PARADIGM pathway analysis of mRNA expression and copy number data
Colon/Rectal Adenocarcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C12J68WF
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): PARADIGM pathway analysis of mRNA expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C12J68WF
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 32 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
TCGA08_retinoblastoma 121
Signaling events mediated by Stem cell factor receptor (c-Kit) 68
BCR signaling pathway 55
Fc-epsilon receptor I signaling in mast cells 51
HIF-1-alpha transcription factor network 44
IGF1 pathway 41
FAS signaling pathway (CD95) 38
Syndecan-1-mediated signaling events 31
Visual signal transduction: Rods 26
Arf6 signaling events 23
Results
Summary Table

The following list describes the columns found in Table 2.

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

  • Significance.Ratio = (Ave.Num.Perturbations)/ (Cohort Size) where Cohort Size is 222 . Pathway is significant if Significance.Ratio > 0.05 .

  • 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. A pathway is defined as significant (red number in Significance.Ratio column) if the Ave.Num.Perturbationsis > 5% of the cohort size ( 222 ).

Pathway.Name Significance.Ratio 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
TCGA08_retinoblastoma 0.5450 121 971 8 -0.35 0.19 1000 -1000 -0.003 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.3063 68 5321 78 -1.1 0.28 1000 -1000 -0.057 -1000
BCR signaling pathway 0.2477 55 5510 99 -0.39 0.034 1000 -1000 -0.064 -1000
Fc-epsilon receptor I signaling in mast cells 0.2297 51 5023 97 -0.35 0.044 1000 -1000 -0.064 -1000
HIF-1-alpha transcription factor network 0.1982 44 3417 76 -0.73 0.041 1000 -1000 -0.076 -1000
IGF1 pathway 0.1847 41 2348 57 -0.28 0.09 1000 -1000 -0.051 -1000
FAS signaling pathway (CD95) 0.1712 38 1787 47 -0.2 0.12 1000 -1000 -0.047 -1000
Syndecan-1-mediated signaling events 0.1396 31 1075 34 -0.31 0.034 1000 -1000 -0.046 -1000
Visual signal transduction: Rods 0.1171 26 1392 52 -0.35 0.07 1000 -1000 -0.033 -1000
Arf6 signaling events 0.1036 23 1474 62 -0.19 0.082 1000 -1000 -0.02 -1000
TCGA08_p53 0.1036 23 166 7 -0.059 0.033 1000 -1000 -0.007 -1000
FOXM1 transcription factor network 0.0991 22 1134 51 -0.51 0.033 1000 -1000 -0.1 -1000
Wnt signaling 0.0946 21 151 7 -0.05 0.033 1000 -1000 -0.013 -1000
Visual signal transduction: Cones 0.0856 19 724 38 -0.14 0.054 1000 -1000 -0.006 -1000
HIF-2-alpha transcription factor network 0.0856 19 859 43 -0.56 0.32 1000 -1000 -0.062 -1000
EGFR-dependent Endothelin signaling events 0.0856 19 410 21 -0.09 0.049 1000 -1000 -0.049 -1000
Glypican 1 network 0.0811 18 881 48 -0.26 0.057 1000 -1000 -0.039 -1000
Syndecan-2-mediated signaling events 0.0766 17 1233 69 -0.29 0.055 1000 -1000 -0.046 -1000
BMP receptor signaling 0.0766 17 1424 81 -0.17 0.065 1000 -1000 -0.053 -1000
Reelin signaling pathway 0.0766 17 967 56 -0.28 0.091 1000 -1000 -0.052 -1000
Endothelins 0.0766 17 1670 96 -0.38 0.096 1000 -1000 -0.053 -1000
IL12-mediated signaling events 0.0676 15 1325 87 -0.38 0.067 1000 -1000 -0.08 -1000
IL4-mediated signaling events 0.0676 15 1377 91 -0.49 0.32 1000 -1000 -0.13 -1000
TRAIL signaling pathway 0.0676 15 765 48 -0.1 0.034 1000 -1000 -0.035 -1000
IL1-mediated signaling events 0.0676 15 945 62 -0.22 0.058 1000 -1000 -0.047 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0676 15 783 52 -0.43 0.12 1000 -1000 -0.042 -1000
IL6-mediated signaling events 0.0676 15 1151 75 -0.25 0.062 1000 -1000 -0.057 -1000
Signaling events mediated by PRL 0.0676 15 533 34 -0.077 0.096 1000 -1000 -0.036 -1000
FOXA2 and FOXA3 transcription factor networks 0.0586 13 606 46 -0.74 0.039 1000 -1000 -0.1 -1000
Syndecan-3-mediated signaling events 0.0586 13 483 35 -0.29 0.071 1000 -1000 -0.028 -1000
Signaling events mediated by the Hedgehog family 0.0541 12 656 52 -0.13 0.086 1000 -1000 -0.044 -1000
IL2 signaling events mediated by PI3K 0.0541 12 714 58 -0.59 0.039 1000 -1000 -0.045 -1000
Regulation of nuclear SMAD2/3 signaling 0.0495 11 1525 136 -1.1 0.12 1000 -1000 -0.04 -1000
Ceramide signaling pathway 0.0495 11 876 76 -0.28 0.088 1000 -1000 -0.037 -1000
Canonical Wnt signaling pathway 0.0495 11 591 51 -0.23 0.18 1000 -1000 -0.058 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0450 10 572 54 -0.28 0.043 1000 -1000 -0.058 -1000
Thromboxane A2 receptor signaling 0.0450 10 1117 105 -0.35 0.069 1000 -1000 -0.051 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0450 10 903 85 -0.13 0.059 1000 -1000 -0.052 -1000
TCR signaling in naïve CD8+ T cells 0.0450 10 931 93 -0.059 0.049 1000 -1000 -0.058 -1000
Presenilin action in Notch and Wnt signaling 0.0405 9 601 61 -0.23 0.12 1000 -1000 -0.058 -1000
p75(NTR)-mediated signaling 0.0405 9 1232 125 -0.31 0.08 1000 -1000 -0.053 -1000
PLK1 signaling events 0.0405 9 814 85 -0.099 0.068 1000 -1000 -0.036 -1000
Glucocorticoid receptor regulatory network 0.0405 9 1053 114 -0.3 0.21 1000 -1000 -0.063 -1000
Glypican 2 network 0.0405 9 36 4 0 0.012 1000 -1000 0 -1000
Aurora B signaling 0.0405 9 603 67 -0.14 0.049 1000 -1000 -0.035 -1000
PLK2 and PLK4 events 0.0360 8 26 3 0.004 0.024 1000 -1000 -0.013 -1000
Osteopontin-mediated events 0.0360 8 321 38 -0.2 0.05 1000 -1000 -0.041 -1000
PDGFR-alpha signaling pathway 0.0360 8 378 44 -0.097 0.077 1000 -1000 -0.032 -1000
amb2 Integrin signaling 0.0360 8 720 82 -0.25 0.054 1000 -1000 -0.036 -1000
Ephrin B reverse signaling 0.0360 8 402 48 -0.093 0.049 1000 -1000 -0.032 -1000
Integrins in angiogenesis 0.0360 8 683 84 -0.28 0.08 1000 -1000 -0.052 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0360 8 594 68 -0.36 0.053 1000 -1000 -0.085 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0360 8 269 33 -0.13 0.077 1000 -1000 -0.053 -1000
Regulation of Androgen receptor activity 0.0360 8 594 70 -0.54 0.063 1000 -1000 -0.048 -1000
Ras signaling in the CD4+ TCR pathway 0.0360 8 144 17 -0.014 0.055 1000 -1000 -0.021 -1000
Noncanonical Wnt signaling pathway 0.0315 7 189 26 -0.05 0.034 1000 -1000 -0.046 -1000
Cellular roles of Anthrax toxin 0.0315 7 311 39 -0.034 0.034 1000 -1000 -0.022 -1000
Signaling events mediated by PTP1B 0.0315 7 544 76 -0.26 0.059 1000 -1000 -0.058 -1000
EPO signaling pathway 0.0315 7 423 55 -0.52 0.034 1000 -1000 -0.048 -1000
Nectin adhesion pathway 0.0315 7 446 63 -0.3 0.078 1000 -1000 -0.043 -1000
Regulation of p38-alpha and p38-beta 0.0315 7 410 54 -0.084 0.062 1000 -1000 -0.055 -1000
Calcium signaling in the CD4+ TCR pathway 0.0315 7 226 31 -0.14 0.04 1000 -1000 -0.059 -1000
Plasma membrane estrogen receptor signaling 0.0315 7 666 86 -0.28 0.1 1000 -1000 -0.055 -1000
ceramide signaling pathway 0.0270 6 308 49 -0.2 0.067 1000 -1000 -0.041 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0270 6 508 83 -0.2 0.087 1000 -1000 -0.035 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0270 6 294 45 -0.1 0.058 1000 -1000 -0.052 -1000
Nongenotropic Androgen signaling 0.0270 6 339 52 -0.057 0.076 1000 -1000 -0.034 -1000
IL27-mediated signaling events 0.0270 6 308 51 -0.15 0.034 1000 -1000 -0.058 -1000
TCGA08_rtk_signaling 0.0270 6 163 26 -0.11 0.069 1000 -1000 -0.018 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0270 6 501 74 -0.28 0.064 1000 -1000 -0.076 -1000
Class I PI3K signaling events 0.0270 6 453 73 -0.23 0.056 1000 -1000 -0.045 -1000
Syndecan-4-mediated signaling events 0.0270 6 451 67 -0.37 0.11 1000 -1000 -0.047 -1000
IL23-mediated signaling events 0.0270 6 397 60 -0.25 0.034 1000 -1000 -0.084 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0225 5 144 28 -0.033 0.043 1000 -1000 -0.023 -1000
a4b1 and a4b7 Integrin signaling 0.0225 5 26 5 0.011 0.045 1000 -1000 0.007 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0225 5 215 37 -0.085 0.079 1000 -1000 -0.035 -1000
Signaling events mediated by HDAC Class III 0.0225 5 213 40 -0.2 0.064 1000 -1000 -0.022 -1000
EPHB forward signaling 0.0225 5 508 85 -0.094 0.11 1000 -1000 -0.068 -1000
Regulation of Telomerase 0.0225 5 574 102 -0.16 0.08 1000 -1000 -0.065 -1000
VEGFR1 specific signals 0.0225 5 331 56 -0.001 0.1 1000 -1000 -0.058 -1000
Canonical NF-kappaB pathway 0.0180 4 162 39 -0.04 0.075 1000 -1000 -0.041 -1000
ErbB4 signaling events 0.0180 4 331 69 -0.21 0.098 1000 -1000 -0.047 -1000
Class I PI3K signaling events mediated by Akt 0.0180 4 312 68 -0.057 0.068 1000 -1000 -0.042 -1000
Signaling mediated by p38-alpha and p38-beta 0.0180 4 202 44 -0.15 0.034 1000 -1000 -0.033 -1000
Effects of Botulinum toxin 0.0180 4 119 26 -0.012 0.063 1000 -1000 -0.018 -1000
E-cadherin signaling in the nascent adherens junction 0.0180 4 306 76 -0.029 0.1 1000 -1000 -0.068 -1000
Arf6 trafficking events 0.0180 4 353 71 -0.11 0.055 1000 -1000 -0.028 -1000
S1P3 pathway 0.0180 4 188 42 -0.031 0.043 1000 -1000 -0.041 -1000
E-cadherin signaling events 0.0180 4 20 5 0.021 0.051 1000 -1000 0 -1000
Caspase cascade in apoptosis 0.0135 3 253 74 -0.09 0.048 1000 -1000 -0.043 -1000
BARD1 signaling events 0.0135 3 177 57 -0.055 0.066 1000 -1000 -0.051 -1000
JNK signaling in the CD4+ TCR pathway 0.0135 3 56 17 -0.013 0.076 1000 -1000 -0.038 -1000
Aurora A signaling 0.0135 3 192 60 -0.002 0.087 1000 -1000 -0.021 -1000
Arf6 downstream pathway 0.0135 3 152 43 -0.047 0.048 1000 -1000 -0.031 -1000
mTOR signaling pathway 0.0135 3 210 53 -0.07 0.046 1000 -1000 -0.058 -1000
IFN-gamma pathway 0.0135 3 223 68 -0.04 0.055 1000 -1000 -0.058 -1000
S1P1 pathway 0.0135 3 141 36 -0.033 0.035 1000 -1000 -0.046 -1000
FoxO family signaling 0.0135 3 240 64 -0.11 0.067 1000 -1000 -0.045 -1000
Signaling mediated by p38-gamma and p38-delta 0.0135 3 57 15 -0.017 0.034 1000 -1000 -0.028 -1000
LPA receptor mediated events 0.0135 3 344 102 -0.1 0.049 1000 -1000 -0.089 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0135 3 276 88 -0.19 0.11 1000 -1000 -0.094 -1000
PDGFR-beta signaling pathway 0.0135 3 373 97 -0.17 0.099 1000 -1000 -0.054 -1000
LPA4-mediated signaling events 0.0090 2 26 12 -0.006 0.029 1000 -1000 -0.022 -1000
ErbB2/ErbB3 signaling events 0.0090 2 139 65 -0.031 0.054 1000 -1000 -0.061 -1000
Coregulation of Androgen receptor activity 0.0090 2 227 76 -0.074 0.068 1000 -1000 -0.017 -1000
Ephrin A reverse signaling 0.0090 2 14 7 0 0.04 1000 -1000 -0.001 -1000
Hedgehog signaling events mediated by Gli proteins 0.0090 2 179 65 -0.052 0.062 1000 -1000 -0.053 -1000
Insulin-mediated glucose transport 0.0090 2 82 32 -0.075 0.053 1000 -1000 -0.026 -1000
S1P5 pathway 0.0090 2 40 17 -0.033 0.034 1000 -1000 -0.016 -1000
Retinoic acid receptors-mediated signaling 0.0090 2 118 58 -0.016 0.068 1000 -1000 -0.06 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0090 2 294 125 -0.02 0.13 1000 -1000 -0.07 -1000
IL2 signaling events mediated by STAT5 0.0090 2 60 22 -0.017 0.069 1000 -1000 -0.051 -1000
Insulin Pathway 0.0090 2 168 74 -0.023 0.1 1000 -1000 -0.048 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0090 2 245 120 -0.019 0.093 1000 -1000 -0.055 -1000
S1P4 pathway 0.0090 2 62 25 -0.033 0.043 1000 -1000 -0.03 -1000
Arf1 pathway 0.0090 2 118 54 -0.001 0.08 1000 -1000 -0.022 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0045 1 33 23 0.011 0.041 1000 -1000 -0.028 -1000
Signaling events mediated by HDAC Class II 0.0045 1 143 75 -0.052 0.067 1000 -1000 -0.028 -1000
Circadian rhythm pathway 0.0045 1 29 22 -0.011 0.078 1000 -1000 -0.031 -1000
Signaling events regulated by Ret tyrosine kinase 0.0045 1 97 82 0 0.069 1000 -1000 -0.074 -1000
Paxillin-dependent events mediated by a4b1 0.0045 1 71 36 -0.069 0.072 1000 -1000 -0.046 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0000 0 26 34 -0.047 0.094 1000 -1000 -0.041 -1000
Aurora C signaling 0.0000 0 4 7 0 0.047 1000 -1000 -0.017 -1000
Signaling events mediated by HDAC Class I 0.0000 0 80 104 -0.066 0.08 1000 -1000 -0.035 -1000
Atypical NF-kappaB pathway 0.0000 0 9 31 0 0.069 1000 -1000 -0.028 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 8 27 0 0.06 1000 -1000 -0.038 -1000
Rapid glucocorticoid signaling 0.0000 0 2 20 0 0.039 1000 -1000 -0.006 -1000
E-cadherin signaling in keratinocytes 0.0000 0 34 43 -0.054 0.1 1000 -1000 -0.045 -1000
Class IB PI3K non-lipid kinase events 0.0000 0 0 3 -0.034 0.034 1000 -1000 -0.009 -1000
p38 MAPK signaling pathway 0.0000 0 30 44 0 0.066 1000 -1000 -0.034 -1000
Alternative NF-kappaB pathway 0.0000 0 3 13 0 0.091 1000 -1000 0 -1000
Total NA 1328 78236 7203 -23 9.6 131000 -131000 -5.7 -131000
TCGA08_retinoblastoma

Figure S1.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S1.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.35 0.22 -10000 0 -0.48 162 162
CDKN2C 0.042 0.029 -10000 0 -10000 0 0
CDKN2A -0.077 0.16 -10000 0 -0.32 65 65
CCND2 0.17 0.1 0.22 160 -0.22 1 161
RB1 -0.15 0.1 0.22 1 -0.23 127 128
CDK4 0.18 0.098 0.23 161 -0.23 1 162
CDK6 0.19 0.1 0.25 160 -10000 0 160
G1/S progression 0.16 0.1 0.23 132 -0.22 1 133
Signaling events mediated by Stem cell factor receptor (c-Kit)

Figure S2.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S2.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.26 0.18 0.28 1 -0.42 106 107
CRKL -0.27 0.2 -10000 0 -0.44 109 109
HRAS -0.23 0.18 -10000 0 -0.4 79 79
mol:PIP3 -0.24 0.18 -10000 0 -0.41 102 102
SPRED1 0.032 0.009 -10000 0 -10000 0 0
SPRED2 0.034 0 -10000 0 -10000 0 0
GAB1 -0.29 0.2 -10000 0 -0.46 113 113
FOXO3 -0.26 0.21 -10000 0 -0.44 101 101
AKT1 -0.28 0.22 -10000 0 -0.47 102 102
BAD -0.26 0.2 -10000 0 -0.44 98 98
megakaryocyte differentiation -0.3 0.21 -10000 0 -0.46 118 118
GSK3B -0.26 0.21 -10000 0 -0.44 98 98
RAF1 -0.19 0.14 -10000 0 -0.38 26 26
SHC1 0.033 0.006 -10000 0 -10000 0 0
STAT3 -0.28 0.2 -10000 0 -0.45 110 110
STAT1 -0.76 0.53 -10000 0 -1.2 111 111
HRAS/SPRED1 -0.18 0.15 -10000 0 -0.37 27 27
cell proliferation -0.28 0.2 -10000 0 -0.44 111 111
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
TEC 0.034 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.28 0.22 -10000 0 -0.46 109 109
HRAS/SPRED2 -0.18 0.15 -10000 0 -0.38 27 27
LYN/TEC/p62DOK -0.25 0.2 -10000 0 -0.44 93 93
MAPK3 -0.13 0.1 -10000 0 -0.29 11 11
STAP1 -0.43 0.25 -10000 0 -0.58 143 143
GRAP2 0.032 0.009 -10000 0 -10000 0 0
JAK2 -0.59 0.41 -10000 0 -0.93 110 110
STAT1 (dimer) -0.74 0.51 -10000 0 -1.2 111 111
mol:Gleevec 0.012 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.28 0.22 -10000 0 -0.46 109 109
actin filament polymerization -0.28 0.2 -10000 0 -0.44 111 111
LYN 0.03 0.012 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.53 0.31 -10000 0 -0.73 142 142
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.24 0.19 -10000 0 -0.41 106 106
PI3K -0.26 0.21 -10000 0 -0.44 107 107
PTEN 0.027 0.052 -10000 0 -0.5 2 2
SCF/KIT/EPO/EPOR -0.84 0.66 -10000 0 -1.5 107 107
MAPK8 -0.29 0.2 -10000 0 -0.45 111 111
STAT3 (dimer) -0.28 0.2 -10000 0 -0.44 110 110
positive regulation of transcription -0.11 0.085 -10000 0 -0.25 6 6
mol:GDP -0.24 0.19 -10000 0 -0.4 108 108
PIK3C2B -0.28 0.21 -10000 0 -0.45 110 110
CBL/CRKL -0.26 0.19 -10000 0 -0.42 108 108
FER -0.29 0.2 -10000 0 -0.46 113 113
SH2B3 -0.28 0.2 -10000 0 -0.46 108 108
PDPK1 -0.22 0.17 -10000 0 -0.38 97 97
SNAI2 -0.27 0.2 -10000 0 -0.45 107 107
positive regulation of cell proliferation -0.51 0.34 -10000 0 -0.79 114 114
KITLG -0.023 0.052 -10000 0 -0.44 2 2
cell motility -0.51 0.34 -10000 0 -0.79 114 114
PTPN6 0.049 0.014 -10000 0 -10000 0 0
EPOR -0.21 0.18 -10000 0 -0.88 4 4
STAT5A (dimer) -0.41 0.28 -10000 0 -0.64 112 112
SOCS1 0.032 0.025 -10000 0 -0.32 1 1
cell migration 0.28 0.2 0.45 108 -10000 0 108
SOS1 0.034 0.002 -10000 0 -10000 0 0
EPO -0.011 0.033 -10000 0 -0.34 1 1
VAV1 -0.014 0.15 -10000 0 -0.51 19 19
GRB10 -0.28 0.2 -10000 0 -0.45 109 109
PTPN11 0.044 0.026 -10000 0 -0.32 1 1
SCF/KIT -0.3 0.21 -10000 0 -0.48 111 111
GO:0007205 0.017 0.01 -10000 0 -10000 0 0
MAP2K1 -0.15 0.11 -10000 0 -0.31 16 16
CBL 0.034 0.005 -10000 0 -10000 0 0
KIT -0.78 0.7 -10000 0 -1.5 108 108
MAP2K2 -0.15 0.11 -10000 0 -0.3 17 17
SHC/Grb2/SOS1 -0.26 0.21 -10000 0 -0.44 103 103
STAT5A -0.42 0.29 -10000 0 -0.66 112 112
GRB2 0.033 0.007 -10000 0 -10000 0 0
response to radiation -0.27 0.2 -10000 0 -0.44 105 105
SHC/GRAP2 0.046 0.016 -10000 0 -10000 0 0
PTPRO -0.3 0.21 -10000 0 -0.47 118 118
SH2B2 -0.28 0.2 -10000 0 -0.45 111 111
DOK1 0.033 0.024 -10000 0 -0.32 1 1
MATK -0.28 0.2 -10000 0 -0.46 108 108
CREBBP -0.08 0.081 -10000 0 -10000 0 0
BCL2 -1.1 0.7 -10000 0 -1.5 148 148
BCR signaling pathway

Figure S3.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S3.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.21 0.26 -10000 0 -0.5 85 85
IKBKB -0.097 0.13 -10000 0 -0.3 16 16
AKT1 -0.12 0.15 0.33 2 -0.28 75 77
IKBKG -0.1 0.13 -10000 0 -0.3 18 18
CALM1 -0.29 0.31 -10000 0 -0.58 100 100
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
MAP3K1 -0.28 0.37 0.48 1 -0.69 87 88
MAP3K7 0.033 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.31 0.34 -10000 0 -0.62 101 101
DOK1 0.033 0.024 -10000 0 -0.32 1 1
AP-1 -0.14 0.14 -10000 0 -0.28 87 87
LYN 0.03 0.012 -10000 0 -10000 0 0
BLNK 0.018 0.089 -10000 0 -0.5 6 6
SHC1 0.033 0.006 -10000 0 -10000 0 0
BCR complex -0.26 0.31 -10000 0 -0.55 108 108
CD22 -0.32 0.4 -10000 0 -0.78 86 86
CAMK2G -0.26 0.28 -10000 0 -0.54 99 99
CSNK2A1 0.027 0.014 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.16 0.22 -10000 0 -0.44 67 67
GO:0007205 -0.32 0.34 -10000 0 -0.64 101 101
SYK 0.032 0.024 -10000 0 -0.32 1 1
ELK1 -0.3 0.32 -10000 0 -0.6 100 100
NFATC1 -0.31 0.35 0.35 1 -0.65 102 103
B-cell antigen/BCR complex -0.26 0.31 -10000 0 -0.55 108 108
PAG1/CSK -0.067 0.18 -10000 0 -0.37 56 56
NFKBIB -0.02 0.053 -10000 0 -0.14 5 5
HRAS -0.25 0.28 0.22 1 -0.53 95 96
NFKBIA -0.018 0.052 -10000 0 -0.14 2 2
NF-kappa-B/RelA/I kappa B beta -0.009 0.045 -10000 0 -10000 0 0
RasGAP/Csk -0.22 0.32 -10000 0 -0.51 108 108
mol:GDP -0.29 0.32 -10000 0 -0.6 101 101
PTEN 0.027 0.052 -10000 0 -0.51 2 2
CD79B -0.16 0.26 -10000 0 -0.5 78 78
NF-kappa-B/RelA/I kappa B alpha -0.008 0.044 -10000 0 -10000 0 0
GRB2 0.033 0.007 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.31 0.35 -10000 0 -0.65 106 106
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
mol:IP3 -0.32 0.35 -10000 0 -0.65 100 100
CSK 0.032 0.009 -10000 0 -10000 0 0
FOS -0.3 0.3 -10000 0 -0.58 103 103
CHUK -0.11 0.14 -10000 0 -0.33 23 23
IBTK 0.033 0.007 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.23 0.28 -10000 0 -0.52 89 89
PTPN6 -0.3 0.38 -10000 0 -0.73 85 85
RELA 0.034 0.005 -10000 0 -10000 0 0
BCL2A1 -0.005 0.032 -10000 0 -10000 0 0
VAV2 -0.38 0.46 0.45 1 -0.84 100 101
ubiquitin-dependent protein catabolic process -0.015 0.052 -10000 0 -0.14 5 5
BTK -0.18 0.45 -10000 0 -1.2 35 35
CD19 -0.39 0.47 -10000 0 -0.84 102 102
MAP4K1 0.033 0.007 -10000 0 -10000 0 0
CD72 0.025 0.062 -10000 0 -0.41 4 4
PAG1 -0.11 0.24 -10000 0 -0.51 57 57
MAPK14 -0.22 0.3 0.38 2 -0.57 85 87
SH3BP5 0.031 0.037 -10000 0 -0.51 1 1
PIK3AP1 -0.32 0.35 -10000 0 -0.67 96 96
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.36 0.41 -10000 0 -0.76 97 97
RAF1 -0.23 0.26 -10000 0 -0.5 94 94
RasGAP/p62DOK/SHIP -0.22 0.3 -10000 0 -0.48 115 115
CD79A -0.22 0.27 -10000 0 -0.5 99 99
re-entry into mitotic cell cycle -0.14 0.14 -10000 0 -0.28 89 89
RASA1 0.031 0.034 -10000 0 -0.32 2 2
MAPK3 -0.19 0.21 -10000 0 -0.43 81 81
MAPK1 -0.19 0.21 -10000 0 -0.43 81 81
CD72/SHP1 -0.27 0.36 0.61 1 -0.69 83 84
NFKB1 0.033 0.006 -10000 0 -10000 0 0
MAPK8 -0.22 0.3 0.45 1 -0.56 85 86
actin cytoskeleton organization -0.29 0.37 0.32 4 -0.66 100 104
NF-kappa-B/RelA -0.01 0.085 -10000 0 -10000 0 0
Calcineurin -0.23 0.27 -10000 0 -0.5 97 97
PI3K -0.26 0.29 -10000 0 -0.56 97 97
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.34 0.37 -10000 0 -0.7 99 99
SOS1 0.034 0.002 -10000 0 -10000 0 0
Bam32/HPK1 -0.32 0.43 -10000 0 -0.83 82 82
DAPP1 -0.38 0.49 -10000 0 -0.97 82 82
cytokine secretion -0.28 0.32 0.35 1 -0.59 102 103
mol:DAG -0.32 0.35 -10000 0 -0.65 100 100
PLCG2 -0.23 0.27 -10000 0 -0.5 105 105
MAP2K1 -0.22 0.23 -10000 0 -0.46 92 92
B-cell antigen/BCR complex/FcgammaRIIB -0.27 0.34 -10000 0 -0.56 114 114
mol:PI-3-4-5-P3 -0.17 0.19 -10000 0 -0.38 93 93
ETS1 -0.24 0.25 -10000 0 -0.49 96 96
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.17 0.26 -10000 0 -0.42 105 105
B-cell antigen/BCR complex/LYN -0.34 0.43 -10000 0 -0.8 91 91
MALT1 0.024 0.016 -10000 0 -10000 0 0
TRAF6 0.034 0.005 -10000 0 -10000 0 0
RAC1 -0.33 0.41 0.32 4 -0.73 100 104
B-cell antigen/BCR complex/LYN/SYK -0.27 0.38 -10000 0 -0.71 84 84
CARD11 -0.29 0.32 -10000 0 -0.6 98 98
FCGR2B -0.086 0.22 -10000 0 -0.5 48 48
PPP3CA 0.033 0.006 -10000 0 -10000 0 0
BCL10 0.033 0.006 -10000 0 -10000 0 0
IKK complex -0.03 0.055 0.12 1 -0.14 2 3
PTPRC 0.003 0.12 -10000 0 -0.51 12 12
PDPK1 -0.11 0.14 0.22 4 -0.27 74 78
PPP3CB 0.033 0.007 -10000 0 -10000 0 0
PPP3CC 0.023 0.039 -10000 0 -0.51 1 1
POU2F2 -0.003 0.031 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

Figure S4.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S4.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.016 0.16 -10000 0 -0.51 20 20
LAT2 -0.22 0.2 -10000 0 -0.4 100 100
AP1 -0.28 0.29 -10000 0 -0.56 93 93
mol:PIP3 -0.29 0.25 0.26 1 -0.52 93 94
IKBKB -0.14 0.14 0.19 8 -0.28 79 87
AKT1 -0.21 0.18 0.33 3 -0.42 79 82
IKBKG -0.15 0.13 0.18 2 -0.28 83 85
MS4A2 -0.3 0.26 -10000 0 -0.51 134 134
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.032 0.004 -10000 0 -10000 0 0
MAP3K1 -0.23 0.21 0.27 1 -0.44 89 90
mol:Ca2+ -0.21 0.18 0.22 3 -0.38 92 95
LYN 0.026 0.012 -10000 0 -10000 0 0
CBLB -0.22 0.2 -10000 0 -0.43 85 85
SHC1 0.033 0.006 -10000 0 -10000 0 0
RasGAP/p62DOK 0.032 0.1 -10000 0 -0.28 19 19
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.24 0.21 0.34 2 -0.44 97 99
PTPN13 -0.26 0.22 -10000 0 -0.57 34 34
PTPN11 0.006 0.039 -10000 0 -0.34 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.17 0.15 0.38 1 -0.34 67 68
SYK 0.028 0.025 -10000 0 -0.33 1 1
GRB2 0.032 0.006 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.28 0.27 -10000 0 -0.54 94 94
LAT -0.22 0.2 -10000 0 -0.43 85 85
PAK2 -0.25 0.24 0.28 1 -0.49 89 90
NFATC2 -0.064 0.066 -10000 0 -10000 0 0
HRAS -0.28 0.26 -10000 0 -0.53 91 91
GAB2 0.034 0.004 -10000 0 -10000 0 0
PLA2G1B 0.036 0.14 -10000 0 -0.87 5 5
Fc epsilon R1 -0.29 0.27 -10000 0 -0.46 146 146
Antigen/IgE/Fc epsilon R1 -0.26 0.24 -10000 0 -0.42 146 146
mol:GDP -0.3 0.28 -10000 0 -0.57 93 93
JUN 0.026 0.053 -10000 0 -0.32 5 5
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.032 0.005 -10000 0 -10000 0 0
FOS -0.027 0.16 -10000 0 -0.49 24 24
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.23 0.21 -10000 0 -0.38 129 129
CHUK -0.15 0.13 0.18 2 -0.28 89 91
KLRG1 -0.2 0.18 -10000 0 -0.4 83 83
VAV1 -0.25 0.22 -10000 0 -0.45 97 97
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.22 0.2 -10000 0 -0.41 98 98
negative regulation of mast cell degranulation -0.19 0.17 -10000 0 -0.37 83 83
BTK -0.31 0.32 -10000 0 -0.62 90 90
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.35 0.33 -10000 0 -0.62 110 110
GAB2/PI3K/SHP2 -0.23 0.2 -10000 0 -0.45 80 80
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.24 0.22 -10000 0 -0.49 86 86
RAF1 0.04 0.16 -10000 0 -0.98 5 5
Fc epsilon R1/FcgammaRIIB/SHIP -0.3 0.29 -10000 0 -0.46 149 149
FCER1G 0.044 0.013 -10000 0 -10000 0 0
FCER1A -0.22 0.28 -10000 0 -0.52 99 99
Antigen/IgE/Fc epsilon R1/Fyn -0.24 0.24 -10000 0 -0.39 146 146
MAPK3 0.037 0.14 -10000 0 -0.87 5 5
MAPK1 0.029 0.15 -10000 0 -0.9 5 5
NFKB1 0.033 0.006 -10000 0 -10000 0 0
MAPK8 -0.19 0.32 -10000 0 -0.78 44 44
DUSP1 -0.011 0.15 -10000 0 -0.51 18 18
NF-kappa-B/RelA -0.082 0.091 0.14 3 -0.2 6 9
actin cytoskeleton reorganization -0.23 0.21 -10000 0 -0.6 8 8
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.24 0.24 -10000 0 -0.48 89 89
FER -0.23 0.2 -10000 0 -0.41 100 100
RELA 0.034 0.005 -10000 0 -10000 0 0
ITK -0.049 0.056 -10000 0 -0.34 2 2
SOS1 0.034 0.002 -10000 0 -10000 0 0
PLCG1 -0.24 0.29 0.27 2 -0.52 89 91
cytokine secretion -0.063 0.06 -10000 0 -10000 0 0
SPHK1 -0.24 0.2 -10000 0 -0.43 95 95
PTK2 -0.24 0.22 -10000 0 -0.64 8 8
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.29 0.28 0.26 1 -0.56 95 96
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.29 0.25 0.25 1 -0.52 98 99
MAP2K2 0.032 0.14 -10000 0 -0.88 5 5
MAP2K1 0.03 0.15 -10000 0 -0.91 5 5
MAP2K7 0.034 0.004 -10000 0 -10000 0 0
KLRG1/SHP2 -0.17 0.17 -10000 0 -0.36 82 82
MAP2K4 -0.2 0.43 -10000 0 -0.95 52 52
Fc epsilon R1/FcgammaRIIB -0.32 0.31 -10000 0 -0.49 149 149
mol:Choline -0.24 0.21 0.33 2 -0.44 97 99
SHC/Grb2/SOS1 -0.2 0.21 -10000 0 -0.42 80 80
FYN 0.03 0.037 -10000 0 -0.51 1 1
DOK1 0.033 0.024 -10000 0 -0.32 1 1
PXN -0.22 0.2 -10000 0 -0.6 7 7
HCLS1 -0.23 0.21 -10000 0 -0.44 87 87
PRKCB -0.21 0.18 0.21 2 -0.38 95 97
FCGR2B -0.086 0.22 -10000 0 -0.5 48 48
IGHE -0.007 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.19 0.17 -10000 0 -0.38 83 83
LCP2 0.026 0.055 -10000 0 -0.37 4 4
PLA2G4A -0.28 0.23 0.19 1 -0.48 104 105
RASA1 0.03 0.034 -10000 0 -0.32 2 2
mol:Phosphatidic acid -0.24 0.21 0.33 2 -0.44 97 99
IKK complex -0.099 0.11 0.18 6 -0.22 29 35
WIPF1 0.032 0.037 -10000 0 -0.51 1 1
HIF-1-alpha transcription factor network

Figure S5.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S5.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.52 0.35 -9999 0 -0.93 65 65
HDAC7 -0.001 0.005 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.41 0.28 -9999 0 -0.83 40 40
SMAD4 0.021 0.04 -9999 0 -0.5 1 1
ID2 -0.52 0.35 -9999 0 -0.93 64 64
AP1 -0.012 0.13 -9999 0 -0.34 28 28
ABCG2 -0.73 0.35 -9999 0 -0.98 121 121
HIF1A -0.084 0.066 -9999 0 -0.43 2 2
TFF3 -0.52 0.35 -9999 0 -0.94 64 64
GATA2 0.031 0.017 -9999 0 -10000 0 0
AKT1 -0.078 0.058 -9999 0 -10000 0 0
response to hypoxia -0.09 0.045 -9999 0 -10000 0 0
MCL1 -0.51 0.35 -9999 0 -0.92 65 65
NDRG1 -0.53 0.38 -9999 0 -0.96 71 71
SERPINE1 -0.53 0.36 -9999 0 -0.92 71 71
FECH -0.51 0.35 -9999 0 -0.92 64 64
FURIN -0.51 0.35 -9999 0 -0.92 64 64
NCOA2 0.031 0.012 -9999 0 -10000 0 0
EP300 -0.084 0.077 -9999 0 -0.27 8 8
HMOX1 -0.54 0.37 -9999 0 -0.97 70 70
BHLHE40 -0.52 0.33 -9999 0 -0.89 73 73
BHLHE41 -0.52 0.33 -9999 0 -0.89 73 73
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.1 0.093 -9999 0 -10000 0 0
ENG -0.099 0.081 -9999 0 -10000 0 0
JUN 0.024 0.054 -9999 0 -0.32 5 5
RORA -0.52 0.35 -9999 0 -0.93 65 65
ABCB1 -0.57 0.6 -9999 0 -1.3 91 91
TFRC -0.52 0.35 -9999 0 -0.92 67 67
CXCR4 -0.52 0.35 -9999 0 -0.94 64 64
TF -0.51 0.34 -9999 0 -0.92 65 65
CITED2 -0.51 0.34 -9999 0 -0.92 65 65
HIF1A/ARNT -0.58 0.39 -9999 0 -1 65 65
LDHA -0.049 0.11 -9999 0 -0.93 3 3
ETS1 -0.51 0.34 -9999 0 -0.92 65 65
PGK1 -0.52 0.35 -9999 0 -0.92 68 68
NOS2 -0.52 0.33 -9999 0 -0.89 73 73
ITGB2 -0.52 0.35 -9999 0 -0.94 64 64
ALDOA -0.51 0.34 -9999 0 -0.92 64 64
Cbp/p300/CITED2 -0.51 0.35 -9999 0 -0.96 58 58
FOS -0.029 0.16 -9999 0 -0.49 24 24
HK2 -0.52 0.34 -9999 0 -0.93 63 63
SP1 -0.019 0.072 -9999 0 -10000 0 0
GCK -0.091 0.11 -9999 0 -10000 0 0
HK1 -0.51 0.34 -9999 0 -0.91 67 67
NPM1 -0.52 0.34 -9999 0 -0.92 65 65
EGLN1 -0.51 0.35 -9999 0 -0.92 64 64
CREB1 0.041 0.003 -9999 0 -10000 0 0
PGM1 -0.55 0.37 -9999 0 -0.96 69 69
SMAD3 0.033 0.01 -9999 0 -10000 0 0
EDN1 -0.15 0.28 -9999 0 -1.3 10 10
IGFBP1 -0.51 0.36 -9999 0 -0.92 69 69
VEGFA -0.38 0.26 -9999 0 -0.77 36 36
HIF1A/JAB1 -0.042 0.053 -9999 0 -0.31 2 2
CP -0.55 0.38 -9999 0 -0.99 72 72
CXCL12 -0.69 0.39 -9999 0 -0.97 117 117
COPS5 0.03 0.012 -9999 0 -10000 0 0
SMAD3/SMAD4 0.031 0.04 -9999 0 -0.36 1 1
BNIP3 -0.53 0.36 -9999 0 -0.94 70 70
EGLN3 -0.59 0.39 -9999 0 -0.96 91 91
CA9 -0.57 0.34 -9999 0 -0.94 75 75
TERT -0.51 0.35 -9999 0 -0.93 63 63
ENO1 -0.52 0.35 -9999 0 -0.92 66 66
PFKL -0.51 0.34 -9999 0 -0.92 65 65
NCOA1 0.03 0.052 -9999 0 -0.5 2 2
ADM -0.52 0.35 -9999 0 -0.92 66 66
ARNT -0.091 0.053 -9999 0 -10000 0 0
HNF4A 0.02 0.019 -9999 0 -10000 0 0
ADFP -0.52 0.33 -9999 0 -0.89 73 73
SLC2A1 -0.39 0.25 -9999 0 -0.74 46 46
LEP -0.51 0.34 -9999 0 -0.92 65 65
HIF1A/ARNT/Cbp/p300 -0.43 0.28 -9999 0 -0.84 43 43
EPO -0.27 0.22 -9999 0 -0.81 16 16
CREBBP -0.084 0.078 -9999 0 -0.26 14 14
HIF1A/ARNT/Cbp/p300/HDAC7 -0.42 0.29 -9999 0 -0.84 43 43
PFKFB3 -0.52 0.35 -9999 0 -0.92 67 67
NT5E -0.52 0.35 -9999 0 -0.94 67 67
IGF1 pathway

Figure S6.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S6.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.034 0 -10000 0 -10000 0 0
PTK2 0.028 0.013 -10000 0 -10000 0 0
CRKL -0.14 0.14 -10000 0 -0.27 121 121
GRB2/SOS1/SHC 0.065 0.018 -10000 0 -10000 0 0
HRAS 0.034 0.005 -10000 0 -10000 0 0
IRS1/Crk -0.14 0.15 -10000 0 -0.26 122 122
IGF-1R heterotetramer/IGF1/PTP1B -0.098 0.14 -10000 0 -0.3 68 68
AKT1 -0.12 0.12 0.28 1 -0.34 4 5
BAD -0.12 0.11 0.27 1 -0.33 4 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.14 0.14 -10000 0 -0.26 122 122
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.14 0.16 -10000 0 -0.27 122 122
RAF1 -0.11 0.14 -10000 0 -0.56 5 5
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.11 0.16 -10000 0 -0.26 117 117
YWHAZ 0.029 0.013 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.15 0.17 -10000 0 -0.29 122 122
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.12 0.12 0.28 1 -0.34 4 5
GNB2L1 0.034 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.077 0.12 0.29 1 -0.43 3 4
PXN 0.034 0.003 -10000 0 -10000 0 0
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.049 0.01 -10000 0 -10000 0 0
HRAS/GTP -0.11 0.14 -10000 0 -0.35 4 4
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.091 0.16 -10000 0 -0.28 4 4
IGF-1R heterotetramer -0.029 0.057 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.13 0.16 -10000 0 -0.27 122 122
Crk/p130 Cas/Paxillin -0.11 0.16 -10000 0 -0.35 5 5
IGF1R -0.029 0.057 -10000 0 -10000 0 0
IGF1 -0.28 0.28 -10000 0 -0.52 123 123
IRS2/Crk -0.098 0.13 -10000 0 -0.26 84 84
PI3K -0.11 0.16 -10000 0 -0.26 114 114
apoptosis 0.09 0.11 0.29 4 -10000 0 4
HRAS/GDP 0.025 0.003 -10000 0 -10000 0 0
PRKCD -0.19 0.19 -10000 0 -0.36 117 117
RAF1/14-3-3 E -0.092 0.13 -10000 0 -0.47 5 5
BAD/14-3-3 -0.095 0.12 -10000 0 -0.31 4 4
PRKCZ -0.13 0.12 0.27 1 -0.34 4 5
Crk/p130 Cas/Paxillin/FAK1 -0.089 0.12 -10000 0 -0.31 4 4
PTPN1 0.018 0.017 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.2 0.2 -10000 0 -0.37 123 123
BCAR1 0.033 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.11 0.16 -10000 0 -0.27 109 109
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.034 0.002 -10000 0 -10000 0 0
IRS1/NCK2 -0.13 0.16 -10000 0 -0.27 122 122
GRB10 0.016 0.07 -10000 0 -0.32 9 9
PTPN11 -0.14 0.14 -10000 0 -0.27 122 122
IRS1 -0.16 0.16 -10000 0 -0.29 122 122
IRS2 -0.099 0.14 -10000 0 -0.27 84 84
IGF-1R heterotetramer/IGF1 -0.2 0.21 -10000 0 -0.39 122 122
GRB2 0.033 0.007 -10000 0 -10000 0 0
PDPK1 -0.13 0.13 0.28 1 -0.36 4 5
YWHAE 0.027 0.014 -10000 0 -10000 0 0
PRKD1 -0.19 0.19 -10000 0 -0.36 117 117
SHC1 0.033 0.006 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

Figure S7.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S7.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.1 0.1 0.21 80 -10000 0 80
RFC1 0.1 0.1 0.21 79 -10000 0 79
PRKDC 0.11 0.13 0.25 82 -10000 0 82
RIPK1 0.035 0.006 -10000 0 -10000 0 0
CASP7 -0.11 0.27 -10000 0 -0.7 35 35
FASLG/FAS/FADD/FAF1 -0.029 0.13 0.2 2 -0.31 28 30
MAP2K4 -0.074 0.16 0.29 1 -0.41 27 28
mol:ceramide -0.052 0.14 -10000 0 -0.37 26 26
GSN 0.069 0.13 0.21 74 -0.29 4 78
FASLG/FAS/FADD/FAF1/Caspase 8 -0.036 0.14 -10000 0 -0.36 24 24
FAS -0.021 0.16 -10000 0 -0.51 20 20
BID -0.023 0.035 0.19 1 -0.24 1 2
MAP3K1 -0.045 0.19 0.24 1 -0.49 24 25
MAP3K7 0.032 0.007 -10000 0 -10000 0 0
RB1 0.12 0.16 0.28 83 -10000 0 83
CFLAR 0.036 0.003 -10000 0 -10000 0 0
HGF/MET -0.098 0.16 -10000 0 -0.35 35 35
ARHGDIB 0.1 0.11 0.22 78 -10000 0 78
FADD 0.031 0.006 -10000 0 -10000 0 0
actin filament polymerization -0.062 0.14 0.29 4 -0.21 74 78
NFKB1 -0.032 0.13 -10000 0 -0.74 6 6
MAPK8 -0.087 0.15 0.28 1 -0.43 21 22
DFFA 0.097 0.1 0.21 78 -10000 0 78
DNA fragmentation during apoptosis 0.098 0.1 0.21 79 -10000 0 79
FAS/FADD/MET -0.072 0.14 -10000 0 -0.35 19 19
CFLAR/RIP1 0.052 0.01 -10000 0 -10000 0 0
FAIM3 0.031 0.034 -10000 0 -0.32 2 2
FAF1 0.029 0.009 -10000 0 -10000 0 0
PARP1 0.1 0.1 0.21 79 -10000 0 79
DFFB 0.095 0.1 0.21 76 -10000 0 76
CHUK -0.031 0.12 -10000 0 -0.69 6 6
FASLG -0.03 0.16 -10000 0 -0.49 24 24
FAS/FADD 0.004 0.12 -10000 0 -0.37 20 20
HGF 0.029 0.034 -10000 0 -0.32 2 2
LMNA 0.089 0.092 0.3 3 -10000 0 3
CASP6 0.1 0.1 0.21 79 -10000 0 79
CASP10 0.031 0.005 -10000 0 -10000 0 0
CASP3 0.12 0.13 0.26 80 -0.21 2 82
PTPN13 -0.076 0.17 -10000 0 -0.33 65 65
CASP8 -0.023 0.015 -10000 0 -10000 0 0
IL6 -0.085 0.15 -10000 0 -0.93 2 2
MET -0.11 0.17 -10000 0 -0.32 87 87
ICAD/CAD 0.065 0.098 0.19 78 -10000 0 78
FASLG/FAS/FADD/FAF1/Caspase 10 -0.053 0.14 -10000 0 -0.38 26 26
activation of caspase activity by cytochrome c -0.023 0.035 0.19 1 -0.24 1 2
PAK2 0.1 0.1 0.21 80 -10000 0 80
BCL2 -0.2 0.26 -10000 0 -0.5 87 87
Syndecan-1-mediated signaling events

Figure S8.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S8.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.033 0.006 -10000 0 -10000 0 0
CCL5 -0.088 0.22 -10000 0 -0.51 48 48
SDCBP 0.03 0.012 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.12 0.1 0.4 1 -0.3 33 34
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.086 0.093 -10000 0 -0.34 13 13
Syndecan-1/Syntenin -0.1 0.098 0.35 1 -0.34 13 14
MAPK3 -0.11 0.096 0.33 1 -0.31 13 14
HGF/MET -0.063 0.13 -10000 0 -0.22 89 89
TGFB1/TGF beta receptor Type II 0.033 0.006 -10000 0 -10000 0 0
BSG 0.033 0.006 -10000 0 -10000 0 0
keratinocyte migration -0.085 0.092 -10000 0 -0.34 13 13
Syndecan-1/RANTES -0.16 0.15 0.35 1 -0.39 53 54
Syndecan-1/CD147 -0.11 0.1 0.35 1 -0.32 13 14
Syndecan-1/Syntenin/PIP2 -0.098 0.094 0.33 1 -0.32 13 14
LAMA5 0.009 0.058 -10000 0 -0.32 6 6
positive regulation of cell-cell adhesion -0.096 0.092 0.32 1 -0.32 13 14
MMP7 -0.31 0.063 -10000 0 -0.32 208 208
HGF 0.029 0.034 -10000 0 -0.32 2 2
Syndecan-1/CASK -0.11 0.093 -10000 0 -0.29 34 34
Syndecan-1/HGF/MET -0.16 0.12 0.31 1 -0.36 28 29
regulation of cell adhesion -0.1 0.099 0.29 2 -0.32 1 3
HPSE -0.052 0.2 -10000 0 -0.51 34 34
positive regulation of cell migration -0.12 0.1 0.4 1 -0.3 33 34
SDC1 -0.12 0.1 0.4 1 -0.31 33 34
Syndecan-1/Collagen -0.12 0.1 0.4 1 -0.3 33 34
PPIB 0.026 0.048 -10000 0 -0.32 4 4
MET -0.11 0.17 -10000 0 -0.32 87 87
PRKACA 0.034 0.005 -10000 0 -10000 0 0
MMP9 0.008 0.064 -10000 0 -0.35 6 6
MAPK1 -0.1 0.095 0.33 1 -0.31 13 14
homophilic cell adhesion -0.11 0.1 0.4 1 -0.3 33 34
MMP1 -0.28 0.11 -10000 0 -0.32 191 191
Visual signal transduction: Rods

Figure S9.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S9.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:K + 0.032 0.008 -10000 0 -10000 0 0
GNAT1/GTP 0.025 0.003 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin -0.21 0.16 -10000 0 -0.31 151 151
PDE6G/GNAT1/GTP 0.044 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.034 0.004 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel -0.18 0.2 -10000 0 -0.47 42 42
mol:Na + -0.088 0.16 -10000 0 -0.39 5 5
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.064 0.17 -10000 0 -0.32 66 66
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.082 0.17 -10000 0 -0.4 5 5
CNGB1 0.034 0.005 -10000 0 -10000 0 0
RDH5 -0.11 0.24 -10000 0 -0.51 57 57
SAG -0.35 0.24 -10000 0 -0.51 153 153
mol:Ca2+ -0.093 0.15 0.42 4 -0.38 5 9
Na + (4 Units) -0.086 0.14 -10000 0 -0.38 5 5
RGS9 -0.14 0.25 -10000 0 -0.51 68 68
GNB1/GNGT1 -0.065 0.13 -10000 0 -0.22 89 89
GNAT1/GDP -0.043 0.16 -10000 0 -0.27 66 66
GUCY2D 0.027 0.014 -10000 0 -10000 0 0
GNGT1 -0.11 0.17 -10000 0 -0.32 89 89
GUCY2F 0.027 0.057 -10000 0 -0.44 3 3
GNB5 0.027 0.042 -10000 0 -0.32 3 3
mol:GMP (4 units) -0.081 0.15 -10000 0 -0.27 82 82
mol:11-cis-retinal -0.11 0.24 -10000 0 -0.5 57 57
mol:cGMP 0.048 0.066 -10000 0 -0.27 4 4
GNB1 0.032 0.008 -10000 0 -10000 0 0
Rhodopsin -0.06 0.18 -10000 0 -0.37 56 56
SLC24A1 0.032 0.008 -10000 0 -10000 0 0
CNGA1 -0.21 0.27 -10000 0 -0.5 97 97
Metarhodopsin II 0.022 0.003 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.058 0.061 -10000 0 -0.29 2 2
RGS9BP 0.025 0.053 -10000 0 -0.32 5 5
Metarhodopsin II/Transducin -0.014 0.054 -10000 0 -10000 0 0
GCAP Family/Ca ++ 0.055 0.049 -10000 0 -0.28 2 2
PDE6A/B -0.11 0.2 -10000 0 -0.37 83 83
mol:Pi -0.065 0.17 -10000 0 -0.31 66 66
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin -0.035 0.11 -10000 0 -10000 0 0
PDE6B 0.033 0.007 -10000 0 -10000 0 0
PDE6A -0.18 0.26 -10000 0 -0.51 83 83
PDE6G 0.033 0.007 -10000 0 -10000 0 0
RHO 0.034 0.005 -10000 0 -10000 0 0
PDE6 -0.14 0.22 -10000 0 -0.5 33 33
GUCA1A 0.032 0.025 -10000 0 -0.32 1 1
GC2/GCAP Family 0.07 0.067 -10000 0 -0.29 4 4
GUCA1C 0.026 0.062 -10000 0 -0.41 4 4
GUCA1B 0.03 0.034 -10000 0 -0.32 2 2
Arf6 signaling events

Figure S10.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S10.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.015 0.025 -10000 0 -0.31 1 1
ARNO/beta Arrestin1-2 -0.071 0.14 -10000 0 -0.24 80 80
EGFR 0.021 0.073 -10000 0 -0.51 4 4
EPHA2 0.016 0.074 -10000 0 -0.32 10 10
USP6 0.027 0.014 -10000 0 -10000 0 0
IQSEC1 0.033 0.006 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.051 0.16 -10000 0 -0.3 56 56
ARRB2 0.012 0.037 -10000 0 -0.48 1 1
mol:GTP 0.007 0.021 0.12 5 -10000 0 5
ARRB1 0.026 0.063 -10000 0 -0.51 3 3
FBXO8 0.033 0.007 -10000 0 -10000 0 0
TSHR 0.031 0.011 -10000 0 -10000 0 0
EGF -0.09 0.21 -10000 0 -0.43 58 58
somatostatin receptor activity 0 0 0.001 2 -0.001 38 40
ARAP2 0 0 0 2 0 46 48
mol:GDP -0.096 0.12 0.19 1 -0.27 51 52
mol:PI-3-4-5-P3 0 0 0.001 1 -0.001 40 41
ITGA2B 0.033 0.007 -10000 0 -10000 0 0
ARF6 0.031 0.01 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.063 0.06 -10000 0 -10000 0 0
ADAP1 0 0 0 1 0 17 18
KIF13B 0.023 0.039 -10000 0 -0.51 1 1
HGF/MET -0.063 0.13 -10000 0 -0.22 89 89
PXN 0.034 0.003 -10000 0 -10000 0 0
ARF6/GTP -0.083 0.12 0.25 1 -0.25 42 43
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.028 0.14 -10000 0 -0.31 32 32
ADRB2 -0.16 0.26 -10000 0 -0.51 77 77
receptor agonist activity 0 0 0 1 0 35 36
actin filament binding 0 0 0.001 1 0 43 44
SRC 0.019 0.017 -10000 0 -10000 0 0
ITGB3 0.033 0.007 -10000 0 -10000 0 0
GNAQ 0 0 0.001 4 -0.001 25 29
EFA6/PI-4-5-P2 0 0 0.001 3 -0.001 20 23
ARF6/GDP -0.053 0.12 -10000 0 -0.34 22 22
ARF6/GDP/GULP/ACAP1 -0.098 0.16 -10000 0 -0.34 45 45
alphaIIb/beta3 Integrin/paxillin/GIT1 0.082 0.023 -10000 0 -10000 0 0
ACAP1 0 0 0 1 -10000 0 1
ACAP2 0 0 0 2 0 41 43
LHCGR/beta Arrestin2 0.013 0.048 -10000 0 -0.25 3 3
EFNA1 0.033 0.006 -10000 0 -10000 0 0
HGF 0.029 0.034 -10000 0 -0.32 2 2
CYTH3 0 0 0.001 2 -0.001 35 37
CYTH2 -0.002 0.002 -10000 0 -0.004 53 53
NCK1 0.034 0.005 -10000 0 -10000 0 0
fibronectin binding 0 0 0 5 0 24 29
endosomal lumen acidification 0 0 0.001 8 0 19 27
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.019 0.16 -10000 0 -0.49 22 22
GNAQ/ARNO -0.002 0.003 0.009 3 -0.007 21 24
mol:Phosphatidic acid 0 0 0 2 0 41 43
PIP3-E 0 0 -10000 0 0 43 43
MET -0.11 0.17 -10000 0 -0.32 87 87
GNA14 0.011 0.11 -10000 0 -0.51 9 9
GNA15 0.024 0.058 -10000 0 -0.32 6 6
GIT1 0.033 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 2 -0.001 28 30
GNA11 0.018 0.089 -10000 0 -0.51 6 6
LHCGR 0.028 0.05 -10000 0 -0.38 3 3
AGTR1 -0.19 0.26 -10000 0 -0.5 89 89
desensitization of G-protein coupled receptor protein signaling pathway 0.013 0.048 -10000 0 -0.25 3 3
IPCEF1/ARNO -0.03 0.1 -10000 0 -0.2 56 56
alphaIIb/beta3 Integrin 0.049 0.011 -10000 0 -10000 0 0
TCGA08_p53

Figure S11.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S11.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.059 0.1 -10000 0 -0.22 65 65
TP53 -0.023 0.058 -10000 0 -0.25 11 11
Senescence -0.051 0.08 -10000 0 -0.2 44 44
Apoptosis -0.051 0.08 -10000 0 -0.2 44 44
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.029 0.063 0.38 2 -10000 0 2
MDM4 0.033 0.006 -10000 0 -10000 0 0
FOXM1 transcription factor network

Figure S12.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S12.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.31 0.37 -9999 0 -1 22 22
PLK1 0.004 0.12 -9999 0 -0.98 3 3
BIRC5 -0.039 0.2 -9999 0 -1 7 7
HSPA1B -0.31 0.37 -9999 0 -0.98 29 29
MAP2K1 -0.007 0.042 -9999 0 -10000 0 0
BRCA2 -0.29 0.4 -9999 0 -1.1 23 23
FOXM1 -0.36 0.45 -9999 0 -1.3 26 26
XRCC1 -0.31 0.37 -9999 0 -1 23 23
FOXM1B/p19 -0.38 0.41 -9999 0 -1.1 36 36
Cyclin D1/CDK4 -0.31 0.36 -9999 0 -0.94 28 28
CDC2 -0.33 0.39 -9999 0 -1.1 26 26
TGFA -0.31 0.37 -9999 0 -0.96 28 28
SKP2 -0.31 0.38 -9999 0 -1.1 21 21
CCNE1 0.008 0.085 -9999 0 -0.33 13 13
CKS1B -0.31 0.38 -9999 0 -1 25 25
RB1 -0.12 0.19 -9999 0 -0.77 5 5
FOXM1C/SP1 -0.37 0.44 -9999 0 -1.2 32 32
AURKB -0.2 0.44 -9999 0 -1 45 45
CENPF -0.31 0.38 -9999 0 -1 23 23
CDK4 -0.009 0.091 -9999 0 -0.33 15 15
MYC -0.34 0.36 -9999 0 -0.92 34 34
CHEK2 -0.008 0.042 -9999 0 -10000 0 0
ONECUT1 -0.32 0.38 -9999 0 -0.96 32 32
CDKN2A -0.074 0.16 -9999 0 -0.32 65 65
LAMA4 -0.31 0.37 -9999 0 -1 22 22
FOXM1B/HNF6 -0.36 0.43 -9999 0 -1.1 31 31
FOS -0.4 0.5 -9999 0 -1.3 42 42
SP1 0.029 0.016 -9999 0 -10000 0 0
CDC25B -0.32 0.39 -9999 0 -1 30 30
response to radiation -0.016 0.021 -9999 0 -10000 0 0
CENPB -0.29 0.37 -9999 0 -1 21 21
CENPA -0.33 0.39 -9999 0 -1.1 22 22
NEK2 -0.35 0.4 -9999 0 -1.1 26 26
HIST1H2BA -0.31 0.37 -9999 0 -1 24 24
CCNA2 -0.022 0.13 -9999 0 -0.33 31 31
EP300 0.032 0.009 -9999 0 -10000 0 0
CCNB1/CDK1 -0.35 0.42 -9999 0 -1.2 24 24
CCNB2 -0.31 0.37 -9999 0 -1 23 23
CCNB1 -0.33 0.4 -9999 0 -1.1 24 24
ETV5 -0.32 0.38 -9999 0 -1 23 23
ESR1 -0.32 0.4 -9999 0 -1.1 25 25
CCND1 -0.32 0.36 -9999 0 -0.94 31 31
GSK3A -0.005 0.038 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.032 0.13 -9999 0 -0.38 12 12
CDK2 -0.006 0.11 -9999 0 -0.32 22 22
G2/M transition of mitotic cell cycle -0.019 0.026 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.32 0.41 -9999 0 -1.1 26 26
GAS1 -0.51 0.58 -9999 0 -1.3 65 65
MMP2 -0.31 0.37 -9999 0 -1 23 23
RB1/FOXM1C -0.31 0.37 -9999 0 -1 26 26
CREBBP 0.033 0.007 -9999 0 -10000 0 0
Wnt signaling

