PARADIGM pathway analysis of mRNASeq expression and copy number data
Stomach Adenocarcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1668BP4
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
Lissencephaly gene (LIS1) in neuronal migration and development 62
FOXA2 and FOXA3 transcription factor networks 51
Aurora C signaling 38
Signaling events regulated by Ret tyrosine kinase 36
Effects of Botulinum toxin 36
IL4-mediated signaling events 34
Wnt signaling 34
Reelin signaling pathway 31
p75(NTR)-mediated signaling 30
Signaling events mediated by Stem cell factor receptor (c-Kit) 30
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 274 . 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 ( 274 ).

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
Lissencephaly gene (LIS1) in neuronal migration and development 0.2263 62 3360 54 -0.26 0.038 1000 -1000 -0.035 -1000
FOXA2 and FOXA3 transcription factor networks 0.1861 51 2354 46 -0.64 0.031 1000 -1000 -0.13 -1000
Aurora C signaling 0.1387 38 272 7 -0.41 0.036 1000 -1000 -0.012 -1000
Signaling events regulated by Ret tyrosine kinase 0.1314 36 3011 82 -0.1 0.027 1000 -1000 -0.05 -1000
Effects of Botulinum toxin 0.1314 36 957 26 -0.12 0.027 1000 -1000 -0.007 -1000
IL4-mediated signaling events 0.1241 34 3134 91 -0.7 0.56 1000 -1000 -0.17 -1000
Wnt signaling 0.1241 34 239 7 -0.068 0.022 1000 -1000 -0.014 -1000
Reelin signaling pathway 0.1131 31 1787 56 -0.1 0.056 1000 -1000 -0.035 -1000
p75(NTR)-mediated signaling 0.1095 30 3858 125 -0.13 0.07 1000 -1000 -0.057 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.1095 30 2355 78 -0.2 0.06 1000 -1000 -0.067 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.1058 29 994 34 -0.058 0.027 1000 -1000 -0.031 -1000
Signaling events mediated by the Hedgehog family 0.1058 29 1539 52 -0.071 0.049 1000 -1000 -0.034 -1000
Fc-epsilon receptor I signaling in mast cells 0.1022 28 2722 97 -0.097 0.034 1000 -1000 -0.052 -1000
Syndecan-1-mediated signaling events 0.0985 27 937 34 -0.1 0.027 1000 -1000 -0.034 -1000
Canonical Wnt signaling pathway 0.0949 26 1343 51 -0.26 0.11 1000 -1000 -0.054 -1000
Ephrin A reverse signaling 0.0912 25 180 7 -0.015 0.008 1000 -1000 -0.01 -1000
Noncanonical Wnt signaling pathway 0.0912 25 654 26 -0.07 0.026 1000 -1000 -0.033 -1000
Syndecan-2-mediated signaling events 0.0876 24 1704 69 -0.14 0.044 1000 -1000 -0.031 -1000
Glypican 1 network 0.0876 24 1152 48 -0.09 0.047 1000 -1000 -0.029 -1000
IL23-mediated signaling events 0.0876 24 1443 60 -0.6 0.027 1000 -1000 -0.14 -1000
Presenilin action in Notch and Wnt signaling 0.0803 22 1401 61 -0.26 0.07 1000 -1000 -0.041 -1000
BMP receptor signaling 0.0803 22 1796 81 -0.2 0.048 1000 -1000 -0.043 -1000
Ephrin B reverse signaling 0.0766 21 1042 48 -0.13 0.065 1000 -1000 -0.024 -1000
Aurora B signaling 0.0766 21 1421 67 -0.3 0.07 1000 -1000 -0.033 -1000
EPHB forward signaling 0.0730 20 1752 85 -0.14 0.1 1000 -1000 -0.06 -1000
BCR signaling pathway 0.0730 20 1991 99 -0.26 0.034 1000 -1000 -0.052 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0657 18 947 52 -0.12 0.055 1000 -1000 -0.038 -1000
Endothelins 0.0657 18 1793 96 -0.21 0.027 1000 -1000 -0.064 -1000
Visual signal transduction: Cones 0.0620 17 668 38 -0.037 0.046 1000 -1000 -0.011 -1000
amb2 Integrin signaling 0.0620 17 1466 82 -0.13 0.04 1000 -1000 -0.033 -1000
HIF-1-alpha transcription factor network 0.0584 16 1231 76 -0.23 0.036 1000 -1000 -0.12 -1000
Glypican 2 network 0.0584 16 66 4 0.004 0.018 1000 -1000 0.008 -1000
LPA receptor mediated events 0.0584 16 1638 102 -0.12 0.037 1000 -1000 -0.067 -1000
TCGA08_retinoblastoma 0.0584 16 130 8 -0.046 0.031 1000 -1000 -0.004 -1000
PDGFR-alpha signaling pathway 0.0547 15 681 44 -0.24 0.21 1000 -1000 -0.045 -1000
TCGA08_p53 0.0547 15 111 7 -0.039 0.027 1000 -1000 -0.01 -1000
TCR signaling in naïve CD8+ T cells 0.0547 15 1426 93 -0.098 0.049 1000 -1000 -0.055 -1000
PLK2 and PLK4 events 0.0511 14 43 3 -0.004 -1000 1000 -1000 -0.011 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0511 14 1758 120 -0.086 0.071 1000 -1000 -0.043 -1000
ErbB2/ErbB3 signaling events 0.0474 13 896 65 -0.085 0.039 1000 -1000 -0.059 -1000
Arf6 signaling events 0.0438 12 747 62 -0.093 0.059 1000 -1000 -0.033 -1000
Nongenotropic Androgen signaling 0.0438 12 654 52 -0.031 0.043 1000 -1000 -0.033 -1000
Glucocorticoid receptor regulatory network 0.0401 11 1362 114 -0.26 0.15 1000 -1000 -0.054 -1000
EGFR-dependent Endothelin signaling events 0.0401 11 237 21 -0.028 0.039 1000 -1000 -0.038 -1000
Visual signal transduction: Rods 0.0401 11 613 52 -0.038 0.035 1000 -1000 -0.028 -1000
PLK1 signaling events 0.0365 10 905 85 -0.025 0.045 1000 -1000 -0.029 -1000
IL1-mediated signaling events 0.0365 10 677 62 -0.049 0.071 1000 -1000 -0.034 -1000
PDGFR-beta signaling pathway 0.0365 10 1007 97 -0.062 0.071 1000 -1000 -0.054 -1000
LPA4-mediated signaling events 0.0328 9 111 12 -0.055 0.007 1000 -1000 -0.024 -1000
ErbB4 signaling events 0.0328 9 689 69 -0.1 0.044 1000 -1000 -0.045 -1000
Osteopontin-mediated events 0.0328 9 353 38 -0.13 0.041 1000 -1000 -0.036 -1000
Ceramide signaling pathway 0.0328 9 704 76 -0.022 0.071 1000 -1000 -0.026 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0328 9 344 37 -0.11 0.061 1000 -1000 -0.027 -1000
ceramide signaling pathway 0.0328 9 452 49 0 0.039 1000 -1000 -0.031 -1000
Syndecan-3-mediated signaling events 0.0328 9 324 35 -0.13 0.07 1000 -1000 -0.023 -1000
Integrins in angiogenesis 0.0328 9 792 84 -0.13 0.063 1000 -1000 -0.041 -1000
Calcium signaling in the CD4+ TCR pathway 0.0328 9 288 31 -0.1 0.027 1000 -1000 -0.04 -1000
IL27-mediated signaling events 0.0328 9 489 51 -0.28 0.074 1000 -1000 -0.051 -1000
Syndecan-4-mediated signaling events 0.0328 9 647 67 -0.13 0.03 1000 -1000 -0.032 -1000
Plasma membrane estrogen receptor signaling 0.0328 9 825 86 -0.048 0.05 1000 -1000 -0.049 -1000
FOXM1 transcription factor network 0.0328 9 505 51 -0.085 0.029 1000 -1000 -0.17 -1000
Regulation of Androgen receptor activity 0.0328 9 668 70 -0.18 0.034 1000 -1000 -0.05 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0292 8 733 85 -0.04 0.035 1000 -1000 -0.044 -1000
Signaling events mediated by PTP1B 0.0292 8 636 76 -0.075 0.034 1000 -1000 -0.033 -1000
Nectin adhesion pathway 0.0292 8 547 63 -0.19 0.051 1000 -1000 -0.047 -1000
FAS signaling pathway (CD95) 0.0292 8 411 47 -0.091 0.04 1000 -1000 -0.042 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0292 8 561 68 -0.19 0.029 1000 -1000 -0.085 -1000
Cellular roles of Anthrax toxin 0.0255 7 277 39 -0.019 0.028 1000 -1000 -0.019 -1000
Class I PI3K signaling events mediated by Akt 0.0255 7 483 68 -0.04 0.045 1000 -1000 -0.031 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0255 7 644 83 -0.26 0.052 1000 -1000 -0.031 -1000
S1P1 pathway 0.0255 7 257 36 -0.031 0.027 1000 -1000 -0.045 -1000
IGF1 pathway 0.0255 7 445 57 -0.023 0.052 1000 -1000 -0.035 -1000
Caspase cascade in apoptosis 0.0219 6 497 74 -0.044 0.062 1000 -1000 -0.033 -1000
Coregulation of Androgen receptor activity 0.0219 6 471 76 -0.047 0.048 1000 -1000 -0.025 -1000
IL12-mediated signaling events 0.0219 6 574 87 -0.06 0.047 1000 -1000 -0.086 -1000
IFN-gamma pathway 0.0219 6 451 68 -0.054 0.039 1000 -1000 -0.048 -1000
IL2 signaling events mediated by PI3K 0.0219 6 382 58 -0.049 0.052 1000 -1000 -0.05 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0219 6 504 74 -0.12 0.061 1000 -1000 -0.058 -1000
Class I PI3K signaling events 0.0219 6 483 73 -0.042 0.05 1000 -1000 -0.036 -1000
Ras signaling in the CD4+ TCR pathway 0.0219 6 113 17 -0.002 0.043 1000 -1000 -0.034 -1000
EPO signaling pathway 0.0182 5 302 55 0.008 0.06 1000 -1000 -0.042 -1000
S1P5 pathway 0.0182 5 88 17 -0.007 0.03 1000 -1000 -0.019 -1000
Retinoic acid receptors-mediated signaling 0.0182 5 346 58 -0.12 0.05 1000 -1000 -0.045 -1000
Regulation of p38-alpha and p38-beta 0.0182 5 290 54 -0.042 0.06 1000 -1000 -0.049 -1000
IL6-mediated signaling events 0.0182 5 435 75 -0.18 0.043 1000 -1000 -0.076 -1000
Regulation of Telomerase 0.0182 5 588 102 -0.1 0.062 1000 -1000 -0.049 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0182 5 197 33 -0.047 0.064 1000 -1000 -0.04 -1000
S1P4 pathway 0.0182 5 134 25 -0.011 0.046 1000 -1000 -0.027 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0146 4 112 28 -0.007 0.046 1000 -1000 -0.021 -1000
JNK signaling in the CD4+ TCR pathway 0.0146 4 83 17 -0.023 0.063 1000 -1000 -0.031 -1000
Thromboxane A2 receptor signaling 0.0146 4 468 105 -0.031 0.044 1000 -1000 -0.045 -1000
Aurora A signaling 0.0146 4 245 60 -0.034 0.054 1000 -1000 -0.023 -1000
Signaling mediated by p38-gamma and p38-delta 0.0146 4 72 15 -0.024 0.027 1000 -1000 -0.033 -1000
Signaling mediated by p38-alpha and p38-beta 0.0146 4 213 44 -0.035 0.027 1000 -1000 -0.028 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0146 4 207 45 0 0.068 1000 -1000 -0.037 -1000
Insulin Pathway 0.0146 4 320 74 -0.024 0.066 1000 -1000 -0.04 -1000
S1P3 pathway 0.0146 4 209 42 -0.01 0.046 1000 -1000 -0.036 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0146 4 394 88 -0.068 0.071 1000 -1000 -0.073 -1000
Signaling events mediated by PRL 0.0146 4 139 34 -0.042 0.039 1000 -1000 -0.039 -1000
E-cadherin signaling in keratinocytes 0.0146 4 213 43 -0.03 0.045 1000 -1000 -0.036 -1000
Class IB PI3K non-lipid kinase events 0.0146 4 12 3 -0.022 0.022 1000 -1000 -0.011 -1000
p38 MAPK signaling pathway 0.0146 4 179 44 -0.045 0.055 1000 -1000 -0.029 -1000
Regulation of nuclear SMAD2/3 signaling 0.0109 3 501 136 -0.092 0.072 1000 -1000 -0.046 -1000
Insulin-mediated glucose transport 0.0109 3 98 32 -0.049 0.051 1000 -1000 -0.025 -1000
mTOR signaling pathway 0.0109 3 203 53 -0.035 0.038 1000 -1000 -0.033 -1000
Signaling events mediated by HDAC Class III 0.0109 3 149 40 -0.049 0.052 1000 -1000 -0.019 -1000
FoxO family signaling 0.0109 3 248 64 -0.039 0.056 1000 -1000 -0.066 -1000
TCGA08_rtk_signaling 0.0109 3 101 26 -0.04 0.073 1000 -1000 -0.015 -1000
E-cadherin signaling in the nascent adherens junction 0.0109 3 268 76 -0.015 0.06 1000 -1000 -0.053 -1000
IL2 signaling events mediated by STAT5 0.0109 3 67 22 0.005 0.038 1000 -1000 -0.045 -1000
Arf6 trafficking events 0.0109 3 241 71 -0.051 0.049 1000 -1000 -0.027 -1000
Canonical NF-kappaB pathway 0.0073 2 103 39 0 0.057 1000 -1000 -0.03 -1000
BARD1 signaling events 0.0073 2 119 57 -0.056 0.065 1000 -1000 -0.038 -1000
Hedgehog signaling events mediated by Gli proteins 0.0073 2 185 65 -0.048 0.061 1000 -1000 -0.052 -1000
Arf6 downstream pathway 0.0073 2 92 43 -0.03 0.046 1000 -1000 -0.026 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0073 2 268 125 0 0.066 1000 -1000 -0.045 -1000
VEGFR1 specific signals 0.0073 2 143 56 -0.013 0.06 1000 -1000 -0.047 -1000
Rapid glucocorticoid signaling 0.0073 2 55 20 -0.008 0.033 1000 -1000 -0.004 -1000
E-cadherin signaling events 0.0073 2 14 5 0.02 0.043 1000 -1000 0.009 -1000
Signaling events mediated by HDAC Class II 0.0036 1 110 75 -0.028 0.07 1000 -1000 -0.027 -1000
Circadian rhythm pathway 0.0036 1 25 22 -0.005 0.057 1000 -1000 -0.035 -1000
TRAIL signaling pathway 0.0036 1 59 48 0 0.057 1000 -1000 -0.034 -1000
HIF-2-alpha transcription factor network 0.0036 1 69 43 -0.076 0.077 1000 -1000 -0.07 -1000
Signaling events mediated by HDAC Class I 0.0036 1 167 104 -0.052 0.065 1000 -1000 -0.029 -1000
Paxillin-dependent events mediated by a4b1 0.0036 1 40 36 -0.051 0.053 1000 -1000 -0.035 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 20 23 0.01 0.045 1000 -1000 -0.028 -1000
a4b1 and a4b7 Integrin signaling 0.0000 0 4 5 0.024 0.038 1000 -1000 0.011 -1000
Atypical NF-kappaB pathway 0.0000 0 23 31 0 0.036 1000 -1000 -0.017 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 9 27 0 0.059 1000 -1000 -0.03 -1000
Arf1 pathway 0.0000 0 53 54 -0.001 0.049 1000 -1000 -0.017 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.072 1000 -1000 0 -1000
Total NA 1470 86794 7203 -12 -990 131000 -131000 -5.3 -131000
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.026 0.006 -10000 0 -10000 0 0
VLDLR -0.009 0.11 -10000 0 -0.37 23 23
LRPAP1 0.026 0.006 -10000 0 -10000 0 0
NUDC 0.026 0.007 -10000 0 -10000 0 0
RELN/LRP8 -0.066 0.14 -10000 0 -0.21 116 116
CaM/Ca2+ 0.02 0.004 -10000 0 -10000 0 0
KATNA1 0.026 0.006 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.069 0.12 0.18 8 -0.25 52 60
IQGAP1/CaM 0.038 0.012 -10000 0 -10000 0 0
DAB1 0.024 0.034 -10000 0 -0.37 2 2
IQGAP1 0.026 0.006 -10000 0 -10000 0 0
PLA2G7 -0.072 0.14 -10000 0 -0.28 87 87
CALM1 0.027 0.005 -10000 0 -10000 0 0
DYNLT1 0.026 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 -0.036 0.11 -10000 0 -0.19 90 90
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.027 0.005 -10000 0 -10000 0 0
CDK5R1 0.023 0.037 -10000 0 -0.28 4 4
LIS1/Poliovirus Protein 3A -0.15 0.098 -10000 0 -0.21 195 195
CDK5R2 -0.073 0.17 -10000 0 -0.36 70 70
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.026 0.14 -10000 0 -0.26 64 64
YWHAE 0.025 0.008 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.087 0.14 0.3 3 -0.3 51 54
MAP1B -0.17 0.12 -10000 0 -0.25 184 184
RAC1 -0.065 0.055 -10000 0 -0.4 1 1
p35/CDK5 -0.06 0.11 0.18 7 -0.29 23 30
RELN -0.057 0.16 -10000 0 -0.37 57 57
PAFAH/LIS1 -0.19 0.13 -10000 0 -0.25 206 206
LIS1/CLIP170 -0.15 0.1 -10000 0 -0.22 194 194
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.18 0.12 -10000 0 -0.3 96 96
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.15 0.17 -10000 0 -0.39 73 73
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.099 0.13 0.18 5 -0.31 53 58
LIS1/IQGAP1 -0.14 0.11 -10000 0 -0.22 187 187
RHOA -0.074 0.07 -10000 0 -0.4 6 6
PAFAH1B1 -0.17 0.12 -10000 0 -0.26 181 181
PAFAH1B3 0.025 0.02 -10000 0 -0.28 1 1
PAFAH1B2 0.026 0.007 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain -0.21 0.14 -10000 0 -0.29 195 195
NDEL1/Katanin 60/Dynein heavy chain -0.079 0.14 0.3 3 -0.29 50 53
LRP8 -0.075 0.14 -10000 0 -0.28 91 91
NDEL1/Katanin 60 -0.086 0.14 0.3 3 -0.3 51 54
P39/CDK5 -0.1 0.14 0.18 5 -0.31 55 60
LIS1/NudC/Dynein intermediate chain/microtubule organizing center -0.15 0.1 -10000 0 -0.22 195 195
CDK5 -0.076 0.1 0.18 10 -0.3 22 32
PPP2R5D 0.026 0.007 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.12 0.088 -10000 0 -0.18 194 194
CSNK2A1 -0.26 0.17 -10000 0 -0.37 195 195
RELN/VLDLR/DAB1/LIS1 -0.16 0.14 -10000 0 -0.24 182 182
RELN/VLDLR -0.063 0.15 -10000 0 -0.28 64 64
CDC42 -0.073 0.07 -10000 0 -0.4 6 6
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.43 0.34 -9999 0 -0.83 88 88
PCK1 -0.34 0.36 -9999 0 -1.1 39 39
HNF4A -0.48 0.44 -9999 0 -1.1 83 83
KCNJ11 -0.42 0.34 -9999 0 -0.85 72 72
AKT1 -0.24 0.2 -9999 0 -0.52 53 53
response to starvation -0.022 0.04 -9999 0 -0.23 6 6
DLK1 -0.42 0.34 -9999 0 -0.85 78 78
NKX2-1 -0.17 0.16 -9999 0 -0.6 6 6
ACADM -0.43 0.34 -9999 0 -0.84 84 84
TAT -0.28 0.24 -9999 0 -0.72 37 37
CEBPB 0.001 0.034 -9999 0 -0.15 2 2
CEBPA -0.007 0.055 -9999 0 -0.3 5 5
TTR -0.58 0.57 -9999 0 -1.2 110 110
PKLR -0.43 0.34 -9999 0 -0.86 79 79
APOA1 -0.64 0.58 -9999 0 -1.4 89 89
CPT1C -0.43 0.34 -9999 0 -0.86 79 79
ALAS1 -0.2 0.15 -9999 0 -0.57 5 5
TFRC -0.32 0.29 -9999 0 -0.89 35 35
FOXF1 0.018 0.06 -9999 0 -0.37 6 6
NF1 0.031 0.005 -9999 0 -10000 0 0
HNF1A (dimer) -0.062 0.1 -9999 0 -0.24 36 36
CPT1A -0.42 0.34 -9999 0 -0.83 83 83
HMGCS1 -0.41 0.34 -9999 0 -0.85 76 76
NR3C1 -0.003 0.059 -9999 0 -0.37 3 3
CPT1B -0.43 0.34 -9999 0 -0.83 88 88
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.024 0.03 -9999 0 -0.17 3 3
GCK -0.44 0.36 -9999 0 -0.85 91 91
CREB1 -0.006 0.059 -9999 0 -0.18 6 6
IGFBP1 -0.26 0.19 -9999 0 -0.61 26 26
PDX1 -0.28 0.33 -9999 0 -1.4 15 15
UCP2 -0.42 0.34 -9999 0 -0.85 77 77
ALDOB -0.51 0.42 -9999 0 -0.96 103 103
AFP -0.098 0.15 -9999 0 -0.46 16 16
BDH1 -0.43 0.34 -9999 0 -0.83 86 86
HADH -0.41 0.33 -9999 0 -0.83 77 77
F2 -0.52 0.43 -9999 0 -1.1 77 77
HNF1A -0.062 0.1 -9999 0 -0.24 36 36
G6PC -0.12 0.25 -9999 0 -1.1 15 15
SLC2A2 -0.63 0.55 -9999 0 -1.2 126 126
INS 0.012 0.028 -9999 0 -10000 0 0
FOXA1 -0.073 0.13 -9999 0 -0.3 54 54
FOXA3 -0.09 0.14 -9999 0 -0.36 41 41
FOXA2 -0.47 0.37 -9999 0 -0.92 83 83
ABCC8 -0.58 0.43 -9999 0 -0.97 130 130
ALB -0.19 0.31 -9999 0 -0.79 50 50
Aurora C signaling

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
INCENP 0.026 0.019 -9999 0 -0.28 1 1
Aurora C/Aurora B/INCENP 0.036 0.047 -9999 0 -0.15 14 14
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.41 0.14 -9999 0 -0.46 244 244
AURKB 0.014 0.06 -9999 0 -0.29 10 10
AURKC 0.023 0.036 -9999 0 -0.31 3 3
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.009 0.077 -10000 0 -0.5 5 5
Crk/p130 Cas/Paxillin -0.072 0.13 -10000 0 -0.27 64 64
JUN -0.064 0.12 -10000 0 -0.34 28 28
HRAS 0.026 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.037 0.14 -10000 0 -0.24 81 81
RAP1A 0.027 0.005 -10000 0 -10000 0 0
FRS2 0.026 0.006 -10000 0 -10000 0 0
RAP1A/GDP 0.02 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.039 0.14 -10000 0 -0.24 84 84
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.034 0.12 -10000 0 -0.21 83 83
RHOA 0.027 0.005 -10000 0 -10000 0 0
RAP1A/GTP -0.034 0.13 -10000 0 -0.21 83 83
GRB7 0.01 0.066 -10000 0 -0.29 12 12
RET51/GFRalpha1/GDNF -0.038 0.14 -10000 0 -0.23 83 83
MAPKKK cascade -0.049 0.13 -10000 0 -0.34 21 21
BCAR1 0.026 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.033 0.12 -10000 0 -0.21 82 82
lamellipodium assembly -0.059 0.12 -10000 0 -0.25 64 64
RET51/GFRalpha1/GDNF/SHC -0.037 0.14 -10000 0 -0.23 84 84
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.033 0.12 -10000 0 -0.21 81 81
RET9/GFRalpha1/GDNF/Shank3 -0.034 0.12 -10000 0 -0.21 83 83
MAPK3 -0.063 0.11 0.2 13 -0.32 18 31
DOK1 0.026 0.019 -10000 0 -0.28 1 1
DOK6 0.019 0.042 -10000 0 -0.28 5 5
PXN 0.024 0.031 -10000 0 -0.32 2 2
neurite development -0.05 0.1 0.18 8 -0.31 18 26
DOK5 0.012 0.055 -10000 0 -0.28 9 9
GFRA1 -0.1 0.19 -10000 0 -0.37 90 90
MAPK8 -0.065 0.13 -10000 0 -0.35 28 28
HRAS/GTP -0.045 0.15 -10000 0 -0.26 78 78
tube development -0.031 0.11 0.21 1 -0.2 79 80
MAPK1 -0.061 0.12 0.23 12 -0.32 18 30
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.048 0.11 -10000 0 -0.22 78 78
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
SRC 0.024 0.009 -10000 0 -10000 0 0
PDLIM7 0.024 0.027 -10000 0 -0.28 2 2
RET51/GFRalpha1/GDNF/Dok6 -0.028 0.13 -10000 0 -0.23 63 63
SHC1 0.026 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.039 0.14 -10000 0 -0.24 84 84
RET51/GFRalpha1/GDNF/Dok5 -0.038 0.13 -10000 0 -0.23 69 69
PRKCA 0.026 0.024 -10000 0 -0.37 1 1
HRAS/GDP 0.02 0.004 -10000 0 -10000 0 0
CREB1 -0.065 0.14 -10000 0 -0.26 80 80
PIK3R1 0.026 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.049 0.12 -10000 0 -0.23 76 76
RET51/GFRalpha1/GDNF/Grb7 -0.04 0.14 -10000 0 -0.25 71 71
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.005 0.1 -10000 0 -0.32 25 25
DOK4 0.025 0.025 -10000 0 -0.37 1 1
JNK cascade -0.065 0.12 0.19 1 -0.33 28 29
RET9/GFRalpha1/GDNF/FRS2 -0.034 0.12 -10000 0 -0.21 82 82
SHANK3 0.026 0.006 -10000 0 -10000 0 0
RASA1 0.025 0.008 -10000 0 -10000 0 0
NCK1 0.027 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.048 0.11 -10000 0 -0.22 78 78
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.058 0.13 -10000 0 -0.35 25 25
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.062 0.14 -10000 0 -0.25 85 85
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.061 0.14 -10000 0 -0.24 85 85
PI3K -0.089 0.18 -10000 0 -0.37 67 67
SOS1 0.027 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.023 0.12 -10000 0 -0.2 79 79
GRB10 0.025 0.019 -10000 0 -0.28 1 1
activation of MAPKK activity -0.055 0.13 -10000 0 -0.35 25 25
RET51/GFRalpha1/GDNF/FRS2 -0.039 0.14 -10000 0 -0.23 83 83
GAB1 0.025 0.025 -10000 0 -0.37 1 1
IRS1 0.026 0.024 -10000 0 -0.37 1 1
IRS2 0.013 0.068 -10000 0 -0.35 9 9
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.064 0.14 -10000 0 -0.26 84 84
RET51/GFRalpha1/GDNF/PKC alpha -0.039 0.14 -10000 0 -0.24 83 83
GRB2 0.027 0.004 -10000 0 -10000 0 0
PRKACA 0.027 0.005 -10000 0 -10000 0 0
GDNF 0.006 0.082 -10000 0 -0.36 13 13
RAC1 0.026 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.039 0.15 -10000 0 -0.24 83 83
Rac1/GTP -0.066 0.15 -10000 0 -0.3 64 64
RET9/GFRalpha1/GDNF -0.049 0.12 -10000 0 -0.23 83 83
GFRalpha1/GDNF -0.061 0.15 -10000 0 -0.28 83 83
Effects of Botulinum toxin

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
STX1A 0.003 0.026 -10000 0 -0.19 5 5
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B -0.057 0.14 -10000 0 -0.26 87 87
STXBP1 0.017 0.054 -10000 0 -0.29 8 8
ACh/CHRNA1 -0.08 0.098 -10000 0 -0.17 139 139
RAB3GAP2/RIMS1/UNC13B -0.032 0.12 -10000 0 -0.22 83 83
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 -0.1 0.18 -10000 0 -0.37 89 89
mol:ACh -0.01 0.049 0.077 24 -0.11 37 61
RAB3GAP2 0.027 0.005 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.044 0.11 -10000 0 -0.26 24 24
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.08 0.098 -10000 0 -0.17 139 139
UNC13B 0.026 0.007 -10000 0 -10000 0 0
CHRNA1 -0.12 0.15 -10000 0 -0.28 132 132
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.029 0.088 -10000 0 -0.18 57 57
SNAP25 -0.029 0.081 -10000 0 -0.21 43 43
VAMP2 0.004 0.001 -10000 0 -10000 0 0
SYT1 -0.039 0.13 -10000 0 -0.3 54 54
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.015 0.042 -10000 0 -0.17 12 12
STX1A/SNAP25 fragment 1/VAMP2 -0.044 0.11 -10000 0 -0.26 24 24
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 -0.49 0.48 -10000 0 -1.2 58 58
STAT6 (cleaved dimer) -0.52 0.51 -10000 0 -1.2 73 73
IGHG1 -0.17 0.16 -10000 0 -0.44 7 7
IGHG3 -0.49 0.46 -10000 0 -1.1 67 67
AKT1 -0.26 0.32 -10000 0 -0.92 34 34
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.22 0.33 -10000 0 -1.1 23 23
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.27 0.34 -10000 0 -1 26 26
THY1 -0.51 0.48 -10000 0 -1.2 58 58
MYB -0.059 0.14 -10000 0 -0.28 76 76
HMGA1 0.023 0.032 -10000 0 -0.28 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.34 0.37 -10000 0 -0.92 48 48
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.27 0.34 -10000 0 -1 25 25
SP1 0.015 0.032 -10000 0 -10000 0 0
INPP5D 0.024 0.035 -10000 0 -0.31 3 3
SOCS5 0.038 0.023 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.51 0.5 -10000 0 -1.2 71 71
SOCS1 -0.34 0.31 -10000 0 -0.76 60 60
SOCS3 -0.28 0.29 -10000 0 -0.9 28 28
FCER2 -0.54 0.58 -10000 0 -1.4 73 73
PARP14 0.019 0.035 -10000 0 -0.28 3 3
CCL17 -0.53 0.52 -10000 0 -1.3 66 66
GRB2 0.027 0.004 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.21 0.25 -10000 0 -0.74 27 27
T cell proliferation -0.5 0.51 -10000 0 -1.3 63 63
IL4R/JAK1 -0.5 0.49 -10000 0 -1.2 65 65
EGR2 -0.54 0.52 -10000 0 -1.3 68 68
JAK2 -0.027 0.04 -10000 0 -10000 0 0
JAK3 0.015 0.06 -10000 0 -0.28 10 10
PIK3R1 0.026 0.007 -10000 0 -10000 0 0
JAK1 -0.001 0.025 -10000 0 -10000 0 0
COL1A2 -0.2 0.23 -10000 0 -0.99 8 8
CCL26 -0.51 0.49 -10000 0 -1.2 63 63
IL4R -0.53 0.52 -10000 0 -1.3 62 62
PTPN6 0.036 0.024 -10000 0 -0.26 1 1
IL13RA2 -0.53 0.48 -10000 0 -1.2 63 63
IL13RA1 -0.03 0.041 -10000 0 -10000 0 0
IRF4 -0.24 0.49 -10000 0 -1.5 35 35
ARG1 -0.13 0.24 -10000 0 -1.3 7 7
CBL -0.31 0.34 -10000 0 -0.86 47 47
GTF3A -0.004 0.039 -10000 0 -10000 0 0
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.033 0.055 -10000 0 -10000 0 0
IRF4/BCL6 -0.21 0.44 -10000 0 -1.3 35 35
CD40LG 0.003 0.081 -10000 0 -0.37 10 10
MAPK14 -0.31 0.35 -10000 0 -0.97 37 37
mitosis -0.25 0.29 -10000 0 -0.84 34 34
STAT6 -0.58 0.58 -10000 0 -1.4 67 67
SPI1 0.027 0.028 -10000 0 -0.28 1 1
RPS6KB1 -0.24 0.28 -10000 0 -0.8 34 34
STAT6 (dimer) -0.58 0.58 -10000 0 -1.4 67 67
STAT6 (dimer)/PARP14 -0.56 0.55 -10000 0 -1.3 72 72
mast cell activation 0.013 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.28 0.35 -10000 0 -1 31 31
FRAP1 -0.26 0.32 -10000 0 -0.92 34 34
LTA -0.51 0.5 -10000 0 -1.2 62 62
FES 0.025 0.019 -10000 0 -0.28 1 1
T-helper 1 cell differentiation 0.56 0.56 1.3 67 -10000 0 67
CCL11 -0.53 0.53 -10000 0 -1.3 69 69
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.26 0.34 -10000 0 -1 29 29
IL2RG 0.014 0.07 -10000 0 -0.35 9 9
IL10 -0.5 0.48 -10000 0 -1.2 61 61
IRS1 0.026 0.024 -10000 0 -0.37 1 1
IRS2 0.013 0.068 -10000 0 -0.35 9 9
IL4 -0.16 0.27 -10000 0 -1.1 16 16
IL5 -0.51 0.48 -10000 0 -1.2 64 64
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.43 0.42 -10000 0 -1 64 64
COL1A1 -0.24 0.22 -10000 0 -1 3 3
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.52 0.51 -10000 0 -1.3 58 58
IL2R gamma/JAK3 0.017 0.069 -10000 0 -0.22 19 19
TFF3 -0.58 0.54 -10000 0 -1.3 72 72
ALOX15 -0.54 0.52 -10000 0 -1.3 66 66
MYBL1 0.014 0.055 -10000 0 -0.28 9 9
T-helper 2 cell differentiation -0.45 0.45 -10000 0 -1 69 69
SHC1 0.026 0.006 -10000 0 -10000 0 0
CEBPB 0.022 0.021 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.26 0.32 -10000 0 -0.97 27 27
mol:PI-3-4-5-P3 -0.26 0.32 -10000 0 -0.92 34 34
PI3K -0.28 0.35 -10000 0 -1 34 34
DOK2 0.023 0.025 -10000 0 -0.37 1 1
ETS1 0.034 0.029 -10000 0 -0.26 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.2 0.23 -10000 0 -0.72 22 22
ITGB3 -0.51 0.48 -10000 0 -1.2 57 57
PIGR -0.7 0.65 -10000 0 -1.4 117 117
IGHE 0.053 0.071 0.17 46 -10000 0 46
MAPKKK cascade -0.19 0.22 -10000 0 -0.7 22 22
BCL6 0.028 0.009 -10000 0 -10000 0 0
OPRM1 -0.5 0.48 -10000 0 -1.2 61 61
RETNLB -0.6 0.56 -10000 0 -1.3 85 85
SELP -0.56 0.56 -10000 0 -1.3 73 73
AICDA -0.51 0.5 -10000 0 -1.2 63 63
Wnt signaling

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
Noncanonical Wnts/FZD -0.068 0.14 -9999 0 -0.27 72 72
FZD6 0.022 0.026 -9999 0 -0.37 1 1
WNT6 -0.036 0.14 -9999 0 -0.36 44 44
WNT4 -0.036 0.14 -9999 0 -0.37 43 43
FZD3 0.022 0.031 -9999 0 -0.32 2 2
WNT5A 0.007 0.076 -9999 0 -0.28 18 18
WNT11 -0.046 0.14 -9999 0 -0.31 59 59
Reelin signaling pathway

