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 103 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
PLK2 and PLK4 events 177
FOXM1 transcription factor network 137
TCGA08_p53 99
HIF-1-alpha transcription factor network 94
Ephrin B reverse signaling 93
LPA receptor mediated events 90
Endothelins 88
Syndecan-1-mediated signaling events 87
Osteopontin-mediated events 86
Wnt signaling 84
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
PLK2 and PLK4 events 177 532 3 -0.011 0.036 1000 -1000 -0.017 -1000
FOXM1 transcription factor network 137 7014 51 -0.508 0.037 1000 -1000 -0.014 -1000
TCGA08_p53 99 694 7 -0.053 0.038 1000 -1000 -0.009 -1000
HIF-1-alpha transcription factor network 94 7178 76 -0.048 0.087 1000 -1000 0 -1000
Ephrin B reverse signaling 93 4483 48 -0.198 0.079 1000 -1000 -0.051 -1000
LPA receptor mediated events 90 9236 102 -0.043 0.04 1000 -1000 -0.04 -1000
Endothelins 88 8532 96 -0.18 0.04 1000 -1000 -0.021 -1000
Syndecan-1-mediated signaling events 87 2963 34 -0.044 0.04 1000 -1000 -0.003 -1000
Osteopontin-mediated events 86 3294 38 -0.19 0.04 1000 -1000 -0.008 -1000
Wnt signaling 84 592 7 -0.017 0.04 1000 -1000 -0.003 -1000
Nectin adhesion pathway 81 5104 63 -0.088 0.063 1000 -1000 -0.012 -1000
amb2 Integrin signaling 79 6520 82 -0.085 0.081 1000 -1000 -0.016 -1000
PDGFR-alpha signaling pathway 78 3441 44 -0.128 0.049 1000 -1000 -0.022 -1000
TCGA08_retinoblastoma 78 626 8 -0.012 0.03 1000 -1000 -0.004 -1000
Thromboxane A2 receptor signaling 76 8047 105 -0.15 0.069 1000 -1000 -0.02 -1000
TRAIL signaling pathway 74 3597 48 -0.02 0.041 1000 -1000 -0.017 -1000
BARD1 signaling events 72 4124 57 -0.039 0.06 1000 -1000 -0.065 -1000
TCGA08_rtk_signaling 71 1857 26 -0.021 0.039 1000 -1000 -0.02 -1000
Paxillin-dependent events mediated by a4b1 70 2539 36 -0.065 0.067 1000 -1000 -0.052 -1000
Nongenotropic Androgen signaling 69 3630 52 -0.122 0.059 1000 -1000 -0.018 -1000
Signaling events mediated by the Hedgehog family 67 3520 52 -0.066 0.058 1000 -1000 -0.024 -1000
Integrins in angiogenesis 67 5644 84 -0.053 0.054 1000 -1000 -0.017 -1000
Ras signaling in the CD4+ TCR pathway 67 1154 17 -0.007 0.053 1000 -1000 -0.003 -1000
IL1-mediated signaling events 66 4143 62 -0.045 0.072 1000 -1000 -0.017 -1000
IL23-mediated signaling events 66 4018 60 -0.168 0.049 1000 -1000 -0.039 -1000
Signaling events mediated by PTP1B 65 4974 76 -0.059 0.068 1000 -1000 -0.036 -1000
IGF1 pathway 65 3707 57 -0.022 0.065 1000 -1000 -0.016 -1000
IL12-mediated signaling events 64 5608 87 -0.184 0.053 1000 -1000 -0.022 -1000
Fc-epsilon receptor I signaling in mast cells 64 6243 97 -0.081 0.046 1000 -1000 -0.038 -1000
Cellular roles of Anthrax toxin 63 2482 39 -0.082 0.04 1000 -1000 -0.015 -1000
Canonical Wnt signaling pathway 63 3228 51 -0.182 0.092 1000 -1000 -0.011 -1000
Syndecan-4-mediated signaling events 63 4246 67 -0.064 0.043 1000 -1000 -0.031 -1000
Syndecan-2-mediated signaling events 60 4183 69 -0.004 0.062 1000 -1000 -0.013 -1000
IL6-mediated signaling events 60 4553 75 -0.141 0.049 1000 -1000 -0.019 -1000
E-cadherin signaling in keratinocytes 60 2584 43 -0.017 0.052 1000 -1000 -0.007 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 59 5041 85 -0.155 0.049 1000 -1000 -0.028 -1000
IL4-mediated signaling events 59 5408 91 -0.224 0.055 1000 -1000 -0.034 -1000
IL2 signaling events mediated by STAT5 59 1307 22 -0.036 0.047 1000 -1000 -0.006 -1000
a4b1 and a4b7 Integrin signaling 58 294 5 0.031 0.038 1000 -1000 0.037 -1000
FoxO family signaling 58 3748 64 -0.195 0.044 1000 -1000 -0.019 -1000
Noncanonical Wnt signaling pathway 57 1491 26 -0.036 0.04 1000 -1000 -0.038 -1000
HIF-2-alpha transcription factor network 57 2459 43 -0.056 0.069 1000 -1000 -0.079 -1000
TCR signaling in naïve CD8+ T cells 57 5348 93 -0.071 0.076 1000 -1000 -0.027 -1000
BMP receptor signaling 56 4600 81 -0.021 0.071 1000 -1000 -0.001 -1000
IFN-gamma pathway 54 3685 68 -0.045 0.062 1000 -1000 -0.031 -1000
Retinoic acid receptors-mediated signaling 54 3167 58 -0.084 0.061 1000 -1000 -0.003 -1000
Plasma membrane estrogen receptor signaling 54 4644 86 -0.086 0.083 1000 -1000 -0.018 -1000
Paxillin-independent events mediated by a4b1 and a4b7 53 1995 37 -0.019 0.069 1000 -1000 -0.01 -1000
EPHB forward signaling 53 4508 85 -0.057 0.138 1000 -1000 -0.038 -1000
FAS signaling pathway (CD95) 51 2431 47 -0.042 0.053 1000 -1000 -0.024 -1000
BCR signaling pathway 51 5059 99 -0.058 0.068 1000 -1000 -0.034 -1000
ErbB4 signaling events 50 3516 69 -0.068 0.055 1000 -1000 -0.03 -1000
E-cadherin signaling in the nascent adherens junction 50 3870 76 -0.056 0.073 1000 -1000 -0.028 -1000
E-cadherin signaling events 49 248 5 0.035 0.052 1000 -1000 0.037 -1000
Caspase cascade in apoptosis 48 3597 74 -0.097 0.051 1000 -1000 -0.017 -1000
Signaling events mediated by PRL 48 1645 34 -0.017 0.04 1000 -1000 -0.024 -1000
Presenilin action in Notch and Wnt signaling 47 2903 61 -0.156 0.076 1000 -1000 -0.025 -1000
IL2 signaling events mediated by PI3K 47 2731 58 -0.06 0.04 1000 -1000 -0.018 -1000
Class I PI3K signaling events 47 3501 73 -0.016 0.049 1000 -1000 -0.017 -1000
EPO signaling pathway 46 2561 55 -0.001 0.071 1000 -1000 -0.012 -1000
Circadian rhythm pathway 45 992 22 -0.08 0.044 1000 -1000 -0.027 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 45 2046 45 -0.059 0.077 1000 -1000 -0.018 -1000
Stabilization and expansion of the E-cadherin adherens junction 45 3359 74 -0.069 0.065 1000 -1000 -0.052 -1000
Aurora B signaling 45 3051 67 -0.058 0.067 1000 -1000 -0.018 -1000
Arf6 signaling events 44 2734 62 0 0.079 1000 -1000 0 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 44 1455 33 -0.003 0.083 1000 -1000 -0.008 -1000
p75(NTR)-mediated signaling 42 5257 125 -0.069 0.093 1000 -1000 -0.036 -1000
S1P3 pathway 42 1773 42 -0.019 0.053 1000 -1000 -0.003 -1000
PLK1 signaling events 41 3557 85 -0.041 0.051 1000 -1000 -0.019 -1000
Reelin signaling pathway 41 2304 56 -0.016 0.091 1000 -1000 -0.006 -1000
RXR and RAR heterodimerization with other nuclear receptor 41 2157 52 -0.045 0.092 1000 -1000 -0.011 -1000
Regulation of p38-alpha and p38-beta 41 2233 54 -0.032 0.091 1000 -1000 -0.001 -1000
Regulation of Telomerase 41 4239 102 -0.114 0.072 1000 -1000 -0.016 -1000
ErbB2/ErbB3 signaling events 40 2650 65 -0.029 0.047 1000 -1000 -0.04 -1000
Canonical NF-kappaB pathway 40 1570 39 -0.036 0.065 1000 -1000 -0.018 -1000
Regulation of Androgen receptor activity 40 2836 70 -0.087 0.063 1000 -1000 -0.023 -1000
EGFR-dependent Endothelin signaling events 38 799 21 -0.016 0.081 1000 -1000 0 -1000
PDGFR-beta signaling pathway 38 3711 97 -0.039 0.083 1000 -1000 -0.034 -1000
JNK signaling in the CD4+ TCR pathway 37 636 17 -0.004 0.072 1000 -1000 -0.001 -1000
Insulin-mediated glucose transport 37 1203 32 -0.018 0.046 1000 -1000 -0.017 -1000
mTOR signaling pathway 37 1976 53 -0.036 0.059 1000 -1000 -0.015 -1000
FOXA2 and FOXA3 transcription factor networks 36 1667 46 -0.131 0.055 1000 -1000 -0.005 -1000
S1P5 pathway 36 614 17 -0.008 0.04 1000 -1000 -0.021 -1000
Neurotrophic factor-mediated Trk receptor signaling 36 4432 120 -0.054 0.087 1000 -1000 -0.019 -1000
Aurora A signaling 35 2100 60 -0.046 0.064 1000 -1000 -0.017 -1000
p38 MAPK signaling pathway 35 1552 44 -0.035 0.073 1000 -1000 0 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 34 1843 54 -0.017 0.055 1000 -1000 -0.017 -1000
Ceramide signaling pathway 34 2596 76 -0.018 0.079 1000 -1000 -0.017 -1000
ceramide signaling pathway 34 1666 49 -0.034 0.06 1000 -1000 -0.007 -1000
Syndecan-3-mediated signaling events 34 1207 35 -0.011 0.067 1000 -1000 -0.017 -1000
S1P4 pathway 34 855 25 -0.014 0.053 1000 -1000 -0.005 -1000
Arf6 downstream pathway 33 1452 43 -0.036 0.057 1000 -1000 -0.045 -1000
Signaling mediated by p38-gamma and p38-delta 33 495 15 -0.04 0.039 1000 -1000 -0.017 -1000
Regulation of nuclear SMAD2/3 signaling 32 4390 136 -0.093 0.088 1000 -1000 -0.049 -1000
Ephrin A reverse signaling 31 220 7 -0.015 0.039 1000 -1000 -0.008 -1000
Hedgehog signaling events mediated by Gli proteins 31 2054 65 -0.002 0.076 1000 -1000 -0.011 -1000
Class I PI3K signaling events mediated by Akt 31 2134 68 -0.032 0.077 1000 -1000 -0.019 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 31 2629 83 -0.011 0.067 1000 -1000 -0.02 -1000
Signaling events mediated by HDAC Class I 31 3256 104 -0.041 0.076 1000 -1000 -0.039 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 30 710 23 -0.015 0.065 1000 -1000 -0.002 -1000
Atypical NF-kappaB pathway 30 946 31 -0.017 0.04 1000 -1000 -0.017 -1000
Glucocorticoid receptor regulatory network 29 3319 114 -0.103 0.074 1000 -1000 -0.042 -1000
Signaling events regulated by Ret tyrosine kinase 29 2396 82 -0.01 0.093 1000 -1000 -0.022 -1000
Sphingosine 1-phosphate (S1P) pathway 28 804 28 -0.019 0.053 1000 -1000 -0.017 -1000
Insulin Pathway 28 2123 74 -0.026 0.1 1000 -1000 -0.028 -1000
Class IB PI3K non-lipid kinase events 28 84 3 -0.039 0.039 1000 -1000 -0.037 -1000
Coregulation of Androgen receptor activity 27 2076 76 -0.011 0.051 1000 -1000 -0.018 -1000
Nephrin/Neph1 signaling in the kidney podocyte 27 923 34 -0.048 0.084 1000 -1000 -0.047 -1000
Glypican 1 network 27 1342 48 -0.039 0.067 1000 -1000 -0.038 -1000
Signaling events mediated by VEGFR1 and VEGFR2 27 3460 125 -0.02 0.069 1000 -1000 -0.017 -1000
LPA4-mediated signaling events 25 307 12 -0.015 0.045 1000 -1000 -0.013 -1000
IL27-mediated signaling events 25 1310 51 -0.009 0.08 1000 -1000 -0.026 -1000
Alternative NF-kappaB pathway 25 329 13 0 0.093 1000 -1000 0 -1000
Signaling events mediated by HDAC Class II 24 1866 75 -0.036 0.092 1000 -1000 -0.024 -1000
Signaling events mediated by HDAC Class III 24 975 40 -0.062 0.071 1000 -1000 -0.055 -1000
VEGFR1 specific signals 24 1375 56 -0.03 0.045 1000 -1000 -0.02 -1000
Angiopoietin receptor Tie2-mediated signaling 24 2192 88 -0.045 0.075 1000 -1000 -0.047 -1000
Sumoylation by RanBP2 regulates transcriptional repression 23 643 27 -0.031 0.083 1000 -1000 -0.023 -1000
Aurora C signaling 22 160 7 0 0.06 1000 -1000 0 -1000
Signaling mediated by p38-alpha and p38-beta 22 984 44 -0.028 0.052 1000 -1000 -0.009 -1000
Effects of Botulinum toxin 22 573 26 -0.01 0.069 1000 -1000 -0.009 -1000
Calcium signaling in the CD4+ TCR pathway 22 700 31 -0.024 0.082 1000 -1000 -0.028 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 22 1512 68 -0.077 0.094 1000 -1000 -0.03 -1000
Rapid glucocorticoid signaling 22 444 20 -0.01 0.046 1000 -1000 -0.01 -1000
S1P1 pathway 21 784 36 0 0.043 1000 -1000 -0.003 -1000
Arf6 trafficking events 19 1363 71 -0.046 0.05 1000 -1000 -0.038 -1000
Arf1 pathway 19 1071 54 -0.009 0.051 1000 -1000 -0.01 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 17 1326 78 -0.017 0.063 1000 -1000 -0.042 -1000
Glypican 2 network 16 64 4 0.039 0.054 1000 -1000 0.037 -1000
Visual signal transduction: Rods 14 736 52 -0.017 0.097 1000 -1000 -0.006 -1000
Visual signal transduction: Cones 13 520 38 -0.01 0.089 1000 -1000 -0.012 -1000
Total 6285 347164 7203 -7.07522783783 8.22199666664 131000 -131000 -2.55295671642 -131000
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.026 0.02 -9999 0 0 207 207
PLK4 0.036 0.014 -9999 0 0 74 74
regulation of centriole replication -0.011 0.01 0 251 -9999 0 251
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 -0.344 0.596 -9999 0 -1.147 159 159
PLK1 -0.045 0.297 -9999 0 -1.206 32 32
BIRC5 -0.053 0.331 -9999 0 -1.311 33 33
HSPA1B -0.345 0.596 -9999 0 -1.101 177 177
MAP2K1 0.003 0.07 -9999 0 -9999 0 0
BRCA2 -0.354 0.608 -9999 0 -1.144 170 170
FOXM1 -0.508 0.878 -9999 0 -1.605 176 176
XRCC1 -0.341 0.602 0.753 1 -1.13 168 169
FOXM1B/p19 -0.432 0.657 -9999 0 -1.262 179 179
Cyclin D1/CDK4 -0.353 0.555 -9999 0 -1.019 183 183
CDC2 -0.404 0.676 -9999 0 -1.26 181 181
TGFA -0.317 0.52 -9999 0 -0.979 169 169
SKP2 -0.34 0.607 -9999 0 -1.138 167 167
CCNE1 0.018 0.028 -9999 0 -0.033 66 66
CKS1B -0.345 0.606 -9999 0 -1.141 168 168
RB1 -0.313 0.47 -9999 0 -0.942 165 165
FOXM1C/SP1 -0.426 0.707 -9999 0 -1.319 178 178
AURKB -0.111 0.413 -9999 0 -1.228 61 61
CENPF -0.381 0.629 -9999 0 -1.168 182 182
CDK4 0.008 0.044 0.108 1 -0.038 188 189
MYC -0.329 0.484 -9999 0 -0.942 177 177
CHEK2 0.006 0.065 -9999 0 -9999 0 0
ONECUT1 -0.352 0.578 -9999 0 -1.092 170 170
CDKN2A 0.026 0.02 0.089 2 -0.033 7 9
LAMA4 -0.385 0.632 -9999 0 -1.167 186 186
FOXM1B/HNF6 -0.445 0.709 -9999 0 -1.369 170 170
FOS -0.418 0.651 -9999 0 -1.154 214 214
SP1 0.035 0.022 -9999 0 -0.032 48 48
CDC25B -0.345 0.604 -9999 0 -1.136 167 167
response to radiation -0.006 0.036 0.088 6 -9999 0 6
CENPB -0.337 0.599 -9999 0 -1.133 163 163
CENPA -0.346 0.601 -9999 0 -1.136 167 167
NEK2 -0.356 0.613 -9999 0 -1.16 169 169
HIST1H2BA -0.339 0.601 -9999 0 -1.132 164 164
CCNA2 0.023 0.03 -9999 0 -0.013 201 201
EP300 0.036 0.014 -9999 0 0 69 69
CCNB1/CDK1 -0.48 0.785 -9999 0 -1.502 175 175
CCNB2 -0.375 0.625 -9999 0 -1.167 178 178
CCNB1 -0.384 0.658 -9999 0 -1.249 169 169
ETV5 -0.354 0.643 -9999 0 -1.154 185 185
ESR1 -0.383 0.615 -9999 0 -1.122 189 189
CCND1 -0.36 0.556 -9999 0 -1.033 183 183
GSK3A 0.005 0.061 0.156 1 -9999 0 1
Cyclin A-E1/CDK1-2 -0.009 0.104 -9999 0 -0.163 116 116
CDK2 0.027 0.029 -9999 0 -0.02 138 138
G2/M transition of mitotic cell cycle -0.007 0.043 0.099 5 -9999 0 5
FOXM1B/Cbp/p300 -0.393 0.664 -9999 0 -1.247 174 174
GAS1 -0.352 0.601 -9999 0 -1.13 171 171
MMP2 -0.424 0.65 -9999 0 -1.156 212 212
RB1/FOXM1C -0.402 0.586 0.666 1 -1.124 180 181
CREBBP 0.037 0.012 -9999 0 0 53 53
TCGA08_p53

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
CDKN2A -0.007 0.005 0 167 -9999 0 167
TP53 -0.052 0.115 0.176 12 -0.238 143 155
Senescence -0.053 0.115 0.176 12 -0.237 145 157
Apoptosis -0.053 0.115 0.176 12 -0.237 145 157
Activated_Oncogenes 0 0 -9999 0 -9999 0 0
MDM2 -0.004 0.044 0.301 11 -9999 0 11
MDM4 0.038 0.012 -9999 0 0 47 47
HIF-1-alpha transcription factor network

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
PKM2 0.046 0.336 0.558 50 -0.54 81 131
HDAC7 -0.001 0.004 -9999 0 -0.039 1 1
HIF1A/ARNT/Cbp/p300/Src-1 0.018 0.313 0.573 3 -0.581 57 60
SMAD4 0.038 0.011 -9999 0 0 43 43
ID2 0.046 0.336 0.558 51 -0.536 81 132
AP1 0.006 0.084 -9999 0 -0.142 118 118
ABCG2 0.042 0.335 0.56 49 -0.541 80 129
HIF1A 0.028 0.106 0.199 43 -0.144 78 121
TFF3 0.024 0.321 0.561 40 -0.537 80 120
GATA2 0.04 0.018 -9999 0 -0.056 11 11
AKT1 0.042 0.098 0.223 32 -0.118 61 93
response to hypoxia 0.004 0.07 0.15 36 -0.115 55 91
MCL1 0.034 0.329 0.549 45 -0.546 80 125
NDRG1 0 0.298 0.533 30 -0.565 70 100
SERPINE1 0 0.307 0.553 30 -0.547 78 108
FECH 0.043 0.336 0.56 50 -0.55 78 128
FURIN 0.046 0.335 0.555 52 -0.541 80 132
NCOA2 0.038 0.014 -9999 0 -0.001 61 61
EP300 0.046 0.121 0.287 48 -0.248 22 70
HMOX1 0.032 0.332 0.554 43 -0.552 81 124
BHLHE40 -0.025 0.289 0.455 50 -0.532 82 132
BHLHE41 -0.025 0.289 0.455 50 -0.532 82 132
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.087 0.152 0.351 13 -0.208 35 48
ENG 0.032 0.121 0.28 26 -0.214 24 50
JUN 0.035 0.018 -9999 0 -0.042 10 10
RORA 0.045 0.335 0.558 49 -0.543 80 129
ABCB1 0.014 0.093 -9999 0 -0.546 4 4
TFRC 0.004 0.312 0.552 32 -0.552 79 111
CXCR4 0.019 0.333 0.552 42 -0.554 83 125
TF 0.04 0.331 0.558 50 -0.535 80 130
CITED2 0.042 0.332 0.551 49 -0.536 81 130
HIF1A/ARNT 0.018 0.37 -9999 0 -0.678 56 56
LDHA -0.048 0.293 -9999 0 -0.93 50 50
ETS1 0.024 0.328 0.545 39 -0.566 78 117
PGK1 0.045 0.344 0.562 50 -0.558 81 131
NOS2 -0.025 0.289 0.455 50 -0.532 82 132
ITGB2 0.025 0.335 0.554 41 -0.555 85 126
ALDOA 0.052 0.339 0.557 54 -0.541 81 135
Cbp/p300/CITED2 0.017 0.332 0.545 32 -0.61 67 99
FOS 0.026 0.022 -9999 0 -0.001 206 206
HK2 0.045 0.338 0.558 51 -0.549 79 130
SP1 0.047 0.009 -9999 0 -9999 0 0
GCK 0.067 0.159 0.529 8 -0.411 1 9
HK1 0.049 0.338 0.553 53 -0.541 81 134
NPM1 0.051 0.34 0.559 53 -0.538 82 135
EGLN1 0.049 0.334 0.554 54 -0.535 80 134
CREB1 0.034 0.042 -9999 0 -0.11 40 40
PGM1 0.038 0.339 0.557 46 -0.559 81 127
SMAD3 0.04 0.009 -9999 0 0 23 23
EDN1 0.037 0.212 0.464 5 -1.049 12 17
IGFBP1 0.051 0.338 0.556 53 -0.54 80 133
VEGFA -0.009 0.259 0.444 34 -0.499 66 100
HIF1A/JAB1 0.035 0.099 0.192 15 -0.135 87 102
CP -0.006 0.314 0.536 36 -0.559 80 116
CXCL12 -0.012 0.311 0.556 27 -0.553 83 110
COPS5 0.036 0.015 -9999 0 -0.001 80 80
SMAD3/SMAD4 0.052 0.032 -9999 0 -0.134 10 10
BNIP3 0.026 0.333 0.559 41 -0.568 77 118
EGLN3 -0.006 0.323 0.548 31 -0.562 88 119
CA9 -0.006 0.306 0.552 28 -0.542 82 110
TERT 0.036 0.326 0.548 46 -0.542 78 124
ENO1 0.048 0.34 0.561 51 -0.551 80 131
PFKL 0.051 0.338 0.558 52 -0.54 81 133
NCOA1 0.04 0.009 -9999 0 -0.001 23 23
ADM 0.011 0.318 0.558 27 -0.547 83 110
ARNT 0.027 0.095 0.194 36 -0.125 69 105
HNF4A 0.041 0.011 -9999 0 -9999 0 0
ADFP 0.01 0.325 0.552 36 -0.55 86 122
SLC2A1 0.013 0.286 0.482 32 -0.517 70 102
LEP 0.049 0.336 0.56 51 -0.546 78 129
HIF1A/ARNT/Cbp/p300 0.01 0.313 0.566 3 -0.602 57 60
EPO 0.039 0.279 0.516 22 -0.533 52 74
CREBBP 0.051 0.118 0.288 51 -0.222 16 67
HIF1A/ARNT/Cbp/p300/HDAC7 0.002 0.304 0.541 3 -0.593 58 61
PFKFB3 0.041 0.337 0.558 49 -0.557 79 128
NT5E -0.027 0.31 0.544 22 -0.555 89 111
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.031 0.018 -9999 0 0 139 139
EPHB2 0.042 0.013 -9999 0 0 38 38
EFNB1 0.001 0.024 0.026 246 -9999 0 246
mol:GTP 0 0 -9999 0 -9999 0 0
Rac1/GDP 0.075 0.066 -9999 0 -0.12 19 19
Ephrin B2/EPHB1-2 0.039 0.068 -9999 0 -0.102 78 78
neuron projection morphogenesis 0.051 0.052 -9999 0 -0.111 24 24
Ephrin B1/EPHB1-2/Tiam1 0.069 0.061 0.195 1 -0.114 29 30
DNM1 0.041 0.011 -9999 0 0 33 33
cell-cell signaling 0.003 0.005 -9999 0 -9999 0 0
MAP2K4 -0.135 0.214 0.226 3 -0.462 159 162
YES1 -0.193 0.326 -9999 0 -0.702 157 157
Ephrin B1/EPHB1-2/NCK2 0.079 0.05 0.194 2 -0.111 15 17
PI3K -0.104 0.223 -9999 0 -0.436 159 159
mol:GDP 0.067 0.059 0.19 1 -0.113 29 30
ITGA2B 0.04 0.008 -9999 0 0 22 22
endothelial cell proliferation 0.024 0.06 -9999 0 -0.109 82 82
FYN -0.198 0.328 -9999 0 -0.705 159 159
MAP3K7 -0.135 0.226 0.22 3 -0.489 155 158
FGR -0.187 0.324 -9999 0 -0.685 161 161
TIAM1 0.036 0.013 -9999 0 0 66 66
PIK3R1 0.034 0.016 -9999 0 0 99 99
RGS3 0.04 0.007 -9999 0 0 15 15
cell adhesion -0.108 0.206 -9999 0 -0.413 159 159
LYN -0.189 0.324 -9999 0 -0.699 155 155
Ephrin B1/EPHB1-2/Src Family Kinases -0.178 0.294 -9999 0 -0.631 160 160
Ephrin B1/EPHB1-2 -0.139 0.243 -9999 0 -0.533 149 149
SRC -0.184 0.322 -9999 0 -0.686 158 158
ITGB3 0.032 0.017 -9999 0 0 116 116
EPHB1 0.04 0.013 -9999 0 0 50 50
EPHB4 0.039 0.008 -9999 0 0 23 23
RAC1 0.039 0.009 -9999 0 0 28 28
Ephrin B2/EPHB4 0.025 0.06 -9999 0 -0.11 82 82
alphaIIb/beta3 Integrin 0.039 0.05 -9999 0 -0.133 35 35
BLK -0.195 0.322 -9999 0 -0.695 158 158
HCK -0.186 0.321 -9999 0 -0.692 155 155
regulation of stress fiber formation -0.076 0.049 0.111 15 -0.188 2 17
MAPK8 -0.133 0.206 0.207 4 -0.445 160 164
Ephrin B1/EPHB1-2/RGS3 0.079 0.05 0.194 2 -0.113 15 17
endothelial cell migration -0.113 0.184 0.187 5 -0.41 145 150
NCK2 0.041 0.004 -9999 0 0 6 6
PTPN13 0.022 0.022 -9999 0 0 271 271
regulation of focal adhesion formation -0.076 0.049 0.111 15 -0.188 2 17
chemotaxis -0.076 0.049 0.112 15 -0.188 2 17
PIK3CA 0.029 0.019 -9999 0 0 166 166
Rac1/GTP 0.064 0.059 -9999 0 -0.114 22 22
angiogenesis -0.141 0.242 -9999 0 -0.527 153 153
LCK -0.186 0.323 -9999 0 -0.682 161 161
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.019 0.078 -9999 0 -0.131 109 109
NF kappa B1 p50/RelA/I kappa B alpha -0.009 0.108 0.209 4 -0.224 67 71
AP1 -0.026 0.067 -9999 0 -0.115 170 170
mol:PIP3 -0.035 0.056 -9999 0 -0.128 122 122
AKT1 0 0.091 0.235 14 -0.238 13 27
PTK2B -0.043 0.105 0.121 3 -0.181 172 175
RHOA 0.002 0.06 0.175 1 -0.309 9 10
PIK3CB 0.034 0.016 -9999 0 0 95 95
mol:Ca2+ -0.009 0.05 0.194 8 -0.145 22 30
MAGI3 0.039 0.009 -9999 0 0 30 30
RELA 0.04 0.006 -9999 0 0 10 10
apoptosis 0.002 0.068 0.072 119 -0.135 94 213
HRAS/GDP 0.029 0.007 -9999 0 -9999 0 0
positive regulation of microtubule depolymerization -0.042 0.1 0.19 17 -0.195 108 125
NF kappa B1 p50/RelA -0.03 0.075 0.101 2 -0.157 112 114
endothelial cell migration -0.041 0.119 -9999 0 -0.293 100 100
ADCY4 -0.021 0.096 0.142 8 -0.193 107 115
ADCY5 -0.019 0.095 0.146 7 -0.192 106 113
ADCY6 -0.021 0.096 0.146 7 -0.195 106 113
ADCY7 -0.02 0.095 0.146 7 -0.193 102 109
ADCY1 -0.02 0.096 0.146 7 -0.195 106 113
ADCY2 -0.016 0.093 0.13 12 -0.189 100 112
ADCY3 -0.021 0.097 0.141 7 -0.195 108 115
ADCY8 -0.006 0.088 0.118 28 -0.178 89 117
ADCY9 -0.024 0.099 0.142 8 -0.199 110 118
GSK3B -0.041 0.106 0.207 14 -0.178 167 181
arachidonic acid secretion -0.029 0.097 0.141 4 -0.187 124 128
GNG2 0.039 0.009 -9999 0 0 29 29
TRIP6 0.013 0.048 -9999 0 -0.241 15 15
GNAO1 0.007 0.071 0.091 114 -0.143 85 199
HRAS 0.039 0.01 -9999 0 0 31 31
NFKBIA -0.032 0.092 0.175 7 -0.242 56 63
GAB1 0.037 0.013 -9999 0 0 58 58
mol:GTP 0 0 -9999 0 -9999 0 0
lamellipodium assembly -0.008 0.256 -9999 0 -0.878 43 43
JUN 0.036 0.014 -9999 0 0 76 76
LPA/LPA2/NHERF2 0.014 0.037 -9999 0 -0.062 96 96
TIAM1 -0.032 0.292 -9999 0 -1.024 43 43
PIK3R1 0.034 0.016 -9999 0 0 99 99
mol:IP3 -0.004 0.044 0.187 9 -0.141 14 23
PLCB3 0.014 0.044 0.167 10 -0.062 95 105
FOS 0.026 0.02 -9999 0 0 201 201
positive regulation of mitosis -0.029 0.097 0.141 4 -0.187 124 128
LPA/LPA1-2-3 -0.017 0.05 -9999 0 -0.121 101 101
mol:Ca ++ 0 0 -9999 0 -9999 0 0
JNK cascade 0 0 -9999 0 -9999 0 0
BCAR1 0.036 0.013 -9999 0 0 65 65
stress fiber formation -0.009 0.096 -9999 0 -0.247 38 38
GNAZ 0.006 0.074 0.092 115 -0.145 90 205
EGFR/PI3K-beta/Gab1 -0.024 0.065 -9999 0 -0.131 123 123
positive regulation of dendritic cell cytokine production -0.017 0.049 -9999 0 -0.12 101 101
LPA/LPA2/MAGI-3 0.015 0.037 -9999 0 -0.06 98 98
ARHGEF1 0.005 0.073 0.205 7 -0.131 90 97
GNAI2 0.006 0.076 0.092 121 -0.144 98 219
GNAI3 0.003 0.08 0.092 117 -0.152 99 216
GNAI1 0.003 0.079 0.092 114 -0.157 91 205
LPA/LPA3 -0.01 0.026 -9999 0 -0.064 101 101
LPA/LPA2 -0.01 0.026 -9999 0 -0.064 101 101
LPA/LPA1 -0.025 0.067 -9999 0 -0.166 101 101
HB-EGF/EGFR 0.023 0.052 -9999 0 -0.126 49 49
HBEGF -0.014 0.01 -9999 0 -9999 0 0
mol:DAG -0.004 0.044 0.187 9 -0.141 14 23
cAMP biosynthetic process -0.024 0.098 0.162 9 -0.192 103 112
NFKB1 0.036 0.013 -9999 0 0 66 66
SRC 0.039 0.009 -9999 0 0 28 28
GNB1 0.039 0.01 -9999 0 0 33 33
LYN -0.025 0.095 0.198 10 -0.232 58 68
GNAQ 0.008 0.032 0.044 116 -0.053 102 218
LPAR2 0 0.001 -9999 0 -9999 0 0
LPAR3 0 0 -9999 0 -9999 0 0
LPAR1 -0.017 0.041 -9999 0 -0.102 101 101
IL8 -0.024 0.172 0.259 4 -0.375 83 87
PTK2 0.007 0.063 0.096 84 -0.125 78 162
Rac1/GDP 0.029 0.009 -9999 0 -0.125 1 1
CASP3 0.002 0.068 0.072 117 -0.135 94 211
EGFR 0.036 0.014 -9999 0 0 67 67
PLCG1 0.005 0.036 -9999 0 -0.094 27 27
PLD2 0.015 0.066 0.095 118 -0.118 90 208
G12/G13 0.02 0.077 -9999 0 -0.133 104 104
PI3K-beta -0.023 0.072 -9999 0 -0.208 38 38
cell migration -0.007 0.086 -9999 0 -0.25 43 43
SLC9A3R2 0.037 0.012 -9999 0 0 54 54
PXN -0.01 0.098 -9999 0 -0.251 38 38
HRAS/GTP -0.029 0.099 0.142 4 -0.191 123 127
RAC1 0.039 0.009 -9999 0 0 28 28
MMP9 0.028 0.019 -9999 0 0 169 169
PRKCE 0.039 0.009 -9999 0 0 28 28
PRKCD -0.018 0.057 0.181 10 -0.161 24 34
Gi(beta/gamma) -0.023 0.103 0.159 4 -0.189 123 127
mol:LPA -0.017 0.041 -9999 0 -0.102 101 101
TRIP6/p130 Cas/FAK1/Paxillin -0.003 0.101 0.187 3 -0.196 75 78
MAPKKK cascade -0.029 0.097 0.141 4 -0.187 124 128
contractile ring contraction involved in cytokinesis 0.001 0.062 0.165 2 -0.306 10 12
mol:GDP 0 0 -9999 0 -9999 0 0
GNA14 0.008 0.033 0.044 116 -0.052 109 225
GNA15 0.008 0.031 0.043 108 -0.054 91 199
GNA12 0.039 0.01 -9999 0 0 33 33
GNA13 0.039 0.008 -9999 0 0 23 23
MAPT -0.042 0.102 0.192 17 -0.2 108 125
GNA11 0.008 0.031 0.043 108 -0.054 95 203
Rac1/GTP -0.011 0.272 -9999 0 -0.934 43 43
MMP2 -0.042 0.12 -9999 0 -0.294 100 100
Endothelins

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
AKT1 -0.01 0.142 0.222 29 -0.237 118 147
PTK2B 0.034 0.016 -9999 0 0 97 97
mol:Ca2+ -0.032 0.199 -9999 0 -0.497 45 45
EDN1 -0.009 0.102 0.222 7 -0.177 126 133
EDN3 0.037 0.013 -9999 0 0 60 60
EDN2 0.037 0.012 -9999 0 0 52 52
HRAS/GDP -0.053 0.19 0.265 2 -0.351 113 115
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.031 0.143 0.224 1 -0.269 104 105
ADCY4 0.006 0.134 0.207 63 -0.23 72 135
ADCY5 0.006 0.133 0.21 55 -0.23 72 127
ADCY6 0.006 0.137 0.208 62 -0.233 74 136
ADCY7 0.005 0.135 0.211 55 -0.234 73 128
ADCY1 0.006 0.137 0.212 57 -0.234 73 130
ADCY2 0.005 0.128 0.215 47 -0.234 61 108
ADCY3 0.005 0.137 0.207 65 -0.235 73 138
ADCY8 -0.004 0.104 0.212 28 -0.226 48 76
ADCY9 0.004 0.136 0.211 56 -0.231 76 132
arachidonic acid secretion -0.104 0.258 0.265 1 -0.488 136 137
ETB receptor/Endothelin-1/Gq/GTP -0.004 0.111 -9999 0 -0.245 61 61
GNAO1 0.035 0.015 -9999 0 0 85 85
HRAS 0.039 0.01 -9999 0 0 31 31
ETA receptor/Endothelin-1/G12/GTP -0.011 0.132 0.341 6 -0.214 126 132
ETA receptor/Endothelin-1/Gs/GTP -0.008 0.124 0.319 7 -0.201 122 129
mol:GTP 0 0.006 -9999 0 -0.025 3 3
COL3A1 -0.06 0.165 0.268 7 -0.355 116 123
EDNRB 0.021 0.053 0.091 5 -0.086 95 100
response to oxidative stress 0 0 -9999 0 -9999 0 0
CYSLTR2 -0.01 0.143 0.279 9 -0.254 99 108
CYSLTR1 -0.021 0.144 0.251 8 -0.258 113 121
SLC9A1 -0.018 0.085 0.199 7 -0.165 98 105
mol:GDP -0.067 0.19 0.253 2 -0.363 116 118
SLC9A3 -0.026 0.192 -9999 0 -0.547 31 31
RAF1 -0.077 0.223 0.262 9 -0.402 140 149
JUN -0.073 0.292 -9999 0 -0.814 56 56
JAK2 -0.013 0.142 0.219 28 -0.244 114 142
mol:IP3 -0.026 0.149 0.205 2 -0.31 81 83
ETA receptor/Endothelin-1 -0.037 0.15 0.383 6 -0.268 135 141
PLCB1 0.033 0.016 -9999 0 0 106 106
PLCB2 0.037 0.014 -9999 0 -0.006 45 45
ETA receptor/Endothelin-3 0.015 0.084 0.186 7 -0.122 118 125
FOS -0.142 0.362 0.33 1 -0.824 109 110
Gai/GDP -0.018 0.212 -9999 0 -0.706 44 44
CRK 0.038 0.012 -9999 0 0 49 49
mol:Ca ++ -0.035 0.193 0.251 27 -0.343 116 143
BCAR1 0.036 0.013 -9999 0 0 65 65
PRKCB1 -0.03 0.15 0.221 7 -0.305 84 91
GNAQ 0.034 0.022 -9999 0 -0.039 30 30
GNAZ 0.038 0.011 -9999 0 0 46 46
GNAL 0.04 0.008 -9999 0 0 22 22
Gs family/GDP -0.052 0.18 0.248 2 -0.338 111 113
ETA receptor/Endothelin-1/Gq/GTP -0.022 0.141 0.214 5 -0.28 84 89
MAPK14 -0.023 0.113 0.23 2 -0.248 75 77
TRPC6 -0.035 0.204 -9999 0 -0.521 44 44
GNAI2 0.04 0.006 -9999 0 0 13 13
GNAI3 0.038 0.011 -9999 0 0 45 45
GNAI1 0.034 0.015 -9999 0 0 93 93
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.018 0.12 -9999 0 -0.251 79 79
ETB receptor/Endothelin-2 0.031 0.054 -9999 0 -0.07 85 85
ETB receptor/Endothelin-3 0.033 0.051 -9999 0 -0.065 82 82
ETB receptor/Endothelin-1 0 0.104 0.198 5 -0.187 100 105
MAPK3 -0.131 0.343 0.317 3 -0.755 112 115
MAPK1 -0.138 0.35 0.317 3 -0.753 117 120
Rac1/GDP -0.054 0.188 0.257 2 -0.352 111 113
cAMP biosynthetic process 0.034 0.127 0.244 43 -0.227 29 72
MAPK8 -0.052 0.234 -9999 0 -0.541 70 70
SRC 0.039 0.009 -9999 0 0 28 28
ETB receptor/Endothelin-1/Gi/GTP -0.01 0.108 -9999 0 -0.259 58 58
p130Cas/CRK/Src/PYK2 -0.06 0.198 0.358 1 -0.405 91 92
mol:K + 0 0 -9999 0 -9999 0 0
G12/GDP -0.054 0.187 0.27 1 -0.35 112 113
COL1A2 -0.079 0.215 0.276 6 -0.488 106 112
EntrezGene:2778 0 0 -9999 0 -9999 0 0
ETA receptor/Endothelin-2 0.012 0.088 0.185 8 -0.127 125 133
mol:DAG -0.026 0.15 0.205 2 -0.31 81 83
MAP2K2 -0.1 0.271 0.292 4 -0.546 124 128
MAP2K1 -0.106 0.276 0.292 4 -0.558 125 129
EDNRA -0.004 0.103 0.221 8 -0.166 134 142
positive regulation of muscle contraction -0.016 0.123 0.214 24 -0.236 81 105
Gq family/GDP -0.019 0.187 -9999 0 -0.319 110 110
HRAS/GTP -0.055 0.184 0.238 3 -0.334 122 125
PRKCH -0.034 0.151 0.196 1 -0.304 91 92
RAC1 0.039 0.009 -9999 0 0 28 28
PRKCA -0.031 0.15 0.233 4 -0.306 85 89
PRKCB -0.03 0.149 0.193 2 -0.292 93 95
PRKCE -0.032 0.149 0.279 5 -0.298 89 94
PRKCD -0.033 0.148 0.241 2 -0.303 87 89
PRKCG -0.033 0.152 0.233 6 -0.304 89 95
regulation of vascular smooth muscle contraction -0.18 0.436 -9999 0 -1.026 106 106
PRKCQ -0.034 0.151 0.264 5 -0.307 88 93
PLA2G4A -0.116 0.282 -9999 0 -0.534 136 136
GNA14 0.035 0.021 -9999 0 -0.038 33 33
GNA15 0.033 0.022 -9999 0 -0.035 29 29
GNA12 0.039 0.01 -9999 0 0 33 33
GNA11 0.033 0.021 -9999 0 -0.012 91 91
Rac1/GTP -0.011 0.132 0.341 6 -0.214 125 131
MMP1 0.023 0.119 0.301 21 -0.579 9 30
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.036 0.014 -9999 0 0 69 69
CCL5 0.029 0.019 -9999 0 0 160 160
SDCBP 0.035 0.014 -9999 0 0 77 77
FGFR/FGF2/Syndecan-1 -0.018 0.123 0.196 14 -0.321 44 58
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 -0.017 0.137 0.227 15 -0.301 59 74
Syndecan-1/Syntenin -0.017 0.142 0.232 21 -0.291 67 88
MAPK3 -0.025 0.131 0.204 22 -0.278 64 86
HGF/MET 0.013 0.074 -9999 0 -0.132 102 102
TGFB1/TGF beta receptor Type II 0.036 0.014 -9999 0 0 69 69
BSG 0.036 0.014 -9999 0 0 74 74
keratinocyte migration -0.016 0.136 0.226 15 -0.297 59 74
Syndecan-1/RANTES -0.021 0.146 0.223 21 -0.29 79 100
Syndecan-1/CD147 -0.004 0.15 0.257 17 -0.29 63 80
Syndecan-1/Syntenin/PIP2 -0.019 0.135 0.206 19 -0.281 67 86
LAMA5 0.036 0.014 -9999 0 0 72 72
positive regulation of cell-cell adhesion -0.019 0.132 0.207 16 -0.276 67 83
MMP7 0.016 0.02 -9999 0 0 333 333
HGF 0.039 0.009 -9999 0 0 27 27
Syndecan-1/CASK -0.044 0.116 0.146 3 -0.288 65 68
Syndecan-1/HGF/MET -0.021 0.146 0.264 14 -0.267 85 99
regulation of cell adhesion -0.033 0.122 0.187 19 -0.284 59 78
HPSE 0.035 0.014 -9999 0 0 79 79
positive regulation of cell migration -0.018 0.123 0.196 14 -0.321 44 58
SDC1 -0.022 0.116 0.167 4 -0.34 38 42
Syndecan-1/Collagen -0.018 0.123 0.196 14 -0.321 44 58
PPIB 0.04 0.007 -9999 0 0 18 18
MET 0.027 0.02 -9999 0 0 191 191
PRKACA 0.035 0.015 -9999 0 0 84 84
MMP9 0.028 0.019 -9999 0 0 169 169
MAPK1 -0.023 0.129 0.196 22 -0.281 62 84
homophilic cell adhesion -0.018 0.128 0.2 22 -0.31 50 72
MMP1 0.03 0.018 -9999 0 0 151 151
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.013 0.132 0.208 7 -0.222 114 121
NF kappa B1 p50/RelA/I kappa B alpha -0.043 0.185 0.28 1 -0.352 117 118
alphaV/beta3 Integrin/Osteopontin/Src -0.007 0.109 -9999 0 -0.179 133 133
AP1 -0.047 0.179 0.268 2 -0.283 150 152
ILK -0.029 0.108 0.202 9 -0.234 72 81
bone resorption -0.042 0.103 0.196 2 -0.251 54 56
PTK2B 0.034 0.016 -9999 0 0 97 97
PYK2/p130Cas 0.006 0.123 -9999 0 -0.201 81 81
ITGAV 0.025 0.033 -9999 0 -0.049 64 64
mol:GTP 0 0 -9999 0 -9999 0 0
CD44/Rho Family GTPase/ROCK2 0.028 0.067 -9999 0 -0.14 68 68
alphaV/beta3 Integrin/Osteopontin -0.005 0.125 -9999 0 -0.174 157 157
MAP3K1 -0.028 0.106 0.201 8 -0.236 70 78
JUN 0.036 0.015 -9999 0 0 76 76
MAPK3 -0.05 0.138 0.188 12 -0.282 113 125
MAPK1 -0.047 0.136 0.188 12 -0.279 109 121
Rac1/GDP 0.029 0.009 -9999 0 -0.125 1 1
NFKB1 0.036 0.013 -9999 0 0 66 66
MAPK8 -0.034 0.105 0.192 9 -0.235 73 82
ITGB3 0.023 0.034 -9999 0 -0.049 76 76
NFKBIA -0.065 0.167 0.192 9 -0.354 114 123
FOS 0.026 0.02 -9999 0 0 201 201
CD44 0.034 0.015 -9999 0 0 90 90
CHUK 0.038 0.011 -9999 0 0 46 46
PLAU -0.19 0.415 -9999 0 -1.025 104 104
NF kappa B1 p50/RelA -0.03 0.204 0.29 1 -0.39 109 110
BCAR1 0.036 0.013 -9999 0 0 65 65
RELA 0.04 0.006 -9999 0 0 10 10
alphaV beta3 Integrin 0.004 0.091 -9999 0 -0.141 130 130
mol:GDP 0 0 -9999 0 -9999 0 0
SYK -0.03 0.104 0.188 12 -0.226 75 87
VAV3 -0.042 0.101 0.169 9 -0.229 88 97
MAP3K14 -0.027 0.124 0.204 10 -0.23 109 119
ROCK2 0.037 0.013 -9999 0 0 58 58
SPP1 0.025 0.032 -9999 0 -0.051 51 51
RAC1 0.039 0.009 -9999 0 0 28 28
Rac1/GTP -0.037 0.106 0.176 10 -0.219 86 96
MMP2 -0.089 0.144 0.224 2 -0.315 124 126
Wnt signaling

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
Noncanonical Wnts/FZD -0.017 0.093 -9999 0 -0.28 38 38
FZD6 0.029 0.019 -9999 0 0 162 162
WNT6 0.04 0.006 -9999 0 0 13 13
WNT4 0.04 0.008 -9999 0 0 19 19
FZD3 0.03 0.019 -9999 0 0 153 153
WNT5A 0.034 0.015 -9999 0 0 89 89
WNT11 0.032 0.017 -9999 0 0 118 118
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.036 0.013 -9999 0 0 65 65
alphaV beta3 Integrin 0.014 0.078 -9999 0 -0.146 93 93
PTK2 -0.047 0.137 -9999 0 -0.308 100 100
positive regulation of JNK cascade -0.038 0.147 -9999 0 -0.28 106 106
CDC42/GDP -0.048 0.199 -9999 0 -0.363 131 131
Rac1/GDP -0.05 0.197 -9999 0 -0.364 126 126
RAP1B 0.037 0.012 -9999 0 0 54 54
RAP1A 0.039 0.01 -9999 0 0 35 35
CTNNB1 0.039 0.01 -9999 0 0 32 32
CDC42/GTP -0.044 0.179 -9999 0 -0.341 105 105
nectin-3/I-afadin 0.011 0.073 -9999 0 -0.137 93 93
RAPGEF1 -0.065 0.183 -9999 0 -0.371 126 126
mol:GTP 0 0 -9999 0 -9999 0 0
CRK -0.073 0.2 -9999 0 -0.41 129 129
PDGFB-D/PDGFRB 0.036 0.013 -9999 0 0 65 65
TLN1 -0.036 0.08 0.19 1 -0.241 55 56
Rap1/GTP -0.048 0.144 -9999 0 -0.286 124 124
IQGAP1 0.036 0.013 -9999 0 0 66 66
Rap1/GTP/I-afadin 0.043 0.063 -9999 0 -0.11 61 61
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.011 0.073 -9999 0 -0.137 93 93
PVR 0.038 0.011 -9999 0 0 39 39
Necl-5(dimer) 0.038 0.011 -9999 0 0 39 39
mol:GDP -0.078 0.223 -9999 0 -0.434 131 131
MLLT4 0.033 0.016 -9999 0 0 109 109
PIK3CA 0.029 0.019 -9999 0 0 166 166
PI3K 0.022 0.086 -9999 0 -0.124 90 90
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.042 0.043 -9999 0 -0.134 22 22
positive regulation of lamellipodium assembly -0.047 0.159 -9999 0 -0.301 115 115
PVRL1 0.04 0.008 -9999 0 0 22 22
PVRL3 0.029 0.019 -9999 0 0 158 158
PVRL2 0.037 0.012 -9999 0 0 51 51
PIK3R1 0.034 0.016 -9999 0 0 99 99
CDH1 0.035 0.014 -9999 0 0 79 79
CLDN1 0.022 0.021 -9999 0 0 249 249
JAM-A/CLDN1 0.011 0.087 -9999 0 -0.122 124 124
SRC -0.088 0.211 -9999 0 -0.444 130 130
ITGB3 0.032 0.017 -9999 0 0 116 116
nectin-1(dimer)/I-afadin/I-afadin 0.042 0.043 -9999 0 -0.134 22 22
FARP2 -0.07 0.225 -9999 0 -0.461 90 90
RAC1 0.039 0.009 -9999 0 0 28 28
CTNNA1 0.039 0.01 -9999 0 0 31 31
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.024 0.075 -9999 0 -0.118 92 92
nectin-1/I-afadin 0.042 0.043 -9999 0 -0.134 22 22
nectin-2/I-afadin 0.038 0.047 -9999 0 -0.137 27 27
RAC1/GTP/IQGAP1/filamentous actin 0.039 0.045 -9999 0 -0.11 40 40
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.026 0.074 -9999 0 -0.119 89 89
CDC42/GTP/IQGAP1/filamentous actin 0.039 0.046 -9999 0 -0.112 42 42
F11R 0.039 0.008 -9999 0 0 24 24
positive regulation of filopodium formation -0.038 0.147 -9999 0 -0.28 106 106
alphaV/beta3 Integrin/Talin -0.033 0.109 0.262 1 -0.224 95 96
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.047 -9999 0 -0.137 27 27
nectin-2(dimer)/I-afadin/I-afadin 0.038 0.047 -9999 0 -0.137 27 27
PIP5K1C -0.03 0.083 -9999 0 -0.17 109 109
VAV2 -0.088 0.244 -9999 0 -0.485 109 109
RAP1/GDP -0.046 0.186 -9999 0 -0.342 128 128
ITGAV 0.033 0.017 -9999 0 0 110 110
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.022 0.075 -9999 0 -0.119 94 94
nectin-3(dimer)/I-afadin/I-afadin 0.011 0.073 -9999 0 -0.137 93 93
Rac1/GTP -0.057 0.192 -9999 0 -0.366 114 114
PTPRM -0.027 0.094 -9999 0 -0.181 117 117
E-cadherin/beta catenin/alpha catenin 0.063 0.085 -9999 0 -0.127 50 50
adherens junction assembly 0 0 -9999 0 -9999 0 0
CDC42 0.04 0.007 -9999 0 0 18 18
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.006 0.084 -9999 0 -0.125 127 127
alphaM/beta2 Integrin/GPIbA 0.051 0.067 -9999 0 -0.114 57 57
alphaM/beta2 Integrin/proMMP-9 0.029 0.081 -9999 0 -0.131 83 83
PLAUR 0.035 0.015 -9999 0 0 82 82
HMGB1 0.041 0.015 -9999 0 -0.053 9 9
alphaM/beta2 Integrin/Talin 0.047 0.075 -9999 0 -0.12 75 75
AGER 0.041 0.015 -9999 0 -0.053 9 9
RAP1A 0.039 0.01 -9999 0 0 35 35
SELPLG 0.039 0.009 -9999 0 0 25 25
mol:LDL 0 0 -9999 0 -9999 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.081 0.08 -9999 0 -0.167 11 11
mol:GTP 0 0 -9999 0 -9999 0 0
MMP9 0.028 0.019 -9999 0 0 169 169
CYR61 0.03 0.018 -9999 0 0 149 149
TLN1 0.038 0.011 -9999 0 0 39 39
Rap1/GTP -0.063 0.173 -9999 0 -0.312 134 134
RHOA 0.04 0.006 -9999 0 0 13 13
P-selectin oligomer 0.039 0.01 -9999 0 0 34 34
MYH2 -0.08 0.171 0.195 2 -0.334 133 135
MST1R 0.038 0.011 -9999 0 0 39 39
leukocyte activation during inflammatory response 0.055 0.063 -9999 0 -0.099 47 47
APOB 0.04 0.007 -9999 0 0 14 14
mol:GDP 0 0 -9999 0 -9999 0 0
complement component iC3b receptor activity 0 0 -9999 0 -9999 0 0
MMP2 0.021 0.021 -9999 0 0 265 265
JAM3 0.038 0.012 -9999 0 0 47 47
GP1BA 0.038 0.011 -9999 0 0 42 42
alphaM/beta2 Integrin/CTGF 0.035 0.079 -9999 0 -0.118 93 93
alphaM/beta2 Integrin -0.066 0.171 -9999 0 -0.35 116 116
JAM3 homodimer 0.038 0.012 -9999 0 0 47 47
ICAM2 0.038 0.01 -9999 0 0 36 36
ICAM1 0.026 0.02 -9999 0 0 206 206
phagocytosis triggered by activation of immune response cell surface activating receptor -0.065 0.171 -9999 0 -0.345 118 118
cell adhesion 0.051 0.067 -9999 0 -0.114 57 57
NFKB1 0.021 0.069 0.303 1 -0.222 20 21
THY1 0.025 0.02 -9999 0 0 216 216
RhoA/GDP 0.029 0.014 -9999 0 -0.125 4 4
Lipoprotein(a) 0.047 0.02 -9999 0 -9999 0 0
alphaM/beta2 Integrin/LRP/tPA 0.024 0.099 -9999 0 -0.126 134 134
IL6 -0.019 0.072 0.301 1 -0.401 10 11
ITGB2 0.034 0.021 -9999 0 -0.051 8 8
elevation of cytosolic calcium ion concentration 0.029 0.102 -9999 0 -0.159 98 98
alphaM/beta2 Integrin/JAM2/JAM3 0.067 0.073 -9999 0 -0.109 52 52
JAM2 0.037 0.012 -9999 0 0 52 52
alphaM/beta2 Integrin/ICAM1 0.05 0.099 -9999 0 -0.137 84 84
alphaM/beta2 Integrin/uPA/Plg 0.038 0.096 -9999 0 -0.138 100 100
RhoA/GTP -0.085 0.18 -9999 0 -0.345 140 140
positive regulation of phagocytosis -0.046 0.151 0.198 2 -0.3 103 105
Ron/MSP 0.054 0.028 -9999 0 -0.134 8 8
alphaM/beta2 Integrin/uPAR/uPA 0.032 0.104 -9999 0 -0.16 98 98
alphaM/beta2 Integrin/uPAR 0.043 0.079 -9999 0 -0.144 63 63
PLAU 0.025 0.02 -9999 0 0 210 210
PLAT 0.026 0.02 -9999 0 0 205 205
actin filament polymerization -0.076 0.165 0.193 2 -0.321 133 135
MST1 0.04 0.007 -9999 0 0 15 15
alphaM/beta2 Integrin/lipoprotein(a) 0.061 0.067 -9999 0 -0.1 47 47
TNF -0.01 0.07 0.29 1 -0.342 7 8
RAP1B 0.037 0.012 -9999 0 0 54 54
alphaM/beta2 Integrin/uPA 0.017 0.092 -9999 0 -0.149 102 102
fibrinolysis 0.036 0.094 -9999 0 -0.137 100 100
HCK 0.036 0.013 -9999 0 0 65 65
dendritic cell antigen processing and presentation -0.065 0.171 -9999 0 -0.345 118 118
VTN 0.039 0.008 -9999 0 0 24 24
alphaM/beta2 Integrin/CYR61 0.024 0.083 -9999 0 -0.119 112 112
LPA 0.035 0.014 -9999 0 0 77 77
LRP1 0.036 0.014 -9999 0 0 69 69
cell migration 0.015 0.092 0.182 10 -0.128 129 139
FN1 0.021 0.021 -9999 0 0 268 268
alphaM/beta2 Integrin/Thy1 0.008 0.091 -9999 0 -0.123 150 150
MPO 0.04 0.007 -9999 0 0 14 14
KNG1 0.034 0.016 -9999 0 0 100 100
RAP1/GDP 0.038 0.05 -9999 0 -0.123 43 43
ROCK1 -0.082 0.172 0.221 3 -0.333 136 139
ELA2 0.036 0.013 -9999 0 0 66 66
PLG 0.038 0.011 -9999 0 0 41 41
CTGF 0.034 0.016 -9999 0 0 101 101
alphaM/beta2 Integrin/Hck 0.05 0.071 -9999 0 -0.133 52 52
ITGAM 0.041 0.015 -9999 0 -0.053 9 9
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.071 0.074 -9999 0 -0.12 51 51
HP 0.01 0.018 -9999 0 0 416 416
leukocyte adhesion 0.017 0.105 -9999 0 -0.175 49 49
SELP 0.039 0.01 -9999 0 0 34 34
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.017 0.035 -9999 0 -0.054 75 75
PDGF/PDGFRA/CRKL 0.013 0.069 -9999 0 -0.134 78 78
positive regulation of JUN kinase activity 0.047 0.081 -9999 0 -0.115 92 92
CRKL 0.038 0.01 -9999 0 0 36 36
PDGF/PDGFRA/Caveolin-3 0.011 0.072 -9999 0 -0.134 88 88
AP1 -0.128 0.25 -9999 0 -0.65 96 96
mol:IP3 -0.018 0.042 0.051 26 -0.098 78 104
PLCG1 -0.018 0.042 0.049 25 -0.098 78 103
PDGF/PDGFRA/alphaV Integrin -0.008 0.09 -9999 0 -0.157 125 125
RAPGEF1 0.039 0.009 -9999 0 0 26 26
CRK 0.038 0.012 -9999 0 0 49 49
mol:Ca2+ -0.018 0.042 0.051 26 -0.098 78 104
CAV3 0.04 0.008 -9999 0 0 19 19
CAV1 0.036 0.014 -9999 0 0 75 75
SHC/Grb2/SOS1 0.049 0.083 -9999 0 -0.116 92 92
PDGF/PDGFRA/Shf 0.012 0.07 -9999 0 -0.134 81 81
FOS -0.124 0.252 0.286 4 -0.642 96 100
JUN -0.031 0.037 0.183 3 -0.198 3 6
oligodendrocyte development -0.008 0.09 -9999 0 -0.157 125 125
GRB2 0.04 0.008 -9999 0 0 21 21
PIK3R1 0.034 0.016 -9999 0 0 99 99
mol:DAG -0.018 0.042 0.051 26 -0.098 78 104
PDGF/PDGFRA 0.017 0.035 -9999 0 -0.054 75 75
actin cytoskeleton reorganization 0.013 0.071 -9999 0 -0.134 85 85
SRF -0.007 0.023 0.032 124 -9999 0 124
SHC1 0.039 0.008 -9999 0 0 23 23
PI3K 0.009 0.079 -9999 0 -0.137 92 92
PDGF/PDGFRA/Crk/C3G 0.033 0.071 -9999 0 -0.113 85 85
JAK1 -0.011 0.02 0.027 36 -9999 0 36
ELK1/SRF -0.025 0.066 0.146 24 -0.15 62 86
SHB 0.04 0.006 -9999 0 0 11 11
SHF 0.039 0.01 -9999 0 0 32 32
CSNK2A1 0.036 0.03 0.084 1 -0.028 59 60
GO:0007205 -0.02 0.053 0.075 7 -0.113 87 94
SOS1 0.037 0.012 -9999 0 0 51 51
Ras protein signal transduction 0.047 0.081 -9999 0 -0.115 92 92
PDGF/PDGFRA/SHB 0.013 0.072 -9999 0 -0.134 85 85
PDGF/PDGFRA/Caveolin-1 0.01 0.074 -9999 0 -0.111 120 120
ITGAV 0.033 0.017 -9999 0 0 110 110
ELK1 -0.031 0.073 0.151 9 -0.175 69 78
PIK3CA 0.029 0.019 -9999 0 0 166 166
PDGF/PDGFRA/Crk 0.012 0.07 -9999 0 -0.105 121 121
JAK-STAT cascade -0.011 0.02 0.027 36 -9999 0 36
cell proliferation 0.012 0.07 -9999 0 -0.134 81 81
TCGA08_retinoblastoma

