PARADIGM pathway analysis of mRNASeq expression and copy number data
Colon Adenocarcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C19P2ZZN
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 46 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
Reelin signaling pathway 63
Ephrin A reverse signaling 39
TCGA08_retinoblastoma 39
Lissencephaly gene (LIS1) in neuronal migration and development 38
Glypican 1 network 34
Osteopontin-mediated events 32
IL4-mediated signaling events 32
Syndecan-1-mediated signaling events 27
Signaling events mediated by the Hedgehog family 25
Signaling events regulated by Ret tyrosine kinase 25
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 232 . 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 ( 232 ).

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
Reelin signaling pathway 0.2716 63 3539 56 -0.32 0.066 1000 -1000 -0.04 -1000
Ephrin A reverse signaling 0.1681 39 276 7 -0.043 0 1000 -1000 -0.016 -1000
TCGA08_retinoblastoma 0.1681 39 319 8 -0.096 0.054 1000 -1000 -0.001 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1638 38 2067 54 -0.32 0.033 1000 -1000 -0.045 -1000
Glypican 1 network 0.1466 34 1671 48 -0.19 0.046 1000 -1000 -0.027 -1000
Osteopontin-mediated events 0.1379 32 1238 38 -0.18 0.035 1000 -1000 -0.047 -1000
IL4-mediated signaling events 0.1379 32 2990 91 -0.75 0.57 1000 -1000 -0.16 -1000
Syndecan-1-mediated signaling events 0.1164 27 949 34 -0.37 0.024 1000 -1000 -0.036 -1000
Signaling events mediated by the Hedgehog family 0.1078 25 1338 52 -0.085 0.083 1000 -1000 -0.031 -1000
Signaling events regulated by Ret tyrosine kinase 0.1078 25 2051 82 -0.099 0.024 1000 -1000 -0.048 -1000
BCR signaling pathway 0.1078 25 2530 99 -0.15 0.03 1000 -1000 -0.051 -1000
HIF-1-alpha transcription factor network 0.1034 24 1893 76 -0.48 0.034 1000 -1000 -0.11 -1000
FOXA2 and FOXA3 transcription factor networks 0.0991 23 1092 46 -0.47 0.028 1000 -1000 -0.11 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0991 23 1817 78 -0.14 0.05 1000 -1000 -0.054 -1000
Fc-epsilon receptor I signaling in mast cells 0.0948 22 2217 97 -0.13 0.044 1000 -1000 -0.06 -1000
p75(NTR)-mediated signaling 0.0905 21 2677 125 -0.37 0.063 1000 -1000 -0.07 -1000
BMP receptor signaling 0.0862 20 1700 81 -0.14 0.045 1000 -1000 -0.047 -1000
IL1-mediated signaling events 0.0862 20 1277 62 -0.15 0.094 1000 -1000 -0.044 -1000
Endothelins 0.0819 19 1857 96 -0.26 0.031 1000 -1000 -0.068 -1000
Visual signal transduction: Cones 0.0776 18 713 38 -0.11 0.041 1000 -1000 -0.016 -1000
Syndecan-2-mediated signaling events 0.0776 18 1259 69 -0.22 0.041 1000 -1000 -0.032 -1000
Wnt signaling 0.0776 18 128 7 -0.058 0.021 1000 -1000 -0.014 -1000
Visual signal transduction: Rods 0.0733 17 892 52 -0.16 0.025 1000 -1000 -0.034 -1000
amb2 Integrin signaling 0.0690 16 1381 82 -0.073 0.041 1000 -1000 -0.028 -1000
TCGA08_p53 0.0690 16 112 7 -0.072 0.031 1000 -1000 -0.007 -1000
LPA receptor mediated events 0.0690 16 1698 102 -0.16 0.032 1000 -1000 -0.06 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0647 15 514 34 -0.023 0.036 1000 -1000 -0.028 -1000
Effects of Botulinum toxin 0.0647 15 392 26 -0.075 0.037 1000 -1000 -0.008 -1000
Glypican 2 network 0.0647 15 60 4 0.001 0.012 1000 -1000 0.003 -1000
Calcium signaling in the CD4+ TCR pathway 0.0647 15 487 31 -0.22 0.024 1000 -1000 -0.041 -1000
Nongenotropic Androgen signaling 0.0647 15 807 52 -0.12 0.045 1000 -1000 -0.039 -1000
Plasma membrane estrogen receptor signaling 0.0647 15 1307 86 -0.26 0.078 1000 -1000 -0.051 -1000
Ras signaling in the CD4+ TCR pathway 0.0647 15 255 17 -0.056 0.045 1000 -1000 -0.026 -1000
LPA4-mediated signaling events 0.0603 14 173 12 -0.075 0.006 1000 -1000 -0.025 -1000
JNK signaling in the CD4+ TCR pathway 0.0603 14 250 17 -0.12 0.039 1000 -1000 -0.026 -1000
Ephrin B reverse signaling 0.0603 14 711 48 -0.071 0.026 1000 -1000 -0.021 -1000
TCR signaling in naïve CD8+ T cells 0.0603 14 1361 93 -0.028 0.035 1000 -1000 -0.047 -1000
Syndecan-4-mediated signaling events 0.0603 14 943 67 -0.28 0.053 1000 -1000 -0.031 -1000
Canonical Wnt signaling pathway 0.0560 13 677 51 -0.19 0.11 1000 -1000 -0.049 -1000
EGFR-dependent Endothelin signaling events 0.0560 13 275 21 -0.061 0.035 1000 -1000 -0.04 -1000
PDGFR-beta signaling pathway 0.0560 13 1335 97 -0.14 0.08 1000 -1000 -0.053 -1000
Noncanonical Wnt signaling pathway 0.0517 12 318 26 -0.058 0.023 1000 -1000 -0.04 -1000
S1P5 pathway 0.0517 12 211 17 -0.12 0.06 1000 -1000 -0.017 -1000
Signaling mediated by p38-alpha and p38-beta 0.0517 12 567 44 -0.041 0.024 1000 -1000 -0.024 -1000
EPHB forward signaling 0.0517 12 1052 85 -0.073 0.08 1000 -1000 -0.061 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0517 12 1073 88 -0.12 0.057 1000 -1000 -0.068 -1000
Coregulation of Androgen receptor activity 0.0474 11 843 76 -0.24 0.063 1000 -1000 -0.023 -1000
HIF-2-alpha transcription factor network 0.0474 11 493 43 -0.27 0.16 1000 -1000 -0.063 -1000
IGF1 pathway 0.0474 11 652 57 -0.042 0.046 1000 -1000 -0.033 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0474 11 1407 120 -0.095 0.088 1000 -1000 -0.045 -1000
S1P4 pathway 0.0474 11 278 25 -0.12 0.037 1000 -1000 -0.027 -1000
Arf6 signaling events 0.0431 10 677 62 -0.13 0.05 1000 -1000 -0.032 -1000
Presenilin action in Notch and Wnt signaling 0.0431 10 666 61 -0.19 0.1 1000 -1000 -0.046 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0431 10 567 52 -0.14 0.054 1000 -1000 -0.04 -1000
S1P1 pathway 0.0431 10 360 36 -0.12 0.024 1000 -1000 -0.044 -1000
Syndecan-3-mediated signaling events 0.0431 10 363 35 -0.22 0.063 1000 -1000 -0.021 -1000
Integrins in angiogenesis 0.0431 10 844 84 -0.18 0.058 1000 -1000 -0.042 -1000
IL23-mediated signaling events 0.0431 10 648 60 -0.3 0.032 1000 -1000 -0.12 -1000
Caspase cascade in apoptosis 0.0388 9 688 74 -0.097 0.058 1000 -1000 -0.041 -1000
PLK1 signaling events 0.0388 9 838 85 -0.008 0.053 1000 -1000 -0.024 -1000
Ceramide signaling pathway 0.0388 9 703 76 -0.061 0.062 1000 -1000 -0.033 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0345 8 239 28 -0.12 0.031 1000 -1000 -0.024 -1000
Thromboxane A2 receptor signaling 0.0345 8 864 105 -0.12 0.06 1000 -1000 -0.053 -1000
Signaling events mediated by PTP1B 0.0345 8 636 76 -0.2 0.041 1000 -1000 -0.035 -1000
Nectin adhesion pathway 0.0345 8 566 63 -0.35 0.066 1000 -1000 -0.041 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0345 8 545 68 -0.24 0.035 1000 -1000 -0.085 -1000
VEGFR1 specific signals 0.0345 8 464 56 -0.014 0.083 1000 -1000 -0.044 -1000
S1P3 pathway 0.0345 8 365 42 -0.12 0.04 1000 -1000 -0.04 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0345 8 285 33 -0.092 0.059 1000 -1000 -0.026 -1000
Signaling events mediated by PRL 0.0345 8 294 34 -0.062 0.073 1000 -1000 -0.038 -1000
Glucocorticoid receptor regulatory network 0.0302 7 908 114 -0.26 0.18 1000 -1000 -0.055 -1000
Regulation of p38-alpha and p38-beta 0.0302 7 385 54 -0.078 0.046 1000 -1000 -0.043 -1000
Regulation of Androgen receptor activity 0.0302 7 550 70 -0.25 0.044 1000 -1000 -0.048 -1000
Aurora B signaling 0.0302 7 495 67 -0.42 0.091 1000 -1000 -0.034 -1000
IL12-mediated signaling events 0.0259 6 548 87 -0.077 0.048 1000 -1000 -0.092 -1000
ErbB4 signaling events 0.0259 6 426 69 -0.18 0.074 1000 -1000 -0.046 -1000
PLK2 and PLK4 events 0.0259 6 18 3 0 0.023 1000 -1000 -0.015 -1000
EPO signaling pathway 0.0259 6 332 55 0.004 0.066 1000 -1000 -0.043 -1000
Regulation of nuclear SMAD2/3 signaling 0.0216 5 735 136 -0.21 0.054 1000 -1000 -0.044 -1000
Cellular roles of Anthrax toxin 0.0216 5 224 39 -0.037 0.026 1000 -1000 -0.018 -1000
PDGFR-alpha signaling pathway 0.0216 5 258 44 -0.011 0.054 1000 -1000 -0.041 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0216 5 192 37 -0.14 0.059 1000 -1000 -0.029 -1000
FAS signaling pathway (CD95) 0.0216 5 251 47 -0.015 0.036 1000 -1000 -0.033 -1000
Signaling mediated by p38-gamma and p38-delta 0.0216 5 75 15 -0.05 0.024 1000 -1000 -0.035 -1000
Retinoic acid receptors-mediated signaling 0.0216 5 319 58 -0.15 0.046 1000 -1000 -0.035 -1000
Class I PI3K signaling events 0.0216 5 384 73 -0.078 0.041 1000 -1000 -0.041 -1000
ErbB2/ErbB3 signaling events 0.0172 4 294 65 -0.056 0.035 1000 -1000 -0.053 -1000
a4b1 and a4b7 Integrin signaling 0.0172 4 22 5 0.014 0.033 1000 -1000 -0.002 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0172 4 421 85 -0.026 0.052 1000 -1000 -0.042 -1000
Insulin-mediated glucose transport 0.0172 4 131 32 -0.14 0.04 1000 -1000 -0.033 -1000
IFN-gamma pathway 0.0172 4 309 68 -0.04 0.035 1000 -1000 -0.05 -1000
Class I PI3K signaling events mediated by Akt 0.0172 4 283 68 -0.049 0.058 1000 -1000 -0.029 -1000
Signaling events mediated by HDAC Class III 0.0172 4 165 40 -0.058 0.046 1000 -1000 -0.016 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0172 4 382 83 -0.16 0.059 1000 -1000 -0.04 -1000
FoxO family signaling 0.0172 4 303 64 -0.085 0.058 1000 -1000 -0.068 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0172 4 519 125 -0.014 0.084 1000 -1000 -0.04 -1000
IL6-mediated signaling events 0.0172 4 345 75 -0.027 0.078 1000 -1000 -0.067 -1000
E-cadherin signaling in the nascent adherens junction 0.0172 4 359 76 -0.005 0.08 1000 -1000 -0.051 -1000
Arf6 trafficking events 0.0172 4 297 71 -0.042 0.043 1000 -1000 -0.025 -1000
Hedgehog signaling events mediated by Gli proteins 0.0129 3 238 65 -0.12 0.047 1000 -1000 -0.047 -1000
Aurora A signaling 0.0129 3 233 60 -0.11 0.067 1000 -1000 -0.023 -1000
Arf6 downstream pathway 0.0129 3 155 43 -0.024 0.038 1000 -1000 -0.028 -1000
ceramide signaling pathway 0.0129 3 151 49 0 0.04 1000 -1000 -0.038 -1000
Atypical NF-kappaB pathway 0.0129 3 94 31 0 0.049 1000 -1000 -0.018 -1000
IL27-mediated signaling events 0.0129 3 200 51 -0.047 0.038 1000 -1000 -0.05 -1000
TCGA08_rtk_signaling 0.0129 3 87 26 -0.023 0.054 1000 -1000 -0.017 -1000
Regulation of Telomerase 0.0129 3 396 102 -0.15 0.057 1000 -1000 -0.052 -1000
FOXM1 transcription factor network 0.0129 3 202 51 -0.097 0.059 1000 -1000 -0.17 -1000
Canonical NF-kappaB pathway 0.0086 2 91 39 -0.019 0.052 1000 -1000 -0.03 -1000
mTOR signaling pathway 0.0086 2 120 53 -0.05 0.035 1000 -1000 -0.032 -1000
IL2 signaling events mediated by PI3K 0.0086 2 124 58 -0.024 0.041 1000 -1000 -0.048 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0086 2 126 45 -0.003 0.067 1000 -1000 -0.043 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0086 2 209 74 -0.061 0.055 1000 -1000 -0.06 -1000
Rapid glucocorticoid signaling 0.0086 2 49 20 -0.016 0.027 1000 -1000 -0.005 -1000
p38 MAPK signaling pathway 0.0086 2 127 44 -0.035 0.054 1000 -1000 -0.026 -1000
Signaling events mediated by HDAC Class II 0.0043 1 122 75 -0.018 0.065 1000 -1000 -0.031 -1000
BARD1 signaling events 0.0043 1 70 57 -0.047 0.064 1000 -1000 -0.038 -1000
TRAIL signaling pathway 0.0043 1 77 48 -0.022 0.054 1000 -1000 -0.033 -1000
Paxillin-dependent events mediated by a4b1 0.0043 1 40 36 -0.049 0.051 1000 -1000 -0.032 -1000
IL2 signaling events mediated by STAT5 0.0043 1 38 22 -0.005 0.037 1000 -1000 -0.045 -1000
Insulin Pathway 0.0043 1 144 74 -0.019 0.074 1000 -1000 -0.049 -1000
Arf1 pathway 0.0043 1 98 54 -0.001 0.045 1000 -1000 -0.017 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 9 23 0.011 0.039 1000 -1000 -0.023 -1000
Circadian rhythm pathway 0.0000 0 2 22 -0.007 0.055 1000 -1000 -0.039 -1000
Aurora C signaling 0.0000 0 0 7 0 0.037 1000 -1000 -0.012 -1000
Signaling events mediated by HDAC Class I 0.0000 0 65 104 -0.047 0.058 1000 -1000 -0.028 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 3 27 0 0.049 1000 -1000 -0.035 -1000
E-cadherin signaling in keratinocytes 0.0000 0 28 43 -0.041 0.077 1000 -1000 -0.035 -1000
Class IB PI3K non-lipid kinase events 0.0000 0 0 3 -0.024 0.024 1000 -1000 -0.006 -1000
E-cadherin signaling events 0.0000 0 0 5 0.024 0.047 1000 -1000 -0.003 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.066 1000 -1000 0 -1000
Total NA 1360 79962 7203 -15 7.2 131000 -131000 -5.2 -131000
Reelin signaling pathway

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
CDK5R1/CDK5 0.031 0.029 -10000 0 -0.27 2 2
VLDLR 0.003 0.077 -10000 0 -0.29 15 15
CRKL 0.023 0.004 -10000 0 -10000 0 0
LRPAP1 0.024 0.004 -10000 0 -10000 0 0
FYN 0.024 0.004 -10000 0 -10000 0 0
ITGA3 0.022 0.027 -10000 0 -0.38 1 1
RELN/VLDLR/Fyn -0.059 0.12 -10000 0 -0.18 102 102
MAPK8IP1/MKK7/MAP3K11/JNK1 0.066 0.019 -10000 0 -10000 0 0
AKT1 -0.08 0.11 -10000 0 -0.29 23 23
MAP2K7 0.024 0.003 -10000 0 -10000 0 0
RAPGEF1 0.024 0.002 -10000 0 -10000 0 0
DAB1 -0.012 0.1 -10000 0 -0.38 16 16
RELN/LRP8/DAB1 -0.24 0.13 0.21 1 -0.28 200 201
LRPAP1/LRP8 -0.22 0.11 0.23 1 -0.27 194 195
RELN/LRP8/DAB1/Fyn -0.22 0.12 0.21 1 -0.27 190 191
DAB1/alpha3/beta1 Integrin -0.22 0.13 -10000 0 -0.33 100 100
long-term memory -0.31 0.16 -10000 0 -0.4 158 158
DAB1/LIS1 -0.22 0.13 0.2 1 -0.33 104 105
DAB1/CRLK/C3G -0.22 0.13 -10000 0 -0.33 103 103
PIK3CA 0.024 0.002 -10000 0 -10000 0 0
DAB1/NCK2 -0.22 0.14 0.21 1 -0.34 103 104
ARHGEF2 0.023 0.004 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.078 0.14 -10000 0 -0.29 68 68
CDK5R1 0.02 0.038 -10000 0 -0.38 2 2
RELN -0.12 0.15 -10000 0 -0.29 105 105
PIK3R1 0.023 0.005 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.24 0.14 0.22 1 -0.3 187 188
GRIN2A/RELN/LRP8/DAB1/Fyn -0.26 0.15 0.22 1 -0.35 139 140
MAPK8 0.024 0.002 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.067 0.12 -10000 0 -0.18 110 110
ITGB1 0.024 0.002 -10000 0 -10000 0 0
MAP1B -0.23 0.13 0.16 1 -0.34 111 112
RELN/LRP8 -0.24 0.14 0.22 1 -0.29 196 197
GRIN2B/RELN/LRP8/DAB1/Fyn -0.28 0.15 -10000 0 -0.33 196 196
PI3K 0.034 0.008 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.034 0.021 -10000 0 -0.27 1 1
RAP1A -0.21 0.11 -10000 0 -0.31 102 102
PAFAH1B1 0.02 0.009 -10000 0 -10000 0 0
MAPK8IP1 0.024 0.003 -10000 0 -10000 0 0
CRLK/C3G 0.035 0.006 -10000 0 -10000 0 0
GRIN2B -0.11 0.19 -10000 0 -0.38 78 78
NCK2 0.024 0 -10000 0 -10000 0 0
neuron differentiation -0.12 0.095 0.14 1 -0.21 92 93
neuron adhesion -0.21 0.11 -10000 0 -0.31 98 98
LRP8 -0.32 0.15 0.31 1 -0.38 195 196
GSK3B -0.079 0.1 -10000 0 -0.28 23 23
RELN/VLDLR/DAB1/Fyn -0.057 0.11 -10000 0 -0.26 26 26
MAP3K11 0.023 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.086 0.12 -10000 0 -0.2 106 106
CDK5 0.023 0.005 -10000 0 -10000 0 0
MAPT -0.034 0.12 0.8 2 -0.27 9 11
neuron migration -0.21 0.14 0.23 1 -0.36 93 94
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.12 0.095 0.14 1 -0.21 92 93
RELN/VLDLR -0.23 0.14 0.23 1 -0.28 183 184
Ephrin A reverse signaling

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
MAPKKK cascade -0.03 0.094 -9999 0 -0.17 66 66
EFNA5 -0.022 0.11 -9999 0 -0.29 33 33
FYN -0.042 0.076 -9999 0 -0.28 6 6
neuron projection morphogenesis -0.03 0.094 -9999 0 -0.17 66 66
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.03 0.094 -9999 0 -0.17 66 66
EPHA5 -0.043 0.11 -9999 0 -0.29 39 39
TCGA08_retinoblastoma

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
CDKN2B -0.025 0.11 -10000 0 -0.26 42 42
CDKN2C 0.033 0.023 -10000 0 -10000 0 0
CDKN2A -0.096 0.19 -10000 0 -0.4 65 65
CCND2 0.043 0.066 0.16 46 -10000 0 46
RB1 -0.042 0.079 0.31 2 -0.19 36 38
CDK4 0.047 0.071 0.17 40 -10000 0 40
CDK6 0.054 0.079 0.18 50 -10000 0 50
G1/S progression 0.037 0.084 0.19 36 -0.31 2 38
Lissencephaly gene (LIS1) in neuronal migration and development

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
DYNC1H1 0.023 0.005 -10000 0 -10000 0 0
VLDLR 0.003 0.077 -10000 0 -0.29 15 15
LRPAP1 0.024 0.004 -10000 0 -10000 0 0
NUDC 0.022 0.006 -10000 0 -10000 0 0
RELN/LRP8 -0.24 0.14 0.22 1 -0.29 196 197
CaM/Ca2+ 0.017 0.004 -10000 0 -10000 0 0
KATNA1 0.024 0.003 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.22 0.12 0.18 2 -0.27 184 186
IQGAP1/CaM 0.033 0.009 -10000 0 -10000 0 0
DAB1 -0.012 0.1 -10000 0 -0.38 16 16
IQGAP1 0.023 0.004 -10000 0 -10000 0 0
PLA2G7 0.024 0.002 -10000 0 -10000 0 0
CALM1 0.023 0.005 -10000 0 -10000 0 0
DYNLT1 0.024 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 -0.22 0.11 0.23 1 -0.27 194 195
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.024 0.002 -10000 0 -10000 0 0
CDK5R1 0.02 0.038 -10000 0 -0.38 2 2
LIS1/Poliovirus Protein 3A 0.006 0.004 -10000 0 -10000 0 0
CDK5R2 -0.02 0.11 -10000 0 -0.3 28 28
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.076 0.13 -10000 0 -0.2 110 110
YWHAE 0.02 0.009 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.19 0.12 0.32 1 -0.3 104 105
MAP1B 0 0.031 -10000 0 -0.21 5 5
RAC1 0.008 0.006 -10000 0 -10000 0 0
p35/CDK5 -0.2 0.11 0.16 1 -0.3 92 93
RELN -0.12 0.15 -10000 0 -0.29 105 105
PAFAH/LIS1 0.019 0.012 -10000 0 -10000 0 0
LIS1/CLIP170 0.019 0.012 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.16 0.1 -10000 0 -0.27 47 47
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.07 0.13 -10000 0 -0.34 23 23
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.21 0.12 0.32 1 -0.31 113 114
LIS1/IQGAP1 0.019 0.012 -10000 0 -10000 0 0
RHOA 0.009 0.006 -10000 0 -10000 0 0
PAFAH1B1 0.008 0.005 -10000 0 -10000 0 0
PAFAH1B3 0.022 0.027 -10000 0 -0.38 1 1
PAFAH1B2 0.024 0.004 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.011 0.035 -10000 0 -0.24 1 1
NDEL1/Katanin 60/Dynein heavy chain -0.19 0.12 0.32 2 -0.29 103 105
LRP8 -0.32 0.15 0.31 1 -0.38 195 196
NDEL1/Katanin 60 -0.2 0.12 0.32 2 -0.3 105 107
P39/CDK5 -0.22 0.12 0.16 1 -0.32 107 108
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.018 0.012 -10000 0 -10000 0 0
CDK5 -0.21 0.11 0.16 1 -0.31 99 100
PPP2R5D 0.024 0.002 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.017 0.01 -10000 0 -10000 0 0
CSNK2A1 0.02 0.009 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.054 0.11 -10000 0 -0.26 24 24
RELN/VLDLR -0.23 0.14 0.23 1 -0.28 183 184
CDC42 0.009 0.006 -10000 0 -10000 0 0
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer 0.022 0.064 -10000 0 -0.18 18 18
fibroblast growth factor receptor signaling pathway 0.022 0.064 -10000 0 -0.18 18 18
LAMA1 -0.022 0.1 -10000 0 -0.29 31 31
PRNP 0.018 0.022 -10000 0 -0.29 1 1
GPC1/SLIT2 -0.034 0.11 -10000 0 -0.2 67 67
SMAD2 0.008 0.021 -10000 0 -0.21 2 2
GPC1/PrPc/Cu2+ 0.026 0.018 -10000 0 -0.16 1 1
GPC1/Laminin alpha1 -0.004 0.082 -10000 0 -0.2 33 33
TDGF1 -0.19 0.2 -10000 0 -0.38 123 123
CRIPTO/GPC1 -0.13 0.16 -10000 0 -0.27 123 123
APP/GPC1 0.032 0.029 -10000 0 -0.27 2 2
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.11 0.12 -10000 0 -0.22 123 123
FLT1 0.019 0.01 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.046 0.026 -10000 0 -0.23 2 2
SERPINC1 0.008 0.032 -10000 0 -0.38 1 1
FYN -0.12 0.12 -10000 0 -0.23 117 117
FGR -0.12 0.12 -10000 0 -0.23 118 118
positive regulation of MAPKKK cascade -0.043 0.11 0.21 13 -0.25 23 36
SLIT2 -0.066 0.14 -10000 0 -0.29 66 66
GPC1/NRG -0.001 0.077 -10000 0 -0.2 29 29
NRG1 -0.018 0.099 -10000 0 -0.29 27 27
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.029 0.054 0.22 1 -0.23 8 9
LYN -0.1 0.12 -10000 0 -0.23 112 112
mol:Spermine 0.004 0.025 -10000 0 -0.27 2 2
cell growth 0.022 0.064 -10000 0 -0.18 18 18
BMP signaling pathway -0.021 0.038 0.38 2 -10000 0 2
SRC -0.053 0.1 -10000 0 -0.22 61 61
TGFBR1 0.024 0.002 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.058 0.14 -10000 0 -0.3 58 58
GPC1 0.021 0.038 -10000 0 -0.38 2 2
TGFBR1 (dimer) 0.024 0.002 -10000 0 -10000 0 0
VEGFA 0.001 0.099 0.31 1 -0.38 14 15
BLK -0.16 0.13 -10000 0 -0.24 156 156
HCK -0.05 0.099 -10000 0 -0.22 58 58
FGF2 -0.004 0.088 -10000 0 -0.29 20 20
FGFR1 0.017 0.036 -10000 0 -0.29 3 3
VEGFR1 homodimer 0.019 0.01 -10000 0 -10000 0 0
TGFBR2 0.024 0.002 -10000 0 -10000 0 0
cell death 0.032 0.029 -10000 0 -0.27 2 2
ATIII/GPC1 0.03 0.029 -10000 0 -0.27 2 2
PLA2G2A/GPC1 -0.029 0.11 -10000 0 -0.21 58 58
LCK -0.12 0.12 -10000 0 -0.23 125 125
neuron differentiation -0.002 0.077 -10000 0 -0.2 29 29
PrPc/Cu2+ 0.014 0.015 -10000 0 -0.19 1 1
APP 0.023 0.004 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.024 0.002 -10000 0 -10000 0 0
Osteopontin-mediated 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
IKK alpha homodimer -0.093 0.12 -10000 0 -0.24 49 49
NF kappa B1 p50/RelA/I kappa B alpha -0.085 0.12 0.32 2 -0.3 3 5
alphaV/beta3 Integrin/Osteopontin/Src -0.12 0.16 -10000 0 -0.28 116 116
AP1 -0.079 0.13 -10000 0 -0.4 4 4
ILK -0.098 0.12 0.19 2 -0.24 48 50
bone resorption -0.081 0.11 0.32 1 -0.25 3 4
PTK2B 0.019 0.01 -10000 0 -10000 0 0
PYK2/p130Cas -0.073 0.12 -10000 0 -0.22 45 45
ITGAV 0.024 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.035 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.098 0.14 -10000 0 -0.24 115 115
MAP3K1 -0.1 0.12 0.19 2 -0.22 113 115
JUN 0.023 0.004 -10000 0 -10000 0 0
MAPK3 -0.11 0.12 -10000 0 -0.27 49 49
MAPK1 -0.11 0.12 -10000 0 -0.27 49 49
Rac1/GDP 0.016 0.006 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.1 0.11 0.19 2 -0.23 49 51
ITGB3 0.017 0.045 -10000 0 -0.28 5 5
NFKBIA -0.1 0.11 -10000 0 -0.26 49 49
FOS 0.023 0.005 -10000 0 -10000 0 0
CD44 0.024 0.003 -10000 0 -10000 0 0
CHUK 0.023 0.005 -10000 0 -10000 0 0
PLAU -0.12 0.15 -10000 0 -0.5 1 1
NF kappa B1 p50/RelA -0.09 0.13 -10000 0 -0.28 47 47
BCAR1 0.024 0.002 -10000 0 -10000 0 0
RELA 0.023 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.029 0.036 -10000 0 -0.19 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.1 0.12 0.19 2 -0.21 115 117
VAV3 -0.12 0.12 0.19 2 -0.25 64 66
MAP3K14 -0.11 0.12 -10000 0 -0.22 115 115
ROCK2 0.024 0.002 -10000 0 -10000 0 0
SPP1 -0.18 0.21 -10000 0 -0.39 116 116
RAC1 0.021 0.008 -10000 0 -10000 0 0
Rac1/GTP -0.092 0.11 0.18 2 -0.23 60 62
MMP2 -0.082 0.1 -10000 0 -0.5 3 3
IL4-mediated signaling events

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
BCL2L1 -0.46 0.44 -10000 0 -1.1 46 46
STAT6 (cleaved dimer) -0.56 0.47 -10000 0 -1.1 84 84
IGHG1 -0.18 0.14 -10000 0 -10000 0 0
IGHG3 -0.5 0.42 -10000 0 -1 72 72
AKT1 -0.28 0.27 -10000 0 -0.74 34 34
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.22 0.22 -10000 0 -0.8 12 12
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.28 0.26 -10000 0 -0.78 24 24
THY1 -0.52 0.43 -10000 0 -1.1 57 57
MYB 0.024 0.004 -10000 0 -10000 0 0
HMGA1 0.019 0.046 -10000 0 -0.38 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.37 0.32 -10000 0 -0.79 61 61
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.28 0.26 -10000 0 -0.81 22 22
SP1 0.02 0.024 -10000 0 -10000 0 0
INPP5D 0.024 0.002 -10000 0 -10000 0 0
SOCS5 0.042 0.022 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.55 0.46 -10000 0 -1.1 80 80
SOCS1 -0.37 0.29 -10000 0 -0.72 58 58
SOCS3 -0.32 0.27 -10000 0 -0.71 48 48
FCER2 -0.68 0.58 -10000 0 -1.3 97 97
PARP14 0.012 0.023 -10000 0 -10000 0 0
CCL17 -0.52 0.43 -10000 0 -1.1 57 57
GRB2 0.024 0.004 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.22 0.2 -10000 0 -0.69 11 11
T cell proliferation -0.52 0.45 -10000 0 -1.1 62 62
IL4R/JAK1 -0.53 0.44 -10000 0 -1.1 59 59
EGR2 -0.57 0.46 -10000 0 -1.2 61 61
JAK2 -0.037 0.035 -10000 0 -10000 0 0
JAK3 0.008 0.057 -10000 0 -0.38 4 4
PIK3R1 0.023 0.005 -10000 0 -10000 0 0
JAK1 -0.009 0.021 -10000 0 -10000 0 0
COL1A2 -0.17 0.15 -10000 0 -10000 0 0
CCL26 -0.54 0.43 -10000 0 -1.1 59 59
IL4R -0.55 0.46 -10000 0 -1.2 55 55
PTPN6 0.035 0.015 -10000 0 -10000 0 0
IL13RA2 -0.53 0.43 -10000 0 -1.1 57 57
IL13RA1 -0.038 0.035 -10000 0 -10000 0 0
IRF4 -0.4 0.57 -10000 0 -1.3 60 60
ARG1 -0.099 0.12 -10000 0 -0.58 1 1
CBL -0.35 0.3 -10000 0 -0.76 59 59
GTF3A 0.002 0.075 0.29 7 -0.38 3 10
PIK3CA 0.024 0.002 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.044 0.049 -10000 0 -10000 0 0
IRF4/BCL6 -0.35 0.53 -10000 0 -1.2 60 60
CD40LG -0.028 0.09 -10000 0 -0.31 15 15
MAPK14 -0.35 0.3 -10000 0 -0.77 55 55
mitosis -0.27 0.26 -10000 0 -0.69 34 34
STAT6 -0.58 0.5 -10000 0 -1.2 68 68
SPI1 0.024 0.029 -10000 0 -0.29 2 2
RPS6KB1 -0.26 0.25 -10000 0 -0.67 34 34
STAT6 (dimer) -0.58 0.5 -10000 0 -1.2 67 67
STAT6 (dimer)/PARP14 -0.58 0.48 -10000 0 -1.2 71 71
mast cell activation 0.014 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.3 0.27 -10000 0 -0.73 36 36
FRAP1 -0.28 0.27 -10000 0 -0.74 34 34
LTA -0.53 0.44 -10000 0 -1.1 56 56
FES 0.023 0.004 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.57 0.48 1.2 67 -10000 0 67
CCL11 -0.57 0.5 -10000 0 -1.2 67 67
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.27 0.24 -10000 0 -0.68 31 31
IL2RG 0.015 0.031 -10000 0 -0.28 1 1
IL10 -0.55 0.47 -10000 0 -1.2 62 62
IRS1 0.024 0 -10000 0 -10000 0 0
IRS2 0.021 0.022 0.31 1 -10000 0 1
IL4 -0.14 0.17 -10000 0 -0.97 6 6
IL5 -0.52 0.43 -10000 0 -1.1 53 53
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.42 0.34 -10000 0 -0.86 57 57
COL1A1 -0.24 0.18 -10000 0 -0.61 9 9
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.53 0.44 -10000 0 -1.2 51 51
IL2R gamma/JAK3 0.013 0.053 -10000 0 -0.26 5 5
TFF3 -0.53 0.44 -10000 0 -1.1 56 56
ALOX15 -0.54 0.46 -10000 0 -1.1 63 63
MYBL1 0.019 0.028 -10000 0 -0.38 1 1
T-helper 2 cell differentiation -0.44 0.36 -10000 0 -0.91 57 57
SHC1 0.023 0.004 -10000 0 -10000 0 0
CEBPB 0.014 0.029 -10000 0 -0.38 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.26 0.26 -10000 0 -0.83 18 18
mol:PI-3-4-5-P3 -0.28 0.27 -10000 0 -0.74 34 34
PI3K -0.3 0.29 -10000 0 -0.79 34 34
DOK2 0.018 0.01 -10000 0 -10000 0 0
ETS1 0.036 0.016 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.21 0.18 -10000 0 -0.62 13 13
ITGB3 -0.53 0.45 -10000 0 -1.2 55 55
PIGR -0.67 0.58 -10000 0 -1.3 86 86
IGHE 0.081 0.075 0.17 78 -10000 0 78
MAPKKK cascade -0.2 0.18 -10000 0 -0.61 13 13
BCL6 0.028 0.008 -10000 0 -10000 0 0
OPRM1 -0.52 0.43 -10000 0 -1.1 56 56
RETNLB -0.75 0.6 -10000 0 -1.3 103 103
SELP -0.62 0.55 -10000 0 -1.3 71 71
AICDA -0.51 0.42 -10000 0 -1.1 56 56
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.024 0.003 -10000 0 -10000 0 0
CCL5 0.011 0.063 -10000 0 -0.3 9 9
SDCBP 0.021 0.008 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.1 0.1 0.23 2 -0.26 32 34
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.085 0.098 0.19 1 -0.25 28 29
Syndecan-1/Syntenin -0.09 0.099 0.19 1 -0.24 29 30
MAPK3 -0.092 0.093 0.18 1 -0.38 5 6
HGF/MET 0.015 0.071 -10000 0 -0.25 15 15
TGFB1/TGF beta receptor Type II 0.024 0.003 -10000 0 -10000 0 0
BSG 0.024 0.002 -10000 0 -10000 0 0
keratinocyte migration -0.084 0.097 0.19 1 -0.25 28 29
Syndecan-1/RANTES -0.099 0.11 0.21 2 -0.26 35 37
Syndecan-1/CD147 -0.091 0.1 0.2 1 -0.24 29 30
Syndecan-1/Syntenin/PIP2 -0.087 0.095 0.18 1 -0.24 29 30
LAMA5 0.015 0.012 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion -0.086 0.093 0.18 1 -0.23 29 30
MMP7 -0.37 0.086 0.31 2 -0.39 225 227
HGF 0.014 0.053 -10000 0 -0.3 6 6
Syndecan-1/CASK -0.097 0.096 0.21 1 -0.24 32 33
Syndecan-1/HGF/MET -0.1 0.11 0.22 2 -0.26 37 39
regulation of cell adhesion -0.092 0.088 0.17 1 -0.36 5 6
HPSE 0.019 0.035 -10000 0 -0.29 3 3
positive regulation of cell migration -0.1 0.1 0.23 2 -0.26 32 34
SDC1 -0.1 0.1 0.25 1 -0.26 32 33
Syndecan-1/Collagen -0.1 0.1 0.23 2 -0.26 32 34
PPIB 0.023 0.004 -10000 0 -10000 0 0
MET 0.007 0.085 0.31 1 -0.38 10 11
PRKACA 0.024 0.002 -10000 0 -10000 0 0
MMP9 -0.01 0.17 0.31 22 -0.38 31 53
MAPK1 -0.091 0.093 0.18 1 -0.37 5 6
homophilic cell adhesion -0.1 0.1 0.23 2 -0.25 32 34
MMP1 -0.24 0.2 0.31 1 -0.38 150 151
Signaling events mediated by the Hedgehog family