Figure S13.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S13.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.045 0.1 -9999 0 -0.29 15 15
FZD6 0.018 0.064 -9999 0 -0.35 6 6
WNT6 0.033 0.024 -9999 0 -0.32 1 1
WNT4 0.016 0.088 -9999 0 -0.45 7 7
FZD3 -0.05 0.15 -9999 0 -0.33 45 45
WNT5A -0.02 0.13 -9999 0 -0.32 33 33
WNT11 -0.038 0.14 -9999 0 -0.32 44 44
Visual signal transduction: Cones

Figure S14.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S14.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.05 0.033 -10000 0 -10000 0 0
RGS9BP 0.025 0.053 -10000 0 -0.32 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
mol:Na + -0.069 0.16 -10000 0 -0.3 64 64
mol:ADP 0.009 0.015 -10000 0 -0.22 1 1
GNAT2 0.028 0.042 -10000 0 -0.32 3 3
RGS9-1/Gbeta5/R9AP -0.064 0.17 -10000 0 -0.32 66 66
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.038 0.037 -10000 0 -0.21 4 4
GRK7 0.032 0.024 -10000 0 -0.32 1 1
CNGB3 0.023 0.048 -10000 0 -0.32 4 4
Cone Metarhodopsin II/X-Arrestin 0.025 0.002 -10000 0 -10000 0 0
mol:Ca2+ -0.05 0.16 -10000 0 -0.28 58 58
Cone PDE6 -0.036 0.17 -10000 0 -0.27 56 56
Cone Metarhodopsin II 0.021 0.013 -10000 0 -0.16 1 1
Na + (4 Units) -0.049 0.15 -10000 0 -0.28 58 58
GNAT2/GDP -0.046 0.16 -10000 0 -0.27 66 66
GNB5 0.027 0.042 -10000 0 -0.32 3 3
mol:GMP (4 units) 0.018 0.04 0.19 4 -0.28 1 5
Cone Transducin 0.054 0.036 -10000 0 -10000 0 0
SLC24A2 0.033 0.006 -10000 0 -10000 0 0
GNB3/GNGT2 0.046 0.019 -10000 0 -10000 0 0
GNB3 0.033 0.007 -10000 0 -10000 0 0
GNAT2/GTP 0.021 0.029 -10000 0 -0.22 3 3
CNGA3 -0.14 0.25 -10000 0 -0.51 68 68
ARR3 0.034 0.002 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel -0.069 0.16 -10000 0 -0.3 64 64
mol:Pi -0.065 0.17 -10000 0 -0.31 66 66
Cone CNG Channel -0.039 0.15 -10000 0 -0.26 57 57
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.033 0.006 -10000 0 -10000 0 0
RGS9 -0.14 0.25 -10000 0 -0.51 68 68
PDE6C 0.031 0.025 -10000 0 -0.32 1 1
GNGT2 0.03 0.037 -10000 0 -0.51 1 1
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.031 0.037 -10000 0 -0.51 1 1
HIF-2-alpha transcription factor network

Figure S15.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S15.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.067 0.22 -10000 0 -0.77 18 18
oxygen homeostasis -0.012 0.009 -10000 0 -10000 0 0
TCEB2 0.033 0.006 -10000 0 -10000 0 0
TCEB1 0.028 0.026 -10000 0 -0.32 1 1
VHL/Elongin B/Elongin C/HIF2A -0.13 0.13 -10000 0 -0.39 15 15
EPO -0.25 0.18 -10000 0 -0.57 19 19
FIH (dimer) 0.002 0.027 -10000 0 -10000 0 0
APEX1 0.001 0.029 -10000 0 -10000 0 0
SERPINE1 -0.31 0.22 -10000 0 -0.66 37 37
FLT1 -0.024 0.12 -10000 0 -0.8 3 3
ADORA2A -0.28 0.19 -10000 0 -0.62 25 25
germ cell development -0.29 0.19 -10000 0 -0.61 26 26
SLC11A2 -0.31 0.21 -10000 0 -0.64 35 35
BHLHE40 -0.3 0.2 -10000 0 -0.57 47 47
HIF1AN 0.003 0.027 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.2 0.15 -10000 0 -0.42 33 33
ETS1 0.043 0.019 -10000 0 -10000 0 0
CITED2 -0.023 0.15 -10000 0 -0.84 6 6
KDR -0.015 0.14 -10000 0 -0.84 5 5
PGK1 -0.3 0.21 -10000 0 -0.65 29 29
SIRT1 0.033 0.007 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT -0.33 0.23 -10000 0 -0.7 35 35
EPAS1 -0.16 0.14 -10000 0 -0.34 68 68
SP1 0.036 0.017 -10000 0 -10000 0 0
ABCG2 -0.56 0.25 -10000 0 -0.7 136 136
EFNA1 -0.3 0.2 -10000 0 -0.64 26 26
FXN -0.29 0.19 -10000 0 -0.62 26 26
POU5F1 -0.3 0.2 -10000 0 -0.62 29 29
neuron apoptosis 0.32 0.23 0.68 34 -10000 0 34
EP300 0.032 0.009 -10000 0 -10000 0 0
EGLN3 -0.16 0.24 -10000 0 -0.52 65 65
EGLN2 0.008 0.026 -10000 0 -10000 0 0
EGLN1 0.003 0.027 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.055 0.035 -10000 0 -10000 0 0
VHL 0.032 0.025 -10000 0 -0.32 1 1
ARNT 0.002 0.03 -10000 0 -10000 0 0
SLC2A1 -0.3 0.2 -10000 0 -0.62 39 39
TWIST1 -0.29 0.21 -10000 0 -0.65 34 34
ELK1 0.036 0.042 -10000 0 -0.31 3 3
HIF2A/ARNT/Cbp/p300 -0.2 0.15 -10000 0 -0.42 33 33
VEGFA -0.3 0.21 -10000 0 -0.64 31 31
CREBBP 0.033 0.007 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

Figure S16.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S16.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.034 0.005 -9999 0 -10000 0 0
EGFR 0.021 0.073 -9999 0 -0.51 4 4
EGF/EGFR -0.067 0.15 -9999 0 -0.3 43 43
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.001 0.14 -9999 0 -0.27 31 31
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.046 0.15 -9999 0 -0.32 49 49
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.09 0.21 -9999 0 -0.42 58 58
EGF/EGFR dimer/SHC -0.028 0.14 -9999 0 -0.31 33 33
mol:GDP -0.005 0.14 -9999 0 -0.27 32 32
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.005 0.12 -9999 0 -0.47 12 12
GRB2/SOS1 0.049 0.01 -9999 0 -10000 0 0
HRAS/GTP -0.017 0.12 -9999 0 -10000 0 0
SHC1 0.033 0.006 -9999 0 -10000 0 0
HRAS/GDP -0.004 0.13 -9999 0 -10000 0 0
FRAP1 -0.062 0.093 -9999 0 -0.26 32 32
EGF/EGFR dimer -0.051 0.16 -9999 0 -0.3 56 56
SOS1 0.034 0.002 -9999 0 -10000 0 0
GRB2 0.033 0.007 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.033 0.14 -9999 0 -0.25 60 60
Glypican 1 network

Figure S17.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S17.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.038 0.082 -10000 0 -0.31 7 7
fibroblast growth factor receptor signaling pathway 0.037 0.082 -10000 0 -0.31 7 7
LAMA1 0.026 0.015 -10000 0 -10000 0 0
PRNP 0.026 0.015 -10000 0 -10000 0 0
GPC1/SLIT2 -0.19 0.2 -10000 0 -0.36 123 123
SMAD2 0.01 0.037 -10000 0 -10000 0 0
GPC1/PrPc/Cu2+ 0.029 0.04 -10000 0 -0.18 5 5
GPC1/Laminin alpha1 0.028 0.053 -10000 0 -0.22 8 8
TDGF1 -0.2 0.17 -10000 0 -0.32 145 145
CRIPTO/GPC1 -0.14 0.13 -10000 0 -0.23 145 145
APP/GPC1 0.037 0.052 -10000 0 -0.22 8 8
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.12 0.099 -10000 0 -0.33 7 7
FLT1 0.007 0.077 -10000 0 -0.32 11 11
GPC1/TGFB/TGFBR1/TGFBR2 0.057 0.049 -10000 0 -10000 0 0
SERPINC1 0.032 0.025 -10000 0 -0.32 1 1
FYN -0.12 0.1 -10000 0 -0.33 8 8
FGR -0.12 0.1 -10000 0 -0.33 7 7
positive regulation of MAPKKK cascade -0.038 0.13 0.29 2 -0.38 7 9
SLIT2 -0.26 0.27 -10000 0 -0.51 117 117
GPC1/NRG 0.03 0.052 -10000 0 -0.22 6 6
NRG1 0.027 0.014 -10000 0 -10000 0 0
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.02 0.083 -10000 0 -0.34 2 2
LYN -0.11 0.1 -10000 0 -0.33 7 7
mol:Spermine 0.001 0.043 -10000 0 -0.22 8 8
cell growth 0.037 0.082 -10000 0 -0.31 7 7
BMP signaling pathway -0.021 0.066 0.32 8 -10000 0 8
SRC -0.055 0.094 -10000 0 -0.33 4 4
TGFBR1 0.034 0.005 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.058 0.19 -10000 0 -0.44 41 41
GPC1 0.021 0.067 -10000 0 -0.32 8 8
TGFBR1 (dimer) 0.034 0.005 -10000 0 -10000 0 0
VEGFA 0.006 0.095 -10000 0 -0.32 17 17
BLK -0.18 0.16 -10000 0 -0.39 59 59
HCK -0.067 0.11 -10000 0 -0.38 10 10
FGF2 0.014 0.098 -10000 0 -0.48 8 8
FGFR1 0.03 0.012 -10000 0 -10000 0 0
VEGFR1 homodimer 0.007 0.077 -10000 0 -0.32 11 11
TGFBR2 0.034 0.003 -10000 0 -10000 0 0
cell death 0.037 0.052 -10000 0 -0.22 8 8
ATIII/GPC1 0.037 0.054 -10000 0 -0.22 9 9
PLA2G2A/GPC1 -0.033 0.15 -10000 0 -0.31 46 46
LCK -0.12 0.1 -10000 0 -0.35 8 8
neuron differentiation 0.03 0.052 -10000 0 -0.22 6 6
PrPc/Cu2+ 0.02 0.011 -10000 0 -10000 0 0
APP 0.032 0.008 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.034 0.003 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

Figure S18.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S18.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.009 0.067 -10000 0 -0.17 24 24
EPHB2 0.021 0.064 -10000 0 -0.35 6 6
Syndecan-2/TACI 0.021 0.039 -10000 0 -0.31 2 2
LAMA1 0.026 0.015 -10000 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 -0.02 0.1 -10000 0 -0.28 2 2
HRAS 0.034 0.005 -10000 0 -10000 0 0
Syndecan-2/CASK 0.01 0.014 -10000 0 -0.17 1 1
ITGA5 0.026 0.053 -10000 0 -0.32 5 5
BAX 0.008 0.02 -10000 0 -10000 0 0
EPB41 0.032 0.009 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.027 0.019 -10000 0 -10000 0 0
LAMA3 0.02 0.051 -10000 0 -0.38 3 3
EZR 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.019 0.072 -10000 0 -0.34 8 8
Syndecan-2/MMP2 0.029 0.029 -10000 0 -0.17 3 3
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 -0.046 0.13 -10000 0 -0.22 76 76
dendrite morphogenesis 0.022 0.044 -10000 0 -0.19 7 7
Syndecan-2/GM-CSF -0.063 0.11 -10000 0 -0.18 101 101
determination of left/right symmetry 0.013 0.018 -10000 0 -0.21 1 1
Syndecan-2/PKC delta 0.031 0.021 -10000 0 -0.17 1 1
GNB2L1 0.034 0.004 -10000 0 -10000 0 0
MAPK3 -0.05 0.12 0.2 17 -0.31 4 21
MAPK1 -0.046 0.12 0.2 17 -0.26 2 19
Syndecan-2/RACK1 0.044 0.026 -10000 0 -10000 0 0
NF1 0.033 0.008 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.013 0.018 -10000 0 -0.21 1 1
ITGA2 -0.092 0.17 -10000 0 -0.32 77 77
MAPK8 0.013 0.017 -10000 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin -0.016 0.099 -10000 0 -0.29 1 1
Syndecan-2/Kininogen 0.023 0.052 -10000 0 -0.26 6 6
ITGB1 0.032 0.024 -10000 0 -0.32 1 1
SRC 0.019 0.038 -10000 0 -10000 0 0
Syndecan-2/CASK/Protein 4.1 0.026 0.02 -10000 0 -10000 0 0
extracellular matrix organization 0.03 0.021 -10000 0 -0.17 1 1
actin cytoskeleton reorganization 0.009 0.066 -10000 0 -0.17 24 24
Syndecan-2/Caveolin-2/Ras 0.036 0.05 -10000 0 -0.28 1 1
Syndecan-2/Laminin alpha3 0.02 0.038 -10000 0 -0.21 4 4
Syndecan-2/RasGAP 0.055 0.037 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.042 0.045 -10000 0 -0.22 6 6
PRKCD 0.034 0.005 -10000 0 -10000 0 0
Syndecan-2 dimer 0.022 0.044 -10000 0 -0.19 7 7
GO:0007205 0.003 0.004 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.023 0.031 -10000 0 -10000 0 0
RHOA 0.034 0.005 -10000 0 -10000 0 0
SDCBP 0.03 0.012 -10000 0 -10000 0 0
TNFRSF13B 0.02 0.064 -10000 0 -0.51 3 3
RASA1 0.03 0.034 -10000 0 -0.32 2 2
alpha2/beta1 Integrin -0.046 0.13 -10000 0 -0.22 76 76
Syndecan-2/Synbindin 0.03 0.021 -10000 0 -10000 0 0
TGFB1 0.033 0.006 -10000 0 -10000 0 0
CASP3 0.041 0.06 0.2 26 -10000 0 26
FN1 -0.005 0.11 -10000 0 -0.32 24 24
Syndecan-2/IL8 -0.12 0.1 -10000 0 -0.18 168 168
SDC2 0.013 0.018 -10000 0 -0.21 1 1
KNG1 0.02 0.085 -10000 0 -0.47 6 6
Syndecan-2/Neurofibromin 0.029 0.022 -10000 0 -0.17 1 1
TRAPPC4 0.034 0.005 -10000 0 -10000 0 0
CSF2 -0.16 0.18 -10000 0 -0.32 116 116
Syndecan-2/TGFB1 0.03 0.021 -10000 0 -0.17 1 1
Syndecan-2/Syntenin/PI-4-5-P2 0.028 0.019 -10000 0 -10000 0 0
Syndecan-2/Ezrin 0.028 0.019 -10000 0 -0.16 1 1
PRKACA 0.045 0.065 0.2 31 -10000 0 31
angiogenesis -0.12 0.1 -10000 0 -0.18 168 168
MMP2 0.03 0.034 -10000 0 -0.32 2 2
IL8 -0.29 0.099 -10000 0 -0.32 196 196
calcineurin-NFAT signaling pathway 0.021 0.039 -10000 0 -0.3 2 2
BMP receptor signaling

Figure S19.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S19.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.021 0.12 -9999 0 -0.3 1 1
SMAD6-7/SMURF1 0.039 0.053 -9999 0 -0.31 1 1
NOG 0.033 0.008 -9999 0 -10000 0 0
SMAD9 -0.068 0.2 -9999 0 -0.5 34 34
SMAD4 0.02 0.039 -9999 0 -0.51 1 1
SMAD5 -0.093 0.16 -9999 0 -0.41 29 29
BMP7/USAG1 -0.14 0.19 -9999 0 -0.36 81 81
SMAD5/SKI -0.084 0.16 -9999 0 -0.41 24 24
SMAD1 -0.014 0.1 -9999 0 -0.51 5 5
BMP2 -0.037 0.17 -9999 0 -0.51 25 25
SMAD1/SMAD1/SMAD4 0.005 0.094 -9999 0 -0.44 4 4
BMPR1A 0.033 0.008 -9999 0 -10000 0 0
BMPR1B 0.029 0.041 -9999 0 -0.32 3 3
BMPR1A-1B/BAMBI 0.03 0.087 -9999 0 -10000 0 0
AHSG 0.034 0.004 -9999 0 -10000 0 0
CER1 0.031 0.025 -9999 0 -0.32 1 1
BMP2-4/CER1 -0.067 0.16 -9999 0 -0.38 32 32
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.024 0.12 -9999 0 -0.36 9 9
BMP2-4 (homodimer) -0.089 0.18 -9999 0 -0.31 74 74
RGMB 0.025 0.053 -9999 0 -0.32 5 5
BMP6/BMPR2/BMPR1A-1B -0.063 0.18 -9999 0 -0.29 82 82
RGMA 0.024 0.064 -9999 0 -0.51 3 3
SMURF1 0.033 0.008 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.035 0.11 -9999 0 -0.27 24 24
BMP2-4/USAG1 -0.17 0.22 -9999 0 -0.4 88 88
SMAD6/SMURF1/SMAD5 -0.085 0.15 -9999 0 -0.41 24 24
SOSTDC1 -0.16 0.26 -9999 0 -0.5 77 77
BMP7/BMPR2/BMPR1A-1B -0.025 0.094 -9999 0 -0.31 1 1
SKI 0.032 0.008 -9999 0 -10000 0 0
BMP6 (homodimer) -0.17 0.26 -9999 0 -0.5 82 82
HFE2 0.034 0.005 -9999 0 -10000 0 0
ZFYVE16 0.034 0.005 -9999 0 -10000 0 0
MAP3K7 0.033 0.007 -9999 0 -10000 0 0
BMP2-4/CHRD -0.065 0.16 -9999 0 -0.37 31 31
SMAD5/SMAD5/SMAD4 -0.08 0.15 -9999 0 -0.42 20 20
MAPK1 0.032 0.009 -9999 0 -10000 0 0
TAK1/TAB family -0.021 0.1 -9999 0 -0.31 7 7
BMP7 (homodimer) -0.075 0.15 -9999 0 -0.32 57 57
NUP214 0.034 0.005 -9999 0 -10000 0 0
BMP6/FETUA -0.11 0.2 -9999 0 -0.37 80 80
SMAD1/SKI -0.005 0.1 -9999 0 -0.52 4 4
SMAD6 0.022 0.058 -9999 0 -0.32 6 6
CTDSP2 0.029 0.052 -9999 0 -0.51 2 2
BMP2-4/FETUA -0.065 0.16 -9999 0 -0.37 31 31
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 0.006 0.093 -9999 0 -0.33 15 15
BMPR2 (homodimer) 0.034 0.002 -9999 0 -10000 0 0
GADD34/PP1CA 0.065 0.023 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) 0.044 0.034 -9999 0 -0.22 3 3
CHRDL1 0.03 0.044 -9999 0 -0.41 2 2
ENDOFIN/SMAD1 -0.004 0.11 -9999 0 -0.53 4 4
SMAD6-7/SMURF1/SMAD1 0.015 0.11 -9999 0 -0.49 4 4
SMAD6/SMURF1 0.033 0.008 -9999 0 -10000 0 0
BAMBI -0.012 0.12 -9999 0 -0.32 28 28
SMURF2 0.013 0.081 -9999 0 -0.32 12 12
BMP2-4/CHRDL1 -0.069 0.16 -9999 0 -0.37 33 33
BMP2-4/GREM1 -0.081 0.17 -9999 0 -0.39 36 36
SMAD7 0.021 0.039 -9999 0 -0.51 1 1
SMAD8A/SMAD8A/SMAD4 -0.067 0.2 -9999 0 -0.46 36 36
SMAD1/SMAD6 -0.006 0.1 -9999 0 -0.53 4 4
TAK1/SMAD6 0.047 0.014 -9999 0 -10000 0 0
BMP7 -0.075 0.15 -9999 0 -0.32 57 57
BMP6 -0.17 0.26 -9999 0 -0.51 82 82
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.039 0.13 -9999 0 -0.37 17 17
PPM1A 0.031 0.01 -9999 0 -10000 0 0
SMAD1/SMURF2 -0.012 0.11 -9999 0 -0.56 4 4
SMAD7/SMURF1 0.032 0.036 -9999 0 -0.37 1 1
CTDSPL 0.029 0.052 -9999 0 -0.51 2 2
PPP1CA 0.032 0.024 -9999 0 -0.32 1 1
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0.034 0.002 -9999 0 -10000 0 0
PPP1R15A 0.034 0.005 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.03 0.11 -9999 0 -0.33 9 9
CHRD 0.034 0.004 -9999 0 -10000 0 0
BMPR2 0.034 0.002 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.032 0.12 -9999 0 -0.29 21 21
BMP4 -0.088 0.17 -9999 0 -0.33 71 71
FST 0.034 0.004 -9999 0 -10000 0 0
BMP2-4/NOG -0.065 0.16 -9999 0 -0.37 32 32
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.018 0.12 -9999 0 -0.3 1 1
Reelin signaling pathway

Figure S20.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S20.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.044 0.029 -10000 0 -0.22 2 2
VLDLR -0.079 0.22 -10000 0 -0.5 45 45
CRKL 0.032 0.009 -10000 0 -10000 0 0
LRPAP1 0.033 0.007 -10000 0 -10000 0 0
FYN 0.03 0.037 -10000 0 -0.51 1 1
ITGA3 0.031 0.025 -10000 0 -0.32 1 1
RELN/VLDLR/Fyn -0.013 0.15 -10000 0 -0.32 39 39
MAPK8IP1/MKK7/MAP3K11/JNK1 0.091 0.038 -10000 0 -10000 0 0
AKT1 -0.026 0.095 -10000 0 -0.36 1 1
MAP2K7 0.034 0.004 -10000 0 -10000 0 0
RAPGEF1 0.034 0.005 -10000 0 -10000 0 0
DAB1 0.033 0.006 -10000 0 -10000 0 0
RELN/LRP8/DAB1 -0.13 0.078 -10000 0 -10000 0 0
LRPAP1/LRP8 -0.19 0.086 -10000 0 -0.22 183 183
RELN/LRP8/DAB1/Fyn -0.12 0.081 -10000 0 -0.41 1 1
DAB1/alpha3/beta1 Integrin -0.16 0.13 -10000 0 -0.38 35 35
long-term memory -0.13 0.098 -10000 0 -0.29 23 23
DAB1/LIS1 -0.16 0.13 -10000 0 -0.39 34 34
DAB1/CRLK/C3G -0.16 0.12 -10000 0 -0.38 33 33
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
DAB1/NCK2 -0.16 0.13 -10000 0 -0.4 34 34
ARHGEF2 0.032 0.025 -10000 0 -0.32 1 1
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.033 0.006 -10000 0 -10000 0 0
CDK5R1 0.033 0.007 -10000 0 -10000 0 0
RELN 0.032 0.008 -10000 0 -10000 0 0
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.14 0.089 -10000 0 -0.31 3 3
GRIN2A/RELN/LRP8/DAB1/Fyn -0.12 0.087 -10000 0 -0.41 1 1
MAPK8 0.033 0.007 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.007 0.13 -10000 0 -0.28 39 39
ITGB1 0.032 0.024 -10000 0 -0.32 1 1
MAP1B -0.17 0.15 -10000 0 -0.42 43 43
RELN/LRP8 -0.14 0.086 -10000 0 -0.23 1 1
GRIN2B/RELN/LRP8/DAB1/Fyn -0.14 0.1 -10000 0 -0.3 24 24
PI3K 0.049 0.01 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.045 0.028 -10000 0 -0.22 2 2
RAP1A -0.15 0.12 -10000 0 -0.37 32 32
PAFAH1B1 0.027 0.014 -10000 0 -10000 0 0
MAPK8IP1 0.032 0.024 -10000 0 -0.32 1 1
CRLK/C3G 0.047 0.014 -10000 0 -10000 0 0
GRIN2B -0.013 0.12 -10000 0 -0.32 28 28
NCK2 0.034 0 -10000 0 -10000 0 0
neuron differentiation -0.029 0.057 -10000 0 -0.32 3 3
neuron adhesion -0.14 0.12 0.36 2 -0.36 31 33
LRP8 -0.28 0.11 -10000 0 -0.32 189 189
GSK3B -0.026 0.094 -10000 0 -0.34 1 1
RELN/VLDLR/DAB1/Fyn 0.003 0.14 -10000 0 -0.27 39 39
MAP3K11 0.034 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.022 0.11 -10000 0 -0.38 2 2
CDK5 0.03 0.034 -10000 0 -0.32 2 2
MAPT 0.022 0.13 0.77 6 -10000 0 6
neuron migration -0.12 0.12 0.24 2 -0.35 34 36
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.03 0.057 -10000 0 -0.32 3 3
RELN/VLDLR -0.18 0.14 -10000 0 -0.39 45 45
Endothelins

Figure S21.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S21.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.14 -10000 0 -0.33 14 14
PTK2B 0.026 0.015 -10000 0 -10000 0 0
mol:Ca2+ 0.023 0.17 -10000 0 -0.78 4 4
EDN1 0.038 0.14 -10000 0 -0.48 12 12
EDN3 -0.15 0.24 -10000 0 -0.51 68 68
EDN2 -0.38 0.23 -10000 0 -0.51 165 165
HRAS/GDP 0.013 0.17 0.34 6 -0.52 7 13
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.001 0.12 0.23 2 -0.36 8 10
ADCY4 -0.021 0.11 -10000 0 -0.3 5 5
ADCY5 -0.017 0.11 -10000 0 -0.29 6 6
ADCY6 -0.018 0.1 -10000 0 -0.3 4 4
ADCY7 -0.019 0.1 -10000 0 -0.3 5 5
ADCY1 -0.016 0.1 -10000 0 -0.3 4 4
ADCY2 -0.019 0.1 -10000 0 -0.3 5 5
ADCY3 -0.027 0.11 -10000 0 -0.3 7 7
ADCY8 -0.022 0.1 -10000 0 -0.3 5 5
ADCY9 -0.022 0.11 -10000 0 -0.32 6 6
arachidonic acid secretion -0.068 0.23 0.38 4 -0.56 27 31
ETB receptor/Endothelin-1/Gq/GTP -0.023 0.13 -10000 0 -0.38 17 17
GNAO1 0.034 0.005 -10000 0 -10000 0 0
HRAS 0.033 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.096 0.17 -10000 0 -0.32 6 6
ETA receptor/Endothelin-1/Gs/GTP 0.064 0.16 -10000 0 -0.28 12 12
mol:GTP 0 0.004 -10000 0 -10000 0 0
COL3A1 -0.013 0.15 -10000 0 -0.42 6 6
EDNRB -0.027 0.14 -10000 0 -0.51 16 16
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.013 0.13 -10000 0 -0.36 5 5
CYSLTR1 -0.014 0.15 -10000 0 -0.45 6 6
SLC9A1 0.009 0.085 -10000 0 -0.34 1 1
mol:GDP 0 0.17 0.31 8 -0.52 8 16
SLC9A3 -0.34 0.32 -10000 0 -0.72 56 56
RAF1 -0.033 0.19 0.36 4 -0.49 16 20
JUN 0.025 0.15 -10000 0 -0.65 2 2
JAK2 -0.011 0.14 -10000 0 -0.34 14 14
mol:IP3 -0.013 0.14 0.24 3 -0.45 9 12
ETA receptor/Endothelin-1 0.094 0.21 -10000 0 -0.39 14 14
PLCB1 -0.047 0.14 -10000 0 -0.32 44 44
PLCB2 0.031 0.011 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.12 0.21 -10000 0 -0.39 74 74
FOS -0.12 0.36 0.43 2 -0.92 33 35
Gai/GDP 0.013 0.13 -10000 0 -0.75 4 4
CRK 0.028 0.014 -10000 0 -10000 0 0
mol:Ca ++ -0.021 0.17 0.39 1 -0.51 10 11
BCAR1 0.034 0.006 -10000 0 -10000 0 0
PRKCB1 -0.009 0.14 0.23 7 -0.44 9 16
GNAQ 0.001 0.005 -10000 0 -10000 0 0
GNAZ 0.032 0.009 -10000 0 -10000 0 0
GNAL 0.027 0.014 -10000 0 -10000 0 0
Gs family/GDP 0.001 0.16 0.36 4 -0.5 7 11
ETA receptor/Endothelin-1/Gq/GTP 0.008 0.12 -10000 0 -0.36 7 7
MAPK14 -0.029 0.12 -10000 0 -0.38 12 12
TRPC6 0.022 0.18 -10000 0 -0.95 3 3
GNAI2 0.034 0.004 -10000 0 -10000 0 0
GNAI3 0.033 0.007 -10000 0 -10000 0 0
GNAI1 -0.033 0.18 -10000 0 -0.51 26 26
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.027 0.12 -10000 0 -0.39 13 13
ETB receptor/Endothelin-2 -0.24 0.19 -10000 0 -0.4 117 117
ETB receptor/Endothelin-3 -0.12 0.2 -10000 0 -0.42 62 62
ETB receptor/Endothelin-1 -0.009 0.16 -10000 0 -0.41 23 23
MAPK3 -0.081 0.29 0.38 4 -0.72 32 36
MAPK1 -0.092 0.31 0.4 3 -0.75 32 35
Rac1/GDP 0.004 0.16 0.31 3 -0.55 6 9
cAMP biosynthetic process 0.006 0.11 0.43 2 -10000 0 2
MAPK8 0.026 0.17 -10000 0 -0.56 10 10
SRC 0.019 0.017 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.011 0.12 -10000 0 -0.36 11 11
p130Cas/CRK/Src/PYK2 0.024 0.19 0.39 9 -0.56 7 16
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP 0.004 0.16 0.31 3 -0.55 6 9
COL1A2 -0.003 0.21 -10000 0 -0.53 11 11
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.3 0.21 -10000 0 -0.4 169 169
mol:DAG -0.013 0.14 0.24 3 -0.45 9 12
MAP2K2 -0.056 0.23 0.4 4 -0.54 30 34
MAP2K1 -0.058 0.24 0.35 4 -0.55 30 34
EDNRA -0.012 0.17 -10000 0 -0.32 49 49
positive regulation of muscle contraction 0.008 0.13 0.28 10 -0.31 5 15
Gq family/GDP -0.006 0.15 -10000 0 -0.48 10 10
HRAS/GTP -0.015 0.16 0.32 5 -0.46 11 16
PRKCH -0.012 0.14 0.24 3 -0.46 8 11
RAC1 0.031 0.011 -10000 0 -10000 0 0
PRKCA -0.007 0.15 0.29 4 -0.53 6 10
PRKCB -0.01 0.14 0.24 4 -0.42 10 14
PRKCE -0.01 0.14 0.28 1 -0.56 5 6
PRKCD -0.009 0.14 0.29 1 -0.45 7 8
PRKCG -0.013 0.14 0.25 4 -0.47 8 12
regulation of vascular smooth muscle contraction -0.14 0.42 0.46 2 -1.1 33 35
PRKCQ -0.01 0.14 0.24 4 -0.45 7 11
PLA2G4A -0.076 0.25 0.38 4 -0.61 27 31
GNA14 0.012 0.11 -10000 0 -0.51 9 9
GNA15 0.024 0.058 -10000 0 -0.32 6 6
GNA12 0.031 0.01 -10000 0 -10000 0 0
GNA11 0.019 0.089 -10000 0 -0.5 6 6
Rac1/GTP 0.095 0.17 -10000 0 -0.32 7 7
MMP1 -0.23 0.095 0.35 1 -10000 0 1
IL12-mediated signaling events

Figure S22.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S22.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.007 0.084 -10000 0 -0.31 1 1
TBX21 -0.38 0.66 -10000 0 -1.3 67 67
B2M 0.012 0.1 -10000 0 -0.5 8 8
TYK2 0.013 0.041 -10000 0 -10000 0 0
IL12RB1 0.013 0.041 -10000 0 -10000 0 0
GADD45B -0.14 0.36 -10000 0 -0.94 25 25
IL12RB2 0.012 0.049 -10000 0 -0.36 1 1
GADD45G -0.14 0.36 -10000 0 -0.89 29 29
natural killer cell activation -0.007 0.024 -10000 0 -10000 0 0
RELB 0.034 0.005 -10000 0 -10000 0 0
RELA 0.034 0.005 -10000 0 -10000 0 0
IL18 -0.026 0.17 -10000 0 -0.5 24 24
IL2RA 0.024 0.058 -10000 0 -0.32 6 6
IFNG -0.041 0.14 -10000 0 -0.32 46 46
STAT3 (dimer) -0.12 0.32 -10000 0 -0.73 34 34
HLA-DRB5 0.011 0.096 -10000 0 -0.5 7 7
FASLG -0.2 0.5 -10000 0 -1.3 31 31
NF kappa B2 p52/RelB -0.14 0.38 -10000 0 -0.83 38 38
CD4 0.028 0.019 -10000 0 -10000 0 0
SOCS1 0.032 0.025 -10000 0 -0.32 1 1
EntrezGene:6955 0 0.008 -10000 0 -10000 0 0
CD3D 0.007 0.11 -10000 0 -0.51 9 9
CD3E 0.03 0.019 -10000 0 -10000 0 0
CD3G 0.006 0.11 -10000 0 -0.49 10 10
IL12Rbeta2/JAK2 0.018 0.068 -10000 0 -0.24 4 4
CCL3 -0.15 0.37 -10000 0 -0.94 27 27
CCL4 -0.16 0.4 -10000 0 -1 26 26
HLA-A 0.022 0.082 -10000 0 -0.5 5 5
IL18/IL18R -0.038 0.21 -10000 0 -0.36 59 59
NOS2 -0.16 0.38 -10000 0 -0.84 38 38
IL12/IL12R/TYK2/JAK2/SPHK2 0.005 0.084 -10000 0 -0.31 1 1
IL1R1 -0.17 0.42 -10000 0 -1.1 29 29
IL4 0.038 0.036 -10000 0 -0.31 1 1
JAK2 0.008 0.056 -10000 0 -0.33 3 3
EntrezGene:6957 0 0.007 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.011 0.17 -10000 0 -0.6 12 12
RAB7A -0.12 0.31 -10000 0 -0.74 28 28
lysosomal transport -0.11 0.3 -10000 0 -0.7 28 28
FOS -0.25 0.55 -10000 0 -1.2 46 46
STAT4 (dimer) -0.13 0.36 -10000 0 -0.84 31 31
STAT5A (dimer) -0.15 0.37 -10000 0 -0.82 38 38
GZMA -0.15 0.37 -10000 0 -0.82 39 39
GZMB -0.15 0.37 -10000 0 -0.95 27 27
HLX 0.033 0.006 -10000 0 -10000 0 0
LCK -0.17 0.4 -10000 0 -0.9 38 38
TCR/CD3/MHC II/CD4 -0.027 0.19 -10000 0 -0.59 16 16
IL2/IL2R 0.067 0.064 -10000 0 -0.29 3 3
MAPK14 -0.15 0.38 -10000 0 -0.9 33 33
CCR5 -0.21 0.5 -10000 0 -1.3 33 33
IL1B -0.048 0.13 -10000 0 -0.31 39 39
STAT6 -0.019 0.12 -10000 0 -0.76 1 1
STAT4 0.032 0.037 -10000 0 -0.51 1 1
STAT3 0.033 0.006 -10000 0 -10000 0 0
STAT1 0.003 0.1 -10000 0 -0.32 19 19
NFKB1 0.033 0.006 -10000 0 -10000 0 0
NFKB2 0.031 0.025 -10000 0 -0.32 1 1
IL12B 0.011 0.051 -10000 0 -0.3 2 2
CD8A 0.001 0.002 -10000 0 -10000 0 0
CD8B 0.036 0.004 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.007 0.084 0.31 1 -10000 0 1
IL2RB 0.032 0.008 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.12 0.33 -10000 0 -0.76 31 31
IL2RG 0.027 0.063 -10000 0 -0.51 3 3
IL12 0.015 0.073 -10000 0 -0.23 3 3
STAT5A 0.033 0.006 -10000 0 -10000 0 0
CD247 0.002 0.12 -10000 0 -0.51 11 11
IL2 0.034 0.005 -10000 0 -10000 0 0
SPHK2 0.031 0.037 -10000 0 -0.51 1 1
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.004 0.067 -10000 0 -0.31 6 6
IL12/IL12R/TYK2/JAK2 -0.18 0.43 -10000 0 -0.94 39 39
MAP2K3 -0.17 0.4 -10000 0 -0.91 37 37
RIPK2 -0.012 0.11 -10000 0 -0.32 25 25
MAP2K6 -0.15 0.38 -10000 0 -0.91 32 32
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.021 0.065 -10000 0 -0.5 3 3
IL18RAP -0.074 0.22 -10000 0 -0.51 43 43
IL12Rbeta1/TYK2 0.022 0.055 -10000 0 -10000 0 0
EOMES 0.025 0.066 -10000 0 -0.56 1 1
STAT1 (dimer) -0.12 0.31 -10000 0 -0.74 30 30
T cell proliferation -0.1 0.28 -10000 0 -0.64 29 29
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.032 0.039 -10000 0 -0.52 1 1
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.12 0.32 -10000 0 -0.71 32 32
ATF2 -0.14 0.35 -10000 0 -0.82 32 32
IL4-mediated signaling events

Figure S23.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S23.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.21 0.46 -10000 0 -1.1 21 21
STAT6 (cleaved dimer) -0.33 0.46 -10000 0 -1.1 37 37
IGHG1 -0.077 0.18 -10000 0 -10000 0 0
IGHG3 -0.28 0.42 -10000 0 -1.1 30 30
AKT1 -0.13 0.26 -10000 0 -0.74 10 10
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.11 0.23 -10000 0 -0.89 6 6
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.13 0.25 -10000 0 -0.97 4 4
THY1 -0.3 0.44 -10000 0 -1.1 27 27
MYB 0.028 0.052 -10000 0 -0.51 2 2
HMGA1 0.034 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.22 0.33 -10000 0 -0.83 28 28
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.14 0.25 -10000 0 -0.95 4 4
SP1 0.024 0.034 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.045 0.029 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.31 0.47 -10000 0 -1.1 35 35
SOCS1 -0.2 0.32 -10000 0 -0.76 20 20
SOCS3 -0.18 0.28 -10000 0 -0.81 11 11
FCER2 -0.25 0.41 -10000 0 -1.1 19 19
PARP14 0.032 0.034 -10000 0 -0.32 2 2
CCL17 -0.3 0.44 -10000 0 -1.2 24 24
GRB2 0.033 0.007 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.1 0.2 -10000 0 -0.65 4 4
T cell proliferation -0.28 0.45 -10000 0 -1.1 28 28
IL4R/JAK1 -0.29 0.44 -10000 0 -1.1 28 28
EGR2 -0.31 0.49 -10000 0 -1.3 25 25
JAK2 -0.01 0.065 -10000 0 -0.35 3 3
JAK3 0.021 0.033 -10000 0 -10000 0 0
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
JAK1 0.011 0.031 -10000 0 -10000 0 0
COL1A2 -0.092 0.17 -10000 0 -10000 0 0
CCL26 -0.3 0.44 -10000 0 -1.1 27 27
IL4R -0.31 0.46 -10000 0 -1.2 28 28
PTPN6 0.038 0.017 -10000 0 -10000 0 0
IL13RA2 -0.32 0.44 -10000 0 -1.2 28 28
IL13RA1 -0.005 0.052 -10000 0 -10000 0 0
IRF4 -0.34 0.62 -10000 0 -1.5 50 50
ARG1 -0.013 0.16 -10000 0 -10000 0 0
CBL -0.21 0.31 -10000 0 -0.79 28 28
GTF3A -0.1 0.15 -10000 0 -0.36 52 52
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.004 0.079 -10000 0 -0.3 2 2
IRF4/BCL6 -0.31 0.58 -10000 0 -1.4 50 50
CD40LG 0.001 0.082 -10000 0 -0.5 2 2
MAPK14 -0.2 0.31 -10000 0 -0.8 25 25
mitosis -0.13 0.25 -10000 0 -0.7 10 10
STAT6 -0.32 0.49 -10000 0 -1.3 30 30
SPI1 0.038 0.015 -10000 0 -10000 0 0
RPS6KB1 -0.12 0.24 -10000 0 -0.74 6 6
STAT6 (dimer) -0.32 0.49 -10000 0 -1.3 30 30
STAT6 (dimer)/PARP14 -0.29 0.47 -10000 0 -1.2 30 30
mast cell activation 0.007 0.013 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.17 0.27 -10000 0 -0.8 13 13
FRAP1 -0.13 0.26 -10000 0 -0.74 10 10
LTA -0.29 0.44 -10000 0 -1.1 25 25
FES 0.028 0.044 -10000 0 -0.41 2 2
T-helper 1 cell differentiation 0.32 0.48 1.2 30 -10000 0 30
CCL11 -0.39 0.6 -10000 0 -1.5 42 42
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.14 0.26 -10000 0 -0.82 9 9
IL2RG 0.014 0.071 -10000 0 -0.51 3 3
IL10 -0.28 0.44 -10000 0 -1.1 29 29
IRS1 0.028 0.048 -10000 0 -0.32 4 4
IRS2 0.025 0.015 -10000 0 -10000 0 0
IL4 -0.044 0.12 -10000 0 -10000 0 0
IL5 -0.3 0.44 -10000 0 -1.1 29 29
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.22 0.35 -10000 0 -0.86 23 23
COL1A1 -0.2 0.22 -10000 0 -0.99 3 3
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.29 0.45 -10000 0 -1.2 24 24
IL2R gamma/JAK3 0.026 0.069 -10000 0 -0.39 3 3
TFF3 -0.3 0.46 -10000 0 -1.2 29 29
ALOX15 -0.29 0.44 -10000 0 -1.1 27 27
MYBL1 0.024 0.042 -10000 0 -0.32 3 3
T-helper 2 cell differentiation -0.23 0.37 -10000 0 -0.88 29 29
SHC1 0.033 0.006 -10000 0 -10000 0 0
CEBPB 0.017 0.039 -10000 0 -0.31 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.11 0.24 -10000 0 -0.85 5 5
mol:PI-3-4-5-P3 -0.13 0.26 -10000 0 -0.74 10 10
PI3K -0.14 0.28 -10000 0 -0.8 10 10
DOK2 0.023 0.039 -10000 0 -0.51 1 1
ETS1 0.04 0.018 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.097 0.19 -10000 0 -0.64 4 4
ITGB3 -0.28 0.44 -10000 0 -1.2 23 23
PIGR -0.33 0.52 -10000 0 -1.3 37 37
IGHE 0.068 0.074 0.2 12 -10000 0 12
MAPKKK cascade -0.095 0.18 -10000 0 -0.63 4 4
BCL6 0.029 0.044 -10000 0 -0.41 2 2
OPRM1 -0.29 0.44 -10000 0 -1.1 27 27
RETNLB -0.49 0.68 -10000 0 -1.5 60 60
SELP -0.38 0.6 -10000 0 -1.4 42 42
AICDA -0.33 0.51 -10000 0 -1.3 35 35
TRAIL signaling pathway

Figure S24.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S24.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.016 0.16 -9999 0 -0.51 20 20
positive regulation of NF-kappaB transcription factor activity -0.004 0.12 -9999 0 -0.35 23 23
MAP2K4 -0.009 0.092 -9999 0 -0.36 8 8
IKBKB 0.029 0.012 -9999 0 -10000 0 0
TNFRSF10B -0.023 0.12 -9999 0 -0.32 30 30
TNFRSF10A -0.009 0.1 -9999 0 -0.32 21 21
SMPD1 -0.1 0.2 -9999 0 -0.42 55 55
IKBKG 0.033 0.006 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.019 0.049 -9999 0 -0.32 4 4
TRAIL/TRAILR2 -0.035 0.15 -9999 0 -0.3 45 45
TRAIL/TRAILR3 -0.029 0.14 -9999 0 -0.3 42 42
TRAIL/TRAILR1 -0.024 0.14 -9999 0 -0.31 38 38
TRAIL/TRAILR4 -0.004 0.12 -9999 0 -0.35 23 23
TRAIL/TRAILR1/DAP3/GTP -0.003 0.11 -9999 0 -0.3 19 19
IKK complex -0.003 0.079 -9999 0 -0.55 1 1
RIPK1 0.034 0.005 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0.025 0.004 -9999 0 -10000 0 0
MAPK3 -0.019 0.12 -9999 0 -0.38 20 20
MAP3K1 -0.005 0.092 -9999 0 -0.33 10 10
TRAILR4 (trimer) 0.019 0.049 -9999 0 -0.32 4 4
TRADD 0.034 0.005 -9999 0 -10000 0 0
TRAILR1 (trimer) -0.009 0.1 -9999 0 -0.32 21 21
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.007 0.094 -9999 0 -0.34 8 8
CFLAR 0.034 0.002 -9999 0 -10000 0 0
MAPK1 -0.013 0.1 -9999 0 -0.37 17 17
TRAIL/TRAILR1/FADD/TRADD/RIP 0.021 0.12 -9999 0 -0.3 14 14
mol:ceramide -0.1 0.2 -9999 0 -0.41 55 55
FADD 0.034 0.004 -9999 0 -10000 0 0
MAPK8 -0.01 0.09 -9999 0 -0.36 7 7
TRAF2 0.033 0.006 -9999 0 -10000 0 0
TRAILR3 (trimer) -0.013 0.11 -9999 0 -0.32 24 24
CHUK 0.033 0.008 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.005 0.13 -9999 0 -0.33 20 20
DAP3 0.033 0.006 -9999 0 -10000 0 0
CASP10 -0.037 0.1 -9999 0 -0.37 15 15
JNK cascade -0.004 0.12 -9999 0 -0.35 23 23
TRAIL (trimer) -0.016 0.16 -9999 0 -0.5 20 20
TNFRSF10C -0.013 0.11 -9999 0 -0.32 24 24
TRAIL/TRAILR1/DAP3/GTP/FADD 0.008 0.12 -9999 0 -0.28 19 19
TRAIL/TRAILR2/FADD -0.015 0.13 -9999 0 -0.34 20 20
cell death -0.1 0.2 -9999 0 -0.41 55 55
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.011 0.095 -9999 0 -0.32 11 11
TRAILR2 (trimer) -0.023 0.12 -9999 0 -0.32 30 30
CASP8 0.026 0.033 -9999 0 -10000 0 0
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.01 0.13 -9999 0 -0.3 19 19
IL1-mediated signaling events

Figure S25.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S25.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.025 0.003 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.033 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.003 0.058 -10000 0 -10000 0 0
IRAK/TOLLIP 0.037 0.022 -10000 0 -10000 0 0
IKBKB 0.029 0.012 -10000 0 -10000 0 0
IKBKG 0.033 0.006 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.22 0.2 -10000 0 -0.33 155 155
IL1A -0.12 0.17 -10000 0 -0.32 94 94
IL1B -0.048 0.12 -10000 0 -0.25 53 53
IRAK/TRAF6/p62/Atypical PKCs 0.058 0.042 -10000 0 -10000 0 0
IL1R2 -0.18 0.26 -10000 0 -0.51 87 87
IL1R1 0.014 0.1 -10000 0 -0.51 8 8
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.003 0.067 -10000 0 -10000 0 0
TOLLIP 0.034 0.005 -10000 0 -10000 0 0
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0.032 0.008 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.022 0.005 -10000 0 -10000 0 0
IKK complex/ELKS 0.034 0.06 -10000 0 -10000 0 0
JUN -0.017 0.053 0.32 1 -10000 0 1
MAP3K7 0.033 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.007 0.13 -10000 0 -0.29 5 5
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.039 0.14 -10000 0 -0.31 12 12
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.026 0.14 -10000 0 -0.32 6 6
IL1 beta fragment/IL1R1/IL1RAP -0.02 0.12 -10000 0 -0.29 22 22
NFKB1 0.033 0.006 -10000 0 -10000 0 0
MAPK8 0 0.055 0.34 1 -0.24 9 10
IRAK1 0.017 0.02 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.041 0.14 -10000 0 -0.24 69 69
IRAK4 0.034 0.004 -10000 0 -10000 0 0
PRKCI 0.026 0.053 -10000 0 -0.32 5 5
TRAF6 0.034 0.005 -10000 0 -10000 0 0
PI3K 0.049 0.01 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.002 0.073 -10000 0 -10000 0 0
CHUK 0.033 0.008 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.02 0.12 -10000 0 -0.29 22 22
IL1 beta/IL1R2 -0.16 0.19 -10000 0 -0.35 91 91
IRAK/TRAF6/TAK1/TAB1/TAB2 0.045 0.023 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.003 0.12 -10000 0 -10000 0 0
IRAK3 0.022 0.062 -10000 0 -0.32 7 7
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.006 0.12 -10000 0 -0.26 22 22
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.014 0.071 -10000 0 -0.3 2 2
IL1 alpha/IL1R1/IL1RAP -0.057 0.14 -10000 0 -0.34 12 12
RELA 0.034 0.005 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.034 0.004 -10000 0 -10000 0 0
MYD88 0.034 0.004 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.053 0.03 -10000 0 -10000 0 0
IL1RAP 0.024 0.058 -10000 0 -0.32 6 6
UBE2N 0.034 0.005 -10000 0 -10000 0 0
IRAK/TRAF6 -0.023 0.1 -10000 0 -10000 0 0
CASP1 0 0.12 -10000 0 -0.44 15 15
IL1RN/IL1R2 -0.19 0.19 -10000 0 -0.32 140 140
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.004 0.13 -10000 0 -0.28 22 22
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.005 0.08 -10000 0 -0.32 8 8
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
IL1RN -0.065 0.16 -10000 0 -0.32 61 61
TRAF6/TAK1/TAB1/TAB2 0.048 0.013 -10000 0 -10000 0 0
MAP2K6 0.009 0.059 0.35 1 -0.25 9 10
RXR and RAR heterodimerization with other nuclear receptor

Figure S26.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S26.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.015 0.055 -10000 0 -10000 0 0
VDR 0.019 0.089 -10000 0 -0.51 6 6
FAM120B 0.033 0.007 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.057 0.028 -10000 0 -10000 0 0
RXRs/LXRs/DNA/Oxysterols 0.063 0.038 -10000 0 -0.37 1 1
MED1 0.032 0.008 -10000 0 -10000 0 0
mol:9cRA 0.006 0.004 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.023 0.071 -10000 0 -0.46 1 1
RXRs/NUR77 0.091 0.038 -10000 0 -10000 0 0
RXRs/PPAR 0.035 0.05 -10000 0 -10000 0 0
NCOR2 0.034 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.014 0.064 -10000 0 -0.36 6 6
RARs/VDR/DNA/Vit D3 0.063 0.064 -10000 0 -0.27 6 6
RARA 0.032 0.008 -10000 0 -10000 0 0
NCOA1 0.029 0.052 -10000 0 -0.51 2 2
VDR/VDR/DNA 0.019 0.089 -10000 0 -0.5 6 6
RARs/RARs/DNA/9cRA 0.057 0.027 -10000 0 -10000 0 0
RARG 0.031 0.034 -10000 0 -0.32 2 2
RPS6KB1 0.021 0.078 0.53 5 -10000 0 5
RARs/THRs/DNA/SMRT 0.024 0.064 -10000 0 -10000 0 0
THRA 0.032 0.008 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.014 0.064 -10000 0 -0.36 6 6
RXRs/PPAR/9cRA/PGJ2/DNA 0.078 0.027 -10000 0 -10000 0 0
NR1H4 -0.43 0.19 -10000 0 -0.51 185 185
RXRs/LXRs/DNA 0.12 0.043 -10000 0 -10000 0 0
NR1H2 0.039 0.009 -10000 0 -10000 0 0
NR1H3 0.04 0.009 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.078 0.063 -10000 0 -0.26 6 6
NR4A1 0.03 0.034 -10000 0 -0.32 2 2
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.18 0.096 -10000 0 -0.23 170 170
RXRG 0.038 0.009 -10000 0 -10000 0 0
RXR alpha/CCPG 0.051 0.014 -10000 0 -10000 0 0
RXRA 0.039 0.008 -10000 0 -10000 0 0
RXRB 0.039 0.01 -10000 0 -10000 0 0
THRB 0.006 0.12 -10000 0 -0.51 11 11
PPARG 0.018 0.089 -10000 0 -0.51 6 6
PPARD 0.034 0.004 -10000 0 -10000 0 0
TNF 0.056 0.035 -10000 0 -10000 0 0
mol:Oxysterols 0.005 0.004 -10000 0 -10000 0 0
cholesterol transport 0.063 0.038 -10000 0 -0.37 1 1
PPARA 0.029 0.038 -10000 0 -0.51 1 1
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.034 0.003 -10000 0 -10000 0 0
RXRs/NUR77/BCL2 -0.11 0.11 -10000 0 -0.23 84 84
SREBF1 0.044 0.042 -10000 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.078 0.027 -10000 0 -10000 0 0
ABCA1 0.051 0.08 -10000 0 -1.1 1 1
RARs/THRs 0.075 0.085 -10000 0 -0.27 10 10
RXRs/FXR -0.22 0.13 -10000 0 -0.28 178 178
BCL2 -0.2 0.26 -10000 0 -0.51 87 87
IL6-mediated signaling events

Figure S27.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S27.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.033 0.15 -10000 0 -10000 0 0
CRP -0.094 0.14 -10000 0 -10000 0 0
cell cycle arrest -0.11 0.14 -10000 0 -0.62 2 2
TIMP1 -0.13 0.15 -10000 0 -0.76 2 2
IL6ST 0.034 0.009 -10000 0 -10000 0 0
Rac1/GDP -0.15 0.16 -10000 0 -0.4 35 35
AP1 0.007 0.13 -10000 0 -0.58 2 2
GAB2 0.038 0.01 -10000 0 -10000 0 0
TNFSF11 -0.071 0.16 -10000 0 -0.65 1 1
HSP90B1 0.018 0.046 -10000 0 -10000 0 0
GAB1 0.031 0.052 -10000 0 -0.5 2 2
MAPK14 -0.14 0.15 -10000 0 -0.47 14 14
AKT1 0.041 0.046 -10000 0 -10000 0 0
FOXO1 0.062 0.092 -10000 0 -10000 0 0
MAP2K6 -0.15 0.16 -10000 0 -0.38 35 35
mol:GTP 0 0.001 -10000 0 -10000 0 0
MAP2K4 -0.15 0.16 -10000 0 -0.44 23 23
MITF -0.15 0.14 -10000 0 -0.35 37 37
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.033 0.006 -10000 0 -10000 0 0
A2M -0.18 0.52 -10000 0 -1.4 32 32
CEBPB 0.018 0.039 -10000 0 -0.31 2 2
GRB2/SOS1/GAB family/SHP2 0.004 0.087 -10000 0 -0.45 2 2
STAT3 -0.12 0.14 -10000 0 -0.65 2 2
STAT1 0.01 0.025 -10000 0 -10000 0 0
CEBPD -0.08 0.14 -10000 0 -10000 0 0
PIK3CA 0.035 0.004 -10000 0 -10000 0 0
PI3K 0.051 0.01 -10000 0 -10000 0 0
JUN 0.025 0.053 -10000 0 -0.32 5 5
PIAS3/MITF -0.14 0.15 -10000 0 -0.36 26 26
MAPK11 -0.14 0.15 -10000 0 -0.49 13 13
STAT3 (dimer)/FOXO1 -0.068 0.17 0.39 1 -0.56 5 6
GRB2/SOS1/GAB family -0.074 0.17 0.32 1 -0.44 7 8
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.12 0.15 -10000 0 -0.34 49 49
GRB2 0.035 0.009 -10000 0 -10000 0 0
JAK2 0.028 0.042 -10000 0 -0.32 3 3
LBP 0.008 0.14 0.5 1 -10000 0 1
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
JAK1 0.033 0.01 -10000 0 -10000 0 0
MYC -0.11 0.16 -10000 0 -0.64 2 2
FGG -0.098 0.13 -10000 0 -10000 0 0
macrophage differentiation -0.11 0.14 -10000 0 -0.62 2 2
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.18 0.18 -10000 0 -0.34 94 94
JUNB -0.096 0.13 -10000 0 -0.54 1 1
FOS -0.028 0.16 -10000 0 -0.49 24 24
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.16 0.15 -10000 0 -0.34 58 58
STAT1/PIAS1 -0.11 0.13 -10000 0 -0.36 13 13
GRB2/SOS1/GAB family/SHP2/PI3K 0.047 0.042 -10000 0 -10000 0 0
STAT3 (dimer) -0.11 0.14 -10000 0 -0.64 2 2
PRKCD -0.14 0.16 0.37 2 -0.5 11 13
IL6R -0.25 0.27 -10000 0 -0.51 114 114
SOCS3 -0.12 0.16 -10000 0 -0.58 3 3
gp130 (dimer)/JAK1/JAK1/LMO4 0.055 0.061 -10000 0 -0.29 2 2
Rac1/GTP -0.15 0.16 -10000 0 -0.43 26 26
HCK 0.005 0.088 -10000 0 -0.5 6 6
MAPKKK cascade 0.037 0.098 -10000 0 -0.52 2 2
bone resorption -0.067 0.16 0.48 1 -0.62 1 2
IRF1 -0.1 0.15 -10000 0 -1.1 1 1
mol:GDP -0.17 0.16 -10000 0 -0.39 47 47
SOS1 0.038 0.009 -10000 0 -10000 0 0
VAV1 -0.17 0.16 -10000 0 -0.39 48 48
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.22 0.21 -10000 0 -0.48 50 50
PTPN11 0.015 0.06 -10000 0 -0.82 1 1
IL6/IL6RA -0.25 0.21 -10000 0 -0.37 146 146
gp130 (dimer)/TYK2/TYK2/LMO4 0.054 0.059 -10000 0 -0.3 2 2
gp130 (dimer)/JAK2/JAK2/LMO4 0.052 0.069 -10000 0 -0.33 5 5
IL6 -0.12 0.17 -10000 0 -0.32 91 91
PIAS3 0.032 0.024 -10000 0 -0.32 1 1
PTPRE 0.032 0.026 -10000 0 -0.31 1 1
PIAS1 0.032 0.008 -10000 0 -10000 0 0
RAC1 0.031 0.011 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.15 0.14 -10000 0 -0.3 80 80
LMO4 0.017 0.081 -10000 0 -0.36 9 9
STAT3 (dimer)/PIAS3 -0.11 0.15 -10000 0 -0.6 3 3
MCL1 0.043 0.053 -10000 0 -10000 0 0
Signaling events mediated by PRL

