PARADIGM pathway analysis of mRNASeq expression and copy number data
Colon Adenocarcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1NS0T35
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1NS0T35
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 39 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 135
Reelin signaling pathway 115
Signaling events regulated by Ret tyrosine kinase 73
Lissencephaly gene (LIS1) in neuronal migration and development 67
Ephrin A reverse signaling 66
IL4-mediated signaling events 62
BCR signaling pathway 60
Fc-epsilon receptor I signaling in mast cells 57
Glypican 1 network 55
Signaling events mediated by Stem cell factor receptor (c-Kit) 53
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 457 . 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 ( 457 ).

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 0.2954 135 1083 8 -0.12 0.096 1000 -1000 -0.007 -1000
Reelin signaling pathway 0.2516 115 6475 56 -0.33 0.074 1000 -1000 -0.054 -1000
Signaling events regulated by Ret tyrosine kinase 0.1597 73 5989 82 -0.13 0.033 1000 -1000 -0.059 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1466 67 3629 54 -0.31 0.036 1000 -1000 -0.056 -1000
Ephrin A reverse signaling 0.1444 66 463 7 -0.052 0 1000 -1000 -0.015 -1000
IL4-mediated signaling events 0.1357 62 5651 91 -0.82 0.58 1000 -1000 -0.17 -1000
BCR signaling pathway 0.1313 60 5964 99 -0.21 0.029 1000 -1000 -0.061 -1000
Fc-epsilon receptor I signaling in mast cells 0.1247 57 5582 97 -0.16 0.05 1000 -1000 -0.065 -1000
Glypican 1 network 0.1204 55 2676 48 -0.16 0.052 1000 -1000 -0.036 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.1160 53 4161 78 -0.19 0.081 1000 -1000 -0.049 -1000
FOXA2 and FOXA3 transcription factor networks 0.1094 50 2345 46 -0.62 0.031 1000 -1000 -0.11 -1000
HIF-1-alpha transcription factor network 0.1007 46 3567 76 -0.56 0.036 1000 -1000 -0.15 -1000
p75(NTR)-mediated signaling 0.1007 46 5804 125 -0.44 0.069 1000 -1000 -0.076 -1000
Visual signal transduction: Rods 0.0897 41 2151 52 -0.22 0.042 1000 -1000 -0.045 -1000
BMP receptor signaling 0.0832 38 3121 81 -0.2 0.051 1000 -1000 -0.052 -1000
Syndecan-1-mediated signaling events 0.0766 35 1197 34 -0.41 0.029 1000 -1000 -0.049 -1000
Signaling events mediated by the Hedgehog family 0.0766 35 1855 52 -0.063 0.063 1000 -1000 -0.042 -1000
JNK signaling in the CD4+ TCR pathway 0.0744 34 580 17 -0.13 0.032 1000 -1000 -0.036 -1000
Syndecan-2-mediated signaling events 0.0744 34 2364 69 -0.24 0.045 1000 -1000 -0.046 -1000
Visual signal transduction: Cones 0.0722 33 1267 38 -0.11 0.037 1000 -1000 -0.019 -1000
Endothelins 0.0722 33 3250 96 -0.25 0.056 1000 -1000 -0.067 -1000
LPA receptor mediated events 0.0700 32 3308 102 -0.16 0.035 1000 -1000 -0.062 -1000
IGF1 pathway 0.0700 32 1838 57 -0.082 0.053 1000 -1000 -0.058 -1000
TCR signaling in naïve CD8+ T cells 0.0678 31 2970 93 -0.045 0.039 1000 -1000 -0.055 -1000
Effects of Botulinum toxin 0.0635 29 764 26 -0.069 0.046 1000 -1000 -0.009 -1000
Plasma membrane estrogen receptor signaling 0.0635 29 2497 86 -0.17 0.072 1000 -1000 -0.056 -1000
amb2 Integrin signaling 0.0613 28 2307 82 -0.083 0.035 1000 -1000 -0.047 -1000
Ras signaling in the CD4+ TCR pathway 0.0591 27 472 17 -0.068 0.048 1000 -1000 -0.033 -1000
Osteopontin-mediated events 0.0569 26 997 38 -0.19 0.039 1000 -1000 -0.047 -1000
Canonical Wnt signaling pathway 0.0569 26 1356 51 -0.26 0.13 1000 -1000 -0.053 -1000
Presenilin action in Notch and Wnt signaling 0.0547 25 1546 61 -0.26 0.13 1000 -1000 -0.047 -1000
IL1-mediated signaling events 0.0525 24 1502 62 -0.14 0.062 1000 -1000 -0.043 -1000
Wnt signaling 0.0525 24 170 7 -0.065 0.023 1000 -1000 -0.019 -1000
IL23-mediated signaling events 0.0525 24 1475 60 -0.28 0.029 1000 -1000 -0.13 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0525 24 2138 88 -0.13 0.061 1000 -1000 -0.069 -1000
Signaling events mediated by PRL 0.0525 24 842 34 -0.056 0.084 1000 -1000 -0.042 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0503 23 859 37 -0.18 0.057 1000 -1000 -0.037 -1000
TCGA08_p53 0.0503 23 166 7 -0.059 0.027 1000 -1000 -0.012 -1000
Calcium signaling in the CD4+ TCR pathway 0.0503 23 715 31 -0.27 0.027 1000 -1000 -0.046 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0481 22 2645 120 -0.11 0.093 1000 -1000 -0.057 -1000
LPA4-mediated signaling events 0.0460 21 261 12 -0.1 0.007 1000 -1000 -0.025 -1000
IL12-mediated signaling events 0.0460 21 1869 87 -0.13 0.048 1000 -1000 -0.095 -1000
EGFR-dependent Endothelin signaling events 0.0460 21 448 21 -0.063 0.039 1000 -1000 -0.045 -1000
Syndecan-3-mediated signaling events 0.0438 20 702 35 -0.24 0.069 1000 -1000 -0.026 -1000
Thromboxane A2 receptor signaling 0.0416 19 2003 105 -0.18 0.07 1000 -1000 -0.05 -1000
Signaling mediated by p38-alpha and p38-beta 0.0416 19 877 44 -0.036 0.028 1000 -1000 -0.035 -1000
EPHB forward signaling 0.0416 19 1628 85 -0.085 0.09 1000 -1000 -0.068 -1000
Nongenotropic Androgen signaling 0.0416 19 1012 52 -0.087 0.064 1000 -1000 -0.04 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0416 19 1336 68 -0.28 0.044 1000 -1000 -0.1 -1000
Arf6 signaling events 0.0394 18 1164 62 -0.13 0.061 1000 -1000 -0.039 -1000
HIF-2-alpha transcription factor network 0.0394 18 806 43 -0.36 0.18 1000 -1000 -0.083 -1000
Syndecan-4-mediated signaling events 0.0394 18 1270 67 -0.25 0.038 1000 -1000 -0.044 -1000
PDGFR-beta signaling pathway 0.0394 18 1746 97 -0.15 0.092 1000 -1000 -0.062 -1000
a4b1 and a4b7 Integrin signaling 0.0372 17 86 5 0.01 0.028 1000 -1000 0.001 -1000
Nectin adhesion pathway 0.0372 17 1106 63 -0.38 0.076 1000 -1000 -0.041 -1000
Glucocorticoid receptor regulatory network 0.0372 17 1965 114 -0.31 0.19 1000 -1000 -0.063 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0372 17 931 52 -0.21 0.059 1000 -1000 -0.054 -1000
Integrins in angiogenesis 0.0350 16 1416 84 -0.19 0.065 1000 -1000 -0.049 -1000
S1P4 pathway 0.0350 16 420 25 -0.087 0.041 1000 -1000 -0.035 -1000
S1P5 pathway 0.0328 15 265 17 -0.087 0.035 1000 -1000 -0.021 -1000
Regulation of Androgen receptor activity 0.0328 15 1107 70 -0.22 0.058 1000 -1000 -0.055 -1000
Caspase cascade in apoptosis 0.0306 14 1108 74 -0.088 0.063 1000 -1000 -0.042 -1000
Signaling events mediated by PTP1B 0.0306 14 1087 76 -0.2 0.047 1000 -1000 -0.046 -1000
Signaling events mediated by HDAC Class III 0.0306 14 561 40 -0.15 0.052 1000 -1000 -0.017 -1000
FAS signaling pathway (CD95) 0.0306 14 672 47 -0.035 0.044 1000 -1000 -0.033 -1000
Regulation of p38-alpha and p38-beta 0.0306 14 776 54 -0.1 0.052 1000 -1000 -0.055 -1000
Glypican 2 network 0.0306 14 57 4 0.013 0.025 1000 -1000 0.001 -1000
IL6-mediated signaling events 0.0306 14 1108 75 -0.072 0.07 1000 -1000 -0.069 -1000
Noncanonical Wnt signaling pathway 0.0284 13 351 26 -0.065 0.027 1000 -1000 -0.05 -1000
Ceramide signaling pathway 0.0284 13 1057 76 -0.079 0.069 1000 -1000 -0.044 -1000
S1P3 pathway 0.0284 13 561 42 -0.086 0.045 1000 -1000 -0.042 -1000
Regulation of nuclear SMAD2/3 signaling 0.0263 12 1703 136 -0.49 0.072 1000 -1000 -0.048 -1000
Ephrin B reverse signaling 0.0263 12 617 48 -0.084 0.032 1000 -1000 -0.043 -1000
Aurora B signaling 0.0263 12 839 67 -0.39 0.09 1000 -1000 -0.036 -1000
ErbB2/ErbB3 signaling events 0.0241 11 759 65 -0.049 0.039 1000 -1000 -0.05 -1000
ErbB4 signaling events 0.0241 11 770 69 -0.16 0.076 1000 -1000 -0.052 -1000
PLK1 signaling events 0.0241 11 941 85 -0.01 0.06 1000 -1000 -0.034 -1000
Class I PI3K signaling events mediated by Akt 0.0241 11 802 68 -0.05 0.06 1000 -1000 -0.036 -1000
S1P1 pathway 0.0241 11 420 36 -0.087 0.042 1000 -1000 -0.049 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0241 11 387 33 -0.07 0.065 1000 -1000 -0.036 -1000
Coregulation of Androgen receptor activity 0.0219 10 789 76 -0.19 0.061 1000 -1000 -0.025 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0219 10 286 28 -0.087 0.043 1000 -1000 -0.027 -1000
Cellular roles of Anthrax toxin 0.0219 10 427 39 -0.04 0.032 1000 -1000 -0.02 -1000
FoxO family signaling 0.0219 10 673 64 -0.12 0.051 1000 -1000 -0.074 -1000
Class I PI3K signaling events 0.0219 10 786 73 -0.1 0.044 1000 -1000 -0.053 -1000
VEGFR1 specific signals 0.0219 10 580 56 -0.015 0.091 1000 -1000 -0.056 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0197 9 747 83 -0.12 0.069 1000 -1000 -0.04 -1000
Signaling mediated by p38-gamma and p38-delta 0.0197 9 143 15 -0.054 0.027 1000 -1000 -0.039 -1000
Retinoic acid receptors-mediated signaling 0.0197 9 527 58 -0.14 0.049 1000 -1000 -0.044 -1000
Insulin-mediated glucose transport 0.0175 8 264 32 -0.14 0.044 1000 -1000 -0.031 -1000
IL27-mediated signaling events 0.0175 8 415 51 -0.066 0.038 1000 -1000 -0.043 -1000
Arf6 trafficking events 0.0175 8 608 71 -0.046 0.048 1000 -1000 -0.03 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0153 7 265 34 -0.028 0.065 1000 -1000 -0.034 -1000
EPO signaling pathway 0.0153 7 405 55 -0.016 0.064 1000 -1000 -0.045 -1000
PDGFR-alpha signaling pathway 0.0153 7 338 44 -0.013 0.062 1000 -1000 -0.045 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0131 6 542 85 -0.039 0.066 1000 -1000 -0.048 -1000
Arf6 downstream pathway 0.0131 6 295 43 -0.028 0.042 1000 -1000 -0.032 -1000
mTOR signaling pathway 0.0131 6 328 53 -0.076 0.038 1000 -1000 -0.036 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0131 6 299 45 -0.017 0.072 1000 -1000 -0.057 -1000
TCGA08_rtk_signaling 0.0131 6 161 26 -0.036 0.061 1000 -1000 -0.021 -1000
Regulation of Telomerase 0.0131 6 706 102 -0.19 0.063 1000 -1000 -0.081 -1000
FOXM1 transcription factor network 0.0131 6 339 51 -0.097 0.11 1000 -1000 -0.15 -1000
Signaling events mediated by HDAC Class II 0.0109 5 385 75 -0.031 0.069 1000 -1000 -0.034 -1000
Hedgehog signaling events mediated by Gli proteins 0.0109 5 374 65 -0.087 0.05 1000 -1000 -0.05 -1000
IFN-gamma pathway 0.0109 5 354 68 -0.035 0.042 1000 -1000 -0.063 -1000
ceramide signaling pathway 0.0109 5 281 49 0 0.044 1000 -1000 -0.044 -1000
IL2 signaling events mediated by PI3K 0.0109 5 344 58 -0.015 0.047 1000 -1000 -0.043 -1000
E-cadherin signaling in the nascent adherens junction 0.0109 5 414 76 -0.012 0.089 1000 -1000 -0.06 -1000
Rapid glucocorticoid signaling 0.0109 5 118 20 -0.017 0.026 1000 -1000 -0.009 -1000
Aurora A signaling 0.0088 4 266 60 -0.083 0.075 1000 -1000 -0.023 -1000
Paxillin-dependent events mediated by a4b1 0.0088 4 175 36 -0.047 0.049 1000 -1000 -0.043 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0088 4 500 125 -0.01 0.096 1000 -1000 -0.058 -1000
Class IB PI3K non-lipid kinase events 0.0088 4 12 3 -0.023 0.023 1000 -1000 -0.009 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0066 3 283 74 -0.079 0.064 1000 -1000 -0.067 -1000
Insulin Pathway 0.0066 3 242 74 -0.03 0.084 1000 -1000 -0.054 -1000
p38 MAPK signaling pathway 0.0066 3 135 44 -0.012 0.059 1000 -1000 -0.036 -1000
PLK2 and PLK4 events 0.0044 2 8 3 0.01 0.026 1000 -1000 -0.015 -1000
TRAIL signaling pathway 0.0044 2 134 48 -0.008 0.059 1000 -1000 -0.042 -1000
IL2 signaling events mediated by STAT5 0.0044 2 60 22 0.005 0.042 1000 -1000 -0.046 -1000
Canonical NF-kappaB pathway 0.0022 1 72 39 0 0.06 1000 -1000 -0.041 -1000
Signaling events mediated by HDAC Class I 0.0022 1 178 104 -0.053 0.065 1000 -1000 -0.041 -1000
Atypical NF-kappaB pathway 0.0022 1 33 31 0 0.055 1000 -1000 -0.03 -1000
Arf1 pathway 0.0022 1 92 54 0 0.042 1000 -1000 -0.021 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 9 23 0.012 0.041 1000 -1000 -0.027 -1000
BARD1 signaling events 0.0000 0 26 57 -0.055 0.078 1000 -1000 -0.048 -1000
Circadian rhythm pathway 0.0000 0 18 22 -0.009 0.064 1000 -1000 -0.041 -1000
Aurora C signaling 0.0000 0 5 7 0 0.041 1000 -1000 -0.013 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 18 27 0 0.052 1000 -1000 -0.038 -1000
E-cadherin signaling in keratinocytes 0.0000 0 28 43 -0.047 0.086 1000 -1000 -0.04 -1000
E-cadherin signaling events 0.0000 0 2 5 0.026 0.053 1000 -1000 0.003 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.075 1000 -1000 -0.002 -1000
Total NA 2527 149224 7203 -16 7.9 131000 -131000 -6.1 -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 -0.12 0.19 -10000 0 -0.36 170 170
CDKN2C 0.034 0.026 -10000 0 -10000 0 0
CDKN2A -0.074 0.19 0.35 2 -0.44 96 98
CCND2 0.086 0.1 0.2 173 -0.35 1 174
RB1 -0.071 0.1 0.27 6 -0.2 141 147
CDK4 0.087 0.1 0.2 166 -0.25 2 168
CDK6 0.096 0.11 0.22 176 -0.38 1 177
G1/S progression 0.075 0.11 0.2 143 -0.27 6 149
Reelin signaling pathway

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
CDK5R1/CDK5 0.038 0.019 -10000 0 -0.3 1 1
VLDLR -0.008 0.12 -10000 0 -0.4 37 37
CRKL 0.026 0.006 -10000 0 -10000 0 0
LRPAP1 0.026 0.005 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
ITGA3 0.026 0.02 -10000 0 -0.4 1 1
RELN/VLDLR/Fyn -0.085 0.16 -10000 0 -0.27 189 189
MAPK8IP1/MKK7/MAP3K11/JNK1 0.074 0.037 -10000 0 -0.56 1 1
AKT1 -0.094 0.13 -10000 0 -0.35 52 52
MAP2K7 0.026 0.02 -10000 0 -0.4 1 1
RAPGEF1 0.026 0.02 -10000 0 -0.4 1 1
DAB1 -0.026 0.14 -10000 0 -0.44 43 43
RELN/LRP8/DAB1 -0.26 0.17 -10000 0 -0.32 374 374
LRPAP1/LRP8 -0.21 0.15 0.26 1 -0.3 326 327
RELN/LRP8/DAB1/Fyn -0.25 0.16 -10000 0 -0.31 368 368
DAB1/alpha3/beta1 Integrin -0.24 0.17 -10000 0 -0.42 170 170
long-term memory -0.33 0.2 -10000 0 -0.47 265 265
DAB1/LIS1 -0.24 0.17 -10000 0 -0.42 175 175
DAB1/CRLK/C3G -0.24 0.17 -10000 0 -0.42 173 173
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
DAB1/NCK2 -0.25 0.18 -10000 0 -0.43 175 175
ARHGEF2 0.027 0.004 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.093 0.18 -10000 0 -0.4 114 114
CDK5R1 0.026 0.022 -10000 0 -0.43 1 1
RELN -0.15 0.21 -10000 0 -0.4 186 186
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.26 0.17 0.25 1 -0.33 362 363
GRIN2A/RELN/LRP8/DAB1/Fyn -0.29 0.19 -10000 0 -0.37 343 343
MAPK8 0.027 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.1 0.16 -10000 0 -0.26 215 215
ITGB1 0.027 0.002 -10000 0 -10000 0 0
MAP1B -0.25 0.18 -10000 0 -0.4 211 211
RELN/LRP8 -0.26 0.17 0.25 1 -0.33 361 362
GRIN2B/RELN/LRP8/DAB1/Fyn -0.3 0.19 -10000 0 -0.37 351 351
PI3K 0.039 0.008 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.039 0.016 -10000 0 -0.28 1 1
RAP1A -0.24 0.15 0.3 1 -0.4 171 172
PAFAH1B1 0.023 0.01 -10000 0 -10000 0 0
MAPK8IP1 0.026 0.02 -10000 0 -0.4 1 1
CRLK/C3G 0.037 0.018 -10000 0 -0.28 1 1
GRIN2B -0.089 0.2 -10000 0 -0.43 114 114
NCK2 0.027 0.001 -10000 0 -10000 0 0
neuron differentiation -0.12 0.12 0.23 1 -0.31 60 61
neuron adhesion -0.23 0.15 0.29 1 -0.39 164 165
LRP8 -0.31 0.2 0.36 1 -0.43 328 329
GSK3B -0.091 0.13 -10000 0 -0.34 51 51
RELN/VLDLR/DAB1/Fyn -0.088 0.16 -10000 0 -0.24 207 207
MAP3K11 0.026 0.02 -10000 0 -0.4 1 1
RELN/VLDLR/DAB1/P13K -0.1 0.14 -10000 0 -0.25 193 193
CDK5 0.026 0.005 -10000 0 -10000 0 0
MAPT -0.056 0.17 0.85 5 -0.35 91 96
neuron migration -0.22 0.17 0.23 3 -0.41 165 168
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.13 0.12 -10000 0 -0.31 60 60
RELN/VLDLR -0.25 0.18 0.26 1 -0.32 355 356
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.02 0.079 -10000 0 -0.4 12 12
Crk/p130 Cas/Paxillin -0.094 0.12 -10000 0 -0.32 44 44
JUN -0.087 0.13 -10000 0 -0.35 51 51
HRAS 0.026 0.02 -10000 0 -0.4 1 1
RET51/GFRalpha1/GDNF/GRB10 -0.072 0.16 -10000 0 -0.26 180 180
RAP1A 0.026 0.005 -10000 0 -10000 0 0
FRS2 0.027 0.003 -10000 0 -10000 0 0
RAP1A/GDP 0.019 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.074 0.17 -10000 0 -0.26 190 190
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.027 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.023 0.01 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.047 0.13 -10000 0 -0.21 161 161
RHOA 0.027 0.004 -10000 0 -10000 0 0
RAP1A/GTP -0.066 0.15 -10000 0 -0.35 47 47
GRB7 0.033 0.044 0.36 8 -10000 0 8
RET51/GFRalpha1/GDNF -0.074 0.17 -10000 0 -0.26 190 190
MAPKKK cascade -0.085 0.15 -10000 0 -0.38 45 45
BCAR1 0.026 0.02 -10000 0 -0.4 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.047 0.13 -10000 0 -0.21 161 161
lamellipodium assembly -0.081 0.12 -10000 0 -0.25 127 127
RET51/GFRalpha1/GDNF/SHC -0.074 0.17 -10000 0 -0.26 188 188
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.046 0.12 -10000 0 -0.21 158 158
RET9/GFRalpha1/GDNF/Shank3 -0.048 0.13 -10000 0 -0.21 161 161
MAPK3 -0.099 0.12 -10000 0 -0.36 42 42
DOK1 0.027 0.002 -10000 0 -10000 0 0
DOK6 0.013 0.053 -10000 0 -0.4 7 7
PXN 0.027 0.002 -10000 0 -10000 0 0
neurite development -0.074 0.11 -10000 0 -0.36 26 26
DOK5 0.011 0.052 0.36 1 -0.4 6 7
GFRA1 -0.13 0.2 -10000 0 -0.4 165 165
MAPK8 -0.091 0.14 -10000 0 -0.36 53 53
HRAS/GTP -0.085 0.18 -10000 0 -0.28 177 177
tube development -0.044 0.12 0.21 1 -0.2 146 147
MAPK1 -0.098 0.12 -10000 0 -0.36 41 41
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.058 0.11 -10000 0 -0.2 157 157
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
SRC 0.017 0.013 -10000 0 -10000 0 0
PDLIM7 0.027 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.054 0.14 -10000 0 -0.28 72 72
SHC1 0.027 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.074 0.17 -10000 0 -0.26 191 191
RET51/GFRalpha1/GDNF/Dok5 -0.058 0.14 0.26 1 -0.26 134 135
PRKCA 0.026 0.006 -10000 0 -10000 0 0
HRAS/GDP 0.019 0.014 -10000 0 -0.28 1 1
CREB1 -0.09 0.15 -10000 0 -0.28 159 159
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.058 0.11 -10000 0 -0.21 155 155
RET51/GFRalpha1/GDNF/Grb7 -0.069 0.17 0.25 4 -0.26 186 190
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.041 0.16 -10000 0 -0.4 72 72
DOK4 0.026 0.02 -10000 0 -0.4 1 1
JNK cascade -0.085 0.13 -10000 0 -0.34 51 51
RET9/GFRalpha1/GDNF/FRS2 -0.047 0.13 -10000 0 -0.21 160 160
SHANK3 0.025 0.021 -10000 0 -0.4 1 1
RASA1 0.026 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.002 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.057 0.11 -10000 0 -0.21 155 155
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.09 0.14 -10000 0 -0.24 191 191
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.091 0.15 -10000 0 -0.25 188 188
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.097 0.16 -10000 0 -0.27 186 186
PI3K -0.12 0.18 -10000 0 -0.36 135 135
SOS1 0.027 0.002 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.035 0.12 -10000 0 -0.2 146 146
GRB10 0.025 0.008 -10000 0 -10000 0 0
activation of MAPKK activity -0.075 0.13 -10000 0 -0.32 46 46
RET51/GFRalpha1/GDNF/FRS2 -0.074 0.17 -10000 0 -0.26 191 191
GAB1 0.027 0.004 -10000 0 -10000 0 0
IRS1 0.027 0.002 -10000 0 -10000 0 0
IRS2 0.021 0.012 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.098 0.16 -10000 0 -0.27 187 187
RET51/GFRalpha1/GDNF/PKC alpha -0.072 0.16 -10000 0 -0.25 189 189
GRB2 0.027 0.004 -10000 0 -10000 0 0
PRKACA 0.027 0.003 -10000 0 -10000 0 0
GDNF 0.014 0.02 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.074 0.17 -10000 0 -0.26 191 191
Rac1/GTP -0.092 0.14 -10000 0 -0.29 127 127
RET9/GFRalpha1/GDNF -0.063 0.13 -10000 0 -0.24 161 161
GFRalpha1/GDNF -0.078 0.15 -10000 0 -0.28 161 161
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.025 0.007 -10000 0 -10000 0 0
VLDLR -0.008 0.12 -10000 0 -0.4 37 37
LRPAP1 0.026 0.005 -10000 0 -10000 0 0
NUDC 0.025 0.007 -10000 0 -10000 0 0
RELN/LRP8 -0.26 0.17 0.25 1 -0.33 361 362
CaM/Ca2+ 0.019 0.005 -10000 0 -10000 0 0
KATNA1 0.027 0.004 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.24 0.16 0.18 8 -0.32 310 318
IQGAP1/CaM 0.036 0.012 -10000 0 -10000 0 0
DAB1 -0.026 0.14 -10000 0 -0.44 43 43
IQGAP1 0.026 0.006 -10000 0 -10000 0 0
PLA2G7 0.022 0.044 -10000 0 -0.4 5 5
CALM1 0.025 0.007 -10000 0 -10000 0 0
DYNLT1 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 -0.21 0.15 0.26 1 -0.3 326 327
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.026 0.02 -10000 0 -0.4 1 1
CDK5R1 0.026 0.022 -10000 0 -0.43 1 1
LIS1/Poliovirus Protein 3A 0.007 0.005 -10000 0 -10000 0 0
CDK5R2 -0.023 0.13 -10000 0 -0.4 45 45
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.11 0.17 -10000 0 -0.28 215 215
YWHAE 0.023 0.01 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.21 0.15 0.32 3 -0.36 161 164
MAP1B 0 0.037 -10000 0 -0.27 8 8
RAC1 0.01 0.007 -10000 0 -10000 0 0
p35/CDK5 -0.21 0.14 0.18 3 -0.38 140 143
RELN -0.15 0.21 -10000 0 -0.4 186 186
PAFAH/LIS1 0.02 0.027 -10000 0 -0.22 4 4
LIS1/CLIP170 0.021 0.018 -10000 0 -0.24 1 1
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.17 0.12 -10000 0 -0.31 140 140
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.09 0.16 -10000 0 -0.37 64 64
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.22 0.15 0.32 3 -0.38 169 172
LIS1/IQGAP1 0.022 0.014 -10000 0 -10000 0 0
RHOA 0.01 0.007 -10000 0 -10000 0 0
PAFAH1B1 0.01 0.006 -10000 0 -10000 0 0
PAFAH1B3 0.02 0.056 -10000 0 -0.43 7 7
PAFAH1B2 0.027 0.004 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.013 0.038 -10000 0 -0.27 1 1
NDEL1/Katanin 60/Dynein heavy chain -0.2 0.15 0.32 3 -0.36 161 164
LRP8 -0.31 0.2 0.36 1 -0.43 328 329
NDEL1/Katanin 60 -0.21 0.15 0.32 3 -0.37 162 165
P39/CDK5 -0.24 0.15 0.18 2 -0.4 165 167
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.021 0.014 -10000 0 -10000 0 0
CDK5 -0.23 0.14 0.18 4 -0.4 142 146
PPP2R5D 0.027 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.018 0.016 -10000 0 -0.2 1 1
CSNK2A1 0.022 0.011 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.085 0.15 -10000 0 -0.34 56 56
RELN/VLDLR -0.25 0.18 0.26 1 -0.32 355 356
CDC42 0.009 0.019 -10000 0 -0.37 1 1
Ephrin A reverse signaling

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
MAPKKK cascade -0.026 0.11 -10000 0 -0.24 92 92
EFNA5 -0.052 0.16 -10000 0 -0.4 82 82
FYN -0.042 0.093 0.18 1 -0.22 90 91
neuron projection morphogenesis -0.026 0.11 -10000 0 -0.24 92 92
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.025 0.11 -10000 0 -0.24 92 92
EPHA5 -0.007 0.073 -10000 0 -0.4 14 14
IL4-mediated signaling events

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
BCL2L1 -0.46 0.49 -10000 0 -1.2 91 91
STAT6 (cleaved dimer) -0.58 0.52 -10000 0 -1.2 151 151
IGHG1 -0.17 0.16 -10000 0 -10000 0 0
IGHG3 -0.5 0.46 -10000 0 -1.1 117 117
AKT1 -0.28 0.29 -10000 0 -0.74 71 71
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.22 0.24 -10000 0 -0.69 41 41
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.28 0.29 -10000 0 -0.84 41 41
THY1 -0.53 0.48 -10000 0 -1.2 97 97
MYB 0.026 0.02 -10000 0 -0.4 1 1
HMGA1 0.028 0.016 0.36 1 -10000 0 1
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.39 0.36 -10000 0 -0.82 136 136
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.28 0.29 -10000 0 -0.89 36 36
SP1 0.027 0.02 -10000 0 -10000 0 0
INPP5D 0.026 0.02 -10000 0 -0.4 1 1
SOCS5 0.046 0.026 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.56 0.51 -10000 0 -1.2 138 138
SOCS1 -0.38 0.31 -10000 0 -0.77 101 101
SOCS3 -0.33 0.3 -10000 0 -0.76 87 87
FCER2 -0.82 0.65 -10000 0 -1.4 244 244
PARP14 0.009 0.03 -10000 0 -10000 0 0
CCL17 -0.53 0.48 -10000 0 -1.2 96 96
GRB2 0.027 0.004 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.22 0.21 -10000 0 -0.71 21 21
T cell proliferation -0.53 0.5 -10000 0 -1.2 111 111
IL4R/JAK1 -0.53 0.49 -10000 0 -1.2 113 113
EGR2 -0.6 0.51 -10000 0 -1.3 115 115
JAK2 -0.034 0.052 -10000 0 -0.43 3 3
JAK3 0.011 0.034 -10000 0 -0.43 1 1
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
JAK1 -0.007 0.025 -10000 0 -10000 0 0
COL1A2 -0.15 0.16 -10000 0 -0.7 1 1
CCL26 -0.54 0.48 -10000 0 -1.2 99 99
IL4R -0.56 0.51 -10000 0 -1.3 109 109
PTPN6 0.038 0.014 -10000 0 -10000 0 0
IL13RA2 -0.54 0.48 -10000 0 -1.2 100 100
IL13RA1 -0.032 0.041 -10000 0 -10000 0 0
IRF4 -0.53 0.67 -10000 0 -1.4 150 150
ARG1 -0.091 0.14 -10000 0 -0.58 6 6
CBL -0.37 0.34 -10000 0 -0.78 134 134
GTF3A 0.022 0.07 0.34 15 -0.42 1 16
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.038 0.061 -10000 0 -0.31 3 3
IRF4/BCL6 -0.46 0.62 -10000 0 -1.3 150 150
CD40LG -0.05 0.12 -10000 0 -0.41 35 35
MAPK14 -0.37 0.34 -10000 0 -0.8 125 125
mitosis -0.27 0.27 -10000 0 -0.7 70 70
STAT6 -0.59 0.57 -10000 0 -1.4 117 117
SPI1 0.023 0.049 -10000 0 -0.39 6 6
RPS6KB1 -0.26 0.26 -10000 0 -0.68 63 63
STAT6 (dimer) -0.59 0.57 -10000 0 -1.4 117 117
STAT6 (dimer)/PARP14 -0.6 0.54 -10000 0 -1.3 127 127
mast cell activation 0.014 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.31 0.29 -10000 0 -0.73 84 84
FRAP1 -0.28 0.29 -10000 0 -0.74 71 71
LTA -0.53 0.49 -10000 0 -1.2 95 95
FES 0.025 0.021 -10000 0 -0.4 1 1
T-helper 1 cell differentiation 0.58 0.55 1.3 117 -10000 0 117
CCL11 -0.56 0.55 -10000 0 -1.3 113 113
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.28 0.27 -10000 0 -0.7 65 65
IL2RG 0.011 0.038 -10000 0 -0.39 2 2
IL10 -0.55 0.52 -10000 0 -1.3 105 105
IRS1 0.027 0.002 -10000 0 -10000 0 0
IRS2 0.021 0.012 -10000 0 -10000 0 0
IL4 -0.14 0.19 -10000 0 -1.1 11 11
IL5 -0.53 0.48 -10000 0 -1.2 96 96
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.42 0.38 -10000 0 -0.93 93 93
COL1A1 -0.19 0.2 -10000 0 -0.58 34 34
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.54 0.5 -10000 0 -1.3 95 95
IL2R gamma/JAK3 0.013 0.047 -10000 0 -0.29 3 3
TFF3 -0.54 0.51 -10000 0 -1.3 101 101
ALOX15 -0.55 0.5 -10000 0 -1.3 106 106
MYBL1 0.022 0.031 -10000 0 -0.43 2 2
T-helper 2 cell differentiation -0.44 0.4 -10000 0 -0.97 108 108
SHC1 0.027 0.004 -10000 0 -10000 0 0
CEBPB 0.017 0.016 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.25 0.28 -10000 0 -0.88 32 32
mol:PI-3-4-5-P3 -0.28 0.29 -10000 0 -0.74 71 71
PI3K -0.3 0.31 -10000 0 -0.8 71 71
DOK2 0.015 0.049 -10000 0 -0.4 6 6
ETS1 0.036 0.028 -10000 0 -0.36 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.2 0.2 -10000 0 -0.63 25 25
ITGB3 -0.53 0.49 -10000 0 -1.3 95 95
PIGR -0.7 0.65 -10000 0 -1.4 169 169
IGHE 0.083 0.073 0.18 117 -10000 0 117
MAPKKK cascade -0.2 0.19 -10000 0 -0.62 25 25
BCL6 0.033 0.01 -10000 0 -10000 0 0
OPRM1 -0.53 0.48 -10000 0 -1.2 94 94
RETNLB -0.75 0.66 -10000 0 -1.4 192 192
SELP -0.59 0.58 -10000 0 -1.4 113 113
AICDA -0.51 0.46 -10000 0 -1.2 96 96
BCR signaling pathway

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
JUN -0.13 0.21 0.2 1 -0.48 96 97
IKBKB -0.039 0.11 0.2 4 -0.28 42 46
AKT1 -0.085 0.11 0.16 4 -0.26 94 98
IKBKG -0.042 0.11 0.22 1 -0.28 45 46
CALM1 -0.11 0.23 0.3 1 -0.54 83 84
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
MAP3K1 -0.16 0.29 0.25 1 -0.65 93 94
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.12 0.25 0.32 1 -0.56 90 91
DOK1 0.027 0.002 -10000 0 -10000 0 0
AP-1 -0.074 0.12 0.21 1 -0.28 83 84
LYN 0.024 0.009 -10000 0 -10000 0 0
BLNK 0.021 0.045 -10000 0 -0.4 5 5
SHC1 0.027 0.004 -10000 0 -10000 0 0
BCR complex -0.11 0.21 -10000 0 -0.36 165 165
CD22 -0.2 0.33 -10000 0 -0.68 116 116
CAMK2G -0.11 0.21 0.27 2 -0.51 81 83
CSNK2A1 0.022 0.011 -10000 0 -10000 0 0
INPP5D 0.026 0.02 -10000 0 -0.4 1 1
SHC/GRB2/SOS1 -0.059 0.14 -10000 0 -0.36 48 48
GO:0007205 -0.12 0.26 0.32 1 -0.57 90 91
SYK 0.027 0.004 -10000 0 -10000 0 0
ELK1 -0.12 0.24 0.3 1 -0.55 86 87
NFATC1 -0.17 0.26 -10000 0 -0.52 131 131
B-cell antigen/BCR complex -0.11 0.21 -10000 0 -0.36 165 165
PAG1/CSK 0.029 0.039 -10000 0 -0.27 6 6
NFKBIB -0.001 0.047 0.11 4 -0.13 19 23
HRAS -0.096 0.2 0.26 2 -0.48 80 82
NFKBIA 0 0.046 0.11 4 -0.12 19 23
NF-kappa-B/RelA/I kappa B beta 0.006 0.04 0.11 4 -10000 0 4
RasGAP/Csk -0.07 0.2 -10000 0 -0.32 158 158
mol:GDP -0.12 0.24 0.31 1 -0.55 87 88
PTEN 0.026 0.006 -10000 0 -10000 0 0
CD79B -0.035 0.15 -10000 0 -0.4 65 65
NF-kappa-B/RelA/I kappa B alpha 0.006 0.039 0.11 4 -10000 0 4
GRB2 0.027 0.004 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.18 0.28 -10000 0 -0.56 131 131
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 -0.13 0.26 0.32 1 -0.57 91 92
CSK 0.026 0.006 -10000 0 -10000 0 0
FOS -0.11 0.22 0.29 1 -0.51 83 84
CHUK -0.05 0.12 0.22 1 -0.3 53 54
IBTK 0.026 0.02 -10000 0 -0.4 1 1
CARD11/BCL10/MALT1/TAK1 -0.082 0.22 0.25 3 -0.52 70 73
PTPN6 -0.19 0.3 -10000 0 -0.64 116 116
RELA 0.027 0.004 -10000 0 -10000 0 0
BCL2A1 0.005 0.029 -10000 0 -0.13 1 1
VAV2 -0.2 0.32 -10000 0 -0.65 128 128
ubiquitin-dependent protein catabolic process 0.002 0.047 0.11 4 -0.12 19 23
BTK -0.12 0.37 -10000 0 -1.1 60 60
CD19 -0.2 0.32 -10000 0 -0.64 128 128
MAP4K1 -0.017 0.13 -10000 0 -0.4 46 46
CD72 0.025 0.021 -10000 0 -0.4 1 1
PAG1 0.017 0.049 -10000 0 -0.4 6 6
MAPK14 -0.13 0.24 0.24 1 -0.54 91 92
SH3BP5 0.024 0.035 -10000 0 -0.4 3 3
PIK3AP1 -0.12 0.26 0.34 2 -0.57 87 89
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.16 0.31 -10000 0 -0.67 90 90
RAF1 -0.092 0.19 0.3 1 -0.45 78 79
RasGAP/p62DOK/SHIP -0.066 0.2 -10000 0 -0.45 72 72
CD79A -0.13 0.2 -10000 0 -0.4 164 164
re-entry into mitotic cell cycle -0.074 0.12 0.21 1 -0.28 84 85
RASA1 0.026 0.005 -10000 0 -10000 0 0
MAPK3 -0.078 0.16 0.27 1 -0.4 67 68
MAPK1 -0.077 0.16 0.27 1 -0.4 66 67
CD72/SHP1 -0.17 0.29 -10000 0 -0.61 113 113
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.13 0.24 0.24 1 -0.54 92 93
actin cytoskeleton organization -0.16 0.27 0.33 1 -0.55 117 118
NF-kappa-B/RelA 0.015 0.078 0.22 4 -0.2 11 15
Calcineurin -0.079 0.2 0.28 1 -0.48 72 73
PI3K -0.17 0.24 -10000 0 -0.49 133 133
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.12 0.27 0.35 1 -0.6 89 90
SOS1 0.027 0.002 -10000 0 -10000 0 0
Bam32/HPK1 -0.19 0.37 -10000 0 -0.88 86 86
DAPP1 -0.21 0.4 -10000 0 -0.98 86 86
cytokine secretion -0.16 0.24 -10000 0 -0.48 131 131
mol:DAG -0.13 0.26 0.32 1 -0.57 91 92
PLCG2 -0.016 0.13 -10000 0 -0.4 45 45
MAP2K1 -0.085 0.17 0.29 1 -0.43 74 75
B-cell antigen/BCR complex/FcgammaRIIB -0.1 0.22 -10000 0 -0.36 165 165
mol:PI-3-4-5-P3 -0.12 0.15 0.17 1 -0.34 121 122
ETS1 -0.098 0.19 0.26 2 -0.47 79 81
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.048 0.16 -10000 0 -0.39 50 50
B-cell antigen/BCR complex/LYN -0.16 0.3 -10000 0 -0.51 145 145
MALT1 0.02 0.023 -10000 0 -0.4 1 1
TRAF6 0.027 0.003 -10000 0 -10000 0 0
RAC1 -0.18 0.29 -10000 0 -0.6 118 118
B-cell antigen/BCR complex/LYN/SYK -0.16 0.3 -10000 0 -0.63 107 107
CARD11 -0.11 0.26 0.27 8 -0.58 81 89
FCGR2B -0.022 0.13 -10000 0 -0.4 51 51
PPP3CA 0.027 0.004 -10000 0 -10000 0 0
BCL10 0.025 0.021 -10000 0 -0.4 1 1
IKK complex -0.012 0.049 0.14 7 -0.12 10 17
PTPRC -0.007 0.12 -10000 0 -0.4 36 36
PDPK1 -0.085 0.1 0.15 4 -0.25 89 93
PPP3CB 0.027 0.004 -10000 0 -10000 0 0
PPP3CC 0.021 0.012 -10000 0 -10000 0 0
POU2F2 0.003 0.032 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.023 0.04 -10000 0 -0.4 4 4
LAT2 -0.093 0.16 -10000 0 -0.32 113 113
AP1 -0.12 0.24 -10000 0 -0.52 97 97
mol:PIP3 -0.12 0.2 0.22 5 -0.46 86 91
IKBKB -0.072 0.14 0.18 25 -0.28 98 123
AKT1 -0.088 0.12 0.29 6 -0.32 52 58
IKBKG -0.084 0.13 0.18 6 -0.28 106 112
MS4A2 -0.098 0.19 -10000 0 -0.4 130 130
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.026 0.003 -10000 0 -10000 0 0
MAP3K1 -0.11 0.18 0.2 5 -0.41 85 90
mol:Ca2+ -0.093 0.15 0.19 6 -0.34 84 90
LYN 0.022 0.011 -10000 0 -10000 0 0
CBLB -0.092 0.16 -10000 0 -0.36 80 80
SHC1 0.027 0.004 -10000 0 -10000 0 0
RasGAP/p62DOK 0.05 0.02 -10000 0 -0.21 2 2
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.026 0.02 -10000 0 -0.4 1 1
PLD2 -0.093 0.14 0.32 6 -0.36 61 67
PTPN13 -0.1 0.19 -10000 0 -0.46 63 63
PTPN11 0.014 0.024 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.079 0.12 0.2 3 -0.3 60 63
SYK 0.025 0.008 -10000 0 -10000 0 0
GRB2 0.026 0.004 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.11 0.21 -10000 0 -0.46 92 92
LAT -0.094 0.16 -10000 0 -0.32 116 116
PAK2 -0.12 0.2 0.21 5 -0.45 89 94
NFATC2 -0.035 0.099 -10000 0 -0.5 14 14
HRAS -0.13 0.22 0.21 6 -0.48 93 99
GAB2 0.027 0.003 -10000 0 -10000 0 0
PLA2G1B 0.021 0.11 -10000 0 -0.89 6 6
Fc epsilon R1 -0.099 0.19 -10000 0 -0.3 188 188
Antigen/IgE/Fc epsilon R1 -0.087 0.17 -10000 0 -0.27 188 188
mol:GDP -0.14 0.24 0.24 2 -0.52 100 102
JUN 0.027 0.005 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
FOS 0.023 0.035 -10000 0 -0.4 3 3
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.094 0.16 -10000 0 -0.33 116 116
CHUK -0.084 0.13 0.15 5 -0.28 103 108
KLRG1 -0.083 0.14 0.14 1 -0.34 71 72
VAV1 -0.1 0.17 -10000 0 -0.34 116 116
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.093 0.16 -10000 0 -0.32 114 114
negative regulation of mast cell degranulation -0.068 0.14 0.17 2 -0.33 71 73
BTK -0.16 0.28 -10000 0 -0.59 101 101
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.14 0.22 -10000 0 -0.4 145 145
GAB2/PI3K/SHP2 -0.1 0.12 -10000 0 -0.34 57 57
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.09 0.16 -10000 0 -0.41 68 68
RAF1 0.024 0.12 -10000 0 -0.97 6 6
Fc epsilon R1/FcgammaRIIB/SHIP -0.088 0.21 -10000 0 -0.34 142 142
FCER1G 0.026 0.047 -10000 0 -0.4 5 5
FCER1A -0.098 0.19 -10000 0 -0.41 125 125
Antigen/IgE/Fc epsilon R1/Fyn -0.074 0.17 -10000 0 -0.28 151 151
MAPK3 0.022 0.11 -10000 0 -0.89 6 6
MAPK1 0.017 0.12 -10000 0 -0.93 6 6
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.11 0.27 -10000 0 -0.69 67 67
DUSP1 0.025 0.028 -10000 0 -0.4 2 2
NF-kappa-B/RelA -0.043 0.083 -10000 0 -0.2 43 43
actin cytoskeleton reorganization -0.097 0.19 -10000 0 -0.45 65 65
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.098 0.2 0.28 2 -0.44 80 82
FER -0.088 0.16 -10000 0 -0.32 107 107
RELA 0.027 0.004 -10000 0 -10000 0 0
ITK -0.035 0.096 -10000 0 -0.38 25 25
SOS1 0.027 0.002 -10000 0 -10000 0 0
PLCG1 -0.092 0.24 0.21 23 -0.48 89 112
cytokine secretion -0.033 0.058 -10000 0 -10000 0 0
SPHK1 -0.11 0.16 -10000 0 -0.33 118 118
PTK2 -0.1 0.19 -10000 0 -0.47 65 65
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.11 0.22 0.2 7 -0.47 92 99
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.12 0.2 0.22 5 -0.45 88 93
MAP2K2 0.017 0.11 -10000 0 -0.88 6 6
MAP2K1 0.016 0.11 -10000 0 -0.9 6 6
MAP2K7 0.026 0.02 -10000 0 -0.4 1 1
KLRG1/SHP2 -0.065 0.13 0.18 2 -0.31 69 71
MAP2K4 -0.15 0.38 -10000 0 -0.91 88 88
Fc epsilon R1/FcgammaRIIB -0.1 0.21 -10000 0 -0.32 195 195
mol:Choline -0.092 0.14 0.32 6 -0.36 61 67
SHC/Grb2/SOS1 -0.063 0.17 -10000 0 -0.37 69 69
FYN 0.027 0.004 -10000 0 -10000 0 0
DOK1 0.027 0.002 -10000 0 -10000 0 0
PXN -0.096 0.18 -10000 0 -0.44 65 65
HCLS1 -0.094 0.16 -10000 0 -0.33 111 111
PRKCB -0.12 0.18 0.18 5 -0.39 108 113
FCGR2B -0.022 0.13 -10000 0 -0.4 51 51
IGHE -0.003 0.005 -10000 0 -10000 0 0
KLRG1/SHIP -0.069 0.15 0.17 2 -0.33 71 73
LCP2 0.022 0.04 -10000 0 -0.4 4 4
PLA2G4A -0.11 0.18 -10000 0 -0.35 136 136
RASA1 0.026 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.092 0.14 0.32 6 -0.36 61 67
IKK complex -0.051 0.11 0.17 26 -0.23 55 81
WIPF1 0.024 0.034 -10000 0 -0.4 3 3
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.028 0.072 -10000 0 -0.23 29 29
fibroblast growth factor receptor signaling pathway 0.028 0.071 -10000 0 -0.23 29 29
LAMA1 -0.058 0.16 -10000 0 -0.4 85 85
PRNP 0.021 0.022 -10000 0 -0.4 1 1
GPC1/SLIT2 -0.043 0.14 -10000 0 -0.28 116 116
SMAD2 0.012 0.025 0.18 3 -0.23 1 4
GPC1/PrPc/Cu2+ 0.028 0.026 -10000 0 -0.24 3 3
GPC1/Laminin alpha1 -0.029 0.12 -10000 0 -0.28 87 87
TDGF1 -0.16 0.22 -10000 0 -0.42 185 185
CRIPTO/GPC1 -0.1 0.17 -10000 0 -0.3 186 186
APP/GPC1 0.037 0.024 -10000 0 -0.29 2 2
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.095 0.13 -10000 0 -0.25 186 186
FLT1 0.021 0.012 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.052 0.026 -10000 0 -0.24 3 3
SERPINC1 0.006 0.051 -10000 0 -0.43 5 5
FYN -0.096 0.13 -10000 0 -0.26 184 184
FGR -0.098 0.14 -10000 0 -0.26 186 186
positive regulation of MAPKKK cascade -0.042 0.13 0.22 29 -0.32 34 63
SLIT2 -0.082 0.18 -10000 0 -0.4 114 114
GPC1/NRG -0.002 0.096 -10000 0 -0.28 47 47
NRG1 -0.022 0.12 -10000 0 -0.4 45 45
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.04 0.033 0.25 1 -0.25 2 3
LYN -0.088 0.13 -10000 0 -0.26 165 165
mol:Spermine 0.006 0.02 -10000 0 -0.29 2 2
cell growth 0.028 0.071 -10000 0 -0.23 29 29
BMP signaling pathway -0.025 0.029 0.41 2 -10000 0 2
SRC -0.051 0.1 -10000 0 -0.26 85 85
TGFBR1 0.026 0.02 -10000 0 -0.4 1 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.068 0.18 -10000 0 -0.4 98 98
GPC1 0.025 0.029 -10000 0 -0.41 2 2
TGFBR1 (dimer) 0.026 0.02 -10000 0 -0.4 1 1
VEGFA 0.028 0.016 0.36 1 -10000 0 1
BLK -0.16 0.16 -10000 0 -0.29 259 259
HCK -0.054 0.11 -10000 0 -0.26 88 88
FGF2 -0.002 0.11 -10000 0 -0.4 30 30
FGFR1 0.02 0.036 -10000 0 -0.4 3 3
VEGFR1 homodimer 0.021 0.012 -10000 0 -10000 0 0
TGFBR2 0.027 0.003 -10000 0 -10000 0 0
cell death 0.037 0.024 -10000 0 -0.29 2 2
ATIII/GPC1 0.031 0.042 -10000 0 -0.3 7 7
PLA2G2A/GPC1 -0.034 0.13 -10000 0 -0.28 100 100
LCK -0.1 0.14 -10000 0 -0.26 190 190
neuron differentiation -0.002 0.096 -10000 0 -0.28 47 47
PrPc/Cu2+ 0.016 0.016 -10000 0 -0.28 1 1
APP 0.026 0.006 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.027 0.003 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.074 0.18 -10000 0 -0.42 80 80
CRKL -0.061 0.17 -10000 0 -0.41 79 79
HRAS -0.048 0.16 -10000 0 -0.37 81 81
mol:PIP3 -0.049 0.16 0.26 2 -0.38 75 77
SPRED1 0.025 0.007 -10000 0 -10000 0 0
SPRED2 0.027 0.002 -10000 0 -10000 0 0
GAB1 -0.063 0.18 -10000 0 -0.43 79 79
FOXO3 -0.057 0.19 0.27 1 -0.41 84 85
AKT1 -0.061 0.2 0.28 1 -0.44 84 85
BAD -0.058 0.19 0.27 1 -0.41 84 85
megakaryocyte differentiation -0.082 0.19 -10000 0 -0.44 83 83
GSK3B -0.057 0.19 0.27 1 -0.41 83 84
RAF1 -0.039 0.14 0.24 1 -0.31 80 81
SHC1 0.027 0.004 -10000 0 -10000 0 0
STAT3 -0.063 0.18 -10000 0 -0.43 78 78
STAT1 -0.16 0.41 -10000 0 -0.97 86 86
HRAS/SPRED1 -0.028 0.14 -10000 0 -0.31 78 78
cell proliferation -0.062 0.17 -10000 0 -0.42 79 79
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
TEC 0.026 0.022 -10000 0 -0.43 1 1
RPS6KB1 -0.057 0.19 -10000 0 -0.43 83 83
HRAS/SPRED2 -0.027 0.14 -10000 0 -0.31 80 80
LYN/TEC/p62DOK -0.026 0.18 -10000 0 -0.41 66 66
MAPK3 -0.026 0.1 0.21 2 -0.26 29 31
STAP1 -0.1 0.2 -10000 0 -0.48 84 84
GRAP2 0.012 0.074 -10000 0 -0.4 14 14
JAK2 -0.13 0.35 -10000 0 -0.82 84 84
STAT1 (dimer) -0.15 0.4 -10000 0 -0.94 86 86
mol:Gleevec 0.002 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.039 0.2 -10000 0 -0.44 77 77
actin filament polymerization -0.061 0.17 0.21 1 -0.42 76 77
LYN 0.024 0.009 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.12 0.26 -10000 0 -0.64 81 81
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.033 0.17 -10000 0 -0.38 76 76
PI3K -0.032 0.19 -10000 0 -0.42 80 80
PTEN 0.026 0.006 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.17 0.48 -10000 0 -1.2 78 78
MAPK8 -0.063 0.18 -10000 0 -0.43 79 79
STAT3 (dimer) -0.062 0.17 -10000 0 -0.42 78 78
positive regulation of transcription -0.019 0.086 0.2 2 -0.21 28 30
mol:GDP -0.045 0.18 -10000 0 -0.39 79 79
PIK3C2B -0.063 0.18 -10000 0 -0.43 79 79
CBL/CRKL -0.045 0.17 -10000 0 -0.39 77 77
FER -0.064 0.18 -10000 0 -0.43 79 79
SH2B3 -0.063 0.18 -10000 0 -0.43 79 79
PDPK1 -0.045 0.15 0.25 3 -0.36 75 78
SNAI2 -0.062 0.17 -10000 0 -0.41 79 79
positive regulation of cell proliferation -0.11 0.3 -10000 0 -0.72 82 82
KITLG 0.009 0.07 -10000 0 -0.42 10 10
cell motility -0.11 0.3 -10000 0 -0.72 82 82
PTPN6 0.029 0.01 -10000 0 -10000 0 0
EPOR -0.019 0.15 -10000 0 -0.85 3 3
STAT5A (dimer) -0.083 0.25 -10000 0 -0.59 80 80
SOCS1 0.017 0.067 -10000 0 -0.43 10 10
cell migration 0.081 0.19 0.46 79 -10000 0 79
SOS1 0.027 0.002 -10000 0 -10000 0 0
EPO 0.012 0.045 0.36 1 -0.43 3 4
VAV1 0.007 0.089 -10000 0 -0.4 21 21
GRB10 -0.062 0.17 -10000 0 -0.42 73 73
PTPN11 0.029 0.007 -10000 0 -10000 0 0
SCF/KIT -0.063 0.18 -10000 0 -0.45 80 80
GO:0007205 0.003 0.009 -10000 0 -10000 0 0
MAP2K1 -0.031 0.11 0.22 2 -0.28 33 35
CBL 0.027 0.004 -10000 0 -10000 0 0
KIT -0.19 0.49 -10000 0 -1.2 80 80
MAP2K2 -0.031 0.11 0.22 2 -0.29 28 30
SHC/Grb2/SOS1 -0.025 0.18 -10000 0 -0.42 74 74
STAT5A -0.088 0.25 -10000 0 -0.61 80 80
GRB2 0.027 0.004 -10000 0 -10000 0 0
response to radiation -0.061 0.17 -10000 0 -0.4 78 78
SHC/GRAP2 0.027 0.056 -10000 0 -0.28 14 14
PTPRO -0.083 0.19 -10000 0 -0.45 83 83
SH2B2 -0.063 0.17 0.21 1 -0.43 76 77
DOK1 0.027 0.002 -10000 0 -10000 0 0
MATK -0.083 0.19 -10000 0 -0.47 80 80
CREBBP 0.014 0.06 -10000 0 -10000 0 0
BCL2 -0.18 0.41 -10000 0 -1.2 51 51
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.27 0.27 -10000 0 -0.77 54 54
PCK1 -0.61 0.6 -10000 0 -1.2 203 203
HNF4A -0.25 0.28 -10000 0 -0.86 37 37
KCNJ11 -0.28 0.28 -10000 0 -0.82 46 46
AKT1 -0.2 0.17 -10000 0 -0.51 44 44
response to starvation -0.016 0.027 -10000 0 -10000 0 0
DLK1 -0.29 0.29 -10000 0 -0.79 63 63
NKX2-1 -0.12 0.14 0.32 5 -0.36 45 50
ACADM -0.28 0.27 -10000 0 -0.76 64 64
TAT -0.62 0.58 -10000 0 -1.3 184 184
CEBPB 0.004 0.032 -10000 0 -10000 0 0
CEBPA 0.001 0.055 -10000 0 -0.4 3 3
TTR -0.31 0.45 0.52 1 -1.1 87 88
PKLR -0.34 0.34 -10000 0 -0.87 99 99
APOA1 -0.29 0.31 -10000 0 -0.9 44 44
CPT1C -0.28 0.27 -10000 0 -0.78 53 53
ALAS1 -0.14 0.15 -10000 0 -0.58 2 2
TFRC -0.28 0.23 -10000 0 -0.63 62 62
FOXF1 0.018 0.059 -10000 0 -0.4 9 9
NF1 0.031 0.006 -10000 0 -10000 0 0
HNF1A (dimer) -0.075 0.057 -10000 0 -0.28 8 8
CPT1A -0.28 0.27 -10000 0 -0.77 55 55
HMGCS1 -0.28 0.27 -10000 0 -0.76 57 57
NR3C1 -0.079 0.13 -10000 0 -0.36 51 51
CPT1B -0.28 0.27 -10000 0 -0.73 70 70
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 -0.063 0.037 -10000 0 -10000 0 0
GCK -0.28 0.28 -10000 0 -0.75 78 78
CREB1 -0.072 0.1 -10000 0 -0.22 89 89
IGFBP1 -0.21 0.19 -10000 0 -0.58 40 40
PDX1 -0.29 0.18 -10000 0 -0.61 22 22
UCP2 -0.28 0.27 -10000 0 -0.74 66 66
ALDOB -0.32 0.32 -10000 0 -0.86 77 77
AFP -0.12 0.13 -10000 0 -0.43 37 37
BDH1 -0.28 0.27 -10000 0 -0.72 75 75
HADH -0.28 0.28 -10000 0 -0.76 63 63
F2 -0.31 0.32 -10000 0 -0.91 48 48
HNF1A -0.075 0.056 -10000 0 -0.28 8 8
G6PC -0.22 0.39 -10000 0 -1.2 57 57
SLC2A2 -0.21 0.18 -10000 0 -0.74 8 8
INS -0.006 0.039 -10000 0 -10000 0 0
FOXA1 -0.034 0.12 -10000 0 -0.39 37 37
FOXA3 -0.16 0.14 -10000 0 -0.34 100 100
FOXA2 -0.32 0.32 -10000 0 -0.83 78 78
ABCC8 -0.33 0.34 -10000 0 -0.91 80 80
ALB -0.12 0.14 -10000 0 -0.44 36 36
HIF-1-alpha 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
PKM2 -0.4 0.28 -9999 0 -0.86 72 72
HDAC7 0.027 0.007 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.32 0.25 -9999 0 -0.81 33 33
SMAD4 0.021 0.012 -9999 0 -10000 0 0
ID2 -0.4 0.29 -9999 0 -0.87 66 66
AP1 0.036 0.028 -9999 0 -0.27 3 3
ABCG2 -0.56 0.32 -9999 0 -0.87 164 164
HIF1A -0.075 0.054 -9999 0 -10000 0 0
TFF3 -0.41 0.3 -9999 0 -0.89 67 67
GATA2 0.018 0.066 -9999 0 -0.4 11 11
AKT1 -0.075 0.058 -9999 0 -0.26 1 1
response to hypoxia -0.079 0.049 -9999 0 -0.22 10 10
MCL1 -0.4 0.29 -9999 0 -0.87 66 66
NDRG1 -0.38 0.29 -9999 0 -0.88 61 61
SERPINE1 -0.44 0.32 -9999 0 -0.88 92 92
FECH -0.4 0.29 -9999 0 -0.87 66 66
FURIN -0.4 0.29 -9999 0 -0.87 67 67
NCOA2 0.023 0.022 -9999 0 -0.4 1 1
EP300 -0.071 0.078 -9999 0 -0.3 25 25
HMOX1 -0.4 0.3 -9999 0 -0.88 69 69
BHLHE40 -0.4 0.29 -9999 0 -0.88 68 68
BHLHE41 -0.41 0.3 -9999 0 -0.89 68 68
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.071 0.087 -9999 0 -10000 0 0
ENG -0.075 0.07 -9999 0 -10000 0 0
JUN 0.027 0.006 -9999 0 -10000 0 0
RORA -0.4 0.3 -9999 0 -0.88 69 69
ABCB1 -0.29 0.43 -9999 0 -1.1 94 94
TFRC -0.4 0.29 -9999 0 -0.87 66 66
CXCR4 -0.4 0.29 -9999 0 -0.87 66 66
TF -0.42 0.31 -9999 0 -0.9 79 79
CITED2 -0.4 0.29 -9999 0 -0.87 66 66
HIF1A/ARNT -0.44 0.33 -9999 0 -0.97 66 66
LDHA -0.037 0.053 -9999 0 -0.67 1 1
ETS1 -0.4 0.29 -9999 0 -0.88 66 66
PGK1 -0.4 0.29 -9999 0 -0.87 66 66
NOS2 -0.41 0.3 -9999 0 -0.88 73 73
ITGB2 -0.4 0.3 -9999 0 -0.88 69 69
ALDOA -0.4 0.29 -9999 0 -0.87 65 65
Cbp/p300/CITED2 -0.4 0.3 -9999 0 -0.97 46 46
FOS 0.023 0.035 -9999 0 -0.4 3 3
HK2 -0.4 0.29 -9999 0 -0.87 66 66
SP1 0.005 0.054 -9999 0 -10000 0 0
GCK -0.096 0.2 -9999 0 -1.3 9 9
HK1 -0.4 0.29 -9999 0 -0.87 65 65
NPM1 -0.4 0.29 -9999 0 -0.87 66 66
EGLN1 -0.4 0.29 -9999 0 -0.87 66 66
CREB1 0.032 0 -9999 0 -10000 0 0
PGM1 -0.4 0.29 -9999 0 -0.86 70 70
SMAD3 0.026 0.007 -9999 0 -10000 0 0
EDN1 -0.079 0.14 -9999 0 -0.72 9 9
IGFBP1 -0.42 0.31 -9999 0 -0.89 82 82
VEGFA -0.29 0.21 -9999 0 -0.74 26 26
HIF1A/JAB1 -0.038 0.045 -9999 0 -10000 0 0
CP -0.48 0.33 -9999 0 -0.87 138 138
CXCL12 -0.43 0.32 -9999 0 -0.88 99 99
COPS5 0.024 0.009 -9999 0 -10000 0 0
SMAD3/SMAD4 0.031 0.019 -9999 0 -10000 0 0
BNIP3 -0.4 0.3 -9999 0 -0.88 67 67
EGLN3 -0.4 0.29 -9999 0 -0.87 67 67
CA9 -0.53 0.32 -9999 0 -0.88 147 147
TERT -0.42 0.31 -9999 0 -0.89 76 76
ENO1 -0.4 0.29 -9999 0 -0.87 66 66
PFKL -0.4 0.29 -9999 0 -0.87 67 67
NCOA1 0.027 0.001 -9999 0 -10000 0 0
ADM -0.4 0.29 -9999 0 -0.87 66 66
ARNT -0.08 0.054 -9999 0 -0.45 1 1
HNF4A 0.015 0.019 -9999 0 -10000 0 0
ADFP -0.4 0.28 -9999 0 -0.86 72 72
SLC2A1 -0.29 0.22 -9999 0 -0.75 34 34
LEP -0.41 0.3 -9999 0 -0.9 73 73
HIF1A/ARNT/Cbp/p300 -0.33 0.25 -9999 0 -0.82 38 38
EPO -0.22 0.18 -9999 0 -0.77 9 9
CREBBP -0.07 0.075 -9999 0 -0.31 20 20
HIF1A/ARNT/Cbp/p300/HDAC7 -0.32 0.25 -9999 0 -0.85 29 29
PFKFB3 -0.4 0.29 -9999 0 -0.87 66 66
NT5E -0.4 0.29 -9999 0 -0.88 68 68
p75(NTR)-mediated 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
Sortilin/TRAF6 0.039 0.009 -10000 0 -10000 0 0
Necdin/E2F1 0.018 0.06 0.26 6 -0.28 12 18
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.01 0.13 -10000 0 -0.38 9 9
NGF (dimer)/p75(NTR)/BEX1 -0.1 0.18 -10000 0 -0.29 196 196
NT-4/5 (dimer)/p75(NTR) -0.059 0.15 -10000 0 -0.29 128 128
IKBKB 0.024 0.009 -10000 0 -10000 0 0
AKT1 -0.049 0.099 -10000 0 -0.38 7 7
IKBKG 0.026 0.02 -10000 0 -0.4 1 1
BDNF 0.013 0.076 -10000 0 -0.43 13 13
MGDIs/NGR/p75(NTR)/LINGO1 -0.046 0.15 -10000 0 -0.25 140 140
FURIN 0.025 0.021 -10000 0 -0.4 1 1
proBDNF (dimer)/p75(NTR)/Sortilin -0.03 0.13 -10000 0 -0.24 126 126
LINGO1 0.005 0.096 -10000 0 -0.43 21 21
Sortilin/TRAF6/NRIF 0.029 0.027 -10000 0 -10000 0 0
proBDNF (dimer) 0.013 0.076 -10000 0 -0.42 13 13
NTRK1 0.018 0.044 -10000 0 -0.43 4 4
RTN4R 0.009 0.086 -10000 0 -0.43 17 17
neuron apoptosis -0.058 0.14 0.3 3 -0.41 28 31
IRAK1 0.027 0.003 -10000 0 -10000 0 0
SHC1 -0.054 0.12 -10000 0 -0.25 117 117
ARHGDIA 0.026 0.02 -10000 0 -0.4 1 1
RhoA/GTP 0.02 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.069 0.032 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.016 0.14 -10000 0 -0.23 117 117
MAGEH1 0.021 0.049 -10000 0 -0.4 6 6
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.022 0.14 -10000 0 -0.24 112 112
Mammalian IAPs/DIABLO 0.063 0.04 -10000 0 -0.22 8 8
proNGF (dimer) 0.008 0.079 -10000 0 -0.4 16 16
MAGED1 0.027 0.003 -10000 0 -10000 0 0
APP 0.026 0.006 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.018 0.091 -10000 0 -0.44 19 19
ZNF274 0.023 0.04 -10000 0 -0.4 4 4
RhoA/GDP/RHOGDI -0.03 0.11 -10000 0 -0.27 19 19
NGF 0.008 0.079 -10000 0 -0.4 16 16
cell cycle arrest -0.038 0.1 0.24 2 -0.34 8 10
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.036 0.11 -10000 0 -0.32 15 15
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.036 0.14 -10000 0 -0.25 128 128
NCSTN 0.027 0.004 -10000 0 -10000 0 0
mol:GTP -0.061 0.16 -10000 0 -0.27 154 154
PSENEN 0.026 0.02 -10000 0 -0.4 1 1
mol:ceramide -0.049 0.11 -10000 0 -0.4 7 7
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.03 0.095 -10000 0 -0.32 16 16
p75(NTR)/beta APP -0.042 0.14 -10000 0 -0.28 114 114
BEX1 -0.099 0.18 -10000 0 -0.4 124 124
mol:GDP -0.071 0.11 -10000 0 -0.24 122 122
NGF (dimer) -0.27 0.11 -10000 0 -0.28 422 422
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.03 0.14 -10000 0 -0.29 35 35
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RAC1/GTP -0.025 0.11 -10000 0 -0.21 109 109
MYD88 0.027 0.003 -10000 0 -10000 0 0
CHUK 0.026 0.006 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.061 0.16 -10000 0 -0.27 154 154
RHOB 0.027 0.001 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.026 0.042 0.26 7 -0.3 2 9
NT3 (dimer) 0.018 0.056 -10000 0 -0.4 8 8
TP53 -0.058 0.093 0.35 3 -0.38 3 6
PRDM4 -0.05 0.11 0.18 1 -0.38 8 9
BDNF (dimer) -0.44 0.14 0.38 1 -0.45 441 442
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
SORT1 0.026 0.005 -10000 0 -10000 0 0
activation of caspase activity -0.014 0.12 -10000 0 -0.38 9 9
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.014 0.13 -10000 0 -0.23 116 116
RHOC 0.026 0.005 -10000 0 -10000 0 0
XIAP 0.027 0.002 -10000 0 -10000 0 0
MAPK10 -0.078 0.16 0.32 4 -0.44 41 45
DIABLO 0.027 0.003 -10000 0 -10000 0 0
SMPD2 -0.049 0.11 -10000 0 -0.4 7 7
APH1B 0.026 0.006 -10000 0 -10000 0 0
APH1A 0.027 0.004 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.029 0.14 -10000 0 -0.25 118 118
PSEN1 0.025 0.007 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.038 0.01 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.046 0.14 -10000 0 -0.28 117 117
MAPK8 -0.054 0.13 0.35 3 -0.36 14 17
MAPK9 -0.053 0.13 0.35 3 -0.37 14 17
APAF1 0.027 0.003 -10000 0 -10000 0 0
NTF3 0.018 0.056 -10000 0 -0.4 8 8
NTF4 -0.018 0.091 -10000 0 -0.44 19 19
NDN 0.01 0.078 -10000 0 -0.4 16 16
RAC1/GDP 0.018 0.006 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.032 0.14 -10000 0 -0.37 27 27
p75 CTF/Sortilin/TRAF6/NRIF 0.063 0.029 -10000 0 -0.21 3 3
RhoA-B-C/GTP -0.061 0.16 -10000 0 -0.27 154 154
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.006 0.13 -10000 0 -0.25 16 16
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.014 0.13 -10000 0 -0.22 126 126
PRKACB -0.026 0.14 -10000 0 -0.4 56 56
proBDNF (dimer)/p75 ECD 0.03 0.058 -10000 0 -0.3 13 13
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.019 0.057 -10000 0 -0.4 8 8
BIRC2 0.027 0.005 -10000 0 -10000 0 0
neuron projection morphogenesis -0.061 0.14 -10000 0 -0.28 82 82
BAD -0.07 0.15 0.32 4 -0.37 39 43
RIPK2 0.023 0.01 -10000 0 -10000 0 0
NGFR -0.081 0.18 -10000 0 -0.4 114 114
CYCS -0.046 0.099 -10000 0 -0.38 7 7
ADAM17 0.027 0.002 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.014 0.12 -10000 0 -0.34 8 8
BCL2L11 -0.07 0.15 0.32 4 -0.37 40 44
BDNF (dimer)/p75(NTR) -0.052 0.15 -10000 0 -0.28 126 126
PI3K -0.013 0.13 -10000 0 -0.37 9 9
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.015 0.13 -10000 0 -0.23 106 106
NDNL2 0.025 0.007 -10000 0 -10000 0 0
YWHAE 0.023 0.01 -10000 0 -10000 0 0
PRKCI 0.025 0.028 -10000 0 -0.4 2 2
NGF (dimer)/p75(NTR) -0.052 0.15 -10000 0 -0.29 122 122
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.012 0.13 -10000 0 -0.23 111 111
TRAF6 0.027 0.003 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCZ 0.026 0.007 -10000 0 -10000 0 0
PLG -0.083 0.17 -10000 0 -0.43 83 83
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.057 0.12 -10000 0 -0.26 107 107
SQSTM1 0.027 0.003 -10000 0 -10000 0 0
NGFRAP1 0.025 0.028 -10000 0 -0.4 2 2
CASP3 -0.068 0.14 0.3 4 -0.35 41 45
E2F1 0.021 0.056 0.36 8 -0.43 2 10
CASP9 0.026 0.007 -10000 0 -10000 0 0
IKK complex -0.003 0.11 -10000 0 -0.37 10 10
NGF (dimer)/TRKA 0.022 0.067 -10000 0 -0.29 20 20
MMP7 -0.41 0.11 0.36 3 -0.43 428 431
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.006 0.13 -10000 0 -0.39 9 9
MMP3 -0.34 0.18 0.36 1 -0.43 365 366
APAF-1/Caspase 9 -0.037 0.091 -10000 0 -0.32 10 10
Visual signal transduction: Rods