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
TGFB2 0.014 0.08 -10000 0 -0.34 9 9
IHH 0.026 0.035 -10000 0 -0.41 1 1
SHH Np/Cholesterol/GAS1 -0.075 0.12 0.18 3 -0.21 98 101
LRPAP1 0.024 0.004 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.075 0.12 0.21 98 -0.18 3 101
SMO/beta Arrestin2 0.004 0.073 -10000 0 -0.4 2 2
SMO -0.006 0.067 -10000 0 -0.42 2 2
AKT1 -0.005 0.096 -10000 0 -0.35 12 12
ARRB2 0.02 0.009 -10000 0 -10000 0 0
BOC -0.017 0.1 -10000 0 -0.29 30 30
ADRBK1 0.023 0.004 -10000 0 -10000 0 0
heart looping -0.006 0.067 -10000 0 -0.41 2 2
STIL -0.049 0.11 0.18 9 -0.29 6 15
DHH N/PTCH2 0.02 0.057 -10000 0 -0.2 14 14
DHH N/PTCH1 0.021 0.068 -10000 0 -0.34 2 2
PIK3CA 0.024 0.002 -10000 0 -10000 0 0
DHH 0.005 0.072 -10000 0 -0.29 13 13
PTHLH 0.011 0.09 -10000 0 -0.69 2 2
determination of left/right symmetry -0.006 0.067 -10000 0 -0.41 2 2
PIK3R1 0.023 0.005 -10000 0 -10000 0 0
skeletal system development 0.011 0.09 -10000 0 -0.69 2 2
IHH N/Hhip -0.016 0.11 -10000 0 -0.23 46 46
DHH N/Hhip -0.02 0.1 -10000 0 -0.21 51 51
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.006 0.067 -10000 0 -0.41 2 2
pancreas development -0.034 0.12 -10000 0 -0.29 42 42
HHAT 0.022 0.021 -10000 0 -0.29 1 1
PI3K 0.034 0.008 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.013 0.1 -10000 0 -0.3 26 26
somite specification -0.006 0.067 -10000 0 -0.41 2 2
SHH Np/Cholesterol/PTCH1 -0.05 0.11 0.19 5 -0.3 6 11
SHH Np/Cholesterol/PTCH2 -0.059 0.11 0.18 4 -0.2 85 89
SHH Np/Cholesterol/Megalin -0.073 0.12 0.17 5 -0.22 94 99
SHH -0.085 0.14 0.26 5 -0.27 84 89
catabolic process 0.02 0.059 -10000 0 -0.38 2 2
SMO/Vitamin D3 -0.045 0.1 -10000 0 -0.3 6 6
SHH Np/Cholesterol/Hhip -0.083 0.12 0.18 4 -0.23 83 87
LRP2 -0.02 0.1 -10000 0 -0.38 16 16
receptor-mediated endocytosis -0.05 0.099 -10000 0 -0.33 5 5
SHH Np/Cholesterol/BOC -0.076 0.12 0.18 5 -0.2 104 109
SHH Np/Cholesterol/CDO -0.058 0.11 0.18 4 -0.2 84 88
mesenchymal cell differentiation 0.083 0.12 0.22 83 -0.18 4 87
mol:Vitamin D3 -0.044 0.12 0.2 9 -0.3 6 15
IHH N/PTCH2 0.028 0.047 -10000 0 -0.2 8 8
CDON 0.024 0.003 -10000 0 -10000 0 0
IHH N/PTCH1 0.027 0.062 -10000 0 -0.38 2 2
Megalin/LRPAP1 0.011 0.077 -10000 0 -0.27 16 16
PTCH2 0.022 0.027 -10000 0 -0.38 1 1
SHH Np/Cholesterol -0.066 0.1 -10000 0 -0.2 84 84
PTCH1 0.02 0.059 -10000 0 -0.38 2 2
HHIP -0.034 0.12 -10000 0 -0.29 42 42
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.014 0.068 -10000 0 -0.37 6 6
Crk/p130 Cas/Paxillin -0.077 0.11 -10000 0 -0.27 21 21
JUN -0.075 0.11 -10000 0 -0.29 29 29
HRAS 0.024 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.045 0.12 -10000 0 -0.22 53 53
RAP1A 0.023 0.004 -10000 0 -10000 0 0
FRS2 0.024 0.002 -10000 0 -10000 0 0
RAP1A/GDP 0.017 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.046 0.13 -10000 0 -0.28 29 29
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.024 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.02 0.009 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.024 0.092 -10000 0 -0.15 79 79
RHOA 0.024 0.004 -10000 0 -10000 0 0
RAP1A/GTP -0.04 0.12 -10000 0 -0.26 26 26
GRB7 0.022 0.057 0.31 3 -0.38 3 6
RET51/GFRalpha1/GDNF -0.047 0.13 -10000 0 -0.27 30 30
MAPKKK cascade -0.062 0.12 -10000 0 -0.3 23 23
BCAR1 0.024 0.002 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.024 0.093 -10000 0 -0.15 81 81
lamellipodium assembly -0.067 0.1 -10000 0 -0.21 67 67
RET51/GFRalpha1/GDNF/SHC -0.046 0.13 -10000 0 -0.28 26 26
PIK3CA 0.024 0.002 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.023 0.091 -10000 0 -0.15 79 79
RET9/GFRalpha1/GDNF/Shank3 -0.024 0.092 -10000 0 -0.15 77 77
MAPK3 -0.075 0.084 -10000 0 -0.25 24 24
DOK1 0.024 0.002 -10000 0 -10000 0 0
DOK6 0.012 0.046 -10000 0 -0.29 5 5
PXN 0.024 0.002 -10000 0 -10000 0 0
neurite development -0.055 0.078 -10000 0 -0.26 13 13
DOK5 0.009 0.053 0.31 1 -0.31 5 6
GFRA1 -0.089 0.15 -10000 0 -0.29 83 83
MAPK8 -0.075 0.12 -10000 0 -0.31 29 29
HRAS/GTP -0.06 0.14 -10000 0 -0.34 25 25
tube development -0.022 0.085 -10000 0 -10000 0 0
MAPK1 -0.074 0.083 -10000 0 -0.25 24 24
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.045 0.093 -10000 0 -0.17 79 79
Rac1/GDP 0.016 0.006 -10000 0 -10000 0 0
SRC 0.016 0.012 -10000 0 -10000 0 0
PDLIM7 0.024 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.033 0.1 -10000 0 -0.28 18 18
SHC1 0.023 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.046 0.13 -10000 0 -0.28 26 26
RET51/GFRalpha1/GDNF/Dok5 -0.036 0.11 0.23 1 -0.29 16 17
PRKCA 0.023 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.018 0.002 -10000 0 -10000 0 0
CREB1 -0.073 0.13 -10000 0 -0.24 79 79
PIK3R1 0.023 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.045 0.092 -10000 0 -0.17 77 77
RET51/GFRalpha1/GDNF/Grb7 -0.045 0.13 0.23 1 -0.27 28 29
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.036 0.13 -10000 0 -0.3 43 43
DOK4 0.024 0.002 -10000 0 -10000 0 0
JNK cascade -0.074 0.11 -10000 0 -0.29 29 29
RET9/GFRalpha1/GDNF/FRS2 -0.024 0.093 -10000 0 -0.15 81 81
SHANK3 0.023 0.004 -10000 0 -10000 0 0
RASA1 0.023 0.005 -10000 0 -10000 0 0
NCK1 0.024 0.002 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.044 0.091 -10000 0 -0.17 77 77
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.073 0.12 -10000 0 -0.32 27 27
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.075 0.13 -10000 0 -0.31 31 31
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.077 0.14 -10000 0 -0.22 94 94
PI3K -0.099 0.15 -10000 0 -0.3 72 72
SOS1 0.024 0.002 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.013 0.092 -10000 0 -10000 0 0
GRB10 0.021 0.008 -10000 0 -10000 0 0
activation of MAPKK activity -0.059 0.1 -10000 0 -0.27 23 23
RET51/GFRalpha1/GDNF/FRS2 -0.047 0.13 -10000 0 -0.28 27 27
GAB1 0.023 0.004 -10000 0 -10000 0 0
IRS1 0.024 0 -10000 0 -10000 0 0
IRS2 0.021 0.022 0.31 1 -10000 0 1
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.078 0.14 -10000 0 -0.22 95 95
RET51/GFRalpha1/GDNF/PKC alpha -0.044 0.12 -10000 0 -0.27 26 26
GRB2 0.024 0.004 -10000 0 -10000 0 0
PRKACA 0.024 0.002 -10000 0 -10000 0 0
GDNF 0.014 0.018 -10000 0 -10000 0 0
RAC1 0.021 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.047 0.13 -10000 0 -0.27 30 30
Rac1/GTP -0.077 0.12 -10000 0 -0.25 67 67
RET9/GFRalpha1/GDNF -0.038 0.093 -10000 0 -0.16 81 81
GFRalpha1/GDNF -0.048 0.11 -10000 0 -0.2 81 81
BCR signaling pathway

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
JUN -0.098 0.19 0.24 1 -0.43 46 47
IKBKB -0.026 0.1 0.22 4 -0.29 13 17
AKT1 -0.067 0.097 0.16 2 -0.24 39 41
IKBKG -0.026 0.094 0.24 1 -0.26 14 15
CALM1 -0.072 0.18 -10000 0 -0.44 37 37
PIK3CA 0.024 0.002 -10000 0 -10000 0 0
MAP3K1 -0.11 0.24 0.27 1 -0.57 41 42
MAP3K7 0.024 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.075 0.2 -10000 0 -0.46 38 38
DOK1 0.024 0.002 -10000 0 -10000 0 0
AP-1 -0.058 0.11 0.18 1 -0.25 43 44
LYN 0.021 0.008 -10000 0 -10000 0 0
BLNK 0.021 0.029 -10000 0 -0.29 2 2
SHC1 0.023 0.004 -10000 0 -10000 0 0
BCR complex -0.054 0.14 -10000 0 -0.26 69 69
CD22 -0.12 0.24 -10000 0 -0.54 48 48
CAMK2G -0.068 0.17 0.25 1 -0.41 37 38
CSNK2A1 0.02 0.009 -10000 0 -10000 0 0
INPP5D 0.024 0.002 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.021 0.089 -10000 0 -0.25 19 19
GO:0007205 -0.077 0.2 -10000 0 -0.47 38 38
SYK 0.024 0.002 -10000 0 -10000 0 0
ELK1 -0.074 0.19 -10000 0 -0.45 37 37
NFATC1 -0.13 0.22 0.2 1 -0.47 53 54
B-cell antigen/BCR complex -0.054 0.14 -10000 0 -0.26 69 69
PAG1/CSK 0.03 0.013 -10000 0 -10000 0 0
NFKBIB 0.002 0.046 0.12 3 -0.13 11 14
HRAS -0.056 0.15 0.24 2 -0.36 37 39
NFKBIA 0.003 0.045 0.12 3 -0.12 11 14
NF-kappa-B/RelA/I kappa B beta 0.008 0.039 0.12 3 -0.092 2 5
RasGAP/Csk -0.025 0.14 -10000 0 -0.29 37 37
mol:GDP -0.071 0.19 -10000 0 -0.45 37 37
PTEN 0.023 0.005 -10000 0 -10000 0 0
CD79B -0.016 0.1 -10000 0 -0.29 29 29
NF-kappa-B/RelA/I kappa B alpha 0.008 0.038 0.12 3 -10000 0 3
GRB2 0.024 0.004 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.14 0.24 0.3 1 -0.52 57 58
PIK3R1 0.023 0.005 -10000 0 -10000 0 0
mol:IP3 -0.077 0.2 -10000 0 -0.47 39 39
CSK 0.023 0.004 -10000 0 -10000 0 0
FOS -0.07 0.17 -10000 0 -0.42 37 37
CHUK -0.033 0.11 0.24 1 -0.29 21 22
IBTK 0.024 0.003 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.047 0.18 0.24 4 -0.42 30 34
PTPN6 -0.12 0.23 -10000 0 -0.52 48 48
RELA 0.023 0.004 -10000 0 -10000 0 0
BCL2A1 0.006 0.028 0.098 1 -10000 0 1
VAV2 -0.13 0.25 -10000 0 -0.56 50 50
ubiquitin-dependent protein catabolic process 0.005 0.046 0.13 3 -0.12 11 14
BTK -0.065 0.29 -10000 0 -1 19 19
CD19 -0.13 0.24 -10000 0 -0.53 52 52
MAP4K1 -0.009 0.095 -10000 0 -0.29 24 24
CD72 0.02 0.034 -10000 0 -0.34 2 2
PAG1 0.021 0.008 -10000 0 -10000 0 0
MAPK14 -0.092 0.2 0.25 1 -0.48 41 42
SH3BP5 0.024 0.002 -10000 0 -10000 0 0
PIK3AP1 -0.069 0.2 0.34 1 -0.46 37 38
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.098 0.24 -10000 0 -0.55 39 39
RAF1 -0.055 0.14 0.23 2 -0.36 34 36
RasGAP/p62DOK/SHIP -0.022 0.14 -10000 0 -0.29 36 36
CD79A -0.067 0.14 -10000 0 -0.29 67 67
re-entry into mitotic cell cycle -0.058 0.11 0.18 1 -0.25 43 44
RASA1 0.023 0.005 -10000 0 -10000 0 0
MAPK3 -0.048 0.12 0.2 3 -0.33 28 31
MAPK1 -0.047 0.12 0.21 2 -0.33 27 29
CD72/SHP1 -0.11 0.22 0.23 1 -0.5 48 49
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.093 0.2 0.25 1 -0.48 41 42
actin cytoskeleton organization -0.11 0.21 -10000 0 -0.47 48 48
NF-kappa-B/RelA 0.019 0.076 0.23 3 -0.19 7 10
Calcineurin -0.045 0.16 -10000 0 -0.39 33 33
PI3K -0.12 0.19 -10000 0 -0.41 56 56
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.075 0.21 0.17 1 -0.48 39 40
SOS1 0.024 0.002 -10000 0 -10000 0 0
Bam32/HPK1 -0.13 0.32 -10000 0 -0.8 37 37
DAPP1 -0.15 0.35 -10000 0 -0.9 36 36
cytokine secretion -0.12 0.2 0.19 1 -0.44 53 54
mol:DAG -0.077 0.2 -10000 0 -0.47 39 39
PLCG2 0.004 0.077 -10000 0 -0.29 15 15
MAP2K1 -0.052 0.13 0.22 2 -0.36 28 30
B-cell antigen/BCR complex/FcgammaRIIB -0.049 0.15 -10000 0 -0.26 71 71
mol:PI-3-4-5-P3 -0.092 0.13 0.16 1 -0.32 42 43
ETS1 -0.063 0.15 0.24 1 -0.38 35 36
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.003 0.11 -10000 0 -0.27 21 21
B-cell antigen/BCR complex/LYN -0.097 0.23 -10000 0 -0.55 39 39
MALT1 0.019 0.01 -10000 0 -10000 0 0
TRAF6 0.024 0.003 -10000 0 -10000 0 0
RAC1 -0.12 0.23 -10000 0 -0.5 48 48
B-cell antigen/BCR complex/LYN/SYK -0.092 0.22 -10000 0 -0.48 47 47
CARD11 -0.069 0.21 0.25 7 -0.44 40 47
FCGR2B -0.015 0.1 -10000 0 -0.29 28 28
PPP3CA 0.024 0.004 -10000 0 -10000 0 0
BCL10 0.023 0.004 -10000 0 -10000 0 0
IKK complex -0.007 0.048 0.15 5 -0.11 5 10
PTPRC 0.003 0.077 -10000 0 -0.29 15 15
PDPK1 -0.065 0.089 0.14 3 -0.23 36 39
PPP3CB 0.024 0.003 -10000 0 -10000 0 0
PPP3CC 0.018 0.01 -10000 0 -10000 0 0
POU2F2 0.006 0.03 0.1 2 -10000 0 2
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.34 0.26 -10000 0 -0.73 36 36
HDAC7 0.02 0.013 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.27 0.24 -10000 0 -0.71 22 22
SMAD4 0.019 0.011 -10000 0 -10000 0 0
ID2 -0.34 0.26 -10000 0 -0.74 34 34
AP1 0.034 0.012 -10000 0 -10000 0 0
ABCG2 -0.43 0.28 -10000 0 -0.75 66 66
HIF1A -0.072 0.052 -10000 0 -0.2 1 1
TFF3 -0.34 0.26 -10000 0 -0.73 39 39
GATA2 0.016 0.05 -10000 0 -0.29 6 6
AKT1 -0.071 0.055 -10000 0 -0.22 5 5
response to hypoxia -0.071 0.047 -10000 0 -0.2 6 6
MCL1 -0.33 0.26 -10000 0 -0.73 36 36
NDRG1 -0.32 0.26 -10000 0 -0.72 34 34
SERPINE1 -0.38 0.29 -10000 0 -0.74 58 58
FECH -0.33 0.26 -10000 0 -0.73 35 35
FURIN -0.34 0.26 -10000 0 -0.74 33 33
NCOA2 0.021 0.009 -10000 0 -10000 0 0
EP300 -0.066 0.074 -10000 0 -0.29 12 12
HMOX1 -0.34 0.26 -10000 0 -0.73 36 36
BHLHE40 -0.34 0.26 -10000 0 -0.74 38 38
BHLHE41 -0.34 0.26 -10000 0 -0.74 35 35
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.063 0.084 -10000 0 -10000 0 0
ENG -0.066 0.073 0.24 2 -10000 0 2
JUN 0.023 0.006 -10000 0 -10000 0 0
RORA -0.34 0.26 -10000 0 -0.74 32 32
ABCB1 -0.21 0.35 -10000 0 -0.99 38 38
TFRC -0.34 0.26 -10000 0 -0.73 36 36
CXCR4 -0.34 0.26 -10000 0 -0.74 38 38
TF -0.36 0.27 -10000 0 -0.76 41 41
CITED2 -0.34 0.26 -10000 0 -0.74 34 34
HIF1A/ARNT -0.35 0.31 -10000 0 -0.82 33 33
LDHA -0.034 0.044 -10000 0 -10000 0 0
ETS1 -0.34 0.26 -10000 0 -0.73 36 36
PGK1 -0.34 0.26 -10000 0 -0.72 39 39
NOS2 -0.35 0.27 -10000 0 -0.74 42 42
ITGB2 -0.34 0.26 -10000 0 -0.74 36 36
ALDOA -0.34 0.26 -10000 0 -0.73 36 36
Cbp/p300/CITED2 -0.34 0.27 -10000 0 -0.8 28 28
FOS 0.023 0.007 -10000 0 -10000 0 0
HK2 -0.34 0.26 -10000 0 -0.74 33 33
SP1 0.009 0.047 -10000 0 -10000 0 0
GCK -0.076 0.18 -10000 0 -1.2 4 4
HK1 -0.34 0.26 -10000 0 -0.73 36 36
NPM1 -0.34 0.26 -10000 0 -0.74 33 33
EGLN1 -0.34 0.26 -10000 0 -0.73 36 36
CREB1 0.029 0 -10000 0 -10000 0 0
PGM1 -0.34 0.26 -10000 0 -0.75 32 32
SMAD3 0.024 0.005 -10000 0 -10000 0 0
EDN1 -0.069 0.11 -10000 0 -0.62 3 3
IGFBP1 -0.34 0.28 -10000 0 -0.74 45 45
VEGFA -0.27 0.23 -10000 0 -0.68 32 32
HIF1A/JAB1 -0.035 0.045 -10000 0 -10000 0 0
CP -0.4 0.28 -10000 0 -0.77 52 52
CXCL12 -0.36 0.28 -10000 0 -0.76 43 43
COPS5 0.021 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4 0.028 0.016 -10000 0 -10000 0 0
BNIP3 -0.34 0.26 -10000 0 -0.74 37 37
EGLN3 -0.34 0.26 -10000 0 -0.73 36 36
CA9 -0.48 0.27 -10000 0 -0.77 77 77
TERT -0.35 0.27 -10000 0 -0.76 41 41
ENO1 -0.34 0.26 -10000 0 -0.73 35 35
PFKL -0.34 0.26 -10000 0 -0.76 29 29
NCOA1 0.024 0.002 -10000 0 -10000 0 0
ADM -0.34 0.26 -10000 0 -0.73 35 35
ARNT -0.071 0.051 -10000 0 -10000 0 0
HNF4A 0.015 0.016 -10000 0 -10000 0 0
ADFP -0.34 0.25 -10000 0 -0.72 40 40
SLC2A1 -0.28 0.23 -10000 0 -0.69 31 31
LEP -0.35 0.27 -10000 0 -0.74 46 46
HIF1A/ARNT/Cbp/p300 -0.28 0.25 -10000 0 -0.73 23 23
EPO -0.19 0.16 -10000 0 -0.74 3 3
CREBBP -0.063 0.072 -10000 0 -0.32 8 8
HIF1A/ARNT/Cbp/p300/HDAC7 -0.28 0.26 -10000 0 -0.73 28 28
PFKFB3 -0.34 0.26 -10000 0 -0.73 36 36
NT5E -0.34 0.26 -10000 0 -0.74 36 36
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.25 0.24 -9999 0 -0.71 30 30
PCK1 -0.47 0.53 -9999 0 -1.1 85 85
HNF4A -0.23 0.25 -9999 0 -0.79 18 18
KCNJ11 -0.27 0.25 -9999 0 -0.76 27 27
AKT1 -0.2 0.15 -9999 0 -0.46 32 32
response to starvation -0.013 0.024 -9999 0 -10000 0 0
DLK1 -0.27 0.26 -9999 0 -0.74 30 30
NKX2-1 -0.15 0.15 -9999 0 -0.55 6 6
ACADM -0.26 0.24 -9999 0 -0.71 31 31
TAT -0.4 0.47 -9999 0 -1.1 62 62
CEBPB 0.001 0.039 -9999 0 -0.38 1 1
CEBPA 0.001 0.048 -9999 0 -0.25 3 3
TTR -0.24 0.42 -9999 0 -1.1 40 40
PKLR -0.31 0.31 -9999 0 -0.8 50 50
APOA1 -0.26 0.28 -9999 0 -0.87 17 17
CPT1C -0.26 0.24 -9999 0 -0.7 31 31
ALAS1 -0.13 0.13 -9999 0 -0.55 1 1
TFRC -0.23 0.21 -9999 0 -0.56 36 36
FOXF1 0.023 0.056 -9999 0 -0.29 6 6
NF1 0.028 0.005 -9999 0 -10000 0 0
HNF1A (dimer) -0.071 0.043 -9999 0 -0.19 7 7
CPT1A -0.26 0.24 -9999 0 -0.71 30 30
HMGCS1 -0.26 0.24 -9999 0 -0.71 30 30
NR3C1 -0.035 0.099 -9999 0 -0.21 41 41
CPT1B -0.26 0.24 -9999 0 -0.71 31 31
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 -0.061 0.029 -9999 0 -10000 0 0
GCK -0.25 0.25 -9999 0 -0.71 34 34
CREB1 -0.056 0.1 -9999 0 -0.21 46 46
IGFBP1 -0.17 0.15 -9999 0 -0.52 15 15
PDX1 -0.28 0.16 -9999 0 -0.58 10 10
UCP2 -0.26 0.24 -9999 0 -0.71 31 31
ALDOB -0.31 0.27 -9999 0 -0.76 36 36
AFP -0.055 0.082 -9999 0 -0.35 2 2
BDH1 -0.26 0.24 -9999 0 -0.73 29 29
HADH -0.26 0.25 -9999 0 -0.74 30 30
F2 -0.28 0.28 -9999 0 -0.84 23 23
HNF1A -0.071 0.043 -9999 0 -0.19 7 7
G6PC -0.16 0.34 -9999 0 -1.1 23 23
SLC2A2 -0.2 0.16 -9999 0 -0.63 5 5
INS -0.01 0.033 -9999 0 -10000 0 0
FOXA1 0.003 0.074 -9999 0 -0.29 10 10
FOXA3 -0.099 0.13 -9999 0 -0.28 49 49
FOXA2 -0.31 0.29 -9999 0 -0.79 38 38
ABCC8 -0.34 0.34 -9999 0 -0.85 54 54
ALB -0.061 0.09 -9999 0 -0.34 5 5
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.052 0.15 -10000 0 -0.38 35 35
CRKL -0.045 0.14 -10000 0 -0.38 35 35
HRAS -0.028 0.14 -10000 0 -0.34 33 33
mol:PIP3 -0.034 0.14 0.25 1 -0.36 33 34
SPRED1 0.023 0.006 -10000 0 -10000 0 0
SPRED2 0.024 0.002 -10000 0 -10000 0 0
GAB1 -0.045 0.15 -10000 0 -0.4 35 35
FOXO3 -0.035 0.16 -10000 0 -0.36 39 39
AKT1 -0.036 0.17 -10000 0 -0.38 41 41
BAD -0.034 0.16 -10000 0 -0.36 39 39
megakaryocyte differentiation -0.062 0.16 -10000 0 -0.42 35 35
GSK3B -0.035 0.16 -10000 0 -0.36 39 39
RAF1 -0.024 0.12 0.24 1 -0.29 33 34
SHC1 0.023 0.004 -10000 0 -10000 0 0
STAT3 -0.046 0.15 -10000 0 -0.4 35 35
STAT1 -0.11 0.35 -10000 0 -0.91 36 36
HRAS/SPRED1 -0.013 0.12 -10000 0 -0.28 33 33
cell proliferation -0.045 0.15 -10000 0 -0.4 35 35
PIK3CA 0.024 0.002 -10000 0 -10000 0 0
TEC 0.024 0.003 -10000 0 -10000 0 0
RPS6KB1 -0.035 0.16 -10000 0 -0.4 35 35
HRAS/SPRED2 -0.012 0.12 -10000 0 -0.29 33 33
LYN/TEC/p62DOK -0.011 0.15 -10000 0 -0.38 29 29
MAPK3 -0.015 0.088 0.21 2 -0.23 10 12
STAP1 -0.06 0.18 -10000 0 -0.47 35 35
GRAP2 0.016 0.046 -10000 0 -0.29 5 5
JAK2 -0.091 0.3 -10000 0 -0.78 35 35
STAT1 (dimer) -0.11 0.34 -10000 0 -0.89 36 36
mol:Gleevec 0.001 0.006 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.017 0.17 -10000 0 -0.4 35 35
actin filament polymerization -0.044 0.15 -10000 0 -0.39 34 34
LYN 0.021 0.008 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.086 0.23 -10000 0 -0.62 35 35
PIK3R1 0.023 0.005 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.021 0.14 -10000 0 -0.36 35 35
PI3K -0.015 0.16 -10000 0 -0.38 35 35
PTEN 0.023 0.005 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.12 0.4 -10000 0 -1.1 35 35
MAPK8 -0.046 0.15 -10000 0 -0.4 35 35
STAT3 (dimer) -0.045 0.15 -10000 0 -0.4 35 35
positive regulation of transcription -0.011 0.074 0.2 2 -0.2 7 9
mol:GDP -0.024 0.14 -10000 0 -0.36 33 33
PIK3C2B -0.044 0.15 -10000 0 -0.41 33 33
CBL/CRKL -0.032 0.14 -10000 0 -0.37 35 35
FER -0.046 0.15 -10000 0 -0.4 35 35
SH2B3 -0.046 0.15 -10000 0 -0.4 35 35
PDPK1 -0.032 0.13 0.23 1 -0.34 33 34
SNAI2 -0.045 0.15 -10000 0 -0.39 34 34
positive regulation of cell proliferation -0.076 0.26 -10000 0 -0.68 35 35
KITLG 0.017 0.024 -10000 0 -10000 0 0
cell motility -0.076 0.26 -10000 0 -0.68 35 35
PTPN6 0.025 0.009 -10000 0 -10000 0 0
EPOR -0.01 0.14 -10000 0 -0.6 4 4
STAT5A (dimer) -0.061 0.21 -10000 0 -0.56 35 35
SOCS1 0.022 0.027 -10000 0 -0.38 1 1
cell migration 0.05 0.16 0.42 35 -10000 0 35
SOS1 0.024 0.002 -10000 0 -10000 0 0
EPO 0.015 0.027 0.31 1 -10000 0 1
VAV1 0.013 0.057 -10000 0 -0.29 8 8
GRB10 -0.047 0.15 -10000 0 -0.39 35 35
PTPN11 0.025 0.007 -10000 0 -10000 0 0
SCF/KIT -0.044 0.16 -10000 0 -0.42 35 35
GO:0007205 0.002 0.008 -10000 0 -10000 0 0
MAP2K1 -0.019 0.095 0.22 2 -0.23 28 30
CBL 0.024 0.003 -10000 0 -10000 0 0
KIT -0.14 0.43 -10000 0 -1.1 35 35
MAP2K2 -0.02 0.096 0.22 2 -0.25 12 14
SHC/Grb2/SOS1 -0.011 0.16 -10000 0 -0.39 32 32
STAT5A -0.062 0.22 -10000 0 -0.58 35 35
GRB2 0.024 0.004 -10000 0 -10000 0 0
response to radiation -0.044 0.14 -10000 0 -0.38 34 34
SHC/GRAP2 0.028 0.035 -10000 0 -0.2 5 5
PTPRO -0.064 0.16 -10000 0 -0.43 35 35
SH2B2 -0.045 0.15 -10000 0 -0.4 34 34
DOK1 0.024 0.002 -10000 0 -10000 0 0
MATK -0.051 0.16 -10000 0 -0.42 35 35
CREBBP 0.016 0.052 -10000 0 -0.17 2 2
BCL2 -0.13 0.32 -10000 0 -1.1 17 17
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.022 0.021 -10000 0 -0.29 1 1
LAT2 -0.071 0.12 -10000 0 -0.27 54 54
AP1 -0.086 0.2 -10000 0 -0.46 38 38
mol:PIP3 -0.088 0.16 0.21 5 -0.37 39 44
IKBKB -0.054 0.12 0.18 13 -0.25 38 51
AKT1 -0.059 0.09 0.25 6 -0.28 1 7
IKBKG -0.066 0.11 0.18 5 -0.24 48 53
MS4A2 -0.051 0.13 -10000 0 -0.29 53 53
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.023 0.002 -10000 0 -10000 0 0
MAP3K1 -0.084 0.14 0.2 4 -0.35 38 42
mol:Ca2+ -0.067 0.13 0.19 5 -0.29 38 43
LYN 0.02 0.009 -10000 0 -10000 0 0
CBLB -0.07 0.12 -10000 0 -0.28 43 43
SHC1 0.023 0.004 -10000 0 -10000 0 0
RasGAP/p62DOK 0.044 0.01 -10000 0 -10000 0 0
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.024 0.002 -10000 0 -10000 0 0
PLD2 -0.055 0.1 0.26 7 -0.24 29 36
PTPN13 -0.089 0.16 -10000 0 -0.53 9 9
PTPN11 0.013 0.021 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.064 0.097 0.2 1 -0.32 4 5
SYK 0.023 0.005 -10000 0 -10000 0 0
GRB2 0.023 0.004 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.078 0.17 -10000 0 -0.38 39 39
LAT -0.071 0.12 -10000 0 -0.26 54 54
PAK2 -0.09 0.16 0.21 4 -0.39 38 42
NFATC2 -0.026 0.093 -10000 0 -0.48 8 8
HRAS -0.093 0.17 0.22 4 -0.42 38 42
GAB2 0.024 0.004 -10000 0 -10000 0 0
PLA2G1B 0.02 0.091 -10000 0 -0.92 2 2
Fc epsilon R1 -0.06 0.13 -10000 0 -0.24 65 65
Antigen/IgE/Fc epsilon R1 -0.051 0.12 -10000 0 -0.22 61 61
mol:GDP -0.1 0.19 0.22 2 -0.45 41 43
JUN 0.023 0.004 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.023 0.005 -10000 0 -10000 0 0
FOS 0.023 0.005 -10000 0 -10000 0 0
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.071 0.13 -10000 0 -0.27 56 56
CHUK -0.066 0.11 0.18 5 -0.25 43 48
KLRG1 -0.063 0.11 -10000 0 -0.27 33 33
VAV1 -0.077 0.13 -10000 0 -0.28 55 55
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.07 0.12 -10000 0 -0.26 53 53
negative regulation of mast cell degranulation -0.052 0.11 0.16 2 -0.26 30 32
BTK -0.11 0.22 -10000 0 -0.51 39 39
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.098 0.17 -10000 0 -0.41 42 42
GAB2/PI3K/SHP2 -0.072 0.077 -10000 0 -0.23 18 18
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.069 0.12 -10000 0 -0.32 32 32
RAF1 0.024 0.097 -10000 0 -0.98 2 2
Fc epsilon R1/FcgammaRIIB/SHIP -0.049 0.15 -10000 0 -0.3 42 42
FCER1G 0.026 0.023 -10000 0 -0.29 1 1
FCER1A -0.071 0.14 -10000 0 -0.3 66 66
Antigen/IgE/Fc epsilon R1/Fyn -0.041 0.12 -10000 0 -0.26 29 29
MAPK3 0.021 0.089 -10000 0 -0.9 2 2
MAPK1 0.017 0.097 -10000 0 -0.96 2 2
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.088 0.23 -10000 0 -0.59 34 34
DUSP1 0.023 0.004 -10000 0 -10000 0 0
NF-kappa-B/RelA -0.033 0.073 0.11 1 -0.17 23 24
actin cytoskeleton reorganization -0.082 0.16 -10000 0 -0.55 7 7
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.074 0.16 0.27 2 -0.35 38 40
FER -0.063 0.12 -10000 0 -0.29 40 40
RELA 0.023 0.004 -10000 0 -10000 0 0
ITK -0.032 0.084 -10000 0 -0.33 14 14
SOS1 0.024 0.002 -10000 0 -10000 0 0
PLCG1 -0.058 0.19 0.22 8 -0.42 32 40
cytokine secretion -0.028 0.05 -10000 0 -0.15 1 1
SPHK1 -0.095 0.13 -10000 0 -0.3 45 45
PTK2 -0.085 0.17 -10000 0 -0.62 6 6
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.077 0.18 0.18 5 -0.39 39 44
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.084 0.16 0.2 6 -0.37 39 45
MAP2K2 0.017 0.09 -10000 0 -0.92 2 2
MAP2K1 0.015 0.09 -10000 0 -0.92 2 2
MAP2K7 0.024 0.003 -10000 0 -10000 0 0
KLRG1/SHP2 -0.047 0.1 0.18 1 -0.24 29 30
MAP2K4 -0.13 0.35 -10000 0 -0.88 40 40
Fc epsilon R1/FcgammaRIIB -0.06 0.15 -10000 0 -0.32 42 42
mol:Choline -0.054 0.1 0.26 7 -0.24 29 36
SHC/Grb2/SOS1 -0.047 0.14 -10000 0 -0.31 31 31
FYN 0.024 0.004 -10000 0 -10000 0 0
DOK1 0.024 0.002 -10000 0 -10000 0 0
PXN -0.081 0.16 -10000 0 -0.56 6 6
HCLS1 -0.072 0.13 -10000 0 -0.27 53 53
PRKCB -0.091 0.15 0.18 5 -0.33 51 56
FCGR2B -0.015 0.1 -10000 0 -0.29 28 28
IGHE -0.002 0.004 -10000 0 -10000 0 0
KLRG1/SHIP -0.053 0.11 0.17 2 -0.27 30 32
LCP2 0.023 0.004 -10000 0 -10000 0 0
PLA2G4A -0.081 0.14 -10000 0 -0.29 59 59
RASA1 0.023 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.054 0.1 0.26 7 -0.24 29 36
IKK complex -0.039 0.098 0.19 12 -0.2 25 37
WIPF1 0.024 0 -10000 0 -10000 0 0
p75(NTR)-mediated 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
Sortilin/TRAF6 0.034 0.007 -10000 0 -10000 0 0
Necdin/E2F1 0.021 0.046 0.23 4 -0.2 5 9
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.008 0.1 -10000 0 -0.26 7 7
NGF (dimer)/p75(NTR)/BEX1 -0.08 0.14 -10000 0 -0.21 113 113
NT-4/5 (dimer)/p75(NTR) -0.05 0.12 -10000 0 -0.22 74 74
IKBKB 0.022 0.021 0.31 1 -10000 0 1
AKT1 -0.054 0.067 -10000 0 -0.27 6 6
IKBKG 0.024 0.002 -10000 0 -10000 0 0
BDNF 0.01 0.075 -10000 0 -0.38 8 8
MGDIs/NGR/p75(NTR)/LINGO1 -0.032 0.12 -10000 0 -0.19 72 72
FURIN 0.023 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.025 0.11 -10000 0 -0.25 9 9
LINGO1 -0.001 0.097 -10000 0 -0.38 14 14
Sortilin/TRAF6/NRIF 0.027 0.019 -10000 0 -10000 0 0
proBDNF (dimer) 0.01 0.074 -10000 0 -0.38 8 8
NTRK1 0.016 0.039 -10000 0 -0.38 2 2
RTN4R 0.022 0.027 -10000 0 -0.38 1 1
neuron apoptosis -0.053 0.12 0.29 2 -0.36 11 13
IRAK1 0.024 0.002 -10000 0 -10000 0 0
SHC1 -0.046 0.09 -10000 0 -0.18 67 67
ARHGDIA 0.024 0.004 -10000 0 -10000 0 0
RhoA/GTP 0.018 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.063 0.024 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.011 0.1 -10000 0 -0.28 6 6
MAGEH1 0.023 0.021 -10000 0 -0.29 1 1
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.015 0.11 -10000 0 -0.28 9 9
Mammalian IAPs/DIABLO 0.058 0.025 -10000 0 -0.21 1 1
proNGF (dimer) 0.006 0.069 -10000 0 -0.29 12 12
MAGED1 0.024 0.003 -10000 0 -10000 0 0
APP 0.023 0.004 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.016 0.084 -10000 0 -0.38 11 11
ZNF274 0.021 0.029 -10000 0 -0.29 2 2
RhoA/GDP/RHOGDI -0.024 0.086 -10000 0 -0.26 6 6
NGF 0.006 0.069 -10000 0 -0.29 12 12
cell cycle arrest -0.027 0.075 0.26 1 -0.23 6 7
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.037 0.098 0.16 1 -0.28 11 12
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.031 0.11 -10000 0 -0.19 74 74
NCSTN 0.023 0.004 -10000 0 -10000 0 0
mol:GTP -0.034 0.12 -10000 0 -0.2 74 74
PSENEN 0.023 0.004 -10000 0 -10000 0 0
mol:ceramide -0.04 0.081 -10000 0 -0.28 6 6
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.034 0.092 0.14 1 -0.29 12 13
p75(NTR)/beta APP -0.034 0.1 -10000 0 -0.2 69 69
BEX1 -0.079 0.14 -10000 0 -0.29 70 70
mol:GDP -0.059 0.081 -10000 0 -0.17 70 70
NGF (dimer) -0.21 0.056 -10000 0 -0.22 222 222
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.018 0.11 -10000 0 -0.27 15 15
PIK3R1 0.023 0.005 -10000 0 -10000 0 0
RAC1/GTP -0.018 0.086 -10000 0 -0.15 62 62
MYD88 0.024 0.002 -10000 0 -10000 0 0
CHUK 0.023 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.034 0.12 -10000 0 -0.2 74 74
RHOB 0.024 0.002 -10000 0 -10000 0 0
RHOA 0.024 0.004 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.026 0.032 0.23 4 -10000 0 4
NT3 (dimer) 0.015 0.049 -10000 0 -0.31 5 5
TP53 -0.043 0.075 0.29 3 -0.29 3 6
PRDM4 -0.042 0.082 -10000 0 -0.28 6 6
BDNF (dimer) -0.36 0.1 0.2 1 -0.37 227 228
PIK3CA 0.024 0.002 -10000 0 -10000 0 0
SORT1 0.023 0.004 -10000 0 -10000 0 0
activation of caspase activity -0.011 0.098 -10000 0 -0.26 7 7
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.011 0.1 -10000 0 -0.28 6 6
RHOC 0.023 0.004 -10000 0 -10000 0 0
XIAP 0.024 0 -10000 0 -10000 0 0
MAPK10 -0.078 0.15 0.37 2 -0.35 34 36
DIABLO 0.024 0.002 -10000 0 -10000 0 0
SMPD2 -0.04 0.081 -10000 0 -0.28 6 6
APH1B 0.023 0.004 -10000 0 -10000 0 0
APH1A 0.023 0.004 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.024 0.11 -10000 0 -0.18 69 69
PSEN1 0.023 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.034 0.009 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.038 0.11 -10000 0 -0.2 71 71
MAPK8 -0.05 0.12 0.37 2 -0.29 13 15
MAPK9 -0.049 0.12 0.37 2 -0.29 12 14
APAF1 0.024 0.003 -10000 0 -10000 0 0
NTF3 0.016 0.049 -10000 0 -0.31 5 5
NTF4 -0.016 0.084 -10000 0 -0.38 11 11
NDN 0.015 0.05 -10000 0 -0.29 6 6
RAC1/GDP 0.016 0.006 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.011 0.11 -10000 0 -0.27 13 13
p75 CTF/Sortilin/TRAF6/NRIF 0.057 0.021 -10000 0 -10000 0 0
RhoA-B-C/GTP -0.034 0.12 -10000 0 -0.19 74 74
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.005 0.1 -10000 0 -0.3 3 3
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.012 0.1 -10000 0 -0.24 8 8
PRKACB 0.004 0.074 -10000 0 -0.29 14 14
proBDNF (dimer)/p75 ECD 0.025 0.056 -10000 0 -0.27 8 8
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.02 0.034 -10000 0 -0.34 2 2
BIRC2 0.023 0.004 -10000 0 -10000 0 0
neuron projection morphogenesis -0.042 0.1 -10000 0 -0.26 16 16
BAD -0.07 0.14 0.37 2 -0.31 30 32
RIPK2 0.022 0.039 0.31 2 -0.38 1 3
NGFR -0.069 0.14 -10000 0 -0.29 69 69
CYCS -0.049 0.066 -10000 0 -0.27 6 6
ADAM17 0.024 0.002 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.01 0.1 0.23 1 -0.27 6 7
BCL2L11 -0.07 0.14 0.37 2 -0.31 30 32
BDNF (dimer)/p75(NTR) -0.044 0.12 -10000 0 -0.21 75 75
PI3K -0.012 0.1 -10000 0 -0.28 6 6
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.011 0.1 -10000 0 -0.28 6 6
NDNL2 0.023 0.005 -10000 0 -10000 0 0
YWHAE 0.02 0.009 -10000 0 -10000 0 0
PRKCI 0.024 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.044 0.12 -10000 0 -0.21 74 74
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.009 0.1 -10000 0 -0.28 6 6
TRAF6 0.024 0.003 -10000 0 -10000 0 0
RAC1 0.021 0.008 -10000 0 -10000 0 0
PRKCZ 0.023 0.005 -10000 0 -10000 0 0
PLG -0.013 0.028 -10000 0 -0.38 1 1
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.053 0.1 0.15 2 -0.32 8 10
SQSTM1 0.024 0.004 -10000 0 -10000 0 0
NGFRAP1 0.023 0.02 -10000 0 -0.29 1 1
CASP3 -0.069 0.13 0.36 2 -0.3 31 33
E2F1 0.021 0.041 0.31 4 -10000 0 4
CASP9 0.023 0.006 -10000 0 -10000 0 0
IKK complex -0.012 0.1 0.19 1 -0.32 7 8
NGF (dimer)/TRKA 0.018 0.058 -10000 0 -0.21 14 14
MMP7 -0.37 0.086 0.31 2 -0.39 225 227
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.004 0.1 -10000 0 -0.27 7 7
MMP3 -0.31 0.16 -10000 0 -0.39 190 190
APAF-1/Caspase 9 -0.048 0.057 -10000 0 -0.27 1 1
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.02 0.15 0.23 29 -0.22 63 92
SMAD6-7/SMURF1 0.037 0.021 -10000 0 -10000 0 0
NOG 0.015 0.031 -10000 0 -0.38 1 1
SMAD9 -0.043 0.16 -10000 0 -0.54 20 20
SMAD4 0.018 0.01 -10000 0 -10000 0 0
SMAD5 -0.035 0.11 -10000 0 -0.35 15 15
BMP7/USAG1 -0.064 0.18 0.23 26 -0.29 79 105
SMAD5/SKI -0.035 0.12 -10000 0 -0.4 10 10
SMAD1 0.01 0.046 -10000 0 -0.34 2 2
BMP2 0.009 0.057 -10000 0 -0.29 8 8
SMAD1/SMAD1/SMAD4 0.022 0.043 -10000 0 -0.3 1 1
BMPR1A 0.023 0.005 -10000 0 -10000 0 0
BMPR1B -0.006 0.097 -10000 0 -0.34 18 18
BMPR1A-1B/BAMBI -0.008 0.11 0.22 1 -0.22 48 49
AHSG -0.005 0.079 -10000 0 -0.38 9 9
CER1 -0.02 0.087 -10000 0 -0.38 12 12
BMP2-4/CER1 -0.005 0.095 -10000 0 -0.22 35 35
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.048 0.12 -10000 0 -0.32 23 23
BMP2-4 (homodimer) -0.003 0.091 -10000 0 -0.25 26 26
RGMB 0.023 0.005 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.037 0.068 -10000 0 -0.21 9 9
RGMA -0.071 0.14 -10000 0 -0.29 70 70
SMURF1 0.023 0.006 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.046 0.12 -10000 0 -0.27 33 33
BMP2-4/USAG1 -0.025 0.1 -10000 0 -0.2 54 54
SMAD6/SMURF1/SMAD5 -0.036 0.12 -10000 0 -0.34 17 17
SOSTDC1 -0.038 0.12 -10000 0 -0.29 43 43
BMP7/BMPR2/BMPR1A-1B -0.016 0.15 0.23 34 -0.22 66 100
SKI 0.023 0.005 -10000 0 -10000 0 0
BMP6 (homodimer) 0.021 0.029 -10000 0 -0.29 2 2
HFE2 -0.006 0.018 -10000 0 -10000 0 0
ZFYVE16 0.023 0.004 -10000 0 -10000 0 0
MAP3K7 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/CHRD 0.007 0.088 -10000 0 -0.22 27 27
SMAD5/SMAD5/SMAD4 -0.03 0.11 -10000 0 -0.33 16 16
MAPK1 0.023 0.004 -10000 0 -10000 0 0
TAK1/TAB family -0.036 0.11 -10000 0 -0.28 20 20
BMP7 (homodimer) -0.046 0.24 0.31 40 -0.37 67 107
NUP214 0.024 0.002 -10000 0 -10000 0 0
BMP6/FETUA 0.019 0.062 -10000 0 -0.26 11 11
SMAD1/SKI 0.017 0.054 -10000 0 -0.33 2 2
SMAD6 0.023 0.005 -10000 0 -10000 0 0
CTDSP2 0.024 0.002 -10000 0 -10000 0 0
BMP2-4/FETUA -0.001 0.093 -10000 0 -0.22 33 33
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.005 0.099 -10000 0 -0.34 18 18
BMPR2 (homodimer) 0.024 0 -10000 0 -10000 0 0
GADD34/PP1CA 0.045 0.013 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0.012 0.073 -10000 0 -0.23 18 18
CHRDL1 -0.14 0.16 -10000 0 -0.29 117 117
ENDOFIN/SMAD1 0.017 0.055 -10000 0 -0.4 1 1
SMAD6-7/SMURF1/SMAD1 0.032 0.054 -10000 0 -0.34 1 1
SMAD6/SMURF1 0.023 0.006 -10000 0 -10000 0 0
BAMBI -0.028 0.14 0.31 1 -0.38 30 31
SMURF2 0.022 0.027 -10000 0 -0.38 1 1
BMP2-4/CHRDL1 -0.079 0.12 -10000 0 -0.19 107 107
BMP2-4/GREM1 -0.009 0.099 -10000 0 -0.21 42 42
SMAD7 0.019 0.01 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.037 0.16 -10000 0 -0.46 26 26
SMAD1/SMAD6 0.017 0.055 -10000 0 -0.33 2 2
TAK1/SMAD6 0.033 0.009 -10000 0 -10000 0 0
BMP7 -0.046 0.24 0.31 40 -0.37 67 107
BMP6 0.021 0.029 -10000 0 -0.29 2 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.054 0.13 -10000 0 -0.34 29 29
PPM1A 0.023 0.005 -10000 0 -10000 0 0
SMAD1/SMURF2 0.016 0.056 -10000 0 -0.32 2 2
SMAD7/SMURF1 0.027 0.015 -10000 0 -10000 0 0
CTDSPL 0.024 0.002 -10000 0 -10000 0 0
PPP1CA 0.023 0.004 -10000 0 -10000 0 0
XIAP 0.024 0 -10000 0 -10000 0 0
CTDSP1 0.024 0 -10000 0 -10000 0 0
PPP1R15A 0.024 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.06 0.14 -10000 0 -0.34 36 36
CHRD 0.019 0.041 -10000 0 -0.29 4 4
BMPR2 0.024 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.057 0.12 -10000 0 -0.29 34 34
BMP4 -0.015 0.12 -10000 0 -0.38 22 22
FST 0.004 0.078 -10000 0 -0.3 14 14
BMP2-4/NOG 0.008 0.084 -10000 0 -0.22 26 26
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.013 0.14 0.23 29 -0.21 61 90
IL1-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
UBC13/UEV1A 0.02 0.016 -10000 0 -10000 0 0
PRKCZ 0.023 0.005 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.023 0.004 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.003 0.046 -10000 0 -10000 0 0
IRAK/TOLLIP 0.016 0.013 -10000 0 -10000 0 0
IKBKB 0.022 0.021 0.31 1 -10000 0 1
IKBKG 0.024 0.002 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.13 0.15 -10000 0 -0.26 133 133
IL1A -0.15 0.2 -10000 0 -0.38 97 97
IL1B -0.042 0.11 -10000 0 -0.27 44 44
IRAK/TRAF6/p62/Atypical PKCs 0.094 0.061 -10000 0 -10000 0 0
IL1R2 -0.033 0.12 -10000 0 -0.29 42 42
IL1R1 0.02 0.035 -10000 0 -0.29 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.028 0.059 0.22 2 -10000 0 2
TOLLIP 0.024 0.003 -10000 0 -10000 0 0
TICAM2 0.018 0.03 -10000 0 -0.29 2 2
MAP3K3 0.024 0.004 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.016 0.002 -10000 0 -10000 0 0
IKK complex/ELKS 0.067 0.082 0.27 6 -10000 0 6
JUN 0.046 0.083 0.16 82 -10000 0 82
MAP3K7 0.024 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.011 0.1 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.054 0.13 -10000 0 -0.21 97 97
PIK3R1 0.023 0.005 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.045 0.13 -10000 0 -0.2 97 97
IL1 beta fragment/IL1R1/IL1RAP -0.01 0.098 -10000 0 -0.21 43 43
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 0.054 0.089 0.17 87 -10000 0 87
IRAK1 0 0.011 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.047 0.14 -10000 0 -0.27 63 63
IRAK4 0.024 0.002 -10000 0 -10000 0 0
PRKCI 0.024 0 -10000 0 -10000 0 0
TRAF6 0.024 0.003 -10000 0 -10000 0 0
PI3K 0.034 0.008 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0 0.049 -10000 0 -10000 0 0
CHUK 0.023 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.01 0.098 -10000 0 -0.21 43 43
IL1 beta/IL1R2 -0.053 0.11 -10000 0 -0.23 44 44
IRAK/TRAF6/TAK1/TAB1/TAB2 0.02 0.017 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.002 0.09 -10000 0 -10000 0 0
IRAK3 0.021 0.029 -10000 0 -0.29 2 2
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.008 0.1 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.022 0.059 -10000 0 -0.26 1 1
IL1 alpha/IL1R1/IL1RAP -0.07 0.14 -10000 0 -0.23 99 99
RELA 0.023 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.024 0.004 -10000 0 -10000 0 0
MYD88 0.024 0.002 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.088 0.067 -10000 0 -10000 0 0
IL1RAP 0.024 0 -10000 0 -10000 0 0
UBE2N 0.024 0.002 -10000 0 -10000 0 0
IRAK/TRAF6 -0.013 0.073 -10000 0 -10000 0 0
CASP1 0.024 0.004 -10000 0 -10000 0 0
IL1RN/IL1R2 -0.085 0.14 -10000 0 -0.25 99 99
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.003 0.099 -10000 0 -0.2 42 42
TMEM189-UBE2V1 0.002 0.016 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.024 0.074 -10000 0 -0.26 1 1
PIK3CA 0.024 0.002 -10000 0 -10000 0 0
IL1RN -0.082 0.18 -10000 0 -0.38 60 60
TRAF6/TAK1/TAB1/TAB2 0.027 0.022 -10000 0 -10000 0 0
MAP2K6 0.059 0.092 0.18 87 -10000 0 87
Endothelins

