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 97 significant pathways identified in this analysis.

Table 1.  Get Full Table Top 10 out of 131 pathways in order of significance.

Pathway.Name Avg.Num.Perturbations
HIF-1-alpha transcription factor network 126
FOXM1 transcription factor network 104
Syndecan-4-mediated signaling events 95
Angiopoietin receptor Tie2-mediated signaling 81
Endothelins 79
TCGA08_p53 71
HIF-2-alpha transcription factor network 68
TCGA08_rtk_signaling 68
Thromboxane A2 receptor signaling 67
PDGFR-alpha signaling pathway 67
Results

The following list describes the columns found in Table 2.

  • Pathway.Name = Full pathway name of curated PARADIGM pathway

  • Avg.Num.Perturbations = Average number of samples with perturbations across the pathway concepts determined by a background permutation model (>2 standard deviations away from the permuted distribution)

  • Total.Perturbations = Total number of perturbed concepts across all samples (>2 standard deviations away from the permuted distribution)

  • Num.Entities = Number of concepts that belong to the pathway

  • Min.Mean.Truth = Minimum IPL for concepts in the pathway among real samples

  • Max.Mean.Truth = Maximum IPL for concepts in the pathway among real samples

  • Min.Mean.Within = Minimum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Max.Mean.Within = Maximum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Min.Mean.Any = Minimum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes)

  • Max.Mean.Any = Maximum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes).

Table 2.  Get Full Table This summary table provides a report of cancer type specific pathway perturbations. Click on the links in the first column to display more detailed results for each pathway.

Pathway.Name Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
HIF-1-alpha transcription factor network 126 9581 76 -0.084 0.105 1000 -1000 -0.01 -1000
FOXM1 transcription factor network 104 5308 51 -0.316 0.055 1000 -1000 -0.053 -1000
Syndecan-4-mediated signaling events 95 6374 67 -0.143 0.036 1000 -1000 -0.031 -1000
Angiopoietin receptor Tie2-mediated signaling 81 7146 88 -0.285 0.051 1000 -1000 -0.052 -1000
Endothelins 79 7662 96 -0.138 0.035 1000 -1000 -0.021 -1000
TCGA08_p53 71 500 7 -0.002 0.032 1000 -1000 -0.01 -1000
HIF-2-alpha transcription factor network 68 2943 43 -0.066 0.046 1000 -1000 -0.044 -1000
TCGA08_rtk_signaling 68 1788 26 -0.026 0.087 1000 -1000 -0.004 -1000
Thromboxane A2 receptor signaling 67 7137 105 -0.061 0.043 1000 -1000 -0.026 -1000
PDGFR-alpha signaling pathway 67 2964 44 -0.093 0.036 1000 -1000 -0.026 -1000
EGFR-dependent Endothelin signaling events 67 1418 21 -0.004 0.093 1000 -1000 -0.01 -1000
Effects of Botulinum toxin 65 1698 26 -0.008 0.05 1000 -1000 -0.01 -1000
PLK2 and PLK4 events 63 189 3 -0.018 0.035 1000 -1000 -0.018 -1000
Arf6 signaling events 62 3852 62 -0.004 0.092 1000 -1000 -0.005 -1000
Wnt signaling 62 434 7 -0.006 0.036 1000 -1000 -0.003 -1000
Syndecan-3-mediated signaling events 61 2146 35 -0.073 0.076 1000 -1000 -0.023 -1000
Canonical Wnt signaling pathway 61 3139 51 -0.1 0.068 1000 -1000 -0.028 -1000
Ras signaling in the CD4+ TCR pathway 60 1027 17 -0.001 0.041 1000 -1000 -0.006 -1000
Ceramide signaling pathway 59 4541 76 -0.084 0.07 1000 -1000 -0.019 -1000
LPA receptor mediated events 58 5926 102 -0.124 0.036 1000 -1000 -0.037 -1000
TCGA08_retinoblastoma 58 467 8 -0.046 0.054 1000 -1000 -0.004 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 57 1904 33 -0.049 0.066 1000 -1000 -0.012 -1000
Syndecan-1-mediated signaling events 56 1933 34 -0.009 0.035 1000 -1000 -0.017 -1000
Nongenotropic Androgen signaling 54 2830 52 -0.086 0.059 1000 -1000 -0.023 -1000
Glypican 2 network 51 206 4 0 0.006 1000 -1000 0 -1000
Syndecan-2-mediated signaling events 50 3481 69 -0.026 0.037 1000 -1000 -0.021 -1000
JNK signaling in the CD4+ TCR pathway 49 834 17 -0.135 0.061 1000 -1000 -0.005 -1000
EPO signaling pathway 49 2705 55 -0.001 0.083 1000 -1000 -0.013 -1000
amb2 Integrin signaling 49 4084 82 -0.018 0.076 1000 -1000 -0.014 -1000
IL2 signaling events mediated by STAT5 49 1081 22 -0.071 0.042 1000 -1000 -0.021 -1000
Fc-epsilon receptor I signaling in mast cells 48 4729 97 -0.122 0.047 1000 -1000 -0.048 -1000
S1P5 pathway 48 828 17 -0.014 0.035 1000 -1000 -0.009 -1000
IL23-mediated signaling events 47 2865 60 -0.052 0.152 1000 -1000 -0.032 -1000
S1P4 pathway 47 1186 25 -0.016 0.035 1000 -1000 -0.008 -1000
FoxO family signaling 46 2967 64 -0.162 0.042 1000 -1000 -0.016 -1000
Osteopontin-mediated events 45 1718 38 -0.065 0.049 1000 -1000 -0.021 -1000
Presenilin action in Notch and Wnt signaling 43 2625 61 -0.08 0.076 1000 -1000 -0.037 -1000
Ephrin B reverse signaling 43 2089 48 -0.065 0.065 1000 -1000 -0.045 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 43 2976 68 -0.1 0.045 1000 -1000 -0.027 -1000
BCR signaling pathway 41 4144 99 -0.048 0.049 1000 -1000 -0.023 -1000
Noncanonical Wnt signaling pathway 40 1056 26 -0.038 0.036 1000 -1000 -0.029 -1000
IL2 signaling events mediated by PI3K 40 2377 58 -0.067 0.037 1000 -1000 -0.019 -1000
EPHB forward signaling 40 3453 85 -0.051 0.08 1000 -1000 -0.041 -1000
Signaling events mediated by VEGFR1 and VEGFR2 40 5062 125 -0.044 0.058 1000 -1000 -0.037 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 39 2146 54 -0.031 0.068 1000 -1000 -0.029 -1000
Reelin signaling pathway 39 2230 56 -0.014 0.065 1000 -1000 -0.014 -1000
E-cadherin signaling in keratinocytes 39 1702 43 -0.035 0.061 1000 -1000 -0.015 -1000
ErbB2/ErbB3 signaling events 38 2519 65 -0.039 0.036 1000 -1000 -0.039 -1000
Regulation of nuclear SMAD2/3 signaling 38 5292 136 -0.199 0.196 1000 -1000 -0.037 -1000
IL12-mediated signaling events 38 3324 87 -0.098 0.099 1000 -1000 -0.021 -1000
Signaling events mediated by PTP1B 38 2930 76 -0.033 0.058 1000 -1000 -0.02 -1000
Glypican 1 network 38 1826 48 -0.036 0.05 1000 -1000 -0.033 -1000
Paxillin-dependent events mediated by a4b1 38 1380 36 -0.058 0.055 1000 -1000 -0.045 -1000
Arf6 downstream pathway 37 1613 43 -0.027 0.051 1000 -1000 -0.029 -1000
mTOR signaling pathway 37 1969 53 -0.028 0.045 1000 -1000 -0.02 -1000
Class I PI3K signaling events 37 2763 73 -0.051 0.056 1000 -1000 -0.017 -1000
Sphingosine 1-phosphate (S1P) pathway 36 1026 28 -0.019 0.035 1000 -1000 -0.019 -1000
BMP receptor signaling 36 2981 81 -0.026 0.056 1000 -1000 -0.009 -1000
Paxillin-independent events mediated by a4b1 and a4b7 36 1361 37 -0.034 0.078 1000 -1000 -0.017 -1000
IL1-mediated signaling events 36 2247 62 -0.039 0.073 1000 -1000 -0.034 -1000
Stabilization and expansion of the E-cadherin adherens junction 36 2667 74 -0.11 0.079 1000 -1000 -0.047 -1000
p38 MAPK signaling pathway 36 1609 44 0 0.041 1000 -1000 -0.006 -1000
IFN-gamma pathway 35 2437 68 -0.037 0.065 1000 -1000 -0.034 -1000
Class I PI3K signaling events mediated by Akt 35 2385 68 -0.033 0.061 1000 -1000 -0.019 -1000
IL6-mediated signaling events 35 2653 75 -0.066 0.096 1000 -1000 -0.027 -1000
IGF1 pathway 35 2041 57 -0.043 0.065 1000 -1000 -0.029 -1000
PLK1 signaling events 34 2960 85 -0.043 0.056 1000 -1000 -0.016 -1000
FAS signaling pathway (CD95) 34 1624 47 -0.143 0.047 1000 -1000 -0.03 -1000
Neurotrophic factor-mediated Trk receptor signaling 34 4158 120 -0.037 0.087 1000 -1000 -0.024 -1000
Hedgehog signaling events mediated by Gli proteins 33 2190 65 -0.025 0.058 1000 -1000 -0.025 -1000
S1P1 pathway 33 1218 36 -0.011 0.049 1000 -1000 -0.016 -1000
Plasma membrane estrogen receptor signaling 33 2915 86 -0.069 0.057 1000 -1000 -0.024 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 32 2754 85 -0.11 0.122 1000 -1000 -0.027 -1000
Regulation of p38-alpha and p38-beta 32 1775 54 -0.008 0.049 1000 -1000 -0.011 -1000
PDGFR-beta signaling pathway 32 3136 97 -0.053 0.067 1000 -1000 -0.041 -1000
Signaling events mediated by PRL 32 1099 34 -0.035 0.047 1000 -1000 -0.022 -1000
ErbB4 signaling events 31 2183 69 -0.081 0.059 1000 -1000 -0.019 -1000
TCR signaling in naïve CD8+ T cells 31 2971 93 -0.273 0.315 1000 -1000 -0.026 -1000
IL4-mediated signaling events 30 2801 91 -0.312 0.059 1000 -1000 -0.046 -1000
Retinoic acid receptors-mediated signaling 30 1762 58 -0.059 0.059 1000 -1000 -0.022 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 30 1371 45 -0.029 0.074 1000 -1000 -0.022 -1000
Caspase cascade in apoptosis 29 2198 74 -0.072 0.056 1000 -1000 -0.024 -1000
p75(NTR)-mediated signaling 29 3699 125 -0.025 0.083 1000 -1000 -0.041 -1000
Signaling events regulated by Ret tyrosine kinase 29 2426 82 -0.052 0.061 1000 -1000 -0.024 -1000
Signaling mediated by p38-gamma and p38-delta 29 449 15 -0.024 0.035 1000 -1000 -0.018 -1000
E-cadherin signaling in the nascent adherens junction 29 2277 76 -0.039 0.089 1000 -1000 -0.036 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 29 2321 78 -0.023 0.072 1000 -1000 -0.028 -1000
Alternative NF-kappaB pathway 29 380 13 0 0.067 1000 -1000 0 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 28 652 23 -0.017 0.053 1000 -1000 -0.009 -1000
Visual signal transduction: Cones 28 1068 38 -0.013 0.058 1000 -1000 -0.01 -1000
a4b1 and a4b7 Integrin signaling 28 140 5 0.027 0.052 1000 -1000 0.032 -1000
Signaling events mediated by HDAC Class III 28 1134 40 -0.05 0.05 1000 -1000 -0.049 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 28 2331 83 -0.034 0.066 1000 -1000 -0.015 -1000
Insulin Pathway 28 2092 74 -0.034 0.08 1000 -1000 -0.03 -1000
LPA4-mediated signaling events 27 330 12 -0.017 0.015 1000 -1000 -0.015 -1000
Aurora A signaling 27 1644 60 -0.026 0.057 1000 -1000 -0.018 -1000
S1P3 pathway 27 1135 42 -0.021 0.036 1000 -1000 -0.025 -1000
Integrins in angiogenesis 26 2253 84 -0.043 0.069 1000 -1000 -0.019 -1000
Aurora B signaling 26 1777 67 -0.033 0.062 1000 -1000 -0.021 -1000
Nectin adhesion pathway 25 1580 63 -0.01 0.08 1000 -1000 -0.024 -1000
Calcium signaling in the CD4+ TCR pathway 25 775 31 -0.022 0.081 1000 -1000 -0.024 -1000
Glucocorticoid receptor regulatory network 24 2753 114 -0.129 0.059 1000 -1000 -0.041 -1000
Regulation of Telomerase 24 2535 102 -0.025 0.076 1000 -1000 -0.036 -1000
BARD1 signaling events 23 1367 57 -0.062 0.081 1000 -1000 -0.056 -1000
Circadian rhythm pathway 23 526 22 -0.009 0.053 1000 -1000 -0.015 -1000
Signaling events mediated by HDAC Class I 23 2406 104 -0.028 0.066 1000 -1000 -0.024 -1000
TRAIL signaling pathway 22 1070 48 -0.023 0.085 1000 -1000 -0.02 -1000
E-cadherin signaling events 22 112 5 0.032 0.061 1000 -1000 0.032 -1000
Insulin-mediated glucose transport 21 676 32 -0.018 0.041 1000 -1000 -0.018 -1000
RXR and RAR heterodimerization with other nuclear receptor 21 1131 52 -0.044 0.103 1000 -1000 -0.017 -1000
Atypical NF-kappaB pathway 19 597 31 -0.021 0.036 1000 -1000 -0.018 -1000
IL27-mediated signaling events 19 1016 51 -0.011 0.05 1000 -1000 -0.031 -1000
Signaling events mediated by HDAC Class II 18 1404 75 -0.029 0.092 1000 -1000 -0.024 -1000
Cellular roles of Anthrax toxin 18 718 39 -0.073 0.036 1000 -1000 -0.015 -1000
Signaling mediated by p38-alpha and p38-beta 18 816 44 -0.013 0.075 1000 -1000 -0.014 -1000
ceramide signaling pathway 17 868 49 -0.012 0.052 1000 -1000 -0.02 -1000
Arf6 trafficking events 17 1218 71 -0.038 0.046 1000 -1000 -0.031 -1000
VEGFR1 specific signals 17 955 56 -0.027 0.04 1000 -1000 -0.021 -1000
Canonical NF-kappaB pathway 16 644 39 -0.031 0.064 1000 -1000 -0.015 -1000
Regulation of Androgen receptor activity 16 1160 70 -0.029 0.066 1000 -1000 -0.03 -1000
Sumoylation by RanBP2 regulates transcriptional repression 15 423 27 -0.032 0.074 1000 -1000 -0.027 -1000
Rapid glucocorticoid signaling 15 319 20 -0.011 0.035 1000 -1000 -0.01 -1000
Arf1 pathway 15 863 54 -0.06 0.044 1000 -1000 -0.011 -1000
Nephrin/Neph1 signaling in the kidney podocyte 14 490 34 -0.053 0.093 1000 -1000 -0.038 -1000
Aurora C signaling 14 102 7 0 0.059 1000 -1000 -0.009 -1000
Signaling events mediated by the Hedgehog family 13 724 52 -0.017 0.078 1000 -1000 -0.021 -1000
Coregulation of Androgen receptor activity 10 799 76 -0.018 0.065 1000 -1000 -0.03 -1000
FOXA2 and FOXA3 transcription factor networks 9 454 46 0 0.099 1000 -1000 -0.046 -1000
Visual signal transduction: Rods 8 426 52 -0.032 0.083 1000 -1000 -0.008 -1000
Class IB PI3K non-lipid kinase events 8 24 3 -0.036 0.036 1000 -1000 -0.033 -1000
Ephrin A reverse signaling 1 13 7 -0.019 0.048 1000 -1000 -0.01 -1000
Total 4924 276661 7203 -6.74617610622 8.26082481898 131000 -131000 -2.94462323897 -131000
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 0.036 0.468 0.614 88 -0.758 82 170
HDAC7 -0.001 0.005 -9999 0 -0.043 5 5
HIF1A/ARNT/Cbp/p300/Src-1 -0.03 0.383 0.573 33 -0.716 68 101
SMAD4 0.033 0.013 0.079 11 -9999 0 11
ID2 0.058 0.482 0.615 114 -0.751 82 196
AP1 0.013 0.082 -9999 0 -0.169 73 73
ABCG2 0.022 0.472 0.612 98 -0.754 85 183
HIF1A 0.045 0.129 0.23 84 -0.16 62 146
TFF3 0.051 0.471 0.615 108 -0.75 80 188
GATA2 0.038 0.013 0.074 24 -0.076 2 26
AKT1 0.053 0.137 0.245 90 -0.203 38 128
response to hypoxia 0.009 0.087 0.166 71 -0.13 37 108
MCL1 0.063 0.48 0.632 102 -0.753 81 183
NDRG1 0.003 0.459 0.613 74 -0.756 87 161
SERPINE1 -0.057 0.399 0.564 46 -0.771 79 125
FECH 0.049 0.474 0.615 107 -0.751 81 188
FURIN 0.063 0.481 0.615 115 -0.753 81 196
NCOA2 0.037 0.005 -9999 0 0 9 9
EP300 0.074 0.191 0.366 92 -0.306 33 125
HMOX1 -0.015 0.458 0.607 75 -0.778 85 160
BHLHE40 -0.056 0.406 0.541 72 -0.734 84 156
BHLHE41 -0.056 0.406 0.541 72 -0.734 84 156
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.071 0.178 0.35 47 -0.234 36 83
ENG 0.037 0.156 0.29 66 -0.251 20 86
JUN 0.035 0.013 0.063 1 -0.002 41 42
RORA 0.032 0.469 0.625 88 -0.753 83 171
ABCB1 -0.056 0.215 -9999 0 -0.863 26 26
TFRC 0.04 0.476 0.632 93 -0.751 84 177
CXCR4 0.022 0.473 0.625 85 -0.765 86 171
TF -0.072 0.414 0.627 47 -0.746 88 135
CITED2 0.021 0.463 0.606 90 -0.76 82 172
HIF1A/ARNT -0.084 0.442 0.651 11 -0.883 73 84
LDHA -0.066 0.279 -9999 0 -0.993 37 37
ETS1 0.065 0.481 0.617 115 -0.76 79 194
PGK1 0.057 0.487 0.629 104 -0.773 81 185
NOS2 -0.056 0.406 0.541 72 -0.734 84 156
ITGB2 0.012 0.465 0.603 89 -0.763 85 174
ALDOA 0.067 0.485 0.631 107 -0.752 82 189
Cbp/p300/CITED2 -0.026 0.454 0.605 61 -0.815 79 140
FOS 0.026 0.018 -9999 0 0 148 148
HK2 0.066 0.485 0.617 117 -0.753 82 199
SP1 0.033 0.057 0.105 33 -0.144 37 70
GCK 0.105 0.249 0.606 38 -0.629 2 40
HK1 0.016 0.459 0.632 81 -0.757 81 162
NPM1 0.062 0.48 0.615 115 -0.756 80 195
EGLN1 0.059 0.478 0.614 111 -0.759 80 191
CREB1 0.031 0.035 -9999 0 -0.103 29 29
PGM1 0.061 0.484 0.619 114 -0.755 82 196
SMAD3 0.037 0.008 0.081 11 -9999 0 11
EDN1 0.056 0.221 0.46 32 -0.525 21 53
IGFBP1 0.002 0.428 0.602 75 -0.749 75 150
VEGFA -0.018 0.339 0.485 73 -0.587 77 150
HIF1A/JAB1 0.045 0.104 0.196 58 -0.165 25 83
CP -0.027 0.448 0.614 66 -0.764 87 153
CXCL12 -0.032 0.416 0.61 50 -0.757 78 128
COPS5 0.036 0.006 -9999 0 0 12 12
SMAD3/SMAD4 0.04 0.05 0.139 5 -0.142 30 35
BNIP3 -0.006 0.45 0.645 71 -0.759 81 152
EGLN3 0.012 0.454 0.605 86 -0.749 82 168
CA9 -0.011 0.432 0.606 62 -0.756 79 141
TERT 0.059 0.48 0.634 103 -0.753 81 184
ENO1 0.057 0.482 0.635 104 -0.763 80 184
PFKL 0.064 0.483 0.634 105 -0.755 81 186
NCOA1 0.033 0.01 -9999 0 0 43 43
ADM -0.015 0.46 0.606 78 -0.764 88 166
ARNT 0.049 0.125 0.236 79 -0.141 57 136
HNF4A 0.038 0.009 -9999 0 -9999 0 0
ADFP -0.024 0.444 0.595 70 -0.77 84 154
SLC2A1 0.017 0.374 0.543 70 -0.618 75 145
LEP 0.024 0.443 0.635 77 -0.756 73 150
HIF1A/ARNT/Cbp/p300 -0.047 0.377 0.573 28 -0.723 69 97
EPO 0.032 0.322 0.552 56 -0.581 45 101
CREBBP 0.081 0.183 0.363 95 -0.264 30 125
HIF1A/ARNT/Cbp/p300/HDAC7 -0.05 0.367 0.54 28 -0.709 70 98
PFKFB3 0.015 0.46 0.616 92 -0.751 83 175
NT5E -0.017 0.45 0.628 68 -0.754 87 155
FOXM1 transcription factor network

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
NFATC3 -0.091 0.651 0.988 29 -1.211 93 122
PLK1 0.052 0.163 0.605 12 -0.758 8 20
BIRC5 -0.072 0.439 0.639 12 -1.228 57 69
HSPA1B -0.091 0.649 0.904 36 -1.181 99 135
MAP2K1 0.045 0.1 0.234 58 -9999 0 58
BRCA2 -0.086 0.657 1.023 30 -1.198 95 125
FOXM1 -0.237 0.967 1.098 32 -1.88 99 131
XRCC1 -0.082 0.66 1.01 31 -1.201 95 126
FOXM1B/p19 -0.316 0.569 -9999 0 -1.376 96 96
Cyclin D1/CDK4 -0.109 0.583 0.818 31 -1.081 99 130
CDC2 -0.109 0.724 1.06 34 -1.306 102 136
TGFA -0.069 0.577 0.837 39 -1.021 98 137
SKP2 -0.089 0.655 0.993 31 -1.195 96 127
CCNE1 0.023 0.036 0.096 21 -0.034 106 127
CKS1B -0.097 0.675 1.017 31 -1.212 101 132
RB1 -0.077 0.369 0.506 15 -1.003 48 63
FOXM1C/SP1 -0.183 0.745 0.874 21 -1.462 101 122
AURKB 0.055 0.15 0.665 10 -1.004 3 13
CENPF -0.113 0.702 1.04 32 -1.239 108 140
CDK4 0.025 0.051 0.146 29 -9999 0 29
MYC -0.109 0.561 0.774 34 -1.009 105 139
CHEK2 0.034 0.087 0.205 49 -9999 0 49
ONECUT1 -0.09 0.632 0.859 40 -1.137 101 141
CDKN2A 0.004 0.015 -9999 0 -0.097 3 3
LAMA4 -0.094 0.654 0.971 30 -1.215 94 124
FOXM1B/HNF6 -0.168 0.766 0.902 33 -1.476 101 134
FOS -0.144 0.701 0.985 30 -1.188 124 154
SP1 0.033 0.019 0.069 1 -0.044 23 24
CDC25B -0.096 0.668 0.96 31 -1.239 96 127
response to radiation 0.023 0.066 0.138 78 -9999 0 78
CENPB -0.085 0.664 0.946 36 -1.221 94 130
CENPA -0.094 0.663 1.03 29 -1.227 94 123
NEK2 -0.084 0.661 1.055 30 -1.189 97 127
HIST1H2BA -0.091 0.649 0.904 36 -1.181 99 135
CCNA2 0.022 0.031 0.09 5 -0.033 74 79
EP300 0.033 0.011 -9999 0 0 49 49
CCNB1/CDK1 -0.189 0.834 1.099 28 -1.595 104 132
CCNB2 -0.11 0.689 0.994 33 -1.288 96 129
CCNB1 -0.121 0.738 1.054 34 -1.342 103 137
ETV5 -0.125 0.686 0.969 32 -1.176 120 152
ESR1 -0.088 0.651 0.964 31 -1.19 97 128
CCND1 -0.107 0.606 0.856 37 -1.107 100 137
GSK3A 0.037 0.082 0.192 55 -9999 0 55
Cyclin A-E1/CDK1-2 0.045 0.1 0.24 23 -0.162 40 63
CDK2 0.024 0.036 0.097 16 -0.034 114 130
G2/M transition of mitotic cell cycle 0.027 0.081 0.167 78 -9999 0 78
FOXM1B/Cbp/p300 -0.163 0.681 0.781 17 -1.352 99 116
GAS1 -0.093 0.668 0.989 33 -1.209 97 130
MMP2 -0.119 0.692 0.959 34 -1.225 111 145
RB1/FOXM1C -0.154 0.603 0.83 25 -1.193 97 122
CREBBP 0.036 0.004 -9999 0 -9999 0 0
Syndecan-4-mediated signaling events

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
PTK2 -0.031 0.158 -9999 0 -0.459 41 41
Syndecan-4/Syndesmos -0.136 0.273 -9999 0 -0.433 171 171
positive regulation of JNK cascade -0.128 0.252 -9999 0 -0.423 159 159
Syndecan-4/ADAM12 -0.13 0.278 -9999 0 -0.437 169 169
CCL5 0.032 0.011 -9999 0 0 50 50
Rac1/GDP 0.018 0.02 -9999 0 -0.132 6 6
DNM2 0.034 0.009 -9999 0 0 34 34
ITGA5 0.032 0.012 -9999 0 0 56 56
SDCBP 0.035 0.007 -9999 0 0 21 21
PLG 0.03 0.02 -9999 0 -0.043 23 23
ADAM12 0.024 0.017 -9999 0 0 169 169
mol:GTP 0 0 -9999 0 -9999 0 0
NUDT16L1 0 0 -9999 0 -9999 0 0
mol:PI-4-5-P2 0 0 -9999 0 -9999 0 0
Syndecan-4/PKC alpha -0.024 0.022 -9999 0 -9999 0 0
Syndecan-4/Laminin alpha1 -0.136 0.273 -9999 0 -0.433 171 171
Syndecan-4/CXCL12/CXCR4 -0.137 0.273 -9999 0 -0.452 159 159
Syndecan-4/Laminin alpha3 -0.122 0.282 -9999 0 -0.444 162 162
MDK 0.029 0.014 -9999 0 0 94 94
Syndecan-4/FZD7 -0.136 0.29 -9999 0 -0.467 162 162
Syndecan-4/Midkine -0.13 0.289 -9999 0 -0.453 169 169
FZD7 0.026 0.016 -9999 0 0 135 135
Syndecan-4/FGFR1/FGF -0.099 0.274 -9999 0 -0.424 159 159
THBS1 0.029 0.014 -9999 0 0 90 90
integrin-mediated signaling pathway -0.126 0.272 -9999 0 -0.436 166 166
positive regulation of MAPKKK cascade -0.128 0.252 -9999 0 -0.423 159 159
Syndecan-4/TACI -0.121 0.286 -9999 0 -0.439 170 170
CXCR4 0.029 0.015 -9999 0 0 97 97
cell adhesion -0.011 0.057 0.206 3 -0.237 20 23
Syndecan-4/Dynamin -0.12 0.278 -9999 0 -0.439 164 164
Syndecan-4/TSP1 -0.131 0.277 -9999 0 -0.442 164 164
Syndecan-4/GIPC -0.12 0.28 -9999 0 -0.44 164 164
Syndecan-4/RANTES -0.128 0.281 -9999 0 -0.442 166 166
ITGB1 0.027 0.016 -9999 0 0 118 118
LAMA1 0 0 -9999 0 -9999 0 0
LAMA3 0.033 0.011 -9999 0 0 45 45
RAC1 0.027 0.016 -9999 0 0 123 123
PRKCA 0 0.103 0.961 5 -9999 0 5
Syndecan-4/alpha-Actinin -0.13 0.288 -9999 0 -0.459 164 164
TFPI 0.029 0.015 -9999 0 0 97 97
F2 0.01 0.04 -9999 0 -0.042 174 174
alpha5/beta1 Integrin 0.03 0.043 -9999 0 -0.139 20 20
positive regulation of cell adhesion -0.127 0.266 -9999 0 -0.429 162 162
ACTN1 0.028 0.015 -9999 0 0 106 106
TNC 0.027 0.016 -9999 0 0 117 117
Syndecan-4/CXCL12 -0.135 0.272 -9999 0 -0.443 161 161
FGF6 0.034 0.009 -9999 0 0 34 34
RHOA 0.035 0.007 -9999 0 0 21 21
CXCL12 0.022 0.018 -9999 0 0 195 195
TNFRSF13B 0.036 0.005 -9999 0 0 8 8
FGF2 0.034 0.008 -9999 0 0 25 25
FGFR1 0.035 0.005 -9999 0 0 11 11
Syndecan-4/PI-4-5-P2 -0.136 0.273 -9999 0 -0.433 171 171
mol:GDP 0 0 -9999 0 -9999 0 0
FN1 0.031 0.019 -9999 0 -0.042 24 24
cell migration -0.01 0.015 -9999 0 -9999 0 0
PRKCD 0.031 0.02 -9999 0 -0.043 21 21
vasculogenesis -0.125 0.263 -9999 0 -0.422 164 164
SDC4 -0.143 0.296 -9999 0 -0.459 173 173
Syndecan-4/Tenascin C -0.133 0.288 -9999 0 -0.458 165 165
Syndecan-4/PI-4-5-P2/PKC alpha -0.019 0.018 -9999 0 -9999 0 0
Syndecan-4/Syntenin -0.123 0.287 -9999 0 -0.442 169 169
MMP9 0.012 0.024 -9999 0 -0.042 39 39
Rac1/GTP -0.012 0.058 0.207 3 -0.242 20 23
cytoskeleton organization -0.129 0.259 -9999 0 -0.414 171 171
GIPC1 0.034 0.009 -9999 0 0 30 30
Syndecan-4/TFPI -0.13 0.283 -9999 0 -0.447 165 165
Angiopoietin receptor Tie2-mediated 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
AKT1 -0.224 0.409 -9999 0 -0.832 132 132
NCK1/PAK1/Dok-R -0.122 0.168 -9999 0 -0.387 122 122
NCK1/Dok-R -0.13 0.352 -9999 0 -0.857 89 89
PIK3CA 0.03 0.014 -9999 0 0 85 85
mol:beta2-estradiol 0.029 0.096 0.226 89 -0.081 1 90
RELA 0.035 0.005 -9999 0 0 10 10
SHC1 0.032 0.011 -9999 0 0 48 48
Rac/GDP 0.018 0.02 -9999 0 -0.132 6 6
F2 0.051 0.111 0.274 82 -0.089 62 144
TNIP2 0.035 0.006 -9999 0 0 13 13
NF kappa B/RelA -0.107 0.354 -9999 0 -0.829 89 89
FN1 0.034 0.009 -9999 0 0 29 29
PLD2 -0.145 0.358 -9999 0 -0.89 89 89
PTPN11 0.036 0.005 -9999 0 0 9 9
GRB14 0.031 0.013 -9999 0 0 67 67
ELK1 -0.138 0.33 -9999 0 -0.821 89 89
GRB7 0.035 0.006 -9999 0 0 13 13
PAK1 0.035 0.007 -9999 0 0 17 17
Tie2/Ang1/alpha5/beta1 Integrin -0.129 0.36 -9999 0 -0.865 89 89
CDKN1A -0.188 0.356 -9999 0 -0.699 136 136
ITGA5 0.032 0.012 -9999 0 0 56 56
mol:GTP 0 0 -9999 0 -9999 0 0
RasGAP/Dok-R -0.134 0.354 -9999 0 -0.863 89 89
CRK 0.035 0.008 -9999 0 0 23 23
mol:NO -0.131 0.32 0.404 4 -0.597 130 134
PLG -0.146 0.357 -9999 0 -0.889 89 89
mol:GDP 0 0 -9999 0 -9999 0 0
chemokinesis -0.172 0.363 -9999 0 -0.757 116 116
GRB2 0.035 0.006 -9999 0 0 16 16
PIK3R1 0.031 0.012 -9999 0 0 61 61
ANGPT2 -0.223 0.453 -9999 0 -1.064 98 98
BMX -0.145 0.358 -9999 0 -0.889 89 89
ANGPT1 -0.157 0.422 -9999 0 -1.036 89 89
tube development -0.206 0.361 -9999 0 -0.706 152 152
ANGPT4 0.023 0.028 -9999 0 -0.034 89 89
response to hypoxia -0.012 0.026 0.034 1 -0.063 89 90
Tie2/Ang1/GRB14 -0.136 0.367 -9999 0 -0.895 89 89
alpha5/beta1 Integrin 0.03 0.043 -9999 0 -0.139 20 20
FGF2 0.035 0.016 -9999 0 -0.011 41 41
STAT5A (dimer) -0.231 0.446 -9999 0 -0.829 156 156
mol:L-citrulline -0.131 0.32 0.404 4 -0.597 130 134
AGTR1 0.021 0.034 -9999 0 -0.047 88 88
MAPK14 -0.151 0.373 -9999 0 -0.9 90 90
Tie2/SHP2 -0.071 0.231 -9999 0 -0.824 29 29
TEK -0.082 0.241 -9999 0 -0.951 26 26
RPS6KB1 -0.199 0.374 -9999 0 -0.774 127 127
Angiotensin II/AT1 0.014 0.036 -9999 0 -0.061 64 64
Tie2/Ang1/GRB2 -0.136 0.372 -9999 0 -0.905 89 89
MAPK3 -0.146 0.335 -9999 0 -0.841 89 89
MAPK1 -0.144 0.334 -9999 0 -0.838 89 89
Tie2/Ang1/GRB7 -0.135 0.373 -9999 0 -0.907 89 89
NFKB1 0.035 0.007 -9999 0 0 17 17
MAPK8 -0.148 0.354 -9999 0 -0.887 89 89
PI3K -0.235 0.438 -9999 0 -0.915 125 125
FES -0.153 0.375 -9999 0 -0.905 90 90
Crk/Dok-R -0.132 0.355 -9999 0 -0.864 89 89
Tie2/Ang1/ABIN2 -0.136 0.373 -9999 0 -0.906 89 89
blood circulation 0 0 -9999 0 -9999 0 0
negative regulation of caspase activity -0.197 0.366 -9999 0 -0.735 135 135
STAT5A 0.036 0.004 -9999 0 0 6 6
mol:ROS 0 0 -9999 0 -9999 0 0
PTK2 -0.199 0.373 -9999 0 -0.775 126 126
Tie2/Ang2 -0.285 0.507 -9999 0 -0.99 148 148
Tie2/Ang1 -0.147 0.378 -9999 0 -0.934 89 89
FOXO1 -0.217 0.392 -9999 0 -0.751 156 156
ELF1 0.028 0.036 0.105 1 -0.045 76 77
ELF2 -0.135 0.352 -9999 0 -0.867 89 89
mol:Choline -0.14 0.347 -9999 0 -0.862 89 89
cell migration -0.065 0.097 -9999 0 -0.216 125 125
FYN -0.242 0.414 -9999 0 -0.818 151 151
DOK2 0 0 -9999 0 -9999 0 0
negative regulation of cell cycle -0.164 0.322 -9999 0 -0.626 136 136
ETS1 0 0.117 -9999 0 -0.246 86 86
PXN -0.169 0.314 -9999 0 -0.65 126 126
ITGB1 0.027 0.016 -9999 0 0 118 118
NOS3 -0.159 0.355 0.421 3 -0.681 129 132
RAC1 0.027 0.016 -9999 0 0 123 123
TNF -0.001 0.117 -9999 0 -0.251 84 84
MAPKKK cascade -0.14 0.347 -9999 0 -0.862 89 89
RASA1 0.034 0.009 -9999 0 0 30 30
Tie2/Ang1/Shc -0.14 0.37 -9999 0 -0.904 89 89
NCK1 0.034 0.008 -9999 0 0 26 26
vasculogenesis -0.113 0.292 0.387 5 -0.536 130 135
mol:Phosphatidic acid -0.14 0.347 -9999 0 -0.862 89 89
mol:Angiotensin II -0.004 0.013 0.021 1 -0.032 72 73
mol:NADP -0.131 0.32 0.404 4 -0.597 130 134
Rac1/GTP -0.173 0.342 -9999 0 -0.714 120 120
MMP2 -0.146 0.363 -9999 0 -0.898 89 89
Endothelins

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
AKT1 -0.019 0.144 0.208 72 -0.26 82 154
PTK2B 0.035 0.006 -9999 0 0 15 15
mol:Ca2+ -0.097 0.25 0.387 1 -0.525 80 81
EDN1 0.004 0.09 0.152 5 -0.155 97 102
EDN3 0.034 0.009 -9999 0 0 30 30
EDN2 0.035 0.006 -9999 0 0 14 14
HRAS/GDP -0.007 0.175 0.292 24 -0.36 57 81
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.002 0.115 0.196 11 -0.236 62 73
ADCY4 -0.035 0.095 0.136 32 -0.199 91 123
ADCY5 -0.035 0.095 0.136 32 -0.199 91 123
ADCY6 -0.005 0.132 0.229 36 -0.237 56 92
ADCY7 -0.011 0.129 0.214 39 -0.24 59 98
ADCY1 0 0.118 0.223 34 -0.249 41 75
ADCY2 -0.005 0.132 0.227 38 -0.238 57 95
ADCY3 -0.035 0.095 0.136 32 -0.199 91 123
ADCY8 -0.008 0.126 0.219 39 -0.238 51 90
ADCY9 -0.007 0.132 0.225 36 -0.238 58 94
arachidonic acid secretion -0.069 0.262 0.321 30 -0.493 101 131
ETB receptor/Endothelin-1/Gq/GTP -0.006 0.106 0.177 11 -0.227 60 71
GNAO1 0.03 0.014 -9999 0 0 81 81
HRAS 0.034 0.009 -9999 0 0 32 32
ETA receptor/Endothelin-1/G12/GTP 0.003 0.123 -9999 0 -0.222 85 85
ETA receptor/Endothelin-1/Gs/GTP 0.005 0.121 -9999 0 -0.202 100 100
mol:GTP 0 0.006 0.024 3 -0.025 3 6
COL3A1 -0.074 0.152 0.189 8 -0.362 96 104
EDNRB 0.023 0.044 0.095 61 -0.082 45 106
response to oxidative stress 0 0 -9999 0 -9999 0 0
CYSLTR2 -0.017 0.141 0.211 69 -0.28 58 127
CYSLTR1 -0.038 0.116 0.18 32 -0.239 89 121
SLC9A1 -0.014 0.087 0.133 2 -0.189 64 66
mol:GDP -0.016 0.172 0.279 27 -0.369 56 83
SLC9A3 -0.116 0.286 -9999 0 -0.653 77 77
RAF1 -0.028 0.208 0.286 36 -0.401 83 119
JUN -0.138 0.329 0.469 1 -0.632 114 115
JAK2 -0.018 0.134 0.211 59 -0.253 76 135
mol:IP3 -0.006 0.116 0.208 17 -0.265 49 66
ETA receptor/Endothelin-1 -0.027 0.139 -9999 0 -0.268 106 106
PLCB1 0.033 0.012 -9999 0 -0.005 38 38
PLCB2 0.028 0.022 -9999 0 -0.022 75 75
ETA receptor/Endothelin-3 0.006 0.089 -9999 0 -0.145 103 103
FOS -0.086 0.354 0.382 24 -0.834 78 102
Gai/GDP -0.07 0.274 -9999 0 -0.736 64 64
CRK 0.035 0.008 -9999 0 0 23 23
mol:Ca ++ -0.018 0.173 0.257 54 -0.331 75 129
BCAR1 0 0 -9999 0 -9999 0 0
PRKCB1 -0.002 0.123 0.227 24 -0.277 46 70
GNAQ 0.027 0.026 -9999 0 -0.033 67 67
GNAZ 0.03 0.013 -9999 0 0 79 79
GNAL 0.035 0.006 -9999 0 0 13 13
Gs family/GDP -0.006 0.164 0.27 26 -0.345 54 80
ETA receptor/Endothelin-1/Gq/GTP -0.008 0.123 0.2 10 -0.256 65 75
MAPK14 -0.01 0.099 0.162 13 -0.251 42 55
TRPC6 -0.102 0.259 0.39 1 -0.549 79 80
GNAI2 0.033 0.01 -9999 0 0 42 42
GNAI3 0.035 0.006 -9999 0 0 12 12
GNAI1 0.018 0.018 -9999 0 0 245 245
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.004 0.102 0.173 15 -0.254 43 58
ETB receptor/Endothelin-2 0.018 0.071 -9999 0 -0.108 95 95
ETB receptor/Endothelin-3 0.016 0.07 -9999 0 -0.109 94 94
ETB receptor/Endothelin-1 -0.001 0.101 0.172 14 -0.16 111 125
MAPK3 -0.068 0.322 0.35 34 -0.722 80 114
MAPK1 -0.082 0.344 0.369 26 -0.772 81 107
Rac1/GDP -0.005 0.157 0.293 20 -0.364 45 65
cAMP biosynthetic process 0.017 0.121 0.222 44 -0.22 46 90
MAPK8 -0.131 0.307 0.339 3 -0.56 140 143
SRC 0.035 0.006 -9999 0 0 13 13
ETB receptor/Endothelin-1/Gi/GTP -0.035 0.14 0.153 6 -0.349 60 66
p130Cas/CRK/Src/PYK2 -0.016 0.184 0.325 22 -0.458 43 65
mol:K + 0 0 -9999 0 -9999 0 0
G12/GDP -0.009 0.162 0.295 18 -0.364 51 69
COL1A2 -0.053 0.169 0.218 1 -0.476 56 57
EntrezGene:2778 0 0 -9999 0 -9999 0 0
ETA receptor/Endothelin-2 0.007 0.089 -9999 0 -0.142 108 108
mol:DAG -0.006 0.116 0.208 17 -0.265 49 66
MAP2K2 -0.042 0.264 0.341 44 -0.555 78 122
MAP2K1 -0.056 0.264 0.315 30 -0.568 81 111
EDNRA -0.007 0.103 0.159 1 -0.194 92 93
positive regulation of muscle contraction 0.011 0.142 0.207 114 -0.236 63 177
Gq family/GDP 0.003 0.157 0.295 4 -0.337 56 60
HRAS/GTP -0.009 0.164 0.265 31 -0.339 58 89
PRKCH -0.007 0.118 0.232 17 -0.287 40 57
RAC1 0.027 0.016 -9999 0 0 123 123
PRKCA -0.011 0.121 0.211 18 -0.275 49 67
PRKCB -0.005 0.118 0.207 22 -0.267 48 70
PRKCE -0.011 0.12 0.21 17 -0.276 48 65
PRKCD -0.008 0.125 0.245 22 -0.279 47 69
PRKCG -0.01 0.121 0.211 19 -0.286 45 64
regulation of vascular smooth muscle contraction -0.112 0.418 0.439 15 -1.008 78 93
PRKCQ -0.003 0.111 0.241 18 -0.282 35 53
PLA2G4A -0.079 0.284 0.332 28 -0.539 101 129
GNA14 0.027 0.026 -9999 0 -0.033 67 67
GNA15 0.029 0.019 -9999 0 -0.034 23 23
GNA12 0.026 0.016 -9999 0 0 136 136
GNA11 0.031 0.017 -9999 0 -0.035 14 14
Rac1/GTP 0.007 0.117 -9999 0 -0.224 73 73
MMP1 0.02 0.073 0.197 26 -9999 0 26
TCGA08_p53

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
CDKN2A -0.002 0.004 0 417 -9999 0 417
TP53 0.004 0.036 -9999 0 -0.253 7 7
Senescence 0.003 0.038 -9999 0 -0.236 9 9
Apoptosis 0.003 0.038 -9999 0 -0.236 9 9
Activated_Oncogenes 0 0 -9999 0 -9999 0 0
MDM2 -0.002 0.005 -9999 0 -9999 0 0
MDM4 0.032 0.012 -9999 0 0 58 58
HIF-2-alpha transcription factor network

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
MMP14 -0.006 0.141 -9999 0 -0.646 20 20
oxygen homeostasis 0.005 0.021 0.045 68 -0.025 30 98
TCEB2 0.036 0.004 -9999 0 0 5 5
TCEB1 0.035 0.007 -9999 0 0 20 20
VHL/Elongin B/Elongin C/HIF2A 0.016 0.137 0.271 37 -0.237 42 79
EPO -0.032 0.202 0.399 20 -0.427 54 74
FIH (dimer) 0.018 0.039 0.108 19 -0.04 57 76
APEX1 0.017 0.041 0.101 8 -0.05 40 48
SERPINE1 -0.066 0.199 0.329 11 -0.452 74 85
FLT1 -0.007 0.144 -9999 0 -0.616 21 21
ADORA2A -0.023 0.232 0.415 42 -0.418 65 107
germ cell development -0.027 0.224 0.394 38 -0.411 67 105
SLC11A2 -0.02 0.243 0.435 39 -0.437 66 105
BHLHE40 -0.03 0.228 0.399 36 -0.424 67 103
HIF1AN 0.018 0.039 0.108 19 -0.04 57 76
HIF2A/ARNT/SIRT1 -0.007 0.159 0.322 23 -0.292 52 75
ETS1 0.046 0.032 0.117 42 -0.107 11 53
CITED2 -0.053 0.259 -9999 0 -0.858 41 41
KDR 0.002 0.159 -9999 0 -0.852 14 14
PGK1 -0.026 0.251 0.435 39 -0.447 72 111
SIRT1 0.026 0.017 -9999 0 0 143 143
response to hypoxia 0 0 -9999 0 -9999 0 0
HIF2A/ARNT -0.015 0.26 0.468 12 -0.477 67 79
EPAS1 0.007 0.132 0.274 48 -0.232 46 94
SP1 0.04 0.011 0.11 8 -9999 0 8
ABCG2 -0.033 0.251 0.44 36 -0.442 81 117
EFNA1 -0.028 0.238 0.413 35 -0.432 72 107
FXN -0.025 0.23 0.407 41 -0.417 67 108
POU5F1 -0.03 0.228 0.399 36 -0.424 67 103
neuron apoptosis 0.014 0.255 0.466 67 -0.461 12 79
EP300 0.033 0.011 -9999 0 0 49 49
EGLN3 0.02 0.039 0.11 16 -0.04 60 76
EGLN2 0.024 0.041 0.108 22 -0.04 50 72
EGLN1 0.025 0.041 0.109 21 -0.039 59 80
VHL/Elongin B/Elongin C 0.044 0.024 -9999 0 -0.115 9 9
VHL 0 0 -9999 0 -9999 0 0
ARNT 0.018 0.041 0.101 8 -0.048 50 58
SLC2A1 -0.046 0.221 0.38 30 -0.437 70 100
TWIST1 -0.063 0.201 0.358 16 -0.417 83 99
ELK1 0.037 0.036 0.112 30 -0.094 25 55
HIF2A/ARNT/Cbp/p300 0.013 0.185 0.369 32 -0.306 51 83
VEGFA -0.03 0.228 0.399 36 -0.424 67 103
CREBBP 0.036 0.004 -9999 0 0 5 5
TCGA08_rtk_signaling

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
PDGFRA 0.024 0.017 -9999 0 0 157 157
HRAS 0.034 0.009 -9999 0 0 32 32
EGFR 0.01 0.016 -9999 0 0 355 355
AKT 0.084 0.111 0.23 111 -0.169 12 123
FOXO3 0 0 -9999 0 -9999 0 0
AKT1 0.032 0.011 -9999 0 0 53 53
FOXO1 0 0 -9999 0 -9999 0 0
AKT3 0.035 0.007 -9999 0 0 21 21
FOXO4 0 0 -9999 0 -9999 0 0
MET 0.023 0.018 -9999 0 0 183 183
PIK3CA 0.03 0.014 -9999 0 0 85 85
PIK3CB 0.035 0.006 -9999 0 0 16 16
NRAS 0.032 0.012 -9999 0 0 58 58
PIK3CG 0.026 0.016 -9999 0 0 139 139
PIK3R3 0.035 0.006 -9999 0 0 14 14
PIK3R2 0.034 0.009 -9999 0 0 31 31
NF1 0.036 0.003 -9999 0 0 4 4
RAS -0.002 0.052 -9999 0 -0.242 10 10
ERBB2 0.036 0.004 -9999 0 0 5 5
proliferation/survival/translation -0.026 0.055 0.232 5 -0.188 19 24
PI3K 0.033 0.08 0.191 63 -0.156 11 74
PIK3R1 0.032 0.012 -9999 0 0 61 61
KRAS 0.033 0.01 -9999 0 0 37 37
FOXO 0.087 0.084 0.189 150 -9999 0 150
AKT2 0.034 0.008 -9999 0 0 26 26
PTEN 0.026 0.016 -9999 0 0 130 130
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.035 0.008 -9999 0 0 24 24
GNB1/GNG2 -0.045 0.076 -9999 0 -0.173 120 120
AKT1 -0.003 0.16 0.28 35 -0.304 35 70
EGF 0.034 0.008 -9999 0 0 24 24
mol:TXA2 0 0.001 0.003 1 -9999 0 1
FGR -0.007 0.08 0.257 30 -0.166 2 32
mol:Ca2+ 0.002 0.187 0.344 28 -0.281 91 119
LYN -0.007 0.083 0.254 33 -0.163 7 40
RhoA/GTP -0.004 0.08 0.152 24 -0.13 94 118
mol:PGI2 0 0 -9999 0 -9999 0 0
SYK -0.012 0.206 0.351 33 -0.323 112 145
GNG2 0 0 -9999 0 -9999 0 0
ARRB2 0.034 0.008 -9999 0 0 27 27
TP alpha/Gq family/GDP/G beta5/gamma2 0.003 0.075 -9999 0 -0.242 31 31
G beta5/gamma2 -0.052 0.101 -9999 0 -0.225 117 117
PRKCH -0.012 0.205 0.35 28 -0.324 112 140
DNM1 0.035 0.008 -9999 0 0 23 23
TXA2/TP beta/beta Arrestin3 0.017 0.019 -9999 0 -9999 0 0
mol:GTP 0.001 0.002 0.005 56 -9999 0 56
PTGDR 0.035 0.007 -9999 0 0 20 20
G12 family/GTP -0.042 0.146 -9999 0 -0.288 103 103
ADRBK1 0.035 0.006 -9999 0 0 14 14
ADRBK2 0.034 0.01 -9999 0 0 36 36
RhoA/GTP/ROCK1 0.043 0.027 -9999 0 -0.125 10 10
mol:GDP -0.01 0.14 0.43 16 -0.283 20 36
mol:NADP 0.027 0.016 -9999 0 0 118 118
RAB11A 0.035 0.006 -9999 0 0 16 16
PRKG1 0.027 0.016 -9999 0 0 124 124
mol:IP3 -0.009 0.219 0.367 28 -0.347 97 125
cell morphogenesis 0.043 0.027 -9999 0 -0.124 10 10
PLCB2 -0.032 0.271 0.43 17 -0.461 102 119
mol:cGMP 0 0.001 -9999 0 -9999 0 0
BLK -0.005 0.084 0.257 34 -9999 0 34
mol:PDG2 0 0 -9999 0 -9999 0 0
HCK -0.012 0.071 0.242 23 -0.17 8 31
RHOA 0.035 0.007 -9999 0 0 21 21
PTGIR 0.034 0.009 -9999 0 0 34 34
PRKCB1 -0.014 0.216 0.359 27 -0.347 106 133
GNAQ 0.034 0.009 -9999 0 0 31 31
mol:L-citrulline 0.027 0.016 -9999 0 0 118 118
TXA2/TXA2-R family -0.042 0.278 0.416 22 -0.476 118 140
LCK -0.005 0.084 0.253 35 -9999 0 35
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.035 0.043 0.188 11 -0.127 1 12
TXA2-R family/G12 family/GDP/G beta/gamma -0.026 0.159 -9999 0 -0.471 52 52
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.032 0.045 0.188 11 -0.127 1 12
MAPK14 0 0.151 0.281 38 -0.221 107 145
TGM2/GTP -0.012 0.236 0.399 21 -0.387 87 108
MAPK11 -0.002 0.15 0.284 37 -0.221 108 145
ARHGEF1 0.006 0.12 0.217 42 -0.175 98 140
GNAI2 0.033 0.01 -9999 0 0 42 42
JNK cascade -0.016 0.223 0.371 28 -0.355 117 145
RAB11/GDP 0.033 0.011 -9999 0 -0.011 24 24
ICAM1 0 0.179 0.312 39 -0.268 112 151
cAMP biosynthetic process -0.01 0.202 0.345 28 -0.325 86 114
Gq family/GTP/EBP50 0.011 0.055 0.247 6 -0.162 31 37
actin cytoskeleton reorganization 0.043 0.027 -9999 0 -0.124 10 10
SRC -0.011 0.073 0.232 28 -9999 0 28
GNB5 0.035 0.007 -9999 0 0 18 18
GNB1 0.033 0.01 -9999 0 0 37 37
EGF/EGFR -0.005 0.113 0.276 29 -0.229 36 65
VCAM1 -0.018 0.208 0.319 35 -0.333 125 160
TP beta/Gq family/GDP/G beta5/gamma2 0.003 0.075 -9999 0 -0.242 31 31
platelet activation -0.004 0.19 0.348 34 -0.285 107 141
PGI2/IP 0.025 0.007 -9999 0 -9999 0 0
PRKACA 0.014 0.023 -9999 0 -9999 0 0
Gq family/GDP/G beta5/gamma2 0.006 0.065 0.179 1 -0.207 31 32
TXA2/TP beta/beta Arrestin2 0.004 0.054 -9999 0 -0.297 10 10
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -9999 0 0
TBXA2R -0.002 0.02 -9999 0 -9999 0 0
mol:DAG -0.018 0.236 0.381 26 -0.381 115 141
EGFR 0.01 0.016 -9999 0 0 355 355
TXA2/TP alpha -0.024 0.256 0.429 18 -0.435 88 106
Gq family/GTP 0.009 0.045 0.198 11 -0.122 27 38
YES1 -0.007 0.084 0.255 33 -0.159 7 40
GNAI2/GTP 0.008 0.047 -9999 0 -0.136 4 4
PGD2/DP 0.026 0.005 -9999 0 -9999 0 0
SLC9A3R1 0.034 0.009 -9999 0 0 34 34
FYN -0.008 0.082 0.252 30 -0.159 18 48
mol:NO 0.027 0.016 -9999 0 0 118 118
GNA15 0.032 0.012 -9999 0 0 59 59
PGK/cGMP 0.029 0.024 -9999 0 -9999 0 0
RhoA/GDP 0.033 0.011 -9999 0 -0.009 29 29
TP alpha/TGM2/GDP/G beta/gamma 0.032 0.045 0.182 9 -0.137 3 12
NOS3 0.027 0.016 -9999 0 0 118 118
RAC1 0.027 0.016 -9999 0 0 123 123
PRKCA -0.012 0.206 0.344 28 -0.325 114 142
PRKCB -0.012 0.206 0.344 28 -0.326 117 145
PRKCE -0.013 0.208 0.351 27 -0.331 114 141
PRKCD -0.016 0.22 0.352 32 -0.352 116 148
PRKCG -0.016 0.219 0.363 28 -0.354 115 143
muscle contraction -0.035 0.262 0.406 23 -0.443 115 138
PRKCZ -0.011 0.202 0.347 28 -0.316 117 145
ARR3 0.036 0 -9999 0 -9999 0 0
TXA2/TP beta 0.038 0.041 0.182 9 -0.133 2 11
PRKCQ -0.02 0.201 0.35 26 -0.328 108 134
MAPKKK cascade -0.027 0.243 0.387 23 -0.405 112 135
SELE -0.006 0.181 0.321 30 -0.275 120 150
TP beta/GNAI2/GDP/G beta/gamma 0.027 0.056 0.184 9 -0.167 15 24
ROCK1 0.035 0.006 -9999 0 0 14 14
GNA14 0.034 0.008 -9999 0 0 28 28
chemotaxis -0.061 0.317 0.465 15 -0.558 125 140
GNA12 0.026 0.016 -9999 0 0 136 136
GNA13 0.035 0.007 -9999 0 0 18 18
GNA11 0.032 0.012 -9999 0 0 60 60
Rac1/GTP 0.019 0.021 -9999 0 -0.133 6 6
PDGFR-alpha signaling pathway

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
PDGFRA 0.017 0.031 0.082 3 -0.056 49 52
PDGF/PDGFRA/CRKL 0.008 0.067 -9999 0 -0.142 64 64
positive regulation of JUN kinase activity 0.024 0.061 -9999 0 -0.114 62 62
CRKL 0.034 0.008 -9999 0 0 25 25
PDGF/PDGFRA/Caveolin-3 0.009 0.068 -9999 0 -0.142 65 65
AP1 -0.085 0.238 0.304 1 -0.602 73 74
mol:IP3 -0.018 0.041 0.051 48 -0.098 56 104
PLCG1 -0.018 0.041 0.051 48 -0.098 56 104
PDGF/PDGFRA/alphaV Integrin 0.004 0.075 -9999 0 -0.154 73 73
RAPGEF1 0.035 0.007 -9999 0 0 18 18
CRK 0.035 0.008 -9999 0 0 23 23
mol:Ca2+ -0.018 0.04 0.051 48 -0.098 56 104
CAV3 0.036 0.005 -9999 0 0 9 9
CAV1 0.016 0.018 -9999 0 0 269 269
SHC/Grb2/SOS1 0.026 0.062 -9999 0 -0.114 62 62
PDGF/PDGFRA/Shf -0.005 0.054 -9999 0 -0.132 65 65
FOS -0.093 0.226 0.283 3 -0.614 68 71
JUN -0.026 0.057 0.217 9 -0.202 16 25
oligodendrocyte development 0.004 0.075 -9999 0 -0.154 73 73
GRB2 0.035 0.006 -9999 0 0 16 16
PIK3R1 0.032 0.012 -9999 0 0 61 61
mol:DAG -0.018 0.041 0.051 48 -0.098 56 104
PDGF/PDGFRA 0.017 0.031 0.082 3 -0.056 49 52
actin cytoskeleton reorganization 0.006 0.066 -9999 0 -0.14 63 63
SRF -0.015 0.02 0.033 65 -9999 0 65
SHC1 0.033 0.011 -9999 0 0 48 48
PI3K 0.006 0.09 -9999 0 -0.15 103 103
PDGF/PDGFRA/Crk/C3G 0.027 0.072 -9999 0 -0.128 72 72
JAK1 -0.011 0.019 0.025 57 -9999 0 57
ELK1/SRF -0.019 0.084 0.138 69 -0.161 56 125
SHB 0.033 0.011 -9999 0 0 48 48
SHF 0 0 -9999 0 -9999 0 0
CSNK2A1 0.026 0.034 0.078 2 -0.031 104 106
GO:0007205 -0.028 0.069 0.104 20 -0.198 53 73
SOS1 0 0 -9999 0 -9999 0 0
Ras protein signal transduction 0.024 0.061 -9999 0 -0.114 62 62
PDGF/PDGFRA/SHB 0.006 0.066 -9999 0 -0.141 63 63
PDGF/PDGFRA/Caveolin-1 -0.013 0.075 -9999 0 -0.153 89 89
ITGAV 0.034 0.009 -9999 0 0 30 30
ELK1 -0.033 0.068 0.088 21 -0.155 84 105
PIK3CA 0.03 0.014 -9999 0 0 85 85
PDGF/PDGFRA/Crk 0.006 0.073 -9999 0 -0.148 73 73
JAK-STAT cascade -0.011 0.019 0.025 57 -9999 0 57
cell proliferation -0.005 0.054 -9999 0 -0.132 65 65
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.034 0.009 -9999 0 0 32 32
EGFR 0.01 0.016 -9999 0 0 355 355
EGF/EGFR 0.002 0.052 -9999 0 -0.111 58 58
EGF/EGFR dimer/SHC/GRB2/SOS1 0.006 0.058 -9999 0 -0.114 60 60
mol:GTP 0 0 -9999 0 -9999 0 0
EDNRA 0.027 0.016 -9999 0 0 117 117
response to oxidative stress 0 0 -9999 0 -9999 0 0
EGF 0.034 0.008 -9999 0 0 24 24
EGF/EGFR dimer/SHC 0 0.056 -9999 0 -0.126 59 59
mol:GDP 0.005 0.055 -9999 0 -0.113 60 60
mol:Ca2+ 0 0 -9999 0 -9999 0 0
EDN1 0.032 0.011 -9999 0 0 50 50
GRB2/SOS1 0.024 0.019 -9999 0 -0.132 7 7
HRAS/GTP -0.004 0.052 -9999 0 -0.114 68 68
SHC1 0.033 0.011 -9999 0 0 48 48
HRAS/GDP 0 0.059 -9999 0 -0.117 68 68
FRAP1 0.093 0.123 0.187 284 -0.185 4 288
EGF/EGFR dimer -0.004 0.057 -9999 0 -0.141 61 61
SOS1 0 0 -9999 0 -9999 0 0
GRB2 0.035 0.006 -9999 0 0 16 16
ETA receptor/Endothelin-1 0.023 0.058 -9999 0 -0.142 47 47
Effects of Botulinum toxin

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
STX1A -0.008 0.005 0 154 -9999 0 154
UniProt:P19321 0 0 -9999 0 -9999 0 0
RIMS1/UNC13B 0.039 0.039 -9999 0 -0.142 17 17
STXBP1 0.029 0.015 -9999 0 0 99 99
ACh/CHRNA1 0.024 0.054 0.096 37 -0.075 92 129
RAB3GAP2/RIMS1/UNC13B 0.05 0.05 -9999 0 -0.132 23 23
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 0.009 -9999 0 0 33 33
mol:ACh 0.013 0.064 0.095 123 -0.089 89 212
RAB3GAP2 0.034 0.008 -9999 0 0 25 25
STX1A/SNAP25/VAMP2 0.018 0.099 0.173 15 -0.154 81 96
UniProt:P10844 0 0 -9999 0 -9999 0 0
muscle contraction 0.024 0.054 0.096 37 -0.075 92 129
UNC13B 0.032 0.012 -9999 0 0 62 62
CHRNA1 0.035 0.006 -9999 0 0 14 14
UniProt:P10845 0 0 -9999 0 -9999 0 0
ACh/Synaptotagmin 1 0.012 0.042 0.097 15 -0.085 42 57
SNAP25 0.002 0.003 -9999 0 0 255 255
VAMP2 0.004 0.001 -9999 0 0 47 47
SYT1 0.018 0.018 -9999 0 0 249 249
UniProt:Q00496 0 0 -9999 0 -9999 0 0
STXIA/STXBP1 0.018 0.016 0.086 1 -9999 0 1
STX1A/SNAP25 fragment 1/VAMP2 0.018 0.099 0.173 15 -0.154 81 96
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.03 0.014 -9999 0 0 81 81
PLK4 0.035 0.007 -9999 0 0 17 17
regulation of centriole replication -0.018 0.009 0 91 -9999 0 91
Arf6 signaling events

