mol:PI-3-4-5-P3 0.023 0.16 -9999 0 -0.689 9 9
NRAS 0.019 0.079 -9999 0 -0.328 9 9
mol:E2 0 0 -9999 0 -9999 0 0
cell adhesion -0.006 0.134 0.401 14 -9999 0 14
GRB2/SOS1 0.051 0.012 -9999 0 -9999 0 0
RhoA/GDP 0.025 0.078 -9999 0 -0.369 4 4
NOS3 0.004 0.145 -9999 0 -0.439 14 14
GNA11 0.028 0.054 -9999 0 -0.39 3 3
MAPKKK cascade 0.044 0.146 -9999 0 -0.48 9 9
E2/ER alpha (dimer)/PELP1/Src 0.063 0.142 0.281 2 -0.405 6 8
ruffle organization -0.025 0.079 -9999 0 -0.296 3 3
ROCK2 -0.022 0.082 -9999 0 -0.283 1 1
GNA14 -0.021 0.149 -9999 0 -0.367 29 29
GNA15 0.02 0.068 -9999 0 -0.259 10 10
GNA13 0.034 0.009 -9999 0 -9999 0 0
MMP9 0.098 0.188 0.384 52 -0.471 3 55
MMP2 0.043 0.152 0.281 3 -0.451 7 10
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.006 0.101 -9999 0 -0.442 7 7
VEGFR1 homodimer/NRP1 -0.007 0.091 -9999 0 -0.505 5 5
mol:DAG 0.007 0.101 -9999 0 -0.545 4 4
VEGFR1 homodimer/NRP1/VEGFR 121 -0.006 0.084 -9999 0 -0.467 5 5
CaM/Ca2+ 0.015 0.1 -9999 0 -0.521 4 4
HIF1A 0.023 0.071 -9999 0 -0.259 10 10
GAB1 0.028 0.054 -9999 0 -0.39 3 3
AKT1 0.031 0.119 0.303 2 -0.518 4 6
PLCG1 0.007 0.102 -9999 0 -0.55 4 4
NOS3 0.082 0.14 0.301 30 -0.518 4 34
CBL 0.035 0.005 -9999 0 -9999 0 0
mol:NO 0.086 0.139 0.301 32 -0.498 4 36
FLT1 -0.006 0.105 -9999 0 -0.577 5 5
PGF 0.025 0.044 -9999 0 -0.204 7 7
VEGFR1 homodimer/NRP2/VEGFR121 0.006 0.093 -9999 0 -0.45 6 6
CALM1 0.032 0.011 -9999 0 -9999 0 0
PIK3CA 0.035 0.006 -9999 0 -9999 0 0
eNOS/Hsp90 0.072 0.135 0.28 31 -0.483 4 35
endothelial cell proliferation 0.082 0.154 0.336 28 -0.548 4 32
mol:Ca2+ 0.007 0.101 -9999 0 -0.54 4 4
MAPK3 -0.006 0.095 0.261 2 -0.447 4 6
MAPK1 -0.004 0.093 0.257 1 -0.486 4 5
PIK3R1 0.028 0.062 -9999 0 -0.483 3 3
PLGF homodimer 0.025 0.044 -9999 0 -0.203 7 7
PRKACA 0.035 0.006 -9999 0 -9999 0 0
RP11-342D11.1 0 0 -9999 0 -9999 0 0
CAV1 0.023 0.064 -9999 0 -0.273 8 8
VEGFA homodimer 0 0 -9999 0 -9999 0 0
VEGFR1 homodimer/VEGFA homodimer -0.007 0.091 -9999 0 -0.505 5 5
platelet activating factor biosynthetic process 0.065 0.149 0.332 24 -0.489 3 27
PI3K 0.067 0.125 -9999 0 -0.408 7 7
PRKCA 0.001 0.097 -9999 0 -0.508 4 4
PRKCB 0.001 0.094 -9999 0 -0.51 4 4
VEGFR1 homodimer/PLGF homodimer 0.006 0.1 -9999 0 -0.479 6 6
VEGFA 0 0 -9999 0 -9999 0 0
VEGFB 0.031 0.051 -9999 0 -0.483 2 2
mol:IP3 0.007 0.101 -9999 0 -0.545 4 4
RASA1 0.034 0.134 -9999 0 -0.396 9 9
NRP2 0.03 0.046 -9999 0 -0.273 4 4
VEGFR1 homodimer -0.005 0.104 -9999 0 -0.575 5 5
VEGFB homodimer 0.031 0.051 -9999 0 -0.482 2 2
NCK1 0.026 0.071 -9999 0 -0.483 4 4
eNOS/Caveolin-1 0.09 0.145 0.308 25 -0.468 5 30
PTPN11 0.029 0.053 -9999 0 -0.39 3 3
mol:PI-3-4-5-P3 0.065 0.123 -9999 0 -0.403 7 7
mol:L-citrulline 0.086 0.139 0.301 32 -0.498 4 36
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.021 0.092 -9999 0 -0.508 4 4
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.005 0.095 -9999 0 -0.426 7 7
CD2AP 0.033 0.036 -9999 0 -0.483 1 1
PI3K/GAB1 0.071 0.129 -9999 0 -0.559 4 4
PDPK1 0.034 0.12 0.351 1 -0.496 4 5
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.005 0.093 -9999 0 -0.411 7 7
mol:NADP 0.086 0.139 0.301 32 -0.498 4 36
HSP90AA1 0 0 -9999 0 -9999 0 0
ubiquitin-dependent protein catabolic process 0.019 0.09 -9999 0 -0.501 4 4
VEGFR1 homodimer/NRP2 0.006 0.101 -9999 0 -0.487 6 6
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0.034 0.017 -9999 0 -0.204 1 1
MKNK1 0.035 0.005 -9999 0 -9999 0 0
mol:PIP3 -0.003 0.066 0.246 2 -0.288 8 10
FRAP1 -0.029 0.178 -9999 0 -0.552 18 18
AKT1 -0.006 0.074 0.218 5 -0.28 8 13
INSR 0.023 0.075 -9999 0 -0.39 6 6
Insulin Receptor/Insulin 0.039 0.046 -9999 0 -0.296 3 3
mol:GTP 0.022 0.082 0.285 2 -0.312 3 5
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.006 0.06 -9999 0 -0.227 7 7
TSC2 0.035 0.005 -9999 0 -9999 0 0
RHEB/GDP 0.01 0.066 -9999 0 -0.285 3 3
TSC1 0.033 0.036 -9999 0 -0.483 1 1
Insulin Receptor/IRS1 0.01 0.09 -9999 0 -0.342 11 11
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.011 0.078 -9999 0 -0.261 7 7
mol:GDP 0 0 -9999 0 -9999 0 0
EIF3A 0 0 -9999 0 -9999 0 0
RPS6KB1 -0.001 0.108 0.252 2 -0.368 9 11
MAP3K5 -0.008 0.071 -9999 0 -0.288 11 11
PIK3R1 0.028 0.062 -9999 0 -0.483 3 3
apoptosis -0.008 0.071 -9999 0 -0.288 11 11
mol:LY294002 0 0 0.001 5 -0.001 7 12
EIF4B 0 0.101 0.252 3 -0.332 9 12
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.01 0.095 0.226 2 -0.322 8 10
eIF4E/eIF4G1/eIF4A1 -0.009 0.105 -9999 0 -0.326 16 16
KIAA1303 0 0 -9999 0 -9999 0 0
PI3K 0.032 0.079 -9999 0 -0.285 10 10
mTOR/RHEB/GTP/Raptor/GBL 0.02 0.07 0.227 4 -0.249 2 6
FKBP1A 0.026 0.039 -9999 0 -0.486 1 1
RHEB/GTP 0.03 0.078 0.262 2 -0.282 3 5
mol:Amino Acids 0 0 0.001 5 -0.001 7 12
FKBP12/Rapamycin 0.019 0.028 -9999 0 -0.351 1 1
PDPK1 -0.014 0.063 0.193 4 -0.272 8 12
EIF4E 0.035 0.006 -9999 0 -9999 0 0
ASK1/PP5C -0.019 0.197 -9999 0 -0.543 21 21
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.027 0.043 -9999 0 -9999 0 0
TSC1/TSC2 0.026 0.089 0.283 3 -0.336 3 6
tumor necrosis factor receptor activity 0 0 0.001 7 -0.001 5 12
RPS6 0.033 0.024 -9999 0 -0.204 2 2
PPP5C 0.034 0.017 -9999 0 -0.204 1 1
EIF4G1 0.027 0.058 -9999 0 -0.315 5 5
IRS1 -0.005 0.072 -9999 0 -0.333 9 9
INS 0.034 0.007 -9999 0 -9999 0 0
PTEN 0.026 0.062 -9999 0 -0.481 3 3
PDK2 -0.015 0.061 0.205 2 -0.272 8 10
EIF4EBP1 -0.052 0.3 -9999 0 -1.121 15 15
PIK3CA 0.035 0.006 -9999 0 -9999 0 0
PPP2R5D -0.022 0.157 -9999 0 -0.48 18 18
peptide biosynthetic process 0.011 0.081 0.189 7 -0.322 9 16
RHEB 0.035 0.006 -9999 0 -9999 0 0
EIF4A1 0.029 0.014 -9999 0 -9999 0 0
mol:Rapamycin 0 0.001 0.004 9 -0.003 8 17
EEF2 0.011 0.081 0.189 7 -0.324 9 16
eIF4E/4E-BP1 -0.031 0.285 -9999 0 -1.044 15 15
RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.021 0.068 -9999 0 -9999 0 0
VDR 0.022 0.081 -9999 0 -0.437 6 6
FAM120B 0 0 -9999 0 -9999 0 0
RXRs/LXRs/DNA/9cRA 0.033 0.085 -9999 0 -0.484 2 2
RXRs/LXRs/DNA/Oxysterols 0.036 0.106 -9999 0 -0.433 7 7
MED1 0 0 -9999 0 -9999 0 0
mol:9cRA 0.003 0.011 -9999 0 -9999 0 0
RARs/THRs/DNA/Src-1 0.013 0.079 -9999 0 -0.238 15 15
RXRs/NUR77 0.062 0.083 -9999 0 -0.263 4 4
RXRs/PPAR 0.003 0.099 -9999 0 -0.281 13 13
NCOR2 0.032 0.04 -9999 0 -0.343 2 2
VDR/VDR/Vit D3 0.016 0.058 -9999 0 -0.311 6 6
RARs/VDR/DNA/Vit D3 0.056 0.08 -9999 0 -0.255 10 10
RARA 0.034 0.009 -9999 0 -9999 0 0
NCOA1 0.026 0.071 -9999 0 -0.483 4 4
VDR/VDR/DNA 0.022 0.081 -9999 0 -0.436 6 6
RARs/RARs/DNA/9cRA 0.049 0.056 -9999 0 -0.251 5 5
RARG 0.029 0.053 -9999 0 -0.39 3 3
RPS6KB1 0.029 0.097 0.543 7 -9999 0 7
RARs/THRs/DNA/SMRT 0.014 0.08 -9999 0 -0.254 12 12
THRA 0.015 0.091 -9999 0 -0.39 9 9
mol:Bile acids 0 0 -9999 0 -9999 0 0
VDR/Vit D3/DNA 0.016 0.058 -9999 0 -0.311 6 6
RXRs/PPAR/9cRA/PGJ2/DNA 0.057 0.072 -9999 0 -0.257 4 4
NR1H4 -0.07 0.174 -9999 0 -0.303 65 65
RXRs/LXRs/DNA 0.092 0.101 -9999 0 -0.378 3 3
NR1H2 0.036 0.019 -9999 0 -9999 0 0
NR1H3 0.029 0.069 -9999 0 -0.432 4 4
RXRs/VDR/DNA/Vit D3 0.062 0.083 -9999 0 -0.251 9 9
NR4A1 0.018 0.062 -9999 0 -0.204 15 15
mol:ATRA 0 0 -9999 0 -9999 0 0
RXRs/FXR/9cRA/MED1 -0.016 0.092 -9999 0 -0.241 24 24
RXRG 0.021 0.079 -9999 0 -0.339 8 8
RXR alpha/CCPG 0.027 0.013 -9999 0 -9999 0 0
RXRA 0.036 0.018 -9999 0 -9999 0 0
RXRB 0.037 0.02 -9999 0 -9999 0 0
THRB 0.022 0.066 -9999 0 -0.266 9 9
PPARG -0.021 0.158 -9999 0 -0.448 24 24
PPARD 0.036 0.004 -9999 0 -9999 0 0
TNF 0.022 0.142 -9999 0 -0.918 3 3
mol:Oxysterols 0.003 0.009 -9999 0 -9999 0 0
cholesterol transport 0.036 0.105 -9999 0 -0.429 7 7
PPARA 0.029 0.04 -9999 0 -0.343 2 2
mol:Vit D3 0 0 -9999 0 -9999 0 0
RARB 0.021 0.078 -9999 0 -0.343 8 8
RXRs/NUR77/BCL2 -0.007 0.077 -9999 0 -0.267 11 11
SREBF1 0.015 0.133 -9999 0 -0.764 4 4
RXRs/RXRs/DNA/9cRA 0.057 0.073 -9999 0 -0.257 4 4
ABCA1 0.022 0.16 -9999 0 -0.955 4 4
RARs/THRs 0.064 0.097 -9999 0 -0.258 12 12
RXRs/FXR 0.004 0.135 -9999 0 -0.284 24 24
BCL2 -0.002 0.098 -9999 0 -0.308 16 16
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.011 0.035 -9999 0 -0.298 3 3
SNTA1 0.013 0.054 -9999 0 -0.39 3 3
response to hypoxia 0 0 -9999 0 -9999 0 0
STMN1 -0.012 0.04 -9999 0 -0.298 4 4
MAPK12 -0.022 0.084 0.212 4 -0.267 17 21
CCND1 -0.003 0.063 -9999 0 -0.412 3 3
p38 gamma/SNTA1 -0.013 0.086 -9999 0 -0.272 16 16
MAP2K3 0.03 0.013 -9999 0 -9999 0 0
PKN1 0.026 0.064 -9999 0 -0.413 4 4
G2/M transition checkpoint -0.022 0.084 0.211 4 -0.265 17 21
MAP2K6 -0.014 0.09 0.243 4 -0.274 19 23
MAPT -0.006 0.052 0.204 2 -0.23 4 6
MAPK13 0.013 0.036 -9999 0 -0.35 2 2
hyperosmotic response 0 0 -9999 0 -9999 0 0
ZAK 0.002 0.072 -9999 0 -0.312 10 10
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.045 0.012 -9999 0 -9999 0 0
response to insulin stimulus 0 0 -9999 0 -9999 0 0
RIPK1 0.036 0.004 -9999 0 -9999 0 0
response to stress 0 0 -9999 0 -9999 0 0
MAP2K6 0.008 0.109 -9999 0 -0.413 12 12
mol:GTP 0 0 -9999 0 -9999 0 0
MAP2K4 0.023 0.052 -9999 0 -0.483 2 2
RAC1-CDC42/GTP/PAK family 0.02 0.021 -9999 0 -0.196 1 1
response to UV 0 0 -9999 0 -9999 0 0
YES1 0.028 0.015 -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 0.034 0.009 -9999 0 -9999 0 0
FYN 0.006 0.108 -9999 0 -0.343 16 16
MAP3K12 0.035 0.005 -9999 0 -9999 0 0
FGR 0.025 0.044 -9999 0 -0.204 7 7
p38 alpha/TAB1 -0.019 0.182 0.251 6 -0.387 27 33
PRKG1 0.035 0.007 -9999 0 -9999 0 0
DUSP8 0.021 0.083 -9999 0 -0.403 7 7
PGK/cGMP/p38 alpha -0.025 0.171 0.202 3 -0.376 27 30
apoptosis -0.018 0.173 0.241 6 -0.369 27 33
RAL/GTP 0.036 0.054 -9999 0 -0.295 5 5
LYN 0.03 0.013 -9999 0 -9999 0 0
DUSP1 0 0.104 -9999 0 -0.259 25 25
PAK1 0.031 0.051 -9999 0 -0.483 2 2
SRC 0.011 0.062 -9999 0 -0.483 3 3
RAC1/OSM/MEKK3/MKK3 0.067 0.041 -9999 0 -9999 0 0
TRAF6 0.036 0.004 -9999 0 -9999 0 0
RAC1 0.033 0.011 -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 0.034 0.009 -9999 0 -9999 0 0
RAC1-CDC42/GTP 0.04 0.021 -9999 0 -9999 0 0
MAPK11 -0.014 0.184 0.317 6 -0.457 17 23
BLK 0.007 0.089 -9999 0 -0.32 12 12
HCK -0.013 0.11 -9999 0 -0.352 17 17
MAP2K3 0.03 0.013 -9999 0 -9999 0 0
DUSP16 0.022 0.075 -9999 0 -0.39 6 6
DUSP10 0.012 0.099 -9999 0 -0.367 12 12
TRAF6/MEKK3 0.043 0.012 -9999 0 -9999 0 0
MAP3K7IP1 0.034 0.009 -9999 0 -9999 0 0
MAPK14 -0.031 0.191 0.253 7 -0.42 27 34
positive regulation of innate immune response -0.03 0.216 0.324 7 -0.542 18 25
LCK -0.015 0.138 -9999 0 -0.354 26 26
p38alpha-beta/MKP7 -0.022 0.216 0.344 6 -0.543 17 23
p38alpha-beta/MKP5 -0.024 0.218 0.331 7 -0.512 20 27
PGK/cGMP 0.026 0.005 -9999 0 -9999 0 0
PAK2 0.035 0.006 -9999 0 -9999 0 0
p38alpha-beta/MKP1 -0.027 0.22 0.344 6 -0.51 21 27
CDC42 0.032 0.019 -9999 0 -0.204 1 1
RALB 0.023 0.08 -9999 0 -0.483 5 5
RALA 0.033 0.01 -9999 0 -9999 0 0
PAK3 0.036 0 -9999 0 -9999 0 0
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.018 0.055 0.214 3 -0.238 6 9
DAPP1 -0.039 0.205 0.242 6 -0.515 21 27
Src family/SYK family/BLNK-LAT/BTK-ITK -0.061 0.244 0.299 1 -0.55 29 30
mol:DAG 0.016 0.116 0.189 36 -0.274 9 45
HRAS 0.032 0.038 -9999 0 -0.326 2 2
RAP1A 0.034 0.012 -9999 0 -9999 0 0
ARF5/GDP 0.041 0.102 -9999 0 -0.27 9 9
PLCG2 -0.012 0.132 -9999 0 -0.328 27 27
PLCG1 0.019 0.018 -9999 0 -9999 0 0
ARF5 0.03 0.051 -9999 0 -0.483 2 2
mol:GTP -0.016 0.05 0.186 3 -0.247 4 7
ARF1/GTP -0.009 0.047 0.187 3 -0.232 4 7
RHOA 0.035 0.004 -9999 0 -9999 0 0
YES1 0.028 0.015 -9999 0 -9999 0 0
RAP1A/GTP -0.012 0.057 0.203 3 -0.244 4 7
ADAP1 -0.017 0.046 0.178 3 -0.236 4 7
ARAP3 -0.016 0.049 0.185 3 -0.243 4 7
INPPL1 0.032 0.04 -9999 0 -0.343 2 2
PREX1 0.002 0.083 -9999 0 -0.378 8 8
ARHGEF6 0.03 0.053 -9999 0 -0.39 3 3
ARHGEF7 0.027 0.016 -9999 0 -9999 0 0
ARF1 0.035 0.006 -9999 0 -9999 0 0
NRAS 0.02 0.08 -9999 0 -0.331 9 9
FYN 0.006 0.108 -9999 0 -0.343 16 16
ARF6 0.028 0.051 -9999 0 -0.483 2 2
FGR 0.025 0.044 -9999 0 -0.204 7 7
mol:Ca2+ 0.016 0.07 0.16 12 -0.139 6 18
mol:IP4 0 0 -9999 0 -9999 0 0
TIAM1 0.028 0.054 -9999 0 -0.39 3 3
ZAP70 0.03 0.053 -9999 0 -0.39 3 3
mol:IP3 0.012 0.087 0.187 11 -0.197 7 18
LYN 0.03 0.013 -9999 0 -9999 0 0
ARF1/GDP 0.044 0.099 -9999 0 -0.27 9 9
RhoA/GDP 0.045 0.08 0.244 3 -0.268 1 4
PDK1/Src/Hsp90 0.02 0.046 -9999 0 -0.295 3 3
BLNK 0.004 0.118 -9999 0 -0.44 13 13
actin cytoskeleton reorganization 0.032 0.103 0.247 4 -0.348 4 8
SRC 0.011 0.062 -9999 0 -0.483 3 3
PLEKHA2 -0.006 0.02 -9999 0 -0.294 1 1
RAC1 0.033 0.011 -9999 0 -9999 0 0
PTEN 0.027 0.06 -9999 0 -0.458 3 3
HSP90AA1 0 0 -9999 0 -9999 0 0
ARF6/GTP -0.017 0.056 0.214 3 -0.238 6 9
RhoA/GTP -0.012 0.058 0.197 3 -0.238 4 7
Src family/SYK family/BLNK-LAT -0.043 0.147 -9999 0 -0.533 12 12
BLK 0.007 0.089 -9999 0 -0.32 12 12
PDPK1 0.032 0.04 -9999 0 -0.343 2 2
CYTH1 -0.017 0.046 0.178 3 -0.236 4 7
HCK -0.013 0.11 -9999 0 -0.352 17 17
CYTH3 -0.017 0.046 0.178 3 -0.236 4 7
CYTH2 -0.017 0.046 0.178 3 -0.236 4 7
KRAS 0.033 0.02 -9999 0 -0.205 1 1
GO:0030676 0 0 -9999 0 -9999 0 0
FOXO3 0.001 0.046 0.179 1 -0.254 4 5
SGK1 0.001 0.048 0.184 1 -0.269 4 5
INPP5D 0 0 -9999 0 -9999 0 0
mol:GDP 0.031 0.097 -9999 0 -0.281 9 9
SOS1 0.036 0.002 -9999 0 -9999 0 0
SYK 0.029 0.053 -9999 0 -0.39 3 3
ARF6/GDP 0.024 0.078 0.23 3 -0.288 2 5
mol:PI-3-4-5-P3 -0.017 0.051 0.233 3 -0.247 4 7
ARAP3/RAP1A/GTP -0.012 0.057 0.204 3 -0.247 4 7
VAV1 -0.004 0.133 -9999 0 -0.421 18 18
mol:PI-3-4-P2 0.008 0.027 -9999 0 -0.24 2 2
RAS family/GTP/PI3K Class I 0.049 0.065 -9999 0 -0.251 4 4
PLEKHA1 -0.007 0.021 -9999 0 -0.294 1 1
Rac1/GDP 0.04 0.097 -9999 0 -0.275 8 8
LAT 0.023 0.064 -9999 0 -0.273 8 8
Rac1/GTP 0.003 0.07 -9999 0 -0.435 3 3
ITK -0.025 0.056 0.182 2 -0.243 8 10
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.006 0.144 0.247 8 -0.385 10 18
LCK -0.015 0.138 -9999 0 -0.354 26 26
BTK -0.035 0.077 0.182 3 -0.259 16 19
Regulation of Telomerase

