PARADIGM pathway analysis of mRNASeq expression and copy number data
Skin Cutaneous Melanoma (Metastatic)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1FF3R52
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 64 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
Ephrin A reverse signaling 59
E-cadherin signaling events 51
TCR signaling in naïve CD8+ T cells 49
IL4-mediated signaling events 43
IL23-mediated signaling events 43
Stabilization and expansion of the E-cadherin adherens junction 42
Signaling events mediated by Stem cell factor receptor (c-Kit) 41
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 38
E-cadherin signaling in the nascent adherens junction 38
Angiopoietin receptor Tie2-mediated signaling 38
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 302 . 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 ( 302 ).

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
Ephrin A reverse signaling 0.1954 59 419 7 -0.05 0.001 1000 -1000 0 -1000
E-cadherin signaling events 0.1689 51 255 5 -0.067 0.029 1000 -1000 0.02 -1000
TCR signaling in naïve CD8+ T cells 0.1623 49 4580 93 -0.23 0.11 1000 -1000 -0.032 -1000
IL4-mediated signaling events 0.1424 43 3994 91 -0.51 0.37 1000 -1000 -0.067 -1000
IL23-mediated signaling events 0.1424 43 2590 60 -0.32 0.029 1000 -1000 -0.065 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.1391 42 3160 74 -0.067 0.064 1000 -1000 -0.038 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.1358 41 3213 78 -0.18 0.06 1000 -1000 -0.025 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1258 38 2646 68 -0.3 0.086 1000 -1000 -0.043 -1000
E-cadherin signaling in the nascent adherens junction 0.1258 38 2951 76 -0.12 0.043 1000 -1000 -0.037 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1258 38 3383 88 -0.2 0.037 1000 -1000 -0.048 -1000
IL12-mediated signaling events 0.1225 37 3286 87 -0.29 0.064 1000 -1000 -0.038 -1000
Signaling events regulated by Ret tyrosine kinase 0.1192 36 2977 82 -0.053 0.034 1000 -1000 -0.03 -1000
Endothelins 0.1192 36 3525 96 -0.12 0.051 1000 -1000 -0.02 -1000
Noncanonical Wnt signaling pathway 0.1126 34 886 26 -0.036 0.028 1000 -1000 -0.022 -1000
Syndecan-1-mediated signaling events 0.1093 33 1146 34 -0.051 0.029 1000 -1000 -0.012 -1000
BCR signaling pathway 0.1093 33 3332 99 -0.16 0.035 1000 -1000 -0.055 -1000
Wnt signaling 0.1060 32 225 7 -0.026 0.022 1000 -1000 0.004 -1000
E-cadherin signaling in keratinocytes 0.1026 31 1353 43 -0.069 0.031 1000 -1000 -0.012 -1000
Nectin adhesion pathway 0.0993 30 1930 63 -0.092 0.043 1000 -1000 -0.024 -1000
Integrins in angiogenesis 0.0960 29 2499 84 -0.12 0.049 1000 -1000 -0.025 -1000
Osteopontin-mediated events 0.0927 28 1101 38 -0.049 0.031 1000 -1000 -0.016 -1000
Glypican 1 network 0.0927 28 1357 48 -0.04 0.039 1000 -1000 -0.021 -1000
Signaling mediated by p38-alpha and p38-beta 0.0894 27 1192 44 -0.06 0.029 1000 -1000 -0.007 -1000
TCGA08_retinoblastoma 0.0894 27 221 8 -0.006 0.047 1000 -1000 -0.006 -1000
Thromboxane A2 receptor signaling 0.0861 26 2806 105 -0.086 0.034 1000 -1000 -0.022 -1000
LPA receptor mediated events 0.0861 26 2750 102 -0.08 0.033 1000 -1000 -0.077 -1000
S1P4 pathway 0.0861 26 659 25 -0.038 0.037 1000 -1000 -0.011 -1000
p75(NTR)-mediated signaling 0.0828 25 3194 125 -0.048 0.073 1000 -1000 -0.036 -1000
Calcium signaling in the CD4+ TCR pathway 0.0828 25 785 31 -0.087 0.029 1000 -1000 -0.032 -1000
Glucocorticoid receptor regulatory network 0.0795 24 2809 114 -0.25 0.13 1000 -1000 -0.036 -1000
EPHB forward signaling 0.0795 24 2122 85 -0.056 0.06 1000 -1000 -0.042 -1000
EGFR-dependent Endothelin signaling events 0.0795 24 523 21 -0.038 0.041 1000 -1000 -0.029 -1000
Caspase cascade in apoptosis 0.0762 23 1730 74 -0.062 0.04 1000 -1000 -0.033 -1000
HIF-1-alpha transcription factor network 0.0762 23 1750 76 -0.027 0.065 1000 -1000 -0.01 -1000
a4b1 and a4b7 Integrin signaling 0.0762 23 115 5 0 0.017 1000 -1000 0.02 -1000
BMP receptor signaling 0.0762 23 1934 81 -0.045 0.05 1000 -1000 -0.021 -1000
FAS signaling pathway (CD95) 0.0762 23 1122 47 -0.048 0.037 1000 -1000 -0.029 -1000
IL27-mediated signaling events 0.0762 23 1189 51 -0.15 0.1 1000 -1000 -0.043 -1000
JNK signaling in the CD4+ TCR pathway 0.0695 21 366 17 -0.087 0.041 1000 -1000 -0.02 -1000
Signaling events mediated by PTP1B 0.0695 21 1621 76 -0.059 0.043 1000 -1000 -0.034 -1000
Glypican 2 network 0.0695 21 85 4 0.011 0.015 1000 -1000 0.019 -1000
Class IB PI3K non-lipid kinase events 0.0695 21 63 3 -0.008 0.008 1000 -1000 -0.024 -1000
Arf6 signaling events 0.0662 20 1248 62 -0.03 0.058 1000 -1000 -0.025 -1000
Ephrin B reverse signaling 0.0662 20 978 48 -0.049 0.039 1000 -1000 -0.029 -1000
Reelin signaling pathway 0.0629 19 1116 56 -0.031 0.056 1000 -1000 -0.019 -1000
S1P5 pathway 0.0629 19 339 17 -0.037 0.033 1000 -1000 -0.004 -1000
IL2 signaling events mediated by PI3K 0.0629 19 1115 58 -0.1 0.042 1000 -1000 -0.033 -1000
Effects of Botulinum toxin 0.0629 19 508 26 -0.016 0.04 1000 -1000 -0.004 -1000
Syndecan-4-mediated signaling events 0.0629 19 1294 67 -0.045 0.037 1000 -1000 -0.027 -1000
Plasma membrane estrogen receptor signaling 0.0629 19 1704 86 -0.12 0.087 1000 -1000 -0.037 -1000
Signaling events mediated by the Hedgehog family 0.0596 18 970 52 -0.045 0.043 1000 -1000 -0.024 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0596 18 1566 85 -0.035 0.036 1000 -1000 -0.022 -1000
Fc-epsilon receptor I signaling in mast cells 0.0596 18 1812 97 -0.051 0.049 1000 -1000 -0.039 -1000
amb2 Integrin signaling 0.0596 18 1496 82 -0.037 0.041 1000 -1000 -0.018 -1000
Ceramide signaling pathway 0.0596 18 1415 76 -0.041 0.041 1000 -1000 -0.017 -1000
TRAIL signaling pathway 0.0596 18 879 48 -0.024 0.044 1000 -1000 -0.021 -1000
S1P1 pathway 0.0596 18 661 36 -0.076 0.029 1000 -1000 -0.017 -1000
IFN-gamma pathway 0.0563 17 1180 68 -0.032 0.037 1000 -1000 -0.03 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0563 17 918 52 -0.061 0.061 1000 -1000 -0.024 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0563 17 797 45 -0.047 0.059 1000 -1000 -0.037 -1000
Class I PI3K signaling events 0.0563 17 1291 73 -0.092 0.051 1000 -1000 -0.019 -1000
ceramide signaling pathway 0.0530 16 812 49 -0.027 0.041 1000 -1000 -0.029 -1000
IL2 signaling events mediated by STAT5 0.0530 16 354 22 -0.04 0.029 1000 -1000 -0.017 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0530 16 1990 120 -0.089 0.069 1000 -1000 -0.035 -1000
ErbB2/ErbB3 signaling events 0.0497 15 981 65 -0.032 0.041 1000 -1000 -0.052 -1000
TCGA08_p53 0.0497 15 107 7 -0.013 0.024 1000 -1000 -0.001 -1000
Signaling mediated by p38-gamma and p38-delta 0.0497 15 235 15 -0.023 0.027 1000 -1000 -0.019 -1000
Ras signaling in the CD4+ TCR pathway 0.0497 15 269 17 -0.021 0.051 1000 -1000 -0.014 -1000
Syndecan-2-mediated signaling events 0.0464 14 979 69 -0.019 0.043 1000 -1000 -0.021 -1000
IL1-mediated signaling events 0.0464 14 914 62 -0.013 0.069 1000 -1000 -0.017 -1000
S1P3 pathway 0.0464 14 602 42 -0.037 0.045 1000 -1000 -0.012 -1000
LPA4-mediated signaling events 0.0430 13 163 12 -0.038 0.006 1000 -1000 -0.017 -1000
EPO signaling pathway 0.0430 13 746 55 -0.001 0.05 1000 -1000 -0.016 -1000
Regulation of p38-alpha and p38-beta 0.0430 13 715 54 -0.057 0.059 1000 -1000 -0.033 -1000
IL6-mediated signaling events 0.0430 13 978 75 -0.03 0.069 1000 -1000 -0.037 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0397 12 684 54 -0.02 0.04 1000 -1000 -0.015 -1000
PDGFR-alpha signaling pathway 0.0397 12 532 44 -0.019 0.054 1000 -1000 -0.021 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0397 12 474 37 -0.032 0.046 1000 -1000 -0.014 -1000
Paxillin-dependent events mediated by a4b1 0.0397 12 442 36 -0.036 0.047 1000 -1000 -0.029 -1000
PDGFR-beta signaling pathway 0.0397 12 1202 97 -0.058 0.065 1000 -1000 -0.032 -1000
Visual signal transduction: Rods 0.0397 12 628 52 -0.002 0.047 1000 -1000 -0.015 -1000
Regulation of Androgen receptor activity 0.0397 12 862 70 -0.088 0.036 1000 -1000 -0.038 -1000
Cellular roles of Anthrax toxin 0.0364 11 452 39 -0.031 0.028 1000 -1000 -0.013 -1000
Nongenotropic Androgen signaling 0.0364 11 574 52 -0.057 0.044 1000 -1000 -0.018 -1000
Regulation of nuclear SMAD2/3 signaling 0.0331 10 1404 136 -0.26 0.074 1000 -1000 -0.036 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0331 10 296 28 -0.037 0.043 1000 -1000 -0.011 -1000
Presenilin action in Notch and Wnt signaling 0.0331 10 614 61 -0.013 0.073 1000 -1000 -0.039 -1000
FOXA2 and FOXA3 transcription factor networks 0.0331 10 494 46 -0.14 0.041 1000 -1000 -0.062 -1000
Atypical NF-kappaB pathway 0.0331 10 328 31 -0.018 0.035 1000 -1000 -0.006 -1000
Canonical Wnt signaling pathway 0.0331 10 512 51 -0.032 0.065 1000 -1000 -0.028 -1000
IGF1 pathway 0.0331 10 602 57 -0.028 0.061 1000 -1000 -0.021 -1000
Hedgehog signaling events mediated by Gli proteins 0.0298 9 620 65 -0.053 0.067 1000 -1000 -0.032 -1000
Signaling events mediated by HDAC Class III 0.0298 9 379 40 -0.054 0.045 1000 -1000 -0.039 -1000
HIF-2-alpha transcription factor network 0.0298 9 402 43 -0.11 0.11 1000 -1000 -0.042 -1000
TCGA08_rtk_signaling 0.0298 9 255 26 -0.023 0.062 1000 -1000 -0.013 -1000
Rapid glucocorticoid signaling 0.0298 9 182 20 -0.008 0.028 1000 -1000 0 -1000
Coregulation of Androgen receptor activity 0.0265 8 638 76 -0.064 0.048 1000 -1000 -0.017 -1000
ErbB4 signaling events 0.0265 8 561 69 -0.066 0.064 1000 -1000 -0.016 -1000
Arf6 downstream pathway 0.0265 8 361 43 -0.039 0.048 1000 -1000 -0.032 -1000
mTOR signaling pathway 0.0265 8 447 53 -0.025 0.036 1000 -1000 -0.019 -1000
Retinoic acid receptors-mediated signaling 0.0265 8 504 58 -0.044 0.054 1000 -1000 -0.023 -1000
Insulin Pathway 0.0265 8 645 74 -0.069 0.07 1000 -1000 -0.03 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0265 8 292 33 -0.006 0.061 1000 -1000 -0.025 -1000
Aurora B signaling 0.0265 8 566 67 -0.071 0.063 1000 -1000 -0.029 -1000
Visual signal transduction: Cones 0.0232 7 271 38 -0.013 0.05 1000 -1000 -0.002 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0232 7 623 83 -0.029 0.054 1000 -1000 -0.014 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0232 7 951 125 -0.024 0.069 1000 -1000 -0.013 -1000
Regulation of Telomerase 0.0232 7 789 102 -0.087 0.058 1000 -1000 -0.037 -1000
FOXM1 transcription factor network 0.0232 7 381 51 -0.019 0.079 1000 -1000 -0.063 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0199 6 217 34 -0.041 0.072 1000 -1000 -0.029 -1000
PLK1 signaling events 0.0199 6 565 85 -0.009 0.05 1000 -1000 -0.02 -1000
FoxO family signaling 0.0199 6 397 64 -0.18 0.042 1000 -1000 -0.042 -1000
Syndecan-3-mediated signaling events 0.0199 6 214 35 0 0.073 1000 -1000 -0.013 -1000
p38 MAPK signaling pathway 0.0199 6 270 44 -0.042 0.047 1000 -1000 -0.015 -1000
Canonical NF-kappaB pathway 0.0166 5 206 39 -0.005 0.058 1000 -1000 -0.02 -1000
BARD1 signaling events 0.0166 5 300 57 -0.055 0.058 1000 -1000 -0.039 -1000
VEGFR1 specific signals 0.0166 5 307 56 -0.028 0.054 1000 -1000 -0.019 -1000
Signaling events mediated by PRL 0.0166 5 173 34 -0.025 0.048 1000 -1000 -0.032 -1000
PLK2 and PLK4 events 0.0132 4 13 3 0.006 -1000 1000 -1000 -0.004 -1000
Insulin-mediated glucose transport 0.0132 4 130 32 -0.021 0.05 1000 -1000 -0.012 -1000
Class I PI3K signaling events mediated by Akt 0.0132 4 276 68 -0.04 0.051 1000 -1000 -0.02 -1000
Aurora A signaling 0.0099 3 223 60 -0.026 0.059 1000 -1000 -0.006 -1000
Signaling events mediated by HDAC Class I 0.0099 3 402 104 -0.053 0.067 1000 -1000 -0.036 -1000
Arf6 trafficking events 0.0099 3 225 71 -0.041 0.053 1000 -1000 -0.035 -1000
Signaling events mediated by HDAC Class II 0.0066 2 207 75 -0.03 0.071 1000 -1000 -0.02 -1000
Circadian rhythm pathway 0.0066 2 49 22 -0.008 0.045 1000 -1000 -0.02 -1000
Aurora C signaling 0.0066 2 18 7 0 0.046 1000 -1000 -0.007 -1000
Arf1 pathway 0.0066 2 135 54 -0.002 0.047 1000 -1000 -0.009 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 14 23 0.005 0.057 1000 -1000 -0.011 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 12 27 -0.01 0.067 1000 -1000 -0.023 -1000
Alternative NF-kappaB pathway 0.0000 0 3 13 0 0.071 1000 -1000 0 -1000
Total NA 2254 132299 7203 -8.1 -990 131000 -131000 -3.1 -131000
Ephrin A reverse signaling

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
MAPKKK cascade -0.029 0.11 -10000 0 -0.21 79 79
EFNA5 0.001 0.097 -10000 0 -0.33 23 23
FYN -0.036 0.098 0.18 8 -0.19 74 82
neuron projection morphogenesis -0.029 0.11 -10000 0 -0.21 79 79
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.028 0.11 -10000 0 -0.21 79 79
EPHA5 -0.05 0.15 0.12 10 -0.33 67 77
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin -0.012 0.12 -10000 0 -0.2 82 82
E-cadherin/beta catenin -0.031 0.12 -10000 0 -0.23 82 82
CTNNB1 0.029 0.003 -10000 0 -10000 0 0
JUP 0.028 0.033 0.12 7 -0.33 2 9
CDH1 -0.067 0.16 -10000 0 -0.33 82 82
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.091 0.31 0.31 13 -0.59 73 86
FYN -0.17 0.41 0.28 8 -0.79 76 84
LAT/GRAP2/SLP76 -0.11 0.31 0.27 3 -0.59 76 79
IKBKB 0.028 0.006 -10000 0 -10000 0 0
AKT1 -0.088 0.24 0.21 6 -0.49 71 77
B2M 0.024 0.016 -10000 0 -10000 0 0
IKBKG -0.016 0.074 0.11 9 -0.14 59 68
MAP3K8 0.023 0.044 -10000 0 -0.33 4 4
mol:Ca2+ -0.017 0.022 0.086 5 -0.054 45 50
integrin-mediated signaling pathway 0.03 0.035 -10000 0 -0.19 6 6
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.15 0.37 0.28 3 -0.72 77 80
TRPV6 0.11 0.35 1.2 29 -10000 0 29
CD28 0.013 0.082 0.12 9 -0.34 15 24
SHC1 -0.16 0.4 0.28 14 -0.76 77 91
receptor internalization -0.19 0.45 0.21 11 -0.83 82 93
PRF1 -0.23 0.51 -10000 0 -1.1 71 71
KRAS 0.028 0.005 -10000 0 -10000 0 0
GRB2 0.028 0.005 -10000 0 -10000 0 0
COT/AKT1 -0.054 0.2 0.18 8 -0.39 68 76
LAT -0.17 0.4 0.22 6 -0.78 77 83
EntrezGene:6955 -0.001 0.004 -10000 0 -10000 0 0
CD3D -0.012 0.12 0.13 19 -0.34 35 54
CD3E -0.009 0.12 0.13 9 -0.34 32 41
CD3G -0.014 0.13 0.13 23 -0.34 38 61
RASGRP2 -0.006 0.051 0.066 1 -0.19 17 18
RASGRP1 -0.093 0.26 0.22 12 -0.53 70 82
HLA-A 0.013 0.051 -10000 0 -0.34 5 5
RASSF5 0.019 0.056 0.12 4 -0.33 7 11
RAP1A/GTP/RAPL 0.03 0.035 -10000 0 -0.19 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.002 0.085 0.15 25 -0.13 57 82
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.055 0.11 -10000 0 -0.24 66 66
PRKCA -0.046 0.14 0.18 9 -0.29 66 75
GRAP2 0.01 0.079 -10000 0 -0.33 15 15
mol:IP3 -0.1 0.21 -10000 0 -0.43 78 78
EntrezGene:6957 -0.001 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.16 0.42 0.17 7 -0.88 65 72
ORAI1 -0.1 0.3 -10000 0 -1 29 29
CSK -0.17 0.41 0.24 3 -0.77 79 82
B7 family/CD28 -0.13 0.42 0.31 4 -0.84 67 71
CHUK 0.025 0.022 -10000 0 -0.33 1 1
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.21 0.49 0.22 7 -0.91 81 88
PTPN6 -0.17 0.42 0.22 6 -0.79 78 84
VAV1 -0.17 0.41 0.22 6 -0.77 80 86
Monovalent TCR/CD3 -0.08 0.25 0.14 15 -0.55 55 70
CBL 0.025 0.01 -10000 0 -10000 0 0
LCK -0.18 0.46 0.27 8 -0.92 70 78
PAG1 -0.17 0.41 0.25 5 -0.78 77 82
RAP1A 0.028 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.21 0.49 0.21 7 -0.93 78 85
CD80 0.007 0.088 -10000 0 -0.34 18 18
CD86 0.008 0.085 0.13 1 -0.34 17 18
PDK1/CARD11/BCL10/MALT1 -0.051 0.14 0.12 7 -0.29 67 74
HRAS 0.028 0.005 -10000 0 -10000 0 0
GO:0035030 -0.12 0.31 0.2 9 -0.66 67 76
CD8A -0.029 0.15 -10000 0 -0.34 53 53
CD8B -0.042 0.16 -10000 0 -0.34 63 63
PTPRC -0.003 0.11 0.12 18 -0.34 28 46
PDK1/PKC theta -0.12 0.3 0.24 6 -0.58 76 82
CSK/PAG1 -0.16 0.4 0.3 9 -0.76 76 85
SOS1 0.029 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.026 0.044 -10000 0 -0.24 5 5
GRAP2/SLP76 -0.14 0.38 0.26 1 -0.7 79 80
STIM1 -0.021 0.058 -10000 0 -10000 0 0
RAS family/GTP -0.001 0.11 0.18 22 -0.18 57 79
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.22 0.51 0.21 9 -0.94 82 91
mol:DAG -0.1 0.18 -10000 0 -0.38 78 78
RAP1A/GDP 0.004 0.04 0.075 17 -0.063 47 64
PLCG1 0.026 0.008 -10000 0 -10000 0 0
CD247 -0.003 0.11 0.13 19 -0.34 28 47
cytotoxic T cell degranulation -0.21 0.48 -10000 0 -1 71 71
RAP1A/GTP -0.002 0.019 -10000 0 -0.07 17 17
mol:PI-3-4-5-P3 -0.11 0.29 0.23 7 -0.57 74 81
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.12 0.29 -10000 0 -0.57 77 77
NRAS 0.027 0.007 -10000 0 -10000 0 0
ZAP70 -0.01 0.13 0.12 31 -0.33 40 71
GRB2/SOS1 0.041 0.009 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.12 0.3 0.21 1 -0.57 78 79
MALT1 0.026 0.03 -10000 0 -0.33 2 2
TRAF6 0.028 0.005 -10000 0 -10000 0 0
CD8 heterodimer -0.041 0.19 0.19 21 -0.38 67 88
CARD11 -0.008 0.12 0.12 22 -0.33 33 55
PRKCB -0.048 0.16 0.18 12 -0.31 67 79
PRKCE -0.045 0.14 0.18 9 -0.29 64 73
PRKCQ -0.14 0.35 0.25 5 -0.68 77 82
LCP2 0.016 0.062 -10000 0 -0.33 9 9
BCL10 0.028 0.005 -10000 0 -10000 0 0
regulation of survival gene product expression -0.069 0.21 0.2 8 -0.41 70 78
IKK complex -0.003 0.073 0.14 17 -0.12 55 72
RAS family/GDP -0.006 0.016 -10000 0 -0.04 30 30
MAP3K14 -0.042 0.15 0.15 8 -0.29 67 75
PDPK1 -0.082 0.23 0.2 8 -0.46 71 79
TCR/CD3/MHC I/CD8/Fyn -0.23 0.52 -10000 0 -1 80 80
IL4-mediated signaling events

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
BCL2L1 -0.32 0.54 -10000 0 -1.2 61 61
STAT6 (cleaved dimer) -0.37 0.57 -10000 0 -1.2 83 83
IGHG1 -0.084 0.19 -10000 0 -0.37 16 16
IGHG3 -0.32 0.52 -10000 0 -1 80 80
AKT1 -0.21 0.41 -10000 0 -0.9 57 57
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.2 0.46 -10000 0 -1 52 52
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.22 0.44 -10000 0 -1 50 50
THY1 -0.33 0.54 -10000 0 -1.2 63 63
MYB 0.019 0.056 0.12 5 -0.33 7 12
HMGA1 0.026 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.26 0.47 -10000 0 -0.89 81 81
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.23 0.46 -10000 0 -1.1 50 50
SP1 0.03 0.025 -10000 0 -0.11 5 5
INPP5D 0.014 0.075 0.12 5 -0.33 13 18
SOCS5 0.024 0.037 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.36 0.57 -10000 0 -1.2 79 79
SOCS1 -0.22 0.36 -10000 0 -0.73 75 75
SOCS3 -0.2 0.4 -10000 0 -0.91 51 51
FCER2 -0.36 0.61 -10000 0 -1.2 84 84
PARP14 0.023 0.04 -10000 0 -0.27 4 4
CCL17 -0.38 0.61 -10000 0 -1.3 74 74
GRB2 0.028 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.16 0.36 -10000 0 -0.82 48 48
T cell proliferation -0.35 0.57 -10000 0 -1.2 73 73
IL4R/JAK1 -0.34 0.54 -10000 0 -1.2 64 64
EGR2 -0.35 0.57 -10000 0 -1.2 69 69
JAK2 -0.011 0.07 -10000 0 -0.35 5 5
JAK3 0.016 0.063 0.13 6 -0.31 9 15
PIK3R1 0.025 0.03 -10000 0 -0.33 2 2
JAK1 0.012 0.032 -10000 0 -10000 0 0
COL1A2 -0.12 0.33 -10000 0 -1.3 15 15
CCL26 -0.32 0.54 -10000 0 -1.2 62 62
IL4R -0.35 0.58 -10000 0 -1.3 63 63
PTPN6 0.009 0.078 0.13 2 -0.32 14 16
IL13RA2 -0.51 0.67 -10000 0 -1.3 112 112
IL13RA1 -0.005 0.062 -10000 0 -0.37 1 1
IRF4 -0.24 0.53 -10000 0 -1.3 55 55
ARG1 -0.089 0.23 -10000 0 -0.69 19 19
CBL -0.24 0.43 -10000 0 -0.84 80 80
GTF3A 0.03 0.024 -10000 0 -0.11 4 4
PIK3CA 0.023 0.042 -10000 0 -0.33 4 4
IL13RA1/JAK2 -0.004 0.086 -10000 0 -0.24 6 6
IRF4/BCL6 -0.21 0.48 -10000 0 -1.2 55 55
CD40LG -0.01 0.12 -10000 0 -0.23 56 56
MAPK14 -0.23 0.44 -10000 0 -0.88 70 70
mitosis -0.19 0.38 -10000 0 -0.83 57 57
STAT6 -0.39 0.68 -10000 0 -1.4 72 72
SPI1 0.021 0.059 -10000 0 -0.33 8 8
RPS6KB1 -0.18 0.36 -10000 0 -0.8 55 55
STAT6 (dimer) -0.39 0.68 -10000 0 -1.4 72 72
STAT6 (dimer)/PARP14 -0.37 0.61 -10000 0 -1.2 76 76
mast cell activation 0.007 0.015 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.24 0.48 -10000 0 -1.1 55 55
FRAP1 -0.21 0.41 -10000 0 -0.9 57 57
LTA -0.37 0.64 -10000 0 -1.4 69 69
FES 0.019 0.055 -10000 0 -0.33 7 7
T-helper 1 cell differentiation 0.37 0.63 1.3 72 -10000 0 72
CCL11 -0.34 0.55 -10000 0 -1.2 67 67
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.22 0.47 -10000 0 -1 54 54
IL2RG -0.016 0.12 0.13 15 -0.32 38 53
IL10 -0.34 0.58 -10000 0 -1.2 68 68
IRS1 0.013 0.073 -10000 0 -0.33 13 13
IRS2 0.025 0.03 -10000 0 -0.33 2 2
IL4 -0.09 0.27 -10000 0 -1.1 14 14
IL5 -0.33 0.54 -10000 0 -1.2 65 65
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.28 0.47 -10000 0 -0.97 70 70
COL1A1 -0.13 0.36 -10000 0 -1.4 16 16
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.34 0.56 -10000 0 -1.3 61 61
IL2R gamma/JAK3 0.003 0.11 0.19 5 -0.24 43 48
TFF3 -0.45 0.65 -10000 0 -1.3 96 96
ALOX15 -0.32 0.54 -10000 0 -1.2 64 64
MYBL1 0.021 0.042 -10000 0 -0.33 4 4
T-helper 2 cell differentiation -0.3 0.52 -10000 0 -1.1 73 73
SHC1 0.026 0.009 -10000 0 -10000 0 0
CEBPB 0.028 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.21 0.44 -10000 0 -1 51 51
mol:PI-3-4-5-P3 -0.21 0.41 -10000 0 -0.9 57 57
PI3K -0.23 0.45 -10000 0 -1 56 56
DOK2 0.01 0.079 0.12 2 -0.33 15 17
ETS1 0.019 0.035 0.15 1 -10000 0 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.15 0.34 -10000 0 -0.77 47 47
ITGB3 -0.43 0.64 -10000 0 -1.3 87 87
PIGR -0.35 0.58 -10000 0 -1.2 75 75
IGHE 0.025 0.068 0.17 28 -0.16 2 30
MAPKKK cascade -0.15 0.32 -10000 0 -0.75 47 47
BCL6 0.028 0.007 -10000 0 -10000 0 0
OPRM1 -0.33 0.54 -10000 0 -1.2 61 61
RETNLB -0.34 0.54 -10000 0 -1.2 63 63
SELP -0.39 0.63 -10000 0 -1.3 82 82
AICDA -0.32 0.52 -10000 0 -1.1 63 63
IL23-mediated signaling events