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
CDKN2B 0.029 0.026 -9999 0 -0.045 39 39
CDKN2C 0.03 0.027 -9999 0 -0.043 46 46
CDKN2A 0.021 0.029 -9999 0 -0.038 60 60
CCND2 0.009 0.045 0.111 79 -0.117 3 82
RB1 -0.012 0.061 0.182 7 -0.135 83 90
CDK4 0.011 0.055 0.13 80 -0.122 17 97
CDK6 0.005 0.064 0.132 81 -0.137 20 101
G1/S progression 0.019 0.068 0.138 103 -0.188 8 111
Thromboxane A2 receptor 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
TGM2 0.033 0.016 -9999 0 0 105 105
GNB1/GNG2 -0.063 0.086 -9999 0 -0.181 185 185
AKT1 -0.026 0.141 0.248 3 -0.232 82 85
EGF 0.038 0.01 -9999 0 0 38 38
mol:TXA2 0 0.001 -9999 0 -9999 0 0
FGR 0.003 0.058 0.187 12 -0.163 3 15
mol:Ca2+ -0.054 0.192 0.307 2 -0.294 192 194
LYN -0.001 0.055 0.192 11 -0.163 6 17
RhoA/GTP -0.021 0.087 0.135 7 -0.133 178 185
mol:PGI2 0 0 -9999 0 -9999 0 0
SYK -0.074 0.205 0.3 2 -0.337 188 190
GNG2 0.039 0.009 -9999 0 0 29 29
ARRB2 0.038 0.011 -9999 0 0 46 46
TP alpha/Gq family/GDP/G beta5/gamma2 -0.027 0.161 -9999 0 -0.508 50 50
G beta5/gamma2 -0.073 0.122 -9999 0 -0.239 185 185
PRKCH -0.074 0.218 0.309 2 -0.354 186 188
DNM1 0.039 0.01 -9999 0 0 33 33
TXA2/TP beta/beta Arrestin3 0.029 0.022 -9999 0 -9999 0 0
mol:GTP 0 0.002 -9999 0 -9999 0 0
PTGDR 0.041 0.005 -9999 0 0 8 8
G12 family/GTP -0.068 0.181 -9999 0 -0.302 187 187
ADRBK1 0.041 0.004 -9999 0 0 6 6
ADRBK2 0.035 0.015 -9999 0 0 84 84
RhoA/GTP/ROCK1 0.05 0.024 -9999 0 -0.109 9 9
mol:GDP 0.035 0.165 0.453 47 -0.247 2 49
mol:NADP 0.038 0.01 -9999 0 0 35 35
RAB11A 0.04 0.008 -9999 0 0 19 19
PRKG1 0.039 0.009 -9999 0 0 30 30
mol:IP3 -0.077 0.231 0.328 2 -0.368 192 194
cell morphogenesis 0.05 0.023 -9999 0 -0.109 9 9
PLCB2 -0.12 0.299 -9999 0 -0.498 191 191
mol:cGMP 0 0.001 -9999 0 -9999 0 0
BLK 0.002 0.053 0.187 12 -0.174 2 14
mol:PDG2 0 0 -9999 0 -9999 0 0
HCK 0 0.056 0.184 12 -0.155 5 17
RHOA 0.04 0.006 -9999 0 0 13 13
PTGIR 0.039 0.009 -9999 0 0 26 26
PRKCB1 -0.08 0.23 0.333 1 -0.375 187 188
GNAQ 0.038 0.012 -9999 0 0 48 48
mol:L-citrulline 0.038 0.01 -9999 0 0 35 35
TXA2/TXA2-R family -0.124 0.301 0.371 1 -0.516 187 188
LCK 0.003 0.058 0.191 12 -0.163 3 15
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.051 0.047 0.187 4 -0.148 7 11
TXA2-R family/G12 family/GDP/G beta/gamma 0.001 0.13 -9999 0 -0.412 46 46
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.047 0.047 0.187 4 -0.148 7 11
MAPK14 -0.044 0.145 0.279 4 -0.229 184 188
TGM2/GTP -0.09 0.248 0.392 1 -0.404 184 185
MAPK11 -0.049 0.139 0.242 3 -0.225 185 188
ARHGEF1 -0.031 0.117 0.193 7 -0.18 180 187
GNAI2 0.04 0.006 -9999 0 0 13 13
JNK cascade -0.08 0.232 0.326 2 -0.38 187 189
RAB11/GDP 0.04 0.008 -9999 0 0 19 19
ICAM1 -0.06 0.195 0.268 8 -0.316 179 187
cAMP biosynthetic process -0.073 0.21 0.311 2 -0.336 191 193
Gq family/GTP/EBP50 0.01 0.049 0.253 2 -0.141 43 45
actin cytoskeleton reorganization 0.05 0.023 -9999 0 -0.109 9 9
SRC 0.001 0.056 0.184 12 -0.163 3 15
GNB5 0.039 0.008 -9999 0 0 23 23
GNB1 0.039 0.01 -9999 0 0 33 33
EGF/EGFR 0.001 0.076 0.22 11 -0.18 22 33
VCAM1 -0.064 0.206 0.266 7 -0.332 186 193
TP beta/Gq family/GDP/G beta5/gamma2 -0.027 0.161 -9999 0 -0.508 50 50
platelet activation -0.059 0.187 0.369 2 -0.296 187 189
PGI2/IP 0.028 0.014 -9999 0 -0.125 4 4
PRKACA 0.019 0.022 -9999 0 -0.158 6 6
Gq family/GDP/G beta5/gamma2 -0.018 0.127 -9999 0 -0.412 46 46
TXA2/TP beta/beta Arrestin2 0.012 0.061 -9999 0 -0.308 13 13
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -9999 0 0
TBXA2R 0.002 0.021 -9999 0 -0.154 6 6
mol:DAG -0.091 0.255 0.355 1 -0.418 187 188
EGFR 0.036 0.014 -9999 0 0 67 67
TXA2/TP alpha -0.106 0.276 0.377 1 -0.455 190 191
Gq family/GTP -0.011 0.066 -9999 0 -0.18 67 67
YES1 0.001 0.056 0.191 12 -0.161 4 16
GNAI2/GTP 0.025 0.046 -9999 0 -0.114 22 22
PGD2/DP 0.03 0.004 -9999 0 -9999 0 0
SLC9A3R1 0.038 0.012 -9999 0 0 49 49
FYN 0 0.055 0.187 12 -0.158 8 20
mol:NO 0.038 0.01 -9999 0 0 35 35
GNA15 0.036 0.014 -9999 0 0 68 68
PGK/cGMP 0.049 0.018 -9999 0 -9999 0 0
RhoA/GDP 0.04 0.007 -9999 0 0 13 13
TP alpha/TGM2/GDP/G beta/gamma 0.057 0.06 0.256 1 -0.175 7 8
NOS3 0.039 0.01 -9999 0 0 35 35
RAC1 0.039 0.009 -9999 0 0 28 28
PRKCA -0.075 0.218 0.323 3 -0.354 186 189
PRKCB -0.072 0.216 0.293 2 -0.35 186 188
PRKCE -0.075 0.221 0.32 4 -0.361 183 187
PRKCD -0.082 0.229 0.327 1 -0.379 184 185
PRKCG -0.081 0.231 0.33 2 -0.38 183 185
muscle contraction -0.113 0.279 0.374 1 -0.476 187 188
PRKCZ -0.071 0.207 0.3 2 -0.339 184 186
ARR3 0.041 0.002 -9999 0 0 1 1
TXA2/TP beta 0.045 0.051 0.234 2 -0.133 10 12
PRKCQ -0.075 0.216 0.345 2 -0.356 180 182
MAPKKK cascade -0.102 0.263 0.353 1 -0.44 188 189
SELE -0.053 0.181 0.268 4 -0.286 187 191
TP beta/GNAI2/GDP/G beta/gamma 0.069 0.057 0.254 2 -0.16 8 10
ROCK1 0.04 0.008 -9999 0 0 21 21
GNA14 0.039 0.009 -9999 0 0 29 29
chemotaxis -0.15 0.343 -9999 0 -0.604 187 187
GNA12 0.039 0.01 -9999 0 0 33 33
GNA13 0.039 0.008 -9999 0 0 23 23
GNA11 0.037 0.013 -9999 0 0 61 61
Rac1/GTP 0.028 0.009 -9999 0 -0.124 1 1
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.021 0.021 -9999 0 0 265 265
positive regulation of NF-kappaB transcription factor activity 0.005 0.065 -9999 0 -0.128 89 89
MAP2K4 -0.008 0.088 0.179 3 -0.27 31 34
IKBKB 0.038 0.011 -9999 0 0 41 41
TNFRSF10B 0.033 0.017 -9999 0 0 111 111
TNFRSF10A 0.032 0.017 -9999 0 0 125 125
SMPD1 -0.007 0.043 -9999 0 -0.1 88 88
IKBKG 0.041 0.002 -9999 0 0 2 2
mol:GTP 0 0 -9999 0 -9999 0 0
TNFRSF10D 0.032 0.017 -9999 0 0 122 122
TRAIL/TRAILR2 0.005 0.066 -9999 0 -0.128 91 91
TRAIL/TRAILR3 0.004 0.066 -9999 0 -0.127 93 93
TRAIL/TRAILR1 0.003 0.067 -9999 0 -0.13 93 93
TRAIL/TRAILR4 0.005 0.065 -9999 0 -0.128 89 89
TRAIL/TRAILR1/DAP3/GTP 0.013 0.064 -9999 0 -0.102 92 92
IKK complex 0.022 0.088 -9999 0 -0.285 29 29
RIPK1 0.039 0.01 -9999 0 0 32 32
response to oxidative stress 0 0 -9999 0 -9999 0 0
DAP3/GTP 0.026 0.021 -9999 0 -0.125 9 9
MAPK3 -0.01 0.01 -9999 0 -9999 0 0
MAP3K1 -0.005 0.096 -9999 0 -0.289 33 33
TRAILR4 (trimer) 0.032 0.017 -9999 0 0 122 122
TRADD 0.037 0.013 -9999 0 0 61 61
TRAILR1 (trimer) 0.032 0.017 -9999 0 0 125 125
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.017 0.08 -9999 0 -0.174 88 88
CFLAR 0.04 0.008 -9999 0 0 19 19
MAPK1 -0.01 0.01 -9999 0 -9999 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP 0.032 0.082 -9999 0 -0.108 79 79
mol:ceramide -0.007 0.043 -9999 0 -0.099 88 88
FADD 0.04 0.008 -9999 0 0 20 20
MAPK8 -0.02 0.097 0.204 3 -0.258 47 50
TRAF2 0.039 0.01 -9999 0 0 32 32
TRAILR3 (trimer) 0.032 0.017 -9999 0 0 119 119
CHUK 0.038 0.011 -9999 0 0 46 46
TRAIL/TRAILR1/FADD 0.014 0.069 -9999 0 -0.113 89 89
DAP3 0.038 0.011 -9999 0 0 40 40
CASP10 -0.006 0.101 0.157 81 -0.198 76 157
JNK cascade 0.005 0.065 -9999 0 -0.128 89 89
TRAIL (trimer) 0.021 0.021 -9999 0 0 265 265
TNFRSF10C 0.032 0.017 -9999 0 0 119 119
TRAIL/TRAILR1/DAP3/GTP/FADD 0.023 0.071 -9999 0 -0.103 87 87
TRAIL/TRAILR2/FADD 0.017 0.068 -9999 0 -0.111 88 88
cell death -0.007 0.043 -9999 0 -0.099 88 88
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.017 0.081 -9999 0 -0.177 85 85
TRAILR2 (trimer) 0.033 0.017 -9999 0 0 111 111
CASP8 -0.005 0.115 -9999 0 -0.611 16 16
negative regulation of caspase activity 0 0 -9999 0 -9999 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.033 0.082 -9999 0 -0.107 76 76
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.039 0.053 -9999 0 -0.137 38 38
ATM 0.036 0.014 -9999 0 0 69 69
UBE2D3 0.039 0.009 -9999 0 0 30 30
PRKDC 0.038 0.011 -9999 0 0 44 44
ATR 0.035 0.015 -9999 0 0 84 84
UBE2L3 0.039 0.01 -9999 0 0 34 34
FANCD2 -0.005 0.09 -9999 0 -0.251 58 58
protein ubiquitination 0.01 0.098 -9999 0 -0.126 147 147
XRCC5 0.038 0.011 -9999 0 0 41 41
XRCC6 0.036 0.014 -9999 0 0 69 69
M/R/N Complex 0.048 0.071 -9999 0 -0.146 50 50
MRE11A 0.038 0.012 -9999 0 0 49 49
DNA-PK 0.051 0.067 -9999 0 -0.138 47 47
FA complex/FANCD2/Ubiquitin -0.002 0.12 -9999 0 -0.376 34 34
FANCF 0.04 0.007 -9999 0 0 18 18
BRCA1 0.034 0.015 -9999 0 0 93 93
CCNE1 0.026 0.02 -9999 0 0 202 202
CDK2/Cyclin E1 0.009 0.074 -9999 0 -0.138 97 97
FANCG 0.04 0.007 -9999 0 0 14 14
BRCA1/BACH1/BARD1 0.027 0.068 -9999 0 -0.138 72 72
FANCE 0.04 0.006 -9999 0 0 12 12
FANCC 0.039 0.009 -9999 0 0 25 25
NBN 0.035 0.015 -9999 0 0 87 87
FANCA 0.034 0.016 -9999 0 0 94 94
DNA repair -0.017 0.134 0.262 21 -0.34 43 64
BRCA1/BARD1/ubiquitin 0.027 0.068 -9999 0 -0.138 72 72
BARD1/DNA-PK 0.06 0.083 -9999 0 -0.142 60 60
FANCL 0.037 0.012 -9999 0 0 52 52
mRNA polyadenylation -0.039 0.052 0.136 38 -9999 0 38
BRCA1/BARD1/CTIP/M/R/N Complex -0.024 0.136 0.156 2 -0.285 80 82
BRCA1/BACH1/BARD1/TopBP1 0.038 0.077 -9999 0 -0.129 80 80
BRCA1/BARD1/P53 0.004 0.103 -9999 0 -0.126 182 182
BARD1/CSTF1/BRCA1 0.039 0.072 -9999 0 -0.121 73 73
BRCA1/BACH1 0.034 0.015 -9999 0 0 93 93
BARD1 0.036 0.013 -9999 0 0 64 64
PCNA 0.034 0.015 -9999 0 0 89 89
BRCA1/BARD1/UbcH5C 0.043 0.071 -9999 0 -0.119 73 73
BRCA1/BARD1/UbcH7 0.043 0.07 -9999 0 -0.119 70 70
BRCA1/BARD1/RAD51/PCNA 0.035 0.095 -9999 0 -0.128 115 115
BARD1/DNA-PK/P53 0.02 0.113 -9999 0 -0.127 170 170
BRCA1/BARD1/Ubiquitin 0.027 0.068 -9999 0 -0.138 72 72
BRCA1/BARD1/CTIP 0.015 0.087 0.18 13 -0.134 116 129
FA complex 0.009 0.086 -9999 0 -0.257 34 34
BARD1/EWS 0.041 0.049 -9999 0 -0.13 34 34
RBBP8 -0.015 0.009 -9999 0 -9999 0 0
TP53 0.026 0.02 -9999 0 0 207 207
TOPBP1 0.037 0.012 -9999 0 0 50 50
G1/S transition of mitotic cell cycle -0.003 0.102 0.125 182 -9999 0 182
BRCA1/BARD1 0.014 0.102 -9999 0 -0.127 147 147
CSTF1 0.037 0.013 -9999 0 0 57 57
BARD1/EWS-Fli1 0.019 0.037 -9999 0 -0.125 33 33
CDK2 0.037 0.013 -9999 0 0 56 56
UniProt:Q9BZD1 0 0 -9999 0 -9999 0 0
RAD51 0.035 0.015 -9999 0 0 83 83
RAD50 0.039 0.01 -9999 0 0 35 35
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.027 0.068 -9999 0 -0.138 72 72
EWSR1 0.038 0.012 -9999 0 0 48 48
TCGA08_rtk_signaling

Figure 18.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 20.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.029 0.019 -9999 0 0 161 161
HRAS 0.039 0.01 -9999 0 0 31 31
EGFR 0.036 0.014 -9999 0 0 67 67
AKT 0.02 0.091 0.206 13 -0.188 35 48
FOXO3 0 0 -9999 0 -9999 0 0
AKT1 0.039 0.01 -9999 0 0 34 34
FOXO1 0 0 -9999 0 -9999 0 0
AKT3 0.03 0.018 -9999 0 0 151 151
FOXO4 0 0 -9999 0 -9999 0 0
MET 0.027 0.02 -9999 0 0 191 191
PIK3CA 0.029 0.019 -9999 0 0 166 166
PIK3CB 0.034 0.016 -9999 0 0 95 95
NRAS 0.039 0.009 -9999 0 0 30 30
PIK3CG 0.033 0.017 -9999 0 0 112 112
PIK3R3 0.034 0.016 -9999 0 0 96 96
PIK3R2 0.036 0.014 -9999 0 0 68 68
NF1 0.034 0.016 -9999 0 0 96 96
RAS 0.002 0.076 0.151 23 -0.226 23 46
ERBB2 0.038 0.012 -9999 0 0 47 47
proliferation/survival/translation -0.021 0.083 0.211 28 -0.206 18 46
PI3K 0.007 0.087 0.172 25 -0.218 39 64
PIK3R1 0.034 0.016 -9999 0 0 99 99
KRAS 0.034 0.016 -9999 0 0 95 95
FOXO 0.039 0.053 0.17 24 -9999 0 24
AKT2 0.037 0.012 -9999 0 0 54 54
PTEN 0.038 0.01 -9999 0 0 36 36
Paxillin-dependent events mediated by a4b1

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
CRKL 0.038 0.01 -9999 0 0 36 36
Rac1/GDP 0.032 0.025 -9999 0 -0.024 67 67
DOCK1 0.037 0.012 -9999 0 0 53 53
ITGA4 0.035 0.015 -9999 0 0 88 88
RAC1 0.039 0.009 -9999 0 0 28 28
alpha4/beta7 Integrin 0.031 0.065 -9999 0 -0.137 66 66
mol:GTP 0 0 -9999 0 -9999 0 0
CRK 0.038 0.012 -9999 0 0 49 49
alpha4/beta1 Integrin 0.045 0.063 -9999 0 -0.116 53 53
alpha4/beta7 Integrin/Paxillin 0.051 0.07 0.18 56 -0.113 53 109
lamellipodium assembly -0.025 0.144 -9999 0 -0.359 65 65
PIK3CA 0.029 0.019 -9999 0 0 166 166
PI3K 0.023 0.06 -9999 0 -0.15 44 44
ARF6 0.04 0.007 -9999 0 0 16 16
TLN1 0.038 0.011 -9999 0 0 39 39
PXN -0.017 0.008 -9999 0 -9999 0 0
PIK3R1 0.034 0.016 -9999 0 0 99 99
ARF6/GTP 0.061 0.071 -9999 0 -0.107 54 54
cell adhesion 0.06 0.079 0.192 50 -0.113 65 115
CRKL/CBL 0.055 0.02 -9999 0 -0.134 1 1
alpha4/beta1 Integrin/Paxillin 0.05 0.068 0.18 52 -0.11 52 104
ITGB1 0.038 0.01 -9999 0 0 36 36
ITGB7 0.038 0.01 -9999 0 0 38 38
ARF6/GDP 0.033 0.025 -9999 0 -0.024 66 66
alpha4/beta1 Integrin/Paxillin/VCAM1 0.021 0.095 0.198 29 -0.133 121 150
p130Cas/Crk/Dock1 0.056 0.052 -9999 0 -0.116 27 27
VCAM1 0.02 0.021 -9999 0 0 281 281
alpha4/beta1 Integrin/Paxillin/Talin 0.062 0.08 0.198 50 -0.114 65 115
alpha4/beta1 Integrin/Paxillin/GIT1 0.067 0.073 0.198 48 -0.108 52 100
BCAR1 0.036 0.013 -9999 0 0 65 65
mol:GDP -0.065 0.072 0.107 52 -0.192 48 100
CBL 0.04 0.008 -9999 0 0 20 20
PRKACA 0.035 0.015 -9999 0 0 84 84
GIT1 0.039 0.009 -9999 0 0 25 25
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.062 0.08 0.198 50 -0.114 65 115
Rac1/GTP -0.03 0.157 -9999 0 -0.399 65 65
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.007 0.005 0 182 -9999 0 182
GNB1/GNG2 0.039 0.068 -9999 0 -0.106 83 83
regulation of S phase of mitotic cell cycle -0.011 0.075 -9999 0 -0.172 83 83
GNAO1 0.035 0.015 -9999 0 0 85 85
HRAS 0.039 0.01 -9999 0 0 31 31
SHBG/T-DHT 0.026 0.007 -9999 0 -9999 0 0
PELP1 0.038 0.011 -9999 0 0 39 39
AKT1 -0.009 0.003 0.002 41 -9999 0 41
MAP2K1 -0.034 0.078 0.168 23 -0.167 77 100
T-DHT/AR 0.006 0.053 -9999 0 -0.125 75 75
G-protein coupled receptor activity 0 0 -9999 0 -9999 0 0
mol:GTP -0.001 0.003 -9999 0 -0.007 100 100
GNAI2 0.04 0.006 -9999 0 0 13 13
GNAI3 0.038 0.011 -9999 0 0 45 45
GNAI1 0.034 0.015 -9999 0 0 93 93
mol:GDP -0.039 0.085 -9999 0 -0.251 66 66
cell proliferation -0.069 0.173 0.244 7 -0.398 103 110
PIK3CA 0.029 0.019 -9999 0 0 166 166
FOS -0.122 0.286 0.284 2 -0.7 103 105
mol:Ca2+ -0.007 0.021 -9999 0 -0.048 83 83
MAPK3 -0.052 0.128 0.232 7 -0.298 94 101
MAPK1 -0.038 0.133 -9999 0 -0.417 33 33
PIK3R1 0.034 0.016 -9999 0 0 99 99
mol:IP3 0 0.002 0.002 12 -0.004 100 112
cAMP biosynthetic process -0.001 0.024 0.203 4 -9999 0 4
GNG2 0.039 0.009 -9999 0 0 29 29
potassium channel inhibitor activity 0 0.002 0.002 12 -0.004 100 112
HRAS/GTP 0.025 0.076 -9999 0 -0.09 137 137
actin cytoskeleton reorganization 0.027 0.05 -9999 0 -0.106 43 43
SRC 0.039 0.009 -9999 0 0 28 28
voltage-gated calcium channel activity 0 0.002 0.002 12 -0.004 100 112
PI3K 0.022 0.051 -9999 0 -0.123 44 44
apoptosis 0.059 0.178 0.388 110 -0.228 3 113
T-DHT/AR/PELP1 0.025 0.056 -9999 0 -0.108 75 75
HRAS/GDP -0.002 0.106 0.149 1 -0.243 67 68
CREB1 -0.074 0.183 0.254 1 -0.415 110 111
RAC1-CDC42/GTP 0.037 0.057 -9999 0 -0.107 43 43
AR 0.032 0.017 -9999 0 0 118 118
GNB1 0.039 0.01 -9999 0 0 33 33
RAF1 -0.021 0.074 0.183 24 -0.179 15 39
RAC1-CDC42/GDP 0.02 0.114 -9999 0 -0.241 65 65
T-DHT/AR/PELP1/Src 0.039 0.064 -9999 0 -0.104 72 72
MAP2K2 -0.028 0.074 0.167 22 -0.168 64 86
T-DHT/AR/PELP1/Src/PI3K -0.011 0.075 -9999 0 -0.173 83 83
GNAZ 0.038 0.011 -9999 0 0 46 46
SHBG 0.038 0.01 -9999 0 0 37 37
Gi family/GNB1/GNG2/GDP -0.007 0.107 -9999 0 -0.312 36 36
mol:T-DHT 0 0.001 -9999 0 -0.003 25 25
RAC1 0.039 0.009 -9999 0 0 28 28
GNRH1 -0.008 0.004 0 107 -9999 0 107
Gi family/GTP -0.019 0.077 -9999 0 -0.179 73 73
CDC42 0.04 0.007 -9999 0 0 18 18
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.066 0.175 -9999 0 -0.39 122 122
IHH 0.021 0.066 -9999 0 -0.098 126 126
SHH Np/Cholesterol/GAS1 0.027 0.025 -9999 0 -0.103 12 12
LRPAP1 0.036 0.014 -9999 0 0 72 72
dorsoventral neural tube patterning -0.027 0.025 0.103 12 -9999 0 12
SMO/beta Arrestin2 0.015 0.118 0.241 2 -0.201 104 106
SMO -0.004 0.109 -9999 0 -0.204 109 109
AKT1 -0.015 0.132 -9999 0 -0.398 35 35
ARRB2 0.038 0.011 -9999 0 0 46 46
BOC 0.035 0.015 -9999 0 0 82 82
ADRBK1 0.041 0.004 -9999 0 0 6 6
heart looping -0.003 0.108 -9999 0 -0.202 109 109
STIL -0.002 0.096 0.208 26 -0.171 104 130
DHH N/PTCH2 0.058 0.014 -9999 0 -9999 0 0
DHH N/PTCH1 0.002 0.107 -9999 0 -0.189 125 125
PIK3CA 0.029 0.019 -9999 0 0 166 166
DHH 0.04 0.006 -9999 0 0 11 11
PTHLH -0.057 0.159 -9999 0 -0.376 108 108
determination of left/right symmetry -0.003 0.108 -9999 0 -0.202 109 109
PIK3R1 0.034 0.016 -9999 0 0 99 99
skeletal system development -0.056 0.159 -9999 0 -0.373 108 108
IHH N/Hhip 0.034 0.054 -9999 0 -0.146 1 1
DHH N/Hhip 0.055 0.02 -9999 0 -0.134 1 1
mol:Cholesterol 0 0 -9999 0 -9999 0 0
heart development -0.003 0.108 -9999 0 -0.202 109 109
pancreas development 0.038 0.011 -9999 0 0 44 44
HHAT 0.039 0.009 -9999 0 0 25 25
PI3K 0.023 0.06 -9999 0 -0.15 44 44
EntrezGene:84976 0 0 -9999 0 -9999 0 0
GAS1 0.036 0.013 -9999 0 0 66 66
somite specification -0.003 0.108 -9999 0 -0.202 109 109
SHH Np/Cholesterol/PTCH1 -0.007 0.085 -9999 0 -0.17 109 109
SHH Np/Cholesterol/PTCH2 0.032 0.015 -9999 0 -0.103 1 1
SHH Np/Cholesterol/Megalin 0.021 0.028 -9999 0 -0.103 15 15
SHH -0.018 0.007 -9999 0 -9999 0 0
catabolic process -0.037 0.095 -9999 0 -0.209 126 126
SMO/Vitamin D3 -0.007 0.1 0.195 17 -0.197 106 123
SHH Np/Cholesterol/Hhip 0.031 0.017 -9999 0 -0.103 2 2
LRP2 0.029 0.019 -9999 0 0 160 160
receptor-mediated endocytosis 0 0.1 0.193 18 -0.183 102 120
SHH Np/Cholesterol/BOC 0.026 0.027 -9999 0 -0.102 16 16
SHH Np/Cholesterol/CDO 0.023 0.033 -9999 0 -0.103 27 27
mesenchymal cell differentiation -0.03 0.017 0.103 2 -9999 0 2
mol:Vitamin D3 -0.015 0.086 0.198 20 -0.171 108 128
IHH N/PTCH2 0.037 0.054 -9999 0 -0.059 121 121
CDON 0.034 0.015 -9999 0 0 91 91
IHH N/PTCH1 -0.021 0.106 -9999 0 -0.21 126 126
Megalin/LRPAP1 0.027 0.054 -9999 0 -0.136 40 40
PTCH2 0.04 0.008 -9999 0 0 19 19
SHH Np/Cholesterol 0.031 0.041 0.196 31 -0.097 1 32
PTCH1 -0.037 0.096 -9999 0 -0.21 126 126
HHIP 0.038 0.011 -9999 0 0 44 44
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.028 0.013 -9999 0 -0.125 3 3
alphaV beta3 Integrin 0.029 0.078 -9999 0 -0.125 91 91
PTK2 -0.014 0.127 0.255 5 -0.281 70 75
IGF1R 0.033 0.017 -9999 0 0 112 112
PI4KB 0 0 -9999 0 -9999 0 0
MFGE8 0.031 0.018 -9999 0 0 137 137
SRC 0.039 0.009 -9999 0 0 28 28
CDKN1B 0.003 0.087 -9999 0 -0.332 29 29
VEGFA 0 0 -9999 0 -9999 0 0
ILK 0.016 0.056 -9999 0 -0.274 12 12
ROCK1 0.04 0.008 -9999 0 0 21 21
AKT1 0.007 0.051 0.212 4 -0.257 11 15
PTK2B -0.014 0.06 0.191 12 -0.176 13 25
alphaV/beta3 Integrin/JAM-A 0.039 0.078 0.198 6 -0.119 85 91
CBL 0.04 0.008 -9999 0 0 20 20
mol:GTP 0 0 -9999 0 -9999 0 0
alphaV beta3 Integrin/ANGPTL3 0.031 0.079 -9999 0 -0.126 91 91
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.054 0.083 -9999 0 -0.119 85 85
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.004 0.084 -9999 0 -0.168 94 94
alphaV/beta3 Integrin/Syndecan-1 0.029 0.079 -9999 0 -0.125 94 94
PI4KA 0 0 -9999 0 -9999 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.018 0.101 -9999 0 -0.142 173 173
PI4 Kinase 0 0 -9999 0 -9999 0 0
PIK3CA 0.029 0.019 -9999 0 0 166 166
alphaV/beta3 Integrin/Osteopontin 0.007 0.098 -9999 0 -0.152 128 128
RPS6KB1 -0.033 0.105 0.273 13 -0.201 58 71
TLN1 0.038 0.011 -9999 0 0 39 39
MAPK3 -0.049 0.153 0.218 3 -0.333 112 115
GPR124 0.037 0.012 -9999 0 0 55 55
MAPK1 -0.048 0.154 0.218 3 -0.341 108 111
PXN 0.04 0.006 -9999 0 0 10 10
PIK3R1 0.034 0.016 -9999 0 0 99 99
alphaV/beta3 Integrin/Tumstatin 0.031 0.079 -9999 0 -0.127 91 91
cell adhesion -0.003 0.098 -9999 0 -0.162 128 128
ANGPTL3 0.04 0.007 -9999 0 0 15 15
VEGFR2 homodimer/VEGFA homodimer/Src 0.05 0.019 -9999 0 -0.109 2 2
IGF-1R heterotetramer 0.033 0.017 -9999 0 0 112 112
Rac1/GDP 0.029 0.009 -9999 0 -0.125 1 1
TGFBR2 0.039 0.01 -9999 0 0 34 34
ITGB3 0.032 0.017 -9999 0 0 116 116
IGF1 0.035 0.014 -9999 0 0 77 77
RAC1 0.039 0.009 -9999 0 0 28 28
regulation of cell-matrix adhesion 0.03 0.075 -9999 0 -0.124 82 82
apoptosis 0.033 0.016 -9999 0 0 110 110
CD47 0.036 0.013 -9999 0 0 65 65
alphaV/beta3 Integrin/CD47 0.023 0.086 -9999 0 -0.139 99 99
VCL 0.039 0.01 -9999 0 0 34 34
alphaV/beta3 Integrin/Del1 0.007 0.082 -9999 0 -0.131 113 113
CSF1 0.035 0.015 -9999 0 0 84 84
PIK3C2A -0.004 0.103 -9999 0 -0.335 43 43
PI4 Kinase/Pyk2 0.006 0.055 -9999 0 -0.109 81 81
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.029 0.073 -9999 0 -0.113 94 94
FAK1/Vinculin 0.005 0.119 0.264 6 -0.239 70 76
alphaV beta3/Integrin/ppsTEM5 0.031 0.075 -9999 0 -0.125 82 82
RHOA 0.04 0.006 -9999 0 0 13 13
VTN 0.039 0.008 -9999 0 0 24 24
BCAR1 0.036 0.013 -9999 0 0 65 65
FGF2 0.039 0.01 -9999 0 0 33 33
F11R -0.019 0.006 -9999 0 -9999 0 0
alphaV/beta3 Integrin/Lactadherin 0.01 0.088 -9999 0 -0.135 123 123
alphaV/beta3 Integrin/TGFBR2 0.027 0.084 -9999 0 -0.136 94 94
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.047 0.089 -9999 0 -0.128 93 93
HSP90AA1 0 0 -9999 0 -9999 0 0
alphaV/beta3 Integrin/Talin 0.026 0.077 -9999 0 -0.118 101 101
mol:GDP 0 0 -9999 0 -9999 0 0
FN1 0.021 0.021 -9999 0 0 268 268
alphaV/beta3 Integrin/Pyk2 0.018 0.067 0.206 1 -0.111 89 90
SDC1 0.039 0.009 -9999 0 0 25 25
VAV3 -0.031 0.072 0.206 15 -0.208 36 51
PTPN11 0.039 0.009 -9999 0 0 29 29
IRS1 0.04 0.008 -9999 0 0 22 22
FAK1/Paxillin 0.007 0.119 0.264 6 -0.235 71 77
cell migration -0.004 0.108 0.248 6 -0.222 70 76
ITGAV 0.033 0.017 -9999 0 0 110 110
PI3K 0.026 0.087 -9999 0 -0.144 68 68
SPP1 0.031 0.018 -9999 0 0 139 139
KDR 0.039 0.009 -9999 0 0 27 27
mol:PI-4-5-P2 0 0 -9999 0 -9999 0 0
alphaV/beta3 Integrin/Caspase 8 0.033 0.017 -9999 0 0 110 110
COL4A3 0.041 0.005 -9999 0 0 7 7
angiogenesis -0.053 0.168 0.255 3 -0.367 111 114
Rac1/GTP -0.033 0.075 0.207 15 -0.197 34 49
EDIL3 0.027 0.02 -9999 0 0 185 185
cell proliferation 0.027 0.083 -9999 0 -0.136 94 94
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.015 0.143 -9999 0 -0.339 29 29
MAP3K8 0.039 0.009 -9999 0 0 24 24
FOS 0.015 0.104 -9999 0 -0.3 21 21
PRKCA 0.026 0.029 -9999 0 -0.015 167 167
PTPN7 0.03 0.032 0.071 1 -0.031 109 110
HRAS 0.039 0.01 -9999 0 0 31 31
PRKCB 0 0.007 0.01 93 -0.013 100 193
NRAS 0.039 0.009 -9999 0 0 30 30
RAS family/GTP 0.053 0.05 -9999 0 -0.108 27 27
MAPK3 0.029 0.078 -9999 0 -0.431 8 8
MAP2K1 0 0.092 0.163 3 -0.269 44 47
ELK1 0.027 0.031 -9999 0 -0.038 101 101
BRAF -0.002 0.065 -9999 0 -0.276 26 26
mol:GTP 0 0.002 0.002 84 -0.004 100 184
MAPK1 0.015 0.105 -9999 0 -0.376 26 26
RAF1 -0.007 0.074 -9999 0 -0.277 35 35
KRAS 0.034 0.016 -9999 0 0 95 95
IL1-mediated signaling events

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
UBC13/UEV1A 0.028 0.019 -9999 0 -0.125 8 8
PRKCZ 0.039 0.009 -9999 0 0 27 27
MAP3K7IP2 0.037 0.012 -9999 0 0 53 53
ERC1 0 0 -9999 0 -9999 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.034 0.134 -9999 0 -0.291 95 95
IRAK/TOLLIP 0.038 0.026 0.19 3 -0.103 10 13
IKBKB 0.038 0.011 -9999 0 0 41 41
IKBKG 0.041 0.002 -9999 0 0 2 2
IL1 alpha/IL1R2 0.046 0.038 -9999 0 -0.134 16 16
IL1A 0.039 0.009 -9999 0 0 30 30
IL1B -0.012 0.01 -9999 0 -9999 0 0
IRAK/TRAF6/p62/Atypical PKCs 0.043 0.076 0.222 2 -0.115 61 63
IL1R2 0.035 0.015 -9999 0 0 80 80
IL1R1 0.031 0.018 -9999 0 0 141 141
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.045 0.14 -9999 0 -0.305 92 92
TOLLIP 0.039 0.01 -9999 0 0 32 32
TICAM2 0.037 0.012 -9999 0 0 51 51
MAP3K3 0.04 0.007 -9999 0 0 14 14
TAK1/TAB1/TAB2 0.061 0.054 -9999 0 -0.14 26 26
IKK complex/ELKS 0.013 0.084 0.278 1 -0.269 25 26
JUN -0.037 0.056 0.155 16 -0.193 17 33
MAP3K7 0.038 0.01 -9999 0 0 38 38
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0 0.113 -9999 0 -0.171 121 121
IL1 alpha/IL1R1/IL1RAP/MYD88 0.037 0.084 -9999 0 -0.122 91 91
PIK3R1 0.034 0.016 -9999 0 0 99 99
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.038 0.098 -9999 0 -0.134 100 100
IL1 beta fragment/IL1R1/IL1RAP -0.011 0.096 0.18 6 -0.148 147 153
NFKB1 0.036 0.013 -9999 0 0 66 66
MAPK8 -0.029 0.052 0.168 15 -0.199 16 31
IRAK1 0.016 0.014 0.069 1 -0.109 6 7
IL1RN/IL1R1 0.022 0.07 -9999 0 -0.136 81 81
IRAK4 0.036 0.014 -9999 0 0 68 68
PRKCI 0.027 0.02 -9999 0 0 192 192
TRAF6 0.04 0.008 -9999 0 0 19 19
PI3K 0.023 0.06 -9999 0 -0.15 44 44
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.036 0.145 0.172 1 -0.307 96 97
CHUK 0.038 0.011 -9999 0 0 46 46
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.011 0.096 0.18 6 -0.148 147 153
IL1 beta/IL1R2 -0.004 0.088 0.242 1 -0.146 131 132
IRAK/TRAF6/TAK1/TAB1/TAB2 0.071 0.068 0.222 1 -0.137 32 33
NF kappa B1 p50/RelA -0.011 0.108 -9999 0 -0.182 116 116
IRAK3 0.034 0.015 -9999 0 0 93 93
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.003 0.117 -9999 0 -0.165 137 137
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.015 0.099 -9999 0 -0.2 97 97
IL1 alpha/IL1R1/IL1RAP 0.017 0.077 -9999 0 -0.129 91 91
RELA 0.04 0.006 -9999 0 0 10 10
MAP3K7IP1 0.037 0.012 -9999 0 0 51 51
SQSTM1 0.038 0.011 -9999 0 0 46 46
MYD88 0.04 0.006 -9999 0 0 12 12
IRAK/TRAF6/MEKK3 0.06 0.036 0.206 3 -0.107 18 21
IL1RAP 0.027 0.02 -9999 0 0 185 185
UBE2N 0.04 0.007 -9999 0 0 16 16
IRAK/TRAF6 -0.022 0.094 -9999 0 -0.163 134 134
CASP1 0.027 0.019 -9999 0 0 184 184
IL1RN/IL1R2 0.041 0.048 -9999 0 -0.137 30 30
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.002 0.103 0.198 6 -0.148 140 146
TMEM189-UBE2V1 0 0 -9999 0 -9999 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.023 0.132 0.206 1 -0.281 94 95
PIK3CA 0.029 0.019 -9999 0 0 166 166
IL1RN 0.038 0.011 -9999 0 0 39 39
TRAF6/TAK1/TAB1/TAB2 0.072 0.066 -9999 0 -0.136 32 32
MAP2K6 -0.025 0.053 0.186 15 -0.205 13 28
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.168 0.613 -9999 0 -1.215 120 120
IL23A -0.112 0.545 -9999 0 -1.226 80 80
NF kappa B1 p50/RelA/I kappa B alpha -0.113 0.544 -9999 0 -1.18 86 86
positive regulation of T cell mediated cytotoxicity -0.132 0.609 -9999 0 -1.318 89 89
ITGA3 -0.156 0.578 -9999 0 -1.145 115 115
IL17F -0.041 0.363 0.494 7 -0.705 87 94
IL12B 0.033 0.072 0.158 8 -0.082 2 10
STAT1 (dimer) -0.147 0.577 -9999 0 -1.278 88 88
CD4 -0.117 0.566 0.665 2 -1.188 96 98
IL23 -0.11 0.523 -9999 0 -1.179 79 79
IL23R 0.037 0.145 -9999 0 -1.23 3 3
IL1B -0.134 0.586 -9999 0 -1.271 93 93
T-helper cell lineage commitment 0 0 -9999 0 -9999 0 0
IL24 -0.099 0.514 -9999 0 -1.138 80 80
TYK2 0.024 0.055 0.128 2 -9999 0 2
STAT4 0.039 0.008 -9999 0 0 24 24
STAT3 0.038 0.011 -9999 0 0 41 41
IL18RAP 0.041 0.007 -9999 0 0 15 15
IL12RB1 0.023 0.057 0.126 3 -9999 0 3
PIK3CA 0.029 0.019 -9999 0 0 166 166
IL12Rbeta1/TYK2 0.035 0.068 -9999 0 -9999 0 0
IL23R/JAK2 0.047 0.172 -9999 0 -1.186 3 3
positive regulation of chronic inflammatory response -0.132 0.609 -9999 0 -1.318 89 89
natural killer cell activation -0.002 0.009 -9999 0 -9999 0 0
JAK2 0.031 0.068 0.158 8 -0.081 3 11
PIK3R1 0.034 0.016 -9999 0 0 99 99
NFKB1 0.038 0.015 -9999 0 0 66 66
RELA 0.042 0.008 -9999 0 0 10 10
positive regulation of dendritic cell antigen processing and presentation -0.098 0.496 -9999 0 -1.101 79 79
ALOX12B -0.099 0.513 -9999 0 -1.126 82 82
CXCL1 -0.133 0.572 -9999 0 -1.171 104 104
T cell proliferation -0.132 0.609 -9999 0 -1.318 89 89
NFKBIA 0.038 0.015 -9999 0 0 64 64
IL17A -0.025 0.296 0.423 10 -0.543 88 98
PI3K -0.15 0.527 -9999 0 -1.189 86 86
IFNG 0.007 0.038 0.101 5 -0.103 13 18
STAT3 (dimer) -0.137 0.504 -9999 0 -1.118 87 87
IL18R1 0.041 0.008 -9999 0 0 19 19
IL23/IL23R/JAK2/TYK2/SOCS3 -0.015 0.337 0.502 4 -0.656 74 78
IL18/IL18R 0.049 0.067 -9999 0 -0.111 61 61
macrophage activation -0.007 0.021 0.033 1 -0.045 74 75
TNF -0.109 0.544 -9999 0 -1.219 80 80
STAT3/STAT4 -0.117 0.558 -9999 0 -1.212 87 87
STAT4 (dimer) -0.129 0.578 -9999 0 -1.269 87 87
IL18 0.031 0.019 -9999 0 0 148 148
IL19 -0.099 0.514 -9999 0 -1.133 81 81
STAT5A (dimer) -0.126 0.583 -9999 0 -1.269 88 88
STAT1 0.034 0.016 -9999 0 0 102 102
SOCS3 0.036 0.013 -9999 0 0 63 63
CXCL9 -0.156 0.607 -9999 0 -1.196 120 120
MPO -0.099 0.514 -9999 0 -1.128 82 82
positive regulation of humoral immune response -0.132 0.609 -9999 0 -1.318 89 89
IL23/IL23R/JAK2/TYK2 -0.168 0.648 -9999 0 -1.434 89 89
IL6 -0.103 0.531 -9999 0 -1.161 84 84
STAT5A 0.038 0.01 -9999 0 0 36 36
IL2 0.039 0.016 -9999 0 -0.032 12 12
positive regulation of tyrosine phosphorylation of STAT protein -0.002 0.009 -9999 0 -9999 0 0
CD3E -0.11 0.54 0.677 1 -1.175 87 88
keratinocyte proliferation -0.132 0.609 -9999 0 -1.318 89 89
NOS2 -0.1 0.514 -9999 0 -1.092 89 89
Signaling events mediated by PTP1B

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
PDGFRB 0.036 0.013 -9999 0 0 65 65
Jak2/Leptin Receptor -0.019 0.149 0.253 1 -0.395 54 55
PTP1B/AKT1 -0.034 0.114 -9999 0 -0.236 87 87
FYN 0.034 0.016 -9999 0 0 94 94
p210 bcr-abl/PTP1B -0.052 0.114 -9999 0 -0.251 95 95
EGFR 0.036 0.017 -9999 0 -0.004 76 76
EGF/EGFR -0.025 0.12 -9999 0 -0.232 90 90
CSF1 0.035 0.015 -9999 0 0 84 84
AKT1 0.039 0.01 -9999 0 0 34 34
INSR 0.038 0.012 -9999 0 0 49 49
PTP1B/N-cadherin -0.054 0.119 -9999 0 -0.239 125 125
Insulin Receptor/Insulin -0.008 0.115 -9999 0 -0.221 64 64
HCK 0.036 0.013 -9999 0 0 65 65
CRK 0.038 0.012 -9999 0 0 49 49
TYK2 -0.037 0.119 0.234 24 -0.25 79 103
EGF 0.037 0.016 -9999 0 -0.009 52 52
YES1 0.037 0.012 -9999 0 0 51 51
CAV1 -0.036 0.106 0.186 1 -0.243 77 78
TXN 0.037 0.012 -9999 0 0 49 49
PTP1B/IRS1/GRB2 -0.027 0.129 -9999 0 -0.242 95 95
cell migration 0.052 0.114 0.251 95 -9999 0 95
STAT3 0.038 0.011 -9999 0 0 41 41
PRLR 0.038 0.016 -9999 0 -9999 0 0
ITGA2B 0.039 0.008 -9999 0 0 22 22
CSF1R 0.034 0.016 -9999 0 0 94 94
Prolactin Receptor/Prolactin 0.056 0.028 -9999 0 -9999 0 0
FGR 0.04 0.007 -9999 0 0 15 15
PTP1B/p130 Cas -0.035 0.118 -9999 0 -0.244 91 91
Crk/p130 Cas -0.028 0.125 -9999 0 -0.244 87 87
DOK1 -0.038 0.108 0.208 2 -0.242 75 77
JAK2 -0.031 0.145 -9999 0 -0.407 56 56
Jak2/Leptin Receptor/Leptin -0.026 0.144 -9999 0 -0.277 80 80
PIK3R1 0.034 0.016 -9999 0 0 99 99
PTPN1 -0.053 0.114 -9999 0 -0.253 95 95
LYN 0.035 0.015 -9999 0 0 83 83
CDH2 0.019 0.021 -9999 0 0 290 290
SRC 0.003 0.101 -9999 0 -0.497 17 17
ITGB3 0.032 0.017 -9999 0 0 116 116
CAT1/PTP1B -0.041 0.131 0.221 7 -0.283 81 88
CAPN1 0.038 0.009 -9999 0 0 25 25
CSK 0.039 0.009 -9999 0 0 25 25
PI3K -0.012 0.107 -9999 0 -0.228 49 49
mol:H2O2 0.002 0.005 -9999 0 -9999 0 0
STAT3 (dimer) -0.022 0.137 -9999 0 -0.263 76 76
negative regulation of transcription -0.03 0.144 -9999 0 -0.402 56 56
FCGR2A 0.032 0.017 -9999 0 0 119 119
FER 0.037 0.011 -9999 0 0 44 44
alphaIIb/beta3 Integrin 0.037 0.05 -9999 0 -0.137 35 35
BLK 0.033 0.017 -9999 0 0 114 114
Insulin Receptor/Insulin/Shc 0.068 0.036 -9999 0 -0.12 5 5
RHOA 0.039 0.006 -9999 0 0 13 13
LEPR 0.039 0.011 -9999 0 0 40 40
BCAR1 0.036 0.013 -9999 0 0 65 65
p210 bcr-abl/Grb2 0.04 0.008 -9999 0 0 21 21
mol:NADPH -0.001 0.002 -9999 0 -9999 0 0
TRPV6 -0.011 0.123 0.205 3 -0.296 49 52
PRL 0.042 0.011 -9999 0 -9999 0 0
SOCS3 -0.029 0.268 -9999 0 -1.174 28 28
SPRY2 0.023 0.021 -9999 0 0 240 240
Insulin Receptor/Insulin/IRS1 0.068 0.038 -9999 0 -0.119 8 8
CSF1/CSF1R -0.043 0.135 -9999 0 -0.261 100 100
Ras protein signal transduction 0.011 0.091 0.599 11 -9999 0 11
IRS1 0.04 0.008 -9999 0 0 22 22
INS 0.039 0.01 -9999 0 0 30 30
LEP 0.039 0.008 -9999 0 0 22 22
STAT5B -0.041 0.126 -9999 0 -0.267 87 87
STAT5A -0.043 0.128 -9999 0 -0.272 88 88
GRB2 0.04 0.008 -9999 0 0 21 21
PDGFB-D/PDGFRB -0.042 0.118 -9999 0 -0.245 94 94
CSN2 0.039 0.06 0.427 1 -9999 0 1
PIK3CA 0.029 0.019 -9999 0 0 166 166
LAT -0.059 0.191 -9999 0 -0.481 85 85
YBX1 0.049 0.019 -9999 0 -0.278 1 1
LCK 0.039 0.009 -9999 0 0 25 25
SHC1 0.039 0.008 -9999 0 0 23 23
NOX4 0.021 0.021 -9999 0 0 277 277
IGF1 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
NCK2 0.041 0.004 -9999 0 0 6 6
PTK2 0.027 0.019 -9999 0 0 182 182
CRKL -0.022 0.051 0.114 12 -0.129 68 80
GRB2/SOS1/SHC 0.065 0.049 -9999 0 -0.124 24 24
HRAS 0.039 0.01 -9999 0 0 31 31
IRS1/Crk 0.011 0.056 -9999 0 -0.122 73 73
IGF-1R heterotetramer/IGF1/PTP1B 0.034 0.07 -9999 0 -0.122 70 70
AKT1 0.008 0.096 0.175 101 -0.174 15 116
BAD 0.001 0.09 0.158 100 -0.171 14 114
mol:GTP 0 0 -9999 0 -9999 0 0
CRK -0.02 0.051 0.118 13 -0.13 64 77
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.013 0.07 0.204 8 -0.131 84 92
RAF1 0.024 0.12 0.276 15 -0.512 11 26
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.045 0.085 0.209 3 -0.13 83 86
YWHAZ 0.034 0.016 -9999 0 0 96 96
IGF-1R heterotetramer/IGF1/IRS1 0.019 0.067 0.178 3 -0.128 82 85
PIK3CA 0.029 0.019 -9999 0 0 166 166
RPS6KB1 0.009 0.098 0.175 105 -0.183 17 122
GNB2L1 0.039 0.009 -9999 0 0 30 30
positive regulation of MAPKKK cascade 0.023 0.111 0.271 20 -0.409 10 30
PXN 0.04 0.006 -9999 0 0 10 10
PIK3R1 0.034 0.016 -9999 0 0 99 99
cell adhesion 0 0 -9999 0 -9999 0 0
GRB2/SOS1 0.047 0.044 -9999 0 -0.142 24 24
HRAS/GTP 0.015 0.065 -9999 0 -0.128 75 75
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.063 0.087 -9999 0 -0.115 77 77
IGF-1R heterotetramer 0.034 0.023 0.099 3 -0.054 13 16
IGF-1R heterotetramer/IGF1/IRS/Nck 0.035 0.075 0.194 3 -0.124 82 85
Crk/p130 Cas/Paxillin 0.043 0.081 0.253 9 -0.126 70 79
IGF1R 0.034 0.023 0.099 3 -0.054 13 16
IGF1 0.027 0.034 0.099 3 -0.053 67 70
IRS2/Crk 0.01 0.054 0.172 3 -0.129 59 62
PI3K 0.023 0.079 0.208 1 -0.121 88 89
apoptosis -0.008 0.094 0.17 8 -0.181 83 91
HRAS/GDP 0.029 0.007 -9999 0 -9999 0 0
PRKCD -0.014 0.092 0.208 3 -0.218 65 68
RAF1/14-3-3 E 0.036 0.115 0.281 14 -0.441 11 25
BAD/14-3-3 0.008 0.097 0.188 83 -0.172 14 97
PRKCZ 0.007 0.095 0.175 100 -0.174 15 115
Crk/p130 Cas/Paxillin/FAK1 0.016 0.08 0.193 18 -0.161 35 53
PTPN1 0.037 0.012 -9999 0 0 55 55
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.012 0.095 -9999 0 -0.22 67 67
BCAR1 0.036 0.013 -9999 0 0 65 65
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.056 0.076 -9999 0 -0.111 72 72
mol:GDP 0 0 -9999 0 -9999 0 0
SOS1 0.037 0.012 -9999 0 0 51 51
IRS1/NCK2 0.025 0.067 0.142 15 -0.123 82 97
GRB10 0.04 0.008 -9999 0 0 22 22
PTPN11 -0.02 0.052 0.118 13 -0.129 66 79
IRS1 0.005 0.06 0.127 17 -0.126 80 97
IRS2 -0.021 0.051 0.117 14 -0.129 67 81
IGF-1R heterotetramer/IGF1 0.021 0.074 0.157 3 -0.158 72 75
GRB2 0.04 0.008 -9999 0 0 21 21
PDPK1 0.015 0.102 0.189 103 -0.179 14 117
YWHAE 0.037 0.013 -9999 0 0 58 58
PRKD1 -0.016 0.095 0.208 1 -0.224 69 70
SHC1 0.039 0.008 -9999 0 0 23 23
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 0.027 0.102 0.213 15 -0.236 33 48
TBX21 -0.026 0.273 -9999 0 -0.69 51 51
B2M 0.038 0.013 -9999 0 -9999 0 0
TYK2 0.024 0.043 -9999 0 -0.048 101 101
IL12RB1 0.023 0.044 -9999 0 -0.049 107 107
GADD45B -0.058 0.343 -9999 0 -0.885 58 58
IL12RB2 0.027 0.045 -9999 0 -0.048 111 111
GADD45G -0.032 0.296 -9999 0 -0.721 59 59
natural killer cell activation 0.002 0.021 0.043 11 -0.033 96 107
RELB 0.039 0.01 -9999 0 0 33 33
RELA 0.04 0.006 -9999 0 0 10 10
IL18 0.03 0.024 -9999 0 -0.042 19 19
IL2RA 0.038 0.01 -9999 0 0 38 38
IFNG 0.037 0.013 -9999 0 0 58 58
STAT3 (dimer) -0.025 0.284 0.403 2 -0.569 84 86
HLA-DRB5 0.016 0.027 -9999 0 -0.006 297 297
FASLG -0.025 0.278 0.521 1 -0.713 49 50
NF kappa B2 p52/RelB -0.013 0.283 -9999 0 -0.559 84 84
CD4 0.025 0.028 -9999 0 -0.013 179 179
SOCS1 0.037 0.012 -9999 0 0 51 51
EntrezGene:6955 -0.001 0.01 -9999 0 -0.026 59 59
CD3D 0.026 0.03 -9999 0 -0.039 67 67
CD3E 0.028 0.029 -9999 0 -0.038 68 68
CD3G 0.025 0.029 -9999 0 -0.041 57 57
IL12Rbeta2/JAK2 0.029 0.074 -9999 0 -0.13 44 44
CCL3 -0.043 0.321 0.47 1 -0.786 61 62
CCL4 -0.03 0.273 -9999 0 -0.557 84 84
HLA-A 0.038 0.013 -9999 0 -9999 0 0
IL18/IL18R 0.053 0.082 -9999 0 -0.117 73 73
NOS2 -0.026 0.266 0.381 2 -0.542 82 84
IL12/IL12R/TYK2/JAK2/SPHK2 0.027 0.103 0.211 17 -0.228 37 54
IL1R1 -0.109 0.428 -9999 0 -0.967 96 96
IL4 0.02 0.044 0.092 6 -0.058 17 23
JAK2 0.023 0.042 -9999 0 -0.049 88 88
EntrezGene:6957 -0.001 0.009 -9999 0 -0.024 36 36
TCR/CD3/MHC I/CD8 -0.013 0.112 -9999 0 -0.422 26 26
RAB7A -0.031 0.27 0.375 1 -0.575 79 80
lysosomal transport -0.027 0.26 0.372 1 -0.548 79 80
FOS -0.184 0.508 -9999 0 -1.065 124 124
STAT4 (dimer) -0.022 0.289 0.397 5 -0.6 77 82
STAT5A (dimer) -0.02 0.278 -9999 0 -0.566 81 81
GZMA -0.051 0.339 -9999 0 -0.871 58 58
GZMB -0.034 0.304 0.427 1 -0.721 63 64
HLX 0 0 -9999 0 -9999 0 0
LCK -0.039 0.282 0.403 3 -0.588 83 86
TCR/CD3/MHC II/CD4 -0.066 0.197 -9999 0 -0.361 128 128
IL2/IL2R 0.045 0.08 -9999 0 -0.11 90 90
MAPK14 -0.047 0.32 -9999 0 -0.7 78 78
CCR5 -0.02 0.249 0.372 2 -0.496 85 87
IL1B 0.023 0.041 -9999 0 -0.048 88 88
STAT6 0.009 0.136 -9999 0 -0.561 13 13
STAT4 0.039 0.008 -9999 0 0 24 24
STAT3 0.038 0.011 -9999 0 0 41 41
STAT1 0.034 0.016 -9999 0 0 102 102
NFKB1 0.036 0.013 -9999 0 0 66 66
NFKB2 0.04 0.007 -9999 0 0 18 18
IL12B 0.027 0.045 -9999 0 -0.048 114 114
CD8A 0.042 0.005 -9999 0 -9999 0 0
CD8B 0.001 0 -9999 0 -9999 0 0
T-helper 1 cell differentiation 0 0 -9999 0 -9999 0 0
natural killer cell mediated cytotoxicity -0.028 0.102 0.234 33 -0.212 16 49
IL2RB 0.035 0.014 -9999 0 0 76 76
proteasomal ubiquitin-dependent protein catabolic process -0.015 0.271 0.393 5 -0.556 77 82
IL2RG 0.028 0.019 -9999 0 0 179 179
IL12 0.024 0.072 -9999 0 -0.128 44 44
STAT5A 0.038 0.01 -9999 0 0 36 36
CD247 -0.001 0.009 -9999 0 -0.024 38 38
IL2 0.039 0.01 -9999 0 0 34 34
SPHK2 0.04 0.008 -9999 0 0 20 20
FRAP1 0.039 0.009 -9999 0 0 28 28
IL12A 0.02 0.04 -9999 0 -0.049 83 83
IL12/IL12R/TYK2/JAK2 -0.047 0.288 -9999 0 -0.631 80 80
MAP2K3 -0.05 0.332 0.408 1 -0.716 79 80
RIPK2 0.032 0.017 -9999 0 0 119 119
MAP2K6 -0.055 0.314 -9999 0 -0.67 83 83
regulation of dendritic cell antigen processing and presentation 0 0 -9999 0 -9999 0 0
HLA-DRA 0.023 0.029 -9999 0 -0.012 203 203
IL18RAP 0.039 0.019 -9999 0 -0.041 23 23
IL12Rbeta1/TYK2 0.038 0.057 -9999 0 -0.079 21 21
EOMES 0.005 0.072 -9999 0 -0.546 7 7
STAT1 (dimer) -0.043 0.282 0.399 2 -0.579 86 88
T cell proliferation -0.021 0.234 0.347 6 -0.476 80 86
T-helper 1 cell lineage commitment 0 0 -9999 0 -9999 0 0
IL18R1 0.039 0.019 -9999 0 -0.041 22 22
CD8-positive alpha-beta T cell lineage commitment 0 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelA -0.029 0.248 -9999 0 -0.531 76 76
ATF2 -0.046 0.3 -9999 0 -0.653 79 79
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.037 0.012 -9999 0 0 53 53
LAT2 -0.019 0.101 0.186 5 -0.215 87 92
AP1 -0.025 0.177 0.284 3 -0.409 66 69
mol:PIP3 -0.031 0.133 0.256 10 -0.309 64 74
IKBKB -0.011 0.09 0.195 25 -0.189 57 82
AKT1 0.02 0.122 0.25 67 -0.209 10 77
IKBKG -0.019 0.084 0.203 8 -0.188 60 68
MS4A2 0.046 0.012 0.07 38 -0.004 10 48
mol:Sphingosine-1-phosphate 0 0 -9999 0 -9999 0 0
PIK3CA 0.029 0.019 -9999 0 0 166 166
MAP3K1 -0.006 0.142 0.237 50 -0.29 61 111
mol:Ca2+ -0.022 0.108 0.223 12 -0.248 58 70
LYN 0.035 0.018 0.078 1 -0.003 92 93
CBLB -0.014 0.095 0.182 7 -0.212 77 84
SHC1 0.039 0.008 -9999 0 0 23 23
RasGAP/p62DOK 0.023 0.071 -9999 0 -0.105 103 103
positive regulation of cell migration -0.01 0.001 -9999 0 -9999 0 0
INPP5D 0 0 -9999 0 -9999 0 0
PLD2 -0.012 0.075 0.293 16 -0.158 4 20
PTPN13 -0.059 0.203 -9999 0 -0.689 33 33
PTPN11 0.039 0.019 0.081 3 -0.033 22 25
GO:0007205 0 0 -9999 0 -9999 0 0
regulation of mast cell degranulation -0.005 0.128 0.282 20 -0.328 30 50
SYK 0.037 0.017 0.078 1 -0.003 74 75
GRB2 0.04 0.008 -9999 0 0 21 21
LAT/PLCgamma1/GRB2/SLP76/GADs -0.024 0.13 0.181 1 -0.274 91 92
LAT -0.017 0.097 0.196 1 -0.21 84 85
PAK2 -0.002 0.152 0.244 58 -0.301 66 124
NFATC2 0.003 0.054 -9999 0 -0.393 9 9
HRAS -0.026 0.142 0.266 3 -0.32 71 74
GAB2 0.031 0.018 -9999 0 0 136 136
PLA2G1B 0.012 0.14 -9999 0 -0.899 12 12
Fc epsilon R1 0.033 0.071 -9999 0 -0.093 111 111
Antigen/IgE/Fc epsilon R1 0.035 0.063 -9999 0 -0.079 102 102
mol:GDP -0.025 0.158 0.233 5 -0.396 58 63
JUN 0.035 0.014 -9999 0 0 76 76
mol:Ca++ 0 0 -9999 0 -9999 0 0
PIK3R1 0.034 0.016 -9999 0 0 99 99
FOS 0.026 0.02 -9999 0 0 201 201
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.011 0.103 0.144 8 -0.218 85 93
CHUK -0.021 0.085 0.189 11 -0.191 66 77
KLRG1 -0.016 0.079 -9999 0 -0.168 84 84
VAV1 -0.013 0.094 0.174 5 -0.215 72 77
calcium-dependent protein kinase C activity 0 0 -9999 0 -9999 0 0
CBL -0.017 0.097 0.181 4 -0.212 82 86
negative regulation of mast cell degranulation -0.021 0.074 -9999 0 -0.193 50 50
BTK -0.033 0.176 -9999 0 -0.484 53 53
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.026 0.103 -9999 0 -0.213 105 105
GAB2/PI3K/SHP2 -0.038 0.053 -9999 0 -0.147 64 64
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP 0 0.058 -9999 0 -0.134 77 77
RAF1 0.015 0.153 -9999 0 -0.989 12 12
Fc epsilon R1/FcgammaRIIB/SHIP 0.032 0.091 -9999 0 -0.12 124 124
FCER1G 0.027 0.02 -9999 0 0 189 189
FCER1A 0.039 0.014 -9999 0 -0.006 41 41
Antigen/IgE/Fc epsilon R1/Fyn 0.04 0.076 -9999 0 -0.09 107 107
MAPK3 0.012 0.142 -9999 0 -0.908 12 12
MAPK1 0.006 0.144 -9999 0 -0.918 12 12
NFKB1 0.036 0.013 -9999 0 0 66 66
MAPK8 -0.035 0.222 -9999 0 -0.582 57 57
DUSP1 0.026 0.02 -9999 0 0 196 196
NF-kappa-B/RelA 0.002 0.069 0.137 16 -0.135 61 77
actin cytoskeleton reorganization -0.052 0.202 -9999 0 -0.73 30 30
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -9999 0 0
PI3K -0.018 0.128 0.255 5 -0.27 75 80
FER -0.017 0.096 0.196 1 -0.217 78 79
RELA 0.04 0.006 -9999 0 0 10 10
ITK -0.002 0.056 -9999 0 -0.29 15 15
SOS1 0.037 0.012 -9999 0 0 51 51
PLCG1 -0.026 0.153 0.301 4 -0.351 69 73
cytokine secretion -0.002 0.047 0.083 8 -0.098 63 71
SPHK1 -0.016 0.098 0.19 6 -0.211 83 89
PTK2 -0.056 0.214 -9999 0 -0.782 30 30
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.018 0.136 -9999 0 -0.28 90 90
EDG1 -0.01 0.001 -9999 0 -9999 0 0
mol:DAG -0.031 0.136 0.257 10 -0.313 67 77
MAP2K2 0.005 0.141 -9999 0 -0.918 12 12
MAP2K1 0.004 0.142 -9999 0 -0.924 12 12
MAP2K7 0.038 0.011 -9999 0 0 41 41
KLRG1/SHP2 0.011 0.09 0.204 30 -0.181 53 83
MAP2K4 -0.081 0.339 -9999 0 -0.898 78 78
Fc epsilon R1/FcgammaRIIB 0.034 0.098 -9999 0 -0.13 124 124
mol:Choline -0.012 0.074 0.291 16 -0.156 4 20
SHC/Grb2/SOS1 0.023 0.13 0.235 1 -0.209 91 92
FYN 0.034 0.016 -9999 0 0 94 94
DOK1 0.04 0.008 -9999 0 0 22 22
PXN -0.054 0.195 -9999 0 -0.705 30 30
HCLS1 -0.012 0.1 0.175 7 -0.244 62 69
PRKCB -0.023 0.107 0.225 10 -0.238 68 78
FCGR2B 0.03 0.019 -9999 0 0 153 153
IGHE 0 0.006 0.037 1 -9999 0 1
KLRG1/SHIP -0.021 0.075 -9999 0 -0.196 50 50
LCP2 0.034 0.016 -9999 0 0 101 101
PLA2G4A -0.008 0.09 0.154 5 -0.219 63 68
RASA1 0.037 0.013 -9999 0 0 56 56
mol:Phosphatidic acid -0.012 0.074 0.291 16 -0.156 4 20
IKK complex -0.014 0.075 0.186 18 -0.162 46 64
WIPF1 0 0 -9999 0 -9999 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.032 0.017 -9999 0 0 116 116
ANTXR2 0.035 0.015 -9999 0 0 87 87
negative regulation of myeloid dendritic cell antigen processing and presentation -0.006 0.011 -9999 0 -0.033 72 72
monocyte activation -0.082 0.168 -9999 0 -0.353 150 150
MAP2K2 -0.041 0.183 -9999 0 -0.585 55 55
MAP2K1 -0.011 0.011 0.008 38 -0.037 68 106
MAP2K7 -0.01 0.011 0.008 36 -0.037 65 101
MAP2K6 -0.009 0.012 0.008 33 -0.039 58 91
CYAA -0.023 0.033 -9999 0 -0.101 72 72
MAP2K4 -0.01 0.012 0.008 32 -0.038 64 96
IL1B -0.01 0.038 0.104 9 -0.084 75 84
Channel 0.022 0.056 -9999 0 -0.11 72 72
NLRP1 -0.006 0.01 -9999 0 -0.031 72 72
CALM1 0.039 0.009 -9999 0 0 26 26
negative regulation of phagocytosis 0.001 0.074 -9999 0 -0.428 15 15
mol:Ca2+ 0 0 -9999 0 -9999 0 0
regulation of endothelial cell proliferation 0.006 0.011 0.033 72 -9999 0 72
MAPK3 -0.011 0.012 0.008 37 -0.037 71 108
MAPK1 -0.01 0.011 0.008 35 -0.037 64 99
PGR -0.008 0.011 0.009 37 -0.037 51 88
PA/Cellular Receptors 0.023 0.062 -9999 0 -0.123 72 72
apoptosis -0.006 0.011 -9999 0 -0.033 72 72
LOC728358 0 0 -9999 0 -9999 0 0
Lethal toxin (unfolded) 0.021 0.056 -9999 0 -0.111 72 72
macrophage activation -0.01 0.03 0.173 10 -0.112 2 12
TNF 0.04 0.008 -9999 0 0 22 22
VCAM1 -0.081 0.169 -9999 0 -0.356 148 148
platelet activation 0.001 0.074 -9999 0 -0.428 15 15
MAPKKK cascade 0.008 0.027 0.083 9 -0.071 19 28
IL18 -0.006 0.038 0.105 10 -0.084 63 73
negative regulation of macrophage activation -0.006 0.011 -9999 0 -0.033 72 72
LEF -0.006 0.011 -9999 0 -0.033 72 72
CASP1 0 0.012 0.019 35 -0.03 48 83
mol:cAMP 0.001 0.074 -9999 0 -0.432 15 15
necrosis -0.006 0.011 -9999 0 -0.033 72 72
intracellular pH reduction 0 0 -9999 0 -9999 0 0
PAGA 0 0 -9999 0 -9999 0 0
Edema toxin (unfolded) 0.023 0.053 -9999 0 -0.102 72 72
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -9999 0 -9999 0 0
Canonical Wnt signaling pathway