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
mol:K + 0.026 0.006 -10000 0 -10000 0 0
GNAT1/GTP 0.013 0.002 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.023 0.023 -10000 0 -0.26 3 3
PDE6G/GNAT1/GTP 0.011 0.067 -10000 0 -0.24 30 30
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 -0.018 0.003 -10000 0 -10000 0 0
GRK1 -0.011 0.031 -10000 0 -0.43 2 2
CNG Channel -0.16 0.17 -10000 0 -0.41 86 86
mol:Na + -0.031 0.13 -10000 0 -0.4 20 20
mol:ADP -0.011 0.031 -10000 0 -0.42 2 2
RGS9-1/Gbeta5/R9AP 0.006 0.1 0.25 1 -0.23 68 69
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.025 0.13 -10000 0 -0.41 20 20
CNGB1 -0.048 0.13 -10000 0 -0.4 56 56
RDH5 -0.012 0.12 -10000 0 -0.4 41 41
SAG -0.009 0.018 -10000 0 -10000 0 0
mol:Ca2+ -0.066 0.11 0.3 7 -0.39 20 27
Na + (4 Units) -0.033 0.12 -10000 0 -0.38 20 20
RGS9 -0.039 0.15 -10000 0 -0.4 68 68
GNB1/GNGT1 -0.045 0.15 0.26 11 -0.3 113 124
GNAT1/GDP 0.013 0.093 0.23 1 -0.21 60 61
GUCY2D -0.004 0.083 -10000 0 -0.43 16 16
GNGT1 -0.09 0.2 0.36 12 -0.43 113 125
GUCY2F -0.016 0.022 -10000 0 -0.43 1 1
GNB5 0.026 0.006 -10000 0 -10000 0 0
mol:GMP (4 units) -0.13 0.13 -10000 0 -0.23 265 265
mol:11-cis-retinal -0.012 0.12 -10000 0 -0.4 41 41
mol:cGMP 0.017 0.079 -10000 0 -0.26 30 30
GNB1 0.026 0.007 -10000 0 -10000 0 0
Rhodopsin 0.002 0.095 -10000 0 -0.28 44 44
SLC24A1 0.026 0.006 -10000 0 -10000 0 0
CNGA1 -0.016 0.13 -10000 0 -0.4 45 45
Metarhodopsin II 0.015 0.031 -10000 0 -0.28 4 4
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.026 0.083 -10000 0 -0.26 31 31
RGS9BP 0.021 0.031 0.36 1 -0.43 1 2
Metarhodopsin II/Transducin -0.019 0.065 0.15 10 -0.22 11 21
GCAP Family/Ca ++ 0.032 0.055 -10000 0 -0.24 18 18
PDE6A/B -0.16 0.17 -10000 0 -0.29 266 266
mol:Pi 0.006 0.1 0.25 1 -0.23 68 69
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin -0.025 0.12 0.23 11 -0.23 113 124
PDE6B 0.006 0.087 -10000 0 -0.4 20 20
PDE6A -0.22 0.21 -10000 0 -0.4 262 262
PDE6G -0.003 0.11 -10000 0 -0.4 30 30
RHO -0.017 0.036 -10000 0 -0.43 3 3
PDE6 -0.14 0.17 -10000 0 -0.41 66 66
GUCA1A -0.001 0.088 0.36 1 -0.43 17 18
GC2/GCAP Family 0.042 0.062 -10000 0 -0.25 18 18
GUCA1C -0.018 0.002 -10000 0 -10000 0 0
GUCA1B 0.027 0.031 0.36 2 -0.43 1 3
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.012 0.16 0.25 58 -0.24 104 162
SMAD6-7/SMURF1 0.04 0.028 -10000 0 -0.24 1 1
NOG 0.014 0.029 -10000 0 -0.43 1 1
SMAD9 -0.049 0.18 -10000 0 -0.56 46 46
SMAD4 0.02 0.012 -10000 0 -10000 0 0
SMAD5 -0.038 0.13 -10000 0 -0.39 37 37
BMP7/USAG1 -0.057 0.2 0.26 56 -0.34 131 187
SMAD5/SKI -0.039 0.14 -10000 0 -0.39 37 37
SMAD1 0.011 0.048 -10000 0 -0.32 4 4
BMP2 0.005 0.083 -10000 0 -0.4 18 18
SMAD1/SMAD1/SMAD4 0.02 0.061 -10000 0 -0.37 4 4
BMPR1A 0.026 0.006 -10000 0 -10000 0 0
BMPR1B -0.01 0.11 -10000 0 -0.42 32 32
BMPR1A-1B/BAMBI 0.009 0.1 -10000 0 -0.25 62 62
AHSG -0.05 0.16 0.36 2 -0.43 64 66
CER1 -0.018 0.085 0.36 1 -0.43 17 18
BMP2-4/CER1 0.001 0.1 -10000 0 -0.26 54 54
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.041 0.13 -10000 0 -0.37 36 36
BMP2-4 (homodimer) 0.001 0.098 -10000 0 -0.3 40 40
RGMB 0.026 0.006 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.024 0.1 -10000 0 -0.22 62 62
RGMA -0.061 0.17 -10000 0 -0.4 92 92
SMURF1 0.026 0.006 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.04 0.12 -10000 0 -0.33 49 49
BMP2-4/USAG1 -0.03 0.13 -10000 0 -0.27 98 98
SMAD6/SMURF1/SMAD5 -0.039 0.14 -10000 0 -0.4 35 35
SOSTDC1 -0.052 0.16 -10000 0 -0.4 79 79
BMP7/BMPR2/BMPR1A-1B -0.009 0.16 0.25 64 -0.24 120 184
SKI 0.026 0.007 -10000 0 -10000 0 0
BMP6 (homodimer) -0.002 0.11 -10000 0 -0.4 31 31
HFE2 -0.008 0.027 -10000 0 -0.43 1 1
ZFYVE16 0.025 0.028 -10000 0 -0.4 2 2
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
BMP2-4/CHRD 0.015 0.09 -10000 0 -0.26 41 41
SMAD5/SMAD5/SMAD4 -0.036 0.13 -10000 0 -0.38 37 37
MAPK1 0.026 0.006 -10000 0 -10000 0 0
TAK1/TAB family -0.028 0.12 -10000 0 -0.33 32 32
BMP7 (homodimer) -0.029 0.25 0.36 75 -0.42 105 180
NUP214 0.027 0.003 -10000 0 -10000 0 0
BMP6/FETUA -0.031 0.14 -10000 0 -0.31 87 87
SMAD1/SKI 0.015 0.073 -10000 0 -0.41 6 6
SMAD6 0.026 0.006 -10000 0 -10000 0 0
CTDSP2 0.027 0.002 -10000 0 -10000 0 0
BMP2-4/FETUA -0.022 0.13 0.25 1 -0.27 89 90
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.002 0.098 -10000 0 -0.41 24 24
BMPR2 (homodimer) 0.026 0.02 -10000 0 -0.4 1 1
GADD34/PP1CA 0.051 0.023 -10000 0 -0.24 2 2
BMPR1A-1B (homodimer) 0.013 0.086 -10000 0 -0.29 32 32
CHRDL1 -0.2 0.21 -10000 0 -0.4 238 238
ENDOFIN/SMAD1 0.014 0.075 -10000 0 -0.42 6 6
SMAD6-7/SMURF1/SMAD1 0.032 0.073 -10000 0 -0.4 5 5
SMAD6/SMURF1 0.026 0.006 -10000 0 -10000 0 0
BAMBI -0.004 0.12 -10000 0 -0.43 31 31
SMURF2 0.025 0.021 -10000 0 -0.4 1 1
BMP2-4/CHRDL1 -0.11 0.16 -10000 0 -0.26 223 223
BMP2-4/GREM1 -0.001 0.11 -10000 0 -0.26 61 61
SMAD7 0.02 0.023 -10000 0 -0.4 1 1
SMAD8A/SMAD8A/SMAD4 -0.047 0.19 -10000 0 -0.5 57 57
SMAD1/SMAD6 0.013 0.075 -10000 0 -0.42 6 6
TAK1/SMAD6 0.038 0.01 -10000 0 -10000 0 0
BMP7 -0.029 0.25 0.36 75 -0.42 105 180
BMP6 -0.002 0.11 -10000 0 -0.4 31 31
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.046 0.14 -10000 0 -0.39 43 43
PPM1A 0.025 0.007 -10000 0 -10000 0 0
SMAD1/SMURF2 0.015 0.074 -10000 0 -0.42 6 6
SMAD7/SMURF1 0.029 0.023 -10000 0 -0.28 1 1
CTDSPL 0.027 0.003 -10000 0 -10000 0 0
PPP1CA 0.027 0.004 -10000 0 -10000 0 0
XIAP 0.027 0.002 -10000 0 -10000 0 0
CTDSP1 0.027 0.001 -10000 0 -10000 0 0
PPP1R15A 0.027 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.055 0.15 -10000 0 -0.4 54 54
CHRD 0.026 0.02 -10000 0 -0.4 1 1
BMPR2 0.026 0.02 -10000 0 -0.4 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.048 0.13 -10000 0 -0.36 45 45
BMP4 -0.001 0.1 -10000 0 -0.42 26 26
FST 0.009 0.084 -10000 0 -0.4 18 18
BMP2-4/NOG 0.013 0.09 -10000 0 -0.26 41 41
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.005 0.16 0.25 58 -0.3 17 75
Syndecan-1-mediated 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
TGFB1 0.026 0.022 -10000 0 -0.43 1 1
CCL5 0.009 0.085 -10000 0 -0.4 19 19
SDCBP 0.023 0.022 -10000 0 -0.4 1 1
FGFR/FGF2/Syndecan-1 -0.11 0.098 0.3 3 -0.29 31 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 -0.084 0.099 0.25 2 -0.35 12 14
Syndecan-1/Syntenin -0.097 0.098 0.28 2 -0.37 12 14
MAPK3 -0.1 0.091 0.26 2 -0.38 9 11
HGF/MET 0.029 0.056 -10000 0 -0.29 13 13
TGFB1/TGF beta receptor Type II 0.026 0.022 -10000 0 -0.42 1 1
BSG 0.026 0.02 -10000 0 -0.4 1 1
keratinocyte migration -0.083 0.098 0.25 2 -0.35 12 14
Syndecan-1/RANTES -0.11 0.1 0.27 3 -0.29 43 46
Syndecan-1/CD147 -0.1 0.1 0.36 1 -0.4 9 10
Syndecan-1/Syntenin/PIP2 -0.094 0.094 0.26 2 -0.36 12 14
LAMA5 0.017 0.042 0.36 3 -0.41 2 5
positive regulation of cell-cell adhesion -0.093 0.092 0.26 2 -0.35 12 14
MMP7 -0.41 0.11 0.36 3 -0.43 428 431
HGF 0.017 0.06 -10000 0 -0.4 9 9
Syndecan-1/CASK -0.11 0.093 0.28 2 -0.29 32 34
Syndecan-1/HGF/MET -0.1 0.1 0.24 1 -0.39 14 15
regulation of cell adhesion -0.099 0.088 0.32 1 -0.37 9 10
HPSE 0.023 0.04 -10000 0 -0.4 4 4
positive regulation of cell migration -0.11 0.098 0.3 3 -0.29 31 34
SDC1 -0.11 0.099 0.3 3 -0.3 31 34
Syndecan-1/Collagen -0.11 0.098 0.3 3 -0.29 31 34
PPIB 0.026 0.006 -10000 0 -10000 0 0
MET 0.023 0.046 0.36 1 -0.43 4 5
PRKACA 0.027 0.003 -10000 0 -10000 0 0
MMP9 -0.002 0.12 0.36 11 -0.42 27 38
MAPK1 -0.098 0.091 0.26 2 -0.38 9 11
homophilic cell adhesion -0.11 0.1 0.3 3 -0.3 32 35
MMP1 -0.26 0.22 0.36 2 -0.43 289 291
Signaling events mediated by the Hedgehog family

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
TGFB2 0.013 0.099 -10000 0 -0.47 10 10
IHH 0.019 0.085 -10000 0 -0.45 13 13
SHH Np/Cholesterol/GAS1 -0.049 0.13 0.19 2 -0.25 120 122
LRPAP1 0.026 0.005 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.048 0.13 0.25 120 -0.18 2 122
SMO/beta Arrestin2 0.018 0.09 -10000 0 -0.48 5 5
SMO 0.006 0.085 -10000 0 -0.51 5 5
AKT1 0 0.11 -10000 0 -0.4 14 14
ARRB2 0.023 0.01 -10000 0 -10000 0 0
BOC 0.019 0.059 -10000 0 -0.4 9 9
ADRBK1 0.027 0.004 -10000 0 -10000 0 0
heart looping 0.007 0.085 -10000 0 -0.5 5 5
STIL -0.017 0.11 -10000 0 -0.37 7 7
DHH N/PTCH2 0.024 0.066 -10000 0 -0.28 20 20
DHH N/PTCH1 0.021 0.091 -10000 0 -0.41 8 8
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
DHH 0.006 0.085 -10000 0 -0.4 19 19
PTHLH 0.007 0.13 -10000 0 -0.74 9 9
determination of left/right symmetry 0.007 0.085 -10000 0 -0.5 5 5
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
skeletal system development 0.008 0.13 -10000 0 -0.74 9 9
IHH N/Hhip -0.039 0.15 -10000 0 -0.32 100 100
DHH N/Hhip -0.039 0.15 -10000 0 -0.3 101 101
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.007 0.085 -10000 0 -0.5 5 5
pancreas development -0.062 0.17 -10000 0 -0.4 93 93
HHAT 0.023 0.04 -10000 0 -0.4 4 4
PI3K 0.039 0.008 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.033 0.15 -10000 0 -0.4 63 63
somite specification 0.007 0.085 -10000 0 -0.5 5 5
SHH Np/Cholesterol/PTCH1 -0.018 0.11 -10000 0 -0.36 9 9
SHH Np/Cholesterol/PTCH2 -0.02 0.1 0.19 4 -0.23 82 86
SHH Np/Cholesterol/Megalin -0.042 0.12 0.18 4 -0.25 110 114
SHH -0.041 0.12 0.27 4 -0.3 80 84
catabolic process 0.018 0.077 -10000 0 -0.4 8 8
SMO/Vitamin D3 -0.014 0.11 -10000 0 -0.44 6 6
SHH Np/Cholesterol/Hhip -0.063 0.13 0.18 4 -0.23 155 159
LRP2 -0.033 0.12 -10000 0 -0.43 40 40
receptor-mediated endocytosis -0.028 0.11 -10000 0 -0.41 10 10
SHH Np/Cholesterol/BOC -0.023 0.1 0.19 3 -0.23 86 89
SHH Np/Cholesterol/CDO -0.019 0.1 0.19 3 -0.23 81 84
mesenchymal cell differentiation 0.063 0.13 0.23 155 -0.18 4 159
mol:Vitamin D3 -0.012 0.12 -10000 0 -0.36 9 9
IHH N/PTCH2 0.031 0.058 -10000 0 -0.27 14 14
CDON 0.027 0.004 -10000 0 -10000 0 0
IHH N/PTCH1 0.026 0.08 -10000 0 -0.4 8 8
Megalin/LRPAP1 0.005 0.097 -10000 0 -0.3 40 40
PTCH2 0.025 0.022 -10000 0 -0.43 1 1
SHH Np/Cholesterol -0.029 0.094 -10000 0 -0.23 81 81
PTCH1 0.018 0.078 -10000 0 -0.4 8 8
HHIP -0.062 0.17 -10000 0 -0.4 93 93
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.026 0.11 -10000 0 -0.27 48 48
MAP4K1 -0.017 0.13 -10000 0 -0.4 46 46
MAP3K8 0.027 0.002 -10000 0 -10000 0 0
PRKCB -0.068 0.18 -10000 0 -0.4 101 101
DBNL 0.025 0.008 -10000 0 -10000 0 0
CRKL 0.026 0.006 -10000 0 -10000 0 0
MAP3K1 -0.012 0.1 -10000 0 -0.34 31 31
JUN -0.13 0.28 -10000 0 -0.6 112 112
MAP3K7 -0.011 0.1 -10000 0 -0.33 31 31
GRAP2 0.012 0.074 -10000 0 -0.4 14 14
CRK 0.023 0.01 -10000 0 -10000 0 0
MAP2K4 -0.019 0.12 0.23 1 -0.37 33 34
LAT 0.024 0.035 -10000 0 -0.4 3 3
LCP2 0.023 0.04 -10000 0 -0.4 4 4
MAPK8 -0.13 0.3 -10000 0 -0.63 113 113
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.007 0.11 -10000 0 -0.35 32 32
LAT/GRAP2/SLP76/HPK1/HIP-55 0.032 0.11 -10000 0 -0.39 11 11
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.01 0.063 -10000 0 -0.25 25 25
EPHB2 0.023 0.031 -10000 0 -0.43 2 2
Syndecan-2/TACI -0.057 0.11 -10000 0 -0.23 134 134
LAMA1 -0.058 0.16 -10000 0 -0.4 85 85
Syndecan-2/alpha2 ITGB1 0.041 0.031 -10000 0 -0.22 1 1
HRAS 0.026 0.02 -10000 0 -0.4 1 1
Syndecan-2/CASK 0.008 0.003 -10000 0 -10000 0 0
ITGA5 0.024 0.037 -10000 0 -0.43 3 3
BAX 0.006 0.003 -10000 0 -10000 0 0
EPB41 0.025 0.007 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.022 0.015 -10000 0 -0.2 1 1
LAMA3 0.019 0.036 -10000 0 -0.4 3 3
EZR 0.027 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.021 0.051 -10000 0 -0.42 6 6
Syndecan-2/MMP2 0.022 0.03 -10000 0 -0.24 5 5
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.039 0.007 -10000 0 -10000 0 0
dendrite morphogenesis 0.022 0.022 -10000 0 -0.25 2 2
Syndecan-2/GM-CSF -0.064 0.14 -10000 0 -0.25 150 150
determination of left/right symmetry 0.011 0.004 -10000 0 -10000 0 0
Syndecan-2/PKC delta 0.025 0.011 -10000 0 -10000 0 0
GNB2L1 0.027 0.003 -10000 0 -10000 0 0
MAPK3 -0.054 0.14 0.19 39 -0.23 148 187
MAPK1 -0.053 0.13 0.19 39 -0.23 148 187
Syndecan-2/RACK1 0.035 0.02 -10000 0 -0.2 1 1
NF1 0.026 0.005 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.011 0.004 -10000 0 -10000 0 0
ITGA2 0.027 0.004 -10000 0 -10000 0 0
MAPK8 0.01 0.004 -10000 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin 0.001 0.089 -10000 0 -10000 0 0
Syndecan-2/Kininogen -0.027 0.1 -10000 0 -0.23 88 88
ITGB1 0.027 0.002 -10000 0 -10000 0 0
SRC 0.018 0.04 0.18 22 -10000 0 22
Syndecan-2/CASK/Protein 4.1 0.022 0.011 -10000 0 -10000 0 0
extracellular matrix organization 0.024 0.017 -10000 0 -0.25 1 1
actin cytoskeleton reorganization 0.01 0.063 -10000 0 -0.25 25 25
Syndecan-2/Caveolin-2/Ras 0.034 0.033 -10000 0 -0.22 5 5
Syndecan-2/Laminin alpha3 0.02 0.019 -10000 0 -0.25 1 1
Syndecan-2/RasGAP 0.045 0.025 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.038 0.028 -10000 0 -0.3 3 3
PRKCD 0.027 0.004 -10000 0 -10000 0 0
Syndecan-2 dimer 0.022 0.022 -10000 0 -0.25 2 2
GO:0007205 0.002 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.021 0.023 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
SDCBP 0.023 0.022 -10000 0 -0.4 1 1
TNFRSF13B -0.13 0.19 -10000 0 -0.4 152 152
RASA1 0.026 0.005 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.039 0.007 -10000 0 -10000 0 0
Syndecan-2/Synbindin 0.025 0.011 -10000 0 -10000 0 0
TGFB1 0.026 0.022 -10000 0 -0.43 1 1
CASP3 0.037 0.06 0.19 57 -10000 0 57
FN1 -0.001 0.11 -10000 0 -0.42 28 28
Syndecan-2/IL8 -0.11 0.15 -10000 0 -0.25 226 226
SDC2 0.011 0.005 -10000 0 -10000 0 0
KNG1 -0.078 0.17 -10000 0 -0.4 101 101
Syndecan-2/Neurofibromin 0.025 0.011 -10000 0 -10000 0 0
TRAPPC4 0.027 0.004 -10000 0 -10000 0 0
CSF2 -0.15 0.22 -10000 0 -0.43 172 172
Syndecan-2/TGFB1 0.024 0.017 -10000 0 -0.25 1 1
Syndecan-2/Syntenin/PI-4-5-P2 0.022 0.015 -10000 0 -0.21 1 1
Syndecan-2/Ezrin 0.038 0.017 -10000 0 -10000 0 0
PRKACA 0.038 0.06 0.19 58 -10000 0 58
angiogenesis -0.11 0.15 -10000 0 -0.25 226 226
MMP2 0.021 0.05 -10000 0 -0.41 6 6
IL8 -0.24 0.23 0.36 1 -0.43 259 260
calcineurin-NFAT signaling pathway -0.057 0.11 -10000 0 -0.23 134 134
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.034 0.051 -10000 0 -0.21 18 18
RGS9BP 0.021 0.031 0.36 1 -0.43 1 2
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 -0.011 0.031 -10000 0 -0.43 2 2
mol:Na + -0.052 0.13 0.23 5 -0.24 130 135
mol:ADP -0.013 0.034 -10000 0 -0.39 3 3
GNAT2 0.015 0.057 -10000 0 -0.43 7 7
RGS9-1/Gbeta5/R9AP 0.006 0.1 0.25 1 -0.23 68 69
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.023 0.039 -10000 0 -0.26 8 8
GRK7 0.009 0.036 -10000 0 -0.43 2 2
CNGB3 -0.013 0.093 0.36 7 -0.43 16 23
Cone Metarhodopsin II/X-Arrestin 0.013 0.021 -10000 0 -0.3 2 2
mol:Ca2+ -0.068 0.14 0.18 40 -0.24 150 190
Cone PDE6 0.02 0.1 0.25 1 -0.23 1 2
Cone Metarhodopsin II 0.019 0.03 -10000 0 -0.3 3 3
Na + (4 Units) -0.057 0.14 0.22 6 -0.24 151 157
GNAT2/GDP 0.013 0.097 0.24 1 -0.2 64 65
GNB5 0.026 0.006 -10000 0 -10000 0 0
mol:GMP (4 units) -0.017 0.033 0.18 2 -0.24 8 10
Cone Transducin 0.037 0.055 -10000 0 -0.22 18 18
SLC24A2 -0.029 0.13 0.36 3 -0.43 40 43
GNB3/GNGT2 0.031 0.051 -10000 0 -0.29 11 11
GNB3 0.023 0.042 -10000 0 -0.42 4 4
GNAT2/GTP 0.014 0.04 -10000 0 -0.3 7 7
CNGA3 -0.11 0.19 -10000 0 -0.4 137 137
ARR3 -0.008 0.034 -10000 0 -0.43 2 2
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel -0.052 0.13 0.23 5 -0.24 130 135
mol:Pi 0.006 0.1 0.25 1 -0.23 68 69
Cone CNG Channel -0.036 0.12 -10000 0 -0.25 24 24
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + -0.029 0.13 0.36 3 -0.42 40 43
RGS9 -0.039 0.15 -10000 0 -0.4 68 68
PDE6C -0.005 0.02 -10000 0 -10000 0 0
GNGT2 0.02 0.053 -10000 0 -0.4 7 7
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H -0.015 0.023 -10000 0 -0.43 1 1
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 -0.03 0.16 0.23 1 -0.43 36 37
PTK2B 0.02 0.023 -10000 0 -0.4 1 1
mol:Ca2+ -0.016 0.25 -10000 0 -0.87 29 29
EDN1 0.016 0.12 -10000 0 -0.29 22 22
EDN3 -0.12 0.19 -10000 0 -0.4 145 145
EDN2 -0.095 0.19 -10000 0 -0.4 127 127
HRAS/GDP 0 0.15 0.29 2 -0.43 18 20
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.011 0.11 -10000 0 -0.39 14 14
ADCY4 -0.043 0.13 -10000 0 -0.39 35 35
ADCY5 -0.12 0.17 -10000 0 -0.4 88 88
ADCY6 -0.044 0.14 -10000 0 -0.39 36 36
ADCY7 -0.043 0.14 -10000 0 -0.39 36 36
ADCY1 -0.045 0.14 0.39 1 -0.4 35 36
ADCY2 -0.059 0.15 -10000 0 -0.41 48 48
ADCY3 -0.044 0.13 -10000 0 -0.38 36 36
ADCY8 -0.044 0.13 0.22 1 -0.39 28 29
ADCY9 -0.044 0.14 -10000 0 -0.39 36 36
arachidonic acid secretion -0.023 0.16 0.26 3 -0.47 27 30
ETB receptor/Endothelin-1/Gq/GTP 0.006 0.077 -10000 0 -0.32 13 13
GNAO1 -0.087 0.19 -10000 0 -0.4 121 121
HRAS 0.026 0.02 -10000 0 -0.4 1 1
ETA receptor/Endothelin-1/G12/GTP 0.056 0.2 0.29 4 -0.4 32 36
ETA receptor/Endothelin-1/Gs/GTP 0.032 0.2 0.3 2 -0.4 37 39
mol:GTP 0.001 0.004 -10000 0 -10000 0 0
COL3A1 -0.034 0.18 -10000 0 -0.45 41 41
EDNRB 0.005 0.076 -10000 0 -0.39 14 14
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.041 0.19 0.25 1 -0.55 39 40
CYSLTR1 -0.074 0.24 -10000 0 -0.55 82 82
SLC9A1 -0.009 0.1 -10000 0 -0.26 40 40
mol:GDP -0.011 0.15 0.23 9 -0.43 23 32
SLC9A3 -0.25 0.33 -10000 0 -0.65 121 121
RAF1 -0.014 0.13 0.27 3 -0.52 9 12
JUN 0.007 0.16 -10000 0 -0.61 11 11
JAK2 -0.032 0.17 0.22 2 -0.42 39 41
mol:IP3 0.021 0.11 0.21 8 -0.5 6 14
ETA receptor/Endothelin-1 0.042 0.25 0.34 4 -0.46 46 50
PLCB1 0.024 0.03 0.36 3 -10000 0 3
PLCB2 0.026 0.007 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.091 0.17 -10000 0 -0.31 148 148
FOS -0.014 0.16 -10000 0 -0.87 9 9
Gai/GDP -0.16 0.34 -10000 0 -0.68 127 127
CRK 0.023 0.01 -10000 0 -10000 0 0
mol:Ca ++ -0.007 0.16 0.23 5 -0.43 28 33
BCAR1 0.026 0.02 -10000 0 -0.4 1 1
PRKCB1 0.018 0.11 0.2 8 -0.53 5 13
GNAQ 0.025 0.023 -10000 0 -0.4 1 1
GNAZ 0.021 0.045 -10000 0 -0.4 5 5
GNAL 0.007 0.078 -10000 0 -0.4 16 16
Gs family/GDP -0.014 0.14 0.29 1 -0.4 25 26
ETA receptor/Endothelin-1/Gq/GTP 0.006 0.12 0.24 1 -0.46 8 9
MAPK14 0.009 0.077 0.23 3 -0.47 4 7
TRPC6 -0.021 0.26 -10000 0 -0.94 29 29
GNAI2 0.027 0.004 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNAI1 0.014 0.071 -10000 0 -0.4 13 13
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.011 0.078 -10000 0 -0.33 10 10
ETB receptor/Endothelin-2 -0.045 0.13 -10000 0 -0.28 101 101
ETB receptor/Endothelin-3 -0.079 0.14 -10000 0 -0.29 135 135
ETB receptor/Endothelin-1 0.016 0.11 -10000 0 -0.36 15 15
MAPK3 -0.011 0.14 0.3 1 -0.67 10 11
MAPK1 -0.017 0.16 -10000 0 -0.79 10 10
Rac1/GDP -0.006 0.14 0.29 2 -0.43 18 20
cAMP biosynthetic process -0.087 0.15 0.24 1 -0.41 47 48
MAPK8 0.003 0.19 -10000 0 -0.62 27 27
SRC 0.017 0.013 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.046 0.14 -10000 0 -0.33 62 62
p130Cas/CRK/Src/PYK2 -0.013 0.19 0.29 11 -0.56 25 36
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.006 0.14 0.25 5 -0.42 19 24
COL1A2 -0.001 0.18 0.34 1 -0.43 32 33
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.078 0.19 -10000 0 -0.32 143 143
mol:DAG 0.021 0.11 0.21 8 -0.5 6 14
MAP2K2 -0.015 0.13 0.27 2 -0.55 11 13
MAP2K1 -0.014 0.13 0.26 3 -0.55 11 14
EDNRA -0.009 0.16 -10000 0 -0.39 44 44
positive regulation of muscle contraction -0.009 0.15 0.25 28 -0.38 30 58
Gq family/GDP 0.001 0.13 -10000 0 -0.54 7 7
HRAS/GTP -0.015 0.13 0.25 2 -0.42 16 18
PRKCH 0.016 0.1 0.2 7 -0.53 5 12
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCA 0.02 0.11 0.22 11 -0.53 5 16
PRKCB -0.018 0.15 0.2 8 -0.39 34 42
PRKCE 0.018 0.11 0.2 7 -0.53 5 12
PRKCD 0.016 0.11 0.2 8 -0.59 4 12
PRKCG -0.046 0.15 0.22 9 -0.42 21 30
regulation of vascular smooth muscle contraction -0.018 0.18 -10000 0 -1 9 9
PRKCQ 0.016 0.11 0.2 7 -0.48 7 14
PLA2G4A -0.027 0.17 0.26 3 -0.51 27 30
GNA14 0.024 0.031 -10000 0 -0.4 2 2
GNA15 0.021 0.049 -10000 0 -0.42 5 5
GNA12 0.025 0.008 -10000 0 -10000 0 0
GNA11 0.024 0.03 -10000 0 -0.4 2 2
Rac1/GTP 0.056 0.2 0.3 3 -0.4 31 34
MMP1 -0.19 0.18 0.29 2 -0.33 232 234
LPA receptor mediated 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
GNB1/GNG2 0.003 0.11 -10000 0 -0.24 67 67
NF kappa B1 p50/RelA/I kappa B alpha -0.01 0.095 0.33 1 -0.36 3 4
AP1 -0.038 0.093 -10000 0 -0.35 9 9
mol:PIP3 -0.027 0.081 -10000 0 -0.33 8 8
AKT1 0.002 0.082 0.24 2 -0.39 3 5
PTK2B -0.053 0.11 0.22 1 -0.34 33 34
RHOA 0.006 0.066 0.22 3 -0.34 9 12
PIK3CB 0.027 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.003 0.055 -10000 0 -0.26 1 1
MAGI3 0.025 0.021 -10000 0 -0.4 1 1
RELA 0.027 0.004 -10000 0 -10000 0 0
apoptosis -0.035 0.11 -10000 0 -0.24 88 88
HRAS/GDP 0.019 0.014 -10000 0 -0.28 1 1
positive regulation of microtubule depolymerization -0.084 0.13 0.2 3 -0.35 53 56
NF kappa B1 p50/RelA -0.039 0.09 -10000 0 -0.39 7 7
endothelial cell migration -0.02 0.099 -10000 0 -0.25 66 66
ADCY4 -0.08 0.18 -10000 0 -0.45 73 73
ADCY5 -0.16 0.24 -10000 0 -0.5 121 121
ADCY6 -0.077 0.18 -10000 0 -0.46 68 68
ADCY7 -0.075 0.18 -10000 0 -0.46 66 66
ADCY1 -0.077 0.17 -10000 0 -0.45 68 68
ADCY2 -0.094 0.2 -10000 0 -0.48 82 82
ADCY3 -0.076 0.18 -10000 0 -0.46 68 68
ADCY8 -0.075 0.17 -10000 0 -0.45 65 65
ADCY9 -0.076 0.18 -10000 0 -0.45 69 69
GSK3B -0.051 0.11 0.2 1 -0.33 30 31
arachidonic acid secretion -0.092 0.19 -10000 0 -0.45 77 77
GNG2 0.009 0.08 -10000 0 -0.39 17 17
TRIP6 0.012 0.02 -10000 0 -0.32 1 1
GNAO1 -0.079 0.16 -10000 0 -0.29 142 142
HRAS 0.026 0.02 -10000 0 -0.4 1 1
NFKBIA -0.028 0.093 0.34 1 -0.33 12 13
GAB1 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.078 0.31 -10000 0 -0.85 62 62
JUN 0.026 0.005 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.035 0.023 -10000 0 -0.24 2 2
TIAM1 -0.11 0.36 -10000 0 -1 62 62
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
mol:IP3 -0.013 0.05 -10000 0 -0.27 1 1
PLCB3 0.015 0.021 0.18 2 -0.22 2 4
FOS 0.022 0.035 -10000 0 -0.4 3 3
positive regulation of mitosis -0.092 0.19 -10000 0 -0.45 77 77
LPA/LPA1-2-3 -0.008 0.12 -10000 0 -0.22 93 93
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade -0.001 0.001 -10000 0 -10000 0 0
BCAR1 0.026 0.02 -10000 0 -0.4 1 1
stress fiber formation -0.033 0.099 0.23 1 -0.3 27 28
GNAZ -0.019 0.093 -10000 0 -0.24 64 64
EGFR/PI3K-beta/Gab1 -0.017 0.089 -10000 0 -0.34 8 8
positive regulation of dendritic cell cytokine production -0.009 0.11 -10000 0 -0.22 93 93
LPA/LPA2/MAGI-3 0.035 0.023 -10000 0 -0.24 2 2
ARHGEF1 0.006 0.097 0.28 4 -0.37 2 6
GNAI2 -0.015 0.087 -10000 0 -0.23 59 59
GNAI3 -0.018 0.089 -10000 0 -0.23 63 63
GNAI1 -0.023 0.1 -10000 0 -0.26 67 67
LPA/LPA3 -0.005 0.08 -10000 0 -0.28 35 35
LPA/LPA2 0.02 0.019 -10000 0 -0.3 1 1
LPA/LPA1 -0.019 0.11 -10000 0 -0.27 67 67
HB-EGF/EGFR 0.003 0.073 0.2 10 -0.26 27 37
HBEGF -0.006 0.088 0.27 11 -0.3 29 40
mol:DAG -0.013 0.05 -10000 0 -0.27 1 1
cAMP biosynthetic process -0.1 0.19 0.32 1 -0.44 85 86
NFKB1 0.027 0.004 -10000 0 -10000 0 0
SRC 0.017 0.013 -10000 0 -10000 0 0
GNB1 0.026 0.007 -10000 0 -10000 0 0
LYN -0.009 0.096 0.3 2 -0.37 6 8
GNAQ -0.003 0.063 -10000 0 -0.21 35 35
LPAR2 0.026 0.022 -10000 0 -0.42 1 1
LPAR3 -0.015 0.11 -10000 0 -0.4 35 35
LPAR1 -0.031 0.15 -10000 0 -0.39 63 63
IL8 -0.09 0.14 0.32 2 -0.37 16 18
PTK2 -0.027 0.089 -10000 0 -0.37 7 7
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
CASP3 -0.035 0.11 -10000 0 -0.24 88 88
EGFR 0.023 0.021 -10000 0 -0.4 1 1
PLCG1 -0.01 0.06 -10000 0 -0.22 30 30
PLD2 -0.033 0.094 0.19 2 -0.36 8 10
G12/G13 0.015 0.091 -10000 0 -0.21 56 56
PI3K-beta -0.011 0.08 -10000 0 -0.37 8 8
cell migration -0.017 0.11 -10000 0 -0.25 58 58
SLC9A3R2 0.026 0.02 -10000 0 -0.4 1 1
PXN -0.033 0.1 0.23 1 -0.3 27 28
HRAS/GTP -0.094 0.2 -10000 0 -0.47 77 77
RAC1 0.025 0.008 -10000 0 -10000 0 0
MMP9 -0.003 0.12 0.36 11 -0.42 27 38
PRKCE 0.027 0.003 -10000 0 -10000 0 0
PRKCD -0.005 0.058 0.31 2 -10000 0 2
Gi(beta/gamma) -0.084 0.19 -10000 0 -0.42 83 83
mol:LPA 0.001 0.014 -10000 0 -0.15 1 1
TRIP6/p130 Cas/FAK1/Paxillin 0.002 0.11 -10000 0 -0.38 9 9
MAPKKK cascade -0.092 0.19 -10000 0 -0.45 77 77
contractile ring contraction involved in cytokinesis 0.007 0.066 0.22 3 -0.34 9 12
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.004 0.065 -10000 0 -0.22 33 33
GNA15 -0.004 0.064 -10000 0 -0.22 31 31
GNA12 0.025 0.008 -10000 0 -10000 0 0
GNA13 0.027 0.004 -10000 0 -10000 0 0
MAPT -0.086 0.13 0.21 2 -0.36 53 55
GNA11 -0.004 0.063 -10000 0 -0.22 32 32
Rac1/GTP -0.084 0.33 -10000 0 -0.9 62 62
MMP2 -0.02 0.1 -10000 0 -0.25 66 66
IGF1 pathway

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
NCK2 0.027 0.001 -10000 0 -10000 0 0
PTK2 0.023 0.01 -10000 0 -10000 0 0
CRKL -0.035 0.092 -10000 0 -0.2 102 102
GRB2/SOS1/SHC 0.053 0.013 -10000 0 -10000 0 0
HRAS 0.026 0.02 -10000 0 -0.4 1 1
IRS1/Crk -0.031 0.097 -10000 0 -0.2 104 104
IGF-1R heterotetramer/IGF1/PTP1B -0.011 0.093 -10000 0 -0.22 67 67
AKT1 -0.05 0.074 0.17 1 -10000 0 1
BAD -0.05 0.071 0.16 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.027 0.084 -10000 0 -0.2 82 82
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.027 0.1 -10000 0 -0.2 111 111
RAF1 -0.033 0.088 -10000 0 -0.45 5 5
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.002 0.11 -10000 0 -0.2 97 97
YWHAZ 0.023 0.01 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.029 0.11 -10000 0 -0.22 112 112
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
RPS6KB1 -0.05 0.075 0.17 1 -10000 0 1
GNB2L1 0.027 0.003 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.015 0.082 0.26 2 -0.38 2 4
PXN 0.027 0.002 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.039 0.007 -10000 0 -10000 0 0
HRAS/GTP -0.019 0.091 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.015 0.11 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.005 0.04 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.014 0.11 -10000 0 -0.2 112 112
Crk/p130 Cas/Paxillin 0 0.11 -10000 0 -10000 0 0
IGF1R 0.005 0.04 -10000 0 -10000 0 0
IGF1 -0.082 0.19 -10000 0 -0.41 112 112
IRS2/Crk -0.022 0.082 -10000 0 -0.2 64 64
PI3K -0.002 0.11 -10000 0 -10000 0 0
apoptosis 0.038 0.062 -10000 0 -10000 0 0
HRAS/GDP 0.019 0.014 -10000 0 -0.28 1 1
PRKCD -0.063 0.14 -10000 0 -0.31 104 104
RAF1/14-3-3 E -0.018 0.083 -10000 0 -0.38 6 6
BAD/14-3-3 -0.04 0.065 -10000 0 -10000 0 0
PRKCZ -0.05 0.074 0.17 1 -10000 0 1
Crk/p130 Cas/Paxillin/FAK1 -0.013 0.08 -10000 0 -10000 0 0
PTPN1 0.016 0.013 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.062 0.15 -10000 0 -0.32 112 112
BCAR1 0.026 0.02 -10000 0 -0.4 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 0 0.11 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.027 0.002 -10000 0 -10000 0 0
IRS1/NCK2 -0.027 0.1 -10000 0 -0.2 112 112
GRB10 0.025 0.008 -10000 0 -10000 0 0
PTPN11 -0.039 0.095 -10000 0 -0.2 111 111
IRS1 -0.043 0.1 -10000 0 -0.22 112 112
IRS2 -0.029 0.084 -10000 0 -0.2 84 84
IGF-1R heterotetramer/IGF1 -0.045 0.14 -10000 0 -0.3 112 112
GRB2 0.027 0.004 -10000 0 -10000 0 0
PDPK1 -0.037 0.087 0.17 1 -10000 0 1
YWHAE 0.023 0.01 -10000 0 -10000 0 0
PRKD1 -0.064 0.14 0.2 1 -0.31 104 105
SHC1 0.027 0.004 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.004 0.16 0.28 6 -0.49 35 41
FYN -0.033 0.2 0.26 2 -0.58 42 44
LAT/GRAP2/SLP76 -0.011 0.17 0.2 1 -0.52 37 38
IKBKB 0.024 0.009 -10000 0 -10000 0 0
AKT1 -0.025 0.14 0.17 2 -0.42 43 45
B2M 0.024 0.022 -10000 0 -0.4 1 1
IKBKG -0.002 0.049 0.091 22 -0.15 19 41
MAP3K8 0.027 0.002 -10000 0 -10000 0 0
mol:Ca2+ -0.02 0.035 0.088 5 -0.11 50 55
integrin-mediated signaling pathway 0.031 0.029 -10000 0 -0.23 5 5
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.041 0.2 0.2 1 -0.61 42 43
TRPV6 -0.015 0.25 1.1 15 -0.42 49 64
CD28 0.01 0.084 -10000 0 -0.4 18 18
SHC1 -0.033 0.2 0.28 7 -0.56 42 49
receptor internalization -0.041 0.22 -10000 0 -0.62 44 44
PRF1 -0.037 0.24 -10000 0 -0.77 33 33
KRAS 0.027 0.003 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
COT/AKT1 -0.009 0.12 0.16 2 -0.34 40 42
LAT -0.037 0.19 0.19 3 -0.56 44 47
EntrezGene:6955 0 0.002 -10000 0 -10000 0 0
CD3D 0.015 0.073 -10000 0 -0.4 13 13
CD3E 0.012 0.08 -10000 0 -0.4 16 16
CD3G -0.007 0.12 -10000 0 -0.4 36 36
RASGRP2 -0.01 0.054 -10000 0 -0.17 42 42
RASGRP1 -0.005 0.15 0.2 7 -0.43 38 45
HLA-A 0 0.003 -10000 0 -10000 0 0
RASSF5 0.022 0.045 -10000 0 -0.4 5 5
RAP1A/GTP/RAPL 0.032 0.029 -10000 0 -0.23 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.017 0.059 0.1 42 -0.12 30 72
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.021 0.069 -10000 0 -0.22 33 33
PRKCA 0.018 0.098 0.13 107 -0.26 27 134
GRAP2 0.012 0.074 -10000 0 -0.4 14 14
mol:IP3 -0.009 0.14 0.2 44 -0.41 30 74
EntrezGene:6957 0 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.033 0.18 -10000 0 -0.57 39 39
ORAI1 -0.004 0.2 0.36 1 -0.96 15 16
CSK -0.032 0.19 0.19 1 -0.56 43 44
B7 family/CD28 -0.008 0.21 -10000 0 -0.62 38 38
CHUK 0.026 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.041 0.22 0.19 1 -0.64 44 45
PTPN6 -0.037 0.19 0.2 5 -0.56 44 49
VAV1 -0.042 0.2 0.22 2 -0.59 44 46
Monovalent TCR/CD3 -0.02 0.15 -10000 0 -0.41 45 45
CBL 0.027 0.004 -10000 0 -10000 0 0
LCK -0.037 0.2 0.23 2 -0.56 46 48
PAG1 -0.022 0.2 0.2 41 -0.55 43 84
RAP1A 0.026 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.04 0.22 0.19 1 -0.63 44 45
CD80 0.025 0.029 -10000 0 -0.4 2 2
CD86 0.018 0.063 -10000 0 -0.4 10 10
PDK1/CARD11/BCL10/MALT1 -0.016 0.087 -10000 0 -0.27 34 34
HRAS 0.026 0.02 -10000 0 -0.4 1 1
GO:0035030 -0.031 0.16 0.16 1 -0.5 40 41
CD8A -0.004 0.11 -10000 0 -0.4 33 33
CD8B 0.014 0.075 -10000 0 -0.4 14 14
PTPRC -0.008 0.12 -10000 0 -0.4 36 36
PDK1/PKC theta -0.023 0.17 0.21 4 -0.5 40 44
CSK/PAG1 -0.019 0.19 0.19 41 -0.58 36 77
SOS1 0.027 0.002 -10000 0 -10000 0 0
peptide-MHC class I 0.017 0.018 -10000 0 -0.28 1 1
GRAP2/SLP76 -0.014 0.2 -10000 0 -0.6 39 39
STIM1 0.015 0.12 1.2 4 -10000 0 4
RAS family/GTP 0.021 0.069 0.14 16 -0.17 24 40
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.045 0.24 -10000 0 -0.67 44 44
mol:DAG -0.024 0.11 -10000 0 -0.36 33 33
RAP1A/GDP 0.011 0.028 0.064 15 -0.064 12 27
PLCG1 0.016 0.013 -10000 0 -10000 0 0
CD247 0.014 0.072 -10000 0 -0.4 13 13
cytotoxic T cell degranulation -0.034 0.22 -10000 0 -0.73 33 33
RAP1A/GTP -0.004 0.02 -10000 0 -0.064 42 42
mol:PI-3-4-5-P3 -0.029 0.17 0.18 3 -0.49 42 45
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.012 0.17 0.22 41 -0.53 30 71
NRAS 0.024 0.029 -10000 0 -0.4 2 2
ZAP70 0.015 0.072 -10000 0 -0.4 13 13
GRB2/SOS1 0.039 0.007 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.021 0.17 0.21 1 -0.52 37 38
MALT1 0.02 0.023 -10000 0 -0.4 1 1
TRAF6 0.027 0.003 -10000 0 -10000 0 0
CD8 heterodimer 0.009 0.11 -10000 0 -0.34 39 39
CARD11 0.002 0.1 0.36 2 -0.41 25 27
PRKCB -0.005 0.12 0.15 27 -0.3 47 74
PRKCE 0.019 0.1 0.13 111 -0.26 29 140
PRKCQ -0.027 0.19 0.2 3 -0.57 40 43
LCP2 0.023 0.04 -10000 0 -0.4 4 4
BCL10 0.025 0.021 -10000 0 -0.4 1 1
regulation of survival gene product expression -0.019 0.12 0.16 3 -0.36 42 45
IKK complex 0.021 0.066 0.11 109 -0.12 25 134
RAS family/GDP -0.003 0.012 -10000 0 -0.062 1 1
MAP3K14 -0.009 0.091 0.13 3 -0.26 37 40
PDPK1 -0.022 0.13 0.17 4 -0.4 39 43
TCR/CD3/MHC I/CD8/Fyn -0.045 0.23 -10000 0 -0.66 43 43
Effects of Botulinum toxin