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
CCL2 -0.23 0.55 -10000 0 -1.2 63 63
IL23A -0.23 0.57 -10000 0 -1.2 57 57
NF kappa B1 p50/RelA/I kappa B alpha -0.22 0.58 -10000 0 -1.2 69 69
positive regulation of T cell mediated cytotoxicity -0.28 0.67 -10000 0 -1.3 69 69
ITGA3 -0.26 0.58 -10000 0 -1.2 72 72
IL17F -0.14 0.36 -10000 0 -0.72 62 62
IL12B 0.018 0.061 0.19 9 -10000 0 9
STAT1 (dimer) -0.26 0.64 -10000 0 -1.3 70 70
CD4 -0.23 0.56 -10000 0 -1.2 64 64
IL23 -0.21 0.55 -10000 0 -1.2 58 58
IL23R 0.01 0.11 -10000 0 -0.88 1 1
IL1B -0.26 0.61 -10000 0 -1.3 63 63
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.24 0.59 0.6 1 -1.2 68 69
TYK2 0.012 0.045 -10000 0 -10000 0 0
STAT4 0.006 0.1 0.12 15 -0.33 23 38
STAT3 0.028 0.005 -10000 0 -10000 0 0
IL18RAP 0.005 0.094 0.13 9 -0.34 18 27
IL12RB1 -0.03 0.14 0.16 5 -0.36 40 45
PIK3CA 0.023 0.042 -10000 0 -0.33 4 4
IL12Rbeta1/TYK2 -0.01 0.11 0.16 2 -0.26 40 42
IL23R/JAK2 0.022 0.13 -10000 0 -0.77 1 1
positive regulation of chronic inflammatory response -0.28 0.67 -10000 0 -1.3 69 69
natural killer cell activation 0.001 0.009 -10000 0 -10000 0 0
JAK2 0.011 0.071 -10000 0 -0.36 5 5
PIK3R1 0.025 0.03 -10000 0 -0.33 2 2
NFKB1 0.028 0.006 -10000 0 -10000 0 0
RELA 0.028 0.007 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.19 0.52 -10000 0 -1.1 60 60
ALOX12B -0.22 0.54 -10000 0 -1.1 63 63
CXCL1 -0.27 0.6 -10000 0 -1.2 74 74
T cell proliferation -0.28 0.67 -10000 0 -1.3 69 69
NFKBIA 0.029 0.005 -10000 0 -10000 0 0
IL17A -0.093 0.29 -10000 0 -0.55 60 60
PI3K -0.24 0.6 -10000 0 -1.2 68 68
IFNG -0.021 0.061 -10000 0 -0.13 59 59
STAT3 (dimer) -0.22 0.57 -10000 0 -1.1 68 68
IL18R1 -0.003 0.098 -10000 0 -0.33 22 22
IL23/IL23R/JAK2/TYK2/SOCS3 -0.14 0.41 -10000 0 -0.81 59 59
IL18/IL18R 0.005 0.13 0.21 10 -0.24 48 58
macrophage activation -0.01 0.022 0.03 1 -0.045 51 52
TNF -0.24 0.6 -10000 0 -1.3 60 60
STAT3/STAT4 -0.25 0.61 -10000 0 -1.2 71 71
STAT4 (dimer) -0.27 0.65 -10000 0 -1.3 71 71
IL18 0.003 0.083 0.13 7 -0.33 15 22
IL19 -0.21 0.55 -10000 0 -1.2 60 60
STAT5A (dimer) -0.27 0.63 -10000 0 -1.3 69 69
STAT1 0.026 0.029 -10000 0 -0.33 2 2
SOCS3 0.021 0.051 -10000 0 -0.33 6 6
CXCL9 -0.31 0.66 -10000 0 -1.3 81 81
MPO -0.24 0.56 -10000 0 -1.2 67 67
positive regulation of humoral immune response -0.28 0.67 -10000 0 -1.3 69 69
IL23/IL23R/JAK2/TYK2 -0.32 0.78 -10000 0 -1.5 69 69
IL6 -0.23 0.58 -10000 0 -1.2 64 64
STAT5A 0.024 0.036 -10000 0 -0.33 3 3
IL2 0.004 0.034 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.001 0.009 -10000 0 -10000 0 0
CD3E -0.27 0.62 -10000 0 -1.3 66 66
keratinocyte proliferation -0.28 0.67 -10000 0 -1.3 69 69
NOS2 -0.24 0.56 -10000 0 -1.1 70 70
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.034 0.094 -10000 0 -0.18 82 82
epithelial cell differentiation -0.004 0.1 -10000 0 -0.16 81 81
CYFIP2 0.014 0.072 0.12 3 -0.33 12 15
ENAH -0.047 0.065 -10000 0 -0.24 7 7
EGFR 0.021 0.071 -10000 0 -0.33 10 10
EPHA2 0.022 0.052 0.12 5 -0.33 6 11
MYO6 -0.049 0.079 0.2 6 -0.17 78 84
CTNNB1 0.029 0.003 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.042 0.052 -10000 0 -0.19 12 12
AQP5 -0.022 0.077 0.33 2 -0.41 1 3
CTNND1 0.029 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.046 0.076 0.2 6 -0.16 77 83
regulation of calcium-dependent cell-cell adhesion -0.045 0.081 0.21 6 -0.16 81 87
EGF -0.03 0.14 -10000 0 -0.33 54 54
NCKAP1 0.029 0.002 -10000 0 -10000 0 0
AQP3 -0.052 0.12 0.38 1 -0.34 28 29
cortical microtubule organization -0.004 0.1 -10000 0 -0.16 81 81
GO:0000145 -0.046 0.071 0.19 6 -0.15 77 83
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0.1 -10000 0 -0.17 81 81
MLLT4 0.022 0.037 -10000 0 -0.33 3 3
ARF6/GDP -0.055 0.06 -10000 0 -0.16 72 72
ARF6 0.028 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.058 0.046 -10000 0 -0.17 7 7
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.035 0.07 0.2 5 -10000 0 5
PVRL2 0.029 0.003 -10000 0 -10000 0 0
ZYX -0.043 0.074 0.2 5 -0.16 71 76
ARF6/GTP 0.064 0.047 -10000 0 -0.16 7 7
CDH1 -0.067 0.16 -10000 0 -0.33 82 82
EGFR/EGFR/EGF/EGF -0.042 0.12 -10000 0 -0.19 112 112
RhoA/GDP -0.002 0.099 -10000 0 -0.16 81 81
actin cytoskeleton organization -0.053 0.079 0.19 6 -0.17 70 76
IGF-1R heterotetramer 0.026 0.03 -10000 0 -0.33 2 2
GIT1 0.028 0.005 -10000 0 -10000 0 0
IGF1R 0.026 0.03 -10000 0 -0.33 2 2
IGF1 0.01 0.085 0.12 6 -0.33 17 23
DIAPH1 -0.037 0.22 -10000 0 -0.54 39 39
Wnt receptor signaling pathway 0.004 0.1 0.16 81 -10000 0 81
RHOA 0.029 0.003 -10000 0 -10000 0 0
RhoA/GTP -0.055 0.061 -10000 0 -0.16 72 72
CTNNA1 0.027 0.007 -10000 0 -10000 0 0
VCL -0.054 0.08 0.19 6 -0.17 70 76
EFNA1 0.025 0.022 -10000 0 -0.33 1 1
LPP -0.051 0.074 0.2 6 -0.16 80 86
Ephrin A1/EPHA2 -0.009 0.093 -10000 0 -0.16 77 77
SEC6/SEC8 -0.05 0.062 -10000 0 -0.16 73 73
MGAT3 -0.046 0.082 0.21 6 -0.16 81 87
HGF/MET -0.025 0.11 -10000 0 -0.18 94 94
HGF 0.019 0.069 -10000 0 -0.33 10 10
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.034 0.095 -10000 0 -0.19 82 82
actin cable formation -0.018 0.1 0.26 14 -0.26 10 24
KIAA1543 -0.05 0.075 0.19 6 -0.16 83 89
KIFC3 -0.05 0.074 0.24 3 -0.16 79 82
NCK1 0.028 0.005 -10000 0 -10000 0 0
EXOC3 0.026 0.009 -10000 0 -10000 0 0
ACTN1 -0.049 0.078 0.2 6 -0.16 81 87
NCK1/GIT1 0.041 0.01 -10000 0 -10000 0 0
mol:GDP -0.004 0.1 -10000 0 -0.16 81 81
EXOC4 0.025 0.009 -10000 0 -10000 0 0
STX4 -0.048 0.077 0.2 6 -0.16 79 85
PIP5K1C -0.047 0.077 0.2 6 -0.16 77 83
LIMA1 0.028 0.004 -10000 0 -10000 0 0
ABI1 0.026 0.009 -10000 0 -10000 0 0
ROCK1 -0.037 0.092 0.35 4 -0.24 1 5
adherens junction assembly -0.045 0.087 0.27 4 -0.29 9 13
IGF-1R heterotetramer/IGF1 -0.018 0.1 -10000 0 -0.17 93 93
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.035 0.03 -10000 0 -0.23 3 3
MET -0.007 0.11 0.12 11 -0.33 30 41
PLEKHA7 -0.05 0.081 0.2 6 -0.16 83 89
mol:GTP 0.056 0.045 -10000 0 -0.17 7 7
establishment of epithelial cell apical/basal polarity -0.02 0.11 0.31 9 -10000 0 9
cortical actin cytoskeleton stabilization -0.034 0.094 -10000 0 -0.18 82 82
regulation of cell-cell adhesion -0.053 0.079 0.19 6 -0.17 70 76
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.034 0.095 -10000 0 -0.19 82 82
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.053 0.17 0.27 8 -0.39 55 63
CRKL -0.05 0.17 0.26 7 -0.39 55 62
HRAS -0.046 0.15 -10000 0 -0.33 60 60
mol:PIP3 -0.019 0.17 0.28 7 -0.35 47 54
SPRED1 0.02 0.051 -10000 0 -0.33 6 6
SPRED2 0.029 0.003 -10000 0 -10000 0 0
GAB1 -0.055 0.18 -10000 0 -0.41 56 56
FOXO3 -0.033 0.17 0.28 2 -0.35 55 57
AKT1 -0.033 0.18 0.29 2 -0.38 57 59
BAD -0.029 0.18 0.31 3 -0.35 56 59
megakaryocyte differentiation -0.06 0.17 -10000 0 -0.4 56 56
GSK3B -0.031 0.17 0.28 2 -0.35 56 58
RAF1 -0.031 0.14 0.24 3 -0.28 55 58
SHC1 0.026 0.009 -10000 0 -10000 0 0
STAT3 -0.056 0.18 -10000 0 -0.41 56 56
STAT1 -0.16 0.41 -10000 0 -0.98 57 57
HRAS/SPRED1 -0.028 0.14 -10000 0 -0.28 56 56
cell proliferation -0.056 0.17 -10000 0 -0.4 57 57
PIK3CA 0.023 0.042 -10000 0 -0.33 4 4
TEC 0.016 0.065 -10000 0 -0.33 10 10
RPS6KB1 -0.042 0.18 0.25 1 -0.39 56 57
HRAS/SPRED2 -0.023 0.14 -10000 0 -0.28 56 56
LYN/TEC/p62DOK -0.031 0.18 -10000 0 -0.39 56 56
MAPK3 -0.018 0.11 0.25 3 -0.21 51 54
STAP1 -0.065 0.18 -10000 0 -0.41 58 58
GRAP2 0.01 0.079 -10000 0 -0.33 15 15
JAK2 -0.13 0.35 -10000 0 -0.82 58 58
STAT1 (dimer) -0.16 0.4 -10000 0 -0.95 57 57
mol:Gleevec 0.001 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.033 0.19 -10000 0 -0.4 55 55
actin filament polymerization -0.058 0.16 -10000 0 -0.38 57 57
LYN 0.022 0.042 -10000 0 -0.33 4 4
STAP1/STAT5A (dimer) -0.11 0.25 0.3 1 -0.56 62 63
PIK3R1 0.025 0.03 -10000 0 -0.33 2 2
CBL/CRKL/GRB2 -0.028 0.17 0.27 5 -0.37 54 59
PI3K -0.023 0.19 -10000 0 -0.38 55 55
PTEN 0.025 0.01 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.17 0.48 -10000 0 -1.2 54 54
MAPK8 -0.058 0.18 -10000 0 -0.4 57 57
STAT3 (dimer) -0.055 0.17 -10000 0 -0.4 57 57
positive regulation of transcription -0.012 0.091 0.23 3 -0.17 48 51
mol:GDP -0.046 0.16 -10000 0 -0.35 58 58
PIK3C2B -0.055 0.17 -10000 0 -0.4 55 55
CBL/CRKL -0.038 0.17 0.27 6 -0.37 55 61
FER -0.059 0.18 -10000 0 -0.41 57 57
SH2B3 -0.057 0.18 -10000 0 -0.4 57 57
PDPK1 -0.019 0.16 0.26 8 -0.33 47 55
SNAI2 -0.059 0.17 -10000 0 -0.4 56 56
positive regulation of cell proliferation -0.12 0.3 -10000 0 -0.7 58 58
KITLG 0.008 0.065 -10000 0 -0.34 8 8
cell motility -0.12 0.3 -10000 0 -0.7 58 58
PTPN6 0.016 0.077 0.13 6 -0.32 14 20
EPOR -0.012 0.13 -10000 0 -0.49 1 1
STAT5A (dimer) -0.091 0.25 0.31 1 -0.57 59 60
SOCS1 0.025 0.043 0.12 5 -0.33 4 9
cell migration 0.06 0.18 0.41 55 -10000 0 55
SOS1 0.029 0.003 -10000 0 -10000 0 0
EPO 0.017 0.029 0.13 2 -10000 0 2
VAV1 -0.004 0.11 0.12 5 -0.33 28 33
GRB10 -0.059 0.17 -10000 0 -0.4 57 57
PTPN11 0.029 0.011 -10000 0 -10000 0 0
SCF/KIT -0.053 0.19 -10000 0 -0.42 57 57
GO:0007205 0.003 0.009 -10000 0 -10000 0 0
MAP2K1 -0.024 0.12 0.25 4 -0.23 53 57
CBL 0.025 0.01 -10000 0 -10000 0 0
KIT -0.18 0.5 -10000 0 -1.2 54 54
MAP2K2 -0.024 0.11 0.22 3 -0.23 53 56
SHC/Grb2/SOS1 -0.023 0.18 -10000 0 -0.39 55 55
STAT5A -0.091 0.26 0.31 1 -0.6 57 58
GRB2 0.028 0.005 -10000 0 -10000 0 0
response to radiation -0.057 0.17 -10000 0 -0.39 56 56
SHC/GRAP2 0.026 0.055 -10000 0 -0.23 12 12
PTPRO -0.061 0.17 -10000 0 -0.41 56 56
SH2B2 -0.059 0.17 -10000 0 -0.39 57 57
DOK1 0.028 0.022 0.12 1 -0.33 1 2
MATK -0.062 0.18 -10000 0 -0.42 55 55
CREBBP 0.018 0.066 -10000 0 -0.12 53 53
BCL2 -0.042 0.25 -10000 0 -1.1 12 12
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.003 0.1 0.13 9 -0.25 33 42
NFATC2 -0.05 0.24 -10000 0 -0.55 45 45
NFATC3 -0.001 0.085 -10000 0 -0.22 20 20
CD40LG -0.16 0.37 -10000 0 -0.75 71 71
ITCH 0.006 0.072 -10000 0 -0.19 33 33
CBLB 0.006 0.075 -10000 0 -0.19 36 36
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.2 0.44 -10000 0 -0.91 71 71
JUNB 0.029 0.008 0.12 2 -10000 0 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.019 0.095 -10000 0 -0.23 37 37
T cell anergy -0.027 0.13 -10000 0 -0.34 37 37
TLE4 -0.04 0.18 0.26 3 -0.47 34 37
Jun/NFAT1-c-4/p21SNFT -0.091 0.35 -10000 0 -0.71 57 57
AP-1/NFAT1-c-4 -0.13 0.43 -10000 0 -0.82 67 67
IKZF1 -0.052 0.21 0.32 1 -0.52 38 39
T-helper 2 cell differentiation -0.14 0.32 -10000 0 -0.74 55 55
AP-1/NFAT1 -0.018 0.19 -10000 0 -0.38 42 42
CALM1 0.019 0.062 -10000 0 -0.14 36 36
EGR2 -0.11 0.34 -10000 0 -0.78 45 45
EGR3 -0.14 0.4 -10000 0 -0.98 43 43
NFAT1/FOXP3 -0.039 0.22 0.28 1 -0.43 58 59
EGR1 0.028 0.029 -10000 0 -0.33 1 1
JUN 0.012 0.036 -10000 0 -10000 0 0
EGR4 0.033 0.029 0.12 21 -10000 0 21
mol:Ca2+ -0.004 0.049 -10000 0 -0.13 37 37
GBP3 -0.063 0.22 -10000 0 -0.53 42 42
FOSL1 0 0.11 0.12 21 -0.33 29 50
NFAT1-c-4/MAF/IRF4 -0.092 0.32 -10000 0 -0.69 53 53
DGKA -0.045 0.18 -10000 0 -0.43 39 39
CREM 0.025 0.023 0.12 1 -0.33 1 2
NFAT1-c-4/PPARG -0.092 0.34 -10000 0 -0.72 54 54
CTLA4 -0.064 0.22 0.26 2 -0.48 52 54
NFAT1-c-4 (dimer)/EGR1 -0.087 0.34 -10000 0 -0.72 54 54
NFAT1-c-4 (dimer)/EGR4 -0.087 0.34 -10000 0 -0.72 54 54
FOS 0.014 0.039 0.13 4 -10000 0 4
IFNG -0.27 0.52 -10000 0 -1.1 82 82
T cell activation -0.059 0.21 -10000 0 -0.59 18 18
MAF 0.028 0.006 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.086 0.27 0.73 32 -10000 0 32
TNF -0.11 0.32 -10000 0 -0.7 55 55
FASLG -0.3 0.64 -10000 0 -1.4 70 70
TBX21 -0.023 0.13 0.16 15 -0.25 64 79
BATF3 0.022 0.043 0.12 2 -0.33 4 6
PRKCQ -0.017 0.13 0.14 6 -0.32 39 45
PTPN1 -0.045 0.17 -10000 0 -0.41 40 40
NFAT1-c-4/ICER1 -0.092 0.33 -10000 0 -0.7 55 55
GATA3 -0.006 0.11 0.13 6 -0.33 30 36
T-helper 1 cell differentiation -0.26 0.5 -10000 0 -1 82 82
IL2RA -0.18 0.41 -10000 0 -0.83 71 71
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.043 0.17 -10000 0 -0.43 34 34
E2F1 0.029 0.023 -10000 0 -0.33 1 1
PPARG 0.026 0.038 -10000 0 -0.33 3 3
SLC3A2 -0.042 0.17 -10000 0 -0.42 35 35
IRF4 -0.011 0.11 -10000 0 -0.33 30 30
PTGS2 -0.15 0.35 -10000 0 -0.72 69 69
CSF2 -0.15 0.35 -10000 0 -0.73 67 67
JunB/Fra1/NFAT1-c-4 -0.093 0.33 -10000 0 -0.7 54 54
IL4 -0.15 0.34 -10000 0 -0.78 55 55
IL5 -0.15 0.35 -10000 0 -0.72 68 68
IL2 -0.06 0.21 -10000 0 -0.6 17 17
IL3 -0.042 0.18 -10000 0 -0.8 14 14
RNF128 -0.01 0.16 -10000 0 -0.43 37 37
NFATC1 -0.086 0.27 -10000 0 -0.73 32 32
CDK4 0.065 0.19 0.56 19 -10000 0 19
PTPRK -0.04 0.17 -10000 0 -0.46 31 31
IL8 -0.15 0.36 -10000 0 -0.73 70 70
POU2F1 0.026 0.009 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.098 0.19 0.23 1 -0.37 91 92
KLHL20 -0.03 0.094 0.18 5 -0.22 24 29
CYFIP2 0.014 0.072 0.12 3 -0.33 12 15
Rac1/GDP -0.046 0.12 0.22 2 -0.23 67 69
ENAH -0.092 0.18 0.22 1 -0.38 81 82
AP1M1 0.029 0.002 -10000 0 -10000 0 0
RAP1B 0.028 0.006 -10000 0 -10000 0 0
RAP1A 0.028 0.006 -10000 0 -10000 0 0
CTNNB1 0.029 0.003 -10000 0 -10000 0 0
CDC42/GTP -0.02 0.082 0.14 1 -0.16 61 62
ABI1/Sra1/Nap1 -0.04 0.054 -10000 0 -0.15 29 29
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.008 0.12 -10000 0 -0.18 90 90
RAPGEF1 -0.078 0.16 0.22 3 -0.34 73 76
CTNND1 0.029 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.095 0.2 -10000 0 -0.38 95 95
CRK -0.087 0.17 0.22 1 -0.35 83 84
E-cadherin/gamma catenin/alpha catenin -0.013 0.12 -10000 0 -0.2 81 81
alphaE/beta7 Integrin 0.029 0.056 -10000 0 -0.23 13 13
IQGAP1 0.028 0.005 -10000 0 -10000 0 0
NCKAP1 0.029 0.002 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.043 0.03 -10000 0 -0.17 3 3
DLG1 -0.098 0.19 -10000 0 -0.37 93 93
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.041 0.048 -10000 0 -0.13 62 62
MLLT4 0.022 0.037 -10000 0 -0.33 3 3
ARF6/GTP/NME1/Tiam1 0.042 0.05 -10000 0 -0.17 14 14
PI3K -0.036 0.071 -10000 0 -0.16 58 58
ARF6 0.028 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin -0.032 0.13 -10000 0 -0.24 82 82
TIAM1 0.011 0.076 -10000 0 -0.33 14 14
E-cadherin(dimer)/Ca2+ 0 0.1 -10000 0 -0.17 81 81
AKT1 -0.025 0.049 0.13 3 -0.14 3 6
PIK3R1 0.025 0.03 -10000 0 -0.33 2 2
CDH1 -0.067 0.16 -10000 0 -0.33 82 82
RhoA/GDP -0.043 0.13 0.27 3 -0.23 70 73
actin cytoskeleton organization -0.021 0.072 0.14 7 -0.16 24 31
CDC42/GDP -0.045 0.13 0.27 3 -0.23 70 73
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.039 0.097 -10000 0 -0.19 83 83
ITGB7 0.014 0.075 0.12 4 -0.33 13 17
RAC1 0.025 0.009 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0 0.11 -10000 0 -0.18 81 81
E-cadherin/Ca2+/beta catenin/alpha catenin -0.009 0.096 -10000 0 -0.16 81 81
mol:GDP -0.062 0.13 0.26 4 -0.26 71 75
CDC42/GTP/IQGAP1 0.037 0.009 -10000 0 -10000 0 0
JUP 0.028 0.033 0.12 7 -0.33 2 9
p120 catenin/RhoA/GDP -0.038 0.13 0.24 3 -0.24 68 71
RAC1/GTP/IQGAP1 0.034 0.014 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.042 0.004 -10000 0 -10000 0 0
RHOA 0.029 0.003 -10000 0 -10000 0 0
CDC42 0.028 0.004 -10000 0 -10000 0 0
CTNNA1 0.027 0.007 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle -0.012 0.056 0.13 8 -0.12 24 32
NME1 0.028 0.005 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.1 0.19 -10000 0 -0.37 94 94
regulation of cell-cell adhesion -0.026 0.067 -10000 0 -0.14 61 61
WASF2 -0.014 0.04 0.091 3 -0.11 3 6
Rap1/GTP -0.021 0.094 0.19 11 -0.17 62 73
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0 0.12 -10000 0 -0.18 88 88
CCND1 -0.015 0.066 0.14 8 -0.14 24 32
VAV2 -0.12 0.25 0.36 1 -0.66 28 29
RAP1/GDP -0.026 0.11 0.25 4 -0.19 66 70
adherens junction assembly -0.098 0.18 -10000 0 -0.36 94 94
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.026 0.009 -10000 0 -10000 0 0
PIP5K1C 0.029 0.003 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.011 0.11 0.25 1 -0.17 87 88
E-cadherin/beta catenin -0.066 0.13 -10000 0 -0.28 80 80
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.094 0.18 0.22 1 -0.37 86 87
PIK3CA 0.023 0.042 -10000 0 -0.33 4 4
Rac1/GTP -0.074 0.13 -10000 0 -0.36 26 26
E-cadherin/beta catenin/alpha catenin -0.013 0.11 -10000 0 -0.2 81 81
ITGAE 0.027 0.008 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.098 0.2 -10000 0 -0.38 95 95
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.12 0.36 -10000 0 -0.8 60 60
NCK1/PAK1/Dok-R -0.087 0.16 -10000 0 -0.4 60 60
NCK1/Dok-R -0.14 0.41 -10000 0 -0.96 59 59
PIK3CA 0.024 0.041 -10000 0 -0.33 4 4
mol:beta2-estradiol 0.036 0.096 0.23 58 -10000 0 58
RELA 0.028 0.005 -10000 0 -10000 0 0
SHC1 0.026 0.009 -10000 0 -10000 0 0
Rac/GDP 0.019 0.007 -10000 0 -10000 0 0
F2 0.031 0.11 0.26 54 -10000 0 54
TNIP2 0.028 0.006 -10000 0 -10000 0 0
NF kappa B/RelA -0.12 0.39 -10000 0 -0.88 60 60
FN1 0.009 0.084 0.12 2 -0.33 17 19
PLD2 -0.16 0.41 -10000 0 -0.96 60 60
PTPN11 0.028 0.004 -10000 0 -10000 0 0
GRB14 0.002 0.11 -10000 0 -0.33 28 28
ELK1 -0.14 0.38 -10000 0 -0.88 60 60
GRB7 0.034 0.028 -10000 0 -10000 0 0
PAK1 0.027 0.008 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.14 0.41 -10000 0 -0.94 60 60
CDKN1A -0.07 0.26 0.38 1 -0.55 60 61
ITGA5 0.026 0.038 -10000 0 -0.33 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.14 0.41 -10000 0 -0.95 59 59
CRK 0.027 0.008 -10000 0 -10000 0 0
mol:NO -0.072 0.28 -10000 0 -0.6 61 61
PLG -0.16 0.4 -10000 0 -0.97 59 59
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.11 0.34 -10000 0 -0.77 60 60
GRB2 0.028 0.005 -10000 0 -10000 0 0
PIK3R1 0.025 0.03 -10000 0 -0.33 2 2
ANGPT2 -0.065 0.25 -10000 0 -0.57 38 38
BMX -0.17 0.41 -10000 0 -0.97 60 60
ANGPT1 -0.2 0.46 -10000 0 -1.1 58 58
tube development -0.086 0.27 -10000 0 -0.59 63 63
ANGPT4 0.016 0.021 0.12 3 -10000 0 3
response to hypoxia -0.012 0.027 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.16 0.44 -10000 0 -1 60 60
alpha5/beta1 Integrin 0.037 0.032 0.18 1 -0.23 3 4
FGF2 -0.035 0.14 -10000 0 -0.33 54 54
STAT5A (dimer) -0.089 0.32 -10000 0 -0.67 63 63
mol:L-citrulline -0.072 0.28 -10000 0 -0.6 61 61
AGTR1 0.005 0.1 -10000 0 -0.33 23 23
MAPK14 -0.16 0.41 -10000 0 -0.95 60 60
Tie2/SHP2 -0.066 0.24 -10000 0 -0.95 16 16
TEK -0.07 0.26 -10000 0 -1 16 16
RPS6KB1 -0.11 0.34 0.42 1 -0.77 60 61
Angiotensin II/AT1 0.007 0.071 0.11 2 -0.23 23 25
Tie2/Ang1/GRB2 -0.15 0.42 -10000 0 -0.98 60 60
MAPK3 -0.15 0.38 -10000 0 -0.9 60 60
MAPK1 -0.15 0.38 -10000 0 -0.89 60 60
Tie2/Ang1/GRB7 -0.15 0.43 -10000 0 -0.99 60 60
NFKB1 0.028 0.005 -10000 0 -10000 0 0
MAPK8 -0.16 0.41 -10000 0 -0.97 59 59
PI3K -0.14 0.4 -10000 0 -0.91 60 60
FES -0.16 0.41 -10000 0 -0.94 61 61
Crk/Dok-R -0.14 0.41 -10000 0 -0.96 59 59
Tie2/Ang1/ABIN2 -0.16 0.42 -10000 0 -0.99 60 60
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.1 0.32 -10000 0 -0.72 60 60
STAT5A 0.025 0.036 -10000 0 -0.33 3 3
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.1 0.35 0.45 2 -0.76 59 61
Tie2/Ang2 -0.12 0.36 -10000 0 -0.77 63 63
Tie2/Ang1 -0.17 0.44 -10000 0 -1 60 60
FOXO1 -0.11 0.33 0.41 1 -0.72 64 65
ELF1 0.023 0.033 -10000 0 -0.12 2 2
ELF2 -0.16 0.4 -10000 0 -0.94 60 60
mol:Choline -0.16 0.39 -10000 0 -0.92 60 60
cell migration -0.045 0.094 -10000 0 -0.22 61 61
FYN -0.1 0.3 -10000 0 -0.66 62 62
DOK2 0.01 0.079 0.12 2 -0.33 15 17
negative regulation of cell cycle -0.06 0.24 0.37 1 -0.5 62 63
ETS1 -0.009 0.1 -10000 0 -0.24 46 46
PXN -0.076 0.3 0.4 3 -0.64 59 62
ITGB1 0.026 0.011 0.12 1 -10000 0 1
NOS3 -0.089 0.32 -10000 0 -0.68 60 60
RAC1 0.025 0.009 -10000 0 -10000 0 0
TNF -0.028 0.14 -10000 0 -0.3 60 60
MAPKKK cascade -0.16 0.39 -10000 0 -0.92 60 60
RASA1 0.025 0.03 -10000 0 -0.33 2 2
Tie2/Ang1/Shc -0.16 0.42 -10000 0 -0.98 60 60
NCK1 0.028 0.005 -10000 0 -10000 0 0
vasculogenesis -0.06 0.26 0.32 2 -0.54 61 63
mol:Phosphatidic acid -0.16 0.39 -10000 0 -0.92 60 60
mol:Angiotensin II 0.001 0.004 -10000 0 -10000 0 0
mol:NADP -0.072 0.28 -10000 0 -0.6 61 61
Rac1/GTP -0.1 0.32 -10000 0 -0.72 60 60
MMP2 -0.17 0.41 -10000 0 -0.97 60 60
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.065 0.19 0.21 9 -0.37 64 73
TBX21 -0.22 0.6 0.48 1 -1.3 59 60
B2M 0.023 0.021 -10000 0 -0.071 1 1
TYK2 0.02 0.042 -10000 0 -10000 0 0
IL12RB1 -0.021 0.14 0.18 5 -0.36 40 45
GADD45B -0.15 0.48 -10000 0 -1.1 55 55
IL12RB2 -0.039 0.14 0.17 3 -0.33 52 55
GADD45G -0.19 0.54 0.47 3 -1.2 60 63
natural killer cell activation 0.005 0.025 -10000 0 -10000 0 0
RELB 0.029 0.003 -10000 0 -10000 0 0
RELA 0.028 0.005 -10000 0 -10000 0 0
IL18 0.01 0.085 0.14 10 -0.34 15 25
IL2RA 0.001 0.095 -10000 0 -0.33 22 22
IFNG -0.025 0.14 -10000 0 -0.33 48 48
STAT3 (dimer) -0.14 0.44 0.39 7 -0.91 63 70
HLA-DRB5 0.004 0.1 -10000 0 -0.33 23 23
FASLG -0.23 0.62 -10000 0 -1.3 66 66
NF kappa B2 p52/RelB -0.19 0.56 0.39 4 -1.2 63 67
CD4 0.016 0.068 0.12 1 -0.33 11 12
SOCS1 0.025 0.043 0.12 5 -0.33 4 9
EntrezGene:6955 -0.001 0.01 -10000 0 -10000 0 0
CD3D -0.013 0.12 0.13 19 -0.33 36 55
CD3E -0.01 0.12 0.13 4 -0.33 32 36
CD3G -0.016 0.13 0.13 23 -0.33 38 61
IL12Rbeta2/JAK2 -0.013 0.12 0.18 3 -0.23 57 60
CCL3 -0.2 0.56 0.46 4 -1.2 59 63
CCL4 -0.21 0.59 0.48 1 -1.3 58 59
HLA-A 0.016 0.05 -10000 0 -0.33 5 5
IL18/IL18R 0.033 0.14 0.25 16 -0.26 42 58
NOS2 -0.19 0.57 -10000 0 -1.2 61 61
IL12/IL12R/TYK2/JAK2/SPHK2 -0.064 0.19 0.2 9 -0.37 63 72
IL1R1 -0.2 0.56 -10000 0 -1.2 60 60
IL4 -0.014 0.037 -10000 0 -10000 0 0
JAK2 0.016 0.06 -10000 0 -0.35 5 5
EntrezGene:6957 -0.001 0.011 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.21 0.49 -10000 0 -1 71 71
RAB7A -0.11 0.4 -10000 0 -0.85 56 56
lysosomal transport -0.1 0.37 -10000 0 -0.8 56 56
FOS -0.13 0.44 -10000 0 -1 51 51
STAT4 (dimer) -0.16 0.51 0.44 5 -1.1 63 68
STAT5A (dimer) -0.21 0.57 0.42 10 -1.2 68 78
GZMA -0.22 0.6 -10000 0 -1.4 58 58
GZMB -0.21 0.59 0.45 1 -1.3 58 59
HLX 0.023 0.03 -10000 0 -0.33 2 2
LCK -0.24 0.66 0.42 8 -1.4 65 73
TCR/CD3/MHC II/CD4 -0.11 0.33 0.15 3 -0.74 54 57
IL2/IL2R 0.015 0.14 0.2 11 -0.28 47 58
MAPK14 -0.17 0.52 0.46 3 -1.1 62 65
CCR5 -0.18 0.55 0.47 2 -1.2 55 57
IL1B -0.002 0.12 -10000 0 -0.36 26 26
STAT6 -0.016 0.16 0.26 5 -0.6 6 11
STAT4 0.006 0.1 0.12 15 -0.33 23 38
STAT3 0.028 0.005 -10000 0 -10000 0 0
STAT1 0.026 0.029 -10000 0 -0.33 2 2
NFKB1 0.028 0.005 -10000 0 -10000 0 0
NFKB2 0.026 0.008 -10000 0 -10000 0 0
IL12B 0.027 0.046 0.16 10 -10000 0 10
CD8A -0.03 0.14 -10000 0 -0.34 53 53
CD8B -0.044 0.15 -10000 0 -0.34 63 63
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.064 0.19 0.36 64 -0.21 9 73
IL2RB 0.006 0.095 0.12 13 -0.33 21 34
proteasomal ubiquitin-dependent protein catabolic process -0.14 0.44 0.43 6 -0.92 63 69
IL2RG -0.012 0.12 0.12 15 -0.33 38 53
IL12 0.027 0.094 0.18 10 -0.25 19 29
STAT5A 0.024 0.036 -10000 0 -0.33 3 3
CD247 -0.005 0.11 0.13 19 -0.33 28 47
IL2 0.022 0.015 -10000 0 -10000 0 0
SPHK2 0.026 0.03 -10000 0 -0.33 2 2
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.002 0.1 0.14 6 -0.35 18 24
IL12/IL12R/TYK2/JAK2 -0.29 0.79 0.46 7 -1.6 63 70
MAP2K3 -0.18 0.54 0.46 3 -1.1 63 66
RIPK2 0.026 0.009 -10000 0 -10000 0 0
MAP2K6 -0.18 0.54 0.44 4 -1.1 63 67
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.002 0.099 -10000 0 -0.33 24 24
IL18RAP 0.012 0.096 0.13 23 -0.34 18 41
IL12Rbeta1/TYK2 0.003 0.12 0.18 5 -0.28 40 45
EOMES -0.1 0.36 -10000 0 -1.2 26 26
STAT1 (dimer) -0.16 0.46 0.42 10 -0.91 71 81
T cell proliferation -0.078 0.35 0.39 7 -0.68 66 73
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.005 0.1 0.14 1 -0.34 22 23
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.11 0.37 0.41 3 -0.76 64 67
ATF2 -0.15 0.46 0.44 3 -0.94 65 68
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.008 0.04 -10000 0 -0.3 2 2
Crk/p130 Cas/Paxillin -0.053 0.11 -10000 0 -0.24 55 55
JUN -0.028 0.11 0.19 3 -0.22 54 57
HRAS 0.028 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 0.012 0.12 0.2 14 -0.2 64 78
RAP1A 0.028 0.006 -10000 0 -10000 0 0
FRS2 0.028 0.006 -10000 0 -10000 0 0
RAP1A/GDP 0.021 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.018 0.13 0.2 15 -0.2 66 81
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.028 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.008 0.11 0.17 11 -0.19 62 73
RHOA 0.029 0.003 -10000 0 -10000 0 0
RAP1A/GTP 0.012 0.11 0.21 1 -0.18 66 67
GRB7 0.034 0.028 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF 0.018 0.13 0.2 15 -0.2 65 80
MAPKKK cascade -0.014 0.12 0.16 3 -0.21 61 64
BCAR1 0.025 0.03 -10000 0 -0.33 2 2
RET9/GFRalpha1/GDNF/IRS1 0 0.12 0.17 10 -0.19 72 82
lamellipodium assembly -0.039 0.11 -10000 0 -0.22 56 56
RET51/GFRalpha1/GDNF/SHC 0.017 0.12 0.2 13 -0.2 58 71
PIK3CA 0.023 0.042 -10000 0 -0.33 4 4
RET9/GFRalpha1/GDNF/SHC 0.009 0.11 0.17 9 -0.2 55 64
RET9/GFRalpha1/GDNF/Shank3 0.008 0.11 0.17 10 -0.19 59 69
MAPK3 -0.03 0.097 0.18 18 -0.32 9 27
DOK1 0.028 0.022 0.12 1 -0.33 1 2
DOK6 0.021 0.083 -10000 0 -0.33 14 14
PXN 0.028 0.004 -10000 0 -10000 0 0
neurite development -0.027 0.09 0.21 6 -0.26 14 20
DOK5 0.022 0.092 -10000 0 -0.33 16 16
GFRA1 0.008 0.12 0.12 50 -0.33 28 78
MAPK8 -0.029 0.11 0.14 1 -0.22 58 59
HRAS/GTP -0.002 0.14 0.22 1 -0.23 65 66
tube development 0.008 0.1 0.17 12 -0.18 58 70
MAPK1 -0.029 0.095 0.18 17 -0.32 9 26
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.021 0.1 0.15 2 -0.21 62 64
Rac1/GDP 0.019 0.007 -10000 0 -10000 0 0
SRC 0.025 0.022 -10000 0 -0.33 1 1
PDLIM7 0.027 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 0.023 0.13 0.27 4 -0.19 66 70
SHC1 0.026 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.014 0.13 0.2 14 -0.2 67 81
RET51/GFRalpha1/GDNF/Dok5 0.013 0.13 0.2 27 -0.2 72 99
PRKCA 0.018 0.063 0.12 3 -0.33 9 12
HRAS/GDP 0.021 0.004 -10000 0 -10000 0 0
CREB1 -0.017 0.11 -10000 0 -0.24 51 51
PIK3R1 0.025 0.03 -10000 0 -0.33 2 2
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.021 0.1 0.15 3 -0.22 58 61
RET51/GFRalpha1/GDNF/Grb7 0.02 0.13 0.2 21 -0.2 65 86
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.024 0.051 0.12 13 -0.33 5 18
DOK4 0.024 0.036 -10000 0 -0.33 3 3
JNK cascade -0.027 0.11 0.19 4 -0.3 20 24
RET9/GFRalpha1/GDNF/FRS2 0.009 0.11 0.17 10 -0.19 61 71
SHANK3 0.025 0.022 -10000 0 -0.33 1 1
RASA1 0.025 0.03 -10000 0 -0.33 2 2
NCK1 0.028 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.02 0.1 0.15 3 -0.22 58 61
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.03 0.12 0.15 2 -0.21 80 82
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.031 0.12 0.15 1 -0.22 75 76
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.017 0.11 0.15 3 -0.22 54 57
PI3K -0.05 0.16 0.23 2 -0.31 59 61
SOS1 0.029 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.017 0.11 0.18 10 -0.18 58 68
GRB10 0.021 0.042 -10000 0 -0.33 4 4
activation of MAPKK activity -0.029 0.12 0.17 1 -0.25 62 63
RET51/GFRalpha1/GDNF/FRS2 0.018 0.12 0.2 14 -0.2 64 78
GAB1 0.026 0.03 -10000 0 -0.33 2 2
IRS1 0.013 0.073 -10000 0 -0.33 13 13
IRS2 0.025 0.03 -10000 0 -0.33 2 2
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.02 0.11 0.15 3 -0.23 59 62
RET51/GFRalpha1/GDNF/PKC alpha 0.014 0.13 0.2 18 -0.21 67 85
GRB2 0.028 0.005 -10000 0 -10000 0 0
PRKACA 0.029 0.002 -10000 0 -10000 0 0
GDNF -0.019 0.13 -10000 0 -0.33 43 43
RAC1 0.025 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.009 0.13 0.2 14 -0.2 75 89
Rac1/GTP -0.04 0.13 -10000 0 -0.26 56 56
RET9/GFRalpha1/GDNF -0.005 0.11 0.16 11 -0.21 62 73
GFRalpha1/GDNF -0.009 0.13 0.18 11 -0.25 62 73
Endothelins

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
AKT1 0.019 0.14 0.28 36 -0.27 31 67
PTK2B 0.027 0.025 0.12 5 -0.33 1 6
mol:Ca2+ -0.018 0.24 0.62 1 -0.6 32 33
EDN1 0.021 0.11 0.22 31 -0.22 31 62
EDN3 -0.004 0.13 0.12 54 -0.33 36 90
EDN2 0.026 0.017 -10000 0 -10000 0 0
HRAS/GDP -0.01 0.17 0.27 8 -0.38 32 40
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.012 0.13 0.18 27 -0.35 24 51
ADCY4 0.02 0.13 0.21 56 -0.25 26 82
ADCY5 0.014 0.14 0.21 51 -0.28 28 79
ADCY6 0.019 0.13 0.21 55 -0.25 27 82
ADCY7 0.018 0.13 0.21 53 -0.24 27 80
ADCY1 -0.004 0.13 0.21 40 -0.25 36 76
ADCY2 0.003 0.15 0.23 38 -0.26 42 80
ADCY3 0.018 0.13 0.21 53 -0.26 25 78
ADCY8 0.019 0.12 0.21 45 -0.27 18 63
ADCY9 0.018 0.13 0.21 55 -0.24 30 85
arachidonic acid secretion -0.009 0.16 0.31 6 -0.4 26 32
ETB receptor/Endothelin-1/Gq/GTP 0.02 0.091 0.15 1 -0.24 23 24
GNAO1 -0.037 0.14 0.12 4 -0.33 55 59
HRAS 0.028 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.051 0.14 0.35 27 -0.25 29 56
ETA receptor/Endothelin-1/Gs/GTP 0.041 0.14 0.33 28 -0.22 42 70
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
COL3A1 0.02 0.15 0.28 37 -0.32 27 64
EDNRB 0.008 0.084 -10000 0 -0.27 22 22
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 0.014 0.16 0.3 34 -0.36 31 65
CYSLTR1 0.012 0.17 0.28 37 -0.36 32 69
SLC9A1 0.015 0.084 0.19 30 -0.21 13 43
mol:GDP -0.021 0.17 0.26 9 -0.39 35 44
SLC9A3 -0.038 0.27 0.43 1 -0.64 36 37
RAF1 -0.018 0.15 0.28 3 -0.39 28 31
JUN -0.02 0.23 0.43 2 -0.58 34 36
JAK2 0.015 0.13 0.28 30 -0.29 27 57
mol:IP3 -0.001 0.14 0.21 4 -0.4 23 27
ETA receptor/Endothelin-1 0.046 0.18 0.39 32 -0.3 34 66
PLCB1 -0.002 0.1 -10000 0 -0.33 26 26
PLCB2 0.019 0.059 0.12 1 -0.33 8 9
ETA receptor/Endothelin-3 0.012 0.12 0.18 28 -0.21 50 78
FOS -0.002 0.13 0.4 2 -0.43 11 13
Gai/GDP -0.12 0.3 -10000 0 -0.66 64 64
CRK 0.027 0.008 -10000 0 -10000 0 0
mol:Ca ++ 0.004 0.17 0.25 26 -0.42 29 55
BCAR1 0.025 0.03 -10000 0 -0.33 2 2
PRKCB1 -0.006 0.14 0.19 5 -0.35 30 35
GNAQ 0.028 0.01 -10000 0 -10000 0 0
GNAZ -0.002 0.1 -10000 0 -0.33 26 26
GNAL 0.009 0.11 -10000 0 -0.33 25 25
Gs family/GDP -0.018 0.16 0.25 9 -0.36 35 44
ETA receptor/Endothelin-1/Gq/GTP 0.034 0.11 0.2 32 -0.3 17 49
MAPK14 -0.008 0.11 0.23 2 -0.36 17 19
TRPC6 -0.021 0.25 0.63 1 -0.64 31 32
GNAI2 0.029 0.003 -10000 0 -10000 0 0
GNAI3 0.028 0.006 -10000 0 -10000 0 0
GNAI1 0.02 0.047 -10000 0 -0.33 5 5
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.002 0.12 0.18 1 -0.37 17 18
ETB receptor/Endothelin-2 0.024 0.065 -10000 0 -0.22 18 18
ETB receptor/Endothelin-3 0 0.11 -10000 0 -0.23 52 52
ETB receptor/Endothelin-1 0.023 0.11 0.2 10 -0.24 28 38
MAPK3 -0.008 0.14 0.4 2 -0.47 14 16
MAPK1 -0.009 0.15 0.4 2 -0.45 17 19
Rac1/GDP -0.011 0.16 0.26 5 -0.38 31 36
cAMP biosynthetic process -0.011 0.16 0.24 33 -0.32 34 67
MAPK8 -0.033 0.27 0.48 1 -0.66 38 39
SRC 0.025 0.022 -10000 0 -0.33 1 1
ETB receptor/Endothelin-1/Gi/GTP -0.032 0.11 0.15 1 -0.28 31 32
p130Cas/CRK/Src/PYK2 -0.014 0.18 0.37 3 -0.47 27 30
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.01 0.16 0.26 5 -0.38 31 36
COL1A2 0.008 0.17 0.28 32 -0.52 17 49
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.036 0.086 0.18 22 -0.18 19 41
mol:DAG -0.001 0.14 0.21 4 -0.4 23 27
MAP2K2 -0.015 0.15 0.37 4 -0.42 20 24
MAP2K1 -0.014 0.15 0.29 4 -0.44 18 22
EDNRA 0.025 0.12 0.22 37 -0.21 35 72
positive regulation of muscle contraction 0.028 0.13 0.25 49 -0.24 26 75
Gq family/GDP 0.017 0.16 0.28 1 -0.43 21 22
HRAS/GTP -0.02 0.16 0.23 7 -0.39 32 39
PRKCH -0.01 0.14 0.19 5 -0.36 29 34
RAC1 0.025 0.009 -10000 0 -10000 0 0
PRKCA -0.012 0.15 0.29 6 -0.34 32 38
PRKCB -0.022 0.16 0.22 4 -0.37 38 42
PRKCE -0.01 0.14 0.2 6 -0.35 30 36
PRKCD -0.01 0.14 0.2 7 -0.34 31 38
PRKCG -0.01 0.14 0.21 2 -0.36 28 30
regulation of vascular smooth muscle contraction -0.008 0.15 0.43 2 -0.52 10 12
PRKCQ -0.019 0.16 0.2 4 -0.38 33 37
PLA2G4A -0.012 0.17 0.33 5 -0.42 26 31
GNA14 0.035 0.049 -10000 0 -0.33 3 3
GNA15 0.019 0.063 0.12 3 -0.33 9 12
GNA12 0.025 0.009 -10000 0 -10000 0 0
GNA11 0.029 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.05 0.14 0.35 26 -0.25 29 55
MMP1 -0.072 0.25 0.33 9 -0.71 37 46
Noncanonical Wnt signaling pathway

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
NFATC2 -0.006 0.11 -10000 0 -0.33 28 28
GNB1/GNG2 -0.011 0.14 0.2 1 -0.24 58 59
mol:DAG -0.028 0.11 0.2 2 -0.22 56 58
PLCG1 -0.029 0.12 0.2 2 -0.23 56 58
YES1 -0.036 0.12 -10000 0 -0.23 61 61
FZD3 0.025 0.03 -10000 0 -0.33 2 2
FZD6 0.006 0.081 -10000 0 -0.33 16 16
G protein -0.004 0.14 0.23 15 -0.23 57 72
MAP3K7 -0.036 0.094 0.16 3 -0.29 19 22
mol:Ca2+ -0.027 0.11 0.19 2 -0.22 56 58
mol:IP3 -0.028 0.11 0.2 2 -0.22 56 58
NLK -0.007 0.12 -10000 0 -0.8 7 7
GNB1 0.028 0.006 -10000 0 -10000 0 0
CAMK2A -0.033 0.1 0.17 3 -0.3 22 25
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.026 0.12 -10000 0 -0.24 63 63
CSNK1A1 0.027 0.007 -10000 0 -10000 0 0
GNAS -0.028 0.11 0.24 3 -0.22 57 60
GO:0007205 -0.032 0.11 0.2 4 -0.29 25 29
WNT6 0.022 0.069 0.12 17 -0.33 10 27
WNT4 -0.002 0.11 0.12 20 -0.33 30 50
NFAT1/CK1 alpha -0.02 0.13 0.25 6 -0.32 24 30
GNG2 0.013 0.073 -10000 0 -0.33 13 13
WNT5A 0.018 0.084 0.12 23 -0.33 15 38
WNT11 0.009 0.088 0.12 11 -0.33 18 29
CDC42 -0.033 0.11 0.18 4 -0.34 19 23
Syndecan-1-mediated signaling events

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
TGFB1 0.024 0.042 -10000 0 -0.33 4 4
CCL5 -0.014 0.12 -10000 0 -0.33 39 39
SDCBP 0.024 0.03 -10000 0 -0.33 2 2
FGFR/FGF2/Syndecan-1 -0.037 0.15 0.24 6 -0.28 57 63
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 -0.04 0.15 0.23 5 -0.35 38 43
Syndecan-1/Syntenin -0.034 0.14 0.21 3 -0.28 54 57
MAPK3 -0.036 0.14 0.22 7 -0.37 27 34
HGF/MET 0.008 0.097 -10000 0 -0.23 40 40
TGFB1/TGF beta receptor Type II 0.024 0.042 -10000 0 -0.33 4 4
BSG 0.029 0.003 -10000 0 -10000 0 0
keratinocyte migration -0.039 0.15 0.23 5 -0.34 38 43
Syndecan-1/RANTES -0.044 0.17 0.24 6 -0.3 66 72
Syndecan-1/CD147 -0.021 0.16 0.24 7 -0.38 27 34
Syndecan-1/Syntenin/PIP2 -0.034 0.14 0.2 3 -0.37 27 30
LAMA5 0.018 0.059 -10000 0 -0.33 8 8
positive regulation of cell-cell adhesion -0.033 0.14 0.19 3 -0.36 28 31
MMP7 0.011 0.099 0.12 34 -0.33 21 55
HGF 0.019 0.069 -10000 0 -0.33 10 10
Syndecan-1/CASK -0.051 0.14 -10000 0 -0.27 61 61
Syndecan-1/HGF/MET -0.043 0.17 0.25 5 -0.4 34 39
regulation of cell adhesion -0.042 0.13 0.2 8 -0.36 25 33
HPSE 0.015 0.068 -10000 0 -0.33 11 11
positive regulation of cell migration -0.037 0.15 0.24 6 -0.28 57 63
SDC1 -0.037 0.14 0.24 1 -0.28 54 55
Syndecan-1/Collagen -0.037 0.15 0.24 6 -0.28 57 63
PPIB 0.029 0.003 -10000 0 -10000 0 0
MET -0.007 0.11 0.12 11 -0.33 30 41
PRKACA 0.029 0.002 -10000 0 -10000 0 0
MMP9 -0.001 0.11 -10000 0 -0.33 29 29
MAPK1 -0.035 0.14 0.22 7 -0.37 25 32
homophilic cell adhesion -0.037 0.15 0.24 6 -0.28 57 63
MMP1 -0.003 0.13 0.12 50 -0.33 37 87
BCR signaling pathway