Figure S28.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S28.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.012 0.084 -10000 0 -0.32 13 13
mol:Halofuginone 0.004 0 -10000 0 -10000 0 0
ITGA1 0.033 0.024 -10000 0 -0.32 1 1
CDKN1A 0.006 0.059 -10000 0 -0.32 6 6
PRL-3/alpha Tubulin -0.015 0.1 -10000 0 -0.22 44 44
mol:Ca2+ -0.07 0.12 -10000 0 -0.23 66 66
AGT -0.077 0.16 -10000 0 -0.32 67 67
CCNA2 0.056 0.11 -10000 0 -10000 0 0
TUBA1B 0.034 0.004 -10000 0 -10000 0 0
EGR1 0.005 0.071 -10000 0 -0.35 7 7
CDK2/Cyclin E1 0.053 0.12 -10000 0 -0.34 3 3
MAPK3 -0.012 0.13 0.23 22 -0.22 45 67
PRL-2 /Rab GGTase beta 0.048 0.013 -10000 0 -10000 0 0
MAPK1 -0.01 0.12 0.23 22 -0.22 44 66
PTP4A1 0.001 0.035 -10000 0 -10000 0 0
PTP4A3 -0.044 0.14 -10000 0 -0.32 44 44
PTP4A2 0.033 0.008 -10000 0 -10000 0 0
ITGB1 -0.011 0.12 0.23 22 -0.22 45 67
SRC 0.019 0.017 -10000 0 -10000 0 0
RAC1 0.016 0.043 -10000 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0.045 0.017 -10000 0 -10000 0 0
PRL-1/ATF-5 0.094 0.099 0.36 2 -10000 0 2
RABGGTA 0.031 0.01 -10000 0 -10000 0 0
BCAR1 0.012 0.057 -10000 0 -10000 0 0
RHOC 0.009 0.066 -10000 0 -0.42 1 1
RHOA 0.017 0.043 -10000 0 -10000 0 0
cell motility 0.044 0.12 0.35 2 -0.41 3 5
PRL-1/alpha Tubulin 0.096 0.1 0.37 3 -10000 0 3
PRL-3/alpha1 Integrin -0.013 0.1 -10000 0 -0.22 44 44
ROCK1 0.044 0.12 0.35 2 -0.42 3 5
RABGGTB 0.033 0.007 -10000 0 -10000 0 0
CDK2 -0.002 0.11 -10000 0 -0.32 22 22
mitosis 0.001 0.034 -10000 0 -10000 0 0
ATF5 0.034 0.005 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

Figure S29.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S29.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.073 0.22 -10000 0 -0.9 5 5
PCK1 -0.68 0.66 -10000 0 -1.2 123 123
HNF4A -0.048 0.25 0.59 3 -0.97 4 7
KCNJ11 -0.06 0.24 -10000 0 -0.96 3 3
AKT1 -0.032 0.14 -10000 0 -0.74 1 1
response to starvation -0.015 0.034 -10000 0 -0.27 2 2
DLK1 -0.058 0.24 -10000 0 -0.96 3 3
NKX2-1 0.034 0.18 -10000 0 -10000 0 0
ACADM -0.077 0.23 -10000 0 -0.93 6 6
TAT -0.12 0.2 -10000 0 -0.79 6 6
CEBPB -0.005 0.042 -10000 0 -0.32 2 2
CEBPA -0.007 0.044 -10000 0 -10000 0 0
TTR -0.74 0.67 0.58 2 -1.3 121 123
PKLR -0.077 0.23 -10000 0 -0.98 4 4
APOA1 -0.061 0.29 -10000 0 -1.2 6 6
CPT1C -0.076 0.23 -10000 0 -0.97 4 4
ALAS1 -0.016 0.14 -10000 0 -0.64 1 1
TFRC -0.11 0.24 -10000 0 -0.95 5 5
FOXF1 0.015 0.099 -10000 0 -0.51 7 7
NF1 0.039 0.009 -10000 0 -10000 0 0
HNF1A (dimer) 0.032 0.042 -10000 0 -10000 0 0
CPT1A -0.075 0.22 -10000 0 -0.95 4 4
HMGCS1 -0.072 0.23 0.59 1 -0.95 4 5
NR3C1 -0.024 0.17 -10000 0 -0.5 24 24
CPT1B -0.074 0.22 -10000 0 -0.95 4 4
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.035 0.023 -10000 0 -10000 0 0
GCK -0.066 0.22 -10000 0 -0.95 4 4
CREB1 -0.12 0.15 -10000 0 -0.26 89 89
IGFBP1 -0.061 0.16 -10000 0 -0.56 7 7
PDX1 -0.003 0.14 -10000 0 -10000 0 0
UCP2 -0.072 0.22 -10000 0 -0.95 4 4
ALDOB -0.11 0.34 -10000 0 -1.1 15 15
AFP -0.14 0.15 -10000 0 -0.47 12 12
BDH1 -0.074 0.23 -10000 0 -1.1 4 4
HADH -0.062 0.24 -10000 0 -1.1 2 2
F2 -0.046 0.26 -10000 0 -1.1 2 2
HNF1A 0.032 0.042 -10000 0 -10000 0 0
G6PC -0.071 0.14 -10000 0 -10000 0 0
SLC2A2 -0.032 0.17 -10000 0 -10000 0 0
INS 0.026 0.022 -10000 0 -10000 0 0
FOXA1 -0.12 0.22 -10000 0 -0.51 53 53
FOXA3 -0.13 0.16 -10000 0 -0.4 27 27
FOXA2 -0.073 0.27 -10000 0 -0.92 6 6
ABCC8 -0.094 0.31 -10000 0 -1 12 12
ALB -0.14 0.15 -10000 0 -0.43 24 24
Syndecan-3-mediated signaling events

Figure S30.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S30.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.034 0.004 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.064 0.15 -9999 0 -0.43 14 14
Syndecan-3/Neurocan 0.013 0.1 -9999 0 -0.37 13 13
POMC 0.032 0.037 -9999 0 -0.51 1 1
EGFR 0.021 0.073 -9999 0 -0.51 4 4
Syndecan-3/EGFR 0.004 0.11 -9999 0 -0.36 15 15
AGRP 0.032 0.024 -9999 0 -0.32 1 1
NCSTN 0.033 0.006 -9999 0 -10000 0 0
PSENEN 0.033 0.007 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.031 0.025 -9999 0 -0.32 1 1
APH1A 0.017 0.092 -9999 0 -0.48 7 7
NCAN 0.034 0.004 -9999 0 -10000 0 0
long-term memory 0.027 0.1 -9999 0 -0.35 13 13
Syndecan-3/IL8 -0.14 0.11 -9999 0 -0.48 14 14
PSEN1 0.031 0.01 -9999 0 -10000 0 0
Src/Cortactin 0.027 0.025 -9999 0 -10000 0 0
FYN 0.03 0.037 -9999 0 -0.51 1 1
limb bud formation -0.009 0.097 -9999 0 -0.38 13 13
MC4R 0.023 0.016 -9999 0 -10000 0 0
SRC 0.019 0.017 -9999 0 -10000 0 0
PTN -0.17 0.26 -9999 0 -0.51 80 80
FGFR/FGF/Syndecan-3 -0.009 0.097 -9999 0 -0.39 13 13
neuron projection morphogenesis -0.023 0.18 -9999 0 -0.44 12 12
Syndecan-3/AgRP 0.012 0.1 -9999 0 -0.37 13 13
Syndecan-3/AgRP/MC4R 0.018 0.1 -9999 0 -0.35 13 13
Fyn/Cortactin 0.046 0.031 -9999 0 -0.37 1 1
SDC3 -0.009 0.098 -9999 0 -0.39 13 13
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.14 0.11 -9999 0 -0.47 14 14
IL8 -0.29 0.099 -9999 0 -0.32 196 196
Syndecan-3/Fyn/Cortactin 0.029 0.11 -9999 0 -0.36 13 13
Syndecan-3/CASK -0.01 0.094 -9999 0 -0.37 13 13
alpha-MSH/MC4R 0.032 0.036 -9999 0 -0.37 1 1
Gamma Secretase 0.071 0.073 -9999 0 -0.27 4 4
Signaling events mediated by the Hedgehog family

Figure S31.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S31.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.023 0.1 -10000 0 -0.49 4 4
IHH 0.035 0.055 -10000 0 -0.62 1 1
SHH Np/Cholesterol/GAS1 -0.087 0.16 -10000 0 -0.31 70 70
LRPAP1 0.033 0.007 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.086 0.16 0.31 70 -10000 0 70
SMO/beta Arrestin2 0.037 0.073 -10000 0 -0.53 1 1
SMO 0.025 0.067 -10000 0 -0.56 1 1
AKT1 0.012 0.11 -10000 0 -10000 0 0
ARRB2 0.027 0.014 -10000 0 -10000 0 0
BOC 0.034 0.004 -10000 0 -10000 0 0
ADRBK1 0.034 0.004 -10000 0 -10000 0 0
heart looping 0.025 0.066 -10000 0 -0.55 1 1
STIL -0.014 0.12 0.37 1 -0.37 7 8
DHH N/PTCH2 0.049 0.009 -10000 0 -10000 0 0
DHH N/PTCH1 0.046 0.067 -10000 0 -0.49 1 1
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
DHH 0.034 0.004 -10000 0 -10000 0 0
PTHLH 0.023 0.1 -10000 0 -0.87 1 1
determination of left/right symmetry 0.025 0.066 -10000 0 -0.55 1 1
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
skeletal system development 0.023 0.099 -10000 0 -0.86 1 1
IHH N/Hhip -0.039 0.19 -10000 0 -0.41 43 43
DHH N/Hhip -0.035 0.17 -10000 0 -0.37 43 43
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.025 0.066 -10000 0 -0.55 1 1
pancreas development -0.074 0.22 -10000 0 -0.5 43 43
HHAT -0.017 0.16 -10000 0 -0.51 20 20
PI3K 0.049 0.01 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.13 0.24 -10000 0 -0.49 67 67
somite specification 0.025 0.066 -10000 0 -0.55 1 1
SHH Np/Cholesterol/PTCH1 0.008 0.098 -10000 0 -0.37 3 3
SHH Np/Cholesterol/PTCH2 0.003 0.094 -10000 0 -0.29 19 19
SHH Np/Cholesterol/Megalin 0.003 0.094 -10000 0 -0.29 19 19
SHH -0.016 0.11 0.23 1 -0.38 19 20
catabolic process 0.03 0.069 -10000 0 -0.54 1 1
SMO/Vitamin D3 0.009 0.098 -10000 0 -0.49 1 1
SHH Np/Cholesterol/Hhip -0.056 0.16 -10000 0 -0.32 53 53
LRP2 0.033 0.024 -10000 0 -0.32 1 1
receptor-mediated endocytosis 0.005 0.097 -10000 0 -0.46 1 1
SHH Np/Cholesterol/BOC 0.005 0.092 -10000 0 -0.29 18 18
SHH Np/Cholesterol/CDO 0.003 0.094 -10000 0 -0.29 19 19
mesenchymal cell differentiation 0.056 0.16 0.32 53 -10000 0 53
mol:Vitamin D3 0.014 0.11 0.39 1 -0.37 3 4
IHH N/PTCH2 0.051 0.035 -10000 0 -0.39 1 1
CDON 0.033 0.006 -10000 0 -10000 0 0
IHH N/PTCH1 0.039 0.072 -10000 0 -0.55 1 1
Megalin/LRPAP1 0.048 0.021 -10000 0 -0.22 1 1
PTCH2 0.034 0.005 -10000 0 -10000 0 0
SHH Np/Cholesterol -0.009 0.089 -10000 0 -0.29 19 19
PTCH1 0.03 0.069 -10000 0 -0.55 1 1
HHIP -0.074 0.22 -10000 0 -0.51 43 43
IL2 signaling events mediated by PI3K

Figure S32.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S32.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.075 0.099 -10000 0 -10000 0 0
UGCG -0.014 0.077 -10000 0 -0.76 2 2
AKT1/mTOR/p70S6K/Hsp90/TERT -0.21 0.2 -10000 0 -0.51 35 35
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.014 0.076 -10000 0 -0.75 2 2
mol:DAG 0.037 0.13 -10000 0 -0.71 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.28 0.22 -10000 0 -0.46 100 100
FRAP1 -0.32 0.25 -10000 0 -0.53 106 106
FOXO3 -0.18 0.16 -10000 0 -0.42 26 26
AKT1 -0.2 0.17 -10000 0 -0.43 41 41
GAB2 0.028 0.005 -10000 0 -10000 0 0
SMPD1 -0.18 0.33 -10000 0 -0.79 47 47
SGMS1 -0.019 0.095 -10000 0 -0.68 4 4
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP -0.013 0.012 -10000 0 -10000 0 0
CALM1 0.03 0.011 -10000 0 -10000 0 0
cell proliferation -0.035 0.11 -10000 0 -0.47 5 5
EIF3A 0.033 0.006 -10000 0 -10000 0 0
PI3K 0.039 0.013 -10000 0 -10000 0 0
RPS6KB1 -0.024 0.15 -10000 0 -0.98 5 5
mol:sphingomyelin 0.037 0.13 -10000 0 -0.71 4 4
natural killer cell activation -0.007 0.004 -10000 0 -0.013 30 30
JAK3 0.03 0.007 -10000 0 -10000 0 0
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
JAK1 0.029 0.008 -10000 0 -10000 0 0
NFKB1 0.033 0.006 -10000 0 -10000 0 0
MYC -0.18 0.16 -10000 0 -0.46 17 17
MYB 0.014 0.13 -10000 0 -1.3 2 2
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.095 0.11 -10000 0 -0.44 4 4
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.016 0.15 -10000 0 -0.9 5 5
mol:PI-3-4-5-P3 -0.094 0.11 -10000 0 -0.43 4 4
Rac1/GDP 0.001 0.023 -10000 0 -10000 0 0
T cell proliferation -0.089 0.1 -10000 0 -0.4 4 4
SHC1 0.027 0.006 -10000 0 -10000 0 0
RAC1 0.03 0.01 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.004 0.007 -10000 0 -0.065 2 2
PRKCZ -0.091 0.1 -10000 0 -0.42 4 4
NF kappa B1 p50/RelA -0.28 0.22 -10000 0 -0.47 96 96
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.016 0.053 -10000 0 -0.41 1 1
HSP90AA1 0.031 0.011 -10000 0 -10000 0 0
RELA 0.034 0.005 -10000 0 -10000 0 0
IL2RA 0.018 0.058 -10000 0 -0.32 6 6
IL2RB 0.028 0.009 -10000 0 -10000 0 0
TERT 0.033 0.008 -10000 0 -10000 0 0
E2F1 0.013 0.061 -10000 0 -0.43 2 2
SOS1 0.028 0.004 -10000 0 -10000 0 0
RPS6 0.03 0.034 -10000 0 -0.32 2 2
mol:cAMP -0.002 0.003 0.031 2 -10000 0 2
PTPN11 0.025 0.025 -10000 0 -0.32 1 1
IL2RG 0.021 0.063 -10000 0 -0.51 3 3
actin cytoskeleton organization -0.089 0.1 -10000 0 -0.4 4 4
GRB2 0.027 0.007 -10000 0 -10000 0 0
IL2 0.028 0.008 -10000 0 -10000 0 0
PIK3CA 0.029 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.004 0.034 -10000 0 -10000 0 0
LCK 0.023 0.045 -10000 0 -0.42 2 2
BCL2 -0.59 0.42 -10000 0 -0.89 142 142
Regulation of nuclear SMAD2/3 signaling

Figure S33.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S33.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.045 0.017 -10000 0 -10000 0 0
HSPA8 0.03 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.012 0.098 -10000 0 -0.35 7 7
AKT1 -0.053 0.057 -10000 0 -10000 0 0
GSC -0.054 0.15 -10000 0 -0.58 6 6
NKX2-5 0.017 0.046 -10000 0 -0.31 1 1
muscle cell differentiation 0.12 0.18 0.6 16 -10000 0 16
SMAD2-3/SMAD4/SP1 -0.1 0.12 -10000 0 -0.4 4 4
SMAD4 -0.025 0.063 -10000 0 -0.38 2 2
CBFB 0.029 0.041 -10000 0 -0.32 3 3
SAP18 0.024 0.015 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.054 0.089 -10000 0 -10000 0 0
SMAD3/SMAD4/VDR 0.052 0.095 -10000 0 -10000 0 0
MYC -0.056 0.14 -10000 0 -0.2 96 96
CDKN2B -1.1 0.62 -10000 0 -1.4 168 168
AP1 -0.03 0.12 -10000 0 -0.35 10 10
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.046 0.14 -10000 0 -0.41 18 18
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.31 0.22 -10000 0 -0.43 153 153
SP3 0.036 0.002 -10000 0 -10000 0 0
CREB1 0.034 0.002 -10000 0 -10000 0 0
FOXH1 0.015 0.036 -10000 0 -10000 0 0
SMAD3/SMAD4/GR -0.051 0.14 -10000 0 -0.37 25 25
GATA3 0.031 0.032 -10000 0 -10000 0 0
SKI/SIN3/HDAC complex/NCoR1 0.015 0.079 -10000 0 -0.46 2 2
MEF2C/TIF2 -0.073 0.19 -10000 0 -0.52 29 29
endothelial cell migration -0.029 0.1 -10000 0 -10000 0 0
MAX 0.032 0.012 -10000 0 -10000 0 0
RBBP7 0.032 0.005 -10000 0 -10000 0 0
RBBP4 0.032 0.007 -10000 0 -10000 0 0
RUNX2 0.034 0.005 -10000 0 -10000 0 0
RUNX3 0.002 0.12 -10000 0 -0.45 13 13
RUNX1 -0.074 0.16 -10000 0 -0.32 65 65
CTBP1 0.033 0.007 -10000 0 -10000 0 0
NR3C1 -0.025 0.17 -10000 0 -0.51 24 24
VDR 0.019 0.089 -10000 0 -0.51 6 6
CDKN1A -0.07 0.19 -10000 0 -1.3 4 4
KAT2B 0.004 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.043 0.085 -10000 0 -0.29 1 1
DCP1A 0.034 0.005 -10000 0 -10000 0 0
SKI 0.031 0.008 -10000 0 -10000 0 0
SERPINE1 0.028 0.1 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF2 -0.016 0.07 -10000 0 -0.29 2 2
SMAD3/SMAD4/ATF3 -0.019 0.076 -10000 0 -0.29 4 4
SAP30 0.031 0.007 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.093 0.051 -10000 0 -10000 0 0
JUN -0.044 0.11 -10000 0 -0.35 10 10
SMAD3/SMAD4/IRF7 -0.006 0.07 -10000 0 -0.32 1 1
TFE3 0.037 0.007 -10000 0 -10000 0 0
COL1A2 -0.031 0.1 -10000 0 -10000 0 0
mesenchymal cell differentiation 0.015 0.069 0.32 1 -10000 0 1
DLX1 0.031 0.034 -10000 0 -0.32 2 2
TCF3 0.033 0.007 -10000 0 -10000 0 0
FOS -0.033 0.17 -10000 0 -0.5 24 24
SMAD3/SMAD4/Max -0.012 0.074 -10000 0 -0.29 2 2
Cbp/p300/SNIP1 0.071 0.029 -10000 0 -10000 0 0
ZBTB17 0.074 0.035 -10000 0 -10000 0 0
LAMC1 -0.02 0.051 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 -0.008 0.061 -10000 0 -10000 0 0
IRF7 0.037 0.005 -10000 0 -10000 0 0
ESR1 0.021 0.082 -10000 0 -0.51 5 5
HNF4A 0.018 0.017 -10000 0 -10000 0 0
MEF2C -0.083 0.2 -10000 0 -0.53 31 31
SMAD2-3/SMAD4 -0.073 0.1 -10000 0 -0.34 3 3
Cbp/p300/Src-1 0.078 0.05 -10000 0 -0.3 2 2
IGHV3OR16-13 -0.008 0.028 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.007 0.062 -10000 0 -0.32 7 7
CREBBP 0.043 0.012 -10000 0 -10000 0 0
SKIL 0.026 0.053 -10000 0 -0.32 5 5
HDAC1 0.031 0.007 -10000 0 -10000 0 0
HDAC2 0.032 0.007 -10000 0 -10000 0 0
SNIP1 0.031 0.006 -10000 0 -10000 0 0
GCN5L2 0.012 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.006 0.069 -10000 0 -0.32 1 1
MSG1/HSC70 0.011 0.086 -10000 0 -0.22 26 26
SMAD2 -0.042 0.06 -10000 0 -0.23 1 1
SMAD3 -0.026 0.046 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 -0.023 0.077 0.28 1 -0.28 4 5
SMAD2/SMAD2/SMAD4 -0.067 0.08 -10000 0 -0.2 33 33
NCOR1 0.026 0.014 -10000 0 -10000 0 0
NCOA2 0.03 0.012 -10000 0 -10000 0 0
NCOA1 0.029 0.052 -10000 0 -0.51 2 2
MYOD/E2A 0.045 0.033 -10000 0 -0.22 3 3
SMAD2-3/SMAD4/SP1/MIZ-1 -0.099 0.13 -10000 0 -0.37 5 5
IFNB1 -0.021 0.048 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C -0.092 0.2 -10000 0 -0.54 31 31
CITED1 -0.009 0.11 -10000 0 -0.32 26 26
SMAD2-3/SMAD4/ARC105 -0.057 0.097 -10000 0 -0.31 3 3
RBL1 0.009 0.058 -10000 0 -0.32 6 6
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.39 0.28 -10000 0 -0.55 149 149
RUNX1-3/PEBPB2 -0.033 0.13 -10000 0 -0.31 12 12
SMAD7 -0.091 0.17 -10000 0 -0.56 10 10
MYC/MIZ-1 0.092 0.12 -10000 0 -0.22 14 14
SMAD3/SMAD4 0.055 0.11 0.33 1 -0.34 2 3
IL10 -0.021 0.06 -10000 0 -10000 0 0
PIASy/HDAC complex 0.002 0.027 -10000 0 -10000 0 0
PIAS3 0.037 0.025 -10000 0 -0.32 1 1
CDK2 0.007 0.11 -10000 0 -0.31 22 22
IL5 -0.033 0.09 -10000 0 -0.32 9 9
CDK4 0.021 0.09 -10000 0 -0.3 15 15
PIAS4 0.002 0.027 -10000 0 -10000 0 0
ATF3 0.027 0.048 -10000 0 -0.32 4 4
SMAD3/SMAD4/SP1 -0.05 0.091 -10000 0 -0.35 4 4
FOXG1 -0.014 0.12 -10000 0 -0.32 27 27
FOXO3 -0.071 0.065 -10000 0 -10000 0 0
FOXO1 -0.06 0.088 -10000 0 -0.46 6 6
FOXO4 -0.07 0.063 -10000 0 -10000 0 0
heart looping -0.082 0.2 -10000 0 -0.52 31 31
CEBPB -0.018 0.046 -10000 0 -0.37 2 2
SMAD3/SMAD4/DLX1 -0.018 0.073 -10000 0 -0.29 3 3
MYOD1 0.029 0.041 -10000 0 -0.32 3 3
SMAD3/SMAD4/HNF4 0 0.048 -10000 0 -10000 0 0
SMAD3/SMAD4/GATA3 -0.007 0.081 -10000 0 -0.32 1 1
SnoN/SIN3/HDAC complex/NCoR1 0.026 0.053 -10000 0 -0.32 5 5
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.057 0.13 -10000 0 -0.34 11 11
SMAD3/SMAD4/SP1-3 -0.034 0.088 -10000 0 -0.32 2 2
MED15 0.032 0.009 -10000 0 -10000 0 0
SP1 -0.026 0.041 -10000 0 -10000 0 0
SIN3B 0.032 0.005 -10000 0 -10000 0 0
SIN3A 0.031 0.008 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.05 0.12 -10000 0 -0.34 14 14
ITGB5 -0.045 0.062 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.021 0.073 -10000 0 -0.49 2 2
SMAD3/SMAD4/AR -0.017 0.072 -10000 0 -0.29 3 3
AR 0.033 0.024 -10000 0 -0.32 1 1
negative regulation of cell growth -0.037 0.099 -10000 0 -0.35 8 8
SMAD3/SMAD4/MYOD -0.018 0.074 -10000 0 -0.3 2 2
E2F5 -0.077 0.16 -10000 0 -0.32 65 65
E2F4 0.032 0.024 -10000 0 -0.32 1 1
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.01 0.087 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 -0.33 0.24 -10000 0 -0.46 156 156
TFDP1 0.019 0.049 -10000 0 -0.32 4 4
SMAD3/SMAD4/AP1 -0.022 0.12 -10000 0 -0.35 10 10
SMAD3/SMAD4/RUNX2 -0.015 0.07 -10000 0 -0.32 1 1
TGIF2 0.007 0.062 -10000 0 -0.32 7 7
TGIF1 -0.011 0.11 -10000 0 -0.32 23 23
ATF2 0.034 0.002 -10000 0 -10000 0 0
Ceramide signaling pathway

Figure S34.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S34.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.006 0.064 -10000 0 -0.37 6 6
MAP4K4 0.015 0.065 -10000 0 -0.37 2 2
BAG4 0.03 0.011 -10000 0 -10000 0 0
PKC zeta/ceramide -0.041 0.095 0.15 1 -0.24 23 24
NFKBIA 0.031 0.01 -10000 0 -10000 0 0
BIRC3 0.01 0.11 -10000 0 -0.47 10 10
BAX -0.005 0.047 -10000 0 -0.29 3 3
RIPK1 0.034 0.005 -10000 0 -10000 0 0
AKT1 0.004 0.013 -10000 0 -10000 0 0
BAD -0.041 0.096 0.16 1 -0.25 23 24
SMPD1 -0.028 0.12 0.33 1 -0.26 40 41
RB1 0.009 0.11 0.19 34 -0.26 12 46
FADD/Caspase 8 0.027 0.058 -10000 0 -0.4 1 1
MAP2K4 -0.038 0.094 -10000 0 -0.34 10 10
NSMAF 0.03 0.012 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.034 0.09 0.19 1 -0.33 8 9
EGF -0.09 0.21 -10000 0 -0.42 58 58
mol:ceramide -0.043 0.1 0.15 5 -0.26 23 28
MADD 0.034 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.006 0.052 -10000 0 -0.37 4 4
ASAH1 0.026 0.015 -10000 0 -10000 0 0
negative regulation of cell cycle 0.01 0.11 0.19 34 -0.25 12 46
cell proliferation -0.14 0.14 -10000 0 -0.32 36 36
BID -0.013 0.18 -10000 0 -0.64 15 15
MAP3K1 -0.041 0.096 -10000 0 -0.25 23 23
EIF2A -0.054 0.095 -10000 0 -0.3 13 13
TRADD 0.034 0.005 -10000 0 -10000 0 0
CRADD 0.029 0.052 -10000 0 -0.51 2 2
MAPK3 -0.028 0.085 -10000 0 -0.49 3 3
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.035 0.087 -10000 0 -0.44 4 4
Cathepsin D/ceramide -0.029 0.11 0.17 1 -0.26 23 24
FADD 0.019 0.058 -10000 0 -0.39 1 1
KSR1 -0.036 0.093 0.19 3 -0.24 21 24
MAPK8 -0.036 0.094 -10000 0 -0.29 12 12
PRKRA -0.042 0.096 0.16 1 -0.25 23 24
PDGFA 0.018 0.082 -10000 0 -0.51 5 5
TRAF2 0.033 0.006 -10000 0 -10000 0 0
IGF1 -0.28 0.27 -10000 0 -0.51 123 123
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.043 0.1 0.15 5 -0.26 23 28
CTSD 0.031 0.037 -10000 0 -0.51 1 1
regulation of nitric oxide biosynthetic process 0.049 0.011 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.15 0.15 -10000 0 -0.34 36 36
PRKCD 0.034 0.005 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.006 0.052 -10000 0 -0.37 4 4
RelA/NF kappa B1 0.049 0.011 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.034 0.004 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.027 0.06 -10000 0 -0.32 3 3
TNFR1A/BAG4/TNF-alpha 0.058 0.026 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.006 0.063 -10000 0 -0.37 6 6
MAP2K1 -0.033 0.086 -10000 0 -0.49 3 3
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.034 0.005 -10000 0 -10000 0 0
CYCS 0.088 0.076 0.19 10 -0.2 1 11
TNFRSF1A 0.033 0.008 -10000 0 -10000 0 0
NFKB1 0.033 0.006 -10000 0 -10000 0 0
TNFR1A/BAG4 0.043 0.019 -10000 0 -10000 0 0
EIF2AK2 -0.045 0.094 -10000 0 -0.31 12 12
TNF-alpha/TNFR1A/FAN 0.057 0.027 -10000 0 -10000 0 0
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.033 0.074 -10000 0 -0.41 4 4
MAP2K2 -0.033 0.085 -10000 0 -0.49 3 3
SMPD3 0.018 0.073 -10000 0 -0.3 8 8
TNF 0.034 0.005 -10000 0 -10000 0 0
PKC zeta/PAR4 0.025 0.003 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.038 0.097 0.21 37 -0.15 2 39
NF kappa B1/RelA/I kappa B alpha 0.07 0.028 -10000 0 -10000 0 0
AIFM1 0.08 0.082 0.2 9 -0.29 1 10
BCL2 -0.2 0.26 -10000 0 -0.51 87 87
Canonical Wnt signaling pathway

Figure S35.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S35.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.058 0.025 -10000 0 -10000 0 0
AES 0.055 0.021 -10000 0 -10000 0 0
FBXW11 0.034 0.004 -10000 0 -10000 0 0
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.046 0.023 -10000 0 -0.22 1 1
SMAD4 0.02 0.039 -10000 0 -0.51 1 1
DKK2 -0.11 0.17 -10000 0 -0.32 86 86
TLE1 0.054 0.018 -10000 0 -10000 0 0
MACF1 0.034 0.005 -10000 0 -10000 0 0
CTNNB1 0.061 0.084 0.42 4 -10000 0 4
WIF1 -0.018 0.12 -10000 0 -0.32 32 32
beta catenin/RanBP3 0.18 0.13 0.35 47 -10000 0 47
KREMEN2 -0.03 0.14 -10000 0 -0.32 39 39
DKK1 -0.055 0.15 -10000 0 -0.32 54 54
beta catenin/beta TrCP1 0.079 0.08 0.41 4 -10000 0 4
FZD1 0.033 0.008 -10000 0 -10000 0 0
AXIN2 -0.16 0.17 -10000 0 -1.6 1 1
AXIN1 0.034 0.007 -10000 0 -10000 0 0
RAN 0.033 0.024 -10000 0 -0.32 1 1
Axin1/APC/GSK3/beta catenin 0.05 0.067 -10000 0 -0.5 2 2
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.001 0.15 0.37 2 -0.6 4 6
Axin1/APC/GSK3 0.065 0.059 0.31 1 -10000 0 1
Axin1/APC/GSK3/beta catenin/Macf1 0.039 0.072 -10000 0 -0.37 1 1
HNF1A 0.055 0.019 -10000 0 -10000 0 0
CTBP1 0.054 0.021 -10000 0 -10000 0 0
MYC -0.057 0.24 0.61 7 -10000 0 7
RANBP3 0.035 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.069 0.14 -10000 0 -0.34 19 19
NKD1 -0.23 0.15 -10000 0 -0.32 160 160
TCF4 0.038 0.031 -10000 0 -10000 0 0
TCF3 0.053 0.021 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.079 0.033 -10000 0 -10000 0 0
Ran/GTP 0.026 0.017 -10000 0 -0.21 1 1
CtBP/CBP/TCF/TLE1/AES 0.14 0.14 0.4 22 -0.44 1 23
LEF1 -0.019 0.15 -10000 0 -0.3 46 46
DVL1 0.049 0.06 -10000 0 -0.48 1 1
CSNK2A1 0.027 0.014 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.007 0.084 -10000 0 -0.56 2 2
DKK1/LRP6/Kremen 2 -0.039 0.14 -10000 0 -0.33 13 13
LRP6 0.032 0.025 -10000 0 -0.32 1 1
CSNK1A1 0.06 0.024 -10000 0 -10000 0 0
NLK 0.029 0.008 -10000 0 -10000 0 0
CCND1 -0.09 0.1 -10000 0 -10000 0 0
WNT1 0.034 0.004 -10000 0 -10000 0 0
GSK3A 0.033 0.006 -10000 0 -10000 0 0
GSK3B 0.032 0.024 -10000 0 -0.32 1 1
FRAT1 0.03 0.037 -10000 0 -0.5 1 1
PPP2R5D 0.13 0.074 0.23 26 -10000 0 26
APC 0.028 0.091 0.56 3 -0.26 6 9
WNT1/LRP6/FZD1 0.046 0.047 0.32 1 -10000 0 1
CREBBP 0.053 0.021 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

Figure S36.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S36.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
DYNC1H1 0.031 0.011 -9999 0 -10000 0 0
VLDLR -0.079 0.22 -9999 0 -0.5 45 45
LRPAP1 0.033 0.007 -9999 0 -10000 0 0
NUDC 0.031 0.01 -9999 0 -10000 0 0
RELN/LRP8 -0.14 0.086 -9999 0 -0.23 1 1
CaM/Ca2+ 0.022 0.008 -9999 0 -10000 0 0
KATNA1 0.033 0.007 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.13 0.074 -9999 0 -10000 0 0
IQGAP1/CaM 0.043 0.019 -9999 0 -10000 0 0
DAB1 0.033 0.006 -9999 0 -10000 0 0
IQGAP1 0.032 0.009 -9999 0 -10000 0 0
PLA2G7 0.001 0.13 -9999 0 -0.51 13 13
CALM1 0.03 0.011 -9999 0 -10000 0 0
DYNLT1 0.033 0.007 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.19 0.086 -9999 0 -0.22 183 183
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.034 0.003 -9999 0 -10000 0 0
CDK5R1 0.033 0.007 -9999 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.009 0.007 -9999 0 -10000 0 0
CDK5R2 0.034 0.002 -9999 0 -10000 0 0
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.011 0.15 -9999 0 -0.31 39 39
YWHAE 0.027 0.014 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.095 0.086 -9999 0 -10000 0 0
MAP1B -0.007 0.063 -9999 0 -0.3 9 9
RAC1 0.012 0.01 -9999 0 -10000 0 0
p35/CDK5 -0.11 0.07 -9999 0 -0.28 1 1
RELN 0.032 0.008 -9999 0 -10000 0 0
PAFAH/LIS1 0.01 0.074 -9999 0 -0.3 11 11
LIS1/CLIP170 0.026 0.019 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.076 0.067 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.028 0.13 -9999 0 -0.35 10 10
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.099 0.082 -9999 0 -10000 0 0
LIS1/IQGAP1 0.026 0.019 -9999 0 -10000 0 0
RHOA 0.013 0.01 -9999 0 -10000 0 0
PAFAH1B1 0.013 0.009 -9999 0 -10000 0 0
PAFAH1B3 -0.003 0.11 -9999 0 -0.32 22 22
PAFAH1B2 0.034 0.005 -9999 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.009 0.058 -9999 0 -0.33 1 1
NDEL1/Katanin 60/Dynein heavy chain -0.096 0.083 -9999 0 -10000 0 0
LRP8 -0.28 0.11 -9999 0 -0.32 189 189
NDEL1/Katanin 60 -0.1 0.083 -9999 0 -10000 0 0
P39/CDK5 -0.12 0.069 -9999 0 -0.28 1 1
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.025 0.019 -9999 0 -10000 0 0
CDK5 -0.13 0.064 -9999 0 -0.29 2 2
PPP2R5D 0.033 0.006 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.023 0.016 -9999 0 -10000 0 0
CSNK2A1 0.027 0.014 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.003 0.13 -9999 0 -10000 0 0
RELN/VLDLR -0.18 0.14 -9999 0 -0.39 45 45
CDC42 0.013 0.01 -9999 0 -10000 0 0
Thromboxane A2 receptor signaling

Figure S37.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S37.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.007 0.062 -10000 0 -0.32 7 7
GNB1/GNG2 -0.051 0.049 -10000 0 -0.19 7 7
AKT1 -0.025 0.1 0.26 4 -0.31 7 11
EGF -0.09 0.21 -10000 0 -0.42 58 58
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR -0.12 0.086 -10000 0 -0.27 1 1
mol:Ca2+ -0.025 0.11 0.29 2 -0.33 5 7
LYN -0.11 0.091 -10000 0 -0.27 1 1
RhoA/GTP -0.006 0.048 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.028 0.11 0.3 3 -0.36 5 8
GNG2 0.031 0.01 -10000 0 -10000 0 0
ARRB2 0.027 0.014 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.059 0.14 -10000 0 -0.54 12 12
G beta5/gamma2 -0.063 0.066 -10000 0 -0.25 7 7
PRKCH -0.034 0.12 0.31 1 -0.42 5 6
DNM1 0.03 0.034 -10000 0 -0.32 2 2
TXA2/TP beta/beta Arrestin3 -0.01 0.051 -10000 0 -0.68 1 1
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.35 0.24 -10000 0 -0.51 152 152
G12 family/GTP -0.026 0.094 -10000 0 -0.32 5 5
ADRBK1 0.034 0.004 -10000 0 -10000 0 0
ADRBK2 0.032 0.008 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.036 0.019 -10000 0 -10000 0 0
mol:GDP 0.069 0.098 0.35 10 -10000 0 10
mol:NADP 0.031 0.025 -10000 0 -0.32 1 1
RAB11A 0.032 0.008 -10000 0 -10000 0 0
PRKG1 0.033 0.006 -10000 0 -10000 0 0
mol:IP3 -0.034 0.13 0.34 1 -0.4 6 7
cell morphogenesis 0.036 0.019 -10000 0 -10000 0 0
PLCB2 -0.049 0.17 -10000 0 -0.54 8 8
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.17 0.13 -10000 0 -0.37 39 39
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.077 0.099 -10000 0 -0.36 5 5
RHOA 0.034 0.005 -10000 0 -10000 0 0
PTGIR 0.033 0.006 -10000 0 -10000 0 0
PRKCB1 -0.029 0.12 0.32 1 -0.39 6 7
GNAQ 0 0 -10000 0 -10000 0 0
mol:L-citrulline 0.031 0.025 -10000 0 -0.32 1 1
TXA2/TXA2-R family -0.045 0.15 -10000 0 -0.56 5 5
LCK -0.13 0.086 -10000 0 -0.27 5 5
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.15 0.11 -10000 0 -0.3 4 4
TXA2-R family/G12 family/GDP/G beta/gamma -0.045 0.13 -10000 0 -0.52 13 13
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.15 0.1 -10000 0 -0.3 4 4
MAPK14 -0.015 0.087 0.3 4 -0.25 3 7
TGM2/GTP -0.039 0.14 0.4 1 -0.47 3 4
MAPK11 -0.017 0.082 0.24 3 -0.25 3 6
ARHGEF1 -0.006 0.07 0.3 1 -0.2 2 3
GNAI2 0.034 0.004 -10000 0 -10000 0 0
JNK cascade -0.031 0.12 0.3 2 -0.41 5 7
RAB11/GDP 0.033 0.008 -10000 0 -10000 0 0
ICAM1 -0.017 0.098 0.26 2 -0.29 5 7
cAMP biosynthetic process -0.035 0.12 0.32 1 -0.39 4 5
Gq family/GTP/EBP50 0 0.068 -10000 0 -0.25 9 9
actin cytoskeleton reorganization 0.036 0.019 -10000 0 -10000 0 0
SRC -0.069 0.09 -10000 0 -0.27 1 1
GNB5 0.027 0.042 -10000 0 -0.32 3 3
GNB1 0.032 0.008 -10000 0 -10000 0 0
EGF/EGFR -0.096 0.11 0.26 2 -0.3 22 24
VCAM1 -0.018 0.1 0.27 2 -0.41 5 7
TP beta/Gq family/GDP/G beta5/gamma2 -0.059 0.14 -10000 0 -0.54 12 12
platelet activation -0.024 0.11 0.34 4 -0.33 3 7
PGI2/IP 0.025 0.004 -10000 0 -10000 0 0
PRKACA -0.18 0.12 -10000 0 -0.25 146 146
Gq family/GDP/G beta5/gamma2 -0.072 0.13 -10000 0 -0.51 13 13
TXA2/TP beta/beta Arrestin2 -0.038 0.069 -10000 0 -0.43 2 2
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.17 0.1 -10000 0 -0.24 144 144
mol:DAG -0.036 0.14 0.34 1 -0.44 7 8
EGFR 0.021 0.073 -10000 0 -0.51 4 4
TXA2/TP alpha -0.048 0.16 0.37 1 -0.52 5 6
Gq family/GTP -0.003 0.071 0.22 2 -0.22 18 20
YES1 -0.12 0.088 -10000 0 -0.27 1 1
GNAI2/GTP -0.14 0.096 -10000 0 -0.29 4 4
PGD2/DP -0.26 0.16 -10000 0 -0.36 152 152
SLC9A3R1 0.026 0.064 -10000 0 -0.51 3 3
FYN -0.12 0.089 -10000 0 -0.31 3 3
mol:NO 0.031 0.025 -10000 0 -0.32 1 1
GNA15 0.024 0.058 -10000 0 -0.32 6 6
PGK/cGMP 0.042 0.019 -10000 0 -0.18 1 1
RhoA/GDP 0.034 0.005 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.097 0.11 -10000 0 -0.33 5 5
NOS3 0.031 0.025 -10000 0 -0.32 1 1
RAC1 0.031 0.011 -10000 0 -10000 0 0
PRKCA -0.027 0.12 0.32 2 -0.37 5 7
PRKCB -0.028 0.11 0.28 1 -0.37 6 7
PRKCE -0.028 0.12 0.28 1 -0.38 5 6
PRKCD -0.029 0.12 0.31 1 -0.4 5 6
PRKCG -0.029 0.13 0.31 2 -0.4 6 8
muscle contraction -0.039 0.15 0.35 1 -0.5 6 7
PRKCZ -0.028 0.11 0.28 2 -0.36 5 7
ARR3 0.034 0.002 -10000 0 -10000 0 0
TXA2/TP beta -0.15 0.11 -10000 0 -0.32 4 4
PRKCQ -0.029 0.12 0.36 2 -0.37 6 8
MAPKKK cascade -0.042 0.14 0.33 1 -0.47 7 8
SELE -0.026 0.11 0.27 2 -0.31 7 9
TP beta/GNAI2/GDP/G beta/gamma -0.14 0.12 -10000 0 -0.31 4 4
ROCK1 0.027 0.014 -10000 0 -10000 0 0
GNA14 0.011 0.11 -10000 0 -0.51 9 9
chemotaxis -0.04 0.16 -10000 0 -0.63 5 5
GNA12 0.031 0.01 -10000 0 -10000 0 0
GNA13 0.032 0.008 -10000 0 -10000 0 0
GNA11 0.018 0.089 -10000 0 -0.51 6 6
Rac1/GTP 0.023 0.008 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

Figure S38.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S38.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.06 0.13 -10000 0 -0.22 87 87
CRKL 0.022 0.1 0.32 4 -0.45 5 9
mol:PIP3 0.003 0.051 0.45 2 -10000 0 2
AKT1 0.001 0.042 0.3 2 -10000 0 2
PTK2B 0.026 0.015 -10000 0 -10000 0 0
RAPGEF1 0.023 0.099 0.31 5 -0.46 4 9
RANBP10 0.034 0.005 -10000 0 -10000 0 0
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.039 0.12 -10000 0 -10000 0 0
MAP3K5 0.034 0.1 0.4 4 -0.5 3 7
HGF/MET/CIN85/CBL/ENDOPHILINS -0.027 0.13 -10000 0 -0.39 4 4
AP1 -0.046 0.13 -10000 0 -0.33 27 27
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.033 0.006 -10000 0 -10000 0 0
apoptosis -0.13 0.32 -10000 0 -0.75 43 43
STAT3 (dimer) 0.006 0.054 0.22 1 -10000 0 1
GAB1/CRKL/SHP2/PI3K 0.059 0.1 0.32 3 -0.49 2 5
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.04 0.1 0.32 3 -0.46 4 7
PTPN11 0.032 0.024 -10000 0 -0.32 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.018 0.017 -10000 0 -10000 0 0
PTEN 0.027 0.052 -10000 0 -0.51 2 2
ELK1 -0.033 0.13 0.35 11 -10000 0 11
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.004 0.046 -10000 0 -0.34 1 1
PAK1 0 0.039 0.28 1 -10000 0 1
HGF/MET/RANBP10 -0.039 0.12 -10000 0 -10000 0 0
HRAS 0.013 0.069 -10000 0 -0.41 1 1
DOCK1 0.02 0.099 0.31 4 -0.46 4 8
GAB1 0.009 0.089 -10000 0 -0.48 5 5
CRK 0.02 0.097 0.33 3 -0.45 5 8
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.01 0.057 -10000 0 -10000 0 0
JUN 0.026 0.053 -10000 0 -0.32 5 5
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.044 0.056 -10000 0 -0.22 1 1
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
cell morphogenesis 0.055 0.11 0.4 6 -10000 0 6
GRB2/SHC -0.02 0.076 -10000 0 -10000 0 0
FOS -0.027 0.16 -10000 0 -0.49 24 24
GLMN 0.001 0.014 -10000 0 -0.16 1 1
cell motility -0.033 0.13 0.35 11 -10000 0 11
HGF/MET/MUC20 -0.05 0.11 -10000 0 -0.18 89 89
cell migration -0.02 0.075 -10000 0 -10000 0 0
GRB2 0.033 0.007 -10000 0 -10000 0 0
CBL 0.034 0.005 -10000 0 -10000 0 0
MET/RANBP10 -0.061 0.13 -10000 0 -0.22 87 87
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.013 0.065 -10000 0 -0.28 1 1
MET/MUC20 -0.074 0.12 -10000 0 -0.22 87 87
RAP1B 0.024 0.099 0.32 6 -0.46 3 9
RAP1A 0.022 0.095 0.3 5 -0.43 4 9
HGF/MET/RANBP9 -0.038 0.12 -10000 0 -10000 0 0
RAF1 0.015 0.069 0.32 1 -10000 0 1
STAT3 0.006 0.054 0.22 1 -10000 0 1
cell proliferation 0.026 0.072 0.34 1 -10000 0 1
RPS6KB1 -0.02 0.062 -10000 0 -0.34 5 5
MAPK3 -0.051 0.13 0.57 5 -10000 0 5
MAPK1 -0.011 0.21 0.62 17 -10000 0 17
RANBP9 0.034 0.005 -10000 0 -10000 0 0
MAPK8 0.038 0.11 0.4 4 -0.51 2 6
SRC 0.009 0.064 -10000 0 -10000 0 0
PI3K -0.02 0.077 -10000 0 -10000 0 0
MET/Glomulin -0.09 0.11 -10000 0 -0.21 88 88
SOS1 0.034 0.002 -10000 0 -10000 0 0
MAP2K1 0.017 0.072 0.37 1 -10000 0 1
MET -0.11 0.17 -10000 0 -0.32 87 87
MAP4K1 0.035 0.1 0.33 4 -0.54 3 7
PTK2 0.028 0.013 -10000 0 -10000 0 0
MAP2K2 0.017 0.074 0.34 2 -10000 0 2
BAD 0 0.039 0.28 1 -10000 0 1
MAP2K4 0.025 0.097 0.39 4 -0.45 3 7
SHP2/GRB2/SOS1/GAB1 0.036 0.094 -10000 0 -0.45 3 3
INPPL1 0.034 0.004 -10000 0 -10000 0 0
PXN 0.034 0.003 -10000 0 -10000 0 0
SH3KBP1 0.024 0.073 -10000 0 -0.51 4 4
HGS -0.04 0.053 -10000 0 -0.2 1 1
PLCgamma1/PKC 0.014 0.013 -10000 0 -10000 0 0
HGF 0.029 0.034 -10000 0 -0.32 2 2
RASA1 0.03 0.034 -10000 0 -0.32 2 2
NCK1 0.034 0.005 -10000 0 -10000 0 0
PTPRJ 0.034 0.004 -10000 0 -10000 0 0
NCK/PLCgamma1 0.006 0.053 -10000 0 -10000 0 0
PDPK1 0.002 0.048 0.35 2 -10000 0 2
HGF/MET/SHIP -0.05 0.11 -10000 0 -0.18 89 89
TCR signaling in naïve CD8+ T cells

Figure S39.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S39.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.012 0.16 0.3 5 -0.48 13 18
FYN -0.036 0.18 0.27 1 -0.57 16 17
LAT/GRAP2/SLP76 0.003 0.15 -10000 0 -0.5 12 12
IKBKB 0.029 0.012 -10000 0 -10000 0 0
AKT1 -0.022 0.14 0.3 2 -0.41 16 18
B2M 0.012 0.1 -10000 0 -0.51 8 8
IKBKG 0 0.046 0.11 1 -0.15 3 4
MAP3K8 -0.013 0.12 -10000 0 -0.32 29 29
mol:Ca2+ -0.009 0.017 0.089 2 -0.085 2 4
integrin-mediated signaling pathway 0.042 0.013 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.035 0.19 0.35 1 -0.6 16 17
TRPV6 0.049 0.25 1.2 10 -10000 0 10
CD28 -0.034 0.18 -10000 0 -0.51 27 27
SHC1 -0.02 0.18 0.31 5 -0.61 13 18
receptor internalization -0.023 0.2 -10000 0 -0.59 18 18
PRF1 -0.021 0.2 -10000 0 -0.77 10 10
KRAS 0.033 0.006 -10000 0 -10000 0 0
GRB2 0.033 0.007 -10000 0 -10000 0 0
COT/AKT1 -0.019 0.13 0.29 2 -0.35 15 17
LAT -0.023 0.17 0.36 1 -0.57 14 15
EntrezGene:6955 0 0.002 -10000 0 -10000 0 0
CD3D 0.012 0.11 -10000 0 -0.51 9 9
CD3E 0.034 0.006 -10000 0 -10000 0 0
CD3G 0.01 0.11 -10000 0 -0.49 10 10
RASGRP2 0.004 0.036 -10000 0 -0.16 8 8
RASGRP1 0.005 0.15 0.31 3 -0.42 13 16
HLA-A 0.022 0.082 -10000 0 -0.51 5 5
RASSF5 0.033 0.006 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.043 0.013 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.027 0.07 0.22 7 -0.13 5 12
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.02 0.061 -10000 0 -0.22 10 10
PRKCA 0.024 0.1 0.17 13 -0.27 10 23
GRAP2 0.032 0.009 -10000 0 -10000 0 0
mol:IP3 -0.027 0.11 -10000 0 -0.41 12 12
EntrezGene:6957 0.001 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.014 0.17 -10000 0 -0.56 14 14
ORAI1 -0.038 0.2 -10000 0 -1 9 9
CSK -0.025 0.18 -10000 0 -0.6 13 13
B7 family/CD28 -0.021 0.23 -10000 0 -0.63 20 20
CHUK 0.033 0.008 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.029 0.2 -10000 0 -0.65 15 15
PTPN6 -0.026 0.18 0.29 1 -0.58 15 16
VAV1 -0.043 0.21 0.26 1 -0.69 15 16
Monovalent TCR/CD3 -0.012 0.16 -10000 0 -0.49 17 17
CBL 0.034 0.005 -10000 0 -10000 0 0
LCK -0.034 0.19 0.24 1 -0.59 16 17
PAG1 -0.059 0.2 0.25 1 -0.57 16 17
RAP1A 0.032 0.008 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.029 0.2 -10000 0 -0.67 15 15
CD80 0.029 0.041 -10000 0 -0.32 3 3
CD86 0.007 0.12 -10000 0 -0.49 11 11
PDK1/CARD11/BCL10/MALT1 -0.015 0.078 -10000 0 -0.27 10 10
HRAS 0.034 0.005 -10000 0 -10000 0 0
GO:0035030 -0.044 0.18 -10000 0 -0.52 20 20
CD8A 0.001 0.003 -10000 0 -10000 0 0
CD8B 0.035 0.003 -10000 0 -10000 0 0
PTPRC 0.003 0.12 -10000 0 -0.51 12 12
PDK1/PKC theta -0.015 0.16 0.4 2 -0.53 13 15
CSK/PAG1 -0.055 0.19 0.25 1 -0.57 14 15
SOS1 0.034 0.002 -10000 0 -10000 0 0
peptide-MHC class I 0.024 0.11 -10000 0 -0.47 9 9
GRAP2/SLP76 0.001 0.18 -10000 0 -0.58 13 13
STIM1 -0.005 0.11 1.2 1 -0.94 1 2
RAS family/GTP 0.03 0.076 0.21 6 -0.18 5 11
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.027 0.22 -10000 0 -0.64 18 18
mol:DAG -0.033 0.096 -10000 0 -0.36 13 13
RAP1A/GDP 0.017 0.035 0.12 6 -10000 0 6
PLCG1 0.018 0.017 -10000 0 -10000 0 0
CD247 0.006 0.12 -10000 0 -0.51 11 11
cytotoxic T cell degranulation -0.019 0.2 -10000 0 -0.72 11 11
RAP1A/GTP 0.002 0.014 -10000 0 -0.064 6 6
mol:PI-3-4-5-P3 -0.025 0.16 0.28 2 -0.49 16 18
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.029 0.14 -10000 0 -0.53 12 12
NRAS 0.029 0.034 -10000 0 -0.32 2 2
ZAP70 0.034 0.002 -10000 0 -10000 0 0
GRB2/SOS1 0.049 0.01 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.019 0.17 0.24 2 -0.52 15 17
MALT1 0.024 0.016 -10000 0 -10000 0 0
TRAF6 0.034 0.005 -10000 0 -10000 0 0
CD8 heterodimer 0.025 0.008 -10000 0 -10000 0 0
CARD11 0.008 0.086 -10000 0 -0.32 14 14
PRKCB -0.025 0.068 -10000 0 -0.25 13 13
PRKCE 0.025 0.1 0.17 13 -0.26 11 24
PRKCQ -0.02 0.18 0.33 2 -0.59 14 16
LCP2 0.027 0.055 -10000 0 -0.36 4 4
BCL10 0.033 0.006 -10000 0 -10000 0 0
regulation of survival gene product expression -0.017 0.12 0.29 2 -0.35 16 18
IKK complex 0.039 0.074 0.14 43 -0.12 2 45
RAS family/GDP -0.001 0.011 -10000 0 -0.058 1 1
MAP3K14 -0.016 0.096 0.25 2 -0.27 13 15
PDPK1 -0.017 0.13 0.46 1 -0.4 14 15
TCR/CD3/MHC I/CD8/Fyn -0.029 0.2 -10000 0 -0.64 15 15
Presenilin action in Notch and Wnt signaling

Figure S40.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S40.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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) 0.026 0.12 -10000 0 -10000 0 0
HDAC1 0.039 0.012 -10000 0 -10000 0 0
AES 0.035 0.007 -10000 0 -10000 0 0
FBXW11 0.034 0.004 -10000 0 -10000 0 0
DTX1 0.034 0.004 -10000 0 -10000 0 0
LRP6/FZD1 0.045 0.023 -10000 0 -0.22 1 1
TLE1 0.035 0.005 -10000 0 -10000 0 0
AP1 -0.098 0.12 0.2 2 -0.3 47 49
NCSTN 0.033 0.006 -10000 0 -10000 0 0
ADAM10 0.032 0.009 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.006 0.11 -10000 0 -0.67 4 4
NICD/RBPSUH 0.023 0.12 -10000 0 -10000 0 0
WIF1 -0.019 0.12 -10000 0 -0.32 32 32
NOTCH1 0.001 0.12 -10000 0 -10000 0 0
PSENEN 0.033 0.007 -10000 0 -10000 0 0
KREMEN2 -0.03 0.14 -10000 0 -0.32 39 39
DKK1 -0.055 0.15 -10000 0 -0.32 54 54
beta catenin/beta TrCP1 0.076 0.07 0.33 2 -10000 0 2
APH1B 0.031 0.025 -10000 0 -0.32 1 1
APH1A 0.017 0.092 -10000 0 -0.48 7 7
AXIN1 -0.021 0.074 -10000 0 -0.49 2 2
CtBP/CBP/TCF1/TLE1/AES 0.056 0.041 -10000 0 -10000 0 0
PSEN1 0.031 0.01 -10000 0 -10000 0 0
FOS -0.027 0.16 -10000 0 -0.49 24 24
JUN 0.026 0.053 -10000 0 -0.32 5 5
MAP3K7 0.036 0.008 -10000 0 -10000 0 0
CTNNB1 0.06 0.071 0.3 3 -10000 0 3
MAPK3 0.029 0.052 -10000 0 -0.51 2 2
DKK2/LRP6/Kremen 2 -0.07 0.14 -10000 0 -0.34 19 19
HNF1A 0.036 0.004 -10000 0 -10000 0 0
CTBP1 0.035 0.007 -10000 0 -10000 0 0
MYC -0.099 0.11 -10000 0 -10000 0 0
NKD1 -0.23 0.15 -10000 0 -0.32 160 160
FZD1 0.032 0.008 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.024 0.12 -10000 0 -10000 0 0
apoptosis -0.098 0.12 0.2 2 -0.3 47 49
Delta 1/NOTCHprecursor 0.022 0.12 -10000 0 -10000 0 0
DLL1 0.033 0.007 -10000 0 -10000 0 0
PPARD 0.018 0.064 -10000 0 -0.86 1 1
Gamma Secretase 0.07 0.073 -10000 0 -0.27 4 4
APC -0.052 0.14 -10000 0 -0.46 18 18
DVL1 0.013 0.071 -10000 0 -0.59 2 2
CSNK2A1 0.026 0.014 -10000 0 -10000 0 0
MAP3K7IP1 0.003 0.004 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.04 0.14 -10000 0 -0.33 13 13
LRP6 0.031 0.025 -10000 0 -0.32 1 1
CSNK1A1 0.033 0.005 -10000 0 -10000 0 0
NLK 0.025 0.011 -10000 0 -10000 0 0
CCND1 -0.02 0.12 -10000 0 -0.8 3 3
WNT1 0.034 0.004 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.01 0.13 0.42 3 -0.44 4 7
DKK2 -0.11 0.17 -10000 0 -0.32 86 86
NOTCH1 precursor/DVL1 0.003 0.15 -10000 0 -0.52 9 9
GSK3B 0.033 0.024 -10000 0 -0.32 1 1
FRAT1 0.031 0.038 -10000 0 -0.51 1 1
NOTCH/Deltex homolog 1 0.027 0.12 -10000 0 -10000 0 0
PPP2R5D 0.12 0.07 0.24 2 -10000 0 2
MAPK1 0.032 0.009 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.044 0.088 -10000 0 -10000 0 0
RBPJ 0.033 0.006 -10000 0 -10000 0 0
CREBBP 0.028 0.008 -10000 0 -10000 0 0
p75(NTR)-mediated signaling