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
Telomerase catalytic core complex -0.057 0.193 -9999 0 -0.945 5 5
RAD9A 0.036 0.004 -9999 0 -9999 0 0
AP1 -0.068 0.163 -9999 0 -0.341 46 46
IFNAR2 0.034 0.02 -9999 0 -0.205 1 1
AKT1 0.023 0.033 -9999 0 -0.171 4 4
ER alpha/Oestrogen 0.019 0.052 -9999 0 -0.346 4 4
NFX1/SIN3/HDAC complex 0.033 0.067 -9999 0 -0.3 2 2
EGF -0.087 0.188 -9999 0 -0.32 72 72
SMG5 0 0 -9999 0 -9999 0 0
SMG6 0 0 -9999 0 -9999 0 0
SP3/HDAC2 0.05 0.033 -9999 0 -0.348 1 1
TERT/c-Abl -0.045 0.185 -9999 0 -0.882 5 5
SAP18 0.026 0.016 -9999 0 -9999 0 0
MRN complex 0.055 0.046 -9999 0 -0.298 2 2
WT1 -0.2 0.221 -9999 0 -0.357 125 125
WRN 0.029 0.014 -9999 0 -9999 0 0
SP1 0.034 0.021 -9999 0 -0.201 1 1
SP3 0.036 0.007 -9999 0 -9999 0 0
TERF2IP 0.036 0.002 -9999 0 -9999 0 0
Telomerase/Nucleolin -0.04 0.181 -9999 0 -0.769 6 6
Mad/Max 0.043 0.044 -9999 0 -0.35 1 1
TERT -0.059 0.2 -9999 0 -0.994 5 5
CCND1 -0.063 0.212 -9999 0 -1.006 7 7
MAX 0.033 0.01 -9999 0 -9999 0 0
RBBP7 0.034 0.023 -9999 0 -0.203 2 2
RBBP4 0.031 0.029 -9999 0 -0.204 3 3
TERF2 0.031 0.034 -9999 0 -0.427 1 1
PTGES3 0.035 0.004 -9999 0 -9999 0 0
SIN3A 0.032 0.019 -9999 0 -0.203 1 1
Telomerase/911 0.035 0.055 -9999 0 -0.362 2 2
CDKN1B -0.08 0.153 -9999 0 -0.334 41 41
RAD1 0.031 0.04 -9999 0 -0.343 2 2
XRCC5 0.036 0.004 -9999 0 -9999 0 0
XRCC6 0.034 0.009 -9999 0 -9999 0 0
SAP30 0.032 0.037 -9999 0 -0.483 1 1
TRF2/PARP2 0.044 0.042 -9999 0 -0.332 2 2
UBE3A 0.033 0.01 -9999 0 -9999 0 0
JUN -0.017 0.15 -9999 0 -0.404 25 25
E6 0 0.002 -9999 0 -9999 0 0
HPV-16 E6/E6AP 0.025 0.011 -9999 0 -9999 0 0
FOS -0.062 0.171 -9999 0 -0.318 56 56
IFN-gamma/IRF1 -0.075 0.179 -9999 0 -0.342 54 54
PARP2 0.031 0.037 -9999 0 -0.483 1 1
BLM 0.021 0.08 -9999 0 -0.483 5 5
Telomerase 0.031 0.045 -9999 0 -9999 0 0
IRF1 0 0.113 -9999 0 -0.285 24 24
ESR1 0.025 0.071 -9999 0 -0.483 4 4
KU/TER 0.05 0.013 -9999 0 -9999 0 0
ATM/TRF2 0.046 0.041 -9999 0 -0.208 4 4
ubiquitin-dependent protein catabolic process 0.014 0.068 -9999 0 -0.294 4 4
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.014 0.069 -9999 0 -0.3 4 4
HDAC1 0.034 0.008 -9999 0 -9999 0 0
HDAC2 0.032 0.039 -9999 0 -0.482 1 1
ATM 0.012 0.033 0.202 1 -0.388 1 2
SMAD3 0.012 0.041 -9999 0 -0.318 3 3
ABL1 0.035 0.005 -9999 0 -9999 0 0
MXD1 0.027 0.054 -9999 0 -0.243 7 7
MRE11A 0.035 0.005 -9999 0 -9999 0 0
HUS1 0.03 0.04 -9999 0 -0.343 2 2
RPS6KB1 0.034 0.008 -9999 0 -9999 0 0
TERT/NF kappa B1/14-3-3 -0.02 0.186 -9999 0 -0.935 4 4
NR2F2 0.031 0.019 -9999 0 -0.201 1 1
MAPK3 0.011 0.052 -9999 0 -0.349 4 4
MAPK1 0.018 0.009 -9999 0 -9999 0 0
TGFB1/TGF beta receptor Type II 0.034 0.017 -9999 0 -0.204 1 1
NFKB1 0.035 0.006 -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 0.033 0.202 1 -0.388 1 2
NBN 0.027 0.038 -9999 0 -0.483 1 1
EGFR 0.016 0.09 -9999 0 -0.413 8 8
mol:Oestrogen 0 0.002 -9999 0 -9999 0 0
EGF/EGFR -0.054 0.149 -9999 0 -0.346 34 34
MYC 0.004 0.111 -9999 0 -0.483 10 10
IL2 0.036 0.014 -9999 0 -9999 0 0
KU 0.05 0.013 -9999 0 -9999 0 0
RAD50 0.03 0.051 -9999 0 -0.483 2 2
HSP90AA1 0 0 -9999 0 -9999 0 0
TGFB1 0.034 0.017 -9999 0 -0.204 1 1
TRF2/BLM 0.038 0.066 -9999 0 -0.331 6 6
FRAP1 0.031 0.037 -9999 0 -0.483 1 1
KU/TERT -0.035 0.193 -9999 0 -0.878 5 5
SP1/HDAC2 0.049 0.038 -9999 0 -0.347 1 1
PINX1 0.024 0.042 -9999 0 -0.343 2 2
Telomerase/EST1A -0.047 0.165 -9999 0 -0.78 5 5
Smad3/Myc 0.011 0.081 -9999 0 -0.314 11 11
911 complex 0.06 0.045 -9999 0 -0.298 2 2
IFNG -0.104 0.197 -9999 0 -0.323 81 81
Telomerase/PinX1 -0.043 0.17 -9999 0 -0.79 5 5
Telomerase/AKT1/mTOR/p70S6K 0.021 0.056 -9999 0 -9999 0 0
SIN3B 0.035 0.006 -9999 0 -9999 0 0
YWHAE 0.03 0.013 -9999 0 -9999 0 0
Telomerase/EST1B -0.047 0.165 -9999 0 -0.78 5 5
response to DNA damage stimulus 0.002 0.023 -9999 0 -0.131 1 1
MRN complex/TRF2/Rap1 0.077 0.059 -9999 0 -0.26 3 3
TRF2/WRN 0.04 0.034 -9999 0 -0.335 1 1
Telomerase/hnRNP C1/C2 -0.047 0.165 -9999 0 -0.78 5 5
E2F1 0.014 0.053 -9999 0 -0.482 2 2
ZNFX1 0 0.001 -9999 0 -9999 0 0
PIF1 0 0 -9999 0 -9999 0 0
NCL 0.026 0.071 -9999 0 -0.483 4 4
DKC1 0.035 0.017 -9999 0 -0.204 1 1
telomeric DNA binding 0 0 -9999 0 -9999 0 0
Insulin 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
CBL/APS/CAP 0.021 0.114 -9999 0 -0.28 21 21
TC10/GTP 0.012 0.085 -9999 0 -0.236 17 17
Insulin Receptor/Insulin/IRS1/Shp2 0.079 0.109 -9999 0 -0.381 8 8
HRAS 0.032 0.04 -9999 0 -0.343 2 2
APS homodimer 0 0 -9999 0 -9999 0 0
GRB14 -0.167 0.219 -9999 0 -0.354 108 108
FOXO3 -0.019 0.026 -9999 0 -9999 0 0
AKT1 -0.076 0.121 0.301 1 -0.375 9 10
INSR 0.037 0.076 -9999 0 -0.417 5 5
Insulin Receptor/Insulin 0.099 0.104 -9999 0 -0.402 2 2
mol:GTP 0 0 -9999 0 -9999 0 0
GRB10 -0.008 0.134 -9999 0 -0.399 20 20
SORBS1 -0.021 0.146 -9999 0 -0.358 29 29
CRK 0.03 0.013 -9999 0 -9999 0 0
PTPN1 0.005 0.052 -9999 0 -0.395 2 2
CAV1 0.022 0.088 0.196 5 -0.288 10 15
CBL/APS/CAP/Crk-II/C3G 0.031 0.097 -9999 0 -0.255 16 16
Insulin Receptor/Insulin/IRS1/NCK2 0.082 0.096 -9999 0 -0.321 8 8
mol:GDP 0 0 -9999 0 -9999 0 0
mol:PI-3-4-5-P3 0.057 0.091 -9999 0 -0.307 9 9
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.067 0.11 -9999 0 -0.535 4 4
RPS6KB1 -0.072 0.111 0.285 1 -0.391 6 7
PARD6A 0.008 0.111 -9999 0 -0.383 14 14
CBL 0.035 0.005 -9999 0 -9999 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -9999 0 0
DOK1 0.026 0.062 -9999 0 -0.82 1 1
PIK3R1 0.028 0.062 -9999 0 -0.483 3 3
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.048 0.128 -9999 0 -0.4 6 6
HRAS/GTP 0.012 0.064 -9999 0 -0.303 5 5
Insulin Receptor 0.037 0.076 -9999 0 -0.416 5 5
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.09 0.097 -9999 0 -0.3 8 8
PRKCI 0.011 0.094 -9999 0 -0.627 3 3
Insulin Receptor/Insulin/GRB14/PDK1 -0.065 0.135 -9999 0 -0.283 33 33
SHC1 0.035 0.007 -9999 0 -9999 0 0
negative regulation of MAPKKK cascade 0.048 0.089 -9999 0 -0.553 3 3
PI3K 0.073 0.097 -9999 0 -0.312 9 9
NCK2 0.035 0.017 -9999 0 -0.204 1 1
RHOQ 0.031 0.043 -9999 0 -0.297 3 3
mol:H2O2 0.001 0.008 -9999 0 -9999 0 0
HRAS/GDP 0.024 0.028 -9999 0 -0.24 2 2
AKT2 -0.071 0.125 0.258 2 -0.366 10 12
PRKCZ -0.002 0.067 -9999 0 -0.746 1 1
SH2B2 0 0 -9999 0 -9999 0 0
SHC/SHIP 0.028 0.076 0.183 3 -0.282 8 11
F2RL2 0.013 0.106 -9999 0 -0.483 9 9
TRIP10 0.035 0.005 -9999 0 -9999 0 0
Insulin Receptor/Insulin/Shc 0.074 0.053 -9999 0 -0.245 3 3
TC10/GTP/CIP4/Exocyst 0.044 0.029 -9999 0 -0.295 1 1
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.104 0.063 -9999 0 -0.244 2 2
RAPGEF1 0.035 0.004 -9999 0 -9999 0 0
RASA1 0.024 0.073 -9999 0 -0.427 5 5
NCK1 0.026 0.071 -9999 0 -0.483 4 4
CBL/APS/CAP/Crk-II 0.019 0.095 -9999 0 -0.269 16 16
TC10/GDP 0.023 0.03 -9999 0 -0.204 3 3
Insulin Receptor/Insulin/SHC/GRB10 0.061 0.108 -9999 0 -0.267 15 15
INPP5D -0.002 0.067 -9999 0 -0.296 8 8
SOS1 0.036 0.002 -9999 0 -9999 0 0
SGK1 -0.01 0.011 -9999 0 -9999 0 0
mol:cAMP 0 0 -9999 0 -9999 0 0
PTPN11 0.029 0.053 -9999 0 -0.39 3 3
IRS1 0.013 0.098 -9999 0 -0.382 11 11
p62DOK/RasGAP 0.048 0.09 -9999 0 -0.559 3 3
INS 0.047 0.02 -9999 0 -9999 0 0
mol:PI-3-4-P2 -0.002 0.066 -9999 0 -0.293 8 8
GRB2 0.034 0.008 -9999 0 -9999 0 0
EIF4EBP1 -0.073 0.113 0.285 1 -0.391 7 8
PTPRA 0.033 0.043 -9999 0 -0.493 1 1
PIK3CA 0.035 0.006 -9999 0 -9999 0 0
TC10/GTP/CIP4 0.044 0.029 -9999 0 -0.295 1 1
PDPK1 0.032 0.04 -9999 0 -0.343 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.035 0.074 -9999 0 -0.407 3 3
Insulin Receptor/Insulin/IRS1 0.062 0.089 -9999 0 -0.318 8 8
Insulin Receptor/Insulin/IRS3 0.064 0.06 -9999 0 -0.34 3 3
Par3/Par6 0.045 0.103 -9999 0 -0.26 19 19
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.033 0.036 -9999 0 -0.483 1 1
mol:S1P 0.001 0.002 -9999 0 -9999 0 0
S1P1/S1P/Gi -0.01 0.116 -9999 0 -0.316 19 19
GNAO1 0.037 0.003 -9999 0 -9999 0 0
S1P/S1P3/G12/G13 0.042 0.017 -9999 0 -9999 0 0
AKT1 -0.016 0.145 -9999 0 -0.384 25 25
AKT3 0.012 0.066 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
PDGFB-D/PDGFRB 0.033 0.036 -9999 0 -0.482 1 1
GNAI2 0.026 0.073 -9999 0 -0.426 5 5
GNAI3 0.031 0.051 -9999 0 -0.486 2 2
GNAI1 -0.012 0.143 -9999 0 -0.397 23 23
mol:GDP 0 0 -9999 0 -9999 0 0
S1PR3 0.001 0.002 -9999 0 -0.012 1 1
S1PR2 0 0 -9999 0 -9999 0 0
EDG1 0.003 0.116 -9999 0 -0.378 16 16
mol:Ca2+ 0 0.099 -9999 0 -0.32 12 12
MAPK3 -0.009 0.1 0.202 1 -0.301 15 16
MAPK1 -0.002 0.091 -9999 0 -0.314 11 11
JAK2 0.031 0.111 0.228 2 -0.354 7 9
CXCR4 -0.033 0.123 -9999 0 -0.315 24 24
FLT1 0.011 0.076 -9999 0 -0.279 11 11
RhoA/GDP 0.026 0.003 -9999 0 -9999 0 0
Rac1/GDP 0.024 0.008 -9999 0 -9999 0 0
SRC 0.001 0.065 -9999 0 -0.295 6 6
S1P/S1P3/Gi 0 0.1 -9999 0 -0.323 12 12
RAC1 0.033 0.011 -9999 0 -9999 0 0
RhoA/GTP 0.017 0.098 -9999 0 -0.303 11 11
VEGFA 0.002 0.003 -9999 0 -0.015 2 2
S1P/S1P2/Gi -0.002 0.098 -9999 0 -0.263 21 21
VEGFR1 homodimer/VEGFA homodimer 0.012 0.055 -9999 0 -0.191 11 11
RHOA 0.035 0.004 -9999 0 -9999 0 0
S1P/S1P3/Gq -0.011 0.087 -9999 0 -0.267 19 19
GNAQ 0 0 -9999 0 -9999 0 0
GNAZ 0.023 0.065 -9999 0 -0.273 8 8
G12/G13 0.046 0.018 -9999 0 -9999 0 0
GNA14 -0.021 0.149 -9999 0 -0.367 29 29
GNA15 0.02 0.068 -9999 0 -0.259 10 10
GNA12 0.033 0.01 -9999 0 -9999 0 0
GNA13 0.034 0.009 -9999 0 -9999 0 0
GNA11 0.028 0.054 -9999 0 -0.39 3 3
Rac1/GTP 0.015 0.095 -9999 0 -0.305 11 11
Regulation of Androgen receptor activity

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
HDAC1 0.018 0.005 -9999 0 -9999 0 0
SMARCC1 0.015 0.065 -9999 0 -0.733 1 1
REL 0.025 0.071 -9999 0 -0.484 4 4
HDAC7 -0.019 0.109 -9999 0 -0.389 11 11
JUN -0.017 0.15 -9999 0 -0.405 25 25
EP300 0.018 0.088 -9999 0 -0.443 7 7
KAT2B 0 0 -9999 0 -9999 0 0
KAT5 0 0 -9999 0 -9999 0 0
MAPK14 -0.002 0.082 -9999 0 -0.371 9 9
FOXO1 0 0 -9999 0 -9999 0 0
T-DHT/AR 0.019 0.131 -9999 0 -0.434 9 9
MAP2K6 0.006 0.112 -9999 0 -0.424 12 12
BRM/BAF57 0.048 0.032 -9999 0 -0.331 1 1
MAP2K4 0.021 0.053 -9999 0 -0.483 2 2
SMARCA2 0.03 0.051 -9999 0 -0.482 2 2
PDE9A -0.099 0.355 -9999 0 -1.014 25 25
NCOA2 0.025 0.052 -9999 0 -0.483 2 2
CEBPA 0.015 0.092 -9999 0 -0.372 10 10
EHMT2 0.036 0.003 -9999 0 -9999 0 0
cell proliferation 0.083 0.167 0.374 12 -0.406 7 19
NR0B1 0.023 0.066 -9999 0 -0.266 9 9
EGR1 -0.053 0.167 -9999 0 -0.314 53 53
RXRs/9cRA 0.056 0.054 -9999 0 -0.269 4 4
AR/RACK1/Src 0.072 0.135 0.358 2 -0.374 8 10
AR/GR 0.001 0.085 -9999 0 -0.261 11 11
GNB2L1 0.035 0.007 -9999 0 -9999 0 0
PKN1 0.027 0.064 -9999 0 -0.413 4 4
RCHY1 0.027 0.058 -9999 0 -0.315 5 5
epidermal growth factor receptor activity 0.001 0 -9999 0 -9999 0 0
MAPK8 0.01 0.031 -9999 0 -0.35 1 1
T-DHT/AR/TIF2/CARM1 0.014 0.1 -9999 0 -0.361 9 9
SRC 0.032 0.126 0.214 4 -0.33 11 15
NR3C1 0.019 0.088 -9999 0 -0.443 7 7
KLK3 -0.048 0.111 -9999 0 -0.458 1 1
APPBP2 0.03 0.018 -9999 0 -9999 0 0
TRIM24 0.03 0.051 -9999 0 -0.483 2 2
T-DHT/AR/TIP60 -0.022 0.08 -9999 0 -0.331 11 11
TMPRSS2 -0.012 0.193 -9999 0 -0.877 7 7
RXRG 0.02 0.078 -9999 0 -0.343 8 8
mol:9cRA 0 0 -9999 0 -9999 0 0
RXRA 0.035 0.006 -9999 0 -9999 0 0
RXRB 0.036 0.004 -9999 0 -9999 0 0
CARM1 0.036 0.006 -9999 0 -9999 0 0
NR2C2 0.035 0.005 -9999 0 -9999 0 0
KLK2 0.044 0.099 0.306 1 -0.462 2 3
AR -0.001 0.063 -9999 0 -0.23 11 11
SENP1 0.035 0.006 -9999 0 -9999 0 0
HSP90AA1 0 0 -9999 0 -9999 0 0
MDM2 0.033 0.017 -9999 0 -0.205 1 1
SRY 0.028 0.046 -9999 0 -0.275 4 4
GATA2 0.029 0.053 -9999 0 -0.39 3 3
MYST2 0.034 0.008 -9999 0 -9999 0 0
HOXB13 -0.104 0.199 -9999 0 -0.335 78 78
T-DHT/AR/RACK1/Src 0.075 0.143 0.332 5 -0.388 8 13
positive regulation of transcription 0.029 0.053 -9999 0 -0.389 3 3
DNAJA1 0.031 0.025 -9999 0 -0.223 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.035 -9999 0 -0.315 2 2
NCOA1 0.03 0.08 -9999 0 -0.536 4 4
SPDEF -0.074 0.182 -9999 0 -0.319 65 65
T-DHT/AR/TIF2 0.001 0.1 0.271 3 -0.411 6 9
T-DHT/AR/Hsp90 -0.022 0.08 -9999 0 -0.33 11 11
GSK3B 0.033 0.036 -9999 0 -0.483 1 1
NR2C1 0.034 0.017 -9999 0 -0.204 1 1
mol:T-DHT -0.015 0.075 0.215 2 -0.32 10 12
SIRT1 0.031 0.04 -9999 0 -0.343 2 2
ZMIZ2 -0.001 0.001 -9999 0 -9999 0 0
POU2F1 0.022 0.079 -9999 0 -0.366 5 5
T-DHT/AR/DAX-1 -0.007 0.103 -9999 0 -0.353 12 12
CREBBP 0.033 0.036 -9999 0 -0.483 1 1
SMARCE1 0.035 0.008 -9999 0 -9999 0 0
Regulation of nuclear SMAD2/3 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
EP300 0.017 0.089 -9999 0 -0.444 7 7
HSPA8 0.035 0.005 -9999 0 -9999 0 0
SMAD3/SMAD4/ER alpha 0.022 0.095 -9999 0 -0.271 7 7
AKT1 0.026 0.034 -9999 0 -0.2 3 3
GSC -0.019 0.162 -9999 0 -1.464 1 1
NKX2-5 0.027 0.033 -9999 0 -0.2 1 1
muscle cell differentiation 0.041 0.165 0.521 10 -9999 0 10
SMAD2-3/SMAD4/SP1 0.026 0.125 -9999 0 -0.335 6 6
SMAD4 0.005 0.076 -9999 0 -0.468 3 3
CBFB 0.036 0.004 -9999 0 -9999 0 0
SAP18 0.026 0.016 -9999 0 -9999 0 0
Cbp/p300/MSG1 0.019 0.108 -9999 0 -0.328 12 12
SMAD3/SMAD4/VDR 0.03 0.121 -9999 0 -0.32 7 7
MYC 0.004 0.111 -9999 0 -0.481 10 10
CDKN2B -0.038 0.221 -9999 0 -1.468 4 4
AP1 -0.062 0.174 -9999 0 -0.452 23 23
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.023 0.14 -9999 0 -0.401 15 15
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.048 0.125 -9999 0 -0.32 20 20
SP3 0.036 0.015 -9999 0 -9999 0 0
CREB1 0.036 0.002 -9999 0 -9999 0 0
FOXH1 0.018 0.05 -9999 0 -0.352 2 2
SMAD3/SMAD4/GR 0.014 0.105 -9999 0 -0.328 10 10
GATA3 0.028 0.058 -9999 0 -0.38 3 3
SKI/SIN3/HDAC complex/NCoR1 0.023 0.082 -9999 0 -0.312 6 6
MEF2C/TIF2 0.006 0.135 -9999 0 -0.488 11 11
endothelial cell migration -0.002 0.147 1.394 2 -9999 0 2
MAX 0.033 0.011 -9999 0 -9999 0 0
RBBP7 0.034 0.023 -9999 0 -0.204 2 2
RBBP4 0.031 0.029 -9999 0 -0.203 3 3
RUNX2 0.034 0.017 -9999 0 -0.204 1 1
RUNX3 -0.024 0.146 -9999 0 -0.348 31 31
RUNX1 0.014 0.089 -9999 0 -0.32 12 12
CTBP1 0.035 0.007 -9999 0 -9999 0 0
NR3C1 0.019 0.089 -9999 0 -0.444 7 7
VDR 0.022 0.081 -9999 0 -0.437 6 6
CDKN1A -0.035 0.222 -9999 0 -1.216 6 6
KAT2B 0 0.003 -9999 0 -9999 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.022 0.086 -9999 0 -0.371 4 4
DCP1A 0.035 0.004 -9999 0 -9999 0 0
SKI 0.034 0.009 -9999 0 -9999 0 0
SERPINE1 0.001 0.149 -9999 0 -1.419 2 2
SMAD3/SMAD4/ATF2 0.023 0.084 -9999 0 -0.258 4 4
SMAD3/SMAD4/ATF3 0.011 0.095 -9999 0 -0.299 5 5
SAP30 0.031 0.037 -9999 0 -0.483 1 1
Cbp/p300/PIAS3 0.047 0.075 -9999 0 -0.297 7 7
JUN -0.073 0.165 -9999 0 -0.452 23 23
SMAD3/SMAD4/IRF7 0.026 0.091 -9999 0 -0.283 3 3
TFE3 0.036 0.024 -9999 0 -9999 0 0
COL1A2 -0.06 0.24 -9999 0 -0.843 17 17
mesenchymal cell differentiation -0.022 0.084 0.254 5 -9999 0 5
DLX1 0.028 0.043 -9999 0 -0.204 7 7
TCF3 0.027 0.062 -9999 0 -0.483 3 3
FOS -0.073 0.171 -9999 0 -0.325 55 55
SMAD3/SMAD4/Max 0.022 0.084 -9999 0 -0.253 5 5
Cbp/p300/SNIP1 0.05 0.072 -9999 0 -0.298 7 7
ZBTB17 0.034 0.011 -9999 0 -9999 0 0
LAMC1 -0.003 0.087 -9999 0 -0.462 4 4
TGIF2/HDAC complex/SMAD3/SMAD4 -0.007 0.102 -9999 0 -0.335 13 13
IRF7 0.036 0.02 -9999 0 -9999 0 0
ESR1 0.029 0.066 -9999 0 -0.421 4 4
HNF4A 0.008 0.071 -9999 0 -0.483 4 4
MEF2C 0.009 0.152 0.342 1 -0.53 10 11
SMAD2-3/SMAD4 0.018 0.094 -9999 0 -0.317 3 3
Cbp/p300/Src-1 0.045 0.084 -9999 0 -0.298 10 10
IGHV3OR16-13 0.004 0.028 -9999 0 -9999 0 0
TGIF2/HDAC complex -0.011 0.118 -9999 0 -0.482 12 12
CREBBP 0.032 0.037 -9999 0 -0.481 1 1
SKIL 0.002 0.121 -9999 0 -0.396 16 16
HDAC1 0.034 0.008 -9999 0 -9999 0 0
HDAC2 0.032 0.036 -9999 0 -0.483 1 1
SNIP1 0.035 0.006 -9999 0 -9999 0 0
GCN5L2 0.032 0.037 -9999 0 -0.484 1 1
SMAD3/SMAD4/TFE3 0.027 0.095 -9999 0 -0.265 6 6
MSG1/HSC70 0.017 0.087 -9999 0 -0.346 5 5
SMAD2 0.018 0.049 -9999 0 -0.543 1 1
SMAD3 0.008 0.071 -9999 0 -0.459 2 2
SMAD3/E2F4-5/DP1/p107/SMAD4 -0.012 0.079 -9999 0 -0.302 7 7
SMAD2/SMAD2/SMAD4 -0.067 0.096 -9999 0 -0.205 60 60
NCOR1 0.029 0.014 -9999 0 -9999 0 0
NCOA2 0.025 0.052 -9999 0 -0.483 2 2
NCOA1 0.026 0.071 -9999 0 -0.483 4 4
MYOD/E2A 0.028 0.078 -9999 0 -0.366 5 5
SMAD2-3/SMAD4/SP1/MIZ-1 0.035 0.127 -9999 0 -0.353 4 4
IFNB1 -0.005 0.084 -9999 0 -0.49 3 3
SMAD3/SMAD4/MEF2C 0.014 0.157 -9999 0 -0.535 10 10
CITED1 -0.01 0.111 -9999 0 -0.245 34 34
SMAD2-3/SMAD4/ARC105 0.019 0.085 -9999 0 -0.28 3 3
RBL1 0.011 0.062 -9999 0 -0.483 3 3
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.002 0.134 -9999 0 -0.441 10 10
RUNX1-3/PEBPB2 0.008 0.119 -9999 0 -0.296 21 21
SMAD7 -0.062 0.188 -9999 0 -0.557 10 10
MYC/MIZ-1 0.021 0.088 -9999 0 -0.346 10 10
SMAD3/SMAD4 -0.044 0.13 0.332 1 -0.454 8 9
IL10 -0.002 0.075 -9999 0 -0.374 1 1
PIASy/HDAC complex 0.03 0.041 -9999 0 -0.339 2 2
PIAS3 0.032 0.025 -9999 0 -0.205 2 2
CDK2 0.019 0.075 -9999 0 -0.287 10 10
IL5 -0.007 0.084 -9999 0 -0.374 1 1
CDK4 0.035 0.009 -9999 0 -9999 0 0
PIAS4 0.031 0.041 -9999 0 -0.339 2 2
ATF3 0.016 0.069 -9999 0 -0.222 15 15
SMAD3/SMAD4/SP1 0.013 0.119 -9999 0 -0.314 10 10
FOXG1 -0.001 0.003 -9999 0 -9999 0 0
FOXO3 0.007 0.022 -9999 0 -9999 0 0
FOXO1 0.007 0.022 -9999 0 -9999 0 0
FOXO4 0.007 0.022 -9999 0 -9999 0 0
heart looping 0.009 0.151 0.34 1 -0.524 10 11
CEBPB 0.015 0.04 -9999 0 -0.482 1 1
SMAD3/SMAD4/DLX1 0.02 0.088 -9999 0 -0.258 6 6
MYOD1 0.014 0.079 -9999 0 -0.236 17 17
SMAD3/SMAD4/HNF4 0.005 0.08 -9999 0 -0.34 5 5
SMAD3/SMAD4/GATA3 0.021 0.101 -9999 0 -0.318 4 4
SnoN/SIN3/HDAC complex/NCoR1 0.002 0.12 -9999 0 -0.395 16 16
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.005 0.135 -9999 0 -0.306 15 15
SMAD3/SMAD4/SP1-3 0.031 0.121 -9999 0 -0.386 4 4
MED15 0 0 -9999 0 -9999 0 0
SP1 0.015 0.063 -9999 0 -0.221 5 5
SIN3B 0.035 0.006 -9999 0 -9999 0 0
SIN3A 0.032 0.019 -9999 0 -0.204 1 1
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.029 0.108 -9999 0 -0.337 9 9
ITGB5 -0.011 0.104 -9999 0 -0.465 5 5
TGIF/SIN3/HDAC complex/CtBP 0.035 0.067 -9999 0 -0.359 2 2
SMAD3/SMAD4/AR 0.012 0.094 -9999 0 -0.266 7 7
AR 0.021 0.07 -9999 0 -0.254 11 11
negative regulation of cell growth -0.009 0.084 -9999 0 -0.414 3 3
SMAD3/SMAD4/MYOD 0.008 0.101 -9999 0 -0.306 7 7
E2F5 0.006 0.106 -9999 0 -0.455 10 10
E2F4 0.034 0.017 -9999 0 -0.204 1 1
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.035 0.1 -9999 0 -0.297 8 8
SMAD2-3/SMAD4/FOXO1-3a-4 -0.012 0.112 -9999 0 -0.407 11 11
TFDP1 0.024 0.039 -9999 0 -0.483 1 1
SMAD3/SMAD4/AP1 -0.05 0.185 -9999 0 -0.457 23 23
SMAD3/SMAD4/RUNX2 0.022 0.085 -9999 0 -0.255 5 5
TGIF2 -0.011 0.118 -9999 0 -0.483 12 12
TGIF1 0 0 -9999 0 -9999 0 0
ATF2 0.036 0.004 -9999 0 -9999 0 0
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.047 0.098 -9999 0 -0.607 1 1
epithelial cell differentiation 0.007 0.126 -9999 0 -0.5 3 3
ITCH 0.021 0.022 -9999 0 -9999 0 0
WWP1 0.009 0.103 -9999 0 -1.31 1 1
FYN 0.006 0.108 -9999 0 -0.343 16 16
EGFR 0.016 0.09 -9999 0 -0.413 8 8
PRL 0.033 0.023 -9999 0 -0.204 2 2
neuron projection morphogenesis 0.04 0.081 0.268 4 -0.434 1 5
PTPRZ1 0.009 0.102 -9999 0 -0.343 14 14
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.06 0.08 -9999 0 -0.468 1 1
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.035 0.066 -9999 0 -0.533 1 1
ADAM17 0.031 0.019 -9999 0 -9999 0 0
ErbB4/ErbB4 0.011 0.063 -9999 0 -0.666 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.06 0.087 -9999 0 -0.607 1 1
NCOR1 0.029 0.014 -9999 0 -9999 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.034 0.088 -9999 0 -0.489 2 2
GRIN2B 0.016 0.089 0.271 1 -0.42 3 4
ErbB4/ErbB2/betacellulin 0.046 0.096 -9999 0 -0.734 1 1
STAT1 0.015 0.067 -9999 0 -0.204 18 18
HBEGF -0.008 0.127 -9999 0 -0.327 25 25
PRLR 0.005 0.118 -9999 0 -0.44 13 13
E4ICDs/ETO2 0.016 0.12 -9999 0 -0.607 1 1
axon guidance -0.001 0.085 0.31 1 -0.784 1 2
NEDD4 0.002 0.103 -9999 0 -0.391 12 12
Prolactin receptor/Prolactin receptor/Prolactin 0.027 0.095 -9999 0 -0.358 11 11
CBFA2T3 -0.073 0.18 -9999 0 -0.317 64 64
ErbB4/ErbB2/HBEGF 0.045 0.091 -9999 0 -0.412 2 2
MAPK3 0.036 0.078 0.271 1 -0.445 1 2
STAT1 (dimer) 0.057 0.084 -9999 0 -0.604 1 1
MAPK1 0.041 0.069 0.271 1 -0.445 1 2
JAK2 0.015 0.078 -9999 0 -0.273 12 12
ErbB4/ErbB2/neuregulin 1 beta 0.032 0.07 -9999 0 -0.412 2 2
NRG1 0.009 0.039 -9999 0 -0.356 2 2
NRG3 0.024 0.073 -9999 0 -0.427 5 5
NRG2 0.028 0.056 -9999 0 -0.343 4 4
NRG4 0.017 0.071 -9999 0 -0.25 12 12
heart development -0.001 0.085 0.31 1 -0.784 1 2
neural crest cell migration 0.032 0.069 -9999 0 -0.408 2 2
ERBB2 0.015 0.029 -9999 0 -0.356 1 1
WWOX/E4ICDs 0.046 0.077 -9999 0 -0.607 1 1
SHC1 0.035 0.007 -9999 0 -9999 0 0
ErbB4/EGFR/neuregulin 4 0.054 0.105 -9999 0 -0.876 1 1
apoptosis -0.013 0.114 0.407 6 -9999 0 6
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.062 0.081 -9999 0 -0.607 1 1
ErbB4/ErbB2/epiregulin -0.034 0.147 -9999 0 -0.353 8 8
ErbB4/ErbB4/betacellulin/betacellulin 0.047 0.104 -9999 0 -0.84 1 1
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.051 0.133 -9999 0 -0.401 4 4
MDM2 0.006 0.059 0.264 1 -0.607 1 2
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.013 0.051 -9999 0 -0.419 1 1
STAT5A 0.013 0.095 0.343 2 -0.756 1 3
ErbB4/EGFR/neuregulin 1 beta 0.035 0.088 -9999 0 -0.734 1 1
DLG4 0.029 0.014 -9999 0 -9999 0 0
GRB2/SHC 0.049 0.015 -9999 0 -9999 0 0
E4ICDs/TAB2/NCoR1 0.064 0.076 -9999 0 -0.56 1 1
STAT5A (dimer) 0.021 0.144 -9999 0 -0.544 3 3
MAP3K7IP2 0.035 0.006 -9999 0 -9999 0 0
STAT5B (dimer) 0.038 0.095 -9999 0 -0.756 1 1
LRIG1 -0.018 0.157 -9999 0 -0.47 22 22
EREG -0.179 0.226 -9999 0 -0.373 109 109
BTC -0.004 0.127 -9999 0 -0.371 20 20
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.004 0.081 -9999 0 -0.794 1 1
ERBB4 0.011 0.063 -9999 0 -0.669 1 1
STAT5B 0.034 0.007 -9999 0 -9999 0 0
YAP1 -0.001 0.081 -9999 0 -0.473 5 5
GRB2 0.034 0.008 -9999 0 -9999 0 0
ErbB4/ErbB2/neuregulin 4 0.053 0.079 -9999 0 -0.587 1 1
glial cell differentiation -0.064 0.075 0.555 1 -9999 0 1
WWOX 0.024 0.039 -9999 0 -0.483 1 1
cell proliferation 0.01 0.109 0.296 1 -0.857 1 2
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.032 0.011 -9999 0 -9999 0 0
VLDLR -0.084 0.198 -9999 0 -0.369 61 61
LRPAP1 0.035 0.007 -9999 0 -9999 0 0
NUDC 0.034 0.009 -9999 0 -9999 0 0
RELN/LRP8 0.047 0.08 -9999 0 -0.298 9 9
CaM/Ca2+ 0.024 0.008 -9999 0 -9999 0 0
KATNA1 0.035 0.006 -9999 0 -9999 0 0
GO:0030286 0 0 -9999 0 -9999 0 0
ABL1 0.012 0.07 -9999 0 -0.271 9 9
IQGAP1/CaM 0.046 0.019 -9999 0 -9999 0 0
DAB1 0.035 0.005 -9999 0 -9999 0 0
IQGAP1 0.034 0.008 -9999 0 -9999 0 0
PLA2G7 -0.05 0.179 -9999 0 -0.379 43 43
CALM1 0.032 0.011 -9999 0 -9999 0 0
DYNLT1 0.035 0.006 -9999 0 -9999 0 0
mol:Ca2+ 0 0 -9999 0 -9999 0 0
LRPAP1/LRP8 0.031 0.084 -9999 0 -0.349 9 9
UniProt:Q4QZ09 0 0 -9999 0 -9999 0 0
CLIP1 0 0 -9999 0 -9999 0 0
CDK5R1 0.035 0.007 -9999 0 -9999 0 0
LIS1/Poliovirus Protein 3A 0.01 0.007 -9999 0 -9999 0 0
CDK5R2 0.036 0.002 -9999 0 -9999 0 0
mol:PP1 0 0 -9999 0 -9999 0 0
RELN/VLDLR/DAB1 -0.015 0.136 -9999 0 -0.298 32 32
YWHAE 0.03 0.013 -9999 0 -9999 0 0
NDEL1/14-3-3 E 0.026 0.075 0.333 3 -9999 0 3
MAP1B 0.005 0.018 0.182 1 -9999 0 1
RAC1 0.013 0.01 -9999 0 -9999 0 0
p35/CDK5 0.018 0.063 -9999 0 -0.244 9 9
RELN 0.033 0.018 -9999 0 -0.204 1 1
PAFAH/LIS1 -0.013 0.099 -9999 0 -0.29 20 20
LIS1/CLIP170 0.01 0.007 -9999 0 -9999 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain 0.02 0.062 -9999 0 -9999 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.016 0.121 -9999 0 -0.264 33 33
GO:0005869 0 0 -9999 0 -9999 0 0
NDEL1 0.013 0.07 0.331 3 -9999 0 3
LIS1/IQGAP1 0.028 0.019 -9999 0 -9999 0 0
RHOA 0.014 0.01 -9999 0 -9999 0 0
PAFAH1B1 0.013 0.009 -9999 0 -9999 0 0
PAFAH1B3 0.033 0.036 -9999 0 -0.483 1 1
PAFAH1B2 0.03 0.043 -9999 0 -0.297 3 3
MAP1B/LIS1/Dynein heavy chain 0.018 0.04 -9999 0 -0.222 2 2
NDEL1/Katanin 60/Dynein heavy chain 0.033 0.087 0.354 4 -9999 0 4
LRP8 0.009 0.109 -9999 0 -0.413 12 12
NDEL1/Katanin 60 0.019 0.08 0.333 3 -9999 0 3
P39/CDK5 0.02 0.064 -9999 0 -0.244 9 9
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.028 0.019 -9999 0 -9999 0 0
CDK5 -0.017 0.06 0.187 5 -0.255 9 14
PPP2R5D 0.034 0.017 -9999 0 -0.204 1 1
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.009 0.006 -9999 0 -9999 0 0
CSNK2A1 0.028 0.015 -9999 0 -9999 0 0
RELN/VLDLR/DAB1/LIS1 0.006 0.128 -9999 0 -0.256 29 29
RELN/VLDLR -0.017 0.145 -9999 0 -0.273 41 41
CDC42 0.013 0.013 -9999 0 -9999 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.005 0.099 -9999 0 -0.301 20 20
CRKL 0.029 0.051 -9999 0 -0.483 2 2
Rac1/GDP 0.024 0.008 -9999 0 -9999 0 0
DOCK1 0.021 0.081 -9999 0 -0.437 6 6
ITGA4 0.01 0.112 -9999 0 -0.458 11 11
alpha4/beta7 Integrin/MAdCAM1 0.03 0.125 -9999 0 -0.28 24 24
EPO 0.032 0.024 -9999 0 -0.204 2 2
alpha4/beta7 Integrin 0.005 0.131 -9999 0 -0.361 23 23
mol:GTP 0 0 -9999 0 -9999 0 0
CRK 0.03 0.013 -9999 0 -9999 0 0
alpha4/beta1 Integrin 0.033 0.084 -9999 0 -0.349 9 9
EPO/EPOR (dimer) 0.045 0.032 -9999 0 -9999 0 0
lamellipodium assembly 0.001 0.106 -9999 0 -0.385 6 6
PIK3CA 0.035 0.006 -9999 0 -9999 0 0
PI3K 0.045 0.049 -9999 0 -0.349 3 3
ARF6 0.028 0.051 -9999 0 -0.483 2 2
JAK2 0.01 0.079 -9999 0 -0.295 10 10
PXN 0.036 0.004 -9999 0 -9999 0 0
PIK3R1 0.028 0.062 -9999 0 -0.483 3 3
MADCAM1 0.016 0.069 -9999 0 -0.222 15 15
cell adhesion 0.028 0.123 -9999 0 -0.279 24 24
CRKL/CBL 0.046 0.041 -9999 0 -0.349 2 2
ITGB1 0.034 0.017 -9999 0 -0.204 1 1
SRC -0.002 0.07 -9999 0 -0.318 8 8
ITGB7 0 0.13 -9999 0 -0.483 14 14
RAC1 0.033 0.011 -9999 0 -9999 0 0
alpha4/beta1 Integrin/VCAM1 0.038 0.111 -9999 0 -0.346 14 14
p130Cas/Crk/Dock1 0.052 0.106 -9999 0 -0.343 3 3
VCAM1 0.013 0.098 -9999 0 -0.382 11 11
RHOA 0.035 0.004 -9999 0 -9999 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.068 0.076 -9999 0 -0.27 8 8
BCAR1 -0.017 0.063 -9999 0 -0.299 8 8
EPOR 0.032 0.029 -9999 0 -0.204 3 3
mol:GDP 0 0 -9999 0 -9999 0 0
CBL 0.035 0.005 -9999 0 -9999 0 0
GIT1 0.033 0.018 -9999 0 -0.204 1 1
Rac1/GTP 0.001 0.108 -9999 0 -0.397 6 6
HIF-2-alpha transcription factor network