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
JUN -0.056 0.2 0.28 10 -0.45 46 56
IKBKB -0.018 0.12 0.27 5 -0.28 28 33
AKT1 -0.036 0.11 0.28 8 -0.23 45 53
IKBKG -0.012 0.11 0.25 5 -0.28 27 32
CALM1 -0.06 0.2 0.33 1 -0.5 39 40
PIK3CA 0.023 0.042 -10000 0 -0.33 4 4
MAP3K1 -0.1 0.28 0.31 7 -0.63 52 59
MAP3K7 0.025 0.022 -10000 0 -0.33 1 1
mol:Ca2+ -0.06 0.21 0.34 1 -0.55 37 38
DOK1 0.028 0.022 0.12 1 -0.33 1 2
AP-1 -0.027 0.12 0.28 2 -0.26 36 38
LYN 0.022 0.042 -10000 0 -0.33 4 4
BLNK -0.004 0.1 -10000 0 -0.33 27 27
SHC1 0.026 0.009 -10000 0 -10000 0 0
BCR complex -0.02 0.17 0.18 29 -0.3 70 99
CD22 -0.081 0.22 0.21 1 -0.53 46 47
CAMK2G -0.054 0.18 0.33 1 -0.48 37 38
CSNK2A1 0.027 0.007 -10000 0 -10000 0 0
INPP5D 0.014 0.075 0.12 5 -0.33 13 18
SHC/GRB2/SOS1 -0.028 0.14 -10000 0 -0.28 55 55
GO:0007205 -0.062 0.22 0.34 1 -0.56 37 38
SYK 0.016 0.066 0.12 5 -0.33 10 15
ELK1 -0.066 0.2 0.33 1 -0.51 40 41
NFATC1 -0.09 0.22 0.28 8 -0.43 67 75
B-cell antigen/BCR complex -0.02 0.17 0.18 29 -0.3 70 99
PAG1/CSK 0.028 0.05 -10000 0 -0.23 10 10
NFKBIB 0.011 0.052 0.15 5 -0.12 14 19
HRAS -0.056 0.19 0.24 3 -0.46 40 43
NFKBIA 0.011 0.051 0.15 5 -0.12 14 19
NF-kappa-B/RelA/I kappa B beta 0.016 0.045 0.15 6 -10000 0 6
RasGAP/Csk 0.016 0.15 -10000 0 -0.22 70 70
mol:GDP -0.063 0.21 0.29 1 -0.52 39 40
PTEN 0.025 0.01 -10000 0 -10000 0 0
CD79B 0.003 0.11 -10000 0 -0.33 29 29
NF-kappa-B/RelA/I kappa B alpha 0.016 0.045 0.15 6 -10000 0 6
GRB2 0.028 0.005 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.099 0.25 0.29 1 -0.53 64 65
PIK3R1 0.025 0.03 -10000 0 -0.33 2 2
mol:IP3 -0.063 0.22 -10000 0 -0.57 37 37
CSK 0.028 0.004 -10000 0 -10000 0 0
FOS -0.063 0.19 0.31 1 -0.48 38 39
CHUK -0.034 0.14 0.25 4 -0.31 47 51
IBTK 0.019 0.051 -10000 0 -0.33 6 6
CARD11/BCL10/MALT1/TAK1 -0.033 0.2 0.26 4 -0.47 40 44
PTPN6 -0.084 0.22 0.22 2 -0.54 46 48
RELA 0.028 0.005 -10000 0 -10000 0 0
BCL2A1 0.009 0.035 0.11 5 -0.1 2 7
VAV2 -0.12 0.26 -10000 0 -0.55 66 66
ubiquitin-dependent protein catabolic process 0.013 0.051 0.16 5 -0.12 14 19
BTK -0.023 0.24 -10000 0 -1 15 15
CD19 -0.098 0.24 0.21 2 -0.51 61 63
MAP4K1 0.01 0.088 0.12 10 -0.33 18 28
CD72 0.017 0.068 0.12 11 -0.33 10 21
PAG1 0.014 0.065 -10000 0 -0.33 10 10
MAPK14 -0.067 0.24 0.33 16 -0.52 50 66
SH3BP5 0.026 0.03 0.12 1 -0.33 2 3
PIK3AP1 -0.057 0.23 -10000 0 -0.64 34 34
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.11 0.33 -10000 0 -0.7 54 54
RAF1 -0.055 0.18 0.26 2 -0.45 38 40
RasGAP/p62DOK/SHIP 0.008 0.16 0.23 5 -0.23 75 80
CD79A -0.038 0.16 -10000 0 -0.33 68 68
re-entry into mitotic cell cycle -0.027 0.12 0.28 2 -0.26 36 38
RASA1 0.025 0.03 -10000 0 -0.33 2 2
MAPK3 -0.047 0.15 0.23 5 -0.39 35 40
MAPK1 -0.04 0.15 0.24 5 -0.4 33 38
CD72/SHP1 -0.066 0.23 0.25 4 -0.51 47 51
NFKB1 0.028 0.005 -10000 0 -10000 0 0
MAPK8 -0.082 0.24 0.29 7 -0.52 53 60
actin cytoskeleton organization -0.087 0.23 0.3 8 -0.46 61 69
NF-kappa-B/RelA 0.035 0.087 0.28 5 -10000 0 5
Calcineurin -0.032 0.18 -10000 0 -0.44 37 37
PI3K -0.09 0.19 -10000 0 -0.41 62 62
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.056 0.24 -10000 0 -0.63 35 35
SOS1 0.029 0.003 -10000 0 -10000 0 0
Bam32/HPK1 -0.12 0.37 -10000 0 -0.86 53 53
DAPP1 -0.16 0.42 -10000 0 -1 52 52
cytokine secretion -0.082 0.2 0.27 8 -0.4 67 75
mol:DAG -0.063 0.22 -10000 0 -0.57 37 37
PLCG2 0.022 0.052 -10000 0 -0.33 6 6
MAP2K1 -0.05 0.16 0.24 4 -0.43 36 40
B-cell antigen/BCR complex/FcgammaRIIB -0.005 0.15 0.18 29 -0.25 71 100
mol:PI-3-4-5-P3 -0.064 0.13 0.17 2 -0.31 47 49
ETS1 -0.052 0.16 0.31 1 -0.45 34 35
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.002 0.18 0.28 9 -0.28 71 80
B-cell antigen/BCR complex/LYN -0.073 0.23 -10000 0 -0.56 42 42
MALT1 0.026 0.03 -10000 0 -0.33 2 2
TRAF6 0.028 0.005 -10000 0 -10000 0 0
RAC1 -0.097 0.24 0.3 4 -0.5 62 66
B-cell antigen/BCR complex/LYN/SYK -0.051 0.23 0.25 5 -0.52 44 49
CARD11 -0.06 0.23 0.27 8 -0.55 42 50
FCGR2B 0.016 0.07 -10000 0 -0.33 11 11
PPP3CA 0.028 0.004 -10000 0 -10000 0 0
BCL10 0.028 0.005 -10000 0 -10000 0 0
IKK complex -0.001 0.055 0.15 8 -0.12 14 22
PTPRC -0.002 0.11 0.12 18 -0.33 28 46
PDPK1 -0.041 0.1 0.24 8 -0.21 46 54
PPP3CB 0.026 0.008 -10000 0 -10000 0 0
PPP3CC 0.027 0.007 -10000 0 -10000 0 0
POU2F2 0.012 0.038 0.15 4 -0.1 2 6
Wnt 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
Noncanonical Wnts/FZD -0.026 0.12 -10000 0 -0.24 63 63
FZD6 0.006 0.081 -10000 0 -0.33 16 16
WNT6 0.022 0.069 0.12 17 -0.33 10 27
WNT4 -0.002 0.11 0.12 20 -0.33 30 50
FZD3 0.025 0.03 -10000 0 -0.33 2 2
WNT5A 0.018 0.084 0.12 23 -0.33 15 38
WNT11 0.009 0.088 0.12 11 -0.33 18 29
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.024 0.073 0.22 2 -0.24 10 12
adherens junction organization -0.052 0.12 0.18 1 -0.22 77 78
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.021 0.077 0.25 1 -0.24 10 11
FMN1 -0.055 0.12 -10000 0 -0.23 79 79
mol:IP3 -0.024 0.068 0.21 1 -0.21 11 12
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.046 0.12 -10000 0 -0.22 78 78
CTNNB1 0.031 0.005 -10000 0 -10000 0 0
AKT1 -0.023 0.084 0.21 1 -0.26 8 9
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.069 0.17 -10000 0 -0.32 78 78
CTNND1 0.029 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.043 0.1 -10000 0 -0.21 70 70
VASP -0.049 0.11 -10000 0 -0.21 78 78
ZYX -0.044 0.1 -10000 0 -0.21 69 69
JUB -0.046 0.11 -10000 0 -0.21 78 78
EGFR(dimer) -0.037 0.12 -10000 0 -0.22 73 73
E-cadherin/beta catenin-gamma catenin -0.008 0.11 -10000 0 -0.18 82 82
mol:PI-3-4-5-P3 -0.009 0.098 -10000 0 -0.27 8 8
PIK3CA 0.024 0.042 -10000 0 -0.34 4 4
PI3K -0.009 0.1 -10000 0 -0.28 8 8
FYN -0.03 0.077 0.21 2 -0.24 22 24
mol:Ca2+ -0.024 0.067 0.21 1 -0.2 11 12
JUP 0.03 0.033 0.12 7 -0.32 2 9
PIK3R1 0.026 0.031 -10000 0 -0.34 2 2
mol:DAG -0.024 0.068 0.21 1 -0.21 11 12
CDH1 -0.067 0.16 0.13 2 -0.33 82 84
RhoA/GDP -0.011 0.088 0.23 3 -0.23 11 14
establishment of polarity of embryonic epithelium -0.048 0.11 -10000 0 -0.21 78 78
SRC 0.025 0.022 -10000 0 -0.33 1 1
RAC1 0.025 0.009 -10000 0 -10000 0 0
RHOA 0.029 0.003 -10000 0 -10000 0 0
EGFR 0.021 0.071 -10000 0 -0.33 10 10
CASR -0.027 0.064 0.18 4 -0.22 7 11
RhoA/GTP -0.012 0.072 0.2 1 -0.21 8 9
AKT2 -0.025 0.085 0.21 1 -0.26 8 9
actin cable formation -0.055 0.12 0.19 4 -0.23 74 78
apoptosis 0.022 0.086 0.25 10 -0.23 3 13
CTNNA1 0.027 0.008 -10000 0 -10000 0 0
mol:GDP -0.029 0.076 0.18 6 -0.24 12 18
PIP5K1A -0.043 0.1 -10000 0 -0.21 70 70
PLCG1 -0.025 0.069 0.21 1 -0.21 11 12
Rac1/GTP -0.03 0.12 -10000 0 -0.21 60 60
homophilic cell adhesion -0.001 0.003 -10000 0 -10000 0 0
Nectin adhesion pathway

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
PDGFRB 0.025 0.031 0.12 1 -0.33 2 3
alphaV beta3 Integrin -0.004 0.11 -10000 0 -0.24 50 50
PTK2 -0.056 0.14 -10000 0 -0.34 45 45
positive regulation of JNK cascade -0.044 0.14 -10000 0 -0.29 53 53
CDC42/GDP -0.054 0.19 -10000 0 -0.39 60 60
Rac1/GDP -0.054 0.18 -10000 0 -0.39 57 57
RAP1B 0.028 0.006 -10000 0 -10000 0 0
RAP1A 0.028 0.006 -10000 0 -10000 0 0
CTNNB1 0.029 0.003 -10000 0 -10000 0 0
CDC42/GTP -0.05 0.17 -10000 0 -0.36 52 52
nectin-3/I-afadin 0.001 0.095 -10000 0 -0.23 42 42
RAPGEF1 -0.061 0.18 0.27 1 -0.39 59 60
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.071 0.2 -10000 0 -0.44 62 62
PDGFB-D/PDGFRB 0.025 0.031 0.12 1 -0.33 2 3
TLN1 -0.017 0.042 0.1 1 -0.13 34 35
Rap1/GTP -0.046 0.13 -10000 0 -0.29 58 58
IQGAP1 0.028 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.043 0.03 -10000 0 -0.17 3 3
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.001 0.095 -10000 0 -0.23 42 42
PVR 0.026 0.03 -10000 0 -0.33 2 2
Necl-5(dimer) 0.026 0.029 -10000 0 -0.33 2 2
mol:GDP -0.08 0.22 -10000 0 -0.48 59 59
MLLT4 0.022 0.037 -10000 0 -0.33 3 3
PIK3CA 0.023 0.042 -10000 0 -0.33 4 4
PI3K 0.033 0.099 -10000 0 -0.18 43 43
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.032 0.031 -10000 0 -0.22 3 3
positive regulation of lamellipodium assembly -0.051 0.15 -10000 0 -0.32 59 59
PVRL1 0.026 0.013 -10000 0 -10000 0 0
PVRL3 -0.019 0.12 0.12 4 -0.33 40 44
PVRL2 0.029 0.003 -10000 0 -10000 0 0
PIK3R1 0.025 0.03 -10000 0 -0.33 2 2
CDH1 -0.067 0.16 -10000 0 -0.33 82 82
CLDN1 -0.017 0.16 0.12 70 -0.33 56 126
JAM-A/CLDN1 0.001 0.13 -10000 0 -0.2 79 79
SRC -0.081 0.21 -10000 0 -0.48 62 62
ITGB3 -0.024 0.13 -10000 0 -0.33 46 46
nectin-1(dimer)/I-afadin/I-afadin 0.032 0.031 -10000 0 -0.22 3 3
FARP2 -0.074 0.22 -10000 0 -0.47 53 53
RAC1 0.025 0.009 -10000 0 -10000 0 0
CTNNA1 0.027 0.007 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.016 0.09 -10000 0 -0.19 44 44
nectin-1/I-afadin 0.032 0.031 -10000 0 -0.22 3 3
nectin-2/I-afadin 0.035 0.03 -10000 0 -0.23 3 3
RAC1/GTP/IQGAP1/filamentous actin 0.033 0.014 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.015 0.087 -10000 0 -0.19 42 42
CDC42/GTP/IQGAP1/filamentous actin 0.037 0.009 -10000 0 -10000 0 0
F11R 0.022 0.042 -10000 0 -0.33 4 4
positive regulation of filopodium formation -0.044 0.14 -10000 0 -0.29 53 53
alphaV/beta3 Integrin/Talin -0.015 0.096 0.24 2 -0.18 46 48
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.035 0.03 -10000 0 -0.23 3 3
nectin-2(dimer)/I-afadin/I-afadin 0.035 0.03 -10000 0 -0.23 3 3
PIP5K1C -0.014 0.051 -10000 0 -0.14 40 40
VAV2 -0.092 0.25 -10000 0 -0.53 58 58
RAP1/GDP -0.045 0.18 -10000 0 -0.36 62 62
ITGAV 0.019 0.058 0.12 1 -0.33 8 9
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.018 0.088 -10000 0 -0.19 42 42
nectin-3(dimer)/I-afadin/I-afadin 0.001 0.095 -10000 0 -0.23 42 42
Rac1/GTP -0.06 0.18 -10000 0 -0.4 57 57
PTPRM -0.01 0.058 -10000 0 -0.15 40 40
E-cadherin/beta catenin/alpha catenin -0.001 0.11 -10000 0 -0.16 80 80
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.028 0.004 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.038 0.03 -10000 0 -0.23 2 2
alphaV beta3 Integrin -0.023 0.14 0.18 1 -0.24 82 83
PTK2 -0.03 0.17 0.3 15 -0.34 45 60
IGF1R 0.026 0.03 -10000 0 -0.33 2 2
PI4KB 0.026 0.008 -10000 0 -10000 0 0
MFGE8 0.026 0.03 0.12 1 -0.33 2 3
SRC 0.025 0.022 -10000 0 -0.33 1 1
CDKN1B -0.015 0.098 -10000 0 -0.44 10 10
VEGFA 0.027 0.028 0.12 8 -0.33 1 9
ILK -0.016 0.098 0.14 1 -0.24 30 31
ROCK1 0.022 0.046 -10000 0 -0.33 5 5
AKT1 -0.022 0.089 0.13 1 -0.38 12 13
PTK2B -0.018 0.091 0.2 25 -0.18 43 68
alphaV/beta3 Integrin/JAM-A -0.008 0.14 0.18 1 -0.21 86 87
CBL 0.025 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.012 0.1 -10000 0 -0.21 49 49
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.044 0.081 -10000 0 -0.18 31 31
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.015 0.088 0.14 1 -0.31 10 11
alphaV/beta3 Integrin/Syndecan-1 0.007 0.11 -10000 0 -0.21 59 59
PI4KA 0.027 0.009 0.12 1 -10000 0 1
IGF-1R heterotetramer/IGF1/IRS1 -0.04 0.15 -10000 0 -0.21 111 111
PI4 Kinase 0.036 0.016 -10000 0 -10000 0 0
PIK3CA 0.023 0.042 -10000 0 -0.33 4 4
alphaV/beta3 Integrin/Osteopontin -0.007 0.13 0.18 4 -0.22 73 77
RPS6KB1 -0.081 0.11 0.32 1 -0.34 30 31
TLN1 0.026 0.009 -10000 0 -10000 0 0
MAPK3 -0.12 0.22 -10000 0 -0.45 81 81
GPR124 0.022 0.042 -10000 0 -0.33 4 4
MAPK1 -0.11 0.21 -10000 0 -0.44 80 80
PXN 0.028 0.004 -10000 0 -10000 0 0
PIK3R1 0.025 0.03 -10000 0 -0.33 2 2
alphaV/beta3 Integrin/Tumstatin 0.007 0.12 0.18 1 -0.22 62 63
cell adhesion 0.004 0.1 -10000 0 -0.22 49 49
ANGPTL3 0.023 0.009 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.047 0.036 -10000 0 -0.2 3 3
IGF-1R heterotetramer 0.026 0.03 -10000 0 -0.33 2 2
Rac1/GDP 0.019 0.007 -10000 0 -10000 0 0
TGFBR2 0.029 0.003 -10000 0 -10000 0 0
ITGB3 -0.024 0.13 -10000 0 -0.33 46 46
IGF1 0.01 0.085 0.12 6 -0.33 17 23
RAC1 0.025 0.009 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.01 0.1 -10000 0 -0.2 52 52
apoptosis 0.019 0.058 0.12 1 -0.33 8 9
CD47 0.028 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.014 0.1 -10000 0 -0.2 50 50
VCL 0.026 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.002 0.14 0.18 7 -0.24 67 74
CSF1 0.022 0.046 -10000 0 -0.33 5 5
PIK3C2A -0.027 0.13 0.14 1 -0.32 32 33
PI4 Kinase/Pyk2 -0.019 0.1 -10000 0 -0.19 63 63
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.027 0.098 0.19 2 -0.18 47 49
FAK1/Vinculin -0.012 0.15 0.3 15 -0.28 42 57
alphaV beta3/Integrin/ppsTEM5 0.01 0.1 -10000 0 -0.2 52 52
RHOA 0.029 0.003 -10000 0 -10000 0 0
VTN 0.029 0.071 0.12 38 -0.33 9 47
BCAR1 0.025 0.03 -10000 0 -0.33 2 2
FGF2 -0.035 0.14 -10000 0 -0.33 54 54
F11R -0.03 0.093 -10000 0 -0.24 50 50
alphaV/beta3 Integrin/Lactadherin 0.013 0.1 -10000 0 -0.21 50 50
alphaV/beta3 Integrin/TGFBR2 0.015 0.1 -10000 0 -0.2 49 49
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.049 0.059 -10000 0 -0.18 15 15
HSP90AA1 0.027 0.021 -10000 0 -0.33 1 1
alphaV/beta3 Integrin/Talin 0.012 0.091 -10000 0 -0.18 49 49
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.009 0.084 0.12 2 -0.33 17 19
alphaV/beta3 Integrin/Pyk2 0.021 0.095 0.18 20 -0.17 47 67
SDC1 0.017 0.069 0.12 6 -0.33 11 17
VAV3 -0.018 0.055 0.18 4 -0.2 16 20
PTPN11 0.028 0.004 -10000 0 -10000 0 0
IRS1 0.013 0.073 -10000 0 -0.33 13 13
FAK1/Paxillin -0.009 0.15 0.3 16 -0.28 40 56
cell migration -0.013 0.14 0.28 16 -0.26 39 55
ITGAV 0.019 0.058 0.12 1 -0.33 8 9
PI3K -0.001 0.14 -10000 0 -0.21 82 82
SPP1 -0.004 0.11 0.12 16 -0.33 31 47
KDR 0.028 0.023 0.12 3 -0.33 1 4
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.019 0.058 0.12 1 -0.33 8 9
COL4A3 0.017 0.096 -10000 0 -0.33 19 19
angiogenesis -0.11 0.23 0.26 1 -0.46 80 81
Rac1/GTP 0.011 0.057 0.17 2 -0.18 16 18
EDIL3 -0.002 0.12 0.12 38 -0.33 34 72
cell proliferation 0.015 0.1 -10000 0 -0.2 49 49
Osteopontin-mediated 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
IKK alpha homodimer -0.019 0.11 0.19 2 -0.19 71 73
NF kappa B1 p50/RelA/I kappa B alpha -0.012 0.11 0.32 1 -0.32 14 15
alphaV/beta3 Integrin/Osteopontin/Src 0.012 0.097 -10000 0 -0.23 38 38
AP1 -0.01 0.14 -10000 0 -0.36 23 23
ILK -0.029 0.1 0.19 4 -0.2 70 74
bone resorption -0.032 0.11 0.18 4 -0.3 22 26
PTK2B 0.027 0.025 0.12 5 -0.33 1 6
PYK2/p130Cas 0.003 0.13 -10000 0 -0.19 79 79
ITGAV 0.02 0.059 0.13 1 -0.33 8 9
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.029 0.056 -10000 0 -0.23 13 13
alphaV/beta3 Integrin/Osteopontin 0 0.13 0.19 4 -0.22 73 77
MAP3K1 -0.033 0.11 0.19 3 -0.2 71 74
JUN 0.029 0.009 0.12 2 -10000 0 2
MAPK3 -0.046 0.092 0.19 2 -0.3 17 19
MAPK1 -0.045 0.088 0.19 2 -0.31 14 16
Rac1/GDP 0.019 0.007 -10000 0 -10000 0 0
NFKB1 0.028 0.005 -10000 0 -10000 0 0
MAPK8 -0.049 0.096 0.19 2 -0.21 58 60
ITGB3 -0.022 0.13 -10000 0 -0.33 46 46
NFKBIA -0.042 0.098 0.18 2 -0.34 16 18
FOS 0.031 0.016 0.12 8 -10000 0 8
CD44 0.023 0.042 -10000 0 -0.33 4 4
CHUK 0.025 0.022 -10000 0 -0.33 1 1
PLAU -0.047 0.18 -10000 0 -0.99 7 7
NF kappa B1 p50/RelA 0.002 0.12 -10000 0 -0.33 12 12
BCAR1 0.025 0.03 -10000 0 -0.33 2 2
RELA 0.028 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0 0.11 -10000 0 -0.24 50 50
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.033 0.11 0.19 4 -0.21 71 75
VAV3 -0.049 0.097 0.19 3 -0.21 60 63
MAP3K14 -0.03 0.1 0.19 2 -0.2 72 74
ROCK2 0.018 0.062 -10000 0 -0.33 9 9
SPP1 -0.003 0.11 0.13 16 -0.33 31 47
RAC1 0.025 0.009 -10000 0 -10000 0 0
Rac1/GTP -0.034 0.098 0.18 1 -0.2 54 55
MMP2 -0.049 0.12 0.31 2 -0.39 24 26
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.005 0.12 0.18 2 -0.2 75 77
fibroblast growth factor receptor signaling pathway -0.005 0.12 0.18 2 -0.2 75 77
LAMA1 -0.019 0.13 -10000 0 -0.33 44 44
PRNP 0.025 0.03 0.12 1 -0.33 2 3
GPC1/SLIT2 0.016 0.094 0.18 2 -0.23 34 36
SMAD2 -0.023 0.043 -10000 0 -0.17 21 21
GPC1/PrPc/Cu2+ 0.021 0.064 0.16 1 -0.19 23 24
GPC1/Laminin alpha1 -0.009 0.12 -10000 0 -0.25 56 56
TDGF1 0.025 0.017 -10000 0 -10000 0 0
CRIPTO/GPC1 0.022 0.073 -10000 0 -0.23 21 21
APP/GPC1 0.014 0.095 -10000 0 -0.26 29 29
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.014 0.058 -10000 0 -0.2 23 23
FLT1 0.027 0.022 0.12 1 -0.33 1 2
GPC1/TGFB/TGFBR1/TGFBR2 0.039 0.067 -10000 0 -0.19 21 21
SERPINC1 0.025 0.015 -10000 0 -10000 0 0
FYN -0.01 0.05 -10000 0 -0.2 18 18
FGR -0.017 0.063 -10000 0 -0.2 30 30
positive regulation of MAPKKK cascade -0.04 0.14 0.23 10 -0.32 45 55
SLIT2 0.017 0.081 0.12 19 -0.33 14 33
GPC1/NRG 0.013 0.1 0.18 3 -0.24 38 41
NRG1 0.014 0.092 -10000 0 -0.33 18 18
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.038 0.07 0.18 2 -0.2 19 21
LYN -0.014 0.057 -10000 0 -0.2 24 24
mol:Spermine -0.008 0.061 -10000 0 -0.23 21 21
cell growth -0.005 0.12 0.18 2 -0.2 75 77
BMP signaling pathway -0.007 0.095 0.33 21 -0.12 15 36
SRC -0.012 0.055 -10000 0 -0.2 22 22
TGFBR1 0.027 0.008 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.009 0.14 0.12 63 -0.33 47 110
GPC1 0.007 0.096 0.12 15 -0.33 21 36
TGFBR1 (dimer) 0.027 0.008 -10000 0 -10000 0 0
VEGFA 0.027 0.028 0.12 8 -0.33 1 9
BLK -0.024 0.082 -10000 0 -0.2 48 48
HCK -0.02 0.065 -10000 0 -0.2 33 33
FGF2 -0.035 0.14 -10000 0 -0.33 54 54
FGFR1 0.026 0.046 -10000 0 -0.33 4 4
VEGFR1 homodimer 0.027 0.022 0.12 1 -0.33 1 2
TGFBR2 0.029 0.003 -10000 0 -10000 0 0
cell death 0.014 0.095 -10000 0 -0.26 29 29
ATIII/GPC1 0.021 0.072 0.18 1 -0.23 20 21
PLA2G2A/GPC1 -0.003 0.13 0.18 1 -0.24 64 65
LCK -0.033 0.085 -10000 0 -0.2 60 60
neuron differentiation 0.013 0.1 0.18 3 -0.24 38 41
PrPc/Cu2+ 0.019 0.021 -10000 0 -0.23 2 2
APP 0.012 0.073 -10000 0 -0.33 13 13
TGFBR2 (dimer) 0.028 0.003 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.039 0.25 0.28 1 -0.76 28 29
MKNK1 0.028 0.004 -10000 0 -10000 0 0
MAPK14 0.01 0.1 -10000 0 -0.3 28 28
ATF2/c-Jun -0.003 0.093 -10000 0 -0.26 28 28
MAPK11 0.007 0.12 -10000 0 -0.33 30 30
MITF -0.027 0.14 -10000 0 -0.3 49 49
MAPKAPK5 -0.004 0.12 -10000 0 -0.35 29 29
KRT8 -0.019 0.14 0.21 1 -0.32 47 48
MAPKAPK3 0.028 0.004 -10000 0 -10000 0 0
MAPKAPK2 0.026 0.009 -10000 0 -10000 0 0
p38alpha-beta/CK2 0.008 0.15 -10000 0 -0.42 30 30
CEBPB -0.007 0.12 -10000 0 -0.35 29 29
SLC9A1 -0.005 0.12 -10000 0 -0.35 29 29
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.002 0.12 0.23 1 -0.35 30 31
p38alpha-beta/MNK1 0.023 0.13 -10000 0 -0.34 30 30
JUN 0.003 0.096 -10000 0 -0.26 28 28
PPARGC1A -0.06 0.17 -10000 0 -0.3 79 79
USF1 -0.001 0.11 0.23 2 -0.34 26 28
RAB5/GDP/GDI1 0.005 0.092 -10000 0 -0.26 29 29
NOS2 -0.018 0.19 -10000 0 -0.54 27 27
DDIT3 -0.003 0.12 0.24 2 -0.35 29 31
RAB5A 0.029 0.003 -10000 0 -10000 0 0
HSPB1 0.001 0.11 0.29 15 -0.29 29 44
p38alpha-beta/HBP1 0.02 0.13 -10000 0 -0.35 29 29
CREB1 -0.005 0.13 -10000 0 -0.38 29 29
RAB5/GDP 0.021 0.002 -10000 0 -10000 0 0
EIF4E 0.007 0.12 0.22 4 -0.33 26 30
RPS6KA4 -0.003 0.12 -10000 0 -0.35 28 28
PLA2G4A -0.004 0.11 0.23 1 -0.3 31 32
GDI1 -0.002 0.12 -10000 0 -0.35 28 28
TP53 -0.019 0.14 0.21 5 -0.44 28 33
RPS6KA5 -0.008 0.13 -10000 0 -0.37 30 30
ESR1 -0.016 0.14 -10000 0 -0.41 31 31
HBP1 0.026 0.009 -10000 0 -10000 0 0
MEF2C -0.008 0.13 -10000 0 -0.36 30 30
MEF2A -0.006 0.13 -10000 0 -0.37 29 29
EIF4EBP1 -0.008 0.13 -10000 0 -0.39 29 29
KRT19 -0.009 0.13 -10000 0 -0.32 37 37
ELK4 0 0.11 0.23 2 -0.34 25 27
ATF6 -0.001 0.11 0.23 2 -0.34 26 28
ATF1 -0.007 0.13 -10000 0 -0.39 30 30
p38alpha-beta/MAPKAPK2 0.023 0.12 -10000 0 -0.33 28 28
p38alpha-beta/MAPKAPK3 0.025 0.13 -10000 0 -0.35 28 28
TCGA08_retinoblastoma