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
HDAC1 0.054 0.062 0.148 116 -0.032 30 146
AES 0.052 0.054 0.132 119 -0.032 13 132
FBXW11 0.04 0.008 -9999 0 0 22 22
mol:GTP 0.001 0.003 0.033 1 -9999 0 1
LRP6/FZD1 0.042 0.048 -9999 0 -0.133 32 32
SMAD4 0.038 0.011 -9999 0 0 43 43
DKK2 0.039 0.01 -9999 0 0 33 33
TLE1 0.052 0.051 0.13 114 -0.033 11 125
MACF1 0.033 0.016 -9999 0 0 106 106
CTNNB1 0.029 0.118 0.303 24 -0.422 12 36
WIF1 0.039 0.009 -9999 0 -0.001 27 27
beta catenin/RanBP3 0.092 0.22 0.459 112 -0.386 10 122
KREMEN2 0.039 0.009 -9999 0 0 29 29
DKK1 0.038 0.011 -9999 0 0 39 39
beta catenin/beta TrCP1 0.049 0.118 0.311 24 -0.397 12 36
FZD1 0.04 0.006 -9999 0 0 13 13
AXIN2 -0.051 0.214 0.801 2 -0.812 25 27
AXIN1 0.039 0.011 -9999 0 0 39 39
RAN 0.04 0.009 0.075 1 0 21 22
Axin1/APC/GSK3/beta catenin 0.02 0.141 0.41 1 -0.477 32 33
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.026 0.173 0.281 8 -0.372 76 84
Axin1/APC/GSK3 0.024 0.079 0.204 13 -0.262 15 28
Axin1/APC/GSK3/beta catenin/Macf1 0.017 0.088 0.281 10 -0.295 14 24
HNF1A 0.018 0.05 0.089 131 -9999 0 131
CTBP1 0.053 0.052 0.132 116 -0.033 11 127
MYC 0.037 0.533 0.645 141 -1.147 67 208
RANBP3 0.039 0.012 0.075 1 0 42 43
DKK2/LRP6/Kremen 2 0.058 0.053 -9999 0 -0.116 29 29
NKD1 0.038 0.011 -9999 0 0 43 43
TCF4 0.054 0.057 0.14 116 -0.032 11 127
TCF3 0.051 0.052 0.13 117 -0.033 12 129
WNT1/LRP6/FZD1/Axin1 0.075 0.061 -9999 0 -0.11 30 30
Ran/GTP 0.03 0.014 0.102 1 -0.122 3 4
CtBP/CBP/TCF/TLE1/AES 0.051 0.299 0.54 110 -0.363 34 144
LEF1 0.036 0.048 0.134 73 -0.032 12 85
DVL1 0.028 0.081 0.234 10 -0.32 13 23
CSNK2A1 0.038 0.012 -9999 0 0 47 47
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.065 0.189 -9999 0 -0.403 91 91
DKK1/LRP6/Kremen 2 0.056 0.053 -9999 0 -0.115 28 28
LRP6 0.034 0.016 -9999 0 0 94 94
CSNK1A1 0.057 0.064 0.148 127 -0.032 33 160
NLK 0.029 0.026 -9999 0 -0.035 68 68
CCND1 -0.182 0.498 0.715 11 -1.21 94 105
WNT1 0.041 0.006 -9999 0 0 10 10
GSK3A 0.038 0.012 0.065 1 0 46 47
GSK3B 0.039 0.008 -9999 0 0 23 23
FRAT1 0.039 0.009 -9999 0 -0.004 19 19
PPP2R5D 0.031 0.071 0.24 2 -0.377 10 12
APC -0.006 0.077 0.2 57 -9999 0 57
WNT1/LRP6/FZD1 0.018 0.064 0.183 3 -0.237 10 13
CREBBP 0.052 0.053 0.133 118 -0.033 14 132
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.064 0.214 -9999 0 -0.35 163 163
Syndecan-4/Syndesmos -0.039 0.189 0.302 2 -0.467 54 56
positive regulation of JNK cascade -0.058 0.186 0.3 1 -0.427 71 72
Syndecan-4/ADAM12 -0.055 0.181 0.302 2 -0.462 58 60
CCL5 0.029 0.019 -9999 0 0 160 160
Rac1/GDP 0.029 0.009 -9999 0 -0.125 1 1
DNM2 0.036 0.014 -9999 0 0 72 72
ITGA5 0.036 0.013 -9999 0 0 64 64
SDCBP 0.035 0.014 -9999 0 0 77 77
PLG 0.033 0.028 -9999 0 -0.042 50 50
ADAM12 0.03 0.018 -9999 0 0 152 152
mol:GTP 0 0 -9999 0 -9999 0 0
NUDT16L1 0.039 0.01 -9999 0 0 33 33
mol:PI-4-5-P2 0 0 -9999 0 -9999 0 0
Syndecan-4/PKC alpha -0.023 0.022 -9999 0 -9999 0 0
Syndecan-4/Laminin alpha1 -0.042 0.182 -9999 0 -0.456 53 53
Syndecan-4/CXCL12/CXCR4 -0.061 0.197 0.313 1 -0.455 70 71
Syndecan-4/Laminin alpha3 -0.049 0.186 0.302 1 -0.473 56 57
MDK 0.039 0.008 -9999 0 0 23 23
Syndecan-4/FZD7 -0.042 0.19 0.302 2 -0.468 56 58
Syndecan-4/Midkine -0.04 0.191 0.302 2 -0.47 55 57
FZD7 0.036 0.013 -9999 0 0 64 64
Syndecan-4/FGFR1/FGF -0.028 0.183 -9999 0 -0.449 48 48
THBS1 0.027 0.02 -9999 0 0 190 190
integrin-mediated signaling pathway -0.056 0.182 0.297 2 -0.415 78 80
positive regulation of MAPKKK cascade -0.058 0.186 0.3 1 -0.427 71 72
Syndecan-4/TACI -0.039 0.19 0.302 2 -0.468 55 57
CXCR4 0.033 0.017 -9999 0 0 115 115
cell adhesion -0.035 0.092 0.21 2 -0.196 120 122
Syndecan-4/Dynamin -0.037 0.183 -9999 0 -0.472 49 49
Syndecan-4/TSP1 -0.059 0.188 0.302 2 -0.464 61 63
Syndecan-4/GIPC -0.037 0.179 -9999 0 -0.475 46 46
Syndecan-4/RANTES -0.051 0.193 0.302 1 -0.47 61 62
ITGB1 0.038 0.01 -9999 0 0 36 36
LAMA1 0.033 0.016 -9999 0 0 104 104
LAMA3 0.03 0.018 -9999 0 0 151 151
RAC1 0.039 0.009 -9999 0 0 28 28
PRKCA 0 0.104 0.903 5 -9999 0 5
Syndecan-4/alpha-Actinin -0.04 0.192 0.302 2 -0.469 56 58
TFPI 0.039 0.01 -9999 0 0 32 32
F2 0.037 0.026 0.087 2 -0.037 49 51
alpha5/beta1 Integrin 0.043 0.046 -9999 0 -0.134 29 29
positive regulation of cell adhesion -0.056 0.17 -9999 0 -0.45 55 55
ACTN1 0.039 0.01 -9999 0 0 32 32
TNC 0.027 0.02 -9999 0 0 189 189
Syndecan-4/CXCL12 -0.058 0.191 0.302 2 -0.461 65 67
FGF6 0.037 0.012 -9999 0 0 55 55
RHOA 0.04 0.006 -9999 0 0 13 13
CXCL12 0.028 0.019 -9999 0 0 174 174
TNFRSF13B 0.037 0.012 -9999 0 0 50 50
FGF2 0.039 0.01 -9999 0 0 33 33
FGFR1 0.033 0.017 -9999 0 0 112 112
Syndecan-4/PI-4-5-P2 -0.062 0.172 -9999 0 -0.461 56 56
mol:GDP 0 0 -9999 0 -9999 0 0
FN1 0.017 0.024 -9999 0 -0.04 24 24
cell migration -0.011 0.013 -9999 0 -9999 0 0
PRKCD 0.033 0.027 -9999 0 -0.042 44 44
vasculogenesis -0.056 0.181 0.297 2 -0.443 62 64
SDC4 -0.055 0.18 -9999 0 -0.501 50 50
Syndecan-4/Tenascin C -0.059 0.189 0.302 2 -0.46 65 67
Syndecan-4/PI-4-5-P2/PKC alpha -0.019 0.017 -9999 0 -9999 0 0
Syndecan-4/Syntenin -0.041 0.189 0.302 2 -0.479 52 54
MMP9 0.027 0.023 -9999 0 -0.038 18 18
Rac1/GTP -0.036 0.094 0.212 2 -0.2 120 122
cytoskeleton organization -0.037 0.182 0.297 2 -0.403 73 75
GIPC1 0.034 0.015 -9999 0 0 92 92
Syndecan-4/TFPI -0.04 0.189 0.302 2 -0.462 57 59
Syndecan-2-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
Syndecan-2/Fibronectin 0.006 0.051 -9999 0 -0.151 42 42
EPHB2 0.038 0.01 -9999 0 0 38 38
Syndecan-2/TACI 0.024 0.041 -9999 0 -0.104 39 39
LAMA1 0.033 0.016 -9999 0 0 104 104
Syndecan-2/alpha2 ITGB1 0.034 0.088 0.189 40 -0.118 88 128
HRAS 0.039 0.01 -9999 0 0 31 31
Syndecan-2/CASK 0 0.028 -9999 0 -0.097 42 42
ITGA5 0.036 0.013 -9999 0 0 64 64
BAX 0.023 0.068 -9999 0 -9999 0 0
EPB41 0.039 0.01 -9999 0 0 31 31
positive regulation of cell-cell adhesion 0.016 0.045 -9999 0 -0.096 67 67
LAMA3 0.03 0.018 -9999 0 0 151 151
EZR 0 0 -9999 0 -9999 0 0
mol:PI-4-5-P2 0 0 -9999 0 -9999 0 0
CAV2 0.033 0.016 -9999 0 0 105 105
Syndecan-2/MMP2 0.007 0.053 -9999 0 -0.155 42 42
RP11-540L11.1 0 0 -9999 0 -9999 0 0
alpha2 ITGB1 0.034 0.057 -9999 0 -0.138 46 46
dendrite morphogenesis 0.024 0.043 -9999 0 -0.113 39 39
Syndecan-2/GM-CSF 0.025 0.041 -9999 0 -0.104 41 41
determination of left/right symmetry 0.01 0.007 -9999 0 -9999 0 0
Syndecan-2/PKC delta 0.023 0.041 -9999 0 -0.107 40 40
GNB2L1 0.039 0.009 -9999 0 0 30 30
MAPK3 0.012 0.077 0.15 108 -0.099 39 147
MAPK1 0.011 0.076 0.151 104 -0.099 38 142
Syndecan-2/RACK1 0.038 0.047 -9999 0 -0.091 44 44
NF1 0.034 0.016 -9999 0 0 96 96
FGFR/FGF/Syndecan-2 0.01 0.007 -9999 0 -9999 0 0
ITGA2 0.033 0.017 -9999 0 0 114 114
MAPK8 -0.004 0.005 -9999 0 -9999 0 0
Syndecan-2/alpha2/beta1 Integrin 0.048 0.08 0.189 50 -0.112 57 107
Syndecan-2/Kininogen 0.022 0.039 -9999 0 -0.104 36 36
ITGB1 0.038 0.01 -9999 0 0 36 36
SRC 0.008 0.076 0.191 66 -9999 0 66
Syndecan-2/CASK/Protein 4.1 0.022 0.037 -9999 0 -0.092 43 43
extracellular matrix organization 0.022 0.042 -9999 0 -0.111 39 39
actin cytoskeleton reorganization 0.006 0.051 -9999 0 -0.15 42 42
Syndecan-2/Caveolin-2/Ras 0.028 0.059 -9999 0 -0.109 64 64
Syndecan-2/Laminin alpha3 0.017 0.046 -9999 0 -0.132 35 35
Syndecan-2/RasGAP 0.062 0.068 0.176 52 -0.092 56 108
alpha5/beta1 Integrin 0.043 0.046 -9999 0 -0.134 29 29
PRKCD 0.037 0.012 -9999 0 0 51 51
Syndecan-2 dimer 0.024 0.043 -9999 0 -0.113 39 39
GO:0007205 0.003 0.001 -9999 0 -9999 0 0
DNA mediated transformation 0 0 -9999 0 -9999 0 0
Syndecan-2/RasGAP/Src 0.039 0.059 0.195 3 -0.097 49 52
RHOA 0.04 0.006 -9999 0 0 13 13
SDCBP 0.035 0.014 -9999 0 0 77 77
TNFRSF13B 0.037 0.012 -9999 0 0 50 50
RASA1 0.037 0.013 -9999 0 0 56 56
alpha2/beta1 Integrin 0.034 0.057 -9999 0 -0.138 46 46
Syndecan-2/Synbindin 0.019 0.044 -9999 0 -0.113 41 41
TGFB1 0.036 0.014 -9999 0 0 69 69
CASP3 0.008 0.075 0.152 94 -0.101 49 143
FN1 0.021 0.021 -9999 0 0 268 268
Syndecan-2/IL8 0.018 0.044 -9999 0 -0.118 39 39
SDC2 0.01 0.007 -9999 0 -9999 0 0
KNG1 0.034 0.016 -9999 0 0 100 100
Syndecan-2/Neurofibromin 0.021 0.042 -9999 0 -0.112 37 37
TRAPPC4 0.034 0.016 -9999 0 0 97 97
CSF2 0.04 0.008 -9999 0 0 21 21
Syndecan-2/TGFB1 0.022 0.042 -9999 0 -0.111 39 39
Syndecan-2/Syntenin/PI-4-5-P2 0.016 0.045 -9999 0 -0.096 67 67
Syndecan-2/Ezrin 0.023 0.038 -9999 0 -0.093 45 45
PRKACA 0.004 0.071 0.149 80 -0.104 53 133
angiogenesis 0.018 0.044 -9999 0 -0.118 39 39
MMP2 0.021 0.021 -9999 0 0 265 265
IL8 0.031 0.018 -9999 0 0 129 129
calcineurin-NFAT signaling pathway 0.024 0.04 -9999 0 -0.104 39 39
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.081 0.346 0.486 2 -0.79 81 83
CRP -0.08 0.33 0.5 1 -0.776 74 75
cell cycle arrest -0.116 0.387 -9999 0 -0.867 91 91
TIMP1 -0.102 0.364 -9999 0 -0.763 107 107
IL6ST 0.025 0.036 -9999 0 -0.043 65 65
Rac1/GDP -0.008 0.171 0.294 7 -0.381 58 65
AP1 -0.027 0.207 -9999 0 -0.479 65 65
GAB2 0.032 0.02 -9999 0 -0.045 2 2
TNFSF11 -0.084 0.328 -9999 0 -0.769 77 77
HSP90B1 0.011 0.093 -9999 0 -1.136 2 2
GAB1 0.038 0.014 -9999 0 -0.04 2 2
MAPK14 -0.029 0.166 -9999 0 -0.619 30 30
AKT1 -0.004 0.152 0.276 3 -0.451 31 34
FOXO1 -0.005 0.145 0.262 3 -0.436 30 33
MAP2K6 -0.021 0.15 0.222 1 -0.416 48 49
mol:GTP 0 0.003 -9999 0 -9999 0 0
MAP2K4 -0.034 0.205 0.312 9 -0.428 79 88
MITF -0.016 0.146 0.227 5 -0.351 58 63
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -9999 0 0
TYK2 0.036 0.013 -9999 0 0 65 65
A2M -0.122 0.41 -9999 0 -1.219 66 66
CEBPB 0.036 0.014 -9999 0 0 72 72
GRB2/SOS1/GAB family/SHP2 -0.009 0.165 0.313 3 -0.404 56 59
STAT3 -0.141 0.42 -9999 0 -0.955 91 91
STAT1 -0.071 0.283 -9999 0 -0.831 64 64
CEBPD -0.083 0.338 0.522 2 -0.793 75 77
PIK3CA 0.029 0.02 -9999 0 -0.047 2 2
PI3K 0.023 0.06 -9999 0 -0.146 46 46
JUN 0.036 0.014 -9999 0 0 76 76
PIAS3/MITF -0.004 0.146 -9999 0 -0.339 53 53
MAPK11 -0.026 0.156 -9999 0 -0.603 30 30
STAT3 (dimer)/FOXO1 -0.089 0.355 0.406 2 -0.739 98 100
GRB2/SOS1/GAB family 0.03 0.128 0.303 4 -0.287 31 35
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK 0.001 0.111 0.188 3 -0.27 54 57
GRB2 0.041 0.01 -9999 0 -0.002 22 22
JAK2 0.034 0.016 -9999 0 0 101 101
LBP -0.031 0.263 0.474 1 -0.574 71 72
PIK3R1 0.034 0.017 -9999 0 -0.001 102 102
JAK1 0.032 0.029 -9999 0 -0.043 58 58
MYC -0.071 0.418 0.499 8 -0.871 97 105
FGG -0.083 0.328 -9999 0 -0.763 78 78
macrophage differentiation -0.116 0.387 -9999 0 -0.867 91 91
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.049 0.103 -9999 0 -0.175 48 48
JUNB -0.097 0.39 0.5 7 -0.859 94 101
FOS 0.026 0.02 -9999 0 0 201 201
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.01 0.157 0.224 5 -0.355 63 68
STAT1/PIAS1 -0.015 0.182 0.283 2 -0.363 76 78
GRB2/SOS1/GAB family/SHP2/PI3K -0.008 0.152 -9999 0 -0.406 43 43
STAT3 (dimer) -0.136 0.41 -9999 0 -0.931 91 91
PRKCD -0.058 0.261 0.338 10 -0.534 93 103
IL6R 0.032 0.028 -9999 0 -0.043 47 47
SOCS3 -0.042 0.22 -9999 0 -1.034 22 22
gp130 (dimer)/JAK1/JAK1/LMO4 0.042 0.088 -9999 0 -0.149 54 54
Rac1/GTP -0.013 0.187 0.3 7 -0.392 68 75
HCK 0.037 0.014 -9999 0 0 65 65
MAPKKK cascade -0.022 0.216 -9999 0 -0.508 67 67
bone resorption -0.077 0.311 -9999 0 -0.718 78 78
IRF1 -0.141 0.422 -9999 0 -0.939 106 106
mol:GDP -0.022 0.152 0.217 4 -0.37 58 62
SOS1 0.039 0.015 -9999 0 -0.001 53 53
VAV1 -0.022 0.154 0.218 4 -0.375 58 62
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.015 0.183 -9999 0 -0.507 48 48
PTPN11 0.001 0.163 -9999 0 -0.786 21 21
IL6/IL6RA 0.03 0.061 -9999 0 -0.13 41 41
gp130 (dimer)/TYK2/TYK2/LMO4 0.048 0.066 -9999 0 -0.111 46 46
gp130 (dimer)/JAK2/JAK2/LMO4 0.039 0.077 -9999 0 -0.131 60 60
IL6 0.023 0.036 -9999 0 -0.044 69 69
PIAS3 0.038 0.012 -9999 0 0 47 47
PTPRE 0.027 0.037 0.097 13 -0.043 66 79
PIAS1 0.039 0.008 -9999 0 0 24 24
RAC1 0.039 0.009 -9999 0 0 28 28
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0.001 0.091 0.161 3 -0.234 43 46
LMO4 0.028 0.037 -9999 0 -0.044 68 68
STAT3 (dimer)/PIAS3 -0.099 0.391 -9999 0 -0.86 89 89
MCL1 0.004 0.162 -9999 0 -0.792 10 10
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0 0.107 0.154 67 -0.303 34 101
adherens junction organization -0.017 0.125 0.194 8 -0.35 45 53
mol:GTP 0 0 -9999 0 -9999 0 0
Rac1/GDP 0.02 0.111 0.217 17 -0.282 27 44
FMN1 -0.012 0.111 0.151 9 -0.278 55 64
mol:IP3 0.009 0.096 0.157 69 -0.236 37 106
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.003 0.121 0.164 9 -0.289 59 68
CTNNB1 0.04 0.011 0.068 3 0 32 35
AKT1 -0.012 0.086 0.207 5 -0.267 35 40
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.002 0.143 -9999 0 -0.419 35 35
CTNND1 0.042 0.009 -9999 0 -0.002 18 18
mol:PI-4-5-P2 -0.005 0.115 0.216 21 -0.32 38 59
VASP -0.013 0.112 0.156 5 -0.286 54 59
ZYX -0.01 0.108 0.151 10 -0.303 44 54
JUB -0.015 0.115 0.151 8 -0.289 57 65
EGFR(dimer) 0.004 0.127 -9999 0 -0.321 46 46
E-cadherin/beta catenin-gamma catenin 0.052 0.058 -9999 0 -0.11 45 45
mol:PI-3-4-5-P3 0.001 0.098 -9999 0 -0.272 37 37
PIK3CA 0.029 0.02 -9999 0 -0.001 169 169
PI3K 0.001 0.1 -9999 0 -0.278 37 37
FYN -0.004 0.12 0.186 17 -0.276 58 75
mol:Ca2+ 0.009 0.095 0.156 69 -0.232 37 106
JUP 0.038 0.013 0.068 1 0 57 58
PIK3R1 0.035 0.017 -9999 0 0 100 100
mol:DAG 0.009 0.096 0.157 69 -0.236 37 106
CDH1 0.036 0.015 -9999 0 0 79 79
RhoA/GDP 0.021 0.113 0.225 17 -0.28 28 45
establishment of polarity of embryonic epithelium -0.011 0.111 0.178 8 -0.28 54 62
SRC 0.039 0.009 -9999 0 0 28 28
RAC1 0.039 0.009 -9999 0 0 28 28
RHOA 0.04 0.006 -9999 0 0 13 13
EGFR 0.036 0.014 -9999 0 0 67 67
CASR 0.003 0.094 0.156 76 -0.267 26 102
RhoA/GTP 0.023 0.1 0.201 11 -0.261 27 38
AKT2 -0.013 0.085 0.22 2 -0.269 34 36
actin cable formation -0.016 0.11 0.236 8 -0.316 41 49
apoptosis -0.007 0.107 0.277 37 -0.166 75 112
CTNNA1 0.04 0.011 -9999 0 -0.001 32 32
mol:GDP 0.002 0.103 0.166 72 -0.248 38 110
PIP5K1A -0.013 0.108 0.152 5 -0.29 49 54
PLCG1 0.008 0.098 0.159 69 -0.241 37 106
Rac1/GTP 0.014 0.126 -9999 0 -0.309 43 43
homophilic cell adhesion 0.001 0.005 -9999 0 -9999 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.011 0.075 -9999 0 -0.137 101 101
CRKL -0.024 0.133 0.278 3 -0.425 33 36
mol:PIP3 0.003 0.109 0.305 1 -0.83 8 9
AKT1 -0.003 0.105 0.372 2 -0.737 8 10
PTK2B 0.034 0.016 -9999 0 0 97 97
RAPGEF1 -0.028 0.126 0.26 3 -0.406 32 35
RANBP10 0.037 0.013 -9999 0 0 58 58
PIK3CA 0.029 0.019 -9999 0 0 166 166
HGF/MET/SHIP2 0.028 0.076 -9999 0 -0.116 100 100
MAP3K5 -0.014 0.128 0.274 1 -0.402 30 31
HGF/MET/CIN85/CBL/ENDOPHILINS 0.049 0.083 -9999 0 -0.109 101 101
AP1 -0.004 0.081 0.158 11 -0.14 102 113
mol:SU11274 0 0 -9999 0 -9999 0 0
SHC1 0.039 0.008 -9999 0 0 23 23
apoptosis -0.155 0.347 -9999 0 -0.764 130 130
STAT3 (dimer) -0.006 0.107 0.188 5 -0.292 34 39
GAB1/CRKL/SHP2/PI3K -0.006 0.138 -9999 0 -0.382 37 37
INPP5D 0 0 -9999 0 -9999 0 0
CBL/CRK -0.004 0.138 0.294 2 -0.4 33 35
PTPN11 0.039 0.009 -9999 0 0 29 29
GO:0007205 0 0 -9999 0 -9999 0 0
PLCG1 0.038 0.011 -9999 0 0 43 43
PTEN 0.038 0.01 -9999 0 0 36 36
ELK1 0.011 0.115 0.349 36 -9999 0 36
mol:SU5416 0 0 -9999 0 -9999 0 0
SHP2/GRB2/SOS1GAB1 -0.011 0.081 0.164 1 -0.227 37 38
PAK1 0.004 0.112 0.334 6 -0.678 8 14
HGF/MET/RANBP10 0.025 0.075 -9999 0 -0.113 101 101
HRAS -0.072 0.213 -9999 0 -0.478 114 114
DOCK1 -0.029 0.131 0.248 7 -0.394 36 43
GAB1 -0.023 0.136 -9999 0 -0.44 33 33
CRK -0.022 0.131 0.29 2 -0.421 32 34
mol:PHA665752 0 0 -9999 0 -9999 0 0
mol:GDP -0.054 0.188 -9999 0 -0.424 105 105
JUN 0.035 0.014 -9999 0 0 76 76
EntrezGene:200958 0 0 -9999 0 -9999 0 0
HGF/MET -0.019 0.07 0.094 4 -0.161 100 104
PIK3R1 0.034 0.016 -9999 0 0 99 99
cell morphogenesis 0 0.147 0.274 35 -0.336 34 69
GRB2/SHC 0.018 0.094 -9999 0 -0.161 103 103
FOS 0.026 0.02 -9999 0 0 201 201
GLMN 0.005 0.006 0.068 5 -9999 0 5
cell motility 0.011 0.115 0.347 36 -9999 0 36
HGF/MET/MUC20 0.015 0.062 -9999 0 -0.108 102 102
cell migration 0.017 0.093 -9999 0 -0.159 103 103
GRB2 0.04 0.008 -9999 0 0 21 21
CBL 0.04 0.008 -9999 0 0 20 20
MET/RANBP10 0.011 0.073 -9999 0 -0.131 102 102
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.015 0.08 -9999 0 -0.176 79 79
MET/MUC20 -0.004 0.06 -9999 0 -0.125 104 104
RAP1B -0.028 0.118 0.332 2 -0.385 29 31
RAP1A -0.032 0.123 0.338 2 -0.39 33 35
HGF/MET/RANBP9 0.027 0.077 -9999 0 -0.118 99 99
RAF1 -0.07 0.206 -9999 0 -0.458 114 114
STAT3 -0.007 0.105 -9999 0 -0.294 33 33
cell proliferation -0.03 0.136 0.26 10 -0.302 75 85
RPS6KB1 -0.01 0.082 -9999 0 -0.265 37 37
MAPK3 -0.008 0.118 0.62 12 -9999 0 12
MAPK1 0.021 0.185 0.712 31 -9999 0 31
RANBP9 0.038 0.012 -9999 0 0 47 47
MAPK8 -0.011 0.14 -9999 0 -0.402 38 38
SRC -0.004 0.093 0.203 10 -0.267 26 36
PI3K 0.002 0.092 -9999 0 -0.178 87 87
MET/Glomulin 0.011 0.047 -9999 0 -0.121 45 45
SOS1 0.037 0.012 -9999 0 0 51 51
MAP2K1 -0.071 0.192 -9999 0 -0.432 114 114
MET 0.027 0.02 -9999 0 0 191 191
MAP4K1 -0.011 0.134 0.271 2 -0.439 28 30
PTK2 0.027 0.019 -9999 0 0 182 182
MAP2K2 -0.07 0.189 -9999 0 -0.424 115 115
BAD -0.008 0.1 0.334 2 -0.707 8 10
MAP2K4 -0.016 0.118 0.258 1 -0.37 30 31
SHP2/GRB2/SOS1/GAB1 -0.009 0.146 -9999 0 -0.353 46 46
INPPL1 0.039 0.009 -9999 0 0 27 27
PXN 0.04 0.006 -9999 0 0 10 10
SH3KBP1 0.04 0.007 -9999 0 0 16 16
HGS -0.026 0.071 0.082 4 -0.161 109 113
PLCgamma1/PKC 0.026 0.02 -9999 0 -0.125 8 8
HGF 0.039 0.009 -9999 0 0 27 27
RASA1 0.037 0.013 -9999 0 0 56 56
NCK1 0.036 0.014 -9999 0 0 70 70
PTPRJ 0.039 0.01 -9999 0 0 33 33
NCK/PLCgamma1 0.014 0.097 -9999 0 -0.169 100 100
PDPK1 -0.004 0.103 -9999 0 -0.774 8 8
HGF/MET/SHIP 0.015 0.062 -9999 0 -0.108 102 102
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.059 0.497 0.758 1 -1.033 69 70
STAT6 (cleaved dimer) -0.105 0.451 -9999 0 -0.954 82 82
IGHG1 0.034 0.232 0.451 3 -0.717 7 10
IGHG3 -0.067 0.45 -9999 0 -0.94 75 75
AKT1 -0.055 0.372 -9999 0 -0.83 67 67
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.046 0.365 0.44 1 -0.857 67 68
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.051 0.402 -9999 0 -0.937 64 64
THY1 -0.224 0.665 -9999 0 -1.161 158 158
MYB 0.034 0.016 -9999 0 0 96 96
HMGA1 0.036 0.013 -9999 0 0 65 65
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.023 0.376 0.518 1 -0.756 66 67
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.055 0.401 -9999 0 -0.903 69 69
SP1 0.021 0.073 -9999 0 -0.125 102 102
INPP5D 0 0 -9999 0 -9999 0 0
SOCS5 0.001 0.05 -9999 0 -0.084 4 4
STAT6 (dimer)/ETS1 -0.082 0.465 -9999 0 -0.971 76 76
SOCS1 -0.026 0.344 -9999 0 -0.668 63 63
SOCS3 -0.038 0.372 0.578 2 -0.977 41 43
FCER2 -0.033 0.391 -9999 0 -0.818 51 51
PARP14 0.033 0.018 -9999 0 0 128 128
CCL17 -0.061 0.474 -9999 0 -1.021 62 62
GRB2 0.04 0.008 -9999 0 0 21 21
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.011 0.3 -9999 0 -0.649 59 59
T cell proliferation -0.085 0.49 -9999 0 -1.024 80 80
IL4R/JAK1 -0.076 0.488 -9999 0 -1.019 77 77
EGR2 -0.057 0.482 -9999 0 -1.038 61 61
JAK2 0.031 0.071 0.177 2 -9999 0 2
JAK3 0.032 0.026 -9999 0 -0.041 32 32
PIK3R1 0.034 0.016 -9999 0 0 99 99
JAK1 0.04 0.041 0.111 3 -0.04 7 10
COL1A2 -0.155 0.566 -9999 0 -1.258 107 107
CCL26 -0.07 0.489 -9999 0 -1.03 71 71
IL4R -0.066 0.523 -9999 0 -1.081 75 75
PTPN6 0.005 0.043 -9999 0 -0.08 2 2
IL13RA2 -0.059 0.473 -9999 0 -0.988 70 70
IL13RA1 0.035 0.074 0.175 6 -9999 0 6
IRF4 0.049 0.172 -9999 0 -0.918 5 5
ARG1 0.047 0.195 -9999 0 -0.779 4 4
CBL -0.026 0.348 -9999 0 -0.712 66 66
GTF3A 0.013 0.079 -9999 0 -0.129 120 120
PIK3CA 0.029 0.019 -9999 0 0 166 166
IL13RA1/JAK2 0.039 0.117 0.247 4 -0.183 27 31
IRF4/BCL6 0.034 0.157 -9999 0 -0.867 5 5
CD40LG 0.048 0.008 -9999 0 -0.054 1 1
MAPK14 -0.032 0.366 0.625 1 -0.775 62 63
mitosis -0.046 0.352 -9999 0 -0.771 67 67
STAT6 -0.063 0.543 0.762 2 -1.109 75 77
SPI1 0.044 0.01 -9999 0 -9999 0 0
RPS6KB1 -0.048 0.341 -9999 0 -0.744 67 67
STAT6 (dimer) -0.06 0.541 0.762 2 -1.103 75 77
STAT6 (dimer)/PARP14 -0.104 0.487 -9999 0 -1.048 76 76
mast cell activation -0.005 0.019 -9999 0 -0.044 9 9
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.074 0.393 -9999 0 -0.876 72 72
FRAP1 -0.055 0.372 -9999 0 -0.831 67 67
LTA -0.06 0.474 -9999 0 -1.003 67 67
FES 0.04 0.008 -9999 0 0 22 22
T-helper 1 cell differentiation 0.055 0.533 1.078 75 -0.761 2 77
CCL11 -0.091 0.497 -9999 0 -1.026 84 84
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.049 0.387 -9999 0 -0.886 65 65
IL2RG 0.026 0.025 -9999 0 -0.047 12 12
IL10 -0.06 0.475 -9999 0 -1.02 63 63
IRS1 0.04 0.008 -9999 0 0 22 22
IRS2 0.039 0.009 -9999 0 0 30 30
IL4 0.042 0.221 -9999 0 -0.921 12 12
IL5 -0.061 0.473 -9999 0 -1.052 55 55
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.044 0.465 0.68 2 -0.899 78 80
COL1A1 -0.212 0.644 -9999 0 -1.283 136 136
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -9999 0 0
IL4/IL4R/JAK1 -0.082 0.492 -9999 0 -1.075 68 68
IL2R gamma/JAK3 0.02 0.073 -9999 0 -0.13 87 87
TFF3 -0.067 0.493 -9999 0 -1.044 70 70
ALOX15 -0.058 0.474 -9999 0 -1.001 67 67
MYBL1 0.036 0.014 -9999 0 0 70 70
T-helper 2 cell differentiation -0.099 0.471 -9999 0 -0.946 86 86
SHC1 0.039 0.008 -9999 0 0 23 23
CEBPB 0.04 0.016 -9999 0 -9999 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.052 0.396 -9999 0 -0.894 69 69
mol:PI-3-4-5-P3 -0.054 0.373 -9999 0 -0.83 67 67
PI3K -0.065 0.399 -9999 0 -0.908 67 67
DOK2 0.032 0.017 -9999 0 0 118 118
ETS1 0 0.046 -9999 0 -0.103 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.008 0.293 0.423 1 -0.63 60 61
ITGB3 -0.093 0.541 -9999 0 -1.128 83 83
PIGR -0.057 0.488 -9999 0 -1.052 63 63
IGHE -0.005 0.087 0.179 41 -0.188 23 64
MAPKKK cascade -0.006 0.288 0.422 1 -0.616 60 61
BCL6 0.031 0.017 -9999 0 0 130 130
OPRM1 -0.062 0.473 -9999 0 -0.998 68 68
RETNLB -0.055 0.477 -9999 0 -1.002 67 67
SELP -0.057 0.476 -9999 0 -1.021 62 62
AICDA -0.051 0.452 -9999 0 -0.963 65 65
IL2 signaling events mediated by STAT5

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
GAB2 0.031 0.018 -9999 0 0 137 137
ELF1 0.047 0.023 -9999 0 -0.264 2 2
CCNA2 0.032 0.017 -9999 0 0 122 122
PIK3CA 0.029 0.019 -9999 0 0 166 166
JAK3 0.037 0.013 -9999 0 -0.001 58 58
PIK3R1 0.034 0.016 -9999 0 0 100 100
JAK1 0.039 0.01 -9999 0 -0.001 34 34
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0 0.133 0.249 1 -0.345 37 38
SHC1 0.04 0.009 -9999 0 -0.001 24 24
SP1 0.042 0.042 -9999 0 -0.27 9 9
IL2RA 0.02 0.032 -9999 0 -0.488 2 2
IL2RB 0.036 0.015 -9999 0 0 77 77
SOS1 0.038 0.013 -9999 0 -0.001 53 53
IL2RG 0.028 0.02 -9999 0 0 180 180
G1/S transition of mitotic cell cycle -0.036 0.178 0.266 5 -0.469 37 42
PTPN11 0.039 0.011 -9999 0 -0.003 32 32
CCND2 0.011 0.062 -9999 0 -0.489 8 8
LCK 0.039 0.01 -9999 0 -0.003 28 28
GRB2 0.04 0.009 -9999 0 -0.003 23 23
IL2 0.039 0.011 -9999 0 -0.002 36 36
CDK6 0.032 0.017 -9999 0 0 126 126
CCND3 0.004 0.14 0.392 1 -0.603 9 10
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.038 0.01 -9999 0 0 36 36
ITGB7 0.038 0.01 -9999 0 0 38 38
ITGA4 0.035 0.015 -9999 0 0 88 88
alpha4/beta7 Integrin 0.031 0.065 -9999 0 -0.137 66 66
alpha4/beta1 Integrin 0.031 0.065 -9999 0 -0.135 66 66
FoxO family signaling

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
G6PC -0.004 0.063 -9999 0 -9999 0 0
PLK1 -0.146 0.378 -9999 0 -0.951 72 72
CDKN1B -0.041 0.204 0.433 2 -0.367 93 95
FOXO3 -0.133 0.35 -9999 0 -0.679 114 114
KAT2B -0.008 0.028 0.041 2 -0.046 171 173
FOXO1/SIRT1 0.015 0.078 0.204 1 -0.225 19 20
CAT -0.151 0.398 0.52 1 -0.97 78 79
CTNNB1 0.039 0.01 -9999 0 0 32 32
AKT1 0.013 0.055 -9999 0 -0.064 144 144
FOXO1 -0.004 0.071 0.214 2 -0.233 16 18
MAPK10 -0.001 0.045 0.192 4 -0.121 22 26
mol:GTP 0 0.003 -9999 0 -9999 0 0
FOXO4 -0.026 0.122 -9999 0 -0.305 59 59
response to oxidative stress -0.006 0.029 -9999 0 -0.051 105 105
FOXO3A/SIRT1 -0.122 0.342 -9999 0 -0.553 170 170
XPO1 0.039 0.01 -9999 0 0 35 35
EP300 0.037 0.014 -9999 0 -9999 0 0
BCL2L11 0.011 0.11 -9999 0 -0.908 6 6
FOXO1/SKP2 0.011 0.076 -9999 0 -0.218 25 25
mol:GDP -0.006 0.029 -9999 0 -0.051 105 105
RAN 0.04 0.008 -9999 0 0 21 21
GADD45A -0.073 0.274 -9999 0 -0.777 51 51
YWHAQ 0.04 0.007 -9999 0 0 18 18
FOXO1/14-3-3 family 0.008 0.149 -9999 0 -0.402 41 41
MST1 0.011 0.055 -9999 0 -0.063 183 183
CSNK1D 0.039 0.008 -9999 0 0 24 24
CSNK1E 0.037 0.012 -9999 0 0 53 53
FOXO4/14-3-3 family -0.002 0.152 -9999 0 -0.445 39 39
YWHAB 0.038 0.011 -9999 0 0 45 45
MAPK8 -0.001 0.047 0.194 5 -0.124 21 26
MAPK9 -0.003 0.048 0.193 5 -0.131 23 28
YWHAG 0.039 0.009 -9999 0 0 25 25
YWHAE 0.037 0.013 -9999 0 0 58 58
YWHAZ 0.034 0.016 -9999 0 0 96 96
SIRT1 0.037 0.018 0.114 2 -0.035 24 26
SOD2 -0.111 0.299 -9999 0 -0.66 94 94
RBL2 -0.123 0.331 -9999 0 -0.774 78 78
RAL/GDP 0.03 0.056 -9999 0 -0.101 41 41
CHUK 0.012 0.053 -9999 0 -0.063 165 165
Ran/GTP 0.026 0.019 -9999 0 -0.123 3 3
CSNK1G2 0.036 0.013 -9999 0 0 64 64
RAL/GTP 0.031 0.056 -9999 0 -0.092 48 48
CSNK1G1 0.04 0.007 -9999 0 0 16 16
FASLG 0.017 0.066 -9999 0 -1.174 1 1
SKP2 0.036 0.014 -9999 0 0 68 68
USP7 0.038 0.012 -9999 0 0 47 47
IKBKB 0.011 0.054 -9999 0 -0.062 171 171
CCNB1 -0.177 0.428 -9999 0 -1.01 92 92
FOXO1-3a-4/beta catenin -0.057 0.204 -9999 0 -0.396 90 90
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.075 -9999 0 -0.217 25 25
CSNK1A1 0.039 0.008 -9999 0 0 23 23
SGK1 -0.008 0.028 0.041 2 -0.046 171 173
CSNK1G3 0.039 0.01 -9999 0 0 31 31
Ran/GTP/Exportin 1 0.044 0.038 -9999 0 -0.101 27 27
ZFAND5 -0.02 0.103 -9999 0 -0.254 58 58
SFN 0.035 0.015 -9999 0 0 83 83
CDK2 0.039 0.013 -9999 0 -9999 0 0
FOXO3A/14-3-3 -0.01 0.156 -9999 0 -0.366 58 58
CREBBP 0.04 0.013 -9999 0 -9999 0 0
FBXO32 -0.195 0.538 -9999 0 -1.084 132 132
BCL6 -0.121 0.344 -9999 0 -0.942 58 58
RALB 0.039 0.009 -9999 0 0 25 25
RALA 0.04 0.008 -9999 0 0 19 19
YWHAH 0.038 0.011 -9999 0 0 46 46
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 0.036 0.014 -9999 0 0 68 68
GNB1/GNG2 0.01 0.121 -9999 0 -0.26 45 45
mol:DAG -0.009 0.102 0.237 7 -0.248 42 49
PLCG1 -0.01 0.103 0.224 6 -0.252 43 49
YES1 -0.019 0.093 -9999 0 -0.264 43 43
FZD3 0.03 0.019 -9999 0 0 153 153
FZD6 0.029 0.019 -9999 0 0 162 162
G protein 0.021 0.125 0.245 30 -0.26 40 70
MAP3K7 -0.03 0.084 0.204 6 -0.225 43 49
mol:Ca2+ -0.009 0.1 0.235 7 -0.242 42 49
mol:IP3 -0.009 0.102 0.237 7 -0.248 42 49
NLK -0.036 0.264 -9999 0 -0.823 54 54
GNB1 0.039 0.01 -9999 0 0 33 33
CAMK2A -0.019 0.092 0.223 7 -0.235 41 48
MAP3K7IP1 0.037 0.012 -9999 0 0 51 51
Noncanonical Wnts/FZD -0.017 0.093 -9999 0 -0.28 38 38
CSNK1A1 0.039 0.008 -9999 0 0 23 23
GNAS -0.014 0.099 0.203 16 -0.267 39 55
GO:0007205 -0.016 0.096 0.234 7 -0.243 45 52
WNT6 0.04 0.006 -9999 0 0 13 13
WNT4 0.04 0.008 -9999 0 0 19 19
NFAT1/CK1 alpha 0 0.117 0.285 4 -0.276 38 42
GNG2 0.039 0.009 -9999 0 0 29 29
WNT5A 0.034 0.015 -9999 0 0 89 89
WNT11 0.032 0.017 -9999 0 0 118 118
CDC42 -0.023 0.091 -9999 0 -0.258 41 41
HIF-2-alpha transcription factor network

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
MMP14 -0.056 0.29 -9999 0 -0.852 61 61
oxygen homeostasis 0.004 0.012 0.034 19 -0.025 6 25
TCEB2 0.039 0.008 -9999 0 0 23 23
TCEB1 0.038 0.011 -9999 0 0 39 39
VHL/Elongin B/Elongin C/HIF2A 0.04 0.135 0.29 11 -0.22 61 72
EPO 0.028 0.177 0.347 13 -0.345 36 49
FIH (dimer) 0.039 0.025 0.087 3 -0.035 41 44
APEX1 0.032 0.033 -9999 0 -0.035 74 74
SERPINE1 0 0.163 0.348 14 -0.315 58 72
FLT1 -0.047 0.256 -9999 0 -0.697 68 68
ADORA2A 0.018 0.172 0.332 34 -0.308 53 87
germ cell development 0.017 0.18 0.344 30 -0.313 64 94
SLC11A2 0.022 0.187 0.345 28 -0.332 59 87
BHLHE40 0.01 0.166 0.328 21 -0.307 60 81
HIF1AN 0.039 0.025 0.087 3 -0.035 41 44
HIF2A/ARNT/SIRT1 0.038 0.151 0.309 12 -0.254 56 68
ETS1 0.042 0.025 0.119 1 -0.107 5 6
CITED2 0.018 0.133 -9999 0 -0.616 20 20
KDR -0.04 0.246 -9999 0 -0.693 64 64
PGK1 0.023 0.191 0.348 30 -0.337 62 92
SIRT1 0.04 0.007 -9999 0 0 16 16
response to hypoxia 0 0 -9999 0 -9999 0 0
HIF2A/ARNT 0.053 0.215 0.467 1 -0.346 56 57
EPAS1 0.006 0.113 0.225 21 -0.221 70 91
SP1 0.034 0.048 -9999 0 -0.108 52 52
ABCG2 0.022 0.18 0.346 26 -0.32 56 82
EFNA1 0.01 0.189 0.341 25 -0.347 69 94
FXN 0.018 0.171 0.333 33 -0.306 56 89
POU5F1 0.016 0.184 0.349 29 -0.322 64 93
neuron apoptosis -0.051 0.211 0.339 56 -0.46 1 57
EP300 0.036 0.014 -9999 0 0 69 69
EGLN3 0.028 0.027 0.086 1 -0.034 23 24
EGLN2 0.038 0.024 0.088 3 -0.033 33 36
EGLN1 0.038 0.025 0.084 5 -0.035 40 45
VHL/Elongin B/Elongin C 0.069 0.038 -9999 0 -0.114 11 11
VHL 0.039 0.008 -9999 0 0 23 23
ARNT 0.032 0.032 -9999 0 -0.035 75 75
SLC2A1 -0.001 0.177 0.344 18 -0.334 67 85
TWIST1 0.017 0.171 0.333 34 -0.308 55 89
ELK1 0.046 0.013 -9999 0 -0.087 3 3
HIF2A/ARNT/Cbp/p300 0.038 0.158 0.326 13 -0.262 51 64
VEGFA 0.01 0.166 0.328 21 -0.307 60 81
CREBBP 0.037 0.012 -9999 0 0 53 53
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.01 0.146 0.24 14 -0.338 55 69
FYN -0.032 0.184 0.257 13 -0.381 84 97
LAT/GRAP2/SLP76 -0.004 0.147 0.24 6 -0.332 66 72
IKBKB 0.038 0.011 -9999 0 0 41 41
AKT1 -0.016 0.135 0.217 10 -0.3 76 86
B2M 0.037 0.016 -9999 0 -0.004 66 66
IKBKG -0.003 0.049 0.12 12 -0.105 56 68
MAP3K8 0.039 0.008 -9999 0 0 24 24
mol:Ca2+ -0.014 0.014 0.038 8 -0.043 43 51
integrin-mediated signaling pathway 0.044 0.035 -9999 0 -0.108 24 24
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.028 0.181 0.239 9 -0.406 77 86
TRPV6 0.076 0.327 1.286 37 -9999 0 37
CD28 0.041 0.007 -9999 0 0 13 13
SHC1 -0.014 0.157 0.227 18 -0.372 62 80
receptor internalization -0.015 0.142 0.172 3 -0.335 69 72
PRF1 -0.01 0.205 -9999 0 -0.755 29 29
KRAS 0.034 0.016 -9999 0 0 95 95
GRB2 0.04 0.008 -9999 0 0 21 21
COT/AKT1 0.003 0.119 0.217 9 -0.246 74 83
LAT -0.019 0.155 0.232 8 -0.363 67 75
EntrezGene:6955 0.001 0.003 -9999 0 -0.023 3 3
CD3D 0.034 0.018 -9999 0 -0.002 105 105
CD3E 0.036 0.016 -9999 0 -0.002 77 77
CD3G 0.032 0.019 -9999 0 -0.002 131 131
RASGRP2 0.009 0.019 0.074 1 -0.163 1 2
RASGRP1 -0.022 0.145 0.23 12 -0.306 82 94
HLA-A 0.038 0.015 -9999 0 -0.004 62 62
RASSF5 0.039 0.009 -9999 0 0 27 27
RAP1A/GTP/RAPL 0.045 0.036 -9999 0 -0.109 24 24
mol:GTP 0 0 -9999 0 -9999 0 0
mol:GDP 0.013 0.059 0.152 15 -0.107 43 58
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.02 0.064 -9999 0 -0.154 80 80
PRKCA -0.008 0.081 0.192 11 -0.198 48 59
GRAP2 0.037 0.012 -9999 0 0 56 56
mol:IP3 -0.015 0.107 -9999 0 -0.263 64 64
EntrezGene:6957 0.001 0.004 -9999 0 -0.021 5 5
TCR/CD3/MHC I/CD8 -0.014 0.12 -9999 0 -0.375 41 41
ORAI1 -0.071 0.278 -9999 0 -1.092 37 37
CSK -0.015 0.155 0.253 7 -0.38 61 68
B7 family/CD28 0.022 0.164 0.264 5 -0.345 66 71
CHUK 0.038 0.011 -9999 0 0 46 46
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.025 0.167 0.203 2 -0.374 75 77
PTPN6 -0.015 0.156 0.198 24 -0.349 69 93
VAV1 -0.018 0.158 0.217 12 -0.388 62 74
Monovalent TCR/CD3 -0.003 0.08 -9999 0 -0.21 60 60
CBL 0.04 0.008 -9999 0 0 20 20
LCK -0.022 0.174 0.246 12 -0.384 72 84
PAG1 -0.013 0.16 0.211 29 -0.371 64 93
RAP1A 0.039 0.01 -9999 0 0 35 35
TCR/CD3/MHC I/CD8/LCK -0.025 0.166 0.194 4 -0.366 77 81
CD80 0.039 0.01 -9999 0 0 32 32
CD86 0.034 0.016 -9999 0 0 99 99
PDK1/CARD11/BCL10/MALT1 -0.009 0.084 -9999 0 -0.183 76 76
HRAS 0.039 0.01 -9999 0 0 31 31
GO:0035030 -0.018 0.126 0.176 13 -0.299 67 80
CD8A 0.041 0.011 -9999 0 -0.018 16 16
CD8B 0.001 0.004 -9999 0 -0.021 6 6
PTPRC 0.025 0.02 -9999 0 0 222 222
PDK1/PKC theta -0.024 0.153 0.24 10 -0.353 71 81
CSK/PAG1 -0.012 0.155 0.217 31 -0.383 57 88
SOS1 0.037 0.012 -9999 0 0 51 51
peptide-MHC class I 0.037 0.071 -9999 0 -0.172 50 50
GRAP2/SLP76 -0.002 0.167 0.253 4 -0.377 66 70
STIM1 -0.013 0.126 1.291 4 -9999 0 4
RAS family/GTP 0.008 0.077 0.181 6 -0.155 53 59
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.016 0.147 0.174 3 -0.348 69 72
mol:DAG -0.027 0.089 -9999 0 -0.234 67 67
RAP1A/GDP 0.01 0.032 0.076 14 -0.057 47 61
PLCG1 0.038 0.011 -9999 0 0 43 43
CD247 0.001 0.003 -9999 0 -0.023 3 3
cytotoxic T cell degranulation -0.008 0.196 -9999 0 -0.695 31 31
RAP1A/GTP 0.003 0.01 -9999 0 -0.034 18 18
mol:PI-3-4-5-P3 -0.02 0.155 0.222 11 -0.345 76 87
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.01 0.138 0.216 1 -0.324 64 65
NRAS 0.039 0.009 -9999 0 0 30 30
ZAP70 0.041 0.005 -9999 0 0 9 9
GRB2/SOS1 0.047 0.044 -9999 0 -0.142 24 24
LAT/GRAP2/SLP76/VAV1 -0.012 0.142 0.25 5 -0.337 63 68
MALT1 0.036 0.014 -9999 0 0 70 70
TRAF6 0.04 0.008 -9999 0 0 19 19
CD8 heterodimer 0.031 0.012 -9999 0 -0.038 8 8
CARD11 0.037 0.012 -9999 0 0 55 55
PRKCB -0.027 0.061 -9999 0 -0.169 67 67
PRKCE -0.006 0.085 0.196 16 -0.199 47 63
PRKCQ -0.026 0.169 0.232 10 -0.386 73 83
LCP2 0.034 0.016 -9999 0 0 101 101
BCL10 0.041 0.005 -9999 0 0 8 8
regulation of survival gene product expression -0.011 0.119 0.2 12 -0.257 77 89
IKK complex 0.003 0.049 0.145 15 -0.091 30 45
RAS family/GDP -0.002 0.014 -9999 0 -0.034 44 44
MAP3K14 -0.003 0.091 0.163 13 -0.195 73 86
PDPK1 -0.018 0.128 0.218 11 -0.286 75 86
TCR/CD3/MHC I/CD8/Fyn -0.037 0.19 -9999 0 -0.472 65 65
BMP receptor signaling

Figure 44.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 46.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.009 0.101 -9999 0 -0.13 145 145
SMAD6-7/SMURF1 0.071 0.037 -9999 0 -0.136 9 9
NOG 0.038 0.012 -9999 0 0 48 48
SMAD9 0.015 0.102 -9999 0 -0.414 25 25
SMAD4 0.038 0.011 -9999 0 0 43 43
SMAD5 -0.001 0.094 0.194 3 -0.273 34 37
BMP7/USAG1 -0.021 0.085 -9999 0 -0.155 137 137
SMAD5/SKI 0.014 0.104 -9999 0 -0.278 33 33
SMAD1 0.007 0.091 -9999 0 -0.308 26 26
BMP2 0.038 0.01 -9999 0 0 38 38
SMAD1/SMAD1/SMAD4 0.031 0.096 -9999 0 -0.293 26 26
BMPR1A 0.036 0.013 -9999 0 0 66 66
BMPR1B 0.031 0.018 -9999 0 0 138 138
BMPR1A-1B/BAMBI 0.008 0.087 -9999 0 -0.136 119 119
AHSG 0.034 0.016 -9999 0 0 101 101
CER1 0.038 0.011 -9999 0 0 41 41
BMP2-4/CER1 0.061 0.043 -9999 0 -0.116 12 12
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.009 0.104 0.183 1 -0.256 54 55
BMP2-4 (homodimer) 0.047 0.035 -9999 0 -0.134 12 12
RGMB 0.039 0.01 -9999 0 0 31 31
BMP6/BMPR2/BMPR1A-1B 0.049 0.086 -9999 0 -0.128 83 83
RGMA 0.039 0.009 -9999 0 0 29 29
SMURF1 0.04 0.006 -9999 0 0 13 13
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.001 0.078 -9999 0 -0.238 32 32
BMP2-4/USAG1 0.022 0.071 -9999 0 -0.122 78 78
SMAD6/SMURF1/SMAD5 0.013 0.106 -9999 0 -0.275 36 36
SOSTDC1 0.023 0.02 -9999 0 0 244 244
BMP7/BMPR2/BMPR1A-1B 0.007 0.1 -9999 0 -0.133 153 153
SKI 0.039 0.009 -9999 0 0 29 29
BMP6 (homodimer) 0.038 0.011 -9999 0 0 46 46
HFE2 0.038 0.01 -9999 0 0 36 36
ZFYVE16 0.035 0.014 -9999 0 0 78 78
MAP3K7 0.038 0.01 -9999 0 0 38 38
BMP2-4/CHRD 0.054 0.044 -9999 0 -0.116 8 8
SMAD5/SMAD5/SMAD4 0.012 0.103 -9999 0 -0.27 35 35
MAPK1 0.038 0.011 -9999 0 0 44 44
TAK1/TAB family 0.036 0.119 -9999 0 -0.242 37 37
BMP7 (homodimer) 0.022 0.021 -9999 0 0 260 260
NUP214 0.038 0.011 -9999 0 0 43 43
BMP6/FETUA 0.045 0.027 -9999 0 -9999 0 0
SMAD1/SKI 0.027 0.095 -9999 0 -0.296 27 27
SMAD6 0.039 0.008 -9999 0 0 24 24
CTDSP2 0.039 0.009 -9999 0 0 29 29
BMP2-4/FETUA 0.054 0.045 -9999 0 -0.116 10 10
MAP3K7IP1 0.037 0.012 -9999 0 0 51 51
GREM1 0.034 0.015 -9999 0 0 91 91
BMPR2 (homodimer) 0.039 0.01 -9999 0 0 31 31
GADD34/PP1CA 0.058 0.054 -9999 0 -0.115 35 35
BMPR1A-1B (homodimer) 0.017 0.077 -9999 0 -0.148 88 88
CHRDL1 0.026 0.02 -9999 0 0 207 207
ENDOFIN/SMAD1 0.023 0.095 -9999 0 -0.299 25 25
SMAD6-7/SMURF1/SMAD1 0.054 0.107 -9999 0 -0.346 17 17
SMAD6/SMURF1 0.04 0.006 -9999 0 0 13 13
BAMBI 0.028 0.019 -9999 0 0 170 170
SMURF2 0.039 0.009 -9999 0 0 28 28
BMP2-4/CHRDL1 0.02 0.076 -9999 0 -0.119 101 101
BMP2-4/GREM1 0.053 0.048 -9999 0 -0.116 17 17
SMAD7 0.038 0.01 -9999 0 0 36 36
SMAD8A/SMAD8A/SMAD4 0.03 0.111 -9999 0 -0.389 30 30
SMAD1/SMAD6 0.027 0.097 -9999 0 -0.304 26 26
TAK1/SMAD6 0.052 0.035 -9999 0 -0.134 15 15
BMP7 0.022 0.021 -9999 0 0 260 260
BMP6 0.038 0.011 -9999 0 0 46 46
MAP3K7IP2 0.037 0.012 -9999 0 0 53 53
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 0.002 0.082 -9999 0 -0.24 33 33
PPM1A 0.04 0.006 -9999 0 0 10 10
SMAD1/SMURF2 0.026 0.097 -9999 0 -0.312 24 24
SMAD7/SMURF1 0.054 0.028 -9999 0 -0.134 8 8
CTDSPL 0.04 0.007 -9999 0 0 15 15
PPP1CA 0.04 0.006 -9999 0 0 11 11
XIAP 0 0 -9999 0 -9999 0 0
CTDSP1 0.04 0.007 -9999 0 0 15 15
PPP1R15A 0.038 0.011 -9999 0 0 41 41
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS 0.002 0.084 0.168 4 -0.247 31 35
CHRD 0.033 0.016 -9999 0 0 105 105
BMPR2 0.039 0.01 -9999 0 0 31 31
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.001 0.085 -9999 0 -0.255 31 31
BMP4 0.036 0.014 -9999 0 0 67 67
FST 0.033 0.017 -9999 0 0 111 111
BMP2-4/NOG 0.059 0.047 -9999 0 -0.116 19 19
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.016 0.106 -9999 0 -0.131 150 150
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.038 0.087 0.244 1 -0.143 65 66
positive regulation of NF-kappaB transcription factor activity 0 0.001 -9999 0 -9999 0 0
CRKL 0.038 0.01 -9999 0 0 36 36
STAT1 (dimer)/Cbp/p300 0.006 0.122 0.267 10 -0.224 79 89
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.039 0.081 -9999 0 -0.152 67 67
antigen processing and presentation of peptide antigen via MHC class I -0.024 0.094 -9999 0 -0.209 79 79
CaM/Ca2+ 0.042 0.087 0.227 1 -0.142 64 65
RAP1A 0.039 0.01 -9999 0 0 35 35
STAT1 (dimer)/SHP2 0.001 0.095 0.221 10 -0.19 62 72
AKT1 0.017 0.114 0.221 54 -0.225 28 82
MAP2K1 -0.023 0.073 0.147 40 -0.181 34 74
MAP3K11 -0.016 0.078 0.166 43 -0.176 30 73
IFNGR1 0.034 0.022 0.08 1 -0.037 19 20
mol:GTP 0 0 -9999 0 -9999 0 0
CaM/Ca2+/CAMKII 0.015 0.098 -9999 0 -0.291 36 36
Rap1/GTP -0.044 0.058 0.066 4 -0.177 48 52
CRKL/C3G 0.055 0.019 -9999 0 -9999 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.062 0.09 -9999 0 -0.141 60 60
CEBPB -0.02 0.161 0.289 2 -0.458 42 44
STAT3 0.038 0.011 -9999 0 0 41 41
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.043 0.162 -9999 0 -0.782 16 16
STAT1 -0.025 0.087 0.175 31 -0.209 47 78
CALM1 0.039 0.009 -9999 0 0 26 26
IFN-gamma (dimer) 0.03 0.027 0.08 1 -0.038 58 59
PIK3CA 0.029 0.019 -9999 0 0 166 166
STAT1 (dimer)/PIAS1 -0.007 0.097 0.226 14 -0.205 50 64
CEBPB/PTGES2/Cbp/p300 -0.007 0.118 -9999 0 -0.313 41 41
mol:Ca2+ 0.034 0.085 0.233 1 -0.142 65 66
MAPK3 -0.014 0.131 -9999 0 -0.685 11 11
STAT1 (dimer) -0.021 0.135 0.182 7 -0.284 78 85
MAPK1 -0.042 0.197 -9999 0 -0.756 31 31
JAK2 0.031 0.024 -9999 0 -0.036 30 30
PIK3R1 0.034 0.016 -9999 0 0 99 99
JAK1 0.035 0.024 0.08 1 -0.037 45 46
CAMK2D 0.036 0.014 -9999 0 0 69 69
DAPK1 -0.019 0.159 0.277 1 -0.494 44 45
SMAD7 0.001 0.075 0.158 43 -0.131 51 94
CBL/CRKL/C3G 0.029 0.09 0.236 15 -0.167 35 50
PI3K 0.019 0.09 -9999 0 -0.184 53 53
IFNG 0.03 0.027 0.08 1 -0.038 58 59
apoptosis -0.007 0.138 0.259 2 -0.414 41 43
CAMK2G 0.04 0.008 -9999 0 0 21 21
STAT3 (dimer) 0.038 0.011 -9999 0 0 41 41
CAMK2A 0.04 0.006 -9999 0 0 12 12
CAMK2B 0.041 0.005 -9999 0 0 9 9
FRAP1 0.008 0.107 0.177 92 -0.214 32 124
PRKCD 0.013 0.118 0.232 49 -0.23 32 81
RAP1B 0.037 0.012 -9999 0 0 54 54
negative regulation of cell growth -0.024 0.094 -9999 0 -0.209 79 79
PTPN2 0.04 0.008 -9999 0 0 19 19
EP300 0.036 0.014 -9999 0 0 69 69
IRF1 -0.045 0.101 0.207 6 -0.277 58 64
STAT1 (dimer)/PIASy -0.024 0.093 0.188 32 -0.217 40 72
SOCS1 -0.002 0.192 -9999 0 -1.099 16 16
mol:GDP 0.026 0.085 0.22 15 -0.162 35 50
CASP1 -0.02 0.083 0.152 21 -0.165 98 119
PTGES2 0.04 0.008 -9999 0 0 22 22
IRF9 -0.005 0.052 0.111 15 -0.131 38 53
mol:PI-3-4-5-P3 0.005 0.08 -9999 0 -0.173 58 58
RAP1/GDP 0.016 0.09 0.202 4 -0.181 48 52
CBL -0.016 0.078 0.166 44 -0.18 26 70
MAP3K1 -0.017 0.076 0.161 40 -0.184 30 70
PIAS1 0.039 0.008 -9999 0 0 24 24
PIAS4 0.037 0.012 -9999 0 0 54 54
antigen processing and presentation of peptide antigen via MHC class II -0.024 0.094 -9999 0 -0.209 79 79
PTPN11 -0.011 0.078 0.173 42 -0.176 30 72
CREBBP 0.037 0.012 -9999 0 0 53 53
RAPGEF1 0.039 0.009 -9999 0 0 26 26
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.038 0.012 -9999 0 0 49 49
HDAC3 0.04 0.006 -9999 0 0 10 10
VDR 0.038 0.011 -9999 0 0 43 43
Cbp/p300/PCAF 0.039 0.043 -9999 0 -0.134 24 24
EP300 0.036 0.014 -9999 0 0 69 69
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.016 0.099 -9999 0 -0.257 56 56
KAT2B 0 0 -9999 0 -9999 0 0
MAPK14 0.04 0.008 -9999 0 0 20 20
AKT1 0.011 0.091 0.193 19 -0.206 28 47
RAR alpha/9cRA/Cyclin H -0.006 0.124 -9999 0 -0.241 77 77
mol:9cRA 0 0 -9999 0 -9999 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.004 0.082 -9999 0 -0.21 54 54
CDC2 0.026 0.023 -9999 0 -0.005 186 186
response to UV -0.001 0.008 -9999 0 -0.027 39 39
RAR alpha/Jnk1 0.015 0.068 -9999 0 -0.152 52 52
NCOR2 0.039 0.01 -9999 0 0 31 31
VDR/VDR/Vit D3 0.023 0.031 -9999 0 -0.125 22 22
RXRs/RARs/NRIP1/9cRA -0.041 0.186 0.277 1 -0.449 77 78
NCOA2 0.037 0.013 -9999 0 0 60 60
NCOA3 0.035 0.015 -9999 0 0 84 84
NCOA1 0.04 0.008 -9999 0 0 22 22
VDR/VDR/DNA 0.038 0.011 -9999 0 0 43 43
RARG 0.035 0.021 -9999 0 -0.018 67 67
RAR gamma1/9cRA 0.041 0.033 -9999 0 -0.109 15 15
MAPK3 0.035 0.022 -9999 0 -0.025 60 60
MAPK1 0.038 0.011 -9999 0 0 44 44
MAPK8 0.034 0.024 -9999 0 -0.026 70 70
mol:Vit D3 0 0 -9999 0 -9999 0 0
RXRs/VDR/DNA/Vit D3 -0.022 0.148 -9999 0 -0.311 95 95
RARA 0.006 0.054 -9999 0 -0.159 41 41
negative regulation of phosphoinositide 3-kinase cascade 0 0 -9999 0 -9999 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.007 0.085 -9999 0 -0.217 55 55
PRKCA 0.03 0.032 -9999 0 -0.074 35 35
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.051 0.2 -9999 0 -0.502 74 74
RXRG 0.013 0.057 -9999 0 -0.18 34 34
RXRA -0.028 0.098 -9999 0 -0.238 58 58
RXRB 0.011 0.059 -9999 0 -0.172 41 41
VDR/Vit D3/DNA 0.023 0.031 -9999 0 -0.125 22 22
RBP1 0.029 0.019 -9999 0 0 159 159
CRBP1/9-cic-RA 0.001 0.057 -9999 0 -0.125 91 91
RARB 0.031 0.026 -9999 0 -0.015 113 113
PRKCG 0.033 0.032 -9999 0 -0.072 41 41
MNAT1 0.04 0.007 -9999 0 0 18 18
RAR alpha/RXRs -0.022 0.161 0.269 2 -0.349 84 86
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.014 0.131 0.24 2 -0.284 72 74
proteasomal ubiquitin-dependent protein catabolic process -0.016 0.106 0.163 2 -0.262 58 60
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.05 0.2 -9999 0 -0.493 77 77
positive regulation of DNA binding -0.012 0.113 -9999 0 -0.224 83 83
NRIP1 -0.084 0.313 -9999 0 -0.951 55 55
RXRs/RARs -0.034 0.169 -9999 0 -0.387 83 83
RXRs/RXRs/DNA/9cRA -0.037 0.138 -9999 0 -0.316 91 91
PRKACA 0.035 0.015 -9999 0 0 84 84
CDK7 0.035 0.015 -9999 0 0 84 84
TFIIH 0.061 0.052 -9999 0 -0.132 25 25
RAR alpha/9cRA 0.036 0.086 -9999 0 -0.19 27 27
CCNH 0.037 0.012 -9999 0 0 51 51
CREBBP 0.037 0.012 -9999 0 0 53 53
RAR gamma2/9cRA 0.046 0.06 -9999 0 -0.126 35 35
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.064 0.064 -9999 0 -0.104 50 50
ER alpha/Gai/GDP/Gbeta gamma -0.024 0.14 -9999 0 -0.302 77 77
AKT1 -0.086 0.263 -9999 0 -0.637 94 94
PIK3CA 0.029 0.019 -9999 0 0 166 166
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.085 0.269 -9999 0 -0.646 95 95
mol:Ca2+ -0.001 0.071 0.183 10 -0.282 24 34
IGF1R 0.033 0.017 -9999 0 0 112 112
E2/ER alpha (dimer)/Striatin 0.034 0.05 -9999 0 -0.112 51 51
SHC1 0.039 0.008 -9999 0 0 23 23
apoptosis 0.083 0.251 0.61 94 -9999 0 94
RhoA/GTP 0.014 0.047 -9999 0 -0.108 57 57
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.009 0.141 0.274 1 -0.294 69 70
regulation of stress fiber formation 0.015 0.069 0.158 16 -0.148 60 76
E2/ERA-ERB (dimer) 0.037 0.045 -9999 0 -0.109 42 42
KRAS 0.034 0.016 -9999 0 0 95 95
G13/GTP 0.033 0.045 -9999 0 -0.098 49 49
pseudopodium formation -0.015 0.069 0.148 60 -0.158 16 76
E2/ER alpha (dimer)/PELP1 0.035 0.046 -9999 0 -0.108 42 42
GRB2 0.04 0.008 -9999 0 0 21 21
GNG2 0.039 0.009 -9999 0 0 29 29
GNAO1 0.035 0.015 -9999 0 0 85 85
HRAS 0.039 0.01 -9999 0 0 31 31
mol:GTP 0 0 -9999 0 -9999 0 0
mol:NO -0.038 0.162 -9999 0 -0.38 79 79
E2/ER beta (dimer) 0.03 0.005 -9999 0 -9999 0 0
mol:GDP -0.002 0.075 0.142 2 -0.229 46 48
mol:NADP -0.038 0.162 -9999 0 -0.38 79 79
PIK3R1 0.034 0.016 -9999 0 0 99 99
mol:IP3 -0.003 0.071 0.183 7 -0.291 24 31
IGF-1R heterotetramer 0.033 0.017 -9999 0 0 112 112
PLCB1 0.004 0.068 -9999 0 -0.292 23 23
PLCB2 0.005 0.067 -9999 0 -0.277 25 25
IGF1 0.035 0.014 -9999 0 0 77 77
mol:L-citrulline -0.038 0.162 -9999 0 -0.38 79 79
RHOA 0.04 0.006 -9999 0 0 13 13
Gai/GDP -0.007 0.179 -9999 0 -0.591 44 44
JNK cascade 0.029 0.005 -9999 0 -9999 0 0
BCAR1 0.036 0.013 -9999 0 0 65 65
ESR2 0.04 0.007 -9999 0 0 15 15
GNAQ 0.038 0.012 -9999 0 0 48 48
ESR1 0.034 0.015 -9999 0 0 91 91
Gq family/GDP/Gbeta gamma -0.048 0.243 -9999 0 -0.662 67 67
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.018 0.116 -9999 0 -0.665 11 11
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.008 0.142 0.255 2 -0.291 73 75
GNAZ 0.038 0.011 -9999 0 0 46 46
E2/ER alpha (dimer) 0.016 0.041 -9999 0 -0.125 42 42
STRN 0.039 0.008 -9999 0 0 23 23
GNAL 0.04 0.008 -9999 0 0 22 22
PELP1 0.038 0.011 -9999 0 0 39 39
MAPK11 0.013 0.008 0.069 1 -9999 0 1
GNAI2 0.04 0.006 -9999 0 0 13 13
GNAI3 0.038 0.011 -9999 0 0 45 45
GNAI1 0.034 0.015 -9999 0 0 93 93
HBEGF -0.018 0.149 0.323 15 -0.332 57 72
cAMP biosynthetic process 0.031 0.038 -9999 0 -0.09 40 40
SRC -0.024 0.139 0.222 17 -0.292 79 96
PI3K 0.023 0.06 -9999 0 -0.15 44 44
GNB1 0.039 0.01 -9999 0 0 33 33
G13/GDP/Gbeta gamma 0.04 0.091 -9999 0 -0.202 47 47
SOS1 0.037 0.012 -9999 0 0 51 51
IGF-1R heterotetramer/IGF1 -0.037 0.103 -9999 0 -0.247 74 74
Gs family/GTP 0.041 0.043 -9999 0 -0.091 40 40
EntrezGene:2778 0 0 -9999 0 -9999 0 0
RAS family/GTP 0.054 0.049 -9999 0 -0.106 27 27
vasodilation -0.035 0.155 -9999 0 -0.364 79 79
mol:DAG -0.003 0.071 0.183 7 -0.291 24 31
Gs family/GDP/Gbeta gamma 0.005 0.078 -9999 0 -0.208 45 45
MSN -0.016 0.072 0.152 60 -0.168 16 76
Gq family/GTP 0.018 0.072 -9999 0 -0.282 25 25
mol:PI-3-4-5-P3 -0.081 0.259 -9999 0 -0.619 96 96
NRAS 0.039 0.009 -9999 0 0 30 30
mol:E2 0 0 -9999 0 -9999 0 0
cell adhesion 0.035 0.155 0.364 79 -9999 0 79
GRB2/SOS1 0.047 0.044 -9999 0 -0.142 24 24
RhoA/GDP 0.016 0.086 -9999 0 -0.218 49 49
NOS3 -0.04 0.169 -9999 0 -0.397 79 79
GNA11 0.037 0.013 -9999 0 0 61 61
MAPKKK cascade -0.03 0.185 -9999 0 -0.464 74 74
E2/ER alpha (dimer)/PELP1/Src -0.014 0.143 0.266 2 -0.296 76 78
ruffle organization -0.015 0.069 0.148 60 -0.158 16 76
ROCK2 -0.009 0.079 0.172 67 -0.168 7 74
GNA14 0.039 0.009 -9999 0 0 29 29
GNA15 0.036 0.014 -9999 0 0 68 68
GNA13 0.039 0.008 -9999 0 0 23 23
MMP9 -0.02 0.149 0.355 15 -0.313 65 80
MMP2 -0.021 0.136 0.228 13 -0.324 57 70
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.001 0.07 0.141 13 -0.182 60 73
CRKL 0.038 0.01 -9999 0 0 36 36
Rac1/GDP 0.029 0.009 -9999 0 -0.125 1 1
DOCK1 0.037 0.012 -9999 0 0 53 53
ITGA4 0.035 0.015 -9999 0 0 88 88
alpha4/beta7 Integrin/MAdCAM1 0.063 0.074 -9999 0 -0.107 68 68
EPO 0.04 0.007 -9999 0 0 14 14
alpha4/beta7 Integrin 0.031 0.065 -9999 0 -0.137 66 66
mol:GTP 0 0 -9999 0 -9999 0 0
CRK 0.038 0.012 -9999 0 0 49 49
alpha4/beta1 Integrin 0.031 0.065 -9999 0 -0.135 66 66
EPO/EPOR (dimer) 0.051 0.025 -9999 0 -0.134 2 2
lamellipodium assembly 0.021 0.107 -9999 0 -0.406 14 14
PIK3CA 0.029 0.019 -9999 0 0 166 166
PI3K 0.023 0.06 -9999 0 -0.15 44 44
ARF6 0.04 0.007 -9999 0 0 16 16
JAK2 0.002 0.075 -9999 0 -0.195 58 58
PXN 0.04 0.006 -9999 0 0 10 10
PIK3R1 0.034 0.016 -9999 0 0 99 99
MADCAM1 0.036 0.014 -9999 0 0 67 67
cell adhesion 0.061 0.072 -9999 0 -0.107 68 68
CRKL/CBL 0.055 0.02 -9999 0 -0.134 1 1
ITGB1 0.038 0.01 -9999 0 0 36 36
SRC -0.019 0.091 0.203 23 -0.191 43 66
ITGB7 0.038 0.01 -9999 0 0 38 38
RAC1 0.039 0.009 -9999 0 0 28 28
alpha4/beta1 Integrin/VCAM1 -0.007 0.096 -9999 0 -0.144 154 154
p130Cas/Crk/Dock1 0.013 0.1 0.226 19 -0.183 45 64
VCAM1 0.02 0.021 -9999 0 0 281 281
RHOA 0.04 0.006 -9999 0 0 13 13
alpha4/beta1 Integrin/Paxillin/GIT1 0.069 0.073 -9999 0 -0.11 65 65
BCAR1 -0.018 0.081 0.198 20 -0.183 39 59
EPOR 0.036 0.014 -9999 0 0 74 74
mol:GDP 0 0 -9999 0 -9999 0 0
CBL 0.04 0.008 -9999 0 0 20 20
GIT1 0.039 0.009 -9999 0 0 25 25
Rac1/GTP 0.02 0.11 -9999 0 -0.436 13 13
EPHB forward 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
Ephrin A5/EPHB2 0.035 0.047 -9999 0 -0.112 43 43
cell-cell adhesion 0.042 0.041 0.17 13 -9999 0 13
Ephrin B/EPHB2/RasGAP 0.052 0.095 -9999 0 -0.118 97 97
ITSN1 0.04 0.007 -9999 0 0 15 15
PIK3CA 0.029 0.019 -9999 0 0 166 166
SHC1 0.039 0.008 -9999 0 0 23 23
Ephrin B1/EPHB3 0.037 0.037 -9999 0 -0.109 21 21
Ephrin B1/EPHB1 0.048 0.023 -9999 0 -0.109 5 5
HRAS/GDP -0.019 0.11 0.194 1 -0.182 131 132
Ephrin B/EPHB1/GRB7 0.056 0.088 -9999 0 -0.114 84 84
Endophilin/SYNJ1 -0.025 0.059 0.189 11 -0.195 6 17
KRAS 0.034 0.016 -9999 0 0 95 95
Ephrin B/EPHB1/Src 0.059 0.087 -9999 0 -0.113 80 80
endothelial cell migration 0.02 0.074 -9999 0 -0.114 94 94
GRB2 0.04 0.008 -9999 0 0 21 21
GRB7 0.037 0.013 -9999 0 0 57 57
PAK1 -0.019 0.071 0.18 27 -0.193 11 38
HRAS 0.039 0.01 -9999 0 0 31 31
RRAS -0.025 0.058 0.194 8 -0.194 11 19
DNM1 0.039 0.01 -9999 0 0 33 33
cell-cell signaling 0 0 -9999 0 -9999 0 0
CRK -0.012 0.07 0.194 31 -0.174 4 35
lamellipodium assembly -0.042 0.041 -9999 0 -0.17 13 13
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.004 0.071 -9999 0 -0.205 13 13
PIK3R1 0.034 0.016 -9999 0 0 99 99
EPHB2 0.038 0.01 -9999 0 0 38 38
EPHB3 0.032 0.017 -9999 0 0 126 126
EPHB1 0.037 0.012 -9999 0 0 50 50
EPHB4 0.039 0.008 -9999 0 0 23 23
mol:GDP -0.043 0.095 0.193 9 -0.225 72 81
Ephrin B/EPHB2 0.045 0.079 -9999 0 -0.108 95 95
Ephrin B/EPHB3 0.035 0.075 -9999 0 -0.107 86 86
JNK cascade -0.008 0.092 0.298 37 -0.182 2 39
Ephrin B/EPHB1 0.047 0.074 -9999 0 -0.106 83 83
RAP1/GDP -0.028 0.115 0.331 2 -0.214 85 87
EFNB2 0.031 0.018 -9999 0 0 139 139
EFNB3 0.036 0.014 -9999 0 0 69 69
EFNB1 0.04 0.007 -9999 0 0 15 15
Ephrin B2/EPHB1-2 0.035 0.067 -9999 0 -0.108 78 78
RAP1B 0.037 0.012 -9999 0 0 54 54
RAP1A 0.039 0.01 -9999 0 0 35 35
CDC42/GTP 0.027 0.098 -9999 0 -0.162 82 82
Rap1/GTP -0.046 0.05 0.06 3 -0.19 15 18
axon guidance 0.035 0.047 -9999 0 -0.112 43 43
MAPK3 -0.004 0.069 0.185 10 -0.216 8 18
MAPK1 -0.001 0.068 0.188 13 -0.21 8 21
Rac1/GDP -0.032 0.107 0.283 4 -0.21 80 84
actin cytoskeleton reorganization -0.053 0.06 -9999 0 -0.165 70 70
CDC42/GDP -0.032 0.108 0.283 4 -0.215 78 82
PI3K 0.023 0.077 -9999 0 -0.115 94 94
EFNA5 0.034 0.015 -9999 0 0 93 93
Ephrin B2/EPHB4 0.023 0.06 -9999 0 -0.112 82 82
Ephrin B/EPHB2/Intersectin/N-WASP 0 0.08 -9999 0 -0.157 96 96
CDC42 0.04 0.007 -9999 0 0 18 18
RAS family/GTP -0.041 0.048 -9999 0 -0.183 15 15
PTK2 0.138 0.256 0.561 146 -0.177 2 148
MAP4K4 -0.008 0.092 0.3 37 -0.183 2 39
SRC 0.039 0.009 -9999 0 0 28 28
KALRN 0.038 0.012 -9999 0 0 47 47
Intersectin/N-WASP 0.056 0.022 -9999 0 -0.134 5 5
neuron projection morphogenesis -0.024 0.088 0.282 16 -0.214 16 32
MAP2K1 -0.003 0.064 0.174 1 -0.202 10 11
WASL 0.04 0.007 -9999 0 0 18 18
Ephrin B1/EPHB1-2/NCK1 0.076 0.063 -9999 0 -0.113 40 40
cell migration -0.011 0.089 0.237 7 -0.242 13 20
NRAS 0.039 0.009 -9999 0 0 30 30
SYNJ1 -0.025 0.06 0.19 11 -0.197 6 17
PXN 0.04 0.006 -9999 0 0 10 10
TF -0.029 0.054 0.17 10 -0.195 6 16
HRAS/GTP 0.031 0.079 -9999 0 -0.115 90 90
Ephrin B1/EPHB1-2 0.062 0.041 -9999 0 -0.107 17 17
cell adhesion mediated by integrin 0.009 0.062 0.169 9 -0.208 14 23
RAC1 0.039 0.009 -9999 0 0 28 28
mol:GTP 0.035 0.081 -9999 0 -0.115 92 92
RAC1-CDC42/GTP -0.041 0.045 -9999 0 -0.196 8 8
RASA1 0.037 0.013 -9999 0 0 56 56
RAC1-CDC42/GDP -0.021 0.114 0.289 4 -0.21 77 81
ruffle organization -0.025 0.077 0.24 11 -0.24 2 13
NCK1 0.036 0.014 -9999 0 0 70 70
receptor internalization -0.03 0.056 0.175 11 -0.189 8 19
Ephrin B/EPHB2/KALRN 0.056 0.092 -9999 0 -0.117 89 89
ROCK1 0.018 0.087 0.193 102 -9999 0 102
RAS family/GDP -0.057 0.063 -9999 0 -0.162 107 107
Rac1/GTP -0.042 0.046 -9999 0 -0.188 11 11
Ephrin B/EPHB1/Src/Paxillin 0.002 0.073 -9999 0 -0.151 83 83
FAS signaling pathway (CD95)