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
MMP14 -0.002 0.189 -9999 0 -0.7 10 10
oxygen homeostasis 0.003 0.011 -9999 0 -9999 0 0
TCEB2 0.035 0.006 -9999 0 -9999 0 0
TCEB1 0.029 0.021 -9999 0 -0.204 1 1
VHL/Elongin B/Elongin C/HIF2A 0.023 0.121 -9999 0 -0.338 3 3
EPO 0.019 0.179 -9999 0 -0.562 3 3
FIH (dimer) 0.032 0.029 -9999 0 -0.218 1 1
APEX1 0.032 0.026 -9999 0 -9999 0 0
SERPINE1 0.001 0.195 -9999 0 -0.64 4 4
FLT1 0.01 0.154 -9999 0 -0.932 4 4
ADORA2A -0.002 0.18 0.388 2 -0.506 7 9
germ cell development 0.005 0.207 0.385 2 -0.557 11 13
SLC11A2 0 0.201 -9999 0 -0.552 8 8
BHLHE40 0 0.182 -9999 0 -0.465 12 12
HIF1AN 0.032 0.029 -9999 0 -0.218 1 1
HIF2A/ARNT/SIRT1 0.025 0.152 -9999 0 -0.399 6 6
ETS1 0.034 0.059 -9999 0 -0.24 7 7
CITED2 0.037 0.09 -9999 0 -0.564 3 3
KDR 0.036 0.126 -9999 0 -0.807 3 3
PGK1 0.009 0.199 0.397 1 -0.539 8 9
SIRT1 0.031 0.04 -9999 0 -0.345 2 2
response to hypoxia 0 0 -9999 0 -9999 0 0
HIF2A/ARNT 0.038 0.23 -9999 0 -0.575 8 8
EPAS1 -0.005 0.111 0.232 1 -0.313 8 9
SP1 0.038 0.023 -9999 0 -0.199 1 1
ABCG2 -0.012 0.221 0.389 2 -0.604 14 16
EFNA1 0 0.201 -9999 0 -0.557 9 9
FXN 0.003 0.181 0.388 2 -0.506 7 9
POU5F1 0.003 0.212 0.397 1 -0.579 11 12
neuron apoptosis -0.037 0.225 0.559 8 -9999 0 8
EP300 0.018 0.088 -9999 0 -0.443 7 7
EGLN3 -0.038 0.155 -9999 0 -0.327 40 40
EGLN2 0.034 0.021 -9999 0 -9999 0 0
EGLN1 0.034 0.022 -9999 0 -9999 0 0
VHL/Elongin B/Elongin C 0.053 0.045 -9999 0 -0.298 1 1
VHL 0.028 0.056 -9999 0 -0.343 4 4
ARNT 0.031 0.043 -9999 0 -0.472 1 1
SLC2A1 -0.018 0.204 0.388 2 -0.533 14 16
TWIST1 -0.015 0.197 0.381 1 -0.527 13 14
ELK1 0.039 0.029 -9999 0 -0.199 3 3
HIF2A/ARNT/Cbp/p300 0.02 0.164 -9999 0 -0.409 6 6
VEGFA 0 0.182 -9999 0 -0.465 12 12
CREBBP 0.032 0.036 -9999 0 -0.483 1 1
Effects of Botulinum toxin

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
STX1A 0.008 0.017 -9999 0 -0.133 3 3
UniProt:P19321 0 0 -9999 0 -9999 0 0
RIMS1/UNC13B 0.047 0.033 -9999 0 -0.349 1 1
STXBP1 0.023 0.064 -9999 0 -0.273 8 8
ACh/CHRNA1 0.018 0.044 -9999 0 -0.15 1 1
RAB3GAP2/RIMS1/UNC13B 0.06 0.05 -9999 0 -0.298 3 3
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 0.034 0.018 -9999 0 -0.204 1 1
mol:ACh 0 0.043 0.087 6 -0.115 12 18
RAB3GAP2 0.03 0.051 -9999 0 -0.483 2 2
STX1A/SNAP25/VAMP2 0.032 0.082 -9999 0 -0.288 1 1
UniProt:P10844 0 0 -9999 0 -9999 0 0
muscle contraction 0.018 0.043 -9999 0 -0.15 1 1
UNC13B 0.031 0.04 -9999 0 -0.343 2 2
CHRNA1 0.032 0.029 -9999 0 -0.204 3 3
UniProt:P10845 0 0 -9999 0 -9999 0 0
ACh/Synaptotagmin 1 -0.061 0.123 -9999 0 -0.29 38 38
SNAP25 0.002 0.029 -9999 0 -0.28 2 2
VAMP2 0.006 0.003 -9999 0 -9999 0 0
SYT1 -0.094 0.196 -9999 0 -0.341 71 71
UniProt:Q00496 0 0 -9999 0 -9999 0 0
STXIA/STXBP1 0.024 0.043 -9999 0 -0.295 2 2
STX1A/SNAP25 fragment 1/VAMP2 0.032 0.082 -9999 0 -0.288 1 1
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.034 0.017 -9999 0 -0.204 1 1
oxygen homeostasis 0 0 -9999 0 -9999 0 0
TCEB2 0.035 0.006 -9999 0 -9999 0 0
TCEB1 0.029 0.021 -9999 0 -0.204 1 1
HIF1A/p53 -0.029 0.112 -9999 0 -0.314 13 13
HIF1A -0.004 0.073 -9999 0 -0.325 8 8
COPS5 0.028 0.038 -9999 0 -0.483 1 1
VHL/Elongin B/Elongin C/RBX1/CUL2 0.075 0.058 -9999 0 -0.258 1 1
FIH (dimer) 0.033 0.018 -9999 0 -0.203 1 1
CDKN2A -0.035 0.154 -9999 0 -0.32 41 41
ARNT/IPAS 0.047 0.033 -9999 0 -0.349 1 1
HIF1AN 0.033 0.018 -9999 0 -0.204 1 1
GNB2L1 0.035 0.006 -9999 0 -9999 0 0
HIF1A/ARNT 0.002 0.084 -9999 0 -0.312 10 10
CUL2 0.036 0.004 -9999 0 -9999 0 0
OS9 0.034 0.017 -9999 0 -0.204 1 1
RACK1/Elongin B/Elongin C 0.057 0.034 -9999 0 -9999 0 0
response to hypoxia 0 0 -9999 0 -9999 0 0
HIF1A/Hsp90 -0.013 0.075 -9999 0 -0.312 9 9
PHD1-3/OS9 0.026 0.11 -9999 0 -0.271 16 16
HIF1A/RACK1/Elongin B/Elongin C 0.027 0.088 -9999 0 -0.354 4 4
VHL 0.028 0.056 -9999 0 -0.343 4 4
HSP90AA1 0 0 -9999 0 -9999 0 0
HIF1A/JAB1 0.005 0.082 -9999 0 -0.31 9 9
EGLN3 -0.038 0.155 -9999 0 -0.329 40 40
EGLN2 0.035 0.006 -9999 0 -9999 0 0
EGLN1 0.035 0.007 -9999 0 -9999 0 0
TP53 -0.048 0.181 -9999 0 -0.466 32 32
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.031 0.098 -9999 0 -0.518 6 6
ARNT 0.032 0.036 -9999 0 -0.483 1 1
ARD1A 0.034 0.023 -9999 0 -0.204 2 2
RBX1 0.033 0.019 -9999 0 -0.204 1 1
HIF1A/p19ARF -0.026 0.107 -9999 0 -0.314 14 14
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.06 0.172 0.305 4 -0.379 9 13
PDGFB-D/PDGFRB/SLAP 0.029 0.068 -9999 0 -0.353 4 4
PDGFB-D/PDGFRB/APS/CBL 0.045 0.026 -9999 0 -0.291 1 1
AKT1 0.054 0.118 0.318 6 -9999 0 6
mol:PI-4-5-P2 0 0.001 -9999 0 -9999 0 0
mol:Sphingosine-1-phosphate 0.053 0.155 0.275 3 -0.375 6 9
PIK3CA 0.035 0.006 -9999 0 -9999 0 0
FGR 0.004 0.152 -9999 0 -0.562 10 10
mol:Ca2+ 0.058 0.132 0.262 1 -0.375 3 4
MYC 0.045 0.262 0.417 21 -0.771 11 32
SHC1 0.035 0.007 -9999 0 -9999 0 0
HRAS/GDP 0.067 0.083 -9999 0 -0.246 1 1
LRP1/PDGFRB/PDGFB 0.064 0.037 -9999 0 -0.293 1 1
GRB10 -0.008 0.134 -9999 0 -0.399 20 20
PTPN11 0.029 0.053 -9999 0 -0.39 3 3
GO:0007205 0.058 0.132 0.262 1 -0.381 3 4
PTEN 0.026 0.062 -9999 0 -0.483 3 3
GRB2 0.034 0.008 -9999 0 -9999 0 0
GRB7 0.028 0.051 -9999 0 -0.483 2 2
PDGFB-D/PDGFRB/SHP2 0.046 0.051 -9999 0 -0.353 3 3
PDGFB-D/PDGFRB/GRB10 0.015 0.108 -9999 0 -0.351 15 15
cell cycle arrest 0.029 0.068 -9999 0 -0.352 4 4
HRAS 0.032 0.04 -9999 0 -0.343 2 2
HIF1A 0.045 0.111 0.299 6 -0.275 1 7
GAB1 0.023 0.168 0.299 3 -0.44 10 13
mol:GTP 0 0 -9999 0 -9999 0 0
DNM2 0.04 0.163 0.329 6 -0.392 9 15
PDGFB-D/PDGFRB 0.024 0.044 -9999 0 -0.304 1 1
mol:GDP 0 0 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.05 0.03 -9999 0 -0.346 1 1
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.006 0.129 -9999 0 -0.351 9 9
positive regulation of MAPKKK cascade 0.045 0.051 -9999 0 -0.352 3 3
PIK3R1 0.028 0.062 -9999 0 -0.483 3 3
mol:IP3 0.058 0.133 0.264 1 -0.384 3 4
E5 0 0.002 -9999 0 -9999 0 0
CSK 0.031 0.01 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/GRB7 0.044 0.05 -9999 0 -0.351 3 3
SHB 0.032 0.029 -9999 0 -0.204 3 3
BLK -0.05 0.186 -9999 0 -0.458 31 31
PTPN2 0.029 0.017 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/SNX15 0.05 0.032 -9999 0 -0.346 1 1
BCAR1 0.034 0.017 -9999 0 -0.204 1 1
VAV2 0.023 0.191 0.306 7 -0.468 11 18
CBL 0.035 0.005 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/DEP1 0.048 0.043 -9999 0 -0.351 2 2
LCK -0.03 0.197 -9999 0 -0.557 21 21
PDGFRB 0.034 0.037 -9999 0 -0.485 1 1
ACP1 0.036 0.004 -9999 0 -9999 0 0
HCK -0.045 0.191 -9999 0 -0.617 18 18
ABL1 0.026 0.168 0.257 4 -0.438 10 14
PDGFB-D/PDGFRB/CBL 0.01 0.173 -9999 0 -0.476 11 11
PTPN1 0.015 0.039 -9999 0 -0.486 1 1
SNX15 0.034 0.017 -9999 0 -0.204 1 1
STAT3 0.034 0.007 -9999 0 -9999 0 0
STAT1 0.015 0.067 -9999 0 -0.204 18 18
cell proliferation 0.049 0.242 0.406 22 -0.648 12 34
SLA 0.012 0.078 -9999 0 -0.273 12 12
actin cytoskeleton reorganization 0.096 0.093 0.352 1 -9999 0 1
SRC 0.004 0.099 -9999 0 -0.697 3 3
PI3K -0.012 0.058 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/GRB7/SHC 0.059 0.05 -9999 0 -0.298 3 3
SH2B2 0 0 -9999 0 -9999 0 0
PLCgamma1/SPHK1 0.053 0.158 0.279 3 -0.387 6 9
LYN 0.015 0.083 -9999 0 -0.559 2 2
LRP1 0.035 0.005 -9999 0 -9999 0 0
SOS1 0.036 0.002 -9999 0 -9999 0 0
STAT5B 0.034 0.007 -9999 0 -9999 0 0
STAT5A 0.027 0.049 -9999 0 -0.259 5 5
NCK1-2/p130 Cas 0.039 0.06 -9999 0 -9999 0 0
SPHK1 -0.035 0.158 -9999 0 -0.323 42 42
EDG1 0.006 0.118 -9999 0 -0.379 16 16
mol:DAG 0.058 0.133 0.264 1 -0.384 3 4
PLCG1 0.058 0.134 -9999 0 -0.392 3 3
NHERF/PDGFRB 0.039 0.094 -9999 0 -0.296 13 13
YES1 -0.042 0.208 -9999 0 -0.575 24 24
cell migration 0.038 0.093 -9999 0 -0.295 13 13
SHC/Grb2/SOS1 0.038 0.056 -9999 0 -0.249 1 1
SLC9A3R2 0.008 0.11 -9999 0 -0.397 13 13
SLC9A3R1 0.025 0.064 -9999 0 -0.413 4 4
NHERF1-2/PDGFRB/PTEN 0.048 0.101 -9999 0 -0.269 15 15
FYN -0.012 0.17 -9999 0 -0.694 10 10
DOK1 0.064 0.09 -9999 0 -0.274 2 2
HRAS/GTP 0.024 0.028 -9999 0 -0.347 1 1
PDGFB 0.032 0.025 -9999 0 -0.204 2 2
RAC1 0.031 0.214 0.403 14 -0.438 19 33
PRKCD 0.065 0.088 -9999 0 -0.275 1 1
FER 0.061 0.093 -9999 0 -0.275 1 1
MAPKKK cascade 0.086 0.104 0.301 11 -9999 0 11
RASA1 0.064 0.088 -9999 0 -0.275 1 1
NCK1 0.026 0.071 -9999 0 -0.483 4 4
NCK2 0.035 0.017 -9999 0 -0.204 1 1
p62DOK/Csk 0.078 0.083 -9999 0 -0.256 2 2
PDGFB-D/PDGFRB/SHB 0.047 0.038 -9999 0 -0.346 1 1
chemotaxis 0.027 0.165 0.253 5 -0.425 10 15
STAT1-3-5/STAT1-3-5 0.016 0.063 -9999 0 -9999 0 0
Bovine Papilomavirus E5/PDGFRB 0.023 0.028 -9999 0 -0.343 1 1
PTPRJ 0.032 0.04 -9999 0 -0.343 2 2
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -9999 0 0
GNAO1 0.036 0.002 -9999 0 -9999 0 0
CDC42/GTP 0.008 0.096 -9999 0 -0.321 9 9
PLCG1 -0.001 0.052 -9999 0 -0.296 3 3
mol:GTP 0 0 -9999 0 -9999 0 0
GNAI2 0.024 0.073 -9999 0 -0.427 5 5
GNAI3 0.03 0.051 -9999 0 -0.483 2 2
G12/G13 0.046 0.018 -9999 0 -9999 0 0
cell migration 0.007 0.094 -9999 0 -0.315 9 9
S1PR5 0 0 -9999 0 -9999 0 0
S1PR4 0 0 -9999 0 -9999 0 0
MAPK3 -0.016 0.097 -9999 0 -0.305 14 14
MAPK1 -0.008 0.089 -9999 0 -0.332 9 9
S1P/S1P5/Gi -0.007 0.097 -9999 0 -0.259 22 22
GNAI1 -0.013 0.142 -9999 0 -0.398 23 23
CDC42/GDP 0.024 0.013 -9999 0 -0.133 1 1
S1P/S1P5/G12 0.022 0.007 -9999 0 -9999 0 0
RHOA 0.041 0.061 0.203 24 -9999 0 24
S1P/S1P4/Gi -0.007 0.097 -9999 0 -0.259 22 22
mol:GDP 0 0 -9999 0 -9999 0 0
GNAZ 0.022 0.064 -9999 0 -0.273 8 8
S1P/S1P4/G12/G13 0.04 0.016 -9999 0 -9999 0 0
GNA12 0.033 0.01 -9999 0 -9999 0 0
GNA13 0.034 0.009 -9999 0 -9999 0 0
CDC42 0.032 0.019 -9999 0 -0.204 1 1
EPO signaling pathway

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
BCL2L1 0.017 0.085 -9999 0 -9999 0 0
CRKL 0.027 0.082 0.313 4 -0.268 3 7
mol:DAG 0.02 0.048 0.251 1 -9999 0 1
HRAS 0.028 0.089 0.291 5 -0.413 1 6
MAPK8 0.049 0.08 0.338 5 -9999 0 5
RAP1A 0.027 0.074 0.316 3 -0.234 2 5
GAB1 0.024 0.081 0.32 3 -0.239 3 6
MAPK14 0.051 0.08 0.338 5 -9999 0 5
EPO 0.032 0.029 -9999 0 -0.209 2 2
PLCG1 0.02 0.048 0.253 1 -9999 0 1
EPOR/TRPC2/IP3 Receptors 0.032 0.033 -9999 0 -0.202 3 3
RAPGEF1 0.035 0.004 -9999 0 -9999 0 0
EPO/EPOR (dimer)/SOCS3 0.045 0.076 -9999 0 -0.312 5 5
GAB1/SHC/GRB2/SOS1 0.054 0.084 0.308 3 -9999 0 3
EPO/EPOR (dimer) 0.045 0.039 -9999 0 -9999 0 0
IRS2 0.006 0.089 0.305 2 -0.246 14 16
STAT1 0.039 0.087 0.261 1 -0.302 1 2
STAT5B 0.041 0.072 0.259 1 -9999 0 1
cell proliferation 0.037 0.082 0.229 21 -9999 0 21
GAB1/SHIP/PIK3R1/SHP2/SHC 0.025 0.08 -9999 0 -0.38 2 2
TEC 0.027 0.076 0.32 3 -0.231 3 6
SOCS3 0.013 0.091 -9999 0 -0.311 13 13
STAT1 (dimer) 0.039 0.086 0.259 1 -0.298 1 2
JAK2 0.017 0.079 -9999 0 -0.274 12 12
PIK3R1 0.028 0.062 -9999 0 -0.483 3 3
EPO/EPOR (dimer)/JAK2 0.045 0.073 -9999 0 -0.24 3 3
EPO/EPOR 0.045 0.039 -9999 0 -9999 0 0
LYN 0.029 0.017 -9999 0 -9999 0 0
TEC/VAV2 0.014 0.107 0.295 2 -0.281 4 6
elevation of cytosolic calcium ion concentration 0.032 0.033 -9999 0 -0.201 3 3
SHC1 0.035 0.007 -9999 0 -9999 0 0
EPO/EPOR (dimer)/LYN 0.055 0.049 -9999 0 -9999 0 0
mol:IP3 0.02 0.048 0.251 1 -9999 0 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.01 0.098 0.291 2 -0.338 5 7
SH2B3 -0.001 0.008 -9999 0 -9999 0 0
NFKB1 0.046 0.073 0.319 3 -9999 0 3
EPO/EPOR (dimer)/JAK2/SOCS3 0.008 0.054 -9999 0 -0.216 8 8
PTPN6 0.024 0.072 0.312 1 -0.239 3 4
TEC/VAV2/GRB2 0.025 0.11 0.301 2 -0.288 3 5
EPOR 0.032 0.033 -9999 0 -0.202 3 3
INPP5D 0 0 -9999 0 -9999 0 0
mol:GDP 0.053 0.085 0.309 3 -9999 0 3
SOS1 0.036 0.002 -9999 0 -9999 0 0
PLCG2 -0.012 0.132 -9999 0 -0.328 27 27
CRKL/CBL/C3G 0.052 0.082 0.294 3 -0.31 1 4
VAV2 0.005 0.109 0.313 4 -0.244 21 25
CBL 0.027 0.078 0.313 4 -0.231 3 7
SHC/Grb2/SOS1 0.025 0.059 -9999 0 -0.238 1 1
STAT5A 0.038 0.083 0.259 1 -0.569 1 2
GRB2 0.034 0.008 -9999 0 -9999 0 0
STAT5 (dimer) 0.043 0.105 -9999 0 -0.345 6 6
LYN/PLCgamma2 0.016 0.089 -9999 0 -0.351 8 8
PTPN11 0.029 0.053 -9999 0 -0.39 3 3
BTK 0.008 0.101 0.301 3 -0.255 11 14
BCL2 -0.019 0.225 -9999 0 -0.796 14 14
Signaling events mediated by HDAC Class III