Figure 14.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 16.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.013 0.035 -9999 0 -0.107 38 38
ARNO/beta Arrestin1-2 0.04 0.026 -9999 0 -0.094 7 7
EGFR 0.01 0.016 -9999 0 0 355 355
EPHA2 0.032 0.011 -9999 0 0 53 53
USP6 0.035 0.007 -9999 0 0 19 19
IQSEC1 0.035 0.007 -9999 0 0 16 16
EGFR/EGFR/EGF/EGF -0.004 0.057 -9999 0 -0.141 61 61
ARRB2 0.012 0.026 -9999 0 -0.2 7 7
mol:GTP 0.002 0.014 0.158 1 -0.064 2 3
ARRB1 0.035 0.005 -9999 0 0 11 11
FBXO8 0 0 -9999 0 -9999 0 0
TSHR 0.034 0.01 -9999 0 0 38 38
EGF 0.035 0.008 -9999 0 0 24 24
somatostatin receptor activity 0 0 0.001 137 0 4 141
ARAP2 0 0 0 125 0 3 128
mol:GDP 0.068 0.065 0.153 116 -0.14 3 119
mol:PI-3-4-5-P3 0 0 0 129 0 4 133
ITGA2B 0.036 0.003 -9999 0 0 3 3
ARF6 0.035 0.007 -9999 0 0 21 21
Ephrin A1/EPHA2/NCK1/GIT1 0.074 0.052 -9999 0 -0.129 21 21
ADAP1 0 0 0 64 -9999 0 64
KIF13B 0.032 0.012 -9999 0 0 62 62
HGF/MET 0.031 0.027 -9999 0 -9999 0 0
PXN 0.036 0.004 -9999 0 0 5 5
ARF6/GTP 0.083 0.084 0.187 126 -0.198 4 130
EGFR/EGFR/EGF/EGF/ARFGEP100 0.002 0.056 -9999 0 -0.124 59 59
ADRB2 0.033 0.01 -9999 0 0 40 40
receptor agonist activity 0 0 0 122 0 4 126
actin filament binding 0 0 0 127 0 4 131
SRC 0.035 0.006 -9999 0 0 13 13
ITGB3 0.036 0.004 -9999 0 0 5 5
GNAQ 0.034 0.009 -9999 0 0 31 31
EFA6/PI-4-5-P2 0.001 0.001 0.001 152 -0.001 3 155
ARF6/GDP 0.038 0.061 0.16 16 -0.193 13 29
ARF6/GDP/GULP/ACAP1 0.056 0.072 0.192 25 -0.158 2 27
alphaIIb/beta3 Integrin/paxillin/GIT1 0.092 0.01 -9999 0 -9999 0 0
ACAP1 0 0 0 52 -9999 0 52
ACAP2 0 0 0 116 0 3 119
LHCGR/beta Arrestin2 0.029 0.025 -9999 0 -0.139 7 7
EFNA1 0.033 0.011 -9999 0 0 47 47
HGF 0.025 0.017 -9999 0 0 157 157
CYTH3 0 0 0.001 136 0 4 140
CYTH2 0 0.001 0.003 5 -0.004 4 9
NCK1 0.034 0.008 -9999 0 0 26 26
fibronectin binding 0 0 0 132 0 3 135
endosomal lumen acidification 0 0 0 127 0 2 129
microtubule-based process 0 0 -9999 0 -9999 0 0
GULP1 0.024 0.017 -9999 0 0 161 161
GNAQ/ARNO 0.026 0.008 0.04 6 0 31 37
mol:Phosphatidic acid 0 0 0 116 0 3 119
PIP3-E 0.03 0.014 -9999 0 0 86 86
MET 0.023 0.018 -9999 0 0 183 183
GNA14 0.034 0.009 -9999 0 0 28 28
GNA15 0.032 0.012 -9999 0 0 59 59
GIT1 0.036 0.003 -9999 0 0 4 4
mol:PI-4-5-P2 0 0 0.001 138 -0.001 4 142
GNA11 0.032 0.012 -9999 0 0 60 60
LHCGR 0.036 0.002 -9999 0 0 2 2
AGTR1 0.035 0.007 -9999 0 0 20 20
desensitization of G-protein coupled receptor protein signaling pathway 0.029 0.025 -9999 0 -0.138 7 7
IPCEF1/ARNO 0.004 0.042 -9999 0 -0.092 48 48
alphaIIb/beta3 Integrin 0.053 0.005 -9999 0 -9999 0 0
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.006 0.088 -9999 0 -0.171 85 85
FZD6 0.027 0.016 -9999 0 0 121 121
WNT6 0.036 0.002 -9999 0 0 2 2
WNT4 0.035 0.007 -9999 0 0 18 18
FZD3 0.028 0.015 -9999 0 0 104 104
WNT5A 0.03 0.014 -9999 0 0 89 89
WNT11 0.035 0.006 -9999 0 0 15 15
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.035 0.006 -9999 0 0 15 15
Syndecan-3/Src/Cortactin -0.024 0.189 -9999 0 -0.45 72 72
Syndecan-3/Neurocan -0.065 0.177 -9999 0 -0.48 73 73
POMC 0.035 0.005 -9999 0 0 10 10
EGFR 0.01 0.016 -9999 0 0 355 355
Syndecan-3/EGFR -0.056 0.162 -9999 0 -0.425 72 72
AGRP 0.036 0.004 -9999 0 0 7 7
NCSTN 0.034 0.008 -9999 0 0 28 28
PSENEN 0.034 0.009 -9999 0 0 33 33
RP11-540L11.1 0 0 -9999 0 -9999 0 0
APH1B 0.035 0.006 -9999 0 0 14 14
APH1A 0.035 0.006 -9999 0 0 16 16
NCAN 0 0 -9999 0 -9999 0 0
long-term memory -0.032 0.201 -9999 0 -0.493 74 74
Syndecan-3/IL8 -0.055 0.18 -9999 0 -0.469 74 74
PSEN1 0.033 0.01 -9999 0 0 41 41
Src/Cortactin 0.05 0.015 -9999 0 -0.142 1 1
FYN 0.03 0.014 -9999 0 0 82 82
limb bud formation -0.065 0.183 -9999 0 -0.496 73 73
MC4R 0.035 0.007 -9999 0 0 17 17
SRC 0.035 0.006 -9999 0 0 13 13
PTN 0.023 0.017 -9999 0 0 178 178
FGFR/FGF/Syndecan-3 -0.066 0.185 -9999 0 -0.501 73 73
neuron projection morphogenesis -0.073 0.16 -9999 0 -0.441 71 71
Syndecan-3/AgRP -0.042 0.19 -9999 0 -0.487 73 73
Syndecan-3/AgRP/MC4R -0.024 0.193 -9999 0 -0.471 74 74
Fyn/Cortactin 0.028 0.061 -9999 0 -0.144 51 51
SDC3 -0.067 0.187 -9999 0 -0.506 73 73
GO:0007205 0 0 -9999 0 -9999 0 0
positive regulation of leukocyte migration -0.054 0.177 -9999 0 -0.462 74 74
IL8 0.019 0.018 -9999 0 0 233 233
Syndecan-3/Fyn/Cortactin -0.033 0.206 -9999 0 -0.505 74 74
Syndecan-3/CASK -0.065 0.177 -9999 0 -0.48 73 73
alpha-MSH/MC4R 0.051 0.012 -9999 0 -9999 0 0
Gamma Secretase 0.076 0.072 -9999 0 -0.151 29 29
Canonical Wnt signaling pathway

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
HDAC1 0.032 0.046 0.121 64 -0.038 83 147
AES 0.03 0.041 0.109 60 -0.035 79 139
FBXW11 0.035 0.007 -9999 0 0 20 20
mol:GTP 0 0.001 -9999 0 -9999 0 0
LRP6/FZD1 0.033 0.027 -9999 0 -0.139 1 1
SMAD4 0.032 0.011 -9999 0 0 53 53
DKK2 0.034 0.009 -9999 0 0 29 29
TLE1 0.031 0.041 0.107 63 -0.035 83 146
MACF1 0.033 0.011 -9999 0 0 48 48
CTNNB1 0.045 0.108 0.265 26 -0.338 14 40
WIF1 0.028 0.015 -9999 0 0 106 106
beta catenin/RanBP3 0.068 0.161 0.411 62 -0.338 9 71
KREMEN2 0.036 0.004 -9999 0 0 5 5
DKK1 0.018 0.018 -9999 0 0 240 240
beta catenin/beta TrCP1 0.059 0.111 0.275 24 -0.343 14 38
FZD1 0.025 0.017 -9999 0 0 155 155
AXIN2 -0.024 0.093 0.116 2 -0.236 64 66
AXIN1 0.036 0.004 -9999 0 0 6 6
RAN 0.036 0.006 -9999 0 0 13 13
Axin1/APC/GSK3/beta catenin 0.011 0.163 -9999 0 -0.584 30 30
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.027 0.128 0.245 12 -0.414 19 31
Axin1/APC/GSK3 0.005 0.092 0.213 6 -0.365 18 24
Axin1/APC/GSK3/beta catenin/Macf1 0.029 0.132 0.262 13 -0.36 31 44
HNF1A 0.007 0.03 0.071 72 -0.035 4 76
CTBP1 0.031 0.042 0.112 59 -0.036 82 141
MYC -0.1 0.405 0.731 13 -1.247 48 61
RANBP3 0.034 0.008 -9999 0 0 27 27
DKK2/LRP6/Kremen 2 0.064 0.026 -9999 0 -0.123 1 1
NKD1 0 0.001 -9999 0 -9999 0 0
TCF4 0.03 0.039 0.108 58 -0.036 67 125
TCF3 0.031 0.042 0.112 60 -0.035 81 141
WNT1/LRP6/FZD1/Axin1 0.061 0.045 -9999 0 -9999 0 0
Ran/GTP 0.025 0.016 -9999 0 -0.129 5 5
CtBP/CBP/TCF/TLE1/AES 0.035 0.191 0.458 63 -0.34 17 80
LEF1 0.033 0.044 0.114 68 -0.036 84 152
DVL1 0.008 0.096 -9999 0 -0.424 16 16
CSNK2A1 0.034 0.009 -9999 0 0 31 31
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.01 0.165 0.268 5 -0.496 29 34
DKK1/LRP6/Kremen 2 0.034 0.037 -9999 0 -9999 0 0
LRP6 0.034 0.01 -9999 0 0 37 37
CSNK1A1 0.034 0.047 0.122 65 -0.037 84 149
NLK 0.026 0.023 -9999 0 -0.032 52 52
CCND1 -0.081 0.353 0.741 3 -1.247 37 40
WNT1 0.035 0.007 -9999 0 0 16 16
GSK3A 0.034 0.009 -9999 0 0 28 28
GSK3B 0.034 0.01 -9999 0 0 35 35
FRAT1 0.026 0.016 -9999 0 0 130 130
PPP2R5D 0.023 0.044 -9999 0 -0.233 7 7
APC 0.037 0.104 0.187 143 -9999 0 143
WNT1/LRP6/FZD1 0.005 0.043 -9999 0 -0.245 8 8
CREBBP 0.033 0.043 0.112 66 -0.035 86 152
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 0.016 0.14 -9999 0 -0.339 30 30
MAP3K8 0.022 0.018 -9999 0 0 182 182
FOS 0.016 0.107 -9999 0 -0.334 18 18
PRKCA 0.028 0.025 -9999 0 -0.029 75 75
PTPN7 0.028 0.029 0.066 52 -0.029 88 140
HRAS 0.034 0.009 -9999 0 0 32 32
PRKCB 0 0.008 0.017 59 -0.013 74 133
NRAS 0.032 0.012 -9999 0 0 58 58
RAS family/GTP 0.041 0.066 -9999 0 -0.135 50 50
MAPK3 0.033 0.057 -9999 0 -0.342 4 4
MAP2K1 0.007 0.058 0.156 1 -0.227 12 13
ELK1 0.026 0.028 -9999 0 -0.039 76 76
BRAF 0.007 0.023 -9999 0 -9999 0 0
mol:GTP 0 0.002 0.003 59 -0.004 74 133
MAPK1 0.006 0.126 -9999 0 -0.434 30 30
RAF1 -0.001 0.068 -9999 0 -0.34 16 16
KRAS 0.033 0.01 -9999 0 0 37 37
Ceramide signaling pathway

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
SPHK2 -0.013 0.011 0 211 -9999 0 211
MAP4K4 0.003 0.054 -9999 0 -0.212 11 11
BAG4 0.035 0.005 -9999 0 0 11 11
PKC zeta/ceramide -0.045 0.13 -9999 0 -0.233 111 111
NFKBIA 0.033 0.011 -9999 0 0 47 47
BIRC3 0.03 0.013 -9999 0 0 77 77
BAX -0.022 0.101 -9999 0 -0.35 32 32
RIPK1 0.035 0.007 -9999 0 0 18 18
AKT1 -0.001 0.088 0.674 6 -9999 0 6
BAD -0.05 0.131 0.219 2 -0.239 110 112
SMPD1 -0.003 0.05 0.153 1 -0.194 15 16
RB1 -0.047 0.135 0.211 10 -0.239 110 120
FADD/Caspase 8 0.015 0.051 -9999 0 -0.229 6 6
MAP2K4 -0.051 0.127 0.186 5 -0.237 107 112
NSMAF 0.034 0.008 -9999 0 0 28 28
response to UV 0 0 -9999 0 -9999 0 0
RAF1 -0.053 0.129 0.191 9 -0.239 108 117
EGF 0.034 0.008 -9999 0 0 24 24
mol:ceramide -0.046 0.139 -9999 0 -0.248 111 111
MADD 0.035 0.006 -9999 0 0 13 13
response to oxidative stress 0 0 -9999 0 -9999 0 0
mol:Free Fatty acid -0.013 0.011 0 207 -9999 0 207
ASAH1 0.035 0.007 -9999 0 0 17 17
negative regulation of cell cycle -0.046 0.133 0.21 10 -0.236 110 120
cell proliferation -0.022 0.119 0.2 5 -0.217 95 100
BID -0.037 0.2 -9999 0 -0.625 46 46
MAP3K1 -0.048 0.132 0.154 3 -0.242 107 110
EIF2A -0.053 0.12 0.189 2 -0.228 108 110
TRADD 0.036 0.004 -9999 0 0 7 7
CRADD 0.035 0.006 -9999 0 0 12 12
MAPK3 -0.045 0.115 0.191 9 -0.222 99 108
response to heat 0 0 -9999 0 -9999 0 0
MAPK1 -0.054 0.126 0.187 10 -0.234 111 121
Cathepsin D/ceramide -0.033 0.139 -9999 0 -0.239 111 111
FADD 0.008 0.048 -9999 0 -0.214 5 5
KSR1 -0.051 0.131 -9999 0 -0.24 111 111
MAPK8 -0.084 0.16 0.161 2 -0.247 178 180
PRKRA -0.053 0.132 -9999 0 -0.243 111 111
PDGFA 0.021 0.018 -9999 0 0 201 201
TRAF2 0.035 0.006 -9999 0 0 14 14
IGF1 0.035 0.007 -9999 0 0 20 20
mol:GD3 0 0 -9999 0 -9999 0 0
ganglioside biosynthetic process -0.046 0.137 0.091 1 -0.246 111 112
CTSD 0.032 0.011 -9999 0 0 55 55
regulation of nitric oxide biosynthetic process 0.049 0.025 -9999 0 -0.141 7 7
response to radiation 0 0 -9999 0 -9999 0 0
ERK1/PKC delta -0.023 0.129 0.214 5 -0.232 95 100
PRKCD 0.034 0.01 -9999 0 0 36 36
PRKCZ 0 0 -9999 0 -9999 0 0
mol:GW4869 0 0 -9999 0 -9999 0 0
mol:sphingosine -0.013 0.011 0 207 -9999 0 207
RelA/NF kappa B1 0.049 0.025 -9999 0 -0.142 7 7
mol:glutathione 0 0 -9999 0 -9999 0 0
PAWR 0.035 0.006 -9999 0 0 13 13
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.018 0.054 -9999 0 -0.232 6 6
TNFR1A/BAG4/TNF-alpha 0.053 0.055 -9999 0 -0.123 39 39
mol:Sphingosine-1-phosphate -0.013 0.011 0 211 -9999 0 211
MAP2K1 -0.057 0.123 0.176 9 -0.234 108 117
mol:C11AG 0 0 -9999 0 -9999 0 0
RELA 0.035 0.005 -9999 0 0 10 10
CYCS -0.013 0.085 0.13 6 -0.248 34 40
TNFRSF1A 0.032 0.012 -9999 0 0 61 61
NFKB1 0.035 0.007 -9999 0 0 17 17
TNFR1A/BAG4 0.034 0.054 -9999 0 -0.142 40 40
EIF2AK2 -0.056 0.126 0.197 2 -0.24 108 110
TNF-alpha/TNFR1A/FAN 0.047 0.066 -9999 0 -0.133 52 52
response to hydrogen peroxide 0 0 -9999 0 -9999 0 0
CASP8 0.033 0.053 -9999 0 -0.298 5 5
MAP2K2 -0.046 0.117 0.181 21 -0.227 99 120
SMPD3 0.006 0.056 0.16 1 -0.287 7 8
TNF 0.036 0.004 -9999 0 0 6 6
PKC zeta/PAR4 0.026 0.004 -9999 0 -9999 0 0
mol:PHOSPHOCHOLINE -0.023 0.075 0.127 7 -0.142 103 110
NF kappa B1/RelA/I kappa B alpha 0.07 0.045 -9999 0 -0.117 18 18
AIFM1 -0.034 0.095 0.121 2 -0.162 121 123
BCL2 0.035 0.007 -9999 0 0 17 17
LPA receptor mediated 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
GNB1/GNG2 0.004 0.058 -9999 0 -0.144 60 60
NF kappa B1 p50/RelA/I kappa B alpha 0.012 0.096 0.204 12 -0.2 42 54
AP1 -0.012 0.074 0.083 6 -0.144 92 98
mol:PIP3 -0.021 0.048 -9999 0 -0.127 66 66
AKT1 -0.006 0.093 0.207 19 -0.236 29 48
PTK2B -0.002 0.059 0.124 4 -0.146 57 61
RHOA 0.011 0.077 0.181 13 -0.339 12 25
PIK3CB 0.035 0.006 -9999 0 0 16 16
mol:Ca2+ -0.009 0.04 0.171 5 -0.137 19 24
MAGI3 0 0 -9999 0 -0.002 1 1
RELA 0.036 0.005 -9999 0 0 10 10
apoptosis 0.001 0.064 0.101 35 -0.161 53 88
HRAS/GDP 0.021 0.029 -9999 0 -0.132 16 16
positive regulation of microtubule depolymerization -0.02 0.074 0.171 9 -0.212 35 44
NF kappa B1 p50/RelA -0.021 0.066 0.08 44 -0.165 54 98
endothelial cell migration -0.018 0.099 -9999 0 -0.301 53 53
ADCY4 -0.016 0.083 0.154 12 -0.244 36 48
ADCY5 -0.016 0.083 0.154 12 -0.244 36 48
ADCY6 -0.003 0.09 0.168 11 -0.242 35 46
ADCY7 -0.006 0.094 0.163 11 -0.236 42 53
ADCY1 -0.01 0.082 0.159 6 -0.25 32 38
ADCY2 -0.005 0.092 0.168 11 -0.239 39 50
ADCY3 -0.016 0.083 0.154 12 -0.244 36 48
ADCY8 -0.006 0.089 0.159 12 -0.24 37 49
ADCY9 -0.004 0.091 0.164 12 -0.238 38 50
GSK3B -0.009 0.064 0.178 5 -0.16 56 61
arachidonic acid secretion -0.021 0.114 0.154 10 -0.252 64 74
GNG2 0 0.001 0.002 2 -0.003 18 20
TRIP6 -0.014 0.082 -9999 0 -0.249 51 51
GNAO1 0.003 0.059 0.127 25 -0.158 47 72
HRAS 0.034 0.009 -9999 0 0 32 32
NFKBIA -0.013 0.083 0.172 14 -0.204 41 55
GAB1 0.031 0.013 -9999 0 0 75 75
mol:GTP 0 0 -9999 0 -9999 0 0
lamellipodium assembly -0.005 0.211 -9999 0 -0.811 30 30
JUN 0.033 0.01 -9999 0 0 39 39
LPA/LPA2/NHERF2 0.018 0.029 -9999 0 -0.061 53 53
TIAM1 -0.016 0.248 -9999 0 -0.979 30 30
PIK3R1 0.032 0.012 -9999 0 0 61 61
mol:IP3 -0.008 0.039 0.179 4 -0.139 19 23
PLCB3 0.006 0.034 0.205 3 -9999 0 3
FOS 0.025 0.017 -9999 0 0 147 147
positive regulation of mitosis -0.021 0.114 0.154 10 -0.252 64 74
LPA/LPA1-2-3 -0.008 0.041 -9999 0 -0.125 53 53
mol:Ca ++ 0 0 -9999 0 -9999 0 0
JNK cascade 0 0.001 -9999 0 -9999 0 0
BCAR1 0 0 -9999 0 -9999 0 0
stress fiber formation 0.009 0.067 -9999 0 -0.285 9 9
GNAZ 0.002 0.063 0.125 26 -0.169 47 73
EGFR/PI3K-beta/Gab1 -0.017 0.052 -9999 0 -0.131 66 66
positive regulation of dendritic cell cytokine production -0.009 0.041 -9999 0 -0.124 53 53
LPA/LPA2/MAGI-3 -0.004 0.017 -9999 0 -0.052 53 53
ARHGEF1 0.018 0.103 0.183 106 -0.163 39 145
GNAI2 0.003 0.07 0.126 38 -0.172 53 91
GNAI3 0.006 0.065 0.126 39 -0.155 53 92
GNAI1 0.002 0.047 0.126 18 -0.157 28 46
LPA/LPA3 -0.006 0.021 -9999 0 -0.066 53 53
LPA/LPA2 -0.006 0.021 -9999 0 -0.066 53 53
LPA/LPA1 -0.013 0.055 -9999 0 -0.171 53 53
HB-EGF/EGFR -0.012 0.058 -9999 0 -0.133 75 75
HBEGF -0.01 0.011 0 264 -9999 0 264
mol:DAG -0.008 0.039 0.179 4 -0.139 19 23
cAMP biosynthetic process -0.004 0.111 0.18 28 -0.257 44 72
NFKB1 0.035 0.007 -9999 0 0 17 17
SRC 0.035 0.006 -9999 0 0 13 13
GNB1 0.033 0.01 -9999 0 0 37 37
LYN -0.02 0.095 0.171 16 -0.222 58 74
GNAQ 0.008 0.027 0.057 37 -0.058 55 92
LPAR2 0 0.001 0.002 1 -0.003 4 5
LPAR3 0 0.001 -9999 0 -0.002 6 6
LPAR1 -0.01 0.033 -9999 0 -0.105 53 53
IL8 -0.124 0.2 0.287 13 -0.392 151 164
PTK2 0.013 0.059 0.123 39 -0.135 51 90
Rac1/GDP 0.018 0.02 -9999 0 -0.132 6 6
CASP3 0.001 0.064 0.101 35 -0.162 53 88
EGFR 0.01 0.016 -9999 0 0 355 355
PLCG1 0.004 0.039 0.061 27 -0.083 56 83
PLD2 0.015 0.054 0.123 37 -0.123 50 87
G12/G13 0.015 0.064 -9999 0 -0.152 52 52
PI3K-beta -0.014 0.071 -9999 0 -0.242 26 26
cell migration 0.001 0.075 -9999 0 -0.246 31 31
SLC9A3R2 0.036 0.004 -9999 0 0 5 5
PXN 0.009 0.068 -9999 0 -0.29 9 9
HRAS/GTP -0.023 0.114 0.152 8 -0.26 62 70
RAC1 0.027 0.016 -9999 0 0 123 123
MMP9 0.017 0.018 -9999 0 0 254 254
PRKCE 0.036 0.004 -9999 0 0 7 7
PRKCD -0.004 0.055 0.181 13 -0.172 5 18
Gi(beta/gamma) -0.014 0.118 0.166 9 -0.27 60 69
mol:LPA -0.01 0.033 -9999 0 -0.105 53 53
TRIP6/p130 Cas/FAK1/Paxillin -0.006 0.082 0.132 1 -0.214 44 45
MAPKKK cascade -0.021 0.114 0.154 10 -0.252 64 74
contractile ring contraction involved in cytokinesis 0.013 0.078 0.189 13 -0.336 12 25
mol:GDP 0 0 -9999 0 -9999 0 0
GNA14 0.008 0.027 0.057 36 -0.058 55 91
GNA15 0.007 0.026 0.056 32 -0.058 53 85
GNA12 0.026 0.016 -9999 0 0 136 136
GNA13 0.035 0.007 -9999 0 0 18 18
MAPT -0.02 0.075 0.172 9 -0.217 35 44
GNA11 0.01 0.023 0.057 36 -0.057 36 72
Rac1/GTP -0.006 0.223 -9999 0 -0.858 30 30
MMP2 -0.018 0.1 -9999 0 -0.303 53 53
TCGA08_retinoblastoma

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
CDKN2B 0.004 0.026 -9999 0 -0.051 56 56
CDKN2C -0.007 0.022 -9999 0 -0.034 104 104
CDKN2A 0.006 0.016 0.086 1 -9999 0 1
CCND2 -0.001 0.02 0.109 7 -9999 0 7
RB1 -0.046 0.089 0.17 1 -0.187 131 132
CDK4 -0.001 0.021 0.127 7 -9999 0 7
CDK6 -0.001 0.021 0.128 7 -9999 0 7
G1/S progression 0.054 0.095 0.189 148 -0.133 5 153
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.033 0.01 -9999 0 0 41 41
oxygen homeostasis 0 0 -9999 0 -9999 0 0
TCEB2 0.036 0.004 -9999 0 0 5 5
TCEB1 0.035 0.007 -9999 0 0 20 20
HIF1A/p53 -0.036 0.123 -9999 0 -0.272 86 86
HIF1A -0.031 0.108 -9999 0 -0.275 73 73
COPS5 0.035 0.006 -9999 0 0 12 12
VHL/Elongin B/Elongin C/RBX1/CUL2 0.05 0.058 -9999 0 -0.13 19 19
FIH (dimer) 0.027 0.016 -9999 0 0 124 124
CDKN2A 0.005 0.013 -9999 0 0 417 417
ARNT/IPAS 0.048 0.016 -9999 0 -9999 0 0
HIF1AN 0.027 0.016 -9999 0 0 124 124
GNB2L1 0.035 0.005 -9999 0 0 11 11
HIF1A/ARNT -0.034 0.126 -9999 0 -0.277 86 86
CUL2 0.026 0.016 -9999 0 0 131 131
OS9 0.03 0.014 -9999 0 0 89 89
RACK1/Elongin B/Elongin C 0.066 0.032 -9999 0 -0.134 9 9
response to hypoxia 0 0 -9999 0 -9999 0 0
HIF1A/Hsp90 -0.049 0.115 -9999 0 -0.271 88 88
PHD1-3/OS9 0.056 0.062 -9999 0 -0.137 25 25
HIF1A/RACK1/Elongin B/Elongin C -0.015 0.14 -9999 0 -0.274 89 89
VHL 0 0 -9999 0 -9999 0 0
HSP90AA1 0 0 -9999 0 -9999 0 0
HIF1A/JAB1 -0.035 0.129 -9999 0 -0.277 90 90
EGLN3 0.03 0.014 -9999 0 0 83 83
EGLN2 0.034 0.008 -9999 0 0 27 27
EGLN1 0.034 0.009 -9999 0 0 31 31
TP53 0.031 0.013 -9999 0 0 75 75
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.007 0.103 -9999 0 -0.607 12 12
ARNT 0.035 0.005 -9999 0 0 10 10
ARD1A 0.036 0.003 -9999 0 0 4 4
RBX1 0.033 0.01 -9999 0 0 41 41
HIF1A/p19ARF -0.045 0.105 -9999 0 -0.265 82 82
Syndecan-1-mediated signaling events

Figure 23.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 25.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.032 0.012 -9999 0 0 62 62
CCL5 0.032 0.011 -9999 0 0 50 50
SDCBP 0.035 0.007 -9999 0 0 21 21
FGFR/FGF2/Syndecan-1 0.014 0.097 0.177 42 -0.236 10 52
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 0.021 0.105 0.2 28 -0.236 12 40
Syndecan-1/Syntenin 0.028 0.11 0.21 37 -0.235 14 51
MAPK3 0.005 0.099 0.182 23 -0.225 18 41
HGF/MET 0.031 0.027 -9999 0 -9999 0 0
TGFB1/TGF beta receptor Type II 0.032 0.012 -9999 0 0 62 62
BSG 0.031 0.013 -9999 0 0 74 74
keratinocyte migration 0.021 0.104 0.199 28 -0.234 12 40
Syndecan-1/RANTES 0.021 0.104 0.213 28 -0.225 12 40
Syndecan-1/CD147 0.024 0.112 0.225 14 -0.232 17 31
Syndecan-1/Syntenin/PIP2 0.025 0.105 0.197 37 -0.226 14 51
LAMA5 0.033 0.011 -9999 0 0 46 46
positive regulation of cell-cell adhesion 0.024 0.103 0.193 37 -0.222 14 51
MMP7 0.026 0.016 -9999 0 0 131 131
HGF 0.024 0.017 -9999 0 0 157 157
Syndecan-1/CASK -0.009 0.078 0.153 3 -0.218 12 15
Syndecan-1/HGF/MET 0.025 0.088 0.239 9 -0.238 5 14
regulation of cell adhesion 0.003 0.112 0.231 40 -0.223 20 60
HPSE 0.032 0.012 -9999 0 0 56 56
positive regulation of cell migration 0.014 0.097 0.177 42 -0.236 10 52
SDC1 0.007 0.089 0.158 26 -0.255 7 33
Syndecan-1/Collagen 0.014 0.097 0.177 42 -0.236 10 52
PPIB 0.034 0.009 -9999 0 0 33 33
MET 0.023 0.018 -9999 0 0 183 183
PRKACA 0.034 0.009 -9999 0 0 29 29
MMP9 0.017 0.018 -9999 0 0 254 254
MAPK1 0.003 0.097 0.182 22 -0.224 19 41
homophilic cell adhesion 0.017 0.1 0.203 30 -0.234 10 40
MMP1 0.031 0.013 -9999 0 0 71 71
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.011 0.003 0 29 -9999 0 29
GNB1/GNG2 0.036 0.032 -9999 0 -0.104 20 20
regulation of S phase of mitotic cell cycle -0.006 0.081 -9999 0 -0.184 72 72
GNAO1 0.03 0.014 -9999 0 0 81 81
HRAS 0.034 0.01 -9999 0 -0.001 33 33
SHBG/T-DHT 0.024 0.005 -9999 0 -9999 0 0
PELP1 0.035 0.008 -9999 0 -0.002 20 20
AKT1 -0.01 0.004 0 53 -9999 0 53
MAP2K1 -0.035 0.076 0.179 14 -0.174 70 84
T-DHT/AR 0.025 0.007 -9999 0 -9999 0 0
G-protein coupled receptor activity 0 0 -9999 0 -9999 0 0
mol:GTP -0.001 0.003 0.002 54 -0.006 73 127
GNAI2 0.033 0.01 -9999 0 0 42 42
GNAI3 0.035 0.006 -9999 0 0 12 12
GNAI1 0.018 0.018 -9999 0 0 245 245
mol:GDP -0.021 0.035 -9999 0 -0.146 14 14
cell proliferation -0.057 0.185 0.272 14 -0.426 80 94
PIK3CA 0.03 0.014 -9999 0 0 85 85
FOS -0.086 0.28 0.329 4 -0.692 79 83
mol:Ca2+ -0.005 0.021 -9999 0 -0.054 63 63
MAPK3 -0.041 0.134 0.255 15 -0.303 76 91
MAPK1 -0.04 0.164 0.245 3 -0.478 39 42
PIK3R1 0.032 0.012 -9999 0 0 61 61
mol:IP3 0 0.002 0.003 57 -0.004 70 127
cAMP biosynthetic process -0.001 0.014 -9999 0 -9999 0 0
GNG2 0 0 -9999 0 -9999 0 0
potassium channel inhibitor activity 0 0.002 0.003 57 -0.004 70 127
HRAS/GTP 0.042 0.066 -9999 0 -0.096 67 67
actin cytoskeleton reorganization 0.019 0.055 -9999 0 -0.121 47 47
SRC 0.035 0.006 -9999 0 0 13 13
voltage-gated calcium channel activity 0 0.002 0.003 57 -0.004 70 127
PI3K 0.016 0.064 -9999 0 -0.127 73 73
apoptosis 0.047 0.19 0.433 79 -0.25 11 90
T-DHT/AR/PELP1 0.043 0.024 -9999 0 -0.119 7 7
HRAS/GDP 0.007 0.062 -9999 0 -0.181 15 15
CREB1 -0.067 0.195 0.253 11 -0.467 79 90
RAC1-CDC42/GTP 0.029 0.061 -9999 0 -0.122 47 47
AR 0.034 0.008 -9999 0 -0.001 22 22
GNB1 0.033 0.01 -9999 0 0 37 37
RAF1 -0.027 0.068 0.19 14 -0.216 14 28
RAC1-CDC42/GDP 0.025 0.057 -9999 0 -0.173 11 11
T-DHT/AR/PELP1/Src 0.059 0.032 -9999 0 -0.116 7 7
MAP2K2 -0.038 0.068 0.171 5 -0.172 67 72
T-DHT/AR/PELP1/Src/PI3K -0.006 0.082 -9999 0 -0.185 72 72
GNAZ 0.03 0.013 -9999 0 0 79 79
SHBG 0.035 0.007 -9999 0 0 18 18
Gi family/GNB1/GNG2/GDP -0.047 0.177 -9999 0 -0.451 58 58
mol:T-DHT 0 0.001 0.002 1 -0.004 20 21
RAC1 0.027 0.016 -9999 0 0 123 123
GNRH1 -0.011 0.002 0.001 12 -9999 0 12
Gi family/GTP -0.01 0.087 -9999 0 -0.195 67 67
CDC42 0.035 0.008 -9999 0 0 22 22
Glypican 2 network

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
MDK 0.029 0.014 -9999 0 0 94 94
GPC2 0 0 -9999 0 -9999 0 0
GPC2/Midkine 0.006 0.05 -9999 0 -0.132 56 56
neuron projection morphogenesis 0.006 0.05 -9999 0 -0.132 56 56
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.014 0.06 -9999 0 -0.132 62 62
EPHB2 0.034 0.009 -9999 0 0 35 35
Syndecan-2/TACI 0.018 0.054 -9999 0 -0.119 59 59
LAMA1 0 0 -9999 0 -9999 0 0
Syndecan-2/alpha2 ITGB1 0.024 0.071 -9999 0 -0.117 76 76
HRAS 0.034 0.009 -9999 0 0 32 32
Syndecan-2/CASK -0.008 0.041 -9999 0 -0.111 62 62
ITGA5 0.032 0.012 -9999 0 0 56 56
BAX -0.009 0.068 -9999 0 -0.832 3 3
EPB41 0.035 0.005 -9999 0 0 10 10
positive regulation of cell-cell adhesion 0.013 0.054 -9999 0 -0.114 66 66
LAMA3 0.033 0.011 -9999 0 0 45 45
EZR 0 0 -9999 0 -9999 0 0
mol:PI-4-5-P2 0 0 -9999 0 -9999 0 0
CAV2 0.019 0.018 -9999 0 0 232 232
Syndecan-2/MMP2 0.009 0.061 -9999 0 -0.141 59 59
RP11-540L11.1 0 0 -9999 0 -9999 0 0
alpha2 ITGB1 0.02 0.053 -9999 0 -0.14 39 39
dendrite morphogenesis 0.016 0.053 -9999 0 -0.119 57 57
Syndecan-2/GM-CSF 0.018 0.054 -9999 0 -0.119 58 58
determination of left/right symmetry 0.007 0.024 0.082 5 -0.239 4 9
Syndecan-2/PKC delta 0.017 0.053 -9999 0 -0.12 56 56
GNB2L1 0.035 0.005 -9999 0 0 11 11
MAPK3 -0.022 0.05 0.111 33 -0.113 57 90
MAPK1 -0.019 0.048 0.113 30 -0.117 44 74
Syndecan-2/RACK1 0.03 0.062 0.137 2 -0.111 70 72
NF1 0.036 0.003 -9999 0 0 4 4
FGFR/FGF/Syndecan-2 0.007 0.024 0.082 5 -0.239 4 9
ITGA2 0.028 0.015 -9999 0 0 108 108
MAPK8 -0.004 0.038 0.125 3 -0.371 3 6
Syndecan-2/alpha2/beta1 Integrin 0.009 0.062 0.137 1 -0.109 85 86
Syndecan-2/Kininogen 0.018 0.054 -9999 0 -0.119 58 58
ITGB1 0.027 0.016 -9999 0 0 118 118
SRC -0.026 0.051 0.165 9 -0.193 9 18
Syndecan-2/CASK/Protein 4.1 0.016 0.049 -9999 0 -0.106 62 62
extracellular matrix organization 0.015 0.051 -9999 0 -0.12 54 54
actin cytoskeleton reorganization 0.014 0.06 -9999 0 -0.132 62 62
Syndecan-2/Caveolin-2/Ras 0.007 0.066 0.144 1 -0.131 70 71
Syndecan-2/Laminin alpha3 0.016 0.052 -9999 0 -0.118 56 56
Syndecan-2/RasGAP 0.037 0.078 -9999 0 -0.123 80 80
alpha5/beta1 Integrin 0.03 0.043 -9999 0 -0.139 20 20
PRKCD 0.034 0.01 -9999 0 0 36 36
Syndecan-2 dimer 0.016 0.053 -9999 0 -0.12 57 57
GO:0007205 0.001 0.011 -9999 0 -0.114 4 4
DNA mediated transformation 0 0 -9999 0 -9999 0 0
Syndecan-2/RasGAP/Src 0.014 0.067 0.186 1 -0.128 72 73
RHOA 0.035 0.007 -9999 0 0 21 21
SDCBP 0.035 0.007 -9999 0 0 21 21
TNFRSF13B 0.036 0.005 -9999 0 0 8 8
RASA1 0.034 0.009 -9999 0 0 30 30
alpha2/beta1 Integrin 0.02 0.053 -9999 0 -0.14 39 39
Syndecan-2/Synbindin 0.017 0.058 -9999 0 -0.128 60 60
TGFB1 0.032 0.012 -9999 0 0 62 62
CASP3 -0.015 0.052 0.112 32 -0.116 47 79
FN1 0.034 0.009 -9999 0 0 29 29
Syndecan-2/IL8 -0.003 0.068 -9999 0 -0.177 55 55
SDC2 0.007 0.024 0.082 5 -0.239 4 9
KNG1 0.035 0.006 -9999 0 0 15 15
Syndecan-2/Neurofibromin 0.017 0.055 -9999 0 -0.119 62 62
TRAPPC4 0.035 0.006 -9999 0 0 14 14
CSF2 0.036 0.005 -9999 0 0 8 8
Syndecan-2/TGFB1 0.015 0.051 -9999 0 -0.12 54 54
Syndecan-2/Syntenin/PI-4-5-P2 0.014 0.054 -9999 0 -0.115 66 66
Syndecan-2/Ezrin 0.015 0.052 -9999 0 -0.112 63 63
PRKACA -0.02 0.048 0.108 33 -0.111 58 91
angiogenesis -0.003 0.068 -9999 0 -0.176 55 55
MMP2 0.029 0.015 -9999 0 0 103 103
IL8 0.019 0.018 -9999 0 0 233 233
calcineurin-NFAT signaling pathway 0.018 0.054 -9999 0 -0.119 59 59
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.066 0.058 -9999 0 -0.115 30 30
MAP4K1 0.034 0.008 -9999 0 0 26 26
MAP3K8 0.023 0.018 -9999 0 0 182 182
PRKCB 0 0 -9999 0 -9999 0 0
DBNL 0 0 -9999 0 -9999 0 0
CRKL 0.034 0.008 -9999 0 0 25 25
MAP3K1 0.002 0.051 -9999 0 -0.147 39 39
JUN -0.135 0.235 0.217 1 -0.51 133 134
MAP3K7 0.002 0.051 -9999 0 -0.157 35 35
GRAP2 0.034 0.009 -9999 0 0 33 33
CRK 0.035 0.008 -9999 0 0 23 23
MAP2K4 -0.013 0.069 0.148 1 -0.226 23 24
LAT 0.036 0.005 -9999 0 0 9 9
LCP2 0.031 0.013 -9999 0 0 71 71
MAPK8 -0.131 0.249 -9999 0 -0.53 133 133
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.012 0.056 -9999 0 -0.15 40 40
LAT/GRAP2/SLP76/HPK1/HIP-55 0.061 0.054 -9999 0 -0.107 30 30
EPO signaling pathway

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
BCL2L1 0.046 0.081 0.341 2 -0.323 1 3
CRKL 0.048 0.097 0.169 168 -9999 0 168
mol:DAG 0.017 0.063 0.203 5 -0.185 26 31
HRAS 0.053 0.106 0.244 65 -0.188 2 67
MAPK8 0.015 0.074 0.162 82 -9999 0 82
RAP1A 0.05 0.098 0.169 172 -9999 0 172
GAB1 0.041 0.092 0.168 147 -9999 0 147
MAPK14 0.025 0.089 0.162 127 -9999 0 127
EPO 0.029 0.02 -9999 0 -0.032 2 2
PLCG1 0.017 0.064 0.205 5 -0.189 26 31
EPOR/TRPC2/IP3 Receptors 0.04 0.015 0.092 2 -0.032 2 4
RAPGEF1 0.035 0.007 -9999 0 0 18 18
EPO/EPOR (dimer)/SOCS3 0.053 0.038 -9999 0 -9999 0 0
GAB1/SHC/GRB2/SOS1 0.06 0.074 0.229 29 -9999 0 29
EPO/EPOR (dimer) 0.04 0.03 -9999 0 -9999 0 0
IRS2 0.038 0.091 0.167 141 -0.16 3 144
STAT1 0.022 0.068 0.237 6 -0.227 7 13
STAT5B 0.02 0.064 0.215 6 -0.205 9 15
cell proliferation 0.012 0.075 0.158 85 -9999 0 85
GAB1/SHIP/PIK3R1/SHP2/SHC 0.035 0.062 0.154 4 -0.176 6 10
TEC 0.05 0.098 0.169 172 -9999 0 172
SOCS3 0.036 0.004 -9999 0 0 5 5
STAT1 (dimer) 0.022 0.067 0.236 6 -0.223 7 13
JAK2 0.035 0.018 0.075 1 -9999 0 1
PIK3R1 0.032 0.012 -9999 0 0 61 61
EPO/EPOR (dimer)/JAK2 0.045 0.052 0.222 8 -9999 0 8
EPO/EPOR 0.04 0.03 -9999 0 -9999 0 0
LYN 0.032 0.014 -9999 0 -9999 0 0
TEC/VAV2 0.063 0.072 0.215 39 -9999 0 39
elevation of cytosolic calcium ion concentration 0.04 0.015 0.092 2 -0.032 2 4
SHC1 0.033 0.011 -9999 0 0 48 48
EPO/EPOR (dimer)/LYN 0.041 0.059 -9999 0 -0.127 28 28
mol:IP3 0.017 0.063 0.203 5 -0.185 26 31
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.043 0.089 0.231 31 -0.17 13 44
SH2B3 -0.001 0.006 0.025 19 -9999 0 19
NFKB1 0.025 0.089 0.162 126 -0.206 1 127
EPO/EPOR (dimer)/JAK2/SOCS3 0.015 0.013 -9999 0 -9999 0 0
PTPN6 0.047 0.095 0.179 152 -9999 0 152
TEC/VAV2/GRB2 0.083 0.074 0.238 37 -9999 0 37
EPOR 0.04 0.015 0.092 2 -0.032 2 4
INPP5D 0 0 -9999 0 -9999 0 0
mol:GDP 0.059 0.074 0.23 29 -9999 0 29
SOS1 0 0 -9999 0 -9999 0 0
PLCG2 0.032 0.012 -9999 0 0 60 60
CRKL/CBL/C3G 0.082 0.073 0.238 37 -9999 0 37
VAV2 0.049 0.097 0.168 172 -9999 0 172
CBL 0.05 0.098 0.169 174 -9999 0 174
SHC/Grb2/SOS1 0.02 0.034 -9999 0 -0.102 9 9
STAT5A 0.02 0.063 0.22 5 -0.184 23 28
GRB2 0.035 0.006 -9999 0 0 16 16
STAT5 (dimer) 0.035 0.072 0.262 8 -0.222 1 9
LYN/PLCgamma2 0.026 0.069 -9999 0 -0.169 49 49
PTPN11 0.036 0.005 -9999 0 0 9 9
BTK 0.047 0.098 0.168 170 -9999 0 170
BCL2 0.047 0.083 0.313 1 -0.323 1 2
amb2 Integrin 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
alphaM/beta2 Integrin/proMMP-2 0.029 0.085 -9999 0 -0.136 84 84
alphaM/beta2 Integrin/GPIbA 0.049 0.068 -9999 0 -0.12 55 55
alphaM/beta2 Integrin/proMMP-9 -0.008 0.09 -9999 0 -0.133 139 139
PLAUR 0.03 0.014 -9999 0 0 89 89
HMGB1 0.039 0.013 0.081 2 -9999 0 2
alphaM/beta2 Integrin/Talin 0.039 0.071 -9999 0 -0.13 53 53
AGER 0.041 0.011 0.081 2 -9999 0 2
RAP1A 0.036 0.005 -9999 0 0 8 8
SELPLG 0.036 0.004 -9999 0 0 6 6
mol:LDL 0 0 -9999 0 -9999 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.076 0.082 -9999 0 -0.116 47 47
mol:GTP 0 0 -9999 0 -9999 0 0
MMP9 0.017 0.018 -9999 0 0 254 254
CYR61 0.024 0.017 -9999 0 0 157 157
TLN1 0.029 0.014 -9999 0 0 94 94
Rap1/GTP 0.028 0.069 -9999 0 -0.221 13 13
RHOA 0.035 0.007 -9999 0 0 21 21
P-selectin oligomer 0.035 0.006 -9999 0 0 14 14
MYH2 0.028 0.07 0.191 5 -0.301 5 10
MST1R 0.035 0.007 -9999 0 0 19 19
leukocyte activation during inflammatory response 0.051 0.061 -9999 0 -0.106 43 43
APOB 0.035 0.006 -9999 0 0 12 12
mol:GDP 0 0 -9999 0 -9999 0 0
complement component iC3b receptor activity 0 0 -9999 0 -9999 0 0
MMP2 0.029 0.015 -9999 0 0 103 103
JAM3 0.032 0.011 -9999 0 0 50 50
GP1BA 0.035 0.006 -9999 0 0 12 12
alphaM/beta2 Integrin/CTGF 0.021 0.085 -9999 0 -0.128 98 98
alphaM/beta2 Integrin 0.025 0.071 -9999 0 -0.239 14 14
JAM3 homodimer 0.032 0.011 -9999 0 0 50 50
ICAM2 0.034 0.009 -9999 0 0 29 29
ICAM1 0.03 0.014 -9999 0 0 89 89
phagocytosis triggered by activation of immune response cell surface activating receptor 0.024 0.071 -9999 0 -0.237 14 14
cell adhesion 0.049 0.067 -9999 0 -0.12 55 55
NFKB1 -0.002 0.078 0.208 19 -0.202 2 21
THY1 0.031 0.013 -9999 0 0 76 76
RhoA/GDP 0.024 0.019 -9999 0 -0.132 7 7
Lipoprotein(a) 0.042 0.017 -9999 0 -9999 0 0
alphaM/beta2 Integrin/LRP/tPA 0.036 0.101 -9999 0 -0.146 94 94
IL6 -0.018 0.036 -9999 0 -9999 0 0
ITGB2 0.033 0.019 0.079 2 -9999 0 2
elevation of cytosolic calcium ion concentration 0.029 0.084 -9999 0 -0.139 64 64
alphaM/beta2 Integrin/JAM2/JAM3 0.048 0.099 -9999 0 -0.152 81 81
JAM2 0.032 0.011 -9999 0 0 53 53
alphaM/beta2 Integrin/ICAM1 0.076 0.072 -9999 0 -0.115 36 36
alphaM/beta2 Integrin/uPA/Plg 0.038 0.081 -9999 0 -0.125 59 59
RhoA/GTP 0.033 0.073 0.195 4 -0.293 6 10
positive regulation of phagocytosis 0.016 0.1 0.172 4 -0.237 44 48
Ron/MSP 0.05 0.013 -9999 0 -9999 0 0
alphaM/beta2 Integrin/uPAR/uPA 0.031 0.086 -9999 0 -0.139 64 64
alphaM/beta2 Integrin/uPAR 0.038 0.074 -9999 0 -0.131 60 60
PLAU 0.02 0.018 -9999 0 0 213 213
PLAT 0.027 0.016 -9999 0 0 124 124
actin filament polymerization 0.029 0.071 0.226 3 -0.29 5 8
MST1 0.034 0.008 -9999 0 0 24 24
alphaM/beta2 Integrin/lipoprotein(a) 0.06 0.064 -9999 0 -0.106 43 43
TNF 0.006 0.088 0.208 41 -9999 0 41
RAP1B 0 0 -9999 0 -9999 0 0
alphaM/beta2 Integrin/uPA 0.021 0.072 -9999 0 -0.132 61 61
fibrinolysis 0.036 0.079 -9999 0 -0.124 59 59
HCK 0.027 0.016 -9999 0 0 123 123
dendritic cell antigen processing and presentation 0.024 0.071 -9999 0 -0.237 14 14
VTN 0.036 0.004 -9999 0 0 5 5
alphaM/beta2 Integrin/CYR61 0.012 0.093 -9999 0 -0.137 116 116
LPA 0.032 0.012 -9999 0 0 56 56
LRP1 0.031 0.013 -9999 0 0 68 68
cell migration -0.001 0.105 0.151 6 -0.143 144 150
FN1 0.034 0.009 -9999 0 0 29 29
alphaM/beta2 Integrin/Thy1 0.031 0.084 -9999 0 -0.133 85 85
MPO 0.036 0.003 -9999 0 0 4 4
KNG1 0.035 0.006 -9999 0 0 15 15
RAP1/GDP 0.024 0.007 -9999 0 -0.107 1 1
ROCK1 0.027 0.072 0.222 1 -0.293 6 7
ELA2 0.033 0.01 -9999 0 0 38 38
PLG 0.034 0.009 -9999 0 0 34 34
CTGF 0.027 0.016 -9999 0 0 128 128
alphaM/beta2 Integrin/Hck 0.03 0.091 -9999 0 -0.171 69 69
ITGAM 0.041 0.01 0.08 3 -9999 0 3
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.071 0.07 -9999 0 -0.116 48 48
HP 0.026 0.016 -9999 0 0 132 132
leukocyte adhesion 0.022 0.115 -9999 0 -0.209 61 61
SELP 0.035 0.006 -9999 0 0 14 14
IL2 signaling events mediated by STAT5

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
GAB2 0.032 0.013 -9999 0 -0.004 52 52
ELF1 0.042 0.015 -9999 0 -9999 0 0
CCNA2 0.028 0.015 -9999 0 0 109 109
PIK3CA 0.029 0.016 -9999 0 -0.002 93 93
JAK3 0.033 0.012 -9999 0 -0.007 38 38
PIK3R1 0.031 0.014 -9999 0 -0.002 66 66
JAK1 0.033 0.012 -9999 0 -0.003 42 42
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.019 0.177 0.233 2 -0.585 31 33
SHC1 0.032 0.014 -9999 0 -0.005 57 57
SP1 -0.013 0.122 -9999 0 -0.272 87 87
IL2RA 0.011 0.012 -9999 0 -9999 0 0
IL2RB 0.032 0.014 -9999 0 -0.003 60 60
SOS1 0 0.002 -9999 0 -9999 0 0
IL2RG 0.034 0.011 -9999 0 -0.029 6 6
G1/S transition of mitotic cell cycle -0.071 0.273 0.284 13 -0.567 95 108
PTPN11 0.035 0.009 -9999 0 -0.03 7 7
CCND2 -0.071 0.191 -9999 0 -0.493 82 82
LCK 0.035 0.01 -9999 0 -0.008 23 23
GRB2 0.034 0.01 -9999 0 -0.009 23 23
IL2 0.035 0.009 -9999 0 -0.014 15 15
CDK6 0.025 0.017 -9999 0 0 156 156
CCND3 -0.026 0.2 0.394 1 -0.804 23 24
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.032 0.012 -9999 0 0 57 57
LAT2 -0.015 0.088 -9999 0 -0.264 43 43
AP1 -0.055 0.175 -9999 0 -0.38 69 69
mol:PIP3 0.021 0.133 0.241 42 -0.278 41 83
IKBKB 0.012 0.092 0.188 36 -0.186 35 71
AKT1 -0.049 0.107 0.25 13 -0.266 45 58
IKBKG 0.01 0.091 0.185 34 -0.186 35 69
MS4A2 0.039 0.007 0.064 5 0 3 8
mol:Sphingosine-1-phosphate 0 0 -9999 0 -9999 0 0
PIK3CA 0.03 0.014 -9999 0 0 85 85
MAP3K1 -0.015 0.117 0.218 13 -0.309 41 54
mol:Ca2+ 0.022 0.112 0.204 54 -0.218 41 95
LYN 0.03 0.015 -9999 0 -0.033 6 6
CBLB -0.02 0.108 0.176 1 -0.273 60 61
SHC1 0.033 0.011 -9999 0 0 48 48
RasGAP/p62DOK 0.047 0.052 -9999 0 -0.117 36 36
positive regulation of cell migration -0.01 0.003 -9999 0 -9999 0 0
INPP5D 0 0 -9999 0 -9999 0 0
PLD2 -0.031 0.07 0.297 10 -0.173 12 22
PTPN13 -0.03 0.182 -9999 0 -0.593 32 32
PTPN11 0.03 0.022 -9999 0 -0.034 45 45
GO:0007205 0 0 -9999 0 -9999 0 0
regulation of mast cell degranulation -0.031 0.111 0.238 6 -0.307 35 41
SYK 0.03 0.015 -9999 0 -0.033 6 6
GRB2 0.035 0.007 -9999 0 0 16 16
LAT/PLCgamma1/GRB2/SLP76/GADs 0.01 0.112 0.213 7 -0.267 52 59
LAT -0.019 0.107 0.176 1 -0.274 58 59
PAK2 -0.014 0.125 0.222 13 -0.33 42 55
NFATC2 -0.012 0.013 -9999 0 -0.042 65 65
HRAS -0.015 0.13 0.197 13 -0.338 47 60
GAB2 0.033 0.01 -9999 0 0 44 44
PLA2G1B -0.005 0.191 -9999 0 -0.91 19 19
Fc epsilon R1 0.041 0.066 -9999 0 -0.11 67 67
Antigen/IgE/Fc epsilon R1 0.042 0.059 -9999 0 -0.093 66 66
mol:GDP -0.007 0.133 0.205 11 -0.355 44 55
JUN 0.033 0.01 -9999 0 0 39 39
mol:Ca++ 0 0 -9999 0 -9999 0 0
PIK3R1 0.032 0.012 -9999 0 0 61 61
FOS 0.025 0.017 -9999 0 0 147 147
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.014 0.114 -9999 0 -0.279 62 62
CHUK 0.013 0.089 0.184 36 -0.184 36 72
KLRG1 -0.017 0.094 0.124 2 -0.263 45 47
VAV1 -0.018 0.105 0.162 4 -0.281 53 57
calcium-dependent protein kinase C activity 0 0 -9999 0 -9999 0 0
CBL -0.021 0.109 0.176 1 -0.272 61 62
negative regulation of mast cell degranulation -0.021 0.088 -9999 0 -0.252 44 44
BTK -0.009 0.129 -9999 0 -0.367 40 40
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.025 0.105 -9999 0 -0.19 109 109
GAB2/PI3K/SHP2 -0.067 0.074 -9999 0 -0.2 83 83
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.004 0.071 -9999 0 -0.184 57 57
RAF1 -0.008 0.197 -9999 0 -0.971 19 19
Fc epsilon R1/FcgammaRIIB/SHIP 0.023 0.093 -9999 0 -0.129 121 121
FCER1G 0.029 0.015 -9999 0 0 106 106
FCER1A 0.033 0.012 -9999 0 -0.032 6 6
Antigen/IgE/Fc epsilon R1/Fyn 0.041 0.081 -9999 0 -0.112 94 94
MAPK3 -0.004 0.188 -9999 0 -0.9 19 19
MAPK1 -0.014 0.199 -9999 0 -0.949 19 19
NFKB1 0.035 0.007 -9999 0 0 17 17
MAPK8 -0.122 0.283 -9999 0 -0.549 141 141
DUSP1 0.031 0.013 -9999 0 0 75 75
NF-kappa-B/RelA 0.018 0.065 0.132 31 -0.127 35 66
actin cytoskeleton reorganization -0.02 0.182 -9999 0 -0.6 30 30
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -9999 0 0
PI3K -0.01 0.141 0.226 4 -0.316 59 63
FER -0.019 0.111 0.159 2 -0.272 62 64
RELA 0.035 0.005 -9999 0 0 10 10
ITK 0.003 0.036 -9999 0 -0.302 2 2
SOS1 0 0 -9999 0 -9999 0 0
PLCG1 -0.002 0.132 0.25 14 -0.345 41 55
cytokine secretion 0.01 0.044 0.085 26 -0.093 35 61
SPHK1 -0.016 0.111 0.153 4 -0.272 60 64
PTK2 -0.023 0.191 -9999 0 -0.634 30 30
NTAL/PLCgamma1/GRB2/SLP76/GADs 0.024 0.12 0.258 9 -0.277 45 54
EDG1 -0.01 0.003 -9999 0 -9999 0 0
mol:DAG 0.004 0.142 0.24 34 -0.298 52 86
MAP2K2 -0.004 0.196 -9999 0 -0.917 19 19
MAP2K1 -0.018 0.185 -9999 0 -0.921 19 19
MAP2K7 0.034 0.009 -9999 0 0 30 30
KLRG1/SHP2 0.004 0.094 0.196 10 -0.253 39 49
MAP2K4 0.021 0.146 -9999 0 -0.88 12 12
Fc epsilon R1/FcgammaRIIB 0.024 0.1 -9999 0 -0.14 121 121
mol:Choline -0.031 0.069 0.295 10 -0.171 12 22
SHC/Grb2/SOS1 0.014 0.122 0.194 1 -0.266 60 61
FYN 0.03 0.014 -9999 0 0 82 82
DOK1 0.036 0.002 -9999 0 0 2 2
PXN -0.025 0.176 -9999 0 -0.583 30 30
HCLS1 -0.022 0.123 0.16 7 -0.303 62 69
PRKCB 0.014 0.112 0.207 41 -0.225 46 87
FCGR2B 0.02 0.018 -9999 0 0 214 214
IGHE -0.001 0.004 0.02 2 -9999 0 2
KLRG1/SHIP -0.021 0.089 -9999 0 -0.257 44 44
LCP2 0.031 0.013 -9999 0 0 71 71
PLA2G4A -0.012 0.113 0.156 7 -0.294 54 61
RASA1 0.034 0.009 -9999 0 0 30 30
mol:Phosphatidic acid -0.031 0.069 0.295 10 -0.171 12 22
IKK complex 0.008 0.077 0.182 25 -0.161 21 46
WIPF1 0 0 -9999 0 -9999 0 0
S1P5 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
mol:S1P 0 0 -9999 0 -9999 0 0
telencephalon oligodendrocyte cell migration -0.003 0.108 0.279 39 -9999 0 39
GNAI2 0.033 0.01 -9999 0 0 42 42
S1P/S1P5/G12 0.011 0.032 -9999 0 -0.107 31 31
mol:GDP 0 0 -9999 0 -9999 0 0
GNAO1 0.03 0.014 -9999 0 0 81 81
RhoA/GTP 0.003 0.11 -9999 0 -0.284 39 39
negative regulation of cAMP metabolic process -0.014 0.102 -9999 0 -0.265 48 48
GNAZ 0.03 0.013 -9999 0 0 79 79
GNAI3 0.035 0.006 -9999 0 0 12 12
GNA12 0.026 0.016 -9999 0 0 136 136
S1PR5 0 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
S1P/S1P5/Gi -0.014 0.103 -9999 0 -0.267 48 48
RhoA/GDP 0.024 0.019 -9999 0 -0.132 7 7
RHOA 0.035 0.007 -9999 0 0 21 21
GNAI1 0.018 0.018 -9999 0 0 245 245
IL23-mediated signaling events

Figure 33.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 35.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.052 0.597 0.747 32 -1.018 120 152
IL23A 0.098 0.368 0.769 20 -0.959 20 40
NF kappa B1 p50/RelA/I kappa B alpha 0.089 0.34 0.637 17 -0.834 22 39
positive regulation of T cell mediated cytotoxicity 0.101 0.387 0.757 36 -0.932 22 58
ITGA3 0.099 0.354 0.72 24 -0.889 19 43
IL17F 0.04 0.267 0.501 36 -0.585 25 61
IL12B 0.061 0.079 0.19 73 -9999 0 73
STAT1 (dimer) 0.078 0.356 0.651 28 -0.887 23 51
CD4 0.082 0.411 0.75 27 -1.042 30 57
IL23 0.098 0.353 0.727 17 -0.928 20 37
IL23R 0.07 0.135 0.29 86 -0.149 8 94
IL1B 0.092 0.399 0.743 30 -1.1 23 53
T-helper cell lineage commitment 0 0 -9999 0 -9999 0 0
IL24 0.097 0.348 0.743 17 -0.869 17 34
TYK2 0.042 0.059 0.148 49 -9999 0 49
STAT4 0.034 0.009 -9999 0 0 30 30
STAT3 0.033 0.01 -9999 0 0 37 37
IL18RAP 0.035 0.008 -9999 0 -0.031 3 3
IL12RB1 0.045 0.059 0.152 46 -9999 0 46
PIK3CA 0.03 0.014 -9999 0 0 85 85
IL12Rbeta1/TYK2 0.052 0.076 0.183 38 -0.135 12 50
IL23R/JAK2 0.101 0.162 0.378 74 -0.191 9 83
positive regulation of chronic inflammatory response 0.101 0.387 0.757 36 -0.932 22 58
natural killer cell activation -0.005 0.011 -9999 0 -0.029 43 43
JAK2 0.055 0.078 0.19 69 -9999 0 69
PIK3R1 0.032 0.012 -9999 0 0 61 61
NFKB1 0.038 0.009 0.065 2 0 17 19
RELA 0.039 0.008 0.065 2 0 10 12
positive regulation of dendritic cell antigen processing and presentation 0.1 0.345 0.711 19 -0.875 21 40
ALOX12B 0.095 0.352 0.739 18 -0.875 18 36
CXCL1 0.104 0.362 0.748 31 -0.876 18 49
T cell proliferation 0.101 0.387 0.757 36 -0.932 22 58
NFKBIA 0.036 0.013 0.065 2 0 47 49
IL17A 0.068 0.243 0.446 55 -0.46 26 81
PI3K 0.047 0.341 0.633 21 -0.868 23 44
IFNG 0.019 0.033 0.097 27 -0.08 5 32
STAT3 (dimer) 0.048 0.339 0.618 22 -0.821 25 47
IL18R1 0.035 0.008 -9999 0 -0.031 4 4
IL23/IL23R/JAK2/TYK2/SOCS3 0.104 0.264 0.557 46 -0.513 16 62
IL18/IL18R 0.06 0.035 -9999 0 -0.12 6 6
macrophage activation -0.002 0.015 0.035 2 -0.042 17 19
TNF 0.101 0.358 0.745 22 -0.883 21 43
STAT3/STAT4 0.077 0.349 0.614 23 -0.852 24 47
STAT4 (dimer) 0.079 0.353 0.635 25 -0.887 23 48
IL18 0.031 0.013 -9999 0 0 69 69
IL19 0.098 0.349 0.724 20 -0.869 17 37
STAT5A (dimer) 0.092 0.36 0.648 28 -0.884 23 51
STAT1 0.033 0.01 -9999 0 0 40 40
SOCS3 0.036 0.004 -9999 0 0 5 5
CXCL9 0.108 0.36 0.753 26 -0.876 18 44
MPO 0.095 0.351 0.724 20 -0.838 21 41
positive regulation of humoral immune response 0.101 0.387 0.757 36 -0.932 22 58
IL23/IL23R/JAK2/TYK2 0.092 0.389 0.763 33 -0.961 22 55
IL6 0.152 0.365 0.744 42 -0.882 17 59
STAT5A 0.036 0.004 -9999 0 0 6 6
IL2 0.021 0.03 0.074 1 -0.035 103 104
positive regulation of tyrosine phosphorylation of STAT protein -0.005 0.011 -9999 0 -0.029 43 43
CD3E 0.095 0.351 0.743 17 -0.885 17 34
keratinocyte proliferation 0.101 0.387 0.757 36 -0.932 22 58
NOS2 0.096 0.352 0.67 36 -0.823 23 59
S1P4 pathway