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
SPTAN1 -0.026 0.053 0.177 2 -0.207 33 35
RFC1 -0.025 0.056 0.18 4 -0.212 35 39
PRKDC -0.019 0.069 0.213 18 -0.209 37 55
RIPK1 0.038 0.01 -9999 0 0 32 32
CASP7 0.006 0.111 -9999 0 -0.575 16 16
FASLG/FAS/FADD/FAF1 0.023 0.08 0.15 100 -0.171 37 137
MAP2K4 0.009 0.113 0.223 6 -0.328 29 35
mol:ceramide 0.017 0.091 -9999 0 -0.307 19 19
GSN -0.026 0.051 0.127 1 -0.207 34 35
FASLG/FAS/FADD/FAF1/Caspase 8 0.024 0.087 0.192 9 -0.235 20 29
FAS 0.035 0.017 -9999 0 -0.002 93 93
BID -0.03 0.018 0.229 1 -9999 0 1
MAP3K1 0.016 0.109 0.254 7 -0.363 22 29
MAP3K7 0.039 0.011 -9999 0 -0.001 39 39
RB1 -0.023 0.059 0.197 7 -0.204 32 39
CFLAR 0.039 0.008 -9999 0 0 19 19
HGF/MET -0.013 0.091 -9999 0 -0.136 167 167
ARHGDIB -0.015 0.073 0.21 24 -0.212 28 52
FADD 0.04 0.012 -9999 0 -0.009 26 26
actin filament polymerization 0.026 0.055 0.208 37 -9999 0 37
NFKB1 -0.035 0.224 -9999 0 -0.667 57 57
MAPK8 0.006 0.114 0.238 1 -0.371 24 25
DFFA -0.024 0.055 0.179 4 -0.206 38 42
DNA fragmentation during apoptosis -0.023 0.058 0.178 4 -0.207 39 43
FAS/FADD/MET 0.018 0.087 -9999 0 -0.128 124 124
CFLAR/RIP1 0.053 0.03 -9999 0 -0.15 8 8
FAIM3 0.04 0.007 -9999 0 0 15 15
FAF1 0.04 0.014 -9999 0 -0.01 33 33
PARP1 -0.021 0.063 0.216 13 -0.202 35 48
DFFB -0.023 0.054 0.179 4 -0.207 36 40
CHUK -0.042 0.208 -9999 0 -0.639 55 55
FASLG 0.04 0.013 -9999 0 -0.011 28 28
FAS/FADD 0.038 0.059 -9999 0 -0.133 52 52
HGF 0.039 0.009 -9999 0 0 27 27
LMNA -0.018 0.066 0.214 15 -0.212 27 42
CASP6 -0.019 0.054 0.135 2 -0.223 23 25
CASP10 0.036 0.016 -9999 0 -0.004 72 72
CASP3 -0.02 0.059 0.164 2 -0.227 37 39
PTPN13 0.021 0.021 -9999 0 0 268 268
CASP8 -0.032 0.016 0.264 1 -9999 0 1
IL6 -0.026 0.232 -9999 0 -0.74 32 32
MET 0.027 0.02 -9999 0 0 191 191
ICAD/CAD -0.026 0.054 0.194 5 -0.198 37 42
FASLG/FAS/FADD/FAF1/Caspase 10 0.017 0.092 -9999 0 -0.311 19 19
activation of caspase activity by cytochrome c -0.03 0.018 0.229 1 -9999 0 1
PAK2 0.005 0.095 0.22 69 -0.208 32 101
BCL2 0.036 0.013 -9999 0 0 67 67
BCR signaling pathway

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
JUN -0.043 0.139 0.296 1 -0.342 64 65
IKBKB 0.021 0.092 0.271 8 -0.275 13 21
AKT1 0.027 0.101 0.239 49 -0.186 14 63
IKBKG 0.021 0.076 0.217 3 -0.252 12 15
CALM1 -0.012 0.114 0.211 6 -0.343 37 43
PIK3CA 0.029 0.019 -9999 0 0 166 166
MAP3K1 -0.032 0.153 -9999 0 -0.422 44 44
MAP3K7 0.038 0.01 -9999 0 0 38 38
mol:Ca2+ -0.01 0.122 0.206 4 -0.344 43 47
DOK1 0.04 0.008 -9999 0 0 22 22
AP-1 -0.022 0.095 0.181 1 -0.217 61 62
LYN 0.035 0.015 -9999 0 0 83 83
BLNK 0.037 0.013 -9999 0 0 62 62
SHC1 0.039 0.008 -9999 0 0 23 23
BCR complex 0.052 0.025 -9999 0 -0.124 3 3
CD22 -0.016 0.094 -9999 0 -0.277 43 43
CAMK2G -0.013 0.111 0.202 14 -0.319 39 53
CSNK2A1 0.038 0.012 -9999 0 0 47 47
INPP5D 0 0 -9999 0 -9999 0 0
SHC/GRB2/SOS1 0.02 0.062 -9999 0 -0.131 57 57
GO:0007205 -0.011 0.124 0.206 4 -0.345 45 49
SYK 0.036 0.014 -9999 0 0 67 67
ELK1 -0.015 0.119 0.216 3 -0.335 44 47
NFATC1 -0.033 0.11 0.211 2 -0.304 45 47
B-cell antigen/BCR complex 0.052 0.025 -9999 0 -0.124 3 3
PAG1/CSK 0.052 0.026 -9999 0 -0.134 4 4
NFKBIB 0.017 0.062 0.126 2 -0.128 64 66
HRAS -0.011 0.101 0.224 4 -0.278 44 48
NFKBIA 0.019 0.057 0.126 2 -0.125 54 56
NF-kappa-B/RelA/I kappa B beta 0.024 0.055 0.125 5 -0.105 60 65
RasGAP/Csk 0.056 0.086 -9999 0 -0.108 83 83
mol:GDP -0.011 0.122 0.203 4 -0.341 44 48
PTEN 0.039 0.01 -9999 0 0 36 36
CD79B 0.04 0.007 -9999 0 0 16 16
NF-kappa-B/RelA/I kappa B alpha 0.026 0.052 0.125 5 -0.104 52 57
GRB2 0.04 0.008 -9999 0 0 21 21
PI3K/BCAP/CD19 -0.026 0.153 -9999 0 -0.423 42 42
PIK3R1 0.034 0.016 -9999 0 0 99 99
mol:IP3 -0.006 0.121 0.207 4 -0.363 38 42
CSK 0.039 0.009 -9999 0 0 25 25
FOS -0.015 0.118 0.221 7 -0.331 43 50
CHUK 0.001 0.109 0.217 3 -0.274 50 53
IBTK 0.036 0.013 -9999 0 0 64 64
CARD11/BCL10/MALT1/TAK1 0.014 0.124 -9999 0 -0.309 38 38
PTPN6 -0.01 0.095 0.179 24 -0.275 36 60
RELA 0.04 0.006 -9999 0 0 10 10
BCL2A1 0.016 0.042 0.098 2 -0.08 60 62
VAV2 -0.025 0.119 -9999 0 -0.326 52 52
ubiquitin-dependent protein catabolic process 0.02 0.06 -9999 0 -0.123 64 64
BTK -0.038 0.253 -9999 0 -1.067 31 31
CD19 -0.019 0.1 -9999 0 -0.29 42 42
MAP4K1 0.036 0.014 -9999 0 0 67 67
CD72 0.04 0.006 -9999 0 0 12 12
PAG1 0.037 0.012 -9999 0 0 50 50
MAPK14 -0.029 0.136 0.309 3 -0.364 45 48
SH3BP5 0.04 0.008 -9999 0 0 22 22
PIK3AP1 -0.01 0.123 0.235 3 -0.39 34 37
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.015 0.163 -9999 0 -0.459 44 44
RAF1 -0.014 0.097 0.211 9 -0.275 40 49
RasGAP/p62DOK/SHIP 0.044 0.077 -9999 0 -0.104 89 89
CD79A 0.036 0.013 -9999 0 0 63 63
re-entry into mitotic cell cycle -0.022 0.094 -9999 0 -0.217 59 59
RASA1 0.037 0.013 -9999 0 0 56 56
MAPK3 -0.019 0.087 0.218 8 -0.25 37 45
MAPK1 -0.017 0.088 0.231 10 -0.254 34 44
CD72/SHP1 0.023 0.122 0.286 20 -0.269 35 55
NFKB1 0.036 0.013 -9999 0 0 66 66
MAPK8 -0.031 0.134 -9999 0 -0.368 43 43
actin cytoskeleton organization -0.026 0.11 0.254 3 -0.297 47 50
NF-kappa-B/RelA 0.04 0.119 -9999 0 -0.228 64 64
Calcineurin 0.013 0.119 0.275 1 -0.302 38 39
PI3K -0.015 0.079 -9999 0 -0.253 26 26
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.001 0.12 0.221 4 -0.376 36 40
SOS1 0.037 0.012 -9999 0 0 51 51
Bam32/HPK1 -0.037 0.23 -9999 0 -0.688 46 46
DAPP1 -0.058 0.252 -9999 0 -0.769 49 49
cytokine secretion -0.03 0.104 0.207 2 -0.286 45 47
mol:DAG -0.006 0.121 0.207 4 -0.363 38 42
PLCG2 0.035 0.015 -9999 0 0 82 82
MAP2K1 -0.017 0.092 0.209 9 -0.269 37 46
B-cell antigen/BCR complex/FcgammaRIIB 0.037 0.07 -9999 0 -0.115 74 74
mol:PI-3-4-5-P3 0.015 0.103 0.229 43 -0.223 14 57
ETS1 -0.011 0.11 0.224 12 -0.317 36 48
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.068 0.082 -9999 0 -0.117 58 58
B-cell antigen/BCR complex/LYN -0.014 0.105 -9999 0 -0.301 42 42
MALT1 0.036 0.014 -9999 0 0 70 70
TRAF6 0.04 0.008 -9999 0 0 19 19
RAC1 -0.027 0.115 0.257 3 -0.312 48 51
B-cell antigen/BCR complex/LYN/SYK 0.046 0.116 0.341 11 -0.247 22 33
CARD11 -0.012 0.118 0.225 5 -0.356 37 42
FCGR2B 0.03 0.019 -9999 0 0 153 153
PPP3CA 0.038 0.011 -9999 0 0 45 45
BCL10 0.041 0.005 -9999 0 0 8 8
IKK complex 0.02 0.051 0.154 19 -0.108 16 35
PTPRC 0.024 0.02 -9999 0 0 222 222
PDPK1 0.018 0.092 0.206 54 -0.166 12 66
PPP3CB 0.039 0.009 -9999 0 0 28 28
PPP3CC 0.033 0.016 -9999 0 0 103 103
POU2F2 0.016 0.042 0.118 8 -0.077 62 70
ErbB4 signaling events

Figure 52.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 54.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.025 0.205 -9999 0 -0.684 39 39
epithelial cell differentiation -0.031 0.189 -9999 0 -0.607 42 42
ITCH 0.038 0.038 0.1 10 -0.094 30 40
WWP1 -0.061 0.275 0.319 1 -1.159 31 32
FYN 0.034 0.016 -9999 0 0 94 94
EGFR 0.036 0.014 -9999 0 0 67 67
PRL 0.039 0.01 -9999 0 0 31 31
neuron projection morphogenesis -0.042 0.156 0.233 9 -0.559 35 44
PTPRZ1 0.039 0.01 -9999 0 0 32 32
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.005 0.185 -9999 0 -0.612 35 35
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.033 0.18 -9999 0 -0.65 37 37
ADAM17 0.037 0.035 0.097 6 -0.08 30 36
ErbB4/ErbB4 -0.05 0.206 -9999 0 -0.838 32 32
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.03 0.2 -9999 0 -0.647 41 41
NCOR1 0.037 0.013 -9999 0 0 58 58
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.026 0.18 -9999 0 -0.595 40 40
GRIN2B -0.034 0.165 0.237 3 -0.555 40 43
ErbB4/ErbB2/betacellulin -0.025 0.184 -9999 0 -0.548 46 46
STAT1 0.034 0.016 -9999 0 0 102 102
HBEGF 0.039 0.009 -9999 0 0 27 27
PRLR 0.035 0.015 -9999 0 0 80 80
E4ICDs/ETO2 -0.029 0.202 -9999 0 -0.683 39 39
axon guidance -0.054 0.224 -9999 0 -0.758 41 41
NEDD4 0.036 0.039 0.103 7 -0.082 39 46
Prolactin receptor/Prolactin receptor/Prolactin 0.05 0.024 -9999 0 -9999 0 0
CBFA2T3 0.035 0.015 -9999 0 0 82 82
ErbB4/ErbB2/HBEGF -0.018 0.184 -9999 0 -0.569 43 43
MAPK3 -0.024 0.165 0.279 4 -0.576 35 39
STAT1 (dimer) -0.034 0.209 -9999 0 -0.518 60 60
MAPK1 -0.024 0.165 0.255 6 -0.576 35 41
JAK2 0.034 0.016 -9999 0 0 101 101
ErbB4/ErbB2/neuregulin 1 beta -0.03 0.174 0.193 2 -0.638 36 38
NRG1 -0.007 0.032 0.035 111 -0.109 21 132
NRG3 0.034 0.015 -9999 0 0 91 91
NRG2 0.041 0.005 -9999 0 0 8 8
NRG4 0.028 0.019 -9999 0 0 169 169
heart development -0.054 0.224 -9999 0 -0.758 41 41
neural crest cell migration -0.029 0.171 0.192 2 -0.628 36 38
ERBB2 -0.009 0.032 0.035 111 -0.098 25 136
WWOX/E4ICDs -0.029 0.195 -9999 0 -0.69 37 37
SHC1 0.039 0.008 -9999 0 0 23 23
ErbB4/EGFR/neuregulin 4 -0.036 0.201 -9999 0 -0.676 38 38
apoptosis 0.03 0.194 0.626 43 -9999 0 43
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.024 0.206 -9999 0 -0.684 39 39
ErbB4/ErbB2/epiregulin -0.018 0.183 -9999 0 -0.575 42 42
ErbB4/ErbB4/betacellulin/betacellulin -0.034 0.205 -9999 0 -0.606 47 47
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.005 0.196 -9999 0 -0.632 36 36
MDM2 -0.042 0.19 0.267 11 -0.724 33 44
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.02 0.164 -9999 0 -0.575 37 37
STAT5A -0.058 0.218 0.238 1 -0.733 42 43
ErbB4/EGFR/neuregulin 1 beta -0.025 0.181 -9999 0 -0.632 37 37
DLG4 0.038 0.01 -9999 0 0 38 38
GRB2/SHC 0.055 0.022 -9999 0 -0.134 4 4
E4ICDs/TAB2/NCoR1 -0.019 0.206 -9999 0 -0.646 41 41
STAT5A (dimer) -0.025 0.215 -9999 0 -0.677 42 42
MAP3K7IP2 0.037 0.012 -9999 0 0 53 53
STAT5B (dimer) -0.037 0.227 -9999 0 -0.735 42 42
LRIG1 0.033 0.017 -9999 0 0 112 112
EREG 0.038 0.011 -9999 0 0 42 42
BTC 0.033 0.016 -9999 0 0 105 105
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.058 0.226 -9999 0 -0.771 41 41
ERBB4 -0.049 0.203 -9999 0 -0.838 31 31
STAT5B 0.039 0.009 -9999 0 0 27 27
YAP1 0.002 0.094 -9999 0 -0.537 14 14
GRB2 0.04 0.008 -9999 0 0 21 21
ErbB4/ErbB2/neuregulin 4 -0.03 0.182 -9999 0 -0.623 38 38
glial cell differentiation 0.019 0.203 0.637 41 -9999 0 41
WWOX 0.029 0.019 -9999 0 0 156 156
cell proliferation -0.068 0.216 0.276 1 -0.6 58 59
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.032 0.138 -9999 0 -0.342 80 80
KLHL20 -0.015 0.102 0.207 12 -0.229 53 65
CYFIP2 0.038 0.011 -9999 0 0 45 45
Rac1/GDP -0.007 0.106 0.256 8 -0.246 45 53
ENAH -0.029 0.136 -9999 0 -0.346 74 74
AP1M1 0.036 0.014 -9999 0 0 72 72
RAP1B 0.037 0.012 -9999 0 0 54 54
RAP1A 0.039 0.01 -9999 0 0 35 35
CTNNB1 0.039 0.01 -9999 0 0 32 32
CDC42/GTP 0.005 0.077 0.158 2 -0.197 31 33
ABI1/Sra1/Nap1 -0.033 0.055 -9999 0 -0.153 69 69
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.068 0.067 -9999 0 -0.111 43 43
RAPGEF1 -0.027 0.124 0.269 4 -0.314 68 72
CTNND1 0.04 0.007 -9999 0 0 17 17
regulation of calcium-dependent cell-cell adhesion -0.019 0.145 -9999 0 -0.346 78 78
CRK -0.023 0.128 0.251 1 -0.338 64 65
E-cadherin/gamma catenin/alpha catenin 0.053 0.063 -9999 0 -0.137 41 41
alphaE/beta7 Integrin 0.048 0.038 -9999 0 -0.132 17 17
IQGAP1 0.036 0.013 -9999 0 0 66 66
NCKAP1 0.039 0.009 -9999 0 0 26 26
Rap1/GTP/I-afadin 0.043 0.063 -9999 0 -0.11 61 61
DLG1 -0.027 0.129 -9999 0 -0.354 63 63
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -9999 0 0
mol:PI-3-4-5-P3 -0.028 0.044 -9999 0 -0.149 40 40
MLLT4 0.033 0.016 -9999 0 0 109 109
ARF6/GTP/NME1/Tiam1 0.047 0.062 -9999 0 -0.107 61 61
PI3K -0.034 0.058 -9999 0 -0.191 40 40
ARF6 0.04 0.007 -9999 0 0 16 16
mol:Ca2+ 0 0 -9999 0 -9999 0 0
E-cadherin/gamma catenin 0.04 0.051 -9999 0 -0.147 30 30
TIAM1 0.036 0.013 -9999 0 0 66 66
E-cadherin(dimer)/Ca2+ 0.065 0.069 -9999 0 -0.125 48 48
AKT1 0.009 0.076 0.161 65 -0.155 16 81
PIK3R1 0.034 0.016 -9999 0 0 99 99
CDH1 0.035 0.015 -9999 0 0 79 79
RhoA/GDP -0.009 0.106 0.253 4 -0.246 48 52
actin cytoskeleton organization -0.009 0.078 0.172 12 -0.167 52 64
CDC42/GDP -0.007 0.107 0.273 6 -0.249 45 51
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.001 0.075 -9999 0 -0.199 56 56
ITGB7 0.038 0.01 -9999 0 0 38 38
RAC1 0.039 0.009 -9999 0 0 28 28
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.07 0.074 -9999 0 -0.134 48 48
E-cadherin/Ca2+/beta catenin/alpha catenin 0.048 0.053 -9999 0 -0.105 45 45
mol:GDP -0.026 0.11 0.249 8 -0.278 48 56
CDC42/GTP/IQGAP1 0.039 0.046 -9999 0 -0.112 42 42
JUP 0.037 0.013 -9999 0 0 57 57
p120 catenin/RhoA/GDP 0.003 0.113 0.264 4 -0.259 44 48
RAC1/GTP/IQGAP1 0.039 0.045 -9999 0 -0.11 40 40
PIP5K1C/AP1M1 0.048 0.026 -9999 0 -0.134 1 1
RHOA 0.04 0.006 -9999 0 0 13 13
CDC42 0.04 0.007 -9999 0 0 18 18
CTNNA1 0.039 0.01 -9999 0 0 31 31
positive regulation of S phase of mitotic cell cycle -0.016 0.058 0.101 4 -0.118 103 107
NME1 0.036 0.014 -9999 0 0 71 71
clathrin coat assembly 0 0 -9999 0 -9999 0 0
TJP1 -0.03 0.138 -9999 0 -0.356 72 72
regulation of cell-cell adhesion -0.009 0.06 -9999 0 -0.154 47 47
WASF2 -0.007 0.043 0.108 13 -0.092 50 63
Rap1/GTP 0.004 0.084 0.189 18 -0.23 26 44
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.073 0.081 -9999 0 -0.123 48 48
CCND1 -0.02 0.071 0.125 2 -0.143 105 107
VAV2 -0.047 0.219 -9999 0 -0.598 56 56
RAP1/GDP 0.004 0.095 0.222 9 -0.26 26 35
adherens junction assembly -0.031 0.135 -9999 0 -0.344 75 75
homophilic cell adhesion 0 0 -9999 0 -9999 0 0
ABI1 0.039 0.009 -9999 0 0 28 28
PIP5K1C 0.037 0.012 -9999 0 0 51 51
regulation of heterotypic cell-cell adhesion 0.045 0.073 0.216 2 -0.123 60 62
E-cadherin/beta catenin 0.007 0.04 0.144 1 -0.228 12 13
mol:GTP 0 0 -9999 0 -9999 0 0
SRC -0.031 0.135 -9999 0 -0.34 77 77
PIK3CA 0.029 0.019 -9999 0 0 166 166
Rac1/GTP -0.056 0.132 -9999 0 -0.351 66 66
E-cadherin/beta catenin/alpha catenin 0.055 0.062 -9999 0 -0.127 45 45
ITGAE 0.038 0.011 -9999 0 0 41 41
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.02 0.147 -9999 0 -0.353 78 78
E-cadherin signaling events

Figure 54.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 56.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.052 0.063 -9999 0 -0.124 47 47
E-cadherin/beta catenin 0.041 0.049 -9999 0 -0.135 33 33
CTNNB1 0.039 0.01 -9999 0 0 32 32
JUP 0.037 0.013 -9999 0 0 57 57
CDH1 0.035 0.014 -9999 0 0 79 79
Caspase cascade in apoptosis

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
TOP1 -0.011 0.138 0.28 2 -0.305 65 67
ACTA1 0.005 0.085 0.205 14 -0.228 21 35
NUMA1 -0.014 0.134 0.252 3 -0.295 71 74
SPTAN1 -0.002 0.083 0.194 11 -0.23 20 31
LIMK1 0.002 0.084 0.198 13 -0.226 21 34
BIRC3 0.025 0.02 -9999 0 0 210 210
BIRC2 0.036 0.014 -9999 0 0 72 72
BAX 0.039 0.008 -9999 0 0 23 23
CASP10 -0.011 0.025 0.059 54 -9999 0 54
CRMA 0 0 -9999 0 -9999 0 0
XIAP 0 0 -9999 0 -9999 0 0
PTK2 -0.031 0.168 0.28 2 -0.375 70 72
DIABLO 0.037 0.013 -9999 0 0 61 61
apoptotic nuclear changes -0.002 0.082 0.193 11 -0.227 20 31
response to UV 0 0 -9999 0 -9999 0 0
CRADD 0.04 0.006 -9999 0 0 10 10
GSN -0.002 0.083 0.198 12 -0.239 20 32
MADD 0.041 0.005 -9999 0 0 9 9
TFAP2A -0.028 0.197 -9999 0 -0.556 51 51
BID 0.002 0.022 -9999 0 -0.094 22 22
MAP3K1 -0.018 0.127 -9999 0 -0.37 56 56
TRADD 0.037 0.013 -9999 0 0 61 61
mol:Ca2+ 0 0 -9999 0 -9999 0 0
APAF-1/Pro-Caspase 9 0.051 0.039 -9999 0 -0.143 18 18
mol:Activated DNA 0 0 -9999 0 -9999 0 0
ARHGDIB 0.007 0.104 0.226 42 -0.223 33 75
CASP9 0.039 0.008 -9999 0 0 24 24
DNA repair -0.012 0.08 0.272 23 -0.161 11 34
neuron apoptosis -0.03 0.193 -9999 0 -0.627 43 43
mol:NAD 0 0 -9999 0 -9999 0 0
DNA fragmentation during apoptosis -0.013 0.118 0.229 6 -0.296 45 51
APAF1 0.039 0.009 -9999 0 0 28 28
CASP6 -0.094 0.326 -9999 0 -0.862 80 80
TRAF2 0.039 0.01 -9999 0 0 32 32
ICAD/CAD -0.002 0.079 0.198 11 -0.223 18 29
CASP7 0.016 0.097 0.184 79 -0.254 17 96
KRT18 -0.012 0.136 -9999 0 -0.572 22 22
apoptosis -0.036 0.158 0.29 11 -0.366 77 88
DFFA 0.002 0.081 0.196 11 -0.223 19 30
DFFB 0.002 0.082 0.2 11 -0.228 20 31
PARP1 0.012 0.08 0.161 11 -0.275 23 34
actin filament polymerization 0.003 0.081 0.227 18 -0.228 10 28
TNF 0.04 0.008 -9999 0 0 22 22
CYCS -0.001 0.067 0.153 9 -0.213 31 40
SATB1 -0.097 0.307 -9999 0 -0.824 79 79
SLK -0.001 0.085 0.224 9 -0.226 22 31
p15 BID/BAX 0.025 0.058 0.182 2 -0.134 38 40
CASP2 0 0.091 0.234 18 -0.241 35 53
JNK cascade 0.018 0.126 0.368 56 -9999 0 56
CASP3 0.007 0.087 0.181 26 -0.213 27 53
LMNB2 -0.047 0.207 0.236 2 -0.41 102 104
RIPK1 0.039 0.01 -9999 0 0 32 32
CASP4 0.033 0.016 -9999 0 0 107 107
Mammalian IAPs/DIABLO 0.011 0.088 -9999 0 -0.131 129 129
negative regulation of DNA binding -0.027 0.193 -9999 0 -0.548 51 51
stress fiber formation -0.001 0.084 0.224 9 -0.223 22 31
GZMB -0.016 0.009 0 125 -9999 0 125
CASP1 -0.012 0.069 -9999 0 -0.197 66 66
LMNB1 -0.046 0.191 0.247 4 -0.351 115 119
APP -0.031 0.197 -9999 0 -0.637 43 43
TNFRSF1A 0.036 0.014 -9999 0 0 72 72
response to stress 0 0 -9999 0 -9999 0 0
CASP8 -0.01 0.002 0 27 -9999 0 27
VIM -0.03 0.161 0.286 11 -0.36 81 92
LMNA -0.018 0.148 0.289 1 -0.371 58 59
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.002 0.086 -9999 0 -0.238 39 39
LRDD 0.039 0.01 -9999 0 0 36 36
SREBF1 0.002 0.082 0.202 10 -0.226 21 31
APAF-1/Caspase 9 0.027 0.156 -9999 0 -0.688 20 20
nuclear fragmentation during apoptosis -0.013 0.132 0.251 3 -0.291 71 74
CFL2 -0.003 0.081 0.23 10 -0.231 18 28
GAS2 0.004 0.086 0.212 17 -0.226 21 38
positive regulation of apoptosis -0.04 0.183 0.238 3 -0.396 88 91
PRF1 0.037 0.013 -9999 0 0 61 61
Signaling events mediated by PRL

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
CCNE1 0.026 0.02 -9999 0 0 202 202
mol:Halofuginone 0.002 0.022 -9999 0 -0.166 9 9
ITGA1 0.032 0.017 -9999 0 0 121 121
CDKN1A 0.021 0.077 -9999 0 -0.354 16 16
PRL-3/alpha Tubulin 0.011 0.038 -9999 0 -0.125 35 35
mol:Ca2+ -0.004 0.072 0.264 35 -9999 0 35
AGT 0.039 0.01 -9999 0 0 35 35
CCNA2 -0.015 0.09 -9999 0 -0.61 7 7
TUBA1B 0 0 -9999 0 -9999 0 0
EGR1 0.006 0.043 -9999 0 -0.315 9 9
CDK2/Cyclin E1 0.023 0.092 -9999 0 -0.357 16 16
MAPK3 -0.012 0.01 0 221 -9999 0 221
PRL-2 /Rab GGTase beta 0.032 0.067 -9999 0 -0.136 70 70
MAPK1 -0.012 0.01 -9999 0 -9999 0 0
PTP4A1 -0.004 0.074 -9999 0 -0.607 7 7
PTP4A3 0.025 0.02 -9999 0 0 209 209
PTP4A2 0.039 0.009 -9999 0 0 30 30
ITGB1 -0.012 0.01 -9999 0 -9999 0 0
SRC 0.039 0.009 -9999 0 0 28 28
RAC1 -0.006 0.107 -9999 0 -0.358 42 42
Rab GGTase beta/Rab GGTase alpha 0.035 0.062 -9999 0 -0.134 62 62
PRL-1/ATF-5 0.017 0.097 0.256 2 -0.539 9 11
RABGGTA 0.04 0.007 -9999 0 0 17 17
BCAR1 -0.005 0.066 0.264 29 -9999 0 29
RHOC -0.005 0.108 -9999 0 -0.367 40 40
RHOA -0.006 0.107 -9999 0 -0.358 42 42
cell motility 0.008 0.118 -9999 0 -0.344 43 43
PRL-1/alpha Tubulin -0.017 0.078 -9999 0 -0.533 9 9
PRL-3/alpha1 Integrin 0.01 0.067 -9999 0 -0.145 69 69
ROCK1 0.008 0.116 -9999 0 -0.345 42 42
RABGGTB 0.035 0.014 -9999 0 0 79 79
CDK2 0.037 0.013 -9999 0 0 56 56
mitosis -0.001 0.077 0.201 6 -0.602 7 13
ATF5 0.038 0.011 -9999 0 0 41 41
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.022 0.144 -9999 0 -0.431 44 44
HDAC1 0.043 0.024 0.083 111 -0.003 54 165
AES 0.038 0.016 0.078 17 0 69 86
FBXW11 0.04 0.008 -9999 0 0 22 22
DTX1 0.041 0.005 -9999 0 0 9 9
LRP6/FZD1 0.042 0.048 -9999 0 -0.133 32 32
TLE1 0.039 0.014 0.076 14 -0.001 51 65
AP1 -0.007 0.082 0.144 2 -0.178 87 89
NCSTN 0.039 0.008 -9999 0 0 22 22
ADAM10 0.039 0.01 -9999 0 0 31 31
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.074 0.223 -9999 0 -0.653 49 49
NICD/RBPSUH -0.006 0.134 -9999 0 -0.436 43 43
WIF1 0.039 0.009 -9999 0 0 26 26
NOTCH1 0.006 0.133 -9999 0 -0.461 39 39
PSENEN 0.034 0.016 -9999 0 0 96 96
KREMEN2 0.039 0.009 -9999 0 0 29 29
DKK1 0.038 0.011 -9999 0 0 39 39
beta catenin/beta TrCP1 0.015 0.093 0.232 1 -0.299 19 20
APH1B 0.035 0.014 -9999 0 0 79 79
APH1A 0.038 0.011 -9999 0 0 42 42
AXIN1 -0.016 0.119 0.23 1 -0.449 28 29
CtBP/CBP/TCF1/TLE1/AES 0.009 0.099 0.18 82 -0.181 51 133
PSEN1 0.039 0.01 -9999 0 0 31 31
FOS 0.026 0.02 -9999 0 0 201 201
JUN 0.035 0.014 -9999 0 0 76 76
MAP3K7 0.041 0.014 0.068 14 0 38 52
CTNNB1 -0.001 0.086 0.221 1 -0.311 17 18
MAPK3 0.04 0.007 -9999 0 0 18 18
DKK2/LRP6/Kremen 2 0.057 0.053 -9999 0 -0.117 29 29
HNF1A 0.002 0.008 0.037 18 -9999 0 18
CTBP1 0.04 0.015 0.078 19 0 49 68
MYC -0.148 0.409 -9999 0 -1.217 69 69
NKD1 0.039 0.012 -9999 0 0 43 43
FZD1 0.04 0.006 -9999 0 0 13 13
NOTCH1 precursor/Deltex homolog 1 0.024 0.146 -9999 0 -0.434 45 45
apoptosis -0.007 0.082 0.143 2 -0.177 87 89
Delta 1/NOTCHprecursor 0.019 0.143 -9999 0 -0.422 46 46
DLL1 0.037 0.013 -9999 0 0 61 61
PPARD 0.009 0.069 -9999 0 -0.869 2 2
Gamma Secretase 0.066 0.084 -9999 0 -0.119 63 63
APC -0.015 0.121 0.23 1 -0.455 28 29
DVL1 0.012 0.068 -9999 0 -0.257 24 24
CSNK2A1 0.037 0.012 -9999 0 0 47 47
MAP3K7IP1 0.04 0.015 0.068 15 0 51 66
DKK1/LRP6/Kremen 2 0.056 0.052 -9999 0 -0.116 28 28
LRP6 0.034 0.016 -9999 0 0 94 94
CSNK1A1 0.039 0.008 -9999 0 0 23 23
NLK 0.026 0.042 -9999 0 -0.215 11 11
CCND1 -0.156 0.439 -9999 0 -1.202 81 81
WNT1 0.04 0.006 -9999 0 0 10 10
Axin1/APC/beta catenin -0.002 0.117 0.27 2 -0.371 26 28
DKK2 0.039 0.01 -9999 0 0 33 33
NOTCH1 precursor/DVL1 0.013 0.147 -9999 0 -0.427 44 44
GSK3B 0.04 0.009 -9999 0 0 23 23
FRAT1 0.041 0.008 -9999 0 0 17 17
NOTCH/Deltex homolog 1 0.027 0.147 -9999 0 -0.439 44 44
PPP2R5D 0.017 0.066 -9999 0 -0.398 10 10
MAPK1 0.038 0.011 -9999 0 0 44 44
WNT1/LRP6/FZD1 0.076 0.059 -9999 0 -0.111 31 31
RBPJ 0 0 -9999 0 -9999 0 0
CREBBP 0.029 0.024 -9999 0 -0.017 85 85
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.012 0.165 -9999 0 -0.703 18 18
UGCG -0.003 0.133 -9999 0 -0.667 18 18
AKT1/mTOR/p70S6K/Hsp90/TERT -0.021 0.177 0.266 2 -0.383 76 78
mol:GTP 0 0.001 -9999 0 -9999 0 0
mol:glucosylceramide -0.002 0.131 -9999 0 -0.657 18 18
mol:DAG -0.008 0.028 0.169 12 -9999 0 12
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.036 0.224 0.285 1 -0.482 81 82
FRAP1 -0.055 0.259 0.288 3 -0.57 81 84
FOXO3 -0.052 0.251 0.263 2 -0.526 90 92
AKT1 -0.06 0.276 0.273 2 -0.578 90 92
GAB2 0.029 0.02 -9999 0 -0.003 149 149
SMPD1 0.002 0.115 -9999 0 -0.614 16 16
SGMS1 -0.003 0.038 0.059 12 -0.079 75 87
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 -0.019 0.034 -9999 0 -0.116 50 50
CALM1 0.039 0.009 -9999 0 0 26 26
cell proliferation 0.005 0.163 0.231 14 -0.306 73 87
EIF3A 0 0 -9999 0 -9999 0 0
PI3K 0.02 0.062 -9999 0 -0.138 52 52
RPS6KB1 -0.022 0.2 -9999 0 -0.877 25 25
mol:sphingomyelin -0.008 0.028 0.169 12 -9999 0 12
natural killer cell activation -0.001 0.004 -9999 0 -0.014 24 24
JAK3 0.034 0.022 -9999 0 -0.046 24 24
PIK3R1 0.031 0.024 -9999 0 -0.041 26 26
JAK1 0.036 0.021 -9999 0 -0.043 24 24
NFKB1 0.036 0.013 -9999 0 0 66 66
MYC -0.035 0.34 0.368 18 -0.805 76 94
MYB -0.047 0.294 -9999 0 -1.091 39 39
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.024 0.173 0.267 2 -0.374 78 80
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.004 0.19 -9999 0 -0.811 25 25
mol:PI-3-4-5-P3 -0.024 0.17 0.266 2 -0.366 78 80
Rac1/GDP 0.008 0.044 -9999 0 -0.109 46 46
T cell proliferation -0.027 0.162 0.278 6 -0.346 78 84
SHC1 0.037 0.016 -9999 0 -0.015 43 43
RAC1 0.039 0.009 -9999 0 0 28 28
positive regulation of cyclin-dependent protein kinase activity 0.001 0.019 0.031 39 -0.064 39 78
PRKCZ -0.027 0.165 0.281 6 -0.359 77 83
NF kappa B1 p50/RelA -0.026 0.236 0.305 2 -0.489 81 83
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.005 0.121 -9999 0 -0.34 39 39
HSP90AA1 0 0 -9999 0 -9999 0 0
RELA 0.04 0.006 -9999 0 0 10 10
IL2RA 0.036 0.017 -9999 0 -0.011 58 58
IL2RB 0.033 0.022 -9999 0 -0.046 20 20
TERT 0.037 0.012 -9999 0 0 53 53
E2F1 -0.006 0.124 -9999 0 -0.413 40 40
SOS1 0.035 0.018 -9999 0 -0.009 71 71
RPS6 0.039 0.01 -9999 0 0 32 32
mol:cAMP -0.001 0.009 0.031 36 -0.016 39 75
PTPN11 0.035 0.02 -9999 0 -0.018 64 64
IL2RG 0.025 0.026 -9999 0 -0.041 28 28
actin cytoskeleton organization -0.027 0.162 0.278 6 -0.346 78 84
GRB2 0.037 0.016 -9999 0 -0.015 41 41
IL2 0.035 0.024 -9999 0 -0.04 38 38
PIK3CA 0.027 0.024 -9999 0 -0.042 21 21
Rac1/GTP 0.029 0.061 -9999 0 -0.106 42 42
LCK 0.035 0.024 -9999 0 -0.039 41 41
BCL2 -0.029 0.198 0.375 1 -0.529 48 49
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.013 0.071 0.149 75 -0.178 5 80
DAPP1 -0.006 0.103 0.202 9 -0.238 51 60
Src family/SYK family/BLNK-LAT/BTK-ITK -0.015 0.143 -9999 0 -0.353 53 53
mol:DAG 0.002 0.075 0.172 21 -0.168 30 51
HRAS 0.04 0.013 0.076 3 -0.004 35 38
RAP1A 0.04 0.012 0.068 4 -0.001 36 40
ARF5/GDP 0.011 0.1 -9999 0 -0.241 42 42
PLCG2 0.035 0.015 -9999 0 0 82 82
PLCG1 0.038 0.011 -9999 0 0 43 43
ARF5 0.038 0.01 -9999 0 0 36 36
mol:GTP -0.014 0.064 0.137 71 -0.181 4 75
ARF1/GTP 0.001 0.063 0.137 80 -0.164 4 84
RHOA 0.04 0.006 -9999 0 0 13 13
YES1 0.037 0.012 -9999 0 0 51 51
RAP1A/GTP -0.006 0.074 0.164 77 -0.18 4 81
ADAP1 -0.015 0.059 0.127 68 -0.172 4 72
ARAP3 -0.014 0.064 0.135 71 -0.178 4 75
INPPL1 0.039 0.009 -9999 0 0 27 27
PREX1 0.038 0.012 -9999 0 0 48 48
ARHGEF6 0.036 0.013 -9999 0 0 64 64
ARHGEF7 0.039 0.009 -9999 0 0 28 28
ARF1 0.038 0.011 -9999 0 0 45 45
NRAS 0.041 0.011 0.069 3 0 30 33
FYN 0.034 0.016 -9999 0 0 94 94
ARF6 0.04 0.007 -9999 0 0 16 16
FGR 0.04 0.007 -9999 0 0 15 15
mol:Ca2+ -0.001 0.049 0.174 14 -0.112 9 23
mol:IP4 0 0 -9999 0 -9999 0 0
TIAM1 0.036 0.013 -9999 0 0 66 66
ZAP70 0.041 0.005 -9999 0 0 9 9
mol:IP3 -0.004 0.062 0.208 14 -0.151 13 27
LYN 0.035 0.015 -9999 0 0 83 83
ARF1/GDP 0.014 0.097 -9999 0 -0.245 37 37
RhoA/GDP 0.032 0.084 0.188 46 -0.166 26 72
PDK1/Src/Hsp90 0.049 0.023 -9999 0 -0.109 6 6
BLNK 0.037 0.013 -9999 0 0 62 62
actin cytoskeleton reorganization 0.002 0.094 0.222 9 -0.26 24 33
SRC 0.039 0.009 -9999 0 0 28 28
PLEKHA2 -0.014 0.006 -9999 0 -9999 0 0
RAC1 0.039 0.009 -9999 0 0 28 28
PTEN 0.032 0.026 -9999 0 -0.03 71 71
HSP90AA1 0 0 -9999 0 -9999 0 0
ARF6/GTP -0.013 0.073 0.151 77 -0.177 4 81
RhoA/GTP -0.01 0.077 0.158 81 -0.177 5 86
Src family/SYK family/BLNK-LAT -0.003 0.097 -9999 0 -0.272 37 37
BLK 0.033 0.017 -9999 0 0 114 114
PDPK1 0.039 0.009 -9999 0 0 29 29
CYTH1 -0.015 0.059 0.127 68 -0.172 4 72
HCK 0.036 0.013 -9999 0 0 65 65
CYTH3 -0.015 0.059 0.127 68 -0.172 4 72
CYTH2 -0.015 0.059 0.127 68 -0.172 4 72
KRAS 0.034 0.017 0.09 1 -0.001 98 99
GO:0030676 0 0 -9999 0 -9999 0 0
FOXO3 0.008 0.047 0.198 1 -0.159 15 16
SGK1 0.008 0.046 -9999 0 -0.168 15 15
INPP5D 0 0 -9999 0 -9999 0 0
mol:GDP -0.005 0.095 -9999 0 -0.254 41 41
SOS1 0.037 0.012 -9999 0 0 51 51
SYK 0.036 0.014 -9999 0 0 67 67
ARF6/GDP -0.003 0.079 0.165 57 -0.177 18 75
mol:PI-3-4-5-P3 -0.015 0.063 0.136 68 -0.18 4 72
ARAP3/RAP1A/GTP -0.006 0.074 0.164 77 -0.181 4 81
VAV1 0.036 0.014 -9999 0 0 69 69
mol:PI-3-4-P2 -0.01 0.002 -9999 0 -9999 0 0
RAS family/GTP/PI3K Class I 0.042 0.063 0.222 23 -0.118 38 61
PLEKHA1 -0.015 0.005 -9999 0 -9999 0 0
Rac1/GDP 0.014 0.101 -9999 0 -0.245 42 42
LAT 0.04 0.006 -9999 0 0 11 11
Rac1/GTP -0.006 0.099 -9999 0 -0.263 50 50
ITK -0.014 0.064 0.132 73 -0.177 5 78
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.003 0.093 0.203 16 -0.223 34 50
LCK 0.039 0.009 -9999 0 0 25 25
BTK -0.016 0.067 0.135 70 -0.185 9 79
EPO signaling pathway

Figure 60.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 62.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.027 0.142 0.35 3 -0.499 23 26
CRKL 0.025 0.086 0.175 114 -0.154 1 115
mol:DAG 0.042 0.074 0.21 5 -0.226 17 22
HRAS 0.023 0.103 0.269 43 -0.175 3 46
MAPK8 0.014 0.083 0.19 83 -0.136 2 85
RAP1A 0.024 0.086 0.176 111 -0.166 3 114
GAB1 0.022 0.083 0.175 105 -0.154 1 106
MAPK14 0.016 0.086 0.192 88 -0.136 2 90
EPO 0.045 0.015 0.081 8 -0.037 7 15
PLCG1 0.042 0.075 0.211 5 -0.23 17 22
EPOR/TRPC2/IP3 Receptors 0.039 0.019 0.082 2 -0.037 6 8
RAPGEF1 0.039 0.009 -9999 0 0 26 26
EPO/EPOR (dimer)/SOCS3 0.063 0.051 -9999 0 -0.126 16 16
GAB1/SHC/GRB2/SOS1 0.067 0.081 0.24 28 -0.172 4 32
EPO/EPOR (dimer) 0.056 0.032 -9999 0 -0.145 2 2
IRS2 0.024 0.085 0.175 111 -0.154 1 112
STAT1 0.038 0.09 0.234 5 -0.244 31 36
STAT5B 0.046 0.079 0.219 6 -0.209 24 30
cell proliferation 0.007 0.081 0.181 83 -0.133 1 84
GAB1/SHIP/PIK3R1/SHP2/SHC 0.032 0.061 0.156 4 -0.159 6 10
TEC 0.019 0.081 0.175 97 -0.171 9 106
SOCS3 0.036 0.013 -9999 0 0 63 63
STAT1 (dimer) 0.038 0.089 0.232 5 -0.239 31 36
JAK2 0.037 0.02 0.081 6 -0.035 4 10
PIK3R1 0.034 0.016 -9999 0 0 99 99
EPO/EPOR (dimer)/JAK2 0.063 0.068 0.236 24 -0.102 30 54
EPO/EPOR 0.056 0.032 -9999 0 -0.145 2 2
LYN 0.035 0.018 -9999 0 -0.036 9 9
TEC/VAV2 0.032 0.076 0.221 22 -0.162 12 34
elevation of cytosolic calcium ion concentration 0.039 0.019 0.082 2 -0.036 6 8
SHC1 0.039 0.008 -9999 0 0 23 23
EPO/EPOR (dimer)/LYN 0.06 0.061 -9999 0 -0.118 28 28
mol:IP3 0.042 0.074 0.21 5 -0.226 17 22
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.045 0.074 0.182 82 -0.134 5 87
SH2B3 -0.001 0.007 0.031 10 -9999 0 10
NFKB1 0.013 0.082 0.193 75 -0.177 5 80
EPO/EPOR (dimer)/JAK2/SOCS3 0.011 0.052 -9999 0 -0.159 36 36
PTPN6 0.035 0.067 0.176 76 -0.102 28 104
TEC/VAV2/GRB2 0.049 0.084 0.234 27 -0.172 10 37
EPOR 0.039 0.019 0.082 2 -0.037 6 8
INPP5D 0 0 -9999 0 -9999 0 0
mol:GDP 0.066 0.081 0.24 28 -0.173 4 32
SOS1 0.037 0.012 -9999 0 0 51 51
PLCG2 0.035 0.015 -9999 0 0 82 82
CRKL/CBL/C3G 0.071 0.076 0.235 37 -0.154 3 40
VAV2 0.021 0.083 0.175 103 -0.16 2 105
CBL 0.025 0.088 0.176 117 -0.225 1 118
SHC/Grb2/SOS1 0.036 0.056 0.168 2 -0.132 11 13
STAT5A 0.045 0.081 0.219 6 -0.218 25 31
GRB2 0.04 0.008 -9999 0 0 21 21
STAT5 (dimer) 0.062 0.093 0.279 4 -0.279 15 19
LYN/PLCgamma2 0.037 0.049 -9999 0 -0.132 32 32
PTPN11 0.039 0.009 -9999 0 0 29 29
BTK 0.023 0.087 0.176 110 -0.169 7 117
BCL2 0.03 0.123 0.341 3 -0.417 15 18
Circadian rhythm pathway