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
CDK5R1/CDK5 0.035 0.029 -10000 0 -0.19 4 4
VLDLR -0.009 0.11 -10000 0 -0.37 23 23
CRKL 0.027 0.005 -10000 0 -10000 0 0
LRPAP1 0.026 0.006 -10000 0 -10000 0 0
FYN 0.027 0.005 -10000 0 -10000 0 0
ITGA3 0.025 0.026 -10000 0 -0.28 2 2
RELN/VLDLR/Fyn -0.025 0.13 -10000 0 -0.25 64 64
MAPK8IP1/MKK7/MAP3K11/JNK1 0.056 0.066 -10000 0 -0.19 15 15
AKT1 -0.041 0.11 -10000 0 -0.23 58 58
MAP2K7 0.026 0.006 -10000 0 -10000 0 0
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
DAB1 0.024 0.034 -10000 0 -0.37 2 2
RELN/LRP8/DAB1 -0.06 0.13 -10000 0 -0.2 119 119
LRPAP1/LRP8 -0.036 0.11 -10000 0 -0.19 90 90
RELN/LRP8/DAB1/Fyn -0.05 0.13 -10000 0 -0.24 56 56
DAB1/alpha3/beta1 Integrin -0.056 0.14 -10000 0 -0.32 32 32
long-term memory -0.1 0.17 -10000 0 -0.35 66 66
DAB1/LIS1 -0.052 0.14 -10000 0 -0.33 33 33
DAB1/CRLK/C3G -0.057 0.14 -10000 0 -0.33 32 32
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
DAB1/NCK2 -0.051 0.15 -10000 0 -0.33 33 33
ARHGEF2 0.027 0.005 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.055 0.16 -10000 0 -0.36 57 57
CDK5R1 0.023 0.037 -10000 0 -0.28 4 4
RELN -0.057 0.16 -10000 0 -0.37 57 57
PIK3R1 0.026 0.007 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.066 0.14 -10000 0 -0.21 118 118
GRIN2A/RELN/LRP8/DAB1/Fyn -0.081 0.17 -10000 0 -0.3 77 77
MAPK8 0.027 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.022 0.12 -10000 0 -0.23 64 64
ITGB1 0.026 0.006 -10000 0 -10000 0 0
MAP1B -0.079 0.13 -10000 0 -0.29 53 53
RELN/LRP8 -0.066 0.14 -10000 0 -0.21 116 116
GRIN2B/RELN/LRP8/DAB1/Fyn -0.064 0.15 -10000 0 -0.3 47 47
PI3K 0.036 0.014 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.037 0.022 -10000 0 -0.19 2 2
RAP1A -0.074 0.12 0.27 4 -0.32 31 35
PAFAH1B1 0.026 0.007 -10000 0 -10000 0 0
MAPK8IP1 -0.001 0.1 -10000 0 -0.36 19 19
CRLK/C3G 0.039 0.01 -10000 0 -10000 0 0
GRIN2B -0.02 0.11 -10000 0 -0.3 37 37
NCK2 0.027 0.003 -10000 0 -10000 0 0
neuron differentiation -0.047 0.11 -10000 0 -0.31 26 26
neuron adhesion -0.069 0.13 0.28 7 -0.31 27 34
LRP8 -0.075 0.14 -10000 0 -0.28 91 91
GSK3B -0.045 0.1 -10000 0 -0.31 19 19
RELN/VLDLR/DAB1/Fyn -0.012 0.12 -10000 0 -0.22 62 62
MAP3K11 0.027 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.043 0.12 -10000 0 -0.24 64 64
CDK5 0.026 0.006 -10000 0 -10000 0 0
MAPT -0.025 0.16 0.73 6 -0.32 29 35
neuron migration -0.083 0.13 -10000 0 -0.32 51 51
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.047 0.12 -10000 0 -0.31 26 26
RELN/VLDLR -0.063 0.15 -10000 0 -0.28 64 64
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.039 0.009 -10000 0 -10000 0 0
Necdin/E2F1 0.025 0.051 -10000 0 -0.2 12 12
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.015 0.14 -10000 0 -0.23 64 64
NGF (dimer)/p75(NTR)/BEX1 -0.13 0.18 -10000 0 -0.27 153 153
NT-4/5 (dimer)/p75(NTR) -0.052 0.13 -10000 0 -0.24 90 90
IKBKB 0.025 0.008 -10000 0 -10000 0 0
AKT1 -0.057 0.11 0.18 16 -0.33 12 28
IKBKG 0.022 0.006 -10000 0 -10000 0 0
BDNF 0.02 0.045 -10000 0 -0.28 6 6
MGDIs/NGR/p75(NTR)/LINGO1 -0.036 0.12 -10000 0 -0.21 90 90
FURIN 0.027 0.005 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.02 0.12 -10000 0 -0.2 77 77
LINGO1 0 0.087 -10000 0 -0.28 24 24
Sortilin/TRAF6/NRIF 0.03 0.024 -10000 0 -10000 0 0
proBDNF (dimer) 0.02 0.045 -10000 0 -0.28 6 6
NTRK1 0.022 0.042 -10000 0 -0.37 3 3
RTN4R 0.019 0.049 -10000 0 -0.28 7 7
neuron apoptosis -0.056 0.15 0.28 1 -0.47 15 16
IRAK1 0.027 0.005 -10000 0 -10000 0 0
SHC1 -0.059 0.12 -10000 0 -0.24 80 80
ARHGDIA 0.027 0.004 -10000 0 -10000 0 0
RhoA/GTP 0.02 0.004 -10000 0 -10000 0 0
Gamma Secretase 0.07 0.03 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.023 0.14 -10000 0 -0.23 74 74
MAGEH1 0.023 0.042 -10000 0 -0.37 3 3
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.024 0.14 -10000 0 -0.23 73 73
Mammalian IAPs/DIABLO 0.062 0.034 -10000 0 -0.19 2 2
proNGF (dimer) -0.009 0.11 -10000 0 -0.36 25 25
MAGED1 0.024 0.034 -10000 0 -0.37 2 2
APP 0.026 0.006 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.004 0.08 -10000 0 -0.28 20 20
ZNF274 0.023 0.034 -10000 0 -0.37 2 2
RhoA/GDP/RHOGDI -0.035 0.11 -10000 0 -0.21 72 72
NGF -0.009 0.11 -10000 0 -0.36 25 25
cell cycle arrest -0.033 0.11 0.27 5 -0.32 12 17
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.032 0.1 -10000 0 -0.22 57 57
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.029 0.12 -10000 0 -0.2 87 87
NCSTN 0.027 0.005 -10000 0 -10000 0 0
mol:GTP -0.039 0.14 -10000 0 -0.24 86 86
PSENEN 0.026 0.007 -10000 0 -10000 0 0
mol:ceramide -0.051 0.11 0.18 4 -0.23 67 71
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.031 0.099 -10000 0 -0.32 16 16
p75(NTR)/beta APP -0.037 0.13 -10000 0 -0.25 72 72
BEX1 -0.13 0.19 -10000 0 -0.36 113 113
mol:GDP -0.077 0.11 -10000 0 -0.23 85 85
NGF (dimer) -0.046 0.12 -10000 0 -0.25 26 26
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.02 0.12 -10000 0 -0.21 60 60
PIK3R1 0.026 0.007 -10000 0 -10000 0 0
RAC1/GTP -0.029 0.12 -10000 0 -0.2 81 81
MYD88 0.027 0.005 -10000 0 -10000 0 0
CHUK 0.027 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.039 0.14 -10000 0 -0.24 86 86
RHOB 0.027 0.004 -10000 0 -10000 0 0
RHOA 0.027 0.005 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.027 0.045 -10000 0 -0.19 10 10
NT3 (dimer) -0.004 0.1 -10000 0 -0.36 21 21
TP53 -0.043 0.089 0.35 1 -0.33 2 3
PRDM4 -0.054 0.12 0.18 4 -0.23 70 74
BDNF (dimer) -0.11 0.12 -10000 0 -0.27 58 58
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
SORT1 0.027 0.005 -10000 0 -10000 0 0
activation of caspase activity -0.019 0.14 -10000 0 -0.23 64 64
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.02 0.13 -10000 0 -0.22 73 73
RHOC 0.026 0.006 -10000 0 -10000 0 0
XIAP 0.027 0.003 -10000 0 -10000 0 0
MAPK10 -0.057 0.15 0.28 5 -0.4 22 27
DIABLO 0.027 0.005 -10000 0 -10000 0 0
SMPD2 -0.051 0.11 0.18 4 -0.23 67 71
APH1B 0.027 0.005 -10000 0 -10000 0 0
APH1A 0.026 0.007 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.037 0.14 -10000 0 -0.23 85 85
PSEN1 0.027 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.039 0.009 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.058 0.15 -10000 0 -0.27 84 84
MAPK8 -0.05 0.13 0.29 5 -0.35 14 19
MAPK9 -0.052 0.13 0.29 4 -0.36 14 18
APAF1 0.027 0.003 -10000 0 -10000 0 0
NTF3 -0.004 0.1 -10000 0 -0.36 21 21
NTF4 0.004 0.08 -10000 0 -0.28 20 20
NDN 0.021 0.048 -10000 0 -0.37 4 4
RAC1/GDP 0.019 0.005 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.016 0.13 -10000 0 -0.2 70 70
p75 CTF/Sortilin/TRAF6/NRIF 0.061 0.032 -10000 0 -0.2 2 2
RhoA-B-C/GTP -0.04 0.14 -10000 0 -0.24 86 86
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.005 0.12 -10000 0 -0.2 51 51
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.004 0.11 -10000 0 -0.2 58 58
PRKACB 0.023 0.042 -10000 0 -0.37 3 3
proBDNF (dimer)/p75 ECD 0.034 0.035 -10000 0 -0.19 6 6
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.021 0.043 -10000 0 -0.32 4 4
BIRC2 0.026 0.006 -10000 0 -10000 0 0
neuron projection morphogenesis -0.033 0.14 0.25 5 -0.27 41 46
BAD -0.061 0.14 0.28 5 -0.36 22 27
RIPK2 0.023 0.02 -10000 0 -0.28 1 1
NGFR -0.074 0.17 -10000 0 -0.35 72 72
CYCS -0.066 0.097 0.18 3 -0.36 10 13
ADAM17 0.027 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.014 0.12 -10000 0 -0.22 63 63
BCL2L11 -0.061 0.14 0.29 5 -0.35 23 28
BDNF (dimer)/p75(NTR) -0.041 0.13 -10000 0 -0.24 77 77
PI3K -0.024 0.13 -10000 0 -0.21 82 82
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.022 0.14 -10000 0 -0.22 73 73
NDNL2 0.027 0.005 -10000 0 -10000 0 0
YWHAE 0.025 0.008 -10000 0 -10000 0 0
PRKCI 0.023 0.027 -10000 0 -0.28 2 2
NGF (dimer)/p75(NTR) -0.06 0.15 -10000 0 -0.28 85 85
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.023 0.14 -10000 0 -0.23 74 74
TRAF6 0.027 0.005 -10000 0 -10000 0 0
RAC1 0.026 0.007 -10000 0 -10000 0 0
PRKCZ 0.026 0.007 -10000 0 -10000 0 0
PLG 0.022 0.019 -10000 0 -0.28 1 1
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.054 0.12 0.15 4 -0.24 70 74
SQSTM1 0.026 0.006 -10000 0 -10000 0 0
NGFRAP1 0.022 0.048 -10000 0 -0.37 4 4
CASP3 -0.061 0.14 0.28 5 -0.34 25 30
E2F1 0.013 0.058 -10000 0 -0.28 10 10
CASP9 0.026 0.006 -10000 0 -10000 0 0
IKK complex -0.007 0.12 -10000 0 -0.34 12 12
NGF (dimer)/TRKA 0.009 0.088 -10000 0 -0.26 27 27
MMP7 -0.1 0.15 -10000 0 -0.28 113 113
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.01 0.14 -10000 0 -0.22 66 66
MMP3 -0.12 0.15 -10000 0 -0.28 124 124
APAF-1/Caspase 9 -0.066 0.079 -10000 0 -0.31 11 11
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 -0.054 0.15 -10000 0 -0.38 44 44
CRKL -0.059 0.16 -10000 0 -0.39 48 48
HRAS -0.036 0.15 -10000 0 -0.34 45 45
mol:PIP3 -0.05 0.15 -10000 0 -0.36 42 42
SPRED1 0.026 0.006 -10000 0 -10000 0 0
SPRED2 0.027 0.003 -10000 0 -10000 0 0
GAB1 -0.06 0.16 -10000 0 -0.41 48 48
FOXO3 -0.056 0.16 -10000 0 -0.37 45 45
AKT1 -0.059 0.17 -10000 0 -0.39 48 48
BAD -0.055 0.16 -10000 0 -0.37 47 47
megakaryocyte differentiation -0.068 0.16 -10000 0 -0.4 48 48
GSK3B -0.053 0.16 -10000 0 -0.36 45 45
RAF1 -0.03 0.12 0.26 2 -0.28 42 44
SHC1 0.026 0.006 -10000 0 -10000 0 0
STAT3 -0.059 0.16 -10000 0 -0.4 46 46
STAT1 -0.16 0.38 -10000 0 -0.95 49 49
HRAS/SPRED1 -0.017 0.13 0.26 1 -0.29 39 40
cell proliferation -0.061 0.16 -10000 0 -0.39 48 48
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
TEC 0.026 0.024 -10000 0 -0.37 1 1
RPS6KB1 -0.054 0.16 -10000 0 -0.39 50 50
HRAS/SPRED2 -0.018 0.13 0.26 1 -0.28 44 45
LYN/TEC/p62DOK -0.022 0.17 -10000 0 -0.38 40 40
MAPK3 -0.019 0.094 0.21 3 -0.25 8 11
STAP1 -0.071 0.18 -10000 0 -0.44 49 49
GRAP2 0.024 0.034 -10000 0 -0.37 2 2
JAK2 -0.13 0.34 -10000 0 -0.84 49 49
STAT1 (dimer) -0.15 0.37 -10000 0 -0.93 49 49
mol:Gleevec 0.002 0.006 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.029 0.18 -10000 0 -0.39 48 48
actin filament polymerization -0.058 0.15 -10000 0 -0.39 44 44
LYN 0.023 0.02 -10000 0 -0.28 1 1
STAP1/STAT5A (dimer) -0.1 0.25 -10000 0 -0.6 50 50
PIK3R1 0.026 0.007 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.03 0.15 -10000 0 -0.36 43 43
PI3K -0.03 0.16 -10000 0 -0.38 43 43
PTEN 0.026 0.006 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.16 0.44 -10000 0 -1.1 49 49
MAPK8 -0.061 0.16 -10000 0 -0.4 47 47
STAT3 (dimer) -0.059 0.16 -10000 0 -0.39 47 47
positive regulation of transcription -0.014 0.08 0.2 3 -0.22 5 8
mol:GDP -0.032 0.16 -10000 0 -0.36 44 44
PIK3C2B -0.059 0.16 -10000 0 -0.4 45 45
CBL/CRKL -0.041 0.15 -10000 0 -0.37 43 43
FER -0.059 0.16 -10000 0 -0.4 48 48
SH2B3 -0.059 0.16 -10000 0 -0.4 48 48
PDPK1 -0.055 0.14 -10000 0 -0.34 41 41
SNAI2 -0.058 0.15 -10000 0 -0.41 39 39
positive regulation of cell proliferation -0.11 0.28 -10000 0 -0.7 49 49
KITLG 0.018 0.026 -10000 0 -10000 0 0
cell motility -0.11 0.28 -10000 0 -0.7 49 49
PTPN6 0.028 0.021 -10000 0 -0.26 1 1
EPOR -0.051 0.21 -10000 0 -0.83 10 10
STAT5A (dimer) -0.089 0.24 -10000 0 -0.57 50 50
SOCS1 0.02 0.048 -10000 0 -0.29 6 6
cell migration 0.06 0.16 0.4 48 -10000 0 48
SOS1 0.027 0.003 -10000 0 -10000 0 0
EPO 0.008 0.052 -10000 0 -0.29 7 7
VAV1 0.023 0.036 -10000 0 -0.31 3 3
GRB10 -0.057 0.16 -10000 0 -0.4 41 41
PTPN11 0.029 0.008 -10000 0 -10000 0 0
SCF/KIT -0.061 0.17 -10000 0 -0.42 48 48
GO:0007205 0.003 0.009 -10000 0 -10000 0 0
MAP2K1 -0.021 0.1 0.23 3 -0.26 11 14
CBL 0.026 0.007 -10000 0 -10000 0 0
KIT -0.2 0.47 -10000 0 -1.1 53 53
MAP2K2 -0.022 0.1 0.23 3 -0.26 11 14
SHC/Grb2/SOS1 -0.024 0.17 -10000 0 -0.39 45 45
STAT5A -0.09 0.24 -10000 0 -0.59 49 49
GRB2 0.027 0.004 -10000 0 -10000 0 0
response to radiation -0.057 0.15 -10000 0 -0.4 40 40
SHC/GRAP2 0.036 0.027 -10000 0 -0.26 2 2
PTPRO -0.068 0.16 -10000 0 -0.41 47 47
SH2B2 -0.057 0.16 -10000 0 -0.41 42 42
DOK1 0.026 0.019 -10000 0 -0.28 1 1
MATK -0.061 0.16 -10000 0 -0.4 48 48
CREBBP 0.015 0.056 -10000 0 -0.17 1 1
BCL2 -0.088 0.28 -10000 0 -0.99 16 16
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.021 0.099 0.22 48 -10000 0 48
KIRREL 0.002 0.052 -10000 0 -0.29 5 5
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.021 0.099 -10000 0 -0.22 48 48
PLCG1 0.024 0.01 -10000 0 -10000 0 0
ARRB2 0.026 0.007 -10000 0 -10000 0 0
WASL 0.026 0.006 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.019 0.12 -10000 0 -0.22 55 55
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.033 0.094 -10000 0 -0.26 13 13
FYN -0.038 0.11 0.2 12 -0.21 54 66
mol:Ca2+ -0.02 0.11 -10000 0 -0.22 48 48
mol:DAG -0.019 0.11 -10000 0 -0.22 48 48
NPHS2 -0.058 0.15 -10000 0 -0.38 50 50
mol:IP3 -0.019 0.11 -10000 0 -0.22 48 48
regulation of endocytosis -0.021 0.1 -10000 0 -0.2 52 52
Nephrin/NEPH1/podocin/Cholesterol -0.029 0.11 -10000 0 -0.21 56 56
establishment of cell polarity -0.021 0.099 -10000 0 -0.22 48 48
Nephrin/NEPH1/podocin/NCK1-2 -0.007 0.12 -10000 0 -0.29 9 9
Nephrin/NEPH1/beta Arrestin2 -0.02 0.11 -10000 0 -0.2 52 52
NPHS1 -0.041 0.12 -10000 0 -0.29 49 49
Nephrin/NEPH1/podocin -0.025 0.11 -10000 0 -0.21 56 56
TJP1 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.004 -10000 0 -10000 0 0
NCK2 0.027 0.003 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.019 0.12 -10000 0 -0.22 48 48
CD2AP 0.026 0.006 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.02 0.12 -10000 0 -0.22 54 54
GRB2 0.027 0.004 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.042 0.11 0.21 12 -0.2 54 66
cytoskeleton organization -0.046 0.1 0.2 2 -0.3 13 15
Nephrin/NEPH1 -0.009 0.069 -10000 0 -0.14 45 45
Nephrin/NEPH1/ZO-1 -0.003 0.086 -10000 0 -0.22 15 15
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.03 0.13 -10000 0 -0.47 11 11
IHH -0.028 0.14 -10000 0 -0.38 35 35
SHH Np/Cholesterol/GAS1 -0.01 0.083 -10000 0 -0.2 42 42
LRPAP1 0.026 0.006 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.01 0.083 0.2 42 -10000 0 42
SMO/beta Arrestin2 -0.022 0.13 -10000 0 -0.4 16 16
SMO -0.034 0.13 -10000 0 -0.36 32 32
AKT1 -0.021 0.14 -10000 0 -0.46 17 17
ARRB2 0.026 0.007 -10000 0 -10000 0 0
BOC 0.005 0.09 -10000 0 -0.35 16 16
ADRBK1 0.026 0.006 -10000 0 -10000 0 0
heart looping -0.032 0.13 -10000 0 -0.35 32 32
STIL -0.058 0.12 0.19 7 -0.32 28 35
DHH N/PTCH2 0.01 0.081 -10000 0 -0.21 33 33
DHH N/PTCH1 -0.01 0.11 -10000 0 -0.33 12 12
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
DHH 0.019 0.054 -10000 0 -0.34 6 6
PTHLH -0.043 0.17 -10000 0 -0.64 13 13
determination of left/right symmetry -0.032 0.13 -10000 0 -0.35 32 32
PIK3R1 0.026 0.007 -10000 0 -10000 0 0
skeletal system development -0.043 0.17 -10000 0 -0.63 13 13
IHH N/Hhip -0.071 0.17 -10000 0 -0.31 81 81
DHH N/Hhip -0.04 0.13 -10000 0 -0.26 70 70
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.032 0.13 -10000 0 -0.35 32 32
pancreas development -0.07 0.17 -10000 0 -0.37 66 66
HHAT 0.024 0.034 -10000 0 -0.37 2 2
PI3K 0.036 0.014 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.002 0.093 -10000 0 -0.34 18 18
somite specification -0.032 0.13 -10000 0 -0.35 32 32
SHH Np/Cholesterol/PTCH1 -0.031 0.11 -10000 0 -0.3 20 20
SHH Np/Cholesterol/PTCH2 -0.017 0.082 -10000 0 -0.17 57 57
SHH Np/Cholesterol/Megalin -0.028 0.091 -10000 0 -0.18 69 69
SHH -0.018 0.086 -10000 0 -0.26 30 30
catabolic process -0.021 0.11 -10000 0 -0.27 34 34
SMO/Vitamin D3 -0.035 0.12 -10000 0 -0.36 19 19
SHH Np/Cholesterol/Hhip -0.049 0.12 -10000 0 -0.23 78 78
LRP2 -0.029 0.12 -10000 0 -0.29 48 48
receptor-mediated endocytosis -0.053 0.12 -10000 0 -0.36 22 22
SHH Np/Cholesterol/BOC -0.009 0.084 -10000 0 -0.2 41 41
SHH Np/Cholesterol/CDO -0.004 0.074 -10000 0 -0.2 29 29
mesenchymal cell differentiation 0.049 0.12 0.23 78 -10000 0 78
mol:Vitamin D3 -0.028 0.11 0.2 7 -0.32 18 25
IHH N/PTCH2 -0.023 0.11 -10000 0 -0.23 56 56
CDON 0.017 0.055 -10000 0 -0.32 7 7
IHH N/PTCH1 -0.014 0.12 -10000 0 -0.28 34 34
Megalin/LRPAP1 -0.003 0.09 -10000 0 -0.2 47 47
PTCH2 -0.005 0.094 -10000 0 -0.28 28 28
SHH Np/Cholesterol -0.008 0.067 -10000 0 -0.19 30 30
PTCH1 -0.021 0.11 -10000 0 -0.28 33 33
HHIP -0.07 0.17 -10000 0 -0.37 66 66
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.026 0.007 -10000 0 -10000 0 0
LAT2 -0.067 0.14 -10000 0 -0.33 46 46
AP1 -0.05 0.18 0.27 1 -0.4 38 39
mol:PIP3 -0.076 0.17 0.34 6 -0.4 37 43
IKBKB -0.038 0.11 0.25 9 -0.23 38 47
AKT1 -0.059 0.13 0.31 12 -0.28 31 43
IKBKG -0.044 0.11 0.23 9 -0.24 35 44
MS4A2 -0.051 0.16 -10000 0 -0.37 53 53
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.025 0.007 -10000 0 -10000 0 0
MAP3K1 -0.05 0.14 0.31 8 -0.32 37 45
mol:Ca2+ -0.057 0.14 0.31 6 -0.3 37 43
LYN 0.022 0.021 -10000 0 -0.28 1 1
CBLB -0.067 0.14 -10000 0 -0.32 48 48
SHC1 0.026 0.006 -10000 0 -10000 0 0
RasGAP/p62DOK 0.034 0.058 -10000 0 -0.19 15 15
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.024 0.035 -10000 0 -0.31 3 3
PLD2 -0.077 0.13 0.3 9 -0.32 39 48
PTPN13 -0.073 0.17 0.34 1 -0.42 35 36
PTPN11 0.015 0.025 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.05 0.12 0.32 7 -0.27 33 40
SYK 0.026 0.008 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.069 0.17 -10000 0 -0.4 39 39
LAT -0.067 0.14 -10000 0 -0.32 49 49
PAK2 -0.053 0.16 0.32 8 -0.35 37 45
NFATC2 -0.023 0.073 -10000 0 -0.7 2 2
HRAS -0.067 0.16 0.36 3 -0.39 39 42
GAB2 0.027 0.005 -10000 0 -10000 0 0
PLA2G1B 0.008 0.065 -10000 0 -0.86 1 1
Fc epsilon R1 -0.069 0.17 -10000 0 -0.29 95 95
Antigen/IgE/Fc epsilon R1 -0.06 0.16 -10000 0 -0.26 95 95
mol:GDP -0.071 0.16 -10000 0 -0.4 40 40
JUN 0.026 0.024 -10000 0 -0.37 1 1
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.025 0.007 -10000 0 -10000 0 0
FOS 0.005 0.089 -10000 0 -0.36 15 15
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.07 0.15 -10000 0 -0.33 53 53
CHUK -0.046 0.11 0.26 6 -0.23 40 46
KLRG1 -0.064 0.12 -10000 0 -0.32 40 40
VAV1 -0.071 0.14 -10000 0 -0.34 48 48
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.068 0.14 -10000 0 -0.32 49 49
negative regulation of mast cell degranulation -0.052 0.13 0.17 3 -0.3 41 44
BTK -0.072 0.16 -10000 0 -0.41 41 41
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.094 0.18 -10000 0 -0.44 47 47
GAB2/PI3K/SHP2 -0.08 0.1 -10000 0 -0.3 32 32
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.073 0.15 -10000 0 -0.37 44 44
RAF1 0.03 0.069 -10000 0 -1 1 1
Fc epsilon R1/FcgammaRIIB/SHIP -0.042 0.17 -10000 0 -0.27 81 81
FCER1G 0.026 0.034 -10000 0 -0.28 3 3
FCER1A -0.097 0.19 -10000 0 -0.38 82 82
Antigen/IgE/Fc epsilon R1/Fyn -0.047 0.15 -10000 0 -0.25 92 92
MAPK3 0.027 0.06 -10000 0 -0.82 1 1
MAPK1 0.025 0.063 -10000 0 -0.88 1 1
NFKB1 0.027 0.005 -10000 0 -10000 0 0
MAPK8 -0.043 0.21 -10000 0 -0.64 24 24
DUSP1 0.003 0.093 -10000 0 -0.37 16 16
NF-kappa-B/RelA -0.019 0.067 0.11 2 -0.15 26 28
actin cytoskeleton reorganization -0.069 0.17 0.35 1 -0.42 37 38
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.052 0.15 -10000 0 -0.36 35 35
FER -0.066 0.14 -10000 0 -0.33 47 47
RELA 0.027 0.004 -10000 0 -10000 0 0
ITK -0.026 0.075 -10000 0 -0.29 14 14
SOS1 0.027 0.003 -10000 0 -10000 0 0
PLCG1 -0.053 0.17 0.31 4 -0.4 37 41
cytokine secretion -0.016 0.047 -10000 0 -0.14 1 1
SPHK1 -0.073 0.14 -10000 0 -0.33 52 52
PTK2 -0.072 0.18 0.35 1 -0.44 37 38
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.07 0.17 -10000 0 -0.4 41 41
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.075 0.17 0.33 5 -0.39 39 44
MAP2K2 0.021 0.063 -10000 0 -0.94 1 1
MAP2K1 0.024 0.056 -10000 0 -0.79 1 1
MAP2K7 0.026 0.006 -10000 0 -10000 0 0
KLRG1/SHP2 -0.049 0.12 0.18 3 -0.28 40 43
MAP2K4 -0.073 0.31 -10000 0 -0.92 31 31
Fc epsilon R1/FcgammaRIIB -0.053 0.17 -10000 0 -0.27 94 94
mol:Choline -0.076 0.13 0.3 9 -0.31 39 48
SHC/Grb2/SOS1 -0.037 0.15 -10000 0 -0.34 36 36
FYN 0.027 0.005 -10000 0 -10000 0 0
DOK1 0.026 0.019 -10000 0 -0.28 1 1
PXN -0.068 0.17 0.34 1 -0.41 37 38
HCLS1 -0.066 0.14 -10000 0 -0.32 47 47
PRKCB -0.064 0.14 0.3 6 -0.32 42 48
FCGR2B 0.021 0.048 -10000 0 -0.37 4 4
IGHE -0.002 0.005 -10000 0 -10000 0 0
KLRG1/SHIP -0.052 0.13 0.18 3 -0.31 41 44
LCP2 0.026 0.006 -10000 0 -10000 0 0
PLA2G4A -0.074 0.14 -10000 0 -0.32 54 54
RASA1 0.025 0.008 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.076 0.13 0.3 9 -0.31 39 48
IKK complex -0.027 0.088 0.21 12 -0.18 28 40
WIPF1 0.024 0.034 -10000 0 -0.37 2 2
Syndecan-1-mediated signaling events

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
TGFB1 0.024 0.025 -10000 0 -0.37 1 1
CCL5 0.018 0.058 -10000 0 -0.37 6 6
SDCBP 0.024 0.009 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.067 0.11 0.22 3 -0.26 41 44
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 -0.07 0.1 -10000 0 -0.28 27 27
Syndecan-1/Syntenin -0.056 0.11 0.26 5 -0.28 19 24
MAPK3 -0.057 0.1 0.21 6 -0.29 17 23
HGF/MET 0.008 0.077 -10000 0 -0.2 33 33
TGFB1/TGF beta receptor Type II 0.024 0.025 -10000 0 -0.37 1 1
BSG 0.026 0.006 -10000 0 -10000 0 0
keratinocyte migration -0.07 0.1 -10000 0 -0.28 27 27
Syndecan-1/RANTES -0.061 0.12 0.24 6 -0.29 25 31
Syndecan-1/CD147 -0.051 0.12 0.29 3 -0.3 18 21
Syndecan-1/Syntenin/PIP2 -0.055 0.1 0.24 5 -0.28 19 24
LAMA5 0.01 0.06 -10000 0 -0.28 11 11
positive regulation of cell-cell adhesion -0.054 0.1 0.23 5 -0.27 19 24
MMP7 -0.1 0.15 -10000 0 -0.28 113 113
HGF 0.021 0.041 -10000 0 -0.28 5 5
Syndecan-1/CASK -0.07 0.098 -10000 0 -0.24 42 42
Syndecan-1/HGF/MET -0.067 0.12 0.24 6 -0.3 27 33
regulation of cell adhesion -0.057 0.1 0.24 6 -0.28 16 22
HPSE 0.006 0.076 -10000 0 -0.28 18 18
positive regulation of cell migration -0.067 0.11 0.22 3 -0.26 41 44
SDC1 -0.07 0.11 -10000 0 -0.26 41 41
Syndecan-1/Collagen -0.067 0.11 0.22 3 -0.26 41 44
PPIB 0.027 0.005 -10000 0 -10000 0 0
MET -0.007 0.094 -10000 0 -0.28 29 29
PRKACA 0.027 0.005 -10000 0 -10000 0 0
MMP9 -0.06 0.13 -10000 0 -0.28 74 74
MAPK1 -0.055 0.11 0.22 7 -0.29 17 24
homophilic cell adhesion -0.062 0.12 0.27 8 -0.26 37 45
MMP1 -0.095 0.15 -10000 0 -0.28 106 106
Canonical Wnt signaling pathway

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
HDAC1 0.027 0.013 -10000 0 -10000 0 0
AES 0.026 0.011 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.035 0.015 -10000 0 -10000 0 0
SMAD4 0.024 0.009 -10000 0 -10000 0 0
DKK2 -0.077 0.14 -10000 0 -0.28 92 92
TLE1 0.027 0.01 -10000 0 -10000 0 0
MACF1 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 -0.028 0.13 0.29 8 -0.45 8 16
WIF1 -0.096 0.18 -10000 0 -0.36 83 83
beta catenin/RanBP3 -0.029 0.12 0.33 9 -0.4 5 14
KREMEN2 -0.036 0.12 -10000 0 -0.28 55 55
DKK1 -0.11 0.16 -10000 0 -0.3 114 114
beta catenin/beta TrCP1 -0.019 0.13 0.29 8 -0.4 8 16
FZD1 0.025 0.009 -10000 0 -10000 0 0
AXIN2 -0.01 0.17 0.6 6 -1.3 3 9
AXIN1 0.026 0.006 -10000 0 -10000 0 0
RAN 0.027 0.005 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin -0.005 0.14 -10000 0 -0.62 12 12
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.016 0.19 0.26 1 -0.64 17 18
Axin1/APC/GSK3 -0.07 0.12 0.22 6 -0.3 23 29
Axin1/APC/GSK3/beta catenin/Macf1 -0.016 0.12 0.26 3 -0.4 12 15
HNF1A 0.018 0.052 -10000 0 -0.29 7 7
CTBP1 0.026 0.012 -10000 0 -10000 0 0
MYC 0.11 0.25 0.59 49 -1.2 1 50
RANBP3 0.027 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.061 0.12 -10000 0 -0.18 129 129
NKD1 -0.012 0.11 -10000 0 -0.32 30 30
TCF4 0.024 0.012 -10000 0 -10000 0 0
TCF3 0.025 0.021 -10000 0 -0.27 1 1
WNT1/LRP6/FZD1/Axin1 0.039 0.069 -10000 0 -0.19 19 19
Ran/GTP 0.02 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.01 0.12 0.38 4 -0.51 6 10
LEF1 0.01 0.068 -10000 0 -0.27 15 15
DVL1 -0.14 0.14 -10000 0 -0.26 121 121
CSNK2A1 -0.26 0.17 -10000 0 -0.37 195 195
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.007 0.16 0.27 1 -0.61 12 13
DKK1/LRP6/Kremen 2 -0.081 0.12 -10000 0 -0.19 144 144
LRP6 0.026 0.007 -10000 0 -10000 0 0
CSNK1A1 0.026 0.013 -10000 0 -10000 0 0
NLK 0.027 0.006 -10000 0 -10000 0 0
CCND1 0.037 0.14 0.59 13 -10000 0 13
WNT1 -0.001 0.099 -10000 0 -0.36 19 19
GSK3A 0.026 0.007 -10000 0 -10000 0 0
GSK3B 0.027 0.005 -10000 0 -10000 0 0
FRAT1 0.027 0.004 -10000 0 -10000 0 0
PPP2R5D -0.042 0.083 0.2 5 -0.28 4 9
APC 0.004 0.087 0.2 30 -0.19 1 31
WNT1/LRP6/FZD1 0.041 0.098 0.19 62 -0.32 2 64
CREBBP 0.026 0.012 -10000 0 -10000 0 0
Ephrin A reverse signaling

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
MAPKKK cascade -0.001 0.088 -10000 0 -0.22 36 36
EFNA5 0.008 0.078 -10000 0 -0.35 12 12
FYN -0.015 0.075 0.18 2 -0.2 33 35
neuron projection morphogenesis -0.001 0.088 -10000 0 -0.22 36 36
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.001 0.088 -10000 0 -0.22 36 36
EPHA5 -0.01 0.11 -10000 0 -0.37 25 25
Noncanonical Wnt signaling pathway

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
NFATC2 0.019 0.035 -10000 0 -0.37 2 2
GNB1/GNG2 -0.052 0.15 -10000 0 -0.36 28 28
mol:DAG -0.053 0.13 0.2 4 -0.35 24 28
PLCG1 -0.054 0.13 0.2 4 -0.36 24 28
YES1 -0.07 0.13 -10000 0 -0.37 28 28
FZD3 0.022 0.031 -10000 0 -0.32 2 2
FZD6 0.022 0.026 -10000 0 -0.37 1 1
G protein -0.029 0.15 0.22 17 -0.38 22 39
MAP3K7 -0.056 0.11 0.18 7 -0.33 21 28
mol:Ca2+ -0.051 0.12 0.2 4 -0.34 24 28
mol:IP3 -0.053 0.13 0.2 4 -0.35 24 28
NLK 0.007 0.054 -10000 0 -0.87 1 1
GNB1 0.026 0.007 -10000 0 -10000 0 0
CAMK2A -0.058 0.12 0.19 7 -0.33 26 33
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.068 0.14 -10000 0 -0.27 72 72
CSNK1A1 0.026 0.006 -10000 0 -10000 0 0
GNAS -0.063 0.13 -10000 0 -0.25 65 65
GO:0007205 -0.055 0.12 0.2 4 -0.34 25 29
WNT6 -0.036 0.14 -10000 0 -0.36 44 44
WNT4 -0.036 0.14 -10000 0 -0.37 43 43
NFAT1/CK1 alpha -0.043 0.14 0.28 5 -0.4 19 24
GNG2 0.026 0.019 -10000 0 -0.28 1 1
WNT5A 0.007 0.076 -10000 0 -0.28 18 18
WNT11 -0.046 0.14 -10000 0 -0.31 59 59
CDC42 -0.062 0.13 -10000 0 -0.36 25 25
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.022 0.078 -10000 0 -0.15 71 71
EPHB2 -0.14 0.15 -10000 0 -0.28 143 143
Syndecan-2/TACI -0.031 0.098 -10000 0 -0.21 61 61
LAMA1 -0.013 0.1 -10000 0 -0.28 34 34
Syndecan-2/alpha2 ITGB1 0.024 0.067 -10000 0 -0.22 7 7
HRAS 0.026 0.006 -10000 0 -10000 0 0
Syndecan-2/CASK 0.008 0.003 -10000 0 -10000 0 0
ITGA5 0.017 0.055 -10000 0 -0.28 9 9
BAX 0.004 0.002 -10000 0 -10000 0 0
EPB41 0.026 0.006 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.022 0.01 -10000 0 -10000 0 0
LAMA3 0.007 0.076 -10000 0 -0.3 16 16
EZR 0.026 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.023 0.031 -10000 0 -0.32 2 2
Syndecan-2/MMP2 0.024 0.015 -10000 0 -0.15 1 1
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.021 0.059 -10000 0 -0.19 19 19
dendrite morphogenesis -0.057 0.086 -10000 0 -0.15 122 122
Syndecan-2/GM-CSF -0.03 0.08 -10000 0 -0.15 82 82
determination of left/right symmetry 0.01 0.004 -10000 0 -10000 0 0
Syndecan-2/PKC delta 0.025 0.011 -10000 0 -10000 0 0
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
MAPK3 -0.017 0.09 0.19 19 -10000 0 19
MAPK1 -0.016 0.09 0.19 19 -10000 0 19
Syndecan-2/RACK1 0.035 0.017 -10000 0 -10000 0 0
NF1 0.027 0.004 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.01 0.004 -10000 0 -10000 0 0
ITGA2 0.004 0.078 -10000 0 -0.28 19 19
MAPK8 0.008 0.004 -10000 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin 0.018 0.071 -10000 0 -0.25 1 1
Syndecan-2/Kininogen 0.001 0.059 -10000 0 -0.15 34 34
ITGB1 0.026 0.006 -10000 0 -10000 0 0
SRC 0.026 0.047 0.18 22 -10000 0 22
Syndecan-2/CASK/Protein 4.1 0.022 0.01 -10000 0 -10000 0 0
extracellular matrix organization 0.024 0.011 -10000 0 -10000 0 0
actin cytoskeleton reorganization -0.022 0.078 -10000 0 -0.15 71 71
Syndecan-2/Caveolin-2/Ras 0.036 0.019 -10000 0 -10000 0 0
Syndecan-2/Laminin alpha3 0.014 0.044 -10000 0 -0.16 14 14
Syndecan-2/RasGAP 0.044 0.024 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.03 0.042 -10000 0 -0.19 9 9
PRKCD 0.027 0.005 -10000 0 -10000 0 0
Syndecan-2 dimer -0.058 0.086 -10000 0 -0.15 122 122
GO:0007205 0.002 0.001 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.029 0.019 0.18 1 -10000 0 1
RHOA 0.027 0.005 -10000 0 -10000 0 0
SDCBP 0.024 0.009 -10000 0 -10000 0 0
TNFRSF13B -0.085 0.18 -10000 0 -0.37 76 76
RASA1 0.025 0.008 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.021 0.059 -10000 0 -0.19 19 19
Syndecan-2/Synbindin 0.024 0.011 -10000 0 -10000 0 0
TGFB1 0.024 0.025 -10000 0 -0.37 1 1
CASP3 0.031 0.055 0.19 28 -10000 0 28
FN1 -0.058 0.14 -10000 0 -0.28 76 76
Syndecan-2/IL8 -0.057 0.087 -10000 0 -0.15 123 123
SDC2 0.01 0.004 -10000 0 -10000 0 0
KNG1 -0.021 0.11 -10000 0 -0.28 41 41
Syndecan-2/Neurofibromin 0.025 0.011 -10000 0 -10000 0 0
TRAPPC4 0.026 0.007 -10000 0 -10000 0 0
CSF2 -0.074 0.14 -10000 0 -0.28 88 88
Syndecan-2/TGFB1 0.024 0.011 -10000 0 -10000 0 0
Syndecan-2/Syntenin/PI-4-5-P2 0.022 0.01 -10000 0 -10000 0 0
Syndecan-2/Ezrin 0.036 0.018 -10000 0 -10000 0 0
PRKACA 0.035 0.057 0.19 32 -10000 0 32
angiogenesis -0.057 0.087 -10000 0 -0.15 123 123
MMP2 0.025 0.02 -10000 0 -0.28 1 1
IL8 -0.13 0.15 -10000 0 -0.28 137 137
calcineurin-NFAT signaling pathway -0.031 0.097 -10000 0 -0.21 61 61
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.04 0.044 -10000 0 -0.17 9 9
fibroblast growth factor receptor signaling pathway 0.04 0.044 -10000 0 -0.17 9 9
LAMA1 -0.013 0.1 -10000 0 -0.28 34 34
PRNP 0.025 0.009 -10000 0 -10000 0 0
GPC1/SLIT2 0.002 0.096 -10000 0 -0.24 37 37
SMAD2 0.011 0.031 0.18 3 -10000 0 3
GPC1/PrPc/Cu2+ 0.028 0.03 -10000 0 -0.16 6 6
GPC1/Laminin alpha1 0.004 0.084 -10000 0 -0.2 38 38
TDGF1 -0.044 0.14 -10000 0 -0.33 53 53
CRIPTO/GPC1 -0.02 0.11 -10000 0 -0.23 58 58
APP/GPC1 0.033 0.035 -10000 0 -0.19 6 6
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.028 0.086 -10000 0 -0.22 32 32
FLT1 0.025 0.019 -10000 0 -0.28 1 1
GPC1/TGFB/TGFBR1/TGFBR2 0.046 0.036 -10000 0 -0.16 6 6
SERPINC1 0.023 0.027 -10000 0 -0.28 2 2
FYN -0.027 0.087 -10000 0 -0.22 33 33
FGR -0.027 0.086 -10000 0 -0.2 51 51
positive regulation of MAPKKK cascade -0.033 0.14 0.19 14 -0.34 34 48
SLIT2 -0.016 0.12 -10000 0 -0.35 31 31
GPC1/NRG -0.045 0.13 -10000 0 -0.25 75 75
NRG1 -0.077 0.17 -10000 0 -0.37 70 70
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.047 0.029 -10000 0 -0.16 3 3
LYN -0.022 0.08 -10000 0 -0.2 43 43
mol:Spermine 0.003 0.028 -10000 0 -0.19 6 6
cell growth 0.04 0.044 -10000 0 -0.17 9 9
BMP signaling pathway -0.02 0.045 0.28 6 -10000 0 6
SRC -0.025 0.084 -10000 0 -0.22 32 32
TGFBR1 0.025 0.019 -10000 0 -0.28 1 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.09 0.16 -10000 0 -0.3 97 97
GPC1 0.02 0.045 -10000 0 -0.28 6 6
TGFBR1 (dimer) 0.025 0.019 -10000 0 -0.28 1 1
VEGFA 0.026 0.007 -10000 0 -10000 0 0
BLK -0.06 0.12 -10000 0 -0.24 78 78
HCK -0.024 0.083 -10000 0 -0.21 44 44
FGF2 0.024 0.031 -10000 0 -0.32 2 2
FGFR1 0.022 0.027 -10000 0 -0.28 2 2
VEGFR1 homodimer 0.025 0.019 -10000 0 -0.28 1 1
TGFBR2 0.027 0.005 -10000 0 -10000 0 0
cell death 0.033 0.035 -10000 0 -0.19 6 6
ATIII/GPC1 0.032 0.04 -10000 0 -0.19 8 8
PLA2G2A/GPC1 -0.053 0.12 -10000 0 -0.21 98 98
LCK -0.03 0.09 -10000 0 -0.23 32 32
neuron differentiation -0.045 0.13 -10000 0 -0.25 75 75
PrPc/Cu2+ 0.018 0.006 -10000 0 -10000 0 0
APP 0.026 0.006 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.027 0.005 -10000 0 -10000 0 0
IL23-mediated signaling events

