PARADIGM pathway analysis of mRNA expression and copy number data
Glioblastoma Multiforme (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1N29V1V
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): PARADIGM pathway analysis of mRNA expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1N29V1V
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 31 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
Glypican 2 network 212
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 94
LPA receptor mediated events 76
amb2 Integrin signaling 75
Endothelins 72
Ceramide signaling pathway 69
TCGA08_retinoblastoma 65
TCGA08_p53 64
BARD1 signaling events 57
HIF-2-alpha transcription factor network 55
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 529 . 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 ( 529 ).

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
Glypican 2 network 0.4008 212 849 4 -0.022 0 1000 -1000 0 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1777 94 6454 68 -0.24 0.065 1000 -1000 -0.047 -1000
LPA receptor mediated events 0.1437 76 7783 102 -0.038 0.046 1000 -1000 -0.06 -1000
amb2 Integrin signaling 0.1418 75 6195 82 -0.043 0.045 1000 -1000 -0.01 -1000
Endothelins 0.1361 72 6963 96 -0.47 0.032 1000 -1000 -0.033 -1000
Ceramide signaling pathway 0.1304 69 5267 76 -0.092 0.065 1000 -1000 -0.021 -1000
TCGA08_retinoblastoma 0.1229 65 525 8 -0.073 0.081 1000 -1000 -0.003 -1000
TCGA08_p53 0.1210 64 449 7 -0.007 0.029 1000 -1000 -0.012 -1000
BARD1 signaling events 0.1078 57 3259 57 -0.043 0.062 1000 -1000 -0.046 -1000
HIF-2-alpha transcription factor network 0.1040 55 2402 43 -0.075 0.043 1000 -1000 -0.029 -1000
EPO signaling pathway 0.1021 54 3002 55 -0.005 0.061 1000 -1000 -0.022 -1000
Arf6 signaling events 0.0870 46 2874 62 0 0.081 1000 -1000 -0.005 -1000
Osteopontin-mediated events 0.0775 41 1566 38 -0.083 0.044 1000 -1000 -0.018 -1000
Syndecan-1-mediated signaling events 0.0756 40 1380 34 -0.035 0.032 1000 -1000 -0.013 -1000
Aurora B signaling 0.0756 40 2703 67 -0.039 0.049 1000 -1000 -0.02 -1000
HIF-1-alpha transcription factor network 0.0737 39 2966 76 -0.095 0.035 1000 -1000 -0.033 -1000
Wnt signaling 0.0737 39 279 7 0 0.032 1000 -1000 0.001 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0737 39 3071 78 -0.037 0.038 1000 -1000 -0.029 -1000
Syndecan-4-mediated signaling events 0.0681 36 2432 67 -0.056 0.032 1000 -1000 -0.03 -1000
Ras signaling in the CD4+ TCR pathway 0.0681 36 616 17 -0.003 0.031 1000 -1000 -0.013 -1000
Caspase cascade in apoptosis 0.0624 33 2487 74 -0.055 0.054 1000 -1000 -0.023 -1000
PDGFR-alpha signaling pathway 0.0624 33 1453 44 -0.04 0.049 1000 -1000 -0.023 -1000
PLK1 signaling events 0.0605 32 2797 85 -0.039 0.056 1000 -1000 -0.014 -1000
VEGFR1 specific signals 0.0605 32 1847 56 -0.037 0.052 1000 -1000 -0.022 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0586 31 1437 45 -0.06 0.054 1000 -1000 -0.018 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0567 30 3818 125 -0.047 0.044 1000 -1000 -0.033 -1000
Signaling events regulated by Ret tyrosine kinase 0.0548 29 2428 82 -0.043 0.048 1000 -1000 -0.019 -1000
FAS signaling pathway (CD95) 0.0548 29 1368 47 -0.15 0.045 1000 -1000 -0.028 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0548 29 987 33 -0.059 0.063 1000 -1000 -0.009 -1000
S1P1 pathway 0.0510 27 982 36 -0.055 0.035 1000 -1000 -0.017 -1000
Signaling mediated by p38-alpha and p38-beta 0.0510 27 1226 44 -0.037 0.059 1000 -1000 -0.016 -1000
Regulation of nuclear SMAD2/3 signaling 0.0491 26 3538 136 -0.21 0.059 1000 -1000 -0.034 -1000
Glypican 1 network 0.0491 26 1290 48 -0.031 0.06 1000 -1000 -0.028 -1000
Fc-epsilon receptor I signaling in mast cells 0.0491 26 2609 97 -0.1 0.056 1000 -1000 -0.037 -1000
Plasma membrane estrogen receptor signaling 0.0491 26 2277 86 -0.43 0.053 1000 -1000 -0.032 -1000
Signaling events mediated by the Hedgehog family 0.0473 25 1322 52 -0.015 0.066 1000 -1000 -0.02 -1000
JNK signaling in the CD4+ TCR pathway 0.0473 25 434 17 -0.12 0.057 1000 -1000 -0.009 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0473 25 934 37 -0.048 0.074 1000 -1000 -0.018 -1000
TCGA08_rtk_signaling 0.0473 25 669 26 -0.044 0.13 1000 -1000 -0.006 -1000
EGFR-dependent Endothelin signaling events 0.0454 24 505 21 -0.012 0.032 1000 -1000 -0.024 -1000
Signaling events mediated by PTP1B 0.0435 23 1816 76 -0.026 0.06 1000 -1000 -0.022 -1000
BMP receptor signaling 0.0435 23 1904 81 -0.03 0.057 1000 -1000 -0.006 -1000
Integrins in angiogenesis 0.0435 23 2007 84 -0.048 0.079 1000 -1000 -0.037 -1000
Canonical Wnt signaling pathway 0.0435 23 1215 51 -0.034 0.11 1000 -1000 -0.023 -1000
E-cadherin signaling in keratinocytes 0.0435 23 1011 43 -0.012 0.075 1000 -1000 -0.016 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0416 22 524 23 -0.021 0.037 1000 -1000 -0.009 -1000
Visual signal transduction: Cones 0.0416 22 836 38 -0.02 0.053 1000 -1000 -0.015 -1000
IL1-mediated signaling events 0.0416 22 1381 62 -0.052 0.056 1000 -1000 -0.034 -1000
Arf6 trafficking events 0.0416 22 1608 71 -0.034 0.041 1000 -1000 -0.03 -1000
Retinoic acid receptors-mediated signaling 0.0397 21 1225 58 -0.013 0.057 1000 -1000 -0.014 -1000
FOXM1 transcription factor network 0.0397 21 1119 51 -0.19 0.032 1000 -1000 -0.13 -1000
Nectin adhesion pathway 0.0378 20 1321 63 -0.015 0.075 1000 -1000 -0.024 -1000
Noncanonical Wnt signaling pathway 0.0359 19 512 26 -0.022 0.032 1000 -1000 -0.019 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0359 19 1636 85 -0.023 0.12 1000 -1000 -0.049 -1000
Arf6 downstream pathway 0.0359 19 855 43 -0.024 0.047 1000 -1000 -0.025 -1000
mTOR signaling pathway 0.0359 19 1057 53 -0.033 0.05 1000 -1000 -0.02 -1000
ceramide signaling pathway 0.0359 19 961 49 -0.016 0.045 1000 -1000 -0.017 -1000
Signaling events mediated by HDAC Class I 0.0359 19 2064 104 -0.041 0.053 1000 -1000 -0.034 -1000
FOXA2 and FOXA3 transcription factor networks 0.0340 18 852 46 0 0.09 1000 -1000 -0.065 -1000
Class I PI3K signaling events mediated by Akt 0.0340 18 1256 68 -0.026 0.06 1000 -1000 -0.021 -1000
TRAIL signaling pathway 0.0340 18 902 48 -0.034 0.072 1000 -1000 -0.02 -1000
IL2 signaling events mediated by PI3K 0.0340 18 1046 58 -0.18 0.042 1000 -1000 -0.031 -1000
TCR signaling in naïve CD8+ T cells 0.0340 18 1688 93 -0.33 0.38 1000 -1000 -0.024 -1000
Regulation of Telomerase 0.0340 18 1857 102 -0.025 0.075 1000 -1000 -0.023 -1000
Coregulation of Androgen receptor activity 0.0321 17 1310 76 -0.047 0.059 1000 -1000 -0.018 -1000
E-cadherin signaling in the nascent adherens junction 0.0321 17 1298 76 -0.036 0.082 1000 -1000 -0.03 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0321 17 463 27 -0.029 0.07 1000 -1000 -0.022 -1000
BCR signaling pathway 0.0321 17 1742 99 -0.048 0.051 1000 -1000 -0.034 -1000
S1P5 pathway 0.0302 16 288 17 -0.033 0.033 1000 -1000 -0.005 -1000
Class I PI3K signaling events 0.0302 16 1237 73 -0.025 0.057 1000 -1000 -0.016 -1000
S1P3 pathway 0.0302 16 696 42 -0.031 0.034 1000 -1000 -0.017 -1000
PDGFR-beta signaling pathway 0.0302 16 1566 97 -0.043 0.066 1000 -1000 -0.035 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0284 15 859 54 -0.02 0.047 1000 -1000 -0.024 -1000
Syndecan-2-mediated signaling events 0.0284 15 1056 69 -0.021 0.054 1000 -1000 -0.019 -1000
Signaling events mediated by HDAC Class III 0.0284 15 614 40 -0.037 0.041 1000 -1000 -0.043 -1000
Syndecan-3-mediated signaling events 0.0284 15 551 35 -0.008 0.072 1000 -1000 -0.012 -1000
EPHB forward signaling 0.0284 15 1302 85 -0.05 0.078 1000 -1000 -0.037 -1000
p75(NTR)-mediated signaling 0.0265 14 1777 125 -0.049 0.072 1000 -1000 -0.036 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0265 14 1206 83 -0.046 0.061 1000 -1000 -0.015 -1000
Paxillin-dependent events mediated by a4b1 0.0265 14 528 36 -0.042 0.046 1000 -1000 -0.034 -1000
Canonical NF-kappaB pathway 0.0246 13 516 39 -0.028 0.065 1000 -1000 -0.011 -1000
Thromboxane A2 receptor signaling 0.0246 13 1374 105 -0.035 0.042 1000 -1000 -0.037 -1000
Hedgehog signaling events mediated by Gli proteins 0.0246 13 852 65 -0.005 0.053 1000 -1000 -0.022 -1000
Presenilin action in Notch and Wnt signaling 0.0246 13 851 61 -0.005 0.071 1000 -1000 -0.023 -1000
IFN-gamma pathway 0.0246 13 941 68 -0.056 0.063 1000 -1000 -0.028 -1000
FoxO family signaling 0.0246 13 854 64 -0.093 0.043 1000 -1000 -0.048 -1000
IL6-mediated signaling events 0.0246 13 1016 75 -0.021 0.071 1000 -1000 -0.063 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0246 13 1000 74 -0.22 0.069 1000 -1000 -0.04 -1000
IL2 signaling events mediated by STAT5 0.0246 13 301 22 -0.018 0.033 1000 -1000 -0.019 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0246 13 1679 120 -0.038 0.084 1000 -1000 -0.035 -1000
Signaling events mediated by PRL 0.0246 13 461 34 -0.026 0.047 1000 -1000 -0.025 -1000
Regulation of p38-alpha and p38-beta 0.0227 12 659 54 -0.019 0.043 1000 -1000 -0.026 -1000
S1P4 pathway 0.0227 12 315 25 -0.033 0.039 1000 -1000 -0.009 -1000
Arf1 pathway 0.0227 12 663 54 -0.063 0.042 1000 -1000 -0.011 -1000
ErbB2/ErbB3 signaling events 0.0208 11 740 65 -0.034 0.039 1000 -1000 -0.052 -1000
Signaling mediated by p38-gamma and p38-delta 0.0208 11 173 15 -0.026 0.032 1000 -1000 -0.022 -1000
Signaling events mediated by HDAC Class II 0.0189 10 778 75 -0.032 0.077 1000 -1000 -0.022 -1000
IL12-mediated signaling events 0.0189 10 916 87 -0.067 0.058 1000 -1000 -0.065 -1000
Cellular roles of Anthrax toxin 0.0189 10 427 39 -0.028 0.032 1000 -1000 -0.013 -1000
Glucocorticoid receptor regulatory network 0.0189 10 1146 114 -0.073 0.12 1000 -1000 -0.035 -1000
Nongenotropic Androgen signaling 0.0189 10 536 52 -0.065 0.055 1000 -1000 -0.019 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0189 10 918 88 -0.063 0.037 1000 -1000 -0.046 -1000
E-cadherin signaling events 0.0189 10 52 5 0.029 0.057 1000 -1000 0.027 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0170 9 310 34 -0.049 0.091 1000 -1000 -0.036 -1000
Aurora A signaling 0.0170 9 566 60 -0.034 0.065 1000 -1000 -0.02 -1000
Atypical NF-kappaB pathway 0.0170 9 279 31 -0.022 0.039 1000 -1000 -0.021 -1000
Effects of Botulinum toxin 0.0170 9 236 26 0 0.053 1000 -1000 -0.011 -1000
Calcium signaling in the CD4+ TCR pathway 0.0170 9 292 31 -0.04 0.034 1000 -1000 -0.013 -1000
Insulin Pathway 0.0170 9 731 74 -0.041 0.078 1000 -1000 -0.027 -1000
Aurora C signaling 0.0151 8 61 7 0 0.05 1000 -1000 0 -1000
IL4-mediated signaling events 0.0151 8 795 91 -0.17 0.069 1000 -1000 -0.14 -1000
Reelin signaling pathway 0.0151 8 451 56 -0.016 0.061 1000 -1000 -0.014 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0132 7 221 28 -0.022 0.034 1000 -1000 -0.021 -1000
Insulin-mediated glucose transport 0.0132 7 236 32 -0.03 0.042 1000 -1000 -0.021 -1000
IGF1 pathway 0.0132 7 405 57 -0.037 0.062 1000 -1000 -0.027 -1000
Regulation of Androgen receptor activity 0.0132 7 522 70 -0.036 0.058 1000 -1000 -0.024 -1000
p38 MAPK signaling pathway 0.0113 6 295 44 0 0.052 1000 -1000 -0.004 -1000
LPA4-mediated signaling events 0.0095 5 65 12 -0.018 0.009 1000 -1000 -0.016 -1000
ErbB4 signaling events 0.0095 5 348 69 -0.027 0.066 1000 -1000 -0.022 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0095 5 282 52 -0.059 0.091 1000 -1000 -0.004 -1000
Ephrin B reverse signaling 0.0095 5 276 48 -0.011 0.05 1000 -1000 -0.039 -1000
Circadian rhythm pathway 0.0076 4 91 22 -0.01 0.046 1000 -1000 -0.022 -1000
IL27-mediated signaling events 0.0076 4 229 51 -0.022 0.056 1000 -1000 -0.037 -1000
Rapid glucocorticoid signaling 0.0076 4 92 20 -0.011 0.032 1000 -1000 -0.011 -1000
a4b1 and a4b7 Integrin signaling 0.0057 3 16 5 0.025 0.046 1000 -1000 0.027 -1000
Alternative NF-kappaB pathway 0.0057 3 44 13 0 0.054 1000 -1000 0 -1000
IL23-mediated signaling events 0.0038 2 142 60 -0.02 0.057 1000 -1000 -0.11 -1000
Visual signal transduction: Rods 0.0019 1 89 52 -0.034 0.074 1000 -1000 -0.024 -1000
PLK2 and PLK4 events 0.0000 0 0 3 -0.016 0.032 1000 -1000 -0.021 -1000
Ephrin A reverse signaling 0.0000 0 3 7 -0.02 0.043 1000 -1000 -0.016 -1000
Class IB PI3K non-lipid kinase events 0.0000 0 0 3 -0.032 0.032 1000 -1000 -0.027 -1000
Total NA 2969 166834 7203 -6.7 7.5 131000 -131000 -3.3 -131000
Glypican 2 network

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
MDK -0.022 0.046 -9999 0 -0.063 283 283
GPC2 0 0 -9999 0 -10000 0 0
GPC2/Midkine -0.012 0.03 -9999 0 -0.039 283 283
neuron projection morphogenesis -0.012 0.03 -9999 0 -0.039 283 283
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.033 0.007 -10000 0 -0.028 6 6
NFATC2 -0.029 0.096 -10000 0 -0.14 199 199
NFATC3 -0.043 0.11 -10000 0 -0.16 215 215
CD40LG -0.14 0.17 0.26 1 -0.33 205 206
ITCH -0.015 0.009 -10000 0 -10000 0 0
CBLB -0.016 0.008 -10000 0 -0.058 1 1
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.13 0.17 -10000 0 -0.39 95 95
JUNB 0.03 0.013 -10000 0 -0.063 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 0.032 0.019 -10000 0 -0.051 14 14
T cell anergy -0.008 0.027 0.17 2 -0.1 5 7
TLE4 -0.021 0.059 0.097 1 -0.094 147 148
Jun/NFAT1-c-4/p21SNFT -0.1 0.21 -10000 0 -0.33 225 225
AP-1/NFAT1-c-4 -0.12 0.22 -10000 0 -0.35 208 208
IKZF1 -0.014 0.051 0.097 1 -0.099 73 74
T-helper 2 cell differentiation -0.13 0.17 -10000 0 -0.48 65 65
AP-1/NFAT1 -0.02 0.071 -10000 0 -0.11 21 21
CALM1 0.03 0.017 -10000 0 -0.045 14 14
EGR2 -0.092 0.18 -10000 0 -0.34 166 166
EGR3 0.005 0.12 -10000 0 -0.61 18 18
NFAT1/FOXP3 -0.006 0.08 -10000 0 -0.11 88 88
EGR1 0.029 0.017 -10000 0 -0.063 15 15
JUN 0.03 0.012 -10000 0 -0.031 8 8
EGR4 0.033 0.001 -10000 0 -10000 0 0
mol:Ca2+ 0.003 0.006 -10000 0 -10000 0 0
GBP3 -0.02 0.053 0.081 2 -0.082 199 201
FOSL1 0.03 0.015 -10000 0 -0.063 12 12
NFAT1-c-4/MAF/IRF4 -0.099 0.22 -10000 0 -0.33 226 226
DGKA -0.021 0.06 0.097 1 -0.1 97 98
CREM 0.025 0.013 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.11 0.22 -10000 0 -0.35 227 227
CTLA4 -0.023 0.054 0.082 1 -0.091 93 94
NFAT1-c-4 (dimer)/EGR1 -0.11 0.22 -10000 0 -0.34 227 227
NFAT1-c-4 (dimer)/EGR4 -0.11 0.22 -10000 0 -0.35 229 229
FOS 0.006 0.041 -10000 0 -0.063 128 128
IFNG -0.05 0.094 -10000 0 -0.26 33 33
T cell activation -0.079 0.11 -10000 0 -10000 0 0
MAF 0.032 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 0.065 0.17 0.32 145 -10000 0 145
TNF -0.13 0.19 -10000 0 -0.33 230 230
FASLG -0.24 0.29 -10000 0 -0.54 235 235
TBX21 0.034 0.005 -10000 0 -0.041 1 1
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ 0.025 0.015 -10000 0 -10000 0 0
PTPN1 -0.021 0.059 0.097 1 -0.098 117 118
NFAT1-c-4/ICER1 -0.12 0.21 -10000 0 -0.35 231 231
GATA3 0.025 0.016 -10000 0 -0.062 2 2
T-helper 1 cell differentiation -0.05 0.093 -10000 0 -0.29 21 21
IL2RA -0.12 0.18 -10000 0 -0.4 96 96
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.032 0.064 0.097 1 -0.1 164 165
E2F1 -0.019 0.04 -10000 0 -0.051 306 306
PPARG 0.031 0.009 -10000 0 -0.063 4 4
SLC3A2 -0.022 0.061 0.097 1 -0.1 116 117
IRF4 0.032 0.006 -10000 0 -0.062 1 1
PTGS2 -0.14 0.17 0.26 1 -0.33 204 205
CSF2 -0.14 0.17 0.26 1 -0.33 205 206
JunB/Fra1/NFAT1-c-4 -0.1 0.22 -10000 0 -0.34 222 222
IL4 -0.13 0.18 -10000 0 -0.5 66 66
IL5 -0.14 0.17 0.26 1 -0.33 204 205
IL2 -0.08 0.11 -10000 0 -10000 0 0
IL3 -0.009 0.072 -10000 0 -0.54 6 6
RNF128 -0.017 0.012 -10000 0 -0.079 14 14
NFATC1 -0.052 0.16 -10000 0 -0.33 123 123
CDK4 0.011 0.11 0.27 66 -10000 0 66
PTPRK -0.02 0.059 0.097 1 -0.091 185 186
IL8 -0.15 0.17 0.26 1 -0.33 206 207
POU2F1 0.035 0.005 -10000 0 -10000 0 0
LPA receptor mediated events

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
GNB1/GNG2 -0.006 0.029 -10000 0 -0.034 258 258
NF kappa B1 p50/RelA/I kappa B alpha -0.007 0.062 0.21 7 -0.18 29 36
AP1 -0.017 0.03 -10000 0 -0.04 293 293
mol:PIP3 -0.013 0.018 -10000 0 -0.057 12 12
AKT1 0.008 0.071 0.2 21 -0.24 7 28
PTK2B -0.009 0.027 0.11 2 -0.2 6 8
RHOA 0.011 0.061 0.14 13 -0.3 10 23
PIK3CB 0.031 0.006 -10000 0 -0.031 2 2
mol:Ca2+ -0.012 0.022 0.2 3 -0.12 7 10
MAGI3 0 0 -10000 0 -0.004 3 3
RELA 0.032 0.004 -10000 0 -10000 0 0
apoptosis -0.015 0.026 -10000 0 -0.037 273 273
HRAS/GDP 0.023 0.005 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.011 0.039 0.17 12 -0.19 6 18
NF kappa B1 p50/RelA -0.038 0.02 -10000 0 -0.11 11 11
endothelial cell migration -0.025 0.041 -10000 0 -0.067 244 244
ADCY4 -0.001 0.007 -10000 0 -0.092 1 1
ADCY5 -0.001 0.007 -10000 0 -0.092 1 1
ADCY6 -0.001 0.01 0.086 2 -0.1 2 4
ADCY7 -0.001 0.01 0.086 3 -0.089 1 4
ADCY1 -0.001 0.007 -10000 0 -0.089 1 1
ADCY2 -0.001 0.01 0.086 3 -0.079 2 5
ADCY3 -0.001 0.007 -10000 0 -0.092 1 1
ADCY8 -0.001 0.009 0.086 2 -0.089 1 3
ADCY9 -0.001 0.01 0.086 3 -0.089 1 4
GSK3B -0.012 0.033 0.17 6 -0.19 6 12
arachidonic acid secretion -0.002 0.014 0.077 3 -0.11 5 8
GNG2 0 0.001 0.002 1 -0.004 27 28
TRIP6 -0.008 0.025 -10000 0 -0.041 167 167
GNAO1 0 0.008 -10000 0 -0.039 16 16
HRAS 0.031 0.007 -10000 0 -10000 0 0
NFKBIA -0.022 0.052 0.18 9 -0.18 28 37
GAB1 0.032 0.008 -10000 0 -0.063 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.002 0.17 -10000 0 -0.74 21 21
JUN 0.032 0.005 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.002 0.022 -10000 0 -0.021 243 243
TIAM1 -0.003 0.2 -10000 0 -0.84 27 27
PIK3R1 0.03 0.01 -10000 0 -0.032 1 1
mol:IP3 -0.012 0.016 0.17 2 -0.12 2 4
PLCB3 -0.019 0.018 0.18 4 -10000 0 4
FOS 0.007 0.04 -10000 0 -0.063 120 120
positive regulation of mitosis -0.002 0.014 0.077 3 -0.11 5 8
LPA/LPA1-2-3 -0.011 0.015 -10000 0 -0.027 250 250
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
stress fiber formation 0.004 0.023 0.13 1 -0.14 3 4
GNAZ -0.01 0.024 -10000 0 -0.039 203 203
EGFR/PI3K-beta/Gab1 -0.013 0.019 0.023 2 -0.062 8 10
positive regulation of dendritic cell cytokine production -0.011 0.015 -10000 0 -0.027 250 250
LPA/LPA2/MAGI-3 -0.005 0.007 -10000 0 -0.012 250 250
ARHGEF1 0.026 0.093 0.17 140 -10000 0 140
GNAI2 -0.013 0.026 -10000 0 -0.039 240 240
GNAI3 -0.016 0.027 -10000 0 -0.041 269 269
GNAI1 -0.008 0.021 -10000 0 -0.039 154 154
LPA/LPA3 -0.007 0.008 -10000 0 -0.015 248 248
LPA/LPA2 -0.007 0.008 -10000 0 -0.015 249 249
LPA/LPA1 -0.016 0.021 -10000 0 -0.038 248 248
HB-EGF/EGFR -0.001 0.024 -10000 0 -0.048 83 83
HBEGF -0.03 0.016 -10000 0 -0.05 165 165
mol:DAG -0.012 0.016 0.17 2 -0.12 2 4
cAMP biosynthetic process 0.046 0.063 0.14 119 -10000 0 119
NFKB1 0.031 0.009 -10000 0 -0.063 4 4
SRC 0.031 0.008 -10000 0 -10000 0 0
GNB1 0.03 0.008 -10000 0 -10000 0 0
LYN -0.017 0.039 0.18 9 -0.16 1 10
GNAQ -0.001 0.013 -10000 0 -0.015 235 235
LPAR2 0 0.001 -10000 0 -0.004 3 3
LPAR3 0 0 -10000 0 -10000 0 0
LPAR1 -0.012 0.013 -10000 0 -0.025 247 247
IL8 -0.038 0.054 0.2 2 -0.29 4 6
PTK2 -0.006 0.025 -10000 0 -0.032 242 242
Rac1/GDP 0.017 0.011 -10000 0 -10000 0 0
CASP3 -0.015 0.026 -10000 0 -0.037 273 273
EGFR 0.012 0.018 -10000 0 -0.063 6 6
PLCG1 0.002 0.008 -10000 0 -0.039 4 4
PLD2 -0.006 0.025 -10000 0 -0.032 245 245
G12/G13 0.003 0.037 -10000 0 -0.042 174 174
PI3K-beta -0.011 0.041 -10000 0 -0.2 13 13
cell migration -0.002 0.048 -10000 0 -0.22 19 19
SLC9A3R2 0.032 0.004 -10000 0 -10000 0 0
PXN 0.004 0.024 0.13 1 -0.14 3 4
HRAS/GTP -0.001 0.012 0.077 3 -0.1 4 7
RAC1 0.023 0.015 -10000 0 -10000 0 0
MMP9 -0.001 0.044 -10000 0 -0.063 165 165
PRKCE 0.032 0.005 -10000 0 -0.027 3 3
PRKCD -0.013 0.037 0.21 10 -0.12 5 15
Gi(beta/gamma) 0 0.014 0.086 3 -0.14 3 6
mol:LPA -0.012 0.013 -10000 0 -0.025 247 247
TRIP6/p130 Cas/FAK1/Paxillin -0.009 0.024 -10000 0 -0.11 6 6
MAPKKK cascade -0.002 0.014 0.077 3 -0.11 5 8
contractile ring contraction involved in cytokinesis 0.013 0.062 0.14 20 -0.29 10 30
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.001 0.013 -10000 0 -0.015 238 238
GNA15 -0.002 0.014 -10000 0 -0.016 234 234
GNA12 0.023 0.015 -10000 0 -10000 0 0
GNA13 0.032 0.007 -10000 0 -0.063 2 2
MAPT -0.014 0.035 0.2 6 -0.19 6 12
GNA11 -0.001 0.013 -10000 0 -0.015 234 234
Rac1/GTP 0.002 0.18 -10000 0 -0.8 19 19
MMP2 -0.025 0.041 -10000 0 -0.067 244 244
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.017 0.057 -10000 0 -0.056 339 339
alphaM/beta2 Integrin/GPIbA 0.016 0.057 -10000 0 -0.049 213 213
alphaM/beta2 Integrin/proMMP-9 -0.005 0.059 -10000 0 -0.057 273 273
PLAUR 0.023 0.027 -10000 0 -0.063 44 44
HMGB1 0.029 0.012 -10000 0 -0.029 11 11
alphaM/beta2 Integrin/Talin 0.007 0.057 -10000 0 -0.051 231 231
AGER 0.03 0.013 -10000 0 -0.039 17 17
RAP1A 0.032 0.004 -10000 0 -10000 0 0
SELPLG 0.032 0.004 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.017 0.072 -10000 0 -0.084 35 35
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.001 0.044 -10000 0 -0.063 165 165
CYR61 0.004 0.043 -10000 0 -0.063 150 150
TLN1 0.021 0.027 -10000 0 -0.063 43 43
Rap1/GTP 0.01 0.037 0.11 2 -0.15 4 6
RHOA 0.032 0.006 -10000 0 -10000 0 0
P-selectin oligomer 0.032 0.006 -10000 0 -0.063 1 1
MYH2 0 0.038 0.14 5 -0.15 5 10
MST1R 0.031 0.008 -10000 0 -0.063 2 2
leukocyte activation during inflammatory response 0.012 0.058 -10000 0 -0.055 38 38
APOB 0.032 0.008 -10000 0 -0.063 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 -0.013 0.047 -10000 0 -0.063 241 241
JAM3 0.03 0.009 -10000 0 -0.063 1 1
GP1BA 0.032 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CTGF 0.008 0.056 -10000 0 -0.051 229 229
alphaM/beta2 Integrin 0.001 0.036 -10000 0 -0.14 8 8
JAM3 homodimer 0.03 0.009 -10000 0 -0.063 1 1
ICAM2 0.032 0.008 -10000 0 -0.063 3 3
ICAM1 0.028 0.018 -10000 0 -0.063 16 16
phagocytosis triggered by activation of immune response cell surface activating receptor 0.001 0.036 -10000 0 -0.13 8 8
cell adhesion 0.016 0.056 -10000 0 -0.049 213 213
NFKB1 -0.041 0.037 0.21 7 -10000 0 7
THY1 0.024 0.015 -10000 0 -10000 0 0
RhoA/GDP 0.023 0.004 -10000 0 -10000 0 0
Lipoprotein(a) 0.04 0.014 -10000 0 -0.042 3 3
alphaM/beta2 Integrin/LRP/tPA -0.011 0.065 -10000 0 -0.058 322 322
IL6 -0.033 0.037 0.16 4 -0.15 2 6
ITGB2 -0.008 0.047 -10000 0 -0.063 214 214
elevation of cytosolic calcium ion concentration -0.009 0.064 -10000 0 -0.061 228 228
alphaM/beta2 Integrin/JAM2/JAM3 0.009 0.066 -10000 0 -0.053 254 254
JAM2 0.018 0.033 -10000 0 -0.063 72 72
alphaM/beta2 Integrin/ICAM1 0.024 0.074 -10000 0 -0.075 12 12
alphaM/beta2 Integrin/uPA/Plg -0.008 0.064 -10000 0 -0.067 114 114
RhoA/GTP 0.005 0.037 0.1 16 -0.13 9 25
positive regulation of phagocytosis -0.002 0.052 0.14 7 -0.12 12 19
Ron/MSP 0.045 0.015 -10000 0 -0.05 8 8
alphaM/beta2 Integrin/uPAR/uPA -0.008 0.065 -10000 0 -0.062 228 228
alphaM/beta2 Integrin/uPAR 0.012 0.058 -10000 0 -0.053 214 214
PLAU 0.007 0.036 -10000 0 -0.063 94 94
PLAT -0.011 0.047 -10000 0 -0.061 238 238
actin filament polymerization 0.001 0.039 0.15 7 -0.15 4 11
MST1 0.031 0.012 -10000 0 -0.063 6 6
alphaM/beta2 Integrin/lipoprotein(a) 0.016 0.061 -10000 0 -0.055 38 38
TNF -0.043 0.035 0.19 7 -10000 0 7
RAP1B 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.004 0.055 -10000 0 -0.057 233 233
fibrinolysis -0.009 0.063 -10000 0 -0.067 117 117
HCK 0.014 0.036 -10000 0 -0.044 120 120
dendritic cell antigen processing and presentation 0.001 0.036 -10000 0 -0.13 8 8
VTN 0.032 0.007 -10000 0 -0.021 6 6
alphaM/beta2 Integrin/CYR61 0 0.061 -10000 0 -0.056 267 267
LPA 0.03 0.008 -10000 0 -10000 0 0
LRP1 0.029 0.016 -10000 0 -0.063 13 13
cell migration -0.032 0.05 -10000 0 -0.064 340 340
FN1 0.014 0.037 -10000 0 -0.063 96 96
alphaM/beta2 Integrin/Thy1 0.007 0.049 -10000 0 -0.049 178 178
MPO 0.032 0.004 -10000 0 -10000 0 0
KNG1 0.032 0.006 -10000 0 -10000 0 0
RAP1/GDP 0.022 0.003 -10000 0 -10000 0 0
ROCK1 0.001 0.043 0.18 9 -0.15 5 14
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.03 0.008 -10000 0 -10000 0 0
CTGF 0.023 0.025 -10000 0 -0.063 36 36
alphaM/beta2 Integrin/Hck 0.01 0.06 -10000 0 -0.058 208 208
ITGAM 0.031 0.01 -10000 0 -0.03 13 13
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.024 0.066 -10000 0 -0.06 35 35
HP 0.017 0.034 -10000 0 -0.063 77 77
leukocyte adhesion -0.008 0.055 -10000 0 -0.1 12 12
SELP 0.032 0.006 -10000 0 -0.063 1 1
Endothelins