Figure S41.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S41.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.031 -10000 0 -0.37 1 1
Necdin/E2F1 -0.037 0.14 -10000 0 -0.37 28 28
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.055 0.054 -10000 0 -0.27 3 3
NGF (dimer)/p75(NTR)/BEX1 0.041 0.036 -10000 0 -0.31 2 2
NT-4/5 (dimer)/p75(NTR) 0.024 0.006 -10000 0 -10000 0 0
IKBKB 0.029 0.012 -10000 0 -10000 0 0
AKT1 0.023 0.029 -10000 0 -10000 0 0
IKBKG 0.033 0.006 -10000 0 -10000 0 0
BDNF 0.008 0.092 -10000 0 -0.32 16 16
MGDIs/NGR/p75(NTR)/LINGO1 0.044 0.065 -10000 0 -0.34 1 1
FURIN 0.032 0.009 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.043 0.071 -10000 0 -0.31 1 1
LINGO1 0.025 0.048 -10000 0 -0.32 4 4
Sortilin/TRAF6/NRIF 0.028 0.056 -10000 0 -10000 0 0
proBDNF (dimer) 0.008 0.092 -10000 0 -0.32 16 16
NTRK1 0.033 0.006 -10000 0 -10000 0 0
RTN4R 0.016 0.074 -10000 0 -0.32 10 10
neuron apoptosis 0.013 0.092 0.28 1 -0.4 3 4
IRAK1 0.03 0.034 -10000 0 -0.32 2 2
SHC1 0.018 0.005 -10000 0 -10000 0 0
ARHGDIA 0.033 0.007 -10000 0 -10000 0 0
RhoA/GTP 0.025 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.071 0.073 -10000 0 -0.27 4 4
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.042 0.078 -10000 0 -0.28 11 11
MAGEH1 0.009 0.11 -10000 0 -0.51 10 10
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.009 0.14 -10000 0 -0.29 38 38
Mammalian IAPs/DIABLO 0.048 0.07 -10000 0 -0.28 8 8
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.032 0.024 -10000 0 -0.32 1 1
APP 0.032 0.008 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.034 0.005 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.045 0.012 -10000 0 -10000 0 0
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest -0.004 0.042 0.2 6 -0.28 1 7
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.025 0.043 -10000 0 -10000 0 0
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.043 0.012 -10000 0 -10000 0 0
NCSTN 0.033 0.006 -10000 0 -10000 0 0
mol:GTP -0.047 0.15 -10000 0 -0.31 52 52
PSENEN 0.033 0.007 -10000 0 -10000 0 0
mol:ceramide 0.022 0.034 -10000 0 -0.28 1 1
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.022 0.038 -10000 0 -10000 0 0
p75(NTR)/beta APP 0.046 0.015 -10000 0 -10000 0 0
BEX1 0.029 0.052 -10000 0 -0.51 2 2
mol:GDP 0.004 0.001 -10000 0 -10000 0 0
NGF (dimer) -0.15 0.047 -10000 0 -0.2 4 4
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.06 0.068 -10000 0 -0.31 1 1
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
RAC1/GTP 0.035 0.014 -10000 0 -10000 0 0
MYD88 0.034 0.004 -10000 0 -10000 0 0
CHUK 0.033 0.008 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.046 0.15 -10000 0 -0.31 52 52
RHOB 0.015 0.081 -10000 0 -0.32 12 12
RHOA 0.034 0.005 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.022 0.041 -10000 0 -0.21 4 4
NT3 (dimer) 0.029 0.034 -10000 0 -0.32 2 2
TP53 0.001 0.06 0.3 1 -10000 0 1
PRDM4 0.024 0.035 -10000 0 -0.28 1 1
BDNF (dimer) -0.31 0.067 -10000 0 -0.33 192 192
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
SORT1 0.03 0.037 -10000 0 -0.51 1 1
activation of caspase activity 0.05 0.051 -10000 0 -0.27 3 3
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.058 0.031 -10000 0 -0.28 1 1
RHOC 0.033 0.008 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 0.019 0.074 0.28 4 -10000 0 4
DIABLO 0.034 0.003 -10000 0 -10000 0 0
SMPD2 0.022 0.034 -10000 0 -0.28 1 1
APH1B 0.031 0.025 -10000 0 -0.32 1 1
APH1A 0.017 0.092 -10000 0 -0.48 7 7
proNGF (dimer)/p75(NTR)/Sortilin 0.041 0.028 -10000 0 -0.31 1 1
PSEN1 0.031 0.01 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.045 0.028 -10000 0 -0.21 2 2
NT3 (dimer)/p75(NTR) 0.044 0.029 -10000 0 -0.22 2 2
MAPK8 0.022 0.07 0.28 4 -10000 0 4
MAPK9 0.021 0.069 0.34 2 -10000 0 2
APAF1 0.031 0.034 -10000 0 -0.32 2 2
NTF3 0.03 0.034 -10000 0 -0.32 2 2
NTF4 0 0 -10000 0 -10000 0 0
NDN -0.069 0.21 -10000 0 -0.51 40 40
RAC1/GDP 0.023 0.008 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.022 0.14 -10000 0 -0.26 51 51
p75 CTF/Sortilin/TRAF6/NRIF 0.08 0.034 -10000 0 -0.29 1 1
RhoA-B-C/GTP -0.047 0.15 -10000 0 -0.31 52 52
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.07 0.076 -10000 0 -0.27 1 1
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.059 0.073 -10000 0 -0.29 1 1
PRKACB -0.1 0.23 -10000 0 -0.51 53 53
proBDNF (dimer)/p75 ECD 0.03 0.071 -10000 0 -0.22 16 16
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.01 0.11 -10000 0 -0.47 10 10
BIRC2 0.033 0.006 -10000 0 -10000 0 0
neuron projection morphogenesis -0.091 0.14 -10000 0 -0.39 22 22
BAD 0.017 0.084 0.4 3 -10000 0 3
RIPK2 -0.012 0.11 -10000 0 -0.32 25 25
NGFR 0.033 0.008 -10000 0 -10000 0 0
CYCS 0.017 0.039 -10000 0 -0.27 2 2
ADAM17 0.034 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.026 0.073 -10000 0 -10000 0 0
BCL2L11 0.017 0.084 0.4 3 -10000 0 3
BDNF (dimer)/p75(NTR) 0.028 0.071 -10000 0 -10000 0 0
PI3K 0.06 0.019 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.054 0.036 -10000 0 -0.28 1 1
NDNL2 0.03 0.025 -10000 0 -0.32 1 1
YWHAE 0.027 0.014 -10000 0 -10000 0 0
PRKCI 0.026 0.053 -10000 0 -0.32 5 5
NGF (dimer)/p75(NTR) 0.024 0.006 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.057 0.034 -10000 0 -0.28 1 1
TRAF6 0.034 0.005 -10000 0 -10000 0 0
RAC1 0.031 0.011 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
PLG 0.033 0.007 -10000 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 0.014 0.047 -10000 0 -0.31 1 1
SQSTM1 0.034 0.004 -10000 0 -10000 0 0
NGFRAP1 0.024 0.073 -10000 0 -0.51 4 4
CASP3 0.016 0.083 0.39 3 -10000 0 3
E2F1 0.014 0.043 -10000 0 -0.32 3 3
CASP9 0.032 0.009 -10000 0 -10000 0 0
IKK complex 0.056 0.043 -10000 0 -10000 0 0
NGF (dimer)/TRKA 0.025 0.004 -10000 0 -10000 0 0
MMP7 -0.31 0.063 -10000 0 -0.32 208 208
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.07 0.035 -10000 0 -0.27 1 1
MMP3 -0.29 0.089 -10000 0 -0.32 200 200
APAF-1/Caspase 9 0.006 0.053 -10000 0 -10000 0 0
PLK1 signaling events

Figure S42.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S42.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.006 0.03 0.12 4 -0.12 1 5
BUB1B -0.014 0.07 0.14 1 -0.21 6 7
PLK1 0.019 0.034 0.098 5 -0.088 1 6
PLK1S1 0.007 0.018 0.056 4 -0.048 1 5
KIF2A 0.015 0.03 -10000 0 -10000 0 0
regulation of mitotic centrosome separation 0.019 0.034 0.1 4 -0.087 1 5
GOLGA2 0.034 0.005 -10000 0 -10000 0 0
Hec1/SPC24 0.025 0.034 -10000 0 -0.16 2 2
WEE1 0.013 0.064 -10000 0 -0.39 3 3
cytokinesis 0.012 0.064 -10000 0 -0.32 1 1
PP2A-alpha B56 0.025 0.12 -10000 0 -0.61 6 6
AURKA 0.027 0.032 0.12 2 -10000 0 2
PICH/PLK1 -0.085 0.14 0.18 11 -0.28 51 62
CENPE 0.008 0.044 -10000 0 -0.18 4 4
RhoA/GTP 0.025 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.015 0.03 -10000 0 -10000 0 0
PPP2CA 0.034 0.005 -10000 0 -10000 0 0
FZR1 0.033 0.006 -10000 0 -10000 0 0
TPX2 0.043 0.053 0.13 28 -10000 0 28
PAK1 0.034 0.005 -10000 0 -10000 0 0
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.034 0.004 -10000 0 -10000 0 0
CLSPN 0.014 0.044 -10000 0 -0.22 6 6
GORASP1 0.034 0.004 -10000 0 -10000 0 0
metaphase 0 0.003 0.019 5 -0.011 1 6
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.007 0.018 0.056 4 -0.048 1 5
G2 phase of mitotic cell cycle 0.001 0.003 0.017 3 -10000 0 3
STAG2 0.024 0.058 -10000 0 -0.32 6 6
GRASP65/GM130/RAB1/GTP 0.01 0.065 -10000 0 -0.52 3 3
spindle elongation 0.019 0.034 0.1 4 -0.087 1 5
ODF2 0.036 0.006 -10000 0 -10000 0 0
BUB1 -0.012 0.12 -10000 0 -0.66 6 6
TPT1 0.027 0.038 0.13 2 -0.19 2 4
CDC25C 0.016 0.041 -10000 0 -0.25 3 3
CDC25B -0.099 0.16 -10000 0 -0.32 77 77
SGOL1 0.006 0.03 0.12 1 -0.12 4 5
RHOA 0.034 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 -0.038 0.094 -10000 0 -0.21 23 23
CDC14B 0.01 0.003 -10000 0 -10000 0 0
CDC20 0.024 0.058 -10000 0 -0.32 6 6
PLK1/PBIP1 0.001 0.054 0.1 2 -0.15 17 19
mitosis -0.002 0.003 -10000 0 -10000 0 0
FBXO5 0 0.049 0.22 2 -0.14 5 7
CDC2 -0.002 0.006 0.01 14 -0.011 25 39
NDC80 0.023 0.036 -10000 0 -0.32 2 2
metaphase plate congression 0 0.075 -10000 0 -0.23 20 20
ERCC6L -0.08 0.13 0.19 1 -0.28 40 41
NLP/gamma Tubulin 0.009 0.02 0.085 4 -10000 0 4
microtubule cytoskeleton organization 0.027 0.038 0.13 2 -0.19 2 4
G2/M transition DNA damage checkpoint 0 0.002 0.014 3 -10000 0 3
PPP1R12A 0.035 0.004 -10000 0 -10000 0 0
interphase 0 0.002 0.014 3 -10000 0 3
PLK1/PRC1-2 0.025 0.084 -10000 0 -0.28 3 3
GRASP65/GM130/RAB1/GTP/PLK1 0.068 0.03 -10000 0 -10000 0 0
RAB1A 0.034 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.024 0.035 0.076 32 -10000 0 32
mitotic prometaphase 0.001 0.006 0.018 20 -10000 0 20
proteasomal ubiquitin-dependent protein catabolic process 0.027 0.059 -10000 0 -0.47 2 2
microtubule-based process 0.013 0.073 -10000 0 -0.17 23 23
Golgi organization 0.019 0.034 0.1 4 -0.087 1 5
Cohesin/SA2 0.029 0.037 -10000 0 -0.15 1 1
PPP1CB/MYPT1 0.051 0.007 -10000 0 -10000 0 0
KIF20A -0.011 0.12 -10000 0 -0.32 27 27
APC/C/CDC20 0.031 0.048 -10000 0 -0.18 6 6
PPP2R1A 0.034 0.005 -10000 0 -10000 0 0
chromosome segregation 0.001 0.053 0.1 2 -0.14 17 19
PRC1 0.024 0.053 -10000 0 -0.32 5 5
ECT2 -0.077 0.091 0.19 2 -0.17 57 59
C13orf34 0.019 0.03 0.079 7 -10000 0 7
NUDC 0 0.075 -10000 0 -0.23 20 20
regulation of attachment of spindle microtubules to kinetochore -0.014 0.069 0.14 1 -0.21 6 7
spindle assembly 0.014 0.03 0.12 5 -10000 0 5
spindle stabilization 0.007 0.018 0.056 4 -0.048 1 5
APC/C/HCDH1 0.032 0.007 -10000 0 -10000 0 0
MKLP2/PLK1 0.013 0.073 -10000 0 -0.17 23 23
CCNB1 -0.042 0.14 -10000 0 -0.32 46 46
PPP1CB 0.035 0.001 -10000 0 -10000 0 0
BTRC 0.033 0.008 -10000 0 -10000 0 0
ROCK2 0.027 0.034 -10000 0 -0.27 1 1
TUBG1 0.017 0.023 0.12 1 -0.15 1 2
G2/M transition of mitotic cell cycle -0.036 0.1 0.17 15 -0.21 20 35
MLF1IP -0.014 0.07 -10000 0 -0.22 22 22
INCENP 0.028 0.042 -10000 0 -0.32 3 3
Glucocorticoid receptor regulatory network

Figure S43.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S43.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.054 0.095 -10000 0 -0.75 1 1
SMARCC2 0.034 0.004 -10000 0 -10000 0 0
SMARCC1 0.027 0.048 -10000 0 -0.32 4 4
TBX21 -0.3 0.39 -10000 0 -0.87 65 65
SUMO2 0.033 0.011 -10000 0 -10000 0 0
STAT1 (dimer) 0.01 0.1 -10000 0 -0.31 19 19
FKBP4 0.033 0.007 -10000 0 -10000 0 0
FKBP5 0.034 0.005 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90 0.086 0.14 0.32 11 -0.31 11 22
PRL -0.028 0.096 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.18 0.23 0.54 36 -10000 0 36
RELA -0.074 0.059 -10000 0 -10000 0 0
FGG 0.12 0.18 0.46 18 -10000 0 18
GR beta/TIF2 0.079 0.15 0.32 15 -0.34 13 28
IFNG -0.15 0.18 -10000 0 -0.59 11 11
apoptosis 0.039 0.13 0.53 2 -0.53 2 4
CREB1 0.043 0.003 -10000 0 -10000 0 0
histone acetylation -0.051 0.1 -10000 0 -0.32 9 9
BGLAP -0.046 0.11 -10000 0 -0.42 1 1
GR/PKAc 0.015 0.2 0.34 7 -0.32 31 38
NF kappa B1 p50/RelA -0.13 0.096 -10000 0 -0.37 4 4
SMARCD1 0.034 0.004 -10000 0 -10000 0 0
MDM2 0.073 0.067 0.23 17 -10000 0 17
GATA3 0.038 0.028 -10000 0 -10000 0 0
AKT1 0.026 0.017 0.24 1 -10000 0 1
CSF2 -0.12 0.14 -10000 0 -0.54 2 2
GSK3B 0.032 0.026 -10000 0 -0.32 1 1
NR1I3 0.041 0.12 0.57 1 -10000 0 1
CSN2 0.09 0.15 0.37 15 -0.32 1 16
BRG1/BAF155/BAF170/BAF60A 0.081 0.038 -10000 0 -10000 0 0
NFATC1 0.027 0.031 -10000 0 -0.31 1 1
POU2F1 0.039 0.01 -10000 0 -10000 0 0
CDKN1A -0.036 0.21 -10000 0 -1.6 3 3
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.005 -10000 0 -10000 0 0
SFN 0.026 0.053 -10000 0 -0.51 2 2
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.089 0.14 0.33 9 -0.31 10 19
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.019 0.19 0.54 1 -0.86 7 8
JUN -0.093 0.12 -10000 0 -0.42 7 7
IL4 -0.048 0.11 -10000 0 -0.47 3 3
CDK5R1 0.033 0.008 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.042 0.14 -10000 0 -0.32 20 20
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.097 0.14 0.33 9 -0.29 10 19
cortisol/GR alpha (monomer) 0.21 0.27 0.61 43 -0.4 2 45
NCOA2 0.03 0.012 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.063 0.16 -10000 0 -0.51 24 24
AP-1/NFAT1-c-4 -0.15 0.16 -10000 0 -0.56 8 8
AFP -0.058 0.1 -10000 0 -10000 0 0
SUV420H1 0.034 0.005 -10000 0 -10000 0 0
IRF1 0.097 0.15 0.47 2 -1 1 3
TP53 0.024 0.082 -10000 0 -0.45 2 2
PPP5C 0.032 0.025 -10000 0 -0.32 1 1
KRT17 -0.12 0.17 -10000 0 -0.6 8 8
KRT14 -0.062 0.1 -10000 0 -10000 0 0
TBP 0.041 0.009 -10000 0 -10000 0 0
CREBBP 0.035 0.015 -10000 0 -10000 0 0
HDAC1 0.031 0.016 -10000 0 -10000 0 0
HDAC2 0.042 0.014 -10000 0 -10000 0 0
AP-1 -0.15 0.16 -10000 0 -0.56 8 8
MAPK14 0.034 0.006 -10000 0 -10000 0 0
MAPK10 0.026 0.062 -10000 0 -0.41 4 4
MAPK11 0.029 0.027 -10000 0 -0.32 1 1
KRT5 -0.12 0.16 -10000 0 -0.61 4 4
interleukin-1 receptor activity 0.009 0.01 -10000 0 -10000 0 0
NCOA1 0.031 0.053 -10000 0 -0.5 2 2
STAT1 0.01 0.1 -10000 0 -0.31 19 19
CGA -0.048 0.11 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.076 0.15 0.4 10 -0.36 2 12
MAPK3 0.029 0.052 -10000 0 -0.5 2 2
MAPK1 0.032 0.01 -10000 0 -10000 0 0
ICAM1 -0.15 0.17 -10000 0 -0.55 15 15
NFKB1 -0.073 0.058 -10000 0 -10000 0 0
MAPK8 -0.091 0.14 0.43 1 -0.4 17 18
MAPK9 0.034 0.006 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.036 0.13 0.53 2 -0.55 2 4
BAX -0.016 0.087 -10000 0 -10000 0 0
POMC -0.072 0.16 -10000 0 -1.3 1 1
EP300 0.035 0.017 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 0.16 0.24 0.55 33 -10000 0 33
proteasomal ubiquitin-dependent protein catabolic process 0.049 0.079 0.33 10 -10000 0 10
SGK1 0.031 0.066 -10000 0 -0.22 1 1
IL13 -0.094 0.14 -10000 0 -0.74 1 1
IL6 -0.2 0.2 -10000 0 -0.58 21 21
PRKACG 0.034 0.005 -10000 0 -10000 0 0
IL5 -0.09 0.14 -10000 0 -0.6 2 2
IL2 -0.12 0.16 -10000 0 -0.59 5 5
CDK5 0.03 0.034 -10000 0 -0.32 2 2
PRKACB -0.1 0.23 -10000 0 -0.51 53 53
HSP90AA1 0.031 0.011 -10000 0 -10000 0 0
IL8 -0.28 0.16 -10000 0 -0.56 28 28
CDK5R1/CDK5 0.044 0.03 -10000 0 -0.22 2 2
NF kappa B1 p50/RelA/PKAc -0.14 0.15 -10000 0 -0.43 27 27
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.18 0.22 0.53 33 -10000 0 33
SMARCA4 0.034 0.004 -10000 0 -10000 0 0
chromatin remodeling 0.1 0.14 0.36 19 -0.34 2 21
NF kappa B1 p50/RelA/Cbp -0.074 0.088 -10000 0 -0.35 1 1
JUN (dimer) -0.093 0.12 -10000 0 -0.42 7 7
YWHAH 0.032 0.008 -10000 0 -10000 0 0
VIPR1 -0.16 0.29 -10000 0 -0.87 28 28
NR3C1 0.098 0.22 0.43 24 -0.43 21 45
NR4A1 0.034 0.061 -10000 0 -0.44 3 3
TIF2/SUV420H1 0.043 0.019 -10000 0 -10000 0 0
MAPKKK cascade 0.039 0.13 0.53 2 -0.53 2 4
cortisol/GR alpha (dimer)/Src-1 0.2 0.24 0.54 42 -0.41 2 44
PBX1 0.029 0.074 -10000 0 -0.5 4 4
POU1F1 0.038 0.038 -10000 0 -0.5 1 1
SELE -0.18 0.2 -10000 0 -0.6 21 21
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.1 0.15 0.36 19 -0.34 2 21
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.18 0.22 0.53 33 -10000 0 33
mol:cortisol 0.12 0.13 0.35 37 -10000 0 37
MMP1 -0.22 0.12 -10000 0 -0.78 4 4
Glypican 2 network

Figure S44.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S44.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.014 0.081 -9999 0 -0.32 12 12
GPC2 0 0 -9999 0 -10000 0 0
GPC2/Midkine 0.012 0.055 -9999 0 -0.22 12 12
neuron projection morphogenesis 0.012 0.055 -9999 0 -0.22 12 12
Aurora B signaling

Figure S45.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S45.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.003 0.056 -9999 0 -0.23 2 2
STMN1 0.013 0.018 -9999 0 -0.22 1 1
Aurora B/RasGAP/Survivin 0.029 0.078 -9999 0 -0.24 3 3
Chromosomal passenger complex/Cul3 protein complex -0.062 0.12 -9999 0 -0.32 20 20
BIRC5 -0.002 0.1 -9999 0 -0.32 21 21
DES -0.14 0.32 -9999 0 -0.69 52 52
Aurora C/Aurora B/INCENP 0.047 0.037 -9999 0 -10000 0 0
Aurora B/TACC1 0.034 0.021 -9999 0 -10000 0 0
Aurora B/PP2A 0.039 0.022 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.01 0.01 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition 0.003 0.004 -9999 0 -10000 0 0
NDC80 0.011 0.025 -9999 0 -0.22 2 2
Cul3 protein complex -0.044 0.17 -9999 0 -0.31 54 54
KIF2C -0.003 0.06 -9999 0 -0.34 3 3
PEBP1 0.034 0.004 -9999 0 -10000 0 0
KIF20A -0.008 0.12 -9999 0 -0.32 27 27
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP 0.037 0.033 -9999 0 -0.22 2 2
SEPT1 0.033 0.006 -9999 0 -10000 0 0
SMC2 0.016 0.077 -9999 0 -0.32 11 11
SMC4 0.031 0.034 -9999 0 -0.32 2 2
NSUN2/NPM1/Nucleolin -0.081 0.21 -9999 0 -0.48 45 45
PSMA3 0.031 0.01 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.004 -9999 0 -10000 0 0
H3F3B 0.016 0.008 -9999 0 -10000 0 0
AURKB 0.027 0.015 -9999 0 -10000 0 0
AURKC 0.033 0.006 -9999 0 -10000 0 0
CDCA8 0.029 0.035 -9999 0 -0.32 2 2
cytokinesis -0.028 0.13 -9999 0 -0.41 15 15
Aurora B/Septin1 -0.027 0.14 -9999 0 -0.4 13 13
AURKA 0.012 0.048 -9999 0 -0.32 4 4
INCENP 0.028 0.042 -9999 0 -0.32 3 3
KLHL13 -0.13 0.24 -9999 0 -0.47 71 71
BUB1 -0.098 0.17 -9999 0 -0.32 82 82
hSgo1/Aurora B/Survivin 0.02 0.084 -9999 0 -0.32 4 4
EVI5 0.033 0.006 -9999 0 -10000 0 0
RhoA/GTP -0.009 0.13 -9999 0 -0.32 15 15
SGOL1 0.015 0.077 -9999 0 -0.32 11 11
CENPA 0.003 0.092 -9999 0 -0.27 9 9
NCAPG 0 0 -9999 0 -10000 0 0
Aurora B/HC8 Proteasome 0.04 0.021 -9999 0 -10000 0 0
NCAPD2 0.032 0.008 -9999 0 -10000 0 0
Aurora B/PP1-gamma 0.04 0.021 -9999 0 -10000 0 0
RHOA 0.034 0.005 -9999 0 -10000 0 0
NCAPH 0.021 0.066 -9999 0 -0.32 8 8
NPM1 -0.044 0.13 -9999 0 -0.35 11 11
RASA1 0.03 0.034 -9999 0 -0.32 2 2
KLHL9 0.033 0.006 -9999 0 -10000 0 0
mitotic prometaphase -0.001 0.003 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.04 0.021 -9999 0 -10000 0 0
PPP1CC 0.034 0.003 -9999 0 -10000 0 0
Centraspindlin -0.021 0.13 -9999 0 -0.33 19 19
RhoA/GDP 0.025 0.003 -9999 0 -10000 0 0
NSUN2 -0.04 0.13 -9999 0 -0.35 10 10
MYLK -0.023 0.12 -9999 0 -0.38 21 21
KIF23 -0.019 0.12 -9999 0 -0.32 31 31
VIM 0.009 0.046 -9999 0 -0.37 3 3
RACGAP1 0.017 0.075 -9999 0 -0.32 10 10
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.043 0.14 -9999 0 -0.48 4 4
Chromosomal passenger complex -0.018 0.085 -9999 0 -0.31 7 7
Chromosomal passenger complex/EVI5 0.049 0.09 -9999 0 -0.3 3 3
TACC1 0.03 0.012 -9999 0 -10000 0 0
PPP2R5D 0.033 0.006 -9999 0 -10000 0 0
CUL3 0.034 0.002 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
PLK2 and PLK4 events

Figure S46.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S46.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.022 0.062 -9999 0 -0.32 7 7
PLK4 0.024 0.058 -9999 0 -0.32 6 6
regulation of centriole replication 0.004 0.056 -9999 0 -0.22 13 13
Osteopontin-mediated events

Figure S47.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S47.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.088 0.099 -10000 0 -0.33 1 1
NF kappa B1 p50/RelA/I kappa B alpha -0.079 0.11 0.42 1 -0.38 1 2
alphaV/beta3 Integrin/Osteopontin/Src -0.13 0.13 -10000 0 -0.24 51 51
AP1 -0.1 0.13 -10000 0 -0.4 2 2
ILK -0.091 0.097 -10000 0 -0.33 1 1
bone resorption -0.078 0.098 0.34 1 -10000 0 1
PTK2B 0.026 0.015 -10000 0 -10000 0 0
PYK2/p130Cas -0.07 0.11 -10000 0 -0.3 1 1
ITGAV 0.034 0.025 -10000 0 -0.32 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.04 0.051 -10000 0 -0.22 8 8
alphaV/beta3 Integrin/Osteopontin -0.094 0.12 -10000 0 -0.36 1 1
MAP3K1 -0.093 0.098 -10000 0 -0.33 1 1
JUN 0.026 0.053 -10000 0 -0.32 5 5
MAPK3 -0.1 0.098 -10000 0 -0.4 3 3
MAPK1 -0.096 0.094 -10000 0 -0.35 1 1
Rac1/GDP 0.023 0.008 -10000 0 -10000 0 0
NFKB1 0.033 0.006 -10000 0 -10000 0 0
MAPK8 -0.087 0.089 -10000 0 -0.32 1 1
ITGB3 0.034 0.008 -10000 0 -10000 0 0
NFKBIA -0.089 0.09 -10000 0 -0.34 2 2
FOS -0.027 0.16 -10000 0 -0.49 24 24
CD44 0.021 0.067 -10000 0 -0.32 8 8
CHUK 0.033 0.008 -10000 0 -10000 0 0
PLAU -0.12 0.15 0.46 1 -0.58 2 3
NF kappa B1 p50/RelA -0.083 0.12 -10000 0 -0.44 1 1
BCAR1 0.033 0.006 -10000 0 -10000 0 0
RELA 0.034 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.05 0.023 -10000 0 -0.23 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.094 0.097 -10000 0 -0.33 1 1
VAV3 -0.13 0.14 -10000 0 -0.42 28 28
MAP3K14 -0.098 0.097 -10000 0 -0.35 1 1
ROCK2 0.034 0.002 -10000 0 -10000 0 0
SPP1 -0.2 0.16 -10000 0 -0.32 144 144
RAC1 0.031 0.011 -10000 0 -10000 0 0
Rac1/GTP -0.11 0.13 -10000 0 -0.39 26 26
MMP2 -0.1 0.1 -10000 0 -0.42 2 2
PDGFR-alpha signaling pathway

Figure S48.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S48.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.021 0.07 -10000 0 -0.51 3 3
PDGF/PDGFRA/CRKL 0.039 0.053 -10000 0 -0.36 3 3
positive regulation of JUN kinase activity 0.074 0.049 -10000 0 -0.27 3 3
CRKL 0.032 0.009 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 0.042 0.053 -10000 0 -0.36 3 3
AP1 -0.07 0.29 -10000 0 -0.79 26 26
mol:IP3 0.015 0.075 0.23 12 -0.37 3 15
PLCG1 0.015 0.075 0.23 12 -0.37 3 15
PDGF/PDGFRA/alphaV Integrin 0.041 0.055 -10000 0 -0.32 4 4
RAPGEF1 0.034 0.005 -10000 0 -10000 0 0
CRK 0.027 0.014 -10000 0 -10000 0 0
mol:Ca2+ 0.015 0.075 0.23 12 -0.37 3 15
CAV3 0.033 0.006 -10000 0 -10000 0 0
CAV1 0.025 0.055 -10000 0 -0.36 4 4
SHC/Grb2/SOS1 0.077 0.05 -10000 0 -0.27 3 3
PDGF/PDGFRA/Shf -0.007 0.11 -10000 0 -0.24 39 39
FOS -0.097 0.27 0.32 5 -0.78 26 31
JUN -0.016 0.041 -10000 0 -0.26 1 1
oligodendrocyte development 0.041 0.055 -10000 0 -0.32 4 4
GRB2 0.033 0.007 -10000 0 -10000 0 0
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
mol:DAG 0.015 0.075 0.23 12 -0.37 3 15
PDGF/PDGFRA 0.021 0.07 -10000 0 -0.51 3 3
actin cytoskeleton reorganization 0.032 0.072 -10000 0 -0.26 11 11
SRF 0.01 0.017 -10000 0 -10000 0 0
SHC1 0.033 0.006 -10000 0 -10000 0 0
PI3K 0.064 0.041 -10000 0 -0.3 2 2
PDGF/PDGFRA/Crk/C3G 0.05 0.053 -10000 0 -0.3 3 3
JAK1 0.011 0.048 -10000 0 -0.36 3 3
ELK1/SRF 0.04 0.084 0.31 3 -0.29 3 6
SHB 0.021 0.067 -10000 0 -0.32 8 8
SHF -0.029 0.13 -10000 0 -0.32 37 37
CSNK2A1 0.019 0.028 -10000 0 -10000 0 0
GO:0007205 0.012 0.081 0.24 15 -0.39 3 18
SOS1 0.034 0.002 -10000 0 -10000 0 0
Ras protein signal transduction 0.074 0.049 -10000 0 -0.27 3 3
PDGF/PDGFRA/SHB 0.032 0.072 -10000 0 -0.26 11 11
PDGF/PDGFRA/Caveolin-1 0.034 0.067 -10000 0 -0.3 7 7
ITGAV 0.033 0.024 -10000 0 -0.32 1 1
ELK1 0.028 0.1 0.24 32 -0.32 4 36
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk 0.033 0.054 -10000 0 -0.36 3 3
JAK-STAT cascade 0.011 0.048 -10000 0 -0.36 3 3
cell proliferation -0.007 0.11 -10000 0 -0.24 39 39
amb2 Integrin signaling

Figure S49.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S49.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.034 0.076 -10000 0 -0.37 4 4
alphaM/beta2 Integrin/GPIbA 0.029 0.071 -10000 0 -0.36 4 4
alphaM/beta2 Integrin/proMMP-9 0.018 0.064 -10000 0 -0.33 3 3
PLAUR 0.032 0.025 -10000 0 -0.32 1 1
HMGB1 0.003 0.036 -10000 0 -0.34 1 1
alphaM/beta2 Integrin/Talin 0.036 0.073 -10000 0 -0.37 4 4
AGER 0.005 0.035 -10000 0 -10000 0 0
RAP1A 0.032 0.008 -10000 0 -10000 0 0
SELPLG 0.027 0.063 -10000 0 -0.51 3 3
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.004 0.09 -10000 0 -0.34 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.008 0.064 -10000 0 -0.35 6 6
CYR61 0.005 0.096 -10000 0 -0.32 17 17
TLN1 0.033 0.006 -10000 0 -10000 0 0
Rap1/GTP 0.021 0.092 -10000 0 -0.44 4 4
RHOA 0.034 0.005 -10000 0 -10000 0 0
P-selectin oligomer -0.034 0.18 -10000 0 -0.5 27 27
MYH2 0.001 0.089 -10000 0 -0.41 5 5
MST1R 0.034 0.004 -10000 0 -10000 0 0
leukocyte activation during inflammatory response 0.049 0.063 -10000 0 -0.32 4 4
APOB 0.034 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.03 0.034 -10000 0 -0.32 2 2
JAM3 0.033 0.006 -10000 0 -10000 0 0
GP1BA 0.027 0.014 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CTGF 0.033 0.076 -10000 0 -0.37 4 4
alphaM/beta2 Integrin 0.005 0.089 -10000 0 -0.56 3 3
JAM3 homodimer 0.033 0.006 -10000 0 -10000 0 0
ICAM2 0.023 0.068 -10000 0 -0.46 4 4
ICAM1 0.015 0.077 -10000 0 -0.32 11 11
phagocytosis triggered by activation of immune response cell surface activating receptor 0.005 0.088 -10000 0 -0.55 3 3
cell adhesion 0.028 0.07 -10000 0 -0.36 4 4
NFKB1 0.005 0.14 0.43 3 -0.36 1 4
THY1 -0.011 0.12 -10000 0 -0.32 27 27
RhoA/GDP 0.025 0.003 -10000 0 -10000 0 0
Lipoprotein(a) 0.044 0.01 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA 0.049 0.075 -10000 0 -0.33 5 5
IL6 -0.053 0.16 -10000 0 -0.47 1 1
ITGB2 -0.005 0.076 -10000 0 -0.5 4 4
elevation of cytosolic calcium ion concentration -0.012 0.13 -10000 0 -0.32 6 6
alphaM/beta2 Integrin/JAM2/JAM3 -0.13 0.18 -10000 0 -0.3 108 108
JAM2 -0.25 0.27 -10000 0 -0.51 114 114
alphaM/beta2 Integrin/ICAM1 0.048 0.1 -10000 0 -0.32 6 6
alphaM/beta2 Integrin/uPA/Plg -0.01 0.13 -10000 0 -0.31 6 6
RhoA/GTP 0.003 0.091 -10000 0 -0.35 8 8
positive regulation of phagocytosis -0.002 0.088 -10000 0 -0.52 3 3
Ron/MSP 0.038 0.057 -10000 0 -0.22 10 10
alphaM/beta2 Integrin/uPAR/uPA -0.01 0.13 -10000 0 -0.32 6 6
alphaM/beta2 Integrin/uPAR 0.035 0.074 -10000 0 -0.37 4 4
PLAU -0.067 0.16 -10000 0 -0.32 61 61
PLAT 0.025 0.045 -10000 0 -0.41 2 2
actin filament polymerization 0 0.088 -10000 0 -0.4 5 5
MST1 0.018 0.074 -10000 0 -0.32 10 10
alphaM/beta2 Integrin/lipoprotein(a) 0.054 0.065 -10000 0 -0.32 4 4
TNF -0.004 0.12 0.38 1 -10000 0 1
RAP1B 0.034 0.004 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.031 0.13 -10000 0 -0.27 17 17
fibrinolysis -0.012 0.13 -10000 0 -0.31 6 6
HCK 0.004 0.088 -10000 0 -0.51 6 6
dendritic cell antigen processing and presentation 0.005 0.088 -10000 0 -0.55 3 3
VTN 0.033 0.008 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CYR61 0.016 0.098 -10000 0 -0.33 6 6
LPA 0.033 0.007 -10000 0 -10000 0 0
LRP1 0.034 0.004 -10000 0 -10000 0 0
cell migration 0.013 0.064 -10000 0 -0.31 5 5
FN1 -0.005 0.11 -10000 0 -0.32 24 24
alphaM/beta2 Integrin/Thy1 0.006 0.11 -10000 0 -0.32 7 7
MPO 0.013 0.081 -10000 0 -0.32 12 12
KNG1 0.02 0.085 -10000 0 -0.47 6 6
RAP1/GDP 0.043 0.012 -10000 0 -10000 0 0
ROCK1 0.005 0.084 -10000 0 -0.4 4 4
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.033 0.007 -10000 0 -10000 0 0
CTGF 0.03 0.034 -10000 0 -0.32 2 2
alphaM/beta2 Integrin/Hck 0.016 0.079 -10000 0 -0.36 7 7
ITGAM 0 0.06 -10000 0 -0.5 2 2
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.013 0.15 -10000 0 -0.33 30 30
HP 0.033 0.006 -10000 0 -10000 0 0
leukocyte adhesion -0.14 0.14 -10000 0 -0.33 45 45
SELP -0.034 0.18 -10000 0 -0.51 27 27
Ephrin B reverse signaling

Figure S50.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S50.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.022 0.039 -10000 0 -0.51 1 1
EPHB2 0.02 0.065 -10000 0 -0.35 6 6
EFNB1 0.014 0.025 -10000 0 -0.22 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.005 0.11 -10000 0 -0.31 3 3
Ephrin B2/EPHB1-2 -0.019 0.097 -10000 0 -0.3 4 4
neuron projection morphogenesis -0.018 0.097 -10000 0 -0.28 6 6
Ephrin B1/EPHB1-2/Tiam1 -0.02 0.12 -10000 0 -0.31 7 7
DNM1 0.03 0.034 -10000 0 -0.32 2 2
cell-cell signaling -0.001 0.005 -10000 0 -10000 0 0
MAP2K4 -0.014 0.08 -10000 0 -0.46 5 5
YES1 -0.028 0.13 -10000 0 -0.68 6 6
Ephrin B1/EPHB1-2/NCK2 -0.016 0.12 -10000 0 -0.29 6 6
PI3K 0.017 0.093 -10000 0 -0.42 6 6
mol:GDP -0.02 0.12 -10000 0 -0.3 7 7
ITGA2B 0.033 0.007 -10000 0 -10000 0 0
endothelial cell proliferation 0.002 0.076 -10000 0 -0.18 28 28
FYN -0.019 0.13 -10000 0 -0.66 7 7
MAP3K7 -0.019 0.079 -10000 0 -0.5 5 5
FGR -0.017 0.11 -10000 0 -0.67 5 5
TIAM1 0.027 0.052 -10000 0 -0.51 2 2
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
RGS3 0.034 0.005 -10000 0 -10000 0 0
cell adhesion 0.01 0.081 -10000 0 -0.43 4 4
LYN -0.015 0.12 -10000 0 -0.67 6 6
Ephrin B1/EPHB1-2/Src Family Kinases -0.02 0.11 -10000 0 -0.57 7 7
Ephrin B1/EPHB1-2 -0.018 0.074 -10000 0 -0.59 3 3
SRC -0.019 0.11 -10000 0 -0.64 6 6
ITGB3 0.033 0.007 -10000 0 -10000 0 0
EPHB1 -0.093 0.17 -10000 0 -0.32 78 78
EPHB4 -0.021 0.13 -10000 0 -0.32 33 33
RAC1 0.031 0.011 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.002 0.076 -10000 0 -0.18 28 28
alphaIIb/beta3 Integrin 0.049 0.011 -10000 0 -10000 0 0
BLK -0.055 0.13 -10000 0 -0.79 4 4
HCK -0.017 0.095 -10000 0 -0.74 3 3
regulation of stress fiber formation 0.017 0.11 0.29 6 -10000 0 6
MAPK8 -0.014 0.082 -10000 0 -0.47 4 4
Ephrin B1/EPHB1-2/RGS3 -0.017 0.11 -10000 0 -0.29 6 6
endothelial cell migration 0.01 0.13 0.3 12 -0.5 3 15
NCK2 0.034 0 -10000 0 -10000 0 0
PTPN13 -0.071 0.16 -10000 0 -0.3 65 65
regulation of focal adhesion formation 0.017 0.11 0.29 6 -10000 0 6
chemotaxis 0.018 0.11 0.29 6 -10000 0 6
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
Rac1/GTP -0.012 0.1 -10000 0 -0.29 5 5
angiogenesis -0.018 0.074 -10000 0 -0.59 3 3
LCK -0.018 0.12 -10000 0 -0.67 6 6
Integrins in angiogenesis

Figure S51.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S51.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.027 0.072 -10000 0 -0.22 16 16
alphaV beta3 Integrin 0.052 0.069 -10000 0 -0.31 6 6
PTK2 0.062 0.11 0.37 7 -10000 0 7
IGF1R 0.032 0.009 -10000 0 -10000 0 0
PI4KB 0.034 0.005 -10000 0 -10000 0 0
MFGE8 0.032 0.009 -10000 0 -10000 0 0
SRC 0.019 0.017 -10000 0 -10000 0 0
CDKN1B 0.026 0.026 -10000 0 -10000 0 0
VEGFA 0.006 0.095 -10000 0 -0.32 17 17
ILK 0.027 0.026 -10000 0 -10000 0 0
ROCK1 0.027 0.014 -10000 0 -10000 0 0
AKT1 0.018 0.024 -10000 0 -10000 0 0
PTK2B 0.012 0.054 0.35 1 -10000 0 1
alphaV/beta3 Integrin/JAM-A 0.062 0.066 -10000 0 -0.27 5 5
CBL 0.034 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.064 0.025 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.13 0.18 -10000 0 -0.29 122 122
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.017 0.066 -10000 0 -0.35 2 2
alphaV/beta3 Integrin/Syndecan-1 0.065 0.023 -10000 0 -10000 0 0
PI4KA 0.032 0.009 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.14 0.18 -10000 0 -0.42 22 22
PI4 Kinase 0.046 0.015 -10000 0 -10000 0 0
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.099 0.12 -10000 0 -0.28 2 2
RPS6KB1 -0.15 0.14 -10000 0 -0.4 21 21
TLN1 0.033 0.006 -10000 0 -10000 0 0
MAPK3 -0.052 0.14 -10000 0 -0.53 13 13
GPR124 0.026 0.035 -10000 0 -0.32 2 2
MAPK1 -0.056 0.14 -10000 0 -0.52 15 15
PXN 0.034 0.003 -10000 0 -10000 0 0
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.062 0.033 -10000 0 -10000 0 0
cell adhesion 0.055 0.028 -10000 0 -10000 0 0
ANGPTL3 0.034 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.028 0.054 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.032 0.009 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.008 -10000 0 -10000 0 0
TGFBR2 0.034 0.003 -10000 0 -10000 0 0
ITGB3 0.033 0.007 -10000 0 -10000 0 0
IGF1 -0.28 0.27 -10000 0 -0.51 123 123
RAC1 0.031 0.011 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.053 0.038 -10000 0 -10000 0 0
apoptosis 0.033 0.024 -10000 0 -0.32 1 1
CD47 0.034 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.064 0.024 -10000 0 -10000 0 0
VCL 0.033 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.023 0.12 -10000 0 -0.31 23 23
CSF1 0.033 0.007 -10000 0 -10000 0 0
PIK3C2A 0.024 0.033 -10000 0 -10000 0 0
PI4 Kinase/Pyk2 0.019 0.07 -10000 0 -0.35 1 1
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.06 0.07 -10000 0 -10000 0 0
FAK1/Vinculin 0.076 0.1 0.32 8 -10000 0 8
alphaV beta3/Integrin/ppsTEM5 0.054 0.039 -10000 0 -10000 0 0
RHOA 0.034 0.005 -10000 0 -10000 0 0
VTN 0.033 0.008 -10000 0 -10000 0 0
BCAR1 0.033 0.006 -10000 0 -10000 0 0
FGF2 0.014 0.098 -10000 0 -0.48 8 8
F11R 0.005 0.07 -10000 0 -0.35 8 8
alphaV/beta3 Integrin/Lactadherin 0.061 0.028 -10000 0 -10000 0 0
alphaV/beta3 Integrin/TGFBR2 0.064 0.024 -10000 0 -10000 0 0
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.08 0.03 -10000 0 -10000 0 0
HSP90AA1 0.031 0.011 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.06 0.024 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.005 0.11 -10000 0 -0.32 24 24
alphaV/beta3 Integrin/Pyk2 0.036 0.064 -10000 0 -10000 0 0
SDC1 0.034 0 -10000 0 -10000 0 0
VAV3 -0.02 0.1 -10000 0 -0.28 30 30
PTPN11 0.032 0.024 -10000 0 -0.32 1 1
IRS1 0.028 0.048 -10000 0 -0.32 4 4
FAK1/Paxillin 0.077 0.098 0.32 7 -10000 0 7
cell migration 0.068 0.094 0.29 9 -10000 0 9
ITGAV 0.033 0.024 -10000 0 -0.32 1 1
PI3K 0.074 0.068 -10000 0 -10000 0 0
SPP1 -0.2 0.16 -10000 0 -0.32 144 144
KDR 0.033 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.033 0.024 -10000 0 -0.32 1 1
COL4A3 0.031 0.034 -10000 0 -0.32 2 2
angiogenesis -0.041 0.14 -10000 0 -0.54 13 13
Rac1/GTP -0.007 0.1 -10000 0 -0.38 1 1
EDIL3 -0.024 0.17 -10000 0 -0.51 23 23
cell proliferation 0.064 0.023 -10000 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

Figure S52.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S52.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.038 0.02 -10000 0 -10000 0 0
NFATC2 0.001 0.11 -10000 0 -0.42 2 2
NFATC3 -0.025 0.086 -10000 0 -0.32 2 2
CD40LG -0.25 0.28 -10000 0 -0.88 15 15
ITCH 0.016 0.042 -10000 0 -10000 0 0
CBLB 0.033 0.039 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.11 0.16 -10000 0 -1 1 1
JUNB 0.029 0.041 -10000 0 -0.32 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 0.036 0.05 -10000 0 -0.27 4 4
T cell anergy 0.044 0.081 -10000 0 -0.38 3 3
TLE4 0.004 0.074 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.11 0.2 -10000 0 -0.84 8 8
AP-1/NFAT1-c-4 -0.27 0.3 -10000 0 -0.98 15 15
IKZF1 0 0.088 -10000 0 -0.77 1 1
T-helper 2 cell differentiation -0.056 0.13 -10000 0 -0.93 1 1
AP-1/NFAT1 -0.059 0.14 -10000 0 -0.46 9 9
CALM1 0.036 0.035 -10000 0 -10000 0 0
EGR2 -0.062 0.29 -10000 0 -1.4 8 8
EGR3 -0.064 0.25 -10000 0 -1.3 6 6
NFAT1/FOXP3 0.016 0.087 -10000 0 -10000 0 0
EGR1 0.013 0.1 -10000 0 -0.45 10 10
JUN -0.042 0.065 -10000 0 -0.36 5 5
EGR4 0.001 0 -10000 0 -10000 0 0
mol:Ca2+ 0.008 0.026 -10000 0 -10000 0 0
GBP3 -0.044 0.22 -10000 0 -0.74 18 18
FOSL1 0.014 0.081 -10000 0 -0.32 12 12
NFAT1-c-4/MAF/IRF4 -0.18 0.28 -10000 0 -0.96 14 14
DGKA 0.003 0.073 -10000 0 -10000 0 0
CREM 0.033 0.003 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.067 0.2 -10000 0 -0.84 7 7
CTLA4 0.045 0.1 -10000 0 -10000 0 0
NFAT1-c-4 (dimer)/EGR1 -0.062 0.21 -10000 0 -0.91 7 7
NFAT1-c-4 (dimer)/EGR4 -0.062 0.19 -10000 0 -0.84 7 7
FOS -0.09 0.16 -10000 0 -0.53 24 24
IFNG -0.19 0.26 -10000 0 -0.69 28 28
T cell activation -0.044 0.15 -10000 0 -10000 0 0
MAF -0.15 0.26 -10000 0 -0.5 73 73
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.053 0.17 0.74 5 -10000 0 5
TNF -0.055 0.19 -10000 0 -0.81 7 7
FASLG -0.18 0.51 -10000 0 -1.4 28 28
TBX21 -0.14 0.24 -10000 0 -0.5 62 62
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ 0.018 0.06 -10000 0 -0.31 4 4
PTPN1 0.004 0.074 -10000 0 -10000 0 0
NFAT1-c-4/ICER1 -0.06 0.2 -10000 0 -0.84 7 7
GATA3 0.036 0.007 -10000 0 -10000 0 0
T-helper 1 cell differentiation -0.19 0.26 -10000 0 -0.68 28 28
IL2RA -0.11 0.16 -10000 0 -0.72 3 3
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.002 0.072 -10000 0 -10000 0 0
E2F1 0.013 0.046 -10000 0 -0.31 3 3
PPARG 0.019 0.089 -10000 0 -0.5 6 6
SLC3A2 0.003 0.079 -10000 0 -0.44 1 1
IRF4 -0.084 0.22 -10000 0 -0.5 47 47
PTGS2 -0.28 0.3 -10000 0 -0.85 22 22
CSF2 -0.32 0.31 -10000 0 -0.86 24 24
JunB/Fra1/NFAT1-c-4 -0.055 0.2 -10000 0 -0.81 7 7
IL4 -0.058 0.14 -10000 0 -0.98 1 1
IL5 -0.26 0.28 -10000 0 -0.84 18 18
IL2 -0.045 0.15 -10000 0 -10000 0 0
IL3 -0.015 0.092 -10000 0 -1 1 1
RNF128 0.021 0.093 -10000 0 -0.6 4 4
NFATC1 -0.053 0.17 -10000 0 -0.74 5 5
CDK4 0.019 0.11 -10000 0 -10000 0 0
PTPRK 0.002 0.072 -10000 0 -10000 0 0
IL8 -0.36 0.29 -10000 0 -0.86 28 28
POU2F1 0.04 0.007 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

Figure S53.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S53.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HIF3A 0.033 0.006 -10000 0 -10000 0 0
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.033 0.006 -10000 0 -10000 0 0
TCEB1 0.028 0.026 -10000 0 -0.32 1 1
HIF1A/p53 -0.016 0.09 0.27 1 -0.36 7 8
HIF1A -0.024 0.08 -10000 0 -0.35 9 9
COPS5 0.03 0.012 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.077 0.049 -10000 0 -10000 0 0
FIH (dimer) 0.033 0.008 -10000 0 -10000 0 0
CDKN2A -0.073 0.16 -10000 0 -0.32 65 65
ARNT/IPAS 0.049 0.01 -10000 0 -10000 0 0
HIF1AN 0.033 0.008 -10000 0 -10000 0 0
GNB2L1 0.034 0.004 -10000 0 -10000 0 0
HIF1A/ARNT -0.021 0.089 -10000 0 -0.34 10 10
CUL2 0.034 0.003 -10000 0 -10000 0 0
OS9 0.034 0.004 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.057 0.031 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 -0.011 0.088 0.27 1 -0.33 10 11
PHD1-3/OS9 -0.04 0.16 -10000 0 -0.28 61 61
HIF1A/RACK1/Elongin B/Elongin C 0.002 0.095 -10000 0 -0.4 5 5
VHL 0.032 0.025 -10000 0 -0.32 1 1
HSP90AA1 0.031 0.011 -10000 0 -10000 0 0
HIF1A/JAB1 -0.015 0.089 0.27 1 -0.34 9 10
EGLN3 -0.13 0.25 -10000 0 -0.51 65 65
EGLN2 0.033 0.006 -10000 0 -10000 0 0
EGLN1 0.033 0.007 -10000 0 -10000 0 0
TP53 0.014 0.067 -10000 0 -0.32 8 8
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.028 0.095 -10000 0 -0.56 4 4
ARNT 0.034 0.005 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.032 0.009 -10000 0 -10000 0 0
HIF1A/p19ARF -0.062 0.11 0.27 1 -0.35 10 11
Regulation of Androgen receptor activity

Figure S54.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S54.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.018 0.005 -10000 0 -10000 0 0
SMARCC1 0.008 0.069 -10000 0 -0.82 1 1
REL 0.034 0 -10000 0 -10000 0 0
HDAC7 -0.092 0.13 -10000 0 -0.44 9 9
JUN 0.026 0.053 -10000 0 -0.32 5 5
EP300 0.032 0.009 -10000 0 -10000 0 0
KAT2B 0 0 -10000 0 -10000 0 0
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 -0.021 0.082 -10000 0 -0.39 9 9
FOXO1 0.01 0.089 -10000 0 -0.5 6 6
T-DHT/AR -0.076 0.15 -10000 0 -0.46 9 9
MAP2K6 -0.011 0.11 -10000 0 -0.52 9 9
BRM/BAF57 0.048 0.015 -10000 0 -10000 0 0
MAP2K4 0.006 0.043 -10000 0 -0.5 1 1
SMARCA2 0.034 0.007 -10000 0 -10000 0 0
PDE9A -0.54 0.57 -10000 0 -1.1 108 108
NCOA2 0.03 0.012 -10000 0 -10000 0 0
CEBPA 0.033 0.007 -10000 0 -10000 0 0
EHMT2 0.034 0.005 -10000 0 -10000 0 0
cell proliferation 0.007 0.18 0.42 9 -0.38 10 19
NR0B1 0.026 0.053 -10000 0 -0.32 5 5
EGR1 0.012 0.1 -10000 0 -0.45 10 10
RXRs/9cRA 0.063 0.017 -10000 0 -10000 0 0
AR/RACK1/Src 0.046 0.13 0.3 5 -0.34 7 12
AR/GR -0.036 0.11 -10000 0 -0.29 22 22
GNB2L1 0.034 0.004 -10000 0 -10000 0 0
PKN1 0.034 0.005 -10000 0 -10000 0 0
RCHY1 0.033 0.006 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 -0.004 0.034 -10000 0 -0.36 1 1
T-DHT/AR/TIF2/CARM1 -0.023 0.097 -10000 0 -0.35 8 8
SRC 0.006 0.1 0.22 2 -0.32 8 10
NR3C1 -0.027 0.17 -10000 0 -0.51 24 24
KLK3 -0.065 0.1 -10000 0 -0.41 1 1
APPBP2 0.008 0.029 -10000 0 -10000 0 0
TRIM24 0.034 0.007 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.049 0.081 -10000 0 -0.34 10 10
TMPRSS2 -0.076 0.19 -10000 0 -0.76 10 10
RXRG 0.034 0.006 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -0.004 1 1
RXRA 0.034 0.005 -10000 0 -10000 0 0
RXRB 0.034 0.005 -10000 0 -10000 0 0
CARM1 0.034 0.005 -10000 0 -10000 0 0
NR2C2 0.034 0.005 -10000 0 -10000 0 0
KLK2 0.027 0.087 0.31 1 -10000 0 1
AR -0.005 0.056 -10000 0 -0.26 2 2
SENP1 0.034 0.005 -10000 0 -10000 0 0
HSP90AA1 0.031 0.011 -10000 0 -10000 0 0
MDM2 0.033 0.004 -10000 0 -10000 0 0
SRY -0.001 0.001 0.009 1 -10000 0 1
GATA2 0.034 0.005 -10000 0 -10000 0 0
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 -0.25 0.14 -10000 0 -0.32 172 172
T-DHT/AR/RACK1/Src 0.049 0.14 0.34 7 -0.35 7 14
positive regulation of transcription 0.034 0.005 -10000 0 -10000 0 0
DNAJA1 0.007 0.037 -10000 0 -0.34 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.008 -10000 0 -10000 0 0
NCOA1 0.033 0.062 -10000 0 -0.58 2 2
SPDEF -0.14 0.25 -10000 0 -0.5 68 68
T-DHT/AR/TIF2 -0.001 0.087 0.28 5 -0.42 2 7
T-DHT/AR/Hsp90 -0.03 0.096 0.27 1 -0.36 9 10
GSK3B 0.03 0.024 -10000 0 -0.32 1 1
NR2C1 0.027 0.048 -10000 0 -0.32 4 4
mol:T-DHT -0.033 0.079 0.22 2 -0.33 10 12
SIRT1 0.033 0.007 -10000 0 -10000 0 0
ZMIZ2 0.03 0.01 -10000 0 -10000 0 0
POU2F1 -0.026 0.073 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.037 0.1 0.27 1 -0.37 8 9
CREBBP 0.033 0.007 -10000 0 -10000 0 0
SMARCE1 0.033 0.008 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

Figure S55.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S55.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.003 0.15 -9999 0 -0.41 11 11
MAP3K8 -0.014 0.12 -9999 0 -0.32 29 29
FOS 0.002 0.11 -9999 0 -0.4 5 5
PRKCA 0.025 0.031 -9999 0 -0.33 1 1
PTPN7 0.012 0.068 -9999 0 -0.32 8 8
HRAS 0.033 0.005 -9999 0 -10000 0 0
PRKCB -0.002 0.006 -9999 0 -0.016 33 33
NRAS 0.029 0.035 -9999 0 -0.32 2 2
RAS family/GTP 0.055 0.031 -9999 0 -10000 0 0
MAPK3 0.02 0.069 -9999 0 -0.44 3 3
MAP2K1 0.004 0.056 -9999 0 -0.26 2 2
ELK1 0.02 0.048 -9999 0 -0.33 3 3
BRAF 0.014 0.021 -9999 0 -10000 0 0
mol:GTP -0.001 0.002 -9999 0 -0.005 33 33
MAPK1 -0.002 0.12 -9999 0 -0.42 14 14
RAF1 0.014 0.021 -9999 0 -10000 0 0
KRAS 0.033 0.006 -9999 0 -10000 0 0
Noncanonical Wnt signaling pathway

Figure S56.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S56.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.018 0.017 -10000 0 -10000 0 0
GNB1/GNG2 -0.031 0.11 -10000 0 -0.32 6 6
mol:DAG -0.023 0.07 -10000 0 -0.32 1 1
PLCG1 -0.023 0.071 -10000 0 -0.33 1 1
YES1 -0.036 0.084 -10000 0 -0.3 5 5
FZD3 -0.05 0.15 -10000 0 -0.33 45 45
FZD6 0.018 0.064 -10000 0 -0.35 6 6
G protein 0.034 0.12 0.29 3 -0.29 4 7
MAP3K7 -0.02 0.063 -10000 0 -10000 0 0
mol:Ca2+ -0.022 0.068 -10000 0 -0.31 1 1
mol:IP3 -0.023 0.07 -10000 0 -0.32 1 1
NLK -0.002 0.1 -10000 0 -0.76 4 4
GNB1 0.032 0.008 -10000 0 -10000 0 0
CAMK2A -0.02 0.068 -10000 0 -0.3 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.045 0.1 -10000 0 -0.29 15 15
CSNK1A1 0.034 0.005 -10000 0 -10000 0 0
GNAS -0.01 0.088 -10000 0 -0.3 6 6
GO:0007205 -0.024 0.067 -10000 0 -0.31 1 1
WNT6 0.033 0.024 -10000 0 -0.32 1 1
WNT4 0.016 0.088 -10000 0 -0.45 7 7
NFAT1/CK1 alpha -0.016 0.077 -10000 0 -0.33 1 1
GNG2 0.031 0.01 -10000 0 -10000 0 0
WNT5A -0.02 0.13 -10000 0 -0.32 33 33
WNT11 -0.038 0.14 -10000 0 -0.32 44 44
CDC42 -0.035 0.078 -10000 0 -0.3 3 3
Cellular roles of Anthrax toxin

Figure S57.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S57.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.015 0.081 -10000 0 -0.32 12 12
ANTXR2 0.026 0.063 -10000 0 -0.51 3 3
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.011 -10000 0 -0.068 3 3
monocyte activation 0.003 0.093 -10000 0 -0.34 14 14
MAP2K2 0.009 0.08 -10000 0 -0.57 4 4
MAP2K1 -0.005 0.011 -10000 0 -10000 0 0
MAP2K7 -0.005 0.011 -10000 0 -10000 0 0
MAP2K6 -0.015 0.054 -10000 0 -0.27 9 9
CYAA -0.015 0.045 -10000 0 -0.17 15 15
MAP2K4 -0.005 0.021 -10000 0 -0.26 1 1
IL1B -0.031 0.06 -10000 0 -0.15 39 39
Channel 0.027 0.06 -10000 0 -0.18 15 15
NLRP1 -0.005 0.014 -10000 0 -0.15 1 1
CALM1 0.03 0.011 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.034 0.13 -10000 0 -0.39 25 25
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.011 0.068 3 -10000 0 3
MAPK3 -0.006 0.028 0.13 1 -0.26 2 3
MAPK1 -0.004 0.011 -10000 0 -10000 0 0
PGR -0.005 0.011 -10000 0 -10000 0 0
PA/Cellular Receptors 0.028 0.066 -10000 0 -0.21 15 15
apoptosis -0.003 0.011 -10000 0 -0.068 3 3
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.027 0.054 -10000 0 -0.16 15 15
macrophage activation -0.003 0.039 0.18 5 -0.26 2 7
TNF 0.034 0.005 -10000 0 -10000 0 0
VCAM1 0.005 0.089 -10000 0 -0.34 13 13
platelet activation -0.034 0.13 -10000 0 -0.39 25 25
MAPKKK cascade 0.004 0.024 0.1 1 -0.13 1 2
IL18 -0.033 0.083 -10000 0 -0.26 24 24
negative regulation of macrophage activation -0.003 0.011 -10000 0 -0.068 3 3
LEF -0.003 0.012 -10000 0 -0.068 3 3
CASP1 -0.005 0.02 -10000 0 -0.079 11 11
mol:cAMP -0.034 0.13 -10000 0 -0.39 25 25
necrosis -0.003 0.011 -10000 0 -0.068 3 3
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.027 0.057 -10000 0 -0.17 15 15
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