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
EP300 0.018 0.088 -9999 0 -0.443 7 7
HDAC4 0.033 0.036 -9999 0 -0.483 1 1
induction of apoptosis 0 0 -9999 0 -9999 0 0
regulation of S phase of mitotic cell cycle -0.007 0.028 0.242 2 -9999 0 2
CDKN1A -0.007 0.105 -9999 0 -0.6 5 5
KAT2B 0 0 -9999 0 -9999 0 0
BAX 0.029 0.046 -9999 0 -0.273 4 4
FOXO3 0.003 0.068 0.393 6 -9999 0 6
FOXO1 0 0 -9999 0 -9999 0 0
FOXO4 0.004 0.052 -9999 0 -0.271 7 7
response to UV 0 0 -9999 0 -9999 0 0
XRCC6 0.034 0.009 -9999 0 -9999 0 0
TAT 0.036 0.004 -9999 0 -9999 0 0
mol:Lysophosphatidic acid 0 0 -9999 0 -9999 0 0
MYOD1 -0.004 0.05 -9999 0 -0.347 2 2
PPARGC1A -0.038 0.161 -9999 0 -0.343 40 40
FHL2 0.016 0.092 -9999 0 -0.371 10 10
response to nutrient levels 0 0 -9999 0 -9999 0 0
KU70/SIRT1 0.045 0.035 -9999 0 -0.351 1 1
HIST2H4A 0.007 0.028 -9999 0 -0.242 2 2
SIRT1/FOXO3a 0.031 0.048 0.264 6 -9999 0 6
SIRT1 0.03 0.042 -9999 0 -0.346 2 2
response to hypoxia 0 0 -9999 0 -9999 0 0
SIRT1/MEF2D/HDAC4 0.061 0.044 -9999 0 -0.297 2 2
SIRT1/Histone H1b 0.016 0.076 -9999 0 -0.286 9 9
apoptosis -0.056 0.049 0.298 2 -9999 0 2
SIRT1/PGC1A -0.005 0.108 -9999 0 -0.289 22 22
p53/SIRT1 -0.027 0.139 -9999 0 -0.352 29 29
SIRT1/FOXO4 0.018 0.065 -9999 0 -0.278 6 6
FOXO1/FHL2/SIRT1 0.03 0.061 -9999 0 -0.269 7 7
HIST1H1E 0.003 0.069 -9999 0 -0.291 10 10
SIRT1/p300 0.034 0.077 -9999 0 -0.407 5 5
muscle cell differentiation -0.007 0.051 0.284 3 -9999 0 3
TP53 -0.048 0.179 0.216 1 -0.459 32 33
KU70/SIRT1/BAX 0.057 0.049 -9999 0 -0.299 2 2
CREBBP 0.032 0.036 -9999 0 -0.483 1 1
MEF2D 0.034 0.007 -9999 0 -9999 0 0
HIV-1 Tat/SIRT1 0.047 0.034 -9999 0 -0.351 1 1
ACSS2 -0.001 0.057 -9999 0 -0.351 5 5
SIRT1/PCAF/MYOD 0.007 0.051 -9999 0 -0.285 3 3
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.014 0.095 -9999 0 -0.343 12 12
positive regulation of NF-kappaB transcription factor activity 0.018 0.084 -9999 0 -0.347 8 8
MAP2K4 0.006 0.067 -9999 0 -0.319 4 4
IKBKB 0.031 0.012 -9999 0 -9999 0 0
TNFRSF10B 0.025 0.027 -9999 0 -0.204 2 2
TNFRSF10A 0.019 0.059 -9999 0 -0.315 5 5
SMPD1 0.003 0.047 -9999 0 -0.216 6 6
IKBKG 0.035 0.017 -9999 0 -0.204 1 1
mol:GTP 0 0 -9999 0 -9999 0 0
TNFRSF10D 0.019 0.052 -9999 0 -0.25 6 6
TRAIL/TRAILR2 0.018 0.08 -9999 0 -0.329 7 7
TRAIL/TRAILR3 -0.015 0.11 -9999 0 -0.341 14 14
TRAIL/TRAILR1 0.016 0.09 -9999 0 -0.387 7 7
TRAIL/TRAILR4 0.018 0.084 -9999 0 -0.348 8 8
TRAIL/TRAILR1/DAP3/GTP 0.031 0.078 -9999 0 -0.302 7 7
IKK complex 0.012 0.082 -9999 0 -0.49 2 2
RIPK1 0.036 0.004 -9999 0 -9999 0 0
response to oxidative stress 0 0 -9999 0 -9999 0 0
DAP3/GTP 0.026 0.005 -9999 0 -9999 0 0
MAPK3 -0.001 0.083 -9999 0 -0.384 8 8
MAP3K1 0.018 0.065 -9999 0 -0.332 4 4
TRAILR4 (trimer) 0.019 0.052 -9999 0 -0.25 6 6
TRADD 0.036 0.004 -9999 0 -9999 0 0
TRAILR1 (trimer) 0.019 0.059 -9999 0 -0.315 5 5
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.014 0.069 -9999 0 -0.281 7 7
CFLAR 0.035 0.004 -9999 0 -9999 0 0
MAPK1 0.005 0.061 -9999 0 -0.349 5 5
TRAIL/TRAILR1/FADD/TRADD/RIP 0.058 0.089 -9999 0 -0.287 7 7
mol:ceramide 0.003 0.047 -9999 0 -0.216 6 6
FADD 0.036 0.004 -9999 0 -9999 0 0
MAPK8 0.005 0.055 -9999 0 -0.333 1 1
TRAF2 0.033 0.024 -9999 0 -0.204 2 2
TRAILR3 (trimer) -0.02 0.116 -9999 0 -0.262 33 33
CHUK 0.027 0.062 -9999 0 -0.483 3 3
TRAIL/TRAILR1/FADD 0.033 0.085 -9999 0 -0.33 7 7
DAP3 0.035 0.007 -9999 0 -9999 0 0
CASP10 -0.004 0.07 -9999 0 -0.397 5 5
JNK cascade 0.018 0.084 -9999 0 -0.347 8 8
TRAIL (trimer) 0.014 0.094 -9999 0 -0.343 12 12
TNFRSF10C -0.02 0.116 -9999 0 -0.263 33 33
TRAIL/TRAILR1/DAP3/GTP/FADD 0.042 0.081 -9999 0 -0.285 7 7
TRAIL/TRAILR2/FADD 0.035 0.076 -9999 0 -0.293 6 6
cell death 0.003 0.047 -9999 0 -0.215 6 6
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.014 0.066 -9999 0 -0.289 3 3
TRAILR2 (trimer) 0.025 0.027 -9999 0 -0.203 2 2
CASP8 0.01 0.101 -9999 0 -0.805 3 3
negative regulation of caspase activity 0 0 -9999 0 -9999 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.061 0.082 -9999 0 -0.253 6 6
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.021 0.04 -9999 0 -9999 0 0
Crk/p130 Cas/Paxillin -0.025 0.076 -9999 0 -0.314 6 6
JUN -0.025 0.103 -9999 0 -0.325 11 11
HRAS 0.032 0.04 -9999 0 -0.343 2 2
RET51/GFRalpha1/GDNF/GRB10 0.019 0.124 -9999 0 -0.293 20 20
RAP1A 0.034 0.008 -9999 0 -9999 0 0
FRS2 0.033 0.024 -9999 0 -0.204 2 2
RAP1A/GDP 0.025 0.006 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF/DOK1 0.042 0.102 -9999 0 -0.297 10 10
EntrezGene:5979 0 0 -9999 0 -9999 0 0
PTPN11 0.029 0.053 -9999 0 -0.39 3 3
mol:GTP 0 0 -9999 0 -9999 0 0
CRK 0.03 0.013 -9999 0 -9999 0 0
RET9/GFRalpha1/GDNF/Enigma 0.053 0.055 -9999 0 -0.27 4 4
RHOA 0.035 0.004 -9999 0 -9999 0 0
RAP1A/GTP 0.03 0.105 -9999 0 -0.267 16 16
GRB7 0.028 0.051 -9999 0 -0.483 2 2
RET51/GFRalpha1/GDNF 0.042 0.099 -9999 0 -0.3 9 9
MAPKKK cascade 0.012 0.088 -9999 0 -0.313 4 4
BCAR1 0.034 0.017 -9999 0 -0.204 1 1
RET9/GFRalpha1/GDNF/IRS1 0.041 0.083 -9999 0 -0.285 11 11
lamellipodium assembly -0.011 0.078 -9999 0 -0.306 5 5
RET51/GFRalpha1/GDNF/SHC 0.046 0.093 -9999 0 -0.296 7 7
PIK3CA 0.035 0.006 -9999 0 -9999 0 0
RET9/GFRalpha1/GDNF/SHC 0.055 0.048 -9999 0 -0.27 3 3
RET9/GFRalpha1/GDNF/Shank3 0.051 0.053 -9999 0 -0.266 4 4
MAPK3 -0.017 0.091 -9999 0 -0.257 18 18
DOK1 0.032 0.039 -9999 0 -0.343 2 2
DOK6 0.021 0.023 -9999 0 -0.204 1 1
PXN 0.036 0.004 -9999 0 -9999 0 0
neurite development -0.001 0.095 0.247 3 -0.347 6 9
DOK5 0.002 0.075 -9999 0 -0.28 11 11
GFRA1 0.03 0.043 -9999 0 -0.297 3 3
MAPK8 0.002 0.083 -9999 0 -0.349 5 5
HRAS/GTP 0.032 0.107 -9999 0 -0.309 11 11
tube development 0.05 0.051 -9999 0 -0.251 3 3
MAPK1 -0.012 0.086 -9999 0 -0.304 5 5
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.024 0.045 -9999 0 -0.242 5 5
Rac1/GDP 0.024 0.008 -9999 0 -9999 0 0
SRC 0.011 0.062 -9999 0 -0.483 3 3
PDLIM7 0.032 0.029 -9999 0 -0.204 3 3
RET51/GFRalpha1/GDNF/Dok6 0.013 0.076 -9999 0 -0.298 4 4
SHC1 0.035 0.007 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF/Dok4 0.033 0.116 -9999 0 -0.299 16 16
RET51/GFRalpha1/GDNF/Dok5 0.007 0.084 -9999 0 -0.3 6 6
PRKCA 0.03 0.04 -9999 0 -0.343 2 2
HRAS/GDP 0.024 0.028 -9999 0 -0.24 2 2
CREB1 0.032 0.053 -9999 0 -0.287 1 1
PIK3R1 0.028 0.062 -9999 0 -0.483 3 3
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.023 0.042 -9999 0 -0.227 4 4
RET51/GFRalpha1/GDNF/Grb7 0.036 0.101 -9999 0 -0.297 10 10
mol:GDP 0 0 -9999 0 -9999 0 0
RET -0.007 0.109 -9999 0 -0.249 31 31
DOK4 0.016 0.1 -9999 0 -0.483 8 8
JNK cascade -0.026 0.102 -9999 0 -0.319 11 11
RET9/GFRalpha1/GDNF/FRS2 0.054 0.054 -9999 0 -0.27 4 4
SHANK3 0.032 0.011 -9999 0 -9999 0 0
RASA1 0.024 0.073 -9999 0 -0.427 5 5
NCK1 0.026 0.071 -9999 0 -0.483 4 4
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.028 0.031 -9999 0 -0.228 2 2
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.011 0.07 -9999 0 -0.286 3 3
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.006 0.088 -9999 0 -0.367 5 5
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.018 0.056 -9999 0 -0.234 6 6
PI3K -0.012 0.11 -9999 0 -0.452 5 5
SOS1 0.036 0.002 -9999 0 -9999 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.063 0.054 -9999 0 -0.251 3 3
GRB10 -0.008 0.134 -9999 0 -0.399 20 20
activation of MAPKK activity 0.016 0.07 -9999 0 -0.301 4 4
RET51/GFRalpha1/GDNF/FRS2 0.042 0.1 -9999 0 -0.3 9 9
GAB1 0.028 0.054 -9999 0 -0.39 3 3
IRS1 0.013 0.098 -9999 0 -0.382 11 11
IRS2 -0.008 0.126 -9999 0 -0.446 15 15
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.013 0.063 -9999 0 -0.232 8 8
RET51/GFRalpha1/GDNF/PKC alpha 0.038 0.098 -9999 0 -0.291 9 9
GRB2 0.034 0.008 -9999 0 -9999 0 0
PRKACA 0.035 0.006 -9999 0 -9999 0 0
GDNF 0.027 0.062 -9999 0 -0.483 3 3
RAC1 0.033 0.011 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF/IRS1 0.029 0.117 -9999 0 -0.298 16 16
Rac1/GTP -0.008 0.095 -9999 0 -0.364 5 5
RET9/GFRalpha1/GDNF 0.037 0.051 -9999 0 -0.295 4 4
GFRalpha1/GDNF 0.04 0.059 -9999 0 -0.349 4 4
S1P5 pathway

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
mol:S1P 0 0 -9999 0 -9999 0 0
telencephalon oligodendrocyte cell migration -0.009 0.094 0.315 9 -9999 0 9
GNAI2 0.024 0.073 -9999 0 -0.427 5 5
S1P/S1P5/G12 0.022 0.007 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
GNAO1 0.036 0.002 -9999 0 -9999 0 0
RhoA/GTP 0.01 0.096 -9999 0 -0.321 9 9
negative regulation of cAMP metabolic process -0.007 0.096 -9999 0 -0.257 22 22
GNAZ 0.022 0.064 -9999 0 -0.273 8 8
GNAI3 0.03 0.051 -9999 0 -0.483 2 2
GNA12 0.033 0.01 -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 -0.007 0.097 -9999 0 -0.259 22 22
RhoA/GDP 0.026 0.003 -9999 0 -9999 0 0
RHOA 0.035 0.004 -9999 0 -9999 0 0
GNAI1 -0.013 0.142 -9999 0 -0.398 23 23
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC -0.001 0.152 -9999 0 -1.369 2 2
PLK1 0.002 0.197 -9999 0 -1.03 3 3
CDKN1B 0.029 0.153 0.389 1 -0.433 5 6
FOXO3 0.005 0.191 -9999 0 -0.685 7 7
KAT2B 0.003 0.018 -9999 0 -0.056 4 4
FOXO1/SIRT1 0.018 0.083 -9999 0 -0.397 4 4
CAT -0.007 0.227 -9999 0 -1.116 5 5
CTNNB1 0.011 0.093 -9999 0 -0.297 15 15
AKT1 0.027 0.043 -9999 0 -0.187 3 3
FOXO1 0.003 0.077 -9999 0 -0.345 5 5
MAPK10 0.016 0.085 0.196 13 -0.256 12 25
mol:GTP 0 0.002 -9999 0 -9999 0 0
FOXO4 0.014 0.109 0.313 2 -0.374 5 7
response to oxidative stress 0.005 0.019 -9999 0 -0.052 6 6
FOXO3A/SIRT1 0.033 0.178 -9999 0 -0.57 9 9
XPO1 0.036 0.001 -9999 0 -9999 0 0
EP300 0.019 0.089 -9999 0 -0.442 7 7
BCL2L11 0.037 0.03 -9999 0 -9999 0 0
FOXO1/SKP2 0.014 0.081 -9999 0 -0.364 3 3
mol:GDP 0.005 0.019 -9999 0 -0.052 6 6
RAN 0.036 0.004 -9999 0 -9999 0 0
GADD45A 0.021 0.21 -9999 0 -0.812 9 9
YWHAQ 0.036 0.002 -9999 0 -9999 0 0
FOXO1/14-3-3 family 0.041 0.14 -9999 0 -0.507 7 7
MST1 0.012 0.082 -9999 0 -0.243 15 15
CSNK1D 0.035 0.007 -9999 0 -9999 0 0
CSNK1E 0.025 0.064 -9999 0 -0.413 4 4
FOXO4/14-3-3 family -0.011 0.118 -9999 0 -0.432 9 9
YWHAB 0.013 0.052 -9999 0 -0.483 2 2
MAPK8 0.029 0.068 0.196 13 -0.268 5 18
MAPK9 0.028 0.074 0.195 13 -0.315 5 18
YWHAG 0.034 0.008 -9999 0 -9999 0 0
YWHAE 0.03 0.013 -9999 0 -9999 0 0
YWHAZ 0.029 0.014 -9999 0 -9999 0 0
SIRT1 0.031 0.043 -9999 0 -0.334 2 2
SOD2 0.013 0.185 -9999 0 -0.741 6 6
RBL2 0.032 0.151 -9999 0 -0.702 2 2
RAL/GDP 0.039 0.061 -9999 0 -0.309 5 5
CHUK 0.024 0.069 -9999 0 -0.485 3 3
Ran/GTP 0.027 0.008 -9999 0 -9999 0 0
CSNK1G2 0.034 0.007 -9999 0 -9999 0 0
RAL/GTP 0.04 0.058 -9999 0 -0.282 5 5
CSNK1G1 0.034 0.008 -9999 0 -9999 0 0
FASLG -0.081 0.382 -9999 0 -1.436 15 15
SKP2 0.022 0.071 -9999 0 -0.308 8 8
USP7 0.021 0.083 -9999 0 -0.403 7 7
IKBKB 0.028 0.032 -9999 0 -9999 0 0
CCNB1 -0.025 0.283 -9999 0 -1.121 10 10
FOXO1-3a-4/beta catenin 0.02 0.158 -9999 0 -0.411 9 9
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.081 -9999 0 -0.361 3 3
CSNK1A1 0.035 0.006 -9999 0 -9999 0 0
SGK1 0.003 0.018 -9999 0 -0.056 4 4
CSNK1G3 0.035 0.006 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0.05 0.009 -9999 0 -9999 0 0
ZFAND5 0.015 0.095 0.27 3 -0.306 5 8
SFN 0.02 0.071 -9999 0 -0.308 8 8
CDK2 0.021 0.076 -9999 0 -0.285 10 10
FOXO3A/14-3-3 -0.005 0.108 -9999 0 -0.448 6 6
CREBBP 0.034 0.039 -9999 0 -0.48 1 1
FBXO32 0.006 0.314 -9999 0 -1.206 10 10
BCL6 -0.001 0.265 -9999 0 -1.157 8 8
RALB 0.024 0.08 -9999 0 -0.484 5 5
RALA 0.033 0.01 -9999 0 -9999 0 0
YWHAH 0.031 0.037 -9999 0 -0.483 1 1
Retinoic acid receptors-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
HDAC1 0.034 0.008 -9999 0 -9999 0 0
HDAC3 0.035 0.006 -9999 0 -9999 0 0
VDR 0.022 0.081 -9999 0 -0.437 6 6
Cbp/p300/PCAF 0.031 0.064 -9999 0 -0.295 7 7
EP300 0.018 0.088 -9999 0 -0.443 7 7
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.006 0.058 -9999 0 -0.236 3 3
KAT2B 0 0 -9999 0 -9999 0 0
MAPK14 0.036 0.004 -9999 0 -9999 0 0
AKT1 0.045 0.085 0.21 26 -0.232 2 28
RAR alpha/9cRA/Cyclin H 0.053 0.077 0.263 1 -0.274 2 3
mol:9cRA 0 0 -9999 0 -9999 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.016 0.077 0.189 1 -0.256 8 9
CDC2 0.033 0.037 -9999 0 -0.483 1 1
response to UV 0.001 0.002 -9999 0 -9999 0 0
RAR alpha/Jnk1 0.038 0.047 -9999 0 -0.331 1 1
NCOR2 0.032 0.04 -9999 0 -0.343 2 2
VDR/VDR/Vit D3 0.016 0.058 -9999 0 -0.311 6 6
RXRs/RARs/NRIP1/9cRA 0.036 0.109 0.387 1 -0.47 5 6
NCOA2 0.025 0.052 -9999 0 -0.483 2 2
NCOA3 0.016 0.039 -9999 0 -0.483 1 1
NCOA1 0.026 0.071 -9999 0 -0.483 4 4
VDR/VDR/DNA 0.022 0.081 -9999 0 -0.436 6 6
RARG 0.03 0.054 -9999 0 -0.39 3 3
RAR gamma1/9cRA 0.043 0.036 -9999 0 -0.295 2 2
MAPK3 0.025 0.073 -9999 0 -0.427 5 5
MAPK1 0.034 0.008 -9999 0 -9999 0 0
MAPK8 0.035 0.009 -9999 0 -9999 0 0
mol:Vit D3 0 0 -9999 0 -9999 0 0
RXRs/VDR/DNA/Vit D3 0.036 0.095 -9999 0 -0.378 5 5
RARA 0.021 0.031 -9999 0 -0.222 2 2
negative regulation of phosphoinositide 3-kinase cascade 0 0 -9999 0 -9999 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.013 0.075 0.189 1 -0.264 8 9
PRKCA 0.032 0.041 -9999 0 -0.341 2 2
RXRs/RARs/NRIP1/9cRA/HDAC1 0.032 0.104 0.322 1 -0.564 3 4
RXRG 0.015 0.066 -9999 0 -0.329 6 6
RXRA 0.024 0.052 -9999 0 -0.217 1 1
RXRB 0.024 0.038 -9999 0 -0.302 2 2
VDR/Vit D3/DNA 0.016 0.058 -9999 0 -0.311 6 6
RBP1 -0.107 0.197 -9999 0 -0.326 82 82
CRBP1/9-cic-RA -0.074 0.14 -9999 0 -0.347 36 36
RARB 0.023 0.078 -9999 0 -0.343 8 8
PRKCG 0.027 0.056 -9999 0 -0.236 8 8
MNAT1 0.033 0.011 -9999 0 -9999 0 0
RAR alpha/RXRs 0.043 0.11 -9999 0 -0.442 4 4
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.041 0.093 0.275 1 -0.382 4 5
proteasomal ubiquitin-dependent protein catabolic process 0.052 0.078 0.246 3 -0.318 1 4
RXRs/RARs/NRIP1/9cRA/HDAC3 0.033 0.104 0.322 1 -0.564 3 4
positive regulation of DNA binding 0.04 0.068 -9999 0 -0.261 2 2
NRIP1 0.032 0.125 -9999 0 -0.956 2 2
RXRs/RARs 0.035 0.098 -9999 0 -0.464 4 4
RXRs/RXRs/DNA/9cRA 0.017 0.081 -9999 0 -0.386 5 5
PRKACA 0.035 0.006 -9999 0 -9999 0 0
CDK7 0.033 0.036 -9999 0 -0.483 1 1
TFIIH 0.062 0.034 -9999 0 -0.298 1 1
RAR alpha/9cRA 0.067 0.061 -9999 0 -0.273 1 1
CCNH 0.035 0.006 -9999 0 -9999 0 0
CREBBP 0.032 0.036 -9999 0 -0.483 1 1
RAR gamma2/9cRA 0.057 0.046 -9999 0 -0.241 3 3
Paxillin-dependent events mediated by a4b1

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
CRKL 0.029 0.051 -9999 0 -0.483 2 2
Rac1/GDP 0.032 0.015 -9999 0 -9999 0 0
DOCK1 0.021 0.081 -9999 0 -0.437 6 6
ITGA4 0.01 0.112 -9999 0 -0.458 11 11
RAC1 0.033 0.011 -9999 0 -9999 0 0
alpha4/beta7 Integrin 0.005 0.131 -9999 0 -0.361 23 23
mol:GTP 0 0 -9999 0 -9999 0 0
CRK 0.03 0.013 -9999 0 -9999 0 0
alpha4/beta1 Integrin 0.052 0.078 -9999 0 -0.298 9 9
alpha4/beta7 Integrin/Paxillin 0.021 0.109 -9999 0 -0.281 23 23
lamellipodium assembly 0.011 0.093 -9999 0 -0.396 6 6
PIK3CA 0.035 0.006 -9999 0 -9999 0 0
PI3K 0.045 0.049 -9999 0 -0.349 3 3
ARF6 0.028 0.051 -9999 0 -0.483 2 2
TLN1 0.035 0.006 -9999 0 -9999 0 0
PXN 0.019 0.003 -9999 0 -9999 0 0
PIK3R1 0.028 0.062 -9999 0 -0.483 3 3
ARF6/GTP 0.052 0.076 -9999 0 -0.237 10 10
cell adhesion 0.06 0.073 -9999 0 -0.254 9 9
CRKL/CBL 0.046 0.041 -9999 0 -0.349 2 2
alpha4/beta1 Integrin/Paxillin 0.042 0.07 -9999 0 -0.272 9 9
ITGB1 0.034 0.017 -9999 0 -0.204 1 1
ITGB7 0 0.13 -9999 0 -0.483 14 14
ARF6/GDP 0.027 0.052 -9999 0 -0.477 2 2
alpha4/beta1 Integrin/Paxillin/VCAM1 0.05 0.104 -9999 0 -0.311 13 13
p130Cas/Crk/Dock1 0.047 0.066 -9999 0 -0.308 5 5
VCAM1 0.013 0.098 -9999 0 -0.382 11 11
alpha4/beta1 Integrin/Paxillin/Talin 0.063 0.075 -9999 0 -0.256 9 9
alpha4/beta1 Integrin/Paxillin/GIT1 0.062 0.073 -9999 0 -0.256 8 8
BCAR1 0.034 0.017 -9999 0 -0.204 1 1
mol:GDP -0.06 0.072 0.254 8 -9999 0 8
CBL 0.035 0.005 -9999 0 -9999 0 0
PRKACA 0.035 0.006 -9999 0 -9999 0 0
GIT1 0.033 0.018 -9999 0 -0.204 1 1
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.063 0.075 -9999 0 -0.256 9 9
Rac1/GTP 0.009 0.101 -9999 0 -0.44 6 6
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.039 0.061 -9999 0 -0.349 4 4
AKT1 0.043 0.167 0.407 4 -0.46 8 12
PTK2B -0.006 0.09 -9999 0 -0.42 4 4
VEGFR2 homodimer/Frs2 0.018 0.089 -9999 0 -0.554 2 2
CAV1 0.023 0.064 -9999 0 -0.273 8 8
CALM1 0.032 0.011 -9999 0 -9999 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.012 0.096 -9999 0 -0.542 2 2
endothelial cell proliferation 0.095 0.182 0.359 26 -0.441 6 32
mol:Ca2+ -0.021 0.106 -9999 0 -0.461 6 6
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.024 0.095 -9999 0 -0.518 2 2
RP11-342D11.1 -0.036 0.127 -9999 0 -0.506 7 7
CDH5 0.032 0.04 -9999 0 -0.343 2 2
VEGFA homodimer 0.047 0.063 -9999 0 -0.326 3 3
SHC1 0.035 0.007 -9999 0 -9999 0 0
SHC2 -0.02 0.133 -9999 0 -0.294 34 34
HRAS/GDP -0.004 0.129 -9999 0 -0.462 6 6
SH2D2A 0.022 0.075 -9999 0 -0.39 6 6
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.061 0.15 0.325 1 -0.546 4 5
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.009 0.106 -9999 0 -0.572 3 3
VEGFR1 homodimer 0.009 0.076 -9999 0 -0.279 11 11
SHC/GRB2/SOS1 0.02 0.145 -9999 0 -0.507 5 5
GRB10 -0.046 0.182 -9999 0 -0.563 18 18
PTPN11 0.029 0.053 -9999 0 -0.39 3 3
GRB2 0.034 0.008 -9999 0 -9999 0 0
PAK1 0.031 0.051 -9999 0 -0.483 2 2
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.022 0.115 -9999 0 -0.437 3 3
HRAS 0.032 0.04 -9999 0 -0.343 2 2
VEGF/Rho/ROCK1/Integrin Complex -0.023 0.103 -9999 0 -0.397 6 6
HIF1A 0.025 0.044 -9999 0 -0.204 7 7
FRS2 0.033 0.024 -9999 0 -0.204 2 2
oxygen and reactive oxygen species metabolic process 0.022 0.094 -9999 0 -0.511 2 2
mol:GTP 0 0 -9999 0 -9999 0 0
FLT4 0.035 0.005 -9999 0 -9999 0 0
Nck/Pak 0.041 0.068 -9999 0 -0.349 6 6
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.002 0.115 -9999 0 -0.426 6 6
mol:GDP 0.006 0.135 -9999 0 -0.492 5 5
mol:NADP 0.061 0.144 0.34 3 -0.504 4 7
eNOS/Hsp90 0.056 0.136 0.32 3 -0.471 4 7
PIK3R1 0.028 0.062 -9999 0 -0.483 3 3
mol:IP3 -0.021 0.107 -9999 0 -0.467 6 6
HIF1A/ARNT 0.037 0.047 -9999 0 -0.332 1 1
SHB 0.032 0.029 -9999 0 -0.204 3 3
VEGFA -0.005 0.021 -9999 0 -9999 0 0
VEGFC -0.002 0.125 -9999 0 -0.401 17 17
FAK1/Vinculin 0.037 0.116 -9999 0 -0.521 2 2
mol:Ca ++ 0 0 -9999 0 -9999 0 0
RHOA 0.035 0.004 -9999 0 -9999 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.022 0.109 -9999 0 -0.446 4 4
PTPN6 0.035 0.006 -9999 0 -9999 0 0
EPAS1 0.016 0.103 -9999 0 -0.478 7 7
mol:L-citrulline 0.061 0.144 0.34 3 -0.504 4 7
ITGAV 0.021 0.083 -9999 0 -0.403 7 7
PIK3CA 0.035 0.006 -9999 0 -9999 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.027 0.099 -9999 0 -0.518 2 2
VEGFR2 homodimer/VEGFA homodimer -0.012 0.152 -9999 0 -0.551 7 7
VEGFR2/3 heterodimer 0.019 0.087 -9999 0 -0.554 2 2
VEGFB 0.031 0.051 -9999 0 -0.483 2 2
MAPK11 -0.05 0.14 -9999 0 -0.522 9 9
VEGFR2 homodimer 0.002 0.094 -9999 0 -0.428 6 6
FLT1 0.009 0.076 -9999 0 -0.28 11 11
NEDD4 -0.002 0.112 -9999 0 -0.411 12 12
MAPK3 0.021 0.138 -9999 0 -0.424 6 6
MAPK1 0.021 0.137 -9999 0 -0.436 6 6
VEGFA145/NRP2 0.015 0.04 -9999 0 -0.225 3 3
VEGFR1/2 heterodimer 0.005 0.095 -9999 0 -0.421 5 5
KDR 0.002 0.094 -9999 0 -0.429 6 6
VEGFA165/NRP1/VEGFR2 homodimer -0.01 0.146 -9999 0 -0.507 8 8
SRC 0.011 0.062 -9999 0 -0.483 3 3
platelet activating factor biosynthetic process 0.032 0.148 0.314 1 -0.443 6 7
PI3K 0.008 0.153 -9999 0 -0.515 9 9
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.008 0.105 -9999 0 -0.468 4 4
FES -0.034 0.148 -9999 0 -0.585 7 7
GAB1 -0.014 0.116 -9999 0 -0.547 5 5
VEGFR2 homodimer/VEGFA homodimer/Src 0.002 0.083 -9999 0 -0.449 4 4
CTNNB1 0.011 0.093 -9999 0 -0.297 15 15
SOS1 0.036 0.002 -9999 0 -9999 0 0
ARNT 0.032 0.036 -9999 0 -0.483 1 1
eNOS/Caveolin-1 0.065 0.148 0.364 2 -0.514 4 6
VEGFR2 homodimer/VEGFA homodimer/Yes 0.004 0.093 -9999 0 -0.542 2 2
PI3K/GAB1 0.007 0.139 -9999 0 -0.484 8 8
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.034 0.115 -9999 0 -0.432 4 4
PRKACA 0.035 0.006 -9999 0 -9999 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.017 0.119 -9999 0 -0.378 8 8
HSP90AA1 0 0 -9999 0 -9999 0 0
CDC42 -0.025 0.137 -9999 0 -0.498 8 8
actin cytoskeleton reorganization 0.009 0.105 -9999 0 -0.566 3 3
PTK2 0.012 0.098 -9999 0 -0.553 2 2
EDG1 -0.039 0.174 -9999 0 -0.575 14 14
mol:DAG -0.021 0.107 -9999 0 -0.467 6 6
CaM/Ca2+ -0.018 0.103 -9999 0 -0.433 6 6
MAP2K3 -0.036 0.13 -9999 0 -0.472 9 9
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.022 0.2 -9999 0 -0.572 18 18
PLCG1 -0.022 0.107 -9999 0 -0.472 6 6
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.009 0.086 -9999 0 -0.428 4 4
IQGAP1 0.034 0.008 -9999 0 -9999 0 0
YES1 0.028 0.015 -9999 0 -9999 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.01 0.1 -9999 0 -0.493 3 3
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.013 0.094 -9999 0 -0.542 2 2
cell migration 0.042 0.112 0.377 1 -0.457 2 3
mol:PI-3-4-5-P3 0.009 0.145 -9999 0 -0.478 9 9
FYN 0.006 0.108 -9999 0 -0.343 16 16
VEGFB/NRP1 -0.021 0.133 -9999 0 -0.48 8 8
mol:NO 0.061 0.144 0.34 3 -0.504 4 7
PXN 0.036 0.004 -9999 0 -9999 0 0
HRAS/GTP -0.021 0.118 -9999 0 -0.46 6 6
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.04 0.187 -9999 0 -0.569 18 18
VHL 0.028 0.056 -9999 0 -0.343 4 4
ITGB3 0.033 0.018 -9999 0 -0.204 1 1
NOS3 0.06 0.157 0.371 2 -0.585 4 6
VEGFR2 homodimer/VEGFA homodimer/Sck -0.017 0.119 -9999 0 -0.419 6 6
RAC1 0.033 0.011 -9999 0 -9999 0 0
PRKCA -0.028 0.1 -9999 0 -0.439 6 6
PRKCB -0.025 0.098 -9999 0 -0.439 6 6
VCL 0.032 0.036 -9999 0 -0.483 1 1
VEGFA165/NRP1 -0.033 0.129 -9999 0 -0.507 7 7
VEGFR1/2 heterodimer/VEGFA homodimer 0.002 0.097 -9999 0 -0.428 5 5
VEGFA165/NRP2 0.015 0.04 -9999 0 -0.225 3 3
MAPKKK cascade -0.034 0.164 -9999 0 -0.507 17 17
NRP2 0.03 0.046 -9999 0 -0.273 4 4
VEGFC homodimer -0.002 0.125 -9999 0 -0.4 17 17
NCK1 0.026 0.071 -9999 0 -0.483 4 4
ROCK1 0.028 0.015 -9999 0 -9999 0 0
FAK1/Paxillin 0.039 0.115 -9999 0 -0.521 2 2
MAP3K13 -0.028 0.142 -9999 0 -0.481 10 10
PDPK1 0.033 0.155 0.266 22 -0.432 9 31
Arf6 trafficking events