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
AKT1 -0.066 0.034 -10000 0 -0.11 90 90
PTK2B 0.032 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.088 0.17 0.36 1 -0.41 98 99
EDN1 -0.036 0.043 -10000 0 -0.061 350 350
EDN3 0.029 0.012 -10000 0 -0.063 3 3
EDN2 0.032 0.006 -10000 0 -0.063 1 1
HRAS/GDP -0.028 0.081 0.23 15 -0.29 15 30
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.014 0.04 -10000 0 -0.17 12 12
ADCY4 -0.053 0.024 0.011 1 -0.074 253 254
ADCY5 -0.053 0.024 0.011 1 -0.074 253 254
ADCY6 -0.057 0.033 0.16 3 -10000 0 3
ADCY7 -0.057 0.036 0.16 4 -10000 0 4
ADCY1 -0.043 0.037 0.15 2 -10000 0 2
ADCY2 -0.056 0.036 0.16 4 -10000 0 4
ADCY3 -0.053 0.024 0.011 1 -0.074 253 254
ADCY8 -0.056 0.036 0.16 4 -10000 0 4
ADCY9 -0.057 0.035 0.16 4 -10000 0 4
arachidonic acid secretion -0.048 0.094 0.28 10 -0.32 19 29
ETB receptor/Endothelin-1/Gq/GTP -0.007 0.033 -10000 0 -0.15 15 15
GNAO1 0.003 0.009 -10000 0 -10000 0 0
HRAS 0.031 0.007 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.032 0.054 -10000 0 -0.086 180 180
ETA receptor/Endothelin-1/Gs/GTP -0.038 0.057 -10000 0 -0.079 235 235
mol:GTP 0 0.001 -10000 0 -10000 0 0
COL3A1 -0.088 0.041 -10000 0 -0.12 232 232
EDNRB -0.008 0.036 -10000 0 -0.041 256 256
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.063 0.035 -10000 0 -0.11 87 87
CYSLTR1 -0.06 0.03 0.04 1 -0.077 340 341
SLC9A1 -0.03 0.03 -10000 0 -0.054 254 254
mol:GDP -0.031 0.079 0.22 15 -0.3 15 30
SLC9A3 -0.074 0.19 -10000 0 -0.62 41 41
RAF1 -0.031 0.082 0.26 12 -0.31 14 26
JUN -0.096 0.19 0.32 2 -0.45 99 101
JAK2 -0.063 0.036 -10000 0 -0.11 84 84
mol:IP3 -0.014 0.046 -10000 0 -0.21 14 14
ETA receptor/Endothelin-1 -0.056 0.067 -10000 0 -0.095 356 356
PLCB1 0.03 0.009 -10000 0 -10000 0 0
PLCB2 0.031 0.006 -10000 0 -0.029 1 1
ETA receptor/Endothelin-3 -0.027 0.046 -10000 0 -0.057 337 337
FOS -0.039 0.097 0.32 10 -0.33 15 25
Gai/GDP -0.47 0.17 -10000 0 -0.52 452 452
CRK 0.032 0.005 -10000 0 -10000 0 0
mol:Ca ++ -0.044 0.05 -10000 0 -0.19 20 20
BCAR1 0 0 -10000 0 -10000 0 0
PRKCB1 -0.016 0.046 -10000 0 -0.23 12 12
GNAQ 0.031 0.007 -10000 0 -0.027 2 2
GNAZ 0.027 0.013 -10000 0 -10000 0 0
GNAL 0.032 0.006 -10000 0 -10000 0 0
Gs family/GDP -0.03 0.074 0.21 14 -0.28 13 27
ETA receptor/Endothelin-1/Gq/GTP -0.021 0.036 -10000 0 -0.14 13 13
MAPK14 -0.011 0.035 -10000 0 -0.2 8 8
TRPC6 -0.091 0.18 0.36 1 -0.42 97 98
GNAI2 0.032 0.006 -10000 0 -10000 0 0
GNAI3 0.021 0.03 -10000 0 -0.063 58 58
GNAI1 0.019 0.016 -10000 0 -0.063 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.004 0.038 -10000 0 -0.18 12 12
ETB receptor/Endothelin-2 0.026 0.031 -10000 0 -0.044 63 63
ETB receptor/Endothelin-3 0.024 0.03 -10000 0 -0.045 59 59
ETB receptor/Endothelin-1 -0.031 0.048 -10000 0 -0.062 346 346
MAPK3 -0.034 0.096 0.32 11 -0.36 10 21
MAPK1 -0.042 0.1 0.32 10 -0.35 17 27
Rac1/GDP -0.026 0.06 0.2 4 -0.28 11 15
cAMP biosynthetic process -0.019 0.043 0.17 8 -0.14 2 10
MAPK8 -0.11 0.22 0.37 1 -0.5 113 114
SRC 0.031 0.008 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.004 0.024 -10000 0 -0.13 17 17
p130Cas/CRK/Src/PYK2 -0.026 0.084 0.28 12 -0.31 12 24
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.026 0.06 0.2 4 -0.28 11 15
COL1A2 -0.054 0.062 -10000 0 -0.13 185 185
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.028 0.047 -10000 0 -0.056 359 359
mol:DAG -0.015 0.046 -10000 0 -0.21 14 14
MAP2K2 -0.035 0.098 0.33 16 -0.32 14 30
MAP2K1 -0.04 0.083 0.26 10 -0.32 14 24
EDNRA -0.047 0.049 -10000 0 -0.073 365 365
positive regulation of muscle contraction -0.009 0.095 0.15 122 -0.12 4 126
Gq family/GDP 0.005 0.08 0.25 3 -0.25 14 17
HRAS/GTP -0.024 0.077 0.21 16 -0.3 16 32
PRKCH -0.02 0.047 0.21 1 -0.26 11 12
RAC1 0.023 0.015 -10000 0 -10000 0 0
PRKCA -0.023 0.053 0.19 2 -0.25 16 18
PRKCB -0.016 0.046 -10000 0 -0.23 12 12
PRKCE -0.024 0.052 -10000 0 -0.25 16 16
PRKCD -0.022 0.05 0.17 2 -0.25 13 15
PRKCG -0.023 0.052 0.21 1 -0.25 16 17
regulation of vascular smooth muscle contraction -0.042 0.11 0.36 9 -0.43 8 17
PRKCQ -0.017 0.041 0.19 3 -0.28 6 9
PLA2G4A -0.05 0.098 0.28 10 -0.34 19 29
GNA14 0.031 0.009 -10000 0 -0.045 4 4
GNA15 0.03 0.013 -10000 0 -0.063 7 7
GNA12 0.023 0.015 -10000 0 -10000 0 0
GNA11 0.031 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.033 0.054 -10000 0 -0.086 181 181
MMP1 0.021 0.045 0.082 41 -0.098 7 48
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.015 0.011 0 176 -0.05 2 178
MAP4K4 -0.008 0.038 -10000 0 -0.18 11 11
BAG4 0.032 0.004 -10000 0 -10000 0 0
PKC zeta/ceramide -0.058 0.11 -10000 0 -0.2 158 158
NFKBIA 0.03 0.009 -10000 0 -0.063 1 1
BIRC3 0.026 0.023 -10000 0 -0.063 30 30
BAX -0.027 0.086 -10000 0 -0.36 24 24
RIPK1 0.03 0.013 -10000 0 -0.063 9 9
AKT1 0 0.07 0.75 4 -10000 0 4
BAD -0.064 0.11 0.19 2 -0.21 158 160
SMPD1 -0.006 0.038 0.12 7 -0.17 15 22
RB1 -0.064 0.11 0.2 1 -0.21 158 159
FADD/Caspase 8 -0.002 0.04 -10000 0 -0.25 6 6
MAP2K4 -0.063 0.11 0.19 4 -0.2 150 154
NSMAF 0.032 0.005 -10000 0 -0.063 1 1
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.065 0.11 0.18 5 -0.2 155 160
EGF 0.032 0.007 -10000 0 -0.063 2 2
mol:ceramide -0.061 0.12 0.094 1 -0.21 158 159
MADD 0.031 0.006 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.015 0.011 0 168 -0.05 2 170
ASAH1 0.032 0.005 -10000 0 -10000 0 0
negative regulation of cell cycle -0.064 0.11 0.2 1 -0.2 158 159
cell proliferation -0.036 0.1 -10000 0 -0.19 142 142
BID -0.026 0.15 -10000 0 -0.65 26 26
MAP3K1 -0.064 0.11 0.2 1 -0.21 157 158
EIF2A -0.064 0.1 0.18 2 -0.19 157 159
TRADD 0.032 0.004 -10000 0 -10000 0 0
CRADD 0.032 0.004 -10000 0 -10000 0 0
MAPK3 -0.059 0.095 0.18 4 -0.19 144 148
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.067 0.1 0.18 4 -0.21 149 153
Cathepsin D/ceramide -0.046 0.12 -10000 0 -0.21 157 157
FADD -0.006 0.033 -10000 0 -0.16 8 8
KSR1 -0.064 0.11 0.2 1 -0.21 158 159
MAPK8 -0.092 0.15 0.15 3 -0.25 194 197
PRKRA -0.064 0.11 -10000 0 -0.21 157 157
PDGFA 0.022 0.016 -10000 0 -0.063 2 2
TRAF2 0.031 0.006 -10000 0 -10000 0 0
IGF1 0.032 0.009 -10000 0 -0.063 4 4
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.061 0.12 0.094 1 -0.21 158 159
CTSD 0.029 0.017 -10000 0 -0.063 15 15
regulation of nitric oxide biosynthetic process 0.046 0.012 -10000 0 -0.049 4 4
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.038 0.11 -10000 0 -0.2 142 142
PRKCD 0.032 0.006 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.015 0.011 0 168 -0.05 2 170
RelA/NF kappa B1 0.046 0.012 -10000 0 -0.05 4 4
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.031 0.006 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.001 0.039 -10000 0 -0.12 34 34
TNFR1A/BAG4/TNF-alpha 0.025 0.054 -10000 0 -0.048 175 175
mol:Sphingosine-1-phosphate -0.015 0.011 0 176 -0.049 2 178
MAP2K1 -0.066 0.1 0.18 5 -0.2 150 155
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.032 0.004 -10000 0 -10000 0 0
CYCS -0.017 0.064 0.11 3 -0.2 40 43
TNFRSF1A 0 0.044 -10000 0 -0.063 165 165
NFKB1 0.031 0.009 -10000 0 -0.063 4 4
TNFR1A/BAG4 0.014 0.045 -10000 0 -0.05 164 164
EIF2AK2 -0.067 0.11 0.18 2 -0.2 157 159
TNF-alpha/TNFR1A/FAN 0.024 0.054 -10000 0 -0.048 165 165
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.02 0.048 -10000 0 -0.25 11 11
MAP2K2 -0.064 0.094 0.17 8 -0.2 149 157
SMPD3 0 0.04 0.096 4 -0.23 10 14
TNF 0.032 0.006 -10000 0 -0.063 2 2
PKC zeta/PAR4 0.023 0.004 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE -0.035 0.066 0.13 3 -0.13 150 153
NF kappa B1/RelA/I kappa B alpha 0.065 0.035 -10000 0 -0.052 2 2
AIFM1 -0.042 0.081 0.11 2 -0.14 153 155
BCL2 0.032 0.006 -10000 0 -10000 0 0
TCGA08_retinoblastoma

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
CDKN2B 0.011 0.019 -10000 0 -0.037 6 6
CDKN2C -0.006 0.028 -10000 0 -0.053 106 106
CDKN2A 0.006 0.025 -10000 0 -0.049 52 52
CCND2 0.002 0.009 0.079 2 -10000 0 2
RB1 -0.073 0.1 0.1 1 -0.22 169 170
CDK4 0.002 0.01 0.09 2 -10000 0 2
CDK6 0.004 0.016 0.11 6 -10000 0 6
G1/S progression 0.081 0.11 0.22 180 -0.1 1 181
TCGA08_p53

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
CDKN2A -0.007 0.012 0 313 -0.039 52 365
TP53 -0.002 0.022 -10000 0 -0.11 13 13
Senescence -0.002 0.024 -10000 0 -0.12 14 14
Apoptosis -0.002 0.024 -10000 0 -0.12 14 14
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.001 0.009 0.022 43 -10000 0 43
MDM4 0.029 0.011 -10000 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 0.023 0.041 -10000 0 -0.05 114 114
ATM 0.027 0.021 -10000 0 -0.063 25 25
UBE2D3 0.032 0.005 -10000 0 -10000 0 0
PRKDC 0.028 0.019 -10000 0 -0.063 21 21
ATR 0.032 0.005 -10000 0 -10000 0 0
UBE2L3 0.031 0.007 -10000 0 -10000 0 0
FANCD2 0.01 0.011 -10000 0 -0.036 25 25
protein ubiquitination 0.043 0.065 -10000 0 -0.078 25 25
XRCC5 0.032 0.002 -10000 0 -10000 0 0
XRCC6 0.03 0.009 -10000 0 -10000 0 0
M/R/N Complex 0.062 0.019 -10000 0 -0.044 1 1
MRE11A 0.032 0.005 -10000 0 -10000 0 0
DNA-PK 0.054 0.034 -10000 0 -0.05 22 22
FA complex/FANCD2/Ubiquitin -0.005 0.08 -10000 0 -0.25 37 37
FANCF 0.031 0.008 -10000 0 -0.063 2 2
BRCA1 0.031 0.01 -10000 0 -0.063 5 5
CCNE1 0.03 0.011 -10000 0 -0.063 4 4
CDK2/Cyclin E1 0.04 0.024 -10000 0 -0.053 23 23
FANCG 0.019 0.03 -10000 0 -0.063 57 57
BRCA1/BACH1/BARD1 0.024 0.042 -10000 0 -0.05 120 120
FANCE 0.032 0.005 -10000 0 -0.063 1 1
FANCC 0.032 0.006 -10000 0 -10000 0 0
NBN 0.032 0.004 -10000 0 -10000 0 0
FANCA 0.031 0.006 -10000 0 -10000 0 0
DNA repair -0.029 0.066 0.18 16 -0.22 26 42
BRCA1/BARD1/ubiquitin 0.024 0.042 -10000 0 -0.05 120 120
BARD1/DNA-PK 0.042 0.062 -10000 0 -0.064 25 25
FANCL 0 0 -10000 0 -10000 0 0
mRNA polyadenylation -0.022 0.041 0.049 114 -10000 0 114
BRCA1/BARD1/CTIP/M/R/N Complex -0.018 0.042 0.1 5 -0.18 16 21
BRCA1/BACH1/BARD1/TopBP1 0.036 0.05 -10000 0 -0.049 126 126
BRCA1/BARD1/P53 0.036 0.065 -10000 0 -0.07 32 32
BARD1/CSTF1/BRCA1 0.035 0.049 -10000 0 -0.049 115 115
BRCA1/BACH1 0.031 0.01 -10000 0 -0.063 5 5
BARD1 0.01 0.041 -10000 0 -0.063 122 122
PCNA -0.026 0.045 -10000 0 -0.063 299 299
BRCA1/BARD1/UbcH5C 0.036 0.05 -10000 0 -0.049 123 123
BRCA1/BARD1/UbcH7 0.035 0.051 -10000 0 -0.05 122 122
BRCA1/BARD1/RAD51/PCNA -0.01 0.064 -10000 0 -0.069 104 104
BARD1/DNA-PK/P53 0.038 0.075 -10000 0 -0.087 11 11
BRCA1/BARD1/Ubiquitin 0.024 0.042 -10000 0 -0.05 120 120
BRCA1/BARD1/CTIP -0.034 0.044 -10000 0 -0.057 392 392
FA complex 0.012 0.034 0.088 8 -0.15 16 24
BARD1/EWS 0.024 0.04 -10000 0 -0.05 107 107
RBBP8 -0.043 0.016 -10000 0 -0.051 379 379
TP53 0.019 0.032 -10000 0 -0.063 65 65
TOPBP1 0.032 0.006 -10000 0 -0.063 1 1
G1/S transition of mitotic cell cycle -0.034 0.063 0.07 32 -10000 0 32
BRCA1/BARD1 0.048 0.069 -10000 0 -0.09 10 10
CSTF1 0.03 0.009 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.009 0.027 -10000 0 -0.039 122 122
CDK2 0.027 0.021 -10000 0 -0.063 24 24
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.032 0.006 -10000 0 -10000 0 0
RAD50 0.032 0.004 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.024 0.042 -10000 0 -0.05 120 120
EWSR1 0.03 0.008 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 -0.014 0.17 -10000 0 -0.64 33 33
oxygen homeostasis -0.003 0.003 -10000 0 -10000 0 0
TCEB2 0.032 0.004 -10000 0 -10000 0 0
TCEB1 0.032 0.005 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.024 0.075 -10000 0 -0.14 99 99
EPO -0.031 0.072 -10000 0 -0.2 49 49
FIH (dimer) 0.02 0.017 -10000 0 -0.027 21 21
APEX1 0.025 0.019 -10000 0 -0.03 44 44
SERPINE1 -0.045 0.071 -10000 0 -0.18 68 68
FLT1 -0.015 0.16 -10000 0 -0.61 35 35
ADORA2A -0.067 0.07 0.3 2 -0.17 107 109
germ cell development -0.062 0.068 -10000 0 -0.16 119 119
SLC11A2 -0.065 0.074 -10000 0 -0.17 119 119
BHLHE40 -0.063 0.069 -10000 0 -0.16 119 119
HIF1AN 0.02 0.017 -10000 0 -0.027 21 21
HIF2A/ARNT/SIRT1 -0.03 0.086 0.17 1 -0.16 102 103
ETS1 0.034 0.014 -10000 0 -10000 0 0
CITED2 -0.025 0.16 -10000 0 -0.59 39 39
KDR 0.016 0.076 -10000 0 -0.55 8 8
PGK1 -0.064 0.077 0.42 1 -0.17 119 120
SIRT1 0.025 0.014 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT -0.032 0.11 -10000 0 -0.19 103 103
EPAS1 -0.03 0.048 0.11 1 -0.12 98 99
SP1 0.034 0.006 -10000 0 -0.038 1 1
ABCG2 -0.064 0.077 0.42 1 -0.17 119 120
EFNA1 -0.065 0.075 -10000 0 -0.17 118 118
FXN -0.067 0.065 -10000 0 -0.17 104 104
POU5F1 -0.063 0.069 -10000 0 -0.16 119 119
neuron apoptosis 0.032 0.11 0.18 103 -10000 0 103
EP300 0.03 0.008 -10000 0 -10000 0 0
EGLN3 0.024 0.017 -10000 0 -0.033 33 33
EGLN2 0.027 0.013 -10000 0 -0.027 23 23
EGLN1 0.026 0.015 -10000 0 -0.029 30 30
VHL/Elongin B/Elongin C 0.043 0.008 -10000 0 -10000 0 0
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.027 0.018 -10000 0 -0.029 41 41
SLC2A1 -0.067 0.066 0.18 1 -0.17 109 110
TWIST1 -0.041 0.057 -10000 0 -0.17 53 53
ELK1 0.033 0.012 -10000 0 -0.038 13 13
HIF2A/ARNT/Cbp/p300 -0.024 0.095 0.19 1 -0.16 99 100
VEGFA -0.075 0.083 0.42 1 -0.18 125 126
CREBBP 0.032 0.004 -10000 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.036 0.046 0.18 19 -0.16 2 21
CRKL 0.026 0.092 0.16 136 -10000 0 136
mol:DAG 0.011 0.028 0.14 4 -0.14 2 6
HRAS 0.019 0.095 0.27 30 -10000 0 30
MAPK8 0.005 0.067 0.15 84 -10000 0 84
RAP1A 0.026 0.09 0.16 140 -10000 0 140
GAB1 0.027 0.093 0.16 140 -10000 0 140
MAPK14 0.02 0.083 0.15 146 -10000 0 146
EPO 0.024 0.016 -10000 0 -10000 0 0
PLCG1 0.011 0.028 0.14 4 -0.14 2 6
EPOR/TRPC2/IP3 Receptors 0.037 0.011 0.084 5 -10000 0 5
RAPGEF1 0.031 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.045 0.032 -10000 0 -0.039 1 1
GAB1/SHC/GRB2/SOS1 0.013 0.085 0.14 142 -10000 0 142
EPO/EPOR (dimer) 0.034 0.024 -10000 0 -10000 0 0
IRS2 0.027 0.091 0.16 139 -10000 0 139
STAT1 0.012 0.031 0.15 4 -0.14 2 6
STAT5B 0.012 0.03 0.15 4 -0.14 2 6
cell proliferation 0.004 0.073 0.16 88 -10000 0 88
GAB1/SHIP/PIK3R1/SHP2/SHC -0.005 0.065 0.11 117 -10000 0 117
TEC 0.027 0.093 0.16 140 -10000 0 140
SOCS3 0.032 0.004 -10000 0 -10000 0 0
STAT1 (dimer) 0.012 0.031 0.15 4 -0.14 2 6
JAK2 0.034 0.015 0.086 6 -10000 0 6
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.051 0.05 0.23 5 -10000 0 5
EPO/EPOR 0.034 0.024 -10000 0 -10000 0 0
LYN 0.022 0.031 -10000 0 -0.062 60 60
TEC/VAV2 0.005 0.07 0.13 110 -10000 0 110
elevation of cytosolic calcium ion concentration 0.037 0.011 0.084 5 -10000 0 5
SHC1 0.024 0.026 -10000 0 -0.063 40 40
EPO/EPOR (dimer)/LYN 0.035 0.043 -10000 0 -0.052 47 47
mol:IP3 0.011 0.028 0.14 4 -0.14 2 6
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.021 0.089 0.15 146 -10000 0 146
SH2B3 0.036 0.016 0.078 3 -0.067 7 10
NFKB1 0.02 0.083 0.15 146 -10000 0 146
EPO/EPOR (dimer)/JAK2/SOCS3 0.012 0.011 -10000 0 -10000 0 0
PTPN6 0.028 0.088 0.16 150 -10000 0 150
TEC/VAV2/GRB2 0.061 0.066 0.16 117 -10000 0 117
EPOR 0.037 0.011 0.084 5 -10000 0 5
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.012 0.086 0.14 142 -10000 0 142
SOS1 0 0 -10000 0 -10000 0 0
PLCG2 0.03 0.014 -10000 0 -0.063 10 10
CRKL/CBL/C3G 0.059 0.067 0.16 114 -10000 0 114
VAV2 0.024 0.088 0.16 135 -10000 0 135
CBL 0.028 0.093 0.16 143 -10000 0 143
SHC/Grb2/SOS1 0.02 0.036 -10000 0 -0.079 1 1
STAT5A 0.012 0.03 0.15 4 -0.14 2 6
GRB2 0.032 0.006 -10000 0 -10000 0 0
STAT5 (dimer) 0.023 0.041 0.18 4 -0.12 1 5
LYN/PLCgamma2 0.035 0.034 -10000 0 -0.053 61 61
PTPN11 0.032 0.003 -10000 0 -10000 0 0
BTK 0.028 0.094 0.16 145 -10000 0 145
BCL2 0.035 0.05 0.17 22 -0.19 6 28
Arf6 signaling events

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
CENTA1/KIF3B 0.021 0.004 -10000 0 -0.031 2 2
ARNO/beta Arrestin1-2 0.04 0.017 -10000 0 -0.063 11 11
EGFR 0.012 0.018 -10000 0 -0.063 6 6
EPHA2 0.029 0.015 -10000 0 -0.063 12 12
USP6 0.032 0.005 -10000 0 -10000 0 0
IQSEC1 0.032 0.006 -10000 0 0 18 18
EGFR/EGFR/EGF/EGF 0.018 0.025 -10000 0 -0.05 8 8
ARRB2 0.013 0.002 -10000 0 -10000 0 0
mol:GTP 0 0.012 0.1 3 -0.064 6 9
ARRB1 0.032 0.004 -10000 0 -10000 0 0
FBXO8 0 0 -10000 0 -10000 0 0
TSHR 0.03 0.012 -10000 0 -0.063 4 4
EGF 0.032 0.007 -10000 0 -0.063 2 2
somatostatin receptor activity 0 0 0 153 0 17 170
ARAP2 0 0 0 148 0 11 159
mol:GDP 0.06 0.064 0.14 140 -0.14 9 149
mol:PI-3-4-5-P3 0 0 0 142 0 14 156
ITGA2B 0.032 0.003 -10000 0 -10000 0 0
ARF6 0.031 0.008 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.067 0.042 -10000 0 -0.072 7 7
ADAP1 0 0 0 87 0 6 93
KIF13B 0.032 0.007 -10000 0 -0.063 2 2
HGF/MET 0.031 0.024 -10000 0 -0.05 3 3
PXN 0.032 0.003 -10000 0 -10000 0 0
ARF6/GTP 0.072 0.088 0.18 145 -0.18 14 159
EGFR/EGFR/EGF/EGF/ARFGEP100 0.023 0.033 -10000 0 -0.045 11 11
ADRB2 0.032 0.006 -10000 0 -0.063 1 1
receptor agonist activity 0 0 0 141 0 15 156
actin filament binding 0 0 0 145 0 17 162
SRC 0.031 0.008 -10000 0 -10000 0 0
ITGB3 0.032 0.003 -10000 0 -10000 0 0
GNAQ 0.032 0.006 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.001 156 -0.001 12 168
ARF6/GDP 0.024 0.068 0.14 24 -0.21 27 51
ARF6/GDP/GULP/ACAP1 0.08 0.063 0.16 126 -0.15 7 133
alphaIIb/beta3 Integrin/paxillin/GIT1 0.081 0.017 -10000 0 -0.055 2 2
ACAP1 0 0 0 46 -10000 0 46
ACAP2 0 0 0 144 0 10 154
LHCGR/beta Arrestin2 0.028 0.016 -10000 0 -0.079 11 11
EFNA1 0.028 0.019 -10000 0 -0.063 20 20
HGF 0.022 0.016 -10000 0 -0.063 1 1
CYTH3 0 0 0.001 142 0 14 156
CYTH2 0 0.001 0.002 3 -0.003 20 23
NCK1 0.03 0.015 -10000 0 -0.063 11 11
fibronectin binding 0 0 0 138 0 17 155
endosomal lumen acidification 0 0 0 150 0 18 168
microtubule-based process 0 0 -10000 0 0 8 8
GULP1 0.032 0.008 -10000 0 -0.063 3 3
GNAQ/ARNO 0.024 0.006 0.043 1 0 19 20
mol:Phosphatidic acid 0 0 0 144 0 10 154
PIP3-E 0 0 0 79 0 15 94
MET 0.022 0.016 -10000 0 -0.063 2 2
GNA14 0.031 0.009 -10000 0 -0.063 2 2
GNA15 0.03 0.013 -10000 0 -0.063 7 7
GIT1 0.032 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 152 -0.001 12 164
GNA11 0.031 0.006 -10000 0 -10000 0 0
LHCGR 0.033 0.001 -10000 0 -10000 0 0
AGTR1 0.032 0.008 -10000 0 -0.063 2 2
desensitization of G-protein coupled receptor protein signaling pathway 0.027 0.016 -10000 0 -0.079 11 11
IPCEF1/ARNO 0.014 0.02 -10000 0 -0.029 8 8
alphaIIb/beta3 Integrin 0.048 0.005 -10000 0 -10000 0 0
Osteopontin-mediated events