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
mol:S1P 0 0 -9999 0 -9999 0 0
GNAO1 0.03 0.014 -9999 0 0 81 81
CDC42/GTP 0.002 0.108 -9999 0 -0.278 39 39
PLCG1 -0.016 0.1 -9999 0 -0.252 50 50
mol:GTP 0 0 -9999 0 -9999 0 0
GNAI2 0.033 0.01 -9999 0 0 42 42
GNAI3 0.035 0.006 -9999 0 0 12 12
G12/G13 0.028 0.049 -9999 0 -0.142 30 30
cell migration 0.001 0.106 -9999 0 -0.273 39 39
S1PR5 0 0 -9999 0 -9999 0 0
S1PR4 0 0 -9999 0 -9999 0 0
MAPK3 -0.016 0.101 -9999 0 -0.199 89 89
MAPK1 -0.009 0.095 -9999 0 -0.247 43 43
S1P/S1P5/Gi -0.014 0.103 -9999 0 -0.267 48 48
GNAI1 0.018 0.018 -9999 0 0 245 245
CDC42/GDP 0.026 0.006 -9999 0 -9999 0 0
S1P/S1P5/G12 0.011 0.032 -9999 0 -0.107 31 31
RHOA 0.02 0.09 0.187 101 -0.181 3 104
S1P/S1P4/Gi -0.014 0.103 -9999 0 -0.267 48 48
mol:GDP 0 0 -9999 0 -9999 0 0
GNAZ 0.03 0.013 -9999 0 0 79 79
S1P/S1P4/G12/G13 0.026 0.038 -9999 0 -0.102 30 30
GNA12 0.026 0.016 -9999 0 0 136 136
GNA13 0.035 0.007 -9999 0 0 18 18
CDC42 0.035 0.008 -9999 0 0 22 22
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0 0.05 -9999 0 -9999 0 0
PLK1 -0.059 0.202 -9999 0 -0.613 24 24
CDKN1B -0.1 0.213 0.432 4 -0.364 135 139
FOXO3 -0.064 0.215 0.318 5 -0.475 82 87
KAT2B -0.001 0.021 0.048 14 -0.04 85 99
FOXO1/SIRT1 0.013 0.055 -9999 0 -0.251 10 10
CAT -0.075 0.258 -9999 0 -0.883 26 26
CTNNB1 0.035 0.007 -9999 0 0 21 21
AKT1 0.021 0.042 -9999 0 -0.059 72 72
FOXO1 0.002 0.054 0.224 1 -0.261 9 10
MAPK10 0.036 0.086 0.186 99 -0.143 19 118
mol:GTP -0.001 0.004 -9999 0 -0.021 1 1
FOXO4 -0.042 0.194 0.267 9 -0.389 81 90
response to oxidative stress 0 0.023 0.051 13 -0.044 63 76
FOXO3A/SIRT1 -0.06 0.217 0.292 4 -0.461 85 89
XPO1 0.036 0.004 -9999 0 0 5 5
EP300 0.033 0.011 -9999 0 -9999 0 0
BCL2L11 0.023 0.031 -9999 0 -9999 0 0
FOXO1/SKP2 0.018 0.057 0.2 1 -0.246 9 10
mol:GDP 0 0.023 0.051 13 -0.044 63 76
RAN 0.034 0.011 -9999 0 -0.013 23 23
GADD45A -0.149 0.331 0.436 1 -0.793 80 81
YWHAQ 0.036 0.005 -9999 0 0 8 8
FOXO1/14-3-3 family 0.005 0.147 -9999 0 -0.508 21 21
MST1 0.021 0.042 0.106 1 -0.059 85 86
CSNK1D 0.035 0.007 -9999 0 0 19 19
CSNK1E 0.031 0.012 -9999 0 0 64 64
FOXO4/14-3-3 family -0.006 0.154 -9999 0 -0.482 26 26
YWHAB 0.035 0.007 -9999 0 0 21 21
MAPK8 0.021 0.074 0.183 64 -0.135 15 79
MAPK9 0.042 0.092 0.184 118 -0.136 20 138
YWHAG 0 0 -9999 0 -9999 0 0
YWHAE 0.034 0.009 -9999 0 0 29 29
YWHAZ 0.035 0.007 -9999 0 0 17 17
SIRT1 0.021 0.022 -9999 0 -0.034 31 31
SOD2 -0.128 0.342 0.402 4 -0.768 89 93
RBL2 -0.079 0.29 -9999 0 -0.918 38 38
RAL/GDP 0.02 0.051 -9999 0 -0.12 26 26
CHUK 0.013 0.039 -9999 0 -0.058 77 77
Ran/GTP 0.018 0.025 -9999 0 -0.054 21 21
CSNK1G2 0.033 0.01 -9999 0 0 37 37
RAL/GTP 0.019 0.052 0.142 2 -0.112 26 28
CSNK1G1 0.036 0.005 -9999 0 0 8 8
FASLG 0.02 0.042 -9999 0 -0.592 1 1
SKP2 0.035 0.006 -9999 0 0 16 16
USP7 0.034 0.01 -9999 0 -0.012 20 20
IKBKB 0.022 0.043 0.106 1 -0.058 91 92
CCNB1 -0.162 0.414 0.486 1 -1.053 80 81
FOXO1-3a-4/beta catenin -0.043 0.211 0.358 12 -0.383 93 105
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.056 0.199 1 -0.245 9 10
CSNK1A1 0.035 0.006 -9999 0 0 12 12
SGK1 -0.001 0.021 0.048 14 -0.04 85 99
CSNK1G3 0.035 0.005 -9999 0 0 11 11
Ran/GTP/Exportin 1 0.038 0.036 -9999 0 -0.138 7 7
ZFAND5 -0.028 0.157 0.243 10 -0.312 80 90
SFN 0.031 0.013 -9999 0 0 74 74
CDK2 0.035 0.012 -9999 0 -0.03 2 2
FOXO3A/14-3-3 -0.013 0.158 -9999 0 -0.444 32 32
CREBBP 0.038 0.007 -9999 0 -0.03 2 2
FBXO32 -0.058 0.2 0.29 5 -0.435 82 87
BCL6 -0.099 0.328 -9999 0 -0.94 51 51
RALB 0.033 0.013 -9999 0 -0.016 30 30
RALA 0.025 0.017 -9999 0 -0.001 147 147
YWHAH 0.031 0.013 -9999 0 0 74 74
Osteopontin-mediated 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
IKK alpha homodimer 0.003 0.077 0.196 2 -0.189 36 38
NF kappa B1 p50/RelA/I kappa B alpha -0.014 0.121 0.245 1 -0.311 42 43
alphaV/beta3 Integrin/Osteopontin/Src 0.026 0.081 -9999 0 -0.15 75 75
AP1 -0.015 0.143 0.275 3 -0.275 79 82
ILK -0.03 0.073 0.197 2 -0.238 31 33
bone resorption -0.04 0.081 0.179 7 -0.232 32 39
PTK2B 0.035 0.006 -9999 0 0 15 15
PYK2/p130Cas 0.044 0.089 -9999 0 -0.166 51 51
ITGAV 0.031 0.026 -9999 0 -0.056 32 32
mol:GTP 0 0 -9999 0 -9999 0 0
CD44/Rho Family GTPase/ROCK2 0.021 0.068 -9999 0 -0.142 68 68
alphaV/beta3 Integrin/Osteopontin 0.049 0.092 -9999 0 -0.158 68 68
MAP3K1 -0.029 0.064 0.198 2 -0.205 25 27
JUN 0.034 0.01 -9999 0 0 39 39
MAPK3 -0.03 0.084 0.177 7 -0.237 38 45
MAPK1 -0.028 0.086 0.166 12 -0.25 37 49
Rac1/GDP 0.018 0.02 -9999 0 -0.132 6 6
NFKB1 0.035 0.007 -9999 0 0 17 17
MAPK8 -0.026 0.06 0.175 3 -0.194 30 33
ITGB3 0.032 0.026 -9999 0 -0.056 37 37
NFKBIA -0.034 0.108 0.179 7 -0.311 43 50
FOS 0.026 0.017 -9999 0 0 147 147
CD44 0.029 0.015 -9999 0 0 102 102
CHUK 0.026 0.016 -9999 0 0 133 133
PLAU -0.065 0.247 -9999 0 -0.989 28 28
NF kappa B1 p50/RelA 0.005 0.126 0.235 2 -0.323 38 40
BCAR1 0 0 -9999 0 -9999 0 0
RELA 0.035 0.005 -9999 0 0 10 10
alphaV beta3 Integrin 0.04 0.058 -9999 0 -0.129 42 42
mol:GDP 0 0 -9999 0 -9999 0 0
SYK -0.031 0.064 0.189 2 -0.23 26 28
VAV3 -0.032 0.066 0.192 1 -0.227 31 32
MAP3K14 -0.027 0.074 0.169 5 -0.207 33 38
ROCK2 0.035 0.007 -9999 0 0 21 21
SPP1 0.03 0.025 -9999 0 -0.057 28 28
RAC1 0.027 0.016 -9999 0 0 123 123
Rac1/GTP -0.023 0.073 0.145 4 -0.219 31 35
MMP2 -0.061 0.121 0.176 2 -0.325 62 64
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.035 0.17 -9999 0 -0.462 64 64
HDAC1 0.026 0.034 0.08 55 -0.038 83 138
AES 0.033 0.013 0.069 8 -0.002 50 58
FBXW11 0.035 0.007 -9999 0 0 20 20
DTX1 0 0 -9999 0 -9999 0 0
LRP6/FZD1 0.033 0.027 -9999 0 -0.141 1 1
TLE1 0.034 0.011 0.067 10 -0.006 26 36
AP1 -0.012 0.077 -9999 0 -0.206 58 58
NCSTN 0.034 0.008 -9999 0 0 28 28
ADAM10 0.032 0.012 -9999 0 0 57 57
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.008 0.127 -9999 0 -0.457 13 13
NICD/RBPSUH -0.041 0.167 -9999 0 -0.462 64 64
WIF1 0.028 0.015 -9999 0 0 106 106
NOTCH1 -0.037 0.177 -9999 0 -0.489 63 63
PSENEN 0.034 0.009 -9999 0 0 33 33
KREMEN2 0.036 0.004 -9999 0 0 5 5
DKK1 0.018 0.018 -9999 0 0 240 240
beta catenin/beta TrCP1 0.057 0.093 0.234 17 -0.298 8 25
APH1B 0.035 0.006 -9999 0 0 14 14
APH1A 0.035 0.006 -9999 0 0 16 16
AXIN1 0.01 0.069 0.235 4 -0.368 1 5
CtBP/CBP/TCF1/TLE1/AES 0.013 0.073 0.172 49 -0.179 18 67
PSEN1 0.033 0.01 -9999 0 0 41 41
FOS 0.025 0.017 -9999 0 0 147 147
JUN 0.033 0.01 -9999 0 0 39 39
MAP3K7 0.032 0.017 0.062 9 -0.01 55 64
CTNNB1 0.044 0.088 0.22 22 -0.307 5 27
MAPK3 0.036 0.003 -9999 0 0 4 4
DKK2/LRP6/Kremen 2 0.064 0.026 -9999 0 -0.123 1 1
HNF1A 0 0.006 0.033 9 -9999 0 9
CTBP1 0.034 0.012 0.071 7 -0.005 28 35
MYC -0.08 0.364 -9999 0 -1.153 49 49
NKD1 0 0.002 -9999 0 -9999 0 0
FZD1 0.025 0.017 -9999 0 0 155 155
NOTCH1 precursor/Deltex homolog 1 -0.041 0.167 -9999 0 -0.462 64 64
apoptosis -0.013 0.077 -9999 0 -0.204 59 59
Delta 1/NOTCHprecursor -0.041 0.167 -9999 0 -0.462 64 64
DLL1 0 0 -9999 0 -9999 0 0
PPARD 0.02 0.066 -9999 0 -0.678 3 3
Gamma Secretase 0.076 0.073 -9999 0 -0.153 29 29
APC -0.022 0.164 0.231 2 -0.638 26 28
DVL1 0.016 0.091 -9999 0 -0.406 15 15
CSNK2A1 0.034 0.01 -9999 0 -0.001 32 32
MAP3K7IP1 0.032 0.017 0.063 9 -0.01 48 57
DKK1/LRP6/Kremen 2 0.033 0.037 -9999 0 -9999 0 0
LRP6 0.033 0.01 -9999 0 0 37 37
CSNK1A1 0.035 0.007 -9999 0 -0.002 13 13
NLK 0.01 0.053 0.13 1 -0.206 22 23
CCND1 -0.054 0.344 -9999 0 -1.129 42 42
WNT1 0.035 0.006 -9999 0 0 16 16
Axin1/APC/beta catenin 0.011 0.135 0.294 4 -0.423 27 31
DKK2 0.034 0.009 -9999 0 0 29 29
NOTCH1 precursor/DVL1 -0.018 0.19 -9999 0 -0.49 53 53
GSK3B 0.034 0.01 -9999 0 0 35 35
FRAT1 0.027 0.016 -9999 0 0 130 130
NOTCH/Deltex homolog 1 -0.035 0.17 -9999 0 -0.462 64 64
PPP2R5D 0.025 0.037 -9999 0 -0.25 4 4
MAPK1 0.033 0.011 -9999 0 0 48 48
WNT1/LRP6/FZD1 0.058 0.044 -9999 0 -9999 0 0
RBPJ 0 0 -9999 0 -9999 0 0
CREBBP 0.032 0.021 0.07 6 -0.018 61 67
Ephrin B reverse 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
EFNB2 0.028 0.015 -9999 0 0 110 110
EPHB2 0.034 0.01 0.055 1 0 35 36
EFNB1 -0.018 0.015 0.023 53 -9999 0 53
mol:GTP 0 0 -9999 0 -9999 0 0
Rac1/GDP 0.052 0.054 -9999 0 -0.15 9 9
Ephrin B2/EPHB1-2 0.031 0.056 -9999 0 -0.105 51 51
neuron projection morphogenesis 0.035 0.042 -9999 0 -0.134 11 11
Ephrin B1/EPHB1-2/Tiam1 0.056 0.049 -9999 0 -0.103 27 27
DNM1 0.035 0.008 -9999 0 0 23 23
cell-cell signaling 0 0.003 0.023 1 -9999 0 1
MAP2K4 -0.053 0.158 0.202 1 -0.52 48 49
YES1 -0.054 0.234 -9999 0 -0.745 49 49
Ephrin B1/EPHB1-2/NCK2 0.06 0.043 -9999 0 -0.101 19 19
PI3K -0.021 0.189 -9999 0 -0.566 48 48
mol:GDP 0.054 0.048 -9999 0 -0.102 27 27
ITGA2B 0.036 0.003 -9999 0 0 3 3
endothelial cell proliferation 0.016 0.048 -9999 0 -0.114 46 46
FYN -0.065 0.239 -9999 0 -0.765 49 49
MAP3K7 -0.05 0.163 -9999 0 -0.54 47 47
FGR -0.05 0.224 -9999 0 -0.722 48 48
TIAM1 0.033 0.01 -9999 0 0 43 43
PIK3R1 0.032 0.012 -9999 0 0 61 61
RGS3 0.035 0.007 -9999 0 0 20 20
cell adhesion -0.033 0.174 -9999 0 -0.536 48 48
LYN -0.059 0.228 -9999 0 -0.734 48 48
Ephrin B1/EPHB1-2/Src Family Kinases -0.055 0.209 -9999 0 -0.677 49 49
Ephrin B1/EPHB1-2 -0.046 0.174 -9999 0 -0.574 47 47
SRC -0.049 0.225 -9999 0 -0.716 49 49
ITGB3 0.036 0.004 -9999 0 0 5 5
EPHB1 0.03 0.014 -9999 0 0 87 87
EPHB4 0.026 0.016 -9999 0 0 141 141
RAC1 0.027 0.016 -9999 0 0 123 123
Ephrin B2/EPHB4 0.016 0.048 -9999 0 -0.114 46 46
alphaIIb/beta3 Integrin 0.053 0.005 -9999 0 -9999 0 0
BLK -0.051 0.226 -9999 0 -0.719 49 49
HCK -0.063 0.23 -9999 0 -0.733 49 49
regulation of stress fiber formation -0.058 0.042 0.101 19 -9999 0 19
MAPK8 -0.056 0.15 -9999 0 -0.499 48 48
Ephrin B1/EPHB1-2/RGS3 0.065 0.033 -9999 0 -0.111 6 6
endothelial cell migration 0.002 0.17 0.196 112 -0.447 44 156
NCK2 0.035 0.007 -9999 0 0 19 19
PTPN13 0.034 0.013 -9999 0 0 56 56
regulation of focal adhesion formation -0.058 0.042 0.101 19 -9999 0 19
chemotaxis -0.063 0.032 0.111 6 -9999 0 6
PIK3CA 0.03 0.014 -9999 0 0 85 85
Rac1/GTP 0.045 0.048 -9999 0 -0.145 9 9
angiogenesis -0.045 0.173 -9999 0 -0.571 47 47
LCK -0.048 0.223 -9999 0 -0.718 48 48
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.041 0.01 -9999 0 -0.041 1 1
NFATC2 0.014 0.156 0.267 5 -0.359 40 45
NFATC3 0.02 0.131 0.258 25 -0.235 68 93
CD40LG -0.011 0.336 0.487 46 -0.687 67 113
ITCH 0.035 0.047 0.19 8 -9999 0 8
CBLB 0.037 0.048 0.193 11 -9999 0 11
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.052 0.255 0.381 13 -0.624 52 65
JUNB 0.03 0.014 -9999 0 0 83 83
CaM/Ca2+/Calcineurin A alpha-beta B1 0.034 0.028 -9999 0 -0.136 6 6
T cell anergy 0.016 0.067 0.255 9 -0.241 1 10
TLE4 0.011 0.108 -9999 0 -0.316 21 21
Jun/NFAT1-c-4/p21SNFT -0.018 0.321 0.442 2 -0.723 67 69
AP-1/NFAT1-c-4 -0.042 0.338 -9999 0 -0.78 63 63
IKZF1 0.007 0.1 0.165 8 -0.24 38 46
T-helper 2 cell differentiation -0.079 0.226 -9999 0 -0.62 39 39
AP-1/NFAT1 0.015 0.147 0.275 19 -0.285 47 66
CALM1 0.045 0.023 0.127 2 -9999 0 2
EGR2 -0.069 0.412 0.494 13 -0.968 71 84
EGR3 -0.054 0.417 0.478 19 -0.976 67 86
NFAT1/FOXP3 0.038 0.125 0.258 2 -0.273 30 32
EGR1 0.029 0.015 0.07 1 0 103 104
JUN 0.033 0.042 0.11 36 -0.049 15 51
EGR4 0.036 0.004 0.07 1 0 5 6
mol:Ca2+ 0.005 0.003 -9999 0 -9999 0 0
GBP3 0.007 0.1 0.165 8 -0.24 38 46
FOSL1 0.032 0.012 -9999 0 0 56 56
NFAT1-c-4/MAF/IRF4 0.011 0.329 -9999 0 -0.71 70 70
DGKA 0.012 0.105 -9999 0 -0.292 23 23
CREM 0.027 0.015 -9999 0 0 121 121
NFAT1-c-4/PPARG -0.004 0.325 -9999 0 -0.724 69 69
CTLA4 0.01 0.093 -9999 0 -0.257 22 22
NFAT1-c-4 (dimer)/EGR1 -0.027 0.335 -9999 0 -0.763 70 70
NFAT1-c-4 (dimer)/EGR4 0.004 0.331 -9999 0 -0.728 69 69
FOS 0.024 0.038 0.102 32 -0.042 51 83
IFNG -0.01 0.132 -9999 0 -0.42 16 16
T cell activation -0.01 0.217 0.422 5 -0.555 28 33
MAF 0.034 0.009 -9999 0 0 34 34
T-helper 2 cell lineage commitment 0 0 -9999 0 -9999 0 0
activation-induced cell death of T cells 0.006 0.276 0.603 67 -0.45 19 86
TNF -0.036 0.306 0.384 15 -0.697 71 86
FASLG -0.094 0.458 0.553 2 -1.102 70 72
TBX21 0.04 0.007 0.107 3 -9999 0 3
BATF3 0 0 -9999 0 -9999 0 0
PRKCQ 0.027 0.017 -9999 0 -9999 0 0
PTPN1 0.008 0.116 -9999 0 -0.342 26 26
NFAT1-c-4/ICER1 -0.026 0.319 -9999 0 -0.729 69 69
GATA3 0.027 0.017 -9999 0 -9999 0 0
T-helper 1 cell differentiation 0.004 0.143 -9999 0 -0.415 16 16
IL2RA -0.066 0.242 0.326 3 -0.599 58 61
T-helper 1 cell lineage commitment 0 0 -9999 0 -9999 0 0
CASP3 0.009 0.114 -9999 0 -0.354 23 23
E2F1 0.036 0.053 -9999 0 -0.243 14 14
PPARG 0.034 0.008 -9999 0 -9999 0 0
SLC3A2 0.008 0.123 0.227 2 -0.383 25 27
IRF4 0.036 0.005 -9999 0 0 8 8
PTGS2 -0.072 0.278 0.434 3 -0.691 63 66
CSF2 -0.011 0.335 0.487 46 -0.687 67 113
JunB/Fra1/NFAT1-c-4 -0.019 0.305 -9999 0 -0.71 66 66
IL4 -0.083 0.232 -9999 0 -0.65 38 38
IL5 -0.012 0.335 0.487 46 -0.687 67 113
IL2 -0.011 0.219 0.43 2 -0.563 28 30
IL3 0.008 0.082 -9999 0 -0.676 4 4
RNF128 0.014 0.022 0.171 1 -9999 0 1
NFATC1 -0.006 0.277 0.451 19 -0.605 67 86
CDK4 -0.015 0.275 0.597 29 -1.037 14 43
PTPRK -0.004 0.145 -9999 0 -0.435 37 37
IL8 -0.1 0.291 0.446 8 -0.729 64 72
POU2F1 0.039 0.008 -9999 0 -9999 0 0
BCR signaling 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
JUN 0 0.114 0.255 3 -0.296 31 34
IKBKB 0.016 0.079 0.263 4 -0.269 10 14
AKT1 0.003 0.089 0.211 38 -0.184 17 55
IKBKG 0.011 0.073 0.226 2 -0.248 11 13
CALM1 -0.024 0.126 0.228 4 -0.374 38 42
PIK3CA 0.03 0.014 -9999 0 0 85 85
MAP3K1 0.024 0.123 0.275 8 -0.348 23 31
MAP3K7 0.033 0.01 -9999 0 0 38 38
mol:Ca2+ -0.022 0.133 0.235 5 -0.386 38 43
DOK1 0.036 0.002 -9999 0 0 2 2
AP-1 -0.01 0.091 0.189 12 -0.213 41 53
LYN 0.031 0.013 -9999 0 0 72 72
BLNK 0.02 0.018 -9999 0 0 219 219
SHC1 0.033 0.011 -9999 0 0 48 48
BCR complex 0.049 0.015 -9999 0 -9999 0 0
CD22 -0.011 0.088 -9999 0 -0.286 30 30
CAMK2G -0.016 0.12 0.222 5 -0.356 38 43
CSNK2A1 0.034 0.009 -9999 0 0 31 31
INPP5D 0 0 -9999 0 -9999 0 0
SHC/GRB2/SOS1 -0.008 0.064 -9999 0 -0.149 52 52
GO:0007205 -0.022 0.135 0.235 5 -0.394 38 43
SYK 0.031 0.013 -9999 0 0 71 71
ELK1 -0.027 0.129 0.243 3 -0.379 38 41
NFATC1 -0.017 0.091 0.232 5 -0.257 33 38
B-cell antigen/BCR complex 0.049 0.015 -9999 0 -9999 0 0
PAG1/CSK 0.023 0.023 -9999 0 -0.132 10 10
NFKBIB 0.021 0.043 0.13 1 -0.131 18 19
HRAS -0.023 0.117 0.222 4 -0.327 40 44
NFKBIA 0.022 0.039 0.13 1 -0.125 14 15
NF-kappa-B/RelA/I kappa B beta 0.026 0.038 0.13 1 -0.103 18 19
RasGAP/Csk 0.044 0.093 -9999 0 -0.12 104 104
mol:GDP -0.02 0.131 0.243 4 -0.372 39 43
PTEN 0.027 0.016 -9999 0 0 130 130
CD79B 0.036 0.005 -9999 0 0 9 9
NF-kappa-B/RelA/I kappa B alpha 0.026 0.037 0.123 2 -0.1 14 16
GRB2 0.035 0.006 -9999 0 0 16 16
PI3K/BCAP/CD19 -0.033 0.155 0.367 1 -0.428 40 41
PIK3R1 0.032 0.012 -9999 0 0 61 61
mol:IP3 -0.022 0.135 0.247 4 -0.4 37 41
CSK 0.035 0.007 -9999 0 0 17 17
FOS -0.025 0.128 0.203 9 -0.368 39 48
CHUK -0.048 0.131 0.226 2 -0.256 107 109
IBTK 0.034 0.008 -9999 0 0 24 24
CARD11/BCL10/MALT1/TAK1 0.001 0.132 0.278 2 -0.342 37 39
PTPN6 -0.02 0.086 0.151 4 -0.295 29 33
RELA 0.036 0.005 -9999 0 0 10 10
BCL2A1 0.018 0.033 0.089 12 -0.091 18 30
VAV2 -0.013 0.097 -9999 0 -0.302 32 32
ubiquitin-dependent protein catabolic process 0.023 0.042 0.131 1 -0.128 18 19
BTK 0.018 0.012 -9999 0 -9999 0 0
CD19 -0.01 0.089 -9999 0 -0.284 30 30
MAP4K1 0.034 0.008 -9999 0 0 26 26
CD72 0.033 0.011 -9999 0 0 48 48
PAG1 0 0 -9999 0 -9999 0 0
MAPK14 0.02 0.111 0.251 9 -0.309 23 32
SH3BP5 0.033 0.011 -9999 0 0 47 47
PIK3AP1 -0.021 0.139 0.252 4 -0.421 37 41
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.03 0.176 -9999 0 -0.526 43 43
RAF1 -0.026 0.113 0.21 8 -0.315 42 50
RasGAP/p62DOK/SHIP 0.036 0.081 -9999 0 -0.111 100 100
CD79A 0.034 0.009 -9999 0 0 35 35
re-entry into mitotic cell cycle -0.01 0.091 0.187 12 -0.215 40 52
RASA1 0.034 0.009 -9999 0 0 30 30
MAPK3 -0.033 0.097 0.193 5 -0.302 34 39
MAPK1 -0.03 0.101 0.21 7 -0.307 34 41
CD72/SHP1 0.007 0.105 0.252 14 -0.281 30 44
NFKB1 0.035 0.007 -9999 0 0 17 17
MAPK8 0.019 0.11 0.251 10 -0.313 21 31
actin cytoskeleton organization 0.026 0.112 0.241 24 -0.291 17 41
NF-kappa-B/RelA 0.045 0.086 0.243 1 -0.24 22 23
Calcineurin -0.005 0.128 0.229 2 -0.334 39 41
PI3K -0.029 0.081 -9999 0 -0.257 30 30
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.017 0.135 0.233 4 -0.372 47 51
SOS1 0 0 -9999 0 -9999 0 0
Bam32/HPK1 0.02 0.139 -9999 0 -0.436 28 28
DAPP1 0 0.142 -9999 0 -0.473 27 27
cytokine secretion -0.015 0.087 0.228 5 -0.243 33 38
mol:DAG -0.022 0.135 0.247 4 -0.4 37 41
PLCG2 0.032 0.012 -9999 0 0 60 60
MAP2K1 -0.03 0.106 0.198 6 -0.308 40 46
B-cell antigen/BCR complex/FcgammaRIIB 0.016 0.072 -9999 0 -0.123 86 86
mol:PI-3-4-5-P3 -0.015 0.074 0.188 22 -0.213 15 37
ETS1 -0.024 0.114 0.208 5 -0.339 36 41
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.036 0.089 -9999 0 -0.152 55 55
B-cell antigen/BCR complex/LYN -0.007 0.092 -9999 0 -0.292 31 31
MALT1 0.034 0.009 -9999 0 0 29 29
TRAF6 0.036 0.005 -9999 0 0 8 8
RAC1 0.023 0.111 0.232 22 -0.307 17 39
B-cell antigen/BCR complex/LYN/SYK 0.025 0.1 0.265 1 -0.27 27 28
CARD11 -0.021 0.129 0.226 5 -0.373 38 43
FCGR2B 0.02 0.018 -9999 0 0 214 214
PPP3CA 0.034 0.009 -9999 0 0 35 35
BCL10 0.035 0.006 -9999 0 0 15 15
IKK complex 0.006 0.043 0.143 4 -0.115 8 12
PTPRC 0.029 0.015 -9999 0 0 103 103
PDPK1 -0.013 0.059 0.158 23 -0.158 13 36
PPP3CB 0.026 0.016 -9999 0 0 132 132
PPP3CC 0.035 0.006 -9999 0 0 14 14
POU2F2 0.016 0.031 0.102 7 -0.081 20 27
Noncanonical Wnt signaling pathway

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
NFATC2 0 0 -9999 0 -9999 0 0
GNB1/GNG2 0.003 0.098 -9999 0 -0.253 26 26
mol:DAG -0.013 0.088 0.189 3 -0.247 26 29
PLCG1 -0.013 0.09 0.191 3 -0.254 26 29
YES1 -0.016 0.084 -9999 0 -0.176 81 81
FZD3 0.028 0.015 -9999 0 0 104 104
FZD6 0.027 0.016 -9999 0 0 121 121
G protein -0.005 0.098 0.208 6 -0.272 26 32
MAP3K7 -0.035 0.075 0.145 7 -0.228 31 38
mol:Ca2+ -0.012 0.086 0.187 3 -0.241 26 29
mol:IP3 -0.013 0.088 0.189 3 -0.247 26 29
NLK -0.038 0.247 -9999 0 -0.767 49 49
GNB1 0.033 0.01 -9999 0 0 37 37
CAMK2A -0.03 0.078 0.184 5 -0.235 26 31
MAP3K7IP1 0.034 0.009 -9999 0 0 33 33
Noncanonical Wnts/FZD -0.006 0.088 -9999 0 -0.171 85 85
CSNK1A1 0.035 0.006 -9999 0 0 12 12
GNAS -0.016 0.081 -9999 0 -0.171 83 83
GO:0007205 -0.02 0.084 0.183 3 -0.249 27 30
WNT6 0.036 0.002 -9999 0 0 2 2
WNT4 0.035 0.007 -9999 0 0 18 18
NFAT1/CK1 alpha -0.005 0.098 0.242 3 -0.264 27 30
GNG2 0 0 -9999 0 -9999 0 0
WNT5A 0.03 0.014 -9999 0 0 89 89
WNT11 0.035 0.006 -9999 0 0 15 15
CDC42 -0.026 0.08 0.158 2 -0.269 22 24
IL2 signaling events mediated by PI3K

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
BCL2L1 0.004 0.093 -9999 0 -0.36 4 4
UGCG -0.027 0.189 -9999 0 -0.738 29 29
AKT1/mTOR/p70S6K/Hsp90/TERT -0.006 0.132 0.262 8 -0.333 38 46
mol:GTP 0 0.001 -9999 0 -9999 0 0
mol:glucosylceramide -0.025 0.185 -9999 0 -0.726 29 29
mol:DAG -0.007 0.031 0.168 14 -9999 0 14
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.024 0.178 0.297 7 -0.414 59 66
FRAP1 -0.034 0.196 0.316 7 -0.468 59 66
FOXO3 -0.034 0.195 0.296 7 -0.457 62 69
AKT1 -0.04 0.207 0.309 4 -0.498 61 65
GAB2 0.029 0.019 -9999 0 -0.012 76 76
SMPD1 0.002 0.095 -9999 0 -0.519 13 13
SGMS1 -0.004 0.034 0.061 20 -0.07 66 86
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 -0.029 0.045 0.098 2 -0.126 73 75
CALM1 0.033 0.011 -9999 0 0 49 49
cell proliferation -0.032 0.189 0.269 10 -0.395 66 76
EIF3A 0 0 -9999 0 -9999 0 0
PI3K 0.015 0.078 -9999 0 -0.154 73 73
RPS6KB1 0.028 0.043 -9999 0 -0.711 1 1
mol:sphingomyelin -0.007 0.031 0.168 14 -9999 0 14
natural killer cell activation 0 0.004 0.007 26 -0.01 44 70
JAK3 0.033 0.017 -9999 0 -0.028 22 22
PIK3R1 0.031 0.019 -9999 0 -0.029 24 24
JAK1 0.032 0.019 -9999 0 -0.028 28 28
NFKB1 0.035 0.007 -9999 0 0 17 17
MYC -0.067 0.294 0.443 7 -0.826 55 62
MYB 0.033 0.041 -9999 0 -9999 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.026 0.159 0.237 8 -0.384 48 56
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.037 0.045 -9999 0 -0.654 1 1
mol:PI-3-4-5-P3 -0.024 0.156 0.249 6 -0.378 47 53
Rac1/GDP 0.005 0.052 0.106 4 -0.127 48 52
T cell proliferation -0.023 0.145 0.235 6 -0.352 47 53
SHC1 0.029 0.019 -9999 0 -0.011 80 80
RAC1 0.027 0.016 -9999 0 0 123 123
positive regulation of cyclin-dependent protein kinase activity 0.005 0.011 0.056 23 -9999 0 23
PRKCZ -0.025 0.15 0.237 6 -0.367 47 53
NF kappa B1 p50/RelA -0.013 0.188 0.314 6 -0.42 59 65
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.006 0.094 -9999 0 -0.292 22 22
HSP90AA1 0 0 -9999 0 -9999 0 0
RELA 0.035 0.005 -9999 0 0 10 10
IL2RA 0.021 0.021 -9999 0 -0.004 189 189
IL2RB 0.031 0.018 -9999 0 -0.028 23 23
TERT 0.035 0.006 -9999 0 0 15 15
E2F1 0.033 0.028 -9999 0 -9999 0 0
SOS1 0 0.003 0.007 32 -0.009 43 75
RPS6 0.031 0.013 -9999 0 0 72 72
mol:cAMP -0.003 0.006 -9999 0 -0.031 24 24
PTPN11 0.032 0.017 -9999 0 -0.023 41 41
IL2RG 0.033 0.017 -9999 0 -0.029 23 23
actin cytoskeleton organization -0.023 0.145 0.235 6 -0.352 47 53
GRB2 0.032 0.016 -9999 0 -0.018 42 42
IL2 0.035 0.016 -9999 0 -0.029 23 23
PIK3CA 0.028 0.02 -9999 0 -0.029 26 26
Rac1/GTP 0.028 0.065 0.158 6 -0.119 48 54
LCK 0.034 0.017 -9999 0 -0.029 24 24
BCL2 -0.021 0.159 0.326 1 -0.452 27 28
EPHB forward signaling

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
Ephrin A5/EPHB2 0.045 0.013 -9999 0 -9999 0 0
cell-cell adhesion 0.032 0.041 0.19 14 -9999 0 14
Ephrin B/EPHB2/RasGAP 0.058 0.089 -9999 0 -0.132 72 72
ITSN1 0.035 0.006 -9999 0 0 16 16
PIK3CA 0.03 0.014 -9999 0 0 85 85
SHC1 0.033 0.011 -9999 0 0 48 48
Ephrin B1/EPHB3 0.045 0.014 -9999 0 -9999 0 0
Ephrin B1/EPHB1 0.039 0.025 -9999 0 -0.115 6 6
HRAS/GDP 0.005 0.082 -9999 0 -0.205 44 44
Ephrin B/EPHB1/GRB7 0.067 0.074 -9999 0 -0.118 45 45
Endophilin/SYNJ1 -0.026 0.055 0.186 12 -0.183 2 14
KRAS 0.033 0.01 -9999 0 0 37 37
Ephrin B/EPHB1/Src 0.064 0.076 -9999 0 -0.117 52 52
endothelial cell migration 0.021 0.072 -9999 0 -0.138 61 61
GRB2 0.035 0.006 -9999 0 0 16 16
GRB7 0.035 0.006 -9999 0 0 13 13
PAK1 -0.027 0.06 0.19 15 -9999 0 15
HRAS 0.034 0.009 -9999 0 0 32 32
RRAS -0.025 0.056 0.196 10 -0.185 11 21
DNM1 0.035 0.008 -9999 0 0 23 23
cell-cell signaling 0 0 -9999 0 -9999 0 0
CRK -0.02 0.063 0.178 14 -0.186 10 24
lamellipodium assembly -0.032 0.041 -9999 0 -0.19 14 14
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.009 0.071 -9999 0 -0.179 48 48
PIK3R1 0.032 0.012 -9999 0 0 61 61
EPHB2 0.034 0.009 -9999 0 0 35 35
EPHB3 0.033 0.01 -9999 0 0 44 44
EPHB1 0.03 0.014 -9999 0 0 87 87
EPHB4 0.026 0.016 -9999 0 0 141 141
mol:GDP 0.014 0.109 0.194 86 -0.224 37 123
Ephrin B/EPHB2 0.05 0.067 -9999 0 -0.108 62 62
Ephrin B/EPHB3 0.051 0.066 -9999 0 -0.109 58 58
JNK cascade -0.006 0.068 0.234 18 -0.193 4 22
Ephrin B/EPHB1 0.051 0.065 -9999 0 -0.11 52 52
RAP1/GDP 0.023 0.117 0.207 83 -0.221 34 117
EFNB2 0.028 0.015 -9999 0 0 110 110
EFNB3 0.034 0.008 -9999 0 0 25 25
EFNB1 0.036 0 -9999 0 -9999 0 0
Ephrin B2/EPHB1-2 0.031 0.058 -9999 0 -0.112 51 51
RAP1B 0 0 -9999 0 -9999 0 0
RAP1A 0.036 0.005 -9999 0 0 8 8
CDC42/GTP 0.043 0.082 -9999 0 -0.188 32 32
Rap1/GTP -0.044 0.052 0.052 8 -0.207 20 28
axon guidance 0.045 0.013 -9999 0 -9999 0 0
MAPK3 -0.01 0.068 0.155 2 -0.259 16 18
MAPK1 -0.009 0.073 0.171 3 -0.261 20 23
Rac1/GDP -0.002 0.1 0.255 23 -0.233 32 55
actin cytoskeleton reorganization -0.039 0.06 -9999 0 -0.2 37 37
CDC42/GDP 0.03 0.128 0.227 88 -0.227 34 122
PI3K 0.024 0.076 -9999 0 -0.139 61 61
EFNA5 0.036 0.003 -9999 0 0 4 4
Ephrin B2/EPHB4 0.016 0.048 -9999 0 -0.115 46 46
Ephrin B/EPHB2/Intersectin/N-WASP 0.002 0.062 -9999 0 -0.171 43 43
CDC42 0.035 0.008 -9999 0 0 22 22
RAS family/GTP -0.051 0.06 -9999 0 -0.238 23 23
PTK2 -0.012 0.078 0.528 8 -0.2 14 22
MAP4K4 -0.006 0.068 0.235 18 -0.195 4 22
SRC 0.035 0.006 -9999 0 0 13 13
KALRN 0.034 0.008 -9999 0 0 24 24
Intersectin/N-WASP 0.033 0.033 -9999 0 -0.142 7 7
neuron projection morphogenesis 0.05 0.157 0.32 100 -0.215 14 114
MAP2K1 -0.002 0.069 -9999 0 -0.178 52 52
WASL 0.025 0.017 -9999 0 0 155 155
Ephrin B1/EPHB1-2/NCK1 0.08 0.038 -9999 0 -0.117 10 10
cell migration -0.014 0.087 0.227 2 -0.274 21 23
NRAS 0.032 0.012 -9999 0 0 58 58
SYNJ1 -0.026 0.056 0.187 12 -0.186 2 14
PXN 0.036 0.004 -9999 0 0 5 5
TF -0.022 0.05 0.194 5 -0.185 19 24
HRAS/GTP 0.032 0.079 -9999 0 -0.142 63 63
Ephrin B1/EPHB1-2 0.053 0.034 -9999 0 -0.11 6 6
cell adhesion mediated by integrin 0.018 0.046 0.147 5 -0.266 4 9
RAC1 0.027 0.016 -9999 0 0 123 123
mol:GTP 0.041 0.077 -9999 0 -0.132 61 61
RAC1-CDC42/GTP -0.034 0.048 -9999 0 -0.196 16 16
RASA1 0.034 0.009 -9999 0 0 30 30
RAC1-CDC42/GDP 0.017 0.102 0.257 22 -0.231 32 54
ruffle organization 0.053 0.159 0.311 106 -0.255 7 113
NCK1 0.034 0.008 -9999 0 0 26 26
receptor internalization -0.031 0.052 0.175 11 -0.184 2 13
Ephrin B/EPHB2/KALRN 0.064 0.078 -9999 0 -0.115 59 59
ROCK1 -0.01 0.043 0.183 15 -9999 0 15
RAS family/GDP -0.042 0.063 -9999 0 -0.206 42 42
Rac1/GTP -0.031 0.046 -9999 0 -0.199 14 14
Ephrin B/EPHB1/Src/Paxillin 0.008 0.066 -9999 0 -0.154 56 56
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.043 0.042 -9999 0 -0.142 23 23
AKT1 -0.019 0.167 0.267 12 -0.418 45 57
PTK2B -0.005 0.109 0.211 39 -0.373 12 51
VEGFR2 homodimer/Frs2 0.025 0.082 -9999 0 -0.325 16 16
CAV1 0.016 0.018 -9999 0 0 269 269
CALM1 0.033 0.011 -9999 0 0 49 49
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.016 0.082 0.19 1 -0.314 17 18
endothelial cell proliferation 0.007 0.142 0.275 23 -0.374 29 52
mol:Ca2+ 0.002 0.123 0.211 73 -0.321 20 93
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.022 0.091 -9999 0 -0.278 22 22
RP11-342D11.1 -0.013 0.095 0.154 45 -0.228 46 91
CDH5 0.03 0.014 -9999 0 0 83 83
VEGFA homodimer 0.035 0.034 -9999 0 -0.094 14 14
SHC1 0.033 0.011 -9999 0 0 48 48
SHC2 0.031 0.013 -9999 0 0 69 69
HRAS/GDP 0.006 0.091 -9999 0 -0.238 45 45
SH2D2A 0.035 0.005 -9999 0 0 11 11
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.015 0.11 -9999 0 -0.349 21 21
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.016 0.083 0.19 1 -0.307 18 19
VEGFR1 homodimer 0.034 0.009 -9999 0 0 31 31
SHC/GRB2/SOS1 0.035 0.103 -9999 0 -0.233 45 45
GRB10 -0.016 0.11 0.203 29 -0.328 35 64
PTPN11 0.036 0.005 -9999 0 0 9 9
GRB2 0.035 0.006 -9999 0 0 16 16
PAK1 0.035 0.007 -9999 0 0 17 17
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.035 0.115 -9999 0 -0.274 35 35
HRAS 0.034 0.009 -9999 0 0 32 32
VEGF/Rho/ROCK1/Integrin Complex 0.008 0.104 -9999 0 -0.322 29 29
HIF1A 0.033 0.01 -9999 0 0 37 37
FRS2 0.035 0.008 -9999 0 0 22 22
oxygen and reactive oxygen species metabolic process 0.02 0.089 -9999 0 -0.276 22 22
mol:GTP 0 0 -9999 0 -9999 0 0
FLT4 0.036 0.005 -9999 0 0 8 8
Nck/Pak 0.048 0.025 -9999 0 -0.142 6 6
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.003 0.096 0.19 1 -0.288 29 30
mol:GDP 0.013 0.091 -9999 0 -0.228 45 45
mol:NADP 0.025 0.117 0.295 15 -0.328 17 32
eNOS/Hsp90 0.023 0.111 0.277 15 -0.312 17 32
PIK3R1 0.032 0.012 -9999 0 0 61 61
mol:IP3 0.002 0.124 0.212 73 -0.325 20 93
HIF1A/ARNT 0.045 0.032 -9999 0 -0.142 11 11
SHB 0.033 0.011 -9999 0 0 48 48
VEGFA -0.003 0.013 -9999 0 -0.041 49 49
VEGFC 0.033 0.011 -9999 0 0 45 45
FAK1/Vinculin 0.011 0.121 0.246 8 -0.454 18 26
mol:Ca ++ 0 0 -9999 0 -9999 0 0
RHOA 0.035 0.007 -9999 0 0 21 21
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.033 0.099 0.203 1 -0.285 24 25
PTPN6 0.032 0.011 -9999 0 0 50 50
EPAS1 0.03 0.062 -9999 0 -0.245 15 15
mol:L-citrulline 0.025 0.117 0.295 15 -0.328 17 32
ITGAV 0.034 0.009 -9999 0 0 30 30
PIK3CA 0.03 0.014 -9999 0 0 85 85
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.036 0.092 0.203 1 -0.302 19 20
VEGFR2 homodimer/VEGFA homodimer 0.012 0.098 -9999 0 -0.248 46 46
VEGFR2/3 heterodimer 0.026 0.083 -9999 0 -0.316 17 17
VEGFB 0.036 0.005 -9999 0 0 9 9
MAPK11 0.004 0.126 0.282 28 -0.333 21 49
VEGFR2 homodimer -0.003 0.083 0.183 2 -0.392 14 16
FLT1 0.034 0.009 -9999 0 0 31 31
NEDD4 0.028 0.033 0.087 5 -0.056 52 57
MAPK3 0.008 0.12 0.269 33 -0.302 19 52
MAPK1 0.008 0.122 0.265 38 -0.295 21 59
VEGFA145/NRP2 0.022 0.022 -9999 0 -0.046 7 7
VEGFR1/2 heterodimer 0.024 0.083 -9999 0 -0.328 16 16
KDR -0.003 0.083 0.183 2 -0.393 14 16
VEGFA165/NRP1/VEGFR2 homodimer 0.022 0.096 -9999 0 -0.227 46 46
SRC 0.035 0.006 -9999 0 0 13 13
platelet activating factor biosynthetic process 0.008 0.122 0.27 34 -0.312 19 53
PI3K -0.009 0.139 0.263 9 -0.365 36 45
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.014 0.083 0.19 1 -0.293 19 20
FES 0.002 0.124 0.241 48 -0.34 17 65
GAB1 0.01 0.116 0.234 15 -0.366 23 38
VEGFR2 homodimer/VEGFA homodimer/Src 0.015 0.083 -9999 0 -0.298 19 19
CTNNB1 0.035 0.007 -9999 0 0 21 21
SOS1 0 0 -9999 0 -9999 0 0
ARNT 0.035 0.005 -9999 0 0 10 10
eNOS/Caveolin-1 0.009 0.094 0.304 4 -0.362 12 16
VEGFR2 homodimer/VEGFA homodimer/Yes 0.011 0.087 0.19 1 -0.316 19 20
PI3K/GAB1 -0.006 0.159 0.264 18 -0.399 43 61
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.058 0.095 -9999 0 -0.278 17 17
PRKACA 0.034 0.009 -9999 0 0 29 29
VEGFR2/3 heterodimer/VEGFC homodimer 0.04 0.08 -9999 0 -0.293 15 15
HSP90AA1 0 0 -9999 0 -9999 0 0
CDC42 0.001 0.123 0.239 46 -0.34 17 63
actin cytoskeleton reorganization 0.015 0.082 0.188 1 -0.305 18 19
PTK2 0.006 0.127 0.239 16 -0.474 18 34
EDG1 -0.005 0.129 0.216 63 -0.346 27 90
mol:DAG 0.002 0.124 0.212 73 -0.325 20 93
CaM/Ca2+ 0.019 0.116 0.247 24 -0.236 47 71
MAP2K3 -0.004 0.118 0.228 45 -0.341 16 61
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.033 0.131 0.223 73 -0.304 43 116
PLCG1 0.002 0.125 0.213 73 -0.328 20 93
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.033 0.089 -9999 0 -0.291 18 18
IQGAP1 0.033 0.01 -9999 0 0 43 43
YES1 0.033 0.01 -9999 0 0 37 37
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.014 0.085 0.19 1 -0.303 20 21
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.012 0.084 0.19 1 -0.3 19 20
cell migration 0.004 0.133 0.243 18 -0.405 27 45
mol:PI-3-4-5-P3 -0.006 0.133 0.25 13 -0.343 36 49
FYN 0.03 0.014 -9999 0 0 82 82
VEGFB/NRP1 0.001 0.115 0.196 72 -0.326 17 89
mol:NO 0.025 0.117 0.295 15 -0.328 17 32
PXN 0.036 0.004 -9999 0 0 5 5
HRAS/GTP -0.044 0.07 -9999 0 -0.236 45 45
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.005 0.102 -9999 0 -0.303 43 43
VHL 0 0 -9999 0 -9999 0 0
ITGB3 0.036 0.004 -9999 0 0 5 5
NOS3 0.024 0.125 0.316 12 -0.365 17 29
VEGFR2 homodimer/VEGFA homodimer/Sck 0.007 0.093 -9999 0 -0.289 28 28
RAC1 0.027 0.016 -9999 0 0 123 123
PRKCA -0.004 0.118 0.221 49 -0.312 20 69
PRKCB 0 0.115 0.222 48 -0.306 20 68
VCL 0.027 0.016 -9999 0 0 127 127
VEGFA165/NRP1 -0.028 0.079 0.113 29 -0.228 46 75
VEGFR1/2 heterodimer/VEGFA homodimer 0.014 0.082 0.19 1 -0.307 18 19
VEGFA165/NRP2 0.022 0.022 -9999 0 -0.046 7 7
MAPKKK cascade -0.033 0.094 0.183 7 -0.316 34 41
NRP2 0.036 0.005 -9999 0 0 9 9
VEGFC homodimer 0.033 0.011 -9999 0 0 45 45
NCK1 0.034 0.008 -9999 0 0 26 26
ROCK1 0.035 0.006 -9999 0 0 14 14
FAK1/Paxillin 0.024 0.128 0.254 12 -0.452 18 30
MAP3K13 0.002 0.124 0.213 71 -0.352 16 87
PDPK1 -0.023 0.125 0.233 23 -0.338 31 54
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.033 0.011 -9999 0 0 45 45
VLDLR 0.027 0.016 -9999 0 0 128 128
LRPAP1 0.035 0.006 -9999 0 0 16 16
NUDC 0.034 0.008 -9999 0 0 25 25
RELN/LRP8 0.041 0.044 -9999 0 -0.132 11 11
CaM/Ca2+ 0.021 0.025 -9999 0 -0.132 12 12
KATNA1 0.033 0.01 -9999 0 0 39 39
GO:0030286 0 0 -9999 0 -9999 0 0
ABL1 0.031 0.098 0.187 117 -0.212 7 124
IQGAP1/CaM 0.032 0.058 -9999 0 -0.148 42 42
DAB1 0.035 0.005 -9999 0 0 11 11
IQGAP1 0.033 0.01 -9999 0 0 43 43
PLA2G7 0.032 0.011 -9999 0 0 51 51
CALM1 0.033 0.011 -9999 0 0 49 49
DYNLT1 0.033 0.01 -9999 0 0 41 41
mol:Ca2+ 0 0 -9999 0 -9999 0 0
LRPAP1/LRP8 0.044 0.036 -9999 0 -0.15 13 13
UniProt:Q4QZ09 0 0 -9999 0 -9999 0 0
CLIP1 0 0 -9999 0 -9999 0 0
CDK5R1 0.035 0.007 -9999 0 0 21 21
LIS1/Poliovirus Protein 3A -0.023 0.029 -9999 0 -0.142 24 24
CDK5R2 0.035 0.006 -9999 0 0 16 16
mol:PP1 0 0 -9999 0 -9999 0 0
RELN/VLDLR/DAB1 0.031 0.05 -9999 0 -0.124 23 23
YWHAE 0.034 0.009 -9999 0 0 29 29
NDEL1/14-3-3 E 0.048 0.157 0.292 116 -0.268 18 134
MAP1B -0.015 0.069 -9999 0 -0.203 52 52
RAC1 -0.004 0.055 -9999 0 -0.245 15 15
p35/CDK5 -0.018 0.072 0.195 26 -0.215 12 38
RELN 0.024 0.017 -9999 0 0 163 163
PAFAH/LIS1 0.021 0.039 -9999 0 -0.15 21 21
LIS1/CLIP170 -0.023 0.029 -9999 0 -0.142 24 24
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.031 0.085 0.135 32 -0.272 26 58
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.015 0.086 -9999 0 -0.223 49 49
GO:0005869 0 0 -9999 0 -9999 0 0
NDEL1 0.041 0.147 0.285 106 -0.267 16 122
LIS1/IQGAP1 0.014 0.059 -9999 0 -0.151 49 49
RHOA -0.007 0.068 -9999 0 -0.329 14 14
PAFAH1B1 -0.02 0.007 -9999 0 -9999 0 0
PAFAH1B3 0.031 0.013 -9999 0 0 72 72
PAFAH1B2 0.036 0.004 -9999 0 0 5 5
MAP1B/LIS1/Dynein heavy chain 0.005 0.079 -9999 0 -0.195 54 54
NDEL1/Katanin 60/Dynein heavy chain 0.068 0.14 0.32 77 -0.26 22 99
LRP8 0.034 0.009 -9999 0 0 35 35
NDEL1/Katanin 60 0.041 0.152 0.288 108 -0.263 19 127
P39/CDK5 -0.016 0.073 0.194 28 -0.215 12 40
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.02 0.053 -9999 0 -0.19 26 26
CDK5 -0.006 0.061 0.186 27 -0.216 7 34
PPP2R5D 0.036 0.004 -9999 0 0 6 6
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.019 0.024 -9999 0 -0.118 24 24
CSNK2A1 0.034 0.009 -9999 0 0 31 31
RELN/VLDLR/DAB1/LIS1 0.031 0.062 0.177 3 -0.132 38 41
RELN/VLDLR 0.043 0.062 -9999 0 -0.12 31 31
CDC42 -0.003 0.047 -9999 0 -0.19 19 19
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.032 0.042 -9999 0 -0.142 18 18
VLDLR 0.027 0.016 -9999 0 0 128 128
CRKL 0.034 0.008 -9999 0 0 25 25
LRPAP1 0.035 0.006 -9999 0 0 16 16
FYN 0.03 0.014 -9999 0 0 82 82
ITGA3 0.032 0.011 -9999 0 0 55 55
RELN/VLDLR/Fyn 0.017 0.063 -9999 0 -0.128 54 54
MAPK8IP1/MKK7/MAP3K11/JNK1 0.065 0.061 -9999 0 -0.109 5 5
AKT1 -0.014 0.069 -9999 0 -0.189 51 51
MAP2K7 0.034 0.009 -9999 0 0 30 30
RAPGEF1 0.035 0.007 -9999 0 0 18 18
DAB1 0.035 0.005 -9999 0 0 11 11
RELN/LRP8/DAB1 0.042 0.036 -9999 0 -0.11 3 3
LRPAP1/LRP8 0.044 0.036 -9999 0 -0.15 13 13
RELN/LRP8/DAB1/Fyn 0.043 0.058 -9999 0 -0.117 30 30
DAB1/alpha3/beta1 Integrin 0.028 0.059 -9999 0 -0.123 24 24
long-term memory 0.043 0.062 -9999 0 -0.125 28 28
DAB1/LIS1 0.046 0.073 -9999 0 -0.132 35 35
DAB1/CRLK/C3G 0.036 0.06 -9999 0 -0.122 30 30
PIK3CA 0.03 0.014 -9999 0 0 85 85
DAB1/NCK2 0.048 0.073 -9999 0 -0.131 33 33
ARHGEF2 0.035 0.007 -9999 0 0 21 21
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -9999 0 0
GRIN2A 0.035 0.006 -9999 0 0 13 13
CDK5R1 0.035 0.007 -9999 0 0 21 21
RELN 0.024 0.017 -9999 0 0 163 163
PIK3R1 0.032 0.012 -9999 0 0 61 61
RELN/LRP8/Fyn 0.031 0.056 -9999 0 -0.131 31 31
GRIN2A/RELN/LRP8/DAB1/Fyn 0.054 0.069 -9999 0 -0.124 30 30
MAPK8 0.026 0.016 -9999 0 0 133 133
RELN/VLDLR/DAB1 0.03 0.046 -9999 0 -0.11 23 23
ITGB1 0.027 0.016 -9999 0 0 118 118
MAP1B 0.017 0.079 0.16 87 -0.206 4 91
RELN/LRP8 0.041 0.044 -9999 0 -0.132 11 11
GRIN2B/RELN/LRP8/DAB1/Fyn 0.054 0.069 -9999 0 -0.125 28 28
PI3K 0.016 0.075 -9999 0 -0.155 73 73
mol:PP2 0 0 -9999 0 -9999 0 0
alpha3/beta1 Integrin 0.035 0.027 -9999 0 -0.142 1 1
RAP1A 0.029 0.108 0.245 35 -0.19 1 36
PAFAH1B1 0.034 0.008 -9999 0 0 26 26
MAPK8IP1 0.034 0.008 -9999 0 0 24 24
CRLK/C3G 0.049 0.015 -9999 0 -9999 0 0
GRIN2B 0.035 0.007 -9999 0 0 18 18
NCK2 0.035 0.007 -9999 0 0 19 19
neuron differentiation 0.005 0.07 -9999 0 -0.245 16 16
neuron adhesion 0.03 0.11 0.248 41 -9999 0 41
LRP8 0.034 0.009 -9999 0 0 35 35
GSK3B -0.01 0.074 -9999 0 -0.199 44 44
RELN/VLDLR/DAB1/Fyn 0.03 0.065 -9999 0 -0.113 53 53
MAP3K11 0.035 0.005 -9999 0 0 11 11
RELN/VLDLR/DAB1/P13K -0.009 0.074 -9999 0 -0.184 57 57
CDK5 0.026 0.016 -9999 0 0 137 137
MAPT -0.009 0.078 0.817 2 -9999 0 2
neuron migration -0.01 0.109 0.206 41 -0.276 31 72
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.005 0.07 -9999 0 -0.247 16 16
RELN/VLDLR 0.043 0.062 -9999 0 -0.12 31 31
E-cadherin signaling in keratinocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
keratinocyte differentiation -0.016 0.107 0.215 4 -0.348 30 34
adherens junction organization 0.002 0.074 0.174 2 -0.3 19 21
mol:GTP 0 0 -9999 0 -9999 0 0
Rac1/GDP 0.038 0.114 0.187 58 -0.283 20 78
FMN1 0.01 0.062 0.151 4 -0.251 16 20
mol:IP3 -0.007 0.077 0.142 3 -0.258 28 31
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.015 0.066 0.158 4 -0.263 16 20
CTNNB1 0.034 0.008 -9999 0 0 21 21
AKT1 -0.005 0.085 -9999 0 -0.318 24 24
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.026 0.065 -9999 0 -0.437 4 4
CTNND1 0.034 0.009 -9999 0 0 30 30
mol:PI-4-5-P2 0.005 0.067 0.15 6 -0.255 19 25
VASP 0.004 0.061 0.154 4 -0.259 15 19
ZYX 0.01 0.052 0.15 4 -0.258 9 13
JUB 0.01 0.062 0.151 4 -0.251 16 20
EGFR(dimer) 0.003 0.061 0.184 1 -0.27 15 16
E-cadherin/beta catenin-gamma catenin 0.061 0.029 -9999 0 -0.115 2 2
mol:PI-3-4-5-P3 0.02 0.09 -9999 0 -0.288 23 23
PIK3CA 0.03 0.015 -9999 0 -0.002 89 89
PI3K 0.02 0.092 -9999 0 -0.293 23 23
FYN -0.035 0.129 0.224 1 -0.308 69 70
mol:Ca2+ -0.006 0.075 0.141 3 -0.253 28 31
JUP 0.033 0.011 -9999 0 0 50 50
PIK3R1 0.031 0.015 -9999 0 -0.003 68 68
mol:DAG -0.007 0.077 0.142 3 -0.258 28 31
CDH1 0.033 0.01 -9999 0 0 37 37
RhoA/GDP 0.059 0.121 0.187 88 -0.284 19 107
establishment of polarity of embryonic epithelium 0.004 0.061 0.153 4 -0.255 16 20
SRC 0.035 0.006 -9999 0 0 13 13
RAC1 0.027 0.016 -9999 0 0 123 123
RHOA 0.035 0.007 -9999 0 0 21 21
EGFR 0.01 0.016 -9999 0 0 355 355
CASR -0.019 0.077 0.143 26 -0.272 23 49
RhoA/GTP 0.012 0.085 -9999 0 -0.264 25 25
AKT2 -0.004 0.076 0.145 1 -0.274 23 24
actin cable formation 0 0.06 0.149 4 -0.253 16 20
apoptosis 0.008 0.098 0.332 27 -0.216 4 31
CTNNA1 0.035 0.008 -9999 0 -0.002 19 19
mol:GDP -0.017 0.068 0.165 7 -0.285 18 25
PIP5K1A 0.005 0.067 0.151 6 -0.259 18 24
PLCG1 -0.007 0.078 0.143 3 -0.264 28 31
Rac1/GTP -0.002 0.067 -9999 0 -0.271 15 15
homophilic cell adhesion -0.001 0.003 -9999 0 -9999 0 0
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.015 0.011 0.018 18 -9999 0 18
RAS family/GTP 0.014 0.105 0.214 1 -0.176 67 68
NFATC4 -0.018 0.069 0.188 18 -0.202 4 22
ERBB2IP 0.034 0.011 -9999 0 -0.002 38 38
HSP90 (dimer) 0 0 -9999 0 -9999 0 0
mammary gland morphogenesis -0.03 0.07 0.171 4 -0.183 14 18
JUN -0.006 0.085 0.2 7 -0.355 7 14
HRAS 0.034 0.01 -9999 0 -0.001 33 33
DOCK7 -0.034 0.064 0.15 7 -0.174 16 23
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.024 0.077 0.212 13 -0.125 77 90
AKT1 -0.009 0.009 0.014 39 -9999 0 39
BAD -0.015 0.007 0.011 4 -9999 0 4
MAPK10 0.004 0.074 0.172 39 -0.156 12 51
mol:GTP 0 0.001 0.003 2 -0.005 24 26
ErbB2/ErbB3/neuregulin 1 beta -0.03 0.077 0.192 6 -0.194 14 20
RAF1 -0.015 0.104 0.234 12 -0.236 31 43
ErbB2/ErbB3/neuregulin 2 0.003 0.071 0.205 14 -0.126 83 97
STAT3 -0.026 0.242 -9999 0 -0.89 35 35
cell migration -0.009 0.071 0.174 25 -0.165 25 50
mol:PI-3-4-5-P3 -0.001 0.002 0.004 15 -0.004 62 77
cell proliferation -0.036 0.238 0.372 3 -0.572 57 60
FOS -0.027 0.205 0.326 10 -0.415 87 97
NRAS 0.032 0.012 -9999 0 -0.001 59 59
mol:Ca2+ -0.03 0.07 0.171 4 -0.183 14 18
MAPK3 -0.014 0.181 0.34 3 -0.477 39 42
MAPK1 -0.039 0.224 0.34 3 -0.567 51 54
JAK2 -0.023 0.072 0.165 13 -0.183 12 25
NF2 0.01 0.009 -9999 0 -9999 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.004 0.076 0.137 10 -0.164 79 89
NRG1 0.035 0.005 -9999 0 0 9 9
GRB2/SOS1 0.024 0.019 -9999 0 -0.133 7 7
MAPK8 -0.022 0.091 0.182 4 -0.222 53 57
MAPK9 0.01 0.079 0.176 48 -0.145 5 53
ERBB2 -0.015 0.069 0.258 29 -9999 0 29
ERBB3 0.017 0.018 -9999 0 0 254 254
SHC1 0.033 0.011 -9999 0 0 48 48
RAC1 0.027 0.016 -9999 0 0 123 123
apoptosis 0.012 0.031 0.196 11 -0.07 1 12
STAT3 (dimer) -0.025 0.237 -9999 0 -0.868 35 35
RNF41 -0.019 0.016 0.08 6 -0.12 1 7
FRAP1 -0.015 0.007 0.011 4 -9999 0 4
RAC1-CDC42/GTP -0.023 0.046 -9999 0 -0.13 49 49
ErbB2/ErbB2/HSP90 (dimer) -0.024 0.008 0.014 3 -9999 0 3
CHRNA1 -0.003 0.152 0.31 6 -0.367 40 46
myelination -0.025 0.082 0.23 19 -0.213 4 23
PPP3CB -0.02 0.067 0.171 13 -0.178 14 27
KRAS 0.034 0.01 -9999 0 0 37 37
RAC1-CDC42/GDP 0.022 0.078 0.218 1 -0.158 54 55
NRG2 0.036 0.005 -9999 0 0 9 9
mol:GDP -0.004 0.076 0.136 10 -0.163 79 89
SOS1 0 0.001 -9999 0 -0.004 7 7
MAP2K2 -0.022 0.101 0.218 14 -0.238 34 48
SRC 0.035 0.006 -9999 0 0 13 13
mol:cAMP -0.001 0.001 0.003 11 -0.004 1 12
PTPN11 -0.028 0.079 0.174 14 -0.211 6 20
MAP2K1 -0.033 0.2 -9999 0 -0.574 33 33
heart morphogenesis -0.03 0.07 0.171 4 -0.183 14 18
RAS family/GDP 0.021 0.107 0.232 1 -0.173 75 76
GRB2 0.035 0.007 -9999 0 0 16 16
PRKACA 0.017 0.01 -9999 0 -9999 0 0
CHRNE 0.001 0.025 0.064 4 -0.126 7 11
HSP90AA1 0 0 -9999 0 -9999 0 0
activation of caspase activity 0.009 0.009 -9999 0 -0.014 39 39
nervous system development -0.03 0.07 0.171 4 -0.183 14 18
CDC42 0.035 0.008 -9999 0 0 22 22
Regulation of nuclear SMAD2/3 signaling

Figure 49.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 51.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.019 0.037 -9999 0 -0.055 87 87
HSPA8 0.035 0.009 -9999 0 0 22 22
SMAD3/SMAD4/ER alpha 0.042 0.085 0.23 9 -0.155 19 28
AKT1 0.03 0.019 -9999 0 -0.029 29 29
GSC 0.004 0.031 0.096 22 -0.063 2 24
NKX2-5 0.033 0.017 0.071 9 -0.059 12 21
muscle cell differentiation -0.019 0.126 0.31 44 -9999 0 44
SMAD2-3/SMAD4/SP1 0.051 0.141 0.325 5 -0.248 44 49
SMAD4 0.021 0.056 0.138 2 -0.128 33 35
CBFB 0.035 0.006 -9999 0 0 12 12
SAP18 0.034 0.01 -9999 0 0 39 39
Cbp/p300/MSG1 0.007 0.086 -9999 0 -0.113 138 138
SMAD3/SMAD4/VDR 0.043 0.117 -9999 0 -0.199 36 36
MYC 0.028 0.014 -9999 0 -9999 0 0
CDKN2B -0.199 0.193 -9999 0 -0.529 30 30
AP1 -0.002 0.1 0.21 2 -0.243 44 46
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.007 0.128 -9999 0 -0.386 32 32
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.001 0.081 -9999 0 -0.279 28 28
SP3 0.035 0.015 0.079 14 -0.051 8 22
CREB1 0.036 0.004 -9999 0 0 6 6
FOXH1 0.034 0.014 0.072 10 -0.053 9 19
SMAD3/SMAD4/GR 0.038 0.091 0.236 2 -0.18 21 23
GATA3 0.028 0.018 -9999 0 -9999 0 0
SKI/SIN3/HDAC complex/NCoR1 -0.003 0.094 -9999 0 -0.299 27 27
MEF2C/TIF2 -0.013 0.08 0.217 20 -0.231 15 35
endothelial cell migration 0.196 0.488 1.153 98 -9999 0 98
MAX 0.027 0.042 0.084 85 -0.053 85 170
RBBP7 0.036 0.005 -9999 0 0 8 8
RBBP4 0.033 0.012 -9999 0 0 53 53
RUNX2 0.036 0.002 -9999 0 0 2 2
RUNX3 0.034 0.009 -9999 0 0 30 30
RUNX1 0.035 0.006 -9999 0 0 12 12
CTBP1 0.035 0.008 -9999 0 0 23 23
NR3C1 0.026 0.042 0.084 80 -0.053 86 166
VDR 0.035 0.007 -9999 0 0 17 17
CDKN1A -0.106 0.364 0.396 1 -1.074 57 58
KAT2B -0.003 0.008 -9999 0 -0.023 13 13
SMAD2/SMAD2/SMAD4/FOXH1 0.047 0.076 0.198 2 -0.161 31 33
DCP1A 0.035 0.007 -9999 0 0 20 20
SKI 0.035 0.007 -9999 0 0 18 18
SERPINE1 -0.198 0.494 -9999 0 -1.168 98 98
SMAD3/SMAD4/ATF2 0.04 0.086 0.215 1 -0.165 28 29
SMAD3/SMAD4/ATF3 0.017 0.102 -9999 0 -0.178 66 66
SAP30 0.035 0.006 -9999 0 0 15 15
Cbp/p300/PIAS3 0.04 0.073 -9999 0 -0.095 89 89
JUN -0.013 0.099 0.201 10 -0.255 39 49
SMAD3/SMAD4/IRF7 0.042 0.09 0.22 1 -0.169 29 30
TFE3 0.017 0.058 0.109 9 -0.093 95 104
COL1A2 -0.056 0.197 -9999 0 -0.629 50 50
mesenchymal cell differentiation -0.04 0.086 0.16 32 -0.213 1 33
DLX1 0 0 -9999 0 -9999 0 0
TCF3 0.033 0.01 -9999 0 0 37 37
FOS 0.021 0.029 0.118 2 -0.048 28 30
SMAD3/SMAD4/Max 0.041 0.086 0.229 3 -0.17 14 17
Cbp/p300/SNIP1 0.043 0.057 -9999 0 -0.068 65 65
ZBTB17 0.035 0.006 -9999 0 -9999 0 0
LAMC1 -0.033 0.102 0.162 10 -0.308 38 48
TGIF2/HDAC complex/SMAD3/SMAD4 0.039 0.085 0.215 1 -0.156 37 38
IRF7 0.034 0.01 -9999 0 -9999 0 0
ESR1 0.041 0.032 0.119 61 -0.001 35 96
HNF4A 0.035 0.006 -9999 0 0 15 15
MEF2C -0.02 0.075 0.208 22 -0.233 16 38
SMAD2-3/SMAD4 0.041 0.094 0.24 1 -0.201 27 28
Cbp/p300/Src-1 0.032 0.075 -9999 0 -0.11 70 70
IGHV3OR16-13 0.005 0.053 -9999 0 -0.49 5 5
TGIF2/HDAC complex 0.034 0.009 -9999 0 0 30 30
CREBBP 0.022 0.034 -9999 0 -0.043 101 101
SKIL 0.035 0.006 -9999 0 0 12 12
HDAC1 0.035 0.007 -9999 0 0 20 20
HDAC2 0.033 0.011 -9999 0 0 50 50
SNIP1 0.036 0.007 -9999 0 0 12 12
GCN5L2 0.021 0.034 -9999 0 -0.045 95 95
SMAD3/SMAD4/TFE3 0.031 0.124 0.258 4 -0.233 48 52
MSG1/HSC70 0.008 0.079 -9999 0 -0.145 95 95
SMAD2 0.034 0.017 0.09 2 -0.052 11 13
SMAD3 0.019 0.059 0.136 2 -0.123 41 43
SMAD3/E2F4-5/DP1/p107/SMAD4 0.003 0.072 -9999 0 -0.2 30 30
SMAD2/SMAD2/SMAD4 -0.011 0.068 0.155 7 -0.203 36 43
NCOR1 0.035 0.008 -9999 0 0 25 25
NCOA2 0.036 0.005 -9999 0 0 9 9
NCOA1 0.033 0.01 -9999 0 0 43 43
MYOD/E2A 0.049 0.015 -9999 0 -9999 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.059 0.144 0.34 4 -0.238 42 46
IFNB1 -0.004 0.06 0.165 8 -0.184 5 13
SMAD3/SMAD4/MEF2C 0.03 0.093 0.239 5 -0.241 17 22
CITED1 0.025 0.017 -9999 0 0 146 146
SMAD2-3/SMAD4/ARC105 0.041 0.085 0.216 2 -0.179 25 27
RBL1 0 0 -9999 0 -9999 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.005 0.103 -9999 0 -0.346 25 25
RUNX1-3/PEBPB2 0.066 0.023 -9999 0 -9999 0 0
SMAD7 -0.037 0.174 0.279 1 -0.441 53 54
MYC/MIZ-1 0.027 0.058 -9999 0 -0.143 47 47
SMAD3/SMAD4 -0.079 0.23 0.206 2 -0.472 107 109
IL10 -0.01 0.063 0.169 10 -0.19 4 14
PIASy/HDAC complex 0.027 0.03 0.07 19 -0.03 84 103
PIAS3 0.024 0.028 -9999 0 -0.03 100 100
CDK2 0.021 0.031 -9999 0 -0.042 84 84
IL5 -0.009 0.064 0.168 11 -0.192 3 14
CDK4 0.021 0.03 -9999 0 -0.045 63 63
PIAS4 0.027 0.03 0.07 18 -0.03 84 102
ATF3 0.027 0.016 -9999 0 0 120 120
SMAD3/SMAD4/SP1 0.029 0.135 0.315 2 -0.252 52 54
FOXG1 0.001 0.007 0.023 21 -9999 0 21
FOXO3 -0.007 0.009 -9999 0 -9999 0 0
FOXO1 -0.007 0.008 -9999 0 -9999 0 0
FOXO4 -0.007 0.008 -9999 0 -9999 0 0
heart looping -0.02 0.075 0.207 22 -0.231 16 38
CEBPB 0.032 0.012 -9999 0 -9999 0 0
SMAD3/SMAD4/DLX1 0.023 0.073 0.19 1 -0.14 47 48
MYOD1 0.036 0.004 -9999 0 0 6 6
SMAD3/SMAD4/HNF4 0.039 0.086 0.215 1 -0.165 28 29
SMAD3/SMAD4/GATA3 0.033 0.085 -9999 0 -0.172 21 21
SnoN/SIN3/HDAC complex/NCoR1 0.035 0.006 -9999 0 0 12 12
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.067 0.093 -9999 0 -0.158 15 15
SMAD3/SMAD4/SP1-3 0.046 0.141 0.32 1 -0.244 50 51
MED15 0 0 -9999 0 -9999 0 0
SP1 0.016 0.073 0.12 19 -0.117 100 119
SIN3B 0.034 0.01 -9999 0 0 35 35
SIN3A 0 0.001 -9999 0 -9999 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.067 0.083 0.242 1 -0.168 28 29
ITGB5 -0.029 0.105 0.212 11 -0.261 39 50
TGIF/SIN3/HDAC complex/CtBP -0.005 0.097 -9999 0 -0.316 28 28
SMAD3/SMAD4/AR 0.038 0.085 0.215 1 -0.166 27 28
AR 0.035 0.007 -9999 0 0 21 21
negative regulation of cell growth -0.017 0.12 0.173 2 -0.295 58 60
SMAD3/SMAD4/MYOD 0.041 0.086 0.215 1 -0.166 27 28
E2F5 0.036 0.004 -9999 0 0 6 6
E2F4 0.036 0.004 -9999 0 0 7 7
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.057 0.097 0.238 1 -0.186 27 28
SMAD2-3/SMAD4/FOXO1-3a-4 -0.007 0.097 -9999 0 -0.319 27 27
TFDP1 0.033 0.011 -9999 0 0 49 49
SMAD3/SMAD4/AP1 0.02 0.117 0.241 3 -0.253 41 44
SMAD3/SMAD4/RUNX2 0.041 0.086 0.215 1 -0.161 32 33
TGIF2 0.034 0.009 -9999 0 0 30 30
TGIF1 0 0 -9999 0 -9999 0 0
ATF2 0.035 0.005 -9999 0 0 10 10
IL12-mediated signaling events