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
chromatin modification -0.048 0.303 -9999 0 -1.016 47 47
CLOCK 0.031 0.031 -9999 0 -0.069 40 40
TIMELESS/CRY2 -0.049 0.309 -9999 0 -1.048 47 47
DEC1/BMAL1 0.044 0.047 -9999 0 -0.133 19 19
ATR 0.035 0.015 -9999 0 0 84 84
NR1D1 -0.013 0.108 -9999 0 -0.634 1 1
ARNTL 0.032 0.031 -9999 0 -0.068 42 42
TIMELESS -0.08 0.316 -9999 0 -1.108 47 47
NPAS2 0.027 0.031 -9999 0 -0.067 36 36
CRY2 0.041 0.004 -9999 0 0 5 5
mol:CO 0.001 0.04 0.131 47 -9999 0 47
CHEK1 0.032 0.017 -9999 0 0 118 118
mol:HEME -0.001 0.04 -9999 0 -0.131 47 47
PER1 0.038 0.011 -9999 0 0 44 44
BMAL/CLOCK/NPAS2 0.029 0.095 -9999 0 -0.132 112 112
BMAL1/CLOCK -0.037 0.196 -9999 0 -0.576 49 49
S phase of mitotic cell cycle -0.048 0.303 -9999 0 -1.016 47 47
TIMELESS/CHEK1/ATR -0.05 0.312 -9999 0 -1.049 47 47
mol:NADPH -0.001 0.04 -9999 0 -0.131 47 47
PER1/TIMELESS -0.052 0.307 -9999 0 -1.046 47 47
PER1-2 / CRY1-2 0 0 -9999 0 -9999 0 0
DEC1 0.04 0.008 -9999 0 0 19 19
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.037 0.012 -9999 0 0 55 55
Caspase 8 (4 units) 0.037 0.092 -9999 0 -0.241 27 27
NEF 0.003 0.005 -9999 0 -0.103 1 1
NFKBIA 0.025 0.043 0.084 9 -0.068 79 88
BIRC3 -0.059 0.101 0.175 5 -0.276 89 94
CYCS -0.004 0.062 0.185 7 -0.258 13 20
RIPK1 0.039 0.01 -9999 0 0 32 32
CD247 0.003 0.005 -9999 0 -0.103 1 1
MAP2K7 -0.006 0.168 -9999 0 -0.562 34 34
protein ubiquitination -0.002 0.098 0.204 5 -0.262 38 43
CRADD 0.04 0.006 -9999 0 0 10 10
DAXX 0.04 0.006 -9999 0 0 11 11
FAS 0.035 0.015 -9999 0 0 88 88
BID 0.005 0.06 0.179 3 -0.261 12 15
NF-kappa-B/RelA/I kappa B alpha 0.027 0.113 -9999 0 -0.174 117 117
TRADD 0.037 0.013 -9999 0 0 61 61
MAP3K5 0.037 0.013 -9999 0 0 60 60
CFLAR 0.04 0.008 -9999 0 0 19 19
FADD 0.04 0.008 -9999 0 0 20 20
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.027 0.113 -9999 0 -0.175 117 117
MAPK8 -0.01 0.155 -9999 0 -0.537 32 32
APAF1 0.039 0.009 -9999 0 0 28 28
TRAF1 0.04 0.007 -9999 0 0 17 17
TRAF2 0.039 0.01 -9999 0 0 32 32
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.013 0.067 -9999 0 -0.271 14 14
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.006 0.115 0.213 1 -0.319 37 38
CHUK -0.003 0.104 0.214 4 -0.281 39 43
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.077 0.083 -9999 0 -0.125 56 56
TCRz/NEF 0.01 0.008 -9999 0 -0.166 1 1
TNF 0.04 0.008 -9999 0 0 22 22
FASLG 0.022 0.014 -9999 0 -0.294 1 1
NFKB1 0.027 0.041 0.095 2 -0.07 68 70
TNFR1A/BAG4/TNF-alpha 0.06 0.045 -9999 0 -0.113 15 15
CASP6 -0.039 0.226 -9999 0 -0.529 84 84
CASP7 -0.042 0.195 0.274 9 -0.41 103 112
RELA 0.027 0.045 0.082 9 -0.066 96 105
CASP2 0.038 0.011 -9999 0 0 41 41
CASP3 -0.054 0.198 0.279 8 -0.408 111 119
TNFRSF1A 0.036 0.014 -9999 0 0 72 72
TNFR1A/BAG4 0.045 0.037 -9999 0 -0.132 14 14
CASP8 0.039 0.009 -9999 0 0 27 27
CASP9 0.039 0.008 -9999 0 0 24 24
MAP3K14 0.003 0.108 0.199 5 -0.301 36 41
APAF-1/Caspase 9 -0.025 0.112 0.192 1 -0.24 92 93
BCL2 -0.009 0.142 -9999 0 -0.487 32 32
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.005 0.067 -9999 0 -0.193 48 48
epithelial cell differentiation 0.058 0.066 -9999 0 -0.124 48 48
CYFIP2 0.038 0.011 -9999 0 0 45 45
ENAH -0.036 0.067 0.191 11 -0.198 7 18
EGFR 0.036 0.014 -9999 0 0 67 67
EPHA2 0.039 0.009 -9999 0 0 26 26
MYO6 -0.029 0.048 0.178 9 -0.201 16 25
CTNNB1 0.039 0.01 -9999 0 0 32 32
ABI1/Sra1/Nap1 0.061 0.057 -9999 0 -0.123 39 39
AQP5 -0.069 0.135 -9999 0 -0.366 88 88
CTNND1 0.04 0.007 -9999 0 0 17 17
mol:PI-4-5-P2 -0.029 0.044 0.175 9 -0.189 12 21
regulation of calcium-dependent cell-cell adhesion -0.029 0.041 0.174 6 -0.189 12 18
EGF 0.038 0.01 -9999 0 0 38 38
NCKAP1 0.039 0.009 -9999 0 0 26 26
AQP3 -0.018 0.048 -9999 0 -0.283 8 8
cortical microtubule organization 0.058 0.066 -9999 0 -0.124 48 48
GO:0000145 -0.028 0.04 0.155 9 -0.181 12 21
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.065 0.069 -9999 0 -0.125 48 48
MLLT4 0.033 0.016 -9999 0 0 109 109
ARF6/GDP -0.052 0.047 -9999 0 -0.189 28 28
ARF6 0.04 0.007 -9999 0 0 16 16
Ephrin A1/EPHA2/NCK1/GIT1 0.06 0.078 -9999 0 -0.121 66 66
mol:Ca2+ 0 0 -9999 0 -9999 0 0
VASP -0.015 0.046 0.17 6 -0.192 15 21
PVRL2 0.037 0.012 -9999 0 0 51 51
ZYX -0.026 0.042 0.178 9 -0.192 8 17
ARF6/GTP 0.065 0.084 -9999 0 -0.121 68 68
CDH1 0.035 0.014 -9999 0 0 79 79
EGFR/EGFR/EGF/EGF 0.039 0.073 -9999 0 -0.123 72 72
RhoA/GDP 0.058 0.068 -9999 0 -0.121 52 52
actin cytoskeleton organization -0.031 0.048 0.156 9 -0.213 17 26
IGF-1R heterotetramer 0.033 0.017 -9999 0 0 112 112
GIT1 0.039 0.009 -9999 0 0 25 25
IGF1R 0.033 0.017 -9999 0 0 112 112
IGF1 0.035 0.014 -9999 0 0 77 77
DIAPH1 -0.003 0.22 -9999 0 -0.556 71 71
Wnt receptor signaling pathway -0.058 0.066 0.124 48 -9999 0 48
RHOA 0.04 0.006 -9999 0 0 13 13
RhoA/GTP -0.051 0.046 -9999 0 -0.185 28 28
CTNNA1 0.039 0.01 -9999 0 0 31 31
VCL -0.031 0.049 0.157 9 -0.218 17 26
EFNA1 0.034 0.016 -9999 0 0 96 96
LPP -0.029 0.044 0.163 8 -0.194 13 21
Ephrin A1/EPHA2 0.035 0.075 -9999 0 -0.123 77 77
SEC6/SEC8 -0.04 0.041 -9999 0 -0.182 18 18
MGAT3 -0.029 0.042 0.176 6 -0.192 12 18
HGF/MET 0.019 0.084 -9999 0 -0.125 110 110
HGF 0.039 0.009 -9999 0 0 27 27
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.005 0.068 -9999 0 -0.194 48 48
actin cable formation 0 0.094 0.249 22 -0.228 23 45
KIAA1543 -0.033 0.042 0.161 8 -0.195 12 20
KIFC3 -0.031 0.044 0.176 9 -0.192 12 21
NCK1 0.036 0.014 -9999 0 0 70 70
EXOC3 0.037 0.012 -9999 0 0 55 55
ACTN1 -0.03 0.048 0.178 10 -0.199 15 25
NCK1/GIT1 0.043 0.047 -9999 0 -0.133 31 31
mol:GDP 0.058 0.066 -9999 0 -0.124 48 48
EXOC4 0.038 0.011 -9999 0 0 41 41
STX4 -0.029 0.032 0.038 7 -0.12 46 53
PIP5K1C -0.029 0.044 0.176 9 -0.192 12 21
LIMA1 0 0 -9999 0 -9999 0 0
ABI1 0.039 0.009 -9999 0 0 28 28
ROCK1 -0.03 0.08 0.224 12 -0.229 6 18
adherens junction assembly -0.043 0.12 -9999 0 -0.384 36 36
IGF-1R heterotetramer/IGF1 0.025 0.08 -9999 0 -0.124 95 95
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.047 -9999 0 -0.137 27 27
MET 0.027 0.02 -9999 0 0 191 191
PLEKHA7 -0.03 0.046 0.178 10 -0.196 13 23
mol:GTP 0.057 0.076 -9999 0 -0.121 66 66
establishment of epithelial cell apical/basal polarity -0.02 0.074 0.146 66 -0.198 13 79
cortical actin cytoskeleton stabilization 0.005 0.067 -9999 0 -0.193 48 48
regulation of cell-cell adhesion -0.031 0.048 0.156 9 -0.213 17 26
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.005 0.068 -9999 0 -0.194 48 48
Aurora B signaling

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
Condensin I complex -0.009 0.038 -9999 0 -0.112 62 62
STMN1 -0.012 0.014 0.024 15 -9999 0 15
Aurora B/RasGAP/Survivin 0.047 0.072 -9999 0 -0.152 49 49
Chromosomal passenger complex/Cul3 protein complex -0.006 0.089 -9999 0 -0.245 44 44
BIRC5 0.037 0.014 -9999 0 -0.003 56 56
DES -0.051 0.279 -9999 0 -0.804 63 63
Aurora C/Aurora B/INCENP 0.059 0.047 -9999 0 -0.112 26 26
Aurora B/TACC1 0.037 0.038 -9999 0 -0.111 22 22
Aurora B/PP2A 0.044 0.048 -9999 0 -0.138 29 29
mol:GTP 0 0 -9999 0 -9999 0 0
CBX5 -0.011 0.061 -9999 0 -0.155 72 72
mitotic metaphase/anaphase transition 0.002 0.006 0.013 109 -9999 0 109
NDC80 -0.005 0.009 0.019 11 -9999 0 11
Cul3 protein complex 0.049 0.06 -9999 0 -0.117 45 45
KIF2C -0.058 0.193 -9999 0 -0.487 78 78
PEBP1 -0.001 0.003 -9999 0 -0.011 38 38
KIF20A 0.032 0.018 -9999 0 0 125 125
mol:GDP 0 0 -9999 0 -9999 0 0
Aurora B/RasGAP 0.037 0.055 -9999 0 -0.137 43 43
SEPT1 0.04 0.007 -9999 0 0 17 17
SMC2 0 0 -9999 0 -9999 0 0
SMC4 0 0 -9999 0 -9999 0 0
NSUN2/NPM1/Nucleolin -0.045 0.198 0.273 1 -0.565 63 64
PSMA3 0.037 0.012 -9999 0 0 51 51
G2/M transition of mitotic cell cycle -0.001 0.003 0.009 36 -0.008 17 53
H3F3B 0.002 0.056 -9999 0 -0.2 38 38
AURKB 0.037 0.016 0.066 1 0 79 80
AURKC 0.039 0.01 -9999 0 0 34 34
CDCA8 0.036 0.015 -9999 0 -0.005 58 58
cytokinesis -0.032 0.181 -9999 0 -0.458 64 64
Aurora B/Septin1 -0.009 0.186 -9999 0 -0.449 61 61
AURKA -0.001 0.003 0.009 36 -0.008 17 53
INCENP 0.038 0.015 -9999 0 -0.029 26 26
KLHL13 0.032 0.017 -9999 0 0 117 117
BUB1 0.037 0.015 -9999 0 0 72 72
hSgo1/Aurora B/Survivin 0.041 0.077 -9999 0 -0.151 59 59
EVI5 0.039 0.01 -9999 0 0 33 33
RhoA/GTP 0 0.165 -9999 0 -0.365 66 66
SGOL1 0.036 0.014 -9999 0 0 69 69
CENPA -0.017 0.113 -9999 0 -0.288 61 61
NCAPG 0 0 -9999 0 -9999 0 0
Aurora B/HC8 Proteasome 0.034 0.063 -9999 0 -0.141 56 56
NCAPD2 0 0 -9999 0 -9999 0 0
Aurora B/PP1-gamma 0.036 0.061 -9999 0 -0.14 53 53
RHOA 0.04 0.006 -9999 0 0 13 13
NCAPH 0 0 -9999 0 -9999 0 0
NPM1 -0.027 0.146 -9999 0 -0.362 70 70
RASA1 0.037 0.013 -9999 0 0 56 56
KLHL9 0.039 0.01 -9999 0 0 34 34
mitotic prometaphase -0.001 0.003 -9999 0 -0.011 38 38
proteasomal ubiquitin-dependent protein catabolic process 0.033 0.063 -9999 0 -0.141 56 56
PPP1CC 0.039 0.01 -9999 0 0 32 32
Centraspindlin -0.012 0.172 -9999 0 -0.38 70 70
RhoA/GDP 0.029 0.014 -9999 0 -0.125 4 4
NSUN2 -0.015 0.12 -9999 0 -0.323 68 68
MYLK 0.001 0.056 -9999 0 -0.199 39 39
KIF23 0.035 0.016 -9999 0 0 93 93
VIM -0.012 0.014 0.023 15 -9999 0 15
RACGAP1 0.037 0.014 -9999 0 -0.004 52 52
mitosis 0 0 -9999 0 -9999 0 0
NCL -0.03 0.13 -9999 0 -0.32 86 86
Chromosomal passenger complex -0.035 0.144 -9999 0 -0.349 67 67
Chromosomal passenger complex/EVI5 0.067 0.095 -9999 0 -0.167 55 55
TACC1 0.035 0.015 -9999 0 0 86 86
PPP2R5D 0.039 0.009 -9999 0 0 26 26
CUL3 0.04 0.008 -9999 0 0 19 19
response to DNA damage stimulus 0 0 -9999 0 -9999 0 0
Arf6 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
CENTA1/KIF3B 0.023 0.012 -9999 0 -0.101 1 1
ARNO/beta Arrestin1-2 0.041 0.033 -9999 0 -0.087 10 10
EGFR 0.036 0.014 -9999 0 0 67 67
EPHA2 0.039 0.009 -9999 0 0 26 26
USP6 0.038 0.011 -9999 0 0 42 42
IQSEC1 0.04 0.006 -9999 0 0 13 13
EGFR/EGFR/EGF/EGF 0.041 0.05 -9999 0 -0.132 35 35
ARRB2 0.016 0.017 -9999 0 -0.196 3 3
mol:GTP 0.002 0.017 0.117 5 -0.06 14 19
ARRB1 0.038 0.012 -9999 0 0 48 48
FBXO8 0.037 0.013 -9999 0 0 59 59
TSHR 0.037 0.012 -9999 0 0 54 54
EGF 0.038 0.01 -9999 0 0 38 38
somatostatin receptor activity 0 0 0 9 -0.001 38 47
ARAP2 0 0 0 11 0 35 46
mol:GDP 0.011 0.072 0.146 3 -0.193 31 34
mol:PI-3-4-5-P3 0 0 0 7 0 37 44
ITGA2B 0.04 0.008 -9999 0 0 22 22
ARF6 0.04 0.007 -9999 0 0 16 16
Ephrin A1/EPHA2/NCK1/GIT1 0.06 0.078 -9999 0 -0.121 66 66
ADAP1 0 0 0 9 0 23 32
KIF13B 0.034 0.016 -9999 0 0 95 95
HGF/MET 0.013 0.074 -9999 0 -0.133 102 102
PXN 0.04 0.006 -9999 0 0 10 10
ARF6/GTP 0.013 0.081 0.189 4 -0.21 38 42
EGFR/EGFR/EGF/EGF/ARFGEP100 0.06 0.053 -9999 0 -0.116 33 33
ADRB2 0.04 0.006 -9999 0 0 11 11
receptor agonist activity 0 0 0 8 0 35 43
actin filament binding 0 0 0 6 0 39 45
SRC 0.039 0.009 -9999 0 0 28 28
ITGB3 0.032 0.017 -9999 0 0 116 116
GNAQ 0.038 0.012 -9999 0 0 48 48
EFA6/PI-4-5-P2 0 0 0.001 13 -0.001 26 39
ARF6/GDP 0.008 0.075 0.178 8 -0.22 29 37
ARF6/GDP/GULP/ACAP1 0.025 0.085 -9999 0 -0.216 24 24
alphaIIb/beta3 Integrin/paxillin/GIT1 0.079 0.057 -9999 0 -0.109 35 35
ACAP1 0 0 0 6 -9999 0 6
ACAP2 0 0 0 8 0 36 44
LHCGR/beta Arrestin2 0.03 0.027 -9999 0 -0.062 37 37
EFNA1 0.034 0.016 -9999 0 0 96 96
HGF 0.039 0.009 -9999 0 0 27 27
CYTH3 0 0 0.001 10 -0.001 35 45
CYTH2 0 0.001 0.003 6 -0.004 36 42
NCK1 0.036 0.014 -9999 0 0 70 70
fibronectin binding 0 0 0 8 0 29 37
endosomal lumen acidification 0 0 0 12 0 17 29
microtubule-based process 0 0 -9999 0 -9999 0 0
GULP1 0.032 0.017 -9999 0 0 127 127
GNAQ/ARNO 0.026 0.008 -9999 0 0 48 48
mol:Phosphatidic acid 0 0 0 8 0 36 44
PIP3-E 0.038 0.011 -9999 0 0 45 45
MET 0.027 0.02 -9999 0 0 191 191
GNA14 0.039 0.009 -9999 0 0 29 29
GNA15 0.036 0.014 -9999 0 0 68 68
GIT1 0.039 0.009 -9999 0 0 25 25
mol:PI-4-5-P2 0 0 0.001 13 -0.001 37 50
GNA11 0.037 0.013 -9999 0 0 61 61
LHCGR 0.04 0.008 -9999 0 0 20 20
AGTR1 0.037 0.013 -9999 0 0 57 57
desensitization of G-protein coupled receptor protein signaling pathway 0.03 0.027 -9999 0 -0.062 37 37
IPCEF1/ARNO 0.051 0.046 -9999 0 -0.086 34 34
alphaIIb/beta3 Integrin 0.039 0.05 -9999 0 -0.133 35 35
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.037 0.012 -9999 0 0 52 52
oxygen homeostasis 0 0 -9999 0 -9999 0 0
TCEB2 0.039 0.008 -9999 0 0 23 23
TCEB1 0.038 0.011 -9999 0 0 39 39
HIF1A/p53 0.004 0.078 0.219 1 -0.248 33 34
HIF1A 0 0.068 0.165 2 -0.251 24 26
COPS5 0.035 0.014 -9999 0 0 79 79
VHL/Elongin B/Elongin C/RBX1/CUL2 0.083 0.071 -9999 0 -0.117 31 31
FIH (dimer) 0.04 0.008 -9999 0 0 20 20
CDKN2A 0.029 0.019 -9999 0 0 167 167
ARNT/IPAS 0.05 0.028 -9999 0 -0.134 4 4
HIF1AN 0.04 0.008 -9999 0 0 20 20
GNB2L1 0.039 0.009 -9999 0 0 30 30
HIF1A/ARNT 0.015 0.076 0.219 1 -0.247 26 27
CUL2 0.039 0.01 -9999 0 0 34 34
OS9 0.039 0.009 -9999 0 0 26 26
RACK1/Elongin B/Elongin C 0.068 0.039 -9999 0 -0.116 11 11
response to hypoxia 0 0 -9999 0 -9999 0 0
HIF1A/Hsp90 -0.003 0.067 0.152 2 -0.296 16 18
PHD1-3/OS9 0.05 0.079 -9999 0 -0.109 88 88
HIF1A/RACK1/Elongin B/Elongin C 0.049 0.084 -9999 0 -0.249 22 22
VHL 0.039 0.008 -9999 0 0 23 23
HSP90AA1 0 0 -9999 0 -9999 0 0
HIF1A/JAB1 0.015 0.074 0.219 1 -0.25 24 25
EGLN3 0.027 0.019 -9999 0 0 182 182
EGLN2 0.038 0.011 -9999 0 0 41 41
EGLN1 0.039 0.009 -9999 0 0 29 29
TP53 0.026 0.02 -9999 0 0 207 207
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.029 0.112 -9999 0 -0.548 18 18
ARNT 0.037 0.012 -9999 0 0 50 50
ARD1A 0.039 0.009 -9999 0 0 30 30
RBX1 0.036 0.014 -9999 0 0 70 70
HIF1A/p19ARF 0.006 0.08 -9999 0 -0.263 29 29
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.046 0.05 -9999 0 -0.14 35 35
Necdin/E2F1 0.043 0.039 -9999 0 -0.141 14 14
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.071 0.059 -9999 0 -0.106 40 40
NGF (dimer)/p75(NTR)/BEX1 0.022 0.052 -9999 0 -0.108 61 61
NT-4/5 (dimer)/p75(NTR) 0.029 0.009 -9999 0 -0.125 1 1
IKBKB 0.038 0.011 -9999 0 0 41 41
AKT1 0.026 0.097 0.192 124 -0.176 6 130
IKBKG 0.041 0.002 -9999 0 0 2 2
BDNF 0.04 0.006 -9999 0 0 12 12
MGDIs/NGR/p75(NTR)/LINGO1 0.048 0.021 -9999 0 -0.109 3 3
FURIN 0.039 0.01 -9999 0 0 31 31
proBDNF (dimer)/p75(NTR)/Sortilin 0.068 0.046 -9999 0 -0.115 25 25
LINGO1 0 0 -9999 0 -9999 0 0
Sortilin/TRAF6/NRIF 0.016 0.068 -9999 0 -0.132 72 72
proBDNF (dimer) 0.04 0.006 -9999 0 0 12 12
NTRK1 0.04 0.007 -9999 0 0 16 16
RTN4R 0.037 0.012 -9999 0 0 50 50
neuron apoptosis -0.069 0.149 -9999 0 -0.381 68 68
IRAK1 0.04 0.008 -9999 0 0 19 19
SHC1 0.017 0.009 0.069 7 -0.109 1 8
ARHGDIA 0.037 0.012 -9999 0 0 53 53
RhoA/GTP 0.029 0.014 -9999 0 -0.125 4 4
Gamma Secretase 0.067 0.085 -9999 0 -0.118 63 63
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.055 0.056 -9999 0 -0.105 49 49
MAGEH1 0.038 0.011 -9999 0 0 44 44
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.051 0.052 -9999 0 -0.102 37 37
Mammalian IAPs/DIABLO 0.012 0.088 -9999 0 -0.13 129 129
proNGF (dimer) 0 0 -9999 0 -9999 0 0
MAGED1 0.039 0.008 -9999 0 0 24 24
APP 0.038 0.011 -9999 0 0 41 41
NT-4/5 (dimer) 0 0 -9999 0 -9999 0 0
ZNF274 0.038 0.01 -9999 0 0 38 38
RhoA/GDP/RHOGDI 0.048 0.027 0.187 3 -0.107 7 10
NGF 0 0 -9999 0 -9999 0 0
cell cycle arrest -0.014 0.045 0.202 8 -9999 0 8
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.01 0.062 -9999 0 -0.164 50 50
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.05 0.024 -9999 0 -0.109 8 8
NCSTN 0.04 0.008 -9999 0 0 22 22
mol:GTP 0.044 0.034 -9999 0 -0.105 23 23
PSENEN 0.034 0.016 -9999 0 0 96 96
mol:ceramide -0.018 0.036 0.196 10 -9999 0 10
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.009 0.09 -9999 0 -0.317 21 21
p75(NTR)/beta APP 0.048 0.043 -9999 0 -0.134 26 26
BEX1 0.026 0.02 -9999 0 0 200 200
mol:GDP -0.008 0.004 -9999 0 -0.101 1 1
NGF (dimer) -0.004 0.074 -9999 0 -0.101 172 172
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.063 0.035 -9999 0 -0.103 7 7
PIK3R1 0.034 0.016 -9999 0 0 99 99
RAC1/GTP 0.044 0.015 -9999 0 -0.09 1 1
MYD88 0.04 0.006 -9999 0 0 12 12
CHUK 0.038 0.011 -9999 0 0 46 46
NGF (dimer)/p75(NTR)/PKA 0.045 0.035 -9999 0 -0.106 23 23
RHOB 0.04 0.007 -9999 0 0 16 16
RHOA 0.04 0.006 -9999 0 0 13 13
MAGE-G1/E2F1 0.052 0.024 -9999 0 -0.134 2 2
NT3 (dimer) 0.031 0.018 -9999 0 0 133 133
TP53 -0.022 0.047 0.171 14 -0.181 13 27
PRDM4 -0.02 0.036 0.197 9 -9999 0 9
BDNF (dimer) 0.016 0.09 -9999 0 -0.108 168 168
PIK3CA 0.029 0.019 -9999 0 0 166 166
SORT1 0.038 0.011 -9999 0 0 42 42
activation of caspase activity 0.064 0.056 -9999 0 -0.105 40 40
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.062 0.048 -9999 0 -0.106 33 33
RHOC 0.04 0.006 -9999 0 0 10 10
XIAP 0 0 -9999 0 -9999 0 0
MAPK10 -0.012 0.057 0.225 7 -0.199 10 17
DIABLO 0.037 0.013 -9999 0 0 61 61
SMPD2 -0.019 0.036 0.196 10 -9999 0 10
APH1B 0.035 0.014 -9999 0 0 79 79
APH1A 0.038 0.011 -9999 0 0 42 42
proNGF (dimer)/p75(NTR)/Sortilin 0.044 0.037 -9999 0 -0.108 26 26
PSEN1 0.039 0.01 -9999 0 0 31 31
APAF-1/Pro-Caspase 9 0.051 0.039 -9999 0 -0.144 18 18
NT3 (dimer)/p75(NTR) 0.042 0.034 -9999 0 -0.134 8 8
MAPK8 -0.017 0.064 0.239 5 -0.231 13 18
MAPK9 -0.017 0.061 0.239 5 -0.213 12 17
APAF1 0.039 0.009 -9999 0 0 28 28
NTF3 0.031 0.018 -9999 0 0 133 133
NTF4 0 0 -9999 0 -9999 0 0
NDN 0.034 0.016 -9999 0 0 99 99
RAC1/GDP 0.029 0.009 -9999 0 -0.125 1 1
RhoA-B-C/GDP 0.073 0.049 -9999 0 -0.103 27 27
p75 CTF/Sortilin/TRAF6/NRIF 0.069 0.075 -9999 0 -0.127 56 56
RhoA-B-C/GTP 0.044 0.034 -9999 0 -0.105 23 23
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.093 0.066 -9999 0 -0.11 32 32
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.085 0.057 -9999 0 -0.112 32 32
PRKACB 0.038 0.011 -9999 0 0 44 44
proBDNF (dimer)/p75 ECD 0.047 0.046 -9999 0 -0.134 31 31
ChemicalAbstracts:86-01-1 0 0 -9999 0 -9999 0 0
BIRC3 0.025 0.02 -9999 0 0 210 210
BIRC2 0.036 0.014 -9999 0 0 72 72
neuron projection morphogenesis -0.018 0.049 0.122 7 -0.162 22 29
BAD -0.019 0.068 0.234 5 -0.212 18 23
RIPK2 0.032 0.017 -9999 0 0 119 119
NGFR 0.039 0.009 -9999 0 0 25 25
CYCS -0.024 0.04 0.201 8 -0.179 5 13
ADAM17 0.037 0.012 -9999 0 0 52 52
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.049 0.056 -9999 0 -0.106 44 44
BCL2L11 -0.02 0.068 0.234 5 -0.213 18 23
BDNF (dimer)/p75(NTR) 0.057 0.017 -9999 0 -0.134 1 1
PI3K 0.034 0.058 -9999 0 -0.114 45 45
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.061 0.046 -9999 0 -0.102 27 27
NDNL2 0.038 0.011 -9999 0 0 40 40
YWHAE 0.037 0.013 -9999 0 0 58 58
PRKCI 0.027 0.02 -9999 0 0 192 192
NGF (dimer)/p75(NTR) 0.029 0.009 -9999 0 -0.125 1 1
ChemicalAbstracts:146-91-8 0 0 -9999 0 -9999 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.06 0.051 -9999 0 -0.105 38 38
TRAF6 0.04 0.008 -9999 0 0 19 19
RAC1 0.039 0.009 -9999 0 0 28 28
PRKCZ 0.039 0.009 -9999 0 0 27 27
PLG 0.038 0.011 -9999 0 0 41 41
oligodendrocyte cell fate commitment 0 0 -9999 0 -9999 0 0
CASP6 0.014 0.044 0.155 8 -0.166 23 31
SQSTM1 0.038 0.011 -9999 0 0 46 46
NGFRAP1 0.04 0.007 -9999 0 0 15 15
CASP3 -0.021 0.071 0.243 4 -0.218 25 29
E2F1 0.038 0.011 -9999 0 0 39 39
CASP9 0.039 0.008 -9999 0 0 24 24
IKK complex 0.045 0.104 -9999 0 -0.248 27 27
NGF (dimer)/TRKA 0.03 0.005 -9999 0 -9999 0 0
MMP7 0.016 0.02 -9999 0 0 333 333
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.074 0.055 -9999 0 -0.103 33 33
MMP3 0.037 0.012 -9999 0 0 53 53
APAF-1/Caspase 9 -0.056 0.059 -9999 0 -0.188 51 51
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.036 0.013 -9999 0 0 65 65
mol:S1P 0.001 0.007 -9999 0 -0.028 23 23
S1P1/S1P/Gi 0.007 0.079 -9999 0 -0.18 62 62
GNAO1 0.034 0.023 -9999 0 -0.009 105 105
S1P/S1P3/G12/G13 0.047 0.03 -9999 0 -0.064 23 23
AKT1 0.015 0.099 -9999 0 -0.453 19 19
AKT3 -0.019 0.227 -9999 0 -0.91 29 29
mol:GTP 0 0 -9999 0 -9999 0 0
PDGFB-D/PDGFRB 0.036 0.013 -9999 0 0 65 65
GNAI2 0.039 0.019 -9999 0 -0.03 35 35
GNAI3 0.037 0.019 -9999 0 -0.013 62 62
GNAI1 0.034 0.022 -9999 0 -0.007 110 110
mol:GDP 0 0 -9999 0 -9999 0 0
S1PR3 0.001 0.007 0.011 3 -0.029 23 26
S1PR2 0 0 -9999 0 -9999 0 0
EDG1 0.04 0.006 -9999 0 0 11 11
mol:Ca2+ 0 0.101 0.156 3 -0.272 46 49
MAPK3 -0.009 0.094 0.139 4 -0.25 51 55
MAPK1 -0.005 0.09 0.139 4 -0.261 41 45
JAK2 -0.015 0.112 0.203 3 -0.288 54 57
CXCR4 -0.01 0.099 0.136 7 -0.273 49 56
FLT1 0.04 0.022 -9999 0 -0.024 48 48
RhoA/GDP 0.029 0.014 -9999 0 -0.125 4 4
Rac1/GDP 0.029 0.009 -9999 0 -0.125 1 1
SRC -0.009 0.093 0.142 3 -0.257 46 49
S1P/S1P3/Gi 0 0.101 0.157 3 -0.276 45 48
RAC1 0.039 0.009 -9999 0 0 28 28
RhoA/GTP 0.012 0.105 -9999 0 -0.244 51 51
VEGFA 0.003 0.01 0.017 98 -0.038 22 120
S1P/S1P2/Gi -0.003 0.088 0.137 3 -0.186 77 80
VEGFR1 homodimer/VEGFA homodimer 0.036 0.032 -9999 0 -0.087 25 25
RHOA 0.04 0.006 -9999 0 0 13 13
S1P/S1P3/Gq 0.017 0.04 -9999 0 -0.148 26 26
GNAQ 0.038 0.012 -9999 0 0 48 48
GNAZ 0.037 0.02 -9999 0 -0.013 64 64
G12/G13 0.053 0.028 -9999 0 -0.134 8 8
GNA14 0.039 0.009 -9999 0 0 29 29
GNA15 0.036 0.014 -9999 0 0 68 68
GNA12 0.039 0.01 -9999 0 0 33 33
GNA13 0.039 0.008 -9999 0 0 23 23
GNA11 0.037 0.013 -9999 0 0 61 61
Rac1/GTP 0.01 0.104 -9999 0 -0.246 49 49
PLK1 signaling events

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
regulation of centriole-centriole cohesion 0.008 0.053 0.176 46 -0.088 3 49
BUB1B -0.024 0.081 -9999 0 -0.207 67 67
PLK1 -0.003 0.036 0.08 2 -0.099 42 44
PLK1S1 -0.002 0.02 0.046 3 -0.054 41 44
KIF2A -0.003 0.032 0.071 2 -0.089 42 44
regulation of mitotic centrosome separation -0.003 0.036 0.08 2 -0.099 42 44
GOLGA2 0.04 0.008 -9999 0 0 22 22
Hec1/SPC24 -0.01 0.025 -9999 0 -0.08 47 47
WEE1 -0.01 0.083 -9999 0 -0.339 22 22
cytokinesis -0.037 0.129 0.148 2 -0.299 89 91
PP2A-alpha B56 0 0.243 -9999 0 -0.699 57 57
AURKA -0.002 0.022 0.051 4 -0.063 34 38
PICH/PLK1 -0.034 0.068 -9999 0 -0.156 106 106
CENPE -0.008 0.035 0.153 2 -0.131 20 22
RhoA/GTP 0.029 0.014 -9999 0 -0.125 4 4
positive regulation of microtubule depolymerization -0.003 0.032 0.071 2 -0.089 42 44
PPP2CA 0.04 0.008 -9999 0 0 22 22
FZR1 0.037 0.012 -9999 0 0 54 54
TPX2 -0.026 0.096 -9999 0 -0.247 84 84
PAK1 0.037 0.014 -9999 0 0 65 65
SPC24 0 0 -9999 0 -9999 0 0
FBXW11 0.04 0.008 -9999 0 0 22 22
CLSPN 0.008 0.034 -9999 0 -0.277 5 5
GORASP1 0.041 0.005 -9999 0 0 8 8
metaphase 0 0.004 0.015 9 -0.013 27 36
mol:GTP 0 0 -9999 0 -9999 0 0
NLP -0.002 0.02 0.046 3 -0.054 41 44
G2 phase of mitotic cell cycle -0.001 0.003 0.012 9 -9999 0 9
STAG2 0.039 0.01 -9999 0 0 34 34
GRASP65/GM130/RAB1/GTP 0.017 0.065 -9999 0 -0.638 4 4
spindle elongation -0.003 0.036 0.08 2 -0.099 42 44
ODF2 0.04 0.009 -9999 0 0 24 24
BUB1 -0.041 0.242 -9999 0 -0.744 57 57
TPT1 -0.002 0.049 -9999 0 -0.19 29 29
CDC25C -0.007 0.088 -9999 0 -0.343 33 33
CDC25B 0.024 0.03 -9999 0 -0.03 114 114
SGOL1 -0.008 0.053 0.088 3 -0.176 46 49
RHOA 0.04 0.006 -9999 0 0 13 13
CCNB1/CDK1 0.005 0.125 -9999 0 -0.21 117 117
CDC14B -0.01 0.006 0.011 31 -9999 0 31
CDC20 0.034 0.016 -9999 0 0 96 96
PLK1/PBIP1 -0.004 0.032 -9999 0 -0.101 34 34
mitosis -0.001 0.003 0.012 6 -0.012 4 10
FBXO5 -0.016 0.063 0.112 2 -0.176 54 56
CDC2 0.027 0.023 -9999 0 -0.028 30 30
NDC80 0 0 -9999 0 -9999 0 0
metaphase plate congression 0.002 0.052 -9999 0 -0.249 19 19
ERCC6L -0.029 0.098 -9999 0 -0.203 113 113
NLP/gamma Tubulin -0.003 0.031 0.062 2 -0.088 46 48
microtubule cytoskeleton organization -0.002 0.049 -9999 0 -0.19 29 29
G2/M transition DNA damage checkpoint 0 0.002 0.011 9 -9999 0 9
PPP1R12A 0.04 0.009 -9999 0 0 24 24
interphase 0 0.002 0.011 9 -9999 0 9
PLK1/PRC1-2 0.013 0.083 -9999 0 -0.152 87 87
GRASP65/GM130/RAB1/GTP/PLK1 0.051 0.058 -9999 0 -0.105 42 42
RAB1A 0.039 0.009 -9999 0 0 26 26
prophase 0 0 -9999 0 -9999 0 0
Aurora A/BORA -0.002 0.025 0.063 5 -0.068 38 43
mitotic prometaphase -0.001 0.004 0.018 19 -9999 0 19
proteasomal ubiquitin-dependent protein catabolic process -0.005 0.078 -9999 0 -0.271 27 27
microtubule-based process 0.014 0.051 0.096 1 -0.143 35 36
Golgi organization -0.003 0.036 0.08 2 -0.099 42 44
Cohesin/SA2 0.013 0.046 0.091 1 -0.096 59 60
PPP1CB/MYPT1 0.051 0.04 -9999 0 -0.137 22 22
KIF20A 0.032 0.017 -9999 0 0 125 125
APC/C/CDC20 0.016 0.05 -9999 0 -0.138 36 36
PPP2R1A 0.039 0.009 -9999 0 0 28 28
chromosome segregation -0.004 0.031 -9999 0 -0.099 34 34
PRC1 0.035 0.015 -9999 0 0 80 80
ECT2 0.034 0.114 0.217 129 -0.151 48 177
C13orf34 -0.002 0.029 0.066 4 -0.078 39 43
NUDC 0.001 0.052 -9999 0 -0.25 19 19
regulation of attachment of spindle microtubules to kinetochore -0.024 0.08 -9999 0 -0.205 67 67
spindle assembly -0.003 0.032 0.072 2 -0.091 40 42
spindle stabilization -0.002 0.02 0.046 3 -0.054 41 44
APC/C/HCDH1 0.031 0.012 -9999 0 -9999 0 0
MKLP2/PLK1 0.014 0.051 0.096 1 -0.144 35 36
CCNB1 0.026 0.027 -9999 0 -0.029 64 64
PPP1CB 0.04 0.008 -9999 0 0 22 22
BTRC 0.04 0.007 -9999 0 0 17 17
ROCK2 -0.007 0.093 -9999 0 -0.329 38 38
TUBG1 -0.003 0.053 -9999 0 -0.211 29 29
G2/M transition of mitotic cell cycle -0.037 0.097 -9999 0 -0.211 112 112
MLF1IP -0.008 0.007 0.012 12 -9999 0 12
INCENP 0.04 0.005 -9999 0 0 6 6
Reelin signaling pathway

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
CDK5R1/CDK5 0.045 0.04 -9999 0 -0.132 19 19
VLDLR 0.032 0.017 -9999 0 0 121 121
CRKL 0.038 0.01 -9999 0 0 36 36
LRPAP1 0.036 0.014 -9999 0 0 72 72
FYN 0.034 0.016 -9999 0 0 94 94
ITGA3 0.034 0.016 -9999 0 0 98 98
RELN/VLDLR/Fyn 0.033 0.067 -9999 0 -0.129 53 53
MAPK8IP1/MKK7/MAP3K11/JNK1 0.091 0.062 -9999 0 -0.109 18 18
AKT1 0.003 0.072 -9999 0 -0.167 54 54
MAP2K7 0.038 0.011 -9999 0 0 41 41
RAPGEF1 0.039 0.009 -9999 0 0 26 26
DAB1 0.04 0.008 -9999 0 0 21 21
RELN/LRP8/DAB1 0.059 0.038 -9999 0 -0.103 6 6
LRPAP1/LRP8 0.041 0.051 -9999 0 -0.139 35 35
RELN/LRP8/DAB1/Fyn 0.065 0.055 -9999 0 -0.103 33 33
DAB1/alpha3/beta1 Integrin 0.029 0.082 -9999 0 -0.176 12 12
long-term memory 0.069 0.069 -9999 0 -0.11 32 32
DAB1/LIS1 0.058 0.081 -9999 0 -0.112 56 56
DAB1/CRLK/C3G 0.046 0.072 -9999 0 -0.182 2 2
PIK3CA 0.029 0.019 -9999 0 0 166 166
DAB1/NCK2 0.064 0.081 -9999 0 -0.181 2 2
ARHGEF2 0.038 0.011 -9999 0 0 39 39
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -9999 0 0
GRIN2A 0.033 0.017 -9999 0 0 111 111
CDK5R1 0.038 0.011 -9999 0 0 40 40
RELN 0.034 0.016 -9999 0 0 96 96
PIK3R1 0.034 0.016 -9999 0 0 99 99
RELN/LRP8/Fyn 0.046 0.056 -9999 0 -0.116 34 34
GRIN2A/RELN/LRP8/DAB1/Fyn 0.073 0.069 -9999 0 -0.109 35 35
MAPK8 0.039 0.009 -9999 0 0 29 29
RELN/VLDLR/DAB1 0.043 0.054 -9999 0 -0.103 38 38
ITGB1 0.038 0.01 -9999 0 0 36 36
MAP1B -0.002 0.062 0.209 21 -0.196 4 25
RELN/LRP8 0.05 0.054 -9999 0 -0.118 29 29
GRIN2B/RELN/LRP8/DAB1/Fyn 0.077 0.067 -9999 0 -0.109 29 29
PI3K 0.023 0.06 -9999 0 -0.15 44 44
mol:PP2 0 0 -9999 0 -9999 0 0
alpha3/beta1 Integrin 0.03 0.065 -9999 0 -0.135 68 68
RAP1A -0.008 0.088 0.281 21 -9999 0 21
PAFAH1B1 0.038 0.012 -9999 0 0 49 49
MAPK8IP1 0.039 0.009 -9999 0 0 30 30
CRLK/C3G 0.055 0.019 -9999 0 -9999 0 0
GRIN2B 0.037 0.013 -9999 0 0 59 59
NCK2 0.041 0.004 -9999 0 0 6 6
neuron differentiation 0.022 0.059 0.168 2 -0.219 9 11
neuron adhesion -0.016 0.097 0.271 26 -0.246 1 27
LRP8 0.039 0.01 -9999 0 0 35 35
GSK3B -0.002 0.074 0.185 7 -0.258 13 20
RELN/VLDLR/DAB1/Fyn 0.05 0.067 -9999 0 -0.113 52 52
MAP3K11 0.04 0.007 -9999 0 0 14 14
RELN/VLDLR/DAB1/P13K -0.003 0.066 -9999 0 -0.165 57 57
CDK5 0.036 0.014 -9999 0 0 69 69
MAPT -0.004 0.074 0.742 5 -9999 0 5
neuron migration -0.001 0.088 0.257 15 -0.243 13 28
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.022 0.058 0.168 2 -0.198 10 12
RELN/VLDLR 0.053 0.072 -9999 0 -0.112 60 60
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.031 0.202 0.327 23 -0.976 21 44
VDR 0.038 0.011 -9999 0 0 43 43
FAM120B 0 0 -9999 0 -9999 0 0
RXRs/LXRs/DNA/9cRA 0.022 0.092 -9999 0 -0.228 53 53
RXRs/LXRs/DNA/Oxysterols 0.012 0.127 -9999 0 -0.342 55 55
MED1 0 0 -9999 0 -9999 0 0
mol:9cRA 0.001 0.015 0.037 2 -0.045 48 50
RARs/THRs/DNA/Src-1 -0.004 0.093 -9999 0 -0.259 34 34
RXRs/NUR77 0.074 0.071 -9999 0 -0.108 38 38
RXRs/PPAR 0.014 0.059 -9999 0 -0.167 20 20
NCOR2 0.039 0.01 -9999 0 0 31 31
VDR/VDR/Vit D3 0.023 0.031 -9999 0 -0.125 22 22
RARs/VDR/DNA/Vit D3 0.065 0.068 -9999 0 -0.111 59 59
RARA 0.039 0.01 -9999 0 0 31 31
NCOA1 0.04 0.008 -9999 0 0 22 22
VDR/VDR/DNA 0.038 0.011 -9999 0 0 43 43
RARs/RARs/DNA/9cRA 0.05 0.053 -9999 0 -0.102 46 46
RARG 0.039 0.009 -9999 0 0 26 26
RPS6KB1 -0.012 0.109 0.56 9 -0.399 21 30
RARs/THRs/DNA/SMRT -0.002 0.088 -9999 0 -0.173 102 102
THRA 0.039 0.01 -9999 0 0 34 34
mol:Bile acids 0 0 -9999 0 -9999 0 0
VDR/Vit D3/DNA 0.023 0.031 -9999 0 -0.125 22 22
RXRs/PPAR/9cRA/PGJ2/DNA 0.063 0.077 0.294 10 -0.146 33 43
NR1H4 0.04 0.006 -9999 0 0 11 11
RXRs/LXRs/DNA 0.092 0.103 -9999 0 -0.192 37 37
NR1H2 0.034 0.031 -9999 0 -0.058 50 50
NR1H3 0.035 0.034 -9999 0 -0.063 53 53
RXRs/VDR/DNA/Vit D3 0.071 0.07 -9999 0 -0.104 47 47
NR4A1 0.034 0.016 -9999 0 0 98 98
mol:ATRA 0 0 -9999 0 -9999 0 0
RXRs/FXR/9cRA/MED1 0.02 0.043 -9999 0 -0.138 10 10
RXRG 0.031 0.03 -9999 0 -0.055 43 43
RXR alpha/CCPG 0.025 0.022 -9999 0 -0.038 40 40
RXRA 0.034 0.031 -9999 0 -0.056 47 47
RXRB 0.036 0.033 -9999 0 -0.06 56 56
THRB 0.033 0.016 -9999 0 0 107 107
PPARG 0.039 0.01 -9999 0 0 32 32
PPARD 0.04 0.006 -9999 0 0 13 13
TNF 0.004 0.126 -9999 0 -0.515 8 8
mol:Oxysterols 0 0.014 -9999 0 -0.04 57 57
cholesterol transport 0.013 0.126 -9999 0 -0.339 55 55
PPARA 0.032 0.017 -9999 0 0 126 126
mol:Vit D3 0 0 -9999 0 -9999 0 0
RARB 0.036 0.014 -9999 0 0 75 75
RXRs/NUR77/BCL2 0.019 0.045 -9999 0 -0.132 24 24
SREBF1 0.004 0.122 -9999 0 -0.351 44 44
RXRs/RXRs/DNA/9cRA 0.063 0.077 0.288 10 -0.146 33 43
ABCA1 -0.045 0.259 -9999 0 -0.816 53 53
RARs/THRs 0.068 0.091 -9999 0 -0.123 81 81
RXRs/FXR 0.085 0.067 -9999 0 -0.106 32 32
BCL2 0.036 0.014 -9999 0 0 67 67
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.05 0.021 -9999 0 -0.109 5 5
response to insulin stimulus 0 0 -9999 0 -9999 0 0
RIPK1 0.039 0.01 -9999 0 0 32 32
response to stress 0 0 -9999 0 -9999 0 0
MAP2K6 0.034 0.016 -9999 0 0 94 94
mol:GTP 0 0 -9999 0 -9999 0 0
MAP2K4 0.036 0.013 -9999 0 0 65 65
RAC1-CDC42/GTP/PAK family 0.007 0.04 -9999 0 -0.139 27 27
response to UV 0 0 -9999 0 -9999 0 0
YES1 0.037 0.012 -9999 0 0 51 51
interleukin-1 receptor activity 0 0 -9999 0 -9999 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -9999 0 0
MAP3K3 0.04 0.007 -9999 0 0 14 14
FYN 0.034 0.016 -9999 0 0 94 94
MAP3K12 0.04 0.006 -9999 0 0 13 13
FGR 0.04 0.007 -9999 0 0 15 15
p38 alpha/TAB1 -0.002 0.121 0.212 1 -0.261 60 61
PRKG1 0.039 0.009 -9999 0 0 30 30
DUSP8 0.039 0.009 -9999 0 0 30 30
PGK/cGMP/p38 alpha -0.007 0.116 0.194 1 -0.256 61 62
apoptosis -0.003 0.116 0.204 1 -0.251 60 61
RAL/GTP 0.046 0.036 -9999 0 -0.112 24 24
LYN 0.035 0.015 -9999 0 0 83 83
DUSP1 0.026 0.02 -9999 0 0 196 196
PAK1 0.036 0.013 -9999 0 0 65 65
SRC 0.039 0.009 -9999 0 0 28 28
RAC1/OSM/MEKK3/MKK3 0.091 0.038 -9999 0 -0.11 1 1
TRAF6 0.04 0.008 -9999 0 0 19 19
RAC1 0.039 0.009 -9999 0 0 28 28
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 0.041 0.005 -9999 0 0 9 9
RAC1-CDC42/GTP 0.05 0.02 -9999 0 -0.138 3 3
MAPK11 -0.032 0.126 0.214 1 -0.283 72 73
BLK 0.033 0.017 -9999 0 0 114 114
HCK 0.036 0.013 -9999 0 0 65 65
MAP2K3 0.038 0.011 -9999 0 0 43 43
DUSP16 0.036 0.014 -9999 0 0 75 75
DUSP10 0.034 0.016 -9999 0 0 102 102
TRAF6/MEKK3 0.048 0.021 -9999 0 -0.097 8 8
MAP3K7IP1 0.037 0.012 -9999 0 0 51 51
MAPK14 -0.015 0.122 0.199 2 -0.276 63 65
positive regulation of innate immune response -0.028 0.143 0.23 2 -0.328 65 67
LCK 0.039 0.009 -9999 0 0 25 25
p38alpha-beta/MKP7 -0.019 0.141 -9999 0 -0.318 63 63
p38alpha-beta/MKP5 -0.023 0.146 -9999 0 -0.31 72 72
PGK/cGMP 0.029 0.007 -9999 0 -9999 0 0
PAK2 0.033 0.017 -9999 0 0 111 111
p38alpha-beta/MKP1 -0.029 0.142 0.257 1 -0.327 66 67
CDC42 0.04 0.007 -9999 0 0 18 18
RALB 0.039 0.009 -9999 0 0 25 25
RALA 0.04 0.008 -9999 0 0 19 19
PAK3 0.037 0.013 -9999 0 0 60 60
Regulation of Telomerase

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
Telomerase catalytic core complex -0.031 0.175 -9999 0 -0.499 23 23
RAD9A 0.041 0.004 -9999 0 0 5 5
AP1 0.002 0.083 -9999 0 -0.147 113 113
IFNAR2 0.029 0.028 -9999 0 -0.033 74 74
AKT1 0.012 0.037 -9999 0 -0.154 5 5
ER alpha/Oestrogen 0.012 0.043 -9999 0 -0.124 42 42
NFX1/SIN3/HDAC complex 0.002 0.079 -9999 0 -0.267 26 26
EGF 0.038 0.011 -9999 0 0 38 38
SMG5 0 0 -9999 0 -9999 0 0
SMG6 0 0 -9999 0 -9999 0 0
SP3/HDAC2 0.044 0.043 -9999 0 -0.132 6 6
TERT/c-Abl -0.021 0.177 -9999 0 -0.474 25 25
SAP18 0.039 0.009 -9999 0 0 24 24
MRN complex 0.048 0.071 -9999 0 -0.146 50 50
WT1 0.029 0.027 -9999 0 -0.033 71 71
WRN 0.033 0.016 -9999 0 0 108 108
SP1 0.031 0.03 -9999 0 -0.041 77 77
SP3 0.04 0.008 -9999 0 -0.005 12 12
TERF2IP 0.037 0.013 -9999 0 0 61 61
Telomerase/Nucleolin -0.019 0.175 -9999 0 -0.44 31 31
Mad/Max 0.054 0.025 -9999 0 -9999 0 0
TERT -0.035 0.176 -9999 0 -0.513 22 22
CCND1 -0.114 0.368 -9999 0 -0.965 81 81
MAX 0.04 0.008 -9999 0 -0.005 14 14
RBBP7 0.039 0.009 -9999 0 0 25 25
RBBP4 0.038 0.011 -9999 0 0 40 40
TERF2 0.036 0.02 0.094 43 0 55 98
PTGES3 0.037 0.012 -9999 0 0 55 55
SIN3A 0.039 0.009 -9999 0 0 30 30
Telomerase/911 0.022 0.078 -9999 0 -0.285 20 20
CDKN1B 0 0.083 0.194 8 -0.323 21 29
RAD1 0.037 0.012 -9999 0 0 51 51
XRCC5 0.038 0.011 -9999 0 0 41 41
XRCC6 0.036 0.014 -9999 0 0 69 69
SAP30 0.038 0.011 -9999 0 0 46 46
TRF2/PARP2 0.049 0.035 -9999 0 -0.128 10 10
UBE3A 0.038 0.011 -9999 0 0 35 35
JUN 0.035 0.015 -9999 0 -0.03 2 2
E6 -0.001 0.004 -9999 0 -9999 0 0
HPV-16 E6/E6AP 0.022 0.022 -9999 0 -0.124 2 2
FOS 0.025 0.02 -9999 0 -0.001 205 205
IFN-gamma/IRF1 0.024 0.081 -9999 0 -0.153 81 81
PARP2 0.038 0.011 -9999 0 0 40 40
BLM 0.036 0.013 -9999 0 0 66 66
Telomerase 0.003 0.062 -9999 0 -0.258 19 19
IRF1 0.029 0.04 -9999 0 -0.142 20 20
ESR1 0.034 0.015 -9999 0 0 91 91
KU/TER 0.04 0.056 -9999 0 -0.162 33 33
ATM/TRF2 0.038 0.056 -9999 0 -0.14 41 41
ubiquitin-dependent protein catabolic process 0.003 0.084 0.176 4 -0.256 27 31
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.002 0.085 0.177 4 -0.262 27 31
HDAC1 0.037 0.012 -9999 0 0 49 49
HDAC2 0.03 0.03 -9999 0 -0.04 74 74
ATM 0.005 0.065 -9999 0 -0.24 33 33
SMAD3 -0.012 0.016 0.025 70 -9999 0 70
ABL1 0.039 0.01 -9999 0 0 32 32
MXD1 0.04 0.008 -9999 0 -0.002 16 16
MRE11A 0.038 0.012 -9999 0 0 49 49
HUS1 0.04 0.006 -9999 0 0 10 10
RPS6KB1 0.038 0.01 -9999 0 0 37 37
TERT/NF kappa B1/14-3-3 -0.007 0.185 -9999 0 -0.494 18 18
NR2F2 0.039 0.012 -9999 0 0 34 34
MAPK3 -0.016 0.014 0.021 50 -0.039 8 58
MAPK1 -0.016 0.014 0.021 45 -0.039 6 51
TGFB1/TGF beta receptor Type II 0.036 0.014 -9999 0 0 69 69
NFKB1 0.036 0.013 -9999 0 0 66 66
HNRNPC 0 0 -9999 0 -9999 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.005 0.065 -9999 0 -0.24 33 33
NBN 0.035 0.015 -9999 0 0 87 87
EGFR 0.036 0.014 -9999 0 0 67 67
mol:Oestrogen 0 0.002 -9999 0 -9999 0 0
EGF/EGFR 0.041 0.051 -9999 0 -0.135 35 35
MYC 0.023 0.021 -9999 0 0 245 245
IL2 0.03 0.031 -9999 0 -0.042 77 77
KU 0.04 0.056 -9999 0 -0.162 33 33
RAD50 0.039 0.01 -9999 0 0 35 35
HSP90AA1 0 0 -9999 0 -9999 0 0
TGFB1 0.036 0.014 -9999 0 0 69 69
TRF2/BLM 0.045 0.042 -9999 0 -0.127 20 20
FRAP1 0.039 0.009 -9999 0 0 28 28
KU/TERT -0.015 0.186 -9999 0 -0.478 25 25
SP1/HDAC2 0.043 0.05 -9999 0 -0.113 16 16
PINX1 0.032 0.017 -9999 0 0 117 117
Telomerase/EST1A -0.025 0.163 -9999 0 -0.432 30 30
Smad3/Myc 0.016 0.038 -9999 0 -0.144 18 18
911 complex 0.072 0.034 -9999 0 -0.116 8 8
IFNG 0.034 0.035 0.111 2 -0.111 24 26
Telomerase/PinX1 -0.026 0.166 -9999 0 -0.43 30 30
Telomerase/AKT1/mTOR/p70S6K 0.001 0.096 -9999 0 -0.264 36 36
SIN3B 0.036 0.014 -9999 0 0 67 67
YWHAE 0.037 0.013 -9999 0 0 58 58
Telomerase/EST1B -0.025 0.163 -9999 0 -0.432 30 30
response to DNA damage stimulus 0 0.035 0.104 3 -0.105 49 52
MRN complex/TRF2/Rap1 0.067 0.08 -9999 0 -0.136 37 37
TRF2/WRN 0.04 0.041 -9999 0 -0.109 23 23
Telomerase/hnRNP C1/C2 -0.025 0.163 -9999 0 -0.432 30 30
E2F1 0.03 0.027 -9999 0 -0.033 73 73
ZNFX1 0 0.001 -9999 0 -9999 0 0
PIF1 0 0 -9999 0 -9999 0 0
NCL 0.039 0.009 -9999 0 0 29 29
DKC1 0.04 0.008 -9999 0 0 20 20
telomeric DNA binding 0 0 -9999 0 -9999 0 0
ErbB2/ErbB3 signaling events

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
USP8 -0.012 0.011 0.016 40 -9999 0 40
RAS family/GTP 0.023 0.102 0.229 1 -0.207 28 29
NFATC4 -0.011 0.09 0.267 26 -0.181 4 30
ERBB2IP 0.036 0.015 -9999 0 -0.003 64 64
HSP90 (dimer) 0 0 -9999 0 -9999 0 0
mammary gland morphogenesis 0.001 0.08 0.195 15 -0.154 51 66
JUN 0.012 0.088 0.225 12 -9999 0 12
HRAS 0.039 0.01 -9999 0 0 31 31
DOCK7 -0.02 0.084 0.206 22 -0.209 10 32
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.041 0.078 0.207 25 -0.122 62 87
AKT1 -0.005 0.012 0.021 39 -9999 0 39
BAD -0.014 0.007 0.011 20 -9999 0 20
MAPK10 -0.003 0.078 0.21 35 -0.153 2 37
mol:GTP 0 0.002 -9999 0 -9999 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.003 0.086 0.21 15 -0.164 49 64
RAF1 0.011 0.106 0.248 22 -0.229 27 49
ErbB2/ErbB3/neuregulin 2 0.028 0.071 0.186 30 -0.122 70 100
STAT3 -0.023 0.247 -9999 0 -0.914 38 38
cell migration -0.003 0.081 0.218 33 -0.179 10 43
mol:PI-3-4-5-P3 -0.001 0.002 0.016 1 -9999 0 1
cell proliferation -0.023 0.232 0.409 3 -0.544 54 57
FOS -0.029 0.219 0.334 10 -0.399 124 134
NRAS 0.039 0.009 -9999 0 0 30 30
mol:Ca2+ 0.001 0.08 0.195 15 -0.154 51 66
MAPK3 -0.006 0.186 0.358 5 -0.467 41 46
MAPK1 -0.016 0.194 0.363 4 -0.471 47 51
JAK2 -0.019 0.081 0.241 14 -0.233 6 20
NF2 0.005 0.076 -9999 0 -0.688 6 6
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0 0.073 0.179 4 -0.173 62 66
NRG1 0.036 0.014 -9999 0 0 74 74
GRB2/SOS1 0.047 0.044 -9999 0 -0.143 24 24
MAPK8 -0.017 0.106 0.237 5 -0.222 71 76
MAPK9 -0.007 0.077 0.206 32 -0.16 4 36
ERBB2 -0.024 0.04 0.261 9 -9999 0 9
ERBB3 0.031 0.018 -9999 0 0 134 134
SHC1 0.04 0.008 -9999 0 0 23 23
RAC1 0.039 0.009 -9999 0 0 28 28
apoptosis 0.005 0.025 0.18 1 -0.206 6 7
STAT3 (dimer) -0.019 0.241 -9999 0 -0.89 38 38
RNF41 -0.016 0.015 0.048 10 -9999 0 10
FRAP1 -0.014 0.008 0.011 20 -9999 0 20
RAC1-CDC42/GTP -0.029 0.056 0.088 29 -0.138 44 73
ErbB2/ErbB2/HSP90 (dimer) -0.023 0.015 0.019 7 -0.12 5 12
CHRNA1 0.01 0.151 0.348 4 -0.352 33 37
myelination -0.004 0.108 0.286 38 -0.212 2 40
PPP3CB -0.016 0.082 0.198 25 -0.199 4 29
KRAS 0.034 0.016 -9999 0 0 95 95
RAC1-CDC42/GDP 0.027 0.097 0.208 1 -0.168 64 65
NRG2 0.041 0.005 -9999 0 0 8 8
mol:GDP 0 0.072 0.179 4 -0.172 62 66
SOS1 0.037 0.012 -9999 0 0 51 51
MAP2K2 -0.002 0.104 0.214 35 -0.221 43 78
SRC 0.039 0.009 -9999 0 0 28 28
mol:cAMP -0.001 0.001 -9999 0 -9999 0 0
PTPN11 -0.019 0.086 0.24 15 -0.203 10 25
MAP2K1 -0.01 0.189 0.375 1 -0.496 32 33
heart morphogenesis 0.001 0.08 0.195 15 -0.154 51 66
RAS family/GDP 0.032 0.102 0.231 1 -0.18 48 49
GRB2 0.04 0.008 -9999 0 0 21 21
PRKACA 0.008 0.079 -9999 0 -0.721 6 6
CHRNE 0.009 0.024 0.084 8 -9999 0 8
HSP90AA1 0 0 -9999 0 -9999 0 0
activation of caspase activity 0.005 0.012 -9999 0 -0.021 39 39
nervous system development 0.001 0.08 0.195 15 -0.154 51 66
CDC42 0.04 0.007 -9999 0 0 18 18
Canonical NF-kappaB 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
FBXW11 0.036 0.027 0.081 2 -0.069 29 31
mol:GTP 0 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.003 0.123 0.258 3 -0.27 57 60
ERC1 0 0 -9999 0 -9999 0 0
RIP2/NOD2 0.014 0.041 -9999 0 -0.125 41 41
NFKBIA -0.036 0.063 0.207 3 -0.272 29 32
BIRC2 0.036 0.014 -9999 0 0 72 72
IKBKB 0.038 0.011 -9999 0 0 41 41
RIPK2 0.032 0.017 -9999 0 0 119 119
IKBKG -0.003 0.108 -9999 0 -0.289 49 49
IKK complex/A20 0.035 0.123 -9999 0 -0.312 30 30
NEMO/A20/RIP2 0.032 0.017 -9999 0 0 119 119
XPO1 0.039 0.01 -9999 0 0 35 35
NEMO/ATM 0.006 0.124 -9999 0 -0.346 36 36
tumor necrosis factor receptor activity 0 0 -9999 0 -9999 0 0
RAN 0.04 0.008 -9999 0 0 21 21
Exportin 1/RanGTP 0.045 0.035 -9999 0 -0.108 24 24
IKK complex/ELKS 0.008 0.113 -9999 0 -0.283 47 47
BCL10/MALT1/TRAF6 0.065 0.047 -9999 0 -0.124 20 20
NOD2 0 0 -9999 0 -9999 0 0
NFKB1 0.033 0.027 -9999 0 -0.071 25 25
RELA 0.036 0.028 0.08 3 -0.068 33 36
MALT1 0.036 0.014 -9999 0 0 70 70
cIAP1/UbcH5C 0.04 0.053 -9999 0 -0.136 39 39
ATM 0.036 0.014 -9999 0 0 69 69
TNF/TNFR1A 0.047 0.038 -9999 0 -0.134 16 16
TRAF6 0.04 0.008 -9999 0 0 19 19
PRKCA 0.035 0.015 -9999 0 0 86 86
CHUK 0.038 0.011 -9999 0 0 46 46
UBE2D3 0.039 0.009 -9999 0 0 30 30
TNF 0.04 0.008 -9999 0 0 22 22
NF kappa B1 p50/RelA 0.058 0.08 -9999 0 -0.151 60 60
BCL10 0.041 0.005 -9999 0 0 8 8
proteasomal ubiquitin-dependent protein catabolic process -0.035 0.063 0.207 3 -0.271 29 32
beta TrCP1/SCF ubiquitin ligase complex 0.036 0.027 0.081 2 -0.069 29 31
TNFRSF1A 0.036 0.014 -9999 0 0 72 72
IKK complex 0.022 0.127 -9999 0 -0.299 47 47
CYLD 0.038 0.011 -9999 0 0 46 46
IKK complex/PKC alpha 0.023 0.132 -9999 0 -0.317 39 39
Regulation of Androgen receptor activity

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
HDAC1 -0.018 0.007 -9999 0 -9999 0 0
SMARCC1 -0.01 0.166 -9999 0 -1.102 12 12
REL 0.039 0.007 -9999 0 0 15 15
HDAC7 -0.049 0.088 0.167 7 -0.216 73 80
JUN 0.036 0.014 -9999 0 0 76 76
EP300 0.036 0.014 -9999 0 0 69 69
KAT2B 0 0 -9999 0 -9999 0 0
KAT5 0 0 -9999 0 -9999 0 0
MAPK14 -0.014 0.018 0.038 6 -0.053 1 7
FOXO1 0 0 -9999 0 -9999 0 0
T-DHT/AR -0.005 0.12 0.261 2 -0.217 86 88
MAP2K6 0.028 0.025 -9999 0 -0.012 146 146
BRM/BAF57 0.031 0.06 -9999 0 -0.132 55 55
MAP2K4 0.03 0.024 -9999 0 -0.015 115 115
SMARCA2 0.032 0.018 -9999 0 -9999 0 0
PDE9A -0.087 0.32 -9999 0 -0.831 82 82
NCOA2 0.037 0.013 -9999 0 0 60 60
CEBPA 0.037 0.012 -9999 0 0 54 54
EHMT2 0.041 0.007 -9999 0 0 14 14
cell proliferation -0.024 0.122 0.284 10 -0.308 36 46
NR0B1 0.038 0.01 -9999 0 0 38 38
EGR1 0.027 0.02 -9999 0 0 188 188
RXRs/9cRA 0.063 0.035 -9999 0 -0.103 3 3
AR/RACK1/Src -0.018 0.087 0.207 24 -0.219 21 45
AR/GR -0.014 0.091 0.203 2 -0.187 85 87
GNB2L1 0.039 0.009 -9999 0 0 30 30
PKN1 0.034 0.016 -9999 0 0 96 96
RCHY1 0.036 0.014 -9999 0 0 67 67
epidermal growth factor receptor activity 0 0 -9999 0 -9999 0 0
MAPK8 -0.014 0.02 0.042 4 -0.06 2 6
T-DHT/AR/TIF2/CARM1 0.002 0.085 0.231 2 -0.215 24 26
SRC -0.021 0.058 0.169 29 -0.153 7 36
NR3C1 0.038 0.011 -9999 0 0 42 42
KLK3 0.003 0.074 -9999 0 -9999 0 0
APPBP2 0.029 0.027 -9999 0 -0.033 67 67
TRIM24 0.039 0.011 -9999 0 0 39 39
T-DHT/AR/TIP60 -0.035 0.059 0.075 3 -0.16 59 62
TMPRSS2 0.014 0.105 -9999 0 -0.55 10 10
RXRG 0.035 0.015 -9999 0 0 81 81
mol:9cRA 0 0 -9999 0 -9999 0 0
RXRA 0.038 0.011 -9999 0 0 43 43
RXRB 0.041 0.005 -9999 0 0 8 8
CARM1 0.036 0.014 -9999 0 0 71 71
NR2C2 0.04 0.007 -9999 0 0 14 14
KLK2 -0.006 0.071 0.215 1 -0.275 8 9
AR -0.019 0.074 0.142 5 -0.187 65 70
SENP1 0.04 0.008 -9999 0 0 19 19
HSP90AA1 0 0 -9999 0 -9999 0 0
MDM2 0.037 0.01 -9999 0 0 36 36
SRY 0.04 0.002 -9999 0 0 2 2
GATA2 0.039 0.01 -9999 0 0 31 31
MYST2 0.04 0.008 -9999 0 0 20 20
HOXB13 0.039 0.011 -9999 0 -9999 0 0
T-DHT/AR/RACK1/Src -0.019 0.088 0.214 24 -0.227 21 45
positive regulation of transcription 0.039 0.01 -9999 0 0 31 31
DNAJA1 0.03 0.026 -9999 0 -0.033 67 67
proteasomal ubiquitin-dependent protein catabolic process -0.008 0.083 -9999 0 -0.258 49 49
NCOA1 0.042 0.032 0.124 1 -0.177 10 11
SPDEF 0.037 0.014 -9999 0 0 72 72
T-DHT/AR/TIF2 -0.017 0.093 0.202 5 -0.256 43 48
T-DHT/AR/Hsp90 -0.035 0.059 0.076 3 -0.16 59 62
GSK3B 0.039 0.008 -9999 0 0 23 23
NR2C1 0.038 0.01 -9999 0 0 33 33
mol:T-DHT -0.025 0.046 0.192 6 -0.156 8 14
SIRT1 0.04 0.007 -9999 0 0 16 16
ZMIZ2 -0.001 0.001 -9999 0 -0.012 1 1
POU2F1 0.032 0.057 0.12 2 -0.107 73 75
T-DHT/AR/DAX-1 -0.026 0.076 0.2 11 -0.212 25 36
CREBBP 0.037 0.012 -9999 0 0 53 53
SMARCE1 0.039 0.01 -9999 0 0 35 35
EGFR-dependent Endothelin 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
HRAS 0.039 0.01 -9999 0 0 31 31
EGFR 0.036 0.014 -9999 0 0 67 67
EGF/EGFR 0.046 0.057 -9999 0 -0.1 51 51
EGF/EGFR dimer/SHC/GRB2/SOS1 0.081 0.075 -9999 0 -0.113 49 49
mol:GTP 0 0 -9999 0 -9999 0 0
EDNRA 0.036 0.014 -9999 0 0 75 75
response to oxidative stress 0 0 -9999 0 -9999 0 0
EGF 0.038 0.01 -9999 0 0 38 38
EGF/EGFR dimer/SHC 0.059 0.054 -9999 0 -0.118 34 34
mol:GDP 0.073 0.071 -9999 0 -0.112 49 49
mol:Ca2+ 0 0 -9999 0 -9999 0 0
EDN1 0.034 0.015 -9999 0 0 89 89
GRB2/SOS1 0.047 0.044 -9999 0 -0.142 24 24
HRAS/GTP 0.048 0.06 -9999 0 -0.109 49 49
SHC1 0.039 0.008 -9999 0 0 23 23
HRAS/GDP 0.068 0.072 -9999 0 -0.113 46 46
FRAP1 -0.016 0.074 0.198 39 -0.18 4 43
EGF/EGFR dimer 0.041 0.05 -9999 0 -0.132 35 35
SOS1 0.037 0.012 -9999 0 0 51 51
GRB2 0.04 0.008 -9999 0 0 21 21
ETA receptor/Endothelin-1 0.038 0.046 -9999 0 -0.137 24 24
PDGFR-beta signaling pathway