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
IKK alpha homodimer -0.035 0.035 0.17 5 -10000 0 5
NF kappa B1 p50/RelA/I kappa B alpha -0.058 0.053 0.22 4 -0.2 17 21
alphaV/beta3 Integrin/Osteopontin/Src 0.01 0.05 -10000 0 -0.057 179 179
AP1 -0.061 0.065 -10000 0 -0.14 61 61
ILK -0.04 0.026 0.16 5 -10000 0 5
bone resorption -0.063 0.029 0.15 4 -10000 0 4
PTK2B 0.032 0.005 -10000 0 -10000 0 0
PYK2/p130Cas 0.01 0.062 0.16 4 -0.085 18 22
ITGAV 0.029 0.017 -10000 0 -0.066 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.029 0.039 -10000 0 -0.05 394 394
alphaV/beta3 Integrin/Osteopontin 0.02 0.061 -10000 0 -0.07 76 76
MAP3K1 -0.041 0.028 0.17 6 -10000 0 6
JUN 0.031 0.005 -10000 0 -10000 0 0
MAPK3 -0.047 0.032 0.16 5 -10000 0 5
MAPK1 -0.044 0.036 0.17 6 -10000 0 6
Rac1/GDP 0.017 0.011 -10000 0 -10000 0 0
NFKB1 0.031 0.009 -10000 0 -0.063 4 4
MAPK8 -0.036 0.032 0.16 4 -10000 0 4
ITGB3 0.031 0.004 -10000 0 -10000 0 0
NFKBIA -0.047 0.043 0.16 5 -0.17 18 23
FOS 0.007 0.04 -10000 0 -0.064 120 120
CD44 -0.043 0.038 -10000 0 -0.063 397 397
CHUK 0.024 0.015 -10000 0 -0.063 1 1
PLAU -0.07 0.065 -10000 0 -0.3 4 4
NF kappa B1 p50/RelA -0.066 0.047 0.18 3 -10000 0 3
BCAR1 0 0 -10000 0 -10000 0 0
RELA 0.032 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.044 0.019 -10000 0 -0.055 15 15
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.041 0.027 0.17 5 -10000 0 5
VAV3 -0.044 0.029 0.16 5 -10000 0 5
MAP3K14 -0.042 0.03 0.17 6 -10000 0 6
ROCK2 0.032 0.003 -10000 0 -10000 0 0
SPP1 -0.003 0.047 -10000 0 -0.066 175 175
RAC1 0.023 0.015 -10000 0 -10000 0 0
Rac1/GTP -0.035 0.032 0.16 3 -10000 0 3
MMP2 -0.083 0.044 0.26 1 -0.16 1 2
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.026 0.022 -10000 0 -0.034 48 48
CCL5 0.028 0.021 -10000 0 -0.063 25 25
SDCBP 0.032 0.004 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.011 0.046 0.1 17 -0.13 33 50
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 -0.009 0.053 0.17 2 -0.18 16 18
Syndecan-1/Syntenin 0.003 0.066 0.2 16 -0.2 11 27
MAPK3 -0.034 0.052 0.16 4 -0.16 31 35
HGF/MET 0.031 0.024 -10000 0 -0.05 3 3
TGFB1/TGF beta receptor Type II 0.026 0.022 -10000 0 -0.034 48 48
BSG 0.031 0.007 -10000 0 -10000 0 0
keratinocyte migration -0.009 0.052 0.17 2 -0.18 16 18
Syndecan-1/RANTES 0.001 0.069 0.2 16 -0.18 19 35
Syndecan-1/CD147 -0.026 0.058 0.19 4 -0.16 28 32
Syndecan-1/Syntenin/PIP2 0.002 0.063 0.19 16 -0.19 11 27
LAMA5 0.027 0.017 -10000 0 -0.063 13 13
positive regulation of cell-cell adhesion 0.002 0.062 0.19 16 -0.19 11 27
MMP7 0.018 0.034 -10000 0 -0.063 75 75
HGF 0.022 0.016 -10000 0 -0.063 1 1
Syndecan-1/CASK -0.013 0.045 0.09 17 -0.19 14 31
Syndecan-1/HGF/MET 0.004 0.058 0.2 5 -0.2 11 16
regulation of cell adhesion -0.034 0.07 0.22 19 -0.2 14 33
HPSE 0.024 0.027 -10000 0 -0.063 44 44
positive regulation of cell migration -0.011 0.046 0.1 17 -0.13 33 50
SDC1 -0.009 0.042 0.1 17 -0.11 28 45
Syndecan-1/Collagen -0.011 0.046 0.1 17 -0.13 33 50
PPIB -0.035 0.043 -10000 0 -0.063 355 355
MET 0.022 0.016 -10000 0 -0.063 2 2
PRKACA 0.032 0.006 -10000 0 -10000 0 0
MMP9 -0.001 0.044 -10000 0 -0.063 165 165
MAPK1 -0.033 0.051 0.16 4 -0.16 29 33
homophilic cell adhesion -0.009 0.052 0.12 23 -0.19 13 36
MMP1 0.025 0.025 -10000 0 -0.063 38 38
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.029 0.047 -10000 0 -0.13 62 62
STMN1 -0.023 0.008 -10000 0 -0.05 24 24
Aurora B/RasGAP/Survivin 0.017 0.057 -10000 0 -0.053 196 196
Chromosomal passenger complex/Cul3 protein complex -0.034 0.056 -10000 0 -0.1 162 162
BIRC5 -0.007 0.048 -10000 0 -0.066 201 201
DES 0.016 0.11 -10000 0 -0.68 11 11
Aurora C/Aurora B/INCENP 0.049 0.033 -10000 0 -0.045 34 34
Aurora B/TACC1 0.038 0.019 -10000 0 -0.04 23 23
Aurora B/PP2A 0.042 0.023 -10000 0 -0.05 26 26
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.006 0.005 -10000 0 -0.014 24 24
mitotic metaphase/anaphase transition -0.001 0.002 0.022 1 -10000 0 1
NDC80 -0.032 0.017 -10000 0 -0.054 164 164
Cul3 protein complex 0.028 0.021 -10000 0 -10000 0 0
KIF2C -0.005 0.042 -10000 0 -0.16 16 16
PEBP1 0.031 0.005 -10000 0 -10000 0 0
KIF20A -0.002 0.046 -10000 0 -0.064 178 178
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.041 0.023 -10000 0 -0.051 23 23
SEPT1 0 0 -10000 0 -10000 0 0
SMC2 0.021 0.03 -10000 0 -0.063 56 56
SMC4 -0.039 0.041 -10000 0 -0.063 378 378
NSUN2/NPM1/Nucleolin -0.009 0.086 -10000 0 -0.55 11 11
PSMA3 0.031 0.008 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.002 0.015 1 -10000 0 1
H3F3B 0.01 0.011 -10000 0 -0.037 25 25
AURKB 0.026 0.023 -10000 0 -0.062 29 29
AURKC 0.03 0.01 -10000 0 -0.063 2 2
CDCA8 0.028 0.018 -10000 0 -0.065 16 16
cytokinesis -0.02 0.064 0.15 1 -0.2 31 32
Aurora B/Septin1 -0.012 0.068 0.14 1 -0.21 28 29
AURKA 0.027 0.018 -10000 0 -0.062 16 16
INCENP 0.032 0.005 0.065 1 -0.026 1 2
KLHL13 0 0 -10000 0 -10000 0 0
BUB1 0.032 0.009 -10000 0 -0.062 4 4
hSgo1/Aurora B/Survivin 0.008 0.039 -10000 0 -0.039 202 202
EVI5 0.031 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.008 0.072 0.16 1 -0.16 28 29
SGOL1 0 0 -10000 0 -10000 0 0
CENPA 0 0.044 -10000 0 -0.16 22 22
NCAPG 0.011 0.039 -10000 0 -0.063 111 111
Aurora B/HC8 Proteasome 0.04 0.023 -10000 0 -0.05 21 21
NCAPD2 0.014 0.037 -10000 0 -0.063 93 93
Aurora B/PP1-gamma 0.041 0.023 -10000 0 -0.05 25 25
RHOA 0.032 0.006 -10000 0 -10000 0 0
NCAPH 0.03 0.016 -10000 0 -0.063 15 15
NPM1 -0.003 0.084 -10000 0 -0.39 17 17
RASA1 0.032 0.006 -10000 0 -10000 0 0
KLHL9 0.021 0.016 -10000 0 -10000 0 0
mitotic prometaphase -0.001 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.04 0.023 -10000 0 -0.05 21 21
PPP1CC 0.032 0.004 -10000 0 -10000 0 0
Centraspindlin 0.002 0.068 0.16 1 -0.16 32 33
RhoA/GDP 0.023 0.004 -10000 0 -10000 0 0
NSUN2 -0.004 0.048 -10000 0 -0.31 11 11
MYLK 0.009 0.013 -10000 0 -0.038 34 34
KIF23 0.017 0.035 -10000 0 -0.066 77 77
VIM -0.019 0.013 0.021 1 -0.05 33 34
RACGAP1 0.002 0.045 -10000 0 -0.065 154 154
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.004 0.048 -10000 0 -0.29 12 12
Chromosomal passenger complex -0.009 0.043 0.086 1 -0.15 29 30
Chromosomal passenger complex/EVI5 0.028 0.075 -10000 0 -0.093 16 16
TACC1 0.032 0.004 -10000 0 -10000 0 0
PPP2R5D 0.032 0.004 -10000 0 -10000 0 0
CUL3 0.033 0.001 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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
PKM2 -0.054 0.17 0.47 14 -0.29 14 28
HDAC7 -0.002 0.002 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.076 0.11 -10000 0 -0.24 72 72
SMAD4 0.009 0.04 -10000 0 -0.063 117 117
ID2 -0.055 0.17 0.5 11 -0.32 5 16
AP1 0.022 0.041 -10000 0 -0.05 117 117
ABCG2 -0.058 0.16 0.48 13 -0.29 15 28
HIF1A -0.013 0.054 0.15 7 -0.085 23 30
TFF3 -0.056 0.16 0.48 14 -0.31 6 20
GATA2 0.031 0.009 -10000 0 -0.027 9 9
AKT1 -0.009 0.055 0.17 6 -0.095 1 7
response to hypoxia -0.018 0.025 0.09 7 -0.057 42 49
MCL1 -0.058 0.16 0.47 12 -0.32 5 17
NDRG1 -0.066 0.15 0.49 6 -0.29 14 20
SERPINE1 -0.052 0.15 0.48 9 -0.3 16 25
FECH -0.05 0.17 0.48 15 -0.29 15 30
FURIN -0.053 0.17 0.48 14 -0.31 6 20
NCOA2 0.033 0.004 -10000 0 -10000 0 0
EP300 0.002 0.055 0.22 13 -0.2 2 15
HMOX1 -0.074 0.16 0.46 13 -0.3 22 35
BHLHE40 -0.094 0.09 -10000 0 -0.2 168 168
BHLHE41 -0.094 0.09 -10000 0 -0.2 168 168
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.01 0.093 0.23 6 -0.1 84 90
ENG -0.035 0.079 0.27 9 -10000 0 9
JUN 0.032 0.005 -10000 0 -10000 0 0
RORA -0.055 0.17 0.5 12 -0.32 5 17
ABCB1 -0.011 0.045 -10000 0 -0.34 5 5
TFRC -0.057 0.16 0.48 14 -0.31 6 20
CXCR4 -0.073 0.16 0.48 9 -0.3 20 29
TF -0.082 0.11 0.4 1 -0.31 6 7
CITED2 -0.059 0.16 0.48 11 -0.31 8 19
HIF1A/ARNT -0.07 0.14 0.27 1 -0.25 108 109
LDHA 0.003 0.057 -10000 0 -0.46 6 6
ETS1 -0.053 0.17 0.48 14 -0.31 6 20
PGK1 -0.054 0.17 0.5 11 -0.32 5 16
NOS2 -0.094 0.09 -10000 0 -0.2 168 168
ITGB2 -0.061 0.17 0.5 11 -0.3 19 30
ALDOA -0.055 0.17 0.48 10 -0.32 5 15
Cbp/p300/CITED2 -0.095 0.1 -10000 0 -0.24 106 106
FOS 0.008 0.04 -10000 0 -0.063 120 120
HK2 -0.054 0.17 0.5 11 -0.32 5 16
SP1 0.034 0.007 -10000 0 -0.041 2 2
GCK 0.004 0.088 0.41 4 -0.37 3 7
HK1 -0.076 0.13 0.46 5 -0.29 16 21
NPM1 -0.058 0.16 0.48 11 -0.31 6 17
EGLN1 -0.058 0.16 0.47 12 -0.31 6 18
CREB1 0.035 0.008 -10000 0 -0.085 2 2
PGM1 -0.054 0.17 0.48 15 -0.29 14 29
SMAD3 0.032 0.005 -10000 0 -10000 0 0
EDN1 -0.017 0.082 0.28 2 -0.3 21 23
IGFBP1 -0.045 0.15 0.47 12 -0.29 13 25
VEGFA -0.076 0.13 0.36 12 -0.28 34 46
HIF1A/JAB1 0.009 0.052 0.14 5 -0.054 152 157
CP -0.064 0.16 0.49 9 -0.3 21 30
CXCL12 -0.066 0.15 0.46 10 -0.29 17 27
COPS5 0.033 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4 0.024 0.041 -10000 0 -0.05 113 113
BNIP3 -0.073 0.13 0.42 4 -0.29 16 20
EGLN3 -0.057 0.16 0.48 12 -0.33 5 17
CA9 -0.058 0.16 0.48 13 -0.31 8 21
TERT -0.051 0.17 0.5 11 -0.32 5 16
ENO1 -0.057 0.16 0.47 14 -0.31 6 20
PFKL -0.052 0.17 0.48 15 -0.32 5 20
NCOA1 0.031 0.007 -10000 0 -10000 0 0
ADM -0.072 0.16 0.47 11 -0.3 21 32
ARNT -0.014 0.055 0.15 7 -0.085 15 22
HNF4A 0.031 0.009 -10000 0 -10000 0 0
ADFP -0.094 0.09 -10000 0 -0.2 168 168
SLC2A1 -0.063 0.13 0.37 13 -0.3 18 31
LEP -0.045 0.14 0.47 10 -0.29 11 21
HIF1A/ARNT/Cbp/p300 -0.077 0.1 -10000 0 -0.24 75 75
EPO -0.032 0.11 0.32 13 -0.34 23 36
CREBBP 0.002 0.055 0.24 9 -0.19 2 11
HIF1A/ARNT/Cbp/p300/HDAC7 -0.082 0.1 -10000 0 -0.23 100 100
PFKFB3 -0.065 0.15 0.46 10 -0.29 15 25
NT5E -0.062 0.16 0.47 11 -0.31 10 21
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 0.039 -9999 0 -0.12 23 23
FZD6 0.014 0.037 -9999 0 -0.063 94 94
WNT6 0.032 0.002 -9999 0 -10000 0 0
WNT4 0.031 0.008 -9999 0 -0.063 2 2
FZD3 0.031 0.01 -9999 0 -0.063 3 3
WNT5A 0.003 0.044 -9999 0 -0.063 155 155
WNT11 0.032 0.007 -9999 0 -0.063 2 2
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.022 0.096 0.19 15 -0.3 47 62
CRKL -0.022 0.095 0.18 1 -0.31 48 49
HRAS -0.006 0.095 0.16 3 -0.26 50 53
mol:PIP3 0.038 0.12 0.25 33 -0.27 40 73
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 0.032 0.003 -10000 0 -10000 0 0
GAB1 -0.014 0.098 -10000 0 -0.31 47 47
FOXO3 0.025 0.13 0.24 28 -0.3 45 73
AKT1 0.03 0.14 0.23 44 -0.31 44 88
BAD 0.024 0.13 0.23 25 -0.3 44 69
megakaryocyte differentiation -0.012 0.089 -10000 0 -0.3 43 43
GSK3B 0.025 0.13 0.24 29 -0.3 45 74
RAF1 -0.012 0.081 0.15 11 -0.23 50 61
SHC1 0.024 0.026 -10000 0 -0.063 40 40
STAT3 -0.016 0.098 -10000 0 -0.31 47 47
STAT1 -0.033 0.17 -10000 0 -0.56 46 46
HRAS/SPRED1 -0.008 0.081 0.14 2 -0.22 50 52
cell proliferation -0.019 0.095 -10000 0 -0.31 47 47
PIK3CA 0.028 0.018 -10000 0 -0.062 17 17
TEC 0.032 0.005 -10000 0 -10000 0 0
RPS6KB1 0.015 0.11 0.2 3 -0.29 46 49
HRAS/SPRED2 0.006 0.091 0.19 3 -0.23 49 52
LYN/TEC/p62DOK 0.024 0.12 -10000 0 -0.31 48 48
MAPK3 -0.007 0.07 0.18 16 -0.17 46 62
STAP1 -0.015 0.098 -10000 0 -0.31 47 47
GRAP2 0.03 0.008 -10000 0 -10000 0 0
JAK2 -0.029 0.16 -10000 0 -0.5 48 48
STAT1 (dimer) -0.031 0.17 -10000 0 -0.55 47 47
mol:Gleevec 0 0.005 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.032 0.12 -10000 0 -0.31 47 47
actin filament polymerization -0.01 0.096 -10000 0 -0.3 47 47
LYN 0.021 0.031 -10000 0 -0.063 60 60
STAP1/STAT5A (dimer) -0.024 0.13 0.21 1 -0.39 49 50
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
CBL/CRKL/GRB2 0.007 0.1 0.21 1 -0.3 48 49
PI3K 0.038 0.12 0.22 3 -0.28 46 49
PTEN 0.023 0.016 -10000 0 -0.063 2 2
SCF/KIT/EPO/EPOR -0.016 0.18 -10000 0 -0.57 47 47
MAPK8 -0.019 0.096 -10000 0 -0.31 47 47
STAT3 (dimer) -0.016 0.097 -10000 0 -0.31 47 47
positive regulation of transcription -0.004 0.061 0.17 16 -0.14 35 51
mol:GDP 0.001 0.099 -10000 0 -0.28 47 47
PIK3C2B -0.017 0.097 -10000 0 -0.31 46 46
CBL/CRKL -0.005 0.1 0.2 4 -0.3 48 52
FER -0.015 0.098 -10000 0 -0.31 46 46
SH2B3 -0.015 0.097 -10000 0 -0.31 47 47
PDPK1 0.032 0.11 0.23 35 -0.26 39 74
SNAI2 -0.021 0.098 -10000 0 -0.32 47 47
positive regulation of cell proliferation -0.029 0.15 -10000 0 -0.47 49 49
KITLG 0.027 0.023 -10000 0 -0.044 45 45
cell motility -0.029 0.15 -10000 0 -0.47 49 49
PTPN6 0.029 0.017 -10000 0 -0.049 18 18
EPOR 0.016 0.077 -10000 0 -0.46 4 4
STAT5A (dimer) -0.018 0.13 -10000 0 -0.4 48 48
SOCS1 0.032 0.004 -10000 0 -10000 0 0
cell migration 0.015 0.095 0.31 45 -10000 0 45
SOS1 0 0 -10000 0 -10000 0 0
EPO 0.02 0.02 -10000 0 -0.033 29 29
VAV1 0.032 0.007 -10000 0 -0.063 1 1
GRB10 -0.011 0.076 -10000 0 -0.32 28 28
PTPN11 0.031 0.01 -10000 0 -0.028 11 11
SCF/KIT -0.008 0.1 -10000 0 -0.32 47 47
GO:0007205 0.001 0.005 -10000 0 -10000 0 0
MAP2K1 -0.017 0.068 0.15 9 -0.19 47 56
CBL 0.032 0.004 -10000 0 -10000 0 0
KIT -0.037 0.2 -10000 0 -0.62 54 54
MAP2K2 -0.015 0.075 0.2 16 -0.19 47 63
SHC/Grb2/SOS1 0.012 0.11 -10000 0 -0.3 48 48
STAT5A -0.017 0.13 -10000 0 -0.41 47 47
GRB2 0.032 0.006 -10000 0 -10000 0 0
response to radiation -0.02 0.096 -10000 0 -0.31 47 47
SHC/GRAP2 0.037 0.028 -10000 0 -0.05 38 38
PTPRO -0.012 0.091 -10000 0 -0.3 43 43
SH2B2 -0.01 0.098 -10000 0 -0.31 47 47
DOK1 0.032 0.002 -10000 0 -10000 0 0
MATK -0.015 0.096 -10000 0 -0.31 45 45
CREBBP 0.026 0.043 -10000 0 -0.1 47 47
BCL2 0.007 0.12 -10000 0 -0.56 13 13
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0 0.059 -10000 0 -0.31 11 11
Syndecan-4/Syndesmos -0.031 0.11 -10000 0 -0.55 13 13
positive regulation of JNK cascade -0.036 0.11 -10000 0 -0.43 18 18
Syndecan-4/ADAM12 -0.022 0.12 -10000 0 -0.52 15 15
CCL5 0.028 0.021 -10000 0 -0.063 25 25
Rac1/GDP 0.017 0.011 -10000 0 -10000 0 0
DNM2 0.031 0.006 -10000 0 -10000 0 0
ITGA5 0.019 0.033 -10000 0 -0.063 68 68
SDCBP 0.032 0.004 -10000 0 -10000 0 0
PLG 0.024 0.022 -10000 0 -0.056 8 8
ADAM12 0.023 0.015 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.037 0.02 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.031 0.11 -10000 0 -0.55 13 13
Syndecan-4/CXCL12/CXCR4 -0.038 0.11 -10000 0 -0.5 15 15
Syndecan-4/Laminin alpha3 -0.016 0.12 -10000 0 -0.55 13 13
MDK -0.022 0.046 -10000 0 -0.063 283 283
Syndecan-4/FZD7 -0.034 0.12 -10000 0 -0.56 13 13
Syndecan-4/Midkine -0.037 0.11 -10000 0 -0.58 12 12
FZD7 -0.012 0.048 -10000 0 -0.062 239 239
Syndecan-4/FGFR1/FGF -0.005 0.12 -10000 0 -0.55 12 12
THBS1 0.024 0.026 -10000 0 -0.063 39 39
integrin-mediated signaling pathway -0.048 0.1 -10000 0 -0.44 19 19
positive regulation of MAPKKK cascade -0.036 0.11 -10000 0 -0.43 18 18
Syndecan-4/TACI -0.015 0.12 -10000 0 -0.56 13 13
CXCR4 -0.017 0.048 -10000 0 -0.063 263 263
cell adhesion -0.007 0.03 0.2 3 -0.085 14 17
Syndecan-4/Dynamin -0.018 0.12 -10000 0 -0.56 13 13
Syndecan-4/TSP1 -0.018 0.12 -10000 0 -0.56 13 13
Syndecan-4/GIPC -0.018 0.12 -10000 0 -0.55 13 13
Syndecan-4/RANTES -0.016 0.12 -10000 0 -0.56 13 13
ITGB1 0.025 0.014 -10000 0 -10000 0 0
LAMA1 0 0 -10000 0 -10000 0 0
LAMA3 0.029 0.017 -10000 0 -0.063 15 15
RAC1 0.023 0.015 -10000 0 -10000 0 0
PRKCA -0.003 0.081 0.8 5 -10000 0 5
Syndecan-4/alpha-Actinin -0.018 0.12 -10000 0 -0.56 13 13
TFPI 0.012 0.039 -10000 0 -0.063 111 111
F2 0.029 0.02 -10000 0 -0.039 28 28
alpha5/beta1 Integrin 0.025 0.034 -10000 0 -0.05 61 61
positive regulation of cell adhesion -0.026 0.11 -10000 0 -0.53 13 13
ACTN1 0.023 0.026 -10000 0 -0.063 40 40
TNC -0.056 0.022 -10000 0 -0.063 469 469
Syndecan-4/CXCL12 -0.022 0.12 -10000 0 -0.56 13 13
FGF6 0.031 0.007 -10000 0 -10000 0 0
RHOA 0.032 0.006 -10000 0 -10000 0 0
CXCL12 0.023 0.019 -10000 0 -0.063 12 12
TNFRSF13B 0.032 0.004 -10000 0 -10000 0 0
FGF2 0.032 0.007 -10000 0 -0.063 2 2
FGFR1 0.032 0.005 -10000 0 -0.063 1 1
Syndecan-4/PI-4-5-P2 -0.031 0.11 -10000 0 -0.55 13 13
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.01 0.039 -10000 0 -0.053 139 139
cell migration -0.019 0.012 -10000 0 -10000 0 0
PRKCD 0.026 0.022 -10000 0 -0.053 10 10
vasculogenesis -0.017 0.12 -10000 0 -0.49 15 15
SDC4 -0.029 0.11 -10000 0 -0.48 19 19
Syndecan-4/Tenascin C -0.049 0.11 -10000 0 -0.46 19 19
Syndecan-4/PI-4-5-P2/PKC alpha -0.03 0.016 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.015 0.12 -10000 0 -0.56 13 13
MMP9 -0.004 0.044 -10000 0 -0.06 179 179
Rac1/GTP -0.007 0.031 0.2 3 -0.084 16 19
cytoskeleton organization -0.03 0.1 -10000 0 -0.53 13 13
GIPC1 0.031 0.006 -10000 0 0 18 18
Syndecan-4/TFPI -0.023 0.12 -10000 0 -0.55 13 13
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.02 0.071 0.3 1 -0.24 13 14
MAP3K8 0.018 0.026 -10000 0 -0.063 37 37
FOS 0.011 0.062 0.25 2 -0.24 13 15
PRKCA 0.031 0.004 -10000 0 0 6 6
PTPN7 0.03 0.008 0.066 1 -0.044 2 3
HRAS 0.031 0.007 -10000 0 -10000 0 0
PRKCB -0.001 0.002 0.018 1 -0.003 121 122
NRAS 0.008 0.041 -10000 0 -0.063 125 125
RAS family/GTP 0.03 0.046 -10000 0 -0.044 119 119
MAPK3 0.026 0.032 -10000 0 -0.36 2 2
MAP2K1 -0.003 0.026 0.12 1 -0.16 3 4
ELK1 0.031 0.005 -10000 0 -0.022 2 2
BRAF 0.004 0.017 0.098 1 -0.23 2 3
mol:GTP 0 0 0.003 1 -0.001 124 125
MAPK1 0 0.1 -10000 0 -0.35 36 36
RAF1 0.006 0.016 0.098 1 -0.22 2 3
KRAS 0.03 0.008 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 -0.016 0.097 0.3 1 -0.32 27 28
ACTA1 -0.045 0.088 0.4 1 -0.24 56 57
NUMA1 -0.014 0.086 0.3 1 -0.31 28 29
SPTAN1 -0.045 0.091 0.21 8 -0.31 33 41
LIMK1 -0.002 0.1 0.18 75 -0.29 25 100
BIRC3 0.026 0.023 -10000 0 -0.063 30 30
BIRC2 0.032 0.004 -10000 0 -10000 0 0
BAX 0.03 0.013 -10000 0 -0.063 6 6
CASP10 -0.02 0.013 -10000 0 -0.051 19 19
CRMA 0 0 -10000 0 -0.001 2 2
XIAP 0 0 0.001 2 -0.001 9 11
PTK2 -0.015 0.086 0.3 1 -0.3 30 31
DIABLO 0.032 0.004 -10000 0 -10000 0 0
apoptotic nuclear changes -0.041 0.094 0.21 8 -0.31 33 41
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.032 0.004 -10000 0 -10000 0 0
GSN -0.048 0.091 0.21 8 -0.26 48 56
MADD 0.031 0.006 -10000 0 -10000 0 0
TFAP2A 0.03 0.09 -10000 0 -0.62 8 8
BID -0.004 0.014 -10000 0 -0.1 7 7
MAP3K1 -0.009 0.056 -10000 0 -0.42 6 6
TRADD 0.032 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.046 0.012 -10000 0 -0.05 3 3
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.049 0.092 0.2 10 -0.25 50 60
CASP9 0.031 0.009 -10000 0 -0.063 3 3
DNA repair 0.026 0.06 0.18 30 -0.14 1 31
neuron apoptosis 0.021 0.069 -10000 0 -0.62 5 5
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.034 0.093 0.28 3 -0.32 33 36
APAF1 0.032 0.004 -10000 0 -10000 0 0
CASP6 0.013 0.1 0.36 1 -0.92 4 5
TRAF2 0.031 0.006 -10000 0 -10000 0 0
ICAD/CAD -0.053 0.091 0.31 5 -0.31 32 37
CASP7 -0.055 0.1 -10000 0 -0.22 134 134
KRT18 0.013 0.059 -10000 0 -0.49 5 5
apoptosis -0.048 0.1 0.6 1 -0.32 34 35
DFFA -0.049 0.089 0.26 3 -0.28 40 43
DFFB -0.049 0.089 0.26 3 -0.28 39 42
PARP1 -0.026 0.061 0.14 1 -0.18 30 31
actin filament polymerization -0.006 0.1 0.27 25 -0.17 75 100
TNF 0.032 0.006 -10000 0 -0.063 2 2
CYCS 0 0.029 0.25 1 -0.18 3 4
SATB1 0.017 0.1 0.37 2 -0.83 4 6
SLK -0.052 0.09 0.42 1 -0.25 54 55
p15 BID/BAX -0.011 0.066 0.21 1 -0.2 39 40
CASP2 0.041 0.088 0.2 116 -0.14 7 123
JNK cascade 0.009 0.056 0.42 6 -10000 0 6
CASP3 -0.047 0.091 0.24 1 -0.24 58 59
LMNB2 0.047 0.082 0.24 11 -0.31 3 14
RIPK1 0.03 0.013 -10000 0 -0.063 9 9
CASP4 0.013 0.038 -10000 0 -0.063 101 101
Mammalian IAPs/DIABLO 0.054 0.028 -10000 0 -0.042 37 37
negative regulation of DNA binding 0.03 0.089 -10000 0 -0.61 8 8
stress fiber formation -0.052 0.089 0.42 1 -0.25 51 52
GZMB -0.018 0.012 0 138 -0.052 19 157
CASP1 -0.011 0.034 -10000 0 -0.053 186 186
LMNB1 0.038 0.1 0.24 12 -0.37 10 22
APP 0.021 0.069 -10000 0 -0.63 5 5
TNFRSF1A 0 0.044 -10000 0 -0.063 165 165
response to stress 0 0 0.001 6 -0.001 21 27
CASP8 -0.012 0.004 0 1 -0.039 9 10
VIM -0.042 0.099 0.43 1 -0.33 32 33
LMNA 0.05 0.081 0.2 38 -0.31 3 41
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.002 0.039 -10000 0 -0.17 11 11
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.051 0.086 0.2 2 -0.3 36 38
APAF-1/Caspase 9 0.021 0.073 -10000 0 -0.62 6 6
nuclear fragmentation during apoptosis -0.014 0.085 0.29 1 -0.3 28 29
CFL2 0.006 0.1 0.17 75 -0.27 25 100
GAS2 -0.052 0.087 0.2 2 -0.29 39 41
positive regulation of apoptosis 0.049 0.09 0.2 39 -0.32 7 46
PRF1 0.022 0.019 -10000 0 -0.063 12 12
PDGFR-alpha signaling pathway