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
STX1A -0.007 0.071 0.27 3 -0.3 23 26
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.033 0.033 -10000 0 -0.3 4 4
STXBP1 0.022 0.048 -10000 0 -0.43 5 5
ACh/CHRNA1 -0.041 0.095 -10000 0 -0.22 65 65
RAB3GAP2/RIMS1/UNC13B 0.046 0.035 -10000 0 -0.25 5 5
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 0.006 0.051 -10000 0 -0.43 5 5
mol:ACh -0.037 0.066 0.078 35 -0.12 147 182
RAB3GAP2 0.026 0.02 -10000 0 -0.4 1 1
STX1A/SNAP25/VAMP2 -0.034 0.11 -10000 0 -0.24 32 32
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.041 0.095 -10000 0 -0.22 65 65
UNC13B 0.027 0.004 -10000 0 -10000 0 0
CHRNA1 -0.012 0.12 -10000 0 -0.4 41 41
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.051 0.11 -10000 0 -0.25 80 80
SNAP25 -0.069 0.11 0.19 1 -0.25 130 131
VAMP2 0.004 0.002 -10000 0 -10000 0 0
SYT1 -0.031 0.14 -10000 0 -0.4 61 61
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.009 0.067 0.2 3 -0.25 26 29
STX1A/SNAP25 fragment 1/VAMP2 -0.034 0.11 -10000 0 -0.24 32 32
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.024 0.094 -10000 0 -0.23 41 41
ER alpha/Gai/GDP/Gbeta gamma -0.12 0.27 -10000 0 -0.63 75 75
AKT1 -0.062 0.28 -10000 0 -0.82 52 52
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.062 0.29 -10000 0 -0.84 52 52
mol:Ca2+ 0.024 0.063 -10000 0 -0.4 2 2
IGF1R 0.026 0.006 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.013 0.075 -10000 0 -0.23 38 38
SHC1 0.027 0.004 -10000 0 -10000 0 0
apoptosis 0.059 0.27 0.78 52 -10000 0 52
RhoA/GTP 0.006 0.059 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.035 0.22 -10000 0 -0.52 57 57
regulation of stress fiber formation 0.019 0.054 0.29 2 -10000 0 2
E2/ERA-ERB (dimer) 0.008 0.08 -10000 0 -0.24 42 42
KRAS 0.027 0.003 -10000 0 -10000 0 0
G13/GTP 0.012 0.068 -10000 0 -0.21 38 38
pseudopodium formation -0.019 0.054 -10000 0 -0.29 2 2
E2/ER alpha (dimer)/PELP1 0.008 0.073 -10000 0 -0.22 39 39
GRB2 0.027 0.004 -10000 0 -10000 0 0
GNG2 0.009 0.081 -10000 0 -0.4 17 17
GNAO1 -0.087 0.19 -10000 0 -0.4 121 121
HRAS 0.026 0.02 -10000 0 -0.4 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.077 0.24 0.24 1 -0.6 61 62
E2/ER beta (dimer) 0.016 0.028 -10000 0 -0.28 4 4
mol:GDP -0.018 0.1 -10000 0 -0.33 40 40
mol:NADP -0.077 0.24 0.24 1 -0.6 61 62
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 0.006 0.039 -10000 0 -0.41 2 2
IGF-1R heterotetramer 0.026 0.006 -10000 0 -10000 0 0
PLCB1 0.008 0.048 -10000 0 -0.44 3 3
PLCB2 0.007 0.054 -10000 0 -0.47 4 4
IGF1 -0.079 0.18 -10000 0 -0.4 112 112
mol:L-citrulline -0.077 0.24 0.24 1 -0.6 61 62
RHOA 0.027 0.004 -10000 0 -10000 0 0
Gai/GDP -0.17 0.34 -10000 0 -0.69 127 127
JNK cascade 0.016 0.028 -10000 0 -0.28 4 4
BCAR1 0.026 0.02 -10000 0 -0.4 1 1
ESR2 0.021 0.041 -10000 0 -0.4 4 4
GNAQ 0.026 0.02 -10000 0 -0.4 1 1
ESR1 -0.012 0.12 -10000 0 -0.4 39 39
Gq family/GDP/Gbeta gamma -0.004 0.14 -10000 0 -0.67 13 13
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.007 0.14 -10000 0 -0.6 12 12
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.032 0.22 -10000 0 -0.52 56 56
GNAZ 0.021 0.045 -10000 0 -0.4 5 5
E2/ER alpha (dimer) -0.006 0.083 -10000 0 -0.28 39 39
STRN 0.027 0.003 -10000 0 -10000 0 0
GNAL 0.007 0.078 -10000 0 -0.4 16 16
PELP1 0.023 0.01 -10000 0 -10000 0 0
MAPK11 0.009 0.03 -10000 0 -0.24 6 6
GNAI2 0.027 0.004 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNAI1 0.014 0.071 -10000 0 -0.4 13 13
HBEGF -0.008 0.26 0.3 104 -0.55 53 157
cAMP biosynthetic process -0.002 0.076 -10000 0 -0.2 51 51
SRC -0.056 0.26 0.21 79 -0.58 63 142
PI3K 0.039 0.008 -10000 0 -10000 0 0
GNB1 0.026 0.007 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.005 0.11 -10000 0 -0.32 36 36
SOS1 0.027 0.002 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.093 0.18 -10000 0 -0.43 80 80
Gs family/GTP 0.003 0.08 -10000 0 -0.2 51 51
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.048 0.025 -10000 0 -0.21 3 3
vasodilation -0.072 0.22 0.23 1 -0.57 61 62
mol:DAG 0.006 0.039 -10000 0 -0.41 2 2
Gs family/GDP/Gbeta gamma -0.019 0.11 -10000 0 -0.32 39 39
MSN -0.02 0.056 -10000 0 -0.32 2 2
Gq family/GTP 0.014 0.06 -10000 0 -0.49 4 4
mol:PI-3-4-5-P3 -0.058 0.27 -10000 0 -0.8 52 52
NRAS 0.024 0.029 -10000 0 -0.4 2 2
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.072 0.22 0.57 61 -0.23 1 62
GRB2/SOS1 0.039 0.007 -10000 0 -10000 0 0
RhoA/GDP -0.003 0.11 -10000 0 -0.31 40 40
NOS3 -0.083 0.25 0.24 1 -0.64 61 62
GNA11 0.025 0.028 -10000 0 -0.4 2 2
MAPKKK cascade -0.036 0.23 0.24 1 -0.61 52 53
E2/ER alpha (dimer)/PELP1/Src -0.035 0.23 0.27 6 -0.53 59 65
ruffle organization -0.019 0.054 -10000 0 -0.29 2 2
ROCK2 -0.019 0.061 -10000 0 -0.34 2 2
GNA14 0.025 0.028 -10000 0 -0.4 2 2
GNA15 0.022 0.048 -10000 0 -0.43 5 5
GNA13 0.027 0.004 -10000 0 -10000 0 0
MMP9 -0.012 0.26 0.37 84 -0.55 50 134
MMP2 -0.053 0.25 0.27 7 -0.57 60 67
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.014 0.1 -10000 0 -0.31 31 31
alphaM/beta2 Integrin/GPIbA 0.007 0.095 -10000 0 -0.29 32 32
alphaM/beta2 Integrin/proMMP-9 -0.001 0.1 0.25 11 -0.28 42 53
PLAUR 0.027 0.003 -10000 0 -10000 0 0
HMGB1 0.014 0.023 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.017 0.094 -10000 0 -0.3 27 27
AGER 0.017 0.034 -10000 0 -0.47 1 1
RAP1A 0.026 0.005 -10000 0 -10000 0 0
SELPLG 0.024 0.035 -10000 0 -0.4 3 3
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.014 0.1 -10000 0 -0.41 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.002 0.12 0.36 11 -0.42 27 38
CYR61 0.022 0.043 -10000 0 -0.43 4 4
TLN1 0.027 0.004 -10000 0 -10000 0 0
Rap1/GTP -0.028 0.11 -10000 0 -0.33 18 18
RHOA 0.027 0.004 -10000 0 -10000 0 0
P-selectin oligomer -0.03 0.14 -10000 0 -0.4 60 60
MYH2 -0.045 0.1 -10000 0 -0.35 13 13
MST1R 0.027 0.004 -10000 0 -10000 0 0
leukocyte activation during inflammatory response -0.022 0.12 -10000 0 -0.24 97 97
APOB -0.049 0.15 -10000 0 -0.4 67 67
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.021 0.05 -10000 0 -0.41 6 6
JAM3 0.027 0.004 -10000 0 -10000 0 0
GP1BA 0.013 0.046 -10000 0 -0.4 5 5
alphaM/beta2 Integrin/CTGF 0.014 0.098 -10000 0 -0.3 31 31
alphaM/beta2 Integrin -0.044 0.11 -10000 0 -0.33 29 29
JAM3 homodimer 0.027 0.004 -10000 0 -10000 0 0
ICAM2 0.027 0.004 -10000 0 -10000 0 0
ICAM1 0.026 0.022 -10000 0 -0.43 1 1
phagocytosis triggered by activation of immune response cell surface activating receptor -0.043 0.11 -10000 0 -0.32 29 29
cell adhesion 0.007 0.095 -10000 0 -0.29 32 32
NFKB1 0.014 0.14 0.32 2 -0.42 13 15
THY1 0.009 0.089 -10000 0 -0.43 18 18
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
Lipoprotein(a) -0.018 0.11 -10000 0 -0.25 79 79
alphaM/beta2 Integrin/LRP/tPA 0.033 0.085 -10000 0 -0.26 28 28
IL6 -0.018 0.16 -10000 0 -0.52 13 13
ITGB2 0.009 0.063 -10000 0 -0.4 9 9
elevation of cytosolic calcium ion concentration 0.014 0.12 -10000 0 -0.28 47 47
alphaM/beta2 Integrin/JAM2/JAM3 -0.017 0.15 -10000 0 -0.4 32 32
JAM2 -0.067 0.17 -10000 0 -0.4 98 98
alphaM/beta2 Integrin/ICAM1 0.004 0.13 -10000 0 -0.33 25 25
alphaM/beta2 Integrin/uPA/Plg -0.045 0.15 -10000 0 -0.26 134 134
RhoA/GTP -0.047 0.11 -10000 0 -0.32 29 29
positive regulation of phagocytosis -0.029 0.1 0.18 2 -0.42 14 16
Ron/MSP -0.013 0.12 -10000 0 -0.3 69 69
alphaM/beta2 Integrin/uPAR/uPA 0.015 0.12 -10000 0 -0.28 47 47
alphaM/beta2 Integrin/uPAR 0.017 0.094 -10000 0 -0.3 27 27
PLAU -0.01 0.12 -10000 0 -0.43 36 36
PLAT 0.022 0.029 -10000 0 -0.4 2 2
actin filament polymerization -0.045 0.1 0.24 2 -0.33 14 16
MST1 -0.043 0.16 -10000 0 -0.43 69 69
alphaM/beta2 Integrin/lipoprotein(a) -0.019 0.13 -10000 0 -0.24 97 97
TNF 0.009 0.14 -10000 0 -0.68 4 4
RAP1B 0.027 0.002 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.005 0.12 -10000 0 -0.29 63 63
fibrinolysis -0.046 0.15 -10000 0 -0.26 134 134
HCK 0.01 0.053 -10000 0 -0.4 7 7
dendritic cell antigen processing and presentation -0.043 0.11 -10000 0 -0.32 29 29
VTN 0.006 0.079 -10000 0 -0.43 14 14
alphaM/beta2 Integrin/CYR61 0.015 0.097 -10000 0 -0.3 31 31
LPA -0.008 0.081 -10000 0 -0.44 14 14
LRP1 0.025 0.028 -10000 0 -0.4 2 2
cell migration -0.006 0.1 0.21 10 -0.3 34 44
FN1 -0.001 0.11 -10000 0 -0.42 28 28
alphaM/beta2 Integrin/Thy1 0.006 0.11 -10000 0 -0.29 44 44
MPO 0.004 0.094 -10000 0 -0.43 20 20
KNG1 -0.078 0.17 -10000 0 -0.4 101 101
RAP1/GDP 0.035 0.007 -10000 0 -10000 0 0
ROCK1 -0.043 0.1 0.2 1 -0.35 12 13
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.083 0.17 -10000 0 -0.43 83 83
CTGF 0.023 0.043 -10000 0 -0.43 4 4
alphaM/beta2 Integrin/Hck 0.007 0.081 -10000 0 -0.3 21 21
ITGAM -0.007 0.1 -10000 0 -0.4 26 26
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.004 0.14 -10000 0 -0.4 26 26
HP -0.006 0.1 -10000 0 -0.43 25 25
leukocyte adhesion -0.036 0.14 -10000 0 -0.45 22 22
SELP -0.031 0.14 -10000 0 -0.4 60 60
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.008 0.14 -9999 0 -0.5 20 20
MAP3K8 0.027 0.002 -9999 0 -10000 0 0
FOS -0.022 0.14 -9999 0 -0.5 20 20
PRKCA 0.026 0.007 -9999 0 -10000 0 0
PTPN7 0.02 0.055 -9999 0 -0.41 7 7
HRAS 0.026 0.02 -9999 0 -0.4 1 1
PRKCB -0.068 0.18 -9999 0 -0.4 101 101
NRAS 0.025 0.029 -9999 0 -0.4 2 2
RAS family/GTP 0.048 0.025 -9999 0 -0.21 3 3
MAPK3 0 0.087 -9999 0 -0.55 5 5
MAP2K1 -0.059 0.16 -9999 0 -0.35 99 99
ELK1 0.027 0.006 -9999 0 -10000 0 0
BRAF -0.052 0.15 -9999 0 -0.34 90 90
mol:GTP 0 0 -9999 0 -0.004 7 7
MAPK1 -0.022 0.15 -9999 0 -0.59 23 23
RAF1 -0.056 0.15 -9999 0 -0.35 94 94
KRAS 0.027 0.003 -9999 0 -10000 0 0
Osteopontin-mediated events

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
IKK alpha homodimer -0.086 0.13 -10000 0 -0.27 31 31
NF kappa B1 p50/RelA/I kappa B alpha -0.071 0.12 0.3 4 -0.32 3 7
alphaV/beta3 Integrin/Osteopontin/Src -0.12 0.17 -10000 0 -0.3 214 214
AP1 -0.068 0.14 -10000 0 -0.46 4 4
ILK -0.096 0.13 -10000 0 -0.31 5 5
bone resorption -0.079 0.12 0.33 1 -0.41 2 3
PTK2B 0.02 0.023 -10000 0 -0.4 1 1
PYK2/p130Cas -0.067 0.14 -10000 0 -0.4 3 3
ITGAV 0.029 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.038 0.022 -10000 0 -0.28 2 2
alphaV/beta3 Integrin/Osteopontin -0.092 0.16 -10000 0 -0.25 210 210
MAP3K1 -0.099 0.13 -10000 0 -0.27 31 31
JUN 0.027 0.005 -10000 0 -10000 0 0
MAPK3 -0.098 0.12 0.2 1 -0.3 33 34
MAPK1 -0.099 0.12 0.2 1 -0.3 31 32
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.096 0.12 0.2 5 -0.31 5 10
ITGB3 0.024 0.044 -10000 0 -0.39 5 5
NFKBIA -0.087 0.11 0.19 1 -0.29 33 34
FOS 0.023 0.035 -10000 0 -0.4 3 3
CD44 0.027 0.003 -10000 0 -10000 0 0
CHUK 0.026 0.006 -10000 0 -10000 0 0
PLAU -0.087 0.13 0.32 1 -0.45 4 5
NF kappa B1 p50/RelA -0.069 0.14 -10000 0 -0.35 1 1
BCAR1 0.026 0.02 -10000 0 -0.4 1 1
RELA 0.027 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.039 0.035 -10000 0 -0.28 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.097 0.13 -10000 0 -0.27 30 30
VAV3 -0.11 0.14 0.19 5 -0.39 36 41
MAP3K14 -0.099 0.13 -10000 0 -0.29 32 32
ROCK2 0.025 0.028 -10000 0 -0.4 2 2
SPP1 -0.19 0.23 -10000 0 -0.42 214 214
RAC1 0.025 0.008 -10000 0 -10000 0 0
Rac1/GTP -0.094 0.13 -10000 0 -0.36 32 32
MMP2 -0.077 0.11 -10000 0 -0.52 5 5
Canonical Wnt signaling pathway

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
HDAC1 0.025 0.01 -10000 0 -10000 0 0
AES 0.026 0.008 -10000 0 -10000 0 0
FBXW11 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.038 0.018 -10000 0 -0.28 1 1
SMAD4 0.02 0.012 -10000 0 -10000 0 0
DKK2 -0.06 0.18 -10000 0 -0.43 84 84
TLE1 0.025 0.021 -10000 0 -0.39 1 1
MACF1 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.04 0.074 0.24 6 -0.46 1 7
WIF1 -0.074 0.17 -10000 0 -0.43 87 87
beta catenin/RanBP3 0.024 0.076 0.28 6 -0.4 1 7
KREMEN2 -0.019 0.14 0.36 2 -0.43 47 49
DKK1 -0.073 0.18 -10000 0 -0.43 93 93
beta catenin/beta TrCP1 0.051 0.071 0.24 5 -0.42 1 6
FZD1 0.025 0.021 -10000 0 -0.4 1 1
AXIN2 -0.004 0.11 0.57 8 -10000 0 8
AXIN1 0.026 0.02 -10000 0 -0.4 1 1
RAN 0.027 0.002 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.031 0.064 -10000 0 -0.49 6 6
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.024 0.15 -10000 0 -0.48 24 24
Axin1/APC/GSK3 0.053 0.066 0.22 8 -0.3 3 11
Axin1/APC/GSK3/beta catenin/Macf1 0.026 0.073 0.33 1 -0.35 3 4
HNF1A 0.025 0.029 -10000 0 -0.4 2 2
CTBP1 0.026 0.008 -10000 0 -10000 0 0
MYC 0.097 0.21 0.56 73 -10000 0 73
RANBP3 0.027 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.035 0.15 0.24 2 -0.27 122 124
NKD1 -0.26 0.22 0.36 4 -0.43 287 291
TCF4 0.019 0.024 -10000 0 -0.4 1 1
TCF3 0.026 0.008 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.061 0.037 -10000 0 -0.23 5 5
Ran/GTP 0.02 0.002 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.015 0.085 -10000 0 -0.4 5 5
LEF1 -0.029 0.15 -10000 0 -0.43 54 54
DVL1 0.025 0.054 -10000 0 -0.38 3 3
CSNK2A1 0.022 0.011 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.024 0.097 -10000 0 -0.58 6 6
DKK1/LRP6/Kremen 2 -0.04 0.15 0.24 2 -0.27 129 131
LRP6 0.027 0.004 -10000 0 -10000 0 0
CSNK1A1 0.026 0.009 -10000 0 -10000 0 0
NLK 0.027 0.005 -10000 0 -10000 0 0
CCND1 0.004 0.048 0.55 1 -10000 0 1
WNT1 0.017 0.039 -10000 0 -0.42 3 3
GSK3A 0.027 0.004 -10000 0 -10000 0 0
GSK3B 0.027 0.002 -10000 0 -10000 0 0
FRAT1 0.026 0.006 -10000 0 -10000 0 0
PPP2R5D 0.13 0.1 0.21 248 -0.24 5 253
APC 0.01 0.056 0.2 9 -10000 0 9
WNT1/LRP6/FZD1 0.039 0.049 0.2 5 -10000 0 5
CREBBP 0.026 0.008 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.024 0.095 -10000 0 -0.35 25 25
HDAC1 0.024 0.006 -10000 0 -10000 0 0
AES 0.026 0.004 -10000 0 -10000 0 0
FBXW11 0.027 0.004 -10000 0 -10000 0 0
DTX1 0.022 0.044 -10000 0 -0.4 5 5
LRP6/FZD1 0.037 0.018 -10000 0 -0.28 1 1
TLE1 0.025 0.02 -10000 0 -0.4 1 1
AP1 -0.078 0.094 0.18 3 -0.29 41 44
NCSTN 0.027 0.004 -10000 0 -10000 0 0
ADAM10 0.026 0.006 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.04 0.083 -10000 0 -0.57 7 7
NICD/RBPSUH 0.025 0.093 -10000 0 -0.35 22 22
WIF1 -0.074 0.17 -10000 0 -0.43 87 87
NOTCH1 0.006 0.092 -10000 0 -0.37 25 25
PSENEN 0.026 0.02 -10000 0 -0.4 1 1
KREMEN2 -0.019 0.14 0.36 2 -0.43 47 49
DKK1 -0.073 0.18 -10000 0 -0.43 93 93
beta catenin/beta TrCP1 0.089 0.076 0.24 12 -0.3 1 13
APH1B 0.026 0.006 -10000 0 -10000 0 0
APH1A 0.027 0.004 -10000 0 -10000 0 0
AXIN1 -0.026 0.068 -10000 0 -0.43 7 7
CtBP/CBP/TCF1/TLE1/AES 0.018 0.027 -10000 0 -0.29 1 1
PSEN1 0.025 0.007 -10000 0 -10000 0 0
FOS 0.023 0.035 -10000 0 -0.4 3 3
JUN 0.027 0.005 -10000 0 -10000 0 0
MAP3K7 0.026 0.004 -10000 0 -10000 0 0
CTNNB1 0.078 0.079 0.24 13 -0.28 2 15
MAPK3 0.026 0.02 -10000 0 -0.4 1 1
DKK2/LRP6/Kremen 2 -0.035 0.15 0.24 2 -0.27 122 124
HNF1A 0.025 0.028 -10000 0 -0.39 2 2
CTBP1 0.026 0.005 -10000 0 -10000 0 0
MYC 0.024 0.038 -10000 0 -10000 0 0
NKD1 -0.26 0.22 0.36 4 -0.43 287 291
FZD1 0.025 0.021 -10000 0 -0.4 1 1
NOTCH1 precursor/Deltex homolog 1 0.022 0.095 -10000 0 -0.35 23 23
apoptosis -0.078 0.094 0.18 3 -0.29 41 44
Delta 1/NOTCHprecursor 0.023 0.095 -10000 0 -0.35 25 25
DLL1 0.024 0.035 -10000 0 -0.4 3 3
PPARD 0.029 0.071 -10000 0 -0.99 2 2
Gamma Secretase 0.07 0.032 -10000 0 -10000 0 0
APC -0.047 0.11 -10000 0 -0.4 33 33
DVL1 0.002 0.083 -10000 0 -0.37 16 16
CSNK2A1 0.022 0.011 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.001 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.041 0.15 0.24 2 -0.27 129 131
LRP6 0.027 0.004 -10000 0 -10000 0 0
CSNK1A1 0.027 0.004 -10000 0 -10000 0 0
NLK 0.012 0.004 -10000 0 -10000 0 0
CCND1 0.019 0.11 -10000 0 -0.82 7 7
WNT1 0.01 0.041 -10000 0 -0.43 3 3
Axin1/APC/beta catenin 0.022 0.11 -10000 0 -0.42 13 13
DKK2 -0.06 0.18 -10000 0 -0.43 84 84
NOTCH1 precursor/DVL1 0.004 0.13 -10000 0 -0.51 19 19
GSK3B 0.027 0.002 -10000 0 -10000 0 0
FRAT1 0.026 0.006 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.024 0.095 -10000 0 -0.35 23 23
PPP2R5D 0.13 0.1 0.22 211 -0.26 5 216
MAPK1 0.026 0.006 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.004 0.12 -10000 0 -0.24 86 86
RBPJ 0.027 0.004 -10000 0 -10000 0 0
CREBBP 0.029 0.005 -10000 0 -10000 0 0
IL1-mediated signaling events

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
UBC13/UEV1A 0.02 0.002 -10000 0 -10000 0 0
PRKCZ 0.026 0.007 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.027 0.004 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.013 0.044 -10000 0 -10000 0 0
IRAK/TOLLIP 0.031 0.006 -10000 0 -10000 0 0
IKBKB 0.024 0.009 -10000 0 -10000 0 0
IKBKG 0.026 0.02 -10000 0 -0.4 1 1
IL1 alpha/IL1R2 -0.14 0.18 -10000 0 -0.31 232 232
IL1A -0.12 0.21 -10000 0 -0.43 148 148
IL1B -0.022 0.099 -10000 0 -0.3 50 50
IRAK/TRAF6/p62/Atypical PKCs 0.062 0.028 -10000 0 -10000 0 0
IL1R2 -0.064 0.17 -10000 0 -0.4 97 97
IL1R1 0.021 0.052 -10000 0 -0.4 7 7
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.009 0.047 -10000 0 -10000 0 0
TOLLIP 0.027 0.003 -10000 0 -10000 0 0
TICAM2 0.015 0.054 -10000 0 -0.4 7 7
MAP3K3 0.027 0.005 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.018 0.002 -10000 0 -10000 0 0
IKK complex/ELKS 0.025 0.052 -10000 0 -10000 0 0
JUN -0.01 0.023 0.16 4 -10000 0 4
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.034 0.095 -10000 0 -0.35 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.034 0.14 -10000 0 -0.24 152 152
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.023 0.14 -10000 0 -0.4 2 2
IL1 beta fragment/IL1R1/IL1RAP 0.01 0.093 -10000 0 -0.23 56 56
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.008 0.024 0.17 4 -10000 0 4
IRAK1 0.014 0.002 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.017 0.13 -10000 0 -0.3 76 76
IRAK4 0.027 0.002 -10000 0 -10000 0 0
PRKCI 0.025 0.028 -10000 0 -0.4 2 2
TRAF6 0.027 0.003 -10000 0 -10000 0 0
PI3K 0.039 0.008 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.011 0.05 -10000 0 -0.33 1 1
CHUK 0.026 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.01 0.093 -10000 0 -0.23 56 56
IL1 beta/IL1R2 -0.055 0.13 -10000 0 -0.25 143 143
IRAK/TRAF6/TAK1/TAB1/TAB2 0.038 0.009 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.023 0.085 -10000 0 -0.31 1 1
IRAK3 0.017 0.065 -10000 0 -0.4 11 11
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.029 0.099 -10000 0 -0.37 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.014 0.066 -10000 0 -0.31 3 3
IL1 alpha/IL1R1/IL1RAP -0.051 0.15 -10000 0 -0.26 152 152
RELA 0.027 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.027 0.003 -10000 0 -10000 0 0
MYD88 0.027 0.003 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.045 0.013 -10000 0 -10000 0 0
IL1RAP 0.027 0.002 -10000 0 -10000 0 0
UBE2N 0.027 0.003 -10000 0 -10000 0 0
IRAK/TRAF6 0.005 0.079 -10000 0 -0.33 1 1
CASP1 0.026 0.02 -10000 0 -0.4 1 1
IL1RN/IL1R2 -0.081 0.16 -10000 0 -0.29 166 166
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.024 0.094 -10000 0 -0.22 46 46
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.004 0.063 -10000 0 -0.31 8 8
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
IL1RN -0.042 0.16 -10000 0 -0.43 69 69
TRAF6/TAK1/TAB1/TAB2 0.039 0.008 -10000 0 -10000 0 0
MAP2K6 0.012 0.025 0.18 4 -10000 0 4
Wnt 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
Noncanonical Wnts/FZD -0.026 0.097 0.17 1 -0.31 24 25
FZD6 0.023 0.01 -10000 0 -10000 0 0
WNT6 -0.002 0.1 -10000 0 -0.41 25 25
WNT4 0.006 0.088 -10000 0 -0.4 20 20
FZD3 0.022 0.033 0.36 2 -0.43 1 3
WNT5A 0.022 0.048 -10000 0 -0.43 5 5
WNT11 -0.065 0.18 -10000 0 -0.42 92 92
IL23-mediated signaling events

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
CCL2 -0.24 0.34 -10000 0 -1.1 35 35
IL23A -0.28 0.34 -10000 0 -1.1 36 36
NF kappa B1 p50/RelA/I kappa B alpha -0.24 0.34 -10000 0 -1 39 39
positive regulation of T cell mediated cytotoxicity -0.25 0.35 -10000 0 -1.1 39 39
ITGA3 -0.24 0.32 -10000 0 -1 30 30
IL17F -0.21 0.25 -10000 0 -0.69 41 41
IL12B -0.017 0.056 -10000 0 -0.44 4 4
STAT1 (dimer) -0.24 0.34 -10000 0 -1 39 39
CD4 -0.25 0.36 -10000 0 -1.1 38 38
IL23 -0.27 0.34 -10000 0 -1 36 36
IL23R -0.078 0.26 -10000 0 -1.1 24 24
IL1B -0.26 0.35 -10000 0 -1.1 34 34
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.27 0.33 -10000 0 -1 33 33
TYK2 -0.006 0.032 -10000 0 -10000 0 0
STAT4 0.006 0.093 -10000 0 -0.4 23 23
STAT3 0.026 0.006 -10000 0 -10000 0 0
IL18RAP 0.003 0.095 -10000 0 -0.4 24 24
IL12RB1 -0.021 0.086 -10000 0 -0.42 17 17
PIK3CA 0.026 0.005 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.013 0.072 -10000 0 -0.31 17 17
IL23R/JAK2 -0.082 0.25 -10000 0 -1.1 22 22
positive regulation of chronic inflammatory response -0.25 0.35 -10000 0 -1.1 39 39
natural killer cell activation 0.005 0.013 0.079 11 -10000 0 11
JAK2 -0.01 0.05 -10000 0 -0.42 3 3
PIK3R1 0.026 0.006 -10000 0 -10000 0 0
NFKB1 0.024 0.005 -10000 0 -10000 0 0
RELA 0.025 0.005 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.26 0.32 -10000 0 -0.98 36 36
ALOX12B -0.23 0.33 -10000 0 -1 34 34
CXCL1 -0.28 0.34 -10000 0 -1 38 38
T cell proliferation -0.25 0.35 -10000 0 -1.1 39 39
NFKBIA 0.023 0.007 -10000 0 -10000 0 0
IL17A -0.19 0.22 -10000 0 -0.56 50 50
PI3K -0.24 0.34 -10000 0 -1 38 38
IFNG -0.01 0.037 0.14 11 -0.11 6 17
STAT3 (dimer) -0.24 0.34 -10000 0 -0.97 40 40
IL18R1 0.017 0.06 -10000 0 -0.39 9 9
IL23/IL23R/JAK2/TYK2/SOCS3 -0.15 0.23 -10000 0 -0.73 31 31
IL18/IL18R 0.029 0.081 -10000 0 -0.23 35 35
macrophage activation -0.018 0.016 -10000 0 -0.044 18 18
TNF -0.26 0.34 -10000 0 -1.1 33 33
STAT3/STAT4 -0.24 0.35 -10000 0 -1 41 41
STAT4 (dimer) -0.25 0.35 -10000 0 -1 42 42
IL18 0.023 0.03 -10000 0 -0.4 2 2
IL19 -0.23 0.32 -10000 0 -1 31 31
STAT5A (dimer) -0.24 0.34 -10000 0 -1 38 38
STAT1 0.026 0.021 -10000 0 -0.43 1 1
SOCS3 0.026 0.022 -10000 0 -0.43 1 1
CXCL9 -0.25 0.34 -10000 0 -1.1 36 36
MPO -0.23 0.32 -10000 0 -1 30 30
positive regulation of humoral immune response -0.25 0.35 -10000 0 -1.1 39 39
IL23/IL23R/JAK2/TYK2 -0.26 0.37 -10000 0 -1.1 39 39
IL6 -0.25 0.36 -10000 0 -1 40 40
STAT5A 0.027 0.004 -10000 0 -10000 0 0
IL2 0.015 0.021 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.005 0.013 0.079 11 -10000 0 11
CD3E -0.25 0.37 -10000 0 -1.1 41 41
keratinocyte proliferation -0.25 0.35 -10000 0 -1.1 39 39
NOS2 -0.26 0.38 -10000 0 -1.2 42 42
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 0.037 0.24 0.43 1 -0.81 28 29
NCK1/PAK1/Dok-R -0.028 0.096 -10000 0 -0.4 25 25
NCK1/Dok-R 0.009 0.26 -10000 0 -0.96 27 27
PIK3CA 0.026 0.003 -10000 0 -10000 0 0
mol:beta2-estradiol 0.002 0.05 0.25 17 -10000 0 17
RELA 0.027 0.004 -10000 0 -10000 0 0
SHC1 0.028 0.005 -10000 0 -10000 0 0
Rac/GDP 0.018 0.006 -10000 0 -10000 0 0
F2 -0.13 0.22 0.29 18 -0.45 137 155
TNIP2 0.026 0.005 -10000 0 -10000 0 0
NF kappa B/RelA 0.044 0.25 -10000 0 -0.89 28 28
FN1 -0.001 0.11 -10000 0 -0.42 28 28
PLD2 -0.026 0.26 -10000 0 -0.98 28 28
PTPN11 0.027 0.003 -10000 0 -10000 0 0
GRB14 -0.007 0.11 -10000 0 -0.4 31 31
ELK1 0.01 0.25 -10000 0 -0.88 29 29
GRB7 0.033 0.044 0.36 8 -10000 0 8
PAK1 0.027 0.003 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0.034 0.28 -10000 0 -0.95 28 28
CDKN1A 0.035 0.2 0.39 8 -0.61 25 33
ITGA5 0.024 0.037 -10000 0 -0.43 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.008 0.26 -10000 0 -0.96 27 27
CRK 0.023 0.01 -10000 0 -10000 0 0
mol:NO 0.049 0.2 0.4 12 -0.6 29 41
PLG -0.053 0.27 -10000 0 -1 29 29
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.028 0.23 -10000 0 -0.78 28 28
GRB2 0.027 0.004 -10000 0 -10000 0 0
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
ANGPT2 -0.028 0.21 0.39 2 -0.56 27 29
BMX -0.071 0.28 -10000 0 -1.1 28 28
ANGPT1 0.012 0.23 -10000 0 -1.1 17 17
tube development 0.026 0.21 0.38 9 -0.66 24 33
ANGPT4 0.011 0.043 -10000 0 -0.42 4 4
response to hypoxia -0.003 0.016 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 0.008 0.29 -10000 0 -1 28 28
alpha5/beta1 Integrin 0.038 0.028 -10000 0 -0.3 3 3
FGF2 -0.003 0.1 -10000 0 -0.39 30 30
STAT5A (dimer) 0.034 0.24 0.43 1 -0.75 25 26
mol:L-citrulline 0.049 0.2 0.4 12 -0.6 29 41
AGTR1 -0.12 0.2 -10000 0 -0.39 153 153
MAPK14 0 0.29 -10000 0 -1 29 29
Tie2/SHP2 0.015 0.22 -10000 0 -1 18 18
TEK -0.011 0.23 -10000 0 -1.1 18 18
RPS6KB1 0.036 0.24 0.57 1 -0.79 28 29
Angiotensin II/AT1 -0.081 0.14 -10000 0 -0.27 153 153
Tie2/Ang1/GRB2 0.019 0.29 -10000 0 -1 28 28
MAPK3 -0.015 0.24 -10000 0 -0.9 28 28
MAPK1 -0.015 0.24 -10000 0 -0.9 28 28
Tie2/Ang1/GRB7 0.022 0.29 -10000 0 -1 28 28
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.023 0.27 -10000 0 -0.99 28 28
PI3K 0.022 0.27 -10000 0 -0.93 29 29
FES -0.011 0.29 -10000 0 -1 29 29
Crk/Dok-R 0.005 0.26 -10000 0 -0.95 27 27
Tie2/Ang1/ABIN2 0.019 0.29 -10000 0 -1 28 28
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.044 0.22 0.39 3 -0.72 29 32
STAT5A 0.027 0.004 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.056 0.24 0.46 10 -0.78 26 36
Tie2/Ang2 -0.012 0.25 0.48 1 -0.93 23 24
Tie2/Ang1 -0.021 0.29 -10000 0 -1.1 28 28
FOXO1 0.061 0.23 0.41 13 -0.74 25 38
ELF1 0.021 0.028 -10000 0 -10000 0 0
ELF2 -0.019 0.27 -10000 0 -0.99 28 28
mol:Choline -0.023 0.25 -10000 0 -0.93 28 28
cell migration -0.014 0.058 -10000 0 -0.22 29 29
FYN 0.019 0.23 0.4 5 -0.77 23 28
DOK2 0.015 0.049 -10000 0 -0.4 6 6
negative regulation of cell cycle 0.038 0.19 0.36 11 -0.55 25 36
ETS1 0.021 0.063 -10000 0 -0.28 17 17
PXN 0.06 0.21 0.4 17 -0.64 28 45
ITGB1 0.027 0.002 -10000 0 -10000 0 0
NOS3 0.045 0.22 0.44 9 -0.69 28 37
RAC1 0.025 0.008 -10000 0 -10000 0 0
TNF 0.021 0.063 -10000 0 -0.28 18 18
MAPKKK cascade -0.023 0.25 -10000 0 -0.93 28 28
RASA1 0.026 0.005 -10000 0 -10000 0 0
Tie2/Ang1/Shc 0.02 0.29 -10000 0 -1 28 28
NCK1 0.027 0.002 -10000 0 -10000 0 0
vasculogenesis 0.051 0.18 0.39 13 -0.54 29 42
mol:Phosphatidic acid -0.023 0.25 -10000 0 -0.93 28 28
mol:Angiotensin II 0.001 0.002 -10000 0 -10000 0 0
mol:NADP 0.049 0.2 0.4 12 -0.6 29 41
Rac1/GTP 0.03 0.21 -10000 0 -0.74 27 27
MMP2 -0.025 0.27 -10000 0 -1 28 28
Signaling events mediated by PRL

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
CCNE1 0.027 0.031 0.36 2 -0.43 1 3
mol:Halofuginone 0.003 0 -10000 0 -10000 0 0
ITGA1 0.027 0.004 -10000 0 -10000 0 0
CDKN1A 0.007 0.048 -10000 0 -0.3 10 10
PRL-3/alpha Tubulin 0.023 0.12 0.26 34 -0.3 40 74
mol:Ca2+ -0.056 0.13 0.17 29 -0.3 82 111
AGT -0.026 0.15 0.36 2 -0.43 53 55
CCNA2 -0.002 0.009 -10000 0 -10000 0 0
TUBA1B 0.027 0.002 -10000 0 -10000 0 0
EGR1 0.015 0.014 -10000 0 -0.27 1 1
CDK2/Cyclin E1 0.072 0.079 0.31 3 -10000 0 3
MAPK3 0.003 0.12 0.27 34 -0.3 41 75
PRL-2 /Rab GGTase beta 0.038 0.01 -10000 0 -10000 0 0
MAPK1 0.004 0.12 0.28 33 -0.3 40 73
PTP4A1 0.002 0.01 -10000 0 -10000 0 0
PTP4A3 0.01 0.16 0.36 34 -0.43 40 74
PTP4A2 0.026 0.006 -10000 0 -10000 0 0
ITGB1 0.004 0.12 0.27 34 -0.3 40 74
SRC 0.017 0.013 -10000 0 -10000 0 0
RAC1 0.025 0.071 0.3 17 -0.3 4 21
Rab GGTase beta/Rab GGTase alpha 0.037 0.012 -10000 0 -10000 0 0
PRL-1/ATF-5 0.082 0.082 -10000 0 -10000 0 0
RABGGTA 0.026 0.007 -10000 0 -10000 0 0
BCAR1 -0.021 0.083 0.15 40 -0.25 35 75
RHOC 0.026 0.085 0.31 22 -0.32 8 30
RHOA 0.027 0.079 0.27 31 -0.3 6 37
cell motility 0.048 0.11 0.31 19 -0.33 9 28
PRL-1/alpha Tubulin 0.084 0.082 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.021 0.12 0.26 32 -0.3 40 72
ROCK1 0.049 0.11 0.31 19 -0.34 7 26
RABGGTB 0.026 0.005 -10000 0 -10000 0 0
CDK2 0.027 0.002 -10000 0 -10000 0 0
mitosis 0.002 0.01 -10000 0 -10000 0 0
ATF5 0.027 0.003 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.003 0.074 -10000 0 -0.29 26 26
CRKL 0.026 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
DOCK1 0.027 0.005 -10000 0 -10000 0 0
ITGA4 0.01 0.083 -10000 0 -0.4 18 18
alpha4/beta7 Integrin/MAdCAM1 -0.082 0.16 -10000 0 -0.24 212 212
EPO 0.005 0.045 0.36 1 -0.43 3 4
alpha4/beta7 Integrin 0.015 0.092 -10000 0 -0.31 32 32
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.023 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.028 0.063 -10000 0 -0.28 18 18
EPO/EPOR (dimer) 0.033 0.035 0.26 1 -0.3 4 5
lamellipodium assembly 0.005 0.078 -10000 0 -0.42 4 4
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
PI3K 0.039 0.008 -10000 0 -10000 0 0
ARF6 0.025 0.007 -10000 0 -10000 0 0
JAK2 0.013 0.059 0.17 1 -0.24 18 19
PXN 0.027 0.002 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
MADCAM1 -0.18 0.21 -10000 0 -0.4 211 211
cell adhesion -0.083 0.16 -10000 0 -0.24 212 212
CRKL/CBL 0.038 0.009 -10000 0 -10000 0 0
ITGB1 0.027 0.002 -10000 0 -10000 0 0
SRC 0.001 0.055 0.18 1 -0.31 12 13
ITGB7 0.01 0.083 -10000 0 -0.4 18 18
RAC1 0.025 0.008 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.036 0.081 -10000 0 -0.31 21 21
p130Cas/Crk/Dock1 0.051 0.08 -10000 0 -0.34 6 6
VCAM1 0.016 0.065 -10000 0 -0.4 11 11
RHOA 0.027 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.057 0.054 -10000 0 -0.21 16 16
BCAR1 -0.014 0.05 0.18 1 -0.38 6 7
EPOR 0.026 0.022 -10000 0 -0.43 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.027 0.004 -10000 0 -10000 0 0
GIT1 0.026 0.02 -10000 0 -0.4 1 1
Rac1/GTP 0.005 0.08 -10000 0 -0.44 4 4
TCGA08_p53

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
CDKN2A -0.059 0.13 0.27 2 -0.31 96 98
TP53 -0.018 0.063 -10000 0 -0.28 21 21
Senescence -0.018 0.063 -10000 0 -0.27 21 21
Apoptosis -0.018 0.063 -10000 0 -0.27 21 21
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.024 0.065 0.26 4 -0.2 1 5
MDM4 0.027 0.004 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.014 0.039 -10000 0 -0.24 3 3
NFATC2 -0.015 0.045 -10000 0 -0.25 10 10
NFATC3 -0.014 0.038 -10000 0 -10000 0 0
CD40LG -0.063 0.21 0.36 1 -0.54 34 35
PTGS2 -0.061 0.21 0.36 1 -0.53 39 40
JUNB 0.025 0.028 -10000 0 -0.4 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.005 0.029 -10000 0 -10000 0 0
CaM/Ca2+ -0.005 0.029 -10000 0 -10000 0 0
CALM1 0.008 0.026 -10000 0 -10000 0 0
JUN 0.008 0.027 -10000 0 -10000 0 0
mol:Ca2+ -0.009 0.012 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.009 0.013 -10000 0 -10000 0 0
FOSL1 -0.27 0.22 -10000 0 -0.43 293 293
CREM 0.027 0.001 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.013 0.14 -10000 0 -0.33 14 14
FOS 0.005 0.042 -10000 0 -0.4 3 3
IFNG -0.067 0.22 0.36 1 -0.52 39 40
AP-1/NFAT1-c-4 -0.057 0.21 -10000 0 -0.46 56 56
FASLG -0.061 0.2 0.36 1 -0.5 27 28
NFAT1-c-4/ICER1 -0.02 0.076 -10000 0 -0.27 6 6
IL2RA -0.054 0.2 0.36 1 -0.52 21 22
FKBP12/FK506 0.016 0.008 -10000 0 -10000 0 0
CSF2 -0.12 0.24 0.36 1 -0.53 61 62
JunB/Fra1/NFAT1-c-4 -0.099 0.16 -10000 0 -0.33 59 59
IL4 -0.054 0.19 0.36 1 -0.5 18 19
IL2 -0.012 0.13 -10000 0 -0.84 11 11
IL3 0.001 0.081 -10000 0 -0.62 7 7
FKBP1A 0.022 0.011 -10000 0 -10000 0 0
BATF3 0.021 0.047 -10000 0 -0.42 5 5
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.027 0.005 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor 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
CRKL 0.026 0.006 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.028 0.096 -10000 0 -0.27 34 34
NT3 (dimer)/TRKC -0.023 0.13 -10000 0 -0.29 81 81
NT3 (dimer)/TRKB -0.095 0.18 -10000 0 -0.3 185 185
SHC/Grb2/SOS1/GAB1/PI3K 0.029 0.01 -10000 0 -10000 0 0
RAPGEF1 0.026 0.02 -10000 0 -0.4 1 1
BDNF 0.013 0.076 -10000 0 -0.43 13 13
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
DYNLT1 0.027 0.004 -10000 0 -10000 0 0
NTRK1 0.018 0.044 -10000 0 -0.43 4 4
NTRK2 -0.093 0.19 -10000 0 -0.4 126 126
NTRK3 -0.055 0.16 -10000 0 -0.4 79 79
NT-4/5 (dimer)/TRKB -0.11 0.18 -10000 0 -0.3 198 198
neuron apoptosis 0.093 0.16 0.38 72 -10000 0 72
SHC 2-3/Grb2 -0.1 0.17 -10000 0 -0.42 72 72
SHC1 0.027 0.004 -10000 0 -10000 0 0
SHC2 -0.1 0.17 -10000 0 -0.43 74 74
SHC3 -0.1 0.16 -10000 0 -0.42 68 68
STAT3 (dimer) 0.031 0.018 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.026 0.13 -10000 0 -0.24 116 116
RIN/GDP -0.005 0.08 0.2 6 -0.24 9 15
GIPC1 0.026 0.02 -10000 0 -0.4 1 1
KRAS 0.027 0.003 -10000 0 -10000 0 0
DNAJA3 -0.068 0.13 -10000 0 -0.28 104 104
RIN/GTP 0.009 0.016 -10000 0 -0.3 1 1
CCND1 0.017 0.029 -10000 0 -0.33 3 3
MAGED1 0.027 0.003 -10000 0 -10000 0 0
PTPN11 0.027 0.003 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.018 0.091 -10000 0 -0.44 19 19
SHC/GRB2/SOS1 0.053 0.013 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.007 0.1 -10000 0 -0.24 66 66
TRKA/NEDD4-2 0.026 0.039 -10000 0 -0.3 5 5
ELMO1 0.022 0.035 -10000 0 -0.4 3 3
RhoG/GTP/ELMO1/DOCK1 0.031 0.025 -10000 0 -0.23 3 3
NGF 0.008 0.079 -10000 0 -0.4 16 16
HRAS 0.026 0.02 -10000 0 -0.4 1 1
DOCK1 0.027 0.005 -10000 0 -10000 0 0
GAB2 0.027 0.003 -10000 0 -10000 0 0
RIT2 -0.012 0.023 -10000 0 -0.43 1 1
RIT1 0.027 0.004 -10000 0 -10000 0 0
FRS2 0.027 0.003 -10000 0 -10000 0 0
DNM1 0.024 0.046 0.36 1 -0.43 4 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.023 0.01 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.051 0.13 -10000 0 -0.28 98 98
mol:GDP -0.013 0.11 0.25 6 -0.36 10 16
NGF (dimer) 0.008 0.079 -10000 0 -0.4 16 16
RhoG/GDP 0.016 0.025 -10000 0 -0.28 3 3
RIT1/GDP -0.001 0.085 0.2 7 -0.24 9 16
TIAM1 -0.013 0.12 -10000 0 -0.4 41 41
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.039 0.13 -10000 0 -0.24 138 138
KIDINS220/CRKL/C3G 0.037 0.018 -10000 0 -0.28 1 1
SHC/RasGAP 0.038 0.009 -10000 0 -10000 0 0
FRS2 family/SHP2 0.054 0.013 0.24 1 -10000 0 1
SHC/GRB2/SOS1/GAB1 0.066 0.018 -10000 0 -10000 0 0
RIT1/GTP 0.02 0.003 -10000 0 -10000 0 0
NT3 (dimer) 0.018 0.056 -10000 0 -0.4 8 8
RAP1/GDP -0.004 0.07 -10000 0 -0.21 7 7
KIDINS220/CRKL 0.026 0.006 -10000 0 -10000 0 0
BDNF (dimer) 0.013 0.076 -10000 0 -0.42 13 13
ubiquitin-dependent protein catabolic process 0.026 0.063 -10000 0 -0.24 21 21
Schwann cell development -0.027 0.029 -10000 0 -10000 0 0
EHD4 0.025 0.007 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.067 0.018 0.25 1 -10000 0 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.016 0.041 0.25 1 -0.24 1 2
RAP1B 0.027 0.002 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.059 0.13 -10000 0 -0.37 29 29
ABL1 0.027 0.004 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.039 0.007 -10000 0 -10000 0 0
Rap1/GTP -0.018 0.1 -10000 0 -0.44 13 13
STAT3 0.031 0.018 -10000 0 -10000 0 0
axon guidance -0.062 0.12 -10000 0 -0.36 29 29
MAPK3 -0.02 0.087 -10000 0 -0.32 2 2
MAPK1 -0.019 0.084 -10000 0 -0.4 1 1
CDC42/GDP 0 0.085 0.2 8 -0.24 9 17
NTF3 0.018 0.056 -10000 0 -0.4 8 8
NTF4 -0.018 0.091 -10000 0 -0.44 19 19
NGF (dimer)/TRKA/FAIM 0.038 0.062 -10000 0 -0.24 20 20
PI3K 0.039 0.008 -10000 0 -10000 0 0
FRS3 0.028 0.016 0.36 1 -10000 0 1
FAIM 0.027 0.003 -10000 0 -10000 0 0
GAB1 0.027 0.004 -10000 0 -10000 0 0
RASGRF1 -0.083 0.14 -10000 0 -0.29 111 111
SOS1 0.027 0.002 -10000 0 -10000 0 0
MCF2L -0.032 0.094 -10000 0 -0.25 69 69
RGS19 0.017 0.013 -10000 0 -10000 0 0
CDC42 0.025 0.021 -10000 0 -0.4 1 1
RAS family/GTP 0.005 0.072 -10000 0 -0.35 5 5
Rac1/GDP -0.006 0.08 0.2 5 -0.25 8 13
NGF (dimer)/TRKA/GRIT 0.021 0.057 -10000 0 -0.24 20 20
neuron projection morphogenesis -0.051 0.14 -10000 0 -0.58 4 4
NGF (dimer)/TRKA/NEDD4-2 0.027 0.064 -10000 0 -0.24 21 21
MAP2K1 0.018 0.03 0.18 15 -10000 0 15
NGFR -0.081 0.18 -10000 0 -0.4 114 114
NGF (dimer)/TRKA/GIPC/GAIP 0.01 0.038 -10000 0 -10000 0 0
RAS family/GTP/PI3K 0.023 0.02 -10000 0 -0.2 3 3
FRS2 family/SHP2/GRB2/SOS1 0.077 0.02 0.25 1 -10000 0 1
NRAS 0.024 0.029 -10000 0 -0.4 2 2
GRB2/SOS1 0.039 0.007 -10000 0 -10000 0 0
PRKCI 0.025 0.028 -10000 0 -0.4 2 2
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCZ 0.026 0.007 -10000 0 -10000 0 0
MAPKKK cascade -0.047 0.15 -10000 0 -0.58 29 29
RASA1 0.026 0.005 -10000 0 -10000 0 0
TRKA/c-Abl 0.035 0.033 -10000 0 -0.3 4 4
SQSTM1 0.027 0.003 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.022 0.13 -10000 0 -0.22 136 136
NGF (dimer)/TRKA/p62/Atypical PKCs 0.058 0.067 -10000 0 -0.41 1 1
MATK -0.021 0.13 -10000 0 -0.4 51 51
NEDD4L 0.02 0.023 -10000 0 -0.4 1 1
RAS family/GDP -0.026 0.046 -10000 0 -0.23 1 1
NGF (dimer)/TRKA -0.064 0.14 -10000 0 -0.29 107 107
Rac1/GTP -0.066 0.1 -10000 0 -0.28 47 47
FRS2 family/SHP2/CRK family 0.065 0.034 -10000 0 -10000 0 0
LPA4-mediated signaling events

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
ADCY4 -0.005 0.001 -10000 0 -10000 0 0
ADCY5 -0.1 0.11 -10000 0 -0.23 187 187
ADCY6 -0.006 0.001 -10000 0 -10000 0 0
ADCY7 -0.006 0.001 -10000 0 -10000 0 0
ADCY1 -0.011 0.039 0.21 1 -0.25 11 12
ADCY2 -0.025 0.063 -10000 0 -0.23 37 37
ADCY3 -0.006 0.001 -10000 0 -10000 0 0
ADCY8 -0.011 0.03 0.21 1 -0.26 6 7
PRKCE 0.007 0.001 -10000 0 -10000 0 0
ADCY9 -0.007 0.015 -10000 0 -0.23 2 2
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.012 0.074 0.2 13 -0.22 3 16
IL12-mediated 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
IL12/IL12R/TYK2/JAK2/SOCS1 0.001 0.11 0.22 1 -0.34 23 24
TBX21 -0.1 0.41 -10000 0 -1.2 44 44
B2M 0.022 0.026 -10000 0 -0.4 1 1
TYK2 0.018 0.032 -10000 0 -10000 0 0
IL12RB1 0.003 0.09 -10000 0 -0.42 17 17
GADD45B -0.043 0.29 -10000 0 -0.89 30 30
IL12RB2 0.012 0.063 -10000 0 -0.43 7 7
GADD45G -0.043 0.29 -10000 0 -0.87 31 31
natural killer cell activation 0 0.019 0.045 7 -0.042 34 41
RELB 0.027 0.003 -10000 0 -10000 0 0
RELA 0.027 0.004 -10000 0 -10000 0 0
IL18 0.025 0.031 -10000 0 -0.39 2 2
IL2RA 0.017 0.065 -10000 0 -0.4 11 11
IFNG -0.023 0.13 -10000 0 -0.43 43 43
STAT3 (dimer) -0.046 0.28 0.34 1 -0.73 46 47
HLA-DRB5 0.001 0.002 -10000 0 -0.022 2 2
FASLG -0.1 0.41 0.58 1 -1.2 47 48
NF kappa B2 p52/RelB -0.067 0.33 -10000 0 -0.9 45 45
CD4 0.011 0.081 -10000 0 -0.4 17 17
SOCS1 0.017 0.067 -10000 0 -0.43 10 10
EntrezGene:6955 0 0.009 -10000 0 -0.037 23 23
CD3D 0.012 0.073 -10000 0 -0.4 13 13
CD3E 0.009 0.08 -10000 0 -0.4 16 16
CD3G -0.009 0.12 -10000 0 -0.4 36 36
IL12Rbeta2/JAK2 0.023 0.069 -10000 0 -0.32 10 10
CCL3 -0.08 0.34 -10000 0 -0.96 39 39
CCL4 -0.075 0.33 -10000 0 -0.96 38 38
HLA-A -0.001 0.009 -10000 0 -0.037 23 23
IL18/IL18R 0.046 0.093 -10000 0 -0.25 34 34
NOS2 -0.092 0.4 -10000 0 -1.2 41 41
IL12/IL12R/TYK2/JAK2/SPHK2 0.004 0.1 0.22 1 -0.33 24 25
IL1R1 -0.084 0.35 -10000 0 -1 41 41
IL4 -0.002 0.035 -10000 0 -10000 0 0
JAK2 0.015 0.049 -10000 0 -0.43 3 3
EntrezGene:6957 0 0.009 -10000 0 -0.037 23 23
TCR/CD3/MHC I/CD8 -0.069 0.29 -10000 0 -0.87 44 44
RAB7A -0.03 0.25 -10000 0 -0.76 27 27
lysosomal transport -0.026 0.24 -10000 0 -0.72 27 27
FOS -0.073 0.31 -10000 0 -0.85 47 47
STAT4 (dimer) -0.046 0.31 0.41 2 -0.84 44 46
STAT5A (dimer) -0.081 0.34 -10000 0 -0.88 48 48
GZMA -0.13 0.45 -10000 0 -1.3 53 53
GZMB -0.1 0.34 -10000 0 -0.96 41 41
HLX 0.026 0.02 -10000 0 -0.4 1 1
LCK -0.089 0.36 -10000 0 -0.96 47 47
TCR/CD3/MHC II/CD4 -0.024 0.16 -10000 0 -0.47 36 36
IL2/IL2R 0.048 0.073 -10000 0 -0.3 16 16
MAPK14 -0.045 0.3 -10000 0 -0.85 38 38
CCR5 -0.051 0.31 -10000 0 -1.1 24 24
IL1B -0.029 0.14 -10000 0 -0.42 49 49
STAT6 0.004 0.096 -10000 0 -10000 0 0
STAT4 0.006 0.093 -10000 0 -0.4 23 23
STAT3 0.027 0.004 -10000 0 -10000 0 0
STAT1 0.026 0.021 -10000 0 -0.43 1 1
NFKB1 0.027 0.004 -10000 0 -10000 0 0
NFKB2 0.026 0.006 -10000 0 -10000 0 0
IL12B 0.01 0.054 -10000 0 -0.42 4 4
CD8A -0.006 0.11 -10000 0 -0.4 33 33
CD8B 0.011 0.076 -10000 0 -0.4 14 14
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.001 0.1 0.33 23 -0.22 1 24
IL2RB 0.017 0.063 -10000 0 -0.4 10 10
proteasomal ubiquitin-dependent protein catabolic process -0.037 0.28 0.41 2 -0.77 42 44
IL2RG 0.025 0.028 -10000 0 -0.4 2 2
IL12 0.02 0.069 -10000 0 -0.3 10 10
STAT5A 0.027 0.004 -10000 0 -10000 0 0
CD247 0.013 0.073 -10000 0 -0.4 13 13
IL2 -0.006 0.02 -10000 0 -10000 0 0
SPHK2 0.026 0.02 -10000 0 -0.4 1 1
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.012 0.06 -10000 0 -0.42 6 6
IL12/IL12R/TYK2/JAK2 -0.09 0.38 0.41 1 -1 47 48
MAP2K3 -0.066 0.32 -10000 0 -0.89 42 42
RIPK2 0.023 0.01 -10000 0 -10000 0 0
MAP2K6 -0.04 0.3 -10000 0 -0.88 33 33
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.001 0.002 -10000 0 -0.026 2 2
IL18RAP 0.004 0.098 -10000 0 -0.4 24 24
IL12Rbeta1/TYK2 0.018 0.078 -10000 0 -0.32 17 17
EOMES -0.055 0.28 -10000 0 -1.1 26 26
STAT1 (dimer) -0.042 0.27 0.35 1 -0.72 43 44
T cell proliferation -0.024 0.23 0.36 2 -0.63 37 39
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.019 0.062 -10000 0 -0.4 9 9
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.031 0.25 -10000 0 -0.7 34 34
ATF2 -0.042 0.28 -10000 0 -0.79 37 37
EGFR-dependent Endothelin signaling events