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
AKT1 -0.047 0.16 0.22 1 -0.34 35 36
PTK2B 0.019 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.011 0.19 -10000 0 -0.76 11 11
EDN1 0.001 0.12 -10000 0 -0.24 22 22
EDN3 -0.082 0.14 -10000 0 -0.29 72 72
EDN2 -0.029 0.12 -10000 0 -0.29 39 39
HRAS/GDP -0.011 0.11 0.2 1 -0.33 10 11
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.006 0.083 -10000 0 -0.24 6 6
ADCY4 -0.052 0.13 0.18 3 -0.34 25 28
ADCY5 -0.082 0.15 0.19 1 -0.32 51 52
ADCY6 -0.052 0.13 0.18 3 -0.34 25 28
ADCY7 -0.051 0.13 0.18 3 -0.34 25 28
ADCY1 -0.051 0.13 0.24 3 -0.34 27 30
ADCY2 -0.066 0.14 0.18 3 -0.34 35 38
ADCY3 -0.051 0.13 0.18 3 -0.32 26 29
ADCY8 -0.05 0.12 0.18 2 -0.3 26 28
ADCY9 -0.051 0.13 0.18 3 -0.33 26 29
arachidonic acid secretion -0.027 0.12 -10000 0 -0.38 11 11
ETB receptor/Endothelin-1/Gq/GTP 0.004 0.056 -10000 0 -0.22 5 5
GNAO1 -0.12 0.16 -10000 0 -0.29 103 103
HRAS 0.024 0.003 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.031 0.19 0.27 2 -0.32 30 32
ETA receptor/Endothelin-1/Gs/GTP 0.011 0.18 0.26 1 -0.3 37 38
mol:GTP 0.001 0.003 -10000 0 -10000 0 0
COL3A1 -0.061 0.19 0.22 1 -0.45 34 35
EDNRB 0.007 0.05 -10000 0 -0.29 5 5
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.05 0.16 -10000 0 -0.4 28 28
CYSLTR1 -0.069 0.2 0.22 1 -0.41 47 48
SLC9A1 -0.017 0.099 0.14 1 -0.23 26 27
mol:GDP -0.02 0.11 0.2 1 -0.35 10 11
SLC9A3 -0.19 0.29 -10000 0 -0.59 55 55
RAF1 -0.022 0.093 -10000 0 -0.33 3 3
JUN 0.004 0.12 -10000 0 -0.5 5 5
JAK2 -0.045 0.16 0.22 1 -0.34 34 35
mol:IP3 0.008 0.077 -10000 0 -0.25 4 4
ETA receptor/Endothelin-1 0.01 0.24 0.3 2 -0.4 35 37
PLCB1 0.02 0.03 0.32 1 -0.29 1 2
PLCB2 0.023 0.006 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.07 0.14 -10000 0 -0.24 79 79
FOS -0.017 0.11 -10000 0 -0.85 2 2
Gai/GDP -0.26 0.34 -10000 0 -0.63 103 103
CRK 0.02 0.009 -10000 0 -10000 0 0
mol:Ca ++ -0.02 0.13 0.2 2 -0.34 18 20
BCAR1 0.024 0.002 -10000 0 -10000 0 0
PRKCB1 0.011 0.077 0.19 1 -0.24 4 5
GNAQ 0.024 0.009 -10000 0 -10000 0 0
GNAZ 0.018 0.041 -10000 0 -0.29 4 4
GNAL 0.006 0.063 -10000 0 -0.29 10 10
Gs family/GDP -0.022 0.11 -10000 0 -0.35 8 8
ETA receptor/Endothelin-1/Gq/GTP -0.002 0.092 -10000 0 -0.26 5 5
MAPK14 0.006 0.057 0.21 1 -0.27 2 3
TRPC6 -0.014 0.2 -10000 0 -0.82 11 11
GNAI2 0.024 0.004 -10000 0 -10000 0 0
GNAI3 0.023 0.004 -10000 0 -10000 0 0
GNAI1 0.018 0.041 -10000 0 -0.29 4 4
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.009 0.058 -10000 0 -0.28 2 2
ETB receptor/Endothelin-2 -0.007 0.078 -10000 0 -0.2 30 30
ETB receptor/Endothelin-3 -0.052 0.1 -10000 0 -0.2 67 67
ETB receptor/Endothelin-1 0.009 0.098 -10000 0 -0.28 9 9
MAPK3 -0.016 0.1 -10000 0 -0.59 2 2
MAPK1 -0.02 0.1 -10000 0 -0.59 2 2
Rac1/GDP -0.013 0.1 -10000 0 -0.33 10 10
cAMP biosynthetic process -0.094 0.14 0.19 3 -0.32 46 49
MAPK8 0.002 0.14 -10000 0 -0.54 7 7
SRC 0.016 0.012 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.062 0.11 -10000 0 -0.29 29 29
p130Cas/CRK/Src/PYK2 -0.022 0.14 0.24 4 -0.41 12 16
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.013 0.1 -10000 0 -0.33 10 10
COL1A2 -0.025 0.17 -10000 0 -0.39 28 28
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.041 0.15 -10000 0 -0.26 57 57
mol:DAG 0.008 0.077 -10000 0 -0.25 4 4
MAP2K2 -0.021 0.095 -10000 0 -0.41 3 3
MAP2K1 -0.02 0.094 -10000 0 -0.41 3 3
EDNRA -0.026 0.17 -10000 0 -0.36 31 31
positive regulation of muscle contraction -0.018 0.15 0.24 16 -0.34 22 38
Gq family/GDP -0.013 0.11 -10000 0 -0.37 6 6
HRAS/GTP -0.022 0.096 0.18 1 -0.31 7 8
PRKCH 0.008 0.077 0.18 2 -0.25 2 4
RAC1 0.021 0.008 -10000 0 -10000 0 0
PRKCA 0.013 0.078 0.19 4 -0.25 1 5
PRKCB -0.013 0.1 0.19 3 -0.3 10 13
PRKCE 0.01 0.079 0.18 3 -0.25 1 4
PRKCD 0.01 0.079 0.18 3 -0.25 1 4
PRKCG -0.065 0.12 0.21 4 -0.32 15 19
regulation of vascular smooth muscle contraction -0.021 0.12 -10000 0 -0.98 2 2
PRKCQ 0.007 0.081 0.18 3 -0.25 1 4
PLA2G4A -0.03 0.13 -10000 0 -0.41 11 11
GNA14 0.022 0.023 -10000 0 -0.29 1 1
GNA15 -0.001 0.098 -10000 0 -0.38 14 14
GNA12 0.021 0.008 -10000 0 -10000 0 0
GNA11 0.023 0.009 -10000 0 -10000 0 0
Rac1/GTP 0.031 0.19 0.27 2 -0.32 30 32
MMP1 -0.17 0.15 0.3 1 -0.3 107 108
Visual signal transduction: Cones

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Cone Metarhodopsin II/Cone Transducin 0.038 0.02 -10000 0 -10000 0 0
RGS9BP 0.021 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 -0.009 0.035 0.31 1 -0.38 1 2
mol:Na + -0.065 0.11 -10000 0 -0.19 95 95
mol:ADP -0.011 0.027 0.26 1 -0.28 1 2
GNAT2 0.02 0.012 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.005 0.083 -10000 0 -0.16 41 41
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.025 0.006 -10000 0 -10000 0 0
GRK7 0.011 0.019 -10000 0 -10000 0 0
CNGB3 -0.028 0.1 0.31 1 -0.38 16 17
Cone Metarhodopsin II/X-Arrestin 0.011 0.019 -10000 0 -0.27 1 1
mol:Ca2+ -0.07 0.11 0.18 17 -0.18 103 120
Cone PDE6 0.016 0.082 -10000 0 -0.2 1 1
Cone Metarhodopsin II 0.019 0.021 0.2 1 -0.21 1 2
Na + (4 Units) -0.063 0.11 -10000 0 -0.18 103 103
GNAT2/GDP 0.015 0.075 -10000 0 -10000 0 0
GNB5 0.023 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.014 0.019 0.18 1 -0.21 1 2
Cone Transducin 0.041 0.022 -10000 0 -10000 0 0
SLC24A2 -0.009 0.092 0.31 1 -0.38 12 13
GNB3/GNGT2 0.032 0.023 -10000 0 -0.2 2 2
GNB3 0.023 0.004 -10000 0 -10000 0 0
GNAT2/GTP 0.017 0.004 -10000 0 -10000 0 0
CNGA3 -0.11 0.15 -10000 0 -0.29 97 97
ARR3 -0.011 0.029 -10000 0 -0.38 1 1
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel -0.065 0.11 -10000 0 -0.19 95 95
mol:Pi 0.005 0.082 -10000 0 -0.16 41 41
Cone CNG Channel -0.046 0.1 -10000 0 -0.26 17 17
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + -0.009 0.092 0.31 1 -0.38 12 13
RGS9 -0.038 0.12 -10000 0 -0.29 45 45
PDE6C -0.007 0.031 -10000 0 -0.38 1 1
GNGT2 0.021 0.029 -10000 0 -0.29 2 2
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H -0.014 0.011 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.001 0.072 -10000 0 -0.22 23 23
EPHB2 0.021 0.027 -10000 0 -0.38 1 1
Syndecan-2/TACI -0.031 0.078 -10000 0 -0.16 62 62
LAMA1 -0.022 0.1 -10000 0 -0.29 31 31
Syndecan-2/alpha2 ITGB1 0.03 0.055 -10000 0 -0.24 7 7
HRAS 0.024 0.003 -10000 0 -10000 0 0
Syndecan-2/CASK 0.007 0.003 -10000 0 -10000 0 0
ITGA5 0.024 0.002 -10000 0 -10000 0 0
BAX 0.004 0.002 -10000 0 -10000 0 0
EPB41 0.023 0.006 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.02 0.008 -10000 0 -10000 0 0
LAMA3 0.016 0.043 -10000 0 -0.35 3 3
EZR 0.024 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.021 0.027 -10000 0 -0.38 1 1
Syndecan-2/MMP2 0.019 0.029 -10000 0 -0.22 3 3
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.025 0.053 -10000 0 -0.27 7 7
dendrite morphogenesis 0.02 0.019 -10000 0 -0.22 1 1
Syndecan-2/GM-CSF -0.063 0.12 -10000 0 -0.22 82 82
determination of left/right symmetry 0.01 0.004 -10000 0 -10000 0 0
Syndecan-2/PKC delta 0.022 0.009 -10000 0 -10000 0 0
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
MAPK3 -0.05 0.12 0.19 19 -0.2 82 101
MAPK1 -0.049 0.12 0.19 19 -0.2 82 101
Syndecan-2/RACK1 0.032 0.014 -10000 0 -10000 0 0
NF1 0.023 0.004 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.01 0.004 -10000 0 -10000 0 0
ITGA2 0.011 0.07 -10000 0 -0.38 7 7
MAPK8 0.008 0.003 -10000 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin 0.01 0.069 -10000 0 -0.19 7 7
Syndecan-2/Kininogen -0.019 0.074 -10000 0 -0.16 50 50
ITGB1 0.024 0.002 -10000 0 -10000 0 0
SRC 0.017 0.039 0.18 12 -10000 0 12
Syndecan-2/CASK/Protein 4.1 0.02 0.009 -10000 0 -10000 0 0
extracellular matrix organization 0.022 0.009 -10000 0 -10000 0 0
actin cytoskeleton reorganization -0.001 0.072 -10000 0 -0.22 23 23
Syndecan-2/Caveolin-2/Ras 0.032 0.022 -10000 0 -0.2 1 1
Syndecan-2/Laminin alpha3 0.017 0.025 -10000 0 -0.22 2 2
Syndecan-2/RasGAP 0.041 0.019 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.035 0.005 -10000 0 -10000 0 0
PRKCD 0.023 0.004 -10000 0 -10000 0 0
Syndecan-2 dimer 0.02 0.019 -10000 0 -0.22 1 1
GO:0007205 0.002 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.019 0.017 -10000 0 -10000 0 0
RHOA 0.024 0.004 -10000 0 -10000 0 0
SDCBP 0.021 0.008 -10000 0 -10000 0 0
TNFRSF13B -0.08 0.14 -10000 0 -0.29 71 71
RASA1 0.023 0.005 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.025 0.053 -10000 0 -0.27 7 7
Syndecan-2/Synbindin 0.022 0.009 -10000 0 -10000 0 0
TGFB1 0.024 0.003 -10000 0 -10000 0 0
CASP3 0.029 0.053 0.19 22 -10000 0 22
FN1 -0.018 0.12 -10000 0 -0.37 25 25
Syndecan-2/IL8 -0.098 0.13 -10000 0 -0.22 119 119
SDC2 0.01 0.004 -10000 0 -10000 0 0
KNG1 -0.06 0.13 -10000 0 -0.29 54 54
Syndecan-2/Neurofibromin 0.022 0.009 -10000 0 -10000 0 0
TRAPPC4 0.024 0.003 -10000 0 -10000 0 0
CSF2 -0.14 0.2 -10000 0 -0.39 91 91
Syndecan-2/TGFB1 0.022 0.009 -10000 0 -10000 0 0
Syndecan-2/Syntenin/PI-4-5-P2 0.02 0.008 -10000 0 -10000 0 0
Syndecan-2/Ezrin 0.034 0.014 -10000 0 -10000 0 0
PRKACA 0.032 0.056 0.19 25 -10000 0 25
angiogenesis -0.098 0.13 -10000 0 -0.22 119 119
MMP2 0.018 0.046 -10000 0 -0.38 3 3
IL8 -0.22 0.2 -10000 0 -0.39 135 135
calcineurin-NFAT signaling pathway -0.031 0.078 -10000 0 -0.16 62 62
Wnt 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
Noncanonical Wnts/FZD -0.036 0.096 -10000 0 -0.24 32 32
FZD6 0.021 0.008 -10000 0 -10000 0 0
WNT6 -0.017 0.1 -10000 0 -0.31 25 25
WNT4 0.01 0.065 -10000 0 -0.31 9 9
FZD3 0.015 0.051 0.31 1 -0.38 3 4
WNT5A 0.004 0.087 -10000 0 -0.38 11 11
WNT11 -0.058 0.16 -10000 0 -0.38 47 47
Visual signal transduction: Rods

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
mol:K + 0.023 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0.011 0.002 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.02 0.017 -10000 0 -0.22 1 1
PDE6G/GNAT1/GTP 0.017 0.037 -10000 0 -0.17 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 -0.017 0.002 -10000 0 -10000 0 0
GRK1 -0.009 0.035 0.31 1 -0.38 1 2
CNG Channel -0.11 0.11 -10000 0 -0.27 47 47
mol:Na + -0.035 0.11 -10000 0 -0.32 15 15
mol:ADP -0.009 0.035 0.31 1 -0.38 1 2
RGS9-1/Gbeta5/R9AP 0.005 0.083 -10000 0 -0.16 41 41
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.03 0.12 -10000 0 -0.33 15 15
CNGB1 -0.058 0.12 -10000 0 -0.29 48 48
RDH5 0.008 0.069 -10000 0 -0.29 12 12
SAG -0.008 0.017 -10000 0 -10000 0 0
mol:Ca2+ -0.067 0.094 0.32 2 -0.32 15 17
Na + (4 Units) -0.037 0.1 -10000 0 -0.31 15 15
RGS9 -0.038 0.12 -10000 0 -0.29 45 45
GNB1/GNGT1 0.01 0.089 0.23 5 -0.27 19 24
GNAT1/GDP 0.011 0.075 -10000 0 -10000 0 0
GUCY2D -0.007 0.082 -10000 0 -0.38 10 10
GNGT1 -0.02 0.12 0.31 5 -0.38 19 24
GUCY2F -0.014 0.01 -10000 0 -10000 0 0
GNB5 0.023 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.087 0.09 -10000 0 -0.27 15 15
mol:11-cis-retinal 0.008 0.069 -10000 0 -0.29 12 12
mol:cGMP 0.003 0.087 -10000 0 -0.23 25 25
GNB1 0.023 0.005 -10000 0 -10000 0 0
Rhodopsin 0.016 0.055 -10000 0 -0.21 13 13
SLC24A1 0.023 0.004 -10000 0 -10000 0 0
CNGA1 0.01 0.063 -10000 0 -0.29 10 10
Metarhodopsin II 0.015 0.025 0.19 1 -0.2 2 3
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.011 0.094 -10000 0 -0.24 26 26
RGS9BP 0.021 0.01 -10000 0 -10000 0 0
Metarhodopsin II/Transducin 0.001 0.041 0.14 5 -0.21 2 7
GCAP Family/Ca ++ 0.017 0.07 -10000 0 -0.21 20 20
PDE6A/B -0.11 0.12 -10000 0 -0.2 138 138
mol:Pi 0.005 0.082 -10000 0 -0.16 41 41
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.018 0.072 0.2 5 -0.21 19 24
PDE6B 0.011 0.06 -10000 0 -0.29 9 9
PDE6A -0.16 0.15 -10000 0 -0.29 136 136
PDE6G 0.011 0.06 -10000 0 -0.29 9 9
RHO -0.015 0.027 -10000 0 -0.38 1 1
PDE6 -0.09 0.12 -10000 0 -0.29 35 35
GUCA1A -0.017 0.11 -10000 0 -0.38 19 19
GC2/GCAP Family 0.025 0.074 -10000 0 -0.22 20 20
GUCA1C -0.017 0.002 -10000 0 -10000 0 0
GUCA1B 0.024 0.033 0.31 1 -0.38 1 2
amb2 Integrin 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
alphaM/beta2 Integrin/proMMP-2 0.027 0.065 -10000 0 -0.2 12 12
alphaM/beta2 Integrin/GPIbA 0.021 0.059 -10000 0 -0.18 11 11
alphaM/beta2 Integrin/proMMP-9 0.004 0.12 0.22 22 -0.23 35 57
PLAUR 0.022 0.027 -10000 0 -0.38 1 1
HMGB1 0.015 0.019 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.03 0.055 -10000 0 -0.18 10 10
AGER 0.018 0.034 -10000 0 -0.42 1 1
RAP1A 0.023 0.004 -10000 0 -10000 0 0
SELPLG 0.024 0.002 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.032 0.068 -10000 0 -0.28 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.01 0.17 0.31 22 -0.38 31 53
CYR61 0.022 0.027 -10000 0 -0.38 1 1
TLN1 0.023 0.004 -10000 0 -10000 0 0
Rap1/GTP -0.024 0.085 -10000 0 -0.26 9 9
RHOA 0.024 0.004 -10000 0 -10000 0 0
P-selectin oligomer -0.032 0.12 -10000 0 -0.29 41 41
MYH2 -0.044 0.09 -10000 0 -0.27 16 16
MST1R 0.024 0.004 -10000 0 -10000 0 0
leukocyte activation during inflammatory response -0.011 0.092 -10000 0 -0.21 18 18
APOB -0.055 0.13 -10000 0 -0.31 48 48
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.018 0.046 -10000 0 -0.38 3 3
JAM3 0.024 0.003 -10000 0 -10000 0 0
GP1BA 0.014 0.04 -10000 0 -0.32 3 3
alphaM/beta2 Integrin/CTGF 0.024 0.067 -10000 0 -0.2 15 15
alphaM/beta2 Integrin -0.039 0.087 -10000 0 -0.23 23 23
JAM3 homodimer 0.024 0.003 -10000 0 -10000 0 0
ICAM2 0.024 0.004 -10000 0 -10000 0 0
ICAM1 0.015 0.059 -10000 0 -0.38 5 5
phagocytosis triggered by activation of immune response cell surface activating receptor -0.038 0.088 -10000 0 -0.24 20 20
cell adhesion 0.021 0.058 -10000 0 -0.18 11 11
NFKB1 0.031 0.1 -10000 0 -0.28 7 7
THY1 0.02 0.038 -10000 0 -0.38 2 2
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
Lipoprotein(a) -0.018 0.087 -10000 0 -0.18 50 50
alphaM/beta2 Integrin/LRP/tPA 0.041 0.052 -10000 0 -0.23 2 2
IL6 0.001 0.13 -10000 0 -0.36 17 17
ITGB2 0.015 0.043 -10000 0 -0.32 3 3
elevation of cytosolic calcium ion concentration -0.018 0.12 -10000 0 -0.22 56 56
alphaM/beta2 Integrin/JAM2/JAM3 -0.001 0.1 -10000 0 -0.25 11 11
JAM2 -0.051 0.13 -10000 0 -0.29 55 55
alphaM/beta2 Integrin/ICAM1 -0.005 0.12 -10000 0 -0.2 52 52
alphaM/beta2 Integrin/uPA/Plg -0.023 0.12 -10000 0 -0.22 56 56
RhoA/GTP -0.046 0.097 0.15 1 -0.27 19 20
positive regulation of phagocytosis -0.02 0.068 0.18 1 -0.26 5 6
Ron/MSP -0.028 0.12 -10000 0 -0.27 48 48
alphaM/beta2 Integrin/uPAR/uPA -0.017 0.12 -10000 0 -0.22 56 56
alphaM/beta2 Integrin/uPAR 0.03 0.057 -10000 0 -0.18 11 11
PLAU -0.073 0.17 -10000 0 -0.38 55 55
PLAT 0.021 0.008 -10000 0 -10000 0 0
actin filament polymerization -0.042 0.089 0.24 1 -0.26 16 17
MST1 -0.061 0.16 -10000 0 -0.38 48 48
alphaM/beta2 Integrin/lipoprotein(a) -0.006 0.095 -10000 0 -0.22 18 18
TNF 0.025 0.1 -10000 0 -0.27 7 7
RAP1B 0.024 0.002 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.031 0.12 -10000 0 -0.23 63 63
fibrinolysis -0.024 0.12 -10000 0 -0.22 56 56
HCK 0.015 0.012 -10000 0 -10000 0 0
dendritic cell antigen processing and presentation -0.038 0.088 -10000 0 -0.24 20 20
VTN 0.005 0.075 -10000 0 -0.38 8 8
alphaM/beta2 Integrin/CYR61 0.03 0.057 -10000 0 -0.19 10 10
LPA 0 0.048 -10000 0 -0.38 3 3
LRP1 0.024 0.002 -10000 0 -10000 0 0
cell migration -0.001 0.11 0.2 22 -0.23 31 53
FN1 -0.018 0.12 -10000 0 -0.37 25 25
alphaM/beta2 Integrin/Thy1 0.029 0.06 -10000 0 -0.19 12 12
MPO 0.004 0.083 -10000 0 -0.38 10 10
KNG1 -0.06 0.13 -10000 0 -0.29 54 54
RAP1/GDP 0.032 0.005 -10000 0 -10000 0 0
ROCK1 -0.044 0.091 -10000 0 -0.26 17 17
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.013 0.028 -10000 0 -0.38 1 1
CTGF 0.015 0.059 -10000 0 -0.38 5 5
alphaM/beta2 Integrin/Hck 0.02 0.042 -10000 0 -0.18 4 4
ITGAM 0.009 0.059 -10000 0 -0.28 8 8
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.011 0.094 -10000 0 -0.26 8 8
HP -0.011 0.11 0.31 1 -0.38 17 18
leukocyte adhesion -0.011 0.091 -10000 0 -0.27 9 9
SELP -0.032 0.12 -10000 0 -0.29 41 41
TCGA08_p53

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
CDKN2A -0.072 0.12 -10000 0 -0.27 65 65
TP53 -0.025 0.068 -10000 0 -0.26 15 15
Senescence -0.025 0.068 -10000 0 -0.26 15 15
Apoptosis -0.025 0.068 -10000 0 -0.26 15 15
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.031 0.061 0.23 2 -10000 0 2
MDM4 0.023 0.004 -10000 0 -10000 0 0
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.015 0.072 -10000 0 -0.27 1 1
NF kappa B1 p50/RelA/I kappa B alpha -0.008 0.074 -10000 0 -0.25 2 2
AP1 -0.025 0.07 -10000 0 -0.22 8 8
mol:PIP3 -0.022 0.06 -10000 0 -0.24 4 4
AKT1 0.007 0.062 0.2 2 -0.24 4 6
PTK2B -0.047 0.098 -10000 0 -0.3 16 16
RHOA 0.006 0.054 -10000 0 -0.32 4 4
PIK3CB 0.024 0 -10000 0 -10000 0 0
mol:Ca2+ -0.003 0.043 -10000 0 -10000 0 0
MAGI3 0.024 0.004 -10000 0 -10000 0 0
RELA 0.023 0.004 -10000 0 -10000 0 0
apoptosis -0.025 0.081 -10000 0 -0.18 47 47
HRAS/GDP 0.018 0.002 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.069 0.11 0.21 2 -0.3 27 29
NF kappa B1 p50/RelA -0.029 0.067 -10000 0 -0.27 4 4
endothelial cell migration -0.011 0.07 -10000 0 -0.33 3 3
ADCY4 -0.087 0.15 -10000 0 -0.37 43 43
ADCY5 -0.16 0.21 -10000 0 -0.4 82 82
ADCY6 -0.083 0.15 -10000 0 -0.39 38 38
ADCY7 -0.082 0.15 -10000 0 -0.39 37 37
ADCY1 -0.083 0.14 -10000 0 -0.37 39 39
ADCY2 -0.12 0.19 -10000 0 -0.4 64 64
ADCY3 -0.081 0.15 -10000 0 -0.38 37 37
ADCY8 -0.076 0.14 -10000 0 -0.37 35 35
ADCY9 -0.081 0.15 -10000 0 -0.38 37 37
GSK3B -0.047 0.094 -10000 0 -0.31 13 13
arachidonic acid secretion -0.099 0.16 -10000 0 -0.4 40 40
GNG2 0.019 0.035 -10000 0 -0.29 3 3
TRIP6 0.012 0.01 -10000 0 -10000 0 0
GNAO1 -0.033 0.1 -10000 0 -0.28 35 35
HRAS 0.024 0.003 -10000 0 -10000 0 0
NFKBIA -0.021 0.069 -10000 0 -0.25 4 4
GAB1 0.023 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.055 0.27 -10000 0 -0.83 25 25
JUN 0.023 0.004 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.032 0.012 -10000 0 -10000 0 0
TIAM1 -0.078 0.31 -10000 0 -0.97 25 25
PIK3R1 0.023 0.005 -10000 0 -10000 0 0
mol:IP3 -0.012 0.038 -10000 0 -10000 0 0
PLCB3 0.012 0.009 -10000 0 -10000 0 0
FOS 0.023 0.005 -10000 0 -10000 0 0
positive regulation of mitosis -0.099 0.16 -10000 0 -0.4 40 40
LPA/LPA1-2-3 0.001 0.088 -10000 0 -0.16 42 42
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.024 0.002 -10000 0 -10000 0 0
stress fiber formation -0.028 0.082 -10000 0 -0.24 15 15
GNAZ -0.01 0.064 -10000 0 -0.16 34 34
EGFR/PI3K-beta/Gab1 -0.01 0.067 -10000 0 -0.25 4 4
positive regulation of dendritic cell cytokine production 0 0.087 -10000 0 -0.16 42 42
LPA/LPA2/MAGI-3 0.032 0.012 -10000 0 -10000 0 0
ARHGEF1 0.012 0.076 0.18 23 -10000 0 23
GNAI2 -0.007 0.06 -10000 0 -0.16 32 32
GNAI3 -0.011 0.063 -10000 0 -0.16 36 36
GNAI1 -0.012 0.068 -10000 0 -0.17 35 35
LPA/LPA3 -0.002 0.064 -10000 0 -0.22 18 18
LPA/LPA2 0.018 0.011 -10000 0 -10000 0 0
LPA/LPA1 -0.009 0.076 -10000 0 -0.19 36 36
HB-EGF/EGFR -0.004 0.1 0.2 19 -0.23 31 50
HBEGF -0.012 0.13 0.26 21 -0.27 35 56
mol:DAG -0.012 0.038 -10000 0 -10000 0 0
cAMP biosynthetic process -0.11 0.16 0.32 1 -0.38 42 43
NFKB1 0.023 0.003 -10000 0 -10000 0 0
SRC 0.016 0.012 -10000 0 -10000 0 0
GNB1 0.023 0.005 -10000 0 -10000 0 0
LYN -0.007 0.072 -10000 0 -0.24 2 2
GNAQ -0.001 0.048 -10000 0 -0.16 18 18
LPAR2 0.024 0.002 -10000 0 -10000 0 0
LPAR3 -0.01 0.091 -10000 0 -0.32 18 18
LPAR1 -0.02 0.11 -10000 0 -0.28 33 33
IL8 -0.081 0.13 0.22 1 -0.34 9 10
PTK2 -0.021 0.065 -10000 0 -0.23 8 8
Rac1/GDP 0.016 0.006 -10000 0 -10000 0 0
CASP3 -0.025 0.082 -10000 0 -0.18 47 47
EGFR 0.021 0.008 -10000 0 -10000 0 0
PLCG1 -0.009 0.046 -10000 0 -0.17 14 14
PLD2 -0.021 0.065 -10000 0 -0.23 8 8
G12/G13 0.019 0.065 -10000 0 -10000 0 0
PI3K-beta -0.001 0.056 -10000 0 -0.26 4 4
cell migration -0.01 0.092 -10000 0 -0.24 25 25
SLC9A3R2 0.024 0.003 -10000 0 -10000 0 0
PXN -0.029 0.083 -10000 0 -0.25 15 15
HRAS/GTP -0.1 0.16 -10000 0 -0.41 40 40
RAC1 0.021 0.008 -10000 0 -10000 0 0
MMP9 -0.01 0.17 0.31 22 -0.38 31 53
PRKCE 0.024 0.002 -10000 0 -10000 0 0
PRKCD -0.006 0.041 -10000 0 -10000 0 0
Gi(beta/gamma) -0.079 0.14 -10000 0 -0.35 40 40
mol:LPA 0.001 0.013 -10000 0 -0.11 3 3
TRIP6/p130 Cas/FAK1/Paxillin -0.008 0.075 -10000 0 -0.27 5 5
MAPKKK cascade -0.099 0.16 -10000 0 -0.4 40 40
contractile ring contraction involved in cytokinesis 0.008 0.056 0.22 1 -0.32 4 5
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.001 0.048 -10000 0 -0.16 18 18
GNA15 -0.01 0.06 -10000 0 -0.16 31 31
GNA12 0.021 0.008 -10000 0 -10000 0 0
GNA13 0.024 0.004 -10000 0 -10000 0 0
MAPT -0.071 0.11 0.23 1 -0.3 27 28
GNA11 -0.001 0.048 -10000 0 -0.16 18 18
Rac1/GTP -0.059 0.29 -10000 0 -0.88 25 25
MMP2 -0.011 0.07 -10000 0 -0.33 3 3
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.002 0.099 0.26 28 -0.2 1 29
KIRREL 0.017 0.022 -10000 0 -10000 0 0
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.001 0.099 0.21 1 -0.26 28 29
PLCG1 0.015 0.012 -10000 0 -10000 0 0
ARRB2 0.02 0.009 -10000 0 -10000 0 0
WASL 0.023 0.005 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.024 0.086 0.2 1 -0.2 26 27
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.009 0.041 0.15 1 -0.18 4 5
FYN -0.012 0.076 0.21 11 -0.17 29 40
mol:Ca2+ 0.011 0.073 -10000 0 -0.2 19 19
mol:DAG 0.012 0.073 -10000 0 -0.2 19 19
NPHS2 -0.009 0.05 -10000 0 -0.38 3 3
mol:IP3 0.012 0.073 -10000 0 -0.2 19 19
regulation of endocytosis 0.014 0.069 0.18 1 -0.16 24 25
Nephrin/NEPH1/podocin/Cholesterol 0.011 0.08 0.18 1 -0.19 29 30
establishment of cell polarity -0.002 0.099 0.2 1 -0.26 28 29
Nephrin/NEPH1/podocin/NCK1-2 0.036 0.084 -10000 0 -0.19 13 13
Nephrin/NEPH1/beta Arrestin2 0.015 0.07 0.19 1 -0.16 24 25
NPHS1 -0.023 0.13 0.28 1 -0.38 26 27
Nephrin/NEPH1/podocin 0.015 0.071 0.19 1 -0.17 29 30
TJP1 0.023 0.005 -10000 0 -10000 0 0
NCK1 0.024 0.002 -10000 0 -10000 0 0
NCK2 0.024 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.012 0.074 -10000 0 -0.2 19 19
CD2AP 0.024 0.002 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.023 0.086 0.2 1 -0.2 28 29
GRB2 0.024 0.004 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.016 0.079 0.21 10 -0.18 27 37
cytoskeleton organization -0.004 0.049 0.18 2 -0.25 1 3
Nephrin/NEPH1 0.004 0.069 0.17 1 -0.18 28 29
Nephrin/NEPH1/ZO-1 0.014 0.084 0.2 1 -0.21 27 28
Effects of Botulinum toxin

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
STX1A 0 0.047 0.26 1 -0.27 6 7
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.024 0.049 -10000 0 -0.27 6 6
STXBP1 0.02 0.038 -10000 0 -0.38 2 2
ACh/CHRNA1 -0.027 0.068 0.1 2 -0.17 21 23
RAB3GAP2/RIMS1/UNC13B 0.037 0.045 -10000 0 -0.23 6 6
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 -0.002 0.07 -10000 0 -0.38 7 7
mol:ACh -0.037 0.063 0.088 16 -0.1 93 109
RAB3GAP2 0.023 0.004 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.04 0.092 -10000 0 -0.2 16 16
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.027 0.068 0.1 2 -0.17 21 23
UNC13B 0.024 0.004 -10000 0 -10000 0 0
CHRNA1 0.004 0.076 -10000 0 -0.29 14 14
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.035 0.081 0.1 2 -0.17 39 41
SNAP25 -0.075 0.1 0.18 1 -0.21 85 86
VAMP2 0.003 0.002 -10000 0 -10000 0 0
SYT1 -0.013 0.1 -10000 0 -0.29 27 27
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.013 0.047 0.2 1 -0.22 8 9
STX1A/SNAP25 fragment 1/VAMP2 -0.04 0.092 -10000 0 -0.2 16 16
Glypican 2 network