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
CCL2 -0.39 0.36 -10000 0 -1.1 32 32
IL23A -0.4 0.37 -10000 0 -1.1 32 32
NF kappa B1 p50/RelA/I kappa B alpha -0.4 0.37 -10000 0 -1.1 36 36
positive regulation of T cell mediated cytotoxicity -0.44 0.41 -10000 0 -1.2 41 41
ITGA3 -0.39 0.36 -10000 0 -1.1 33 33
IL17F -0.33 0.26 -10000 0 -0.7 52 52
IL12B -0.036 0.071 -10000 0 -0.38 9 9
STAT1 (dimer) -0.42 0.4 -10000 0 -1.1 41 41
CD4 -0.39 0.35 -10000 0 -1.1 32 32
IL23 -0.39 0.36 -10000 0 -1.1 32 32
IL23R -0.09 0.22 -10000 0 -1.1 11 11
IL1B -0.41 0.38 -10000 0 -1.2 32 32
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.4 0.36 -10000 0 -1.1 31 31
TYK2 -0.019 0.028 -10000 0 -10000 0 0
STAT4 0.025 0.03 -10000 0 -0.32 2 2
STAT3 0.025 0.008 -10000 0 -10000 0 0
IL18RAP 0.014 0.057 -10000 0 -0.35 6 6
IL12RB1 -0.02 0.028 -10000 0 -10000 0 0
PIK3CA 0.025 0.009 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.017 0.04 -10000 0 -10000 0 0
IL23R/JAK2 -0.094 0.2 -10000 0 -1.1 9 9
positive regulation of chronic inflammatory response -0.44 0.41 -10000 0 -1.2 41 41
natural killer cell activation 0.008 0.011 0.079 5 -10000 0 5
JAK2 -0.021 0.033 -10000 0 -10000 0 0
PIK3R1 0.024 0.009 -10000 0 -10000 0 0
NFKB1 0.024 0.005 -10000 0 -10000 0 0
RELA 0.024 0.005 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.38 0.34 -10000 0 -1 32 32
ALOX12B -0.42 0.37 -10000 0 -1.1 36 36
CXCL1 -0.44 0.36 -10000 0 -1.1 38 38
T cell proliferation -0.44 0.41 -10000 0 -1.2 41 41
NFKBIA 0.024 0.004 -10000 0 -10000 0 0
IL17A -0.3 0.22 -10000 0 -0.58 68 68
PI3K -0.42 0.38 -10000 0 -1.1 42 42
IFNG -0.022 0.04 0.12 7 -0.11 11 18
STAT3 (dimer) -0.42 0.37 -10000 0 -1.1 43 43
IL18R1 0.022 0.023 -10000 0 -0.28 1 1
IL23/IL23R/JAK2/TYK2/SOCS3 -0.25 0.24 -10000 0 -0.72 29 29
IL18/IL18R 0.024 0.062 -10000 0 -0.19 10 10
macrophage activation -0.023 0.015 -10000 0 -0.045 19 19
TNF -0.41 0.38 -10000 0 -1.1 33 33
STAT3/STAT4 -0.41 0.38 -10000 0 -1.1 42 42
STAT4 (dimer) -0.42 0.4 -10000 0 -1.1 42 42
IL18 0.017 0.042 -10000 0 -0.3 4 4
IL19 -0.6 0.55 -10000 0 -1.2 108 108
STAT5A (dimer) -0.42 0.4 -10000 0 -1.1 41 41
STAT1 0.018 0.052 -10000 0 -0.28 8 8
SOCS3 0.027 0.004 -10000 0 -10000 0 0
CXCL9 -0.43 0.36 -10000 0 -1.1 36 36
MPO -0.4 0.36 -10000 0 -1.1 33 33
positive regulation of humoral immune response -0.44 0.41 -10000 0 -1.2 41 41
IL23/IL23R/JAK2/TYK2 -0.45 0.44 -10000 0 -1.2 41 41
IL6 -0.43 0.41 -10000 0 -1.2 43 43
STAT5A 0.027 0.005 -10000 0 -10000 0 0
IL2 0.018 0.022 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.008 0.011 0.079 5 -10000 0 5
CD3E -0.39 0.36 -10000 0 -1.1 33 33
keratinocyte proliferation -0.44 0.41 -10000 0 -1.2 41 41
NOS2 -0.41 0.36 -10000 0 -1 38 38
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.033 0.073 -10000 0 -0.36 8 8
HDAC1 0.025 0.006 -10000 0 -10000 0 0
AES 0.026 0.006 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
DTX1 0.022 0.04 -10000 0 -0.3 4 4
LRP6/FZD1 0.035 0.015 -10000 0 -10000 0 0
TLE1 0.026 0.005 -10000 0 -10000 0 0
AP1 -0.014 0.09 -10000 0 -0.25 28 28
NCSTN 0.027 0.005 -10000 0 -10000 0 0
ADAM10 0.027 0.005 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.022 0.17 -10000 0 -0.7 15 15
NICD/RBPSUH 0.032 0.075 -10000 0 -0.37 8 8
WIF1 -0.095 0.18 -10000 0 -0.36 83 83
NOTCH1 0.016 0.062 -10000 0 -0.38 6 6
PSENEN 0.026 0.007 -10000 0 -10000 0 0
KREMEN2 -0.036 0.12 -10000 0 -0.28 55 55
DKK1 -0.11 0.16 -10000 0 -0.3 114 114
beta catenin/beta TrCP1 -0.099 0.1 0.24 1 -0.32 12 13
APH1B 0.027 0.005 -10000 0 -10000 0 0
APH1A 0.026 0.007 -10000 0 -10000 0 0
AXIN1 -0.018 0.084 -10000 0 -0.38 11 11
CtBP/CBP/TCF1/TLE1/AES 0.013 0.037 -10000 0 -10000 0 0
PSEN1 0.027 0.005 -10000 0 -10000 0 0
FOS 0.005 0.089 -10000 0 -0.36 15 15
JUN 0.026 0.024 -10000 0 -0.37 1 1
MAP3K7 0.026 0.006 -10000 0 -10000 0 0
CTNNB1 -0.1 0.1 0.24 1 -0.32 15 16
MAPK3 0.027 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.061 0.12 -10000 0 -0.18 129 129
HNF1A 0.018 0.053 -10000 0 -0.3 7 7
CTBP1 0.025 0.007 -10000 0 -10000 0 0
MYC 0.007 0.1 -10000 0 -1.1 2 2
NKD1 -0.012 0.11 -10000 0 -0.32 30 30
FZD1 0.025 0.009 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.029 0.076 -10000 0 -0.37 8 8
apoptosis -0.014 0.09 -10000 0 -0.25 28 28
Delta 1/NOTCHprecursor 0.031 0.074 -10000 0 -0.36 8 8
DLL1 0.025 0.02 -10000 0 -0.28 1 1
PPARD 0 0.14 -10000 0 -0.86 7 7
Gamma Secretase 0.07 0.03 -10000 0 -10000 0 0
APC -0.03 0.11 -10000 0 -0.4 18 18
DVL1 -0.25 0.18 -10000 0 -0.36 191 191
CSNK2A1 -0.26 0.17 -10000 0 -0.37 195 195
MAP3K7IP1 -0.001 0.001 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.081 0.12 -10000 0 -0.19 140 140
LRP6 0.026 0.007 -10000 0 -10000 0 0
CSNK1A1 0.026 0.006 -10000 0 -10000 0 0
NLK 0.012 0.005 -10000 0 -10000 0 0
CCND1 0.001 0.12 -10000 0 -0.84 4 4
WNT1 0 0.099 -10000 0 -0.36 19 19
Axin1/APC/beta catenin -0.16 0.14 -10000 0 -0.45 24 24
DKK2 -0.077 0.14 -10000 0 -0.28 92 92
NOTCH1 precursor/DVL1 -0.21 0.17 -10000 0 -0.57 19 19
GSK3B 0.027 0.005 -10000 0 -10000 0 0
FRAT1 0.027 0.004 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.031 0.076 -10000 0 -0.37 8 8
PPP2R5D -0.073 0.092 0.22 3 -0.31 5 8
MAPK1 0.027 0.005 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.029 0.12 -10000 0 -0.2 86 86
RBPJ 0.027 0.004 -10000 0 -10000 0 0
CREBBP 0.027 0.008 -10000 0 -10000 0 0
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.015 0.12 -9999 0 -0.22 54 54
SMAD6-7/SMURF1 0.045 0.023 -9999 0 -10000 0 0
NOG 0.002 0.093 -9999 0 -0.34 19 19
SMAD9 -0.015 0.14 -9999 0 -0.59 12 12
SMAD4 0.024 0.009 -9999 0 -10000 0 0
SMAD5 -0.025 0.11 -9999 0 -0.3 25 25
BMP7/USAG1 -0.16 0.18 -9999 0 -0.31 146 146
SMAD5/SKI -0.031 0.13 -9999 0 -0.33 31 31
SMAD1 0.009 0.071 -9999 0 -0.39 6 6
BMP2 0.02 0.042 -9999 0 -0.37 3 3
SMAD1/SMAD1/SMAD4 0.024 0.06 -9999 0 -0.33 3 3
BMPR1A 0.025 0.024 -9999 0 -0.37 1 1
BMPR1B -0.023 0.13 -9999 0 -0.35 35 35
BMPR1A-1B/BAMBI -0.015 0.11 -9999 0 -0.2 71 71
AHSG 0.005 0.071 -9999 0 -0.28 16 16
CER1 0.018 0.02 -9999 0 -0.28 1 1
BMP2-4/CER1 0.033 0.048 -9999 0 -0.18 10 10
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.042 0.13 -9999 0 -0.34 31 31
BMP2-4 (homodimer) 0.026 0.049 -9999 0 -0.21 10 10
RGMB 0.024 0.025 -9999 0 -0.37 1 1
BMP6/BMPR2/BMPR1A-1B 0.03 0.088 -9999 0 -0.2 28 28
RGMA -0.061 0.16 -9999 0 -0.36 61 61
SMURF1 0.025 0.008 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.034 0.12 -9999 0 -0.32 29 29
BMP2-4/USAG1 -0.11 0.13 -9999 0 -0.22 150 150
SMAD6/SMURF1/SMAD5 -0.031 0.13 -9999 0 -0.32 32 32
SOSTDC1 -0.2 0.19 -9999 0 -0.37 156 156
BMP7/BMPR2/BMPR1A-1B -0.015 0.12 -9999 0 -0.22 55 55
SKI 0.026 0.007 -9999 0 -10000 0 0
BMP6 (homodimer) 0.026 0.007 -9999 0 -10000 0 0
HFE2 0.021 0.026 -9999 0 -0.28 2 2
ZFYVE16 0.026 0.007 -9999 0 -10000 0 0
MAP3K7 0.026 0.006 -9999 0 -10000 0 0
BMP2-4/CHRD 0.035 0.054 -9999 0 -0.2 10 10
SMAD5/SMAD5/SMAD4 -0.031 0.13 -9999 0 -0.32 32 32
MAPK1 0.027 0.005 -9999 0 -10000 0 0
TAK1/TAB family -0.023 0.11 -9999 0 -0.29 24 24
BMP7 (homodimer) -0.045 0.14 -9999 0 -0.35 48 48
NUP214 0.027 0.005 -9999 0 -10000 0 0
BMP6/FETUA 0.022 0.053 -9999 0 -0.18 16 16
SMAD1/SKI 0.017 0.082 -9999 0 -0.38 7 7
SMAD6 0.027 0.004 -9999 0 -10000 0 0
CTDSP2 0.027 0.005 -9999 0 -10000 0 0
BMP2-4/FETUA 0.028 0.059 -9999 0 -0.17 18 18
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.043 0.13 -9999 0 -0.29 60 60
BMPR2 (homodimer) 0.028 0.002 -9999 0 -10000 0 0
GADD34/PP1CA 0.048 0.02 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) 0.001 0.098 -9999 0 -0.25 34 34
CHRDL1 -0.1 0.19 -9999 0 -0.37 90 90
ENDOFIN/SMAD1 0.018 0.081 -9999 0 -0.41 6 6
SMAD6-7/SMURF1/SMAD1 0.037 0.073 -9999 0 -0.37 3 3
SMAD6/SMURF1 0.025 0.008 -9999 0 -10000 0 0
BAMBI -0.022 0.11 -9999 0 -0.28 43 43
SMURF2 0.027 0.004 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.036 0.13 -9999 0 -0.23 80 80
BMP2-4/GREM1 -0.007 0.094 -9999 0 -0.17 67 67
SMAD7 0.025 0.009 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.009 0.14 -9999 0 -0.53 16 16
SMAD1/SMAD6 0.017 0.074 -9999 0 -0.37 4 4
TAK1/SMAD6 0.036 0.014 -9999 0 -10000 0 0
BMP7 -0.045 0.14 -9999 0 -0.35 48 48
BMP6 0.026 0.007 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.029 0.12 -9999 0 -0.33 26 26
PPM1A 0.027 0.005 -9999 0 -10000 0 0
SMAD1/SMURF2 0.018 0.08 -9999 0 -0.42 5 5
SMAD7/SMURF1 0.033 0.016 -9999 0 -10000 0 0
CTDSPL 0.027 0.005 -9999 0 -10000 0 0
PPP1CA 0.027 0.005 -9999 0 -10000 0 0
XIAP 0.027 0.003 -9999 0 -10000 0 0
CTDSP1 0.027 0.004 -9999 0 -10000 0 0
PPP1R15A 0.026 0.006 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.055 0.15 -9999 0 -0.37 39 39
CHRD 0.023 0.034 -9999 0 -0.37 2 2
BMPR2 0.028 0.002 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.046 0.12 -9999 0 -0.33 32 32
BMP4 0.02 0.045 -9999 0 -0.28 6 6
FST 0.008 0.074 -9999 0 -0.3 14 14
BMP2-4/NOG 0.023 0.077 -9999 0 -0.19 28 28
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.008 0.12 -9999 0 -0.21 50 50
Ephrin B reverse signaling

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
EFNB2 0.025 0.02 -10000 0 -0.28 1 1
EPHB2 -0.13 0.15 -10000 0 -0.28 143 143
EFNB1 0.003 0.036 -10000 0 -0.19 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.06 0.12 -10000 0 -0.24 40 40
Ephrin B2/EPHB1-2 -0.067 0.11 -10000 0 -0.17 130 130
neuron projection morphogenesis -0.063 0.1 -10000 0 -0.23 41 41
Ephrin B1/EPHB1-2/Tiam1 -0.068 0.12 -10000 0 -0.26 43 43
DNM1 0.018 0.052 -10000 0 -0.28 8 8
cell-cell signaling 0 0.004 -10000 0 -10000 0 0
MAP2K4 -0.02 0.1 -10000 0 -0.43 14 14
YES1 -0.021 0.16 -10000 0 -0.65 15 15
Ephrin B1/EPHB1-2/NCK2 -0.065 0.12 -10000 0 -0.25 42 42
PI3K 0.012 0.11 -10000 0 -0.41 15 15
mol:GDP -0.068 0.12 -10000 0 -0.26 43 43
ITGA2B 0.019 0.056 -10000 0 -0.35 6 6
endothelial cell proliferation 0.03 0.023 -10000 0 -0.16 3 3
FYN -0.022 0.16 -10000 0 -0.65 15 15
MAP3K7 -0.022 0.11 0.22 1 -0.45 15 16
FGR -0.021 0.15 -10000 0 -0.64 15 15
TIAM1 0.024 0.031 -10000 0 -0.32 2 2
PIK3R1 0.026 0.007 -10000 0 -10000 0 0
RGS3 0.026 0.006 -10000 0 -10000 0 0
cell adhesion 0 0.1 -10000 0 -0.4 13 13
LYN -0.019 0.15 -10000 0 -0.66 14 14
Ephrin B1/EPHB1-2/Src Family Kinases -0.026 0.14 -10000 0 -0.58 16 16
Ephrin B1/EPHB1-2 -0.018 0.11 -10000 0 -0.53 12 12
SRC -0.021 0.15 -10000 0 -0.65 15 15
ITGB3 0.026 0.019 -10000 0 -0.28 1 1
EPHB1 -0.024 0.11 -10000 0 -0.28 45 45
EPHB4 0.023 0.027 -10000 0 -0.28 2 2
RAC1 0.026 0.007 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.03 0.024 -10000 0 -0.16 3 3
alphaIIb/beta3 Integrin 0.033 0.045 -10000 0 -0.24 7 7
BLK -0.042 0.16 -10000 0 -0.67 15 15
HCK -0.019 0.15 -10000 0 -0.66 14 14
regulation of stress fiber formation 0.065 0.12 0.25 42 -10000 0 42
MAPK8 -0.022 0.099 -10000 0 -0.41 14 14
Ephrin B1/EPHB1-2/RGS3 -0.065 0.12 -10000 0 -0.25 41 41
endothelial cell migration 0.001 0.11 0.23 19 -0.41 11 30
NCK2 0.027 0.003 -10000 0 -10000 0 0
PTPN13 0.017 0.071 -10000 0 -0.44 6 6
regulation of focal adhesion formation 0.065 0.12 0.25 42 -10000 0 42
chemotaxis 0.065 0.12 0.25 41 -10000 0 41
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
Rac1/GTP -0.061 0.11 -10000 0 -0.24 40 40
angiogenesis -0.02 0.11 -10000 0 -0.51 13 13
LCK -0.024 0.16 -10000 0 -0.64 16 16
Aurora B signaling

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
Condensin I complex 0.001 0.06 -9999 0 -0.26 6 6
STMN1 0.006 0.044 -9999 0 -0.22 9 9
Aurora B/RasGAP/Survivin 0.036 0.07 -9999 0 -0.2 18 18
Chromosomal passenger complex/Cul3 protein complex -0.022 0.09 -9999 0 -0.27 17 17
BIRC5 0.011 0.071 -9999 0 -0.29 14 14
DES -0.3 0.32 -9999 0 -0.6 140 140
Aurora C/Aurora B/INCENP 0.041 0.049 -9999 0 -0.15 14 14
Aurora B/TACC1 0.029 0.035 -9999 0 -0.15 8 8
Aurora B/PP2A 0.033 0.042 -9999 0 -0.19 8 8
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.11 0.054 -9999 0 -0.13 223 223
mitotic metaphase/anaphase transition 0.002 0.005 -9999 0 -10000 0 0
NDC80 -0.019 0.083 -9999 0 -0.21 39 39
Cul3 protein complex 0.015 0.089 -9999 0 -0.21 35 35
KIF2C -0.012 0.072 -9999 0 -0.23 13 13
PEBP1 0.026 0.006 -9999 0 -10000 0 0
KIF20A -0.02 0.11 -9999 0 -0.28 42 42
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP 0.03 0.047 -9999 0 -0.19 10 10
SEPT1 0.023 0.036 -9999 0 -0.31 3 3
SMC2 0.024 0.027 -9999 0 -0.28 2 2
SMC4 0.024 0.027 -9999 0 -0.28 2 2
NSUN2/NPM1/Nucleolin -0.03 0.15 -9999 0 -0.54 21 21
PSMA3 0.027 0.005 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.003 -9999 0 -10000 0 0
H3F3B -0.22 0.1 -9999 0 -0.26 227 227
AURKB 0.019 0.062 -9999 0 -0.29 10 10
AURKC 0.023 0.036 -9999 0 -0.31 3 3
CDCA8 0.013 0.064 -9999 0 -0.28 12 12
cytokinesis -0.042 0.11 -9999 0 -0.36 17 17
Aurora B/Septin1 -0.021 0.12 -9999 0 -0.33 19 19
AURKA 0.013 0.052 -9999 0 -0.28 8 8
INCENP 0.026 0.021 -9999 0 -0.28 1 1
KLHL13 -0.027 0.14 -9999 0 -0.36 38 38
BUB1 -0.062 0.14 -9999 0 -0.28 80 80
hSgo1/Aurora B/Survivin 0.011 0.098 -9999 0 -0.18 48 48
EVI5 0.028 0.005 -9999 0 -10000 0 0
RhoA/GTP -0.009 0.12 -9999 0 -0.28 19 19
SGOL1 -0.02 0.11 -9999 0 -0.28 42 42
CENPA 0.002 0.071 -9999 0 -0.24 13 13
NCAPG 0.008 0.074 -9999 0 -0.28 17 17
Aurora B/HC8 Proteasome 0.032 0.046 -9999 0 -0.19 10 10
NCAPD2 0.025 0.019 -9999 0 -0.28 1 1
Aurora B/PP1-gamma 0.033 0.046 -9999 0 -0.19 10 10
RHOA 0.027 0.005 -9999 0 -10000 0 0
NCAPH 0.005 0.08 -9999 0 -0.28 20 20
NPM1 -0.023 0.13 -9999 0 -0.4 20 20
RASA1 0.025 0.008 -9999 0 -10000 0 0
KLHL9 0.024 0.009 -9999 0 -10000 0 0
mitotic prometaphase -0.001 0.003 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.032 0.046 -9999 0 -0.19 10 10
PPP1CC 0.027 0.004 -9999 0 -10000 0 0
Centraspindlin -0.018 0.12 -9999 0 -0.28 24 24
RhoA/GDP 0.02 0.004 -9999 0 -10000 0 0
NSUN2 -0.014 0.1 -9999 0 -0.35 18 18
MYLK -0.002 0.057 -9999 0 -0.27 8 8
KIF23 -0.046 0.13 -9999 0 -0.28 65 65
VIM 0.006 0.04 -9999 0 -0.19 10 10
RACGAP1 0.025 0.027 -9999 0 -0.28 2 2
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.013 0.094 -9999 0 -0.32 19 19
Chromosomal passenger complex -0.013 0.08 -9999 0 -0.25 16 16
Chromosomal passenger complex/EVI5 0.07 0.097 -9999 0 -0.29 10 10
TACC1 0.025 0.009 -9999 0 -10000 0 0
PPP2R5D 0.026 0.007 -9999 0 -10000 0 0
CUL3 0.027 0.003 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.075 0.11 -10000 0 -0.17 144 144
cell-cell adhesion 0.081 0.082 0.23 38 -10000 0 38
Ephrin B/EPHB2/RasGAP -0.042 0.11 -10000 0 -0.26 10 10
ITSN1 0.027 0.005 -10000 0 -10000 0 0
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
SHC1 0.026 0.006 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.031 0.027 -10000 0 -0.17 4 4
Ephrin B1/EPHB1 0.003 0.072 -10000 0 -0.16 45 45
HRAS/GDP -0.014 0.098 -10000 0 -0.27 15 15
Ephrin B/EPHB1/GRB7 0.011 0.097 -10000 0 -0.23 14 14
Endophilin/SYNJ1 -0.063 0.081 0.17 6 -0.28 6 12
KRAS 0.024 0.009 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.022 0.089 -10000 0 -0.23 10 10
endothelial cell migration 0.044 0.031 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
GRB7 0.01 0.066 -10000 0 -0.29 12 12
PAK1 -0.062 0.087 0.18 9 -0.29 6 15
HRAS 0.026 0.006 -10000 0 -10000 0 0
RRAS -0.065 0.078 0.17 4 -0.29 5 9
DNM1 0.017 0.052 -10000 0 -0.28 8 8
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.022 0.079 0.2 15 -0.27 4 19
lamellipodium assembly -0.081 0.082 -10000 0 -0.23 38 38
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.006 0.056 -10000 0 -0.24 1 1
PIK3R1 0.026 0.007 -10000 0 -10000 0 0
EPHB2 -0.14 0.15 -10000 0 -0.28 143 143
EPHB3 0.021 0.04 -10000 0 -0.3 4 4
EPHB1 -0.024 0.11 -10000 0 -0.28 45 45
EPHB4 0.023 0.027 -10000 0 -0.28 2 2
mol:GDP -0.037 0.082 0.18 5 -0.27 15 20
Ephrin B/EPHB2 -0.047 0.1 -10000 0 -0.26 10 10
Ephrin B/EPHB3 0.04 0.058 -10000 0 -0.2 9 9
JNK cascade -0.089 0.1 0.25 6 -0.25 36 42
Ephrin B/EPHB1 0.015 0.086 -10000 0 -0.22 10 10
RAP1/GDP -0.028 0.097 0.24 5 -0.27 11 16
EFNB2 0.025 0.02 -10000 0 -0.28 1 1
EFNB3 0.007 0.078 -10000 0 -0.32 14 14
EFNB1 0.027 0.004 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.068 0.12 -10000 0 -0.18 134 134
RAP1B 0.026 0.006 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.058 0.11 -10000 0 -0.3 8 8
Rap1/GTP -0.067 0.096 -10000 0 -0.24 30 30
axon guidance -0.074 0.11 -10000 0 -0.17 144 144
MAPK3 -0.002 0.047 -10000 0 -0.22 1 1
MAPK1 -0.002 0.047 -10000 0 -0.22 1 1
Rac1/GDP -0.036 0.088 0.26 2 -0.27 11 13
actin cytoskeleton reorganization -0.066 0.081 -10000 0 -0.26 12 12
CDC42/GDP -0.032 0.094 0.24 5 -0.27 13 18
PI3K 0.048 0.034 -10000 0 -10000 0 0
EFNA5 0.008 0.078 -10000 0 -0.35 12 12
Ephrin B2/EPHB4 0.03 0.024 -10000 0 -0.16 3 3
Ephrin B/EPHB2/Intersectin/N-WASP -0.03 0.061 -10000 0 -0.22 9 9
CDC42 0.026 0.007 -10000 0 -10000 0 0
RAS family/GTP -0.065 0.093 -10000 0 -0.24 30 30
PTK2 0.1 0.21 0.62 39 -10000 0 39
MAP4K4 -0.09 0.1 0.25 6 -0.26 36 42
SRC 0.024 0.009 -10000 0 -10000 0 0
KALRN 0.023 0.042 -10000 0 -0.37 3 3
Intersectin/N-WASP 0.038 0.011 -10000 0 -10000 0 0
neuron projection morphogenesis -0.045 0.1 0.26 10 -0.28 5 15
MAP2K1 0.003 0.05 -10000 0 -0.23 1 1
WASL 0.026 0.006 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.069 0.12 -10000 0 -0.27 36 36
cell migration 0.006 0.082 0.22 9 -0.28 3 12
NRAS 0.027 0.005 -10000 0 -10000 0 0
SYNJ1 -0.063 0.082 0.17 6 -0.29 6 12
PXN 0.024 0.031 -10000 0 -0.32 2 2
TF -0.1 0.1 0.16 3 -0.28 43 46
HRAS/GTP -0.061 0.11 -10000 0 -0.24 39 39
Ephrin B1/EPHB1-2 -0.074 0.12 -10000 0 -0.17 144 144
cell adhesion mediated by integrin 0.004 0.059 0.2 7 -0.2 10 17
RAC1 0.026 0.007 -10000 0 -10000 0 0
mol:GTP -0.063 0.11 -10000 0 -0.25 39 39
RAC1-CDC42/GTP -0.072 0.092 -10000 0 -0.24 36 36
RASA1 0.025 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.032 0.089 0.25 2 -0.28 8 10
ruffle organization -0.055 0.13 0.32 15 -0.33 5 20
NCK1 0.027 0.004 -10000 0 -10000 0 0
receptor internalization -0.065 0.083 0.16 6 -0.27 12 18
Ephrin B/EPHB2/KALRN -0.045 0.11 -10000 0 -0.25 13 13
ROCK1 0.025 0.05 0.18 21 -0.16 4 25
RAS family/GDP -0.072 0.073 -10000 0 -0.26 12 12
Rac1/GTP -0.072 0.096 -10000 0 -0.25 37 37
Ephrin B/EPHB1/Src/Paxillin 0.001 0.054 -10000 0 -0.21 9 9
BCR signaling pathway

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
JUN 0.029 0.19 0.29 13 -0.39 27 40
IKBKB -0.018 0.099 0.47 2 -0.28 15 17
AKT1 -0.04 0.11 0.34 6 -0.22 19 25
IKBKG -0.014 0.084 0.62 1 -0.3 6 7
CALM1 -0.043 0.12 0.27 1 -0.37 19 20
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
MAP3K1 -0.072 0.19 0.46 2 -0.52 27 29
MAP3K7 0.026 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.044 0.12 -10000 0 -0.36 23 23
DOK1 0.026 0.019 -10000 0 -0.28 1 1
AP-1 0.032 0.14 0.25 16 -0.26 24 40
LYN 0.023 0.02 -10000 0 -0.28 1 1
BLNK 0.015 0.067 -10000 0 -0.37 8 8
SHC1 0.026 0.006 -10000 0 -10000 0 0
BCR complex -0.056 0.15 -10000 0 -0.28 81 81
CD22 -0.073 0.15 -10000 0 -0.48 17 17
CAMK2G -0.039 0.11 0.26 1 -0.34 17 18
CSNK2A1 -0.26 0.17 -10000 0 -0.37 195 195
INPP5D 0.024 0.035 -10000 0 -0.31 3 3
SHC/GRB2/SOS1 -0.029 0.1 -10000 0 -0.33 11 11
GO:0007205 -0.046 0.13 0.29 1 -0.36 25 26
SYK 0.026 0.006 -10000 0 -10000 0 0
ELK1 -0.045 0.12 0.27 1 -0.37 20 21
NFATC1 -0.067 0.14 0.26 3 -0.38 29 32
B-cell antigen/BCR complex -0.056 0.15 -10000 0 -0.28 81 81
PAG1/CSK 0.034 0.02 -10000 0 -0.19 1 1
NFKBIB 0.008 0.045 0.23 2 -0.12 9 11
HRAS -0.041 0.11 0.38 1 -0.34 19 20
NFKBIA 0.008 0.045 0.23 2 -0.12 9 11
NF-kappa-B/RelA/I kappa B beta 0.013 0.04 0.23 2 -10000 0 2
RasGAP/Csk -0.012 0.13 -10000 0 -0.21 72 72
mol:GDP -0.043 0.12 0.27 1 -0.37 20 21
PTEN 0.026 0.006 -10000 0 -10000 0 0
CD79B 0.001 0.093 -10000 0 -0.33 20 20
NF-kappa-B/RelA/I kappa B alpha 0.013 0.04 0.23 2 -10000 0 2
GRB2 0.027 0.004 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.1 0.2 0.44 2 -0.46 43 45
PIK3R1 0.026 0.007 -10000 0 -10000 0 0
mol:IP3 -0.045 0.13 -10000 0 -0.36 24 24
CSK 0.027 0.005 -10000 0 -10000 0 0
FOS -0.049 0.13 0.29 4 -0.38 21 25
CHUK -0.016 0.094 0.62 1 -0.3 12 13
IBTK 0.026 0.006 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.022 0.13 0.32 2 -0.36 16 18
PTPN6 -0.072 0.14 -10000 0 -0.47 17 17
RELA 0.027 0.004 -10000 0 -10000 0 0
BCL2A1 0.008 0.031 0.27 1 -10000 0 1
VAV2 -0.081 0.18 -10000 0 -0.48 31 31
ubiquitin-dependent protein catabolic process 0.011 0.045 0.23 2 -0.12 9 11
BTK 0.009 0.12 -10000 0 -0.96 4 4
CD19 -0.08 0.17 -10000 0 -0.44 34 34
MAP4K1 0.021 0.043 -10000 0 -0.32 4 4
CD72 0.014 0.058 -10000 0 -0.28 10 10
PAG1 0.023 0.021 -10000 0 -0.28 1 1
MAPK14 -0.059 0.17 0.52 2 -0.44 27 29
SH3BP5 0.027 0.002 -10000 0 -10000 0 0
PIK3AP1 -0.05 0.13 -10000 0 -0.38 23 23
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.082 0.19 -10000 0 -0.36 70 70
RAF1 -0.039 0.11 0.3 2 -0.33 17 19
RasGAP/p62DOK/SHIP -0.012 0.14 -10000 0 -0.39 11 11
CD79A -0.084 0.18 -10000 0 -0.37 76 76
re-entry into mitotic cell cycle 0.031 0.14 0.28 11 -0.26 24 35
RASA1 0.025 0.008 -10000 0 -10000 0 0
MAPK3 -0.033 0.096 0.35 2 -0.29 14 16
MAPK1 -0.032 0.093 0.24 3 -0.29 14 17
CD72/SHP1 -0.061 0.14 0.25 1 -0.41 22 23
NFKB1 0.027 0.005 -10000 0 -10000 0 0
MAPK8 -0.061 0.16 0.52 2 -0.44 27 29
actin cytoskeleton organization -0.063 0.16 0.26 2 -0.41 30 32
NF-kappa-B/RelA 0.028 0.075 0.38 2 -0.19 5 7
Calcineurin -0.014 0.11 -10000 0 -0.33 13 13
PI3K -0.067 0.14 -10000 0 -0.35 32 32
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.041 0.14 -10000 0 -0.4 23 23
SOS1 0.027 0.003 -10000 0 -10000 0 0
Bam32/HPK1 -0.086 0.25 -10000 0 -0.79 23 23
DAPP1 -0.11 0.27 -10000 0 -0.86 26 26
cytokine secretion -0.062 0.14 0.26 3 -0.36 29 32
mol:DAG -0.045 0.13 -10000 0 -0.36 24 24
PLCG2 0.02 0.044 -10000 0 -0.3 5 5
MAP2K1 -0.037 0.1 0.28 2 -0.31 16 18
B-cell antigen/BCR complex/FcgammaRIIB -0.038 0.14 -10000 0 -0.24 81 81
mol:PI-3-4-5-P3 -0.059 0.094 -10000 0 -0.26 25 25
ETS1 -0.035 0.1 0.27 3 -0.33 15 18
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.01 0.13 -10000 0 -0.22 58 58
B-cell antigen/BCR complex/LYN -0.059 0.15 -10000 0 -0.52 15 15
MALT1 0.024 0.02 -10000 0 -0.28 1 1
TRAF6 0.027 0.005 -10000 0 -10000 0 0
RAC1 -0.069 0.16 0.29 1 -0.44 30 31
B-cell antigen/BCR complex/LYN/SYK -0.048 0.15 -10000 0 -0.46 15 15
CARD11 -0.045 0.13 0.35 2 -0.41 18 20
FCGR2B 0.021 0.048 -10000 0 -0.37 4 4
PPP3CA 0.027 0.005 -10000 0 -10000 0 0
BCL10 0.027 0.004 -10000 0 -10000 0 0
IKK complex 0.001 0.054 0.23 5 -0.12 5 10
PTPRC 0.017 0.055 -10000 0 -0.28 9 9
PDPK1 -0.042 0.084 0.19 8 -0.21 18 26
PPP3CB 0.027 0.005 -10000 0 -10000 0 0
PPP3CC 0.024 0.009 -10000 0 -10000 0 0
POU2F2 0.01 0.033 0.37 1 -10000 0 1
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.011 0.086 0.36 3 -1.1 1 4
VDR 0.026 0.019 -10000 0 -0.28 1 1
FAM120B 0.026 0.007 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.046 0.11 -10000 0 -0.29 16 16
RXRs/LXRs/DNA/Oxysterols -0.038 0.11 -10000 0 -0.36 10 10
MED1 0.026 0.007 -10000 0 -10000 0 0
mol:9cRA 0.002 0.007 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.01 0.061 -10000 0 -0.2 20 20
RXRs/NUR77 -0.034 0.13 -10000 0 -0.2 89 89
RXRs/PPAR -0.052 0.11 -10000 0 -0.22 51 51
NCOR2 0.027 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.019 0.013 -10000 0 -0.19 1 1
RARs/VDR/DNA/Vit D3 0.055 0.031 -10000 0 -0.19 1 1
RARA 0.025 0.008 -10000 0 -10000 0 0
NCOA1 0.027 0.004 -10000 0 -10000 0 0
VDR/VDR/DNA 0.025 0.019 -10000 0 -0.28 1 1
RARs/RARs/DNA/9cRA 0.043 0.025 -10000 0 -0.16 2 2
RARG 0.025 0.019 -10000 0 -0.28 1 1
RPS6KB1 0.023 0.055 0.53 2 -0.41 1 3
RARs/THRs/DNA/SMRT 0.01 0.063 -10000 0 -0.2 20 20
THRA 0.025 0.008 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.019 0.013 -10000 0 -0.19 1 1
RXRs/PPAR/9cRA/PGJ2/DNA -0.034 0.12 0.28 1 -0.2 87 88
NR1H4 -0.032 0.13 -10000 0 -0.32 45 45
RXRs/LXRs/DNA -0.013 0.13 -10000 0 -0.27 8 8
NR1H2 0.026 0.015 -10000 0 -10000 0 0
NR1H3 0.027 0.015 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.025 0.12 -10000 0 -0.18 83 83
NR4A1 0.014 0.071 -10000 0 -0.37 9 9
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.069 0.12 -10000 0 -0.27 38 38
RXRG -0.12 0.19 -10000 0 -0.37 97 97
RXR alpha/CCPG 0.037 0.023 -10000 0 -0.26 1 1
RXRA 0.025 0.028 -10000 0 -0.36 1 1
RXRB 0.026 0.015 -10000 0 -10000 0 0
THRB -0.001 0.1 -10000 0 -0.36 20 20
PPARG 0.024 0.034 -10000 0 -0.37 2 2
PPARD 0.026 0.006 -10000 0 -10000 0 0
TNF -0.044 0.15 -10000 0 -0.62 9 9
mol:Oxysterols 0.002 0.007 -10000 0 -10000 0 0
cholesterol transport -0.037 0.11 -10000 0 -0.36 10 10
PPARA 0.026 0.006 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.026 0.024 -10000 0 -0.37 1 1
RXRs/NUR77/BCL2 -0.066 0.12 -10000 0 -0.22 99 99
SREBF1 -0.034 0.1 -10000 0 -0.5 2 2
RXRs/RXRs/DNA/9cRA -0.034 0.12 0.27 1 -0.2 87 88
ABCA1 -0.037 0.1 -10000 0 -0.44 4 4
RARs/THRs 0.051 0.076 -10000 0 -0.2 19 19
RXRs/FXR -0.058 0.15 -10000 0 -0.22 101 101
BCL2 0.024 0.025 -10000 0 -0.37 1 1
Endothelins

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
AKT1 -0.03 0.13 0.25 5 -0.37 15 20
PTK2B 0.024 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0.002 0.14 -10000 0 -0.57 7 7
EDN1 -0.003 0.1 0.21 3 -0.32 8 11
EDN3 -0.065 0.16 -10000 0 -0.37 60 60
EDN2 -0.033 0.14 -10000 0 -0.36 42 42
HRAS/GDP -0.018 0.14 0.28 4 -0.51 10 14
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.002 0.097 0.17 1 -0.35 10 11
ADCY4 -0.027 0.12 0.2 10 -0.33 18 28
ADCY5 -0.066 0.15 0.19 9 -0.32 46 55
ADCY6 -0.026 0.12 0.2 11 -0.33 18 29
ADCY7 -0.028 0.12 0.2 9 -0.33 18 27
ADCY1 -0.029 0.12 0.2 8 -0.32 20 28
ADCY2 -0.04 0.13 0.2 7 -0.33 29 36
ADCY3 -0.027 0.12 0.2 11 -0.33 18 29
ADCY8 -0.027 0.11 0.19 6 -0.33 14 20
ADCY9 -0.028 0.12 0.2 7 -0.33 18 25
arachidonic acid secretion -0.027 0.16 0.42 1 -0.51 19 20
ETB receptor/Endothelin-1/Gq/GTP -0.003 0.077 -10000 0 -0.27 12 12
GNAO1 -0.007 0.11 -10000 0 -0.34 25 25
HRAS 0.026 0.006 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.018 0.15 0.32 5 -0.34 14 19
ETA receptor/Endothelin-1/Gs/GTP 0.008 0.15 0.3 5 -0.35 18 23
mol:GTP 0.001 0.003 -10000 0 -10000 0 0
COL3A1 -0.051 0.17 0.25 6 -0.37 43 49
EDNRB -0.002 0.072 -10000 0 -0.37 7 7
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.034 0.15 0.25 6 -0.42 15 21
CYSLTR1 -0.052 0.18 0.25 6 -0.44 34 40
SLC9A1 -0.011 0.082 0.17 4 -0.23 14 18
mol:GDP -0.03 0.14 0.28 4 -0.53 11 15
SLC9A3 -0.21 0.28 -10000 0 -0.52 100 100
RAF1 -0.035 0.15 0.26 5 -0.47 19 24
JUN -0.002 0.15 -10000 0 -0.66 8 8
JAK2 -0.028 0.13 0.25 5 -0.37 15 20
mol:IP3 -0.007 0.11 -10000 0 -0.5 8 8
ETA receptor/Endothelin-1 -0.001 0.18 0.35 6 -0.4 18 24
PLCB1 0.018 0.047 -10000 0 -0.31 5 5
PLCB2 0.026 0.009 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.062 0.14 -10000 0 -0.28 74 74
FOS -0.051 0.22 0.39 1 -0.82 18 19
Gai/GDP -0.063 0.26 -10000 0 -0.71 34 34
CRK 0.026 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.026 0.13 0.22 3 -0.4 15 18
BCAR1 0.026 0.007 -10000 0 -10000 0 0
PRKCB1 -0.006 0.11 -10000 0 -0.51 7 7
GNAQ 0.027 0.008 -10000 0 -10000 0 0
GNAZ 0.008 0.084 -10000 0 -0.37 13 13
GNAL 0.01 0.077 -10000 0 -0.36 11 11
Gs family/GDP -0.028 0.14 0.29 3 -0.42 16 19
ETA receptor/Endothelin-1/Gq/GTP -0.002 0.095 0.19 3 -0.34 8 11
MAPK14 -0.005 0.086 0.19 1 -0.38 7 8
TRPC6 0.001 0.14 -10000 0 -0.6 7 7
GNAI2 0.027 0.005 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.019 0.053 -10000 0 -0.37 5 5
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.002 0.082 -10000 0 -0.36 6 6
ETB receptor/Endothelin-2 -0.027 0.11 -10000 0 -0.27 46 46
ETB receptor/Endothelin-3 -0.05 0.13 -10000 0 -0.27 62 62
ETB receptor/Endothelin-1 -0.002 0.11 -10000 0 -0.3 12 12
MAPK3 -0.048 0.21 0.4 1 -0.71 20 21
MAPK1 -0.051 0.22 0.41 1 -0.75 20 21
Rac1/GDP -0.02 0.13 0.24 2 -0.5 10 12
cAMP biosynthetic process -0.045 0.14 0.26 6 -0.33 30 36
MAPK8 -0.003 0.16 0.35 1 -0.6 13 14
SRC 0.024 0.009 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.025 0.11 -10000 0 -0.35 17 17
p130Cas/CRK/Src/PYK2 -0.021 0.16 0.32 5 -0.56 10 15
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.019 0.13 0.23 3 -0.5 10 13
COL1A2 -0.047 0.16 0.25 3 -0.4 24 27
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.039 0.14 -10000 0 -0.26 59 59
mol:DAG -0.007 0.11 -10000 0 -0.5 8 8
MAP2K2 -0.041 0.17 0.41 1 -0.55 21 22
MAP2K1 -0.041 0.17 0.41 1 -0.55 21 22
EDNRA -0.017 0.12 0.21 3 -0.32 22 25
positive regulation of muscle contraction -0.017 0.12 0.22 13 -0.32 14 27
Gq family/GDP -0.004 0.13 -10000 0 -0.46 9 9
HRAS/GTP -0.031 0.14 0.3 3 -0.52 12 15
PRKCH -0.003 0.1 0.24 1 -0.49 6 7
RAC1 0.026 0.007 -10000 0 -10000 0 0
PRKCA -0.007 0.11 -10000 0 -0.51 7 7
PRKCB -0.014 0.12 -10000 0 -0.49 11 11
PRKCE -0.006 0.11 0.27 2 -0.51 7 9
PRKCD -0.002 0.093 -10000 0 -0.54 4 4
PRKCG -0.05 0.13 0.22 4 -0.43 13 17
regulation of vascular smooth muscle contraction -0.064 0.26 0.4 1 -0.97 18 19
PRKCQ -0.008 0.1 -10000 0 -0.54 6 6
PLA2G4A -0.031 0.18 0.43 1 -0.55 19 20
GNA14 0.021 0.046 -10000 0 -0.34 4 4
GNA15 0.025 0.027 -10000 0 -0.28 2 2
GNA12 0.026 0.007 -10000 0 -10000 0 0
GNA11 0.027 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.019 0.15 0.32 5 -0.34 14 19
MMP1 -0.094 0.17 0.4 2 -0.31 71 73
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.042 0.03 -10000 0 -0.17 4 4
RGS9BP -0.02 0.12 -10000 0 -0.37 31 31
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.019 0.019 -10000 0 -0.28 1 1
mol:Na + -0.015 0.093 -10000 0 -0.2 54 54
mol:ADP -0.009 0.025 -10000 0 -0.19 4 4
GNAT2 0.023 0.036 -10000 0 -0.31 3 3
RGS9-1/Gbeta5/R9AP 0.005 0.11 -10000 0 -0.25 39 39
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.027 0.031 -10000 0 -0.17 6 6
GRK7 0.023 0.027 -10000 0 -0.28 2 2
CNGB3 -0.005 0.087 -10000 0 -0.28 25 25
Cone Metarhodopsin II/X-Arrestin 0.02 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.037 0.11 0.18 19 -0.24 33 52
Cone PDE6 0.022 0.1 -10000 0 -0.21 39 39
Cone Metarhodopsin II 0.025 0.022 -10000 0 -0.14 4 4
Na + (4 Units) -0.031 0.11 -10000 0 -0.18 83 83
GNAT2/GDP 0.015 0.099 -10000 0 -0.21 40 40
GNB5 0.027 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) -0.001 0.037 0.18 6 -0.16 3 9
Cone Transducin 0.046 0.032 -10000 0 -0.18 4 4
SLC24A2 -0.023 0.11 -10000 0 -0.29 41 41
GNB3/GNGT2 0.037 0.026 -10000 0 -0.35 1 1
GNB3 0.025 0.019 -10000 0 -0.28 1 1
GNAT2/GTP 0.017 0.024 -10000 0 -0.21 3 3
CNGA3 -0.029 0.14 -10000 0 -0.36 39 39
ARR3 0.027 0.004 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel -0.015 0.093 -10000 0 -0.2 54 54
mol:Pi 0.005 0.11 -10000 0 -0.24 39 39
Cone CNG Channel 0.004 0.093 -10000 0 -0.2 28 28
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + -0.023 0.11 -10000 0 -0.29 41 41
RGS9 0.003 0.095 -10000 0 -0.36 17 17
PDE6C 0.026 0.005 -10000 0 -10000 0 0
GNGT2 0.026 0.019 -10000 0 -0.28 1 1
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.017 0.032 -10000 0 -0.28 3 3
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.028 0.06 -10000 0 -0.19 9 9
alphaM/beta2 Integrin/GPIbA 0.014 0.08 -10000 0 -0.21 22 22
alphaM/beta2 Integrin/proMMP-9 -0.028 0.1 -10000 0 -0.17 73 73
PLAUR 0.024 0.027 -10000 0 -0.28 2 2
HMGB1 0.016 0.028 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.028 0.059 -10000 0 -0.19 8 8
AGER 0.015 0.03 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
SELPLG 0.027 0.004 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.023 0.099 -10000 0 -0.29 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.06 0.13 -10000 0 -0.28 74 74
CYR61 0.022 0.043 -10000 0 -0.32 4 4
TLN1 0.026 0.007 -10000 0 -10000 0 0
Rap1/GTP -0.024 0.083 -10000 0 -0.29 7 7
RHOA 0.027 0.005 -10000 0 -10000 0 0
P-selectin oligomer -0.016 0.12 -10000 0 -0.37 29 29
MYH2 -0.045 0.089 -10000 0 -0.28 18 18
MST1R 0.021 0.045 -10000 0 -0.35 4 4
leukocyte activation during inflammatory response -0.053 0.12 -10000 0 -0.2 88 88
APOB -0.13 0.18 -10000 0 -0.34 112 112
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.025 0.02 -10000 0 -0.28 1 1
JAM3 0.025 0.019 -10000 0 -0.28 1 1
GP1BA 0.004 0.087 -10000 0 -0.34 16 16
alphaM/beta2 Integrin/CTGF 0.027 0.065 -10000 0 -0.2 11 11
alphaM/beta2 Integrin -0.037 0.08 -10000 0 -0.25 17 17
JAM3 homodimer 0.025 0.019 -10000 0 -0.28 1 1
ICAM2 0.026 0.019 -10000 0 -0.28 1 1
ICAM1 0.016 0.058 -10000 0 -0.28 10 10
phagocytosis triggered by activation of immune response cell surface activating receptor -0.036 0.081 -10000 0 -0.25 16 16
cell adhesion 0.014 0.08 -10000 0 -0.21 22 22
NFKB1 -0.014 0.14 0.38 1 -0.37 27 28
THY1 -0.009 0.097 -10000 0 -0.28 31 31
RhoA/GDP 0.02 0.004 -10000 0 -10000 0 0
Lipoprotein(a) -0.065 0.12 -10000 0 -0.2 115 115
alphaM/beta2 Integrin/LRP/tPA 0.04 0.06 -10000 0 -0.22 4 4
IL6 -0.045 0.19 -10000 0 -0.54 27 27
ITGB2 0.009 0.051 -10000 0 -0.29 5 5
elevation of cytosolic calcium ion concentration 0.023 0.082 -10000 0 -0.21 11 11
alphaM/beta2 Integrin/JAM2/JAM3 0.03 0.08 -10000 0 -0.2 18 18
JAM2 0.005 0.09 -10000 0 -0.37 15 15
alphaM/beta2 Integrin/ICAM1 0.035 0.085 -10000 0 -0.26 5 5
alphaM/beta2 Integrin/uPA/Plg 0.022 0.083 -10000 0 -0.21 11 11
RhoA/GTP -0.048 0.092 -10000 0 -0.28 20 20
positive regulation of phagocytosis -0.02 0.075 -10000 0 -0.31 5 5
Ron/MSP 0.025 0.058 -10000 0 -0.2 16 16
alphaM/beta2 Integrin/uPAR/uPA 0.024 0.083 -10000 0 -0.21 11 11
alphaM/beta2 Integrin/uPAR 0.027 0.061 -10000 0 -0.23 4 4
PLAU 0 0.087 -10000 0 -0.28 24 24
PLAT 0.023 0.025 -10000 0 -0.37 1 1
actin filament polymerization -0.043 0.087 -10000 0 -0.27 18 18
MST1 0.013 0.063 -10000 0 -0.28 12 12
alphaM/beta2 Integrin/lipoprotein(a) -0.051 0.12 -10000 0 -0.2 88 88
TNF -0.03 0.15 -10000 0 -0.4 26 26
RAP1B 0.026 0.006 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.011 0.082 -10000 0 -0.18 31 31
fibrinolysis 0.02 0.082 -10000 0 -0.21 11 11
HCK 0.025 0.009 -10000 0 -10000 0 0
dendritic cell antigen processing and presentation -0.036 0.081 -10000 0 -0.25 16 16
VTN -0.011 0.11 -10000 0 -0.3 31 31
alphaM/beta2 Integrin/CYR61 0.026 0.067 -10000 0 -0.2 12 12
LPA 0.017 0.045 -10000 0 -0.28 6 6
LRP1 0.027 0.004 -10000 0 -10000 0 0
cell migration -0.027 0.089 -10000 0 -0.22 14 14
FN1 -0.058 0.14 -10000 0 -0.28 76 76
alphaM/beta2 Integrin/Thy1 0.006 0.085 -10000 0 -0.18 31 31
MPO 0.024 0.03 -10000 0 -0.32 2 2
KNG1 -0.021 0.11 -10000 0 -0.28 41 41
RAP1/GDP 0.035 0.01 -10000 0 -10000 0 0
ROCK1 -0.043 0.088 -10000 0 -0.27 18 18
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.022 0.019 -10000 0 -0.28 1 1
CTGF 0.023 0.039 -10000 0 -0.34 3 3
alphaM/beta2 Integrin/Hck 0.027 0.055 -10000 0 -0.19 7 7
ITGAM 0.012 0.047 -10000 0 -0.29 4 4
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.018 0.097 -10000 0 -0.21 32 32
HP -0.028 0.12 -10000 0 -0.3 44 44
leukocyte adhesion -0.005 0.098 -10000 0 -0.29 7 7
SELP -0.016 0.12 -10000 0 -0.37 29 29
HIF-1-alpha transcription factor network