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
HRAS 0.026 0.02 -9999 0 -0.4 1 1
EGFR 0.024 0.021 -9999 0 -0.4 1 1
EGF/EGFR -0.012 0.11 -9999 0 -0.21 93 93
EGF/EGFR dimer/SHC/GRB2/SOS1 0.017 0.11 -9999 0 -0.22 15 15
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.001 0.11 -9999 0 -0.43 26 26
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.063 0.17 -9999 0 -0.4 90 90
EGF/EGFR dimer/SHC -0.005 0.11 -9999 0 -0.24 80 80
mol:GDP 0.013 0.1 -9999 0 -0.22 15 15
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.025 0.028 -9999 0 -0.4 2 2
GRB2/SOS1 0.039 0.007 -9999 0 -10000 0 0
HRAS/GTP 0 0.091 -9999 0 -10000 0 0
SHC1 0.027 0.004 -9999 0 -10000 0 0
HRAS/GDP 0.012 0.1 -9999 0 -10000 0 0
FRAP1 -0.043 0.071 -9999 0 -0.21 15 15
EGF/EGFR dimer -0.024 0.12 -9999 0 -0.28 82 82
SOS1 0.027 0.002 -9999 0 -10000 0 0
GRB2 0.027 0.004 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.018 0.083 -9999 0 -0.3 28 28
Syndecan-3-mediated signaling events

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
CTTN 0.027 0.004 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.002 0.1 -10000 0 -0.38 14 14
Syndecan-3/Neurocan 0.006 0.09 -10000 0 -0.37 23 23
POMC 0.008 0.086 -10000 0 -0.4 19 19
EGFR 0.024 0.021 -10000 0 -0.4 1 1
Syndecan-3/EGFR 0.007 0.088 -10000 0 -0.36 23 23
AGRP -0.004 0.041 -10000 0 -0.43 3 3
NCSTN 0.027 0.004 -10000 0 -10000 0 0
PSENEN 0.026 0.02 -10000 0 -0.4 1 1
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.026 0.006 -10000 0 -10000 0 0
APH1A 0.027 0.004 -10000 0 -10000 0 0
NCAN 0.002 0.036 -10000 0 -0.43 2 2
long-term memory 0.026 0.089 -10000 0 -0.35 23 23
Syndecan-3/IL8 -0.12 0.14 0.23 1 -0.45 26 27
PSEN1 0.025 0.007 -10000 0 -10000 0 0
Src/Cortactin 0.024 0.02 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
limb bud formation -0.006 0.086 -10000 0 -0.38 23 23
MC4R -0.008 0.043 -10000 0 -0.43 4 4
SRC 0.017 0.013 -10000 0 -10000 0 0
PTN -0.042 0.16 -10000 0 -0.4 72 72
FGFR/FGF/Syndecan-3 -0.007 0.087 -10000 0 -0.38 23 23
neuron projection morphogenesis 0.024 0.12 -10000 0 -0.38 14 14
Syndecan-3/AgRP 0.005 0.091 -10000 0 -0.36 24 24
Syndecan-3/AgRP/MC4R 0.009 0.091 -10000 0 -0.34 25 25
Fyn/Cortactin 0.039 0.008 -10000 0 -10000 0 0
SDC3 -0.007 0.088 -10000 0 -0.38 23 23
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration -0.12 0.14 0.23 1 -0.44 26 27
IL8 -0.24 0.23 0.36 1 -0.43 259 260
Syndecan-3/Fyn/Cortactin 0.027 0.091 -10000 0 -0.35 23 23
Syndecan-3/CASK -0.008 0.084 -10000 0 -0.35 25 25
alpha-MSH/MC4R 0.011 0.069 -10000 0 -0.28 23 23
Gamma Secretase 0.069 0.032 -10000 0 -10000 0 0
Thromboxane A2 receptor 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
TGM2 0.013 0.038 -10000 0 -0.43 3 3
GNB1/GNG2 -0.053 0.05 -10000 0 -0.19 17 17
AKT1 -0.043 0.093 -10000 0 -0.29 32 32
EGF -0.063 0.17 -10000 0 -0.4 90 90
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR -0.071 0.08 -10000 0 -0.31 2 2
mol:Ca2+ -0.055 0.096 -10000 0 -0.29 31 31
LYN -0.061 0.077 -10000 0 -10000 0 0
RhoA/GTP -0.024 0.043 -10000 0 -0.14 6 6
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.06 0.1 -10000 0 -0.34 15 15
GNG2 0.009 0.081 -10000 0 -0.4 17 17
ARRB2 0.023 0.01 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.028 0.12 -10000 0 -0.68 10 10
G beta5/gamma2 -0.061 0.067 -10000 0 -0.27 14 14
PRKCH -0.057 0.1 -10000 0 -0.34 19 19
DNM1 0.024 0.046 0.36 1 -0.43 4 5
TXA2/TP beta/beta Arrestin3 -0.01 0.047 -10000 0 -0.62 2 2
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.18 0.21 -10000 0 -0.4 221 221
G12 family/GTP -0.054 0.089 -10000 0 -0.3 17 17
ADRBK1 0.027 0.004 -10000 0 -10000 0 0
ADRBK2 0.026 0.006 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.029 0.019 -10000 0 -0.23 1 1
mol:GDP 0.07 0.1 0.34 29 -10000 0 29
mol:NADP 0.018 0.066 0.36 1 -0.42 9 10
RAB11A 0.026 0.006 -10000 0 -10000 0 0
PRKG1 0.006 0.087 -10000 0 -0.4 20 20
mol:IP3 -0.067 0.12 -10000 0 -0.36 31 31
cell morphogenesis 0.029 0.019 -10000 0 -0.23 1 1
PLCB2 -0.092 0.15 -10000 0 -0.49 31 31
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.11 0.11 -10000 0 -0.3 74 74
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.042 0.073 -10000 0 -0.29 4 4
RHOA 0.027 0.004 -10000 0 -10000 0 0
PTGIR 0.026 0.022 -10000 0 -0.43 1 1
PRKCB1 -0.061 0.11 -10000 0 -0.35 20 20
GNAQ 0.026 0.02 -10000 0 -0.4 1 1
mol:L-citrulline 0.018 0.066 0.36 1 -0.42 9 10
TXA2/TXA2-R family -0.087 0.14 -10000 0 -0.5 18 18
LCK -0.074 0.082 -10000 0 -0.3 5 5
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.079 0.1 -10000 0 -0.24 4 4
TXA2-R family/G12 family/GDP/G beta/gamma -0.033 0.12 -10000 0 -0.49 25 25
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.073 0.1 -10000 0 -0.23 4 4
MAPK14 -0.042 0.071 -10000 0 -0.23 12 12
TGM2/GTP -0.077 0.12 -10000 0 -0.41 22 22
MAPK11 -0.042 0.071 -10000 0 -0.24 12 12
ARHGEF1 -0.035 0.055 -10000 0 -0.18 11 11
GNAI2 0.027 0.004 -10000 0 -10000 0 0
JNK cascade -0.067 0.11 -10000 0 -0.37 18 18
RAB11/GDP 0.027 0.006 -10000 0 -10000 0 0
ICAM1 -0.045 0.082 -10000 0 -0.28 13 13
cAMP biosynthetic process -0.07 0.11 -10000 0 -0.34 31 31
Gq family/GTP/EBP50 0.016 0.049 0.24 4 -0.32 5 9
actin cytoskeleton reorganization 0.029 0.019 -10000 0 -0.23 1 1
SRC -0.041 0.069 -10000 0 -10000 0 0
GNB5 0.026 0.006 -10000 0 -10000 0 0
GNB1 0.026 0.007 -10000 0 -10000 0 0
EGF/EGFR -0.065 0.1 0.17 5 -0.28 26 31
VCAM1 -0.05 0.092 -10000 0 -0.38 12 12
TP beta/Gq family/GDP/G beta5/gamma2 -0.028 0.12 -10000 0 -0.68 10 10
platelet activation -0.054 0.094 -10000 0 -0.31 14 14
PGI2/IP 0.019 0.015 -10000 0 -0.3 1 1
PRKACA -0.096 0.11 -10000 0 -0.21 214 214
Gq family/GDP/G beta5/gamma2 -0.033 0.11 -10000 0 -0.6 10 10
TXA2/TP beta/beta Arrestin2 -0.027 0.064 -10000 0 -0.36 4 4
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.092 0.1 -10000 0 -0.2 210 210
mol:DAG -0.069 0.12 -10000 0 -0.39 23 23
EGFR 0.024 0.021 -10000 0 -0.4 1 1
TXA2/TP alpha -0.091 0.15 -10000 0 -0.46 31 31
Gq family/GTP 0.01 0.054 0.3 3 -0.3 6 9
YES1 -0.066 0.078 -10000 0 -10000 0 0
GNAI2/GTP -0.071 0.094 -10000 0 -0.23 2 2
PGD2/DP -0.13 0.15 -10000 0 -0.28 221 221
SLC9A3R1 0.027 0.004 -10000 0 -10000 0 0
FYN -0.072 0.078 -10000 0 -10000 0 0
mol:NO 0.018 0.066 0.36 1 -0.42 9 10
GNA15 0.022 0.048 -10000 0 -0.43 5 5
PGK/cGMP 0.016 0.068 -10000 0 -0.25 27 27
RhoA/GDP 0.027 0.004 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.043 0.1 -10000 0 -0.34 8 8
NOS3 0.018 0.066 0.36 1 -0.43 9 10
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCA -0.057 0.1 -10000 0 -0.33 16 16
PRKCB -0.08 0.12 -10000 0 -0.39 26 26
PRKCE -0.054 0.1 -10000 0 -0.33 17 17
PRKCD -0.06 0.1 -10000 0 -0.37 15 15
PRKCG -0.085 0.13 -10000 0 -0.39 21 21
muscle contraction -0.084 0.14 -10000 0 -0.46 22 22
PRKCZ -0.061 0.099 -10000 0 -0.34 15 15
ARR3 -0.008 0.034 -10000 0 -0.43 2 2
TXA2/TP beta -0.073 0.1 -10000 0 -0.24 3 3
PRKCQ -0.056 0.1 -10000 0 -0.34 18 18
MAPKKK cascade -0.08 0.13 -10000 0 -0.43 26 26
SELE -0.058 0.096 -10000 0 -0.29 17 17
TP beta/GNAI2/GDP/G beta/gamma -0.073 0.12 -10000 0 -0.32 14 14
ROCK1 0.022 0.022 -10000 0 -0.4 1 1
GNA14 0.025 0.028 -10000 0 -0.4 2 2
chemotaxis -0.088 0.15 -10000 0 -0.58 14 14
GNA12 0.025 0.008 -10000 0 -10000 0 0
GNA13 0.027 0.004 -10000 0 -10000 0 0
GNA11 0.025 0.028 -10000 0 -0.4 2 2
Rac1/GTP 0.018 0.006 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.009 0.13 -10000 0 -0.81 4 4
MKNK1 0.027 0.004 -10000 0 -10000 0 0
MAPK14 0.008 0.087 -10000 0 -0.29 22 22
ATF2/c-Jun 0.004 0.064 -10000 0 -10000 0 0
MAPK11 0.007 0.09 -10000 0 -0.31 24 24
MITF -0.007 0.1 -10000 0 -0.33 29 29
MAPKAPK5 -0.001 0.095 -10000 0 -0.32 29 29
KRT8 0 0.093 -10000 0 -0.32 27 27
MAPKAPK3 0.027 0.004 -10000 0 -10000 0 0
MAPKAPK2 0.027 0.004 -10000 0 -10000 0 0
p38alpha-beta/CK2 0.008 0.12 -10000 0 -0.42 25 25
CEBPB -0.003 0.073 -10000 0 -0.33 15 15
SLC9A1 -0.003 0.099 -10000 0 -0.36 27 27
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.002 0.093 -10000 0 -0.32 24 24
p38alpha-beta/MNK1 0.025 0.11 -10000 0 -0.34 23 23
JUN 0.003 0.062 -10000 0 -10000 0 0
PPARGC1A -0.036 0.14 -10000 0 -0.39 34 34
USF1 0.003 0.088 -10000 0 -0.33 24 24
RAB5/GDP/GDI1 0.007 0.074 -10000 0 -0.24 23 23
NOS2 -0.036 0.22 -10000 0 -0.92 25 25
DDIT3 -0.001 0.096 -10000 0 -0.33 28 28
RAB5A 0.026 0.02 -10000 0 -0.4 1 1
HSPB1 0.002 0.092 0.28 15 -0.27 25 40
p38alpha-beta/HBP1 0.024 0.11 -10000 0 -0.34 22 22
CREB1 0.001 0.099 -10000 0 -0.36 26 26
RAB5/GDP 0.019 0.014 -10000 0 -0.28 1 1
EIF4E -0.005 0.085 -10000 0 -0.3 23 23
RPS6KA4 -0.001 0.095 -10000 0 -0.33 29 29
PLA2G4A -0.023 0.1 -10000 0 -0.35 20 20
GDI1 0 0.093 -10000 0 -0.32 28 28
TP53 -0.016 0.11 -10000 0 -0.42 23 23
RPS6KA5 -0.002 0.099 -10000 0 -0.36 26 26
ESR1 -0.023 0.13 -10000 0 -0.39 29 29
HBP1 0.026 0.005 -10000 0 -10000 0 0
MEF2C -0.007 0.1 -10000 0 -0.35 28 28
MEF2A -0.001 0.098 -10000 0 -0.34 27 27
EIF4EBP1 -0.003 0.099 -10000 0 -0.37 25 25
KRT19 -0.001 0.095 -10000 0 -0.33 29 29
ELK4 0.003 0.088 -10000 0 -0.33 24 24
ATF6 0.003 0.088 -10000 0 -0.33 24 24
ATF1 0.001 0.098 -10000 0 -0.36 26 26
p38alpha-beta/MAPKAPK2 0.028 0.1 -10000 0 -0.34 20 20
p38alpha-beta/MAPKAPK3 0.025 0.11 -10000 0 -0.34 23 23
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.017 0.1 -10000 0 -0.23 84 84
cell-cell adhesion 0.041 0.07 0.36 3 -10000 0 3
Ephrin B/EPHB2/RasGAP 0.046 0.051 -10000 0 -0.22 4 4
ITSN1 0.026 0.005 -10000 0 -10000 0 0
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
SHC1 0.027 0.004 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.021 0.066 -10000 0 -0.25 24 24
Ephrin B1/EPHB1 -0.035 0.13 0.23 2 -0.26 112 114
HRAS/GDP -0.027 0.1 -10000 0 -0.3 16 16
Ephrin B/EPHB1/GRB7 0.005 0.11 0.26 4 -0.22 56 60
Endophilin/SYNJ1 0.044 0.075 0.19 24 -10000 0 24
KRAS 0.027 0.003 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.009 0.087 0.26 1 -0.23 37 38
endothelial cell migration 0.043 0.026 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
GRB7 0.033 0.044 0.36 8 -10000 0 8
PAK1 0.03 0.084 0.19 27 -10000 0 27
HRAS 0.026 0.02 -10000 0 -0.4 1 1
RRAS 0.047 0.077 0.2 29 -10000 0 29
DNM1 0.024 0.046 0.36 1 -0.43 4 5
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.013 0.1 0.19 3 -0.4 1 4
lamellipodium assembly -0.041 0.07 -10000 0 -0.36 3 3
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.014 0.059 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
EPHB2 0.023 0.031 -10000 0 -0.43 2 2
EPHB3 0.003 0.1 -10000 0 -0.43 24 24
EPHB1 -0.085 0.2 0.36 2 -0.43 112 114
EPHB4 0.026 0.006 -10000 0 -10000 0 0
mol:GDP -0.017 0.089 -10000 0 -0.29 16 16
Ephrin B/EPHB2 0.037 0.044 -10000 0 -0.21 7 7
Ephrin B/EPHB3 0.026 0.07 -10000 0 -0.22 27 27
JNK cascade -0.045 0.1 0.33 2 -0.38 3 5
Ephrin B/EPHB1 -0.005 0.1 0.24 1 -0.22 75 76
RAP1/GDP -0.003 0.11 0.3 9 -0.27 12 21
EFNB2 0.021 0.011 -10000 0 -10000 0 0
EFNB3 0.016 0.05 -10000 0 -0.4 6 6
EFNB1 0.027 0.002 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.009 0.1 0.24 2 -0.24 71 73
RAP1B 0.027 0.002 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.011 0.097 -10000 0 -0.31 5 5
Rap1/GTP -0.019 0.082 -10000 0 -0.37 3 3
axon guidance -0.017 0.1 -10000 0 -0.23 84 84
MAPK3 0.007 0.053 0.19 2 -10000 0 2
MAPK1 0.007 0.05 -10000 0 -10000 0 0
Rac1/GDP -0.018 0.097 0.24 3 -0.28 13 16
actin cytoskeleton reorganization -0.037 0.076 -10000 0 -0.27 4 4
CDC42/GDP -0.009 0.11 0.29 11 -0.27 15 26
PI3K 0.047 0.029 -10000 0 -10000 0 0
EFNA5 -0.052 0.16 -10000 0 -0.4 82 82
Ephrin B2/EPHB4 0.028 0.016 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.017 0.027 -10000 0 -0.2 3 3
CDC42 0.025 0.021 -10000 0 -0.4 1 1
RAS family/GTP -0.023 0.082 -10000 0 -0.36 4 4
PTK2 0.09 0.21 0.58 66 -10000 0 66
MAP4K4 -0.045 0.11 0.34 2 -0.39 3 5
SRC 0.017 0.013 -10000 0 -10000 0 0
KALRN 0.026 0.02 -10000 0 -0.4 1 1
Intersectin/N-WASP 0.038 0.01 -10000 0 -10000 0 0
neuron projection morphogenesis -0.008 0.096 0.27 15 -10000 0 15
MAP2K1 0.01 0.054 -10000 0 -10000 0 0
WASL 0.026 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.011 0.13 -10000 0 -0.24 112 112
cell migration 0.028 0.082 0.25 7 -10000 0 7
NRAS 0.024 0.029 -10000 0 -0.4 2 2
SYNJ1 0.044 0.075 0.19 24 -10000 0 24
PXN 0.027 0.002 -10000 0 -10000 0 0
TF 0.008 0.1 0.19 22 -0.39 2 24
HRAS/GTP -0.008 0.094 -10000 0 -0.38 3 3
Ephrin B1/EPHB1-2 -0.022 0.12 0.24 2 -0.24 112 114
cell adhesion mediated by integrin -0.038 0.095 0.23 4 -0.21 96 100
RAC1 0.025 0.008 -10000 0 -10000 0 0
mol:GTP -0.007 0.098 -10000 0 -0.4 3 3
RAC1-CDC42/GTP -0.036 0.095 -10000 0 -0.38 12 12
RASA1 0.026 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.011 0.098 0.31 1 -0.27 13 14
ruffle organization -0.006 0.12 0.36 20 -0.37 3 23
NCK1 0.027 0.002 -10000 0 -10000 0 0
receptor internalization 0.027 0.08 0.19 23 -10000 0 23
Ephrin B/EPHB2/KALRN 0.046 0.053 -10000 0 -0.22 4 4
ROCK1 0 0.055 0.18 1 -0.22 25 26
RAS family/GDP -0.044 0.062 -10000 0 -0.28 1 1
Rac1/GTP -0.025 0.082 -10000 0 -0.38 3 3
Ephrin B/EPHB1/Src/Paxillin 0.002 0.051 0.17 1 -10000 0 1
Nongenotropic Androgen signaling

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
PTK2 0.006 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.021 0.079 -10000 0 -0.22 40 40
regulation of S phase of mitotic cell cycle 0.006 0.042 -10000 0 -0.2 15 15
GNAO1 -0.087 0.19 -10000 0 -0.4 121 121
HRAS 0.026 0.02 -10000 0 -0.4 1 1
SHBG/T-DHT 0.011 0.033 -10000 0 -0.32 4 4
PELP1 0.023 0.01 -10000 0 -10000 0 0
AKT1 0.007 0.002 -10000 0 -10000 0 0
MAP2K1 0.048 0.097 0.18 136 -10000 0 136
T-DHT/AR 0.001 0.07 -10000 0 -0.28 26 26
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -0.009 7 7
GNAI2 0.027 0.004 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNAI1 0.014 0.071 -10000 0 -0.4 13 13
mol:GDP -0.014 0.072 -10000 0 -0.3 24 24
cell proliferation 0.044 0.11 0.29 2 -0.36 4 6
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
FOS 0.035 0.12 0.26 1 -0.74 7 8
mol:Ca2+ -0.013 0.029 -10000 0 -0.078 44 44
MAPK3 0.048 0.098 0.3 4 -0.31 1 5
MAPK1 0.021 0.1 0.21 1 -0.39 18 19
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.005 7 7
cAMP biosynthetic process 0.006 0.038 0.11 2 -0.29 4 6
GNG2 0.009 0.081 -10000 0 -0.4 17 17
potassium channel inhibitor activity 0 0.001 -10000 0 -0.005 7 7
HRAS/GTP 0.02 0.051 -10000 0 -0.19 17 17
actin cytoskeleton reorganization 0.034 0.02 -10000 0 -10000 0 0
SRC 0.017 0.013 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.005 7 7
PI3K 0.036 0.007 -10000 0 -10000 0 0
apoptosis -0.043 0.094 0.35 8 -0.28 1 9
T-DHT/AR/PELP1 0.015 0.062 -10000 0 -0.23 26 26
HRAS/GDP -0.003 0.072 -10000 0 -0.3 20 20
CREB1 0.043 0.098 0.28 1 -0.38 8 9
RAC1-CDC42/GTP 0.043 0.024 -10000 0 -10000 0 0
AR -0.004 0.099 -10000 0 -0.4 26 26
GNB1 0.026 0.007 -10000 0 -10000 0 0
RAF1 0.064 0.097 0.2 43 -10000 0 43
RAC1-CDC42/GDP 0.036 0.086 -10000 0 -0.33 15 15
T-DHT/AR/PELP1/Src 0.019 0.053 -10000 0 -0.21 17 17
MAP2K2 0.049 0.098 0.18 139 -0.34 1 140
T-DHT/AR/PELP1/Src/PI3K 0.006 0.042 -10000 0 -0.2 15 15
GNAZ 0.021 0.045 -10000 0 -0.4 5 5
SHBG 0.01 0.054 -10000 0 -0.52 4 4
Gi family/GNB1/GNG2/GDP -0.077 0.19 -10000 0 -0.39 99 99
mol:T-DHT 0 0.001 -10000 0 -0.005 7 7
RAC1 0.025 0.008 -10000 0 -10000 0 0
GNRH1 0.005 0.004 -10000 0 -10000 0 0
Gi family/GTP -0.049 0.11 -10000 0 -0.3 46 46
CDC42 0.025 0.021 -10000 0 -0.4 1 1
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.008 0.1 -10000 0 -0.46 19 19
NFATC2 -0.004 0.13 -10000 0 -0.62 7 7
NFATC3 -0.022 0.069 -10000 0 -0.3 4 4
CD40LG -0.19 0.28 -10000 0 -0.8 40 40
ITCH 0.018 0.019 -10000 0 -10000 0 0
CBLB 0.029 0.028 -10000 0 -0.49 1 1
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.12 0.21 -10000 0 -0.78 23 23
JUNB 0.025 0.028 -10000 0 -0.4 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.037 0.022 -10000 0 -0.24 2 2
T cell anergy 0.038 0.056 -10000 0 -0.32 1 1
TLE4 -0.004 0.09 -10000 0 -0.49 7 7
Jun/NFAT1-c-4/p21SNFT -0.084 0.18 -10000 0 -0.76 11 11
AP-1/NFAT1-c-4 -0.21 0.27 -10000 0 -0.86 31 31
IKZF1 -0.017 0.14 -10000 0 -0.66 17 17
T-helper 2 cell differentiation -0.066 0.17 -10000 0 -0.7 15 15
AP-1/NFAT1 -0.035 0.1 -10000 0 -0.42 6 6
CALM1 0.034 0.016 -10000 0 -10000 0 0
EGR2 -0.046 0.18 -10000 0 -1.1 9 9
EGR3 -0.046 0.18 -10000 0 -0.95 11 11
NFAT1/FOXP3 -0.002 0.12 -10000 0 -0.48 14 14
EGR1 0.027 0.021 -10000 0 -0.39 1 1
JUN -0.031 0.045 -10000 0 -10000 0 0
EGR4 -0.053 0.17 -10000 0 -0.42 79 79
mol:Ca2+ 0.009 0.01 -10000 0 -10000 0 0
GBP3 -0.023 0.15 -10000 0 -0.62 23 23
FOSL1 -0.27 0.22 -10000 0 -0.43 293 293
NFAT1-c-4/MAF/IRF4 -0.092 0.2 -10000 0 -0.78 19 19
DGKA -0.004 0.085 -10000 0 -0.48 4 4
CREM 0.027 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.048 0.16 -10000 0 -0.76 9 9
CTLA4 -0.016 0.12 -10000 0 -0.48 18 18
NFAT1-c-4 (dimer)/EGR1 -0.044 0.16 -10000 0 -0.77 9 9
NFAT1-c-4 (dimer)/EGR4 -0.077 0.18 -10000 0 -0.81 9 9
FOS -0.032 0.055 -10000 0 -0.42 3 3
IFNG -0.064 0.19 -10000 0 -0.66 23 23
T cell activation -0.028 0.14 -10000 0 -0.6 2 2
MAF 0.016 0.068 -10000 0 -0.4 12 12
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.044 0.15 0.81 11 -10000 0 11
TNF -0.069 0.16 -10000 0 -0.83 7 7
FASLG -0.11 0.37 -10000 0 -1.2 40 40
TBX21 -0.005 0.1 -10000 0 -0.4 27 27
BATF3 0.021 0.047 -10000 0 -0.42 5 5
PRKCQ 0.018 0.05 -10000 0 -0.39 4 4
PTPN1 -0.003 0.084 -10000 0 -0.45 6 6
NFAT1-c-4/ICER1 -0.047 0.16 -10000 0 -0.76 9 9
GATA3 0.022 0.045 -10000 0 -0.4 5 5
T-helper 1 cell differentiation -0.063 0.18 -10000 0 -0.65 23 23
IL2RA -0.11 0.21 -10000 0 -0.74 26 26
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.005 0.084 -10000 0 -0.45 6 6
E2F1 0.024 0.056 0.36 8 -0.42 2 10
PPARG 0.024 0.035 -10000 0 -0.4 3 3
SLC3A2 -0.003 0.085 -10000 0 -0.48 4 4
IRF4 -0.11 0.2 -10000 0 -0.4 143 143
PTGS2 -0.19 0.28 -10000 0 -0.76 48 48
CSF2 -0.25 0.32 -10000 0 -0.76 68 68
JunB/Fra1/NFAT1-c-4 -0.16 0.19 -10000 0 -0.79 14 14
IL4 -0.068 0.17 -10000 0 -0.73 15 15
IL5 -0.18 0.27 -10000 0 -0.77 33 33
IL2 -0.028 0.14 -10000 0 -0.6 2 2
IL3 -0.035 0.092 -10000 0 -0.69 6 6
RNF128 0.029 0.028 -10000 0 -0.49 1 1
NFATC1 -0.044 0.15 -10000 0 -0.81 11 11
CDK4 0.025 0.1 0.64 4 -10000 0 4
PTPRK -0.003 0.084 -10000 0 -0.45 6 6
IL8 -0.28 0.32 -10000 0 -0.76 75 75
POU2F1 0.027 0.005 -10000 0 -10000 0 0
Arf6 signaling events

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
CENTA1/KIF3B 0.026 0.028 -10000 0 -0.44 1 1
ARNO/beta Arrestin1-2 0.002 0.094 -10000 0 -0.8 2 2
EGFR 0.024 0.021 -10000 0 -0.4 1 1
EPHA2 0.025 0.022 -10000 0 -0.43 1 1
USP6 0.022 0.024 -10000 0 -0.43 1 1
IQSEC1 0.027 0.004 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.024 0.12 -10000 0 -0.28 82 82
ARRB2 0.008 0.004 -10000 0 -10000 0 0
mol:GTP 0.004 0.041 0.12 5 -0.2 4 9
ARRB1 0.026 0.02 -10000 0 -0.4 1 1
FBXO8 0.025 0.021 -10000 0 -0.4 1 1
TSHR 0.008 0.054 -10000 0 -0.4 7 7
EGF -0.063 0.17 -10000 0 -0.4 90 90
somatostatin receptor activity 0 0 0.001 22 -0.001 24 46
ARAP2 0.026 0.02 -10000 0 -0.4 1 1
mol:GDP -0.037 0.11 0.2 7 -0.27 43 50
mol:PI-3-4-5-P3 0 0 0.001 14 -0.001 11 25
ITGA2B 0.005 0.089 -10000 0 -0.43 18 18
ARF6 0.025 0.007 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.061 0.03 -10000 0 -0.22 2 2
ADAP1 0.024 0.021 -10000 0 -0.4 1 1
KIF13B 0.02 0.023 -10000 0 -0.4 1 1
HGF/MET 0.029 0.056 -10000 0 -0.29 13 13
PXN 0.027 0.002 -10000 0 -10000 0 0
ARF6/GTP -0.025 0.11 0.22 20 -0.28 25 45
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.006 0.11 -10000 0 -0.24 82 82
ADRB2 -0.039 0.15 -10000 0 -0.4 69 69
receptor agonist activity 0 0 0 6 0 21 27
actin filament binding 0 0 0 21 -0.001 23 44
SRC 0.017 0.013 -10000 0 -10000 0 0
ITGB3 0.022 0.045 -10000 0 -0.4 5 5
GNAQ 0.026 0.02 -10000 0 -0.4 1 1
EFA6/PI-4-5-P2 0 0.001 0.001 29 -0.001 12 41
ARF6/GDP -0.05 0.17 0.22 1 -0.42 55 56
ARF6/GDP/GULP/ACAP1 -0.027 0.12 0.23 2 -0.34 23 25
alphaIIb/beta3 Integrin/paxillin/GIT1 0.052 0.066 -10000 0 -0.23 22 22
ACAP1 0.011 0.068 -10000 0 -0.4 12 12
ACAP2 0.026 0.02 -10000 0 -0.4 1 1
LHCGR/beta Arrestin2 0.007 0.026 -10000 0 -10000 0 0
EFNA1 0.027 0.004 -10000 0 -10000 0 0
HGF 0.017 0.06 -10000 0 -0.4 9 9
CYTH3 0.006 0.002 -10000 0 -10000 0 0
CYTH2 0.015 0.068 -10000 0 -1 2 2
NCK1 0.027 0.002 -10000 0 -10000 0 0
fibronectin binding 0 0 0 31 0 14 45
endosomal lumen acidification 0 0 0 34 -0.001 12 46
microtubule-based process 0 0 -10000 0 0 1 1
GULP1 0.006 0.091 -10000 0 -0.4 22 22
GNAQ/ARNO 0.03 0.065 -10000 0 -0.93 2 2
mol:Phosphatidic acid 0 0 0 5 -10000 0 5
PIP3-E 0 0 0 9 0 5 14
MET 0.023 0.046 0.36 1 -0.43 4 5
GNA14 0.025 0.028 -10000 0 -0.4 2 2
GNA15 0.022 0.048 -10000 0 -0.43 5 5
GIT1 0.026 0.02 -10000 0 -0.4 1 1
mol:PI-4-5-P2 0 0 0.001 24 -0.001 18 42
GNA11 0.025 0.028 -10000 0 -0.4 2 2
LHCGR -0.012 0.015 -10000 0 -10000 0 0
AGTR1 -0.13 0.2 -10000 0 -0.4 153 153
desensitization of G-protein coupled receptor protein signaling pathway 0.007 0.026 -10000 0 -10000 0 0
IPCEF1/ARNO -0.001 0.098 -10000 0 -0.85 2 2
alphaIIb/beta3 Integrin 0.022 0.075 -10000 0 -0.3 23 23
HIF-2-alpha transcription factor network

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
MMP14 -0.031 0.16 -10000 0 -0.63 26 26
oxygen homeostasis -0.011 0.01 -10000 0 -10000 0 0
TCEB2 0.026 0.022 -10000 0 -0.43 1 1
TCEB1 0.023 0.01 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.043 0.073 -10000 0 -0.34 1 1
EPO -0.15 0.15 -10000 0 -0.54 12 12
FIH (dimer) 0.007 0.023 -10000 0 -10000 0 0
APEX1 -0.015 0.023 -10000 0 -10000 0 0
SERPINE1 -0.2 0.22 -10000 0 -0.67 43 43
FLT1 -0.002 0.087 -10000 0 -0.65 6 6
ADORA2A -0.16 0.17 0.36 1 -0.52 42 43
germ cell development -0.16 0.17 -10000 0 -0.52 44 44
SLC11A2 -0.16 0.17 -10000 0 -0.53 41 41
BHLHE40 -0.17 0.18 -10000 0 -0.54 44 44
HIF1AN 0.007 0.023 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.091 0.11 -10000 0 -0.39 4 4
ETS1 0.035 0.022 -10000 0 -0.39 1 1
CITED2 -0.006 0.1 -10000 0 -0.72 8 8
KDR -0.012 0.13 -10000 0 -0.67 15 15
PGK1 -0.16 0.17 -10000 0 -0.53 42 42
SIRT1 0.027 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT -0.18 0.2 -10000 0 -0.61 42 42
EPAS1 -0.052 0.065 -10000 0 -0.28 3 3
SP1 0.031 0.01 -10000 0 -10000 0 0
ABCG2 -0.36 0.24 -10000 0 -0.64 114 114
EFNA1 -0.16 0.17 -10000 0 -0.53 42 42
FXN -0.16 0.17 0.36 1 -0.52 42 43
POU5F1 -0.17 0.18 -10000 0 -0.54 45 45
neuron apoptosis 0.18 0.2 0.59 42 -10000 0 42
EP300 0.026 0.006 -10000 0 -10000 0 0
EGLN3 0.003 0.04 -10000 0 -0.4 3 3
EGLN2 0.007 0.03 -10000 0 -0.4 1 1
EGLN1 0.008 0.023 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.046 0.021 -10000 0 -10000 0 0
VHL 0.027 0.003 -10000 0 -10000 0 0
ARNT -0.015 0.031 -10000 0 -0.41 1 1
SLC2A1 -0.16 0.18 0.36 1 -0.53 49 50
TWIST1 -0.16 0.19 0.36 1 -0.61 44 45
ELK1 0.032 0.003 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.091 0.11 -10000 0 -0.4 3 3
VEGFA -0.16 0.17 -10000 0 -0.53 41 41
CREBBP 0.027 0.004 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

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
PTK2 0.015 0.077 -10000 0 -0.38 7 7
Syndecan-4/Syndesmos 0.035 0.13 0.31 4 -0.5 3 7
positive regulation of JNK cascade 0.009 0.15 0.3 4 -0.46 5 9
Syndecan-4/ADAM12 -0.068 0.18 0.28 3 -0.4 31 34
CCL5 0.009 0.085 -10000 0 -0.4 19 19
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
DNM2 0.027 0.003 -10000 0 -10000 0 0
ITGA5 0.024 0.037 -10000 0 -0.43 3 3
SDCBP 0.023 0.022 -10000 0 -0.4 1 1
PLG -0.089 0.17 -10000 0 -0.45 83 83
ADAM12 -0.25 0.22 -10000 0 -0.43 270 270
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.027 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.041 0.049 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.013 0.13 0.31 4 -0.42 8 12
Syndecan-4/CXCL12/CXCR4 0.01 0.15 0.31 4 -0.53 4 8
Syndecan-4/Laminin alpha3 0.022 0.12 0.31 4 -0.5 3 7
MDK 0.023 0.043 -10000 0 -0.43 4 4
Syndecan-4/FZD7 0.036 0.13 0.31 4 -0.5 3 7
Syndecan-4/Midkine 0.033 0.13 0.31 4 -0.49 3 7
FZD7 0.027 0 -10000 0 -10000 0 0
Syndecan-4/FGFR1/FGF 0.013 0.13 0.3 3 -0.45 4 7
THBS1 0.024 0.022 -10000 0 -0.43 1 1
integrin-mediated signaling pathway 0.03 0.13 0.3 4 -0.45 6 10
positive regulation of MAPKKK cascade 0.009 0.15 0.3 4 -0.46 5 9
Syndecan-4/TACI -0.039 0.14 0.31 2 -0.42 16 18
CXCR4 0.027 0.003 -10000 0 -10000 0 0
cell adhesion 0.009 0.052 0.2 12 -0.24 6 18
Syndecan-4/Dynamin 0.035 0.13 0.31 4 -0.5 3 7
Syndecan-4/TSP1 0.034 0.13 0.31 4 -0.47 4 8
Syndecan-4/GIPC 0.035 0.13 0.31 4 -0.5 3 7
Syndecan-4/RANTES 0.027 0.13 0.31 4 -0.47 4 8
ITGB1 0.027 0.002 -10000 0 -10000 0 0
LAMA1 -0.058 0.16 -10000 0 -0.4 85 85
LAMA3 0.019 0.036 -10000 0 -0.4 3 3
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCA 0.022 0.13 0.77 13 -10000 0 13
Syndecan-4/alpha-Actinin 0.031 0.13 0.31 4 -0.5 3 7
TFPI 0.024 0.035 -10000 0 -0.4 3 3
F2 -0.11 0.21 0.4 1 -0.41 144 145
alpha5/beta1 Integrin 0.038 0.028 -10000 0 -0.3 3 3
positive regulation of cell adhesion -0.014 0.13 0.3 4 -0.41 9 13
ACTN1 0.026 0.007 -10000 0 -10000 0 0
TNC 0.015 0.071 -10000 0 -0.41 12 12
Syndecan-4/CXCL12 0.005 0.15 0.31 4 -0.48 6 10
FGF6 -0.017 0.027 0.36 1 -0.43 1 2
RHOA 0.027 0.004 -10000 0 -10000 0 0
CXCL12 -0.048 0.16 -10000 0 -0.4 80 80
TNFRSF13B -0.13 0.19 -10000 0 -0.4 152 152
FGF2 -0.002 0.11 -10000 0 -0.4 30 30
FGFR1 0.02 0.036 -10000 0 -0.4 3 3
Syndecan-4/PI-4-5-P2 -0.011 0.096 0.29 4 -0.5 3 7
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.014 0.11 -10000 0 -0.42 28 28
cell migration -0.021 0.02 -10000 0 -10000 0 0
PRKCD 0.013 0.024 -10000 0 -10000 0 0
vasculogenesis 0.034 0.12 0.3 4 -0.45 4 8
SDC4 -0.008 0.1 0.32 4 -0.53 3 7
Syndecan-4/Tenascin C 0.03 0.14 0.31 4 -0.46 6 10
Syndecan-4/PI-4-5-P2/PKC alpha -0.033 0.038 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.026 0.12 0.31 3 -0.5 3 6
MMP9 -0.003 0.12 0.37 11 -0.42 27 38
Rac1/GTP 0.009 0.053 0.2 12 -0.24 6 18
cytoskeleton organization 0.034 0.13 0.3 4 -0.48 3 7
GIPC1 0.026 0.02 -10000 0 -0.4 1 1
Syndecan-4/TFPI 0.035 0.13 0.31 4 -0.47 4 8
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.038 0.1 0.22 26 -0.31 1 27
PDGFB-D/PDGFRB/SLAP 0.03 0.044 -10000 0 -0.3 7 7
PDGFB-D/PDGFRB/APS/CBL 0.047 0.044 0.26 1 -0.25 8 9
AKT1 0.054 0.093 0.25 14 -10000 0 14
mol:PI-4-5-P2 0.001 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.066 0.12 0.24 59 -0.38 1 60
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
FGR 0.007 0.12 0.34 1 -0.47 18 19
mol:Ca2+ 0.061 0.11 0.24 59 -0.45 1 60
MYC 0.092 0.16 0.39 62 -10000 0 62
SHC1 0.027 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.062 0.076 -10000 0 -10000 0 0
LRP1/PDGFRB/PDGFB 0.048 0.043 -10000 0 -0.25 8 8
GRB10 0.025 0.008 -10000 0 -10000 0 0
PTPN11 0.027 0.003 -10000 0 -10000 0 0
GO:0007205 0.061 0.11 0.24 57 -0.46 1 58
PTEN 0.026 0.006 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
GRB7 0.033 0.044 0.36 8 -10000 0 8
PDGFB-D/PDGFRB/SHP2 0.037 0.037 -10000 0 -0.3 5 5
PDGFB-D/PDGFRB/GRB10 0.034 0.035 -10000 0 -0.3 4 4
cell cycle arrest 0.03 0.044 -10000 0 -0.29 7 7
HRAS 0.026 0.02 -10000 0 -0.4 1 1
HIF1A 0.048 0.087 0.21 20 -10000 0 20
GAB1 0.044 0.12 0.25 14 -0.32 3 17
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.058 0.12 0.23 69 -0.29 1 70
PDGFB-D/PDGFRB 0.026 0.042 -10000 0 -0.26 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.037 0.037 -10000 0 -0.3 5 5
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.006 0.06 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.037 0.037 -10000 0 -0.3 5 5
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 0.061 0.11 0.24 57 -0.46 1 58
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.024 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.041 0.047 0.26 8 -0.3 5 13
SHB 0.027 0.004 -10000 0 -10000 0 0
BLK -0.15 0.23 -10000 0 -0.47 148 148
PTPN2 0.024 0.012 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.037 0.037 -10000 0 -0.3 5 5
BCAR1 0.026 0.02 -10000 0 -0.4 1 1
VAV2 0.054 0.13 0.26 69 -0.35 3 72
CBL 0.027 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.037 0.037 -10000 0 -0.3 5 5
LCK 0.016 0.11 0.34 1 -0.43 14 15
PDGFRB 0.024 0.048 -10000 0 -0.43 5 5
ACP1 0.027 0.002 -10000 0 -10000 0 0
HCK 0.004 0.08 -10000 0 -0.5 8 8
ABL1 0.037 0.13 0.23 59 -0.33 9 68
PDGFB-D/PDGFRB/CBL 0.033 0.12 0.32 1 -0.38 4 5
PTPN1 0.016 0.013 -10000 0 -10000 0 0
SNX15 0.027 0.004 -10000 0 -10000 0 0
STAT3 0.027 0.004 -10000 0 -10000 0 0
STAT1 0.026 0.021 -10000 0 -0.43 1 1
cell proliferation 0.091 0.15 0.38 64 -10000 0 64
SLA 0.021 0.03 -10000 0 -0.4 2 2
actin cytoskeleton reorganization 0.084 0.086 0.34 3 -10000 0 3
SRC 0.011 0.041 -10000 0 -10000 0 0
PI3K -0.003 0.026 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC 0.053 0.043 0.25 7 -0.25 5 12
SH2B2 0.024 0.041 0.36 1 -0.43 3 4
PLCgamma1/SPHK1 0.067 0.13 0.25 58 -0.39 1 59
LYN 0.021 0.079 0.34 1 -0.56 3 4
LRP1 0.025 0.028 -10000 0 -0.4 2 2
SOS1 0.027 0.002 -10000 0 -10000 0 0
STAT5B 0.027 0.004 -10000 0 -10000 0 0
STAT5A 0.027 0.004 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.039 0.051 -10000 0 -10000 0 0
SPHK1 -0.002 0.12 -10000 0 -0.42 32 32
EDG1 0.003 0.004 -10000 0 -10000 0 0
mol:DAG 0.061 0.11 0.24 57 -0.46 1 58
PLCG1 0.061 0.12 0.24 57 -0.48 1 58
NHERF/PDGFRB 0.05 0.037 -10000 0 -0.25 6 6
YES1 -0.008 0.15 0.34 1 -0.5 30 31
cell migration 0.049 0.037 -10000 0 -0.25 6 6
SHC/Grb2/SOS1 0.038 0.05 -10000 0 -10000 0 0
SLC9A3R2 0.026 0.02 -10000 0 -0.4 1 1
SLC9A3R1 0.027 0.004 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.061 0.04 -10000 0 -0.23 6 6
FYN 0.02 0.081 0.34 1 -0.38 7 8
DOK1 0.057 0.084 0.18 59 -0.23 5 64
HRAS/GTP 0.019 0.014 -10000 0 -0.28 1 1
PDGFB 0.025 0.022 -10000 0 -0.43 1 1
RAC1 0.069 0.14 0.35 45 -0.38 1 46
PRKCD 0.056 0.085 0.18 127 -0.23 5 132
FER 0.056 0.085 0.19 59 -0.24 2 61
MAPKKK cascade 0.063 0.099 0.32 9 -10000 0 9
RASA1 0.056 0.085 0.18 118 -0.23 5 123
NCK1 0.027 0.002 -10000 0 -10000 0 0
NCK2 0.027 0.001 -10000 0 -10000 0 0
p62DOK/Csk 0.064 0.074 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0.037 0.037 -10000 0 -0.3 5 5
chemotaxis 0.037 0.12 0.23 59 -0.32 9 68
STAT1-3-5/STAT1-3-5 0.031 0.045 -10000 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.018 0.034 -10000 0 -0.3 5 5
PTPRJ 0.027 0.003 -10000 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.027 0.002 -9999 0 -10000 0 0
ITGB7 0.01 0.083 -9999 0 -0.4 18 18
ITGA4 0.01 0.083 -9999 0 -0.4 18 18
alpha4/beta7 Integrin 0.015 0.092 -9999 0 -0.31 32 32
alpha4/beta1 Integrin 0.028 0.063 -9999 0 -0.28 18 18
Nectin adhesion 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
PDGFRB 0.022 0.048 -10000 0 -0.43 5 5
alphaV beta3 Integrin 0.036 0.034 -10000 0 -0.28 5 5
PTK2 0.016 0.067 -10000 0 -0.34 9 9
positive regulation of JNK cascade 0.026 0.069 -10000 0 -0.28 7 7
CDC42/GDP 0.054 0.097 -10000 0 -0.34 13 13
Rac1/GDP 0.049 0.096 -10000 0 -0.34 12 12
RAP1B 0.027 0.002 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
CDC42/GTP 0.046 0.086 -10000 0 -0.34 7 7
nectin-3/I-afadin 0.031 0.052 -10000 0 -0.28 12 12
RAPGEF1 0.031 0.092 0.28 2 -0.36 12 14
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.005 0.084 -10000 0 -0.39 15 15
PDGFB-D/PDGFRB 0.022 0.048 -10000 0 -0.42 5 5
TLN1 -0.001 0.029 -10000 0 -0.27 3 3
Rap1/GTP 0.02 0.066 -10000 0 -0.3 5 5
IQGAP1 0.026 0.006 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.049 0.013 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.031 0.052 -10000 0 -0.28 12 12
PVR 0.027 0.003 -10000 0 -10000 0 0
Necl-5(dimer) 0.027 0.003 -10000 0 -10000 0 0
mol:GDP 0.047 0.11 -10000 0 -0.4 15 15
MLLT4 0.027 0.004 -10000 0 -10000 0 0
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
PI3K 0.065 0.057 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.039 0.008 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.026 0.08 -10000 0 -0.27 16 16
PVRL1 0.027 0.004 -10000 0 -10000 0 0
PVRL3 0.016 0.068 -10000 0 -0.4 12 12
PVRL2 0.027 0.003 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
CDH1 0.027 0.002 -10000 0 -10000 0 0
CLDN1 -0.38 0.13 0.36 1 -0.43 409 410
JAM-A/CLDN1 -0.21 0.094 -10000 0 -0.24 388 388
SRC 0.006 0.096 -10000 0 -0.41 20 20
ITGB3 0.022 0.045 -10000 0 -0.4 5 5
nectin-1(dimer)/I-afadin/I-afadin 0.039 0.008 -10000 0 -10000 0 0
FARP2 0.049 0.11 -10000 0 -0.45 8 8
RAC1 0.025 0.008 -10000 0 -10000 0 0
CTNNA1 0.027 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.045 0.048 -10000 0 -0.24 12 12
nectin-1/I-afadin 0.039 0.008 -10000 0 -10000 0 0
nectin-2/I-afadin 0.039 0.007 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.032 0.013 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.045 0.048 -10000 0 -0.24 12 12
CDC42/GTP/IQGAP1/filamentous actin 0.032 0.017 -10000 0 -0.23 1 1
F11R 0.027 0.004 -10000 0 -10000 0 0
positive regulation of filopodium formation 0.026 0.069 -10000 0 -0.28 7 7
alphaV/beta3 Integrin/Talin 0.008 0.07 -10000 0 -0.29 3 3
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.039 0.007 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.039 0.007 -10000 0 -10000 0 0
PIP5K1C 0.002 0.032 -10000 0 -0.29 3 3
VAV2 0.04 0.12 -10000 0 -0.41 19 19
RAP1/GDP 0.057 0.091 -10000 0 -0.33 9 9
ITGAV 0.027 0.002 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.045 0.048 -10000 0 -0.24 12 12
nectin-3(dimer)/I-afadin/I-afadin 0.031 0.052 -10000 0 -0.28 12 12
Rac1/GTP 0.034 0.096 -10000 0 -0.33 14 14
PTPRM 0.006 0.039 -10000 0 -0.36 3 3
E-cadherin/beta catenin/alpha catenin 0.076 0.022 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.025 0.021 -10000 0 -0.4 1 1
Glucocorticoid receptor regulatory network

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
PCK2 0.056 0.061 -10000 0 -10000 0 0
SMARCC2 0.024 0.019 -10000 0 -10000 0 0
SMARCC1 0.024 0.019 -10000 0 -10000 0 0
TBX21 -0.1 0.18 0.32 1 -0.68 31 32
SUMO2 0.027 0.008 -10000 0 -10000 0 0
STAT1 (dimer) 0.032 0.021 -10000 0 -0.42 1 1
FKBP4 0.027 0.016 0.36 1 -10000 0 1
FKBP5 0.026 0.02 -10000 0 -0.4 1 1
GR alpha/HSP90/FKBP51/HSP90 0.087 0.1 0.3 16 -0.26 13 29
PRL -0.043 0.091 -10000 0 -0.54 1 1
cortisol/GR alpha (dimer)/TIF2 0.16 0.18 0.51 42 -0.39 3 45
RELA -0.042 0.07 -10000 0 -0.23 1 1
FGG 0.08 0.18 0.44 20 -0.44 12 32
GR beta/TIF2 0.075 0.11 0.3 17 -0.3 16 33
IFNG -0.18 0.16 -10000 0 -0.57 33 33
apoptosis -0.001 0.15 0.48 14 -0.5 6 20
CREB1 0.025 0.025 -10000 0 -10000 0 0
histone acetylation -0.043 0.1 0.33 6 -0.35 18 24
BGLAP -0.044 0.088 -10000 0 -0.42 2 2
GR/PKAc 0.062 0.14 0.3 10 -0.37 14 24
NF kappa B1 p50/RelA -0.069 0.12 -10000 0 -0.31 21 21
SMARCD1 0.024 0.02 -10000 0 -10000 0 0
MDM2 0.057 0.058 0.21 24 -0.26 1 25
GATA3 0.023 0.049 -10000 0 -0.4 5 5
AKT1 0.021 0.006 -10000 0 -10000 0 0
CSF2 -0.11 0.12 -10000 0 -0.48 2 2
GSK3B 0.028 0.007 -10000 0 -10000 0 0
NR1I3 0.003 0.16 0.48 12 -0.7 5 17
CSN2 0.073 0.12 0.36 18 -0.4 1 19
BRG1/BAF155/BAF170/BAF60A 0.061 0.056 -10000 0 -0.27 4 4
NFATC1 0.019 0.036 -10000 0 -0.4 3 3
POU2F1 0.026 0.019 -10000 0 -10000 0 0
CDKN1A -0.013 0.11 -10000 0 -1.4 2 2
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.007 -10000 0 -10000 0 0
SFN 0.023 0.029 -10000 0 -0.4 2 2
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.091 0.1 0.3 12 -0.3 4 16
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.001 0.14 0.45 11 -0.66 2 13
JUN -0.18 0.12 -10000 0 -0.42 39 39
IL4 -0.052 0.083 -10000 0 -0.45 4 4
CDK5R1 0.026 0.022 -10000 0 -0.42 1 1
PRKACA 0.027 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.22 0.15 -10000 0 -0.4 121 121
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.097 0.1 0.3 15 -0.29 5 20
cortisol/GR alpha (monomer) 0.19 0.21 0.6 43 -0.43 3 46
NCOA2 0.023 0.022 -10000 0 -0.4 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.069 0.05 -10000 0 -0.44 3 3
AP-1/NFAT1-c-4 -0.26 0.16 -10000 0 -0.55 65 65
AFP -0.13 0.1 -10000 0 -10000 0 0
SUV420H1 0.027 0.004 -10000 0 -10000 0 0
IRF1 0.093 0.1 0.4 9 -10000 0 9
TP53 0.033 0.029 -10000 0 -0.48 1 1
PPP5C 0.027 0.003 -10000 0 -10000 0 0
KRT17 -0.31 0.16 -10000 0 -0.56 65 65
KRT14 -0.083 0.21 0.41 3 -1.1 12 15
TBP 0.033 0.008 -10000 0 -10000 0 0
CREBBP 0.033 0.075 0.32 9 -0.25 18 27
HDAC1 0.025 0.008 -10000 0 -10000 0 0
HDAC2 0.034 0.013 -10000 0 -10000 0 0
AP-1 -0.27 0.16 -10000 0 -0.55 65 65
MAPK14 0.028 0.007 -10000 0 -10000 0 0
MAPK10 -0.03 0.14 -10000 0 -0.39 61 61
MAPK11 0.024 0.032 -10000 0 -0.43 2 2
KRT5 -0.2 0.17 -10000 0 -0.58 38 38
interleukin-1 receptor activity 0.008 0.011 -10000 0 -10000 0 0
NCOA1 0.029 0.001 -10000 0 -10000 0 0
STAT1 0.032 0.021 -10000 0 -0.42 1 1
CGA -0.059 0.096 -10000 0 -0.42 4 4
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.078 0.14 0.34 24 -0.42 10 34
MAPK3 0.027 0.022 -10000 0 -0.4 1 1
MAPK1 0.027 0.009 -10000 0 -10000 0 0
ICAM1 -0.1 0.13 -10000 0 -0.5 12 12
NFKB1 -0.042 0.07 -10000 0 -0.23 1 1
MAPK8 -0.13 0.11 -10000 0 -0.38 30 30
MAPK9 0.028 0.007 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.002 0.16 0.48 14 -0.53 6 20
BAX -0.008 0.075 -10000 0 -10000 0 0
POMC -0.1 0.26 0.44 1 -1.3 17 18
EP300 0.032 0.075 0.32 9 -0.25 18 27
cortisol/GR alpha (dimer)/p53 0.16 0.19 0.53 38 -0.43 1 39
proteasomal ubiquitin-dependent protein catabolic process 0.035 0.058 0.24 17 -0.23 1 18
SGK1 -0.006 0.28 -10000 0 -1.2 22 22
IL13 -0.14 0.12 -10000 0 -0.49 18 18
IL6 -0.13 0.19 0.34 1 -0.5 69 70
PRKACG -0.005 0.028 -10000 0 -0.43 1 1
IL5 -0.11 0.11 -10000 0 -0.61 3 3
IL2 -0.17 0.14 -10000 0 -0.56 18 18
CDK5 0.027 0.006 -10000 0 -10000 0 0
PRKACB -0.026 0.14 -10000 0 -0.4 56 56
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
IL8 -0.21 0.19 -10000 0 -0.49 68 68
CDK5R1/CDK5 0.039 0.02 -10000 0 -0.3 1 1
NF kappa B1 p50/RelA/PKAc -0.064 0.12 -10000 0 -0.34 15 15
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.18 0.18 0.52 39 -0.4 1 40
SMARCA4 0.024 0.019 -10000 0 -10000 0 0
chromatin remodeling 0.079 0.15 0.35 23 -0.49 16 39
NF kappa B1 p50/RelA/Cbp -0.018 0.13 0.38 4 -0.38 8 12
JUN (dimer) -0.18 0.12 -10000 0 -0.42 39 39
YWHAH 0.026 0.006 -10000 0 -10000 0 0
VIPR1 -0.097 0.18 -10000 0 -0.74 27 27
NR3C1 0.093 0.16 0.42 25 -0.39 22 47
NR4A1 0.004 0.12 -10000 0 -0.5 23 23
TIF2/SUV420H1 0.034 0.021 -10000 0 -0.28 1 1
MAPKKK cascade -0.001 0.15 0.48 14 -0.5 6 20
cortisol/GR alpha (dimer)/Src-1 0.19 0.18 0.52 45 -0.44 1 46
PBX1 0.016 0.068 -10000 0 -0.4 11 11
POU1F1 0.002 0.036 -10000 0 -0.51 1 1
SELE -0.13 0.18 -10000 0 -0.54 34 34
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.079 0.16 0.35 23 -0.49 16 39
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.18 0.18 0.52 39 -0.4 1 40
mol:cortisol 0.093 0.11 0.33 45 -10000 0 45
MMP1 -0.22 0.16 -10000 0 -0.48 33 33
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.018 0.068 0.44 6 -10000 0 6
VDR 0.027 0.003 -10000 0 -10000 0 0
FAM120B 0.027 0.004 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.046 0.11 -10000 0 -0.36 5 5
RXRs/LXRs/DNA/Oxysterols -0.031 0.11 -10000 0 -0.4 7 7
MED1 0.027 0.016 0.36 1 -10000 0 1
mol:9cRA 0.003 0.006 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.036 0.11 0.17 1 -0.35 5 6
RXRs/NUR77 -0.039 0.14 -10000 0 -0.39 6 6
RXRs/PPAR -0.058 0.12 -10000 0 -0.3 20 20
NCOR2 0.026 0.02 -10000 0 -0.4 1 1
VDR/VDR/Vit D3 0.02 0.002 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.059 0.032 0.24 1 -10000 0 1
RARA 0.026 0.026 0.36 1 -0.4 1 2
NCOA1 0.027 0.001 -10000 0 -10000 0 0
VDR/VDR/DNA 0.027 0.003 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.045 0.031 0.22 1 -0.2 5 6
RARG 0.027 0.002 -10000 0 -10000 0 0
RPS6KB1 0.033 0.083 0.6 8 -0.38 1 9
RARs/THRs/DNA/SMRT -0.036 0.11 0.17 1 -0.36 6 7
THRA 0.027 0.016 0.36 1 -10000 0 1
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.02 0.002 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.041 0.13 -10000 0 -0.32 1 1
NR1H4 -0.21 0.2 -10000 0 -0.4 245 245
RXRs/LXRs/DNA -0.017 0.14 -10000 0 -0.37 2 2
NR1H2 0.029 0.023 -10000 0 -0.39 1 1
NR1H3 0.03 0.011 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.033 0.13 -10000 0 -0.26 1 1
NR4A1 0.019 0.06 -10000 0 -0.42 8 8
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.16 0.15 -10000 0 -0.37 107 107
RXRG -0.13 0.2 -10000 0 -0.39 168 168
RXR alpha/CCPG 0.04 0.019 -10000 0 -0.28 1 1
RXRA 0.029 0.023 -10000 0 -0.39 1 1
RXRB 0.03 0.011 -10000 0 -10000 0 0
THRB -0.093 0.19 -10000 0 -0.4 127 127
PPARG 0.024 0.035 -10000 0 -0.4 3 3
PPARD 0.026 0.02 -10000 0 -0.4 1 1
TNF -0.034 0.11 -10000 0 -0.78 3 3
mol:Oxysterols 0.003 0.006 -10000 0 -10000 0 0
cholesterol transport -0.031 0.11 -10000 0 -0.4 7 7
PPARA 0.026 0.006 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.023 0.04 -10000 0 -0.4 4 4
RXRs/NUR77/BCL2 -0.08 0.13 -10000 0 -0.32 50 50
SREBF1 -0.024 0.091 -10000 0 -0.5 1 1
RXRs/RXRs/DNA/9cRA -0.041 0.13 -10000 0 -0.32 1 1
ABCA1 -0.038 0.14 -10000 0 -0.98 5 5
RARs/THRs -0.003 0.13 0.26 1 -0.39 2 3
RXRs/FXR -0.17 0.17 -10000 0 -0.4 104 104
BCL2 0.012 0.06 -10000 0 -0.4 9 9
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.039 0.02 0.26 1 -0.28 1 2
alphaV beta3 Integrin 0.031 0.08 -10000 0 -0.25 33 33
PTK2 0.028 0.11 0.3 12 -0.39 3 15
IGF1R 0.026 0.006 -10000 0 -10000 0 0
PI4KB 0.027 0.004 -10000 0 -10000 0 0
MFGE8 0.026 0.005 -10000 0 -10000 0 0
SRC 0.017 0.013 -10000 0 -10000 0 0
CDKN1B 0.011 0.043 -10000 0 -0.4 1 1
VEGFA 0.028 0.016 0.36 1 -10000 0 1
ILK 0.011 0.039 -10000 0 -10000 0 0
ROCK1 0.022 0.022 -10000 0 -0.4 1 1
AKT1 0.005 0.033 -10000 0 -10000 0 0
PTK2B 0.01 0.032 0.18 6 -10000 0 6
alphaV/beta3 Integrin/JAM-A 0.03 0.082 -10000 0 -0.4 2 2
CBL 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.044 0.038 -10000 0 -0.24 7 7
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.003 0.12 -10000 0 -0.21 102 102
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.017 0.04 -10000 0 -0.36 3 3
alphaV/beta3 Integrin/Syndecan-1 0.051 0.032 -10000 0 -0.24 5 5
PI4KA 0.026 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.032 0.15 -10000 0 -0.39 30 30
PI4 Kinase 0.038 0.01 -10000 0 -10000 0 0
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.099 0.16 -10000 0 -0.26 219 219
RPS6KB1 -0.077 0.11 -10000 0 -0.37 30 30
TLN1 0.027 0.004 -10000 0 -10000 0 0
MAPK3 -0.044 0.15 -10000 0 -0.51 38 38
GPR124 0.022 0.022 -10000 0 -0.4 1 1
MAPK1 -0.044 0.15 -10000 0 -0.51 39 39
PXN 0.027 0.002 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.021 0.092 -10000 0 -0.24 50 50
cell adhesion 0.039 0.037 -10000 0 -0.24 5 5
ANGPTL3 -0.003 0.036 -10000 0 -0.43 2 2
VEGFR2 homodimer/VEGFA homodimer/Src 0.033 0.027 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.026 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
TGFBR2 0.027 0.003 -10000 0 -10000 0 0
ITGB3 0.022 0.045 -10000 0 -0.4 5 5
IGF1 -0.079 0.18 -10000 0 -0.4 112 112
RAC1 0.025 0.008 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.042 0.037 -10000 0 -0.23 6 6
apoptosis 0.027 0.002 -10000 0 -10000 0 0
CD47 0.027 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.05 0.032 -10000 0 -0.24 5 5
VCL 0.027 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.002 0.12 -10000 0 -0.25 81 81
CSF1 0.025 0.021 -10000 0 -0.4 1 1
PIK3C2A 0.011 0.043 -10000 0 -0.4 1 1
PI4 Kinase/Pyk2 0.011 0.069 -10000 0 -0.36 2 2
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.063 0.035 0.26 1 -0.21 5 6
FAK1/Vinculin 0.04 0.1 0.24 25 -0.32 3 28
alphaV beta3/Integrin/ppsTEM5 0.042 0.038 -10000 0 -0.23 6 6
RHOA 0.027 0.004 -10000 0 -10000 0 0
VTN 0.006 0.079 -10000 0 -0.43 14 14
BCAR1 0.026 0.02 -10000 0 -0.4 1 1
FGF2 -0.002 0.11 -10000 0 -0.4 30 30
F11R -0.006 0.072 -10000 0 -0.28 29 29
alphaV/beta3 Integrin/Lactadherin 0.049 0.033 -10000 0 -0.23 5 5
alphaV/beta3 Integrin/TGFBR2 0.05 0.032 -10000 0 -0.24 5 5
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.065 0.025 -10000 0 -0.21 2 2
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.047 0.03 -10000 0 -0.21 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.001 0.11 -10000 0 -0.42 28 28
alphaV/beta3 Integrin/Pyk2 0.037 0.039 -10000 0 -10000 0 0
SDC1 0.027 0.001 -10000 0 -10000 0 0
VAV3 -0.008 0.066 -10000 0 -10000 0 0
PTPN11 0.027 0.003 -10000 0 -10000 0 0
IRS1 0.027 0.002 -10000 0 -10000 0 0
FAK1/Paxillin 0.04 0.1 0.24 24 -0.32 3 27
cell migration 0.035 0.097 0.22 35 -0.29 3 38
ITGAV 0.027 0.002 -10000 0 -10000 0 0
PI3K 0.043 0.084 -10000 0 -0.37 2 2
SPP1 -0.19 0.23 -10000 0 -0.43 214 214
KDR 0.026 0.02 -10000 0 -0.4 1 1
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.027 0.002 -10000 0 -10000 0 0
COL4A3 -0.023 0.13 -10000 0 -0.4 45 45
angiogenesis -0.039 0.16 -10000 0 -0.52 37 37
Rac1/GTP 0.004 0.064 -10000 0 -10000 0 0
EDIL3 -0.052 0.16 -10000 0 -0.4 83 83
cell proliferation 0.05 0.032 -10000 0 -0.24 5 5
S1P4 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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 -0.087 0.19 -10000 0 -0.4 121 121
CDC42/GTP -0.04 0.13 -10000 0 -0.35 31 31
PLCG1 -0.034 0.1 -10000 0 -0.36 20 20
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.027 0.004 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
G12/G13 0.036 0.013 -10000 0 -10000 0 0
cell migration -0.04 0.12 -10000 0 -0.34 31 31
S1PR5 0.02 0.056 -10000 0 -0.43 7 7
S1PR4 0.017 0.063 -10000 0 -0.4 10 10
MAPK3 -0.055 0.12 -10000 0 -0.36 33 33
MAPK1 -0.045 0.12 -10000 0 -0.38 22 22
S1P/S1P5/Gi -0.048 0.12 -10000 0 -0.35 29 29
GNAI1 0.014 0.071 -10000 0 -0.4 13 13
CDC42/GDP 0.018 0.015 -10000 0 -0.28 1 1
S1P/S1P5/G12 0.028 0.037 -10000 0 -0.25 7 7
RHOA 0.028 0.062 0.18 48 -10000 0 48
S1P/S1P4/Gi -0.052 0.13 -10000 0 -0.37 33 33
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.021 0.045 -10000 0 -0.4 5 5
S1P/S1P4/G12/G13 0.041 0.038 -10000 0 -0.21 8 8
GNA12 0.025 0.008 -10000 0 -10000 0 0
GNA13 0.027 0.004 -10000 0 -10000 0 0
CDC42 0.025 0.021 -10000 0 -0.4 1 1
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.035 0.12 0.32 27 -10000 0 27
GNAI2 0.027 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.028 0.037 -10000 0 -0.25 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.087 0.19 -10000 0 -0.4 121 121
RhoA/GTP -0.035 0.12 -10000 0 -0.32 27 27
negative regulation of cAMP metabolic process -0.048 0.12 -10000 0 -0.34 29 29
GNAZ 0.021 0.045 -10000 0 -0.4 5 5
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNA12 0.025 0.008 -10000 0 -10000 0 0
S1PR5 0.02 0.056 -10000 0 -0.43 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.048 0.12 -10000 0 -0.35 29 29
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
GNAI1 0.014 0.071 -10000 0 -0.4 13 13
Regulation of Androgen receptor activity