Figure S58.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S58.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.034 0.005 -10000 0 -10000 0 0
Jak2/Leptin Receptor 0.043 0.074 -10000 0 -0.34 1 1
PTP1B/AKT1 0.015 0.082 -10000 0 -0.32 3 3
FYN 0.03 0.037 -10000 0 -0.51 1 1
p210 bcr-abl/PTP1B 0.007 0.088 0.22 2 -0.3 5 7
EGFR 0.014 0.075 -10000 0 -0.51 4 4
EGF/EGFR -0.031 0.14 -10000 0 -0.32 29 29
CSF1 0.033 0.007 -10000 0 -10000 0 0
AKT1 0.032 0.011 -10000 0 -10000 0 0
INSR 0.027 0.064 -10000 0 -0.51 3 3
PTP1B/N-cadherin 0.005 0.085 0.22 1 -0.32 3 4
Insulin Receptor/Insulin 0.04 0.084 -10000 0 -0.35 3 3
HCK 0.004 0.088 -10000 0 -0.51 6 6
CRK 0.027 0.014 -10000 0 -10000 0 0
TYK2 0.007 0.089 0.28 4 -0.37 2 6
EGF -0.09 0.21 -10000 0 -0.43 58 58
YES1 0.027 0.014 -10000 0 -10000 0 0
CAV1 0.02 0.12 0.27 8 -0.35 4 12
TXN 0.032 0.005 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.03 0.096 -10000 0 -0.36 2 2
cell migration -0.007 0.088 0.3 5 -0.22 2 7
STAT3 0.034 0.006 -10000 0 -10000 0 0
PRLR 0.033 0.034 -10000 0 -0.31 2 2
ITGA2B 0.032 0.007 -10000 0 -10000 0 0
CSF1R 0.034 0.005 -10000 0 -10000 0 0
Prolactin Receptor/Prolactin 0.053 0.034 -10000 0 -10000 0 0
FGR 0.031 0.01 -10000 0 -10000 0 0
PTP1B/p130 Cas 0.015 0.089 0.22 1 -0.32 3 4
Crk/p130 Cas 0.021 0.086 -10000 0 -0.35 2 2
DOK1 0.015 0.082 0.22 1 -0.31 3 4
JAK2 0.034 0.07 0.25 1 -0.33 2 3
Jak2/Leptin Receptor/Leptin 0.035 0.1 -10000 0 -0.37 1 1
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
PTPN1 0.007 0.089 0.22 2 -0.3 5 7
LYN 0.03 0.012 -10000 0 -10000 0 0
CDH2 0.018 0.051 -10000 0 -0.33 4 4
SRC 0.02 0.1 -10000 0 -0.46 4 4
ITGB3 0.032 0.007 -10000 0 -10000 0 0
CAT1/PTP1B 0.009 0.17 0.27 18 -0.41 14 32
CAPN1 0.032 0.005 -10000 0 -10000 0 0
CSK 0.032 0.009 -10000 0 -10000 0 0
PI3K 0.053 0.083 -10000 0 -0.35 2 2
mol:H2O2 -0.001 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.034 0.098 -10000 0 -0.33 1 1
negative regulation of transcription 0.034 0.07 0.24 1 -0.32 2 3
FCGR2A 0.012 0.084 -10000 0 -0.32 13 13
FER 0.019 0.066 -10000 0 -0.32 8 8
alphaIIb/beta3 Integrin 0.046 0.01 -10000 0 -10000 0 0
BLK -0.084 0.21 -10000 0 -0.51 44 44
Insulin Receptor/Insulin/Shc 0.059 0.043 -10000 0 -0.32 2 2
RHOA 0.033 0.005 -10000 0 -10000 0 0
LEPR 0.025 0.063 -10000 0 -0.5 3 3
BCAR1 0.033 0.006 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.033 0.007 -10000 0 -10000 0 0
mol:NADPH -0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.061 0.22 0.24 9 -0.49 29 38
PRL 0.036 0.024 -10000 0 -0.31 1 1
SOCS3 -0.013 0.2 -10000 0 -1.1 7 7
SPRY2 0.019 0.052 -10000 0 -0.38 3 3
Insulin Receptor/Insulin/IRS1 0.056 0.054 -10000 0 -0.32 2 2
CSF1/CSF1R 0.035 0.093 -10000 0 -0.36 2 2
Ras protein signal transduction -0.001 0.063 0.47 3 -10000 0 3
IRS1 0.028 0.048 -10000 0 -0.32 4 4
INS 0.033 0.008 -10000 0 -10000 0 0
LEP 0.028 0.052 -10000 0 -0.51 2 2
STAT5B 0.025 0.08 0.23 2 -0.31 3 5
STAT5A 0.025 0.08 0.23 2 -0.31 3 5
GRB2 0.033 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.016 0.091 0.22 1 -0.33 3 4
CSN2 0.024 0.043 -10000 0 -10000 0 0
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
LAT 0.03 0.07 -10000 0 -0.54 2 2
YBX1 0.044 0.009 -10000 0 -10000 0 0
LCK 0.029 0.044 -10000 0 -0.41 2 2
SHC1 0.033 0.006 -10000 0 -10000 0 0
NOX4 -0.26 0.13 -10000 0 -0.32 179 179
EPO signaling pathway

Figure S59.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S59.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.13 0.14 -10000 0 -10000 0 0
CRKL -0.033 0.081 0.34 1 -10000 0 1
mol:DAG -0.018 0.063 -10000 0 -10000 0 0
HRAS -0.031 0.086 0.47 1 -10000 0 1
MAPK8 0.014 0.073 -10000 0 -10000 0 0
RAP1A -0.035 0.081 0.28 2 -10000 0 2
GAB1 -0.039 0.085 0.28 2 -0.35 2 4
MAPK14 0.013 0.072 -10000 0 -10000 0 0
EPO 0.008 0.036 -10000 0 -0.33 1 1
PLCG1 -0.019 0.064 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.011 0.029 -10000 0 -10000 0 0
RAPGEF1 0.034 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.016 0.062 -10000 0 -10000 0 0
GAB1/SHC/GRB2/SOS1 -0.021 0.093 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.009 0.043 -10000 0 -0.24 1 1
IRS2 -0.026 0.068 0.23 1 -10000 0 1
STAT1 -0.093 0.13 -10000 0 -0.36 8 8
STAT5B -0.062 0.1 -10000 0 -10000 0 0
cell proliferation 0.011 0.075 0.22 6 -10000 0 6
GAB1/SHIP/PIK3R1/SHP2/SHC -0.031 0.078 -10000 0 -10000 0 0
TEC -0.036 0.082 0.28 2 -10000 0 2
SOCS3 0.02 0.067 -10000 0 -0.32 8 8
STAT1 (dimer) -0.092 0.13 -10000 0 -0.36 8 8
JAK2 0.022 0.044 -10000 0 -0.32 3 3
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 -0.026 0.095 -10000 0 -10000 0 0
EPO/EPOR 0.009 0.043 -10000 0 -0.24 1 1
LYN 0.006 0.027 -10000 0 -10000 0 0
TEC/VAV2 -0.038 0.085 -10000 0 -0.34 2 2
elevation of cytosolic calcium ion concentration 0.011 0.029 -10000 0 -10000 0 0
SHC1 0.033 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.002 0.055 -10000 0 -10000 0 0
mol:IP3 -0.018 0.063 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.019 0.07 -10000 0 -10000 0 0
SH2B3 0.028 0.015 -10000 0 -10000 0 0
NFKB1 0.014 0.072 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2/SOCS3 0.011 0.032 -10000 0 -10000 0 0
PTPN6 -0.04 0.078 0.25 1 -10000 0 1
TEC/VAV2/GRB2 -0.029 0.094 -10000 0 -0.33 2 2
EPOR 0.011 0.029 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP -0.022 0.093 -10000 0 -10000 0 0
SOS1 0.034 0.002 -10000 0 -10000 0 0
PLCG2 -0.23 0.27 -10000 0 -0.51 105 105
CRKL/CBL/C3G -0.025 0.087 -10000 0 -10000 0 0
VAV2 -0.041 0.088 0.28 2 -0.35 2 4
CBL -0.037 0.081 0.28 2 -10000 0 2
SHC/Grb2/SOS1 -0.032 0.076 -10000 0 -10000 0 0
STAT5A -0.062 0.1 -10000 0 -10000 0 0
GRB2 0.033 0.007 -10000 0 -10000 0 0
STAT5 (dimer) -0.12 0.17 -10000 0 -0.35 2 2
LYN/PLCgamma2 -0.15 0.2 -10000 0 -0.37 90 90
PTPN11 0.032 0.024 -10000 0 -0.32 1 1
BTK -0.076 0.12 0.23 1 -0.33 25 26
BCL2 -0.52 0.42 -10000 0 -0.82 141 141
Nectin adhesion pathway

Figure S60.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S60.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.034 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.047 0.021 -10000 0 -0.22 1 1
PTK2 0.01 0.099 -10000 0 -0.39 8 8
positive regulation of JNK cascade 0.022 0.094 -10000 0 -0.31 6 6
CDC42/GDP 0.059 0.13 0.33 1 -0.4 8 9
Rac1/GDP 0.05 0.13 -10000 0 -0.4 7 7
RAP1B 0.034 0.004 -10000 0 -10000 0 0
RAP1A 0.032 0.008 -10000 0 -10000 0 0
CTNNB1 0.026 0.053 -10000 0 -0.32 5 5
CDC42/GTP 0.043 0.12 -10000 0 -0.38 6 6
nectin-3/I-afadin 0.027 0.092 -10000 0 -0.37 11 11
RAPGEF1 0.029 0.12 -10000 0 -0.42 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.013 0.13 -10000 0 -0.47 9 9
PDGFB-D/PDGFRB 0.034 0.005 -10000 0 -10000 0 0
TLN1 -0.003 0.048 -10000 0 -0.38 2 2
Rap1/GTP 0.018 0.089 -10000 0 -0.32 6 6
IQGAP1 0.032 0.009 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.06 0.02 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.027 0.092 -10000 0 -0.37 11 11
PVR 0.034 0.005 -10000 0 -10000 0 0
Necl-5(dimer) 0.034 0.005 -10000 0 -10000 0 0
mol:GDP 0.048 0.15 0.34 1 -0.47 10 11
MLLT4 0.033 0.007 -10000 0 -10000 0 0
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
PI3K 0.075 0.085 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.048 0.013 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.027 0.1 -10000 0 -0.32 8 8
PVRL1 0.034 0.005 -10000 0 -10000 0 0
PVRL3 0.006 0.12 -10000 0 -0.51 11 11
PVRL2 0.032 0.024 -10000 0 -0.32 1 1
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
CDH1 0.021 0.081 -10000 0 -0.51 5 5
CLDN1 -0.3 0.072 -10000 0 -0.32 205 205
JAM-A/CLDN1 -0.16 0.077 -10000 0 -0.4 11 11
SRC -0.005 0.13 -10000 0 -0.51 10 10
ITGB3 0.033 0.007 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin 0.048 0.013 -10000 0 -10000 0 0
FARP2 0.048 0.15 -10000 0 -0.5 6 6
RAC1 0.031 0.011 -10000 0 -10000 0 0
CTNNA1 0.034 0.005 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.047 0.082 -10000 0 -0.31 10 10
nectin-1/I-afadin 0.048 0.013 -10000 0 -10000 0 0
nectin-2/I-afadin 0.047 0.022 -10000 0 -0.22 1 1
RAC1/GTP/IQGAP1/filamentous actin 0.039 0.017 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.045 0.085 -10000 0 -0.31 11 11
CDC42/GTP/IQGAP1/filamentous actin 0.04 0.016 -10000 0 -10000 0 0
F11R 0.033 0.006 -10000 0 -10000 0 0
positive regulation of filopodium formation 0.022 0.094 -10000 0 -0.31 6 6
alphaV/beta3 Integrin/Talin 0.009 0.084 -10000 0 -0.36 2 2
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.047 0.022 -10000 0 -0.22 1 1
nectin-2(dimer)/I-afadin/I-afadin 0.047 0.022 -10000 0 -0.22 1 1
PIP5K1C -0.001 0.053 -10000 0 -0.41 2 2
VAV2 0.043 0.16 -10000 0 -0.53 6 6
RAP1/GDP 0.063 0.12 0.3 2 -0.38 5 7
ITGAV 0.033 0.024 -10000 0 -0.32 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.046 0.084 -10000 0 -0.31 10 10
nectin-3(dimer)/I-afadin/I-afadin 0.027 0.092 -10000 0 -0.37 11 11
Rac1/GTP 0.034 0.12 -10000 0 -0.39 8 8
PTPRM 0.002 0.061 -10000 0 -0.24 11 11
E-cadherin/beta catenin/alpha catenin 0.078 0.072 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.032 0.009 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

Figure S61.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S61.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.043 0.012 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.034 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.01 0.11 -10000 0 -0.51 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.024 0.039 -10000 0 -0.51 1 1
RAC1-CDC42/GTP/PAK family 0.021 0.011 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.027 0.014 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.032 0.008 -10000 0 -10000 0 0
FYN 0.03 0.037 -10000 0 -0.51 1 1
MAP3K12 0.034 0.004 -10000 0 -10000 0 0
FGR 0.031 0.01 -10000 0 -10000 0 0
p38 alpha/TAB1 -0.081 0.14 -10000 0 -0.36 37 37
PRKG1 0.033 0.006 -10000 0 -10000 0 0
DUSP8 0.031 0.037 -10000 0 -0.51 1 1
PGK/cGMP/p38 alpha -0.029 0.17 0.19 2 -0.38 29 31
apoptosis -0.078 0.14 -10000 0 -0.34 37 37
RAL/GTP 0.041 0.015 -10000 0 -10000 0 0
LYN 0.03 0.012 -10000 0 -10000 0 0
DUSP1 -0.011 0.15 -10000 0 -0.51 18 18
PAK1 0.034 0.004 -10000 0 -10000 0 0
SRC 0.019 0.017 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.062 0.041 -10000 0 -10000 0 0
TRAF6 0.034 0.005 -10000 0 -10000 0 0
RAC1 0.031 0.011 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.031 0.01 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.038 0.018 -10000 0 -10000 0 0
MAPK11 -0.013 0.19 0.31 10 -0.44 19 29
BLK -0.084 0.21 -10000 0 -0.51 44 44
HCK 0.004 0.088 -10000 0 -0.51 6 6
MAP2K3 0.028 0.013 -10000 0 -10000 0 0
DUSP16 0.033 0.007 -10000 0 -10000 0 0
DUSP10 -0.004 0.11 -10000 0 -0.32 23 23
TRAF6/MEKK3 0.041 0.012 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.031 0.2 0.24 14 -0.4 34 48
positive regulation of innate immune response -0.029 0.22 0.34 9 -0.49 23 32
LCK 0.029 0.044 -10000 0 -0.41 2 2
p38alpha-beta/MKP7 -0.02 0.21 0.33 7 -0.49 20 27
p38alpha-beta/MKP5 -0.032 0.22 0.33 8 -0.49 22 30
PGK/cGMP 0.025 0.005 -10000 0 -10000 0 0
PAK2 0.034 0.005 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.035 0.24 0.33 8 -0.52 26 34
CDC42 0.032 0.009 -10000 0 -10000 0 0
RALB 0.034 0 -10000 0 -10000 0 0
RALA 0.031 0.011 -10000 0 -10000 0 0
PAK3 0.034 0.003 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

Figure S62.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S62.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.014 0.04 -10000 0 -0.2 1 1
NFATC2 -0.011 0.028 -10000 0 -10000 0 0
NFATC3 -0.016 0.041 -10000 0 -10000 0 0
CD40LG -0.08 0.22 0.43 1 -0.56 12 13
PTGS2 -0.11 0.25 0.43 1 -0.55 27 28
JUNB 0.029 0.041 -10000 0 -0.32 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.003 0.032 -10000 0 -10000 0 0
CaM/Ca2+ -0.003 0.032 -10000 0 -10000 0 0
CALM1 0.015 0.028 -10000 0 -10000 0 0
JUN 0.01 0.058 -10000 0 -0.32 5 5
mol:Ca2+ -0.011 0.013 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.013 0.013 -10000 0 -10000 0 0
FOSL1 0.014 0.081 -10000 0 -0.32 12 12
CREM 0.034 0.003 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.043 0.1 -10000 0 -10000 0 0
FOS -0.043 0.16 -10000 0 -0.5 24 24
IFNG -0.1 0.24 0.43 1 -0.54 26 27
AP-1/NFAT1-c-4 -0.095 0.24 -10000 0 -0.52 25 25
FASLG -0.1 0.24 0.43 1 -0.55 21 22
NFAT1-c-4/ICER1 -0.018 0.075 -10000 0 -10000 0 0
IL2RA -0.083 0.22 -10000 0 -0.58 11 11
FKBP12/FK506 0.02 0.011 -10000 0 -10000 0 0
CSF2 -0.14 0.26 0.43 1 -0.54 34 35
JunB/Fra1/NFAT1-c-4 0.007 0.12 -10000 0 -0.32 2 2
IL4 -0.08 0.22 0.43 1 -0.55 11 12
IL2 -0.002 0.14 -10000 0 -0.91 5 5
IL3 0.023 0.086 -10000 0 -0.9 1 1
FKBP1A 0.027 0.014 -10000 0 -10000 0 0
BATF3 0 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.04 0.007 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

Figure S63.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S63.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.06 0.058 -10000 0 -0.26 5 5
ER alpha/Gai/GDP/Gbeta gamma -0.019 0.14 -10000 0 -0.48 10 10
AKT1 0.003 0.2 -10000 0 -0.75 13 13
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K 0.007 0.2 -10000 0 -0.75 13 13
mol:Ca2+ -0.016 0.12 0.23 2 -0.38 8 10
IGF1R 0.032 0.009 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.034 0.058 -10000 0 -0.27 7 7
SHC1 0.033 0.006 -10000 0 -10000 0 0
apoptosis -0.004 0.19 0.72 13 -10000 0 13
RhoA/GTP 0.022 0.045 -10000 0 -0.24 3 3
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.054 0.14 0.26 3 -0.38 8 11
regulation of stress fiber formation 0.001 0.058 -10000 0 -0.3 2 2
E2/ERA-ERB (dimer) 0.032 0.055 -10000 0 -0.31 5 5
KRAS 0.033 0.006 -10000 0 -10000 0 0
G13/GTP 0.032 0.05 -10000 0 -0.28 5 5
pseudopodium formation -0.001 0.058 0.3 2 -10000 0 2
E2/ER alpha (dimer)/PELP1 0.028 0.055 -10000 0 -0.3 5 5
GRB2 0.033 0.007 -10000 0 -10000 0 0
GNG2 0.031 0.01 -10000 0 -10000 0 0
GNAO1 0.034 0.005 -10000 0 -10000 0 0
HRAS 0.034 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0 0.15 0.3 1 -0.48 13 14
E2/ER beta (dimer) 0.023 0.008 -10000 0 -10000 0 0
mol:GDP 0.008 0.072 -10000 0 -0.39 5 5
mol:NADP 0 0.15 0.3 1 -0.48 13 14
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
mol:IP3 -0.027 0.11 0.24 1 -0.4 8 9
IGF-1R heterotetramer 0.032 0.009 -10000 0 -10000 0 0
PLCB1 -0.031 0.12 -10000 0 -0.39 10 10
PLCB2 -0.01 0.095 -10000 0 -0.41 9 9
IGF1 -0.28 0.27 -10000 0 -0.51 123 123
mol:L-citrulline 0 0.15 0.3 1 -0.48 13 14
RHOA 0.034 0.005 -10000 0 -10000 0 0
Gai/GDP 0.011 0.12 -10000 0 -0.68 4 4
JNK cascade 0.023 0.008 -10000 0 -10000 0 0
BCAR1 0.033 0.006 -10000 0 -10000 0 0
ESR2 0.031 0.01 -10000 0 -10000 0 0
GNAQ 0 0 -10000 0 -10000 0 0
ESR1 0.02 0.081 -10000 0 -0.51 5 5
Gq family/GDP/Gbeta gamma -0.013 0.15 -10000 0 -0.58 10 10
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.038 0.1 -10000 0 -0.53 3 3
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.052 0.14 0.26 3 -0.39 7 10
GNAZ 0.032 0.009 -10000 0 -10000 0 0
E2/ER alpha (dimer) 0.015 0.059 -10000 0 -0.36 5 5
STRN 0.031 0.034 -10000 0 -0.32 2 2
GNAL 0.027 0.014 -10000 0 -10000 0 0
PELP1 0.027 0.014 -10000 0 -10000 0 0
MAPK11 0.016 0.015 -10000 0 -0.18 1 1
GNAI2 0.034 0.004 -10000 0 -10000 0 0
GNAI3 0.033 0.007 -10000 0 -10000 0 0
GNAI1 -0.033 0.18 -10000 0 -0.51 26 26
HBEGF 0.1 0.18 0.34 56 -0.41 3 59
cAMP biosynthetic process 0.023 0.045 -10000 0 -0.24 5 5
SRC 0.048 0.13 -10000 0 -0.4 4 4
PI3K 0.049 0.01 -10000 0 -10000 0 0
GNB1 0.032 0.008 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.04 0.078 -10000 0 -0.34 5 5
SOS1 0.034 0.002 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.1 0.13 -10000 0 -0.38 20 20
Gs family/GTP 0.031 0.048 -10000 0 -0.25 5 5
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.058 0.029 -10000 0 -10000 0 0
vasodilation 0.002 0.14 0.3 1 -0.45 14 15
mol:DAG -0.027 0.11 0.24 1 -0.4 8 9
Gs family/GDP/Gbeta gamma 0.015 0.066 -10000 0 -0.33 5 5
MSN -0.001 0.06 0.31 2 -10000 0 2
Gq family/GTP -0.006 0.1 -10000 0 -0.41 10 10
mol:PI-3-4-5-P3 0.008 0.19 -10000 0 -0.72 13 13
NRAS 0.029 0.034 -10000 0 -0.32 2 2
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.002 0.14 0.45 14 -0.3 1 15
GRB2/SOS1 0.049 0.01 -10000 0 -10000 0 0
RhoA/GDP 0.026 0.079 -10000 0 -0.37 5 5
NOS3 -0.001 0.16 0.31 1 -0.51 13 14
GNA11 0.018 0.089 -10000 0 -0.51 6 6
MAPKKK cascade 0.034 0.16 0.37 2 -0.51 12 14
E2/ER alpha (dimer)/PELP1/Src 0.052 0.14 0.28 3 -0.39 8 11
ruffle organization -0.001 0.058 0.3 2 -10000 0 2
ROCK2 0.02 0.062 0.32 2 -10000 0 2
GNA14 0.011 0.11 -10000 0 -0.51 9 9
GNA15 0.024 0.058 -10000 0 -0.32 6 6
GNA13 0.032 0.008 -10000 0 -10000 0 0
MMP9 0.086 0.19 0.39 49 -0.42 3 52
MMP2 0.045 0.14 0.28 4 -0.43 4 8
ceramide signaling pathway

Figure S64.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S64.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.019 0.087 -10000 0 -0.48 2 2
BAG4 0.03 0.011 -10000 0 -10000 0 0
BAD -0.005 0.057 0.21 1 -0.21 2 3
NFKBIA 0.031 0.01 -10000 0 -10000 0 0
BIRC3 0.01 0.11 -10000 0 -0.47 10 10
BAX -0.004 0.065 0.25 3 -0.21 3 6
EnzymeConsortium:3.1.4.12 0.01 0.024 0.12 2 -0.11 1 3
IKBKB 0.034 0.096 0.34 1 -0.46 2 3
MAP2K2 0.001 0.062 0.21 4 -10000 0 4
MAP2K1 0.001 0.059 0.21 4 -10000 0 4
SMPD1 -0.035 0.098 0.18 1 -0.22 46 47
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.027 0.086 -10000 0 -0.45 2 2
MAP2K4 -0.004 0.052 0.21 1 -0.21 2 3
protein ubiquitination 0.028 0.091 0.4 1 -0.46 2 3
EnzymeConsortium:2.7.1.37 0.003 0.063 0.22 5 -10000 0 5
response to UV 0 0.001 0.002 8 -10000 0 8
RAF1 0.001 0.063 0.2 7 -0.21 1 8
CRADD 0.029 0.052 -10000 0 -0.51 2 2
mol:ceramide -0.005 0.06 0.22 1 -0.18 4 5
I-kappa-B-alpha/RELA/p50/ubiquitin 0.041 0.015 -10000 0 -10000 0 0
MADD 0.034 0.004 -10000 0 -10000 0 0
MAP3K1 -0.005 0.057 0.22 1 -0.19 2 3
TRADD 0.034 0.005 -10000 0 -10000 0 0
RELA/p50 0.034 0.005 -10000 0 -10000 0 0
MAPK3 0.006 0.062 0.21 4 -10000 0 4
MAPK1 0.001 0.068 0.22 3 -0.29 1 4
p50/RELA/I-kappa-B-alpha 0.045 0.016 -10000 0 -10000 0 0
FADD 0.022 0.083 -10000 0 -0.58 1 1
KSR1 -0.001 0.064 0.21 6 -0.2 2 8
MAPK8 -0.005 0.054 0.2 2 -0.2 1 3
TRAF2 0.033 0.006 -10000 0 -10000 0 0
response to radiation 0 0 0.002 4 -10000 0 4
CHUK 0.016 0.081 -10000 0 -0.45 2 2
TNF R/SODD 0.043 0.019 -10000 0 -10000 0 0
TNF 0.034 0.005 -10000 0 -10000 0 0
CYCS 0.067 0.08 0.18 29 -10000 0 29
IKBKG 0.022 0.087 -10000 0 -0.46 2 2
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.024 0.088 -10000 0 -0.47 2 2
RELA 0.034 0.005 -10000 0 -10000 0 0
RIPK1 0.034 0.005 -10000 0 -10000 0 0
AIFM1 0.063 0.076 0.17 22 -10000 0 22
TNF/TNF R/SODD 0.058 0.026 -10000 0 -10000 0 0
TNFRSF1A 0.033 0.008 -10000 0 -10000 0 0
response to heat 0 0 0.002 4 -10000 0 4
CASP8 0.032 0.1 -10000 0 -0.62 5 5
NSMAF 0.039 0.099 0.28 1 -0.56 1 2
response to hydrogen peroxide 0 0.001 0.002 8 -10000 0 8
BCL2 -0.2 0.26 -10000 0 -0.51 87 87
Role of Calcineurin-dependent NFAT signaling in lymphocytes

Figure S65.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S65.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.02 0.017 -10000 0 -10000 0 0
NFATC1 -0.021 0.14 0.44 1 -0.38 17 18
NFATC2 0.042 0.05 0.17 3 -10000 0 3
NFATC3 0.015 0.006 -10000 0 -10000 0 0
YWHAE 0.027 0.014 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.011 0.065 0.27 1 -0.26 3 4
Exportin 1/Ran/NUP214 0.067 0.021 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.045 0.069 0.24 1 -10000 0 1
BCL2/BAX -0.16 0.18 -10000 0 -0.36 86 86
CaM/Ca2+/Calcineurin A alpha-beta B1 0.023 0.009 -10000 0 -10000 0 0
CaM/Ca2+ 0.023 0.009 -10000 0 -10000 0 0
BAX 0.032 0.024 -10000 0 -0.32 1 1
MAPK14 0.034 0.005 -10000 0 -10000 0 0
BAD 0.034 0.005 -10000 0 -10000 0 0
CABIN1/MEF2D 0.026 0.067 0.25 1 -0.29 1 2
Calcineurin A alpha-beta B1/BCL2 -0.2 0.26 -10000 0 -0.5 87 87
FKBP8 0.034 0.004 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.025 0.067 0.28 1 -0.25 1 2
KPNB1 0.025 0.053 -10000 0 -0.32 5 5
KPNA2 0.019 0.067 -10000 0 -0.32 8 8
XPO1 0.034 0 -10000 0 -10000 0 0
SFN 0.026 0.053 -10000 0 -0.51 2 2
MAP3K8 -0.013 0.12 -10000 0 -0.32 29 29
NFAT4/CK1 alpha 0.034 0.029 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 0.087 0.059 -10000 0 -10000 0 0
CABIN1 0.011 0.065 0.27 1 -0.27 3 4
CALM1 0.031 0.011 -10000 0 -10000 0 0
RAN 0.033 0.024 -10000 0 -0.32 1 1
MAP3K1 0.034 0.005 -10000 0 -10000 0 0
CAMK4 0.033 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0.001 0.001 -10000 0 -10000 0 0
MAPK3 0.029 0.052 -10000 0 -0.51 2 2
YWHAH 0.032 0.008 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.037 0.058 -10000 0 -0.37 4 4
YWHAB 0.018 0.017 -10000 0 -10000 0 0
MAPK8 0.034 0.007 -10000 0 -10000 0 0
MAPK9 0.034 0.004 -10000 0 -10000 0 0
YWHAG 0.033 0.008 -10000 0 -10000 0 0
FKBP1A 0.027 0.014 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.008 0.13 0.44 1 -0.37 5 6
PRKCH 0.026 0.053 -10000 0 -0.51 2 2
CABIN1/Cbp/p300 0.047 0.016 -10000 0 -10000 0 0
CASP3 0.032 0.009 -10000 0 -10000 0 0
PIM1 0.034 0.005 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.018 0.01 -10000 0 -10000 0 0
apoptosis -0.019 0.054 -10000 0 -0.34 1 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.039 0.048 -10000 0 -10000 0 0
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.034 0.004 -10000 0 -10000 0 0
JNK2/NFAT4 0.029 0.025 -10000 0 -10000 0 0
BAD/BCL-XL 0.029 0.025 -10000 0 -10000 0 0
PRKCD 0.034 0.005 -10000 0 -10000 0 0
NUP214 0.034 0.005 -10000 0 -10000 0 0
PRKCZ 0 0.001 -10000 0 -10000 0 0
PRKCA 0.031 0.025 -10000 0 -0.32 1 1
PRKCG 0.027 0.048 -10000 0 -0.32 4 4
PRKCQ 0.027 0.048 -10000 0 -0.32 4 4
FKBP38/BCL2 -0.16 0.18 -10000 0 -0.37 86 86
EP300 0.032 0.009 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.027 0.014 -10000 0 -10000 0 0
NFATc/JNK1 -0.003 0.14 0.43 1 -0.37 12 13
CaM/Ca2+/FKBP38 0.041 0.016 -10000 0 -10000 0 0
FKBP12/FK506 0.02 0.011 -10000 0 -10000 0 0
CSNK1A1 0.018 0.008 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.041 0.017 -10000 0 -10000 0 0
NFATc/ERK1 -0.009 0.14 0.43 1 -0.38 11 12
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.048 0.07 0.24 1 -10000 0 1
NR4A1 0.054 0.059 0.3 2 -10000 0 2
GSK3B 0.033 0.024 -10000 0 -0.32 1 1
positive T cell selection 0.015 0.006 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.037 0.039 -10000 0 -10000 0 0
RCH1/ KPNB1 0.032 0.067 -10000 0 -0.23 12 12
YWHAQ 0.034 0 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
AKAP5 0.021 0.073 -10000 0 -0.51 4 4
MEF2D 0.034 0.006 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.029 0.013 -10000 0 -10000 0 0
NFATc/p38 alpha -0.007 0.14 0.43 1 -0.37 12 13
CREBBP 0.034 0.007 -10000 0 -10000 0 0
BCL2 -0.2 0.26 -10000 0 -0.51 87 87
HIV-1 Nef: Negative effector of Fas and TNF-alpha

Figure S66.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S66.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.03 0.011 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.006 0.13 -10000 0 -0.38 11 11
NEF -0.012 0.047 -10000 0 -10000 0 0
NFKBIA 0.027 0.03 -10000 0 -10000 0 0
BIRC3 0.004 0.11 -10000 0 -0.55 8 8
CYCS -0.017 0.13 -10000 0 -0.4 10 10
RIPK1 0.034 0.005 -10000 0 -10000 0 0
CD247 -0.011 0.15 -10000 0 -0.36 26 26
MAP2K7 0.004 0.14 -10000 0 -0.79 3 3
protein ubiquitination 0.036 0.071 0.48 2 -10000 0 2
CRADD 0.029 0.052 -10000 0 -0.51 2 2
DAXX 0.034 0.005 -10000 0 -10000 0 0
FAS -0.018 0.16 -10000 0 -0.51 20 20
BID -0.025 0.13 0.2 4 -0.34 22 26
NF-kappa-B/RelA/I kappa B alpha 0.054 0.074 -10000 0 -0.28 7 7
TRADD 0.034 0.005 -10000 0 -10000 0 0
MAP3K5 0.03 0.034 -10000 0 -0.32 2 2
CFLAR 0.034 0.002 -10000 0 -10000 0 0
FADD 0.034 0.004 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.054 0.074 -10000 0 -0.28 7 7
MAPK8 0.006 0.13 0.45 1 -0.71 3 4
APAF1 0.031 0.034 -10000 0 -0.32 2 2
TRAF1 0.034 0.005 -10000 0 -10000 0 0
TRAF2 0.033 0.006 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.019 0.14 0.2 4 -0.33 26 30
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.039 0.058 -10000 0 -0.36 1 1
CHUK 0.036 0.064 0.55 1 -10000 0 1
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.058 0.11 -10000 0 -0.28 19 19
TCRz/NEF -0.02 0.15 -10000 0 -0.39 26 26
TNF 0.034 0.005 -10000 0 -10000 0 0
FASLG -0.053 0.22 -10000 0 -0.59 28 28
NFKB1 0.03 0.028 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.058 0.026 -10000 0 -10000 0 0
CASP6 0.021 0.13 -10000 0 -0.65 3 3
CASP7 -0.047 0.19 0.46 1 -0.5 21 22
RELA 0.03 0.029 -10000 0 -10000 0 0
CASP2 0.033 0.007 -10000 0 -10000 0 0
CASP3 -0.015 0.15 0.46 1 -0.53 11 12
TNFRSF1A 0.033 0.008 -10000 0 -10000 0 0
TNFR1A/BAG4 0.043 0.019 -10000 0 -10000 0 0
CASP8 0.034 0.002 -10000 0 -10000 0 0
CASP9 0.032 0.009 -10000 0 -10000 0 0
MAP3K14 0.037 0.063 -10000 0 -10000 0 0
APAF-1/Caspase 9 -0.009 0.13 -10000 0 -0.38 12 12
BCL2 -0.1 0.15 -10000 0 -0.48 10 10
Nongenotropic Androgen signaling

Figure S67.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S67.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.008 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.055 0.027 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.016 0.018 -10000 0 -10000 0 0
GNAO1 0.034 0.005 -10000 0 -10000 0 0
HRAS 0.033 0.005 -10000 0 -10000 0 0
SHBG/T-DHT 0.018 0.01 -10000 0 -10000 0 0
PELP1 0.027 0.014 -10000 0 -10000 0 0
AKT1 0.009 0.003 -10000 0 -10000 0 0
MAP2K1 0.059 0.092 0.22 1 -10000 0 1
T-DHT/AR 0.023 0.017 -10000 0 -0.22 1 1
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.008 33 33
GNAI2 0.034 0.004 -10000 0 -10000 0 0
GNAI3 0.033 0.007 -10000 0 -10000 0 0
GNAI1 -0.033 0.18 -10000 0 -0.51 26 26
mol:GDP 0.005 0.007 -10000 0 -10000 0 0
cell proliferation 0.022 0.17 0.29 4 -0.41 15 19
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
FOS -0.057 0.31 -10000 0 -0.81 31 31
mol:Ca2+ -0.006 0.026 -10000 0 -0.083 14 14
MAPK3 0.043 0.13 0.29 5 -0.33 3 8
MAPK1 0.006 0.13 -10000 0 -0.42 8 8
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
mol:IP3 -0.001 0.002 -10000 0 -0.005 33 33
cAMP biosynthetic process 0.003 0.02 -10000 0 -10000 0 0
GNG2 0.031 0.01 -10000 0 -10000 0 0
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.005 33 33
HRAS/GTP 0.025 0.04 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.043 0.022 -10000 0 -10000 0 0
SRC 0.018 0.017 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.005 33 33
PI3K 0.045 0.009 -10000 0 -10000 0 0
apoptosis -0.012 0.17 0.37 26 -0.24 1 27
T-DHT/AR/PELP1 0.035 0.023 -10000 0 -0.16 1 1
HRAS/GDP 0.023 0.028 -10000 0 -10000 0 0
CREB1 0.01 0.18 -10000 0 -0.4 26 26
RAC1-CDC42/GTP 0.053 0.028 -10000 0 -10000 0 0
AR 0.032 0.024 -10000 0 -0.32 1 1
GNB1 0.032 0.008 -10000 0 -10000 0 0
RAF1 0.076 0.089 0.23 1 -10000 0 1
RAC1-CDC42/GDP 0.068 0.046 -10000 0 -10000 0 0
T-DHT/AR/PELP1/Src 0.03 0.033 -10000 0 -10000 0 0
MAP2K2 0.061 0.092 -10000 0 -10000 0 0
T-DHT/AR/PELP1/Src/PI3K 0.016 0.018 -10000 0 -10000 0 0
GNAZ 0.032 0.009 -10000 0 -10000 0 0
SHBG 0.027 0.014 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.006 0.095 -10000 0 -0.5 2 2
mol:T-DHT -0.001 0.002 -10000 0 -0.004 27 27
RAC1 0.031 0.011 -10000 0 -10000 0 0
GNRH1 0.007 0.004 -10000 0 -10000 0 0
Gi family/GTP -0.012 0.088 -10000 0 -0.25 14 14
CDC42 0.032 0.009 -10000 0 -10000 0 0
IL27-mediated signaling events

Figure S68.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S68.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.04 0.012 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.015 0.082 0.45 1 -10000 0 1
IL27/IL27R/JAK1 -0.018 0.11 -10000 0 -10000 0 0
TBX21 -0.15 0.2 -10000 0 -0.44 57 57
IL12B 0.03 0.034 -10000 0 -0.32 2 2
IL12A 0.001 0.038 -10000 0 -0.22 6 6
IL6ST 0.029 0.007 -10000 0 -10000 0 0
IL27RA/JAK1 0.004 0.046 -10000 0 -10000 0 0
IL27 -0.005 0.13 -10000 0 -0.46 15 15
TYK2 0.022 0.022 -10000 0 -10000 0 0
T-helper cell lineage commitment 0.012 0.14 1.1 2 -10000 0 2
T-helper 2 cell differentiation 0.015 0.082 0.45 1 -10000 0 1
T cell proliferation during immune response 0.015 0.082 0.45 1 -10000 0 1
MAPKKK cascade -0.015 0.082 -10000 0 -0.45 1 1
STAT3 0.033 0.006 -10000 0 -10000 0 0
STAT2 0.034 0.004 -10000 0 -10000 0 0
STAT1 0.002 0.099 -10000 0 -0.32 19 19
IL12RB1 0.033 0.004 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.082 0.13 0.38 1 -0.45 3 4
IL27/IL27R/JAK2/TYK2 -0.015 0.083 -10000 0 -0.46 1 1
positive regulation of T cell mediated cytotoxicity -0.015 0.082 -10000 0 -0.45 1 1
STAT1 (dimer) -0.079 0.17 -10000 0 -0.59 2 2
JAK2 0.025 0.043 -10000 0 -0.33 3 3
JAK1 0.032 0.006 -10000 0 -10000 0 0
STAT2 (dimer) -0.005 0.089 -10000 0 -0.44 1 1
T cell proliferation -0.065 0.12 -10000 0 -0.42 5 5
IL12/IL12R/TYK2/JAK2 0.011 0.14 -10000 0 -0.72 6 6
IL17A 0.012 0.14 1.1 2 -10000 0 2
mast cell activation 0.015 0.082 0.45 1 -10000 0 1
IFNG -0.001 0.029 -10000 0 -10000 0 0
T cell differentiation -0.005 0.005 -10000 0 -0.02 1 1
STAT3 (dimer) -0.005 0.091 -10000 0 -0.44 1 1
STAT5A (dimer) -0.005 0.091 -10000 0 -0.44 1 1
STAT4 (dimer) -0.005 0.093 -10000 0 -0.44 1 1
STAT4 0.032 0.037 -10000 0 -0.51 1 1
T cell activation -0.007 0.005 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.006 0.069 -10000 0 -10000 0 0
GATA3 0.007 0.058 0.56 2 -10000 0 2
IL18 -0.032 0.12 -10000 0 -0.36 24 24
positive regulation of mast cell cytokine production -0.005 0.09 -10000 0 -0.43 1 1
IL27/EBI3 0.013 0.099 -10000 0 -0.34 15 15
IL27RA -0.002 0.04 -10000 0 -10000 0 0
IL6 -0.11 0.17 -10000 0 -0.31 91 91
STAT5A 0.033 0.006 -10000 0 -10000 0 0
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 -0.008 0.018 -10000 0 -10000 0 0
IL1B -0.031 0.087 -10000 0 -0.22 39 39
EBI3 0.029 0.007 -10000 0 -10000 0 0
TNF 0.01 0.002 -10000 0 -10000 0 0
TCGA08_rtk_signaling

Figure S69.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S69.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.026 0.063 -10000 0 -0.51 3 3
HRAS 0.034 0.005 -10000 0 -10000 0 0
EGFR 0.021 0.073 -10000 0 -0.51 4 4
AKT 0.041 0.086 0.3 9 -10000 0 9
FOXO3 0.033 0.007 -10000 0 -10000 0 0
AKT1 0.031 0.011 -10000 0 -10000 0 0
FOXO1 0.01 0.089 -10000 0 -0.51 6 6
AKT3 0.033 0.006 -10000 0 -10000 0 0
FOXO4 0.034 0.002 -10000 0 -10000 0 0
MET -0.11 0.17 -10000 0 -0.32 87 87
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
PIK3CB 0.034 0.005 -10000 0 -10000 0 0
NRAS 0.029 0.034 -10000 0 -0.32 2 2
PIK3CG 0.02 0.081 -10000 0 -0.51 5 5
PIK3R3 0.034 0.005 -10000 0 -10000 0 0
PIK3R2 0.034 0.004 -10000 0 -10000 0 0
NF1 0.033 0.008 -10000 0 -10000 0 0
RAS 0.006 0.07 0.24 6 -0.21 5 11
ERBB2 0.03 0.038 -10000 0 -0.51 1 1
proliferation/survival/translation -0.035 0.075 0.28 3 -0.26 3 6
PI3K 0.031 0.089 0.27 16 -10000 0 16
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
KRAS 0.033 0.006 -10000 0 -10000 0 0
FOXO 0.069 0.075 0.27 11 -10000 0 11
AKT2 0.033 0.007 -10000 0 -10000 0 0
PTEN 0.027 0.052 -10000 0 -0.51 2 2
Stabilization and expansion of the E-cadherin adherens junction

Figure S70.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S70.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.004 0.089 -10000 0 -0.25 20 20
epithelial cell differentiation 0.056 0.063 -10000 0 -0.27 5 5
CYFIP2 0.029 0.052 -10000 0 -0.51 2 2
ENAH -0.015 0.06 0.28 1 -10000 0 1
EGFR 0.021 0.073 -10000 0 -0.51 4 4
EPHA2 0.016 0.074 -10000 0 -0.32 10 10
MYO6 0.009 0.051 -10000 0 -0.26 5 5
CTNNB1 0.026 0.053 -10000 0 -0.32 5 5
ABI1/Sra1/Nap1 0.063 0.042 -10000 0 -0.31 2 2
AQP5 0.007 0.055 -10000 0 -0.37 1 1
CTNND1 0.034 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.011 0.053 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.003 0.068 -10000 0 -10000 0 0
EGF -0.09 0.21 -10000 0 -0.42 58 58
NCKAP1 0.033 0.024 -10000 0 -0.32 1 1
AQP3 0.008 0.052 -10000 0 -10000 0 0
cortical microtubule organization 0.056 0.063 -10000 0 -0.27 5 5
GO:0000145 -0.012 0.047 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.063 0.065 -10000 0 -0.27 5 5
MLLT4 0.033 0.007 -10000 0 -10000 0 0
ARF6/GDP -0.023 0.054 -10000 0 -0.35 2 2
ARF6 0.031 0.01 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.063 0.06 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.004 0.043 -10000 0 -10000 0 0
PVRL2 0.032 0.024 -10000 0 -0.32 1 1
ZYX 0.008 0.051 -10000 0 -10000 0 0
ARF6/GTP 0.064 0.063 -10000 0 -10000 0 0
CDH1 0.021 0.081 -10000 0 -0.51 5 5
EGFR/EGFR/EGF/EGF -0.024 0.13 -10000 0 -0.26 31 31
RhoA/GDP 0.058 0.062 -10000 0 -0.25 5 5
actin cytoskeleton organization 0 0.047 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.032 0.009 -10000 0 -10000 0 0
GIT1 0.033 0.007 -10000 0 -10000 0 0
IGF1R 0.032 0.009 -10000 0 -10000 0 0
IGF1 -0.28 0.27 -10000 0 -0.51 123 123
DIAPH1 0.057 0.11 -10000 0 -0.68 2 2
Wnt receptor signaling pathway -0.056 0.063 0.27 5 -10000 0 5
RHOA 0.034 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.024 0.055 -10000 0 -0.35 2 2
CTNNA1 0.034 0.005 -10000 0 -10000 0 0
VCL 0 0.048 -10000 0 -10000 0 0
EFNA1 0.033 0.006 -10000 0 -10000 0 0
LPP -0.012 0.049 -10000 0 -10000 0 0
Ephrin A1/EPHA2 0.038 0.079 -10000 0 -0.32 5 5
SEC6/SEC8 0.007 0.047 -10000 0 -10000 0 0
MGAT3 0.003 0.069 -10000 0 -10000 0 0
HGF/MET -0.036 0.11 -10000 0 -0.35 3 3
HGF 0.029 0.034 -10000 0 -0.32 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.004 0.089 -10000 0 -0.25 20 20
actin cable formation 0.013 0.084 0.32 6 -0.31 1 7
KIAA1543 -0.012 0.048 -10000 0 -10000 0 0
KIFC3 0.006 0.057 -10000 0 -0.28 2 2
NCK1 0.034 0.005 -10000 0 -10000 0 0
EXOC3 0.033 0.008 -10000 0 -10000 0 0
ACTN1 0.011 0.052 -10000 0 -10000 0 0
NCK1/GIT1 0.048 0.013 -10000 0 -10000 0 0
mol:GDP 0.056 0.063 -10000 0 -0.27 5 5
EXOC4 0.033 0.008 -10000 0 -10000 0 0
STX4 0.01 0.048 -10000 0 -10000 0 0
PIP5K1C 0.011 0.054 -10000 0 -10000 0 0
LIMA1 -0.009 0.15 -10000 0 -0.51 17 17
ABI1 0.034 0.004 -10000 0 -10000 0 0
ROCK1 -0.01 0.071 0.3 3 -10000 0 3
adherens junction assembly 0.007 0.061 0.28 3 -10000 0 3
IGF-1R heterotetramer/IGF1 -0.12 0.16 -10000 0 -0.44 5 5
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.047 0.022 -10000 0 -0.22 1 1
MET -0.11 0.17 -10000 0 -0.32 87 87
PLEKHA7 0.011 0.054 -10000 0 -10000 0 0
mol:GTP 0.06 0.059 -10000 0 -10000 0 0
establishment of epithelial cell apical/basal polarity -0.003 0.067 0.33 1 -10000 0 1
cortical actin cytoskeleton stabilization 0.004 0.089 -10000 0 -0.25 20 20
regulation of cell-cell adhesion 0 0.047 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.004 0.089 -10000 0 -0.25 20 20
Class I PI3K signaling events

Figure S71.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S71.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.019 0.035 0.24 3 -10000 0 3
DAPP1 -0.014 0.18 0.24 9 -0.43 20 29
Src family/SYK family/BLNK-LAT/BTK-ITK -0.056 0.23 0.3 1 -0.6 20 21
mol:DAG -0.026 0.11 0.19 21 -0.24 14 35
HRAS 0.035 0.006 -10000 0 -10000 0 0
RAP1A 0.034 0.009 -10000 0 -10000 0 0
ARF5/GDP 0.052 0.092 0.25 1 -0.29 4 5
PLCG2 -0.23 0.27 -10000 0 -0.51 105 105
PLCG1 0.018 0.017 -10000 0 -10000 0 0
ARF5 0.033 0.007 -10000 0 -10000 0 0
mol:GTP -0.008 0.039 0.22 3 -10000 0 3
ARF1/GTP -0.001 0.033 0.22 3 -10000 0 3
RHOA 0.034 0.005 -10000 0 -10000 0 0
YES1 0.027 0.014 -10000 0 -10000 0 0
RAP1A/GTP -0.006 0.041 0.21 2 -10000 0 2
ADAP1 -0.008 0.037 0.21 3 -10000 0 3
ARAP3 -0.008 0.038 0.22 3 -10000 0 3
INPPL1 0.034 0.004 -10000 0 -10000 0 0
PREX1 0.019 0.017 -10000 0 -10000 0 0
ARHGEF6 0.029 0.052 -10000 0 -0.51 2 2
ARHGEF7 0.025 0.015 -10000 0 -10000 0 0
ARF1 0.033 0.007 -10000 0 -10000 0 0
NRAS 0.031 0.035 -10000 0 -0.32 2 2
FYN 0.03 0.037 -10000 0 -0.51 1 1
ARF6 0.031 0.01 -10000 0 -10000 0 0
FGR 0.031 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.008 0.062 0.16 4 -10000 0 4
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.027 0.052 -10000 0 -0.51 2 2
ZAP70 0.034 0.002 -10000 0 -10000 0 0
mol:IP3 -0.016 0.081 0.18 5 -0.19 4 9
LYN 0.03 0.012 -10000 0 -10000 0 0
ARF1/GDP 0.052 0.093 0.25 1 -0.29 4 5
RhoA/GDP 0.053 0.063 0.24 4 -10000 0 4
PDK1/Src/Hsp90 0.035 0.035 -10000 0 -10000 0 0
BLNK 0.018 0.089 -10000 0 -0.51 6 6
actin cytoskeleton reorganization 0.048 0.089 0.29 5 -0.39 1 6
SRC 0.019 0.017 -10000 0 -10000 0 0
PLEKHA2 0.004 0.019 0.21 1 -0.18 1 2
RAC1 0.031 0.011 -10000 0 -10000 0 0
PTEN 0.026 0.051 -10000 0 -0.48 2 2
HSP90AA1 0.031 0.011 -10000 0 -10000 0 0
ARF6/GTP 0.02 0.037 0.24 3 -10000 0 3
RhoA/GTP -0.005 0.045 0.23 3 -10000 0 3
Src family/SYK family/BLNK-LAT -0.034 0.13 -10000 0 -0.44 12 12
BLK -0.084 0.21 -10000 0 -0.51 44 44
PDPK1 0.033 0.006 -10000 0 -10000 0 0
CYTH1 -0.008 0.037 0.21 3 -10000 0 3
HCK 0.004 0.088 -10000 0 -0.51 6 6
CYTH3 -0.008 0.037 0.21 3 -10000 0 3
CYTH2 -0.008 0.037 0.21 3 -10000 0 3
KRAS 0.035 0.008 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.008 0.032 0.19 1 -10000 0 1
SGK1 0.008 0.034 0.2 1 -10000 0 1
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.041 0.091 0.25 1 -0.3 4 5
SOS1 0.034 0.002 -10000 0 -10000 0 0
SYK 0.032 0.024 -10000 0 -0.32 1 1
ARF6/GDP 0.038 0.061 0.25 5 -10000 0 5
mol:PI-3-4-5-P3 -0.008 0.041 0.26 3 -10000 0 3
ARAP3/RAP1A/GTP -0.006 0.041 0.21 2 -10000 0 2
VAV1 -0.014 0.15 -10000 0 -0.51 19 19
mol:PI-3-4-P2 0.01 0.001 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.056 0.046 -10000 0 -10000 0 0
PLEKHA1 0.005 0.001 -10000 0 -10000 0 0
Rac1/GDP 0.048 0.089 0.25 1 -0.29 4 5
LAT 0.032 0.025 -10000 0 -0.32 1 1
Rac1/GTP 0.005 0.064 -10000 0 -0.42 2 2
ITK -0.009 0.035 0.23 2 -10000 0 2
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.042 0.14 0.21 20 -0.32 18 38
LCK 0.029 0.044 -10000 0 -0.41 2 2
BTK -0.045 0.092 0.19 2 -0.26 30 32
Syndecan-4-mediated signaling events

Figure S72.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S72.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.036 0.047 -10000 0 -10000 0 0
Syndecan-4/Syndesmos 0.11 0.11 0.38 1 -0.43 1 2
positive regulation of JNK cascade -0.068 0.14 -10000 0 -0.57 2 2
Syndecan-4/ADAM12 0.07 0.15 0.38 2 -0.45 3 5
CCL5 -0.088 0.22 -10000 0 -0.51 48 48
Rac1/GDP 0.023 0.008 -10000 0 -10000 0 0
DNM2 0.034 0.005 -10000 0 -10000 0 0
ITGA5 0.026 0.053 -10000 0 -0.32 5 5
SDCBP 0.03 0.012 -10000 0 -10000 0 0
PLG 0.005 0.032 -10000 0 -10000 0 0
ADAM12 -0.1 0.17 -10000 0 -0.32 81 81
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.033 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.022 0.026 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.08 0.11 -10000 0 -10000 0 0
Syndecan-4/CXCL12/CXCR4 -0.071 0.15 -10000 0 -0.61 2 2
Syndecan-4/Laminin alpha3 0.078 0.11 0.38 1 -10000 0 1
MDK 0.014 0.081 -10000 0 -0.32 12 12
Syndecan-4/FZD7 0.11 0.12 0.38 2 -0.43 1 3
Syndecan-4/Midkine 0.11 0.12 0.38 2 -0.43 1 3
FZD7 0.019 0.077 -10000 0 -0.36 8 8
Syndecan-4/FGFR1/FGF 0.097 0.12 0.37 1 -10000 0 1
THBS1 0.028 0.044 -10000 0 -0.41 2 2
integrin-mediated signaling pathway 0.1 0.11 0.37 1 -0.42 1 2
positive regulation of MAPKKK cascade -0.068 0.14 -10000 0 -0.57 2 2
Syndecan-4/TACI 0.085 0.11 0.38 1 -10000 0 1
CXCR4 0.016 0.077 -10000 0 -0.32 11 11
cell adhesion 0.008 0.047 0.19 4 -10000 0 4
Syndecan-4/Dynamin 0.11 0.11 0.38 2 -0.43 1 3
Syndecan-4/TSP1 0.1 0.12 0.38 2 -0.42 1 3
Syndecan-4/GIPC 0.11 0.12 0.38 2 -0.43 1 3
Syndecan-4/RANTES 0.053 0.14 0.38 1 -0.66 1 2
ITGB1 0.032 0.024 -10000 0 -0.32 1 1
LAMA1 0.026 0.015 -10000 0 -10000 0 0
LAMA3 0.02 0.051 -10000 0 -0.38 3 3
RAC1 0.031 0.011 -10000 0 -10000 0 0
PRKCA 0.013 0.11 0.66 6 -10000 0 6
Syndecan-4/alpha-Actinin 0.099 0.11 0.38 1 -0.43 1 2
TFPI 0.033 0.024 -10000 0 -0.32 1 1
F2 0.055 0.023 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.042 0.045 -10000 0 -0.22 6 6
positive regulation of cell adhesion 0.068 0.11 -10000 0 -10000 0 0
ACTN1 0.031 0.01 -10000 0 -10000 0 0
TNC 0.026 0.053 -10000 0 -0.32 5 5
Syndecan-4/CXCL12 -0.064 0.14 -10000 0 -0.62 2 2
FGF6 0.031 0.025 -10000 0 -0.32 1 1
RHOA 0.034 0.005 -10000 0 -10000 0 0
CXCL12 -0.37 0.24 -10000 0 -0.51 159 159
TNFRSF13B 0.02 0.064 -10000 0 -0.51 3 3
FGF2 0.014 0.098 -10000 0 -0.48 8 8
FGFR1 0.03 0.012 -10000 0 -10000 0 0
Syndecan-4/PI-4-5-P2 0.01 0.062 -10000 0 -0.43 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.034 0.11 -10000 0 -0.33 24 24
cell migration -0.012 0.014 -10000 0 -10000 0 0
PRKCD 0.006 0.032 -10000 0 -10000 0 0
vasculogenesis 0.1 0.12 0.37 2 -0.4 1 3
SDC4 0.019 0.06 -10000 0 -0.45 1 1
Syndecan-4/Tenascin C 0.11 0.12 0.38 1 -0.43 1 2
Syndecan-4/PI-4-5-P2/PKC alpha -0.018 0.021 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.092 0.11 0.38 1 -10000 0 1
MMP9 0.009 0.063 -10000 0 -0.34 6 6
Rac1/GTP 0.008 0.048 0.2 4 -10000 0 4
cytoskeleton organization 0.1 0.11 0.37 1 -0.42 1 2
GIPC1 0.031 0.037 -10000 0 -0.51 1 1
Syndecan-4/TFPI 0.11 0.11 0.38 2 -0.43 1 3
IL23-mediated signaling events

Figure S73.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S73.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.22 0.35 -10000 0 -1.2 16 16
IL23A -0.24 0.28 -10000 0 -1.2 5 5
NF kappa B1 p50/RelA/I kappa B alpha -0.18 0.28 -10000 0 -1.1 6 6
positive regulation of T cell mediated cytotoxicity -0.2 0.29 -10000 0 -1.2 6 6
ITGA3 -0.19 0.27 -10000 0 -1.1 5 5
IL17F -0.13 0.2 -10000 0 -0.69 6 6
IL12B -0.002 0.053 -10000 0 -0.35 2 2
STAT1 (dimer) -0.2 0.3 -10000 0 -1.1 7 7
CD4 -0.17 0.26 -10000 0 -1.1 5 5
IL23 -0.24 0.28 -10000 0 -1.1 5 5
IL23R -0.051 0.24 -10000 0 -1.2 8 8
IL1B -0.23 0.29 -10000 0 -1.2 5 5
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.18 0.28 -10000 0 -1 7 7
TYK2 0.001 0.034 -10000 0 -10000 0 0
STAT4 0.032 0.037 -10000 0 -0.51 1 1
STAT3 0.034 0.006 -10000 0 -10000 0 0
IL18RAP -0.074 0.22 -10000 0 -0.5 43 43
IL12RB1 0.002 0.034 -10000 0 -10000 0 0
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.01 0.044 -10000 0 -10000 0 0
IL23R/JAK2 -0.053 0.23 -10000 0 -1.2 7 7
positive regulation of chronic inflammatory response -0.2 0.29 -10000 0 -1.2 6 6
natural killer cell activation 0.004 0.012 0.082 4 -10000 0 4
JAK2 -0.004 0.057 -10000 0 -0.35 3 3
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
NFKB1 0.032 0.006 -10000 0 -10000 0 0
RELA 0.032 0.006 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.23 0.27 -10000 0 -1 6 6
ALOX12B -0.18 0.26 -10000 0 -1.1 5 5
CXCL1 -0.25 0.28 -10000 0 -1.1 6 6
T cell proliferation -0.2 0.29 -10000 0 -1.2 6 6
NFKBIA 0.029 0.01 -10000 0 -10000 0 0
IL17A -0.1 0.17 -10000 0 -0.55 4 4
PI3K -0.17 0.28 -10000 0 -1.1 6 6
IFNG -0.023 0.039 0.15 3 -0.11 3 6
STAT3 (dimer) -0.14 0.28 -10000 0 -1.1 5 5
IL18R1 0.031 0.037 -10000 0 -0.5 1 1
IL23/IL23R/JAK2/TYK2/SOCS3 -0.11 0.18 -10000 0 -0.77 4 4
IL18/IL18R -0.063 0.19 -10000 0 -0.35 59 59
macrophage activation -0.018 0.015 -10000 0 -0.045 3 3
TNF -0.22 0.28 -10000 0 -1.2 5 5
STAT3/STAT4 -0.17 0.28 -10000 0 -1.1 6 6
STAT4 (dimer) -0.19 0.29 -10000 0 -1.2 6 6
IL18 -0.027 0.17 -10000 0 -0.5 24 24
IL19 -0.18 0.26 -10000 0 -1.1 4 4
STAT5A (dimer) -0.18 0.28 -10000 0 -1.1 6 6
STAT1 0.003 0.1 -10000 0 -0.32 19 19
SOCS3 0.02 0.067 -10000 0 -0.32 8 8
CXCL9 -0.24 0.37 -10000 0 -1.2 18 18
MPO -0.18 0.26 -10000 0 -1.1 5 5
positive regulation of humoral immune response -0.2 0.29 -10000 0 -1.2 6 6
IL23/IL23R/JAK2/TYK2 -0.2 0.3 -10000 0 -1.3 6 6
IL6 -0.22 0.3 -10000 0 -1.1 5 5
STAT5A 0.033 0.006 -10000 0 -10000 0 0
IL2 0.03 0.018 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.004 0.012 0.082 4 -10000 0 4
CD3E -0.18 0.26 -10000 0 -1.1 5 5
keratinocyte proliferation -0.2 0.29 -10000 0 -1.2 6 6
NOS2 -0.18 0.26 -10000 0 -1 6 6
Sphingosine 1-phosphate (S1P) pathway