Figure 50.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 52.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.042 0.088 0.221 30 -0.196 12 42
TBX21 0.072 0.197 0.56 6 -0.577 3 9
B2M 0.035 0.007 -9999 0 0 19 19
TYK2 0.035 0.039 0.116 14 -0.054 11 25
IL12RB1 0.036 0.04 0.116 15 -0.051 31 46
GADD45B 0.064 0.279 0.563 10 -0.994 21 31
IL12RB2 0.039 0.04 0.114 21 -0.053 15 36
GADD45G 0.093 0.186 0.54 8 -0.551 3 11
natural killer cell activation 0.012 0.024 0.054 75 -0.036 11 86
RELB 0.034 0.009 -9999 0 0 33 33
RELA 0.035 0.005 -9999 0 0 10 10
IL18 0.034 0.021 0.086 2 -0.041 15 17
IL2RA 0.024 0.017 -9999 0 0 162 162
IFNG 0.034 0.009 -9999 0 0 32 32
STAT3 (dimer) 0.076 0.221 0.446 26 -0.524 24 50
HLA-DRB5 -0.001 0.009 -9999 0 -0.023 45 45
FASLG 0.077 0.197 0.505 13 -0.522 9 22
NF kappa B2 p52/RelB 0.057 0.186 0.419 13 -0.464 16 29
CD4 0.024 0.027 -9999 0 -0.039 56 56
SOCS1 0.036 0.004 -9999 0 0 7 7
EntrezGene:6955 -0.001 0.01 -9999 0 -0.025 61 61
CD3D 0.025 0.028 -9999 0 -0.042 64 64
CD3E 0.027 0.027 -9999 0 -0.036 74 74
CD3G 0.026 0.029 -9999 0 -0.042 67 67
IL12Rbeta2/JAK2 0.053 0.058 0.184 15 -9999 0 15
CCL3 0.074 0.198 0.446 28 -0.472 16 44
CCL4 0.044 0.329 0.563 17 -1.028 30 47
HLA-A 0.035 0.007 -9999 0 0 19 19
IL18/IL18R 0.088 0.064 0.207 28 -0.121 7 35
NOS2 0.076 0.189 0.423 35 -0.433 16 51
IL12/IL12R/TYK2/JAK2/SPHK2 0.039 0.087 0.216 27 -0.208 11 38
IL1R1 0.074 0.199 0.53 12 -0.549 5 17
IL4 0.003 0.048 -9999 0 -0.074 74 74
JAK2 0.033 0.037 0.113 12 -0.05 20 32
EntrezGene:6957 -0.001 0.009 -9999 0 -0.023 45 45
TCR/CD3/MHC I/CD8 0.007 0.041 0.106 1 -0.155 14 15
RAB7A 0.096 0.202 0.443 28 -0.532 18 46
lysosomal transport 0.096 0.198 0.438 29 -0.51 18 47
FOS -0.098 0.473 0.463 18 -1.05 86 104
STAT4 (dimer) 0.092 0.205 0.451 31 -0.493 15 46
STAT5A (dimer) 0.079 0.19 0.416 14 -0.469 16 30
GZMA 0.072 0.2 0.543 12 -0.549 5 17
GZMB 0.071 0.197 0.563 11 -0.539 6 17
HLX 0 0 -9999 0 -9999 0 0
LCK 0.058 0.2 0.452 27 -0.49 16 43
TCR/CD3/MHC II/CD4 -0.021 0.117 0.16 22 -0.203 117 139
IL2/IL2R 0.058 0.049 -9999 0 -9999 0 0
MAPK14 0.099 0.224 0.495 21 -0.622 18 39
CCR5 0.079 0.175 0.388 39 -0.39 17 56
IL1B 0.029 0.037 0.112 7 -0.05 27 34
STAT6 0.046 0.1 0.275 16 -0.437 3 19
STAT4 0.034 0.009 -9999 0 0 30 30
STAT3 0.033 0.01 -9999 0 0 37 37
STAT1 0.033 0.01 -9999 0 0 40 40
NFKB1 0.035 0.007 -9999 0 0 17 17
NFKB2 0.027 0.016 -9999 0 0 127 127
IL12B 0.04 0.04 0.116 21 -0.051 27 48
CD8A 0 0 -9999 0 -9999 0 0
CD8B 0 0 -9999 0 -9999 0 0
T-helper 1 cell differentiation 0 0 -9999 0 -9999 0 0
natural killer cell mediated cytotoxicity -0.042 0.087 0.195 12 -0.221 30 42
IL2RB 0.032 0.011 -9999 0 0 53 53
proteasomal ubiquitin-dependent protein catabolic process 0.092 0.199 0.439 34 -0.465 15 49
IL2RG 0.034 0.008 -9999 0 0 24 24
IL12 0.062 0.059 0.178 22 -9999 0 22
STAT5A 0.036 0.004 -9999 0 0 6 6
CD247 -0.001 0.009 -9999 0 -0.023 45 45
IL2 0.036 0.005 -9999 0 0 8 8
SPHK2 0.034 0.01 -9999 0 0 36 36
FRAP1 0.035 0.006 -9999 0 0 14 14
IL12A 0.038 0.04 0.116 14 -0.051 32 46
IL12/IL12R/TYK2/JAK2 0.064 0.206 0.495 24 -0.513 16 40
MAP2K3 0.093 0.224 0.482 23 -0.617 18 41
RIPK2 0.035 0.005 -9999 0 0 11 11
MAP2K6 0.097 0.217 0.492 20 -0.585 18 38
regulation of dendritic cell antigen processing and presentation 0 0 -9999 0 -9999 0 0
HLA-DRA 0.02 0.027 -9999 0 -0.011 183 183
IL18RAP 0.038 0.019 0.086 2 -0.04 19 21
IL12Rbeta1/TYK2 0.047 0.063 0.173 7 -0.152 15 22
EOMES -0.02 0.038 0.074 2 -0.098 48 50
STAT1 (dimer) 0.085 0.187 0.437 24 -0.437 13 37
T cell proliferation 0.08 0.179 0.396 35 -0.406 18 53
T-helper 1 cell lineage commitment 0 0 -9999 0 -9999 0 0
IL18R1 0.039 0.019 0.086 2 -0.04 19 21
CD8-positive alpha-beta T cell lineage commitment 0 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelA 0.043 0.165 -9999 0 -0.468 21 21
ATF2 0.09 0.212 0.464 21 -0.589 18 39
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.034 0.008 -9999 0 0 25 25
Jak2/Leptin Receptor 0.002 0.127 -9999 0 -0.329 40 40
PTP1B/AKT1 0 0.111 -9999 0 -0.253 48 48
FYN 0.03 0.014 -9999 0 0 82 82
p210 bcr-abl/PTP1B -0.011 0.107 0.174 1 -0.268 42 43
EGFR 0.009 0.017 -9999 0 -0.03 3 3
EGF/EGFR -0.033 0.09 -9999 0 -0.275 38 38
CSF1 0.036 0.004 -9999 0 0 5 5
AKT1 0.033 0.012 -9999 0 0 53 53
INSR 0.034 0.009 -9999 0 -0.001 29 29
PTP1B/N-cadherin -0.006 0.119 -9999 0 -0.267 52 52
Insulin Receptor/Insulin 0.018 0.108 -9999 0 -0.259 33 33
HCK 0.027 0.016 -9999 0 0 123 123
CRK 0.035 0.008 -9999 0 0 23 23
TYK2 -0.007 0.124 0.271 25 -0.289 40 65
EGF 0.026 0.024 -9999 0 -0.022 89 89
YES1 0.033 0.01 -9999 0 0 37 37
CAV1 0.005 0.136 0.215 27 -0.284 51 78
TXN 0.034 0.01 -9999 0 0 38 38
PTP1B/IRS1/GRB2 0.007 0.123 -9999 0 -0.278 40 40
cell migration 0.011 0.107 0.268 42 -0.174 1 43
STAT3 0.034 0.01 -9999 0 0 37 37
PRLR 0.038 0.005 -9999 0 -9999 0 0
ITGA2B 0.036 0.003 -9999 0 0 3 3
CSF1R 0.027 0.016 -9999 0 0 121 121
Prolactin Receptor/Prolactin 0.056 0.012 -9999 0 -9999 0 0
FGR 0.032 0.011 -9999 0 0 52 52
PTP1B/p130 Cas -0.012 0.101 0.152 1 -0.251 44 45
Crk/p130 Cas -0.002 0.111 -9999 0 -0.254 46 46
DOK1 -0.008 0.104 0.183 6 -0.291 32 38
JAK2 -0.01 0.125 -9999 0 -0.338 42 42
Jak2/Leptin Receptor/Leptin -0.009 0.12 -9999 0 -0.318 30 30
PIK3R1 0.032 0.012 -9999 0 0 61 61
PTPN1 -0.011 0.108 0.174 1 -0.27 42 43
LYN 0.031 0.013 -9999 0 0 72 72
CDH2 0.032 0.011 -9999 0 0 53 53
SRC 0.015 0.099 -9999 0 -0.478 15 15
ITGB3 0.036 0.004 -9999 0 0 5 5
CAT1/PTP1B -0.014 0.166 0.256 13 -0.371 58 71
CAPN1 0.035 0.005 -9999 0 0 8 8
CSK 0.035 0.007 -9999 0 0 17 17
PI3K 0.009 0.123 -9999 0 -0.285 39 39
mol:H2O2 0.003 0.005 0.021 5 -9999 0 5
STAT3 (dimer) -0.007 0.111 -9999 0 -0.291 30 30
negative regulation of transcription -0.009 0.123 -9999 0 -0.333 42 42
FCGR2A 0.028 0.015 -9999 0 0 105 105
FER 0.036 0.007 -9999 0 0 14 14
alphaIIb/beta3 Integrin 0.053 0.006 -9999 0 -9999 0 0
BLK 0.035 0.007 -9999 0 0 17 17
Insulin Receptor/Insulin/Shc 0.058 0.035 -9999 0 -0.128 7 7
RHOA 0.034 0.008 -9999 0 0 21 21
LEPR 0.035 0.007 -9999 0 0 18 18
BCAR1 0 0 -9999 0 -9999 0 0
p210 bcr-abl/Grb2 0.035 0.006 -9999 0 0 16 16
mol:NADPH 0 0.003 -9999 0 -9999 0 0
TRPV6 -0.009 0.151 0.21 5 -0.358 56 61
PRL 0.037 0.006 -9999 0 -9999 0 0
SOCS3 0.024 0.015 -9999 0 -9999 0 0
SPRY2 0.029 0.018 -9999 0 0 129 129
Insulin Receptor/Insulin/IRS1 0.054 0.047 -9999 0 -0.126 23 23
CSF1/CSF1R -0.003 0.126 -9999 0 -0.274 49 49
Ras protein signal transduction -0.005 0.085 0.593 8 -9999 0 8
IRS1 0.032 0.011 -9999 0 0 51 51
INS 0.035 0.007 -9999 0 -0.002 16 16
LEP 0.026 0.016 -9999 0 0 131 131
STAT5B -0.003 0.102 0.169 1 -0.291 26 27
STAT5A -0.003 0.101 -9999 0 -0.296 25 25
GRB2 0.035 0.006 -9999 0 0 16 16
PDGFB-D/PDGFRB 0 0.114 -9999 0 -0.27 42 42
CSN2 0.013 0.041 -9999 0 -9999 0 0
PIK3CA 0.03 0.014 -9999 0 0 85 85
LAT -0.025 0.172 -9999 0 -0.472 57 57
YBX1 0.038 0.04 -9999 0 -0.287 7 7
LCK 0.035 0.007 -9999 0 0 17 17
SHC1 0.033 0.011 -9999 0 0 48 48
NOX4 0.034 0.015 -9999 0 0 78 78
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.051 0.056 -9999 0 -0.131 35 35
fibroblast growth factor receptor signaling pathway 0.05 0.056 -9999 0 -0.131 35 35
LAMA1 0 0 -9999 0 -9999 0 0
PRNP 0.032 0.011 -9999 0 0 54 54
GPC1/SLIT2 0.031 0.046 -9999 0 -0.142 24 24
SMAD2 -0.023 0.049 0.177 10 -0.201 3 13
GPC1/PrPc/Cu2+ 0.024 0.059 -9999 0 -0.136 53 53
GPC1/Laminin alpha1 0.014 0.041 -9999 0 -0.132 35 35
TDGF1 0.035 0.006 -9999 0 0 16 16
CRIPTO/GPC1 0.037 0.048 -9999 0 -0.142 30 30
APP/GPC1 0.033 0.059 -9999 0 -0.159 38 38
mol:NO 0 0 -9999 0 -9999 0 0
YES1 -0.023 0.034 0.089 22 -0.123 24 46
FLT1 0.034 0.009 -9999 0 0 31 31
GPC1/TGFB/TGFBR1/TGFBR2 0.05 0.053 -9999 0 -0.123 34 34
SERPINC1 0.035 0.005 -9999 0 0 10 10
FYN -0.017 0.029 0.089 24 -0.123 8 32
FGR -0.022 0.034 0.089 23 -0.123 22 45
positive regulation of MAPKKK cascade -0.036 0.123 0.18 11 -0.301 58 69
SLIT2 0.029 0.014 -9999 0 0 96 96
GPC1/NRG 0.036 0.051 -9999 0 -0.142 35 35
NRG1 0.036 0.005 -9999 0 0 9 9
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.031 0.044 -9999 0 -0.115 35 35
LYN -0.022 0.035 0.089 22 -0.123 25 47
mol:Spermine -0.01 0.004 -9999 0 -9999 0 0
cell growth 0.05 0.056 -9999 0 -0.131 35 35
BMP signaling pathway -0.032 0.012 0 62 -9999 0 62
SRC -0.025 0.036 0.089 24 -0.123 30 54
TGFBR1 0.035 0.006 -9999 0 0 15 15
mol:Cu2+ 0 0 -9999 0 -9999 0 0
PLA2G2A 0.017 0.018 -9999 0 0 256 256
GPC1 0.032 0.012 -9999 0 0 62 62
TGFBR1 (dimer) 0.035 0.006 -9999 0 0 15 15
VEGFA 0 0 -9999 0 -9999 0 0
BLK -0.024 0.036 0.089 25 -0.123 28 53
HCK -0.018 0.032 0.089 20 -0.123 17 37
FGF2 0.034 0.008 -9999 0 0 25 25
FGFR1 0.035 0.005 -9999 0 0 11 11
VEGFR1 homodimer 0.034 0.009 -9999 0 0 31 31
TGFBR2 0.034 0.008 -9999 0 0 27 27
cell death 0.033 0.059 -9999 0 -0.158 38 38
ATIII/GPC1 0.036 0.05 -9999 0 -0.142 33 33
PLA2G2A/GPC1 -0.006 0.074 -9999 0 -0.15 91 91
LCK -0.024 0.034 0.089 23 -0.123 25 48
neuron differentiation 0.036 0.051 -9999 0 -0.141 35 35
PrPc/Cu2+ 0.016 0.038 -9999 0 -0.132 30 30
APP 0.035 0.007 -9999 0 0 19 19
TGFBR2 (dimer) 0.034 0.008 -9999 0 0 27 27
Paxillin-dependent events mediated by a4b1

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
CRKL 0.034 0.008 -9999 0 0 25 25
Rac1/GDP 0.027 0.02 -9999 0 -0.024 14 14
DOCK1 0.023 0.017 -9999 0 0 178 178
ITGA4 0.035 0.006 -9999 0 0 12 12
RAC1 0.027 0.016 -9999 0 0 123 123
alpha4/beta7 Integrin 0.052 0.011 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
CRK 0.035 0.008 -9999 0 0 23 23
alpha4/beta1 Integrin 0.053 0.033 -9999 0 -9999 0 0
alpha4/beta7 Integrin/Paxillin 0.051 0.018 -9999 0 -9999 0 0
lamellipodium assembly -0.051 0.146 -9999 0 -0.363 72 72
PIK3CA 0.03 0.014 -9999 0 0 85 85
PI3K 0.016 0.075 -9999 0 -0.155 73 73
ARF6 0.035 0.007 -9999 0 0 21 21
TLN1 0.029 0.014 -9999 0 0 94 94
PXN -0.021 0.006 -9999 0 -9999 0 0
PIK3R1 0.032 0.012 -9999 0 0 61 61
ARF6/GTP 0.052 0.047 -9999 0 -0.113 1 1
cell adhesion 0.046 0.049 -9999 0 -0.115 12 12
CRKL/CBL 0.05 0.013 -9999 0 -9999 0 0
alpha4/beta1 Integrin/Paxillin 0.04 0.026 -9999 0 -9999 0 0
ITGB1 0.027 0.016 -9999 0 0 118 118
ITGB7 0.035 0.005 -9999 0 0 10 10
ARF6/GDP 0.034 0.016 -9999 0 -0.025 16 16
alpha4/beta1 Integrin/Paxillin/VCAM1 0.014 0.077 -9999 0 -0.114 104 104
p130Cas/Crk/Dock1 0.026 0.036 -9999 0 -0.115 17 17
VCAM1 0.022 0.018 -9999 0 0 186 186
alpha4/beta1 Integrin/Paxillin/Talin 0.047 0.051 -9999 0 -0.116 12 12
alpha4/beta1 Integrin/Paxillin/GIT1 0.055 0.046 -9999 0 -9999 0 0
BCAR1 0 0 -9999 0 -9999 0 0
mol:GDP -0.053 0.045 -9999 0 -9999 0 0
CBL 0.036 0.004 -9999 0 0 6 6
PRKACA 0.034 0.009 -9999 0 0 29 29
GIT1 0.036 0.003 -9999 0 0 4 4
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.047 0.051 -9999 0 -0.116 12 12
Rac1/GTP -0.058 0.162 -9999 0 -0.404 72 72
Arf6 downstream 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
PLAUR -0.013 0.184 -9999 0 -0.809 22 22
regulation of axonogenesis 0.002 0.063 0.217 31 -9999 0 31
myoblast fusion -0.016 0.093 0.346 26 -0.176 3 29
mol:GTP 0.016 0.064 -9999 0 -0.182 42 42
regulation of calcium-dependent cell-cell adhesion -0.027 0.073 0.149 57 -0.155 2 59
ARF1/GTP 0.035 0.061 -9999 0 -0.142 45 45
mol:GM1 0.004 0.046 0.088 1 -0.136 41 42
mol:Choline -0.014 0.04 0.083 4 -0.131 36 40
lamellipodium assembly -0.007 0.103 -9999 0 -0.373 32 32
MAPK3 0.014 0.079 0.135 35 -0.215 38 73
ARF6/GTP/NME1/Tiam1 0.028 0.073 0.158 2 -0.15 57 59
ARF1 0.035 0.007 -9999 0 0 21 21
ARF6/GDP 0.016 0.093 0.177 3 -0.347 26 29
ARF1/GDP 0.016 0.099 0.179 1 -0.28 42 43
ARF6 0.039 0.042 0.107 1 -0.13 24 25
RAB11A 0.035 0.006 -9999 0 0 16 16
TIAM1 0.029 0.021 -9999 0 -0.044 28 28
fibronectin binding 0 0 -9999 0 -9999 0 0
MAPK1 0.013 0.078 0.136 34 -0.301 22 56
actin filament bundle formation -0.021 0.103 0.29 42 -9999 0 42
KALRN 0.006 0.069 0.123 3 -0.256 27 30
RAB11FIP3/RAB11A 0.046 0.035 -9999 0 -0.16 12 12
RhoA/GDP 0.022 0.104 -9999 0 -0.292 42 42
NME1 -0.001 0.008 -9999 0 -0.03 23 23
Rac1/GDP 0.017 0.092 -9999 0 -0.296 31 31
substrate adhesion-dependent cell spreading 0.016 0.064 -9999 0 -0.182 42 42
cortical actin cytoskeleton organization -0.007 0.104 -9999 0 -0.375 32 32
RAC1 0.027 0.016 -9999 0 0 123 123
liver development 0.016 0.064 -9999 0 -0.182 42 42
ARF6/GTP 0.016 0.064 -9999 0 -0.182 42 42
RhoA/GTP 0.034 0.062 -9999 0 -0.148 45 45
mol:GDP -0.002 0.095 0.17 2 -0.3 38 40
ARF6/GTP/RAB11FIP3/RAB11A 0.051 0.067 -9999 0 -0.132 48 48
RHOA 0.035 0.007 -9999 0 0 21 21
PLD1 0.013 0.051 -9999 0 -0.144 40 40
RAB11FIP3 0.035 0.007 -9999 0 0 19 19
tube morphogenesis -0.007 0.103 -9999 0 -0.373 32 32
ruffle organization -0.002 0.063 -9999 0 -0.217 31 31
regulation of epithelial cell migration 0.016 0.064 -9999 0 -0.182 42 42
PLD2 0.014 0.05 -9999 0 -0.143 39 39
PIP5K1A -0.002 0.063 -9999 0 -0.217 31 31
mol:Phosphatidic acid -0.014 0.04 0.083 4 -0.131 36 40
Rac1/GTP -0.008 0.104 -9999 0 -0.376 32 32
mTOR 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
GBL 0.035 0.005 -9999 0 0 11 11
MKNK1 0.034 0.009 -9999 0 0 31 31
mol:PIP3 -0.02 0.057 0.092 3 -0.221 22 25
FRAP1 0.024 0.105 0.257 1 -0.438 17 18
AKT1 0.004 0.103 0.17 81 -0.252 30 111
INSR 0.034 0.008 -9999 0 0 28 28
Insulin Receptor/Insulin 0.045 0.014 -9999 0 -9999 0 0
mol:GTP 0.028 0.111 0.204 47 -0.254 30 77
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.007 0.049 -9999 0 -0.17 25 25
TSC2 0.034 0.008 -9999 0 0 26 26
RHEB/GDP 0.005 0.079 -9999 0 -0.223 32 32
TSC1 0.034 0.01 -9999 0 0 36 36
Insulin Receptor/IRS1 0.02 0.062 -9999 0 -0.252 23 23
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.02 0.073 0.15 4 -0.199 23 27
mol:GDP 0 0 -9999 0 -9999 0 0
EIF3A 0 0 -9999 0 -9999 0 0
RPS6KB1 0.029 0.085 0.249 13 -0.268 7 20
MAP3K5 -0.023 0.082 0.166 1 -0.227 64 65
PIK3R1 0.032 0.012 -9999 0 0 61 61
apoptosis -0.023 0.082 0.166 1 -0.226 64 65
mol:LY294002 0 0 0.001 18 -0.001 21 39
EIF4B 0.024 0.083 0.236 16 -0.271 7 23
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.027 0.072 0.228 9 -0.229 6 15
eIF4E/eIF4G1/eIF4A1 0.007 0.077 -9999 0 -0.289 20 20
KIAA1303 0 0 -9999 0 -9999 0 0
PI3K 0.018 0.082 -9999 0 -0.211 37 37
mTOR/RHEB/GTP/Raptor/GBL 0.011 0.065 0.192 13 -0.187 13 26
FKBP1A 0.033 0.011 -9999 0 0 46 46
RHEB/GTP 0.02 0.092 0.252 7 -0.23 29 36
mol:Amino Acids 0 0 0.001 18 -0.001 21 39
FKBP12/Rapamycin 0.021 0.025 -9999 0 -0.134 11 11
PDPK1 -0.022 0.061 0.148 16 -0.217 21 37
EIF4E 0.034 0.009 -9999 0 0 35 35
ASK1/PP5C -0.028 0.228 -9999 0 -0.555 72 72
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.01 0.094 -9999 0 -0.313 31 31
TSC1/TSC2 0.031 0.119 0.221 47 -0.272 30 77
tumor necrosis factor receptor activity 0 0 0.001 21 -0.001 18 39
RPS6 0.031 0.013 -9999 0 0 72 72
PPP5C 0.033 0.01 -9999 0 0 39 39
EIF4G1 0.033 0.01 -9999 0 0 44 44
IRS1 0 0.06 -9999 0 -0.263 23 23
INS 0.035 0.006 -9999 0 0 15 15
PTEN 0.026 0.016 -9999 0 0 130 130
PDK2 -0.022 0.061 0.148 16 -0.217 21 37
EIF4EBP1 -0.028 0.261 -9999 0 -1.117 26 26
PIK3CA 0.03 0.014 -9999 0 0 85 85
PPP2R5D 0.019 0.097 0.28 2 -0.398 17 19
peptide biosynthetic process -0.019 0.017 0.182 3 -9999 0 3
RHEB 0.028 0.015 -9999 0 0 115 115
EIF4A1 0.035 0.007 -9999 0 0 20 20
mol:Rapamycin 0 0.001 0.003 30 -0.002 18 48
EEF2 -0.019 0.018 0.183 3 -9999 0 3
eIF4E/4E-BP1 -0.011 0.253 -9999 0 -1.064 26 26
Class I PI3K signaling events

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
ARF5/GTP -0.022 0.055 0.155 20 -0.221 10 30
DAPP1 -0.024 0.122 -9999 0 -0.29 62 62
Src family/SYK family/BLNK-LAT/BTK-ITK -0.046 0.191 0.243 2 -0.487 56 58
mol:DAG -0.012 0.091 0.194 21 -0.211 42 63
HRAS 0.034 0.019 0.085 1 -0.032 24 25
RAP1A 0.037 0.014 0.063 2 -0.022 19 21
ARF5/GDP -0.002 0.101 -9999 0 -0.32 32 32
PLCG2 0.032 0.012 -9999 0 0 60 60
PLCG1 0.035 0.007 -9999 0 0 20 20
ARF5 0.026 0.016 -9999 0 0 138 138
mol:GTP -0.024 0.053 0.143 21 -0.195 11 32
ARF1/GTP -0.018 0.053 0.135 23 -0.2 14 37
RHOA 0.035 0.007 -9999 0 0 21 21
YES1 0.033 0.01 -9999 0 0 37 37
RAP1A/GTP -0.023 0.056 0.162 21 -0.193 11 32
ADAP1 -0.024 0.049 0.136 18 -0.186 11 29
ARAP3 -0.024 0.052 0.141 21 -0.192 11 32
INPPL1 0.035 0.006 -9999 0 0 12 12
PREX1 0 0 -9999 0 -9999 0 0
ARHGEF6 0.033 0.011 -9999 0 0 47 47
ARHGEF7 0.032 0.012 -9999 0 0 56 56
ARF1 0.035 0.007 -9999 0 0 21 21
NRAS 0.033 0.017 -9999 0 -0.032 11 11
FYN 0.03 0.014 -9999 0 0 82 82
ARF6 0.035 0.007 -9999 0 0 21 21
FGR 0.032 0.011 -9999 0 0 52 52
mol:Ca2+ 0.004 0.062 0.159 30 -0.127 11 41
mol:IP4 0 0 -9999 0 -9999 0 0
TIAM1 0.033 0.01 -9999 0 0 43 43
ZAP70 0.036 0.003 -9999 0 0 3 3
mol:IP3 -0.007 0.07 0.183 24 -0.171 18 42
LYN 0.031 0.013 -9999 0 0 72 72
ARF1/GDP 0.005 0.114 -9999 0 -0.329 37 37
RhoA/GDP 0.021 0.091 0.182 15 -0.213 31 46
PDK1/Src/Hsp90 0.047 0.009 -9999 0 -9999 0 0
BLNK 0.02 0.018 -9999 0 0 219 219
actin cytoskeleton reorganization 0.001 0.105 0.203 21 -0.307 23 44
SRC 0.035 0.006 -9999 0 0 13 13
PLEKHA2 -0.016 0.005 -9999 0 -9999 0 0
RAC1 0.027 0.016 -9999 0 0 123 123
PTEN 0.026 0.022 -9999 0 -0.032 21 21
HSP90AA1 0 0 -9999 0 -9999 0 0
ARF6/GTP -0.025 0.057 0.153 23 -0.198 11 34
RhoA/GTP -0.027 0.059 0.162 22 -0.204 12 34
Src family/SYK family/BLNK-LAT -0.051 0.156 -9999 0 -0.347 79 79
BLK 0.035 0.007 -9999 0 0 17 17
PDPK1 0.036 0.003 -9999 0 0 4 4
CYTH1 -0.024 0.049 0.136 18 -0.186 11 29
HCK 0.027 0.016 -9999 0 0 123 123
CYTH3 -0.024 0.049 0.136 18 -0.186 11 29
CYTH2 -0.024 0.049 0.136 18 -0.186 11 29
KRAS 0.033 0.02 0.085 1 -0.032 27 28
GO:0030676 0 0 -9999 0 -9999 0 0
FOXO3 -0.002 0.031 0.175 2 -0.146 2 4
SGK1 0.001 0.032 0.18 2 -0.154 2 4
INPP5D 0 0 -9999 0 -9999 0 0
mol:GDP -0.012 0.109 0.167 3 -0.322 39 42
SOS1 0 0 -9999 0 -9999 0 0
SYK 0.031 0.013 -9999 0 0 71 71
ARF6/GDP -0.027 0.07 0.166 20 -0.216 27 47
mol:PI-3-4-5-P3 -0.025 0.052 0.145 18 -0.195 11 29
ARAP3/RAP1A/GTP -0.023 0.056 0.162 21 -0.195 11 32
VAV1 0.033 0.01 -9999 0 0 38 38
mol:PI-3-4-P2 -0.011 0.002 -9999 0 -9999 0 0
RAS family/GTP/PI3K Class I 0.056 0.089 0.207 85 -0.14 40 125
PLEKHA1 -0.011 0.009 -9999 0 -9999 0 0
Rac1/GDP -0.002 0.105 -9999 0 -0.314 34 34
LAT 0.036 0.005 -9999 0 0 9 9
Rac1/GTP -0.012 0.152 0.16 1 -0.409 43 44
ITK -0.027 0.052 0.137 21 -0.193 11 32
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.024 0.116 0.227 14 -0.283 48 62
LCK 0.035 0.007 -9999 0 0 17 17
BTK -0.027 0.052 0.136 21 -0.193 11 32
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.034 0.01 -9999 0 0 36 36
SPHK1 0.033 0.011 -9999 0 0 47 47
GNAI2 0.033 0.01 -9999 0 0 42 42
mol:S1P 0.018 0.015 -9999 0 -9999 0 0
GNAO1 0.03 0.014 -9999 0 0 81 81
mol:Sphinganine-1-P -0.019 0.008 -9999 0 -9999 0 0
growth factor activity 0 0 -9999 0 -9999 0 0
S1P/S1P2/G12/G13 0.032 0.046 -9999 0 -0.16 3 3
GNAI3 0.035 0.006 -9999 0 0 12 12
G12/G13 0.028 0.049 -9999 0 -0.142 30 30
S1PR3 0 0 -9999 0 -9999 0 0
S1PR2 0 0 -9999 0 -9999 0 0
EDG1 0.033 0.01 -9999 0 0 38 38
S1P1/S1P 0.035 0.034 -9999 0 -9999 0 0
S1PR5 0 0 -9999 0 -9999 0 0
S1PR4 0 0 -9999 0 -9999 0 0
GNAI1 0.018 0.018 -9999 0 0 245 245
S1P/S1P5/G12 0.019 0.039 -9999 0 -0.163 3 3
S1P/S1P3/Gq 0.024 0.04 0.147 6 -0.215 8 14
S1P/S1P4/Gi -0.006 0.108 0.147 2 -0.288 43 45
GNAQ 0.034 0.009 -9999 0 0 31 31
GNAZ 0.03 0.013 -9999 0 0 79 79
GNA14 0.034 0.008 -9999 0 0 28 28
GNA15 0.032 0.012 -9999 0 0 59 59
GNA12 0.026 0.016 -9999 0 0 136 136
GNA13 0.035 0.007 -9999 0 0 18 18
GNA11 0.032 0.012 -9999 0 0 60 60
ABCC1 0.035 0.007 -9999 0 0 19 19
BMP receptor 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
BMP7/BMPR2/BMPR1A-1B/FS 0.065 0.064 -9999 0 -0.115 13 13
SMAD6-7/SMURF1 0.048 0.036 -9999 0 -0.124 2 2
NOG 0 0 -9999 0 -9999 0 0
SMAD9 -0.012 0.133 -9999 0 -0.444 39 39
SMAD4 0.032 0.011 -9999 0 0 53 53
SMAD5 -0.022 0.094 -9999 0 -0.323 31 31
BMP7/USAG1 0.035 0.025 -9999 0 -9999 0 0
SMAD5/SKI -0.015 0.105 -9999 0 -0.305 38 38
SMAD1 -0.026 0.147 -9999 0 -0.393 46 46
BMP2 0.028 0.015 -9999 0 0 109 109
SMAD1/SMAD1/SMAD4 -0.008 0.13 -9999 0 -0.393 34 34
BMPR1A 0.026 0.016 -9999 0 0 142 142
BMPR1B 0.035 0.005 -9999 0 0 11 11
BMPR1A-1B/BAMBI 0.02 0.062 -9999 0 -0.126 52 52
AHSG 0.035 0.007 -9999 0 0 18 18
CER1 0.032 0.012 -9999 0 0 61 61
BMP2-4/CER1 0.038 0.054 -9999 0 -0.121 33 33
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.009 0.078 -9999 0 -0.241 29 29
BMP2-4 (homodimer) 0.028 0.051 -9999 0 -0.141 33 33
RGMB 0 0 -9999 0 -9999 0 0
BMP6/BMPR2/BMPR1A-1B 0.056 0.056 -9999 0 -0.116 13 13
RGMA 0 0 -9999 0 -9999 0 0
SMURF1 0.026 0.016 -9999 0 0 136 136
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.017 0.067 -9999 0 -0.166 53 53
BMP2-4/USAG1 0.034 0.046 -9999 0 -0.123 16 16
SMAD6/SMURF1/SMAD5 -0.012 0.093 -9999 0 -0.292 33 33
SOSTDC1 0.025 0.017 -9999 0 0 155 155
BMP7/BMPR2/BMPR1A-1B 0.056 0.057 -9999 0 -0.116 15 15
SKI 0.035 0.007 -9999 0 0 18 18
BMP6 (homodimer) 0.034 0.008 -9999 0 0 25 25
HFE2 0 0 -9999 0 -9999 0 0
ZFYVE16 0.034 0.009 -9999 0 0 35 35
MAP3K7 0.033 0.01 -9999 0 0 38 38
BMP2-4/CHRD 0.042 0.054 -9999 0 -0.123 32 32
SMAD5/SMAD5/SMAD4 -0.019 0.107 -9999 0 -0.31 40 40
MAPK1 0.033 0.011 -9999 0 0 48 48
TAK1/TAB family 0.018 0.087 -9999 0 -0.203 23 23
BMP7 (homodimer) 0.035 0.007 -9999 0 0 19 19
NUP214 0.035 0.008 -9999 0 0 23 23
BMP6/FETUA 0.049 0.015 -9999 0 -9999 0 0
SMAD1/SKI -0.008 0.15 0.226 1 -0.388 44 45
SMAD6 0.036 0.004 -9999 0 0 6 6
CTDSP2 0.03 0.013 -9999 0 0 77 77
BMP2-4/FETUA 0.042 0.054 -9999 0 -0.123 33 33
MAP3K7IP1 0.034 0.009 -9999 0 0 33 33
GREM1 0.032 0.012 -9999 0 0 63 63
BMPR2 (homodimer) 0.035 0.006 -9999 0 0 16 16
GADD34/PP1CA 0.049 0.054 -9999 0 -0.129 31 31
BMPR1A-1B (homodimer) 0.035 0.032 -9999 0 -0.142 7 7
CHRDL1 0 0 -9999 0 -9999 0 0
ENDOFIN/SMAD1 -0.01 0.156 0.226 1 -0.403 45 46
SMAD6-7/SMURF1/SMAD1 0.008 0.143 0.241 1 -0.413 33 34
SMAD6/SMURF1 0.026 0.016 -9999 0 0 136 136
BAMBI 0.018 0.018 -9999 0 0 237 237
SMURF2 0.035 0.007 -9999 0 0 18 18
BMP2-4/CHRDL1 0.027 0.043 -9999 0 -0.114 33 33
BMP2-4/GREM1 0.037 0.054 -9999 0 -0.122 31 31
SMAD7 0.034 0.01 -9999 0 0 36 36
SMAD8A/SMAD8A/SMAD4 -0.005 0.142 -9999 0 -0.409 48 48
SMAD1/SMAD6 -0.011 0.14 0.226 1 -0.428 33 34
TAK1/SMAD6 0.033 0.035 -9999 0 -0.142 10 10
BMP7 0.035 0.007 -9999 0 0 19 19
BMP6 0.034 0.008 -9999 0 0 25 25
MAP3K7IP2 0.033 0.01 -9999 0 0 42 42
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.005 0.058 -9999 0 -0.222 17 17
PPM1A 0.034 0.008 -9999 0 0 25 25
SMAD1/SMURF2 -0.009 0.155 0.226 1 -0.407 43 44
SMAD7/SMURF1 0.035 0.028 -9999 0 -0.142 2 2
CTDSPL 0.034 0.009 -9999 0 0 29 29
PPP1CA 0.035 0.008 -9999 0 0 22 22
XIAP 0 0 -9999 0 -9999 0 0
CTDSP1 0.035 0.006 -9999 0 0 14 14
PPP1R15A 0.032 0.012 -9999 0 0 59 59
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.012 0.07 -9999 0 -0.216 26 26
CHRD 0.035 0.007 -9999 0 0 17 17
BMPR2 0.035 0.006 -9999 0 0 16 16
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.017 0.069 -9999 0 -0.175 50 50
BMP4 0.033 0.011 -9999 0 0 46 46
FST 0.033 0.01 -9999 0 0 43 43
BMP2-4/NOG 0.027 0.043 -9999 0 -0.114 33 33
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.052 0.063 -9999 0 -0.113 12 12
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.004 0.038 -9999 0 -9999 0 0
CRKL 0.034 0.008 -9999 0 0 25 25
Rac1/GDP 0.018 0.02 -9999 0 -0.132 6 6
DOCK1 0.023 0.017 -9999 0 0 178 178
ITGA4 0.035 0.006 -9999 0 0 12 12
alpha4/beta7 Integrin/MAdCAM1 0.078 0.039 -9999 0 -0.117 7 7
EPO 0.026 0.016 -9999 0 0 138 138
alpha4/beta7 Integrin 0.052 0.011 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
CRK 0.035 0.008 -9999 0 0 23 23
alpha4/beta1 Integrin 0.04 0.024 -9999 0 -9999 0 0
EPO/EPOR (dimer) 0.037 0.025 -9999 0 -9999 0 0
lamellipodium assembly -0.011 0.098 -9999 0 -0.334 21 21
PIK3CA 0.03 0.014 -9999 0 0 85 85
PI3K 0.016 0.075 -9999 0 -0.155 73 73
ARF6 0.035 0.007 -9999 0 0 21 21
JAK2 0.009 0.029 -9999 0 -9999 0 0
PXN 0.036 0.004 -9999 0 0 5 5
PIK3R1 0.032 0.012 -9999 0 0 61 61
MADCAM1 0.033 0.01 -9999 0 0 40 40
cell adhesion 0.075 0.038 -9999 0 -0.117 7 7
CRKL/CBL 0.05 0.013 -9999 0 -9999 0 0
ITGB1 0.027 0.016 -9999 0 0 118 118
SRC -0.034 0.059 0.169 4 -9999 0 4
ITGB7 0.035 0.005 -9999 0 0 10 10
RAC1 0.027 0.016 -9999 0 0 123 123
alpha4/beta1 Integrin/VCAM1 0.004 0.077 -9999 0 -0.121 117 117
p130Cas/Crk/Dock1 -0.031 0.063 0.181 4 -0.192 8 12
VCAM1 0.022 0.018 -9999 0 0 186 186
RHOA 0.035 0.007 -9999 0 0 21 21
alpha4/beta1 Integrin/Paxillin/GIT1 0.065 0.048 -9999 0 -9999 0 0
BCAR1 -0.032 0.052 0.157 4 -9999 0 4
EPOR 0.034 0.009 -9999 0 0 34 34
mol:GDP 0 0 -9999 0 -9999 0 0
CBL 0.036 0.004 -9999 0 0 6 6
GIT1 0.036 0.003 -9999 0 0 4 4
Rac1/GTP -0.012 0.101 -9999 0 -0.352 20 20
IL1-mediated signaling events

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
UBC13/UEV1A 0.024 0.019 -9999 0 -0.132 7 7
PRKCZ 0 0 -9999 0 -9999 0 0
MAP3K7IP2 0.033 0.01 -9999 0 0 42 42
ERC1 0 0 -9999 0 -9999 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.008 0.113 -9999 0 -0.285 54 54
IRAK/TOLLIP 0.029 0.032 0.178 1 -0.118 19 20
IKBKB 0.036 0.004 -9999 0 0 6 6
IKBKG 0.036 0 -9999 0 -9999 0 0
IL1 alpha/IL1R2 0.043 0.022 -9999 0 -9999 0 0
IL1A 0.035 0.008 -9999 0 0 23 23
IL1B -0.014 0.011 -9999 0 -9999 0 0
IRAK/TRAF6/p62/Atypical PKCs 0.053 0.05 0.183 1 -0.131 27 28
IL1R2 0.03 0.014 -9999 0 0 85 85
IL1R1 0.035 0.006 -9999 0 0 13 13
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.013 0.097 -9999 0 -0.283 38 38
TOLLIP 0.034 0.009 -9999 0 0 30 30
TICAM2 0 0 -9999 0 -9999 0 0
MAP3K3 0.036 0.004 -9999 0 0 5 5
TAK1/TAB1/TAB2 0.055 0.049 -9999 0 -0.138 21 21
IKK complex/ELKS -0.036 0.091 -9999 0 -0.262 10 10
JUN -0.039 0.041 0.15 2 -0.208 9 11
MAP3K7 0.033 0.01 -9999 0 0 38 38
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.025 0.104 -9999 0 -0.143 108 108
IL1 alpha/IL1R1/IL1RAP/MYD88 0.064 0.068 -9999 0 -0.126 48 48
PIK3R1 0.032 0.012 -9999 0 0 61 61
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.073 0.074 -9999 0 -0.124 47 47
IL1 beta fragment/IL1R1/IL1RAP 0.023 0.08 -9999 0 -0.137 80 80
NFKB1 0.035 0.007 -9999 0 0 17 17
MAPK8 -0.033 0.035 0.167 2 -0.2 7 9
IRAK1 -0.018 0.011 -9999 0 -0.115 5 5
IL1RN/IL1R1 0.052 0.01 -9999 0 -9999 0 0
IRAK4 0.035 0.007 -9999 0 0 17 17
PRKCI 0.034 0.008 -9999 0 0 25 25
TRAF6 0.036 0.005 -9999 0 0 8 8
PI3K 0.016 0.075 -9999 0 -0.155 73 73
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.007 0.112 -9999 0 -0.271 57 57
CHUK 0.026 0.016 -9999 0 0 133 133
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.023 0.08 -9999 0 -0.137 80 80
IL1 beta/IL1R2 0.018 0.071 -9999 0 -0.135 66 66
IRAK/TRAF6/TAK1/TAB1/TAB2 0.059 0.068 0.204 1 -0.138 34 35
NF kappa B1 p50/RelA 0.011 0.096 -9999 0 -0.15 101 101
IRAK3 0.034 0.008 -9999 0 0 26 26
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.037 0.082 -9999 0 -0.128 78 78
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.01 0.072 -9999 0 -0.177 48 48
IL1 alpha/IL1R1/IL1RAP 0.048 0.053 -9999 0 -0.124 32 32
RELA 0.035 0.005 -9999 0 0 10 10
MAP3K7IP1 0.034 0.009 -9999 0 0 33 33
SQSTM1 0.034 0.009 -9999 0 0 33 33
MYD88 0.034 0.009 -9999 0 0 31 31
IRAK/TRAF6/MEKK3 0.05 0.037 0.191 1 -0.117 20 21
IL1RAP 0.03 0.014 -9999 0 0 85 85
UBE2N 0.035 0.005 -9999 0 0 11 11
IRAK/TRAF6 -0.038 0.061 0.061 68 -0.186 24 92
CASP1 0.029 0.015 -9999 0 0 102 102
IL1RN/IL1R2 0.044 0.021 -9999 0 -9999 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.037 0.095 -9999 0 -0.145 87 87
TMEM189-UBE2V1 0 0 -9999 0 -9999 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.003 0.092 -9999 0 -0.292 33 33
PIK3CA 0.03 0.014 -9999 0 0 85 85
IL1RN 0.036 0.004 -9999 0 0 6 6
TRAF6/TAK1/TAB1/TAB2 0.065 0.06 -9999 0 -0.14 23 23
MAP2K6 -0.038 0.034 0.173 3 -0.205 7 10
Stabilization and expansion of the E-cadherin adherens junction

Figure 61.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 63.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
adherens junction organization 0.009 0.056 -9999 0 -0.222 20 20
epithelial cell differentiation 0.062 0.049 -9999 0 -0.139 20 20
CYFIP2 0.031 0.013 -9999 0 0 73 73
ENAH -0.034 0.078 0.244 16 -0.234 10 26
EGFR 0.01 0.016 -9999 0 0 355 355
EPHA2 0.032 0.011 -9999 0 0 53 53
MYO6 -0.025 0.053 0.174 14 -0.218 11 25
CTNNB1 0.035 0.007 -9999 0 0 21 21
ABI1/Sra1/Nap1 0.031 0.066 -9999 0 -0.126 57 57
AQP5 -0.015 0.052 0.176 1 -0.282 7 8
CTNND1 0.034 0.009 -9999 0 0 30 30
mol:PI-4-5-P2 -0.025 0.049 0.173 13 -0.211 10 23
regulation of calcium-dependent cell-cell adhesion -0.023 0.05 0.172 15 -0.193 7 22
EGF 0.034 0.008 -9999 0 0 24 24
NCKAP1 0.036 0.002 -9999 0 0 1 1
AQP3 -0.029 0.076 -9999 0 -0.295 28 28
cortical microtubule organization 0.062 0.049 -9999 0 -0.139 20 20
GO:0000145 -0.024 0.045 0.155 13 -0.202 10 23
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.069 0.051 -9999 0 -0.14 20 20
MLLT4 0.034 0.009 -9999 0 0 35 35
ARF6/GDP -0.049 0.039 -9999 0 -0.226 10 10
ARF6 0.035 0.007 -9999 0 0 21 21
Ephrin A1/EPHA2/NCK1/GIT1 0.074 0.052 -9999 0 -0.129 21 21
mol:Ca2+ 0 0 -9999 0 -9999 0 0
VASP -0.025 0.082 0.171 8 -0.303 27 35
PVRL2 0.034 0.01 -9999 0 0 36 36
ZYX -0.019 0.047 0.174 11 -0.21 12 23
ARF6/GTP 0.079 0.057 -9999 0 -0.13 20 20
CDH1 0.033 0.01 -9999 0 0 37 37
EGFR/EGFR/EGF/EGF 0.001 0.057 -9999 0 -0.122 59 59
RhoA/GDP 0.062 0.054 -9999 0 -0.143 24 24
actin cytoskeleton organization -0.021 0.049 0.154 12 -0.227 11 23
IGF-1R heterotetramer 0.032 0.012 -9999 0 0 56 56
GIT1 0.036 0.003 -9999 0 0 4 4
IGF1R 0.032 0.012 -9999 0 0 56 56
IGF1 0.035 0.007 -9999 0 0 20 20
DIAPH1 -0.11 0.266 -9999 0 -0.505 130 130
Wnt receptor signaling pathway -0.062 0.049 0.139 20 -9999 0 20
RHOA 0.035 0.007 -9999 0 0 21 21
RhoA/GTP -0.05 0.041 -9999 0 -0.235 11 11
CTNNA1 0.035 0.007 -9999 0 0 18 18
VCL -0.022 0.05 0.155 12 -0.232 11 23
EFNA1 0.033 0.011 -9999 0 0 47 47
LPP -0.027 0.05 0.161 9 -0.237 12 21
Ephrin A1/EPHA2 0.045 0.059 -9999 0 -0.136 34 34
SEC6/SEC8 -0.04 0.028 -9999 0 -0.142 21 21
MGAT3 -0.023 0.05 0.174 15 -0.195 7 22
HGF/MET 0.035 0.045 -9999 0 -0.138 11 11
HGF 0.024 0.017 -9999 0 0 157 157
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.009 0.056 -9999 0 -0.224 20 20
actin cable formation -0.033 0.105 0.298 12 -0.296 29 41
KIAA1543 -0.021 0.04 0.15 13 -0.18 7 20
KIFC3 -0.026 0.048 0.174 12 -0.195 7 19
NCK1 0.034 0.008 -9999 0 0 26 26
EXOC3 0.035 0.006 -9999 0 0 16 16
ACTN1 -0.024 0.053 0.174 11 -0.222 14 25
NCK1/GIT1 0.049 0.024 -9999 0 -0.142 6 6
mol:GDP 0.062 0.049 -9999 0 -0.139 20 20
EXOC4 0 0 -9999 0 -9999 0 0
STX4 -0.026 0.03 0.055 22 -0.133 20 42
PIP5K1C -0.025 0.05 0.174 13 -0.214 10 23
LIMA1 0 0 -9999 0 -9999 0 0
ABI1 0.027 0.016 -9999 0 0 126 126
ROCK1 -0.026 0.091 0.273 21 -0.273 6 27
adherens junction assembly -0.018 0.07 0.214 5 -0.3 13 18
IGF-1R heterotetramer/IGF1 0.048 0.059 -9999 0 -0.141 33 33
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.046 0.023 -9999 0 -0.142 3 3
MET 0.023 0.018 -9999 0 0 183 183
PLEKHA7 -0.026 0.03 0.055 22 -0.133 20 42
mol:GTP 0.071 0.05 -9999 0 -0.129 21 21
establishment of epithelial cell apical/basal polarity -0.032 0.044 0.127 20 -0.184 8 28
cortical actin cytoskeleton stabilization 0.009 0.056 -9999 0 -0.222 20 20
regulation of cell-cell adhesion -0.021 0.049 0.154 12 -0.227 11 23
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.009 0.056 -9999 0 -0.224 20 20
p38 MAPK signaling pathway

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
TRAF6/ASK1 0.012 0.05 -9999 0 -0.109 60 60
TRAF2/ASK1 0.032 0.043 -9999 0 -0.115 34 34
ATM 0.034 0.01 -9999 0 0 36 36
MAP2K3 0.01 0.099 -9999 0 -0.291 29 29
response to stress 0 0 -9999 0 -9999 0 0
MAP2K6 0.009 0.091 0.215 1 -0.269 28 29
hyperosmotic response 0 0 -9999 0 -9999 0 0
response to oxidative stress 0 0 -9999 0 -9999 0 0
GADD45G 0.031 0.012 -9999 0 0 64 64
TXN 0.007 0.002 -9999 0 0 38 38
CALM1 0.033 0.011 -9999 0 0 49 49
GADD45A 0.031 0.013 -9999 0 0 74 74
GADD45B 0.029 0.014 -9999 0 0 90 90
MAP3K1 0.035 0.007 -9999 0 0 18 18
MAP3K6 0.035 0.007 -9999 0 0 20 20
MAP3K7 0.033 0.01 -9999 0 0 38 38
MAP3K4 0.032 0.012 -9999 0 0 61 61
mol:Ca2+ 0 0 -9999 0 -9999 0 0
ASK1/ASK2 0.033 0.052 -9999 0 -0.141 35 35
TAK1/TAB family 0.006 0.061 -9999 0 -0.265 18 18
RAC1/OSM/MEKK3 0.033 0.025 -9999 0 -0.102 6 6
TRAF2 0.035 0.006 -9999 0 0 14 14
RAC1/OSM/MEKK3/MKK3 0.011 0.08 -9999 0 -0.254 23 23
TRAF6 0.009 0.032 -9999 0 -0.2 11 11
RAC1 0.027 0.016 -9999 0 0 123 123
mol:LPS 0 0 -9999 0 -9999 0 0
CAMK2B 0.019 0.018 -9999 0 0 236 236
CCM2 0 0 -9999 0 -9999 0 0
CaM/Ca2+/CAMKIIB 0.009 0.057 -9999 0 -0.128 58 58
MAPK11 0.033 0.011 -9999 0 0 48 48
response to DNA damage stimulus 0 0 -9999 0 -9999 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.012 0.07 -9999 0 -0.133 69 69
OSM/MEKK3 0.027 0.003 -9999 0 -9999 0 0
TAOK1 0.007 0.002 -9999 0 0 36 36
TAOK2 0.012 0.024 -9999 0 -0.2 6 6
TAOK3 0.006 0.042 -9999 0 -0.2 19 19
MAP3K7IP1 0.034 0.009 -9999 0 0 33 33
MAPK14 0.036 0.004 -9999 0 0 6 6
MAP3K7IP2 0.033 0.01 -9999 0 0 42 42
MAP3K5 0.03 0.014 -9999 0 0 81 81
MAP3K10 0.034 0.008 -9999 0 0 25 25
MAP3K3 0.036 0.004 -9999 0 0 5 5
TRX/ASK1 0.022 0.035 -9999 0 -0.162 13 13
GADD45/MTK1/MTK1 0.041 0.074 -9999 0 -0.127 62 62
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.051 0.071 -9999 0 -0.123 35 35
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -9999 0 0
CRKL 0.034 0.008 -9999 0 0 25 25
STAT1 (dimer)/Cbp/p300 0.028 0.084 0.252 8 -0.217 16 24
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.043 0.06 -9999 0 -0.138 35 35
antigen processing and presentation of peptide antigen via MHC class I -0.029 0.078 -9999 0 -0.182 62 62
CaM/Ca2+ 0.048 0.077 -9999 0 -0.14 35 35
RAP1A 0.036 0.005 -9999 0 0 8 8
STAT1 (dimer)/SHP2 -0.019 0.063 0.158 27 -0.187 8 35
AKT1 -0.023 0.092 0.202 28 -0.219 29 57
MAP2K1 -0.022 0.063 0.152 33 -0.192 8 41
MAP3K11 -0.016 0.067 0.167 31 -0.177 6 37
IFNGR1 0.032 0.018 -9999 0 -0.035 16 16
mol:GTP 0 0 -9999 0 -9999 0 0
CaM/Ca2+/CAMKII -0.035 0.127 -9999 0 -0.306 60 60
Rap1/GTP -0.037 0.035 -9999 0 -0.164 6 6
CRKL/C3G 0.049 0.015 -9999 0 -9999 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.065 0.074 -9999 0 -0.127 31 31
CEBPB -0.003 0.125 0.323 6 -0.408 23 29
STAT3 0.033 0.01 -9999 0 0 37 37
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.06 0.09 -9999 0 -0.741 3 3
STAT1 -0.019 0.066 0.178 25 -0.187 8 33
CALM1 0.033 0.011 -9999 0 0 49 49
IFN-gamma (dimer) 0.03 0.021 -9999 0 -0.036 34 34
PIK3CA 0.03 0.014 -9999 0 0 85 85
STAT1 (dimer)/PIAS1 -0.019 0.076 0.187 27 -0.203 13 40
CEBPB/PTGES2/Cbp/p300 0.009 0.091 -9999 0 -0.292 22 22
mol:Ca2+ 0.047 0.068 -9999 0 -0.122 35 35
MAPK3 0.012 0.086 0.335 2 -0.726 2 4
STAT1 (dimer) -0.029 0.111 0.187 6 -0.255 53 59
MAPK1 -0.037 0.208 0.346 1 -0.744 34 35
JAK2 0.026 0.022 -9999 0 -0.036 31 31
PIK3R1 0.032 0.012 -9999 0 0 61 61
JAK1 0.033 0.017 -9999 0 -0.035 16 16
CAMK2D 0 0 -9999 0 -9999 0 0
DAPK1 0.003 0.1 0.297 7 -0.395 11 18
SMAD7 -0.008 0.064 0.162 25 -0.145 14 39
CBL/CRKL/C3G 0.027 0.073 0.254 8 -0.177 5 13
PI3K 0.027 0.091 -9999 0 -0.186 30 30
IFNG 0.03 0.021 -9999 0 -0.036 34 34
apoptosis 0.015 0.092 0.304 5 -0.44 8 13
CAMK2G 0.025 0.017 -9999 0 0 155 155
STAT3 (dimer) 0.033 0.01 -9999 0 0 37 37
CAMK2A 0.036 0.004 -9999 0 0 7 7
CAMK2B 0.019 0.018 -9999 0 0 236 236
FRAP1 -0.03 0.085 0.179 29 -0.21 30 59
PRKCD -0.023 0.09 0.214 27 -0.2 22 49
RAP1B 0 0 -9999 0 -9999 0 0
negative regulation of cell growth -0.029 0.078 -9999 0 -0.182 62 62
PTPN2 0.035 0.006 -9999 0 0 16 16
EP300 0.033 0.012 -9999 0 -0.001 50 50
IRF1 -0.03 0.062 0.201 8 -0.291 9 17
STAT1 (dimer)/PIASy -0.018 0.071 0.225 13 -0.189 7 20
SOCS1 0.017 0.085 -9999 0 -1.039 3 3
mol:GDP -0.016 0.072 0.175 29 -0.186 3 32
CASP1 -0.018 0.077 0.156 26 -0.165 58 84
PTGES2 0.035 0.007 -9999 0 0 18 18
IRF9 0 0.046 0.126 18 -0.122 22 40
mol:PI-3-4-5-P3 0.014 0.079 -9999 0 -0.157 47 47
RAP1/GDP -0.027 0.054 0.108 21 -0.177 4 25
CBL -0.016 0.066 0.166 31 -0.177 5 36
MAP3K1 -0.016 0.065 0.166 29 -0.176 5 34
PIAS1 0.035 0.008 -9999 0 0 23 23
PIAS4 0.034 0.009 -9999 0 0 32 32
antigen processing and presentation of peptide antigen via MHC class II -0.029 0.078 -9999 0 -0.182 62 62
PTPN11 -0.01 0.068 0.169 37 -0.178 5 42
CREBBP 0.036 0.005 -9999 0 -0.005 6 6
RAPGEF1 0.035 0.007 -9999 0 0 18 18
Class I PI3K signaling events mediated by Akt

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
BCL2L1 -0.02 0.007 -9999 0 -9999 0 0
BAD/BCL-XL/YWHAZ 0.047 0.034 -9999 0 -0.124 12 12
CDKN1B -0.026 0.119 0.197 5 -0.331 56 61
CDKN1A -0.026 0.119 -9999 0 -0.328 58 58
FRAP1 0.035 0.006 -9999 0 0 14 14
PRKDC 0.033 0.01 -9999 0 0 42 42
FOXO3 -0.022 0.114 -9999 0 -0.31 60 60
AKT1 -0.022 0.119 -9999 0 -0.327 59 59
BAD 0.035 0.006 -9999 0 0 16 16
AKT3 0.015 0.003 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
FOXO4 -0.022 0.114 -9999 0 -0.31 60 60
AKT1/ASK1 -0.011 0.126 -9999 0 -0.321 59 59
BAD/YWHAZ 0.061 0.038 -9999 0 -0.131 12 12
RICTOR 0 0 -9999 0 -9999 0 0
RAF1 0.034 0.009 -9999 0 0 31 31
JNK cascade 0.011 0.122 0.312 59 -9999 0 59
TSC1 -0.027 0.117 -9999 0 -0.333 55 55
YWHAZ 0.035 0.007 -9999 0 0 17 17
AKT1/RAF1 -0.005 0.133 -9999 0 -0.333 61 61
EP300 0.033 0.011 -9999 0 0 49 49
mol:GDP -0.021 0.118 -9999 0 -0.323 59 59
mol:PI-3-4-5-P3 0 0 -9999 0 -9999 0 0
TSC2 -0.03 0.12 -9999 0 -0.329 61 61
YWHAQ 0.036 0.005 -9999 0 0 8 8
TBC1D4 -0.002 0.016 0.104 11 -9999 0 11
MAP3K5 0.03 0.014 -9999 0 0 81 81
MAPKAP1 0.034 0.008 -9999 0 0 26 26
negative regulation of cell cycle 0.007 0.106 0.327 26 -9999 0 26
YWHAH 0.031 0.013 -9999 0 0 74 74
AKT1S1 -0.022 0.114 -9999 0 -0.31 60 60
CASP9 -0.024 0.115 0.197 1 -0.321 57 58
YWHAB 0.035 0.007 -9999 0 0 21 21
p27Kip1/KPNA1 -0.01 0.13 0.267 4 -0.323 59 63
GBL 0.035 0.005 -9999 0 0 11 11
PDK1/Src/Hsp90 0.047 0.009 -9999 0 -9999 0 0
YWHAE 0.034 0.009 -9999 0 0 29 29
SRC 0.035 0.006 -9999 0 0 13 13
AKT2/p21CIP1 -0.026 0.107 0.236 1 -0.285 58 59
KIAA1303 0 0 -9999 0 -9999 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.016 0.063 -9999 0 -0.467 5 5
CHUK -0.025 0.107 -9999 0 -0.322 50 50
BAD/BCL-XL 0 0.124 -9999 0 -0.313 59 59
mTORC2 0.061 0.03 -9999 0 -0.12 7 7
AKT2 0.014 0.004 -9999 0 -9999 0 0
FOXO1-3a-4/14-3-3 family -0.009 0.13 -9999 0 -0.403 27 27
PDPK1 0.036 0.003 -9999 0 0 4 4
MDM2 -0.01 0.123 0.201 33 -0.318 53 86
MAPKKK cascade 0.005 0.13 0.327 61 -9999 0 61
MDM2/Cbp/p300 0.019 0.134 0.256 2 -0.312 53 55
TSC1/TSC2 -0.033 0.126 0.236 7 -0.336 60 67
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.128 0.245 2 -0.299 53 55
glucose import -0.008 0.02 0.204 2 -9999 0 2
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.008 0.081 -9999 0 -0.357 8 8
response to stress 0 0 -9999 0 -9999 0 0
SLC2A4 -0.008 0.021 0.204 2 -9999 0 2
GSK3A -0.023 0.115 0.197 9 -0.32 55 64
FOXO1 -0.022 0.114 -9999 0 -0.31 60 60
GSK3B -0.028 0.123 0.2 2 -0.335 59 61
SFN 0.031 0.013 -9999 0 0 74 74
G1/S transition of mitotic cell cycle -0.029 0.129 0.244 10 -0.329 61 71
p27Kip1/14-3-3 family 0.009 0.11 -9999 0 -0.535 12 12
PRKACA 0.034 0.009 -9999 0 0 29 29
KPNA1 0.035 0.007 -9999 0 0 21 21
HSP90AA1 0 0 -9999 0 -9999 0 0
YWHAG 0 0 -9999 0 -9999 0 0
RHEB 0.028 0.015 -9999 0 0 115 115
CREBBP 0.036 0.004 -9999 0 0 5 5
IL6-mediated signaling events