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
SLC2A4 0.005 0.096 -9999 0 -0.323 14 14
CLTC -0.007 0.133 -9999 0 -0.436 17 17
calcium ion-dependent exocytosis 0.001 0.073 -9999 0 -0.279 5 5
Dynamin 2/GTP 0.026 0.04 -9999 0 -0.269 3 3
EXOC4 0.034 0.007 -9999 0 -9999 0 0
CD59 -0.009 0.113 -9999 0 -0.385 16 16
CPE -0.049 0.112 -9999 0 -0.297 30 30
CTNNB1 0.011 0.093 -9999 0 -0.297 15 15
membrane fusion 0.018 0.033 -9999 0 -9999 0 0
CTNND1 0.014 0.042 0.188 4 -0.253 3 7
DNM2 0.035 0.006 -9999 0 -9999 0 0
mol:PI-4-5-P2 -0.002 0.084 -9999 0 -0.33 7 7
TSHR 0.013 0.038 -9999 0 -0.295 3 3
INS 0.02 0.027 -9999 0 -9999 0 0
BIN1 0.016 0.1 -9999 0 -0.483 8 8
mol:Choline 0.018 0.033 -9999 0 -9999 0 0
growth hormone secretagogue receptor activity 0 0 -9999 0 -9999 0 0
mol:GDP 0.012 0.039 -9999 0 -0.294 3 3
membrane depolarization 0 0 -9999 0 -9999 0 0
ARF6 0.028 0.051 -9999 0 -0.483 2 2
mol:Ca2+ 0.026 0.04 -9999 0 -0.267 3 3
JUP -0.008 0.114 -9999 0 -0.385 16 16
ASAP2/amphiphysin II 0.025 0.068 -9999 0 -0.267 10 10
ARF6/GTP 0.021 0.037 -9999 0 -0.347 2 2
CDH1 -0.019 0.119 -9999 0 -0.385 16 16
clathrin-independent pinocytosis 0.02 0.037 -9999 0 -0.346 2 2
MAPK8IP3 0.028 0.062 -9999 0 -0.483 3 3
positive regulation of endocytosis 0.02 0.037 -9999 0 -0.346 2 2
EXOC2 0.033 0.036 -9999 0 -0.483 1 1
substrate adhesion-dependent cell spreading 0.022 0.06 -9999 0 -0.422 1 1
insulin receptor binding 0 0 -9999 0 -9999 0 0
SPAG9 0.034 0.008 -9999 0 -9999 0 0
regulation of calcium-dependent cell-cell adhesion 0.003 0.133 0.362 18 -9999 0 18
positive regulation of phagocytosis 0.013 0.033 -9999 0 -0.293 2 2
ARF6/GTP/JIP3 0.035 0.051 -9999 0 -0.295 4 4
ACAP1 0.017 0.035 -9999 0 -0.168 2 2
mol:GTP 0 0 -9999 0 -9999 0 0
CHRM2 -0.036 0.138 -9999 0 -0.416 17 17
clathrin heavy chain/ACAP1 -0.006 0.114 -9999 0 -0.363 16 16
JIP4/KLC1 0.036 0.037 -9999 0 -0.267 2 2
EXOC1 0.035 0.004 -9999 0 -9999 0 0
exocyst 0.025 0.056 -9999 0 -0.428 1 1
RALA/GTP 0.024 0.007 -9999 0 -9999 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.037 0.04 -9999 0 -0.295 2 2
receptor recycling 0.02 0.037 -9999 0 -0.346 2 2
CTNNA1 0.014 0.042 0.188 4 -0.253 3 7
NME1 0.012 0.04 -9999 0 -0.295 3 3
clathrin coat assembly -0.01 0.136 -9999 0 -0.423 18 18
IL2RA -0.032 0.131 -9999 0 -0.406 17 17
VAMP3 0.013 0.033 -9999 0 -0.294 2 2
GLUT4/clathrin heavy chain/ACAP1 -0.004 0.118 -9999 0 -0.335 17 17
EXOC6 0.03 0.051 -9999 0 -0.483 2 2
PLD1 0.011 0.034 -9999 0 -0.261 2 2
PLD2 0.015 0.016 -9999 0 -9999 0 0
EXOC5 0.033 0.01 -9999 0 -9999 0 0
PIP5K1C 0 0.082 -9999 0 -0.334 7 7
SDC1 -0.01 0.114 -9999 0 -0.385 16 16
ARF6/GDP 0.025 0.04 -9999 0 -0.295 3 3
EXOC7 0.034 0.008 -9999 0 -9999 0 0
E-cadherin/beta catenin -0.002 0.137 -9999 0 -0.373 18 18
mol:Phosphatidic acid 0.018 0.033 -9999 0 -9999 0 0
endocytosis -0.024 0.068 0.266 10 -9999 0 10
SCAMP2 0.033 0.01 -9999 0 -9999 0 0
ADRB2 -0.025 0.142 0.341 2 -0.425 17 19
EXOC3 0.035 0.006 -9999 0 -9999 0 0
ASAP2 0 0 -9999 0 -9999 0 0
Dynamin 2/GDP 0.031 0.042 -9999 0 -0.267 3 3
KLC1 0 0 -9999 0 -9999 0 0
AVPR2 -0.014 0.133 0.385 1 -0.412 17 18
RALA 0.033 0.01 -9999 0 -9999 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.004 0.13 -9999 0 -0.432 7 7
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.025 0.073 0.426 5 -9999 0 5
PI3K Class IB/PDE3B 0.025 0.073 -9999 0 -0.427 5 5
PDE3B 0.025 0.073 -9999 0 -0.427 5 5
LPA4-mediated signaling events

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
ADCY4 -0.023 0.069 -9999 0 -0.296 12 12
ADCY5 -0.008 0.022 -9999 0 -0.295 1 1
ADCY6 -0.007 0.02 -9999 0 -0.295 1 1
ADCY7 -0.011 0.037 -9999 0 -0.296 3 3
ADCY1 -0.007 0.02 -9999 0 -0.295 1 1
ADCY2 -0.007 0.021 -9999 0 -0.295 1 1
ADCY3 -0.021 0.065 -9999 0 -0.296 11 11
ADCY8 -0.01 0.041 -9999 0 -0.296 4 4
PRKCE 0.008 0.025 -9999 0 -0.347 1 1
ADCY9 -0.012 0.042 -9999 0 -0.296 4 4
mol:DAG 0 0 -9999 0 -9999 0 0
cAMP biosynthetic process 0.017 0.074 0.184 10 -0.349 1 11
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.005 0.015 -9999 0 -9999 0 0
RAS family/GTP 0.023 0.098 -9999 0 -0.338 3 3
NFATC4 -0.01 0.058 0.208 1 -0.376 1 2
ERBB2IP 0.021 0.086 -9999 0 -0.478 6 6
HSP90 (dimer) 0 0 -9999 0 -9999 0 0
mammary gland morphogenesis 0.011 0.07 0.226 2 -0.337 3 5
JUN 0 0.076 -9999 0 -9999 0 0
HRAS 0.032 0.04 -9999 0 -0.343 2 2
DOCK7 -0.007 0.064 -9999 0 -0.473 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.05 0.073 0.266 3 -0.375 3 6
AKT1 0.007 0.018 -9999 0 -0.134 3 3
BAD -0.006 0.016 -9999 0 -9999 0 0
MAPK10 -0.004 0.071 0.216 6 -0.208 5 11
mol:GTP -0.001 0.002 -9999 0 -9999 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.013 0.076 0.243 2 -0.364 3 5
RAF1 -0.001 0.089 -9999 0 -0.316 3 3
ErbB2/ErbB3/neuregulin 2 0.038 0.074 0.255 6 -0.448 3 9
STAT3 0.003 0.142 -9999 0 -0.988 4 4
cell migration 0.006 0.069 0.253 5 -0.222 1 6
mol:PI-3-4-5-P3 -0.001 0.001 -9999 0 -9999 0 0
cell proliferation -0.075 0.238 -9999 0 -0.593 25 25
FOS -0.087 0.217 -9999 0 -0.44 49 49
NRAS 0.019 0.08 -9999 0 -0.328 9 9
mol:Ca2+ 0.011 0.07 0.226 2 -0.337 3 5
MAPK3 -0.045 0.189 -9999 0 -0.506 18 18
MAPK1 -0.054 0.206 -9999 0 -0.546 19 19
JAK2 -0.012 0.071 -9999 0 -0.331 3 3
NF2 0.011 0.046 -9999 0 -0.641 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.018 0.052 -9999 0 -0.28 4 4
NRG1 0.022 0.054 -9999 0 -0.39 3 3
GRB2/SOS1 0.05 0.012 -9999 0 -9999 0 0
MAPK8 0 0.081 -9999 0 -0.309 3 3
MAPK9 0.004 0.065 0.214 7 -0.238 1 8
ERBB2 -0.014 0.069 0.356 6 -0.372 1 7
ERBB3 0.029 0.051 -9999 0 -0.487 2 2
SHC1 0.034 0.007 -9999 0 -9999 0 0
RAC1 0.033 0.011 -9999 0 -9999 0 0
apoptosis 0.001 0.016 -9999 0 -9999 0 0
STAT3 (dimer) 0.004 0.138 -9999 0 -0.96 4 4
RNF41 -0.007 0.014 -9999 0 -9999 0 0
FRAP1 -0.005 0.014 -9999 0 -9999 0 0
RAC1-CDC42/GTP -0.01 0.041 -9999 0 -0.337 1 1
ErbB2/ErbB2/HSP90 (dimer) -0.013 0.048 0.233 6 -0.313 1 7
CHRNA1 -0.024 0.148 -9999 0 -0.404 6 6
myelination -0.005 0.065 0.267 3 -0.371 1 4
PPP3CB -0.006 0.062 -9999 0 -0.438 1 1
KRAS 0.033 0.018 -9999 0 -0.204 1 1
RAC1-CDC42/GDP 0.034 0.073 -9999 0 -0.372 1 1
NRG2 0.028 0.056 -9999 0 -0.343 4 4
mol:GDP 0.018 0.052 -9999 0 -0.279 4 4
SOS1 0.036 0.003 -9999 0 -9999 0 0
MAP2K2 -0.015 0.091 -9999 0 -0.298 2 2
SRC 0.011 0.062 -9999 0 -0.483 3 3
mol:cAMP -0.001 0.001 -9999 0 -9999 0 0
PTPN11 -0.017 0.07 -9999 0 -0.458 2 2
MAP2K1 -0.062 0.213 -9999 0 -0.635 15 15
heart morphogenesis 0.011 0.07 0.226 2 -0.337 3 5
RAS family/GDP 0.036 0.099 -9999 0 -0.35 3 3
GRB2 0.034 0.008 -9999 0 -9999 0 0
PRKACA 0.015 0.049 -9999 0 -0.685 1 1
CHRNE 0.008 0.018 -9999 0 -9999 0 0
HSP90AA1 0 0 -9999 0 -9999 0 0
activation of caspase activity -0.007 0.018 0.134 3 -9999 0 3
nervous system development 0.011 0.07 0.226 2 -0.337 3 5
CDC42 0.032 0.019 -9999 0 -0.204 1 1
Coregulation of Androgen receptor activity

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
NRIP1 0.031 0.037 -9999 0 -0.482 1 1
SVIL 0.023 0.071 -9999 0 -0.307 8 8
ZNF318 0.032 0.006 -9999 0 -9999 0 0
JMJD2C 0.033 0.054 -9999 0 -0.386 3 3
T-DHT/AR/Ubc9 0.042 0.055 -9999 0 -0.249 3 3
CARM1 0.035 0.006 -9999 0 -9999 0 0
PRDX1 0.035 0.004 -9999 0 -9999 0 0
PELP1 0.029 0.014 -9999 0 -9999 0 0
CTNNB1 0.012 0.093 -9999 0 -0.296 15 15
AKT1 0.028 0.03 -9999 0 -0.205 3 3
PTK2B 0.029 0.015 -9999 0 -9999 0 0
MED1 -0.001 0.001 -9999 0 -9999 0 0
MAK 0.029 0.029 -9999 0 -0.207 3 3
response to oxidative stress 0 0 -9999 0 -9999 0 0
HIP1 0.034 0.019 -9999 0 -0.202 1 1
GSN 0.014 0.088 -9999 0 -0.277 15 15
NCOA2 0.025 0.052 -9999 0 -0.483 2 2
NCOA6 0.004 0.086 -9999 0 -0.482 6 6
DNA-PK 0.056 0.03 -9999 0 -9999 0 0
NCOA4 0.033 0.036 -9999 0 -0.483 1 1
PIAS3 0.034 0.024 -9999 0 -0.202 2 2
cell proliferation 0.02 0.034 -9999 0 -0.38 1 1
XRCC5 0.035 0.003 -9999 0 -9999 0 0
UBE3A 0.035 0.01 -9999 0 -9999 0 0
T-DHT/AR/SNURF 0.021 0.048 -9999 0 -0.251 3 3
FHL2 0.007 0.173 -9999 0 -0.892 7 7
RANBP9 0.037 0.003 -9999 0 -9999 0 0
JMJD1A 0.041 0.023 -9999 0 -9999 0 0
CDK6 0.025 0.066 -9999 0 -0.372 5 5
TGFB1I1 0.023 0.076 -9999 0 -0.362 7 7
T-DHT/AR/CyclinD1 0.036 0.068 -9999 0 -0.266 5 5
XRCC6 0.033 0.009 -9999 0 -9999 0 0
T-DHT/AR 0.033 0.061 -9999 0 -0.187 11 11
CTDSP1 0.036 0.003 -9999 0 -9999 0 0
CTDSP2 0.024 0.066 -9999 0 -0.373 5 5
BRCA1 0.036 0.008 -9999 0 -9999 0 0
TCF4 0.019 0.032 -9999 0 -0.205 3 3
CDKN2A -0.036 0.154 -9999 0 -0.321 41 41
SRF 0.031 0.052 -9999 0 -0.34 2 2
NKX3-1 0.021 0.036 -9999 0 -0.219 3 3
KLK3 0.024 0.045 -9999 0 -9999 0 0
TMF1 0.036 0.005 -9999 0 -9999 0 0
HNRNPA1 -0.001 0.001 -9999 0 -9999 0 0
AOF2 0.031 0.04 -9999 0 -0.342 2 2
APPL1 0.005 0.017 -9999 0 -0.135 3 3
T-DHT/AR/Caspase 8 0.037 0.067 -9999 0 -0.271 6 6
AR 0.022 0.072 -9999 0 -0.252 11 11
UBA3 0 0 -9999 0 -9999 0 0
PATZ1 -0.001 0.001 -9999 0 -9999 0 0
PAWR 0.033 0.036 -9999 0 -0.483 1 1
PRKDC 0.029 0.02 -9999 0 -0.205 1 1
PA2G4 0.032 0.036 -9999 0 -0.484 1 1
UBE2I 0.035 0.006 -9999 0 -9999 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.039 0.051 -9999 0 -0.229 3 3
RPS6KA3 0.035 0.036 -9999 0 -0.482 1 1
T-DHT/AR/ARA70 0.041 0.059 -9999 0 -0.262 4 4
LATS2 0.006 0.091 -9999 0 -0.371 10 10
T-DHT/AR/PRX1 0.04 0.049 -9999 0 -0.23 3 3
Cyclin D3/CDK11 p58 0.025 0.012 -9999 0 -0.133 1 1
VAV3 -0.076 0.203 -9999 0 -0.417 51 51
KLK2 0.033 0.048 -9999 0 -0.416 1 1
CASP8 0.028 0.062 -9999 0 -0.484 3 3
T-DHT/AR/TIF2/CARM1 0.048 0.066 -9999 0 -0.284 3 3
TMPRSS2 0.027 0.12 -9999 0 -0.934 3 3
CCND1 0.024 0.064 -9999 0 -0.273 8 8
PIAS1 0.035 0.01 -9999 0 -9999 0 0
mol:T-DHT 0.002 0.014 -9999 0 -0.06 9 9
CDC2L1 0 0 -9999 0 -9999 0 0
PIAS4 0.033 0.041 -9999 0 -0.341 2 2
T-DHT/AR/CDK6 0.035 0.069 -9999 0 -0.26 7 7
CMTM2 0.029 0.04 -9999 0 -0.204 6 6
SNURF 0 0 -9999 0 -9999 0 0
ZMIZ1 0.002 0.014 -9999 0 -0.06 9 9
CCND3 0.034 0.017 -9999 0 -0.204 1 1
TGIF1 -0.001 0.001 -9999 0 -9999 0 0
FKBP4 0.033 0.037 -9999 0 -0.483 1 1
BARD1 signaling events

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
BARD1/CSTF1 0.026 0.037 -9999 0 -0.349 1 1
ATM 0.03 0.043 -9999 0 -0.297 3 3
UBE2D3 0.032 0.036 -9999 0 -0.483 1 1
PRKDC 0.03 0.021 -9999 0 -0.204 1 1
ATR 0.034 0.017 -9999 0 -0.204 1 1
UBE2L3 0.034 0.007 -9999 0 -9999 0 0
FANCD2 0.026 0.028 -9999 0 -0.304 1 1
protein ubiquitination 0.065 0.08 -9999 0 -0.255 7 7
XRCC5 0.036 0.004 -9999 0 -9999 0 0
XRCC6 0.034 0.009 -9999 0 -9999 0 0
M/R/N Complex 0.055 0.046 -9999 0 -0.298 2 2
MRE11A 0.035 0.005 -9999 0 -9999 0 0
DNA-PK 0.059 0.031 -9999 0 -9999 0 0
FA complex/FANCD2/Ubiquitin 0.023 0.074 -9999 0 -0.377 3 3
FANCF 0.021 0.087 -9999 0 -0.483 6 6
BRCA1 0.035 0.006 -9999 0 -9999 0 0
CCNE1 0.026 0.058 -9999 0 -0.315 5 5
CDK2/Cyclin E1 0.032 0.074 -9999 0 -0.333 6 6
FANCG 0.032 0.036 -9999 0 -0.483 1 1
BRCA1/BACH1/BARD1 0.049 0.03 -9999 0 -0.349 1 1
FANCE 0.034 0.017 -9999 0 -0.204 1 1
FANCC 0.03 0.043 -9999 0 -0.297 3 3
NBN 0.027 0.038 -9999 0 -0.483 1 1
FANCA 0.02 0.084 -9999 0 -0.378 8 8
DNA repair 0.025 0.113 0.293 5 -0.369 3 8
BRCA1/BARD1/ubiquitin 0.049 0.03 -9999 0 -0.349 1 1
BARD1/DNA-PK 0.073 0.045 -9999 0 -0.272 1 1
FANCL 0.036 0 -9999 0 -9999 0 0
mRNA polyadenylation -0.026 0.037 0.349 1 -9999 0 1
BRCA1/BARD1/CTIP/M/R/N Complex 0.019 0.066 -9999 0 -0.32 2 2
BRCA1/BACH1/BARD1/TopBP1 0.068 0.03 -9999 0 -0.298 1 1
BRCA1/BARD1/P53 0.015 0.129 -9999 0 -0.272 31 31
BARD1/CSTF1/BRCA1 0.036 0.043 -9999 0 -0.298 1 1
BRCA1/BACH1 0.035 0.006 -9999 0 -9999 0 0
BARD1 0.033 0.036 -9999 0 -0.483 1 1
PCNA 0.009 0.094 -9999 0 -0.448 8 8
BRCA1/BARD1/UbcH5C 0.065 0.04 -9999 0 -0.298 2 2
BRCA1/BARD1/UbcH7 0.066 0.032 -9999 0 -0.298 1 1
BRCA1/BARD1/RAD51/PCNA 0.041 0.098 -9999 0 -0.321 10 10
BARD1/DNA-PK/P53 0.026 0.119 -9999 0 -0.258 24 24
BRCA1/BARD1/Ubiquitin 0.049 0.03 -9999 0 -0.349 1 1
BRCA1/BARD1/CTIP 0.033 0.058 -9999 0 -0.272 5 5
FA complex 0.024 0.061 -9999 0 -9999 0 0
BARD1/EWS 0.045 0.038 -9999 0 -0.349 1 1
RBBP8 0.005 0.053 -9999 0 -0.35 4 4
TP53 -0.048 0.181 -9999 0 -0.466 32 32
TOPBP1 0.036 0.004 -9999 0 -9999 0 0
G1/S transition of mitotic cell cycle -0.013 0.127 0.27 31 -9999 0 31
BRCA1/BARD1 0.073 0.084 -9999 0 -0.257 7 7
CSTF1 0.019 0.018 -9999 0 -9999 0 0
BARD1/EWS-Fli1 0.025 0.026 -9999 0 -0.347 1 1
CDK2 0.02 0.075 -9999 0 -0.287 10 10
UniProt:Q9BZD1 0 0 -9999 0 -9999 0 0
RAD51 0.015 0.095 -9999 0 -0.448 8 8
RAD50 0.03 0.051 -9999 0 -0.483 2 2
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.049 0.03 -9999 0 -0.349 1 1
EWSR1 0.03 0.03 -9999 0 -0.204 3 3
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.045 0.044 -9999 0 -0.349 2 2
CRKL 0.035 0.095 -9999 0 -0.519 3 3
mol:PIP3 -0.006 0.113 0.427 3 -0.8 3 6
AKT1 -0.012 0.098 0.29 3 -0.702 3 6
PTK2B 0.028 0.015 -9999 0 -9999 0 0
RAPGEF1 0.036 0.092 -9999 0 -0.585 2 2
RANBP10 0.032 0.029 -9999 0 -0.204 3 3
PIK3CA 0.035 0.006 -9999 0 -9999 0 0
HGF/MET/SHIP2 0.058 0.061 -9999 0 -0.32 4 4
MAP3K5 0.037 0.095 -9999 0 -0.531 2 2
HGF/MET/CIN85/CBL/ENDOPHILINS 0.056 0.099 -9999 0 -0.278 15 15
AP1 -0.062 0.147 -9999 0 -0.303 46 46
mol:SU11274 0 0 -9999 0 -9999 0 0
SHC1 0.035 0.007 -9999 0 -9999 0 0
apoptosis -0.18 0.356 -9999 0 -0.746 58 58
STAT3 (dimer) 0.013 0.041 -9999 0 -9999 0 0
GAB1/CRKL/SHP2/PI3K 0.075 0.112 -9999 0 -0.596 3 3
INPP5D 0 0 -9999 0 -9999 0 0
CBL/CRK 0.06 0.094 -9999 0 -0.585 2 2
PTPN11 0.029 0.053 -9999 0 -0.39 3 3
GO:0007205 0 0 -9999 0 -9999 0 0
PLCG1 0.019 0.018 -9999 0 -9999 0 0
PTEN 0.026 0.062 -9999 0 -0.483 3 3
ELK1 0.002 0.087 0.299 10 -9999 0 10
mol:SU5416 0 0 -9999 0 -9999 0 0
SHP2/GRB2/SOS1GAB1 0.013 0.041 -9999 0 -0.242 2 2
PAK1 -0.014 0.095 -9999 0 -0.67 3 3
HGF/MET/RANBP10 0.059 0.06 -9999 0 -0.358 3 3
HRAS 0.029 0.081 -9999 0 -0.677 2 2
DOCK1 0.029 0.1 -9999 0 -0.585 2 2
GAB1 0.032 0.088 -9999 0 -0.545 3 3
CRK 0.033 0.088 0.271 1 -0.519 3 4
mol:PHA665752 0 0 -9999 0 -9999 0 0
mol:GDP 0.032 0.078 -9999 0 -0.565 3 3
JUN -0.017 0.15 -9999 0 -0.405 25 25
EntrezGene:200958 0 0 -9999 0 -9999 0 0
HGF/MET -0.012 0.046 -9999 0 -0.268 4 4
PIK3R1 0.028 0.062 -9999 0 -0.483 3 3
cell morphogenesis 0.062 0.115 0.38 1 -0.616 2 3
GRB2/SHC 0.014 0.061 -9999 0 -0.25 3 3
FOS -0.063 0.171 -9999 0 -0.318 56 56
GLMN 0.001 0.023 -9999 0 -0.326 1 1
cell motility 0.002 0.087 0.297 10 -9999 0 10
HGF/MET/MUC20 0.039 0.049 -9999 0 -0.326 3 3
cell migration 0.011 0.058 -9999 0 -0.246 3 3
GRB2 0.034 0.008 -9999 0 -9999 0 0
CBL 0.035 0.005 -9999 0 -9999 0 0
MET/RANBP10 0.043 0.052 -9999 0 -0.4 2 2
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.021 0.047 -9999 0 -0.273 1 1
MET/MUC20 0.02 0.04 -9999 0 -0.24 4 4
RAP1B 0.035 0.088 0.288 1 -0.544 2 3
RAP1A 0.033 0.089 0.359 1 -0.544 2 3
HGF/MET/RANBP9 0.061 0.054 -9999 0 -0.328 3 3
RAF1 0.032 0.08 -9999 0 -0.636 2 2
STAT3 0.012 0.041 -9999 0 -9999 0 0
cell proliferation 0.047 0.076 0.285 4 -0.402 1 5
RPS6KB1 0.003 0.042 -9999 0 -0.252 4 4
MAPK3 -0.01 0.118 0.633 5 -9999 0 5
MAPK1 0.005 0.148 0.604 10 -9999 0 10
RANBP9 0.036 0.002 -9999 0 -9999 0 0
MAPK8 0.04 0.106 -9999 0 -0.44 4 4
SRC 0.009 0.048 -9999 0 -9999 0 0
PI3K 0.01 0.07 -9999 0 -0.239 7 7
MET/Glomulin -0.016 0.061 -9999 0 -0.21 9 9
SOS1 0.036 0.002 -9999 0 -9999 0 0
MAP2K1 0.029 0.075 -9999 0 -0.587 2 2
MET 0.027 0.056 -9999 0 -0.343 4 4
MAP4K1 0.052 0.091 -9999 0 -0.575 2 2
PTK2 0.03 0.013 -9999 0 -9999 0 0
MAP2K2 0.032 0.078 -9999 0 -0.581 2 2
BAD -0.013 0.094 -9999 0 -0.67 3 3
MAP2K4 0.025 0.088 -9999 0 -0.479 2 2
SHP2/GRB2/SOS1/GAB1 0.064 0.094 -9999 0 -0.564 2 2
INPPL1 0.032 0.04 -9999 0 -0.343 2 2
PXN 0.036 0.004 -9999 0 -9999 0 0
SH3KBP1 0.005 0.122 -9999 0 -0.462 13 13
HGS -0.013 0.039 -9999 0 -0.259 3 3
PLCgamma1/PKC 0.014 0.013 -9999 0 -9999 0 0
HGF 0.03 0.043 -9999 0 -0.297 3 3
RASA1 0.024 0.073 -9999 0 -0.427 5 5
NCK1 0.026 0.071 -9999 0 -0.483 4 4
PTPRJ 0.032 0.04 -9999 0 -0.343 2 2
NCK/PLCgamma1 0.03 0.045 -9999 0 -0.243 2 2
PDPK1 -0.008 0.106 0.333 3 -0.742 3 6
HGF/MET/SHIP 0.039 0.049 -9999 0 -0.326 3 3
Aurora A signaling