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
CDKN2B 0.019 0.052 0.13 13 -0.3 5 18
CDKN2C 0.02 0.018 -10000 0 -10000 0 0
CDKN2A 0.005 0.091 0.13 7 -0.31 20 27
CCND2 0.003 0.048 0.16 20 -0.14 2 22
RB1 -0.006 0.054 0.19 1 -0.18 21 22
CDK4 0.006 0.054 0.18 21 -0.2 1 22
CDK6 0.003 0.057 0.18 20 -0.13 8 28
G1/S progression 0.047 0.091 0.19 81 -0.19 1 82
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.019 0.056 0.12 4 -0.33 7 11
GNB1/GNG2 -0.041 0.077 -10000 0 -0.19 61 61
AKT1 -0.014 0.11 0.28 1 -0.23 39 40
EGF -0.03 0.14 -10000 0 -0.33 54 54
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.005 0.08 0.39 2 -0.24 11 13
mol:Ca2+ -0.032 0.15 0.25 1 -0.31 65 66
LYN -0.006 0.065 0.26 1 -0.23 8 9
RhoA/GTP -0.011 0.064 -10000 0 -0.13 55 55
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.045 0.17 0.24 1 -0.35 61 62
GNG2 0.013 0.073 -10000 0 -0.33 13 13
ARRB2 0.027 0.009 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.011 0.089 -10000 0 -0.35 14 14
G beta5/gamma2 -0.048 0.1 -10000 0 -0.24 61 61
PRKCH -0.042 0.17 0.25 1 -0.35 64 65
DNM1 0.025 0.039 0.12 7 -0.33 3 10
TXA2/TP beta/beta Arrestin3 0.008 0.022 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR 0.017 0.07 0.12 8 -0.33 11 19
G12 family/GTP -0.041 0.14 -10000 0 -0.3 63 63
ADRBK1 0.028 0.005 -10000 0 -10000 0 0
ADRBK2 0.017 0.058 -10000 0 -0.33 8 8
RhoA/GTP/ROCK1 0.034 0.03 -10000 0 -0.19 5 5
mol:GDP 0.025 0.14 0.34 32 -0.28 1 33
mol:NADP 0.021 0.042 -10000 0 -0.33 4 4
RAB11A 0.028 0.004 -10000 0 -10000 0 0
PRKG1 0.012 0.079 -10000 0 -0.33 14 14
mol:IP3 -0.046 0.19 0.27 1 -0.39 65 66
cell morphogenesis 0.034 0.03 -10000 0 -0.19 5 5
PLCB2 -0.077 0.25 -10000 0 -0.53 65 65
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.009 0.087 0.3 4 -0.24 12 16
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.008 0.078 0.39 2 -0.24 12 14
RHOA 0.029 0.003 -10000 0 -10000 0 0
PTGIR 0.025 0.036 -10000 0 -0.33 3 3
PRKCB1 -0.046 0.18 0.25 1 -0.38 64 65
GNAQ 0.027 0.008 -10000 0 -10000 0 0
mol:L-citrulline 0.021 0.042 -10000 0 -0.33 4 4
TXA2/TXA2-R family -0.074 0.24 -10000 0 -0.53 61 61
LCK -0.016 0.095 0.23 2 -0.26 23 25
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.017 0.059 -10000 0 -0.17 21 21
TXA2-R family/G12 family/GDP/G beta/gamma 0.002 0.096 -10000 0 -0.45 11 11
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.02 0.058 0.17 1 -0.19 12 13
MAPK14 -0.012 0.12 0.22 9 -0.24 53 62
TGM2/GTP -0.053 0.2 -10000 0 -0.42 63 63
MAPK11 -0.021 0.12 0.22 6 -0.24 58 64
ARHGEF1 -0.019 0.086 0.16 1 -0.18 61 62
GNAI2 0.029 0.003 -10000 0 -10000 0 0
JNK cascade -0.047 0.18 0.26 1 -0.39 61 62
RAB11/GDP 0.028 0.004 -10000 0 -10000 0 0
ICAM1 -0.031 0.14 0.22 1 -0.3 60 61
cAMP biosynthetic process -0.044 0.17 0.26 1 -0.36 64 65
Gq family/GTP/EBP50 -0.001 0.067 -10000 0 -0.19 29 29
actin cytoskeleton reorganization 0.034 0.03 -10000 0 -0.19 5 5
SRC -0.002 0.068 0.39 2 -0.21 6 8
GNB5 0.024 0.036 -10000 0 -0.33 3 3
GNB1 0.028 0.006 -10000 0 -10000 0 0
EGF/EGFR -0.029 0.13 0.27 9 -0.28 40 49
VCAM1 -0.036 0.15 0.22 1 -0.32 60 61
TP beta/Gq family/GDP/G beta5/gamma2 -0.011 0.089 -10000 0 -0.35 14 14
platelet activation -0.022 0.16 0.3 4 -0.3 63 67
PGI2/IP 0.018 0.025 -10000 0 -0.23 3 3
PRKACA 0.009 0.045 -10000 0 -0.19 14 14
Gq family/GDP/G beta5/gamma2 -0.008 0.085 -10000 0 -0.32 14 14
TXA2/TP beta/beta Arrestin2 -0.007 0.084 -10000 0 -0.4 11 11
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.006 0.054 -10000 0 -0.18 23 23
mol:DAG -0.054 0.2 0.27 1 -0.43 64 65
EGFR 0.021 0.071 -10000 0 -0.33 10 10
TXA2/TP alpha -0.066 0.23 -10000 0 -0.49 64 64
Gq family/GTP 0.007 0.047 0.23 2 -0.21 10 12
YES1 -0.005 0.063 -10000 0 -0.22 4 4
GNAI2/GTP 0.004 0.061 -10000 0 -0.16 28 28
PGD2/DP 0.013 0.048 0.089 8 -0.23 11 19
SLC9A3R1 0.027 0.022 0.12 1 -0.33 1 2
FYN 0.002 0.067 0.39 2 -0.22 4 6
mol:NO 0.021 0.042 -10000 0 -0.33 4 4
GNA15 0.019 0.062 0.12 3 -0.33 9 12
PGK/cGMP 0.021 0.052 -10000 0 -0.19 15 15
RhoA/GDP 0.028 0.004 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.022 0.083 -10000 0 -0.24 14 14
NOS3 0.021 0.042 -10000 0 -0.33 4 4
RAC1 0.025 0.009 -10000 0 -10000 0 0
PRKCA -0.041 0.17 0.25 1 -0.35 63 64
PRKCB -0.047 0.18 -10000 0 -0.37 64 64
PRKCE -0.04 0.17 0.26 1 -0.35 64 65
PRKCD -0.045 0.18 0.25 1 -0.38 64 65
PRKCG -0.047 0.18 0.29 1 -0.39 63 64
muscle contraction -0.068 0.23 0.31 1 -0.49 64 65
PRKCZ -0.043 0.16 0.28 1 -0.34 61 62
ARR3 0.02 0.01 -10000 0 -10000 0 0
TXA2/TP beta 0.017 0.067 0.18 1 -0.17 28 29
PRKCQ -0.053 0.18 0.26 1 -0.37 64 65
MAPKKK cascade -0.065 0.22 -10000 0 -0.47 64 64
SELE -0.039 0.16 0.22 1 -0.34 60 61
TP beta/GNAI2/GDP/G beta/gamma 0.029 0.075 0.19 1 -0.18 21 22
ROCK1 0.022 0.046 -10000 0 -0.33 5 5
GNA14 0.034 0.048 -10000 0 -0.33 3 3
chemotaxis -0.086 0.27 -10000 0 -0.6 60 60
GNA12 0.025 0.009 -10000 0 -10000 0 0
GNA13 0.028 0.005 -10000 0 -10000 0 0
GNA11 0.029 0.003 -10000 0 -10000 0 0
Rac1/GTP 0.019 0.007 -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 0.025 0.097 -10000 0 -0.2 38 38
NF kappa B1 p50/RelA/I kappa B alpha -0.004 0.1 0.23 1 -0.29 8 9
AP1 0.01 0.094 0.16 1 -0.17 56 57
mol:PIP3 -0.024 0.08 -10000 0 -0.18 50 50
AKT1 0.005 0.083 0.26 5 -0.28 7 12
PTK2B -0.021 0.095 0.18 1 -0.24 29 30
RHOA 0.01 0.061 0.22 5 -0.27 5 10
PIK3CB 0.028 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.011 0.079 0.21 9 -0.24 11 20
MAGI3 0.025 0.03 -10000 0 -0.33 2 2
RELA 0.028 0.005 -10000 0 -10000 0 0
apoptosis -0.021 0.094 0.18 1 -0.2 58 59
HRAS/GDP 0.021 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.037 0.098 0.22 3 -0.25 28 31
NF kappa B1 p50/RelA -0.008 0.1 0.17 1 -0.22 33 34
endothelial cell migration -0.009 0.11 -10000 0 -0.32 28 28
ADCY4 -0.05 0.14 0.24 1 -0.32 48 49
ADCY5 -0.064 0.16 0.24 1 -0.35 55 56
ADCY6 -0.051 0.14 0.24 1 -0.32 48 49
ADCY7 -0.049 0.13 0.24 1 -0.32 46 47
ADCY1 -0.075 0.14 -10000 0 -0.33 57 57
ADCY2 -0.08 0.17 0.24 1 -0.35 67 68
ADCY3 -0.05 0.13 0.24 1 -0.31 47 48
ADCY8 -0.043 0.13 0.25 2 -0.31 43 45
ADCY9 -0.052 0.14 0.24 1 -0.32 48 49
GSK3B -0.022 0.092 0.21 3 -0.28 19 22
arachidonic acid secretion -0.061 0.14 0.2 1 -0.32 52 53
GNG2 0.013 0.073 -10000 0 -0.33 13 13
TRIP6 0.01 0.048 -10000 0 -0.26 8 8
GNAO1 -0.033 0.1 -10000 0 -0.2 71 71
HRAS 0.028 0.005 -10000 0 -10000 0 0
NFKBIA -0.025 0.1 0.22 1 -0.24 29 30
GAB1 0.026 0.03 -10000 0 -0.33 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.027 0.25 -10000 0 -0.87 24 24
JUN 0.029 0.009 0.12 2 -10000 0 2
LPA/LPA2/NHERF2 0.033 0.037 -10000 0 -0.12 12 12
TIAM1 -0.05 0.3 -10000 0 -1 24 24
PIK3R1 0.025 0.03 -10000 0 -0.33 2 2
mol:IP3 -0.011 0.073 0.2 7 -0.19 25 32
PLCB3 0.011 0.036 0.18 5 -0.18 4 9
FOS 0.031 0.016 0.12 8 -10000 0 8
positive regulation of mitosis -0.061 0.14 0.2 1 -0.32 52 53
LPA/LPA1-2-3 0.019 0.11 0.18 2 -0.18 59 61
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.025 0.03 -10000 0 -0.33 2 2
stress fiber formation -0.012 0.098 0.19 1 -0.33 15 16
GNAZ -0.016 0.09 0.12 1 -0.22 45 46
EGFR/PI3K-beta/Gab1 -0.012 0.09 -10000 0 -0.18 51 51
positive regulation of dendritic cell cytokine production 0.017 0.11 0.17 2 -0.18 59 61
LPA/LPA2/MAGI-3 0.032 0.037 -10000 0 -0.11 14 14
ARHGEF1 0.016 0.089 0.21 30 -0.2 20 50
GNAI2 -0.003 0.073 -10000 0 -0.21 29 29
GNAI3 -0.004 0.071 -10000 0 -0.21 29 29
GNAI1 -0.008 0.079 -10000 0 -0.22 32 32
LPA/LPA3 0.004 0.084 0.1 1 -0.19 39 40
LPA/LPA2 0.016 0.034 -10000 0 -0.12 13 13
LPA/LPA1 0.004 0.092 0.14 2 -0.24 32 34
HB-EGF/EGFR 0.006 0.078 0.15 6 -0.19 36 42
HBEGF -0.006 0.067 -10000 0 -0.23 23 23
mol:DAG -0.011 0.073 0.2 7 -0.19 25 32
cAMP biosynthetic process -0.065 0.14 0.22 4 -0.3 58 62
NFKB1 0.028 0.005 -10000 0 -10000 0 0
SRC 0.025 0.022 -10000 0 -0.33 1 1
GNB1 0.028 0.006 -10000 0 -10000 0 0
LYN -0.02 0.11 0.24 5 -0.26 36 41
GNAQ -0.006 0.069 0.16 1 -0.2 32 33
LPAR2 0.025 0.036 0.12 1 -0.33 3 4
LPAR3 0.007 0.12 -10000 0 -0.33 30 30
LPAR1 0.006 0.11 0.14 2 -0.3 27 29
IL8 -0.035 0.16 0.32 3 -0.4 36 39
PTK2 -0.018 0.077 0.19 5 -0.18 46 51
Rac1/GDP 0.019 0.007 -10000 0 -10000 0 0
CASP3 -0.021 0.094 0.18 1 -0.2 58 59
EGFR 0.021 0.071 -10000 0 -0.33 10 10
PLCG1 -0.011 0.078 0.17 3 -0.21 34 37
PLD2 -0.018 0.082 0.19 5 -0.18 49 54
G12/G13 0.031 0.081 -10000 0 -0.19 28 28
PI3K-beta -0.002 0.073 -10000 0 -0.28 10 10
cell migration -0.007 0.086 0.2 1 -0.26 21 22
SLC9A3R2 0.028 0.022 -10000 0 -0.33 1 1
PXN -0.013 0.1 0.19 1 -0.33 15 16
HRAS/GTP -0.064 0.14 -10000 0 -0.33 52 52
RAC1 0.025 0.009 -10000 0 -10000 0 0
MMP9 -0.001 0.11 -10000 0 -0.33 29 29
PRKCE 0.028 0.004 -10000 0 -10000 0 0
PRKCD -0.017 0.079 0.2 10 -0.25 8 18
Gi(beta/gamma) -0.051 0.13 0.22 1 -0.3 49 50
mol:LPA -0.003 0.027 -10000 0 -0.11 15 15
TRIP6/p130 Cas/FAK1/Paxillin 0 0.1 0.21 1 -0.31 13 14
MAPKKK cascade -0.061 0.14 0.2 1 -0.32 52 53
contractile ring contraction involved in cytokinesis 0.011 0.061 0.22 5 -0.26 5 10
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.004 0.074 0.17 2 -0.19 35 37
GNA15 -0.011 0.079 0.16 1 -0.2 40 41
GNA12 0.025 0.009 -10000 0 -10000 0 0
GNA13 0.028 0.005 -10000 0 -10000 0 0
MAPT -0.037 0.1 0.22 3 -0.26 28 31
GNA11 -0.006 0.07 0.16 1 -0.19 33 34
Rac1/GTP -0.03 0.27 -10000 0 -0.94 23 23
MMP2 -0.009 0.11 -10000 0 -0.32 28 28
S1P4 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 -0.037 0.14 0.12 4 -0.33 55 59
CDC42/GTP -0.028 0.12 -10000 0 -0.23 59 59
PLCG1 -0.036 0.11 0.22 1 -0.22 66 67
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.029 0.003 -10000 0 -10000 0 0
GNAI3 0.028 0.006 -10000 0 -10000 0 0
G12/G13 0.037 0.015 -10000 0 -10000 0 0
cell migration -0.028 0.12 -10000 0 -0.22 59 59
S1PR5 0.026 0.05 -10000 0 -0.33 5 5
S1PR4 0.005 0.099 -10000 0 -0.33 23 23
MAPK3 -0.037 0.11 -10000 0 -0.22 72 72
MAPK1 -0.038 0.11 -10000 0 -0.21 72 72
S1P/S1P5/Gi -0.025 0.11 -10000 0 -0.21 68 68
GNAI1 0.02 0.047 -10000 0 -0.33 5 5
CDC42/GDP 0.021 0.003 -10000 0 -10000 0 0
S1P/S1P5/G12 0.033 0.032 -10000 0 -0.19 4 4
RHOA 0.002 0.079 0.2 33 -0.16 17 50
S1P/S1P4/Gi -0.034 0.12 -10000 0 -0.22 72 72
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ -0.002 0.1 -10000 0 -0.33 26 26
S1P/S1P4/G12/G13 0.036 0.058 -10000 0 -0.17 18 18
GNA12 0.025 0.009 -10000 0 -10000 0 0
GNA13 0.028 0.005 -10000 0 -10000 0 0
CDC42 0.028 0.004 -10000 0 -10000 0 0
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.031 0.05 -10000 0 -0.23 10 10
Necdin/E2F1 0.019 0.07 -10000 0 -0.23 21 21
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.038 0.1 -10000 0 -0.17 51 51
NGF (dimer)/p75(NTR)/BEX1 0.031 0.11 0.2 15 -0.21 47 62
NT-4/5 (dimer)/p75(NTR) 0.025 0.083 0.18 2 -0.23 25 27
IKBKB 0.028 0.006 -10000 0 -10000 0 0
AKT1 -0.02 0.079 0.2 15 -0.32 3 18
IKBKG 0.029 0.003 -10000 0 -10000 0 0
BDNF -0.009 0.14 -10000 0 -0.33 42 42
MGDIs/NGR/p75(NTR)/LINGO1 -0.009 0.13 -10000 0 -0.23 68 68
FURIN 0.028 0.005 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.006 0.12 0.18 8 -0.21 70 78
LINGO1 -0.011 0.11 0.12 2 -0.33 33 35
Sortilin/TRAF6/NRIF 0.025 0.042 -10000 0 -0.16 12 12
proBDNF (dimer) -0.009 0.14 -10000 0 -0.33 42 42
NTRK1 0.022 0.059 0.12 14 -0.33 7 21
RTN4R -0.004 0.1 0.12 6 -0.33 27 33
neuron apoptosis -0.032 0.12 0.34 5 -0.35 13 18
IRAK1 0.029 0.003 -10000 0 -10000 0 0
SHC1 -0.002 0.066 0.2 2 -0.2 26 28
ARHGDIA 0.027 0.021 -10000 0 -0.33 1 1
RhoA/GTP 0.021 0.002 -10000 0 -10000 0 0
Gamma Secretase 0.073 0.035 -10000 0 -0.16 2 2
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.037 0.1 0.19 4 -0.19 45 49
MAGEH1 0.025 0.036 -10000 0 -0.33 3 3
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.023 0.12 0.19 4 -0.2 56 60
Mammalian IAPs/DIABLO 0.04 0.094 -10000 0 -0.21 33 33
proNGF (dimer) 0.016 0.07 0.12 8 -0.33 11 19
MAGED1 0.027 0.021 -10000 0 -0.33 1 1
APP 0.012 0.073 -10000 0 -0.33 13 13
NT-4/5 (dimer) 0.025 0.018 -10000 0 -10000 0 0
ZNF274 0.028 0.005 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.017 0.07 0.18 2 -0.17 34 36
NGF 0.016 0.07 0.12 8 -0.33 11 19
cell cycle arrest -0.021 0.095 0.3 14 -0.2 11 25
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.01 0.067 -10000 0 -0.19 27 27
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.04 0.077 0.18 2 -0.2 25 27
NCSTN 0.026 0.008 -10000 0 -10000 0 0
mol:GTP 0.03 0.093 0.18 5 -0.2 38 43
PSENEN 0.029 0.003 -10000 0 -10000 0 0
mol:ceramide -0.02 0.076 0.22 10 -0.18 35 45
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.001 0.076 -10000 0 -0.29 9 9
p75(NTR)/beta APP 0.015 0.099 -10000 0 -0.24 36 36
BEX1 0.026 0.093 0.12 57 -0.33 16 73
mol:GDP -0.024 0.064 -10000 0 -0.2 34 34
NGF (dimer) 0.037 0.08 0.19 1 -0.18 29 30
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.004 0.13 -10000 0 -0.22 68 68
PIK3R1 0.025 0.03 -10000 0 -0.33 2 2
RAC1/GTP 0.026 0.075 0.16 5 -0.17 33 38
MYD88 0.027 0.021 -10000 0 -0.33 1 1
CHUK 0.025 0.022 -10000 0 -0.33 1 1
NGF (dimer)/p75(NTR)/PKA 0.031 0.094 0.18 5 -0.2 38 43
RHOB 0.028 0.004 -10000 0 -10000 0 0
RHOA 0.029 0.003 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.037 0.021 -10000 0 -0.23 1 1
NT3 (dimer) 0.033 0.036 0.12 27 -0.33 1 28
TP53 -0.036 0.086 0.19 11 -0.3 6 17
PRDM4 -0.025 0.081 0.22 10 -0.18 43 53
BDNF (dimer) 0.008 0.13 0.19 17 -0.19 78 95
PIK3CA 0.023 0.042 -10000 0 -0.33 4 4
SORT1 0.016 0.065 -10000 0 -0.33 10 10
activation of caspase activity 0.032 0.1 -10000 0 -0.17 51 51
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.039 0.098 0.19 4 -0.18 43 47
RHOC 0.028 0.006 -10000 0 -10000 0 0
XIAP 0.026 0.029 -10000 0 -0.33 2 2
MAPK10 -0.035 0.14 0.32 10 -0.29 35 45
DIABLO 0.028 0.004 -10000 0 -10000 0 0
SMPD2 -0.02 0.077 0.22 10 -0.18 35 45
APH1B 0.026 0.029 -10000 0 -0.33 2 2
APH1A 0.026 0.008 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.025 0.099 0.18 4 -0.2 43 47
PSEN1 0.028 0.004 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.038 0.029 -10000 0 -0.23 3 3
NT3 (dimer)/p75(NTR) 0.03 0.087 0.18 8 -0.23 26 34
MAPK8 -0.03 0.13 0.34 9 -0.28 31 40
MAPK9 -0.026 0.13 0.35 9 -0.28 30 39
APAF1 0.025 0.036 -10000 0 -0.33 3 3
NTF3 0.033 0.036 0.12 27 -0.33 1 28
NTF4 0.025 0.018 -10000 0 -10000 0 0
NDN -0.001 0.098 -10000 0 -0.33 24 24
RAC1/GDP 0.019 0.007 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.046 0.085 -10000 0 -0.16 37 37
p75 CTF/Sortilin/TRAF6/NRIF 0.059 0.049 -10000 0 -0.18 10 10
RhoA-B-C/GTP 0.03 0.092 0.18 5 -0.2 38 43
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.03 0.12 0.2 8 -0.18 67 75
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.021 0.12 0.19 8 -0.19 69 77
PRKACB 0.023 0.042 -10000 0 -0.33 4 4
proBDNF (dimer)/p75 ECD 0.012 0.1 -10000 0 -0.23 42 42
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.004 0.11 0.12 21 -0.33 31 52
BIRC2 0.019 0.051 -10000 0 -0.33 6 6
neuron projection morphogenesis -0.036 0.085 0.16 3 -0.21 45 48
BAD -0.039 0.14 0.32 9 -0.29 35 44
RIPK2 0.026 0.009 -10000 0 -10000 0 0
NGFR 0.01 0.11 0.12 40 -0.33 25 65
CYCS -0.025 0.077 0.24 9 -0.18 37 46
ADAM17 0.028 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.047 0.083 0.19 5 -0.18 27 32
BCL2L11 -0.04 0.14 0.32 9 -0.29 36 45
BDNF (dimer)/p75(NTR) -0.001 0.13 0.18 10 -0.24 62 72
PI3K 0.042 0.094 0.19 5 -0.19 36 41
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.038 0.097 0.19 4 -0.18 42 46
NDNL2 0.028 0.005 -10000 0 -10000 0 0
YWHAE 0.027 0.008 -10000 0 -10000 0 0
PRKCI 0.027 0.021 -10000 0 -0.33 1 1
NGF (dimer)/p75(NTR) 0.019 0.097 0.18 5 -0.24 34 39
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.038 0.099 0.19 4 -0.18 44 48
TRAF6 0.028 0.005 -10000 0 -10000 0 0
RAC1 0.025 0.009 -10000 0 -10000 0 0
PRKCZ 0.015 0.065 -10000 0 -0.33 10 10
PLG 0.017 0.011 0.12 2 -10000 0 2
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.033 0.1 0.15 3 -0.2 79 82
SQSTM1 0.026 0.022 -10000 0 -0.33 1 1
NGFRAP1 0.019 0.058 -10000 0 -0.33 8 8
CASP3 -0.036 0.13 0.3 10 -0.28 35 45
E2F1 0.025 0.022 -10000 0 -0.33 1 1
CASP9 0.028 0.005 -10000 0 -10000 0 0
IKK complex 0.021 0.099 -10000 0 -0.24 18 18
NGF (dimer)/TRKA 0.028 0.066 0.18 1 -0.23 16 17
MMP7 0.011 0.099 0.12 34 -0.33 21 55
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.047 0.099 0.2 4 -0.18 43 47
MMP3 0.005 0.11 0.12 42 -0.33 27 69
APAF-1/Caspase 9 -0.048 0.078 -10000 0 -0.2 44 44
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.01 0.051 -10000 0 -0.15 19 19
NFATC2 -0.019 0.07 -10000 0 -0.2 30 30
NFATC3 -0.003 0.035 -10000 0 -0.091 10 10
CD40LG -0.078 0.22 0.3 3 -0.46 58 61
PTGS2 -0.073 0.2 0.28 2 -0.42 60 62
JUNB 0.029 0.008 0.12 2 -10000 0 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.005 0.028 -10000 0 -0.058 8 8
CaM/Ca2+ 0.005 0.028 -10000 0 -0.058 8 8
CALM1 0.014 0.026 -10000 0 -10000 0 0
JUN 0.014 0.028 0.12 2 -10000 0 2
mol:Ca2+ -0.005 0.011 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.014 0.013 -10000 0 -10000 0 0
FOSL1 -0.001 0.11 0.12 21 -0.33 29 50
CREM 0.025 0.023 0.12 1 -0.33 1 2
Jun/NFAT1-c-4/p21SNFT -0.017 0.15 -10000 0 -0.29 45 45
FOS 0.017 0.032 0.13 4 -10000 0 4
IFNG -0.087 0.23 0.35 1 -0.44 71 72
AP-1/NFAT1-c-4 -0.041 0.25 0.3 1 -0.47 56 57
FASLG -0.081 0.22 0.35 1 -0.48 58 59
NFAT1-c-4/ICER1 -0.021 0.1 0.18 1 -0.22 42 43
IL2RA -0.08 0.22 0.35 1 -0.44 61 62
FKBP12/FK506 0.02 0.005 -10000 0 -10000 0 0
CSF2 -0.069 0.2 0.35 1 -0.42 53 54
JunB/Fra1/NFAT1-c-4 -0.019 0.12 -10000 0 -0.21 56 56
IL4 -0.072 0.19 0.35 1 -0.42 53 54
IL2 0.001 0.13 -10000 0 -0.95 5 5
IL3 -0.022 0.17 -10000 0 -0.79 14 14
FKBP1A 0.027 0.007 -10000 0 -10000 0 0
BATF3 0.022 0.043 0.12 2 -0.33 4 6
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.026 0.009 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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
PCK2 0.049 0.083 0.25 2 -10000 0 2
SMARCC2 0.028 0.011 -10000 0 -10000 0 0
SMARCC1 0.028 0.017 -10000 0 -0.15 2 2
TBX21 -0.079 0.21 0.5 1 -0.59 34 35
SUMO2 0.03 0.01 -10000 0 -10000 0 0
STAT1 (dimer) 0.026 0.048 -10000 0 -0.22 10 10
FKBP4 0.028 0.005 -10000 0 -10000 0 0
FKBP5 0.004 0.086 0.12 1 -0.33 18 19
GR alpha/HSP90/FKBP51/HSP90 0.052 0.11 0.25 29 -0.22 6 35
PRL -0.015 0.089 -10000 0 -0.33 2 2
cortisol/GR alpha (dimer)/TIF2 0.1 0.21 0.46 55 -0.47 1 56
RELA 0.002 0.082 -10000 0 -0.18 43 43
FGG 0.095 0.19 0.4 54 -0.31 1 55
GR beta/TIF2 0.051 0.12 0.25 39 -0.29 4 43
IFNG -0.24 0.41 -10000 0 -0.92 67 67
apoptosis 0.044 0.14 0.51 17 -10000 0 17
CREB1 0.03 0.006 -10000 0 -10000 0 0
histone acetylation 0 0.13 0.34 17 -0.28 20 37
BGLAP -0.031 0.1 -10000 0 -0.36 2 2
GR/PKAc 0.074 0.11 0.26 30 -0.24 6 36
NF kappa B1 p50/RelA 0.004 0.14 -10000 0 -0.28 52 52
SMARCD1 0.028 0.011 -10000 0 -0.088 2 2
MDM2 0.053 0.086 0.2 52 -0.28 1 53
GATA3 -0.004 0.11 0.16 1 -0.33 30 31
AKT1 0.024 0.004 -10000 0 -10000 0 0
CSF2 -0.023 0.1 -10000 0 -10000 0 0
GSK3B 0.03 0.01 -10000 0 -10000 0 0
NR1I3 0.071 0.16 0.5 20 -10000 0 20
CSN2 0.076 0.16 0.34 47 -0.28 1 48
BRG1/BAF155/BAF170/BAF60A 0.073 0.033 -10000 0 -0.27 2 2
NFATC1 0.018 0.062 -10000 0 -0.33 9 9
POU2F1 0.03 0.012 -10000 0 -10000 0 0
CDKN1A -0.008 0.19 0.76 1 -1.3 5 6
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.002 0.009 -10000 0 -10000 0 0
SFN 0.028 0.084 -10000 0 -0.33 13 13
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.062 0.11 0.27 21 -0.21 6 27
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.06 0.14 0.47 16 -0.74 1 17
JUN -0.092 0.16 -10000 0 -0.34 59 59
IL4 -0.058 0.13 -10000 0 -0.46 8 8
CDK5R1 0.022 0.051 -10000 0 -0.33 6 6
PRKACA 0.029 0.002 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.037 0.11 0.2 30 -0.25 26 56
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.066 0.11 0.26 24 -0.19 7 31
cortisol/GR alpha (monomer) 0.13 0.25 0.52 61 -0.36 1 62
NCOA2 0.021 0.042 -10000 0 -0.33 4 4
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.021 0.084 0.19 1 -0.14 20 21
AP-1/NFAT1-c-4 -0.16 0.27 -10000 0 -0.48 103 103
AFP -0.087 0.13 -10000 0 -10000 0 0
SUV420H1 0.026 0.022 -10000 0 -0.33 1 1
IRF1 0.074 0.15 0.34 26 -0.58 5 31
TP53 0.026 0.074 -10000 0 -0.4 8 8
PPP5C 0.028 0.004 -10000 0 -10000 0 0
KRT17 -0.18 0.33 -10000 0 -0.74 59 59
KRT14 -0.22 0.45 -10000 0 -1.2 52 52
TBP 0.031 0.012 -10000 0 -10000 0 0
CREBBP 0.058 0.11 0.3 48 -0.3 2 50
HDAC1 0.026 0.021 -10000 0 -0.33 1 1
HDAC2 0.024 0.01 -10000 0 -10000 0 0
AP-1 -0.16 0.28 -10000 0 -0.48 103 103
MAPK14 0.027 0.012 -10000 0 -10000 0 0
MAPK10 0.021 0.083 0.12 28 -0.33 14 42
MAPK11 0.023 0.042 -10000 0 -0.32 4 4
KRT5 -0.25 0.43 -10000 0 -0.93 73 73
interleukin-1 receptor activity -0.001 0.002 -10000 0 -10000 0 0
NCOA1 0.029 0.005 -10000 0 -10000 0 0
STAT1 0.026 0.048 -10000 0 -0.22 10 10
CGA -0.043 0.11 -10000 0 -0.34 7 7
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.063 0.14 0.33 42 -0.27 1 43
MAPK3 0.03 0.01 -10000 0 -10000 0 0
MAPK1 0.028 0.01 -10000 0 -10000 0 0
ICAM1 -0.095 0.22 -10000 0 -0.57 36 36
NFKB1 0 0.088 -10000 0 -0.19 37 37
MAPK8 -0.07 0.14 -10000 0 -0.31 53 53
MAPK9 0.029 0.011 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.041 0.14 0.52 15 -10000 0 15
BAX -0.005 0.075 -10000 0 -0.39 1 1
POMC -0.13 0.36 -10000 0 -1.4 20 20
EP300 0.056 0.11 0.3 46 -0.27 1 47
cortisol/GR alpha (dimer)/p53 0.11 0.22 0.47 54 -10000 0 54
proteasomal ubiquitin-dependent protein catabolic process 0.03 0.076 0.18 33 -0.25 1 34
SGK1 0.058 0.19 0.37 18 -1.1 3 21
IL13 -0.15 0.25 -10000 0 -0.68 33 33
IL6 -0.082 0.23 -10000 0 -0.64 29 29
PRKACG 0.018 0.009 0.12 1 -10000 0 1
IL5 -0.13 0.22 -10000 0 -0.57 38 38
IL2 -0.14 0.24 -10000 0 -0.55 48 48
CDK5 0.027 0.01 -10000 0 -10000 0 0
PRKACB 0.023 0.042 -10000 0 -0.33 4 4
HSP90AA1 0.027 0.021 -10000 0 -0.33 1 1
IL8 -0.1 0.24 -10000 0 -0.67 32 32
CDK5R1/CDK5 0.034 0.042 -10000 0 -0.23 6 6
NF kappa B1 p50/RelA/PKAc 0.032 0.13 -10000 0 -0.23 40 40
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.12 0.21 0.44 60 -10000 0 60
SMARCA4 0.028 0.017 -10000 0 -0.13 3 3
chromatin remodeling 0.08 0.14 0.31 45 -0.35 1 46
NF kappa B1 p50/RelA/Cbp 0.058 0.16 0.36 35 -0.27 26 61
JUN (dimer) -0.091 0.16 -10000 0 -0.34 59 59
YWHAH 0.027 0.006 -10000 0 -10000 0 0
VIPR1 -0.044 0.15 0.53 1 -0.48 14 15
NR3C1 0.079 0.16 0.33 56 -0.36 2 58
NR4A1 -0.004 0.14 -10000 0 -0.47 23 23
TIF2/SUV420H1 0.032 0.038 -10000 0 -0.23 5 5
MAPKKK cascade 0.044 0.14 0.51 17 -10000 0 17
cortisol/GR alpha (dimer)/Src-1 0.12 0.22 0.46 63 -0.31 1 64
PBX1 0.035 0.036 0.16 4 -0.33 1 5
POU1F1 0.024 0.01 -10000 0 -10000 0 0
SELE -0.11 0.28 -10000 0 -0.73 41 41
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.08 0.14 0.31 45 -0.36 1 46
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.12 0.21 0.44 60 -10000 0 60
mol:cortisol 0.073 0.14 0.29 67 -10000 0 67
MMP1 -0.18 0.4 -10000 0 -0.98 54 54
EPHB forward 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
Ephrin A5/EPHB2 0.007 0.079 -10000 0 -0.19 39 39
cell-cell adhesion 0.041 0.067 0.17 55 -10000 0 55
Ephrin B/EPHB2/RasGAP 0.037 0.1 -10000 0 -0.17 50 50
ITSN1 0.028 0.005 -10000 0 -10000 0 0
PIK3CA 0.023 0.042 -10000 0 -0.33 4 4
SHC1 0.026 0.009 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.025 0.058 -10000 0 -0.19 19 19
Ephrin B1/EPHB1 0.033 0.055 -10000 0 -0.19 15 15
HRAS/GDP -0.001 0.1 0.19 1 -0.21 37 38
Ephrin B/EPHB1/GRB7 0.047 0.1 0.25 1 -0.17 48 49
Endophilin/SYNJ1 -0.03 0.066 0.18 7 -0.16 43 50
KRAS 0.028 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.038 0.1 0.25 1 -0.17 47 48
endothelial cell migration 0.043 0.054 -10000 0 -0.18 13 13
GRB2 0.028 0.005 -10000 0 -10000 0 0
GRB7 0.034 0.028 -10000 0 -10000 0 0
PAK1 -0.031 0.069 0.17 9 -0.3 2 11
HRAS 0.028 0.005 -10000 0 -10000 0 0
RRAS -0.029 0.066 0.18 7 -0.28 1 8
DNM1 0.025 0.039 0.12 7 -0.33 3 10
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.028 0.064 0.18 5 -0.17 38 43
lamellipodium assembly -0.041 0.067 -10000 0 -0.17 55 55
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.001 0.082 -10000 0 -0.23 12 12
PIK3R1 0.025 0.03 -10000 0 -0.33 2 2
EPHB2 0.008 0.084 -10000 0 -0.33 17 17
EPHB3 0.007 0.089 0.12 6 -0.33 19 25
EPHB1 0.019 0.086 -10000 0 -0.33 15 15
EPHB4 0.016 0.062 -10000 0 -0.33 9 9
mol:GDP -0.027 0.087 0.23 1 -0.23 35 36
Ephrin B/EPHB2 0.028 0.091 0.18 2 -0.17 48 50
Ephrin B/EPHB3 0.026 0.094 0.18 2 -0.17 52 54
JNK cascade -0.023 0.068 0.23 7 -0.19 25 32
Ephrin B/EPHB1 0.032 0.094 0.19 5 -0.17 48 53
RAP1/GDP 0.002 0.11 0.22 15 -0.27 12 27
EFNB2 0.03 0.016 0.12 8 -10000 0 8
EFNB3 -0.008 0.12 -10000 0 -0.33 34 34
EFNB1 0.029 0.008 0.12 2 -10000 0 2
Ephrin B2/EPHB1-2 0.035 0.08 0.17 4 -0.2 27 31
RAP1B 0.028 0.006 -10000 0 -10000 0 0
RAP1A 0.028 0.006 -10000 0 -10000 0 0
CDC42/GTP 0.009 0.11 0.2 1 -0.21 49 50
Rap1/GTP -0.008 0.078 -10000 0 -0.17 49 49
axon guidance 0.007 0.079 -10000 0 -0.19 39 39
MAPK3 -0.007 0.08 0.21 8 -0.28 5 13
MAPK1 -0.001 0.083 0.21 14 -0.3 4 18
Rac1/GDP -0.016 0.097 0.22 7 -0.28 12 19
actin cytoskeleton reorganization -0.043 0.067 -10000 0 -0.19 35 35
CDC42/GDP -0.005 0.11 0.22 18 -0.28 12 30
PI3K 0.048 0.056 -10000 0 -0.18 13 13
EFNA5 0.001 0.097 -10000 0 -0.33 23 23
Ephrin B2/EPHB4 0.029 0.042 -10000 0 -0.19 9 9
Ephrin B/EPHB2/Intersectin/N-WASP -0.013 0.089 -10000 0 -0.19 53 53
CDC42 0.028 0.004 -10000 0 -10000 0 0
RAS family/GTP -0.012 0.075 -10000 0 -0.26 5 5
PTK2 0.06 0.18 0.56 35 -10000 0 35
MAP4K4 -0.023 0.069 0.23 7 -0.19 25 32
SRC 0.025 0.022 -10000 0 -0.33 1 1
KALRN 0.026 0.045 0.12 8 -0.33 4 12
Intersectin/N-WASP 0.036 0.021 -10000 0 -0.23 1 1
neuron projection morphogenesis -0.011 0.12 0.29 24 -0.28 11 35
MAP2K1 -0.005 0.078 0.23 2 -0.22 12 14
WASL 0.025 0.022 -10000 0 -0.33 1 1
Ephrin B1/EPHB1-2/NCK1 0.051 0.085 0.19 1 -0.2 27 28
cell migration -0.001 0.11 0.24 11 -0.33 5 16
NRAS 0.027 0.007 -10000 0 -10000 0 0
SYNJ1 -0.03 0.066 0.18 7 -0.16 43 50
PXN 0.028 0.004 -10000 0 -10000 0 0
TF -0.056 0.094 0.18 6 -0.19 72 78
HRAS/GTP 0.012 0.094 0.18 1 -0.16 57 58
Ephrin B1/EPHB1-2 0.035 0.079 0.17 1 -0.2 27 28
cell adhesion mediated by integrin 0.029 0.057 0.17 33 -0.19 3 36
RAC1 0.025 0.009 -10000 0 -10000 0 0
mol:GTP 0.016 0.1 0.2 3 -0.17 60 63
RAC1-CDC42/GTP -0.048 0.072 -10000 0 -0.17 55 55
RASA1 0.025 0.03 -10000 0 -0.33 2 2
RAC1-CDC42/GDP -0.007 0.099 0.22 7 -0.27 12 19
ruffle organization -0.012 0.12 0.32 17 -0.26 9 26
NCK1 0.028 0.005 -10000 0 -10000 0 0
receptor internalization -0.033 0.064 0.17 7 -0.16 42 49
Ephrin B/EPHB2/KALRN 0.037 0.1 -10000 0 -0.17 51 51
ROCK1 0.001 0.052 0.18 2 -0.18 22 24
RAS family/GDP -0.046 0.067 -10000 0 -0.19 36 36
Rac1/GTP -0.041 0.072 -10000 0 -0.18 55 55
Ephrin B/EPHB1/Src/Paxillin -0.004 0.088 -10000 0 -0.2 47 47
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.028 0.005 -10000 0 -10000 0 0
EGFR 0.021 0.071 -10000 0 -0.33 10 10
EGF/EGFR 0.001 0.1 -10000 0 -0.17 66 66
EGF/EGFR dimer/SHC/GRB2/SOS1 0.028 0.1 -10000 0 -0.18 50 50
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.023 0.058 -10000 0 -0.33 7 7
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF -0.03 0.14 -10000 0 -0.33 54 54
EGF/EGFR dimer/SHC 0.007 0.1 0.18 2 -0.2 53 55
mol:GDP 0.024 0.099 -10000 0 -0.18 50 50
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.018 0.061 -10000 0 -0.33 8 8
GRB2/SOS1 0.041 0.009 -10000 0 -10000 0 0
HRAS/GTP 0.009 0.084 -10000 0 -0.17 49 49
SHC1 0.026 0.009 -10000 0 -10000 0 0
HRAS/GDP 0.022 0.095 -10000 0 -0.17 49 49
FRAP1 -0.038 0.062 0.17 1 -0.17 50 51
EGF/EGFR dimer -0.01 0.12 0.18 2 -0.24 59 61
SOS1 0.029 0.003 -10000 0 -10000 0 0
GRB2 0.028 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 0.028 0.065 0.18 1 -0.26 12 13
Caspase cascade in apoptosis

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
TOP1 -0.025 0.14 -10000 0 -0.4 28 28
ACTA1 -0.047 0.16 0.18 2 -0.39 41 43
NUMA1 -0.031 0.16 -10000 0 -0.45 29 29
SPTAN1 -0.052 0.15 -10000 0 -0.39 41 41
LIMK1 -0.038 0.16 0.19 19 -0.39 39 58
BIRC3 -0.004 0.11 0.12 21 -0.33 31 52
BIRC2 0.019 0.051 -10000 0 -0.33 6 6
BAX 0.028 0.004 -10000 0 -10000 0 0
CASP10 -0.043 0.1 -10000 0 -0.29 38 38
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.026 0.029 -10000 0 -0.33 2 2
PTK2 -0.029 0.15 -10000 0 -0.41 30 30
DIABLO 0.028 0.004 -10000 0 -10000 0 0
apoptotic nuclear changes -0.051 0.15 -10000 0 -0.38 41 41
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.029 0.007 0.12 1 -10000 0 1
GSN -0.053 0.16 -10000 0 -0.4 41 41
MADD 0.028 0.005 -10000 0 -10000 0 0
TFAP2A -0.061 0.24 -10000 0 -0.57 46 46
BID -0.014 0.063 -10000 0 -0.19 31 31
MAP3K1 -0.026 0.12 -10000 0 -0.5 14 14
TRADD 0.028 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.038 0.029 -10000 0 -0.23 3 3
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.053 0.16 0.23 3 -0.4 41 44
CASP9 0.028 0.005 -10000 0 -10000 0 0
DNA repair -0.001 0.063 0.19 9 -0.16 11 20
neuron apoptosis -0.028 0.18 -10000 0 -0.65 22 22
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.043 0.17 0.3 1 -0.5 28 29
APAF1 0.025 0.036 -10000 0 -0.33 3 3
CASP6 -0.013 0.16 -10000 0 -0.81 7 7
TRAF2 0.027 0.008 -10000 0 -10000 0 0
ICAD/CAD -0.05 0.16 0.31 5 -0.38 41 46
CASP7 0.005 0.12 0.26 27 -0.25 16 43
KRT18 -0.049 0.2 -10000 0 -0.56 36 36
apoptosis -0.04 0.14 -10000 0 -0.4 27 27
DFFA -0.051 0.16 0.19 4 -0.39 41 45
DFFB -0.051 0.16 0.22 4 -0.39 41 45
PARP1 0.001 0.063 0.16 11 -0.19 9 20
actin filament polymerization 0.039 0.15 0.36 39 -0.21 7 46
TNF 0.009 0.089 0.12 16 -0.33 18 34
CYCS -0.009 0.057 -10000 0 -0.18 18 18
SATB1 -0.028 0.17 -10000 0 -0.66 12 12
SLK -0.052 0.15 -10000 0 -0.38 42 42
p15 BID/BAX -0.008 0.082 -10000 0 -0.23 26 26
CASP2 -0.006 0.1 0.21 15 -0.29 18 33
JNK cascade 0.025 0.12 0.5 14 -10000 0 14
CASP3 -0.053 0.16 -10000 0 -0.41 41 41
LMNB2 0.017 0.12 0.26 9 -0.37 14 23
RIPK1 0.025 0.01 -10000 0 -10000 0 0
CASP4 0.023 0.03 -10000 0 -0.33 2 2
Mammalian IAPs/DIABLO 0.04 0.094 -10000 0 -0.21 33 33
negative regulation of DNA binding -0.055 0.24 -10000 0 -0.57 46 46
stress fiber formation -0.051 0.15 -10000 0 -0.38 42 42
GZMB -0.025 0.12 0.089 16 -0.32 37 53
CASP1 -0.002 0.066 -10000 0 -0.27 16 16
LMNB1 0.004 0.16 0.26 10 -0.46 22 32
APP -0.029 0.18 -10000 0 -0.66 22 22
TNFRSF1A 0.028 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.005 0.014 -10000 0 -0.23 1 1
VIM -0.035 0.14 -10000 0 -0.4 27 27
LMNA 0.014 0.12 0.26 8 -0.36 15 23
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.014 0.099 -10000 0 -0.26 28 28
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.051 0.15 0.18 1 -0.39 41 42
APAF-1/Caspase 9 0.022 0.089 0.37 3 -0.66 3 6
nuclear fragmentation during apoptosis -0.03 0.15 -10000 0 -0.44 29 29
CFL2 -0.041 0.16 0.21 7 -0.38 39 46
GAS2 -0.062 0.16 -10000 0 -0.38 46 46
positive regulation of apoptosis 0.016 0.14 0.26 9 -0.39 19 28
PRF1 -0.002 0.11 -10000 0 -0.33 28 28
HIF-1-alpha transcription factor network

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
PKM2 -0.001 0.27 0.4 1 -0.62 29 30
HDAC7 0.028 0.022 -10000 0 -0.33 1 1
HIF1A/ARNT/Cbp/p300/Src-1 0.038 0.3 0.48 6 -0.63 27 33
SMAD4 0.029 0.003 -10000 0 -10000 0 0
ID2 0 0.27 0.4 1 -0.62 30 31
AP1 0.042 0.024 0.18 1 -0.085 2 3
ABCG2 -0.003 0.28 0.4 1 -0.62 31 32
HIF1A 0.016 0.068 -10000 0 -0.15 7 7
TFF3 -0.019 0.3 0.4 1 -0.6 41 42
GATA2 0.024 0.05 0.12 4 -0.34 5 9
AKT1 0.015 0.082 -10000 0 -0.21 12 12
response to hypoxia -0.002 0.067 0.12 1 -0.15 28 29
MCL1 -0.01 0.27 -10000 0 -0.62 28 28
NDRG1 0.006 0.27 0.4 1 -0.62 27 28
SERPINE1 -0.004 0.28 0.4 2 -0.65 30 32
FECH 0.001 0.27 0.4 1 -0.61 30 31
FURIN -0.003 0.27 0.4 1 -0.63 28 29
NCOA2 0.022 0.042 -10000 0 -0.33 4 4
EP300 0.013 0.1 0.2 1 -0.33 16 17
HMOX1 0.001 0.27 0.4 2 -0.64 28 30
BHLHE40 0 0.28 0.4 1 -0.61 31 32
BHLHE41 -0.007 0.28 0.4 1 -0.6 34 35
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.065 0.11 -10000 0 -0.21 4 4
ENG 0.026 0.083 0.27 4 -0.23 1 5
JUN 0.028 0.015 0.12 2 -10000 0 2
RORA -0.003 0.28 0.4 2 -0.62 30 32
ABCB1 -0.027 0.25 -10000 0 -0.94 18 18
TFRC 0.002 0.27 0.4 1 -0.62 29 30
CXCR4 -0.002 0.28 0.4 2 -0.63 31 33
TF -0.018 0.32 0.4 1 -0.63 41 42
CITED2 -0.001 0.27 0.4 1 -0.62 29 30
HIF1A/ARNT 0.055 0.37 0.6 8 -0.78 22 30
LDHA 0.022 0.12 -10000 0 -0.65 7 7
ETS1 -0.002 0.27 0.4 1 -0.62 29 30
PGK1 0.001 0.27 0.4 1 -0.62 29 30
NOS2 0 0.28 0.4 3 -0.62 31 34
ITGB2 -0.005 0.29 0.4 1 -0.64 31 32
ALDOA 0.001 0.27 0.4 1 -0.62 29 30
Cbp/p300/CITED2 0.001 0.31 0.42 2 -0.72 28 30
FOS 0.03 0.02 0.12 8 -10000 0 8
HK2 -0.001 0.28 0.4 1 -0.64 29 30
SP1 0.026 0.035 -10000 0 -0.12 13 13
GCK -0.005 0.3 -10000 0 -1.3 14 14
HK1 -0.001 0.27 0.4 1 -0.62 29 30
NPM1 0 0.27 0.4 1 -0.62 29 30
EGLN1 -0.008 0.26 -10000 0 -0.62 28 28
CREB1 0.033 0.009 -10000 0 -0.11 1 1
PGM1 -0.005 0.28 0.4 1 -0.64 29 30
SMAD3 0.027 0.03 -10000 0 -0.33 2 2
EDN1 0.008 0.23 0.4 1 -0.81 16 17
IGFBP1 -0.004 0.27 0.43 2 -0.62 29 31
VEGFA 0.019 0.23 0.41 3 -0.54 25 28
HIF1A/JAB1 0.031 0.054 -10000 0 -0.14 2 2
CP -0.014 0.3 0.4 2 -0.63 37 39
CXCL12 -0.006 0.28 0.4 2 -0.63 31 33
COPS5 0.027 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4 0.041 0.023 -10000 0 -0.23 2 2
BNIP3 -0.004 0.27 -10000 0 -0.62 29 29
EGLN3 -0.002 0.28 0.4 1 -0.64 30 31
CA9 -0.006 0.29 0.43 2 -0.59 37 39
TERT -0.005 0.28 0.4 1 -0.62 32 33
ENO1 -0.004 0.27 0.4 1 -0.62 30 31
PFKL 0.001 0.27 0.4 1 -0.62 29 30
NCOA1 0.028 0.005 -10000 0 -10000 0 0
ADM -0.004 0.28 0.4 1 -0.64 31 32
ARNT 0.017 0.064 -10000 0 -0.14 4 4
HNF4A 0.023 0.035 0.13 10 -0.11 10 20
ADFP -0.019 0.26 0.38 1 -0.61 30 31
SLC2A1 0.022 0.24 0.4 4 -0.55 26 30
LEP 0 0.27 0.4 1 -0.62 29 30
HIF1A/ARNT/Cbp/p300 0.034 0.31 0.49 5 -0.65 27 32
EPO 0.029 0.2 -10000 0 -0.54 14 14
CREBBP 0.016 0.1 0.2 1 -0.29 18 19
HIF1A/ARNT/Cbp/p300/HDAC7 0.045 0.3 0.49 5 -0.65 25 30
PFKFB3 -0.003 0.27 0.4 1 -0.62 29 30
NT5E -0.002 0.28 0.43 2 -0.64 31 33
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.026 0.011 0.12 1 -10000 0 1
ITGB7 0.014 0.075 0.12 4 -0.33 13 17
ITGA4 0 0.1 0.12 7 -0.33 26 33
alpha4/beta7 Integrin 0.009 0.094 -10000 0 -0.23 38 38
alpha4/beta1 Integrin 0.017 0.077 -10000 0 -0.22 26 26
BMP receptor 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
BMP7/BMPR2/BMPR1A-1B/FS -0.003 0.15 0.2 28 -0.19 103 131
SMAD6-7/SMURF1 0.049 0.031 -10000 0 -0.2 3 3
NOG 0.034 0.037 -10000 0 -0.33 1 1
SMAD9 -0.022 0.15 -10000 0 -0.5 24 24
SMAD4 0.029 0.003 -10000 0 -10000 0 0
SMAD5 -0.029 0.13 0.19 2 -0.36 25 27
BMP7/USAG1 0.005 0.13 0.18 28 -0.24 61 89
SMAD5/SKI -0.017 0.14 0.21 3 -0.36 23 26
SMAD1 0.012 0.075 -10000 0 -0.35 6 6
BMP2 0.013 0.091 -10000 0 -0.33 18 18
SMAD1/SMAD1/SMAD4 0.024 0.069 -10000 0 -0.29 8 8
BMPR1A 0.025 0.022 -10000 0 -0.33 1 1
BMPR1B -0.03 0.15 -10000 0 -0.33 59 59
BMPR1A-1B/BAMBI -0.001 0.12 -10000 0 -0.2 72 72
AHSG 0.024 0.018 0.12 8 -10000 0 8
CER1 0.018 0.009 -10000 0 -10000 0 0
BMP2-4/CER1 0.031 0.074 0.18 1 -0.19 24 25
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.027 0.12 -10000 0 -0.35 23 23
BMP2-4 (homodimer) 0.024 0.084 0.18 1 -0.24 25 26
RGMB 0.028 0.01 0.12 2 -10000 0 2
BMP6/BMPR2/BMPR1A-1B 0.025 0.1 0.19 4 -0.18 52 56
RGMA 0.021 0.073 0.12 21 -0.33 11 32
SMURF1 0.026 0.008 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.026 0.11 -10000 0 -0.31 22 22
BMP2-4/USAG1 0.027 0.11 0.19 12 -0.21 47 59
SMAD6/SMURF1/SMAD5 -0.021 0.14 0.27 1 -0.35 23 24
SOSTDC1 0.017 0.12 -10000 0 -0.33 28 28
BMP7/BMPR2/BMPR1A-1B 0.004 0.13 0.19 7 -0.19 85 92
SKI 0.028 0.006 -10000 0 -10000 0 0
BMP6 (homodimer) 0.031 0.026 0.12 20 -10000 0 20
HFE2 0.021 0.016 -10000 0 -10000 0 0
ZFYVE16 0.023 0.042 -10000 0 -0.33 4 4
MAP3K7 0.025 0.022 -10000 0 -0.33 1 1
BMP2-4/CHRD 0.036 0.087 0.24 1 -0.21 30 31
SMAD5/SMAD5/SMAD4 -0.017 0.14 0.23 4 -0.36 24 28
MAPK1 0.027 0.007 -10000 0 -10000 0 0
TAK1/TAB family -0.014 0.11 -10000 0 -0.26 24 24
BMP7 (homodimer) 0.003 0.14 0.12 75 -0.33 39 114
NUP214 0.027 0.008 -10000 0 -10000 0 0
BMP6/FETUA 0.038 0.025 -10000 0 -10000 0 0
SMAD1/SKI 0.022 0.078 -10000 0 -0.32 7 7
SMAD6 0.027 0.031 -10000 0 -0.33 2 2
CTDSP2 0.028 0.006 -10000 0 -10000 0 0
BMP2-4/FETUA 0.037 0.077 0.18 2 -0.2 24 26
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.003 0.11 0.12 21 -0.33 31 52
BMPR2 (homodimer) 0.029 0.002 -10000 0 -10000 0 0
GADD34/PP1CA 0.05 0.034 -10000 0 -0.2 4 4
BMPR1A-1B (homodimer) -0.006 0.11 -10000 0 -0.23 60 60
CHRDL1 -0.028 0.15 -10000 0 -0.33 57 57
ENDOFIN/SMAD1 0.022 0.078 -10000 0 -0.33 6 6
SMAD6-7/SMURF1/SMAD1 0.041 0.082 -10000 0 -0.31 8 8
SMAD6/SMURF1 0.026 0.008 -10000 0 -10000 0 0
BAMBI 0.009 0.076 -10000 0 -0.33 14 14
SMURF2 0.027 0.021 -10000 0 -0.33 1 1
BMP2-4/CHRDL1 0.003 0.13 0.18 6 -0.23 67 73
BMP2-4/GREM1 0.019 0.11 0.18 8 -0.21 49 57
SMAD7 0.027 0.021 -10000 0 -0.33 1 1
SMAD8A/SMAD8A/SMAD4 -0.011 0.15 -10000 0 -0.46 26 26
SMAD1/SMAD6 0.019 0.077 -10000 0 -0.33 7 7
TAK1/SMAD6 0.035 0.022 -10000 0 -0.23 1 1
BMP7 0.003 0.14 0.12 75 -0.33 39 114
BMP6 0.031 0.027 0.12 20 -10000 0 20
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.017 0.11 -10000 0 -0.31 23 23
PPM1A 0.028 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.022 0.081 -10000 0 -0.33 7 7
SMAD7/SMURF1 0.037 0.02 -10000 0 -0.23 1 1
CTDSPL 0.029 0.003 -10000 0 -10000 0 0
PPP1CA 0.028 0.005 -10000 0 -10000 0 0
XIAP 0.026 0.029 -10000 0 -0.33 2 2
CTDSP1 0.029 0.003 -10000 0 -10000 0 0
PPP1R15A 0.029 0.007 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.045 0.16 0.18 2 -0.41 32 34
CHRD 0.021 0.061 0.12 9 -0.33 8 17
BMPR2 0.029 0.002 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.031 0.12 -10000 0 -0.34 22 22
BMP4 0.023 0.062 -10000 0 -0.33 8 8
FST 0.003 0.12 0.12 52 -0.33 34 86
BMP2-4/NOG 0.042 0.082 0.19 6 -0.2 25 31
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.011 0.12 0.2 5 -0.18 78 83
FAS signaling pathway (CD95)