Figure 65.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 67.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.058 0.264 0.538 17 -0.688 23 40
CRP 0.054 0.257 0.568 10 -0.722 19 29
cell cycle arrest 0.047 0.286 0.525 15 -0.747 29 44
TIMP1 -0.001 0.367 0.558 13 -0.79 69 82
IL6ST 0.028 0.032 0.089 1 -0.045 38 39
Rac1/GDP 0.05 0.112 0.302 18 -0.302 10 28
AP1 0.017 0.19 -9999 0 -0.524 38 38
GAB2 0.034 0.012 -9999 0 -0.041 1 1
TNFSF11 0.053 0.256 0.561 8 -0.733 19 27
HSP90B1 0.002 0.216 0.335 1 -0.84 27 28
GAB1 0.031 0.014 -9999 0 -0.041 1 1
MAPK14 0.03 0.065 0.211 1 -0.318 2 3
AKT1 -0.013 0.168 -9999 0 -0.554 29 29
FOXO1 -0.009 0.162 -9999 0 -0.52 30 30
MAP2K6 0.032 0.072 0.183 4 -0.241 8 12
mol:GTP 0 0.004 -9999 0 -0.023 2 2
MAP2K4 0.041 0.139 0.327 26 -0.343 17 43
MITF 0.034 0.083 0.211 14 -0.267 9 23
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -9999 0 0
TYK2 0.032 0.011 -9999 0 0 54 54
A2M -0.066 0.32 -9999 0 -1.151 38 38
CEBPB 0.032 0.012 -9999 0 0 62 62
GRB2/SOS1/GAB family/SHP2 0.023 0.125 0.222 1 -0.45 22 23
STAT3 0.029 0.291 0.533 13 -0.8 29 42
STAT1 0.022 0.068 -9999 0 -0.74 3 3
CEBPD 0.02 0.333 0.573 7 -0.893 41 48
PIK3CA 0.03 0.015 -9999 0 -0.041 1 1
PI3K 0.017 0.076 -9999 0 -0.155 73 73
JUN 0.033 0.01 -9999 0 0 39 39
PIAS3/MITF 0.075 0.106 0.256 23 -0.27 10 33
MAPK11 0.026 0.063 0.21 2 -0.318 2 4
STAT3 (dimer)/FOXO1 -0.014 0.264 0.435 10 -0.609 52 62
GRB2/SOS1/GAB family 0.04 0.114 0.218 3 -0.264 31 34
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK 0.005 0.103 0.179 10 -0.253 43 53
GRB2 0.036 0.008 -9999 0 -0.041 1 1
JAK2 0.03 0.014 -9999 0 0 86 86
LBP 0.06 0.248 0.499 18 -0.613 26 44
PIK3R1 0.032 0.013 -9999 0 -0.041 1 1
JAK1 0.029 0.026 -9999 0 -0.041 47 47
MYC 0.009 0.363 0.582 11 -0.884 54 65
FGG 0.053 0.255 0.573 7 -0.747 18 25
macrophage differentiation 0.047 0.286 0.525 15 -0.747 29 44
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.055 0.073 -9999 0 -0.163 7 7
JUNB 0.052 0.292 0.527 22 -0.84 24 46
FOS 0.025 0.017 -9999 0 0 147 147
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 0.036 0.086 0.217 18 -0.274 9 27
STAT1/PIAS1 0.073 0.123 0.285 17 -0.323 7 24
GRB2/SOS1/GAB family/SHP2/PI3K -0.001 0.167 -9999 0 -0.513 31 31
STAT3 (dimer) 0.032 0.29 0.516 15 -0.788 29 44
PRKCD 0.096 0.217 0.405 83 -0.415 25 108
IL6R 0.03 0.026 -9999 0 -0.04 56 56
SOCS3 0.057 0.083 0.416 3 -9999 0 3
gp130 (dimer)/JAK1/JAK1/LMO4 0.043 0.088 0.181 1 -0.17 42 43
Rac1/GTP 0.042 0.115 0.3 10 -0.321 11 21
HCK 0.027 0.016 -9999 0 0 123 123
MAPKKK cascade 0.017 0.179 0.335 1 -0.558 34 35
bone resorption 0.055 0.248 0.534 10 -0.69 19 29
IRF1 0.046 0.293 0.54 15 -0.864 24 39
mol:GDP 0.033 0.088 0.218 20 -0.264 9 29
SOS1 0.001 0.005 0.025 11 -0.022 1 12
VAV1 0.031 0.087 0.22 18 -0.267 9 27
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.024 0.076 -9999 0 -0.328 12 12
PTPN11 0.023 0.078 -9999 0 -0.761 4 4
IL6/IL6RA 0.025 0.038 -9999 0 -9999 0 0
gp130 (dimer)/TYK2/TYK2/LMO4 0.045 0.075 -9999 0 -0.152 42 42
gp130 (dimer)/JAK2/JAK2/LMO4 0.046 0.062 -9999 0 -0.124 31 31
IL6 0.017 0.028 -9999 0 -0.041 21 21
PIAS3 0.035 0.007 -9999 0 0 17 17
PTPRE 0.009 0.029 -9999 0 -0.049 52 52
PIAS1 0.035 0.008 -9999 0 0 23 23
RAC1 0.027 0.016 -9999 0 0 123 123
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0.028 0.059 0.168 6 -0.224 5 11
LMO4 0.029 0.032 0.089 1 -0.047 35 36
STAT3 (dimer)/PIAS3 0.02 0.266 0.461 5 -0.727 30 35
MCL1 -0.005 0.167 0.396 1 -0.767 13 14
IGF1 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
NCK2 0.035 0.007 -9999 0 0 19 19
PTK2 0.034 0.008 -9999 0 0 28 28
CRKL -0.017 0.044 0.098 28 -0.147 23 51
GRB2/SOS1/SHC 0.04 0.03 -9999 0 -0.123 12 12
HRAS 0.034 0.009 -9999 0 0 32 32
IRS1/Crk 0.016 0.047 -9999 0 -0.141 35 35
IGF-1R heterotetramer/IGF1/PTP1B 0.051 0.056 -9999 0 -0.144 28 28
AKT1 -0.03 0.079 0.152 36 -0.216 30 66
BAD -0.035 0.075 0.142 32 -0.22 28 60
mol:GTP 0 0 -9999 0 -9999 0 0
CRK -0.017 0.046 0.1 28 -0.155 24 52
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.025 0.05 0.219 2 -0.144 29 31
RAF1 -0.032 0.145 -9999 0 -0.544 27 27
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.043 0.055 -9999 0 -0.134 28 28
YWHAZ 0.035 0.007 -9999 0 0 17 17
IGF-1R heterotetramer/IGF1/IRS1 0.032 0.049 -9999 0 -0.155 24 24
PIK3CA 0.03 0.014 -9999 0 0 85 85
RPS6KB1 -0.029 0.076 0.154 39 -0.2 22 61
GNB2L1 0.035 0.005 -9999 0 0 11 11
positive regulation of MAPKKK cascade -0.03 0.117 0.229 4 -0.42 27 31
PXN 0.036 0.004 -9999 0 0 5 5
PIK3R1 0.032 0.012 -9999 0 0 61 61
cell adhesion 0 0 -9999 0 -9999 0 0
GRB2/SOS1 0.024 0.019 -9999 0 -0.132 7 7
HRAS/GTP 0.015 0.053 -9999 0 -0.135 41 41
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.065 0.055 -9999 0 -0.117 31 31
IGF-1R heterotetramer 0.036 0.014 -9999 0 -9999 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck 0.046 0.061 -9999 0 -0.14 35 35
Crk/p130 Cas/Paxillin 0.036 0.056 0.216 1 -0.134 35 36
IGF1R 0.036 0.014 -9999 0 -9999 0 0
IGF1 0.032 0.026 -9999 0 -0.055 33 33
IRS2/Crk -0.029 0.057 0.086 34 -0.186 30 64
PI3K 0.035 0.087 -9999 0 -0.138 77 77
apoptosis 0.033 0.081 0.21 29 -0.158 30 59
HRAS/GDP 0.021 0.029 -9999 0 -0.132 16 16
PRKCD -0.001 0.059 0.127 4 -0.213 22 26
RAF1/14-3-3 E -0.01 0.133 -9999 0 -0.467 27 27
BAD/14-3-3 -0.034 0.085 0.164 30 -0.221 29 59
PRKCZ -0.024 0.074 0.153 38 -0.194 22 60
Crk/p130 Cas/Paxillin/FAK1 -0.043 0.076 0.129 32 -0.214 30 62
PTPN1 0.034 0.008 -9999 0 0 26 26
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.005 0.06 -9999 0 -0.216 23 23
BCAR1 0 0 -9999 0 -9999 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.039 0.073 -9999 0 -0.141 46 46
mol:GDP 0 0 -9999 0 -9999 0 0
SOS1 0 0 -9999 0 -9999 0 0
IRS1/NCK2 0.024 0.051 0.131 2 -0.141 34 36
GRB10 0.022 0.018 -9999 0 0 185 185
PTPN11 -0.018 0.046 0.099 29 -0.152 24 53
IRS1 0.009 0.042 0.121 2 -0.155 24 26
IRS2 -0.018 0.05 0.101 22 -0.191 23 45
IGF-1R heterotetramer/IGF1 0.038 0.052 -9999 0 -0.171 24 24
GRB2 0.035 0.006 -9999 0 0 16 16
PDPK1 -0.023 0.081 0.166 40 -0.206 21 61
YWHAE 0.034 0.009 -9999 0 0 29 29
PRKD1 -0.003 0.063 0.129 2 -0.236 24 26
SHC1 0.033 0.011 -9999 0 0 48 48
PLK1 signaling events

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
regulation of centriole-centriole cohesion 0 0.009 -9999 0 -0.034 13 13
BUB1B -0.022 0.083 0.115 18 -0.215 59 77
PLK1 0.004 0.022 0.083 12 -0.069 3 15
PLK1S1 0.002 0.013 0.048 16 -0.039 2 18
KIF2A 0.004 0.02 0.073 12 -0.062 3 15
regulation of mitotic centrosome separation 0.005 0.022 0.083 12 -0.069 3 15
GOLGA2 0.034 0.008 -9999 0 0 24 24
Hec1/SPC24 -0.004 0.01 -9999 0 -0.053 5 5
WEE1 -0.03 0.131 -9999 0 -0.462 35 35
cytokinesis -0.022 0.111 0.143 11 -0.297 57 68
PP2A-alpha B56 0.056 0.067 -9999 0 -0.481 4 4
AURKA 0.002 0.015 0.055 16 -0.041 2 18
PICH/PLK1 -0.034 0.073 0.066 8 -0.175 82 90
CENPE 0.004 0.046 0.119 46 -0.101 11 57
RhoA/GTP 0.024 0.019 -9999 0 -0.132 7 7
positive regulation of microtubule depolymerization 0.004 0.02 0.073 12 -0.062 3 15
PPP2CA 0.035 0.007 -9999 0 0 20 20
FZR1 0.034 0.009 -9999 0 0 33 33
TPX2 -0.026 0.089 0.12 1 -0.222 81 82
PAK1 0.035 0.007 -9999 0 0 17 17
SPC24 0 0 -9999 0 -9999 0 0
FBXW11 0.035 0.007 -9999 0 0 20 20
CLSPN 0.01 0.027 -9999 0 -0.204 6 6
GORASP1 0.034 0.008 -9999 0 0 28 28
metaphase 0.001 0.003 0.013 11 -0.01 1 12
mol:GTP 0 0 -9999 0 -9999 0 0
NLP 0.002 0.013 0.048 16 -0.039 2 18
G2 phase of mitotic cell cycle -0.001 0.002 0.01 8 -9999 0 8
STAG2 0.035 0.007 -9999 0 0 21 21
GRASP65/GM130/RAB1/GTP -0.017 0.14 -9999 0 -0.601 23 23
spindle elongation 0.005 0.022 0.083 12 -0.069 3 15
ODF2 0.035 0.008 -9999 0 0 26 26
BUB1 0.026 0.045 -9999 0 -0.573 2 2
TPT1 -0.002 0.049 -9999 0 -0.181 31 31
CDC25C 0.012 0.026 -9999 0 -0.214 5 5
CDC25B 0.014 0.031 -9999 0 -0.029 150 150
SGOL1 0 0.009 0.034 13 -9999 0 13
RHOA 0.035 0.007 -9999 0 0 21 21
CCNB1/CDK1 -0.015 0.125 -9999 0 -0.222 99 99
CDC14B -0.011 0.004 0.011 6 -9999 0 6
CDC20 0.027 0.016 -9999 0 0 117 117
PLK1/PBIP1 -0.015 0.036 0.059 5 -0.09 75 80
mitosis -0.001 0.003 0.012 9 -9999 0 9
FBXO5 -0.015 0.06 0.114 13 -0.163 47 60
CDC2 0.017 0.023 -9999 0 -0.03 40 40
NDC80 0 0 -9999 0 -9999 0 0
metaphase plate congression 0.001 0.059 -9999 0 -0.26 22 22
ERCC6L -0.041 0.1 -9999 0 -0.218 93 93
NLP/gamma Tubulin 0.002 0.027 0.07 9 -0.105 19 28
microtubule cytoskeleton organization -0.002 0.049 -9999 0 -0.181 31 31
G2/M transition DNA damage checkpoint -0.001 0.002 0.01 4 -9999 0 4
PPP1R12A 0.035 0.008 -9999 0 0 21 21
interphase -0.001 0.002 0.01 4 -9999 0 4
PLK1/PRC1-2 0.008 0.075 -9999 0 -0.142 84 84
GRASP65/GM130/RAB1/GTP/PLK1 0.047 0.053 -9999 0 -0.121 29 29
RAB1A 0.035 0.007 -9999 0 0 17 17
prophase 0 0 -9999 0 -9999 0 0
Aurora A/BORA 0.002 0.018 0.065 15 -0.051 1 16
mitotic prometaphase 0 0.005 0.021 22 -9999 0 22
proteasomal ubiquitin-dependent protein catabolic process -0.041 0.098 0.174 2 -0.207 97 99
microtubule-based process 0.019 0.024 0.095 4 -0.061 3 7
Golgi organization 0.005 0.022 0.083 12 -0.069 3 15
Cohesin/SA2 0.02 0.032 0.092 6 -0.093 21 27
PPP1CB/MYPT1 0.046 0.036 -9999 0 -0.153 14 14
KIF20A 0.029 0.015 -9999 0 0 101 101
APC/C/CDC20 0.02 0.024 0.104 5 -0.059 2 7
PPP2R1A 0.032 0.012 -9999 0 0 61 61
chromosome segregation -0.015 0.036 0.059 5 -0.089 75 80
PRC1 0.028 0.015 -9999 0 0 113 113
ECT2 0 0.057 0.135 47 -0.105 31 78
C13orf34 0.003 0.019 0.069 14 -0.056 2 16
NUDC 0.001 0.059 -9999 0 -0.261 22 22
regulation of attachment of spindle microtubules to kinetochore -0.021 0.082 0.114 18 -0.213 59 77
spindle assembly 0.002 0.024 0.075 14 -0.078 13 27
spindle stabilization 0.002 0.013 0.048 16 -0.039 2 18
APC/C/HCDH1 0.023 0.027 0.087 1 -0.116 15 16
MKLP2/PLK1 0.019 0.024 0.095 4 -0.061 3 7
CCNB1 0.016 0.027 -9999 0 -0.028 94 94
PPP1CB 0.036 0.006 -9999 0 0 12 12
BTRC 0.027 0.016 -9999 0 0 124 124
ROCK2 0.016 0.029 -9999 0 -0.208 3 3
TUBG1 0.002 0.049 0.099 1 -0.224 20 21
G2/M transition of mitotic cell cycle -0.043 0.105 0.131 16 -0.229 89 105
MLF1IP -0.008 0.006 0.009 3 -9999 0 3
INCENP 0.036 0.003 -9999 0 0 4 4
FAS signaling pathway (CD95)

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
SPTAN1 -0.02 0.057 0.221 5 -0.215 23 28
RFC1 -0.021 0.051 0.185 2 -0.216 25 27
PRKDC -0.017 0.058 0.192 7 -0.222 23 30
RIPK1 0.032 0.012 -9999 0 -0.013 30 30
CASP7 -0.143 0.276 -9999 0 -0.576 138 138
FASLG/FAS/FADD/FAF1 -0.006 0.085 0.158 32 -0.178 40 72
MAP2K4 -0.035 0.139 0.209 1 -0.333 35 36
mol:ceramide 0.008 0.092 0.178 5 -0.242 20 25
GSN -0.008 0.06 0.19 9 -0.224 20 29
FASLG/FAS/FADD/FAF1/Caspase 8 -0.007 0.096 0.18 12 -0.256 24 36
FAS 0.022 0.02 -9999 0 -9999 0 0
BID -0.03 0.033 0.077 9 -0.131 20 29
MAP3K1 -0.087 0.187 -9999 0 -0.365 140 140
MAP3K7 0.034 0.01 -9999 0 0 38 38
RB1 -0.014 0.056 0.224 9 -0.211 24 33
CFLAR 0.033 0.01 -9999 0 -0.016 18 18
HGF/MET 0.033 0.049 -9999 0 -0.124 21 21
ARHGDIB -0.017 0.06 0.222 7 -0.224 22 29
FADD 0.038 0.008 -9999 0 0 13 13
actin filament polymerization 0.008 0.06 0.223 20 -0.189 9 29
NFKB1 0.029 0.109 -9999 0 -0.651 10 10
MAPK8 -0.026 0.136 0.231 1 -0.364 21 22
DFFA -0.019 0.051 0.222 3 -0.213 25 28
DNA fragmentation during apoptosis -0.018 0.047 0.223 1 -0.21 24 25
FAS/FADD/MET 0.025 0.049 -9999 0 -0.122 22 22
CFLAR/RIP1 0.047 0.019 -9999 0 -0.134 2 2
FAIM3 0.035 0.006 -9999 0 0 13 13
FAF1 0.038 0.011 -9999 0 -9999 0 0
PARP1 -0.019 0.052 0.221 3 -0.215 26 29
DFFB -0.018 0.047 0.224 1 -0.211 24 25
CHUK 0.017 0.101 -9999 0 -0.613 10 10
FASLG 0.039 0.008 -9999 0 -9999 0 0
FAS/FADD 0.024 0.053 -9999 0 -0.143 32 32
HGF 0.024 0.017 -9999 0 0 157 157
LMNA -0.02 0.052 0.195 6 -0.198 24 30
CASP6 -0.018 0.049 0.173 3 -0.21 24 27
CASP10 0.039 0.004 -9999 0 -9999 0 0
CASP3 -0.01 0.048 -9999 0 -0.242 19 19
PTPN13 0.032 0.012 -9999 0 0 56 56
CASP8 -0.03 0.007 -9999 0 -9999 0 0
IL6 0.025 0.129 -9999 0 -0.689 4 4
MET 0.023 0.018 -9999 0 0 183 183
ICAD/CAD -0.023 0.05 0.269 3 -0.206 24 27
FASLG/FAS/FADD/FAF1/Caspase 10 0.008 0.093 0.179 5 -0.245 20 25
activation of caspase activity by cytochrome c -0.03 0.033 0.077 9 -0.13 20 29
PAK2 -0.012 0.057 0.213 8 -0.211 23 31
BCL2 0.035 0.007 -9999 0 0 17 17
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.034 0.008 -9999 0 0 25 25
RAS family/GTP/Tiam1 -0.006 0.086 -9999 0 -0.202 63 63
NT3 (dimer)/TRKC 0.046 0.026 -9999 0 -0.142 6 6
NT3 (dimer)/TRKB 0.027 0.068 -9999 0 -0.124 67 67
SHC/Grb2/SOS1/GAB1/PI3K -0.008 0.091 -9999 0 -0.21 66 66
RAPGEF1 0.035 0.007 -9999 0 0 18 18
BDNF 0.032 0.012 -9999 0 0 61 61
PIK3CA 0.03 0.014 -9999 0 0 85 85
DYNLT1 0.033 0.01 -9999 0 0 41 41
NTRK1 0.035 0.006 -9999 0 0 12 12
NTRK2 0.027 0.016 -9999 0 0 126 126
NTRK3 0.034 0.009 -9999 0 0 32 32
NT-4/5 (dimer)/TRKB 0.014 0.057 -9999 0 -0.115 70 70
neuron apoptosis -0.007 0.122 0.309 40 -0.211 1 41
SHC 2-3/Grb2 0.006 0.131 -9999 0 -0.333 40 40
SHC1 0.033 0.011 -9999 0 0 48 48
SHC2 -0.011 0.123 -9999 0 -0.434 29 29
SHC3 -0.012 0.119 -9999 0 -0.408 29 29
STAT3 (dimer) 0.02 0.087 -9999 0 -0.285 35 35
NT3 (dimer)/TRKA 0.059 0.029 -9999 0 -9999 0 0
RIN/GDP 0.003 0.071 0.176 4 -0.217 23 27
GIPC1 0.034 0.009 -9999 0 0 30 30
KRAS 0.033 0.01 -9999 0 0 37 37
DNAJA3 -0.004 0.04 0.142 3 -0.13 1 4
RIN/GTP 0.011 0.036 -9999 0 -0.132 26 26
CCND1 -0.012 0.112 -9999 0 -0.493 25 25
MAGED1 0.034 0.008 -9999 0 0 26 26
PTPN11 0.036 0.005 -9999 0 0 9 9
RICS 0.033 0.01 -9999 0 0 41 41
NT-4/5 (dimer) 0 0 -9999 0 -9999 0 0
SHC/GRB2/SOS1 0.04 0.03 -9999 0 -0.123 12 12
GRB2 0.035 0.006 -9999 0 0 16 16
NGF (dimer)/TRKA/MATK 0.044 0.014 -9999 0 -9999 0 0
TRKA/NEDD4-2 0.047 0.019 -9999 0 -0.142 1 1
ELMO1 0.02 0.018 -9999 0 0 219 219
RhoG/GTP/ELMO1/DOCK1 0.009 0.046 -9999 0 -0.116 43 43
NGF 0 0 -9999 0 -9999 0 0
HRAS 0.034 0.009 -9999 0 0 32 32
DOCK1 0.023 0.017 -9999 0 0 178 178
GAB2 0.033 0.01 -9999 0 0 44 44
RIT2 0.024 0.017 -9999 0 0 157 157
RIT1 0.032 0.012 -9999 0 0 61 61
FRS2 0.035 0.008 -9999 0 0 22 22
DNM1 0.035 0.008 -9999 0 0 23 23
mol:GTP 0 0 -9999 0 -9999 0 0
CRK 0.035 0.008 -9999 0 0 23 23
SH2B1 (homopentamer) 0 0 -9999 0 -9999 0 0
RhoG/GTP 0.012 0.048 0.156 2 -0.169 11 13
mol:GDP 0.001 0.101 0.215 10 -0.309 23 33
NGF (dimer) 0 0 -9999 0 -9999 0 0
RhoG/GDP 0.003 0.044 -9999 0 -0.132 43 43
RIT1/GDP 0.011 0.08 0.193 8 -0.216 24 32
TIAM1 0.033 0.01 -9999 0 0 43 43
PIK3R1 0.032 0.012 -9999 0 0 61 61
BDNF (dimer)/TRKB 0.028 0.069 -9999 0 -0.126 67 67
KIDINS220/CRKL/C3G 0.049 0.015 -9999 0 -9999 0 0
SHC/RasGAP 0.037 0.051 -9999 0 -0.153 29 29
FRS2 family/SHP2 0.067 0.027 -9999 0 -0.124 6 6
SHC/GRB2/SOS1/GAB1 0.046 0.044 -9999 0 -0.114 19 19
RIT1/GTP 0.014 0.042 -9999 0 -0.132 36 36
NT3 (dimer) 0.034 0.008 -9999 0 0 23 23
RAP1/GDP 0 0.059 -9999 0 -0.174 25 25
KIDINS220/CRKL 0.034 0.008 -9999 0 0 25 25
BDNF (dimer) 0.032 0.012 -9999 0 0 61 61
ubiquitin-dependent protein catabolic process 0.042 0.017 -9999 0 -0.115 1 1
Schwann cell development -0.011 0.016 -9999 0 -0.053 39 39
EHD4 0.033 0.01 -9999 0 0 37 37
FRS2 family/GRB2/SOS1 0.063 0.027 -9999 0 -0.11 7 7
FRS2 family/SHP2/CRK family/C3G/GAB2 0.01 0.068 -9999 0 -0.262 16 16
RAP1B 0 0 -9999 0 -9999 0 0
RAP1A 0.036 0.005 -9999 0 0 8 8
CDC42/GTP 0.017 0.08 -9999 0 -0.144 74 74
ABL1 0.031 0.013 -9999 0 0 67 67
SH2B family/GRB2/SOS1 0.024 0.019 -9999 0 -0.132 7 7
Rap1/GTP 0.007 0.065 -9999 0 -0.204 21 21
STAT3 0.02 0.087 -9999 0 -0.284 35 35
axon guidance 0.005 0.07 -9999 0 -0.139 76 76
MAPK3 -0.005 0.058 0.183 41 -9999 0 41
MAPK1 -0.005 0.054 0.183 35 -9999 0 35
CDC42/GDP 0.012 0.078 0.183 9 -0.209 23 32
NTF3 0.035 0.008 -9999 0 0 23 23
NTF4 0 0 -9999 0 -9999 0 0
NGF (dimer)/TRKA/FAIM 0.043 0.024 -9999 0 -0.115 8 8
PI3K 0.016 0.075 -9999 0 -0.155 73 73
FRS3 0.036 0.002 -9999 0 0 2 2
FAIM 0.034 0.008 -9999 0 0 27 27
GAB1 0.031 0.013 -9999 0 0 75 75
RASGRF1 -0.004 0.041 0.142 2 -0.13 2 4
SOS1 0 0 -9999 0 -9999 0 0
MCF2L -0.018 0.021 0.089 11 -0.123 2 13
RGS19 0.034 0.008 -9999 0 0 24 24
CDC42 0.035 0.008 -9999 0 0 22 22
RAS family/GTP 0.013 0.097 0.227 1 -0.347 23 24
Rac1/GDP 0.011 0.071 0.189 9 -0.222 19 28
NGF (dimer)/TRKA/GRIT 0.039 0.035 -9999 0 -0.115 21 21
neuron projection morphogenesis -0.037 0.244 -9999 0 -0.863 35 35
NGF (dimer)/TRKA/NEDD4-2 0.043 0.017 -9999 0 -0.115 1 1
MAP2K1 0.002 0.074 0.184 48 -0.188 5 53
NGFR 0.031 0.013 -9999 0 0 67 67
NGF (dimer)/TRKA/GIPC/GAIP 0.012 0.047 -9999 0 -0.225 10 10
RAS family/GTP/PI3K -0.024 0.103 -9999 0 -0.206 96 96
FRS2 family/SHP2/GRB2/SOS1 0.076 0.038 -9999 0 -0.144 9 9
NRAS 0.032 0.012 -9999 0 0 58 58
GRB2/SOS1 0.024 0.019 -9999 0 -0.132 7 7
PRKCI 0.034 0.008 -9999 0 0 25 25
ChemicalAbstracts:146-91-8 0 0 -9999 0 -9999 0 0
RAC1 0.027 0.016 -9999 0 0 123 123
PRKCZ 0 0 -9999 0 -9999 0 0
MAPKKK cascade 0.014 0.086 -9999 0 -0.492 11 11
RASA1 0.034 0.009 -9999 0 0 30 30
TRKA/c-Abl 0.031 0.058 -9999 0 -0.142 47 47
SQSTM1 0.034 0.009 -9999 0 0 33 33
BDNF (dimer)/TRKB/GIPC 0.049 0.072 -9999 0 -0.118 58 58
NGF (dimer)/TRKA/p62/Atypical PKCs 0.053 0.033 -9999 0 -0.102 14 14
MATK 0.034 0.009 -9999 0 0 35 35
NEDD4L 0.033 0.011 -9999 0 0 47 47
RAS family/GDP -0.019 0.055 -9999 0 -0.158 44 44
NGF (dimer)/TRKA 0.008 0.039 0.153 4 -0.13 2 6
Rac1/GTP -0.014 0.058 -9999 0 -0.207 26 26
FRS2 family/SHP2/CRK family 0.087 0.055 -9999 0 -0.125 17 17
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.035 0.007 -9999 0 0 20 20
HDAC2 0.032 0.011 -9999 0 0 50 50
GNB1/GNG2 0.029 0.035 -9999 0 -0.115 16 16
forebrain development 0.036 0.071 0.264 7 -0.375 3 10
GNAO1 0.03 0.014 -9999 0 0 81 81
SMO/beta Arrestin2 0.036 0.03 -9999 0 -0.14 4 4
SMO 0.026 0.016 -9999 0 0 134 134
ARRB2 0.034 0.008 -9999 0 0 27 27
GLI3/SPOP 0.004 0.11 -9999 0 -0.293 41 41
mol:GTP 0 0.001 -9999 0 -9999 0 0
GSK3B 0.034 0.009 -9999 0 0 35 35
GNAI2 0.033 0.01 -9999 0 0 42 42
SIN3/HDAC complex 0.054 0.042 -9999 0 -0.125 18 18
GNAI1 0.018 0.018 -9999 0 0 245 245
XPO1 0.037 0.005 -9999 0 0 5 5
GLI1/Su(fu) 0.012 0.05 0.244 1 -0.279 5 6
SAP30 0.035 0.006 -9999 0 0 15 15
mol:GDP 0.026 0.016 -9999 0 0 134 134
MIM/GLI2A 0.041 0.013 0.117 11 -9999 0 11
IFT88 0.034 0.009 -9999 0 0 29 29
GNAI3 0.035 0.006 -9999 0 0 12 12
GLI2 0.005 0.088 0.23 1 -0.349 18 19
GLI3 -0.011 0.1 -9999 0 -0.282 41 41
CSNK1D 0.035 0.007 -9999 0 0 19 19
CSNK1E 0.031 0.012 -9999 0 0 64 64
SAP18 0.033 0.01 -9999 0 0 39 39
embryonic digit morphogenesis 0.034 0.009 -9999 0 0 29 29
GNG2 0 0 -9999 0 -9999 0 0
Gi family/GTP -0.014 0.097 -9999 0 -0.264 43 43
SIN3B 0.034 0.009 -9999 0 0 35 35
SIN3A 0 0 -9999 0 -9999 0 0
GLI3/Su(fu) -0.011 0.077 0.14 2 -0.268 27 29
GLI2/Su(fu) -0.001 0.073 -9999 0 -0.31 17 17
FOXA2 0.045 0.055 -9999 0 -0.49 1 1
neural tube patterning 0.036 0.071 0.264 7 -0.375 3 10
SPOP 0.035 0.007 -9999 0 0 21 21
Su(fu)/PIAS1 0.042 0.036 0.096 115 -0.123 4 119
GNB1 0.033 0.01 -9999 0 0 37 37
CSNK1G2 0.033 0.01 -9999 0 0 37 37
CSNK1G3 0.035 0.005 -9999 0 0 11 11
MTSS1 0.041 0.013 0.117 11 -9999 0 11
embryonic limb morphogenesis 0.036 0.071 0.264 7 -0.375 3 10
SUFU 0.002 0.01 -9999 0 -0.107 4 4
LGALS3 0.028 0.015 -9999 0 0 106 106
catabolic process 0.013 0.14 0.273 2 -0.412 34 36
GLI3A/CBP 0.043 0.008 -9999 0 -9999 0 0
KIF3A 0.032 0.011 -9999 0 0 51 51
GLI1 0.035 0.071 0.273 6 -0.382 3 9
RAB23 0.034 0.009 -9999 0 0 29 29
CSNK1A1 0.035 0.006 -9999 0 0 12 12
IFT172 0 0 -9999 0 -9999 0 0
RBBP7 0.036 0.005 -9999 0 0 8 8
Su(fu)/Galectin3 0.034 0.039 0.096 93 -0.13 8 101
GNAZ 0.03 0.013 -9999 0 0 79 79
RBBP4 0.032 0.011 -9999 0 0 53 53
CSNK1G1 0.036 0.005 -9999 0 0 8 8
PIAS1 0.035 0.008 -9999 0 0 23 23
PRKACA 0.034 0.009 -9999 0 0 29 29
GLI2/SPOP 0.019 0.096 0.221 1 -0.325 22 23
STK36 0.001 0.003 0.024 5 -9999 0 5
Gi family/GNB1/GNG2/GDP -0.025 0.111 -9999 0 -0.337 40 40
PTCH1 0.034 0.066 0.244 8 -0.345 3 11
MIM/GLI1 0.058 0.076 0.347 3 -0.348 3 6
CREBBP 0.043 0.008 -9999 0 -9999 0 0
Su(fu)/SIN3/HDAC complex -0.001 0.098 0.167 1 -0.312 29 30
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.018 0.05 -9999 0 -0.183 25 25
PDGFRB 0.035 0.009 -9999 0 -0.001 26 26
SPHK1 0.018 0.021 -9999 0 -9999 0 0
mol:S1P 0.019 0.028 -9999 0 -9999 0 0
S1P1/S1P/Gi -0.005 0.14 0.239 11 -0.441 29 40
GNAO1 0.032 0.015 0.063 1 0 81 82
PDGFB-D/PDGFRB/PLCgamma1 0.023 0.143 0.248 21 -0.361 33 54
PLCG1 -0.011 0.129 0.221 13 -0.394 31 44
mol:GTP 0 0 -9999 0 -9999 0 0
PDGFB-D/PDGFRB 0.035 0.009 -9999 0 -0.001 26 26
GNAI2 0.035 0.012 -9999 0 0 42 42
GNAI3 0.037 0.007 -9999 0 0 12 12
GNAI1 0.019 0.019 -9999 0 0 245 245
mol:GDP 0 0 -9999 0 -9999 0 0
EDG1 0.011 0.072 0.115 11 -0.267 25 36
S1P1/S1P 0.026 0.073 0.21 4 -0.266 14 18
negative regulation of cAMP metabolic process -0.004 0.137 0.238 11 -0.429 29 40
MAPK3 -0.006 0.135 0.273 8 -0.421 28 36
calcium-dependent phospholipase C activity 0 0.003 -9999 0 -9999 0 0
Rac1/GDP 0.018 0.02 -9999 0 -0.132 6 6
RhoA/GDP 0.024 0.019 -9999 0 -0.132 7 7
KDR 0.028 0.033 0.086 9 -0.127 15 24
PLCB2 0.033 0.082 0.22 13 -0.249 14 27
RAC1 0.027 0.016 -9999 0 0 123 123
RhoA/GTP 0.018 0.063 -9999 0 -0.234 15 15
receptor internalization 0.024 0.069 0.2 4 -0.252 14 18
PTGS2 0.028 0.15 0.358 8 -0.464 15 23
Rac1/GTP 0.013 0.055 -9999 0 -0.254 10 10
RHOA 0.035 0.007 -9999 0 0 21 21
VEGFA -0.001 0.021 -9999 0 -0.098 20 20
negative regulation of T cell proliferation -0.004 0.137 0.238 11 -0.429 29 40
GO:0007205 0 0 -9999 0 -9999 0 0
GNAZ 0.032 0.015 -9999 0 0 79 79
MAPK1 -0.002 0.134 0.27 10 -0.442 24 34
S1P1/S1P/PDGFB-D/PDGFRB 0.049 0.096 0.261 7 -0.276 19 26
ABCC1 0.036 0.008 -9999 0 0 19 19
Plasma membrane estrogen receptor signaling

Figure 72.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 74.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.049 0.039 -9999 0 -0.099 20 20
ER alpha/Gai/GDP/Gbeta gamma -0.046 0.176 -9999 0 -0.471 50 50
AKT1 -0.058 0.227 -9999 0 -0.616 58 58
PIK3CA 0.03 0.014 -9999 0 0 85 85
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.052 0.235 -9999 0 -0.632 57 57
mol:Ca2+ 0.004 0.044 0.173 4 -0.211 3 7
IGF1R 0.032 0.012 -9999 0 0 56 56
E2/ER alpha (dimer)/Striatin 0.045 0.013 -9999 0 -9999 0 0
SHC1 0.033 0.011 -9999 0 0 48 48
apoptosis 0.057 0.217 0.577 61 -9999 0 61
RhoA/GTP 0.01 0.055 -9999 0 -0.132 51 51
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.021 0.153 -9999 0 -0.359 56 56
regulation of stress fiber formation 0.035 0.062 0.182 21 -0.175 6 27
E2/ERA-ERB (dimer) 0.044 0.015 -9999 0 -9999 0 0
KRAS 0.033 0.01 -9999 0 0 37 37
G13/GTP 0.042 0.014 -9999 0 -9999 0 0
pseudopodium formation -0.035 0.062 0.175 6 -0.182 21 27
E2/ER alpha (dimer)/PELP1 0.042 0.024 -9999 0 -0.113 7 7
GRB2 0.035 0.006 -9999 0 0 16 16
GNG2 0 0 -9999 0 -9999 0 0
GNAO1 0.03 0.014 -9999 0 0 81 81
HRAS 0.034 0.009 -9999 0 0 32 32
mol:GTP 0 0 -9999 0 -9999 0 0
mol:NO -0.022 0.163 -9999 0 -0.419 47 47
E2/ER beta (dimer) 0.025 0.006 -9999 0 -9999 0 0
mol:GDP 0.005 0.056 0.132 4 -0.192 21 25
mol:NADP -0.022 0.163 -9999 0 -0.419 47 47
PIK3R1 0.032 0.012 -9999 0 0 61 61
mol:IP3 0.004 0.04 -9999 0 -0.203 1 1
IGF-1R heterotetramer 0.032 0.012 -9999 0 0 56 56
PLCB1 0.011 0.04 -9999 0 -0.202 1 1
PLCB2 0.011 0.04 -9999 0 -0.202 1 1
IGF1 0.035 0.007 -9999 0 0 20 20
mol:L-citrulline -0.022 0.163 -9999 0 -0.419 47 47
RHOA 0.035 0.007 -9999 0 0 21 21
Gai/GDP -0.069 0.238 -9999 0 -0.643 66 66
JNK cascade 0.025 0.006 -9999 0 -9999 0 0
BCAR1 0 0 -9999 0 -9999 0 0
ESR2 0.034 0.009 -9999 0 0 29 29
GNAQ 0.034 0.009 -9999 0 0 31 31
ESR1 0.034 0.009 -9999 0 0 34 34
Gq family/GDP/Gbeta gamma -0.008 0.157 -9999 0 -0.469 37 37
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.012 0.138 -9999 0 -0.714 14 14
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.008 0.161 0.251 4 -0.377 51 55
GNAZ 0.03 0.013 -9999 0 0 79 79
E2/ER alpha (dimer) 0.025 0.007 -9999 0 -9999 0 0
STRN 0.036 0.002 -9999 0 0 2 2
GNAL 0.035 0.006 -9999 0 0 13 13
PELP1 0.035 0.007 -9999 0 0 19 19
MAPK11 -0.015 0.006 -9999 0 -9999 0 0
GNAI2 0.033 0.01 -9999 0 0 42 42
GNAI3 0.035 0.006 -9999 0 0 12 12
GNAI1 0.018 0.018 -9999 0 0 245 245
HBEGF -0.027 0.18 0.32 11 -0.428 52 63
cAMP biosynthetic process 0.036 0.016 -9999 0 -9999 0 0
SRC -0.05 0.167 0.207 2 -0.444 52 54
PI3K 0.016 0.075 -9999 0 -0.155 73 73
GNB1 0.033 0.01 -9999 0 0 37 37
G13/GDP/Gbeta gamma 0.021 0.066 -9999 0 -0.173 28 28
SOS1 0 0 -9999 0 -9999 0 0
IGF-1R heterotetramer/IGF1 -0.031 0.121 -9999 0 -0.309 53 53
Gs family/GTP 0.046 0.02 -9999 0 -9999 0 0
EntrezGene:2778 0 0 -9999 0 -9999 0 0
RAS family/GTP 0.041 0.064 -9999 0 -0.131 50 50
vasodilation -0.019 0.156 -9999 0 -0.399 47 47
mol:DAG 0.004 0.04 -9999 0 -0.203 1 1
Gs family/GDP/Gbeta gamma 0.003 0.059 -9999 0 -0.179 28 28
MSN -0.033 0.064 0.18 6 -0.194 21 27
Gq family/GTP 0.023 0.042 -9999 0 -0.205 1 1
mol:PI-3-4-5-P3 -0.05 0.225 -9999 0 -0.607 57 57
NRAS 0.032 0.012 -9999 0 0 58 58
mol:E2 0 0 -9999 0 -9999 0 0
cell adhesion 0.019 0.156 0.399 47 -9999 0 47
GRB2/SOS1 0.024 0.019 -9999 0 -0.132 7 7
RhoA/GDP 0.02 0.066 -9999 0 -0.193 24 24
NOS3 -0.024 0.172 -9999 0 -0.442 47 47
GNA11 0.032 0.012 -9999 0 0 60 60
MAPKKK cascade -0.004 0.15 -9999 0 -0.456 36 36
E2/ER alpha (dimer)/PELP1/Src -0.012 0.166 0.247 6 -0.387 52 58
ruffle organization -0.035 0.062 0.175 6 -0.182 21 27
ROCK2 -0.028 0.068 0.193 7 -0.193 13 20
GNA14 0.034 0.008 -9999 0 0 28 28
GNA15 0.032 0.012 -9999 0 0 59 59
GNA13 0.035 0.007 -9999 0 0 18 18
MMP9 -0.034 0.173 0.374 2 -0.399 61 63
MMP2 -0.035 0.174 0.234 8 -0.425 55 63
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.03 0.034 -9999 0 -0.142 8 8
CRKL 0.039 0.106 0.264 6 -0.41 16 22
mol:PIP3 -0.018 0.134 0.336 1 -0.777 13 14
AKT1 -0.027 0.12 -9999 0 -0.689 13 13
PTK2B 0.035 0.006 -9999 0 0 15 15
RAPGEF1 0.036 0.104 0.26 11 -0.386 16 27
RANBP10 0.036 0.004 -9999 0 0 6 6
PIK3CA 0.03 0.014 -9999 0 0 85 85
HGF/MET/SHIP2 0.041 0.038 -9999 0 -0.124 2 2
MAP3K5 0.039 0.107 0.27 5 -0.392 16 21
HGF/MET/CIN85/CBL/ENDOPHILINS 0.04 0.035 -9999 0 -9999 0 0
AP1 0.034 0.08 0.146 84 -0.144 46 130
mol:SU11274 0 0 -9999 0 -9999 0 0
SHC1 0.033 0.011 -9999 0 0 48 48
apoptosis -0.11 0.349 -9999 0 -0.781 99 99
STAT3 (dimer) 0.012 0.056 -9999 0 -0.214 17 17
GAB1/CRKL/SHP2/PI3K 0.053 0.121 0.27 2 -0.412 16 18
INPP5D 0 0 -9999 0 -9999 0 0
CBL/CRK 0.054 0.108 0.272 2 -0.397 16 18
PTPN11 0.036 0.005 -9999 0 0 9 9
GO:0007205 0 0 -9999 0 -9999 0 0
PLCG1 0.035 0.007 -9999 0 0 20 20
PTEN 0.026 0.016 -9999 0 0 130 130
ELK1 0.117 0.18 0.346 172 -9999 0 172
mol:SU5416 0 0 -9999 0 -9999 0 0
SHP2/GRB2/SOS1GAB1 0.011 0.032 0.142 1 -0.143 12 13
PAK1 -0.03 0.116 -9999 0 -0.661 13 13
HGF/MET/RANBP10 0.042 0.036 -9999 0 -9999 0 0
HRAS 0.012 0.079 -9999 0 -0.47 9 9
DOCK1 0.028 0.101 0.244 8 -0.399 15 23
GAB1 0.04 0.104 -9999 0 -0.426 15 15
CRK 0.038 0.106 0.269 2 -0.411 16 18
mol:PHA665752 0 0 -9999 0 -9999 0 0
mol:GDP 0.019 0.062 -9999 0 -0.409 8 8
JUN 0.033 0.01 -9999 0 0 39 39
EntrezGene:200958 0 0 -9999 0 -9999 0 0
HGF/MET 0.011 0.017 -9999 0 -9999 0 0
PIK3R1 0.032 0.012 -9999 0 0 61 61
cell morphogenesis 0.026 0.107 0.264 25 -0.329 12 37
GRB2/SHC 0.075 0.059 0.164 92 -0.123 1 93
FOS 0.025 0.017 -9999 0 0 147 147
GLMN 0.004 0.004 0.068 2 -9999 0 2
cell motility 0.116 0.179 0.344 172 -9999 0 172
HGF/MET/MUC20 0.028 0.024 -9999 0 -9999 0 0
cell migration 0.074 0.058 0.161 92 -0.121 1 93
GRB2 0.035 0.006 -9999 0 0 16 16
CBL 0.036 0.004 -9999 0 0 6 6
MET/RANBP10 0.033 0.026 -9999 0 -9999 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.013 0.044 -9999 0 -0.174 17 17
MET/MUC20 0.017 0.013 -9999 0 -9999 0 0
RAP1B 0.036 0.099 0.25 11 -0.364 16 27
RAP1A 0.031 0.1 0.252 12 -0.37 16 28
HGF/MET/RANBP9 0.039 0.041 -9999 0 -0.124 7 7
RAF1 0.031 0.096 -9999 0 -0.436 12 12
STAT3 0.012 0.056 -9999 0 -0.216 17 17
cell proliferation 0.036 0.075 0.226 15 -0.296 6 21
RPS6KB1 0.014 0.021 -9999 0 -0.26 1 1
MAPK3 0.086 0.166 0.388 30 -9999 0 30
MAPK1 0.122 0.214 0.521 63 -9999 0 63
RANBP9 0.035 0.006 -9999 0 0 15 15
MAPK8 -0.049 0.16 0.253 2 -0.334 72 74
SRC 0.01 0.045 -9999 0 -0.171 17 17
PI3K 0.057 0.069 0.164 74 -0.152 7 81
MET/Glomulin 0.017 0.024 -9999 0 -0.094 11 11
SOS1 0 0 -9999 0 -9999 0 0
MAP2K1 0.024 0.098 0.283 2 -0.417 13 15
MET 0.023 0.018 -9999 0 0 183 183
MAP4K1 0.048 0.106 0.277 3 -0.395 16 19
PTK2 0.034 0.008 -9999 0 0 28 28
MAP2K2 0.036 0.104 0.288 14 -0.404 11 25
BAD -0.032 0.116 -9999 0 -0.655 13 13
MAP2K4 0.033 0.102 0.27 7 -0.361 16 23
SHP2/GRB2/SOS1/GAB1 0.016 0.081 -9999 0 -0.342 17 17
INPPL1 0.035 0.006 -9999 0 0 12 12
PXN 0.036 0.004 -9999 0 0 5 5
SH3KBP1 0 0 -9999 0 -9999 0 0
HGS 0.002 0.017 0.074 17 -9999 0 17
PLCgamma1/PKC 0.025 0.013 -9999 0 -0.132 3 3
HGF 0.024 0.017 -9999 0 0 157 157
RASA1 0.034 0.009 -9999 0 0 30 30
NCK1 0.034 0.008 -9999 0 0 26 26
PTPRJ 0.036 0.005 -9999 0 0 8 8
NCK/PLCgamma1 0.079 0.053 0.161 95 -0.097 5 100
PDPK1 -0.021 0.126 -9999 0 -0.724 13 13
HGF/MET/SHIP 0.028 0.024 -9999 0 -9999 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.047 0.01 -9999 0 -9999 0 0
response to insulin stimulus 0 0 -9999 0 -9999 0 0
RIPK1 0.035 0.007 -9999 0 0 18 18
response to stress 0 0 -9999 0 -9999 0 0
MAP2K6 0.036 0.003 -9999 0 0 4 4
mol:GTP 0 0 -9999 0 -9999 0 0
MAP2K4 0.035 0.007 -9999 0 0 20 20
RAC1-CDC42/GTP/PAK family -0.002 0.051 -9999 0 -0.14 47 47
response to UV 0 0 -9999 0 -9999 0 0
YES1 0.033 0.01 -9999 0 0 37 37
interleukin-1 receptor activity 0 0 -9999 0 -9999 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -9999 0 0
MAP3K3 0.036 0.004 -9999 0 0 5 5
FYN 0.03 0.014 -9999 0 0 82 82
MAP3K12 0.036 0.005 -9999 0 0 9 9
FGR 0.032 0.011 -9999 0 0 52 52
p38 alpha/TAB1 0.014 0.108 0.183 2 -0.261 36 38
PRKG1 0.027 0.016 -9999 0 0 124 124
DUSP8 0.033 0.01 -9999 0 0 38 38
PGK/cGMP/p38 alpha 0.002 0.098 -9999 0 -0.252 36 36
apoptosis 0.013 0.103 0.175 2 -0.252 36 38
RAL/GTP 0.029 0.038 -9999 0 -0.12 20 20
LYN 0.031 0.013 -9999 0 0 72 72
DUSP1 0.031 0.013 -9999 0 0 75 75
PAK1 0.035 0.007 -9999 0 0 17 17
SRC 0.035 0.006 -9999 0 0 13 13
RAC1/OSM/MEKK3/MKK3 0.049 0.036 -9999 0 -0.11 6 6
TRAF6 0.036 0.005 -9999 0 0 8 8
RAC1 0.027 0.016 -9999 0 0 123 123
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 0 -9999 0 -9999 0 0
RAC1-CDC42/GTP 0.034 0.027 -9999 0 -0.115 6 6
MAPK11 -0.008 0.127 0.2 3 -0.317 44 47
BLK 0.035 0.007 -9999 0 0 17 17
HCK 0.027 0.016 -9999 0 0 123 123
MAP2K3 0.035 0.005 -9999 0 0 10 10
DUSP16 0 0 -9999 0 -9999 0 0
DUSP10 0.033 0.011 -9999 0 0 47 47
TRAF6/MEKK3 0.045 0.01 -9999 0 -0.102 1 1
MAP3K7IP1 0.034 0.009 -9999 0 0 33 33
MAPK14 0.005 0.107 0.178 5 -0.261 42 47
positive regulation of innate immune response -0.005 0.141 0.212 3 -0.34 47 50
LCK 0.035 0.007 -9999 0 0 17 17
p38alpha-beta/MKP7 -0.007 0.135 0.201 3 -0.326 47 50
p38alpha-beta/MKP5 0.008 0.139 0.231 2 -0.327 44 46
PGK/cGMP 0.02 0.012 -9999 0 -9999 0 0
PAK2 0.034 0.009 -9999 0 0 35 35
p38alpha-beta/MKP1 -0.001 0.144 0.231 2 -0.336 48 50
CDC42 0.035 0.008 -9999 0 0 22 22
RALB 0.035 0.006 -9999 0 0 15 15
RALA 0.026 0.017 -9999 0 0 143 143
PAK3 0.026 0.016 -9999 0 0 134 134
PDGFR-beta signaling pathway

Figure 75.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 77.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.03 0.112 0.331 11 -0.32 21 32
PDGFB-D/PDGFRB/SLAP 0.018 0.073 -9999 0 -0.156 67 67
PDGFB-D/PDGFRB/APS/CBL 0.044 0.024 -9999 0 -0.118 8 8
AKT1 -0.022 0.095 0.27 16 -0.237 15 31
mol:PI-4-5-P2 0 0.001 -9999 0 -9999 0 0
mol:Sphingosine-1-phosphate 0.021 0.106 0.311 9 -0.348 20 29
PIK3CA 0.03 0.014 -9999 0 0 85 85
FGR 0.004 0.096 0.269 2 -0.506 11 13
mol:Ca2+ 0.012 0.105 0.256 11 -0.38 20 31
MYC -0.003 0.256 0.387 24 -0.674 50 74
SHC1 0.033 0.011 -9999 0 0 48 48
HRAS/GDP 0.013 0.064 0.174 20 -0.17 16 36
LRP1/PDGFRB/PDGFB 0.047 0.056 -9999 0 -0.137 31 31
GRB10 0.022 0.018 -9999 0 0 185 185
PTPN11 0.036 0.005 -9999 0 0 9 9
GO:0007205 0.012 0.106 0.256 11 -0.385 20 31
PTEN 0.026 0.016 -9999 0 0 130 130
GRB2 0.035 0.006 -9999 0 0 16 16
GRB7 0.035 0.006 -9999 0 0 13 13
PDGFB-D/PDGFRB/SHP2 0.046 0.035 -9999 0 -0.144 14 14
PDGFB-D/PDGFRB/GRB10 0.021 0.054 -9999 0 -0.146 36 36
cell cycle arrest 0.018 0.073 -9999 0 -0.156 67 67
HRAS 0.034 0.009 -9999 0 0 32 32
HIF1A -0.027 0.088 0.237 18 -0.243 14 32
GAB1 0.009 0.125 0.292 10 -0.376 28 38
mol:GTP 0 0 -9999 0 -9999 0 0
DNM2 0.01 0.123 0.276 23 -0.318 31 54
PDGFB-D/PDGFRB 0.054 0.053 -9999 0 -0.135 14 14
mol:GDP 0 0 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.043 0.041 -9999 0 -0.145 20 20
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.025 0.118 0.305 4 -0.279 35 39
positive regulation of MAPKKK cascade 0.046 0.035 -9999 0 -0.144 14 14
PIK3R1 0.032 0.012 -9999 0 0 61 61
mol:IP3 0.012 0.107 0.257 11 -0.388 20 31
E5 -0.001 0.001 -9999 0 -9999 0 0
CSK 0.034 0.011 -9999 0 -0.01 25 25
PDGFB-D/PDGFRB/GRB7 0.049 0.024 -9999 0 -0.145 5 5
SHB 0.033 0.011 -9999 0 0 48 48
BLK 0.012 0.075 0.316 1 -0.453 6 7
PTPN2 0.033 0.015 -9999 0 -0.017 36 36
PDGFB-D/PDGFRB/SNX15 0.049 0.027 -9999 0 -0.141 8 8
BCAR1 0 0 -9999 0 -9999 0 0
VAV2 -0.005 0.156 0.293 14 -0.406 44 58
CBL 0.036 0.004 -9999 0 0 6 6
PDGFB-D/PDGFRB/DEP1 0.048 0.028 -9999 0 -0.143 8 8
LCK 0.014 0.063 0.255 3 -0.339 5 8
PDGFRB 0.031 0.021 0.062 1 -0.018 68 69
ACP1 0.034 0.008 -9999 0 0 28 28
HCK -0.043 0.182 -9999 0 -0.506 57 57
ABL1 0.004 0.115 0.271 10 -0.35 27 37
PDGFB-D/PDGFRB/CBL 0.008 0.134 0.293 7 -0.435 26 33
PTPN1 0.032 0.016 -9999 0 -0.013 46 46
SNX15 0.036 0.004 -9999 0 0 6 6
STAT3 0.033 0.01 -9999 0 0 37 37
STAT1 0.033 0.01 -9999 0 0 40 40
cell proliferation 0.005 0.235 0.368 27 -0.595 51 78
SLA 0.027 0.016 -9999 0 0 122 122
actin cytoskeleton reorganization -0.016 0.069 0.204 29 -0.194 7 36
SRC 0.017 0.049 0.308 1 -9999 0 1
PI3K -0.047 0.045 -9999 0 -0.166 38 38
PDGFB-D/PDGFRB/GRB7/SHC 0.06 0.037 -9999 0 -0.125 10 10
SH2B2 0 0 -9999 0 -9999 0 0
PLCgamma1/SPHK1 0.021 0.108 0.315 9 -0.359 20 29
LYN -0.034 0.16 0.221 2 -0.472 49 51
LRP1 0.031 0.013 -9999 0 0 68 68
SOS1 0 0 -9999 0 -9999 0 0
STAT5B 0.036 0.004 -9999 0 0 6 6
STAT5A 0.036 0.004 -9999 0 0 6 6
NCK1-2/p130 Cas 0.065 0.065 -9999 0 -0.138 25 25
SPHK1 0.033 0.011 0.059 2 0 47 49
EDG1 0.034 0.011 0.059 2 0 38 40
mol:DAG 0.012 0.107 0.257 11 -0.388 20 31
PLCG1 0.011 0.109 0.259 11 -0.398 20 31
NHERF/PDGFRB 0.062 0.037 -9999 0 -0.124 12 12
YES1 -0.009 0.131 0.233 3 -0.527 24 27
cell migration 0.061 0.037 -9999 0 -0.124 12 12
SHC/Grb2/SOS1 0.067 0.06 -9999 0 -0.135 18 18
SLC9A3R2 0.036 0.004 -9999 0 0 5 5
SLC9A3R1 0.034 0.009 -9999 0 0 34 34
NHERF1-2/PDGFRB/PTEN 0.059 0.054 -9999 0 -0.115 13 13
FYN -0.053 0.187 -9999 0 -0.452 75 75
DOK1 -0.018 0.05 0.173 21 -0.129 2 23
HRAS/GTP 0.021 0.029 -9999 0 -0.132 16 16
PDGFB 0.034 0.009 -9999 0 0 35 35
RAC1 0.017 0.188 0.33 29 -0.427 51 80
PRKCD -0.015 0.051 0.179 21 -0.133 2 23
FER -0.016 0.051 0.175 20 -0.133 3 23
MAPKKK cascade -0.011 0.064 0.161 44 -0.172 5 49
RASA1 -0.016 0.052 0.175 21 -0.17 6 27
NCK1 0.034 0.008 -9999 0 0 26 26
NCK2 0.035 0.007 -9999 0 0 19 19
p62DOK/Csk -0.013 0.059 0.18 22 -0.196 3 25
PDGFB-D/PDGFRB/SHB 0.045 0.028 -9999 0 -0.142 6 6
chemotaxis 0.004 0.113 0.261 11 -0.341 27 38
STAT1-3-5/STAT1-3-5 0.06 0.072 -9999 0 -0.14 30 30
Bovine Papilomavirus E5/PDGFRB 0.02 0.026 -9999 0 -0.139 8 8
PTPRJ 0.036 0.005 -9999 0 0 8 8
Signaling events mediated by PRL

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
CCNE1 0.032 0.012 -9999 0 0 61 61
mol:Halofuginone -0.002 0.03 -9999 0 -0.176 14 14
ITGA1 0 0 -9999 0 -9999 0 0
CDKN1A -0.033 0.155 -9999 0 -0.405 62 62
PRL-3/alpha Tubulin 0.018 0.031 -9999 0 -0.132 18 18
mol:Ca2+ -0.018 0.041 0.262 9 -9999 0 9
AGT 0.029 0.015 -9999 0 0 100 100
CCNA2 -0.034 0.107 -9999 0 -0.607 13 13
TUBA1B 0 0 -9999 0 -9999 0 0
EGR1 0.001 0.058 0.109 4 -0.326 14 18
CDK2/Cyclin E1 -0.008 0.149 -9999 0 -0.366 58 58
MAPK3 -0.019 0.008 -9999 0 -9999 0 0
PRL-2 /Rab GGTase beta 0.047 0.034 -9999 0 -0.161 11 11
MAPK1 -0.017 0.009 0 108 -9999 0 108
PTP4A1 -0.024 0.104 -9999 0 -0.63 13 13
PTP4A3 0.031 0.012 -9999 0 0 66 66
PTP4A2 0.035 0.006 -9999 0 0 16 16
ITGB1 -0.015 0.011 0 168 -9999 0 168
SRC 0.035 0.006 -9999 0 0 13 13
RAC1 -0.002 0.09 -9999 0 -0.392 21 21
Rab GGTase beta/Rab GGTase alpha 0.046 0.031 -9999 0 -0.142 10 10
PRL-1/ATF-5 -0.035 0.103 -9999 0 -0.555 14 14
RABGGTA 0.034 0.009 -9999 0 0 30 30
BCAR1 -0.01 0.052 0.252 18 -9999 0 18
RHOC -0.006 0.111 -9999 0 -0.39 31 31
RHOA -0.009 0.129 -9999 0 -0.449 31 31
cell motility -0.004 0.119 -9999 0 -0.412 27 27
PRL-1/alpha Tubulin -0.035 0.101 -9999 0 -0.574 14 14
PRL-3/alpha1 Integrin 0.018 0.031 -9999 0 -0.132 18 18
ROCK1 -0.004 0.119 -9999 0 -0.415 27 27
RABGGTB 0.035 0.007 -9999 0 0 19 19
CDK2 0.033 0.01 -9999 0 0 40 40
mitosis -0.023 0.103 -9999 0 -0.624 13 13
ATF5 0.033 0.01 -9999 0 0 38 38
ErbB4 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
ErbB4/ErbB4/HBEGF/HBEGF 0.021 0.128 -9999 0 -0.626 17 17
epithelial cell differentiation -0.006 0.138 -9999 0 -0.637 17 17
ITCH 0.03 0.031 0.108 1 -0.098 22 23
WWP1 -0.023 0.214 -9999 0 -1.133 17 17
FYN 0.03 0.014 -9999 0 0 82 82
EGFR 0.01 0.016 -9999 0 0 355 355
PRL 0.035 0.006 -9999 0 0 14 14
neuron projection morphogenesis -0.025 0.104 0.236 6 -0.468 18 24
PTPRZ1 0.022 0.018 -9999 0 0 184 184
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.053 0.118 -9999 0 -0.516 17 17
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.005 0.112 -9999 0 -0.567 17 17
ADAM17 0.03 0.03 -9999 0 -0.098 22 22
ErbB4/ErbB4 -0.002 0.132 -9999 0 -0.681 17 17
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.01 0.117 -9999 0 -0.619 17 17
NCOR1 0.034 0.008 -9999 0 0 25 25
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.017 0.117 -9999 0 -0.573 17 17
GRIN2B -0.008 0.11 0.229 2 -0.542 17 19
ErbB4/ErbB2/betacellulin 0.026 0.113 -9999 0 -0.546 17 17
STAT1 0.033 0.01 -9999 0 0 40 40
HBEGF 0.035 0.008 -9999 0 0 22 22
PRLR 0.036 0.004 -9999 0 0 7 7
E4ICDs/ETO2 0.021 0.128 -9999 0 -0.625 17 17
axon guidance -0.028 0.158 -9999 0 -0.793 17 17
NEDD4 0.028 0.031 0.108 1 -0.105 20 21
Prolactin receptor/Prolactin receptor/Prolactin 0.052 0.011 -9999 0 -9999 0 0
CBFA2T3 0.034 0.008 -9999 0 0 26 26
ErbB4/ErbB2/HBEGF 0.024 0.113 0.213 1 -0.546 17 18
MAPK3 -0.016 0.109 0.255 5 -0.493 17 22
STAT1 (dimer) 0.02 0.127 -9999 0 -0.623 17 17
MAPK1 -0.018 0.108 0.255 5 -0.477 18 23
JAK2 0.03 0.014 -9999 0 0 86 86
ErbB4/ErbB2/neuregulin 1 beta 0.004 0.108 0.206 1 -0.546 17 18
NRG1 -0.022 0.018 0.042 7 -0.083 17 24
NRG3 0 0 -9999 0 -9999 0 0
NRG2 0.036 0.005 -9999 0 0 9 9
NRG4 0 0 -9999 0 -9999 0 0
heart development -0.028 0.158 -9999 0 -0.793 17 17
neural crest cell migration 0.004 0.107 0.205 1 -0.539 17 18
ERBB2 -0.022 0.02 0.056 10 -0.083 17 27
WWOX/E4ICDs 0.011 0.111 -9999 0 -0.538 17 17
SHC1 0.033 0.011 -9999 0 0 48 48
ErbB4/EGFR/neuregulin 4 -0.012 0.095 -9999 0 -0.459 17 17
apoptosis -0.006 0.115 0.578 17 -9999 0 17
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.023 0.128 -9999 0 -0.626 17 17
ErbB4/ErbB2/epiregulin 0.024 0.113 -9999 0 -0.546 17 17
ErbB4/ErbB4/betacellulin/betacellulin 0.023 0.128 -9999 0 -0.626 17 17
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.059 0.126 -9999 0 -0.547 17 17
MDM2 0.01 0.138 0.263 37 -0.604 17 54
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.021 0.103 -9999 0 -0.504 17 17
STAT5A -0.033 0.152 -9999 0 -0.769 17 17
ErbB4/EGFR/neuregulin 1 beta -0.002 0.085 -9999 0 -0.416 17 17
DLG4 0.035 0.006 -9999 0 0 13 13
GRB2/SHC 0.043 0.035 -9999 0 -0.151 12 12
E4ICDs/TAB2/NCoR1 0.031 0.132 -9999 0 -0.62 17 17
STAT5A (dimer) 0.002 0.155 -9999 0 -0.703 17 17
MAP3K7IP2 0.033 0.01 -9999 0 0 42 42
STAT5B (dimer) -0.013 0.161 0.281 1 -0.769 17 18
LRIG1 0.03 0.014 -9999 0 0 81 81
EREG 0.035 0.007 -9999 0 0 21 21
BTC 0.036 0.005 -9999 0 0 8 8
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.029 0.159 -9999 0 -0.804 17 17
ERBB4 -0.002 0.133 -9999 0 -0.684 17 17
STAT5B 0.036 0.004 -9999 0 0 6 6
YAP1 -0.081 0.205 -9999 0 -0.511 85 85
GRB2 0.035 0.006 -9999 0 0 16 16
ErbB4/ErbB2/neuregulin 4 0.002 0.106 -9999 0 -0.539 17 17
glial cell differentiation -0.031 0.131 0.613 17 -9999 0 17
WWOX 0.024 0.017 -9999 0 0 160 160
cell proliferation -0.011 0.112 -9999 0 -0.567 17 17
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.028 0.069 0.183 28 -0.227 9 37
FYN -0.009 0.097 0.211 10 -0.294 28 38
LAT/GRAP2/SLP76 0.021 0.07 0.214 5 -0.26 11 16
IKBKB 0.036 0.004 -9999 0 0 6 6
AKT1 0.005 0.084 0.204 15 -0.241 20 35
B2M 0.036 0.008 -9999 0 0 19 19
IKBKG -0.003 0.034 0.094 13 -0.109 5 18
MAP3K8 0.023 0.018 -9999 0 0 182 182
mol:Ca2+ -0.011 0.009 -9999 0 -0.04 4 4
integrin-mediated signaling pathway 0.024 0.007 -9999 0 -0.107 1 1
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.009 0.099 0.236 15 -0.275 23 38
TRPV6 0.315 0.564 1.281 123 -9999 0 123
CD28 0.037 0.001 -9999 0 -9999 0 0
SHC1 0.018 0.07 0.193 29 -0.273 7 36
receptor internalization 0.02 0.054 0.173 9 -0.26 6 15
PRF1 -0.127 0.3 -9999 0 -0.606 130 130
KRAS 0.033 0.01 -9999 0 0 37 37
GRB2 0.035 0.006 -9999 0 0 16 16
COT/AKT1 0.006 0.064 0.194 5 -0.211 17 22
LAT 0.011 0.065 0.192 13 -0.279 8 21
EntrezGene:6955 0.001 0.004 0.014 40 -9999 0 40
CD3D 0.034 0.011 -9999 0 -9999 0 0
CD3E 0.037 0.006 -9999 0 0 6 6
CD3G 0.037 0.007 -9999 0 -9999 0 0
RASGRP2 0.007 0.019 0.074 2 -0.148 4 6
RASGRP1 -0.024 0.127 0.214 28 -0.245 90 118
HLA-A 0.036 0.009 -9999 0 -9999 0 0
RASSF5 0 0 -9999 0 -9999 0 0
RAP1A/GTP/RAPL 0.024 0.007 -9999 0 -0.107 1 1
mol:GTP 0 0 -9999 0 -9999 0 0
mol:GDP 0.009 0.054 0.126 43 -0.097 20 63
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.006 0.036 -9999 0 -0.12 25 25
PRKCA -0.001 0.056 0.163 23 -0.167 6 29
GRAP2 0.034 0.009 -9999 0 0 33 33
mol:IP3 0.005 0.054 -9999 0 -0.215 10 10
EntrezGene:6957 0.001 0.004 0.014 40 -9999 0 40
TCR/CD3/MHC I/CD8 0.019 0.044 0.148 12 -0.162 5 17
ORAI1 -0.273 0.478 0.378 4 -1.089 123 127
CSK 0.012 0.064 0.191 12 -0.279 8 20
B7 family/CD28 0.06 0.091 0.253 19 -0.272 8 27
CHUK 0.026 0.016 -9999 0 0 133 133
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.016 0.066 0.191 9 -0.284 9 18
PTPN6 0.01 0.071 0.215 15 -0.288 9 24
VAV1 0.021 0.076 0.197 37 -0.284 7 44
Monovalent TCR/CD3 0.022 0.017 0.11 1 -9999 0 1
CBL 0.036 0.004 -9999 0 0 6 6
LCK 0.007 0.082 0.211 14 -0.257 16 30
PAG1 0.014 0.064 0.196 11 -0.275 8 19
RAP1A 0.036 0.005 -9999 0 0 8 8
TCR/CD3/MHC I/CD8/LCK 0.016 0.069 0.197 12 -0.276 10 22
CD80 0.036 0.006 -9999 0 0 12 12
CD86 0.032 0.012 -9999 0 0 59 59
PDK1/CARD11/BCL10/MALT1 0.001 0.046 -9999 0 -0.144 22 22
HRAS 0.034 0.009 -9999 0 0 32 32
GO:0035030 0.012 0.068 0.182 24 -0.212 12 36
CD8A 0.001 0.004 0.014 40 -9999 0 40
CD8B 0.001 0.004 0.015 40 -9999 0 40
PTPRC 0.029 0.015 -9999 0 0 103 103
PDK1/PKC theta 0.007 0.09 0.22 24 -0.279 12 36
CSK/PAG1 0.01 0.063 0.197 9 -0.269 8 17
SOS1 0 0 -9999 0 -9999 0 0
peptide-MHC class I 0.049 0.033 -9999 0 -0.146 11 11
GRAP2/SLP76 0.03 0.078 0.234 4 -0.278 12 16
STIM1 -0.047 0.158 1.24 5 -9999 0 5
RAS family/GTP 0.004 0.071 0.149 24 -0.16 35 59
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.02 0.053 0.164 8 -0.27 6 14
mol:DAG -0.019 0.036 -9999 0 -0.193 10 10
RAP1A/GDP 0.008 0.028 0.068 32 -0.05 17 49
PLCG1 0.035 0.007 -9999 0 0 20 20
CD247 0.001 0.004 0.014 40 -9999 0 40
cytotoxic T cell degranulation -0.122 0.292 -9999 0 -0.584 132 132
RAP1A/GTP 0.004 0.007 -9999 0 -0.055 4 4
mol:PI-3-4-5-P3 0.011 0.09 0.22 17 -0.243 22 39
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.015 0.068 0.172 1 -0.253 10 11
NRAS 0.032 0.012 -9999 0 0 58 58
ZAP70 0.036 0.003 -9999 0 0 3 3
GRB2/SOS1 0.024 0.019 -9999 0 -0.132 7 7
LAT/GRAP2/SLP76/VAV1 0.014 0.068 0.188 9 -0.257 9 18
MALT1 0.034 0.009 -9999 0 0 29 29
TRAF6 0.036 0.005 -9999 0 0 8 8
CD8 heterodimer 0.003 0.008 0.027 41 -9999 0 41
CARD11 0 0 -9999 0 -9999 0 0
PRKCB -0.016 0.027 -9999 0 -0.138 11 11
PRKCE -0.001 0.056 0.165 22 -0.167 6 28
PRKCQ 0.009 0.094 0.225 25 -0.294 13 38
LCP2 0.031 0.013 -9999 0 0 71 71
BCL10 0.035 0.006 -9999 0 0 15 15
regulation of survival gene product expression 0.006 0.077 0.195 15 -0.218 18 33
IKK complex 0.001 0.038 0.122 16 -0.093 2 18
RAS family/GDP -0.004 0.015 -9999 0 -0.038 41 41
MAP3K14 0.008 0.063 0.17 24 -0.17 17 41
PDPK1 0.006 0.079 0.202 16 -0.226 17 33
TCR/CD3/MHC I/CD8/Fyn 0.01 0.062 -9999 0 -0.271 10 10
IL4-mediated signaling events