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
PKM2 -0.18 0.28 0.4 1 -0.76 19 20
HDAC7 0.024 0.013 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.15 0.3 -10000 0 -0.83 18 18
SMAD4 0.024 0.01 -10000 0 -10000 0 0
ID2 -0.18 0.28 0.4 1 -0.76 19 20
AP1 0.022 0.072 -10000 0 -0.27 15 15
ABCG2 -0.18 0.29 0.4 1 -0.75 27 28
HIF1A -0.033 0.069 -10000 0 -0.22 2 2
TFF3 -0.23 0.31 0.4 1 -0.75 39 40
GATA2 0.025 0.026 -10000 0 -0.37 1 1
AKT1 -0.037 0.08 -10000 0 -0.23 11 11
response to hypoxia -0.045 0.066 -10000 0 -0.21 15 15
MCL1 -0.18 0.28 -10000 0 -0.76 19 19
NDRG1 -0.16 0.27 0.4 1 -0.78 17 18
SERPINE1 -0.19 0.28 0.4 1 -0.76 22 23
FECH -0.18 0.28 0.4 1 -0.76 19 20
FURIN -0.18 0.28 0.4 1 -0.77 18 19
NCOA2 0.024 0.011 -10000 0 -10000 0 0
EP300 -0.037 0.1 -10000 0 -0.34 16 16
HMOX1 -0.18 0.28 0.4 1 -0.76 20 21
BHLHE40 -0.18 0.28 0.4 1 -0.76 19 20
BHLHE41 -0.17 0.28 -10000 0 -0.76 19 19
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.005 0.098 -10000 0 -10000 0 0
ENG -0.015 0.082 0.29 2 -10000 0 2
JUN 0.026 0.025 -10000 0 -0.37 1 1
RORA -0.18 0.28 0.4 1 -0.76 20 21
ABCB1 -0.054 0.14 -10000 0 -0.7 8 8
TFRC -0.18 0.28 0.4 1 -0.77 19 20
CXCR4 -0.18 0.28 0.4 1 -0.76 20 21
TF -0.22 0.32 0.4 1 -0.76 39 40
CITED2 -0.18 0.28 0.4 1 -0.78 18 19
HIF1A/ARNT -0.17 0.34 -10000 0 -0.85 18 18
LDHA -0.024 0.12 -10000 0 -0.71 6 6
ETS1 -0.18 0.28 0.4 1 -0.76 19 20
PGK1 -0.18 0.28 0.4 1 -0.77 18 19
NOS2 -0.19 0.3 0.4 1 -0.77 26 27
ITGB2 -0.18 0.28 0.4 1 -0.75 21 22
ALDOA -0.18 0.28 0.4 1 -0.77 18 19
Cbp/p300/CITED2 -0.19 0.32 0.4 1 -0.89 22 23
FOS 0.005 0.09 -10000 0 -0.36 15 15
HK2 -0.18 0.29 0.4 1 -0.77 22 23
SP1 0.029 0.02 -10000 0 -0.14 1 1
GCK -0.089 0.29 -10000 0 -1.1 18 18
HK1 -0.18 0.28 0.4 1 -0.78 17 18
NPM1 -0.18 0.28 0.4 1 -0.77 18 19
EGLN1 -0.18 0.28 -10000 0 -0.76 19 19
CREB1 0.032 0.003 -10000 0 -10000 0 0
PGM1 -0.18 0.29 0.4 1 -0.77 21 22
SMAD3 0.028 0.005 -10000 0 -10000 0 0
EDN1 -0.058 0.18 -10000 0 -0.62 14 14
IGFBP1 -0.21 0.3 0.4 1 -0.75 29 30
VEGFA -0.14 0.25 0.36 1 -0.74 16 17
HIF1A/JAB1 -0.004 0.053 -10000 0 -10000 0 0
CP -0.18 0.29 0.4 1 -0.75 22 23
CXCL12 -0.19 0.29 0.4 1 -0.77 24 25
COPS5 0.024 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4 0.036 0.015 -10000 0 -10000 0 0
BNIP3 -0.18 0.28 0.4 1 -0.76 21 22
EGLN3 -0.18 0.28 0.4 1 -0.77 18 19
CA9 -0.23 0.31 0.4 1 -0.77 33 34
TERT -0.2 0.3 0.4 1 -0.76 30 31
ENO1 -0.18 0.28 0.4 1 -0.76 19 20
PFKL -0.18 0.28 0.4 1 -0.76 19 20
NCOA1 0.027 0.004 -10000 0 -10000 0 0
ADM -0.18 0.28 0.4 1 -0.76 21 22
ARNT -0.028 0.065 -10000 0 -10000 0 0
HNF4A 0.01 0.062 -10000 0 -0.34 7 7
ADFP -0.19 0.27 -10000 0 -0.71 27 27
SLC2A1 -0.16 0.27 0.36 1 -0.72 25 26
LEP -0.19 0.29 0.4 1 -0.75 24 25
HIF1A/ARNT/Cbp/p300 -0.16 0.3 -10000 0 -0.84 19 19
EPO -0.093 0.2 -10000 0 -0.73 5 5
CREBBP -0.039 0.11 -10000 0 -0.34 18 18
HIF1A/ARNT/Cbp/p300/HDAC7 -0.15 0.3 -10000 0 -0.85 19 19
PFKFB3 -0.17 0.28 0.4 1 -0.76 18 19
NT5E -0.18 0.29 0.4 1 -0.77 22 23
Glypican 2 network

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
MDK 0.021 0.044 -9999 0 -0.3 5 5
GPC2 0.004 0.078 -9999 0 -0.28 19 19
GPC2/Midkine 0.018 0.065 -9999 0 -0.2 21 21
neuron projection morphogenesis 0.018 0.065 -9999 0 -0.2 21 21
LPA receptor mediated events

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
GNB1/GNG2 0.036 0.061 -10000 0 -0.19 15 15
NF kappa B1 p50/RelA/I kappa B alpha -0.019 0.11 -10000 0 -0.35 7 7
AP1 -0.029 0.097 -10000 0 -0.2 38 38
mol:PIP3 -0.029 0.084 -10000 0 -0.33 7 7
AKT1 0.015 0.07 0.28 4 -0.28 3 7
PTK2B -0.02 0.084 0.2 1 -0.27 17 18
RHOA 0.002 0.072 0.21 4 -0.39 6 10
PIK3CB 0.027 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.026 0.088 0.23 3 -0.48 3 6
MAGI3 0.027 0.005 -10000 0 -10000 0 0
RELA 0.027 0.004 -10000 0 -10000 0 0
apoptosis -0.033 0.097 -10000 0 -0.22 57 57
HRAS/GDP 0.02 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.035 0.1 0.2 8 -0.31 12 20
NF kappa B1 p50/RelA -0.041 0.099 -10000 0 -0.35 7 7
endothelial cell migration 0.003 0.056 -10000 0 -0.21 17 17
ADCY4 -0.019 0.098 -10000 0 -0.35 17 17
ADCY5 -0.057 0.14 -10000 0 -0.4 31 31
ADCY6 -0.019 0.098 -10000 0 -0.34 17 17
ADCY7 -0.02 0.097 -10000 0 -0.35 17 17
ADCY1 -0.022 0.096 -10000 0 -0.35 17 17
ADCY2 -0.031 0.11 -10000 0 -0.38 20 20
ADCY3 -0.02 0.098 -10000 0 -0.35 17 17
ADCY8 -0.021 0.09 -10000 0 -0.32 17 17
ADCY9 -0.02 0.099 -10000 0 -0.34 18 18
GSK3B -0.017 0.083 0.19 5 -0.29 12 17
arachidonic acid secretion -0.023 0.1 -10000 0 -0.33 20 20
GNG2 0.025 0.019 -10000 0 -0.28 1 1
TRIP6 0.018 0.009 -10000 0 -10000 0 0
GNAO1 -0.015 0.08 -10000 0 -0.21 38 38
HRAS 0.026 0.006 -10000 0 -10000 0 0
NFKBIA -0.039 0.11 0.3 1 -0.37 8 9
GAB1 0.025 0.025 -10000 0 -0.37 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.003 0.19 -10000 0 -0.79 14 14
JUN 0.025 0.024 -10000 0 -0.37 1 1
LPA/LPA2/NHERF2 0.035 0.012 -10000 0 -10000 0 0
TIAM1 -0.014 0.21 -10000 0 -0.92 14 14
PIK3R1 0.026 0.007 -10000 0 -10000 0 0
mol:IP3 -0.024 0.074 0.21 4 -0.26 1 5
PLCB3 0.017 0.021 0.18 4 -10000 0 4
FOS 0.005 0.089 -10000 0 -0.36 15 15
positive regulation of mitosis -0.023 0.1 -10000 0 -0.33 20 20
LPA/LPA1-2-3 -0.004 0.1 -10000 0 -0.2 54 54
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.026 0.007 -10000 0 -10000 0 0
stress fiber formation -0.019 0.1 0.25 1 -0.35 13 14
GNAZ -0.006 0.072 -10000 0 -0.22 27 27
EGFR/PI3K-beta/Gab1 -0.02 0.092 -10000 0 -0.35 7 7
positive regulation of dendritic cell cytokine production -0.005 0.1 -10000 0 -0.2 54 54
LPA/LPA2/MAGI-3 0.036 0.011 -10000 0 -10000 0 0
ARHGEF1 0.017 0.063 0.19 17 -0.19 1 18
GNAI2 0.005 0.053 -10000 0 -0.21 15 15
GNAI3 0.005 0.051 -10000 0 -0.21 14 14
GNAI1 0 0.066 -10000 0 -0.24 17 17
LPA/LPA3 -0.028 0.1 -10000 0 -0.25 49 49
LPA/LPA2 0.021 0.006 -10000 0 -10000 0 0
LPA/LPA1 0.008 0.065 -10000 0 -0.24 17 17
HB-EGF/EGFR -0.03 0.083 -10000 0 -0.16 71 71
HBEGF -0.044 0.089 -10000 0 -0.19 73 73
mol:DAG -0.024 0.074 0.21 4 -0.26 1 5
cAMP biosynthetic process -0.032 0.12 0.34 3 -0.34 21 24
NFKB1 0.027 0.005 -10000 0 -10000 0 0
SRC 0.024 0.009 -10000 0 -10000 0 0
GNB1 0.026 0.007 -10000 0 -10000 0 0
LYN -0.031 0.11 0.32 2 -0.34 10 12
GNAQ -0.02 0.081 -10000 0 -0.2 43 43
LPAR2 0.027 0.005 -10000 0 -10000 0 0
LPAR3 -0.044 0.15 -10000 0 -0.36 48 48
LPAR1 0.005 0.093 -10000 0 -0.36 16 16
IL8 -0.12 0.13 -10000 0 -0.38 21 21
PTK2 -0.025 0.077 0.18 1 -0.22 5 6
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
CASP3 -0.033 0.098 -10000 0 -0.22 57 57
EGFR 0.012 0.069 -10000 0 -0.36 9 9
PLCG1 -0.025 0.082 0.16 1 -0.21 41 42
PLD2 -0.029 0.083 0.18 2 -0.29 3 5
G12/G13 0.037 0.06 -10000 0 -0.19 16 16
PI3K-beta 0.006 0.059 -10000 0 -0.32 3 3
cell migration -0.002 0.071 0.18 1 -0.24 12 13
SLC9A3R2 0.026 0.006 -10000 0 -10000 0 0
PXN -0.02 0.1 0.25 1 -0.36 13 14
HRAS/GTP -0.022 0.1 -10000 0 -0.34 18 18
RAC1 0.026 0.007 -10000 0 -10000 0 0
MMP9 -0.061 0.13 -10000 0 -0.28 74 74
PRKCE 0.027 0.004 -10000 0 -10000 0 0
PRKCD -0.029 0.085 0.21 3 -0.45 3 6
Gi(beta/gamma) -0.013 0.09 -10000 0 -0.31 17 17
mol:LPA 0.002 0.006 -10000 0 -10000 0 0
TRIP6/p130 Cas/FAK1/Paxillin -0.01 0.097 -10000 0 -0.35 6 6
MAPKKK cascade -0.023 0.1 -10000 0 -0.33 20 20
contractile ring contraction involved in cytokinesis 0.003 0.075 0.21 4 -0.37 7 11
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.023 0.083 -10000 0 -0.2 46 46
GNA15 -0.021 0.081 -10000 0 -0.2 44 44
GNA12 0.026 0.007 -10000 0 -10000 0 0
GNA13 0.027 0.004 -10000 0 -10000 0 0
MAPT -0.036 0.1 0.2 8 -0.32 12 20
GNA11 -0.02 0.08 -10000 0 -0.2 42 42
Rac1/GTP 0.002 0.2 -10000 0 -0.83 14 14
MMP2 0.003 0.056 -10000 0 -0.21 17 17
TCGA08_retinoblastoma

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
CDKN2B 0.018 0.051 -10000 0 -0.31 6 6
CDKN2C 0.031 0.02 -10000 0 -10000 0 0
CDKN2A -0.046 0.13 -10000 0 -0.28 62 62
CCND2 0.013 0.039 0.15 9 -10000 0 9
RB1 -0.014 0.039 -10000 0 -0.17 6 6
CDK4 0.016 0.042 0.16 9 -10000 0 9
CDK6 0.016 0.043 0.15 11 -10000 0 11
G1/S progression 0.027 0.063 0.18 26 -0.28 1 27
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.035 0.021 -10000 0 -10000 0 0
PDGF/PDGFRA/CRKL 0.044 0.02 -10000 0 -10000 0 0
positive regulation of JUN kinase activity 0.068 0.024 -10000 0 -10000 0 0
CRKL 0.027 0.005 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 0.04 0.02 -10000 0 -10000 0 0
AP1 0.1 0.19 0.34 16 -0.63 13 29
mol:IP3 0.027 0.026 0.12 2 -10000 0 2
PLCG1 0.027 0.026 0.12 2 -10000 0 2
PDGF/PDGFRA/alphaV Integrin 0.044 0.02 -10000 0 -10000 0 0
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0.027 0.026 0.12 2 -10000 0 2
CAV3 0.022 0.006 -10000 0 -10000 0 0
CAV1 0.023 0.027 -10000 0 -0.28 2 2
SHC/Grb2/SOS1 0.07 0.025 -10000 0 -10000 0 0
PDGF/PDGFRA/Shf 0.035 0.055 -10000 0 -0.26 8 8
FOS 0.097 0.19 0.31 24 -0.62 13 37
JUN 0.21 0.14 0.3 192 -10000 0 192
oligodendrocyte development 0.043 0.02 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
PIK3R1 0.026 0.007 -10000 0 -10000 0 0
mol:DAG 0.027 0.026 0.12 2 -10000 0 2
PDGF/PDGFRA 0.035 0.021 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.042 0.021 -10000 0 -10000 0 0
SRF -0.16 0.12 -10000 0 -0.25 184 184
SHC1 0.026 0.006 -10000 0 -10000 0 0
PI3K 0.054 0.023 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk/C3G 0.056 0.022 -10000 0 -10000 0 0
JAK1 0.021 0.014 -10000 0 -10000 0 0
ELK1/SRF -0.085 0.065 0.15 2 -0.2 4 6
SHB 0.026 0.007 -10000 0 -10000 0 0
SHF 0.015 0.067 -10000 0 -0.37 8 8
CSNK2A1 -0.24 0.16 -10000 0 -0.35 195 195
GO:0007205 0.022 0.024 0.12 2 -10000 0 2
SOS1 0.027 0.003 -10000 0 -10000 0 0
Ras protein signal transduction 0.068 0.024 -10000 0 -10000 0 0
PDGF/PDGFRA/SHB 0.042 0.021 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-1 0.04 0.029 -10000 0 -0.18 2 2
ITGAV 0.027 0.005 -10000 0 -10000 0 0
ELK1 0.024 0.029 -10000 0 -10000 0 0
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk 0.043 0.02 -10000 0 -10000 0 0
JAK-STAT cascade 0.021 0.014 -10000 0 -10000 0 0
cell proliferation 0.034 0.055 -10000 0 -0.26 8 8
TCGA08_p53

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
CDKN2A -0.039 0.081 -10000 0 -0.19 62 62
TP53 -0.014 0.054 0.15 1 -0.24 12 13
Senescence -0.016 0.055 0.15 1 -0.24 12 13
Apoptosis -0.016 0.055 0.15 1 -0.24 12 13
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.022 0.073 0.33 7 -0.25 3 10
MDM4 0.027 0.005 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.022 0.14 0.28 10 -0.42 15 25
FYN 0 0.16 0.28 9 -0.52 15 24
LAT/GRAP2/SLP76 0.018 0.14 0.25 8 -0.44 15 23
IKBKB 0.025 0.008 -10000 0 -10000 0 0
AKT1 -0.004 0.12 0.24 7 -0.37 18 25
B2M 0.027 0.006 -10000 0 -10000 0 0
IKBKG -0.003 0.039 0.092 6 -0.13 6 12
MAP3K8 0.026 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.018 0.018 -10000 0 -0.079 6 6
integrin-mediated signaling pathway 0.033 0.018 -10000 0 -0.21 1 1
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.005 0.16 0.27 9 -0.54 15 24
TRPV6 -0.098 0.23 1.2 4 -0.37 82 86
CD28 0.022 0.044 -10000 0 -0.3 5 5
SHC1 -0.003 0.16 0.27 10 -0.49 18 28
receptor internalization -0.01 0.17 0.23 1 -0.53 20 21
PRF1 0.002 0.16 -10000 0 -0.77 8 8
KRAS 0.024 0.009 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
COT/AKT1 0.011 0.097 0.21 6 -0.29 14 20
LAT -0.004 0.16 0.26 8 -0.52 17 25
EntrezGene:6955 0 0.002 -10000 0 -10000 0 0
CD3D 0.019 0.054 -10000 0 -0.38 5 5
CD3E 0.024 0.035 -10000 0 -0.38 2 2
CD3G 0.022 0.042 -10000 0 -0.37 3 3
RASGRP2 0.007 0.03 0.072 3 -0.15 7 10
RASGRP1 0.011 0.13 0.29 8 -0.39 15 23
HLA-A 0.026 0.025 -10000 0 -0.37 1 1
RASSF5 0.025 0.025 -10000 0 -0.37 1 1
RAP1A/GTP/RAPL 0.034 0.018 -10000 0 -0.22 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.028 0.056 0.14 22 -0.12 10 32
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.015 0.054 -10000 0 -0.19 14 14
PRKCA 0.017 0.077 0.16 30 -0.23 8 38
GRAP2 0.024 0.034 -10000 0 -0.37 2 2
mol:IP3 0.03 0.12 0.19 58 -0.32 13 71
EntrezGene:6957 0.001 0.002 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.005 0.14 -10000 0 -0.59 11 11
ORAI1 0.049 0.16 0.49 3 -0.98 4 7
CSK -0.005 0.16 0.24 8 -0.51 18 26
B7 family/CD28 0.01 0.15 0.27 4 -0.46 15 19
CHUK 0.027 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.015 0.17 0.21 1 -0.57 18 19
PTPN6 -0.01 0.15 0.24 6 -0.5 17 23
VAV1 -0.01 0.16 0.24 7 -0.51 18 25
Monovalent TCR/CD3 0.008 0.086 -10000 0 -0.39 9 9
CBL 0.026 0.007 -10000 0 -10000 0 0
LCK -0.004 0.16 0.28 9 -0.54 15 24
PAG1 0 0.16 0.25 7 -0.5 18 25
RAP1A 0.027 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.015 0.17 0.21 1 -0.55 18 19
CD80 -0.028 0.12 -10000 0 -0.28 49 49
CD86 0.025 0.027 -10000 0 -0.28 2 2
PDK1/CARD11/BCL10/MALT1 -0.008 0.07 -10000 0 -0.22 14 14
HRAS 0.026 0.006 -10000 0 -10000 0 0
GO:0035030 -0.014 0.12 0.22 6 -0.4 15 21
CD8A 0.01 0.084 -10000 0 -0.37 13 13
CD8B 0.006 0.092 -10000 0 -0.35 17 17
PTPRC 0.017 0.055 -10000 0 -0.28 9 9
PDK1/PKC theta -0.005 0.14 0.34 6 -0.46 15 21
CSK/PAG1 -0.001 0.16 0.22 14 -0.51 16 30
SOS1 0.027 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.038 0.022 -10000 0 -0.26 1 1
GRAP2/SLP76 0.017 0.16 0.27 4 -0.49 17 21
STIM1 0.032 0.12 1.3 2 -10000 0 2
RAS family/GTP 0.026 0.072 0.18 16 -0.18 12 28
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.013 0.18 -10000 0 -0.56 20 20
mol:DAG -0.002 0.084 0.11 1 -0.28 15 16
RAP1A/GDP 0.017 0.027 0.074 18 -0.062 2 20
PLCG1 0.024 0.01 -10000 0 -10000 0 0
CD247 0.018 0.059 -10000 0 -0.37 6 6
cytotoxic T cell degranulation 0.003 0.16 -10000 0 -0.74 8 8
RAP1A/GTP 0.002 0.011 -10000 0 -0.057 7 7
mol:PI-3-4-5-P3 0.001 0.14 0.26 9 -0.45 15 24
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.034 0.14 0.2 55 -0.41 13 68
NRAS 0.027 0.005 -10000 0 -10000 0 0
ZAP70 0.018 0.057 -10000 0 -0.33 7 7
GRB2/SOS1 0.039 0.008 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.009 0.13 0.24 4 -0.43 15 19
MALT1 0.024 0.02 -10000 0 -0.28 1 1
TRAF6 0.027 0.005 -10000 0 -10000 0 0
CD8 heterodimer 0.014 0.11 -10000 0 -0.35 20 20
CARD11 0.001 0.084 -10000 0 -0.28 22 22
PRKCB 0.009 0.085 0.16 17 -0.27 12 29
PRKCE 0.016 0.079 0.15 31 -0.24 8 39
PRKCQ 0.001 0.16 0.3 8 -0.52 15 23
LCP2 0.026 0.006 -10000 0 -10000 0 0
BCL10 0.027 0.004 -10000 0 -10000 0 0
regulation of survival gene product expression 0 0.11 0.22 8 -0.31 18 26
IKK complex 0.02 0.057 0.13 32 -0.12 5 37
RAS family/GDP 0.001 0.008 -10000 0 -10000 0 0
MAP3K14 0.006 0.076 0.16 8 -0.23 13 21
PDPK1 -0.006 0.12 0.25 8 -0.36 16 24
TCR/CD3/MHC I/CD8/Fyn -0.02 0.2 -10000 0 -0.68 18 18
PLK2 and PLK4 events

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
PLK2 0.019 0.045 -9999 0 -0.28 6 6
PLK4 0.007 0.074 -9999 0 -0.28 17 17
regulation of centriole replication -0.004 0.06 -9999 0 -0.21 20 20
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.027 0.005 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.015 0.072 -10000 0 -0.24 12 12
NT3 (dimer)/TRKC -0.029 0.13 -10000 0 -0.27 59 59
NT3 (dimer)/TRKB -0.067 0.17 -10000 0 -0.28 96 96
SHC/Grb2/SOS1/GAB1/PI3K 0.025 0.018 -10000 0 -0.19 1 1
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
BDNF 0.02 0.045 -10000 0 -0.28 6 6
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
DYNLT1 0.026 0.006 -10000 0 -10000 0 0
NTRK1 0.022 0.042 -10000 0 -0.37 3 3
NTRK2 -0.034 0.14 -10000 0 -0.36 43 43
NTRK3 -0.034 0.14 -10000 0 -0.36 42 42
NT-4/5 (dimer)/TRKB -0.062 0.16 -10000 0 -0.24 102 102
neuron apoptosis 0.067 0.16 0.37 46 -10000 0 46
SHC 2-3/Grb2 -0.073 0.18 -10000 0 -0.4 46 46
SHC1 0.026 0.006 -10000 0 -10000 0 0
SHC2 -0.086 0.19 -10000 0 -0.42 53 53
SHC3 -0.076 0.17 -10000 0 -0.39 49 49
STAT3 (dimer) 0.025 0.043 -10000 0 -0.23 7 7
NT3 (dimer)/TRKA -0.036 0.13 -10000 0 -0.23 83 83
RIN/GDP 0.006 0.09 0.21 9 -0.25 7 16
GIPC1 0.027 0.004 -10000 0 -10000 0 0
KRAS 0.024 0.009 -10000 0 -10000 0 0
DNAJA3 -0.061 0.13 -10000 0 -0.27 64 64
RIN/GTP 0.013 0.013 -10000 0 -0.19 1 1
CCND1 0.016 0.018 -10000 0 -0.26 1 1
MAGED1 0.024 0.034 -10000 0 -0.37 2 2
PTPN11 0.027 0.004 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.004 0.08 -10000 0 -0.28 20 20
SHC/GRB2/SOS1 0.052 0.015 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.023 0.082 -10000 0 -0.21 28 28
TRKA/NEDD4-2 0.031 0.038 -10000 0 -0.26 4 4
ELMO1 0.025 0.019 -10000 0 -0.28 1 1
RhoG/GTP/ELMO1/DOCK1 0.034 0.015 -10000 0 -0.16 1 1
NGF -0.009 0.11 -10000 0 -0.36 25 25
HRAS 0.026 0.006 -10000 0 -10000 0 0
DOCK1 0.027 0.005 -10000 0 -10000 0 0
GAB2 0.027 0.005 -10000 0 -10000 0 0
RIT2 0.018 0.019 -10000 0 -0.28 1 1
RIT1 0.027 0.005 -10000 0 -10000 0 0
FRS2 0.026 0.006 -10000 0 -10000 0 0
DNM1 0.017 0.052 -10000 0 -0.28 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.048 0.13 -10000 0 -0.28 53 53
mol:GDP -0.003 0.12 0.26 8 -0.36 9 17
NGF (dimer) -0.009 0.11 -10000 0 -0.36 25 25
RhoG/GDP 0.019 0.013 -10000 0 -0.19 1 1
RIT1/GDP 0.004 0.086 0.18 5 -0.25 6 11
TIAM1 0.024 0.031 -10000 0 -0.32 2 2
PIK3R1 0.026 0.007 -10000 0 -10000 0 0
BDNF (dimer)/TRKB 0.006 0.099 -10000 0 -0.2 47 47
KIDINS220/CRKL/C3G 0.039 0.01 -10000 0 -10000 0 0
SHC/RasGAP 0.036 0.014 -10000 0 -10000 0 0
FRS2 family/SHP2 0.05 0.018 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.062 0.028 -10000 0 -0.2 1 1
RIT1/GTP 0.02 0.004 -10000 0 -10000 0 0
NT3 (dimer) -0.004 0.1 -10000 0 -0.36 21 21
RAP1/GDP 0 0.07 0.12 3 -0.21 6 9
KIDINS220/CRKL 0.027 0.005 -10000 0 -10000 0 0
BDNF (dimer) 0.02 0.045 -10000 0 -0.28 6 6
ubiquitin-dependent protein catabolic process 0.02 0.081 -10000 0 -0.21 28 28
Schwann cell development -0.021 0.026 -10000 0 -10000 0 0
EHD4 0.027 0.005 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.062 0.024 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.026 0.04 -10000 0 -0.33 1 1
RAP1B 0.026 0.006 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.03 0.12 -10000 0 -0.33 22 22
ABL1 0.027 0.005 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.039 0.008 -10000 0 -10000 0 0
Rap1/GTP 0.013 0.076 -10000 0 -0.42 4 4
STAT3 0.025 0.043 -10000 0 -0.23 7 7
axon guidance -0.037 0.12 -10000 0 -0.32 22 22
MAPK3 -0.004 0.069 0.18 6 -0.2 26 32
MAPK1 -0.003 0.069 0.18 7 -0.2 25 32
CDC42/GDP 0.008 0.091 0.21 9 -0.25 7 16
NTF3 -0.004 0.1 -10000 0 -0.36 21 21
NTF4 0.004 0.08 -10000 0 -0.28 20 20
NGF (dimer)/TRKA/FAIM 0.024 0.081 -10000 0 -0.22 27 27
PI3K 0.036 0.014 -10000 0 -10000 0 0
FRS3 0.026 0.006 -10000 0 -10000 0 0
FAIM 0.027 0.005 -10000 0 -10000 0 0
GAB1 0.025 0.025 -10000 0 -0.37 1 1
RASGRF1 -0.067 0.13 -10000 0 -0.27 64 64
SOS1 0.027 0.003 -10000 0 -10000 0 0
MCF2L -0.035 0.1 -10000 0 -0.23 54 54
RGS19 0.021 0.021 -10000 0 -0.28 1 1
CDC42 0.026 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.012 0.094 -10000 0 -0.45 4 4
Rac1/GDP 0.004 0.088 0.2 7 -0.25 7 14
NGF (dimer)/TRKA/GRIT 0.01 0.074 -10000 0 -0.21 27 27
neuron projection morphogenesis -0.055 0.15 -10000 0 -0.67 4 4
NGF (dimer)/TRKA/NEDD4-2 0.02 0.082 -10000 0 -0.21 28 28
MAP2K1 0.001 0.057 0.21 16 -10000 0 16
NGFR -0.074 0.17 -10000 0 -0.35 72 72
NGF (dimer)/TRKA/GIPC/GAIP 0.004 0.06 -10000 0 -0.19 20 20
RAS family/GTP/PI3K 0.02 0.012 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.071 0.029 -10000 0 -10000 0 0
NRAS 0.027 0.005 -10000 0 -10000 0 0
GRB2/SOS1 0.039 0.008 -10000 0 -10000 0 0
PRKCI 0.023 0.027 -10000 0 -0.28 2 2
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.026 0.007 -10000 0 -10000 0 0
PRKCZ 0.026 0.007 -10000 0 -10000 0 0
MAPKKK cascade -0.059 0.19 -10000 0 -0.54 35 35
RASA1 0.025 0.008 -10000 0 -10000 0 0
TRKA/c-Abl 0.035 0.033 -10000 0 -0.26 3 3
SQSTM1 0.026 0.006 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.02 0.097 -10000 0 -0.2 37 37
NGF (dimer)/TRKA/p62/Atypical PKCs 0.041 0.078 -10000 0 -0.19 22 22
MATK 0.023 0.034 -10000 0 -0.37 2 2
NEDD4L 0.023 0.025 -10000 0 -0.37 1 1
RAS family/GDP -0.025 0.045 -10000 0 -0.17 5 5
NGF (dimer)/TRKA -0.064 0.13 -10000 0 -0.27 69 69
Rac1/GTP -0.05 0.092 -10000 0 -0.23 32 32
FRS2 family/SHP2/CRK family 0.067 0.032 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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
USP8 -0.005 0.01 -10000 0 -10000 0 0
RAS family/GTP -0.025 0.1 -10000 0 -0.34 3 3
NFATC4 -0.034 0.09 0.27 5 -0.36 1 6
ERBB2IP 0.025 0.025 -10000 0 -0.36 1 1
HSP90 (dimer) 0.026 0.006 -10000 0 -10000 0 0
mammary gland morphogenesis -0.046 0.09 -10000 0 -0.21 52 52
JUN -0.009 0.062 0.22 3 -10000 0 3
HRAS 0.026 0.006 -10000 0 -10000 0 0
DOCK7 -0.047 0.094 0.27 1 -0.45 1 2
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.018 0.1 -10000 0 -0.21 55 55
AKT1 0.003 0.009 -10000 0 -10000 0 0
BAD -0.005 0.007 -10000 0 -10000 0 0
MAPK10 -0.018 0.077 0.2 12 -0.21 4 16
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.045 0.1 -10000 0 -0.22 52 52
RAF1 -0.036 0.1 0.22 5 -0.32 4 9
ErbB2/ErbB3/neuregulin 2 -0.043 0.1 -10000 0 -0.21 68 68
STAT3 0.022 0.068 -10000 0 -0.74 2 2
cell migration -0.012 0.083 0.22 13 -0.21 3 16
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.078 0.17 0.31 1 -0.61 9 10
FOS -0.056 0.14 0.27 2 -0.46 16 18
NRAS 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.046 0.09 -10000 0 -0.21 52 52
MAPK3 -0.063 0.15 0.29 1 -0.59 7 8
MAPK1 -0.068 0.16 0.32 1 -0.63 9 10
JAK2 -0.045 0.086 -10000 0 -0.45 1 1
NF2 -0.008 0.098 -10000 0 -0.65 6 6
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.032 0.1 0.18 5 -0.22 54 59
NRG1 -0.077 0.17 -10000 0 -0.37 70 70
GRB2/SOS1 0.039 0.008 -10000 0 -10000 0 0
MAPK8 -0.043 0.11 0.2 1 -0.24 53 54
MAPK9 -0.014 0.075 0.2 13 -0.23 1 14
ERBB2 -0.02 0.031 0.32 1 -0.28 2 3
ERBB3 0.021 0.039 -10000 0 -0.34 3 3
SHC1 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.026 0.007 -10000 0 -10000 0 0
apoptosis 0.008 0.011 -10000 0 -10000 0 0
STAT3 (dimer) 0.022 0.066 -10000 0 -0.72 2 2
RNF41 -0.008 0.011 -10000 0 -10000 0 0
FRAP1 -0.003 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.037 0.064 -10000 0 -0.33 1 1
ErbB2/ErbB2/HSP90 (dimer) -0.006 0.03 0.23 1 -0.23 2 3
CHRNA1 -0.074 0.14 0.28 1 -0.46 7 8
myelination -0.019 0.11 0.29 15 -0.36 1 16
PPP3CB -0.046 0.086 -10000 0 -0.42 1 1
KRAS 0.024 0.009 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.008 0.1 -10000 0 -0.38 2 2
NRG2 -0.085 0.18 -10000 0 -0.37 76 76
mol:GDP -0.031 0.1 0.18 5 -0.22 54 59
SOS1 0.027 0.003 -10000 0 -10000 0 0
MAP2K2 -0.044 0.098 0.21 5 -0.33 4 9
SRC 0.024 0.009 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.047 0.093 0.26 1 -0.45 1 2
MAP2K1 -0.07 0.16 -10000 0 -0.57 10 10
heart morphogenesis -0.046 0.09 -10000 0 -0.21 52 52
RAS family/GDP -0.003 0.11 -10000 0 -0.38 2 2
GRB2 0.027 0.004 -10000 0 -10000 0 0
PRKACA -0.008 0.11 -10000 0 -0.67 7 7
CHRNE 0.003 0.016 0.085 1 -10000 0 1
HSP90AA1 0.026 0.006 -10000 0 -10000 0 0
activation of caspase activity -0.003 0.009 -10000 0 -10000 0 0
nervous system development -0.046 0.09 -10000 0 -0.21 52 52
CDC42 0.026 0.007 -10000 0 -10000 0 0
Arf6 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
CENTA1/KIF3B 0.031 0.014 -10000 0 -10000 0 0
ARNO/beta Arrestin1-2 -0.033 0.15 -10000 0 -0.82 6 6
EGFR 0.012 0.069 -10000 0 -0.36 9 9
EPHA2 0.024 0.031 -10000 0 -0.32 2 2
USP6 0.013 0.063 -10000 0 -0.3 10 10
IQSEC1 0.027 0.003 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.001 0.089 -10000 0 -0.22 39 39
ARRB2 0.009 0.018 -10000 0 -10000 0 0
mol:GTP 0.015 0.04 0.14 12 -0.13 2 14
ARRB1 0.027 0.005 -10000 0 -10000 0 0
FBXO8 0.026 0.007 -10000 0 -10000 0 0
TSHR 0.003 0.093 -10000 0 -0.37 16 16
EGF -0.013 0.1 -10000 0 -0.3 32 32
somatostatin receptor activity 0 0 0.001 4 -0.001 18 22
ARAP2 0.025 0.026 -10000 0 -0.28 2 2
mol:GDP -0.048 0.11 0.26 2 -0.26 38 40
mol:PI-3-4-5-P3 0 0 0.001 1 -0.001 11 12
ITGA2B 0.019 0.056 -10000 0 -0.35 6 6
ARF6 0.026 0.006 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.058 0.039 -10000 0 -0.2 1 1
ADAP1 0.025 0.008 -10000 0 -10000 0 0
KIF13B 0.025 0.009 -10000 0 -10000 0 0
HGF/MET 0.008 0.077 -10000 0 -0.2 33 33
PXN 0.024 0.031 -10000 0 -0.32 2 2
ARF6/GTP -0.036 0.11 0.3 4 -0.27 19 23
EGFR/EGFR/EGF/EGF/ARFGEP100 0.014 0.083 -10000 0 -0.18 39 39
ADRB2 -0.093 0.18 -10000 0 -0.37 82 82
receptor agonist activity 0 0 0 5 0 18 23
actin filament binding 0 0 0.001 4 0 20 24
SRC 0.024 0.009 -10000 0 -10000 0 0
ITGB3 0.026 0.019 -10000 0 -0.28 1 1
GNAQ 0.026 0.005 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.002 7 -0.001 13 20
ARF6/GDP -0.018 0.13 0.23 3 -0.41 16 19
ARF6/GDP/GULP/ACAP1 -0.03 0.13 0.26 2 -0.32 23 25
alphaIIb/beta3 Integrin/paxillin/GIT1 0.059 0.047 -10000 0 -0.2 6 6
ACAP1 0.023 0.027 -10000 0 -0.28 2 2
ACAP2 0.026 0.007 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.014 0.032 -10000 0 -0.15 6 6
EFNA1 0.022 0.037 -10000 0 -0.28 4 4
HGF 0.021 0.041 -10000 0 -0.28 5 5
CYTH3 0.006 0.002 -10000 0 -10000 0 0
CYTH2 -0.004 0.15 -10000 0 -0.99 6 6
NCK1 0.027 0.004 -10000 0 -10000 0 0
fibronectin binding 0 0 0.001 5 0 14 19
endosomal lumen acidification 0 0 0.001 17 0 8 25
microtubule-based process 0 0 -10000 0 0 1 1
GULP1 0.011 0.078 -10000 0 -0.37 11 11
GNAQ/ARNO 0.012 0.14 -10000 0 -0.92 6 6
mol:Phosphatidic acid 0 0 0 2 -10000 0 2
PIP3-E 0 0 0.001 2 0 3 5
MET -0.007 0.094 -10000 0 -0.28 29 29
GNA14 0.021 0.045 -10000 0 -0.35 4 4
GNA15 0.024 0.027 -10000 0 -0.28 2 2
GIT1 0.027 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 5 -0.001 15 20
GNA11 0.026 0.006 -10000 0 -10000 0 0
LHCGR 0.017 0.045 -10000 0 -0.28 6 6
AGTR1 -0.067 0.16 -10000 0 -0.35 67 67
desensitization of G-protein coupled receptor protein signaling pathway 0.014 0.032 -10000 0 -0.15 6 6
IPCEF1/ARNO -0.003 0.14 -10000 0 -0.85 6 6
alphaIIb/beta3 Integrin 0.033 0.045 -10000 0 -0.24 7 7
Nongenotropic Androgen signaling