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
MDK 0.017 0.053 -10000 0 -0.38 4 4
GPC2 0.001 0.1 0.31 2 -0.38 14 16
GPC2/Midkine 0.012 0.084 0.23 2 -0.27 18 20
neuron projection morphogenesis 0.012 0.084 0.23 2 -0.27 18 20
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.013 0.033 -9999 0 -0.2 1 1
NFATC2 -0.014 0.038 -9999 0 -0.2 5 5
NFATC3 -0.014 0.034 -9999 0 -10000 0 0
CD40LG -0.049 0.19 -9999 0 -0.41 29 29
PTGS2 -0.047 0.19 -9999 0 -0.41 30 30
JUNB 0.024 0.002 -9999 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.005 0.026 -9999 0 -10000 0 0
CaM/Ca2+ -0.005 0.026 -9999 0 -10000 0 0
CALM1 0.007 0.024 -9999 0 -10000 0 0
JUN 0.007 0.024 -9999 0 -10000 0 0
mol:Ca2+ -0.008 0.011 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.006 0.012 -9999 0 -10000 0 0
FOSL1 -0.22 0.2 -9999 0 -0.39 138 138
CREM 0.024 0.002 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.039 0.11 -9999 0 -0.32 10 10
FOS 0.007 0.024 -9999 0 -10000 0 0
IFNG -0.062 0.2 -9999 0 -0.43 32 32
AP-1/NFAT1-c-4 -0.05 0.19 -9999 0 -0.42 27 27
FASLG -0.043 0.18 -9999 0 -0.39 28 28
NFAT1-c-4/ICER1 -0.027 0.065 -9999 0 -0.24 2 2
IL2RA -0.044 0.18 -9999 0 -0.39 27 27
FKBP12/FK506 0.015 0.007 -9999 0 -10000 0 0
CSF2 -0.1 0.23 -9999 0 -0.41 60 60
JunB/Fra1/NFAT1-c-4 -0.08 0.14 -9999 0 -0.27 57 57
IL4 -0.047 0.18 -9999 0 -0.38 27 27
IL2 -0.013 0.13 -9999 0 -0.8 6 6
IL3 0 0.079 -9999 0 -0.66 3 3
FKBP1A 0.02 0.009 -9999 0 -10000 0 0
BATF3 0.015 0.059 -9999 0 -0.38 5 5
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.023 0.004 -9999 0 -10000 0 0
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.005 0.002 -10000 0 -10000 0 0
GNB1/GNG2 0.006 0.078 -10000 0 -0.16 39 39
regulation of S phase of mitotic cell cycle -0.007 0.057 -10000 0 -0.17 23 23
GNAO1 -0.12 0.16 -10000 0 -0.29 103 103
HRAS 0.024 0.003 -10000 0 -10000 0 0
SHBG/T-DHT 0.009 0.035 -10000 0 -0.29 3 3
PELP1 0.02 0.009 -10000 0 -10000 0 0
AKT1 0.006 0.001 -10000 0 -10000 0 0
MAP2K1 0.034 0.094 0.17 62 -10000 0 62
T-DHT/AR -0.021 0.081 -10000 0 -0.2 41 41
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -0.01 2 2
GNAI2 0.024 0.004 -10000 0 -10000 0 0
GNAI3 0.023 0.004 -10000 0 -10000 0 0
GNAI1 0.018 0.041 -10000 0 -0.29 4 4
mol:GDP -0.04 0.095 -10000 0 -0.25 35 35
cell proliferation 0.027 0.099 0.24 4 -0.29 1 5
PIK3CA 0.024 0.002 -10000 0 -10000 0 0
FOS 0.027 0.094 0.25 1 -0.66 2 3
mol:Ca2+ -0.02 0.03 -10000 0 -0.073 43 43
MAPK3 0.03 0.094 0.2 13 -10000 0 13
MAPK1 0.017 0.086 0.21 1 -0.36 7 8
PIK3R1 0.023 0.005 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.006 2 2
cAMP biosynthetic process 0.004 0.038 0.1 1 -0.24 3 4
GNG2 0.019 0.036 -10000 0 -0.29 3 3
potassium channel inhibitor activity 0 0.001 -10000 0 -0.006 2 2
HRAS/GTP 0.01 0.053 -10000 0 -0.18 1 1
actin cytoskeleton reorganization 0.029 0.016 -10000 0 -10000 0 0
SRC 0.016 0.012 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.006 2 2
PI3K 0.031 0.007 -10000 0 -10000 0 0
apoptosis -0.032 0.083 0.3 3 -0.27 1 4
T-DHT/AR/PELP1 -0.006 0.072 -10000 0 -0.16 41 41
HRAS/GDP -0.029 0.095 -10000 0 -0.28 23 23
CREB1 0.031 0.085 0.28 1 -0.31 3 4
RAC1-CDC42/GTP 0.037 0.02 -10000 0 -10000 0 0
AR -0.036 0.12 -10000 0 -0.29 41 41
GNB1 0.023 0.005 -10000 0 -10000 0 0
RAF1 0.045 0.094 0.18 62 -10000 0 62
RAC1-CDC42/GDP -0.001 0.11 -10000 0 -0.27 23 23
T-DHT/AR/PELP1/Src 0.007 0.057 -10000 0 -0.15 22 22
MAP2K2 0.034 0.094 0.17 61 -10000 0 61
T-DHT/AR/PELP1/Src/PI3K -0.007 0.057 -10000 0 -0.17 23 23
GNAZ 0.018 0.041 -10000 0 -0.29 4 4
SHBG 0.01 0.058 -10000 0 -0.48 3 3
Gi family/GNB1/GNG2/GDP -0.12 0.19 -10000 0 -0.39 53 53
mol:T-DHT 0 0 -10000 0 -0.005 2 2
RAC1 0.021 0.008 -10000 0 -10000 0 0
GNRH1 0.005 0.003 -10000 0 -10000 0 0
Gi family/GTP -0.075 0.11 -10000 0 -0.28 43 43
CDC42 0.023 0.006 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.031 0.063 -10000 0 -0.27 2 2
ER alpha/Gai/GDP/Gbeta gamma -0.14 0.24 -10000 0 -0.56 40 40
AKT1 -0.061 0.26 -10000 0 -0.81 24 24
PIK3CA 0.024 0.002 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.061 0.26 -10000 0 -0.83 24 24
mol:Ca2+ 0.017 0.067 0.17 24 -0.27 2 26
IGF1R 0.023 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.016 0.054 -10000 0 -0.16 19 19
SHC1 0.023 0.004 -10000 0 -10000 0 0
apoptosis 0.057 0.25 0.77 24 -10000 0 24
RhoA/GTP 0.01 0.042 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.052 0.2 -10000 0 -0.48 28 28
regulation of stress fiber formation 0.017 0.036 -10000 0 -0.14 5 5
E2/ERA-ERB (dimer) 0.012 0.059 -10000 0 -0.17 22 22
KRAS 0.024 0.003 -10000 0 -10000 0 0
G13/GTP 0.015 0.048 -10000 0 -0.14 19 19
pseudopodium formation -0.017 0.036 0.14 5 -10000 0 5
E2/ER alpha (dimer)/PELP1 0.012 0.052 -10000 0 -0.15 20 20
GRB2 0.024 0.004 -10000 0 -10000 0 0
GNG2 0.019 0.036 -10000 0 -0.29 3 3
GNAO1 -0.12 0.16 -10000 0 -0.29 103 103
HRAS 0.024 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.083 0.21 0.22 1 -0.63 25 26
E2/ER beta (dimer) 0.014 0.024 -10000 0 -0.19 3 3
mol:GDP -0.011 0.087 -10000 0 -0.27 21 21
mol:NADP -0.083 0.21 0.22 1 -0.63 25 26
PIK3R1 0.023 0.005 -10000 0 -10000 0 0
mol:IP3 -0.001 0.042 0.16 1 -0.28 2 3
IGF-1R heterotetramer 0.023 0.004 -10000 0 -10000 0 0
PLCB1 0.002 0.044 0.17 1 -0.29 2 3
PLCB2 0.004 0.042 -10000 0 -0.29 2 2
IGF1 -0.042 0.13 -10000 0 -0.29 48 48
mol:L-citrulline -0.083 0.21 0.22 1 -0.63 25 26
RHOA 0.024 0.004 -10000 0 -10000 0 0
Gai/GDP -0.26 0.34 -10000 0 -0.63 104 104
JNK cascade 0.014 0.024 -10000 0 -0.19 3 3
BCAR1 0.024 0.002 -10000 0 -10000 0 0
ESR2 0.019 0.036 -10000 0 -0.29 3 3
GNAQ 0.024 0.002 -10000 0 -10000 0 0
ESR1 -0.004 0.088 -10000 0 -0.29 20 20
Gq family/GDP/Gbeta gamma 0.008 0.077 -10000 0 -0.45 3 3
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.005 0.1 -10000 0 -0.6 3 3
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.048 0.2 -10000 0 -0.48 28 28
GNAZ 0.018 0.041 -10000 0 -0.29 4 4
E2/ER alpha (dimer) -0.001 0.059 -10000 0 -0.19 20 20
STRN 0.024 0.002 -10000 0 -10000 0 0
GNAL 0.006 0.063 -10000 0 -0.29 10 10
PELP1 0.02 0.009 -10000 0 -10000 0 0
MAPK11 0.009 0.02 -10000 0 -0.16 3 3
GNAI2 0.024 0.004 -10000 0 -10000 0 0
GNAI3 0.023 0.004 -10000 0 -10000 0 0
GNAI1 0.018 0.041 -10000 0 -0.29 4 4
HBEGF -0.04 0.24 0.3 41 -0.46 34 75
cAMP biosynthetic process 0.003 0.058 -10000 0 -0.16 21 21
SRC -0.076 0.23 0.2 33 -0.57 28 61
PI3K 0.034 0.008 -10000 0 -10000 0 0
GNB1 0.023 0.005 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.014 0.089 -10000 0 -0.25 19 19
SOS1 0.024 0.002 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.085 0.16 -10000 0 -0.44 27 27
Gs family/GTP 0.008 0.061 -10000 0 -0.16 21 21
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.044 0.01 -10000 0 -10000 0 0
vasodilation -0.078 0.2 0.22 1 -0.59 25 26
mol:DAG -0.001 0.042 0.16 1 -0.28 2 3
Gs family/GDP/Gbeta gamma -0.009 0.086 -10000 0 -0.28 16 16
MSN -0.018 0.038 0.15 5 -10000 0 5
Gq family/GTP 0.011 0.041 -10000 0 -0.29 1 1
mol:PI-3-4-5-P3 -0.057 0.25 -10000 0 -0.79 24 24
NRAS 0.024 0.004 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.078 0.2 0.59 25 -0.22 1 26
GRB2/SOS1 0.035 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.001 0.089 -10000 0 -0.27 19 19
NOS3 -0.089 0.23 0.23 1 -0.67 25 26
GNA11 0.024 0.002 -10000 0 -10000 0 0
MAPKKK cascade -0.041 0.21 0.24 1 -0.61 23 24
E2/ER alpha (dimer)/PELP1/Src -0.052 0.21 0.23 4 -0.5 28 32
ruffle organization -0.017 0.036 0.14 5 -10000 0 5
ROCK2 -0.017 0.041 -10000 0 -10000 0 0
GNA14 0.023 0.021 -10000 0 -0.29 1 1
GNA15 -0.001 0.097 -10000 0 -0.38 14 14
GNA13 0.024 0.004 -10000 0 -10000 0 0
MMP9 -0.049 0.25 0.35 38 -0.49 32 70
MMP2 -0.072 0.22 0.2 36 -0.54 28 64
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.006 0.12 -9999 0 -0.43 10 10
MAP3K8 0.024 0.003 -9999 0 -10000 0 0
FOS -0.02 0.12 -9999 0 -0.48 8 8
PRKCA 0.024 0.004 -9999 0 -10000 0 0
PTPN7 0.006 0.083 -9999 0 -0.36 11 11
HRAS 0.024 0.003 -9999 0 -10000 0 0
PRKCB -0.051 0.13 -9999 0 -0.29 56 56
NRAS 0.024 0.004 -9999 0 -10000 0 0
RAS family/GTP 0.045 0.01 -9999 0 -10000 0 0
MAPK3 -0.001 0.074 -9999 0 -0.48 2 2
MAP2K1 -0.056 0.15 -9999 0 -0.31 55 55
ELK1 0.024 0.005 -9999 0 -10000 0 0
BRAF -0.05 0.13 -9999 0 -0.3 50 50
mol:GTP 0 0 -9999 0 -0.003 2 2
MAPK1 -0.017 0.13 -9999 0 -0.61 8 8
RAF1 -0.056 0.14 -9999 0 -0.31 53 53
KRAS 0.024 0.003 -9999 0 -10000 0 0
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.006 0.001 -10000 0 -10000 0 0
ADCY5 -0.075 0.078 -10000 0 -0.16 102 102
ADCY6 -0.006 0.001 -10000 0 -10000 0 0
ADCY7 -0.006 0.001 -10000 0 -10000 0 0
ADCY1 -0.01 0.037 0.21 1 -0.22 6 7
ADCY2 -0.039 0.064 -10000 0 -0.16 49 49
ADCY3 -0.006 0 -10000 0 -10000 0 0
ADCY8 -0.009 0.004 -10000 0 -10000 0 0
PRKCE 0.006 0 -10000 0 -10000 0 0
ADCY9 -0.007 0.01 -10000 0 -0.16 1 1
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.014 0.072 0.18 14 -10000 0 14
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 0.033 0.074 -10000 0 -0.28 4 4
MAP4K1 -0.009 0.095 -10000 0 -0.29 24 24
MAP3K8 0.024 0.003 -10000 0 -10000 0 0
PRKCB -0.052 0.13 -10000 0 -0.29 56 56
DBNL 0.021 0.008 -10000 0 -10000 0 0
CRKL 0.023 0.004 -10000 0 -10000 0 0
MAP3K1 -0.004 0.077 -10000 0 -0.27 10 10
JUN -0.12 0.26 -10000 0 -0.55 59 59
MAP3K7 -0.002 0.074 -10000 0 -0.27 9 9
GRAP2 0.016 0.046 -10000 0 -0.29 5 5
CRK 0.02 0.009 -10000 0 -10000 0 0
MAP2K4 -0.01 0.086 0.17 1 -0.3 10 11
LAT 0.024 0.002 -10000 0 -10000 0 0
LCP2 0.023 0.004 -10000 0 -10000 0 0
MAPK8 -0.12 0.27 -10000 0 -0.58 59 59
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.001 0.084 -10000 0 -0.28 11 11
LAT/GRAP2/SLP76/HPK1/HIP-55 0.039 0.067 -10000 0 -0.27 2 2
Ephrin B reverse signaling

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
EFNB2 0.02 0.009 -10000 0 -10000 0 0
EPHB2 0.021 0.027 -10000 0 -0.38 1 1
EFNB1 0.006 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.015 0.11 -10000 0 -0.22 26 26
Ephrin B2/EPHB1-2 -0.003 0.087 -10000 0 -0.2 36 36
neuron projection morphogenesis -0.023 0.096 -10000 0 -0.21 26 26
Ephrin B1/EPHB1-2/Tiam1 -0.022 0.11 -10000 0 -0.21 52 52
DNM1 0.024 0.003 -10000 0 -10000 0 0
cell-cell signaling 0 0.004 -10000 0 -10000 0 0
MAP2K4 -0.01 0.062 -10000 0 -0.36 6 6
YES1 -0.009 0.11 -10000 0 -0.59 7 7
Ephrin B1/EPHB1-2/NCK2 -0.008 0.1 -10000 0 -0.19 48 48
PI3K 0.022 0.081 -10000 0 -0.32 11 11
mol:GDP -0.023 0.11 -10000 0 -0.21 52 52
ITGA2B 0.005 0.075 -10000 0 -0.38 8 8
endothelial cell proliferation 0.025 0.013 -10000 0 -10000 0 0
FYN -0.01 0.11 -10000 0 -0.57 8 8
MAP3K7 -0.01 0.066 -10000 0 -0.4 6 6
FGR -0.015 0.12 -10000 0 -0.58 9 9
TIAM1 -0.001 0.083 -10000 0 -0.29 18 18
PIK3R1 0.023 0.005 -10000 0 -10000 0 0
RGS3 0.024 0.002 -10000 0 -10000 0 0
cell adhesion 0.003 0.092 -10000 0 -0.36 9 9
LYN -0.011 0.11 -10000 0 -0.56 9 9
Ephrin B1/EPHB1-2/Src Family Kinases -0.009 0.087 -10000 0 -0.49 7 7
Ephrin B1/EPHB1-2 -0.006 0.058 -10000 0 -0.5 3 3
SRC -0.006 0.093 -10000 0 -0.57 6 6
ITGB3 0.017 0.045 -10000 0 -0.29 5 5
EPHB1 -0.071 0.17 -10000 0 -0.38 55 55
EPHB4 0.023 0.006 -10000 0 -10000 0 0
RAC1 0.021 0.008 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.026 0.014 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.019 0.065 -10000 0 -0.24 13 13
BLK -0.045 0.12 -10000 0 -0.6 6 6
HCK -0.005 0.087 -10000 0 -0.58 5 5
regulation of stress fiber formation 0.009 0.1 0.19 48 -10000 0 48
MAPK8 -0.009 0.063 -10000 0 -0.35 6 6
Ephrin B1/EPHB1-2/RGS3 -0.008 0.1 -10000 0 -0.19 49 49
endothelial cell migration 0.02 0.086 0.22 26 -0.4 2 28
NCK2 0.024 0 -10000 0 -10000 0 0
PTPN13 0.003 0.078 -10000 0 -0.34 11 11
regulation of focal adhesion formation 0.009 0.1 0.19 48 -10000 0 48
chemotaxis 0.009 0.1 0.19 49 -10000 0 49
PIK3CA 0.024 0.002 -10000 0 -10000 0 0
Rac1/GTP -0.018 0.1 -10000 0 -0.21 26 26
angiogenesis -0.009 0.067 -10000 0 -0.45 5 5
LCK -0.014 0.11 -10000 0 -0.57 9 9
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 0.006 0.14 0.28 6 -0.41 15 21
FYN -0.015 0.16 0.29 2 -0.48 16 18
LAT/GRAP2/SLP76 0 0.14 0.18 3 -0.45 13 16
IKBKB 0.022 0.021 0.31 1 -10000 0 1
AKT1 -0.014 0.12 0.19 2 -0.36 16 18
B2M 0.023 0.008 -10000 0 -10000 0 0
IKBKG -0.002 0.044 0.091 14 -0.13 10 24
MAP3K8 0.024 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.02 0.034 0.088 3 -0.097 32 35
integrin-mediated signaling pathway 0.03 0.007 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.023 0.16 0.21 3 -0.47 19 22
TRPV6 -0.006 0.28 1.2 10 -10000 0 10
CD28 0.015 0.054 -10000 0 -0.29 7 7
SHC1 -0.016 0.16 0.3 6 -0.49 16 22
receptor internalization -0.025 0.18 0.17 1 -0.49 22 23
PRF1 -0.019 0.19 -10000 0 -0.82 9 9
KRAS 0.024 0.003 -10000 0 -10000 0 0
GRB2 0.024 0.004 -10000 0 -10000 0 0
COT/AKT1 -0.001 0.1 0.18 2 -0.31 14 16
LAT -0.02 0.15 0.19 3 -0.45 19 22
EntrezGene:6955 0 0.002 -10000 0 -10000 0 0
CD3D 0.015 0.055 -10000 0 -0.3 7 7
CD3E 0.014 0.055 -10000 0 -0.3 7 7
CD3G -0.001 0.084 -10000 0 -0.29 18 18
RASGRP2 -0.021 0.064 -10000 0 -0.16 37 37
RASGRP1 0.006 0.13 0.23 5 -0.38 13 18
HLA-A 0.024 0.007 -10000 0 -10000 0 0
RASSF5 0.023 0.004 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.031 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.016 0.056 0.15 9 -0.13 9 18
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.018 0.059 -10000 0 -0.21 13 13
PRKCA 0.02 0.082 0.12 48 -0.26 8 56
GRAP2 0.016 0.046 -10000 0 -0.29 5 5
mol:IP3 0.007 0.11 0.19 30 -0.38 10 40
EntrezGene:6957 0 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.018 0.14 -10000 0 -0.42 19 19
ORAI1 -0.013 0.22 -10000 0 -0.99 10 10
CSK -0.017 0.15 0.2 2 -0.46 17 19
B7 family/CD28 0 0.17 0.21 1 -0.51 15 16
CHUK 0.023 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.022 0.17 0.2 2 -0.48 21 23
PTPN6 -0.02 0.15 0.21 3 -0.49 15 18
VAV1 -0.023 0.16 0.22 4 -0.48 18 22
Monovalent TCR/CD3 -0.014 0.12 -10000 0 -0.3 24 24
CBL 0.024 0.003 -10000 0 -10000 0 0
LCK -0.018 0.16 0.26 2 -0.47 17 19
PAG1 -0.006 0.16 0.2 21 -0.46 17 38
RAP1A 0.023 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.021 0.17 0.19 2 -0.48 20 22
CD80 0.003 0.09 -10000 0 -0.38 12 12
CD86 0.021 0.029 -10000 0 -0.29 2 2
PDK1/CARD11/BCL10/MALT1 -0.013 0.074 -10000 0 -0.25 13 13
HRAS 0.024 0.003 -10000 0 -10000 0 0
GO:0035030 -0.024 0.13 0.16 2 -0.4 17 19
CD8A 0.008 0.073 -10000 0 -0.3 12 12
CD8B 0.014 0.06 -10000 0 -0.32 7 7
PTPRC 0.003 0.078 -10000 0 -0.29 15 15
PDK1/PKC theta -0.011 0.14 0.21 4 -0.44 14 18
CSK/PAG1 -0.004 0.15 0.2 21 -0.44 16 37
SOS1 0.024 0.002 -10000 0 -10000 0 0
peptide-MHC class I 0.034 0.012 -10000 0 -10000 0 0
GRAP2/SLP76 0.001 0.16 0.2 1 -0.51 14 15
STIM1 0.013 0.12 1.2 2 -10000 0 2
RAS family/GTP 0.024 0.062 0.16 8 -0.18 7 15
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.028 0.19 0.17 1 -0.52 22 23
mol:DAG -0.012 0.084 0.099 1 -0.34 10 11
RAP1A/GDP 0.01 0.027 0.073 8 -0.064 3 11
PLCG1 0.015 0.012 -10000 0 -10000 0 0
CD247 0.014 0.055 -10000 0 -0.29 7 7
cytotoxic T cell degranulation -0.017 0.18 -10000 0 -0.78 9 9
RAP1A/GTP -0.008 0.024 -10000 0 -0.062 36 36
mol:PI-3-4-5-P3 -0.016 0.14 0.19 4 -0.41 17 21
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.007 0.14 0.2 29 -0.48 10 39
NRAS 0.024 0.004 -10000 0 -10000 0 0
ZAP70 0.012 0.064 -10000 0 -0.32 8 8
GRB2/SOS1 0.035 0.006 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.007 0.13 0.21 2 -0.43 14 16
MALT1 0.019 0.01 -10000 0 -10000 0 0
TRAF6 0.024 0.003 -10000 0 -10000 0 0
CD8 heterodimer 0.017 0.074 -10000 0 -0.24 17 17
CARD11 -0.009 0.12 0.31 4 -0.36 21 25
PRKCB 0.003 0.094 0.12 40 -0.26 15 55
PRKCE 0.02 0.082 0.12 50 -0.26 8 58
PRKCQ -0.011 0.15 0.22 4 -0.48 15 19
LCP2 0.023 0.004 -10000 0 -10000 0 0
BCL10 0.023 0.004 -10000 0 -10000 0 0
regulation of survival gene product expression -0.01 0.1 0.17 3 -0.31 16 19
IKK complex 0.021 0.06 0.11 50 -0.12 7 57
RAS family/GDP -0.002 0.01 -10000 0 -10000 0 0
MAP3K14 -0.003 0.077 0.14 3 -0.25 12 15
PDPK1 -0.012 0.11 0.18 3 -0.35 15 18
TCR/CD3/MHC I/CD8/Fyn -0.021 0.17 -10000 0 -0.53 17 17
Syndecan-4-mediated signaling 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
PTK2 0.009 0.075 0.19 3 -0.29 5 8
Syndecan-4/Syndesmos 0.051 0.13 0.29 14 -0.28 1 15
positive regulation of JNK cascade 0.028 0.14 0.28 13 -0.29 3 16
Syndecan-4/ADAM12 -0.039 0.19 0.27 14 -0.35 19 33
CCL5 0.011 0.063 -10000 0 -0.3 9 9
Rac1/GDP 0.016 0.006 -10000 0 -10000 0 0
DNM2 0.024 0.002 -10000 0 -10000 0 0
ITGA5 0.024 0.002 -10000 0 -10000 0 0
SDCBP 0.021 0.008 -10000 0 -10000 0 0
PLG -0.012 0.035 -10000 0 -0.38 1 1
ADAM12 -0.28 0.18 -10000 0 -0.38 169 169
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.024 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.037 0.045 -10000 0 -0.15 1 1
Syndecan-4/Laminin alpha1 0.022 0.12 0.29 11 -0.28 1 12
Syndecan-4/CXCL12/CXCR4 0.03 0.15 0.3 13 -0.3 3 16
Syndecan-4/Laminin alpha3 0.033 0.13 0.3 12 -0.31 2 14
MDK 0.017 0.053 -10000 0 -0.38 4 4
Syndecan-4/FZD7 0.053 0.13 0.29 14 -0.28 1 15
Syndecan-4/Midkine 0.049 0.13 0.28 13 -0.31 2 15
FZD7 0.024 0 -10000 0 -10000 0 0
Syndecan-4/FGFR1/FGF 0.023 0.12 0.29 9 -10000 0 9
THBS1 0.021 0.027 -10000 0 -0.38 1 1
integrin-mediated signaling pathway 0.046 0.14 0.28 14 -0.3 7 21
positive regulation of MAPKKK cascade 0.028 0.14 0.28 13 -0.29 3 16
Syndecan-4/TACI -0.002 0.13 0.29 9 -0.31 6 15
CXCR4 0.012 0.07 -10000 0 -0.38 7 7
cell adhesion 0 0.046 0.19 3 -0.2 3 6
Syndecan-4/Dynamin 0.052 0.13 0.29 14 -0.28 1 15
Syndecan-4/TSP1 0.051 0.13 0.29 14 -0.31 2 16
Syndecan-4/GIPC 0.052 0.13 0.29 14 -0.28 1 15
Syndecan-4/RANTES 0.045 0.13 0.29 13 -0.28 1 14
ITGB1 0.024 0.002 -10000 0 -10000 0 0
LAMA1 -0.022 0.1 -10000 0 -0.29 31 31
LAMA3 0.016 0.043 -10000 0 -0.35 3 3
RAC1 0.021 0.008 -10000 0 -10000 0 0
PRKCA 0.009 0.094 0.68 4 -10000 0 4
Syndecan-4/alpha-Actinin 0.046 0.13 0.29 13 -0.28 1 14
TFPI 0.022 0.027 -10000 0 -0.38 1 1
F2 -0.091 0.18 -10000 0 -0.37 70 70
alpha5/beta1 Integrin 0.035 0.005 -10000 0 -10000 0 0
positive regulation of cell adhesion 0.014 0.12 0.29 10 -0.3 2 12
ACTN1 0.023 0.005 -10000 0 -10000 0 0
TNC 0.007 0.078 -10000 0 -0.34 11 11
Syndecan-4/CXCL12 0.037 0.14 0.3 13 -0.29 2 15
FGF6 -0.016 0.006 -10000 0 -10000 0 0
RHOA 0.024 0.004 -10000 0 -10000 0 0
CXCL12 -0.023 0.11 -10000 0 -0.29 35 35
TNFRSF13B -0.08 0.14 -10000 0 -0.29 71 71
FGF2 -0.004 0.088 -10000 0 -0.29 20 20
FGFR1 0.017 0.036 -10000 0 -0.29 3 3
Syndecan-4/PI-4-5-P2 0.009 0.1 0.28 10 -0.27 1 11
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.036 0.12 -10000 0 -0.37 25 25
cell migration -0.019 0.019 -10000 0 -10000 0 0
PRKCD 0.007 0.026 -10000 0 -10000 0 0
vasculogenesis 0.05 0.13 0.29 14 -0.3 2 16
SDC4 0.013 0.11 0.3 13 -0.29 1 14
Syndecan-4/Tenascin C 0.046 0.14 0.29 14 -0.31 7 21
Syndecan-4/PI-4-5-P2/PKC alpha -0.03 0.035 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.04 0.12 0.29 12 -0.28 1 13
MMP9 -0.01 0.17 0.33 22 -0.38 31 53
Rac1/GTP 0 0.047 0.19 3 -0.2 3 6
cytoskeleton organization 0.051 0.13 0.29 14 -0.27 1 15
GIPC1 0.024 0.002 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.052 0.13 0.29 14 -0.31 2 16
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.028 0.013 -10000 0 -10000 0 0
AES 0.029 0.01 -10000 0 -10000 0 0
FBXW11 0.023 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.033 0.01 -10000 0 -10000 0 0
SMAD4 0.018 0.01 -10000 0 -10000 0 0
DKK2 -0.032 0.14 -10000 0 -0.38 32 32
TLE1 0.028 0.01 -10000 0 -10000 0 0
MACF1 0.024 0.004 -10000 0 -10000 0 0
CTNNB1 0.038 0.076 0.23 9 -0.28 1 10
WIF1 -0.074 0.16 -10000 0 -0.38 49 49
beta catenin/RanBP3 0.062 0.1 0.28 14 -10000 0 14
KREMEN2 -0.035 0.14 -10000 0 -0.38 33 33
DKK1 -0.068 0.17 -10000 0 -0.38 50 50
beta catenin/beta TrCP1 0.047 0.072 0.23 7 -10000 0 7
FZD1 0.023 0.006 -10000 0 -10000 0 0
AXIN2 -0.066 0.13 0.58 2 -10000 0 2
AXIN1 0.024 0.003 -10000 0 -10000 0 0
RAN 0.024 0.002 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.027 0.065 -10000 0 -0.5 3 3
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.027 0.14 -10000 0 -0.38 17 17
Axin1/APC/GSK3 0.05 0.067 0.22 9 -0.27 2 11
Axin1/APC/GSK3/beta catenin/Macf1 0.024 0.072 0.24 4 -0.4 1 5
HNF1A 0.028 0.01 -10000 0 -10000 0 0
CTBP1 0.028 0.011 -10000 0 -10000 0 0
MYC 0.072 0.2 0.55 31 -10000 0 31
RANBP3 0.024 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.029 0.13 -10000 0 -0.24 60 60
NKD1 -0.19 0.21 0.32 3 -0.38 126 129
TCF4 0.022 0.015 -10000 0 -10000 0 0
TCF3 0.028 0.01 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.054 0.031 -10000 0 -0.21 2 2
Ran/GTP 0.018 0.002 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.014 0.1 0.34 2 -0.36 2 4
LEF1 -0.085 0.18 -10000 0 -0.38 64 64
DVL1 0.023 0.057 0.18 3 -0.48 1 4
CSNK2A1 0.02 0.009 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0 0.078 -10000 0 -0.48 2 2
DKK1/LRP6/Kremen 2 -0.047 0.15 -10000 0 -0.26 71 71
LRP6 0.024 0.004 -10000 0 -10000 0 0
CSNK1A1 0.029 0.013 -10000 0 -10000 0 0
NLK 0.023 0.004 -10000 0 -10000 0 0
CCND1 -0.011 0.06 0.5 1 -10000 0 1
WNT1 0.011 0.041 -10000 0 -0.38 2 2
GSK3A 0.024 0.004 -10000 0 -10000 0 0
GSK3B 0.024 0.001 -10000 0 -10000 0 0
FRAT1 0.023 0.004 -10000 0 -10000 0 0
PPP2R5D 0.11 0.1 0.22 51 -0.24 4 55
APC 0.005 0.054 0.19 15 -10000 0 15
WNT1/LRP6/FZD1 0.037 0.049 0.19 4 -10000 0 4
CREBBP 0.028 0.011 -10000 0 -10000 0 0
EGFR-dependent Endothelin 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
HRAS 0.024 0.003 -9999 0 -10000 0 0
EGFR 0.021 0.008 -9999 0 -10000 0 0
EGF/EGFR -0.02 0.098 -9999 0 -0.2 33 33
EGF/EGFR dimer/SHC/GRB2/SOS1 0.012 0.091 -9999 0 -0.2 14 14
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.01 0.11 -9999 0 -0.38 19 19
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.061 0.14 -9999 0 -0.32 56 56
EGF/EGFR dimer/SHC -0.008 0.093 -9999 0 -0.18 48 48
mol:GDP 0.008 0.088 -9999 0 -0.2 14 14
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.017 0.053 -9999 0 -0.38 4 4
GRB2/SOS1 0.035 0.006 -9999 0 -10000 0 0
HRAS/GTP -0.001 0.076 -9999 0 -10000 0 0
SHC1 0.023 0.004 -9999 0 -10000 0 0
HRAS/GDP 0.009 0.084 -9999 0 -10000 0 0
FRAP1 -0.038 0.058 -9999 0 -0.19 14 14
EGF/EGFR dimer -0.025 0.1 -9999 0 -0.22 50 50
SOS1 0.024 0.002 -9999 0 -10000 0 0
GRB2 0.024 0.004 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.004 0.091 -9999 0 -0.27 23 23
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.024 0.1 0.2 29 -0.26 2 31
PDGFB-D/PDGFRB/SLAP 0.025 0.041 -10000 0 -0.27 4 4
PDGFB-D/PDGFRB/APS/CBL 0.04 0.038 -10000 0 -0.22 4 4
AKT1 0.047 0.094 0.25 10 -10000 0 10
mol:PI-4-5-P2 0.001 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.051 0.12 0.23 45 -0.36 1 46
PIK3CA 0.024 0.002 -10000 0 -10000 0 0
FGR 0.008 0.11 0.34 2 -0.5 7 9
mol:Ca2+ 0.052 0.11 0.22 44 -0.44 1 45
MYC 0.08 0.15 0.38 25 -10000 0 25
SHC1 0.023 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.05 0.072 0.17 55 -0.19 4 59
LRP1/PDGFRB/PDGFB 0.042 0.037 -10000 0 -0.22 4 4
GRB10 0.021 0.008 -10000 0 -10000 0 0
PTPN11 0.024 0.003 -10000 0 -10000 0 0
GO:0007205 0.052 0.11 0.22 44 -0.44 1 45
PTEN 0.023 0.005 -10000 0 -10000 0 0
GRB2 0.024 0.004 -10000 0 -10000 0 0
GRB7 0.022 0.057 0.31 3 -0.38 3 6
PDGFB-D/PDGFRB/SHP2 0.03 0.04 -10000 0 -0.27 4 4
PDGFB-D/PDGFRB/GRB10 0.028 0.036 -10000 0 -0.27 3 3
cell cycle arrest 0.025 0.041 -10000 0 -0.27 4 4
HRAS 0.024 0.003 -10000 0 -10000 0 0
HIF1A 0.041 0.088 0.2 19 -10000 0 19
GAB1 0.034 0.11 0.22 27 -0.31 3 30
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.045 0.11 0.22 41 -0.27 1 42
PDGFB-D/PDGFRB 0.022 0.042 -10000 0 -0.23 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.03 0.04 -10000 0 -0.27 4 4
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.002 0.069 0.18 8 -0.24 1 9
positive regulation of MAPKKK cascade 0.03 0.04 -10000 0 -0.27 4 4
PIK3R1 0.023 0.005 -10000 0 -10000 0 0
mol:IP3 0.052 0.11 0.22 44 -0.45 1 45
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.021 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.028 0.058 0.23 3 -0.27 7 10
SHB 0.023 0.004 -10000 0 -10000 0 0
BLK -0.14 0.22 -10000 0 -0.44 79 79
PTPN2 0.021 0.01 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.03 0.04 -10000 0 -0.27 4 4
BCAR1 0.024 0.002 -10000 0 -10000 0 0
VAV2 0.042 0.12 0.24 34 -0.33 3 37
CBL 0.024 0.003 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.03 0.04 -10000 0 -0.27 4 4
LCK 0.017 0.094 0.34 2 -0.45 4 6
PDGFRB 0.018 0.054 -10000 0 -0.38 4 4
ACP1 0.024 0.003 -10000 0 -10000 0 0
HCK 0.012 0.044 -10000 0 -10000 0 0
ABL1 0.029 0.12 0.22 30 -0.29 7 37
PDGFB-D/PDGFRB/CBL 0.024 0.11 0.22 23 -0.32 6 29
PTPN1 0.015 0.012 -10000 0 -10000 0 0
SNX15 0.023 0.004 -10000 0 -10000 0 0
STAT3 0.023 0.004 -10000 0 -10000 0 0
STAT1 0.017 0.053 -10000 0 -0.38 4 4
cell proliferation 0.079 0.14 0.36 28 -10000 0 28
SLA 0.021 0.008 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.069 0.089 0.2 25 -10000 0 25
SRC 0.008 0.041 -10000 0 -10000 0 0
PI3K -0.013 0.024 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC 0.04 0.053 0.22 3 -0.22 7 10
SH2B2 0.023 0.006 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.052 0.13 0.23 44 -0.37 1 45
LYN 0.022 0.078 0.34 1 -0.64 1 2
LRP1 0.024 0.002 -10000 0 -10000 0 0
SOS1 0.024 0.002 -10000 0 -10000 0 0
STAT5B 0.024 0.004 -10000 0 -10000 0 0
STAT5A 0.024 0.004 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.037 0.047 -10000 0 -10000 0 0
SPHK1 -0.031 0.14 -10000 0 -0.38 33 33
EDG1 0.002 0.004 -10000 0 -10000 0 0
mol:DAG 0.052 0.11 0.22 44 -0.45 1 45
PLCG1 0.052 0.11 0.23 38 -0.46 1 39
NHERF/PDGFRB 0.043 0.037 -10000 0 -0.22 4 4
YES1 0 0.13 0.34 2 -0.53 10 12
cell migration 0.042 0.037 -10000 0 -0.22 4 4
SHC/Grb2/SOS1 0.034 0.047 -10000 0 -10000 0 0
SLC9A3R2 0.024 0.003 -10000 0 -10000 0 0
SLC9A3R1 0.024 0.004 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.053 0.038 -10000 0 -0.2 4 4
FYN 0.021 0.078 0.33 1 -0.36 3 4
DOK1 0.039 0.082 0.18 56 -0.2 4 60
HRAS/GTP 0.018 0.002 -10000 0 -10000 0 0
PDGFB 0.023 0.004 -10000 0 -10000 0 0
RAC1 0.059 0.14 0.29 36 -0.33 2 38
PRKCD 0.038 0.084 0.18 54 -0.21 4 58
FER 0.039 0.084 0.18 55 -0.21 4 59
MAPKKK cascade 0.057 0.1 0.21 28 -10000 0 28
RASA1 0.038 0.084 0.18 54 -0.21 4 58
NCK1 0.024 0.002 -10000 0 -10000 0 0
NCK2 0.024 0 -10000 0 -10000 0 0
p62DOK/Csk 0.055 0.073 0.17 59 -0.19 4 63
PDGFB-D/PDGFRB/SHB 0.03 0.04 -10000 0 -0.27 4 4
chemotaxis 0.029 0.11 0.22 31 -0.28 7 38
STAT1-3-5/STAT1-3-5 0.025 0.05 -10000 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.013 0.037 -10000 0 -0.27 4 4
PTPRJ 0.024 0.002 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