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
BCL2L1 -0.051 0.379 0.751 2 -0.991 24 26
STAT6 (cleaved dimer) -0.066 0.345 -9999 0 -0.897 32 32
IGHG1 -0.009 0.248 0.424 20 -0.763 20 40
IGHG3 -0.06 0.356 0.623 1 -0.878 33 34
AKT1 -0.022 0.272 0.504 5 -0.701 31 36
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.018 0.19 0.453 5 -0.559 7 12
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.006 0.26 0.508 3 -0.718 20 23
THY1 -0.124 0.502 0.774 2 -1.18 63 65
MYB 0.032 0.011 -9999 0 0 50 50
HMGA1 0.035 0.006 -9999 0 0 12 12
IL4/IL4R/JAK1/IL2R gamma/JAK3 0.002 0.255 0.518 11 -0.561 20 31
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.004 0.251 0.506 2 -0.77 15 17
SP1 0.029 0.075 0.116 92 -0.14 66 158
INPP5D 0 0 -9999 0 -9999 0 0
SOCS5 0.008 0.044 -9999 0 -9999 0 0
STAT6 (dimer)/ETS1 -0.046 0.362 -9999 0 -0.92 29 29
SOCS1 -0.033 0.294 0.511 3 -0.656 30 33
SOCS3 -0.002 0.22 -9999 0 -0.6 5 5
FCER2 -0.024 0.319 0.646 1 -0.758 15 16
PARP14 0.001 0.001 -9999 0 -9999 0 0
CCL17 -0.059 0.376 0.711 1 -1.002 23 24
GRB2 0.035 0.006 -9999 0 0 16 16
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP 0.006 0.215 0.456 7 -0.565 17 24
T cell proliferation -0.064 0.369 0.655 1 -0.937 32 33
IL4R/JAK1 -0.064 0.379 0.656 1 -0.983 27 28
EGR2 -0.109 0.491 0.714 1 -1.227 52 53
JAK2 0.02 0.064 0.15 17 -9999 0 17
JAK3 0.032 0.019 -9999 0 -0.036 17 17
PIK3R1 0.032 0.012 -9999 0 0 61 61
JAK1 0.027 0.039 0.107 7 -9999 0 7
COL1A2 -0.106 0.469 0.523 2 -1.162 70 72
CCL26 -0.057 0.377 0.671 2 -0.909 33 35
IL4R -0.053 0.403 0.79 3 -1.049 24 27
PTPN6 0.015 0.036 -9999 0 -0.055 10 10
IL13RA2 -0.312 0.654 0.748 3 -1.109 172 175
IL13RA1 0.024 0.066 0.152 16 -9999 0 16
IRF4 0.043 0.118 -9999 0 -0.564 1 1
ARG1 0.007 0.209 0.514 2 -0.811 8 10
CBL -0.007 0.237 0.475 6 -0.539 20 26
GTF3A 0.048 0.034 0.12 69 -0.147 3 72
PIK3CA 0.03 0.014 -9999 0 0 85 85
IL13RA1/JAK2 0.024 0.1 0.228 10 -0.158 20 30
IRF4/BCL6 0.037 0.116 -9999 0 -0.459 1 1
CD40LG 0.041 0.004 0.134 1 -9999 0 1
MAPK14 -0.004 0.237 0.483 5 -0.556 15 20
mitosis -0.018 0.261 0.501 5 -0.656 31 36
STAT6 -0.061 0.422 0.806 4 -1.012 33 37
SPI1 0.037 0.013 -9999 0 -9999 0 0
RPS6KB1 -0.021 0.253 0.477 5 -0.644 30 35
STAT6 (dimer) -0.061 0.422 0.806 4 -1.009 33 37
STAT6 (dimer)/PARP14 -0.078 0.371 -9999 0 -0.952 33 33
mast cell activation -0.002 0.016 -9999 0 -0.04 20 20
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 0.008 0.213 0.476 4 -0.532 8 12
FRAP1 -0.022 0.271 0.504 5 -0.695 31 36
LTA -0.059 0.376 0.711 1 -1.002 23 24
FES 0.035 0.006 -9999 0 0 14 14
T-helper 1 cell differentiation 0.059 0.418 0.993 33 -0.783 5 38
CCL11 -0.061 0.356 -9999 0 -0.957 24 24
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES 0.012 0.215 0.494 5 -0.55 6 11
IL2RG 0.032 0.018 -9999 0 -0.035 18 18
IL10 -0.054 0.379 0.704 3 -1.002 23 26
IRS1 0.032 0.011 -9999 0 0 51 51
IRS2 0.029 0.014 -9999 0 0 93 93
IL4 0.026 0.175 0.561 1 -0.874 5 6
IL5 -0.059 0.376 0.711 1 -1.002 23 24
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.052 0.378 0.652 11 -0.868 36 47
COL1A1 0.02 0.259 0.597 5 -0.942 9 14
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -9999 0 0
IL4/IL4R/JAK1 -0.068 0.378 -9999 0 -1.041 23 23
IL2R gamma/JAK3 0.051 0.021 -9999 0 -9999 0 0
TFF3 -0.054 0.375 0.711 1 -0.99 23 24
ALOX15 -0.059 0.376 0.711 1 -1.012 22 23
MYBL1 0.029 0.014 -9999 0 0 92 92
T-helper 2 cell differentiation -0.041 0.335 0.627 4 -0.761 32 36
SHC1 0.033 0.011 -9999 0 0 48 48
CEBPB 0.035 0.014 -9999 0 -9999 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.014 0.258 0.523 4 -0.753 19 23
mol:PI-3-4-5-P3 -0.021 0.272 0.507 5 -0.695 31 36
PI3K -0.026 0.283 0.51 5 -0.743 31 36
DOK2 0 0 -9999 0 -9999 0 0
ETS1 0.004 0.046 -9999 0 -0.086 9 9
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 0.007 0.212 0.436 8 -0.544 21 29
ITGB3 -0.059 0.377 0.711 1 -0.999 23 24
PIGR -0.054 0.379 0.707 2 -1.002 23 25
IGHE -0.008 0.077 0.172 32 -0.183 14 46
MAPKKK cascade 0.009 0.21 0.426 10 -0.534 21 31
BCL6 0.03 0.013 -9999 0 0 72 72
OPRM1 -0.058 0.376 0.711 1 -0.998 23 24
RETNLB -0.057 0.377 0.671 2 -0.909 33 35
SELP -0.055 0.379 0.771 2 -1.002 23 25
AICDA -0.058 0.355 -9999 0 -0.939 24 24
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.035 0.007 -9999 0 0 20 20
HDAC3 0.036 0.005 -9999 0 0 8 8
VDR 0.035 0.007 -9999 0 0 17 17
Cbp/p300/PCAF 0.041 0.026 -9999 0 -0.115 9 9
EP300 0.033 0.011 -9999 0 0 49 49
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.001 0.055 -9999 0 -0.219 11 11
KAT2B 0 0 -9999 0 -9999 0 0
MAPK14 0.036 0.004 -9999 0 0 6 6
AKT1 0.007 0.079 0.2 5 -0.218 10 15
RAR alpha/9cRA/Cyclin H -0.026 0.126 -9999 0 -0.287 41 41
mol:9cRA 0 0 -9999 0 -9999 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.005 0.059 -9999 0 -0.206 24 24
CDC2 0.02 0.02 -9999 0 -0.002 214 214
response to UV -0.001 0.007 0.02 1 -0.026 33 34
RAR alpha/Jnk1 0.018 0.033 -9999 0 -9999 0 0
NCOR2 0.036 0.003 -9999 0 0 4 4
VDR/VDR/Vit D3 0.026 0.005 -9999 0 -9999 0 0
RXRs/RARs/NRIP1/9cRA -0.034 0.155 -9999 0 -0.529 35 35
NCOA2 0.036 0.005 -9999 0 0 9 9
NCOA3 0.035 0.008 -9999 0 0 22 22
NCOA1 0.033 0.01 -9999 0 0 43 43
VDR/VDR/DNA 0.035 0.007 -9999 0 0 17 17
RARG 0.032 0.017 -9999 0 -0.024 41 41
RAR gamma1/9cRA 0.045 0.013 -9999 0 -9999 0 0
MAPK3 0.031 0.018 -9999 0 -0.035 33 33
MAPK1 0.033 0.011 -9999 0 0 48 48
MAPK8 0.023 0.022 -9999 0 -0.006 155 155
mol:Vit D3 0 0 -9999 0 -9999 0 0
RXRs/VDR/DNA/Vit D3 -0.028 0.125 -9999 0 -0.338 45 45
RARA 0.005 0.038 -9999 0 -0.202 11 11
negative regulation of phosphoinositide 3-kinase cascade 0 0 -9999 0 -9999 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.003 0.044 -9999 0 -0.177 12 12
PRKCA 0.03 0.028 0.078 3 -0.071 33 36
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.036 0.171 -9999 0 -0.575 38 38
RXRG 0.016 0.029 -9999 0 -9999 0 0
RXRA -0.017 0.084 -9999 0 -0.279 28 28
RXRB 0.016 0.027 -9999 0 -9999 0 0
VDR/Vit D3/DNA 0.026 0.005 -9999 0 -9999 0 0
RBP1 0.026 0.016 -9999 0 0 132 132
CRBP1/9-cic-RA -0.004 0.06 -9999 0 -0.132 88 88
RARB 0.031 0.022 0.074 1 -0.046 33 34
PRKCG 0.028 0.029 0.076 4 -0.071 33 37
MNAT1 0.034 0.009 -9999 0 0 35 35
RAR alpha/RXRs -0.02 0.13 0.267 2 -0.402 30 32
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.01 0.096 -9999 0 -0.301 28 28
proteasomal ubiquitin-dependent protein catabolic process -0.01 0.061 -9999 0 -0.182 25 25
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.036 0.171 -9999 0 -0.599 35 35
positive regulation of DNA binding -0.03 0.115 -9999 0 -0.27 42 42
NRIP1 -0.059 0.278 -9999 0 -1.055 33 33
RXRs/RARs -0.017 0.125 -9999 0 -0.401 37 37
RXRs/RXRs/DNA/9cRA -0.04 0.118 -9999 0 -0.338 47 47
PRKACA 0.034 0.009 -9999 0 0 29 29
CDK7 0.035 0.008 -9999 0 0 22 22
TFIIH 0.059 0.051 -9999 0 -0.169 18 18
RAR alpha/9cRA 0.019 0.09 -9999 0 -0.182 26 26
CCNH 0.035 0.006 -9999 0 0 16 16
CREBBP 0.036 0.004 -9999 0 0 5 5
RAR gamma2/9cRA 0.055 0.05 -9999 0 -0.156 16 16
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.035 0.005 -9999 0 0 11 11
Caspase 8 (4 units) -0.004 0.093 -9999 0 -0.23 22 22
NEF 0.002 0 -9999 0 -9999 0 0
NFKBIA 0.039 0.019 0.078 62 -9999 0 62
BIRC3 -0.024 0.031 0.177 4 -0.199 2 6
CYCS -0.004 0.081 0.178 46 -0.228 13 59
RIPK1 0.035 0.007 -9999 0 0 18 18
CD247 0.002 0 -9999 0 -9999 0 0
MAP2K7 -0.01 0.102 -9999 0 -0.373 9 9
protein ubiquitination 0.011 0.067 0.212 2 -0.229 8 10
CRADD 0.035 0.006 -9999 0 0 12 12
DAXX 0.036 0.004 -9999 0 0 7 7
FAS 0.021 0.018 -9999 0 0 207 207
BID -0.001 0.053 0.123 1 -0.162 37 38
NF-kappa-B/RelA/I kappa B alpha 0.074 0.053 -9999 0 -0.137 15 15
TRADD 0.036 0.004 -9999 0 0 7 7
MAP3K5 0.03 0.014 -9999 0 0 81 81
CFLAR 0.036 0.005 -9999 0 0 9 9
FADD 0.035 0.006 -9999 0 0 13 13
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.074 0.053 -9999 0 -0.137 15 15
MAPK8 -0.007 0.093 -9999 0 -0.353 9 9
APAF1 0.036 0.003 -9999 0 0 4 4
TRAF1 0.034 0.008 -9999 0 0 24 24
TRAF2 0.035 0.006 -9999 0 0 14 14
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.004 0.058 -9999 0 -0.161 43 43
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.027 0.076 -9999 0 -0.255 12 12
CHUK 0.012 0.069 0.217 2 -0.253 7 9
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.043 0.081 -9999 0 -0.121 54 54
TCRz/NEF 0.007 0.001 -9999 0 -9999 0 0
TNF 0.036 0.004 -9999 0 0 6 6
FASLG 0.018 0.003 -9999 0 -9999 0 0
NFKB1 0.041 0.016 0.078 69 -9999 0 69
TNFR1A/BAG4/TNF-alpha 0.053 0.055 -9999 0 -0.123 39 39
CASP6 0.009 0.106 -9999 0 -0.564 6 6
CASP7 -0.029 0.143 0.275 10 -0.308 38 48
RELA 0.042 0.016 0.079 71 -9999 0 71
CASP2 0.026 0.016 -9999 0 0 130 130
CASP3 0.002 0.114 0.255 14 -0.309 19 33
TNFRSF1A 0.032 0.012 -9999 0 0 61 61
TNFR1A/BAG4 0.034 0.054 -9999 0 -0.142 40 40
CASP8 0.035 0.006 -9999 0 0 13 13
CASP9 0.034 0.009 -9999 0 0 31 31
MAP3K14 0.022 0.079 0.198 3 -0.252 12 15
APAF-1/Caspase 9 0.001 0.086 0.169 7 -0.206 21 28
BCL2 -0.015 0.092 0.271 2 -0.333 9 11
Caspase cascade in apoptosis

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
TOP1 -0.008 0.087 -9999 0 -0.275 30 30
ACTA1 -0.032 0.086 -9999 0 -0.3 25 25
NUMA1 -0.002 0.084 -9999 0 -0.315 19 19
SPTAN1 -0.041 0.087 0.211 4 -0.297 28 32
LIMK1 0.009 0.107 0.191 65 -0.357 12 77
BIRC3 0.031 0.013 -9999 0 0 77 77
BIRC2 0.036 0.005 -9999 0 0 11 11
BAX 0.033 0.011 -9999 0 0 46 46
CASP10 -0.008 0.032 0.083 47 -9999 0 47
CRMA 0 0 -9999 0 -9999 0 0
XIAP 0 0 -9999 0 -9999 0 0
PTK2 -0.009 0.088 -9999 0 -0.28 31 31
DIABLO 0.036 0.004 -9999 0 0 5 5
apoptotic nuclear changes -0.041 0.086 0.21 4 -0.293 28 32
response to UV 0 0 -9999 0 -9999 0 0
CRADD 0.035 0.006 -9999 0 0 12 12
GSN -0.032 0.092 0.207 5 -0.317 24 29
MADD 0.035 0.006 -9999 0 0 13 13
TFAP2A 0.041 0.071 -9999 0 -0.541 6 6
BID -0.002 0.04 -9999 0 -0.186 18 18
MAP3K1 -0.001 0.048 -9999 0 -0.382 4 4
TRADD 0.036 0.004 -9999 0 0 7 7
mol:Ca2+ 0 0 -9999 0 -9999 0 0
APAF-1/Pro-Caspase 9 0.049 0.018 -9999 0 -0.141 2 2
mol:Activated DNA 0 0 -9999 0 -9999 0 0
ARHGDIB -0.038 0.094 0.196 12 -0.304 29 41
CASP9 0.034 0.009 -9999 0 0 31 31
DNA repair 0.03 0.066 0.233 21 -9999 0 21
neuron apoptosis 0.016 0.111 -9999 0 -0.608 14 14
mol:NAD 0 0 -9999 0 -9999 0 0
DNA fragmentation during apoptosis -0.022 0.086 -9999 0 -0.323 23 23
APAF1 0.036 0.003 -9999 0 0 4 4
CASP6 0.021 0.117 -9999 0 -0.864 6 6
TRAF2 0.035 0.006 -9999 0 0 14 14
ICAD/CAD -0.043 0.082 0.294 2 -0.303 24 26
CASP7 -0.072 0.105 -9999 0 -0.231 125 125
KRT18 0.024 0.052 -9999 0 -0.468 4 4
apoptosis -0.033 0.091 -9999 0 -0.348 19 19
DFFA -0.04 0.082 0.195 1 -0.304 25 26
DFFB -0.039 0.081 0.195 1 -0.313 23 24
PARP1 -0.03 0.067 -9999 0 -0.235 21 21
actin filament polymerization -0.014 0.103 0.333 12 -0.18 66 78
TNF 0.036 0.004 -9999 0 0 6 6
CYCS 0.01 0.039 0.135 6 -0.239 3 9
SATB1 0.014 0.108 -9999 0 -0.753 6 6
SLK -0.025 0.08 -9999 0 -0.296 25 25
p15 BID/BAX -0.001 0.069 0.152 2 -0.178 47 49
CASP2 0.046 0.096 0.215 92 -0.239 8 100
JNK cascade 0.001 0.047 0.379 4 -9999 0 4
CASP3 -0.036 0.086 -9999 0 -0.314 25 25
LMNB2 0.051 0.088 0.22 17 -0.271 8 25
RIPK1 0.035 0.007 -9999 0 0 18 18
CASP4 0.03 0.014 -9999 0 0 86 86
Mammalian IAPs/DIABLO 0.056 0.035 -9999 0 -0.153 6 6
negative regulation of DNA binding 0.041 0.071 -9999 0 -0.535 6 6
stress fiber formation -0.034 0.08 -9999 0 -0.292 25 25
GZMB -0.013 0.011 0 194 -9999 0 194
CASP1 -0.01 0.066 -9999 0 -0.2 51 51
LMNB1 0.033 0.125 0.229 13 -0.302 32 45
APP 0.016 0.112 -9999 0 -0.616 14 14
TNFRSF1A 0.032 0.012 -9999 0 0 61 61
response to stress 0 0 -9999 0 -9999 0 0
CASP8 -0.011 0.002 0 13 -9999 0 13
VIM -0.032 0.094 -9999 0 -0.344 22 22
LMNA 0.056 0.088 0.234 11 -0.344 5 16
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.017 0.057 -9999 0 -0.217 13 13
LRDD 0.035 0.007 -9999 0 0 18 18
SREBF1 -0.038 0.083 0.184 1 -0.309 24 25
APAF-1/Caspase 9 0.012 0.102 -9999 0 -0.609 12 12
nuclear fragmentation during apoptosis -0.002 0.083 -9999 0 -0.31 19 19
CFL2 0.014 0.104 0.181 65 -0.341 12 77
GAS2 -0.03 0.086 0.23 1 -0.302 24 25
positive regulation of apoptosis 0.051 0.1 0.224 21 -0.348 8 29
PRF1 0.023 0.017 -9999 0 0 174 174
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.05 0.022 -9999 0 -0.142 5 5
Necdin/E2F1 -0.016 0.084 -9999 0 -0.142 142 142
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.071 0.047 -9999 0 -0.123 22 22
NGF (dimer)/p75(NTR)/BEX1 0.01 0.063 -9999 0 -0.115 93 93
NT-4/5 (dimer)/p75(NTR) 0.023 0.009 -9999 0 -9999 0 0
IKBKB 0.036 0.004 -9999 0 0 6 6
AKT1 -0.011 0.083 0.191 36 -0.198 22 58
IKBKG 0.036 0 -9999 0 -9999 0 0
BDNF 0.032 0.012 -9999 0 0 61 61
MGDIs/NGR/p75(NTR)/LINGO1 0.021 0.008 -9999 0 -9999 0 0
FURIN 0.036 0.005 -9999 0 0 9 9
proBDNF (dimer)/p75(NTR)/Sortilin 0.055 0.034 -9999 0 -0.124 2 2
LINGO1 0 0 -9999 0 -9999 0 0
Sortilin/TRAF6/NRIF 0.021 0.068 -9999 0 -0.159 45 45
proBDNF (dimer) 0.032 0.012 -9999 0 0 61 61
NTRK1 0.035 0.006 -9999 0 0 12 12
RTN4R 0 0 -9999 0 -9999 0 0
neuron apoptosis -0.005 0.122 -9999 0 -0.347 39 39
IRAK1 0.035 0.006 -9999 0 0 16 16
SHC1 -0.003 0.035 0.091 58 -9999 0 58
ARHGDIA 0.035 0.007 -9999 0 0 19 19
RhoA/GTP 0.024 0.019 -9999 0 -0.132 7 7
Gamma Secretase 0.076 0.072 -9999 0 -0.151 29 29
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.041 0.056 -9999 0 -0.11 47 47
MAGEH1 0.032 0.012 -9999 0 0 63 63
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.002 0.073 -9999 0 -0.11 131 131
Mammalian IAPs/DIABLO 0.056 0.035 -9999 0 -0.152 6 6
proNGF (dimer) 0 0 -9999 0 -9999 0 0
MAGED1 0.034 0.008 -9999 0 0 26 26
APP 0.035 0.007 -9999 0 0 19 19
NT-4/5 (dimer) 0 0 -9999 0 -9999 0 0
ZNF274 0.031 0.013 -9999 0 0 69 69
RhoA/GDP/RHOGDI 0.05 0.03 0.174 1 -0.102 6 7
NGF 0 0 -9999 0 -9999 0 0
cell cycle arrest 0.005 0.053 0.194 8 -9999 0 8
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.016 0.056 -9999 0 -0.175 32 32
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.041 0.019 -9999 0 -0.115 1 1
NCSTN 0.034 0.008 -9999 0 0 28 28
mol:GTP 0.031 0.041 -9999 0 -0.115 29 29
PSENEN 0.034 0.009 -9999 0 0 33 33
mol:ceramide -0.006 0.043 0.099 63 -9999 0 63
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.013 0.052 -9999 0 -0.272 9 9
p75(NTR)/beta APP 0.042 0.032 -9999 0 -0.142 9 9
BEX1 0.028 0.015 -9999 0 0 111 111
mol:GDP -0.008 0.003 -9999 0 -9999 0 0
NGF (dimer) 0.046 0.033 -9999 0 -9999 0 0
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.039 0.017 -9999 0 -9999 0 0
PIK3R1 0.032 0.012 -9999 0 0 61 61
RAC1/GTP 0.026 0.024 -9999 0 -0.095 6 6
MYD88 0.034 0.009 -9999 0 0 31 31
CHUK 0.026 0.016 -9999 0 0 133 133
NGF (dimer)/p75(NTR)/PKA 0.031 0.041 -9999 0 -0.115 29 29
RHOB 0.031 0.013 -9999 0 0 72 72
RHOA 0.035 0.007 -9999 0 0 21 21
MAGE-G1/E2F1 0.026 0.005 -9999 0 -9999 0 0
NT3 (dimer) 0.034 0.008 -9999 0 0 23 23
TP53 -0.007 0.074 0.204 24 -0.205 6 30
PRDM4 -0.006 0.045 0.099 69 -9999 0 69
BDNF (dimer) 0.076 0.033 -9999 0 -9999 0 0
PIK3CA 0.03 0.014 -9999 0 0 85 85
SORT1 0.035 0.005 -9999 0 0 11 11
activation of caspase activity 0.064 0.045 -9999 0 -0.122 22 22
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.057 0.03 -9999 0 -0.11 4 4
RHOC 0.035 0.006 -9999 0 0 16 16
XIAP 0 0 -9999 0 -9999 0 0
MAPK10 0.012 0.109 0.233 34 -0.315 17 51
DIABLO 0.036 0.004 -9999 0 0 5 5
SMPD2 -0.006 0.043 0.1 63 -9999 0 63
APH1B 0.035 0.006 -9999 0 0 14 14
APH1A 0.035 0.006 -9999 0 0 16 16
proNGF (dimer)/p75(NTR)/Sortilin 0.041 0.021 -9999 0 -0.115 3 3
PSEN1 0.033 0.01 -9999 0 0 41 41
APAF-1/Pro-Caspase 9 0.049 0.018 -9999 0 -0.142 2 2
NT3 (dimer)/p75(NTR) 0.044 0.021 -9999 0 -9999 0 0
MAPK8 -0.003 0.078 0.217 16 -0.262 8 24
MAPK9 0.023 0.096 0.232 37 -0.267 11 48
APAF1 0.036 0.003 -9999 0 0 4 4
NTF3 0.035 0.008 -9999 0 0 23 23
NTF4 0 0 -9999 0 -9999 0 0
NDN 0.018 0.018 -9999 0 0 247 247
RAC1/GDP 0.018 0.02 -9999 0 -0.132 6 6
RhoA-B-C/GDP 0.046 0.073 -9999 0 -0.146 52 52
p75 CTF/Sortilin/TRAF6/NRIF 0.07 0.057 -9999 0 -0.12 29 29
RhoA-B-C/GTP 0.03 0.041 -9999 0 -0.115 29 29
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.079 0.06 -9999 0 -0.12 23 23
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.083 0.027 -9999 0 -0.117 2 2
PRKACB 0.033 0.011 -9999 0 0 45 45
proBDNF (dimer)/p75 ECD 0.046 0.019 -9999 0 -9999 0 0
ChemicalAbstracts:86-01-1 0 0 -9999 0 -9999 0 0
BIRC3 0.03 0.013 -9999 0 0 77 77
BIRC2 0.035 0.005 -9999 0 0 11 11
neuron projection morphogenesis -0.013 0.069 0.131 29 -0.163 24 53
BAD 0.007 0.098 0.233 25 -0.287 15 40
RIPK2 0.035 0.005 -9999 0 0 11 11
NGFR 0.031 0.013 -9999 0 0 67 67
CYCS -0.011 0.044 0.176 5 -0.187 3 8
ADAM17 0.035 0.006 -9999 0 0 12 12
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.057 0.029 -9999 0 -0.11 3 3
BCL2L11 0.007 0.097 0.234 24 -0.292 14 38
BDNF (dimer)/p75(NTR) 0.041 0.023 -9999 0 -9999 0 0
PI3K 0.025 0.068 -9999 0 -0.121 71 71
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.039 0.02 -9999 0 -0.102 3 3
NDNL2 0 0 -9999 0 -9999 0 0
YWHAE 0.034 0.009 -9999 0 0 29 29
PRKCI 0.034 0.008 -9999 0 0 25 25
NGF (dimer)/p75(NTR) 0.023 0.009 -9999 0 -9999 0 0
ChemicalAbstracts:146-91-8 0 0 -9999 0 -9999 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.049 0.047 -9999 0 -0.116 26 26
TRAF6 0.036 0.005 -9999 0 0 8 8
RAC1 0.027 0.016 -9999 0 0 123 123
PRKCZ 0 0 -9999 0 -9999 0 0
PLG 0.034 0.009 -9999 0 0 34 34
oligodendrocyte cell fate commitment 0 0 -9999 0 -9999 0 0
CASP6 0.032 0.034 0.141 15 -0.148 2 17
SQSTM1 0.034 0.009 -9999 0 0 33 33
NGFRAP1 0.035 0.006 -9999 0 0 13 13
CASP3 0.007 0.095 0.225 25 -0.279 16 41
E2F1 0.035 0.006 -9999 0 0 16 16
CASP9 0.034 0.009 -9999 0 0 31 31
IKK complex 0.041 0.066 -9999 0 -0.255 8 8
NGF (dimer)/TRKA 0.026 0.004 -9999 0 -9999 0 0
MMP7 0.026 0.016 -9999 0 0 131 131
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.064 0.052 -9999 0 -0.112 28 28
MMP3 0.035 0.007 -9999 0 0 21 21
APAF-1/Caspase 9 -0.025 0.04 -9999 0 -0.202 6 6
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.009 0.092 -9999 0 -0.392 23 23
Crk/p130 Cas/Paxillin -0.052 0.089 -9999 0 -0.193 103 103
JUN -0.015 0.05 -9999 0 -0.238 13 13
HRAS 0.034 0.009 -9999 0 0 32 32
RET51/GFRalpha1/GDNF/GRB10 0.037 0.06 -9999 0 -0.114 30 30
RAP1A 0.036 0.005 -9999 0 0 8 8
FRS2 0.035 0.008 -9999 0 0 22 22
RAP1A/GDP 0.026 0.008 -9999 0 -0.132 1 1
RET51/GFRalpha1/GDNF/DOK1 0.061 0.046 -9999 0 -9999 0 0
EntrezGene:5979 0 0 -9999 0 -9999 0 0
PTPN11 0.036 0.005 -9999 0 0 9 9
mol:GTP 0 0 -9999 0 -9999 0 0
CRK 0.035 0.008 -9999 0 0 23 23
RET9/GFRalpha1/GDNF/Enigma 0.048 0.032 -9999 0 -9999 0 0
RHOA 0.035 0.007 -9999 0 0 21 21
RAP1A/GTP 0.054 0.048 -9999 0 -0.111 1 1
GRB7 0.035 0.006 -9999 0 0 13 13
RET51/GFRalpha1/GDNF 0.059 0.047 -9999 0 -9999 0 0
MAPKKK cascade -0.005 0.072 -9999 0 -0.171 12 12
BCAR1 0 0 -9999 0 -9999 0 0
RET9/GFRalpha1/GDNF/IRS1 0.038 0.046 -9999 0 -0.106 23 23
lamellipodium assembly -0.027 0.085 -9999 0 -0.189 67 67
RET51/GFRalpha1/GDNF/SHC 0.056 0.05 -9999 0 -0.117 7 7
PIK3CA 0.03 0.014 -9999 0 0 85 85
RET9/GFRalpha1/GDNF/SHC 0.041 0.038 -9999 0 -0.11 7 7
RET9/GFRalpha1/GDNF/Shank3 0.032 0.022 -9999 0 -9999 0 0
MAPK3 -0.022 0.046 0.185 17 -9999 0 17
DOK1 0.036 0.002 -9999 0 0 2 2
DOK6 0 0 -9999 0 -9999 0 0
PXN 0.036 0.004 -9999 0 0 5 5
neurite development -0.019 0.048 0.234 4 -0.208 10 14
DOK5 0.03 0.014 -9999 0 0 85 85
GFRA1 0.025 0.017 -9999 0 0 147 147
MAPK8 0.001 0.047 -9999 0 -0.17 23 23
HRAS/GTP 0.021 0.091 -9999 0 -0.175 9 9
tube development 0.027 0.03 0.204 5 -0.1 7 12
MAPK1 -0.02 0.045 0.186 16 -9999 0 16
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.01 0.061 -9999 0 -0.215 11 11
Rac1/GDP 0.018 0.02 -9999 0 -0.132 6 6
SRC 0.035 0.006 -9999 0 0 13 13
PDLIM7 0.036 0.004 -9999 0 0 7 7
RET51/GFRalpha1/GDNF/Dok6 0.056 0.043 -9999 0 -9999 0 0
SHC1 0.033 0.011 -9999 0 0 48 48
RET51/GFRalpha1/GDNF/Dok4 0.061 0.046 -9999 0 -9999 0 0
RET51/GFRalpha1/GDNF/Dok5 0.038 0.071 -9999 0 -0.113 60 60
PRKCA 0.036 0.004 -9999 0 0 5 5
HRAS/GDP 0.021 0.029 -9999 0 -0.132 16 16
CREB1 -0.028 0.094 -9999 0 -0.189 105 105
PIK3R1 0.032 0.012 -9999 0 0 61 61
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.008 0.06 -9999 0 -0.165 21 21
RET51/GFRalpha1/GDNF/Grb7 0.06 0.046 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
RET 0.027 0.016 -9999 0 0 127 127
DOK4 0.036 0.005 -9999 0 0 9 9
JNK cascade -0.016 0.05 -9999 0 -0.227 15 15
RET9/GFRalpha1/GDNF/FRS2 0.047 0.033 -9999 0 -9999 0 0
SHANK3 0 0 -9999 0 -9999 0 0
RASA1 0.034 0.009 -9999 0 0 30 30
NCK1 0.034 0.008 -9999 0 0 26 26
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.012 0.056 -9999 0 -0.162 14 14
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.024 0.09 -9999 0 -0.188 99 99
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.03 0.095 -9999 0 -0.188 113 113
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.008 0.045 -9999 0 -0.164 14 14
PI3K -0.045 0.128 0.196 3 -0.255 94 97
SOS1 0 0 -9999 0 -9999 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.039 0.038 -9999 0 -0.101 7 7
GRB10 0.022 0.018 -9999 0 0 185 185
activation of MAPKK activity 0.013 0.045 -9999 0 -0.254 10 10
RET51/GFRalpha1/GDNF/FRS2 0.059 0.047 -9999 0 -9999 0 0
GAB1 0.031 0.013 -9999 0 0 75 75
IRS1 0.032 0.011 -9999 0 0 51 51
IRS2 0.029 0.014 -9999 0 0 93 93
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.01 0.048 -9999 0 -0.158 19 19
RET51/GFRalpha1/GDNF/PKC alpha 0.06 0.046 -9999 0 -9999 0 0
GRB2 0.035 0.006 -9999 0 0 16 16
PRKACA 0.034 0.009 -9999 0 0 29 29
GDNF 0.036 0.004 -9999 0 0 6 6
RAC1 0.027 0.016 -9999 0 0 123 123
RET51/GFRalpha1/GDNF/IRS1 0.052 0.057 -9999 0 -0.11 22 22
Rac1/GTP -0.027 0.102 0.19 1 -0.224 62 63
RET9/GFRalpha1/GDNF 0.034 0.023 -9999 0 -9999 0 0
GFRalpha1/GDNF 0.037 0.025 -9999 0 -9999 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.016 0.005 0 46 -9999 0 46
SNTA1 0.032 0.012 -9999 0 0 57 57
response to hypoxia 0 0 -9999 0 -9999 0 0
STMN1 -0.013 0.034 0.083 52 -9999 0 52
MAPK12 -0.01 0.032 0.204 4 -0.166 10 14
CCND1 -0.022 0.106 -9999 0 -0.371 40 40
p38 gamma/SNTA1 -0.008 0.041 0.197 4 -0.162 10 14
MAP2K3 0.035 0.005 -9999 0 0 10 10
PKN1 0.032 0.012 -9999 0 0 58 58
G2/M transition checkpoint -0.01 0.032 0.204 4 -0.165 10 14
MAP2K6 -0.007 0.028 0.104 1 -0.176 11 12
MAPT -0.024 0.077 0.161 3 -0.198 72 75
MAPK13 -0.02 0.007 0 46 -9999 0 46
hyperosmotic response 0 0 -9999 0 -9999 0 0
ZAK 0.009 0.032 -9999 0 -0.2 11 11
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.007 0.071 -9999 0 -0.288 22 22
KLHL20 0.041 0.092 0.198 61 -0.194 21 82
CYFIP2 0.031 0.013 -9999 0 0 73 73
Rac1/GDP 0.008 0.063 0.195 2 -0.247 14 16
ENAH 0.007 0.074 -9999 0 -0.309 20 20
AP1M1 0 0 -9999 0 -9999 0 0
RAP1B 0 0 0 57 0 10 67
RAP1A 0.036 0.005 -9999 0 0 8 8
CTNNB1 0.035 0.007 -9999 0 0 21 21
CDC42/GTP -0.024 0.05 0.119 11 -0.207 16 27
ABI1/Sra1/Nap1 -0.016 0.036 -9999 0 -0.135 31 31
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.081 0.038 -9999 0 -0.131 6 6
RAPGEF1 -0.005 0.073 -9999 0 -0.275 21 21
CTNND1 0.034 0.009 -9999 0 0 30 30
regulation of calcium-dependent cell-cell adhesion 0.019 0.076 -9999 0 -0.289 23 23
CRK 0.002 0.075 0.197 1 -0.29 21 22
E-cadherin/gamma catenin/alpha catenin 0.061 0.035 -9999 0 -0.124 8 8
alphaE/beta7 Integrin 0.049 0.024 -9999 0 -0.142 6 6
IQGAP1 0.033 0.01 -9999 0 0 43 43
NCKAP1 0.036 0.002 -9999 0 0 1 1
Rap1/GTP/I-afadin 0.042 0.015 -9999 0 -0.101 1 1
DLG1 0.006 0.075 -9999 0 -0.293 23 23
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -9999 0 0
mol:PI-3-4-5-P3 -0.032 0.043 -9999 0 -0.175 28 28
MLLT4 0.034 0.009 -9999 0 0 35 35
ARF6/GTP/NME1/Tiam1 0.036 0.033 -9999 0 -0.102 23 23
PI3K -0.039 0.056 -9999 0 -0.225 28 28
ARF6 0.035 0.007 -9999 0 0 21 21
mol:Ca2+ 0 0 0.001 67 0 26 93
E-cadherin/gamma catenin 0.047 0.018 -9999 0 -9999 0 0
TIAM1 0.033 0.01 -9999 0 0 43 43
E-cadherin(dimer)/Ca2+ 0.07 0.051 -9999 0 -0.141 20 20
AKT1 -0.017 0.057 0.131 15 -0.17 25 40
PIK3R1 0.032 0.012 -9999 0 0 61 61
CDH1 0.034 0.01 -9999 0 0 37 37
RhoA/GDP 0.012 0.071 0.237 3 -0.233 17 20
actin cytoskeleton organization 0.034 0.073 0.163 62 -0.143 21 83
CDC42/GDP 0.011 0.067 0.195 2 -0.228 16 18
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.012 0.048 -9999 0 -0.202 19 19
ITGB7 0.035 0.005 -9999 0 0 10 10
RAC1 0.027 0.016 -9999 0 0 123 123
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.075 0.055 -9999 0 -0.15 20 20
E-cadherin/Ca2+/beta catenin/alpha catenin 0.053 0.032 -9999 0 -0.111 9 9
mol:GDP -0.005 0.072 0.218 4 -0.261 16 20
CDC42/GTP/IQGAP1 0.035 0.042 -9999 0 -0.115 32 32
JUP 0.032 0.011 -9999 0 0 50 50
p120 catenin/RhoA/GDP 0.025 0.077 0.249 3 -0.238 17 20
RAC1/GTP/IQGAP1 0.026 0.044 -9999 0 -0.117 32 32
PIP5K1C/AP1M1 0.018 0.031 -9999 0 -0.132 19 19
RHOA 0.035 0.007 -9999 0 0 21 21
CDC42 0.035 0.008 -9999 0 0 22 22
CTNNA1 0.035 0.007 -9999 0 0 18 18
positive regulation of S phase of mitotic cell cycle 0.01 0.046 0.112 9 -0.122 31 40
NME1 0 0 -9999 0 0 30 30
clathrin coat assembly 0 0 -9999 0 -9999 0 0
TJP1 0.008 0.073 -9999 0 -0.297 21 21
regulation of cell-cell adhesion -0.026 0.039 -9999 0 -0.166 22 22
WASF2 -0.009 0.02 -9999 0 -0.074 31 31
Rap1/GTP -0.022 0.058 0.151 16 -0.249 13 29
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.089 0.05 -9999 0 -0.129 12 12
CCND1 0.012 0.054 0.132 8 -0.149 31 39
VAV2 0.016 0.116 -9999 0 -0.561 11 11
RAP1/GDP -0.008 0.064 0.17 17 -0.253 12 29
adherens junction assembly 0.008 0.071 -9999 0 -0.289 21 21
homophilic cell adhesion 0 0 -9999 0 -9999 0 0
ABI1 0.027 0.016 -9999 0 0 126 126
PIP5K1C 0.032 0.012 -9999 0 0 58 58
regulation of heterotypic cell-cell adhesion 0.062 0.046 0.198 2 -0.136 12 14
E-cadherin/beta catenin 0.008 0.019 -9999 0 -0.096 6 6
mol:GTP 0 0 0.001 60 0 30 90
SRC 0.006 0.072 -9999 0 -0.287 23 23
PIK3CA 0.03 0.014 -9999 0 0 85 85
Rac1/GTP -0.009 0.077 0.177 2 -0.301 21 23
E-cadherin/beta catenin/alpha catenin 0.061 0.037 -9999 0 -0.134 9 9
ITGAE 0.035 0.007 -9999 0 0 19 19
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.019 0.077 -9999 0 -0.294 23 23
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 0.032 0.116 0.283 26 -0.36 20 46
CRKL 0.028 0.107 0.253 14 -0.374 20 34
HRAS 0.036 0.101 0.265 8 -0.323 20 28
mol:PIP3 0.036 0.152 0.308 29 -0.372 33 62
SPRED1 0 0 -9999 0 -9999 0 0
SPRED2 0.036 0.004 -9999 0 0 7 7
GAB1 0.025 0.101 0.234 9 -0.386 20 29
FOXO3 0.037 0.164 0.298 25 -0.376 40 65
AKT1 0.037 0.174 0.312 24 -0.404 40 64
BAD 0.032 0.167 0.307 24 -0.385 40 64
megakaryocyte differentiation 0.026 0.099 0.23 10 -0.389 18 28
GSK3B 0.03 0.17 0.306 23 -0.399 41 64
RAF1 0.024 0.09 0.25 12 -0.275 20 32
SHC1 0.033 0.011 -9999 0 0 48 48
STAT3 0.019 0.1 0.239 4 -0.396 20 24
STAT1 0.011 0.192 -9999 0 -0.866 19 19
HRAS/SPRED1 0.026 0.087 0.221 7 -0.266 21 28
cell proliferation 0.011 0.093 0.253 3 -0.382 20 23
PIK3CA 0.03 0.014 -9999 0 0 85 85
TEC 0.036 0.004 -9999 0 0 6 6
RPS6KB1 0.049 0.117 0.267 13 -0.376 18 31
HRAS/SPRED2 0.046 0.098 0.258 10 -0.275 20 30
LYN/TEC/p62DOK 0.065 0.119 0.276 2 -0.396 20 22
MAPK3 0.024 0.088 0.256 21 -0.217 17 38
STAP1 0.026 0.099 0.231 3 -0.386 20 23
GRAP2 0.034 0.009 -9999 0 0 33 33
JAK2 0.013 0.169 -9999 0 -0.738 19 19
STAT1 (dimer) 0.019 0.192 -9999 0 -0.847 19 19
mol:Gleevec -0.003 0.006 -9999 0 -0.022 2 2
GRB2/SOCS1/VAV1 0.072 0.112 0.289 2 -0.382 20 22
actin filament polymerization 0.028 0.099 0.244 4 -0.378 20 24
LYN 0.031 0.013 -9999 0 0 72 72
STAP1/STAT5A (dimer) 0.026 0.132 0.281 1 -0.537 19 20
PIK3R1 0.032 0.012 -9999 0 0 61 61
CBL/CRKL/GRB2 0.066 0.113 0.322 10 -0.363 19 29
PI3K 0.054 0.129 0.303 9 -0.384 19 28
PTEN 0.026 0.016 -9999 0 0 130 130
SCF/KIT/EPO/EPOR 0.027 0.218 -9999 0 -0.988 19 19
MAPK8 0.01 0.094 0.254 3 -0.389 20 23
STAT3 (dimer) 0.02 0.099 0.238 4 -0.388 20 24
positive regulation of transcription 0.024 0.078 0.236 22 -0.18 16 38
mol:GDP 0.042 0.096 0.258 2 -0.336 19 21
PIK3C2B 0.019 0.099 0.264 5 -0.384 20 25
CBL/CRKL 0.054 0.112 0.309 11 -0.367 19 30
FER 0.024 0.102 0.255 5 -0.392 20 25
SH2B3 0.026 0.099 0.231 3 -0.386 20 23
PDPK1 0.031 0.14 0.296 27 -0.334 34 61
SNAI2 0.029 0.104 0.239 9 -0.393 19 28
positive regulation of cell proliferation 0.03 0.163 0.349 2 -0.665 19 21
KITLG 0.039 0.02 -9999 0 -0.05 18 18
cell motility 0.03 0.163 0.349 2 -0.665 19 21
PTPN6 0.022 0.025 -9999 0 -0.032 70 70
EPOR 0.048 0.08 -9999 0 -9999 0 0
STAT5A (dimer) 0.034 0.139 0.313 3 -0.544 19 22
SOCS1 0.036 0.004 -9999 0 0 7 7
cell migration -0.023 0.098 0.372 20 -0.296 4 24
SOS1 0 0 -9999 0 -9999 0 0
EPO 0.027 0.021 -9999 0 -0.035 13 13
VAV1 0.033 0.01 -9999 0 0 38 38
GRB10 0.016 0.086 0.239 4 -0.352 17 21
PTPN11 0.027 0.021 -9999 0 -0.032 53 53
SCF/KIT 0.03 0.105 0.245 3 -0.404 20 23
GO:0007205 -0.002 0.007 0.021 17 -0.02 4 21
MAP2K1 0.018 0.081 0.225 14 -0.224 22 36
CBL 0.036 0.004 -9999 0 0 6 6
KIT 0.013 0.236 -9999 0 -1.093 19 19
MAP2K2 0.023 0.091 0.297 20 -0.228 18 38
SHC/Grb2/SOS1 0.055 0.103 0.271 2 -0.357 20 22
STAT5A 0.034 0.141 0.315 3 -0.559 19 22
GRB2 0.035 0.006 -9999 0 0 16 16
response to radiation 0.029 0.103 0.238 9 -0.385 19 28
SHC/GRAP2 0.043 0.029 -9999 0 -0.142 7 7
PTPRO 0.025 0.099 0.227 9 -0.396 18 27
SH2B2 0.026 0.099 0.231 3 -0.386 20 23
DOK1 0.036 0.002 -9999 0 0 2 2
MATK 0.02 0.097 0.24 2 -0.379 20 22
CREBBP 0.052 0.043 0.142 1 -0.118 19 20
BCL2 0.042 0.125 -9999 0 -0.837 5 5
Alternative NF-kappaB pathway

Figure 88.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 90.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.038 0.027 -9999 0 -0.142 2 2
FBXW11 0.035 0.007 -9999 0 0 20 20
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.035 0.007 -9999 0 0 20 20
CHUK 0.026 0.016 -9999 0 0 133 133
NF kappa B2 p100/RelB 0.067 0.061 -9999 0 -0.116 11 11
NFKB1 0.035 0.007 -9999 0 0 17 17
MAP3K14 0.035 0.006 -9999 0 0 12 12
NF kappa B1 p50/RelB 0.047 0.025 -9999 0 -0.142 5 5
RELB 0.034 0.009 -9999 0 0 33 33
NFKB2 0.027 0.016 -9999 0 0 127 127
NF kappa B2 p52/RelB 0.035 0.022 -9999 0 -9999 0 0
regulation of B cell activation 0.034 0.022 -9999 0 -9999 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.032 0.011 -9999 0 0 53 53
SMAD2 -0.017 0.068 0.167 2 -0.254 17 19
SMAD3 0.011 0.064 -9999 0 -0.344 6 6
SMAD3/SMAD4 -0.004 0.164 -9999 0 -0.487 41 41
SMAD4/Ubc9/PIASy 0.053 0.051 -9999 0 -0.124 30 30
SMAD2/SMAD2/SMAD4 0.024 0.105 -9999 0 -0.253 25 25
PPM1A 0.034 0.008 -9999 0 0 25 25
CALM1 0.033 0.011 -9999 0 0 49 49
SMAD2/SMAD4 0 0.07 -9999 0 -0.206 27 27
MAP3K1 0.035 0.007 -9999 0 0 18 18
TRAP-1/SMAD4 0.037 0.051 -9999 0 -0.142 34 34
MAPK3 0.036 0.003 -9999 0 0 4 4
MAPK1 0.033 0.011 -9999 0 0 48 48
NUP214 0.035 0.008 -9999 0 0 23 23
CTDSP1 0.035 0.006 -9999 0 0 14 14
CTDSP2 0.03 0.013 -9999 0 0 77 77
CTDSPL 0.034 0.009 -9999 0 0 29 29
KPNB1 0.035 0.008 -9999 0 0 23 23
TGFBRAP1 0.035 0.005 -9999 0 0 10 10
UBE2I 0.036 0.003 -9999 0 0 3 3
NUP153 0.034 0.008 -9999 0 0 28 28
KPNA2 0.034 0.009 -9999 0 0 34 34
PIAS4 0.034 0.009 -9999 0 0 32 32
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.041 0.01 -9999 0 -9999 0 0
RGS9BP 0 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
GRK1 0 0 -9999 0 -9999 0 0
mol:Na + 0.01 0.06 -9999 0 -0.115 83 83
mol:ADP 0 0 -9999 0 -9999 0 0
GNAT2 0.036 0.004 -9999 0 0 6 6
RGS9-1/Gbeta5/R9AP 0.045 0.014 -9999 0 -0.115 1 1
mol:GDP 0 0 -9999 0 -9999 0 0
PDE6H/GNAT2/GTP 0.046 0.011 -9999 0 -9999 0 0
GRK7 0 0 -9999 0 -9999 0 0
CNGB3 0.036 0.004 -9999 0 0 7 7
Cone Metarhodopsin II/X-Arrestin 0.027 0 -9999 0 -9999 0 0
mol:Ca2+ -0.013 0.056 0.093 73 -0.11 68 141
Cone PDE6 0.055 0.046 -9999 0 -0.109 1 1
Cone Metarhodopsin II 0 0 -9999 0 -9999 0 0
Na + (4 Units) 0.016 0.064 -9999 0 -0.107 82 82
GNAT2/GDP 0.058 0.02 -9999 0 -0.102 1 1
GNB5 0.035 0.007 -9999 0 0 18 18
mol:GMP (4 units) -0.011 0.034 0.183 13 -9999 0 13
Cone Transducin 0.044 0.01 -9999 0 -9999 0 0
SLC24A2 0.029 0.014 -9999 0 0 92 92
GNB3/GNGT2 0.026 0.005 -9999 0 -9999 0 0
GNB3 0.035 0.007 -9999 0 0 20 20
GNAT2/GTP 0.026 0.003 -9999 0 -9999 0 0
CNGA3 0.022 0.018 -9999 0 0 187 187
ARR3 0.036 0 -9999 0 -9999 0 0
absorption of light 0 0 -9999 0 -9999 0 0
cGMP/Cone CNG Channel 0.01 0.06 -9999 0 -0.115 83 83
mol:Pi 0.045 0.014 -9999 0 -0.115 1 1
Cone CNG Channel 0.028 0.074 -9999 0 -0.109 78 78
mol:all-trans-retinal 0 0 -9999 0 -9999 0 0
mol:K + 0.029 0.014 -9999 0 0 92 92
RGS9 0.035 0.006 -9999 0 0 15 15
PDE6C 0.027 0.016 -9999 0 0 127 127
GNGT2 0 0 -9999 0 -9999 0 0
mol:cGMP (4 units) 0 0 -9999 0 -9999 0 0
PDE6H 0.035 0.007 -9999 0 0 20 20
a4b1 and a4b7 Integrin signaling

Figure 91.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 93.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.027 0.016 -9999 0 0 118 118
ITGB7 0.035 0.005 -9999 0 0 10 10
ITGA4 0.035 0.006 -9999 0 0 12 12
alpha4/beta7 Integrin 0.052 0.011 -9999 0 -9999 0 0
alpha4/beta1 Integrin 0.04 0.024 -9999 0 -9999 0 0
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 0.033 0.011 -9999 0 0 49 49
HDAC4 0.034 0.008 -9999 0 0 24 24
induction of apoptosis 0 0 -9999 0 -9999 0 0
regulation of S phase of mitotic cell cycle -0.001 0.037 -9999 0 -0.124 38 38
CDKN1A -0.037 0.117 -9999 0 -0.457 34 34
KAT2B 0 0 -9999 0 -9999 0 0
BAX 0.033 0.011 -9999 0 0 46 46
FOXO3 0.001 0.036 0.255 8 -9999 0 8
FOXO1 0 0 -9999 0 -9999 0 0
FOXO4 0.005 0.026 -9999 0 -0.181 9 9
response to UV 0 0 -9999 0 -9999 0 0
XRCC6 0.033 0.01 -9999 0 0 37 37
TAT 0.035 0.005 -9999 0 0 11 11
mol:Lysophosphatidic acid 0 0 -9999 0 -9999 0 0
MYOD1 -0.011 0.001 -9999 0 -9999 0 0
PPARGC1A 0.031 0.013 -9999 0 0 75 75
FHL2 0.027 0.016 -9999 0 0 118 118
response to nutrient levels 0 0 -9999 0 -9999 0 0
KU70/SIRT1 0.041 0.044 0.163 27 -0.172 4 31
HIST2H4A 0.001 0.037 0.124 38 -9999 0 38
SIRT1/FOXO3a 0.028 0.043 0.151 41 -0.181 1 42
SIRT1 0.033 0.046 0.177 38 -9999 0 38
response to hypoxia 0 0 -9999 0 -9999 0 0
SIRT1/MEF2D/HDAC4 0.049 0.053 0.172 23 -0.127 14 37
SIRT1/Histone H1b 0.027 0.047 0.16 3 -0.165 7 10
apoptosis -0.05 0.048 0.126 6 -0.17 24 30
SIRT1/PGC1A 0.031 0.042 0.144 25 -0.115 13 38
p53/SIRT1 0.038 0.083 0.339 26 -0.149 19 45
SIRT1/FOXO4 0.024 0.046 0.145 27 -0.138 16 43
FOXO1/FHL2/SIRT1 0.024 0.042 0.137 21 -0.102 20 41
HIST1H1E 0.012 0.026 -9999 0 -0.177 8 8
SIRT1/p300 0.038 0.049 0.16 30 -0.152 11 41
muscle cell differentiation 0.004 0.037 0.118 4 -0.112 38 42
TP53 0.039 0.045 0.183 39 -9999 0 39
KU70/SIRT1/BAX 0.05 0.049 0.172 24 -0.126 6 30
CREBBP 0.036 0.004 -9999 0 0 5 5
MEF2D 0.035 0.006 -9999 0 0 13 13
HIV-1 Tat/SIRT1 0.042 0.043 0.16 30 -0.145 4 34
ACSS2 0.001 0.037 0.124 38 -9999 0 38
SIRT1/PCAF/MYOD -0.004 0.037 0.113 38 -0.118 4 42
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.034 0.009 -9999 0 0 30 30
NFATC1 0.001 0.105 0.218 2 -0.411 21 23
NFATC2 -0.034 0.081 0.116 1 -0.166 100 101
NFATC3 0.009 0.018 -9999 0 -0.101 12 12
YWHAE 0.034 0.009 -9999 0 0 29 29
Calcineurin A alpha-beta B1/CABIN1 -0.007 0.081 0.163 5 -0.207 42 47
Exportin 1/Ran/NUP214 0.066 0.031 -9999 0 -0.154 6 6
mol:DAG 0 0 -9999 0 -9999 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.021 0.093 -9999 0 -0.211 26 26
BCL2/BAX 0.046 0.023 -9999 0 -0.142 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 0.021 0.025 -9999 0 -0.131 12 12
CaM/Ca2+ 0.021 0.025 -9999 0 -0.131 12 12
BAX 0.033 0.011 -9999 0 0 46 46
MAPK14 0.036 0.004 -9999 0 0 6 6
BAD 0.035 0.006 -9999 0 0 16 16
CABIN1/MEF2D 0.007 0.086 0.185 1 -0.201 40 41
Calcineurin A alpha-beta B1/BCL2 0.035 0.007 -9999 0 0 17 17
FKBP8 0.033 0.01 -9999 0 0 37 37
activation-induced cell death of T cells -0.007 0.085 0.199 40 -0.184 1 41
KPNB1 0.035 0.008 -9999 0 0 23 23
KPNA2 0.034 0.009 -9999 0 0 34 34
XPO1 0.036 0.004 -9999 0 0 5 5
SFN 0.031 0.013 -9999 0 0 74 74
MAP3K8 0.023 0.018 -9999 0 0 182 182
NFAT4/CK1 alpha 0.025 0.042 0.17 1 -0.163 15 16
MEF2D/NFAT1/Cbp/p300 0.008 0.108 0.226 1 -0.208 38 39
CABIN1 -0.006 0.081 0.163 5 -0.209 41 46
CALM1 0.033 0.011 -9999 0 0 49 49
RAN 0.035 0.006 -9999 0 0 13 13
MAP3K1 0.035 0.007 -9999 0 0 18 18
CAMK4 0.036 0.004 -9999 0 0 7 7
mol:Ca2+ 0 0.001 -9999 0 -9999 0 0
MAPK3 0.036 0.003 -9999 0 0 4 4
YWHAH 0.031 0.013 -9999 0 0 74 74
Calcineurin A alpha-beta B1/AKAP79/PKA 0.048 0.017 -9999 0 -9999 0 0
YWHAB 0.035 0.007 -9999 0 0 21 21
MAPK8 0.026 0.016 -9999 0 0 133 133
MAPK9 0.035 0.006 -9999 0 0 12 12
YWHAG 0 0 -9999 0 -9999 0 0
FKBP1A 0.033 0.011 -9999 0 0 46 46
NFAT1-c-4/YWHAQ 0 0.107 0.205 2 -0.365 21 23
PRKCH 0.033 0.01 -9999 0 0 38 38
CABIN1/Cbp/p300 0.046 0.03 -9999 0 -0.142 9 9
CASP3 0.034 0.009 -9999 0 0 30 30
PIM1 0.035 0.005 -9999 0 0 10 10
Calcineurin A alpha-beta B1/FKBP12/FK506 0.02 0.02 -9999 0 -0.107 11 11
apoptosis 0.018 0.036 -9999 0 -0.167 12 12
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.096 -9999 0 -0.326 24 24
PRKCB 0 0 -9999 0 -9999 0 0
PRKCE 0.036 0.004 -9999 0 0 7 7
JNK2/NFAT4 0.027 0.034 -9999 0 -0.117 17 17
BAD/BCL-XL 0.047 0.026 -9999 0 -0.142 6 6
PRKCD 0.034 0.01 -9999 0 0 36 36
NUP214 0.035 0.008 -9999 0 0 23 23
PRKCZ 0 0 -9999 0 -9999 0 0
PRKCA 0.036 0.004 -9999 0 0 5 5
PRKCG 0.033 0.01 -9999 0 0 38 38
PRKCQ 0.025 0.017 -9999 0 0 146 146
FKBP38/BCL2 0.048 0.017 -9999 0 -9999 0 0
EP300 0.033 0.011 -9999 0 0 49 49
PRKCB1 0.03 0.013 -9999 0 0 80 80
CSNK2A1 0.034 0.009 -9999 0 0 31 31
NFATc/JNK1 0.009 0.103 -9999 0 -0.391 21 21
CaM/Ca2+/FKBP38 0.038 0.03 -9999 0 -0.115 12 12
FKBP12/FK506 0.021 0.024 -9999 0 -0.132 11 11
CSNK1A1 -0.015 0.021 0.087 12 -0.115 8 20
CaM/Ca2+/CAMK IV 0.041 0.028 -9999 0 -0.115 12 12
NFATc/ERK1 0.019 0.106 -9999 0 -0.392 21 21
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.021 0.094 -9999 0 -0.212 28 28
NR4A1 -0.025 0.079 0.164 8 -0.197 33 41
GSK3B 0.034 0.009 -9999 0 0 35 35
positive T cell selection 0.01 0.019 -9999 0 -0.101 12 12
NFAT1/CK1 alpha -0.02 0.069 0.093 1 -0.172 45 46
RCH1/ KPNB1 0.035 0.057 -9999 0 -0.15 41 41
YWHAQ 0.036 0.005 -9999 0 0 8 8
PRKACA 0.034 0.009 -9999 0 0 29 29
AKAP5 0.034 0.008 -9999 0 0 24 24
MEF2D 0.035 0.006 -9999 0 0 13 13
mol:FK506 0 0 -9999 0 -9999 0 0
YWHAZ 0.035 0.007 -9999 0 0 17 17
NFATc/p38 alpha 0.02 0.107 0.251 1 -0.391 21 22
CREBBP 0.036 0.004 -9999 0 0 5 5
BCL2 0.035 0.007 -9999 0 0 17 17
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.032 0.049 -9999 0 -0.109 23 23
TC10/GTP 0.029 0.046 -9999 0 -0.116 19 19
Insulin Receptor/Insulin/IRS1/Shp2 0.072 0.058 -9999 0 -0.127 28 28
HRAS 0.034 0.009 -9999 0 0 32 32
APS homodimer 0 0 -9999 0 -9999 0 0
GRB14 0.031 0.013 -9999 0 0 67 67
FOXO3 -0.009 0.016 0.02 3 -0.054 32 35
AKT1 -0.019 0.091 0.224 17 -0.209 23 40
INSR 0.031 0.021 0.074 4 -0.037 34 38
Insulin Receptor/Insulin 0.056 0.061 0.225 4 -0.135 34 38
mol:GTP 0 0 -9999 0 -9999 0 0
GRB10 0.022 0.018 -9999 0 0 185 185
SORBS1 0.027 0.016 -9999 0 0 126 126
CRK 0.035 0.008 -9999 0 0 23 23
PTPN1 -0.022 0.048 0.143 21 -0.251 6 27
CAV1 -0.011 0.041 0.174 9 -0.19 8 17
CBL/APS/CAP/Crk-II/C3G 0.052 0.053 -9999 0 -0.107 13 13
Insulin Receptor/Insulin/IRS1/NCK2 0.069 0.063 -9999 0 -0.139 31 31
mol:GDP 0 0 -9999 0 -9999 0 0
mol:PI-3-4-5-P3 0.03 0.078 -9999 0 -0.13 76 76
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.02 0.066 -9999 0 -0.317 11 11
RPS6KB1 -0.026 0.084 0.2 18 -0.201 23 41
PARD6A 0.035 0.007 -9999 0 0 17 17
CBL 0.036 0.004 -9999 0 0 6 6
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -9999 0 0
DOK1 0.023 0.018 -9999 0 -9999 0 0
PIK3R1 0.032 0.012 -9999 0 0 61 61
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.031 0.085 0.17 30 -0.209 24 54
HRAS/GTP -0.034 0.032 0.033 6 -0.121 39 45
Insulin Receptor 0.031 0.021 0.074 4 -0.037 34 38
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.08 0.066 -9999 0 -0.129 30 30
PRKCI 0.026 0.084 -9999 0 -0.43 14 14
Insulin Receptor/Insulin/GRB14/PDK1 0.012 0.066 -9999 0 -0.133 72 72
SHC1 0.033 0.011 -9999 0 0 48 48
negative regulation of MAPKKK cascade 0.036 0.053 -9999 0 -9999 0 0
PI3K 0.041 0.085 -9999 0 -0.132 76 76
NCK2 0.035 0.007 -9999 0 0 19 19
RHOQ 0.035 0.006 -9999 0 0 14 14
mol:H2O2 -0.004 0.006 -9999 0 -0.034 6 6
HRAS/GDP 0.021 0.029 -9999 0 -0.132 16 16
AKT2 -0.022 0.081 0.221 12 -0.192 12 24
PRKCZ 0.004 0.073 -9999 0 -0.41 13 13
SH2B2 0 0 -9999 0 -9999 0 0
SHC/SHIP -0.014 0.052 0.158 25 -0.148 4 29
F2RL2 0.036 0.004 -9999 0 0 6 6
TRIP10 0.033 0.01 -9999 0 0 39 39
Insulin Receptor/Insulin/Shc 0.056 0.036 -9999 0 -0.116 8 8
TC10/GTP/CIP4/Exocyst 0.041 0.029 -9999 0 -0.115 13 13
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.071 0.044 -9999 0 -0.128 11 11
RAPGEF1 0.035 0.007 -9999 0 0 18 18
RASA1 0.034 0.009 -9999 0 0 30 30
NCK1 0.034 0.008 -9999 0 0 26 26
CBL/APS/CAP/Crk-II 0.046 0.04 -9999 0 -0.108 13 13
TC10/GDP 0.023 0.023 -9999 0 -0.132 10 10
Insulin Receptor/Insulin/SHC/GRB10 0.047 0.066 -9999 0 -0.133 32 32
INPP5D -0.02 0.028 0.065 20 -0.109 23 43
SOS1 0 0 -9999 0 -9999 0 0
SGK1 -0.005 0.005 -9999 0 -9999 0 0
mol:cAMP 0 0 -9999 0 -9999 0 0
PTPN11 0.036 0.005 -9999 0 0 9 9
IRS1 0.032 0.011 -9999 0 0 51 51
p62DOK/RasGAP 0.036 0.053 -9999 0 -9999 0 0
INS 0.033 0.022 0.087 14 -0.037 34 48
mol:PI-3-4-P2 -0.02 0.028 0.065 20 -0.108 23 43
GRB2 0.035 0.006 -9999 0 0 16 16
EIF4EBP1 -0.028 0.083 0.196 17 -0.211 22 39
PTPRA 0.034 0.015 0.074 2 -0.047 6 8
PIK3CA 0.03 0.014 -9999 0 0 85 85
TC10/GTP/CIP4 0.041 0.029 -9999 0 -0.115 13 13
PDPK1 0.036 0.003 -9999 0 0 4 4
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.013 0.051 -9999 0 -0.16 30 30
Insulin Receptor/Insulin/IRS1 0.052 0.046 -9999 0 -0.114 25 25
Insulin Receptor/Insulin/IRS3 0.045 0.03 -9999 0 -0.069 5 5
Par3/Par6 0.072 0.04 -9999 0 -0.109 15 15
LPA4-mediated signaling events