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
HDAC1 0.009 0.011 -10000 0 -10000 0 0
SMARCC1 0.013 0.01 -10000 0 -10000 0 0
REL 0.029 0.008 -10000 0 -10000 0 0
HDAC7 -0.022 0.086 -10000 0 -0.38 4 4
JUN 0.025 0.006 -10000 0 -10000 0 0
EP300 0.026 0.006 -10000 0 -10000 0 0
KAT2B 0.01 0.081 -10000 0 -0.4 17 17
KAT5 0.027 0.004 -10000 0 -10000 0 0
MAPK14 0.001 0.035 -10000 0 -0.3 4 4
FOXO1 0.02 0.023 -10000 0 -0.4 1 1
T-DHT/AR -0.004 0.1 -10000 0 -0.39 4 4
MAP2K6 0.015 0.045 -10000 0 -0.41 4 4
BRM/BAF57 0.027 0.032 -10000 0 -0.31 1 1
MAP2K4 0.015 0.019 -10000 0 -10000 0 0
SMARCA2 0.018 0.028 -10000 0 -0.41 1 1
PDE9A -0.16 0.39 -10000 0 -0.96 81 81
NCOA2 0.023 0.022 -10000 0 -0.4 1 1
CEBPA 0.024 0.035 -10000 0 -0.39 3 3
EHMT2 0.026 0.017 0.36 1 -10000 0 1
cell proliferation 0.031 0.13 0.26 23 -0.42 2 25
NR0B1 -0.008 0.053 -10000 0 -0.43 6 6
EGR1 0.02 0.026 -10000 0 -0.4 1 1
RXRs/9cRA -0.058 0.12 -10000 0 -0.22 164 164
AR/RACK1/Src 0.05 0.099 0.3 2 -0.35 1 3
AR/GR -0.017 0.09 -10000 0 -0.31 17 17
GNB2L1 0.027 0.004 -10000 0 -10000 0 0
PKN1 0.027 0.003 -10000 0 -10000 0 0
RCHY1 0.027 0.005 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -10000 0 -0.012 1 1
MAPK8 0.003 0.018 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.006 0.063 -10000 0 -0.31 3 3
SRC 0.024 0.086 0.19 87 -0.26 3 90
NR3C1 -0.001 0.11 -10000 0 -0.4 30 30
KLK3 -0.22 0.42 -10000 0 -1.2 71 71
APPBP2 0.018 0.028 -10000 0 -0.39 1 1
TRIM24 0.019 0.019 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.005 0.058 0.2 1 -0.32 3 4
TMPRSS2 -0.017 0.13 -10000 0 -0.73 7 7
RXRG -0.15 0.19 -10000 0 -0.4 168 168
mol:9cRA -0.001 0.002 -10000 0 -10000 0 0
RXRA 0.026 0.02 -10000 0 -0.4 1 1
RXRB 0.027 0.003 -10000 0 -10000 0 0
CARM1 0.027 0.003 -10000 0 -10000 0 0
NR2C2 0.027 0.004 -10000 0 -10000 0 0
KLK2 0.023 0.087 -10000 0 -0.35 2 2
AR -0.011 0.064 0.16 1 -0.26 24 25
SENP1 0.027 0.003 -10000 0 -10000 0 0
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
MDM2 0.03 0.023 -10000 0 -0.4 1 1
SRY 0.004 0.011 0.028 74 -10000 0 74
GATA2 0.017 0.065 -10000 0 -0.4 11 11
MYST2 0 0.001 -10000 0 -10000 0 0
HOXB13 -0.14 0.22 0.36 3 -0.43 155 158
T-DHT/AR/RACK1/Src 0.058 0.1 0.3 4 -0.31 3 7
positive regulation of transcription 0.017 0.065 -10000 0 -0.4 11 11
DNAJA1 0.019 0.02 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.019 0.016 -10000 0 -0.29 1 1
NCOA1 0.025 0.019 -10000 0 -10000 0 0
SPDEF -0.059 0.17 -10000 0 -0.4 86 86
T-DHT/AR/TIF2 -0.002 0.068 -10000 0 -0.28 7 7
T-DHT/AR/Hsp90 -0.006 0.055 -10000 0 -0.32 3 3
GSK3B 0.026 0.004 -10000 0 -10000 0 0
NR2C1 0.028 0.004 -10000 0 -10000 0 0
mol:T-DHT -0.016 0.034 -10000 0 -0.27 3 3
SIRT1 0.026 0.005 -10000 0 -10000 0 0
ZMIZ2 0.028 0.014 -10000 0 -10000 0 0
POU2F1 0.014 0.052 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.015 0.061 -10000 0 -0.31 4 4
CREBBP 0.026 0.004 -10000 0 -10000 0 0
SMARCE1 0.019 0.019 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 -0.036 0.1 -10000 0 -0.32 29 29
ACTA1 -0.053 0.1 -10000 0 -0.34 26 26
NUMA1 -0.035 0.11 -10000 0 -0.36 24 24
SPTAN1 -0.053 0.1 -10000 0 -0.34 25 25
LIMK1 -0.047 0.1 0.27 3 -0.34 23 26
BIRC3 0.019 0.057 -10000 0 -0.4 8 8
BIRC2 0.026 0.005 -10000 0 -10000 0 0
BAX 0.027 0.003 -10000 0 -10000 0 0
CASP10 -0.074 0.12 -10000 0 -0.27 111 111
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.027 0.002 -10000 0 -10000 0 0
PTK2 -0.034 0.11 -10000 0 -0.33 32 32
DIABLO 0.027 0.003 -10000 0 -10000 0 0
apoptotic nuclear changes -0.052 0.1 -10000 0 -0.33 25 25
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.027 0.003 -10000 0 -10000 0 0
GSN -0.057 0.11 -10000 0 -0.35 29 29
MADD 0.027 0.003 -10000 0 -10000 0 0
TFAP2A 0.002 0.082 -10000 0 -0.57 7 7
BID -0.027 0.063 -10000 0 -0.22 18 18
MAP3K1 -0.019 0.076 -10000 0 -0.4 12 12
TRADD 0.027 0.002 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.038 0.011 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.053 0.1 -10000 0 -0.34 25 25
CASP9 0.026 0.007 -10000 0 -10000 0 0
DNA repair 0.008 0.041 0.2 2 -10000 0 2
neuron apoptosis -0.014 0.16 -10000 0 -0.69 22 22
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.045 0.11 -10000 0 -0.35 28 28
APAF1 0.027 0.003 -10000 0 -10000 0 0
CASP6 -0.021 0.15 -10000 0 -0.88 12 12
TRAF2 0.026 0.02 -10000 0 -0.4 1 1
ICAD/CAD -0.052 0.096 -10000 0 -0.33 24 24
CASP7 0.002 0.058 0.24 6 -0.27 5 11
KRT18 0.012 0.03 -10000 0 -10000 0 0
apoptosis -0.048 0.11 0.35 1 -0.38 27 28
DFFA -0.053 0.099 -10000 0 -0.34 25 25
DFFB -0.053 0.1 0.19 1 -0.34 25 26
PARP1 -0.008 0.041 -10000 0 -0.2 2 2
actin filament polymerization 0.046 0.097 0.32 20 -0.25 2 22
TNF 0.025 0.029 -10000 0 -0.4 2 2
CYCS -0.013 0.055 0.19 1 -0.19 7 8
SATB1 -0.025 0.14 -10000 0 -0.82 12 12
SLK -0.053 0.1 0.34 1 -0.34 25 26
p15 BID/BAX -0.017 0.069 -10000 0 -0.22 14 14
CASP2 0.022 0.046 0.21 13 -10000 0 13
JNK cascade 0.019 0.075 0.4 12 -10000 0 12
CASP3 -0.055 0.11 -10000 0 -0.35 26 26
LMNB2 0.012 0.1 0.28 1 -0.6 7 8
RIPK1 0.027 0.003 -10000 0 -10000 0 0
CASP4 0.027 0.004 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.063 0.04 -10000 0 -0.22 8 8
negative regulation of DNA binding 0.002 0.081 -10000 0 -0.57 7 7
stress fiber formation -0.053 0.099 0.34 1 -0.33 25 26
GZMB -0.07 0.15 -10000 0 -0.32 111 111
CASP1 0.014 0.014 -10000 0 -0.28 1 1
LMNB1 0.009 0.1 0.28 1 -0.5 9 10
APP -0.015 0.16 -10000 0 -0.7 22 22
TNFRSF1A 0.027 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.007 0 -10000 0 -10000 0 0
VIM -0.046 0.11 -10000 0 -0.38 28 28
LMNA 0.019 0.063 0.28 1 -0.29 2 3
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.023 0.033 -10000 0 -0.22 1 1
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.049 0.098 -10000 0 -0.33 24 24
APAF-1/Caspase 9 -0.022 0.15 -10000 0 -0.62 26 26
nuclear fragmentation during apoptosis -0.034 0.11 -10000 0 -0.36 24 24
CFL2 -0.047 0.098 0.25 2 -0.33 20 22
GAS2 -0.088 0.14 -10000 0 -0.38 51 51
positive regulation of apoptosis 0.018 0.089 0.24 2 -0.4 13 15
PRF1 0.019 0.057 -10000 0 -0.4 8 8
Signaling events mediated by PTP1B

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
PDGFRB 0.022 0.048 -10000 0 -0.43 5 5
Jak2/Leptin Receptor 0.023 0.085 -10000 0 -0.4 7 7
PTP1B/AKT1 0.017 0.074 0.18 3 -0.29 4 7
FYN 0.027 0.004 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.013 0.08 0.2 8 -0.32 4 12
EGFR 0.018 0.027 -10000 0 -0.4 1 1
EGF/EGFR -0.013 0.12 -10000 0 -0.27 34 34
CSF1 0.025 0.021 -10000 0 -0.4 1 1
AKT1 0.026 0.008 -10000 0 -10000 0 0
INSR 0.027 0.004 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.005 0.081 0.2 5 -0.28 10 15
Insulin Receptor/Insulin 0.029 0.067 -10000 0 -0.32 2 2
HCK 0.01 0.053 -10000 0 -0.4 7 7
CRK 0.023 0.01 -10000 0 -10000 0 0
TYK2 0.011 0.078 0.24 7 -0.33 3 10
EGF -0.06 0.17 -10000 0 -0.4 90 90
YES1 0.022 0.022 -10000 0 -0.4 1 1
CAV1 0.022 0.1 0.21 37 -0.3 4 41
TXN 0.027 0.004 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.028 0.084 0.2 2 -0.36 2 4
cell migration -0.013 0.08 0.32 4 -0.2 8 12
STAT3 0.027 0.004 -10000 0 -10000 0 0
PRLR 0.018 0.06 -10000 0 -0.4 9 9
ITGA2B 0.005 0.089 -10000 0 -0.42 18 18
CSF1R 0 0.1 -10000 0 -0.4 28 28
Prolactin Receptor/Prolactin 0.019 0.07 -10000 0 -0.29 21 21
FGR 0.021 0.041 -10000 0 -0.4 4 4
PTP1B/p130 Cas 0.019 0.081 0.2 6 -0.28 5 11
Crk/p130 Cas 0.018 0.078 0.19 3 -0.31 3 6
DOK1 0.016 0.073 0.21 2 -0.32 3 5
JAK2 0.015 0.085 0.22 1 -0.35 11 12
Jak2/Leptin Receptor/Leptin 0.021 0.092 -10000 0 -0.34 3 3
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
PTPN1 0.013 0.08 0.2 8 -0.32 4 12
LYN 0.024 0.009 -10000 0 -10000 0 0
CDH2 0.004 0.084 -10000 0 -0.4 18 18
SRC 0.024 0.087 -10000 0 -0.4 12 12
ITGB3 0.022 0.045 -10000 0 -0.4 5 5
CAT1/PTP1B 0 0.16 0.24 54 -0.44 18 72
CAPN1 0.026 0.004 -10000 0 -10000 0 0
CSK 0.026 0.006 -10000 0 -10000 0 0
PI3K 0.042 0.065 -10000 0 -0.34 1 1
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.023 0.084 -10000 0 -0.33 2 2
negative regulation of transcription 0.015 0.084 0.22 1 -0.34 11 12
FCGR2A 0.024 0.037 -10000 0 -0.43 3 3
FER 0.025 0.007 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.021 0.074 -10000 0 -0.3 23 23
BLK -0.1 0.19 -10000 0 -0.4 129 129
Insulin Receptor/Insulin/Shc 0.046 0.013 -10000 0 -10000 0 0
RHOA 0.026 0.004 -10000 0 -10000 0 0
LEPR 0.021 0.044 -10000 0 -0.39 5 5
BCAR1 0.026 0.02 -10000 0 -0.4 1 1
p210 bcr-abl/Grb2 0.027 0.004 -10000 0 -10000 0 0
mol:NADPH 0 0.003 -10000 0 -10000 0 0
TRPV6 -0.073 0.19 0.24 14 -0.41 65 79
PRL -0.006 0.073 -10000 0 -0.42 12 12
SOCS3 0.011 0.12 -10000 0 -1.1 5 5
SPRY2 0.022 0.012 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.047 0.011 -10000 0 -10000 0 0
CSF1/CSF1R 0.015 0.097 0.21 4 -0.33 8 12
Ras protein signal transduction -0.005 0.055 0.44 5 -10000 0 5
IRS1 0.027 0.002 -10000 0 -10000 0 0
INS 0.007 0.017 -10000 0 -10000 0 0
LEP -0.016 0.11 -10000 0 -0.4 32 32
STAT5B 0.02 0.076 0.18 7 -0.31 6 13
STAT5A 0.02 0.077 0.19 6 -0.31 6 12
GRB2 0.027 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.017 0.086 0.2 7 -0.31 7 14
CSN2 -0.007 0.051 -10000 0 -10000 0 0
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
LAT 0.028 0.059 -10000 0 -0.46 4 4
YBX1 0.035 0.008 -10000 0 -10000 0 0
LCK 0.017 0.063 -10000 0 -0.42 9 9
SHC1 0.027 0.004 -10000 0 -10000 0 0
NOX4 -0.2 0.23 0.35 1 -0.43 228 229
Signaling events mediated by HDAC Class III

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
EP300 0.026 0.006 -10000 0 -10000 0 0
HDAC4 0.027 0.002 -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 0.033 0.3 4 -0.27 1 5
CDKN1A -0.009 0.036 -10000 0 -0.53 2 2
KAT2B 0.011 0.081 -10000 0 -0.4 17 17
BAX 0.027 0.003 -10000 0 -10000 0 0
FOXO3 -0.005 0.003 -10000 0 -10000 0 0
FOXO1 0.02 0.023 -10000 0 -0.4 1 1
FOXO4 0.015 0.004 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.026 0.006 -10000 0 -10000 0 0
TAT -0.15 0.2 -10000 0 -0.4 173 173
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.024 0.052 -10000 0 -0.28 17 17
PPARGC1A -0.027 0.14 -10000 0 -0.4 57 57
FHL2 0.027 0 -10000 0 -10000 0 0
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.036 0.012 -10000 0 -10000 0 0
HIST2H4A 0.009 0.033 0.27 1 -0.3 4 5
SIRT1/FOXO3a 0.018 0.025 -10000 0 -0.2 2 2
SIRT1 0.024 0.01 0.2 1 -10000 0 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.052 0.013 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.016 0.045 -10000 0 -0.2 3 3
apoptosis -0.049 0.016 -10000 0 -10000 0 0
SIRT1/PGC1A 0 0.089 -10000 0 -0.23 57 57
p53/SIRT1 0.026 0.021 0.38 1 -10000 0 1
SIRT1/FOXO4 0.023 0.032 -10000 0 -0.2 2 2
FOXO1/FHL2/SIRT1 0.038 0.026 -10000 0 -0.21 1 1
HIST1H1E 0.007 0.035 0.2 2 -0.24 1 3
SIRT1/p300 0.036 0.012 -10000 0 -10000 0 0
muscle cell differentiation -0.02 0.054 0.24 17 -0.21 3 20
TP53 0.02 0.012 0.2 1 -10000 0 1
KU70/SIRT1/BAX 0.05 0.016 -10000 0 -10000 0 0
CREBBP 0.027 0.004 -10000 0 -10000 0 0
MEF2D 0.027 0.004 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.086 0.15 -10000 0 -0.28 172 172
ACSS2 0.008 0.017 0.35 1 -10000 0 1
SIRT1/PCAF/MYOD 0.02 0.055 0.22 3 -0.24 17 20
FAS signaling pathway (CD95)

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
SPTAN1 0.002 0.038 0.21 13 -10000 0 13
RFC1 0.001 0.032 0.19 12 -10000 0 12
PRKDC 0.019 0.071 0.23 44 -10000 0 44
RIPK1 0.027 0.004 -10000 0 -10000 0 0
CASP7 0.005 0.1 -10000 0 -0.54 12 12
FASLG/FAS/FADD/FAF1 0.004 0.066 0.21 11 -0.23 21 32
MAP2K4 -0.02 0.1 -10000 0 -0.37 17 17
mol:ceramide 0 0.086 -10000 0 -0.29 27 27
GSN 0 0.044 0.21 13 -0.22 4 17
FASLG/FAS/FADD/FAF1/Caspase 8 0 0.076 0.27 1 -0.29 19 20
FAS 0.02 0.045 -10000 0 -0.4 5 5
BID -0.008 0.054 0.26 17 -0.27 1 18
MAP3K1 0.004 0.085 0.21 5 -0.36 12 17
MAP3K7 0.026 0.004 -10000 0 -10000 0 0
RB1 0.027 0.08 0.22 60 -10000 0 60
CFLAR 0.028 0.002 -10000 0 -10000 0 0
HGF/MET 0.032 0.075 -10000 0 -0.26 27 27
ARHGDIB 0.002 0.037 0.21 12 -10000 0 12
FADD 0.025 0.008 -10000 0 -10000 0 0
actin filament polymerization 0.002 0.054 0.22 4 -0.22 15 19
NFKB1 -0.007 0.12 -10000 0 -0.71 11 11
MAPK8 -0.028 0.11 -10000 0 -0.42 18 18
DFFA 0.001 0.032 0.2 9 -10000 0 9
DNA fragmentation during apoptosis 0 0.047 0.21 13 -10000 0 13
FAS/FADD/MET 0.044 0.046 0.25 1 -0.25 9 10
CFLAR/RIP1 0.041 0.006 -10000 0 -10000 0 0
FAIM3 0.004 0.095 -10000 0 -0.4 24 24
FAF1 0.02 0.017 -10000 0 -10000 0 0
PARP1 0.001 0.032 0.19 12 -10000 0 12
DFFB 0.002 0.035 0.2 11 -10000 0 11
CHUK -0.009 0.11 -10000 0 -0.66 11 11
FASLG -0.006 0.1 -10000 0 -0.4 28 28
FAS/FADD 0.033 0.036 -10000 0 -0.28 5 5
HGF 0.017 0.06 -10000 0 -0.4 9 9
LMNA -0.002 0.042 0.26 4 -10000 0 4
CASP6 0.001 0.032 0.19 12 -10000 0 12
CASP10 0.026 0.007 -10000 0 -10000 0 0
CASP3 0.006 0.048 0.25 15 -10000 0 15
PTPN13 0.011 0.08 -10000 0 -0.42 15 15
CASP8 -0.002 0.076 0.32 23 -10000 0 23
IL6 -0.035 0.2 -10000 0 -0.91 14 14
MET 0.023 0.046 0.36 1 -0.43 4 5
ICAD/CAD 0 0.031 0.23 3 -10000 0 3
FASLG/FAS/FADD/FAF1/Caspase 10 -0.001 0.087 -10000 0 -0.29 27 27
activation of caspase activity by cytochrome c -0.008 0.054 0.25 17 -0.26 1 18
PAK2 0.002 0.035 0.19 14 -10000 0 14
BCL2 0.012 0.06 -10000 0 -0.4 9 9
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.035 0.007 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.027 0.003 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.023 0.04 -10000 0 -0.4 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.022 0.011 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.014 0.012 -10000 0 -0.18 1 1
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.022 0.022 -10000 0 -0.4 1 1
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.027 0.005 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
MAP3K12 0.027 0.002 -10000 0 -10000 0 0
FGR 0.021 0.041 -10000 0 -0.4 4 4
p38 alpha/TAB1 -0.064 0.11 -10000 0 -0.33 53 53
PRKG1 0.006 0.087 -10000 0 -0.4 20 20
DUSP8 0.026 0.02 -10000 0 -0.4 1 1
PGK/cGMP/p38 alpha -0.032 0.14 0.16 8 -0.36 46 54
apoptosis -0.062 0.11 -10000 0 -0.32 53 53
RAL/GTP 0.034 0.011 -10000 0 -10000 0 0
LYN 0.024 0.009 -10000 0 -10000 0 0
DUSP1 0.025 0.028 -10000 0 -0.4 2 2
PAK1 0.027 0.003 -10000 0 -10000 0 0
SRC 0.017 0.013 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.052 0.033 -10000 0 -10000 0 0
TRAF6 0.027 0.003 -10000 0 -10000 0 0
RAC1 0.025 0.008 -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 0.024 0.021 -10000 0 -0.4 1 1
RAC1-CDC42/GTP 0.03 0.019 -10000 0 -0.23 1 1
MAPK11 -0.011 0.15 0.22 35 -0.36 28 63
BLK -0.1 0.19 -10000 0 -0.4 129 129
HCK 0.01 0.053 -10000 0 -0.4 7 7
MAP2K3 0.023 0.01 -10000 0 -10000 0 0
DUSP16 0.027 0.004 -10000 0 -10000 0 0
DUSP10 0.023 0.043 -10000 0 -0.43 4 4
TRAF6/MEKK3 0.034 0.007 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.023 0.16 0.21 28 -0.37 46 74
positive regulation of innate immune response -0.023 0.18 0.25 32 -0.42 39 71
LCK 0.017 0.063 -10000 0 -0.42 9 9
p38alpha-beta/MKP7 -0.014 0.18 0.26 32 -0.41 37 69
p38alpha-beta/MKP5 -0.014 0.17 0.26 32 -0.41 37 69
PGK/cGMP 0.006 0.061 -10000 0 -0.28 20 20
PAK2 0.027 0.002 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.015 0.18 0.26 32 -0.43 33 65
CDC42 0.025 0.021 -10000 0 -0.4 1 1
RALB 0.027 0.001 -10000 0 -10000 0 0
RALA 0.025 0.008 -10000 0 -10000 0 0
PAK3 0.009 0.022 -10000 0 -10000 0 0
Glypican 2 network

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
MDK 0.023 0.043 -10000 0 -0.43 4 4
GPC2 0.013 0.08 0.36 1 -0.43 14 15
GPC2/Midkine 0.025 0.069 0.26 1 -0.3 18 19
neuron projection morphogenesis 0.025 0.068 0.26 1 -0.3 18 19
IL6-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
BCL2L1 0.066 0.16 0.42 1 -0.66 2 3
CRP 0.003 0.14 0.48 1 -0.72 3 4
cell cycle arrest 0.002 0.14 -10000 0 -0.75 4 4
TIMP1 0.006 0.15 -10000 0 -0.6 5 5
IL6ST 0.021 0.057 -10000 0 -0.39 8 8
Rac1/GDP -0.037 0.13 -10000 0 -0.38 29 29
AP1 0.053 0.09 -10000 0 -0.46 4 4
GAB2 0.027 0.004 -10000 0 -10000 0 0
TNFSF11 0.032 0.18 0.48 1 -0.87 5 6
HSP90B1 0.035 0.051 -10000 0 -0.58 1 1
GAB1 0.027 0.005 -10000 0 -10000 0 0
MAPK14 -0.035 0.12 -10000 0 -0.39 18 18
AKT1 0.033 0.041 -10000 0 -0.4 1 1
FOXO1 0.061 0.077 0.25 3 -0.36 1 4
MAP2K6 -0.045 0.12 -10000 0 -0.37 25 25
mol:GTP 0 0.001 -10000 0 -10000 0 0
MAP2K4 -0.032 0.12 0.4 1 -0.45 13 14
MITF -0.045 0.12 0.18 2 -0.37 27 29
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.027 0.003 -10000 0 -10000 0 0
A2M 0.003 0.17 -10000 0 -1.2 9 9
CEBPB 0.019 0.016 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.023 0.082 0.25 1 -0.39 7 8
STAT3 -0.006 0.15 -10000 0 -0.8 4 4
STAT1 0.02 0.017 -10000 0 -10000 0 0
CEBPD 0.02 0.15 -10000 0 -0.98 2 2
PIK3CA 0.028 0.002 -10000 0 -10000 0 0
PI3K 0.041 0.008 -10000 0 -10000 0 0
JUN 0.026 0.005 -10000 0 -10000 0 0
PIAS3/MITF -0.028 0.13 0.22 1 -0.37 26 27
MAPK11 -0.032 0.12 -10000 0 -0.4 16 16
STAT3 (dimer)/FOXO1 0.049 0.15 0.35 14 -0.56 4 18
GRB2/SOS1/GAB family 0.014 0.13 0.24 2 -0.4 15 17
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.031 0.12 0.23 2 -0.37 26 28
GRB2 0.027 0.005 -10000 0 -10000 0 0
JAK2 0.024 0.035 -10000 0 -0.4 3 3
LBP 0.07 0.16 0.39 9 -0.58 1 10
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
JAK1 0.028 0.008 -10000 0 -10000 0 0
MYC 0.031 0.15 0.45 2 -0.77 2 4
FGG -0.012 0.14 -10000 0 -0.69 4 4
macrophage differentiation 0.002 0.14 -10000 0 -0.75 4 4
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.026 0.15 0.26 4 -0.29 50 54
JUNB 0.001 0.14 -10000 0 -0.94 3 3
FOS 0.022 0.035 -10000 0 -0.4 3 3
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.04 0.13 0.2 2 -0.38 29 31
STAT1/PIAS1 -0.008 0.12 -10000 0 -0.38 17 17
GRB2/SOS1/GAB family/SHP2/PI3K 0.037 0.04 -10000 0 -0.34 3 3
STAT3 (dimer) 0 0.15 -10000 0 -0.78 4 4
PRKCD -0.012 0.14 0.32 20 -0.5 9 29
IL6R -0.065 0.17 -10000 0 -0.39 99 99
SOCS3 -0.031 0.12 -10000 0 -0.5 5 5
gp130 (dimer)/JAK1/JAK1/LMO4 0.053 0.044 -10000 0 -0.23 8 8
Rac1/GTP -0.035 0.13 -10000 0 -0.39 27 27
HCK 0.01 0.053 -10000 0 -0.4 7 7
MAPKKK cascade 0.041 0.082 -10000 0 -0.5 4 4
bone resorption 0.033 0.17 0.48 1 -0.81 5 6
IRF1 0.004 0.13 -10000 0 -0.76 2 2
mol:GDP -0.04 0.13 0.19 2 -0.38 34 36
SOS1 0.027 0.003 -10000 0 -10000 0 0
VAV1 -0.048 0.13 0.19 2 -0.38 34 36
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.069 0.17 -10000 0 -0.37 89 89
PTPN11 0.016 0.068 -10000 0 -0.79 3 3
IL6/IL6RA -0.072 0.17 0.26 4 -0.3 147 151
gp130 (dimer)/TYK2/TYK2/LMO4 0.05 0.042 -10000 0 -0.23 8 8
gp130 (dimer)/JAK2/JAK2/LMO4 0.048 0.048 -10000 0 -0.23 11 11
IL6 -0.038 0.17 0.36 5 -0.42 69 74
PIAS3 0.026 0.006 -10000 0 -10000 0 0
PTPRE 0.022 0.01 -10000 0 -10000 0 0
PIAS1 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.045 0.12 0.18 3 -0.25 82 85
LMO4 0.029 0.009 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 0.006 0.15 -10000 0 -0.75 4 4
MCL1 0.034 0.047 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

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
NFATC2 0.007 0.062 -10000 0 -0.4 10 10
GNB1/GNG2 -0.021 0.11 -10000 0 -0.32 18 18
mol:DAG -0.021 0.08 0.19 1 -0.34 8 9
PLCG1 -0.021 0.082 0.19 1 -0.35 8 9
YES1 -0.029 0.087 -10000 0 -0.3 20 20
FZD3 0.022 0.033 0.36 2 -0.43 1 3
FZD6 0.023 0.01 -10000 0 -10000 0 0
G protein 0.025 0.12 0.28 8 -0.33 11 19
MAP3K7 -0.029 0.075 -10000 0 -0.34 5 5
mol:Ca2+ -0.02 0.078 0.19 1 -0.33 8 9
mol:IP3 -0.021 0.08 0.19 1 -0.34 8 9
NLK 0 0.079 -10000 0 -0.74 5 5
GNB1 0.026 0.007 -10000 0 -10000 0 0
CAMK2A -0.028 0.081 -10000 0 -0.33 9 9
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.026 0.097 0.17 1 -0.31 24 25
CSNK1A1 0.027 0.004 -10000 0 -10000 0 0
GNAS -0.016 0.084 0.33 1 -0.32 15 16
GO:0007205 -0.023 0.078 -10000 0 -0.34 8 8
WNT6 -0.002 0.1 -10000 0 -0.41 25 25
WNT4 0.006 0.088 -10000 0 -0.4 20 20
NFAT1/CK1 alpha -0.012 0.089 -10000 0 -0.4 7 7
GNG2 0.009 0.081 -10000 0 -0.4 17 17
WNT5A 0.022 0.048 -10000 0 -0.43 5 5
WNT11 -0.065 0.18 -10000 0 -0.42 92 92
CDC42 -0.03 0.084 -10000 0 -0.33 11 11
Ceramide signaling pathway

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
SPHK2 0.012 0.014 -10000 0 -0.28 1 1
MAP4K4 0.018 0.036 -10000 0 -10000 0 0
BAG4 0.023 0.01 -10000 0 -10000 0 0
PKC zeta/ceramide -0.015 0.068 -10000 0 -0.19 46 46
NFKBIA 0.025 0.007 -10000 0 -10000 0 0
BIRC3 0.019 0.057 -10000 0 -0.4 8 8
BAX -0.003 0.039 -10000 0 -0.34 3 3
RIPK1 0.027 0.003 -10000 0 -10000 0 0
AKT1 -0.002 0.012 -10000 0 -10000 0 0
BAD -0.03 0.061 -10000 0 -0.19 47 47
SMPD1 0.021 0.046 0.15 5 -0.24 4 9
RB1 0.013 0.089 0.19 65 -0.19 24 89
FADD/Caspase 8 0.026 0.036 0.2 1 -10000 0 1
MAP2K4 -0.028 0.058 -10000 0 -0.22 12 12
NSMAF 0.024 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.025 0.063 0.18 8 -0.23 9 17
EGF -0.063 0.17 -10000 0 -0.4 90 90
mol:ceramide -0.029 0.065 -10000 0 -0.2 47 47
MADD 0.027 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.01 0.006 -10000 0 -10000 0 0
ASAH1 0.021 0.012 -10000 0 -10000 0 0
negative regulation of cell cycle 0.012 0.089 0.19 65 -0.19 24 89
cell proliferation -0.044 0.097 0.19 1 -0.3 9 10
BID -0.001 0.13 -10000 0 -0.59 20 20
MAP3K1 -0.03 0.061 -10000 0 -0.19 48 48
EIF2A -0.03 0.058 0.17 1 -0.22 10 11
TRADD 0.027 0.002 -10000 0 -10000 0 0
CRADD 0.027 0.003 -10000 0 -10000 0 0
MAPK3 -0.021 0.06 0.18 8 -0.22 8 16
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.026 0.063 0.17 6 -0.22 9 15
Cathepsin D/ceramide -0.015 0.068 -10000 0 -0.19 47 47
FADD 0.019 0.036 0.21 1 -10000 0 1
KSR1 -0.024 0.066 0.19 7 -0.19 44 51
MAPK8 -0.025 0.067 -10000 0 -0.22 16 16
PRKRA -0.03 0.061 -10000 0 -0.19 47 47
PDGFA 0.025 0.008 -10000 0 -10000 0 0
TRAF2 0.026 0.02 -10000 0 -0.4 1 1
IGF1 -0.079 0.18 -10000 0 -0.4 112 112
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.029 0.065 -10000 0 -0.2 47 47
CTSD 0.026 0.02 -10000 0 -0.4 1 1
regulation of nitric oxide biosynthetic process 0.039 0.008 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.046 0.1 -10000 0 -0.33 9 9
PRKCD 0.027 0.004 -10000 0 -10000 0 0
PRKCZ 0.026 0.007 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.01 0.006 -10000 0 -10000 0 0
RelA/NF kappa B1 0.039 0.008 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.027 0.003 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.023 0.03 -10000 0 -0.24 1 1
TNFR1A/BAG4/TNF-alpha 0.044 0.028 -10000 0 -0.24 2 2
mol:Sphingosine-1-phosphate 0.012 0.014 -10000 0 -0.28 1 1
MAP2K1 -0.025 0.061 0.19 4 -0.22 8 12
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.027 0.004 -10000 0 -10000 0 0
CYCS 0.018 0.05 0.16 7 -10000 0 7
TNFRSF1A 0.027 0.004 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.034 0.015 -10000 0 -10000 0 0
EIF2AK2 -0.03 0.059 0.18 1 -0.23 11 12
TNF-alpha/TNFR1A/FAN 0.045 0.028 -10000 0 -0.24 2 2
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.03 0.047 -10000 0 -0.29 1 1
MAP2K2 -0.026 0.061 0.18 5 -0.22 8 13
SMPD3 0.02 0.057 0.19 1 -0.29 10 11
TNF 0.025 0.029 -10000 0 -0.4 2 2
PKC zeta/PAR4 0.038 0.011 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.028 0.082 0.2 62 -10000 0 62
NF kappa B1/RelA/I kappa B alpha 0.069 0.03 -10000 0 -10000 0 0
AIFM1 0.01 0.059 0.15 7 -0.15 4 11
BCL2 0.012 0.06 -10000 0 -0.4 9 9
S1P3 pathway

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
PDGFRB 0.022 0.048 -10000 0 -0.43 5 5
mol:S1P 0.001 0.002 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.038 0.11 -10000 0 -0.31 35 35
GNAO1 -0.086 0.19 -10000 0 -0.4 121 121
S1P/S1P3/G12/G13 0.045 0.025 -10000 0 -0.23 1 1
AKT1 -0.028 0.14 -10000 0 -0.46 36 36
AKT3 -0.015 0.16 -10000 0 -1.2 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.022 0.048 -10000 0 -0.42 5 5
GNAI2 0.027 0.009 -10000 0 -10000 0 0
GNAI3 0.026 0.008 -10000 0 -10000 0 0
GNAI1 0.014 0.071 -10000 0 -0.4 13 13
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.026 0.023 -10000 0 -0.42 1 1
S1PR2 0.027 0.003 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.042 0.13 -10000 0 -0.37 33 33
MAPK3 -0.046 0.12 -10000 0 -0.36 34 34
MAPK1 -0.038 0.12 -10000 0 -0.38 24 24
JAK2 0.001 0.14 0.23 8 -0.36 30 38
CXCR4 -0.045 0.12 -10000 0 -0.36 33 33
FLT1 0.021 0.015 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
SRC -0.032 0.1 -10000 0 -0.35 23 23
S1P/S1P3/Gi -0.042 0.13 -10000 0 -0.38 33 33
RAC1 0.025 0.008 -10000 0 -10000 0 0
RhoA/GTP -0.031 0.13 -10000 0 -0.34 34 34
VEGFA 0.028 0.019 0.36 1 -10000 0 1
S1P/S1P2/Gi -0.044 0.13 -10000 0 -0.35 34 34
VEGFR1 homodimer/VEGFA homodimer 0.033 0.025 0.26 1 -10000 0 1
RHOA 0.027 0.004 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.022 0.037 -10000 0 -0.6 1 1
GNAQ 0.026 0.02 -10000 0 -0.4 1 1
GNAZ 0.021 0.045 -10000 0 -0.4 5 5
G12/G13 0.036 0.013 -10000 0 -10000 0 0
GNA14 0.025 0.028 -10000 0 -0.4 2 2
GNA15 0.022 0.048 -10000 0 -0.43 5 5
GNA12 0.025 0.008 -10000 0 -10000 0 0
GNA13 0.027 0.004 -10000 0 -10000 0 0
GNA11 0.025 0.028 -10000 0 -0.4 2 2
Rac1/GTP -0.032 0.12 -10000 0 -0.35 33 33
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.025 0.023 -10000 0 -10000 0 0
HSPA8 0.026 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.003 0.11 -10000 0 -0.31 31 31
AKT1 -0.012 0.055 -10000 0 -10000 0 0
GSC -0.037 0.13 -10000 0 -0.58 4 4
NKX2-5 0 0.01 -10000 0 -10000 0 0
muscle cell differentiation 0.042 0.12 0.35 17 -10000 0 17
SMAD2-3/SMAD4/SP1 -0.015 0.12 -10000 0 -0.29 3 3
SMAD4 0 0.048 -10000 0 -10000 0 0
CBFB 0.027 0.002 -10000 0 -10000 0 0
SAP18 0.021 0.011 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.033 0.14 -10000 0 -0.25 131 131
SMAD3/SMAD4/VDR 0.058 0.059 -10000 0 -10000 0 0
MYC 0.049 0.06 0.37 5 -0.36 2 7
CDKN2B -0.49 0.64 -10000 0 -1.3 179 179
AP1 0.014 0.054 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.018 0.12 -10000 0 -0.37 30 30
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.16 0.23 -10000 0 -0.43 164 164
SP3 0.029 0.001 -10000 0 -10000 0 0
CREB1 0.027 0 -10000 0 -10000 0 0
FOXH1 0.005 0.078 0.36 1 -0.4 14 15
SMAD3/SMAD4/GR 0.008 0.1 -10000 0 -0.3 26 26
GATA3 0.016 0.058 -10000 0 -0.42 5 5
SKI/SIN3/HDAC complex/NCoR1 0.019 0.066 -10000 0 -0.44 4 4
MEF2C/TIF2 -0.003 0.086 -10000 0 -0.4 8 8
endothelial cell migration 0.02 0.12 -10000 0 -10000 0 0
MAX 0.029 0.012 -10000 0 -10000 0 0
RBBP7 0.026 0.003 -10000 0 -10000 0 0
RBBP4 0.026 0.006 -10000 0 -10000 0 0
RUNX2 0.027 0.003 -10000 0 -10000 0 0
RUNX3 0.024 0.021 -10000 0 -0.4 1 1
RUNX1 0.026 0.006 -10000 0 -10000 0 0
CTBP1 0.026 0.005 -10000 0 -10000 0 0
NR3C1 0.002 0.11 -10000 0 -0.4 30 30
VDR 0.027 0.003 -10000 0 -10000 0 0
CDKN1A -0.014 0.11 -10000 0 -1 3 3
KAT2B 0.012 0.08 -10000 0 -0.39 17 17
SMAD2/SMAD2/SMAD4/FOXH1 -0.004 0.081 0.28 1 -0.3 9 10
DCP1A 0.027 0.004 -10000 0 -10000 0 0
SKI 0.025 0.006 -10000 0 -10000 0 0
SERPINE1 -0.021 0.12 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF2 0.018 0.065 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.016 0.069 -10000 0 -0.28 2 2
SAP30 0.026 0.006 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.054 0.048 -10000 0 -10000 0 0
JUN 0.003 0.046 -10000 0 -10000 0 0
SMAD3/SMAD4/IRF7 0.017 0.067 -10000 0 -0.26 1 1
TFE3 0.018 0.024 -10000 0 -10000 0 0
COL1A2 0.003 0.08 -10000 0 -10000 0 0
mesenchymal cell differentiation -0.017 0.065 -10000 0 -10000 0 0
DLX1 -0.001 0.084 -10000 0 -0.43 16 16
TCF3 0.027 0.004 -10000 0 -10000 0 0
FOS 0.02 0.038 -10000 0 -0.4 3 3
SMAD3/SMAD4/Max 0.026 0.07 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.054 0.019 -10000 0 -10000 0 0
ZBTB17 0.046 0.039 -10000 0 -0.4 1 1
LAMC1 -0.004 0.043 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.016 0.057 0.28 3 -0.31 1 4
IRF7 0.026 0.02 -10000 0 -0.4 1 1
ESR1 -0.012 0.12 -10000 0 -0.4 39 39
HNF4A 0.016 0.014 -10000 0 -10000 0 0
MEF2C -0.002 0.096 -10000 0 -0.42 8 8
SMAD2-3/SMAD4 -0.005 0.092 -10000 0 -0.28 2 2
Cbp/p300/Src-1 0.058 0.025 -10000 0 -10000 0 0
IGHV3OR16-13 0.011 0.011 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.021 0.049 0.36 7 -0.42 1 8
CREBBP 0.028 0.014 -10000 0 -10000 0 0
SKIL 0.026 0.02 -10000 0 -0.4 1 1
HDAC1 0.026 0.006 -10000 0 -10000 0 0
HDAC2 0.026 0.004 -10000 0 -10000 0 0
SNIP1 0.025 0.006 -10000 0 -10000 0 0
GCN5L2 0.004 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.015 0.063 -10000 0 -10000 0 0
MSG1/HSC70 -0.065 0.16 -10000 0 -0.31 133 133
SMAD2 -0.009 0.049 -10000 0 -10000 0 0
SMAD3 0 0.051 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.004 0.047 0.21 4 -0.25 2 6
SMAD2/SMAD2/SMAD4 -0.052 0.12 -10000 0 -0.32 44 44
NCOR1 0.022 0.011 -10000 0 -10000 0 0
NCOA2 0.023 0.022 -10000 0 -0.4 1 1
NCOA1 0.027 0.001 -10000 0 -10000 0 0
MYOD/E2A 0.032 0.006 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 -0.005 0.12 -10000 0 -0.32 1 1
IFNB1 -0.008 0.045 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C 0.004 0.11 -10000 0 -0.43 8 8
CITED1 -0.11 0.21 -10000 0 -0.43 133 133
SMAD2-3/SMAD4/ARC105 0.006 0.091 -10000 0 -10000 0 0
RBL1 0.017 0.013 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.16 0.28 -10000 0 -0.52 159 159
RUNX1-3/PEBPB2 0.05 0.017 -10000 0 -10000 0 0
SMAD7 -0.009 0.096 -10000 0 -0.47 4 4
MYC/MIZ-1 0.072 0.079 0.2 41 -0.3 2 43
SMAD3/SMAD4 0.008 0.11 0.26 8 -0.34 5 13
IL10 -0.022 0.12 -10000 0 -0.45 27 27
PIASy/HDAC complex 0.012 0.025 -10000 0 -10000 0 0
PIAS3 0.028 0.007 -10000 0 -10000 0 0
CDK2 0.03 0.009 -10000 0 -10000 0 0
IL5 -0.014 0.078 -10000 0 -0.38 6 6
CDK4 0.026 0.028 -10000 0 -0.42 1 1
PIAS4 0.012 0.025 -10000 0 -10000 0 0
ATF3 0.024 0.037 -10000 0 -0.43 3 3
SMAD3/SMAD4/SP1 0 0.084 -10000 0 -10000 0 0
FOXG1 -0.072 0.15 -10000 0 -0.44 65 65
FOXO3 -0.028 0.061 -10000 0 -10000 0 0
FOXO1 -0.019 0.052 -10000 0 -0.35 1 1
FOXO4 -0.027 0.059 -10000 0 -10000 0 0
heart looping -0.002 0.095 -10000 0 -0.42 8 8
CEBPB 0 0.029 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.006 0.083 -10000 0 -0.28 9 9
MYOD1 -0.018 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.013 0.049 -10000 0 -10000 0 0
SMAD3/SMAD4/GATA3 0.009 0.094 -10000 0 -0.3 12 12
SnoN/SIN3/HDAC complex/NCoR1 0.026 0.02 -10000 0 -0.4 1 1
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.035 0.069 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1-3 0.013 0.085 -10000 0 -10000 0 0
MED15 0.025 0.021 -10000 0 -0.4 1 1
SP1 0 0.039 -10000 0 -10000 0 0
SIN3B 0.027 0.003 -10000 0 -10000 0 0
SIN3A 0.026 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.002 0.079 0.26 1 -0.27 13 14
ITGB5 -0.011 0.056 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.027 0.052 -10000 0 -0.44 2 2
SMAD3/SMAD4/AR 0.001 0.094 -10000 0 -0.31 16 16
AR -0.004 0.099 -10000 0 -0.4 26 26
negative regulation of cell growth -0.007 0.068 -10000 0 -0.3 8 8
SMAD3/SMAD4/MYOD 0.012 0.065 -10000 0 -10000 0 0
E2F5 0.026 0.05 0.36 6 -0.43 2 8
E2F4 0.027 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.02 0.076 0.27 1 -0.25 7 8
SMAD2-3/SMAD4/FOXO1-3a-4 -0.13 0.24 -10000 0 -0.43 163 163
TFDP1 0.021 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.026 0.065 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX2 0.018 0.065 -10000 0 -10000 0 0
TGIF2 0.021 0.049 0.36 7 -0.43 1 8
TGIF1 0.022 0.011 -10000 0 -10000 0 0
ATF2 0.027 0.002 -10000 0 -10000 0 0
Ephrin B reverse signaling

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
EFNB2 0.021 0.011 -10000 0 -10000 0 0
EPHB2 0.023 0.031 -10000 0 -0.43 2 2
EFNB1 0.01 0.033 0.28 1 -0.29 4 5
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.024 0.13 -10000 0 -0.38 11 11
Ephrin B2/EPHB1-2 -0.007 0.1 0.25 2 -0.23 71 73
neuron projection morphogenesis -0.034 0.12 -10000 0 -0.37 11 11
Ephrin B1/EPHB1-2/Tiam1 -0.036 0.14 0.24 1 -0.38 14 15
DNM1 0.024 0.045 0.36 1 -0.42 4 5
cell-cell signaling 0 0.004 -10000 0 -10000 0 0
MAP2K4 -0.007 0.065 -10000 0 -0.41 10 10
YES1 -0.008 0.11 -10000 0 -0.63 12 12
Ephrin B1/EPHB1-2/NCK2 -0.013 0.12 0.26 2 -0.33 5 7
PI3K 0.032 0.08 -10000 0 -0.42 10 10
mol:GDP -0.037 0.14 0.24 1 -0.38 14 15
ITGA2B 0.005 0.089 -10000 0 -0.43 18 18
endothelial cell proliferation 0.028 0.016 -10000 0 -10000 0 0
FYN -0.005 0.11 -10000 0 -0.61 13 13
MAP3K7 -0.011 0.069 -10000 0 -0.42 12 12
FGR -0.01 0.11 -10000 0 -0.62 14 14
TIAM1 -0.013 0.12 -10000 0 -0.4 41 41
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RGS3 0.027 0.003 -10000 0 -10000 0 0
cell adhesion 0.01 0.088 -10000 0 -0.41 10 10
LYN -0.006 0.11 -10000 0 -0.6 14 14
Ephrin B1/EPHB1-2/Src Family Kinases -0.009 0.093 -10000 0 -0.52 14 14
Ephrin B1/EPHB1-2 -0.011 0.075 -10000 0 -0.46 12 12
SRC -0.009 0.1 -10000 0 -0.58 14 14
ITGB3 0.022 0.045 -10000 0 -0.4 5 5
EPHB1 -0.084 0.2 0.36 2 -0.42 112 114
EPHB4 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.028 0.016 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.022 0.075 -10000 0 -0.3 23 23
BLK -0.046 0.12 -10000 0 -0.65 12 12
HCK -0.011 0.1 -10000 0 -0.6 13 13
regulation of stress fiber formation 0.014 0.12 0.33 5 -0.26 2 7
MAPK8 -0.006 0.064 -10000 0 -0.39 10 10
Ephrin B1/EPHB1-2/RGS3 -0.013 0.12 0.26 2 -0.33 5 7
endothelial cell migration 0.02 0.087 0.28 16 -0.35 6 22
NCK2 0.027 0.001 -10000 0 -10000 0 0
PTPN13 0.01 0.076 -10000 0 -0.39 15 15
regulation of focal adhesion formation 0.014 0.12 0.33 5 -0.26 2 7
chemotaxis 0.014 0.12 0.33 5 -0.26 2 7
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
Rac1/GTP -0.029 0.12 -10000 0 -0.38 11 11
angiogenesis -0.01 0.075 -10000 0 -0.46 12 12
LCK -0.009 0.11 -10000 0 -0.61 14 14
Aurora B signaling