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
Aurora A/GADD45A 0.028 0.057 -9999 0 -0.286 5 5
BIRC5 0.023 0.073 -9999 0 -0.427 5 5
NFKBIA 0.004 0.036 0.245 1 -0.28 2 3
CPEB1 0.028 0.051 -9999 0 -0.483 2 2
AKT1 0.004 0.026 -9999 0 -0.269 1 1
NDEL1 0.029 0.014 -9999 0 -9999 0 0
Aurora A/BRCA1 0.031 0.024 -9999 0 -0.244 1 1
NDEL1/TACC3 0.039 0.045 -9999 0 -0.239 3 3
GADD45A 0.02 0.079 -9999 0 -0.328 9 9
GSK3B 0.032 0.037 -9999 0 -0.492 1 1
PAK1/Aurora A 0.035 0.041 -9999 0 -0.283 3 3
MDM2 0.034 0.017 -9999 0 -0.204 1 1
JUB 0.017 0.088 -9999 0 -0.443 7 7
TPX2 0.003 0.05 -9999 0 -0.35 4 4
TP53 -0.031 0.121 -9999 0 -0.295 35 35
DLG7 -0.005 0.059 0.245 1 -0.266 9 10
AURKAIP1 0 0 -9999 0 -9999 0 0
ARHGEF7 0.027 0.016 -9999 0 -9999 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -9999 0 0
Aurora A/NDEL1/TACC3 0.042 0.047 -9999 0 -0.255 3 3
G2/M transition of mitotic cell cycle 0.031 0.024 -9999 0 -0.242 1 1
AURKA 0.014 0.028 -9999 0 -0.318 1 1
AURKB 0.009 0.05 -9999 0 -0.275 5 5
CDC25B -0.017 0.109 0.184 1 -0.345 18 19
G2/M transition checkpoint 0.019 0.055 -9999 0 -0.259 7 7
mRNA polyadenylation 0.026 0.037 -9999 0 -0.254 3 3
Aurora A/CPEB 0.026 0.037 -9999 0 -0.256 3 3
Aurora A/TACC1/TRAP/chTOG 0.051 0.071 -9999 0 -0.248 7 7
BRCA1 0.035 0.006 -9999 0 -9999 0 0
centrosome duplication 0.035 0.041 -9999 0 -0.282 3 3
regulation of centrosome cycle 0.038 0.045 -9999 0 -0.237 3 3
spindle assembly 0.05 0.07 -9999 0 -0.246 7 7
TDRD7 0.033 0.036 -9999 0 -0.483 1 1
Aurora A/RasGAP/Survivin 0.054 0.067 -9999 0 -0.293 4 4
CENPA 0.011 0.053 -9999 0 -0.343 4 4
Aurora A/PP2A 0.037 0.021 -9999 0 -9999 0 0
meiosis 0 0 -9999 0 -9999 0 0
protein catabolic process -0.012 0.057 -9999 0 -0.262 3 3
negative regulation of DNA binding -0.055 0.131 -9999 0 -0.294 35 35
prophase 0 0 -9999 0 -9999 0 0
GIT1/beta-PIX 0.039 0.024 -9999 0 -9999 0 0
RASA1 0.024 0.073 -9999 0 -0.427 5 5
Ajuba/Aurora A 0.02 0.056 -9999 0 -0.26 7 7
mitotic prometaphase 0.01 0.03 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.028 -9999 0 -0.317 1 1
TACC1 0.009 0.095 -9999 0 -0.333 13 13
TACC3 0.027 0.056 -9999 0 -0.343 4 4
Aurora A/Antizyme1 0.031 0.023 -9999 0 -0.244 1 1
Aurora A/RasGAP 0.03 0.059 -9999 0 -0.349 4 4
OAZ1 0.034 0.007 -9999 0 -9999 0 0
RAN 0.036 0.004 -9999 0 -9999 0 0
mitosis 0 0 -9999 0 -9999 0 0
PRKACA 0.034 0.009 -9999 0 -9999 0 0
GIT1 0.033 0.018 -9999 0 -0.204 1 1
GIT1/beta-PIX/PAK1 0.049 0.047 -9999 0 -0.298 2 2
Importin alpha/Importin beta/TPX2 0.003 0.05 -9999 0 -0.349 4 4
PPP2R5D 0.034 0.017 -9999 0 -0.204 1 1
Aurora A/TPX2 0.008 0.036 -9999 0 -0.232 4 4
PAK1 0.031 0.051 -9999 0 -0.483 2 2
CKAP5 0.036 0.004 -9999 0 -9999 0 0
Aurora C signaling

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
INCENP 0.015 0.097 -9999 0 -0.399 10 10
Aurora C/Aurora B/INCENP 0.036 0.078 -9999 0 -0.261 11 11
metaphase 0 0 -9999 0 -9999 0 0
mitosis 0 0 -9999 0 -9999 0 0
H3F3B 0.003 0.066 -9999 0 -0.433 4 4
AURKB 0.022 0.063 -9999 0 -0.483 3 3
AURKC 0.033 0.024 -9999 0 -0.204 2 2
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.001 0.035 0.185 6 -9999 0 6
BUB1B -0.009 0.072 -9999 0 -0.257 10 10
PLK1 0.002 0.028 -9999 0 -0.121 5 5
PLK1S1 0.001 0.015 -9999 0 -0.066 5 5
KIF2A 0.002 0.025 -9999 0 -0.109 5 5
regulation of mitotic centrosome separation 0.002 0.028 -9999 0 -0.12 5 5
GOLGA2 0.033 0.036 -9999 0 -0.483 1 1
Hec1/SPC24 -0.007 0.019 -9999 0 -0.093 7 7
WEE1 0.008 0.087 -9999 0 -0.755 2 2
cytokinesis -0.004 0.086 -9999 0 -0.455 4 4
PP2A-alpha B56 0.02 0.229 -9999 0 -0.767 15 15
AURKA 0.001 0.017 -9999 0 -0.081 4 4
PICH/PLK1 -0.017 0.095 -9999 0 -0.349 12 12
CENPE 0 0.025 -9999 0 -9999 0 0
RhoA/GTP 0.026 0.003 -9999 0 -9999 0 0
positive regulation of microtubule depolymerization 0.002 0.025 -9999 0 -0.108 5 5
PPP2CA 0.035 0.006 -9999 0 -9999 0 0
FZR1 0.034 0.007 -9999 0 -9999 0 0
TPX2 0.017 0.051 -9999 0 -0.301 4 4
PAK1 0.031 0.052 -9999 0 -0.493 2 2
SPC24 0 0 -9999 0 -9999 0 0
FBXW11 0.036 0.004 -9999 0 -9999 0 0
CLSPN 0.004 0.052 -9999 0 -0.283 6 6
GORASP1 0.036 0.004 -9999 0 -9999 0 0
metaphase 0 0.002 0.017 2 -0.02 1 3
mol:GTP 0 0 -9999 0 -9999 0 0
NLP 0.001 0.015 -9999 0 -0.066 5 5
G2 phase of mitotic cell cycle -0.001 0.002 0.014 2 -9999 0 2
STAG2 0.025 0.073 -9999 0 -0.427 5 5
GRASP65/GM130/RAB1/GTP 0.025 0.052 -9999 0 -0.427 2 2
spindle elongation 0.002 0.028 -9999 0 -0.12 5 5
ODF2 0.029 0.054 -9999 0 -0.396 3 3
BUB1 -0.026 0.237 -9999 0 -0.835 15 15
TPT1 0.017 0.025 -9999 0 -0.18 1 1
CDC25C 0.003 0.072 -9999 0 -0.365 7 7
CDC25B 0.007 0.103 -9999 0 -0.463 9 9
SGOL1 0.001 0.035 -9999 0 -0.186 6 6
RHOA 0.035 0.004 -9999 0 -9999 0 0
CCNB1/CDK1 0.02 0.134 -9999 0 -0.421 12 12
CDC14B 0.007 0.025 -9999 0 -0.351 1 1
CDC20 0.03 0.051 -9999 0 -0.483 2 2
PLK1/PBIP1 -0.011 0.064 -9999 0 -0.235 13 13
mitosis -0.001 0.002 0.012 1 -0.011 1 2
FBXO5 -0.002 0.055 -9999 0 -0.262 5 5
CDC2 0.029 0.041 -9999 0 -0.506 1 1
NDC80 0 0 -9999 0 -9999 0 0
metaphase plate congression -0.003 0.068 -9999 0 -0.248 14 14
ERCC6L -0.014 0.113 -9999 0 -0.399 12 12
NLP/gamma Tubulin 0.006 0.019 -9999 0 -0.085 2 2
microtubule cytoskeleton organization 0.017 0.025 -9999 0 -0.179 1 1
G2/M transition DNA damage checkpoint -0.001 0.002 0.013 2 -9999 0 2
PPP1R12A 0.036 0.005 -9999 0 -9999 0 0
interphase -0.001 0.002 0.013 2 -9999 0 2
PLK1/PRC1-2 0.035 0.065 -9999 0 -0.388 3 3
GRASP65/GM130/RAB1/GTP/PLK1 0.055 0.042 -9999 0 -0.226 1 1
RAB1A 0.036 0 -9999 0 -9999 0 0
prophase 0 0 -9999 0 -9999 0 0
Aurora A/BORA 0.001 0.02 -9999 0 -0.088 5 5
mitotic prometaphase 0 0.005 0.018 14 -0.013 1 15
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.054 -9999 0 -0.353 2 2
microtubule-based process 0.017 0.056 -9999 0 -0.283 5 5
Golgi organization 0.002 0.028 -9999 0 -0.12 5 5
Cohesin/SA2 0.016 0.047 -9999 0 -0.22 5 5
PPP1CB/MYPT1 0.05 0.029 -9999 0 -0.353 1 1
KIF20A 0.025 0.071 -9999 0 -0.483 4 4
APC/C/CDC20 0.021 0.047 -9999 0 -0.272 3 3
PPP2R1A 0.035 0.006 -9999 0 -9999 0 0
chromosome segregation -0.01 0.063 -9999 0 -0.232 13 13
PRC1 0.031 0.037 -9999 0 -0.483 1 1
ECT2 -0.005 0.052 0.225 1 -0.278 5 6
C13orf34 0.001 0.022 -9999 0 -0.092 6 6
NUDC -0.003 0.068 -9999 0 -0.249 14 14
regulation of attachment of spindle microtubules to kinetochore -0.008 0.072 -9999 0 -0.254 10 10
spindle assembly 0.004 0.027 0.088 2 -0.102 5 7
spindle stabilization 0.001 0.015 -9999 0 -0.066 5 5
APC/C/HCDH1 0.03 0.024 -9999 0 -0.296 1 1
MKLP2/PLK1 0.017 0.056 -9999 0 -0.285 5 5
CCNB1 0.016 0.096 -9999 0 -0.495 7 7
PPP1CB 0.034 0.036 -9999 0 -0.485 1 1
BTRC 0.034 0.008 -9999 0 -9999 0 0
ROCK2 -0.006 0.101 -9999 0 -0.402 12 12
TUBG1 0.011 0.017 -9999 0 -9999 0 0
G2/M transition of mitotic cell cycle -0.022 0.113 -9999 0 -0.411 12 12
MLF1IP -0.012 0.082 -9999 0 -0.321 13 13
INCENP 0.014 0.098 -9999 0 -0.403 10 10
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.01 0.01 -9999 0 -9999 0 0
BAD/BCL-XL/YWHAZ 0.028 0.032 -9999 0 -9999 0 0
CDKN1B 0.023 0.08 -9999 0 -0.344 2 2
CDKN1A 0.023 0.072 -9999 0 -9999 0 0
FRAP1 0.031 0.037 -9999 0 -0.483 1 1
PRKDC 0.03 0.021 -9999 0 -0.204 1 1
FOXO3 0.026 0.072 -9999 0 -0.311 2 2
AKT1 0.027 0.072 -9999 0 -0.326 2 2
BAD 0.034 0.017 -9999 0 -0.204 1 1
AKT3 0.014 0.031 -9999 0 -0.254 2 2
mol:GTP 0 0 -9999 0 -9999 0 0
FOXO4 0.026 0.072 -9999 0 -0.311 2 2
AKT1/ASK1 0.038 0.113 -9999 0 -0.41 4 4
BAD/YWHAZ 0.057 0.032 -9999 0 -9999 0 0
RICTOR 0.033 0.018 -9999 0 -0.204 1 1
RAF1 0.035 0.006 -9999 0 -9999 0 0
JNK cascade -0.037 0.11 0.397 4 -9999 0 4
TSC1 0.025 0.075 -9999 0 -0.369 1 1
YWHAZ 0.029 0.014 -9999 0 -9999 0 0
AKT1/RAF1 0.054 0.1 0.297 1 -0.369 1 2
EP300 0.018 0.088 -9999 0 -0.443 7 7
mol:GDP 0.027 0.072 -9999 0 -0.322 2 2
mol:PI-3-4-5-P3 0 0 -9999 0 -9999 0 0
TSC2 0.028 0.071 -9999 0 -0.369 1 1
YWHAQ 0.036 0.002 -9999 0 -9999 0 0
TBC1D4 0.056 0.116 0.243 49 -0.277 7 56
MAP3K5 0.011 0.101 -9999 0 -0.354 13 13
MAPKAP1 0.028 0.049 -9999 0 -0.259 5 5
negative regulation of cell cycle -0.054 0.1 0.335 4 -0.218 15 19
YWHAH 0.031 0.037 -9999 0 -0.483 1 1
AKT1S1 0.03 0.079 0.27 3 -0.369 1 4
CASP9 0.025 0.07 -9999 0 -0.369 1 1
YWHAB 0.013 0.052 -9999 0 -0.483 2 2
p27Kip1/KPNA1 0.051 0.107 0.464 1 -0.33 2 3
GBL 0.034 0.017 -9999 0 -0.204 1 1
PDK1/Src/Hsp90 0.02 0.046 -9999 0 -0.295 3 3
YWHAE 0.03 0.013 -9999 0 -9999 0 0
SRC 0.011 0.062 -9999 0 -0.483 3 3
AKT2/p21CIP1 0.02 0.077 0.264 1 -0.266 2 3
KIAA1303 0 0 -9999 0 -9999 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.045 0.062 -9999 0 -0.625 1 1
CHUK 0.024 0.078 -9999 0 -0.414 2 2
BAD/BCL-XL 0.019 0.065 -9999 0 -9999 0 0
mTORC2 0.071 0.057 -9999 0 -0.272 2 2
AKT2 0.018 0.024 -9999 0 -0.312 1 1
FOXO1-3a-4/14-3-3 family 0.052 0.128 0.257 14 -0.47 4 18
PDPK1 0.032 0.04 -9999 0 -0.343 2 2
MDM2 0.028 0.076 0.273 1 -0.356 1 2
MAPKKK cascade -0.054 0.099 0.362 1 -0.295 1 2
MDM2/Cbp/p300 0.048 0.117 0.284 1 -0.379 3 4
TSC1/TSC2 0.023 0.07 0.245 1 -0.361 1 2
proteasomal ubiquitin-dependent protein catabolic process 0.046 0.112 0.273 1 -0.363 3 4
glucose import 0.024 0.105 0.211 34 -0.335 7 41
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.037 0.091 0.332 1 -0.369 5 6
response to stress 0 0 -9999 0 -9999 0 0
SLC2A4 0.024 0.106 0.211 34 -0.337 7 41
GSK3A 0.029 0.078 0.273 3 -0.369 1 4
FOXO1 0.026 0.072 -9999 0 -0.311 2 2
GSK3B 0.027 0.074 -9999 0 -0.369 1 1
SFN 0.02 0.071 -9999 0 -0.308 8 8
G1/S transition of mitotic cell cycle 0.034 0.095 0.295 4 -0.361 1 5
p27Kip1/14-3-3 family 0.045 0.08 -9999 0 -0.338 4 4
PRKACA 0.035 0.006 -9999 0 -9999 0 0
KPNA1 0.036 0.004 -9999 0 -9999 0 0
HSP90AA1 0 0 -9999 0 -9999 0 0
YWHAG 0.034 0.008 -9999 0 -9999 0 0
RHEB 0.035 0.006 -9999 0 -9999 0 0
CREBBP 0.032 0.036 -9999 0 -0.483 1 1
ceramide signaling pathway