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
SPTAN1 0.007 0.057 0.18 26 -0.18 2 28
RFC1 0.009 0.06 0.18 30 -0.18 2 32
PRKDC 0.022 0.085 0.22 41 -0.18 2 43
RIPK1 0.025 0.01 -10000 0 -10000 0 0
CASP7 -0.027 0.18 -10000 0 -0.6 25 25
FASLG/FAS/FADD/FAF1 -0.002 0.088 0.17 19 -0.23 26 45
MAP2K4 -0.028 0.17 0.24 2 -0.42 35 37
mol:ceramide -0.012 0.12 -10000 0 -0.31 37 37
GSN 0.007 0.058 0.18 26 -0.18 3 29
FASLG/FAS/FADD/FAF1/Caspase 8 -0.006 0.1 0.22 1 -0.28 27 28
FAS 0.019 0.047 -10000 0 -0.33 5 5
BID 0.009 0.095 0.27 31 -0.2 1 32
MAP3K1 -0.024 0.16 0.23 3 -0.43 28 31
MAP3K7 0.024 0.023 -10000 0 -0.33 1 1
RB1 0.01 0.064 0.18 32 -0.18 3 35
CFLAR 0.029 0.003 -10000 0 -10000 0 0
HGF/MET 0.013 0.11 -10000 0 -0.22 48 48
ARHGDIB 0.009 0.074 0.19 31 -0.2 6 37
FADD 0.026 0.013 -10000 0 -10000 0 0
actin filament polymerization -0.007 0.058 0.18 3 -0.18 26 29
NFKB1 -0.007 0.13 -10000 0 -0.65 9 9
MAPK8 -0.034 0.18 0.23 2 -0.46 34 36
DFFA 0.01 0.062 0.18 31 -0.18 2 33
DNA fragmentation during apoptosis 0.01 0.061 0.18 30 -0.18 2 32
FAS/FADD/MET 0.018 0.081 -10000 0 -0.19 34 34
CFLAR/RIP1 0.037 0.015 -10000 0 -10000 0 0
FAIM3 -0.009 0.11 -10000 0 -0.33 32 32
FAF1 0.027 0.013 -10000 0 -10000 0 0
PARP1 0.012 0.064 0.18 33 -0.18 2 35
DFFB 0.01 0.061 0.18 30 -0.18 2 32
CHUK -0.012 0.11 -10000 0 -0.61 8 8
FASLG -0.016 0.13 -10000 0 -0.33 40 40
FAS/FADD 0.032 0.037 -10000 0 -0.23 4 4
HGF 0.019 0.069 -10000 0 -0.33 10 10
LMNA 0.005 0.053 0.23 6 -10000 0 6
CASP6 0.008 0.057 0.18 27 -0.18 1 28
CASP10 0.02 0.052 -10000 0 -0.33 6 6
CASP3 0.017 0.07 0.22 29 -0.16 1 30
PTPN13 0.01 0.079 -10000 0 -0.33 15 15
CASP8 0.011 0.1 0.3 32 -0.24 1 33
IL6 -0.048 0.29 -10000 0 -1.1 18 18
MET -0.007 0.11 0.12 11 -0.33 30 41
ICAD/CAD 0.007 0.059 0.27 6 -0.17 2 8
FASLG/FAS/FADD/FAF1/Caspase 10 -0.013 0.13 -10000 0 -0.31 37 37
activation of caspase activity by cytochrome c 0.009 0.094 0.27 31 -0.2 1 32
PAK2 0.01 0.061 0.18 30 -0.18 2 32
BCL2 0.019 0.058 0.12 1 -0.33 8 9
IL27-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
TGFB1 0.024 0.042 -10000 0 -0.33 4 4
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.1 0.24 0.6 39 -10000 0 39
IL27/IL27R/JAK1 -0.057 0.25 -10000 0 -0.93 17 17
TBX21 -0.1 0.19 -10000 0 -0.52 38 38
IL12B 0.021 0.027 0.13 10 -10000 0 10
IL12A -0.011 0.057 -10000 0 -0.23 18 18
IL6ST -0.007 0.09 -10000 0 -0.34 19 19
IL27RA/JAK1 -0.044 0.24 -10000 0 -1.1 13 13
IL27 -0.002 0.086 0.13 1 -0.34 16 17
TYK2 0.017 0.027 -10000 0 -10000 0 0
T-helper cell lineage commitment 0.027 0.1 0.42 6 -0.5 1 7
T-helper 2 cell differentiation 0.1 0.24 0.6 39 -10000 0 39
T cell proliferation during immune response 0.1 0.24 0.6 39 -10000 0 39
MAPKKK cascade -0.1 0.24 -10000 0 -0.6 39 39
STAT3 0.028 0.005 -10000 0 -10000 0 0
STAT2 0.028 0.005 -10000 0 -10000 0 0
STAT1 0.026 0.029 -10000 0 -0.33 2 2
IL12RB1 -0.021 0.12 -10000 0 -0.33 40 40
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.12 0.21 0.41 1 -0.49 46 47
IL27/IL27R/JAK2/TYK2 -0.1 0.25 -10000 0 -0.62 38 38
positive regulation of T cell mediated cytotoxicity -0.1 0.24 -10000 0 -0.6 39 39
STAT1 (dimer) -0.081 0.27 -10000 0 -0.76 27 27
JAK2 0.01 0.051 -10000 0 -0.33 5 5
JAK1 0.028 0.006 -10000 0 -10000 0 0
STAT2 (dimer) -0.087 0.24 -10000 0 -0.6 35 35
T cell proliferation -0.1 0.23 -10000 0 -0.59 38 38
IL12/IL12R/TYK2/JAK2 -0.09 0.26 -10000 0 -0.82 21 21
IL17A 0.027 0.1 0.42 6 -0.5 1 7
mast cell activation 0.1 0.24 0.6 39 -10000 0 39
IFNG -0.024 0.057 0.082 1 -0.12 66 67
T cell differentiation -0.006 0.009 -10000 0 -0.023 58 58
STAT3 (dimer) -0.09 0.24 -10000 0 -0.59 38 38
STAT5A (dimer) -0.091 0.24 -10000 0 -0.6 36 36
STAT4 (dimer) -0.096 0.25 -10000 0 -0.58 45 45
STAT4 0.006 0.1 0.12 15 -0.33 23 38
T cell activation -0.003 0.021 0.12 8 -0.045 1 9
IL27R/JAK2/TYK2 -0.046 0.24 -10000 0 -0.99 15 15
GATA3 -0.15 0.41 -10000 0 -1.2 40 40
IL18 -0.007 0.052 -10000 0 -0.23 15 15
positive regulation of mast cell cytokine production -0.087 0.23 -10000 0 -0.56 39 39
IL27/EBI3 -0.005 0.11 0.19 2 -0.26 37 39
IL27RA -0.058 0.25 -10000 0 -1.2 13 13
IL6 0.018 0.076 -10000 0 -0.33 12 12
STAT5A 0.024 0.036 -10000 0 -0.33 3 3
monocyte differentiation -0.001 0.003 -10000 0 -0.013 1 1
IL2 0.014 0.098 0.46 13 -10000 0 13
IL1B -0.013 0.067 -10000 0 -0.23 26 26
EBI3 -0.009 0.1 -10000 0 -0.33 27 27
TNF -0.008 0.057 -10000 0 -0.23 18 18
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.034 0.11 0.2 6 -0.24 35 41
MAP4K1 0.01 0.088 0.12 10 -0.33 18 28
MAP3K8 0.023 0.044 -10000 0 -0.33 4 4
PRKCB 0.003 0.11 -10000 0 -0.33 26 26
DBNL 0.026 0.009 -10000 0 -10000 0 0
CRKL 0.027 0.009 -10000 0 -10000 0 0
MAP3K1 -0.015 0.12 -10000 0 -0.37 20 20
JUN -0.084 0.28 -10000 0 -0.65 52 52
MAP3K7 -0.008 0.1 -10000 0 -0.36 17 17
GRAP2 0.01 0.079 -10000 0 -0.33 15 15
CRK 0.027 0.008 -10000 0 -10000 0 0
MAP2K4 -0.013 0.14 0.22 10 -0.41 22 32
LAT 0.018 0.078 -10000 0 -0.33 13 13
LCP2 0.016 0.062 -10000 0 -0.33 9 9
MAPK8 -0.087 0.29 -10000 0 -0.68 52 52
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.005 0.12 -10000 0 -0.36 24 24
LAT/GRAP2/SLP76/HPK1/HIP-55 0.041 0.11 0.25 1 -0.22 32 33
Signaling events mediated by PTP1B

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
PDGFRB 0.025 0.031 0.12 1 -0.33 2 3
Jak2/Leptin Receptor -0.05 0.19 -10000 0 -0.41 53 53
PTP1B/AKT1 -0.019 0.11 0.29 1 -0.26 31 32
FYN 0.025 0.009 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.032 0.11 0.31 1 -0.27 32 33
EGFR 0.013 0.074 -10000 0 -0.34 10 10
EGF/EGFR -0.039 0.14 0.22 1 -0.26 54 55
CSF1 0.022 0.046 -10000 0 -0.33 5 5
AKT1 0.028 0.005 -10000 0 -10000 0 0
INSR 0.028 0.021 -10000 0 -0.34 1 1
PTP1B/N-cadherin -0.037 0.13 0.29 1 -0.27 52 53
Insulin Receptor/Insulin -0.004 0.1 0.27 1 -0.26 18 19
HCK 0.01 0.076 0.12 1 -0.33 14 15
CRK 0.027 0.008 -10000 0 -10000 0 0
TYK2 -0.033 0.1 0.24 3 -0.27 30 33
EGF -0.033 0.15 0.14 3 -0.34 54 57
YES1 0.021 0.046 -10000 0 -0.33 5 5
CAV1 -0.024 0.12 0.26 6 -0.3 27 33
TXN 0.026 0.008 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.019 0.12 -10000 0 -0.26 35 35
cell migration 0.032 0.11 0.27 32 -0.31 1 33
STAT3 0.028 0.005 -10000 0 -10000 0 0
PRLR 0.014 0.1 -10000 0 -0.33 22 22
ITGA2B 0.019 0.075 0.12 24 -0.33 11 35
CSF1R 0.019 0.055 0.12 2 -0.33 7 9
Prolactin Receptor/Prolactin 0.025 0.079 0.18 3 -0.23 21 24
FGR 0.014 0.075 -10000 0 -0.33 13 13
PTP1B/p130 Cas -0.022 0.11 0.29 1 -0.26 32 33
Crk/p130 Cas -0.015 0.11 0.29 1 -0.26 28 29
DOK1 -0.028 0.11 0.28 1 -0.28 30 31
JAK2 -0.059 0.19 0.29 1 -0.44 50 51
Jak2/Leptin Receptor/Leptin -0.027 0.15 -10000 0 -0.35 34 34
PIK3R1 0.025 0.03 -10000 0 -0.33 2 2
PTPN1 -0.032 0.11 0.32 1 -0.28 32 33
LYN 0.022 0.042 -10000 0 -0.33 4 4
CDH2 -0.04 0.15 -10000 0 -0.33 63 63
SRC 0.015 0.055 -10000 0 -0.56 1 1
ITGB3 -0.024 0.13 -10000 0 -0.33 46 46
CAT1/PTP1B -0.041 0.19 0.28 9 -0.41 44 53
CAPN1 0.026 0.022 -10000 0 -0.34 1 1
CSK 0.028 0.004 -10000 0 -10000 0 0
PI3K 0.007 0.11 0.24 1 -0.3 12 13
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.025 0.14 -10000 0 -0.33 33 33
negative regulation of transcription -0.058 0.19 0.29 1 -0.43 50 51
FCGR2A 0.02 0.052 -10000 0 -0.33 6 6
FER 0.021 0.047 -10000 0 -0.34 5 5
alphaIIb/beta3 Integrin -0.005 0.12 0.18 3 -0.24 56 59
BLK 0.003 0.12 0.12 45 -0.33 31 76
Insulin Receptor/Insulin/Shc 0.043 0.023 -10000 0 -0.2 1 1
RHOA 0.028 0.004 -10000 0 -10000 0 0
LEPR 0.022 0.051 0.12 1 -0.33 6 7
BCAR1 0.025 0.03 -10000 0 -0.33 2 2
p210 bcr-abl/Grb2 0.028 0.005 -10000 0 -10000 0 0
mol:NADPH -0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.044 0.21 0.24 10 -0.47 45 55
PRL 0.015 0.032 0.12 12 -10000 0 12
SOCS3 -0.017 0.24 -10000 0 -1.3 10 10
SPRY2 0.025 0.037 -10000 0 -0.34 3 3
Insulin Receptor/Insulin/IRS1 0.036 0.054 -10000 0 -0.2 14 14
CSF1/CSF1R -0.016 0.12 -10000 0 -0.27 34 34
Ras protein signal transduction 0.014 0.096 0.58 7 -10000 0 7
IRS1 0.013 0.073 -10000 0 -0.33 13 13
INS 0.007 0.017 -10000 0 -10000 0 0
LEP 0.027 0.04 0.12 27 -0.33 1 28
STAT5B -0.038 0.14 0.31 1 -0.33 37 38
STAT5A -0.039 0.14 0.31 1 -0.33 37 38
GRB2 0.028 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.018 0.11 0.29 1 -0.26 34 35
CSN2 0.017 0.063 -10000 0 -10000 0 0
PIK3CA 0.023 0.042 -10000 0 -0.33 4 4
LAT -0.017 0.15 -10000 0 -0.52 20 20
YBX1 0.035 0.006 -10000 0 -10000 0 0
LCK -0.018 0.13 0.12 22 -0.33 44 66
SHC1 0.026 0.009 -10000 0 -10000 0 0
NOX4 -0.009 0.12 -10000 0 -0.34 32 32
Glypican 2 network

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
MDK 0.014 0.082 -9999 0 -0.33 15 15
GPC2 0.011 0.077 -9999 0 -0.33 14 14
GPC2/Midkine 0.015 0.084 -9999 0 -0.24 28 28
neuron projection morphogenesis 0.015 0.084 -9999 0 -0.24 28 28
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.008 0.086 0.33 18 -0.12 3 21
PI3K Class IB/PDE3B 0.008 0.086 0.12 3 -0.33 18 21
PDE3B 0.008 0.086 0.12 3 -0.33 18 21
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.026 0.043 -10000 0 -0.19 10 10
ARNO/beta Arrestin1-2 0.033 0.078 -10000 0 -0.83 2 2
EGFR 0.021 0.071 -10000 0 -0.33 10 10
EPHA2 0.022 0.052 0.12 5 -0.33 6 11
USP6 0.027 0.008 -10000 0 -10000 0 0
IQSEC1 0.028 0.003 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.01 0.12 0.18 2 -0.24 59 61
ARRB2 0.01 0.005 -10000 0 -10000 0 0
mol:GTP -0.006 0.059 0.18 2 -0.15 27 29
ARRB1 0.026 0.022 -10000 0 -0.33 1 1
FBXO8 0.028 0.004 -10000 0 -10000 0 0
TSHR 0.013 0.088 0.12 8 -0.33 17 25
EGF -0.03 0.14 -10000 0 -0.33 54 54
somatostatin receptor activity 0 0 0.001 20 -0.001 28 48
ARAP2 0.005 0.088 -10000 0 -0.33 19 19
mol:GDP -0.006 0.1 0.18 15 -0.26 26 41
mol:PI-3-4-5-P3 0 0 0.001 13 -0.001 16 29
ITGA2B 0.022 0.074 0.12 24 -0.33 11 35
ARF6 0.028 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.058 0.046 -10000 0 -0.17 7 7
ADAP1 0.015 0.066 -10000 0 -0.33 10 10
KIF13B 0.027 0.007 -10000 0 -10000 0 0
HGF/MET 0.008 0.097 -10000 0 -0.23 40 40
PXN 0.028 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.009 0.11 0.22 20 -0.26 29 49
EGFR/EGFR/EGF/EGF/ARFGEP100 0.007 0.11 0.18 2 -0.2 59 61
ADRB2 0.025 0.045 0.12 8 -0.33 4 12
receptor agonist activity 0 0 0 9 0 29 38
actin filament binding 0 0 0 20 0 28 48
SRC 0.025 0.022 -10000 0 -0.33 1 1
ITGB3 -0.024 0.13 -10000 0 -0.33 46 46
GNAQ 0.027 0.008 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.002 20 -0.001 22 42
ARF6/GDP -0.021 0.16 0.21 5 -0.37 40 45
ARF6/GDP/GULP/ACAP1 0.006 0.13 0.21 7 -0.3 30 37
alphaIIb/beta3 Integrin/paxillin/GIT1 0.029 0.1 0.19 3 -0.18 56 59
ACAP1 0.006 0.1 0.12 26 -0.33 24 50
ACAP2 0.027 0.021 -10000 0 -0.33 1 1
LHCGR/beta Arrestin2 0.015 0.019 -10000 0 -10000 0 0
EFNA1 0.025 0.022 -10000 0 -0.33 1 1
HGF 0.019 0.069 -10000 0 -0.33 10 10
CYTH3 0.003 0.019 -10000 0 -0.23 2 2
CYTH2 0.013 0.086 -10000 0 -1 2 2
NCK1 0.028 0.005 -10000 0 -10000 0 0
fibronectin binding 0 0 0.001 19 0 27 46
endosomal lumen acidification 0 0 0 20 0 20 40
microtubule-based process 0 0 -10000 0 0 1 1
GULP1 0.006 0.088 -10000 0 -0.33 19 19
GNAQ/ARNO 0.029 0.081 -10000 0 -0.94 2 2
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
PIP3-E 0 0 0 10 0 9 19
MET -0.007 0.11 0.12 11 -0.33 30 41
GNA14 0.034 0.048 -10000 0 -0.33 3 3
GNA15 0.019 0.063 0.12 3 -0.33 9 12
GIT1 0.028 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 20 -0.001 23 43
GNA11 0.028 0.003 -10000 0 -10000 0 0
LHCGR 0.012 0.018 0.12 2 -10000 0 2
AGTR1 0.004 0.1 -10000 0 -0.33 23 23
desensitization of G-protein coupled receptor protein signaling pathway 0.015 0.019 -10000 0 -10000 0 0
IPCEF1/ARNO 0.008 0.11 -10000 0 -0.87 2 2
alphaIIb/beta3 Integrin -0.003 0.12 0.18 3 -0.23 56 59
Ephrin B reverse signaling

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
EFNB2 0.03 0.016 0.12 8 -10000 0 8
EPHB2 0.008 0.085 0.13 1 -0.33 17 18
EFNB1 -0.006 0.028 -10000 0 -0.23 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.03 0.094 -10000 0 -0.2 33 33
Ephrin B2/EPHB1-2 0.035 0.08 0.17 4 -0.2 27 31
neuron projection morphogenesis 0.015 0.082 -10000 0 -0.19 35 35
Ephrin B1/EPHB1-2/Tiam1 0.028 0.097 0.18 1 -0.2 39 40
DNM1 0.026 0.039 0.12 7 -0.33 3 10
cell-cell signaling 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.031 0.13 0.2 1 -0.5 20 21
YES1 -0.036 0.2 -10000 0 -0.76 20 20
Ephrin B1/EPHB1-2/NCK2 0.039 0.083 0.18 1 -0.19 29 30
PI3K 0.004 0.15 -10000 0 -0.52 20 20
mol:GDP 0.025 0.096 0.17 1 -0.2 39 40
ITGA2B 0.022 0.074 0.12 24 -0.33 11 35
endothelial cell proliferation 0.029 0.042 -10000 0 -0.19 9 9
FYN -0.042 0.19 -10000 0 -0.75 20 20
MAP3K7 -0.03 0.14 0.22 1 -0.54 19 20
FGR -0.038 0.19 -10000 0 -0.74 20 20
TIAM1 0.011 0.076 -10000 0 -0.33 14 14
PIK3R1 0.025 0.03 -10000 0 -0.33 2 2
RGS3 0.026 0.022 -10000 0 -0.33 1 1
cell adhesion -0.035 0.15 -10000 0 -0.5 22 22
LYN -0.033 0.19 -10000 0 -0.74 19 19
Ephrin B1/EPHB1-2/Src Family Kinases -0.037 0.18 -10000 0 -0.69 20 20
Ephrin B1/EPHB1-2 -0.032 0.15 -10000 0 -0.59 19 19
SRC -0.032 0.19 -10000 0 -0.73 20 20
ITGB3 -0.024 0.13 -10000 0 -0.33 46 46
EPHB1 0.019 0.086 0.13 1 -0.33 15 16
EPHB4 0.016 0.062 -10000 0 -0.33 9 9
RAC1 0.025 0.009 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.029 0.042 -10000 0 -0.19 9 9
alphaIIb/beta3 Integrin -0.003 0.12 0.18 3 -0.23 56 59
BLK -0.044 0.2 -10000 0 -0.75 20 20
HCK -0.039 0.19 -10000 0 -0.73 20 20
regulation of stress fiber formation -0.037 0.081 0.19 29 -0.17 1 30
MAPK8 -0.033 0.12 0.2 1 -0.48 20 21
Ephrin B1/EPHB1-2/RGS3 0.038 0.083 0.18 1 -0.2 28 29
endothelial cell migration -0.019 0.12 0.19 20 -0.46 18 38
NCK2 0.029 0.003 -10000 0 -10000 0 0
PTPN13 0.007 0.1 -10000 0 -0.45 14 14
regulation of focal adhesion formation -0.037 0.081 0.19 29 -0.17 1 30
chemotaxis -0.036 0.082 0.19 28 -0.17 1 29
PIK3CA 0.023 0.042 -10000 0 -0.33 4 4
Rac1/GTP 0.023 0.088 -10000 0 -0.19 35 35
angiogenesis -0.032 0.14 -10000 0 -0.58 19 19
LCK -0.049 0.19 -10000 0 -0.74 20 20
Reelin signaling pathway

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
CDK5R1/CDK5 0.032 0.04 -10000 0 -0.23 6 6
VLDLR 0.01 0.074 -10000 0 -0.33 13 13
CRKL 0.027 0.009 -10000 0 -10000 0 0
LRPAP1 0.028 0.006 -10000 0 -10000 0 0
FYN 0.025 0.009 -10000 0 -10000 0 0
ITGA3 0.009 0.088 0.12 9 -0.33 18 27
RELN/VLDLR/Fyn 0.021 0.093 -10000 0 -0.19 41 41
MAPK8IP1/MKK7/MAP3K11/JNK1 0.054 0.062 -10000 0 -0.17 15 15
AKT1 -0.019 0.089 0.14 2 -0.22 34 36
MAP2K7 0.029 0.003 -10000 0 -10000 0 0
RAPGEF1 0.027 0.008 -10000 0 -10000 0 0
DAB1 0.033 0.032 -10000 0 -10000 0 0
RELN/LRP8/DAB1 0.037 0.082 0.17 11 -0.18 31 42
LRPAP1/LRP8 0.039 0.019 -10000 0 -0.23 1 1
RELN/LRP8/DAB1/Fyn 0.044 0.081 0.18 11 -0.16 31 42
DAB1/alpha3/beta1 Integrin 0.017 0.095 -10000 0 -0.18 47 47
long-term memory 0.049 0.091 0.24 7 -0.16 33 40
DAB1/LIS1 0.038 0.095 -10000 0 -0.17 38 38
DAB1/CRLK/C3G 0.025 0.085 -10000 0 -0.17 36 36
PIK3CA 0.023 0.042 -10000 0 -0.33 4 4
DAB1/NCK2 0.042 0.096 -10000 0 -0.17 38 38
ARHGEF2 0.026 0.008 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.03 0.059 -10000 0 -0.33 6 6
CDK5R1 0.021 0.051 -10000 0 -0.33 6 6
RELN 0.005 0.12 0.12 51 -0.33 31 82
PIK3R1 0.025 0.03 -10000 0 -0.33 2 2
RELN/LRP8/Fyn 0.034 0.083 -10000 0 -0.19 31 31
GRIN2A/RELN/LRP8/DAB1/Fyn 0.055 0.098 0.25 7 -0.17 35 42
MAPK8 0.022 0.037 -10000 0 -0.33 3 3
RELN/VLDLR/DAB1 0.023 0.091 0.17 11 -0.18 41 52
ITGB1 0.026 0.011 0.12 1 -10000 0 1
MAP1B -0.009 0.086 0.17 19 -0.19 41 60
RELN/LRP8 0.035 0.083 -10000 0 -0.19 30 30
GRIN2B/RELN/LRP8/DAB1/Fyn 0.056 0.089 0.23 2 -0.16 30 32
PI3K 0.035 0.042 -10000 0 -0.27 5 5
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.023 0.066 -10000 0 -0.23 18 18
RAP1A -0.009 0.096 0.23 19 -0.29 3 22
PAFAH1B1 0.027 0.008 -10000 0 -10000 0 0
MAPK8IP1 0.013 0.074 -10000 0 -0.33 13 13
CRLK/C3G 0.037 0.015 -10000 0 -10000 0 0
GRIN2B 0.028 0.024 -10000 0 -10000 0 0
NCK2 0.029 0.003 -10000 0 -10000 0 0
neuron differentiation -0.005 0.11 0.19 1 -0.34 16 17
neuron adhesion -0.018 0.099 0.26 10 -0.28 7 17
LRP8 0.027 0.021 -10000 0 -0.33 1 1
GSK3B -0.018 0.086 0.22 1 -0.31 10 11
RELN/VLDLR/DAB1/Fyn 0.031 0.091 0.18 11 -0.16 41 52
MAP3K11 0.027 0.021 -10000 0 -0.33 1 1
RELN/VLDLR/DAB1/P13K -0.009 0.094 0.15 2 -0.22 42 44
CDK5 0.026 0.009 -10000 0 -10000 0 0
MAPT -0.031 0.12 0.74 3 -0.3 35 38
neuron migration -0.014 0.12 0.26 19 -0.28 29 48
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.005 0.11 0.19 1 -0.35 16 17
RELN/VLDLR 0.032 0.095 -10000 0 -0.19 39 39
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.017 0.11 0.2 51 -0.18 1 52
GNAI2 0.029 0.003 -10000 0 -10000 0 0
S1P/S1P5/G12 0.033 0.032 -10000 0 -0.19 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.037 0.14 0.12 4 -0.33 55 59
RhoA/GTP -0.016 0.11 0.18 1 -0.21 51 52
negative regulation of cAMP metabolic process -0.024 0.11 -10000 0 -0.2 68 68
GNAZ -0.002 0.1 -10000 0 -0.33 26 26
GNAI3 0.028 0.006 -10000 0 -10000 0 0
GNA12 0.025 0.009 -10000 0 -10000 0 0
S1PR5 0.026 0.05 -10000 0 -0.33 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.025 0.11 -10000 0 -0.21 68 68
RhoA/GDP 0.021 0.002 -10000 0 -10000 0 0
RHOA 0.029 0.003 -10000 0 -10000 0 0
GNAI1 0.02 0.047 -10000 0 -0.33 5 5
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.03 0.19 -10000 0 -0.59 22 22
UGCG -0.037 0.21 -10000 0 -0.74 22 22
AKT1/mTOR/p70S6K/Hsp90/TERT -0.027 0.2 0.27 2 -0.47 39 41
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.036 0.2 -10000 0 -0.72 22 22
mol:DAG -0.1 0.3 -10000 0 -0.89 38 38
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.016 0.19 0.28 2 -0.45 42 44
FRAP1 -0.031 0.22 0.3 2 -0.52 42 44
FOXO3 -0.031 0.2 0.3 2 -0.5 40 42
AKT1 -0.032 0.22 0.31 2 -0.54 40 42
GAB2 0.027 0.009 -10000 0 -10000 0 0
SMPD1 -0.002 0.14 -10000 0 -0.91 6 6
SGMS1 -0.076 0.26 -10000 0 -0.74 38 38
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP -0.008 0.03 -10000 0 -0.22 5 5
CALM1 0.028 0.005 -10000 0 -10000 0 0
cell proliferation -0.05 0.23 0.3 1 -0.59 37 38
EIF3A 0.026 0.009 -10000 0 -10000 0 0
PI3K 0.037 0.043 -10000 0 -0.27 5 5
RPS6KB1 0 0.14 -10000 0 -0.92 6 6
mol:sphingomyelin -0.1 0.3 -10000 0 -0.89 38 38
natural killer cell activation 0 0.001 -10000 0 -0.012 2 2
JAK3 0.021 0.064 0.13 6 -0.33 9 15
PIK3R1 0.026 0.03 -10000 0 -0.33 2 2
JAK1 0.03 0.005 -10000 0 -10000 0 0
NFKB1 0.028 0.005 -10000 0 -10000 0 0
MYC -0.004 0.2 0.4 2 -0.48 33 35
MYB -0.007 0.2 -10000 0 -1.1 9 9
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.037 0.22 -10000 0 -0.52 43 43
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.026 0.13 -10000 0 -0.83 6 6
mol:PI-3-4-5-P3 -0.035 0.21 -10000 0 -0.51 42 42
Rac1/GDP 0.016 0.032 -10000 0 -0.2 5 5
T cell proliferation -0.037 0.2 0.29 2 -0.48 43 45
SHC1 0.026 0.009 -10000 0 -10000 0 0
RAC1 0.025 0.009 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.002 0.011 0.023 6 -0.064 8 14
PRKCZ -0.04 0.21 0.28 1 -0.51 42 43
NF kappa B1 p50/RelA -0.006 0.2 0.3 2 -0.45 41 43
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.039 0.2 -10000 0 -0.5 41 41
HSP90AA1 0.027 0.021 -10000 0 -0.33 1 1
RELA 0.028 0.005 -10000 0 -10000 0 0
IL2RA 0.001 0.095 -10000 0 -0.33 22 22
IL2RB 0.007 0.095 0.12 13 -0.33 21 34
TERT 0.007 0.088 0.12 11 -0.33 18 29
E2F1 0.012 0.085 -10000 0 -0.44 9 9
SOS1 0.029 0.005 -10000 0 -10000 0 0
RPS6 0.025 0.01 -10000 0 -10000 0 0
mol:cAMP -0.001 0.005 0.032 7 -0.013 6 13
PTPN11 0.028 0.006 -10000 0 -10000 0 0
IL2RG -0.011 0.12 0.13 15 -0.33 38 53
actin cytoskeleton organization -0.037 0.2 0.29 2 -0.48 43 45
GRB2 0.028 0.007 -10000 0 -10000 0 0
IL2 0.022 0.018 -10000 0 -10000 0 0
PIK3CA 0.025 0.042 -10000 0 -0.33 4 4
Rac1/GTP 0.042 0.04 -10000 0 -0.19 5 5
LCK -0.017 0.13 0.12 22 -0.33 44 66
BCL2 -0.029 0.21 -10000 0 -0.52 36 36
Effects of Botulinum toxin

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
STX1A 0.007 0.016 -10000 0 -0.23 1 1
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.033 0.026 -10000 0 -0.23 1 1
STXBP1 0.025 0.022 -10000 0 -0.33 1 1
ACh/CHRNA1 -0.002 0.086 0.1 37 -0.15 58 95
RAB3GAP2/RIMS1/UNC13B 0.04 0.037 -10000 0 -0.2 3 3
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 0.024 0.021 0.12 11 -10000 0 11
mol:ACh -0.001 0.048 0.092 30 -0.1 31 61
RAB3GAP2 0.023 0.03 -10000 0 -0.33 2 2
STX1A/SNAP25/VAMP2 0.018 0.066 0.18 4 -0.14 26 30
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.002 0.086 0.1 37 -0.15 58 95
UNC13B 0.024 0.023 -10000 0 -0.33 1 1
CHRNA1 -0.008 0.13 0.12 37 -0.33 40 77
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.02 0.066 0.12 22 -0.12 34 56
SNAP25 -0.016 0.074 -10000 0 -0.23 32 32
VAMP2 0.004 0.001 -10000 0 -10000 0 0
SYT1 0.032 0.077 -10000 0 -0.33 10 10
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.022 0.021 -10000 0 -0.19 2 2
STX1A/SNAP25 fragment 1/VAMP2 0.018 0.066 0.18 4 -0.14 26 30
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.002 0.11 -10000 0 -0.37 21 21
Syndecan-4/Syndesmos -0.019 0.18 -10000 0 -0.46 31 31
positive regulation of JNK cascade -0.012 0.18 -10000 0 -0.45 32 32
Syndecan-4/ADAM12 -0.021 0.18 -10000 0 -0.48 31 31
CCL5 -0.014 0.12 -10000 0 -0.33 39 39
Rac1/GDP 0.019 0.007 -10000 0 -10000 0 0
DNM2 0.029 0.003 -10000 0 -10000 0 0
ITGA5 0.026 0.038 -10000 0 -0.33 3 3
SDCBP 0.024 0.03 -10000 0 -0.33 2 2
PLG 0.011 0.021 0.12 1 -0.088 1 2
ADAM12 0.018 0.056 -10000 0 -0.33 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.028 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.028 0.018 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.026 0.19 -10000 0 -0.46 35 35
Syndecan-4/CXCL12/CXCR4 -0.013 0.19 -10000 0 -0.48 32 32
Syndecan-4/Laminin alpha3 -0.019 0.18 -10000 0 -0.47 30 30
MDK 0.014 0.082 -10000 0 -0.33 15 15
Syndecan-4/FZD7 -0.019 0.18 -10000 0 -0.46 34 34
Syndecan-4/Midkine -0.022 0.19 -10000 0 -0.48 33 33
FZD7 0.024 0.053 0.12 7 -0.33 6 13
Syndecan-4/FGFR1/FGF -0.032 0.19 -10000 0 -0.45 38 38
THBS1 0.015 0.073 0.12 7 -0.33 12 19
integrin-mediated signaling pathway -0.022 0.18 0.29 1 -0.46 35 36
positive regulation of MAPKKK cascade -0.012 0.18 -10000 0 -0.45 32 32
Syndecan-4/TACI -0.023 0.18 -10000 0 -0.48 32 32
CXCR4 0.022 0.056 -10000 0 -0.33 7 7
cell adhesion -0.004 0.072 0.19 4 -0.25 18 22
Syndecan-4/Dynamin -0.018 0.18 -10000 0 -0.46 31 31
Syndecan-4/TSP1 -0.021 0.18 -10000 0 -0.47 32 32
Syndecan-4/GIPC -0.018 0.18 -10000 0 -0.46 31 31
Syndecan-4/RANTES -0.028 0.19 -10000 0 -0.49 33 33
ITGB1 0.026 0.011 0.12 1 -10000 0 1
LAMA1 -0.019 0.13 -10000 0 -0.33 44 44
LAMA3 0.024 0.063 0.12 18 -0.33 8 26
RAC1 0.025 0.009 -10000 0 -10000 0 0
PRKCA 0.005 0.13 0.77 7 -0.31 7 14
Syndecan-4/alpha-Actinin -0.019 0.18 -10000 0 -0.46 31 31
TFPI 0.024 0.053 0.12 7 -0.33 6 13
F2 0.019 0.027 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.037 0.032 0.18 1 -0.23 3 4
positive regulation of cell adhesion -0.045 0.18 -10000 0 -0.46 34 34
ACTN1 0.025 0.036 -10000 0 -0.33 3 3
TNC -0.003 0.1 -10000 0 -0.33 26 26
Syndecan-4/CXCL12 -0.021 0.18 -10000 0 -0.48 31 31
FGF6 0.017 0.004 -10000 0 -10000 0 0
RHOA 0.029 0.003 -10000 0 -10000 0 0
CXCL12 0.015 0.066 0.12 3 -0.33 10 13
TNFRSF13B 0.001 0.12 -10000 0 -0.33 31 31
FGF2 -0.035 0.14 -10000 0 -0.33 54 54
FGFR1 0.026 0.046 -10000 0 -0.33 4 4
Syndecan-4/PI-4-5-P2 -0.043 0.16 -10000 0 -0.46 31 31
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.005 0.081 0.12 2 -0.31 17 19
cell migration -0.014 0.012 -10000 0 -10000 0 0
PRKCD 0.022 0.035 -10000 0 -0.31 2 2
vasculogenesis -0.019 0.18 -10000 0 -0.45 32 32
SDC4 -0.035 0.17 -10000 0 -0.48 30 30
Syndecan-4/Tenascin C -0.024 0.19 0.29 1 -0.48 35 36
Syndecan-4/PI-4-5-P2/PKC alpha -0.022 0.014 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.02 0.17 -10000 0 -0.47 29 29
MMP9 -0.001 0.11 -10000 0 -0.33 29 29
Rac1/GTP -0.004 0.073 0.19 4 -0.26 18 22
cytoskeleton organization -0.017 0.17 -10000 0 -0.44 31 31
GIPC1 0.029 0.002 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.018 0.18 -10000 0 -0.47 31 31
Plasma membrane estrogen 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
GNB1/GNG2 0.043 0.073 -10000 0 -0.17 25 25
ER alpha/Gai/GDP/Gbeta gamma -0.088 0.2 -10000 0 -0.45 50 50
AKT1 -0.093 0.29 -10000 0 -0.74 46 46
PIK3CA 0.023 0.042 -10000 0 -0.33 4 4
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.091 0.29 -10000 0 -0.76 46 46
mol:Ca2+ -0.004 0.084 0.18 9 -0.37 9 18
IGF1R 0.026 0.03 -10000 0 -0.33 2 2
E2/ER alpha (dimer)/Striatin 0.024 0.048 -10000 0 -0.19 13 13
SHC1 0.026 0.009 -10000 0 -10000 0 0
apoptosis 0.087 0.27 0.7 47 -10000 0 47
RhoA/GTP 0.018 0.033 -10000 0 -0.15 9 9
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.047 0.18 0.25 1 -0.39 41 42
regulation of stress fiber formation 0.011 0.06 -10000 0 -0.16 25 25
E2/ERA-ERB (dimer) 0.028 0.055 -10000 0 -0.2 13 13
KRAS 0.028 0.005 -10000 0 -10000 0 0
G13/GTP 0.026 0.037 -10000 0 -0.17 9 9
pseudopodium formation -0.011 0.06 0.16 25 -10000 0 25
E2/ER alpha (dimer)/PELP1 0.027 0.039 -10000 0 -0.19 8 8
GRB2 0.028 0.005 -10000 0 -10000 0 0
GNG2 0.013 0.073 -10000 0 -0.33 13 13
GNAO1 -0.037 0.14 0.12 4 -0.33 55 59
HRAS 0.028 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.066 0.2 0.25 2 -0.49 45 47
E2/ER beta (dimer) 0.023 0.038 -10000 0 -0.23 5 5
mol:GDP -0.008 0.083 -10000 0 -0.21 36 36
mol:NADP -0.066 0.2 0.25 2 -0.49 45 47
PIK3R1 0.025 0.03 -10000 0 -0.33 2 2
mol:IP3 -0.01 0.081 0.21 1 -0.38 9 10
IGF-1R heterotetramer 0.026 0.03 -10000 0 -0.33 2 2
PLCB1 -0.002 0.075 0.22 1 -0.33 9 10
PLCB2 0.005 0.072 -10000 0 -0.38 8 8
IGF1 0.01 0.085 0.12 6 -0.33 17 23
mol:L-citrulline -0.066 0.2 0.25 2 -0.49 45 47
RHOA 0.029 0.003 -10000 0 -10000 0 0
Gai/GDP -0.12 0.29 -10000 0 -0.65 65 65
JNK cascade 0.023 0.038 -10000 0 -0.23 5 5
BCAR1 0.025 0.03 -10000 0 -0.33 2 2
ESR2 0.031 0.055 -10000 0 -0.33 5 5
GNAQ 0.027 0.008 -10000 0 -10000 0 0
ESR1 0.015 0.062 0.12 1 -0.33 9 10
Gq family/GDP/Gbeta gamma 0.008 0.11 -10000 0 -0.42 12 12
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.016 0.089 -10000 0 -0.57 4 4
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.045 0.17 -10000 0 -0.38 41 41
GNAZ -0.002 0.1 -10000 0 -0.33 26 26
E2/ER alpha (dimer) 0.012 0.043 -10000 0 -0.23 9 9
STRN 0.022 0.046 -10000 0 -0.33 5 5
GNAL 0.009 0.11 -10000 0 -0.33 25 25
PELP1 0.027 0.008 -10000 0 -10000 0 0
MAPK11 0.009 0.034 -10000 0 -0.19 8 8
GNAI2 0.029 0.003 -10000 0 -10000 0 0
GNAI3 0.028 0.006 -10000 0 -10000 0 0
GNAI1 0.02 0.047 -10000 0 -0.33 5 5
HBEGF -0.07 0.22 0.33 15 -0.46 48 63
cAMP biosynthetic process 0.012 0.067 0.11 8 -0.16 35 43
SRC -0.077 0.19 0.22 11 -0.44 48 59
PI3K 0.035 0.042 -10000 0 -0.27 5 5
GNB1 0.028 0.006 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.013 0.094 -10000 0 -0.26 17 17
SOS1 0.029 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.062 0.13 -10000 0 -0.32 46 46
Gs family/GTP 0.019 0.072 0.14 8 -0.16 35 43
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.05 0.017 -10000 0 -10000 0 0
vasodilation -0.062 0.2 0.24 3 -0.47 45 48
mol:DAG -0.01 0.081 0.21 1 -0.38 9 10
Gs family/GDP/Gbeta gamma -0.015 0.094 -10000 0 -0.26 20 20
MSN -0.012 0.062 0.16 24 -10000 0 24
Gq family/GTP 0.018 0.067 -10000 0 -0.37 6 6
mol:PI-3-4-5-P3 -0.087 0.28 -10000 0 -0.73 46 46
NRAS 0.027 0.007 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.062 0.2 0.47 45 -0.24 3 48
GRB2/SOS1 0.041 0.009 -10000 0 -10000 0 0
RhoA/GDP 0.006 0.089 -10000 0 -0.26 15 15
NOS3 -0.07 0.22 0.28 1 -0.52 45 46
GNA11 0.029 0.003 -10000 0 -10000 0 0
MAPKKK cascade -0.053 0.21 0.29 4 -0.52 42 46
E2/ER alpha (dimer)/PELP1/Src -0.049 0.18 0.26 4 -0.4 44 48
ruffle organization -0.011 0.06 0.16 25 -10000 0 25
ROCK2 -0.008 0.065 0.26 4 -10000 0 4
GNA14 0.034 0.048 -10000 0 -0.33 3 3
GNA15 0.019 0.062 0.12 3 -0.33 9 12
GNA13 0.028 0.005 -10000 0 -10000 0 0
MMP9 -0.076 0.21 0.36 11 -0.44 49 60
MMP2 -0.072 0.19 0.29 6 -0.42 48 54
Signaling events mediated by the Hedgehog family