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
ADCY4 -0.009 0.001 0 7 -9999 0 7
ADCY5 -0.009 0.001 0 7 -9999 0 7
ADCY6 -0.017 0.004 0 22 -9999 0 22
ADCY7 -0.016 0.005 0 44 -9999 0 44
ADCY1 -0.013 0.008 0 126 -9999 0 126
ADCY2 -0.017 0.004 0 20 -9999 0 20
ADCY3 -0.009 0.001 0 7 -9999 0 7
ADCY8 -0.015 0.006 0 74 -9999 0 74
PRKCE -0.011 0.001 0 7 -9999 0 7
ADCY9 -0.017 0.003 -9999 0 -9999 0 0
mol:DAG 0 0 -9999 0 -9999 0 0
cAMP biosynthetic process 0.015 0.044 0.159 16 -9999 0 16
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.023 0.056 0.156 1 -0.198 23 24
BIRC5 0.029 0.015 -9999 0 0 102 102
NFKBIA -0.007 0.04 0.142 8 -0.178 13 21
CPEB1 0.032 0.011 -9999 0 0 54 54
AKT1 -0.005 0.029 0.175 2 -0.178 4 6
NDEL1 0.035 0.007 -9999 0 0 19 19
Aurora A/BRCA1 0.023 0.041 -9999 0 -0.15 19 19
NDEL1/TACC3 0.037 0.056 0.154 1 -0.17 21 22
GADD45A 0.031 0.013 -9999 0 0 74 74
GSK3B 0.034 0.015 0.088 23 0 35 58
PAK1/Aurora A 0.03 0.047 0.156 1 -0.164 20 21
MDM2 0.033 0.011 -9999 0 0 49 49
JUB 0 0 -9999 0 -9999 0 0
TPX2 -0.016 0.01 -9999 0 -9999 0 0
TP53 0.002 0.069 -9999 0 -0.233 30 30
DLG7 -0.003 0.041 0.104 38 -0.178 11 49
AURKAIP1 0 0 -9999 0 -9999 0 0
ARHGEF7 0.032 0.012 -9999 0 0 56 56
G2 phase of mitotic cell cycle 0 0 -9999 0 -9999 0 0
Aurora A/NDEL1/TACC3 0.039 0.059 0.163 1 -0.155 32 33
G2/M transition of mitotic cell cycle 0.023 0.04 -9999 0 -0.149 19 19
AURKA 0.007 0.047 0.131 22 -0.207 16 38
AURKB 0.008 0.035 -9999 0 -0.136 25 25
CDC25B 0 0.074 0.116 1 -0.293 25 26
G2/M transition checkpoint 0.002 0.034 0.076 22 -0.139 20 42
mRNA polyadenylation 0.015 0.049 -9999 0 -0.127 42 42
Aurora A/CPEB 0.015 0.049 -9999 0 -0.128 42 42
Aurora A/TACC1/TRAP/chTOG 0.05 0.079 -9999 0 -0.167 43 43
BRCA1 0.035 0.006 -9999 0 0 16 16
centrosome duplication 0.03 0.047 0.156 1 -0.164 20 21
regulation of centrosome cycle 0.035 0.055 0.15 1 -0.169 21 22
spindle assembly 0.048 0.078 -9999 0 -0.166 43 43
TDRD7 0.033 0.01 -9999 0 0 40 40
Aurora A/RasGAP/Survivin 0.035 0.072 -9999 0 -0.187 22 22
CENPA 0.003 0.061 -9999 0 -0.263 22 22
Aurora A/PP2A 0.031 0.047 0.156 1 -0.161 21 22
meiosis 0 0 -9999 0 -9999 0 0
protein catabolic process -0.006 0.049 0.14 1 -0.214 14 15
negative regulation of DNA binding 0 0.072 -9999 0 -0.237 33 33
prophase 0 0 -9999 0 -9999 0 0
GIT1/beta-PIX 0.04 0.045 -9999 0 -0.142 26 26
RASA1 0.034 0.009 -9999 0 0 30 30
Ajuba/Aurora A 0.002 0.034 0.076 22 -0.14 20 42
mitotic prometaphase -0.004 0.01 0.067 9 -9999 0 9
proteasomal ubiquitin-dependent protein catabolic process 0.007 0.047 0.131 22 -0.206 16 38
TACC1 0.035 0.008 -9999 0 0 22 22
TACC3 0.032 0.011 -9999 0 0 55 55
Aurora A/Antizyme1 0.023 0.041 -9999 0 -0.151 19 19
Aurora A/RasGAP 0.028 0.057 0.156 1 -0.223 19 20
OAZ1 0.033 0.01 -9999 0 0 41 41
RAN 0.035 0.006 -9999 0 0 13 13
mitosis 0 0 -9999 0 -9999 0 0
PRKACA 0.035 0.015 0.088 25 0 29 54
GIT1 0.036 0.003 -9999 0 0 4 4
GIT1/beta-PIX/PAK1 0.057 0.047 -9999 0 -0.123 25 25
Importin alpha/Importin beta/TPX2 -0.016 0.01 -9999 0 -9999 0 0
PPP2R5D 0.036 0.004 -9999 0 0 6 6
Aurora A/TPX2 -0.026 0.052 0.093 2 -0.221 18 20
PAK1 0.035 0.007 -9999 0 0 17 17
CKAP5 0.034 0.009 -9999 0 0 33 33
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.034 0.008 -9999 0 0 25 25
mol:S1P 0.001 0.002 0.019 4 -9999 0 4
S1P1/S1P/Gi -0.021 0.109 -9999 0 -0.358 34 34
GNAO1 0.031 0.014 -9999 0 -9999 0 0
S1P/S1P3/G12/G13 0.027 0.039 -9999 0 -0.102 30 30
AKT1 -0.017 0.165 -9999 0 -0.49 46 46
AKT3 0.01 0.075 -9999 0 -0.468 1 1
mol:GTP 0 0 -9999 0 -9999 0 0
PDGFB-D/PDGFRB 0.034 0.008 -9999 0 0 25 25
GNAI2 0.034 0.011 -9999 0 -9999 0 0
GNAI3 0.036 0.006 -9999 0 -9999 0 0
GNAI1 0.018 0.019 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
S1PR3 0.001 0.002 0.02 4 -9999 0 4
S1PR2 0 0 -9999 0 -9999 0 0
EDG1 0.033 0.01 -9999 0 0 38 38
mol:Ca2+ -0.008 0.104 0.2 1 -0.294 38 39
MAPK3 -0.011 0.101 0.185 1 -0.286 38 39
MAPK1 -0.004 0.095 0.185 1 -0.291 30 31
JAK2 -0.016 0.111 0.171 1 -0.314 41 42
CXCR4 -0.009 0.101 0.185 1 -0.291 37 38
FLT1 0.035 0.01 -9999 0 -9999 0 0
RhoA/GDP 0.024 0.019 -9999 0 -0.132 7 7
Rac1/GDP 0.018 0.02 -9999 0 -0.132 6 6
SRC -0.011 0.1 0.185 1 -0.287 37 38
S1P/S1P3/Gi -0.008 0.104 0.201 1 -0.296 38 39
RAC1 0.027 0.016 -9999 0 0 123 123
RhoA/GTP 0.008 0.11 0.189 1 -0.281 39 40
VEGFA 0.002 0.002 0.028 4 -9999 0 4
S1P/S1P2/Gi -0.012 0.103 0.161 1 -0.298 38 39
VEGFR1 homodimer/VEGFA homodimer 0.029 0.009 0.093 4 -9999 0 4
RHOA 0.035 0.007 -9999 0 0 21 21
S1P/S1P3/Gq 0.014 0.04 -9999 0 -0.147 25 25
GNAQ 0.034 0.009 -9999 0 0 31 31
GNAZ 0.031 0.014 -9999 0 -9999 0 0
G12/G13 0.028 0.049 -9999 0 -0.142 30 30
GNA14 0.034 0.008 -9999 0 0 28 28
GNA15 0.032 0.012 -9999 0 0 59 59
GNA12 0.026 0.016 -9999 0 0 136 136
GNA13 0.035 0.007 -9999 0 0 18 18
GNA11 0.032 0.012 -9999 0 0 60 60
Rac1/GTP -0.001 0.099 -9999 0 -0.291 31 31
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.019 0.024 -9999 0 -0.132 10 10
alphaV beta3 Integrin 0.059 0.048 -9999 0 -0.131 25 25
PTK2 0.005 0.085 0.223 4 -0.293 20 24
IGF1R 0.032 0.012 -9999 0 0 56 56
PI4KB 0 0 -9999 0 -9999 0 0
MFGE8 0.035 0.006 -9999 0 0 13 13
SRC 0.035 0.006 -9999 0 0 13 13
CDKN1B 0.002 0.089 -9999 0 -0.32 32 32
VEGFA 0 0 -9999 0 -9999 0 0
ILK 0.01 0.072 -9999 0 -0.296 23 23
ROCK1 0.035 0.006 -9999 0 0 14 14
AKT1 -0.004 0.069 -9999 0 -0.313 20 20
PTK2B -0.008 0.066 0.181 35 -0.187 4 39
alphaV/beta3 Integrin/JAM-A 0.069 0.047 -9999 0 -0.115 20 20
CBL 0.036 0.004 -9999 0 0 6 6
mol:GTP 0 0 -9999 0 -9999 0 0
alphaV beta3 Integrin/ANGPTL3 0.061 0.044 -9999 0 -0.123 23 23
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.066 0.068 -9999 0 -0.133 44 44
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.006 0.057 -9999 0 -0.282 11 11
alphaV/beta3 Integrin/Syndecan-1 0.054 0.043 -9999 0 -0.124 15 15
PI4KA 0 0 -9999 0 -9999 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.047 0.083 -9999 0 -0.146 65 65
PI4 Kinase 0 0 -9999 0 -9999 0 0
PIK3CA 0.03 0.014 -9999 0 0 85 85
alphaV/beta3 Integrin/Osteopontin 0.047 0.069 -9999 0 -0.14 55 55
RPS6KB1 -0.043 0.066 0.24 3 -0.209 18 21
TLN1 0.029 0.014 -9999 0 0 94 94
MAPK3 0.002 0.086 -9999 0 -0.332 25 25
GPR124 0.034 0.008 -9999 0 0 24 24
MAPK1 -0.001 0.087 -9999 0 -0.348 23 23
PXN 0.036 0.004 -9999 0 0 5 5
PIK3R1 0.032 0.012 -9999 0 0 61 61
alphaV/beta3 Integrin/Tumstatin 0.062 0.043 -9999 0 -0.124 23 23
cell adhesion 0.047 0.054 -9999 0 -0.157 27 27
ANGPTL3 0.036 0.005 -9999 0 0 8 8
VEGFR2 homodimer/VEGFA homodimer/Src 0.037 0.029 -9999 0 -0.115 10 10
IGF-1R heterotetramer 0.032 0.012 -9999 0 0 56 56
Rac1/GDP 0.018 0.02 -9999 0 -0.132 6 6
TGFBR2 0.034 0.008 -9999 0 0 27 27
ITGB3 0.036 0.004 -9999 0 0 5 5
IGF1 0.035 0.007 -9999 0 0 20 20
RAC1 0.027 0.016 -9999 0 0 123 123
regulation of cell-matrix adhesion 0.058 0.045 -9999 0 -0.123 23 23
apoptosis 0.034 0.009 -9999 0 0 30 30
CD47 0.034 0.008 -9999 0 0 25 25
alphaV/beta3 Integrin/CD47 0.058 0.048 -9999 0 -0.13 26 26
VCL 0.027 0.016 -9999 0 0 127 127
alphaV/beta3 Integrin/Del1 0.062 0.043 -9999 0 -0.124 23 23
CSF1 0.036 0.004 -9999 0 0 5 5
PIK3C2A 0.01 0.018 -9999 0 -9999 0 0
PI4 Kinase/Pyk2 0.026 0.041 -9999 0 -0.122 27 27
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.047 0.05 -9999 0 -0.125 27 27
FAK1/Vinculin 0.013 0.074 0.224 3 -0.26 17 20
alphaV beta3/Integrin/ppsTEM5 0.059 0.045 -9999 0 -0.124 23 23
RHOA 0.035 0.007 -9999 0 0 21 21
VTN 0.036 0.004 -9999 0 0 5 5
BCAR1 0 0 -9999 0 -9999 0 0
FGF2 0.034 0.008 -9999 0 0 25 25
F11R -0.019 0.008 -9999 0 -9999 0 0
alphaV/beta3 Integrin/Lactadherin 0.06 0.046 -9999 0 -0.127 24 24
alphaV/beta3 Integrin/TGFBR2 0.058 0.047 -9999 0 -0.123 26 26
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.059 0.04 -9999 0 -0.109 23 23
HSP90AA1 0 0 -9999 0 -9999 0 0
alphaV/beta3 Integrin/Talin 0.045 0.051 -9999 0 -0.117 31 31
mol:GDP 0 0 -9999 0 -9999 0 0
FN1 0.034 0.009 -9999 0 0 29 29
alphaV/beta3 Integrin/Pyk2 0.059 0.058 0.19 29 -0.12 27 56
SDC1 0.03 0.014 -9999 0 0 81 81
VAV3 -0.025 0.03 0.179 2 -0.188 5 7
PTPN11 0.036 0.005 -9999 0 0 9 9
IRS1 0.032 0.011 -9999 0 0 51 51
FAK1/Paxillin 0.023 0.079 0.22 4 -0.247 20 24
cell migration -0.004 0.068 0.196 4 -0.276 11 15
ITGAV 0.034 0.009 -9999 0 0 30 30
PI3K 0.051 0.085 -9999 0 -0.136 59 59
SPP1 0.032 0.011 -9999 0 0 51 51
KDR 0.03 0.014 -9999 0 0 86 86
mol:PI-4-5-P2 0 0 -9999 0 -9999 0 0
alphaV/beta3 Integrin/Caspase 8 0.034 0.009 -9999 0 0 30 30
COL4A3 0.036 0 -9999 0 -9999 0 0
angiogenesis 0 0.096 0.217 1 -0.377 24 25
Rac1/GTP -0.028 0.036 0.18 1 -0.189 7 8
EDIL3 0.036 0.003 -9999 0 0 4 4
cell proliferation 0.057 0.047 -9999 0 -0.123 26 26
Aurora B signaling

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
Condensin I complex 0.001 0.012 -9999 0 -0.093 8 8
STMN1 -0.019 0.01 0.059 2 -9999 0 2
Aurora B/RasGAP/Survivin 0.033 0.075 -9999 0 -0.137 70 70
Chromosomal passenger complex/Cul3 protein complex -0.033 0.077 -9999 0 -0.195 61 61
BIRC5 0.029 0.015 -9999 0 0 102 102
DES 0.025 0.091 -9999 0 -0.645 8 8
Aurora C/Aurora B/INCENP 0.057 0.026 -9999 0 -9999 0 0
Aurora B/TACC1 0.041 0.025 -9999 0 -0.116 8 8
Aurora B/PP2A 0.049 0.016 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
CBX5 -0.004 0.052 -9999 0 -0.192 31 31
mitotic metaphase/anaphase transition -0.001 0.003 0.009 19 -0.009 1 20
NDC80 -0.01 0.006 0.014 2 -9999 0 2
Cul3 protein complex 0.026 0.034 -9999 0 -0.134 10 10
KIF2C -0.018 0.121 -9999 0 -0.451 31 31
PEBP1 -0.001 0.003 0.009 14 -0.009 9 23
KIF20A 0.028 0.015 -9999 0 0 101 101
mol:GDP 0 0 -9999 0 -9999 0 0
Aurora B/RasGAP 0.039 0.045 -9999 0 -0.144 24 24
SEPT1 0 0 -9999 0 -9999 0 0
SMC2 0 0 -9999 0 -9999 0 0
SMC4 0 0 -9999 0 -9999 0 0
NSUN2/NPM1/Nucleolin -0.002 0.078 -9999 0 -0.484 8 8
PSMA3 0.034 0.009 -9999 0 0 32 32
G2/M transition of mitotic cell cycle -0.001 0.002 0.009 8 -0.006 1 9
H3F3B 0.009 0.032 -9999 0 -0.2 11 11
AURKB 0.032 0.015 -9999 0 -0.008 52 52
AURKC 0.033 0.011 -9999 0 0 47 47
CDCA8 0.032 0.013 -9999 0 -0.003 53 53
cytokinesis -0.025 0.142 0.18 5 -0.406 49 54
Aurora B/Septin1 -0.013 0.138 0.199 1 -0.411 42 43
AURKA -0.001 0.002 0.009 8 -0.006 1 9
INCENP 0.034 0.014 0.057 1 -0.025 22 23
KLHL13 0 0 -9999 0 -9999 0 0
BUB1 0.036 0.006 0.058 1 0 11 12
hSgo1/Aurora B/Survivin 0.022 0.05 -9999 0 -0.111 55 55
EVI5 0.035 0.006 -9999 0 0 11 11
RhoA/GTP 0.009 0.127 -9999 0 -0.32 50 50
SGOL1 0 0 -9999 0 -9999 0 0
CENPA -0.006 0.077 0.124 1 -0.283 29 30
NCAPG 0 0 -9999 0 -9999 0 0
Aurora B/HC8 Proteasome 0.044 0.031 -9999 0 -0.144 9 9
NCAPD2 0 0 -9999 0 -9999 0 0
Aurora B/PP1-gamma 0.047 0.026 -9999 0 -0.147 6 6
RHOA 0.035 0.007 -9999 0 0 21 21
NCAPH 0 0 -9999 0 -9999 0 0
NPM1 0.006 0.065 -9999 0 -0.322 14 14
RASA1 0.034 0.009 -9999 0 0 30 30
KLHL9 0.022 0.018 -9999 0 0 196 196
mitotic prometaphase -0.001 0.003 0.009 14 -0.009 9 23
proteasomal ubiquitin-dependent protein catabolic process 0.044 0.031 -9999 0 -0.144 9 9
PPP1CC 0.036 0.005 -9999 0 0 8 8
Centraspindlin 0.002 0.128 -9999 0 -0.335 50 50
RhoA/GDP 0.024 0.019 -9999 0 -0.132 7 7
NSUN2 0.002 0.041 -9999 0 -0.29 8 8
MYLK -0.013 0.067 -9999 0 -0.199 56 56
KIF23 0.028 0.017 -9999 0 -0.005 93 93
VIM -0.015 0.011 0.016 1 -9999 0 1
RACGAP1 0.031 0.015 -9999 0 -0.003 77 77
mitosis 0 0 -9999 0 -9999 0 0
NCL 0.002 0.066 -9999 0 -0.289 22 22
Chromosomal passenger complex -0.015 0.097 0.127 4 -0.244 59 63
Chromosomal passenger complex/EVI5 0.062 0.084 -9999 0 -0.15 54 54
TACC1 0.035 0.008 -9999 0 0 22 22
PPP2R5D 0.036 0.004 -9999 0 0 6 6
CUL3 0.036 0.002 -9999 0 0 2 2
response to DNA damage stimulus 0 0 -9999 0 -9999 0 0
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.034 0.008 -9999 0 0 25 25
alphaV beta3 Integrin 0.043 0.042 -9999 0 -0.142 23 23
PTK2 0.015 0.107 -9999 0 -0.327 27 27
positive regulation of JNK cascade 0.023 0.09 -9999 0 -0.277 21 21
CDC42/GDP 0.038 0.123 -9999 0 -0.346 34 34
Rac1/GDP 0.029 0.109 -9999 0 -0.356 20 20
RAP1B 0 0 -9999 0 -9999 0 0
RAP1A 0.036 0.005 -9999 0 0 8 8
CTNNB1 0.035 0.007 -9999 0 0 21 21
CDC42/GTP 0.031 0.11 -9999 0 -0.341 20 20
nectin-3/I-afadin 0.043 0.026 -9999 0 -0.138 4 4
RAPGEF1 0.006 0.119 -9999 0 -0.358 37 37
mol:GTP 0 0 -9999 0 -9999 0 0
CRK 0.006 0.126 -9999 0 -0.394 37 37
PDGFB-D/PDGFRB 0.034 0.008 -9999 0 0 25 25
TLN1 -0.01 0.052 0.093 38 -0.235 13 51
Rap1/GTP -0.002 0.085 -9999 0 -0.269 38 38
IQGAP1 0.033 0.01 -9999 0 0 43 43
Rap1/GTP/I-afadin 0.042 0.015 -9999 0 -0.102 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.043 0.026 -9999 0 -0.138 4 4
PVR 0.034 0.009 -9999 0 0 30 30
Necl-5(dimer) 0.034 0.009 -9999 0 0 30 30
mol:GDP 0.023 0.137 -9999 0 -0.412 33 33
MLLT4 0.034 0.009 -9999 0 0 35 35
PIK3CA 0.03 0.014 -9999 0 0 85 85
PI3K 0.053 0.088 -9999 0 -0.132 70 70
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.049 0.015 -9999 0 -9999 0 0
positive regulation of lamellipodium assembly 0.019 0.087 -9999 0 -0.281 22 22
PVRL1 0.036 0.004 -9999 0 0 5 5
PVRL3 0.032 0.012 -9999 0 0 56 56
PVRL2 0.034 0.01 -9999 0 0 36 36
PIK3R1 0.032 0.012 -9999 0 0 61 61
CDH1 0.033 0.01 -9999 0 0 37 37
CLDN1 0.034 0.008 -9999 0 0 27 27
JAM-A/CLDN1 0.073 0.043 -9999 0 -0.114 8 8
SRC 0.013 0.135 -9999 0 -0.421 37 37
ITGB3 0.036 0.004 -9999 0 0 5 5
nectin-1(dimer)/I-afadin/I-afadin 0.049 0.015 -9999 0 -9999 0 0
FARP2 0.029 0.136 -9999 0 -0.438 21 21
RAC1 0.027 0.016 -9999 0 0 123 123
CTNNA1 0.035 0.007 -9999 0 0 18 18
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.057 0.034 -9999 0 -0.12 4 4
nectin-1/I-afadin 0.049 0.015 -9999 0 -9999 0 0
nectin-2/I-afadin 0.046 0.023 -9999 0 -0.142 3 3
RAC1/GTP/IQGAP1/filamentous actin 0.026 0.044 -9999 0 -0.117 32 32
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.059 0.032 -9999 0 -0.12 4 4
CDC42/GTP/IQGAP1/filamentous actin 0.035 0.042 -9999 0 -0.115 32 32
F11R 0.032 0.011 -9999 0 0 52 52
positive regulation of filopodium formation 0.023 0.09 -9999 0 -0.277 21 21
alphaV/beta3 Integrin/Talin 0.032 0.091 0.207 38 -0.211 27 65
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.046 0.023 -9999 0 -0.142 3 3
nectin-2(dimer)/I-afadin/I-afadin 0.046 0.023 -9999 0 -0.142 3 3
PIP5K1C -0.01 0.04 0.091 5 -0.216 13 18
VAV2 0.025 0.145 -9999 0 -0.463 23 23
RAP1/GDP 0.027 0.112 0.265 1 -0.321 35 36
ITGAV 0.034 0.009 -9999 0 0 30 30
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.056 0.037 -9999 0 -0.137 6 6
nectin-3(dimer)/I-afadin/I-afadin 0.043 0.026 -9999 0 -0.138 4 4
Rac1/GTP 0.025 0.105 -9999 0 -0.348 19 19
PTPRM 0.008 0.044 -9999 0 -0.232 14 14
E-cadherin/beta catenin/alpha catenin 0.08 0.058 -9999 0 -0.124 11 11
adherens junction assembly 0 0 -9999 0 -9999 0 0
CDC42 0.035 0.008 -9999 0 0 22 22
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.001 0.038 0.096 27 -0.098 9 36
NFATC2 0 0.027 0.084 16 -0.095 9 25
NFATC3 -0.002 0.038 0.096 27 -0.101 10 37
CD40LG 0.012 0.115 0.283 38 -0.239 2 40
PTGS2 -0.022 0.066 0.234 7 -0.239 2 9
JUNB 0.03 0.014 -9999 0 0 83 83
CaM/Ca2+/Calcineurin A alpha-beta B1 0.026 0.026 -9999 0 -0.12 11 11
CaM/Ca2+ 0.026 0.026 -9999 0 -0.12 11 11
CALM1 0.035 0.013 0.065 4 0 49 53
JUN 0.036 0.012 -9999 0 -9999 0 0
mol:Ca2+ 0 0.002 -9999 0 -9999 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.021 0.021 -9999 0 -0.107 11 11
FOSL1 0.032 0.012 -9999 0 0 56 56
CREM 0.027 0.016 -9999 0 0 121 121
Jun/NFAT1-c-4/p21SNFT 0.058 0.07 0.259 13 -0.18 3 16
FOS 0.027 0.019 -9999 0 -9999 0 0
IFNG 0.009 0.11 0.288 32 -0.239 2 34
AP-1/NFAT1-c-4 0.081 0.111 0.354 7 -0.261 2 9
FASLG 0.01 0.112 0.281 35 -0.239 2 37
NFAT1-c-4/ICER1 0.04 0.051 0.21 12 -9999 0 12
IL2RA 0.002 0.087 0.246 20 -0.239 2 22
FKBP12/FK506 0.021 0.024 -9999 0 -0.132 11 11
CSF2 0.011 0.114 0.284 37 -0.239 2 39
JunB/Fra1/NFAT1-c-4 0.047 0.056 0.219 6 -0.184 1 7
IL4 0.011 0.114 0.284 37 -0.239 2 39
IL2 0.014 0.079 -9999 0 -0.832 4 4
IL3 0.031 0.075 -9999 0 -0.587 6 6
FKBP1A 0.033 0.011 -9999 0 0 46 46
BATF3 0 0 -9999 0 -9999 0 0
mol:FK506 0 0 -9999 0 -9999 0 0
POU2F1 0.038 0.008 -9999 0 -9999 0 0
Glucocorticoid receptor regulatory network

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
PCK2 -0.023 0.104 -9999 0 -0.482 16 16
SMARCC2 0.033 0.011 -9999 0 0 45 45
SMARCC1 0.034 0.009 -9999 0 0 33 33
TBX21 0.031 0.052 -9999 0 -9999 0 0
SUMO2 0.033 0.018 0.073 1 -0.029 30 31
STAT1 (dimer) 0.035 0.037 -9999 0 -0.169 12 12
FKBP4 0.034 0.009 -9999 0 0 34 34
FKBP5 0.028 0.015 -9999 0 0 115 115
GR alpha/HSP90/FKBP51/HSP90 -0.024 0.064 -9999 0 -0.181 10 10
PRL 0.039 0.052 -9999 0 -9999 0 0
cortisol/GR alpha (dimer)/TIF2 -0.041 0.115 -9999 0 -0.323 1 1
RELA 0.017 0.108 0.171 33 -0.162 115 148
FGG -0.049 0.1 -9999 0 -0.32 2 2
GR beta/TIF2 -0.024 0.074 -9999 0 -0.219 2 2
IFNG 0.035 0.078 0.344 1 -9999 0 1
apoptosis -0.024 0.194 0.425 23 -0.506 31 54
CREB1 0.042 0.009 -9999 0 -9999 0 0
histone acetylation 0.021 0.053 -9999 0 -0.238 1 1
BGLAP 0.039 0.059 -9999 0 -9999 0 0
GR/PKAc 0.019 0.089 -9999 0 -0.18 19 19
NF kappa B1 p50/RelA 0.031 0.175 0.284 30 -0.262 110 140
SMARCD1 0.035 0.007 -9999 0 0 17 17
MDM2 -0.008 0.035 -9999 0 -9999 0 0
GATA3 0.032 0.02 -9999 0 -9999 0 0
AKT1 0.028 0.029 0.156 8 -0.086 17 25
CSF2 0.006 0.033 -9999 0 -9999 0 0
GSK3B 0.032 0.019 0.073 1 -0.03 26 27
NR1I3 -0.016 0.179 0.456 14 -0.495 17 31
CSN2 -0.045 0.087 -9999 0 -0.29 2 2
BRG1/BAF155/BAF170/BAF60A 0.059 0.074 -9999 0 -0.166 36 36
NFATC1 0.04 0.008 -9999 0 -9999 0 0
POU2F1 0.039 0.012 -9999 0 -9999 0 0
CDKN1A -0.129 0.416 -9999 0 -1.243 57 57
response to stress 0 0 -9999 0 -9999 0 0
response to UV 0.001 0.008 0.028 29 -9999 0 29
SFN 0.031 0.013 -9999 0 0 74 74
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.007 0.065 -9999 0 -0.151 7 7
prolactin receptor activity 0 0 -9999 0 -9999 0 0
EGR1 -0.071 0.272 0.433 14 -0.662 68 82
JUN 0.025 0.053 0.323 4 -9999 0 4
IL4 0.036 0.051 -9999 0 -9999 0 0
CDK5R1 0.035 0.008 -9999 0 0 21 21
PRKACA 0.034 0.009 -9999 0 0 29 29
cortisol/GR alpha (monomer)/AP-1 -0.048 0.053 -9999 0 -0.214 15 15
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.001 0.071 -9999 0 -0.16 15 15
cortisol/GR alpha (monomer) -0.056 0.12 -9999 0 -0.372 2 2
NCOA2 0.036 0.005 -9999 0 0 9 9
response to hypoxia 0 0 -9999 0 -9999 0 0
FOS 0.039 0.031 0.165 7 -9999 0 7
AP-1/NFAT1-c-4 0.051 0.073 0.425 2 -9999 0 2
AFP 0.023 0.066 -9999 0 -9999 0 0
SUV420H1 0.032 0.011 -9999 0 0 52 52
IRF1 -0.029 0.124 -9999 0 -0.631 14 14
TP53 -0.015 0.172 -9999 0 -0.49 54 54
PPP5C 0.033 0.01 -9999 0 0 39 39
KRT17 0.04 0.079 0.433 1 -9999 0 1
KRT14 0.031 0.067 -9999 0 -9999 0 0
TBP 0.042 0.017 -9999 0 -9999 0 0
CREBBP 0.029 0.018 -9999 0 -0.09 10 10
HDAC1 0.032 0.007 -9999 0 -9999 0 0
HDAC2 0.032 0.011 -9999 0 -9999 0 0
AP-1 0.051 0.073 0.426 2 -9999 0 2
MAPK14 0.034 0.018 0.073 1 -0.03 28 29
MAPK10 0.029 0.02 0.072 1 -0.03 23 24
MAPK11 0.03 0.02 0.073 1 -0.03 28 29
KRT5 0.039 0.077 0.433 1 -9999 0 1
interleukin-1 receptor activity -0.001 0 -9999 0 -9999 0 0
NCOA1 0.032 0.019 0.077 3 -0.067 10 13
STAT1 0.035 0.037 -9999 0 -0.169 12 12
CGA 0.037 0.053 -9999 0 -9999 0 0
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.033 0.07 -9999 0 -0.364 8 8
MAPK3 0.033 0.019 0.074 2 -0.03 33 35
MAPK1 0.03 0.019 -9999 0 -0.03 27 27
ICAM1 0.029 0.131 0.329 14 -9999 0 14
NFKB1 0.017 0.107 0.169 31 -0.162 113 144
MAPK8 0.034 0.058 0.278 2 -9999 0 2
MAPK9 0.033 0.018 0.073 1 -0.029 28 29
cortisol/GR alpha (dimer) -0.028 0.198 0.431 22 -0.517 34 56
BAX -0.033 0.176 -9999 0 -0.879 9 9
POMC 0.032 0.071 0.501 1 -9999 0 1
EP300 0.026 0.019 -9999 0 -0.09 10 10
cortisol/GR alpha (dimer)/p53 -0.071 0.132 -9999 0 -0.42 18 18
proteasomal ubiquitin-dependent protein catabolic process -0.005 0.069 0.241 29 -9999 0 29
SGK1 -0.017 0.062 -9999 0 -0.243 15 15
IL13 0.027 0.064 -9999 0 -9999 0 0
IL6 0.03 0.128 0.329 16 -9999 0 16
PRKACG 0.035 0.006 -9999 0 0 14 14
IL5 0.018 0.075 0.4 1 -9999 0 1
IL2 0.04 0.075 -9999 0 -9999 0 0
CDK5 0.026 0.017 -9999 0 0 137 137
PRKACB 0.033 0.011 -9999 0 0 45 45
HSP90AA1 0 0 -9999 0 -9999 0 0
IL8 -0.113 0.389 0.323 18 -0.785 117 135
CDK5R1/CDK5 0.033 0.042 -9999 0 -0.139 18 18
NF kappa B1 p50/RelA/PKAc 0.055 0.161 0.295 23 -0.207 99 122
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 -0.037 0.103 -9999 0 -0.371 1 1
SMARCA4 0.031 0.013 -9999 0 0 76 76
chromatin remodeling -0.036 0.105 -9999 0 -0.357 26 26
NF kappa B1 p50/RelA/Cbp 0.045 0.161 0.287 16 -0.217 106 122
JUN (dimer) 0.025 0.053 0.322 4 -9999 0 4
YWHAH 0.031 0.013 -9999 0 0 74 74
VIPR1 0.034 0.062 0.367 4 -9999 0 4
NR3C1 -0.039 0.083 -9999 0 -0.346 1 1
NR4A1 0.039 0.008 -9999 0 -9999 0 0
TIF2/SUV420H1 0.036 0.053 -9999 0 -0.142 38 38
MAPKKK cascade -0.024 0.194 0.425 23 -0.506 31 54
cortisol/GR alpha (dimer)/Src-1 -0.047 0.122 -9999 0 -0.388 2 2
PBX1 0.04 0.01 -9999 0 -9999 0 0
POU1F1 0.041 0.011 -9999 0 -9999 0 0
SELE 0.026 0.129 0.328 2 -9999 0 2
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A -0.036 0.105 -9999 0 -0.37 24 24
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.037 0.103 -9999 0 -0.371 1 1
mol:cortisol -0.034 0.059 -9999 0 -9999 0 0
MMP1 0.036 0.072 0.339 1 -0.488 3 4
Regulation of Telomerase

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
Telomerase catalytic core complex 0.026 0.154 -9999 0 -0.57 8 8
RAD9A 0.035 0.006 -9999 0 0 12 12
AP1 0.009 0.082 -9999 0 -0.171 72 72
IFNAR2 0.033 0.02 -9999 0 -0.035 35 35
AKT1 0.011 0.056 -9999 0 -0.252 19 19
ER alpha/Oestrogen 0.023 0.014 -9999 0 -9999 0 0
NFX1/SIN3/HDAC complex -0.005 0.086 -9999 0 -0.266 33 33
EGF 0.033 0.015 -9999 0 -0.031 18 18
SMG5 0 0 -9999 0 -9999 0 0
SMG6 0 0 -9999 0 -9999 0 0
SP3/HDAC2 0.038 0.052 -9999 0 -0.167 19 19
TERT/c-Abl 0.033 0.162 -9999 0 -0.522 16 16
SAP18 0.034 0.01 -9999 0 0 39 39
MRN complex 0.068 0.024 -9999 0 -0.124 4 4
WT1 0.032 0.02 -9999 0 -0.034 36 36
WRN 0.034 0.009 -9999 0 0 31 31
SP1 0.033 0.023 -9999 0 -0.042 37 37
SP3 0.033 0.016 -9999 0 -0.03 25 25
TERF2IP 0.034 0.009 -9999 0 0 34 34
Telomerase/Nucleolin 0.038 0.155 -9999 0 -0.499 17 17
Mad/Max 0.047 0.027 -9999 0 -9999 0 0
TERT 0.022 0.155 -9999 0 -0.584 8 8
CCND1 -0.015 0.288 -9999 0 -0.949 38 38
MAX 0.031 0.018 -9999 0 -0.029 30 30
RBBP7 0.036 0.005 -9999 0 0 8 8
RBBP4 0.032 0.011 -9999 0 0 53 53
TERF2 0.028 0.011 0.084 5 -9999 0 5
PTGES3 0.035 0.008 -9999 0 0 22 22
SIN3A 0 0.001 -9999 0 -9999 0 0
Telomerase/911 0.04 0.1 -9999 0 -0.421 13 13
CDKN1B -0.025 0.083 0.098 35 -0.317 28 63
RAD1 0.035 0.007 -9999 0 0 18 18
XRCC5 0.036 0.004 -9999 0 0 7 7
XRCC6 0.033 0.01 -9999 0 0 37 37
SAP30 0.035 0.006 -9999 0 0 15 15
TRF2/PARP2 0.03 0.057 -9999 0 -0.142 43 43
UBE3A 0.034 0.012 -9999 0 -0.029 10 10
JUN 0.032 0.016 -9999 0 -0.03 19 19
E6 0 0.003 -9999 0 -9999 0 0
HPV-16 E6/E6AP 0.024 0.02 -9999 0 -0.131 3 3
FOS 0.024 0.02 -9999 0 -0.03 18 18
IFN-gamma/IRF1 0.033 0.069 -9999 0 -0.187 36 36
PARP2 0.033 0.01 -9999 0 0 41 41
BLM 0.029 0.015 -9999 0 0 98 98
Telomerase 0.014 0.056 -9999 0 -0.32 9 9
IRF1 0.025 0.039 -9999 0 -0.112 29 29
ESR1 0.034 0.009 -9999 0 0 34 34
KU/TER 0.047 0.026 -9999 0 -0.142 6 6
ATM/TRF2 0.043 0.028 -9999 0 -0.108 8 8
ubiquitin-dependent protein catabolic process 0.001 0.083 -9999 0 -0.279 25 25
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.001 0.085 -9999 0 -0.285 25 25
HDAC1 0.035 0.007 -9999 0 0 20 20
HDAC2 0.03 0.023 -9999 0 -0.041 35 35
ATM 0.021 0.038 0.133 36 -0.18 5 41
SMAD3 -0.018 0.012 0.022 24 -9999 0 24
ABL1 0.031 0.013 -9999 0 0 67 67
MXD1 0.033 0.017 -9999 0 -0.029 30 30
MRE11A 0.036 0.004 -9999 0 0 7 7
HUS1 0.027 0.016 -9999 0 0 125 125
RPS6KB1 0.036 0.005 -9999 0 0 8 8
TERT/NF kappa B1/14-3-3 0.042 0.17 -9999 0 -0.564 13 13
NR2F2 0.022 0.023 -9999 0 -0.029 48 48
MAPK3 -0.017 0.015 0.021 62 -9999 0 62
MAPK1 -0.014 0.017 0.024 59 -9999 0 59
TGFB1/TGF beta receptor Type II 0.031 0.012 -9999 0 0 62 62
NFKB1 0.035 0.007 -9999 0 0 17 17
HNRNPC 0 0 -9999 0 -9999 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.021 0.038 0.133 36 -0.18 5 41
NBN 0.035 0.005 -9999 0 0 11 11
EGFR 0.01 0.016 -9999 0 -9999 0 0
mol:Oestrogen 0 0.002 -9999 0 -9999 0 0
EGF/EGFR -0.004 0.057 -9999 0 -0.139 61 61
MYC 0.028 0.019 -9999 0 -0.029 20 20
IL2 0.033 0.022 -9999 0 -0.042 35 35
KU 0.047 0.026 -9999 0 -0.142 6 6
RAD50 0.035 0.006 -9999 0 0 12 12
HSP90AA1 0 0 -9999 0 -9999 0 0
TGFB1 0.031 0.012 -9999 0 0 62 62
TRF2/BLM 0.012 0.077 -9999 0 -0.148 86 86
FRAP1 0.035 0.006 -9999 0 0 14 14
KU/TERT 0.05 0.162 -9999 0 -0.53 11 11
SP1/HDAC2 0.042 0.045 -9999 0 -0.139 11 11
PINX1 0 0 -9999 0 -9999 0 0
Telomerase/EST1A 0.02 0.139 -9999 0 -0.471 16 16
Smad3/Myc 0.012 0.049 -9999 0 -0.126 41 41
911 complex 0.05 0.037 -9999 0 -0.124 4 4
IFNG 0.027 0.039 -9999 0 -0.106 33 33
Telomerase/PinX1 0.02 0.139 -9999 0 -0.471 16 16
Telomerase/AKT1/mTOR/p70S6K 0.022 0.096 -9999 0 -0.479 9 9
SIN3B 0.034 0.01 -9999 0 0 35 35
YWHAE 0.034 0.009 -9999 0 0 29 29
Telomerase/EST1B 0.02 0.139 -9999 0 -0.471 16 16
response to DNA damage stimulus 0.009 0.018 -9999 0 -0.082 10 10
MRN complex/TRF2/Rap1 0.076 0.071 -9999 0 -0.139 39 39
TRF2/WRN 0.034 0.045 -9999 0 -0.113 38 38
Telomerase/hnRNP C1/C2 0.02 0.139 -9999 0 -0.471 16 16
E2F1 0.033 0.02 -9999 0 -0.034 34 34
ZNFX1 0 0.001 -9999 0 -9999 0 0
PIF1 0 0 -9999 0 -9999 0 0
NCL 0.035 0.007 -9999 0 0 17 17
DKC1 0.035 0.007 -9999 0 0 18 18
telomeric DNA binding 0 0 -9999 0 -9999 0 0
BARD1 signaling events

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
BARD1/CSTF1 0.046 0.036 -9999 0 -0.142 16 16
ATM 0.034 0.01 -9999 0 0 36 36
UBE2D3 0.035 0.005 -9999 0 0 11 11
PRKDC 0.033 0.01 -9999 0 0 42 42
ATR 0.034 0.008 -9999 0 0 24 24
UBE2L3 0.034 0.009 -9999 0 0 33 33
FANCD2 0.008 0.035 -9999 0 -0.2 13 13
protein ubiquitination 0.074 0.054 -9999 0 -0.128 18 18
XRCC5 0.036 0.004 -9999 0 0 7 7
XRCC6 0.033 0.01 -9999 0 0 37 37
M/R/N Complex 0.068 0.024 -9999 0 -0.124 4 4
MRE11A 0.036 0.004 -9999 0 0 7 7
DNA-PK 0.057 0.047 -9999 0 -0.142 19 19
FA complex/FANCD2/Ubiquitin 0.002 0.085 -9999 0 -0.286 23 23
FANCF 0.035 0.007 -9999 0 0 20 20
BRCA1 0.035 0.006 -9999 0 0 16 16
CCNE1 0.032 0.012 -9999 0 0 61 61
CDK2/Cyclin E1 0.044 0.024 -9999 0 -0.142 2 2
FANCG 0.03 0.014 -9999 0 0 81 81
BRCA1/BACH1/BARD1 0.045 0.036 -9999 0 -0.142 16 16
FANCE 0.036 0.004 -9999 0 0 6 6
FANCC 0.035 0.006 -9999 0 0 16 16
NBN 0.035 0.005 -9999 0 0 11 11
FANCA 0.035 0.007 -9999 0 0 18 18
DNA repair -0.016 0.085 0.224 8 -0.304 13 21
BRCA1/BARD1/ubiquitin 0.045 0.036 -9999 0 -0.142 16 16
BARD1/DNA-PK 0.069 0.063 -9999 0 -0.139 30 30
FANCL 0 0 -9999 0 -9999 0 0
mRNA polyadenylation -0.045 0.036 0.141 16 -9999 0 16
BRCA1/BARD1/CTIP/M/R/N Complex 0.011 0.064 -9999 0 -0.224 23 23
BRCA1/BACH1/BARD1/TopBP1 0.051 0.061 -9999 0 -0.135 42 42
BRCA1/BARD1/P53 0.064 0.067 -9999 0 -0.132 41 41
BARD1/CSTF1/BRCA1 0.062 0.039 -9999 0 -0.124 16 16
BRCA1/BACH1 0.035 0.006 -9999 0 0 16 16
BARD1 0.035 0.007 -9999 0 0 18 18
PCNA 0.033 0.01 -9999 0 0 44 44
BRCA1/BARD1/UbcH5C 0.063 0.041 -9999 0 -0.134 17 17
BRCA1/BARD1/UbcH7 0.059 0.044 -9999 0 -0.133 19 19
BRCA1/BARD1/RAD51/PCNA 0.069 0.061 -9999 0 -0.13 32 32
BARD1/DNA-PK/P53 0.066 0.081 -9999 0 -0.133 51 51
BRCA1/BARD1/Ubiquitin 0.045 0.036 -9999 0 -0.142 16 16
BRCA1/BARD1/CTIP 0.039 0.058 -9999 0 -0.136 41 41
FA complex 0.013 0.056 -9999 0 -0.196 21 21
BARD1/EWS 0.043 0.037 -9999 0 -0.142 16 16
RBBP8 -0.019 0.008 -9999 0 -9999 0 0
TP53 0.031 0.013 -9999 0 0 75 75
TOPBP1 0.033 0.011 -9999 0 0 48 48
G1/S transition of mitotic cell cycle -0.062 0.066 0.131 41 -9999 0 41
BRCA1/BARD1 0.081 0.058 -9999 0 -0.129 18 18
CSTF1 0.035 0.006 -9999 0 0 14 14
BARD1/EWS-Fli1 0.021 0.028 -9999 0 -0.132 16 16
CDK2 0.033 0.01 -9999 0 0 40 40
UniProt:Q9BZD1 0 0 -9999 0 -9999 0 0
RAD51 0.035 0.007 -9999 0 0 17 17
RAD50 0.035 0.006 -9999 0 0 12 12
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.045 0.036 -9999 0 -0.142 16 16
EWSR1 0.033 0.01 -9999 0 0 37 37
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.029 0.156 -9999 0 -0.987 10 10
CLOCK 0.033 0.019 -9999 0 -0.066 10 10
TIMELESS/CRY2 0.023 0.16 -9999 0 -1.02 10 10
DEC1/BMAL1 0.032 0.057 -9999 0 -0.128 49 49
ATR 0.034 0.008 -9999 0 0 24 24
NR1D1 0.013 0.064 -9999 0 -0.381 2 2
ARNTL 0.031 0.02 -9999 0 -0.069 8 8
TIMELESS -0.002 0.163 -9999 0 -1.085 10 10
NPAS2 0.036 0.017 -9999 0 -0.066 10 10
CRY2 0.035 0.007 -9999 0 0 21 21
mol:CO -0.009 0.027 0.127 10 -0.069 44 54
CHEK1 0.033 0.011 -9999 0 0 49 49
mol:HEME 0.009 0.027 0.069 44 -0.127 10 54
PER1 0.032 0.011 -9999 0 0 51 51
BMAL/CLOCK/NPAS2 0.053 0.075 0.228 1 -0.143 48 49
BMAL1/CLOCK 0.008 0.121 -9999 0 -0.512 18 18
S phase of mitotic cell cycle 0.029 0.156 -9999 0 -0.987 10 10
TIMELESS/CHEK1/ATR 0.029 0.161 -9999 0 -1.017 10 10
mol:NADPH 0.009 0.027 0.069 44 -0.127 10 54
PER1/TIMELESS 0.021 0.16 -9999 0 -1.026 10 10
PER1-2 / CRY1-2 0 0 -9999 0 -9999 0 0
DEC1 0.035 0.006 -9999 0 0 13 13
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.052 0.095 -9999 0 -0.197 50 50
Ran/GTP/Exportin 1/HDAC1 -0.028 0.022 -9999 0 -0.112 25 25
NF kappa B1 p50/RelA/I kappa B alpha 0.006 0.107 -9999 0 -0.257 52 52
SUMO1 0.036 0.003 -9999 0 0 3 3
ZFPM1 0 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.007 0.033 -9999 0 -0.146 20 20
FKBP3 0.034 0.009 -9999 0 0 30 30
Histones 0.034 0.075 -9999 0 -0.236 22 22
YY1/LSF 0.013 0.065 -9999 0 -0.139 65 65
SMG5 0 0 -9999 0 -9999 0 0
RAN 0.035 0.006 -9999 0 0 13 13
I kappa B alpha/HDAC3 0.001 0.077 -9999 0 -0.205 49 49
I kappa B alpha/HDAC1 0.011 0.094 -9999 0 -0.23 52 52
SAP18 0.033 0.01 -9999 0 0 39 39
RELA -0.004 0.081 0.187 1 -0.281 18 19
HDAC1/Smad7 0.045 0.04 -9999 0 -0.124 7 7
RANGAP1 0.033 0.01 -9999 0 0 43 43
HDAC3/TR2 0.026 0.07 -9999 0 -0.26 19 19
NuRD/MBD3 Complex -0.009 0.116 -9999 0 -0.337 37 37
NF kappa B1 p50/RelA 0.01 0.09 -9999 0 -0.319 16 16
EntrezGene:23225 0 0 -9999 0 -9999 0 0
GATA2 0.035 0.006 -9999 0 0 14 14
GATA1 0.036 0 -9999 0 -9999 0 0
Mad/Max 0.051 0.012 -9999 0 -9999 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.008 0.111 -9999 0 -0.342 34 34
RBBP7 0.036 0.005 -9999 0 0 8 8
NPC 0.017 0.021 -9999 0 -0.088 18 18
RBBP4 0.032 0.011 -9999 0 0 53 53
MAX 0.034 0.008 -9999 0 0 24 24
EntrezGene:9972 0 0 -9999 0 -9999 0 0
FBXW11 0.035 0.007 -9999 0 0 20 20
NFKBIA 0.002 0.078 -9999 0 -0.328 21 21
KAT2B 0 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
SIN3/HDAC complex -0.007 0.087 -9999 0 -0.294 27 27
SIN3 complex 0.054 0.042 -9999 0 -0.124 18 18
SMURF1 0.026 0.016 -9999 0 0 136 136
CHD3 0.035 0.006 -9999 0 0 12 12
SAP30 0.035 0.006 -9999 0 0 15 15
EntrezGene:23636 0 0 -9999 0 -9999 0 0
NCOR1 0.034 0.008 -9999 0 0 25 25
YY1/HDAC3 -0.003 0.078 -9999 0 -0.252 28 28
YY1/HDAC2 0.013 0.063 -9999 0 -0.139 59 59
YY1/HDAC1 0.015 0.064 -9999 0 -0.217 20 20
NuRD/MBD2 Complex (MeCP1) -0.002 0.096 -9999 0 -0.285 34 34
PPARG -0.001 0.08 -9999 0 -0.209 54 54
HDAC8/hEST1B 0.023 0.006 -9999 0 -9999 0 0
UBE2I 0.036 0.003 -9999 0 0 3 3
beta TrCP1/SCF ubiquitin ligase complex 0.035 0.007 -9999 0 0 20 20
TNFRSF1A 0.032 0.012 -9999 0 0 61 61
HDAC3/SMRT (N-CoR2) 0.025 0.071 -9999 0 -0.26 19 19
MBD3L2 0 0 -9999 0 -9999 0 0
ubiquitin-dependent protein catabolic process 0.044 0.04 -9999 0 -0.123 7 7
CREBBP 0.036 0.004 -9999 0 0 5 5
NuRD/MBD3/MBD3L2 Complex -0.005 0.108 -9999 0 -0.297 41 41
HDAC1 0.035 0.007 -9999 0 0 20 20
HDAC3 0.007 0.061 -9999 0 -0.296 13 13
HDAC2 0.032 0.011 -9999 0 0 50 50
YY1 0.009 0.035 -9999 0 -0.227 9 9
HDAC8 0 0 -9999 0 -9999 0 0
SMAD7 0.034 0.01 -9999 0 0 36 36
NCOR2 0.036 0.003 -9999 0 0 4 4
MXD1 0.036 0.003 -9999 0 0 4 4
STAT3 0.004 0.066 -9999 0 -0.225 34 34
NFKB1 0.035 0.007 -9999 0 0 17 17
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.034 0.008 -9999 0 0 24 24
YY1/LSF/HDAC1 0.028 0.072 -9999 0 -0.212 20 20
YY1/SAP30/HDAC1 0.029 0.071 -9999 0 -0.206 20 20
EP300 0.033 0.011 -9999 0 0 49 49
STAT3 (dimer non-phopshorylated) 0.004 0.066 -9999 0 -0.225 34 34
proteasomal ubiquitin-dependent protein catabolic process 0 0.081 -9999 0 -0.321 24 24
histone deacetylation -0.003 0.097 -9999 0 -0.271 38 38
STAT3 (dimer non-phopshorylated)/HDAC3 -0.001 0.095 -9999 0 -0.319 26 26
nuclear export -0.023 0.006 -9999 0 -9999 0 0
PRKACA 0.034 0.009 -9999 0 0 29 29
GATAD2B 0 0 -9999 0 -9999 0 0
GATAD2A 0.032 0.012 -9999 0 0 59 59
GATA2/HDAC3 0.025 0.07 -9999 0 -0.255 19 19
GATA1/HDAC1 0.05 0.023 -9999 0 -0.142 6 6
GATA1/HDAC3 0.026 0.071 -9999 0 -0.26 19 19
CHD4 0.033 0.01 -9999 0 0 38 38
TNF-alpha/TNFR1A 0.035 0.055 -9999 0 -0.141 41 41
SIN3/HDAC complex/Mad/Max -0.001 0.085 -9999 0 -0.299 23 23
NuRD Complex -0.003 0.11 -9999 0 -0.338 33 33
positive regulation of chromatin silencing 0.032 0.074 -9999 0 -0.233 22 22
SIN3B 0.034 0.009 -9999 0 0 35 35
MTA2 0.036 0.004 -9999 0 0 7 7
SIN3A 0 0 -9999 0 -9999 0 0
XPO1 0.036 0.004 -9999 0 0 5 5
SUMO1/HDAC1 0.036 0.054 -9999 0 -0.22 5 5
HDAC complex 0.066 0.07 -9999 0 -0.152 36 36
GATA1/Fog1 0.027 0 -9999 0 -9999 0 0
FKBP25/HDAC1/HDAC2 0.055 0.047 -9999 0 -0.143 18 18
TNF 0.036 0.004 -9999 0 0 6 6
negative regulation of cell growth -0.001 0.084 -9999 0 -0.291 24 24
NuRD/MBD2/PRMT5 Complex -0.002 0.096 -9999 0 -0.285 34 34
Ran/GTP/Exportin 1 0.035 0.058 -9999 0 -0.159 20 20
NF kappa B/RelA/I kappa B alpha -0.008 0.097 -9999 0 -0.259 51 51
SIN3/HDAC complex/NCoR1 -0.001 0.093 -9999 0 -0.321 24 24
TFCP2 0.035 0.008 -9999 0 0 22 22
NR2C1 0.036 0.004 -9999 0 0 5 5
MBD3 0.032 0.011 -9999 0 0 51 51
MBD2 0.035 0.006 -9999 0 0 15 15
TRAIL signaling pathway

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
TNFSF10 0.029 0.015 -9999 0 0 97 97
positive regulation of NF-kappaB transcription factor activity 0.035 0.044 -9999 0 -0.141 23 23
MAP2K4 0.014 0.054 0.212 2 -0.25 6 8
IKBKB 0.036 0.004 -9999 0 0 6 6
TNFRSF10B 0.034 0.008 -9999 0 0 24 24
TNFRSF10A 0 0 -9999 0 -9999 0 0
SMPD1 0.014 0.027 -9999 0 -0.106 18 18
IKBKG 0.036 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
TNFRSF10D 0.035 0.005 -9999 0 0 11 11
TRAIL/TRAILR2 0.035 0.044 -9999 0 -0.141 22 22
TRAIL/TRAILR3 0.035 0.044 -9999 0 -0.141 23 23
TRAIL/TRAILR1 0.015 0.035 -9999 0 -0.132 24 24
TRAIL/TRAILR4 0.035 0.044 -9999 0 -0.141 23 23
TRAIL/TRAILR1/DAP3/GTP 0.029 0.039 -9999 0 -0.105 31 31
IKK complex -0.023 0.11 -9999 0 -0.22 106 106
RIPK1 0.035 0.007 -9999 0 0 18 18
response to oxidative stress 0 0 -9999 0 -9999 0 0
DAP3/GTP 0.022 0.024 -9999 0 -0.132 11 11
MAPK3 -0.018 0.009 -9999 0 -9999 0 0
MAP3K1 0.022 0.053 -9999 0 -0.244 7 7
TRAILR4 (trimer) 0.035 0.005 -9999 0 0 11 11
TRADD 0.036 0.004 -9999 0 0 7 7
TRAILR1 (trimer) 0 0 -9999 0 -9999 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.017 0.048 -9999 0 -0.164 23 23
CFLAR 0.036 0.005 -9999 0 0 9 9
MAPK1 -0.016 0.01 -9999 0 -9999 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP 0.069 0.046 -9999 0 -0.107 24 24
mol:ceramide 0.014 0.027 -9999 0 -0.105 18 18
FADD 0.035 0.006 -9999 0 0 13 13
MAPK8 0.008 0.041 0.193 1 -0.247 5 6
TRAF2 0.035 0.006 -9999 0 0 14 14
TRAILR3 (trimer) 0.035 0.006 -9999 0 0 15 15
CHUK 0.026 0.016 -9999 0 0 133 133
TRAIL/TRAILR1/FADD 0.033 0.038 -9999 0 -0.115 24 24
DAP3 0.034 0.008 -9999 0 0 28 28
CASP10 -0.005 0.05 0.136 14 -0.165 21 35
JNK cascade 0.035 0.044 -9999 0 -0.141 23 23
TRAIL (trimer) 0.029 0.014 -9999 0 0 97 97
TNFRSF10C 0.035 0.006 -9999 0 0 15 15
TRAIL/TRAILR1/DAP3/GTP/FADD 0.041 0.047 -9999 0 -0.107 31 31
TRAIL/TRAILR2/FADD 0.05 0.048 -9999 0 -0.122 22 22
cell death 0.014 0.027 -9999 0 -0.105 18 18
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.022 0.051 -9999 0 -0.219 6 6
TRAILR2 (trimer) 0.034 0.008 -9999 0 0 24 24
CASP8 0.015 0.029 -9999 0 -9999 0 0
negative regulation of caspase activity 0 0 -9999 0 -9999 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.085 0.055 -9999 0 -0.114 22 22
E-cadherin signaling events