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
MAP4K4 0.009 0.093 -9999 0 -0.426 3 3
BAG4 0.027 0.051 -9999 0 -0.483 2 2
BAD 0.011 0.033 -9999 0 -9999 0 0
NFKBIA 0.028 0.044 -9999 0 -0.297 3 3
BIRC3 -0.011 0.126 -9999 0 -0.304 28 28
BAX 0.013 0.047 0.199 4 -0.279 1 5
EnzymeConsortium:3.1.4.12 0.006 0.022 -9999 0 -0.09 2 2
IKBKB 0.024 0.092 0.238 1 -0.365 2 3
MAP2K2 0.017 0.05 0.19 10 -9999 0 10
MAP2K1 0.013 0.041 0.174 6 -9999 0 6
SMPD1 0.009 0.027 -9999 0 -0.209 1 1
GO:0005551 0 0 -9999 0 -9999 0 0
FADD/Caspase 8 0.019 0.087 -9999 0 -0.416 2 2
MAP2K4 0.004 0.035 -9999 0 -0.205 2 2
protein ubiquitination 0.014 0.087 -9999 0 -0.416 2 2
EnzymeConsortium:2.7.1.37 0.015 0.049 0.176 9 -9999 0 9
response to UV 0 0.001 0.002 8 -0.002 1 9
RAF1 0.015 0.043 0.182 6 -9999 0 6
CRADD 0.026 0.071 -9999 0 -0.484 4 4
mol:ceramide 0.014 0.033 -9999 0 -0.141 1 1
I-kappa-B-alpha/RELA/p50/ubiquitin 0.04 0.032 -9999 0 -0.295 1 1
MADD 0.036 0.003 -9999 0 -9999 0 0
MAP3K1 0.01 0.033 -9999 0 -9999 0 0
TRADD 0.036 0.004 -9999 0 -9999 0 0
RELA/p50 0.035 0.004 -9999 0 -9999 0 0
MAPK3 0.019 0.048 0.179 9 -9999 0 9
MAPK1 0.017 0.05 0.179 8 -9999 0 8
p50/RELA/I-kappa-B-alpha 0.044 0.037 -9999 0 -0.349 1 1
FADD 0.015 0.08 -9999 0 -0.418 1 1
KSR1 0.016 0.041 0.177 5 -9999 0 5
MAPK8 0.005 0.038 -9999 0 -0.194 1 1
TRAF2 0.033 0.024 -9999 0 -0.203 2 2
response to radiation 0 0 0.002 1 -9999 0 1
CHUK 0.003 0.089 -9999 0 -0.401 3 3
TNF R/SODD 0.042 0.044 -9999 0 -0.35 2 2
TNF 0.023 0.066 -9999 0 -0.266 9 9
CYCS 0.04 0.057 0.161 8 -0.173 1 9
IKBKG 0.006 0.089 -9999 0 -0.405 3 3
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.017 0.086 -9999 0 -0.372 2 2
RELA 0.035 0.004 -9999 0 -9999 0 0
RIPK1 0.036 0.004 -9999 0 -9999 0 0
AIFM1 0.034 0.051 0.133 13 -0.175 1 14
TNF/TNF R/SODD 0.05 0.063 -9999 0 -0.294 4 4
TNFRSF1A 0.035 0.007 -9999 0 -9999 0 0
response to heat 0 0 0.002 1 -9999 0 1
CASP8 0.028 0.113 -9999 0 -0.605 6 6
NSMAF 0.035 0.094 0.237 2 -0.412 1 3
response to hydrogen peroxide 0 0.001 0.002 8 -0.002 1 9
BCL2 -0.002 0.098 -9999 0 -0.308 16 16
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.019 0.018 -9999 0 -9999 0 0
NFATC1 -0.04 0.141 0.427 1 -0.427 13 14
NFATC2 0.039 0.053 0.18 1 -9999 0 1
NFATC3 0.013 0.027 -9999 0 -0.367 1 1
YWHAE 0.03 0.013 -9999 0 -9999 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.014 0.106 -9999 0 -0.348 11 11
Exportin 1/Ran/NUP214 0.07 0.018 -9999 0 -9999 0 0
mol:DAG 0 0.001 -9999 0 -9999 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.021 0.105 -9999 0 -0.33 6 6
BCL2/BAX 0.004 0.086 -9999 0 -0.349 7 7
CaM/Ca2+/Calcineurin A alpha-beta B1 0.024 0.009 -9999 0 -9999 0 0
CaM/Ca2+ 0.024 0.009 -9999 0 -9999 0 0
BAX 0.029 0.046 -9999 0 -0.273 4 4
MAPK14 0.036 0.004 -9999 0 -9999 0 0
BAD 0.034 0.017 -9999 0 -0.204 1 1
CABIN1/MEF2D 0.003 0.103 -9999 0 -0.336 8 8
Calcineurin A alpha-beta B1/BCL2 -0.002 0.097 -9999 0 -0.308 16 16
FKBP8 0.035 0.006 -9999 0 -9999 0 0
activation-induced cell death of T cells -0.003 0.102 0.332 8 -9999 0 8
KPNB1 0.021 0.066 -9999 0 -0.266 9 9
KPNA2 0.034 0.008 -9999 0 -9999 0 0
XPO1 0.036 0 -9999 0 -9999 0 0
SFN 0.02 0.071 -9999 0 -0.308 8 8
MAP3K8 0.005 0.106 -9999 0 -0.312 18 18
NFAT4/CK1 alpha 0.03 0.038 -9999 0 -0.214 1 1
MEF2D/NFAT1/Cbp/p300 0.069 0.092 -9999 0 -0.302 2 2
CABIN1 -0.015 0.107 -9999 0 -0.35 11 11
CALM1 0.032 0.011 -9999 0 -9999 0 0
RAN 0.036 0.004 -9999 0 -9999 0 0
MAP3K1 0.031 0.033 -9999 0 -0.204 4 4
CAMK4 0.035 0.006 -9999 0 -9999 0 0
mol:Ca2+ 0 0.002 -9999 0 -9999 0 0
MAPK3 0.024 0.073 -9999 0 -0.427 5 5
YWHAH 0.031 0.037 -9999 0 -0.483 1 1
Calcineurin A alpha-beta B1/AKAP79/PKA 0.012 0.106 -9999 0 -0.349 14 14
YWHAB 0.013 0.052 -9999 0 -0.483 2 2
MAPK8 0.035 0.007 -9999 0 -9999 0 0
MAPK9 0.033 0.036 -9999 0 -0.483 1 1
YWHAG 0.034 0.008 -9999 0 -9999 0 0
FKBP1A 0.026 0.038 -9999 0 -0.483 1 1
NFAT1-c-4/YWHAQ -0.005 0.133 0.435 1 -0.373 10 11
PRKCH 0.018 0.087 -9999 0 -0.483 6 6
CABIN1/Cbp/p300 0.034 0.075 -9999 0 -0.348 7 7
CASP3 0.031 0.037 -9999 0 -0.483 1 1
PIM1 0.03 0.043 -9999 0 -0.297 3 3
Calcineurin A alpha-beta B1/FKBP12/FK506 0.017 0.025 -9999 0 -0.293 1 1
apoptosis 0.005 0.03 -9999 0 -0.224 1 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.035 0.067 -9999 0 -0.305 3 3
PRKCB 0 0 -9999 0 -9999 0 0
PRKCE 0.033 0.036 -9999 0 -0.483 1 1
JNK2/NFAT4 0.027 0.041 -9999 0 -0.296 2 2
BAD/BCL-XL 0.028 0.029 -9999 0 -9999 0 0
PRKCD 0.035 0.004 -9999 0 -9999 0 0
NUP214 0.034 0.017 -9999 0 -0.203 1 1
PRKCZ 0 0.001 -9999 0 -9999 0 0
PRKCA 0.03 0.04 -9999 0 -0.343 2 2
PRKCG 0.025 0.056 -9999 0 -0.239 8 8
PRKCQ -0.013 0.14 -9999 0 -0.378 24 24
FKBP38/BCL2 0.01 0.081 -9999 0 -0.349 6 6
EP300 0.018 0.088 -9999 0 -0.442 7 7
PRKCB1 0.01 0.094 -9999 0 -0.291 16 16
CSNK2A1 0.028 0.015 -9999 0 -9999 0 0
NFATc/JNK1 -0.022 0.142 0.42 1 -0.402 13 14
CaM/Ca2+/FKBP38 0.042 0.017 -9999 0 -9999 0 0
FKBP12/FK506 0.019 0.028 -9999 0 -0.347 1 1
CSNK1A1 0.016 0.011 -9999 0 -9999 0 0
CaM/Ca2+/CAMK IV 0.042 0.017 -9999 0 -9999 0 0
NFATc/ERK1 -0.028 0.144 0.42 1 -0.404 13 14
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.021 0.111 -9999 0 -0.351 7 7
NR4A1 0.036 0.088 0.256 3 -0.283 2 5
GSK3B 0.033 0.036 -9999 0 -0.483 1 1
positive T cell selection 0.013 0.027 -9999 0 -0.366 1 1
NFAT1/CK1 alpha 0.036 0.043 -9999 0 -9999 0 0
RCH1/ KPNB1 0.04 0.053 -9999 0 -0.349 2 2
YWHAQ 0.036 0.002 -9999 0 -9999 0 0
PRKACA 0.035 0.006 -9999 0 -9999 0 0
AKAP5 -0.01 0.134 -9999 0 -0.39 21 21
MEF2D 0.035 0.007 -9999 0 -9999 0 0
mol:FK506 0 0 -9999 0 -9999 0 0
YWHAZ 0.029 0.014 -9999 0 -9999 0 0
NFATc/p38 alpha -0.025 0.141 0.42 1 -0.392 13 14
CREBBP 0.033 0.036 -9999 0 -0.482 1 1
BCL2 -0.002 0.098 -9999 0 -0.308 16 16
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.035 0.017 -9999 0 -0.204 1 1
PTK2 0.03 0.013 -9999 0 -9999 0 0
CRKL 0.001 0.06 0.168 1 -0.261 6 7
GRB2/SOS1/SHC 0.067 0.021 -9999 0 -9999 0 0
HRAS 0.032 0.04 -9999 0 -0.343 2 2
IRS1/Crk 0.008 0.06 -9999 0 -0.243 5 5
IGF-1R heterotetramer/IGF1/PTP1B 0.024 0.05 -9999 0 -0.328 1 1
AKT1 -0.023 0.053 0.171 1 -0.231 3 4
BAD -0.025 0.052 0.16 1 -0.296 1 2
mol:GTP 0 0 -9999 0 -9999 0 0
CRK 0.001 0.052 -9999 0 -0.243 5 5
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.017 0.071 -9999 0 -0.281 6 6
RAF1 -0.002 0.08 -9999 0 -0.431 4 4
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.048 0.077 -9999 0 -0.244 4 4
YWHAZ 0.029 0.014 -9999 0 -9999 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.021 0.067 -9999 0 -0.212 11 11
PIK3CA 0.035 0.006 -9999 0 -9999 0 0
RPS6KB1 -0.022 0.054 0.171 1 -0.231 3 4
GNB2L1 0.035 0.006 -9999 0 -9999 0 0
positive regulation of MAPKKK cascade 0.01 0.076 -9999 0 -0.359 2 2
PXN 0.036 0.004 -9999 0 -9999 0 0
PIK3R1 0.028 0.062 -9999 0 -0.483 3 3
cell adhesion 0 0 -9999 0 -9999 0 0
GRB2/SOS1 0.051 0.012 -9999 0 -9999 0 0
HRAS/GTP 0.018 0.06 -9999 0 -0.227 4 4
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.083 0.055 -9999 0 -0.23 3 3
IGF-1R heterotetramer 0.022 0.049 -9999 0 -0.35 2 2
IGF-1R heterotetramer/IGF1/IRS/Nck 0.036 0.073 -9999 0 -0.255 4 4
Crk/p130 Cas/Paxillin 0.049 0.076 -9999 0 -0.229 4 4
IGF1R 0.022 0.049 -9999 0 -0.351 2 2
IGF1 0.009 0.084 -9999 0 -0.266 14 14
IRS2/Crk -0.008 0.08 -9999 0 -0.261 15 15
PI3K 0.046 0.083 -9999 0 -0.245 7 7
apoptosis -0.001 0.05 0.264 1 -9999 0 1
HRAS/GDP 0.024 0.028 -9999 0 -0.347 1 1
PRKCD 0.007 0.065 -9999 0 -0.296 4 4
RAF1/14-3-3 E 0.011 0.08 -9999 0 -0.384 4 4
BAD/14-3-3 0.001 0.053 -9999 0 -0.279 1 1
PRKCZ -0.02 0.055 0.166 1 -0.225 7 8
Crk/p130 Cas/Paxillin/FAK1 0.017 0.061 -9999 0 -9999 0 0
PTPN1 0.015 0.039 -9999 0 -0.483 1 1
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.006 0.068 -9999 0 -0.299 5 5
BCAR1 0.034 0.017 -9999 0 -0.204 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.034 0.107 -9999 0 -0.28 16 16
mol:GDP 0 0 -9999 0 -9999 0 0
SOS1 0.036 0.002 -9999 0 -9999 0 0
IRS1/NCK2 0.018 0.065 -9999 0 -0.253 4 4
GRB10 -0.008 0.134 -9999 0 -0.399 20 20
PTPN11 0 0.064 0.168 1 -0.281 6 7
IRS1 0 0.061 -9999 0 -0.212 11 11
IRS2 -0.015 0.079 -9999 0 -0.252 18 18
IGF-1R heterotetramer/IGF1 0.024 0.075 -9999 0 -0.369 4 4
GRB2 0.034 0.008 -9999 0 -9999 0 0
PDPK1 0.001 0.063 -9999 0 -0.236 7 7
YWHAE 0.03 0.013 -9999 0 -9999 0 0
PRKD1 -0.01 0.088 -9999 0 -0.384 6 6
SHC1 0.035 0.007 -9999 0 -9999 0 0
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 0.049 0.11 -9999 0 -0.708 2 2
NCK1/PAK1/Dok-R -0.016 0.049 -9999 0 -0.349 2 2
NCK1/Dok-R 0.056 0.109 -9999 0 -1.027 1 1
PIK3CA 0.035 0.005 -9999 0 -9999 0 0
mol:beta2-estradiol -0.009 0.02 0.236 1 -9999 0 1
RELA 0.035 0.004 -9999 0 -9999 0 0
SHC1 0.035 0.007 -9999 0 -9999 0 0
Rac/GDP 0.024 0.008 -9999 0 -9999 0 0
F2 -0.002 0.076 0.279 1 -0.384 6 7
TNIP2 0.033 0.018 -9999 0 -0.204 1 1
NF kappa B/RelA 0.099 0.097 -9999 0 -0.978 1 1
FN1 -0.016 0.132 -9999 0 -0.3 32 32
PLD2 0.025 0.087 -9999 0 -1.061 1 1
PTPN11 0.029 0.053 -9999 0 -0.39 3 3
GRB14 -0.167 0.219 -9999 0 -0.354 108 108
ELK1 0.05 0.091 -9999 0 -0.958 1 1
GRB7 0.028 0.051 -9999 0 -0.483 2 2
PAK1 0.031 0.051 -9999 0 -0.483 2 2
Tie2/Ang1/alpha5/beta1 Integrin 0.078 0.12 -9999 0 -1.018 1 1
CDKN1A 0.031 0.165 -9999 0 -0.782 6 6
ITGA5 0.025 0.049 -9999 0 -0.204 9 9
mol:GTP 0 0 -9999 0 -9999 0 0
RasGAP/Dok-R 0.052 0.108 -9999 0 -1.027 1 1
CRK 0.03 0.013 -9999 0 -9999 0 0
mol:NO 0.058 0.103 -9999 0 -0.55 2 2
PLG 0.027 0.089 -9999 0 -1.061 1 1
mol:GDP 0 0 -9999 0 -9999 0 0
chemokinesis 0.066 0.106 -9999 0 -0.802 1 1
GRB2 0.034 0.008 -9999 0 -9999 0 0
PIK3R1 0.028 0.062 -9999 0 -0.484 3 3
ANGPT2 -0.007 0.142 -9999 0 -1.055 1 1
BMX 0.012 0.095 -9999 0 -1.061 1 1
ANGPT1 0.025 0.103 -9999 0 -1.301 1 1
tube development 0.023 0.12 -9999 0 -0.698 1 1
ANGPT4 0.021 0.063 -9999 0 -0.483 3 3
response to hypoxia 0.002 0.008 -9999 0 -9999 0 0
Tie2/Ang1/GRB14 -0.016 0.149 -9999 0 -1.094 1 1
alpha5/beta1 Integrin 0.043 0.041 -9999 0 -9999 0 0
FGF2 -0.004 0.115 -9999 0 -0.297 24 24
STAT5A (dimer) 0.044 0.146 -9999 0 -0.706 2 2
mol:L-citrulline 0.058 0.103 -9999 0 -0.55 2 2
AGTR1 0.014 0.071 -9999 0 -0.202 20 20
MAPK14 0.053 0.092 -9999 0 -0.938 1 1
Tie2/SHP2 0.057 0.063 -9999 0 -9999 0 0
TEK 0.036 0.057 -9999 0 -9999 0 0
RPS6KB1 0.06 0.111 -9999 0 -0.765 1 1
Angiotensin II/AT1 0.014 0.048 -9999 0 -0.131 20 20
Tie2/Ang1/GRB2 0.068 0.097 -9999 0 -1.094 1 1
MAPK3 0.02 0.089 -9999 0 -0.987 1 1
MAPK1 0.022 0.081 -9999 0 -0.987 1 1
Tie2/Ang1/GRB7 0.065 0.102 -9999 0 -1.094 1 1
NFKB1 0.035 0.006 -9999 0 -9999 0 0
MAPK8 0.028 0.087 -9999 0 -1.061 1 1
PI3K 0.053 0.114 -9999 0 -0.883 1 1
FES 0.028 0.14 -9999 0 -0.972 2 2
Crk/Dok-R 0.051 0.103 -9999 0 -1.027 1 1
Tie2/Ang1/ABIN2 0.069 0.097 -9999 0 -1.094 1 1
blood circulation 0 0 -9999 0 -9999 0 0
negative regulation of caspase activity 0.054 0.106 -9999 0 -0.645 2 2
STAT5A 0.027 0.049 -9999 0 -0.259 5 5
mol:ROS 0 0 -9999 0 -9999 0 0
PTK2 0.078 0.121 -9999 0 -0.765 1 1
Tie2/Ang2 0.014 0.129 -9999 0 -0.943 1 1
Tie2/Ang1 0.034 0.093 -9999 0 -1.128 1 1
FOXO1 0.059 0.113 -9999 0 -0.713 2 2
ELF1 0.027 0.054 -9999 0 -0.478 2 2
ELF2 0.032 0.086 -9999 0 -1.033 1 1
mol:Choline 0.025 0.084 -9999 0 -1.018 1 1
cell migration -0.009 0.037 -9999 0 -0.212 2 2
FYN 0.018 0.127 -9999 0 -0.796 1 1
DOK2 0.011 0.066 -9999 0 -0.225 13 13
negative regulation of cell cycle 0.035 0.151 -9999 0 -0.692 6 6
ETS1 0.033 0.06 -9999 0 -0.237 8 8
PXN 0.081 0.116 0.419 1 -0.646 1 2
ITGB1 0.034 0.017 -9999 0 -0.204 1 1
NOS3 0.057 0.11 -9999 0 -0.617 2 2
RAC1 0.033 0.011 -9999 0 -9999 0 0
TNF 0.031 0.071 -9999 0 -0.257 10 10
MAPKKK cascade 0.025 0.084 -9999 0 -1.018 1 1
RASA1 0.024 0.073 -9999 0 -0.427 5 5
Tie2/Ang1/Shc 0.069 0.097 -9999 0 -1.095 1 1
NCK1 0.026 0.071 -9999 0 -0.483 4 4
vasculogenesis 0.057 0.097 -9999 0 -0.498 2 2
mol:Phosphatidic acid 0.025 0.084 -9999 0 -1.018 1 1
mol:Angiotensin II 0.001 0.004 -9999 0 -9999 0 0
mol:NADP 0.058 0.103 -9999 0 -0.55 2 2
Rac1/GTP 0.06 0.103 -9999 0 -0.718 1 1
MMP2 0.02 0.103 -9999 0 -1.254 1 1
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.029 0.051 -9999 0 -0.483 2 2
RAS family/GTP/Tiam1 0.007 0.064 -9999 0 -0.287 1 1
NT3 (dimer)/TRKC 0.028 0.077 -9999 0 -0.346 6 6
NT3 (dimer)/TRKB 0.023 0.093 -9999 0 -0.299 8 8
SHC/Grb2/SOS1/GAB1/PI3K 0.03 0.045 -9999 0 -0.223 5 5
RAPGEF1 0.035 0.004 -9999 0 -9999 0 0
BDNF 0.017 0.084 -9999 0 -0.297 12 12
PIK3CA 0.035 0.006 -9999 0 -9999 0 0
DYNLT1 0.035 0.006 -9999 0 -9999 0 0
NTRK1 0.033 0.018 -9999 0 -0.204 1 1
NTRK2 0 0.084 -9999 0 -0.204 30 30
NTRK3 0.031 0.025 -9999 0 -0.204 2 2
NT-4/5 (dimer)/TRKB 0.022 0.057 -9999 0 -0.21 1 1
neuron apoptosis 0.013 0.143 0.345 25 -9999 0 25
SHC 2-3/Grb2 -0.016 0.154 -9999 0 -0.373 25 25
SHC1 0.035 0.007 -9999 0 -9999 0 0
SHC2 -0.015 0.153 -9999 0 -0.526 14 14
SHC3 -0.016 0.142 -9999 0 -0.461 16 16
STAT3 (dimer) 0.033 0.05 -9999 0 -0.317 3 3
NT3 (dimer)/TRKA 0.048 0.068 -9999 0 -0.28 5 5
RIN/GDP 0.036 0.077 0.26 5 -0.309 1 6
GIPC1 0.029 0.053 -9999 0 -0.39 3 3
KRAS 0.033 0.018 -9999 0 -0.204 1 1
DNAJA3 0.011 0.045 0.213 4 -0.232 1 5
RIN/GTP 0.017 0.013 -9999 0 -9999 0 0
CCND1 0.011 0.09 -9999 0 -0.664 3 3
MAGED1 0.024 0.075 -9999 0 -0.39 6 6
PTPN11 0.029 0.053 -9999 0 -0.39 3 3
RICS 0.03 0.051 -9999 0 -0.483 2 2
NT-4/5 (dimer) 0 0 -9999 0 -9999 0 0
SHC/GRB2/SOS1 0.067 0.021 -9999 0 -9999 0 0
GRB2 0.034 0.008 -9999 0 -9999 0 0
NGF (dimer)/TRKA/MATK 0.041 0.029 -9999 0 -0.21 1 1
TRKA/NEDD4-2 0.026 0.055 -9999 0 -0.349 3 3
ELMO1 0.033 0.011 -9999 0 -9999 0 0
RhoG/GTP/ELMO1/DOCK1 0.032 0.056 -9999 0 -0.295 5 5
NGF 0 0 -9999 0 -9999 0 0
HRAS 0.032 0.04 -9999 0 -0.343 2 2
DOCK1 0.021 0.081 -9999 0 -0.437 6 6
GAB2 0.036 0.004 -9999 0 -9999 0 0
RIT2 0.023 0.017 -9999 0 -9999 0 0
RIT1 0.032 0.024 -9999 0 -0.204 2 2
FRS2 0.033 0.024 -9999 0 -0.204 2 2
DNM1 0.029 0.037 -9999 0 -0.204 5 5
mol:GTP 0 0 -9999 0 -9999 0 0
CRK 0.03 0.013 -9999 0 -9999 0 0
SH2B1 (homopentamer) 0 0 -9999 0 -9999 0 0
RhoG/GTP 0.034 0.048 0.227 4 -9999 0 4
mol:GDP 0.052 0.104 0.314 5 -0.376 3 8
NGF (dimer) 0 0 -9999 0 -9999 0 0
RhoG/GDP 0.024 0.008 -9999 0 -9999 0 0
RIT1/GDP 0.05 0.074 0.217 3 -0.286 2 5
TIAM1 0.028 0.054 -9999 0 -0.39 3 3
PIK3R1 0.028 0.062 -9999 0 -0.483 3 3
BDNF (dimer)/TRKB 0.022 0.092 -9999 0 -0.276 8 8
KIDINS220/CRKL/C3G 0.046 0.041 -9999 0 -0.349 2 2
SHC/RasGAP 0.041 0.058 -9999 0 -0.349 4 4
FRS2 family/SHP2 0.064 0.046 -9999 0 -0.343 2 2
SHC/GRB2/SOS1/GAB1 0.077 0.048 -9999 0 -0.272 2 2
RIT1/GTP 0.024 0.016 -9999 0 -0.133 2 2
NT3 (dimer) 0.01 0.097 -9999 0 -0.323 14 14
RAP1/GDP 0.042 0.062 0.167 4 -0.229 2 6
KIDINS220/CRKL 0.029 0.051 -9999 0 -0.482 2 2
BDNF (dimer) 0.017 0.084 -9999 0 -0.296 12 12
ubiquitin-dependent protein catabolic process 0.024 0.047 -9999 0 -0.294 3 3
Schwann cell development -0.008 0.018 -9999 0 -9999 0 0
EHD4 0.028 0.054 -9999 0 -0.39 3 3
FRS2 family/GRB2/SOS1 0.083 0.032 -9999 0 -9999 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.016 0.073 -9999 0 -0.446 2 2
RAP1B 0.035 0.004 -9999 0 -9999 0 0
RAP1A 0.034 0.008 -9999 0 -9999 0 0
CDC42/GTP 0 0.1 -9999 0 -0.353 8 8
ABL1 0.035 0.005 -9999 0 -9999 0 0
SH2B family/GRB2/SOS1 0.051 0.012 -9999 0 -9999 0 0
Rap1/GTP 0.017 0.099 -9999 0 -0.429 6 6
STAT3 0.033 0.05 -9999 0 -0.317 3 3
axon guidance -0.01 0.089 -9999 0 -0.327 9 9
MAPK3 0.02 0.057 0.189 9 -0.254 5 14
MAPK1 0.025 0.041 0.189 9 -0.19 1 10
CDC42/GDP 0.053 0.082 0.258 6 -0.262 3 9
NTF3 0.01 0.097 -9999 0 -0.323 14 14
NTF4 0 0 -9999 0 -9999 0 0
NGF (dimer)/TRKA/FAIM 0.038 0.05 -9999 0 -0.295 4 4
PI3K 0.045 0.049 -9999 0 -0.349 3 3
FRS3 0.035 0.006 -9999 0 -9999 0 0
FAIM 0.022 0.081 -9999 0 -0.437 6 6
GAB1 0.028 0.054 -9999 0 -0.39 3 3
RASGRF1 0.005 0.048 0.213 4 -0.232 1 5
SOS1 0.036 0.002 -9999 0 -9999 0 0
MCF2L -0.001 0.063 -9999 0 -0.297 7 7
RGS19 0.014 0.038 -9999 0 -0.204 5 5
CDC42 0.032 0.019 -9999 0 -0.204 1 1
RAS family/GTP 0.047 0.079 0.387 1 -9999 0 1
Rac1/GDP 0.047 0.076 0.224 5 -0.268 2 7
NGF (dimer)/TRKA/GRIT 0.042 0.04 -9999 0 -0.341 2 2
neuron projection morphogenesis 0.031 0.084 -9999 0 -0.862 1 1
NGF (dimer)/TRKA/NEDD4-2 0.024 0.048 -9999 0 -0.295 3 3
MAP2K1 0.028 0.052 -9999 0 -0.256 2 2
NGFR 0.033 0.018 -9999 0 -0.204 1 1
NGF (dimer)/TRKA/GIPC/GAIP 0.012 0.031 -9999 0 -0.227 2 2
RAS family/GTP/PI3K 0.021 0.055 -9999 0 -0.247 7 7
FRS2 family/SHP2/GRB2/SOS1 0.092 0.053 -9999 0 -0.298 2 2
NRAS 0.019 0.079 -9999 0 -0.328 9 9
GRB2/SOS1 0.051 0.012 -9999 0 -9999 0 0
PRKCI 0.028 0.056 -9999 0 -0.343 4 4
ChemicalAbstracts:146-91-8 0 0 -9999 0 -9999 0 0
RAC1 0.033 0.011 -9999 0 -9999 0 0
PRKCZ 0 0 -9999 0 -9999 0 0
MAPKKK cascade -0.007 0.078 -9999 0 -0.444 4 4
RASA1 0.024 0.073 -9999 0 -0.427 5 5
TRKA/c-Abl 0.049 0.018 -9999 0 -9999 0 0
SQSTM1 0.034 0.017 -9999 0 -0.204 1 1
BDNF (dimer)/TRKB/GIPC 0.039 0.095 -9999 0 -0.273 7 7
NGF (dimer)/TRKA/p62/Atypical PKCs 0.055 0.041 -9999 0 -0.294 2 2
MATK 0.03 0.033 -9999 0 -0.204 4 4
NEDD4L 0.015 0.065 -9999 0 -0.413 4 4
RAS family/GDP -0.013 0.038 -9999 0 -0.237 2 2
NGF (dimer)/TRKA 0.017 0.044 0.236 4 -9999 0 4
Rac1/GTP -0.004 0.054 -9999 0 -0.261 1 1
FRS2 family/SHP2/CRK family 0.076 0.074 -9999 0 -0.362 3 3
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.017 0.063 -9999 0 -0.483 3 3
SMAD2 0.013 0.064 -9999 0 -0.248 5 5
SMAD3 0.003 0.086 -9999 0 -0.408 5 5
SMAD3/SMAD4 0.005 0.116 -9999 0 -0.519 7 7
SMAD4/Ubc9/PIASy 0.038 0.063 -9999 0 -0.294 4 4
SMAD2/SMAD2/SMAD4 0.035 0.082 -9999 0 -0.274 1 1
PPM1A 0.032 0.011 -9999 0 -9999 0 0
CALM1 0.032 0.011 -9999 0 -9999 0 0
SMAD2/SMAD4 0.008 0.065 -9999 0 -0.273 4 4
MAP3K1 0.031 0.033 -9999 0 -0.204 4 4
TRAP-1/SMAD4 0.017 0.083 -9999 0 -0.346 9 9
MAPK3 0.024 0.073 -9999 0 -0.427 5 5
MAPK1 0.034 0.008 -9999 0 -9999 0 0
NUP214 0.034 0.017 -9999 0 -0.204 1 1
CTDSP1 0.036 0.002 -9999 0 -9999 0 0
CTDSP2 0.025 0.066 -9999 0 -0.371 5 5
CTDSPL 0.016 0.091 -9999 0 -0.39 9 9
KPNB1 0.021 0.066 -9999 0 -0.266 9 9
TGFBRAP1 0.021 0.087 -9999 0 -0.483 6 6
UBE2I 0.035 0.006 -9999 0 -9999 0 0
NUP153 0.033 0.036 -9999 0 -0.483 1 1
KPNA2 0.034 0.008 -9999 0 -9999 0 0
PIAS4 0.031 0.04 -9999 0 -0.343 2 2
Ephrin A reverse signaling