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
PTK2 0.006 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.028 0.07 -10000 0 -0.2 22 22
regulation of S phase of mitotic cell cycle 0.005 0.055 -10000 0 -0.2 17 17
GNAO1 -0.007 0.11 -10000 0 -0.34 25 25
HRAS 0.026 0.007 -10000 0 -10000 0 0
SHBG/T-DHT 0.005 0.049 -10000 0 -0.19 16 16
PELP1 0.026 0.007 -10000 0 -10000 0 0
AKT1 0.007 0.002 -10000 0 -10000 0 0
MAP2K1 -0.003 0.078 0.18 27 -0.27 2 29
T-DHT/AR -0.004 0.077 -10000 0 -0.26 23 23
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -0.007 16 16
GNAI2 0.027 0.005 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.019 0.053 -10000 0 -0.37 5 5
mol:GDP -0.024 0.089 -10000 0 -0.28 28 28
cell proliferation -0.009 0.12 0.29 4 -0.42 13 17
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
FOS -0.022 0.18 -10000 0 -0.74 15 15
mol:Ca2+ -0.006 0.023 -10000 0 -0.066 25 25
MAPK3 -0.004 0.098 0.3 4 -0.29 12 16
MAPK1 -0.004 0.1 0.22 2 -0.43 9 11
PIK3R1 0.026 0.007 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.004 16 16
cAMP biosynthetic process -0.008 0.045 -10000 0 -0.17 16 16
GNG2 0.026 0.019 -10000 0 -0.28 1 1
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 16 16
HRAS/GTP 0.025 0.062 -10000 0 -0.18 19 19
actin cytoskeleton reorganization 0.034 0.018 -10000 0 -10000 0 0
SRC 0.024 0.009 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 16 16
PI3K 0.033 0.013 -10000 0 -10000 0 0
apoptosis 0.003 0.12 0.41 15 -0.26 3 18
T-DHT/AR/PELP1 0.013 0.07 -10000 0 -0.21 23 23
HRAS/GDP -0.011 0.089 -10000 0 -0.28 25 25
CREB1 -0.004 0.12 0.29 2 -0.44 15 17
RAC1-CDC42/GTP 0.043 0.022 -10000 0 -10000 0 0
AR -0.007 0.11 -10000 0 -0.37 23 23
GNB1 0.026 0.007 -10000 0 -10000 0 0
RAF1 0.016 0.078 0.19 28 -0.24 2 30
RAC1-CDC42/GDP 0.015 0.096 -10000 0 -0.29 20 20
T-DHT/AR/PELP1/Src 0.026 0.064 -10000 0 -0.19 19 19
MAP2K2 -0.003 0.077 0.18 26 -0.27 2 28
T-DHT/AR/PELP1/Src/PI3K 0.005 0.055 -10000 0 -0.2 17 17
GNAZ 0.008 0.084 -10000 0 -0.37 13 13
SHBG 0.004 0.084 -10000 0 -0.33 16 16
Gi family/GNB1/GNG2/GDP -0.031 0.15 -10000 0 -0.49 18 18
mol:T-DHT 0 0.001 -10000 0 -0.004 11 11
RAC1 0.026 0.007 -10000 0 -10000 0 0
GNRH1 0.004 0.023 -10000 0 -0.26 2 2
Gi family/GTP -0.018 0.082 -10000 0 -0.24 25 25
CDC42 0.026 0.007 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.049 0.064 -10000 0 -10000 0 0
SMARCC2 0.026 0.015 -10000 0 -10000 0 0
SMARCC1 0.026 0.015 -10000 0 -10000 0 0
TBX21 -0.054 0.1 -10000 0 -0.4 7 7
SUMO2 0.028 0.009 -10000 0 -10000 0 0
STAT1 (dimer) 0.023 0.052 -10000 0 -0.27 8 8
FKBP4 0.026 0.007 -10000 0 -10000 0 0
FKBP5 0.024 0.034 -10000 0 -0.37 2 2
GR alpha/HSP90/FKBP51/HSP90 0.081 0.086 0.25 14 -0.19 1 15
PRL -0.035 0.088 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.13 0.18 0.48 22 -10000 0 22
RELA -0.038 0.074 -10000 0 -0.23 11 11
FGG 0.041 0.21 0.4 16 -0.4 33 49
GR beta/TIF2 0.069 0.088 0.27 13 -10000 0 13
IFNG -0.19 0.19 -10000 0 -0.54 36 36
apoptosis 0.013 0.14 0.48 9 -0.48 6 15
CREB1 0.014 0.063 -10000 0 -0.3 7 7
histone acetylation -0.007 0.12 0.33 11 -0.31 11 22
BGLAP -0.04 0.087 -10000 0 -10000 0 0
GR/PKAc 0.086 0.088 0.26 12 -10000 0 12
NF kappa B1 p50/RelA -0.059 0.12 -10000 0 -0.3 28 28
SMARCD1 0.026 0.015 -10000 0 -10000 0 0
MDM2 0.049 0.066 0.2 20 -10000 0 20
GATA3 0.023 0.049 -10000 0 -0.29 6 6
AKT1 0.022 0.005 -10000 0 -10000 0 0
CSF2 -0.077 0.12 -10000 0 -0.42 3 3
GSK3B 0.027 0.009 -10000 0 -10000 0 0
NR1I3 0.023 0.14 0.47 8 -0.52 1 9
CSN2 0.068 0.13 0.34 17 -0.27 1 18
BRG1/BAF155/BAF170/BAF60A 0.064 0.046 -10000 0 -0.23 5 5
NFATC1 0.026 0.02 -10000 0 -10000 0 0
POU2F1 0.026 0.025 -10000 0 -0.27 1 1
CDKN1A -0.011 0.16 -10000 0 -1.3 4 4
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.007 -10000 0 -10000 0 0
SFN 0.014 0.066 -10000 0 -0.34 9 9
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.081 0.096 0.27 10 -0.24 3 13
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.007 0.16 0.46 7 -0.7 6 13
JUN -0.14 0.11 0.32 1 -0.36 18 19
IL4 -0.042 0.086 -10000 0 -10000 0 0
CDK5R1 0.023 0.037 -10000 0 -0.28 4 4
PRKACA 0.027 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.13 0.14 0.21 3 -0.3 71 74
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.088 0.085 0.27 10 -10000 0 10
cortisol/GR alpha (monomer) 0.15 0.21 0.55 28 -10000 0 28
NCOA2 0.024 0.009 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.075 0.092 -10000 0 -0.41 15 15
AP-1/NFAT1-c-4 -0.22 0.17 -10000 0 -0.5 37 37
AFP -0.1 0.1 -10000 0 -10000 0 0
SUV420H1 0.026 0.006 -10000 0 -10000 0 0
IRF1 0.079 0.1 0.38 3 -10000 0 3
TP53 0.031 0.055 -10000 0 -0.48 3 3
PPP5C 0.026 0.007 -10000 0 -10000 0 0
KRT17 -0.26 0.2 -10000 0 -0.59 35 35
KRT14 -0.16 0.33 -10000 0 -1.1 28 28
TBP 0.031 0.009 -10000 0 -10000 0 0
CREBBP 0.061 0.091 0.31 24 -0.25 4 28
HDAC1 0.024 0.008 -10000 0 -10000 0 0
HDAC2 0.033 0.013 -10000 0 -10000 0 0
AP-1 -0.22 0.17 -10000 0 -0.5 38 38
MAPK14 0.027 0.01 -10000 0 -10000 0 0
MAPK10 0.009 0.081 -10000 0 -0.36 12 12
MAPK11 0.027 0.01 -10000 0 -10000 0 0
KRT5 -0.18 0.19 -10000 0 -0.55 33 33
interleukin-1 receptor activity 0.007 0.011 -10000 0 -10000 0 0
NCOA1 0.029 0.004 -10000 0 -10000 0 0
STAT1 0.023 0.052 -10000 0 -0.27 8 8
CGA -0.076 0.19 -10000 0 -1 8 8
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.092 0.13 0.32 33 -0.46 1 34
MAPK3 0.028 0.009 -10000 0 -10000 0 0
MAPK1 0.027 0.01 -10000 0 -10000 0 0
ICAM1 -0.097 0.14 -10000 0 -0.42 23 23
NFKB1 -0.037 0.072 -10000 0 -0.21 14 14
MAPK8 -0.1 0.11 0.46 1 -0.32 17 18
MAPK9 0.027 0.009 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.012 0.15 0.48 9 -0.51 6 15
BAX 0.006 0.07 -10000 0 -10000 0 0
POMC -0.11 0.29 0.42 1 -1.3 13 14
EP300 0.063 0.09 0.31 24 -0.25 4 28
cortisol/GR alpha (dimer)/p53 0.14 0.18 0.49 24 -10000 0 24
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.052 0.18 7 -10000 0 7
SGK1 0.045 0.2 0.39 9 -1.2 5 14
IL13 -0.12 0.14 -10000 0 -0.61 6 6
IL6 -0.14 0.25 -10000 0 -0.75 31 31
PRKACG 0.019 0.037 -10000 0 -0.28 4 4
IL5 -0.1 0.12 -10000 0 -0.56 4 4
IL2 -0.15 0.16 -10000 0 -0.6 11 11
CDK5 0.027 0.007 -10000 0 -10000 0 0
PRKACB 0.023 0.042 -10000 0 -0.37 3 3
HSP90AA1 0.026 0.006 -10000 0 -10000 0 0
IL8 -0.17 0.17 -10000 0 -0.46 31 31
CDK5R1/CDK5 0.035 0.031 -10000 0 -0.19 4 4
NF kappa B1 p50/RelA/PKAc -0.028 0.11 -10000 0 -0.34 9 9
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.14 0.18 0.47 28 -10000 0 28
SMARCA4 0.026 0.015 -10000 0 -10000 0 0
chromatin remodeling 0.079 0.12 0.32 19 -0.39 3 22
NF kappa B1 p50/RelA/Cbp 0.02 0.15 0.36 15 -0.38 9 24
JUN (dimer) -0.14 0.11 0.32 1 -0.36 18 19
YWHAH 0.027 0.004 -10000 0 -10000 0 0
VIPR1 -0.071 0.16 -10000 0 -0.63 14 14
NR3C1 0.088 0.13 0.36 21 -0.3 1 22
NR4A1 -0.003 0.13 -10000 0 -0.46 18 18
TIF2/SUV420H1 0.035 0.015 -10000 0 -10000 0 0
MAPKKK cascade 0.013 0.14 0.48 9 -0.48 6 15
cortisol/GR alpha (dimer)/Src-1 0.15 0.18 0.48 29 -10000 0 29
PBX1 0.016 0.069 -10000 0 -0.37 8 8
POU1F1 0.025 0.017 -10000 0 -10000 0 0
SELE -0.11 0.17 -10000 0 -0.47 26 26
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.079 0.12 0.32 19 -0.4 3 22
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.14 0.18 0.47 28 -10000 0 28
mol:cortisol 0.073 0.12 0.3 30 -0.18 3 33
MMP1 -0.16 0.22 -10000 0 -0.6 29 29
EGFR-dependent Endothelin 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
HRAS 0.026 0.006 -9999 0 -10000 0 0
EGFR 0.012 0.069 -9999 0 -0.36 9 9
EGF/EGFR 0.004 0.082 -9999 0 -0.2 17 17
EGF/EGFR dimer/SHC/GRB2/SOS1 0.036 0.081 -9999 0 -0.19 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.007 0.074 -9999 0 -0.28 17 17
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.012 0.1 -9999 0 -0.3 32 32
EGF/EGFR dimer/SHC 0.016 0.08 -9999 0 -0.18 36 36
mol:GDP 0.031 0.077 -9999 0 -0.19 12 12
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.02 0.044 -9999 0 -0.3 5 5
GRB2/SOS1 0.039 0.008 -9999 0 -10000 0 0
HRAS/GTP 0.017 0.066 -9999 0 -0.18 12 12
SHC1 0.026 0.006 -9999 0 -10000 0 0
HRAS/GDP 0.03 0.075 -9999 0 -0.18 12 12
FRAP1 -0.028 0.047 -9999 0 -0.18 12 12
EGF/EGFR dimer -0.001 0.089 -9999 0 -0.22 39 39
SOS1 0.027 0.003 -9999 0 -10000 0 0
GRB2 0.027 0.004 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.018 0.064 -9999 0 -0.19 22 22
Visual signal transduction: Rods

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
mol:K + 0.027 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0.013 0.03 -10000 0 -0.18 6 6
Metarhodopsin II/Arrestin 0.03 0.007 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.027 0.035 -10000 0 -0.16 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.017 0.041 -10000 0 -0.28 5 5
GRK1 0.019 0.019 -10000 0 -0.28 1 1
CNG Channel 0.011 0.082 -10000 0 -0.2 25 25
mol:Na + -0.007 0.094 -10000 0 -0.3 4 4
mol:ADP 0.019 0.019 -10000 0 -0.28 1 1
RGS9-1/Gbeta5/R9AP 0.005 0.11 -10000 0 -0.25 39 39
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0 0.1 -10000 0 -0.3 4 4
CNGB1 0.009 0.073 -10000 0 -0.31 13 13
RDH5 0.027 0.004 -10000 0 -10000 0 0
SAG 0.024 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.032 0.11 0.35 12 -0.35 2 14
Na + (4 Units) -0.01 0.088 -10000 0 -0.28 4 4
RGS9 0.003 0.095 -10000 0 -0.36 17 17
GNB1/GNGT1 -0.011 0.091 -10000 0 -0.19 56 56
GNAT1/GDP 0.011 0.098 -10000 0 -0.21 39 39
GUCY2D 0.014 0.058 -10000 0 -0.28 10 10
GNGT1 -0.038 0.12 -10000 0 -0.28 55 55
GUCY2F 0.022 0.005 -10000 0 -10000 0 0
GNB5 0.027 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) 0.012 0.046 -10000 0 -0.22 5 5
mol:11-cis-retinal 0.027 0.004 -10000 0 -10000 0 0
mol:cGMP 0.014 0.08 -10000 0 -0.21 16 16
GNB1 0.026 0.007 -10000 0 -10000 0 0
Rhodopsin 0.035 0.008 -10000 0 -10000 0 0
SLC24A1 0.027 0.004 -10000 0 -10000 0 0
CNGA1 0.001 0.098 -10000 0 -0.37 18 18
Metarhodopsin II 0.024 0.016 -10000 0 -0.14 2 2
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.023 0.087 -10000 0 -0.22 16 16
RGS9BP -0.02 0.12 -10000 0 -0.37 31 31
Metarhodopsin II/Transducin -0.01 0.051 -10000 0 -0.19 11 11
GCAP Family/Ca ++ 0.019 0.073 -10000 0 -0.18 31 31
PDE6A/B 0.026 0.053 -10000 0 -0.21 12 12
mol:Pi 0.005 0.11 -10000 0 -0.24 39 39
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.002 0.078 -10000 0 -0.14 56 56
PDE6B 0.018 0.054 -10000 0 -0.34 6 6
PDE6A 0.019 0.049 -10000 0 -0.28 7 7
PDE6G 0.024 0.032 -10000 0 -0.28 3 3
RHO 0.021 0.006 -10000 0 -10000 0 0
PDE6 0.02 0.11 -10000 0 -0.31 10 10
GUCA1A 0.005 0.08 -10000 0 -0.3 17 17
GC2/GCAP Family 0.03 0.079 -10000 0 -0.21 15 15
GUCA1C -0.001 0.086 -10000 0 -0.36 15 15
GUCA1B 0.024 0.025 -10000 0 -0.37 1 1
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.004 0.034 0.11 5 -0.092 2 7
BUB1B -0.017 0.059 0.11 1 -0.14 20 21
PLK1 0.011 0.03 0.083 18 -10000 0 18
PLK1S1 0.014 0.034 0.11 7 -0.2 3 10
KIF2A 0.008 0.032 0.14 5 -10000 0 5
regulation of mitotic centrosome separation 0.011 0.03 0.083 18 -10000 0 18
GOLGA2 0.026 0.006 -10000 0 -10000 0 0
Hec1/SPC24 0.015 0.065 -10000 0 -0.16 14 14
WEE1 0.01 0.065 0.15 2 -0.32 8 10
cytokinesis -0.009 0.071 0.14 2 -0.24 10 12
PP2A-alpha B56 0.011 0.075 -10000 0 -0.47 4 4
AURKA 0.011 0.023 -10000 0 -10000 0 0
PICH/PLK1 -0.016 0.069 0.16 1 -0.21 12 13
CENPE -0.025 0.07 0.19 2 -0.14 55 57
RhoA/GTP 0.02 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.009 0.032 0.14 5 -10000 0 5
PPP2CA 0 0 -10000 0 -10000 0 0
FZR1 0.026 0.006 -10000 0 -10000 0 0
TPX2 0.008 0.039 0.099 18 -10000 0 18
PAK1 0.027 0.006 -10000 0 -10000 0 0
SPC24 0.025 0.027 -10000 0 -0.28 2 2
FBXW11 0.026 0.006 -10000 0 -10000 0 0
CLSPN -0.003 0.046 0.13 1 -0.23 4 5
GORASP1 0.027 0.005 -10000 0 -10000 0 0
metaphase 0 0.004 0.017 9 -10000 0 9
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.005 0.017 0.047 20 -0.042 1 21
G2 phase of mitotic cell cycle 0 0.003 0.012 9 -10000 0 9
STAG2 0.027 0.003 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.009 0.077 -10000 0 -0.5 6 6
spindle elongation 0.011 0.03 0.083 18 -10000 0 18
ODF2 0.028 0.007 -10000 0 -10000 0 0
BUB1 -0.002 0.076 -10000 0 -0.51 4 4
TPT1 0.012 0.029 0.12 3 -0.18 3 6
CDC25C 0.001 0.061 -10000 0 -0.25 13 13
CDC25B 0.022 0.028 -10000 0 -0.28 2 2
SGOL1 -0.004 0.034 0.092 2 -0.11 5 7
RHOA 0.027 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 0.026 0.045 -10000 0 -10000 0 0
CDC14B 0.006 0.004 -10000 0 -10000 0 0
CDC20 0.018 0.052 -10000 0 -0.28 8 8
PLK1/PBIP1 0.006 0.028 0.078 4 -0.13 4 8
mitosis -0.001 0.003 0.016 3 -10000 0 3
FBXO5 0.008 0.037 0.11 11 -0.13 3 14
CDC2 0 0.003 -10000 0 -0.01 4 4
NDC80 -0.015 0.1 -10000 0 -0.28 36 36
metaphase plate congression -0.002 0.066 -10000 0 -0.23 19 19
ERCC6L -0.014 0.071 -10000 0 -0.23 10 10
NLP/gamma Tubulin 0.008 0.02 0.069 12 -0.079 1 13
microtubule cytoskeleton organization 0.012 0.029 0.12 3 -0.18 3 6
G2/M transition DNA damage checkpoint 0 0.003 0.015 3 -10000 0 3
PPP1R12A 0.027 0.005 -10000 0 -10000 0 0
interphase 0 0.003 0.015 3 -10000 0 3
PLK1/PRC1-2 -0.006 0.093 -10000 0 -0.22 29 29
GRASP65/GM130/RAB1/GTP/PLK1 0.045 0.034 -10000 0 -10000 0 0
RAB1A 0.027 0.003 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.013 0.03 0.071 41 -10000 0 41
mitotic prometaphase 0 0.005 0.016 19 -10000 0 19
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.028 0.17 1 -10000 0 1
microtubule-based process 0.001 0.063 0.1 3 -0.14 33 36
Golgi organization 0.011 0.03 0.083 18 -10000 0 18
Cohesin/SA2 0.022 0.027 0.096 3 -10000 0 3
PPP1CB/MYPT1 0.039 0.01 -10000 0 -10000 0 0
KIF20A -0.021 0.11 -10000 0 -0.28 42 42
APC/C/CDC20 0.02 0.043 0.11 2 -0.17 8 10
PPP2R1A 0.026 0.006 -10000 0 -10000 0 0
chromosome segregation 0.006 0.028 0.077 4 -0.12 4 8
PRC1 -0.016 0.11 -10000 0 -0.28 38 38
ECT2 -0.013 0.095 0.22 20 -0.15 58 78
C13orf34 0.011 0.027 0.071 24 -10000 0 24
NUDC -0.002 0.066 -10000 0 -0.23 19 19
regulation of attachment of spindle microtubules to kinetochore -0.017 0.058 0.11 1 -0.14 20 21
spindle assembly 0.01 0.028 0.094 14 -10000 0 14
spindle stabilization 0.014 0.034 0.11 7 -0.2 3 10
APC/C/HCDH1 0.024 0.007 -10000 0 -10000 0 0
MKLP2/PLK1 0.001 0.063 0.1 3 -0.14 33 36
CCNB1 0.02 0.046 -10000 0 -0.28 6 6
PPP1CB 0.028 0.004 -10000 0 -10000 0 0
BTRC 0.027 0.004 -10000 0 -10000 0 0
ROCK2 0.014 0.047 0.14 1 -0.3 3 4
TUBG1 0.012 0.022 0.11 1 -0.19 1 2
G2/M transition of mitotic cell cycle -0.002 0.035 -10000 0 -10000 0 0
MLF1IP 0.002 0.024 -10000 0 -0.19 4 4
INCENP 0.026 0.019 -10000 0 -0.28 1 1
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.032 0.017 -10000 0 -10000 0 0
PRKCZ 0.026 0.007 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.026 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.008 0.049 -10000 0 -0.22 5 5
IRAK/TOLLIP 0.025 0.014 -10000 0 -10000 0 0
IKBKB 0.025 0.008 -10000 0 -10000 0 0
IKBKG 0.022 0.006 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.049 0.12 -10000 0 -0.22 94 94
IL1A -0.042 0.13 -10000 0 -0.28 61 61
IL1B -0.009 0.066 -10000 0 -0.21 27 27
IRAK/TRAF6/p62/Atypical PKCs 0.071 0.055 -10000 0 -10000 0 0
IL1R2 -0.022 0.13 -10000 0 -0.36 35 35
IL1R1 0.026 0.019 -10000 0 -0.28 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.015 0.063 -10000 0 -0.61 1 1
TOLLIP 0.027 0.005 -10000 0 -10000 0 0
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0.027 0.004 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.018 0.004 -10000 0 -10000 0 0
IKK complex/ELKS 0.047 0.067 0.25 7 -10000 0 7
JUN 0.018 0.069 0.16 52 -10000 0 52
MAP3K7 0.026 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.034 0.075 -10000 0 -0.2 6 6
IL1 alpha/IL1R1/IL1RAP/MYD88 0.012 0.093 -10000 0 -0.27 3 3
PIK3R1 0.026 0.007 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.02 0.094 -10000 0 -0.26 3 3
IL1 beta fragment/IL1R1/IL1RAP 0.015 0.069 -10000 0 -0.22 7 7
NFKB1 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.022 0.074 0.17 53 -10000 0 53
IRAK1 0.013 0.007 -10000 0 -10000 0 0
IL1RN/IL1R1 0.014 0.084 -10000 0 -0.25 25 25
IRAK4 0.027 0.005 -10000 0 -10000 0 0
PRKCI 0.023 0.027 -10000 0 -0.28 2 2
TRAF6 0.027 0.005 -10000 0 -10000 0 0
PI3K 0.036 0.014 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.009 0.048 -10000 0 -0.23 3 3
CHUK 0.027 0.004 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.015 0.069 -10000 0 -0.22 7 7
IL1 beta/IL1R2 -0.016 0.1 0.22 1 -0.21 57 58
IRAK/TRAF6/TAK1/TAB1/TAB2 0.03 0.018 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.023 0.066 -10000 0 -0.23 2 2
IRAK3 0.022 0.042 -10000 0 -0.37 3 3
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.024 0.067 -10000 0 -0.2 7 7
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.004 0.044 -10000 0 -0.19 1 1
IL1 alpha/IL1R1/IL1RAP -0.001 0.093 -10000 0 -0.17 63 63
RELA 0.027 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.026 0.006 -10000 0 -10000 0 0
MYD88 0.027 0.005 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.068 0.053 -10000 0 -10000 0 0
IL1RAP 0.015 0.055 -10000 0 -0.28 9 9
UBE2N 0.027 0.004 -10000 0 -10000 0 0
IRAK/TRAF6 0.009 0.049 -10000 0 -0.23 2 2
CASP1 0.025 0.019 -10000 0 -0.28 1 1
IL1RN/IL1R2 -0.02 0.13 -10000 0 -0.29 49 49
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.026 0.072 -10000 0 -0.2 7 7
TMEM189-UBE2V1 0.022 0.011 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.02 0.061 -10000 0 -0.26 4 4
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
IL1RN -0.007 0.11 -10000 0 -0.36 24 24
TRAF6/TAK1/TAB1/TAB2 0.041 0.024 -10000 0 -10000 0 0
MAP2K6 0.027 0.078 0.18 55 -10000 0 55
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.035 0.089 0.23 18 -0.32 2 20
PDGFB-D/PDGFRB/SLAP 0.016 0.062 -10000 0 -0.18 22 22
PDGFB-D/PDGFRB/APS/CBL 0.033 0.058 -10000 0 -0.15 21 21
AKT1 0.027 0.099 0.24 25 -10000 0 25
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.039 0.098 0.25 13 -0.38 2 15
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
FGR 0.003 0.11 0.33 2 -0.45 11 13
mol:Ca2+ 0.031 0.098 0.24 13 -0.37 4 17
MYC 0.071 0.14 0.39 20 -0.75 1 21
SHC1 0.026 0.006 -10000 0 -10000 0 0
HRAS/GDP 0.033 0.065 0.17 30 -10000 0 30
LRP1/PDGFRB/PDGFB 0.035 0.061 -10000 0 -0.16 21 21
GRB10 0.025 0.019 -10000 0 -0.28 1 1
PTPN11 0.027 0.004 -10000 0 -10000 0 0
GO:0007205 0.031 0.098 0.24 13 -0.37 4 17
PTEN 0.026 0.006 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
GRB7 0.01 0.066 -10000 0 -0.29 12 12
PDGFB-D/PDGFRB/SHP2 0.021 0.062 -10000 0 -0.18 22 22
PDGFB-D/PDGFRB/GRB10 0.02 0.061 -10000 0 -0.19 21 21
cell cycle arrest 0.016 0.062 -10000 0 -0.18 22 22
HRAS 0.026 0.006 -10000 0 -10000 0 0
HIF1A 0.021 0.091 0.23 24 -10000 0 24
GAB1 0.028 0.095 0.26 5 -0.38 2 7
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.032 0.093 0.25 15 -0.31 2 17
PDGFB-D/PDGFRB 0.027 0.056 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.022 0.061 -10000 0 -0.18 21 21
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.014 0.056 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.021 0.062 -10000 0 -0.18 22 22
PIK3R1 0.026 0.007 -10000 0 -10000 0 0
mol:IP3 0.031 0.099 0.24 13 -0.38 4 17
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.025 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.007 0.075 -10000 0 -0.19 33 33
SHB 0.026 0.007 -10000 0 -10000 0 0
BLK -0.062 0.19 0.32 1 -0.48 42 43
PTPN2 0.027 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.021 0.062 -10000 0 -0.18 22 22
BCAR1 0.026 0.007 -10000 0 -10000 0 0
VAV2 0.034 0.1 0.26 10 -0.41 2 12
CBL 0.026 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.021 0.063 -10000 0 -0.18 23 23
LCK 0.009 0.1 0.33 2 -0.45 8 10
PDGFRB 0.003 0.083 -10000 0 -0.28 22 22
ACP1 0.027 0.004 -10000 0 -10000 0 0
HCK 0.019 0.059 0.34 2 -10000 0 2
ABL1 0.025 0.1 0.24 13 -0.38 3 16
PDGFB-D/PDGFRB/CBL 0.025 0.099 0.26 4 -0.38 5 9
PTPN1 0.022 0.011 -10000 0 -10000 0 0
SNX15 0.027 0.004 -10000 0 -10000 0 0
STAT3 0.027 0.005 -10000 0 -10000 0 0
STAT1 0.018 0.052 -10000 0 -0.28 8 8
cell proliferation 0.07 0.13 0.35 26 -0.66 1 27
SLA 0.022 0.021 -10000 0 -0.28 1 1
actin cytoskeleton reorganization 0.045 0.088 0.32 9 -10000 0 9
SRC 0.016 0.064 0.33 2 -0.34 1 3
PI3K -0.005 0.035 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC 0.021 0.07 -10000 0 -0.17 9 9
SH2B2 0.025 0.02 -10000 0 -0.28 1 1
PLCgamma1/SPHK1 0.04 0.1 0.26 13 -0.39 2 15
LYN 0.011 0.086 0.3 3 -0.38 6 9
LRP1 0.027 0.004 -10000 0 -10000 0 0
SOS1 0.027 0.003 -10000 0 -10000 0 0
STAT5B 0.027 0.005 -10000 0 -10000 0 0
STAT5A 0.027 0.005 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.045 0.061 -10000 0 -10000 0 0
SPHK1 0.013 0.068 -10000 0 -0.28 14 14
EDG1 0.001 0.003 -10000 0 -10000 0 0
mol:DAG 0.031 0.099 0.24 13 -0.38 4 17
PLCG1 0.031 0.1 0.26 8 -0.38 4 12
NHERF/PDGFRB 0.034 0.058 -10000 0 -10000 0 0
YES1 0.009 0.099 0.32 1 -0.57 5 6
cell migration 0.034 0.058 -10000 0 -10000 0 0
SHC/Grb2/SOS1 0.044 0.062 -10000 0 -10000 0 0
SLC9A3R2 0.026 0.006 -10000 0 -10000 0 0
SLC9A3R1 0.027 0.004 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.046 0.06 -10000 0 -10000 0 0
FYN 0.007 0.097 0.3 3 -0.39 9 12
DOK1 0.026 0.075 0.18 42 -10000 0 42
HRAS/GTP 0.02 0.004 -10000 0 -10000 0 0
PDGFB 0.025 0.026 -10000 0 -0.28 2 2
RAC1 0.044 0.12 0.34 13 -0.39 3 16
PRKCD 0.028 0.077 0.18 44 -10000 0 44
FER 0.024 0.073 0.18 37 -10000 0 37
MAPKKK cascade 0.014 0.087 0.26 10 -10000 0 10
RASA1 0.023 0.073 0.18 36 -10000 0 36
NCK1 0.027 0.004 -10000 0 -10000 0 0
NCK2 0.027 0.003 -10000 0 -10000 0 0
p62DOK/Csk 0.039 0.071 0.17 15 -10000 0 15
PDGFB-D/PDGFRB/SHB 0.02 0.062 -10000 0 -0.18 22 22
chemotaxis 0.025 0.099 0.24 13 -0.37 3 16
STAT1-3-5/STAT1-3-5 0.031 0.062 -10000 0 -0.24 1 1
Bovine Papilomavirus E5/PDGFRB 0.004 0.055 -10000 0 -0.18 22 22
PTPRJ 0.026 0.019 -10000 0 -0.28 1 1
LPA4-mediated signaling events

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
ADCY4 -0.006 0.001 -10000 0 -10000 0 0
ADCY5 -0.055 0.088 -10000 0 -0.21 64 64
ADCY6 -0.006 0.001 -10000 0 -10000 0 0
ADCY7 -0.006 0.002 -10000 0 -10000 0 0
ADCY1 -0.012 0.03 -10000 0 -0.16 11 11
ADCY2 -0.019 0.051 -10000 0 -0.21 18 18
ADCY3 -0.006 0.001 -10000 0 -10000 0 0
ADCY8 -0.007 0.004 -10000 0 -10000 0 0
PRKCE 0.007 0.001 -10000 0 -10000 0 0
ADCY9 -0.006 0.002 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.007 0.082 0.23 17 -0.26 1 18
ErbB4 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
ErbB4/ErbB4/HBEGF/HBEGF 0.013 0.067 -10000 0 -10000 0 0
epithelial cell differentiation 0.007 0.077 -10000 0 -10000 0 0
ITCH 0.031 0.018 -10000 0 -10000 0 0
WWP1 0.006 0.063 -10000 0 -10000 0 0
FYN 0.027 0.005 -10000 0 -10000 0 0
EGFR 0.012 0.069 -10000 0 -0.36 9 9
PRL 0.018 0.045 -10000 0 -0.28 6 6
neuron projection morphogenesis -0.024 0.11 0.29 12 -10000 0 12
PTPRZ1 -0.1 0.18 -10000 0 -0.37 89 89
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.017 0.1 -10000 0 -10000 0 0
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.042 0.095 -10000 0 -0.27 12 12
ADAM17 0.033 0.016 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.006 0.055 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.001 0.088 -10000 0 -0.34 3 3
NCOR1 0.025 0.008 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.034 0.098 -10000 0 -10000 0 0
GRIN2B -0.05 0.11 0.25 3 -0.28 5 8
ErbB4/ErbB2/betacellulin 0.008 0.067 -10000 0 -0.3 2 2
STAT1 0.018 0.052 -10000 0 -0.28 8 8
HBEGF 0.023 0.034 -10000 0 -0.37 2 2
PRLR -0.024 0.13 -10000 0 -0.36 34 34
E4ICDs/ETO2 0.005 0.076 -10000 0 -0.31 1 1
axon guidance 0.023 0.081 0.36 4 -0.34 1 5
NEDD4 0.03 0.032 -10000 0 -0.28 2 2
Prolactin receptor/Prolactin receptor/Prolactin -0.005 0.098 -10000 0 -0.25 37 37
CBFA2T3 0.004 0.089 -10000 0 -0.36 15 15
ErbB4/ErbB2/HBEGF 0.014 0.054 -10000 0 -10000 0 0
MAPK3 -0.023 0.11 0.3 9 -10000 0 9
STAT1 (dimer) 0.012 0.075 -10000 0 -10000 0 0
MAPK1 -0.021 0.11 0.29 10 -10000 0 10
JAK2 0.024 0.01 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.039 0.091 -10000 0 -0.27 12 12
NRG1 -0.057 0.12 -10000 0 -0.26 70 70
NRG3 -0.01 0.11 -10000 0 -0.35 26 26
NRG2 -0.085 0.18 -10000 0 -0.37 76 76
NRG4 -0.033 0.14 -10000 0 -0.37 41 41
heart development 0.023 0.081 0.36 4 -0.34 1 5
neural crest cell migration -0.039 0.09 -10000 0 -0.26 12 12
ERBB2 0.012 0.026 -10000 0 -0.26 2 2
WWOX/E4ICDs 0.014 0.067 -10000 0 -10000 0 0
SHC1 0.026 0.006 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.011 0.1 -10000 0 -0.29 11 11
apoptosis 0.013 0.11 0.36 17 -10000 0 17
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.039 0.11 -10000 0 -0.31 15 15
ErbB4/ErbB2/epiregulin -0.008 0.08 -10000 0 -0.34 1 1
ErbB4/ErbB4/betacellulin/betacellulin 0.007 0.083 -10000 0 -0.3 3 3
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.009 0.098 -10000 0 -10000 0 0
MDM2 0.001 0.067 0.26 7 -10000 0 7
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.034 0.091 -10000 0 -10000 0 0
STAT5A 0.025 0.081 0.33 4 -0.32 1 5
ErbB4/EGFR/neuregulin 1 beta -0.035 0.099 -10000 0 -0.32 4 4
DLG4 0.026 0.007 -10000 0 -10000 0 0
GRB2/SHC 0.038 0.01 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.012 0.062 -10000 0 -10000 0 0
STAT5A (dimer) 0.02 0.096 0.3 3 -10000 0 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.044 0.09 0.32 5 -0.32 1 6
LRIG1 0.024 0.034 -10000 0 -0.37 2 2
EREG -0.045 0.13 -10000 0 -0.29 62 62
BTC 0.005 0.09 -10000 0 -0.37 15 15
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.013 0.071 0.33 3 -0.34 1 4
ERBB4 -0.006 0.055 -10000 0 -10000 0 0
STAT5B 0.027 0.005 -10000 0 -10000 0 0
YAP1 0.001 0.068 -10000 0 -0.44 5 5
GRB2 0.027 0.004 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.009 0.086 -10000 0 -0.27 9 9
glial cell differentiation -0.012 0.061 -10000 0 -10000 0 0
WWOX 0.026 0.007 -10000 0 -10000 0 0
cell proliferation -0.022 0.13 0.28 9 -0.46 3 12
Osteopontin-mediated events

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
IKK alpha homodimer -0.051 0.087 0.19 1 -10000 0 1
NF kappa B1 p50/RelA/I kappa B alpha -0.038 0.086 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin/Src -0.079 0.11 -10000 0 -0.19 143 143
AP1 -0.046 0.1 -10000 0 -0.37 2 2
ILK -0.06 0.082 -10000 0 -10000 0 0
bone resorption -0.038 0.083 0.22 1 -10000 0 1
PTK2B 0.024 0.009 -10000 0 -10000 0 0
PYK2/p130Cas -0.029 0.099 -10000 0 -10000 0 0
ITGAV 0.028 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.037 0.018 -10000 0 -0.19 1 1
alphaV/beta3 Integrin/Osteopontin -0.055 0.11 -10000 0 -0.19 18 18
MAP3K1 -0.056 0.082 0.19 2 -10000 0 2
JUN 0.026 0.024 -10000 0 -0.37 1 1
MAPK3 -0.063 0.077 0.19 1 -0.22 1 2
MAPK1 -0.061 0.078 0.19 1 -0.22 1 2
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
NFKB1 0.027 0.005 -10000 0 -10000 0 0
MAPK8 -0.058 0.074 0.19 2 -10000 0 2
ITGB3 0.028 0.019 -10000 0 -0.27 1 1
NFKBIA -0.054 0.072 0.19 1 -10000 0 1
FOS 0.005 0.089 -10000 0 -0.36 15 15
CD44 0.026 0.007 -10000 0 -10000 0 0
CHUK 0.027 0.004 -10000 0 -10000 0 0
PLAU -0.057 0.096 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.038 0.098 -10000 0 -10000 0 0
BCAR1 0.026 0.007 -10000 0 -10000 0 0
RELA 0.027 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.041 0.018 -10000 0 -0.18 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.061 0.082 0.19 2 -10000 0 2
VAV3 -0.069 0.076 -10000 0 -0.24 7 7
MAP3K14 -0.062 0.085 0.19 2 -0.2 1 3
ROCK2 0.026 0.019 -10000 0 -0.28 1 1
SPP1 -0.13 0.15 -10000 0 -0.28 139 139
RAC1 0.026 0.007 -10000 0 -10000 0 0
Rac1/GTP -0.055 0.076 -10000 0 -0.23 6 6
MMP2 -0.052 0.077 -10000 0 -0.37 2 2
Ceramide signaling pathway