Figure S74.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S74.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.031 0.037 -9999 0 -0.51 1 1
SPHK1 -0.011 0.12 -9999 0 -0.32 27 27
GNAI2 0.034 0.004 -9999 0 -10000 0 0
mol:S1P -0.003 0.05 -9999 0 -0.37 1 1
GNAO1 0.034 0.005 -9999 0 -10000 0 0
mol:Sphinganine-1-P -0.013 0.085 -9999 0 -0.23 27 27
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.023 0.055 -9999 0 -0.28 1 1
GNAI3 0.033 0.007 -9999 0 -10000 0 0
G12/G13 0.043 0.018 -9999 0 -10000 0 0
S1PR3 0 0 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.008 0.043 -9999 0 -0.32 1 1
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
GNAI1 -0.033 0.18 -9999 0 -0.51 26 26
S1P/S1P5/G12 0.01 0.05 -9999 0 -0.3 1 1
S1P/S1P3/Gq -0.002 0.088 -9999 0 -0.29 13 13
S1P/S1P4/Gi -0.013 0.099 -9999 0 -0.43 4 4
GNAQ 0 0 -9999 0 -10000 0 0
GNAZ 0.032 0.009 -9999 0 -10000 0 0
GNA14 0.011 0.11 -9999 0 -0.51 9 9
GNA15 0.024 0.058 -9999 0 -0.32 6 6
GNA12 0.031 0.01 -9999 0 -10000 0 0
GNA13 0.032 0.008 -9999 0 -10000 0 0
GNA11 0.018 0.089 -9999 0 -0.51 6 6
ABCC1 -0.001 0.1 -9999 0 -0.32 21 21
a4b1 and a4b7 Integrin signaling

Figure S75.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S75.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.032 0.024 -9999 0 -0.32 1 1
ITGB7 0.011 0.11 -9999 0 -0.51 9 9
ITGA4 0.029 0.052 -9999 0 -0.51 2 2
alpha4/beta7 Integrin 0.029 0.092 -9999 0 -0.37 11 11
alpha4/beta1 Integrin 0.045 0.044 -9999 0 -0.32 3 3
Paxillin-independent events mediated by a4b1 and a4b7

Figure S76.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S76.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.012 0.067 -9999 0 -0.28 10 10
CRKL 0.032 0.009 -9999 0 -10000 0 0
Rac1/GDP 0.023 0.008 -9999 0 -10000 0 0
DOCK1 0.028 0.052 -9999 0 -0.51 2 2
ITGA4 0.029 0.052 -9999 0 -0.51 2 2
alpha4/beta7 Integrin/MAdCAM1 -0.013 0.18 -9999 0 -0.32 51 51
EPO 0.031 0.025 -9999 0 -0.32 1 1
alpha4/beta7 Integrin 0.029 0.092 -9999 0 -0.37 11 11
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.027 0.014 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.045 0.044 -9999 0 -0.32 3 3
EPO/EPOR (dimer) 0.046 0.022 -9999 0 -0.22 1 1
lamellipodium assembly 0.006 0.091 -9999 0 -0.56 1 1
PIK3CA 0.034 0.004 -9999 0 -10000 0 0
PI3K 0.049 0.01 -9999 0 -10000 0 0
ARF6 0.031 0.01 -9999 0 -10000 0 0
JAK2 0.029 0.035 -9999 0 -0.24 2 2
PXN 0.034 0.003 -9999 0 -10000 0 0
PIK3R1 0.034 0.005 -9999 0 -10000 0 0
MADCAM1 -0.085 0.22 -9999 0 -0.51 47 47
cell adhesion -0.015 0.17 -9999 0 -0.31 51 51
CRKL/CBL 0.047 0.014 -9999 0 -10000 0 0
ITGB1 0.032 0.024 -9999 0 -0.32 1 1
SRC 0.004 0.054 -9999 0 -0.35 4 4
ITGB7 0.011 0.11 -9999 0 -0.51 9 9
RAC1 0.031 0.011 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.053 0.075 -9999 0 -0.36 6 6
p130Cas/Crk/Dock1 0.064 0.089 -9999 0 -0.48 1 1
VCAM1 0.021 0.081 -9999 0 -0.51 5 5
RHOA 0.034 0.005 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.079 0.044 -9999 0 -0.29 2 2
BCAR1 -0.003 0.049 -9999 0 -0.33 4 4
EPOR 0.034 0.005 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.034 0.005 -9999 0 -10000 0 0
GIT1 0.033 0.007 -9999 0 -10000 0 0
Rac1/GTP 0.006 0.093 -9999 0 -0.58 1 1
Signaling events mediated by HDAC Class III

Figure S77.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S77.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.032 0.009 -10000 0 -10000 0 0
HDAC4 0.034 0.004 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.009 0.013 -10000 0 -10000 0 0
CDKN1A -0.01 0.066 0.31 1 -0.65 2 3
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.032 0.024 -10000 0 -0.32 1 1
FOXO3 -0.007 0.004 -10000 0 -10000 0 0
FOXO1 0.01 0.089 -10000 0 -0.51 6 6
FOXO4 0.02 0.007 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.032 0.009 -10000 0 -10000 0 0
TAT 0.034 0.005 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.007 0.027 -10000 0 -0.22 3 3
PPARGC1A -0.2 0.27 -10000 0 -0.51 91 91
FHL2 0.033 0.024 -10000 0 -0.32 1 1
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.044 0.017 -10000 0 -10000 0 0
HIST2H4A 0.009 0.013 -10000 0 -10000 0 0
SIRT1/FOXO3a 0.024 0.028 0.27 1 -10000 0 1
SIRT1 0.031 0.017 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.064 0.021 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.026 0.043 -10000 0 -10000 0 0
apoptosis -0.058 0.028 -10000 0 -10000 0 0
SIRT1/PGC1A -0.11 0.17 -10000 0 -0.31 89 89
p53/SIRT1 0.022 0.057 0.41 1 -10000 0 1
SIRT1/FOXO4 0.029 0.04 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 0.035 0.066 -10000 0 -0.31 6 6
HIST1H1E 0.019 0.012 -10000 0 -10000 0 0
SIRT1/p300 0.044 0.017 -10000 0 -10000 0 0
muscle cell differentiation -0.018 0.026 -10000 0 -10000 0 0
TP53 0.011 0.068 0.22 1 -0.32 8 9
KU70/SIRT1/BAX 0.059 0.028 -10000 0 -10000 0 0
CREBBP 0.033 0.007 -10000 0 -10000 0 0
MEF2D 0.033 0.006 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.047 0.016 -10000 0 -10000 0 0
ACSS2 0.009 0.037 0.36 1 -0.37 1 2
SIRT1/PCAF/MYOD 0.018 0.026 -10000 0 -10000 0 0
EPHB forward signaling

Figure S78.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S78.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.033 0.049 -10000 0 -0.22 7 7
cell-cell adhesion 0.048 0.082 -10000 0 -10000 0 0
Ephrin B/EPHB2/RasGAP 0.049 0.067 -10000 0 -0.26 2 2
ITSN1 0.033 0.007 -10000 0 -10000 0 0
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
SHC1 0.033 0.006 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.017 0.079 -10000 0 -0.2 25 25
Ephrin B1/EPHB1 -0.037 0.11 -10000 0 -0.18 78 78
HRAS/GDP -0.04 0.11 -10000 0 -0.4 4 4
Ephrin B/EPHB1/GRB7 0.007 0.1 -10000 0 -10000 0 0
Endophilin/SYNJ1 0.055 0.082 -10000 0 -10000 0 0
KRAS 0.033 0.006 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.012 0.078 -10000 0 -10000 0 0
endothelial cell migration 0.021 0.077 -10000 0 -0.26 1 1
GRB2 0.033 0.007 -10000 0 -10000 0 0
GRB7 0.03 0.025 -10000 0 -0.32 1 1
PAK1 0.062 0.087 0.36 1 -10000 0 1
HRAS 0.034 0.005 -10000 0 -10000 0 0
RRAS 0.058 0.083 -10000 0 -10000 0 0
DNM1 0.03 0.034 -10000 0 -0.32 2 2
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.004 0.098 0.36 1 -0.31 1 2
lamellipodium assembly -0.048 0.082 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.015 0.056 -10000 0 -10000 0 0
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
EPHB2 0.021 0.064 -10000 0 -0.35 6 6
EPHB3 -0.01 0.12 -10000 0 -0.34 25 25
EPHB1 -0.094 0.17 -10000 0 -0.32 78 78
EPHB4 -0.021 0.13 -10000 0 -0.32 33 33
mol:GDP -0.03 0.11 0.33 1 -0.4 4 5
Ephrin B/EPHB2 0.039 0.055 -10000 0 -0.26 2 2
Ephrin B/EPHB3 0.025 0.075 -10000 0 -0.26 3 3
JNK cascade -0.042 0.11 0.36 4 -0.31 7 11
Ephrin B/EPHB1 -0.007 0.093 -10000 0 -0.25 1 1
RAP1/GDP -0.014 0.13 0.34 2 -0.38 3 5
EFNB2 0.022 0.039 -10000 0 -0.51 1 1
EFNB3 0.027 0.014 -10000 0 -10000 0 0
EFNB1 0.034 0.002 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.019 0.098 -10000 0 -0.3 4 4
RAP1B 0.034 0.004 -10000 0 -10000 0 0
RAP1A 0.032 0.008 -10000 0 -10000 0 0
CDC42/GTP -0.014 0.093 -10000 0 -0.31 1 1
Rap1/GTP -0.023 0.076 -10000 0 -10000 0 0
axon guidance 0.032 0.049 -10000 0 -0.22 7 7
MAPK3 0.017 0.06 -10000 0 -10000 0 0
MAPK1 0.02 0.054 -10000 0 -10000 0 0
Rac1/GDP -0.026 0.11 -10000 0 -0.37 4 4
actin cytoskeleton reorganization -0.053 0.082 -10000 0 -0.29 4 4
CDC42/GDP -0.018 0.13 0.35 3 -0.39 3 6
PI3K 0.024 0.08 -10000 0 -0.27 1 1
EFNA5 0.031 0.037 -10000 0 -0.51 1 1
Ephrin B2/EPHB4 0.003 0.076 -10000 0 -0.18 28 28
Ephrin B/EPHB2/Intersectin/N-WASP 0.016 0.048 -10000 0 -0.32 1 1
CDC42 0.032 0.009 -10000 0 -10000 0 0
RAS family/GTP -0.026 0.074 -10000 0 -10000 0 0
PTK2 0.11 0.22 0.6 37 -10000 0 37
MAP4K4 -0.043 0.11 0.36 4 -0.31 7 11
SRC 0.019 0.017 -10000 0 -10000 0 0
KALRN 0.034 0.005 -10000 0 -10000 0 0
Intersectin/N-WASP 0.045 0.032 -10000 0 -0.37 1 1
neuron projection morphogenesis -0.008 0.13 0.4 9 -10000 0 9
MAP2K1 0.018 0.055 -10000 0 -10000 0 0
WASL 0.03 0.037 -10000 0 -0.51 1 1
Ephrin B1/EPHB1-2/NCK1 -0.014 0.12 -10000 0 -0.31 5 5
cell migration 0.046 0.093 0.36 4 -10000 0 4
NRAS 0.029 0.034 -10000 0 -0.32 2 2
SYNJ1 0.056 0.082 -10000 0 -10000 0 0
PXN 0.034 0.003 -10000 0 -10000 0 0
TF 0.038 0.086 0.2 2 -10000 0 2
HRAS/GTP -0.012 0.089 -10000 0 -0.27 2 2
Ephrin B1/EPHB1-2 -0.026 0.11 -10000 0 -0.31 5 5
cell adhesion mediated by integrin -0.045 0.094 0.25 1 -0.2 50 51
RAC1 0.031 0.011 -10000 0 -10000 0 0
mol:GTP -0.011 0.094 -10000 0 -0.28 2 2
RAC1-CDC42/GTP -0.041 0.084 -10000 0 -0.36 3 3
RASA1 0.03 0.034 -10000 0 -0.32 2 2
RAC1-CDC42/GDP -0.019 0.12 -10000 0 -0.38 3 3
ruffle organization -0.009 0.14 0.44 8 -10000 0 8
NCK1 0.034 0.005 -10000 0 -10000 0 0
receptor internalization 0.037 0.087 0.2 2 -10000 0 2
Ephrin B/EPHB2/KALRN 0.05 0.064 -10000 0 -0.26 2 2
ROCK1 0.002 0.057 -10000 0 -0.28 3 3
RAS family/GDP -0.051 0.077 -10000 0 -0.3 3 3
Rac1/GTP -0.047 0.089 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/Paxillin 0.007 0.042 -10000 0 -10000 0 0
Regulation of Telomerase

Figure S79.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S79.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.006 0.11 -10000 0 -10000 0 0
RAD9A 0.034 0.005 -10000 0 -10000 0 0
AP1 -0.009 0.14 -10000 0 -0.34 28 28
IFNAR2 0.034 0.008 -10000 0 -10000 0 0
AKT1 0.019 0.052 -10000 0 -0.44 2 2
ER alpha/Oestrogen 0.016 0.059 -10000 0 -0.36 5 5
NFX1/SIN3/HDAC complex 0.044 0.055 -10000 0 -10000 0 0
EGF -0.09 0.21 -10000 0 -0.42 58 58
SMG5 0.033 0.006 -10000 0 -10000 0 0
SMG6 0.027 0.014 -10000 0 -10000 0 0
SP3/HDAC2 0.05 0.012 -10000 0 -10000 0 0
TERT/c-Abl 0.013 0.11 -10000 0 -10000 0 0
SAP18 0.025 0.015 -10000 0 -10000 0 0
MRN complex 0.057 0.027 -10000 0 -10000 0 0
WT1 -0.16 0.18 -10000 0 -0.32 116 116
WRN 0.027 0.014 -10000 0 -10000 0 0
SP1 0.035 0.006 -10000 0 -10000 0 0
SP3 0.035 0.003 -10000 0 -10000 0 0
TERF2IP 0.034 0.005 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.002 0.13 -10000 0 -10000 0 0
Mad/Max 0.024 0.096 -10000 0 -0.36 12 12
TERT 0.005 0.11 -10000 0 -10000 0 0
CCND1 -0.009 0.12 -10000 0 -10000 0 0
MAX 0.031 0.01 -10000 0 -10000 0 0
RBBP7 0.034 0.005 -10000 0 -10000 0 0
RBBP4 0.033 0.007 -10000 0 -10000 0 0
TERF2 0.031 0.011 -10000 0 -10000 0 0
PTGES3 0.034 0.004 -10000 0 -10000 0 0
SIN3A 0.032 0.009 -10000 0 -10000 0 0
Telomerase/911 0.028 0.062 0.3 1 -10000 0 1
CDKN1B -0.016 0.088 -10000 0 -0.3 3 3
RAD1 0.023 0.058 -10000 0 -0.32 6 6
XRCC5 0.034 0.002 -10000 0 -10000 0 0
XRCC6 0.032 0.009 -10000 0 -10000 0 0
SAP30 0.033 0.008 -10000 0 -10000 0 0
TRF2/PARP2 0.044 0.017 -10000 0 -10000 0 0
UBE3A 0.032 0.009 -10000 0 -10000 0 0
JUN 0.026 0.053 -10000 0 -0.32 5 5
E6 0 0.001 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.024 0.008 -10000 0 -10000 0 0
FOS -0.027 0.16 -10000 0 -0.49 24 24
IFN-gamma/IRF1 -0.002 0.11 -10000 0 -0.37 2 2
PARP2 0.031 0.01 -10000 0 -10000 0 0
BLM 0.029 0.035 -10000 0 -0.32 2 2
Telomerase -0.021 0.12 -10000 0 -0.68 3 3
IRF1 0.034 0.045 -10000 0 -0.4 2 2
ESR1 0.02 0.081 -10000 0 -0.5 5 5
KU/TER 0.047 0.013 -10000 0 -10000 0 0
ATM/TRF2 0.048 0.012 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.038 0.069 -10000 0 -0.29 2 2
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.039 0.07 -10000 0 -0.3 2 2
HDAC1 0.033 0.007 -10000 0 -10000 0 0
HDAC2 0.034 0.008 -10000 0 -10000 0 0
ATM 0.013 0.005 -10000 0 -10000 0 0
SMAD3 0.017 0.006 -10000 0 -10000 0 0
ABL1 0.034 0.005 -10000 0 -10000 0 0
MXD1 0.005 0.12 -10000 0 -0.51 12 12
MRE11A 0.034 0.005 -10000 0 -10000 0 0
HUS1 0.031 0.01 -10000 0 -10000 0 0
RPS6KB1 0.032 0.008 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.022 0.13 -10000 0 -10000 0 0
NR2F2 0.031 0.009 -10000 0 -10000 0 0
MAPK3 0.016 0.037 -10000 0 -0.37 2 2
MAPK1 0.018 0.006 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.033 0.006 -10000 0 -10000 0 0
NFKB1 0.033 0.006 -10000 0 -10000 0 0
HNRNPC 0.031 0.01 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.013 0.005 -10000 0 -10000 0 0
NBN 0.029 0.012 -10000 0 -10000 0 0
EGFR 0.021 0.073 -10000 0 -0.51 4 4
mol:Oestrogen 0 0.001 -10000 0 -10000 0 0
EGF/EGFR -0.05 0.16 -10000 0 -0.3 56 56
MYC -0.13 0.17 -10000 0 -0.32 96 96
IL2 0.035 0.007 -10000 0 -10000 0 0
KU 0.047 0.013 -10000 0 -10000 0 0
RAD50 0.034 0.005 -10000 0 -10000 0 0
HSP90AA1 0.031 0.011 -10000 0 -10000 0 0
TGFB1 0.033 0.006 -10000 0 -10000 0 0
TRF2/BLM 0.044 0.029 -10000 0 -0.21 2 2
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.028 0.12 -10000 0 -10000 0 0
SP1/HDAC2 0.051 0.015 -10000 0 -10000 0 0
PINX1 0.024 0.028 -10000 0 -0.32 1 1
Telomerase/EST1A -0.003 0.12 -10000 0 -10000 0 0
Smad3/Myc -0.066 0.1 -10000 0 -0.26 1 1
911 complex 0.052 0.047 -10000 0 -10000 0 0
IFNG -0.037 0.14 -10000 0 -0.31 46 46
Telomerase/PinX1 -0.009 0.12 -10000 0 -10000 0 0
Telomerase/AKT1/mTOR/p70S6K -0.009 0.12 0.29 1 -0.51 5 6
SIN3B 0.034 0.005 -10000 0 -10000 0 0
YWHAE 0.027 0.014 -10000 0 -10000 0 0
Telomerase/EST1B 0.002 0.13 -10000 0 -10000 0 0
response to DNA damage stimulus 0.002 0.022 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.08 0.039 -10000 0 -10000 0 0
TRF2/WRN 0.038 0.022 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.003 0.13 -10000 0 -10000 0 0
E2F1 0.015 0.043 -10000 0 -0.32 3 3
ZNFX1 0.019 0.017 -10000 0 -10000 0 0
PIF1 0.026 0.048 -10000 0 -0.32 4 4
NCL 0.034 0.003 -10000 0 -10000 0 0
DKC1 -0.069 0.16 -10000 0 -0.32 63 63
telomeric DNA binding 0 0 -10000 0 -10000 0 0
VEGFR1 specific signals

Figure S80.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S80.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.015 0.067 -10000 0 -0.4 2 2
VEGFR1 homodimer/NRP1 -0.001 0.06 -10000 0 -0.39 2 2
mol:DAG 0.013 0.083 -10000 0 -0.4 3 3
VEGFR1 homodimer/NRP1/VEGFR 121 0.008 0.074 -10000 0 -0.4 3 3
CaM/Ca2+ 0.025 0.084 -10000 0 -0.41 2 2
HIF1A 0.026 0.061 -10000 0 -0.46 2 2
GAB1 0.029 0.052 -10000 0 -0.51 2 2
AKT1 0.038 0.096 0.34 1 -0.52 1 2
PLCG1 0.013 0.083 -10000 0 -0.4 3 3
NOS3 0.084 0.12 0.3 24 -0.42 1 25
CBL 0.034 0.005 -10000 0 -10000 0 0
mol:NO 0.09 0.12 0.31 27 -0.4 1 28
FLT1 0.001 0.073 -10000 0 -0.46 2 2
PGF 0.016 0.072 -10000 0 -0.32 9 9
VEGFR1 homodimer/NRP2/VEGFR121 0.021 0.087 -10000 0 -0.45 3 3
CALM1 0.03 0.011 -10000 0 -10000 0 0
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
eNOS/Hsp90 0.1 0.12 0.35 9 -0.4 1 10
endothelial cell proliferation 0.086 0.14 0.34 28 -0.42 1 29
mol:Ca2+ 0.013 0.083 -10000 0 -0.4 3 3
MAPK3 0.01 0.097 0.34 4 -0.43 2 6
MAPK1 0.011 0.089 0.34 4 -0.45 1 5
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
PLGF homodimer 0.016 0.072 -10000 0 -0.32 9 9
PRKACA 0.034 0.005 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.025 0.055 -10000 0 -0.36 4 4
VEGFA homodimer 0.006 0.095 -10000 0 -0.32 17 17
VEGFR1 homodimer/VEGFA homodimer 0.008 0.082 -10000 0 -0.44 3 3
platelet activating factor biosynthetic process 0.066 0.14 0.34 23 -0.42 2 25
PI3K 0.073 0.1 -10000 0 -0.48 1 1
PRKCA 0.018 0.094 0.36 4 -0.47 1 5
PRKCB 0.007 0.077 -10000 0 -0.4 2 2
VEGFR1 homodimer/PLGF homodimer 0.01 0.081 -10000 0 -0.44 3 3
VEGFA 0.006 0.095 -10000 0 -0.32 17 17
VEGFB 0.034 0.005 -10000 0 -10000 0 0
mol:IP3 0.013 0.083 -10000 0 -0.4 3 3
RASA1 0.045 0.1 -10000 0 -0.36 2 2
NRP2 0.033 0.024 -10000 0 -0.32 1 1
VEGFR1 homodimer 0.001 0.072 -10000 0 -0.46 2 2
VEGFB homodimer 0.034 0.005 -10000 0 -10000 0 0
NCK1 0.034 0.005 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.092 0.12 0.3 22 -0.4 1 23
PTPN11 0.032 0.024 -10000 0 -0.32 1 1
mol:PI-3-4-5-P3 0.071 0.1 -10000 0 -0.47 1 1
mol:L-citrulline 0.09 0.12 0.31 27 -0.4 1 28
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.072 0.1 -10000 0 -0.41 2 2
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.021 0.082 -10000 0 -0.4 3 3
CD2AP 0.034 0.005 -10000 0 -10000 0 0
PI3K/GAB1 0.081 0.11 -10000 0 -0.69 1 1
PDPK1 0.039 0.099 0.35 1 -0.45 1 2
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.022 0.082 -10000 0 -0.4 3 3
mol:NADP 0.09 0.12 0.31 27 -0.4 1 28
HSP90AA1 0.031 0.011 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.07 0.1 -10000 0 -0.41 2 2
VEGFR1 homodimer/NRP2 0.014 0.072 -10000 0 -0.47 2 2
Canonical NF-kappaB pathway

Figure S81.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S81.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.037 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.056 0.086 0.4 3 -10000 0 3
ERC1 0.033 0.007 -10000 0 -10000 0 0
RIP2/NOD2 -0.033 0.13 -10000 0 -0.23 59 59
NFKBIA 0.019 0.008 -10000 0 -10000 0 0
BIRC2 0.033 0.006 -10000 0 -10000 0 0
IKBKB 0.029 0.012 -10000 0 -10000 0 0
RIPK2 -0.012 0.11 -10000 0 -0.32 25 25
IKBKG 0.017 0.051 -10000 0 -10000 0 0
IKK complex/A20 0.052 0.063 -10000 0 -10000 0 0
NEMO/A20/RIP2 -0.012 0.11 -10000 0 -0.32 25 25
XPO1 0.034 0 -10000 0 -10000 0 0
NEMO/ATM 0.039 0.064 0.28 2 -10000 0 2
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.032 0.024 -10000 0 -0.32 1 1
Exportin 1/RanGTP 0.045 0.016 -10000 0 -0.18 1 1
IKK complex/ELKS 0.042 0.054 -10000 0 -10000 0 0
BCL10/MALT1/TRAF6 0.047 0.033 -10000 0 -10000 0 0
NOD2 -0.04 0.14 -10000 0 -0.32 45 45
NFKB1 0.036 0.006 -10000 0 -10000 0 0
RELA 0.036 0.006 -10000 0 -10000 0 0
MALT1 0.024 0.016 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.048 0.012 -10000 0 -10000 0 0
ATM 0.033 0.007 -10000 0 -10000 0 0
TNF/TNFR1A 0.048 0.013 -10000 0 -10000 0 0
TRAF6 0.034 0.005 -10000 0 -10000 0 0
PRKCA 0.031 0.025 -10000 0 -0.32 1 1
CHUK 0.033 0.008 -10000 0 -10000 0 0
UBE2D3 0.033 0.006 -10000 0 -10000 0 0
TNF 0.034 0.005 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.075 0.019 -10000 0 -10000 0 0
BCL10 0.033 0.006 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.019 0.008 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.037 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.033 0.008 -10000 0 -10000 0 0
IKK complex 0.044 0.059 -10000 0 -10000 0 0
CYLD 0.034 0.004 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.052 0.065 -10000 0 -10000 0 0
ErbB4 signaling events

Figure S82.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S82.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.069 0.047 -10000 0 -10000 0 0
epithelial cell differentiation 0.062 0.061 -10000 0 -10000 0 0
ITCH 0.021 0.019 -10000 0 -10000 0 0
WWP1 0.019 0.038 -10000 0 -10000 0 0
FYN 0.03 0.037 -10000 0 -0.51 1 1
EGFR 0.021 0.073 -10000 0 -0.51 4 4
PRL 0.032 0.024 -10000 0 -0.32 1 1
neuron projection morphogenesis 0.046 0.051 0.29 1 -10000 0 1
PTPRZ1 -0.018 0.16 -10000 0 -0.49 21 21
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.07 0.054 -10000 0 -10000 0 0
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.044 0.035 -10000 0 -10000 0 0
ADAM17 0.03 0.01 -10000 0 -10000 0 0
ErbB4/ErbB4 0.02 0.025 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.07 0.046 -10000 0 -10000 0 0
NCOR1 0.027 0.014 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.055 0.043 -10000 0 -10000 0 0
GRIN2B 0.022 0.064 -10000 0 -10000 0 0
ErbB4/ErbB2/betacellulin 0.062 0.061 -10000 0 -10000 0 0
STAT1 0.003 0.1 -10000 0 -0.32 19 19
HBEGF 0.029 0.041 -10000 0 -0.32 3 3
PRLR 0.03 0.034 -10000 0 -0.32 2 2
E4ICDs/ETO2 -0.034 0.15 -10000 0 -10000 0 0
axon guidance 0.018 0.057 -10000 0 -10000 0 0
NEDD4 0.017 0.058 -10000 0 -0.32 6 6
Prolactin receptor/Prolactin receptor/Prolactin 0.044 0.033 -10000 0 -0.22 3 3
CBFA2T3 -0.16 0.26 -10000 0 -0.5 76 76
ErbB4/ErbB2/HBEGF 0.066 0.05 -10000 0 -10000 0 0
MAPK3 0.043 0.051 0.27 1 -10000 0 1
STAT1 (dimer) 0.057 0.071 -10000 0 -10000 0 0
MAPK1 0.046 0.043 -10000 0 -10000 0 0
JAK2 0.028 0.042 -10000 0 -0.32 3 3
ErbB4/ErbB2/neuregulin 1 beta 0.035 0.042 -10000 0 -10000 0 0
NRG1 0.014 0.008 -10000 0 -10000 0 0
NRG3 0.031 0.037 -10000 0 -0.51 1 1
NRG2 0.021 0.081 -10000 0 -0.51 5 5
NRG4 0.02 0.075 -10000 0 -0.41 6 6
heart development 0.018 0.057 -10000 0 -10000 0 0
neural crest cell migration 0.035 0.042 -10000 0 -10000 0 0
ERBB2 0.022 0.045 0.23 6 -0.37 1 7
WWOX/E4ICDs 0.07 0.039 -10000 0 -10000 0 0
SHC1 0.033 0.006 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.063 0.072 -10000 0 -10000 0 0
apoptosis -0.053 0.077 0.36 4 -10000 0 4
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.065 0.061 -10000 0 -10000 0 0
ErbB4/ErbB2/epiregulin -0.036 0.11 -10000 0 -0.39 1 1
ErbB4/ErbB4/betacellulin/betacellulin 0.065 0.056 -10000 0 -10000 0 0
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.098 0.062 -10000 0 -10000 0 0
MDM2 0.016 0.021 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.024 0.026 -10000 0 -10000 0 0
STAT5A 0.036 0.063 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta 0.047 0.053 -10000 0 -10000 0 0
DLG4 0.027 0.014 -10000 0 -10000 0 0
GRB2/SHC 0.048 0.013 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.051 0.041 -10000 0 -10000 0 0
STAT5A (dimer) 0.08 0.073 0.32 1 -10000 0 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.063 0.066 -10000 0 -10000 0 0
LRIG1 0.011 0.11 -10000 0 -0.51 9 9
EREG -0.21 0.17 -10000 0 -0.32 146 146
BTC 0.021 0.081 -10000 0 -0.51 5 5
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.017 0.055 -10000 0 -10000 0 0
ERBB4 0.02 0.025 -10000 0 -10000 0 0
STAT5B 0.033 0.006 -10000 0 -10000 0 0
YAP1 0.005 0.069 -10000 0 -0.42 5 5
GRB2 0.033 0.007 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.059 0.062 -10000 0 -10000 0 0
glial cell differentiation -0.051 0.04 -10000 0 -10000 0 0
WWOX 0.033 0.006 -10000 0 -10000 0 0
cell proliferation 0.04 0.069 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

Figure S83.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S83.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.018 0.23 1 -10000 0 1
BAD/BCL-XL/YWHAZ 0.031 0.032 -10000 0 -10000 0 0
CDKN1B 0.037 0.082 0.28 1 -0.63 1 2
CDKN1A 0.033 0.087 -10000 0 -0.63 1 1
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.022 0.054 -10000 0 -0.32 5 5
FOXO3 0.04 0.066 -10000 0 -10000 0 0
AKT1 0.028 0.08 -10000 0 -0.66 1 1
BAD 0.034 0.005 -10000 0 -10000 0 0
AKT3 0.019 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.034 0.086 -10000 0 -0.63 1 1
AKT1/ASK1 0.044 0.11 0.28 1 -0.6 1 2
BAD/YWHAZ 0.056 0.028 -10000 0 -10000 0 0
RICTOR 0.031 0.025 -10000 0 -0.32 1 1
RAF1 0.033 0.006 -10000 0 -10000 0 0
JNK cascade -0.042 0.11 0.57 1 -0.27 1 2
TSC1 0.034 0.086 -10000 0 -0.63 1 1
YWHAZ 0.029 0.013 -10000 0 -10000 0 0
AKT1/RAF1 0.052 0.11 0.3 2 -0.63 1 3
EP300 0.032 0.009 -10000 0 -10000 0 0
mol:GDP 0.028 0.079 -10000 0 -0.65 1 1
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.034 0.083 -10000 0 -0.63 1 1
YWHAQ 0.034 0 -10000 0 -10000 0 0
TBC1D4 0.066 0.11 0.24 55 -0.29 1 56
MAP3K5 0.03 0.034 -10000 0 -0.32 2 2
MAPKAP1 0.03 0.034 -10000 0 -0.32 2 2
negative regulation of cell cycle -0.057 0.1 0.3 4 -0.25 16 20
YWHAH 0.032 0.008 -10000 0 -10000 0 0
AKT1S1 0.038 0.085 0.28 1 -0.63 1 2
CASP9 0.035 0.077 -10000 0 -0.63 1 1
YWHAB 0.018 0.017 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.052 0.12 0.38 3 -0.6 1 4
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.035 0.035 -10000 0 -10000 0 0
YWHAE 0.027 0.014 -10000 0 -10000 0 0
SRC 0.019 0.017 -10000 0 -10000 0 0
AKT2/p21CIP1 0.019 0.086 -10000 0 -0.57 1 1
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.025 0.035 -10000 0 -10000 0 0
CHUK 0.039 0.066 -10000 0 -10000 0 0
BAD/BCL-XL 0.022 0.08 -10000 0 -0.6 1 1
mTORC2 0.038 0.026 -10000 0 -0.16 3 3
AKT2 0.019 0.005 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.068 0.14 0.34 14 -0.4 5 19
PDPK1 0.033 0.006 -10000 0 -10000 0 0
MDM2 0.037 0.084 0.28 1 -0.63 1 2
MAPKKK cascade -0.052 0.11 0.61 1 -0.29 2 3
MDM2/Cbp/p300 0.054 0.11 -10000 0 -0.58 1 1
TSC1/TSC2 0.031 0.083 0.35 1 -0.61 1 2
proteasomal ubiquitin-dependent protein catabolic process 0.052 0.1 -10000 0 -0.55 1 1
glucose import -0.022 0.14 0.21 28 -0.27 40 68
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.038 0.063 0.25 3 -0.35 1 4
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.022 0.14 0.21 28 -0.27 40 68
GSK3A 0.038 0.086 0.28 1 -0.63 1 2
FOXO1 0.055 0.12 0.28 17 -0.63 1 18
GSK3B 0.036 0.089 0.28 1 -0.63 1 2
SFN 0.026 0.053 -10000 0 -0.51 2 2
G1/S transition of mitotic cell cycle 0.039 0.11 0.37 4 -0.61 1 5
p27Kip1/14-3-3 family 0.055 0.06 0.29 1 -10000 0 1
PRKACA 0.034 0.005 -10000 0 -10000 0 0
KPNA1 0.034 0.005 -10000 0 -10000 0 0
HSP90AA1 0.031 0.011 -10000 0 -10000 0 0
YWHAG 0.033 0.008 -10000 0 -10000 0 0
RHEB 0.033 0.007 -10000 0 -10000 0 0
CREBBP 0.033 0.007 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

Figure S84.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S84.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.036 0.12 -10000 0 -10000 0 0
MKNK1 0.034 0.005 -10000 0 -10000 0 0
MAPK14 -0.001 0.07 -10000 0 -10000 0 0
ATF2/c-Jun -0.004 0.067 -10000 0 -0.38 2 2
MAPK11 -0.001 0.069 -10000 0 -0.3 1 1
MITF -0.004 0.066 -10000 0 -10000 0 0
MAPKAPK5 -0.004 0.068 -10000 0 -0.27 1 1
KRT8 -0.007 0.073 -10000 0 -0.29 4 4
MAPKAPK3 0.034 0.004 -10000 0 -10000 0 0
MAPKAPK2 0.033 0.006 -10000 0 -10000 0 0
p38alpha-beta/CK2 0 0.091 -10000 0 -10000 0 0
CEBPB -0.004 0.059 -10000 0 -10000 0 0
SLC9A1 -0.006 0.065 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.004 0.071 -10000 0 -0.33 1 1
p38alpha-beta/MNK1 0.016 0.084 -10000 0 -10000 0 0
JUN -0.005 0.066 -10000 0 -0.38 2 2
PPARGC1A -0.15 0.19 -10000 0 -0.36 91 91
USF1 -0.01 0.075 -10000 0 -10000 0 0
RAB5/GDP/GDI1 0.007 0.055 -10000 0 -10000 0 0
NOS2 -0.012 0.065 -10000 0 -0.27 1 1
DDIT3 -0.005 0.066 -10000 0 -10000 0 0
RAB5A 0.034 0.005 -10000 0 -10000 0 0
HSPB1 0.001 0.079 0.29 8 -10000 0 8
p38alpha-beta/HBP1 0.016 0.083 -10000 0 -10000 0 0
CREB1 -0.002 0.065 -10000 0 -0.36 1 1
RAB5/GDP 0.025 0.004 -10000 0 -10000 0 0
EIF4E -0.007 0.058 -10000 0 -10000 0 0
RPS6KA4 -0.002 0.062 -10000 0 -10000 0 0
PLA2G4A -0.076 0.13 -10000 0 -0.3 37 37
GDI1 -0.002 0.063 -10000 0 -10000 0 0
TP53 -0.021 0.064 -10000 0 -10000 0 0
RPS6KA5 -0.01 0.075 -10000 0 -0.35 4 4
ESR1 -0.01 0.079 -10000 0 -0.31 6 6
HBP1 0.033 0.008 -10000 0 -10000 0 0
MEF2C -0.055 0.14 -10000 0 -0.34 32 32
MEF2A -0.004 0.066 -10000 0 -0.27 1 1
EIF4EBP1 -0.009 0.077 -10000 0 -0.34 3 3
KRT19 -0.01 0.081 -10000 0 -0.34 5 5
ELK4 -0.003 0.068 -10000 0 -10000 0 0
ATF6 -0.002 0.065 -10000 0 -0.27 1 1
ATF1 -0.002 0.066 -10000 0 -0.36 1 1
p38alpha-beta/MAPKAPK2 0.02 0.081 -10000 0 -10000 0 0
p38alpha-beta/MAPKAPK3 0.017 0.085 -10000 0 -10000 0 0
Effects of Botulinum toxin

Figure S85.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S85.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.001 0.043 -10000 0 -0.22 8 8
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.048 0.013 -10000 0 -10000 0 0
STXBP1 0.013 0.084 -10000 0 -0.32 13 13
ACh/CHRNA1 0.018 0.041 -10000 0 -10000 0 0
RAB3GAP2/RIMS1/UNC13B 0.063 0.02 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.033 0.007 -10000 0 -10000 0 0
mol:ACh 0 0.046 0.1 8 -0.11 12 20
RAB3GAP2 0.033 0.006 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.019 0.079 -10000 0 -10000 0 0
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.018 0.041 -10000 0 -10000 0 0
UNC13B 0.033 0.006 -10000 0 -10000 0 0
CHRNA1 0.034 0.002 -10000 0 -10000 0 0
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.01 0.078 -10000 0 -0.19 27 27
SNAP25 0.002 0.029 -10000 0 -0.29 2 2
VAMP2 0.005 0.003 -10000 0 -10000 0 0
SYT1 -0.012 0.12 -10000 0 -0.32 28 28
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.01 0.063 -10000 0 -0.18 21 21
STX1A/SNAP25 fragment 1/VAMP2 0.019 0.079 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

Figure S86.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S86.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.017 0.084 -10000 0 -0.46 5 5
KLHL20 0.045 0.092 0.23 12 -0.23 4 16
CYFIP2 0.029 0.052 -10000 0 -0.51 2 2
Rac1/GDP 0.074 0.098 0.29 6 -10000 0 6
ENAH 0.013 0.086 -10000 0 -0.46 5 5
AP1M1 0.034 0.004 -10000 0 -10000 0 0
RAP1B 0.034 0.004 -10000 0 -10000 0 0
RAP1A 0.032 0.008 -10000 0 -10000 0 0
CTNNB1 0.026 0.053 -10000 0 -0.32 5 5
CDC42/GTP 0.051 0.067 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.015 0.036 -10000 0 -0.18 5 5
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.04 0.098 -10000 0 -0.28 14 14
RAPGEF1 0.059 0.11 0.32 4 -0.41 4 8
CTNND1 0.034 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.024 0.087 -10000 0 -0.48 5 5
CRK 0.054 0.11 -10000 0 -0.44 4 4
E-cadherin/gamma catenin/alpha catenin 0.056 0.06 -10000 0 -0.31 5 5
alphaE/beta7 Integrin 0.024 0.083 -10000 0 -0.36 9 9
IQGAP1 0.032 0.009 -10000 0 -10000 0 0
NCKAP1 0.033 0.024 -10000 0 -0.32 1 1
Rap1/GTP/I-afadin 0.06 0.02 -10000 0 -10000 0 0
DLG1 0.017 0.084 -10000 0 -0.46 5 5
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0.026 -10000 0 -10000 0 0
MLLT4 0.033 0.007 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.05 0.045 -10000 0 -0.28 2 2
PI3K 0.003 0.035 -10000 0 -10000 0 0
ARF6 0.031 0.01 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.038 0.064 -10000 0 -0.37 5 5
TIAM1 0.027 0.052 -10000 0 -0.51 2 2
E-cadherin(dimer)/Ca2+ 0.062 0.065 -10000 0 -0.27 5 5
AKT1 0.035 0.052 0.18 4 -10000 0 4
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
CDH1 0.021 0.081 -10000 0 -0.51 5 5
RhoA/GDP 0.092 0.1 0.31 8 -10000 0 8
actin cytoskeleton organization 0.042 0.08 0.22 15 -0.17 4 19
CDC42/GDP 0.086 0.11 0.31 9 -10000 0 9
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.02 0.041 -10000 0 -0.24 5 5
ITGB7 0.011 0.11 -10000 0 -0.51 9 9
RAC1 0.031 0.011 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.067 0.07 -10000 0 -0.29 5 5
E-cadherin/Ca2+/beta catenin/alpha catenin 0.045 0.059 -10000 0 -0.27 5 5
mol:GDP 0.08 0.11 0.32 9 -0.33 1 10
CDC42/GTP/IQGAP1 0.04 0.016 -10000 0 -10000 0 0
JUP 0.033 0.007 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.1 0.1 0.33 7 -10000 0 7
RAC1/GTP/IQGAP1 0.039 0.017 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.05 0.008 -10000 0 -10000 0 0
RHOA 0.034 0.005 -10000 0 -10000 0 0
CDC42 0.032 0.009 -10000 0 -10000 0 0
CTNNA1 0.034 0.005 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.025 0.08 0.18 18 -0.16 2 20
NME1 0.029 0.035 -10000 0 -0.32 2 2
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.015 0.084 -10000 0 -0.46 5 5
regulation of cell-cell adhesion 0.009 0.035 -10000 0 -10000 0 0
WASF2 0.018 0.04 0.11 10 -0.13 1 11
Rap1/GTP 0.085 0.089 0.3 3 -10000 0 3
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.057 0.093 -10000 0 -0.27 10 10
CCND1 0.028 0.094 0.2 18 -0.2 2 20
VAV2 0.078 0.16 0.42 1 -0.72 4 5
RAP1/GDP 0.096 0.099 0.32 6 -10000 0 6
adherens junction assembly 0.016 0.081 -10000 0 -0.45 5 5
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.034 0.004 -10000 0 -10000 0 0
PIP5K1C 0.033 0.006 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.037 0.088 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.008 0.058 -10000 0 -0.36 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
SRC 0.008 0.072 -10000 0 -0.46 4 4
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
Rac1/GTP -0.029 0.072 -10000 0 -0.36 5 5
E-cadherin/beta catenin/alpha catenin 0.051 0.069 -10000 0 -0.31 5 5
ITGAE 0.027 0.014 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.024 0.089 -10000 0 -0.49 5 5
Arf6 trafficking events

Figure S87.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S87.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.11 0.23 -10000 0 -0.51 53 53
CLTC -0.008 0.12 -10000 0 -0.39 17 17
calcium ion-dependent exocytosis -0.006 0.083 -10000 0 -0.33 6 6
Dynamin 2/GTP 0.029 0.022 -10000 0 -10000 0 0
EXOC4 0.033 0.008 -10000 0 -10000 0 0
CD59 -0.008 0.1 -10000 0 -0.35 16 16
CPE -0.012 0.091 -10000 0 -0.28 21 21
CTNNB1 0.026 0.053 -10000 0 -0.32 5 5
membrane fusion 0.009 0.059 -10000 0 -0.34 2 2
CTNND1 0.019 0.03 0.19 4 -10000 0 4
DNM2 0.034 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.003 0.074 -10000 0 -0.29 4 4
TSHR 0.018 0.006 -10000 0 -10000 0 0
INS 0.013 0.056 -10000 0 -0.5 2 2
BIN1 0.034 0 -10000 0 -10000 0 0
mol:Choline 0.009 0.059 -10000 0 -0.34 2 2
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.015 0.019 -10000 0 -0.18 1 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.031 0.01 -10000 0 -10000 0 0
mol:Ca2+ 0.029 0.022 -10000 0 -10000 0 0
JUP -0.008 0.1 -10000 0 -0.34 16 16
ASAP2/amphiphysin II 0.04 0.013 -10000 0 -10000 0 0
ARF6/GTP 0.023 0.008 -10000 0 -10000 0 0
CDH1 -0.013 0.11 -10000 0 -0.34 17 17
clathrin-independent pinocytosis 0.023 0.008 -10000 0 -10000 0 0
MAPK8IP3 0.033 0.007 -10000 0 -10000 0 0
positive regulation of endocytosis 0.023 0.008 -10000 0 -10000 0 0
EXOC2 0.033 0.006 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.028 0.051 -10000 0 -0.31 2 2
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.032 0.008 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.013 0.12 0.4 6 -10000 0 6
positive regulation of phagocytosis 0.016 0.007 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.041 0.015 -10000 0 -10000 0 0
ACAP1 0.009 0.055 -10000 0 -0.29 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.017 0.11 -10000 0 -0.36 17 17
clathrin heavy chain/ACAP1 -0.009 0.11 -10000 0 -0.33 15 15
JIP4/KLC1 0.055 0.024 -10000 0 -10000 0 0
EXOC1 0.033 0.006 -10000 0 -10000 0 0
exocyst 0.028 0.052 -10000 0 -0.31 2 2
RALA/GTP 0.023 0.008 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.04 0.016 -10000 0 -10000 0 0
receptor recycling 0.023 0.008 -10000 0 -10000 0 0
CTNNA1 0.019 0.03 0.19 4 -10000 0 4
NME1 0.015 0.019 -10000 0 -0.18 1 1
clathrin coat assembly -0.009 0.12 -10000 0 -0.39 17 17
IL2RA -0.01 0.1 -10000 0 -0.34 16 16
VAMP3 0.017 0.007 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.063 0.14 -10000 0 -0.36 11 11
EXOC6 0.033 0.007 -10000 0 -10000 0 0
PLD1 -0.015 0.093 -10000 0 -0.3 20 20
PLD2 0.014 0.011 -10000 0 -10000 0 0
EXOC5 0.031 0.01 -10000 0 -10000 0 0
PIP5K1C 0.002 0.067 -10000 0 -0.27 2 2
SDC1 -0.008 0.1 -10000 0 -0.34 16 16
ARF6/GDP 0.026 0.022 -10000 0 -0.18 1 1
EXOC7 0.033 0.007 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.014 0.13 -10000 0 -0.43 5 5
mol:Phosphatidic acid 0.009 0.059 -10000 0 -0.34 2 2
endocytosis -0.038 0.013 -10000 0 -10000 0 0
SCAMP2 0.032 0.009 -10000 0 -10000 0 0
ADRB2 -0.098 0.18 0.39 1 -0.49 23 24
EXOC3 0.033 0.008 -10000 0 -10000 0 0
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.033 0.023 -10000 0 -10000 0 0
KLC1 0.031 0.011 -10000 0 -10000 0 0
AVPR2 -0.005 0.13 0.37 2 -0.37 17 19
RALA 0.031 0.011 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.008 0.12 -10000 0 -0.43 4 4
S1P3 pathway

Figure S88.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S88.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.034 0.005 -10000 0 -10000 0 0
mol:S1P 0.001 0 -10000 0 -10000 0 0
S1P1/S1P/Gi 0 0.088 -10000 0 -0.24 25 25
GNAO1 0.035 0.005 -10000 0 -10000 0 0
S1P/S1P3/G12/G13 0.04 0.017 -10000 0 -10000 0 0
AKT1 -0.011 0.13 -10000 0 -0.38 23 23
AKT3 0.023 0.051 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.034 0.005 -10000 0 -10000 0 0
GNAI2 0.035 0.004 -10000 0 -10000 0 0
GNAI3 0.034 0.007 -10000 0 -10000 0 0
GNAI1 -0.031 0.18 -10000 0 -0.5 26 26
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.002 0 -10000 0 -10000 0 0
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0.002 0.09 -10000 0 -0.34 4 4
MAPK3 -0.005 0.087 -10000 0 -0.35 3 3
MAPK1 0.003 0.08 -10000 0 -0.34 3 3
JAK2 0.042 0.098 0.23 3 -0.34 2 5
CXCR4 -0.01 0.089 -10000 0 -0.34 4 4
FLT1 0.008 0.077 -10000 0 -0.32 11 11
RhoA/GDP 0.025 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.008 -10000 0 -10000 0 0
SRC 0.004 0.05 -10000 0 -0.26 1 1
S1P/S1P3/Gi 0.002 0.091 -10000 0 -0.34 4 4
RAC1 0.031 0.011 -10000 0 -10000 0 0
RhoA/GTP 0.016 0.09 -10000 0 -0.38 2 2
VEGFA 0.008 0.095 -10000 0 -0.32 17 17
S1P/S1P2/Gi -0.001 0.091 -10000 0 -0.34 4 4
VEGFR1 homodimer/VEGFA homodimer 0.017 0.082 -10000 0 -0.24 18 18
RHOA 0.034 0.005 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.001 0.073 -10000 0 -0.26 14 14
GNAQ 0 0 -10000 0 -10000 0 0
GNAZ 0.033 0.009 -10000 0 -10000 0 0
G12/G13 0.043 0.018 -10000 0 -10000 0 0
GNA14 0.011 0.11 -10000 0 -0.51 9 9
GNA15 0.024 0.058 -10000 0 -0.32 6 6
GNA12 0.031 0.01 -10000 0 -10000 0 0
GNA13 0.032 0.008 -10000 0 -10000 0 0
GNA11 0.018 0.089 -10000 0 -0.51 6 6
Rac1/GTP 0.011 0.087 -10000 0 -0.34 3 3
E-cadherin signaling events

Figure S89.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S89.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.051 0.069 -9999 0 -0.31 5 5
E-cadherin/beta catenin 0.033 0.074 -9999 0 -0.37 5 5
CTNNB1 0.026 0.053 -9999 0 -0.32 5 5
JUP 0.033 0.007 -9999 0 -10000 0 0
CDH1 0.021 0.081 -9999 0 -0.51 5 5
Caspase cascade in apoptosis

Figure S90.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S90.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.01 0.069 -10000 0 -0.32 4 4
ACTA1 -0.019 0.073 -10000 0 -0.33 1 1
NUMA1 0.015 0.091 -10000 0 -0.51 3 3
SPTAN1 -0.002 0.059 -10000 0 -10000 0 0
LIMK1 0 0.075 0.34 2 -10000 0 2
BIRC3 0.01 0.11 -10000 0 -0.47 10 10
BIRC2 0.033 0.006 -10000 0 -10000 0 0
BAX 0.032 0.024 -10000 0 -0.32 1 1
CASP10 -0.003 0.039 -10000 0 -10000 0 0
CRMA 0 0 -10000 0 -0.001 1 1
XIAP 0 0 -10000 0 -0.001 7 7
PTK2 0.016 0.071 -10000 0 -0.36 3 3
DIABLO 0.034 0.003 -10000 0 -10000 0 0
apoptotic nuclear changes -0.001 0.058 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.029 0.052 -10000 0 -0.51 2 2
GSN -0.044 0.11 -10000 0 -0.34 12 12
MADD 0.034 0.004 -10000 0 -10000 0 0
TFAP2A 0.032 0.075 -10000 0 -0.63 2 2
BID 0.002 0.035 -10000 0 -0.21 4 4
MAP3K1 0.009 0.054 -10000 0 -0.36 3 3
TRADD 0.034 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.045 0.028 -10000 0 -0.21 2 2
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.001 0.066 0.33 1 -10000 0 1
CASP9 0.032 0.009 -10000 0 -10000 0 0
DNA repair 0.003 0.054 0.21 1 -0.18 4 5
neuron apoptosis -0.007 0.17 -10000 0 -0.64 14 14
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.007 0.084 -10000 0 -0.83 1 1
APAF1 0.031 0.034 -10000 0 -0.32 2 2
CASP6 0.017 0.14 -10000 0 -0.83 5 5
TRAF2 0.033 0.006 -10000 0 -10000 0 0
ICAD/CAD -0.005 0.054 -10000 0 -10000 0 0
CASP7 -0.05 0.16 0.26 4 -0.43 28 32
KRT18 0.024 0.047 -10000 0 -0.51 1 1
apoptosis -0.008 0.09 0.34 1 -0.44 3 4
DFFA -0.001 0.055 -10000 0 -10000 0 0
DFFB -0.003 0.056 -10000 0 -10000 0 0
PARP1 -0.003 0.054 0.18 4 -0.21 1 5
actin filament polymerization 0.005 0.072 0.3 1 -0.31 1 2
TNF 0.034 0.005 -10000 0 -10000 0 0
CYCS 0.02 0.042 0.19 1 -0.28 1 2
SATB1 -0.004 0.14 -10000 0 -0.8 5 5
SLK -0.002 0.056 -10000 0 -10000 0 0
p15 BID/BAX 0.013 0.054 -10000 0 -0.24 2 2
CASP2 0.024 0.064 0.22 6 -0.31 2 8
JNK cascade -0.009 0.054 0.36 3 -10000 0 3
CASP3 -0.002 0.059 -10000 0 -10000 0 0
LMNB2 0.034 0.11 0.37 3 -0.76 2 5
RIPK1 0.034 0.005 -10000 0 -10000 0 0
CASP4 0.033 0.006 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.048 0.071 -10000 0 -0.28 8 8
negative regulation of DNA binding 0.032 0.074 -10000 0 -0.62 2 2
stress fiber formation -0.002 0.056 -10000 0 -10000 0 0
GZMB 0.007 0.049 -10000 0 -0.27 1 1
CASP1 0 0.074 -10000 0 -0.32 10 10
LMNB1 0.028 0.093 0.41 2 -0.5 3 5
APP -0.008 0.17 -10000 0 -0.65 14 14
TNFRSF1A 0.033 0.008 -10000 0 -10000 0 0
response to stress 0 0 0.001 15 -0.001 2 17
CASP8 0.01 0.001 -10000 0 -10000 0 0
VIM -0.006 0.095 0.32 2 -0.41 5 7
LMNA 0.04 0.082 0.42 2 -0.5 2 4
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.022 0.06 -10000 0 -0.32 2 2
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 0.002 0.049 -10000 0 -10000 0 0
APAF-1/Caspase 9 -0.007 0.16 -10000 0 -0.59 15 15
nuclear fragmentation during apoptosis 0.015 0.089 -10000 0 -0.5 3 3
CFL2 -0.005 0.073 0.31 1 -0.31 1 2
GAS2 -0.09 0.089 -10000 0 -0.38 1 1
positive regulation of apoptosis 0.038 0.095 0.37 3 -0.63 2 5
PRF1 0.028 0.042 -10000 0 -0.32 3 3
BARD1 signaling events

Figure S91.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S91.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.028 0.025 -10000 0 -10000 0 0
ATM 0.033 0.007 -10000 0 -10000 0 0
UBE2D3 0.033 0.006 -10000 0 -10000 0 0
PRKDC 0.022 0.054 -10000 0 -0.32 5 5
ATR 0.032 0.024 -10000 0 -0.32 1 1
UBE2L3 0.032 0.009 -10000 0 -10000 0 0
FANCD2 0.027 0.014 -10000 0 -10000 0 0
protein ubiquitination 0.044 0.096 -10000 0 -0.29 3 3
XRCC5 0.034 0.002 -10000 0 -10000 0 0
XRCC6 0.032 0.009 -10000 0 -10000 0 0
M/R/N Complex 0.057 0.027 -10000 0 -10000 0 0
MRE11A 0.034 0.005 -10000 0 -10000 0 0
DNA-PK 0.051 0.045 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.017 0.072 -10000 0 -0.52 1 1
FANCF 0.029 0.052 -10000 0 -0.51 2 2
BRCA1 0.028 0.042 -10000 0 -0.32 3 3
CCNE1 0.012 0.084 -10000 0 -0.32 13 13
CDK2/Cyclin E1 0.006 0.1 -10000 0 -0.24 32 32
FANCG 0.02 0.067 -10000 0 -0.32 8 8
BRCA1/BACH1/BARD1 0.046 0.033 -10000 0 -0.22 3 3
FANCE 0.032 0.024 -10000 0 -0.32 1 1
FANCC 0.034 0.005 -10000 0 -10000 0 0
NBN 0.029 0.012 -10000 0 -10000 0 0
FANCA -0.045 0.15 -10000 0 -0.32 48 48
DNA repair 0.031 0.09 0.32 2 -10000 0 2
BRCA1/BARD1/ubiquitin 0.046 0.033 -10000 0 -0.22 3 3
BARD1/DNA-PK 0.066 0.05 -10000 0 -10000 0 0
FANCL 0.034 0 -10000 0 -10000 0 0
mRNA polyadenylation -0.027 0.025 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.027 0.053 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1/TopBP1 0.063 0.033 -10000 0 -10000 0 0
BRCA1/BARD1/P53 0.057 0.063 -10000 0 -0.31 1 1
BARD1/CSTF1/BRCA1 0.037 0.035 -10000 0 -10000 0 0
BRCA1/BACH1 0.028 0.041 -10000 0 -0.32 3 3
BARD1 0.034 0.002 -10000 0 -10000 0 0
PCNA 0.021 0.043 -10000 0 -0.32 3 3
BRCA1/BARD1/UbcH5C 0.062 0.033 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.06 0.035 -10000 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.057 0.051 -10000 0 -10000 0 0
BARD1/DNA-PK/P53 0.065 0.072 -10000 0 -0.3 1 1
BRCA1/BARD1/Ubiquitin 0.046 0.033 -10000 0 -0.22 3 3
BRCA1/BARD1/CTIP 0.04 0.035 -10000 0 -10000 0 0
FA complex 0.014 0.058 -10000 0 -0.27 2 2
BARD1/EWS 0.046 0.022 -10000 0 -0.22 1 1
RBBP8 0.014 0.009 -10000 0 -10000 0 0
TP53 0.014 0.067 -10000 0 -0.32 8 8
TOPBP1 0.034 0.005 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.055 0.061 0.31 1 -10000 0 1
BRCA1/BARD1 0.051 0.1 -10000 0 -0.3 3 3
CSTF1 0.019 0.017 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.025 0.002 -10000 0 -10000 0 0
CDK2 -0.002 0.11 -10000 0 -0.32 22 22
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.032 0.009 -10000 0 -10000 0 0
RAD50 0.034 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.046 0.033 -10000 0 -0.22 3 3
EWSR1 0.03 0.025 -10000 0 -0.32 1 1
JNK signaling in the CD4+ TCR pathway

Figure S92.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S92.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.071 0.05 -10000 0 -0.29 1 1
MAP4K1 0.033 0.007 -10000 0 -10000 0 0
MAP3K8 -0.013 0.12 -10000 0 -0.32 29 29
PRKCB 0 0 -10000 0 -10000 0 0
DBNL 0.031 0.01 -10000 0 -10000 0 0
CRKL 0.032 0.009 -10000 0 -10000 0 0
MAP3K1 0.018 0.048 -10000 0 -0.29 1 1
JUN -0.004 0.11 -10000 0 -0.57 7 7
MAP3K7 0.019 0.046 -10000 0 -0.29 1 1
GRAP2 0.032 0.009 -10000 0 -10000 0 0
CRK 0.027 0.014 -10000 0 -10000 0 0
MAP2K4 0.009 0.071 0.33 2 -0.32 2 4
LAT 0.032 0.025 -10000 0 -0.32 1 1
LCP2 0.027 0.055 -10000 0 -0.36 4 4
MAPK8 0.003 0.11 -10000 0 -0.58 7 7
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.025 0.051 -10000 0 -0.31 1 1
LAT/GRAP2/SLP76/HPK1/HIP-55 0.076 0.057 -10000 0 -10000 0 0
Aurora A signaling