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
Condensin I complex 0.009 0.048 -10000 0 -0.38 1 1
STMN1 0.013 0.016 -10000 0 -0.28 1 1
Aurora B/RasGAP/Survivin 0.051 0.028 0.25 1 -10000 0 1
Chromosomal passenger complex/Cul3 protein complex -0.013 0.084 0.16 1 -0.28 19 20
BIRC5 0.03 0.016 0.36 1 -10000 0 1
DES -0.39 0.32 -10000 0 -0.6 299 299
Aurora C/Aurora B/INCENP 0.046 0.03 -10000 0 -0.21 2 2
Aurora B/TACC1 0.03 0.018 -10000 0 -10000 0 0
Aurora B/PP2A 0.036 0.018 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.009 0.005 -10000 0 -10000 0 0
mitotic metaphase/anaphase transition 0.001 0.004 -10000 0 -10000 0 0
NDC80 0.013 0.008 -10000 0 -10000 0 0
Cul3 protein complex 0.017 0.097 -10000 0 -0.23 58 58
KIF2C 0.014 0.052 -10000 0 -0.35 7 7
PEBP1 0.029 0.002 -10000 0 -10000 0 0
KIF20A 0.028 0.005 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.036 0.018 -10000 0 -10000 0 0
SEPT1 0.021 0.049 -10000 0 -0.4 6 6
SMC2 0.026 0.02 -10000 0 -0.4 1 1
SMC4 0.025 0.028 -10000 0 -0.4 2 2
NSUN2/NPM1/Nucleolin -0.072 0.2 -10000 0 -0.49 80 80
PSMA3 0.026 0.007 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.003 -10000 0 -10000 0 0
H3F3B 0.014 0.007 -10000 0 -10000 0 0
AURKB 0.027 0.014 -10000 0 -10000 0 0
AURKC 0.023 0.03 -10000 0 -0.4 2 2
CDCA8 0.029 0.006 -10000 0 -10000 0 0
cytokinesis 0.007 0.038 -10000 0 -0.37 2 2
Aurora B/Septin1 0.002 0.11 -10000 0 -0.32 9 9
AURKA 0.016 0.014 -10000 0 -10000 0 0
INCENP 0.029 0.005 -10000 0 -10000 0 0
KLHL13 -0.028 0.14 -10000 0 -0.4 58 58
BUB1 0.029 0.004 -10000 0 -10000 0 0
hSgo1/Aurora B/Survivin 0.049 0.029 0.24 1 -0.21 1 2
EVI5 0.028 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.046 0.063 -10000 0 -0.29 1 1
SGOL1 0.026 0.022 -10000 0 -0.43 1 1
CENPA 0.032 0.056 -10000 0 -0.18 5 5
NCAPG 0.026 0.005 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.036 0.018 -10000 0 -10000 0 0
NCAPD2 0.027 0.004 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.037 0.018 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
NCAPH 0.027 0 -10000 0 -10000 0 0
NPM1 -0.041 0.14 -10000 0 -0.31 77 77
RASA1 0.026 0.005 -10000 0 -10000 0 0
KLHL9 0.026 0.005 -10000 0 -10000 0 0
mitotic prometaphase 0.001 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.036 0.018 -10000 0 -10000 0 0
PPP1CC 0.027 0.003 -10000 0 -10000 0 0
Centraspindlin 0.042 0.063 -10000 0 -0.31 1 1
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
NSUN2 -0.035 0.11 -10000 0 -0.28 63 63
MYLK -0.023 0.095 -10000 0 -0.27 58 58
KIF23 0.026 0.022 -10000 0 -0.43 1 1
VIM 0.013 0.008 -10000 0 -10000 0 0
RACGAP1 0.028 0.004 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.035 0.11 -10000 0 -0.28 76 76
Chromosomal passenger complex 0.019 0.049 0.17 1 -0.19 2 3
Chromosomal passenger complex/EVI5 0.09 0.055 0.3 1 -10000 0 1
TACC1 0.023 0.01 -10000 0 -10000 0 0
PPP2R5D 0.027 0.004 -10000 0 -10000 0 0
CUL3 0.027 0.001 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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
USP8 -0.006 0.016 -10000 0 -0.22 2 2
RAS family/GTP 0.01 0.092 0.23 1 -0.26 7 8
NFATC4 -0.022 0.061 0.25 2 -10000 0 2
ERBB2IP 0.021 0.048 -10000 0 -0.39 6 6
HSP90 (dimer) 0.025 0.007 -10000 0 -10000 0 0
mammary gland morphogenesis -0.001 0.074 0.2 1 -10000 0 1
JUN 0.005 0.064 -10000 0 -0.18 1 1
HRAS 0.026 0.02 -10000 0 -0.4 1 1
DOCK7 -0.028 0.066 0.17 1 -10000 0 1
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.014 0.081 0.22 4 -0.22 41 45
AKT1 0.004 0.006 -10000 0 -10000 0 0
BAD -0.006 0.012 -10000 0 -0.24 1 1
MAPK10 -0.022 0.072 0.18 5 -0.24 12 17
mol:GTP 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.001 0.08 0.21 1 -10000 0 1
RAF1 -0.007 0.087 0.25 2 -0.3 7 9
ErbB2/ErbB3/neuregulin 2 -0.002 0.087 0.21 8 -0.22 51 59
STAT3 0.019 0.043 -10000 0 -0.79 1 1
cell migration -0.015 0.07 0.19 7 -0.21 12 19
mol:PI-3-4-5-P3 -0.001 0.001 -10000 0 -10000 0 0
cell proliferation -0.046 0.22 -10000 0 -0.59 55 55
FOS -0.019 0.14 -10000 0 -0.35 58 58
NRAS 0.024 0.029 -10000 0 -0.4 2 2
mol:Ca2+ -0.001 0.074 0.2 1 -10000 0 1
MAPK3 -0.027 0.17 -10000 0 -0.49 41 41
MAPK1 -0.045 0.2 -10000 0 -0.54 52 52
JAK2 -0.029 0.067 0.17 1 -10000 0 1
NF2 0.003 0.065 -10000 0 -0.6 5 5
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.006 0.072 0.18 1 -0.22 41 42
NRG1 -0.022 0.13 -10000 0 -0.4 45 45
GRB2/SOS1 0.039 0.007 -10000 0 -10000 0 0
MAPK8 -0.018 0.092 -10000 0 -0.24 33 33
MAPK9 -0.006 0.054 0.18 5 -10000 0 5
ERBB2 -0.013 0.047 0.29 10 -10000 0 10
ERBB3 0.026 0.003 -10000 0 -10000 0 0
SHC1 0.027 0.004 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
apoptosis 0.004 0.013 0.21 1 -10000 0 1
STAT3 (dimer) 0.019 0.042 -10000 0 -0.77 1 1
RNF41 -0.009 0.014 -10000 0 -0.2 2 2
FRAP1 -0.003 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.011 0.05 -10000 0 -10000 0 0
ErbB2/ErbB2/HSP90 (dimer) 0.011 0.036 0.22 10 -10000 0 10
CHRNA1 -0.036 0.2 0.25 1 -0.59 45 46
myelination -0.019 0.063 0.24 3 -10000 0 3
PPP3CB -0.027 0.063 0.16 1 -10000 0 1
KRAS 0.027 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.01 0.081 0.24 1 -10000 0 1
NRG2 -0.04 0.14 -10000 0 -0.4 59 59
mol:GDP -0.006 0.072 0.18 1 -0.22 41 42
SOS1 0.027 0.002 -10000 0 -10000 0 0
MAP2K2 -0.015 0.092 0.24 2 -0.33 9 11
SRC 0.017 0.013 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.028 0.067 -10000 0 -10000 0 0
MAP2K1 -0.049 0.2 -10000 0 -0.56 42 42
heart morphogenesis -0.001 0.074 0.2 1 -10000 0 1
RAS family/GDP 0.014 0.093 0.25 1 -10000 0 1
GRB2 0.027 0.004 -10000 0 -10000 0 0
PRKACA 0.006 0.069 -10000 0 -0.64 5 5
CHRNE 0.005 0.023 -10000 0 -0.14 7 7
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
activation of caspase activity -0.004 0.006 -10000 0 -10000 0 0
nervous system development -0.001 0.074 0.2 1 -10000 0 1
CDC42 0.025 0.021 -10000 0 -0.4 1 1
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.055 0.054 -10000 0 -0.58 1 1
epithelial cell differentiation 0.046 0.077 -10000 0 -0.63 1 1
ITCH 0.018 0.015 -10000 0 -10000 0 0
WWP1 0.013 0.067 -10000 0 -1.2 1 1
FYN 0.027 0.004 -10000 0 -10000 0 0
EGFR 0.024 0.021 -10000 0 -0.4 1 1
PRL -0.008 0.073 -10000 0 -0.43 12 12
neuron projection morphogenesis 0.024 0.085 0.29 11 -0.38 2 13
PTPRZ1 -0.12 0.19 -10000 0 -0.4 144 144
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.031 0.08 -10000 0 -0.46 1 1
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.005 0.071 -10000 0 -0.51 1 1
ADAM17 0.023 0.011 -10000 0 -10000 0 0
ErbB4/ErbB4 0.015 0.039 -10000 0 -0.64 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.052 0.052 -10000 0 -0.59 1 1
NCOR1 0.022 0.011 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.018 0.075 -10000 0 -0.49 1 1
GRIN2B -0.037 0.11 0.26 3 -0.38 8 11
ErbB4/ErbB2/betacellulin 0.052 0.048 0.26 2 -0.49 1 3
STAT1 0.026 0.021 -10000 0 -0.43 1 1
HBEGF 0.025 0.03 -10000 0 -0.43 2 2
PRLR 0.018 0.059 -10000 0 -0.4 9 9
E4ICDs/ETO2 0.034 0.085 -10000 0 -0.58 1 1
axon guidance 0.039 0.085 0.29 11 -0.72 1 12
NEDD4 0.021 0.012 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin 0.02 0.07 -10000 0 -0.29 21 21
CBFA2T3 -0.031 0.14 -10000 0 -0.4 61 61
ErbB4/ErbB2/HBEGF 0.053 0.047 0.26 2 -0.49 1 3
MAPK3 0.021 0.081 0.27 8 -0.39 2 10
STAT1 (dimer) 0.057 0.052 -10000 0 -0.58 1 1
MAPK1 0.02 0.08 0.27 8 -0.44 1 9
JAK2 0.024 0.035 -10000 0 -0.4 3 3
ErbB4/ErbB2/neuregulin 1 beta 0.005 0.069 0.24 2 -0.49 1 3
NRG1 -0.024 0.087 -10000 0 -0.28 45 45
NRG3 0.004 0.03 -10000 0 -0.43 1 1
NRG2 -0.04 0.14 -10000 0 -0.4 59 59
NRG4 -0.025 0.12 -10000 0 -0.4 44 44
heart development 0.039 0.085 0.29 11 -0.72 1 12
neural crest cell migration 0.005 0.069 0.24 2 -0.48 1 3
ERBB2 0.01 0.029 0.28 4 -10000 0 4
WWOX/E4ICDs 0.053 0.053 -10000 0 -0.58 1 1
SHC1 0.027 0.004 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.037 0.082 -10000 0 -0.55 1 1
apoptosis -0.038 0.079 0.37 9 -10000 0 9
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.032 0.082 -10000 0 -0.38 3 3
ErbB4/ErbB2/epiregulin -0.033 0.12 0.29 4 -0.34 4 8
ErbB4/ErbB4/betacellulin/betacellulin 0.054 0.055 -10000 0 -0.58 1 1
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.069 0.078 -10000 0 -0.52 1 1
MDM2 0.011 0.036 0.25 1 -0.58 1 2
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.002 0.061 -10000 0 -0.4 1 1
STAT5A 0.047 0.086 0.28 12 -0.7 1 13
ErbB4/EGFR/neuregulin 1 beta 0.016 0.074 -10000 0 -0.49 1 1
DLG4 0.021 0.024 -10000 0 -0.43 1 1
GRB2/SHC 0.039 0.009 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.041 0.046 -10000 0 -0.55 1 1
STAT5A (dimer) 0.073 0.096 0.31 3 -0.69 1 4
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.076 0.088 0.28 12 -0.7 1 13
LRIG1 0.027 0.003 -10000 0 -10000 0 0
EREG -0.16 0.23 0.36 2 -0.43 183 185
BTC 0.023 0.04 -10000 0 -0.4 4 4
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.024 0.073 0.29 5 -0.73 1 6
ERBB4 0.01 0.033 -10000 0 -0.64 1 1
STAT5B 0.027 0.004 -10000 0 -10000 0 0
YAP1 0.012 0.053 -10000 0 -0.44 5 5
GRB2 0.027 0.004 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.032 0.075 0.26 2 -0.49 1 3
glial cell differentiation -0.041 0.046 0.54 1 -10000 0 1
WWOX 0.024 0.009 -10000 0 -10000 0 0
cell proliferation 0.019 0.096 0.31 8 -0.53 1 9
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.01 0.019 0.11 7 -0.12 1 8
BUB1B 0.018 0.038 -10000 0 -10000 0 0
PLK1 0.023 0.027 0.07 46 -0.099 2 48
PLK1S1 0.022 0.047 0.098 50 -0.17 14 64
KIF2A 0.018 0.026 0.25 1 -10000 0 1
regulation of mitotic centrosome separation 0.023 0.027 0.07 46 -0.098 2 48
GOLGA2 0.027 0.003 -10000 0 -10000 0 0
Hec1/SPC24 0.039 0.042 -10000 0 -0.19 7 7
WEE1 0.031 0.035 -10000 0 -0.3 1 1
cytokinesis 0.026 0.034 0.19 1 -10000 0 1
PP2A-alpha B56 0.054 0.083 -10000 0 -0.5 9 9
AURKA 0.025 0.022 -10000 0 -10000 0 0
PICH/PLK1 0.019 0.05 0.18 14 -0.19 3 17
CENPE 0.018 0.026 -10000 0 -0.22 1 1
RhoA/GTP 0.02 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.019 0.027 0.25 1 -10000 0 1
PPP2CA 0.027 0.004 -10000 0 -10000 0 0
FZR1 0.026 0.02 -10000 0 -0.4 1 1
TPX2 0.04 0.04 0.1 59 -10000 0 59
PAK1 0.028 0.004 -10000 0 -10000 0 0
SPC24 0.02 0.062 0.36 1 -0.43 8 9
FBXW11 0.027 0.004 -10000 0 -10000 0 0
CLSPN 0.014 0.046 -10000 0 -0.21 16 16
GORASP1 0.027 0.003 -10000 0 -10000 0 0
metaphase 0 0.002 0.016 5 -0.011 1 6
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.011 0.015 0.038 46 -0.052 2 48
G2 phase of mitotic cell cycle 0.001 0.003 0.015 7 -10000 0 7
STAG2 0.027 0.003 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.014 0.051 -10000 0 -0.45 5 5
spindle elongation 0.023 0.027 0.07 46 -0.098 2 48
ODF2 0.029 0.004 -10000 0 -10000 0 0
BUB1 0.018 0.081 -10000 0 -0.53 9 9
TPT1 0.027 0.038 0.099 23 -0.16 7 30
CDC25C 0.019 0.036 -10000 0 -0.24 7 7
CDC25B 0.017 0.098 0.36 12 -0.42 15 27
SGOL1 0.01 0.02 0.12 1 -0.11 7 8
RHOA 0.027 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.037 0.05 0.24 12 -10000 0 12
CDC14B 0.007 0.014 -10000 0 -0.28 1 1
CDC20 0.027 0.004 -10000 0 -10000 0 0
PLK1/PBIP1 0.018 0.02 -10000 0 -10000 0 0
mitosis -0.001 0.001 -10000 0 -10000 0 0
FBXO5 0.017 0.028 0.13 1 -10000 0 1
CDC2 0.002 0.003 0.015 12 -10000 0 12
NDC80 0.022 0.011 -10000 0 -10000 0 0
metaphase plate congression 0.005 0.066 -10000 0 -0.22 35 35
ERCC6L 0.021 0.048 0.19 12 -0.24 1 13
NLP/gamma Tubulin 0.012 0.015 0.075 3 -10000 0 3
microtubule cytoskeleton organization 0.027 0.037 0.099 23 -0.16 7 30
G2/M transition DNA damage checkpoint 0 0.002 0.014 6 -10000 0 6
PPP1R12A 0.026 0.029 -10000 0 -0.4 2 2
interphase 0 0.002 0.014 6 -10000 0 6
PLK1/PRC1-2 0.049 0.026 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0.06 0.023 -10000 0 -10000 0 0
RAB1A 0.027 0.002 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.026 0.03 0.075 59 -10000 0 59
mitotic prometaphase 0.001 0.005 0.018 35 -10000 0 35
proteasomal ubiquitin-dependent protein catabolic process 0.028 0.026 0.17 1 -0.21 1 2
microtubule-based process 0.036 0.025 -10000 0 -10000 0 0
Golgi organization 0.023 0.027 0.07 46 -0.098 2 48
Cohesin/SA2 0.035 0.021 -10000 0 -10000 0 0
PPP1CB/MYPT1 0.039 0.03 -10000 0 -0.39 2 2
KIF20A 0.027 0.004 -10000 0 -10000 0 0
APC/C/CDC20 0.037 0.025 -10000 0 -10000 0 0
PPP2R1A 0.027 0.003 -10000 0 -10000 0 0
chromosome segregation 0.017 0.02 -10000 0 -10000 0 0
PRC1 0.026 0.006 -10000 0 -10000 0 0
ECT2 0.017 0.031 0.19 1 -0.2 3 4
C13orf34 0.022 0.025 0.064 56 -10000 0 56
NUDC 0.005 0.067 -10000 0 -0.22 35 35
regulation of attachment of spindle microtubules to kinetochore 0.018 0.038 -10000 0 -10000 0 0
spindle assembly 0.018 0.023 0.084 8 -0.085 2 10
spindle stabilization 0.022 0.047 0.098 50 -0.17 14 64
APC/C/HCDH1 0.024 0.018 -10000 0 -0.23 2 2
MKLP2/PLK1 0.036 0.025 -10000 0 -10000 0 0
CCNB1 0.027 0.008 -10000 0 -10000 0 0
PPP1CB 0.027 0.02 -10000 0 -0.4 1 1
BTRC 0.026 0.006 -10000 0 -10000 0 0
ROCK2 0.025 0.036 -10000 0 -0.36 2 2
TUBG1 0.018 0.017 0.096 1 -0.13 1 2
G2/M transition of mitotic cell cycle 0.013 0.041 0.18 12 -10000 0 12
MLF1IP 0.007 0.003 -10000 0 -10000 0 0
INCENP 0.027 0.004 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.008 0.007 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.025 0.026 -10000 0 -10000 0 0
CDKN1B 0.023 0.064 -10000 0 -0.3 12 12
CDKN1A 0.022 0.067 0.2 1 -0.29 14 15
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.024 0.009 -10000 0 -10000 0 0
FOXO3 0.024 0.057 -10000 0 -0.27 11 11
AKT1 0.002 0.059 -10000 0 -0.31 14 14
BAD 0.026 0.02 -10000 0 -0.4 1 1
AKT3 0.01 0.036 -10000 0 -0.27 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.024 0.064 -10000 0 -0.3 12 12
AKT1/ASK1 0.041 0.092 0.22 1 -0.29 15 16
BAD/YWHAZ 0.045 0.025 -10000 0 -0.24 1 1
RICTOR 0.023 0.04 -10000 0 -0.4 4 4
RAF1 0.027 0.003 -10000 0 -10000 0 0
JNK cascade -0.038 0.088 0.28 15 -0.21 1 16
TSC1 0.022 0.067 -10000 0 -0.3 12 12
YWHAZ 0.023 0.01 -10000 0 -10000 0 0
AKT1/RAF1 0.044 0.095 0.22 4 -0.31 14 18
EP300 0.026 0.006 -10000 0 -10000 0 0
mol:GDP 0.024 0.069 -10000 0 -0.3 14 14
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.023 0.064 -10000 0 -0.3 12 12
YWHAQ 0.027 0.002 -10000 0 -10000 0 0
TBC1D4 0.057 0.095 0.24 97 -10000 0 97
MAP3K5 0.027 0.004 -10000 0 -10000 0 0
MAPKAP1 0.027 0.004 -10000 0 -10000 0 0
negative regulation of cell cycle -0.05 0.094 0.3 8 -0.2 49 57
YWHAH 0.026 0.006 -10000 0 -10000 0 0
AKT1S1 0.023 0.066 0.2 1 -0.3 13 14
CASP9 0.024 0.058 -10000 0 -0.33 7 7
YWHAB 0.016 0.014 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.042 0.093 0.23 6 -0.3 12 18
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.032 0.027 -10000 0 -10000 0 0
YWHAE 0.023 0.01 -10000 0 -10000 0 0
SRC 0.017 0.013 -10000 0 -10000 0 0
AKT2/p21CIP1 0.02 0.076 0.23 2 -0.29 12 14
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.016 0.03 -10000 0 -0.24 1 1
CHUK 0.025 0.053 -10000 0 -0.28 7 7
BAD/BCL-XL 0.017 0.065 -10000 0 -0.43 2 2
mTORC2 0.031 0.024 -10000 0 -0.21 4 4
AKT2 0.014 0.003 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.06 0.12 0.24 70 -0.35 14 84
PDPK1 0.027 0.003 -10000 0 -10000 0 0
MDM2 0.023 0.066 -10000 0 -0.3 11 11
MAPKKK cascade -0.044 0.093 0.3 14 -0.21 4 18
MDM2/Cbp/p300 0.05 0.091 -10000 0 -0.49 2 2
TSC1/TSC2 0.021 0.063 0.34 1 -0.31 9 10
proteasomal ubiquitin-dependent protein catabolic process 0.047 0.087 -10000 0 -0.46 2 2
glucose import 0.014 0.097 0.21 64 -0.2 39 103
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.024 0.047 0.18 4 -0.34 1 5
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 0.014 0.098 0.21 64 -0.2 39 103
GSK3A 0.024 0.065 0.2 2 -0.3 12 14
FOXO1 0.024 0.071 0.2 22 -0.3 10 32
GSK3B 0.023 0.068 0.2 1 -0.29 14 15
SFN 0.023 0.029 -10000 0 -0.4 2 2
G1/S transition of mitotic cell cycle 0.035 0.078 0.24 4 -0.32 11 15
p27Kip1/14-3-3 family 0.045 0.052 -10000 0 -10000 0 0
PRKACA 0.027 0.003 -10000 0 -10000 0 0
KPNA1 0.027 0.002 -10000 0 -10000 0 0
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
YWHAG 0.026 0.005 -10000 0 -10000 0 0
RHEB 0.026 0.005 -10000 0 -10000 0 0
CREBBP 0.027 0.004 -10000 0 -10000 0 0
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.04 0.02 0.26 1 -0.27 1 2
PDGFRB 0.023 0.048 -10000 0 -0.43 5 5
SPHK1 -0.001 0.054 -10000 0 -0.6 3 3
mol:S1P -0.004 0.049 -10000 0 -0.5 3 3
S1P1/S1P/Gi -0.039 0.15 0.28 1 -0.41 34 35
GNAO1 -0.087 0.19 -10000 0 -0.4 121 121
PDGFB-D/PDGFRB/PLCgamma1 0.01 0.16 0.28 14 -0.42 17 31
PLCG1 -0.045 0.12 0.3 5 -0.44 19 24
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.023 0.048 -10000 0 -0.43 5 5
GNAI2 0.028 0.006 -10000 0 -10000 0 0
GNAI3 0.027 0.007 -10000 0 -10000 0 0
GNAI1 0.014 0.072 -10000 0 -0.4 13 13
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 0.006 0.016 0.2 1 -0.22 1 2
S1P1/S1P 0.023 0.059 0.21 3 -0.29 3 6
negative regulation of cAMP metabolic process -0.038 0.15 0.28 1 -0.39 35 36
MAPK3 -0.043 0.16 0.26 3 -0.46 26 29
calcium-dependent phospholipase C activity -0.001 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
KDR 0.026 0.02 -10000 0 -0.39 1 1
PLCB2 0.024 0.061 0.24 7 -0.32 1 8
RAC1 0.025 0.008 -10000 0 -10000 0 0
RhoA/GTP 0.017 0.047 -10000 0 -0.3 1 1
receptor internalization 0.021 0.055 0.19 2 -0.27 3 5
PTGS2 -0.039 0.17 -10000 0 -0.62 13 13
Rac1/GTP 0.014 0.046 -10000 0 -0.3 1 1
RHOA 0.027 0.004 -10000 0 -10000 0 0
VEGFA 0.028 0.016 0.36 1 -10000 0 1
negative regulation of T cell proliferation -0.038 0.15 0.28 1 -0.39 35 36
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.022 0.046 -10000 0 -0.4 5 5
MAPK1 -0.038 0.15 0.27 1 -0.47 23 24
S1P1/S1P/PDGFB-D/PDGFRB 0.042 0.081 0.24 8 -0.28 2 10
ABCC1 0.028 0.004 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.051 0.16 -10000 0 -0.4 82 82
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.026 0.022 -10000 0 -0.43 1 1
TCEB1 0.023 0.01 -10000 0 -10000 0 0
HIF1A/p53 0.013 0.058 -10000 0 -0.25 18 18
HIF1A 0.004 0.046 -10000 0 -0.26 12 12
COPS5 0.024 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.065 0.033 -10000 0 -10000 0 0
FIH (dimer) 0.026 0.006 -10000 0 -10000 0 0
CDKN2A -0.07 0.19 0.36 2 -0.43 96 98
ARNT/IPAS -0.018 0.12 -10000 0 -0.28 80 80
HIF1AN 0.026 0.006 -10000 0 -10000 0 0
GNB2L1 0.027 0.003 -10000 0 -10000 0 0
HIF1A/ARNT 0.011 0.063 -10000 0 -0.26 18 18
CUL2 0.027 0.001 -10000 0 -10000 0 0
OS9 0.027 0.002 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.046 0.021 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.016 0.059 -10000 0 -0.26 17 17
PHD1-3/OS9 0.059 0.035 -10000 0 -0.21 4 4
HIF1A/RACK1/Elongin B/Elongin C 0.03 0.066 -10000 0 -0.29 5 5
VHL 0.027 0.003 -10000 0 -10000 0 0
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
HIF1A/JAB1 0.01 0.061 -10000 0 -0.26 16 16
EGLN3 0.022 0.035 -10000 0 -0.4 3 3
EGLN2 0.026 0.02 -10000 0 -0.4 1 1
EGLN1 0.026 0.005 -10000 0 -10000 0 0
TP53 0.022 0.011 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.03 0.074 -10000 0 -0.51 7 7
ARNT 0.026 0.02 -10000 0 -0.4 1 1
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.025 0.021 -10000 0 -0.4 1 1
HIF1A/p19ARF -0.032 0.11 0.22 1 -0.31 22 23
Coregulation of Androgen receptor activity

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
NRIP1 0.007 0.05 -10000 0 -0.4 2 2
SVIL 0.012 0.036 -10000 0 -10000 0 0
ZNF318 0.049 0.057 0.18 43 -10000 0 43
JMJD2C 0.004 0.019 -10000 0 -0.07 18 18
T-DHT/AR/Ubc9 0.024 0.067 -10000 0 -0.23 26 26
CARM1 0.019 0.02 -10000 0 -10000 0 0
PRDX1 0.028 0.006 -10000 0 -10000 0 0
PELP1 0.026 0.015 -10000 0 -10000 0 0
CTNNB1 0.013 0.033 -10000 0 -10000 0 0
AKT1 0.031 0.019 -10000 0 -10000 0 0
PTK2B 0.012 0.032 -10000 0 -0.4 1 1
MED1 0.035 0.026 0.36 1 -10000 0 1
MAK 0.033 0.1 0.22 5 -0.42 15 20
response to oxidative stress 0.002 0.005 -10000 0 -10000 0 0
HIP1 0.01 0.041 -10000 0 -0.4 1 1
GSN 0 0.076 -10000 0 -0.42 10 10
NCOA2 0.017 0.026 -10000 0 -0.4 1 1
NCOA6 0.01 0.027 -10000 0 -10000 0 0
DNA-PK 0.061 0.053 -10000 0 -10000 0 0
NCOA4 0.023 0.022 -10000 0 -0.4 1 1
PIAS3 0.013 0.033 -10000 0 -10000 0 0
cell proliferation 0.028 0.071 0.27 1 -0.38 4 5
XRCC5 0.033 0.013 -10000 0 -10000 0 0
UBE3A 0.007 0.05 -10000 0 -0.4 1 1
T-DHT/AR/SNURF -0.001 0.1 -10000 0 -0.25 57 57
FHL2 0.043 0.054 -10000 0 -10000 0 0
RANBP9 0.009 0.045 -10000 0 -0.4 1 1
JMJD1A 0.002 0.011 -10000 0 -0.13 2 2
CDK6 0.027 0.007 -10000 0 -10000 0 0
TGFB1I1 0.012 0.036 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 0.008 0.074 -10000 0 -0.24 29 29
XRCC6 0.031 0.015 -10000 0 -10000 0 0
T-DHT/AR 0.032 0.073 -10000 0 -0.23 26 26
CTDSP1 0.017 0.023 -10000 0 -10000 0 0
CTDSP2 0.042 0.038 -10000 0 -10000 0 0
BRCA1 0.013 0.035 -10000 0 -10000 0 0
TCF4 0.027 0.034 -10000 0 -0.4 1 1
CDKN2A -0.061 0.19 0.36 2 -0.42 96 98
SRF 0.04 0.021 -10000 0 -10000 0 0
NKX3-1 -0.002 0.031 -10000 0 -0.16 6 6
KLK3 -0.19 0.48 -10000 0 -1.3 71 71
TMF1 0.018 0.027 -10000 0 -0.4 1 1
HNRNPA1 0.036 0.022 -10000 0 -10000 0 0
AOF2 -0.012 0.029 -10000 0 -0.079 71 71
APPL1 0.024 0.041 0.15 3 -0.28 2 5
T-DHT/AR/Caspase 8 0.033 0.072 -10000 0 -0.23 26 26
AR 0.001 0.1 -10000 0 -0.4 26 26
UBA3 0.017 0.023 -10000 0 -10000 0 0
PATZ1 0.034 0.022 -10000 0 -10000 0 0
PAWR 0.019 0.018 -10000 0 -10000 0 0
PRKDC 0.028 0.015 -10000 0 -10000 0 0
PA2G4 0.037 0.024 -10000 0 -10000 0 0
UBE2I 0.027 0.004 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.029 0.064 -10000 0 -0.21 26 26
RPS6KA3 0.009 0.043 -10000 0 -10000 0 0
T-DHT/AR/ARA70 0.017 0.068 -10000 0 -0.23 27 27
LATS2 0.028 0.024 -10000 0 -10000 0 0
T-DHT/AR/PRX1 0.035 0.072 0.17 3 -0.21 24 27
Cyclin D3/CDK11 p58 0.022 0.005 -10000 0 -10000 0 0
VAV3 -0.026 0.13 -10000 0 -0.4 43 43
KLK2 0.003 0.065 -10000 0 -0.33 4 4
CASP8 0.031 0.008 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.021 0.068 -10000 0 -0.22 23 23
TMPRSS2 0.009 0.062 -10000 0 -0.82 2 2
CCND1 0.013 0.044 -10000 0 -0.42 3 3
PIAS1 0.007 0.048 -10000 0 -10000 0 0
mol:T-DHT 0.002 0.009 -10000 0 -0.061 3 3
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.002 0.069 -10000 0 -10000 0 0
T-DHT/AR/CDK6 0.026 0.069 -10000 0 -0.23 26 26
CMTM2 0.01 0.09 -10000 0 -0.42 18 18
SNURF -0.019 0.11 -10000 0 -0.4 36 36
ZMIZ1 0.027 0.016 -10000 0 -10000 0 0
CCND3 0.028 0.004 -10000 0 -10000 0 0
TGIF1 0.029 0.023 -10000 0 -10000 0 0
FKBP4 0.01 0.045 0.36 1 -10000 0 1
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.026 0.02 -9999 0 -0.4 1 1
SPHK1 -0.006 0.12 -9999 0 -0.43 32 32
GNAI2 0.027 0.004 -9999 0 -10000 0 0
mol:S1P 0.006 0.034 -9999 0 -0.24 1 1
GNAO1 -0.087 0.19 -9999 0 -0.4 121 121
mol:Sphinganine-1-P -0.01 0.082 -9999 0 -0.3 33 33
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.043 0.046 -9999 0 -10000 0 0
GNAI3 0.026 0.005 -9999 0 -10000 0 0
G12/G13 0.036 0.013 -9999 0 -10000 0 0
S1PR3 0.026 0.022 -9999 0 -0.43 1 1
S1PR2 0.027 0.003 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P 0.001 0.031 -9999 0 -0.21 1 1
S1PR5 0.02 0.056 -9999 0 -0.43 7 7
S1PR4 0.017 0.063 -9999 0 -0.4 10 10
GNAI1 0.014 0.071 -9999 0 -0.4 13 13
S1P/S1P5/G12 0.028 0.054 -9999 0 -0.25 7 7
S1P/S1P3/Gq 0.024 0.055 -9999 0 -0.36 6 6
S1P/S1P4/Gi -0.049 0.13 -9999 0 -0.37 38 38
GNAQ 0.026 0.02 -9999 0 -0.4 1 1
GNAZ 0.021 0.045 -9999 0 -0.4 5 5
GNA14 0.025 0.028 -9999 0 -0.4 2 2
GNA15 0.022 0.048 -9999 0 -0.43 5 5
GNA12 0.025 0.008 -9999 0 -10000 0 0
GNA13 0.027 0.004 -9999 0 -10000 0 0
GNA11 0.025 0.028 -9999 0 -0.4 2 2
ABCC1 0.027 0.003 -9999 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.021 0.052 -10000 0 -0.42 6 6
ANTXR2 0.026 0.02 -10000 0 -0.4 1 1
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0.006 -10000 0 -0.052 7 7
monocyte activation -0.005 0.094 -10000 0 -0.33 35 35
MAP2K2 0.006 0.079 -10000 0 -0.58 8 8
MAP2K1 -0.003 0.006 -10000 0 -10000 0 0
MAP2K7 -0.004 0.011 -10000 0 -0.2 1 1
MAP2K6 -0.005 0.019 -10000 0 -0.2 4 4
CYAA -0.008 0.025 -10000 0 -0.21 7 7
MAP2K4 -0.003 0.006 -10000 0 -10000 0 0
IL1B -0.025 0.066 -10000 0 -0.21 49 49
Channel 0.03 0.033 -10000 0 -0.22 7 7
NLRP1 -0.004 0.018 -10000 0 -0.21 3 3
CALM1 0.025 0.007 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.018 0.1 -10000 0 -0.38 34 34
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0.006 0.052 7 -10000 0 7
MAPK3 -0.004 0.011 -10000 0 -0.2 1 1
MAPK1 -0.003 0.006 -10000 0 -10000 0 0
PGR -0.04 0.076 -10000 0 -0.2 84 84
PA/Cellular Receptors 0.032 0.036 -10000 0 -0.25 7 7
apoptosis -0.001 0.006 -10000 0 -0.052 7 7
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.03 0.029 -10000 0 -0.2 7 7
macrophage activation -0.004 0.02 0.18 4 -0.19 1 5
TNF 0.025 0.029 -10000 0 -0.4 2 2
VCAM1 -0.006 0.095 -10000 0 -0.33 35 35
platelet activation -0.018 0.1 -10000 0 -0.38 34 34
MAPKKK cascade 0.001 0.014 0.14 1 -0.07 7 8
IL18 -0.003 0.017 -10000 0 -0.19 2 2
negative regulation of macrophage activation -0.001 0.006 -10000 0 -0.052 7 7
LEF -0.001 0.006 -10000 0 -0.052 7 7
CASP1 0 0.011 -10000 0 -0.1 4 4
mol:cAMP -0.018 0.1 -10000 0 -0.38 34 34
necrosis -0.001 0.006 -10000 0 -0.052 7 7
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.03 0.031 -10000 0 -0.21 7 7
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
FoxO family signaling

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
G6PC -0.12 0.4 -10000 0 -1.2 55 55
PLK1 0.017 0.13 -10000 0 -0.68 4 4
CDKN1B 0.045 0.12 0.28 3 -0.36 9 12
FOXO3 0.026 0.13 -10000 0 -0.71 5 5
KAT2B 0.015 0.083 -10000 0 -0.39 17 17
FOXO1/SIRT1 -0.003 0.15 -10000 0 -0.37 50 50
CAT 0.018 0.13 -10000 0 -0.65 5 5
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
AKT1 0.019 0.034 -10000 0 -10000 0 0
FOXO1 -0.015 0.15 -10000 0 -0.39 54 54
MAPK10 0.005 0.089 0.19 35 -0.2 55 90
mol:GTP 0.001 0 -10000 0 -10000 0 0
FOXO4 0.032 0.077 -10000 0 -10000 0 0
response to oxidative stress 0 0.022 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.04 0.12 -10000 0 -0.56 7 7
XPO1 0.028 0.001 -10000 0 -10000 0 0
EP300 0.015 0.033 -10000 0 -10000 0 0
BCL2L11 0.031 0.025 -10000 0 -10000 0 0
FOXO1/SKP2 -0.003 0.14 -10000 0 -0.39 39 39
mol:GDP 0 0.022 -10000 0 -10000 0 0
RAN 0.028 0.002 -10000 0 -10000 0 0
GADD45A 0.039 0.14 -10000 0 -0.59 12 12
YWHAQ 0.027 0.002 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.034 0.12 0.21 12 -0.45 12 24
MST1 -0.039 0.16 -10000 0 -0.42 69 69
CSNK1D 0.027 0.004 -10000 0 -10000 0 0
CSNK1E 0.026 0.006 -10000 0 -10000 0 0
FOXO4/14-3-3 family -0.009 0.11 -10000 0 -0.44 17 17
YWHAB 0.016 0.014 -10000 0 -10000 0 0
MAPK8 0.035 0.052 0.19 42 -10000 0 42
MAPK9 0.034 0.052 0.19 42 -10000 0 42
YWHAG 0.026 0.005 -10000 0 -10000 0 0
YWHAE 0.023 0.01 -10000 0 -10000 0 0
YWHAZ 0.023 0.01 -10000 0 -10000 0 0
SIRT1 0.028 0.015 -10000 0 -10000 0 0
SOD2 0.041 0.12 -10000 0 -0.5 1 1
RBL2 0.041 0.12 -10000 0 -0.78 2 2
RAL/GDP 0.033 0.026 -10000 0 -10000 0 0
CHUK 0.03 0.017 -10000 0 -10000 0 0
Ran/GTP 0.023 0.002 -10000 0 -10000 0 0
CSNK1G2 0.026 0.02 -10000 0 -0.4 1 1
RAL/GTP 0.037 0.025 -10000 0 -10000 0 0
CSNK1G1 0.025 0.021 -10000 0 -0.4 1 1
FASLG -0.049 0.32 -10000 0 -1.3 29 29
SKP2 0.027 0.004 -10000 0 -10000 0 0
USP7 0.028 0.003 -10000 0 -10000 0 0
IKBKB 0.028 0.018 -10000 0 -10000 0 0
CCNB1 0.019 0.13 -10000 0 -0.79 2 2
FOXO1-3a-4/beta catenin 0.051 0.12 0.28 13 -10000 0 13
proteasomal ubiquitin-dependent protein catabolic process -0.003 0.14 -10000 0 -0.39 39 39
CSNK1A1 0.027 0.004 -10000 0 -10000 0 0
SGK1 0.012 0.089 -10000 0 -0.39 20 20
CSNK1G3 0.026 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.041 0.004 -10000 0 -10000 0 0
ZFAND5 0.031 0.072 0.36 1 -10000 0 1
SFN 0.023 0.029 -10000 0 -0.4 2 2
CDK2 0.012 0.043 -10000 0 -10000 0 0
FOXO3A/14-3-3 -0.001 0.1 -10000 0 -0.46 11 11
CREBBP 0.011 0.043 -10000 0 -0.2 1 1
FBXO32 0.046 0.16 -10000 0 -0.81 4 4
BCL6 0.041 0.11 -10000 0 -0.72 2 2
RALB 0.028 0.001 -10000 0 -10000 0 0
RALA 0.026 0.008 -10000 0 -10000 0 0
YWHAH 0.026 0.006 -10000 0 -10000 0 0
Class I PI3K signaling events

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
ARF5/GTP -0.004 0.049 -10000 0 -10000 0 0
DAPP1 -0.017 0.15 0.22 20 -0.39 31 51
Src family/SYK family/BLNK-LAT/BTK-ITK -0.069 0.2 0.24 12 -0.52 45 57
mol:DAG -0.006 0.095 0.18 50 -0.24 14 64
HRAS 0.026 0.021 -10000 0 -0.4 1 1
RAP1A 0.027 0.008 -10000 0 -10000 0 0
ARF5/GDP 0.028 0.12 0.18 3 -0.41 18 21
PLCG2 -0.016 0.13 -10000 0 -0.4 45 45
PLCG1 0.016 0.013 -10000 0 -10000 0 0
ARF5 0.026 0.005 -10000 0 -10000 0 0
mol:GTP -0.014 0.026 -10000 0 -10000 0 0
ARF1/GTP 0.004 0.039 0.24 1 -10000 0 1
RHOA 0.027 0.004 -10000 0 -10000 0 0
YES1 0.022 0.022 -10000 0 -0.4 1 1
RAP1A/GTP -0.014 0.027 0.16 7 -10000 0 7
ADAP1 -0.014 0.029 -10000 0 -0.36 1 1
ARAP3 -0.014 0.026 -10000 0 -10000 0 0
INPPL1 0.027 0.003 -10000 0 -10000 0 0
PREX1 0.015 0.024 -10000 0 -0.4 1 1
ARHGEF6 0.017 0.065 -10000 0 -0.4 11 11
ARHGEF7 0.021 0.012 -10000 0 -10000 0 0
ARF1 0.026 0.005 -10000 0 -10000 0 0
NRAS 0.025 0.029 -10000 0 -0.4 2 2
FYN 0.027 0.004 -10000 0 -10000 0 0
ARF6 0.025 0.007 -10000 0 -10000 0 0
FGR 0.021 0.041 -10000 0 -0.4 4 4
mol:Ca2+ 0.002 0.058 0.15 14 -10000 0 14
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.013 0.12 -10000 0 -0.4 41 41
ZAP70 0.015 0.071 -10000 0 -0.4 13 13
mol:IP3 -0.005 0.073 0.17 17 -0.2 2 19
LYN 0.024 0.009 -10000 0 -10000 0 0
ARF1/GDP 0.028 0.12 0.18 3 -0.41 19 22
RhoA/GDP 0.039 0.07 0.23 4 -0.3 3 7
PDK1/Src/Hsp90 0.032 0.027 -10000 0 -10000 0 0
BLNK 0.021 0.045 -10000 0 -0.4 5 5
actin cytoskeleton reorganization 0.034 0.095 0.23 24 -0.36 7 31
SRC 0.017 0.013 -10000 0 -10000 0 0
PLEKHA2 -0.007 0.003 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
PTEN 0.026 0.009 -10000 0 -10000 0 0
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
ARF6/GTP -0.014 0.032 -10000 0 -10000 0 0
RhoA/GTP -0.014 0.027 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.036 0.11 -10000 0 -0.4 20 20
BLK -0.1 0.19 -10000 0 -0.4 129 129
PDPK1 0.027 0.003 -10000 0 -10000 0 0
CYTH1 -0.015 0.026 -10000 0 -10000 0 0
HCK 0.01 0.053 -10000 0 -0.4 7 7
CYTH3 -0.014 0.025 -10000 0 -10000 0 0
CYTH2 -0.015 0.026 -10000 0 -10000 0 0
KRAS 0.027 0.006 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.006 0.08 -10000 0 -0.38 18 18
SGK1 -0.005 0.087 -10000 0 -0.4 19 19
INPP5D 0.026 0.02 -10000 0 -0.4 1 1
mol:GDP 0.017 0.12 0.18 4 -0.43 19 23
SOS1 0.027 0.002 -10000 0 -10000 0 0
SYK 0.027 0.004 -10000 0 -10000 0 0
ARF6/GDP 0.024 0.066 0.22 4 -0.3 3 7
mol:PI-3-4-5-P3 -0.014 0.026 -10000 0 -10000 0 0
ARAP3/RAP1A/GTP -0.014 0.027 0.16 7 -10000 0 7
VAV1 0.007 0.089 -10000 0 -0.4 21 21
mol:PI-3-4-P2 0.013 0.014 -10000 0 -0.28 1 1
RAS family/GTP/PI3K Class I 0.044 0.04 -10000 0 -10000 0 0
PLEKHA1 -0.009 0.011 -10000 0 -0.24 1 1
Rac1/GDP 0.021 0.12 -10000 0 -0.44 16 16
LAT 0.024 0.035 -10000 0 -0.4 3 3
Rac1/GTP -0.017 0.11 -10000 0 -0.49 17 17
ITK -0.023 0.041 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.017 0.12 0.2 47 -0.32 21 68
LCK 0.017 0.063 -10000 0 -0.42 9 9
BTK -0.037 0.064 -10000 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.025 0.016 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 0.011 0.006 -10000 0 -10000 0 0
mol:DAG 0.015 0.057 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0.023 0.017 0.23 1 -10000 0 1
CaM/Ca2+ 0.024 0.057 -10000 0 -10000 0 0
HIF1A 0.031 0.009 -10000 0 -10000 0 0
GAB1 0.027 0.004 -10000 0 -10000 0 0
AKT1 0.039 0.073 -10000 0 -10000 0 0
PLCG1 0.015 0.057 -10000 0 -10000 0 0
NOS3 0.08 0.11 0.3 61 -10000 0 61
CBL 0.027 0.004 -10000 0 -10000 0 0
mol:NO 0.08 0.11 0.29 62 -0.4 1 63
FLT1 0.014 0.009 -10000 0 -10000 0 0
PGF 0.011 0.079 -10000 0 -0.43 14 14
VEGFR1 homodimer/NRP2/VEGFR121 0.035 0.032 0.24 1 -10000 0 1
CALM1 0.025 0.007 -10000 0 -10000 0 0
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
eNOS/Hsp90 0.091 0.11 0.29 62 -0.37 1 63
endothelial cell proliferation 0.046 0.12 0.33 42 -10000 0 42
mol:Ca2+ 0.015 0.057 -10000 0 -10000 0 0
MAPK3 0.002 0.054 -10000 0 -10000 0 0
MAPK1 0.002 0.052 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
PLGF homodimer 0.011 0.079 -10000 0 -0.42 14 14
PRKACA 0.027 0.003 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.023 0.04 -10000 0 -0.4 4 4
VEGFA homodimer 0.028 0.016 0.36 1 -10000 0 1
VEGFR1 homodimer/VEGFA homodimer 0.025 0.019 0.25 1 -10000 0 1
platelet activating factor biosynthetic process 0.07 0.13 0.34 55 -10000 0 55
PI3K 0.039 0.05 -10000 0 -10000 0 0
PRKCA 0.004 0.056 0.19 27 -10000 0 27
PRKCB -0.015 0.075 0.19 21 -10000 0 21
VEGFR1 homodimer/PLGF homodimer 0.019 0.047 -10000 0 -0.25 11 11
VEGFA 0.028 0.016 0.36 1 -10000 0 1
VEGFB 0.027 0.004 -10000 0 -10000 0 0
mol:IP3 0.015 0.057 -10000 0 -10000 0 0
RASA1 0.049 0.072 -10000 0 -10000 0 0
NRP2 0.025 0.034 -10000 0 -0.4 3 3
VEGFR1 homodimer 0.014 0.009 -10000 0 -10000 0 0
VEGFB homodimer 0.027 0.004 -10000 0 -10000 0 0
NCK1 0.027 0.002 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.085 0.1 0.28 54 -0.39 1 55
PTPN11 0.027 0.003 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.038 0.049 -10000 0 -10000 0 0
mol:L-citrulline 0.08 0.11 0.29 62 -0.4 1 63
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.042 0.046 0.25 1 -10000 0 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.036 0.025 0.24 1 -10000 0 1
CD2AP 0.016 0.068 -10000 0 -0.4 12 12
PI3K/GAB1 0.081 0.068 -10000 0 -10000 0 0
PDPK1 0.041 0.078 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.036 0.025 0.24 1 -10000 0 1
mol:NADP 0.08 0.11 0.29 62 -0.4 1 63
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.04 0.045 0.24 1 -10000 0 1
VEGFR1 homodimer/NRP2 0.023 0.026 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.017 0.013 -10000 0 -10000 0 0
NFATC1 -0.015 0.13 0.25 1 -0.39 29 30
NFATC2 0.033 0.052 0.14 2 -0.22 4 6
NFATC3 0.02 0.008 -10000 0 -10000 0 0
YWHAE 0.023 0.01 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.053 0.11 -10000 0 -0.28 53 53
Exportin 1/Ran/NUP214 0.055 0.008 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.036 0.12 -10000 0 -0.35 27 27
BCL2/BAX 0.024 0.047 -10000 0 -0.28 9 9
CaM/Ca2+/Calcineurin A alpha-beta B1 0.019 0.007 -10000 0 -10000 0 0
CaM/Ca2+ 0.019 0.007 -10000 0 -10000 0 0
BAX 0.027 0.003 -10000 0 -10000 0 0
MAPK14 0.027 0.003 -10000 0 -10000 0 0
BAD 0.026 0.02 -10000 0 -0.4 1 1
CABIN1/MEF2D -0.041 0.11 -10000 0 -0.35 20 20
Calcineurin A alpha-beta B1/BCL2 0.012 0.059 -10000 0 -0.4 9 9
FKBP8 0.026 0.02 -10000 0 -0.4 1 1
activation-induced cell death of T cells 0.04 0.11 0.34 20 -10000 0 20
KPNB1 0.027 0.004 -10000 0 -10000 0 0
KPNA2 0.027 0.016 0.36 1 -10000 0 1
XPO1 0.027 0.001 -10000 0 -10000 0 0
SFN 0.023 0.029 -10000 0 -0.4 2 2
MAP3K8 0.027 0.002 -10000 0 -10000 0 0
NFAT4/CK1 alpha 0.027 0.024 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 0.069 0.067 -10000 0 -0.29 2 2
CABIN1 -0.054 0.11 -10000 0 -0.28 53 53
CALM1 0.025 0.007 -10000 0 -10000 0 0
RAN 0.027 0.002 -10000 0 -10000 0 0
MAP3K1 0.026 0.02 -10000 0 -0.4 1 1
CAMK4 0.001 0.097 -10000 0 -0.4 25 25
mol:Ca2+ 0 0.002 -10000 0 -10000 0 0
MAPK3 0.026 0.02 -10000 0 -0.4 1 1
YWHAH 0.026 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.025 0.063 -10000 0 -0.28 18 18
YWHAB 0.016 0.014 -10000 0 -10000 0 0
MAPK8 0.027 0.004 -10000 0 -10000 0 0
MAPK9 0.027 0.003 -10000 0 -10000 0 0
YWHAG 0.026 0.005 -10000 0 -10000 0 0
FKBP1A 0.022 0.011 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.014 0.13 -10000 0 -0.39 20 20
PRKCH 0.024 0.021 -10000 0 -0.4 1 1
CABIN1/Cbp/p300 0.038 0.013 -10000 0 -10000 0 0
CASP3 0.026 0.007 -10000 0 -10000 0 0
PIM1 0.027 0.003 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.015 0.007 -10000 0 -10000 0 0
apoptosis 0.01 0.016 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.031 0.045 -10000 0 -0.37 1 1
PRKCB -0.068 0.18 -10000 0 -0.4 101 101
PRKCE 0.027 0.003 -10000 0 -10000 0 0
JNK2/NFAT4 0.024 0.039 -10000 0 -10000 0 0
BAD/BCL-XL 0.024 0.025 -10000 0 -0.28 1 1
PRKCD 0.027 0.004 -10000 0 -10000 0 0
NUP214 0.027 0.003 -10000 0 -10000 0 0
PRKCZ 0.026 0.007 -10000 0 -10000 0 0
PRKCA 0.026 0.006 -10000 0 -10000 0 0
PRKCG -0.12 0.22 0.36 4 -0.43 146 150
PRKCQ 0.023 0.04 -10000 0 -0.4 4 4
FKBP38/BCL2 0.024 0.049 -10000 0 -0.28 10 10
EP300 0.026 0.008 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.022 0.011 -10000 0 -10000 0 0
NFATc/JNK1 -0.001 0.12 0.25 1 -0.37 28 29
CaM/Ca2+/FKBP38 0.034 0.017 -10000 0 -0.24 1 1
FKBP12/FK506 0.016 0.008 -10000 0 -10000 0 0
CSNK1A1 0.014 0.006 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.018 0.061 -10000 0 -0.23 25 25
NFATc/ERK1 -0.002 0.12 0.25 1 -0.37 27 28
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.039 0.12 -10000 0 -0.34 31 31
NR4A1 0.039 0.073 0.23 3 -0.37 8 11
GSK3B 0.027 0.002 -10000 0 -10000 0 0
positive T cell selection 0.02 0.008 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.031 0.038 -10000 0 -10000 0 0
RCH1/ KPNB1 0.04 0.007 -10000 0 -10000 0 0
YWHAQ 0.027 0.002 -10000 0 -10000 0 0
PRKACA 0.027 0.003 -10000 0 -10000 0 0
AKAP5 0.008 0.083 -10000 0 -0.4 18 18
MEF2D 0.026 0.007 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.023 0.01 -10000 0 -10000 0 0
NFATc/p38 alpha -0.002 0.13 0.25 1 -0.37 27 28
CREBBP 0.027 0.007 -10000 0 -10000 0 0
BCL2 0.012 0.06 -10000 0 -0.4 9 9
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.007 0.003 -10000 0 -10000 0 0
SNTA1 0.016 0.024 -10000 0 -0.4 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.007 0.011 -10000 0 -0.24 1 1
MAPK12 -0.007 0.037 -10000 0 -0.27 8 8
CCND1 0.007 0.038 -10000 0 -0.32 4 4
p38 gamma/SNTA1 0.008 0.043 0.19 4 -0.24 9 13
MAP2K3 0.023 0.01 -10000 0 -10000 0 0
PKN1 0.027 0.003 -10000 0 -10000 0 0
G2/M transition checkpoint -0.004 0.044 0.2 6 -0.26 8 14
MAP2K6 0.001 0.021 -10000 0 -0.22 4 4
MAPT -0.054 0.12 0.18 7 -0.28 91 98
MAPK13 0.012 0.005 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.007 0.001 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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
HDAC1 0.026 0.006 -10000 0 -10000 0 0
HDAC3 0.027 0.004 -10000 0 -10000 0 0
VDR 0.027 0.003 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.041 0.056 -10000 0 -0.23 17 17
EP300 0.026 0.006 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.004 0.038 -10000 0 -0.32 1 1
KAT2B 0.011 0.081 -10000 0 -0.4 17 17
MAPK14 0.027 0.003 -10000 0 -10000 0 0
AKT1 -0.002 0.047 0.19 1 -0.22 1 2
RAR alpha/9cRA/Cyclin H 0.012 0.068 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.007 0.054 0.18 1 -0.22 11 12
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.002 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.002 0.054 -10000 0 -0.25 2 2
NCOR2 0.026 0.02 -10000 0 -0.4 1 1
VDR/VDR/Vit D3 0.02 0.002 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.027 0.082 0.3 1 -0.45 5 6
NCOA2 0.023 0.022 -10000 0 -0.4 1 1
NCOA3 0.016 0.013 -10000 0 -10000 0 0
NCOA1 0.027 0.001 -10000 0 -10000 0 0
VDR/VDR/DNA 0.027 0.003 -10000 0 -10000 0 0
RARG 0.028 0.004 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.037 0.006 -10000 0 -10000 0 0
MAPK3 0.026 0.02 -10000 0 -0.4 1 1
MAPK1 0.026 0.006 -10000 0 -10000 0 0
MAPK8 0.027 0.006 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.027 0.08 0.26 1 -0.36 6 7
RARA -0.012 0.055 0.18 3 -0.21 7 10
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.004 0.05 0.18 1 -0.22 10 11
PRKCA 0.028 0.009 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.033 0.086 0.32 1 -0.46 5 6
RXRG -0.14 0.16 0.28 3 -0.32 166 169
RXRA -0.008 0.055 0.26 1 -0.2 2 3
RXRB -0.027 0.082 0.27 4 -0.34 3 7
VDR/Vit D3/DNA 0.02 0.002 -10000 0 -10000 0 0
RBP1 0.001 0.11 0.36 1 -0.43 27 28
CRBP1/9-cic-RA 0.001 0.077 0.24 1 -0.3 27 28
RARB 0.024 0.04 -10000 0 -0.4 4 4
PRKCG -0.12 0.22 0.36 4 -0.42 146 150
MNAT1 0.024 0.022 -10000 0 -0.43 1 1
RAR alpha/RXRs -0.027 0.077 -10000 0 -0.4 6 6
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.02 0.072 0.3 1 -0.36 4 5
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.072 0.24 4 -0.27 3 7
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.032 0.086 0.32 1 -0.45 5 6
positive regulation of DNA binding 0.006 0.061 -10000 0 -10000 0 0
NRIP1 -0.033 0.1 -10000 0 -1.1 2 2
RXRs/RARs -0.032 0.086 0.34 1 -0.38 6 7
RXRs/RXRs/DNA/9cRA -0.037 0.072 -10000 0 -0.36 6 6
PRKACA 0.027 0.003 -10000 0 -10000 0 0
CDK7 0.027 0.004 -10000 0 -10000 0 0
TFIIH 0.049 0.022 -10000 0 -0.26 1 1
RAR alpha/9cRA 0.02 0.066 0.23 1 -0.25 2 3
CCNH 0.027 0.005 -10000 0 -10000 0 0
CREBBP 0.027 0.004 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.048 0.022 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.1 0.18 -10000 0 -0.4 79 79
CaM/Ca2+ 0.019 0.005 -10000 0 -10000 0 0
AKT1 0.025 0.007 -10000 0 -10000 0 0
AKT2 0.027 0.004 -10000 0 -10000 0 0
STXBP4 0.026 0.02 -10000 0 -0.4 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.12 0.18 -10000 0 -0.42 87 87
YWHAZ 0.023 0.01 -10000 0 -10000 0 0
CALM1 0.025 0.007 -10000 0 -10000 0 0
YWHAQ 0.027 0.002 -10000 0 -10000 0 0
TBC1D4 0.01 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.026 0.006 -10000 0 -10000 0 0
YWHAB 0.016 0.014 -10000 0 -10000 0 0
SNARE/Synip 0.044 0.026 -10000 0 -0.24 1 1
YWHAG 0.026 0.005 -10000 0 -10000 0 0
ASIP 0.003 0.041 0.36 2 -0.43 2 4
PRKCI 0.025 0.028 -10000 0 -0.4 2 2
AS160/CaM/Ca2+ 0.019 0.005 -10000 0 -10000 0 0
RHOQ 0.027 0.003 -10000 0 -10000 0 0
GYS1 0.011 0.004 -10000 0 -10000 0 0
PRKCZ 0.026 0.007 -10000 0 -10000 0 0
TRIP10 0.027 0.004 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.036 0.006 -10000 0 -10000 0 0
AS160/14-3-3 0.013 0.041 -10000 0 -0.3 1 1
VAMP2 0.022 0.011 -10000 0 -10000 0 0
SLC2A4 -0.14 0.2 -10000 0 -0.48 87 87
STX4 0.027 0.003 -10000 0 -10000 0 0
GSK3B 0.02 0.007 -10000 0 -10000 0 0
SFN 0.023 0.029 -10000 0 -0.4 2 2
LNPEP 0.026 0.006 -10000 0 -10000 0 0
YWHAE 0.023 0.01 -10000 0 -10000 0 0
IL27-mediated 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
TGFB1 -0.002 0.064 -10000 0 -0.43 1 1
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.007 0.093 0.41 4 -10000 0 4
IL27/IL27R/JAK1 0.03 0.11 -10000 0 -0.56 1 1
TBX21 -0.026 0.13 -10000 0 -0.51 17 17
IL12B 0.014 0.045 -10000 0 -0.43 4 4
IL12A 0.001 0.033 -10000 0 -0.28 6 6
IL6ST 0.018 0.058 -10000 0 -0.41 8 8
IL27RA/JAK1 0.022 0.027 -10000 0 -10000 0 0
IL27 0.007 0.079 -10000 0 -0.43 14 14
TYK2 0.023 0.015 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.041 0.14 0.43 1 -10000 0 1
T-helper 2 cell differentiation 0.007 0.093 0.41 4 -10000 0 4
T cell proliferation during immune response 0.007 0.093 0.41 4 -10000 0 4
MAPKKK cascade -0.007 0.093 -10000 0 -0.41 4 4
STAT3 0.027 0.004 -10000 0 -10000 0 0
STAT2 0.027 0.002 -10000 0 -10000 0 0
STAT1 0.027 0.022 -10000 0 -0.43 1 1
IL12RB1 0.011 0.081 -10000 0 -0.4 17 17
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.019 0.12 -10000 0 -0.53 9 9
IL27/IL27R/JAK2/TYK2 -0.007 0.094 -10000 0 -0.42 4 4
positive regulation of T cell mediated cytotoxicity -0.007 0.093 -10000 0 -0.41 4 4
STAT1 (dimer) 0.029 0.16 -10000 0 -0.6 5 5
JAK2 0.022 0.038 -10000 0 -0.4 3 3
JAK1 0.027 0.005 -10000 0 -10000 0 0
STAT2 (dimer) 0.004 0.098 -10000 0 -0.42 3 3
T cell proliferation -0.049 0.12 -10000 0 -0.41 15 15
IL12/IL12R/TYK2/JAK2 0.006 0.14 -10000 0 -0.77 11 11
IL17A -0.041 0.14 0.43 1 -10000 0 1
mast cell activation 0.007 0.093 0.41 4 -10000 0 4
IFNG 0.002 0.026 -10000 0 -0.12 1 1
T cell differentiation -0.001 0.004 -10000 0 -0.018 3 3
STAT3 (dimer) 0.004 0.097 -10000 0 -0.42 3 3
STAT5A (dimer) 0.004 0.097 -10000 0 -0.42 3 3
STAT4 (dimer) -0.005 0.12 -10000 0 -0.4 16 16
STAT4 0.006 0.093 -10000 0 -0.4 23 23
T cell activation -0.006 0.002 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.038 0.059 -10000 0 -10000 0 0
GATA3 -0.015 0.12 -10000 0 -1.2 4 4
IL18 0.005 0.019 -10000 0 -0.28 2 2
positive regulation of mast cell cytokine production 0.004 0.096 -10000 0 -0.41 3 3
IL27/EBI3 -0.001 0.11 -10000 0 -0.29 50 50
IL27RA 0.008 0.025 -10000 0 -10000 0 0
IL6 -0.066 0.18 0.33 5 -0.44 69 74
STAT5A 0.027 0.004 -10000 0 -10000 0 0
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 -0.015 0.014 -10000 0 -10000 0 0
IL1B -0.027 0.095 -10000 0 -0.3 49 49
EBI3 -0.008 0.12 -10000 0 -0.4 37 37
TNF 0.005 0.019 -10000 0 -0.28 2 2
Arf6 trafficking events