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
PDGFRA 0.015 0.027 -10000 0 -0.032 103 103
PDGF/PDGFRA/CRKL 0.037 0.021 -10000 0 -0.051 5 5
positive regulation of JUN kinase activity 0.039 0.035 -10000 0 -0.044 42 42
CRKL 0.031 0.007 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 0.038 0.021 -10000 0 -0.051 5 5
AP1 -0.027 0.073 0.14 58 -0.13 97 155
mol:IP3 -0.022 0.014 0.033 4 -0.066 2 6
PLCG1 -0.022 0.015 0.033 4 -0.066 2 6
PDGF/PDGFRA/alphaV Integrin 0.036 0.026 -10000 0 -0.053 20 20
RAPGEF1 0.031 0.006 -10000 0 -10000 0 0
CRK 0.032 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.022 0.014 0.033 4 -0.066 2 6
CAV3 0.032 0.004 -10000 0 -10000 0 0
CAV1 -0.018 0.041 -10000 0 -0.063 218 218
SHC/Grb2/SOS1 0.041 0.036 -10000 0 -0.044 42 42
PDGF/PDGFRA/Shf 0.019 0.011 -10000 0 -0.04 6 6
FOS -0.04 0.048 0.17 4 -0.12 98 102
JUN -0.026 0.021 0.025 36 -10000 0 36
oligodendrocyte development 0.036 0.025 -10000 0 -0.053 20 20
GRB2 0.032 0.006 -10000 0 0 15 15
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
mol:DAG -0.022 0.014 0.033 4 -0.066 2 6
PDGF/PDGFRA 0.015 0.027 -10000 0 -0.032 103 103
actin cytoskeleton reorganization 0.036 0.022 -10000 0 -0.05 4 4
SRF -0.021 0.007 0.02 1 -10000 0 1
SHC1 0.024 0.026 -10000 0 -0.063 40 40
PI3K 0.045 0.034 -10000 0 -0.05 22 22
PDGF/PDGFRA/Crk/C3G 0.049 0.031 -10000 0 -0.043 9 9
JAK1 -0.018 0.014 0.022 25 -0.055 2 27
ELK1/SRF -0.01 0.059 0.13 72 -10000 0 72
SHB 0.03 0.009 -10000 0 -10000 0 0
SHF 0 0 -10000 0 -10000 0 0
CSNK2A1 0.026 0.024 -10000 0 -0.03 65 65
GO:0007205 -0.016 0.011 0.023 4 -0.057 5 9
SOS1 0 0 -10000 0 -10000 0 0
Ras protein signal transduction 0.039 0.035 -10000 0 -0.044 42 42
PDGF/PDGFRA/SHB 0.036 0.022 -10000 0 -0.05 4 4
PDGF/PDGFRA/Caveolin-1 -0.009 0.038 -10000 0 -0.054 186 186
ITGAV 0.03 0.016 -10000 0 -0.063 15 15
ELK1 -0.022 0.015 0.026 4 -0.07 2 6
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
PDGF/PDGFRA/Crk 0.038 0.021 -10000 0 -0.05 5 5
JAK-STAT cascade -0.018 0.014 0.022 25 -0.055 2 27
cell proliferation 0.019 0.011 -10000 0 -0.04 6 6
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.001 0.009 -10000 0 -0.028 33 33
BUB1B -0.012 0.035 0.083 13 -0.12 22 35
PLK1 0.007 0.023 0.071 35 -0.092 4 39
PLK1S1 0.003 0.014 0.042 35 -0.047 4 39
KIF2A -0.001 0.025 0.13 8 -0.097 3 11
regulation of mitotic centrosome separation 0.007 0.023 0.071 35 -0.092 4 39
GOLGA2 0.031 0.006 -10000 0 -10000 0 0
Hec1/SPC24 0.008 0.028 0.11 2 -0.079 9 11
WEE1 -0.018 0.066 -10000 0 -0.34 15 15
cytokinesis -0.011 0.04 0.16 3 -0.16 10 13
PP2A-alpha B56 0.056 0.077 -10000 0 -0.56 7 7
AURKA 0.007 0.017 0.092 4 -0.18 1 5
PICH/PLK1 -0.031 0.021 0.098 2 -0.088 11 13
CENPE -0.003 0.026 0.18 4 -0.12 3 7
RhoA/GTP 0.023 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.001 0.026 0.13 9 -0.096 3 12
PPP2CA 0.032 0.005 -10000 0 -10000 0 0
FZR1 0.031 0.006 -10000 0 -10000 0 0
TPX2 -0.01 0.025 0.13 1 -0.09 1 2
PAK1 0.032 0.005 -10000 0 -10000 0 0
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.032 0.005 -10000 0 -10000 0 0
CLSPN 0.009 0.031 0.1 2 -0.23 7 9
GORASP1 0.032 0.005 -10000 0 -10000 0 0
metaphase 0 0.002 0.015 5 -0.011 3 8
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.003 0.014 0.042 35 -0.047 4 39
G2 phase of mitotic cell cycle -0.001 0.002 0.01 8 -0.011 1 9
STAG2 0.028 0.021 -10000 0 -0.063 26 26
GRASP65/GM130/RAB1/GTP 0.011 0.067 -10000 0 -0.51 8 8
spindle elongation 0.007 0.023 0.071 35 -0.092 4 39
ODF2 0.032 0.007 -10000 0 -10000 0 0
BUB1 0.023 0.074 -10000 0 -0.59 7 7
TPT1 -0.005 0.055 0.084 3 -0.19 39 42
CDC25C 0.011 0.031 -10000 0 -0.25 6 6
CDC25B 0.026 0.018 -10000 0 -0.059 17 17
SGOL1 0.001 0.009 0.028 33 -10000 0 33
RHOA 0.032 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 -0.011 0.047 -10000 0 -0.089 38 38
CDC14B -0.011 0.004 0.009 11 -10000 0 11
CDC20 -0.022 0.047 -10000 0 -0.063 287 287
PLK1/PBIP1 -0.017 0.015 0.054 3 -0.069 12 15
mitosis -0.003 0.003 0.015 5 -10000 0 5
FBXO5 -0.013 0.033 0.11 7 -0.097 33 40
CDC2 -0.001 0.002 -10000 0 -0.01 3 3
NDC80 0 0.045 -10000 0 -0.063 170 170
metaphase plate congression 0.009 0.033 -10000 0 -0.23 8 8
ERCC6L -0.024 0.036 -10000 0 -0.097 32 32
NLP/gamma Tubulin 0.004 0.016 0.063 12 -0.064 6 18
microtubule cytoskeleton organization -0.005 0.055 0.084 3 -0.19 39 42
G2/M transition DNA damage checkpoint 0 0.002 0.011 5 -10000 0 5
PPP1R12A 0.032 0.006 -10000 0 -10000 0 0
interphase 0 0.002 0.011 5 -10000 0 5
PLK1/PRC1-2 0.007 0.047 0.13 3 -0.086 17 20
GRASP65/GM130/RAB1/GTP/PLK1 0.053 0.029 0.14 1 -0.086 5 6
RAB1A 0.032 0.004 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.006 0.022 0.066 44 -0.06 4 48
mitotic prometaphase -0.001 0.003 0.019 8 -10000 0 8
proteasomal ubiquitin-dependent protein catabolic process -0.039 0.097 0.13 3 -0.23 100 103
microtubule-based process 0.009 0.031 0.12 3 -0.081 10 13
Golgi organization 0.007 0.023 0.071 35 -0.092 4 39
Cohesin/SA2 0.021 0.022 0.09 4 -0.07 6 10
PPP1CB/MYPT1 0.047 0.01 -10000 0 -0.046 1 1
KIF20A -0.001 0.045 -10000 0 -0.063 178 178
APC/C/CDC20 -0.001 0.03 0.12 1 -0.076 13 14
PPP2R1A 0.03 0.009 -10000 0 -10000 0 0
chromosome segregation -0.017 0.015 0.054 3 -0.068 12 15
PRC1 -0.008 0.047 -10000 0 -0.063 213 213
ECT2 -0.005 0.036 0.18 12 -0.12 3 15
C13orf34 0.005 0.02 0.064 35 -0.068 4 39
NUDC 0.009 0.033 -10000 0 -0.23 8 8
regulation of attachment of spindle microtubules to kinetochore -0.012 0.034 0.082 13 -0.12 22 35
spindle assembly 0.004 0.02 0.062 31 -0.077 4 35
spindle stabilization 0.003 0.014 0.042 35 -0.047 4 39
APC/C/HCDH1 0.025 0.007 -10000 0 -10000 0 0
MKLP2/PLK1 0.009 0.031 0.12 3 -0.081 10 13
CCNB1 -0.02 0.048 -10000 0 -0.063 280 280
PPP1CB 0.032 0.007 -10000 0 -0.058 2 2
BTRC 0.024 0.014 -10000 0 -10000 0 0
ROCK2 0.016 0.025 0.14 1 -0.22 2 3
TUBG1 0.009 0.022 0.084 3 -0.18 4 7
G2/M transition of mitotic cell cycle -0.025 0.029 -10000 0 -0.094 30 30
MLF1IP -0.034 0.012 -10000 0 -0.04 420 420
INCENP 0.032 0.004 -10000 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.027 0.02 -10000 0 -0.045 2 2
VEGFR1 homodimer/NRP1 -0.013 0.005 -10000 0 -10000 0 0
mol:DAG -0.024 0.017 0.18 2 -10000 0 2
VEGFR1 homodimer/NRP1/VEGFR 121 -0.01 0.035 -10000 0 -0.041 273 273
CaM/Ca2+ -0.027 0.019 0.18 2 -10000 0 2
HIF1A 0.035 0.011 -10000 0 -0.061 2 2
GAB1 0.032 0.008 -10000 0 -0.063 3 3
AKT1 -0.023 0.034 0.13 15 -0.19 1 16
PLCG1 -0.024 0.017 0.18 2 -10000 0 2
NOS3 -0.007 0.042 0.18 4 -0.21 14 18
CBL 0.032 0.004 -10000 0 -10000 0 0
mol:NO 0.006 0.055 0.15 20 -0.2 15 35
FLT1 -0.016 0.006 -10000 0 -10000 0 0
PGF 0.027 0.02 -10000 0 -0.063 19 19
VEGFR1 homodimer/NRP2/VEGFR121 -0.007 0.049 -10000 0 -0.057 33 33
CALM1 0.029 0.01 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
eNOS/Hsp90 0.022 0.075 0.19 12 -0.22 24 36
endothelial cell proliferation -0.011 0.047 0.12 33 -0.14 20 53
mol:Ca2+ -0.024 0.017 0.18 2 -10000 0 2
MAPK3 -0.035 0.017 0.15 2 -10000 0 2
MAPK1 -0.033 0.019 0.15 2 -10000 0 2
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
PLGF homodimer 0.027 0.02 -10000 0 -0.063 19 19
PRKACA 0.032 0.006 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.018 0.041 -10000 0 -0.063 218 218
VEGFA homodimer -0.019 0.047 -10000 0 -0.063 274 274
VEGFR1 homodimer/VEGFA homodimer -0.012 0.039 -10000 0 -0.046 269 269
platelet activating factor biosynthetic process -0.037 0.02 0.14 2 -10000 0 2
PI3K 0.044 0.047 0.17 1 -0.077 1 2
PRKCA -0.028 0.018 0.17 2 -10000 0 2
PRKCB -0.022 0.016 0.17 2 -10000 0 2
VEGFR1 homodimer/PLGF homodimer 0.026 0.021 -10000 0 -0.045 21 21
VEGFA -0.019 0.047 -10000 0 -0.063 274 274
VEGFB 0.032 0.004 -10000 0 -10000 0 0
mol:IP3 -0.024 0.017 0.18 2 -10000 0 2
RASA1 -0.027 0.015 0.18 2 -10000 0 2
NRP2 0.032 0.004 -10000 0 -0.063 1 1
VEGFR1 homodimer -0.016 0.006 -10000 0 -10000 0 0
VEGFB homodimer 0.032 0.004 -10000 0 -10000 0 0
NCK1 0.03 0.015 -10000 0 -0.063 11 11
eNOS/Caveolin-1 -0.015 0.051 0.17 1 -0.22 17 18
PTPN11 0.032 0.003 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.042 0.046 0.16 1 -0.077 1 2
mol:L-citrulline 0.006 0.055 0.15 20 -0.2 15 35
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.008 0.059 -10000 0 -0.077 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.008 0.049 -10000 0 -0.058 35 35
CD2AP 0.023 0.028 -10000 0 -0.063 48 48
PI3K/GAB1 0.052 0.055 0.18 1 -10000 0 1
PDPK1 -0.031 0.035 0.15 16 -10000 0 16
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.006 0.049 -10000 0 -0.058 33 33
mol:NADP 0.006 0.055 0.15 20 -0.2 15 35
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.009 0.058 -10000 0 -0.075 2 2
VEGFR1 homodimer/NRP2 0.027 0.021 -10000 0 -0.045 3 3
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.032 0.004 -10000 0 -10000 0 0
Caspase 8 (4 units) -0.005 0.078 0.15 3 -0.12 139 142
NEF 0.002 0.001 -10000 0 -10000 0 0
NFKBIA 0.027 0.017 -10000 0 -0.035 27 27
BIRC3 -0.033 0.021 0.17 3 -10000 0 3
CYCS 0.004 0.068 0.17 61 -0.1 43 104
RIPK1 0.03 0.013 -10000 0 -0.063 9 9
CD247 0.033 0.008 -10000 0 -0.063 2 2
MAP2K7 -0.007 0.088 -10000 0 -0.4 7 7
protein ubiquitination 0.002 0.05 0.2 7 -0.24 8 15
CRADD 0.032 0.004 -10000 0 -10000 0 0
DAXX 0.032 0.005 -10000 0 -0.063 1 1
FAS 0.013 0.03 -10000 0 -0.063 55 55
BID -0.018 0.044 0.14 4 -0.1 94 98
NF-kappa-B/RelA/I kappa B alpha 0.054 0.042 -10000 0 -0.062 35 35
TRADD 0.032 0.004 -10000 0 -10000 0 0
MAP3K5 0.03 0.009 -10000 0 -10000 0 0
CFLAR 0.032 0.01 -10000 0 -0.063 5 5
FADD 0.032 0.006 -10000 0 -0.063 1 1
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.054 0.042 -10000 0 -0.062 35 35
MAPK8 -0.004 0.085 0.54 1 -0.38 8 9
APAF1 0.032 0.004 -10000 0 -10000 0 0
TRAF1 0.031 0.008 -10000 0 -0.063 1 1
TRAF2 0.031 0.006 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.007 0.024 0.15 4 -0.13 6 10
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.014 0.05 -10000 0 -0.23 10 10
CHUK 0.003 0.05 0.2 7 -0.25 7 14
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.038 0.071 -10000 0 -0.071 3 3
TCRz/NEF 0.028 0.006 -10000 0 -0.039 2 2
TNF 0.032 0.006 -10000 0 -0.063 2 2
FASLG -0.016 0.003 -10000 0 -10000 0 0
NFKB1 0.028 0.018 -10000 0 -0.037 32 32
TNFR1A/BAG4/TNF-alpha 0.025 0.054 -10000 0 -0.048 175 175
CASP6 0.008 0.086 -10000 0 -0.44 5 5
CASP7 -0.06 0.11 0.18 5 -0.24 131 136
RELA 0.029 0.016 -10000 0 -0.033 30 30
CASP2 0.023 0.015 -10000 0 -10000 0 0
CASP3 -0.03 0.071 0.18 4 -0.22 30 34
TNFRSF1A 0 0.044 -10000 0 -0.063 165 165
TNFR1A/BAG4 0.014 0.045 -10000 0 -0.05 164 164
CASP8 0.031 0.013 -10000 0 -0.063 9 9
CASP9 0.031 0.009 -10000 0 -0.063 3 3
MAP3K14 0.01 0.054 0.18 1 -0.25 10 11
APAF-1/Caspase 9 -0.017 0.071 0.13 65 -0.16 7 72
BCL2 -0.016 0.086 0.33 3 -0.36 8 11
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.045 0.018 -10000 0 -0.05 15 15
AKT1 -0.023 0.074 0.22 6 -0.27 16 22
PTK2B -0.034 0.059 0.16 38 -10000 0 38
VEGFR2 homodimer/Frs2 0.025 0.024 -10000 0 -0.089 13 13
CAV1 -0.018 0.041 -10000 0 -0.063 218 218
CALM1 0.029 0.01 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.004 0.05 -10000 0 -0.081 29 29
endothelial cell proliferation -0.005 0.079 0.21 25 -0.25 10 35
mol:Ca2+ -0.03 0.052 0.15 33 -0.12 2 35
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.002 0.059 0.17 12 -0.1 14 26
RP11-342D11.1 -0.032 0.037 0.16 15 -0.098 11 26
CDH5 0.027 0.022 -10000 0 -0.063 29 29
VEGFA homodimer 0.002 0.052 -10000 0 -0.043 274 274
SHC1 0.024 0.026 -10000 0 -0.063 40 40
SHC2 0.031 0.007 -10000 0 -10000 0 0
HRAS/GDP -0.017 0.053 -10000 0 -0.096 29 29
SH2D2A 0.032 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.007 0.06 0.2 2 -0.2 4 6
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.005 0.051 -10000 0 -0.082 30 30
VEGFR1 homodimer 0.03 0.008 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.003 0.068 0.16 13 -0.11 16 29
GRB10 -0.021 0.047 0.16 24 -0.12 1 25
PTPN11 0.032 0.003 -10000 0 -10000 0 0
GRB2 0.032 0.006 -10000 0 -10000 0 0
PAK1 0.032 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.005 0.076 0.18 12 -0.11 21 33
HRAS 0.031 0.007 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.004 0.046 0.13 11 -0.21 8 19
HIF1A 0.03 0.01 -10000 0 -0.063 2 2
FRS2 0.031 0.007 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.002 0.058 0.17 12 -0.1 14 26
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.032 0.004 -10000 0 -10000 0 0
Nck/Pak 0.044 0.017 -10000 0 -0.05 11 11
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.007 0.05 -10000 0 -0.074 46 46
mol:GDP -0.011 0.056 -10000 0 -0.094 29 29
mol:NADP 0.005 0.058 0.25 4 -0.2 1 5
eNOS/Hsp90 0.014 0.06 0.26 4 -0.2 1 5
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
mol:IP3 -0.03 0.052 0.15 33 -0.12 2 35
HIF1A/ARNT 0.044 0.015 -10000 0 -0.05 2 2
SHB 0.03 0.009 -10000 0 -10000 0 0
VEGFA -0.019 0.048 -10000 0 -0.064 274 274
VEGFC 0.03 0.015 -10000 0 -0.063 11 11
FAK1/Vinculin -0.004 0.059 0.2 11 -0.2 9 20
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.032 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.003 0.067 0.17 13 -0.1 14 27
PTPN6 0.029 0.015 -10000 0 -0.063 11 11
EPAS1 0.034 0.019 -10000 0 -0.072 16 16
mol:L-citrulline 0.005 0.058 0.25 4 -0.2 1 5
ITGAV 0.03 0.016 -10000 0 -0.063 15 15
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.004 0.065 0.17 13 -0.1 12 25
VEGFR2 homodimer/VEGFA homodimer -0.005 0.055 -10000 0 -0.083 42 42
VEGFR2/3 heterodimer 0.026 0.024 -10000 0 -0.089 14 14
VEGFB 0.032 0.004 -10000 0 -10000 0 0
MAPK11 -0.03 0.06 0.16 28 -0.17 14 42
VEGFR2 homodimer -0.02 0.015 -10000 0 -0.099 14 14
FLT1 0.03 0.008 -10000 0 -10000 0 0
NEDD4 0.028 0.019 -10000 0 -0.044 29 29
MAPK3 -0.019 0.065 0.19 15 -10000 0 15
MAPK1 -0.021 0.062 0.19 12 -10000 0 12
VEGFA145/NRP2 -0.005 0.049 -10000 0 -0.05 275 275
VEGFR1/2 heterodimer 0.024 0.025 -10000 0 -0.089 14 14
KDR -0.02 0.015 -10000 0 -0.1 14 14
VEGFA165/NRP1/VEGFR2 homodimer -0.002 0.06 0.16 14 -0.089 28 42
SRC 0.031 0.008 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.018 0.066 0.2 14 -10000 0 14
PI3K -0.019 0.064 0.17 8 -0.16 23 31
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.006 0.051 -10000 0 -0.08 33 33
FES -0.032 0.054 0.16 36 -0.12 2 38
GAB1 -0.018 0.067 0.16 10 -0.19 31 41
VEGFR2 homodimer/VEGFA homodimer/Src -0.003 0.05 -10000 0 -0.083 29 29
CTNNB1 0.032 0.005 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
ARNT 0.032 0.005 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.008 0.047 0.27 3 -0.19 2 5
VEGFR2 homodimer/VEGFA homodimer/Yes -0.013 0.051 -10000 0 -0.076 65 65
PI3K/GAB1 -0.02 0.076 0.17 8 -0.23 20 28
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.006 0.073 0.18 12 -0.1 11 23
PRKACA 0.032 0.006 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.041 0.031 -10000 0 -0.071 24 24
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
CDC42 -0.032 0.052 0.16 33 -0.12 2 35
actin cytoskeleton reorganization -0.005 0.051 -10000 0 -0.082 30 30
PTK2 -0.011 0.059 0.15 29 -0.19 11 40
EDG1 -0.032 0.037 0.16 15 -0.098 11 26
mol:DAG -0.03 0.052 0.15 33 -0.12 2 35
CaM/Ca2+ -0.031 0.051 0.15 30 -0.13 1 31
MAP2K3 -0.036 0.05 0.14 33 -10000 0 33
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.043 0.095 0.18 133 -0.1 17 150
PLCG1 -0.03 0.052 0.16 33 -0.12 2 35
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.003 0.065 0.17 11 -0.1 14 25
IQGAP1 0.01 0.04 -10000 0 -0.063 120 120
YES1 0.017 0.034 -10000 0 -0.063 75 75
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.005 0.051 -10000 0 -0.081 31 31
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.007 0.051 -10000 0 -0.08 34 34
cell migration -0.009 0.075 0.18 19 -0.2 28 47
mol:PI-3-4-5-P3 -0.018 0.062 0.16 8 -0.15 23 31
FYN 0.029 0.011 -10000 0 -0.063 1 1
VEGFB/NRP1 -0.03 0.051 0.15 35 -0.12 2 37
mol:NO 0.005 0.058 0.25 4 -0.2 1 5
PXN 0.032 0.003 -10000 0 -10000 0 0
HRAS/GTP -0.047 0.023 -10000 0 -0.096 29 29
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.008 0.04 -10000 0 -0.095 22 22
VHL 0 0 -10000 0 -10000 0 0
ITGB3 0.032 0.003 -10000 0 -10000 0 0
NOS3 0.004 0.061 0.26 4 -0.22 1 5
VEGFR2 homodimer/VEGFA homodimer/Sck -0.004 0.05 -10000 0 -0.081 30 30
RAC1 0.023 0.015 -10000 0 -10000 0 0
PRKCA -0.033 0.05 0.14 34 -10000 0 34
PRKCB -0.028 0.048 0.14 33 -0.12 1 34
VCL 0.025 0.014 -10000 0 -10000 0 0
VEGFA165/NRP1 -0.031 0.041 0.17 17 -0.12 2 19
VEGFR1/2 heterodimer/VEGFA homodimer -0.006 0.051 -10000 0 -0.075 44 44
VEGFA165/NRP2 -0.005 0.049 -10000 0 -0.05 275 275
MAPKKK cascade -0.033 0.039 0.18 6 -10000 0 6
NRP2 0.032 0.004 -10000 0 -0.063 1 1
VEGFC homodimer 0.029 0.015 -10000 0 -0.063 11 11
NCK1 0.03 0.015 -10000 0 -0.063 11 11
ROCK1 0.032 0.005 -10000 0 -10000 0 0
FAK1/Paxillin -0.002 0.068 0.2 14 -0.2 9 23
MAP3K13 -0.033 0.052 0.16 32 -0.12 2 34
PDPK1 -0.034 0.053 0.15 8 -0.16 14 22
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.013 0.052 -10000 0 -0.35 10 10
Crk/p130 Cas/Paxillin -0.037 0.081 -10000 0 -0.18 117 117
JUN -0.012 0.029 -10000 0 -0.18 7 7
HRAS 0.031 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 0.043 0.05 -10000 0 -0.056 3 3
RAP1A 0.032 0.004 -10000 0 -10000 0 0
FRS2 0.031 0.007 -10000 0 -10000 0 0
RAP1A/GDP 0.024 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.048 0.058 -10000 0 -0.058 1 1
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.032 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.032 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.036 0.042 -10000 0 -0.032 138 138
RHOA 0.032 0.006 -10000 0 -10000 0 0
RAP1A/GTP 0.044 0.056 -10000 0 -10000 0 0
GRB7 0.032 0.005 -10000 0 -0.063 1 1
RET51/GFRalpha1/GDNF 0.048 0.057 -10000 0 -0.058 1 1
MAPKKK cascade -0.005 0.076 -10000 0 -0.13 126 126
BCAR1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.036 0.042 -10000 0 -0.032 138 138
lamellipodium assembly -0.013 0.061 -10000 0 -0.17 49 49
RET51/GFRalpha1/GDNF/SHC 0.038 0.061 -10000 0 -0.062 6 6
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
RET9/GFRalpha1/GDNF/SHC 0.029 0.046 -10000 0 -0.034 165 165
RET9/GFRalpha1/GDNF/Shank3 0.024 0.029 -10000 0 -0.024 137 137
MAPK3 -0.038 0.03 0.2 4 -10000 0 4
DOK1 0.032 0.002 -10000 0 -10000 0 0
DOK6 0 0 -10000 0 -10000 0 0
PXN 0.032 0.003 -10000 0 -10000 0 0
neurite development -0.027 0.029 0.2 5 -10000 0 5
DOK5 0.028 0.011 -10000 0 -10000 0 0
GFRA1 0.024 0.015 -10000 0 -0.063 1 1
MAPK8 0.001 0.03 -10000 0 -0.12 25 25
HRAS/GTP 0.019 0.097 -10000 0 -0.14 131 131
tube development 0.02 0.035 0.16 10 -10000 0 10
MAPK1 -0.033 0.046 0.28 6 -10000 0 6
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.009 0.055 -10000 0 -0.11 122 122
Rac1/GDP 0.017 0.011 -10000 0 -10000 0 0
SRC 0.031 0.008 -10000 0 -10000 0 0
PDLIM7 0.032 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 0.046 0.05 -10000 0 -10000 0 0
SHC1 0.024 0.026 -10000 0 -0.063 40 40
RET51/GFRalpha1/GDNF/Dok4 0.047 0.058 -10000 0 -0.058 1 1
RET51/GFRalpha1/GDNF/Dok5 0.047 0.053 -10000 0 -10000 0 0
PRKCA 0.032 0.004 -10000 0 0 6 6
HRAS/GDP 0.023 0.005 -10000 0 -10000 0 0
CREB1 -0.036 0.096 -10000 0 -0.2 125 125
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.013 0.055 -10000 0 -0.11 124 124
RET51/GFRalpha1/GDNF/Grb7 0.048 0.058 -10000 0 -0.062 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.025 0.014 -10000 0 -0.063 1 1
DOK4 0.032 0.005 -10000 0 -10000 0 0
JNK cascade -0.012 0.029 -10000 0 -0.18 7 7
RET9/GFRalpha1/GDNF/FRS2 0.036 0.041 -10000 0 -0.039 5 5
SHANK3 0 0 -10000 0 -10000 0 0
RASA1 0.032 0.006 -10000 0 -10000 0 0
NCK1 0.03 0.015 -10000 0 -0.063 11 11
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.016 0.053 -10000 0 -0.1 125 125
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.027 0.095 -10000 0 -0.19 125 125
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.032 0.098 -10000 0 -0.19 136 136
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.007 0.033 -10000 0 -0.12 26 26
PI3K -0.043 0.11 -10000 0 -0.23 120 120
SOS1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.033 0.039 -10000 0 -0.029 131 131
GRB10 0.021 0.018 -10000 0 -0.063 6 6
activation of MAPKK activity -0.014 0.069 0.1 7 -0.15 102 109
RET51/GFRalpha1/GDNF/FRS2 0.047 0.057 -10000 0 -0.058 1 1
GAB1 0.032 0.008 -10000 0 -0.063 3 3
IRS1 0.032 0.009 -10000 0 -0.063 4 4
IRS2 0.03 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.009 0.036 -10000 0 -0.12 28 28
RET51/GFRalpha1/GDNF/PKC alpha 0.048 0.058 -10000 0 -0.056 2 2
GRB2 0.032 0.006 -10000 0 0 15 15
PRKACA 0.032 0.006 -10000 0 -10000 0 0
GDNF 0.032 0.004 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.047 0.058 -10000 0 -0.061 4 4
Rac1/GTP -0.013 0.071 -10000 0 -0.2 49 49
RET9/GFRalpha1/GDNF 0.032 0.02 -10000 0 -0.04 1 1
GFRalpha1/GDNF 0.035 0.022 -10000 0 -0.05 1 1
FAS signaling pathway (CD95)