Figure 78.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 80.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.058 0.104 0.296 20 -0.262 15 35
PDGFB-D/PDGFRB/SLAP 0.033 0.038 -9999 0 -0.133 10 10
PDGFB-D/PDGFRB/APS/CBL 0.047 0.024 -9999 0 -0.11 4 4
AKT1 0.033 0.108 0.251 53 -0.177 1 54
mol:PI-4-5-P2 0 0.001 -9999 0 -9999 0 0
mol:Sphingosine-1-phosphate 0.043 0.095 0.272 18 -0.303 13 31
PIK3CA 0.029 0.019 -9999 0 0 166 166
FGR 0.022 0.09 0.227 17 -0.394 12 29
mol:Ca2+ 0.025 0.09 0.251 15 -0.341 13 28
MYC 0.001 0.277 0.326 23 -0.66 71 94
SHC1 0.039 0.008 -9999 0 0 23 23
HRAS/GDP 0.039 0.057 0.181 43 -0.105 12 55
LRP1/PDGFRB/PDGFB 0.053 0.056 -9999 0 -0.116 35 35
GRB10 0.04 0.008 -9999 0 0 22 22
PTPN11 0.039 0.009 -9999 0 0 29 29
GO:0007205 0.024 0.09 0.25 15 -0.345 13 28
PTEN 0.038 0.01 -9999 0 0 36 36
GRB2 0.04 0.008 -9999 0 0 21 21
GRB7 0.037 0.013 -9999 0 0 57 57
PDGFB-D/PDGFRB/SHP2 0.046 0.042 -9999 0 -0.136 21 21
PDGFB-D/PDGFRB/GRB10 0.05 0.034 -9999 0 -0.147 9 9
cell cycle arrest 0.033 0.038 -9999 0 -0.133 10 10
HRAS 0.039 0.01 -9999 0 0 31 31
HIF1A 0.019 0.099 0.229 49 -0.197 5 54
GAB1 0.022 0.103 0.271 11 -0.276 24 35
mol:GTP 0 0 -9999 0 -9999 0 0
DNM2 0.024 0.112 0.248 44 -0.248 29 73
PDGFB-D/PDGFRB 0.055 0.051 -9999 0 -0.115 6 6
mol:GDP 0 0 -9999 0 -9999 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.047 0.04 -9999 0 -0.134 18 18
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.048 0.121 0.286 23 -0.245 40 63
positive regulation of MAPKKK cascade 0.046 0.042 -9999 0 -0.136 21 21
PIK3R1 0.034 0.016 -9999 0 0 99 99
mol:IP3 0.025 0.091 0.252 15 -0.348 13 28
E5 0 0.002 -9999 0 -9999 0 0
CSK 0.038 0.011 -9999 0 -0.005 29 29
PDGFB-D/PDGFRB/GRB7 0.046 0.036 -9999 0 -0.135 11 11
SHB 0.04 0.006 -9999 0 0 11 11
BLK -0.039 0.164 0.261 3 -0.373 91 94
PTPN2 0.039 0.014 -9999 0 -0.013 34 34
PDGFB-D/PDGFRB/SNX15 0.053 0.025 -9999 0 -0.136 3 3
BCAR1 0.036 0.013 -9999 0 0 65 65
VAV2 0.007 0.132 0.27 16 -0.312 51 67
CBL 0.04 0.008 -9999 0 0 20 20
PDGFB-D/PDGFRB/DEP1 0.046 0.04 -9999 0 -0.132 19 19
LCK 0.026 0.077 0.265 5 -0.364 7 12
PDGFRB 0.036 0.019 0.068 1 -0.006 81 82
ACP1 0.039 0.01 -9999 0 0 34 34
HCK 0.014 0.092 0.335 1 -0.466 12 13
ABL1 0.018 0.092 0.244 18 -0.233 24 42
PDGFB-D/PDGFRB/CBL 0.021 0.108 0.29 6 -0.308 25 31
PTPN1 0.035 0.017 -9999 0 -0.007 70 70
SNX15 0.041 0.004 -9999 0 0 6 6
STAT3 0.038 0.011 -9999 0 0 41 41
STAT1 0.034 0.016 -9999 0 0 102 102
cell proliferation 0.009 0.253 0.307 30 -0.59 71 101
SLA 0.028 0.019 -9999 0 0 179 179
actin cytoskeleton reorganization 0.008 0.093 0.223 62 -0.18 1 63
SRC 0.024 0.053 0.334 1 -9999 0 1
PI3K -0.026 0.036 -9999 0 -0.119 35 35
PDGFB-D/PDGFRB/GRB7/SHC 0.061 0.044 -9999 0 -0.118 12 12
SH2B2 0 0 -9999 0 -9999 0 0
PLCgamma1/SPHK1 0.043 0.097 0.278 17 -0.311 13 30
LYN -0.001 0.118 0.278 2 -0.423 31 33
LRP1 0.036 0.014 -9999 0 0 69 69
SOS1 0.037 0.012 -9999 0 0 51 51
STAT5B 0.039 0.009 -9999 0 0 27 27
STAT5A 0.038 0.01 -9999 0 0 36 36
NCK1-2/p130 Cas 0.073 0.074 -9999 0 -0.117 21 21
SPHK1 0.041 0.009 0.063 1 0 24 25
EDG1 0.042 0.007 0.063 1 0 11 12
mol:DAG 0.025 0.091 0.252 15 -0.348 13 28
PLCG1 0.024 0.092 0.253 15 -0.355 13 28
NHERF/PDGFRB 0.057 0.049 -9999 0 -0.118 19 19
YES1 0.003 0.122 0.262 5 -0.428 30 35
cell migration 0.056 0.049 -9999 0 -0.118 19 19
SHC/Grb2/SOS1 0.083 0.071 -9999 0 -0.126 21 21
SLC9A3R2 0.037 0.012 -9999 0 0 54 54
SLC9A3R1 0.038 0.012 -9999 0 0 49 49
NHERF1-2/PDGFRB/PTEN 0.075 0.058 -9999 0 -0.113 30 30
FYN -0.012 0.132 0.261 3 -0.392 48 51
DOK1 0.006 0.067 0.188 52 -9999 0 52
HRAS/GTP 0.029 0.007 -9999 0 -9999 0 0
PDGFB 0.037 0.012 -9999 0 0 54 54
RAC1 -0.032 0.235 0.289 10 -0.53 76 86
PRKCD 0.006 0.067 0.191 50 -9999 0 50
FER 0.006 0.066 0.187 50 -9999 0 50
MAPKKK cascade 0 0.083 0.235 32 -0.175 4 36
RASA1 0.006 0.065 0.187 48 -9999 0 48
NCK1 0.036 0.014 -9999 0 0 70 70
NCK2 0.041 0.004 -9999 0 0 6 6
p62DOK/Csk 0.054 0.056 0.194 54 -0.109 11 65
PDGFB-D/PDGFRB/SHB 0.052 0.026 -9999 0 -0.136 3 3
chemotaxis 0.019 0.091 0.242 18 -0.228 24 42
STAT1-3-5/STAT1-3-5 0.051 0.079 -9999 0 -0.124 52 52
Bovine Papilomavirus E5/PDGFRB 0.025 0.019 -9999 0 -0.035 24 24
PTPRJ 0.039 0.01 -9999 0 0 33 33
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.063 0.067 -9999 0 -0.11 44 44
MAP4K1 0.036 0.014 -9999 0 0 67 67
MAP3K8 0.039 0.008 -9999 0 0 24 24
PRKCB 0 0 -9999 0 -9999 0 0
DBNL 0.04 0.006 -9999 0 0 12 12
CRKL 0.038 0.01 -9999 0 0 36 36
MAP3K1 0.007 0.066 0.174 2 -0.176 45 47
JUN -0.004 0.106 -9999 0 -0.499 21 21
MAP3K7 0.008 0.067 0.195 5 -0.221 18 23
GRAP2 0.037 0.013 -9999 0 0 56 56
CRK 0.038 0.012 -9999 0 0 49 49
MAP2K4 0 0.083 0.173 7 -0.27 26 33
LAT 0.04 0.006 -9999 0 0 11 11
LCP2 0.034 0.016 -9999 0 0 101 101
MAPK8 0.001 0.112 -9999 0 -0.539 21 21
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.019 0.068 -9999 0 -0.163 49 49
LAT/GRAP2/SLP76/HPK1/HIP-55 0.072 0.077 -9999 0 -0.114 42 42
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.017 0.136 0.26 3 -0.336 38 41
CaM/Ca2+ 0.028 0.016 -9999 0 -0.125 5 5
AKT1 0.039 0.01 -9999 0 0 34 34
AKT2 0.037 0.012 -9999 0 0 54 54
STXBP4 0.038 0.011 -9999 0 0 43 43
mol:GTP 0 0 -9999 0 -9999 0 0
mol:glucose 0.004 0.135 0.251 3 -0.362 38 41
YWHAZ 0.034 0.016 -9999 0 0 96 96
CALM1 0.039 0.009 -9999 0 0 26 26
YWHAQ 0.04 0.007 -9999 0 0 18 18
TBC1D4 -0.018 0.007 -9999 0 -9999 0 0
mol:Ca2+ 0 0 -9999 0 -9999 0 0
YWHAH 0.038 0.011 -9999 0 0 46 46
YWHAB 0.038 0.011 -9999 0 0 45 45
SNARE/Synip 0.044 0.029 -9999 0 -0.109 9 9
YWHAG 0.039 0.009 -9999 0 0 25 25
ASIP 0.038 0.011 -9999 0 0 46 46
PRKCI 0.027 0.02 -9999 0 0 192 192
AS160/CaM/Ca2+ 0.028 0.016 -9999 0 -0.125 5 5
RHOQ 0.039 0.009 -9999 0 0 25 25
GYS1 0.007 0.021 0.253 1 -0.172 5 6
PRKCZ 0.039 0.009 -9999 0 0 27 27
TRIP10 0.038 0.012 -9999 0 0 49 49
TC10/GTP/CIP4/Exocyst 0.046 0.029 -9999 0 -0.109 12 12
AS160/14-3-3 0.014 0.083 0.187 3 -0.272 23 26
VAMP2 0.036 0.014 -9999 0 0 69 69
SLC2A4 0.001 0.148 0.269 2 -0.404 38 40
STX4 0 0 -9999 0 -9999 0 0
GSK3B 0.022 0.024 -9999 0 -0.196 5 5
SFN 0.035 0.015 -9999 0 0 83 83
LNPEP 0.035 0.014 -9999 0 0 77 77
YWHAE 0.037 0.013 -9999 0 0 58 58
mTOR signaling pathway

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
GBL 0.039 0.009 -9999 0 0 26 26
MKNK1 0.04 0.007 -9999 0 0 15 15
mol:PIP3 -0.013 0.037 0.139 2 -0.156 15 17
FRAP1 0.028 0.107 -9999 0 -0.415 23 23
AKT1 0.023 0.086 0.171 112 -0.173 10 122
INSR 0.038 0.012 -9999 0 0 49 49
Insulin Receptor/Insulin 0.047 0.023 -9999 0 -0.109 4 4
mol:GTP 0.054 0.092 0.24 31 -0.158 11 42
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.006 0.053 -9999 0 -0.185 30 30
TSC2 0.039 0.01 -9999 0 0 35 35
RHEB/GDP 0.03 0.069 0.159 6 -0.156 15 21
TSC1 0.039 0.01 -9999 0 0 31 31
Insulin Receptor/IRS1 0.034 0.031 -9999 0 -0.23 6 6
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.016 0.074 0.189 1 -0.217 28 29
mol:GDP 0 0 -9999 0 -9999 0 0
EIF3A 0 0 -9999 0 -9999 0 0
RPS6KB1 0.032 0.113 0.245 20 -0.326 26 46
MAP3K5 -0.006 0.061 0.186 5 -0.219 37 42
PIK3R1 0.034 0.016 -9999 0 0 99 99
apoptosis -0.006 0.061 0.186 5 -0.219 37 42
mol:LY294002 0 0 0.001 3 -0.001 6 9
EIF4B 0.028 0.105 0.246 16 -0.297 26 42
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.04 0.1 0.229 16 -0.266 29 45
eIF4E/eIF4G1/eIF4A1 0.012 0.065 -9999 0 -0.264 21 21
KIAA1303 0 0 -9999 0 -9999 0 0
PI3K 0.027 0.052 -9999 0 -0.146 18 18
mTOR/RHEB/GTP/Raptor/GBL 0.028 0.077 0.202 20 -0.18 23 43
FKBP1A 0.038 0.011 -9999 0 0 44 44
RHEB/GTP 0.052 0.087 0.234 19 -0.158 14 33
mol:Amino Acids 0 0 0.001 3 -0.001 6 9
FKBP12/Rapamycin 0.028 0.013 -9999 0 -0.127 2 2
PDPK1 0.01 0.077 0.158 99 -0.166 11 110
EIF4E 0.039 0.01 -9999 0 0 31 31
ASK1/PP5C 0.02 0.187 -9999 0 -0.565 43 43
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.005 0.108 -9999 0 -0.555 10 10
TSC1/TSC2 0.059 0.099 0.259 31 -0.168 11 42
tumor necrosis factor receptor activity 0 0 0.001 6 -0.001 3 9
RPS6 0.039 0.01 -9999 0 0 32 32
PPP5C 0.039 0.009 -9999 0 0 27 27
EIF4G1 0.032 0.017 -9999 0 0 116 116
IRS1 0.011 0.028 -9999 0 -0.24 6 6
INS 0.039 0.009 -9999 0 0 30 30
PTEN 0.038 0.01 -9999 0 0 36 36
PDK2 0.012 0.077 0.158 100 -0.169 10 110
EIF4EBP1 -0.036 0.271 -9999 0 -1.063 35 35
PIK3CA 0.029 0.019 -9999 0 0 166 166
PPP2R5D 0.028 0.104 0.277 4 -0.384 22 26
peptide biosynthetic process -0.014 0.029 0.189 9 -9999 0 9
RHEB 0.037 0.012 -9999 0 0 53 53
EIF4A1 0.038 0.011 -9999 0 0 42 42
mol:Rapamycin 0 0.001 0.003 51 -0.002 3 54
EEF2 -0.014 0.03 0.19 9 -9999 0 9
eIF4E/4E-BP1 -0.016 0.258 -9999 0 -0.991 35 35
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.041 0.25 0.481 1 -0.544 64 65
PCK1 -0.111 0.413 -9999 0 -1.05 78 78
HNF4A -0.077 0.348 0.595 2 -0.762 89 91
KCNJ11 -0.008 0.233 -9999 0 -0.521 37 37
AKT1 0.005 0.167 -9999 0 -0.315 42 42
response to starvation -0.015 0.043 -9999 0 -0.114 75 75
DLK1 -0.002 0.235 0.642 3 -0.529 35 38
NKX2-1 -0.002 0.147 0.349 3 -0.298 40 43
ACADM -0.055 0.27 0.54 1 -0.588 69 70
TAT -0.024 0.184 -9999 0 -0.529 17 17
CEBPB 0.039 0.017 -9999 0 -0.072 2 2
CEBPA 0.042 0.016 -9999 0 -0.069 2 2
TTR 0.035 0.168 0.619 2 -0.821 4 6
PKLR -0.028 0.245 0.477 4 -0.547 45 49
APOA1 -0.131 0.476 -9999 0 -1.069 95 95
CPT1C -0.036 0.241 -9999 0 -0.558 49 49
ALAS1 -0.005 0.163 -9999 0 -0.798 3 3
TFRC -0.063 0.365 -9999 0 -0.864 75 75
FOXF1 0.034 0.015 -9999 0 -9999 0 0
NF1 0.038 0.02 -9999 0 -0.155 1 1
HNF1A (dimer) 0.009 0.001 -9999 0 -9999 0 0
CPT1A -0.046 0.264 0.54 1 -0.574 66 67
HMGCS1 -0.034 0.261 0.501 3 -0.582 57 60
NR3C1 0.048 0.014 -9999 0 -9999 0 0
CPT1B -0.034 0.228 -9999 0 -0.573 42 42
chromatin remodeling 0 0 -9999 0 -9999 0 0
SP1 0.04 0.007 -9999 0 -9999 0 0
GCK -0.036 0.241 0.457 1 -0.555 48 49
CREB1 0.019 0.095 -9999 0 -0.207 77 77
IGFBP1 -0.004 0.149 -9999 0 -0.486 4 4
PDX1 0.009 0.141 0.395 1 -0.289 28 29
UCP2 -0.062 0.304 0.485 5 -0.654 81 86
ALDOB -0.007 0.23 -9999 0 -0.517 37 37
AFP 0.015 0.049 -9999 0 -9999 0 0
BDH1 -0.024 0.286 0.477 13 -0.597 64 77
HADH -0.008 0.229 -9999 0 -0.473 57 57
F2 -0.038 0.308 -9999 0 -0.742 37 37
HNF1A 0.009 0.001 -9999 0 -9999 0 0
G6PC 0.021 0.087 -9999 0 -9999 0 0
SLC2A2 0.028 0.165 -9999 0 -0.427 1 1
INS 0.029 0.013 0.177 1 -9999 0 1
FOXA1 0.055 0.016 -9999 0 -9999 0 0
FOXA3 0.019 0.122 -9999 0 -0.202 114 114
FOXA2 0.01 0.288 -9999 0 -0.555 54 54
ABCC8 -0.008 0.232 -9999 0 -0.517 37 37
ALB 0.015 0.049 -9999 0 -9999 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -9999 0 0
telencephalon oligodendrocyte cell migration -0.008 0.084 0.168 72 -9999 0 72
GNAI2 0.04 0.006 -9999 0 0 13 13
S1P/S1P5/G12 0.026 0.007 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
GNAO1 0.035 0.015 -9999 0 0 85 85
RhoA/GTP 0.008 0.085 -9999 0 -0.171 72 72
negative regulation of cAMP metabolic process -0.008 0.078 -9999 0 -0.183 69 69
GNAZ 0.038 0.011 -9999 0 0 46 46
GNAI3 0.038 0.011 -9999 0 0 45 45
GNA12 0.039 0.01 -9999 0 0 33 33
S1PR5 0 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
S1P/S1P5/Gi -0.008 0.078 -9999 0 -0.184 69 69
RhoA/GDP 0.029 0.014 -9999 0 -0.125 4 4
RHOA 0.04 0.006 -9999 0 0 13 13
GNAI1 0.034 0.015 -9999 0 0 93 93
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.038 0.01 -9999 0 0 36 36
RAS family/GTP/Tiam1 0.011 0.059 -9999 0 -0.161 38 38
NT3 (dimer)/TRKC 0.041 0.034 -9999 0 -0.134 7 7
NT3 (dimer)/TRKB 0.056 0.043 -9999 0 -0.116 8 8
SHC/Grb2/SOS1/GAB1/PI3K -0.002 0.079 -9999 0 -0.196 56 56
RAPGEF1 0.039 0.009 -9999 0 0 26 26
BDNF 0.04 0.006 -9999 0 0 12 12
PIK3CA 0.029 0.019 -9999 0 0 166 166
DYNLT1 0.036 0.014 -9999 0 0 75 75
NTRK1 0.04 0.007 -9999 0 0 16 16
NTRK2 0.039 0.01 -9999 0 0 35 35
NTRK3 0.038 0.011 -9999 0 0 45 45
NT-4/5 (dimer)/TRKB 0.05 0.017 -9999 0 -0.085 1 1
neuron apoptosis -0.031 0.099 0.246 27 -0.226 2 29
SHC 2-3/Grb2 0.032 0.105 0.235 2 -0.263 27 29
SHC1 0.039 0.008 -9999 0 0 23 23
SHC2 0.006 0.118 0.214 2 -0.346 47 49
SHC3 0.03 0.083 0.214 2 -0.399 13 15
STAT3 (dimer) 0.001 0.11 -9999 0 -0.265 79 79
NT3 (dimer)/TRKA 0.057 0.043 -9999 0 -0.116 8 8
RIN/GDP 0.044 0.083 0.218 18 -0.201 22 40
GIPC1 0.034 0.015 -9999 0 0 92 92
KRAS 0.034 0.016 -9999 0 0 95 95
DNAJA3 0.013 0.052 0.143 13 -0.15 10 23
RIN/GTP 0.028 0.008 -9999 0 -9999 0 0
CCND1 -0.054 0.179 -9999 0 -0.489 79 79
MAGED1 0.039 0.008 -9999 0 0 24 24
PTPN11 0.039 0.009 -9999 0 0 29 29
RICS 0.036 0.014 -9999 0 0 70 70
NT-4/5 (dimer) 0 0 -9999 0 -9999 0 0
SHC/GRB2/SOS1 0.065 0.049 -9999 0 -0.124 24 24
GRB2 0.04 0.008 -9999 0 0 21 21
NGF (dimer)/TRKA/MATK 0.049 0.018 -9999 0 -9999 0 0
TRKA/NEDD4-2 0.047 0.038 -9999 0 -0.134 17 17
ELMO1 0.036 0.014 -9999 0 0 75 75
RhoG/GTP/ELMO1/DOCK1 0.035 0.046 -9999 0 -0.111 41 41
NGF 0 0 -9999 0 -9999 0 0
HRAS 0.039 0.01 -9999 0 0 31 31
DOCK1 0.037 0.012 -9999 0 0 53 53
GAB2 0.031 0.018 -9999 0 0 136 136
RIT2 0.038 0.01 -9999 0 0 37 37
RIT1 0.037 0.012 -9999 0 0 50 50
FRS2 0.038 0.011 -9999 0 0 41 41
DNM1 0.039 0.01 -9999 0 0 33 33
mol:GTP 0 0 -9999 0 -9999 0 0
CRK 0.038 0.012 -9999 0 0 49 49
SH2B1 (homopentamer) 0 0 -9999 0 -9999 0 0
RhoG/GTP 0.031 0.06 0.168 9 -0.151 9 18
mol:GDP 0.039 0.108 0.261 16 -0.298 23 39
NGF (dimer) 0 0 -9999 0 -9999 0 0
RhoG/GDP 0.022 0.029 -9999 0 -0.125 18 18
RIT1/GDP 0.041 0.083 0.213 14 -0.206 24 38
TIAM1 0.036 0.013 -9999 0 0 66 66
PIK3R1 0.034 0.016 -9999 0 0 99 99
BDNF (dimer)/TRKB 0.072 0.03 -9999 0 -0.116 1 1
KIDINS220/CRKL/C3G 0.055 0.019 -9999 0 -9999 0 0
SHC/RasGAP 0.048 0.038 -9999 0 -0.132 18 18
FRS2 family/SHP2 0.065 0.049 -9999 0 -0.123 25 25
SHC/GRB2/SOS1/GAB1 0.076 0.061 -9999 0 -0.118 31 31
RIT1/GTP 0.024 0.026 -9999 0 -0.125 15 15
NT3 (dimer) 0.031 0.018 -9999 0 0 133 133
RAP1/GDP 0.03 0.073 0.176 9 -0.183 26 35
KIDINS220/CRKL 0.038 0.01 -9999 0 0 36 36
BDNF (dimer) 0.04 0.006 -9999 0 0 12 12
ubiquitin-dependent protein catabolic process 0.043 0.033 -9999 0 -0.108 17 17
Schwann cell development -0.007 0.011 -9999 0 -0.044 11 11
EHD4 0.039 0.01 -9999 0 0 35 35
FRS2 family/GRB2/SOS1 0.079 0.059 -9999 0 -0.122 28 28
FRS2 family/SHP2/CRK family/C3G/GAB2 0.003 0.081 -9999 0 -0.207 38 38
RAP1B 0.037 0.012 -9999 0 0 54 54
RAP1A 0.039 0.01 -9999 0 0 35 35
CDC42/GTP 0.067 0.051 0.204 2 -0.109 9 11
ABL1 0.039 0.01 -9999 0 0 32 32
SH2B family/GRB2/SOS1 0.047 0.044 -9999 0 -0.142 24 24
Rap1/GTP 0.005 0.111 -9999 0 -0.266 52 52
STAT3 0.001 0.11 -9999 0 -0.265 79 79
axon guidance 0.041 0.036 -9999 0 -0.106 9 9
MAPK3 -0.014 0.031 0.191 11 -9999 0 11
MAPK1 -0.013 0.032 0.191 12 -9999 0 12
CDC42/GDP 0.046 0.086 0.217 21 -0.2 24 45
NTF3 0.031 0.018 -9999 0 0 133 133
NTF4 0 0 -9999 0 -9999 0 0
NGF (dimer)/TRKA/FAIM 0.05 0.019 -9999 0 -0.109 2 2
PI3K 0.023 0.06 -9999 0 -0.15 44 44
FRS3 0.04 0.008 -9999 0 0 21 21
FAIM 0.038 0.011 -9999 0 0 43 43
GAB1 0.037 0.013 -9999 0 0 58 58
RASGRF1 0.013 0.052 0.143 13 -0.15 10 23
SOS1 0.037 0.012 -9999 0 0 51 51
MCF2L 0.004 0.058 0.179 35 -0.116 7 42
RGS19 0.037 0.013 -9999 0 0 59 59
CDC42 0.04 0.007 -9999 0 0 18 18
RAS family/GTP 0.033 0.118 0.293 3 -0.354 29 32
Rac1/GDP 0.045 0.085 0.217 21 -0.197 24 45
NGF (dimer)/TRKA/GRIT 0.043 0.034 -9999 0 -0.109 19 19
neuron projection morphogenesis -0.048 0.241 -9999 0 -0.827 39 39
NGF (dimer)/TRKA/NEDD4-2 0.043 0.033 -9999 0 -0.109 17 17
MAP2K1 -0.007 0.079 0.198 58 -0.183 3 61
NGFR 0.039 0.009 -9999 0 0 25 25
NGF (dimer)/TRKA/GIPC/GAIP 0.015 0.041 -9999 0 -0.149 23 23
RAS family/GTP/PI3K -0.005 0.07 -9999 0 -0.194 49 49
FRS2 family/SHP2/GRB2/SOS1 0.087 0.074 -9999 0 -0.131 38 38
NRAS 0.039 0.009 -9999 0 0 30 30
GRB2/SOS1 0.047 0.044 -9999 0 -0.142 24 24
PRKCI 0.027 0.02 -9999 0 0 192 192
ChemicalAbstracts:146-91-8 0 0 -9999 0 -9999 0 0
RAC1 0.039 0.009 -9999 0 0 28 28
PRKCZ 0.039 0.009 -9999 0 0 27 27
MAPKKK cascade 0.026 0.049 -9999 0 -0.501 2 2
RASA1 0.037 0.013 -9999 0 0 56 56
TRKA/c-Abl 0.053 0.031 -9999 0 -0.134 11 11
SQSTM1 0.038 0.011 -9999 0 0 46 46
BDNF (dimer)/TRKB/GIPC 0.07 0.059 -9999 0 -0.112 23 23
NGF (dimer)/TRKA/p62/Atypical PKCs 0.045 0.068 -9999 0 -0.107 54 54
MATK 0.037 0.013 -9999 0 0 56 56
NEDD4L 0.036 0.014 -9999 0 0 74 74
RAS family/GDP -0.01 0.039 -9999 0 -0.142 24 24
NGF (dimer)/TRKA 0.004 0.04 0.155 6 -0.152 10 16
Rac1/GTP -0.003 0.049 -9999 0 -0.154 14 14
FRS2 family/SHP2/CRK family 0.087 0.067 -9999 0 -0.115 23 23
Aurora A signaling

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
Aurora A/GADD45A 0.04 0.039 0.17 2 -0.147 10 12
BIRC5 0.037 0.012 -9999 0 0 52 52
NFKBIA -0.004 0.027 0.247 1 -0.175 5 6
CPEB1 0.039 0.009 -9999 0 0 28 28
AKT1 -0.002 0.041 0.262 9 -0.174 6 15
NDEL1 0.038 0.011 -9999 0 0 40 40
Aurora A/BRCA1 0.026 0.048 0.15 2 -0.098 52 54
NDEL1/TACC3 0.045 0.051 0.171 1 -0.109 30 31
GADD45A 0.036 0.013 -9999 0 0 66 66
GSK3B 0.038 0.012 0.091 14 0 23 37
PAK1/Aurora A 0.041 0.039 0.17 2 -0.161 9 11
MDM2 0.038 0.01 -9999 0 0 36 36
JUB 0.037 0.013 -9999 0 0 62 62
TPX2 -0.015 0.009 -9999 0 -9999 0 0
TP53 -0.045 0.115 0.162 1 -0.24 134 135
DLG7 -0.002 0.026 0.247 1 -0.172 3 4
AURKAIP1 0 0 -9999 0 -9999 0 0
ARHGEF7 0.039 0.009 -9999 0 0 28 28
G2 phase of mitotic cell cycle 0 0 -9999 0 -9999 0 0
Aurora A/NDEL1/TACC3 0.047 0.054 0.181 1 -0.117 30 31
G2/M transition of mitotic cell cycle 0.026 0.048 0.149 2 -0.098 52 54
AURKA 0.01 0.029 0.129 12 -0.202 6 18
AURKB -0.002 0.063 -9999 0 -0.188 49 49
CDC25B 0.005 0.047 -9999 0 -0.216 19 19
G2/M transition checkpoint 0.032 0.043 0.149 2 -0.106 31 33
mRNA polyadenylation 0.038 0.033 0.149 2 -0.131 10 12
Aurora A/CPEB 0.039 0.034 0.15 2 -0.131 10 12
Aurora A/TACC1/TRAP/chTOG 0.051 0.073 -9999 0 -0.173 14 14
BRCA1 0.034 0.015 -9999 0 0 93 93
centrosome duplication 0.041 0.039 0.169 2 -0.161 9 11
regulation of centrosome cycle 0.044 0.05 0.167 1 -0.108 30 31
spindle assembly 0.049 0.072 -9999 0 -0.172 14 14
TDRD7 0.034 0.015 -9999 0 0 89 89
Aurora A/RasGAP/Survivin 0.044 0.071 0.186 1 -0.163 8 9
CENPA 0.009 0.053 -9999 0 -0.324 11 11
Aurora A/PP2A 0.044 0.038 0.17 2 -0.147 10 12
meiosis 0 0 -9999 0 -9999 0 0
protein catabolic process -0.013 0.057 0.17 4 -0.205 14 18
negative regulation of DNA binding -0.046 0.115 0.161 1 -0.238 137 138
prophase 0 0 -9999 0 -9999 0 0
GIT1/beta-PIX 0.055 0.018 -9999 0 -9999 0 0
RASA1 0.037 0.013 -9999 0 0 56 56
Ajuba/Aurora A 0.032 0.043 0.15 2 -0.106 31 33
mitotic prometaphase 0.004 0.025 0.073 62 -9999 0 62
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.029 0.129 12 -0.202 6 18
TACC1 0.035 0.015 -9999 0 0 86 86
TACC3 0.033 0.016 -9999 0 0 103 103
Aurora A/Antizyme1 0.029 0.043 0.147 1 -0.102 34 35
Aurora A/RasGAP 0.041 0.04 0.17 2 -0.156 10 12
OAZ1 0.033 0.016 -9999 0 0 105 105
RAN 0.04 0.008 -9999 0 0 21 21
mitosis 0 0 -9999 0 -9999 0 0
PRKACA 0.034 0.016 0.091 12 0 84 96
GIT1 0.039 0.009 -9999 0 0 25 25
GIT1/beta-PIX/PAK1 0.064 0.044 -9999 0 -0.115 16 16
Importin alpha/Importin beta/TPX2 -0.015 0.009 -9999 0 -9999 0 0
PPP2R5D 0.039 0.009 -9999 0 0 26 26
Aurora A/TPX2 0.017 0.034 0.152 1 -0.17 10 11
PAK1 0.036 0.013 -9999 0 0 65 65
CKAP5 0.038 0.011 -9999 0 0 45 45
p38 MAPK signaling pathway

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
TRAF6/ASK1 0.019 0.052 -9999 0 -0.13 47 47
TRAF2/ASK1 0.044 0.033 -9999 0 -0.106 18 18
ATM 0.036 0.014 -9999 0 0 69 69
MAP2K3 -0.029 0.151 -9999 0 -0.328 84 84
response to stress 0 0 -9999 0 -9999 0 0
MAP2K6 -0.035 0.136 0.207 2 -0.328 65 67
hyperosmotic response 0 0 -9999 0 -9999 0 0
response to oxidative stress 0 0 -9999 0 -9999 0 0
GADD45G 0.037 0.013 -9999 0 0 58 58
TXN 0.009 0.003 -9999 0 -9999 0 0
CALM1 0.039 0.009 -9999 0 0 26 26
GADD45A 0.036 0.013 -9999 0 0 66 66
GADD45B 0.034 0.015 -9999 0 0 92 92
MAP3K1 0.036 0.013 -9999 0 0 63 63
MAP3K6 0.04 0.008 -9999 0 0 19 19
MAP3K7 0.038 0.01 -9999 0 0 38 38
MAP3K4 0.038 0.011 -9999 0 0 43 43
mol:Ca2+ 0 0 -9999 0 -9999 0 0
ASK1/ASK2 0.048 0.039 -9999 0 -0.134 19 19
TAK1/TAB family 0.016 0.07 0.166 2 -0.276 21 23
RAC1/OSM/MEKK3 0.073 0.023 -9999 0 -0.103 1 1
TRAF2 0.039 0.01 -9999 0 0 32 32
RAC1/OSM/MEKK3/MKK3 0.002 0.137 -9999 0 -0.269 81 81
TRAF6 0.008 0.044 -9999 0 -0.196 24 24
RAC1 0.039 0.009 -9999 0 0 28 28
mol:LPS 0 0 -9999 0 -9999 0 0
CAMK2B 0.041 0.005 -9999 0 0 9 9
CCM2 0.041 0.005 -9999 0 0 9 9
CaM/Ca2+/CAMKIIB 0.052 0.017 -9999 0 -0.109 3 3
MAPK11 0.029 0.019 -9999 0 0 157 157
response to DNA damage stimulus 0 0 -9999 0 -9999 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.063 0.042 -9999 0 -0.102 21 21
OSM/MEKK3 0.059 0.012 -9999 0 -9999 0 0
TAOK1 0.004 0.052 -9999 0 -0.196 34 34
TAOK2 0.004 0.052 -9999 0 -0.196 34 34
TAOK3 0.001 0.058 -9999 0 -0.196 43 43
MAP3K7IP1 0.037 0.012 -9999 0 0 51 51
MAPK14 0.04 0.008 -9999 0 0 20 20
MAP3K7IP2 0.037 0.012 -9999 0 0 53 53
MAP3K5 0.037 0.013 -9999 0 0 60 60
MAP3K10 0.037 0.013 -9999 0 0 57 57
MAP3K3 0.04 0.007 -9999 0 0 14 14
TRX/ASK1 0.022 0.047 -9999 0 -0.149 34 34
GADD45/MTK1/MTK1 0.056 0.066 -9999 0 -0.103 55 55
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.038 0.01 -9999 0 0 37 37
VLDLR 0.032 0.017 -9999 0 0 121 121
LRPAP1 0.036 0.014 -9999 0 0 72 72
NUDC 0.039 0.009 -9999 0 0 25 25
RELN/LRP8 0.05 0.054 -9999 0 -0.118 29 29
CaM/Ca2+ 0.028 0.016 -9999 0 -0.125 5 5
KATNA1 0.037 0.012 -9999 0 0 51 51
GO:0030286 0 0 -9999 0 -9999 0 0
ABL1 -0.006 0.059 0.191 24 -0.189 1 25
IQGAP1/CaM 0.041 0.054 -9999 0 -0.136 43 43
DAB1 0.04 0.008 -9999 0 0 21 21
IQGAP1 0.036 0.013 -9999 0 0 66 66
PLA2G7 0.03 0.018 -9999 0 0 149 149
CALM1 0.039 0.009 -9999 0 0 26 26
DYNLT1 0.036 0.014 -9999 0 0 75 75
mol:Ca2+ 0 0 -9999 0 -9999 0 0
LRPAP1/LRP8 0.041 0.051 -9999 0 -0.139 35 35
UniProt:Q4QZ09 0 0 -9999 0 -9999 0 0
CLIP1 0 0 -9999 0 -9999 0 0
CDK5R1 0.038 0.011 -9999 0 0 40 40
LIS1/Poliovirus Protein 3A -0.015 0.013 -9999 0 -0.126 5 5
CDK5R2 0.04 0.006 -9999 0 0 11 11
mol:PP1 0 0 -9999 0 -9999 0 0
RELN/VLDLR/DAB1 0.045 0.058 -9999 0 -0.116 38 38
YWHAE 0.037 0.013 -9999 0 0 58 58
NDEL1/14-3-3 E 0.028 0.076 0.25 25 -0.169 6 31
MAP1B -0.006 0.049 0.182 3 -0.185 36 39
RAC1 0.011 0.041 -9999 0 -0.581 1 1
p35/CDK5 -0.011 0.062 0.179 23 -0.179 1 24
RELN 0.034 0.016 -9999 0 0 96 96
PAFAH/LIS1 0.025 0.027 -9999 0 -0.151 5 5
LIS1/CLIP170 -0.015 0.013 -9999 0 -0.126 5 5
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain 0.02 0.075 0.193 8 -0.182 14 22
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.001 0.093 -9999 0 -0.215 60 60
GO:0005869 0 0 -9999 0 -9999 0 0
NDEL1 -0.001 0.069 0.208 32 -9999 0 32
LIS1/IQGAP1 0.03 0.026 -9999 0 -0.15 5 5
RHOA 0.011 0.043 0.117 18 -0.119 27 45
PAFAH1B1 -0.017 0.008 -9999 0 -9999 0 0
PAFAH1B3 0.034 0.016 -9999 0 0 94 94
PAFAH1B2 0.039 0.009 -9999 0 0 28 28
MAP1B/LIS1/Dynein heavy chain 0.014 0.059 0.182 1 -0.14 40 41
NDEL1/Katanin 60/Dynein heavy chain 0.034 0.084 0.276 15 -0.175 9 24
LRP8 0.039 0.01 -9999 0 0 35 35
NDEL1/Katanin 60 0.024 0.074 0.24 22 -0.167 10 32
P39/CDK5 -0.011 0.066 0.189 25 -0.179 1 26
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.033 0.025 -9999 0 -0.15 5 5
CDK5 -0.012 0.05 0.183 16 -0.182 1 17
PPP2R5D 0.039 0.009 -9999 0 0 26 26
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.012 0.011 -9999 0 -0.105 5 5
CSNK2A1 0.038 0.012 -9999 0 0 47 47
RELN/VLDLR/DAB1/LIS1 0.055 0.064 0.198 19 -0.109 36 55
RELN/VLDLR 0.053 0.072 -9999 0 -0.112 60 60
CDC42 0.01 0.047 0.117 19 -0.125 32 51
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.018 0.007 0 74 -9999 0 74
MAP4K4 -0.006 0.079 -9999 0 -0.241 31 31
BAG4 0.037 0.012 -9999 0 0 55 55
PKC zeta/ceramide 0.029 0.032 -9999 0 -0.184 8 8
NFKBIA 0.036 0.013 -9999 0 0 64 64
BIRC3 0.025 0.02 -9999 0 0 210 210
BAX 0.007 0.067 -9999 0 -0.341 19 19
RIPK1 0.039 0.01 -9999 0 0 32 32
AKT1 0.002 0.121 0.69 16 -9999 0 16
BAD -0.001 0.028 0.216 2 -0.183 7 9
SMPD1 0.008 0.059 0.159 14 -0.168 28 42
RB1 -0.003 0.043 0.201 8 -0.184 8 16
FADD/Caspase 8 -0.008 0.109 0.241 8 -0.3 43 51
MAP2K4 -0.007 0.028 -9999 0 -0.181 8 8
NSMAF 0.037 0.012 -9999 0 0 55 55
response to UV 0 0 -9999 0 -9999 0 0
RAF1 -0.003 0.042 0.185 15 -0.19 8 23
EGF 0.038 0.01 -9999 0 0 38 38
mol:ceramide 0.005 0.027 -9999 0 -0.19 8 8
MADD 0.041 0.005 -9999 0 0 9 9
response to oxidative stress 0 0 -9999 0 -9999 0 0
mol:Free Fatty acid -0.015 0.009 0 151 -9999 0 151
ASAH1 0.033 0.016 -9999 0 0 106 106
negative regulation of cell cycle -0.003 0.043 0.2 8 -0.183 8 16
cell proliferation 0.026 0.054 0.195 11 -0.21 6 17
BID -0.017 0.184 -9999 0 -0.648 36 36
MAP3K1 -0.002 0.027 -9999 0 -0.184 8 8
EIF2A 0.007 0.078 0.189 60 -0.215 8 68
TRADD 0.037 0.013 -9999 0 0 61 61
CRADD 0.04 0.006 -9999 0 0 10 10
MAPK3 -0.002 0.044 0.179 14 -0.209 6 20
response to heat 0 0 -9999 0 -9999 0 0
MAPK1 -0.007 0.048 0.18 13 -0.186 7 20
Cathepsin D/ceramide 0.028 0.032 -9999 0 -0.184 8 8
FADD -0.005 0.082 0.223 4 -0.241 32 36
KSR1 0 0.033 0.214 5 -0.184 8 13
MAPK8 0.002 0.053 -9999 0 -0.197 15 15
PRKRA 0.003 0.046 0.197 18 -0.184 8 26
PDGFA 0.037 0.013 -9999 0 0 57 57
TRAF2 0.039 0.01 -9999 0 0 32 32
IGF1 0.035 0.014 -9999 0 0 77 77
mol:GD3 0 0 -9999 0 -9999 0 0
ganglioside biosynthetic process 0.005 0.027 -9999 0 -0.189 8 8
CTSD 0.037 0.012 -9999 0 0 55 55
regulation of nitric oxide biosynthetic process 0.044 0.049 -9999 0 -0.134 34 34
response to radiation 0 0 -9999 0 -9999 0 0
ERK1/PKC delta 0.029 0.057 0.209 11 -0.223 6 17
PRKCD 0.037 0.012 -9999 0 0 51 51
PRKCZ 0.039 0.009 -9999 0 0 27 27
mol:GW4869 0 0 -9999 0 -9999 0 0
mol:sphingosine -0.015 0.009 0 151 -9999 0 151
RelA/NF kappa B1 0.044 0.049 -9999 0 -0.134 34 34
mol:glutathione 0 0 -9999 0 -9999 0 0
PAWR 0.04 0.006 -9999 0 0 11 11
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.001 0.084 -9999 0 -0.254 30 30
TNFR1A/BAG4/TNF-alpha 0.06 0.045 -9999 0 -0.113 15 15
mol:Sphingosine-1-phosphate -0.018 0.007 0 74 -9999 0 74
MAP2K1 -0.008 0.041 0.174 15 -0.192 7 22
mol:C11AG 0 0 -9999 0 -9999 0 0
RELA 0.04 0.006 -9999 0 0 10 10
CYCS 0.003 0.047 -9999 0 -0.178 14 14
TNFRSF1A 0.036 0.014 -9999 0 0 72 72
NFKB1 0.036 0.013 -9999 0 0 66 66
TNFR1A/BAG4 0.045 0.037 -9999 0 -0.132 14 14
EIF2AK2 -0.003 0.055 0.184 23 -0.189 10 33
TNF-alpha/TNFR1A/FAN 0.059 0.052 -9999 0 -0.137 21 21
response to hydrogen peroxide 0 0 -9999 0 -9999 0 0
CASP8 -0.005 0.137 -9999 0 -0.397 48 48
MAP2K2 -0.005 0.04 0.176 14 -0.193 6 20
SMPD3 -0.004 0.101 0.189 4 -0.294 47 51
TNF 0.04 0.008 -9999 0 0 22 22
PKC zeta/PAR4 0.057 0.017 -9999 0 -0.134 1 1
mol:PHOSPHOCHOLINE 0.004 0.031 0.148 2 -0.135 7 9
NF kappa B1/RelA/I kappa B alpha 0.079 0.081 -9999 0 -0.116 59 59
AIFM1 0.004 0.042 0.125 1 -0.173 14 15
BCL2 0.036 0.014 -9999 0 0 67 67
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.025 0.134 0.272 1 -0.375 42 43
BAG4 0.037 0.012 -9999 0 0 55 55
BAD -0.009 0.047 0.19 4 -0.134 30 34
NFKBIA 0.036 0.013 -9999 0 0 64 64
BIRC3 0.025 0.02 -9999 0 0 210 210
BAX -0.008 0.045 0.168 3 -0.133 28 31
EnzymeConsortium:3.1.4.12 -0.003 0.031 0.064 2 -0.084 38 40
IKBKB -0.025 0.128 0.22 12 -0.368 40 52
MAP2K2 -0.007 0.043 0.16 10 -0.145 8 18
MAP2K1 -0.011 0.045 0.162 10 -0.145 9 19
SMPD1 -0.003 0.036 -9999 0 -0.105 32 32
GO:0005551 0 0 -9999 0 -9999 0 0
FADD/Caspase 8 -0.016 0.139 0.249 9 -0.368 43 52
MAP2K4 -0.009 0.04 -9999 0 -0.136 21 21
protein ubiquitination -0.031 0.129 0.256 1 -0.371 42 43
EnzymeConsortium:2.7.1.37 -0.011 0.046 0.16 9 -0.16 5 14
response to UV 0 0 0.002 9 -0.002 3 12
RAF1 -0.009 0.047 0.166 10 -0.14 15 25
CRADD 0.04 0.006 -9999 0 0 10 10
mol:ceramide -0.004 0.046 0.124 1 -0.126 37 38
I-kappa-B-alpha/RELA/p50/ubiquitin 0.041 0.042 -9999 0 -0.111 35 35
MADD 0.041 0.005 -9999 0 0 9 9
MAP3K1 -0.009 0.043 0.116 1 -0.13 33 34
TRADD 0.037 0.013 -9999 0 0 61 61
RELA/p50 0.04 0.006 -9999 0 0 10 10
MAPK3 -0.007 0.046 0.164 9 -0.169 6 15
MAPK1 -0.01 0.052 0.164 8 -0.177 15 23
p50/RELA/I-kappa-B-alpha 0.044 0.05 -9999 0 -0.137 35 35
FADD -0.021 0.136 0.242 9 -0.369 42 51
KSR1 -0.006 0.044 0.156 5 -0.132 24 29
MAPK8 -0.015 0.044 0.177 3 -0.147 12 15
TRAF2 0.039 0.01 -9999 0 0 32 32
response to radiation 0 0 -9999 0 -9999 0 0
CHUK -0.034 0.128 0.255 1 -0.353 46 47
TNF R/SODD 0.045 0.037 -9999 0 -0.131 14 14
TNF 0.04 0.008 -9999 0 0 22 22
CYCS -0.01 0.048 0.152 3 -0.142 25 28
IKBKG -0.032 0.127 0.255 1 -0.374 39 40
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.02 0.14 -9999 0 -0.389 42 42
RELA 0.04 0.006 -9999 0 0 10 10
RIPK1 0.039 0.01 -9999 0 0 32 32
AIFM1 -0.009 0.046 0.132 6 -0.135 23 29
TNF/TNF R/SODD 0.06 0.045 -9999 0 -0.113 15 15
TNFRSF1A 0.036 0.014 -9999 0 0 72 72
response to heat 0 0 -9999 0 -9999 0 0
CASP8 0.017 0.132 -9999 0 -0.654 18 18
NSMAF -0.017 0.136 0.235 15 -0.378 41 56
response to hydrogen peroxide 0 0 0.002 9 -0.002 3 12
BCL2 0.036 0.014 -9999 0 0 67 67
Syndecan-3-mediated signaling events

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
CTTN 0.039 0.009 -9999 0 0 30 30
Syndecan-3/Src/Cortactin 0.022 0.091 -9999 0 -0.354 13 13
Syndecan-3/Neurocan 0.001 0.064 -9999 0 -0.408 12 12
POMC 0.04 0.006 -9999 0 0 12 12
EGFR 0.036 0.014 -9999 0 0 67 67
Syndecan-3/EGFR 0.032 0.075 -9999 0 -0.425 12 12
AGRP 0.037 0.012 -9999 0 0 55 55
NCSTN 0.04 0.008 -9999 0 0 22 22
PSENEN 0.034 0.016 -9999 0 0 96 96
RP11-540L11.1 0 0 -9999 0 -9999 0 0
APH1B 0.035 0.014 -9999 0 0 79 79
APH1A 0.038 0.011 -9999 0 0 42 42
NCAN 0 0 -9999 0 -9999 0 0
long-term memory 0.042 0.081 -9999 0 -0.392 12 12
Syndecan-3/IL8 0.026 0.073 -9999 0 -0.413 12 12
PSEN1 0.039 0.01 -9999 0 0 31 31
Src/Cortactin 0.052 0.032 -9999 0 -0.134 11 11
FYN 0.034 0.016 -9999 0 0 94 94
limb bud formation 0.002 0.065 -9999 0 -0.437 11 11
MC4R 0 0 -9999 0 -9999 0 0
SRC 0.039 0.009 -9999 0 0 28 28
PTN 0.023 0.02 -9999 0 0 241 241
FGFR/FGF/Syndecan-3 0.002 0.065 -9999 0 -0.441 11 11
neuron projection morphogenesis -0.011 0.068 -9999 0 -0.383 10 10
Syndecan-3/AgRP 0.034 0.073 -9999 0 -0.41 12 12
Syndecan-3/AgRP/MC4R 0.032 0.071 -9999 0 -0.397 12 12
Fyn/Cortactin 0.037 0.055 -9999 0 -0.134 44 44
SDC3 0.003 0.064 -9999 0 -0.455 10 10
GO:0007205 0 0 -9999 0 -9999 0 0
positive regulation of leukocyte migration 0.026 0.072 -9999 0 -0.407 12 12
IL8 0.031 0.018 -9999 0 0 129 129
Syndecan-3/Fyn/Cortactin 0.043 0.083 -9999 0 -0.401 12 12
Syndecan-3/CASK 0.001 0.064 -9999 0 -0.408 12 12
alpha-MSH/MC4R 0.03 0.004 -9999 0 -9999 0 0
Gamma Secretase 0.067 0.085 -9999 0 -0.118 63 63
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -9999 0 0
GNAO1 0.035 0.015 -9999 0 0 85 85
CDC42/GTP 0.009 0.084 -9999 0 -0.17 70 70
PLCG1 -0.014 0.072 -9999 0 -0.178 68 68
mol:GTP 0 0 -9999 0 -9999 0 0
GNAI2 0.04 0.006 -9999 0 0 13 13
GNAI3 0.038 0.011 -9999 0 0 45 45
G12/G13 0.053 0.028 -9999 0 -0.134 8 8
cell migration 0.008 0.083 -9999 0 -0.167 70 70
S1PR5 0 0 -9999 0 -9999 0 0
S1PR4 0 0 -9999 0 -9999 0 0
MAPK3 -0.013 0.073 -9999 0 -0.182 66 66
MAPK1 -0.008 0.065 -9999 0 -0.168 58 58
S1P/S1P5/Gi -0.008 0.078 -9999 0 -0.184 69 69
GNAI1 0.034 0.015 -9999 0 0 93 93
CDC42/GDP 0.029 0.012 -9999 0 -0.125 3 3
S1P/S1P5/G12 0.026 0.007 -9999 0 -9999 0 0
RHOA -0.014 0.03 0.192 9 -0.171 1 10
S1P/S1P4/Gi -0.008 0.078 -9999 0 -0.184 69 69
mol:GDP 0 0 -9999 0 -9999 0 0
GNAZ 0.038 0.011 -9999 0 0 46 46
S1P/S1P4/G12/G13 0.046 0.023 -9999 0 -0.097 8 8
GNA12 0.039 0.01 -9999 0 0 33 33
GNA13 0.039 0.008 -9999 0 0 23 23
CDC42 0.04 0.007 -9999 0 0 18 18
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR -0.033 0.202 -9999 0 -0.802 34 34
regulation of axonogenesis -0.002 0.048 0.245 11 -9999 0 11
myoblast fusion -0.013 0.103 0.354 36 -9999 0 36
mol:GTP 0.016 0.066 -9999 0 -0.201 43 43
regulation of calcium-dependent cell-cell adhesion -0.036 0.089 0.203 40 -9999 0 40
ARF1/GTP 0.037 0.059 -9999 0 -0.161 38 38
mol:GM1 0.003 0.046 -9999 0 -0.154 40 40
mol:Choline -0.001 0.034 -9999 0 -0.144 26 26
lamellipodium assembly -0.009 0.121 -9999 0 -0.403 44 44
MAPK3 0.009 0.083 -9999 0 -0.276 40 40
ARF6/GTP/NME1/Tiam1 0.037 0.089 -9999 0 -0.204 40 40
ARF1 0.038 0.011 -9999 0 0 45 45
ARF6/GDP 0.013 0.103 -9999 0 -0.355 36 36
ARF1/GDP 0.018 0.102 -9999 0 -0.318 40 40
ARF6 0.042 0.045 -9999 0 -0.127 33 33
RAB11A 0.04 0.008 -9999 0 0 19 19
TIAM1 0.032 0.023 -9999 0 -0.045 28 28
fibronectin binding 0 0 -9999 0 -9999 0 0
MAPK1 0.011 0.079 -9999 0 -0.277 35 35
actin filament bundle formation -0.025 0.107 0.319 44 -9999 0 44
KALRN 0.003 0.074 -9999 0 -0.263 35 35
RAB11FIP3/RAB11A 0.054 0.026 -9999 0 -0.134 6 6
RhoA/GDP 0.026 0.108 -9999 0 -0.321 44 44
NME1 0.031 0.024 -9999 0 -0.047 33 33
Rac1/GDP 0.025 0.107 -9999 0 -0.317 44 44
substrate adhesion-dependent cell spreading 0.016 0.066 -9999 0 -0.201 43 43
cortical actin cytoskeleton organization -0.009 0.121 -9999 0 -0.407 43 43
RAC1 0.039 0.009 -9999 0 0 28 28
liver development 0.016 0.066 -9999 0 -0.201 43 43
ARF6/GTP 0.016 0.066 -9999 0 -0.201 43 43
RhoA/GTP 0.04 0.062 -9999 0 -0.163 43 43
mol:GDP -0.003 0.097 -9999 0 -0.345 37 37
ARF6/GTP/RAB11FIP3/RAB11A 0.057 0.065 -9999 0 -0.14 43 43
RHOA 0.04 0.006 -9999 0 0 13 13
PLD1 0.008 0.047 -9999 0 -0.168 31 31
RAB11FIP3 0.038 0.01 -9999 0 0 37 37
tube morphogenesis -0.009 0.121 -9999 0 -0.403 44 44
ruffle organization 0.002 0.048 -9999 0 -0.245 11 11
regulation of epithelial cell migration 0.016 0.066 -9999 0 -0.201 43 43
PLD2 0.015 0.047 -9999 0 -0.153 36 36
PIP5K1A 0.002 0.048 -9999 0 -0.247 11 11
mol:Phosphatidic acid -0.001 0.034 -9999 0 -0.144 26 26
Rac1/GTP -0.009 0.122 -9999 0 -0.408 43 43
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.019 0.015 0.059 14 -9999 0 14
SNTA1 0.039 0.01 -9999 0 0 34 34
response to hypoxia 0 0 -9999 0 -9999 0 0
STMN1 -0.018 0.016 0.059 15 -9999 0 15
MAPK12 -0.008 0.038 0.208 4 -0.162 12 16
CCND1 -0.04 0.13 -9999 0 -0.372 70 70
p38 gamma/SNTA1 0.023 0.068 0.222 8 -0.169 28 36
MAP2K3 0.038 0.011 -9999 0 0 43 43
PKN1 0.034 0.016 -9999 0 0 96 96
G2/M transition checkpoint -0.008 0.038 0.208 4 -0.161 12 16
MAP2K6 0.002 0.04 0.245 2 -0.173 19 21
MAPT 0 0.047 0.145 8 -0.191 13 21
MAPK13 -0.017 0.007 0 84 -9999 0 84
hyperosmotic response 0 0 -9999 0 -9999 0 0
ZAK 0.004 0.048 -9999 0 -0.197 29 29
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.036 0.016 0.078 1 -0.056 3 4
HSPA8 0.039 0.01 -9999 0 0 34 34
SMAD3/SMAD4/ER alpha 0.063 0.091 0.232 34 -0.159 18 52
AKT1 0.04 0.017 -9999 0 -0.098 5 5
GSC 0.026 0.1 -9999 0 -0.728 5 5
NKX2-5 0.038 0.018 0.082 2 -0.055 14 16
muscle cell differentiation -0.045 0.093 0.282 11 -9999 0 11
SMAD2-3/SMAD4/SP1 0.072 0.115 -9999 0 -0.201 9 9
SMAD4 0.036 0.047 -9999 0 -0.103 11 11
CBFB 0.036 0.014 -9999 0 0 67 67
SAP18 0.039 0.008 -9999 0 0 24 24
Cbp/p300/MSG1 0.059 0.055 -9999 0 -0.144 22 22
SMAD3/SMAD4/VDR 0.077 0.099 -9999 0 -0.209 12 12
MYC 0.022 0.021 0.108 5 -0.042 2 7
CDKN2B -0.037 0.161 -9999 0 -1.265 5 5
AP1 0.005 0.092 -9999 0 -0.219 41 41
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.006 0.121 0.186 3 -0.322 42 45
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.014 0.059 -9999 0 -0.208 26 26
SP3 0.036 0.023 0.081 1 -0.053 32 33
CREB1 0.04 0.007 -9999 0 0 17 17
FOXH1 0.028 0.025 -9999 0 -0.059 15 15
SMAD3/SMAD4/GR 0.053 0.078 -9999 0 -0.149 19 19
GATA3 0.042 0.012 -9999 0 -9999 0 0
SKI/SIN3/HDAC complex/NCoR1 0.003 0.094 -9999 0 -0.27 34 34
MEF2C/TIF2 0.062 0.101 0.218 101 -0.213 16 117
endothelial cell migration -0.03 0.106 0.939 5 -9999 0 5
MAX 0.029 0.027 0.097 3 -0.035 77 80
RBBP7 0.039 0.009 -9999 0 0 25 25
RBBP4 0.038 0.011 -9999 0 0 40 40
RUNX2 0.038 0.011 -9999 0 0 40 40
RUNX3 0.039 0.01 -9999 0 0 33 33
RUNX1 0.039 0.01 -9999 0 0 33 33
CTBP1 0.038 0.012 -9999 0 0 49 49
NR3C1 0.026 0.027 0.097 3 -0.035 77 80
VDR 0.038 0.011 -9999 0 0 43 43
CDKN1A 0.013 0.075 -9999 0 -0.646 2 2
KAT2B 0 0.002 -9999 0 -9999 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.056 0.062 -9999 0 -0.222 3 3
DCP1A 0.04 0.007 -9999 0 0 17 17
SKI 0.039 0.009 -9999 0 0 29 29
SERPINE1 0.028 0.106 -9999 0 -0.95 5 5
SMAD3/SMAD4/ATF2 0.062 0.074 -9999 0 -0.153 13 13
SMAD3/SMAD4/ATF3 0.058 0.068 -9999 0 -0.137 7 7
SAP30 0.038 0.011 -9999 0 0 46 46
Cbp/p300/PIAS3 0.057 0.058 0.174 1 -0.14 27 28
JUN 0.001 0.087 0.183 9 -0.224 38 47
SMAD3/SMAD4/IRF7 0.07 0.07 -9999 0 -0.146 7 7
TFE3 0.038 0.033 0.114 1 -0.082 34 35
COL1A2 -0.093 0.251 -9999 0 -0.608 103 103
mesenchymal cell differentiation -0.062 0.069 0.135 9 -9999 0 9
DLX1 0.04 0.008 -9999 0 0 19 19
TCF3 0.036 0.014 -9999 0 0 74 74
FOS 0.025 0.029 -9999 0 -0.05 28 28
SMAD3/SMAD4/Max 0.062 0.068 -9999 0 -0.14 6 6
Cbp/p300/SNIP1 0.058 0.055 -9999 0 -0.142 24 24
ZBTB17 0.038 0.01 0.102 3 -0.04 4 7
LAMC1 0.01 0.075 -9999 0 -0.257 26 26
TGIF2/HDAC complex/SMAD3/SMAD4 0.059 0.075 -9999 0 -0.156 13 13
IRF7 0.04 0.012 0.087 1 -9999 0 1
ESR1 0.046 0.037 0.122 90 0 91 181
HNF4A 0.038 0.01 -9999 0 0 38 38
MEF2C 0.049 0.106 0.203 145 -0.226 14 159
SMAD2-3/SMAD4 0.07 0.073 -9999 0 -0.144 6 6
Cbp/p300/Src-1 0.058 0.06 -9999 0 -0.141 31 31
IGHV3OR16-13 0.01 0.057 -9999 0 -0.447 8 8
TGIF2/HDAC complex 0.037 0.012 -9999 0 0 50 50
CREBBP 0.037 0.014 -9999 0 -0.045 2 2
SKIL 0.025 0.02 -9999 0 0 215 215
HDAC1 0.037 0.012 -9999 0 0 49 49
HDAC2 0.038 0.01 -9999 0 0 38 38
SNIP1 0.039 0.009 -9999 0 0 28 28
GCN5L2 0.039 0.012 -9999 0 -0.045 3 3
SMAD3/SMAD4/TFE3 0.076 0.083 -9999 0 -0.163 21 21
MSG1/HSC70 0.052 0.026 -9999 0 -0.134 5 5
SMAD2 0.039 0.024 -9999 0 -0.065 20 20
SMAD3 0.034 0.047 -9999 0 -0.102 13 13
SMAD3/E2F4-5/DP1/p107/SMAD4 0.019 0.065 0.16 1 -0.197 19 20
SMAD2/SMAD2/SMAD4 -0.003 0.056 0.159 9 -0.166 32 41
NCOR1 0.037 0.013 -9999 0 0 58 58
NCOA2 0.037 0.013 -9999 0 0 60 60
NCOA1 0.04 0.008 -9999 0 0 22 22
MYOD/E2A 0.051 0.024 -9999 0 -0.134 1 1
SMAD2-3/SMAD4/SP1/MIZ-1 0.084 0.121 -9999 0 -0.196 9 9
IFNB1 0.013 0.049 0.168 1 -0.158 2 3
SMAD3/SMAD4/MEF2C 0.088 0.111 0.267 47 -0.222 13 60
CITED1 0.039 0.01 -9999 0 0 35 35
SMAD2-3/SMAD4/ARC105 0.068 0.066 -9999 0 -0.129 4 4
RBL1 0.037 0.012 -9999 0 0 54 54
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.025 0.072 -9999 0 -0.408 7 7
RUNX1-3/PEBPB2 0.065 0.041 -9999 0 -0.107 13 13
SMAD7 -0.001 0.137 -9999 0 -0.364 29 29
MYC/MIZ-1 0.019 0.058 0.198 3 -0.137 49 52
SMAD3/SMAD4 -0.002 0.101 0.255 2 -0.339 22 24
IL10 0.022 0.061 0.226 15 -9999 0 15
PIASy/HDAC complex 0.036 0.014 -9999 0 -0.038 4 4
PIAS3 0.038 0.013 -9999 0 -0.002 50 50
CDK2 0.037 0.014 -9999 0 -0.042 3 3
IL5 0.023 0.061 0.233 13 -9999 0 13
CDK4 0.038 0.013 -9999 0 -0.045 3 3
PIAS4 0.036 0.014 -9999 0 -0.038 4 4
ATF3 0.036 0.013 -9999 0 0 63 63
SMAD3/SMAD4/SP1 0.054 0.106 -9999 0 -0.183 21 21
FOXG1 -0.001 0.001 -9999 0 -9999 0 0
FOXO3 0.01 0.012 -9999 0 -0.109 5 5
FOXO1 0.01 0.012 -9999 0 -0.108 5 5
FOXO4 0.01 0.012 -9999 0 -0.108 5 5
heart looping 0.049 0.105 0.202 145 -0.224 14 159
CEBPB 0.036 0.017 -9999 0 -0.061 5 5
SMAD3/SMAD4/DLX1 0.067 0.067 -9999 0 -0.138 6 6
MYOD1 0.04 0.007 -9999 0 0 16 16
SMAD3/SMAD4/HNF4 0.064 0.068 -9999 0 -0.138 6 6
SMAD3/SMAD4/GATA3 0.077 0.07 -9999 0 -0.164 1 1
SnoN/SIN3/HDAC complex/NCoR1 0.025 0.02 -9999 0 0 215 215
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.088 0.082 -9999 0 -0.145 1 1
SMAD3/SMAD4/SP1-3 0.07 0.118 -9999 0 -0.211 21 21
MED15 0 0 -9999 0 -9999 0 0
SP1 0.018 0.066 -9999 0 -0.099 122 122
SIN3B 0.036 0.014 -9999 0 0 67 67
SIN3A 0.039 0.009 -9999 0 0 30 30
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.071 0.077 -9999 0 -0.169 11 11
ITGB5 -0.004 0.091 0.207 13 -0.268 29 42
TGIF/SIN3/HDAC complex/CtBP 0.008 0.087 -9999 0 -0.261 30 30
SMAD3/SMAD4/AR 0.04 0.088 -9999 0 -0.155 30 30
AR 0.032 0.017 -9999 0 0 118 118
negative regulation of cell growth 0.019 0.076 0.188 1 -0.248 21 22
SMAD3/SMAD4/MYOD 0.068 0.067 -9999 0 -0.138 6 6
E2F5 0.036 0.013 -9999 0 0 64 64
E2F4 0.036 0.013 -9999 0 0 64 64
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.069 0.079 -9999 0 -0.153 5 5
SMAD2-3/SMAD4/FOXO1-3a-4 0.026 0.051 -9999 0 -0.293 7 7
TFDP1 0.037 0.012 -9999 0 0 55 55
SMAD3/SMAD4/AP1 0.031 0.11 0.258 3 -0.23 37 40
SMAD3/SMAD4/RUNX2 0.063 0.07 -9999 0 -0.136 9 9
TGIF2 0.037 0.012 -9999 0 0 50 50
TGIF1 0 0 -9999 0 -9999 0 0
ATF2 0.039 0.009 -9999 0 0 30 30
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0.037 0.042 -9999 0 -0.108 33 33
EFNA5 0.034 0.015 -9999 0 0 93 93
FYN -0.015 0.033 0.176 4 -9999 0 4
neuron projection morphogenesis 0.037 0.042 -9999 0 -0.108 33 33
cell-cell signaling 0 0 -9999 0 -9999 0 0
Ephrin A5/EPHA5 0.038 0.042 -9999 0 -0.108 33 33
EPHA5 0.039 0.008 -9999 0 0 24 24
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.037 0.012 -9999 0 0 49 49
HDAC2 0.038 0.01 -9999 0 0 38 38
GNB1/GNG2 0.068 0.042 -9999 0 -0.116 16 16
forebrain development 0.011 0.108 -9999 0 -0.376 29 29
GNAO1 0.035 0.015 -9999 0 0 85 85
SMO/beta Arrestin2 0.054 0.025 -9999 0 -0.133 4 4
SMO 0.04 0.009 -9999 0 -0.001 24 24
ARRB2 0.038 0.012 -9999 0 0 46 46
GLI3/SPOP 0.025 0.122 0.234 1 -0.336 29 30
mol:GTP 0 0.001 -9999 0 -9999 0 0
GSK3B 0.039 0.008 -9999 0 0 23 23
GNAI2 0.04 0.006 -9999 0 0 13 13
SIN3/HDAC complex 0.076 0.053 -9999 0 -0.113 12 12
GNAI1 0.034 0.016 -9999 0 0 93 93
XPO1 0.039 0.012 -9999 0 -0.003 38 38
GLI1/Su(fu) 0.017 0.112 -9999 0 -0.404 24 24
SAP30 0.038 0.011 -9999 0 0 46 46
mol:GDP 0.04 0.009 -9999 0 -0.001 24 24
MIM/GLI2A 0.032 0.025 -9999 0 -0.121 2 2
IFT88 0.037 0.013 -9999 0 0 61 61
GNAI3 0.038 0.011 -9999 0 0 45 45
GLI2 0.015 0.077 0.176 5 -0.265 17 22
GLI3 0.007 0.118 0.21 3 -0.346 29 32
CSNK1D 0.039 0.008 -9999 0 0 24 24
CSNK1E 0.037 0.012 -9999 0 0 53 53
SAP18 0.039 0.008 -9999 0 0 24 24
embryonic digit morphogenesis 0.037 0.013 -9999 0 0 61 61
GNG2 0.039 0.009 -9999 0 0 29 29
Gi family/GTP 0.002 0.077 -9999 0 -0.247 28 28
SIN3B 0.036 0.014 -9999 0 0 67 67
SIN3A 0.039 0.009 -9999 0 0 30 30
GLI3/Su(fu) 0.019 0.115 0.21 3 -0.328 32 35
GLI2/Su(fu) 0.022 0.086 0.18 2 -0.265 23 25
FOXA2 0.022 0.1 -9999 0 -0.57 13 13
neural tube patterning 0.011 0.108 -9999 0 -0.376 29 29
SPOP 0.04 0.008 -9999 0 0 21 21
Su(fu)/PIAS1 0.041 0.055 -9999 0 -0.191 20 20
GNB1 0.039 0.01 -9999 0 0 33 33
CSNK1G2 0.036 0.013 -9999 0 0 64 64
CSNK1G3 0.039 0.01 -9999 0 0 31 31
MTSS1 0.032 0.025 -9999 0 -0.121 2 2
embryonic limb morphogenesis 0.011 0.108 -9999 0 -0.376 29 29
SUFU 0.022 0.039 -9999 0 -0.239 10 10
LGALS3 0.036 0.014 -9999 0 0 67 67
catabolic process 0.027 0.13 -9999 0 -0.359 31 31
GLI3A/CBP 0.046 0.015 -9999 0 -9999 0 0
KIF3A 0.038 0.011 -9999 0 0 46 46
GLI1 0.01 0.11 -9999 0 -0.383 29 29
RAB23 0.04 0.006 -9999 0 0 13 13
CSNK1A1 0.039 0.008 -9999 0 0 23 23
IFT172 0.039 0.009 -9999 0 0 28 28
RBBP7 0.039 0.009 -9999 0 0 25 25
Su(fu)/Galectin3 0.037 0.053 -9999 0 -0.182 19 19
GNAZ 0.038 0.012 -9999 0 0 46 46
RBBP4 0.038 0.011 -9999 0 0 40 40
CSNK1G1 0.04 0.007 -9999 0 0 16 16
PIAS1 0.039 0.008 -9999 0 0 24 24
PRKACA 0.035 0.015 -9999 0 0 84 84
GLI2/SPOP 0.032 0.086 -9999 0 -0.271 20 20
STK36 0.039 0.011 -9999 0 -0.003 33 33
Gi family/GNB1/GNG2/GDP -0.002 0.087 -9999 0 -0.238 38 38
PTCH1 0.011 0.1 -9999 0 -0.346 29 29
MIM/GLI1 0.024 0.101 -9999 0 -0.353 21 21
CREBBP 0.046 0.015 -9999 0 -9999 0 0
Su(fu)/SIN3/HDAC complex 0.004 0.107 0.168 4 -0.322 34 38
Class I PI3K signaling events mediated by Akt