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
TGFB2 0.014 0.12 -10000 0 -0.45 17 17
IHH 0.031 0.051 0.14 4 -0.13 22 26
SHH Np/Cholesterol/GAS1 0.017 0.028 -10000 0 -0.18 5 5
LRPAP1 0.028 0.006 -10000 0 -10000 0 0
dorsoventral neural tube patterning -0.016 0.028 0.17 5 -10000 0 5
SMO/beta Arrestin2 0.006 0.13 -10000 0 -0.36 17 17
SMO -0.015 0.12 -10000 0 -0.38 18 18
AKT1 0 0.1 -10000 0 -0.4 10 10
ARRB2 0.027 0.009 -10000 0 -10000 0 0
BOC 0.018 0.071 -10000 0 -0.33 11 11
ADRBK1 0.028 0.005 -10000 0 -10000 0 0
heart looping -0.015 0.12 -10000 0 -0.37 18 18
STIL 0.018 0.09 0.19 33 -0.26 14 47
DHH N/PTCH2 0.034 0.07 0.18 2 -0.23 17 19
DHH N/PTCH1 0.021 0.11 -10000 0 -0.33 21 21
PIK3CA 0.023 0.042 -10000 0 -0.33 4 4
DHH 0.022 0.081 -10000 0 -0.33 13 13
PTHLH -0.006 0.18 -10000 0 -0.64 20 20
determination of left/right symmetry -0.015 0.12 -10000 0 -0.37 18 18
PIK3R1 0.025 0.03 -10000 0 -0.33 2 2
skeletal system development -0.006 0.18 -10000 0 -0.63 20 20
IHH N/Hhip 0.043 0.041 0.18 1 -10000 0 1
DHH N/Hhip 0.038 0.065 0.18 4 -0.23 13 17
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.015 0.12 -10000 0 -0.37 18 18
pancreas development 0.031 0.024 0.12 18 -10000 0 18
HHAT 0.02 0.047 -10000 0 -0.33 5 5
PI3K 0.035 0.042 -10000 0 -0.27 5 5
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.024 0.037 0.12 1 -0.33 3 4
somite specification -0.015 0.12 -10000 0 -0.37 18 18
SHH Np/Cholesterol/PTCH1 0.009 0.074 -10000 0 -0.26 17 17
SHH Np/Cholesterol/PTCH2 0.019 0.033 0.16 2 -0.18 6 8
SHH Np/Cholesterol/Megalin -0.007 0.1 0.19 11 -0.18 70 81
SHH -0.008 0.028 -10000 0 -0.23 3 3
catabolic process 0.011 0.1 -10000 0 -0.35 21 21
SMO/Vitamin D3 0.005 0.1 0.25 4 -0.3 18 22
SHH Np/Cholesterol/Hhip 0.016 0.036 0.16 6 -0.18 3 9
LRP2 -0.045 0.18 0.12 82 -0.33 82 164
receptor-mediated endocytosis -0.034 0.13 0.21 3 -0.38 21 24
SHH Np/Cholesterol/BOC 0.015 0.045 -10000 0 -0.19 11 11
SHH Np/Cholesterol/CDO 0.015 0.032 -10000 0 -0.18 7 7
mesenchymal cell differentiation -0.016 0.036 0.17 3 -0.16 6 9
mol:Vitamin D3 0.035 0.1 0.22 37 -0.26 17 54
IHH N/PTCH2 0.038 0.05 -10000 0 -0.25 4 4
CDON 0.021 0.042 -10000 0 -0.33 4 4
IHH N/PTCH1 0.021 0.11 -10000 0 -0.36 21 21
Megalin/LRPAP1 -0.017 0.14 -10000 0 -0.23 82 82
PTCH2 0.025 0.044 0.12 6 -0.33 4 10
SHH Np/Cholesterol 0.01 0.02 -10000 0 -0.17 3 3
PTCH1 0.011 0.1 -10000 0 -0.35 21 21
HHIP 0.031 0.024 0.12 18 -10000 0 18
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.015 0.076 -10000 0 -0.23 24 24
CRKL 0.013 0.13 0.31 10 -0.45 8 18
mol:PIP3 0.002 0.011 -10000 0 -10000 0 0
AKT1 -0.006 0.02 -10000 0 -10000 0 0
PTK2B 0.027 0.025 0.12 5 -0.33 1 6
RAPGEF1 0.011 0.13 0.3 9 -0.43 8 17
RANBP10 0.028 0.006 -10000 0 -10000 0 0
PIK3CA 0.023 0.042 -10000 0 -0.33 4 4
HGF/MET/SHIP2 0.022 0.088 -10000 0 -0.19 38 38
MAP3K5 -0.006 0.14 0.29 7 -0.41 18 25
HGF/MET/CIN85/CBL/ENDOPHILINS 0.031 0.09 -10000 0 -0.18 40 40
AP1 0.034 0.053 0.15 14 -10000 0 14
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.026 0.009 -10000 0 -10000 0 0
apoptosis 0.018 0.14 -10000 0 -0.81 7 7
STAT3 (dimer) -0.003 0.095 0.18 5 -0.22 37 42
GAB1/CRKL/SHP2/PI3K 0.036 0.13 0.31 5 -0.5 6 11
INPP5D 0.014 0.075 0.12 5 -0.33 13 18
CBL/CRK 0.014 0.12 0.31 3 -0.43 8 11
PTPN11 0.028 0.004 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.026 0.008 -10000 0 -10000 0 0
PTEN 0.025 0.01 -10000 0 -10000 0 0
ELK1 0.02 0.13 0.36 33 -10000 0 33
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.005 0.063 -10000 0 -0.23 9 9
PAK1 0.001 0.045 -10000 0 -10000 0 0
HGF/MET/RANBP10 0.023 0.089 -10000 0 -0.19 40 40
HRAS -0.035 0.17 -10000 0 -0.5 34 34
DOCK1 0.01 0.12 0.3 9 -0.45 7 16
GAB1 0.001 0.12 0.25 1 -0.46 9 10
CRK 0.004 0.12 0.29 4 -0.44 9 13
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.031 0.16 -10000 0 -0.44 40 40
JUN 0.029 0.009 0.12 2 -10000 0 2
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.016 0.071 0.11 1 -0.19 39 40
PIK3R1 0.025 0.03 -10000 0 -0.33 2 2
cell morphogenesis 0.013 0.14 0.38 13 -0.41 7 20
GRB2/SHC 0.016 0.085 0.18 13 -0.18 35 48
FOS 0.031 0.016 0.12 8 -10000 0 8
GLMN 0 0.026 -10000 0 -0.2 5 5
cell motility 0.02 0.13 0.36 33 -10000 0 33
HGF/MET/MUC20 0.01 0.082 -10000 0 -0.19 40 40
cell migration 0.016 0.084 0.17 13 -0.18 35 48
GRB2 0.028 0.005 -10000 0 -10000 0 0
CBL 0.025 0.01 -10000 0 -10000 0 0
MET/RANBP10 0.012 0.084 -10000 0 -0.23 30 30
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.005 0.082 -10000 0 -0.2 39 39
MET/MUC20 -0.003 0.076 -10000 0 -0.23 30 30
RAP1B 0.013 0.12 0.31 12 -0.43 7 19
RAP1A 0.012 0.12 0.31 10 -0.42 7 17
HGF/MET/RANBP9 0.023 0.084 -10000 0 -0.19 34 34
RAF1 -0.022 0.18 0.28 1 -0.48 34 35
STAT3 -0.005 0.094 0.16 3 -0.22 38 41
cell proliferation 0.004 0.14 0.27 14 -0.32 34 48
RPS6KB1 -0.007 0.057 -10000 0 -0.3 7 7
MAPK3 0.01 0.13 0.5 12 -10000 0 12
MAPK1 0.016 0.14 0.52 15 -10000 0 15
RANBP9 0.025 0.01 -10000 0 -10000 0 0
MAPK8 -0.024 0.17 0.3 7 -0.42 32 39
SRC -0.012 0.079 0.19 4 -0.2 38 42
PI3K 0.012 0.092 0.18 13 -0.18 40 53
MET/Glomulin -0.007 0.076 -10000 0 -0.19 38 38
SOS1 0.029 0.003 -10000 0 -10000 0 0
MAP2K1 -0.018 0.17 0.3 2 -0.45 33 35
MET -0.007 0.11 0.12 11 -0.33 30 41
MAP4K1 -0.006 0.16 0.31 7 -0.43 19 26
PTK2 0.025 0.01 -10000 0 -10000 0 0
MAP2K2 -0.018 0.17 0.3 2 -0.45 33 35
BAD -0.005 0.03 -10000 0 -10000 0 0
MAP2K4 -0.006 0.13 0.28 8 -0.37 18 26
SHP2/GRB2/SOS1/GAB1 0.007 0.12 -10000 0 -0.3 33 33
INPPL1 0.027 0.007 -10000 0 -10000 0 0
PXN 0.028 0.004 -10000 0 -10000 0 0
SH3KBP1 0.027 0.021 -10000 0 -0.33 1 1
HGS -0.02 0.065 0.096 1 -0.18 39 40
PLCgamma1/PKC 0.02 0.006 -10000 0 -10000 0 0
HGF 0.019 0.069 -10000 0 -0.33 10 10
RASA1 0.025 0.03 -10000 0 -0.33 2 2
NCK1 0.028 0.005 -10000 0 -10000 0 0
PTPRJ 0.026 0.03 -10000 0 -0.33 2 2
NCK/PLCgamma1 0.021 0.087 0.18 15 -0.18 38 53
PDPK1 -0.002 0.023 -10000 0 -10000 0 0
HGF/MET/SHIP 0.015 0.11 -10000 0 -0.22 47 47
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.028 0.006 -10000 0 -10000 0 0
LAT2 -0.012 0.12 0.2 5 -0.38 21 26
AP1 -0.009 0.2 -10000 0 -0.48 35 35
mol:PIP3 0 0.17 0.27 22 -0.44 24 46
IKBKB 0.008 0.11 0.21 28 -0.27 20 48
AKT1 0.002 0.12 0.32 23 -0.28 4 27
IKBKG 0.006 0.11 0.21 23 -0.27 19 42
MS4A2 0.022 0.044 0.12 11 -0.33 3 14
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.023 0.042 -10000 0 -0.33 4 4
MAP3K1 -0.01 0.14 0.24 9 -0.4 24 33
mol:Ca2+ 0.007 0.13 0.24 23 -0.33 23 46
LYN 0.022 0.044 -10000 0 -0.34 4 4
CBLB -0.011 0.1 0.18 2 -0.33 20 22
SHC1 0.026 0.009 -10000 0 -10000 0 0
RasGAP/p62DOK 0.049 0.031 -10000 0 -0.17 4 4
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.014 0.075 0.12 5 -0.33 13 18
PLD2 0.004 0.11 0.3 26 -0.2 13 39
PTPN13 0.001 0.14 0.3 2 -0.49 14 16
PTPN11 0.026 0.018 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.009 0.099 0.26 15 -0.28 10 25
SYK 0.017 0.069 0.12 5 -0.34 10 15
GRB2 0.028 0.006 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.009 0.15 0.18 1 -0.44 25 26
LAT -0.014 0.12 0.18 2 -0.35 23 25
PAK2 -0.011 0.16 0.25 7 -0.46 23 30
NFATC2 -0.033 0.13 -10000 0 -0.45 25 25
HRAS -0.013 0.17 0.27 5 -0.48 25 30
GAB2 0.027 0.008 -10000 0 -10000 0 0
PLA2G1B 0.008 0.11 -10000 0 -0.88 4 4
Fc epsilon R1 0.036 0.088 0.18 7 -0.22 27 34
Antigen/IgE/Fc epsilon R1 0.035 0.081 0.17 7 -0.19 27 34
mol:GDP -0.023 0.18 -10000 0 -0.53 25 25
JUN 0.029 0.009 0.12 2 -10000 0 2
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.025 0.03 -10000 0 -0.33 2 2
FOS 0.031 0.016 0.12 8 -10000 0 8
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.005 0.11 -10000 0 -0.34 21 21
CHUK 0.005 0.11 0.22 21 -0.27 19 40
KLRG1 -0.012 0.097 -10000 0 -0.26 29 29
VAV1 -0.02 0.13 0.19 1 -0.41 22 23
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.005 0.094 -10000 0 -0.34 15 15
negative regulation of mast cell degranulation 0.01 0.12 0.19 9 -0.36 20 29
BTK -0.023 0.19 -10000 0 -0.61 23 23
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.014 0.13 -10000 0 -0.33 31 31
GAB2/PI3K/SHP2 -0.027 0.053 -10000 0 -0.2 18 18
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.009 0.11 -10000 0 -0.29 30 30
RAF1 0.006 0.12 -10000 0 -0.97 4 4
Fc epsilon R1/FcgammaRIIB/SHIP 0.045 0.12 0.25 1 -0.23 38 39
FCER1G 0.019 0.072 0.12 18 -0.34 10 28
FCER1A 0.007 0.092 -10000 0 -0.34 18 18
Antigen/IgE/Fc epsilon R1/Fyn 0.041 0.08 0.18 7 -0.18 27 34
MAPK3 0.008 0.11 -10000 0 -0.89 4 4
MAPK1 0.006 0.11 -10000 0 -0.89 4 4
NFKB1 0.028 0.005 -10000 0 -10000 0 0
MAPK8 -0.051 0.25 -10000 0 -0.65 39 39
DUSP1 0.027 0.025 -10000 0 -0.33 1 1
NF-kappa-B/RelA 0.011 0.065 0.14 11 -0.17 17 28
actin cytoskeleton reorganization 0.01 0.14 0.31 1 -0.51 13 14
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.005 0.15 -10000 0 -0.43 23 23
FER -0.01 0.1 0.19 1 -0.32 20 21
RELA 0.028 0.005 -10000 0 -10000 0 0
ITK -0.033 0.12 -10000 0 -0.32 41 41
SOS1 0.029 0.003 -10000 0 -10000 0 0
PLCG1 -0.005 0.18 0.28 10 -0.52 24 34
cytokine secretion 0 0.041 -10000 0 -0.14 11 11
SPHK1 -0.012 0.11 0.18 1 -0.37 19 20
PTK2 0.009 0.14 0.31 1 -0.54 13 14
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.004 0.15 0.21 2 -0.45 24 26
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.004 0.17 0.27 23 -0.43 24 47
MAP2K2 0.002 0.11 -10000 0 -0.91 4 4
MAP2K1 0.004 0.11 -10000 0 -0.91 4 4
MAP2K7 0.029 0.003 -10000 0 -10000 0 0
KLRG1/SHP2 0.004 0.097 0.21 5 -0.26 23 28
MAP2K4 -0.018 0.22 -10000 0 -0.86 19 19
Fc epsilon R1/FcgammaRIIB 0.044 0.1 0.19 8 -0.22 32 40
mol:Choline 0.004 0.11 0.3 26 -0.2 13 39
SHC/Grb2/SOS1 0.033 0.11 -10000 0 -0.32 17 17
FYN 0.025 0.009 -10000 0 -10000 0 0
DOK1 0.028 0.022 0.12 1 -0.33 1 2
PXN 0.008 0.13 0.3 1 -0.5 13 14
HCLS1 -0.016 0.12 0.18 1 -0.39 22 23
PRKCB 0.001 0.14 0.25 21 -0.36 22 43
FCGR2B 0.016 0.07 -10000 0 -0.33 11 11
IGHE 0 0.006 -10000 0 -10000 0 0
KLRG1/SHIP 0.01 0.13 0.19 9 -0.37 20 29
LCP2 0.016 0.062 -10000 0 -0.33 9 9
PLA2G4A -0.012 0.1 0.18 2 -0.34 18 20
RASA1 0.025 0.03 -10000 0 -0.33 2 2
mol:Phosphatidic acid 0.004 0.11 0.3 26 -0.2 13 39
IKK complex 0.009 0.092 0.2 25 -0.22 15 40
WIPF1 0.016 0.068 -10000 0 -0.33 11 11
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.025 0.11 0.21 3 -0.31 24 27
alphaM/beta2 Integrin/GPIbA 0.03 0.1 0.19 2 -0.27 24 26
alphaM/beta2 Integrin/proMMP-9 0.015 0.12 0.21 3 -0.28 36 39
PLAUR 0.023 0.058 0.12 10 -0.33 7 17
HMGB1 0.022 0.026 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.03 0.084 0.19 2 -0.28 15 17
AGER 0.021 0.028 0.13 3 -10000 0 3
RAP1A 0.028 0.006 -10000 0 -10000 0 0
SELPLG 0.017 0.065 -10000 0 -0.33 10 10
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.035 0.12 0.23 1 -0.26 35 36
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.001 0.11 -10000 0 -0.33 29 29
CYR61 0.027 0.04 -10000 0 -0.33 3 3
TLN1 0.026 0.009 -10000 0 -10000 0 0
Rap1/GTP -0.01 0.12 -10000 0 -0.34 22 22
RHOA 0.029 0.003 -10000 0 -10000 0 0
P-selectin oligomer -0.008 0.12 0.12 22 -0.33 34 56
MYH2 -0.024 0.12 0.2 3 -0.36 18 21
MST1R 0.017 0.096 0.12 37 -0.33 19 56
leukocyte activation during inflammatory response 0.03 0.078 -10000 0 -0.26 15 15
APOB 0.028 0.025 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.015 0.083 -10000 0 -0.33 15 15
JAM3 0.013 0.068 0.12 1 -0.33 11 12
GP1BA 0.023 0.083 -10000 0 -0.33 13 13
alphaM/beta2 Integrin/CTGF 0.027 0.1 0.19 2 -0.3 20 22
alphaM/beta2 Integrin -0.028 0.14 -10000 0 -0.39 23 23
JAM3 homodimer 0.013 0.068 0.12 1 -0.33 11 12
ICAM2 0.028 0.024 -10000 0 -0.33 1 1
ICAM1 0.017 0.065 -10000 0 -0.33 10 10
phagocytosis triggered by activation of immune response cell surface activating receptor -0.029 0.14 -10000 0 -0.38 25 25
cell adhesion 0.029 0.1 0.19 2 -0.27 24 26
NFKB1 0.007 0.16 0.36 7 -0.38 33 40
THY1 0.023 0.039 0.12 5 -0.33 3 8
RhoA/GDP 0.021 0.002 -10000 0 -10000 0 0
Lipoprotein(a) 0.028 0.02 0.16 1 -10000 0 1
alphaM/beta2 Integrin/LRP/tPA 0.04 0.094 0.2 2 -0.26 19 21
IL6 -0.012 0.17 0.35 7 -0.44 31 38
ITGB2 0.008 0.08 -10000 0 -0.33 14 14
elevation of cytosolic calcium ion concentration 0.039 0.1 0.21 6 -0.3 20 26
alphaM/beta2 Integrin/JAM2/JAM3 0.035 0.1 0.2 2 -0.26 26 28
JAM2 0.026 0.038 0.12 4 -0.33 3 7
alphaM/beta2 Integrin/ICAM1 0.039 0.12 0.2 1 -0.24 40 41
alphaM/beta2 Integrin/uPA/Plg 0.036 0.093 0.25 2 -0.3 16 18
RhoA/GTP -0.03 0.13 -10000 0 -0.36 21 21
positive regulation of phagocytosis -0.013 0.14 0.19 4 -0.43 22 26
Ron/MSP 0.03 0.082 0.18 1 -0.25 21 22
alphaM/beta2 Integrin/uPAR/uPA 0.041 0.1 0.22 6 -0.3 20 26
alphaM/beta2 Integrin/uPAR 0.03 0.099 0.19 2 -0.28 21 23
PLAU 0.024 0.045 -10000 0 -0.33 4 4
PLAT 0.021 0.056 0.12 5 -0.33 7 12
actin filament polymerization -0.024 0.12 0.2 3 -0.36 17 20
MST1 0.024 0.042 0.12 1 -0.33 4 5
alphaM/beta2 Integrin/lipoprotein(a) 0.035 0.081 -10000 0 -0.26 15 15
TNF -0.037 0.18 0.39 2 -0.5 33 35
RAP1B 0.028 0.006 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.03 0.097 0.25 2 -0.33 16 18
fibrinolysis 0.034 0.092 0.24 2 -0.3 16 18
HCK 0.01 0.076 0.12 1 -0.33 14 15
dendritic cell antigen processing and presentation -0.029 0.14 -10000 0 -0.38 25 25
VTN 0.029 0.071 0.12 38 -0.33 9 47
alphaM/beta2 Integrin/CYR61 0.032 0.092 0.19 2 -0.3 16 18
LPA 0.017 0.011 -10000 0 -10000 0 0
LRP1 0.028 0.005 -10000 0 -10000 0 0
cell migration -0.001 0.13 0.19 3 -0.28 40 43
FN1 0.009 0.084 0.12 2 -0.33 17 19
alphaM/beta2 Integrin/Thy1 0.027 0.091 0.22 2 -0.27 19 21
MPO 0.017 0.066 -10000 0 -0.33 10 10
KNG1 0.022 0.016 -10000 0 -10000 0 0
RAP1/GDP 0.036 0.011 -10000 0 -10000 0 0
ROCK1 -0.032 0.12 0.24 2 -0.36 19 21
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.017 0.011 0.12 2 -10000 0 2
CTGF 0.02 0.062 0.12 11 -0.33 8 19
alphaM/beta2 Integrin/Hck 0.023 0.12 0.22 2 -0.38 18 20
ITGAM 0.012 0.069 0.13 1 -0.32 10 11
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.017 0.14 0.21 4 -0.27 41 45
HP 0.009 0.11 0.12 50 -0.33 27 77
leukocyte adhesion 0.014 0.12 0.24 1 -0.33 23 24
SELP -0.008 0.12 0.12 22 -0.33 34 56
Ceramide signaling 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
SPHK2 -0.004 0.06 -10000 0 -0.23 19 19
MAP4K4 -0.019 0.1 -10000 0 -0.34 18 18
BAG4 0.021 0.046 -10000 0 -0.33 5 5
PKC zeta/ceramide -0.011 0.084 -10000 0 -0.21 37 37
NFKBIA 0.029 0.003 -10000 0 -10000 0 0
BIRC3 -0.004 0.11 0.12 21 -0.33 31 52
BAX 0.001 0.043 -10000 0 -0.29 3 3
RIPK1 0.025 0.01 -10000 0 -10000 0 0
AKT1 -0.006 0.014 -10000 0 -10000 0 0
BAD -0.021 0.077 0.2 5 -0.19 35 40
SMPD1 0.015 0.089 0.17 32 -0.26 12 44
RB1 -0.023 0.078 0.19 5 -0.19 37 42
FADD/Caspase 8 -0.014 0.11 0.23 3 -0.35 19 22
MAP2K4 -0.026 0.072 0.18 3 -0.18 38 41
NSMAF 0.026 0.008 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.026 0.069 0.18 1 -0.19 33 34
EGF -0.03 0.14 -10000 0 -0.33 54 54
mol:ceramide -0.022 0.077 0.12 1 -0.2 35 36
MADD 0.028 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.002 0.055 -10000 0 -0.23 16 16
ASAH1 0.023 0.036 -10000 0 -0.33 3 3
negative regulation of cell cycle -0.023 0.077 0.18 5 -0.19 37 42
cell proliferation -0.008 0.08 -10000 0 -0.21 13 13
BID -0.012 0.16 -10000 0 -0.61 14 14
MAP3K1 -0.025 0.075 0.19 2 -0.19 39 41
EIF2A -0.026 0.067 0.17 3 -0.19 27 30
TRADD 0.028 0.006 -10000 0 -10000 0 0
CRADD 0.029 0.007 0.12 1 -10000 0 1
MAPK3 -0.021 0.067 0.17 1 -0.19 22 23
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.022 0.066 0.17 1 -0.19 21 22
Cathepsin D/ceramide -0.008 0.081 -10000 0 -0.2 35 35
FADD -0.015 0.095 0.2 2 -0.33 15 17
KSR1 -0.023 0.072 0.19 1 -0.2 34 35
MAPK8 -0.041 0.1 -10000 0 -0.26 33 33
PRKRA -0.024 0.071 -10000 0 -0.19 34 34
PDGFA 0.007 0.085 -10000 0 -0.33 17 17
TRAF2 0.027 0.008 -10000 0 -10000 0 0
IGF1 0.01 0.085 0.12 6 -0.33 17 23
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.022 0.076 0.12 1 -0.2 35 36
CTSD 0.028 0.024 -10000 0 -0.33 1 1
regulation of nitric oxide biosynthetic process 0.04 0.01 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.007 0.086 -10000 0 -0.25 9 9
PRKCD 0.026 0.03 -10000 0 -0.33 2 2
PRKCZ 0.015 0.065 -10000 0 -0.33 10 10
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.002 0.055 -10000 0 -0.23 16 16
RelA/NF kappa B1 0.04 0.01 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR -0.013 0.11 -10000 0 -0.33 34 34
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.01 0.1 -10000 0 -0.38 14 14
TNFR1A/BAG4/TNF-alpha 0.032 0.071 -10000 0 -0.19 23 23
mol:Sphingosine-1-phosphate -0.004 0.06 -10000 0 -0.23 19 19
MAP2K1 -0.025 0.068 0.17 3 -0.19 31 34
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.028 0.005 -10000 0 -10000 0 0
CYCS 0.002 0.046 0.14 7 -0.17 6 13
TNFRSF1A 0.028 0.005 -10000 0 -10000 0 0
NFKB1 0.028 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.035 0.037 -10000 0 -0.23 5 5
EIF2AK2 -0.026 0.067 -10000 0 -0.19 32 32
TNF-alpha/TNFR1A/FAN 0.036 0.065 -10000 0 -0.2 18 18
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.002 0.098 -10000 0 -0.4 11 11
MAP2K2 -0.026 0.067 0.17 3 -0.19 32 35
SMPD3 0.004 0.1 0.16 23 -0.33 16 39
TNF 0.009 0.089 0.12 16 -0.33 18 34
PKC zeta/PAR4 0 0.097 -10000 0 -0.23 44 44
mol:PHOSPHOCHOLINE 0.027 0.084 0.18 53 -0.14 18 71
NF kappa B1/RelA/I kappa B alpha 0.041 0.089 -10000 0 -0.17 42 42
AIFM1 -0.006 0.057 0.15 8 -0.17 10 18
BCL2 0.019 0.058 0.12 1 -0.33 8 9
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.006 0.088 -10000 0 -0.33 19 19
positive regulation of NF-kappaB transcription factor activity 0.026 0.079 -10000 0 -0.22 24 24
MAP2K4 -0.003 0.091 -10000 0 -0.32 15 15
IKBKB 0.028 0.006 -10000 0 -10000 0 0
TNFRSF10B 0.01 0.076 -10000 0 -0.33 14 14
TNFRSF10A 0.005 0.097 -10000 0 -0.33 22 22
SMPD1 -0.005 0.056 -10000 0 -0.16 32 32
IKBKG 0.029 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.033 0.058 0.12 37 -0.33 5 42
TRAIL/TRAILR2 0.011 0.087 -10000 0 -0.24 32 32
TRAIL/TRAILR3 0.011 0.095 -10000 0 -0.24 34 34
TRAIL/TRAILR1 0.008 0.1 -10000 0 -0.26 35 35
TRAIL/TRAILR4 0.027 0.079 -10000 0 -0.23 24 24
TRAIL/TRAILR1/DAP3/GTP 0.023 0.081 -10000 0 -0.19 33 33
IKK complex -0.007 0.078 -10000 0 -0.3 10 10
RIPK1 0.025 0.01 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.019 0.006 -10000 0 -10000 0 0
MAPK3 -0.003 0.059 -10000 0 -0.23 19 19
MAP3K1 -0.008 0.095 -10000 0 -0.28 24 24
TRAILR4 (trimer) 0.033 0.058 0.12 37 -0.33 5 42
TRADD 0.028 0.006 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.005 0.097 -10000 0 -0.33 22 22
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.006 0.09 -10000 0 -0.24 34 34
CFLAR 0.029 0.002 -10000 0 -10000 0 0
MAPK1 -0.002 0.055 -10000 0 -0.23 16 16
TRAIL/TRAILR1/FADD/TRADD/RIP 0.043 0.086 -10000 0 -0.18 30 30
mol:ceramide -0.005 0.055 -10000 0 -0.16 32 32
FADD 0.027 0.007 -10000 0 -10000 0 0
MAPK8 -0.002 0.085 0.27 1 -0.3 14 15
TRAF2 0.027 0.008 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.01 0.089 -10000 0 -0.33 18 18
CHUK 0.025 0.022 -10000 0 -0.33 1 1
TRAIL/TRAILR1/FADD 0.025 0.091 -10000 0 -0.22 33 33
DAP3 0.026 0.008 -10000 0 -10000 0 0
CASP10 -0.024 0.099 0.16 9 -0.3 22 31
JNK cascade 0.026 0.079 -10000 0 -0.22 24 24
TRAIL (trimer) 0.006 0.088 -10000 0 -0.33 19 19
TNFRSF10C 0.01 0.089 -10000 0 -0.33 18 18
TRAIL/TRAILR1/DAP3/GTP/FADD 0.034 0.079 -10000 0 -0.18 31 31
TRAIL/TRAILR2/FADD 0.027 0.077 -10000 0 -0.2 29 29
cell death -0.005 0.055 -10000 0 -0.16 32 32
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.001 0.077 -10000 0 -0.22 30 30
TRAILR2 (trimer) 0.01 0.076 -10000 0 -0.33 14 14
CASP8 0.008 0.078 -10000 0 -0.63 3 3
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.044 0.077 -10000 0 -0.17 26 26
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.036 0.034 -10000 0 -0.23 2 2
PDGFRB 0.025 0.031 0.12 1 -0.34 2 3
SPHK1 -0.02 0.14 -10000 0 -0.69 12 12
mol:S1P -0.021 0.13 -10000 0 -0.6 12 12
S1P1/S1P/Gi -0.055 0.17 0.2 2 -0.33 60 62
GNAO1 -0.04 0.14 0.13 3 -0.33 55 58
PDGFB-D/PDGFRB/PLCgamma1 -0.028 0.17 0.27 10 -0.35 40 50
PLCG1 -0.056 0.16 0.25 4 -0.32 55 59
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.025 0.031 0.12 1 -0.34 2 3
GNAI2 0.026 0.015 -10000 0 -10000 0 0
GNAI3 0.025 0.015 -10000 0 -10000 0 0
GNAI1 0.017 0.049 -10000 0 -0.34 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.005 0.02 -10000 0 -0.19 2 2
S1P1/S1P -0.012 0.1 0.17 1 -0.41 12 13
negative regulation of cAMP metabolic process -0.053 0.16 0.2 2 -0.32 60 62
MAPK3 -0.07 0.21 0.32 3 -0.5 40 43
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.021 0.002 -10000 0 -10000 0 0
KDR 0.026 0.026 0.12 3 -0.33 1 4
PLCB2 0.004 0.12 0.24 13 -0.39 12 25
RAC1 0.025 0.009 -10000 0 -10000 0 0
RhoA/GTP -0.011 0.087 -10000 0 -0.34 13 13
receptor internalization -0.013 0.096 -10000 0 -0.37 13 13
PTGS2 -0.076 0.29 0.33 8 -0.78 34 42
Rac1/GTP -0.012 0.086 -10000 0 -0.35 12 12
RHOA 0.029 0.003 -10000 0 -10000 0 0
VEGFA 0.025 0.03 0.12 8 -0.33 1 9
negative regulation of T cell proliferation -0.053 0.16 0.2 2 -0.32 60 62
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ -0.005 0.1 -10000 0 -0.33 26 26
MAPK1 -0.065 0.19 0.25 2 -0.48 39 41
S1P1/S1P/PDGFB-D/PDGFRB 0.004 0.11 0.23 5 -0.32 16 21
ABCC1 0.019 0.055 -10000 0 -0.33 7 7
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.022 0.092 0.21 1 -0.16 49 50
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.027 0.009 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.016 0.089 0.28 2 -0.22 12 14
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.03 0.052 -10000 0 -0.21 5 5
antigen processing and presentation of peptide antigen via MHC class I -0.018 0.075 -10000 0 -0.21 23 23
CaM/Ca2+ 0.023 0.09 0.19 1 -0.16 48 49
RAP1A 0.028 0.006 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.005 0.08 0.16 1 -0.17 46 47
AKT1 -0.026 0.081 0.27 4 -0.34 4 8
MAP2K1 -0.032 0.075 0.17 5 -0.28 9 14
MAP3K11 -0.029 0.068 0.16 8 -0.18 14 22
IFNGR1 0.018 0.024 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.019 0.13 -10000 0 -0.31 41 41
Rap1/GTP -0.011 0.056 -10000 0 -0.15 31 31
CRKL/C3G 0.037 0.015 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.03 0.098 -10000 0 -0.17 49 49
CEBPB 0 0.13 0.34 3 -0.44 13 16
STAT3 0.028 0.005 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.022 0.16 -10000 0 -0.99 5 5
STAT1 -0.03 0.072 0.16 8 -0.18 31 39
CALM1 0.028 0.005 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.029 0.14 -10000 0 -0.33 48 48
PIK3CA 0.023 0.042 -10000 0 -0.33 4 4
STAT1 (dimer)/PIAS1 -0.003 0.081 0.2 3 -0.17 38 41
CEBPB/PTGES2/Cbp/p300 0.009 0.086 -10000 0 -0.3 12 12
mol:Ca2+ 0.019 0.09 0.2 1 -0.16 49 50
MAPK3 -0.008 0.11 0.39 1 -0.59 4 5
STAT1 (dimer) -0.018 0.1 -10000 0 -0.28 22 22
MAPK1 -0.014 0.12 0.39 1 -0.64 6 7
JAK2 0.012 0.051 -10000 0 -0.34 5 5
PIK3R1 0.025 0.03 -10000 0 -0.33 2 2
JAK1 0.019 0.024 -10000 0 -10000 0 0
CAMK2D 0.027 0.021 -10000 0 -0.33 1 1
DAPK1 -0.001 0.12 0.32 2 -0.54 9 11
SMAD7 -0.005 0.051 0.16 6 -0.14 12 18
CBL/CRKL/C3G 0.011 0.078 0.27 2 -0.16 31 33
PI3K 0.017 0.096 -10000 0 -0.17 45 45
IFNG -0.029 0.14 -10000 0 -0.33 48 48
apoptosis 0.002 0.099 0.28 2 -0.43 9 11
CAMK2G 0.026 0.008 -10000 0 -10000 0 0
STAT3 (dimer) 0.028 0.005 -10000 0 -10000 0 0
CAMK2A 0.02 0.08 0.12 28 -0.33 13 41
CAMK2B 0.023 0.073 0.12 29 -0.33 10 39
FRAP1 -0.028 0.075 0.26 4 -0.27 6 10
PRKCD -0.027 0.083 0.26 5 -0.28 7 12
RAP1B 0.028 0.006 -10000 0 -10000 0 0
negative regulation of cell growth -0.018 0.075 -10000 0 -0.21 23 23
PTPN2 0.026 0.022 -10000 0 -0.33 1 1
EP300 0.026 0.009 -10000 0 -10000 0 0
IRF1 -0.013 0.089 0.26 6 -0.3 10 16
STAT1 (dimer)/PIASy -0.002 0.084 0.21 5 -0.21 10 15
SOCS1 0.008 0.16 -10000 0 -1.2 5 5
mol:GDP 0.009 0.074 0.26 2 -0.16 31 33
CASP1 -0.01 0.064 0.16 5 -0.21 17 22
PTGES2 0.027 0.007 -10000 0 -10000 0 0
IRF9 0.018 0.053 0.17 8 -0.14 6 14
mol:PI-3-4-5-P3 0.005 0.086 -10000 0 -0.17 45 45
RAP1/GDP 0.007 0.066 -10000 0 -0.16 10 10
CBL -0.024 0.065 0.2 3 -0.17 25 28
MAP3K1 -0.031 0.076 0.2 3 -0.27 9 12
PIAS1 0.028 0.004 -10000 0 -10000 0 0
PIAS4 0.028 0.003 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.018 0.075 -10000 0 -0.21 23 23
PTPN11 -0.013 0.076 0.17 10 -0.16 45 55
CREBBP 0.028 0.004 -10000 0 -10000 0 0
RAPGEF1 0.027 0.008 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.009 0.14 -10000 0 -1.1 4 4
VDR 0.022 0.046 -10000 0 -0.33 5 5
FAM120B 0.025 0.01 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.026 0.12 -10000 0 -0.32 25 25
RXRs/LXRs/DNA/Oxysterols -0.029 0.14 -10000 0 -0.44 23 23
MED1 0.028 0.005 -10000 0 -10000 0 0
mol:9cRA 0 0.016 -10000 0 -0.14 1 1
RARs/THRs/DNA/Src-1 0.006 0.078 -10000 0 -0.21 28 28
RXRs/NUR77 0.009 0.1 -10000 0 -0.18 55 55
RXRs/PPAR -0.021 0.09 -10000 0 -0.19 60 60
NCOR2 0.028 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.017 0.032 -10000 0 -0.23 5 5
RARs/VDR/DNA/Vit D3 0.046 0.067 -10000 0 -0.17 24 24
RARA 0.028 0.005 -10000 0 -10000 0 0
NCOA1 0.028 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.022 0.046 -10000 0 -0.33 5 5
RARs/RARs/DNA/9cRA 0.034 0.057 -10000 0 -0.17 20 20
RARG 0.028 0.004 -10000 0 -10000 0 0
RPS6KB1 0.01 0.088 0.56 5 -0.41 4 9
RARs/THRs/DNA/SMRT 0.006 0.079 -10000 0 -0.2 36 36
THRA 0.028 0.005 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.017 0.032 -10000 0 -0.23 5 5
RXRs/PPAR/9cRA/PGJ2/DNA 0.001 0.099 0.29 1 -0.17 67 68
NR1H4 0.026 0.02 0.12 11 -10000 0 11
RXRs/LXRs/DNA 0.016 0.12 -10000 0 -0.25 18 18
NR1H2 0.025 0.032 -10000 0 -0.35 1 1
NR1H3 0.025 0.035 0.13 1 -0.26 2 3
RXRs/VDR/DNA/Vit D3 0.005 0.097 -10000 0 -0.17 58 58
NR4A1 0.025 0.036 -10000 0 -0.33 3 3
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.022 0.086 -10000 0 -0.18 60 60
RXRG -0.051 0.15 0.13 2 -0.33 64 66
RXR alpha/CCPG 0.034 0.024 -10000 0 -10000 0 0
RXRA 0.024 0.025 -10000 0 -0.13 1 1
RXRB 0.023 0.025 -10000 0 -10000 0 0
THRB 0.023 0.084 -10000 0 -0.33 14 14
PPARG 0.026 0.038 -10000 0 -0.33 3 3
PPARD 0.026 0.011 0.12 1 -10000 0 1
TNF -0.061 0.24 -10000 0 -0.92 20 20
mol:Oxysterols 0 0.014 -10000 0 -0.11 1 1
cholesterol transport -0.029 0.14 -10000 0 -0.43 23 23
PPARA 0.026 0.008 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.006 0.091 -10000 0 -0.33 20 20
RXRs/NUR77/BCL2 -0.028 0.096 -10000 0 -0.2 60 60
SREBF1 -0.03 0.14 -10000 0 -0.57 9 9
RXRs/RXRs/DNA/9cRA 0.001 0.099 0.28 1 -0.17 67 68
ABCA1 -0.034 0.16 -10000 0 -0.66 12 12
RARs/THRs 0.061 0.089 -10000 0 -0.19 29 29
RXRs/FXR 0.009 0.1 -10000 0 -0.18 55 55
BCL2 0.019 0.058 0.12 1 -0.33 8 9
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.021 0.046 -10000 0 -0.33 5 5
Caspase 8 (4 units) 0.006 0.1 -10000 0 -0.28 16 16
NEF -0.016 0.051 -10000 0 -0.16 28 28
NFKBIA 0.018 0.037 -10000 0 -0.13 1 1
BIRC3 -0.018 0.12 0.18 1 -0.38 30 31
CYCS -0.006 0.097 0.18 20 -0.25 30 50
RIPK1 0.025 0.01 -10000 0 -10000 0 0
CD247 -0.018 0.14 0.14 11 -0.31 47 58
MAP2K7 0.002 0.14 0.3 3 -0.42 11 14
protein ubiquitination 0.01 0.11 0.24 11 -0.3 16 27
CRADD 0.029 0.007 0.12 1 -10000 0 1
DAXX 0.025 0.009 -10000 0 -10000 0 0
FAS 0.02 0.047 -10000 0 -0.33 5 5
BID -0.013 0.095 0.18 7 -0.26 31 38
NF-kappa-B/RelA/I kappa B alpha 0.036 0.088 -10000 0 -0.22 30 30
TRADD 0.028 0.006 -10000 0 -10000 0 0
MAP3K5 0.025 0.025 -10000 0 -0.33 1 1
CFLAR 0.029 0.002 -10000 0 -10000 0 0
FADD 0.027 0.007 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.036 0.089 -10000 0 -0.22 30 30
MAPK8 0.001 0.13 0.3 2 -0.38 11 13
APAF1 0.025 0.036 -10000 0 -0.33 3 3
TRAF1 0.028 0.054 -10000 0 -0.33 5 5
TRAF2 0.027 0.008 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.01 0.11 0.19 9 -0.27 35 44
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.003 0.12 0.19 2 -0.39 17 19
CHUK 0.011 0.11 0.25 11 -0.33 15 26
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.059 0.049 -10000 0 -0.17 5 5
TCRz/NEF -0.021 0.13 0.14 11 -0.31 47 58
TNF 0.009 0.089 0.12 16 -0.33 18 34
FASLG -0.047 0.18 -10000 0 -0.44 46 46
NFKB1 0.018 0.036 -10000 0 -0.13 1 1
TNFR1A/BAG4/TNF-alpha 0.032 0.071 -10000 0 -0.19 23 23
CASP6 0.017 0.13 -10000 0 -0.54 7 7
CASP7 -0.038 0.19 0.33 5 -0.42 51 56
RELA 0.017 0.036 -10000 0 -10000 0 0
CASP2 0.025 0.022 -10000 0 -0.33 1 1
CASP3 -0.029 0.18 0.3 7 -0.43 39 46
TNFRSF1A 0.028 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.035 0.037 -10000 0 -0.23 5 5
CASP8 0.027 0.021 -10000 0 -0.33 1 1
CASP9 0.028 0.005 -10000 0 -10000 0 0
MAP3K14 -0.001 0.12 0.24 3 -0.35 18 21
APAF-1/Caspase 9 -0.015 0.13 0.19 1 -0.3 35 36
BCL2 -0.003 0.12 0.28 2 -0.36 10 12
Class I PI3K signaling events

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
ARF5/GTP -0.011 0.059 0.29 4 -10000 0 4
DAPP1 -0.057 0.24 0.29 7 -0.53 45 52
Src family/SYK family/BLNK-LAT/BTK-ITK -0.092 0.31 0.32 6 -0.65 57 63
mol:DAG -0.015 0.13 0.26 15 -0.25 46 61
HRAS 0.029 0.014 -10000 0 -10000 0 0
RAP1A 0.028 0.013 -10000 0 -10000 0 0
ARF5/GDP 0.007 0.12 0.2 1 -0.33 23 24
PLCG2 0.022 0.052 -10000 0 -0.33 6 6
PLCG1 0.026 0.008 -10000 0 -10000 0 0
ARF5 0.026 0.009 -10000 0 -10000 0 0
mol:GTP -0.011 0.065 0.21 18 -10000 0 18
ARF1/GTP -0.002 0.062 0.3 6 -0.18 1 7
RHOA 0.029 0.003 -10000 0 -10000 0 0
YES1 0.021 0.046 -10000 0 -0.33 5 5
RAP1A/GTP -0.017 0.046 0.17 11 -10000 0 11
ADAP1 -0.018 0.056 0.25 5 -0.17 6 11
ARAP3 -0.011 0.065 0.21 18 -10000 0 18
INPPL1 0.027 0.007 -10000 0 -10000 0 0
PREX1 0.019 0.051 -10000 0 -0.33 6 6
ARHGEF6 0.011 0.079 -10000 0 -0.33 15 15
ARHGEF7 0.028 0.006 -10000 0 -10000 0 0
ARF1 0.026 0.009 -10000 0 -10000 0 0
NRAS 0.027 0.014 -10000 0 -10000 0 0
FYN 0.025 0.009 -10000 0 -10000 0 0
ARF6 0.028 0.004 -10000 0 -10000 0 0
FGR 0.014 0.075 -10000 0 -0.33 13 13
mol:Ca2+ 0.001 0.075 0.17 24 -0.14 28 52
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.011 0.076 -10000 0 -0.33 14 14
ZAP70 -0.01 0.13 0.12 31 -0.33 40 71
mol:IP3 -0.004 0.096 0.2 22 -0.18 38 60
LYN 0.022 0.042 -10000 0 -0.33 4 4
ARF1/GDP 0.008 0.11 -10000 0 -0.33 22 22
RhoA/GDP 0.02 0.084 0.24 9 -0.26 10 19
PDK1/Src/Hsp90 0.051 0.023 -10000 0 -0.17 1 1
BLNK -0.004 0.1 -10000 0 -0.33 27 27
actin cytoskeleton reorganization 0.013 0.12 0.25 18 -0.36 13 31
SRC 0.025 0.022 -10000 0 -0.33 1 1
PLEKHA2 -0.018 0.038 -10000 0 -0.21 10 10
RAC1 0.025 0.009 -10000 0 -10000 0 0
PTEN 0.023 0.018 -10000 0 -10000 0 0
HSP90AA1 0.027 0.021 -10000 0 -0.33 1 1
ARF6/GTP -0.014 0.064 0.29 7 -10000 0 7
RhoA/GTP -0.012 0.066 0.22 18 -10000 0 18
Src family/SYK family/BLNK-LAT -0.089 0.28 0.18 1 -0.57 58 59
BLK 0.003 0.12 0.12 45 -0.33 31 76
PDPK1 0.029 0.003 -10000 0 -10000 0 0
CYTH1 -0.012 0.062 0.28 8 -10000 0 8
HCK 0.01 0.076 0.12 1 -0.33 14 15
CYTH3 -0.015 0.05 0.25 5 -0.17 1 6
CYTH2 -0.013 0.062 0.27 9 -10000 0 9
KRAS 0.029 0.014 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.007 0.072 0.21 6 -0.35 8 14
SGK1 -0.001 0.097 0.22 6 -0.35 18 24
INPP5D 0.014 0.075 0.12 5 -0.33 13 18
mol:GDP -0.003 0.12 0.22 4 -0.32 26 30
SOS1 0.029 0.003 -10000 0 -10000 0 0
SYK 0.016 0.066 0.12 5 -0.33 10 15
ARF6/GDP 0.012 0.088 0.27 13 -0.26 10 23
mol:PI-3-4-5-P3 -0.011 0.063 0.27 9 -10000 0 9
ARAP3/RAP1A/GTP -0.017 0.046 0.17 11 -10000 0 11
VAV1 -0.004 0.11 0.12 5 -0.33 28 33
mol:PI-3-4-P2 0.004 0.044 -10000 0 -0.23 10 10
RAS family/GTP/PI3K Class I 0.051 0.07 0.2 39 -0.15 12 51
PLEKHA1 -0.016 0.03 -10000 0 -0.2 8 8
Rac1/GDP 0.005 0.12 0.2 1 -0.31 25 26
LAT 0.018 0.078 -10000 0 -0.33 13 13
Rac1/GTP -0.014 0.14 -10000 0 -0.4 25 25
ITK -0.024 0.07 0.28 6 -0.28 2 8
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.035 0.17 0.27 13 -0.35 50 63
LCK -0.018 0.13 0.12 22 -0.33 44 66
BTK -0.018 0.07 0.26 9 -0.18 10 19
ceramide signaling 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
MAP4K4 -0.016 0.14 0.27 3 -0.38 25 28
BAG4 0.021 0.046 -10000 0 -0.33 5 5
BAD 0.002 0.059 0.16 12 -0.15 16 28
NFKBIA 0.029 0.003 -10000 0 -10000 0 0
BIRC3 -0.005 0.11 0.12 21 -0.33 31 52
BAX 0.001 0.058 0.15 11 -0.14 18 29
EnzymeConsortium:3.1.4.12 0 0.038 0.077 12 -0.093 21 33
IKBKB -0.015 0.14 0.36 2 -0.38 21 23
MAP2K2 -0.001 0.062 0.22 6 -0.19 8 14
MAP2K1 0 0.062 0.2 8 -0.19 8 16
SMPD1 0.001 0.043 0.11 3 -0.13 12 15
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.007 0.15 0.32 7 -0.4 20 27
MAP2K4 0 0.061 0.16 13 -0.18 12 25
protein ubiquitination -0.016 0.14 0.28 3 -0.38 23 26
EnzymeConsortium:2.7.1.37 -0.001 0.067 0.2 8 -0.2 8 16
response to UV 0 0.001 0.002 9 -0.002 7 16
RAF1 0 0.059 0.15 10 -0.17 11 21
CRADD 0.029 0.007 0.12 1 -10000 0 1
mol:ceramide 0.002 0.058 0.13 10 -0.14 20 30
I-kappa-B-alpha/RELA/p50/ubiquitin 0.037 0.008 -10000 0 -10000 0 0
MADD 0.028 0.005 -10000 0 -10000 0 0
MAP3K1 0 0.064 0.15 12 -0.16 21 33
TRADD 0.028 0.006 -10000 0 -10000 0 0
RELA/p50 0.028 0.005 -10000 0 -10000 0 0
MAPK3 0.003 0.063 0.22 6 -0.19 8 14
MAPK1 0.002 0.064 0.22 6 -0.2 9 15
p50/RELA/I-kappa-B-alpha 0.041 0.009 -10000 0 -10000 0 0
FADD -0.014 0.14 0.25 6 -0.37 23 29
KSR1 0.001 0.059 0.15 10 -0.16 16 26
MAPK8 -0.003 0.062 0.18 7 -0.23 8 15
TRAF2 0.027 0.008 -10000 0 -10000 0 0
response to radiation 0 0.001 0.002 4 -0.002 2 6
CHUK -0.017 0.14 0.25 3 -0.37 23 26
TNF R/SODD 0.035 0.037 -10000 0 -0.23 5 5
TNF 0.009 0.09 0.12 2 -0.33 18 20
CYCS 0.008 0.063 0.14 16 -0.15 15 31
IKBKG -0.016 0.14 0.26 4 -0.38 22 26
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.027 0.14 -10000 0 -0.34 37 37
RELA 0.028 0.005 -10000 0 -10000 0 0
RIPK1 0.025 0.01 -10000 0 -10000 0 0
AIFM1 0.002 0.059 0.14 14 -0.15 15 29
TNF/TNF R/SODD 0.032 0.071 -10000 0 -0.19 23 23
TNFRSF1A 0.028 0.005 -10000 0 -10000 0 0
response to heat 0 0.001 0.002 4 -0.002 2 6
CASP8 0.014 0.11 -10000 0 -0.63 6 6
NSMAF -0.011 0.14 0.22 11 -0.37 24 35
response to hydrogen peroxide 0 0.001 0.002 9 -0.002 7 16
BCL2 0.019 0.058 0.12 1 -0.33 8 9
IL2 signaling events mediated by STAT5