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
MAPKKK cascade 0.037 0.047 -9999 0 -0.294 3 3
EFNA5 0.028 0.054 -9999 0 -0.39 3 3
FYN -0.002 0.073 -9999 0 -0.294 10 10
neuron projection morphogenesis 0.037 0.047 -9999 0 -0.294 3 3
cell-cell signaling 0 0 -9999 0 -9999 0 0
Ephrin A5/EPHA5 0.037 0.047 -9999 0 -0.295 3 3
EPHA5 0.029 0.046 -9999 0 -0.273 4 4
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.015 0.096 -9999 0 -0.421 9 9
HRAS 0.032 0.04 -9999 0 -0.343 2 2
EGFR 0.016 0.09 -9999 0 -0.413 8 8
AKT 0.051 0.085 0.26 6 -0.302 2 8
FOXO3 0 0 -9999 0 -9999 0 0
AKT1 0.029 0.03 -9999 0 -0.204 3 3
FOXO1 0 0 -9999 0 -9999 0 0
AKT3 0.028 0.04 -9999 0 -0.204 6 6
FOXO4 0 0 -9999 0 -9999 0 0
MET 0.027 0.056 -9999 0 -0.343 4 4
PIK3CA 0.035 0.006 -9999 0 -9999 0 0
PIK3CB 0.033 0.036 -9999 0 -0.483 1 1
NRAS 0.019 0.079 -9999 0 -0.328 9 9
PIK3CG 0.024 0.068 -9999 0 -0.343 6 6
PIK3R3 0.026 0.066 -9999 0 -0.371 5 5
PIK3R2 0.035 0.005 -9999 0 -9999 0 0
NF1 0.034 0.008 -9999 0 -9999 0 0
RAS 0.016 0.067 -9999 0 -0.266 5 5
ERBB2 0.031 0.037 -9999 0 -0.483 1 1
proliferation/survival/translation -0.027 0.057 0.175 1 -0.244 1 2
PI3K 0.037 0.08 0.235 11 -0.242 4 15
PIK3R1 0.028 0.062 -9999 0 -0.483 3 3
KRAS 0.033 0.018 -9999 0 -0.204 1 1
FOXO 0.058 0.055 0.222 9 -9999 0 9
AKT2 0.035 0.006 -9999 0 -9999 0 0
PTEN 0.026 0.062 -9999 0 -0.483 3 3
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.004 0.055 -9999 0 -0.304 3 3
adherens junction organization 0.02 0.085 -9999 0 -0.348 3 3
mol:GTP 0 0 -9999 0 -9999 0 0
Rac1/GDP 0.009 0.07 -9999 0 -0.351 3 3
FMN1 0.03 0.079 -9999 0 -0.244 11 11
mol:IP3 0.003 0.051 -9999 0 -0.267 3 3
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.034 0.083 -9999 0 -0.256 11 11
CTNNB1 0.012 0.093 -9999 0 -0.294 15 15
AKT1 0.047 0.084 0.196 1 -0.384 1 2
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.039 0.161 -9999 0 -0.466 12 12
CTNND1 0.039 0.006 -9999 0 -9999 0 0
mol:PI-4-5-P2 0.032 0.081 -9999 0 -0.316 2 2
VASP 0.025 0.086 -9999 0 -0.323 2 2
ZYX 0.03 0.082 -9999 0 -0.323 2 2
JUB 0.021 0.095 -9999 0 -0.44 3 3
EGFR(dimer) 0.041 0.103 -9999 0 -0.407 4 4
E-cadherin/beta catenin-gamma catenin 0.03 0.098 -9999 0 -0.287 15 15
mol:PI-3-4-5-P3 0.089 0.099 -9999 0 -0.401 1 1
PIK3CA 0.039 0.008 -9999 0 -9999 0 0
PI3K 0.091 0.101 -9999 0 -0.409 1 1
FYN -0.002 0.076 -9999 0 -0.38 5 5
mol:Ca2+ 0.003 0.05 -9999 0 -0.262 3 3
JUP 0.035 0.019 -9999 0 -0.205 1 1
PIK3R1 0.032 0.063 -9999 0 -0.486 3 3
mol:DAG 0.003 0.051 -9999 0 -0.267 3 3
CDH1 0.012 0.111 -9999 0 -0.484 10 10
RhoA/GDP 0.013 0.073 -9999 0 -0.351 3 3
establishment of polarity of embryonic epithelium 0.025 0.085 -9999 0 -0.316 2 2
SRC 0.011 0.062 -9999 0 -0.483 3 3
RAC1 0.033 0.011 -9999 0 -9999 0 0
RHOA 0.035 0.004 -9999 0 -9999 0 0
EGFR 0.016 0.09 -9999 0 -0.413 8 8
CASR -0.001 0.057 -9999 0 -0.553 1 1
RhoA/GTP 0.013 0.055 -9999 0 -0.33 1 1
AKT2 0.053 0.083 0.196 1 -0.384 1 2
actin cable formation 0.023 0.083 -9999 0 -0.314 2 2
apoptosis -0.044 0.08 0.285 3 -0.215 2 5
CTNNA1 0.039 0.007 -9999 0 -9999 0 0
mol:GDP -0.001 0.065 -9999 0 -0.371 3 3
PIP5K1A 0.032 0.082 -9999 0 -0.323 2 2
PLCG1 0.003 0.052 -9999 0 -0.272 3 3
Rac1/GTP 0.048 0.1 -9999 0 -0.379 4 4
homophilic cell adhesion 0.003 0.004 -9999 0 -9999 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.02 0.055 -9999 0 -0.239 7 7
TRAF2/ASK1 0.03 0.065 -9999 0 -0.295 6 6
ATM 0.03 0.043 -9999 0 -0.297 3 3
MAP2K3 0.014 0.091 -9999 0 -0.339 6 6
response to stress 0 0 -9999 0 -9999 0 0
MAP2K6 0.002 0.094 0.233 1 -0.302 5 6
hyperosmotic response 0 0 -9999 0 -9999 0 0
response to oxidative stress 0 0 -9999 0 -9999 0 0
GADD45G 0.014 0.086 -9999 0 -0.283 14 14
TXN 0.01 0.001 -9999 0 -9999 0 0
CALM1 0.032 0.011 -9999 0 -9999 0 0
GADD45A 0.02 0.079 -9999 0 -0.328 9 9
GADD45B 0.019 0.07 -9999 0 -0.254 11 11
MAP3K1 0.031 0.033 -9999 0 -0.204 4 4
MAP3K6 0.025 0.064 -9999 0 -0.413 4 4
MAP3K7 0.033 0.036 -9999 0 -0.483 1 1
MAP3K4 0.035 0.006 -9999 0 -9999 0 0
mol:Ca2+ 0 0 -9999 0 -9999 0 0
ASK1/ASK2 0.024 0.095 -9999 0 -0.379 9 9
TAK1/TAB family 0.021 0.021 -9999 0 -0.207 1 1
RAC1/OSM/MEKK3 0.059 0.025 -9999 0 -9999 0 0
TRAF2 0.033 0.024 -9999 0 -0.204 2 2
RAC1/OSM/MEKK3/MKK3 0.032 0.08 -9999 0 -0.298 3 3
TRAF6 0.02 0.003 -9999 0 -9999 0 0
RAC1 0.033 0.011 -9999 0 -9999 0 0
mol:LPS 0 0 -9999 0 -9999 0 0
CAMK2B 0.026 0.049 -9999 0 -0.259 5 5
CCM2 0.034 0.009 -9999 0 -9999 0 0
CaM/Ca2+/CAMKIIB 0.036 0.035 -9999 0 -0.295 1 1
MAPK11 0.031 0.02 -9999 0 -0.204 1 1
response to DNA damage stimulus 0 0 -9999 0 -9999 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.038 0.073 -9999 0 -0.28 7 7
OSM/MEKK3 0.047 0.017 -9999 0 -9999 0 0
TAOK1 0.013 0.041 -9999 0 -0.312 3 3
TAOK2 0.017 0.025 -9999 0 -0.312 1 1
TAOK3 0.017 0.025 -9999 0 -0.312 1 1
MAP3K7IP1 0.034 0.009 -9999 0 -9999 0 0
MAPK14 0.036 0.004 -9999 0 -9999 0 0
MAP3K7IP2 0.035 0.006 -9999 0 -9999 0 0
MAP3K5 0.011 0.101 -9999 0 -0.354 13 13
MAP3K10 0.03 0.033 -9999 0 -0.204 4 4
MAP3K3 0.034 0.009 -9999 0 -9999 0 0
TRX/ASK1 0.017 0.062 -9999 0 -0.267 8 8
GADD45/MTK1/MTK1 0.041 0.091 -9999 0 -0.254 10 10
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.075 0.039 -9999 0 -9999 0 0
HDAC3 0.035 0.006 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0.007 0.024 -9999 0 -0.224 2 2
GATA1/HDAC4 0.044 0.057 -9999 0 -0.349 4 4
GATA1/HDAC5 0.044 0.055 -9999 0 -0.377 3 3
GATA2/HDAC5 0.044 0.046 -9999 0 -0.349 2 2
HDAC5/BCL6/BCoR 0.046 0.081 -9999 0 -0.298 8 8
HDAC9 0.029 0.041 -9999 0 -0.343 2 2
Glucocorticoid receptor/Hsp90/HDAC6 0.036 0.06 -9999 0 -0.295 6 6
HDAC4/ANKRA2 0.049 0.032 -9999 0 -0.349 1 1
HDAC5/YWHAB 0.022 0.045 -9999 0 -0.349 2 2
NPC/RanGAP1/SUMO1/Ubc9 0.017 0.021 -9999 0 -0.2 1 1
GATA2 0.029 0.053 -9999 0 -0.39 3 3
HDAC4/RFXANK 0.05 0.029 -9999 0 -0.349 1 1
BCOR 0.033 0.036 -9999 0 -0.483 1 1
mol:GTP 0 0 -9999 0 -9999 0 0
HDAC10 0.03 0.025 -9999 0 -0.204 2 2
HDAC5 0.032 0.024 -9999 0 -0.204 2 2
GNB1/GNG2 0.045 0.019 -9999 0 -9999 0 0
Histones 0.024 0.05 -9999 0 -0.254 2 2
ADRBK1 0.036 0.004 -9999 0 -9999 0 0
HDAC4 0.033 0.036 -9999 0 -0.483 1 1
XPO1 0.036 0 -9999 0 -9999 0 0
HDAC5/ANKRA2 0.048 0.025 -9999 0 -9999 0 0
HDAC4/Ubc9 0.049 0.031 -9999 0 -0.349 1 1
HDAC7 0 0 -9999 0 -9999 0 0
HDAC5/14-3-3 E 0.042 0.028 -9999 0 -9999 0 0
TUBA1B 0 0 -9999 0 -9999 0 0
HDAC6 0.035 0.017 -9999 0 -0.204 1 1
HDAC5/RFXANK 0.049 0.022 -9999 0 -9999 0 0
CAMK4 0.035 0.006 -9999 0 -9999 0 0
Tubulin/HDAC6 0.04 0.043 -9999 0 -0.295 2 2
SUMO1 0.036 0.004 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 0 0
YWHAB 0.013 0.052 -9999 0 -0.483 2 2
GATA1 0.027 0.064 -9999 0 -0.413 4 4
EntrezGene:8021 0 0 -9999 0 -9999 0 0
YWHAE 0.03 0.013 -9999 0 -9999 0 0
NR3C1 0.019 0.088 -9999 0 -0.443 7 7
SUMO1/HDAC4 0.046 0.045 -9999 0 -0.226 1 1
SRF 0.031 0.04 -9999 0 -0.343 2 2
HDAC4/YWHAB 0.02 0.052 -9999 0 -0.349 3 3
Tubulin 0.019 0.044 -9999 0 -0.194 7 7
HDAC4/14-3-3 E 0.041 0.035 -9999 0 -0.349 1 1
GNB1 0.034 0.008 -9999 0 -9999 0 0
RANGAP1 0.029 0.034 -9999 0 -0.204 4 4
BCL6/BCoR 0.029 0.085 -9999 0 -0.349 8 8
HDAC4/HDAC3/SMRT (N-CoR2) 0.064 0.041 -9999 0 -0.298 2 2
HDAC4/SRF 0.064 0.049 -9999 0 -0.555 1 1
HDAC4/ER alpha 0.042 0.062 -9999 0 -0.349 5 5
EntrezGene:23225 0 0 -9999 0 -9999 0 0
positive regulation of chromatin silencing 0.024 0.05 -9999 0 -0.252 2 2
cell motility 0.04 0.042 -9999 0 -0.294 2 2
EntrezGene:23636 0 0 -9999 0 -9999 0 0
UBE2I 0.035 0.006 -9999 0 -9999 0 0
HDAC7/HDAC3 0.026 0.004 -9999 0 -9999 0 0
BCL6 0.008 0.104 -9999 0 -0.326 16 16
HDAC4/CaMK II delta B 0.033 0.036 -9999 0 -0.482 1 1
Hsp90/HDAC6 0.026 0.011 -9999 0 -0.133 1 1
ESR1 0.025 0.071 -9999 0 -0.483 4 4
HDAC6/HDAC11 0.049 0.024 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0.049 0.042 -9999 0 -9999 0 0
NPC 0.019 0.02 -9999 0 -0.249 1 1
MEF2C -0.003 0.124 -9999 0 -0.357 20 20
RAN 0.036 0.004 -9999 0 -9999 0 0
HDAC4/MEF2C 0.066 0.095 -9999 0 -0.256 12 12
GNG2 0.033 0.01 -9999 0 -9999 0 0
NCOR2 0.032 0.04 -9999 0 -0.343 2 2
TUBB2A 0.025 0.062 -9999 0 -0.283 7 7
HDAC11 0.033 0.024 -9999 0 -0.204 2 2
HSP90AA1 0 0 -9999 0 -9999 0 0
RANBP2 0.032 0.039 -9999 0 -0.343 2 2
ANKRA2 0.034 0.017 -9999 0 -0.204 1 1
RFXANK 0.035 0.005 -9999 0 -9999 0 0
nuclear import -0.017 0.044 0.286 3 -9999 0 3
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.007 0.114 -9999 0 -0.294 10 10
CaM/Ca2+ 0.024 0.008 -9999 0 -9999 0 0
AKT1 0.029 0.03 -9999 0 -0.204 3 3
AKT2 0.035 0.006 -9999 0 -9999 0 0
STXBP4 0.034 0.008 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
mol:glucose -0.01 0.111 -9999 0 -0.269 18 18
YWHAZ 0.029 0.014 -9999 0 -9999 0 0
CALM1 0.032 0.011 -9999 0 -9999 0 0
YWHAQ 0.036 0.002 -9999 0 -9999 0 0
TBC1D4 0.001 0.063 -9999 0 -0.35 6 6
mol:Ca2+ 0 0 -9999 0 -9999 0 0
YWHAH 0.031 0.037 -9999 0 -0.483 1 1
YWHAB 0.013 0.052 -9999 0 -0.483 2 2
SNARE/Synip 0.039 0.019 -9999 0 -9999 0 0
YWHAG 0.034 0.008 -9999 0 -9999 0 0
ASIP 0 0 -9999 0 -9999 0 0
PRKCI 0.028 0.056 -9999 0 -0.343 4 4
AS160/CaM/Ca2+ 0.024 0.008 -9999 0 -9999 0 0
RHOQ 0.031 0.043 -9999 0 -0.297 3 3
GYS1 0.015 0.027 0.252 1 -0.263 1 2
PRKCZ 0 0 -9999 0 -9999 0 0
TRIP10 0.035 0.005 -9999 0 -9999 0 0
TC10/GTP/CIP4/Exocyst 0.044 0.029 -9999 0 -0.295 1 1
AS160/14-3-3 0.006 0.059 -9999 0 -0.299 2 2
VAMP2 0.029 0.014 -9999 0 -9999 0 0
SLC2A4 -0.013 0.12 -9999 0 -0.295 18 18
STX4 0 0 -9999 0 -9999 0 0
GSK3B 0.024 0.027 -9999 0 -0.305 1 1
SFN 0.02 0.071 -9999 0 -0.308 8 8
LNPEP 0.034 0.007 -9999 0 -9999 0 0
YWHAE 0.03 0.013 -9999 0 -9999 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.066 0.072 -9999 0 -0.306 2 2
Ran/GTP/Exportin 1/HDAC1 0.008 0.017 -9999 0 -0.223 1 1
NF kappa B1 p50/RelA/I kappa B alpha 0.033 0.075 -9999 0 -0.285 2 2
SUMO1 0.036 0.004 -9999 0 -9999 0 0
ZFPM1 0.034 0.017 -9999 0 -0.204 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.017 0.021 -9999 0 -0.2 1 1
FKBP3 0.032 0.011 -9999 0 -9999 0 0
Histones 0.077 0.051 -9999 0 -9999 0 0
YY1/LSF 0.008 0.08 -9999 0 -0.251 11 11
SMG5 0 0 -9999 0 -9999 0 0
RAN 0.036 0.004 -9999 0 -9999 0 0
I kappa B alpha/HDAC3 0.027 0.039 -9999 0 -0.235 3 3
I kappa B alpha/HDAC1 0.025 0.068 -9999 0 -0.332 1 1
SAP18 0.026 0.016 -9999 0 -9999 0 0
RELA 0.021 0.057 -9999 0 -0.235 4 4
HDAC1/Smad7 0.045 0.042 -9999 0 -0.298 1 1
RANGAP1 0.029 0.034 -9999 0 -0.204 4 4
HDAC3/TR2 0.043 0.041 -9999 0 -9999 0 0
NuRD/MBD3 Complex 0.021 0.067 -9999 0 -0.37 2 2
NF kappa B1 p50/RelA 0.029 0.078 -9999 0 -0.262 4 4
EntrezGene:23225 0 0 -9999 0 -9999 0 0
GATA2 0.029 0.053 -9999 0 -0.39 3 3
GATA1 0.027 0.064 -9999 0 -0.413 4 4
Mad/Max 0.042 0.043 -9999 0 -0.349 1 1
NuRD/MBD3 Complex/GATA1/Fog1 0.019 0.088 -9999 0 -0.464 2 2
RBBP7 0.034 0.023 -9999 0 -0.204 2 2
NPC 0.019 0.02 -9999 0 -0.249 1 1
RBBP4 0.031 0.029 -9999 0 -0.204 3 3
MAX 0.033 0.01 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 0 0
FBXW11 0.036 0.004 -9999 0 -9999 0 0
NFKBIA 0.023 0.038 -9999 0 -0.362 1 1
KAT2B 0 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
SIN3/HDAC complex 0.042 0.059 -9999 0 -0.36 1 1
SIN3 complex 0.058 0.051 -9999 0 -0.272 1 1
SMURF1 0.034 0.008 -9999 0 -9999 0 0
CHD3 0.028 0.021 -9999 0 -0.204 1 1
SAP30 0.031 0.037 -9999 0 -0.483 1 1
EntrezGene:23636 0 0 -9999 0 -9999 0 0
NCOR1 0.029 0.014 -9999 0 -9999 0 0
YY1/HDAC3 0.012 0.066 -9999 0 -0.29 2 2
YY1/HDAC2 0.009 0.077 -9999 0 -0.25 10 10
YY1/HDAC1 0.01 0.075 -9999 0 -0.249 9 9
NuRD/MBD2 Complex (MeCP1) 0.009 0.069 -9999 0 -0.393 1 1
PPARG -0.012 0.114 -9999 0 -0.313 23 23
HDAC8/hEST1B 0.047 0.007 -9999 0 -9999 0 0
UBE2I 0.035 0.006 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.036 0.004 -9999 0 -9999 0 0
TNFRSF1A 0.035 0.007 -9999 0 -9999 0 0
HDAC3/SMRT (N-CoR2) 0.041 0.046 -9999 0 -0.249 1 1
MBD3L2 0.017 0.09 -9999 0 -0.413 8 8
ubiquitin-dependent protein catabolic process 0.045 0.042 -9999 0 -0.297 1 1
CREBBP 0.032 0.036 -9999 0 -0.483 1 1
NuRD/MBD3/MBD3L2 Complex 0.016 0.093 -9999 0 -0.478 2 2
HDAC1 0.034 0.008 -9999 0 -9999 0 0
HDAC3 0.028 0.025 -9999 0 -9999 0 0
HDAC2 0.032 0.036 -9999 0 -0.483 1 1
YY1 0.007 0.058 -9999 0 -0.274 8 8
HDAC8 0.036 0 -9999 0 -9999 0 0
SMAD7 0.022 0.039 -9999 0 -0.483 1 1
NCOR2 0.032 0.04 -9999 0 -0.343 2 2
MXD1 0.027 0.054 -9999 0 -0.244 7 7
STAT3 0.015 0.061 -9999 0 -0.304 7 7
NFKB1 0.035 0.006 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.032 0.039 -9999 0 -0.343 2 2
YY1/LSF/HDAC1 0.023 0.082 -9999 0 -0.236 10 10
YY1/SAP30/HDAC1 0.024 0.08 -9999 0 -0.232 10 10
EP300 0.018 0.088 -9999 0 -0.443 7 7
STAT3 (dimer non-phopshorylated) 0.015 0.061 -9999 0 -0.304 7 7
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.038 -9999 0 -0.36 1 1
histone deacetylation 0.009 0.068 -9999 0 -0.389 1 1
STAT3 (dimer non-phopshorylated)/HDAC3 0.026 0.061 -9999 0 -0.251 1 1
nuclear export -0.047 0.007 -9999 0 -9999 0 0
PRKACA 0.035 0.006 -9999 0 -9999 0 0
GATAD2B 0.035 0.007 -9999 0 -9999 0 0
GATAD2A 0.033 0.036 -9999 0 -0.483 1 1
GATA2/HDAC3 0.04 0.05 -9999 0 -0.249 2 2
GATA1/HDAC1 0.044 0.051 -9999 0 -0.349 3 3
GATA1/HDAC3 0.039 0.054 -9999 0 -0.249 3 3
CHD4 0.035 0.007 -9999 0 -9999 0 0
TNF-alpha/TNFR1A 0.041 0.052 -9999 0 -0.349 2 2
SIN3/HDAC complex/Mad/Max 0.032 0.072 -9999 0 -0.316 4 4
NuRD Complex -0.011 0.11 -9999 0 -0.386 6 6
positive regulation of chromatin silencing 0.074 0.049 -9999 0 -9999 0 0
SIN3B 0.035 0.006 -9999 0 -9999 0 0
MTA2 0.03 0.051 -9999 0 -0.483 2 2
SIN3A 0.032 0.019 -9999 0 -0.204 1 1
XPO1 0.036 0 -9999 0 -9999 0 0
SUMO1/HDAC1 0.046 0.04 -9999 0 -9999 0 0
HDAC complex 0.079 0.045 -9999 0 -0.272 1 1
GATA1/Fog1 0.045 0.052 -9999 0 -0.349 3 3
FKBP25/HDAC1/HDAC2 0.057 0.039 -9999 0 -0.298 1 1
TNF 0.023 0.066 -9999 0 -0.266 9 9
negative regulation of cell growth 0.032 0.072 -9999 0 -0.314 4 4
NuRD/MBD2/PRMT5 Complex 0.009 0.069 -9999 0 -0.393 1 1
Ran/GTP/Exportin 1 0.049 0.042 -9999 0 -9999 0 0
NF kappa B/RelA/I kappa B alpha 0.018 0.061 -9999 0 -0.281 3 3
SIN3/HDAC complex/NCoR1 0.007 0.073 -9999 0 -0.302 6 6
TFCP2 0.03 0.051 -9999 0 -0.483 2 2
NR2C1 0.035 0.017 -9999 0 -0.204 1 1
MBD3 0.034 0.008 -9999 0 -9999 0 0
MBD2 0.024 0.017 -9999 0 -9999 0 0
Atypical NF-kappaB 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
BCL3/RelA 0.041 0.063 -9999 0 -0.349 5 5
FBXW11 0.036 0.004 -9999 0 -9999 0 0
NF kappa B1 p50/c-Rel 0.032 0.036 -9999 0 -0.298 2 2
NF kappa B1 p50/RelA/I kappa B alpha 0.044 0.089 -9999 0 -0.389 1 1
NFKBIA 0.039 0.08 -9999 0 -0.281 4 4
MAPK14 0.036 0.004 -9999 0 -9999 0 0
NF kappa B1 p105/p50 0.035 0.015 -9999 0 -9999 0 0
ARRB2 0.015 0.024 -9999 0 -0.313 1 1
REL 0.026 0.071 -9999 0 -0.483 4 4
response to oxidative stress 0 0 -9999 0 -9999 0 0
BCL3/NF kappa B1 p50 0.029 0.044 -9999 0 -0.298 3 3
response to UV 0 0 -9999 0 -9999 0 0
NF kappa B1 p105/RelA 0.034 0.015 -9999 0 -9999 0 0
PIK3CA 0.035 0.006 -9999 0 -9999 0 0
NF kappa B1 p50 dimer 0.024 0.01 -9999 0 -9999 0 0
PIK3R1 0.028 0.062 -9999 0 -0.483 3 3
NFKB1 0.016 0.007 -9999 0 -9999 0 0
RELA 0.035 0.004 -9999 0 -9999 0 0
positive regulation of anti-apoptosis 0.03 0.074 -9999 0 -0.399 1 1
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.036 0.086 -9999 0 -0.318 1 1
SRC 0.011 0.062 -9999 0 -0.483 3 3
PI3K 0.045 0.049 -9999 0 -0.349 3 3
NF kappa B1 p50/RelA 0.03 0.074 -9999 0 -0.403 1 1
IKBKB 0.031 0.012 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.036 0.004 -9999 0 -9999 0 0
SYK 0.029 0.053 -9999 0 -0.39 3 3
I kappa B alpha/PIK3R1 0.041 0.108 -9999 0 -0.329 8 8
cell death 0.035 0.083 -9999 0 -0.305 1 1
NF kappa B1 p105/c-Rel 0.032 0.036 -9999 0 -0.298 2 2
LCK -0.015 0.138 -9999 0 -0.354 26 26
BCL3 0.021 0.081 -9999 0 -0.437 6 6
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.043 0.037 -9999 0 -9999 0 0
KIRREL 0.034 0.018 -9999 0 -9999 0 0
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.043 0.037 -9999 0 -9999 0 0
PLCG1 0.019 0.018 -9999 0 -9999 0 0
ARRB2 0.027 0.038 -9999 0 -0.483 1 1
WASL 0.032 0.036 -9999 0 -0.483 1 1
Nephrin/NEPH1/podocin/CD2AP 0.074 0.049 -9999 0 -0.293 1 1
ChemicalAbstracts:57-88-5 0 0 -9999 0 -9999 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.028 0.043 -9999 0 -9999 0 0
FYN 0.021 0.072 0.302 5 -0.199 7 12
mol:Ca2+ 0.039 0.046 -9999 0 -9999 0 0
mol:DAG 0.04 0.047 -9999 0 -9999 0 0
NPHS2 0.032 0.03 -9999 0 -0.213 2 2
mol:IP3 0.04 0.047 -9999 0 -9999 0 0
regulation of endocytosis 0.041 0.067 -9999 0 -0.247 1 1
Nephrin/NEPH1/podocin/Cholesterol 0.053 0.041 -9999 0 -9999 0 0
establishment of cell polarity 0.043 0.037 -9999 0 -9999 0 0
Nephrin/NEPH1/podocin/NCK1-2 0.085 0.069 -9999 0 -0.27 4 4
Nephrin/NEPH1/beta Arrestin2 0.043 0.069 -9999 0 -0.25 1 1
NPHS1 0.03 0.038 -9999 0 -0.204 4 4
Nephrin/NEPH1/podocin 0.046 0.063 -9999 0 -0.199 7 7
TJP1 0.033 0.009 -9999 0 -9999 0 0
NCK1 0.026 0.071 -9999 0 -0.483 4 4
NCK2 0.035 0.017 -9999 0 -0.204 1 1
heterophilic cell adhesion 0 0 -9999 0 -9999 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.041 0.048 -9999 0 -9999 0 0
CD2AP 0.033 0.036 -9999 0 -0.483 1 1
Nephrin/NEPH1/podocin/GRB2 0.075 0.044 -9999 0 -9999 0 0
GRB2 0.034 0.008 -9999 0 -9999 0 0
homophilic cell adhesion 0 0 -9999 0 -9999 0 0
TRPC6 0.016 0.08 0.313 5 -0.301 5 10
cytoskeleton organization 0.019 0.049 0.214 5 -9999 0 5
Nephrin/NEPH1 0.037 0.027 -9999 0 -9999 0 0
Nephrin/NEPH1/ZO-1 0.059 0.036 -9999 0 -9999 0 0
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 0.037 0.014 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.056 0.073 -9999 0 -0.295 1 1
ERC1 0 0 -9999 0 -9999 0 0
RIP2/NOD2 0.017 0.045 -9999 0 -0.347 3 3
NFKBIA 0.014 0.044 -9999 0 -0.536 1 1
BIRC2 0.034 0.018 -9999 0 -0.204 1 1
IKBKB 0.031 0.012 -9999 0 -9999 0 0
RIPK2 0.022 0.063 -9999 0 -0.483 3 3
IKBKG 0.027 0.046 -9999 0 -0.31 1 1
IKK complex/A20 0.068 0.056 -9999 0 -9999 0 0
NEMO/A20/RIP2 0.022 0.063 -9999 0 -0.482 3 3
XPO1 0.036 0 -9999 0 -9999 0 0
NEMO/ATM 0.049 0.054 -9999 0 -0.285 1 1
tumor necrosis factor receptor activity 0 0 -9999 0 -9999 0 0
RAN 0.036 0.004 -9999 0 -9999 0 0
Exportin 1/RanGTP 0.048 0.005 -9999 0 -9999 0 0
IKK complex/ELKS 0.039 0.052 -9999 0 -0.276 1 1
BCL10/MALT1/TRAF6 0.043 0.051 -9999 0 -0.298 2 2
NOD2 0 0 -9999 0 -9999 0 0
NFKB1 0.036 0.014 -9999 0 -9999 0 0
RELA 0.037 0.014 -9999 0 -9999 0 0
MALT1 0.021 0.039 -9999 0 -0.483 1 1
cIAP1/UbcH5C 0.048 0.033 -9999 0 -0.349 1 1
ATM 0.03 0.043 -9999 0 -0.297 3 3
TNF/TNFR1A 0.041 0.052 -9999 0 -0.349 2 2
TRAF6 0.036 0.004 -9999 0 -9999 0 0
PRKCA 0.03 0.04 -9999 0 -0.343 2 2
CHUK 0.027 0.062 -9999 0 -0.483 3 3
UBE2D3 0.032 0.036 -9999 0 -0.483 1 1
TNF 0.023 0.066 -9999 0 -0.266 9 9
NF kappa B1 p50/RelA 0.076 0.036 -9999 0 -0.276 1 1
BCL10 0.033 0.036 -9999 0 -0.483 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.044 -9999 0 -0.532 1 1
beta TrCP1/SCF ubiquitin ligase complex 0.037 0.014 -9999 0 -9999 0 0
TNFRSF1A 0.035 0.007 -9999 0 -9999 0 0
IKK complex 0.054 0.061 -9999 0 -0.291 1 1
CYLD 0.036 0 -9999 0 -9999 0 0
IKK complex/PKC alpha 0.062 0.067 -9999 0 -9999 0 0
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.056 0.062 -9999 0 -9999 0 0
CLOCK 0.035 0.04 -9999 0 -0.339 2 2
TIMELESS/CRY2 0.05 0.025 -9999 0 -9999 0 0
DEC1/BMAL1 0.051 0.034 -9999 0 -0.346 1 1
ATR 0.034 0.017 -9999 0 -0.204 1 1
NR1D1 0.029 0.023 -9999 0 -9999 0 0
ARNTL 0.036 0.036 -9999 0 -0.479 1 1
TIMELESS 0.031 0.018 -9999 0 -9999 0 0
NPAS2 0.026 0.08 -9999 0 -0.482 5 5
CRY2 0.036 0.002 -9999 0 -9999 0 0
mol:CO -0.012 0.003 -9999 0 -9999 0 0
CHEK1 0.015 0.1 -9999 0 -0.483 8 8
mol:HEME 0.012 0.003 -9999 0 -9999 0 0
PER1 0.029 0.014 -9999 0 -9999 0 0
BMAL/CLOCK/NPAS2 0.073 0.071 -9999 0 -0.294 7 7
BMAL1/CLOCK 0.04 0.053 -9999 0 -9999 0 0
S phase of mitotic cell cycle 0.056 0.062 -9999 0 -9999 0 0
TIMELESS/CHEK1/ATR 0.057 0.063 -9999 0 -9999 0 0
mol:NADPH 0.012 0.003 -9999 0 -9999 0 0
PER1/TIMELESS 0.04 0.031 -9999 0 -9999 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -9999 0 0
DEC1 0.034 0.017 -9999 0 -0.204 1 1
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.044 0.05 -9999 0 -0.349 3 3
FBXW11 0.036 0.004 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.036 0.004 -9999 0 -9999 0 0
CHUK 0.027 0.062 -9999 0 -0.483 3 3
NF kappa B2 p100/RelB 0.09 0.059 -9999 0 -0.257 4 4
NFKB1 0.035 0.006 -9999 0 -9999 0 0
MAP3K14 0.035 0.006 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.049 0.03 -9999 0 -0.349 1 1
RELB 0.033 0.036 -9999 0 -0.483 1 1
NFKB2 0.033 0.018 -9999 0 -0.204 1 1
NF kappa B2 p52/RelB 0.043 0.029 -9999 0 -0.295 1 1
regulation of B cell activation 0.042 0.029 -9999 0 -0.294 1 1
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.034 0.008 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0.004 0.027 -9999 0 -0.23 2 2
MDM2/SUMO1 0.046 0.04 -9999 0 -9999 0 0
HDAC4 0.033 0.036 -9999 0 -0.483 1 1
Ran/GTP/Exportin 1/HDAC1 0.005 0.023 -9999 0 -0.25 1 1
SUMO1 0.036 0.004 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1 0.014 0.018 -9999 0 -0.206 1 1
mol:GTP 0 0 -9999 0 -9999 0 0
XPO1 0.008 0.028 -9999 0 -9999 0 0
EntrezGene:23636 0 0 -9999 0 -9999 0 0
RAN 0.036 0.004 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.032 0.039 -9999 0 -0.343 2 2
SUMO1/HDAC4 0.046 0.045 -9999 0 -0.226 1 1
SUMO1/HDAC1 0.046 0.04 -9999 0 -9999 0 0
RANGAP1 0.029 0.034 -9999 0 -0.204 4 4
MDM2/SUMO1/SUMO1 0.049 0.062 -9999 0 -0.272 2 2
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.017 0.021 -9999 0 -0.2 1 1
Ran/GTP 0.032 0.036 -9999 0 -9999 0 0
EntrezGene:23225 0 0 -9999 0 -9999 0 0
MDM2 0.034 0.017 -9999 0 -0.204 1 1
UBE2I 0.035 0.006 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0.029 0.035 -9999 0 -9999 0 0
NPC 0.019 0.02 -9999 0 -0.249 1 1
PIAS2 0.012 0.064 -9999 0 -0.273 8 8
PIAS1 0.034 0.009 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.043 0.034 -9999 0 -9999 0 0
MAPK9 0.009 0.023 -9999 0 -0.32 1 1
adrenocorticotropin secretion 0.008 0.01 -9999 0 -0.133 1 1
GNB1/GNG2 0.041 0.017 -9999 0 -9999 0 0
GNB1 0.034 0.008 -9999 0 -9999 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
MAPK14 0.01 0.001 -9999 0 -9999 0 0
Gs family/GTP 0.014 0.019 -9999 0 -0.091 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 0.001 0.004 0.029 4 -9999 0 4
GNAL 0.022 0.035 -9999 0 -0.204 4 4
GNG2 0.033 0.01 -9999 0 -9999 0 0
CRH 0.029 0.021 -9999 0 -0.204 1 1
mol:cortisol 0 0 -9999 0 -9999 0 0
MAPK8 0.01 0.002 -9999 0 -9999 0 0
MAPK11 0.009 0.007 -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 0.067 0.068 -9999 0 -9999 0 0
EntrezGene:79658 0 0 -9999 0 -9999 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.01 0.038 0.134 3 -0.188 2 5
AP2 0.048 0.032 -9999 0 -0.349 1 1
mol:DAG 0 0 -9999 0 -9999 0 0
Arfaptin 2/Rac/GTP 0.042 0.016 -9999 0 -9999 0 0
CLTB 0.035 0.005 -9999 0 -9999 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.026 0.009 -9999 0 -9999 0 0
CD4 0.035 0.007 -9999 0 -9999 0 0
CLTA 0.035 0.006 -9999 0 -9999 0 0
mol:GTP -0.001 0.002 -9999 0 -9999 0 0
ARFGAP1 0.005 0.005 -9999 0 -9999 0 0
mol:PI-4-5-P2 0.007 0.007 -9999 0 -9999 0 0
ARF1/GTP 0.023 0.009 -9999 0 -9999 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.029 0.053 0.175 24 -9999 0 24
mol:Choline 0.007 0.007 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
ARF1 0.035 0.007 -9999 0 -9999 0 0
DDEF1 0.005 0.005 -9999 0 -9999 0 0
ARF1/GDP 0.002 0.016 -9999 0 -9999 0 0
AP2M1 0.032 0.04 -9999 0 -0.343 2 2
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 0.009 -9999 0 -9999 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.026 0.026 -9999 0 -9999 0 0
ARFIP2 0.023 0.025 -9999 0 -9999 0 0
COPA 0.034 0.007 -9999 0 -9999 0 0
RAC1 0.033 0.011 -9999 0 -9999 0 0
ARF1/GTP/coatomer protein complex 0.021 0.022 -9999 0 -9999 0 0
ARF1/GTP/ARHGAP10 0.023 0.006 -9999 0 -9999 0 0
GGA3 0.034 0.008 -9999 0 -9999 0 0
ARF1/GTP/Membrin 0.024 0.04 -9999 0 -0.254 4 4
AP2A1 0.035 0.006 -9999 0 -9999 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.011 0.019 -9999 0 -9999 0 0
ARF1/GDP/Membrin 0.025 0.047 -9999 0 -0.301 4 4
Arfaptin 2/Rac/GDP 0.041 0.016 -9999 0 -9999 0 0
CYTH2 -0.001 0.002 -9999 0 -9999 0 0
ARF1/GTP/GGA3 0.045 0.013 -9999 0 -9999 0 0
mol:ATP 0 0 -9999 0 -9999 0 0
Rac/GDP 0.024 0.008 -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 0.032 0.025 -9999 0 -9999 0 0
PLD2 0.007 0.007 -9999 0 -9999 0 0
ARF-GAP1/v-SNARE 0.005 0.005 -9999 0 -9999 0 0
PIP5K1A 0.007 0.007 -9999 0 -9999 0 0
ARF1/GTP/Membrin/GBF1/p115 0.011 0.03 -9999 0 -0.136 1 1
mol:Phosphatic acid 0 0 -9999 0 -9999 0 0
mol:Phosphatidic acid 0.007 0.007 -9999 0 -9999 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.005 0.005 -9999 0 -9999 0 0
GOSR2 0.015 0.008 -9999 0 -9999 0 0
USO1 0.003 0.003 -9999 0 -9999 0 0
GBF1 0.002 0.068 -9999 0 -0.355 7 7
ARF1/GTP/Arfaptin 2 0.046 0.01 -9999 0 -9999 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.065 0.034 -9999 0 -0.298 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/COADREAD/350103/1.GDAC_MergeDataFiles.Finished/COADREAD.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/COADREAD/718074/1.GetReducedSegments.Finished/COADREAD.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)