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
BCL2L1 -0.016 0.009 -9999 0 -9999 0 0
BAD/BCL-XL/YWHAZ 0.062 0.06 0.18 72 -0.109 16 88
CDKN1B 0.013 0.091 0.206 31 -0.33 24 55
CDKN1A 0.004 0.084 0.202 9 -0.317 28 37
FRAP1 0.039 0.009 -9999 0 0 28 28
PRKDC 0.038 0.011 -9999 0 0 44 44
FOXO3 0.005 0.081 -9999 0 -0.309 30 30
AKT1 0.006 0.081 -9999 0 -0.336 26 26
BAD 0.041 0.005 -9999 0 0 7 7
AKT3 0.004 0.046 -9999 0 -0.197 26 26
mol:GTP 0 0 -9999 0 -9999 0 0
FOXO4 0.005 0.081 -9999 0 -0.309 30 30
AKT1/ASK1 0.026 0.09 -9999 0 -0.307 31 31
BAD/YWHAZ 0.056 0.042 -9999 0 -0.112 6 6
RICTOR 0.037 0.013 -9999 0 0 59 59
RAF1 0.04 0.008 -9999 0 0 22 22
JNK cascade -0.025 0.087 0.298 31 -9999 0 31
TSC1 0.002 0.078 0.255 1 -0.324 25 26
YWHAZ 0.034 0.016 -9999 0 0 96 96
AKT1/RAF1 0.032 0.093 0.237 1 -0.322 29 30
EP300 0.036 0.014 -9999 0 0 69 69
mol:GDP 0.004 0.083 -9999 0 -0.32 30 30
mol:PI-3-4-5-P3 0 0 -9999 0 -9999 0 0
TSC2 0 0.082 0.255 1 -0.315 30 31
YWHAQ 0.04 0.007 -9999 0 0 18 18
TBC1D4 0.004 0.03 0.245 4 -0.172 7 11
MAP3K5 0.037 0.013 -9999 0 0 60 60
MAPKAP1 0.04 0.008 -9999 0 0 21 21
negative regulation of cell cycle -0.022 0.087 0.296 17 -0.216 2 19
YWHAH 0.038 0.011 -9999 0 0 46 46
AKT1S1 0.002 0.077 0.273 1 -0.327 24 25
CASP9 0 0.079 -9999 0 -0.322 27 27
YWHAB 0.038 0.011 -9999 0 0 45 45
p27Kip1/KPNA1 0.033 0.106 0.288 6 -0.323 28 34
GBL 0.039 0.009 -9999 0 0 26 26
PDK1/Src/Hsp90 0.049 0.023 -9999 0 -0.109 6 6
YWHAE 0.037 0.013 -9999 0 0 58 58
SRC 0.039 0.009 -9999 0 0 28 28
AKT2/p21CIP1 0.007 0.077 0.201 8 -0.286 26 34
KIAA1303 0 0 -9999 0 -9999 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.018 0.097 -9999 0 -0.365 27 27
CHUK -0.002 0.084 -9999 0 -0.324 30 30
BAD/BCL-XL 0.025 0.086 0.234 1 -0.309 26 27
mTORC2 0.077 0.061 -9999 0 -0.114 32 32
AKT2 0.014 0.025 -9999 0 -0.196 7 7
FOXO1-3a-4/14-3-3 family 0.024 0.108 0.237 3 -0.351 20 23
PDPK1 0.039 0.009 -9999 0 0 29 29
MDM2 0.005 0.088 0.204 15 -0.325 28 43
MAPKKK cascade -0.032 0.092 0.316 29 -0.235 1 30
MDM2/Cbp/p300 0.04 0.104 0.334 3 -0.325 28 31
TSC1/TSC2 -0.003 0.083 0.28 5 -0.309 30 35
proteasomal ubiquitin-dependent protein catabolic process 0.038 0.1 0.322 3 -0.312 28 31
glucose import -0.004 0.036 0.209 11 -0.161 7 18
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.014 0.089 0.249 1 -0.343 11 12
response to stress 0 0 -9999 0 -9999 0 0
SLC2A4 -0.005 0.033 0.208 8 -0.162 7 15
GSK3A 0.005 0.084 0.218 11 -0.323 26 37
FOXO1 0.005 0.081 -9999 0 -0.309 30 30
GSK3B 0.004 0.087 0.22 13 -0.322 28 41
SFN 0.035 0.015 -9999 0 0 83 83
G1/S transition of mitotic cell cycle 0.008 0.097 0.285 11 -0.32 27 38
p27Kip1/14-3-3 family 0.02 0.08 0.22 1 -0.346 11 12
PRKACA 0.035 0.015 -9999 0 0 84 84
KPNA1 0.039 0.009 -9999 0 0 28 28
HSP90AA1 0 0 -9999 0 -9999 0 0
YWHAG 0.039 0.009 -9999 0 0 25 25
RHEB 0.037 0.012 -9999 0 0 53 53
CREBBP 0.037 0.012 -9999 0 0 53 53
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.037 0.013 -9999 0 0 58 58
NFATC1 0.014 0.102 0.265 5 -0.339 16 21
NFATC2 0.023 0.061 0.157 12 -0.192 15 27
NFATC3 0.025 0.016 -9999 0 -9999 0 0
YWHAE 0.037 0.013 -9999 0 0 58 58
Calcineurin A alpha-beta B1/CABIN1 -0.007 0.087 0.169 2 -0.252 32 34
Exportin 1/Ran/NUP214 0.064 0.051 -9999 0 -0.114 32 32
mol:DAG 0.001 0.002 -9999 0 -9999 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.026 0.1 -9999 0 -0.255 23 23
BCL2/BAX 0.051 0.023 -9999 0 -0.134 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 0.029 0.019 -9999 0 -0.125 5 5
CaM/Ca2+ 0.029 0.019 -9999 0 -0.125 5 5
BAX 0.039 0.008 -9999 0 0 23 23
MAPK14 0.04 0.008 -9999 0 0 20 20
BAD 0.041 0.005 -9999 0 0 7 7
CABIN1/MEF2D 0.011 0.093 -9999 0 -0.252 29 29
Calcineurin A alpha-beta B1/BCL2 0.036 0.014 -9999 0 0 67 67
FKBP8 0.036 0.014 -9999 0 0 71 71
activation-induced cell death of T cells -0.011 0.092 0.249 29 -9999 0 29
KPNB1 0.039 0.009 -9999 0 0 25 25
KPNA2 0.035 0.014 -9999 0 0 79 79
XPO1 0.039 0.01 -9999 0 0 35 35
SFN 0.035 0.015 -9999 0 0 83 83
MAP3K8 0.04 0.009 -9999 0 0 24 24
NFAT4/CK1 alpha 0.027 0.044 0.185 1 -0.152 10 11
MEF2D/NFAT1/Cbp/p300 0.067 0.093 0.238 3 -0.205 14 17
CABIN1 -0.006 0.087 0.169 2 -0.254 32 34
CALM1 0.04 0.009 -9999 0 0 26 26
RAN 0.04 0.008 -9999 0 0 21 21
MAP3K1 0.036 0.013 -9999 0 0 63 63
CAMK4 0.037 0.012 -9999 0 0 55 55
mol:Ca2+ 0.001 0.004 -9999 0 -9999 0 0
MAPK3 0.04 0.007 -9999 0 0 18 18
YWHAH 0.038 0.011 -9999 0 0 46 46
Calcineurin A alpha-beta B1/AKAP79/PKA 0.05 0.026 -9999 0 -0.134 2 2
YWHAB 0.038 0.011 -9999 0 0 45 45
MAPK8 0.04 0.01 -9999 0 0 29 29
MAPK9 0.038 0.011 -9999 0 0 39 39
YWHAG 0.039 0.009 -9999 0 0 25 25
FKBP1A 0.038 0.011 -9999 0 0 44 44
NFAT1-c-4/YWHAQ 0.028 0.112 0.257 4 -0.29 25 29
PRKCH 0.038 0.01 -9999 0 0 36 36
CABIN1/Cbp/p300 0.043 0.051 -9999 0 -0.163 24 24
CASP3 0.037 0.013 -9999 0 0 62 62
PIM1 0.038 0.01 -9999 0 0 36 36
Calcineurin A alpha-beta B1/FKBP12/FK506 0.026 0.011 -9999 0 -0.101 2 2
apoptosis 0.017 0.035 -9999 0 -0.188 10 10
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.023 0.075 -9999 0 -0.279 15 15
PRKCB 0 0 -9999 0 -9999 0 0
PRKCE 0.039 0.009 -9999 0 0 28 28
JNK2/NFAT4 0.027 0.066 -9999 0 -0.147 61 61
BAD/BCL-XL 0.051 0.031 -9999 0 -0.134 10 10
PRKCD 0.037 0.012 -9999 0 0 51 51
NUP214 0.038 0.011 -9999 0 0 43 43
PRKCZ 0.04 0.009 -9999 0 0 27 27
PRKCA 0.035 0.015 -9999 0 0 86 86
PRKCG 0.039 0.009 -9999 0 0 27 27
PRKCQ 0.035 0.015 -9999 0 0 85 85
FKBP38/BCL2 0.046 0.028 -9999 0 -0.134 2 2
EP300 0.037 0.014 -9999 0 0 69 69
PRKCB1 0.038 0.011 -9999 0 0 46 46
CSNK2A1 0.038 0.012 -9999 0 0 47 47
NFATc/JNK1 0.028 0.108 0.257 4 -0.323 17 21
CaM/Ca2+/FKBP38 0.047 0.027 -9999 0 -0.131 4 4
FKBP12/FK506 0.028 0.012 -9999 0 -0.125 2 2
CSNK1A1 0.017 0.018 0.097 5 -0.108 4 9
CaM/Ca2+/CAMK IV 0.048 0.027 -9999 0 -0.109 7 7
NFATc/ERK1 0.029 0.108 0.275 5 -0.325 16 21
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.023 0.101 -9999 0 -0.245 27 27
NR4A1 0.012 0.074 0.195 15 -0.218 22 37
GSK3B 0.04 0.009 -9999 0 0 23 23
positive T cell selection 0.025 0.015 -9999 0 -9999 0 0
NFAT1/CK1 alpha 0.021 0.049 0.123 9 -0.187 12 21
RCH1/ KPNB1 0.036 0.062 -9999 0 -0.138 58 58
YWHAQ 0.04 0.007 -9999 0 0 18 18
PRKACA 0.035 0.015 -9999 0 0 84 84
AKAP5 0.04 0.007 -9999 0 0 14 14
MEF2D 0.041 0.008 -9999 0 0 18 18
mol:FK506 0 0 -9999 0 -9999 0 0
YWHAZ 0.034 0.016 -9999 0 0 96 96
NFATc/p38 alpha 0.03 0.107 0.275 5 -0.308 17 22
CREBBP 0.038 0.013 -9999 0 0 53 53
BCL2 0.036 0.014 -9999 0 0 67 67
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.053 0.094 -9999 0 -0.202 39 39
Ran/GTP/Exportin 1/HDAC1 -0.029 0.032 -9999 0 -0.124 45 45
NF kappa B1 p50/RelA/I kappa B alpha 0.022 0.103 0.237 1 -0.282 35 36
SUMO1 0.04 0.007 -9999 0 0 14 14
ZFPM1 0.035 0.015 -9999 0 0 86 86
NPC/RanGAP1/SUMO1/Ubc9 0.009 0.034 -9999 0 -0.142 25 25
FKBP3 0.039 0.009 -9999 0 0 30 30
Histones 0.069 0.085 0.24 1 -0.242 13 14
YY1/LSF 0.01 0.084 -9999 0 -0.23 42 42
SMG5 0 0 -9999 0 -9999 0 0
RAN 0.04 0.008 -9999 0 0 21 21
I kappa B alpha/HDAC3 0.016 0.059 -9999 0 -0.175 38 38
I kappa B alpha/HDAC1 0.029 0.088 0.214 1 -0.233 44 45
SAP18 0.039 0.008 -9999 0 0 24 24
RELA 0.015 0.083 0.231 2 -0.253 24 26
HDAC1/Smad7 0.063 0.051 -9999 0 -0.116 31 31
RANGAP1 0.037 0.012 -9999 0 0 54 54
HDAC3/TR2 0.045 0.061 0.214 1 -0.226 14 15
NuRD/MBD3 Complex 0.008 0.094 -9999 0 -0.287 30 30
NF kappa B1 p50/RelA 0.019 0.103 0.225 2 -0.272 38 40
EntrezGene:23225 0 0 -9999 0 -9999 0 0
GATA2 0.039 0.01 -9999 0 0 31 31
GATA1 0.041 0.002 -9999 0 0 1 1
Mad/Max 0.058 0.013 -9999 0 -9999 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.002 0.105 -9999 0 -0.273 43 43
RBBP7 0.039 0.009 -9999 0 0 25 25
NPC 0.019 0.022 -9999 0 -0.083 23 23
RBBP4 0.038 0.011 -9999 0 0 40 40
MAX 0.04 0.006 -9999 0 0 12 12
EntrezGene:9972 0 0 -9999 0 -9999 0 0
FBXW11 0.04 0.008 -9999 0 0 22 22
NFKBIA 0.01 0.066 -9999 0 -0.259 28 28
KAT2B 0 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
SIN3/HDAC complex 0.009 0.084 -9999 0 -0.268 26 26
SIN3 complex 0.076 0.053 -9999 0 -0.113 12 12
SMURF1 0.04 0.006 -9999 0 0 13 13
CHD3 0.037 0.013 -9999 0 0 56 56
SAP30 0.038 0.011 -9999 0 0 46 46
EntrezGene:23636 0 0 -9999 0 -9999 0 0
NCOR1 0.037 0.013 -9999 0 0 58 58
YY1/HDAC3 0.015 0.077 -9999 0 -0.244 27 27
YY1/HDAC2 0.013 0.078 -9999 0 -0.216 39 39
YY1/HDAC1 0.01 0.08 -9999 0 -0.221 39 39
NuRD/MBD2 Complex (MeCP1) 0.01 0.095 -9999 0 -0.291 30 30
PPARG 0.027 0.066 0.25 2 -0.202 26 28
HDAC8/hEST1B 0.041 0.035 -9999 0 -0.109 20 20
UBE2I 0.039 0.009 -9999 0 0 27 27
beta TrCP1/SCF ubiquitin ligase complex 0.039 0.008 -9999 0 0 22 22
TNFRSF1A 0.036 0.014 -9999 0 0 72 72
HDAC3/SMRT (N-CoR2) 0.046 0.06 0.214 1 -0.225 13 14
MBD3L2 0.038 0.011 -9999 0 0 43 43
ubiquitin-dependent protein catabolic process 0.063 0.051 -9999 0 -0.116 31 31
CREBBP 0.037 0.012 -9999 0 0 53 53
NuRD/MBD3/MBD3L2 Complex 0.004 0.108 0.183 8 -0.27 46 54
HDAC1 0.038 0.012 -9999 0 0 49 49
HDAC3 0.023 0.031 -9999 0 -0.239 4 4
HDAC2 0.038 0.01 -9999 0 0 38 38
YY1 0.005 0.056 -9999 0 -0.24 23 23
HDAC8 0.039 0.009 -9999 0 0 26 26
SMAD7 0.038 0.01 -9999 0 0 36 36
NCOR2 0.039 0.01 -9999 0 0 31 31
MXD1 0.04 0.007 -9999 0 0 15 15
STAT3 0.008 0.067 -9999 0 -0.238 33 33
NFKB1 0.036 0.013 -9999 0 0 66 66
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.039 0.009 -9999 0 0 30 30
YY1/LSF/HDAC1 0.021 0.093 -9999 0 -0.215 46 46
YY1/SAP30/HDAC1 0.024 0.086 -9999 0 -0.205 40 40
EP300 0.036 0.014 -9999 0 0 69 69
STAT3 (dimer non-phopshorylated) 0.008 0.066 -9999 0 -0.238 33 33
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.066 -9999 0 -0.258 28 28
histone deacetylation 0.011 0.095 0.167 5 -0.288 30 35
STAT3 (dimer non-phopshorylated)/HDAC3 0.018 0.083 -9999 0 -0.278 22 22
nuclear export -0.041 0.035 0.108 20 -9999 0 20
PRKACA 0.035 0.015 -9999 0 0 84 84
GATAD2B 0.038 0.011 -9999 0 0 41 41
GATAD2A 0.037 0.012 -9999 0 0 54 54
GATA2/HDAC3 0.046 0.059 0.214 1 -0.211 15 16
GATA1/HDAC1 0.05 0.041 -9999 0 -0.134 24 24
GATA1/HDAC3 0.049 0.06 0.214 1 -0.211 17 18
CHD4 0.036 0.014 -9999 0 0 69 69
TNF-alpha/TNFR1A 0.047 0.038 -9999 0 -0.134 16 16
SIN3/HDAC complex/Mad/Max 0.015 0.08 -9999 0 -0.258 23 23
NuRD Complex 0.001 0.106 0.183 7 -0.281 40 47
positive regulation of chromatin silencing 0.065 0.082 0.231 1 -0.238 13 14
SIN3B 0.036 0.014 -9999 0 0 67 67
MTA2 0.04 0.006 -9999 0 0 10 10
SIN3A 0.039 0.009 -9999 0 0 30 30
XPO1 0.039 0.01 -9999 0 0 35 35
SUMO1/HDAC1 0.034 0.066 -9999 0 -0.183 25 25
HDAC complex 0.073 0.074 -9999 0 -0.133 51 51
GATA1/Fog1 0.051 0.022 -9999 0 -9999 0 0
FKBP25/HDAC1/HDAC2 0.058 0.06 -9999 0 -0.127 41 41
TNF 0.04 0.008 -9999 0 0 22 22
negative regulation of cell growth 0.015 0.081 0.167 1 -0.255 24 25
NuRD/MBD2/PRMT5 Complex 0.01 0.095 -9999 0 -0.291 30 30
Ran/GTP/Exportin 1 0.035 0.071 -9999 0 -0.176 36 36
NF kappa B/RelA/I kappa B alpha 0.005 0.078 -9999 0 -0.26 31 31
SIN3/HDAC complex/NCoR1 0.001 0.093 -9999 0 -0.239 44 44
TFCP2 0.039 0.01 -9999 0 0 35 35
NR2C1 0.039 0.01 -9999 0 0 33 33
MBD3 0.036 0.014 -9999 0 0 69 69
MBD2 0.039 0.01 -9999 0 0 32 32
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.038 0.011 -9999 0 0 43 43
SMAD2 0.012 0.052 0.187 7 -0.231 3 10
SMAD3 0.014 0.054 0.281 1 -0.302 4 5
SMAD3/SMAD4 -0.015 0.162 -9999 0 -0.389 78 78
SMAD4/Ubc9/PIASy 0.065 0.041 -9999 0 -0.126 9 9
SMAD2/SMAD2/SMAD4 0.053 0.083 0.271 1 -0.18 9 10
PPM1A 0.04 0.006 -9999 0 0 10 10
CALM1 0.039 0.009 -9999 0 0 26 26
SMAD2/SMAD4 0.03 0.051 0.218 2 -0.179 7 9
MAP3K1 0.036 0.013 -9999 0 0 63 63
TRAP-1/SMAD4 0.049 0.041 -9999 0 -0.139 21 21
MAPK3 0.04 0.007 -9999 0 0 18 18
MAPK1 0.038 0.011 -9999 0 0 44 44
NUP214 0.038 0.011 -9999 0 0 43 43
CTDSP1 0.04 0.007 -9999 0 0 15 15
CTDSP2 0.039 0.009 -9999 0 0 29 29
CTDSPL 0.04 0.007 -9999 0 0 15 15
KPNB1 0.039 0.009 -9999 0 0 25 25
TGFBRAP1 0.04 0.008 -9999 0 0 20 20
UBE2I 0.039 0.009 -9999 0 0 27 27
NUP153 0.037 0.013 -9999 0 0 57 57
KPNA2 0.035 0.014 -9999 0 0 79 79
PIAS4 0.037 0.012 -9999 0 0 54 54
Atypical NF-kappaB 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
BCL3/RelA 0.053 0.025 -9999 0 -0.134 4 4
FBXW11 0.04 0.008 -9999 0 0 22 22
NF kappa B1 p50/c-Rel 0.028 0.036 -9999 0 -0.116 26 26
NF kappa B1 p50/RelA/I kappa B alpha 0.019 0.077 0.261 1 -0.22 21 22
NFKBIA 0.003 0.06 -9999 0 -0.147 53 53
MAPK14 0.04 0.008 -9999 0 0 20 20
NF kappa B1 p105/p50 0.027 0.039 -9999 0 -0.126 27 27
ARRB2 0.014 0.028 -9999 0 -0.196 9 9
REL 0.04 0.007 -9999 0 0 15 15
response to oxidative stress 0 0 -9999 0 -9999 0 0
BCL3/NF kappa B1 p50 0.027 0.035 -9999 0 -0.12 23 23
response to UV 0 0 -9999 0 -9999 0 0
NF kappa B1 p105/RelA 0.028 0.038 -9999 0 -0.119 29 29
PIK3CA 0.029 0.019 -9999 0 0 166 166
NF kappa B1 p50 dimer 0.019 0.039 -9999 0 -0.138 28 28
PIK3R1 0.034 0.016 -9999 0 0 99 99
NFKB1 -0.017 0.008 -9999 0 -9999 0 0
RELA 0.04 0.006 -9999 0 0 10 10
positive regulation of anti-apoptosis 0.012 0.051 0.135 1 -0.184 12 13
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.018 0.081 0.229 1 -0.223 24 25
SRC 0.039 0.009 -9999 0 0 28 28
PI3K 0.023 0.06 -9999 0 -0.15 44 44
NF kappa B1 p50/RelA 0.012 0.051 0.136 1 -0.185 12 13
IKBKB 0.038 0.011 -9999 0 0 41 41
beta TrCP1/SCF ubiquitin ligase complex 0.039 0.008 -9999 0 0 22 22
SYK 0.036 0.014 -9999 0 0 67 67
I kappa B alpha/PIK3R1 0.016 0.068 0.268 1 -0.238 12 13
cell death 0.017 0.078 0.221 1 -0.215 24 25
NF kappa B1 p105/c-Rel 0.028 0.036 -9999 0 -0.116 26 26
LCK 0.039 0.009 -9999 0 0 25 25
BCL3 0.037 0.012 -9999 0 0 51 51
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 -0.02 0.076 -9999 0 -0.388 10 10
SMARCC2 0.039 0.009 -9999 0 0 29 29
SMARCC1 0.04 0.007 -9999 0 0 18 18
TBX21 0.04 0.06 0.411 2 -0.265 1 3
SUMO2 0.037 0.015 -9999 0 -0.014 36 36
STAT1 (dimer) 0.022 0.064 -9999 0 -0.18 45 45
FKBP4 0.036 0.014 -9999 0 0 73 73
FKBP5 0.03 0.018 -9999 0 0 142 142
GR alpha/HSP90/FKBP51/HSP90 -0.034 0.074 0.208 3 -0.214 17 20
PRL 0.044 0.063 -9999 0 -9999 0 0
cortisol/GR alpha (dimer)/TIF2 -0.056 0.119 0.401 4 -0.343 2 6
RELA 0.012 0.095 -9999 0 -0.163 117 117
FGG -0.053 0.111 0.35 4 -0.321 1 5
GR beta/TIF2 -0.032 0.08 0.25 2 -0.237 6 8
IFNG 0.045 0.105 -9999 0 -0.411 1 1
apoptosis -0.053 0.172 -9999 0 -0.413 75 75
CREB1 0.048 0.009 -9999 0 -9999 0 0
histone acetylation 0.023 0.079 0.327 6 -0.387 6 12
BGLAP 0.045 0.083 -9999 0 -0.882 2 2
GR/PKAc 0.031 0.083 0.298 1 -0.154 22 23
NF kappa B1 p50/RelA 0.011 0.169 -9999 0 -0.292 115 115
SMARCD1 0.04 0.007 -9999 0 0 17 17
MDM2 -0.013 0.047 0.128 7 -0.241 8 15
GATA3 0.049 0.013 -9999 0 -9999 0 0
AKT1 0.035 0.015 0.168 2 -0.048 6 8
CSF2 0.012 0.052 -9999 0 -9999 0 0
GSK3B 0.037 0.014 -9999 0 -0.012 38 38
NR1I3 -0.045 0.154 -9999 0 -0.411 29 29
CSN2 -0.049 0.096 0.278 6 -0.296 2 8
BRG1/BAF155/BAF170/BAF60A 0.074 0.065 -9999 0 -0.131 30 30
NFATC1 0.043 0.017 -9999 0 -9999 0 0
POU2F1 0.045 0.008 -9999 0 -9999 0 0
CDKN1A -0.043 0.121 -9999 0 -9999 0 0
response to stress 0 0 -9999 0 -9999 0 0
response to UV -0.001 0.004 -9999 0 -9999 0 0
SFN 0.035 0.015 -9999 0 0 83 83
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.03 0.079 0.234 2 -0.196 24 26
prolactin receptor activity 0 0 -9999 0 -9999 0 0
EGR1 -0.103 0.276 -9999 0 -0.701 89 89
JUN 0.04 0.096 0.333 8 -0.277 4 12
IL4 0.042 0.057 -9999 0 -9999 0 0
CDK5R1 0.038 0.011 -9999 0 0 40 40
PRKACA 0.035 0.015 -9999 0 0 84 84
cortisol/GR alpha (monomer)/AP-1 -0.039 0.067 0.199 11 -0.219 23 34
GR alpha/HSP90/FKBP51/HSP90/PP5C -0.024 0.079 0.238 2 -0.199 17 19
cortisol/GR alpha (monomer) -0.069 0.129 0.424 5 -0.398 1 6
NCOA2 0.037 0.013 -9999 0 0 60 60
response to hypoxia 0 0 -9999 0 -9999 0 0
FOS 0.032 0.055 -9999 0 -0.13 29 29
AP-1/NFAT1-c-4 0.038 0.139 -9999 0 -0.38 18 18
AFP 0.03 0.094 -9999 0 -9999 0 0
SUV420H1 0.039 0.009 -9999 0 0 30 30
IRF1 -0.102 0.216 -9999 0 -0.572 82 82
TP53 0.035 0.028 -9999 0 -9999 0 0
PPP5C 0.039 0.009 -9999 0 0 27 27
KRT17 0.028 0.156 -9999 0 -0.772 11 11
KRT14 0.023 0.186 0.501 8 -1.064 12 20
TBP 0.043 0.027 -9999 0 -0.325 2 2
CREBBP 0.03 0.054 0.331 13 -9999 0 13
HDAC1 0.033 0.012 -9999 0 -0.058 2 2
HDAC2 0.037 0.01 -9999 0 -9999 0 0
AP-1 0.038 0.139 -9999 0 -0.382 18 18
MAPK14 0.037 0.015 -9999 0 -0.015 39 39
MAPK10 0.033 0.02 -9999 0 -0.009 90 90
MAPK11 0.027 0.021 -9999 0 -0.002 170 170
KRT5 -0.01 0.255 -9999 0 -0.827 43 43
interleukin-1 receptor activity -0.001 0 -9999 0 -9999 0 0
NCOA1 0.04 0.011 -9999 0 -0.068 2 2
STAT1 0.022 0.064 -9999 0 -0.18 45 45
CGA 0.045 0.065 0.303 1 -9999 0 1
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.059 0.111 0.295 4 -0.344 37 41
MAPK3 0.035 0.019 -9999 0 -0.019 52 52
MAPK1 0.035 0.017 -9999 0 -0.01 65 65
ICAM1 -0.079 0.316 -9999 0 -0.771 89 89
NFKB1 0.006 0.108 -9999 0 -0.194 111 111
MAPK8 0.049 0.083 0.476 2 -0.257 3 5
MAPK9 0.035 0.017 -9999 0 -0.01 59 59
cortisol/GR alpha (dimer) -0.056 0.178 -9999 0 -0.425 79 79
BAX -0.05 0.118 -9999 0 -9999 0 0
POMC 0.052 0.092 0.487 2 -9999 0 2
EP300 0.028 0.047 0.317 10 -9999 0 10
cortisol/GR alpha (dimer)/p53 -0.073 0.123 0.408 4 -0.361 1 5
proteasomal ubiquitin-dependent protein catabolic process -0.026 0.047 0.253 5 -0.222 8 13
SGK1 -0.025 0.114 0.342 10 -0.299 47 57
IL13 0.047 0.094 -9999 0 -9999 0 0
IL6 0.011 0.155 -9999 0 -0.645 15 15
PRKACG 0.04 0.008 -9999 0 0 22 22
IL5 0.046 0.096 -9999 0 -9999 0 0
IL2 0.037 0.124 -9999 0 -0.53 6 6
CDK5 0.035 0.014 -9999 0 0 69 69
PRKACB 0.038 0.011 -9999 0 0 44 44
HSP90AA1 0 0 -9999 0 -9999 0 0
IL8 -0.013 0.219 -9999 0 -0.799 32 32
CDK5R1/CDK5 0.044 0.04 -9999 0 -0.131 19 19
NF kappa B1 p50/RelA/PKAc 0.042 0.15 -9999 0 -0.222 91 91
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 -0.043 0.11 0.37 5 -0.313 1 6
SMARCA4 0.034 0.015 -9999 0 0 92 92
chromatin remodeling -0.03 0.091 0.272 4 -0.358 10 14
NF kappa B1 p50/RelA/Cbp 0.025 0.159 0.414 6 -0.249 102 108
JUN (dimer) 0.04 0.096 0.333 8 -0.276 4 12
YWHAH 0.038 0.011 -9999 0 0 46 46
VIPR1 0.041 0.057 0.401 1 -0.265 1 2
NR3C1 -0.044 0.091 0.299 3 -0.321 3 6
NR4A1 0.038 0.018 -9999 0 -9999 0 0
TIF2/SUV420H1 0.042 0.051 -9999 0 -0.137 36 36
MAPKKK cascade -0.053 0.172 -9999 0 -0.413 75 75
cortisol/GR alpha (dimer)/Src-1 -0.052 0.126 0.401 5 -0.344 1 6
PBX1 0.043 0.012 -9999 0 -9999 0 0
POU1F1 0.046 0.008 -9999 0 -9999 0 0
SELE 0.023 0.114 -9999 0 -0.397 4 4
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A -0.03 0.091 0.273 4 -0.361 10 14
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.043 0.11 0.37 5 -0.313 1 6
mol:cortisol -0.042 0.066 0.21 7 -9999 0 7
MMP1 0.008 0.16 -9999 0 -0.752 19 19
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.016 0.088 -9999 0 -0.378 23 23
Crk/p130 Cas/Paxillin 0.005 0.037 -9999 0 -0.175 4 4
JUN 0.002 0.062 0.19 4 -0.227 13 17
HRAS 0.039 0.01 -9999 0 0 31 31
RET51/GFRalpha1/GDNF/GRB10 0.088 0.039 -9999 0 -0.11 5 5
RAP1A 0.039 0.01 -9999 0 0 35 35
FRS2 0.038 0.011 -9999 0 0 41 41
RAP1A/GDP 0.023 0.031 -9999 0 -0.125 22 22
RET51/GFRalpha1/GDNF/DOK1 0.088 0.039 -9999 0 -0.11 5 5
EntrezGene:5979 0 0 -9999 0 -9999 0 0
PTPN11 0.039 0.009 -9999 0 0 29 29
mol:GTP 0 0 -9999 0 -9999 0 0
CRK 0.038 0.012 -9999 0 0 49 49
RET9/GFRalpha1/GDNF/Enigma 0.064 0.033 -9999 0 -0.103 2 2
RHOA 0.04 0.006 -9999 0 0 13 13
RAP1A/GTP 0.075 0.05 -9999 0 -0.104 15 15
GRB7 0.037 0.013 -9999 0 0 57 57
RET51/GFRalpha1/GDNF 0.078 0.045 -9999 0 -0.11 3 3
MAPKKK cascade 0.032 0.046 -9999 0 -0.145 3 3
BCAR1 0.036 0.013 -9999 0 0 65 65
RET9/GFRalpha1/GDNF/IRS1 0.063 0.034 -9999 0 -0.103 5 5
lamellipodium assembly 0.03 0.05 -9999 0 -0.185 3 3
RET51/GFRalpha1/GDNF/SHC 0.088 0.036 -9999 0 -0.11 1 1
PIK3CA 0.029 0.019 -9999 0 0 166 166
RET9/GFRalpha1/GDNF/SHC 0.064 0.033 -9999 0 -0.103 2 2
RET9/GFRalpha1/GDNF/Shank3 0.05 0.039 -9999 0 -0.103 1 1
MAPK3 -0.009 0.063 0.182 38 -9999 0 38
DOK1 0.04 0.008 -9999 0 0 22 22
DOK6 0.038 0.011 -9999 0 0 45 45
PXN 0.04 0.006 -9999 0 0 10 10
neurite development 0 0.059 0.218 13 -0.205 4 17
DOK5 0.022 0.021 -9999 0 0 260 260
GFRA1 0.037 0.012 -9999 0 0 54 54
MAPK8 0.013 0.059 0.203 1 -0.234 10 11
HRAS/GTP 0.08 0.046 -9999 0 -0.147 3 3
tube development 0.047 0.043 0.236 9 -0.103 2 11
MAPK1 -0.01 0.061 0.184 34 -9999 0 34
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.02 0.046 -9999 0 -0.171 24 24
Rac1/GDP 0.029 0.009 -9999 0 -0.125 1 1
SRC 0.039 0.009 -9999 0 0 28 28
PDLIM7 0.039 0.009 -9999 0 0 30 30
RET51/GFRalpha1/GDNF/Dok6 0.093 0.052 -9999 0 -0.109 1 1
SHC1 0.039 0.008 -9999 0 0 23 23
RET51/GFRalpha1/GDNF/Dok4 0.086 0.039 -9999 0 -0.11 1 1
RET51/GFRalpha1/GDNF/Dok5 0.039 0.078 -9999 0 -0.11 88 88
PRKCA 0.035 0.015 -9999 0 0 86 86
HRAS/GDP 0.029 0.007 -9999 0 -9999 0 0
CREB1 0.036 0.06 -9999 0 -0.367 4 4
PIK3R1 0.034 0.016 -9999 0 0 99 99
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.024 0.032 -9999 0 -0.144 11 11
RET51/GFRalpha1/GDNF/Grb7 0.083 0.044 -9999 0 -0.11 6 6
mol:GDP 0 0 -9999 0 -9999 0 0
RET 0.039 0.008 -9999 0 0 23 23
DOK4 0.038 0.01 -9999 0 0 37 37
JNK cascade 0.002 0.062 0.18 6 -0.224 13 19
RET9/GFRalpha1/GDNF/FRS2 0.059 0.04 -9999 0 -0.103 11 11
SHANK3 0.03 0.018 -9999 0 0 152 152
RASA1 0.037 0.013 -9999 0 0 56 56
NCK1 0.036 0.014 -9999 0 0 70 70
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.023 0.037 -9999 0 -0.138 22 22
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.026 0.048 -9999 0 -0.17 24 24
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.018 0.056 -9999 0 -0.161 35 35
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.029 0.039 -9999 0 -0.148 19 19
PI3K 0.045 0.064 0.222 8 -0.253 2 10
SOS1 0.037 0.012 -9999 0 0 51 51
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.062 0.047 -9999 0 -0.103 2 2
GRB10 0.04 0.008 -9999 0 0 22 22
activation of MAPKK activity 0.029 0.052 -9999 0 -0.31 5 5
RET51/GFRalpha1/GDNF/FRS2 0.083 0.046 -9999 0 -0.11 11 11
GAB1 0.037 0.013 -9999 0 0 58 58
IRS1 0.04 0.008 -9999 0 0 22 22
IRS2 0.039 0.009 -9999 0 0 30 30
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.029 0.034 -9999 0 -0.173 1 1
RET51/GFRalpha1/GDNF/PKC alpha 0.075 0.057 -9999 0 -0.11 30 30
GRB2 0.04 0.008 -9999 0 0 21 21
PRKACA 0.035 0.015 -9999 0 0 84 84
GDNF 0.039 0.01 -9999 0 0 35 35
RAC1 0.039 0.009 -9999 0 0 28 28
RET51/GFRalpha1/GDNF/IRS1 0.088 0.038 -9999 0 -0.11 5 5
Rac1/GTP 0.044 0.063 0.195 4 -0.215 3 7
RET9/GFRalpha1/GDNF 0.047 0.021 -9999 0 -0.109 1 1
GFRalpha1/GDNF 0.051 0.024 -9999 0 -0.134 1 1
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.04 0.008 -9999 0 0 20 20
SPHK1 0.039 0.008 -9999 0 0 24 24
GNAI2 0.04 0.006 -9999 0 0 13 13
mol:S1P 0.015 0.025 -9999 0 -0.172 9 9
GNAO1 0.035 0.015 -9999 0 0 85 85
mol:Sphinganine-1-P -0.019 0.006 -9999 0 -9999 0 0
growth factor activity 0 0 -9999 0 -9999 0 0
S1P/S1P2/G12/G13 0.05 0.048 -9999 0 -0.164 10 10
GNAI3 0.038 0.011 -9999 0 0 45 45
G12/G13 0.053 0.028 -9999 0 -0.134 8 8
S1PR3 0 0 -9999 0 -9999 0 0
S1PR2 0 0 -9999 0 -9999 0 0
EDG1 0.04 0.006 -9999 0 0 11 11
S1P1/S1P 0.036 0.043 0.164 1 -0.116 35 36
S1PR5 0 0 -9999 0 -9999 0 0
S1PR4 0 0 -9999 0 -9999 0 0
GNAI1 0.034 0.015 -9999 0 0 93 93
S1P/S1P5/G12 0.031 0.039 -9999 0 -0.145 10 10
S1P/S1P3/Gq 0.016 0.074 0.166 1 -0.244 35 36
S1P/S1P4/Gi -0.009 0.091 0.151 1 -0.204 68 69
GNAQ 0.038 0.012 -9999 0 0 48 48
GNAZ 0.038 0.011 -9999 0 0 46 46
GNA14 0.039 0.009 -9999 0 0 29 29
GNA15 0.036 0.014 -9999 0 0 68 68
GNA12 0.039 0.01 -9999 0 0 33 33
GNA13 0.039 0.008 -9999 0 0 23 23
GNA11 0.037 0.013 -9999 0 0 61 61
ABCC1 0.039 0.009 -9999 0 0 27 27
Insulin 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
CBL/APS/CAP 0.059 0.041 -9999 0 -0.116 10 10
TC10/GTP 0.051 0.035 -9999 0 -0.101 11 11
Insulin Receptor/Insulin/IRS1/Shp2 0.086 0.058 -9999 0 -0.119 22 22
HRAS 0.039 0.01 -9999 0 0 31 31
APS homodimer 0 0 -9999 0 -9999 0 0
GRB14 0.038 0.012 -9999 0 0 49 49
FOXO3 -0.004 0.009 0.022 12 -0.036 6 18
AKT1 0.022 0.1 0.208 56 -0.173 3 59
INSR 0.041 0.016 0.081 10 -0.049 1 11
Insulin Receptor/Insulin 0.084 0.058 0.24 37 -0.136 4 41
mol:GTP 0 0 -9999 0 -9999 0 0
GRB10 0.04 0.008 -9999 0 0 22 22
SORBS1 0.039 0.009 -9999 0 0 30 30
CRK 0.038 0.012 -9999 0 0 49 49
PTPN1 -0.007 0.04 0.152 28 -0.239 1 29
CAV1 -0.007 0.042 0.173 17 -9999 0 17
CBL/APS/CAP/Crk-II/C3G 0.08 0.04 -9999 0 -0.105 6 6
Insulin Receptor/Insulin/IRS1/NCK2 0.093 0.046 -9999 0 -0.105 9 9
mol:GDP 0 0 -9999 0 -9999 0 0
mol:PI-3-4-5-P3 0.037 0.063 -9999 0 -0.107 44 44
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.023 0.097 0.223 1 -0.308 36 37
RPS6KB1 0.012 0.093 0.156 126 -0.184 8 134
PARD6A 0.037 0.013 -9999 0 0 61 61
CBL 0.04 0.008 -9999 0 0 20 20
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -9999 0 0
DOK1 0.023 0.078 -9999 0 -0.703 6 6
PIK3R1 0.034 0.016 -9999 0 0 99 99
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.054 0.083 0.199 25 -0.182 11 36
HRAS/GTP -0.026 0.032 0.049 2 -0.109 19 21
Insulin Receptor 0.041 0.015 0.081 10 -0.049 1 11
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.1 0.06 -9999 0 -0.112 9 9
PRKCI -0.013 0.136 -9999 0 -0.373 61 61
Insulin Receptor/Insulin/GRB14/PDK1 0.017 0.051 -9999 0 -0.115 41 41
SHC1 0.039 0.008 -9999 0 0 23 23
negative regulation of MAPKKK cascade 0.049 0.079 -9999 0 -0.529 6 6
PI3K 0.047 0.071 -9999 0 -0.108 44 44
NCK2 0.041 0.004 -9999 0 0 6 6
RHOQ 0.039 0.009 -9999 0 0 25 25
mol:H2O2 -0.002 0.004 0.019 1 -0.032 1 2
HRAS/GDP 0.029 0.007 -9999 0 -9999 0 0
AKT2 0.018 0.094 0.199 47 -0.173 3 50
PRKCZ 0.025 0.108 -9999 0 -0.327 41 41
SH2B2 0 0 -9999 0 -9999 0 0
SHC/SHIP -0.008 0.04 0.156 16 -0.122 1 17
F2RL2 0.036 0.013 -9999 0 0 63 63
TRIP10 0.038 0.012 -9999 0 0 49 49
Insulin Receptor/Insulin/Shc 0.07 0.037 -9999 0 -0.101 5 5
TC10/GTP/CIP4/Exocyst 0.046 0.029 -9999 0 -0.109 12 12
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.092 0.069 -9999 0 -0.115 20 20
RAPGEF1 0.039 0.009 -9999 0 0 26 26
RASA1 0.037 0.013 -9999 0 0 56 56
NCK1 0.036 0.014 -9999 0 0 70 70
CBL/APS/CAP/Crk-II 0.065 0.034 -9999 0 -0.113 6 6
TC10/GDP 0.027 0.019 -9999 0 -0.125 8 8
Insulin Receptor/Insulin/SHC/GRB10 0.089 0.051 -9999 0 -0.104 11 11
INPP5D -0.013 0.017 0.053 11 -0.091 8 19
SOS1 0.037 0.012 -9999 0 0 51 51
SGK1 -0.004 0.004 -9999 0 -9999 0 0
mol:cAMP 0 0 -9999 0 -9999 0 0
PTPN11 0.039 0.009 -9999 0 0 29 29
IRS1 0.04 0.008 -9999 0 0 22 22
p62DOK/RasGAP 0.05 0.079 -9999 0 -0.535 6 6
INS 0.043 0.014 0.082 13 -0.002 31 44
mol:PI-3-4-P2 -0.013 0.017 0.053 11 -0.09 8 19
GRB2 0.04 0.008 -9999 0 0 21 21
EIF4EBP1 0.009 0.085 0.153 111 -0.162 3 114
PTPRA 0.042 0.013 0.083 3 -0.049 1 4
PIK3CA 0.029 0.019 -9999 0 0 166 166
TC10/GTP/CIP4 0.046 0.029 -9999 0 -0.109 12 12
PDPK1 0.039 0.009 -9999 0 0 29 29
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.02 0.055 -9999 0 -0.158 27 27
Insulin Receptor/Insulin/IRS1 0.069 0.038 -9999 0 -0.099 8 8
Insulin Receptor/Insulin/IRS3 0.058 0.031 -9999 0 -0.12 4 4
Par3/Par6 0.069 0.049 -9999 0 -0.098 14 14
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.039 0.009 0 28 -9999 0 28
PI3K Class IB/PDE3B 0.039 0.009 -9999 0 0 28 28
PDE3B 0.039 0.009 -9999 0 0 28 28
Coregulation of Androgen receptor activity

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
NRIP1 0.035 0.016 -9999 0 -9999 0 0
SVIL 0.036 0.015 -9999 0 -9999 0 0
ZNF318 0.037 0.009 -9999 0 -0.032 2 2
JMJD2C 0.041 0.016 -9999 0 -9999 0 0
T-DHT/AR/Ubc9 0.037 0.06 -9999 0 -0.103 74 74
CARM1 0.036 0.014 -9999 0 0 71 71
PRDX1 0.039 0.009 -9999 0 0 31 31
PELP1 0.038 0.011 -9999 0 0 39 39
CTNNB1 0.04 0.01 -9999 0 -9999 0 0
AKT1 0.038 0.01 -9999 0 0 34 34
PTK2B 0.034 0.016 -9999 0 -9999 0 0
MED1 -0.001 0 -9999 0 -9999 0 0
MAK 0.033 0.014 -9999 0 -0.032 2 2
response to oxidative stress 0 0 -9999 0 -9999 0 0
HIP1 0.04 0.01 -9999 0 -9999 0 0
GSN 0.039 0.011 -9999 0 -9999 0 0
NCOA2 0.037 0.013 -9999 0 0 60 60
NCOA6 0.039 0.011 -9999 0 -9999 0 0
DNA-PK 0.049 0.067 -9999 0 -0.14 47 47
NCOA4 0.039 0.009 -9999 0 0 26 26
PIAS3 0.038 0.012 -9999 0 -9999 0 0
cell proliferation 0.019 0.042 -9999 0 -0.435 4 4
XRCC5 0.038 0.011 -9999 0 0 41 41
UBE3A 0.04 0.01 -9999 0 -9999 0 0
T-DHT/AR/SNURF 0.034 0.062 -9999 0 -0.106 74 74
FHL2 0.026 0.061 -9999 0 -0.583 4 4
RANBP9 0.039 0.012 -9999 0 -9999 0 0
JMJD1A 0.051 0.018 -9999 0 -0.137 1 1
CDK6 0.032 0.017 -9999 0 0 126 126
TGFB1I1 0.041 0.006 -9999 0 -9999 0 0
T-DHT/AR/CyclinD1 0.013 0.077 -9999 0 -0.116 125 125
XRCC6 0.036 0.014 -9999 0 0 69 69
T-DHT/AR 0.037 0.056 -9999 0 -0.099 68 68
CTDSP1 0.04 0.007 -9999 0 0 15 15
CTDSP2 0.038 0.009 -9999 0 -9999 0 0
BRCA1 0.035 0.016 -9999 0 -9999 0 0
TCF4 0.036 0.012 -9999 0 0 54 54
CDKN2A 0.028 0.019 -9999 0 0 167 167
SRF 0.043 0.019 -9999 0 -0.143 3 3
NKX3-1 0.014 0.083 -9999 0 -0.299 30 30
KLK3 0.004 0.048 -9999 0 -9999 0 0
TMF1 0.039 0.01 -9999 0 0 37 37
HNRNPA1 -0.001 0 -9999 0 -9999 0 0
AOF2 0.04 0.009 -9999 0 -9999 0 0
APPL1 -0.011 0.003 -9999 0 -9999 0 0
T-DHT/AR/Caspase 8 0.033 0.064 -9999 0 -0.106 86 86
AR 0.037 0.02 -9999 0 -0.042 1 1
UBA3 0 0 -9999 0 -9999 0 0
PATZ1 -0.001 0 -9999 0 -9999 0 0
PAWR 0.041 0.006 -9999 0 0 11 11
PRKDC 0.037 0.011 -9999 0 0 44 44
PA2G4 0.038 0.009 -9999 0 0 28 28
UBE2I 0.039 0.009 -9999 0 0 27 27
T-DHT/AR/Cyclin D3/CDK11 p58 0.034 0.056 -9999 0 -0.092 77 77
RPS6KA3 0.038 0.013 -9999 0 -9999 0 0
T-DHT/AR/ARA70 0.034 0.065 -9999 0 -0.105 88 88
LATS2 0.039 0.007 -9999 0 0 17 17
T-DHT/AR/PRX1 0.031 0.059 -9999 0 -0.094 88 88
Cyclin D3/CDK11 p58 0.028 0.015 -9999 0 -0.125 4 4
VAV3 0.034 0.017 -9999 0 -9999 0 0
KLK2 0.02 0.063 -9999 0 -0.297 16 16
CASP8 0.039 0.009 -9999 0 0 27 27
T-DHT/AR/TIF2/CARM1 0.043 0.07 -9999 0 -0.105 65 65
TMPRSS2 0.013 0.09 -9999 0 -0.308 34 34
CCND1 0.031 0.018 -9999 0 -9999 0 0
PIAS1 0.041 0.009 -9999 0 -9999 0 0
mol:T-DHT 0.005 0.005 -9999 0 -0.036 3 3
CDC2L1 0 0 -9999 0 -9999 0 0
PIAS4 0.039 0.013 -9999 0 -9999 0 0
T-DHT/AR/CDK6 0.017 0.075 -9999 0 -0.114 117 117
CMTM2 0.036 0.013 -9999 0 0 60 60
SNURF 0.038 0.011 -9999 0 0 45 45
ZMIZ1 0.005 0.005 -9999 0 -0.036 3 3
CCND3 0.039 0.01 -9999 0 0 31 31
TGIF1 -0.001 0 -9999 0 -9999 0 0
FKBP4 0.037 0.014 -9999 0 -9999 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.048 0.043 0.145 16 -9999 0 16
KIRREL 0.043 0.015 0.083 1 -9999 0 1
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.048 0.043 -9999 0 -0.145 16 16
PLCG1 0.038 0.011 -9999 0 0 43 43
ARRB2 0.038 0.011 -9999 0 0 46 46
WASL 0.04 0.007 -9999 0 0 18 18
Nephrin/NEPH1/podocin/CD2AP 0.073 0.067 -9999 0 -0.114 34 34
ChemicalAbstracts:57-88-5 0 0 -9999 0 -9999 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.021 0.05 0.144 1 -0.146 30 31
FYN 0.006 0.065 0.163 68 -0.123 14 82
mol:Ca2+ 0.075 0.06 -9999 0 -0.12 22 22
mol:DAG 0.076 0.061 0.208 1 -0.12 22 23
NPHS2 0.043 0.018 0.086 2 -0.042 15 17
mol:IP3 0.076 0.061 0.208 1 -0.12 22 23
regulation of endocytosis 0.053 0.056 -9999 0 -0.116 17 17
Nephrin/NEPH1/podocin/Cholesterol 0.062 0.047 0.185 1 -0.105 17 18
establishment of cell polarity 0.048 0.043 -9999 0 -0.145 16 16
Nephrin/NEPH1/podocin/NCK1-2 0.084 0.076 -9999 0 -0.108 37 37
Nephrin/NEPH1/beta Arrestin2 0.055 0.058 -9999 0 -0.117 17 17
NPHS1 0.037 0.021 0.085 4 -0.043 14 18
Nephrin/NEPH1/podocin 0.054 0.053 0.217 1 -0.122 15 16
TJP1 0.036 0.013 -9999 0 0 63 63
NCK1 0.036 0.014 -9999 0 0 70 70
NCK2 0.041 0.004 -9999 0 0 6 6
heterophilic cell adhesion 0 0 -9999 0 -9999 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.078 0.062 0.212 1 -0.12 22 23
CD2AP 0.037 0.013 -9999 0 0 62 62
Nephrin/NEPH1/podocin/GRB2 0.082 0.058 0.212 1 -0.118 16 17
GRB2 0.04 0.008 -9999 0 0 21 21
homophilic cell adhesion 0 0 -9999 0 -9999 0 0
TRPC6 0.008 0.07 0.166 76 -0.121 2 78
cytoskeleton organization 0.017 0.054 0.219 10 -0.168 11 21
Nephrin/NEPH1 0.041 0.033 -9999 0 -0.092 17 17
Nephrin/NEPH1/ZO-1 0.054 0.06 -9999 0 -0.127 34 34
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.056 0.049 -9999 0 -0.11 22 22
fibroblast growth factor receptor signaling pathway 0.055 0.049 -9999 0 -0.11 22 22
LAMA1 0.033 0.016 -9999 0 0 104 104
PRNP 0.036 0.013 -9999 0 0 63 63
GPC1/SLIT2 0.018 0.07 -9999 0 -0.134 87 87
SMAD2 -0.02 0.036 0.192 9 -9999 0 9
GPC1/PrPc/Cu2+ 0.04 0.041 -9999 0 -0.109 32 32
GPC1/Laminin alpha1 0.045 0.031 -9999 0 -0.129 6 6
TDGF1 0.04 0.006 -9999 0 0 13 13
CRIPTO/GPC1 0.056 0.018 -9999 0 -0.134 1 1
APP/GPC1 0.046 0.044 -9999 0 -0.134 27 27
mol:NO 0 0 -9999 0 -9999 0 0
YES1 -0.017 0.027 0.19 6 -0.116 1 7
FLT1 0.039 0.009 -9999 0 0 28 28
GPC1/TGFB/TGFBR1/TGFBR2 0.067 0.042 -9999 0 -0.114 17 17
SERPINC1 0.04 0.008 -9999 0 0 19 19
FYN -0.015 0.028 0.19 6 -0.116 1 7
FGR -0.018 0.027 0.19 6 -0.116 1 7
positive regulation of MAPKKK cascade 0.002 0.074 0.201 19 -0.185 25 44
SLIT2 0.028 0.019 -9999 0 0 176 176
GPC1/NRG 0.05 0.025 -9999 0 -0.134 1 1
NRG1 0.036 0.014 -9999 0 0 74 74
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.049 0.023 -9999 0 -0.109 6 6
LYN -0.016 0.025 0.19 5 -0.116 1 6
mol:Spermine -0.01 0.002 -9999 0 -9999 0 0
cell growth 0.055 0.049 -9999 0 -0.11 22 22
BMP signaling pathway -0.039 0.01 0 31 -9999 0 31
SRC -0.018 0.025 0.19 5 -0.116 1 6
TGFBR1 0.039 0.008 -9999 0 0 23 23
mol:Cu2+ 0 0 -9999 0 -9999 0 0
PLA2G2A 0.036 0.014 -9999 0 0 67 67
GPC1 0.039 0.01 -9999 0 0 31 31
TGFBR1 (dimer) 0.039 0.008 -9999 0 0 23 23
VEGFA 0 0 -9999 0 -9999 0 0
BLK -0.015 0.024 0.19 4 -0.116 1 5
HCK -0.017 0.025 0.19 5 -9999 0 5
FGF2 0.039 0.01 -9999 0 0 33 33
FGFR1 0.033 0.017 -9999 0 0 112 112
VEGFR1 homodimer 0.039 0.009 -9999 0 0 28 28
TGFBR2 0.039 0.01 -9999 0 0 34 34
cell death 0.046 0.044 -9999 0 -0.134 27 27
ATIII/GPC1 0.055 0.019 -9999 0 -0.134 1 1
PLA2G2A/GPC1 0.05 0.027 -9999 0 -0.134 3 3
LCK -0.018 0.027 0.19 6 -9999 0 6
neuron differentiation 0.049 0.025 -9999 0 -0.134 1 1
PrPc/Cu2+ 0.02 0.036 -9999 0 -0.125 31 31
APP 0.038 0.011 -9999 0 0 41 41
TGFBR2 (dimer) 0.039 0.01 -9999 0 0 34 34
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.014 0.078 -9999 0 -0.146 93 93
AKT1 0.018 0.108 0.268 5 -0.308 20 25
PTK2B -0.012 0.078 0.198 13 -0.313 7 20
VEGFR2 homodimer/Frs2 0.033 0.057 -9999 0 -0.371 4 4
CAV1 0.036 0.014 -9999 0 0 75 75
CALM1 0.039 0.009 -9999 0 0 26 26
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.031 0.058 -9999 0 -0.355 4 4
endothelial cell proliferation 0.036 0.098 0.284 15 -0.295 9 24
mol:Ca2+ 0.023 0.068 0.255 3 -0.294 7 10
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.046 0.076 -9999 0 -0.211 20 20
RP11-342D11.1 -0.009 0.052 0.173 13 -0.325 5 18
CDH5 0.036 0.013 -9999 0 0 65 65
VEGFA homodimer 0.06 0.048 -9999 0 -0.111 27 27
SHC1 0.039 0.008 -9999 0 0 23 23
SHC2 0.036 0.014 -9999 0 0 67 67
HRAS/GDP 0.037 0.067 -9999 0 -0.242 10 10
SH2D2A 0.04 0.007 -9999 0 0 17 17
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.055 0.087 0.296 1 -0.373 6 7
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.036 0.055 -9999 0 -0.32 5 5
VEGFR1 homodimer 0.039 0.009 -9999 0 0 28 28
SHC/GRB2/SOS1 0.069 0.083 -9999 0 -0.247 11 11
GRB10 0.024 0.072 0.263 2 -0.349 8 10
PTPN11 0.039 0.009 -9999 0 0 29 29
GRB2 0.04 0.008 -9999 0 0 21 21
PAK1 0.036 0.013 -9999 0 0 65 65
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.051 0.086 -9999 0 -0.211 21 21
HRAS 0.039 0.01 -9999 0 0 31 31
VEGF/Rho/ROCK1/Integrin Complex -0.016 0.11 -9999 0 -0.259 76 76
HIF1A 0.038 0.01 -9999 0 0 37 37
FRS2 0.038 0.011 -9999 0 0 41 41
oxygen and reactive oxygen species metabolic process 0.044 0.075 -9999 0 -0.209 20 20
mol:GTP 0 0 -9999 0 -9999 0 0
FLT4 0.04 0.008 -9999 0 0 22 22
Nck/Pak 0.036 0.056 -9999 0 -0.139 44 44
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.024 0.061 -9999 0 -0.271 7 7
mol:GDP 0.053 0.074 -9999 0 -0.241 11 11
mol:NADP 0.04 0.083 0.277 5 -0.331 7 12
eNOS/Hsp90 0.037 0.078 0.26 5 -0.314 7 12
PIK3R1 0.034 0.016 -9999 0 0 99 99
mol:IP3 0.023 0.069 0.256 3 -0.297 7 10
HIF1A/ARNT 0.046 0.044 -9999 0 -0.143 22 22
SHB 0.04 0.006 -9999 0 0 11 11
VEGFA 0.002 0.004 -9999 0 -0.037 6 6
VEGFC 0.036 0.014 -9999 0 0 69 69
FAK1/Vinculin 0.01 0.124 0.264 3 -0.304 37 40
mol:Ca ++ 0 0 -9999 0 -9999 0 0
RHOA 0.04 0.006 -9999 0 0 13 13
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.023 0.087 -9999 0 -0.206 33 33
PTPN6 0.037 0.013 -9999 0 0 56 56
EPAS1 0.043 0.031 -9999 0 -0.271 3 3
mol:L-citrulline 0.04 0.083 0.277 5 -0.331 7 12
ITGAV 0.033 0.017 -9999 0 0 110 110
PIK3CA 0.029 0.019 -9999 0 0 166 166
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.053 0.068 -9999 0 -0.307 5 5
VEGFR2 homodimer/VEGFA homodimer 0.041 0.061 -9999 0 -0.285 8 8
VEGFR2/3 heterodimer 0.034 0.057 -9999 0 -0.329 5 5
VEGFB 0.038 0.011 -9999 0 0 40 40
MAPK11 -0.003 0.078 0.249 8 -0.319 10 18
VEGFR2 homodimer 0.019 0.044 -9999 0 -0.377 5 5
FLT1 0.039 0.009 -9999 0 0 28 28
NEDD4 0.039 0.016 -9999 0 -0.053 5 5
MAPK3 0.001 0.074 0.245 6 -0.273 8 14
MAPK1 0.001 0.074 0.24 7 -0.297 7 14
VEGFA145/NRP2 0.015 0.045 -9999 0 -0.113 54 54
VEGFR1/2 heterodimer 0.034 0.058 -9999 0 -0.286 7 7
KDR 0.019 0.044 -9999 0 -0.378 5 5
VEGFA165/NRP1/VEGFR2 homodimer 0.03 0.071 -9999 0 -0.209 19 19
SRC 0.039 0.009 -9999 0 0 28 28
platelet activating factor biosynthetic process 0.003 0.079 0.239 8 -0.304 7 15
PI3K 0.013 0.081 -9999 0 -0.312 9 9
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.026 0.062 -9999 0 -0.25 10 10
FES 0.024 0.068 0.257 3 -0.326 5 8
GAB1 0.02 0.083 0.26 2 -0.304 17 19
VEGFR2 homodimer/VEGFA homodimer/Src 0.035 0.053 -9999 0 -0.282 5 5
CTNNB1 0.039 0.01 -9999 0 0 32 32
SOS1 0.037 0.012 -9999 0 0 51 51
ARNT 0.037 0.012 -9999 0 0 50 50
eNOS/Caveolin-1 0.047 0.084 0.31 2 -0.351 6 8
VEGFR2 homodimer/VEGFA homodimer/Yes 0.028 0.062 -9999 0 -0.267 8 8
PI3K/GAB1 0.027 0.113 0.268 3 -0.312 20 23
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.048 0.082 -9999 0 -0.212 13 13
PRKACA 0.035 0.015 -9999 0 0 84 84
VEGFR2/3 heterodimer/VEGFC homodimer 0.051 0.066 -9999 0 -0.289 6 6
HSP90AA1 0 0 -9999 0 -9999 0 0
CDC42 0.024 0.068 0.257 3 -0.334 5 8
actin cytoskeleton reorganization 0.035 0.054 -9999 0 -0.318 5 5
PTK2 -0.007 0.107 0.233 1 -0.322 33 34
EDG1 0.023 0.065 0.238 2 -0.331 5 7
mol:DAG 0.023 0.069 0.256 3 -0.297 7 10
CaM/Ca2+ 0.038 0.069 0.249 3 -0.264 8 11
MAP2K3 -0.006 0.063 0.183 28 -0.327 5 33
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.042 0.07 0.239 5 -0.337 9 14
PLCG1 0.023 0.069 0.257 3 -0.3 7 10
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.058 0.062 -9999 0 -0.271 5 5
IQGAP1 0.036 0.013 -9999 0 0 66 66
YES1 0.037 0.012 -9999 0 0 51 51
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.031 0.06 -9999 0 -0.28 7 7
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.034 0.053 -9999 0 -0.307 5 5
cell migration 0 0.127 0.264 4 -0.329 38 42
mol:PI-3-4-5-P3 0.013 0.078 -9999 0 -0.295 9 9
FYN 0.034 0.016 -9999 0 0 94 94
VEGFB/NRP1 0.028 0.064 0.225 2 -0.234 10 12
mol:NO 0.04 0.083 0.277 5 -0.331 7 12
PXN 0.04 0.006 -9999 0 0 10 10
HRAS/GTP 0.016 0.056 -9999 0 -0.232 11 11
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.025 0.061 -9999 0 -0.337 9 9
VHL 0.039 0.008 -9999 0 0 23 23
ITGB3 0.032 0.017 -9999 0 0 116 116
NOS3 0.04 0.088 0.291 4 -0.369 7 11
VEGFR2 homodimer/VEGFA homodimer/Sck 0.031 0.055 -9999 0 -0.312 5 5
RAC1 0.039 0.009 -9999 0 0 28 28
PRKCA -0.006 0.067 0.176 35 -0.334 5 40
PRKCB -0.002 0.066 0.176 37 -0.328 5 42
VCL 0.039 0.01 -9999 0 0 34 34
VEGFA165/NRP1 0.006 0.048 0.171 5 -0.262 8 13
VEGFR1/2 heterodimer/VEGFA homodimer 0.034 0.057 -9999 0 -0.28 7 7
VEGFA165/NRP2 0.015 0.045 -9999 0 -0.113 54 54
MAPKKK cascade -0.02 0.07 0.185 24 -0.341 7 31
NRP2 0.034 0.015 -9999 0 0 93 93
VEGFC homodimer 0.036 0.014 -9999 0 0 69 69
NCK1 0.036 0.014 -9999 0 0 70 70
ROCK1 0.04 0.008 -9999 0 0 21 21
FAK1/Paxillin 0.012 0.124 0.264 3 -0.314 33 36
MAP3K13 0.017 0.065 0.257 3 -0.291 7 10
PDPK1 0.001 0.068 0.242 1 -0.276 7 8
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.015 0.005 -9999 0 -9999 0 0
ADCY5 -0.014 0.006 -9999 0 -9999 0 0
ADCY6 -0.015 0.004 -9999 0 -9999 0 0
ADCY7 -0.014 0.005 0 68 -9999 0 68
ADCY1 -0.015 0.004 0 39 -9999 0 39
ADCY2 -0.014 0.006 -9999 0 -9999 0 0
ADCY3 -0.015 0.004 0 44 -9999 0 44
ADCY8 -0.009 0.008 -9999 0 -9999 0 0
PRKCE -0.01 0.002 0 28 -9999 0 28
ADCY9 -0.014 0.006 0 71 -9999 0 71
mol:DAG 0 0 -9999 0 -9999 0 0
cAMP biosynthetic process 0.045 0.078 0.203 52 -0.199 5 57
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 0.036 0.014 -9999 0 0 69 69
CD4-positive alpha-beta T cell lineage commitment 0 0 -9999 0 -9999 0 0
cytokine production during immune response -0.001 0.112 0.438 13 -9999 0 13
IL27/IL27R/JAK1 0.08 0.107 -9999 0 -0.885 2 2
TBX21 0.006 0.104 0.381 4 -0.556 2 6
IL12B 0.041 0.008 -9999 0 0 18 18
IL12A -0.006 0.006 0.012 26 -9999 0 26
IL6ST 0.036 0.017 -9999 0 -0.032 2 2
IL27RA/JAK1 0.05 0.098 -9999 0 -1.036 2 2
IL27 0.043 0.009 -9999 0 -0.032 2 2
TYK2 0.038 0.015 -9999 0 -0.033 2 2
T-helper cell lineage commitment 0.005 0.059 0.195 17 -0.179 29 46
T-helper 2 cell differentiation -0.001 0.112 0.438 13 -9999 0 13
T cell proliferation during immune response -0.001 0.112 0.438 13 -9999 0 13
MAPKKK cascade 0.001 0.112 -9999 0 -0.438 13 13
STAT3 0.038 0.011 -9999 0 0 41 41
STAT2 0.038 0.012 -9999 0 0 49 49
STAT1 0.034 0.016 -9999 0 0 102 102
IL12RB1 0.038 0.012 -9999 0 0 50 50
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -9999 0 -9999 0 0
IL12RB2 0.002 0.1 0.4 1 -0.515 2 3
IL27/IL27R/JAK2/TYK2 0.001 0.114 -9999 0 -0.444 13 13
positive regulation of T cell mediated cytotoxicity 0.001 0.112 -9999 0 -0.438 13 13
STAT1 (dimer) 0.062 0.125 -9999 0 -0.777 2 2
JAK2 0.035 0.018 -9999 0 -9999 0 0
JAK1 0.039 0.01 -9999 0 0 33 33
STAT2 (dimer) 0.019 0.129 -9999 0 -0.42 15 15
T cell proliferation 0.002 0.11 0.339 1 -0.422 13 14
IL12/IL12R/TYK2/JAK2 0.009 0.171 -9999 0 -0.724 25 25
IL17A 0.006 0.055 0.196 17 -0.177 26 43
mast cell activation -0.001 0.112 0.438 13 -9999 0 13
IFNG 0.013 0.031 0.106 1 -0.092 9 10
T cell differentiation -0.001 0.003 0.014 2 -0.016 5 7
STAT3 (dimer) 0.024 0.129 -9999 0 -0.422 14 14
STAT5A (dimer) 0.025 0.129 -9999 0 -0.428 13 13
STAT4 (dimer) 0.025 0.128 -9999 0 -0.423 13 13
STAT4 0.039 0.008 -9999 0 0 24 24
T cell activation -0.008 0.01 -9999 0 -0.045 29 29
IL27R/JAK2/TYK2 0.048 0.096 -9999 0 -0.926 2 2
GATA3 0.015 0.116 0.637 17 -9999 0 17
IL18 -0.006 0.006 0.002 179 -9999 0 179
positive regulation of mast cell cytokine production 0.024 0.127 -9999 0 -0.414 14 14
IL27/EBI3 0.058 0.022 -9999 0 -9999 0 0
IL27RA 0.022 0.1 -9999 0 -1.116 2 2
IL6 0.034 0.016 -9999 0 0 100 100
STAT5A 0.038 0.01 -9999 0 0 36 36
monocyte differentiation 0 0 -9999 0 -9999 0 0
IL2 -0.009 0.034 0.488 2 -9999 0 2
IL1B -0.007 0.006 0.002 145 -9999 0 145
EBI3 0.039 0.014 -9999 0 -9999 0 0
TNF -0.008 0.005 0.006 60 -9999 0 60
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.047 0.044 -9999 0 -0.134 27 27
FBXW11 0.04 0.008 -9999 0 0 22 22
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.039 0.008 -9999 0 0 22 22
CHUK 0.038 0.011 -9999 0 0 46 46
NF kappa B2 p100/RelB 0.093 0.066 -9999 0 -0.112 32 32
NFKB1 0.036 0.013 -9999 0 0 66 66
MAP3K14 0.04 0.008 -9999 0 0 20 20
NF kappa B1 p50/RelB 0.043 0.048 -9999 0 -0.133 33 33
RELB 0.039 0.01 -9999 0 0 33 33
NFKB2 0.04 0.007 -9999 0 0 18 18
NF kappa B2 p52/RelB 0.05 0.023 -9999 0 -0.126 5 5
regulation of B cell activation 0.049 0.022 -9999 0 -0.126 5 5
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.088 0.048 -9999 0 -0.115 17 17
HDAC3 0.04 0.006 -9999 0 0 10 10
Ran/GTP/Exportin 1/HDAC4 -0.026 0.024 -9999 0 -0.113 32 32
GATA1/HDAC4 0.058 0.013 -9999 0 -9999 0 0
GATA1/HDAC5 0.059 0.012 -9999 0 -9999 0 0
GATA2/HDAC5 0.055 0.018 -9999 0 -9999 0 0
HDAC5/BCL6/BCoR 0.053 0.056 -9999 0 -0.122 33 33
HDAC9 0.036 0.014 -9999 0 0 74 74
Glucocorticoid receptor/Hsp90/HDAC6 0.044 0.038 -9999 0 -0.109 29 29
HDAC4/ANKRA2 0.049 0.031 -9999 0 -0.134 8 8
HDAC5/YWHAB 0.052 0.027 -9999 0 -0.134 6 6
NPC/RanGAP1/SUMO1/Ubc9 0.009 0.034 -9999 0 -0.142 25 25
GATA2 0.039 0.01 -9999 0 0 31 31
HDAC4/RFXANK 0.046 0.039 -9999 0 -0.132 18 18
BCOR 0.041 0.005 -9999 0 0 8 8
mol:GTP 0 0 -9999 0 -9999 0 0
HDAC10 0.029 0.019 -9999 0 0 157 157
HDAC5 0.04 0.008 -9999 0 0 21 21
GNB1/GNG2 0.05 0.036 -9999 0 -0.134 16 16
Histones -0.01 0.07 -9999 0 -0.191 37 37
ADRBK1 0.041 0.004 -9999 0 0 6 6
HDAC4 0.039 0.009 -9999 0 0 25 25
XPO1 0.039 0.01 -9999 0 0 35 35
HDAC5/ANKRA2 0.049 0.031 -9999 0 -0.134 8 8
HDAC4/Ubc9 0.055 0.019 -9999 0 -0.134 1 1
HDAC7 0 0 -9999 0 -9999 0 0
HDAC5/14-3-3 E 0.052 0.029 -9999 0 -0.134 7 7
TUBA1B 0 0 -9999 0 -9999 0 0
HDAC6 0.04 0.007 -9999 0 0 14 14
HDAC5/RFXANK 0.046 0.04 -9999 0 -0.132 20 20
CAMK4 0.037 0.012 -9999 0 0 55 55
Tubulin/HDAC6 0.051 0.016 -9999 0 -9999 0 0
SUMO1 0.04 0.007 -9999 0 0 14 14
EntrezGene:9972 0 0 -9999 0 -9999 0 0
YWHAB 0.038 0.011 -9999 0 0 45 45
GATA1 0.041 0.002 -9999 0 0 1 1
EntrezGene:8021 0 0 -9999 0 -9999 0 0
YWHAE 0.037 0.013 -9999 0 0 58 58
NR3C1 0.038 0.011 -9999 0 0 42 42
SUMO1/HDAC4 0.037 0.063 -9999 0 -0.18 17 17
SRF 0.038 0.01 -9999 0 0 37 37
HDAC4/YWHAB 0.052 0.027 -9999 0 -0.134 6 6
Tubulin 0.029 0.007 -9999 0 -9999 0 0
HDAC4/14-3-3 E 0.051 0.029 -9999 0 -0.134 7 7
GNB1 0.039 0.01 -9999 0 0 33 33
RANGAP1 0.037 0.012 -9999 0 0 54 54
BCL6/BCoR 0.038 0.051 -9999 0 -0.14 33 33
HDAC4/HDAC3/SMRT (N-CoR2) 0.073 0.032 -9999 0 -0.116 5 5
HDAC4/SRF 0.067 0.035 -9999 0 -0.116 2 2
HDAC4/ER alpha 0.038 0.053 -9999 0 -0.134 41 41
EntrezGene:23225 0 0 -9999 0 -9999 0 0
positive regulation of chromatin silencing -0.01 0.07 -9999 0 -0.189 37 37
cell motility 0.05 0.015 -9999 0 -9999 0 0
EntrezGene:23636 0 0 -9999 0 -9999 0 0
UBE2I 0.039 0.009 -9999 0 0 27 27
HDAC7/HDAC3 0.029 0.01 -9999 0 -0.125 2 2
BCL6 0.031 0.018 -9999 0 0 130 130
HDAC4/CaMK II delta B 0.039 0.009 -9999 0 0 25 25
Hsp90/HDAC6 0.03 0.005 -9999 0 -9999 0 0
ESR1 0.034 0.015 -9999 0 0 91 91
HDAC6/HDAC11 0.056 0.025 -9999 0 -0.134 7 7
Ran/GTP/Exportin 1 0.035 0.071 -9999 0 -0.176 36 36
NPC 0.019 0.022 -9999 0 -0.083 23 23
MEF2C 0.037 0.013 -9999 0 0 61 61
RAN 0.04 0.008 -9999 0 0 21 21
HDAC4/MEF2C 0.092 0.061 -9999 0 -0.114 16 16
GNG2 0.039 0.009 -9999 0 0 29 29
NCOR2 0.039 0.01 -9999 0 0 31 31
TUBB2A 0.039 0.01 -9999 0 0 33 33
HDAC11 0.04 0.008 -9999 0 0 21 21
HSP90AA1 0 0 -9999 0 -9999 0 0
RANBP2 0.039 0.009 -9999 0 0 30 30
ANKRA2 0.036 0.014 -9999 0 0 72 72
RFXANK 0.036 0.014 -9999 0 0 74 74
nuclear import -0.036 0.039 0.177 12 -9999 0 12
Signaling events mediated by HDAC Class III