Figure S93.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S93.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.067 0.048 -10000 0 -10000 0 0
BIRC5 -0.002 0.1 -10000 0 -0.32 21 21
NFKBIA 0.018 0.039 -10000 0 -10000 0 0
CPEB1 0.002 0.12 -10000 0 -0.51 12 12
AKT1 0.018 0.038 -10000 0 -10000 0 0
NDEL1 0.027 0.014 -10000 0 -10000 0 0
Aurora A/BRCA1 0.035 0.039 -10000 0 -10000 0 0
NDEL1/TACC3 0.06 0.053 -10000 0 -10000 0 0
GADD45A 0.03 0.034 -10000 0 -0.32 2 2
GSK3B 0.031 0.024 -10000 0 -0.31 1 1
PAK1/Aurora A 0.072 0.042 -10000 0 -10000 0 0
MDM2 0.034 0.004 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.046 0.11 0.23 45 -0.22 12 57
TP53 0.018 0.048 -10000 0 -0.25 1 1
DLG7 0.022 0.042 -10000 0 -10000 0 0
AURKAIP1 0.032 0.008 -10000 0 -10000 0 0
ARHGEF7 0.025 0.015 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.064 0.056 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.034 0.039 -10000 0 -10000 0 0
AURKA 0.031 0.051 -10000 0 -10000 0 0
AURKB 0.006 0.037 -10000 0 -0.17 7 7
CDC25B -0.001 0.052 -10000 0 -10000 0 0
G2/M transition checkpoint 0.008 0.013 -10000 0 -10000 0 0
mRNA polyadenylation 0.018 0.07 -10000 0 -0.27 6 6
Aurora A/CPEB 0.018 0.071 -10000 0 -0.27 6 6
Aurora A/TACC1/TRAP/chTOG 0.087 0.054 -10000 0 -10000 0 0
BRCA1 0.028 0.042 -10000 0 -0.32 3 3
centrosome duplication 0.072 0.042 -10000 0 -10000 0 0
regulation of centrosome cycle 0.059 0.052 -10000 0 -10000 0 0
spindle assembly 0.085 0.053 -10000 0 -10000 0 0
TDRD7 0.034 0.005 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.072 0.079 -10000 0 -0.28 1 1
CENPA 0.013 0.029 -10000 0 -10000 0 0
Aurora A/PP2A 0.07 0.042 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.045 0.049 0.19 4 -10000 0 4
negative regulation of DNA binding 0.009 0.064 -10000 0 -0.25 1 1
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.036 0.023 -10000 0 -10000 0 0
RASA1 0.03 0.034 -10000 0 -0.32 2 2
Ajuba/Aurora A 0.008 0.013 -10000 0 -10000 0 0
mitotic prometaphase 0.013 0.03 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.031 0.051 -10000 0 -10000 0 0
TACC1 0.03 0.012 -10000 0 -10000 0 0
TACC3 0.028 0.042 -10000 0 -0.32 3 3
Aurora A/Antizyme1 0.081 0.044 -10000 0 -10000 0 0
Aurora A/RasGAP 0.069 0.048 -10000 0 -10000 0 0
OAZ1 0.033 0.006 -10000 0 -10000 0 0
RAN 0.032 0.024 -10000 0 -0.32 1 1
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.033 0.006 -10000 0 -10000 0 0
GIT1 0.033 0.007 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.049 0.032 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.046 0.11 0.23 45 -0.22 12 57
PPP2R5D 0.033 0.006 -10000 0 -10000 0 0
Aurora A/TPX2 0.023 0.071 0.29 7 -10000 0 7
PAK1 0.034 0.004 -10000 0 -10000 0 0
CKAP5 0.034 0.004 -10000 0 -10000 0 0
Arf6 downstream pathway

Figure S94.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S94.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.022 0.042 -10000 0 -10000 0 0
regulation of axonogenesis 0.007 0.074 0.33 5 -10000 0 5
myoblast fusion -0.029 0.023 -10000 0 -10000 0 0
mol:GTP 0.012 0.05 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.047 0.064 0.3 3 -10000 0 3
ARF1/GTP 0.031 0.047 -10000 0 -10000 0 0
mol:GM1 0.003 0.036 -10000 0 -10000 0 0
mol:Choline -0.011 0.083 -10000 0 -0.29 17 17
lamellipodium assembly -0.005 0.096 -10000 0 -0.34 16 16
MAPK3 0.019 0.049 -10000 0 -0.32 2 2
ARF6/GTP/NME1/Tiam1 0.048 0.064 -10000 0 -0.3 3 3
ARF1 0.033 0.007 -10000 0 -10000 0 0
ARF6/GDP 0.029 0.023 -10000 0 -10000 0 0
ARF1/GDP 0.02 0.069 -10000 0 -0.26 1 1
ARF6 0.038 0.014 -10000 0 -10000 0 0
RAB11A 0.032 0.008 -10000 0 -10000 0 0
TIAM1 0.029 0.052 -10000 0 -0.5 2 2
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.023 0.033 -10000 0 -10000 0 0
actin filament bundle formation -0.025 0.072 0.26 1 -10000 0 1
KALRN 0.019 0.015 -10000 0 -10000 0 0
RAB11FIP3/RAB11A 0.046 0.015 -10000 0 -10000 0 0
RhoA/GDP 0.026 0.072 -10000 0 -0.26 1 1
NME1 0.03 0.035 -10000 0 -0.32 2 2
Rac1/GDP 0.023 0.07 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.013 0.049 -10000 0 -10000 0 0
cortical actin cytoskeleton organization -0.005 0.096 -10000 0 -0.34 16 16
RAC1 0.031 0.011 -10000 0 -10000 0 0
liver development 0.013 0.049 -10000 0 -10000 0 0
ARF6/GTP 0.013 0.049 -10000 0 -10000 0 0
RhoA/GTP 0.032 0.047 -10000 0 -10000 0 0
mol:GDP 0.005 0.059 -10000 0 -0.28 1 1
ARF6/GTP/RAB11FIP3/RAB11A 0.048 0.049 -10000 0 -10000 0 0
RHOA 0.034 0.005 -10000 0 -10000 0 0
PLD1 -0.023 0.12 -10000 0 -0.34 23 23
RAB11FIP3 0.033 0.007 -10000 0 -10000 0 0
tube morphogenesis -0.005 0.096 -10000 0 -0.34 16 16
ruffle organization -0.007 0.074 -10000 0 -0.33 5 5
regulation of epithelial cell migration 0.013 0.049 -10000 0 -10000 0 0
PLD2 0.021 0.021 -10000 0 -10000 0 0
PIP5K1A -0.007 0.075 -10000 0 -0.33 5 5
mol:Phosphatidic acid -0.011 0.083 -10000 0 -0.29 17 17
Rac1/GTP -0.005 0.097 -10000 0 -0.34 16 16
mTOR signaling pathway

Figure S95.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S95.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0 -10000 0 -10000 0 0
MKNK1 0.034 0.005 -10000 0 -10000 0 0
mol:PIP3 0.01 0.031 0.25 2 -10000 0 2
FRAP1 -0.018 0.13 -10000 0 -0.44 18 18
AKT1 0.007 0.044 0.2 1 -10000 0 1
INSR 0.026 0.063 -10000 0 -0.51 3 3
Insulin Receptor/Insulin 0.039 0.037 -10000 0 -0.31 2 2
mol:GTP 0.038 0.055 0.27 1 -10000 0 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.005 0.048 -10000 0 -0.25 1 1
TSC2 0.033 0.006 -10000 0 -10000 0 0
RHEB/GDP 0.022 0.036 -10000 0 -10000 0 0
TSC1 0.034 0.005 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.024 0.042 -10000 0 -0.23 5 5
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.019 0.06 -10000 0 -0.28 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.033 0.006 -10000 0 -10000 0 0
RPS6KB1 0.01 0.094 0.26 3 -0.39 4 7
MAP3K5 0.004 0.042 0.19 2 -0.18 7 9
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
apoptosis 0.004 0.042 0.19 2 -0.18 7 9
mol:LY294002 0 0 -10000 0 -0.001 2 2
EIF4B 0.011 0.089 0.3 4 -0.37 3 7
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.031 0.088 0.25 3 -0.34 4 7
eIF4E/eIF4G1/eIF4A1 0 0.082 -10000 0 -0.27 16 16
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.046 0.032 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.017 0.048 0.28 3 -10000 0 3
FKBP1A 0.027 0.014 -10000 0 -10000 0 0
RHEB/GTP 0.044 0.051 0.24 1 -10000 0 1
mol:Amino Acids 0 0 -10000 0 -0.001 2 2
FKBP12/Rapamycin 0.02 0.011 -10000 0 -10000 0 0
PDPK1 -0.002 0.032 0.19 3 -10000 0 3
EIF4E 0.034 0.005 -10000 0 -10000 0 0
ASK1/PP5C -0.006 0.16 -10000 0 -0.51 13 13
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.018 0.036 -10000 0 -10000 0 0
TSC1/TSC2 0.042 0.06 0.29 1 -10000 0 1
tumor necrosis factor receptor activity 0 0 0.001 2 -10000 0 2
RPS6 0.03 0.034 -10000 0 -0.32 2 2
PPP5C 0.032 0.025 -10000 0 -0.32 1 1
EIF4G1 0.034 0.004 -10000 0 -10000 0 0
IRS1 0.007 0.024 -10000 0 -0.21 2 2
INS 0.032 0.008 -10000 0 -10000 0 0
PTEN 0.027 0.052 -10000 0 -0.5 2 2
PDK2 -0.002 0.03 0.21 1 -10000 0 1
EIF4EBP1 -0.07 0.31 -10000 0 -1 20 20
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
PPP2R5D -0.011 0.12 0.27 2 -0.4 17 19
peptide biosynthetic process 0.024 0.044 0.19 8 -0.28 2 10
RHEB 0.033 0.007 -10000 0 -10000 0 0
EIF4A1 0.027 0.014 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.003 7 -10000 0 7
EEF2 0.024 0.045 0.19 8 -0.28 2 10
eIF4E/4E-BP1 -0.049 0.3 -10000 0 -0.97 20 20
IFN-gamma pathway

Figure S96.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S96.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.033 0.093 -10000 0 -0.26 3 3
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.032 0.009 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.016 0.11 0.32 1 -0.36 4 5
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.055 0.042 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.005 0.067 -10000 0 -0.27 1 1
CaM/Ca2+ 0.028 0.09 -10000 0 -10000 0 0
RAP1A 0.032 0.008 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.002 0.1 -10000 0 -0.35 5 5
AKT1 -0.003 0.075 0.33 3 -10000 0 3
MAP2K1 -0.008 0.073 0.36 2 -10000 0 2
MAP3K11 -0.002 0.079 0.36 2 -10000 0 2
IFNGR1 0.032 0.013 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.024 0.068 -10000 0 -10000 0 0
Rap1/GTP -0.003 0.059 -10000 0 -10000 0 0
CRKL/C3G 0.047 0.014 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.025 0.1 -10000 0 -0.28 3 3
CEBPB 0.047 0.12 0.46 2 -0.48 1 3
STAT3 0.033 0.006 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.05 0.12 -10000 0 -0.72 3 3
STAT1 -0.015 0.1 0.36 2 -0.35 5 7
CALM1 0.03 0.011 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.04 0.14 -10000 0 -0.32 46 46
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.001 0.1 0.36 2 -0.35 4 6
CEBPB/PTGES2/Cbp/p300 0.049 0.079 -10000 0 -10000 0 0
mol:Ca2+ 0.03 0.091 -10000 0 -0.25 3 3
MAPK3 0.007 0.11 0.4 1 -0.87 2 3
STAT1 (dimer) 0.002 0.094 -10000 0 -0.37 1 1
MAPK1 -0.032 0.2 0.42 1 -0.73 14 15
JAK2 0.028 0.044 -10000 0 -0.34 3 3
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
JAK1 0.033 0.013 -10000 0 -10000 0 0
CAMK2D 0.034 0.005 -10000 0 -10000 0 0
DAPK1 0.046 0.093 0.37 3 -10000 0 3
SMAD7 0.004 0.05 0.22 2 -0.27 1 3
CBL/CRKL/C3G 0.023 0.088 0.36 2 -10000 0 2
PI3K 0.033 0.09 -10000 0 -10000 0 0
IFNG -0.04 0.14 -10000 0 -0.32 46 46
apoptosis 0.031 0.095 0.36 2 -0.38 3 5
CAMK2G 0.033 0.007 -10000 0 -10000 0 0
STAT3 (dimer) 0.033 0.006 -10000 0 -10000 0 0
CAMK2A 0.034 0.005 -10000 0 -10000 0 0
CAMK2B 0.029 0.026 -10000 0 -0.32 1 1
FRAP1 -0.012 0.068 0.31 3 -10000 0 3
PRKCD -0.003 0.077 0.34 3 -10000 0 3
RAP1B 0.034 0.004 -10000 0 -10000 0 0
negative regulation of cell growth -0.005 0.067 -10000 0 -0.27 1 1
PTPN2 0.027 0.014 -10000 0 -10000 0 0
EP300 0.032 0.009 -10000 0 -10000 0 0
IRF1 -0.009 0.094 0.36 3 -0.45 2 5
STAT1 (dimer)/PIASy -0.003 0.1 0.42 1 -0.35 4 5
SOCS1 0.023 0.13 -10000 0 -1 3 3
mol:GDP 0.02 0.083 0.34 2 -10000 0 2
CASP1 -0.004 0.075 0.22 2 -0.26 11 13
PTGES2 0.034 0.005 -10000 0 -10000 0 0
IRF9 0.036 0.056 0.22 6 -10000 0 6
mol:PI-3-4-5-P3 0.018 0.079 -10000 0 -10000 0 0
RAP1/GDP 0.017 0.073 -10000 0 -10000 0 0
CBL -0.003 0.079 0.36 2 -10000 0 2
MAP3K1 -0.001 0.079 0.36 2 -10000 0 2
PIAS1 0.032 0.008 -10000 0 -10000 0 0
PIAS4 0.033 0.006 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.005 0.067 -10000 0 -0.27 1 1
PTPN11 -0.006 0.073 -10000 0 -0.25 3 3
CREBBP 0.034 0.007 -10000 0 -10000 0 0
RAPGEF1 0.034 0.005 -10000 0 -10000 0 0
S1P1 pathway

Figure S97.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S97.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.026 0.072 -10000 0 -0.22 16 16
PDGFRB 0.035 0.007 -10000 0 -10000 0 0
SPHK1 -0.013 0.09 -10000 0 -0.57 5 5
mol:S1P -0.01 0.091 -10000 0 -0.5 4 4
S1P1/S1P/Gi -0.014 0.1 -10000 0 -0.33 3 3
GNAO1 0.033 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/PLCgamma1 0.029 0.14 0.33 5 -10000 0 5
PLCG1 0.015 0.12 0.27 3 -0.33 1 4
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.035 0.007 -10000 0 -10000 0 0
GNAI2 0.033 0.006 -10000 0 -10000 0 0
GNAI3 0.033 0.008 -10000 0 -10000 0 0
GNAI1 -0.033 0.18 -10000 0 -0.51 26 26
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.011 0.052 0.18 1 -0.19 3 4
S1P1/S1P -0.014 0.091 -10000 0 -0.37 4 4
negative regulation of cAMP metabolic process -0.014 0.1 -10000 0 -0.33 3 3
MAPK3 -0.031 0.12 -10000 0 -0.38 2 2
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.025 0.003 -10000 0 -10000 0 0
KDR 0.033 0.006 -10000 0 -10000 0 0
PLCB2 -0.002 0.1 0.33 4 -0.4 2 6
RAC1 0.031 0.011 -10000 0 -10000 0 0
RhoA/GTP -0.014 0.079 -10000 0 -0.38 2 2
receptor internalization -0.014 0.086 -10000 0 -0.34 4 4
PTGS2 -0.032 0.15 0.48 2 -10000 0 2
Rac1/GTP -0.015 0.076 -10000 0 -0.38 2 2
RHOA 0.034 0.005 -10000 0 -10000 0 0
VEGFA 0.005 0.095 -10000 0 -0.32 17 17
negative regulation of T cell proliferation -0.014 0.1 -10000 0 -0.33 3 3
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.032 0.01 -10000 0 -10000 0 0
MAPK1 -0.018 0.11 0.42 1 -10000 0 1
S1P1/S1P/PDGFB-D/PDGFRB 0.011 0.12 0.35 5 -0.38 2 7
ABCC1 0 0.1 -10000 0 -0.32 21 21
FoxO family signaling

Figure S98.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S98.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.035 0.095 0.55 1 -10000 0 1
PLK1 -0.014 0.19 -10000 0 -0.79 4 4
CDKN1B 0.05 0.15 0.4 2 -0.39 1 3
FOXO3 -0.017 0.21 -10000 0 -0.61 13 13
KAT2B -0.001 0.019 -10000 0 -0.053 9 9
FOXO1/SIRT1 0.046 0.089 0.33 3 -0.33 1 4
CAT -0.02 0.21 -10000 0 -0.99 4 4
CTNNB1 0.026 0.053 -10000 0 -0.32 5 5
AKT1 0.028 0.032 -10000 0 -10000 0 0
FOXO1 0.037 0.099 0.43 3 -0.36 1 4
MAPK10 0.042 0.064 0.21 2 -0.26 2 4
mol:GTP 0.002 0.001 -10000 0 -10000 0 0
FOXO4 0.064 0.079 0.33 5 -10000 0 5
response to oxidative stress 0.004 0.019 -10000 0 -0.051 7 7
FOXO3A/SIRT1 0.013 0.18 -10000 0 -0.53 12 12
XPO1 0.035 0 -10000 0 -10000 0 0
EP300 0.034 0.01 -10000 0 -10000 0 0
BCL2L11 0.034 0.033 -10000 0 -10000 0 0
FOXO1/SKP2 0.03 0.1 0.29 2 -0.34 2 4
mol:GDP 0.004 0.019 -10000 0 -0.051 7 7
RAN 0.034 0.024 -10000 0 -0.32 1 1
GADD45A 0.048 0.15 -10000 0 -0.6 4 4
YWHAQ 0.034 0 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.053 0.14 0.33 4 -0.48 6 10
MST1 0.01 0.079 -10000 0 -0.31 10 10
CSNK1D 0.033 0.007 -10000 0 -10000 0 0
CSNK1E 0.03 0.025 -10000 0 -0.32 1 1
FOXO4/14-3-3 family -0.013 0.12 -10000 0 -0.43 4 4
YWHAB 0.018 0.017 -10000 0 -10000 0 0
MAPK8 0.047 0.055 0.21 1 -10000 0 1
MAPK9 0.048 0.055 0.21 1 -10000 0 1
YWHAG 0.033 0.008 -10000 0 -10000 0 0
YWHAE 0.027 0.014 -10000 0 -10000 0 0
YWHAZ 0.029 0.013 -10000 0 -10000 0 0
SIRT1 0.035 0.019 -10000 0 -10000 0 0
SOD2 0.044 0.16 0.58 1 -0.49 3 4
RBL2 0.032 0.14 -10000 0 -0.56 1 1
RAL/GDP 0.046 0.024 -10000 0 -10000 0 0
CHUK 0.025 0.033 -10000 0 -10000 0 0
Ran/GTP 0.027 0.017 -10000 0 -0.21 1 1
CSNK1G2 0.033 0.006 -10000 0 -10000 0 0
RAL/GTP 0.049 0.025 -10000 0 -10000 0 0
CSNK1G1 0.032 0.008 -10000 0 -10000 0 0
FASLG -0.11 0.46 -10000 0 -1.5 22 22
SKP2 0.005 0.095 -10000 0 -0.32 17 17
USP7 0.032 0.037 -10000 0 -0.5 1 1
IKBKB 0.024 0.031 -10000 0 -10000 0 0
CCNB1 -0.036 0.2 -10000 0 -0.89 4 4
FOXO1-3a-4/beta catenin 0.067 0.16 0.4 8 -0.44 1 9
proteasomal ubiquitin-dependent protein catabolic process 0.03 0.1 0.29 2 -0.34 2 4
CSNK1A1 0.034 0.005 -10000 0 -10000 0 0
SGK1 -0.001 0.019 -10000 0 -0.053 9 9
CSNK1G3 0.034 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.05 0.017 -10000 0 -0.18 1 1
ZFAND5 0.061 0.074 -10000 0 -10000 0 0
SFN 0.026 0.053 -10000 0 -0.51 2 2
CDK2 0.001 0.11 -10000 0 -0.31 22 22
FOXO3A/14-3-3 -0.013 0.12 -10000 0 -0.46 5 5
CREBBP 0.036 0.007 -10000 0 -10000 0 0
FBXO32 -0.058 0.41 -10000 0 -1.3 19 19
BCL6 0.027 0.16 -10000 0 -1.3 1 1
RALB 0.035 0.001 -10000 0 -10000 0 0
RALA 0.031 0.011 -10000 0 -10000 0 0
YWHAH 0.032 0.008 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

Figure S99.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S99.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.006 0.003 -10000 0 -10000 0 0
SNTA1 0.019 0.017 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 0.005 0.013 -10000 0 -10000 0 0
MAPK12 -0.017 0.075 0.21 4 -0.28 10 14
CCND1 -0.004 0.047 -10000 0 -0.32 1 1
p38 gamma/SNTA1 -0.002 0.066 -10000 0 -0.27 8 8
MAP2K3 0.028 0.013 -10000 0 -10000 0 0
PKN1 0.034 0.005 -10000 0 -10000 0 0
G2/M transition checkpoint -0.017 0.075 0.21 4 -0.28 10 14
MAP2K6 -0.011 0.079 0.24 4 -0.29 10 14
MAPT 0.001 0.053 0.25 3 -0.26 2 5
MAPK13 0.016 0.008 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.001 0.048 -10000 0 -0.28 1 1
LPA receptor mediated events

Figure S100.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S100.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.041 0.024 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.026 0.059 -10000 0 -10000 0 0
AP1 -0.037 0.079 -10000 0 -0.25 23 23
mol:PIP3 0.003 0.044 -10000 0 -0.25 6 6
AKT1 0.036 0.047 0.26 3 -10000 0 3
PTK2B -0.027 0.08 -10000 0 -0.17 45 45
RHOA 0.02 0.057 0.27 2 -0.3 3 5
PIK3CB 0.033 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.009 0.041 0.21 3 -0.22 1 4
MAGI3 0.03 0.037 -10000 0 -0.51 1 1
RELA 0.033 0.005 -10000 0 -10000 0 0
apoptosis 0.016 0.012 -10000 0 -10000 0 0
HRAS/GDP 0.025 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.02 0.078 0.22 3 -0.27 1 4
NF kappa B1 p50/RelA -0.012 0.027 -10000 0 -10000 0 0
endothelial cell migration 0.02 0.029 -10000 0 -0.28 2 2
ADCY4 -0.003 0.065 -10000 0 -0.27 3 3
ADCY5 0.001 0.055 -10000 0 -10000 0 0
ADCY6 0.001 0.058 -10000 0 -10000 0 0
ADCY7 0.001 0.058 -10000 0 -10000 0 0
ADCY1 -0.002 0.054 -10000 0 -10000 0 0
ADCY2 0.002 0.055 -10000 0 -10000 0 0
ADCY3 -0.002 0.058 -10000 0 -10000 0 0
ADCY8 0.005 0.047 -10000 0 -10000 0 0
ADCY9 -0.002 0.06 -10000 0 -10000 0 0
GSK3B -0.025 0.079 0.19 2 -0.22 5 7
arachidonic acid secretion 0.001 0.058 -10000 0 -0.25 1 1
GNG2 0.031 0.01 -10000 0 -10000 0 0
TRIP6 0.014 0.016 -10000 0 -10000 0 0
GNAO1 0.021 0.015 -10000 0 -10000 0 0
HRAS 0.034 0.005 -10000 0 -10000 0 0
NFKBIA 0.003 0.05 -10000 0 -10000 0 0
GAB1 0.029 0.052 -10000 0 -0.51 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.012 0.24 -10000 0 -0.83 16 16
JUN 0.025 0.053 -10000 0 -0.32 5 5
LPA/LPA2/NHERF2 0.023 0.009 -10000 0 -10000 0 0
TIAM1 -0.034 0.27 -10000 0 -0.95 17 17
PIK3R1 0.033 0.005 -10000 0 -10000 0 0
mol:IP3 0.001 0.039 0.22 3 -0.23 1 4
PLCB3 0.024 0.027 0.19 5 -10000 0 5
FOS -0.028 0.16 -10000 0 -0.49 24 24
positive regulation of mitosis 0.001 0.058 -10000 0 -0.25 1 1
LPA/LPA1-2-3 -0.001 0.011 -10000 0 -0.12 2 2
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade -0.001 0 -10000 0 -10000 0 0
BCAR1 0.033 0.006 -10000 0 -10000 0 0
stress fiber formation 0.01 0.049 -10000 0 -0.24 1 1
GNAZ 0.02 0.016 -10000 0 -10000 0 0
EGFR/PI3K-beta/Gab1 0.011 0.047 -10000 0 -0.26 6 6
positive regulation of dendritic cell cytokine production -0.001 0.011 -10000 0 -0.12 2 2
LPA/LPA2/MAGI-3 0.021 0.025 -10000 0 -0.31 1 1
ARHGEF1 0.044 0.059 0.37 1 -10000 0 1
GNAI2 0.022 0.015 -10000 0 -10000 0 0
GNAI3 0.021 0.016 -10000 0 -10000 0 0
GNAI1 -0.019 0.11 -10000 0 -0.3 26 26
LPA/LPA3 -0.001 0.006 -10000 0 -0.062 2 2
LPA/LPA2 -0.001 0.006 -10000 0 -0.062 2 2
LPA/LPA1 -0.001 0.015 -10000 0 -0.16 2 2
HB-EGF/EGFR 0.007 0.055 -10000 0 -0.31 3 3
HBEGF 0 0.049 -10000 0 -0.24 8 8
mol:DAG 0.001 0.039 0.22 3 -0.23 1 4
cAMP biosynthetic process 0.002 0.07 0.29 3 -10000 0 3
NFKB1 0.033 0.006 -10000 0 -10000 0 0
SRC 0.019 0.017 -10000 0 -10000 0 0
GNB1 0.032 0.008 -10000 0 -10000 0 0
LYN 0.027 0.056 0.26 2 -10000 0 2
GNAQ 0.001 0.005 -10000 0 -0.045 2 2
LPAR2 -0.001 0 -10000 0 -10000 0 0
LPAR3 -0.001 0 -10000 0 -10000 0 0
LPAR1 0.003 0.01 -10000 0 -0.098 2 2
IL8 -0.1 0.1 -10000 0 -0.41 7 7
PTK2 0.019 0.016 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.008 -10000 0 -10000 0 0
CASP3 0.017 0.012 -10000 0 -10000 0 0
EGFR 0.02 0.073 -10000 0 -0.51 4 4
PLCG1 0 0.031 -10000 0 -0.13 10 10
PLD2 0.019 0.016 -10000 0 -10000 0 0
G12/G13 0.042 0.024 -10000 0 -10000 0 0
PI3K-beta 0.018 0.029 -10000 0 -10000 0 0
cell migration 0.022 0.082 -10000 0 -0.24 11 11
SLC9A3R2 0.033 0.006 -10000 0 -10000 0 0
PXN 0.01 0.05 -10000 0 -0.24 1 1
HRAS/GTP 0 0.058 -10000 0 -0.26 1 1
RAC1 0.031 0.011 -10000 0 -10000 0 0
MMP9 0.007 0.064 -10000 0 -0.35 6 6
PRKCE 0.034 0.004 -10000 0 -10000 0 0
PRKCD 0.01 0.044 0.21 4 -10000 0 4
Gi(beta/gamma) 0 0.067 -10000 0 -0.3 2 2
mol:LPA 0.003 0.01 -10000 0 -0.098 2 2
TRIP6/p130 Cas/FAK1/Paxillin 0.049 0.055 -10000 0 -10000 0 0
MAPKKK cascade 0.001 0.058 -10000 0 -0.25 1 1
contractile ring contraction involved in cytokinesis 0.021 0.058 0.27 2 -0.3 3 5
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.002 0.059 -10000 0 -0.28 9 9
GNA15 0.01 0.023 -10000 0 -0.12 6 6
GNA12 0.031 0.01 -10000 0 -10000 0 0
GNA13 0.032 0.008 -10000 0 -10000 0 0
MAPT -0.021 0.079 0.22 3 -0.28 1 4
GNA11 0.006 0.049 -10000 0 -0.28 6 6
Rac1/GTP -0.014 0.25 -10000 0 -0.88 16 16
MMP2 0.02 0.029 -10000 0 -0.28 2 2
Angiopoietin receptor Tie2-mediated signaling

Figure S101.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S101.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.073 0.084 -10000 0 -10000 0 0
NCK1/PAK1/Dok-R -0.005 0.021 -10000 0 -10000 0 0
NCK1/Dok-R 0.077 0.064 -10000 0 -10000 0 0
PIK3CA 0.033 0.004 -10000 0 -10000 0 0
mol:beta2-estradiol -0.011 0.008 -10000 0 -10000 0 0
RELA 0.034 0.005 -10000 0 -10000 0 0
SHC1 0.035 0.006 -10000 0 -10000 0 0
Rac/GDP 0.023 0.008 -10000 0 -10000 0 0
F2 0.005 0.027 -10000 0 -10000 0 0
TNIP2 0.033 0.007 -10000 0 -10000 0 0
NF kappa B/RelA 0.11 0.05 -10000 0 -10000 0 0
FN1 -0.005 0.11 -10000 0 -0.32 24 24
PLD2 0.032 0.036 -10000 0 -10000 0 0
PTPN11 0.032 0.024 -10000 0 -0.32 1 1
GRB14 -0.023 0.14 -10000 0 -0.37 30 30
ELK1 0.065 0.059 -10000 0 -10000 0 0
GRB7 0.03 0.025 -10000 0 -0.32 1 1
PAK1 0.034 0.004 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0.097 0.08 -10000 0 -10000 0 0
CDKN1A 0.033 0.14 -10000 0 -0.82 3 3
ITGA5 0.026 0.053 -10000 0 -0.32 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.075 0.066 -10000 0 -10000 0 0
CRK 0.027 0.014 -10000 0 -10000 0 0
mol:NO 0.083 0.094 0.5 2 -10000 0 2
PLG 0.036 0.036 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.076 0.073 -10000 0 -10000 0 0
GRB2 0.033 0.007 -10000 0 -10000 0 0
PIK3R1 0.035 0.006 -10000 0 -10000 0 0
ANGPT2 -0.069 0.15 -10000 0 -0.5 1 1
BMX -0.098 0.12 -10000 0 -10000 0 0
ANGPT1 0.034 0.03 -10000 0 -10000 0 0
tube development 0.03 0.11 0.43 1 -10000 0 1
ANGPT4 0.028 0.015 -10000 0 -10000 0 0
response to hypoxia 0.002 0.007 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 0.069 0.081 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.042 0.045 -10000 0 -0.22 6 6
FGF2 0.013 0.098 -10000 0 -0.48 8 8
STAT5A (dimer) 0.041 0.13 -10000 0 -10000 0 0
mol:L-citrulline 0.083 0.094 0.5 2 -10000 0 2
AGTR1 -0.19 0.26 -10000 0 -0.5 89 89
MAPK14 0.061 0.073 -10000 0 -10000 0 0
Tie2/SHP2 0.07 0.036 -10000 0 -10000 0 0
TEK 0.043 0.032 -10000 0 -10000 0 0
RPS6KB1 0.076 0.087 -10000 0 -10000 0 0
Angiotensin II/AT1 -0.13 0.19 -10000 0 -0.36 89 89
Tie2/Ang1/GRB2 0.087 0.046 -10000 0 -10000 0 0
MAPK3 0.032 0.047 -10000 0 -10000 0 0
MAPK1 0.034 0.042 -10000 0 -10000 0 0
Tie2/Ang1/GRB7 0.084 0.047 -10000 0 -10000 0 0
NFKB1 0.033 0.006 -10000 0 -10000 0 0
MAPK8 0.036 0.036 -10000 0 -10000 0 0
PI3K 0.069 0.08 -10000 0 -10000 0 0
FES 0.049 0.088 -10000 0 -10000 0 0
Crk/Dok-R 0.069 0.064 -10000 0 -10000 0 0
Tie2/Ang1/ABIN2 0.086 0.047 -10000 0 -10000 0 0
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.078 0.082 -10000 0 -10000 0 0
STAT5A 0.033 0.006 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.099 0.11 -10000 0 -10000 0 0
Tie2/Ang2 0.012 0.1 -10000 0 -10000 0 0
Tie2/Ang1 0.042 0.039 -10000 0 -10000 0 0
FOXO1 0.094 0.11 -10000 0 -10000 0 0
ELF1 0.031 0.019 -10000 0 -10000 0 0
ELF2 0.038 0.038 -10000 0 -10000 0 0
mol:Choline 0.032 0.035 -10000 0 -10000 0 0
cell migration -0.002 0.022 -10000 0 -10000 0 0
FYN 0.029 0.11 -10000 0 -10000 0 0
DOK2 0.023 0.039 -10000 0 -0.51 1 1
negative regulation of cell cycle 0.036 0.13 0.42 1 -0.72 3 4
ETS1 0.043 0.012 -10000 0 -10000 0 0
PXN 0.096 0.1 0.43 2 -10000 0 2
ITGB1 0.032 0.024 -10000 0 -0.32 1 1
NOS3 0.081 0.09 -10000 0 -10000 0 0
RAC1 0.031 0.011 -10000 0 -10000 0 0
TNF 0.045 0.012 -10000 0 -10000 0 0
MAPKKK cascade 0.032 0.035 -10000 0 -10000 0 0
RASA1 0.03 0.034 -10000 0 -0.32 2 2
Tie2/Ang1/Shc 0.088 0.048 -10000 0 -10000 0 0
NCK1 0.034 0.005 -10000 0 -10000 0 0
vasculogenesis 0.081 0.091 0.49 2 -10000 0 2
mol:Phosphatidic acid 0.032 0.035 -10000 0 -10000 0 0
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP 0.083 0.094 0.5 2 -10000 0 2
Rac1/GTP 0.069 0.072 -10000 0 -10000 0 0
MMP2 0.036 0.038 -10000 0 -10000 0 0
PDGFR-beta signaling pathway

Figure S102.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S102.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.021 0.098 0.25 1 -10000 0 1
PDGFB-D/PDGFRB/SLAP 0.041 0.02 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/APS/CBL 0.044 0.009 -10000 0 -10000 0 0
AKT1 0.06 0.1 0.32 6 -10000 0 6
mol:PI-4-5-P2 0.001 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.054 0.12 0.27 4 -10000 0 4
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
FGR -0.007 0.15 0.33 1 -0.48 15 16
mol:Ca2+ 0.051 0.12 0.27 4 -0.35 1 5
MYC -0.011 0.17 0.39 7 -0.39 4 11
SHC1 0.033 0.006 -10000 0 -10000 0 0
HRAS/GDP 0.07 0.075 -10000 0 -10000 0 0
LRP1/PDGFRB/PDGFB 0.061 0.026 -10000 0 -10000 0 0
GRB10 0.016 0.07 -10000 0 -0.32 9 9
PTPN11 0.032 0.024 -10000 0 -0.32 1 1
GO:0007205 0.05 0.12 0.27 4 -0.36 1 5
PTEN 0.027 0.052 -10000 0 -0.51 2 2
GRB2 0.033 0.007 -10000 0 -10000 0 0
GRB7 0.03 0.025 -10000 0 -0.32 1 1
PDGFB-D/PDGFRB/SHP2 0.047 0.02 -10000 0 -0.22 1 1
PDGFB-D/PDGFRB/GRB10 0.033 0.055 -10000 0 -0.22 9 9
cell cycle arrest 0.041 0.019 -10000 0 -10000 0 0
HRAS 0.034 0.005 -10000 0 -10000 0 0
HIF1A 0.05 0.098 0.3 6 -0.33 1 7
GAB1 0.011 0.12 -10000 0 -0.37 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.027 0.12 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.026 0.031 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.049 0.007 -10000 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.017 0.061 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.047 0.02 -10000 0 -0.22 1 1
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
mol:IP3 0.051 0.12 0.27 4 -0.36 1 5
E5 -0.001 0.001 -10000 0 -10000 0 0
CSK 0.031 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.045 0.023 -10000 0 -0.22 1 1
SHB 0.021 0.067 -10000 0 -0.32 8 8
BLK -0.17 0.27 0.35 1 -0.53 69 70
PTPN2 0.027 0.015 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.048 0.01 -10000 0 -10000 0 0
BCAR1 0.033 0.006 -10000 0 -10000 0 0
VAV2 0.005 0.14 0.32 2 -0.37 4 6
CBL 0.034 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.049 0.009 -10000 0 -10000 0 0
LCK 0.01 0.13 0.33 1 -0.45 11 12
PDGFRB 0.033 0.006 -10000 0 -10000 0 0
ACP1 0.034 0 -10000 0 -10000 0 0
HCK -0.008 0.12 -10000 0 -0.6 7 7
ABL1 0.014 0.14 0.25 5 -0.38 6 11
PDGFB-D/PDGFRB/CBL 0.002 0.13 -10000 0 -0.38 4 4
PTPN1 0.017 0.016 -10000 0 -10000 0 0
SNX15 0.034 0.005 -10000 0 -10000 0 0
STAT3 0.033 0.006 -10000 0 -10000 0 0
STAT1 0.003 0.1 -10000 0 -0.32 19 19
cell proliferation -0.008 0.16 0.36 9 -0.35 6 15
SLA 0.028 0.013 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.099 0.085 0.34 4 -10000 0 4
SRC 0.006 0.035 -10000 0 -10000 0 0
PI3K -0.002 0.038 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC 0.06 0.027 -10000 0 -10000 0 0
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.054 0.12 0.28 4 -10000 0 4
LYN 0.019 0.088 -10000 0 -0.52 3 3
LRP1 0.034 0.004 -10000 0 -10000 0 0
SOS1 0.034 0.002 -10000 0 -10000 0 0
STAT5B 0.033 0.006 -10000 0 -10000 0 0
STAT5A 0.033 0.006 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.043 0.049 -10000 0 -10000 0 0
SPHK1 -0.009 0.12 -10000 0 -0.32 27 27
EDG1 0.002 0.004 -10000 0 -10000 0 0
mol:DAG 0.051 0.12 0.27 4 -0.36 1 5
PLCG1 0.05 0.12 0.27 4 -0.37 1 5
NHERF/PDGFRB 0.057 0.049 -10000 0 -0.32 3 3
YES1 -0.034 0.19 0.33 1 -0.5 25 26
cell migration 0.056 0.049 -10000 0 -0.31 3 3
SHC/Grb2/SOS1 0.041 0.049 -10000 0 -10000 0 0
SLC9A3R2 0.033 0.007 -10000 0 -10000 0 0
SLC9A3R1 0.026 0.064 -10000 0 -0.51 3 3
NHERF1-2/PDGFRB/PTEN 0.066 0.065 -10000 0 -0.28 5 5
FYN 0.01 0.12 0.32 1 -0.51 8 9
DOK1 0.066 0.08 -10000 0 -10000 0 0
HRAS/GTP 0.025 0.003 -10000 0 -10000 0 0
PDGFB 0.03 0.025 -10000 0 -0.32 1 1
RAC1 -0.005 0.16 0.35 5 -0.4 6 11
PRKCD 0.063 0.082 -10000 0 -10000 0 0
FER 0.057 0.088 -10000 0 -10000 0 0
MAPKKK cascade 0.076 0.099 0.35 6 -10000 0 6
RASA1 0.061 0.085 -10000 0 -10000 0 0
NCK1 0.034 0.005 -10000 0 -10000 0 0
NCK2 0.034 0 -10000 0 -10000 0 0
p62DOK/Csk 0.076 0.076 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0.038 0.052 -10000 0 -0.22 8 8
chemotaxis 0.014 0.13 0.25 6 -0.37 6 12
STAT1-3-5/STAT1-3-5 0.016 0.063 -10000 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.023 0.005 -10000 0 -10000 0 0
PTPRJ 0.034 0.004 -10000 0 -10000 0 0
LPA4-mediated signaling events

Figure S103.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S103.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.003 0.022 -10000 0 -0.31 1 1
ADCY5 0.005 0.001 -10000 0 -10000 0 0
ADCY6 0.005 0.001 -10000 0 -10000 0 0
ADCY7 0.005 0.001 -10000 0 -10000 0 0
ADCY1 0.005 0.002 -10000 0 -10000 0 0
ADCY2 0.004 0.013 -10000 0 -0.18 1 1
ADCY3 -0.006 0.044 -10000 0 -0.18 13 13
ADCY8 0.003 0.013 -10000 0 -0.18 1 1
PRKCE 0.01 0.001 -10000 0 -10000 0 0
ADCY9 0.001 0.037 -10000 0 -0.31 3 3
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.029 0.064 0.24 7 -10000 0 7
ErbB2/ErbB3 signaling events

Figure S104.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S104.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.002 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.042 0.072 -10000 0 -10000 0 0
NFATC4 -0.006 0.044 0.25 1 -10000 0 1
ERBB2IP 0.026 0.063 -10000 0 -0.5 3 3
HSP90 (dimer) 0.031 0.011 -10000 0 -10000 0 0
mammary gland morphogenesis 0.028 0.051 -10000 0 -10000 0 0
JUN 0.025 0.073 0.25 2 -10000 0 2
HRAS 0.034 0.005 -10000 0 -10000 0 0
DOCK7 0.006 0.046 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.054 0.049 0.27 2 -0.28 1 3
AKT1 0.009 0.004 -10000 0 -10000 0 0
BAD 0.002 0.005 -10000 0 -10000 0 0
MAPK10 0.015 0.055 0.24 5 -10000 0 5
mol:GTP 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.031 0.056 -10000 0 -10000 0 0
RAF1 0.024 0.067 0.32 2 -10000 0 2
ErbB2/ErbB3/neuregulin 2 0.038 0.068 0.26 3 -0.3 6 9
STAT3 0.017 0.084 -10000 0 -0.81 2 2
cell migration 0.017 0.057 0.23 7 -10000 0 7
mol:PI-3-4-5-P3 0 0.001 -10000 0 -10000 0 0
cell proliferation -0.004 0.18 0.39 2 -0.53 8 10
FOS -0.031 0.21 0.35 2 -0.49 31 33
NRAS 0.029 0.035 -10000 0 -0.32 2 2
mol:Ca2+ 0.028 0.051 -10000 0 -10000 0 0
MAPK3 0.018 0.12 0.37 2 -10000 0 2
MAPK1 -0.004 0.17 0.38 2 -0.69 6 8
JAK2 0.004 0.049 -10000 0 -10000 0 0
NF2 0.009 0.063 -10000 0 -0.64 2 2
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.023 0.028 -10000 0 -10000 0 0
NRG1 0.028 0.014 -10000 0 -10000 0 0
GRB2/SOS1 0.049 0.01 -10000 0 -10000 0 0
MAPK8 0.013 0.068 -10000 0 -10000 0 0
MAPK9 0.017 0.052 0.24 5 -10000 0 5
ERBB2 -0.012 0.064 0.26 9 -0.38 1 10
ERBB3 0.034 0.004 -10000 0 -10000 0 0
SHC1 0.034 0.006 -10000 0 -10000 0 0
RAC1 0.031 0.011 -10000 0 -10000 0 0
apoptosis -0.002 0.006 -10000 0 -10000 0 0
STAT3 (dimer) 0.017 0.082 -10000 0 -0.79 2 2
RNF41 -0.004 0.006 -10000 0 -10000 0 0
FRAP1 0.001 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.006 0.027 -10000 0 -10000 0 0
ErbB2/ErbB2/HSP90 (dimer) 0.026 0.046 0.26 3 -0.32 1 4
CHRNA1 0.021 0.11 0.36 2 -10000 0 2
myelination -0.001 0.053 0.32 2 -10000 0 2
PPP3CB 0.007 0.044 -10000 0 -10000 0 0
KRAS 0.033 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.037 0.059 -10000 0 -10000 0 0
NRG2 0.021 0.081 -10000 0 -0.51 5 5
mol:GDP 0.023 0.028 -10000 0 -10000 0 0
SOS1 0.034 0.002 -10000 0 -10000 0 0
MAP2K2 0.016 0.066 0.39 1 -10000 0 1
SRC 0.019 0.017 -10000 0 -10000 0 0
mol:cAMP 0 0.001 -10000 0 -10000 0 0
PTPN11 0.006 0.048 -10000 0 -10000 0 0
MAP2K1 -0.016 0.2 0.38 1 -0.63 14 15
heart morphogenesis 0.028 0.051 -10000 0 -10000 0 0
RAS family/GDP 0.051 0.071 -10000 0 -10000 0 0
GRB2 0.033 0.007 -10000 0 -10000 0 0
PRKACA 0.013 0.067 -10000 0 -0.68 2 2
CHRNE 0.014 0.018 -10000 0 -10000 0 0
HSP90AA1 0.031 0.011 -10000 0 -10000 0 0
activation of caspase activity -0.009 0.004 -10000 0 -10000 0 0
nervous system development 0.028 0.051 -10000 0 -10000 0 0
CDC42 0.032 0.009 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

Figure S105.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S105.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.032 0.011 -9999 0 -10000 0 0
SVIL 0.03 0.052 -9999 0 -0.5 2 2
ZNF318 0.031 0.006 -9999 0 -10000 0 0
JMJD2C 0.006 0.001 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 0.052 0.027 -9999 0 -10000 0 0
CARM1 0.034 0.005 -9999 0 -10000 0 0
PRDX1 0.034 0.005 -9999 0 -10000 0 0
PELP1 0.027 0.014 -9999 0 -10000 0 0
CTNNB1 0.027 0.053 -9999 0 -0.32 5 5
AKT1 0.03 0.01 -9999 0 -10000 0 0
PTK2B 0.027 0.015 -9999 0 -10000 0 0
MED1 0.032 0.008 -9999 0 -10000 0 0
MAK 0.025 0.048 -9999 0 -0.32 4 4
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.032 0.025 -9999 0 -0.32 1 1
GSN -0.053 0.2 -9999 0 -0.5 35 35
NCOA2 0.03 0.012 -9999 0 -10000 0 0
NCOA6 0.02 0.018 -9999 0 -10000 0 0
DNA-PK 0.049 0.044 -9999 0 -10000 0 0
NCOA4 0.034 0.005 -9999 0 -10000 0 0
PIAS3 0.033 0.024 -9999 0 -0.32 1 1
cell proliferation 0.019 0.043 -9999 0 -0.37 2 2
XRCC5 0.034 0.002 -9999 0 -10000 0 0
UBE3A 0.033 0.01 -9999 0 -10000 0 0
T-DHT/AR/SNURF 0.032 0.017 -9999 0 -0.17 1 1
FHL2 0.042 0.023 -9999 0 -10000 0 0
RANBP9 0.035 0.006 -9999 0 -10000 0 0
JMJD1A 0.006 0.01 -9999 0 -0.14 1 1
CDK6 0.031 0.025 -9999 0 -0.32 1 1
TGFB1I1 0.035 0.005 -9999 0 -10000 0 0
T-DHT/AR/CyclinD1 0.021 0.083 -9999 0 -10000 0 0
XRCC6 0.031 0.009 -9999 0 -10000 0 0
T-DHT/AR 0.068 0.028 -9999 0 -10000 0 0
CTDSP1 0.035 0.002 -9999 0 -10000 0 0
CTDSP2 0.027 0.052 -9999 0 -0.51 2 2
BRCA1 0.03 0.042 -9999 0 -0.32 3 3
TCF4 0.022 0.016 -9999 0 -10000 0 0
CDKN2A -0.074 0.16 -9999 0 -0.32 65 65
SRF 0.039 0.01 -9999 0 -10000 0 0
NKX3-1 0.013 0.018 -9999 0 -0.23 1 1
KLK3 0.019 0.044 -9999 0 -10000 0 0
TMF1 0.034 0.006 -9999 0 -10000 0 0
HNRNPA1 0.033 0.004 -9999 0 -10000 0 0
AOF2 0.002 0.001 -9999 0 -0.019 1 1
APPL1 0.016 0.006 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 0.054 0.02 -9999 0 -10000 0 0
AR 0.038 0.025 -9999 0 -0.31 1 1
UBA3 0 0 -9999 0 -10000 0 0
PATZ1 0.031 0.008 -9999 0 -10000 0 0
PAWR 0.034 0.004 -9999 0 -10000 0 0
PRKDC 0.021 0.054 -9999 0 -0.32 5 5
PA2G4 0.031 0.024 -9999 0 -0.32 1 1
UBE2I 0.031 0.025 -9999 0 -0.32 1 1
T-DHT/AR/Cyclin D3/CDK11 p58 0.05 0.02 -9999 0 -10000 0 0
RPS6KA3 0.035 0.006 -9999 0 -10000 0 0
T-DHT/AR/ARA70 0.055 0.021 -9999 0 -10000 0 0
LATS2 0.025 0.015 -9999 0 -10000 0 0
T-DHT/AR/PRX1 0.05 0.019 -9999 0 -10000 0 0
Cyclin D3/CDK11 p58 0.025 0.004 -9999 0 -10000 0 0
VAV3 -0.044 0.19 -9999 0 -0.5 31 31
KLK2 0.031 0.012 -9999 0 -10000 0 0
CASP8 0.034 0.002 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.064 0.033 -9999 0 -10000 0 0
TMPRSS2 0.024 0.071 -9999 0 -0.94 1 1
CCND1 -0.02 0.13 -9999 0 -0.32 33 33
PIAS1 0.034 0.01 -9999 0 -10000 0 0
mol:T-DHT 0.005 0.005 -9999 0 -0.063 1 1
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.036 0.008 -9999 0 -10000 0 0
T-DHT/AR/CDK6 0.051 0.028 -9999 0 -0.17 1 1
CMTM2 0.027 0.048 -9999 0 -0.32 4 4
SNURF 0 0 -9999 0 -10000 0 0
ZMIZ1 0.037 0.012 -9999 0 -10000 0 0
CCND3 0.033 0.006 -9999 0 -10000 0 0
TGIF1 -0.012 0.11 -9999 0 -0.32 23 23
FKBP4 0.034 0.008 -9999 0 -10000 0 0
Ephrin A reverse signaling

Figure S106.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S106.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.039 0.034 -9999 0 -0.22 3 3
EFNA5 0.031 0.037 -9999 0 -0.51 1 1
FYN 0.016 0.036 -9999 0 -0.28 2 2
neuron projection morphogenesis 0.039 0.034 -9999 0 -0.22 3 3
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 0.04 0.034 -9999 0 -0.22 3 3
EPHA5 0.03 0.034 -9999 0 -0.32 2 2
Hedgehog signaling events mediated by Gli proteins

Figure S107.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S107.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.033 0.007 -10000 0 -10000 0 0
HDAC2 0.033 0.007 -10000 0 -10000 0 0
GNB1/GNG2 0.051 0.047 -10000 0 -0.31 1 1
forebrain development -0.019 0.16 -10000 0 -0.63 8 8
GNAO1 0.034 0.005 -10000 0 -10000 0 0
SMO/beta Arrestin2 0.032 0.047 -10000 0 -0.26 4 4
SMO 0.025 0.056 -10000 0 -0.37 4 4
ARRB2 0.027 0.014 -10000 0 -10000 0 0
GLI3/SPOP 0.055 0.099 0.28 1 -10000 0 1
mol:GTP 0 0.002 -10000 0 -10000 0 0
GSK3B 0.032 0.024 -10000 0 -0.32 1 1
GNAI2 0.034 0.004 -10000 0 -10000 0 0
SIN3/HDAC complex 0.059 0.042 -10000 0 -10000 0 0
GNAI1 -0.033 0.18 -10000 0 -0.51 26 26
XPO1 0.033 0.012 -10000 0 -10000 0 0
GLI1/Su(fu) -0.021 0.14 -10000 0 -0.74 4 4
SAP30 0.033 0.008 -10000 0 -10000 0 0
mol:GDP 0.025 0.056 -10000 0 -0.37 4 4
MIM/GLI2A 0.01 0.062 -10000 0 -0.5 2 2
IFT88 0.025 0.015 -10000 0 -10000 0 0
GNAI3 0.033 0.007 -10000 0 -10000 0 0
GLI2 0.023 0.062 -10000 0 -0.35 2 2
GLI3 0.044 0.1 0.32 2 -0.34 1 3
CSNK1D 0.033 0.007 -10000 0 -10000 0 0
CSNK1E 0.03 0.025 -10000 0 -0.32 1 1
SAP18 0.025 0.015 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.025 0.015 -10000 0 -10000 0 0
GNG2 0.031 0.01 -10000 0 -10000 0 0
Gi family/GTP -0.007 0.094 -10000 0 -0.3 7 7
SIN3B 0.034 0.005 -10000 0 -10000 0 0
SIN3A 0.032 0.009 -10000 0 -10000 0 0
GLI3/Su(fu) 0.054 0.089 0.37 1 -10000 0 1
GLI2/Su(fu) 0.026 0.074 -10000 0 -0.41 3 3
FOXA2 -0.052 0.19 -10000 0 -0.89 6 6
neural tube patterning -0.019 0.16 -10000 0 -0.63 8 8
SPOP 0.033 0.008 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.029 0.053 -10000 0 -10000 0 0
GNB1 0.032 0.008 -10000 0 -10000 0 0
CSNK1G2 0.033 0.006 -10000 0 -10000 0 0
CSNK1G3 0.034 0.005 -10000 0 -10000 0 0
MTSS1 0.01 0.062 -10000 0 -0.5 2 2
embryonic limb morphogenesis -0.019 0.16 -10000 0 -0.63 8 8
SUFU 0.021 0.027 -10000 0 -10000 0 0
LGALS3 0.016 0.089 -10000 0 -0.51 6 6
catabolic process 0.062 0.11 0.34 1 -0.4 1 2
GLI3A/CBP 0.018 0.089 -10000 0 -0.35 12 12
KIF3A 0.032 0.024 -10000 0 -0.32 1 1
GLI1 -0.019 0.16 -10000 0 -0.65 8 8
RAB23 0.021 0.067 -10000 0 -0.32 8 8
CSNK1A1 0.034 0.005 -10000 0 -10000 0 0
IFT172 0.032 0.037 -10000 0 -0.51 1 1
RBBP7 0.034 0.005 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.022 0.074 -10000 0 -0.3 6 6
GNAZ 0.032 0.009 -10000 0 -10000 0 0
RBBP4 0.033 0.007 -10000 0 -10000 0 0
CSNK1G1 0.032 0.008 -10000 0 -10000 0 0
PIAS1 0.032 0.008 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
GLI2/SPOP 0.037 0.068 -10000 0 -0.35 3 3
STK36 0.031 0.026 -10000 0 -0.32 1 1
Gi family/GNB1/GNG2/GDP -0.004 0.097 -10000 0 -0.39 5 5
PTCH1 -0.014 0.15 -10000 0 -0.74 3 3
MIM/GLI1 -0.026 0.18 -10000 0 -0.66 9 9
CREBBP 0.018 0.089 -10000 0 -0.34 12 12
Su(fu)/SIN3/HDAC complex 0.032 0.095 -10000 0 -0.39 6 6
Insulin-mediated glucose transport

Figure S108.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S108.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.051 0.14 0.23 1 -0.29 12 13
CaM/Ca2+ 0.022 0.008 -10000 0 -10000 0 0
AKT1 0.031 0.011 -10000 0 -10000 0 0
AKT2 0.033 0.007 -10000 0 -10000 0 0
STXBP4 0.033 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.067 0.14 0.24 1 -0.29 23 24
YWHAZ 0.029 0.013 -10000 0 -10000 0 0
CALM1 0.03 0.011 -10000 0 -10000 0 0
YWHAQ 0.034 0 -10000 0 -10000 0 0
TBC1D4 0.016 0.057 0.23 8 -0.26 4 12
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.032 0.008 -10000 0 -10000 0 0
YWHAB 0.018 0.017 -10000 0 -10000 0 0
SNARE/Synip 0.053 0.03 -10000 0 -10000 0 0
YWHAG 0.033 0.008 -10000 0 -10000 0 0
ASIP 0 0 -10000 0 -10000 0 0
PRKCI 0.026 0.053 -10000 0 -0.32 5 5
AS160/CaM/Ca2+ 0.022 0.008 -10000 0 -10000 0 0
RHOQ 0.034 0.004 -10000 0 -10000 0 0
GYS1 0.015 0.01 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
TRIP10 0.034 0.004 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.045 0.008 -10000 0 -10000 0 0
AS160/14-3-3 0.013 0.054 -10000 0 -0.3 2 2
VAMP2 0.027 0.014 -10000 0 -10000 0 0
SLC2A4 -0.075 0.15 0.24 1 -0.32 23 24
STX4 0.034 0.005 -10000 0 -10000 0 0
GSK3B 0.025 0.014 -10000 0 -10000 0 0
SFN 0.026 0.053 -10000 0 -0.51 2 2
LNPEP 0.033 0.006 -10000 0 -10000 0 0
YWHAE 0.027 0.014 -10000 0 -10000 0 0
S1P5 pathway

Figure S109.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S109.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.007 0.088 0.34 3 -10000 0 3
GNAI2 0.034 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.021 0.007 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.034 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.008 0.09 -10000 0 -0.34 3 3
negative regulation of cAMP metabolic process -0.007 0.09 -10000 0 -0.34 4 4
GNAZ 0.032 0.009 -10000 0 -10000 0 0
GNAI3 0.033 0.007 -10000 0 -10000 0 0
GNA12 0.031 0.01 -10000 0 -10000 0 0
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.007 0.091 -10000 0 -0.35 4 4
RhoA/GDP 0.025 0.003 -10000 0 -10000 0 0
RHOA 0.034 0.005 -10000 0 -10000 0 0
GNAI1 -0.033 0.18 -10000 0 -0.51 26 26
Retinoic acid receptors-mediated signaling

Figure S110.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S110.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.033 0.007 -10000 0 -10000 0 0
HDAC3 0.034 0.005 -10000 0 -10000 0 0
VDR 0.019 0.089 -10000 0 -0.51 6 6
Cbp/p300/PCAF 0.042 0.014 -10000 0 -10000 0 0
EP300 0.032 0.009 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.017 0.04 -10000 0 -10000 0 0
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.034 0.005 -10000 0 -10000 0 0
AKT1 0.025 0.065 0.23 8 -10000 0 8
RAR alpha/9cRA/Cyclin H 0.058 0.061 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.032 0.051 0.22 3 -0.27 2 5
CDC2 0.001 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.038 0.041 -10000 0 -0.32 1 1
NCOR2 0.034 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.014 0.064 -10000 0 -0.36 6 6
RXRs/RARs/NRIP1/9cRA 0.045 0.064 0.4 1 -10000 0 1
NCOA2 0.03 0.012 -10000 0 -10000 0 0
NCOA3 0.018 0.017 -10000 0 -10000 0 0
NCOA1 0.029 0.052 -10000 0 -0.51 2 2
VDR/VDR/DNA 0.019 0.089 -10000 0 -0.5 6 6
RARG 0.032 0.034 -10000 0 -0.32 2 2
RAR gamma1/9cRA 0.044 0.023 -10000 0 -0.18 2 2
MAPK3 0.029 0.052 -10000 0 -0.5 2 2
MAPK1 0.032 0.009 -10000 0 -10000 0 0
MAPK8 0.034 0.007 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.045 0.072 -10000 0 -0.44 1 1
RARA 0.025 0.022 -10000 0 -10000 0 0
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.028 0.04 0.2 2 -0.21 1 3
PRKCA 0.034 0.025 -10000 0 -0.31 1 1
RXRs/RARs/NRIP1/9cRA/HDAC1 0.05 0.067 0.38 2 -10000 0 2
RXRG 0.028 0.021 -10000 0 -10000 0 0
RXRA 0.025 0.036 -10000 0 -10000 0 0
RXRB 0.028 0.021 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.014 0.064 -10000 0 -0.36 6 6
RBP1 -0.016 0.14 -10000 0 -0.39 25 25
CRBP1/9-cic-RA -0.01 0.1 -10000 0 -0.28 25 25
RARB 0.036 0.004 -10000 0 -10000 0 0
PRKCG 0.03 0.048 -10000 0 -0.31 4 4
MNAT1 0.031 0.01 -10000 0 -10000 0 0
RAR alpha/RXRs 0.04 0.069 0.35 1 -10000 0 1
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.046 0.064 0.4 1 -10000 0 1
proteasomal ubiquitin-dependent protein catabolic process 0.064 0.071 0.31 5 -0.31 1 6
RXRs/RARs/NRIP1/9cRA/HDAC3 0.051 0.066 0.38 2 -10000 0 2
positive regulation of DNA binding 0.044 0.052 -10000 0 -10000 0 0
NRIP1 0.053 0.062 -10000 0 -10000 0 0
RXRs/RARs 0.05 0.056 -10000 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.03 0.048 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
CDK7 0.034 0.005 -10000 0 -10000 0 0
TFIIH 0.061 0.023 -10000 0 -10000 0 0
RAR alpha/9cRA 0.068 0.053 -10000 0 -10000 0 0
CCNH 0.034 0.005 -10000 0 -10000 0 0
CREBBP 0.033 0.007 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.058 0.032 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