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
SPTAN1 -0.018 0.042 0.21 8 -0.19 12 20
RFC1 -0.022 0.035 0.17 2 -0.19 14 16
PRKDC -0.023 0.035 0.17 2 -0.19 14 16
RIPK1 0.03 0.013 -10000 0 -0.062 9 9
CASP7 -0.15 0.26 -10000 0 -0.59 132 132
FASLG/FAS/FADD/FAF1 -0.022 0.057 0.11 1 -0.12 124 125
MAP2K4 -0.059 0.12 0.34 2 -0.24 128 130
mol:ceramide -0.014 0.061 -10000 0 -0.16 21 21
GSN -0.019 0.043 0.21 8 -0.19 13 21
FASLG/FAS/FADD/FAF1/Caspase 8 -0.027 0.062 0.14 1 -0.12 128 129
FAS 0.013 0.03 -10000 0 -0.064 55 55
BID -0.031 0.014 0.2 1 -10000 0 1
MAP3K1 -0.1 0.18 0.42 1 -0.39 135 136
MAP3K7 0.031 0.008 -10000 0 -0.063 1 1
RB1 -0.02 0.034 0.17 2 -0.19 13 15
CFLAR 0.032 0.009 -10000 0 -0.061 5 5
HGF/MET 0.037 0.037 -10000 0 -0.049 23 23
ARHGDIB -0.02 0.044 0.21 9 -0.2 11 20
FADD 0.032 0.006 -10000 0 -0.062 1 1
actin filament polymerization 0.019 0.043 0.19 13 -0.21 8 21
NFKB1 0.014 0.072 -10000 0 -0.62 6 6
MAPK8 -0.064 0.12 0.42 2 -0.24 124 126
DFFA -0.02 0.038 0.2 4 -0.2 13 17
DNA fragmentation during apoptosis -0.021 0.036 0.19 3 -0.2 13 16
FAS/FADD/MET 0.026 0.04 -10000 0 -0.048 53 53
CFLAR/RIP1 0.045 0.017 -10000 0 -0.048 14 14
FAIM3 0.031 0.007 -10000 0 -0.063 1 1
FAF1 0.031 0.006 -10000 0 -10000 0 0
PARP1 -0.023 0.037 0.22 2 -0.19 15 17
DFFB -0.021 0.036 0.19 3 -0.2 13 16
CHUK 0.005 0.067 -10000 0 -0.59 6 6
FASLG 0.032 0.005 -10000 0 -10000 0 0
FAS/FADD 0.024 0.034 -10000 0 -0.051 56 56
HGF 0.022 0.016 -10000 0 -0.063 1 1
LMNA -0.027 0.034 0.19 2 -0.18 13 15
CASP6 -0.023 0.033 0.17 2 -0.19 12 14
CASP10 0.032 0.002 -10000 0 -10000 0 0
CASP3 -0.016 0.033 0.16 1 -0.22 9 10
PTPN13 0.027 0.021 -10000 0 -0.063 26 26
CASP8 -0.03 0.007 0.053 1 -0.058 9 10
IL6 -0.025 0.092 -10000 0 -0.52 7 7
MET 0.022 0.016 -10000 0 -0.063 2 2
ICAD/CAD -0.026 0.04 0.25 4 -0.19 13 17
FASLG/FAS/FADD/FAF1/Caspase 10 -0.015 0.061 -10000 0 -0.16 21 21
activation of caspase activity by cytochrome c -0.031 0.014 0.2 1 -10000 0 1
PAK2 -0.02 0.041 0.21 7 -0.19 12 19
BCL2 0.032 0.006 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.031 0.007 -10000 0 -10000 0 0
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.032 0.004 -10000 0 -10000 0 0
TCEB1 0.032 0.005 -10000 0 -10000 0 0
HIF1A/p53 -0.05 0.14 0.22 2 -0.27 128 130
HIF1A -0.048 0.13 -10000 0 -0.32 90 90
COPS5 0.032 0.004 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.048 0.05 -10000 0 -10000 0 0
FIH (dimer) 0.024 0.014 -10000 0 -10000 0 0
CDKN2A 0.003 0.026 -10000 0 -0.063 52 52
ARNT/IPAS 0.045 0.013 -10000 0 -10000 0 0
HIF1AN 0.024 0.014 -10000 0 -10000 0 0
GNB2L1 0.032 0.004 -10000 0 -10000 0 0
HIF1A/ARNT -0.045 0.14 0.16 1 -0.27 124 125
CUL2 0.025 0.014 -10000 0 -10000 0 0
OS9 0.028 0.012 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.063 0.017 -10000 0 -0.053 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 -0.044 0.14 0.2 3 -0.27 128 131
PHD1-3/OS9 0.059 0.043 -10000 0 -10000 0 0
HIF1A/RACK1/Elongin B/Elongin C -0.023 0.15 -10000 0 -0.27 126 126
VHL 0 0 -10000 0 -10000 0 0
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
HIF1A/JAB1 -0.045 0.14 0.22 2 -0.27 127 129
EGLN3 0.03 0.011 -10000 0 -0.063 4 4
EGLN2 0.031 0.006 -10000 0 -10000 0 0
EGLN1 0.032 0.007 -10000 0 -0.063 1 1
TP53 0.019 0.032 -10000 0 -0.063 65 65
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.002 0.07 -10000 0 -0.57 3 3
ARNT 0.032 0.005 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.03 0.009 -10000 0 -10000 0 0
HIF1A/p19ARF -0.059 0.13 0.2 3 -0.27 127 130
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.004 0.047 -10000 0 -0.049 258 258
PDGFRB 0.032 0.007 -10000 0 -0.064 2 2
SPHK1 0.011 0.018 -10000 0 -10000 0 0
mol:S1P 0.005 0.023 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.041 0.068 -10000 0 -0.28 20 20
GNAO1 0.003 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/PLCgamma1 -0.037 0.08 0.2 16 -0.28 12 28
PLCG1 -0.04 0.061 -10000 0 -0.25 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.032 0.007 -10000 0 -0.064 2 2
GNAI2 0.035 0.007 -10000 0 -10000 0 0
GNAI3 0.021 0.03 -10000 0 -0.062 58 58
GNAI1 0.019 0.016 -10000 0 -0.06 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.025 0.014 0.01 3 -0.039 184 187
S1P1/S1P -0.003 0.033 0.2 2 -10000 0 2
negative regulation of cAMP metabolic process -0.04 0.067 -10000 0 -0.27 20 20
MAPK3 -0.05 0.069 -10000 0 -0.32 14 14
calcium-dependent phospholipase C activity -0.001 0.001 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.023 0.004 -10000 0 -10000 0 0
KDR 0.028 0.018 -10000 0 -0.062 14 14
PLCB2 0.001 0.052 0.17 22 -10000 0 22
RAC1 0.023 0.015 -10000 0 -10000 0 0
RhoA/GTP -0.002 0.032 -10000 0 -10000 0 0
receptor internalization -0.003 0.032 0.19 2 -10000 0 2
PTGS2 -0.055 0.072 -10000 0 -0.36 9 9
Rac1/GTP -0.007 0.025 -10000 0 -10000 0 0
RHOA 0.032 0.006 -10000 0 -10000 0 0
VEGFA -0.018 0.047 -10000 0 -0.061 274 274
negative regulation of T cell proliferation -0.04 0.067 -10000 0 -0.27 20 20
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.027 0.013 -10000 0 -10000 0 0
MAPK1 -0.047 0.068 -10000 0 -0.36 11 11
S1P1/S1P/PDGFB-D/PDGFRB 0.01 0.054 0.2 11 -10000 0 11
ABCC1 0.031 0.012 -10000 0 -0.063 8 8
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0.014 0.026 0.077 3 -0.093 25 28
MKNK1 0.032 0.005 -10000 0 -10000 0 0
MAPK14 0.032 0.024 0.091 5 -0.067 26 31
ATF2/c-Jun 0.004 0.041 -10000 0 -0.11 51 51
MAPK11 0.029 0.025 0.09 4 -0.067 25 29
MITF 0.016 0.017 0.082 5 -0.043 28 33
MAPKAPK5 0.016 0.016 0.076 3 -0.043 26 29
KRT8 0.013 0.021 0.076 3 -0.045 45 48
MAPKAPK3 0.032 0.007 -10000 0 -0.063 1 1
MAPKAPK2 0.032 0.006 -10000 0 -10000 0 0
p38alpha-beta/CK2 0.04 0.033 -10000 0 -0.083 25 25
CEBPB 0.014 0.019 0.082 3 -0.05 30 33
SLC9A1 0.016 0.016 0.081 1 -0.043 26 27
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.017 0.02 0.11 9 -0.046 25 34
p38alpha-beta/MNK1 0.053 0.036 -10000 0 -0.07 25 25
JUN -0.001 0.039 -10000 0 -0.11 51 51
PPARGC1A 0.016 0.017 0.082 5 -0.044 28 33
USF1 0.012 0.016 0.077 5 -0.045 26 31
RAB5/GDP/GDI1 0.013 0.048 -10000 0 -0.12 46 46
NOS2 0.012 0.015 0.077 5 -0.044 26 31
DDIT3 0.014 0.018 0.074 2 -0.045 28 30
RAB5A 0.032 0.004 -10000 0 -10000 0 0
HSPB1 0.059 0.12 0.27 121 -10000 0 121
p38alpha-beta/HBP1 0.038 0.04 -10000 0 -0.071 20 20
CREB1 0.004 0.057 -10000 0 -0.2 36 36
RAB5/GDP 0.024 0.003 -10000 0 -10000 0 0
EIF4E -0.031 0.029 0.22 6 -10000 0 6
RPS6KA4 0.016 0.017 0.082 5 -0.043 26 31
PLA2G4A -0.037 0.024 0.21 3 -10000 0 3
GDI1 0.016 0.015 0.082 5 -0.044 17 22
TP53 -0.015 0.017 0.063 6 -0.071 25 31
RPS6KA5 0.016 0.017 0.082 5 -0.043 26 31
ESR1 0.016 0.017 0.082 5 -0.043 25 30
HBP1 0.023 0.015 -10000 0 -10000 0 0
MEF2C 0.014 0.015 0.082 3 -0.044 17 20
MEF2A 0.016 0.017 0.082 5 -0.043 26 31
EIF4EBP1 -0.009 0.058 -10000 0 -0.21 35 35
KRT19 0.014 0.021 0.082 5 -0.044 45 50
ELK4 0.016 0.016 0.076 3 -0.043 25 28
ATF6 0.016 0.016 0.076 3 -0.043 25 28
ATF1 0.001 0.058 -10000 0 -0.19 38 38
p38alpha-beta/MAPKAPK2 0.053 0.036 -10000 0 -0.07 24 24
p38alpha-beta/MAPKAPK3 0.053 0.037 -10000 0 -0.07 25 25
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.022 0.019 -10000 0 -0.026 53 53
HSPA8 0.032 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.038 0.061 -10000 0 -0.088 5 5
AKT1 0.031 0.009 -10000 0 -10000 0 0
GSC 0.007 0.026 0.1 20 -10000 0 20
NKX2-5 0.036 0.012 0.089 9 -10000 0 9
muscle cell differentiation -0.013 0.07 0.25 19 -10000 0 19
SMAD2-3/SMAD4/SP1 0.018 0.076 0.2 1 -0.11 11 12
SMAD4 -0.008 0.05 0.11 2 -0.081 102 104
CBFB 0.031 0.009 -10000 0 -0.063 4 4
SAP18 0.031 0.008 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.05 0.031 -10000 0 -0.049 34 34
SMAD3/SMAD4/VDR 0.042 0.075 -10000 0 -10000 0 0
MYC 0.008 0.04 -10000 0 -0.064 119 119
CDKN2B -0.21 0.19 -10000 0 -0.36 291 291
AP1 -0.003 0.048 0.15 5 -0.085 13 18
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.002 0.07 -10000 0 -0.22 32 32
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.012 0.061 0.14 3 -0.25 23 26
SP3 0.018 0.034 -10000 0 -0.061 81 81
CREB1 0.033 0.001 -10000 0 -10000 0 0
FOXH1 0.035 0.011 0.1 5 -10000 0 5
SMAD3/SMAD4/GR 0.033 0.059 -10000 0 -0.084 13 13
GATA3 0.025 0.015 -10000 0 -0.063 2 2
SKI/SIN3/HDAC complex/NCoR1 -0.003 0.068 -10000 0 -0.17 44 44
MEF2C/TIF2 -0.034 0.039 0.22 8 -10000 0 8
endothelial cell migration 0.034 0.067 0.45 2 -10000 0 2
MAX 0.034 0.01 -10000 0 -10000 0 0
RBBP7 0.033 0.002 -10000 0 -10000 0 0
RBBP4 0.015 0.036 -10000 0 -0.063 89 89
RUNX2 0.032 0.004 -10000 0 -10000 0 0
RUNX3 0.031 0.009 -10000 0 -0.063 3 3
RUNX1 0.032 0.005 -10000 0 -10000 0 0
CTBP1 0.032 0.006 -10000 0 -10000 0 0
NR3C1 0.035 0.006 -10000 0 -10000 0 0
VDR 0.031 0.006 -10000 0 -10000 0 0
CDKN1A -0.015 0.053 0.33 3 -10000 0 3
KAT2B -0.001 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.029 0.05 0.26 1 -0.061 20 21
DCP1A 0.032 0.006 -10000 0 -10000 0 0
SKI 0.031 0.007 -10000 0 -10000 0 0
SERPINE1 -0.032 0.067 -10000 0 -0.46 2 2
SMAD3/SMAD4/ATF2 0.024 0.06 -10000 0 -0.08 23 23
SMAD3/SMAD4/ATF3 0.008 0.064 -10000 0 -0.081 61 61
SAP30 0.032 0.006 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.052 0.023 -10000 0 -0.043 10 10
JUN -0.026 0.037 0.14 9 -10000 0 9
SMAD3/SMAD4/IRF7 0.024 0.063 -10000 0 -0.086 23 23
TFE3 -0.006 0.037 -10000 0 -0.039 275 275
COL1A2 -0.025 0.052 0.11 1 -0.093 174 175
mesenchymal cell differentiation -0.023 0.06 0.08 23 -10000 0 23
DLX1 0 0 -10000 0 -10000 0 0
TCF3 0.031 0.006 -10000 0 -10000 0 0
FOS 0.004 0.044 -10000 0 -0.061 150 150
SMAD3/SMAD4/Max 0.031 0.061 -10000 0 -0.086 13 13
Cbp/p300/SNIP1 0.057 0.022 -10000 0 -0.039 10 10
ZBTB17 0.031 0.005 -10000 0 -10000 0 0
LAMC1 -0.05 0.042 0.14 4 -0.12 9 13
TGIF2/HDAC complex/SMAD3/SMAD4 0.024 0.058 -10000 0 -0.081 24 24
IRF7 0.029 0.016 -10000 0 -0.064 12 12
ESR1 0.037 0.014 0.13 3 -10000 0 3
HNF4A 0.03 0.008 -10000 0 -10000 0 0
MEF2C -0.03 0.04 0.2 11 -10000 0 11
SMAD2-3/SMAD4 0.026 0.061 0.18 1 -0.083 16 17
Cbp/p300/Src-1 0.053 0.024 -10000 0 -0.041 12 12
IGHV3OR16-13 0.006 0.008 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.03 0.012 -10000 0 -0.063 4 4
CREBBP 0.03 0.006 -10000 0 -0.026 2 2
SKIL 0.032 0.005 -10000 0 -10000 0 0
HDAC1 0.021 0.031 -10000 0 -0.063 61 61
HDAC2 0.03 0.012 -10000 0 -0.063 4 4
SNIP1 0.032 0.005 -10000 0 -10000 0 0
GCN5L2 -0.002 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0 0.072 -10000 0 -0.09 87 87
MSG1/HSC70 0.044 0.022 -10000 0 -0.049 24 24
SMAD2 0.036 0.012 0.13 3 -10000 0 3
SMAD3 0.001 0.039 -10000 0 -0.065 8 8
SMAD3/E2F4-5/DP1/p107/SMAD4 -0.001 0.042 -10000 0 -0.14 29 29
SMAD2/SMAD2/SMAD4 -0.01 0.039 0.12 9 -0.18 10 19
NCOR1 0.032 0.004 -10000 0 -10000 0 0
NCOA2 0.032 0.004 -10000 0 -10000 0 0
NCOA1 0.031 0.007 -10000 0 -10000 0 0
MYOD/E2A 0.046 0.011 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.035 0.081 0.21 1 -0.11 4 5
IFNB1 -0.022 0.033 0.14 8 -10000 0 8
SMAD3/SMAD4/MEF2C -0.009 0.054 0.2 3 -10000 0 3
CITED1 0.028 0.02 -10000 0 -0.063 24 24
SMAD2-3/SMAD4/ARC105 0.041 0.066 0.19 1 -0.086 7 8
RBL1 0 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.001 0.051 0.19 1 -0.25 12 13
RUNX1-3/PEBPB2 0.059 0.025 -10000 0 -0.049 8 8
SMAD7 -0.024 0.064 -10000 0 -0.19 33 33
MYC/MIZ-1 0.022 0.041 -10000 0 -0.051 116 116
SMAD3/SMAD4 -0.045 0.066 -10000 0 -0.24 31 31
IL10 -0.032 0.04 0.16 13 -10000 0 13
PIASy/HDAC complex 0.033 0.006 -10000 0 -10000 0 0
PIAS3 0.031 0.004 -10000 0 -10000 0 0
CDK2 0.025 0.021 -10000 0 -0.064 24 24
IL5 -0.033 0.04 0.16 13 -10000 0 13
CDK4 -0.021 0.044 -10000 0 -0.064 251 251
PIAS4 0.033 0.006 -10000 0 -10000 0 0
ATF3 0.012 0.038 -10000 0 -0.063 103 103
SMAD3/SMAD4/SP1 -0.003 0.069 -10000 0 -0.11 30 30
FOXG1 0.027 0.012 -10000 0 -10000 0 0
FOXO3 -0.019 0.007 -10000 0 -10000 0 0
FOXO1 -0.019 0.008 -10000 0 -10000 0 0
FOXO4 -0.02 0.006 -10000 0 -10000 0 0
heart looping -0.03 0.04 0.2 11 -10000 0 11
CEBPB 0.029 0.016 -10000 0 -0.062 11 11
SMAD3/SMAD4/DLX1 0.007 0.047 -10000 0 -0.067 38 38
MYOD1 0.032 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.024 0.058 -10000 0 -0.08 22 22
SMAD3/SMAD4/GATA3 0.017 0.065 -10000 0 -0.087 27 27
SnoN/SIN3/HDAC complex/NCoR1 0.032 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.052 0.07 -10000 0 -0.09 1 1
SMAD3/SMAD4/SP1-3 0.01 0.081 -10000 0 -0.12 28 28
MED15 0.031 0.007 -10000 0 -10000 0 0
SP1 -0.004 0.036 -10000 0 -0.052 47 47
SIN3B 0.031 0.007 -10000 0 -10000 0 0
SIN3A 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.04 0.06 -10000 0 -10000 0 0
ITGB5 -0.043 0.052 0.24 9 -10000 0 9
TGIF/SIN3/HDAC complex/CtBP -0.019 0.06 -10000 0 -0.16 53 53
SMAD3/SMAD4/AR 0.023 0.061 -10000 0 -0.08 30 30
AR 0.031 0.012 -10000 0 -0.063 8 8
negative regulation of cell growth -0.003 0.048 -10000 0 -0.24 12 12
SMAD3/SMAD4/MYOD 0.023 0.06 -10000 0 -0.08 25 25
E2F5 0.032 0.004 -10000 0 -10000 0 0
E2F4 0.032 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.043 0.066 0.27 1 -10000 0 1
SMAD2-3/SMAD4/FOXO1-3a-4 -0.001 0.042 0.13 2 -0.2 11 13
TFDP1 0.029 0.015 -10000 0 -0.063 11 11
SMAD3/SMAD4/AP1 0.012 0.064 -10000 0 -0.085 14 14
SMAD3/SMAD4/RUNX2 0.024 0.06 -10000 0 -0.08 23 23
TGIF2 0.03 0.012 -10000 0 -0.063 4 4
TGIF1 -0.033 0.043 -10000 0 -0.063 343 343
ATF2 0.032 0.002 -10000 0 -10000 0 0
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.061 0.022 -10000 0 -0.048 10 10
fibroblast growth factor receptor signaling pathway 0.06 0.022 -10000 0 -0.048 10 10
LAMA1 0 0 -10000 0 -10000 0 0
PRNP 0.028 0.011 -10000 0 -10000 0 0
GPC1/SLIT2 0.03 0.024 -10000 0 -0.05 5 5
SMAD2 -0.027 0.029 0.17 10 -10000 0 10
GPC1/PrPc/Cu2+ 0.037 0.018 -10000 0 -0.04 7 7
GPC1/Laminin alpha1 0.023 0.008 -10000 0 -0.039 7 7
TDGF1 0.031 0.008 -10000 0 -0.063 2 2
CRIPTO/GPC1 0.045 0.016 -10000 0 -0.05 9 9
APP/GPC1 0.046 0.014 -10000 0 -0.05 7 7
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.028 0.011 -10000 0 -0.049 76 76
FLT1 0.03 0.008 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.059 0.026 -10000 0 -0.048 13 13
SERPINC1 0.032 0.006 -10000 0 -0.063 1 1
FYN -0.024 0.009 -10000 0 -10000 0 0
FGR -0.026 0.008 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.007 0.06 0.18 32 -0.2 6 38
SLIT2 0.021 0.017 -10000 0 -0.063 3 3
GPC1/NRG 0.046 0.014 -10000 0 -0.05 7 7
NRG1 0.032 0.004 -10000 0 -10000 0 0
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0 0.056 -10000 0 -0.049 276 276
LYN -0.028 0.01 -10000 0 -0.069 1 1
mol:Spermine -0.012 0.003 -10000 0 -0.039 7 7
cell growth 0.06 0.022 -10000 0 -0.048 10 10
BMP signaling pathway -0.031 0.012 0.063 7 -10000 0 7
SRC -0.024 0.008 -10000 0 -10000 0 0
TGFBR1 0.032 0.006 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.002 0.045 -10000 0 -0.058 194 194
GPC1 0.031 0.012 -10000 0 -0.063 7 7
TGFBR1 (dimer) 0.032 0.006 -10000 0 -10000 0 0
VEGFA -0.019 0.047 -10000 0 -0.063 274 274
BLK -0.025 0.007 -10000 0 -10000 0 0
HCK -0.028 0.013 -10000 0 -0.048 91 91
FGF2 0.032 0.007 -10000 0 -0.063 2 2
FGFR1 0.032 0.005 -10000 0 -0.063 1 1
VEGFR1 homodimer 0.03 0.008 -10000 0 -10000 0 0
TGFBR2 0.031 0.01 -10000 0 -0.063 5 5
cell death 0.045 0.014 -10000 0 -0.049 7 7
ATIII/GPC1 0.046 0.014 -10000 0 -0.05 8 8
PLA2G2A/GPC1 0.011 0.047 -10000 0 -0.05 182 182
LCK -0.026 0.007 -10000 0 -0.069 1 1
neuron differentiation 0.046 0.014 -10000 0 -0.049 7 7
PrPc/Cu2+ 0.021 0.008 -10000 0 -10000 0 0
APP 0.032 0.005 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.031 0.01 -10000 0 -0.063 5 5
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.032 0.006 -10000 0 -0.063 1 1
LAT2 -0.015 0.03 0.12 4 -0.13 7 11
AP1 -0.031 0.11 -10000 0 -0.26 44 44
mol:PIP3 0.026 0.1 0.25 40 -0.18 1 41
IKBKB 0.016 0.074 0.19 39 -0.14 1 40
AKT1 -0.033 0.077 0.3 12 -10000 0 12
IKBKG 0.016 0.073 0.2 35 -0.14 1 36
MS4A2 0.035 0.005 0.069 1 -10000 0 1
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
MAP3K1 -0.01 0.06 0.22 14 -0.2 6 20
mol:Ca2+ 0.025 0.09 0.23 40 -0.14 1 41
LYN 0.02 0.032 0.086 1 -0.065 62 63
CBLB -0.015 0.036 0.14 7 -0.13 9 16
SHC1 0.024 0.026 -10000 0 -0.063 40 40
RasGAP/p62DOK 0.056 0.024 -10000 0 -0.042 21 21
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.031 0.06 0.32 11 -10000 0 11
PTPN13 0.005 0.074 0.32 1 -0.57 5 6
PTPN11 0.032 0.01 -10000 0 -0.029 9 9
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.009 0.074 0.31 9 -0.28 5 14
SYK 0.024 0.025 -10000 0 -0.064 35 35
GRB2 0.032 0.006 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs 0.013 0.066 0.18 18 -0.16 5 23
LAT -0.015 0.037 0.14 7 -0.12 10 17
PAK2 -0.006 0.061 0.21 16 -0.21 6 22
NFATC2 -0.012 0.005 -10000 0 -10000 0 0
HRAS -0.002 0.057 0.18 18 -0.21 7 25
GAB2 0.032 0.006 -10000 0 -10000 0 0
PLA2G1B 0.021 0.064 -10000 0 -0.81 2 2
Fc epsilon R1 0.009 0.058 -10000 0 -0.05 242 242
Antigen/IgE/Fc epsilon R1 0.011 0.055 -10000 0 -0.045 239 239
mol:GDP 0.003 0.051 0.18 16 -0.19 1 17
JUN 0.032 0.005 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
FOS 0.007 0.04 -10000 0 -0.063 120 120
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.007 0.036 0.12 3 -0.12 7 10
CHUK 0.007 0.068 0.2 31 -0.14 1 32
KLRG1 -0.012 0.026 0.082 3 -0.095 3 6
VAV1 -0.015 0.037 0.12 10 -0.13 9 19
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.014 0.036 0.14 7 -0.13 6 13
negative regulation of mast cell degranulation -0.013 0.027 0.076 2 -0.1 4 6
BTK 0.007 0.04 0.2 1 -10000 0 1
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.008 0.029 -10000 0 -0.11 6 6
GAB2/PI3K/SHP2 -0.052 0.024 0.027 1 -10000 0 1
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.009 0.03 -10000 0 -0.084 33 33
RAF1 0.024 0.061 -10000 0 -0.89 2 2
Fc epsilon R1/FcgammaRIIB/SHIP 0.006 0.065 -10000 0 -0.06 145 145
FCER1G -0.014 0.049 -10000 0 -0.065 242 242
FCER1A 0.03 0.015 -10000 0 -0.06 12 12
Antigen/IgE/Fc epsilon R1/Fyn 0.008 0.062 -10000 0 -0.055 33 33
MAPK3 0.024 0.063 -10000 0 -0.82 2 2
MAPK1 0.014 0.07 -10000 0 -0.82 2 2
NFKB1 0.031 0.009 -10000 0 -0.063 4 4
MAPK8 -0.1 0.25 -10000 0 -0.51 130 130
DUSP1 0.029 0.017 -10000 0 -0.063 16 16
NF-kappa-B/RelA 0.007 0.051 0.12 30 -0.099 1 31
actin cytoskeleton reorganization 0.012 0.076 0.33 1 -0.59 5 6
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.001 0.066 0.2 16 -0.19 7 23
FER -0.015 0.036 0.14 7 -0.12 8 15
RELA 0.032 0.004 -10000 0 -10000 0 0
ITK 0.001 0.025 -10000 0 -0.23 5 5
SOS1 0 0 -10000 0 -10000 0 0
PLCG1 0.015 0.074 0.25 23 -0.19 1 24
cytokine secretion 0.001 0.032 0.072 25 -0.073 1 26
SPHK1 -0.016 0.035 0.13 6 -0.13 9 15
PTK2 0.012 0.079 0.34 1 -0.62 5 6
NTAL/PLCgamma1/GRB2/SLP76/GADs 0.02 0.08 0.23 20 -0.16 5 25
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.02 0.091 0.25 33 -0.24 2 35
MAP2K2 0.02 0.07 -10000 0 -0.84 2 2
MAP2K1 0.015 0.059 -10000 0 -0.84 2 2
MAP2K7 0.031 0.006 -10000 0 -10000 0 0
KLRG1/SHP2 -0.001 0.045 0.2 11 -0.1 2 13
MAP2K4 0.001 0.18 -10000 0 -0.76 26 26
Fc epsilon R1/FcgammaRIIB 0.007 0.071 -10000 0 -0.065 150 150
mol:Choline -0.03 0.06 0.32 11 -10000 0 11
SHC/Grb2/SOS1 0.008 0.058 0.18 3 -0.13 5 8
FYN 0.029 0.011 -10000 0 -0.063 1 1
DOK1 0.032 0.002 -10000 0 -10000 0 0
PXN 0.007 0.078 0.4 3 -0.57 5 8
HCLS1 -0.018 0.039 0.14 7 -0.13 9 16
PRKCB 0.021 0.084 0.21 39 -0.18 1 40
FCGR2B 0.01 0.04 -10000 0 -0.063 120 120
IGHE -0.001 0.004 0.053 1 -10000 0 1
KLRG1/SHIP -0.014 0.027 0.077 2 -0.11 4 6
LCP2 0.027 0.023 -10000 0 -0.063 29 29
PLA2G4A -0.02 0.038 0.14 7 -0.13 9 16
RASA1 0.032 0.006 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.03 0.06 0.32 11 -10000 0 11
IKK complex 0.007 0.068 0.21 26 -10000 0 26
WIPF1 0.03 0.014 -10000 0 -0.063 11 11
Plasma membrane estrogen receptor 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
GNB1/GNG2 0.045 0.031 -10000 0 -0.038 14 14
ER alpha/Gai/GDP/Gbeta gamma -0.089 0.13 -10000 0 -0.38 60 60
AKT1 -0.032 0.18 -10000 0 -0.71 31 31
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.028 0.18 -10000 0 -0.73 31 31
mol:Ca2+ -0.004 0.045 0.17 18 -0.23 9 27
IGF1R 0.032 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.041 0.011 -10000 0 -10000 0 0
SHC1 0.024 0.026 -10000 0 -0.063 40 40
apoptosis 0.03 0.17 0.68 31 -10000 0 31
RhoA/GTP -0.039 0.014 -10000 0 -0.076 1 1
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.071 0.12 0.18 9 -0.29 63 72
regulation of stress fiber formation 0.045 0.044 -10000 0 -0.16 8 8
E2/ERA-ERB (dimer) 0.039 0.014 -10000 0 -10000 0 0
KRAS 0.031 0.008 -10000 0 -10000 0 0
G13/GTP 0.037 0.017 -10000 0 -0.025 32 32
pseudopodium formation -0.045 0.044 0.16 8 -10000 0 8
E2/ER alpha (dimer)/PELP1 0.04 0.012 -10000 0 -10000 0 0
GRB2 0.032 0.006 -10000 0 0 15 15
GNG2 0 0 -10000 0 -10000 0 0
GNAO1 0.003 0.009 -10000 0 -10000 0 0
HRAS 0.031 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.055 0.14 0.21 2 -0.44 40 42
E2/ER beta (dimer) 0.023 0.006 -10000 0 -10000 0 0
mol:GDP -0.005 0.058 0.13 5 -0.17 45 50
mol:NADP -0.055 0.14 0.21 2 -0.44 40 42
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
mol:IP3 -0.01 0.032 -10000 0 -0.24 9 9
IGF-1R heterotetramer 0.032 0.004 -10000 0 -10000 0 0
PLCB1 0.008 0.016 -10000 0 -0.23 1 1
PLCB2 0.009 0.016 -10000 0 -0.23 1 1
IGF1 0.032 0.009 -10000 0 -0.063 4 4
mol:L-citrulline -0.055 0.14 0.21 2 -0.44 40 42
RHOA 0.032 0.006 -10000 0 -10000 0 0
Gai/GDP -0.43 0.16 -10000 0 -0.48 449 449
JNK cascade 0.022 0.006 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 0.03 0.008 -10000 0 -10000 0 0
GNAQ 0.031 0.006 -10000 0 -10000 0 0
ESR1 0.031 0.008 -10000 0 -10000 0 0
Gq family/GDP/Gbeta gamma 0.014 0.07 -10000 0 -0.26 21 21
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.004 0.071 -10000 0 -0.58 5 5
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.07 0.12 0.2 10 -0.3 63 73
GNAZ 0.027 0.013 -10000 0 -10000 0 0
E2/ER alpha (dimer) 0.023 0.006 -10000 0 -10000 0 0
STRN 0.032 0.002 -10000 0 -10000 0 0
GNAL 0.032 0.006 -10000 0 -10000 0 0
PELP1 0.032 0.005 -10000 0 -10000 0 0
MAPK11 -0.015 0.006 -10000 0 -10000 0 0
GNAI2 0.032 0.006 -10000 0 -10000 0 0
GNAI3 0.021 0.03 -10000 0 -0.063 58 58
GNAI1 0.019 0.016 -10000 0 -0.063 1 1
HBEGF -0.11 0.13 0.24 16 -0.34 63 79
cAMP biosynthetic process 0.03 0.021 -10000 0 -0.035 15 15
SRC -0.098 0.12 0.2 1 -0.36 62 63
PI3K 0.039 0.023 -10000 0 -0.05 16 16
GNB1 0.031 0.008 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.024 0.059 -10000 0 -0.15 46 46
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.078 0.091 -10000 0 -0.24 71 71
Gs family/GTP 0.039 0.025 -10000 0 -0.036 15 15
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.031 0.046 -10000 0 -0.043 119 119
vasodilation -0.053 0.13 0.21 2 -0.42 40 42
mol:DAG -0.01 0.032 -10000 0 -0.24 9 9
Gs family/GDP/Gbeta gamma -0.005 0.056 -10000 0 -0.16 46 46
MSN -0.051 0.039 0.16 8 -10000 0 8
Gq family/GTP 0.022 0.019 -10000 0 -0.24 1 1
mol:PI-3-4-5-P3 -0.026 0.18 -10000 0 -0.7 31 31
NRAS 0.009 0.041 -10000 0 -0.063 125 125
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.053 0.13 0.42 40 -0.21 2 42
GRB2/SOS1 0.023 0.004 -10000 0 -10000 0 0
RhoA/GDP 0.017 0.063 0.14 5 -0.17 46 51
NOS3 -0.058 0.14 0.22 2 -0.47 40 42
GNA11 0.031 0.006 -10000 0 -10000 0 0
MAPKKK cascade -0.035 0.14 0.24 1 -0.49 35 36
E2/ER alpha (dimer)/PELP1/Src -0.07 0.12 0.21 11 -0.31 60 71
ruffle organization -0.045 0.044 0.16 8 -10000 0 8
ROCK2 -0.032 0.052 0.16 23 -10000 0 23
GNA14 0.031 0.009 -10000 0 -0.063 2 2
GNA15 0.03 0.013 -10000 0 -0.063 7 7
GNA13 0.032 0.007 -10000 0 -0.063 2 2
MMP9 -0.11 0.12 0.37 1 -0.35 60 61
MMP2 -0.11 0.12 0.19 1 -0.36 60 61
Signaling events mediated by the Hedgehog family