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
NFATC2 0.005 0.053 -10000 0 -0.29 7 7
GNB1/GNG2 -0.029 0.1 -10000 0 -0.27 17 17
mol:DAG -0.02 0.077 0.18 2 -0.29 8 10
PLCG1 -0.021 0.079 0.18 2 -0.3 8 10
YES1 -0.037 0.085 -10000 0 -0.25 19 19
FZD3 0.015 0.051 0.31 1 -0.38 3 4
FZD6 0.021 0.008 -10000 0 -10000 0 0
G protein 0.019 0.12 0.2 33 -0.3 8 41
MAP3K7 -0.027 0.072 0.16 2 -0.29 7 9
mol:Ca2+ -0.02 0.076 0.18 2 -0.28 8 10
mol:IP3 -0.02 0.077 0.18 2 -0.29 8 10
NLK 0.001 0.074 -10000 0 -0.79 2 2
GNB1 0.023 0.005 -10000 0 -10000 0 0
CAMK2A -0.023 0.077 0.17 3 -0.3 8 11
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.036 0.096 -10000 0 -0.24 32 32
CSNK1A1 0.023 0.004 -10000 0 -10000 0 0
GNAS -0.017 0.084 -10000 0 -0.3 10 10
GO:0007205 -0.023 0.074 0.18 2 -0.27 9 11
WNT6 -0.017 0.1 -10000 0 -0.31 25 25
WNT4 0.01 0.065 -10000 0 -0.31 9 9
NFAT1/CK1 alpha -0.018 0.082 -10000 0 -0.3 7 7
GNG2 0.019 0.036 -10000 0 -0.29 3 3
WNT5A 0.004 0.087 -10000 0 -0.38 11 11
WNT11 -0.058 0.16 -10000 0 -0.38 47 47
CDC42 -0.036 0.077 -10000 0 -0.25 13 13
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.06 0.11 0.26 21 -10000 0 21
GNAI2 0.024 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.017 0.053 -10000 0 -0.22 10 10
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.12 0.16 -10000 0 -0.29 103 103
RhoA/GTP -0.061 0.11 -10000 0 -0.26 21 21
negative regulation of cAMP metabolic process -0.07 0.11 -10000 0 -0.29 19 19
GNAZ 0.018 0.041 -10000 0 -0.29 4 4
GNAI3 0.023 0.004 -10000 0 -10000 0 0
GNA12 0.021 0.008 -10000 0 -10000 0 0
S1PR5 0.006 0.083 -10000 0 -0.38 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.07 0.11 -10000 0 -0.3 19 19
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
RHOA 0.024 0.004 -10000 0 -10000 0 0
GNAI1 0.018 0.041 -10000 0 -0.29 4 4
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.017 0.15 -10000 0 -0.53 14 14
MKNK1 0.023 0.004 -10000 0 -10000 0 0
MAPK14 0.001 0.089 -10000 0 -0.26 19 19
ATF2/c-Jun 0 0.066 -10000 0 -0.23 1 1
MAPK11 0.002 0.086 -10000 0 -0.27 17 17
MITF -0.011 0.11 -10000 0 -0.34 17 17
MAPKAPK5 -0.004 0.092 -10000 0 -0.31 16 16
KRT8 -0.002 0.089 -10000 0 -0.31 15 15
MAPKAPK3 0.024 0.004 -10000 0 -10000 0 0
MAPKAPK2 0.023 0.004 -10000 0 -10000 0 0
p38alpha-beta/CK2 0.001 0.12 -10000 0 -0.38 17 17
CEBPB -0.008 0.077 -10000 0 -0.3 12 12
SLC9A1 -0.007 0.097 -10000 0 -0.33 16 16
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.003 0.095 -10000 0 -0.3 18 18
p38alpha-beta/MNK1 0.018 0.1 -10000 0 -0.31 17 17
JUN -0.002 0.064 -10000 0 -10000 0 0
PPARGC1A -0.029 0.13 -10000 0 -0.37 19 19
USF1 0.001 0.084 -10000 0 -0.31 13 13
RAB5/GDP/GDI1 0.004 0.074 -10000 0 -0.22 18 18
NOS2 -0.041 0.21 -10000 0 -0.8 14 14
DDIT3 -0.002 0.092 -10000 0 -0.32 15 15
RAB5A 0.024 0.002 -10000 0 -10000 0 0
HSPB1 0.002 0.09 0.27 9 -0.26 15 24
p38alpha-beta/HBP1 0.018 0.1 -10000 0 -0.3 16 16
CREB1 -0.006 0.1 -10000 0 -0.35 17 17
RAB5/GDP 0.018 0.002 -10000 0 -10000 0 0
EIF4E -0.011 0.083 0.2 1 -0.28 16 17
RPS6KA4 -0.004 0.091 -10000 0 -0.31 16 16
PLA2G4A -0.008 0.079 0.2 1 -0.3 12 13
GDI1 -0.002 0.089 -10000 0 -0.31 15 15
TP53 -0.018 0.1 -10000 0 -0.38 15 15
RPS6KA5 -0.006 0.098 -10000 0 -0.33 16 16
ESR1 -0.027 0.13 -10000 0 -0.41 19 19
HBP1 0.023 0.005 -10000 0 -10000 0 0
MEF2C -0.008 0.099 -10000 0 -0.32 17 17
MEF2A -0.005 0.095 -10000 0 -0.32 16 16
EIF4EBP1 -0.007 0.11 -10000 0 -0.37 16 16
KRT19 -0.004 0.091 -10000 0 -0.31 16 16
ELK4 0 0.086 -10000 0 -0.31 14 14
ATF6 0.001 0.084 -10000 0 -0.31 13 13
ATF1 -0.006 0.1 -10000 0 -0.34 17 17
p38alpha-beta/MAPKAPK2 0.021 0.1 -10000 0 -0.31 15 15
p38alpha-beta/MAPKAPK3 0.019 0.1 -10000 0 -0.3 17 17
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.001 0.068 -10000 0 -0.16 34 34
cell-cell adhesion 0.035 0.06 0.32 1 -10000 0 1
Ephrin B/EPHB2/RasGAP 0.043 0.043 -10000 0 -0.2 2 2
ITSN1 0.024 0.003 -10000 0 -10000 0 0
PIK3CA 0.024 0.002 -10000 0 -10000 0 0
SHC1 0.023 0.004 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.006 0.079 -10000 0 -0.22 24 24
Ephrin B1/EPHB1 -0.029 0.11 -10000 0 -0.23 55 55
HRAS/GDP -0.023 0.093 -10000 0 -0.28 7 7
Ephrin B/EPHB1/GRB7 0.008 0.097 0.23 1 -0.2 37 38
Endophilin/SYNJ1 0.025 0.074 0.18 41 -10000 0 41
KRAS 0.024 0.003 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.015 0.077 -10000 0 -0.2 20 20
endothelial cell migration 0.039 0.023 -10000 0 -10000 0 0
GRB2 0.024 0.004 -10000 0 -10000 0 0
GRB7 0.022 0.057 0.31 3 -0.38 3 6
PAK1 0.022 0.075 0.18 40 -10000 0 40
HRAS 0.024 0.003 -10000 0 -10000 0 0
RRAS 0.025 0.074 0.18 40 -10000 0 40
DNM1 0.024 0.002 -10000 0 -10000 0 0
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.016 0.087 0.18 21 -0.36 1 22
lamellipodium assembly -0.035 0.06 -10000 0 -0.32 1 1
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.013 0.055 -10000 0 -10000 0 0
PIK3R1 0.023 0.005 -10000 0 -10000 0 0
EPHB2 0.021 0.027 -10000 0 -0.38 1 1
EPHB3 -0.018 0.12 -10000 0 -0.38 24 24
EPHB1 -0.073 0.17 -10000 0 -0.38 55 55
EPHB4 0.023 0.006 -10000 0 -10000 0 0
mol:GDP -0.009 0.086 0.25 2 -0.27 7 9
Ephrin B/EPHB2 0.034 0.037 -10000 0 -0.19 3 3
Ephrin B/EPHB3 0.014 0.073 -10000 0 -0.19 23 23
JNK cascade -0.056 0.078 -10000 0 -0.26 1 1
Ephrin B/EPHB1 0.001 0.089 -10000 0 -0.2 35 35
RAP1/GDP 0 0.11 0.26 7 -0.25 6 13
EFNB2 0.02 0.009 -10000 0 -10000 0 0
EFNB3 0.015 0.043 -10000 0 -0.35 3 3
EFNB1 0.024 0.002 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.004 0.088 -10000 0 -0.2 36 36
RAP1B 0.024 0.002 -10000 0 -10000 0 0
RAP1A 0.023 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.008 0.083 -10000 0 -0.3 1 1
Rap1/GTP -0.014 0.071 -10000 0 -0.33 1 1
axon guidance 0 0.068 -10000 0 -0.16 34 34
MAPK3 0.008 0.05 0.18 3 -10000 0 3
MAPK1 0.007 0.048 0.17 2 -10000 0 2
Rac1/GDP -0.018 0.088 0.2 1 -0.26 6 7
actin cytoskeleton reorganization -0.044 0.059 -10000 0 -0.22 6 6
CDC42/GDP -0.003 0.1 0.26 8 -0.26 7 15
PI3K 0.042 0.025 -10000 0 -10000 0 0
EFNA5 -0.022 0.11 -10000 0 -0.29 33 33
Ephrin B2/EPHB4 0.026 0.013 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.015 0.02 -10000 0 -10000 0 0
CDC42 0.023 0.006 -10000 0 -10000 0 0
RAS family/GTP -0.017 0.07 -10000 0 -0.32 1 1
PTK2 0.08 0.2 0.58 31 -10000 0 31
MAP4K4 -0.056 0.079 -10000 0 -0.26 1 1
SRC 0.016 0.012 -10000 0 -10000 0 0
KALRN 0.023 0.02 -10000 0 -0.29 1 1
Intersectin/N-WASP 0.034 0.008 -10000 0 -10000 0 0
neuron projection morphogenesis -0.015 0.09 0.27 10 -10000 0 10
MAP2K1 0.009 0.049 -10000 0 -10000 0 0
WASL 0.023 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.006 0.11 -10000 0 -0.21 55 55
cell migration 0.024 0.08 0.21 16 -10000 0 16
NRAS 0.024 0.004 -10000 0 -10000 0 0
SYNJ1 0.026 0.075 0.18 41 -10000 0 41
PXN 0.024 0.002 -10000 0 -10000 0 0
TF 0.004 0.086 0.17 35 -0.35 1 36
HRAS/GTP -0.004 0.08 -10000 0 -0.34 1 1
Ephrin B1/EPHB1-2 -0.017 0.11 -10000 0 -0.2 56 56
cell adhesion mediated by integrin -0.026 0.086 0.18 2 -0.2 38 40
RAC1 0.021 0.008 -10000 0 -10000 0 0
mol:GTP -0.003 0.084 -10000 0 -0.19 28 28
RAC1-CDC42/GTP -0.051 0.075 -10000 0 -0.3 5 5
RASA1 0.023 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.011 0.089 0.2 1 -0.25 6 7
ruffle organization 0.003 0.12 0.35 13 -0.33 1 14
NCK1 0.024 0.002 -10000 0 -10000 0 0
receptor internalization 0.023 0.073 0.17 41 -10000 0 41
Ephrin B/EPHB2/KALRN 0.042 0.045 -10000 0 -0.2 2 2
ROCK1 -0.011 0.064 -10000 0 -0.2 24 24
RAS family/GDP -0.041 0.054 -10000 0 -0.25 1 1
Rac1/GTP -0.019 0.07 -10000 0 -0.34 1 1
Ephrin B/EPHB1/Src/Paxillin 0.004 0.045 -10000 0 -0.17 4 4
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 0.035 0.22 -10000 0 -0.81 12 12
NCK1/PAK1/Dok-R -0.023 0.088 -10000 0 -0.39 12 12
NCK1/Dok-R 0.016 0.22 -10000 0 -0.83 13 13
PIK3CA 0.023 0.002 -10000 0 -10000 0 0
mol:beta2-estradiol 0 0.042 0.25 6 -10000 0 6
RELA 0.023 0.004 -10000 0 -10000 0 0
SHC1 0.024 0.005 -10000 0 -10000 0 0
Rac/GDP 0.016 0.006 -10000 0 -10000 0 0
F2 -0.11 0.19 0.28 6 -0.4 68 74
TNIP2 0.024 0.004 -10000 0 -10000 0 0
NF kappa B/RelA 0.044 0.22 -10000 0 -0.8 13 13
FN1 -0.018 0.12 -10000 0 -0.37 25 25
PLD2 -0.019 0.22 -10000 0 -0.87 13 13
PTPN11 0.024 0.003 -10000 0 -10000 0 0
GRB14 -0.008 0.096 -10000 0 -0.32 19 19
ELK1 0.015 0.21 -10000 0 -0.82 13 13
GRB7 0.022 0.057 0.31 3 -0.38 3 6
PAK1 0.024 0.003 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0.028 0.23 -10000 0 -0.85 13 13
CDKN1A 0.027 0.18 0.36 1 -0.6 12 13
ITGA5 0.024 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.016 0.22 -10000 0 -0.83 13 13
CRK 0.02 0.009 -10000 0 -10000 0 0
mol:NO 0.048 0.18 0.38 8 -0.6 12 20
PLG -0.016 0.22 -10000 0 -0.87 13 13
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.022 0.2 -10000 0 -0.75 13 13
GRB2 0.024 0.004 -10000 0 -10000 0 0
PIK3R1 0.024 0.005 -10000 0 -10000 0 0
ANGPT2 -0.05 0.21 -10000 0 -0.64 15 15
BMX -0.034 0.24 -10000 0 -0.96 13 13
ANGPT1 0.019 0.18 -10000 0 -1 6 6
tube development 0.014 0.19 0.34 3 -0.67 12 15
ANGPT4 0.002 0.04 -10000 0 -0.38 2 2
response to hypoxia -0.002 0.015 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 0.015 0.24 -10000 0 -0.91 13 13
alpha5/beta1 Integrin 0.035 0.005 -10000 0 -10000 0 0
FGF2 -0.004 0.087 -10000 0 -0.29 20 20
STAT5A (dimer) 0.023 0.22 -10000 0 -0.76 12 12
mol:L-citrulline 0.048 0.18 0.38 8 -0.6 12 20
AGTR1 -0.12 0.15 -10000 0 -0.29 108 108
MAPK14 0.006 0.26 -10000 0 -0.99 13 13
Tie2/SHP2 0.013 0.2 -10000 0 -0.92 9 9
TEK -0.007 0.21 -10000 0 -1 9 9
RPS6KB1 0.031 0.21 -10000 0 -0.8 12 12
Angiotensin II/AT1 -0.081 0.1 -10000 0 -0.19 108 108
Tie2/Ang1/GRB2 0.024 0.23 -10000 0 -0.88 13 13
MAPK3 -0.014 0.2 -10000 0 -0.81 13 13
MAPK1 -0.011 0.2 -10000 0 -0.83 12 12
Tie2/Ang1/GRB7 0.025 0.23 -10000 0 -0.86 13 13
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.013 0.22 -10000 0 -0.88 13 13
PI3K 0.02 0.24 -10000 0 -0.94 12 12
FES -0.002 0.26 -10000 0 -1 13 13
Crk/Dok-R 0.013 0.22 -10000 0 -0.85 12 12
Tie2/Ang1/ABIN2 0.024 0.24 -10000 0 -0.89 13 13
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.041 0.2 0.36 1 -0.73 12 13
STAT5A 0.024 0.004 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.05 0.22 0.43 6 -0.79 11 17
Tie2/Ang2 -0.014 0.23 -10000 0 -0.9 12 12
Tie2/Ang1 -0.01 0.24 -10000 0 -0.93 13 13
FOXO1 0.057 0.21 0.39 9 -0.73 11 20
ELF1 0.019 0.027 -10000 0 -10000 0 0
ELF2 -0.01 0.22 -10000 0 -0.88 13 13
mol:Choline -0.017 0.21 -10000 0 -0.84 13 13
cell migration -0.013 0.054 -10000 0 -0.22 12 12
FYN 0.007 0.21 0.37 1 -0.76 12 13
DOK2 0.018 0.01 -10000 0 -10000 0 0
negative regulation of cell cycle 0.029 0.17 0.33 4 -0.54 12 16
ETS1 0.022 0.047 -10000 0 -0.26 6 6
PXN 0.052 0.19 0.4 7 -0.66 11 18
ITGB1 0.024 0.002 -10000 0 -10000 0 0
NOS3 0.045 0.2 0.45 4 -0.68 12 16
RAC1 0.021 0.008 -10000 0 -10000 0 0
TNF 0.021 0.054 -10000 0 -0.28 7 7
MAPKKK cascade -0.017 0.21 -10000 0 -0.84 13 13
RASA1 0.023 0.005 -10000 0 -10000 0 0
Tie2/Ang1/Shc 0.024 0.24 -10000 0 -0.89 13 13
NCK1 0.024 0.002 -10000 0 -10000 0 0
vasculogenesis 0.05 0.17 0.37 8 -0.54 12 20
mol:Phosphatidic acid -0.017 0.21 -10000 0 -0.84 13 13
mol:Angiotensin II 0.001 0.002 -10000 0 -10000 0 0
mol:NADP 0.048 0.18 0.38 8 -0.6 12 20
Rac1/GTP 0.023 0.19 -10000 0 -0.73 12 12
MMP2 -0.015 0.22 -10000 0 -0.88 13 13
Coregulation of Androgen receptor activity

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
NRIP1 0 0.045 -10000 0 -10000 0 0
SVIL 0.001 0.047 -10000 0 -0.29 2 2
ZNF318 0.054 0.062 0.18 47 -10000 0 47
JMJD2C 0.006 0.019 0.04 2 -0.066 10 12
T-DHT/AR/Ubc9 0 0.078 -10000 0 -0.16 38 38
CARM1 0.014 0.02 -10000 0 -10000 0 0
PRDX1 0.026 0.006 -10000 0 -10000 0 0
PELP1 0.024 0.014 -10000 0 -10000 0 0
CTNNB1 0.006 0.035 -10000 0 -10000 0 0
AKT1 0.031 0.019 -10000 0 -10000 0 0
PTK2B 0.008 0.028 -10000 0 -10000 0 0
MED1 0.035 0.03 0.35 1 -10000 0 1
MAK 0.042 0.092 0.18 46 -0.38 6 52
response to oxidative stress 0.002 0.005 -10000 0 -10000 0 0
HIP1 0.004 0.038 -10000 0 -10000 0 0
GSN -0.001 0.055 -10000 0 -0.34 2 2
NCOA2 0.014 0.018 -10000 0 -10000 0 0
NCOA6 0.007 0.027 -10000 0 -10000 0 0
DNA-PK 0.063 0.063 0.2 34 -0.23 1 35
NCOA4 0.018 0.014 -10000 0 -10000 0 0
PIAS3 0.006 0.035 -10000 0 -10000 0 0
cell proliferation 0.03 0.071 -10000 0 -0.37 2 2
XRCC5 0.031 0.014 -10000 0 -10000 0 0
UBE3A -0.001 0.05 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.012 0.092 -10000 0 -0.18 45 45
FHL2 0.037 0.059 -10000 0 -10000 0 0
RANBP9 0.002 0.044 -10000 0 -10000 0 0
JMJD1A 0.002 0.021 -10000 0 -0.12 5 5
CDK6 0.022 0.027 -10000 0 -0.37 1 1
TGFB1I1 0.002 0.043 -10000 0 -0.29 1 1
T-DHT/AR/CyclinD1 -0.019 0.087 -10000 0 -0.18 44 44
XRCC6 0.03 0.015 -10000 0 -10000 0 0
T-DHT/AR 0.009 0.088 -10000 0 -0.23 5 5
CTDSP1 0.012 0.024 -10000 0 -10000 0 0
CTDSP2 0.044 0.041 -10000 0 -10000 0 0
BRCA1 0.001 0.055 -10000 0 -0.42 2 2
TCF4 0.029 0.029 -10000 0 -10000 0 0
CDKN2A -0.08 0.19 -10000 0 -0.38 65 65
SRF 0.039 0.021 -10000 0 -10000 0 0
NKX3-1 -0.027 0.12 -10000 0 -0.4 17 17
KLK3 -0.24 0.49 -10000 0 -1.2 48 48
TMF1 0.014 0.019 -10000 0 -10000 0 0
HNRNPA1 0.036 0.024 -10000 0 -10000 0 0
AOF2 -0.016 0.032 -10000 0 -0.077 48 48
APPL1 0.027 0.038 0.12 7 -10000 0 7
T-DHT/AR/Caspase 8 0.01 0.084 -10000 0 -0.16 33 33
AR -0.031 0.12 -10000 0 -0.29 39 39
UBA3 0.012 0.024 -10000 0 -10000 0 0
PATZ1 0.035 0.024 -10000 0 -10000 0 0
PAWR 0.015 0.019 -10000 0 -10000 0 0
PRKDC 0.026 0.037 0.33 1 -0.38 1 2
PA2G4 0.037 0.027 -10000 0 -10000 0 0
UBE2I 0.024 0.003 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.009 0.074 -10000 0 -0.14 32 32
RPS6KA3 0.001 0.045 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.007 0.078 -10000 0 -0.16 41 41
LATS2 0.028 0.024 -10000 0 -10000 0 0
T-DHT/AR/PRX1 0.016 0.081 0.14 14 -0.14 30 44
Cyclin D3/CDK11 p58 0.02 0.005 -10000 0 -10000 0 0
VAV3 -0.033 0.1 -10000 0 -0.29 29 29
KLK2 -0.007 0.063 -10000 0 -0.26 9 9
CASP8 0.028 0.008 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.002 0.077 -10000 0 -0.18 13 13
TMPRSS2 -0.004 0.069 -10000 0 -0.52 2 2
CCND1 0.004 0.058 -10000 0 -0.39 4 4
PIAS1 -0.003 0.052 -10000 0 -10000 0 0
mol:T-DHT 0.001 0.012 -10000 0 -0.059 5 5
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.014 0.075 -10000 0 -0.16 48 48
T-DHT/AR/CDK6 0.002 0.081 -10000 0 -0.16 40 40
CMTM2 0.011 0.079 -10000 0 -0.38 9 9
SNURF -0.001 0.074 -10000 0 -0.3 13 13
ZMIZ1 0.023 0.02 -10000 0 -10000 0 0
CCND3 0.025 0.003 -10000 0 -10000 0 0
TGIF1 0.028 0.023 -10000 0 -10000 0 0
FKBP4 0.002 0.049 0.32 1 -10000 0 1
HIF-2-alpha transcription factor network

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
MMP14 -0.027 0.14 -10000 0 -0.61 10 10
oxygen homeostasis -0.01 0.011 -10000 0 -10000 0 0
TCEB2 0.024 0.003 -10000 0 -10000 0 0
TCEB1 0.021 0.008 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.034 0.073 -10000 0 -10000 0 0
EPO -0.13 0.17 -10000 0 -0.54 11 11
FIH (dimer) 0.003 0.024 -10000 0 -10000 0 0
APEX1 -0.013 0.026 -10000 0 -10000 0 0
SERPINE1 -0.18 0.23 -10000 0 -0.55 46 46
FLT1 0.001 0.071 -10000 0 -0.56 3 3
ADORA2A -0.14 0.19 -10000 0 -0.53 24 24
germ cell development -0.15 0.19 -10000 0 -0.53 26 26
SLC11A2 -0.15 0.19 -10000 0 -0.54 24 24
BHLHE40 -0.15 0.2 -10000 0 -0.56 25 25
HIF1AN 0.003 0.024 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.075 0.11 -10000 0 -0.34 6 6
ETS1 0.033 0.004 -10000 0 -10000 0 0
CITED2 -0.004 0.087 -10000 0 -0.66 3 3
KDR -0.008 0.1 -10000 0 -0.53 8 8
PGK1 -0.15 0.19 -10000 0 -0.54 25 25
SIRT1 0.024 0.002 -10000 0 -10000 0 0
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT -0.16 0.23 -10000 0 -0.62 25 25
EPAS1 -0.045 0.068 -10000 0 -0.23 3 3
SP1 0.026 0.014 -10000 0 -10000 0 0
ABCG2 -0.27 0.25 -10000 0 -0.56 64 64
EFNA1 -0.15 0.19 -10000 0 -0.54 24 24
FXN -0.15 0.18 -10000 0 -0.53 24 24
POU5F1 -0.15 0.2 -10000 0 -0.55 26 26
neuron apoptosis 0.16 0.22 0.6 25 -10000 0 25
EP300 0.023 0.005 -10000 0 -10000 0 0
EGLN3 0.002 0.025 -10000 0 -10000 0 0
EGLN2 0.003 0.025 -10000 0 -10000 0 0
EGLN1 0.003 0.024 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.042 0.017 -10000 0 -10000 0 0
VHL 0.024 0.002 -10000 0 -10000 0 0
ARNT -0.011 0.026 -10000 0 -10000 0 0
SLC2A1 -0.16 0.2 -10000 0 -0.55 29 29
TWIST1 -0.15 0.21 -10000 0 -0.58 29 29
ELK1 0.028 0.003 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.076 0.12 -10000 0 -0.36 5 5
VEGFA -0.16 0.21 -10000 0 -0.56 28 28
CREBBP 0.024 0.004 -10000 0 -10000 0 0
IGF1 pathway

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
NCK2 0.024 0 -10000 0 -10000 0 0
PTK2 0.021 0.009 -10000 0 -10000 0 0
CRKL -0.019 0.065 -10000 0 -0.15 44 44
GRB2/SOS1/SHC 0.046 0.011 -10000 0 -10000 0 0
HRAS 0.024 0.003 -10000 0 -10000 0 0
IRS1/Crk -0.012 0.066 -10000 0 -0.15 44 44
IGF-1R heterotetramer/IGF1/PTP1B 0.002 0.066 -10000 0 -0.16 27 27
AKT1 -0.033 0.049 -10000 0 -10000 0 0
BAD -0.033 0.047 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.013 0.057 -10000 0 -0.15 32 32
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.009 0.074 -10000 0 -0.16 42 42
RAF1 -0.02 0.067 -10000 0 -0.47 2 2
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.016 0.081 -10000 0 -10000 0 0
YWHAZ 0.021 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.009 0.08 -10000 0 -0.16 48 48
PIK3CA 0.024 0.002 -10000 0 -10000 0 0
RPS6KB1 -0.034 0.05 -10000 0 -10000 0 0
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.002 0.072 -10000 0 -0.38 2 2
PXN 0.024 0.002 -10000 0 -10000 0 0
PIK3R1 0.023 0.005 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.035 0.006 -10000 0 -10000 0 0
HRAS/GTP -0.002 0.064 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.03 0.077 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.009 0.031 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck 0.003 0.081 -10000 0 -0.15 48 48
Crk/p130 Cas/Paxillin 0.015 0.078 -10000 0 -10000 0 0
IGF1R 0.009 0.032 -10000 0 -10000 0 0
IGF1 0.016 0.039 -10000 0 -0.38 2 2
IRS2/Crk -0.007 0.057 0.18 1 -10000 0 1
PI3K 0.012 0.082 -10000 0 -10000 0 0
apoptosis 0.029 0.041 -10000 0 -10000 0 0
HRAS/GDP 0.018 0.002 -10000 0 -10000 0 0
PRKCD -0.04 0.11 -10000 0 -0.26 39 39
RAF1/14-3-3 E -0.005 0.062 -10000 0 -0.41 2 2
BAD/14-3-3 -0.03 0.042 -10000 0 -10000 0 0
PRKCZ -0.034 0.05 -10000 0 -10000 0 0
Crk/p130 Cas/Paxillin/FAK1 -0.001 0.057 -10000 0 -10000 0 0
PTPN1 0.015 0.012 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.04 0.12 -10000 0 -0.27 46 46
BCAR1 0.024 0.002 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.015 0.075 -10000 0 -0.17 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.024 0.002 -10000 0 -10000 0 0
IRS1/NCK2 -0.009 0.074 -10000 0 -0.15 48 48
GRB10 0.021 0.008 -10000 0 -10000 0 0
PTPN11 -0.022 0.067 -10000 0 -0.15 48 48
IRS1 -0.023 0.073 0.12 1 -0.16 48 49
IRS2 -0.015 0.061 0.19 1 -0.15 37 38
IGF-1R heterotetramer/IGF1 -0.018 0.1 -10000 0 -0.22 48 48
GRB2 0.024 0.004 -10000 0 -10000 0 0
PDPK1 -0.036 0.053 -10000 0 -10000 0 0
YWHAE 0.02 0.009 -10000 0 -10000 0 0
PRKD1 -0.042 0.11 -10000 0 -0.27 40 40
SHC1 0.023 0.004 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.023 0.004 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.024 0.077 -10000 0 -0.22 15 15
NT3 (dimer)/TRKC -0.024 0.11 -10000 0 -0.21 54 54
NT3 (dimer)/TRKB -0.067 0.14 -10000 0 -0.22 99 99
SHC/Grb2/SOS1/GAB1/PI3K 0.024 0.009 -10000 0 -10000 0 0
RAPGEF1 0.024 0.002 -10000 0 -10000 0 0
BDNF 0.01 0.075 -10000 0 -0.38 8 8
PIK3CA 0.024 0.002 -10000 0 -10000 0 0
DYNLT1 0.024 0.003 -10000 0 -10000 0 0
NTRK1 0.016 0.039 -10000 0 -0.38 2 2
NTRK2 -0.06 0.14 -10000 0 -0.3 60 60
NTRK3 -0.056 0.13 -10000 0 -0.29 55 55
NT-4/5 (dimer)/TRKB -0.078 0.14 -10000 0 -0.23 102 102
neuron apoptosis 0.088 0.14 0.34 41 -10000 0 41
SHC 2-3/Grb2 -0.094 0.16 -10000 0 -0.37 41 41
SHC1 0.023 0.004 -10000 0 -10000 0 0
SHC2 -0.088 0.15 -10000 0 -0.37 39 39
SHC3 -0.095 0.15 -10000 0 -0.38 40 40
STAT3 (dimer) 0.025 0.027 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.022 0.1 -10000 0 -0.17 71 71
RIN/GDP -0.009 0.075 0.19 3 -0.24 4 7
GIPC1 0.024 0.002 -10000 0 -10000 0 0
KRAS 0.024 0.003 -10000 0 -10000 0 0
DNAJA3 -0.067 0.11 -10000 0 -0.24 62 62
RIN/GTP 0.009 0.005 -10000 0 -10000 0 0
CCND1 0.01 0.041 -10000 0 -0.3 4 4
MAGED1 0.024 0.003 -10000 0 -10000 0 0
PTPN11 0.024 0.003 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.016 0.084 -10000 0 -0.38 11 11
SHC/GRB2/SOS1 0.046 0.011 -10000 0 -10000 0 0
GRB2 0.024 0.004 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.013 0.078 -10000 0 -0.17 34 34
TRKA/NEDD4-2 0.024 0.031 -10000 0 -0.27 2 2
ELMO1 0.02 0.022 -10000 0 -0.29 1 1
RhoG/GTP/ELMO1/DOCK1 0.028 0.017 -10000 0 -0.16 1 1
NGF 0.006 0.069 -10000 0 -0.29 12 12
HRAS 0.024 0.003 -10000 0 -10000 0 0
DOCK1 0.024 0.003 -10000 0 -10000 0 0
GAB2 0.024 0.004 -10000 0 -10000 0 0
RIT2 -0.011 0.011 -10000 0 -10000 0 0
RIT1 0.023 0.004 -10000 0 -10000 0 0
FRS2 0.024 0.002 -10000 0 -10000 0 0
DNM1 0.024 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.02 0.009 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.052 0.12 -10000 0 -0.24 58 58
mol:GDP -0.018 0.1 0.24 4 -0.38 4 8
NGF (dimer) 0.006 0.069 -10000 0 -0.29 12 12
RhoG/GDP 0.015 0.015 -10000 0 -0.19 1 1
RIT1/GDP -0.009 0.076 0.19 2 -0.25 4 6
TIAM1 -0.001 0.083 -10000 0 -0.29 18 18
PIK3R1 0.023 0.005 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.018 0.1 -10000 0 -0.25 14 14
KIDINS220/CRKL/C3G 0.035 0.006 -10000 0 -10000 0 0
SHC/RasGAP 0.033 0.009 -10000 0 -10000 0 0
FRS2 family/SHP2 0.048 0.007 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.058 0.016 -10000 0 -10000 0 0
RIT1/GTP 0.017 0.003 -10000 0 -10000 0 0
NT3 (dimer) 0.015 0.049 -10000 0 -0.31 5 5
RAP1/GDP -0.009 0.064 0.12 1 -0.21 4 5
KIDINS220/CRKL 0.023 0.004 -10000 0 -10000 0 0
BDNF (dimer) 0.01 0.074 -10000 0 -0.38 8 8
ubiquitin-dependent protein catabolic process 0.023 0.054 -10000 0 -0.17 14 14
Schwann cell development -0.025 0.025 -10000 0 -10000 0 0
EHD4 0.023 0.005 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.06 0.012 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.011 0.035 -10000 0 -10000 0 0
RAP1B 0.024 0.002 -10000 0 -10000 0 0
RAP1A 0.023 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.045 0.1 -10000 0 -0.27 16 16
ABL1 0.024 0.002 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.035 0.006 -10000 0 -10000 0 0
Rap1/GTP -0.01 0.08 -10000 0 -0.4 5 5
STAT3 0.025 0.027 -10000 0 -10000 0 0
axon guidance -0.048 0.093 -10000 0 -0.26 16 16
MAPK3 -0.01 0.067 0.18 6 -0.21 3 9
MAPK1 -0.01 0.065 0.18 5 -0.21 3 8
CDC42/GDP -0.004 0.079 0.18 5 -0.25 4 9
NTF3 0.016 0.049 -10000 0 -0.31 5 5
NTF4 -0.016 0.084 -10000 0 -0.38 11 11
NGF (dimer)/TRKA/FAIM 0.032 0.054 -10000 0 -0.17 14 14
PI3K 0.034 0.008 -10000 0 -10000 0 0
FRS3 0.024 0.002 -10000 0 -10000 0 0
FAIM 0.024 0 -10000 0 -10000 0 0
GAB1 0.023 0.004 -10000 0 -10000 0 0
RASGRF1 -0.082 0.12 -10000 0 -0.25 65 65
SOS1 0.024 0.002 -10000 0 -10000 0 0
MCF2L -0.03 0.079 0.22 1 -0.18 46 47
RGS19 0.015 0.012 -10000 0 -10000 0 0
CDC42 0.023 0.006 -10000 0 -10000 0 0
RAS family/GTP -0.005 0.07 -10000 0 -0.35 3 3
Rac1/GDP -0.011 0.072 0.17 2 -0.23 4 6
NGF (dimer)/TRKA/GRIT 0.018 0.049 -10000 0 -0.17 14 14
neuron projection morphogenesis -0.061 0.14 -10000 0 -0.7 2 2
NGF (dimer)/TRKA/NEDD4-2 0.023 0.054 -10000 0 -0.17 14 14
MAP2K1 -0.004 0.039 0.18 10 -10000 0 10
NGFR -0.069 0.14 -10000 0 -0.29 69 69
NGF (dimer)/TRKA/GIPC/GAIP 0.006 0.04 -10000 0 -0.17 10 10
RAS family/GTP/PI3K 0.021 0.006 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.069 0.015 -10000 0 -10000 0 0
NRAS 0.024 0.004 -10000 0 -10000 0 0
GRB2/SOS1 0.035 0.006 -10000 0 -10000 0 0
PRKCI 0.024 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.021 0.008 -10000 0 -10000 0 0
PRKCZ 0.023 0.005 -10000 0 -10000 0 0
MAPKKK cascade -0.052 0.15 -10000 0 -0.54 18 18
RASA1 0.023 0.005 -10000 0 -10000 0 0
TRKA/c-Abl 0.031 0.029 -10000 0 -0.27 2 2
SQSTM1 0.024 0.004 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.003 0.1 -10000 0 -0.23 14 14
NGF (dimer)/TRKA/p62/Atypical PKCs 0.051 0.056 -10000 0 -0.2 2 2
MATK -0.005 0.091 -10000 0 -0.29 21 21
NEDD4L 0.019 0.01 -10000 0 -10000 0 0
RAS family/GDP -0.027 0.042 -10000 0 -0.19 3 3
NGF (dimer)/TRKA -0.064 0.12 -10000 0 -0.25 69 69
Rac1/GTP -0.064 0.092 -10000 0 -0.23 35 35
FRS2 family/SHP2/CRK family 0.058 0.028 -10000 0 -10000 0 0
S1P4 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 -0.12 0.16 -10000 0 -0.29 103 103
CDC42/GTP -0.06 0.11 -10000 0 -0.28 19 19
PLCG1 -0.042 0.087 -10000 0 -0.3 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.024 0.004 -10000 0 -10000 0 0
GNAI3 0.023 0.004 -10000 0 -10000 0 0
G12/G13 0.031 0.012 -10000 0 -10000 0 0
cell migration -0.059 0.11 -10000 0 -0.27 19 19
S1PR5 0.006 0.083 -10000 0 -0.38 10 10
S1PR4 0.017 0.045 -10000 0 -0.29 5 5
MAPK3 -0.069 0.11 -10000 0 -0.3 17 17
MAPK1 -0.061 0.099 -10000 0 -0.3 12 12
S1P/S1P5/Gi -0.07 0.11 -10000 0 -0.3 19 19
GNAI1 0.018 0.041 -10000 0 -0.29 4 4
CDC42/GDP 0.017 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.017 0.053 -10000 0 -0.22 10 10
RHOA 0.028 0.058 0.18 27 -10000 0 27
S1P/S1P4/Gi -0.069 0.11 -10000 0 -0.31 17 17
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.018 0.041 -10000 0 -0.29 4 4
S1P/S1P4/G12/G13 0.037 0.029 -10000 0 -0.15 4 4
GNA12 0.021 0.008 -10000 0 -10000 0 0
GNA13 0.024 0.004 -10000 0 -10000 0 0
CDC42 0.023 0.006 -10000 0 -10000 0 0
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.024 0.015 -10000 0 -10000 0 0
ARNO/beta Arrestin1-2 0.012 0.075 -10000 0 -0.81 1 1
EGFR 0.021 0.008 -10000 0 -10000 0 0
EPHA2 0.014 0.059 -10000 0 -0.38 5 5
USP6 0.02 0.009 -10000 0 -10000 0 0
IQSEC1 0.024 0.002 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.025 0.1 -10000 0 -0.22 50 50
ARRB2 0.007 0.003 -10000 0 -10000 0 0
mol:GTP 0.004 0.035 0.12 1 -0.11 8 9
ARRB1 0.024 0.003 -10000 0 -10000 0 0
FBXO8 0.023 0.006 -10000 0 -10000 0 0
TSHR 0.011 0.032 -10000 0 -0.38 1 1
EGF -0.061 0.14 -10000 0 -0.32 56 56
somatostatin receptor activity 0 0 0.001 16 -0.001 8 24
ARAP2 0.023 0.004 -10000 0 -10000 0 0
mol:GDP -0.039 0.094 0.15 8 -0.22 20 28
mol:PI-3-4-5-P3 0 0 0.001 6 -0.001 2 8
ITGA2B 0.005 0.075 -10000 0 -0.38 8 8
ARF6 0.023 0.006 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.05 0.044 0.23 1 -0.21 5 6
ADAP1 0.021 0.008 -10000 0 -10000 0 0
KIF13B 0.019 0.01 -10000 0 -10000 0 0
HGF/MET 0.015 0.071 -10000 0 -0.25 15 15
PXN 0.024 0.002 -10000 0 -10000 0 0
ARF6/GTP -0.026 0.097 0.18 16 -0.23 8 24
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.008 0.094 -10000 0 -0.18 50 50
ADRB2 -0.013 0.1 -10000 0 -0.29 27 27
receptor agonist activity 0 0 0 4 0 7 11
actin filament binding 0 0 0 16 0 11 27
SRC 0.016 0.012 -10000 0 -10000 0 0
ITGB3 0.017 0.045 -10000 0 -0.29 5 5
GNAQ 0.024 0.002 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.001 18 -0.001 3 21
ARF6/GDP -0.048 0.14 0.19 1 -0.33 34 35
ARF6/GDP/GULP/ACAP1 -0.027 0.097 -10000 0 -0.32 4 4
alphaIIb/beta3 Integrin/paxillin/GIT1 0.046 0.057 -10000 0 -0.2 9 9
ACAP1 0.01 0.053 -10000 0 -0.29 7 7
ACAP2 0.024 0 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.005 0.024 -10000 0 -10000 0 0
EFNA1 0.025 0.019 0.31 1 -10000 0 1
HGF 0.014 0.053 -10000 0 -0.3 6 6
CYTH3 0.005 0.002 -10000 0 -10000 0 0
CYTH2 0.012 0.068 -10000 0 -1 1 1
NCK1 0.024 0.002 -10000 0 -10000 0 0
fibronectin binding 0 0 0 23 0 6 29
endosomal lumen acidification 0 0 0 20 0 5 25
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 0.02 0.035 -10000 0 -0.29 3 3
GNAQ/ARNO 0.027 0.065 -10000 0 -0.95 1 1
mol:Phosphatidic acid 0 0 0 2 -10000 0 2
PIP3-E 0 0 0 6 0 1 7
MET 0.007 0.085 0.31 1 -0.38 10 11
GNA14 0.023 0.021 -10000 0 -0.29 1 1
GNA15 -0.001 0.097 -10000 0 -0.38 14 14
GIT1 0.023 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 18 -0.001 5 23
GNA11 0.024 0.002 -10000 0 -10000 0 0
LHCGR -0.012 0.013 -10000 0 -10000 0 0
AGTR1 -0.13 0.15 -10000 0 -0.29 108 108
desensitization of G-protein coupled receptor protein signaling pathway 0.005 0.024 -10000 0 -10000 0 0
IPCEF1/ARNO -0.004 0.088 -10000 0 -0.88 1 1
alphaIIb/beta3 Integrin 0.019 0.065 -10000 0 -0.24 13 13
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.024 0.081 -10000 0 -0.36 9 9
HDAC1 0.022 0.005 -10000 0 -10000 0 0
AES 0.024 0.002 -10000 0 -10000 0 0
FBXW11 0.023 0.004 -10000 0 -10000 0 0
DTX1 0.019 0.039 -10000 0 -0.32 3 3
LRP6/FZD1 0.033 0.01 -10000 0 -10000 0 0
TLE1 0.024 0.002 -10000 0 -10000 0 0
AP1 -0.054 0.083 0.16 3 -0.25 17 20
NCSTN 0.023 0.004 -10000 0 -10000 0 0
ADAM10 0.023 0.005 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.03 0.087 -10000 0 -0.59 4 4
NICD/RBPSUH 0.023 0.078 -10000 0 -0.35 9 9
WIF1 -0.074 0.16 -10000 0 -0.38 49 49
NOTCH1 0.009 0.078 -10000 0 -0.38 9 9
PSENEN 0.024 0.004 -10000 0 -10000 0 0
KREMEN2 -0.035 0.14 -10000 0 -0.38 33 33
DKK1 -0.068 0.17 -10000 0 -0.38 50 50
beta catenin/beta TrCP1 0.071 0.071 0.22 6 -10000 0 6
APH1B 0.023 0.004 -10000 0 -10000 0 0
APH1A 0.023 0.004 -10000 0 -10000 0 0
AXIN1 -0.018 0.063 -10000 0 -0.42 3 3
CtBP/CBP/TCF1/TLE1/AES 0.02 0.013 -10000 0 -10000 0 0
PSEN1 0.023 0.005 -10000 0 -10000 0 0
FOS 0.023 0.005 -10000 0 -10000 0 0
JUN 0.023 0.004 -10000 0 -10000 0 0
MAP3K7 0.023 0.003 -10000 0 -10000 0 0
CTNNB1 0.062 0.074 0.23 6 -0.24 1 7
MAPK3 0.024 0.002 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.029 0.13 -10000 0 -0.24 60 60
HNF1A 0.024 0.002 -10000 0 -10000 0 0
CTBP1 0.023 0.004 -10000 0 -10000 0 0
MYC 0.014 0.053 -10000 0 -10000 0 0
NKD1 -0.19 0.21 0.31 3 -0.38 126 129
FZD1 0.023 0.006 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.021 0.08 -10000 0 -0.36 9 9
apoptosis -0.054 0.083 0.16 3 -0.25 17 20
Delta 1/NOTCHprecursor 0.022 0.08 -10000 0 -0.36 9 9
DLL1 0.021 0.034 -10000 0 -0.34 2 2
PPARD 0.026 0.052 -10000 0 -0.74 1 1
Gamma Secretase 0.063 0.024 -10000 0 -10000 0 0
APC -0.036 0.11 -10000 0 -0.4 15 15
DVL1 0.004 0.047 -10000 0 -0.24 7 7
CSNK2A1 0.02 0.009 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.048 0.15 -10000 0 -0.26 71 71
LRP6 0.024 0.004 -10000 0 -10000 0 0
CSNK1A1 0.024 0.004 -10000 0 -10000 0 0
NLK 0.01 0.004 -10000 0 -10000 0 0
CCND1 0.006 0.13 -10000 0 -0.86 5 5
WNT1 0.01 0.041 -10000 0 -0.38 2 2
Axin1/APC/beta catenin 0.022 0.1 0.23 1 -0.41 6 7
DKK2 -0.032 0.14 -10000 0 -0.38 32 32
NOTCH1 precursor/DVL1 0.009 0.11 -10000 0 -0.49 7 7
GSK3B 0.024 0 -10000 0 -10000 0 0
FRAT1 0.023 0.004 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.024 0.081 -10000 0 -0.36 9 9
PPP2R5D 0.1 0.1 0.23 27 -0.27 4 31
MAPK1 0.023 0.004 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.001 0.11 -10000 0 -0.21 48 48
RBPJ 0.024 0.003 -10000 0 -10000 0 0
CREBBP 0.025 0.005 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.015 0.073 0.44 5 -10000 0 5
VDR 0.024 0.002 -10000 0 -10000 0 0
FAM120B 0.024 0.003 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.044 0.094 -10000 0 -0.23 2 2
RXRs/LXRs/DNA/Oxysterols -0.028 0.087 -10000 0 -10000 0 0
MED1 0.025 0.019 0.31 1 -10000 0 1
mol:9cRA 0.003 0.002 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.023 0.088 0.16 1 -0.17 58 59
RXRs/NUR77 -0.032 0.11 -10000 0 -0.28 8 8
RXRs/PPAR -0.055 0.099 -10000 0 -0.25 8 8
NCOR2 0.024 0.002 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.018 0.002 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.054 0.018 -10000 0 -10000 0 0
RARA 0.023 0.004 -10000 0 -10000 0 0
NCOA1 0.024 0.002 -10000 0 -10000 0 0
VDR/VDR/DNA 0.024 0.002 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.042 0.015 -10000 0 -0.14 1 1
RARG 0.024 0.002 -10000 0 -10000 0 0
RPS6KB1 0.028 0.066 0.58 3 -10000 0 3
RARs/THRs/DNA/SMRT -0.023 0.088 0.16 1 -0.33 2 3
THRA 0.026 0.027 0.31 2 -10000 0 2
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.018 0.002 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.029 0.095 -10000 0 -10000 0 0
NR1H4 -0.14 0.15 -10000 0 -0.29 113 113
RXRs/LXRs/DNA -0.009 0.1 -10000 0 -10000 0 0
NR1H2 0.027 0.005 -10000 0 -10000 0 0
NR1H3 0.027 0.004 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.023 0.096 -10000 0 -10000 0 0
NR4A1 0.01 0.075 -10000 0 -0.38 8 8
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.13 0.12 -10000 0 -0.31 49 49
RXRG -0.11 0.15 -10000 0 -0.28 98 98
RXR alpha/CCPG 0.038 0.006 -10000 0 -10000 0 0
RXRA 0.027 0.004 -10000 0 -10000 0 0
RXRB 0.027 0.004 -10000 0 -10000 0 0
THRB -0.055 0.14 -10000 0 -0.29 58 58
PPARG 0.024 0.002 -10000 0 -10000 0 0
PPARD 0.024 0.002 -10000 0 -10000 0 0
TNF -0.028 0.08 -10000 0 -10000 0 0
mol:Oxysterols 0.004 0.001 -10000 0 -10000 0 0
cholesterol transport -0.028 0.087 -10000 0 -10000 0 0
PPARA 0.023 0.004 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.023 0.021 -10000 0 -0.29 1 1
RXRs/NUR77/BCL2 -0.073 0.11 -10000 0 -0.19 97 97
SREBF1 -0.018 0.071 -10000 0 -10000 0 0
RXRs/RXRs/DNA/9cRA -0.029 0.095 -10000 0 -10000 0 0
ABCA1 -0.027 0.079 -10000 0 -10000 0 0
RARs/THRs 0.016 0.094 0.23 1 -0.27 1 2
RXRs/FXR -0.11 0.12 -10000 0 -0.28 47 47
BCL2 0.016 0.03 -10000 0 -0.29 2 2
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.018 0.074 0.23 1 -0.27 14 15
PDGFRB 0.017 0.054 -10000 0 -0.38 4 4
SPHK1 -0.008 0.065 -10000 0 -0.66 2 2
mol:S1P -0.011 0.058 -10000 0 -0.56 2 2
S1P1/S1P/Gi -0.084 0.16 0.28 1 -0.37 29 30
GNAO1 -0.12 0.16 -10000 0 -0.29 103 103
PDGFB-D/PDGFRB/PLCgamma1 -0.031 0.16 0.29 5 -0.37 17 22
PLCG1 -0.07 0.13 0.37 1 -0.4 17 18
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.017 0.054 -10000 0 -0.38 4 4
GNAI2 0.024 0.009 -10000 0 -10000 0 0
GNAI3 0.023 0.009 -10000 0 -10000 0 0
GNAI1 0.017 0.042 -10000 0 -0.29 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.011 0.055 0.2 1 -0.22 14 15
S1P1/S1P 0.004 0.074 0.2 1 -0.4 1 2
negative regulation of cAMP metabolic process -0.082 0.15 0.28 1 -0.36 29 30
MAPK3 -0.086 0.17 0.27 1 -0.5 17 18
calcium-dependent phospholipase C activity -0.001 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.016 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
KDR 0.024 0.006 -10000 0 -10000 0 0
PLCB2 0.003 0.071 0.28 2 -0.34 1 3
RAC1 0.021 0.008 -10000 0 -10000 0 0
RhoA/GTP -0.007 0.056 -10000 0 -0.34 1 1
receptor internalization 0.003 0.069 -10000 0 -0.3 2 2
PTGS2 -0.084 0.2 -10000 0 -0.71 12 12
Rac1/GTP -0.007 0.054 -10000 0 -0.34 1 1
RHOA 0.024 0.004 -10000 0 -10000 0 0
VEGFA 0.001 0.099 0.31 1 -0.38 14 15
negative regulation of T cell proliferation -0.082 0.15 0.28 1 -0.36 29 30
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.017 0.042 -10000 0 -0.29 4 4
MAPK1 -0.086 0.16 0.27 1 -0.49 17 18
S1P1/S1P/PDGFB-D/PDGFRB 0.016 0.092 0.22 2 -0.3 3 5
ABCC1 0.024 0.006 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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
CTTN 0.023 0.004 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.001 0.089 -9999 0 -0.37 7 7
Syndecan-3/Neurocan 0.004 0.086 -9999 0 -0.36 12 12
POMC 0.01 0.066 -9999 0 -0.3 10 10
EGFR 0.021 0.008 -9999 0 -10000 0 0
Syndecan-3/EGFR 0.005 0.083 -9999 0 -0.34 12 12
AGRP -0.002 0.02 -9999 0 -10000 0 0
NCSTN 0.023 0.004 -9999 0 -10000 0 0
PSENEN 0.023 0.004 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.023 0.004 -9999 0 -10000 0 0
APH1A 0.023 0.004 -9999 0 -10000 0 0
NCAN 0.006 0.033 -9999 0 -0.38 1 1
long-term memory 0.023 0.086 -9999 0 -0.35 11 11
Syndecan-3/IL8 -0.1 0.13 -9999 0 -0.4 14 14
PSEN1 0.023 0.005 -9999 0 -10000 0 0
Src/Cortactin 0.022 0.017 -9999 0 -10000 0 0
FYN 0.024 0.004 -9999 0 -10000 0 0
limb bud formation -0.007 0.083 -9999 0 -0.38 11 11
MC4R -0.012 0.058 -9999 0 -0.38 5 5
SRC 0.016 0.012 -9999 0 -10000 0 0
PTN -0.034 0.12 -9999 0 -0.29 42 42
FGFR/FGF/Syndecan-3 -0.007 0.084 -9999 0 -0.38 11 11
neuron projection morphogenesis 0.02 0.11 -9999 0 -0.36 7 7
Syndecan-3/AgRP 0.004 0.085 -9999 0 -0.36 12 12
Syndecan-3/AgRP/MC4R 0.006 0.085 -9999 0 -0.34 11 11
Fyn/Cortactin 0.034 0.008 -9999 0 -10000 0 0
SDC3 -0.007 0.084 -9999 0 -0.38 11 11
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.1 0.12 -9999 0 -0.39 14 14
IL8 -0.22 0.2 -9999 0 -0.39 135 135
Syndecan-3/Fyn/Cortactin 0.024 0.087 -9999 0 -0.35 11 11
Syndecan-3/CASK -0.009 0.081 -9999 0 -0.35 12 12
alpha-MSH/MC4R 0.008 0.065 -9999 0 -0.23 14 14
Gamma Secretase 0.063 0.024 -9999 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.017 0.074 0.23 1 -0.27 14 15
alphaV beta3 Integrin 0.025 0.068 -10000 0 -0.18 22 22
PTK2 0.017 0.1 0.26 11 -0.32 4 15
IGF1R 0.023 0.004 -10000 0 -10000 0 0
PI4KB 0.023 0.004 -10000 0 -10000 0 0
MFGE8 0.022 0.027 -10000 0 -0.38 1 1
SRC 0.016 0.012 -10000 0 -10000 0 0
CDKN1B 0.007 0.041 -10000 0 -0.34 1 1
VEGFA 0.001 0.099 0.31 1 -0.38 14 15
ILK 0.008 0.034 -10000 0 -10000 0 0
ROCK1 0.021 0.008 -10000 0 -10000 0 0
AKT1 0.002 0.029 -10000 0 -10000 0 0
PTK2B -0.021 0.05 0.17 2 -10000 0 2
alphaV/beta3 Integrin/JAM-A 0.022 0.072 -10000 0 -0.2 9 9
CBL 0.024 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.039 0.032 -10000 0 -0.17 5 5
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.016 0.086 -10000 0 -0.21 2 2
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.009 0.042 0.14 1 -0.3 1 2
alphaV/beta3 Integrin/Syndecan-1 0.043 0.032 -10000 0 -0.16 5 5
PI4KA 0.023 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.024 0.12 -10000 0 -0.28 18 18
PI4 Kinase 0.034 0.008 -10000 0 -10000 0 0
PIK3CA 0.024 0.002 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.097 0.14 -10000 0 -0.23 121 121
RPS6KB1 -0.065 0.084 -10000 0 -0.27 17 17
TLN1 0.023 0.004 -10000 0 -10000 0 0
MAPK3 -0.044 0.13 -10000 0 -0.41 24 24
GPR124 0.02 0.009 -10000 0 -10000 0 0
MAPK1 -0.043 0.13 -10000 0 -0.42 23 23
PXN 0.024 0.002 -10000 0 -10000 0 0
PIK3R1 0.023 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.007 0.087 -10000 0 -0.18 41 41
cell adhesion 0.034 0.037 -10000 0 -0.18 4 4
ANGPTL3 0.001 0.02 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.021 0.057 0.22 1 -0.23 9 10
IGF-1R heterotetramer 0.023 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.016 0.006 -10000 0 -10000 0 0
TGFBR2 0.024 0.002 -10000 0 -10000 0 0
ITGB3 0.017 0.045 -10000 0 -0.29 5 5
IGF1 -0.042 0.13 -10000 0 -0.29 48 48
RAC1 0.021 0.008 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.037 0.034 -10000 0 -0.16 4 4
apoptosis 0.024 0 -10000 0 -10000 0 0
CD47 0.024 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.043 0.032 -10000 0 -0.16 5 5
VCL 0.024 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.011 0.086 -10000 0 -0.19 34 34
CSF1 0.022 0.021 -10000 0 -0.29 1 1
PIK3C2A 0.008 0.034 -10000 0 -10000 0 0
PI4 Kinase/Pyk2 -0.004 0.077 -10000 0 -0.28 4 4
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.039 0.072 0.23 1 -0.21 14 15
FAK1/Vinculin 0.029 0.099 0.24 14 -0.26 4 18
alphaV beta3/Integrin/ppsTEM5 0.037 0.034 -10000 0 -0.16 4 4
RHOA 0.024 0.004 -10000 0 -10000 0 0
VTN 0.005 0.075 -10000 0 -0.38 8 8
BCAR1 0.024 0.002 -10000 0 -10000 0 0
FGF2 -0.004 0.088 -10000 0 -0.29 20 20
F11R -0.007 0.058 -10000 0 -0.2 20 20
alphaV/beta3 Integrin/Lactadherin 0.042 0.036 -10000 0 -0.18 5 5
alphaV/beta3 Integrin/TGFBR2 0.043 0.032 -10000 0 -0.16 5 5
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.058 0.019 -10000 0 -0.15 1 1
HSP90AA1 0.023 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.04 0.03 -10000 0 -0.15 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.018 0.12 -10000 0 -0.37 25 25
alphaV/beta3 Integrin/Pyk2 0.017 0.062 0.19 1 -0.2 11 12
SDC1 0.024 0.002 -10000 0 -10000 0 0
VAV3 -0.009 0.02 0.18 2 -10000 0 2
PTPN11 0.024 0.003 -10000 0 -10000 0 0
IRS1 0.024 0 -10000 0 -10000 0 0
FAK1/Paxillin 0.029 0.099 0.24 14 -0.26 4 18
cell migration 0.025 0.094 0.23 14 -0.24 4 18
ITGAV 0.024 0 -10000 0 -10000 0 0
PI3K 0.03 0.072 -10000 0 -0.25 1 1
SPP1 -0.18 0.21 -10000 0 -0.39 116 116
KDR 0.023 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.024 0 -10000 0 -10000 0 0
COL4A3 -0.035 0.12 -10000 0 -0.31 36 36
angiogenesis -0.04 0.14 -10000 0 -0.43 21 21
Rac1/GTP 0.001 0.05 -10000 0 -10000 0 0
EDIL3 -0.025 0.11 -10000 0 -0.29 36 36
cell proliferation 0.043 0.032 -10000 0 -0.16 5 5
IL23-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
CCL2 -0.24 0.29 -10000 0 -1.1 12 12
IL23A -0.3 0.3 -10000 0 -0.98 17 17
NF kappa B1 p50/RelA/I kappa B alpha -0.26 0.29 -10000 0 -0.92 18 18
positive regulation of T cell mediated cytotoxicity -0.26 0.3 -10000 0 -0.97 18 18
ITGA3 -0.25 0.28 -10000 0 -0.95 13 13
IL17F -0.22 0.22 -10000 0 -0.64 26 26
IL12B -0.019 0.041 -10000 0 -0.39 1 1
STAT1 (dimer) -0.25 0.3 -10000 0 -0.94 18 18
CD4 -0.24 0.29 -10000 0 -0.95 15 15
IL23 -0.29 0.3 -10000 0 -0.95 17 17
IL23R -0.069 0.21 -10000 0 -0.97 10 10
IL1B -0.29 0.31 -10000 0 -1 16 16
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.27 0.29 -10000 0 -0.9 17 17
TYK2 -0.011 0.029 -10000 0 -10000 0 0
STAT4 0.023 0.02 -10000 0 -0.29 1 1
STAT3 0.023 0.006 -10000 0 -10000 0 0
IL18RAP 0.007 0.064 -10000 0 -0.29 10 10
IL12RB1 -0.023 0.066 -10000 0 -0.33 8 8
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.018 0.056 -10000 0 -0.24 7 7
IL23R/JAK2 -0.076 0.2 -10000 0 -0.94 9 9
positive regulation of chronic inflammatory response -0.26 0.3 -10000 0 -0.97 18 18
natural killer cell activation 0.005 0.01 0.077 3 -10000 0 3
JAK2 -0.014 0.033 -10000 0 -10000 0 0
PIK3R1 0.022 0.006 -10000 0 -10000 0 0
NFKB1 0.021 0.004 -10000 0 -10000 0 0
RELA 0.021 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.28 0.29 -10000 0 -0.91 17 17
ALOX12B -0.24 0.27 -10000 0 -0.94 12 12
CXCL1 -0.29 0.29 -10000 0 -0.93 16 16
T cell proliferation -0.26 0.3 -10000 0 -0.97 18 18
NFKBIA 0.02 0.006 -10000 0 -10000 0 0
IL17A -0.22 0.2 -10000 0 -0.53 34 34
PI3K -0.25 0.29 -10000 0 -0.92 18 18
IFNG -0.013 0.03 0.12 3 -0.12 2 5
STAT3 (dimer) -0.25 0.29 -10000 0 -0.89 19 19
IL18R1 0.018 0.031 -10000 0 -0.28 2 2
IL23/IL23R/JAK2/TYK2/SOCS3 -0.16 0.2 -10000 0 -0.74 10 10
IL18/IL18R 0.032 0.053 -10000 0 -0.16 10 10
macrophage activation -0.02 0.015 -10000 0 -0.043 11 11
TNF -0.28 0.29 -10000 0 -0.95 16 16
STAT3/STAT4 -0.24 0.29 -10000 0 -0.92 17 17
STAT4 (dimer) -0.25 0.3 -10000 0 -0.95 17 17
IL18 0.02 0.014 -10000 0 -10000 0 0
IL19 -0.24 0.27 -10000 0 -0.97 10 10
STAT5A (dimer) -0.24 0.3 -10000 0 -0.96 16 16
STAT1 0.017 0.053 -10000 0 -0.38 4 4
SOCS3 0.024 0.003 -10000 0 -10000 0 0
CXCL9 -0.27 0.3 -10000 0 -1 16 16
MPO -0.24 0.28 -10000 0 -0.92 14 14
positive regulation of humoral immune response -0.26 0.3 -10000 0 -0.97 18 18
IL23/IL23R/JAK2/TYK2 -0.26 0.31 -10000 0 -1 17 17
IL6 -0.25 0.32 -10000 0 -1 18 18
STAT5A 0.024 0.004 -10000 0 -10000 0 0
IL2 0.012 0.02 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.005 0.01 0.077 3 -10000 0 3
CD3E -0.26 0.33 -10000 0 -1.1 17 17
keratinocyte proliferation -0.26 0.3 -10000 0 -0.97 18 18
NOS2 -0.27 0.34 -10000 0 -1.1 21 21
Caspase cascade in apoptosis