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
GAB2 0.027 0.008 -10000 0 -10000 0 0
ELF1 0.005 0.094 -10000 0 -0.28 29 29
CCNA2 0.025 0.036 -10000 0 -0.33 3 3
PIK3CA 0.024 0.042 -10000 0 -0.33 4 4
JAK3 0.02 0.063 0.12 6 -0.33 9 15
PIK3R1 0.026 0.03 -10000 0 -0.33 2 2
JAK1 0.029 0.004 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.04 0.22 -10000 0 -0.52 45 45
SHC1 0.026 0.009 -10000 0 -10000 0 0
SP1 0.026 0.059 -10000 0 -0.32 8 8
IL2RA -0.026 0.16 -10000 0 -0.61 21 21
IL2RB 0.006 0.095 0.12 13 -0.33 21 34
SOS1 0.029 0.003 -10000 0 -10000 0 0
IL2RG -0.012 0.12 0.12 15 -0.33 38 53
G1/S transition of mitotic cell cycle -0.008 0.15 0.28 2 -0.46 22 24
PTPN11 0.029 0.004 -10000 0 -10000 0 0
CCND2 0.005 0.097 0.29 1 -0.61 7 8
LCK -0.018 0.13 0.12 22 -0.33 44 66
GRB2 0.028 0.006 -10000 0 -10000 0 0
IL2 0.022 0.015 -10000 0 -10000 0 0
CDK6 0.012 0.071 -10000 0 -0.33 12 12
CCND3 -0.012 0.2 0.33 1 -0.53 29 30
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.027 0.009 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 0.005 0.055 -10000 0 -0.18 14 14
NT3 (dimer)/TRKC 0.039 0.067 0.18 8 -0.23 13 21
NT3 (dimer)/TRKB 0.031 0.11 0.19 16 -0.22 40 56
SHC/Grb2/SOS1/GAB1/PI3K 0.021 0.043 -10000 0 -0.32 3 3
RAPGEF1 0.027 0.008 -10000 0 -10000 0 0
BDNF -0.009 0.14 -10000 0 -0.33 42 42
PIK3CA 0.023 0.042 -10000 0 -0.33 4 4
DYNLT1 0.026 0.009 -10000 0 -10000 0 0
NTRK1 0.022 0.059 0.12 14 -0.33 7 21
NTRK2 0.01 0.098 0.12 26 -0.33 21 47
NTRK3 0.021 0.077 0.12 26 -0.33 12 38
NT-4/5 (dimer)/TRKB 0.027 0.11 0.19 10 -0.22 39 49
neuron apoptosis 0.063 0.18 0.33 69 -0.24 2 71
SHC 2-3/Grb2 -0.069 0.19 0.28 1 -0.36 69 70
SHC1 0.026 0.009 -10000 0 -10000 0 0
SHC2 -0.089 0.21 -10000 0 -0.46 60 60
SHC3 -0.056 0.18 0.22 1 -0.41 48 49
STAT3 (dimer) 0.028 0.047 -10000 0 -0.29 6 6
NT3 (dimer)/TRKA 0.039 0.086 0.19 10 -0.19 29 39
RIN/GDP 0.025 0.096 0.26 15 -0.22 10 25
GIPC1 0.029 0.002 -10000 0 -10000 0 0
KRAS 0.028 0.005 -10000 0 -10000 0 0
DNAJA3 -0.018 0.087 0.18 1 -0.22 40 41
RIN/GTP 0.013 0.003 -10000 0 -10000 0 0
CCND1 0.009 0.085 0.29 3 -0.61 5 8
MAGED1 0.027 0.021 -10000 0 -0.33 1 1
PTPN11 0.028 0.004 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.025 0.018 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.051 0.02 -10000 0 -10000 0 0
GRB2 0.028 0.005 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.028 0.091 0.18 2 -0.22 32 34
TRKA/NEDD4-2 0.033 0.051 -10000 0 -0.23 9 9
ELMO1 0.015 0.062 -10000 0 -0.33 9 9
RhoG/GTP/ELMO1/DOCK1 0.026 0.04 -10000 0 -0.18 9 9
NGF 0.016 0.07 0.12 8 -0.33 11 19
HRAS 0.028 0.005 -10000 0 -10000 0 0
DOCK1 0.026 0.009 -10000 0 -10000 0 0
GAB2 0.027 0.008 -10000 0 -10000 0 0
RIT2 0.018 0.004 -10000 0 -10000 0 0
RIT1 0.026 0.008 -10000 0 -10000 0 0
FRS2 0.028 0.006 -10000 0 -10000 0 0
DNM1 0.025 0.039 0.12 7 -0.33 3 10
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.008 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.001 0.1 -10000 0 -0.23 40 40
mol:GDP 0.025 0.13 0.31 16 -0.31 12 28
NGF (dimer) 0.016 0.07 0.12 8 -0.33 11 19
RhoG/GDP 0.012 0.043 -10000 0 -0.23 9 9
RIT1/GDP 0.016 0.082 0.22 6 -0.22 10 16
TIAM1 0.011 0.076 -10000 0 -0.33 14 14
PIK3R1 0.025 0.03 -10000 0 -0.33 2 2
BDNF (dimer)/TRKB 0.013 0.12 0.18 8 -0.21 57 65
KIDINS220/CRKL/C3G 0.037 0.015 -10000 0 -10000 0 0
SHC/RasGAP 0.035 0.026 -10000 0 -0.23 2 2
FRS2 family/SHP2 0.049 0.022 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.062 0.033 -10000 0 -0.18 2 2
RIT1/GTP 0.019 0.006 -10000 0 -10000 0 0
NT3 (dimer) 0.033 0.036 0.12 27 -0.33 1 28
RAP1/GDP 0.012 0.067 0.14 4 -0.19 9 13
KIDINS220/CRKL 0.027 0.009 -10000 0 -10000 0 0
BDNF (dimer) -0.009 0.14 -10000 0 -0.33 42 42
ubiquitin-dependent protein catabolic process 0.04 0.065 0.18 1 -0.19 18 19
Schwann cell development -0.017 0.022 -10000 0 -10000 0 0
EHD4 0.027 0.006 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.06 0.029 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.019 0.046 -10000 0 -0.19 6 6
RAP1B 0.028 0.006 -10000 0 -10000 0 0
RAP1A 0.028 0.006 -10000 0 -10000 0 0
CDC42/GTP -0.001 0.12 0.18 3 -0.19 74 77
ABL1 0.027 0.008 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.041 0.009 -10000 0 -10000 0 0
Rap1/GTP 0.005 0.083 -10000 0 -0.3 7 7
STAT3 0.028 0.047 -10000 0 -0.29 6 6
axon guidance -0.015 0.1 -10000 0 -0.18 74 74
MAPK3 -0.012 0.091 0.2 26 -0.2 32 58
MAPK1 -0.011 0.083 0.19 24 -0.19 30 54
CDC42/GDP 0.029 0.097 0.26 15 -0.22 10 25
NTF3 0.033 0.036 0.12 27 -0.33 1 28
NTF4 0.025 0.018 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.038 0.071 0.18 1 -0.2 20 21
PI3K 0.035 0.042 -10000 0 -0.27 5 5
FRS3 0.026 0.009 -10000 0 -10000 0 0
FAIM 0.02 0.055 -10000 0 -0.33 7 7
GAB1 0.026 0.03 -10000 0 -0.33 2 2
RASGRF1 -0.032 0.099 0.16 2 -0.2 65 67
SOS1 0.029 0.003 -10000 0 -10000 0 0
MCF2L -0.006 0.081 0.22 5 -0.2 37 42
RGS19 0.026 0.008 -10000 0 -10000 0 0
CDC42 0.028 0.004 -10000 0 -10000 0 0
RAS family/GTP 0.04 0.088 0.32 4 -0.44 3 7
Rac1/GDP 0.021 0.09 0.25 12 -0.22 10 22
NGF (dimer)/TRKA/GRIT 0.026 0.056 0.16 1 -0.19 16 17
neuron projection morphogenesis -0.014 0.17 -10000 0 -0.82 8 8
NGF (dimer)/TRKA/NEDD4-2 0.04 0.065 0.18 1 -0.19 18 19
MAP2K1 0.005 0.068 0.19 34 -0.17 2 36
NGFR 0.01 0.11 0.12 40 -0.33 25 65
NGF (dimer)/TRKA/GIPC/GAIP 0.007 0.068 0.15 1 -0.21 24 25
RAS family/GTP/PI3K 0.018 0.034 -10000 0 -0.22 5 5
FRS2 family/SHP2/GRB2/SOS1 0.069 0.034 -10000 0 -10000 0 0
NRAS 0.027 0.007 -10000 0 -10000 0 0
GRB2/SOS1 0.041 0.009 -10000 0 -10000 0 0
PRKCI 0.027 0.021 -10000 0 -0.33 1 1
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.025 0.009 -10000 0 -10000 0 0
PRKCZ 0.015 0.065 -10000 0 -0.33 10 10
MAPKKK cascade -0.039 0.18 -10000 0 -0.57 29 29
RASA1 0.025 0.03 -10000 0 -0.33 2 2
TRKA/c-Abl 0.033 0.045 -10000 0 -0.22 7 7
SQSTM1 0.026 0.022 -10000 0 -0.33 1 1
BDNF (dimer)/TRKB/GIPC 0.028 0.11 0.19 8 -0.19 55 63
NGF (dimer)/TRKA/p62/Atypical PKCs 0.049 0.078 -10000 0 -0.17 26 26
MATK 0.005 0.099 -10000 0 -0.33 23 23
NEDD4L 0.026 0.03 -10000 0 -0.33 2 2
RAS family/GDP -0.014 0.042 -10000 0 -0.15 13 13
NGF (dimer)/TRKA -0.013 0.091 0.19 1 -0.22 41 42
Rac1/GTP -0.025 0.077 -10000 0 -0.2 34 34
FRS2 family/SHP2/CRK family 0.064 0.038 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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
USP8 -0.009 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.024 0.093 -10000 0 -0.25 7 7
NFATC4 -0.032 0.071 0.2 5 -0.21 11 16
ERBB2IP 0.025 0.036 -10000 0 -0.33 3 3
HSP90 (dimer) 0.027 0.021 -10000 0 -0.33 1 1
mammary gland morphogenesis 0.003 0.084 0.2 4 -0.19 36 40
JUN 0.019 0.078 0.22 7 -0.35 3 10
HRAS 0.028 0.006 -10000 0 -10000 0 0
DOCK7 -0.031 0.071 0.16 4 -0.19 26 30
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.02 0.083 0.23 3 -0.19 34 37
AKT1 -0.005 0.007 -10000 0 -10000 0 0
BAD -0.009 0.004 -10000 0 -10000 0 0
MAPK10 -0.012 0.065 0.17 10 -0.18 2 12
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.005 0.09 0.21 4 -0.2 36 40
RAF1 0.01 0.1 0.26 11 -0.27 9 20
ErbB2/ErbB3/neuregulin 2 0.003 0.084 0.22 2 -0.21 35 37
STAT3 0.007 0.15 -10000 0 -0.94 7 7
cell migration -0.008 0.071 0.22 11 -0.16 4 15
mol:PI-3-4-5-P3 -0.001 0.001 -10000 0 -10000 0 0
cell proliferation -0.022 0.24 0.39 3 -0.6 40 43
FOS 0.006 0.15 0.33 4 -0.33 40 44
NRAS 0.027 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0.003 0.084 0.2 4 -0.19 36 40
MAPK3 -0.012 0.2 0.35 4 -0.46 41 45
MAPK1 -0.016 0.2 0.38 2 -0.48 39 41
JAK2 -0.03 0.064 -10000 0 -0.2 20 20
NF2 0.01 0.012 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.006 0.069 -10000 0 -0.2 28 28
NRG1 0.012 0.093 -10000 0 -0.33 18 18
GRB2/SOS1 0.041 0.009 -10000 0 -10000 0 0
MAPK8 -0.009 0.089 0.23 2 -0.24 27 29
MAPK9 -0.011 0.056 0.18 6 -0.17 1 7
ERBB2 -0.024 0.048 0.3 3 -0.24 7 10
ERBB3 0.01 0.079 -10000 0 -0.33 15 15
SHC1 0.026 0.009 -10000 0 -10000 0 0
RAC1 0.025 0.009 -10000 0 -10000 0 0
apoptosis 0.007 0.009 -10000 0 -10000 0 0
STAT3 (dimer) 0.008 0.14 -10000 0 -0.91 7 7
RNF41 -0.013 0.007 -10000 0 -10000 0 0
FRAP1 -0.005 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.027 0.047 -10000 0 -0.15 28 28
ErbB2/ErbB2/HSP90 (dimer) -0.021 0.041 0.22 3 -0.2 8 11
CHRNA1 -0.027 0.24 0.33 4 -0.6 40 44
myelination -0.032 0.07 0.23 3 -0.25 4 7
PPP3CB -0.027 0.066 0.16 4 -0.18 26 30
KRAS 0.028 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.024 0.078 -10000 0 -0.18 22 22
NRG2 0.003 0.09 -10000 0 -0.33 20 20
mol:GDP -0.006 0.069 -10000 0 -0.2 29 29
SOS1 0.029 0.003 -10000 0 -10000 0 0
MAP2K2 -0.005 0.11 0.25 9 -0.31 10 19
SRC 0.025 0.022 -10000 0 -0.33 1 1
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.032 0.071 0.16 5 -0.19 29 34
MAP2K1 -0.006 0.18 0.4 1 -0.55 12 13
heart morphogenesis 0.003 0.084 0.2 4 -0.19 36 40
RAS family/GDP 0.029 0.091 -10000 0 -0.23 7 7
GRB2 0.028 0.006 -10000 0 -10000 0 0
PRKACA 0.015 0.007 -10000 0 -10000 0 0
CHRNE 0.011 0.027 0.079 10 -0.15 3 13
HSP90AA1 0.027 0.021 -10000 0 -0.33 1 1
activation of caspase activity 0.005 0.007 -10000 0 -10000 0 0
nervous system development 0.003 0.084 0.2 4 -0.19 36 40
CDC42 0.028 0.004 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.008 0.06 -10000 0 -0.23 20 20
TP53 -0.009 0.055 0.16 3 -0.21 13 16
Senescence -0.013 0.062 0.16 3 -0.21 18 21
Apoptosis -0.013 0.062 0.16 3 -0.21 18 21
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.009 0.07 0.21 26 -0.23 2 28
MDM4 0.024 0.023 -10000 0 -0.33 1 1
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.014 0.022 -10000 0 -0.2 4 4
SNTA1 0.023 0.037 0.12 1 -0.33 3 4
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.015 0.027 -10000 0 -0.2 6 6
MAPK12 -0.008 0.071 0.21 14 -0.19 24 38
CCND1 -0.002 0.067 -10000 0 -0.35 8 8
p38 gamma/SNTA1 0.008 0.071 0.2 13 -0.18 26 39
MAP2K3 0.027 0.007 -10000 0 -10000 0 0
PKN1 0.027 0.021 -10000 0 -0.33 1 1
G2/M transition checkpoint -0.008 0.07 0.2 14 -0.19 24 38
MAP2K6 -0.003 0.057 0.24 4 -0.21 16 20
MAPT -0.023 0.12 0.16 24 -0.27 41 65
MAPK13 0.008 0.029 -10000 0 -0.23 4 4
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.007 0.043 -10000 0 -0.25 8 8
Ras signaling in the CD4+ TCR 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
ERK1-2/ELK1 0.003 0.19 0.28 1 -0.53 27 28
MAP3K8 0.023 0.044 -10000 0 -0.33 4 4
FOS -0.015 0.19 0.25 1 -0.55 27 28
PRKCA 0.019 0.063 0.12 3 -0.33 9 12
PTPN7 0.003 0.097 -10000 0 -0.33 22 22
HRAS 0.028 0.005 -10000 0 -10000 0 0
PRKCB 0.003 0.11 -10000 0 -0.33 26 26
NRAS 0.027 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.051 0.017 -10000 0 -10000 0 0
MAPK3 -0.021 0.19 -10000 0 -0.56 29 29
MAP2K1 -0.011 0.14 -10000 0 -0.37 33 33
ELK1 0.03 0.003 -10000 0 -10000 0 0
BRAF -0.013 0.11 -10000 0 -0.35 27 27
mol:GTP 0 0 -10000 0 -10000 0 0
MAPK1 -0.02 0.19 -10000 0 -0.55 30 30
RAF1 -0.015 0.12 -10000 0 -0.36 30 30
KRAS 0.028 0.005 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.01 0.061 -10000 0 -0.2 23 23
EPHB2 0.008 0.084 -10000 0 -0.33 17 17
Syndecan-2/TACI 0.008 0.079 0.16 3 -0.19 37 40
LAMA1 -0.019 0.13 -10000 0 -0.33 44 44
Syndecan-2/alpha2 ITGB1 0.037 0.079 0.18 6 -0.19 24 30
HRAS 0.028 0.005 -10000 0 -10000 0 0
Syndecan-2/CASK 0.002 0.035 -10000 0 -0.18 10 10
ITGA5 0.026 0.038 -10000 0 -0.33 3 3
BAX -0.007 0.038 -10000 0 -10000 0 0
EPB41 0.026 0.03 -10000 0 -0.33 2 2
positive regulation of cell-cell adhesion 0.017 0.037 -10000 0 -0.17 11 11
LAMA3 0.024 0.063 0.12 18 -0.33 8 26
EZR 0.022 0.037 -10000 0 -0.33 3 3
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.025 0.022 -10000 0 -0.33 1 1
Syndecan-2/MMP2 0.014 0.068 0.24 1 -0.21 21 22
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.025 0.063 0.18 1 -0.23 16 17
dendrite morphogenesis 0.01 0.064 -10000 0 -0.21 21 21
Syndecan-2/GM-CSF 0.02 0.041 0.13 1 -0.19 9 10
determination of left/right symmetry 0.003 0.043 -10000 0 -0.22 10 10
Syndecan-2/PKC delta 0.018 0.044 -10000 0 -0.19 12 12
GNB2L1 0.027 0.007 -10000 0 -10000 0 0
MAPK3 0.015 0.06 0.19 23 -0.17 9 32
MAPK1 0.015 0.058 0.19 22 -0.17 7 29
Syndecan-2/RACK1 0.032 0.038 -10000 0 -0.16 9 9
NF1 0.024 0.036 -10000 0 -0.33 3 3
FGFR/FGF/Syndecan-2 0.003 0.043 -10000 0 -0.22 10 10
ITGA2 0.011 0.083 0.12 7 -0.33 16 23
MAPK8 -0.001 0.038 -10000 0 -0.18 12 12
Syndecan-2/alpha2/beta1 Integrin 0.012 0.1 0.2 6 -0.18 55 61
Syndecan-2/Kininogen 0.016 0.041 -10000 0 -0.19 10 10
ITGB1 0.026 0.011 0.12 1 -10000 0 1
SRC 0.019 0.052 0.18 22 -0.16 7 29
Syndecan-2/CASK/Protein 4.1 0.017 0.039 -10000 0 -0.17 12 12
extracellular matrix organization 0.019 0.051 -10000 0 -0.24 10 10
actin cytoskeleton reorganization 0.01 0.061 -10000 0 -0.19 23 23
Syndecan-2/Caveolin-2/Ras 0.03 0.043 -10000 0 -0.17 10 10
Syndecan-2/Laminin alpha3 0.02 0.058 0.13 1 -0.23 13 14
Syndecan-2/RasGAP 0.043 0.047 0.17 4 -0.15 11 15
alpha5/beta1 Integrin 0.037 0.032 0.18 1 -0.23 3 4
PRKCD 0.026 0.03 -10000 0 -0.33 2 2
Syndecan-2 dimer 0.01 0.064 -10000 0 -0.21 21 21
GO:0007205 0.002 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.027 0.043 0.18 2 -0.15 10 12
RHOA 0.029 0.003 -10000 0 -10000 0 0
SDCBP 0.024 0.03 -10000 0 -0.33 2 2
TNFRSF13B 0.001 0.12 -10000 0 -0.33 31 31
RASA1 0.025 0.03 -10000 0 -0.33 2 2
alpha2/beta1 Integrin 0.025 0.063 0.18 1 -0.23 16 17
Syndecan-2/Synbindin 0.018 0.04 -10000 0 -0.18 10 10
TGFB1 0.024 0.042 -10000 0 -0.33 4 4
CASP3 0.021 0.065 0.19 27 -0.17 12 39
FN1 0.009 0.084 0.12 2 -0.33 17 19
Syndecan-2/IL8 0.015 0.062 0.13 1 -0.19 21 22
SDC2 0.003 0.043 -10000 0 -0.22 10 10
KNG1 0.022 0.016 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.017 0.045 -10000 0 -0.19 13 13
TRAPPC4 0.025 0.009 -10000 0 -10000 0 0
CSF2 0.027 0.021 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.019 0.051 -10000 0 -0.24 10 10
Syndecan-2/Syntenin/PI-4-5-P2 0.018 0.038 -10000 0 -0.17 11 11
Syndecan-2/Ezrin 0.029 0.046 -10000 0 -0.17 13 13
PRKACA 0.02 0.065 0.19 26 -0.17 13 39
angiogenesis 0.015 0.061 0.13 1 -0.19 21 22
MMP2 0.015 0.083 -10000 0 -0.33 15 15
IL8 0.014 0.085 -10000 0 -0.33 16 16
calcineurin-NFAT signaling pathway 0.008 0.079 0.16 3 -0.19 37 40
IL1-mediated signaling events

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
UBC13/UEV1A 0.035 0.013 -10000 0 -10000 0 0
PRKCZ 0.015 0.065 -10000 0 -0.33 10 10
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.028 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.003 0.096 -10000 0 -0.3 19 19
IRAK/TOLLIP 0.027 0.011 -10000 0 -10000 0 0
IKBKB 0.028 0.006 -10000 0 -10000 0 0
IKBKG 0.029 0.003 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.033 0.072 0.18 5 -0.23 18 23
IL1A 0.035 0.028 0.12 27 -10000 0 27
IL1B -0.013 0.086 -10000 0 -0.26 29 29
IRAK/TRAF6/p62/Atypical PKCs 0.062 0.062 -10000 0 -0.18 10 10
IL1R2 0.011 0.089 0.12 14 -0.33 18 32
IL1R1 0.017 0.065 -10000 0 -0.33 10 10
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.007 0.099 0.23 2 -0.37 14 16
TOLLIP 0.028 0.005 -10000 0 -10000 0 0
TICAM2 0.021 0.046 -10000 0 -0.33 5 5
MAP3K3 0.028 0.005 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.017 0.013 -10000 0 -0.19 1 1
IKK complex/ELKS 0.022 0.079 0.25 2 -0.31 2 4
JUN -0.008 0.055 0.15 26 -10000 0 26
MAP3K7 0.025 0.022 -10000 0 -0.33 1 1
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.025 0.11 -10000 0 -0.21 47 47
IL1 alpha/IL1R1/IL1RAP/MYD88 0.059 0.073 0.19 1 -0.19 21 22
PIK3R1 0.025 0.03 -10000 0 -0.33 2 2
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.069 0.073 -10000 0 -0.18 21 21
IL1 beta fragment/IL1R1/IL1RAP 0.005 0.1 -10000 0 -0.22 47 47
NFKB1 0.028 0.005 -10000 0 -10000 0 0
MAPK8 -0.004 0.06 0.16 28 -0.16 3 31
IRAK1 0.002 0.015 -10000 0 -10000 0 0
IL1RN/IL1R1 0.023 0.078 -10000 0 -0.24 23 23
IRAK4 0.028 0.005 -10000 0 -10000 0 0
PRKCI 0.027 0.021 -10000 0 -0.33 1 1
TRAF6 0.028 0.005 -10000 0 -10000 0 0
PI3K 0.035 0.042 -10000 0 -0.27 5 5
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.009 0.1 -10000 0 -0.3 25 25
CHUK 0.025 0.022 -10000 0 -0.33 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.005 0.1 -10000 0 -0.22 47 47
IL1 beta/IL1R2 -0.004 0.1 -10000 0 -0.22 48 48
IRAK/TRAF6/TAK1/TAB1/TAB2 0.031 0.02 -10000 0 -0.16 1 1
NF kappa B1 p50/RelA 0.012 0.1 -10000 0 -0.22 36 36
IRAK3 0.019 0.063 -10000 0 -0.33 9 9
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.026 0.11 -10000 0 -0.2 47 47
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.014 0.065 -10000 0 -0.2 22 22
IL1 alpha/IL1R1/IL1RAP 0.046 0.072 0.18 1 -0.2 20 21
RELA 0.028 0.005 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.026 0.022 -10000 0 -0.33 1 1
MYD88 0.027 0.021 -10000 0 -0.33 1 1
IRAK/TRAF6/MEKK3 0.057 0.042 0.18 27 -10000 0 27
IL1RAP 0.017 0.069 0.12 6 -0.33 11 17
UBE2N 0.028 0.004 -10000 0 -10000 0 0
IRAK/TRAF6 0.001 0.083 -10000 0 -0.2 34 34
CASP1 0.008 0.079 -10000 0 -0.33 15 15
IL1RN/IL1R2 0.019 0.09 0.18 2 -0.24 31 33
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.019 0.11 0.19 1 -0.21 46 47
TMEM189-UBE2V1 0.021 0.009 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.018 0.084 -10000 0 -0.32 12 12
PIK3CA 0.023 0.042 -10000 0 -0.33 4 4
IL1RN 0.015 0.079 -10000 0 -0.33 14 14
TRAF6/TAK1/TAB1/TAB2 0.042 0.026 -10000 0 -0.16 1 1
MAP2K6 0.002 0.064 0.17 31 -0.16 8 39
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.025 0.031 0.12 1 -0.33 2 3
mol:S1P 0.001 0.002 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.03 0.098 -10000 0 -0.2 67 67
GNAO1 -0.037 0.14 0.12 4 -0.33 55 59
S1P/S1P3/G12/G13 0.045 0.034 -10000 0 -0.18 3 3
AKT1 -0.01 0.13 -10000 0 -0.5 16 16
AKT3 0.009 0.09 -10000 0 -1.1 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.025 0.031 0.12 1 -0.33 2 3
GNAI2 0.029 0.006 -10000 0 -10000 0 0
GNAI3 0.028 0.007 -10000 0 -10000 0 0
GNAI1 0.021 0.047 -10000 0 -0.33 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.027 0.041 0.12 9 -0.33 3 12
S1PR2 0.029 0.002 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.014 0.11 0.23 1 -0.23 42 43
MAPK3 -0.02 0.1 0.22 1 -0.22 41 42
MAPK1 -0.022 0.098 0.22 1 -0.22 42 43
JAK2 -0.031 0.13 0.21 6 -0.33 32 38
CXCR4 -0.022 0.1 0.22 1 -0.3 17 18
FLT1 0.028 0.023 0.13 1 -0.33 1 2
RhoA/GDP 0.021 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.007 -10000 0 -10000 0 0
SRC -0.018 0.1 0.22 4 -0.31 15 19
S1P/S1P3/Gi -0.015 0.11 0.23 1 -0.23 42 43
RAC1 0.025 0.009 -10000 0 -10000 0 0
RhoA/GTP -0.016 0.12 0.21 1 -0.28 26 27
VEGFA 0.028 0.028 0.12 8 -0.19 2 10
S1P/S1P2/Gi -0.019 0.1 -10000 0 -0.2 65 65
VEGFR1 homodimer/VEGFA homodimer 0.041 0.032 0.18 1 -0.18 3 4
RHOA 0.029 0.003 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.016 0.065 -10000 0 -0.26 13 13
GNAQ 0.027 0.008 -10000 0 -10000 0 0
GNAZ -0.002 0.1 -10000 0 -0.33 26 26
G12/G13 0.037 0.015 -10000 0 -10000 0 0
GNA14 0.034 0.048 -10000 0 -0.33 3 3
GNA15 0.019 0.062 0.12 3 -0.33 9 12
GNA12 0.025 0.009 -10000 0 -10000 0 0
GNA13 0.028 0.005 -10000 0 -10000 0 0
GNA11 0.029 0.003 -10000 0 -10000 0 0
Rac1/GTP -0.021 0.11 -10000 0 -0.28 25 25
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.01 0.019 -10000 0 -0.19 3 3
ADCY5 -0.022 0.057 0.24 1 -0.19 28 29
ADCY6 -0.011 0.018 -10000 0 -0.19 3 3
ADCY7 -0.009 0.011 -10000 0 -0.19 1 1
ADCY1 -0.033 0.064 -10000 0 -0.19 42 42
ADCY2 -0.038 0.083 0.24 2 -0.19 63 65
ADCY3 -0.009 0.011 -10000 0 -0.19 1 1
ADCY8 -0.006 0.01 -10000 0 -10000 0 0
PRKCE 0.006 0.001 -10000 0 -10000 0 0
ADCY9 -0.01 0.011 -10000 0 -0.19 1 1
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.007 0.076 0.2 13 -0.19 5 18
EPO signaling pathway

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
BCL2L1 0.029 0.091 0.36 1 -0.4 3 4
CRKL 0.006 0.061 0.16 23 -0.2 5 28
mol:DAG 0.013 0.06 -10000 0 -0.29 6 6
HRAS 0.007 0.084 0.27 10 -0.25 3 13
MAPK8 0.019 0.068 0.17 38 -0.2 6 44
RAP1A 0.007 0.064 0.16 25 -0.2 5 30
GAB1 0.005 0.069 0.16 25 -0.24 7 32
MAPK14 0.016 0.061 0.17 31 -0.2 4 35
EPO 0.022 0.026 0.13 6 -10000 0 6
PLCG1 0.013 0.061 -10000 0 -0.3 6 6
EPOR/TRPC2/IP3 Receptors 0.027 0.018 -10000 0 -10000 0 0
RAPGEF1 0.027 0.008 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.043 0.048 -10000 0 -0.22 6 6
GAB1/SHC/GRB2/SOS1 0.044 0.064 0.25 3 -0.23 4 7
EPO/EPOR (dimer) 0.035 0.029 -10000 0 -10000 0 0
IRS2 0.006 0.069 0.16 27 -0.2 8 35
STAT1 0.022 0.08 -10000 0 -0.28 13 13
STAT5B 0.016 0.068 -10000 0 -0.3 6 6
cell proliferation -0.001 0.063 0.17 27 -0.19 6 33
GAB1/SHIP/PIK3R1/SHP2/SHC 0.027 0.075 -10000 0 -0.26 12 12
TEC 0.001 0.069 0.16 22 -0.21 11 33
SOCS3 0.021 0.051 -10000 0 -0.33 6 6
STAT1 (dimer) 0.024 0.08 -10000 0 -0.28 13 13
JAK2 0.019 0.048 -10000 0 -0.33 5 5
PIK3R1 0.025 0.03 -10000 0 -0.33 2 2
EPO/EPOR (dimer)/JAK2 0.05 0.071 0.22 3 -0.17 17 20
EPO/EPOR 0.035 0.029 -10000 0 -10000 0 0
LYN 0.021 0.043 -10000 0 -0.33 4 4
TEC/VAV2 0.017 0.074 0.2 4 -0.19 18 22
elevation of cytosolic calcium ion concentration 0.027 0.018 -10000 0 -10000 0 0
SHC1 0.026 0.009 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.045 0.045 -10000 0 -0.22 4 4
mol:IP3 0.013 0.06 -10000 0 -0.29 6 6
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.033 0.09 0.27 4 -0.24 17 21
SH2B3 0.023 0.041 -10000 0 -0.35 3 3
NFKB1 0.022 0.067 0.17 41 -0.2 4 45
EPO/EPOR (dimer)/JAK2/SOCS3 0.009 0.036 -10000 0 -0.2 7 7
PTPN6 0.019 0.059 0.16 24 -0.21 7 31
TEC/VAV2/GRB2 0.027 0.073 0.22 3 -0.18 16 19
EPOR 0.027 0.019 -10000 0 -10000 0 0
INPP5D 0.014 0.075 0.12 5 -0.33 13 18
mol:GDP 0.043 0.064 0.25 3 -0.23 4 7
SOS1 0.029 0.003 -10000 0 -10000 0 0
PLCG2 0.022 0.052 -10000 0 -0.33 6 6
CRKL/CBL/C3G 0.032 0.059 0.23 2 -0.19 5 7
VAV2 0.006 0.069 0.16 27 -0.19 11 38
CBL 0.006 0.061 0.16 21 -0.21 6 27
SHC/Grb2/SOS1 0.027 0.05 -10000 0 -0.19 3 3
STAT5A 0.014 0.072 -10000 0 -0.27 11 11
GRB2 0.028 0.005 -10000 0 -10000 0 0
STAT5 (dimer) 0.026 0.086 -10000 0 -0.34 10 10
LYN/PLCgamma2 0.03 0.056 -10000 0 -0.28 8 8
PTPN11 0.028 0.004 -10000 0 -10000 0 0
BTK 0 0.08 0.16 25 -0.23 16 41
BCL2 0.02 0.15 0.34 1 -0.63 12 13
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.033 0.014 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.025 0.01 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.017 0.062 -10000 0 -0.33 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.027 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.015 0.01 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.021 0.046 -10000 0 -0.33 5 5
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.028 0.005 -10000 0 -10000 0 0
FYN 0.025 0.009 -10000 0 -10000 0 0
MAP3K12 0.028 0.004 -10000 0 -10000 0 0
FGR 0.014 0.075 -10000 0 -0.33 13 13
p38 alpha/TAB1 -0.057 0.13 -10000 0 -0.31 43 43
PRKG1 0.012 0.079 -10000 0 -0.33 14 14
DUSP8 0.017 0.074 -10000 0 -0.33 12 12
PGK/cGMP/p38 alpha -0.011 0.15 0.19 10 -0.32 37 47
apoptosis -0.055 0.12 -10000 0 -0.3 43 43
RAL/GTP 0.035 0.013 -10000 0 -10000 0 0
LYN 0.022 0.042 -10000 0 -0.33 4 4
DUSP1 0.027 0.025 -10000 0 -0.33 1 1
PAK1 0.027 0.008 -10000 0 -10000 0 0
SRC 0.025 0.022 -10000 0 -0.33 1 1
RAC1/OSM/MEKK3/MKK3 0.059 0.03 -10000 0 -10000 0 0
TRAF6 0.028 0.005 -10000 0 -10000 0 0
RAC1 0.025 0.009 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.026 0.009 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.034 0.014 -10000 0 -10000 0 0
MAPK11 -0.017 0.17 0.25 11 -0.38 37 48
BLK 0.003 0.12 0.12 45 -0.33 31 76
HCK 0.01 0.076 0.12 1 -0.33 14 15
MAP2K3 0.027 0.007 -10000 0 -10000 0 0
DUSP16 0.028 0.005 -10000 0 -10000 0 0
DUSP10 0.016 0.058 -10000 0 -0.33 8 8
TRAF6/MEKK3 0.035 0.008 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.01 0.17 0.2 18 -0.35 40 58
positive regulation of innate immune response -0.016 0.2 0.24 18 -0.4 42 60
LCK -0.018 0.13 0.12 22 -0.33 44 66
p38alpha-beta/MKP7 -0.007 0.19 0.26 12 -0.4 40 52
p38alpha-beta/MKP5 -0.016 0.18 0.25 7 -0.4 40 47
PGK/cGMP 0.009 0.054 -10000 0 -0.23 14 14
PAK2 0.029 0.003 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.005 0.19 0.27 13 -0.39 40 53
CDC42 0.028 0.004 -10000 0 -10000 0 0
RALB 0.029 0.002 -10000 0 -10000 0 0
RALA 0.026 0.009 -10000 0 -10000 0 0
PAK3 0.034 0.028 0.12 26 -10000 0 26
IL6-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
BCL2L1 0.035 0.2 0.54 3 -0.66 8 11
CRP 0.036 0.2 0.52 6 -0.63 10 16
cell cycle arrest 0.021 0.22 0.47 3 -0.69 13 16
TIMP1 0.043 0.19 0.54 1 -0.73 7 8
IL6ST 0.003 0.089 -10000 0 -0.3 22 22
Rac1/GDP 0.011 0.12 0.23 3 -0.34 19 22
AP1 0.069 0.12 -10000 0 -0.5 7 7
GAB2 0.028 0.009 -10000 0 -10000 0 0
TNFSF11 -0.018 0.31 0.54 1 -0.93 27 28
HSP90B1 0.037 0.11 -10000 0 -0.72 5 5
GAB1 0.027 0.03 -10000 0 -0.33 2 2
MAPK14 -0.001 0.13 0.26 1 -0.5 11 12
AKT1 0.023 0.089 -10000 0 -0.46 7 7
FOXO1 0.022 0.089 -10000 0 -0.44 7 7
MAP2K6 -0.006 0.1 0.28 1 -0.38 13 14
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 0.007 0.14 0.28 3 -0.36 21 24
MITF -0.005 0.1 0.23 4 -0.3 16 20
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.029 0.002 -10000 0 -10000 0 0
A2M -0.03 0.27 -10000 0 -1.3 12 12
CEBPB 0.03 0.012 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.028 0.1 -10000 0 -0.51 6 6
STAT3 0.017 0.23 0.48 3 -0.75 13 16
STAT1 0.016 0.084 -10000 0 -0.78 3 3
CEBPD 0.028 0.21 0.54 1 -0.67 14 15
PIK3CA 0.024 0.042 -10000 0 -0.33 4 4
PI3K 0.036 0.042 -10000 0 -0.27 5 5
JUN 0.029 0.009 0.12 2 -10000 0 2
PIAS3/MITF 0.016 0.12 0.23 20 -0.3 15 35
MAPK11 -0.001 0.13 0.26 1 -0.5 11 12
STAT3 (dimer)/FOXO1 0.017 0.18 -10000 0 -0.51 17 17
GRB2/SOS1/GAB family 0.042 0.12 -10000 0 -0.3 14 14
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.008 0.11 -10000 0 -0.24 39 39
GRB2 0.029 0.006 -10000 0 -10000 0 0
JAK2 0.018 0.047 -10000 0 -0.33 5 5
LBP 0.052 0.21 0.53 3 -0.7 12 15
PIK3R1 0.026 0.03 -10000 0 -0.33 2 2
JAK1 0.026 0.02 -10000 0 -10000 0 0
MYC 0.041 0.2 0.54 1 -0.67 10 11
FGG 0.022 0.19 0.48 2 -0.62 11 13
macrophage differentiation 0.021 0.22 0.47 3 -0.69 13 16
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.034 0.099 -10000 0 -0.18 39 39
JUNB 0.024 0.18 0.52 1 -0.6 11 12
FOS 0.031 0.016 0.12 8 -10000 0 8
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 0.006 0.095 0.17 1 -0.29 14 15
STAT1/PIAS1 0.033 0.11 0.31 1 -0.28 13 14
GRB2/SOS1/GAB family/SHP2/PI3K 0.027 0.093 -10000 0 -0.52 6 6
STAT3 (dimer) 0.019 0.23 0.47 3 -0.74 13 16
PRKCD 0.031 0.18 0.34 24 -0.44 20 44
IL6R 0.015 0.06 -10000 0 -0.28 10 10
SOCS3 0.004 0.2 0.45 3 -1 8 11
gp130 (dimer)/JAK1/JAK1/LMO4 0.033 0.081 -10000 0 -0.19 28 28
Rac1/GTP 0.01 0.13 0.23 1 -0.34 21 22
HCK 0.01 0.076 0.12 1 -0.33 14 15
MAPKKK cascade 0.042 0.12 0.34 1 -0.59 6 7
bone resorption -0.011 0.29 0.54 1 -0.86 27 28
IRF1 0.012 0.24 0.5 2 -0.77 16 18
mol:GDP 0.006 0.12 -10000 0 -0.34 19 19
SOS1 0.03 0.005 -10000 0 -10000 0 0
VAV1 0 0.11 0.17 1 -0.34 19 20
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.006 0.12 0.27 1 -0.39 15 16
PTPN11 0.015 0.092 -10000 0 -0.74 4 4
IL6/IL6RA 0.023 0.075 -10000 0 -0.24 18 18
gp130 (dimer)/TYK2/TYK2/LMO4 0.035 0.074 -10000 0 -0.19 25 25
gp130 (dimer)/JAK2/JAK2/LMO4 0.028 0.083 -10000 0 -0.22 25 25
IL6 0.017 0.08 0.13 18 -0.34 12 30
PIAS3 0.026 0.009 -10000 0 -10000 0 0
PTPRE 0.008 0.047 -10000 0 -0.31 5 5
PIAS1 0.028 0.004 -10000 0 -10000 0 0
RAC1 0.026 0.01 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0 0.077 0.14 1 -0.19 34 35
LMO4 0.021 0.048 -10000 0 -0.26 6 6
STAT3 (dimer)/PIAS3 0.016 0.2 -10000 0 -0.66 13 13
MCL1 0.038 0.097 0.32 2 -0.51 4 6
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.028 0.005 -10000 0 -10000 0 0
VLDLR 0.01 0.074 -10000 0 -0.33 13 13
LRPAP1 0.028 0.006 -10000 0 -10000 0 0
NUDC 0.028 0.004 -10000 0 -10000 0 0
RELN/LRP8 0.035 0.083 -10000 0 -0.19 30 30
CaM/Ca2+ 0.021 0.003 -10000 0 -10000 0 0
KATNA1 0.026 0.009 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0 0.083 0.2 29 -0.18 25 54
IQGAP1/CaM 0.04 0.01 -10000 0 -10000 0 0
DAB1 0.033 0.032 -10000 0 -10000 0 0
IQGAP1 0.028 0.005 -10000 0 -10000 0 0
PLA2G7 0 0.1 -10000 0 -0.33 24 24
CALM1 0.028 0.005 -10000 0 -10000 0 0
DYNLT1 0.026 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.039 0.019 -10000 0 -0.23 1 1
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.027 0.021 -10000 0 -0.33 1 1
CDK5R1 0.021 0.051 -10000 0 -0.33 6 6
LIS1/Poliovirus Protein 3A -0.008 0.003 -10000 0 -10000 0 0
CDK5R2 0.005 0.11 0.12 32 -0.33 27 59
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.023 0.099 0.18 11 -0.2 41 52
YWHAE 0.027 0.008 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.01 0.12 0.33 17 -0.25 10 27
MAP1B 0 0.036 -10000 0 -0.23 7 7
RAC1 0.01 0.006 -10000 0 -10000 0 0
p35/CDK5 -0.02 0.065 0.18 8 -0.22 5 13
RELN 0.005 0.12 0.12 51 -0.33 31 82
PAFAH/LIS1 0.011 0.06 -10000 0 -0.19 22 22
LIS1/CLIP170 0.026 0.01 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.002 0.078 -10000 0 -0.24 7 7
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.02 0.11 0.19 1 -0.28 32 33
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.003 0.11 0.26 28 -0.21 21 49
LIS1/IQGAP1 0.026 0.011 -10000 0 -10000 0 0
RHOA 0.012 0.005 -10000 0 -10000 0 0
PAFAH1B1 0.011 0.004 -10000 0 -10000 0 0
PAFAH1B3 0.028 0.004 -10000 0 -10000 0 0
PAFAH1B2 0.023 0.031 -10000 0 -0.33 2 2
MAP1B/LIS1/Dynein heavy chain 0.013 0.041 -10000 0 -0.15 7 7
NDEL1/Katanin 60/Dynein heavy chain 0.016 0.12 0.34 15 -0.25 10 25
LRP8 0.027 0.021 -10000 0 -0.33 1 1
NDEL1/Katanin 60 0.008 0.12 0.33 16 -0.25 11 27
P39/CDK5 -0.015 0.092 0.25 13 -0.18 17 30
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.026 0.011 -10000 0 -10000 0 0
CDK5 -0.017 0.057 0.18 9 -0.17 23 32
PPP2R5D 0.026 0.009 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.023 0.009 -10000 0 -10000 0 0
CSNK2A1 0.027 0.007 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.03 0.091 0.25 3 -0.17 38 41
RELN/VLDLR 0.032 0.095 -10000 0 -0.19 39 39
CDC42 0.012 0.005 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