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
TGFB2 0.018 0.027 0.16 9 -0.077 19 28
IHH 0.038 0.021 0.11 17 -0.044 13 30
SHH Np/Cholesterol/GAS1 0.014 0.02 -10000 0 -0.041 37 37
LRPAP1 0.032 0.003 -10000 0 -10000 0 0
dorsoventral neural tube patterning -0.013 0.02 0.041 37 -10000 0 37
SMO/beta Arrestin2 0.066 0.056 0.16 120 -0.14 1 121
SMO 0.014 0.019 0.14 3 -10000 0 3
AKT1 0.003 0.083 -10000 0 -0.31 25 25
ARRB2 0.032 0.005 -10000 0 -10000 0 0
BOC 0 0 -10000 0 -10000 0 0
ADRBK1 0.032 0.004 -10000 0 -10000 0 0
heart looping 0.014 0.019 0.14 3 -10000 0 3
STIL 0.024 0.085 0.17 125 -10000 0 125
DHH N/PTCH2 0.024 0.003 -10000 0 0 10 10
DHH N/PTCH1 0.017 0.014 -10000 0 -0.056 7 7
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
DHH 0 0 -10000 0 -10000 0 0
PTHLH 0.015 0.024 0.15 8 -0.094 6 14
determination of left/right symmetry 0.014 0.019 0.14 3 -10000 0 3
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
skeletal system development 0.015 0.024 0.15 8 -0.093 6 14
IHH N/Hhip 0.025 0.012 0.071 17 -0.021 7 24
DHH N/Hhip 0 0 -10000 0 -10000 0 0
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.014 0.019 0.14 3 -10000 0 3
pancreas development 0 0 -10000 0 -10000 0 0
HHAT 0.032 0.006 -10000 0 -10000 0 0
PI3K 0.039 0.023 -10000 0 -0.05 16 16
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.021 0.03 -10000 0 -0.063 55 55
somite specification 0.014 0.019 0.14 3 -10000 0 3
SHH Np/Cholesterol/PTCH1 0.014 0.017 -10000 0 -0.06 5 5
SHH Np/Cholesterol/PTCH2 0.018 0.014 -10000 0 -0.031 4 4
SHH Np/Cholesterol/Megalin 0.018 0.014 -10000 0 -0.033 5 5
SHH -0.015 0.011 -10000 0 -10000 0 0
catabolic process 0.02 0.017 -10000 0 -0.063 13 13
SMO/Vitamin D3 0.016 0.032 0.18 14 -10000 0 14
SHH Np/Cholesterol/Hhip -0.011 0.007 0 163 -10000 0 163
LRP2 0.032 0.005 -10000 0 -0.063 1 1
receptor-mediated endocytosis 0.012 0.027 0.15 13 -10000 0 13
SHH Np/Cholesterol/BOC -0.011 0.007 0 163 -10000 0 163
SHH Np/Cholesterol/CDO 0.018 0.014 -10000 0 -0.031 4 4
mesenchymal cell differentiation 0.011 0.007 -10000 0 0 163 163
mol:Vitamin D3 0.041 0.096 0.19 146 -10000 0 146
IHH N/PTCH2 0.05 0.012 0.11 8 -0.036 1 9
CDON 0.032 0.004 -10000 0 -10000 0 0
IHH N/PTCH1 0.036 0.021 -10000 0 -0.06 20 20
Megalin/LRPAP1 0.047 0.007 -10000 0 -0.05 1 1
PTCH2 0.032 0.005 -10000 0 0 10 10
SHH Np/Cholesterol -0.011 0.007 -10000 0 -10000 0 0
PTCH1 0.02 0.017 -10000 0 -0.063 13 13
HHIP 0 0 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.061 0.047 -10000 0 -0.058 1 1
MAP4K1 0.031 0.008 -10000 0 -0.063 1 1
MAP3K8 0.018 0.026 -10000 0 -0.063 37 37
PRKCB 0 0 -10000 0 -10000 0 0
DBNL 0 0 -10000 0 -10000 0 0
CRKL 0.031 0.007 -10000 0 -10000 0 0
MAP3K1 0.001 0.034 0.076 14 -0.12 28 42
JUN -0.12 0.23 0.22 3 -0.52 121 124
MAP3K7 0.002 0.033 -10000 0 -0.12 24 24
GRAP2 0.03 0.008 -10000 0 -10000 0 0
CRK 0.032 0.005 -10000 0 -10000 0 0
MAP2K4 -0.02 0.063 0.15 5 -0.22 32 37
LAT 0.032 0.005 -10000 0 -0.063 1 1
LCP2 0.026 0.022 -10000 0 -0.063 29 29
MAPK8 -0.12 0.24 -10000 0 -0.55 121 121
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.015 0.035 -10000 0 -0.14 16 16
LAT/GRAP2/SLP76/HPK1/HIP-55 0.057 0.044 -10000 0 -0.054 1 1
Paxillin-independent events mediated by a4b1 and a4b7

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.004 0.043 -10000 0 -0.084 113 113
CRKL 0.031 0.007 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.011 -10000 0 -10000 0 0
DOCK1 0.023 0.015 -10000 0 -10000 0 0
ITGA4 0.031 0.01 -10000 0 -0.063 5 5
alpha4/beta7 Integrin/MAdCAM1 0.074 0.031 -10000 0 -0.069 2 2
EPO 0.023 0.015 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.046 0.013 -10000 0 -0.06 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.032 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.036 0.022 -10000 0 -0.05 4 4
EPO/EPOR (dimer) 0.033 0.023 -10000 0 -10000 0 0
lamellipodium assembly -0.006 0.082 -10000 0 -0.3 30 30
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
PI3K 0.039 0.023 -10000 0 -0.05 16 16
ARF6 0.031 0.008 -10000 0 -10000 0 0
JAK2 0.009 0.028 -10000 0 -0.091 31 31
PXN 0.032 0.003 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
MADCAM1 0.031 0.007 -10000 0 -10000 0 0
cell adhesion 0.072 0.03 -10000 0 -0.069 2 2
CRKL/CBL 0.045 0.012 -10000 0 -10000 0 0
ITGB1 0.025 0.014 -10000 0 -10000 0 0
SRC -0.041 0.02 0.17 2 -10000 0 2
ITGB7 0.032 0.008 -10000 0 -0.063 2 2
RAC1 0.023 0.015 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.02 0.05 -10000 0 -0.05 335 335
p130Cas/Crk/Dock1 -0.048 0.023 0.18 3 -10000 0 3
VCAM1 -0.03 0.045 -10000 0 -0.063 333 333
RHOA 0.032 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.054 0.053 -10000 0 -10000 0 0
BCAR1 -0.037 0.035 0.27 4 -10000 0 4
EPOR 0.031 0.006 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.032 0.004 -10000 0 -10000 0 0
GIT1 0.032 0.004 -10000 0 -10000 0 0
Rac1/GTP -0.007 0.084 -10000 0 -0.31 30 30
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.026 0.015 -10000 0 -0.063 6 6
HRAS 0.031 0.007 -10000 0 -10000 0 0
EGFR 0.012 0.018 -10000 0 -0.063 6 6
AKT 0.12 0.092 0.21 198 -0.14 1 199
FOXO3 0.03 0.008 -10000 0 -10000 0 0
AKT1 0.03 0.008 -10000 0 -10000 0 0
FOXO1 0.028 0.016 -10000 0 -0.063 11 11
AKT3 0.031 0.007 -10000 0 -10000 0 0
FOXO4 0.032 0.002 -10000 0 -10000 0 0
MET 0.022 0.016 -10000 0 -0.063 2 2
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
PIK3CB 0.032 0.005 -10000 0 -10000 0 0
NRAS 0.009 0.041 -10000 0 -0.063 125 125
PIK3CG 0.023 0.015 -10000 0 -10000 0 0
PIK3R3 0.032 0.006 -10000 0 -0.063 1 1
PIK3R2 0.031 0.006 -10000 0 -10000 0 0
NF1 0.032 0.003 -10000 0 -10000 0 0
RAS 0.006 0.024 -10000 0 -0.084 9 9
ERBB2 0.032 0.003 -10000 0 -10000 0 0
proliferation/survival/translation -0.044 0.07 0.3 9 -0.21 14 23
PI3K 0.049 0.072 0.17 93 -10000 0 93
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
KRAS 0.031 0.008 -10000 0 -10000 0 0
FOXO 0.13 0.082 0.22 175 -10000 0 175
AKT2 0.031 0.006 -10000 0 -10000 0 0
PTEN 0.023 0.016 -10000 0 -0.063 2 2
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.031 0.007 -9999 0 -10000 0 0
EGFR 0.012 0.018 -9999 0 -0.063 6 6
EGF/EGFR 0.007 0.035 -9999 0 -0.056 8 8
EGF/EGFR dimer/SHC/GRB2/SOS1 0.021 0.04 -9999 0 -0.047 33 33
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.005 0.043 -9999 0 -0.063 146 146
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF 0.032 0.007 -9999 0 -0.063 2 2
EGF/EGFR dimer/SHC 0.018 0.035 -9999 0 -0.048 35 35
mol:GDP 0.019 0.037 -9999 0 -0.047 33 33
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.03 0.013 -9999 0 -0.063 9 9
GRB2/SOS1 0.023 0.004 -9999 0 0 15 15
HRAS/GTP 0.011 0.03 -9999 0 -0.059 3 3
SHC1 0.024 0.026 -9999 0 -0.063 40 40
HRAS/GDP 0.017 0.038 -9999 0 -0.067 1 1
FRAP1 -0.012 0.015 -9999 0 -0.056 2 2
EGF/EGFR dimer 0.018 0.025 -9999 0 -0.05 8 8
SOS1 0 0 -9999 0 -10000 0 0
GRB2 0.032 0.006 -9999 0 0 15 15
ETA receptor/Endothelin-1 0.018 0.045 -9999 0 -0.05 149 149
Signaling events mediated by PTP1B

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
PDGFRB 0.032 0.007 -10000 0 -0.063 2 2
Jak2/Leptin Receptor 0.019 0.12 -10000 0 -0.28 56 56
PTP1B/AKT1 0.039 0.059 0.17 8 -0.25 9 17
FYN 0.029 0.011 -10000 0 -0.063 1 1
p210 bcr-abl/PTP1B 0.026 0.06 0.18 8 -0.25 9 17
EGFR 0.012 0.019 -10000 0 -0.052 9 9
EGF/EGFR 0.01 0.041 -10000 0 -0.19 10 10
CSF1 0.032 0.004 -10000 0 -10000 0 0
AKT1 0.031 0.009 -10000 0 -0.026 2 2
INSR 0.031 0.008 -10000 0 -0.026 5 5
PTP1B/N-cadherin 0.038 0.061 0.17 6 -0.23 11 17
Insulin Receptor/Insulin 0.054 0.064 0.18 2 -0.2 15 17
HCK 0.014 0.036 -10000 0 -0.044 120 120
CRK 0.032 0.005 -10000 0 -10000 0 0
TYK2 0.026 0.077 0.27 25 -0.25 9 34
EGF 0.034 0.008 -10000 0 -0.053 3 3
YES1 0.017 0.034 -10000 0 -0.063 75 75
CAV1 0.05 0.085 0.17 90 -0.25 10 100
TXN 0.033 0.007 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.056 0.065 0.2 4 -0.23 11 15
cell migration -0.026 0.06 0.25 9 -0.18 8 17
STAT3 0.031 0.014 -10000 0 -0.062 10 10
PRLR 0.033 0.005 -10000 0 -10000 0 0
ITGA2B 0.032 0.003 -10000 0 -10000 0 0
CSF1R 0.025 0.026 -10000 0 -0.063 40 40
Prolactin Receptor/Prolactin 0.049 0.014 -10000 0 -10000 0 0
FGR 0.029 0.017 -10000 0 -0.063 15 15
PTP1B/p130 Cas 0.022 0.055 0.12 31 -0.19 16 47
Crk/p130 Cas 0.038 0.06 0.17 8 -0.22 11 19
DOK1 0.022 0.062 0.18 14 -0.25 12 26
JAK2 0.005 0.12 0.2 2 -0.3 57 59
Jak2/Leptin Receptor/Leptin 0.026 0.076 -10000 0 -0.24 18 18
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
PTPN1 0.026 0.06 0.14 26 -0.23 11 37
LYN 0.021 0.031 -10000 0 -0.063 60 60
CDH2 0.031 0.009 -10000 0 -0.063 2 2
SRC 0.033 0.059 -10000 0 -0.41 7 7
ITGB3 0.032 0.003 -10000 0 -10000 0 0
CAT1/PTP1B 0.045 0.094 0.24 40 -0.29 11 51
CAPN1 0.032 0.004 -10000 0 -10000 0 0
CSK 0.032 0.005 -10000 0 -10000 0 0
PI3K 0.053 0.07 -10000 0 -0.2 15 15
mol:H2O2 0.003 0.004 0.036 1 -10000 0 1
STAT3 (dimer) 0.025 0.07 -10000 0 -0.22 18 18
negative regulation of transcription 0.005 0.12 0.2 2 -0.29 57 59
FCGR2A -0.015 0.047 -10000 0 -0.063 253 253
FER 0.034 0.005 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.048 0.005 -10000 0 -10000 0 0
BLK 0.032 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.05 0.038 -10000 0 -0.046 57 57
RHOA 0.032 0.006 -10000 0 -10000 0 0
LEPR 0.031 0.009 -10000 0 -0.063 3 3
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.032 0.006 -10000 0 0 15 15
mol:NADPH 0.001 0.002 -10000 0 -10000 0 0
TRPV6 0.031 0.08 0.2 25 -0.28 11 36
PRL 0.033 0.011 -10000 0 -0.061 5 5
SOCS3 0.019 0.015 -10000 0 -10000 0 0
SPRY2 0.032 0.015 -10000 0 -0.061 8 8
Insulin Receptor/Insulin/IRS1 0.06 0.024 -10000 0 -0.041 21 21
CSF1/CSF1R 0.051 0.067 0.2 3 -0.23 11 14
Ras protein signal transduction -0.012 0.082 0.46 13 -10000 0 13
IRS1 0.032 0.009 -10000 0 -0.063 4 4
INS 0.032 0.007 -10000 0 -0.026 1 1
LEP 0.023 0.015 -10000 0 0 158 158
STAT5B 0.023 0.075 0.2 4 -0.26 19 23
STAT5A 0.023 0.075 0.2 4 -0.24 21 25
GRB2 0.032 0.006 -10000 0 0 15 15
PDGFB-D/PDGFRB 0.041 0.062 0.18 8 -0.23 11 19
CSN2 0 0.034 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
LAT 0.009 0.044 -10000 0 -0.29 2 2
YBX1 0.037 0.017 -10000 0 -0.061 12 12
LCK 0.031 0.01 -10000 0 -0.063 4 4
SHC1 0.024 0.026 -10000 0 -0.063 40 40
NOX4 0.022 0.033 -10000 0 -0.06 70 70
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.054 0.063 -10000 0 -10000 0 0
SMAD6-7/SMURF1 0.043 0.033 -10000 0 -0.037 11 11
NOG 0 0 -10000 0 -10000 0 0
SMAD9 -0.03 0.16 -10000 0 -0.49 53 53
SMAD4 0.01 0.04 -10000 0 -0.063 117 117
SMAD5 -0.028 0.093 0.12 2 -0.31 39 41
BMP7/USAG1 0.031 0.024 -10000 0 -0.05 6 6
SMAD5/SKI -0.016 0.097 -10000 0 -0.3 39 39
SMAD1 -0.01 0.072 -10000 0 -0.25 26 26
BMP2 0.022 0.027 -10000 0 -0.063 44 44
SMAD1/SMAD1/SMAD4 0 0.071 -10000 0 -0.25 19 19
BMPR1A 0.023 0.017 -10000 0 -0.063 6 6
BMPR1B 0.032 0.006 -10000 0 -0.063 1 1
BMPR1A-1B/BAMBI 0.029 0.052 -10000 0 -0.044 164 164
AHSG 0.031 0.008 -10000 0 -0.063 2 2
CER1 0.029 0.011 -10000 0 -10000 0 0
BMP2-4/CER1 0.039 0.045 -10000 0 -0.043 103 103
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.003 0.061 -10000 0 -0.19 40 40
BMP2-4 (homodimer) 0.033 0.031 -10000 0 -0.05 47 47
RGMB 0 0 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.048 0.056 -10000 0 -0.058 4 4
RGMA 0 0 -10000 0 -10000 0 0
SMURF1 0.023 0.015 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.016 0.058 -10000 0 -0.12 102 102
BMP2-4/USAG1 0.032 0.041 -10000 0 -0.05 49 49
SMAD6/SMURF1/SMAD5 -0.008 0.087 -10000 0 -0.3 34 34
SOSTDC1 0.022 0.017 -10000 0 -0.063 6 6
BMP7/BMPR2/BMPR1A-1B 0.05 0.053 -10000 0 -0.057 3 3
SKI 0.031 0.007 -10000 0 -10000 0 0
BMP6 (homodimer) 0.032 0.007 -10000 0 -0.063 2 2
HFE2 0 0 -10000 0 -10000 0 0
ZFYVE16 0.031 0.01 -10000 0 -0.063 5 5
MAP3K7 0.031 0.008 -10000 0 -0.063 1 1
BMP2-4/CHRD 0.044 0.041 -10000 0 -0.045 71 71
SMAD5/SMAD5/SMAD4 -0.022 0.099 -10000 0 -0.31 40 40
MAPK1 0.03 0.009 -10000 0 -10000 0 0
TAK1/TAB family 0.01 0.053 -10000 0 -0.18 20 20
BMP7 (homodimer) 0.03 0.01 -10000 0 -0.063 1 1
NUP214 0.031 0.007 -10000 0 -10000 0 0
BMP6/FETUA 0.045 0.014 -10000 0 -0.05 4 4
SMAD1/SKI 0.003 0.081 -10000 0 -0.25 28 28
SMAD6 0.032 0.005 -10000 0 -10000 0 0
CTDSP2 0.028 0.011 -10000 0 -10000 0 0
BMP2-4/FETUA 0.044 0.041 -10000 0 -0.045 74 74
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.027 0.02 -10000 0 -0.063 22 22
BMPR2 (homodimer) 0.032 0.001 -10000 0 -10000 0 0
GADD34/PP1CA 0.057 0.028 -10000 0 -0.038 34 34
BMPR1A-1B (homodimer) 0.034 0.023 -10000 0 -0.05 5 5
CHRDL1 0 0 -10000 0 -10000 0 0
ENDOFIN/SMAD1 0.002 0.084 0.29 1 -0.25 30 31
SMAD6-7/SMURF1/SMAD1 0.016 0.079 -10000 0 -0.26 18 18
SMAD6/SMURF1 0.023 0.015 -10000 0 -10000 0 0
BAMBI 0.02 0.024 -10000 0 -0.063 27 27
SMURF2 0.032 0.005 -10000 0 -0.063 1 1
BMP2-4/CHRDL1 0.03 0.027 -10000 0 -0.04 50 50
BMP2-4/GREM1 0.039 0.045 -10000 0 -0.046 100 100
SMAD7 0.031 0.007 -10000 0 -0.063 1 1
SMAD8A/SMAD8A/SMAD4 -0.027 0.16 -10000 0 -0.46 59 59
SMAD1/SMAD6 0.002 0.068 -10000 0 -0.25 20 20
TAK1/SMAD6 0.033 0.023 -10000 0 -0.05 1 1
BMP7 0.03 0.01 -10000 0 -0.063 1 1
BMP6 0.032 0.007 -10000 0 -0.063 2 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.005 0.051 -10000 0 -0.13 49 49
PPM1A 0.031 0.008 -10000 0 -10000 0 0
SMAD1/SMURF2 0.003 0.083 0.29 1 -0.25 29 30
SMAD7/SMURF1 0.033 0.023 -10000 0 -0.05 1 1
CTDSPL 0.032 0.005 -10000 0 -10000 0 0
PPP1CA 0.032 0.004 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
CTDSP1 0.032 0.007 -10000 0 -0.063 3 3
PPP1R15A 0.031 0.009 -10000 0 -0.063 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.015 0.059 -10000 0 -0.12 103 103
CHRD 0.031 0.006 -10000 0 -10000 0 0
BMPR2 0.033 0.001 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.018 0.059 -10000 0 -0.12 108 108
BMP4 0.029 0.014 -10000 0 -0.063 8 8
FST 0.029 0.017 -10000 0 -0.063 16 16
BMP2-4/NOG 0.03 0.027 -10000 0 -0.04 50 50
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.05 0.055 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.006 0.047 -10000 0 -0.051 258 258
alphaV beta3 Integrin 0.06 0.025 -10000 0 -0.048 17 17
PTK2 -0.01 0.063 0.29 7 -0.26 6 13
IGF1R 0.032 0.004 -10000 0 -10000 0 0
PI4KB 0.032 0.005 -10000 0 -10000 0 0
MFGE8 0.032 0.007 -10000 0 -0.063 2 2
SRC 0.031 0.008 -10000 0 -10000 0 0
CDKN1B 0.013 0.051 -10000 0 -0.26 17 17
VEGFA -0.019 0.047 -10000 0 -0.063 274 274
ILK 0.014 0.048 -10000 0 -0.26 15 15
ROCK1 0.032 0.005 -10000 0 -10000 0 0
AKT1 0.001 0.041 -10000 0 -0.25 13 13
PTK2B -0.029 0.058 0.16 40 -10000 0 40
alphaV/beta3 Integrin/JAM-A 0.055 0.041 0.17 6 -10000 0 6
CBL 0.032 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.06 0.024 -10000 0 -0.048 15 15
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.079 0.023 -10000 0 -10000 0 0
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.009 0.044 -10000 0 -0.16 24 24
alphaV/beta3 Integrin/Syndecan-1 0.051 0.038 -10000 0 -0.048 62 62
PI4KA 0.012 0.016 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.043 0.06 -10000 0 -0.094 2 2
PI4 Kinase 0.017 0.023 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
alphaV/beta3 Integrin/Osteopontin 0.022 0.055 -10000 0 -0.049 186 186
RPS6KB1 -0.048 0.043 0.68 1 -10000 0 1
TLN1 0.021 0.027 -10000 0 -0.063 43 43
MAPK3 0 0.039 -10000 0 -0.28 8 8
GPR124 0.032 0.007 -10000 0 -0.063 2 2
MAPK1 -0.001 0.039 -10000 0 -0.28 8 8
PXN 0.032 0.003 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.061 0.022 -10000 0 -0.046 19 19
cell adhesion 0.047 0.03 -10000 0 -0.082 4 4
ANGPTL3 0.032 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.003 0.054 -10000 0 -0.049 237 237
IGF-1R heterotetramer 0.032 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.011 -10000 0 -10000 0 0
TGFBR2 0.031 0.01 -10000 0 -0.063 5 5
ITGB3 0.032 0.003 -10000 0 -10000 0 0
IGF1 0.032 0.009 -10000 0 -0.063 4 4
RAC1 0.023 0.015 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.059 0.024 -10000 0 -0.048 18 18
apoptosis 0.029 0.016 -10000 0 -0.063 15 15
CD47 0.031 0.008 -10000 0 -0.063 2 2
alphaV/beta3 Integrin/CD47 0.059 0.026 -10000 0 -0.044 26 26
VCL 0.025 0.014 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.06 0.024 -10000 0 -0.048 15 15
CSF1 0.032 0.004 -10000 0 -10000 0 0
PIK3C2A 0.009 0.013 -10000 0 -0.25 1 1
PI4 Kinase/Pyk2 -0.02 0.034 0.098 8 -10000 0 8
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.005 0.064 -10000 0 -0.07 18 18
FAK1/Vinculin -0.005 0.056 0.28 6 -0.23 6 12
alphaV beta3/Integrin/ppsTEM5 0.06 0.024 -10000 0 -0.048 18 18
RHOA 0.032 0.006 -10000 0 -10000 0 0
VTN 0.032 0.007 -10000 0 -0.063 2 2
BCAR1 0 0 -10000 0 -10000 0 0
FGF2 0.032 0.007 -10000 0 -0.063 2 2
F11R -0.024 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Lactadherin 0.06 0.025 -10000 0 -0.048 17 17
alphaV/beta3 Integrin/TGFBR2 0.059 0.027 -10000 0 -0.048 20 20
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.057 0.023 -10000 0 -0.042 16 16
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.043 0.039 -10000 0 -0.044 55 55
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.014 0.037 -10000 0 -0.063 96 96
alphaV/beta3 Integrin/Pyk2 0.002 0.067 0.17 34 -0.088 1 35
SDC1 0.024 0.027 -10000 0 -0.063 45 45
VAV3 -0.028 0.021 0.18 5 -10000 0 5
PTPN11 0.032 0.003 -10000 0 -10000 0 0
IRS1 0.032 0.009 -10000 0 -0.063 4 4
FAK1/Paxillin -0.003 0.062 0.26 7 -0.22 6 13
cell migration -0.016 0.051 0.25 7 -0.21 6 13
ITGAV 0.03 0.016 -10000 0 -0.063 15 15
PI3K 0.061 0.049 0.16 5 -10000 0 5
SPP1 -0.001 0.045 -10000 0 -0.063 175 175
KDR 0.028 0.017 -10000 0 -0.063 14 14
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.029 0.016 -10000 0 -0.063 15 15
COL4A3 0.033 0.001 -10000 0 -10000 0 0
angiogenesis 0.002 0.044 0.18 3 -0.31 8 11
Rac1/GTP -0.023 0.024 0.18 4 -10000 0 4
EDIL3 0.032 0.004 -10000 0 -10000 0 0
cell proliferation 0.058 0.027 -10000 0 -0.048 20 20
Canonical Wnt signaling pathway

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
HDAC1 0.023 0.031 -10000 0 -0.057 61 61
AES 0.034 0.009 -10000 0 -10000 0 0
FBXW11 0.032 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.032 0.024 -10000 0 -0.05 4 4
SMAD4 0.01 0.04 -10000 0 -0.063 117 117
DKK2 0.031 0.012 -10000 0 -0.063 8 8
TLE1 0.034 0.008 -10000 0 -10000 0 0
MACF1 0.032 0.006 -10000 0 -10000 0 0
CTNNB1 0.096 0.099 0.22 146 -0.27 6 152
WIF1 0.004 0.01 -10000 0 -10000 0 0
beta catenin/RanBP3 0.098 0.078 0.23 51 -0.3 3 54
KREMEN2 0.032 0.003 -10000 0 -10000 0 0
DKK1 0.006 0.037 -10000 0 -0.062 101 101
beta catenin/beta TrCP1 0.11 0.095 0.22 141 -0.26 6 147
FZD1 0.022 0.017 -10000 0 -0.063 4 4
AXIN2 -0.014 0.022 -10000 0 -0.13 2 2
AXIN1 0.034 0.004 -10000 0 -10000 0 0
RAN 0.032 0.004 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.045 0.085 -10000 0 -0.45 9 9
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.064 0.07 0.24 18 -0.25 5 23
Axin1/APC/GSK3 0.041 0.063 0.16 70 -0.3 3 73
Axin1/APC/GSK3/beta catenin/Macf1 0.065 0.092 0.19 125 -0.22 10 135
HNF1A 0.035 0.007 -10000 0 -10000 0 0
CTBP1 0.034 0.008 -10000 0 -10000 0 0
MYC -0.025 0.098 0.45 15 -10000 0 15
RANBP3 0.032 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.06 0.023 -10000 0 -0.043 14 14
NKD1 -0.001 0.001 -10000 0 -10000 0 0
TCF4 0.034 0.009 -10000 0 -10000 0 0
TCF3 0.034 0.009 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.053 0.042 -10000 0 -0.06 1 1
Ran/GTP 0.024 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.035 0.05 0.21 2 -0.19 3 5
LEF1 0.034 0.01 -10000 0 -0.059 3 3
DVL1 0.023 0.023 -10000 0 -0.14 1 1
CSNK2A1 0.031 0.008 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.067 0.062 0.26 16 -0.22 2 18
DKK1/LRP6/Kremen 2 0.025 0.047 -10000 0 -0.047 107 107
LRP6 0.032 0.007 -10000 0 -10000 0 0
CSNK1A1 0.037 0.008 -10000 0 -10000 0 0
NLK 0.032 0.004 -10000 0 -10000 0 0
CCND1 -0.034 0.058 0.41 3 -10000 0 3
WNT1 0.032 0.006 -10000 0 -10000 0 0
GSK3A 0.032 0.007 -10000 0 -10000 0 0
GSK3B 0.032 0.006 -10000 0 -10000 0 0
FRAT1 0.024 0.014 -10000 0 -10000 0 0
PPP2R5D 0.032 0.037 -10000 0 -0.26 4 4
APC 0.032 0.11 0.18 150 -10000 0 150
WNT1/LRP6/FZD1 0 0.025 -10000 0 -0.24 4 4
CREBBP 0.035 0.007 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.004 0.038 0.15 15 -0.19 7 22
adherens junction organization 0.007 0.041 0.13 7 -0.16 17 24
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.046 0.071 0.16 130 -0.15 5 135
FMN1 0.013 0.038 0.13 7 -0.14 16 23
mol:IP3 0.004 0.024 0.085 1 -0.12 9 10
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.018 0.04 0.14 7 -0.15 16 23
CTNNB1 0.032 0.006 -10000 0 -10000 0 0
AKT1 0.012 0.035 0.1 29 -0.16 6 35
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.024 0.06 -10000 0 -0.26 14 14
CTNND1 0.031 0.014 -10000 0 -0.064 10 10
mol:PI-4-5-P2 0.007 0.037 0.13 7 -0.15 16 23
VASP 0.007 0.034 0.13 7 -0.14 14 21
ZYX 0.001 0.03 0.13 2 -0.17 9 11
JUB 0.013 0.038 0.13 7 -0.14 16 23
EGFR(dimer) 0.011 0.035 0.15 2 -0.16 9 11
E-cadherin/beta catenin-gamma catenin 0.058 0.026 -10000 0 -0.052 19 19
mol:PI-3-4-5-P3 0.041 0.049 0.16 31 -0.15 8 39
PIK3CA 0.029 0.019 -10000 0 -0.057 21 21
PI3K 0.042 0.05 0.16 31 -0.15 8 39
FYN -0.011 0.054 0.15 11 -0.2 28 39
mol:Ca2+ 0.004 0.025 0.085 1 -0.13 10 11
JUP 0.03 0.017 -10000 0 -0.062 16 16
PIK3R1 0.031 0.01 -10000 0 -10000 0 0
mol:DAG 0.004 0.024 0.085 1 -0.12 9 10
CDH1 0.031 0.013 -10000 0 -0.061 8 8
RhoA/GDP 0.075 0.077 0.16 224 -0.14 6 230
establishment of polarity of embryonic epithelium 0.006 0.035 0.13 7 -0.14 16 23
SRC 0.031 0.008 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
RHOA 0.032 0.006 -10000 0 -10000 0 0
EGFR 0.012 0.018 -10000 0 -0.063 6 6
CASR -0.012 0.033 0.15 12 -0.14 7 19
RhoA/GTP 0.02 0.037 0.14 12 -0.13 8 20
AKT2 0.01 0.034 0.1 22 -0.15 7 29
actin cable formation 0.004 0.034 0.12 7 -0.14 16 23
apoptosis -0.01 0.043 0.17 9 -0.17 12 21
CTNNA1 0.033 0.005 -10000 0 -10000 0 0
mol:GDP -0.008 0.021 0.14 1 -0.14 8 9
PIP5K1A 0.007 0.038 0.13 7 -0.15 16 23
PLCG1 0.004 0.025 0.086 1 -0.13 9 10
Rac1/GTP 0.015 0.039 0.15 2 -0.16 9 11
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.01 0.04 -10000 0 -0.063 117 117
SMAD2 -0.021 0.058 0.14 1 -0.22 28 29
SMAD3 0.013 0.042 0.1 30 -0.098 27 57
SMAD3/SMAD4 0.026 0.056 -10000 0 -0.5 4 4
SMAD4/Ubc9/PIASy 0.037 0.048 -10000 0 -0.048 108 108
SMAD2/SMAD2/SMAD4 0.017 0.084 -10000 0 -0.19 38 38
PPM1A 0.031 0.008 -10000 0 -10000 0 0
CALM1 0.029 0.01 -10000 0 -10000 0 0
SMAD2/SMAD4 -0.014 0.063 -10000 0 -0.19 39 39
MAP3K1 0.032 0.006 -10000 0 -0.063 1 1
TRAP-1/SMAD4 0.024 0.041 -10000 0 -0.05 116 116
MAPK3 0.032 0.002 -10000 0 -10000 0 0
MAPK1 0.03 0.009 -10000 0 -10000 0 0
NUP214 0.031 0.007 -10000 0 -10000 0 0
CTDSP1 0.032 0.007 -10000 0 -0.063 3 3
CTDSP2 0.028 0.011 -10000 0 -10000 0 0
CTDSPL 0.032 0.005 -10000 0 -10000 0 0
KPNB1 0.032 0.003 -10000 0 -10000 0 0
TGFBRAP1 0.032 0.003 -10000 0 -10000 0 0
UBE2I 0.032 0.003 -10000 0 -10000 0 0
NUP153 0.032 0.005 -10000 0 -0.063 1 1
KPNA2 0.03 0.014 -10000 0 -0.063 11 11
PIAS4 0.032 0.006 -10000 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.036 0.011 -10000 0 -0.022 9 9
RGS9BP 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
mol:Na + 0.013 0.039 -10000 0 -0.039 179 179
mol:ADP 0 0 -10000 0 -10000 0 0
GNAT2 0.032 0.004 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.042 0.01 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.041 0.011 -10000 0 -10000 0 0
GRK7 0 0 -10000 0 -10000 0 0
CNGB3 0.032 0.004 -10000 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0.024 0.002 -10000 0 0 2 2
mol:Ca2+ -0.02 0.033 0.18 11 -10000 0 11
Cone PDE6 0.044 0.051 -10000 0 -10000 0 0
Cone Metarhodopsin II 0 0 -10000 0 -10000 0 0
Na + (4 Units) 0.014 0.051 -10000 0 -0.041 229 229
GNAT2/GDP 0.053 0.018 -10000 0 -10000 0 0
GNB5 0.031 0.006 -10000 0 -10000 0 0
mol:GMP (4 units) -0.013 0.03 0.18 11 -10000 0 11
Cone Transducin 0.039 0.012 -10000 0 -0.023 9 9
SLC24A2 0.027 0.013 -10000 0 -10000 0 0
GNB3/GNGT2 0.023 0.005 -10000 0 0 22 22
GNB3 0.031 0.007 -10000 0 -10000 0 0
GNAT2/GTP 0.024 0.003 -10000 0 -10000 0 0
CNGA3 -0.001 0.045 -10000 0 -0.063 179 179
ARR3 0.032 0.002 -10000 0 0 2 2
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.014 0.04 -10000 0 -0.04 179 179
mol:Pi 0.041 0.009 -10000 0 -10000 0 0
Cone CNG Channel 0.014 0.064 -10000 0 -0.065 4 4
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.027 0.013 -10000 0 -10000 0 0
RGS9 0.032 0.004 -10000 0 -10000 0 0
PDE6C 0.024 0.014 -10000 0 -10000 0 0
GNGT2 0 0 -10000 0 -10000 0 0
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.031 0.007 -10000 0 -10000 0 0
IL1-mediated signaling events