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
EP300 0.036 0.014 -9999 0 0 69 69
HDAC4 0.039 0.009 -9999 0 0 25 25
induction of apoptosis 0 0 -9999 0 -9999 0 0
regulation of S phase of mitotic cell cycle 0.013 0.004 -9999 0 -9999 0 0
CDKN1A 0.016 0.051 0.371 4 -9999 0 4
KAT2B 0 0 -9999 0 -9999 0 0
BAX 0.039 0.008 -9999 0 0 23 23
FOXO3 0.002 0.04 0.248 14 -9999 0 14
FOXO1 0 0 -9999 0 -9999 0 0
FOXO4 0.005 0.033 -9999 0 -0.178 17 17
response to UV 0 0 -9999 0 -9999 0 0
XRCC6 0.036 0.014 -9999 0 0 69 69
TAT 0.036 0.013 -9999 0 0 65 65
mol:Lysophosphatidic acid 0 0 -9999 0 -9999 0 0
MYOD1 -0.01 0.002 -9999 0 -9999 0 0
PPARGC1A 0.037 0.012 -9999 0 0 52 52
FHL2 0.04 0.008 -9999 0 0 19 19
response to nutrient levels 0 0 -9999 0 -9999 0 0
KU70/SIRT1 0.045 0.042 -9999 0 -0.168 16 16
HIST2H4A -0.013 0.004 -9999 0 -9999 0 0
SIRT1/FOXO3a 0.038 0.044 0.151 57 -0.201 2 59
SIRT1 0.037 0.007 -9999 0 -9999 0 0
response to hypoxia 0 0 -9999 0 -9999 0 0
SIRT1/MEF2D/HDAC4 0.071 0.033 -9999 0 -0.12 8 8
SIRT1/Histone H1b 0.002 0.09 -9999 0 -0.195 70 70
apoptosis -0.062 0.046 0.145 16 -9999 0 16
SIRT1/PGC1A 0.045 0.025 -9999 0 -0.112 8 8
p53/SIRT1 -0.008 0.087 -9999 0 -0.145 152 152
SIRT1/FOXO4 0.007 0.076 -9999 0 -0.152 86 86
FOXO1/FHL2/SIRT1 0.045 0.024 -9999 0 -0.1 12 12
HIST1H1E -0.004 0.068 -9999 0 -0.203 51 51
SIRT1/p300 0.044 0.041 -9999 0 -0.135 22 22
muscle cell differentiation -0.018 0.023 0.112 9 -0.208 2 11
TP53 0.023 0.018 -9999 0 -9999 0 0
KU70/SIRT1/BAX 0.063 0.046 -9999 0 -0.146 16 16
CREBBP 0.037 0.012 -9999 0 0 53 53
MEF2D 0.04 0.007 -9999 0 0 18 18
HIV-1 Tat/SIRT1 0.048 0.029 -9999 0 -0.131 8 8
ACSS2 -0.021 0.009 0.04 1 -9999 0 1
SIRT1/PCAF/MYOD 0.018 0.023 0.209 2 -0.112 9 11
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.035 0.052 -9999 0 -0.398 5 5
VEGFR1 homodimer/NRP1 0.009 0.046 -9999 0 -0.391 5 5
mol:DAG -0.024 0.039 0.194 1 -0.305 6 7
VEGFR1 homodimer/NRP1/VEGFR 121 0.008 0.042 -9999 0 -0.357 5 5
CaM/Ca2+ 0.026 0.05 -9999 0 -0.277 7 7
HIF1A 0.045 0.033 -9999 0 -0.274 5 5
GAB1 0.037 0.013 -9999 0 0 58 58
AKT1 0.01 0.094 0.226 15 -0.267 16 31
PLCG1 -0.024 0.039 0.194 1 -0.307 6 7
NOS3 0.025 0.071 0.318 3 -0.263 10 13
CBL 0.04 0.008 -9999 0 0 20 20
mol:NO 0.029 0.076 0.3 7 -0.256 10 17
FLT1 0.018 0.044 -9999 0 -0.489 4 4
PGF 0.039 0.008 -9999 0 0 23 23
VEGFR1 homodimer/NRP2/VEGFR121 0.018 0.061 -9999 0 -0.305 8 8
CALM1 0.039 0.009 -9999 0 0 26 26
PIK3CA 0.029 0.019 -9999 0 0 166 166
eNOS/Hsp90 0.02 0.067 0.225 2 -0.254 9 11
endothelial cell proliferation -0.003 0.062 0.292 2 -0.295 10 12
mol:Ca2+ -0.024 0.039 0.193 1 -0.303 6 7
MAPK3 -0.03 0.049 0.202 4 -0.247 9 13
MAPK1 -0.028 0.048 0.202 4 -0.253 8 12
PIK3R1 0.034 0.016 -9999 0 0 99 99
PLGF homodimer 0.039 0.008 -9999 0 0 23 23
PRKACA 0.035 0.015 -9999 0 0 84 84
RP11-342D11.1 0 0 -9999 0 -9999 0 0
CAV1 0.036 0.014 -9999 0 0 75 75
VEGFA homodimer 0 0 -9999 0 -9999 0 0
VEGFR1 homodimer/VEGFA homodimer 0.009 0.046 -9999 0 -0.391 5 5
platelet activating factor biosynthetic process -0.027 0.056 0.324 1 -0.276 6 7
PI3K 0.037 0.077 -9999 0 -0.244 15 15
PRKCA -0.02 0.046 0.215 4 -0.262 8 12
PRKCB -0.022 0.036 0.176 1 -0.283 6 7
VEGFR1 homodimer/PLGF homodimer 0.035 0.053 -9999 0 -0.398 5 5
VEGFA 0 0 -9999 0 -9999 0 0
VEGFB 0.038 0.011 -9999 0 0 40 40
mol:IP3 -0.024 0.039 0.194 1 -0.305 6 7
RASA1 -0.021 0.045 0.194 2 -0.317 7 9
NRP2 0.034 0.015 -9999 0 0 93 93
VEGFR1 homodimer 0.018 0.044 -9999 0 -0.488 4 4
VEGFB homodimer 0.038 0.011 -9999 0 0 40 40
NCK1 0.036 0.014 -9999 0 0 70 70
eNOS/Caveolin-1 0.045 0.083 0.321 6 -0.255 10 16
PTPN11 0.039 0.009 -9999 0 0 29 29
mol:PI-3-4-5-P3 0.036 0.076 -9999 0 -0.234 16 16
mol:L-citrulline 0.029 0.076 0.3 7 -0.256 10 17
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.041 0.065 -9999 0 -0.272 9 9
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.023 0.058 -9999 0 -0.28 10 10
CD2AP 0.037 0.013 -9999 0 0 62 62
PI3K/GAB1 0.042 0.085 -9999 0 -0.239 16 16
PDPK1 0.007 0.094 0.175 93 -0.304 7 100
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.028 0.054 -9999 0 -0.283 9 9
mol:NADP 0.029 0.076 0.3 7 -0.256 10 17
HSP90AA1 0 0 -9999 0 -9999 0 0
ubiquitin-dependent protein catabolic process 0.039 0.063 -9999 0 -0.27 9 9
VEGFR1 homodimer/NRP2 0.028 0.057 -9999 0 -0.335 8 8
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.014 0.171 -9999 0 -0.686 14 14
NCK1/PAK1/Dok-R -0.031 0.073 -9999 0 -0.334 14 14
NCK1/Dok-R 0.051 0.097 -9999 0 -0.872 2 2
PIK3CA 0.028 0.019 -9999 0 0 166 166
mol:beta2-estradiol -0.008 0.008 -9999 0 -9999 0 0
RELA 0.04 0.006 -9999 0 0 10 10
SHC1 0.04 0.009 -9999 0 0 23 23
Rac/GDP 0.029 0.009 -9999 0 -0.125 1 1
F2 0.011 0.037 -9999 0 -0.082 1 1
TNIP2 0.038 0.011 -9999 0 0 43 43
NF kappa B/RelA 0.075 0.102 -9999 0 -0.833 2 2
FN1 0.021 0.021 -9999 0 0 268 268
PLD2 0.032 0.079 -9999 0 -0.894 2 2
PTPN11 0.039 0.009 -9999 0 0 29 29
GRB14 0.038 0.012 -9999 0 0 49 49
ELK1 0.033 0.081 -9999 0 -0.844 2 2
GRB7 0.037 0.013 -9999 0 0 57 57
PAK1 0.036 0.013 -9999 0 0 65 65
Tie2/Ang1/alpha5/beta1 Integrin 0.023 0.111 -9999 0 -0.86 2 2
CDKN1A 0.012 0.188 -9999 0 -0.619 38 38
ITGA5 0.036 0.013 -9999 0 0 64 64
mol:GTP 0 0 -9999 0 -9999 0 0
RasGAP/Dok-R 0.056 0.096 -9999 0 -0.872 2 2
CRK 0.038 0.012 -9999 0 0 49 49
mol:NO 0.023 0.146 -9999 0 -0.515 15 15
PLG 0.031 0.077 -9999 0 -0.894 2 2
mol:GDP 0 0 -9999 0 -9999 0 0
chemokinesis 0.027 0.144 -9999 0 -0.749 6 6
GRB2 0.04 0.008 -9999 0 0 21 21
PIK3R1 0.034 0.016 -9999 0 0 99 99
ANGPT2 -0.045 0.285 -9999 0 -1.034 37 37
BMX 0.031 0.078 -9999 0 -0.894 2 2
ANGPT1 0.013 0.047 -9999 0 -9999 0 0
tube development -0.002 0.207 -9999 0 -0.702 38 38
ANGPT4 0.035 0.02 -9999 0 -0.014 71 71
response to hypoxia 0.001 0.008 0.033 1 -0.062 2 3
Tie2/Ang1/GRB14 0.051 0.089 -9999 0 -0.907 2 2
alpha5/beta1 Integrin 0.043 0.046 -9999 0 -0.134 29 29
FGF2 0.039 0.011 -9999 0 0 33 33
STAT5A (dimer) 0.015 0.239 -9999 0 -0.799 38 38
mol:L-citrulline 0.023 0.146 -9999 0 -0.515 15 15
AGTR1 0.032 0.025 -9999 0 -0.018 93 93
MAPK14 0.041 0.127 -9999 0 -1.034 4 4
Tie2/SHP2 0.039 0.107 -9999 0 -0.757 3 3
TEK 0.028 0.102 -9999 0 -0.801 3 3
RPS6KB1 0.014 0.156 -9999 0 -0.647 12 12
Angiotensin II/AT1 0.025 0.024 -9999 0 -0.059 33 33
Tie2/Ang1/GRB2 0.056 0.091 -9999 0 -0.907 2 2
MAPK3 0.026 0.076 -9999 0 -0.845 2 2
MAPK1 0.028 0.079 -9999 0 -0.845 2 2
Tie2/Ang1/GRB7 0.053 0.089 -9999 0 -0.907 2 2
NFKB1 0.036 0.013 -9999 0 0 66 66
MAPK8 0.031 0.081 -9999 0 -0.894 2 2
PI3K 0.011 0.165 -9999 0 -0.928 6 6
FES 0.043 0.109 -9999 0 -1.021 2 2
Crk/Dok-R 0.058 0.094 -9999 0 -0.872 2 2
Tie2/Ang1/ABIN2 0.054 0.09 -9999 0 -0.907 2 2
blood circulation 0 0 -9999 0 -9999 0 0
negative regulation of caspase activity 0.018 0.16 -9999 0 -0.612 15 15
STAT5A 0.039 0.01 -9999 0 0 36 36
mol:ROS 0 0 -9999 0 -9999 0 0
PTK2 0.054 0.175 -9999 0 -0.634 9 9
Tie2/Ang2 -0.012 0.268 -9999 0 -0.948 38 38
Tie2/Ang1 0.039 0.081 -9999 0 -0.939 2 2
FOXO1 0.012 0.184 -9999 0 -0.608 37 37
ELF1 0.047 0.018 -9999 0 -0.126 2 2
ELF2 0.036 0.079 -9999 0 -0.894 2 2
mol:Choline 0.032 0.077 -9999 0 -0.866 2 2
cell migration -0.017 0.047 -9999 0 -0.187 13 13
FYN -0.01 0.231 -9999 0 -0.802 38 38
DOK2 0.032 0.017 -9999 0 0 118 118
negative regulation of cell cycle 0.015 0.173 -9999 0 -0.561 38 38
ETS1 0.041 0.021 -9999 0 -9999 0 0
PXN 0.053 0.162 0.394 2 -0.548 9 11
ITGB1 0.038 0.01 -9999 0 0 36 36
NOS3 0.02 0.157 -9999 0 -0.586 14 14
RAC1 0.039 0.009 -9999 0 0 28 28
TNF 0.048 0.013 -9999 0 -9999 0 0
MAPKKK cascade 0.032 0.077 -9999 0 -0.866 2 2
RASA1 0.037 0.013 -9999 0 0 56 56
Tie2/Ang1/Shc 0.058 0.091 -9999 0 -0.909 2 2
NCK1 0.036 0.014 -9999 0 0 70 70
vasculogenesis 0.025 0.137 -9999 0 -0.467 15 15
mol:Phosphatidic acid 0.032 0.077 -9999 0 -0.866 2 2
mol:Angiotensin II 0 0.008 -9999 0 -0.033 30 30
mol:NADP 0.023 0.146 -9999 0 -0.515 15 15
Rac1/GTP 0.028 0.151 -9999 0 -0.647 9 9
MMP2 0.032 0.088 -9999 0 -0.894 2 2
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.038 0.012 -9999 0 0 49 49
Ran/GTP/Exportin 1/HDAC4 -0.028 0.033 -9999 0 -0.14 33 33
MDM2/SUMO1 0.036 0.063 -9999 0 -0.181 19 19
HDAC4 0.039 0.009 -9999 0 0 25 25
Ran/GTP/Exportin 1/HDAC1 -0.031 0.039 -9999 0 -0.142 46 46
SUMO1 0.04 0.007 -9999 0 0 14 14
NPC/RanGAP1/SUMO1 0.007 0.033 -9999 0 -0.137 25 25
mol:GTP 0 0 -9999 0 -9999 0 0
XPO1 -0.001 0.031 -9999 0 -0.144 12 12
EntrezGene:23636 0 0 -9999 0 -9999 0 0
RAN 0.04 0.008 -9999 0 0 21 21
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.039 0.009 -9999 0 0 30 30
SUMO1/HDAC4 0.037 0.063 -9999 0 -0.18 17 17
SUMO1/HDAC1 0.034 0.066 -9999 0 -0.183 25 25
RANGAP1 0.037 0.012 -9999 0 0 54 54
MDM2/SUMO1/SUMO1 0.083 0.053 -9999 0 -0.124 17 17
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.009 0.034 -9999 0 -0.142 25 25
Ran/GTP 0.02 0.057 -9999 0 -0.149 35 35
EntrezGene:23225 0 0 -9999 0 -9999 0 0
MDM2 0.038 0.01 -9999 0 0 36 36
UBE2I 0.039 0.009 -9999 0 0 27 27
Ran/GTP/Exportin 1 0.015 0.066 0.204 8 -0.176 36 44
NPC 0.019 0.022 -9999 0 -0.083 23 23
PIAS2 0.038 0.011 -9999 0 0 42 42
PIAS1 0.039 0.008 -9999 0 0 24 24
EntrezGene:9972 0 0 -9999 0 -9999 0 0
Aurora C signaling

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
INCENP 0.041 0.004 -9999 0 0 6 6
Aurora C/Aurora B/INCENP 0.06 0.045 -9999 0 -0.103 26 26
metaphase 0 0 -9999 0 -9999 0 0
mitosis 0 0 -9999 0 -9999 0 0
H3F3B 0.003 0.068 -9999 0 -0.382 16 16
AURKB 0.035 0.014 -9999 0 0 78 78
AURKC 0.039 0.01 -9999 0 0 34 34
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0.007 0.112 -9999 0 -0.808 9 9
MKNK1 0.04 0.007 -9999 0 0 15 15
MAPK14 0.041 0.052 0.174 1 -0.13 32 33
ATF2/c-Jun -0.026 0.104 -9999 0 -0.309 44 44
MAPK11 0.029 0.051 -9999 0 -0.128 29 29
MITF 0.018 0.06 -9999 0 -0.291 14 14
MAPKAPK5 0.018 0.057 -9999 0 -0.259 16 16
KRT8 0.014 0.061 -9999 0 -0.225 25 25
MAPKAPK3 0.04 0.006 -9999 0 0 11 11
MAPKAPK2 0.04 0.007 -9999 0 0 14 14
p38alpha-beta/CK2 0.04 0.075 -9999 0 -0.283 14 14
CEBPB 0.02 0.053 -9999 0 -0.287 10 10
SLC9A1 0.019 0.054 -9999 0 -0.275 13 13
mol:GDP 0 0 -9999 0 -9999 0 0
ATF2 0.012 0.074 0.229 1 -0.241 28 29
p38alpha-beta/MNK1 0.051 0.075 -9999 0 -0.303 9 9
JUN -0.028 0.101 -9999 0 -0.308 44 44
PPARGC1A 0.02 0.054 -9999 0 -0.277 12 12
USF1 0.018 0.056 -9999 0 -0.265 15 15
RAB5/GDP/GDI1 -0.001 0.078 -9999 0 -0.188 30 30
NOS2 0.014 0.051 -9999 0 -0.277 12 12
DDIT3 0.015 0.059 -9999 0 -0.223 23 23
RAB5A 0.04 0.006 -9999 0 0 13 13
HSPB1 0.002 0.05 0.305 2 -0.227 15 17
p38alpha-beta/HBP1 0.042 0.081 -9999 0 -0.258 13 13
CREB1 -0.012 0.1 -9999 0 -0.196 107 107
RAB5/GDP 0.029 0.012 -9999 0 -0.125 3 3
EIF4E -0.01 0.056 0.201 11 -0.29 8 19
RPS6KA4 0.019 0.055 -9999 0 -0.274 13 13
PLA2G4A -0.01 0.054 0.237 5 -0.316 9 14
GDI1 0.016 0.06 -9999 0 -0.249 20 20
TP53 0.002 0.058 -9999 0 -0.354 10 10
RPS6KA5 0.017 0.058 -9999 0 -0.247 18 18
ESR1 0.007 0.072 -9999 0 -0.227 38 38
HBP1 0.038 0.011 -9999 0 0 43 43
MEF2C 0.014 0.067 -9999 0 -0.28 19 19
MEF2A 0.017 0.057 -9999 0 -0.258 16 16
EIF4EBP1 -0.008 0.094 -9999 0 -0.197 94 94
KRT19 0.008 0.076 -9999 0 -0.229 39 39
ELK4 0.018 0.055 -9999 0 -0.271 14 14
ATF6 0.018 0.055 -9999 0 -0.254 15 15
ATF1 -0.011 0.098 -9999 0 -0.298 18 18
p38alpha-beta/MAPKAPK2 0.051 0.075 -9999 0 -0.262 11 11
p38alpha-beta/MAPKAPK3 0.052 0.074 -9999 0 -0.293 9 9
Effects of Botulinum toxin

Figure 121.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 123.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
STX1A -0.01 0.001 0 11 -9999 0 11
UniProt:P19321 0 0 -9999 0 -9999 0 0
RIMS1/UNC13B 0.056 0.02 -9999 0 -0.134 2 2
STXBP1 0.038 0.011 -9999 0 0 42 42
ACh/CHRNA1 0.027 0.025 0.091 1 -0.048 39 40
RAB3GAP2/RIMS1/UNC13B 0.069 0.041 -9999 0 -0.116 15 15
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 0.039 0.009 -9999 0 0 29 29
mol:ACh 0.002 0.023 0.072 24 -0.085 4 28
RAB3GAP2 0.039 0.01 -9999 0 0 35 35
STX1A/SNAP25/VAMP2 0.053 0.057 0.18 1 -0.105 24 25
UniProt:P10844 0 0 -9999 0 -9999 0 0
muscle contraction 0.027 0.025 0.091 1 -0.048 39 40
UNC13B 0.04 0.007 -9999 0 0 15 15
CHRNA1 0.037 0.013 -9999 0 0 57 57
UniProt:P10845 0 0 -9999 0 -9999 0 0
ACh/Synaptotagmin 1 0.028 0.025 0.091 1 -0.048 39 40
SNAP25 0.006 0.002 -9999 0 0 58 58
VAMP2 0.005 0.002 -9999 0 0 69 69
SYT1 0.038 0.011 -9999 0 0 42 42
UniProt:Q00496 0 0 -9999 0 -9999 0 0
STXIA/STXBP1 0.033 0.011 -9999 0 -9999 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.053 0.057 0.18 1 -0.105 24 25
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 0.019 0.02 0.076 5 -0.092 3 8
NFATC2 0.019 0.02 0.084 1 -0.108 3 4
NFATC3 0.02 0.02 0.077 6 -0.082 4 10
CD40LG 0.03 0.104 0.303 20 -0.24 1 21
PTGS2 0.011 0.093 0.334 12 -0.261 6 18
JUNB 0.029 0.019 -9999 0 0 159 159
CaM/Ca2+/Calcineurin A alpha-beta B1 0.032 0.016 -9999 0 -0.124 3 3
CaM/Ca2+ 0.032 0.016 -9999 0 -0.124 3 3
CALM1 0.041 0.011 -9999 0 -0.002 28 28
JUN 0.038 0.016 0.103 1 -0.035 1 2
mol:Ca2+ 0.001 0.003 -9999 0 -9999 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.027 0.011 0.067 1 -0.101 2 3
FOSL1 0.04 0.007 -9999 0 0 18 18
CREM 0.039 0.007 -9999 0 0 19 19
Jun/NFAT1-c-4/p21SNFT 0.054 0.066 0.223 3 -9999 0 3
FOS 0.028 0.022 0.103 1 0 201 202
IFNG 0.02 0.094 0.309 11 -0.24 1 12
AP-1/NFAT1-c-4 0.082 0.114 -9999 0 -0.228 3 3
FASLG 0.027 0.101 0.306 16 -0.241 2 18
NFAT1-c-4/ICER1 0.054 0.056 0.211 7 -9999 0 7
IL2RA 0.027 0.104 0.328 17 -0.244 2 19
FKBP12/FK506 0.028 0.012 -9999 0 -0.125 2 2
CSF2 0.029 0.102 0.304 19 -0.24 1 20
JunB/Fra1/NFAT1-c-4 0.046 0.072 0.227 3 -0.176 3 6
IL4 0.029 0.102 0.305 18 -0.24 1 19
IL2 -0.024 0.205 -9999 0 -0.869 30 30
IL3 0.027 0.121 -9999 0 -0.598 19 19
FKBP1A 0.038 0.011 -9999 0 0 44 44
BATF3 0 0 -9999 0 -9999 0 0
mol:FK506 0 0 -9999 0 -9999 0 0
POU2F1 0.045 0.008 -9999 0 -9999 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.046 0.01 -9999 0 -0.051 3 3
NFATC2 0.046 0.179 0.412 5 -0.382 38 43
NFATC3 0.071 0.066 0.288 26 -0.241 3 29
CD40LG 0.083 0.154 0.503 4 -0.688 2 6
ITCH 0.022 0.053 0.2 5 -0.204 21 26
CBLB 0.019 0.061 0.199 6 -0.256 20 26
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment 0.043 0.14 0.368 1 -0.5 5 6
JUNB 0.029 0.019 -9999 0 0 159 159
CaM/Ca2+/Calcineurin A alpha-beta B1 0.044 0.048 -9999 0 -0.178 22 22
T cell anergy 0.002 0.066 0.247 5 -0.285 17 22
TLE4 0.007 0.153 0.278 3 -0.412 44 47
Jun/NFAT1-c-4/p21SNFT 0.085 0.149 -9999 0 -0.698 2 2
AP-1/NFAT1-c-4 0.09 0.186 -9999 0 -0.756 2 2
IKZF1 0.021 0.108 0.215 17 -0.25 38 55
T-helper 2 cell differentiation 0.034 0.137 0.45 1 -0.489 1 2
AP-1/NFAT1 0.035 0.143 0.326 2 -0.251 39 41
CALM1 0.042 0.034 -9999 0 -0.108 23 23
EGR2 0.061 0.156 0.585 6 -1.088 2 8
EGR3 0.055 0.134 0.582 5 -0.523 1 6
NFAT1/FOXP3 0.057 0.143 0.325 3 -0.268 35 38
EGR1 0.027 0.021 0.074 1 0 190 191
JUN 0.04 0.026 0.14 2 -0.054 4 6
EGR4 0.041 0.009 -9999 0 -0.035 2 2
mol:Ca2+ 0.005 0.022 -9999 0 -0.099 22 22
GBP3 -0.021 0.211 0.32 21 -0.451 91 112
FOSL1 0.04 0.007 -9999 0 0 18 18
NFAT1-c-4/MAF/IRF4 0.09 0.151 -9999 0 -0.683 2 2
DGKA 0.025 0.125 0.287 7 -0.296 33 40
CREM 0.039 0.008 -9999 0 -0.002 20 20
NFAT1-c-4/PPARG 0.086 0.144 -9999 0 -0.689 2 2
CTLA4 0.023 0.102 -9999 0 -0.227 32 32
NFAT1-c-4 (dimer)/EGR1 0.062 0.147 -9999 0 -0.753 2 2
NFAT1-c-4 (dimer)/EGR4 0.094 0.15 -9999 0 -0.719 2 2
FOS 0.029 0.029 0.127 3 -0.042 7 10
IFNG 0.033 0.133 -9999 0 -0.492 7 7
T cell activation 0.054 0.121 0.604 1 -9999 0 1
MAF 0.036 0.015 -9999 0 0 80 80
T-helper 2 cell lineage commitment 0 0 -9999 0 -9999 0 0
activation-induced cell death of T cells -0.064 0.124 0.532 2 -0.505 22 24
TNF 0.048 0.132 0.459 2 -0.692 2 4
FASLG 0.055 0.164 0.698 1 -1.026 3 4
TBX21 0.046 0.013 0.093 1 -9999 0 1
BATF3 0 0 -9999 0 -9999 0 0
PRKCQ 0.037 0.018 -9999 0 -0.125 1 1
PTPN1 0.028 0.119 0.288 7 -0.271 29 36
NFAT1-c-4/ICER1 0.087 0.146 -9999 0 -0.72 2 2
GATA3 0.041 0.011 -9999 0 -9999 0 0
T-helper 1 cell differentiation 0.035 0.133 -9999 0 -0.486 7 7
IL2RA 0.05 0.146 -9999 0 -0.497 6 6
T-helper 1 cell lineage commitment 0 0 -9999 0 -9999 0 0
CASP3 0.023 0.117 0.274 2 -0.299 30 32
E2F1 0.031 0.05 -9999 0 -0.18 27 27
PPARG 0.039 0.01 -9999 0 -9999 0 0
SLC3A2 0.024 0.126 0.286 5 -0.296 36 41
IRF4 0.038 0.012 -9999 0 0 46 46
PTGS2 0.055 0.139 0.692 1 -0.725 2 3
CSF2 0.079 0.152 0.503 4 -0.688 2 6
JunB/Fra1/NFAT1-c-4 0.076 0.151 -9999 0 -0.693 2 2
IL4 0.033 0.138 -9999 0 -0.504 1 1
IL5 0.078 0.151 0.487 3 -0.688 2 5
IL2 0.054 0.121 0.605 1 -9999 0 1
IL3 0.036 0.078 -9999 0 -0.406 13 13
RNF128 0.022 0.042 0.197 4 -0.153 22 26
NFATC1 0.064 0.124 0.505 22 -0.534 2 24
CDK4 -0.077 0.288 0.467 3 -1.239 28 31
PTPRK 0.011 0.15 0.278 3 -0.392 45 48
IL8 0.048 0.142 0.576 3 -0.566 3 6
POU2F1 0.046 0.008 -9999 0 -9999 0 0
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.06 0.035 -9999 0 -0.096 15 15
MAPK9 0.009 0.002 -9999 0 0 39 39
adrenocorticotropin secretion -0.01 0.003 0 42 -9999 0 42
GNB1/GNG2 0.046 0.031 -9999 0 -0.109 16 16
GNB1 0.039 0.01 -9999 0 0 33 33
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
MAPK14 0.009 0.002 -9999 0 0 20 20
Gs family/GTP 0.025 0.005 -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 0.04 0.008 -9999 0 0 22 22
GNG2 0.039 0.009 -9999 0 0 29 29
CRH 0.038 0.011 -9999 0 0 42 42
mol:cortisol 0 0 -9999 0 -9999 0 0
MAPK8 0.009 0.002 -9999 0 0 29 29
MAPK11 0.007 0.004 -9999 0 0 157 157
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.037 0.017 -9999 0 -0.13 3 3
PDGFRB 0.037 0.014 -9999 0 0 65 65
SPHK1 0.011 0.085 -9999 0 -0.627 9 9
mol:S1P 0.009 0.076 -9999 0 -0.529 9 9
S1P1/S1P/Gi 0.025 0.081 -9999 0 -0.307 18 18
GNAO1 0.035 0.017 -9999 0 -0.003 92 92
PDGFB-D/PDGFRB/PLCgamma1 0.013 0.103 0.25 7 -0.266 31 38
PLCG1 0.01 0.087 0.208 11 -0.297 19 30
mol:GTP 0 0 -9999 0 -9999 0 0
PDGFB-D/PDGFRB 0.037 0.014 -9999 0 0 65 65
GNAI2 0.04 0.012 -9999 0 -0.014 22 22
GNAI3 0.038 0.015 -9999 0 -0.006 54 54
GNAI1 0.034 0.018 -9999 0 -0.002 100 100
mol:GDP 0 0 -9999 0 -9999 0 0
EDG1 0.024 0.016 -9999 0 -0.117 3 3
S1P1/S1P 0.021 0.068 0.2 1 -0.328 11 12
negative regulation of cAMP metabolic process 0.025 0.08 -9999 0 -0.3 18 18
MAPK3 0.011 0.106 -9999 0 -0.469 14 14
calcium-dependent phospholipase C activity 0 0.002 -9999 0 -9999 0 0
Rac1/GDP 0.029 0.009 -9999 0 -0.125 1 1
RhoA/GDP 0.029 0.014 -9999 0 -0.125 4 4
KDR 0.043 0.01 -9999 0 -9999 0 0
PLCB2 0.016 0.064 -9999 0 -0.307 10 10
RAC1 0.039 0.009 -9999 0 0 28 28
RhoA/GTP 0.019 0.06 -9999 0 -0.28 12 12
receptor internalization 0.02 0.064 0.189 2 -0.309 11 13
PTGS2 0.003 0.149 0.342 1 -0.811 11 12
Rac1/GTP 0.019 0.06 -9999 0 -0.29 11 11
RHOA 0.04 0.006 -9999 0 0 13 13
VEGFA 0.004 0.002 -9999 0 -9999 0 0
negative regulation of T cell proliferation 0.025 0.08 -9999 0 -0.3 18 18
GO:0007205 0 0 -9999 0 -9999 0 0
GNAZ 0.038 0.015 -9999 0 -0.005 55 55
MAPK1 0.014 0.097 0.262 1 -0.438 12 13
S1P1/S1P/PDGFB-D/PDGFRB 0.032 0.076 0.231 2 -0.268 13 15
ABCC1 0.04 0.009 -9999 0 0 27 27
Arf6 trafficking events

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
SLC2A4 0.039 0.01 -9999 0 0 35 35
CLTC 0.011 0.086 -9999 0 -0.465 11 11
calcium ion-dependent exocytosis 0.016 0.046 0.176 2 -0.193 9 11
Dynamin 2/GTP 0.021 0.041 -9999 0 -0.107 44 44
EXOC4 0.038 0.011 -9999 0 0 41 41
CD59 0.009 0.057 -9999 0 -0.346 10 10
CPE 0.012 0.013 -9999 0 -0.109 4 4
CTNNB1 0.039 0.01 -9999 0 0 32 32
membrane fusion 0.004 0.033 0.108 2 -0.147 12 14
CTNND1 -0.009 0.066 0.174 50 -0.201 3 53
DNM2 0.036 0.014 -9999 0 0 72 72
mol:PI-4-5-P2 0.015 0.053 0.175 3 -0.217 12 15
TSHR 0.014 0.015 -9999 0 -0.109 7 7
INS 0.004 0.103 -9999 0 -0.449 26 26
BIN1 0.04 0.007 -9999 0 0 18 18
mol:Choline 0.004 0.033 0.108 2 -0.147 12 14
growth hormone secretagogue receptor activity 0 0 -9999 0 -9999 0 0
mol:GDP 0.014 0.013 -9999 0 -0.108 5 5
membrane depolarization 0 0 -9999 0 -9999 0 0
ARF6 0.04 0.007 -9999 0 0 16 16
mol:Ca2+ 0.021 0.041 -9999 0 -0.107 44 44
JUP 0.008 0.058 -9999 0 -0.347 9 9
ASAP2/amphiphysin II 0.047 0.023 -9999 0 -0.096 11 11
ARF6/GTP 0.028 0.019 -9999 0 -0.125 8 8
CDH1 0.006 0.063 -9999 0 -0.381 10 10
clathrin-independent pinocytosis 0.028 0.019 -9999 0 -0.124 8 8
MAPK8IP3 0.039 0.009 -9999 0 0 29 29
positive regulation of endocytosis 0.028 0.019 -9999 0 -0.124 8 8
EXOC2 0.038 0.011 -9999 0 0 41 41
substrate adhesion-dependent cell spreading 0.012 0.105 -9999 0 -0.274 46 46
insulin receptor binding 0 0 -9999 0 -9999 0 0
SPAG9 0.039 0.009 -9999 0 0 30 30
regulation of calcium-dependent cell-cell adhesion -0.031 0.081 0.33 12 -9999 0 12
positive regulation of phagocytosis 0.015 0.015 -9999 0 -0.108 7 7
ARF6/GTP/JIP3 0.05 0.024 -9999 0 -0.109 8 8
ACAP1 0.004 0.033 -9999 0 -0.174 8 8
mol:GTP 0 0 -9999 0 -9999 0 0
CHRM2 0.012 0.057 -9999 0 -0.331 10 10
clathrin heavy chain/ACAP1 0.012 0.074 0.246 1 -0.369 11 12
JIP4/KLC1 0.045 0.029 -9999 0 -0.097 19 19
EXOC1 0.038 0.011 -9999 0 0 46 46
exocyst 0.011 0.106 -9999 0 -0.277 46 46
RALA/GTP 0.027 0.02 -9999 0 -0.125 9 9
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.047 0.032 -9999 0 -0.109 19 19
receptor recycling 0.028 0.019 -9999 0 -0.124 8 8
CTNNA1 -0.009 0.065 0.174 48 -0.201 3 51
NME1 0.014 0.013 -9999 0 -0.109 5 5
clathrin coat assembly 0.012 0.086 -9999 0 -0.457 11 11
IL2RA 0.012 0.055 -9999 0 -0.326 9 9
VAMP3 0.015 0.015 -9999 0 -0.109 7 7
GLUT4/clathrin heavy chain/ACAP1 0.035 0.079 -9999 0 -0.36 10 10
EXOC6 0.038 0.011 -9999 0 0 46 46
PLD1 0 0.048 -9999 0 -0.194 28 28
PLD2 0.014 0.025 -9999 0 -0.187 3 3
EXOC5 0.04 0.008 -9999 0 0 20 20
PIP5K1C 0.011 0.049 0.178 2 -0.223 11 13
SDC1 0.01 0.058 -9999 0 -0.346 10 10
ARF6/GDP 0.026 0.038 -9999 0 -0.114 35 35
EXOC7 0.04 0.007 -9999 0 0 18 18
E-cadherin/beta catenin 0.034 0.084 -9999 0 -0.34 12 12
mol:Phosphatidic acid 0.004 0.033 0.108 2 -0.147 12 14
endocytosis -0.046 0.023 0.096 11 -9999 0 11
SCAMP2 0.039 0.009 -9999 0 0 25 25
ADRB2 0.005 0.084 0.243 2 -0.434 11 13
EXOC3 0.037 0.012 -9999 0 0 55 55
ASAP2 0 0 -9999 0 -9999 0 0
Dynamin 2/GDP 0.025 0.045 0.19 4 -0.107 44 48
KLC1 0 0 -9999 0 -9999 0 0
AVPR2 0.006 0.083 0.252 1 -0.431 11 12
RALA 0.04 0.008 -9999 0 0 19 19
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.017 0.086 -9999 0 -0.368 12 12
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.018 0.042 0.148 49 -0.123 1 50
EntrezGene:79658 0 0 -9999 0 -9999 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.016 0.035 0.125 6 -0.164 3 9
AP2 0.039 0.043 -9999 0 -0.134 21 21
mol:DAG 0 0 -9999 0 -9999 0 0
Arfaptin 2/Rac/GTP 0.051 0.018 -9999 0 -0.112 1 1
CLTB 0.04 0.008 -9999 0 0 22 22
coatomer protein complex/ARF1/GTP/ER cargo protein 0.02 0.03 -9999 0 -0.152 13 13
CD4 0.032 0.017 -9999 0 0 121 121
CLTA 0.04 0.006 -9999 0 0 10 10
mol:GTP -0.003 0.003 0.013 5 -0.02 1 6
ARFGAP1 -0.009 0.003 0 56 -9999 0 56
mol:PI-4-5-P2 0.009 0.014 0.079 15 -9999 0 15
ARF1/GTP 0.021 0.012 0.078 1 -0.136 1 2
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.022 0.05 0.173 45 -0.166 4 49
mol:Choline 0.008 0.014 0.079 15 -9999 0 15
mol:GDP 0 0 -9999 0 -9999 0 0
ARF1 0.039 0.012 -9999 0 0 45 45
DDEF1 0.004 0.009 0.079 6 -9999 0 6
ARF1/GDP 0.006 0.015 0.058 2 -0.087 8 10
AP2M1 0.032 0.017 -9999 0 0 125 125
EntrezGene:1313 0 0 -9999 0 -9999 0 0
actin filament polymerization -0.009 0.017 0.049 11 -0.102 2 13
Rac/GTP 0.029 0.01 -9999 0 -0.131 1 1
ARF1/GTP/GGA3/ARF-GAP1 0.046 0.024 -9999 0 -0.101 1 1
ARFIP2 0.033 0.021 -9999 0 -0.039 36 36
COPA 0.039 0.009 -9999 0 0 26 26
RAC1 0.039 0.009 -9999 0 0 28 28
ARF1/GTP/coatomer protein complex 0.015 0.038 0.138 2 -0.196 10 12
ARF1/GTP/ARHGAP10 0.025 0.01 -9999 0 -0.11 1 1
GGA3 0.04 0.008 -9999 0 0 21 21
ARF1/GTP/Membrin 0.023 0.044 -9999 0 -0.223 14 14
AP2A1 0.039 0.01 -9999 0 0 32 32
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.012 0.032 -9999 0 -0.17 11 11
ARF1/GDP/Membrin 0.029 0.051 -9999 0 -0.254 15 15
Arfaptin 2/Rac/GDP 0.05 0.018 -9999 0 -0.109 1 1
CYTH2 -0.003 0.003 0.013 5 -0.02 1 6
ARF1/GTP/GGA3 0.048 0.02 -9999 0 -0.117 2 2
mol:ATP 0 0 -9999 0 -9999 0 0
Rac/GDP 0.029 0.009 -9999 0 -0.125 1 1
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 0.005 0.055 -9999 0 -0.301 7 7
PLD2 0.008 0.014 0.079 15 -9999 0 15
ARF-GAP1/v-SNARE -0.009 0.003 0 56 -9999 0 56
PIP5K1A 0.009 0.014 0.079 15 -9999 0 15
ARF1/GTP/Membrin/GBF1/p115 0.017 0.026 -9999 0 -0.074 22 22
mol:Phosphatic acid 0 0 -9999 0 -9999 0 0
mol:Phosphatidic acid 0.008 0.014 0.079 15 -9999 0 15
KDEL Receptor/Ligand/ARF-GAP1 -0.009 0.003 0 56 -9999 0 56
GOSR2 0.013 0.036 -9999 0 -0.31 6 6
USO1 0.003 0.007 0.04 17 -0.029 1 18
GBF1 0.005 0.066 -9999 0 -0.351 18 18
ARF1/GTP/Arfaptin 2 0.05 0.019 -9999 0 -0.121 1 1
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.038 0.063 -9999 0 -0.124 45 45
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 0.027 0.078 0.296 10 -0.288 1 11
CRKL 0.018 0.064 0.246 2 -0.34 2 4
HRAS 0.028 0.076 0.245 2 -0.293 5 7
mol:PIP3 0.015 0.106 0.314 4 -0.376 15 19
SPRED1 0.035 0.014 -9999 0 0 78 78
SPRED2 0.04 0.008 -9999 0 0 22 22
GAB1 0.018 0.054 -9999 0 -0.306 1 1
FOXO3 0.02 0.093 -9999 0 -0.418 11 11
AKT1 0.021 0.098 -9999 0 -0.452 11 11
BAD 0.016 0.094 -9999 0 -0.424 11 11
megakaryocyte differentiation 0.021 0.057 0.237 1 -0.3 1 2
GSK3B 0.02 0.097 0.277 5 -0.41 11 16
RAF1 0.023 0.073 0.254 7 -0.274 3 10
SHC1 0.039 0.008 -9999 0 0 23 23
STAT3 0.017 0.06 -9999 0 -0.435 2 2
STAT1 0.027 0.11 -9999 0 -0.923 3 3
HRAS/SPRED1 0.034 0.082 0.259 3 -0.306 3 6
cell proliferation 0.017 0.062 0.252 2 -0.426 2 4
PIK3CA 0.029 0.019 -9999 0 0 166 166
TEC 0.033 0.017 -9999 0 0 114 114
RPS6KB1 0.022 0.094 -9999 0 -0.375 7 7
HRAS/SPRED2 0.039 0.082 0.252 3 -0.272 4 7
LYN/TEC/p62DOK 0.038 0.095 -9999 0 -0.357 4 4
MAPK3 0.016 0.063 0.227 6 -0.264 3 9
STAP1 0.02 0.059 -9999 0 -0.43 2 2
GRAP2 0.037 0.013 -9999 0 0 56 56
JAK2 0.026 0.107 -9999 0 -0.761 3 3
STAT1 (dimer) 0.029 0.11 -9999 0 -0.902 3 3
mol:Gleevec -0.002 0.003 -9999 0 -9999 0 0
GRB2/SOCS1/VAV1 0.058 0.089 -9999 0 -0.385 3 3
actin filament polymerization 0.02 0.06 -9999 0 -0.421 2 2
LYN 0.035 0.015 -9999 0 0 83 83
STAP1/STAT5A (dimer) 0.017 0.094 -9999 0 -0.553 4 4
PIK3R1 0.034 0.016 -9999 0 0 99 99
CBL/CRKL/GRB2 0.05 0.084 0.286 1 -0.355 2 3
PI3K 0.023 0.099 -9999 0 -0.327 10 10
PTEN 0.038 0.01 -9999 0 0 36 36
SCF/KIT/EPO/EPOR 0.056 0.133 -9999 0 -1.289 2 2
MAPK8 0.016 0.063 0.253 2 -0.435 2 4
STAT3 (dimer) 0.017 0.059 -9999 0 -0.426 2 2
positive regulation of transcription 0.015 0.057 0.212 6 -0.24 2 8
mol:GDP 0.037 0.082 -9999 0 -0.335 3 3
PIK3C2B 0.016 0.062 -9999 0 -0.435 2 2
CBL/CRKL 0.036 0.077 0.275 1 -0.36 2 3
FER 0.018 0.06 -9999 0 -0.435 2 2
SH2B3 0.02 0.059 -9999 0 -0.43 2 2
PDPK1 0.014 0.1 0.297 5 -0.332 15 20
SNAI2 0.021 0.067 0.243 2 -0.503 2 4
positive regulation of cell proliferation 0.019 0.107 -9999 0 -0.736 3 3
KITLG 0.043 0.014 -9999 0 -0.042 3 3
cell motility 0.019 0.107 -9999 0 -0.736 3 3
PTPN6 0.034 0.015 -9999 0 -0.005 67 67
EPOR 0.006 0.17 -9999 0 -0.99 2 2
STAT5A (dimer) 0.021 0.101 -9999 0 -0.565 4 4
SOCS1 0.037 0.012 -9999 0 0 51 51
cell migration -0.017 0.058 0.426 2 -9999 0 2
SOS1 0.037 0.012 -9999 0 0 51 51
EPO 0.043 0.01 -9999 0 -0.036 3 3
VAV1 0.036 0.014 -9999 0 0 69 69
GRB10 0.017 0.061 -9999 0 -0.436 2 2
PTPN11 0.037 0.011 -9999 0 -0.004 33 33
SCF/KIT 0.024 0.064 -9999 0 -0.451 2 2
GO:0007205 -0.002 0.004 -9999 0 -9999 0 0
MAP2K1 0.014 0.064 0.235 6 -0.244 2 8
CBL 0.04 0.008 -9999 0 0 20 20
KIT 0.015 0.158 -9999 0 -0.726 5 5
MAP2K2 0.014 0.061 0.235 6 -0.244 2 8
SHC/Grb2/SOS1 0.063 0.09 -9999 0 -0.395 2 2
STAT5A 0.024 0.097 -9999 0 -0.583 4 4
GRB2 0.04 0.008 -9999 0 0 21 21
response to radiation 0.025 0.07 0.241 3 -0.492 2 5
SHC/GRAP2 0.052 0.023 -9999 0 -0.134 1 1
PTPRO 0.019 0.055 0.239 1 -0.305 1 2
SH2B2 0.02 0.059 -9999 0 -0.43 2 2
DOK1 0.04 0.008 -9999 0 0 22 22
MATK 0.016 0.059 -9999 0 -0.435 2 2
CREBBP 0.058 0.029 -9999 0 -0.143 3 3
BCL2 -0.013 0.213 -9999 0 -0.673 22 22
Glypican 2 network

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
MDK 0.039 0.008 -9999 0 0 23 23
GPC2 0.04 0.006 -9999 0 0 13 13
GPC2/Midkine 0.054 0.032 -9999 0 -0.134 14 14
neuron projection morphogenesis 0.054 0.032 -9999 0 -0.134 14 14
Visual signal transduction: Rods

Figure 130.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table 132.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:K + 0.04 0.007 -9999 0 0 15 15
GNAT1/GTP 0.03 0.005 -9999 0 -9999 0 0
Metarhodopsin II/Arrestin 0.052 0.013 -9999 0 -9999 0 0
PDE6G/GNAT1/GTP 0.049 0.02 -9999 0 -0.109 2 2
mol:GTP 0 0 -9999 0 -9999 0 0
absorption of light 0 0 -9999 0 -9999 0 0
GNAT1 0.04 0.006 -9999 0 0 13 13
GRK1 0 0 -9999 0 -9999 0 0
CNG Channel 0.066 0.037 -9999 0 -0.106 2 2
mol:Na + 0.068 0.041 -9999 0 -0.11 1 1
mol:ADP 0 0 -9999 0 -9999 0 0
RGS9-1/Gbeta5/R9AP 0.067 0.034 -9999 0 -0.116 1 1
mol:GDP 0 0 -9999 0 -9999 0 0
cGMP/CNG Channel 0.084 0.049 -9999 0 -0.112 1 1
CNGB1 0.038 0.01 -9999 0 0 38 38
RDH5 0.036 0.013 -9999 0 0 65 65
SAG 0.04 0.006 -9999 0 0 12 12
mol:Ca2+ -0.017 0.081 0.324 19 -9999 0 19
Na + (4 Units) 0.056 0.037 -9999 0 -0.111 1 1
RGS9 0.038 0.01 -9999 0 0 37 37
GNB1/GNGT1 0.054 0.024 -9999 0 -0.134 4 4
GNAT1/GDP 0.079 0.038 -9999 0 -0.102 1 1
GUCY2D 0.038 0.011 -9999 0 0 42 42
GNGT1 0.039 0.009 -9999 0 0 26 26
GUCY2F 0.041 0.002 -9999 0 0 1 1
GNB5 0.039 0.008 -9999 0 0 23 23
mol:GMP (4 units) 0.035 0.023 0.164 7 -0.102 2 9
mol:11-cis-retinal 0.036 0.013 -9999 0 0 65 65
mol:cGMP 0.075 0.034 0.196 3 -0.109 1 4
GNB1 0.039 0.01 -9999 0 0 33 33
Rhodopsin 0.05 0.03 -9999 0 -0.134 7 7
SLC24A1 0.04 0.007 -9999 0 0 15 15
CNGA1 0.04 0.008 -9999 0 0 20 20
Metarhodopsin II 0.025 0.005 -9999 0 -9999 0 0
mol:Ca ++ 0 0 -9999 0 -9999 0 0
GC1/GCAP Family 0.09 0.038 -9999 0 -0.11 1 1
RGS9BP 0.037 0.013 -9999 0 0 56 56
Metarhodopsin II/Transducin 0.023 0.02 -9999 0 -0.142 6 6
GCAP Family/Ca ++ 0.072 0.024 -9999 0 -0.103 1 1
PDE6A/B 0.055 0.019 -9999 0 -9999 0 0
mol:Pi 0.066 0.033 -9999 0 -0.116 1 1
mol:all-trans-retinal 0 0 -9999 0 -9999 0 0
Transducin 0.07 0.029 -9999 0 -0.103 4 4
PDE6B 0.038 0.011 -9999 0 0 45 45
PDE6A 0.04 0.007 -9999 0 0 15 15
PDE6G 0.037 0.012 -9999 0 0 55 55
RHO 0.04 0.008 -9999 0 0 20 20
PDE6 0.09 0.056 -9999 0 -0.146 2 2
GUCA1A 0.039 0.008 -9999 0 0 24 24
GC2/GCAP Family 0.097 0.031 -9999 0 -0.11 1 1
GUCA1C 0.039 0.009 -9999 0 0 27 27
GUCA1B 0.04 0.008 -9999 0 0 21 21
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.062 0.027 -9999 0 -0.096 1 1
RGS9BP 0.037 0.013 -9999 0 0 56 56
mol:GTP 0 0 -9999 0 -9999 0 0
GRK1 0 0 -9999 0 -9999 0 0
mol:Na + 0.05 0.016 -9999 0 -9999 0 0
mol:ADP -0.01 0.003 -9999 0 -9999 0 0
GNAT2 0.041 0.004 -9999 0 0 6 6
RGS9-1/Gbeta5/R9AP 0.067 0.034 -9999 0 -0.116 1 1
mol:GDP 0 0 -9999 0 -9999 0 0
PDE6H/GNAT2/GTP 0.05 0.017 -9999 0 -9999 0 0
GRK7 0.038 0.011 -9999 0 0 40 40
CNGB3 0.038 0.012 -9999 0 0 49 49
Cone Metarhodopsin II/X-Arrestin 0.03 0.001 -9999 0 -9999 0 0
mol:Ca2+ -0.004 0.055 0.191 40 -9999 0 40
Cone PDE6 0.089 0.055 -9999 0 -0.109 1 1
Cone Metarhodopsin II 0.024 0.007 -9999 0 -9999 0 0
Na + (4 Units) 0.067 0.028 -9999 0 -9999 0 0
GNAT2/GDP 0.08 0.037 -9999 0 -0.102 1 1
GNB5 0.039 0.008 -9999 0 0 23 23
mol:GMP (4 units) -0.003 0.058 0.191 45 -9999 0 45
Cone Transducin 0.067 0.029 -9999 0 -0.103 1 1
SLC24A2 0.039 0.01 -9999 0 0 33 33
GNB3/GNGT2 0.052 0.022 -9999 0 -0.134 1 1
GNB3 0.037 0.012 -9999 0 0 55 55
GNAT2/GTP 0.03 0.003 -9999 0 -9999 0 0
CNGA3 0.041 0.004 -9999 0 0 4 4
ARR3 0.041 0.002 -9999 0 0 1 1
absorption of light 0 0 -9999 0 -9999 0 0
cGMP/Cone CNG Channel 0.05 0.016 -9999 0 -9999 0 0
mol:Pi 0.066 0.033 -9999 0 -0.116 1 1
Cone CNG Channel 0.081 0.043 -9999 0 -9999 0 0
mol:all-trans-retinal 0 0 -9999 0 -9999 0 0
mol:K + 0.039 0.01 -9999 0 0 33 33
RGS9 0.038 0.01 -9999 0 0 37 37
PDE6C 0.04 0.007 -9999 0 0 18 18
GNGT2 0.039 0.008 -9999 0 0 23 23
mol:cGMP (4 units) 0 0 -9999 0 -9999 0 0
PDE6H 0.037 0.012 -9999 0 0 50 50
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/OV/856530/1.GDAC_MergeDataFiles.Finished/OV.exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data.data.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/writeReducedSegments/OV/868533/1.GetReducedSegments.Finished/OV.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)