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
TOP1 -0.04 0.09 -10000 0 -0.3 12 12
ACTA1 -0.061 0.095 -10000 0 -0.28 19 19
NUMA1 -0.043 0.096 -10000 0 -0.31 13 13
SPTAN1 -0.063 0.092 -10000 0 -0.29 16 16
LIMK1 -0.054 0.094 0.22 3 -0.3 13 16
BIRC3 0.02 0.034 -10000 0 -0.34 2 2
BIRC2 0.023 0.004 -10000 0 -10000 0 0
BAX 0.024 0.004 -10000 0 -10000 0 0
CASP10 -0.086 0.11 -10000 0 -0.24 74 74
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.024 0 -10000 0 -10000 0 0
PTK2 -0.041 0.093 -10000 0 -0.31 12 12
DIABLO 0.024 0.002 -10000 0 -10000 0 0
apoptotic nuclear changes -0.062 0.091 -10000 0 -0.29 16 16
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.024 0.003 -10000 0 -10000 0 0
GSN -0.064 0.094 -10000 0 -0.3 16 16
MADD 0.024 0.002 -10000 0 -10000 0 0
TFAP2A -0.003 0.064 -10000 0 -0.49 3 3
BID -0.035 0.062 -10000 0 -0.22 10 10
MAP3K1 -0.025 0.083 -10000 0 -0.46 6 6
TRADD 0.024 0.002 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.034 0.009 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.062 0.094 0.19 1 -0.29 16 17
CASP9 0.023 0.006 -10000 0 -10000 0 0
DNA repair 0.012 0.036 0.15 2 -10000 0 2
neuron apoptosis -0.008 0.13 -10000 0 -0.68 8 8
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.053 0.1 0.19 2 -0.3 16 18
APAF1 0.024 0.003 -10000 0 -10000 0 0
CASP6 -0.02 0.13 -10000 0 -0.88 4 4
TRAF2 0.024 0.002 -10000 0 -10000 0 0
ICAD/CAD -0.06 0.091 0.18 2 -0.29 15 17
CASP7 0.003 0.045 -10000 0 -0.23 6 6
KRT18 0.009 0.026 -10000 0 -10000 0 0
apoptosis -0.053 0.1 0.35 1 -0.32 15 16
DFFA -0.062 0.091 -10000 0 -0.29 16 16
DFFB -0.061 0.094 0.19 2 -0.29 16 18
PARP1 -0.012 0.037 -10000 0 -0.16 2 2
actin filament polymerization 0.058 0.096 0.28 17 -0.2 5 22
TNF 0.022 0.027 -10000 0 -0.38 1 1
CYCS -0.017 0.052 0.19 1 -0.16 5 6
SATB1 -0.024 0.12 -10000 0 -0.83 4 4
SLK -0.061 0.095 0.34 1 -0.29 16 17
p15 BID/BAX -0.022 0.064 -10000 0 -0.2 9 9
CASP2 0.024 0.045 0.2 10 -10000 0 10
JNK cascade 0.025 0.082 0.46 6 -10000 0 6
CASP3 -0.064 0.098 0.16 1 -0.29 19 20
LMNB2 0.017 0.057 -10000 0 -0.26 5 5
RIPK1 0.024 0.003 -10000 0 -10000 0 0
CASP4 0.024 0.004 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.058 0.025 -10000 0 -0.21 1 1
negative regulation of DNA binding -0.003 0.063 -10000 0 -0.49 3 3
stress fiber formation -0.06 0.094 0.34 1 -0.29 16 17
GZMB -0.088 0.14 -10000 0 -0.28 77 77
CASP1 0.012 0.002 -10000 0 -10000 0 0
LMNB1 0.006 0.1 -10000 0 -0.4 9 9
APP -0.008 0.14 -10000 0 -0.7 8 8
TNFRSF1A 0.024 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.006 0 -10000 0 -10000 0 0
VIM -0.051 0.1 -10000 0 -0.32 15 15
LMNA 0.018 0.054 0.17 4 -0.25 4 8
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.022 0.023 -10000 0 -10000 0 0
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.059 0.09 -10000 0 -0.28 16 16
APAF-1/Caspase 9 -0.022 0.14 -10000 0 -0.61 12 12
nuclear fragmentation during apoptosis -0.042 0.095 -10000 0 -0.31 13 13
CFL2 -0.06 0.097 0.2 5 -0.29 17 22
GAS2 -0.097 0.14 -10000 0 -0.36 35 35
positive regulation of apoptosis 0.018 0.074 0.18 4 -0.39 4 8
PRF1 0.016 0.051 -10000 0 -0.33 5 5
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.008 0.017 0.11 2 -10000 0 2
BUB1B 0.015 0.041 0.093 13 -0.12 5 18
PLK1 0.02 0.03 0.069 31 -0.11 2 33
PLK1S1 0.021 0.048 0.1 26 -0.17 7 33
KIF2A 0.016 0.031 0.18 2 -10000 0 2
regulation of mitotic centrosome separation 0.02 0.03 0.07 29 -0.11 2 31
GOLGA2 0.024 0.002 -10000 0 -10000 0 0
Hec1/SPC24 0.034 0.037 -10000 0 -0.17 3 3
WEE1 0.027 0.036 0.17 1 -10000 0 1
cytokinesis 0.021 0.039 0.19 1 -0.2 2 3
PP2A-alpha B56 0.046 0.084 -10000 0 -0.5 5 5
AURKA 0.025 0.029 0.12 6 -10000 0 6
PICH/PLK1 0.004 0.079 0.18 15 -0.2 9 24
CENPE 0.005 0.05 0.1 1 -0.18 11 12
RhoA/GTP 0.018 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.016 0.031 0.18 2 -10000 0 2
PPP2CA 0.023 0.004 -10000 0 -10000 0 0
FZR1 0.024 0.002 -10000 0 -10000 0 0
TPX2 0.044 0.056 0.12 76 -10000 0 76
PAK1 0.024 0.004 -10000 0 -10000 0 0
SPC24 0.019 0.046 -10000 0 -0.38 3 3
FBXW11 0.023 0.004 -10000 0 -10000 0 0
CLSPN 0.006 0.049 -10000 0 -0.22 8 8
GORASP1 0.024 0.002 -10000 0 -10000 0 0
metaphase 0 0.002 0.013 2 -10000 0 2
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.009 0.016 0.037 29 -0.058 2 31
G2 phase of mitotic cell cycle 0.001 0.003 0.01 6 -10000 0 6
STAG2 0.024 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.011 0.045 -10000 0 -0.45 2 2
spindle elongation 0.02 0.03 0.07 29 -0.11 2 31
ODF2 0.026 0.003 -10000 0 -10000 0 0
BUB1 0.014 0.079 -10000 0 -0.57 4 4
TPT1 0.023 0.041 0.095 31 -0.16 4 35
CDC25C 0.016 0.039 -10000 0 -0.24 4 4
CDC25B 0.003 0.14 0.31 14 -0.38 20 34
SGOL1 0.008 0.017 -10000 0 -0.11 2 2
RHOA 0.024 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.029 0.069 0.21 14 -0.17 1 15
CDC14B 0.006 0.004 -10000 0 -10000 0 0
CDC20 0.022 0.027 -10000 0 -0.38 1 1
PLK1/PBIP1 0.013 0.026 0.085 1 -0.19 1 2
mitosis -0.002 0.002 -10000 0 -10000 0 0
FBXO5 0.013 0.033 0.13 2 -0.12 2 4
CDC2 0.002 0.004 0.014 14 -10000 0 14
NDC80 0.02 0.009 -10000 0 -10000 0 0
metaphase plate congression 0.004 0.065 -10000 0 -0.22 16 16
ERCC6L 0.007 0.077 0.18 14 -0.2 9 23
NLP/gamma Tubulin 0.01 0.018 0.069 4 -0.07 2 6
microtubule cytoskeleton organization 0.023 0.041 0.095 30 -0.16 4 34
G2/M transition DNA damage checkpoint 0 0.002 0.013 3 -10000 0 3
PPP1R12A 0.025 0.003 -10000 0 -10000 0 0
interphase 0 0.002 0.013 3 -10000 0 3
PLK1/PRC1-2 0.041 0.036 -10000 0 -0.2 2 2
GRASP65/GM130/RAB1/GTP/PLK1 0.053 0.026 -10000 0 -10000 0 0
RAB1A 0.024 0.002 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.023 0.032 0.065 78 -0.073 1 79
mitotic prometaphase 0.001 0.005 0.018 16 -10000 0 16
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.026 -10000 0 -0.21 2 2
microtubule-based process 0.028 0.035 0.11 1 -0.2 2 3
Golgi organization 0.02 0.03 0.07 29 -0.11 2 31
Cohesin/SA2 0.029 0.024 0.1 1 -10000 0 1
PPP1CB/MYPT1 0.036 0.005 -10000 0 -10000 0 0
KIF20A 0.02 0.038 -10000 0 -0.38 2 2
APC/C/CDC20 0.03 0.032 0.11 1 -0.2 1 2
PPP2R1A 0.024 0.003 -10000 0 -10000 0 0
chromosome segregation 0.013 0.026 0.084 1 -0.18 1 2
PRC1 0.023 0.004 -10000 0 -10000 0 0
ECT2 -0.001 0.061 0.1 1 -0.18 19 20
C13orf34 0.019 0.027 0.064 31 -0.079 2 33
NUDC 0.004 0.065 -10000 0 -0.22 16 16
regulation of attachment of spindle microtubules to kinetochore 0.015 0.041 0.087 26 -0.12 5 31
spindle assembly 0.015 0.025 0.092 5 -0.093 2 7
spindle stabilization 0.021 0.048 0.1 26 -0.17 7 33
APC/C/HCDH1 0.023 0.003 -10000 0 -10000 0 0
MKLP2/PLK1 0.028 0.036 0.11 1 -0.2 2 3
CCNB1 0.02 0.038 -10000 0 -0.38 2 2
PPP1CB 0.025 0.002 -10000 0 -10000 0 0
BTRC 0.023 0.005 -10000 0 -10000 0 0
ROCK2 0.022 0.033 -10000 0 -0.28 1 1
TUBG1 0.015 0.023 -10000 0 -0.15 2 2
G2/M transition of mitotic cell cycle 0.008 0.061 0.18 14 -0.16 1 15
MLF1IP 0.003 0.019 -10000 0 -0.27 1 1
INCENP 0.024 0.004 -10000 0 -10000 0 0
Ceramide signaling pathway