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
UBC13/UEV1A 0.024 0.003 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.031 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.002 0.053 -10000 0 -0.18 29 29
IRAK/TOLLIP 0.03 0.009 -10000 0 -0.031 4 4
IKBKB 0.032 0.003 -10000 0 -10000 0 0
IKBKG 0.032 0.003 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.04 0.027 -10000 0 -0.05 40 40
IL1A 0.032 0.008 -10000 0 -0.063 3 3
IL1B -0.032 0.014 -10000 0 -0.051 171 171
IRAK/TRAF6/p62/Atypical PKCs 0.056 0.026 0.17 4 -10000 0 4
IL1R2 0.025 0.025 -10000 0 -0.063 37 37
IL1R1 0.032 0.008 -10000 0 -0.063 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.011 0.047 -10000 0 -0.17 22 22
TOLLIP 0.031 0.006 -10000 0 -10000 0 0
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0.032 0.003 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.021 0.005 -10000 0 -0.031 1 1
IKK complex/ELKS -0.026 0.096 -10000 0 -0.19 120 120
JUN -0.025 0.022 0.14 4 -10000 0 4
MAP3K7 0.031 0.008 -10000 0 -0.063 1 1
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.019 0.068 0.18 2 -0.091 6 8
IL1 alpha/IL1R1/IL1RAP/MYD88 0.051 0.057 -10000 0 -0.069 11 11
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.056 0.066 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP 0.009 0.05 -10000 0 -0.054 186 186
NFKB1 0.031 0.009 -10000 0 -0.063 4 4
MAPK8 -0.022 0.023 0.16 5 -10000 0 5
IRAK1 -0.017 0.003 -10000 0 -10000 0 0
IL1RN/IL1R1 0.048 0.008 -10000 0 -0.05 3 3
IRAK4 0.031 0.008 -10000 0 -0.063 1 1
PRKCI 0.032 0.006 -10000 0 -0.063 1 1
TRAF6 0.032 0.005 -10000 0 -10000 0 0
PI3K 0.039 0.023 -10000 0 -0.05 16 16
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.004 0.047 0.13 1 -0.19 20 21
CHUK 0.024 0.015 -10000 0 -0.063 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.009 0.05 -10000 0 -0.054 186 186
IL1 beta/IL1R2 0.004 0.044 -10000 0 -0.072 21 21
IRAK/TRAF6/TAK1/TAB1/TAB2 0.038 0.023 0.16 4 -10000 0 4
NF kappa B1 p50/RelA 0.007 0.064 -10000 0 -0.098 7 7
IRAK3 0.031 0.008 -10000 0 -0.063 1 1
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.015 0.057 0.16 2 -0.084 4 6
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.007 0.041 -10000 0 -0.12 37 37
IL1 alpha/IL1R1/IL1RAP 0.053 0.036 -10000 0 -0.049 46 46
RELA 0.032 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.032 0.006 -10000 0 -0.063 1 1
MYD88 0.019 0.032 -10000 0 -0.063 67 67
IRAK/TRAF6/MEKK3 0.05 0.018 0.18 4 -10000 0 4
IL1RAP 0.024 0.026 -10000 0 -0.063 41 41
UBE2N 0.032 0.004 -10000 0 -10000 0 0
IRAK/TRAF6 -0.052 0.016 0.035 1 -0.092 4 5
CASP1 0.001 0.044 -10000 0 -0.063 166 166
IL1RN/IL1R2 0.041 0.026 -10000 0 -0.05 37 37
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.011 0.064 0.17 2 -0.09 13 15
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.007 0.048 -10000 0 -0.23 11 11
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
IL1RN 0.032 0.002 -10000 0 -10000 0 0
TRAF6/TAK1/TAB1/TAB2 0.042 0.02 -10000 0 -0.035 5 5
MAP2K6 -0.023 0.025 0.17 8 -10000 0 8
Arf6 trafficking 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
SLC2A4 0.032 0.005 -10000 0 -10000 0 0
CLTC 0.008 0.089 -10000 0 -0.34 29 29
calcium ion-dependent exocytosis 0.022 0.045 0.093 89 -0.19 6 95
Dynamin 2/GTP 0.022 0.012 -10000 0 -0.023 28 28
EXOC4 0 0 -10000 0 -10000 0 0
CD59 0.006 0.075 -10000 0 -0.28 28 28
CPE -0.015 0.007 -10000 0 -10000 0 0
CTNNB1 0.032 0.005 -10000 0 -10000 0 0
membrane fusion 0.026 0.044 0.093 126 -0.2 3 129
CTNND1 -0.021 0.006 -10000 0 -10000 0 0
DNM2 0.031 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.012 0.055 0.13 9 -0.17 28 37
TSHR -0.017 0.005 0 40 -0.04 4 44
INS 0.004 0.095 -10000 0 -0.46 19 19
BIN1 0.03 0.009 -10000 0 -10000 0 0
mol:Choline 0.026 0.044 0.093 126 -0.2 3 129
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP -0.008 0.002 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.031 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0.021 0.012 -10000 0 -0.023 28 28
JUP 0.005 0.072 -10000 0 -0.28 27 27
ASAP2/amphiphysin II 0.035 0.018 -10000 0 -0.023 27 27
ARF6/GTP 0.023 0.006 -10000 0 -10000 0 0
CDH1 0.006 0.072 -10000 0 -0.28 27 27
clathrin-independent pinocytosis 0.023 0.006 -10000 0 -10000 0 0
MAPK8IP3 0.032 0.004 -10000 0 -10000 0 0
positive regulation of endocytosis 0.023 0.006 -10000 0 -10000 0 0
EXOC2 0.032 0.004 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.003 0.04 -10000 0 -0.13 34 34
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.032 0.005 -10000 0 -0.063 1 1
regulation of calcium-dependent cell-cell adhesion -0.033 0.076 0.27 28 -10000 0 28
positive regulation of phagocytosis -0.016 0.006 0 63 -10000 0 63
ARF6/GTP/JIP3 0.041 0.011 -10000 0 -10000 0 0
ACAP1 0.027 0.042 0.091 126 -0.2 3 129
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.001 0.066 -10000 0 -0.29 21 21
clathrin heavy chain/ACAP1 0.017 0.077 0.18 9 -0.25 28 37
JIP4/KLC1 0.041 0.033 -10000 0 -0.039 11 11
EXOC1 0.03 0.009 -10000 0 -0.063 1 1
exocyst 0.003 0.041 -10000 0 -0.13 34 34
RALA/GTP 0.015 0.014 -10000 0 -0.039 11 11
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.041 0.011 -10000 0 -0.04 1 1
receptor recycling 0.023 0.006 -10000 0 -10000 0 0
CTNNA1 -0.021 0.005 -10000 0 -10000 0 0
NME1 -0.008 0.002 -10000 0 -10000 0 0
clathrin coat assembly 0.009 0.088 0.18 1 -0.33 29 30
IL2RA -0.003 0.08 -10000 0 -0.33 26 26
VAMP3 -0.016 0.006 0 63 -10000 0 63
GLUT4/clathrin heavy chain/ACAP1 0.034 0.075 -10000 0 -0.25 28 28
EXOC6 0 0 -10000 0 -10000 0 0
PLD1 0.006 0.012 -10000 0 -0.054 13 13
PLD2 0.006 0.011 -10000 0 -0.054 11 11
EXOC5 0.028 0.018 -10000 0 -0.063 15 15
PIP5K1C 0.011 0.051 0.12 4 -0.17 26 30
SDC1 0.003 0.074 -10000 0 -0.28 28 28
ARF6/GDP 0.023 0.006 -10000 0 0 29 29
EXOC7 0.032 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.035 0.079 -10000 0 -0.28 28 28
mol:Phosphatidic acid 0.026 0.044 0.093 126 -0.2 3 129
endocytosis -0.034 0.018 0.023 27 -10000 0 27
SCAMP2 0.032 0.005 -10000 0 -10000 0 0
ADRB2 0.003 0.085 0.22 2 -0.32 29 31
EXOC3 0.032 0.006 -10000 0 -10000 0 0
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.019 0.011 -10000 0 -0.023 28 28
KLC1 0.023 0.015 -10000 0 -10000 0 0
AVPR2 0.004 0.086 0.2 4 -0.32 29 33
RALA 0.021 0.019 -10000 0 -0.063 11 11
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.02 0.076 0.22 2 -0.27 28 30
Retinoic acid receptors-mediated 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
HDAC1 0.02 0.031 -10000 0 -0.063 61 61
HDAC3 0.032 0.004 -10000 0 -10000 0 0
VDR 0.031 0.006 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.04 0.012 -10000 0 -10000 0 0
EP300 0.03 0.008 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.002 0.057 0.09 5 -0.16 45 50
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.032 0.005 -10000 0 -0.063 1 1
AKT1 0.004 0.053 0.14 5 -0.19 17 22
RAR alpha/9cRA/Cyclin H 0.007 0.088 0.2 3 -0.17 39 42
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.003 0.052 0.091 7 -0.15 43 50
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.017 0.045 0.15 1 -0.16 22 23
NCOR2 0.032 0.004 -10000 0 0 6 6
VDR/VDR/Vit D3 0.023 0.005 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.002 0.073 0.3 3 -0.28 17 20
NCOA2 0.032 0.004 -10000 0 0 9 9
NCOA3 0.03 0.011 -10000 0 -0.003 43 43
NCOA1 0.031 0.007 -10000 0 -10000 0 0
VDR/VDR/DNA 0.031 0.006 -10000 0 -10000 0 0
RARG 0.032 0.005 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.042 0.01 -10000 0 -10000 0 0
MAPK3 0.033 0.003 -10000 0 -10000 0 0
MAPK1 0.03 0.009 -10000 0 -10000 0 0
MAPK8 0.025 0.014 -10000 0 -0.027 1 1
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.009 0.072 -10000 0 -0.29 17 17
RARA 0.011 0.007 -10000 0 -10000 0 0
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.002 0.051 0.098 8 -0.15 40 48
PRKCA 0.033 0.007 -10000 0 -0.036 4 4
RXRs/RARs/NRIP1/9cRA/HDAC1 0.002 0.069 0.27 2 -0.28 18 20
RXRG 0.019 0.007 -10000 0 -0.033 2 2
RXRA -0.013 0.044 0.1 8 -0.093 111 119
RXRB 0.019 0.007 -10000 0 -0.04 1 1
VDR/Vit D3/DNA 0.023 0.005 -10000 0 -10000 0 0
RBP1 -0.01 0.046 -10000 0 -0.063 222 222
CRBP1/9-cic-RA -0.004 0.031 -10000 0 -0.039 222 222
RARB 0.032 0.007 -10000 0 -0.025 4 4
PRKCG 0.031 0.01 -10000 0 -0.036 4 4
MNAT1 0.03 0.009 -10000 0 -0.063 1 1
RAR alpha/RXRs 0.003 0.08 0.2 1 -0.33 17 18
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.002 0.067 0.24 2 -0.25 19 21
proteasomal ubiquitin-dependent protein catabolic process -0.009 0.064 0.16 3 -0.18 35 38
RXRs/RARs/NRIP1/9cRA/HDAC3 0.003 0.068 0.3 1 -0.27 18 19
positive regulation of DNA binding 0.001 0.08 0.15 2 -0.16 39 41
NRIP1 0.008 0.068 0.3 2 -0.33 6 8
RXRs/RARs 0.008 0.067 -10000 0 -0.27 20 20
RXRs/RXRs/DNA/9cRA -0.004 0.065 -10000 0 -0.28 18 18
PRKACA 0.032 0.006 -10000 0 -10000 0 0
CDK7 0.032 0.007 -10000 0 -0.063 2 2
TFIIH 0.057 0.029 -10000 0 -0.048 8 8
RAR alpha/9cRA 0.024 0.082 -10000 0 -0.13 40 40
CCNH 0.032 0.004 -10000 0 -10000 0 0
CREBBP 0.032 0.004 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.053 0.034 -10000 0 -10000 0 0
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.16 0.2 -10000 0 -0.7 14 14
PLK1 0 0.11 -10000 0 -0.86 7 7
BIRC5 -0.028 0.073 -10000 0 -10000 0 0
HSPA1B -0.16 0.2 -10000 0 -0.67 19 19
MAP2K1 -0.013 0.038 -10000 0 -10000 0 0
BRCA2 -0.16 0.2 -10000 0 -0.7 13 13
FOXM1 -0.18 0.22 -10000 0 -0.74 22 22
XRCC1 -0.16 0.2 0.36 1 -0.7 13 14
FOXM1B/p19 -0.17 0.2 -10000 0 -0.7 18 18
Cyclin D1/CDK4 -0.16 0.19 -10000 0 -0.65 15 15
CDC2 -0.17 0.2 -10000 0 -0.71 16 16
TGFA -0.16 0.19 -10000 0 -0.62 20 20
SKP2 -0.16 0.2 -10000 0 -0.7 15 15
CCNE1 0.015 0.026 -10000 0 -0.072 4 4
CKS1B -0.17 0.2 -10000 0 -0.69 20 20
RB1 -0.11 0.19 -10000 0 -0.59 46 46
FOXM1C/SP1 -0.17 0.22 -10000 0 -0.72 21 21
AURKB -0.009 0.14 -10000 0 -0.92 11 11
CENPF -0.17 0.21 -10000 0 -0.69 19 19
CDK4 -0.028 0.046 -10000 0 -0.072 246 246
MYC -0.16 0.19 -10000 0 -0.62 20 20
CHEK2 -0.012 0.04 -10000 0 -0.1 15 15
ONECUT1 -0.16 0.2 -10000 0 -0.67 17 17
CDKN2A 0.003 0.026 -10000 0 -0.061 52 52
LAMA4 -0.16 0.2 -10000 0 -0.7 14 14
FOXM1B/HNF6 -0.17 0.21 -10000 0 -0.72 18 18
FOS -0.18 0.2 -10000 0 -0.74 14 14
SP1 0.031 0.006 -10000 0 -0.025 2 2
CDC25B -0.16 0.2 0.36 1 -0.69 13 14
response to radiation -0.011 0.013 -10000 0 -10000 0 0
CENPB -0.16 0.2 -10000 0 -0.7 12 12
CENPA -0.17 0.21 -10000 0 -0.7 20 20
NEK2 -0.16 0.2 -10000 0 -0.71 14 14
HIST1H2BA -0.16 0.2 -10000 0 -0.67 19 19
CCNA2 0.001 0.046 -10000 0 -0.072 135 135
EP300 0.03 0.008 -10000 0 -10000 0 0
CCNB1/CDK1 -0.18 0.21 -10000 0 -0.76 15 15
CCNB2 -0.19 0.21 -10000 0 -0.7 21 21
CCNB1 -0.18 0.21 -10000 0 -0.72 16 16
ETV5 -0.16 0.2 -10000 0 -0.68 16 16
ESR1 -0.16 0.2 -10000 0 -0.7 14 14
CCND1 -0.16 0.2 -10000 0 -0.65 18 18
GSK3A -0.009 0.036 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.013 0.06 -10000 0 -0.1 10 10
CDK2 0.014 0.03 -10000 0 -0.073 24 24
G2/M transition of mitotic cell cycle -0.014 0.016 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.16 0.22 -10000 0 -0.7 20 20
GAS1 -0.17 0.2 0.36 1 -0.71 15 16
MMP2 -0.18 0.2 -10000 0 -0.7 18 18
RB1/FOXM1C -0.18 0.21 -10000 0 -0.67 25 25
CREBBP 0.032 0.004 -10000 0 -10000 0 0
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.032 0.007 -10000 0 -0.063 2 2
alphaV beta3 Integrin 0.045 0.018 -10000 0 -0.05 15 15
PTK2 0.016 0.078 -10000 0 -0.23 42 42
positive regulation of JNK cascade 0.021 0.081 -10000 0 -0.24 40 40
CDC42/GDP 0.035 0.11 0.35 2 -0.33 38 40
Rac1/GDP 0.024 0.093 0.29 1 -0.33 21 22
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.032 0.004 -10000 0 -10000 0 0
CTNNB1 0.032 0.005 -10000 0 -10000 0 0
CDC42/GTP 0.028 0.099 -10000 0 -0.29 40 40
nectin-3/I-afadin 0.044 0.015 -10000 0 -0.05 1 1
RAPGEF1 0.006 0.11 0.24 6 -0.34 40 46
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.004 0.11 -10000 0 -0.37 40 40
PDGFB-D/PDGFRB 0.032 0.007 -10000 0 -0.063 2 2
TLN1 -0.015 0.015 -10000 0 -0.075 19 19
Rap1/GTP 0.001 0.077 -10000 0 -0.26 39 39
IQGAP1 0.01 0.04 -10000 0 -0.063 120 120
Rap1/GTP/I-afadin 0.036 0.018 -10000 0 -0.023 40 40
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.044 0.015 -10000 0 -0.05 1 1
PVR 0.031 0.007 -10000 0 -10000 0 0
Necl-5(dimer) 0.031 0.007 -10000 0 -10000 0 0
mol:GDP 0.021 0.13 0.33 3 -0.39 39 42
MLLT4 0.03 0.008 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
PI3K 0.07 0.052 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.044 0.014 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.015 0.076 -10000 0 -0.27 21 21
PVRL1 0.032 0.004 -10000 0 -10000 0 0
PVRL3 0.032 0.006 -10000 0 -0.063 1 1
PVRL2 0.031 0.007 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
CDH1 0.03 0.013 -10000 0 -0.063 8 8
CLDN1 0.03 0.014 -10000 0 -0.063 9 9
JAM-A/CLDN1 0.062 0.047 -10000 0 -0.066 12 12
SRC 0.01 0.12 -10000 0 -0.4 40 40
ITGB3 0.032 0.003 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin 0.044 0.014 -10000 0 -10000 0 0
FARP2 0.026 0.12 0.37 1 -0.38 34 35
RAC1 0.023 0.015 -10000 0 -10000 0 0
CTNNA1 0.032 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.055 0.031 -10000 0 -0.038 44 44
nectin-1/I-afadin 0.044 0.014 -10000 0 -10000 0 0
nectin-2/I-afadin 0.043 0.015 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.016 0.032 -10000 0 -0.04 89 89
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.056 0.03 -10000 0 -0.036 46 46
CDC42/GTP/IQGAP1/filamentous actin 0.023 0.035 -10000 0 -0.04 118 118
F11R 0.026 0.023 -10000 0 -0.063 31 31
positive regulation of filopodium formation 0.021 0.081 -10000 0 -0.24 40 40
alphaV/beta3 Integrin/Talin 0.024 0.065 0.2 27 -0.17 9 36
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.043 0.015 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.043 0.015 -10000 0 -10000 0 0
PIP5K1C -0.011 0.014 -10000 0 -0.062 32 32
VAV2 0.021 0.14 0.31 2 -0.43 32 34
RAP1/GDP 0.025 0.1 0.32 2 -0.31 38 40
ITGAV 0.03 0.016 -10000 0 -0.063 15 15
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.055 0.031 -10000 0 -0.038 44 44
nectin-3(dimer)/I-afadin/I-afadin 0.044 0.015 -10000 0 -0.05 1 1
Rac1/GTP 0.021 0.092 0.25 1 -0.33 21 22
PTPRM 0.006 0.019 -10000 0 -0.061 35 35
E-cadherin/beta catenin/alpha catenin 0.075 0.052 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.031 0.006 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0 0 -10000 0 -10000 0 0
GNB1/GNG2 0.008 0.048 -10000 0 -0.14 13 13
mol:DAG -0.005 0.039 0.14 4 -0.14 9 13
PLCG1 -0.006 0.04 0.14 4 -0.14 9 13
YES1 -0.014 0.034 -10000 0 -0.12 24 24
FZD3 0.031 0.01 -10000 0 -0.063 3 3
FZD6 0.014 0.037 -10000 0 -0.063 94 94
G protein 0.01 0.06 0.17 34 -0.14 10 44
MAP3K7 -0.022 0.037 0.17 7 -0.14 9 16
mol:Ca2+ -0.005 0.039 0.14 4 -0.14 9 13
mol:IP3 -0.005 0.039 0.14 4 -0.14 9 13
NLK 0.007 0.08 -10000 0 -0.72 6 6
GNB1 0.031 0.008 -10000 0 -10000 0 0
CAMK2A -0.019 0.039 0.19 8 -0.14 9 17
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD 0 0.039 -10000 0 -0.12 23 23
CSNK1A1 0.032 0.004 -10000 0 -10000 0 0
GNAS -0.009 0.03 -10000 0 -0.13 16 16
GO:0007205 -0.009 0.034 0.14 4 -0.13 11 15
WNT6 0.032 0.002 -10000 0 -10000 0 0
WNT4 0.031 0.008 -10000 0 -0.063 2 2
NFAT1/CK1 alpha -0.006 0.053 0.2 7 -0.15 13 20
GNG2 0 0 -10000 0 -10000 0 0
WNT5A 0.003 0.044 -10000 0 -0.063 155 155
WNT11 0.032 0.007 -10000 0 -0.063 2 2
CDC42 -0.022 0.031 0.18 3 -0.14 7 10
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.032 0.023 -10000 0 -0.05 2 2
CRKL 0.049 0.083 0.28 4 -0.43 5 9
mol:PIP3 0.012 0.039 -10000 0 -0.76 1 1
AKT1 0.004 0.037 -10000 0 -0.5 1 1
PTK2B 0.032 0.005 -10000 0 -10000 0 0
RAPGEF1 0.047 0.085 0.3 13 -0.38 5 18
RANBP10 0.032 0.004 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
HGF/MET/SHIP2 0.042 0.033 -10000 0 -0.041 8 8
MAP3K5 0.048 0.08 0.24 6 -0.38 5 11
HGF/MET/CIN85/CBL/ENDOPHILINS 0.04 0.031 -10000 0 -0.035 9 9
AP1 0.012 0.074 0.14 114 -10000 0 114
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.024 0.026 -10000 0 -0.063 40 40
apoptosis -0.023 0.22 -10000 0 -0.72 42 42
STAT3 (dimer) 0.012 0.028 -10000 0 -0.13 8 8
GAB1/CRKL/SHP2/PI3K 0.079 0.081 0.3 2 -0.4 5 7
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.067 0.081 0.27 3 -0.41 5 8
PTPN11 0.032 0.003 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.03 0.009 -10000 0 -10000 0 0
PTEN 0.023 0.016 -10000 0 -0.063 2 2
ELK1 0.11 0.18 0.35 168 -10000 0 168
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.009 0.029 0.16 1 -0.16 10 11
PAK1 -0.001 0.041 -10000 0 -0.48 1 1
HGF/MET/RANBP10 0.042 0.033 -10000 0 -0.04 8 8
HRAS 0.015 0.039 -10000 0 -0.3 4 4
DOCK1 0.036 0.078 0.28 5 -0.41 5 10
GAB1 0.051 0.078 0.22 2 -0.47 4 6
CRK 0.052 0.081 0.26 3 -0.43 5 8
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.02 0.036 -10000 0 -0.35 3 3
JUN 0.032 0.005 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.007 0.016 0.081 8 -0.051 16 24
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
cell morphogenesis 0.044 0.089 0.27 32 -0.3 3 35
GRB2/SHC 0.059 0.062 0.16 104 -0.11 10 114
FOS 0.007 0.04 -10000 0 -0.063 120 120
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility 0.11 0.18 0.35 168 -10000 0 168
HGF/MET/MUC20 0.028 0.022 -10000 0 -0.04 3 3
cell migration 0.058 0.061 0.15 104 -0.11 10 114
GRB2 0.032 0.006 -10000 0 0 15 15
CBL 0.032 0.004 -10000 0 -10000 0 0
MET/RANBP10 0.032 0.023 -10000 0 -0.05 2 2
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.016 0.021 -10000 0 -0.12 6 6
MET/MUC20 0.016 0.012 -10000 0 -0.039 2 2
RAP1B 0.046 0.081 0.29 13 -0.36 5 18
RAP1A 0.042 0.084 0.31 15 -0.38 4 19
HGF/MET/RANBP9 0.042 0.033 -10000 0 -0.048 3 3
RAF1 0.038 0.061 0.24 1 -0.31 3 4
STAT3 0.012 0.027 -10000 0 -0.14 7 7
cell proliferation 0.03 0.061 0.21 16 -0.25 2 18
RPS6KB1 0.01 0.015 -10000 0 -10000 0 0
MAPK3 0.076 0.16 0.44 5 -10000 0 5
MAPK1 0.12 0.21 0.59 46 -10000 0 46
RANBP9 0.032 0.004 -10000 0 -10000 0 0
MAPK8 -0.023 0.14 0.24 5 -0.32 55 60
SRC 0.004 0.017 -10000 0 -0.12 7 7
PI3K 0.058 0.059 0.16 96 -0.11 9 105
MET/Glomulin 0.015 0.025 0.085 1 -0.086 19 20
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 0.035 0.062 0.25 5 -0.32 2 7
MET 0.022 0.016 -10000 0 -0.063 2 2
MAP4K1 0.056 0.085 0.27 4 -0.44 5 9
PTK2 0.031 0.006 -10000 0 -10000 0 0
MAP2K2 0.04 0.073 0.28 12 -0.3 3 15
BAD -0.002 0.037 -10000 0 -0.48 1 1
MAP2K4 0.043 0.077 0.23 13 -0.34 5 18
SHP2/GRB2/SOS1/GAB1 0.028 0.052 -10000 0 -0.36 5 5
INPPL1 0.032 0.004 -10000 0 -10000 0 0
PXN 0.032 0.003 -10000 0 -10000 0 0
SH3KBP1 0 0 -10000 0 -10000 0 0
HGS -0.004 0.014 0.071 8 -0.11 2 10
PLCgamma1/PKC 0.022 0.006 -10000 0 -10000 0 0
HGF 0.022 0.016 -10000 0 -0.063 1 1
RASA1 0.032 0.006 -10000 0 -10000 0 0
NCK1 0.03 0.015 -10000 0 -0.063 11 11
PTPRJ 0.032 0.006 -10000 0 -10000 0 0
NCK/PLCgamma1 0.066 0.056 0.16 112 -0.11 10 122
PDPK1 0.011 0.036 -10000 0 -0.53 1 1
HGF/MET/SHIP 0.028 0.022 -10000 0 -0.04 3 3
Arf6 downstream 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
PLAUR 0 0.037 -10000 0 -0.1 59 59
regulation of axonogenesis 0.01 0.059 0.26 26 -10000 0 26
myoblast fusion -0.014 0.038 0.28 4 -10000 0 4
mol:GTP 0.009 0.05 -10000 0 -0.18 29 29
regulation of calcium-dependent cell-cell adhesion -0.024 0.041 0.12 25 -10000 0 25
ARF1/GTP 0.027 0.047 -10000 0 -0.14 27 27
mol:GM1 -0.001 0.034 -10000 0 -0.13 29 29
mol:Choline -0.021 0.026 0.033 1 -0.13 25 26
lamellipodium assembly -0.006 0.064 -10000 0 -0.38 13 13
MAPK3 0.006 0.039 -10000 0 -0.11 32 32
ARF6/GTP/NME1/Tiam1 0.024 0.041 -10000 0 -0.12 25 25
ARF1 0.032 0.006 -10000 0 -10000 0 0
ARF6/GDP 0.014 0.038 -10000 0 -0.28 4 4
ARF1/GDP 0.008 0.067 -10000 0 -0.24 27 27
ARF6 0.033 0.024 -10000 0 -0.039 44 44
RAB11A 0.032 0.005 -10000 0 -10000 0 0
TIAM1 0.029 0.011 -10000 0 -0.031 8 8
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.008 0.034 -10000 0 -0.11 21 21
actin filament bundle formation -0.016 0.071 0.25 28 -10000 0 28
KALRN -0.001 0.047 -10000 0 -0.26 14 14
RAB11FIP3/RAB11A 0.047 0.009 -10000 0 -10000 0 0
RhoA/GDP 0.016 0.071 -10000 0 -0.25 28 28
NME1 -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.013 0.055 -10000 0 -0.24 15 15
substrate adhesion-dependent cell spreading 0.009 0.05 -10000 0 -0.18 29 29
cortical actin cytoskeleton organization -0.006 0.064 -10000 0 -0.38 13 13
RAC1 0.023 0.015 -10000 0 -10000 0 0
liver development 0.009 0.05 -10000 0 -0.18 29 29
ARF6/GTP 0.009 0.05 -10000 0 -0.18 29 29
RhoA/GTP 0.027 0.047 -10000 0 -0.14 28 28
mol:GDP -0.009 0.062 -10000 0 -0.26 27 27
ARF6/GTP/RAB11FIP3/RAB11A 0.043 0.052 -10000 0 -0.13 29 29
RHOA 0.032 0.006 -10000 0 -10000 0 0
PLD1 0.005 0.039 -10000 0 -0.14 28 28
RAB11FIP3 0.032 0.004 -10000 0 -10000 0 0
tube morphogenesis -0.006 0.064 -10000 0 -0.38 13 13
ruffle organization -0.01 0.059 -10000 0 -0.26 26 26
regulation of epithelial cell migration 0.009 0.05 -10000 0 -0.18 29 29
PLD2 0.006 0.038 -10000 0 -0.14 26 26
PIP5K1A -0.011 0.06 -10000 0 -0.26 26 26
mol:Phosphatidic acid -0.021 0.026 0.033 1 -0.13 25 26
Rac1/GTP -0.006 0.065 -10000 0 -0.38 13 13
mTOR 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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.032 0.005 -10000 0 -10000 0 0
mol:PIP3 -0.008 0.014 -10000 0 -10000 0 0
FRAP1 0.04 0.06 0.22 5 -0.44 2 7
AKT1 0.033 0.08 0.16 123 -0.13 9 132
INSR 0.032 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.041 0.011 -10000 0 -10000 0 0
mol:GTP 0.036 0.088 0.18 125 -0.14 1 126
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.009 0.023 -10000 0 -0.17 2 2
TSC2 0.032 0.004 -10000 0 -10000 0 0
RHEB/GDP -0.007 0.042 0.11 41 -0.13 5 46
TSC1 0.031 0.008 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.03 0.009 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.043 0.042 0.14 5 -0.18 2 7
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.024 0.015 -10000 0 -10000 0 0
RPS6KB1 0.05 0.07 0.2 32 -0.25 2 34
MAP3K5 -0.012 0.056 0.16 2 -0.2 40 42
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
apoptosis -0.012 0.056 0.16 2 -0.2 40 42
mol:LY294002 0 0 0.001 1 -0.001 1 2
EIF4B 0.044 0.069 0.19 39 -0.23 2 41
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.036 0.045 0.23 4 -0.23 1 5
eIF4E/eIF4G1/eIF4A1 0.025 0.032 -10000 0 -0.24 3 3
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.046 0.026 0.15 1 -10000 0 1
mTOR/RHEB/GTP/Raptor/GBL 0.009 0.046 0.12 57 -10000 0 57
FKBP1A 0.03 0.009 -10000 0 -0.063 1 1
RHEB/GTP 0.034 0.051 0.15 52 -0.13 5 57
mol:Amino Acids 0 0 0.001 1 -0.001 1 2
FKBP12/Rapamycin 0.023 0.007 -10000 0 -0.001 37 37
PDPK1 -0.013 0.021 0.16 5 -10000 0 5
EIF4E 0.031 0.009 -10000 0 -0.063 4 4
ASK1/PP5C 0.013 0.16 -10000 0 -0.52 42 42
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.016 0.031 -10000 0 -0.24 4 4
TSC1/TSC2 0.041 0.096 0.19 126 -0.15 1 127
tumor necrosis factor receptor activity 0 0 0.001 1 -0.001 1 2
RPS6 0.028 0.011 -10000 0 0 66 66
PPP5C 0.031 0.007 -10000 0 -10000 0 0
EIF4G1 0.031 0.006 -10000 0 -10000 0 0
IRS1 0.01 0.007 -10000 0 -10000 0 0
INS 0.031 0.006 -10000 0 -10000 0 0
PTEN 0.023 0.016 -10000 0 -0.062 2 2
PDK2 -0.013 0.021 0.16 5 -10000 0 5
EIF4EBP1 -0.033 0.094 -10000 0 -0.97 3 3
PIK3CA 0.029 0.018 -10000 0 -0.063 17 17
PPP2R5D 0.033 0.058 0.22 6 -0.4 2 8
peptide biosynthetic process -0.022 0.016 0.18 3 -10000 0 3
RHEB 0.022 0.015 -10000 0 -10000 0 0
EIF4A1 0.03 0.014 -10000 0 -0.063 10 10
mol:Rapamycin 0 0.001 0.002 108 -0.003 1 109
EEF2 -0.022 0.016 0.18 3 -10000 0 3
eIF4E/4E-BP1 -0.023 0.094 -10000 0 -0.91 3 3
ceramide signaling 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
MAP4K4 -0.003 0.051 -10000 0 -0.28 8 8
BAG4 0.032 0.004 -10000 0 -10000 0 0
BAD -0.008 0.025 0.14 3 -0.12 8 11
NFKBIA 0.03 0.009 -10000 0 -0.063 1 1
BIRC3 0.026 0.023 -10000 0 -0.063 30 30
BAX -0.005 0.037 0.18 12 -0.12 8 20
EnzymeConsortium:3.1.4.12 0 0.016 0.062 4 -0.064 10 14
IKBKB -0.008 0.053 0.2 3 -0.27 8 11
MAP2K2 -0.012 0.045 0.16 24 -0.14 6 30
MAP2K1 -0.016 0.034 0.16 10 -0.14 6 16
SMPD1 -0.002 0.025 0.11 2 -0.1 18 20
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0 0.056 0.29 1 -0.28 10 11
MAP2K4 -0.012 0.027 0.16 5 -0.13 6 11
protein ubiquitination -0.01 0.059 0.5 1 -0.28 8 9
EnzymeConsortium:2.7.1.37 -0.016 0.042 0.16 12 -0.15 6 18
response to UV 0 0 0.002 13 -0.002 2 15
RAF1 -0.012 0.033 0.17 8 -0.13 7 15
CRADD 0.032 0.004 -10000 0 -10000 0 0
mol:ceramide -0.002 0.025 0.1 3 -0.1 13 16
I-kappa-B-alpha/RELA/p50/ubiquitin 0.041 0.012 -10000 0 -0.04 1 1
MADD 0.031 0.006 -10000 0 -10000 0 0
MAP3K1 -0.008 0.027 0.15 4 -0.12 8 12
TRADD 0.032 0.004 -10000 0 -10000 0 0
RELA/p50 0.032 0.004 -10000 0 -10000 0 0
MAPK3 -0.009 0.04 0.16 11 -0.14 5 16
MAPK1 -0.016 0.047 0.16 10 -0.16 13 23
p50/RELA/I-kappa-B-alpha 0.045 0.013 -10000 0 -0.05 1 1
FADD -0.002 0.049 0.24 1 -0.27 6 7
KSR1 -0.008 0.026 0.12 4 -0.12 10 14
MAPK8 -0.012 0.031 0.18 5 -0.13 7 12
TRAF2 0.031 0.006 -10000 0 -10000 0 0
response to radiation 0 0 0.002 1 -10000 0 1
CHUK -0.009 0.049 -10000 0 -0.27 8 8
TNF R/SODD 0.014 0.045 -10000 0 -0.05 164 164
TNF 0.032 0.006 -10000 0 -0.063 2 2
CYCS 0.011 0.045 0.14 19 -0.12 5 24
IKBKG -0.008 0.053 0.19 3 -0.27 8 11
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.005 0.054 0.15 1 -0.27 9 10
RELA 0.032 0.004 -10000 0 -10000 0 0
RIPK1 0.03 0.013 -10000 0 -0.063 9 9
AIFM1 -0.009 0.031 0.12 13 -0.12 6 19
TNF/TNF R/SODD 0.025 0.054 -10000 0 -0.048 172 172
TNFRSF1A 0 0.044 -10000 0 -0.063 165 165
response to heat 0 0 0.002 1 -10000 0 1
CASP8 0.027 0.073 -10000 0 -0.61 6 6
NSMAF -0.002 0.054 0.19 4 -0.27 8 12
response to hydrogen peroxide 0 0 0.002 13 -0.002 2 15
BCL2 0.032 0.006 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.022 0.071 -10000 0 -0.14 22 22
Ran/GTP/Exportin 1/HDAC1 -0.026 0.007 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.002 0.062 0.16 1 -0.18 24 25
SUMO1 0.033 0.001 -10000 0 -10000 0 0
ZFPM1 0 0 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.003 0.028 -10000 0 -0.095 39 39
FKBP3 0.03 0.008 -10000 0 -10000 0 0
Histones 0.032 0.044 -10000 0 -0.2 7 7
YY1/LSF 0.012 0.061 -10000 0 -0.15 59 59
SMG5 0.032 0.005 -10000 0 -10000 0 0
RAN 0.032 0.004 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 -0.001 0.036 -10000 0 -0.1 32 32
I kappa B alpha/HDAC1 0 0.059 -10000 0 -0.18 34 34
SAP18 0.031 0.008 -10000 0 -10000 0 0
RELA 0 0.05 0.11 13 -0.15 37 50
HDAC1/Smad7 0.035 0.04 -10000 0 -0.047 47 47
RANGAP1 0.03 0.008 -10000 0 0 37 37
HDAC3/TR2 0.016 0.044 -10000 0 -0.21 8 8
NuRD/MBD3 Complex 0.002 0.048 -10000 0 -0.16 28 28
NF kappa B1 p50/RelA 0.016 0.059 0.17 1 -0.15 44 45
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.032 0.005 -10000 0 -10000 0 0
GATA1 0.032 0.002 -10000 0 -10000 0 0
Mad/Max 0.045 0.012 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.002 0.048 -10000 0 -0.15 28 28
RBBP7 0.032 0.002 -10000 0 -10000 0 0
NPC 0.019 0.001 -10000 0 -10000 0 0
RBBP4 0.015 0.036 -10000 0 -0.063 89 89
MAX 0.03 0.008 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.032 0.005 -10000 0 -10000 0 0
NFKBIA 0.006 0.019 -10000 0 -0.055 5 5
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex -0.006 0.052 -10000 0 -0.13 59 59
SIN3 complex 0.053 0.028 -10000 0 -0.039 5 5
SMURF1 0.023 0.015 -10000 0 -10000 0 0
CHD3 0.032 0.005 -10000 0 -10000 0 0
SAP30 0.032 0.006 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.032 0.004 -10000 0 -10000 0 0
YY1/HDAC3 -0.003 0.051 -10000 0 -0.18 24 24
YY1/HDAC2 0.012 0.06 -10000 0 -0.15 54 54
YY1/HDAC1 0.007 0.061 -10000 0 -0.15 55 55
NuRD/MBD2 Complex (MeCP1) 0.002 0.052 -10000 0 -0.16 29 29
PPARG 0.004 0.038 0.12 10 -0.15 14 24
HDAC8/hEST1B 0.042 0.01 -10000 0 -10000 0 0
UBE2I 0.032 0.003 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.032 0.005 -10000 0 -10000 0 0
TNFRSF1A 0 0.044 -10000 0 -0.063 165 165
HDAC3/SMRT (N-CoR2) 0.016 0.044 -10000 0 -0.21 8 8
MBD3L2 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.035 0.039 -10000 0 -0.047 47 47
CREBBP 0.032 0.004 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.003 0.047 -10000 0 -0.15 23 23
HDAC1 0.02 0.031 -10000 0 -0.063 61 61
HDAC3 0.007 0.02 -10000 0 -0.059 7 7
HDAC2 0.03 0.012 -10000 0 -0.063 4 4
YY1 0.01 0.004 -10000 0 -10000 0 0
HDAC8 0 0 -10000 0 -10000 0 0
SMAD7 0.031 0.007 -10000 0 -0.063 1 1
NCOR2 0.032 0.004 -10000 0 0 6 6
MXD1 0.033 0.001 -10000 0 -10000 0 0
STAT3 0.017 0.009 -10000 0 -0.035 8 8
NFKB1 0.031 0.009 -10000 0 -0.063 4 4
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.032 0.002 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.021 0.066 -10000 0 -0.14 58 58
YY1/SAP30/HDAC1 0.02 0.067 -10000 0 -0.14 59 59
EP300 0.03 0.008 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.017 0.009 -10000 0 -0.035 8 8
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.019 -10000 0 -0.055 5 5
histone deacetylation 0.002 0.051 -10000 0 -0.16 29 29
STAT3 (dimer non-phopshorylated)/HDAC3 0.012 0.041 -10000 0 -0.11 42 42
nuclear export -0.041 0.01 -10000 0 -10000 0 0
PRKACA 0.032 0.006 -10000 0 -10000 0 0
GATAD2B 0 0 -10000 0 -10000 0 0
GATAD2A 0.023 0.027 -10000 0 -0.063 43 43
GATA2/HDAC3 0.016 0.044 -10000 0 -0.21 8 8
GATA1/HDAC1 0.035 0.032 -10000 0 -0.05 61 61
GATA1/HDAC3 0.016 0.045 -10000 0 -0.21 8 8
CHD4 0.031 0.007 -10000 0 0 24 24
TNF-alpha/TNFR1A 0.014 0.045 -10000 0 -0.05 166 166
SIN3/HDAC complex/Mad/Max -0.006 0.067 -10000 0 -0.18 47 47
NuRD Complex 0.004 0.051 -10000 0 -0.19 17 17
positive regulation of chromatin silencing 0.031 0.042 -10000 0 -0.2 7 7
SIN3B 0.031 0.006 -10000 0 -10000 0 0
MTA2 0.032 0.004 -10000 0 -10000 0 0
SIN3A 0 0 -10000 0 -10000 0 0
XPO1 0.033 0.001 -10000 0 0 1 1
SUMO1/HDAC1 0.03 0.043 -10000 0 -0.1 38 38
HDAC complex 0.04 0.063 -10000 0 -0.066 28 28
GATA1/Fog1 0.024 0.002 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.04 0.046 -10000 0 -0.044 112 112
TNF 0.032 0.006 -10000 0 -0.063 2 2
negative regulation of cell growth -0.006 0.067 -10000 0 -0.18 47 47
NuRD/MBD2/PRMT5 Complex 0.002 0.052 -10000 0 -0.16 29 29
Ran/GTP/Exportin 1 0.037 0.039 -10000 0 -0.096 39 39
NF kappa B/RelA/I kappa B alpha -0.005 0.049 -10000 0 -0.17 26 26
SIN3/HDAC complex/NCoR1 0.006 0.044 -10000 0 -0.17 21 21
TFCP2 0.032 0.005 -10000 0 -10000 0 0
NR2C1 0.032 0.004 -10000 0 -10000 0 0
MBD3 0.031 0.006 -10000 0 -10000 0 0
MBD2 0.032 0.006 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.042 0.06 0.23 35 -10000 0 35
PCK1 0.037 0.031 -10000 0 -10000 0 0
HNF4A 0.035 0.043 0.24 8 -10000 0 8
KCNJ11 0.055 0.061 0.26 28 -10000 0 28
AKT1 0.068 0.042 -10000 0 -0.25 1 1
response to starvation 0.002 0.004 -10000 0 -0.075 1 1
DLK1 0.049 0.072 0.26 32 -10000 0 32
NKX2-1 0.04 0.048 0.21 4 -10000 0 4
ACADM 0.042 0.06 0.23 35 -10000 0 35
TAT 0.043 0.043 -10000 0 -10000 0 0
CEBPB 0.029 0.017 -10000 0 -0.061 11 11
CEBPA 0.03 0.018 -10000 0 -0.061 15 15
TTR 0.053 0.092 0.35 34 -0.44 1 35
PKLR 0.045 0.065 0.23 43 -10000 0 43
APOA1 0.06 0.071 0.41 10 -10000 0 10
CPT1C 0.044 0.056 0.24 29 -10000 0 29
ALAS1 0.047 0.058 -10000 0 -0.62 1 1
TFRC 0.055 0.051 0.21 25 -10000 0 25
FOXF1 0.023 0.024 -10000 0 -0.063 35 35
NF1 0.034 0.01 -10000 0 -0.17 1 1
HNF1A (dimer) 0.039 0.005 -10000 0 -10000 0 0
CPT1A 0.042 0.06 0.23 36 -10000 0 36
HMGCS1 0.043 0.061 0.23 37 -10000 0 37
NR3C1 0.035 0.014 -10000 0 -10000 0 0
CPT1B 0.035 0.053 0.23 24 -10000 0 24
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.034 0.005 -10000 0 -10000 0 0
GCK 0.077 0.098 0.25 119 -10000 0 119
CREB1 0.035 0.009 -10000 0 -10000 0 0
IGFBP1 0.05 0.047 -10000 0 -10000 0 0
PDX1 0.045 0.052 -10000 0 -0.31 1 1
UCP2 0.037 0.066 0.23 35 -10000 0 35
ALDOB 0.061 0.071 0.26 44 -10000 0 44
AFP 0.01 0.009 -10000 0 -0.082 4 4
BDH1 0.046 0.067 0.24 45 -10000 0 45
HADH 0.059 0.068 0.26 39 -10000 0 39
F2 0.058 0.074 0.41 10 -10000 0 10
HNF1A 0.039 0.005 -10000 0 -10000 0 0
G6PC 0.021 0.03 -10000 0 -10000 0 0
SLC2A2 0.061 0.051 0.2 35 -10000 0 35
INS 0.028 0.01 0.18 1 -10000 0 1
FOXA1 0.006 0.006 -10000 0 -0.087 1 1
FOXA3 0.015 0.011 -10000 0 -0.1 3 3
FOXA2 0.09 0.071 0.29 28 -10000 0 28
ABCC8 0.058 0.066 0.25 37 -10000 0 37
ALB 0.01 0.009 -10000 0 -0.082 4 4
Class I PI3K signaling events mediated by Akt