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
SPHK2 0.011 0.013 -10000 0 -0.19 1 1
MAP4K4 0.012 0.054 -10000 0 -0.32 4 4
BAG4 0.025 0.009 -10000 0 -10000 0 0
PKC zeta/ceramide -0.004 0.069 -10000 0 -0.2 25 25
NFKBIA 0.027 0.004 -10000 0 -10000 0 0
BIRC3 0.021 0.043 -10000 0 -0.32 4 4
BAX -0.005 0.062 -10000 0 -0.35 7 7
RIPK1 0.026 0.006 -10000 0 -10000 0 0
AKT1 -0.005 0.011 -10000 0 -10000 0 0
BAD -0.02 0.066 0.2 2 -0.2 26 28
SMPD1 0.012 0.068 0.2 6 -0.29 7 13
RB1 -0.011 0.068 0.18 9 -0.2 20 29
FADD/Caspase 8 0.021 0.08 0.21 10 -0.36 6 16
MAP2K4 -0.022 0.058 -10000 0 -0.19 22 22
NSMAF 0.024 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.016 0.063 0.18 7 -0.19 23 30
EGF -0.012 0.1 -10000 0 -0.3 32 32
mol:ceramide -0.02 0.068 -10000 0 -0.21 26 26
MADD 0.027 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.009 0.018 -10000 0 -0.19 2 2
ASAH1 0.024 0.01 -10000 0 -10000 0 0
negative regulation of cell cycle -0.011 0.068 0.18 9 -0.2 20 29
cell proliferation -0.011 0.08 0.18 4 -0.24 8 12
BID 0 0.16 -10000 0 -0.82 9 9
MAP3K1 -0.021 0.063 -10000 0 -0.19 26 26
EIF2A -0.015 0.07 0.18 12 -0.26 5 17
TRADD 0.026 0.007 -10000 0 -10000 0 0
CRADD 0.027 0.004 -10000 0 -10000 0 0
MAPK3 -0.014 0.062 0.17 7 -0.23 5 12
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.016 0.063 0.17 7 -0.24 5 12
Cathepsin D/ceramide -0.005 0.07 -10000 0 -0.2 26 26
FADD 0.013 0.049 -10000 0 -0.34 3 3
KSR1 -0.017 0.063 0.2 4 -0.19 24 28
MAPK8 -0.016 0.069 -10000 0 -0.22 14 14
PRKRA -0.02 0.066 0.2 2 -0.2 26 28
PDGFA 0.023 0.027 -10000 0 -0.28 2 2
TRAF2 0.027 0.005 -10000 0 -10000 0 0
IGF1 -0.019 0.12 -10000 0 -0.31 37 37
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.02 0.067 -10000 0 -0.21 26 26
CTSD 0.026 0.006 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.039 0.009 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.01 0.085 0.19 4 -0.26 8 12
PRKCD 0.027 0.005 -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 0.009 0.018 -10000 0 -0.19 2 2
RelA/NF kappa B1 0.039 0.009 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.027 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.015 0.047 -10000 0 -0.35 3 3
TNFR1A/BAG4/TNF-alpha 0.036 0.049 -10000 0 -0.17 11 11
mol:Sphingosine-1-phosphate 0.011 0.013 -10000 0 -0.19 1 1
MAP2K1 -0.017 0.062 0.17 8 -0.19 15 23
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.027 0.004 -10000 0 -10000 0 0
CYCS 0.003 0.048 0.16 1 -0.21 5 6
TNFRSF1A 0.026 0.006 -10000 0 -10000 0 0
NFKB1 0.027 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.035 0.015 -10000 0 -10000 0 0
EIF2AK2 -0.02 0.065 0.19 4 -0.2 24 28
TNF-alpha/TNFR1A/FAN 0.037 0.047 -10000 0 -0.17 10 10
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.028 0.054 -10000 0 -0.32 3 3
MAP2K2 -0.018 0.06 0.17 7 -0.19 14 21
SMPD3 -0.003 0.09 0.14 1 -0.28 22 23
TNF 0.011 0.07 -10000 0 -0.31 12 12
PKC zeta/PAR4 0.038 0.011 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.002 0.06 0.18 7 -0.15 12 19
NF kappa B1/RelA/I kappa B alpha 0.071 0.028 -10000 0 -10000 0 0
AIFM1 -0.001 0.058 0.14 3 -0.23 6 9
BCL2 0.024 0.025 -10000 0 -0.37 1 1
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.018 0.02 -10000 0 -0.26 1 1
CRKL 0.027 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
DOCK1 0.027 0.005 -10000 0 -10000 0 0
ITGA4 0.027 0.004 -10000 0 -10000 0 0
alpha4/beta7 Integrin/MAdCAM1 -0.031 0.13 -10000 0 -0.2 94 94
EPO 0.014 0.048 -10000 0 -0.28 7 7
alpha4/beta7 Integrin 0.036 0.027 -10000 0 -0.26 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.038 0.01 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.03 0.035 -10000 0 -0.19 6 6
lamellipodium assembly 0.011 0.084 -10000 0 -0.42 8 8
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
PI3K 0.036 0.014 -10000 0 -10000 0 0
ARF6 0.026 0.006 -10000 0 -10000 0 0
JAK2 0.017 0.027 -10000 0 -0.23 2 2
PXN 0.024 0.031 -10000 0 -0.32 2 2
PIK3R1 0.026 0.007 -10000 0 -10000 0 0
MADCAM1 -0.11 0.19 -10000 0 -0.37 95 95
cell adhesion -0.032 0.12 -10000 0 -0.2 94 94
CRKL/CBL 0.038 0.011 -10000 0 -10000 0 0
ITGB1 0.026 0.006 -10000 0 -10000 0 0
SRC 0.012 0.033 0.18 5 -10000 0 5
ITGB7 0.024 0.034 -10000 0 -0.37 2 2
RAC1 0.026 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.046 0.035 -10000 0 -0.16 6 6
p130Cas/Crk/Dock1 0.026 0.032 -10000 0 -10000 0 0
VCAM1 0.019 0.049 -10000 0 -0.28 7 7
RHOA 0.027 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.061 0.03 -10000 0 -0.2 1 1
BCAR1 -0.01 0.031 0.18 4 -10000 0 4
EPOR 0.027 0.005 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.026 0.007 -10000 0 -10000 0 0
GIT1 0.027 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.011 0.087 -10000 0 -0.43 8 8
ceramide signaling pathway

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
MAP4K4 0.002 0.12 0.21 2 -0.51 10 12
BAG4 0.025 0.009 -10000 0 -10000 0 0
BAD 0.008 0.045 0.18 5 -0.2 5 10
NFKBIA 0.027 0.004 -10000 0 -10000 0 0
BIRC3 0.021 0.043 -10000 0 -0.32 4 4
BAX 0.012 0.053 0.18 11 -0.19 5 16
EnzymeConsortium:3.1.4.12 0.005 0.027 0.067 6 -0.1 10 16
IKBKB 0.012 0.12 0.21 15 -0.47 10 25
MAP2K2 0.009 0.053 0.2 10 -0.23 3 13
MAP2K1 0.01 0.053 0.2 11 -0.21 4 15
SMPD1 0.005 0.036 0.1 3 -0.17 7 10
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.018 0.12 0.22 12 -0.51 10 22
MAP2K4 0.008 0.037 0.14 3 -0.21 3 6
protein ubiquitination 0.009 0.12 0.2 2 -0.5 10 12
EnzymeConsortium:2.7.1.37 0.009 0.056 0.2 11 -0.25 3 14
response to UV 0 0.001 0.002 11 -0.002 3 14
RAF1 0.01 0.055 0.2 10 -0.22 4 14
CRADD 0.027 0.004 -10000 0 -10000 0 0
mol:ceramide 0.009 0.044 0.11 7 -0.18 8 15
I-kappa-B-alpha/RELA/p50/ubiquitin 0.036 0.008 -10000 0 -10000 0 0
MADD 0.027 0.004 -10000 0 -10000 0 0
MAP3K1 0.007 0.041 0.13 4 -0.2 5 9
TRADD 0.026 0.007 -10000 0 -10000 0 0
RELA/p50 0.027 0.004 -10000 0 -10000 0 0
MAPK3 0.011 0.056 0.2 11 -0.26 3 14
MAPK1 0.01 0.06 0.2 11 -0.25 5 16
p50/RELA/I-kappa-B-alpha 0.039 0.009 -10000 0 -10000 0 0
FADD 0.014 0.12 0.21 12 -0.5 9 21
KSR1 0.011 0.053 0.2 8 -0.21 5 13
MAPK8 0.006 0.044 0.24 3 -0.22 2 5
TRAF2 0.027 0.005 -10000 0 -10000 0 0
response to radiation 0 0 0.002 5 -10000 0 5
CHUK 0.006 0.11 0.21 3 -0.5 9 12
TNF R/SODD 0.035 0.015 -10000 0 -10000 0 0
TNF 0.011 0.07 -10000 0 -0.31 12 12
CYCS 0.019 0.054 0.15 20 -0.16 4 24
IKBKG 0.007 0.11 0.2 8 -0.48 10 18
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.006 0.12 -10000 0 -0.56 9 9
RELA 0.027 0.004 -10000 0 -10000 0 0
RIPK1 0.026 0.006 -10000 0 -10000 0 0
AIFM1 0.016 0.05 0.15 15 -0.16 4 19
TNF/TNF R/SODD 0.036 0.048 -10000 0 -0.17 11 11
TNFRSF1A 0.026 0.006 -10000 0 -10000 0 0
response to heat 0 0 0.002 5 -10000 0 5
CASP8 0.024 0.076 -10000 0 -0.63 3 3
NSMAF 0.015 0.11 0.21 14 -0.47 9 23
response to hydrogen peroxide 0 0.001 0.002 11 -0.002 3 14
BCL2 0.024 0.025 -10000 0 -0.37 1 1
Syndecan-3-mediated signaling events

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
CTTN 0.026 0.007 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.027 0.088 -9999 0 -0.34 8 8
Syndecan-3/Neurocan 0.016 0.075 -9999 0 -0.37 9 9
POMC 0.007 0.085 -9999 0 -0.36 14 14
EGFR 0.012 0.069 -9999 0 -0.36 9 9
Syndecan-3/EGFR 0.01 0.077 -9999 0 -0.37 8 8
AGRP 0.023 0.027 -9999 0 -0.28 2 2
NCSTN 0.027 0.005 -9999 0 -10000 0 0
PSENEN 0.026 0.007 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.027 0.005 -9999 0 -10000 0 0
APH1A 0.026 0.007 -9999 0 -10000 0 0
NCAN 0.025 0.019 -9999 0 -0.28 1 1
long-term memory 0.032 0.072 -9999 0 -0.34 8 8
Syndecan-3/IL8 -0.052 0.1 -9999 0 -0.47 9 9
PSEN1 0.027 0.005 -9999 0 -10000 0 0
Src/Cortactin 0.034 0.016 -9999 0 -10000 0 0
FYN 0.027 0.005 -9999 0 -10000 0 0
limb bud formation 0 0.07 -9999 0 -0.38 9 9
MC4R 0.021 0.008 -9999 0 -10000 0 0
SRC 0.024 0.009 -9999 0 -10000 0 0
PTN -0.011 0.12 -9999 0 -0.37 26 26
FGFR/FGF/Syndecan-3 -0.001 0.071 -9999 0 -0.38 9 9
neuron projection morphogenesis 0.012 0.087 -9999 0 -0.34 8 8
Syndecan-3/AgRP 0.016 0.073 -9999 0 -0.36 9 9
Syndecan-3/AgRP/MC4R 0.027 0.075 -9999 0 -0.34 9 9
Fyn/Cortactin 0.037 0.013 -9999 0 -10000 0 0
SDC3 -0.001 0.072 -9999 0 -0.38 9 9
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.052 0.1 -9999 0 -0.46 9 9
IL8 -0.13 0.15 -9999 0 -0.28 137 137
Syndecan-3/Fyn/Cortactin 0.033 0.074 -9999 0 -0.35 8 8
Syndecan-3/CASK -0.002 0.069 -9999 0 -0.36 9 9
alpha-MSH/MC4R 0.019 0.063 -9999 0 -0.25 14 14
Gamma Secretase 0.07 0.03 -9999 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.036 0.018 -10000 0 -0.19 1 1
alphaV beta3 Integrin 0.05 0.028 -10000 0 -0.18 3 3
PTK2 0.031 0.1 0.31 16 -10000 0 16
IGF1R 0.027 0.005 -10000 0 -10000 0 0
PI4KB 0.026 0.006 -10000 0 -10000 0 0
MFGE8 0.027 0.005 -10000 0 -10000 0 0
SRC 0.024 0.009 -10000 0 -10000 0 0
CDKN1B -0.004 0.086 -10000 0 -0.36 13 13
VEGFA 0.026 0.007 -10000 0 -10000 0 0
ILK -0.002 0.083 -10000 0 -0.37 11 11
ROCK1 0.026 0.006 -10000 0 -10000 0 0
AKT1 -0.006 0.07 -10000 0 -0.35 9 9
PTK2B 0 0.046 0.18 16 -10000 0 16
alphaV/beta3 Integrin/JAM-A 0.032 0.068 -10000 0 -0.18 9 9
CBL 0.026 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.02 0.088 -10000 0 -0.21 34 34
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.036 0.082 -10000 0 -0.21 12 12
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.008 0.054 -10000 0 -0.33 3 3
alphaV/beta3 Integrin/Syndecan-1 0.051 0.025 -10000 0 -0.19 2 2
PI4KA 0.027 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.019 0.11 -10000 0 -0.26 18 18
PI4 Kinase 0.038 0.012 -10000 0 -10000 0 0
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.06 0.11 -10000 0 -0.16 140 140
RPS6KB1 -0.054 0.089 0.24 3 -0.3 4 7
TLN1 0.026 0.007 -10000 0 -10000 0 0
MAPK3 -0.013 0.072 -10000 0 -0.42 3 3
GPR124 0.022 0.027 -10000 0 -0.28 2 2
MAPK1 -0.012 0.07 -10000 0 -0.42 3 3
PXN 0.024 0.031 -10000 0 -0.32 2 2
PIK3R1 0.026 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.028 0.077 -10000 0 -0.2 28 28
cell adhesion 0.018 0.076 -10000 0 -0.21 1 1
ANGPTL3 -0.021 0.13 -10000 0 -0.36 33 33
VEGFR2 homodimer/VEGFA homodimer/Src 0.044 0.026 -10000 0 -0.16 1 1
IGF-1R heterotetramer 0.027 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
TGFBR2 0.027 0.005 -10000 0 -10000 0 0
ITGB3 0.026 0.019 -10000 0 -0.28 1 1
IGF1 -0.019 0.12 -10000 0 -0.31 37 37
RAC1 0.026 0.007 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.045 0.029 -10000 0 -0.16 3 3
apoptosis 0.027 0.005 -10000 0 -10000 0 0
CD47 0.027 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.052 0.018 -10000 0 -0.16 1 1
VCL 0.025 0.019 -10000 0 -0.28 1 1
alphaV/beta3 Integrin/Del1 0.044 0.042 -10000 0 -0.21 6 6
CSF1 0.027 0.005 -10000 0 -10000 0 0
PIK3C2A -0.002 0.083 -10000 0 -0.37 11 11
PI4 Kinase/Pyk2 0.016 0.058 -10000 0 -0.24 1 1
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.06 0.03 -10000 0 -10000 0 0
FAK1/Vinculin 0.039 0.096 0.29 17 -10000 0 17
alphaV beta3/Integrin/ppsTEM5 0.046 0.029 -10000 0 -0.16 3 3
RHOA 0.027 0.005 -10000 0 -10000 0 0
VTN -0.011 0.11 -10000 0 -0.3 31 31
BCAR1 0.026 0.007 -10000 0 -10000 0 0
FGF2 0.024 0.031 -10000 0 -0.32 2 2
F11R 0.011 0.021 -10000 0 -0.22 2 2
alphaV/beta3 Integrin/Lactadherin 0.052 0.019 -10000 0 -0.16 1 1
alphaV/beta3 Integrin/TGFBR2 0.052 0.019 -10000 0 -0.16 1 1
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.063 0.023 -10000 0 -10000 0 0
HSP90AA1 0.026 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.047 0.02 -10000 0 -0.14 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.058 0.14 -10000 0 -0.28 76 76
alphaV/beta3 Integrin/Pyk2 0.046 0.038 -10000 0 -10000 0 0
SDC1 0.025 0.024 -10000 0 -0.37 1 1
VAV3 -0.012 0.044 0.18 8 -10000 0 8
PTPN11 0.027 0.004 -10000 0 -10000 0 0
IRS1 0.026 0.024 -10000 0 -0.37 1 1
FAK1/Paxillin 0.041 0.096 0.29 17 -10000 0 17
cell migration 0.033 0.092 0.26 22 -10000 0 22
ITGAV 0.027 0.005 -10000 0 -10000 0 0
PI3K 0.039 0.067 -10000 0 -10000 0 0
SPP1 -0.13 0.15 -10000 0 -0.28 139 139
KDR 0.023 0.032 -10000 0 -0.28 3 3
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.027 0.005 -10000 0 -10000 0 0
COL4A3 -0.01 0.11 -10000 0 -0.33 28 28
angiogenesis -0.011 0.079 -10000 0 -0.41 4 4
Rac1/GTP 0.021 0.04 0.18 1 -10000 0 1
EDIL3 0.018 0.053 -10000 0 -0.37 5 5
cell proliferation 0.051 0.019 -10000 0 -0.16 1 1
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.014 0.03 -9999 0 -10000 0 0
NFATC2 -0.013 0.033 -9999 0 -0.23 2 2
NFATC3 -0.014 0.03 -9999 0 -10000 0 0
CD40LG -0.071 0.16 -9999 0 -0.39 24 24
PTGS2 -0.076 0.17 -9999 0 -0.44 26 26
JUNB 0.025 0.024 -9999 0 -0.37 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.006 0.025 -9999 0 -10000 0 0
CaM/Ca2+ -0.006 0.025 -9999 0 -10000 0 0
CALM1 0.013 0.023 -9999 0 -10000 0 0
JUN 0.013 0.033 -9999 0 -0.38 1 1
mol:Ca2+ -0.008 0.009 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.013 0.01 -9999 0 -10000 0 0
FOSL1 0.001 0.087 -9999 0 -0.29 22 22
CREM 0.026 0.006 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.03 0.1 -9999 0 -0.25 13 13
FOS -0.007 0.091 -9999 0 -0.37 15 15
IFNG -0.094 0.18 -9999 0 -0.42 37 37
AP-1/NFAT1-c-4 -0.065 0.18 -9999 0 -0.44 21 21
FASLG -0.068 0.16 -9999 0 -0.42 20 20
NFAT1-c-4/ICER1 -0.025 0.062 -9999 0 -0.25 1 1
IL2RA -0.068 0.16 -9999 0 -0.45 18 18
FKBP12/FK506 0.018 0.007 -9999 0 -10000 0 0
CSF2 -0.1 0.18 -9999 0 -0.43 37 37
JunB/Fra1/NFAT1-c-4 -0.02 0.084 -9999 0 -0.24 4 4
IL4 -0.067 0.15 -9999 0 -0.41 18 18
IL2 -0.016 0.17 -9999 0 -0.85 11 11
IL3 -0.022 0.15 -9999 0 -0.61 16 16
FKBP1A 0.024 0.009 -9999 0 -10000 0 0
BATF3 0.027 0.005 -9999 0 -10000 0 0
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.026 0.019 -9999 0 -0.28 1 1
IL27-mediated signaling events

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
TGFB1 -0.066 0.19 -10000 0 -0.42 57 57
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.012 0.084 0.35 2 -10000 0 2
IL27/IL27R/JAK1 0.055 0.11 -10000 0 -10000 0 0
TBX21 0.019 0.11 0.36 1 -10000 0 1
IL12B 0.01 0.067 -10000 0 -0.35 9 9
IL12A -0.009 0.054 -10000 0 -0.26 12 12
IL6ST 0.024 0.013 -10000 0 -10000 0 0
IL27RA/JAK1 0.019 0.036 -10000 0 -10000 0 0
IL27 0.013 0.059 -10000 0 -0.28 10 10
TYK2 0.016 0.022 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.28 0.54 0.41 3 -1.2 62 65
T-helper 2 cell differentiation 0.012 0.084 0.35 2 -10000 0 2
T cell proliferation during immune response 0.012 0.084 0.35 2 -10000 0 2
MAPKKK cascade -0.012 0.084 -10000 0 -0.35 2 2
STAT3 0.027 0.005 -10000 0 -10000 0 0
STAT2 0.026 0.019 -10000 0 -0.28 1 1
STAT1 0.02 0.052 -10000 0 -0.28 8 8
IL12RB1 0.026 0.005 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.01 0.11 0.36 1 -0.35 4 5
IL27/IL27R/JAK2/TYK2 -0.012 0.084 -10000 0 -0.35 2 2
positive regulation of T cell mediated cytotoxicity -0.012 0.084 -10000 0 -0.35 2 2
STAT1 (dimer) 0.074 0.17 0.42 27 -10000 0 27
JAK2 0.014 0.021 -10000 0 -10000 0 0
JAK1 0.029 0.005 -10000 0 -10000 0 0
STAT2 (dimer) -0.005 0.092 -10000 0 -0.33 3 3
T cell proliferation -0.063 0.11 -10000 0 -0.39 10 10
IL12/IL12R/TYK2/JAK2 -0.059 0.22 -10000 0 -0.74 23 23
IL17A -0.28 0.54 0.41 3 -1.3 62 65
mast cell activation 0.012 0.084 0.35 2 -10000 0 2
IFNG -0.01 0.033 -10000 0 -0.11 6 6
T cell differentiation -0.002 0.005 -10000 0 -0.015 7 7
STAT3 (dimer) -0.004 0.091 -10000 0 -0.33 3 3
STAT5A (dimer) -0.004 0.091 -10000 0 -0.33 3 3
STAT4 (dimer) -0.007 0.092 -10000 0 -0.34 3 3
STAT4 0.025 0.03 -10000 0 -0.32 2 2
T cell activation -0.005 0.004 0.039 1 -10000 0 1
IL27R/JAK2/TYK2 0.025 0.054 -10000 0 -10000 0 0
GATA3 0.014 0.14 0.63 9 -1.2 1 10
IL18 0 0.026 -10000 0 -0.2 4 4
positive regulation of mast cell cytokine production -0.004 0.09 -10000 0 -0.33 3 3
IL27/EBI3 0.017 0.063 -10000 0 -0.21 16 16
IL27RA 0.003 0.022 -10000 0 -10000 0 0
IL6 -0.097 0.21 -10000 0 -0.43 74 74
STAT5A 0.027 0.005 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.002 -10000 0 -10000 0 0
IL2 -0.009 0.017 -10000 0 -10000 0 0
IL1B -0.018 0.064 -10000 0 -0.2 29 29
EBI3 0.018 0.055 -10000 0 -0.34 6 6
TNF -0.006 0.045 -10000 0 -0.21 12 12
Syndecan-4-mediated signaling events

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
PTK2 -0.016 0.073 -10000 0 -0.29 4 4
Syndecan-4/Syndesmos -0.012 0.1 -10000 0 -0.43 1 1
positive regulation of JNK cascade -0.016 0.12 0.28 1 -0.38 3 4
Syndecan-4/ADAM12 -0.069 0.13 -10000 0 -0.39 7 7
CCL5 0.018 0.058 -10000 0 -0.37 6 6
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
DNM2 0.027 0.005 -10000 0 -10000 0 0
ITGA5 0.017 0.055 -10000 0 -0.28 9 9
SDCBP 0.024 0.009 -10000 0 -10000 0 0
PLG 0.014 0.029 -10000 0 -0.28 1 1
ADAM12 -0.13 0.15 -10000 0 -0.28 138 138
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.026 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.044 0.033 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.025 0.12 0.29 1 -0.38 3 4
Syndecan-4/CXCL12/CXCR4 -0.016 0.12 0.29 1 -0.4 3 4
Syndecan-4/Laminin alpha3 -0.017 0.11 0.29 1 -0.43 3 4
MDK 0.021 0.044 -10000 0 -0.3 5 5
Syndecan-4/FZD7 -0.011 0.11 0.29 1 -0.42 2 3
Syndecan-4/Midkine -0.012 0.11 0.29 1 -0.58 1 2
FZD7 0.022 0.043 -10000 0 -0.32 4 4
Syndecan-4/FGFR1/FGF -0.015 0.1 -10000 0 -0.38 3 3
THBS1 0.015 0.061 -10000 0 -0.3 10 10
integrin-mediated signaling pathway -0.022 0.11 -10000 0 -0.38 2 2
positive regulation of MAPKKK cascade -0.016 0.12 0.28 1 -0.38 3 4
Syndecan-4/TACI -0.052 0.12 -10000 0 -0.4 7 7
CXCR4 0.019 0.049 -10000 0 -0.28 7 7
cell adhesion -0.014 0.056 0.19 4 -10000 0 4
Syndecan-4/Dynamin -0.008 0.11 0.29 1 -0.43 1 2
Syndecan-4/TSP1 -0.012 0.11 0.29 1 -0.43 1 2
Syndecan-4/GIPC -0.007 0.11 0.29 1 -0.43 1 2
Syndecan-4/RANTES -0.012 0.11 0.29 1 -0.43 1 2
ITGB1 0.026 0.006 -10000 0 -10000 0 0
LAMA1 -0.013 0.1 -10000 0 -0.28 34 34
LAMA3 0.007 0.076 -10000 0 -0.3 16 16
RAC1 0.026 0.007 -10000 0 -10000 0 0
PRKCA 0.015 0.092 0.73 4 -0.34 1 5
Syndecan-4/alpha-Actinin -0.009 0.11 -10000 0 -0.43 1 1
TFPI 0.022 0.043 -10000 0 -0.32 4 4
F2 -0.006 0.098 -10000 0 -0.28 31 31
alpha5/beta1 Integrin 0.03 0.042 -10000 0 -0.19 9 9
positive regulation of cell adhesion -0.033 0.12 0.28 1 -0.4 5 6
ACTN1 0.023 0.032 -10000 0 -0.28 3 3
TNC -0.006 0.095 -10000 0 -0.28 29 29
Syndecan-4/CXCL12 -0.019 0.11 0.29 1 -0.39 3 4
FGF6 0.015 0.032 -10000 0 -0.28 3 3
RHOA 0.027 0.005 -10000 0 -10000 0 0
CXCL12 0.002 0.096 -10000 0 -0.37 17 17
TNFRSF13B -0.085 0.18 -10000 0 -0.37 76 76
FGF2 0.024 0.031 -10000 0 -0.32 2 2
FGFR1 0.022 0.027 -10000 0 -0.28 2 2
Syndecan-4/PI-4-5-P2 -0.037 0.079 -10000 0 -0.43 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.066 0.14 -10000 0 -0.28 76 76
cell migration -0.02 0.014 -10000 0 -10000 0 0
PRKCD 0.019 0.024 -10000 0 -10000 0 0
vasculogenesis -0.012 0.11 0.28 1 -0.42 1 2
SDC4 -0.034 0.08 -10000 0 -0.45 1 1
Syndecan-4/Tenascin C -0.023 0.12 -10000 0 -0.4 2 2
Syndecan-4/PI-4-5-P2/PKC alpha -0.035 0.026 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.012 0.1 0.29 1 -0.42 1 2
MMP9 -0.06 0.13 -10000 0 -0.28 74 74
Rac1/GTP -0.014 0.057 0.19 4 -10000 0 4
cytoskeleton organization -0.011 0.1 -10000 0 -0.42 1 1
GIPC1 0.027 0.004 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.013 0.1 -10000 0 -0.43 1 1
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.05 0.047 -10000 0 -0.18 8 8
ER alpha/Gai/GDP/Gbeta gamma -0.032 0.17 -10000 0 -0.52 18 18
AKT1 -0.011 0.18 -10000 0 -0.74 15 15
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.008 0.19 -10000 0 -0.75 15 15
mol:Ca2+ 0.017 0.068 0.18 18 -0.32 5 23
IGF1R 0.027 0.005 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.029 0.038 -10000 0 -0.22 6 6
SHC1 0.026 0.006 -10000 0 -10000 0 0
apoptosis 0.009 0.18 0.71 15 -10000 0 15
RhoA/GTP 0.018 0.027 -10000 0 -0.17 3 3
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.002 0.14 -10000 0 -0.44 15 15
regulation of stress fiber formation -0.005 0.057 -10000 0 -0.15 24 24
E2/ERA-ERB (dimer) 0.027 0.043 -10000 0 -0.21 8 8
KRAS 0.024 0.009 -10000 0 -10000 0 0
G13/GTP 0.028 0.034 -10000 0 -0.19 6 6
pseudopodium formation 0.005 0.057 0.15 24 -10000 0 24
E2/ER alpha (dimer)/PELP1 0.028 0.038 -10000 0 -0.21 6 6
GRB2 0.027 0.004 -10000 0 -10000 0 0
GNG2 0.026 0.019 -10000 0 -0.28 1 1
GNAO1 -0.007 0.11 -10000 0 -0.34 25 25
HRAS 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.019 0.16 -10000 0 -0.52 18 18
E2/ER beta (dimer) 0.018 0.024 -10000 0 -0.26 2 2
mol:GDP 0.008 0.059 -10000 0 -0.3 8 8
mol:NADP -0.019 0.16 -10000 0 -0.52 18 18
PIK3R1 0.026 0.007 -10000 0 -10000 0 0
mol:IP3 0.003 0.051 -10000 0 -0.33 5 5
IGF-1R heterotetramer 0.027 0.005 -10000 0 -10000 0 0
PLCB1 0.011 0.048 -10000 0 -0.37 3 3
PLCB2 0.015 0.045 -10000 0 -0.37 3 3
IGF1 -0.019 0.12 -10000 0 -0.31 37 37
mol:L-citrulline -0.019 0.16 -10000 0 -0.52 18 18
RHOA 0.027 0.005 -10000 0 -10000 0 0
Gai/GDP -0.048 0.22 -10000 0 -0.6 33 33
JNK cascade 0.018 0.024 -10000 0 -0.26 2 2
BCAR1 0.026 0.007 -10000 0 -10000 0 0
ESR2 0.024 0.034 -10000 0 -0.37 2 2
GNAQ 0.027 0.005 -10000 0 -10000 0 0
ESR1 0.018 0.058 -10000 0 -0.37 6 6
Gq family/GDP/Gbeta gamma -0.01 0.16 -10000 0 -0.66 14 14
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.021 0.11 -10000 0 -0.77 4 4
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.002 0.14 -10000 0 -0.44 15 15
GNAZ 0.008 0.084 -10000 0 -0.37 13 13
E2/ER alpha (dimer) 0.013 0.041 -10000 0 -0.26 6 6
STRN 0.027 0.004 -10000 0 -10000 0 0
GNAL 0.01 0.077 -10000 0 -0.36 11 11
PELP1 0.026 0.007 -10000 0 -10000 0 0
MAPK11 0.012 0.02 -10000 0 -0.22 2 2
GNAI2 0.027 0.005 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.019 0.053 -10000 0 -0.37 5 5
HBEGF -0.012 0.18 0.32 23 -0.53 15 38
cAMP biosynthetic process 0.015 0.053 -10000 0 -0.18 18 18
SRC -0.016 0.16 0.21 17 -0.59 12 29
PI3K 0.036 0.014 -10000 0 -10000 0 0
GNB1 0.026 0.007 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.034 0.064 -10000 0 -0.26 8 8
SOS1 0.027 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.031 0.11 -10000 0 -0.37 15 15
Gs family/GTP 0.021 0.056 -10000 0 -0.18 18 18
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.044 0.021 -10000 0 -10000 0 0
vasodilation -0.017 0.15 -10000 0 -0.49 18 18
mol:DAG 0.003 0.051 -10000 0 -0.33 5 5
Gs family/GDP/Gbeta gamma 0.007 0.067 -10000 0 -0.27 9 9
MSN 0.005 0.059 0.16 24 -10000 0 24
Gq family/GTP 0.02 0.048 -10000 0 -0.38 3 3
mol:PI-3-4-5-P3 -0.007 0.18 -10000 0 -0.72 15 15
NRAS 0.027 0.005 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.017 0.15 0.49 18 -10000 0 18
GRB2/SOS1 0.039 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.021 0.06 -10000 0 -0.28 7 7
NOS3 -0.022 0.17 -10000 0 -0.56 18 18
GNA11 0.026 0.006 -10000 0 -10000 0 0
MAPKKK cascade 0.003 0.15 0.27 2 -0.56 14 16
E2/ER alpha (dimer)/PELP1/Src 0.003 0.15 0.26 5 -0.47 15 20
ruffle organization 0.005 0.057 0.15 24 -10000 0 24
ROCK2 0.009 0.065 0.17 24 -10000 0 24
GNA14 0.021 0.045 -10000 0 -0.35 4 4
GNA15 0.024 0.027 -10000 0 -0.28 2 2
GNA13 0.027 0.004 -10000 0 -10000 0 0
MMP9 -0.029 0.18 0.35 19 -0.5 17 36
MMP2 -0.01 0.16 0.3 6 -0.53 13 19
FOXM1 transcription factor network

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
NFATC3 -0.046 0.31 -10000 0 -0.98 10 10
PLK1 -0.011 0.2 -10000 0 -1.1 6 6
BIRC5 0.006 0.16 -10000 0 -1.1 4 4
HSPA1B -0.045 0.31 -10000 0 -0.98 10 10
MAP2K1 0.02 0.039 -10000 0 -10000 0 0
BRCA2 -0.049 0.32 -10000 0 -1 10 10
FOXM1 -0.061 0.35 -10000 0 -1.2 11 11
XRCC1 -0.044 0.31 -10000 0 -0.98 10 10
FOXM1B/p19 -0.085 0.32 -10000 0 -0.99 13 13
Cyclin D1/CDK4 -0.054 0.29 -10000 0 -0.92 9 9
CDC2 -0.052 0.32 -10000 0 -1 10 10
TGFA -0.052 0.29 -10000 0 -0.87 11 11
SKP2 -0.035 0.31 0.54 1 -0.98 10 11
CCNE1 0.01 0.063 -10000 0 -0.29 11 11
CKS1B -0.045 0.31 -10000 0 -0.99 10 10
RB1 -0.011 0.19 -10000 0 -0.91 5 5
FOXM1C/SP1 -0.05 0.34 -10000 0 -1.1 10 10
AURKB -0.042 0.26 -10000 0 -0.88 21 21
CENPF -0.085 0.33 -10000 0 -1 11 11
CDK4 0.021 0.023 -10000 0 -10000 0 0
MYC -0.036 0.26 -10000 0 -0.84 9 9
CHEK2 0.018 0.049 -10000 0 -0.33 2 2
ONECUT1 -0.056 0.31 -10000 0 -0.97 11 11
CDKN2A -0.048 0.13 -10000 0 -0.28 62 62
LAMA4 -0.051 0.31 -10000 0 -0.98 10 10
FOXM1B/HNF6 -0.066 0.34 -10000 0 -1.1 11 11
FOS -0.083 0.38 -10000 0 -1.1 21 21
SP1 0.027 0.006 -10000 0 -10000 0 0
CDC25B -0.036 0.31 0.54 1 -0.98 9 10
response to radiation 0.003 0.022 -10000 0 -10000 0 0
CENPB -0.034 0.3 0.54 1 -0.96 10 11
CENPA -0.054 0.32 -10000 0 -1 11 11
NEK2 -0.058 0.32 -10000 0 -1 11 11
HIST1H2BA -0.051 0.31 -10000 0 -0.99 10 10
CCNA2 0.011 0.066 -10000 0 -0.29 12 12
EP300 0.027 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 -0.059 0.34 -10000 0 -1.1 10 10
CCNB2 -0.051 0.31 -10000 0 -1 10 10
CCNB1 -0.052 0.32 -10000 0 -1 10 10
ETV5 -0.041 0.32 -10000 0 -1 9 9
ESR1 -0.06 0.35 -10000 0 -1.1 15 15
CCND1 -0.06 0.3 -10000 0 -0.91 11 11
GSK3A 0.021 0.035 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.029 0.076 -10000 0 -0.21 15 15
CDK2 0.024 0.016 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.002 0.026 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.041 0.33 -10000 0 -1 11 11
GAS1 -0.08 0.38 -10000 0 -1.1 21 21
MMP2 -0.047 0.31 -10000 0 -0.98 10 10
RB1/FOXM1C -0.048 0.3 -10000 0 -1 9 9
CREBBP 0.026 0.007 -10000 0 -10000 0 0
Regulation of Androgen receptor activity

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
HDAC1 0.011 0.006 -10000 0 -10000 0 0
SMARCC1 0.014 0.01 -10000 0 -10000 0 0
REL 0.027 0.003 -10000 0 -10000 0 0
HDAC7 -0.013 0.089 0.23 1 -0.34 6 7
JUN 0.026 0.024 -10000 0 -0.37 1 1
EP300 0.027 0.005 -10000 0 -10000 0 0
KAT2B 0.023 0.041 -10000 0 -0.37 3 3
KAT5 0.027 0.004 -10000 0 -10000 0 0
MAPK14 0.005 0.031 -10000 0 -0.29 2 2
FOXO1 0.026 0.007 -10000 0 -10000 0 0
T-DHT/AR 0.009 0.1 0.25 1 -0.3 13 14
MAP2K6 0.018 0.039 -10000 0 -0.39 2 2
BRM/BAF57 0.034 0.016 -10000 0 -10000 0 0
MAP2K4 0.019 0.019 -10000 0 -10000 0 0
SMARCA2 0.024 0.009 -10000 0 -10000 0 0
PDE9A -0.072 0.28 -10000 0 -0.83 30 30
NCOA2 0.024 0.009 -10000 0 -10000 0 0
CEBPA 0.02 0.044 -10000 0 -0.3 5 5
EHMT2 0.026 0.007 -10000 0 -10000 0 0
cell proliferation 0.014 0.13 0.28 16 -0.37 6 22
NR0B1 0.019 0.026 -10000 0 -0.28 2 2
EGR1 0.018 0.056 -10000 0 -0.35 6 6
RXRs/9cRA -0.038 0.12 -10000 0 -0.19 95 95
AR/RACK1/Src 0.016 0.081 0.22 4 -0.33 2 6
AR/GR -0.004 0.089 0.19 2 -0.27 19 21
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
PKN1 0.027 0.004 -10000 0 -10000 0 0
RCHY1 0.027 0.005 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -10000 0 -0.016 1 1
MAPK8 0.007 0.018 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.015 0.064 0.26 2 -0.35 1 3
SRC -0.015 0.032 0.21 1 -0.25 2 3
NR3C1 0.022 0.042 -10000 0 -0.37 3 3
KLK3 -0.083 0.1 -10000 0 -0.43 4 4
APPBP2 0.021 0.018 -10000 0 -10000 0 0
TRIM24 0.025 0.019 -10000 0 -0.28 1 1
T-DHT/AR/TIP60 0.001 0.061 0.23 1 -0.35 2 3
TMPRSS2 -0.066 0.27 -10000 0 -0.87 25 25
RXRG -0.12 0.19 -10000 0 -0.37 97 97
mol:9cRA 0 0.001 -10000 0 -10000 0 0
RXRA 0.025 0.025 -10000 0 -0.37 1 1
RXRB 0.026 0.006 -10000 0 -10000 0 0
CARM1 0.027 0.006 -10000 0 -10000 0 0
NR2C2 0.027 0.002 -10000 0 -10000 0 0
KLK2 0.008 0.073 0.33 1 -0.32 1 2
AR -0.014 0.077 0.23 1 -0.26 22 23
SENP1 0.027 0.005 -10000 0 -10000 0 0
HSP90AA1 0.026 0.006 -10000 0 -10000 0 0
MDM2 0.023 0.032 -10000 0 -0.28 3 3
SRY 0 0.003 0.012 12 -10000 0 12
GATA2 0.026 0.024 -10000 0 -0.37 1 1
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 -0.18 0.14 -10000 0 -0.28 187 187
T-DHT/AR/RACK1/Src 0.019 0.085 0.25 7 -0.34 2 9
positive regulation of transcription 0.025 0.024 -10000 0 -0.37 1 1
DNAJA1 0.02 0.019 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.011 -10000 0 -10000 0 0
NCOA1 0.031 0.014 -10000 0 -10000 0 0
SPDEF -0.052 0.16 -10000 0 -0.37 53 53
T-DHT/AR/TIF2 0.008 0.07 0.23 4 -0.34 3 7
T-DHT/AR/Hsp90 0.001 0.062 0.23 1 -0.35 2 3
GSK3B 0.027 0.005 -10000 0 -10000 0 0
NR2C1 0.027 0.004 -10000 0 -10000 0 0
mol:T-DHT -0.015 0.037 0.31 1 -0.26 2 3
SIRT1 0.027 0.005 -10000 0 -10000 0 0
ZMIZ2 0.026 0.007 -10000 0 -10000 0 0
POU2F1 0.017 0.049 -10000 0 -0.2 3 3
T-DHT/AR/DAX-1 -0.003 0.065 0.26 2 -0.35 2 4
CREBBP 0.026 0.007 -10000 0 -10000 0 0
SMARCE1 0.026 0.007 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.013 0.07 -10000 0 -0.19 28 28
CRKL 0.007 0.12 0.32 2 -0.48 11 13
mol:PIP3 -0.002 0.047 -10000 0 -0.76 1 1
AKT1 -0.016 0.058 -10000 0 -0.67 1 1
PTK2B 0.024 0.009 -10000 0 -10000 0 0
RAPGEF1 0.009 0.12 0.28 3 -0.46 11 14
RANBP10 0.026 0.007 -10000 0 -10000 0 0
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.022 0.072 -10000 0 -0.16 33 33
MAP3K5 0.013 0.12 0.3 2 -0.45 11 13
HGF/MET/CIN85/CBL/ENDOPHILINS 0.035 0.073 -10000 0 -0.27 1 1
AP1 0.01 0.072 0.18 2 -0.24 13 15
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.026 0.006 -10000 0 -10000 0 0
apoptosis -0.04 0.24 -10000 0 -0.77 25 25
STAT3 (dimer) 0.005 0.055 -10000 0 -0.28 4 4
GAB1/CRKL/SHP2/PI3K 0.032 0.12 0.33 1 -0.44 10 11
INPP5D 0.024 0.035 -10000 0 -0.31 3 3
CBL/CRK 0.021 0.12 0.29 3 -0.46 10 13
PTPN11 0.027 0.004 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.024 0.01 -10000 0 -10000 0 0
PTEN 0.026 0.006 -10000 0 -10000 0 0
ELK1 0.004 0.12 0.34 25 -0.29 1 26
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.005 0.047 -10000 0 -0.21 7 7
PAK1 -0.01 0.064 -10000 0 -0.64 1 1
HGF/MET/RANBP10 0.023 0.071 -10000 0 -0.16 32 32
HRAS -0.001 0.1 -10000 0 -0.43 11 11
DOCK1 0.009 0.12 0.28 6 -0.45 11 17
GAB1 0.003 0.11 -10000 0 -0.57 8 8
CRK 0.006 0.12 0.29 3 -0.5 10 13
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.005 0.086 -10000 0 -0.41 8 8
JUN 0.026 0.024 -10000 0 -0.37 1 1
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.005 0.035 -10000 0 -0.13 5 5
PIK3R1 0.026 0.007 -10000 0 -10000 0 0
cell morphogenesis 0.025 0.11 0.29 14 -0.38 6 20
GRB2/SHC 0.02 0.053 0.17 2 -10000 0 2
FOS 0.005 0.089 -10000 0 -0.36 15 15
GLMN 0.002 0.007 -10000 0 -10000 0 0
cell motility 0.004 0.12 0.33 25 -0.29 1 26
HGF/MET/MUC20 0.01 0.065 -10000 0 -0.16 33 33
cell migration 0.02 0.052 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
CBL 0.026 0.007 -10000 0 -10000 0 0
MET/RANBP10 0.012 0.07 -10000 0 -0.19 28 28
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.009 0.044 -10000 0 -0.26 3 3
MET/MUC20 -0.003 0.064 -10000 0 -0.19 29 29
RAP1B 0.014 0.12 0.26 7 -0.46 9 16
RAP1A 0.008 0.11 0.27 3 -0.46 9 12
HGF/MET/RANBP9 0.023 0.071 -10000 0 -0.16 31 31
RAF1 0.004 0.1 -10000 0 -0.42 10 10
STAT3 0.005 0.056 -10000 0 -0.28 4 4
cell proliferation 0.014 0.07 0.29 4 -0.38 2 6
RPS6KB1 0.007 0.027 -10000 0 -0.33 1 1
MAPK3 -0.004 0.13 0.64 7 -10000 0 7
MAPK1 0.006 0.15 0.63 12 -10000 0 12
RANBP9 0.026 0.006 -10000 0 -10000 0 0
MAPK8 0.021 0.11 0.29 3 -0.44 8 11
SRC 0.001 0.035 -10000 0 -10000 0 0
PI3K 0.019 0.052 0.17 1 -10000 0 1
MET/Glomulin -0.009 0.062 -10000 0 -0.17 30 30
SOS1 0.027 0.003 -10000 0 -10000 0 0
MAP2K1 0.002 0.096 -10000 0 -0.39 10 10
MET -0.007 0.094 -10000 0 -0.28 29 29
MAP4K1 0.011 0.13 0.31 2 -0.47 12 14
PTK2 0.023 0.01 -10000 0 -10000 0 0
MAP2K2 0.002 0.093 -10000 0 -0.4 9 9
BAD -0.016 0.057 -10000 0 -0.64 1 1
MAP2K4 0.01 0.11 0.28 2 -0.42 10 12
SHP2/GRB2/SOS1/GAB1 0.018 0.11 -10000 0 -0.45 9 9
INPPL1 0.026 0.006 -10000 0 -10000 0 0
PXN 0.024 0.031 -10000 0 -0.32 2 2
SH3KBP1 0.027 0.004 -10000 0 -10000 0 0
HGS -0.007 0.032 -10000 0 -0.14 1 1
PLCgamma1/PKC 0.017 0.007 -10000 0 -10000 0 0
HGF 0.021 0.041 -10000 0 -0.28 5 5
RASA1 0.025 0.008 -10000 0 -10000 0 0
NCK1 0.027 0.004 -10000 0 -10000 0 0
PTPRJ 0.026 0.019 -10000 0 -0.28 1 1
NCK/PLCgamma1 0.026 0.049 0.17 2 -10000 0 2
PDPK1 -0.014 0.062 -10000 0 -0.7 1 1
HGF/MET/SHIP 0.021 0.075 -10000 0 -0.16 36 36
Signaling events mediated by PTP1B