Figure S111.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S111.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.047 0.021 -10000 0 -0.22 1 1
AKT1 0.085 0.12 0.4 7 -10000 0 7
PTK2B 0.005 0.068 -10000 0 -10000 0 0
VEGFR2 homodimer/Frs2 0.03 0.063 -10000 0 -10000 0 0
CAV1 0.025 0.055 -10000 0 -0.36 4 4
CALM1 0.03 0.011 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.031 0.088 -10000 0 -10000 0 0
endothelial cell proliferation 0.13 0.15 0.36 33 -10000 0 33
mol:Ca2+ -0.005 0.063 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.043 0.084 -10000 0 -10000 0 0
RP11-342D11.1 -0.014 0.081 -10000 0 -0.41 2 2
CDH5 0.034 0.005 -10000 0 -10000 0 0
VEGFA homodimer 0.054 0.077 -10000 0 -0.31 1 1
SHC1 0.033 0.006 -10000 0 -10000 0 0
SHC2 0.015 0.077 -10000 0 -0.32 11 11
HRAS/GDP 0.024 0.087 -10000 0 -0.37 1 1
SH2D2A 0.024 0.058 -10000 0 -0.32 6 6
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.096 0.11 0.34 1 -10000 0 1
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.025 0.092 -10000 0 -10000 0 0
VEGFR1 homodimer 0.007 0.077 -10000 0 -0.32 11 11
SHC/GRB2/SOS1 0.049 0.11 -10000 0 -0.4 2 2
GRB10 -0.004 0.09 -10000 0 -0.41 1 1
PTPN11 0.032 0.024 -10000 0 -0.32 1 1
GRB2 0.033 0.007 -10000 0 -10000 0 0
PAK1 0.034 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.053 0.1 -10000 0 -0.38 1 1
HRAS 0.034 0.005 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.007 0.099 -10000 0 -0.35 4 4
HIF1A 0.028 0.035 -10000 0 -0.32 2 2
FRS2 0.034 0.004 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.041 0.083 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.034 0.004 -10000 0 -10000 0 0
Nck/Pak 0.049 0.009 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.029 0.091 -10000 0 -0.36 1 1
mol:GDP 0.033 0.097 -10000 0 -0.39 2 2
mol:NADP 0.085 0.11 0.34 6 -10000 0 6
eNOS/Hsp90 0.089 0.1 0.34 6 -10000 0 6
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
mol:IP3 -0.005 0.064 -10000 0 -10000 0 0
HIF1A/ARNT 0.042 0.03 -10000 0 -0.22 2 2
SHB 0.021 0.067 -10000 0 -0.32 8 8
VEGFA 0.003 0.097 -10000 0 -0.32 17 17
VEGFC 0.025 0.064 -10000 0 -0.51 3 3
FAK1/Vinculin 0.052 0.097 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.034 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.045 0.092 -10000 0 -10000 0 0
PTPN6 0.033 0.007 -10000 0 -10000 0 0
EPAS1 0.022 0.09 -10000 0 -0.49 6 6
mol:L-citrulline 0.085 0.11 0.34 6 -10000 0 6
ITGAV 0.033 0.024 -10000 0 -0.32 1 1
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.046 0.091 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer 0.022 0.11 -10000 0 -0.45 2 2
VEGFR2/3 heterodimer 0.03 0.062 -10000 0 -10000 0 0
VEGFB 0.034 0.005 -10000 0 -10000 0 0
MAPK11 -0.02 0.084 -10000 0 -0.43 2 2
VEGFR2 homodimer 0.013 0.067 -10000 0 -0.35 6 6
FLT1 0.007 0.077 -10000 0 -0.32 11 11
NEDD4 0.019 0.063 -10000 0 -0.32 6 6
MAPK3 0.04 0.11 0.33 3 -10000 0 3
MAPK1 0.04 0.11 0.33 3 -10000 0 3
VEGFA145/NRP2 0.027 0.078 -10000 0 -0.23 17 17
VEGFR1/2 heterodimer 0.009 0.072 -10000 0 -10000 0 0
KDR 0.013 0.067 -10000 0 -0.35 6 6
VEGFA165/NRP1/VEGFR2 homodimer 0.026 0.1 -10000 0 -0.4 2 2
SRC 0.019 0.017 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.05 0.11 0.34 4 -10000 0 4
PI3K 0.043 0.092 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.032 0.086 -10000 0 -10000 0 0
FES -0.002 0.096 -10000 0 -0.54 2 2
GAB1 0.011 0.079 -10000 0 -0.47 1 1
VEGFR2 homodimer/VEGFA homodimer/Src 0.015 0.068 -10000 0 -10000 0 0
CTNNB1 0.026 0.053 -10000 0 -0.32 5 5
SOS1 0.034 0.002 -10000 0 -10000 0 0
ARNT 0.034 0.005 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.084 0.1 0.34 3 -10000 0 3
VEGFR2 homodimer/VEGFA homodimer/Yes 0.021 0.085 -10000 0 -10000 0 0
PI3K/GAB1 0.048 0.082 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.061 0.093 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.042 0.073 -10000 0 -10000 0 0
HSP90AA1 0.031 0.011 -10000 0 -10000 0 0
CDC42 -0.001 0.089 -10000 0 -0.42 2 2
actin cytoskeleton reorganization 0.024 0.091 -10000 0 -10000 0 0
PTK2 0.028 0.073 -10000 0 -10000 0 0
EDG1 -0.014 0.081 -10000 0 -0.41 2 2
mol:DAG -0.005 0.064 -10000 0 -10000 0 0
CaM/Ca2+ 0.003 0.064 -10000 0 -10000 0 0
MAP2K3 -0.009 0.079 -10000 0 -0.39 2 2
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.036 0.12 -10000 0 -0.41 1 1
PLCG1 -0.005 0.064 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.02 0.076 -10000 0 -10000 0 0
IQGAP1 0.032 0.009 -10000 0 -10000 0 0
YES1 0.027 0.014 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.03 0.089 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.029 0.088 -10000 0 -10000 0 0
cell migration 0.062 0.099 0.39 1 -10000 0 1
mol:PI-3-4-5-P3 0.044 0.09 -10000 0 -10000 0 0
FYN 0.03 0.037 -10000 0 -0.51 1 1
VEGFB/NRP1 0.003 0.085 -10000 0 -0.38 2 2
mol:NO 0.085 0.11 0.34 6 -10000 0 6
PXN 0.034 0.003 -10000 0 -10000 0 0
HRAS/GTP 0.004 0.076 -10000 0 -0.37 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.016 0.1 -10000 0 -0.41 1 1
VHL 0.032 0.025 -10000 0 -0.32 1 1
ITGB3 0.033 0.007 -10000 0 -10000 0 0
NOS3 0.086 0.11 0.37 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/Sck 0.02 0.1 -10000 0 -0.38 1 1
RAC1 0.031 0.011 -10000 0 -10000 0 0
PRKCA -0.003 0.07 -10000 0 -10000 0 0
PRKCB -0.011 0.056 -10000 0 -10000 0 0
VCL 0.033 0.007 -10000 0 -10000 0 0
VEGFA165/NRP1 0.002 0.089 -10000 0 -0.41 2 2
VEGFR1/2 heterodimer/VEGFA homodimer 0.013 0.086 -10000 0 -10000 0 0
VEGFA165/NRP2 0.027 0.078 -10000 0 -0.23 17 17
MAPKKK cascade 0.016 0.089 -10000 0 -10000 0 0
NRP2 0.033 0.024 -10000 0 -0.32 1 1
VEGFC homodimer 0.025 0.063 -10000 0 -0.5 3 3
NCK1 0.034 0.005 -10000 0 -10000 0 0
ROCK1 0.027 0.014 -10000 0 -10000 0 0
FAK1/Paxillin 0.052 0.098 -10000 0 -10000 0 0
MAP3K13 0 0.089 -10000 0 -0.42 2 2
PDPK1 0.067 0.11 0.27 24 -10000 0 24
IL2 signaling events mediated by STAT5

Figure S112.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S112.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.035 0.004 -10000 0 -10000 0 0
ELF1 0.026 0.033 -10000 0 -10000 0 0
CCNA2 -0.017 0.12 -10000 0 -0.32 31 31
PIK3CA 0.035 0.004 -10000 0 -10000 0 0
JAK3 0.035 0.004 -10000 0 -10000 0 0
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
JAK1 0.034 0.006 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.068 0.075 -10000 0 -0.54 1 1
SHC1 0.034 0.006 -10000 0 -10000 0 0
SP1 0.024 0.071 -10000 0 -0.32 7 7
IL2RA 0.014 0.047 -10000 0 -10000 0 0
IL2RB 0.033 0.009 -10000 0 -10000 0 0
SOS1 0.035 0.002 -10000 0 -10000 0 0
IL2RG 0.027 0.063 -10000 0 -0.5 3 3
G1/S transition of mitotic cell cycle 0.008 0.13 0.4 2 -0.67 5 7
PTPN11 0.033 0.024 -10000 0 -0.32 1 1
CCND2 -0.001 0.13 -10000 0 -0.78 5 5
LCK 0.029 0.044 -10000 0 -0.41 2 2
GRB2 0.034 0.007 -10000 0 -10000 0 0
IL2 0.034 0.005 -10000 0 -10000 0 0
CDK6 0.031 0.025 -10000 0 -0.32 1 1
CCND3 0.069 0.079 0.43 1 -0.46 1 2
Insulin Pathway

Figure S113.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S113.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.04 0.091 -10000 0 -0.29 12 12
TC10/GTP 0.024 0.071 -10000 0 -0.25 12 12
Insulin Receptor/Insulin/IRS1/Shp2 0.088 0.064 -10000 0 -0.27 2 2
HRAS 0.034 0.005 -10000 0 -10000 0 0
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 -0.023 0.14 -10000 0 -0.37 30 30
FOXO3 -0.004 0.11 -10000 0 -0.55 8 8
AKT1 0.005 0.083 -10000 0 -0.36 1 1
INSR 0.04 0.066 -10000 0 -0.5 3 3
Insulin Receptor/Insulin 0.089 0.088 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.016 0.07 -10000 0 -0.32 9 9
SORBS1 0.001 0.13 -10000 0 -0.49 13 13
CRK 0.027 0.014 -10000 0 -10000 0 0
PTPN1 0.01 0.037 -10000 0 -10000 0 0
CAV1 0.031 0.064 0.2 2 -0.29 4 6
CBL/APS/CAP/Crk-II/C3G 0.042 0.084 -10000 0 -0.27 12 12
Insulin Receptor/Insulin/IRS1/NCK2 0.09 0.061 -10000 0 -0.27 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.069 0.052 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.073 0.094 -10000 0 -0.47 3 3
RPS6KB1 -0.01 0.073 -10000 0 -0.33 1 1
PARD6A 0.019 0.07 -10000 0 -0.32 9 9
CBL 0.034 0.005 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.024 0.016 -10000 0 -10000 0 0
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.027 0.085 -10000 0 -0.34 1 1
HRAS/GTP 0.021 0.034 -10000 0 -10000 0 0
Insulin Receptor 0.04 0.065 -10000 0 -0.5 3 3
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.097 0.066 -10000 0 -10000 0 0
PRKCI 0.035 0.059 -10000 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 0.015 0.083 -10000 0 -0.38 1 1
SHC1 0.033 0.006 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.053 0.035 -10000 0 -10000 0 0
PI3K 0.085 0.058 -10000 0 -10000 0 0
NCK2 0.034 0 -10000 0 -10000 0 0
RHOQ 0.034 0.004 -10000 0 -10000 0 0
mol:H2O2 0.002 0.007 -10000 0 -10000 0 0
HRAS/GDP 0.025 0.003 -10000 0 -10000 0 0
AKT2 0.005 0.082 -10000 0 -0.36 1 1
PRKCZ 0.017 0.05 -10000 0 -0.38 1 1
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP 0.036 0.049 -10000 0 -0.24 2 2
F2RL2 0.027 0.048 -10000 0 -0.32 4 4
TRIP10 0.034 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.073 0.046 -10000 0 -0.27 2 2
TC10/GTP/CIP4/Exocyst 0.045 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.1 0.056 -10000 0 -10000 0 0
RAPGEF1 0.034 0.005 -10000 0 -10000 0 0
RASA1 0.03 0.034 -10000 0 -0.32 2 2
NCK1 0.034 0.005 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.03 0.082 -10000 0 -0.28 12 12
TC10/GDP 0.025 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.073 0.072 -10000 0 -0.27 2 2
INPP5D 0.008 0.04 -10000 0 -0.25 2 2
SOS1 0.034 0.002 -10000 0 -10000 0 0
SGK1 -0.003 0.007 -10000 0 -10000 0 0
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.032 0.024 -10000 0 -0.32 1 1
IRS1 0.028 0.048 -10000 0 -0.32 4 4
p62DOK/RasGAP 0.054 0.036 -10000 0 -10000 0 0
INS 0.045 0.019 -10000 0 -10000 0 0
mol:PI-3-4-P2 0.008 0.039 -10000 0 -0.24 2 2
GRB2 0.033 0.007 -10000 0 -10000 0 0
EIF4EBP1 -0.011 0.076 -10000 0 -0.33 1 1
PTPRA 0.033 0.022 -10000 0 -10000 0 0
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.045 0.008 -10000 0 -10000 0 0
PDPK1 0.033 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.044 0.04 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.07 0.056 -10000 0 -0.27 2 2
Insulin Receptor/Insulin/IRS3 0.063 0.052 -10000 0 -0.37 2 2
Par3/Par6 0.063 0.057 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

Figure S114.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S114.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.032 0.009 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 0.021 0.041 -10000 0 -10000 0 0
NT3 (dimer)/TRKC 0.043 0.03 -10000 0 -0.22 2 2
NT3 (dimer)/TRKB 0.043 0.081 -10000 0 -0.3 8 8
SHC/Grb2/SOS1/GAB1/PI3K 0.035 0.034 -10000 0 -10000 0 0
RAPGEF1 0.034 0.005 -10000 0 -10000 0 0
BDNF 0.008 0.092 -10000 0 -0.32 16 16
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
DYNLT1 0.033 0.007 -10000 0 -10000 0 0
NTRK1 0.033 0.006 -10000 0 -10000 0 0
NTRK2 0.007 0.11 -10000 0 -0.45 12 12
NTRK3 0.032 0.009 -10000 0 -10000 0 0
NT-4/5 (dimer)/TRKB 0.027 0.071 -10000 0 -0.27 11 11
neuron apoptosis -0.019 0.08 0.33 1 -10000 0 1
SHC 2-3/Grb2 0.02 0.085 -10000 0 -0.35 1 1
SHC1 0.033 0.006 -10000 0 -10000 0 0
SHC2 0.009 0.071 -10000 0 -10000 0 0
SHC3 0.008 0.077 -10000 0 -0.41 4 4
STAT3 (dimer) 0.011 0.069 -10000 0 -10000 0 0
NT3 (dimer)/TRKA 0.06 0.032 -10000 0 -10000 0 0
RIN/GDP 0.053 0.08 0.3 8 -0.24 1 9
GIPC1 0.031 0.037 -10000 0 -0.51 1 1
KRAS 0.033 0.006 -10000 0 -10000 0 0
DNAJA3 0.009 0.029 -10000 0 -10000 0 0
RIN/GTP 0.017 0.012 -10000 0 -10000 0 0
CCND1 -0.019 0.1 -10000 0 -10000 0 0
MAGED1 0.032 0.024 -10000 0 -0.32 1 1
PTPN11 0.032 0.024 -10000 0 -0.32 1 1
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.065 0.018 -10000 0 -10000 0 0
GRB2 0.033 0.007 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.044 0.01 -10000 0 -10000 0 0
TRKA/NEDD4-2 0.002 0.1 -10000 0 -0.37 13 13
ELMO1 0.031 0.011 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.036 0.037 -10000 0 -0.31 2 2
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.034 0.005 -10000 0 -10000 0 0
DOCK1 0.028 0.052 -10000 0 -0.51 2 2
GAB2 0.034 0.004 -10000 0 -10000 0 0
RIT2 0.023 0.016 -10000 0 -10000 0 0
RIT1 0.033 0.006 -10000 0 -10000 0 0
FRS2 0.034 0.004 -10000 0 -10000 0 0
DNM1 0.03 0.034 -10000 0 -0.32 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.014 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.03 0.033 -10000 0 -10000 0 0
mol:GDP 0.066 0.1 0.33 10 -0.35 2 12
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.023 0.008 -10000 0 -10000 0 0
RIT1/GDP 0.058 0.071 0.22 9 -0.25 1 10
TIAM1 0.027 0.052 -10000 0 -0.51 2 2
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
BDNF (dimer)/TRKB 0.026 0.1 -10000 0 -0.31 10 10
KIDINS220/CRKL/C3G 0.047 0.014 -10000 0 -10000 0 0
SHC/RasGAP 0.046 0.028 -10000 0 -0.22 2 2
FRS2 family/SHP2 0.066 0.022 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.078 0.043 -10000 0 -0.29 2 2
RIT1/GTP 0.025 0.004 -10000 0 -10000 0 0
NT3 (dimer) 0.029 0.034 -10000 0 -0.32 2 2
RAP1/GDP 0.045 0.055 0.16 3 -0.21 1 4
KIDINS220/CRKL 0.032 0.009 -10000 0 -10000 0 0
BDNF (dimer) 0.008 0.092 -10000 0 -0.32 16 16
ubiquitin-dependent protein catabolic process 0.004 0.087 -10000 0 -0.31 13 13
Schwann cell development -0.004 0.014 -10000 0 -10000 0 0
EHD4 0.032 0.009 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.082 0.024 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.018 0.051 -10000 0 -10000 0 0
RAP1B 0.034 0.004 -10000 0 -10000 0 0
RAP1A 0.032 0.008 -10000 0 -10000 0 0
CDC42/GTP 0.016 0.077 -10000 0 -0.27 2 2
ABL1 0.034 0.005 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.049 0.01 -10000 0 -10000 0 0
Rap1/GTP 0.012 0.096 -10000 0 -0.43 4 4
STAT3 0.011 0.069 -10000 0 -10000 0 0
axon guidance 0.006 0.068 -10000 0 -0.26 2 2
MAPK3 0.022 0.039 -10000 0 -0.28 2 2
MAPK1 0.024 0.026 -10000 0 -10000 0 0
CDC42/GDP 0.065 0.083 0.27 12 -0.25 1 13
NTF3 0.03 0.034 -10000 0 -0.32 2 2
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.043 0.018 -10000 0 -10000 0 0
PI3K 0.049 0.01 -10000 0 -10000 0 0
FRS3 0.033 0.006 -10000 0 -10000 0 0
FAIM 0.03 0.034 -10000 0 -0.32 2 2
GAB1 0.029 0.052 -10000 0 -0.51 2 2
RASGRF1 0 0.041 -10000 0 -10000 0 0
SOS1 0.034 0.002 -10000 0 -10000 0 0
MCF2L 0.014 0.022 -10000 0 -10000 0 0
RGS19 0.019 0.017 -10000 0 -10000 0 0
CDC42 0.032 0.009 -10000 0 -10000 0 0
RAS family/GTP 0.052 0.085 0.49 2 -10000 0 2
Rac1/GDP 0.052 0.074 0.26 7 -0.25 1 8
NGF (dimer)/TRKA/GRIT 0.023 0.004 -10000 0 -10000 0 0
neuron projection morphogenesis 0.027 0.095 -10000 0 -0.86 2 2
NGF (dimer)/TRKA/NEDD4-2 0.004 0.087 -10000 0 -0.31 13 13
MAP2K1 0.023 0.043 -10000 0 -10000 0 0
NGFR 0.033 0.008 -10000 0 -10000 0 0
NGF (dimer)/TRKA/GIPC/GAIP 0.016 0.026 -10000 0 -0.23 1 1
RAS family/GTP/PI3K 0.031 0.022 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.093 0.033 -10000 0 -10000 0 0
NRAS 0.029 0.034 -10000 0 -0.32 2 2
GRB2/SOS1 0.049 0.01 -10000 0 -10000 0 0
PRKCI 0.026 0.053 -10000 0 -0.32 5 5
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.031 0.011 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade 0.012 0.026 -10000 0 -10000 0 0
RASA1 0.03 0.034 -10000 0 -0.32 2 2
TRKA/c-Abl 0.049 0.011 -10000 0 -10000 0 0
SQSTM1 0.034 0.004 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.044 0.1 -10000 0 -0.32 8 8
NGF (dimer)/TRKA/p62/Atypical PKCs 0.054 0.032 -10000 0 -10000 0 0
MATK 0.033 0.006 -10000 0 -10000 0 0
NEDD4L -0.009 0.13 -10000 0 -0.51 13 13
RAS family/GDP -0.006 0.025 -10000 0 -10000 0 0
NGF (dimer)/TRKA 0.015 0.025 -10000 0 -10000 0 0
Rac1/GTP 0.004 0.045 -10000 0 -0.27 1 1
FRS2 family/SHP2/CRK family 0.074 0.048 -10000 0 -10000 0 0
S1P4 pathway

Figure S115.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S115.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -10000 0 -10000 0 0
GNAO1 0.034 0.005 -10000 0 -10000 0 0
CDC42/GTP 0.007 0.089 -10000 0 -0.34 3 3
PLCG1 0.007 0.064 0.19 10 -0.27 1 11
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.034 0.004 -10000 0 -10000 0 0
GNAI3 0.033 0.007 -10000 0 -10000 0 0
G12/G13 0.043 0.018 -10000 0 -10000 0 0
cell migration 0.007 0.087 -10000 0 -0.34 3 3
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
MAPK3 -0.014 0.087 -10000 0 -0.3 6 6
MAPK1 -0.005 0.08 -10000 0 -0.35 3 3
S1P/S1P5/Gi -0.007 0.091 -10000 0 -0.35 4 4
GNAI1 -0.033 0.18 -10000 0 -0.51 26 26
CDC42/GDP 0.023 0.007 -10000 0 -10000 0 0
S1P/S1P5/G12 0.021 0.007 -10000 0 -10000 0 0
RHOA 0.042 0.062 0.37 2 -10000 0 2
S1P/S1P4/Gi -0.007 0.091 -10000 0 -0.35 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.032 0.009 -10000 0 -10000 0 0
S1P/S1P4/G12/G13 0.038 0.016 -10000 0 -10000 0 0
GNA12 0.031 0.01 -10000 0 -10000 0 0
GNA13 0.032 0.008 -10000 0 -10000 0 0
CDC42 0.032 0.009 -10000 0 -10000 0 0
Arf1 pathway

Figure S116.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S116.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.067 0.069 0.17 10 -10000 0 10
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.013 0.037 -10000 0 -10000 0 0
AP2 0.049 0.01 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.039 0.016 -10000 0 -10000 0 0
CLTB 0.034 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.026 0.008 -10000 0 -10000 0 0
CD4 0.033 0.007 -10000 0 -10000 0 0
CLTA 0.033 0.006 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -10000 0 0
ARFGAP1 0.005 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.007 0.007 -10000 0 -10000 0 0
ARF1/GTP 0.022 0.008 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.08 0.08 0.18 87 -10000 0 87
mol:Choline 0.006 0.007 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.034 0.007 -10000 0 -10000 0 0
DDEF1 0.005 0.006 -10000 0 -10000 0 0
ARF1/GDP 0.009 0.031 0.16 8 -10000 0 8
AP2M1 0.034 0.004 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.015 0.007 -10000 0 -10000 0 0
Rac/GTP 0.024 0.009 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.033 0.037 -10000 0 -10000 0 0
ARFIP2 0.02 0.025 -10000 0 -10000 0 0
COPA 0.033 0.006 -10000 0 -10000 0 0
RAC1 0.031 0.011 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.02 0.021 -10000 0 -10000 0 0
ARF1/GTP/ARHGAP10 0.023 0.006 -10000 0 -10000 0 0
GGA3 0.033 0.007 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.024 0.039 -10000 0 -0.24 4 4
AP2A1 0.034 0.005 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.016 0.027 -10000 0 -10000 0 0
ARF1/GDP/Membrin 0.023 0.046 -10000 0 -0.29 4 4
Arfaptin 2/Rac/GDP 0.039 0.015 -10000 0 -10000 0 0
CYTH2 -0.001 0.003 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.044 0.012 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.023 0.008 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.032 0.02 -10000 0 -10000 0 0
PLD2 0.006 0.007 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.005 0.005 -10000 0 -10000 0 0
PIP5K1A 0.007 0.007 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.012 0.03 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.006 0.007 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.005 0.005 -10000 0 -10000 0 0
GOSR2 0.012 0.024 -10000 0 -0.31 1 1
USO1 0.012 0.024 -10000 0 -0.31 1 1
GBF1 0.009 0.039 -10000 0 -0.31 3 3
ARF1/GTP/Arfaptin 2 0.043 0.011 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.065 0.018 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

Figure S117.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S117.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.02 0.039 -9999 0 -0.51 1 1
SMAD2 0.012 0.047 -9999 0 -0.26 1 1
SMAD3 0.018 0.057 -9999 0 -0.57 1 1
SMAD3/SMAD4 0.013 0.099 -9999 0 -0.46 7 7
SMAD4/Ubc9/PIASy 0.041 0.046 -9999 0 -0.31 1 1
SMAD2/SMAD2/SMAD4 0.032 0.074 -9999 0 -10000 0 0
PPM1A 0.031 0.01 -9999 0 -10000 0 0
CALM1 0.03 0.011 -9999 0 -10000 0 0
SMAD2/SMAD4 0.011 0.049 -9999 0 -0.26 1 1
MAP3K1 0.034 0.005 -9999 0 -10000 0 0
TRAP-1/SMAD4 0.031 0.039 -9999 0 -0.37 1 1
MAPK3 0.029 0.052 -9999 0 -0.51 2 2
MAPK1 0.032 0.009 -9999 0 -10000 0 0
NUP214 0.034 0.005 -9999 0 -10000 0 0
CTDSP1 0.034 0.002 -9999 0 -10000 0 0
CTDSP2 0.029 0.052 -9999 0 -0.51 2 2
CTDSPL 0.029 0.052 -9999 0 -0.51 2 2
KPNB1 0.025 0.053 -9999 0 -0.32 5 5
TGFBRAP1 0.034 0 -9999 0 -10000 0 0
UBE2I 0.031 0.025 -9999 0 -0.32 1 1
NUP153 0.034 0.005 -9999 0 -10000 0 0
KPNA2 0.019 0.067 -9999 0 -0.32 8 8
PIAS4 0.033 0.006 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class II

Figure S118.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S118.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.073 0.034 -9999 0 -10000 0 0
HDAC3 0.034 0.005 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.008 0.014 -9999 0 -10000 0 0
GATA1/HDAC4 0.048 0.02 -9999 0 -0.22 1 1
GATA1/HDAC5 0.047 0.022 -9999 0 -0.22 1 1
GATA2/HDAC5 0.048 0.012 -9999 0 -10000 0 0
HDAC5/BCL6/BCoR 0.062 0.035 -9999 0 -0.31 1 1
HDAC9 0.031 0.011 -9999 0 -10000 0 0
Glucocorticoid receptor/Hsp90/HDAC6 0.019 0.12 -9999 0 -0.31 24 24
HDAC4/ANKRA2 0.049 0.009 -9999 0 -10000 0 0
HDAC5/YWHAB 0.026 0.026 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.017 0.013 -9999 0 -10000 0 0
GATA2 0.034 0.005 -9999 0 -10000 0 0
HDAC4/RFXANK 0.05 0.008 -9999 0 -10000 0 0
BCOR 0.034 0.004 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.027 0.042 -9999 0 -0.32 3 3
HDAC5 0.033 0.007 -9999 0 -10000 0 0
GNB1/GNG2 0.043 0.018 -9999 0 -10000 0 0
Histones 0.031 0.045 -9999 0 -0.26 2 2
ADRBK1 0.034 0.004 -9999 0 -10000 0 0
HDAC4 0.034 0.004 -9999 0 -10000 0 0
XPO1 0.034 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.048 0.012 -9999 0 -10000 0 0
HDAC4/Ubc9 0.047 0.022 -9999 0 -0.22 1 1
HDAC7 0 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.039 0.021 -9999 0 -10000 0 0
TUBA1B 0.034 0.004 -9999 0 -10000 0 0
HDAC6 0.034 0.004 -9999 0 -10000 0 0
HDAC5/RFXANK 0.048 0.011 -9999 0 -10000 0 0
CAMK4 0.033 0.006 -9999 0 -10000 0 0
Tubulin/HDAC6 0.067 0.015 -9999 0 -10000 0 0
SUMO1 0.034 0.002 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.018 0.017 -9999 0 -10000 0 0
GATA1 0.032 0.024 -9999 0 -0.32 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.027 0.014 -9999 0 -10000 0 0
NR3C1 -0.027 0.17 -9999 0 -0.51 24 24
SUMO1/HDAC4 0.044 0.042 -9999 0 -10000 0 0
SRF 0.033 0.006 -9999 0 -10000 0 0
HDAC4/YWHAB 0.026 0.026 -9999 0 -10000 0 0
Tubulin 0.049 0.009 -9999 0 -10000 0 0
HDAC4/14-3-3 E 0.04 0.021 -9999 0 -10000 0 0
GNB1 0.032 0.008 -9999 0 -10000 0 0
RANGAP1 0.027 0.042 -9999 0 -0.32 3 3
BCL6/BCoR 0.046 0.035 -9999 0 -0.37 1 1
HDAC4/HDAC3/SMRT (N-CoR2) 0.066 0.015 -9999 0 -10000 0 0
HDAC4/SRF 0.065 0.018 -9999 0 -10000 0 0
HDAC4/ER alpha 0.038 0.064 -9999 0 -0.37 5 5
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.031 0.045 -9999 0 -0.25 2 2
cell motility 0.066 0.015 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.031 0.025 -9999 0 -0.32 1 1
HDAC7/HDAC3 0.025 0.003 -9999 0 -10000 0 0
BCL6 0.03 0.044 -9999 0 -0.41 2 2
HDAC4/CaMK II delta B 0.034 0.004 -9999 0 -10000 0 0
Hsp90/HDAC6 0.045 0.017 -9999 0 -10000 0 0
ESR1 0.02 0.081 -9999 0 -0.51 5 5
HDAC6/HDAC11 0.049 0.01 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.045 0.044 -9999 0 -10000 0 0
NPC 0.02 0.012 -9999 0 -10000 0 0
MEF2C -0.052 0.2 -9999 0 -0.51 34 34
RAN 0.032 0.024 -9999 0 -0.32 1 1
HDAC4/MEF2C 0.041 0.13 -9999 0 -0.27 30 30
GNG2 0.031 0.01 -9999 0 -10000 0 0
NCOR2 0.034 0.005 -9999 0 -10000 0 0
TUBB2A 0.034 0.005 -9999 0 -10000 0 0
HDAC11 0.033 0.006 -9999 0 -10000 0 0
HSP90AA1 0.031 0.011 -9999 0 -10000 0 0
RANBP2 0.033 0.024 -9999 0 -0.32 1 1
ANKRA2 0.034 0.005 -9999 0 -10000 0 0
RFXANK 0.034 0.004 -9999 0 -10000 0 0
nuclear import -0.021 0.024 -9999 0 -10000 0 0
Circadian rhythm pathway

Figure S119.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S119.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.042 0.069 -9999 0 -10000 0 0
CLOCK 0.035 0.011 -9999 0 -10000 0 0
TIMELESS/CRY2 0.048 0.034 -9999 0 -10000 0 0
DEC1/BMAL1 0.05 0.024 -9999 0 -0.27 1 1
ATR 0.032 0.024 -9999 0 -0.32 1 1
NR1D1 0.027 0.027 -9999 0 -10000 0 0
ARNTL 0.035 0.01 -9999 0 -10000 0 0
TIMELESS 0.028 0.03 -9999 0 -10000 0 0
NPAS2 0.036 0.009 -9999 0 -10000 0 0
CRY2 0.034 0.004 -9999 0 -10000 0 0
mol:CO -0.011 0.008 -9999 0 -10000 0 0
CHEK1 -0.009 0.11 -9999 0 -0.32 26 26
mol:HEME 0.011 0.008 -9999 0 -10000 0 0
PER1 0.027 0.014 -9999 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.078 0.025 -9999 0 -10000 0 0
BMAL1/CLOCK 0.04 0.047 -9999 0 -10000 0 0
S phase of mitotic cell cycle 0.042 0.069 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.043 0.07 -9999 0 -10000 0 0
mol:NADPH 0.011 0.008 -9999 0 -10000 0 0
PER1/TIMELESS 0.038 0.036 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 0.032 0.029 -9999 0 -0.39 1 1
Signaling events regulated by Ret tyrosine kinase

Figure S120.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S120.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.025 0.038 -10000 0 -10000 0 0
Crk/p130 Cas/Paxillin 0.002 0.041 -10000 0 -10000 0 0
JUN 0.015 0.05 -10000 0 -10000 0 0
HRAS 0.034 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 0.052 0.079 -10000 0 -0.29 4 4
RAP1A 0.032 0.008 -10000 0 -10000 0 0
FRS2 0.034 0.004 -10000 0 -10000 0 0
RAP1A/GDP 0.024 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.067 0.07 -10000 0 -0.29 5 5
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.032 0.024 -10000 0 -0.32 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.014 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.059 0.024 -10000 0 -10000 0 0
RHOA 0.034 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.058 0.068 -10000 0 -0.26 4 4
GRB7 0.03 0.025 -10000 0 -0.32 1 1
RET51/GFRalpha1/GDNF 0.066 0.069 -10000 0 -0.29 5 5
MAPKKK cascade 0.037 0.058 -10000 0 -10000 0 0
BCAR1 0.033 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.056 0.036 -10000 0 -10000 0 0
lamellipodium assembly 0.014 0.046 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC 0.066 0.069 -10000 0 -0.29 5 5
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC 0.06 0.02 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3 0.057 0.023 -10000 0 -10000 0 0
MAPK3 0.01 0.063 -10000 0 -10000 0 0
DOK1 0.033 0.024 -10000 0 -0.32 1 1
DOK6 0.023 0.016 -10000 0 -10000 0 0
PXN 0.034 0.003 -10000 0 -10000 0 0
neurite development 0.021 0.065 -10000 0 -0.32 2 2
DOK5 0.01 0.053 -10000 0 -0.32 5 5
GFRA1 0.033 0.007 -10000 0 -10000 0 0
MAPK8 0.024 0.048 -10000 0 -10000 0 0
HRAS/GTP 0.061 0.068 -10000 0 -0.29 4 4
tube development 0.056 0.029 -10000 0 -10000 0 0
MAPK1 0.013 0.066 0.35 2 -10000 0 2
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.031 0.014 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.008 -10000 0 -10000 0 0
SRC 0.019 0.017 -10000 0 -10000 0 0
PDLIM7 0.032 0.024 -10000 0 -0.32 1 1
RET51/GFRalpha1/GDNF/Dok6 0.033 0.061 -10000 0 -0.27 1 1
SHC1 0.033 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.064 0.074 -10000 0 -0.29 6 6
RET51/GFRalpha1/GDNF/Dok5 0.029 0.066 -10000 0 -0.29 2 2
PRKCA 0.031 0.025 -10000 0 -0.32 1 1
HRAS/GDP 0.025 0.003 -10000 0 -10000 0 0
CREB1 0.038 0.036 -10000 0 -10000 0 0
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.028 0.029 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Grb7 0.062 0.069 -10000 0 -0.29 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.015 0.093 -10000 0 -0.42 9 9
DOK4 0.026 0.063 -10000 0 -0.51 3 3
JNK cascade 0.015 0.049 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/FRS2 0.061 0.018 -10000 0 -10000 0 0
SHANK3 0.032 0.01 -10000 0 -10000 0 0
RASA1 0.03 0.034 -10000 0 -0.32 2 2
NCK1 0.034 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.031 0.013 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.026 0.051 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.028 0.048 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.028 0.046 -10000 0 -10000 0 0
PI3K 0.021 0.061 -10000 0 -10000 0 0
SOS1 0.034 0.002 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.069 0.03 -10000 0 -10000 0 0
GRB10 0.016 0.07 -10000 0 -0.32 9 9
activation of MAPKK activity 0.031 0.046 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/FRS2 0.067 0.069 -10000 0 -0.29 5 5
GAB1 0.029 0.052 -10000 0 -0.51 2 2
IRS1 0.028 0.048 -10000 0 -0.32 4 4
IRS2 0.025 0.015 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.025 0.054 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/PKC alpha 0.063 0.068 -10000 0 -0.29 4 4
GRB2 0.033 0.007 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
GDNF 0.033 0.007 -10000 0 -10000 0 0
RAC1 0.031 0.011 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.062 0.075 -10000 0 -0.29 5 5
Rac1/GTP 0.023 0.057 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF 0.043 0.013 -10000 0 -10000 0 0
GFRalpha1/GDNF 0.047 0.014 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

Figure S121.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S121.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.032 0.009 -10000 0 -10000 0 0
Rac1/GDP 0.029 0.012 -10000 0 -10000 0 0
DOCK1 0.028 0.052 -10000 0 -0.51 2 2
ITGA4 0.029 0.052 -10000 0 -0.51 2 2
RAC1 0.031 0.011 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.029 0.092 -10000 0 -0.37 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.014 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.063 0.042 -10000 0 -0.31 2 2
alpha4/beta7 Integrin/Paxillin 0.041 0.076 -10000 0 -0.28 11 11
lamellipodium assembly 0.017 0.078 -10000 0 -0.42 4 4
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
PI3K 0.049 0.01 -10000 0 -10000 0 0
ARF6 0.031 0.01 -10000 0 -10000 0 0
TLN1 0.033 0.006 -10000 0 -10000 0 0
PXN 0.019 0.003 -10000 0 -10000 0 0
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
ARF6/GTP 0.061 0.043 -10000 0 -10000 0 0
cell adhesion 0.069 0.042 -10000 0 -0.27 2 2
CRKL/CBL 0.047 0.014 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.053 0.038 -10000 0 -0.29 2 2
ITGB1 0.032 0.024 -10000 0 -0.32 1 1
ITGB7 0.011 0.11 -10000 0 -0.51 9 9
ARF6/GDP 0.029 0.013 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.063 0.071 -10000 0 -0.31 6 6
p130Cas/Crk/Dock1 0.049 0.046 -10000 0 -0.3 2 2
VCAM1 0.021 0.081 -10000 0 -0.51 5 5
alpha4/beta1 Integrin/Paxillin/Talin 0.072 0.043 -10000 0 -0.27 2 2
alpha4/beta1 Integrin/Paxillin/GIT1 0.071 0.043 -10000 0 -0.27 2 2
BCAR1 0.033 0.006 -10000 0 -10000 0 0
mol:GDP -0.069 0.042 0.27 2 -10000 0 2
CBL 0.034 0.005 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
GIT1 0.033 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.072 0.043 -10000 0 -0.27 2 2
Rac1/GTP 0.016 0.085 -10000 0 -0.46 4 4
Nephrin/Neph1 signaling in the kidney podocyte

Figure S122.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S122.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.047 0.03 0.22 2 -10000 0 2
KIRREL 0.036 0.012 -10000 0 -10000 0 0
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.047 0.03 -10000 0 -0.22 2 2
PLCG1 0.018 0.017 -10000 0 -10000 0 0
ARRB2 0.027 0.014 -10000 0 -10000 0 0
WASL 0.03 0.037 -10000 0 -0.51 1 1
Nephrin/NEPH1/podocin/CD2AP 0.079 0.036 -10000 0 -10000 0 0
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.035 0.025 -10000 0 -10000 0 0
FYN 0.029 0.051 0.31 4 -0.21 1 5
mol:Ca2+ 0.043 0.045 -10000 0 -10000 0 0
mol:DAG 0.044 0.046 -10000 0 -10000 0 0
NPHS2 0.036 0.012 -10000 0 -10000 0 0
mol:IP3 0.044 0.046 -10000 0 -10000 0 0
regulation of endocytosis 0.053 0.04 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/Cholesterol 0.059 0.03 -10000 0 -10000 0 0
establishment of cell polarity 0.047 0.03 -10000 0 -0.22 2 2
Nephrin/NEPH1/podocin/NCK1-2 0.094 0.039 -10000 0 -10000 0 0
Nephrin/NEPH1/beta Arrestin2 0.056 0.042 -10000 0 -10000 0 0
NPHS1 0.032 0.035 -10000 0 -0.32 2 2
Nephrin/NEPH1/podocin 0.06 0.031 -10000 0 -0.21 1 1
TJP1 0.032 0.009 -10000 0 -10000 0 0
NCK1 0.034 0.005 -10000 0 -10000 0 0
NCK2 0.034 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.045 0.047 -10000 0 -10000 0 0
CD2AP 0.034 0.005 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.077 0.037 -10000 0 -10000 0 0
GRB2 0.033 0.007 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.029 0.064 0.32 6 -0.28 2 8
cytoskeleton organization 0.026 0.032 0.22 3 -10000 0 3
Nephrin/NEPH1 0.04 0.022 -10000 0 -10000 0 0
Nephrin/NEPH1/ZO-1 0.059 0.033 -10000 0 -10000 0 0
Aurora C signaling

Figure S123.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S123.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.029 0.041 -9999 0 -0.32 3 3
Aurora C/Aurora B/INCENP 0.047 0.038 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.014 0.023 -9999 0 -0.3 1 1
AURKB 0.027 0.014 -9999 0 -10000 0 0
AURKC 0.033 0.006 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class I

Figure S124.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S124.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.073 0.051 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0.008 0.014 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.041 0.064 -10000 0 -0.3 1 1
SUMO1 0.034 0.002 -10000 0 -10000 0 0
ZFPM1 0.033 0.006 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.017 0.013 -10000 0 -10000 0 0
FKBP3 0.031 0.011 -10000 0 -10000 0 0
Histones 0.079 0.038 -10000 0 -10000 0 0
YY1/LSF 0.016 0.06 -10000 0 -0.3 1 1
SMG5 0.033 0.006 -10000 0 -10000 0 0
RAN 0.032 0.024 -10000 0 -0.32 1 1
I kappa B alpha/HDAC3 0.033 0.015 -10000 0 -10000 0 0
I kappa B alpha/HDAC1 0.03 0.06 -10000 0 -10000 0 0
SAP18 0.025 0.015 -10000 0 -10000 0 0
RELA 0.033 0.022 -10000 0 -10000 0 0
HDAC1/Smad7 0.045 0.041 -10000 0 -0.31 1 1
RANGAP1 0.027 0.042 -10000 0 -0.32 3 3
HDAC3/TR2 0.044 0.04 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.026 0.057 -10000 0 -0.46 1 1
NF kappa B1 p50/RelA 0.038 0.072 0.32 1 -0.34 2 3
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.034 0.005 -10000 0 -10000 0 0
GATA1 0.032 0.024 -10000 0 -0.32 1 1
Mad/Max 0.023 0.096 -10000 0 -0.36 12 12
NuRD/MBD3 Complex/GATA1/Fog1 0.022 0.077 -10000 0 -0.37 2 2
RBBP7 0.034 0.005 -10000 0 -10000 0 0
NPC 0.02 0.012 -10000 0 -10000 0 0
RBBP4 0.033 0.007 -10000 0 -10000 0 0
MAX 0.031 0.01 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.034 0.004 -10000 0 -10000 0 0
NFKBIA 0.028 0.012 -10000 0 -10000 0 0
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.046 0.052 -10000 0 -0.35 1 1
SIN3 complex 0.059 0.042 -10000 0 -10000 0 0
SMURF1 0.033 0.008 -10000 0 -10000 0 0
CHD3 0.025 0.031 -10000 0 -0.39 1 1
SAP30 0.033 0.008 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.027 0.014 -10000 0 -10000 0 0
YY1/HDAC3 0.022 0.045 -10000 0 -10000 0 0
YY1/HDAC2 0.017 0.057 -10000 0 -0.24 2 2
YY1/HDAC1 0.016 0.059 -10000 0 -0.28 1 1
NuRD/MBD2 Complex (MeCP1) 0.018 0.069 -10000 0 -0.52 2 2
PPARG 0.02 0.064 -10000 0 -0.3 6 6
HDAC8/hEST1B 0.066 0.015 -10000 0 -10000 0 0
UBE2I 0.031 0.025 -10000 0 -0.32 1 1
beta TrCP1/SCF ubiquitin ligase complex 0.034 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.033 0.008 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.047 0.031 -10000 0 -10000 0 0
MBD3L2 0.034 0.004 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.044 0.041 -10000 0 -0.31 1 1
CREBBP 0.033 0.007 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.023 0.082 -10000 0 -0.38 3 3
HDAC1 0.033 0.007 -10000 0 -10000 0 0
HDAC3 0.031 0.009 -10000 0 -10000 0 0
HDAC2 0.033 0.007 -10000 0 -10000 0 0
YY1 0.018 0.009 -10000 0 -10000 0 0
HDAC8 0.034 0.002 -10000 0 -10000 0 0
SMAD7 0.021 0.039 -10000 0 -0.51 1 1
NCOR2 0.034 0.005 -10000 0 -10000 0 0
MXD1 0.004 0.12 -10000 0 -0.51 12 12
STAT3 0.026 0.01 -10000 0 -10000 0 0
NFKB1 0.033 0.006 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.033 0.024 -10000 0 -0.32 1 1
YY1/LSF/HDAC1 0.032 0.062 -10000 0 -0.26 1 1
YY1/SAP30/HDAC1 0.033 0.061 -10000 0 -0.24 1 1
EP300 0.032 0.009 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.026 0.01 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.028 0.012 -10000 0 -10000 0 0
histone deacetylation 0.011 0.08 -10000 0 -0.51 2 2
STAT3 (dimer non-phopshorylated)/HDAC3 0.038 0.032 -10000 0 -10000 0 0
nuclear export -0.066 0.015 -10000 0 -10000 0 0
PRKACA 0.034 0.005 -10000 0 -10000 0 0
GATAD2B 0.034 0.005 -10000 0 -10000 0 0
GATAD2A 0.034 0.004 -10000 0 -10000 0 0
GATA2/HDAC3 0.047 0.031 -10000 0 -10000 0 0
GATA1/HDAC1 0.047 0.022 -10000 0 -0.22 1 1
GATA1/HDAC3 0.047 0.034 -10000 0 -10000 0 0
CHD4 0.033 0.008 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.048 0.013 -10000 0 -10000 0 0
SIN3/HDAC complex/Mad/Max 0.029 0.073 -10000 0 -0.33 2 2
NuRD Complex -0.008 0.11 -10000 0 -0.42 3 3
positive regulation of chromatin silencing 0.075 0.037 -10000 0 -10000 0 0
SIN3B 0.034 0.005 -10000 0 -10000 0 0
MTA2 0.033 0.006 -10000 0 -10000 0 0
SIN3A 0.032 0.009 -10000 0 -10000 0 0
XPO1 0.034 0 -10000 0 -10000 0 0
SUMO1/HDAC1 0.043 0.042 -10000 0 -10000 0 0
HDAC complex 0.08 0.027 -10000 0 -10000 0 0
GATA1/Fog1 0.048 0.021 -10000 0 -0.22 1 1
FKBP25/HDAC1/HDAC2 0.057 0.027 -10000 0 -10000 0 0
TNF 0.034 0.005 -10000 0 -10000 0 0
negative regulation of cell growth 0.027 0.077 -10000 0 -0.33 2 2
NuRD/MBD2/PRMT5 Complex 0.018 0.069 -10000 0 -0.52 2 2
Ran/GTP/Exportin 1 0.045 0.044 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.025 0.052 -10000 0 -0.31 1 1
SIN3/HDAC complex/NCoR1 0.009 0.061 -10000 0 -0.35 2 2
TFCP2 0.034 0.004 -10000 0 -10000 0 0
NR2C1 0.028 0.048 -10000 0 -0.32 4 4
MBD3 0.033 0.007 -10000 0 -10000 0 0
MBD2 0.023 0.016 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

Figure S125.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S125.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.049 0.011 -10000 0 -10000 0 0
FBXW11 0.034 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.034 0.018 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.065 0.057 0.26 1 -10000 0 1
NFKBIA 0.053 0.053 -10000 0 -10000 0 0
MAPK14 0.034 0.005 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.034 0.018 -10000 0 -10000 0 0
ARRB2 0.016 0.008 -10000 0 -10000 0 0
REL 0.034 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.033 0.019 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.033 0.019 -10000 0 -10000 0 0
PIK3CA 0.034 0.004 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.024 0.01 -10000 0 -10000 0 0
PIK3R1 0.034 0.005 -10000 0 -10000 0 0
NFKB1 0.017 0.016 0.23 1 -10000 0 1
RELA 0.034 0.005 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.046 0.044 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.056 0.059 0.23 1 -10000 0 1
SRC 0.019 0.017 -10000 0 -10000 0 0
PI3K 0.049 0.01 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.046 0.044 -10000 0 -10000 0 0
IKBKB 0.029 0.012 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.034 0.004 -10000 0 -10000 0 0
SYK 0.032 0.024 -10000 0 -0.32 1 1
I kappa B alpha/PIK3R1 0.069 0.056 0.24 2 -10000 0 2
cell death 0.054 0.057 0.22 1 -10000 0 1
NF kappa B1 p105/c-Rel 0.034 0.018 -10000 0 -10000 0 0
LCK 0.029 0.044 -10000 0 -0.41 2 2
BCL3 0.034 0.005 -10000 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

Figure S126.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S126.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.033 0.007 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.004 0.019 -9999 0 -10000 0 0
MDM2/SUMO1 0.044 0.042 -9999 0 -10000 0 0
HDAC4 0.034 0.004 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0.004 0.019 -9999 0 -10000 0 0
SUMO1 0.034 0.002 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.015 0.013 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.014 0.012 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.032 0.024 -9999 0 -0.32 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.033 0.024 -9999 0 -0.32 1 1
SUMO1/HDAC4 0.044 0.042 -9999 0 -10000 0 0
SUMO1/HDAC1 0.043 0.042 -9999 0 -10000 0 0
RANGAP1 0.027 0.042 -9999 0 -0.32 3 3
MDM2/SUMO1/SUMO1 0.06 0.041 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.017 0.013 -9999 0 -10000 0 0
Ran/GTP 0.029 0.039 -9999 0 -0.2 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.034 0.004 -9999 0 -10000 0 0
UBE2I 0.031 0.025 -9999 0 -0.32 1 1
Ran/GTP/Exportin 1 0.027 0.038 -9999 0 -10000 0 0
NPC 0.02 0.012 -9999 0 -0.15 1 1
PIAS2 0.024 0.016 -9999 0 -10000 0 0
PIAS1 0.032 0.008 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Rapid glucocorticoid signaling

Figure S127.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S127.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.045 0.027 -9999 0 -10000 0 0
MAPK9 0.01 0.001 -9999 0 -10000 0 0
adrenocorticotropin secretion 0.008 0.016 -9999 0 -0.22 1 1
GNB1/GNG2 0.039 0.017 -9999 0 -10000 0 0
GNB1 0.032 0.008 -9999 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
MAPK14 0.01 0.001 -9999 0 -10000 0 0
Gs family/GTP 0.017 0.009 -9999 0 -10000 0 0
EntrezGene:2778 0 0 -9999 0 -10000 0 0
vasopressin secretion 0 0 -9999 0 -10000 0 0
G-protein coupled receptor activity 0 0 -9999 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
glutamate secretion 0 0 -9999 0 -10000 0 0
GNAL 0.027 0.014 -9999 0 -10000 0 0
GNG2 0.031 0.01 -9999 0 -10000 0 0
CRH 0.028 0.027 -9999 0 -0.32 1 1
mol:cortisol 0 0 -9999 0 -10000 0 0
MAPK8 0.01 0.002 -9999 0 -10000 0 0
MAPK11 0.009 0.009 -9999 0 -10000 0 0
E-cadherin signaling in keratinocytes

Figure S128.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S128.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.02 0.04 0.22 1 -10000 0 1
adherens junction organization 0.042 0.059 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.025 0.055 -10000 0 -10000 0 0
FMN1 0.041 0.053 -10000 0 -10000 0 0
mol:IP3 0.013 0.028 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.046 0.056 -10000 0 -10000 0 0
CTNNB1 0.026 0.053 -10000 0 -0.32 5 5
AKT1 0.06 0.061 0.26 1 -10000 0 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.067 0.1 -10000 0 -0.4 5 5
CTNND1 0.037 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.043 0.055 -10000 0 -10000 0 0
VASP 0.043 0.056 -10000 0 -10000 0 0
ZYX 0.04 0.056 -10000 0 -10000 0 0
JUB 0.041 0.053 -10000 0 -10000 0 0
EGFR(dimer) 0.049 0.072 -10000 0 -0.29 1 1
E-cadherin/beta catenin-gamma catenin 0.047 0.067 -10000 0 -0.3 5 5
mol:PI-3-4-5-P3 0.1 0.072 0.26 1 -10000 0 1
PIK3CA 0.038 0.006 -10000 0 -10000 0 0
PI3K 0.1 0.074 0.26 1 -10000 0 1
FYN 0.016 0.056 0.22 1 -0.31 1 2
mol:Ca2+ 0.012 0.028 -10000 0 -10000 0 0
JUP 0.034 0.007 -10000 0 -10000 0 0
PIK3R1 0.038 0.007 -10000 0 -10000 0 0
mol:DAG 0.013 0.028 -10000 0 -10000 0 0
CDH1 0.022 0.082 -10000 0 -0.5 5 5
RhoA/GDP 0.027 0.057 -10000 0 -10000 0 0
establishment of polarity of embryonic epithelium 0.043 0.055 -10000 0 -10000 0 0
SRC 0.019 0.017 -10000 0 -10000 0 0
RAC1 0.031 0.011 -10000 0 -10000 0 0
RHOA 0.034 0.005 -10000 0 -10000 0 0
EGFR 0.021 0.073 -10000 0 -0.51 4 4
CASR 0.015 0.046 0.22 1 -0.36 1 2
RhoA/GTP 0.029 0.043 -10000 0 -10000 0 0
AKT2 0.065 0.06 -10000 0 -10000 0 0
actin cable formation 0.04 0.054 -10000 0 -10000 0 0
apoptosis -0.054 0.058 -10000 0 -0.24 1 1
CTNNA1 0.037 0.006 -10000 0 -10000 0 0
mol:GDP 0.015 0.047 -10000 0 -10000 0 0
PIP5K1A 0.043 0.056 -10000 0 -10000 0 0
PLCG1 0.013 0.029 -10000 0 -10000 0 0
Rac1/GTP 0.057 0.071 -10000 0 -10000 0 0
homophilic cell adhesion 0.003 0.004 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

Figure S129.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S129.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.034 0.005 -9999 0 -9999 0 0
PI3K Class IB/PDE3B 0.034 0.005 -9999 0 -9999 0 0
PDE3B 0.034 0.005 -9999 0 -9999 0 0
p38 MAPK signaling pathway

Figure S130.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S130.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.024 0.022 -10000 0 -10000 0 0
TRAF2/ASK1 0.041 0.025 -10000 0 -0.18 2 2
ATM 0.033 0.007 -10000 0 -10000 0 0
MAP2K3 0.018 0.09 0.37 2 -0.45 2 4
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.017 0.092 0.36 2 -0.43 3 5
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.026 0.053 -10000 0 -0.32 5 5
TXN 0.01 0.001 -10000 0 -10000 0 0
CALM1 0.03 0.011 -10000 0 -10000 0 0
GADD45A 0.03 0.034 -10000 0 -0.32 2 2
GADD45B 0.033 0.006 -10000 0 -10000 0 0
MAP3K1 0.034 0.005 -10000 0 -10000 0 0
MAP3K6 0.031 0.01 -10000 0 -10000 0 0
MAP3K7 0.033 0.007 -10000 0 -10000 0 0
MAP3K4 0.033 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.042 0.03 -10000 0 -0.22 2 2
TAK1/TAB family 0 0.017 -10000 0 -10000 0 0
RAC1/OSM/MEKK3 0.056 0.024 -10000 0 -10000 0 0
TRAF2 0.033 0.006 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.029 0.073 -10000 0 -0.42 1 1
TRAF6 0.01 0.001 -10000 0 -10000 0 0
RAC1 0.031 0.011 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.029 0.026 -10000 0 -0.32 1 1
CCM2 0.031 0.01 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.036 0.024 -10000 0 -0.18 1 1
MAPK11 0.03 0.026 -10000 0 -0.32 1 1
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.049 0.037 -10000 0 -10000 0 0
OSM/MEKK3 0.044 0.018 -10000 0 -10000 0 0
TAOK1 0.017 0.024 -10000 0 -0.32 1 1
TAOK2 0.019 0.005 -10000 0 -10000 0 0
TAOK3 0.019 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.034 0.005 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.03 0.034 -10000 0 -0.32 2 2
MAP3K10 0.031 0.025 -10000 0 -0.32 1 1
MAP3K3 0.032 0.008 -10000 0 -10000 0 0
TRX/ASK1 0.028 0.024 -10000 0 -0.17 2 2
GADD45/MTK1/MTK1 0.066 0.047 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

Figure S131.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S131.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.014 -9999 0 -10000 0 0
FBXW11 0.034 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.034 0.004 -9999 0 -10000 0 0
CHUK 0.033 0.008 -9999 0 -10000 0 0
NF kappa B2 p100/RelB 0.091 0.035 -9999 0 -10000 0 0
NFKB1 0.033 0.006 -9999 0 -10000 0 0
MAP3K14 0.033 0.007 -9999 0 -10000 0 0
NF kappa B1 p50/RelB 0.049 0.01 -9999 0 -10000 0 0
RELB 0.034 0.005 -9999 0 -10000 0 0
NFKB2 0.031 0.025 -9999 0 -0.32 1 1
NF kappa B2 p52/RelB 0.042 0.019 -9999 0 -0.18 1 1
regulation of B cell activation 0.042 0.019 -9999 0 -0.18 1 1
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 215 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.AY.4071 TCGA.AY.4070 TCGA.AG.A032 TCGA.AG.A02X
109_MAP3K5 0.16 0.13 0.027 -0.12
47_PPARGC1A 0.034 -0.51 0.034 -0.51
105_BMP4 0.034 0.034 0.034 0.034
105_BMP6 0.034 0.034 -0.51 -0.51
105_BMP7 0 0 0 0.034
105_BMP2 0 0.034 0.034 0.034
131_RELN/VLDLR -0.43 0 -0.16 -0.16
30_TGFB1/TGF beta receptor Type II 0.034 0.036 0.034 0.033
84_STAT5B 0.087 0.025 0.076 0.062
84_STAT5A 0.087 0.025 0.076 0.062
Methods & Data
Input

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

  • mRNA Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/COADREAD-TP/3348409/GDAC_MergeDataFiles_3202301/COADREAD-TP.transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/COADREAD-TP/3471834/all_data_by_genes.txt

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.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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)
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