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
SLC2A4 -0.02 0.13 -10000 0 -0.4 45 45
CLTC -0.005 0.11 -10000 0 -0.4 30 30
calcium ion-dependent exocytosis 0.016 0.038 -10000 0 -10000 0 0
Dynamin 2/GTP 0.021 0.037 0.19 1 -0.23 9 10
EXOC4 0.026 0.005 -10000 0 -10000 0 0
CD59 0.001 0.078 -10000 0 -0.31 23 23
CPE -0.004 0.062 -10000 0 -0.23 30 30
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
membrane fusion 0.019 0.03 -10000 0 -10000 0 0
CTNND1 0.009 0.038 0.18 7 -0.21 9 16
DNM2 0.027 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.002 0.069 -10000 0 -0.32 10 10
TSHR 0.003 0.032 -10000 0 -0.23 7 7
INS 0.007 0.04 -10000 0 -0.51 2 2
BIN1 0.026 0.02 -10000 0 -0.4 1 1
mol:Choline 0.019 0.03 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.009 0.038 0.23 1 -0.25 9 10
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.025 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0.02 0.037 0.18 1 -0.22 9 10
JUP 0.001 0.078 0.21 1 -0.31 23 24
ASAP2/amphiphysin II 0.048 0.019 -10000 0 -0.21 1 1
ARF6/GTP 0.019 0.005 -10000 0 -10000 0 0
CDH1 0.001 0.077 -10000 0 -0.31 23 23
clathrin-independent pinocytosis 0.019 0.005 -10000 0 -10000 0 0
MAPK8IP3 0.025 0.029 -10000 0 -0.41 2 2
positive regulation of endocytosis 0.019 0.005 -10000 0 -10000 0 0
EXOC2 0.026 0.02 -10000 0 -0.4 1 1
substrate adhesion-dependent cell spreading 0.025 0.045 -10000 0 -0.4 3 3
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.027 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.017 0.097 0.32 29 -10000 0 29
positive regulation of phagocytosis 0.013 0.005 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.033 0.021 -10000 0 -0.24 2 2
ACAP1 0.019 0.033 -10000 0 -0.28 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.039 0.11 -10000 0 -0.39 25 25
clathrin heavy chain/ACAP1 -0.002 0.095 0.19 1 -0.33 28 29
JIP4/KLC1 0.047 0.016 -10000 0 -10000 0 0
EXOC1 0.026 0.02 -10000 0 -0.4 1 1
exocyst 0.022 0.042 -10000 0 -0.41 3 3
RALA/GTP 0.018 0.006 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.034 0.011 -10000 0 -10000 0 0
receptor recycling 0.019 0.005 -10000 0 -10000 0 0
CTNNA1 0.009 0.038 0.18 7 -0.22 6 13
NME1 0.009 0.039 0.23 1 -0.25 9 10
clathrin coat assembly -0.004 0.11 -10000 0 -0.39 30 30
IL2RA -0.002 0.08 -10000 0 -0.31 23 23
VAMP3 0.013 0.005 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.011 0.1 -10000 0 -0.3 31 31
EXOC6 0.026 0.006 -10000 0 -10000 0 0
PLD1 0.012 0.013 -10000 0 -0.24 1 1
PLD2 0.011 0.007 -10000 0 -10000 0 0
EXOC5 0.023 0.035 -10000 0 -0.4 3 3
PIP5K1C 0.006 0.059 -10000 0 -0.31 5 5
SDC1 0.001 0.077 -10000 0 -0.31 23 23
ARF6/GDP 0.018 0.04 0.2 1 -0.25 9 10
EXOC7 0.027 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.019 0.1 -10000 0 -0.33 29 29
mol:Phosphatidic acid 0.019 0.03 -10000 0 -10000 0 0
endocytosis -0.046 0.019 0.21 1 -10000 0 1
SCAMP2 0.026 0.006 -10000 0 -10000 0 0
ADRB2 -0.034 0.13 -10000 0 -0.44 30 30
EXOC3 0.027 0.004 -10000 0 -10000 0 0
ASAP2 0.027 0.002 -10000 0 -10000 0 0
Dynamin 2/GDP 0.024 0.038 0.21 1 -0.22 9 10
KLC1 0.025 0.007 -10000 0 -10000 0 0
AVPR2 -0.019 0.12 0.24 2 -0.39 30 32
RALA 0.025 0.008 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.014 0.094 -10000 0 -0.34 19 19
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.028 0.061 0.3 14 -0.24 1 15
KIRREL 0.022 0.047 -10000 0 -0.41 5 5
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.028 0.061 0.24 1 -0.3 14 15
PLCG1 0.016 0.013 -10000 0 -10000 0 0
ARRB2 0.023 0.01 -10000 0 -10000 0 0
WASL 0.026 0.005 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.044 0.075 0.23 1 -0.23 28 29
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.021 0.032 0.16 1 -0.21 4 5
FYN 0.012 0.061 0.27 11 -0.23 6 17
mol:Ca2+ 0.028 0.056 -10000 0 -0.32 2 2
mol:DAG 0.029 0.056 -10000 0 -0.32 2 2
NPHS2 0.013 0.045 -10000 0 -0.42 4 4
mol:IP3 0.029 0.056 -10000 0 -0.32 2 2
regulation of endocytosis 0.036 0.049 0.21 1 -0.24 3 4
Nephrin/NEPH1/podocin/Cholesterol 0.036 0.054 0.21 1 -0.23 16 17
establishment of cell polarity 0.028 0.061 0.24 1 -0.3 14 15
Nephrin/NEPH1/podocin/NCK1-2 0.065 0.058 -10000 0 -0.38 1 1
Nephrin/NEPH1/beta Arrestin2 0.038 0.051 0.22 1 -0.24 3 4
NPHS1 0.015 0.067 0.33 1 -0.43 9 10
Nephrin/NEPH1/podocin 0.038 0.049 0.21 1 -0.2 16 17
TJP1 0.026 0.007 -10000 0 -10000 0 0
NCK1 0.027 0.002 -10000 0 -10000 0 0
NCK2 0.027 0.001 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.029 0.057 -10000 0 -0.32 2 2
CD2AP 0.016 0.068 -10000 0 -0.4 12 12
Nephrin/NEPH1/podocin/GRB2 0.051 0.059 0.23 1 -0.23 16 17
GRB2 0.027 0.004 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.012 0.078 0.28 9 -0.24 23 32
cytoskeleton organization 0.01 0.042 0.2 5 -0.24 5 10
Nephrin/NEPH1 0.025 0.043 0.19 1 -0.2 14 15
Nephrin/NEPH1/ZO-1 0.04 0.053 0.22 1 -0.24 12 13
EPO signaling 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
BCL2L1 0.023 0.062 -10000 0 -10000 0 0
CRKL 0.021 0.049 0.3 1 -0.29 2 3
mol:DAG 0.018 0.031 -10000 0 -10000 0 0
HRAS 0.011 0.056 0.27 2 -0.29 1 3
MAPK8 0.038 0.064 0.19 49 -10000 0 49
RAP1A 0.02 0.049 0.3 1 -0.29 2 3
GAB1 0.02 0.049 0.3 1 -0.29 2 3
MAPK14 0.039 0.064 0.19 50 -10000 0 50
EPO 0.02 0.042 0.34 1 -0.43 3 4
PLCG1 0.019 0.031 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.026 0.024 -10000 0 -0.39 1 1
RAPGEF1 0.026 0.02 -10000 0 -0.4 1 1
EPO/EPOR (dimer)/SOCS3 0.047 0.038 0.24 1 -0.25 5 6
GAB1/SHC/GRB2/SOS1 0.051 0.05 0.27 1 -0.3 1 2
EPO/EPOR (dimer) 0.034 0.038 0.25 1 -0.3 4 5
IRS2 0.014 0.039 -10000 0 -0.33 1 1
STAT1 0.028 0.05 -10000 0 -10000 0 0
STAT5B 0.026 0.046 -10000 0 -10000 0 0
cell proliferation 0.02 0.075 0.19 67 -10000 0 67
GAB1/SHIP/PIK3R1/SHP2/SHC 0.041 0.045 -10000 0 -0.29 1 1
TEC 0.02 0.05 0.3 1 -0.29 2 3
SOCS3 0.026 0.022 -10000 0 -0.43 1 1
STAT1 (dimer) 0.028 0.05 -10000 0 -10000 0 0
JAK2 0.024 0.037 -10000 0 -0.4 3 3
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.064 0.053 0.24 1 -0.3 2 3
EPO/EPOR 0.034 0.038 0.25 1 -0.3 4 5
LYN 0.023 0.013 -10000 0 -10000 0 0
TEC/VAV2 0.031 0.055 0.28 1 -0.25 1 2
elevation of cytosolic calcium ion concentration 0.026 0.024 -10000 0 -0.39 1 1
SHC1 0.027 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.045 0.038 0.24 1 -0.23 3 4
mol:IP3 0.018 0.031 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.035 0.046 -10000 0 -0.31 1 1
SH2B3 0.028 0.011 -10000 0 -10000 0 0
NFKB1 0.038 0.064 0.19 49 -10000 0 49
EPO/EPOR (dimer)/JAK2/SOCS3 0.011 0.031 -10000 0 -0.26 3 3
PTPN6 0.02 0.049 -10000 0 -0.3 2 2
TEC/VAV2/GRB2 0.042 0.058 0.28 1 -10000 0 1
EPOR 0.026 0.024 -10000 0 -0.39 1 1
INPP5D 0.026 0.02 -10000 0 -0.4 1 1
mol:GDP 0.05 0.051 0.27 1 -0.31 1 2
SOS1 0.027 0.002 -10000 0 -10000 0 0
PLCG2 -0.016 0.13 -10000 0 -0.4 45 45
CRKL/CBL/C3G 0.047 0.05 0.28 1 -10000 0 1
VAV2 0.017 0.054 0.3 1 -0.26 1 2
CBL 0.02 0.05 0.3 1 -0.29 2 3
SHC/Grb2/SOS1 0.037 0.043 -10000 0 -0.28 2 2
STAT5A 0.026 0.046 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
STAT5 (dimer) 0.039 0.069 -10000 0 -0.31 1 1
LYN/PLCgamma2 0.008 0.088 -10000 0 -0.28 38 38
PTPN11 0.027 0.003 -10000 0 -10000 0 0
BTK -0.005 0.086 0.3 1 -0.3 9 10
BCL2 0.01 0.17 -10000 0 -0.72 22 22
PDGFR-alpha 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
PDGFRA 0.021 0.069 -10000 0 -0.39 12 12
PDGF/PDGFRA/CRKL 0.034 0.051 -10000 0 -0.26 12 12
positive regulation of JUN kinase activity 0.06 0.045 -10000 0 -0.2 9 9
CRKL 0.026 0.006 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 0.027 0.055 -10000 0 -0.27 14 14
AP1 0.022 0.087 0.29 2 -0.52 3 5
mol:IP3 0.003 0.042 -10000 0 -0.28 9 9
PLCG1 0.003 0.042 -10000 0 -0.28 9 9
PDGF/PDGFRA/alphaV Integrin 0.035 0.051 -10000 0 -0.26 12 12
RAPGEF1 0.026 0.02 -10000 0 -0.4 1 1
CRK 0.023 0.01 -10000 0 -10000 0 0
mol:Ca2+ 0.003 0.042 -10000 0 -0.28 9 9
CAV3 -0.013 0.032 -10000 0 -0.43 2 2
CAV1 0.023 0.04 -10000 0 -0.4 4 4
SHC/Grb2/SOS1 0.062 0.046 -10000 0 -0.2 9 9
PDGF/PDGFRA/Shf 0.022 0.078 -10000 0 -0.29 26 26
FOS -0.004 0.071 0.31 9 -0.52 3 12
JUN -0.006 0.02 -10000 0 -10000 0 0
oligodendrocyte development 0.035 0.051 -10000 0 -0.26 12 12
GRB2 0.027 0.004 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:DAG 0.003 0.042 -10000 0 -0.28 9 9
PDGF/PDGFRA 0.021 0.069 -10000 0 -0.39 12 12
actin cytoskeleton reorganization 0.034 0.051 -10000 0 -0.26 12 12
SRF 0.005 0.012 -10000 0 -10000 0 0
SHC1 0.027 0.004 -10000 0 -10000 0 0
PI3K 0.049 0.045 -10000 0 -0.23 8 8
PDGF/PDGFRA/Crk/C3G 0.04 0.05 -10000 0 -0.22 11 11
JAK1 0.01 0.045 -10000 0 -0.27 11 11
ELK1/SRF 0.022 0.075 0.23 2 -10000 0 2
SHB 0.027 0.004 -10000 0 -10000 0 0
SHF 0.012 0.078 -10000 0 -0.42 14 14
CSNK2A1 0.013 0.02 -10000 0 -10000 0 0
GO:0007205 -0.002 0.044 -10000 0 -0.31 9 9
SOS1 0.027 0.002 -10000 0 -10000 0 0
Ras protein signal transduction 0.06 0.045 -10000 0 -0.2 9 9
PDGF/PDGFRA/SHB 0.034 0.051 -10000 0 -0.26 12 12
PDGF/PDGFRA/Caveolin-1 0.032 0.058 -10000 0 -0.28 13 13
ITGAV 0.027 0.002 -10000 0 -10000 0 0
ELK1 -0.007 0.039 0.25 1 -0.26 9 10
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk 0.028 0.051 -10000 0 -0.26 12 12
JAK-STAT cascade 0.01 0.045 -10000 0 -0.27 11 11
cell proliferation 0.022 0.078 -10000 0 -0.28 26 26
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.035 0.038 0.26 1 -0.3 5 6
CRKL 0.028 0.089 0.29 3 -0.44 9 12
mol:PIP3 -0.004 0.04 -10000 0 -0.82 1 1
AKT1 -0.009 0.038 -10000 0 -0.72 1 1
PTK2B 0.02 0.023 -10000 0 -0.4 1 1
RAPGEF1 0.03 0.088 0.28 4 -0.42 9 13
RANBP10 0.027 0.001 -10000 0 -10000 0 0
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.044 0.051 -10000 0 -0.24 13 13
MAP3K5 0.014 0.11 0.24 1 -0.43 14 15
HGF/MET/CIN85/CBL/ENDOPHILINS 0.057 0.051 -10000 0 -0.22 11 11
AP1 0.028 0.033 -10000 0 -0.25 2 2
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.027 0.004 -10000 0 -10000 0 0
apoptosis -0.039 0.24 -10000 0 -0.75 43 43
STAT3 (dimer) 0.007 0.048 -10000 0 -0.28 4 4
GAB1/CRKL/SHP2/PI3K 0.066 0.087 0.34 1 -0.41 8 9
INPP5D 0.026 0.02 -10000 0 -0.4 1 1
CBL/CRK 0.049 0.089 0.28 4 -0.42 9 13
PTPN11 0.027 0.003 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.016 0.013 -10000 0 -10000 0 0
PTEN 0.026 0.006 -10000 0 -10000 0 0
ELK1 0.004 0.087 0.29 30 -10000 0 30
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.009 0.037 -10000 0 -0.21 3 3
PAK1 -0.009 0.038 -10000 0 -0.69 1 1
HGF/MET/RANBP10 0.044 0.051 -10000 0 -0.24 13 13
HRAS 0.021 0.059 0.33 1 -0.42 2 3
DOCK1 0.03 0.084 0.3 2 -0.42 9 11
GAB1 0.02 0.083 -10000 0 -0.46 9 9
CRK 0.025 0.085 0.32 2 -0.45 8 10
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.02 0.075 0.26 1 -0.41 11 12
JUN 0.027 0.005 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.011 0.038 -10000 0 -0.18 10 10
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
cell morphogenesis 0.049 0.095 0.25 28 -0.4 2 30
GRB2/SHC 0.011 0.053 -10000 0 -0.2 3 3
FOS 0.023 0.035 -10000 0 -0.4 3 3
GLMN 0.002 0.01 -10000 0 -0.22 1 1
cell motility 0.004 0.087 0.29 30 -10000 0 30
HGF/MET/MUC20 0.027 0.047 -10000 0 -0.24 13 13
cell migration 0.01 0.052 -10000 0 -0.2 3 3
GRB2 0.027 0.004 -10000 0 -10000 0 0
CBL 0.027 0.004 -10000 0 -10000 0 0
MET/RANBP10 0.037 0.035 0.26 1 -0.3 4 5
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.014 0.045 -10000 0 -0.24 11 11
MET/MUC20 0.017 0.032 0.24 1 -0.3 4 5
RAP1B 0.028 0.085 0.3 2 -0.4 9 11
RAP1A 0.027 0.083 0.28 3 -0.4 9 12
HGF/MET/RANBP9 0.043 0.053 -10000 0 -0.24 14 14
RAF1 0.024 0.061 0.31 1 -0.4 2 3
STAT3 0.007 0.048 -10000 0 -0.29 4 4
cell proliferation 0.025 0.064 0.26 1 -0.34 5 6
RPS6KB1 0.004 0.034 -10000 0 -0.26 5 5
MAPK3 -0.014 0.076 0.54 4 -10000 0 4
MAPK1 0.018 0.16 0.66 24 -10000 0 24
RANBP9 0.026 0.02 -10000 0 -0.4 1 1
MAPK8 0.025 0.1 0.24 2 -0.43 8 10
SRC 0.006 0.034 -10000 0 -0.26 4 4
PI3K 0.011 0.053 -10000 0 -10000 0 0
MET/Glomulin -0.013 0.054 0.2 1 -0.19 14 15
SOS1 0.027 0.002 -10000 0 -10000 0 0
MAP2K1 0.022 0.059 0.3 1 -0.38 2 3
MET 0.023 0.046 0.36 1 -0.43 4 5
MAP4K1 0.015 0.12 0.25 1 -0.46 15 16
PTK2 0.023 0.01 -10000 0 -10000 0 0
MAP2K2 0.022 0.061 0.3 1 -0.37 3 4
BAD -0.01 0.037 -10000 0 -0.69 1 1
MAP2K4 0.009 0.1 0.24 2 -0.41 11 13
SHP2/GRB2/SOS1/GAB1 0.049 0.078 -10000 0 -0.38 9 9
INPPL1 0.027 0.003 -10000 0 -10000 0 0
PXN 0.027 0.002 -10000 0 -10000 0 0
SH3KBP1 0.027 0.003 -10000 0 -10000 0 0
HGS -0.013 0.034 -10000 0 -0.21 3 3
PLCgamma1/PKC 0.012 0.01 -10000 0 -10000 0 0
HGF 0.017 0.06 -10000 0 -0.4 9 9
RASA1 0.026 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.002 -10000 0 -10000 0 0
PTPRJ 0.027 0.003 -10000 0 -10000 0 0
NCK/PLCgamma1 0.026 0.033 -10000 0 -10000 0 0
PDPK1 -0.008 0.041 -10000 0 -0.76 1 1
HGF/MET/SHIP 0.043 0.053 -10000 0 -0.24 14 14
Arf6 downstream 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
PLAUR 0.015 0.029 -10000 0 -10000 0 0
regulation of axonogenesis -0.008 0.032 0.23 7 -10000 0 7
myoblast fusion -0.028 0.019 -10000 0 -10000 0 0
mol:GTP 0.014 0.034 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.017 0.095 0.25 44 -10000 0 44
ARF1/GTP 0.027 0.037 -10000 0 -10000 0 0
mol:GM1 0.003 0.029 -10000 0 -10000 0 0
mol:Choline 0.008 0.019 -10000 0 -0.22 1 1
lamellipodium assembly 0.001 0.088 -10000 0 -0.34 27 27
MAPK3 0.017 0.028 -10000 0 -0.24 1 1
ARF6/GTP/NME1/Tiam1 0.017 0.096 -10000 0 -0.25 44 44
ARF1 0.026 0.005 -10000 0 -10000 0 0
ARF6/GDP 0.028 0.019 -10000 0 -10000 0 0
ARF1/GDP 0.022 0.06 -10000 0 -0.24 8 8
ARF6 0.032 0.009 -10000 0 -10000 0 0
RAB11A 0.026 0.006 -10000 0 -10000 0 0
TIAM1 -0.012 0.12 -10000 0 -0.4 41 41
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.018 0.024 -10000 0 -10000 0 0
actin filament bundle formation -0.023 0.06 0.24 8 -10000 0 8
KALRN 0.02 0.019 -10000 0 -0.2 1 1
RAB11FIP3/RAB11A 0.038 0.01 -10000 0 -10000 0 0
RhoA/GDP 0.023 0.061 -10000 0 -0.24 8 8
NME1 0.019 0.066 0.36 1 -0.42 9 10
Rac1/GDP 0.021 0.059 -10000 0 -0.27 1 1
substrate adhesion-dependent cell spreading 0.014 0.034 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0.002 0.087 -10000 0 -0.34 25 25
RAC1 0.025 0.008 -10000 0 -10000 0 0
liver development 0.014 0.034 -10000 0 -10000 0 0
ARF6/GTP 0.014 0.034 -10000 0 -10000 0 0
RhoA/GTP 0.027 0.037 -10000 0 -10000 0 0
mol:GDP 0.011 0.051 -10000 0 -0.26 1 1
ARF6/GTP/RAB11FIP3/RAB11A 0.042 0.037 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
PLD1 0.012 0.035 -10000 0 -0.25 1 1
RAB11FIP3 0.027 0.004 -10000 0 -10000 0 0
tube morphogenesis 0.001 0.088 -10000 0 -0.34 27 27
ruffle organization 0.008 0.032 -10000 0 -0.23 7 7
regulation of epithelial cell migration 0.014 0.034 -10000 0 -10000 0 0
PLD2 0.015 0.019 -10000 0 -10000 0 0
PIP5K1A 0.008 0.032 -10000 0 -0.23 7 7
mol:Phosphatidic acid 0.008 0.019 -10000 0 -0.22 1 1
Rac1/GTP 0.002 0.087 -10000 0 -0.34 25 25
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.027 0.004 -10000 0 -10000 0 0
mol:PIP3 0.007 0.012 -10000 0 -10000 0 0
FRAP1 -0.009 0.11 -10000 0 -0.43 25 25
AKT1 0.002 0.026 0.16 4 -10000 0 4
INSR 0.027 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.029 0.006 -10000 0 -10000 0 0
mol:GTP 0.03 0.042 0.23 1 -10000 0 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.006 0.039 -10000 0 -0.22 5 5
TSC2 0.027 0.003 -10000 0 -10000 0 0
RHEB/GDP 0.016 0.029 -10000 0 -10000 0 0
TSC1 0.027 0.003 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.023 0.017 -10000 0 -0.18 2 2
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.017 0.048 -10000 0 -0.25 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.027 0.004 -10000 0 -10000 0 0
RPS6KB1 0.007 0.071 0.21 1 -0.3 13 14
MAP3K5 0.005 0.026 0.2 2 -0.17 7 9
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
apoptosis 0.006 0.026 0.2 2 -0.17 7 9
mol:LY294002 0 0 -10000 0 -0.001 2 2
EIF4B 0.007 0.065 0.19 2 -0.27 13 15
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.028 0.065 0.2 1 -0.3 6 7
eIF4E/eIF4G1/eIF4A1 0.004 0.065 -10000 0 -0.26 22 22
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.038 0.021 -10000 0 -0.2 1 1
mTOR/RHEB/GTP/Raptor/GBL 0.008 0.03 0.16 6 -10000 0 6
FKBP1A 0.022 0.011 -10000 0 -10000 0 0
RHEB/GTP 0.034 0.038 0.2 1 -10000 0 1
mol:Amino Acids 0 0 -10000 0 -0.001 2 2
FKBP12/Rapamycin 0.016 0.008 -10000 0 -10000 0 0
PDPK1 -0.005 0.016 0.16 2 -10000 0 2
EIF4E 0.025 0.028 -10000 0 -0.4 2 2
ASK1/PP5C 0.009 0.12 -10000 0 -0.43 30 30
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.01 0.048 -10000 0 -0.31 4 4
TSC1/TSC2 0.033 0.045 0.24 1 -10000 0 1
tumor necrosis factor receptor activity 0 0 0.001 2 -10000 0 2
RPS6 0.025 0.022 -10000 0 -0.43 1 1
PPP5C 0.027 0.003 -10000 0 -10000 0 0
EIF4G1 0.027 0.002 -10000 0 -10000 0 0
IRS1 0.007 0.015 -10000 0 -0.21 2 2
INS -0.017 0.003 -10000 0 -10000 0 0
PTEN 0.026 0.006 -10000 0 -10000 0 0
PDK2 -0.006 0.02 0.16 2 -10000 0 2
EIF4EBP1 -0.076 0.31 -10000 0 -1 42 42
PIK3CA 0.027 0.002 -10000 0 -10000 0 0
PPP2R5D -0.006 0.098 -10000 0 -0.39 25 25
peptide biosynthetic process -0.007 0.033 0.18 12 -0.24 1 13
RHEB 0.027 0.005 -10000 0 -10000 0 0
EIF4A1 0.022 0.011 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.002 17 -10000 0 17
EEF2 -0.007 0.033 0.18 12 -0.24 1 13
eIF4E/4E-BP1 -0.059 0.29 -10000 0 -0.96 42 42
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.023 0.01 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.028 0.072 -10000 0 -0.33 5 5
NEF -0.006 0.038 -10000 0 -0.26 2 2
NFKBIA 0.025 0.018 -10000 0 -10000 0 0
BIRC3 0.013 0.062 -10000 0 -0.44 8 8
CYCS 0.01 0.085 0.18 39 -0.36 5 44
RIPK1 0.027 0.003 -10000 0 -10000 0 0
CD247 0.007 0.093 -10000 0 -0.47 13 13
MAP2K7 0.018 0.11 -10000 0 -0.58 9 9
protein ubiquitination 0.027 0.045 0.2 6 -0.29 1 7
CRADD 0.027 0.003 -10000 0 -10000 0 0
DAXX 0.027 0.003 -10000 0 -10000 0 0
FAS 0.021 0.045 -10000 0 -0.4 5 5
BID 0.001 0.074 0.19 7 -0.25 27 34
NF-kappa-B/RelA/I kappa B alpha 0.051 0.044 -10000 0 -0.24 7 7
TRADD 0.027 0.002 -10000 0 -10000 0 0
MAP3K5 0.027 0.004 -10000 0 -10000 0 0
CFLAR 0.027 0 -10000 0 -10000 0 0
FADD 0.027 0.004 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.051 0.044 -10000 0 -0.24 7 7
MAPK8 0.016 0.1 -10000 0 -0.56 8 8
APAF1 0.027 0.003 -10000 0 -10000 0 0
TRAF1 0.027 0.003 -10000 0 -10000 0 0
TRAF2 0.026 0.02 -10000 0 -0.4 1 1
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.007 0.079 0.2 8 -0.26 27 35
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.033 0.045 -10000 0 -0.39 1 1
CHUK 0.028 0.047 0.23 2 -0.31 1 3
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.072 0.036 -10000 0 -10000 0 0
TCRz/NEF 0.001 0.093 -10000 0 -0.32 33 33
TNF 0.025 0.029 -10000 0 -0.4 2 2
FASLG -0.017 0.14 -10000 0 -0.48 33 33
NFKB1 0.026 0.017 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.044 0.028 -10000 0 -0.24 2 2
CASP6 0.033 0.099 -10000 0 -0.52 4 4
CASP7 0.013 0.095 -10000 0 -0.44 10 10
RELA 0.027 0.017 -10000 0 -10000 0 0
CASP2 0.026 0.005 -10000 0 -10000 0 0
CASP3 0.01 0.095 -10000 0 -0.44 10 10
TNFRSF1A 0.027 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.034 0.015 -10000 0 -10000 0 0
CASP8 0.027 0.001 -10000 0 -10000 0 0
CASP9 0.026 0.007 -10000 0 -10000 0 0
MAP3K14 0.031 0.049 0.2 4 -0.36 1 5
APAF-1/Caspase 9 0.021 0.08 -10000 0 -0.34 3 3
BCL2 0.008 0.091 -10000 0 -0.5 8 8
TCGA08_rtk_signaling

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
PDGFRA 0.015 0.068 -10000 0 -0.4 12 12
HRAS 0.026 0.02 -10000 0 -0.4 1 1
EGFR 0.024 0.021 -10000 0 -0.4 1 1
AKT 0.036 0.073 0.26 8 -0.3 5 13
FOXO3 0.027 0.004 -10000 0 -10000 0 0
AKT1 0.025 0.007 -10000 0 -10000 0 0
FOXO1 0.02 0.023 -10000 0 -0.4 1 1
AKT3 0.02 0.053 -10000 0 -0.4 7 7
FOXO4 0.027 0.002 -10000 0 -10000 0 0
MET 0.023 0.046 0.36 1 -0.43 4 5
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
PIK3CB 0.027 0.003 -10000 0 -10000 0 0
NRAS 0.024 0.029 -10000 0 -0.4 2 2
PIK3CG -0.036 0.15 -10000 0 -0.4 65 65
PIK3R3 0.027 0.004 -10000 0 -10000 0 0
PIK3R2 0.027 0.003 -10000 0 -10000 0 0
NF1 0.026 0.005 -10000 0 -10000 0 0
RAS 0.023 0.04 0.18 4 -0.28 1 5
ERBB2 0.029 0.032 0.36 4 -10000 0 4
proliferation/survival/translation -0.025 0.069 0.26 12 -0.23 1 13
PI3K 0.022 0.062 0.24 12 -0.22 6 18
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
KRAS 0.027 0.003 -10000 0 -10000 0 0
FOXO 0.061 0.051 0.22 14 -10000 0 14
AKT2 0.027 0.004 -10000 0 -10000 0 0
PTEN 0.026 0.006 -10000 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex 0.002 0.13 -10000 0 -1.1 2 2
RAD9A 0.027 0.004 -10000 0 -10000 0 0
AP1 0.035 0.028 -10000 0 -0.27 3 3
IFNAR2 0.024 0.013 -10000 0 -10000 0 0
AKT1 -0.004 0.067 -10000 0 -0.31 12 12
ER alpha/Oestrogen -0.007 0.084 -10000 0 -0.28 39 39
NFX1/SIN3/HDAC complex 0.037 0.048 -10000 0 -0.29 2 2
EGF -0.061 0.17 -10000 0 -0.4 90 90
SMG5 0.027 0.004 -10000 0 -10000 0 0
SMG6 0.023 0.01 -10000 0 -10000 0 0
SP3/HDAC2 0.037 0.019 -10000 0 -10000 0 0
TERT/c-Abl 0.012 0.13 -10000 0 -1 2 2
SAP18 0.021 0.011 -10000 0 -10000 0 0
MRN complex 0.044 0.026 -10000 0 -0.24 1 1
WT1 -0.19 0.23 0.36 4 -0.43 218 222
WRN 0.02 0.023 -10000 0 -0.4 1 1
SP1 0.024 0.016 -10000 0 -10000 0 0
SP3 0.027 0.004 -10000 0 -10000 0 0
TERF2IP 0.027 0.002 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.029 0.12 -10000 0 -0.89 2 2
Mad/Max 0.036 0.025 -10000 0 -0.28 2 2
TERT 0.002 0.13 -10000 0 -1.1 2 2
CCND1 0.002 0.12 -10000 0 -0.92 2 2
MAX 0.025 0.008 -10000 0 -10000 0 0
RBBP7 0.027 0.003 -10000 0 -10000 0 0
RBBP4 0.026 0.006 -10000 0 -10000 0 0
TERF2 0.024 0.007 -10000 0 -10000 0 0
PTGES3 0.027 0.002 -10000 0 -10000 0 0
SIN3A 0.026 0.006 -10000 0 -10000 0 0
Telomerase/911 0.041 0.048 -10000 0 -0.3 3 3
CDKN1B -0.005 0.08 -10000 0 -0.26 12 12
RAD1 0.027 0.016 0.36 1 -10000 0 1
XRCC5 0.027 0.001 -10000 0 -10000 0 0
XRCC6 0.026 0.006 -10000 0 -10000 0 0
SAP30 0.026 0.006 -10000 0 -10000 0 0
TRF2/PARP2 0.037 0.011 -10000 0 -10000 0 0
UBE3A 0.024 0.021 -10000 0 -0.4 1 1
JUN 0.026 0.006 -10000 0 -10000 0 0
E6 0 0.002 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.017 0.018 -10000 0 -0.28 1 1
FOS 0.022 0.035 -10000 0 -0.4 3 3
IFN-gamma/IRF1 0.012 0.1 -10000 0 -0.3 43 43
PARP2 0.026 0.007 -10000 0 -10000 0 0
BLM 0.026 0.006 -10000 0 -10000 0 0
Telomerase -0.003 0.12 -10000 0 -0.64 10 10
IRF1 0.03 0.006 -10000 0 -10000 0 0
ESR1 -0.011 0.12 -10000 0 -0.4 39 39
KU/TER 0.038 0.009 -10000 0 -10000 0 0
ATM/TRF2 0.04 0.006 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.032 0.06 -10000 0 -0.3 5 5
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.033 0.06 -10000 0 -0.31 5 5
HDAC1 0.026 0.006 -10000 0 -10000 0 0
HDAC2 0.024 0.016 -10000 0 -10000 0 0
ATM 0.01 0.002 -10000 0 -10000 0 0
SMAD3 0.012 0.016 -10000 0 -0.3 1 1
ABL1 0.027 0.004 -10000 0 -10000 0 0
MXD1 0.025 0.028 -10000 0 -0.4 2 2
MRE11A 0.027 0.004 -10000 0 -10000 0 0
HUS1 0.025 0.008 -10000 0 -10000 0 0
RPS6KB1 0.026 0.021 -10000 0 -0.4 1 1
TERT/NF kappa B1/14-3-3 0.013 0.14 -10000 0 -0.86 3 3
NR2F2 0.026 0.007 -10000 0 -10000 0 0
MAPK3 -0.008 0.018 -10000 0 -0.29 1 1
MAPK1 -0.007 0.013 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.026 0.022 -10000 0 -0.43 1 1
NFKB1 0.027 0.004 -10000 0 -10000 0 0
HNRNPC 0.026 0.007 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.01 0.002 -10000 0 -10000 0 0
NBN 0.022 0.022 -10000 0 -0.4 1 1
EGFR 0.024 0.021 -10000 0 -0.4 1 1
mol:Oestrogen 0 0.001 -10000 0 -10000 0 0
EGF/EGFR -0.024 0.12 -10000 0 -0.28 82 82
MYC 0.025 0.048 0.36 5 -0.42 2 7
IL2 0.016 0.017 -10000 0 -10000 0 0
KU 0.038 0.009 -10000 0 -10000 0 0
RAD50 0.027 0.004 -10000 0 -10000 0 0
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
TGFB1 0.026 0.022 -10000 0 -0.43 1 1
TRF2/BLM 0.038 0.01 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.023 0.13 -10000 0 -1 2 2
SP1/HDAC2 0.036 0.023 -10000 0 -10000 0 0
PINX1 0.021 0.012 -10000 0 -10000 0 0
Telomerase/EST1A 0.024 0.12 -10000 0 -0.89 2 2
Smad3/Myc 0.024 0.035 0.25 5 -0.26 3 8
911 complex 0.049 0.021 0.25 1 -10000 0 1
IFNG -0.015 0.13 -10000 0 -0.42 43 43
Telomerase/PinX1 0.018 0.12 -10000 0 -0.89 2 2
Telomerase/AKT1/mTOR/p70S6K 0.001 0.1 0.22 1 -0.4 16 17
SIN3B 0.027 0.003 -10000 0 -10000 0 0
YWHAE 0.023 0.01 -10000 0 -10000 0 0
Telomerase/EST1B 0.028 0.12 -10000 0 -0.89 2 2
response to DNA damage stimulus 0.003 0.014 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.063 0.033 -10000 0 -10000 0 0
TRF2/WRN 0.03 0.022 -10000 0 -0.26 1 1
Telomerase/hnRNP C1/C2 0.03 0.12 -10000 0 -0.89 2 2
E2F1 0.02 0.057 0.36 8 -0.43 2 10
ZNFX1 0.016 0.013 -10000 0 -10000 0 0
PIF1 0.016 0.067 -10000 0 -0.43 10 10
NCL 0.027 0.002 -10000 0 -10000 0 0
DKC1 0.027 0.003 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 0.068 0.23 -10000 0 -1 1 1
PLK1 0.041 0.089 -10000 0 -0.83 4 4
BIRC5 0.039 0.098 -10000 0 -0.8 5 5
HSPA1B 0.061 0.24 -10000 0 -1 1 1
MAP2K1 0.035 0.036 -10000 0 -10000 0 0
BRCA2 0.11 0.24 -10000 0 -1 1 1
FOXM1 0.069 0.26 -10000 0 -1.1 2 2
XRCC1 0.07 0.23 -10000 0 -1 1 1
FOXM1B/p19 0.033 0.26 -10000 0 -0.94 3 3
Cyclin D1/CDK4 0.077 0.22 -10000 0 -0.93 1 1
CDC2 0.069 0.24 -10000 0 -0.94 2 2
TGFA 0.068 0.22 -10000 0 -0.89 1 1
SKP2 0.071 0.23 -10000 0 -1 1 1
CCNE1 0.029 0.032 0.35 2 -0.42 1 3
CKS1B 0.069 0.23 -10000 0 -0.85 3 3
RB1 0.055 0.13 -10000 0 -0.7 2 2
FOXM1C/SP1 0.074 0.25 -10000 0 -1.1 1 1
AURKB -0.097 0.33 -10000 0 -0.8 78 78
CENPF 0.072 0.23 -10000 0 -1 1 1
CDK4 0.029 0.027 -10000 0 -0.41 1 1
MYC 0.053 0.21 -10000 0 -0.89 1 1
CHEK2 0.035 0.036 -10000 0 -10000 0 0
ONECUT1 0.069 0.23 -10000 0 -0.98 1 1
CDKN2A -0.073 0.19 0.36 2 -0.44 96 98
LAMA4 0.068 0.23 -10000 0 -1 1 1
FOXM1B/HNF6 0.068 0.24 -10000 0 -1.1 1 1
FOS 0.059 0.27 -10000 0 -1.1 8 8
SP1 0.027 0.007 -10000 0 -10000 0 0
CDC25B 0.088 0.24 -10000 0 -1.1 1 1
response to radiation 0.012 0.02 -10000 0 -10000 0 0
CENPB 0.093 0.24 -10000 0 -1 1 1
CENPA 0.068 0.23 -10000 0 -1 1 1
NEK2 0.072 0.23 -10000 0 -1 1 1
HIST1H2BA 0.064 0.23 -10000 0 -1 1 1
CCNA2 0.028 0.012 -10000 0 -10000 0 0
EP300 0.026 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 0.065 0.25 -10000 0 -1.2 1 1
CCNB2 0.068 0.23 -10000 0 -1 1 1
CCNB1 0.069 0.24 -10000 0 -1.1 1 1
ETV5 0.066 0.23 -10000 0 -1 1 1
ESR1 0.007 0.39 -10000 0 -1.1 40 40
CCND1 0.068 0.22 -10000 0 -0.95 1 1
GSK3A 0.033 0.033 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.063 0.041 0.22 2 -0.23 1 3
CDK2 0.029 0.011 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.014 0.024 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 0.078 0.24 -10000 0 -1.1 1 1
GAS1 -0.026 0.44 -10000 0 -1.1 59 59
MMP2 0.064 0.25 -10000 0 -1.2 3 3
RB1/FOXM1C 0.054 0.21 -10000 0 -0.99 1 1
CREBBP 0.027 0.004 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.05 0.058 -10000 0 -0.21 14 14
HDAC3 0.027 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.008 0.001 -10000 0 -10000 0 0
GATA1/HDAC4 0.037 0.006 -10000 0 -10000 0 0
GATA1/HDAC5 0.036 0.017 -10000 0 -0.28 1 1
GATA2/HDAC5 0.031 0.052 -10000 0 -0.28 12 12
HDAC5/BCL6/BCoR 0.053 0.017 -10000 0 -0.24 1 1
HDAC9 -0.031 0.14 -10000 0 -0.4 59 59
Glucocorticoid receptor/Hsp90/HDAC6 0.032 0.072 -10000 0 -0.24 24 24
HDAC4/ANKRA2 0.039 0.007 -10000 0 -10000 0 0
HDAC5/YWHAB 0.022 0.025 -10000 0 -0.28 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.014 0.013 -10000 0 -0.18 2 2
GATA2 0.017 0.065 -10000 0 -0.4 11 11
HDAC4/RFXANK 0.04 0.005 -10000 0 -10000 0 0
BCOR 0.027 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.025 0.021 -10000 0 -0.4 1 1
HDAC5 0.026 0.02 -10000 0 -0.4 1 1
GNB1/GNG2 0.024 0.061 -10000 0 -0.28 17 17
Histones 0.003 0.082 -10000 0 -0.32 7 7
ADRBK1 0.027 0.004 -10000 0 -10000 0 0
HDAC4 0.027 0.002 -10000 0 -10000 0 0
XPO1 0.027 0.001 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.038 0.017 -10000 0 -0.28 1 1
HDAC4/Ubc9 0.04 0.006 -10000 0 -10000 0 0
HDAC7 0.027 0.002 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.033 0.021 -10000 0 -0.28 1 1
TUBA1B 0.027 0.002 -10000 0 -10000 0 0
HDAC6 0.027 0.003 -10000 0 -10000 0 0
HDAC5/RFXANK 0.039 0.016 -10000 0 -0.28 1 1
CAMK4 0.001 0.097 -10000 0 -0.4 25 25
Tubulin/HDAC6 0.048 0.042 -10000 0 -0.26 8 8
SUMO1 0.025 0.028 -10000 0 -0.4 2 2
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.016 0.014 -10000 0 -10000 0 0
GATA1 0.011 0.022 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.023 0.01 -10000 0 -10000 0 0
NR3C1 -0.001 0.11 -10000 0 -0.4 30 30
SUMO1/HDAC4 0.037 0.036 -10000 0 -0.28 2 2
SRF 0.027 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.023 0.02 -10000 0 -10000 0 0
Tubulin 0.034 0.046 -10000 0 -0.3 8 8
HDAC4/14-3-3 E 0.033 0.015 -10000 0 -10000 0 0
GNB1 0.026 0.007 -10000 0 -10000 0 0
RANGAP1 0.026 0.006 -10000 0 -10000 0 0
BCL6/BCoR 0.04 0.006 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.053 0.017 -10000 0 -0.24 1 1
HDAC4/SRF 0.035 0.067 -10000 0 -0.24 25 25
HDAC4/ER alpha 0.011 0.09 -10000 0 -0.28 39 39
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.003 0.082 -10000 0 -0.31 7 7
cell motility 0.048 0.042 -10000 0 -0.26 8 8
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.027 0.004 -10000 0 -10000 0 0
HDAC7/HDAC3 0.04 0.006 -10000 0 -10000 0 0
BCL6 0.027 0.002 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.027 0.002 -10000 0 -10000 0 0
Hsp90/HDAC6 0.037 0.011 -10000 0 -10000 0 0
ESR1 -0.012 0.12 -10000 0 -0.4 39 39
HDAC6/HDAC11 0.04 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.038 0.032 -10000 0 -10000 0 0
NPC 0.016 0 -10000 0 -10000 0 0
MEF2C 0.017 0.063 -10000 0 -0.4 10 10
RAN 0.027 0.002 -10000 0 -10000 0 0
HDAC4/MEF2C 0.069 0.048 -10000 0 -10000 0 0
GNG2 0.009 0.081 -10000 0 -0.4 17 17
NCOR2 0.026 0.02 -10000 0 -0.4 1 1
TUBB2A 0.019 0.06 -10000 0 -0.43 8 8
HDAC11 0.027 0.003 -10000 0 -10000 0 0
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
RANBP2 0.027 0 -10000 0 -10000 0 0
ANKRA2 0.027 0.004 -10000 0 -10000 0 0
RFXANK 0.027 0.003 -10000 0 -10000 0 0
nuclear import -0.019 0.022 0.24 1 -10000 0 1
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.026 0.006 -10000 0 -10000 0 0
HDAC2 0.027 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.037 0.056 -10000 0 -0.23 16 16
forebrain development 0.005 0.092 -10000 0 -0.54 5 5
GNAO1 -0.087 0.19 -10000 0 -0.4 121 121
SMO/beta Arrestin2 0.034 0.018 -10000 0 -10000 0 0
SMO 0.027 0.007 -10000 0 -10000 0 0
ARRB2 0.023 0.011 -10000 0 -10000 0 0
GLI3/SPOP 0.044 0.084 0.24 2 -0.31 3 5
mol:GTP 0 0.001 -10000 0 -10000 0 0
GSK3B 0.027 0.002 -10000 0 -10000 0 0
GNAI2 0.027 0.005 -10000 0 -10000 0 0
SIN3/HDAC complex 0.05 0.032 -10000 0 -10000 0 0
GNAI1 0.014 0.071 -10000 0 -0.4 13 13
XPO1 0.028 0.008 -10000 0 -10000 0 0
GLI1/Su(fu) 0.002 0.096 -10000 0 -0.58 3 3
SAP30 0.026 0.006 -10000 0 -10000 0 0
mol:GDP 0.027 0.007 -10000 0 -10000 0 0
MIM/GLI2A 0.02 0.047 -10000 0 -0.39 5 5
IFT88 0.021 0.011 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GLI2 0.012 0.06 0.18 1 -0.28 11 12
GLI3 0.032 0.086 0.24 3 -0.34 4 7
CSNK1D 0.027 0.004 -10000 0 -10000 0 0
CSNK1E 0.026 0.006 -10000 0 -10000 0 0
SAP18 0.021 0.011 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.021 0.011 -10000 0 -10000 0 0
GNG2 0.009 0.081 -10000 0 -0.4 17 17
Gi family/GTP -0.044 0.12 -10000 0 -0.34 33 33
SIN3B 0.027 0.003 -10000 0 -10000 0 0
SIN3A 0.026 0.006 -10000 0 -10000 0 0
GLI3/Su(fu) 0.038 0.075 0.24 3 -0.32 3 6
GLI2/Su(fu) 0.021 0.062 -10000 0 -0.34 6 6
FOXA2 -0.004 0.16 -10000 0 -0.79 11 11
neural tube patterning 0.005 0.092 -10000 0 -0.54 5 5
SPOP 0.027 0.004 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.028 0.039 -10000 0 -10000 0 0
GNB1 0.026 0.007 -10000 0 -10000 0 0
CSNK1G2 0.026 0.02 -10000 0 -0.4 1 1
CSNK1G3 0.026 0.005 -10000 0 -10000 0 0
MTSS1 0.021 0.047 -10000 0 -0.4 5 5
embryonic limb morphogenesis 0.005 0.092 -10000 0 -0.54 5 5
SUFU 0.02 0.011 -10000 0 -10000 0 0
LGALS3 0.025 0.021 -10000 0 -0.4 1 1
catabolic process 0.048 0.098 0.25 1 -0.36 6 7
GLI3A/CBP 0.031 0.029 -10000 0 -0.32 3 3
KIF3A 0.027 0.005 -10000 0 -10000 0 0
GLI1 0.004 0.094 -10000 0 -0.56 5 5
RAB23 0.027 0.003 -10000 0 -10000 0 0
CSNK1A1 0.027 0.004 -10000 0 -10000 0 0
IFT172 0.027 0.001 -10000 0 -10000 0 0
RBBP7 0.027 0.003 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.027 0.04 -10000 0 -10000 0 0
GNAZ 0.022 0.045 -10000 0 -0.4 5 5
RBBP4 0.026 0.006 -10000 0 -10000 0 0
CSNK1G1 0.025 0.021 -10000 0 -0.4 1 1
PIAS1 0.026 0.006 -10000 0 -10000 0 0
PRKACA 0.027 0.003 -10000 0 -10000 0 0
GLI2/SPOP 0.027 0.06 -10000 0 -0.32 4 4
STK36 0.028 0.008 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.046 0.14 -10000 0 -0.37 46 46
PTCH1 0.003 0.11 -10000 0 -1 3 3
MIM/GLI1 0.012 0.11 -10000 0 -0.64 4 4
CREBBP 0.031 0.029 -10000 0 -0.32 3 3
Su(fu)/SIN3/HDAC complex 0.024 0.088 0.24 1 -0.36 15 16
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.035 0.079 -10000 0 -0.23 1 1
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.026 0.006 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.029 0.073 0.3 1 -0.34 1 2
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.039 0.043 -10000 0 -0.24 3 3
antigen processing and presentation of peptide antigen via MHC class I -0.004 0.055 -10000 0 -0.28 1 1
CaM/Ca2+ 0.035 0.077 -10000 0 -0.22 1 1
RAP1A 0.026 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.011 0.07 -10000 0 -0.37 1 1
AKT1 -0.008 0.057 -10000 0 -10000 0 0
MAP2K1 -0.014 0.062 0.29 1 -0.26 1 2
MAP3K11 -0.004 0.065 0.29 1 -10000 0 1
IFNGR1 0.022 0.019 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.023 0.14 -10000 0 -0.39 40 40
Rap1/GTP 0.002 0.054 -10000 0 -10000 0 0
CRKL/C3G 0.037 0.018 -10000 0 -0.28 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.035 0.088 -10000 0 -10000 0 0
CEBPB 0.017 0.14 0.27 3 -0.55 11 14
STAT3 0.027 0.004 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.042 0.11 -10000 0 -0.67 3 3
STAT1 -0.003 0.066 0.29 1 -0.37 1 2
CALM1 0.025 0.007 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.018 0.13 -10000 0 -0.42 43 43
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.01 0.068 0.29 1 -0.36 1 2
CEBPB/PTGES2/Cbp/p300 0.023 0.095 -10000 0 -0.38 6 6
mol:Ca2+ 0.032 0.077 -10000 0 -0.22 1 1
MAPK3 -0.006 0.093 -10000 0 -0.74 3 3
STAT1 (dimer) 0.004 0.078 -10000 0 -0.39 1 1
MAPK1 -0.035 0.17 -10000 0 -0.73 22 22
JAK2 0.019 0.039 -10000 0 -0.4 3 3
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
JAK1 0.022 0.019 -10000 0 -10000 0 0
CAMK2D 0.027 0.005 -10000 0 -10000 0 0
DAPK1 0.008 0.15 0.29 4 -0.56 23 27
SMAD7 0.003 0.033 0.13 1 -0.24 1 2
CBL/CRKL/C3G 0.02 0.071 0.29 1 -10000 0 1
PI3K 0.035 0.076 -10000 0 -10000 0 0
IFNG -0.018 0.13 -10000 0 -0.42 43 43
apoptosis 0.003 0.13 0.25 4 -0.43 30 34
CAMK2G 0.027 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.027 0.004 -10000 0 -10000 0 0
CAMK2A -0.009 0.11 -10000 0 -0.4 34 34
CAMK2B -0.012 0.11 0.36 1 -0.4 34 35
FRAP1 -0.02 0.05 -10000 0 -10000 0 0
PRKCD -0.008 0.06 0.28 1 -10000 0 1
RAP1B 0.027 0.002 -10000 0 -10000 0 0
negative regulation of cell growth -0.004 0.055 -10000 0 -0.28 1 1
PTPN2 0.022 0.011 -10000 0 -10000 0 0
EP300 0.026 0.006 -10000 0 -10000 0 0
IRF1 -0.005 0.057 0.26 2 -10000 0 2
STAT1 (dimer)/PIASy 0.009 0.068 0.29 1 -0.36 1 2
SOCS1 0.017 0.093 -10000 0 -1 3 3
mol:GDP 0.018 0.067 0.27 1 -10000 0 1
CASP1 0.002 0.036 0.13 1 -0.27 1 2
PTGES2 0.027 0.003 -10000 0 -10000 0 0
IRF9 0.023 0.049 0.14 6 -0.18 1 7
mol:PI-3-4-5-P3 0.022 0.068 -10000 0 -10000 0 0
RAP1/GDP 0.02 0.063 -10000 0 -10000 0 0
CBL -0.004 0.064 0.29 1 -10000 0 1
MAP3K1 -0.004 0.065 0.29 1 -0.24 1 2
PIAS1 0.026 0.006 -10000 0 -10000 0 0
PIAS4 0.027 0.004 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.004 0.055 -10000 0 -0.28 1 1
PTPN11 -0.004 0.065 -10000 0 -0.23 1 1
CREBBP 0.027 0.004 -10000 0 -10000 0 0
RAPGEF1 0.026 0.02 -10000 0 -0.4 1 1
ceramide signaling pathway

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
MAP4K4 0.023 0.053 -10000 0 -0.33 1 1
BAG4 0.023 0.01 -10000 0 -10000 0 0
BAD 0.013 0.03 0.12 1 -0.36 1 2
NFKBIA 0.025 0.007 -10000 0 -10000 0 0
BIRC3 0.019 0.057 -10000 0 -0.4 8 8
BAX 0.015 0.032 0.18 5 -0.19 1 6
EnzymeConsortium:3.1.4.12 0.009 0.015 0.06 4 -10000 0 4
IKBKB 0.037 0.07 0.24 3 -0.31 1 4
MAP2K2 0.014 0.042 0.19 12 -0.31 1 13
MAP2K1 0.013 0.039 0.19 12 -10000 0 12
SMPD1 0.009 0.028 0.12 3 -0.18 6 9
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.029 0.056 -10000 0 -0.36 1 1
MAP2K4 0.009 0.026 0.14 1 -0.23 1 2
protein ubiquitination 0.028 0.057 -10000 0 -0.31 2 2
EnzymeConsortium:2.7.1.37 0.015 0.042 0.19 14 -0.23 1 15
response to UV 0 0 0.002 14 -10000 0 14
RAF1 0.016 0.04 0.19 12 -10000 0 12
CRADD 0.027 0.003 -10000 0 -10000 0 0
mol:ceramide 0.016 0.029 0.11 5 -0.2 1 6
I-kappa-B-alpha/RELA/p50/ubiquitin 0.034 0.011 -10000 0 -10000 0 0
MADD 0.027 0.003 -10000 0 -10000 0 0
MAP3K1 0.013 0.029 0.12 1 -0.22 2 3
TRADD 0.027 0.002 -10000 0 -10000 0 0
RELA/p50 0.027 0.004 -10000 0 -10000 0 0
MAPK3 0.018 0.041 0.19 13 -0.24 1 14
MAPK1 0.014 0.043 0.19 11 -0.24 1 12
p50/RELA/I-kappa-B-alpha 0.037 0.012 -10000 0 -10000 0 0
FADD 0.025 0.051 0.21 1 -0.3 1 2
KSR1 0.017 0.039 0.19 12 -0.19 1 13
MAPK8 0.009 0.028 0.14 1 -0.22 1 2
TRAF2 0.026 0.02 -10000 0 -0.4 1 1
response to radiation 0 0 0.002 5 -10000 0 5
CHUK 0.022 0.05 -10000 0 -10000 0 0
TNF R/SODD 0.034 0.015 -10000 0 -10000 0 0
TNF 0.025 0.029 -10000 0 -0.4 2 2
CYCS 0.036 0.048 0.13 37 -0.28 1 38
IKBKG 0.022 0.055 -10000 0 -0.36 2 2
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.027 0.055 -10000 0 -0.32 2 2
RELA 0.027 0.004 -10000 0 -10000 0 0
RIPK1 0.027 0.003 -10000 0 -10000 0 0
AIFM1 0.031 0.044 0.13 25 -0.28 1 26
TNF/TNF R/SODD 0.044 0.028 -10000 0 -0.24 2 2
TNFRSF1A 0.027 0.004 -10000 0 -10000 0 0
response to heat 0 0 0.002 5 -10000 0 5
CASP8 0.025 0.09 -10000 0 -0.55 10 10
NSMAF 0.043 0.077 0.25 7 -0.32 1 8
response to hydrogen peroxide 0 0 0.002 14 -10000 0 14
BCL2 0.012 0.06 -10000 0 -0.4 9 9
IL2 signaling events mediated by PI3K