Figure 108.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 110.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.061 0.029 -9999 0 -0.124 2 2
E-cadherin/beta catenin 0.047 0.021 -9999 0 -0.142 2 2
CTNNB1 0.035 0.007 -9999 0 0 21 21
JUP 0.032 0.011 -9999 0 0 50 50
CDH1 0.033 0.01 -9999 0 0 37 37
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.026 0.078 -9999 0 -0.222 25 25
CaM/Ca2+ 0.021 0.025 -9999 0 -0.132 12 12
AKT1 0.032 0.011 -9999 0 0 53 53
AKT2 0.034 0.008 -9999 0 0 26 26
STXBP4 0 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
mol:glucose 0.006 0.075 0.167 1 -0.233 27 28
YWHAZ 0.035 0.007 -9999 0 0 17 17
CALM1 0.033 0.011 -9999 0 0 49 49
YWHAQ 0.036 0.005 -9999 0 0 8 8
TBC1D4 -0.018 0.008 -9999 0 -9999 0 0
mol:Ca2+ 0 0 -9999 0 -9999 0 0
YWHAH 0.031 0.013 -9999 0 0 74 74
YWHAB 0.035 0.007 -9999 0 0 21 21
SNARE/Synip 0.02 0.018 -9999 0 -0.107 8 8
YWHAG 0 0 -9999 0 -9999 0 0
ASIP 0.035 0.006 -9999 0 0 16 16
PRKCI 0.034 0.008 -9999 0 0 25 25
AS160/CaM/Ca2+ 0.021 0.025 -9999 0 -0.132 12 12
RHOQ 0.035 0.006 -9999 0 0 14 14
GYS1 0.001 0.036 0.246 1 -0.213 5 6
PRKCZ 0 0 -9999 0 -9999 0 0
TRIP10 0.033 0.01 -9999 0 0 39 39
TC10/GTP/CIP4/Exocyst 0.041 0.029 -9999 0 -0.115 13 13
AS160/14-3-3 -0.006 0.098 -9999 0 -0.4 18 18
VAMP2 0.033 0.011 -9999 0 0 47 47
SLC2A4 0.005 0.08 0.172 1 -0.254 27 28
STX4 0 0 -9999 0 -9999 0 0
GSK3B 0.004 0.077 -9999 0 -0.307 25 25
SFN 0.031 0.013 -9999 0 0 74 74
LNPEP 0.036 0.005 -9999 0 0 9 9
YWHAE 0.034 0.009 -9999 0 0 29 29
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.012 0.15 0.348 21 -1 8 29
VDR 0.035 0.007 -9999 0 0 17 17
FAM120B 0 0 -9999 0 -9999 0 0
RXRs/LXRs/DNA/9cRA 0.011 0.098 0.244 2 -0.272 39 41
RXRs/LXRs/DNA/Oxysterols 0.005 0.139 0.298 2 -0.393 44 46
MED1 0 0 -9999 0 -9999 0 0
mol:9cRA 0 0.016 0.045 3 -0.047 43 46
RARs/THRs/DNA/Src-1 0.018 0.051 -9999 0 -0.155 35 35
RXRs/NUR77 0.077 0.065 -9999 0 -0.112 31 31
RXRs/PPAR 0.018 0.048 -9999 0 -0.185 5 5
NCOR2 0.036 0.003 -9999 0 0 4 4
VDR/VDR/Vit D3 0.026 0.005 -9999 0 -9999 0 0
RARs/VDR/DNA/Vit D3 0.081 0.022 -9999 0 -9999 0 0
RARA 0.036 0.003 -9999 0 0 3 3
NCOA1 0.033 0.01 -9999 0 0 43 43
VDR/VDR/DNA 0.035 0.007 -9999 0 0 17 17
RARs/RARs/DNA/9cRA 0.055 0.032 -9999 0 -9999 0 0
RARG 0.036 0.005 -9999 0 0 8 8
RPS6KB1 -0.005 0.081 0.498 6 -0.401 8 14
RARs/THRs/DNA/SMRT 0.03 0.024 -9999 0 -0.177 5 5
THRA 0.035 0.005 -9999 0 0 11 11
mol:Bile acids 0 0 -9999 0 -9999 0 0
VDR/Vit D3/DNA 0.026 0.005 -9999 0 -9999 0 0
RXRs/PPAR/9cRA/PGJ2/DNA 0.057 0.074 0.285 3 -0.152 39 42
NR1H4 0.036 0.003 -9999 0 0 3 3
RXRs/LXRs/DNA 0.081 0.104 0.305 2 -0.213 39 41
NR1H2 0.028 0.031 0.088 2 -0.06 45 47
NR1H3 0.03 0.032 0.089 2 -0.067 42 44
RXRs/VDR/DNA/Vit D3 0.07 0.061 0.203 1 -0.103 36 37
NR4A1 0.035 0.006 -9999 0 0 12 12
mol:ATRA 0 0 -9999 0 -9999 0 0
RXRs/FXR/9cRA/MED1 0.016 0.04 0.129 1 -0.148 4 5
RXRG 0.03 0.029 0.087 2 -0.058 44 46
RXR alpha/CCPG 0.022 0.021 -9999 0 -0.062 6 6
RXRA 0.03 0.03 0.087 2 -0.059 44 46
RXRB 0.031 0.032 0.088 1 -0.064 47 48
THRB 0.036 0.004 -9999 0 0 6 6
PPARG 0.034 0.008 -9999 0 0 24 24
PPARD 0.036 0.003 -9999 0 0 3 3
TNF 0 0.128 -9999 0 -0.379 39 39
mol:Oxysterols 0 0.015 0.045 3 -0.041 47 50
cholesterol transport 0.005 0.138 0.297 2 -0.389 44 46
PPARA 0.033 0.01 -9999 0 0 44 44
mol:Vit D3 0 0 -9999 0 -9999 0 0
RARB 0.035 0.005 -9999 0 0 10 10
RXRs/NUR77/BCL2 0.02 0.03 -9999 0 -0.159 1 1
SREBF1 -0.01 0.163 -9999 0 -0.468 40 40
RXRs/RXRs/DNA/9cRA 0.057 0.074 0.281 3 -0.152 39 42
ABCA1 -0.044 0.256 -9999 0 -0.82 45 45
RARs/THRs 0.103 0.025 -9999 0 -0.116 1 1
RXRs/FXR 0.078 0.065 -9999 0 -0.112 31 31
BCL2 0.035 0.007 -9999 0 0 17 17
Atypical NF-kappaB 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
BCL3/RelA 0.049 0.019 -9999 0 -0.142 2 2
FBXW11 0.035 0.007 -9999 0 0 20 20
NF kappa B1 p50/c-Rel 0.032 0.018 -9999 0 -0.123 5 5
NF kappa B1 p50/RelA/I kappa B alpha 0.024 0.065 -9999 0 -0.257 11 11
NFKBIA 0.004 0.053 -9999 0 -0.173 24 24
MAPK14 0.036 0.004 -9999 0 0 6 6
NF kappa B1 p105/p50 0.028 0.031 -9999 0 -0.129 16 16
ARRB2 0.011 0.026 -9999 0 -0.2 7 7
REL 0.036 0.002 -9999 0 0 2 2
response to oxidative stress 0 0 -9999 0 -9999 0 0
BCL3/NF kappa B1 p50 0.031 0.019 -9999 0 -0.123 5 5
response to UV 0 0 -9999 0 -9999 0 0
NF kappa B1 p105/RelA 0.031 0.021 -9999 0 -0.124 7 7
PIK3CA 0.03 0.014 -9999 0 0 85 85
NF kappa B1 p50 dimer 0.023 0.025 0.172 6 -0.142 5 11
PIK3R1 0.032 0.012 -9999 0 0 61 61
NFKB1 -0.021 0.005 -9999 0 -9999 0 0
RELA 0.035 0.005 -9999 0 0 10 10
positive regulation of anti-apoptosis 0.013 0.036 -9999 0 -0.137 18 18
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.025 0.069 -9999 0 -0.252 12 12
SRC 0.035 0.006 -9999 0 0 13 13
PI3K 0.016 0.075 -9999 0 -0.155 73 73
NF kappa B1 p50/RelA 0.013 0.036 -9999 0 -0.138 18 18
IKBKB 0.036 0.004 -9999 0 0 6 6
beta TrCP1/SCF ubiquitin ligase complex 0.035 0.007 -9999 0 0 20 20
SYK 0.031 0.013 -9999 0 0 71 71
I kappa B alpha/PIK3R1 0.016 0.067 -9999 0 -0.204 29 29
cell death 0.024 0.067 -9999 0 -0.242 12 12
NF kappa B1 p105/c-Rel 0.032 0.018 -9999 0 -0.123 5 5
LCK 0.035 0.007 -9999 0 0 17 17
BCL3 0.034 0.009 -9999 0 0 31 31
IL27-mediated signaling events

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
TGFB1 0.032 0.012 -9999 0 0 62 62
CD4-positive alpha-beta T cell lineage commitment 0 0 -9999 0 -9999 0 0
cytokine production during immune response -0.005 0.058 0.408 2 -9999 0 2
IL27/IL27R/JAK1 0.041 0.064 -9999 0 -9999 0 0
TBX21 -0.007 0.099 0.345 19 -9999 0 19
IL12B 0.036 0.004 -9999 0 0 6 6
IL12A -0.011 0.002 0.013 2 -9999 0 2
IL6ST 0.034 0.011 -9999 0 -0.032 1 1
IL27RA/JAK1 0.03 0.051 -9999 0 -9999 0 0
IL27 0 0.004 -9999 0 -9999 0 0
TYK2 0.033 0.012 -9999 0 -0.032 1 1
T-helper cell lineage commitment 0.05 0.074 0.172 109 -0.181 2 111
T-helper 2 cell differentiation -0.005 0.058 0.408 2 -9999 0 2
T cell proliferation during immune response -0.005 0.058 0.408 2 -9999 0 2
MAPKKK cascade 0.005 0.058 -9999 0 -0.408 2 2
STAT3 0.033 0.01 -9999 0 0 37 37
STAT2 0.035 0.007 -9999 0 0 17 17
STAT1 0.033 0.01 -9999 0 0 40 40
IL12RB1 0.034 0.009 -9999 0 0 30 30
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -9999 0 -9999 0 0
IL12RB2 -0.007 0.099 0.346 19 -9999 0 19
IL27/IL27R/JAK2/TYK2 0.005 0.058 -9999 0 -0.412 2 2
positive regulation of T cell mediated cytotoxicity 0.005 0.058 -9999 0 -0.408 2 2
STAT1 (dimer) 0.046 0.08 -9999 0 -9999 0 0
JAK2 0.029 0.014 -9999 0 -0.031 1 1
JAK1 0.033 0.01 -9999 0 0 37 37
STAT2 (dimer) 0.021 0.096 -9999 0 -0.331 10 10
T cell proliferation 0.007 0.06 -9999 0 -0.313 4 4
IL12/IL12R/TYK2/JAK2 0.005 0.183 -9999 0 -0.764 25 25
IL17A 0.043 0.07 0.175 88 -0.12 7 95
mast cell activation -0.005 0.058 0.408 2 -9999 0 2
IFNG 0.004 0.028 -9999 0 -0.089 19 19
T cell differentiation -0.001 0.003 -9999 0 -0.017 10 10
STAT3 (dimer) 0.017 0.104 -9999 0 -0.379 11 11
STAT5A (dimer) 0.022 0.097 -9999 0 -0.331 10 10
STAT4 (dimer) 0.021 0.095 -9999 0 -0.341 7 7
STAT4 0.034 0.009 -9999 0 0 30 30
T cell activation -0.004 0.005 -9999 0 -0.083 1 1
IL27R/JAK2/TYK2 0.035 0.064 -9999 0 -9999 0 0
GATA3 0.003 0.073 0.632 6 -9999 0 6
IL18 -0.01 0.004 0 69 -9999 0 69
positive regulation of mast cell cytokine production 0.017 0.103 -9999 0 -0.373 11 11
IL27/EBI3 0.024 0.012 -9999 0 -9999 0 0
IL27RA 0.005 0.037 -9999 0 -9999 0 0
IL6 0.021 0.018 -9999 0 0 199 199
STAT5A 0.036 0.004 -9999 0 0 6 6
monocyte differentiation 0 0 -9999 0 -9999 0 0
IL2 -0.007 0.028 -9999 0 -9999 0 0
IL1B -0.009 0.004 0 99 -9999 0 99
EBI3 0.033 0.012 -9999 0 -0.032 1 1
TNF -0.011 0.001 0 6 -9999 0 6
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.057 0.04 -9999 0 -0.114 19 19
HDAC3 0.036 0.005 -9999 0 0 8 8
Ran/GTP/Exportin 1/HDAC4 -0.029 0.023 -9999 0 -0.106 33 33
GATA1/HDAC4 0.047 0.032 -9999 0 -0.142 13 13
GATA1/HDAC5 0.052 0.013 -9999 0 -0.142 1 1
GATA2/HDAC5 0.05 0.015 -9999 0 -0.142 1 1
HDAC5/BCL6/BCoR 0.05 0.052 -9999 0 -0.127 29 29
HDAC9 0.023 0.017 -9999 0 0 178 178
Glucocorticoid receptor/Hsp90/HDAC6 0.043 0.029 -9999 0 -0.115 15 15
HDAC4/ANKRA2 0.044 0.038 -9999 0 -0.142 18 18
HDAC5/YWHAB 0.048 0.027 -9999 0 -0.16 6 6
NPC/RanGAP1/SUMO1/Ubc9 0.007 0.033 -9999 0 -0.146 20 20
GATA2 0.035 0.006 -9999 0 0 14 14
HDAC4/RFXANK 0.038 0.047 -9999 0 -0.146 27 27
BCOR 0.034 0.009 -9999 0 0 35 35
mol:GTP 0 0 -9999 0 -9999 0 0
HDAC10 0 0 -9999 0 -9999 0 0
HDAC5 0.035 0.006 -9999 0 0 15 15
GNB1/GNG2 0.019 0.032 -9999 0 -0.132 20 20
Histones 0.019 0.064 -9999 0 -0.161 39 39
ADRBK1 0.035 0.006 -9999 0 0 14 14
HDAC4 0.034 0.008 -9999 0 0 24 24
XPO1 0.036 0.004 -9999 0 0 5 5
HDAC5/ANKRA2 0.049 0.024 -9999 0 -0.142 6 6
HDAC4/Ubc9 0.047 0.033 -9999 0 -0.142 13 13
HDAC7 0 0 -9999 0 -9999 0 0
HDAC5/14-3-3 E 0.046 0.031 -9999 0 -0.142 11 11
TUBA1B 0 0 -9999 0 -9999 0 0
HDAC6 0.036 0 -9999 0 -9999 0 0
HDAC5/RFXANK 0.042 0.037 -9999 0 -0.142 16 16
CAMK4 0.036 0.004 -9999 0 0 7 7
Tubulin/HDAC6 0.036 0.044 -9999 0 -0.115 37 37
SUMO1 0.036 0.003 -9999 0 0 3 3
EntrezGene:9972 0 0 -9999 0 -9999 0 0
YWHAB 0.035 0.007 -9999 0 0 21 21
GATA1 0.036 0 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
YWHAE 0.034 0.009 -9999 0 0 29 29
NR3C1 0.034 0.008 -9999 0 0 24 24
SUMO1/HDAC4 0.034 0.056 -9999 0 -0.222 5 5
SRF 0.036 0.002 -9999 0 0 2 2
HDAC4/YWHAB 0.044 0.04 -9999 0 -0.154 17 17
Tubulin 0.014 0.042 -9999 0 -0.132 37 37
HDAC4/14-3-3 E 0.042 0.043 -9999 0 -0.147 22 22
GNB1 0.033 0.01 -9999 0 0 37 37
RANGAP1 0.033 0.01 -9999 0 0 43 43
BCL6/BCoR 0.034 0.048 -9999 0 -0.142 29 29
HDAC4/HDAC3/SMRT (N-CoR2) 0.065 0.036 -9999 0 -0.123 14 14
HDAC4/SRF 0.066 0.033 -9999 0 -0.124 12 12
HDAC4/ER alpha 0.044 0.034 -9999 0 -0.139 13 13
EntrezGene:23225 0 0 -9999 0 -9999 0 0
positive regulation of chromatin silencing 0.019 0.064 -9999 0 -0.16 39 39
cell motility 0.035 0.044 -9999 0 -0.115 37 37
EntrezGene:23636 0 0 -9999 0 -9999 0 0
UBE2I 0.036 0.003 -9999 0 0 3 3
HDAC7/HDAC3 0.026 0.008 -9999 0 -0.132 1 1
BCL6 0.031 0.013 -9999 0 0 72 72
HDAC4/CaMK II delta B 0.034 0.008 -9999 0 0 24 24
Hsp90/HDAC6 0.027 0 -9999 0 -9999 0 0
ESR1 0.034 0.009 -9999 0 0 34 34
HDAC6/HDAC11 0.053 0.006 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0.035 0.058 -9999 0 -0.159 20 20
NPC 0.017 0.021 -9999 0 -0.088 18 18
MEF2C 0.034 0.008 -9999 0 0 27 27
RAN 0.035 0.006 -9999 0 0 13 13
HDAC4/MEF2C 0.092 0.053 -9999 0 -0.119 24 24
GNG2 0 0 -9999 0 -9999 0 0
NCOR2 0.036 0.003 -9999 0 0 4 4
TUBB2A 0.033 0.011 -9999 0 0 45 45
HDAC11 0.036 0.004 -9999 0 0 6 6
HSP90AA1 0 0 -9999 0 -9999 0 0
RANBP2 0.034 0.008 -9999 0 0 24 24
ANKRA2 0.035 0.006 -9999 0 0 12 12
RFXANK 0.033 0.011 -9999 0 0 46 46
nuclear import -0.029 0.057 0.212 23 -9999 0 23
Cellular roles of Anthrax toxin

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
ANTXR1 0.035 0.007 -9999 0 0 17 17
ANTXR2 0 0 -9999 0 -9999 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0 -9999 0 -9999 0 0
monocyte activation -0.07 0.163 -9999 0 -0.339 130 130
MAP2K2 0.018 0.04 -9999 0 -0.587 2 2
MAP2K1 -0.008 0.002 -9999 0 -9999 0 0
MAP2K7 -0.008 0.003 -9999 0 -9999 0 0
MAP2K6 -0.008 0.002 -9999 0 -9999 0 0
CYAA -0.007 0.001 -9999 0 -9999 0 0
MAP2K4 -0.008 0.002 -9999 0 -9999 0 0
IL1B 0.001 0.04 0.083 69 -0.075 53 122
Channel 0.022 0.004 -9999 0 -9999 0 0
NLRP1 -0.001 0 -9999 0 -9999 0 0
CALM1 0.033 0.011 -9999 0 0 49 49
negative regulation of phagocytosis -0.017 0.115 -9999 0 -0.411 38 38
mol:Ca2+ 0 0 -9999 0 -9999 0 0
regulation of endothelial cell proliferation 0.001 0 -9999 0 -9999 0 0
MAPK3 -0.008 0.002 -9999 0 -9999 0 0
MAPK1 -0.008 0.003 -9999 0 -9999 0 0
PGR -0.008 0.002 -9999 0 -9999 0 0
PA/Cellular Receptors 0.024 0.005 -9999 0 -9999 0 0
apoptosis -0.001 0 -9999 0 -9999 0 0
LOC728358 0 0 -9999 0 -9999 0 0
Lethal toxin (unfolded) 0.022 0.004 -9999 0 -9999 0 0
macrophage activation -0.012 0.012 0.07 8 -9999 0 8
TNF 0.036 0.004 -9999 0 0 6 6
VCAM1 -0.073 0.162 -9999 0 -0.342 128 128
platelet activation -0.017 0.115 -9999 0 -0.411 38 38
MAPKKK cascade 0.002 0.022 0.064 3 -0.07 33 36
IL18 -0.005 0.035 0.085 38 -0.075 56 94
negative regulation of macrophage activation -0.001 0 -9999 0 -9999 0 0
LEF -0.001 0 -9999 0 -9999 0 0
CASP1 0.003 0.004 0.025 12 -9999 0 12
mol:cAMP -0.017 0.116 -9999 0 -0.414 38 38
necrosis -0.001 0 -9999 0 -9999 0 0
intracellular pH reduction 0 0 -9999 0 -9999 0 0
PAGA 0 0 -9999 0 -9999 0 0
Edema toxin (unfolded) 0.022 0.004 -9999 0 -9999 0 0
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -9999 0 -9999 0 0
Signaling mediated by p38-alpha and p38-beta

Figure 115.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 117.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTGS2 0.045 0.063 -9999 0 -9999 0 0
MKNK1 0.034 0.009 -9999 0 0 31 31
MAPK14 0.046 0.037 0.156 3 -0.082 22 25
ATF2/c-Jun 0 0.093 -9999 0 -0.319 31 31
MAPK11 0.043 0.038 0.156 3 -0.082 22 25
MITF 0.032 0.048 0.191 2 -0.205 6 8
MAPKAPK5 0.034 0.038 0.18 3 -9999 0 3
KRT8 0.035 0.039 0.205 2 -9999 0 2
MAPKAPK3 0.035 0.006 -9999 0 0 16 16
MAPKAPK2 0.035 0.006 -9999 0 0 14 14
p38alpha-beta/CK2 0.061 0.056 0.224 3 -9999 0 3
CEBPB 0.025 0.068 0.219 2 -0.211 24 26
SLC9A1 0.032 0.041 0.162 1 -0.255 2 3
mol:GDP 0 0 -9999 0 -9999 0 0
ATF2 0.032 0.054 0.261 4 -0.259 1 5
p38alpha-beta/MNK1 0.064 0.067 -9999 0 -0.144 17 17
JUN -0.004 0.091 -9999 0 -0.321 30 30
PPARGC1A 0.032 0.057 0.182 6 -0.212 13 19
USF1 0.028 0.037 0.174 3 -9999 0 3
RAB5/GDP/GDI1 0.013 0.076 -9999 0 -0.213 26 26
NOS2 0.028 0.037 0.174 3 -9999 0 3
DDIT3 0.025 0.058 0.18 3 -0.198 17 20
RAB5A 0.034 0.009 -9999 0 0 29 29
HSPB1 0.075 0.127 0.285 119 -0.153 5 124
p38alpha-beta/HBP1 0.055 0.058 0.221 2 -9999 0 2
CREB1 0.024 0.068 0.224 1 -0.184 32 33
RAB5/GDP 0.019 0.034 -9999 0 -0.132 23 23
EIF4E -0.013 0.057 0.186 10 -0.192 7 17
RPS6KA4 0.034 0.038 0.18 3 -9999 0 3
PLA2G4A -0.012 0.052 0.19 5 -0.186 9 14
GDI1 0.023 0.061 0.219 1 -0.229 18 19
TP53 0.01 0.05 0.167 11 -9999 0 11
RPS6KA5 0.035 0.039 0.175 4 -9999 0 4
ESR1 0.032 0.038 0.191 2 -9999 0 2
HBP1 0.026 0.016 -9999 0 0 138 138
MEF2C 0.031 0.049 0.191 2 -0.217 7 9
MEF2A 0.03 0.048 0.219 1 -0.217 7 8
EIF4EBP1 0.021 0.073 0.224 1 -0.198 29 30
KRT19 0.035 0.039 0.191 3 -9999 0 3
ELK4 0.033 0.037 -9999 0 -9999 0 0
ATF6 0.033 0.037 0.161 2 -9999 0 2
ATF1 0.02 0.071 0.224 1 -0.189 28 29
p38alpha-beta/MAPKAPK2 0.072 0.055 0.211 2 -9999 0 2
p38alpha-beta/MAPKAPK3 0.072 0.056 0.217 3 -0.133 1 4
ceramide signaling pathway

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
MAP4K4 0.004 0.081 -9999 0 -0.292 17 17
BAG4 0.035 0.005 -9999 0 0 11 11
BAD -0.002 0.034 0.139 3 -0.135 9 12
NFKBIA 0.033 0.011 -9999 0 0 47 47
BIRC3 0.03 0.013 -9999 0 0 77 77
BAX 0.004 0.048 0.193 18 -0.134 7 25
EnzymeConsortium:3.1.4.12 0.004 0.021 -9999 0 -0.078 9 9
IKBKB -0.004 0.082 0.212 5 -0.288 16 21
MAP2K2 -0.004 0.058 0.167 36 -0.156 6 42
MAP2K1 -0.012 0.042 0.163 10 -0.158 7 17
SMPD1 0.003 0.027 -9999 0 -0.12 9 9
GO:0005551 0 0 -9999 0 -9999 0 0
FADD/Caspase 8 0.012 0.076 -9999 0 -0.315 8 8
MAP2K4 -0.006 0.034 0.179 2 -0.154 2 4
protein ubiquitination -0.005 0.081 0.209 1 -0.297 15 16
EnzymeConsortium:2.7.1.37 -0.01 0.05 0.158 13 -0.164 6 19
response to UV 0 0 0.002 15 -0.002 2 17
RAF1 -0.007 0.042 0.174 10 -0.144 8 18
CRADD 0.035 0.006 -9999 0 0 12 12
mol:ceramide 0.003 0.031 -9999 0 -0.119 10 10
I-kappa-B-alpha/RELA/p50/ubiquitin 0.04 0.031 -9999 0 -0.114 15 15
MADD 0.035 0.006 -9999 0 0 13 13
MAP3K1 -0.001 0.032 0.162 2 -0.138 4 6
TRADD 0.036 0.004 -9999 0 0 7 7
RELA/p50 0.035 0.005 -9999 0 0 10 10
MAPK3 -0.003 0.051 0.161 16 -0.156 6 22
MAPK1 -0.01 0.061 0.163 15 -0.202 14 29
p50/RELA/I-kappa-B-alpha 0.044 0.036 -9999 0 -0.141 15 15
FADD 0.009 0.071 -9999 0 -0.304 6 6
KSR1 -0.003 0.03 -9999 0 -0.132 6 6
MAPK8 -0.009 0.029 0.167 2 -0.156 1 3
TRAF2 0.035 0.006 -9999 0 0 14 14
response to radiation 0 0 0.002 1 -9999 0 1
CHUK -0.007 0.077 0.209 1 -0.292 14 15
TNF R/SODD 0.034 0.054 -9999 0 -0.142 40 40
TNF 0.036 0.004 -9999 0 0 6 6
CYCS 0.014 0.052 0.148 22 -0.142 4 26
IKBKG -0.005 0.079 0.209 1 -0.288 16 17
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.015 0.082 -9999 0 -0.333 9 9
RELA 0.035 0.005 -9999 0 0 10 10
RIPK1 0.035 0.007 -9999 0 0 18 18
AIFM1 -0.002 0.04 0.125 18 -0.125 9 27
TNF/TNF R/SODD 0.052 0.055 -9999 0 -0.123 39 39
TNFRSF1A 0.032 0.012 -9999 0 0 61 61
response to heat 0 0 0.002 1 -9999 0 1
CASP8 0.035 0.081 -9999 0 -0.597 7 7
NSMAF 0.007 0.081 0.219 6 -0.299 14 20
response to hydrogen peroxide 0 0 0.002 15 -0.002 2 17
BCL2 0.035 0.007 -9999 0 0 17 17
Arf6 trafficking events

Figure 117.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 119.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 0.035 0.006 -9999 0 0 13 13
CLTC 0.013 0.087 -9999 0 -0.35 20 20
calcium ion-dependent exocytosis 0.014 0.063 0.126 1 -0.223 15 16
Dynamin 2/GTP 0.025 0.011 -9999 0 -0.102 1 1
EXOC4 0 0 -9999 0 -9999 0 0
CD59 0.004 0.076 -9999 0 -0.29 22 22
CPE -0.014 0.008 -9999 0 -0.115 1 1
CTNNB1 0.035 0.007 -9999 0 0 21 21
membrane fusion 0.017 0.062 -9999 0 -0.165 28 28
CTNND1 -0.018 0.011 0.087 1 -0.181 1 2
DNM2 0.034 0.009 -9999 0 0 34 34
mol:PI-4-5-P2 0.011 0.068 0.157 2 -0.229 19 21
TSHR -0.016 0.008 0.091 1 -0.115 1 2
INS 0.01 0.083 -9999 0 -0.432 15 15
BIN1 0.031 0.013 -9999 0 0 73 73
mol:Choline 0.017 0.062 -9999 0 -0.165 28 28
growth hormone secretagogue receptor activity 0 0 -9999 0 -9999 0 0
mol:GDP -0.009 0.005 -9999 0 -0.106 1 1
membrane depolarization 0 0 -9999 0 -9999 0 0
ARF6 0.035 0.007 -9999 0 0 21 21
mol:Ca2+ 0.025 0.011 -9999 0 -0.102 1 1
JUP 0.012 0.068 -9999 0 -0.277 19 19
ASAP2/amphiphysin II 0.028 0.045 -9999 0 -0.104 46 46
ARF6/GTP 0.025 0.009 -9999 0 -0.132 1 1
CDH1 0.01 0.068 -9999 0 -0.28 19 19
clathrin-independent pinocytosis 0.025 0.009 -9999 0 -0.132 1 1
MAPK8IP3 0.036 0.004 -9999 0 0 5 5
positive regulation of endocytosis 0.025 0.009 -9999 0 -0.132 1 1
EXOC2 0.035 0.008 -9999 0 0 22 22
substrate adhesion-dependent cell spreading 0.001 0.052 -9999 0 -0.293 5 5
insulin receptor binding 0 0 -9999 0 -9999 0 0
SPAG9 0.034 0.009 -9999 0 0 32 32
regulation of calcium-dependent cell-cell adhesion -0.038 0.073 0.286 17 -9999 0 17
positive regulation of phagocytosis -0.015 0.006 -9999 0 -9999 0 0
ARF6/GTP/JIP3 0.046 0.013 -9999 0 -0.115 1 1
ACAP1 0.018 0.059 -9999 0 -0.222 13 13
mol:GTP 0 0 -9999 0 -9999 0 0
CHRM2 0.006 0.062 -9999 0 -0.285 14 14
clathrin heavy chain/ACAP1 0.017 0.084 0.194 7 -0.266 20 27
JIP4/KLC1 0.036 0.034 -9999 0 -0.105 24 24
EXOC1 0.033 0.01 -9999 0 0 42 42
exocyst 0.001 0.053 -9999 0 -0.297 5 5
RALA/GTP 0.014 0.03 -9999 0 -0.132 17 17
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.038 0.038 -9999 0 -0.119 24 24
receptor recycling 0.025 0.009 -9999 0 -0.132 1 1
CTNNA1 -0.019 0.011 0.087 1 -0.181 1 2
NME1 -0.009 0.005 -9999 0 -0.107 1 1
clathrin coat assembly 0.014 0.086 -9999 0 -0.345 20 20
IL2RA 0.006 0.068 -9999 0 -0.34 13 13
VAMP3 -0.015 0.006 -9999 0 -9999 0 0
GLUT4/clathrin heavy chain/ACAP1 0.031 0.082 -9999 0 -0.245 24 24
EXOC6 0 0 -9999 0 -9999 0 0
PLD1 0 0.041 -9999 0 -0.214 12 12
PLD2 0 0.041 -9999 0 -0.214 12 12
EXOC5 0.03 0.014 -9999 0 0 81 81
PIP5K1C 0.009 0.063 -9999 0 -0.24 16 16
SDC1 0.014 0.07 -9999 0 -0.28 19 19
ARF6/GDP 0.026 0.005 -9999 0 0 21 21
EXOC7 0.036 0.004 -9999 0 0 5 5
E-cadherin/beta catenin 0.041 0.076 -9999 0 -0.294 17 17
mol:Phosphatidic acid 0.017 0.062 -9999 0 -0.165 28 28
endocytosis -0.027 0.044 0.104 46 -9999 0 46
SCAMP2 0.034 0.008 -9999 0 0 24 24
ADRB2 0.013 0.086 0.234 1 -0.341 19 20
EXOC3 0.035 0.006 -9999 0 0 16 16
ASAP2 0 0 -9999 0 -9999 0 0
Dynamin 2/GDP 0.022 0.01 0.088 1 -0.102 1 2
KLC1 0 0 -9999 0 -9999 0 0
AVPR2 0.007 0.083 -9999 0 -0.335 20 20
RALA 0.026 0.017 -9999 0 0 143 143
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.022 0.08 0.216 2 -0.291 18 20
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.033 0.028 -9999 0 -9999 0 0
VEGFR1 homodimer/NRP1 0.009 0.019 -9999 0 -9999 0 0
mol:DAG -0.018 0.033 0.187 1 -9999 0 1
VEGFR1 homodimer/NRP1/VEGFR 121 0.008 0.017 -9999 0 -9999 0 0
CaM/Ca2+ -0.022 0.042 0.189 1 -0.192 2 3
HIF1A 0.04 0.012 -9999 0 -9999 0 0
GAB1 0.031 0.013 -9999 0 0 75 75
AKT1 -0.025 0.091 0.197 6 -0.306 22 28
PLCG1 -0.018 0.033 0.187 1 -9999 0 1
NOS3 0.005 0.069 -9999 0 -0.3 5 5
CBL 0.036 0.004 -9999 0 0 6 6
mol:NO 0.01 0.072 -9999 0 -0.291 5 5
FLT1 0.016 0.008 -9999 0 -9999 0 0
PGF 0.032 0.012 -9999 0 0 61 61
VEGFR1 homodimer/NRP2/VEGFR121 0.029 0.025 -9999 0 -9999 0 0
CALM1 0.033 0.011 -9999 0 0 49 49
PIK3CA 0.03 0.014 -9999 0 0 85 85
eNOS/Hsp90 0.002 0.068 -9999 0 -0.283 5 5
endothelial cell proliferation -0.003 0.046 0.193 2 -0.246 2 4
mol:Ca2+ -0.018 0.033 0.186 1 -9999 0 1
MAPK3 -0.027 0.031 0.153 1 -9999 0 1
MAPK1 -0.026 0.035 0.153 1 -0.19 2 3
PIK3R1 0.032 0.012 -9999 0 0 61 61
PLGF homodimer 0.032 0.012 -9999 0 0 61 61
PRKACA 0.034 0.009 -9999 0 0 29 29
RP11-342D11.1 0 0 -9999 0 -9999 0 0
CAV1 0.016 0.018 -9999 0 0 269 269
VEGFA homodimer 0 0 -9999 0 -9999 0 0
VEGFR1 homodimer/VEGFA homodimer 0.009 0.019 -9999 0 -9999 0 0
platelet activating factor biosynthetic process -0.027 0.044 -9999 0 -0.19 2 2
PI3K 0.034 0.078 -9999 0 -0.198 15 15
PRKCA -0.023 0.032 0.171 1 -9999 0 1
PRKCB -0.016 0.03 0.172 1 -9999 0 1
VEGFR1 homodimer/PLGF homodimer 0.03 0.028 -9999 0 -9999 0 0
VEGFA 0 0 -9999 0 -9999 0 0
VEGFB 0.036 0.005 -9999 0 0 9 9
mol:IP3 -0.018 0.033 0.187 1 -9999 0 1
RASA1 -0.025 0.027 0.187 1 -0.2 5 6
NRP2 0.036 0.005 -9999 0 0 9 9
VEGFR1 homodimer 0.016 0.008 -9999 0 -9999 0 0
VEGFB homodimer 0.036 0.005 -9999 0 0 9 9
NCK1 0.034 0.008 -9999 0 0 26 26
eNOS/Caveolin-1 0.006 0.07 -9999 0 -0.281 11 11
PTPN11 0.036 0.005 -9999 0 0 9 9
mol:PI-3-4-5-P3 0.032 0.077 -9999 0 -0.197 15 15
mol:L-citrulline 0.01 0.072 -9999 0 -0.291 5 5
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.04 0.043 -9999 0 -0.188 3 3
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.027 0.029 -9999 0 -0.193 1 1
CD2AP 0.033 0.01 -9999 0 0 43 43
PI3K/GAB1 0.037 0.086 -9999 0 -0.197 21 21
PDPK1 -0.026 0.072 0.237 4 -0.262 2 6
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.028 0.029 -9999 0 -0.193 1 1
mol:NADP 0.01 0.072 -9999 0 -0.291 5 5
HSP90AA1 0 0 -9999 0 -9999 0 0
ubiquitin-dependent protein catabolic process 0.039 0.042 -9999 0 -0.186 3 3
VEGFR1 homodimer/NRP2 0.032 0.028 -9999 0 -9999 0 0
Canonical NF-kappaB pathway

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
FBXW11 0.033 0.019 0.079 9 -0.055 14 23
mol:GTP 0 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.007 0.08 -9999 0 -0.245 17 17
ERC1 0 0 -9999 0 -9999 0 0
RIP2/NOD2 0.026 0.011 -9999 0 -0.132 2 2
NFKBIA -0.031 0.047 0.201 3 -0.277 12 15
BIRC2 0.035 0.005 -9999 0 0 11 11
IKBKB 0.036 0.004 -9999 0 0 6 6
RIPK2 0.035 0.005 -9999 0 0 11 11
IKBKG 0.019 0.05 -9999 0 -0.253 11 11
IKK complex/A20 0.058 0.073 -9999 0 -0.273 5 5
NEMO/A20/RIP2 0.035 0.005 -9999 0 0 11 11
XPO1 0.036 0.004 -9999 0 0 5 5
NEMO/ATM 0.037 0.057 -9999 0 -0.306 6 6
tumor necrosis factor receptor activity 0 0 -9999 0 -9999 0 0
RAN 0.035 0.006 -9999 0 0 13 13
Exportin 1/RanGTP 0.046 0.023 -9999 0 -0.146 6 6
IKK complex/ELKS 0.03 0.052 -9999 0 -0.254 4 4
BCL10/MALT1/TRAF6 0.063 0.034 -9999 0 -0.124 10 10
NOD2 0 0 -9999 0 -9999 0 0
NFKB1 0.034 0.019 0.079 10 -0.056 15 25
RELA 0.034 0.019 0.079 10 -0.055 16 26
MALT1 0.034 0.009 -9999 0 0 29 29
cIAP1/UbcH5C 0.049 0.028 -9999 0 -0.178 6 6
ATM 0.034 0.01 -9999 0 0 36 36
TNF/TNFR1A 0.035 0.055 -9999 0 -0.141 41 41
TRAF6 0.036 0.005 -9999 0 0 8 8
PRKCA 0.036 0.004 -9999 0 0 5 5
CHUK 0.026 0.016 -9999 0 0 133 133
UBE2D3 0.035 0.005 -9999 0 0 11 11
TNF 0.036 0.004 -9999 0 0 6 6
NF kappa B1 p50/RelA 0.064 0.059 -9999 0 -0.166 25 25
BCL10 0.035 0.006 -9999 0 0 15 15
proteasomal ubiquitin-dependent protein catabolic process -0.031 0.047 0.201 3 -0.276 12 15
beta TrCP1/SCF ubiquitin ligase complex 0.033 0.019 0.079 9 -0.055 14 23
TNFRSF1A 0.032 0.012 -9999 0 0 61 61
IKK complex 0.041 0.06 -9999 0 -0.269 4 4
CYLD 0.035 0.006 -9999 0 0 15 15
IKK complex/PKC alpha 0.051 0.067 -9999 0 -0.268 4 4
Regulation of Androgen receptor activity

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
HDAC1 -0.01 0.002 0.012 1 -9999 0 1
SMARCC1 -0.005 0.121 -9999 0 -1.154 4 4
REL 0.035 0.004 -9999 0 -0.01 3 3
HDAC7 -0.029 0.057 0.171 5 -0.211 18 23
JUN 0.034 0.01 -9999 0 0 39 39
EP300 0.033 0.011 -9999 0 0 49 49
KAT2B 0 0 -9999 0 -9999 0 0
KAT5 0 0 -9999 0 -9999 0 0
MAPK14 -0.017 0.018 0.044 11 -9999 0 11
FOXO1 0 0 -9999 0 -9999 0 0
T-DHT/AR 0.018 0.078 0.235 3 -0.221 18 21
MAP2K6 0.035 0.011 -9999 0 -0.035 10 10
BRM/BAF57 0.046 0.024 -9999 0 -0.141 3 3
MAP2K4 0.034 0.013 -9999 0 -0.034 11 11
SMARCA2 0.032 0.012 -9999 0 -9999 0 0
PDE9A -0.013 0.19 -9999 0 -0.787 26 26
NCOA2 0.036 0.005 -9999 0 0 9 9
CEBPA 0.028 0.015 -9999 0 0 115 115
EHMT2 0.036 0.004 -9999 0 0 5 5
cell proliferation -0.024 0.086 0.251 2 -0.319 12 14
NR0B1 0.03 0.014 -9999 0 0 83 83
EGR1 0.029 0.015 -9999 0 -9999 0 0
RXRs/9cRA 0.066 0.019 -9999 0 -0.109 1 1
AR/RACK1/Src -0.021 0.05 0.171 7 -0.221 2 9
AR/GR 0.002 0.06 0.159 1 -0.2 24 25
GNB2L1 0.036 0.005 -9999 0 0 11 11
PKN1 0.032 0.012 -9999 0 0 58 58
RCHY1 0.035 0.006 -9999 0 0 14 14
epidermal growth factor receptor activity 0 0 -9999 0 -9999 0 0
MAPK8 -0.012 0.016 0.032 15 -0.053 1 16
T-DHT/AR/TIF2/CARM1 0.014 0.054 0.204 3 -0.194 4 7
SRC -0.022 0.029 0.177 3 -9999 0 3
NR3C1 0.034 0.008 -9999 0 0 24 24
KLK3 -0.011 0.077 0.417 1 -9999 0 1
APPBP2 0.034 0.014 -9999 0 -0.033 14 14
TRIM24 0.025 0.017 -9999 0 -9999 0 0
T-DHT/AR/TIP60 -0.023 0.029 0.083 2 -0.149 8 10
TMPRSS2 0.015 0.081 -9999 0 -0.563 7 7
RXRG 0.035 0.006 -9999 0 0 13 13
mol:9cRA 0 0 -9999 0 -9999 0 0
RXRA 0.035 0.007 -9999 0 0 18 18
RXRB 0.036 0.002 -9999 0 0 2 2
CARM1 0.034 0.01 -9999 0 0 36 36
NR2C2 0.036 0.004 -9999 0 0 6 6
KLK2 0.001 0.041 -9999 0 -0.235 2 2
AR -0.004 0.043 0.143 3 -0.192 18 21
SENP1 0 0 -9999 0 -9999 0 0
HSP90AA1 0 0 -9999 0 -9999 0 0
MDM2 0.032 0.011 -9999 0 -0.001 50 50
SRY 0.035 0.004 -9999 0 -0.009 4 4
GATA2 0.035 0.006 -9999 0 0 14 14
MYST2 0.034 0.009 -9999 0 0 32 32
HOXB13 0.037 0.003 -9999 0 -9999 0 0
T-DHT/AR/RACK1/Src -0.023 0.051 0.171 9 -0.228 2 11
positive regulation of transcription 0.035 0.006 -9999 0 0 14 14
DNAJA1 0.031 0.016 -9999 0 -0.033 14 14
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.033 -9999 0 -0.266 6 6
NCOA1 0.039 0.023 0.132 5 -0.176 2 7
SPDEF 0.037 0.004 -9999 0 -9999 0 0
T-DHT/AR/TIF2 -0.027 0.082 0.167 1 -0.247 37 38
T-DHT/AR/Hsp90 -0.023 0.029 0.083 2 -0.149 8 10
GSK3B 0.034 0.01 -9999 0 0 35 35
NR2C1 0.036 0.004 -9999 0 0 5 5
mol:T-DHT -0.019 0.025 0.077 8 -0.123 4 12
SIRT1 0.026 0.017 -9999 0 0 143 143
ZMIZ2 -0.001 0.001 -9999 0 -0.019 1 1
POU2F1 0.037 0.033 0.116 12 -0.109 19 31
T-DHT/AR/DAX-1 -0.021 0.036 0.184 1 -0.192 2 3
CREBBP 0.036 0.004 -9999 0 0 5 5
SMARCE1 0.036 0.004 -9999 0 -9999 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.035 0.007 -9999 0 0 20 20
Ran/GTP/Exportin 1/HDAC4 -0.032 0.03 -9999 0 -0.128 33 33
MDM2/SUMO1 0.033 0.052 -9999 0 -0.218 4 4
HDAC4 0.034 0.008 -9999 0 0 24 24
Ran/GTP/Exportin 1/HDAC1 -0.031 0.03 -9999 0 -0.14 25 25
SUMO1 0.036 0.003 -9999 0 0 3 3
NPC/RanGAP1/SUMO1 0.005 0.033 -9999 0 -0.149 20 20
mol:GTP 0 0 -9999 0 -9999 0 0
XPO1 -0.008 0.041 -9999 0 -0.155 20 20
EntrezGene:23636 0 0 -9999 0 -9999 0 0
RAN 0.035 0.006 -9999 0 0 13 13
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.034 0.008 -9999 0 0 24 24
SUMO1/HDAC4 0.034 0.056 -9999 0 -0.222 5 5
SUMO1/HDAC1 0.036 0.054 -9999 0 -0.22 5 5
RANGAP1 0.033 0.01 -9999 0 0 43 43
MDM2/SUMO1/SUMO1 0.074 0.047 -9999 0 -0.123 14 14
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.007 0.033 -9999 0 -0.146 20 20
Ran/GTP 0.019 0.049 -9999 0 -0.146 20 20
EntrezGene:23225 0 0 -9999 0 -9999 0 0
MDM2 0.033 0.011 -9999 0 0 49 49
UBE2I 0.036 0.003 -9999 0 0 3 3
Ran/GTP/Exportin 1 0.013 0.052 0.211 2 -0.159 20 22
NPC 0.017 0.021 -9999 0 -0.088 18 18
PIAS2 0.035 0.006 -9999 0 0 15 15
PIAS1 0.035 0.008 -9999 0 0 23 23
EntrezGene:9972 0 0 -9999 0 -9999 0 0
Rapid glucocorticoid signaling

Figure 122.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 124.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.035 0.029 -9999 0 -0.095 20 20
MAPK9 0.008 0.001 -9999 0 0 12 12
adrenocorticotropin secretion -0.011 0.002 0 15 -9999 0 15
GNB1/GNG2 0.018 0.026 -9999 0 -0.107 20 20
GNB1 0.033 0.01 -9999 0 0 37 37
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 0.008 0.001 -9999 0 0 6 6
Gs family/GTP 0.023 0.004 -9999 0 -9999 0 0
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 0.002 0 -9999 0 -9999 0 0
GNAL 0.035 0.006 -9999 0 0 13 13
GNG2 0 0 -9999 0 -9999 0 0
CRH 0.035 0.006 -9999 0 0 15 15
mol:cortisol 0 0 -9999 0 -9999 0 0
MAPK8 0.006 0.003 -9999 0 0 133 133
MAPK11 0.007 0.002 -9999 0 0 48 48
Arf1 pathway

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
coatomer protein complex 0.004 0.026 0.136 11 -0.178 3 14
EntrezGene:79658 0 0 -9999 0 -9999 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A -0.006 0.044 0.118 3 -0.154 10 13
AP2 0.021 0.027 -9999 0 -0.132 14 14
mol:DAG 0 0 -9999 0 -9999 0 0
Arfaptin 2/Rac/GTP 0.031 0.037 -9999 0 -0.118 17 17
CLTB 0.036 0.005 -9999 0 0 8 8
coatomer protein complex/ARF1/GTP/ER cargo protein 0.014 0.031 -9999 0 -0.176 11 11
CD4 0.031 0.013 -9999 0 0 71 71
CLTA 0.033 0.01 -9999 0 0 38 38
mol:GTP -0.003 0.002 0.007 1 -0.018 7 8
ARFGAP1 -0.011 0.002 0 17 -9999 0 17
mol:PI-4-5-P2 0.008 0.018 0.104 11 -9999 0 11
ARF1/GTP 0.018 0.017 -9999 0 -0.107 7 7
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.001 0.033 -9999 0 -0.175 10 10
mol:Choline 0.007 0.018 0.101 14 -9999 0 14
mol:GDP 0 0 -9999 0 -9999 0 0
ARF1 0.035 0.008 -9999 0 0 21 21
DDEF1 0.005 0.017 0.097 12 -9999 0 12
ARF1/GDP 0.006 0.014 -9999 0 -0.087 7 7
AP2M1 0.034 0.01 -9999 0 0 36 36
EntrezGene:1313 0 0 -9999 0 -9999 0 0
actin filament polymerization -0.012 0.019 0.065 1 -0.113 10 11
Rac/GTP 0.018 0.021 -9999 0 -0.138 6 6
ARF1/GTP/GGA3/ARF-GAP1 0.043 0.023 -9999 0 -0.104 8 8
ARFIP2 0.031 0.016 -9999 0 -0.037 17 17
COPA 0.035 0.006 -9999 0 0 13 13
RAC1 0.027 0.016 -9999 0 0 123 123
ARF1/GTP/coatomer protein complex 0.005 0.042 -9999 0 -0.181 10 10
ARF1/GTP/ARHGAP10 0.021 0.016 -9999 0 -0.113 6 6
GGA3 0.036 0.004 -9999 0 0 7 7
ARF1/GTP/Membrin 0.028 0.023 -9999 0 -0.246 2 2
AP2A1 0 0 -9999 0 -9999 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.005 0.037 -9999 0 -0.182 11 11
ARF1/GDP/Membrin 0.031 0.026 -9999 0 -0.277 2 2
Arfaptin 2/Rac/GDP 0.03 0.036 -9999 0 -0.119 17 17
CYTH2 -0.003 0.002 0.007 1 -0.018 7 8
ARF1/GTP/GGA3 0.044 0.021 -9999 0 -0.122 6 6
mol:ATP 0 0 -9999 0 -9999 0 0
Rac/GDP 0.018 0.02 -9999 0 -0.132 6 6
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 0.003 0.059 -9999 0 -0.187 31 31
PLD2 0.007 0.018 0.101 14 -9999 0 14
ARF-GAP1/v-SNARE -0.011 0.002 0 17 -9999 0 17
PIP5K1A 0.008 0.018 0.105 11 -9999 0 11
ARF1/GTP/Membrin/GBF1/p115 0.005 0.034 -9999 0 -0.106 6 6
mol:Phosphatic acid 0 0 -9999 0 -9999 0 0
mol:Phosphatidic acid 0.007 0.018 0.101 14 -9999 0 14
KDEL Receptor/Ligand/ARF-GAP1 -0.011 0.002 0 17 -9999 0 17
GOSR2 0.015 0.018 -9999 0 -0.315 1 1
USO1 0.001 0.005 0.034 5 -0.03 4 9
GBF1 -0.06 0.139 -9999 0 -0.314 112 112
ARF1/GTP/Arfaptin 2 0.041 0.034 -9999 0 -0.121 17 17
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.03 0.045 -9999 0 -0.124 32 32
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.053 0.018 -9999 0 -9999 0 0
KIRREL 0.038 0.009 -9999 0 -0.041 1 1
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.053 0.018 -9999 0 -9999 0 0
PLCG1 0.035 0.007 -9999 0 0 20 20
ARRB2 0.034 0.008 -9999 0 0 27 27
WASL 0.025 0.017 -9999 0 0 155 155
Nephrin/NEPH1/podocin/CD2AP 0.081 0.049 -9999 0 -0.122 15 15
ChemicalAbstracts:57-88-5 0 0 -9999 0 -9999 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.015 0.034 -9999 0 -0.194 6 6
FYN -0.005 0.049 0.174 30 -9999 0 30
mol:Ca2+ 0.084 0.036 -9999 0 -0.125 3 3
mol:DAG 0.086 0.037 -9999 0 -0.126 3 3
NPHS2 0.039 0.008 -9999 0 -0.041 1 1
mol:IP3 0.086 0.037 -9999 0 -0.126 3 3
regulation of endocytosis 0.051 0.05 -9999 0 -0.136 5 5
Nephrin/NEPH1/podocin/Cholesterol 0.068 0.027 -9999 0 -9999 0 0
establishment of cell polarity 0.053 0.018 -9999 0 -9999 0 0
Nephrin/NEPH1/podocin/NCK1-2 0.093 0.058 -9999 0 -0.137 16 16
Nephrin/NEPH1/beta Arrestin2 0.053 0.052 -9999 0 -0.138 5 5
NPHS1 0.038 0.011 0.076 6 -9999 0 6
Nephrin/NEPH1/podocin 0.051 0.044 -9999 0 -0.107 1 1
TJP1 0.034 0.009 -9999 0 0 34 34
NCK1 0.034 0.008 -9999 0 0 26 26
NCK2 0.035 0.007 -9999 0 0 19 19
heterophilic cell adhesion 0 0 -9999 0 -9999 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.087 0.037 -9999 0 -0.126 3 3
CD2AP 0.033 0.01 -9999 0 0 43 43
Nephrin/NEPH1/podocin/GRB2 0.086 0.04 -9999 0 -0.131 5 5
GRB2 0.035 0.006 -9999 0 0 16 16
homophilic cell adhesion 0 0 -9999 0 -9999 0 0
TRPC6 -0.011 0.054 0.173 33 -9999 0 33
cytoskeleton organization -0.01 0.03 0.203 4 -0.204 2 6
Nephrin/NEPH1 0.045 0.015 -9999 0 -9999 0 0
Nephrin/NEPH1/ZO-1 0.063 0.037 -9999 0 -0.14 8 8
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.036 0.003 -9999 0 0 4 4
Aurora C/Aurora B/INCENP 0.059 0.026 -9999 0 -9999 0 0
metaphase 0 0 -9999 0 -9999 0 0
mitosis 0 0 -9999 0 -9999 0 0
H3F3B 0.004 0.064 -9999 0 -0.392 12 12
AURKB 0.033 0.01 -9999 0 0 39 39
AURKC 0.033 0.011 -9999 0 0 47 47
Signaling events mediated by the Hedgehog family

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
TGFB2 0.033 0.03 -9999 0 -9999 0 0
IHH 0.051 0.012 -9999 0 -9999 0 0
SHH Np/Cholesterol/GAS1 0.017 0.027 -9999 0 -0.11 15 15
LRPAP1 0.035 0.006 -9999 0 0 16 16
dorsoventral neural tube patterning -0.017 0.027 0.109 15 -9999 0 15
SMO/beta Arrestin2 0.078 0.055 0.25 5 -9999 0 5
SMO 0.027 0.031 -9999 0 -9999 0 0
AKT1 -0.014 0.136 -9999 0 -0.459 30 30
ARRB2 0.034 0.008 -9999 0 0 27 27
BOC 0 0 -9999 0 -9999 0 0
ADRBK1 0.035 0.006 -9999 0 0 14 14
heart looping 0.027 0.031 -9999 0 -9999 0 0
STIL 0.031 0.079 0.182 89 -9999 0 89
DHH N/PTCH2 0.027 0.003 -9999 0 -9999 0 0
DHH N/PTCH1 0.016 0.019 -9999 0 -9999 0 0
PIK3CA 0.03 0.014 -9999 0 0 85 85
DHH 0 0 -9999 0 -9999 0 0
PTHLH 0.023 0.01 -9999 0 -9999 0 0
determination of left/right symmetry 0.027 0.031 -9999 0 -9999 0 0
PIK3R1 0.032 0.012 -9999 0 0 61 61
skeletal system development 0.03 0.033 -9999 0 -9999 0 0
IHH N/Hhip 0.033 0.007 -9999 0 -9999 0 0
DHH N/Hhip 0 0 -9999 0 -9999 0 0
mol:Cholesterol 0 0 -9999 0 -9999 0 0
heart development 0.027 0.031 -9999 0 -9999 0 0
pancreas development 0 0 -9999 0 -9999 0 0
HHAT 0.035 0.007 -9999 0 0 20 20
PI3K 0.016 0.075 -9999 0 -0.155 73 73
EntrezGene:84976 0 0 -9999 0 -9999 0 0
GAS1 0.03 0.014 -9999 0 0 83 83
somite specification 0.027 0.031 -9999 0 -9999 0 0
SHH Np/Cholesterol/PTCH1 0.021 0.027 0.162 2 -9999 0 2
SHH Np/Cholesterol/PTCH2 0.024 0.014 -9999 0 -9999 0 0
SHH Np/Cholesterol/Megalin 0.024 0.014 -9999 0 -9999 0 0
SHH -0.017 0.01 -9999 0 -9999 0 0
catabolic process 0.02 0.025 0.136 21 -9999 0 21
SMO/Vitamin D3 0.023 0.035 0.185 12 -9999 0 12
SHH Np/Cholesterol/Hhip -0.012 0.007 -9999 0 -9999 0 0
LRP2 0.035 0.006 -9999 0 0 12 12
receptor-mediated endocytosis 0.024 0.038 0.249 3 -9999 0 3
SHH Np/Cholesterol/BOC -0.012 0.007 -9999 0 -9999 0 0
SHH Np/Cholesterol/CDO 0.024 0.014 -9999 0 -9999 0 0
mesenchymal cell differentiation 0.012 0.007 -9999 0 -9999 0 0
mol:Vitamin D3 0.055 0.074 0.192 102 -9999 0 102
IHH N/PTCH2 0.06 0.01 -9999 0 -9999 0 0
CDON 0.036 0.003 -9999 0 0 4 4
IHH N/PTCH1 0.046 0.027 -9999 0 -9999 0 0
Megalin/LRPAP1 0.048 0.028 -9999 0 -0.142 9 9
PTCH2 0.036 0.004 -9999 0 0 5 5
SHH Np/Cholesterol 0.014 0.008 -9999 0 -9999 0 0
PTCH1 0.02 0.025 0.136 21 -9999 0 21
HHIP 0 0 -9999 0 -9999 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.033 0.012 -9999 0 -9999 0 0
SVIL 0.024 0.018 -9999 0 -9999 0 0
ZNF318 0.034 0.005 -9999 0 -0.045 1 1
JMJD2C 0.035 0.014 -9999 0 -9999 0 0
T-DHT/AR/Ubc9 0.052 0.04 -9999 0 -9999 0 0
CARM1 0.034 0.01 -9999 0 -9999 0 0
PRDX1 0.035 0.007 -9999 0 0 19 19
PELP1 0.035 0.007 -9999 0 0 19 19
CTNNB1 0.035 0.007 -9999 0 -9999 0 0
AKT1 0.032 0.012 -9999 0 -0.031 1 1
PTK2B 0.036 0.006 -9999 0 -9999 0 0
MED1 0 0 -9999 0 -9999 0 0
MAK 0.033 0.008 -9999 0 -0.045 1 1
response to oxidative stress 0 0 -9999 0 -9999 0 0
HIP1 0.022 0.018 -9999 0 -9999 0 0
GSN 0.032 0.013 -9999 0 -9999 0 0
NCOA2 0.036 0.005 -9999 0 -9999 0 0
NCOA6 0.034 0.01 -9999 0 -9999 0 0
DNA-PK 0.055 0.047 -9999 0 -0.143 19 19
NCOA4 0.027 0.016 -9999 0 0 121 121
PIAS3 0.035 0.007 -9999 0 -9999 0 0
cell proliferation 0.021 0.046 -9999 0 -0.443 4 4
XRCC5 0.035 0.004 -9999 0 0 7 7
UBE3A 0.036 0.007 -9999 0 -9999 0 0
T-DHT/AR/SNURF 0.031 0.032 0.114 1 -0.071 31 32
FHL2 -0.018 0.175 -9999 0 -0.684 31 31
RANBP9 0.036 0.006 -9999 0 -9999 0 0
JMJD1A 0.044 0.011 -9999 0 -9999 0 0
CDK6 0.024 0.017 -9999 0 0 156 156
TGFB1I1 0.033 0.012 -9999 0 -9999 0 0
T-DHT/AR/CyclinD1 0.033 0.056 -9999 0 -0.114 29 29
XRCC6 0.033 0.01 -9999 0 0 37 37
T-DHT/AR 0.047 0.058 0.208 1 -0.13 31 32
CTDSP1 0.035 0.006 -9999 0 -9999 0 0
CTDSP2 0.029 0.013 -9999 0 -0.039 1 1
BRCA1 0.036 0.007 -9999 0 -9999 0 0
TCF4 0.031 0.012 -9999 0 -0.035 1 1
CDKN2A 0.005 0.012 -9999 0 -9999 0 0
SRF 0.039 0.054 -9999 0 -0.147 31 31
NKX3-1 0.026 0.068 -9999 0 -0.303 14 14
KLK3 0.014 0.05 -9999 0 -9999 0 0
TMF1 0.035 0.007 -9999 0 -9999 0 0
HNRNPA1 -0.001 0 -9999 0 -9999 0 0
AOF2 0.034 0.011 -9999 0 -9999 0 0
APPL1 -0.011 0.004 -9999 0 -9999 0 0
T-DHT/AR/Caspase 8 0.05 0.04 -9999 0 -9999 0 0
AR 0.035 0.03 -9999 0 -0.068 31 31
UBA3 0 0 -9999 0 -9999 0 0
PATZ1 -0.001 0 -9999 0 -9999 0 0
PAWR 0.035 0.006 -9999 0 -9999 0 0
PRKDC 0.033 0.01 -9999 0 0 42 42
PA2G4 0.034 0.008 -9999 0 -0.032 1 1
UBE2I 0.036 0.003 -9999 0 0 3 3
T-DHT/AR/Cyclin D3/CDK11 p58 0.044 0.044 -9999 0 -0.101 11 11
RPS6KA3 0.036 0.007 -9999 0 -9999 0 0
T-DHT/AR/ARA70 0.04 0.045 -9999 0 -0.1 5 5
LATS2 -0.001 0 -9999 0 -9999 0 0
T-DHT/AR/PRX1 0.045 0.042 -9999 0 -0.115 8 8
Cyclin D3/CDK11 p58 0.021 0.028 -9999 0 -0.132 16 16
VAV3 0.029 0.015 -9999 0 -9999 0 0
KLK2 0.025 0.054 -9999 0 -0.321 9 9
CASP8 0.035 0.006 -9999 0 0 13 13
T-DHT/AR/TIF2/CARM1 0.065 0.048 -9999 0 -0.107 1 1
TMPRSS2 0.024 0.068 -9999 0 -0.303 14 14
CCND1 0.028 0.015 -9999 0 -9999 0 0
PIAS1 0.036 0.008 -9999 0 -9999 0 0
mol:T-DHT 0.004 0.016 0.051 1 -0.049 31 32
CDC2L1 0 0 -9999 0 -9999 0 0
PIAS4 0.035 0.009 -9999 0 -9999 0 0
T-DHT/AR/CDK6 0.038 0.039 -9999 0 -9999 0 0
CMTM2 0 0 -9999 0 -9999 0 0
SNURF 0 0 -9999 0 -9999 0 0
ZMIZ1 0.004 0.016 0.051 1 -0.049 31 32
CCND3 0.034 0.008 -9999 0 0 25 25
TGIF1 -0.001 0 -9999 0 -9999 0 0
FKBP4 0.034 0.009 -9999 0 -9999 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.043 0.18 0.462 2 -0.664 15 17
PCK1 0.048 0.119 0.484 3 -0.586 3 6
HNF4A 0.055 0.157 0.575 2 -0.673 6 8
KCNJ11 0.064 0.173 0.458 3 -0.583 13 16
AKT1 0.062 0.124 0.359 1 -0.381 11 12
response to starvation 0.003 0.002 -9999 0 -9999 0 0
DLK1 0.076 0.18 0.578 2 -0.67 7 9
NKX2-1 0.031 0.101 0.274 3 -0.347 8 11
ACADM 0.049 0.168 0.525 1 -0.749 8 9
TAT 0.046 0.131 0.546 1 -0.643 5 6
CEBPB 0.034 0.014 0.117 1 -9999 0 1
CEBPA 0.031 0.017 -9999 0 -9999 0 0
TTR 0.028 0.172 0.45 10 -0.601 11 21
PKLR 0.055 0.159 0.525 1 -0.678 6 7
APOA1 0.073 0.197 0.62 3 -0.823 6 9
CPT1C 0.052 0.154 0.442 3 -0.561 11 14
ALAS1 0.033 0.228 -9999 0 -1.253 12 12
TFRC 0.018 0.291 0.574 2 -0.966 33 35
FOXF1 0.031 0.013 -9999 0 -9999 0 0
NF1 0.035 0.033 -9999 0 -0.166 12 12
HNF1A (dimer) 0.006 0.005 0.107 1 -9999 0 1
CPT1A 0.051 0.154 0.525 1 -0.692 5 6
HMGCS1 0.055 0.162 0.51 3 -0.678 6 9
NR3C1 0.046 0.02 -9999 0 -9999 0 0
CPT1B 0.043 0.151 0.462 2 -0.678 6 8
chromatin remodeling 0 0 -9999 0 -9999 0 0
SP1 0.035 0.005 -9999 0 -9999 0 0
GCK 0.08 0.173 0.49 8 -0.619 6 14
CREB1 0.043 0.013 0.147 1 -9999 0 1
IGFBP1 0.053 0.127 0.519 1 -0.629 5 6
PDX1 0.053 0.103 0.32 3 -0.333 6 9
UCP2 0.026 0.231 0.499 3 -0.664 37 40
ALDOB 0.068 0.177 0.489 2 -0.729 6 8
AFP 0.015 0.031 0.296 1 -9999 0 1
BDH1 0.046 0.184 0.51 2 -0.668 15 17
HADH 0.064 0.173 0.458 3 -0.583 13 16
F2 0.072 0.197 0.757 1 -0.842 6 7
HNF1A 0.006 0.005 0.107 1 -9999 0 1
G6PC 0.008 0.081 0.414 1 -9999 0 1
SLC2A2 0.06 0.122 0.429 1 -0.46 1 2
INS 0.024 0.041 0.183 12 -0.092 35 47
FOXA1 0.014 0.012 0.14 2 -9999 0 2
FOXA3 0.019 0.056 0.251 2 -0.181 23 25
FOXA2 0.099 0.213 0.62 3 -0.67 13 16
ABCC8 0.065 0.175 0.525 1 -0.628 10 11
ALB 0.016 0.032 0.296 1 -9999 0 1
Visual signal transduction: Rods

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
mol:K + 0.036 0.005 -9999 0 0 8 8
GNAT1/GTP 0.026 0.004 -9999 0 -9999 0 0
Metarhodopsin II/Arrestin 0.047 0.01 -9999 0 -9999 0 0
PDE6G/GNAT1/GTP 0.047 0.008 -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 0.035 0.006 -9999 0 0 12 12
GRK1 0 0 -9999 0 -9999 0 0
CNG Channel 0.068 0.023 -9999 0 -9999 0 0
mol:Na + 0.043 0.015 -9999 0 -9999 0 0
mol:ADP 0 0 -9999 0 -9999 0 0
RGS9-1/Gbeta5/R9AP 0.045 0.014 -9999 0 -0.115 1 1
mol:GDP 0 0 -9999 0 -9999 0 0
cGMP/CNG Channel 0.054 0.018 -9999 0 -9999 0 0
CNGB1 0.035 0.006 -9999 0 0 12 12
RDH5 0.034 0.008 -9999 0 0 24 24
SAG 0.036 0.005 -9999 0 0 9 9
mol:Ca2+ -0.032 0.028 0.159 9 -9999 0 9
Na + (4 Units) 0.041 0.017 -9999 0 -9999 0 0
RGS9 0.035 0.006 -9999 0 0 15 15
GNB1/GNGT1 0.03 0.039 -9999 0 -0.141 14 14
GNAT1/GDP 0.058 0.02 -9999 0 -0.102 1 1
GUCY2D 0.035 0.005 -9999 0 0 11 11
GNGT1 0.025 0.017 -9999 0 0 148 148
GUCY2F 0.036 0 -9999 0 -9999 0 0
GNB5 0.035 0.007 -9999 0 0 18 18
mol:GMP (4 units) 0.028 0.008 -9999 0 -9999 0 0
mol:11-cis-retinal 0.034 0.008 -9999 0 0 24 24
mol:cGMP 0.028 0.006 -9999 0 -9999 0 0
GNB1 0.033 0.01 -9999 0 0 37 37
Rhodopsin 0.05 0.014 -9999 0 -9999 0 0
SLC24A1 0.036 0.005 -9999 0 0 8 8
CNGA1 0.036 0.004 -9999 0 0 7 7
Metarhodopsin II 0.023 0.004 -9999 0 -9999 0 0
mol:Ca ++ 0 0 -9999 0 -9999 0 0
GC1/GCAP Family 0.045 0.008 -9999 0 -9999 0 0
RGS9BP 0 0 -9999 0 -9999 0 0
Metarhodopsin II/Transducin 0.006 0.037 -9999 0 -0.157 16 16
GCAP Family/Ca ++ 0.023 0.002 -9999 0 -9999 0 0
PDE6A/B 0.052 0.01 -9999 0 -9999 0 0
mol:Pi 0.045 0.014 -9999 0 -0.115 1 1
mol:all-trans-retinal 0 0 -9999 0 -9999 0 0
Transducin 0.041 0.042 -9999 0 -0.109 14 14
PDE6B 0.035 0.006 -9999 0 0 12 12
PDE6A 0.036 0.004 -9999 0 0 6 6
PDE6G 0.036 0.003 -9999 0 0 3 3
RHO 0.035 0.006 -9999 0 0 12 12
PDE6 0.083 0.026 -9999 0 -0.11 1 1
GUCA1A 0 0 -9999 0 -9999 0 0
GC2/GCAP Family 0.046 0.004 -9999 0 -9999 0 0
GUCA1C 0 0 -9999 0 -9999 0 0
GUCA1B 0.036 0.003 -9999 0 0 3 3
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.036 0.005 0 8 -9999 0 8
PI3K Class IB/PDE3B 0.036 0.005 -9999 0 0 8 8
PDE3B 0.036 0.005 -9999 0 0 8 8
Ephrin A reverse signaling

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
MAPKKK cascade 0.047 0.007 -9999 0 -9999 0 0
EFNA5 0.036 0.003 -9999 0 0 4 4
FYN -0.019 0.013 0.183 1 -9999 0 1
neuron projection morphogenesis 0.047 0.007 -9999 0 -9999 0 0
cell-cell signaling 0 0 -9999 0 -9999 0 0
Ephrin A5/EPHA5 0.048 0.007 -9999 0 -9999 0 0
EPHA5 0.036 0.005 -9999 0 0 8 8
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/GBM/407045/1.GDAC_MergeDataFiles.Finished/GBM.transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data.data.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/writeReducedSegments/GBM/868470/1.GetReducedSegments.Finished/GBM.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)