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
SPHK2 0.01 0.004 -10000 0 -10000 0 0
MAP4K4 0.017 0.026 -10000 0 -10000 0 0
BAG4 0.02 0.009 -10000 0 -10000 0 0
PKC zeta/ceramide -0.022 0.069 -10000 0 -0.19 30 30
NFKBIA 0.023 0.006 -10000 0 -10000 0 0
BIRC3 0.02 0.034 -10000 0 -0.34 2 2
BAX -0.007 0.042 -10000 0 -0.34 2 2
RIPK1 0.024 0.003 -10000 0 -10000 0 0
AKT1 -0.001 0.012 -10000 0 -10000 0 0
BAD -0.035 0.063 -10000 0 -0.19 31 31
SMPD1 0.021 0.035 0.15 3 -10000 0 3
RB1 0.003 0.089 0.18 34 -0.18 19 53
FADD/Caspase 8 0.024 0.022 -10000 0 -10000 0 0
MAP2K4 -0.032 0.059 -10000 0 -0.18 24 24
NSMAF 0.021 0.008 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.032 0.063 0.17 3 -0.18 29 32
EGF -0.061 0.14 -10000 0 -0.32 56 56
mol:ceramide -0.034 0.067 -10000 0 -0.2 31 31
MADD 0.024 0.002 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.008 0.005 -10000 0 -10000 0 0
ASAH1 0.018 0.01 -10000 0 -10000 0 0
negative regulation of cell cycle 0.003 0.088 0.18 34 -0.18 19 53
cell proliferation -0.036 0.078 -10000 0 -0.23 10 10
BID 0.006 0.11 -10000 0 -0.63 6 6
MAP3K1 -0.034 0.063 -10000 0 -0.19 31 31
EIF2A -0.035 0.059 0.17 1 -0.21 5 6
TRADD 0.024 0.002 -10000 0 -10000 0 0
CRADD 0.024 0.003 -10000 0 -10000 0 0
MAPK3 -0.028 0.06 0.19 2 -0.2 4 6
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.032 0.062 0.19 1 -0.21 6 7
Cathepsin D/ceramide -0.022 0.07 -10000 0 -0.19 31 31
FADD 0.018 0.022 -10000 0 -10000 0 0
KSR1 -0.031 0.067 0.18 3 -0.19 30 33
MAPK8 -0.027 0.064 -10000 0 -0.2 7 7
PRKRA -0.035 0.063 -10000 0 -0.19 31 31
PDGFA 0.021 0.008 -10000 0 -10000 0 0
TRAF2 0.024 0.002 -10000 0 -10000 0 0
IGF1 -0.042 0.13 -10000 0 -0.29 48 48
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.034 0.067 -10000 0 -0.2 31 31
CTSD 0.024 0.003 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.034 0.008 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.038 0.083 -10000 0 -0.25 10 10
PRKCD 0.023 0.004 -10000 0 -10000 0 0
PRKCZ 0.023 0.005 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.008 0.005 -10000 0 -10000 0 0
RelA/NF kappa B1 0.034 0.008 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.024 0.002 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.023 0.009 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.04 0.019 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.01 0.004 -10000 0 -10000 0 0
MAP2K1 -0.032 0.061 0.19 2 -0.18 19 21
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.023 0.004 -10000 0 -10000 0 0
CYCS 0.011 0.044 0.14 3 -10000 0 3
TNFRSF1A 0.024 0.004 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.03 0.014 -10000 0 -10000 0 0
EIF2AK2 -0.035 0.062 0.18 1 -0.18 30 31
TNF-alpha/TNFR1A/FAN 0.042 0.017 -10000 0 -10000 0 0
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.025 0.049 -10000 0 -0.29 1 1
MAP2K2 -0.033 0.06 0.17 2 -0.2 5 7
SMPD3 0.021 0.037 0.19 1 -0.25 2 3
TNF 0.022 0.027 -10000 0 -0.38 1 1
PKC zeta/PAR4 0.034 0.008 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.024 0.079 0.16 38 -0.12 16 54
NF kappa B1/RelA/I kappa B alpha 0.062 0.025 -10000 0 -10000 0 0
AIFM1 0.002 0.056 0.13 2 -0.14 4 6
BCL2 0.016 0.03 -10000 0 -0.29 2 2
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.024 0.003 -10000 0 -10000 0 0
SPHK1 -0.035 0.14 -10000 0 -0.38 33 33
GNAI2 0.024 0.004 -10000 0 -10000 0 0
mol:S1P -0.003 0.039 -10000 0 -10000 0 0
GNAO1 -0.12 0.16 -10000 0 -0.29 103 103
mol:Sphinganine-1-P -0.029 0.098 -10000 0 -0.27 33 33
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.028 0.049 -10000 0 -10000 0 0
GNAI3 0.023 0.004 -10000 0 -10000 0 0
G12/G13 0.031 0.012 -10000 0 -10000 0 0
S1PR3 0.024 0.002 -10000 0 -10000 0 0
S1PR2 0.024 0.002 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P -0.006 0.034 -10000 0 -10000 0 0
S1PR5 0.006 0.083 -10000 0 -0.38 10 10
S1PR4 0.017 0.045 -10000 0 -0.29 5 5
GNAI1 0.018 0.041 -10000 0 -0.29 4 4
S1P/S1P5/G12 0.01 0.067 0.18 1 -0.23 10 11
S1P/S1P3/Gq 0.014 0.044 -10000 0 -0.29 2 2
S1P/S1P4/Gi -0.067 0.11 -10000 0 -0.31 19 19
GNAQ 0.024 0.002 -10000 0 -10000 0 0
GNAZ 0.018 0.041 -10000 0 -0.29 4 4
GNA14 0.023 0.021 -10000 0 -0.29 1 1
GNA15 -0.001 0.097 -10000 0 -0.38 14 14
GNA12 0.021 0.008 -10000 0 -10000 0 0
GNA13 0.024 0.004 -10000 0 -10000 0 0
GNA11 0.024 0.002 -10000 0 -10000 0 0
ABCC1 0.024 0.002 -10000 0 -10000 0 0
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.011 0.039 -10000 0 -0.38 2 2
GNB1/GNG2 -0.05 0.044 -10000 0 -0.17 5 5
AKT1 -0.041 0.079 0.19 1 -0.26 13 14
EGF -0.061 0.14 -10000 0 -0.32 56 56
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR -0.053 0.061 -10000 0 -0.24 1 1
mol:Ca2+ -0.055 0.086 -10000 0 -0.3 10 10
LYN -0.045 0.058 -10000 0 -10000 0 0
RhoA/GTP -0.026 0.038 -10000 0 -0.13 2 2
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.064 0.089 -10000 0 -0.32 6 6
GNG2 0.019 0.036 -10000 0 -0.29 3 3
ARRB2 0.02 0.009 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.011 0.053 -10000 0 -0.29 3 3
G beta5/gamma2 -0.059 0.057 -10000 0 -0.24 3 3
PRKCH -0.058 0.091 -10000 0 -0.34 7 7
DNM1 0.024 0.002 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin3 -0.006 0.044 -10000 0 -0.63 1 1
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.12 0.16 -10000 0 -0.29 103 103
G12 family/GTP -0.058 0.075 -10000 0 -0.28 6 6
ADRBK1 0.023 0.004 -10000 0 -10000 0 0
ADRBK2 0.023 0.004 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.027 0.012 -10000 0 -10000 0 0
mol:GDP 0.06 0.089 0.3 15 -10000 0 15
mol:NADP 0.022 0.033 0.31 1 -0.38 1 2
RAB11A 0.023 0.004 -10000 0 -10000 0 0
PRKG1 0.009 0.066 -10000 0 -0.29 11 11
mol:IP3 -0.068 0.1 -10000 0 -0.37 10 10
cell morphogenesis 0.027 0.011 -10000 0 -10000 0 0
PLCB2 -0.09 0.13 -10000 0 -0.51 10 10
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.054 0.086 -10000 0 -0.23 35 35
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.033 0.053 -10000 0 -10000 0 0
RHOA 0.024 0.004 -10000 0 -10000 0 0
PTGIR 0.024 0.004 -10000 0 -10000 0 0
PRKCB1 -0.063 0.098 -10000 0 -0.35 8 8
GNAQ 0.024 0.002 -10000 0 -10000 0 0
mol:L-citrulline 0.022 0.033 0.31 1 -0.38 1 2
TXA2/TXA2-R family -0.088 0.12 -10000 0 -0.48 6 6
LCK -0.059 0.066 -10000 0 -0.26 3 3
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.052 0.084 -10000 0 -0.19 1 1
TXA2-R family/G12 family/GDP/G beta/gamma -0.016 0.099 -10000 0 -0.48 9 9
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.046 0.082 -10000 0 -0.19 1 1
MAPK14 -0.046 0.063 -10000 0 -0.22 5 5
TGM2/GTP -0.078 0.1 -10000 0 -0.4 10 10
MAPK11 -0.045 0.063 -10000 0 -0.22 4 4
ARHGEF1 -0.036 0.049 -10000 0 -0.18 4 4
GNAI2 0.024 0.004 -10000 0 -10000 0 0
JNK cascade -0.069 0.098 -10000 0 -0.35 6 6
RAB11/GDP 0.024 0.004 -10000 0 -10000 0 0
ICAM1 -0.05 0.077 -10000 0 -0.27 6 6
cAMP biosynthetic process -0.07 0.098 -10000 0 -0.34 10 10
Gq family/GTP/EBP50 0.009 0.029 -10000 0 -0.18 2 2
actin cytoskeleton reorganization 0.027 0.011 -10000 0 -10000 0 0
SRC -0.035 0.054 -10000 0 -10000 0 0
GNB5 0.023 0.004 -10000 0 -10000 0 0
GNB1 0.023 0.005 -10000 0 -10000 0 0
EGF/EGFR -0.046 0.088 0.19 2 -0.23 16 18
VCAM1 -0.053 0.078 -10000 0 -0.32 3 3
TP beta/Gq family/GDP/G beta5/gamma2 -0.011 0.053 -10000 0 -0.29 3 3
platelet activation -0.058 0.083 -10000 0 -0.29 6 6
PGI2/IP 0.017 0.003 -10000 0 -10000 0 0
PRKACA -0.063 0.089 -10000 0 -0.16 98 98
Gq family/GDP/G beta5/gamma2 -0.018 0.055 -10000 0 -0.24 7 7
TXA2/TP beta/beta Arrestin2 -0.022 0.058 -10000 0 -0.22 6 6
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.063 0.082 -10000 0 -0.16 98 98
mol:DAG -0.07 0.11 -10000 0 -0.4 8 8
EGFR 0.021 0.008 -10000 0 -10000 0 0
TXA2/TP alpha -0.09 0.13 -10000 0 -0.47 10 10
Gq family/GTP 0.006 0.027 -10000 0 -0.17 2 2
YES1 -0.045 0.059 -10000 0 -10000 0 0
GNAI2/GTP -0.047 0.077 -10000 0 -10000 0 0
PGD2/DP -0.078 0.1 -10000 0 -0.2 103 103
SLC9A3R1 0.024 0.004 -10000 0 -10000 0 0
FYN -0.053 0.06 -10000 0 -10000 0 0
mol:NO 0.022 0.033 0.31 1 -0.38 1 2
GNA15 -0.001 0.097 -10000 0 -0.38 14 14
PGK/cGMP 0.021 0.047 0.21 1 -0.17 12 13
RhoA/GDP 0.024 0.004 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.022 0.08 -10000 0 -0.28 2 2
NOS3 0.022 0.033 0.31 1 -0.38 1 2
RAC1 0.021 0.008 -10000 0 -10000 0 0
PRKCA -0.06 0.093 0.24 1 -0.34 7 8
PRKCB -0.075 0.098 -10000 0 -0.36 9 9
PRKCE -0.057 0.092 -10000 0 -0.35 5 5
PRKCD -0.06 0.095 -10000 0 -0.35 6 6
PRKCG -0.091 0.12 -10000 0 -0.34 12 12
muscle contraction -0.086 0.12 -10000 0 -0.44 8 8
PRKCZ -0.062 0.089 -10000 0 -0.32 5 5
ARR3 -0.011 0.029 -10000 0 -0.38 1 1
TXA2/TP beta -0.047 0.086 -10000 0 -10000 0 0
PRKCQ -0.059 0.094 -10000 0 -0.34 6 6
MAPKKK cascade -0.079 0.12 -10000 0 -0.43 9 9
SELE -0.067 0.092 -10000 0 -0.28 9 9
TP beta/GNAI2/GDP/G beta/gamma -0.04 0.095 -10000 0 -0.25 3 3
ROCK1 0.021 0.008 -10000 0 -10000 0 0
GNA14 0.023 0.021 -10000 0 -0.29 1 1
chemotaxis -0.092 0.13 -10000 0 -0.51 5 5
GNA12 0.021 0.008 -10000 0 -10000 0 0
GNA13 0.024 0.004 -10000 0 -10000 0 0
GNA11 0.024 0.002 -10000 0 -10000 0 0
Rac1/GTP 0.015 0.006 -10000 0 -10000 0 0
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 0.016 0.053 -10000 0 -0.38 4 4
Jak2/Leptin Receptor 0.015 0.076 -10000 0 -0.34 4 4
PTP1B/AKT1 0.011 0.071 0.17 5 -0.27 2 7
FYN 0.024 0.004 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.008 0.075 0.18 7 -0.28 2 9
EGFR 0.015 0.017 -10000 0 -10000 0 0
EGF/EGFR -0.019 0.096 -10000 0 -0.23 18 18
CSF1 0.022 0.021 -10000 0 -0.29 1 1
AKT1 0.023 0.006 -10000 0 -10000 0 0
INSR 0.024 0.003 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.001 0.077 0.18 3 -0.26 9 12
Insulin Receptor/Insulin 0.016 0.066 -10000 0 -0.24 2 2
HCK 0.015 0.012 -10000 0 -10000 0 0
CRK 0.02 0.009 -10000 0 -10000 0 0
TYK2 0.005 0.073 0.19 7 -0.27 2 9
EGF -0.054 0.14 -10000 0 -0.32 51 51
YES1 0.02 0.009 -10000 0 -10000 0 0
CAV1 0.017 0.1 0.22 16 -0.26 4 20
TXN 0.024 0.003 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.019 0.079 0.19 5 -0.33 1 6
cell migration -0.008 0.075 0.28 2 -0.18 7 9
STAT3 0.024 0.004 -10000 0 -10000 0 0
PRLR 0.015 0.05 -10000 0 -0.29 6 6
ITGA2B 0.005 0.075 -10000 0 -0.38 8 8
CSF1R 0.017 0.045 -10000 0 -0.29 5 5
Prolactin Receptor/Prolactin 0.009 0.075 -10000 0 -0.25 18 18
FGR 0.019 0.034 -10000 0 -0.34 2 2
PTP1B/p130 Cas 0.013 0.075 0.18 5 -0.27 2 7
Crk/p130 Cas 0.009 0.071 0.19 4 -0.33 1 5
DOK1 0.011 0.072 0.17 6 -0.29 2 8
JAK2 0.011 0.076 -10000 0 -0.31 5 5
Jak2/Leptin Receptor/Leptin 0.009 0.083 -10000 0 -0.29 2 2
PIK3R1 0.023 0.005 -10000 0 -10000 0 0
PTPN1 0.008 0.075 0.18 7 -0.28 2 9
LYN 0.021 0.008 -10000 0 -10000 0 0
CDH2 0.001 0.078 -10000 0 -0.33 12 12
SRC 0.024 0.088 -10000 0 -0.44 6 6
ITGB3 0.017 0.046 -10000 0 -0.29 5 5
CAT1/PTP1B 0 0.15 0.24 26 -0.36 9 35
CAPN1 0.023 0.004 -10000 0 -10000 0 0
CSK 0.023 0.004 -10000 0 -10000 0 0
PI3K 0.032 0.063 -10000 0 -0.26 1 1
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.01 0.077 -10000 0 -0.28 1 1
negative regulation of transcription 0.011 0.075 -10000 0 -0.31 5 5
FCGR2A 0.02 0.038 -10000 0 -0.38 2 2
FER 0.022 0.006 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.018 0.064 -10000 0 -0.24 13 13
BLK -0.078 0.14 -10000 0 -0.29 70 70
Insulin Receptor/Insulin/Shc 0.04 0.012 -10000 0 -10000 0 0
RHOA 0.023 0.004 -10000 0 -10000 0 0
LEPR 0.022 0.021 -10000 0 -0.29 1 1
BCAR1 0.024 0.002 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.024 0.004 -10000 0 -10000 0 0
mol:NADPH 0 0.003 -10000 0 -10000 0 0
TRPV6 -0.062 0.16 0.25 6 -0.33 34 40
PRL -0.014 0.089 -10000 0 -0.38 12 12
SOCS3 0.012 0.1 -10000 0 -1 2 2
SPRY2 0.02 0.01 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.041 0.01 -10000 0 -10000 0 0
CSF1/CSF1R 0.016 0.082 0.19 6 -0.26 4 10
Ras protein signal transduction -0.005 0.048 0.43 2 -10000 0 2
IRS1 0.024 0 -10000 0 -10000 0 0
INS -0.008 0.015 -10000 0 -10000 0 0
LEP -0.029 0.11 -10000 0 -0.32 28 28
STAT5B 0.013 0.072 0.17 6 -0.28 3 9
STAT5A 0.013 0.072 0.17 6 -0.28 3 9
GRB2 0.024 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.01 0.082 0.18 6 -0.3 4 10
CSN2 -0.011 0.05 -10000 0 -10000 0 0
PIK3CA 0.024 0.002 -10000 0 -10000 0 0
LAT 0.027 0.034 -10000 0 -10000 0 0
YBX1 0.032 0.007 -10000 0 -10000 0 0
LCK 0.009 0.074 -10000 0 -0.38 8 8
SHC1 0.023 0.004 -10000 0 -10000 0 0
NOX4 -0.2 0.2 0.31 1 -0.38 127 128
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 0.016 0.053 -10000 0 -0.38 4 4
alphaV beta3 Integrin 0.03 0.034 -10000 0 -0.2 5 5
PTK2 0.012 0.063 -10000 0 -0.3 5 5
positive regulation of JNK cascade 0.024 0.061 -10000 0 -0.26 4 4
CDC42/GDP 0.051 0.087 -10000 0 -0.34 4 4
Rac1/GDP 0.044 0.085 -10000 0 -0.33 4 4
RAP1B 0.024 0.002 -10000 0 -10000 0 0
RAP1A 0.023 0.004 -10000 0 -10000 0 0
CTNNB1 0.024 0.002 -10000 0 -10000 0 0
CDC42/GTP 0.04 0.077 -10000 0 -0.31 4 4
nectin-3/I-afadin 0.029 0.037 -10000 0 -0.2 6 6
RAPGEF1 0.026 0.086 -10000 0 -0.35 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.003 0.08 -10000 0 -0.37 8 8
PDGFB-D/PDGFRB 0.016 0.053 -10000 0 -0.38 4 4
TLN1 -0.002 0.027 -10000 0 -0.26 2 2
Rap1/GTP 0.017 0.063 -10000 0 -0.28 4 4
IQGAP1 0.023 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.044 0.01 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.029 0.037 -10000 0 -0.2 6 6
PVR 0.024 0.003 -10000 0 -10000 0 0
Necl-5(dimer) 0.024 0.003 -10000 0 -10000 0 0
mol:GDP 0.045 0.098 -10000 0 -0.4 4 4
MLLT4 0.024 0.004 -10000 0 -10000 0 0
PIK3CA 0.024 0.002 -10000 0 -10000 0 0
PI3K 0.056 0.05 -10000 0 -0.2 4 4
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.034 0.007 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.021 0.066 -10000 0 -0.26 5 5
PVRL1 0.024 0.003 -10000 0 -10000 0 0
PVRL3 0.016 0.05 -10000 0 -0.29 6 6
PVRL2 0.024 0.003 -10000 0 -10000 0 0
PIK3R1 0.023 0.005 -10000 0 -10000 0 0
CDH1 0.024 0.002 -10000 0 -10000 0 0
CLDN1 -0.35 0.11 -10000 0 -0.38 214 214
JAM-A/CLDN1 -0.18 0.082 -10000 0 -0.21 206 206
SRC 0.003 0.09 -10000 0 -0.39 10 10
ITGB3 0.017 0.045 -10000 0 -0.29 5 5
nectin-1(dimer)/I-afadin/I-afadin 0.034 0.007 -10000 0 -10000 0 0
FARP2 0.046 0.094 -10000 0 -0.39 4 4
RAC1 0.021 0.008 -10000 0 -10000 0 0
CTNNA1 0.024 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.041 0.035 -10000 0 -0.16 6 6
nectin-1/I-afadin 0.034 0.007 -10000 0 -10000 0 0
nectin-2/I-afadin 0.034 0.007 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.028 0.011 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.041 0.035 -10000 0 -10000 0 0
CDC42/GTP/IQGAP1/filamentous actin 0.03 0.009 -10000 0 -10000 0 0
F11R 0.023 0.004 -10000 0 -10000 0 0
positive regulation of filopodium formation 0.024 0.061 -10000 0 -0.26 4 4
alphaV/beta3 Integrin/Talin 0.007 0.065 0.19 2 -0.24 3 5
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.034 0.007 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.034 0.007 -10000 0 -10000 0 0
PIP5K1C 0.001 0.031 -10000 0 -0.28 2 2
VAV2 0.042 0.1 -10000 0 -0.4 5 5
RAP1/GDP 0.052 0.084 -10000 0 -0.32 4 4
ITGAV 0.024 0 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.041 0.035 -10000 0 -0.16 6 6
nectin-3(dimer)/I-afadin/I-afadin 0.029 0.037 -10000 0 -0.2 6 6
Rac1/GTP 0.033 0.082 -10000 0 -0.32 4 4
PTPRM 0.008 0.019 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin 0.066 0.02 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.023 0.006 -10000 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.035 0.15 -10000 0 -0.41 30 30
NFATC2 0.01 0.085 -10000 0 -0.6 1 1
NFATC3 -0.021 0.06 -10000 0 -0.27 3 3
CD40LG -0.15 0.24 -10000 0 -0.7 15 15
ITCH 0.018 0.014 -10000 0 -10000 0 0
CBLB 0.028 0.007 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.1 0.17 -10000 0 -0.7 8 8
JUNB 0.024 0.002 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.035 0.008 -10000 0 -10000 0 0
T cell anergy 0.031 0.043 -10000 0 -10000 0 0
TLE4 0.006 0.055 -10000 0 -0.42 1 1
Jun/NFAT1-c-4/p21SNFT -0.065 0.15 -10000 0 -0.72 2 2
AP-1/NFAT1-c-4 -0.17 0.23 -10000 0 -0.73 12 12
IKZF1 0.001 0.083 -10000 0 -0.54 4 4
T-helper 2 cell differentiation -0.039 0.14 -10000 0 -0.71 5 5
AP-1/NFAT1 -0.026 0.089 -10000 0 -0.44 1 1
CALM1 0.032 0.007 -10000 0 -10000 0 0
EGR2 -0.025 0.12 -10000 0 -1.3 1 1
EGR3 -0.029 0.13 -10000 0 -0.81 4 4
NFAT1/FOXP3 -0.018 0.12 -10000 0 -0.44 7 7
EGR1 0.021 0.034 -10000 0 -0.34 2 2
JUN -0.03 0.041 -10000 0 -10000 0 0
EGR4 -0.069 0.17 -10000 0 -0.38 51 51
mol:Ca2+ 0.009 0.001 -10000 0 -10000 0 0
GBP3 -0.002 0.09 -10000 0 -0.53 5 5
FOSL1 -0.22 0.2 -10000 0 -0.38 138 138
NFAT1-c-4/MAF/IRF4 -0.044 0.13 -10000 0 -0.76 2 2
DGKA 0.005 0.055 -10000 0 -0.42 1 1
CREM 0.024 0.002 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.029 0.12 -10000 0 -0.86 1 1
CTLA4 -0.038 0.13 -10000 0 -0.4 18 18
NFAT1-c-4 (dimer)/EGR1 -0.029 0.12 -10000 0 -0.85 1 1
NFAT1-c-4 (dimer)/EGR4 -0.063 0.14 -10000 0 -0.85 1 1
FOS -0.028 0.041 -10000 0 -10000 0 0
IFNG -0.046 0.14 -10000 0 -0.62 6 6
T cell activation -0.004 0.12 -10000 0 -10000 0 0
MAF 0.023 0.021 -10000 0 -0.29 1 1
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.025 0.1 1.1 1 -10000 0 1
TNF -0.057 0.12 -10000 0 -0.78 1 1
FASLG -0.049 0.25 -10000 0 -1.1 10 10
TBX21 0.004 0.066 -10000 0 -0.3 8 8
BATF3 0.015 0.059 -10000 0 -0.38 5 5
PRKCQ 0.013 0.062 -10000 0 -0.37 5 5
PTPN1 0.005 0.055 -10000 0 -0.42 1 1
NFAT1-c-4/ICER1 -0.03 0.12 -10000 0 -0.86 1 1
GATA3 0.018 0.047 -10000 0 -0.34 4 4
T-helper 1 cell differentiation -0.044 0.14 -10000 0 -0.61 6 6
IL2RA -0.093 0.17 -10000 0 -0.64 10 10
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.004 0.055 -10000 0 -0.42 1 1
E2F1 0.023 0.041 0.32 4 -10000 0 4
PPARG 0.024 0.002 -10000 0 -10000 0 0
SLC3A2 0.006 0.054 -10000 0 -0.42 1 1
IRF4 -0.05 0.13 -10000 0 -0.29 55 55
PTGS2 -0.14 0.24 -10000 0 -0.68 15 15
CSF2 -0.2 0.29 -10000 0 -0.66 35 35
JunB/Fra1/NFAT1-c-4 -0.12 0.15 -10000 0 -0.67 3 3
IL4 -0.041 0.14 -10000 0 -0.74 5 5
IL5 -0.14 0.23 -10000 0 -0.69 12 12
IL2 -0.005 0.12 -10000 0 -10000 0 0
IL3 -0.031 0.08 -10000 0 -0.52 4 4
RNF128 0.027 0.006 -10000 0 -10000 0 0
NFATC1 -0.025 0.1 -10000 0 -1.1 1 1
CDK4 0.015 0.073 0.72 1 -10000 0 1
PTPRK 0.006 0.054 -10000 0 -0.42 1 1
IL8 -0.24 0.28 -10000 0 -0.67 34 34
POU2F1 0.023 0.004 -10000 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.023 0.013 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 0.009 0.005 -10000 0 -10000 0 0
mol:DAG 0.013 0.057 0.19 14 -10000 0 14
VEGFR1 homodimer/NRP1/VEGFR 121 0.017 0.047 0.2 1 -0.2 8 9
CaM/Ca2+ 0.022 0.055 -10000 0 -10000 0 0
HIF1A 0.029 0.007 -10000 0 -10000 0 0
GAB1 0.023 0.004 -10000 0 -10000 0 0
AKT1 0.031 0.073 -10000 0 -10000 0 0
PLCG1 0.013 0.057 0.19 14 -10000 0 14
NOS3 0.072 0.1 0.3 28 -10000 0 28
CBL 0.024 0.003 -10000 0 -10000 0 0
mol:NO 0.074 0.1 0.29 29 -10000 0 29
FLT1 0.013 0.007 -10000 0 -10000 0 0
PGF 0.005 0.083 -10000 0 -0.38 10 10
VEGFR1 homodimer/NRP2/VEGFR121 0.028 0.054 0.22 1 -10000 0 1
CALM1 0.023 0.005 -10000 0 -10000 0 0
PIK3CA 0.024 0.002 -10000 0 -10000 0 0
eNOS/Hsp90 0.083 0.1 0.29 29 -10000 0 29
endothelial cell proliferation 0.039 0.11 0.32 21 -10000 0 21
mol:Ca2+ 0.013 0.057 0.19 14 -10000 0 14
MAPK3 0 0.052 0.17 14 -10000 0 14
MAPK1 -0.001 0.051 0.17 13 -10000 0 13
PIK3R1 0.023 0.005 -10000 0 -10000 0 0
PLGF homodimer 0.005 0.083 -10000 0 -0.38 10 10
PRKACA 0.024 0.002 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.016 0.045 -10000 0 -0.29 5 5
VEGFA homodimer 0.001 0.099 0.31 1 -0.38 14 15
VEGFR1 homodimer/VEGFA homodimer 0.018 0.052 0.22 1 -0.22 8 9
platelet activating factor biosynthetic process 0.037 0.12 0.28 40 -10000 0 40
PI3K 0.034 0.049 -10000 0 -10000 0 0
PRKCA 0.001 0.055 0.18 14 -10000 0 14
PRKCB -0.014 0.061 0.18 9 -10000 0 9
VEGFR1 homodimer/PLGF homodimer 0.015 0.048 -10000 0 -0.22 8 8
VEGFA 0.001 0.099 0.31 1 -0.38 14 15
VEGFB 0.023 0.004 -10000 0 -10000 0 0
mol:IP3 0.013 0.057 0.19 14 -10000 0 14
RASA1 0.044 0.071 0.19 42 -10000 0 42
NRP2 0.022 0.027 -10000 0 -0.38 1 1
VEGFR1 homodimer 0.013 0.007 -10000 0 -10000 0 0
VEGFB homodimer 0.023 0.004 -10000 0 -10000 0 0
NCK1 0.024 0.002 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.073 0.093 0.28 23 -10000 0 23
PTPN11 0.024 0.003 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.033 0.048 -10000 0 -10000 0 0
mol:L-citrulline 0.074 0.1 0.29 29 -10000 0 29
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.038 0.053 0.22 1 -10000 0 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.029 0.051 0.22 1 -10000 0 1
CD2AP 0.024 0.002 -10000 0 -10000 0 0
PI3K/GAB1 0.071 0.067 -10000 0 -10000 0 0
PDPK1 0.034 0.076 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.029 0.051 0.22 1 -10000 0 1
mol:NADP 0.074 0.1 0.29 29 -10000 0 29
HSP90AA1 0.023 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.037 0.052 0.22 1 -10000 0 1
VEGFR1 homodimer/NRP2 0.022 0.021 -10000 0 -0.22 1 1
S1P3 pathway

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
PDGFRB 0.016 0.053 -10000 0 -0.38 4 4
mol:S1P 0.001 0.002 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.063 0.1 -10000 0 -0.29 19 19
GNAO1 -0.12 0.16 -10000 0 -0.29 103 103
S1P/S1P3/G12/G13 0.04 0.019 -10000 0 -10000 0 0
AKT1 -0.034 0.12 -10000 0 -0.46 15 15
AKT3 -0.029 0.14 -10000 0 -1.1 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.016 0.053 -10000 0 -0.38 4 4
GNAI2 0.024 0.008 -10000 0 -10000 0 0
GNAI3 0.024 0.007 -10000 0 -10000 0 0
GNAI1 0.018 0.042 -10000 0 -0.29 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.024 0.007 -10000 0 -10000 0 0
S1PR2 0.024 0.002 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.063 0.12 -10000 0 -0.32 18 18
MAPK3 -0.063 0.11 -10000 0 -0.3 18 18
MAPK1 -0.057 0.1 -10000 0 -0.32 13 13
JAK2 -0.025 0.12 0.22 3 -0.3 14 17
CXCR4 -0.068 0.11 -10000 0 -0.3 20 20
FLT1 0.019 0.013 -10000 0 -10000 0 0
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.016 0.006 -10000 0 -10000 0 0
SRC -0.042 0.09 -10000 0 -0.29 11 11
S1P/S1P3/Gi -0.063 0.12 -10000 0 -0.32 18 18
RAC1 0.021 0.008 -10000 0 -10000 0 0
RhoA/GTP -0.054 0.11 -10000 0 -0.29 18 18
VEGFA 0.001 0.1 0.32 1 -0.38 14 15
S1P/S1P2/Gi -0.063 0.11 -10000 0 -0.3 18 18
VEGFR1 homodimer/VEGFA homodimer 0.02 0.06 0.24 1 -0.27 8 9
RHOA 0.024 0.004 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.016 0.029 -10000 0 -0.17 1 1
GNAQ 0.024 0.002 -10000 0 -10000 0 0
GNAZ 0.018 0.041 -10000 0 -0.29 4 4
G12/G13 0.031 0.012 -10000 0 -10000 0 0
GNA14 0.023 0.021 -10000 0 -0.29 1 1
GNA15 -0.001 0.097 -10000 0 -0.38 14 14
GNA12 0.021 0.008 -10000 0 -10000 0 0
GNA13 0.024 0.004 -10000 0 -10000 0 0
GNA11 0.024 0.002 -10000 0 -10000 0 0
Rac1/GTP -0.049 0.11 -10000 0 -0.29 18 18
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.09 0.15 -10000 0 -0.29 84 84
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.024 0.003 -10000 0 -10000 0 0
TCEB1 0.021 0.008 -10000 0 -10000 0 0
HIF1A/p53 0.013 0.05 0.18 1 -0.24 7 8
HIF1A 0.003 0.045 -10000 0 -0.26 6 6
COPS5 0.021 0.008 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.059 0.028 -10000 0 -10000 0 0
FIH (dimer) 0.023 0.005 -10000 0 -10000 0 0
CDKN2A -0.092 0.18 -10000 0 -0.39 65 65
ARNT/IPAS -0.049 0.11 -10000 0 -0.2 82 82
HIF1AN 0.023 0.005 -10000 0 -10000 0 0
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
HIF1A/ARNT 0.013 0.051 -10000 0 -0.26 7 7
CUL2 0.024 0.002 -10000 0 -10000 0 0
OS9 0.024 0.002 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.041 0.018 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.016 0.051 0.18 1 -0.25 7 8
PHD1-3/OS9 0.056 0.019 -10000 0 -10000 0 0
HIF1A/RACK1/Elongin B/Elongin C 0.029 0.056 -10000 0 -0.25 7 7
VHL 0.024 0.002 -10000 0 -10000 0 0
HSP90AA1 0.023 0.005 -10000 0 -10000 0 0
HIF1A/JAB1 0.011 0.052 -10000 0 -0.26 7 7
EGLN3 0.023 0.006 -10000 0 -10000 0 0
EGLN2 0.024 0.004 -10000 0 -10000 0 0
EGLN1 0.023 0.004 -10000 0 -10000 0 0
TP53 0.02 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.031 0.056 -10000 0 -0.52 2 2
ARNT 0.023 0.004 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.023 0.005 -10000 0 -10000 0 0
HIF1A/p19ARF -0.039 0.099 -10000 0 -0.3 9 9
Signaling events mediated by PRL

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
CCNE1 0.021 0.054 0.31 2 -0.38 3 5
mol:Halofuginone 0.003 0 -10000 0 -10000 0 0
ITGA1 0.023 0.004 -10000 0 -10000 0 0
CDKN1A 0.006 0.047 -10000 0 -0.3 5 5
PRL-3/alpha Tubulin 0.03 0.071 0.23 10 -0.27 8 18
mol:Ca2+ -0.062 0.12 0.22 8 -0.27 50 58
AGT -0.045 0.16 0.31 3 -0.39 41 44
CCNA2 -0.004 0.015 -10000 0 -10000 0 0
TUBA1B 0.024 0.002 -10000 0 -10000 0 0
EGR1 0.011 0.022 -10000 0 -0.22 2 2
CDK2/Cyclin E1 0.066 0.076 0.27 5 -0.27 4 9
MAPK3 0.011 0.074 0.26 10 -0.27 8 18
PRL-2 /Rab GGTase beta 0.034 0.008 -10000 0 -10000 0 0
MAPK1 0.011 0.074 0.26 10 -0.27 8 18
PTP4A1 0 0.016 -10000 0 -10000 0 0
PTP4A3 0.02 0.097 0.31 10 -0.38 8 18
PTP4A2 0.023 0.005 -10000 0 -10000 0 0
ITGB1 0.012 0.08 0.29 10 -0.27 8 18
SRC 0.016 0.012 -10000 0 -10000 0 0
RAC1 0.013 0.049 0.29 3 -0.3 2 5
Rab GGTase beta/Rab GGTase alpha 0.033 0.01 -10000 0 -10000 0 0
PRL-1/ATF-5 0.071 0.081 -10000 0 -10000 0 0
RABGGTA 0.023 0.005 -10000 0 -10000 0 0
BCAR1 -0.02 0.051 0.14 8 -0.22 10 18
RHOC 0.018 0.059 0.29 6 -0.3 2 8
RHOA 0.015 0.06 0.29 5 -0.3 3 8
cell motility 0.047 0.092 0.29 6 -0.3 3 9
PRL-1/alpha Tubulin 0.073 0.082 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.027 0.068 0.23 8 -0.27 8 16
ROCK1 0.049 0.088 0.23 15 -0.31 2 17
RABGGTB 0.023 0.005 -10000 0 -10000 0 0
CDK2 0.024 0.002 -10000 0 -10000 0 0
mitosis 0 0.016 -10000 0 -10000 0 0
ATF5 0.024 0.003 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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
PCK2 0.051 0.056 -10000 0 -0.29 1 1
SMARCC2 0.025 0.005 -10000 0 -10000 0 0
SMARCC1 0.024 0.006 -10000 0 -10000 0 0
TBX21 -0.077 0.12 -10000 0 -0.45 15 15
SUMO2 0.024 0.006 -10000 0 -10000 0 0
STAT1 (dimer) 0.022 0.053 -10000 0 -0.38 4 4
FKBP4 0.025 0.02 0.31 1 -10000 0 1
FKBP5 0.024 0.002 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90 0.089 0.074 0.26 11 -0.2 1 12
PRL -0.047 0.093 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.16 0.15 0.46 25 -10000 0 25
RELA -0.045 0.064 -10000 0 -0.19 1 1
FGG 0.085 0.14 0.4 12 -0.34 5 17
GR beta/TIF2 0.077 0.077 0.26 13 -0.21 1 14
IFNG -0.17 0.15 -10000 0 -0.53 19 19
apoptosis -0.001 0.13 0.47 6 -0.45 3 9
CREB1 0.023 0.022 -10000 0 -10000 0 0
histone acetylation -0.035 0.065 -10000 0 -0.27 4 4
BGLAP -0.042 0.072 -10000 0 -0.38 1 1
GR/PKAc 0.084 0.09 0.26 9 -0.31 2 11
NF kappa B1 p50/RelA -0.073 0.11 -10000 0 -0.28 10 10
SMARCD1 0.025 0.006 -10000 0 -10000 0 0
MDM2 0.051 0.05 0.19 14 -10000 0 14
GATA3 0.018 0.051 -10000 0 -0.33 4 4
AKT1 0.019 0.004 -10000 0 -10000 0 0
CSF2 -0.095 0.1 -10000 0 -0.37 7 7
GSK3B 0.025 0.005 -10000 0 -10000 0 0
NR1I3 0.005 0.12 0.49 5 -0.46 1 6
CSN2 0.071 0.1 0.33 11 -10000 0 11
BRG1/BAF155/BAF170/BAF60A 0.064 0.019 -10000 0 -10000 0 0
NFATC1 0.018 0.023 -10000 0 -0.29 1 1
POU2F1 0.02 0.024 -10000 0 -10000 0 0
CDKN1A -0.007 0.068 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.006 -10000 0 -10000 0 0
SFN 0.022 0.006 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.094 0.074 0.26 9 -10000 0 9
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.001 0.12 0.44 5 -0.8 1 6
JUN -0.15 0.1 -10000 0 -0.4 11 11
IL4 -0.044 0.066 -10000 0 -0.39 1 1
CDK5R1 0.02 0.038 -10000 0 -0.38 2 2
PRKACA 0.024 0.002 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.18 0.12 -10000 0 -0.32 63 63
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.097 0.074 0.27 9 -10000 0 9
cortisol/GR alpha (monomer) 0.18 0.18 0.52 26 -10000 0 26
NCOA2 0.021 0.008 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.062 0.04 -10000 0 -10000 0 0
AP-1/NFAT1-c-4 -0.23 0.15 -10000 0 -0.48 29 29
AFP -0.1 0.07 -10000 0 -10000 0 0
SUV420H1 0.024 0.004 -10000 0 -10000 0 0
IRF1 0.086 0.083 0.36 4 -10000 0 4
TP53 0.031 0.014 -10000 0 -10000 0 0
PPP5C 0.024 0.003 -10000 0 -10000 0 0
KRT17 -0.26 0.16 -10000 0 -0.58 18 18
KRT14 -0.065 0.09 0.39 1 -0.51 3 4
TBP 0.029 0.004 -10000 0 -10000 0 0
CREBBP 0.035 0.027 -10000 0 -0.24 1 1
HDAC1 0.022 0.007 -10000 0 -10000 0 0
HDAC2 0.031 0.012 -10000 0 -10000 0 0
AP-1 -0.23 0.15 -10000 0 -0.49 29 29
MAPK14 0.025 0.005 -10000 0 -10000 0 0
MAPK10 -0.034 0.12 -10000 0 -0.29 43 43
MAPK11 0.024 0.007 -10000 0 -10000 0 0
KRT5 -0.17 0.16 -10000 0 -0.58 13 13
interleukin-1 receptor activity 0.007 0.011 -10000 0 -10000 0 0
NCOA1 0.026 0.002 -10000 0 -10000 0 0
STAT1 0.022 0.053 -10000 0 -0.38 4 4
CGA -0.057 0.082 -10000 0 -0.39 2 2
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.077 0.11 0.32 11 -0.35 2 13
MAPK3 0.025 0.007 -10000 0 -10000 0 0
MAPK1 0.024 0.007 -10000 0 -10000 0 0
ICAM1 -0.1 0.13 -10000 0 -0.59 6 6
NFKB1 -0.045 0.065 -10000 0 -0.2 2 2
MAPK8 -0.12 0.095 -10000 0 -0.36 11 11
MAPK9 0.024 0.006 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.002 0.13 0.47 6 -0.47 3 9
BAX -0.007 0.073 -10000 0 -10000 0 0
POMC -0.098 0.24 0.53 1 -1.2 9 10
EP300 0.034 0.028 -10000 0 -0.24 1 1
cortisol/GR alpha (dimer)/p53 0.15 0.16 0.47 21 -10000 0 21
proteasomal ubiquitin-dependent protein catabolic process 0.031 0.052 0.22 9 -10000 0 9
SGK1 0.037 0.11 -10000 0 -0.95 2 2
IL13 -0.12 0.12 -10000 0 -0.55 4 4
IL6 -0.11 0.17 -10000 0 -0.55 18 18
PRKACG -0.003 0.019 -10000 0 -10000 0 0
IL5 -0.1 0.1 -10000 0 -0.74 1 1
IL2 -0.16 0.13 -10000 0 -0.52 12 12
CDK5 0.023 0.006 -10000 0 -10000 0 0
PRKACB 0.004 0.074 -10000 0 -0.29 14 14
HSP90AA1 0.023 0.005 -10000 0 -10000 0 0
IL8 -0.2 0.18 -10000 0 -0.41 59 59
CDK5R1/CDK5 0.032 0.03 -10000 0 -0.27 2 2
NF kappa B1 p50/RelA/PKAc -0.052 0.099 -10000 0 -0.26 4 4
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.17 0.15 0.46 25 -10000 0 25
SMARCA4 0.025 0.005 -10000 0 -10000 0 0
chromatin remodeling 0.092 0.1 0.33 13 -0.42 2 15
NF kappa B1 p50/RelA/Cbp -0.015 0.1 -10000 0 -0.29 1 1
JUN (dimer) -0.15 0.1 -10000 0 -0.4 11 11
YWHAH 0.023 0.004 -10000 0 -10000 0 0
VIPR1 -0.078 0.13 -10000 0 -0.52 13 13
NR3C1 0.096 0.11 0.36 15 -0.31 4 19
NR4A1 -0.005 0.13 -10000 0 -0.47 15 15
TIF2/SUV420H1 0.031 0.013 -10000 0 -10000 0 0
MAPKKK cascade -0.001 0.13 0.47 6 -0.45 3 9
cortisol/GR alpha (dimer)/Src-1 0.18 0.15 0.46 26 -10000 0 26
PBX1 0.011 0.058 -10000 0 -0.29 7 7
POU1F1 0.002 0.041 -10000 0 -0.46 1 1
SELE -0.14 0.17 -10000 0 -0.44 30 30
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.093 0.1 0.33 13 -0.42 2 15
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.17 0.15 0.46 25 -10000 0 25
mol:cortisol 0.082 0.095 0.29 22 -10000 0 22
MMP1 -0.2 0.15 -10000 0 -0.45 15 15
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.031 0.006 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.024 0.003 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.024 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.02 0.009 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.012 0.006 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.02 0.009 -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 0.024 0.004 -10000 0 -10000 0 0
FYN 0.024 0.004 -10000 0 -10000 0 0
MAP3K12 0.024 0.002 -10000 0 -10000 0 0
FGR 0.019 0.034 -10000 0 -0.34 2 2
p38 alpha/TAB1 -0.056 0.095 -10000 0 -0.29 25 25
PRKG1 0.009 0.066 -10000 0 -0.29 11 11
DUSP8 0.024 0.003 -10000 0 -10000 0 0
PGK/cGMP/p38 alpha -0.027 0.12 -10000 0 -0.31 23 23
apoptosis -0.054 0.092 -10000 0 -0.28 25 25
RAL/GTP 0.029 0.011 -10000 0 -10000 0 0
LYN 0.021 0.008 -10000 0 -10000 0 0
DUSP1 0.023 0.004 -10000 0 -10000 0 0
PAK1 0.024 0.003 -10000 0 -10000 0 0
SRC 0.016 0.012 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.046 0.027 -10000 0 -10000 0 0
TRAF6 0.024 0.003 -10000 0 -10000 0 0
RAC1 0.021 0.008 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.021 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.027 0.013 -10000 0 -10000 0 0
MAPK11 -0.001 0.13 0.22 20 -0.32 8 28
BLK -0.078 0.14 -10000 0 -0.29 70 70
HCK 0.015 0.012 -10000 0 -10000 0 0
MAP2K3 0.02 0.009 -10000 0 -10000 0 0
DUSP16 0.024 0.004 -10000 0 -10000 0 0
DUSP10 0.018 0.046 -10000 0 -0.38 3 3
TRAF6/MEKK3 0.03 0.006 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.015 0.14 0.2 17 -0.33 22 39
positive regulation of innate immune response -0.012 0.15 0.24 19 -0.37 16 35
LCK 0.009 0.074 -10000 0 -0.38 8 8
p38alpha-beta/MKP7 -0.005 0.15 0.25 19 -0.36 16 35
p38alpha-beta/MKP5 -0.004 0.15 0.25 19 -0.36 16 35
PGK/cGMP 0.008 0.045 -10000 0 -0.19 11 11
PAK2 0.024 0 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.005 0.15 0.25 19 -0.36 16 35
CDC42 0.023 0.006 -10000 0 -10000 0 0
RALB 0.024 0.002 -10000 0 -10000 0 0
RALA 0.021 0.008 -10000 0 -10000 0 0
PAK3 0.009 0.02 -10000 0 -10000 0 0
Regulation of Androgen receptor activity