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
BCL2L1 0.08 0.1 -10000 0 -0.54 1 1
UGCG 0.022 0.045 -10000 0 -0.58 2 2
AKT1/mTOR/p70S6K/Hsp90/TERT 0.011 0.13 -10000 0 -0.43 22 22
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.022 0.045 -10000 0 -0.58 2 2
mol:DAG -0.004 0.12 -10000 0 -0.82 9 9
CaM/Ca2+/Calcineurin A alpha-beta B1 0.023 0.13 -10000 0 -0.4 27 27
FRAP1 0.013 0.14 -10000 0 -0.45 30 30
FOXO3 0.018 0.11 -10000 0 -0.4 14 14
AKT1 0.02 0.12 -10000 0 -0.41 16 16
GAB2 0.027 0.004 -10000 0 -10000 0 0
SMPD1 0.014 0.083 -10000 0 -0.62 7 7
SGMS1 0.012 0.093 -10000 0 -0.62 9 9
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 0.007 0.006 -10000 0 -10000 0 0
CALM1 0.025 0.007 -10000 0 -10000 0 0
cell proliferation 0.035 0.084 -10000 0 -0.41 7 7
EIF3A 0.027 0.004 -10000 0 -10000 0 0
PI3K 0.043 0.009 -10000 0 -10000 0 0
RPS6KB1 0.015 0.1 -10000 0 -0.83 6 6
mol:sphingomyelin -0.004 0.12 -10000 0 -0.82 9 9
natural killer cell activation 0 0.002 -10000 0 -10000 0 0
JAK3 0.028 0.022 -10000 0 -0.42 1 1
PIK3R1 0.028 0.006 -10000 0 -10000 0 0
JAK1 0.028 0.006 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MYC 0.047 0.12 0.29 6 -0.45 4 10
MYB 0.031 0.064 -10000 0 -1.1 1 1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.027 0.093 -10000 0 -0.41 9 9
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.043 0.098 -10000 0 -0.76 6 6
mol:PI-3-4-5-P3 0.026 0.093 -10000 0 -0.4 9 9
Rac1/GDP 0.021 0.013 -10000 0 -10000 0 0
T cell proliferation 0.025 0.08 -10000 0 -0.42 5 5
SHC1 0.027 0.005 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0.003 -10000 0 -0.065 1 1
PRKCZ 0.026 0.081 -10000 0 -0.44 5 5
NF kappa B1 p50/RelA 0.036 0.13 -10000 0 -0.41 24 24
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.026 0.056 -10000 0 -0.39 5 5
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
RELA 0.027 0.004 -10000 0 -10000 0 0
IL2RA 0.017 0.065 -10000 0 -0.4 11 11
IL2RB 0.018 0.063 -10000 0 -0.4 10 10
TERT -0.015 0.13 0.36 2 -0.42 42 44
E2F1 0.033 0.041 -10000 0 -0.4 1 1
SOS1 0.027 0.003 -10000 0 -10000 0 0
RPS6 0.025 0.022 -10000 0 -0.43 1 1
mol:cAMP -0.002 0.002 0.031 1 -10000 0 1
PTPN11 0.027 0.003 -10000 0 -10000 0 0
IL2RG 0.027 0.029 -10000 0 -0.4 2 2
actin cytoskeleton organization 0.025 0.08 -10000 0 -0.42 5 5
GRB2 0.027 0.005 -10000 0 -10000 0 0
IL2 0.019 0.012 -10000 0 -10000 0 0
PIK3CA 0.029 0.003 -10000 0 -10000 0 0
Rac1/GTP 0.047 0.024 -10000 0 -10000 0 0
LCK 0.019 0.063 -10000 0 -0.42 9 9
BCL2 -0.001 0.2 -10000 0 -0.8 23 23
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.022 0.035 -10000 0 -0.31 3 3
KLHL20 0.042 0.075 0.21 28 -0.23 7 35
CYFIP2 0.026 0.02 -10000 0 -0.4 1 1
Rac1/GDP 0.068 0.08 0.29 4 -10000 0 4
ENAH 0.022 0.035 -10000 0 -0.31 3 3
AP1M1 0.027 0.003 -10000 0 -10000 0 0
RAP1B 0.027 0.002 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
CDC42/GTP 0.019 0.022 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.008 0.028 -10000 0 -0.16 7 7
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.049 0.056 -10000 0 -0.21 7 7
RAPGEF1 0.056 0.082 0.31 6 -10000 0 6
CTNND1 0.027 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.03 0.037 -10000 0 -0.31 3 3
CRK 0.056 0.076 -10000 0 -0.3 1 1
E-cadherin/gamma catenin/alpha catenin 0.053 0.018 -10000 0 -0.24 1 1
alphaE/beta7 Integrin 0.022 0.061 -10000 0 -0.27 18 18
IQGAP1 0.026 0.006 -10000 0 -10000 0 0
NCKAP1 0.027 0 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.05 0.013 -10000 0 -10000 0 0
DLG1 0.022 0.036 -10000 0 -0.31 3 3
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.005 0.01 -10000 0 -10000 0 0
MLLT4 0.027 0.004 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.019 0.086 -10000 0 -0.23 44 44
PI3K 0.009 0.014 -10000 0 -10000 0 0
ARF6 0.025 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.039 0.016 -10000 0 -0.28 1 1
TIAM1 -0.012 0.12 -10000 0 -0.4 41 41
E-cadherin(dimer)/Ca2+ 0.062 0.014 -10000 0 -10000 0 0
AKT1 0.032 0.041 0.1 25 -10000 0 25
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
CDH1 0.027 0.002 -10000 0 -10000 0 0
RhoA/GDP 0.081 0.081 0.28 7 -10000 0 7
actin cytoskeleton organization 0.04 0.062 0.17 31 -0.17 7 38
CDC42/GDP 0.075 0.08 0.27 6 -10000 0 6
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.02 0.012 -10000 0 -0.2 1 1
ITGB7 0.01 0.083 -10000 0 -0.4 18 18
RAC1 0.025 0.008 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.067 0.015 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0.047 0.009 -10000 0 -10000 0 0
mol:GDP 0.072 0.088 0.3 6 -0.29 1 7
CDC42/GTP/IQGAP1 0.033 0.017 -10000 0 -0.23 1 1
JUP 0.026 0.02 -10000 0 -0.4 1 1
p120 catenin/RhoA/GDP 0.089 0.081 0.29 6 -10000 0 6
RAC1/GTP/IQGAP1 0.032 0.013 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.039 0.016 -10000 0 -0.28 1 1
RHOA 0.027 0.004 -10000 0 -10000 0 0
CDC42 0.025 0.021 -10000 0 -0.4 1 1
CTNNA1 0.027 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.032 0.047 0.14 32 -0.16 3 35
NME1 0.019 0.066 0.36 1 -0.43 9 10
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.021 0.035 -10000 0 -0.31 3 3
regulation of cell-cell adhesion 0.012 0.016 -10000 0 -10000 0 0
WASF2 0.015 0.026 -10000 0 -10000 0 0
Rap1/GTP 0.08 0.071 0.29 5 -10000 0 5
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.057 0.058 -10000 0 -10000 0 0
CCND1 0.036 0.054 0.15 31 -0.2 3 34
VAV2 0.071 0.14 -10000 0 -0.59 12 12
RAP1/GDP 0.088 0.078 0.3 6 -10000 0 6
adherens junction assembly 0.02 0.035 -10000 0 -0.3 3 3
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.027 0.002 -10000 0 -10000 0 0
PIP5K1C 0.026 0.02 -10000 0 -0.4 1 1
regulation of heterotypic cell-cell adhesion 0.044 0.052 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.013 0.011 -10000 0 -0.15 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
SRC 0.014 0.03 -10000 0 -0.31 2 2
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
Rac1/GTP -0.004 0.066 -10000 0 -0.36 9 9
E-cadherin/beta catenin/alpha catenin 0.054 0.01 -10000 0 -10000 0 0
ITGAE 0.023 0.01 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.03 0.037 -10000 0 -0.32 3 3
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.021 0.066 -10000 0 -0.21 30 30
MAPK9 0.007 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.01 0.02 -10000 0 -0.3 2 2
GNB1/GNG2 0.022 0.052 -10000 0 -0.23 17 17
GNB1 0.026 0.007 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.007 0.001 -10000 0 -10000 0 0
Gs family/GTP 0.006 0.042 -10000 0 -0.21 16 16
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.003 0.011 0.058 16 -10000 0 16
GNAL 0.007 0.078 -10000 0 -0.4 16 16
GNG2 0.009 0.081 -10000 0 -0.4 17 17
CRH -0.017 0.029 -10000 0 -0.43 2 2
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.007 0.001 -10000 0 -10000 0 0
MAPK11 0.006 0.011 -10000 0 -0.15 2 2
Aurora A 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
Aurora A/GADD45A 0.046 0.036 -10000 0 -10000 0 0
BIRC5 0.027 0.016 0.36 1 -10000 0 1
NFKBIA 0.005 0.012 0.25 1 -10000 0 1
CPEB1 -0.083 0.18 -10000 0 -0.4 107 107
AKT1 0.005 0.004 -10000 0 -10000 0 0
NDEL1 0.022 0.01 -10000 0 -10000 0 0
Aurora A/BRCA1 0.017 0.016 -10000 0 -10000 0 0
NDEL1/TACC3 0.053 0.036 -10000 0 -10000 0 0
GADD45A 0.026 0.005 -10000 0 -10000 0 0
GSK3B 0.025 0.002 -10000 0 -10000 0 0
PAK1/Aurora A 0.048 0.036 -10000 0 -10000 0 0
MDM2 0.026 0.02 -10000 0 -0.4 1 1
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.011 0.026 0.27 4 -10000 0 4
TP53 0.013 0.012 -10000 0 -10000 0 0
DLG7 0.006 0.005 -10000 0 -10000 0 0
AURKAIP1 0.026 0.007 -10000 0 -10000 0 0
ARHGEF7 0.021 0.012 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.056 0.037 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.017 0.016 -10000 0 -10000 0 0
AURKA 0.01 0.009 -10000 0 -10000 0 0
AURKB 0.009 0.009 -10000 0 -10000 0 0
CDC25B 0.015 0.046 0.3 10 -10000 0 10
G2/M transition checkpoint 0.006 0.008 -10000 0 -10000 0 0
mRNA polyadenylation -0.028 0.081 -10000 0 -0.2 65 65
Aurora A/CPEB -0.028 0.082 -10000 0 -0.2 65 65
Aurora A/TACC1/TRAP/chTOG 0.069 0.041 -10000 0 -10000 0 0
BRCA1 0.027 0.003 -10000 0 -10000 0 0
centrosome duplication 0.047 0.036 -10000 0 -10000 0 0
regulation of centrosome cycle 0.052 0.035 -10000 0 -10000 0 0
spindle assembly 0.067 0.04 -10000 0 -10000 0 0
TDRD7 0.027 0.004 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.075 0.033 -10000 0 -10000 0 0
CENPA 0.011 0.01 -10000 0 -10000 0 0
Aurora A/PP2A 0.047 0.036 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.035 0.04 0.2 1 -10000 0 1
negative regulation of DNA binding 0.012 0.018 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.03 0.023 -10000 0 -0.28 1 1
RASA1 0.026 0.005 -10000 0 -10000 0 0
Ajuba/Aurora A 0.006 0.008 -10000 0 -10000 0 0
mitotic prometaphase 0.011 0.028 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.009 -10000 0 -10000 0 0
TACC1 0.023 0.01 -10000 0 -10000 0 0
TACC3 0.026 0.005 -10000 0 -10000 0 0
Aurora A/Antizyme1 0.066 0.034 -10000 0 -10000 0 0
Aurora A/RasGAP 0.047 0.036 -10000 0 -10000 0 0
OAZ1 0.027 0.004 -10000 0 -10000 0 0
RAN 0.027 0.002 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.025 0.003 -10000 0 -10000 0 0
GIT1 0.026 0.02 -10000 0 -0.4 1 1
GIT1/beta-PIX/PAK1 0.041 0.028 -10000 0 -0.24 1 1
Importin alpha/Importin beta/TPX2 0.011 0.026 0.27 4 -10000 0 4
PPP2R5D 0.027 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 0.015 0.028 0.28 4 -10000 0 4
PAK1 0.027 0.003 -10000 0 -10000 0 0
CKAP5 0.027 0.003 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.026 0.006 -9999 0 -10000 0 0
Rac1/GDP 0.025 0.011 -9999 0 -10000 0 0
DOCK1 0.027 0.005 -9999 0 -10000 0 0
ITGA4 0.01 0.083 -9999 0 -0.4 18 18
RAC1 0.025 0.008 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.015 0.092 -9999 0 -0.31 32 32
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.023 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.043 0.057 -9999 0 -0.24 18 18
alpha4/beta7 Integrin/Paxillin 0.025 0.075 -9999 0 -0.24 31 31
lamellipodium assembly 0.01 0.074 -9999 0 -0.41 9 9
PIK3CA 0.027 0.003 -9999 0 -10000 0 0
PI3K 0.039 0.008 -9999 0 -10000 0 0
ARF6 0.025 0.007 -9999 0 -10000 0 0
TLN1 0.027 0.004 -9999 0 -10000 0 0
PXN 0.014 0.002 -9999 0 -10000 0 0
PIK3R1 0.026 0.005 -9999 0 -10000 0 0
ARF6/GTP 0.045 0.048 -9999 0 -10000 0 0
cell adhesion 0.046 0.052 -9999 0 -10000 0 0
CRKL/CBL 0.038 0.009 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.035 0.052 -9999 0 -0.21 18 18
ITGB1 0.027 0.002 -9999 0 -10000 0 0
ITGB7 0.01 0.083 -9999 0 -0.4 18 18
ARF6/GDP 0.026 0.01 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.042 0.074 -9999 0 -0.39 8 8
p130Cas/Crk/Dock1 0.044 0.026 -9999 0 -0.24 1 1
VCAM1 0.016 0.065 -9999 0 -0.4 11 11
alpha4/beta1 Integrin/Paxillin/Talin 0.048 0.053 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.049 0.05 -9999 0 -10000 0 0
BCAR1 0.026 0.02 -9999 0 -0.4 1 1
mol:GDP -0.047 0.05 -9999 0 -10000 0 0
CBL 0.027 0.004 -9999 0 -10000 0 0
PRKACA 0.027 0.003 -9999 0 -10000 0 0
GIT1 0.026 0.02 -9999 0 -0.4 1 1
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.048 0.053 -9999 0 -10000 0 0
Rac1/GTP 0.009 0.08 -9999 0 -0.45 9 9
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.036 0.034 -10000 0 -0.28 5 5
AKT1 0.089 0.09 0.26 60 -0.4 1 61
PTK2B 0.014 0.037 -10000 0 -0.49 1 1
VEGFR2 homodimer/Frs2 0.034 0.03 -10000 0 -0.58 1 1
CAV1 0.023 0.04 -10000 0 -0.4 4 4
CALM1 0.025 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.051 0.032 0.25 1 -0.53 1 2
endothelial cell proliferation 0.094 0.12 0.27 111 -0.33 1 112
mol:Ca2+ 0.013 0.022 -10000 0 -0.33 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.056 0.039 -10000 0 -0.51 1 1
RP11-342D11.1 0.011 0.029 -10000 0 -0.49 1 1
CDH5 0.027 0.001 -10000 0 -10000 0 0
VEGFA homodimer 0.064 0.025 0.26 1 -10000 0 1
SHC1 0.027 0.004 -10000 0 -10000 0 0
SHC2 0.018 0.062 -10000 0 -0.41 9 9
HRAS/GDP 0.045 0.032 -10000 0 -0.44 1 1
SH2D2A 0.027 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.096 0.083 0.28 8 -0.38 2 10
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.05 0.033 0.25 1 -0.53 1 2
VEGFR1 homodimer 0.021 0.012 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.073 0.04 -10000 0 -0.48 1 1
GRB10 0.021 0.03 -10000 0 -0.49 1 1
PTPN11 0.027 0.003 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
PAK1 0.027 0.003 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.073 0.038 -10000 0 -0.49 1 1
HRAS 0.026 0.02 -10000 0 -0.4 1 1
VEGF/Rho/ROCK1/Integrin Complex 0.004 0.077 -10000 0 -0.54 2 2
HIF1A 0.025 0.007 -10000 0 -10000 0 0
FRS2 0.027 0.003 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.054 0.038 -10000 0 -0.5 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.023 0.04 -10000 0 -0.4 4 4
Nck/Pak 0.04 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.05 0.032 0.25 1 -0.53 1 2
mol:GDP 0.058 0.035 -10000 0 -0.46 1 1
mol:NADP 0.086 0.088 0.29 15 -0.4 1 16
eNOS/Hsp90 0.09 0.085 0.29 15 -0.36 1 16
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 0.013 0.022 -10000 0 -0.33 1 1
HIF1A/ARNT 0.036 0.019 -10000 0 -0.28 1 1
SHB 0.027 0.004 -10000 0 -10000 0 0
VEGFA 0.029 0.016 0.36 1 -10000 0 1
VEGFC 0.02 0.049 -10000 0 -0.4 6 6
FAK1/Vinculin 0.056 0.075 0.28 5 -0.57 1 6
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.062 0.042 -10000 0 -0.51 1 1
PTPN6 0.027 0.004 -10000 0 -10000 0 0
EPAS1 0.033 0.017 -10000 0 -0.31 1 1
mol:L-citrulline 0.086 0.088 0.29 15 -0.4 1 16
ITGAV 0.027 0.002 -10000 0 -10000 0 0
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.064 0.034 0.25 1 -0.51 1 2
VEGFR2 homodimer/VEGFA homodimer 0.052 0.034 -10000 0 -0.54 1 1
VEGFR2/3 heterodimer 0.032 0.039 -10000 0 -0.58 1 1
VEGFB 0.027 0.004 -10000 0 -10000 0 0
MAPK11 0.007 0.04 0.43 1 -0.53 1 2
VEGFR2 homodimer 0.02 0.032 -10000 0 -0.65 1 1
FLT1 0.021 0.012 -10000 0 -10000 0 0
NEDD4 0.027 0.007 -10000 0 -10000 0 0
MAPK3 0.033 0.08 0.3 4 -0.32 1 5
MAPK1 0.034 0.079 0.29 5 -0.32 1 6
VEGFA145/NRP2 0.039 0.028 0.26 1 -0.28 3 4
VEGFR1/2 heterodimer 0.026 0.033 -10000 0 -0.58 1 1
KDR 0.02 0.032 -10000 0 -0.66 1 1
VEGFA165/NRP1/VEGFR2 homodimer 0.052 0.038 0.24 1 -0.49 1 2
SRC 0.017 0.013 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.046 0.085 0.36 4 -0.33 1 5
PI3K 0.049 0.056 0.3 1 -0.41 1 2
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.051 0.032 0.25 1 -0.53 1 2
FES 0.022 0.032 -10000 0 -0.51 1 1
GAB1 0.03 0.037 -10000 0 -0.55 1 1
VEGFR2 homodimer/VEGFA homodimer/Src 0.031 0.033 -10000 0 -0.36 1 1
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
SOS1 0.027 0.002 -10000 0 -10000 0 0
ARNT 0.026 0.02 -10000 0 -0.4 1 1
eNOS/Caveolin-1 0.088 0.084 0.31 7 -0.38 1 8
VEGFR2 homodimer/VEGFA homodimer/Yes 0.042 0.043 0.25 1 -0.71 1 2
PI3K/GAB1 0.053 0.054 0.27 1 -0.44 1 2
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.075 0.036 -10000 0 -0.49 1 1
PRKACA 0.027 0.003 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.041 0.051 -10000 0 -0.47 2 2
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
CDC42 0.022 0.031 -10000 0 -0.51 1 1
actin cytoskeleton reorganization 0.049 0.032 0.25 1 -0.53 1 2
PTK2 0.028 0.054 0.28 1 -0.6 1 2
EDG1 0.011 0.029 -10000 0 -0.49 1 1
mol:DAG 0.013 0.022 -10000 0 -0.33 1 1
CaM/Ca2+ 0.022 0.028 -10000 0 -0.31 1 1
MAP2K3 0.013 0.035 -10000 0 -0.49 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.065 0.06 -10000 0 -0.51 1 1
PLCG1 0.013 0.022 -10000 0 -0.34 1 1
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.039 0.039 -10000 0 -0.34 1 1
IQGAP1 0.026 0.006 -10000 0 -10000 0 0
YES1 0.022 0.022 -10000 0 -0.4 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.051 0.032 0.25 1 -0.53 1 2
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.05 0.032 0.25 1 -0.53 1 2
cell migration 0.063 0.08 0.28 8 -0.5 1 9
mol:PI-3-4-5-P3 0.054 0.055 0.29 1 -0.39 1 2
FYN 0.027 0.004 -10000 0 -10000 0 0
VEGFB/NRP1 0.027 0.029 -10000 0 -0.47 1 1
mol:NO 0.086 0.088 0.29 15 -0.4 1 16
PXN 0.027 0.002 -10000 0 -10000 0 0
HRAS/GTP 0.026 0.027 -10000 0 -0.44 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.039 0.034 -10000 0 -0.51 1 1
VHL 0.027 0.003 -10000 0 -10000 0 0
ITGB3 0.022 0.045 -10000 0 -0.4 5 5
NOS3 0.088 0.092 0.35 8 -0.44 1 9
VEGFR2 homodimer/VEGFA homodimer/Sck 0.044 0.049 -10000 0 -0.53 1 1
RAC1 0.025 0.008 -10000 0 -10000 0 0
PRKCA 0.007 0.023 -10000 0 -0.32 1 1
PRKCB -0.01 0.055 -10000 0 -0.32 1 1
VCL 0.027 0.004 -10000 0 -10000 0 0
VEGFA165/NRP1 0.031 0.031 0.23 1 -0.49 1 2
VEGFR1/2 heterodimer/VEGFA homodimer 0.039 0.038 0.25 1 -0.53 1 2
VEGFA165/NRP2 0.039 0.028 0.26 1 -0.28 3 4
MAPKKK cascade 0.033 0.04 -10000 0 -0.44 1 1
NRP2 0.025 0.034 -10000 0 -0.4 3 3
VEGFC homodimer 0.02 0.049 -10000 0 -0.4 6 6
NCK1 0.027 0.002 -10000 0 -10000 0 0
ROCK1 0.022 0.022 -10000 0 -0.4 1 1
FAK1/Paxillin 0.056 0.076 0.28 5 -0.57 1 6
MAP3K13 0.023 0.03 -10000 0 -0.51 1 1
PDPK1 0.08 0.088 0.26 64 -0.35 1 65
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.023 0.04 0.39 4 -10000 0 4
PI3K Class IB/PDE3B 0.023 0.04 -10000 0 -0.4 4 4
PDE3B 0.023 0.04 -10000 0 -0.4 4 4
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.022 0.027 -10000 0 -0.2 6 6
epithelial cell differentiation 0.056 0.013 -10000 0 -10000 0 0
CYFIP2 0.026 0.02 -10000 0 -0.4 1 1
ENAH -0.01 0.026 -10000 0 -10000 0 0
EGFR 0.024 0.021 -10000 0 -0.4 1 1
EPHA2 0.025 0.022 -10000 0 -0.43 1 1
MYO6 0.013 0.011 -10000 0 -10000 0 0
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.054 0.016 -10000 0 -0.24 1 1
AQP5 -0.006 0.043 -10000 0 -10000 0 0
CTNND1 0.027 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.012 0.015 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.003 0.042 -10000 0 -10000 0 0
EGF -0.063 0.17 -10000 0 -0.4 90 90
NCKAP1 0.027 0 -10000 0 -10000 0 0
AQP3 0.011 0.036 0.24 1 -0.43 1 2
cortical microtubule organization 0.056 0.013 -10000 0 -10000 0 0
GO:0000145 -0.008 0.015 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.062 0.014 -10000 0 -10000 0 0
MLLT4 0.027 0.004 -10000 0 -10000 0 0
ARF6/GDP -0.015 0.013 -10000 0 -10000 0 0
ARF6 0.025 0.007 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.061 0.03 -10000 0 -0.22 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.006 0.011 -10000 0 -10000 0 0
PVRL2 0.027 0.003 -10000 0 -10000 0 0
ZYX 0.012 0.009 -10000 0 -10000 0 0
ARF6/GTP 0.064 0.034 -10000 0 -10000 0 0
CDH1 0.027 0.002 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.001 0.093 -10000 0 -10000 0 0
RhoA/GDP 0.057 0.014 -10000 0 -10000 0 0
actin cytoskeleton organization -0.008 0.012 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.026 0.006 -10000 0 -10000 0 0
GIT1 0.026 0.02 -10000 0 -0.4 1 1
IGF1R 0.026 0.006 -10000 0 -10000 0 0
IGF1 -0.079 0.18 -10000 0 -0.4 112 112
DIAPH1 0.042 0.092 -10000 0 -0.52 7 7
Wnt receptor signaling pathway -0.056 0.013 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.015 0.013 -10000 0 -10000 0 0
CTNNA1 0.027 0.004 -10000 0 -10000 0 0
VCL -0.008 0.013 -10000 0 -10000 0 0
EFNA1 0.027 0.004 -10000 0 -10000 0 0
LPP -0.01 0.016 -10000 0 -10000 0 0
Ephrin A1/EPHA2 0.047 0.021 -10000 0 -10000 0 0
SEC6/SEC8 0.014 0.006 -10000 0 -10000 0 0
MGAT3 0.003 0.042 -10000 0 -10000 0 0
HGF/MET 0.042 0.044 -10000 0 -10000 0 0
HGF 0.017 0.06 -10000 0 -0.4 9 9
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.023 0.027 -10000 0 -0.2 6 6
actin cable formation 0.01 0.052 0.22 11 -0.29 1 12
KIAA1543 -0.008 0.013 -10000 0 -10000 0 0
KIFC3 0.004 0.044 -10000 0 -10000 0 0
NCK1 0.027 0.002 -10000 0 -10000 0 0
EXOC3 0.027 0.004 -10000 0 -10000 0 0
ACTN1 0.012 0.012 -10000 0 -10000 0 0
NCK1/GIT1 0.038 0.017 -10000 0 -0.28 1 1
mol:GDP 0.056 0.013 -10000 0 -10000 0 0
EXOC4 0.026 0.005 -10000 0 -10000 0 0
STX4 0.013 0.011 -10000 0 -10000 0 0
PIP5K1C 0.012 0.015 -10000 0 -10000 0 0
LIMA1 0.022 0.049 -10000 0 -0.4 6 6
ABI1 0.027 0.002 -10000 0 -10000 0 0
ROCK1 -0.007 0.038 0.29 1 -10000 0 1
adherens junction assembly 0.003 0.037 0.27 1 -0.3 1 2
IGF-1R heterotetramer/IGF1 -0.009 0.1 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.039 0.007 -10000 0 -10000 0 0
MET 0.023 0.046 0.36 1 -0.43 4 5
PLEKHA7 0.013 0.011 -10000 0 -10000 0 0
mol:GTP 0.059 0.029 -10000 0 -0.22 2 2
establishment of epithelial cell apical/basal polarity -0.002 0.05 0.32 3 -10000 0 3
cortical actin cytoskeleton stabilization 0.022 0.027 -10000 0 -0.2 6 6
regulation of cell-cell adhesion -0.008 0.012 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.023 0.027 -10000 0 -0.2 6 6
Insulin 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
CBL/APS/CAP 0.049 0.049 -10000 0 -10000 0 0
TC10/GTP 0.034 0.045 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 0.076 0.026 -10000 0 -10000 0 0
HRAS 0.026 0.02 -10000 0 -0.4 1 1
APS homodimer 0.024 0.041 0.36 1 -0.42 3 4
GRB14 -0.007 0.11 -10000 0 -0.4 31 31
FOXO3 -0.009 0.14 -10000 0 -0.57 27 27
AKT1 -0.003 0.06 0.24 2 -10000 0 2
INSR 0.038 0.015 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.074 0.069 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.025 0.008 -10000 0 -10000 0 0
SORBS1 0.016 0.065 -10000 0 -0.4 11 11
CRK 0.023 0.01 -10000 0 -10000 0 0
PTPN1 0.006 0.024 0.31 1 -10000 0 1
CAV1 0.014 0.044 0.19 9 -10000 0 9
CBL/APS/CAP/Crk-II/C3G 0.054 0.058 0.26 1 -10000 0 1
Insulin Receptor/Insulin/IRS1/NCK2 0.077 0.026 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.059 0.022 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.065 0.066 -10000 0 -10000 0 0
RPS6KB1 -0.007 0.055 0.21 3 -10000 0 3
PARD6A 0.023 0.043 -10000 0 -0.43 4 4
CBL 0.027 0.004 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.019 0.008 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.029 0.057 -10000 0 -10000 0 0
HRAS/GTP 0.021 0.015 -10000 0 -10000 0 0
Insulin Receptor 0.038 0.015 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.084 0.032 -10000 0 -10000 0 0
PRKCI 0.027 0.056 -10000 0 -0.41 3 3
Insulin Receptor/Insulin/GRB14/PDK1 0.022 0.057 -10000 0 -10000 0 0
SHC1 0.027 0.004 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.042 0.03 -10000 0 -0.35 1 1
PI3K 0.072 0.026 -10000 0 -10000 0 0
NCK2 0.027 0.001 -10000 0 -10000 0 0
RHOQ 0.027 0.003 -10000 0 -10000 0 0
mol:H2O2 0.001 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.019 0.014 -10000 0 -0.28 1 1
AKT2 -0.003 0.06 0.24 2 -10000 0 2
PRKCZ 0.017 0.075 -10000 0 -0.4 2 2
SH2B2 0.024 0.041 0.36 1 -0.43 3 4
SHC/SHIP 0.044 0.033 0.29 1 -10000 0 1
F2RL2 -0.008 0.12 -10000 0 -0.43 34 34
TRIP10 0.027 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.059 0.024 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.036 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.083 0.032 -10000 0 -10000 0 0
RAPGEF1 0.026 0.02 -10000 0 -0.4 1 1
RASA1 0.026 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.002 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.047 0.055 0.26 1 -0.22 11 12
TC10/GDP 0.02 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.067 0.033 -10000 0 -10000 0 0
INPP5D 0.016 0.043 0.19 9 -10000 0 9
SOS1 0.027 0.002 -10000 0 -10000 0 0
SGK1 -0.03 0.18 -10000 0 -0.75 27 27
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.027 0.003 -10000 0 -10000 0 0
IRS1 0.027 0.002 -10000 0 -10000 0 0
p62DOK/RasGAP 0.042 0.03 -10000 0 -0.35 1 1
INS 0.028 0.014 -10000 0 -10000 0 0
mol:PI-3-4-P2 0.016 0.042 0.19 9 -10000 0 9
GRB2 0.027 0.004 -10000 0 -10000 0 0
EIF4EBP1 -0.009 0.052 0.18 3 -10000 0 3
PTPRA 0.028 0.016 -10000 0 -10000 0 0
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.036 0.006 -10000 0 -10000 0 0
PDPK1 0.027 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.036 0.018 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.06 0.023 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS3 0.05 0.025 -10000 0 -10000 0 0
Par3/Par6 0.038 0.08 -10000 0 -0.22 38 38
p38 MAPK signaling 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
TRAF6/ASK1 0.021 0.008 -10000 0 -10000 0 0
TRAF2/ASK1 0.035 0.014 -10000 0 -0.23 1 1
ATM 0.027 0.004 -10000 0 -10000 0 0
MAP2K3 0.01 0.067 -10000 0 -0.32 6 6
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.017 0.06 0.23 1 -0.35 4 5
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.026 0.033 0.36 1 -0.41 2 3
TXN 0.007 0.001 -10000 0 -10000 0 0
CALM1 0.025 0.007 -10000 0 -10000 0 0
GADD45A 0.026 0.005 -10000 0 -10000 0 0
GADD45B 0.027 0.004 -10000 0 -10000 0 0
MAP3K1 0.026 0.02 -10000 0 -0.4 1 1
MAP3K6 0.024 0.021 -10000 0 -0.4 1 1
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
MAP3K4 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.036 0.019 -10000 0 -0.28 1 1
TAK1/TAB family 0 0.016 -10000 0 -0.14 1 1
RAC1/OSM/MEKK3 0.045 0.022 -10000 0 -0.21 1 1
TRAF2 0.026 0.02 -10000 0 -0.4 1 1
RAC1/OSM/MEKK3/MKK3 0.02 0.061 -10000 0 -0.29 3 3
TRAF6 0.007 0.001 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.012 0.11 0.36 1 -0.4 34 35
CCM2 0.024 0.021 -10000 0 -0.4 1 1
CaM/Ca2+/CAMKIIB 0.011 0.072 0.23 1 -0.23 34 35
MAPK11 0.024 0.031 -10000 0 -0.43 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.024 0.07 0.24 1 -0.21 33 34
OSM/MEKK3 0.035 0.02 -10000 0 -0.28 1 1
TAOK1 0.014 0.003 -10000 0 -10000 0 0
TAOK2 0.015 0.003 -10000 0 -10000 0 0
TAOK3 0.015 0.002 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.027 0.003 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.027 0.004 -10000 0 -10000 0 0
MAP3K10 0.027 0.004 -10000 0 -10000 0 0
MAP3K3 0.027 0.005 -10000 0 -10000 0 0
TRX/ASK1 0.025 0.009 -10000 0 -10000 0 0
GADD45/MTK1/MTK1 0.059 0.027 0.24 1 -0.21 2 3
PLK2 and PLK4 events

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
PLK2 0.023 0.043 -9999 0 -0.43 4 4
PLK4 0.026 0.005 -9999 0 -10000 0 0
regulation of centriole replication 0.01 0.03 -9999 0 -0.3 4 4
TRAIL signaling pathway

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
TNFSF10 0.025 0.028 -9999 0 -0.4 2 2
positive regulation of NF-kappaB transcription factor activity 0.029 0.027 -9999 0 -0.28 2 2
MAP2K4 0.018 0.025 -9999 0 -10000 0 0
IKBKB 0.024 0.009 -9999 0 -10000 0 0
TNFRSF10B 0.021 0.012 -9999 0 -10000 0 0
TNFRSF10A 0.021 0.012 -9999 0 -10000 0 0
SMPD1 0.007 0.044 -9999 0 -0.38 5 5
IKBKG 0.026 0.02 -9999 0 -0.4 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.021 0.012 -9999 0 -10000 0 0
TRAIL/TRAILR2 0.029 0.027 -9999 0 -0.28 2 2
TRAIL/TRAILR3 0.008 0.085 -9999 0 -0.3 30 30
TRAIL/TRAILR1 0.029 0.027 -9999 0 -0.28 2 2
TRAIL/TRAILR4 0.029 0.027 -9999 0 -0.28 2 2
TRAIL/TRAILR1/DAP3/GTP 0.038 0.029 -9999 0 -0.21 2 2
IKK complex 0.019 0.043 -9999 0 -0.34 2 2
RIPK1 0.027 0.003 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0.02 0.003 -9999 0 -10000 0 0
MAPK3 0.012 0.024 -9999 0 -0.28 3 3
MAP3K1 0.021 0.029 -9999 0 -10000 0 0
TRAILR4 (trimer) 0.021 0.012 -9999 0 -10000 0 0
TRADD 0.027 0.002 -9999 0 -10000 0 0
TRAILR1 (trimer) 0.021 0.012 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.022 0.023 -9999 0 -10000 0 0
CFLAR 0.027 0 -9999 0 -10000 0 0
MAPK1 0.012 0.014 -9999 0 -0.28 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP 0.059 0.04 -9999 0 -10000 0 0
mol:ceramide 0.007 0.043 -9999 0 -0.38 5 5
FADD 0.027 0.004 -9999 0 -10000 0 0
MAPK8 0.014 0.028 -9999 0 -10000 0 0
TRAF2 0.026 0.02 -9999 0 -0.4 1 1
TRAILR3 (trimer) -0.008 0.11 -9999 0 -0.42 28 28
CHUK 0.026 0.006 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.04 0.03 -9999 0 -0.24 2 2
DAP3 0.027 0.004 -9999 0 -10000 0 0
CASP10 0.006 0.02 -9999 0 -0.26 2 2
JNK cascade 0.029 0.027 -9999 0 -0.28 2 2
TRAIL (trimer) 0.025 0.028 -9999 0 -0.4 2 2
TNFRSF10C -0.008 0.11 -9999 0 -0.43 28 28
TRAIL/TRAILR1/DAP3/GTP/FADD 0.047 0.033 -9999 0 -0.2 2 2
TRAIL/TRAILR2/FADD 0.04 0.03 -9999 0 -0.24 2 2
cell death 0.007 0.043 -9999 0 -0.38 5 5
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.022 0.023 -9999 0 -10000 0 0
TRAILR2 (trimer) 0.021 0.012 -9999 0 -10000 0 0
CASP8 0.014 0.027 -9999 0 -0.48 1 1
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.059 0.04 -9999 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.027 0.003 -10000 0 -10000 0 0
ELF1 0.02 0.045 -10000 0 -0.32 7 7
CCNA2 0.027 0.004 -10000 0 -10000 0 0
PIK3CA 0.028 0.002 -10000 0 -10000 0 0
JAK3 0.026 0.022 -10000 0 -0.42 1 1
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
JAK1 0.027 0.005 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.042 0.092 -10000 0 -0.45 7 7
SHC1 0.027 0.004 -10000 0 -10000 0 0
SP1 0.029 0.037 -10000 0 -0.32 5 5
IL2RA 0.005 0.084 -10000 0 -0.66 7 7
IL2RB 0.017 0.063 -10000 0 -0.4 10 10
SOS1 0.028 0.002 -10000 0 -10000 0 0
IL2RG 0.026 0.028 -10000 0 -0.4 2 2
G1/S transition of mitotic cell cycle 0.025 0.081 0.3 1 -0.63 4 5
PTPN11 0.028 0.003 -10000 0 -10000 0 0
CCND2 0.013 0.064 -10000 0 -0.66 4 4
LCK 0.018 0.063 -10000 0 -0.42 9 9
GRB2 0.027 0.004 -10000 0 -10000 0 0
IL2 0.019 0.008 -10000 0 -10000 0 0
CDK6 0.026 0.006 -10000 0 -10000 0 0
CCND3 0.041 0.087 0.34 1 -0.55 2 3
Canonical NF-kappaB pathway

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
FBXW11 0.029 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 0.053 0.075 0.22 26 -0.27 1 27
ERC1 0.027 0.004 -10000 0 -10000 0 0
RIP2/NOD2 0.026 0.054 -10000 0 -0.3 11 11
NFKBIA 0.013 0.006 -10000 0 -10000 0 0
BIRC2 0.027 0.005 -10000 0 -10000 0 0
IKBKB 0.024 0.009 -10000 0 -10000 0 0
RIPK2 0.023 0.01 -10000 0 -10000 0 0
IKBKG 0.028 0.047 -10000 0 -0.34 3 3
IKK complex/A20 0.054 0.06 -10000 0 -0.35 1 1
NEMO/A20/RIP2 0.023 0.01 -10000 0 -10000 0 0
XPO1 0.027 0.001 -10000 0 -10000 0 0
NEMO/ATM 0.046 0.057 0.27 1 -0.33 4 5
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.027 0.002 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.037 0.003 -10000 0 -10000 0 0
IKK complex/ELKS 0.044 0.052 -10000 0 -0.34 1 1
BCL10/MALT1/TRAF6 0.04 0.03 -10000 0 -0.24 2 2
NOD2 0.015 0.073 -10000 0 -0.42 12 12
NFKB1 0.029 0.005 -10000 0 -10000 0 0
RELA 0.029 0.004 -10000 0 -10000 0 0
MALT1 0.02 0.023 -10000 0 -0.4 1 1
cIAP1/UbcH5C 0.039 0.009 -10000 0 -10000 0 0
ATM 0.027 0.004 -10000 0 -10000 0 0
TNF/TNFR1A 0.038 0.022 -10000 0 -0.28 2 2
TRAF6 0.027 0.003 -10000 0 -10000 0 0
PRKCA 0.026 0.006 -10000 0 -10000 0 0
CHUK 0.026 0.006 -10000 0 -10000 0 0
UBE2D3 0.027 0.004 -10000 0 -10000 0 0
TNF 0.025 0.029 -10000 0 -0.4 2 2
NF kappa B1 p50/RelA 0.06 0.015 -10000 0 -10000 0 0
BCL10 0.025 0.021 -10000 0 -0.4 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.006 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.029 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.027 0.004 -10000 0 -10000 0 0
IKK complex 0.047 0.055 -10000 0 -0.34 2 2
CYLD 0.026 0.02 -10000 0 -0.4 1 1
IKK complex/PKC alpha 0.054 0.058 -10000 0 -0.35 1 1
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.059 0.042 -10000 0 -0.26 2 2
Ran/GTP/Exportin 1/HDAC1 -0.007 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.033 0.05 -10000 0 -10000 0 0
SUMO1 0.025 0.028 -10000 0 -0.4 2 2
ZFPM1 0.018 0.064 -10000 0 -0.43 9 9
NPC/RanGAP1/SUMO1/Ubc9 0.014 0.013 -10000 0 -0.18 2 2
FKBP3 0.024 0.021 -10000 0 -0.4 1 1
Histones 0.061 0.035 -10000 0 -10000 0 0
YY1/LSF 0.01 0.07 -10000 0 -0.3 6 6
SMG5 0.027 0.004 -10000 0 -10000 0 0
RAN 0.027 0.002 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.025 0.018 -10000 0 -10000 0 0
I kappa B alpha/HDAC1 0.026 0.046 -10000 0 -10000 0 0
SAP18 0.021 0.011 -10000 0 -10000 0 0
RELA 0.025 0.023 -10000 0 -10000 0 0
HDAC1/Smad7 0.039 0.028 -10000 0 -0.24 1 1
RANGAP1 0.026 0.006 -10000 0 -10000 0 0
HDAC3/TR2 0.036 0.03 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.019 0.039 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.03 0.054 0.19 1 -0.26 4 5
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.017 0.065 -10000 0 -0.4 11 11
GATA1 0.011 0.022 -10000 0 -10000 0 0
Mad/Max 0.036 0.024 -10000 0 -0.28 2 2
NuRD/MBD3 Complex/GATA1/Fog1 0.012 0.068 -10000 0 -0.32 4 4
RBBP7 0.027 0.003 -10000 0 -10000 0 0
NPC 0.016 0 -10000 0 -10000 0 0
RBBP4 0.026 0.006 -10000 0 -10000 0 0
MAX 0.025 0.007 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.027 0.004 -10000 0 -10000 0 0
NFKBIA 0.021 0.014 -10000 0 -10000 0 0
KAT2B 0.011 0.081 -10000 0 -0.4 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.021 0.014 -10000 0 -10000 0 0
SIN3 complex 0.051 0.032 -10000 0 -10000 0 0
SMURF1 0.026 0.006 -10000 0 -10000 0 0
CHD3 0.022 0.011 -10000 0 -10000 0 0
SAP30 0.026 0.006 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.022 0.011 -10000 0 -10000 0 0
YY1/HDAC3 0.013 0.058 -10000 0 -0.31 4 4
YY1/HDAC2 0.011 0.068 -10000 0 -0.32 5 5
YY1/HDAC1 0.011 0.067 -10000 0 -0.32 5 5
NuRD/MBD2 Complex (MeCP1) 0.016 0.046 -10000 0 -0.44 2 2
PPARG 0.021 0.036 -10000 0 -0.25 5 5
HDAC8/hEST1B 0.053 0.011 -10000 0 -10000 0 0
UBE2I 0.027 0.004 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.027 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.027 0.004 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.035 0.031 -10000 0 -10000 0 0
MBD3L2 -0.018 0.002 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.039 0.028 -10000 0 -0.24 1 1
CREBBP 0.027 0.004 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.011 0.071 -10000 0 -0.32 6 6
HDAC1 0.026 0.006 -10000 0 -10000 0 0
HDAC3 0.023 0.013 -10000 0 -10000 0 0
HDAC2 0.027 0.004 -10000 0 -10000 0 0
YY1 0.008 0.054 -10000 0 -0.26 17 17
HDAC8 0.027 0.002 -10000 0 -10000 0 0
SMAD7 0.02 0.023 -10000 0 -0.4 1 1
NCOR2 0.026 0.02 -10000 0 -0.4 1 1
MXD1 0.025 0.028 -10000 0 -0.4 2 2
STAT3 0.02 0.006 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.027 0 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.025 0.069 -10000 0 -0.29 5 5
YY1/SAP30/HDAC1 0.025 0.066 -10000 0 -0.29 5 5
EP300 0.026 0.006 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.02 0.006 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.014 -10000 0 -10000 0 0
histone deacetylation 0.016 0.046 -10000 0 -0.44 2 2
STAT3 (dimer non-phopshorylated)/HDAC3 0.03 0.018 -10000 0 -10000 0 0
nuclear export -0.053 0.011 -10000 0 -10000 0 0
PRKACA 0.027 0.003 -10000 0 -10000 0 0
GATAD2B 0.027 0.004 -10000 0 -10000 0 0
GATAD2A 0.027 0.003 -10000 0 -10000 0 0
GATA2/HDAC3 0.03 0.046 -10000 0 -10000 0 0
GATA1/HDAC1 0.036 0.01 -10000 0 -10000 0 0
GATA1/HDAC3 0.033 0.028 -10000 0 -10000 0 0
CHD4 0.027 0.004 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.038 0.022 -10000 0 -0.28 2 2
SIN3/HDAC complex/Mad/Max 0.033 0.046 -10000 0 -0.33 2 2
NuRD Complex -0.006 0.092 -10000 0 -0.3 19 19
positive regulation of chromatin silencing 0.058 0.034 -10000 0 -10000 0 0
SIN3B 0.027 0.003 -10000 0 -10000 0 0
MTA2 0.027 0.004 -10000 0 -10000 0 0
SIN3A 0.026 0.006 -10000 0 -10000 0 0
XPO1 0.027 0.001 -10000 0 -10000 0 0
SUMO1/HDAC1 0.037 0.033 -10000 0 -0.28 2 2
HDAC complex 0.065 0.019 -10000 0 -10000 0 0
GATA1/Fog1 0.03 0.049 -10000 0 -0.31 9 9
FKBP25/HDAC1/HDAC2 0.048 0.023 -10000 0 -0.24 1 1
TNF 0.025 0.029 -10000 0 -0.4 2 2
negative regulation of cell growth 0.033 0.046 -10000 0 -0.33 2 2
NuRD/MBD2/PRMT5 Complex 0.016 0.046 -10000 0 -0.44 2 2
Ran/GTP/Exportin 1 0.038 0.032 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.02 0.04 -10000 0 -0.26 2 2
SIN3/HDAC complex/NCoR1 0.008 0.058 -10000 0 -0.31 10 10
TFCP2 0.026 0.02 -10000 0 -0.4 1 1
NR2C1 0.027 0.003 -10000 0 -10000 0 0
MBD3 0.026 0.02 -10000 0 -0.4 1 1
MBD2 0.021 0.012 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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
BCL3/RelA 0.039 0.007 -10000 0 -10000 0 0
FBXW11 0.027 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.026 0.011 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.053 0.056 0.21 6 -10000 0 6
NFKBIA 0.045 0.055 -10000 0 -0.18 1 1
MAPK14 0.027 0.003 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.026 0.011 -10000 0 -10000 0 0
ARRB2 0.012 0.006 -10000 0 -10000 0 0
REL 0.027 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.026 0.011 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.026 0.011 -10000 0 -10000 0 0
PIK3CA 0.027 0.003 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.018 0.008 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
NFKB1 0.012 0.005 -10000 0 -10000 0 0
RELA 0.027 0.004 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.038 0.045 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.045 0.055 0.2 6 -10000 0 6
SRC 0.017 0.013 -10000 0 -10000 0 0
PI3K 0.039 0.008 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.038 0.045 -10000 0 -10000 0 0
IKBKB 0.024 0.009 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.027 0.004 -10000 0 -10000 0 0
SYK 0.027 0.004 -10000 0 -10000 0 0
I kappa B alpha/PIK3R1 0.055 0.06 0.21 6 -10000 0 6
cell death 0.042 0.053 0.19 5 -10000 0 5
NF kappa B1 p105/c-Rel 0.026 0.011 -10000 0 -10000 0 0
LCK 0.017 0.063 -10000 0 -0.42 9 9
BCL3 0.027 0.003 -10000 0 -10000 0 0
Arf1 pathway

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
coatomer protein complex 0.057 0.071 0.18 11 -0.31 1 12
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.01 0.034 0.14 9 -0.17 1 10
AP2 0.039 0.016 -10000 0 -0.28 1 1
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.032 0.013 -10000 0 -10000 0 0
CLTB 0.027 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.02 0.006 -10000 0 -10000 0 0
CD4 0.011 0.081 -10000 0 -0.4 17 17
CLTA 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0.003 -10000 0 -10000 0 0
ARFGAP1 0.004 0.019 0.27 1 -0.28 1 2
mol:PI-4-5-P2 0.006 0.007 -10000 0 -10000 0 0
ARF1/GTP 0.035 0.01 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.007 0.016 0.19 1 -0.25 1 2
mol:Choline 0.005 0.007 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.028 0.006 -10000 0 -10000 0 0
DDEF1 0.004 0.007 -10000 0 -10000 0 0
ARF1/GDP 0.002 0.017 0.18 1 -0.23 1 2
AP2M1 0.027 0.002 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.012 0.006 -10000 0 -10000 0 0
Rac/GTP 0.02 0.007 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.024 0.024 0.19 1 -0.2 1 2
ARFIP2 0.016 0.021 -10000 0 -10000 0 0
COPA 0.027 0.004 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.014 0.019 -10000 0 -0.17 1 1
ARF1/GTP/ARHGAP10 0.02 0.006 -10000 0 -10000 0 0
GGA3 0.027 0.004 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.024 0.026 -10000 0 -0.24 4 4
AP2A1 0.026 0.02 -10000 0 -0.4 1 1
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.01 0.018 0.14 1 -0.21 1 2
ARF1/GDP/Membrin 0.018 0.033 -10000 0 -0.28 4 4
Arfaptin 2/Rac/GDP 0.031 0.012 -10000 0 -10000 0 0
CYTH2 0.029 0.006 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.037 0.01 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.018 0.006 -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 0.018 0.041 -10000 0 -10000 0 0
PLD2 0.005 0.007 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.004 0.018 0.27 1 -0.28 1 2
PIP5K1A 0.006 0.007 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.013 0.027 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.005 0.007 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.004 0.018 0.27 1 -0.28 1 2
GOSR2 0.011 0.016 -10000 0 -0.31 1 1
USO1 0.009 0.027 -10000 0 -0.31 3 3
GBF1 0.007 0.038 -10000 0 -0.31 6 6
ARF1/GTP/Arfaptin 2 0.037 0.009 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.042 0.058 -10000 0 -0.24 18 18
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.02 0.012 -10000 0 -10000 0 0
SMAD2 0.012 0.032 -10000 0 -10000 0 0
SMAD3 0.019 0.018 -10000 0 -10000 0 0
SMAD3/SMAD4 0.026 0.058 -10000 0 -0.43 6 6
SMAD4/Ubc9/PIASy 0.041 0.025 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.04 0.048 -10000 0 -10000 0 0
PPM1A 0.025 0.007 -10000 0 -10000 0 0
CALM1 0.025 0.007 -10000 0 -10000 0 0
SMAD2/SMAD4 0.015 0.026 -10000 0 -10000 0 0
MAP3K1 0.026 0.02 -10000 0 -0.4 1 1
TRAP-1/SMAD4 0.03 0.018 -10000 0 -10000 0 0
MAPK3 0.026 0.02 -10000 0 -0.4 1 1
MAPK1 0.026 0.006 -10000 0 -10000 0 0
NUP214 0.027 0.003 -10000 0 -10000 0 0
CTDSP1 0.027 0.001 -10000 0 -10000 0 0
CTDSP2 0.027 0.002 -10000 0 -10000 0 0
CTDSPL 0.027 0.003 -10000 0 -10000 0 0
KPNB1 0.027 0.004 -10000 0 -10000 0 0
TGFBRAP1 0.027 0 -10000 0 -10000 0 0
UBE2I 0.027 0.004 -10000 0 -10000 0 0
NUP153 0.027 0.004 -10000 0 -10000 0 0
KPNA2 0.027 0.016 0.36 1 -10000 0 1
PIAS4 0.027 0.004 -10000 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 0.024 0.02 -10000 0 -10000 0 0
ATM 0.027 0.004 -10000 0 -10000 0 0
UBE2D3 0.027 0.004 -10000 0 -10000 0 0
PRKDC 0.024 0.009 -10000 0 -10000 0 0
ATR 0.027 0.002 -10000 0 -10000 0 0
UBE2L3 0.026 0.006 -10000 0 -10000 0 0
FANCD2 0.021 0.014 -10000 0 -0.27 1 1
protein ubiquitination 0.071 0.024 -10000 0 -10000 0 0
XRCC5 0.027 0.001 -10000 0 -10000 0 0
XRCC6 0.026 0.006 -10000 0 -10000 0 0
M/R/N Complex 0.044 0.026 -10000 0 -0.24 1 1
MRE11A 0.027 0.004 -10000 0 -10000 0 0
DNA-PK 0.046 0.021 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.03 0.046 -10000 0 -0.39 4 4
FANCF 0.027 0.003 -10000 0 -10000 0 0
BRCA1 0.027 0.003 -10000 0 -10000 0 0
CCNE1 0.027 0.031 0.36 2 -0.43 1 3
CDK2/Cyclin E1 0.04 0.023 0.26 2 -0.3 1 3
FANCG 0.027 0.004 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.04 0.005 -10000 0 -10000 0 0
FANCE 0.027 0.003 -10000 0 -10000 0 0
FANCC 0.027 0.004 -10000 0 -10000 0 0
NBN 0.022 0.022 -10000 0 -0.4 1 1
FANCA 0.027 0.003 -10000 0 -10000 0 0
DNA repair 0.047 0.064 0.26 5 -10000 0 5
BRCA1/BARD1/ubiquitin 0.04 0.005 -10000 0 -10000 0 0
BARD1/DNA-PK 0.058 0.027 -10000 0 -10000 0 0
FANCL 0.027 0.001 -10000 0 -10000 0 0
mRNA polyadenylation -0.024 0.02 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.027 0.043 -10000 0 -0.26 4 4
BRCA1/BACH1/BARD1/TopBP1 0.054 0.008 -10000 0 -10000 0 0
BRCA1/BARD1/P53 0.057 0.028 -10000 0 -10000 0 0
BARD1/CSTF1/BRCA1 0.032 0.027 -10000 0 -10000 0 0
BRCA1/BACH1 0.027 0.003 -10000 0 -10000 0 0
BARD1 0.027 0.001 -10000 0 -10000 0 0
PCNA 0.022 0.011 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.054 0.011 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.052 0.013 -10000 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.053 0.03 -10000 0 -10000 0 0
BARD1/DNA-PK/P53 0.058 0.037 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin 0.04 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP 0.036 0.022 -10000 0 -0.21 1 1
FA complex 0.031 0.015 -10000 0 -10000 0 0
BARD1/EWS 0.039 0.009 -10000 0 -10000 0 0
RBBP8 0.01 0.015 -10000 0 -0.28 1 1
TP53 0.022 0.011 -10000 0 -10000 0 0
TOPBP1 0.027 0.002 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.055 0.027 -10000 0 -10000 0 0
BRCA1/BARD1 0.078 0.025 0.26 2 -10000 0 2
CSTF1 0.016 0.013 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.02 0.001 -10000 0 -10000 0 0
CDK2 0.027 0.002 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.025 0.007 -10000 0 -10000 0 0
RAD50 0.027 0.004 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.04 0.005 -10000 0 -10000 0 0
EWSR1 0.026 0.006 -10000 0 -10000 0 0
Circadian rhythm pathway

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
chromatin modification 0.054 0.014 -10000 0 -10000 0 0
CLOCK 0.028 0.006 -10000 0 -10000 0 0
TIMELESS/CRY2 0.039 0.012 -10000 0 -10000 0 0
DEC1/BMAL1 0.031 0.042 -10000 0 -0.3 7 7
ATR 0.027 0.002 -10000 0 -10000 0 0
NR1D1 0.023 0.01 -10000 0 -10000 0 0
ARNTL 0.029 0.005 -10000 0 -10000 0 0
TIMELESS 0.023 0.009 -10000 0 -10000 0 0
NPAS2 0.029 0.003 -10000 0 -10000 0 0
CRY2 0.027 0.003 -10000 0 -10000 0 0
mol:CO -0.009 0.004 0.066 1 -10000 0 1
CHEK1 0.027 0.004 -10000 0 -10000 0 0
mol:HEME 0.009 0.004 -10000 0 -0.066 1 1
PER1 0.021 0.022 -10000 0 -0.4 1 1
BMAL/CLOCK/NPAS2 0.064 0.014 -10000 0 -10000 0 0
BMAL1/CLOCK 0.023 0.046 -10000 0 -10000 0 0
S phase of mitotic cell cycle 0.054 0.014 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.054 0.014 -10000 0 -10000 0 0
mol:NADPH 0.009 0.004 -10000 0 -0.066 1 1
PER1/TIMELESS 0.033 0.02 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 -0.009 0.057 -10000 0 -0.43 7 7
Aurora C 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
INCENP 0.027 0.004 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.041 0.027 -9999 0 -0.21 2 2
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.01 0.016 -9999 0 -0.3 1 1
AURKB 0.022 0.01 -9999 0 -10000 0 0
AURKC 0.023 0.03 -9999 0 -0.4 2 2
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.026 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.006 0.01 -10000 0 -10000 0 0
MDM2/SUMO1 0.036 0.04 -10000 0 -0.36 2 2
HDAC4 0.027 0.002 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0.006 0.009 -10000 0 -10000 0 0
SUMO1 0.025 0.028 -10000 0 -0.4 2 2
NPC/RanGAP1/SUMO1 0.012 0.013 -10000 0 -0.18 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.01 0.012 -10000 0 -0.17 2 2
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.027 0.002 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.027 0 -10000 0 -10000 0 0
SUMO1/HDAC4 0.037 0.036 -10000 0 -0.28 2 2
SUMO1/HDAC1 0.037 0.033 -10000 0 -0.28 2 2
RANGAP1 0.026 0.006 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.052 0.039 -10000 0 -0.31 2 2
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.014 0.013 -10000 0 -0.18 2 2
Ran/GTP 0.024 0.028 -10000 0 -10000 0 0
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.026 0.02 -10000 0 -0.4 1 1
UBE2I 0.027 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.022 0.029 0.19 1 -10000 0 1
NPC 0.016 0 -10000 0 -10000 0 0
PIAS2 0.021 0.012 -10000 0 -10000 0 0
PIAS1 0.026 0.006 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.012 0.019 -10000 0 -10000 0 0
adherens junction organization 0.036 0.039 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.024 -10000 0 -10000 0 0
FMN1 0.036 0.034 -10000 0 -10000 0 0
mol:IP3 0.013 0.017 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.043 0.036 -10000 0 -0.22 1 1
CTNNB1 0.028 0.004 -10000 0 -10000 0 0
AKT1 0.052 0.047 0.18 4 -10000 0 4
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.062 0.064 -10000 0 -0.48 1 1
CTNND1 0.03 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.038 0.036 -10000 0 -10000 0 0
VASP 0.037 0.035 -10000 0 -10000 0 0
ZYX 0.036 0.035 -10000 0 -10000 0 0
JUB 0.039 0.035 -10000 0 -0.21 1 1
EGFR(dimer) 0.05 0.041 -10000 0 -10000 0 0
E-cadherin/beta catenin-gamma catenin 0.05 0.017 -10000 0 -0.22 1 1
mol:PI-3-4-5-P3 0.084 0.059 0.21 5 -10000 0 5
PIK3CA 0.031 0.005 -10000 0 -10000 0 0
PI3K 0.086 0.06 0.22 5 -10000 0 5
FYN -0.005 0.048 -10000 0 -0.32 1 1
mol:Ca2+ 0.012 0.017 -10000 0 -10000 0 0
JUP 0.027 0.02 -10000 0 -0.4 1 1
PIK3R1 0.03 0.007 -10000 0 -10000 0 0
mol:DAG 0.013 0.017 -10000 0 -10000 0 0
CDH1 0.028 0.002 -10000 0 -10000 0 0
RhoA/GDP 0.023 0.033 -10000 0 -10000 0 0
establishment of polarity of embryonic epithelium 0.038 0.036 -10000 0 -10000 0 0
SRC 0.017 0.013 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
EGFR 0.024 0.021 -10000 0 -0.4 1 1
CASR -0.007 0.048 -10000 0 -10000 0 0
RhoA/GTP 0.02 0.023 -10000 0 -10000 0 0
AKT2 0.055 0.047 0.18 4 -10000 0 4
actin cable formation 0.032 0.034 -10000 0 -10000 0 0
apoptosis -0.047 0.046 -10000 0 -0.18 3 3
CTNNA1 0.03 0.005 -10000 0 -10000 0 0
mol:GDP 0.01 0.017 -10000 0 -10000 0 0
PIP5K1A 0.037 0.035 -10000 0 -10000 0 0
PLCG1 0.013 0.017 -10000 0 -10000 0 0
Rac1/GTP 0.055 0.042 -10000 0 -10000 0 0
homophilic cell adhesion 0.002 0.004 -10000 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.053 0.017 -9999 0 -0.24 1 1
E-cadherin/beta catenin 0.04 0.005 -9999 0 -10000 0 0
CTNNB1 0.027 0.003 -9999 0 -10000 0 0
JUP 0.026 0.02 -9999 0 -0.4 1 1
CDH1 0.027 0.002 -9999 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 0.038 0.01 -9999 0 -9999 0 0
FBXW11 0.027 0.004 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.027 0.004 -9999 0 -9999 0 0
CHUK 0.026 0.006 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.075 0.022 -9999 0 -9999 0 0
NFKB1 0.027 0.004 -9999 0 -9999 0 0
MAP3K14 0.027 0.004 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.039 0.008 -9999 0 -9999 0 0
RELB 0.027 0.003 -9999 0 -9999 0 0
NFKB2 0.026 0.006 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.035 0.009 -9999 0 -9999 0 0
regulation of B cell activation 0.034 0.009 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 448 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.WS.AB45 TCGA.T9.A92H TCGA.SS.A7HO TCGA.RU.A8FL
109_MAP3K5 0.031 0.031 -0.19 -0.17
47_PPARGC1A 0.027 0.027 0.027 0.027
105_BMP4 0.027 0 0 0.027
105_BMP6 0.027 0.027 -0.4 0.027
105_BMP7 -0.4 0.027 0.027 0.36
105_BMP2 0.027 0.027 0 -0.4
131_RELN/VLDLR -0.23 -0.23 -0.045 -0.24
30_TGFB1/TGF beta receptor Type II 0.027 0.027 0.029 0.031
84_STAT5B 0.0083 0.028 0 0.038
84_STAT5A 0.0083 0.028 0 0.038
Methods & Data
Input

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/COAD-TP/19438977/COAD-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/COAD-TP/19775082/Gistic2_Analysis_19775673/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

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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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