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
PDGFRB 0.002 0.083 -10000 0 -0.28 22 22
Jak2/Leptin Receptor -0.03 0.13 -10000 0 -0.38 18 18
PTP1B/AKT1 0.011 0.071 0.2 2 -0.26 7 9
FYN 0.027 0.005 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.001 0.074 0.2 3 -0.28 7 10
EGFR 0.011 0.07 -10000 0 -0.36 9 9
EGF/EGFR -0.006 0.086 -10000 0 -0.29 7 7
CSF1 0.027 0.005 -10000 0 -10000 0 0
AKT1 0.027 0.006 -10000 0 -10000 0 0
INSR 0.027 0.006 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.003 0.079 0.2 2 -0.32 6 8
Insulin Receptor/Insulin 0.019 0.066 -10000 0 -0.26 5 5
HCK 0.025 0.009 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
TYK2 0 0.072 0.22 4 -0.29 5 9
EGF -0.013 0.1 -10000 0 -0.29 32 32
YES1 0.026 0.007 -10000 0 -10000 0 0
CAV1 0.009 0.091 0.23 11 -0.29 8 19
TXN 0.027 0.006 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.018 0.08 0.21 2 -0.31 4 6
cell migration -0.001 0.074 0.28 7 -0.2 3 10
STAT3 0.027 0.005 -10000 0 -10000 0 0
PRLR -0.025 0.13 -10000 0 -0.36 34 34
ITGA2B 0.019 0.057 -10000 0 -0.36 6 6
CSF1R 0.022 0.042 -10000 0 -0.37 3 3
Prolactin Receptor/Prolactin -0.006 0.1 -10000 0 -0.25 37 37
FGR 0.026 0.007 -10000 0 -10000 0 0
PTP1B/p130 Cas 0.01 0.071 -10000 0 -0.28 6 6
Crk/p130 Cas 0.016 0.074 -10000 0 -0.3 4 4
DOK1 -0.002 0.076 0.19 2 -0.29 7 9
JAK2 -0.041 0.14 -10000 0 -0.38 21 21
Jak2/Leptin Receptor/Leptin 0.004 0.1 -10000 0 -0.34 6 6
PIK3R1 0.026 0.007 -10000 0 -10000 0 0
PTPN1 0 0.074 0.2 3 -0.28 7 10
LYN 0.023 0.02 -10000 0 -0.28 1 1
CDH2 0.012 0.068 -10000 0 -0.3 12 12
SRC 0.016 0.085 -10000 0 -0.51 6 6
ITGB3 0.026 0.019 -10000 0 -0.28 1 1
CAT1/PTP1B -0.037 0.14 0.22 12 -0.42 17 29
CAPN1 0.027 0.005 -10000 0 -10000 0 0
CSK 0.027 0.005 -10000 0 -10000 0 0
PI3K 0.031 0.061 -10000 0 -0.25 3 3
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.005 0.093 -10000 0 -0.32 6 6
negative regulation of transcription -0.041 0.13 -10000 0 -0.38 21 21
FCGR2A 0.019 0.049 -10000 0 -0.28 7 7
FER 0.025 0.008 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.032 0.045 -10000 0 -0.24 7 7
BLK -0.042 0.14 -10000 0 -0.35 47 47
Insulin Receptor/Insulin/Shc 0.034 0.011 -10000 0 -10000 0 0
RHOA 0.026 0.006 -10000 0 -10000 0 0
LEPR 0.027 0.004 -10000 0 -10000 0 0
BCAR1 0.026 0.007 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.027 0.004 -10000 0 -10000 0 0
mol:NADPH 0 0.003 -10000 0 -10000 0 0
TRPV6 -0.062 0.17 0.23 2 -0.45 23 25
PRL 0.015 0.046 -10000 0 -0.28 6 6
SOCS3 0.013 0.13 -10000 0 -1.1 4 4
SPRY2 0.025 0.026 -10000 0 -0.38 1 1
Insulin Receptor/Insulin/IRS1 0.034 0.018 -10000 0 -0.22 1 1
CSF1/CSF1R 0.017 0.079 0.21 2 -0.29 4 6
Ras protein signal transduction -0.001 0.058 0.5 3 -10000 0 3
IRS1 0.026 0.024 -10000 0 -0.37 1 1
INS 0 0.002 -10000 0 -10000 0 0
LEP 0 0.093 -10000 0 -0.34 19 19
STAT5B -0.009 0.087 0.2 1 -0.34 9 10
STAT5A -0.009 0.087 0.2 1 -0.34 9 10
GRB2 0.027 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0 0.084 0.2 2 -0.27 7 9
CSN2 -0.016 0.076 -10000 0 -0.38 1 1
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
LAT 0.019 0.064 -10000 0 -0.47 3 3
YBX1 0.034 0.007 -10000 0 -10000 0 0
LCK 0.02 0.048 -10000 0 -0.29 6 6
SHC1 0.026 0.006 -10000 0 -10000 0 0
NOX4 -0.075 0.14 -10000 0 -0.28 91 91
Nectin adhesion pathway

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
PDGFRB 0.002 0.083 -10000 0 -0.28 22 22
alphaV beta3 Integrin 0.039 0.016 -10000 0 -0.19 1 1
PTK2 0.013 0.072 -10000 0 -0.32 5 5
positive regulation of JNK cascade 0.014 0.079 -10000 0 -0.28 4 4
CDC42/GDP 0.036 0.11 -10000 0 -0.36 7 7
Rac1/GDP 0.035 0.11 -10000 0 -0.36 7 7
RAP1B 0.026 0.006 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.027 0.005 -10000 0 -10000 0 0
CDC42/GTP 0.027 0.098 -10000 0 -0.33 4 4
nectin-3/I-afadin 0.026 0.059 -10000 0 -0.26 11 11
RAPGEF1 0.017 0.099 0.29 2 -0.36 9 11
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.008 0.097 -10000 0 -0.4 9 9
PDGFB-D/PDGFRB 0.002 0.083 -10000 0 -0.28 22 22
TLN1 -0.001 0.02 -10000 0 -10000 0 0
Rap1/GTP 0.012 0.072 -10000 0 -0.27 7 7
IQGAP1 0.026 0.006 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.047 0.017 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.026 0.059 -10000 0 -0.26 11 11
PVR 0.024 0.027 -10000 0 -0.28 2 2
Necl-5(dimer) 0.024 0.027 -10000 0 -0.28 2 2
mol:GDP 0.025 0.12 -10000 0 -0.43 9 9
MLLT4 0.026 0.007 -10000 0 -10000 0 0
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
PI3K 0.041 0.078 -10000 0 -0.19 7 7
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.025 0.052 -10000 0 -0.19 14 14
positive regulation of lamellipodium assembly 0.018 0.085 -10000 0 -0.3 8 8
PVRL1 0.01 0.068 -10000 0 -0.28 14 14
PVRL3 0.011 0.078 -10000 0 -0.37 11 11
PVRL2 0.025 0.02 -10000 0 -0.28 1 1
PIK3R1 0.026 0.007 -10000 0 -10000 0 0
CDH1 0.02 0.048 -10000 0 -0.37 4 4
CLDN1 -0.19 0.14 -10000 0 -0.28 193 193
JAM-A/CLDN1 -0.094 0.095 -10000 0 -0.25 12 12
SRC 0.007 0.11 -10000 0 -0.41 15 15
ITGB3 0.026 0.019 -10000 0 -0.28 1 1
nectin-1(dimer)/I-afadin/I-afadin 0.025 0.052 -10000 0 -0.19 14 14
FARP2 0.024 0.13 -10000 0 -0.43 4 4
RAC1 0.026 0.007 -10000 0 -10000 0 0
CTNNA1 0.026 0.006 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.039 0.053 -10000 0 -0.2 11 11
nectin-1/I-afadin 0.025 0.052 -10000 0 -0.19 14 14
nectin-2/I-afadin 0.036 0.019 -10000 0 -0.19 1 1
RAC1/GTP/IQGAP1/filamentous actin 0.033 0.012 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.031 0.065 -10000 0 -0.18 22 22
CDC42/GTP/IQGAP1/filamentous actin 0.034 0.011 -10000 0 -10000 0 0
F11R 0.027 0.005 -10000 0 -10000 0 0
positive regulation of filopodium formation 0.014 0.079 -10000 0 -0.28 4 4
alphaV/beta3 Integrin/Talin 0.034 0.053 0.2 9 -10000 0 9
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.036 0.019 -10000 0 -0.19 1 1
nectin-2(dimer)/I-afadin/I-afadin 0.036 0.019 -10000 0 -0.19 1 1
PIP5K1C 0.002 0.025 -10000 0 -10000 0 0
VAV2 0.024 0.13 -10000 0 -0.49 8 8
RAP1/GDP 0.038 0.1 -10000 0 -0.34 5 5
ITGAV 0.027 0.005 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.041 0.049 -10000 0 -0.21 9 9
nectin-3(dimer)/I-afadin/I-afadin 0.026 0.059 -10000 0 -0.26 11 11
Rac1/GTP 0.025 0.1 -10000 0 -0.37 8 8
PTPRM 0.007 0.031 -10000 0 -0.15 10 10
E-cadherin/beta catenin/alpha catenin 0.051 0.061 -10000 0 -0.25 1 1
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.026 0.007 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 -0.001 0.038 0.22 5 -0.18 3 8
RFC1 -0.004 0.026 0.16 2 -0.18 3 5
PRKDC 0.008 0.064 0.22 17 -0.22 4 21
RIPK1 0.027 0.007 -10000 0 -10000 0 0
CASP7 0.008 0.086 -10000 0 -0.64 4 4
FASLG/FAS/FADD/FAF1 0.01 0.042 0.18 2 -0.2 4 6
MAP2K4 -0.016 0.13 -10000 0 -0.37 23 23
mol:ceramide 0.008 0.07 -10000 0 -0.25 10 10
GSN -0.006 0.041 0.22 2 -0.22 6 8
FASLG/FAS/FADD/FAF1/Caspase 8 0.011 0.056 -10000 0 -0.24 5 5
FAS 0.021 0.024 -10000 0 -0.28 1 1
BID -0.015 0.025 0.24 1 -0.17 1 2
MAP3K1 0.002 0.089 0.2 1 -0.42 5 6
MAP3K7 0.025 0.009 -10000 0 -10000 0 0
RB1 0.005 0.051 0.24 10 -0.18 2 12
CFLAR 0.028 0.003 -10000 0 -10000 0 0
HGF/MET 0.017 0.08 -10000 0 -0.17 39 39
ARHGDIB -0.001 0.038 0.21 5 -0.18 3 8
FADD 0.022 0.016 -10000 0 -10000 0 0
actin filament polymerization 0.014 0.055 0.19 19 -0.22 2 21
NFKB1 -0.005 0.12 -10000 0 -0.67 6 6
MAPK8 -0.03 0.17 -10000 0 -0.47 28 28
DFFA -0.001 0.037 0.21 5 -0.18 3 8
DNA fragmentation during apoptosis -0.01 0.051 0.21 4 -0.18 3 7
FAS/FADD/MET 0.02 0.069 -10000 0 -0.16 28 28
CFLAR/RIP1 0.04 0.011 -10000 0 -10000 0 0
FAIM3 0.012 0.066 -10000 0 -0.29 12 12
FAF1 0.021 0.02 -10000 0 -10000 0 0
PARP1 -0.004 0.027 0.17 1 -0.18 3 4
DFFB -0.001 0.034 0.21 4 -0.18 3 7
CHUK -0.005 0.1 -10000 0 -0.65 5 5
FASLG 0.013 0.057 -10000 0 -0.35 6 6
FAS/FADD 0.031 0.026 -10000 0 -0.19 1 1
HGF 0.021 0.041 -10000 0 -0.28 5 5
LMNA -0.011 0.04 0.19 1 -10000 0 1
CASP6 -0.003 0.023 0.17 1 -0.18 2 3
CASP10 0.02 0.037 -10000 0 -0.37 2 2
CASP3 0.001 0.021 0.19 2 -10000 0 2
PTPN13 0.016 0.061 -10000 0 -0.36 7 7
CASP8 -0.013 0.039 0.16 12 -10000 0 12
IL6 -0.091 0.36 -10000 0 -1.1 28 28
MET -0.007 0.094 -10000 0 -0.28 29 29
ICAD/CAD 0 0.05 0.36 4 -10000 0 4
FASLG/FAS/FADD/FAF1/Caspase 10 0.008 0.071 -10000 0 -0.26 10 10
activation of caspase activity by cytochrome c -0.015 0.025 0.24 1 -0.17 1 2
PAK2 0.004 0.052 0.23 11 -0.19 3 14
BCL2 0.024 0.025 -10000 0 -0.37 1 1
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.002 0.076 -10000 0 -0.38 6 6
NFATC2 0.011 0.1 -10000 0 -0.53 2 2
NFATC3 -0.017 0.07 -10000 0 -0.27 10 10
CD40LG -0.14 0.23 -10000 0 -0.72 14 14
ITCH 0.017 0.042 -10000 0 -10000 0 0
CBLB 0.02 0.043 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.092 0.18 -10000 0 -0.59 13 13
JUNB 0.025 0.024 -10000 0 -0.37 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 0.025 0.054 -10000 0 -0.24 10 10
T cell anergy 0.013 0.074 -10000 0 -0.34 10 10
TLE4 0.007 0.065 -10000 0 -0.36 2 2
Jun/NFAT1-c-4/p21SNFT -0.056 0.2 -10000 0 -0.74 11 11
AP-1/NFAT1-c-4 -0.14 0.25 -10000 0 -0.8 12 12
IKZF1 0.003 0.088 -10000 0 -0.55 4 4
T-helper 2 cell differentiation -0.027 0.12 -10000 0 -0.63 2 2
AP-1/NFAT1 -0.026 0.11 -10000 0 -0.33 5 5
CALM1 0.027 0.036 -10000 0 -10000 0 0
EGR2 -0.028 0.16 -10000 0 -0.87 5 5
EGR3 -0.055 0.26 -10000 0 -1.1 15 15
NFAT1/FOXP3 0.009 0.11 -10000 0 -0.36 6 6
EGR1 0.016 0.057 -10000 0 -0.35 6 6
JUN -0.018 0.046 -10000 0 -0.37 1 1
EGR4 -0.045 0.13 -10000 0 -0.29 60 60
mol:Ca2+ 0.002 0.029 -10000 0 -10000 0 0
GBP3 0 0.097 -10000 0 -0.57 5 5
FOSL1 0.001 0.087 -10000 0 -0.29 22 22
NFAT1-c-4/MAF/IRF4 -0.028 0.2 -10000 0 -0.76 12 12
DGKA 0.007 0.065 -10000 0 -0.41 1 1
CREM 0.026 0.006 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.024 0.18 -10000 0 -0.72 11 11
CTLA4 -0.024 0.12 -10000 0 -0.34 16 16
NFAT1-c-4 (dimer)/EGR1 -0.025 0.19 -10000 0 -0.76 11 11
NFAT1-c-4 (dimer)/EGR4 -0.05 0.2 -10000 0 -0.77 12 12
FOS -0.037 0.093 -10000 0 -0.38 15 15
IFNG -0.06 0.16 -10000 0 -0.8 5 5
T cell activation -0.024 0.12 -10000 0 -10000 0 0
MAF 0.021 0.042 -10000 0 -0.37 3 3
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.029 0.14 0.62 11 -10000 0 11
TNF -0.067 0.19 -10000 0 -0.72 13 13
FASLG -0.061 0.29 -10000 0 -1 18 18
TBX21 0.004 0.051 -10000 0 -0.28 3 3
BATF3 0.027 0.005 -10000 0 -10000 0 0
PRKCQ 0.019 0.057 -10000 0 -0.38 5 5
PTPN1 0.007 0.067 -10000 0 -0.37 2 2
NFAT1-c-4/ICER1 -0.022 0.18 -10000 0 -0.72 11 11
GATA3 0.019 0.048 -10000 0 -0.29 6 6
T-helper 1 cell differentiation -0.059 0.16 -10000 0 -0.78 5 5
IL2RA -0.074 0.16 -10000 0 -0.56 9 9
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.005 0.064 -10000 0 -0.41 1 1
E2F1 0.016 0.058 -10000 0 -0.28 10 10
PPARG 0.024 0.034 -10000 0 -0.37 2 2
SLC3A2 0.008 0.067 -10000 0 -0.43 1 1
IRF4 -0.013 0.12 -10000 0 -0.37 27 27
PTGS2 -0.14 0.24 -10000 0 -0.71 19 19
CSF2 -0.17 0.25 -10000 0 -0.68 22 22
JunB/Fra1/NFAT1-c-4 -0.02 0.18 -10000 0 -0.72 11 11
IL4 -0.028 0.12 -10000 0 -0.66 2 2
IL5 -0.13 0.22 -10000 0 -0.7 14 14
IL2 -0.024 0.12 -10000 0 -10000 0 0
IL3 -0.041 0.14 -10000 0 -0.55 15 15
RNF128 0.008 0.095 -10000 0 -0.45 11 11
NFATC1 -0.029 0.14 -10000 0 -0.62 11 11
CDK4 0.014 0.094 -10000 0 -10000 0 0
PTPRK 0.007 0.066 -10000 0 -0.41 1 1
IL8 -0.19 0.25 -10000 0 -0.68 22 22
POU2F1 0.026 0.019 -10000 0 -0.28 1 1
Cellular roles of Anthrax toxin

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
ANTXR1 0.02 0.049 -10000 0 -0.28 7 7
ANTXR2 0.022 0.042 -10000 0 -0.37 3 3
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.007 -10000 0 -0.039 10 10
monocyte activation -0.004 0.089 -10000 0 -0.36 15 15
MAP2K2 -0.013 0.13 -10000 0 -0.56 14 14
MAP2K1 -0.004 0.007 -10000 0 -10000 0 0
MAP2K7 -0.004 0.007 -10000 0 -10000 0 0
MAP2K6 -0.006 0.016 -10000 0 -0.18 2 2
CYAA -0.01 0.027 -10000 0 -0.14 10 10
MAP2K4 -0.004 0.006 -10000 0 -10000 0 0
IL1B -0.015 0.045 0.19 2 -0.14 26 28
Channel 0.027 0.037 -10000 0 -0.16 10 10
NLRP1 -0.007 0.02 -10000 0 -0.14 5 5
CALM1 0.027 0.005 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.005 0.078 -10000 0 -0.38 11 11
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.007 0.039 10 -10000 0 10
MAPK3 -0.004 0.007 -10000 0 -10000 0 0
MAPK1 -0.004 0.007 -10000 0 -10000 0 0
PGR -0.019 0.049 -10000 0 -0.18 24 24
PA/Cellular Receptors 0.028 0.041 -10000 0 -0.17 10 10
apoptosis -0.002 0.007 -10000 0 -0.039 10 10
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.027 0.034 -10000 0 -0.14 10 10
macrophage activation -0.007 0.007 -10000 0 -10000 0 0
TNF 0.011 0.07 -10000 0 -0.31 12 12
VCAM1 0.002 0.075 -10000 0 -0.34 11 11
platelet activation -0.005 0.078 -10000 0 -0.38 11 11
MAPKKK cascade 0.002 0.014 -10000 0 -0.067 4 4
IL18 -0.004 0.025 0.19 1 -0.16 4 5
negative regulation of macrophage activation -0.002 0.007 -10000 0 -0.039 10 10
LEF -0.002 0.007 -10000 0 -0.039 10 10
CASP1 -0.001 0.011 -10000 0 -0.075 4 4
mol:cAMP -0.005 0.078 -10000 0 -0.38 11 11
necrosis -0.002 0.007 -10000 0 -0.039 10 10
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.027 0.035 -10000 0 -0.14 10 10
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.011 0.005 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.034 0.02 -10000 0 -10000 0 0
CDKN1B 0.003 0.067 0.2 1 -0.3 10 11
CDKN1A 0.002 0.07 0.2 1 -0.34 7 8
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.022 0.027 -10000 0 -0.28 2 2
FOXO3 0.003 0.064 -10000 0 -0.32 7 7
AKT1 0.003 0.056 -10000 0 -0.32 6 6
BAD 0.027 0.004 -10000 0 -10000 0 0
AKT3 -0.001 0.061 -10000 0 -0.26 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.002 0.069 -10000 0 -0.31 9 9
AKT1/ASK1 0.024 0.081 -10000 0 -0.3 9 9
BAD/YWHAZ 0.045 0.022 -10000 0 -10000 0 0
RICTOR 0.025 0.009 -10000 0 -10000 0 0
RAF1 0.027 0.003 -10000 0 -10000 0 0
JNK cascade -0.022 0.079 0.29 9 -10000 0 9
TSC1 0.004 0.064 -10000 0 -0.3 9 9
YWHAZ 0.023 0.01 -10000 0 -10000 0 0
AKT1/RAF1 0.026 0.087 0.26 1 -0.31 9 10
EP300 0.027 0.005 -10000 0 -10000 0 0
mol:GDP 0.005 0.069 -10000 0 -0.31 10 10
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.005 0.06 -10000 0 -0.33 5 5
YWHAQ 0.027 0.004 -10000 0 -10000 0 0
TBC1D4 -0.006 0.051 0.14 1 -0.2 16 17
MAP3K5 0.027 0.005 -10000 0 -10000 0 0
MAPKAP1 0.027 0.005 -10000 0 -10000 0 0
negative regulation of cell cycle -0.032 0.082 0.32 5 -0.19 13 18
YWHAH 0.027 0.004 -10000 0 -10000 0 0
AKT1S1 0.002 0.07 0.2 1 -0.31 9 10
CASP9 0.009 0.053 0.2 2 -0.28 4 6
YWHAB 0.023 0.011 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.028 0.088 0.34 2 -0.3 8 10
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.032 0.061 -10000 0 -0.21 14 14
YWHAE 0.025 0.008 -10000 0 -10000 0 0
SRC 0.024 0.009 -10000 0 -10000 0 0
AKT2/p21CIP1 -0.003 0.083 0.22 2 -0.32 8 10
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0 0.072 -10000 0 -0.33 10 10
CHUK 0.002 0.067 -10000 0 -0.31 8 8
BAD/BCL-XL 0.023 0.077 0.26 1 -0.29 9 10
mTORC2 0.031 0.012 -10000 0 -10000 0 0
AKT2 -0.001 0.059 -10000 0 -0.26 13 13
FOXO1-3a-4/14-3-3 family 0.032 0.11 0.24 14 -0.39 8 22
PDPK1 0.004 0.089 -10000 0 -0.36 15 15
MDM2 0.007 0.07 0.2 3 -0.32 7 10
MAPKKK cascade -0.026 0.086 0.3 9 -0.26 1 10
MDM2/Cbp/p300 0.038 0.085 0.3 1 -0.32 4 5
TSC1/TSC2 0.005 0.055 -10000 0 -0.34 4 4
proteasomal ubiquitin-dependent protein catabolic process 0.036 0.082 0.29 1 -0.31 4 5
glucose import -0.032 0.094 0.21 10 -0.2 50 60
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.007 0.065 0.18 2 -0.33 4 6
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.04 0.083 0.12 1 -0.2 50 51
GSK3A 0.003 0.069 0.2 2 -0.3 10 12
FOXO1 0.005 0.074 0.2 6 -0.3 11 17
GSK3B 0.002 0.067 0.2 1 -0.31 8 9
SFN 0.014 0.066 -10000 0 -0.34 9 9
G1/S transition of mitotic cell cycle 0.007 0.079 0.24 5 -0.31 7 12
p27Kip1/14-3-3 family 0.029 0.053 -10000 0 -0.4 1 1
PRKACA 0.027 0.005 -10000 0 -10000 0 0
KPNA1 0.027 0.005 -10000 0 -10000 0 0
HSP90AA1 0.026 0.006 -10000 0 -10000 0 0
YWHAG 0.026 0.007 -10000 0 -10000 0 0
RHEB 0.026 0.006 -10000 0 -10000 0 0
CREBBP 0.026 0.007 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.024 0.009 -10000 0 -10000 0 0
NFATC1 -0.2 0.16 -10000 0 -0.46 37 37
NFATC2 0.018 0.061 0.15 3 -0.27 6 9
NFATC3 0.019 0.008 -10000 0 -10000 0 0
YWHAE 0.025 0.008 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.021 0.086 0.24 1 -0.31 12 13
Exportin 1/Ran/NUP214 0.052 0.014 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.007 0.087 -10000 0 -0.31 9 9
BCL2/BAX 0.034 0.023 -10000 0 -0.26 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 0.019 0.008 -10000 0 -10000 0 0
CaM/Ca2+ 0.019 0.008 -10000 0 -10000 0 0
BAX 0.026 0.006 -10000 0 -10000 0 0
MAPK14 0.027 0.006 -10000 0 -10000 0 0
BAD 0.027 0.004 -10000 0 -10000 0 0
CABIN1/MEF2D -0.013 0.084 -10000 0 -0.3 10 10
Calcineurin A alpha-beta B1/BCL2 0.024 0.025 -10000 0 -0.37 1 1
FKBP8 0.027 0.004 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.013 0.083 0.3 10 -10000 0 10
KPNB1 0.028 0 -10000 0 -10000 0 0
KPNA2 0.017 0.055 -10000 0 -0.28 9 9
XPO1 0.027 0.003 -10000 0 -10000 0 0
SFN 0.014 0.066 -10000 0 -0.34 9 9
MAP3K8 0.026 0.006 -10000 0 -10000 0 0
NFAT4/CK1 alpha 0.027 0.02 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 0.05 0.078 -10000 0 -0.27 2 2
CABIN1 -0.021 0.086 0.24 1 -0.31 12 13
CALM1 0.027 0.006 -10000 0 -10000 0 0
RAN 0.027 0.005 -10000 0 -10000 0 0
MAP3K1 0.026 0.007 -10000 0 -10000 0 0
CAMK4 0.018 0.053 -10000 0 -0.37 5 5
mol:Ca2+ 0 0.002 -10000 0 -10000 0 0
MAPK3 0.027 0.004 -10000 0 -10000 0 0
YWHAH 0.027 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.034 0.032 -10000 0 -0.19 5 5
YWHAB 0.023 0.011 -10000 0 -10000 0 0
MAPK8 0.027 0.005 -10000 0 -10000 0 0
MAPK9 0.026 0.006 -10000 0 -10000 0 0
YWHAG 0.026 0.007 -10000 0 -10000 0 0
FKBP1A 0.024 0.009 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.15 0.14 -10000 0 -0.42 31 31
PRKCH 0.027 0.005 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.036 0.017 -10000 0 -10000 0 0
CASP3 0.025 0.008 -10000 0 -10000 0 0
PIM1 0.025 0.025 -10000 0 -0.37 1 1
Calcineurin A alpha-beta B1/FKBP12/FK506 0.016 0.007 -10000 0 -10000 0 0
apoptosis 0.017 0.014 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.011 0.035 -10000 0 -10000 0 0
PRKCB 0.005 0.09 -10000 0 -0.37 15 15
PRKCE 0.027 0.004 -10000 0 -10000 0 0
JNK2/NFAT4 0.024 0.041 -10000 0 -10000 0 0
BAD/BCL-XL 0.036 0.014 -10000 0 -10000 0 0
PRKCD 0.027 0.005 -10000 0 -10000 0 0
NUP214 0.027 0.005 -10000 0 -10000 0 0
PRKCZ 0.026 0.007 -10000 0 -10000 0 0
PRKCA 0.026 0.024 -10000 0 -0.37 1 1
PRKCG -0.092 0.15 -10000 0 -0.28 104 104
PRKCQ 0.019 0.053 -10000 0 -0.37 5 5
FKBP38/BCL2 0.035 0.022 -10000 0 -0.26 1 1
EP300 0.026 0.01 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 -0.26 0.17 -10000 0 -0.37 195 195
NFATc/JNK1 -0.18 0.16 -10000 0 -0.44 35 35
CaM/Ca2+/FKBP38 0.034 0.013 -10000 0 -10000 0 0
FKBP12/FK506 0.018 0.007 -10000 0 -10000 0 0
CSNK1A1 0.013 0.008 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.028 0.037 -10000 0 -0.22 5 5
NFATc/ERK1 -0.18 0.16 -10000 0 -0.44 36 36
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.007 0.091 0.21 1 -0.3 10 11
NR4A1 0.019 0.089 0.21 4 -0.36 10 14
GSK3B 0.027 0.005 -10000 0 -10000 0 0
positive T cell selection 0.019 0.008 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.02 0.043 0.14 2 -0.2 4 6
RCH1/ KPNB1 0.033 0.042 -10000 0 -0.19 9 9
YWHAQ 0.027 0.004 -10000 0 -10000 0 0
PRKACA 0.027 0.005 -10000 0 -10000 0 0
AKAP5 0.021 0.041 -10000 0 -0.28 5 5
MEF2D 0.025 0.011 -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 -0.18 0.16 -10000 0 -0.44 36 36
CREBBP 0.025 0.011 -10000 0 -10000 0 0
BCL2 0.024 0.025 -10000 0 -0.37 1 1
S1P1 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
VEGFR2 homodimer/VEGFA homodimer 0.036 0.019 -10000 0 -0.2 1 1
PDGFRB 0.002 0.083 -10000 0 -0.28 22 22
SPHK1 -0.004 0.081 -10000 0 -0.62 4 4
mol:S1P -0.007 0.071 -10000 0 -0.53 4 4
S1P1/S1P/Gi -0.02 0.13 -10000 0 -0.44 15 15
GNAO1 -0.008 0.11 -10000 0 -0.34 25 25
PDGFB-D/PDGFRB/PLCgamma1 -0.005 0.14 0.26 11 -0.4 12 23
PLCG1 -0.029 0.11 -10000 0 -0.41 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.002 0.083 -10000 0 -0.28 22 22
GNAI2 0.026 0.008 -10000 0 -10000 0 0
GNAI3 0.026 0.008 -10000 0 -10000 0 0
GNAI1 0.018 0.054 -10000 0 -0.37 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.004 0.013 -10000 0 -0.17 1 1
S1P1/S1P -0.001 0.059 -10000 0 -0.33 4 4
negative regulation of cAMP metabolic process -0.019 0.13 -10000 0 -0.42 15 15
MAPK3 -0.028 0.14 0.33 1 -0.49 15 16
calcium-dependent phospholipase C activity -0.001 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.005 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.004 -10000 0 -10000 0 0
KDR 0.023 0.033 -10000 0 -0.28 3 3
PLCB2 0.011 0.07 0.21 6 -0.3 4 10
RAC1 0.026 0.007 -10000 0 -10000 0 0
RhoA/GTP -0.001 0.051 -10000 0 -0.28 4 4
receptor internalization -0.002 0.056 -10000 0 -0.31 4 4
PTGS2 -0.031 0.18 0.37 1 -0.75 10 11
Rac1/GTP 0.001 0.051 -10000 0 -0.29 4 4
RHOA 0.027 0.005 -10000 0 -10000 0 0
VEGFA 0.025 0.008 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.019 0.13 -10000 0 -0.42 15 15
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.007 0.085 -10000 0 -0.37 13 13
MAPK1 -0.028 0.14 -10000 0 -0.49 15 15
S1P1/S1P/PDGFB-D/PDGFRB 0.008 0.08 0.23 4 -0.28 3 7
ABCC1 0.027 0.005 -10000 0 -10000 0 0
IGF1 pathway