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
PDGFRA 0.01 0.088 0.14 1 -0.33 18 19
PDGF/PDGFRA/CRKL 0.027 0.061 -10000 0 -0.22 16 16
positive regulation of JUN kinase activity 0.052 0.054 -10000 0 -0.17 12 12
CRKL 0.027 0.009 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 0.022 0.065 -10000 0 -0.22 18 18
AP1 -0.008 0.054 -10000 0 -10000 0 0
mol:IP3 -0.018 0.053 0.25 1 -0.23 15 16
PLCG1 -0.018 0.053 0.25 1 -0.23 15 16
PDGF/PDGFRA/alphaV Integrin 0.021 0.081 -10000 0 -0.24 24 24
RAPGEF1 0.027 0.008 -10000 0 -10000 0 0
CRK 0.027 0.008 -10000 0 -10000 0 0
mol:Ca2+ -0.018 0.053 0.25 1 -0.23 15 16
CAV3 0.02 0.013 0.12 4 -10000 0 4
CAV1 0.025 0.022 -10000 0 -0.33 1 1
SHC/Grb2/SOS1 0.054 0.055 -10000 0 -0.17 12 12
PDGF/PDGFRA/Shf 0.023 0.073 -10000 0 -0.22 23 23
FOS -0.013 0.047 0.31 1 -10000 0 1
JUN -0.019 0.015 -10000 0 -10000 0 0
oligodendrocyte development 0.021 0.08 -10000 0 -0.24 24 24
GRB2 0.028 0.005 -10000 0 -10000 0 0
PIK3R1 0.025 0.03 -10000 0 -0.33 2 2
mol:DAG -0.018 0.053 0.25 1 -0.23 15 16
PDGF/PDGFRA 0.01 0.088 0.14 1 -0.33 18 19
actin cytoskeleton reorganization 0.015 0.081 -10000 0 -0.22 29 29
SRF -0.01 0.008 -10000 0 -10000 0 0
SHC1 0.026 0.009 -10000 0 -10000 0 0
PI3K 0.038 0.07 -10000 0 -0.2 20 20
PDGF/PDGFRA/Crk/C3G 0.039 0.06 -10000 0 -0.18 18 18
JAK1 -0.019 0.053 -10000 0 -0.22 18 18
ELK1/SRF -0.013 0.053 0.15 15 -0.19 12 27
SHB 0.013 0.073 -10000 0 -0.33 12 12
SHF 0.023 0.047 0.12 3 -0.33 5 8
CSNK2A1 0.024 0.015 -10000 0 -10000 0 0
GO:0007205 -0.015 0.06 0.28 1 -0.26 15 16
SOS1 0.029 0.003 -10000 0 -10000 0 0
Ras protein signal transduction 0.052 0.054 -10000 0 -0.17 12 12
PDGF/PDGFRA/SHB 0.015 0.081 -10000 0 -0.22 29 29
PDGF/PDGFRA/Caveolin-1 0.025 0.062 -10000 0 -0.22 16 16
ITGAV 0.019 0.058 0.12 1 -0.33 8 9
ELK1 -0.015 0.051 0.24 2 -0.22 14 16
PIK3CA 0.023 0.042 -10000 0 -0.33 4 4
PDGF/PDGFRA/Crk 0.026 0.064 -10000 0 -0.22 18 18
JAK-STAT cascade -0.019 0.053 -10000 0 -0.22 18 18
cell proliferation 0.022 0.073 -10000 0 -0.22 23 23
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.01 0.082 -10000 0 -0.24 30 30
CRKL 0.027 0.009 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.007 -10000 0 -10000 0 0
DOCK1 0.026 0.009 -10000 0 -10000 0 0
ITGA4 0 0.1 0.12 7 -0.33 26 33
alpha4/beta7 Integrin/MAdCAM1 0.044 0.088 0.19 2 -0.18 37 39
EPO 0.025 0.019 0.12 8 -10000 0 8
alpha4/beta7 Integrin 0.009 0.094 -10000 0 -0.23 38 38
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.008 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.017 0.077 -10000 0 -0.22 26 26
EPO/EPOR (dimer) 0.038 0.017 -10000 0 -10000 0 0
lamellipodium assembly 0.006 0.074 -10000 0 -0.46 5 5
PIK3CA 0.023 0.042 -10000 0 -0.33 4 4
PI3K 0.035 0.042 -10000 0 -0.27 5 5
ARF6 0.028 0.004 -10000 0 -10000 0 0
JAK2 -0.001 0.08 -10000 0 -0.25 24 24
PXN 0.028 0.004 -10000 0 -10000 0 0
PIK3R1 0.025 0.03 -10000 0 -0.33 2 2
MADCAM1 0.032 0.023 -10000 0 -10000 0 0
cell adhesion 0.042 0.087 0.19 2 -0.18 37 39
CRKL/CBL 0.035 0.017 -10000 0 -10000 0 0
ITGB1 0.026 0.011 0.12 1 -10000 0 1
SRC -0.032 0.071 0.18 3 -0.2 37 40
ITGB7 0.014 0.075 0.12 4 -0.33 13 17
RAC1 0.025 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.02 0.099 -10000 0 -0.22 38 38
p130Cas/Crk/Dock1 0.012 0.082 0.19 3 -0.2 25 28
VCAM1 0.006 0.092 0.12 7 -0.33 20 27
RHOA 0.029 0.003 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.046 0.073 -10000 0 -0.17 26 26
BCAR1 -0.032 0.066 0.17 4 -0.19 35 39
EPOR 0.029 0.003 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.025 0.01 -10000 0 -10000 0 0
GIT1 0.028 0.005 -10000 0 -10000 0 0
Rac1/GTP 0.006 0.076 -10000 0 -0.48 5 5
Paxillin-dependent events mediated by a4b1

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
CRKL 0.027 0.009 -10000 0 -10000 0 0
Rac1/GDP 0.028 0.013 -10000 0 -10000 0 0
DOCK1 0.026 0.009 -10000 0 -10000 0 0
ITGA4 0 0.1 0.12 7 -0.33 26 33
RAC1 0.025 0.009 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.009 0.094 -10000 0 -0.23 38 38
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.008 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.033 0.072 -10000 0 -0.19 26 26
alpha4/beta7 Integrin/Paxillin 0.019 0.077 -10000 0 -0.18 37 37
lamellipodium assembly -0.002 0.1 -10000 0 -0.4 16 16
PIK3CA 0.023 0.042 -10000 0 -0.33 4 4
PI3K 0.035 0.042 -10000 0 -0.27 5 5
ARF6 0.028 0.004 -10000 0 -10000 0 0
TLN1 0.026 0.009 -10000 0 -10000 0 0
PXN 0.012 0.002 -10000 0 -10000 0 0
PIK3R1 0.025 0.03 -10000 0 -0.33 2 2
ARF6/GTP 0.037 0.063 -10000 0 -0.16 25 25
cell adhesion 0.035 0.065 -10000 0 -0.16 25 25
CRKL/CBL 0.035 0.017 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.025 0.064 -10000 0 -0.17 26 26
ITGB1 0.026 0.011 0.12 1 -10000 0 1
ITGB7 0.014 0.075 0.12 4 -0.33 13 17
ARF6/GDP 0.031 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.027 0.091 -10000 0 -0.19 38 38
p130Cas/Crk/Dock1 0.047 0.03 -10000 0 -0.2 2 2
VCAM1 0.006 0.092 0.12 7 -0.33 20 27
alpha4/beta1 Integrin/Paxillin/Talin 0.038 0.067 -10000 0 -0.16 25 25
alpha4/beta1 Integrin/Paxillin/GIT1 0.039 0.068 -10000 0 -0.17 26 26
BCAR1 0.025 0.03 -10000 0 -0.33 2 2
mol:GDP -0.036 0.066 0.16 26 -10000 0 26
CBL 0.025 0.01 -10000 0 -10000 0 0
PRKACA 0.029 0.002 -10000 0 -10000 0 0
GIT1 0.028 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.038 0.067 -10000 0 -0.16 25 25
Rac1/GTP -0.004 0.12 -10000 0 -0.44 16 16
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.009 0.12 0.21 15 -0.36 21 36
PDGFB-D/PDGFRB/SLAP 0.026 0.054 -10000 0 -0.22 12 12
PDGFB-D/PDGFRB/APS/CBL 0.039 0.046 -10000 0 -0.19 8 8
AKT1 0.009 0.088 0.33 9 -0.39 1 10
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.017 0.14 0.24 16 -0.4 21 37
PIK3CA 0.023 0.042 -10000 0 -0.33 4 4
FGR -0.004 0.15 0.3 3 -0.52 16 19
mol:Ca2+ 0.008 0.14 0.24 14 -0.45 19 33
MYC 0.045 0.15 0.4 15 -0.4 12 27
SHC1 0.026 0.009 -10000 0 -10000 0 0
HRAS/GDP 0.04 0.057 0.17 35 -0.2 4 39
LRP1/PDGFRB/PDGFB 0.049 0.03 -10000 0 -0.2 2 2
GRB10 0.021 0.042 -10000 0 -0.33 4 4
PTPN11 0.028 0.004 -10000 0 -10000 0 0
GO:0007205 0.007 0.14 0.24 14 -0.46 19 33
PTEN 0.025 0.01 -10000 0 -10000 0 0
GRB2 0.028 0.005 -10000 0 -10000 0 0
GRB7 0.034 0.028 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHP2 0.039 0.026 -10000 0 -0.23 2 2
PDGFB-D/PDGFRB/GRB10 0.032 0.04 -10000 0 -0.22 6 6
cell cycle arrest 0.026 0.054 -10000 0 -0.22 12 12
HRAS 0.028 0.005 -10000 0 -10000 0 0
HIF1A 0.003 0.082 0.28 11 -0.35 1 12
GAB1 0.004 0.14 0.29 6 -0.46 18 24
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.006 0.13 0.28 11 -0.4 18 29
PDGFB-D/PDGFRB 0.046 0.036 -10000 0 -0.21 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.038 0.026 -10000 0 -0.23 2 2
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.002 0.1 -10000 0 -0.32 20 20
positive regulation of MAPKKK cascade 0.038 0.026 -10000 0 -0.23 2 2
PIK3R1 0.025 0.03 -10000 0 -0.33 2 2
mol:IP3 0.007 0.14 0.24 14 -0.46 19 33
E5 -0.001 0.002 -10000 0 -10000 0 0
CSK 0.027 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.043 0.033 -10000 0 -0.24 2 2
SHB 0.013 0.073 -10000 0 -0.33 12 12
BLK -0.041 0.2 0.28 2 -0.51 38 40
PTPN2 0.027 0.022 -10000 0 -0.34 1 1
PDGFB-D/PDGFRB/SNX15 0.038 0.026 -10000 0 -0.23 2 2
BCAR1 0.025 0.03 -10000 0 -0.33 2 2
VAV2 0.005 0.16 0.29 11 -0.49 18 29
CBL 0.025 0.01 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.036 0.034 -10000 0 -0.23 4 4
LCK -0.058 0.22 -10000 0 -0.56 44 44
PDGFRB 0.025 0.032 0.12 1 -0.34 2 3
ACP1 0.028 0.004 -10000 0 -10000 0 0
HCK -0.014 0.16 -10000 0 -0.63 15 15
ABL1 -0.001 0.14 0.24 14 -0.41 21 35
PDGFB-D/PDGFRB/CBL -0.008 0.16 0.27 3 -0.52 21 24
PTPN1 0.027 0.011 0.12 1 -10000 0 1
SNX15 0.028 0.005 -10000 0 -10000 0 0
STAT3 0.028 0.005 -10000 0 -10000 0 0
STAT1 0.026 0.029 -10000 0 -0.33 2 2
cell proliferation 0.045 0.15 0.36 20 -0.36 13 33
SLA 0.014 0.065 -10000 0 -0.33 10 10
actin cytoskeleton reorganization 0.024 0.074 0.26 8 -0.24 2 10
SRC 0.012 0.063 -10000 0 -0.51 1 1
PI3K -0.021 0.032 -10000 0 -0.22 5 5
PDGFB-D/PDGFRB/GRB7/SHC 0.051 0.036 -10000 0 -0.2 2 2
SH2B2 0.019 0.051 -10000 0 -0.33 6 6
PLCgamma1/SPHK1 0.016 0.14 0.25 14 -0.41 21 35
LYN 0.009 0.091 0.34 1 -0.57 4 5
LRP1 0.028 0.005 -10000 0 -10000 0 0
SOS1 0.029 0.003 -10000 0 -10000 0 0
STAT5B 0.028 0.005 -10000 0 -10000 0 0
STAT5A 0.024 0.036 -10000 0 -0.33 3 3
NCK1-2/p130 Cas 0.065 0.05 -10000 0 -0.17 5 5
SPHK1 0.022 0.062 0.12 10 -0.33 8 18
EDG1 0.001 0.003 -10000 0 -10000 0 0
mol:DAG 0.007 0.14 0.24 14 -0.46 19 33
PLCG1 0.007 0.15 0.25 13 -0.48 19 32
NHERF/PDGFRB 0.05 0.034 -10000 0 -0.19 4 4
YES1 0.002 0.13 0.34 2 -0.57 10 12
cell migration 0.05 0.034 -10000 0 -0.19 4 4
SHC/Grb2/SOS1 0.061 0.048 -10000 0 -0.17 3 3
SLC9A3R2 0.028 0.022 -10000 0 -0.33 1 1
SLC9A3R1 0.027 0.022 0.12 1 -0.33 1 2
NHERF1-2/PDGFRB/PTEN 0.056 0.042 -10000 0 -0.18 4 4
FYN -0.027 0.17 0.28 2 -0.49 29 31
DOK1 0.017 0.067 0.18 39 -0.19 4 43
HRAS/GTP 0.021 0.004 -10000 0 -10000 0 0
PDGFB 0.027 0.011 -10000 0 -10000 0 0
RAC1 0.024 0.16 0.33 13 -0.45 18 31
PRKCD 0.025 0.064 0.18 37 -0.19 4 41
FER 0.022 0.067 0.18 35 -0.21 6 41
MAPKKK cascade 0.022 0.093 0.27 18 -10000 0 18
RASA1 0.024 0.066 0.18 37 -0.22 4 41
NCK1 0.028 0.005 -10000 0 -10000 0 0
NCK2 0.029 0.003 -10000 0 -10000 0 0
p62DOK/Csk 0.044 0.055 0.17 38 -0.17 4 42
PDGFB-D/PDGFRB/SHB 0.027 0.059 -10000 0 -0.23 13 13
chemotaxis 0 0.14 0.24 14 -0.4 21 35
STAT1-3-5/STAT1-3-5 0.052 0.048 -10000 0 -0.19 6 6
Bovine Papilomavirus E5/PDGFRB 0.018 0.022 0.089 1 -0.23 2 3
PTPRJ 0.026 0.03 -10000 0 -0.33 2 2
Visual signal transduction: Rods

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
mol:K + 0.028 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0.016 0.007 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.024 0.007 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.016 0.065 0.16 1 -0.19 25 26
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.021 0.01 0.12 2 -10000 0 2
GRK1 0.018 0.006 -10000 0 -10000 0 0
CNG Channel 0.022 0.08 -10000 0 -0.18 34 34
mol:Na + 0.033 0.057 0.16 1 -0.16 17 18
mol:ADP 0.018 0.006 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.04 0.072 -10000 0 -0.19 23 23
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.044 0.063 0.2 1 -0.17 17 18
CNGB1 0.025 0.016 -10000 0 -10000 0 0
RDH5 0.029 0.053 0.12 21 -0.33 5 26
SAG 0.018 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.004 0.11 0.3 34 -10000 0 34
Na + (4 Units) 0.026 0.052 -10000 0 -0.16 17 17
RGS9 0.018 0.085 0.12 26 -0.33 15 41
GNB1/GNGT1 0.029 0.041 -10000 0 -0.23 6 6
GNAT1/GDP 0.045 0.066 -10000 0 -0.16 23 23
GUCY2D 0.031 0.025 -10000 0 -10000 0 0
GNGT1 0.015 0.052 0.12 4 -0.33 6 10
GUCY2F 0.019 0.007 -10000 0 -10000 0 0
GNB5 0.024 0.036 -10000 0 -0.33 3 3
mol:GMP (4 units) -0.002 0.072 0.2 1 -0.19 34 35
mol:11-cis-retinal 0.029 0.053 0.12 21 -0.33 5 26
mol:cGMP 0.035 0.054 -10000 0 -0.17 15 15
GNB1 0.028 0.006 -10000 0 -10000 0 0
Rhodopsin 0.034 0.04 -10000 0 -0.23 5 5
SLC24A1 0.028 0.004 -10000 0 -10000 0 0
CNGA1 0.031 0.039 0.12 22 -0.33 2 24
Metarhodopsin II 0.023 0.008 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.047 0.062 0.18 1 -0.18 15 16
RGS9BP 0.018 0.062 0.12 3 -0.33 9 12
Metarhodopsin II/Transducin 0.008 0.029 -10000 0 -0.19 6 6
GCAP Family/Ca ++ 0.033 0.052 -10000 0 -0.18 15 15
PDE6A/B 0.027 0.064 -10000 0 -0.23 16 16
mol:Pi 0.039 0.071 -10000 0 -0.19 23 23
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.038 0.036 -10000 0 -0.18 6 6
PDE6B 0.009 0.082 -10000 0 -0.33 16 16
PDE6A 0.029 0.02 -10000 0 -10000 0 0
PDE6G 0.001 0.1 0.12 12 -0.33 25 37
RHO 0.019 0.006 -10000 0 -10000 0 0
PDE6 0.03 0.11 -10000 0 -0.19 51 51
GUCA1A 0.028 0.022 0.12 13 -10000 0 13
GC2/GCAP Family 0.043 0.057 -10000 0 -0.18 15 15
GUCA1C 0.018 0.008 0.12 1 -10000 0 1
GUCA1B 0.008 0.078 -10000 0 -0.33 15 15
Regulation of Androgen receptor activity

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
HDAC1 0.011 0.014 -10000 0 -0.23 1 1
SMARCC1 0.011 0.011 -10000 0 -10000 0 0
REL 0.026 0.03 -10000 0 -0.33 2 2
HDAC7 -0.011 0.094 0.18 18 -0.29 7 25
JUN 0.029 0.009 0.12 2 -10000 0 2
EP300 0.026 0.009 -10000 0 -10000 0 0
KAT2B 0.015 0.068 -10000 0 -0.33 11 11
KAT5 0.028 0.005 -10000 0 -10000 0 0
MAPK14 -0.003 0.044 -10000 0 -0.23 9 9
FOXO1 0.027 0.022 -10000 0 -0.33 1 1
T-DHT/AR 0.015 0.11 0.27 3 -0.22 19 22
MAP2K6 0.01 0.064 -10000 0 -0.33 9 9
BRM/BAF57 0.036 0.022 -10000 0 -0.23 1 1
MAP2K4 0.02 0.021 -10000 0 -10000 0 0
SMARCA2 0.024 0.023 -10000 0 -0.33 1 1
PDE9A -0.088 0.32 -10000 0 -0.89 38 38
NCOA2 0.021 0.042 -10000 0 -0.33 4 4
CEBPA 0.012 0.08 -10000 0 -0.33 15 15
EHMT2 0.026 0.009 -10000 0 -10000 0 0
cell proliferation 0.003 0.16 0.31 21 -0.34 22 43
NR0B1 -0.026 0.15 -10000 0 -0.33 53 53
EGR1 0.029 0.028 -10000 0 -0.33 1 1
RXRs/9cRA 0.001 0.087 -10000 0 -0.17 55 55
AR/RACK1/Src 0.019 0.091 0.21 16 -0.21 8 24
AR/GR 0.008 0.082 0.22 1 -0.23 20 21
GNB2L1 0.027 0.007 -10000 0 -10000 0 0
PKN1 0.028 0.021 -10000 0 -0.33 1 1
RCHY1 0.029 0.003 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -10000 0 -0.011 1 1
MAPK8 0.002 0.031 -10000 0 -0.23 3 3
T-DHT/AR/TIF2/CARM1 0.014 0.086 0.25 3 -0.21 16 19
SRC 0 0.073 0.18 33 -0.17 8 41
NR3C1 0.02 0.051 -10000 0 -0.33 6 6
KLK3 -0.028 0.089 -10000 0 -10000 0 0
APPBP2 0.021 0.02 -10000 0 -10000 0 0
TRIM24 0.026 0.009 -10000 0 -10000 0 0
T-DHT/AR/TIP60 0.004 0.078 0.19 19 -0.2 14 33
TMPRSS2 -0.036 0.22 -10000 0 -0.83 19 19
RXRG -0.05 0.15 0.12 2 -0.33 64 66
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.027 0.008 -10000 0 -10000 0 0
RXRB 0.026 0.009 -10000 0 -10000 0 0
CARM1 0.028 0.006 -10000 0 -10000 0 0
NR2C2 0.026 0.03 -10000 0 -0.33 2 2
KLK2 0.005 0.13 0.25 5 -0.49 12 17
AR 0.004 0.069 0.14 21 -0.24 12 33
SENP1 0.028 0.005 -10000 0 -10000 0 0
HSP90AA1 0.027 0.021 -10000 0 -0.33 1 1
MDM2 0.024 0.03 -10000 0 -0.33 2 2
SRY -0.001 0.002 -10000 0 -10000 0 0
GATA2 0.023 0.048 0.12 5 -0.33 5 10
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 -0.068 0.16 0.12 3 -0.33 83 86
T-DHT/AR/RACK1/Src 0.016 0.089 0.21 20 -0.21 7 27
positive regulation of transcription 0.023 0.048 0.12 5 -0.33 5 10
DNAJA1 0.019 0.021 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.02 -10000 0 -0.21 2 2
NCOA1 0.031 0.011 -10000 0 -10000 0 0
SPDEF 0.028 0.022 0.13 5 -10000 0 5
T-DHT/AR/TIF2 0.008 0.11 0.24 13 -0.3 16 29
T-DHT/AR/Hsp90 0.006 0.079 0.19 17 -0.2 11 28
GSK3B 0.028 0.007 -10000 0 -10000 0 0
NR2C1 0.028 0.004 -10000 0 -10000 0 0
mol:T-DHT -0.017 0.046 0.21 4 -0.18 9 13
SIRT1 0.024 0.03 -10000 0 -0.33 2 2
ZMIZ2 0.025 0.009 -10000 0 -10000 0 0
POU2F1 0.019 0.051 -10000 0 -0.1 36 36
T-DHT/AR/DAX-1 -0.019 0.1 0.23 10 -0.22 22 32
CREBBP 0.028 0.004 -10000 0 -10000 0 0
SMARCE1 0.028 0.005 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 0.016 0.068 -10000 0 -0.33 11 11
ANTXR2 0.023 0.052 0.12 5 -0.33 6 11
negative regulation of myeloid dendritic cell antigen processing and presentation -0.004 0.011 -10000 0 -0.048 16 16
monocyte activation -0.031 0.15 -10000 0 -0.42 37 37
MAP2K2 0.014 0.035 -10000 0 -0.57 1 1
MAP2K1 -0.007 0.01 -10000 0 -0.074 1 1
MAP2K7 -0.007 0.01 -10000 0 -0.074 1 1
MAP2K6 -0.012 0.028 -10000 0 -0.15 10 10
CYAA -0.016 0.037 -10000 0 -0.17 16 16
MAP2K4 -0.006 0.009 -10000 0 -10000 0 0
IL1B -0.022 0.064 0.11 2 -0.2 28 30
Channel 0.025 0.051 -10000 0 -0.18 16 16
NLRP1 -0.01 0.027 -10000 0 -0.18 7 7
CALM1 0.028 0.005 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.001 0.066 -10000 0 -0.39 8 8
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.004 0.011 0.048 16 -10000 0 16
MAPK3 -0.007 0.01 -10000 0 -0.074 1 1
MAPK1 -0.006 0.009 -10000 0 -0.074 1 1
PGR -0.011 0.028 -10000 0 -0.16 9 9
PA/Cellular Receptors 0.026 0.056 -10000 0 -0.2 16 16
apoptosis -0.004 0.011 -10000 0 -0.048 16 16
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.025 0.049 -10000 0 -0.18 16 16
macrophage activation -0.001 0.04 0.17 15 -10000 0 15
TNF 0.009 0.089 0.12 16 -0.33 18 34
VCAM1 -0.031 0.15 -10000 0 -0.42 36 36
platelet activation -0.001 0.066 -10000 0 -0.39 8 8
MAPKKK cascade 0.004 0.02 0.079 2 -0.066 11 13
IL18 -0.013 0.046 0.11 2 -0.19 15 17
negative regulation of macrophage activation -0.004 0.011 -10000 0 -0.048 16 16
LEF -0.004 0.011 -10000 0 -0.049 16 16
CASP1 -0.007 0.032 -10000 0 -0.12 17 17
mol:cAMP -0.001 0.066 -10000 0 -0.39 8 8
necrosis -0.004 0.011 -10000 0 -0.048 16 16
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.025 0.048 -10000 0 -0.17 16 16
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.006 0.002 -10000 0 -10000 0 0
GNB1/GNG2 0.037 0.067 -10000 0 -0.17 25 25
regulation of S phase of mitotic cell cycle 0.011 0.054 -10000 0 -0.2 16 16
GNAO1 -0.037 0.14 0.12 4 -0.33 55 59
HRAS 0.028 0.005 -10000 0 -10000 0 0
SHBG/T-DHT 0.017 0.019 -10000 0 -0.19 2 2
PELP1 0.027 0.008 -10000 0 -10000 0 0
AKT1 0.006 0.001 -10000 0 -10000 0 0
MAP2K1 0.002 0.063 0.18 27 -10000 0 27
T-DHT/AR 0.016 0.052 0.089 21 -0.23 12 33
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.029 0.003 -10000 0 -10000 0 0
GNAI3 0.028 0.006 -10000 0 -10000 0 0
GNAI1 0.02 0.047 -10000 0 -0.33 5 5
mol:GDP -0.009 0.065 -10000 0 -0.29 13 13
cell proliferation 0.015 0.07 0.26 8 -10000 0 8
PIK3CA 0.023 0.042 -10000 0 -0.33 4 4
FOS 0.022 0.051 -10000 0 -10000 0 0
mol:Ca2+ -0.009 0.024 0.036 1 -0.05 61 62
MAPK3 0.008 0.065 0.29 3 -10000 0 3
MAPK1 0.015 0.053 0.2 2 -0.31 4 6
PIK3R1 0.025 0.03 -10000 0 -0.33 2 2
mol:IP3 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.001 0.026 0.22 1 -0.15 2 3
GNG2 0.013 0.073 -10000 0 -0.33 13 13
potassium channel inhibitor activity 0 0 -10000 0 -10000 0 0
HRAS/GTP 0.044 0.046 -10000 0 -0.15 11 11
actin cytoskeleton reorganization 0.033 0.034 -10000 0 -0.18 5 5
SRC 0.025 0.022 -10000 0 -0.33 1 1
voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
PI3K 0.032 0.036 -10000 0 -0.22 5 5
apoptosis -0.023 0.056 0.22 1 -0.25 3 4
T-DHT/AR/PELP1 0.032 0.047 -10000 0 -0.19 11 11
HRAS/GDP 0.007 0.066 -10000 0 -0.28 13 13
CREB1 0.023 0.057 0.25 3 -0.24 1 4
RAC1-CDC42/GTP 0.042 0.038 -10000 0 -0.19 5 5
AR 0.02 0.076 -10000 0 -0.33 12 12
GNB1 0.028 0.006 -10000 0 -10000 0 0
RAF1 0.005 0.066 0.19 27 -10000 0 27
RAC1-CDC42/GDP 0.027 0.069 -10000 0 -0.27 11 11
T-DHT/AR/PELP1/Src 0.043 0.049 -10000 0 -0.17 11 11
MAP2K2 0.001 0.063 0.18 26 -10000 0 26
T-DHT/AR/PELP1/Src/PI3K 0.011 0.054 -10000 0 -0.2 16 16
GNAZ -0.002 0.1 -10000 0 -0.33 26 26
SHBG 0.025 0.032 -10000 0 -0.33 2 2
Gi family/GNB1/GNG2/GDP -0.057 0.14 -10000 0 -0.31 56 56
mol:T-DHT 0 0 -10000 0 -10000 0 0
RAC1 0.025 0.009 -10000 0 -10000 0 0
GNRH1 -0.002 0.042 -10000 0 -0.23 10 10
Gi family/GTP -0.032 0.088 -10000 0 -0.22 37 37
CDC42 0.028 0.004 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 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
EP300 0.026 0.017 -10000 0 -10000 0 0
HSPA8 0.024 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.036 0.078 0.21 7 -0.21 12 19
AKT1 0.016 0.039 -10000 0 -10000 0 0
GSC -0.035 0.26 -10000 0 -1.2 12 12
NKX2-5 -0.01 0.14 -10000 0 -0.33 43 43
muscle cell differentiation -0.015 0.084 0.32 5 -10000 0 5
SMAD2-3/SMAD4/SP1 0.055 0.1 -10000 0 -0.2 13 13
SMAD4 0.017 0.048 -10000 0 -0.14 5 5
CBFB 0.028 0.006 -10000 0 -10000 0 0
SAP18 0.027 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.025 0.088 -10000 0 -0.19 37 37
SMAD3/SMAD4/VDR 0.074 0.063 -10000 0 -0.21 6 6
MYC 0.024 0.031 -10000 0 -0.33 1 1
CDKN2B -0.26 0.51 -10000 0 -1.5 39 39
AP1 0.037 0.05 0.2 2 -0.17 2 4
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.007 0.073 -10000 0 -0.31 5 5
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.027 0.12 -10000 0 -0.33 35 35
SP3 0.026 0.031 -10000 0 -0.33 2 2
CREB1 0.029 0.002 -10000 0 -10000 0 0
FOXH1 0.017 0.047 -10000 0 -0.16 14 14
SMAD3/SMAD4/GR 0.039 0.07 -10000 0 -0.19 10 10
GATA3 -0.009 0.12 -10000 0 -0.32 34 34
SKI/SIN3/HDAC complex/NCoR1 0.013 0.058 -10000 0 -0.35 3 3
MEF2C/TIF2 -0.01 0.1 0.24 4 -0.26 20 24
endothelial cell migration 0.01 0.24 1.1 12 -10000 0 12
MAX 0.026 0.015 -10000 0 -10000 0 0
RBBP7 0.029 0.003 -10000 0 -10000 0 0
RBBP4 0.028 0.005 -10000 0 -10000 0 0
RUNX2 0.016 0.058 -10000 0 -0.33 8 8
RUNX3 -0.013 0.11 -10000 0 -0.33 34 34
RUNX1 0.021 0.051 -10000 0 -0.33 6 6
CTBP1 0.027 0.006 -10000 0 -10000 0 0
NR3C1 0.018 0.052 -10000 0 -0.33 6 6
VDR 0.022 0.046 -10000 0 -0.33 5 5
CDKN1A -0.007 0.16 -10000 0 -1 6 6
KAT2B 0.015 0.068 -10000 0 -0.33 11 11
SMAD2/SMAD2/SMAD4/FOXH1 0.033 0.086 -10000 0 -0.26 15 15
DCP1A 0.028 0.004 -10000 0 -10000 0 0
SKI 0.027 0.006 -10000 0 -10000 0 0
SERPINE1 -0.011 0.24 -10000 0 -1.1 12 12
SMAD3/SMAD4/ATF2 0.043 0.065 -10000 0 -0.18 8 8
SMAD3/SMAD4/ATF3 0.041 0.064 -10000 0 -0.2 6 6
SAP30 0.029 0.007 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.048 0.036 0.2 1 -10000 0 1
JUN 0.019 0.042 0.17 1 -0.17 2 3
SMAD3/SMAD4/IRF7 0.042 0.07 -10000 0 -0.2 8 8
TFE3 0.029 0.018 -10000 0 -10000 0 0
COL1A2 0.003 0.13 -10000 0 -0.72 9 9
mesenchymal cell differentiation -0.035 0.073 0.21 12 -10000 0 12
DLX1 -0.005 0.12 -10000 0 -0.33 36 36
TCF3 0.028 0.004 -10000 0 -10000 0 0
FOS 0.033 0.022 0.14 7 -10000 0 7
SMAD3/SMAD4/Max 0.046 0.064 -10000 0 -0.18 4 4
Cbp/p300/SNIP1 0.051 0.025 -10000 0 -10000 0 0
ZBTB17 0.026 0.016 -10000 0 -10000 0 0
LAMC1 0.012 0.043 0.18 1 -0.2 1 2
TGIF2/HDAC complex/SMAD3/SMAD4 0.042 0.06 -10000 0 -0.19 4 4
IRF7 0.023 0.047 -10000 0 -0.33 5 5
ESR1 0.014 0.065 0.13 2 -0.33 9 11
HNF4A 0.025 0.022 0.12 12 -10000 0 12
MEF2C -0.007 0.11 0.22 22 -0.27 19 41
SMAD2-3/SMAD4 0.038 0.082 -10000 0 -0.2 8 8
Cbp/p300/Src-1 0.052 0.029 -10000 0 -10000 0 0
IGHV3OR16-13 0.003 0.034 -10000 0 -0.33 2 2
TGIF2/HDAC complex 0.025 0.022 -10000 0 -0.33 1 1
CREBBP 0.028 0.014 -10000 0 -10000 0 0
SKIL 0.014 0.071 -10000 0 -0.33 12 12
HDAC1 0.027 0.021 -10000 0 -0.33 1 1
HDAC2 0.026 0.009 -10000 0 -10000 0 0
SNIP1 0.028 0.005 -10000 0 -10000 0 0
GCN5L2 0.001 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.051 0.065 -10000 0 -0.17 4 4
MSG1/HSC70 0.006 0.094 -10000 0 -0.23 40 40
SMAD2 0.014 0.046 -10000 0 -0.13 12 12
SMAD3 0.018 0.052 -10000 0 -0.2 6 6
SMAD3/E2F4-5/DP1/p107/SMAD4 0.014 0.047 -10000 0 -0.19 10 10
SMAD2/SMAD2/SMAD4 0.008 0.06 0.2 3 -0.22 11 14
NCOR1 0.027 0.007 -10000 0 -10000 0 0
NCOA2 0.021 0.042 -10000 0 -0.33 4 4
NCOA1 0.028 0.005 -10000 0 -10000 0 0
MYOD/E2A 0.041 0.018 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.061 0.11 -10000 0 -0.18 23 23
IFNB1 0.006 0.043 0.21 1 -0.2 3 4
SMAD3/SMAD4/MEF2C 0.015 0.12 0.24 2 -0.26 18 20
CITED1 -0.013 0.13 -10000 0 -0.33 40 40
SMAD2-3/SMAD4/ARC105 0.051 0.079 -10000 0 -0.16 6 6
RBL1 0.024 0.03 -10000 0 -0.33 2 2
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.033 0.18 -10000 0 -0.49 37 37
RUNX1-3/PEBPB2 0.02 0.087 -10000 0 -0.2 39 39
SMAD7 0.031 0.072 -10000 0 -0.48 2 2
MYC/MIZ-1 0.035 0.039 0.18 5 -0.23 1 6
SMAD3/SMAD4 0.015 0.099 0.28 8 -0.34 11 19
IL10 -0.013 0.11 -10000 0 -0.29 29 29
PIASy/HDAC complex 0.023 0.019 -10000 0 -10000 0 0
PIAS3 0.025 0.013 -10000 0 -10000 0 0
CDK2 0.017 0.063 -10000 0 -0.33 9 9
IL5 -0.012 0.081 -10000 0 -0.22 29 29
CDK4 0.027 0.015 -10000 0 -10000 0 0
PIAS4 0.023 0.019 -10000 0 -10000 0 0
ATF3 0.025 0.033 0.12 5 -0.33 2 7
SMAD3/SMAD4/SP1 0.047 0.081 -10000 0 -0.19 10 10
FOXG1 0.003 0.091 -10000 0 -0.33 17 17
FOXO3 0.001 0.038 -10000 0 -0.13 4 4
FOXO1 0 0.041 -10000 0 -0.15 4 4
FOXO4 0 0.041 -10000 0 -0.13 5 5
heart looping -0.007 0.11 0.22 22 -0.26 19 41
CEBPB 0.018 0.027 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.023 0.1 0.2 1 -0.21 39 40
MYOD1 0.028 0.022 0.12 14 -10000 0 14
SMAD3/SMAD4/HNF4 0.042 0.059 -10000 0 -0.18 3 3
SMAD3/SMAD4/GATA3 0.022 0.12 -10000 0 -0.24 39 39
SnoN/SIN3/HDAC complex/NCoR1 0.014 0.071 -10000 0 -0.33 12 12
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.035 0.1 -10000 0 -0.19 39 39
SMAD3/SMAD4/SP1-3 0.061 0.087 -10000 0 -0.19 10 10
MED15 0.027 0.008 -10000 0 -10000 0 0
SP1 0.02 0.037 -10000 0 -0.12 10 10
SIN3B 0.029 0.003 -10000 0 -10000 0 0
SIN3A 0.028 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.021 0.12 -10000 0 -0.2 54 54
ITGB5 0.004 0.064 0.18 1 -0.27 6 7
TGIF/SIN3/HDAC complex/CtBP 0.019 0.053 -10000 0 -0.35 2 2
SMAD3/SMAD4/AR 0.041 0.082 -10000 0 -0.21 15 15
AR 0.02 0.076 -10000 0 -0.33 12 12
negative regulation of cell growth 0.024 0.054 -10000 0 -0.27 3 3
SMAD3/SMAD4/MYOD 0.046 0.061 -10000 0 -0.17 5 5
E2F5 0.018 0.055 -10000 0 -0.33 7 7
E2F4 0.028 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.051 0.08 -10000 0 -0.19 15 15
SMAD2-3/SMAD4/FOXO1-3a-4 -0.02 0.13 -10000 0 -0.36 35 35
TFDP1 0.027 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.058 0.06 0.23 1 -0.18 2 3
SMAD3/SMAD4/RUNX2 0.035 0.073 -10000 0 -0.21 12 12
TGIF2 0.025 0.022 -10000 0 -0.33 1 1
TGIF1 0.026 0.022 -10000 0 -0.33 1 1
ATF2 0.025 0.036 -10000 0 -0.33 3 3
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.026 0.03 -10000 0 -0.33 2 2
SPHK1 0.021 0.061 0.12 10 -0.33 8 18
GNAI2 0.029 0.003 -10000 0 -10000 0 0
mol:S1P 0.002 0.057 -10000 0 -0.24 15 15
GNAO1 -0.037 0.14 0.12 4 -0.33 55 59
mol:Sphinganine-1-P 0.005 0.045 -10000 0 -0.23 10 10
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.043 0.062 -10000 0 -0.18 14 14
GNAI3 0.028 0.006 -10000 0 -10000 0 0
G12/G13 0.037 0.015 -10000 0 -10000 0 0
S1PR3 0.026 0.04 0.12 9 -0.33 3 12
S1PR2 0.029 0.002 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P -0.003 0.051 -10000 0 -0.2 15 15
S1PR5 0.026 0.05 -10000 0 -0.33 5 5
S1PR4 0.005 0.099 -10000 0 -0.33 23 23
GNAI1 0.02 0.047 -10000 0 -0.33 5 5
S1P/S1P5/G12 0.031 0.066 -10000 0 -0.19 17 17
S1P/S1P3/Gq -0.004 0.12 -10000 0 -0.36 26 26
S1P/S1P4/Gi -0.032 0.13 0.19 2 -0.36 25 27
GNAQ 0.027 0.008 -10000 0 -10000 0 0
GNAZ -0.002 0.1 -10000 0 -0.33 26 26
GNA14 0.034 0.048 -10000 0 -0.33 3 3
GNA15 0.019 0.062 0.12 3 -0.33 9 12
GNA12 0.025 0.009 -10000 0 -10000 0 0
GNA13 0.028 0.005 -10000 0 -10000 0 0
GNA11 0.029 0.003 -10000 0 -10000 0 0
ABCC1 0.02 0.055 -10000 0 -0.33 7 7