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
HDAC1 0.005 0.012 -10000 0 -10000 0 0
SMARCC1 0.01 0.011 -10000 0 -10000 0 0
REL 0.027 0.008 -10000 0 -10000 0 0
HDAC7 -0.028 0.071 -10000 0 -0.25 1 1
JUN 0.022 0.005 -10000 0 -10000 0 0
EP300 0.023 0.005 -10000 0 -10000 0 0
KAT2B 0.023 0.002 -10000 0 -10000 0 0
KAT5 0.024 0.004 -10000 0 -10000 0 0
MAPK14 0 0.019 -10000 0 -10000 0 0
FOXO1 0.019 0.01 -10000 0 -10000 0 0
T-DHT/AR -0.014 0.086 -10000 0 -0.26 1 1
MAP2K6 0.016 0.018 -10000 0 -10000 0 0
BRM/BAF57 0.02 0.03 -10000 0 -10000 0 0
MAP2K4 0.014 0.017 -10000 0 -10000 0 0
SMARCA2 0.014 0.02 -10000 0 -10000 0 0
PDE9A -0.14 0.35 -10000 0 -0.84 44 44
NCOA2 0.021 0.008 -10000 0 -10000 0 0
CEBPA 0.022 0.029 -10000 0 -0.28 2 2
EHMT2 0.02 0.011 -10000 0 -10000 0 0
cell proliferation 0.02 0.12 0.25 9 -0.42 1 10
NR0B1 -0.001 0.032 -10000 0 -0.38 1 1
EGR1 0.012 0.038 -10000 0 -0.34 2 2
RXRs/9cRA -0.05 0.091 -10000 0 -0.15 96 96
AR/RACK1/Src 0.034 0.087 0.19 17 -10000 0 17
AR/GR -0.029 0.087 -10000 0 -0.25 16 16
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
PKN1 0.024 0.002 -10000 0 -10000 0 0
RCHY1 0.024 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity -0.001 0.002 -10000 0 -0.011 1 1
MAPK8 0.001 0.017 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.004 0.052 -10000 0 -10000 0 0
SRC -0.01 0.028 0.21 2 -10000 0 2
NR3C1 0.013 0.057 -10000 0 -0.29 8 8
KLK3 -0.25 0.44 -10000 0 -1.1 49 49
APPBP2 0.017 0.018 -10000 0 -10000 0 0
TRIM24 0.014 0.02 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.014 0.046 -10000 0 -10000 0 0
TMPRSS2 -0.016 0.12 -10000 0 -0.56 7 7
RXRG -0.12 0.14 -10000 0 -0.29 98 98
mol:9cRA -0.001 0.002 -10000 0 -10000 0 0
RXRA 0.023 0.002 -10000 0 -10000 0 0
RXRB 0.023 0.002 -10000 0 -10000 0 0
CARM1 0.024 0.002 -10000 0 -10000 0 0
NR2C2 0.023 0.002 -10000 0 -10000 0 0
KLK2 0.014 0.074 -10000 0 -0.28 1 1
AR -0.026 0.071 -10000 0 -0.2 31 31
SENP1 0.023 0.004 -10000 0 -10000 0 0
HSP90AA1 0.023 0.005 -10000 0 -10000 0 0
MDM2 0.03 0.012 -10000 0 -10000 0 0
SRY 0.006 0.012 0.027 52 -10000 0 52
GATA2 0.016 0.05 -10000 0 -0.29 6 6
MYST2 0.001 0.002 -10000 0 -10000 0 0
HOXB13 -0.004 0.072 -10000 0 -0.3 12 12
T-DHT/AR/RACK1/Src 0.044 0.094 0.19 35 -10000 0 35
positive regulation of transcription 0.016 0.05 -10000 0 -0.29 6 6
DNAJA1 0.017 0.018 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.006 -10000 0 -10000 0 0
NCOA1 0.019 0.02 -10000 0 -10000 0 0
SPDEF -0.052 0.13 -10000 0 -0.29 51 51
T-DHT/AR/TIF2 -0.002 0.046 -10000 0 -10000 0 0
T-DHT/AR/Hsp90 -0.016 0.045 -10000 0 -10000 0 0
GSK3B 0.023 0.004 -10000 0 -10000 0 0
NR2C1 0.025 0.004 -10000 0 -10000 0 0
mol:T-DHT -0.016 0.022 -10000 0 -10000 0 0
SIRT1 0.024 0.002 -10000 0 -10000 0 0
ZMIZ2 0.026 0.016 -10000 0 -10000 0 0
POU2F1 0.014 0.049 -10000 0 -0.17 1 1
T-DHT/AR/DAX-1 -0.021 0.047 -10000 0 -10000 0 0
CREBBP 0.023 0.004 -10000 0 -10000 0 0
SMARCE1 0.014 0.02 -10000 0 -10000 0 0
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.006 0.042 -10000 0 -0.17 1 1
STMN1 0.012 0.006 -10000 0 -10000 0 0
Aurora B/RasGAP/Survivin 0.048 0.026 0.22 1 -10000 0 1
Chromosomal passenger complex/Cul3 protein complex -0.011 0.073 0.14 2 -0.23 10 12
BIRC5 0.028 0.019 0.31 1 -10000 0 1
DES -0.42 0.28 -10000 0 -0.57 174 174
Aurora C/Aurora B/INCENP 0.044 0.023 -10000 0 -10000 0 0
Aurora B/TACC1 0.028 0.017 -10000 0 -10000 0 0
Aurora B/PP2A 0.034 0.016 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.008 0.004 -10000 0 -10000 0 0
mitotic metaphase/anaphase transition 0.001 0.004 -10000 0 -10000 0 0
NDC80 0.011 0.007 -10000 0 -10000 0 0
Cul3 protein complex 0.02 0.074 -10000 0 -0.17 27 27
KIF2C 0.015 0.042 -10000 0 -0.27 3 3
PEBP1 0.026 0.002 -10000 0 -10000 0 0
KIF20A 0.022 0.038 -10000 0 -0.38 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.033 0.016 -10000 0 -10000 0 0
SEPT1 0.023 0.021 -10000 0 -0.29 1 1
SMC2 0.024 0.002 -10000 0 -10000 0 0
SMC4 0.024 0 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.077 0.19 -10000 0 -0.49 39 39
PSMA3 0.023 0.005 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.003 -10000 0 -10000 0 0
H3F3B 0.013 0.006 -10000 0 -10000 0 0
AURKB 0.026 0.013 -10000 0 -10000 0 0
AURKC 0.023 0.007 -10000 0 -10000 0 0
CDCA8 0.027 0.019 0.31 1 -10000 0 1
cytokinesis 0.002 0.046 -10000 0 -0.43 2 2
Aurora B/Septin1 0.004 0.096 -10000 0 -0.33 4 4
AURKA 0.02 0.052 0.31 5 -0.38 1 6
INCENP 0.026 0.006 -10000 0 -10000 0 0
KLHL13 -0.018 0.11 -10000 0 -0.3 30 30
BUB1 0.024 0.027 -10000 0 -0.38 1 1
hSgo1/Aurora B/Survivin 0.045 0.033 0.21 1 -0.19 2 3
EVI5 0.025 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.042 0.067 -10000 0 -0.33 2 2
SGOL1 0.02 0.038 -10000 0 -0.38 2 2
CENPA 0.03 0.058 0.15 4 -0.25 3 7
NCAPG 0.02 0.038 -10000 0 -0.38 2 2
Aurora B/HC8 Proteasome 0.033 0.016 -10000 0 -10000 0 0
NCAPD2 0.024 0.004 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.034 0.016 -10000 0 -10000 0 0
RHOA 0.024 0.004 -10000 0 -10000 0 0
NCAPH 0.021 0.038 -10000 0 -0.38 2 2
NPM1 -0.049 0.15 -10000 0 -0.35 35 35
RASA1 0.023 0.005 -10000 0 -10000 0 0
KLHL9 0.023 0.004 -10000 0 -10000 0 0
mitotic prometaphase 0.001 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.033 0.016 -10000 0 -10000 0 0
PPP1CC 0.024 0.002 -10000 0 -10000 0 0
Centraspindlin 0.039 0.068 -10000 0 -0.36 2 2
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
NSUN2 -0.035 0.097 -10000 0 -0.27 34 34
MYLK -0.045 0.1 -10000 0 -0.22 55 55
KIF23 0.021 0.038 -10000 0 -0.39 2 2
VIM 0.012 0.007 -10000 0 -10000 0 0
RACGAP1 0.025 0.005 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.037 0.098 -10000 0 -0.26 36 36
Chromosomal passenger complex 0.019 0.052 0.15 2 -0.21 4 6
Chromosomal passenger complex/EVI5 0.091 0.054 0.28 2 -10000 0 2
TACC1 0.021 0.009 -10000 0 -10000 0 0
PPP2R5D 0.024 0.002 -10000 0 -10000 0 0
CUL3 0.024 0 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 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 0.006 0.079 -10000 0 -0.3 7 7
TBX21 -0.065 0.28 -10000 0 -0.96 13 13
B2M 0.02 0.018 -10000 0 -10000 0 0
TYK2 0.017 0.027 -10000 0 -10000 0 0
IL12RB1 0.005 0.069 -10000 0 -0.33 8 8
GADD45B -0.021 0.2 -10000 0 -0.87 5 5
IL12RB2 0.01 0.062 -10000 0 -0.41 4 4
GADD45G -0.02 0.19 -10000 0 -0.72 7 7
natural killer cell activation -0.001 0.015 -10000 0 -10000 0 0
RELB 0.024 0.003 -10000 0 -10000 0 0
RELA 0.023 0.004 -10000 0 -10000 0 0
IL18 0.023 0.013 -10000 0 -10000 0 0
IL2RA 0.015 0.055 -10000 0 -0.32 6 6
IFNG -0.034 0.14 -10000 0 -0.38 30 30
STAT3 (dimer) -0.029 0.19 -10000 0 -0.64 10 10
HLA-DRB5 0.001 0.092 -10000 0 -0.34 15 15
FASLG -0.063 0.27 -10000 0 -0.96 13 13
NF kappa B2 p52/RelB -0.039 0.22 -10000 0 -0.72 11 11
CD4 0.021 0.029 -10000 0 -0.29 2 2
SOCS1 0.022 0.027 -10000 0 -0.38 1 1
EntrezGene:6955 -0.001 0.01 -10000 0 -10000 0 0
CD3D 0.011 0.056 -10000 0 -0.29 7 7
CD3E 0.011 0.056 -10000 0 -0.29 7 7
CD3G -0.003 0.086 -10000 0 -0.3 18 18
IL12Rbeta2/JAK2 0.021 0.057 -10000 0 -0.3 4 4
CCL3 -0.053 0.23 -10000 0 -0.81 9 9
CCL4 -0.05 0.23 -10000 0 -0.87 8 8
HLA-A 0.02 0.018 -10000 0 -10000 0 0
IL18/IL18R 0.048 0.063 -10000 0 -0.18 5 5
NOS2 -0.07 0.31 -10000 0 -1.1 15 15
IL12/IL12R/TYK2/JAK2/SPHK2 0.007 0.074 -10000 0 -0.28 6 6
IL1R1 -0.056 0.24 -10000 0 -0.91 10 10
IL4 0 0.029 -10000 0 -10000 0 0
JAK2 0.016 0.027 -10000 0 -10000 0 0
EntrezGene:6957 -0.001 0.011 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.059 0.26 -10000 0 -0.8 21 21
RAB7A -0.017 0.18 -10000 0 -0.75 4 4
lysosomal transport -0.015 0.17 -10000 0 -0.71 4 4
FOS -0.045 0.24 -10000 0 -0.93 11 11
STAT4 (dimer) -0.016 0.2 -10000 0 -0.7 9 9
STAT5A (dimer) -0.061 0.24 -10000 0 -0.7 14 14
GZMA -0.07 0.29 -10000 0 -1 14 14
GZMB -0.077 0.23 -10000 0 -0.91 7 7
HLX 0.023 0.004 -10000 0 -10000 0 0
LCK -0.059 0.23 -10000 0 -0.72 14 14
TCR/CD3/MHC II/CD4 -0.018 0.14 -10000 0 -0.45 16 16
IL2/IL2R 0.043 0.054 -10000 0 -0.24 5 5
MAPK14 -0.023 0.21 -10000 0 -0.84 6 6
CCR5 -0.025 0.2 -10000 0 -0.79 6 6
IL1B -0.059 0.16 -10000 0 -0.38 44 44
STAT6 0.002 0.074 -10000 0 -10000 0 0
STAT4 0.023 0.02 -10000 0 -0.29 1 1
STAT3 0.023 0.004 -10000 0 -10000 0 0
STAT1 0.017 0.053 -10000 0 -0.38 4 4
NFKB1 0.024 0.004 -10000 0 -10000 0 0
NFKB2 0.023 0.005 -10000 0 -10000 0 0
IL12B 0.011 0.039 -10000 0 -0.39 1 1
CD8A 0.004 0.075 -10000 0 -0.31 12 12
CD8B 0.01 0.063 -10000 0 -0.33 7 7
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.006 0.078 0.3 7 -10000 0 7
IL2RB 0.016 0.049 -10000 0 -0.31 5 5
proteasomal ubiquitin-dependent protein catabolic process -0.013 0.19 -10000 0 -0.65 9 9
IL2RG 0.023 0.021 -10000 0 -0.29 1 1
IL12 0.021 0.047 -10000 0 -0.24 2 2
STAT5A 0.024 0.004 -10000 0 -10000 0 0
CD247 0.011 0.057 -10000 0 -0.3 7 7
IL2 -0.005 0.018 -10000 0 -10000 0 0
SPHK2 0.024 0.003 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.015 0.034 -10000 0 -0.29 1 1
IL12/IL12R/TYK2/JAK2 -0.051 0.24 -10000 0 -0.8 12 12
MAP2K3 -0.042 0.22 -10000 0 -0.82 9 9
RIPK2 0.022 0.039 0.31 2 -0.38 1 3
MAP2K6 -0.016 0.2 -10000 0 -0.76 7 7
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.023 0.021 -10000 0 -0.29 1 1
IL18RAP 0.01 0.065 -10000 0 -0.29 10 10
IL12Rbeta1/TYK2 0.017 0.06 -10000 0 -0.23 8 8
EOMES -0.057 0.27 -10000 0 -1 16 16
STAT1 (dimer) -0.029 0.2 -10000 0 -0.72 7 7
T cell proliferation -0.008 0.16 -10000 0 -0.59 6 6
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.021 0.032 -10000 0 -0.3 2 2
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.013 0.18 -10000 0 -0.6 8 8
ATF2 -0.023 0.19 -10000 0 -0.78 6 6
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.049 0.052 -10000 0 -10000 0 0
epithelial cell differentiation 0.036 0.071 -10000 0 -0.29 1 1
ITCH 0.017 0.013 -10000 0 -10000 0 0
WWP1 0.016 0.04 -10000 0 -10000 0 0
FYN 0.024 0.004 -10000 0 -10000 0 0
EGFR 0.021 0.008 -10000 0 -10000 0 0
PRL -0.014 0.089 -10000 0 -0.38 12 12
neuron projection morphogenesis 0.021 0.072 0.28 7 -10000 0 7
PTPRZ1 -0.1 0.14 -10000 0 -0.29 87 87
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.031 0.061 -10000 0 -10000 0 0
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.021 0.027 -10000 0 -10000 0 0
ADAM17 0.013 0.018 -10000 0 -10000 0 0
ErbB4/ErbB4 0.013 0.018 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.051 0.038 -10000 0 -10000 0 0
NCOR1 0.02 0.009 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.019 0.056 -10000 0 -10000 0 0
GRIN2B -0.044 0.098 0.24 2 -0.3 4 6
ErbB4/ErbB2/betacellulin 0.049 0.035 0.23 1 -10000 0 1
STAT1 0.017 0.053 -10000 0 -0.38 4 4
HBEGF 0.017 0.053 -10000 0 -0.38 4 4
PRLR 0.016 0.05 -10000 0 -0.29 6 6
E4ICDs/ETO2 0.04 0.059 -10000 0 -10000 0 0
axon guidance 0.04 0.071 0.28 4 -10000 0 4
NEDD4 0.012 0.018 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin 0.01 0.076 -10000 0 -0.25 18 18
CBFA2T3 -0.019 0.11 -10000 0 -0.3 30 30
ErbB4/ErbB2/HBEGF 0.046 0.044 0.23 1 -10000 0 1
MAPK3 0.022 0.064 0.27 4 -10000 0 4
STAT1 (dimer) 0.05 0.051 -10000 0 -10000 0 0
MAPK1 0.021 0.064 0.27 4 -10000 0 4
JAK2 0.024 0.003 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta 0.009 0.05 0.22 1 -10000 0 1
NRG1 -0.021 0.066 -10000 0 -0.2 27 27
NRG3 0.009 0.019 -10000 0 -10000 0 0
NRG2 -0.056 0.12 -10000 0 -0.29 51 51
NRG4 0.016 0.016 -10000 0 -10000 0 0
heart development 0.04 0.071 0.28 4 -10000 0 4
neural crest cell migration 0.009 0.05 0.22 1 -10000 0 1
ERBB2 0.007 0.027 0.27 2 -10000 0 2
WWOX/E4ICDs 0.053 0.04 -10000 0 -10000 0 0
SHC1 0.023 0.004 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.053 0.036 -10000 0 -10000 0 0
apoptosis -0.034 0.071 0.34 3 -10000 0 3
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.037 0.044 -10000 0 -10000 0 0
ErbB4/ErbB2/epiregulin -0.041 0.11 -10000 0 -10000 0 0
ErbB4/ErbB4/betacellulin/betacellulin 0.052 0.041 -10000 0 -10000 0 0
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.058 0.078 -10000 0 -0.34 1 1
MDM2 0.011 0.019 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.002 0.044 -10000 0 -10000 0 0
STAT5A 0.05 0.077 0.28 7 -10000 0 7
ErbB4/EGFR/neuregulin 1 beta 0.017 0.055 -10000 0 -10000 0 0
DLG4 0.02 0.009 -10000 0 -10000 0 0
GRB2/SHC 0.034 0.008 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.039 0.035 -10000 0 -10000 0 0
STAT5A (dimer) 0.063 0.09 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.074 0.076 0.26 8 -10000 0 8
LRIG1 0.024 0.003 -10000 0 -10000 0 0
EREG -0.18 0.2 -10000 0 -0.38 119 119
BTC 0.022 0.021 -10000 0 -0.29 1 1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.027 0.062 0.28 4 -10000 0 4
ERBB4 0.011 0.01 -10000 0 -10000 0 0
STAT5B 0.024 0.004 -10000 0 -10000 0 0
YAP1 0.005 0.054 -10000 0 -0.46 3 3
GRB2 0.024 0.004 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.049 0.031 0.23 1 -10000 0 1
glial cell differentiation -0.038 0.034 -10000 0 -10000 0 0
WWOX 0.024 0.002 -10000 0 -10000 0 0
cell proliferation 0.023 0.075 0.32 4 -10000 0 4
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.008 0.079 -9999 0 -0.38 9 9
PLK4 0.023 0.004 -9999 0 -10000 0 0
regulation of centriole replication 0 0.054 -9999 0 -0.27 9 9
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.025 0.058 -10000 0 -0.49 1 1
CRKL 0.024 0.04 0.15 15 -10000 0 15
mol:DAG 0.019 0.026 -10000 0 -10000 0 0
HRAS 0.005 0.052 0.18 6 -10000 0 6
MAPK8 0.029 0.063 0.18 33 -10000 0 33
RAP1A 0.023 0.039 0.15 14 -10000 0 14
GAB1 0.023 0.039 0.15 14 -10000 0 14
MAPK14 0.029 0.063 0.18 33 -10000 0 33
EPO 0.012 0.028 0.29 1 -10000 0 1
PLCG1 0.019 0.026 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.026 0.008 -10000 0 -10000 0 0
RAPGEF1 0.024 0.002 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.046 0.02 0.21 1 -10000 0 1
GAB1/SHC/GRB2/SOS1 0.05 0.035 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.035 0.018 0.22 1 -10000 0 1
IRS2 0.017 0.031 0.16 9 -10000 0 9
STAT1 0.029 0.044 0.18 1 -0.3 1 2
STAT5B 0.028 0.036 0.18 1 -0.24 1 2
cell proliferation 0.02 0.077 0.19 36 -10000 0 36
GAB1/SHIP/PIK3R1/SHP2/SHC 0.041 0.029 -10000 0 -10000 0 0
TEC 0.024 0.04 0.15 18 -10000 0 18
SOCS3 0.024 0.003 -10000 0 -10000 0 0
STAT1 (dimer) 0.028 0.044 0.18 1 -0.3 1 2
JAK2 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.023 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.066 0.035 0.21 5 -10000 0 5
EPO/EPOR 0.035 0.018 0.22 1 -10000 0 1
LYN 0.021 0.01 -10000 0 -10000 0 0
TEC/VAV2 0.037 0.038 0.17 4 -10000 0 4
elevation of cytosolic calcium ion concentration 0.026 0.008 -10000 0 -10000 0 0
SHC1 0.023 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.045 0.026 0.21 1 -10000 0 1
mol:IP3 0.019 0.026 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.036 0.034 0.2 1 -10000 0 1
SH2B3 0.026 0.007 -10000 0 -10000 0 0
NFKB1 0.028 0.062 0.18 32 -10000 0 32
EPO/EPOR (dimer)/JAK2/SOCS3 0.012 0.017 0.15 1 -10000 0 1
PTPN6 0.023 0.037 0.16 14 -10000 0 14
TEC/VAV2/GRB2 0.048 0.039 0.18 1 -10000 0 1
EPOR 0.026 0.008 -10000 0 -10000 0 0
INPP5D 0.024 0.002 -10000 0 -10000 0 0
mol:GDP 0.049 0.035 -10000 0 -10000 0 0
SOS1 0.024 0.002 -10000 0 -10000 0 0
PLCG2 0.004 0.077 -10000 0 -0.29 15 15
CRKL/CBL/C3G 0.049 0.037 -10000 0 -10000 0 0
VAV2 0.024 0.04 0.15 15 -10000 0 15
CBL 0.024 0.04 0.15 18 -10000 0 18
SHC/Grb2/SOS1 0.037 0.023 -10000 0 -10000 0 0
STAT5A 0.028 0.036 0.18 1 -0.24 1 2
GRB2 0.024 0.004 -10000 0 -10000 0 0
STAT5 (dimer) 0.044 0.051 -10000 0 -0.34 2 2
LYN/PLCgamma2 0.019 0.054 -10000 0 -0.2 13 13
PTPN11 0.024 0.003 -10000 0 -10000 0 0
BTK 0.021 0.041 0.15 14 -0.25 1 15
BCL2 0.032 0.11 -10000 0 -0.7 4 4
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.017 0.021 -10000 0 -10000 0 0
HSPA8 0.024 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.02 0.086 -10000 0 -0.22 4 4
AKT1 0.007 0.041 -10000 0 -10000 0 0
GSC -0.013 0.1 -10000 0 -0.46 1 1
NKX2-5 0.005 0.064 -10000 0 -0.38 6 6
muscle cell differentiation 0.02 0.1 0.29 7 -10000 0 7
SMAD2-3/SMAD4/SP1 0.016 0.093 -10000 0 -10000 0 0
SMAD4 0.011 0.038 -10000 0 -10000 0 0
CBFB 0.024 0.002 -10000 0 -10000 0 0
SAP18 0.021 0.022 0.31 1 -10000 0 1
Cbp/p300/MSG1 -0.04 0.12 -10000 0 -0.23 68 68
SMAD3/SMAD4/VDR 0.054 0.049 -10000 0 -10000 0 0
MYC 0.033 0.074 0.32 7 -0.32 4 11
CDKN2B -0.21 0.47 -10000 0 -1.1 46 46
AP1 0.025 0.04 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.013 0.12 -10000 0 -0.34 18 18
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.08 0.18 -10000 0 -0.41 45 45
SP3 0.025 0 -10000 0 -10000 0 0
CREB1 0.024 0 -10000 0 -10000 0 0
FOXH1 0.009 0.063 0.32 1 -0.31 7 8
SMAD3/SMAD4/GR 0.035 0.072 -10000 0 -0.23 6 6
GATA3 0.012 0.057 -10000 0 -0.35 4 4
SKI/SIN3/HDAC complex/NCoR1 0.02 0.053 -10000 0 -0.34 1 1
MEF2C/TIF2 0.006 0.06 -10000 0 -0.3 1 1
endothelial cell migration 0.039 0.11 0.54 1 -10000 0 1
MAX 0.027 0.01 -10000 0 -10000 0 0
RBBP7 0.024 0.002 -10000 0 -10000 0 0
RBBP4 0.023 0.005 -10000 0 -10000 0 0
RUNX2 0.024 0.002 -10000 0 -10000 0 0
RUNX3 0.023 0.006 -10000 0 -10000 0 0
RUNX1 0.018 0.046 -10000 0 -0.38 3 3
CTBP1 0.024 0.004 -10000 0 -10000 0 0
NR3C1 0.017 0.059 -10000 0 -0.29 8 8
VDR 0.024 0.002 -10000 0 -10000 0 0
CDKN1A 0.006 0.049 -10000 0 -10000 0 0
KAT2B 0.024 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.017 0.064 0.25 1 -0.22 3 4
DCP1A 0.023 0.004 -10000 0 -10000 0 0
SKI 0.023 0.005 -10000 0 -10000 0 0
SERPINE1 -0.04 0.11 -10000 0 -0.55 1 1
SMAD3/SMAD4/ATF2 0.032 0.051 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.031 0.053 -10000 0 -10000 0 0
SAP30 0.023 0.005 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.038 0.042 -10000 0 -10000 0 0
JUN 0.014 0.033 -10000 0 -10000 0 0
SMAD3/SMAD4/IRF7 0.032 0.051 -10000 0 -10000 0 0
TFE3 0.013 0.023 -10000 0 -10000 0 0
COL1A2 -0.01 0.089 -10000 0 -10000 0 0
mesenchymal cell differentiation -0.032 0.051 -10000 0 -10000 0 0
DLX1 -0.001 0.085 -10000 0 -0.38 11 11
TCF3 0.024 0.002 -10000 0 -10000 0 0
FOS 0.022 0.013 -10000 0 -10000 0 0
SMAD3/SMAD4/Max 0.041 0.057 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.046 0.015 -10000 0 -10000 0 0
ZBTB17 0.032 0.025 -10000 0 -10000 0 0
LAMC1 0.004 0.033 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.031 0.059 0.25 6 -0.23 1 7
IRF7 0.024 0.003 -10000 0 -10000 0 0
ESR1 -0.004 0.088 -10000 0 -0.29 20 20
HNF4A 0.015 0.012 -10000 0 -10000 0 0
MEF2C 0.007 0.077 0.23 4 -0.31 1 5
SMAD2-3/SMAD4 0.023 0.07 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.046 0.02 -10000 0 -10000 0 0
IGHV3OR16-13 0.009 0.01 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.029 0.07 0.31 11 -0.38 1 12
CREBBP 0.017 0.019 -10000 0 -10000 0 0
SKIL 0.024 0 -10000 0 -10000 0 0
HDAC1 0.023 0.005 -10000 0 -10000 0 0
HDAC2 0.024 0.004 -10000 0 -10000 0 0
SNIP1 0.023 0.005 -10000 0 -10000 0 0
GCN5L2 0.001 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.028 0.049 -10000 0 -10000 0 0
MSG1/HSC70 -0.059 0.14 -10000 0 -0.27 70 70
SMAD2 0.005 0.037 -10000 0 -10000 0 0
SMAD3 0.013 0.04 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.011 0.036 0.17 1 -0.22 1 2
SMAD2/SMAD2/SMAD4 -0.033 0.076 -10000 0 -0.21 20 20
NCOR1 0.02 0.009 -10000 0 -10000 0 0
NCOA2 0.021 0.008 -10000 0 -10000 0 0
NCOA1 0.024 0.002 -10000 0 -10000 0 0
MYOD/E2A 0.028 0.003 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.03 0.094 -10000 0 -10000 0 0
IFNB1 0.002 0.033 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C 0.019 0.086 -10000 0 -0.3 1 1
CITED1 -0.1 0.19 -10000 0 -0.39 70 70
SMAD2-3/SMAD4/ARC105 0.033 0.07 -10000 0 -10000 0 0
RBL1 0.022 0.04 0.31 4 -10000 0 4
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.061 0.21 -10000 0 -0.49 39 39
RUNX1-3/PEBPB2 0.041 0.034 -10000 0 -0.23 3 3
SMAD7 0.015 0.056 -10000 0 -10000 0 0
MYC/MIZ-1 0.048 0.068 0.19 35 -0.27 2 37
SMAD3/SMAD4 -0.019 0.088 -10000 0 -0.33 1 1
IL10 -0.009 0.089 -10000 0 -0.32 13 13
PIASy/HDAC complex 0.018 0.019 -10000 0 -10000 0 0
PIAS3 0.024 0.004 -10000 0 -10000 0 0
CDK2 0.02 0.016 -10000 0 -10000 0 0
IL5 -0.005 0.066 -10000 0 -0.33 4 4
CDK4 0.018 0.019 -10000 0 -10000 0 0
PIAS4 0.018 0.019 -10000 0 -10000 0 0
ATF3 0.022 0.027 -10000 0 -0.38 1 1
SMAD3/SMAD4/SP1 0.016 0.071 -10000 0 -10000 0 0
FOXG1 -0.057 0.13 -10000 0 -0.4 28 28
FOXO3 -0.007 0.046 -10000 0 -0.15 3 3
FOXO1 -0.003 0.036 -10000 0 -10000 0 0
FOXO4 -0.006 0.044 -10000 0 -0.15 1 1
heart looping 0.007 0.076 0.23 4 -0.31 1 5
CEBPB 0.007 0.034 -10000 0 -0.38 1 1
SMAD3/SMAD4/DLX1 0.02 0.073 -10000 0 -0.23 7 7
MYOD1 -0.017 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.023 0.043 -10000 0 -10000 0 0
SMAD3/SMAD4/GATA3 0.024 0.079 -10000 0 -0.26 5 5
SnoN/SIN3/HDAC complex/NCoR1 0.024 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.042 0.064 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1-3 0.028 0.073 -10000 0 -10000 0 0
MED15 0.023 0.004 -10000 0 -10000 0 0
SP1 0.006 0.038 -10000 0 -10000 0 0
SIN3B 0.024 0.002 -10000 0 -10000 0 0
SIN3A 0.023 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.017 0.073 0.25 1 -10000 0 1
ITGB5 -0.001 0.047 0.21 1 -10000 0 1
TGIF/SIN3/HDAC complex/CtBP 0.025 0.043 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.002 0.097 -10000 0 -0.23 15 15
AR -0.036 0.12 -10000 0 -0.29 41 41
negative regulation of cell growth 0.003 0.058 -10000 0 -0.27 4 4
SMAD3/SMAD4/MYOD 0.027 0.05 -10000 0 -10000 0 0
E2F5 0.023 0.054 0.31 4 -0.38 2 6
E2F4 0.024 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.033 0.061 0.24 1 -10000 0 1
SMAD2-3/SMAD4/FOXO1-3a-4 -0.046 0.19 -10000 0 -0.43 40 40
TFDP1 0.02 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.039 0.05 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX2 0.032 0.051 -10000 0 -10000 0 0
TGIF2 0.029 0.07 0.31 11 -0.38 1 12
TGIF1 0.02 0.009 -10000 0 -10000 0 0
ATF2 0.024 0 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.015 0.059 -10000 0 -0.38 5 5
ANTXR2 0.024 0.004 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.007 -10000 0 -0.046 5 5
monocyte activation 0 0.076 -10000 0 -0.31 13 13
MAP2K2 0.011 0.038 -10000 0 -0.56 1 1
MAP2K1 -0.004 0.006 -10000 0 -10000 0 0
MAP2K7 -0.004 0.006 -10000 0 -10000 0 0
MAP2K6 -0.004 0.006 -10000 0 -10000 0 0
CYAA -0.009 0.027 -10000 0 -0.19 5 5
MAP2K4 -0.004 0.006 -10000 0 -10000 0 0
IL1B -0.037 0.072 -10000 0 -0.18 44 44
Channel 0.025 0.034 -10000 0 -0.2 5 5
NLRP1 -0.005 0.016 -10000 0 -0.16 2 2
CALM1 0.023 0.005 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.009 0.084 -10000 0 -0.38 11 11
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.007 0.046 5 -10000 0 5
MAPK3 -0.004 0.006 -10000 0 -10000 0 0
MAPK1 -0.004 0.006 -10000 0 -10000 0 0
PGR -0.032 0.054 -10000 0 -0.13 50 50
PA/Cellular Receptors 0.026 0.038 -10000 0 -0.22 5 5
apoptosis -0.002 0.007 -10000 0 -0.046 5 5
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.025 0.03 -10000 0 -0.17 5 5
macrophage activation -0.005 0.018 0.18 2 -10000 0 2
TNF 0.022 0.027 -10000 0 -0.38 1 1
VCAM1 0 0.076 -10000 0 -0.31 13 13
platelet activation -0.009 0.084 -10000 0 -0.38 11 11
MAPKKK cascade 0.001 0.012 -10000 0 -0.069 4 4
IL18 -0.003 0.01 -10000 0 -10000 0 0
negative regulation of macrophage activation -0.002 0.007 -10000 0 -0.046 5 5
LEF -0.002 0.007 -10000 0 -0.046 5 5
CASP1 -0.001 0.009 -10000 0 -0.099 1 1
mol:cAMP -0.009 0.084 -10000 0 -0.38 11 11
necrosis -0.002 0.007 -10000 0 -0.046 5 5
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.025 0.032 -10000 0 -0.19 5 5
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
PDGFR-alpha 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
PDGFRA 0.018 0.056 -10000 0 -0.29 7 7
PDGF/PDGFRA/CRKL 0.029 0.043 -10000 0 -0.19 8 8
positive regulation of JUN kinase activity 0.052 0.038 -10000 0 -10000 0 0
CRKL 0.023 0.004 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 0.023 0.047 -10000 0 -0.2 9 9
AP1 0.018 0.073 0.29 1 -0.34 1 2
mol:IP3 0.001 0.036 -10000 0 -0.2 7 7
PLCG1 0.001 0.036 -10000 0 -0.2 7 7
PDGF/PDGFRA/alphaV Integrin 0.03 0.043 -10000 0 -0.19 8 8
RAPGEF1 0.024 0.002 -10000 0 -10000 0 0
CRK 0.02 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0.001 0.036 -10000 0 -0.2 7 7
CAV3 -0.011 0.029 -10000 0 -0.38 1 1
CAV1 0.016 0.045 -10000 0 -0.29 5 5
SHC/Grb2/SOS1 0.054 0.039 -10000 0 -10000 0 0
PDGF/PDGFRA/Shf 0.012 0.082 -10000 0 -0.24 21 21
FOS -0.003 0.047 0.31 3 -10000 0 3
JUN -0.007 0.018 -10000 0 -10000 0 0
oligodendrocyte development 0.03 0.043 -10000 0 -0.19 8 8
GRB2 0.024 0.004 -10000 0 -10000 0 0
PIK3R1 0.023 0.005 -10000 0 -10000 0 0
mol:DAG 0.001 0.036 -10000 0 -0.2 7 7
PDGF/PDGFRA 0.018 0.056 -10000 0 -0.29 7 7
actin cytoskeleton reorganization 0.029 0.043 -10000 0 -0.19 8 8
SRF 0.004 0.011 -10000 0 -10000 0 0
SHC1 0.023 0.004 -10000 0 -10000 0 0
PI3K 0.041 0.04 -10000 0 -0.16 7 7
PDGF/PDGFRA/Crk/C3G 0.036 0.04 -10000 0 -0.16 6 6
JAK1 0.008 0.036 -10000 0 -0.19 7 7
ELK1/SRF 0.016 0.07 0.15 43 -10000 0 43
SHB 0.023 0.004 -10000 0 -10000 0 0
SHF 0 0.094 -10000 0 -0.38 13 13
CSNK2A1 0.012 0.018 -10000 0 -10000 0 0
GO:0007205 -0.004 0.041 -10000 0 -0.23 7 7
SOS1 0.024 0.002 -10000 0 -10000 0 0
Ras protein signal transduction 0.052 0.038 -10000 0 -10000 0 0
PDGF/PDGFRA/SHB 0.029 0.043 -10000 0 -0.19 8 8
PDGF/PDGFRA/Caveolin-1 0.025 0.056 -10000 0 -0.22 10 10
ITGAV 0.024 0 -10000 0 -10000 0 0
ELK1 -0.009 0.034 -10000 0 -0.2 7 7
PIK3CA 0.024 0.002 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk 0.025 0.042 -10000 0 -0.19 7 7
JAK-STAT cascade 0.008 0.036 -10000 0 -0.19 7 7
cell proliferation 0.012 0.082 -10000 0 -0.24 21 21
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.013 0.032 -10000 0 -0.2 5 5
CRKL 0.023 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.016 0.006 -10000 0 -10000 0 0
DOCK1 0.024 0.003 -10000 0 -10000 0 0
ITGA4 0.02 0.035 -10000 0 -0.29 3 3
alpha4/beta7 Integrin/MAdCAM1 -0.057 0.11 -10000 0 -0.3 8 8
EPO 0.01 0.028 0.31 1 -10000 0 1
alpha4/beta7 Integrin 0.026 0.05 -10000 0 -0.22 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.02 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.033 0.027 -10000 0 -0.2 3 3
EPO/EPOR (dimer) 0.032 0.016 0.23 1 -10000 0 1
lamellipodium assembly 0.006 0.073 -10000 0 -0.33 7 7
PIK3CA 0.024 0.002 -10000 0 -10000 0 0
PI3K 0.034 0.008 -10000 0 -10000 0 0
ARF6 0.023 0.006 -10000 0 -10000 0 0
JAK2 0.019 0.024 0.16 1 -0.16 3 4
PXN 0.024 0.002 -10000 0 -10000 0 0
PIK3R1 0.023 0.005 -10000 0 -10000 0 0
MADCAM1 -0.14 0.15 -10000 0 -0.29 123 123
cell adhesion -0.057 0.11 -10000 0 -0.29 8 8
CRKL/CBL 0.034 0.007 -10000 0 -10000 0 0
ITGB1 0.024 0.002 -10000 0 -10000 0 0
SRC 0.005 0.025 -10000 0 -0.28 1 1
ITGB7 0.014 0.053 -10000 0 -0.29 7 7
RAC1 0.021 0.008 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.042 0.035 -10000 0 -0.2 4 4
p130Cas/Crk/Dock1 0.016 0.027 -10000 0 -0.23 1 1
VCAM1 0.02 0.029 -10000 0 -0.29 2 2
RHOA 0.024 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.059 0.018 -10000 0 -0.15 1 1
BCAR1 -0.01 0.022 -10000 0 -0.26 1 1
EPOR 0.024 0.002 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.024 0.003 -10000 0 -10000 0 0
GIT1 0.023 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.005 0.075 -10000 0 -0.47 3 3
FAS signaling pathway (CD95)

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
SPTAN1 -0.003 0.015 0.15 2 -10000 0 2
RFC1 -0.003 0.015 0.15 2 -10000 0 2
PRKDC 0.012 0.059 0.21 18 -0.21 1 19
RIPK1 0.024 0.004 -10000 0 -10000 0 0
CASP7 0.008 0.07 -10000 0 -0.56 3 3
FASLG/FAS/FADD/FAF1 0.012 0.044 0.16 5 -0.18 5 10
MAP2K4 -0.007 0.084 -10000 0 -0.28 11 11
mol:ceramide 0.012 0.058 -10000 0 -0.23 8 8
GSN -0.003 0.018 0.15 2 -0.15 1 3
FASLG/FAS/FADD/FAF1/Caspase 8 0.009 0.055 -10000 0 -0.23 6 6
FAS 0.022 0.009 -10000 0 -10000 0 0
BID -0.013 0.037 0.24 4 -0.24 1 5
MAP3K1 0.007 0.071 0.19 1 -0.41 4 5
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
RB1 0.021 0.068 0.21 26 -10000 0 26
CFLAR 0.024 0.002 -10000 0 -10000 0 0
HGF/MET 0.013 0.089 -10000 0 -0.22 27 27
ARHGDIB -0.003 0.015 0.15 2 -10000 0 2
FADD 0.023 0.008 -10000 0 -10000 0 0
actin filament polymerization 0.003 0.018 -10000 0 -0.15 2 2
NFKB1 0.002 0.092 -10000 0 -0.56 5 5
MAPK8 -0.013 0.098 -10000 0 -0.41 7 7
DFFA -0.003 0.015 0.15 2 -10000 0 2
DNA fragmentation during apoptosis -0.001 0.025 0.18 4 -10000 0 4
FAS/FADD/MET 0.032 0.059 0.22 1 -0.22 10 11
CFLAR/RIP1 0.036 0.006 -10000 0 -10000 0 0
FAIM3 0.016 0.049 -10000 0 -0.31 5 5
FAF1 0.02 0.013 -10000 0 -10000 0 0
PARP1 -0.003 0.015 0.15 2 -10000 0 2
DFFB -0.001 0.025 0.18 4 -10000 0 4
CHUK -0.001 0.084 -10000 0 -0.52 5 5
FASLG 0.007 0.065 -10000 0 -0.31 9 9
FAS/FADD 0.033 0.013 -10000 0 -10000 0 0
HGF 0.014 0.053 -10000 0 -0.3 6 6
LMNA -0.008 0.031 0.19 1 -10000 0 1
CASP6 -0.003 0.015 0.15 2 -10000 0 2
CASP10 0.023 0.008 -10000 0 -10000 0 0
CASP3 -0.001 0.018 0.18 2 -10000 0 2
PTPN13 0 0.091 -10000 0 -0.36 14 14
CASP8 -0.012 0.041 0.26 5 -10000 0 5
IL6 -0.015 0.18 -10000 0 -0.98 6 6
MET 0.007 0.085 0.31 1 -0.38 10 11
ICAD/CAD -0.002 0.023 0.19 2 -10000 0 2
FASLG/FAS/FADD/FAF1/Caspase 10 0.012 0.059 -10000 0 -0.23 8 8
activation of caspase activity by cytochrome c -0.013 0.037 0.24 4 -0.24 1 5
PAK2 -0.003 0.015 0.15 2 -10000 0 2
BCL2 0.016 0.03 -10000 0 -0.29 2 2
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.008 0.003 -10000 0 -10000 0 0
SNTA1 0.015 0.012 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.008 0.004 -10000 0 -10000 0 0
MAPK12 -0.002 0.037 0.21 2 -0.2 6 8
CCND1 0.003 0.042 -10000 0 -0.32 3 3
p38 gamma/SNTA1 0.007 0.035 0.19 1 -0.18 6 7
MAP2K3 0.02 0.009 -10000 0 -10000 0 0
PKN1 0.024 0.002 -10000 0 -10000 0 0
G2/M transition checkpoint -0.002 0.037 0.21 2 -0.2 6 8
MAP2K6 0.006 0.001 -10000 0 -10000 0 0
MAPT -0.05 0.1 0.14 2 -0.25 47 49
MAPK13 0.01 0.004 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.013 0.001 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.023 0.005 -10000 0 -10000 0 0
HDAC3 0.024 0.004 -10000 0 -10000 0 0
VDR 0.024 0.002 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.046 0.011 -10000 0 -10000 0 0
EP300 0.023 0.005 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.003 0.026 -10000 0 -0.19 1 1
KAT2B 0.024 0.002 -10000 0 -10000 0 0
MAPK14 0.024 0 -10000 0 -10000 0 0
AKT1 0.001 0.042 0.19 1 -10000 0 1
RAR alpha/9cRA/Cyclin H -0.001 0.059 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.009 0.028 0.17 1 -10000 0 1
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.013 0.049 -10000 0 -0.16 1 1
NCOR2 0.024 0.002 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.018 0.002 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.028 0.068 0.29 1 -0.35 2 3
NCOA2 0.021 0.008 -10000 0 -10000 0 0
NCOA3 0.015 0.012 -10000 0 -10000 0 0
NCOA1 0.024 0.002 -10000 0 -10000 0 0
VDR/VDR/DNA 0.024 0.002 -10000 0 -10000 0 0
RARG 0.024 0.002 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.033 0.004 -10000 0 -10000 0 0
MAPK3 0.024 0.002 -10000 0 -10000 0 0
MAPK1 0.023 0.004 -10000 0 -10000 0 0
MAPK8 0.025 0.002 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.035 0.067 -10000 0 -0.32 2 2
RARA -0.02 0.05 0.15 4 -0.2 1 5
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.006 0.028 0.17 1 -0.19 1 2
PRKCA 0.025 0.004 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.037 0.071 0.31 1 -0.34 2 3
RXRG -0.15 0.15 0.22 1 -0.3 96 97
RXRA -0.017 0.05 0.25 1 -10000 0 1
RXRB -0.04 0.08 0.27 3 -0.3 1 4
VDR/Vit D3/DNA 0.018 0.002 -10000 0 -10000 0 0
RBP1 -0.038 0.15 -10000 0 -0.38 35 35
CRBP1/9-cic-RA -0.025 0.1 -10000 0 -0.27 35 35
RARB 0.024 0.021 -10000 0 -0.29 1 1
PRKCG -0.15 0.21 0.32 3 -0.38 104 107
MNAT1 0.023 0.005 -10000 0 -10000 0 0
RAR alpha/RXRs -0.022 0.067 -10000 0 -0.38 2 2
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.022 0.064 0.29 1 -0.31 2 3
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.061 0.22 3 -0.23 2 5
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.036 0.073 0.31 1 -0.36 2 3
positive regulation of DNA binding -0.005 0.052 -10000 0 -10000 0 0
NRIP1 -0.035 0.069 -10000 0 -10000 0 0
RXRs/RARs -0.037 0.075 0.33 1 -0.34 3 4
RXRs/RXRs/DNA/9cRA -0.04 0.062 -10000 0 -0.33 2 2
PRKACA 0.024 0.002 -10000 0 -10000 0 0
CDK7 0.023 0.004 -10000 0 -10000 0 0
TFIIH 0.045 0.014 -10000 0 -10000 0 0
RAR alpha/9cRA 0.006 0.059 0.22 1 -10000 0 1
CCNH 0.023 0.005 -10000 0 -10000 0 0
CREBBP 0.024 0.004 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.044 0.014 -10000 0 -10000 0 0
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.004 0.047 -10000 0 -10000 0 0
DAPP1 -0.006 0.12 0.18 31 -0.3 10 41
Src family/SYK family/BLNK-LAT/BTK-ITK -0.056 0.17 0.24 4 -0.48 17 21
mol:DAG 0.001 0.082 0.18 26 -0.21 6 32
HRAS 0.024 0.004 -10000 0 -10000 0 0
RAP1A 0.024 0.005 -10000 0 -10000 0 0
ARF5/GDP 0.033 0.088 0.22 1 -0.36 4 5
PLCG2 0.004 0.077 -10000 0 -0.29 15 15
PLCG1 0.015 0.012 -10000 0 -10000 0 0
ARF5 0.023 0.005 -10000 0 -10000 0 0
mol:GTP -0.014 0.019 0.14 3 -10000 0 3
ARF1/GTP 0.006 0.039 0.24 1 -10000 0 1
RHOA 0.024 0.004 -10000 0 -10000 0 0
YES1 0.02 0.009 -10000 0 -10000 0 0
RAP1A/GTP -0.014 0.02 0.16 3 -10000 0 3
ADAP1 -0.013 0.019 0.15 1 -10000 0 1
ARAP3 -0.014 0.019 0.14 3 -10000 0 3
INPPL1 0.024 0.004 -10000 0 -10000 0 0
PREX1 0.015 0.012 -10000 0 -10000 0 0
ARHGEF6 0.02 0.035 -10000 0 -0.29 3 3
ARHGEF7 0.02 0.009 -10000 0 -10000 0 0
ARF1 0.023 0.004 -10000 0 -10000 0 0
NRAS 0.024 0.005 -10000 0 -10000 0 0
FYN 0.024 0.004 -10000 0 -10000 0 0
ARF6 0.023 0.006 -10000 0 -10000 0 0
FGR 0.019 0.034 -10000 0 -0.34 2 2
mol:Ca2+ 0.005 0.051 0.15 7 -10000 0 7
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.001 0.083 -10000 0 -0.29 18 18
ZAP70 0.012 0.064 -10000 0 -0.32 8 8
mol:IP3 0.001 0.063 0.14 28 -0.16 4 32
LYN 0.021 0.008 -10000 0 -10000 0 0
ARF1/GDP 0.036 0.09 0.22 1 -0.35 5 6
RhoA/GDP 0.041 0.053 0.25 2 -10000 0 2
PDK1/Src/Hsp90 0.031 0.024 -10000 0 -10000 0 0
BLNK 0.021 0.029 -10000 0 -0.29 2 2
actin cytoskeleton reorganization 0.04 0.074 0.23 10 -0.28 1 11
SRC 0.016 0.012 -10000 0 -10000 0 0
PLEKHA2 -0.008 0.003 -10000 0 -10000 0 0
RAC1 0.021 0.008 -10000 0 -10000 0 0
PTEN 0.023 0.007 -10000 0 -10000 0 0
HSP90AA1 0.023 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.014 0.028 -10000 0 -10000 0 0
RhoA/GTP -0.015 0.021 0.15 3 -10000 0 3
Src family/SYK family/BLNK-LAT -0.031 0.089 -10000 0 -0.33 9 9
BLK -0.078 0.14 -10000 0 -0.29 70 70
PDPK1 0.024 0.003 -10000 0 -10000 0 0
CYTH1 -0.015 0.021 0.15 1 -10000 0 1
HCK 0.015 0.012 -10000 0 -10000 0 0
CYTH3 -0.013 0.019