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
NCK2 0.027 0.003 -10000 0 -10000 0 0
PTK2 0.023 0.01 -10000 0 -10000 0 0
CRKL -0.003 0.055 0.16 2 -0.2 11 13
GRB2/SOS1/SHC 0.052 0.015 -10000 0 -10000 0 0
HRAS 0.026 0.006 -10000 0 -10000 0 0
IRS1/Crk 0.004 0.058 -10000 0 -0.2 12 12
IGF-1R heterotetramer/IGF1/PTP1B 0.017 0.07 -10000 0 -0.16 32 32
AKT1 -0.021 0.071 0.18 13 -0.3 1 14
BAD -0.023 0.067 0.17 13 -0.28 1 14
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.003 0.053 0.16 2 -0.21 9 11
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.011 0.062 -10000 0 -0.2 12 12
RAF1 -0.006 0.073 0.28 1 -10000 0 1
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.036 0.071 -10000 0 -0.19 12 12
YWHAZ 0.023 0.01 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.011 0.065 -10000 0 -0.22 12 12
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
RPS6KB1 -0.02 0.072 0.18 14 -0.3 1 15
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.003 0.08 0.35 3 -0.28 1 4
PXN 0.024 0.031 -10000 0 -0.32 2 2
PIK3R1 0.026 0.007 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.039 0.008 -10000 0 -10000 0 0
HRAS/GTP 0.011 0.056 -10000 0 -0.18 10 10
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.046 0.074 -10000 0 -0.2 1 1
IGF-1R heterotetramer 0.018 0.028 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck 0.025 0.068 -10000 0 -0.2 12 12
Crk/p130 Cas/Paxillin 0.033 0.071 0.22 2 -0.19 9 11
IGF1R 0.018 0.028 -10000 0 -10000 0 0
IGF1 -0.017 0.12 -10000 0 -0.31 37 37
IRS2/Crk -0.003 0.065 0.16 1 -0.2 17 18
PI3K 0.033 0.068 -10000 0 -0.2 9 9
apoptosis 0.018 0.056 0.25 1 -0.17 10 11
HRAS/GDP 0.02 0.004 -10000 0 -10000 0 0
PRKCD -0.005 0.068 -10000 0 -0.3 11 11
RAF1/14-3-3 E 0.004 0.083 0.33 2 -0.31 2 4
BAD/14-3-3 -0.018 0.058 0.18 9 -0.27 1 10
PRKCZ -0.023 0.068 0.18 11 -0.3 1 12
Crk/p130 Cas/Paxillin/FAK1 0.008 0.063 -10000 0 -0.27 1 1
PTPN1 0.022 0.011 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.005 0.078 -10000 0 -0.3 14 14
BCAR1 0.026 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.034 0.072 -10000 0 -0.19 11 11
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.027 0.003 -10000 0 -10000 0 0
IRS1/NCK2 0.012 0.063 -10000 0 -0.2 12 12
GRB10 0.025 0.019 -10000 0 -0.28 1 1
PTPN11 -0.004 0.056 0.16 2 -0.2 12 14
IRS1 -0.003 0.061 -10000 0 -0.22 11 11
IRS2 -0.011 0.065 0.16 1 -0.2 20 21
IGF-1R heterotetramer/IGF1 0.005 0.089 -10000 0 -0.22 35 35
GRB2 0.027 0.004 -10000 0 -10000 0 0
PDPK1 -0.008 0.073 0.18 11 -0.31 1 12
YWHAE 0.025 0.008 -10000 0 -10000 0 0
PRKD1 -0.007 0.072 -10000 0 -0.29 13 13
SHC1 0.026 0.006 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 -0.006 0.086 -10000 0 -0.34 12 12
ACTA1 -0.015 0.066 -10000 0 -0.28 5 5
NUMA1 -0.007 0.11 -10000 0 -0.38 13 13
SPTAN1 -0.009 0.065 0.19 6 -0.26 5 11
LIMK1 -0.009 0.068 0.19 8 -0.27 4 12
BIRC3 0.021 0.043 -10000 0 -0.32 4 4
BIRC2 0.026 0.006 -10000 0 -10000 0 0
BAX 0.026 0.006 -10000 0 -10000 0 0
CASP10 -0.019 0.04 -10000 0 -0.17 16 16
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.027 0.003 -10000 0 -10000 0 0
PTK2 -0.01 0.11 -10000 0 -0.44 12 12
DIABLO 0.027 0.005 -10000 0 -10000 0 0
apoptotic nuclear changes -0.009 0.065 0.19 6 -0.27 4 10
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.027 0.004 -10000 0 -10000 0 0
GSN -0.016 0.071 0.19 3 -0.31 6 9
MADD 0.027 0.004 -10000 0 -10000 0 0
TFAP2A -0.044 0.19 -10000 0 -0.69 18 18
BID 0.001 0.022 -10000 0 -0.14 2 2
MAP3K1 -0.021 0.11 -10000 0 -0.42 19 19
TRADD 0.026 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.039 0.009 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.01 0.065 0.18 6 -0.25 5 11
CASP9 0.026 0.006 -10000 0 -10000 0 0
DNA repair -0.004 0.03 0.18 1 -10000 0 1
neuron apoptosis -0.005 0.14 -10000 0 -0.66 11 11
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.01 0.097 -10000 0 -0.41 8 8
APAF1 0.027 0.003 -10000 0 -10000 0 0
CASP6 -0.015 0.18 -10000 0 -0.92 10 10
TRAF2 0.027 0.005 -10000 0 -10000 0 0
ICAD/CAD -0.011 0.07 0.32 4 -0.28 3 7
CASP7 -0.002 0.052 0.25 1 -0.24 7 8
KRT18 -0.003 0.12 -10000 0 -0.57 9 9
apoptosis -0.01 0.1 0.39 2 -0.42 11 13
DFFA -0.012 0.063 0.19 4 -0.27 4 8
DFFB -0.013 0.062 0.19 3 -0.28 3 6
PARP1 0.004 0.03 -10000 0 -0.18 1 1
actin filament polymerization 0.012 0.069 0.29 2 -0.19 4 6
TNF 0.011 0.07 -10000 0 -0.31 12 12
CYCS 0.011 0.033 0.16 2 -0.16 1 3
SATB1 -0.016 0.18 0.29 1 -0.88 10 11
SLK -0.013 0.063 0.26 2 -0.26 5 7
p15 BID/BAX 0.016 0.038 -10000 0 -0.19 2 2
CASP2 0.009 0.058 0.21 3 -0.32 5 8
JNK cascade 0.02 0.11 0.42 19 -10000 0 19
CASP3 -0.014 0.063 -10000 0 -0.25 7 7
LMNB2 -0.001 0.13 0.2 4 -0.44 18 22
RIPK1 0.026 0.006 -10000 0 -10000 0 0
CASP4 0.026 0.006 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.062 0.034 -10000 0 -0.19 2 2
negative regulation of DNA binding -0.042 0.19 -10000 0 -0.68 18 18
stress fiber formation -0.012 0.063 0.26 2 -0.25 5 7
GZMB 0 0.051 -10000 0 -0.2 16 16
CASP1 0.014 0.008 -10000 0 -10000 0 0
LMNB1 -0.01 0.16 0.23 1 -0.53 18 19
APP -0.005 0.14 -10000 0 -0.67 11 11
TNFRSF1A 0.026 0.006 -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 -0.01 0.1 0.31 2 -0.42 12 14
LMNA 0.011 0.11 0.23 1 -0.41 13 14
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.011 0.061 -10000 0 -0.32 6 6
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.012 0.061 0.2 2 -0.26 5 7
APAF-1/Caspase 9 0.012 0.081 -10000 0 -0.64 4 4
nuclear fragmentation during apoptosis -0.007 0.1 -10000 0 -0.38 13 13
CFL2 -0.012 0.07 0.19 4 -0.3 2 6
GAS2 -0.021 0.07 0.18 2 -0.25 7 9
positive regulation of apoptosis 0.001 0.14 0.2 4 -0.54 14 18
PRF1 0.027 0.005 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.024 0.013 -9999 0 -10000 0 0
SVIL 0.018 0.046 -9999 0 -0.28 6 6
ZNF318 0.027 0.011 -9999 0 -10000 0 0
JMJD2C 0 0.014 -9999 0 -0.063 12 12
T-DHT/AR/Ubc9 0.008 0.082 -9999 0 -0.23 24 24
CARM1 0.027 0.005 -9999 0 -10000 0 0
PRDX1 0.027 0.003 -9999 0 -10000 0 0
PELP1 0.026 0.007 -9999 0 -10000 0 0
CTNNB1 0.025 0.012 -9999 0 -10000 0 0
AKT1 0.026 0.007 -9999 0 -10000 0 0
PTK2B 0.022 0.013 -9999 0 -10000 0 0
MED1 0.026 0.008 -9999 0 -10000 0 0
MAK 0.023 0.038 -9999 0 -0.28 4 4
response to oxidative stress 0 0.001 -9999 0 -10000 0 0
HIP1 0.024 0.013 -9999 0 -10000 0 0
GSN 0.016 0.059 -9999 0 -0.37 6 6
NCOA2 0.024 0.009 -9999 0 -10000 0 0
NCOA6 0.023 0.013 -9999 0 -10000 0 0
DNA-PK 0.048 0.027 -9999 0 -0.16 1 1
NCOA4 0.027 0.004 -9999 0 -10000 0 0
PIAS3 0.025 0.011 -9999 0 -10000 0 0
cell proliferation -0.005 0.092 -9999 0 -0.46 9 9
XRCC5 0.028 0.003 -9999 0 -10000 0 0
UBE3A 0.024 0.014 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.005 0.076 -9999 0 -0.21 28 28
FHL2 0.006 0.1 -9999 0 -0.77 4 4
RANBP9 0.024 0.012 -9999 0 -10000 0 0
JMJD1A -0.002 0.037 -9999 0 -0.13 20 20
CDK6 0.02 0.038 -9999 0 -0.28 4 4
TGFB1I1 0.021 0.04 -9999 0 -0.34 3 3
T-DHT/AR/CyclinD1 0.007 0.081 -9999 0 -0.22 24 24
XRCC6 0.027 0.005 -9999 0 -10000 0 0
T-DHT/AR 0.014 0.099 -9999 0 -0.25 24 24
CTDSP1 0.027 0.004 -9999 0 -10000 0 0
CTDSP2 0.027 0.007 -9999 0 -10000 0 0
BRCA1 0.022 0.034 -9999 0 -0.28 3 3
TCF4 0.025 0.01 -9999 0 -10000 0 0
CDKN2A -0.047 0.13 -9999 0 -0.28 62 62
SRF 0.029 0.016 -9999 0 -0.14 1 1
NKX3-1 -0.017 0.13 -9999 0 -0.53 11 11
KLK3 0.001 0.062 -9999 0 -10000 0 0
TMF1 0.027 0.004 -9999 0 -10000 0 0
HNRNPA1 0.027 0.006 -9999 0 -10000 0 0
AOF2 0 0.004 -9999 0 -10000 0 0
APPL1 0.013 0.006 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 0.01 0.083 -9999 0 -0.23 23 23
AR -0.013 0.12 -9999 0 -0.38 23 23
UBA3 0.027 0.005 -9999 0 -10000 0 0
PATZ1 0.027 0.005 -9999 0 -10000 0 0
PAWR 0.027 0.005 -9999 0 -10000 0 0
PRKDC 0.023 0.027 -9999 0 -0.27 2 2
PA2G4 0.027 0.006 -9999 0 -10000 0 0
UBE2I 0.026 0.006 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.009 0.075 -9999 0 -0.2 24 24
RPS6KA3 0.025 0.012 -9999 0 -10000 0 0
T-DHT/AR/ARA70 0.01 0.082 -9999 0 -0.23 23 23
LATS2 0.026 0.007 -9999 0 -10000 0 0
T-DHT/AR/PRX1 0.011 0.075 -9999 0 -0.21 23 23
Cyclin D3/CDK11 p58 0.019 0.005 -9999 0 -10000 0 0
VAV3 0.008 0.072 -9999 0 -0.28 15 15
KLK2 -0.007 0.067 -9999 0 -0.38 3 3
CASP8 0.028 0.002 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.022 0.076 -9999 0 -0.21 18 18
TMPRSS2 -0.043 0.21 -9999 0 -0.78 19 19
CCND1 0.024 0.02 -9999 0 -0.28 1 1
PIAS1 0.025 0.013 -9999 0 -10000 0 0
mol:T-DHT -0.003 0.02 -9999 0 -0.063 23 23
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.024 0.017 -9999 0 -10000 0 0
T-DHT/AR/CDK6 0.006 0.08 -9999 0 -0.22 25 25
CMTM2 0.023 0.032 -9999 0 -0.28 3 3
SNURF 0 0 -9999 0 -10000 0 0
ZMIZ1 0.02 0.03 -9999 0 -10000 0 0
CCND3 0.026 0.007 -9999 0 -10000 0 0
TGIF1 0.026 0.007 -9999 0 -10000 0 0
FKBP4 0.024 0.012 -9999 0 -10000 0 0
IL12-mediated 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
IL12/IL12R/TYK2/JAK2/SOCS1 0.002 0.093 -10000 0 -0.33 9 9
TBX21 -0.029 0.22 -10000 0 -1 6 6
B2M 0.022 0.017 -10000 0 -10000 0 0
TYK2 0.022 0.025 -10000 0 -10000 0 0
IL12RB1 0.022 0.026 -10000 0 -10000 0 0
GADD45B -0.015 0.2 -10000 0 -0.93 6 6
IL12RB2 0.011 0.067 -10000 0 -0.29 11 11
GADD45G -0.016 0.21 -10000 0 -0.87 8 8
natural killer cell activation 0.002 0.014 -10000 0 -10000 0 0
RELB 0.026 0.007 -10000 0 -10000 0 0
RELA 0.027 0.004 -10000 0 -10000 0 0
IL18 0.021 0.041 -10000 0 -0.3 4 4
IL2RA 0.012 0.063 -10000 0 -0.28 12 12
IFNG -0.056 0.14 -10000 0 -0.28 72 72
STAT3 (dimer) -0.013 0.19 -10000 0 -0.72 8 8
HLA-DRB5 0.016 0.057 -10000 0 -0.36 6 6
FASLG -0.029 0.25 -10000 0 -0.99 10 10
NF kappa B2 p52/RelB -0.02 0.22 -10000 0 -0.8 10 10
CD4 0.024 0.013 -10000 0 -10000 0 0
SOCS1 0.02 0.048 -10000 0 -0.29 6 6
EntrezGene:6955 -0.001 0.008 -10000 0 -10000 0 0
CD3D 0.014 0.056 -10000 0 -0.37 5 5
CD3E 0.018 0.038 -10000 0 -0.37 2 2
CD3G 0.016 0.045 -10000 0 -0.37 3 3
IL12Rbeta2/JAK2 0.027 0.052 -10000 0 -0.19 8 8
CCL3 -0.044 0.23 -10000 0 -1 6 6
CCL4 -0.025 0.22 -10000 0 -1.1 5 5
HLA-A 0.021 0.029 -10000 0 -0.37 1 1
IL18/IL18R 0.043 0.067 -10000 0 -0.21 7 7
NOS2 -0.033 0.22 -10000 0 -0.89 8 8
IL12/IL12R/TYK2/JAK2/SPHK2 0.004 0.091 -10000 0 -0.31 10 10
IL1R1 -0.027 0.21 -10000 0 -0.98 6 6
IL4 0.007 0.045 -10000 0 -0.29 4 4
JAK2 0.02 0.025 -10000 0 -10000 0 0
EntrezGene:6957 -0.001 0.008 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.026 0.19 -10000 0 -0.8 12 12
RAB7A -0.005 0.18 -10000 0 -0.73 5 5
lysosomal transport -0.003 0.18 -10000 0 -0.66 6 6
FOS -0.06 0.32 -10000 0 -1.1 20 20
STAT4 (dimer) -0.007 0.21 0.38 2 -0.75 9 11
STAT5A (dimer) -0.045 0.23 -10000 0 -0.8 11 11
GZMA -0.043 0.26 -10000 0 -1.1 10 10
GZMB -0.037 0.23 -10000 0 -1.1 6 6
HLX 0.024 0.027 -10000 0 -0.28 2 2
LCK -0.033 0.23 -10000 0 -0.88 10 10
TCR/CD3/MHC II/CD4 -0.002 0.11 -10000 0 -0.5 9 9
IL2/IL2R 0.047 0.06 -10000 0 -0.2 6 6
MAPK14 -0.013 0.21 -10000 0 -0.78 9 9
CCR5 -0.012 0.2 -10000 0 -1.1 4 4
IL1B -0.011 0.11 -10000 0 -0.31 29 29
STAT6 0.006 0.1 -10000 0 -1.3 1 1
STAT4 0.025 0.03 -10000 0 -0.32 2 2
STAT3 0.027 0.005 -10000 0 -10000 0 0
STAT1 0.018 0.052 -10000 0 -0.28 8 8
NFKB1 0.027 0.005 -10000 0 -10000 0 0
NFKB2 0.027 0.005 -10000 0 -10000 0 0
IL12B 0.009 0.071 -10000 0 -0.34 9 9
CD8A 0.005 0.085 -10000 0 -0.37 13 13
CD8B 0.001 0.092 -10000 0 -0.35 17 17
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.002 0.092 0.33 9 -10000 0 9
IL2RB 0.027 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.003 0.2 0.36 3 -0.68 9 12
IL2RG 0.014 0.069 -10000 0 -0.36 9 9
IL12 0.012 0.085 -10000 0 -0.26 19 19
STAT5A 0.027 0.005 -10000 0 -10000 0 0
CD247 0.012 0.061 -10000 0 -0.38 6 6
IL2 0.024 0.007 -10000 0 -10000 0 0
SPHK2 0.026 0.006 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.005 0.086 -10000 0 -0.38 12 12
IL12/IL12R/TYK2/JAK2 -0.03 0.25 -10000 0 -0.94 10 10
MAP2K3 -0.022 0.22 -10000 0 -0.82 10 10
RIPK2 0.023 0.02 -10000 0 -0.28 1 1
MAP2K6 -0.011 0.21 -10000 0 -0.83 7 7
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.019 0.047 -10000 0 -0.34 4 4
IL18RAP 0.019 0.057 -10000 0 -0.35 6 6
IL12Rbeta1/TYK2 0.034 0.035 -10000 0 -10000 0 0
EOMES -0.018 0.16 -10000 0 -0.96 6 6
STAT1 (dimer) -0.03 0.2 -10000 0 -0.72 8 8
T cell proliferation 0.007 0.16 0.4 2 -0.6 5 7
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.026 0.022 -10000 0 -0.28 1 1
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.002 0.17 -10000 0 -0.65 5 5
ATF2 -0.012 0.2 -10000 0 -0.72 9 9
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.013 0.08 0.2 1 -0.18 2 3
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.027 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.014 0.084 0.29 2 -10000 0 2
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.026 0.044 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.019 0.053 -10000 0 -10000 0 0
CaM/Ca2+ 0.014 0.078 -10000 0 -0.17 2 2
RAP1A 0.027 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.006 0.075 -10000 0 -0.23 6 6
AKT1 -0.009 0.078 0.19 13 -10000 0 13
MAP2K1 -0.021 0.064 0.17 13 -10000 0 13
MAP3K11 -0.014 0.063 0.16 1 -10000 0 1
IFNGR1 0.015 0.024 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.04 0.12 -10000 0 -0.29 33 33
Rap1/GTP -0.01 0.053 -10000 0 -10000 0 0
CRKL/C3G 0.039 0.01 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.014 0.09 -10000 0 -0.19 2 2
CEBPB 0.015 0.11 0.29 1 -0.52 5 6
STAT3 0.027 0.005 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.001 0.16 -10000 0 -0.75 8 8
STAT1 -0.016 0.07 0.17 2 -0.23 6 8
CALM1 0.027 0.005 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.054 0.14 -10000 0 -0.28 72 72
PIK3CA 0.026 0.007 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0 0.08 0.28 2 -0.22 6 8
CEBPB/PTGES2/Cbp/p300 0.015 0.072 -10000 0 -0.33 5 5
mol:Ca2+ 0.011 0.078 0.19 1 -0.18 2 3
MAPK3 -0.007 0.1 -10000 0 -0.65 4 4
STAT1 (dimer) -0.019 0.073 -10000 0 -10000 0 0
MAPK1 -0.017 0.12 -10000 0 -0.64 8 8
JAK2 0.012 0.023 -10000 0 -10000 0 0
PIK3R1 0.026 0.007 -10000 0 -10000 0 0
JAK1 0.016 0.024 -10000 0 -10000 0 0
CAMK2D 0.027 0.005 -10000 0 -10000 0 0
DAPK1 0.016 0.095 0.3 2 -0.47 5 7
SMAD7 0.001 0.045 0.14 9 -10000 0 9
CBL/CRKL/C3G 0.009 0.076 0.28 1 -10000 0 1
PI3K 0.01 0.075 -10000 0 -10000 0 0
IFNG -0.054 0.14 -10000 0 -0.28 72 72
apoptosis 0.008 0.098 0.26 2 -0.43 8 10
CAMK2G 0.026 0.006 -10000 0 -10000 0 0
STAT3 (dimer) 0.027 0.005 -10000 0 -10000 0 0
CAMK2A 0.006 0.082 -10000 0 -0.32 16 16
CAMK2B -0.045 0.15 -10000 0 -0.36 49 49
FRAP1 -0.011 0.072 0.17 15 -10000 0 15
PRKCD -0.011 0.078 0.18 17 -10000 0 17
RAP1B 0.026 0.006 -10000 0 -10000 0 0
negative regulation of cell growth -0.019 0.053 -10000 0 -10000 0 0
PTPN2 0.025 0.008 -10000 0 -10000 0 0
EP300 0.027 0.005 -10000 0 -10000 0 0
IRF1 -0.014 0.062 0.26 1 -0.35 1 2
STAT1 (dimer)/PIASy 0 0.082 0.28 2 -0.22 6 8
SOCS1 -0.01 0.2 -10000 0 -1.1 8 8
mol:GDP 0.007 0.072 0.26 1 -10000 0 1
CASP1 0 0.045 0.14 8 -0.17 1 9
PTGES2 0.026 0.006 -10000 0 -10000 0 0
IRF9 0.019 0.043 0.15 7 -0.15 1 8
mol:PI-3-4-5-P3 0 0.066 -10000 0 -10000 0 0
RAP1/GDP 0.003 0.063 -10000 0 -10000 0 0
CBL -0.014 0.063 0.17 2 -10000 0 2
MAP3K1 -0.012 0.062 0.17 2 -10000 0 2
PIAS1 0.027 0.004 -10000 0 -10000 0 0
PIAS4 0.026 0.006 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.019 0.053 -10000 0 -10000 0 0
PTPN11 -0.007 0.075 0.18 16 -0.18 2 18
CREBBP 0.026 0.007 -10000 0 -10000 0 0
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.03 0.069 -10000 0 -10000 0 0
UGCG 0.007 0.1 -10000 0 -0.61 7 7
AKT1/mTOR/p70S6K/Hsp90/TERT 0.005 0.11 0.27 2 -0.43 8 10
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.008 0.1 -10000 0 -0.61 7 7
mol:DAG 0.001 0.1 -10000 0 -0.79 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.03 0.095 0.28 1 -0.42 5 6
FRAP1 0.02 0.1 0.31 1 -0.47 5 6
FOXO3 0.021 0.098 0.3 1 -0.46 5 6
AKT1 0.023 0.11 0.31 1 -0.48 6 7
GAB2 0.027 0.006 -10000 0 -10000 0 0
SMPD1 -0.002 0.14 -10000 0 -0.68 10 10
SGMS1 0.014 0.075 -10000 0 -0.58 4 4
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.003 0.006 -10000 0 -10000 0 0
CALM1 0.027 0.005 -10000 0 -10000 0 0
cell proliferation 0.036 0.091 0.28 2 -0.36 9 11
EIF3A 0.027 0.005 -10000 0 -10000 0 0
PI3K 0.038 0.015 -10000 0 -10000 0 0
RPS6KB1 0.001 0.064 -10000 0 -0.82 1 1
mol:sphingomyelin 0.001 0.1 -10000 0 -0.79 4 4
natural killer cell activation 0 0.001 -10000 0 -10000 0 0
JAK3 0.017 0.058 -10000 0 -0.28 10 10
PIK3R1 0.027 0.008 -10000 0 -10000 0 0
JAK1 0.029 0.004 -10000 0 -10000 0 0
NFKB1 0.027 0.005 -10000 0 -10000 0 0
MYC 0.052 0.13 0.43 2 -0.58 4 6
MYB -0.04 0.11 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.023 0.084 -10000 0 -0.49 3 3
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.023 0.069 -10000 0 -0.76 1 1
mol:PI-3-4-5-P3 0.025 0.083 -10000 0 -0.47 3 3
Rac1/GDP 0.02 0.011 -10000 0 -10000 0 0
T cell proliferation 0.028 0.069 0.24 3 -0.46 2 5
SHC1 0.027 0.006 -10000 0 -10000 0 0
RAC1 0.026 0.007 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.006 0.014 -10000 0 -0.027 81 81
PRKCZ 0.028 0.069 0.22 2 -0.48 2 4
NF kappa B1 p50/RelA 0.042 0.098 -10000 0 -0.43 4 4
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.021 0.049 -10000 0 -0.38 2 2
HSP90AA1 0.026 0.006 -10000 0 -10000 0 0
RELA 0.027 0.004 -10000 0 -10000 0 0
IL2RA 0.013 0.063 -10000 0 -0.28 12 12
IL2RB 0.028 0.005 -10000 0 -10000 0 0
TERT -0.049 0.13 -10000 0 -0.28 64 64
E2F1 -0.018 0.074 -10000 0 -0.31 1 1
SOS1 0.027 0.004 -10000 0 -10000 0 0
RPS6 0.025 0.008 -10000 0 -10000 0 0
mol:cAMP 0.003 0.007 0.013 80 -10000 0 80
PTPN11 0.027 0.004 -10000 0 -10000 0 0
IL2RG 0.016 0.069 -10000 0 -0.36 9 9
actin cytoskeleton organization 0.028 0.069 0.24 3 -0.46 2 5
GRB2 0.027 0.004 -10000 0 -10000 0 0
IL2 0.026 0.007 -10000 0 -10000 0 0
PIK3CA 0.027 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.043 0.023 -10000 0 -10000 0 0
LCK 0.021 0.048 -10000 0 -0.29 6 6
BCL2 0.02 0.097 -10000 0 -0.56 3 3
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.019 0.028 -10000 0 -0.19 4 4
epithelial cell differentiation 0.048 0.035 -10000 0 -0.18 4 4
CYFIP2 0.021 0.045 -10000 0 -0.35 4 4
ENAH -0.004 0.055 0.22 6 -0.23 1 7
EGFR 0.012 0.069 -10000 0 -0.36 9 9
EPHA2 0.024 0.031 -10000 0 -0.32 2 2
MYO6 -0.004 0.044 0.18 11 -10000 0 11
CTNNB1 0.027 0.005 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.046 0.036 -10000 0 -0.2 4 4
AQP5 -0.12 0.19 -10000 0 -0.4 77 77
CTNND1 0.027 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.005 0.042 0.18 10 -10000 0 10
regulation of calcium-dependent cell-cell adhesion -0.008 0.046 0.18 10 -10000 0 10
EGF -0.012 0.1 -10000 0 -0.3 32 32
NCKAP1 0.027 0.004 -10000 0 -10000 0 0
AQP3 -0.008 0.088 -10000 0 -0.42 8 8
cortical microtubule organization 0.048 0.035 -10000 0 -0.18 4 4
GO:0000145 -0.005 0.039 0.16 10 -10000 0 10
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.053 0.037 -10000 0 -0.19 4 4
MLLT4 0.026 0.007 -10000 0 -10000 0 0
ARF6/GDP -0.02 0.028 -10000 0 -0.31 1 1
ARF6 0.026 0.006 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.058 0.039 -10000 0 -0.2 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.005 0.038 0.18 8 -10000 0 8
PVRL2 0.025 0.02 -10000 0 -0.28 1 1
ZYX -0.004 0.044 0.18 11 -10000 0 11
ARF6/GTP 0.061 0.042 -10000 0 -0.19 1 1
CDH1 0.02 0.048 -10000 0 -0.37 4 4
EGFR/EGFR/EGF/EGF 0.012 0.073 -10000 0 -0.23 3 3
RhoA/GDP 0.049 0.035 -10000 0 -0.18 3 3
actin cytoskeleton organization -0.006 0.04 0.16 10 -10000 0 10
IGF-1R heterotetramer 0.027 0.005 -10000 0 -10000 0 0
GIT1 0.027 0.004 -10000 0 -10000 0 0
IGF1R 0.027 0.005 -10000 0 -10000 0 0
IGF1 -0.019 0.12 -10000 0 -0.31 37 37
DIAPH1 0.01 0.15 -10000 0 -0.54 12 12
Wnt receptor signaling pathway -0.048 0.035 0.18 4 -10000 0 4
RHOA 0.027 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.02 0.027 -10000 0 -0.29 1 1
CTNNA1 0.026 0.006 -10000 0 -10000 0 0
VCL -0.007 0.041 0.17 10 -10000 0 10
EFNA1 0.022 0.037 -10000 0 -0.28 4 4
LPP -0.011 0.045 0.17 8 -0.24 2 10
Ephrin A1/EPHA2 0.038 0.044 -10000 0 -0.33 1 1
SEC6/SEC8 -0.015 0.021 -10000 0 -10000 0 0
MGAT3 -0.008 0.046 0.18 10 -10000 0 10
HGF/MET 0.02 0.064 -10000 0 -0.24 1 1
HGF 0.021 0.041 -10000 0 -0.28 5 5
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.019 0.028 -10000 0 -0.19 4 4
actin cable formation 0.018 0.081 0.26 13 -0.29 2 15
KIAA1543 -0.005 0.041 0.17 11 -10000 0 11
KIFC3 -0.007 0.039 0.18 8 -10000 0 8
NCK1 0.027 0.004 -10000 0 -10000 0 0
EXOC3 0.025 0.009 -10000 0 -10000 0 0
ACTN1 -0.006 0.046 0.18 11 -10000 0 11
NCK1/GIT1 0.039 0.009 -10000 0 -10000 0 0
mol:GDP 0.048 0.035 -10000 0 -0.18 4 4
EXOC4 0.027 0.005 -10000 0 -10000 0 0
STX4 -0.006 0.041 0.18 9 -10000 0 9
PIP5K1C -0.005 0.042 0.18 10 -10000 0 10
LIMA1 0.027 0.004 -10000 0 -10000 0 0
ABI1 0.026 0.007 -10000 0 -10000 0 0
ROCK1 0.002 0.069 0.31 5 -0.26 1 6
adherens junction assembly -0.008 0.091 0.28 2 -0.54 4 6
IGF-1R heterotetramer/IGF1 0.018 0.071 -10000 0 -0.18 14 14
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.036 0.019 -10000 0 -0.19 1 1
MET -0.007 0.094 -10000 0 -0.28 29 29
PLEKHA7 -0.004 0.044 0.18 11 -10000 0 11
mol:GTP 0.056 0.038 -10000 0 -0.2 1 1
establishment of epithelial cell apical/basal polarity 0.015 0.08 0.29 8 -10000 0 8
cortical actin cytoskeleton stabilization 0.019 0.028 -10000 0 -0.19 4 4
regulation of cell-cell adhesion -0.006 0.04 0.16 10 -10000 0 10
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.019 0.028 -10000 0 -0.19 4 4
Class I PI3K signaling events

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
ARF5/GTP -0.002 0.052 0.16 1 -10000 0 1
DAPP1 0.007 0.12 0.24 7 -0.34 13 20
Src family/SYK family/BLNK-LAT/BTK-ITK -0.005 0.15 0.26 2 -0.46 17 19
mol:DAG 0.018 0.08 0.18 23 -0.2 7 30
HRAS 0.028 0.007 -10000 0 -10000 0 0
RAP1A 0.028 0.007 -10000 0 -10000 0 0
ARF5/GDP 0.042 0.059 0.18 4 -0.28 2 6
PLCG2 0.02 0.044 -10000 0 -0.3 5 5
PLCG1 0.024 0.01 -10000 0 -10000 0 0
ARF5 0.027 0.005 -10000 0 -10000 0 0
mol:GTP -0.001 0.049 0.15 16 -10000 0 16
ARF1/GTP 0.006 0.047 0.22 6 -10000 0 6
RHOA 0.027 0.005 -10000 0 -10000 0 0
YES1 0.026 0.007 -10000 0 -10000 0 0
RAP1A/GTP 0 0.051 0.15 26 -10000 0 26
ADAP1 -0.003 0.044 0.15 5 -10000 0 5
ARAP3 -0.001 0.048 0.15 16 -10000 0 16
INPPL1 0.026 0.006 -10000 0 -10000 0 0
PREX1 0.023 0.01 -10000 0 -10000 0 0
ARHGEF6 0.025 0.024 -10000 0 -0.37 1 1
ARHGEF7 0.026 0.007 -10000 0 -10000 0 0
ARF1 0.027 0.005 -10000 0 -10000 0 0
NRAS 0.028 0.007 -10000 0 -10000 0 0
FYN 0.027 0.005 -10000 0 -10000 0 0
ARF6 0.026 0.006 -10000 0 -10000 0 0
FGR 0.026 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0.012 0.047 0.15 10 -10000 0 10
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.024 0.031 -10000 0 -0.32 2 2
ZAP70 0.018 0.057 -10000 0 -0.33 7 7
mol:IP3 0.011 0.059 0.14 23 -0.15 3 26
LYN 0.023 0.02 -10000 0 -0.28 1 1
ARF1/GDP 0.043 0.06 0.19 4 -0.28 2 6
RhoA/GDP 0.05 0.057 0.22 13 -10000 0 13
PDK1/Src/Hsp90 0.032 0.061 -10000 0 -0.21 14 14
BLNK 0.015 0.067 -10000 0 -0.37 8 8
actin cytoskeleton reorganization 0.042 0.076 0.24 19 -10000 0 19
SRC 0.024 0.009 -10000 0 -10000 0 0
PLEKHA2 -0.009 0.012 -10000 0 -0.16 1 1
RAC1 0.026 0.007 -10000 0 -10000 0 0
PTEN 0.022 0.016 -10000 0 -10000 0 0
HSP90AA1 0.026 0.006 -10000 0 -10000 0 0
ARF6/GTP -0.002 0.051 0.16 1 -10000 0 1
RhoA/GTP -0.001 0.051 0.15 15 -10000 0 15
Src family/SYK family/BLNK-LAT -0.008 0.11 -10000 0 -0.39 15 15
BLK -0.042 0.14 -10000 0 -0.35 47 47
PDPK1 0.004 0.089 -10000 0 -0.36 15 15
CYTH1 -0.001 0.05 0.16 6 -10000 0 6
HCK 0.025 0.009 -10000 0 -10000 0 0
CYTH3 -0.004 0.044 0.15 4 -10000 0 4
CYTH2 -0.001 0.048 0.16 6 -10000 0 6
KRAS 0.025 0.01 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.004 0.073 -10000 0 -0.39 4 4
SGK1 0.005 0.083 -10000 0 -0.38 6 6
INPP5D 0.024 0.035 -10000 0 -0.31 3 3
mol:GDP 0.031 0.06 0.17 6 -0.29 2 8
SOS1 0.027 0.003 -10000 0 -10000 0 0
SYK 0.026 0.006 -10000 0 -10000 0 0
ARF6/GDP 0.036 0.056 0.21 14 -10000 0 14
mol:PI-3-4-5-P3 -0.002 0.045 0.15 1 -10000 0 1
ARAP3/RAP1A/GTP 0 0.051 0.16 26 -10000 0 26
VAV1 0.023 0.036 -10000 0 -0.31 3 3
mol:PI-3-4-P2 0.01 0.023 -10000 0 -0.2 3 3
RAS family/GTP/PI3K Class I 0.038 0.033 0.2 1 -10000 0 1
PLEKHA1 -0.01 0.012 -10000 0 -0.16 1 1
Rac1/GDP 0.039 0.057 0.18 2 -0.28 2 4
LAT 0.027 0.005 -10000 0 -10000 0 0
Rac1/GTP 0.018 0.045 -10000 0 -0.26 2 2
ITK -0.006 0.051 0.16 3 -10000 0 3
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.014 0.092 0.2 18 -0.28 8 26
LCK 0.02 0.048 -10000 0 -0.29 6 6
BTK -0.003 0.051 0.15 5 -10000 0 5
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 0.023 0.12 0.3 1 -0.46 9 10
MAP3K8 0.026 0.006 -10000 0 -10000 0 0
FOS 0.013 0.1 0.32 1 -0.42 8 9
PRKCA 0.024 0.026 -10000 0 -0.37 1 1
PTPN7 0.02 0.039 -10000 0 -0.28 4 4
HRAS 0.026 0.006 -10000 0 -10000 0 0
PRKCB 0.003 0.091 -10000 0 -0.37 15 15
NRAS 0.027 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.043 0.022 -10000 0 -10000 0 0
MAPK3 0.017 0.082 -10000 0 -0.48 5 5
MAP2K1 0.004 0.094 -10000 0 -0.35 14 14
ELK1 0.025 0.012 -10000 0 -10000 0 0
BRAF -0.002 0.085 -10000 0 -0.34 15 15
mol:GTP 0 0.001 -10000 0 -0.004 16 16
MAPK1 0.011 0.1 -10000 0 -0.48 9 9
RAF1 -0.001 0.085 -10000 0 -0.34 15 15
KRAS 0.024 0.009 -10000 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.041 0.05 0.27 1 -10000 0 1
CRKL 0.028 0.054 0.21 10 -10000 0 10
mol:DAG 0.025 0.034 -10000 0 -10000 0 0
HRAS 0.011 0.063 0.26 6 -0.25 1 7
MAPK8 0.032 0.058 0.18 32 -10000 0 32
RAP1A 0.03 0.053 0.21 10 -10000 0 10
GAB1 0.026 0.053 0.21 7 -0.28 1 8
MAPK14 0.032 0.056 0.18 31 -10000 0 31
EPO 0.017 0.048 -10000 0 -0.27 7 7
PLCG1 0.026 0.034 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.029 0.012 -10000 0 -10000 0 0
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.048 0.033 -10000 0 -10000 0 0
GAB1/SHC/GRB2/SOS1 0.055 0.048 0.27 2 -0.26 1 3
EPO/EPOR (dimer) 0.034 0.037 -10000 0 -0.19 6 6
IRS2 0.021 0.056 0.19 7 -0.28 1 8
STAT1 0.03 0.042 0.24 1 -10000 0 1
STAT5B 0.03 0.036 -10000 0 -10000 0 0
cell proliferation 0.017 0.076 0.19 37 -10000 0 37
GAB1/SHIP/PIK3R1/SHP2/SHC 0.042 0.044 -10000 0 -0.35 1 1
TEC 0.029 0.056 0.21 10 -10000 0 10
SOCS3 0.027 0.004 -10000 0 -10000 0 0
STAT1 (dimer) 0.03 0.041 0.24 1 -10000 0 1
JAK2 0.026 0.014 -10000 0 -10000 0 0
PIK3R1 0.026 0.007 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.06 0.046 0.22 3 -10000 0 3
EPO/EPOR 0.034 0.037 -10000 0 -0.19 6 6
LYN 0.024 0.021 -10000 0 -0.28 1 1
TEC/VAV2 0.039 0.051 0.22 6 -10000 0 6
elevation of cytosolic calcium ion concentration 0.029 0.012 -10000 0 -10000 0 0
SHC1 0.026 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.045 0.038 -10000 0 -10000 0 0
mol:IP3 0.025 0.034 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.041 0.062 0.3 1 -0.37 1 2
SH2B3 0.029 0.011 -10000 0 -10000 0 0
NFKB1 0.034 0.059 0.18 33 -10000 0 33
EPO/EPOR (dimer)/JAK2/SOCS3 0.008 0.029 -10000 0 -0.22 3 3
PTPN6 0.028 0.048 0.16 20 -10000 0 20
TEC/VAV2/GRB2 0.048 0.053 0.22 6 -10000 0 6
EPOR 0.029 0.012 -10000 0 -10000 0 0
INPP5D 0.024 0.035 -10000 0 -0.31 3 3
mol:GDP 0.054 0.048 0.27 2 -0.26 1 3
SOS1 0.027 0.003 -10000 0 -10000 0 0
PLCG2 0.02 0.044 -10000 0 -0.3 5 5
CRKL/CBL/C3G 0.05 0.049 0.26 4 -10000 0 4
VAV2 0.026 0.053 0.2 9 -10000 0 9
CBL 0.027 0.051 0.22 8 -10000 0 8
SHC/Grb2/SOS1 0.036 0.031 -10000 0 -10000 0 0
STAT5A 0.03 0.036 -10000 0 -10000 0 0
GRB2 0.027 0.004 -10000 0 -10000 0 0
STAT5 (dimer) 0.047 0.044 0.25 1 -10000 0 1
LYN/PLCgamma2 0.031 0.033 -10000 0 -0.18 5 5
PTPN11 0.027 0.004 -10000 0 -10000 0 0
BTK 0.027 0.058 0.21 9 -0.23 1 10
BCL2 0.044 0.075 -10000 0 -0.7 1 1
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.001 0.081 0.27 9 -10000 0 9
GNAI2 0.027 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 0.03 0.028 -10000 0 -0.16 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.007 0.11 -10000 0 -0.34 25 25
RhoA/GTP 0.001 0.083 -10000 0 -0.27 9 9
negative regulation of cAMP metabolic process -0.005 0.077 -10000 0 -0.29 8 8
GNAZ 0.008 0.084 -10000 0 -0.37 13 13
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNA12 0.026 0.007 -10000 0 -10000 0 0
S1PR5 0.02 0.045 -10000 0 -0.28 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.005 0.078 -10000 0 -0.29 8 8
RhoA/GDP 0.02 0.004 -10000 0 -10000 0 0
RHOA 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.019 0.053 -10000 0 -0.37 5 5
Retinoic acid receptors-mediated signaling

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
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC3 0.026 0.006 -10000 0 -10000 0 0
VDR 0.026 0.019 -10000 0 -0.28 1 1
Cbp/p300/PCAF 0.048 0.032 -10000 0 -0.22 3 3
EP300 0.027 0.005 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.007 0.056 -10000 0 -0.32 4 4
KAT2B 0.023 0.041 -10000 0 -0.37 3 3
MAPK14 0.027 0.005 -10000 0 -10000 0 0
AKT1 -0.002 0.057 0.24 3 -0.22 4 7
RAR alpha/9cRA/Cyclin H 0.009 0.067 -10000 0 -0.24 1 1
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.007 0.055 0.22 1 -0.31 3 4
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.003 0.053 0.15 1 -10000 0 1
NCOR2 0.027 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.019 0.013 -10000 0 -0.19 1 1
RXRs/RARs/NRIP1/9cRA -0.029 0.091 -10000 0 -0.45 4 4
NCOA2 0.024 0.009 -10000 0 -10000 0 0
NCOA3 0.023 0.01 -10000 0 -10000 0 0
NCOA1 0.027 0.004 -10000 0 -10000 0 0
VDR/VDR/DNA 0.025 0.019 -10000 0 -0.28 1 1
RARG 0.026 0.019 -10000 0 -0.28 1 1
RAR gamma1/9cRA 0.035 0.015 -10000 0 -0.16 1 1
MAPK3 0.027 0.004 -10000 0 -10000 0 0
MAPK1 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.028 0.004 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.036 0.097 -10000 0 -0.42 8 8
RARA -0.015 0.048 -10000 0 -0.19 8 8
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.005 0.051 -10000 0 -0.31 3 3
PRKCA 0.027 0.024 -10000 0 -0.37 1 1
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.033 0.099 0.34 1 -0.44 6 7
RXRG -0.12 0.15 -10000 0 -0.31 96 96
RXRA -0.009 0.052 -10000 0 -0.22 3 3
RXRB -0.029 0.069 -10000 0 -0.26 8 8
VDR/Vit D3/DNA 0.019 0.013 -10000 0 -0.19 1 1
RBP1 0.012 0.068 -10000 0 -0.3 12 12
CRBP1/9-cic-RA 0.01 0.047 -10000 0 -0.2 12 12
RARB 0.027 0.024 -10000 0 -0.37 1 1
PRKCG -0.09 0.15 -10000 0 -0.28 104 104
MNAT1 0.027 0.005 -10000 0 -10000 0 0
RAR alpha/RXRs -0.035 0.093 0.33 1 -0.42 8 9
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.026 0.093 0.21 1 -0.37 8 9
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.067 0.24 2 -0.32 2 4
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.033 0.098 0.34 1 -0.43 6 7
positive regulation of DNA binding 0.003 0.059 -10000 0 -0.23 1 1
NRIP1 -0.029 0.093 -10000 0 -0.44 4 4
RXRs/RARs -0.034 0.097 -10000 0 -0.41 7 7
RXRs/RXRs/DNA/9cRA -0.045 0.09 -10000 0 -0.42 8 8
PRKACA 0.027 0.005 -10000 0 -10000 0 0
CDK7 0.026 0.007 -10000 0 -10000 0 0
TFIIH 0.05 0.018 -10000 0 -10000 0 0
RAR alpha/9cRA 0.018 0.063 0.2 1 -10000 0 1
CCNH 0.025 0.008 -10000 0 -10000 0 0
CREBBP 0.026 0.007 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.046 0.024 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
RIP1/MEKK3 0.035 0.01 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.026 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.024 0.034 -10000 0 -0.37 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.025 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.004 0.044 -10000 0 -0.17 15 15
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.026 0.007 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.027 0.004 -10000 0 -10000 0 0
FYN 0.027 0.005 -10000 0 -10000 0 0
MAP3K12 0.027 0.005 -10000 0 -10000 0 0
FGR 0.026 0.007 -10000 0 -10000 0 0
p38 alpha/TAB1 -0.038 0.1 -10000 0 -0.43 14 14
PRKG1 0.025 0.027 -10000 0 -0.28 2 2
DUSP8 0.022 0.042 -10000 0 -0.37 3 3
PGK/cGMP/p38 alpha 0.005 0.12 0.16 2 -0.43 13 15
apoptosis -0.036 0.1 -10000 0 -0.4 14 14
RAL/GTP 0.035 0.009 -10000 0 -10000 0 0
LYN 0.023 0.02 -10000 0 -0.28 1 1
DUSP1 0.003 0.093 -10000 0 -0.37 16 16
PAK1 0.026 0.006 -10000 0 -10000 0 0
SRC 0.024 0.009 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.06 0.026 -10000 0 -10000 0 0
TRAF6 0.027 0.005 -10000 0 -10000 0 0
RAC1 0.026 0.007 -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 0.026 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.033 0.012 -10000 0 -10000 0 0
MAPK11 0.008 0.13 0.24 10 -0.41 13 23
BLK -0.042 0.14 -10000 0 -0.35 47 47
HCK 0.025 0.009 -10000 0 -10000 0 0
MAP2K3 0.026 0.007 -10000 0 -10000 0 0
DUSP16 0.026 0.007 -10000 0 -10000 0 0
DUSP10 0.023 0.032 -10000 0 -0.28 3 3
TRAF6/MEKK3 0.034 0.008 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.003 0.14 0.2 9 -0.48 13 22
positive regulation of innate immune response 0.007 0.15 0.25 10 -0.52 12 22
LCK 0.02 0.048 -10000 0 -0.29 6 6
p38alpha-beta/MKP7 0.017 0.15 0.26 8 -0.51 11 19
p38alpha-beta/MKP5 0.015 0.15 0.25 9 -0.53 10 19
PGK/cGMP 0.018 0.018 -10000 0 -0.19 2 2
PAK2 0.026 0.007 -10000 0 -10000 0 0
p38alpha-beta/MKP1 0.011 0.16 0.25 9 -0.52 12 21
CDC42 0.026 0.007 -10000 0 -10000 0 0
RALB 0.027 0.003 -10000 0 -10000 0 0
RALA 0.026 0.006 -10000 0 -10000 0 0
PAK3 -0.006 0.11 -10000 0 -0.35 24 24
IL6-mediated 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.