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
BCL2L1 -0.021 0.006 0 41 -10000 0 41
BAD/BCL-XL/YWHAZ 0.043 0.017 -10000 0 -10000 0 0
CDKN1B -0.006 0.084 0.2 7 -0.33 29 36
CDKN1A -0.012 0.085 -10000 0 -0.33 32 32
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.028 0.019 -10000 0 -0.063 21 21
FOXO3 -0.005 0.08 0.2 4 -0.33 26 30
AKT1 -0.002 0.088 -10000 0 -0.34 31 31
BAD 0.032 0.004 -10000 0 -10000 0 0
AKT3 0.012 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 -0.009 0.084 -10000 0 -0.33 31 31
AKT1/ASK1 0.014 0.09 -10000 0 -0.32 33 33
BAD/YWHAZ 0.06 0.02 -10000 0 -10000 0 0
RICTOR 0 0 -10000 0 -10000 0 0
RAF1 0.032 0.004 -10000 0 -10000 0 0
JNK cascade -0.013 0.087 0.31 33 -10000 0 33
TSC1 -0.01 0.085 0.19 1 -0.33 32 33
YWHAZ 0.032 0.006 -10000 0 -10000 0 0
AKT1/RAF1 0.016 0.093 -10000 0 -0.33 33 33
EP300 0.03 0.008 -10000 0 -10000 0 0
mol:GDP -0.002 0.087 -10000 0 -0.34 31 31
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 -0.011 0.085 -10000 0 -0.33 33 33
YWHAQ 0.032 0.004 -10000 0 -10000 0 0
TBC1D4 -0.006 0.002 -10000 0 -10000 0 0
MAP3K5 0.03 0.009 -10000 0 -10000 0 0
MAPKAP1 0.031 0.007 -10000 0 -10000 0 0
negative regulation of cell cycle 0.013 0.054 0.18 24 -0.16 2 26
YWHAH 0.015 0.016 -10000 0 -10000 0 0
AKT1S1 -0.003 0.084 -10000 0 -0.32 31 31
CASP9 -0.008 0.085 0.2 3 -0.33 31 34
YWHAB 0.03 0.009 -10000 0 0 39 39
p27Kip1/KPNA1 0.013 0.093 0.23 10 -0.31 33 43
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.055 0.029 -10000 0 -0.044 2 2
YWHAE 0.032 0.005 -10000 0 -10000 0 0
SRC 0.031 0.008 -10000 0 -10000 0 0
AKT2/p21CIP1 -0.01 0.079 0.23 1 -0.3 33 34
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.005 0.029 -10000 0 -0.13 12 12
CHUK -0.004 0.062 -10000 0 -0.34 16 16
BAD/BCL-XL 0.013 0.09 -10000 0 -0.32 32 32
mTORC2 0.02 0.006 -10000 0 -0.016 8 8
AKT2 0.012 0.003 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family -0.026 0.08 0.17 1 -0.26 36 37
PDPK1 0.032 0.004 -10000 0 -10000 0 0
MDM2 0.006 0.099 0.2 41 -0.33 30 71
MAPKKK cascade -0.016 0.092 0.32 33 -10000 0 33
MDM2/Cbp/p300 0.038 0.11 0.22 44 -0.3 33 77
TSC1/TSC2 -0.01 0.094 0.25 12 -0.32 33 45
proteasomal ubiquitin-dependent protein catabolic process 0.036 0.1 0.21 44 -0.29 33 77
glucose import -0.01 0.019 0.2 4 -10000 0 4
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.007 0.053 -10000 0 -0.19 33 33
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.011 0.017 0.2 3 -10000 0 3
GSK3A -0.007 0.081 0.2 4 -0.33 28 32
FOXO1 -0.007 0.077 -10000 0 -0.33 26 26
GSK3B -0.008 0.086 0.2 4 -0.33 32 36
SFN 0.026 0.023 -10000 0 -0.063 31 31
G1/S transition of mitotic cell cycle -0.011 0.093 0.22 16 -0.33 33 49
p27Kip1/14-3-3 family 0.006 0.033 -10000 0 -0.22 7 7
PRKACA 0.032 0.006 -10000 0 -10000 0 0
KPNA1 0.032 0.005 -10000 0 -10000 0 0
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
RHEB 0.022 0.015 -10000 0 -10000 0 0
CREBBP 0.032 0.004 -10000 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.024 0.027 -10000 0 -0.063 45 45
positive regulation of NF-kappaB transcription factor activity 0.038 0.028 -10000 0 -0.049 44 44
MAP2K4 0.008 0.037 0.2 2 -0.16 11 13
IKBKB 0.032 0.003 -10000 0 -10000 0 0
TNFRSF10B 0.031 0.01 -10000 0 -0.063 5 5
TNFRSF10A 0 0 -10000 0 -10000 0 0
SMPD1 0.007 0.013 -10000 0 -0.058 7 7
IKBKG 0.032 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.032 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR2 0.037 0.03 -10000 0 -0.05 48 48
TRAIL/TRAILR3 0.038 0.029 -10000 0 -0.05 44 44
TRAIL/TRAILR1 0.018 0.018 -10000 0 -0.039 45 45
TRAIL/TRAILR4 0.038 0.029 -10000 0 -0.05 44 44
TRAIL/TRAILR1/DAP3/GTP 0.033 0.023 -10000 0 -0.034 46 46
IKK complex -0.034 0.11 -10000 0 -0.23 123 123
RIPK1 0.03 0.013 -10000 0 -0.063 9 9
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.024 0.004 -10000 0 -10000 0 0
MAPK3 -0.024 0.009 -10000 0 -0.049 45 45
MAP3K1 0.014 0.035 -10000 0 -0.14 20 20
TRAILR4 (trimer) 0.032 0.005 -10000 0 -10000 0 0
TRADD 0.032 0.004 -10000 0 -10000 0 0
TRAILR1 (trimer) 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.012 0.029 -10000 0 -0.11 20 20
CFLAR 0.032 0.01 -10000 0 -0.063 5 5
MAPK1 -0.022 0.01 -10000 0 -0.049 40 40
TRAIL/TRAILR1/FADD/TRADD/RIP 0.059 0.043 -10000 0 -0.064 3 3
mol:ceramide 0.007 0.013 -10000 0 -0.058 7 7
FADD 0.032 0.006 -10000 0 -0.063 1 1
MAPK8 -0.001 0.031 0.19 1 -0.16 8 9
TRAF2 0.031 0.006 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.032 0.005 -10000 0 -10000 0 0
CHUK 0.024 0.015 -10000 0 -0.063 1 1
TRAIL/TRAILR1/FADD 0.035 0.025 -10000 0 -0.04 45 45
DAP3 0.032 0.005 -10000 0 -10000 0 0
CASP10 -0.013 0.026 0.14 10 -0.092 7 17
JNK cascade 0.038 0.028 -10000 0 -0.049 44 44
TRAIL (trimer) 0.023 0.027 -10000 0 -0.063 45 45
TNFRSF10C 0.032 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP/FADD 0.046 0.031 -10000 0 -0.04 44 44
TRAIL/TRAILR2/FADD 0.051 0.038 -10000 0 -0.049 49 49
cell death 0.007 0.012 -10000 0 -0.058 7 7
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.015 0.033 -10000 0 -0.11 22 22
TRAILR2 (trimer) 0.031 0.01 -10000 0 -0.063 5 5
CASP8 0.016 0.021 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.072 0.055 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.01 0.047 0.2 10 -0.2 5 15
UGCG 0.008 0.072 -10000 0 -0.58 7 7
AKT1/mTOR/p70S6K/Hsp90/TERT -0.003 0.092 0.24 2 -0.31 25 27
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.008 0.071 -10000 0 -0.57 7 7
mol:DAG -0.18 0.35 -10000 0 -0.8 122 122
CaM/Ca2+/Calcineurin A alpha-beta B1 0.003 0.077 0.26 2 -0.24 14 16
FRAP1 -0.007 0.079 0.28 2 -0.25 18 20
FOXO3 -0.013 0.079 0.25 3 -0.26 20 23
AKT1 -0.01 0.08 0.26 1 -0.27 19 20
GAB2 0.031 0.006 -10000 0 -10000 0 0
SMPD1 -0.001 0.1 -10000 0 -0.59 15 15
SGMS1 -0.13 0.26 -10000 0 -0.6 122 122
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 -0.016 0.007 -10000 0 -0.04 16 16
CALM1 0.029 0.01 -10000 0 -10000 0 0
cell proliferation -0.063 0.16 -10000 0 -0.35 108 108
EIF3A 0.024 0.015 -10000 0 -10000 0 0
PI3K 0.04 0.023 -10000 0 -0.049 16 16
RPS6KB1 0.02 0.037 -10000 0 -0.74 1 1
mol:sphingomyelin -0.18 0.35 -10000 0 -0.8 122 122
natural killer cell activation 0 0.001 -10000 0 -0.004 5 5
JAK3 0.032 0.006 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
JAK1 0.032 0.006 -10000 0 -10000 0 0
NFKB1 0.031 0.009 -10000 0 -0.063 4 4
MYC -0.015 0.085 0.25 3 -0.28 13 16
MYB 0.015 0.026 -10000 0 -0.34 1 1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.009 0.071 0.14 3 -0.21 27 30
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.042 0.047 -10000 0 -0.71 1 1
mol:PI-3-4-5-P3 -0.009 0.07 0.14 3 -0.2 27 30
Rac1/GDP 0.005 0.019 -10000 0 -0.045 4 4
T cell proliferation -0.009 0.066 -10000 0 -0.19 27 27
SHC1 0.024 0.026 -10000 0 -0.064 40 40
RAC1 0.023 0.015 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.001 0.002 -10000 0 -10000 0 0
PRKCZ -0.01 0.067 0.13 3 -0.2 27 30
NF kappa B1 p50/RelA 0.008 0.091 0.28 2 -0.24 17 19
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.014 0.044 -10000 0 -0.2 11 11
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
RELA 0.032 0.004 -10000 0 -10000 0 0
IL2RA 0.023 0.017 -10000 0 -0.063 6 6
IL2RB 0.03 0.012 -10000 0 -0.064 4 4
TERT 0.032 0.006 -10000 0 0 16 16
E2F1 0.024 0.024 -10000 0 -0.38 1 1
SOS1 0 0.001 -10000 0 -0.003 4 4
RPS6 0.028 0.011 -10000 0 0 66 66
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 0.032 0.003 -10000 0 -10000 0 0
IL2RG 0.031 0.013 -10000 0 -0.064 9 9
actin cytoskeleton organization -0.009 0.066 -10000 0 -0.19 27 27
GRB2 0.031 0.006 -10000 0 -10000 0 0
IL2 0.032 0.004 -10000 0 -10000 0 0
PIK3CA 0.029 0.018 -10000 0 -0.063 17 17
Rac1/GTP 0.032 0.032 -10000 0 -10000 0 0
LCK 0.031 0.01 -10000 0 -0.063 4 4
BCL2 -0.005 0.074 0.26 7 -0.24 10 17
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.02 0.051 0.21 10 -0.23 7 17
FYN 0.002 0.057 0.22 6 -0.25 9 15
LAT/GRAP2/SLP76 0.023 0.051 0.2 3 -0.25 7 10
IKBKB 0.032 0.003 -10000 0 -10000 0 0
AKT1 0.001 0.06 0.23 6 -0.22 12 18
B2M 0.032 0.006 -10000 0 -10000 0 0
IKBKG -0.01 0.023 0.084 12 -0.087 5 17
MAP3K8 0.018 0.026 -10000 0 -0.063 37 37
mol:Ca2+ -0.011 0.009 -10000 0 -0.039 2 2
integrin-mediated signaling pathway 0.021 0.003 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.003 0.066 0.21 10 -0.25 13 23
TRPV6 0.38 0.59 1.3 155 -10000 0 155
CD28 0.033 0.002 -10000 0 -10000 0 0
SHC1 0.007 0.052 0.24 9 -0.27 6 15
receptor internalization 0.014 0.05 -10000 0 -0.36 6 6
PRF1 -0.13 0.27 -10000 0 -0.6 126 126
KRAS 0.031 0.008 -10000 0 -10000 0 0
GRB2 0.032 0.006 -10000 0 0 15 15
COT/AKT1 0.007 0.05 0.17 5 -0.19 13 18
LAT 0.007 0.049 0.19 5 -0.28 7 12
EntrezGene:6955 0 0.001 -10000 0 -10000 0 0
CD3D 0.029 0.019 -10000 0 -0.064 20 20
CD3E 0.032 0.006 -10000 0 -0.064 1 1
CD3G 0.032 0.006 -10000 0 -0.068 1 1
RASGRP2 0.004 0.016 -10000 0 -0.14 5 5
RASGRP1 -0.045 0.086 0.22 12 -0.23 25 37
HLA-A 0.032 0.006 -10000 0 -0.063 1 1
RASSF5 0 0 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.022 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.003 0.042 0.14 18 -0.092 12 30
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.006 0.027 -10000 0 -0.11 13 13
PRKCA -0.012 0.039 0.18 4 -0.16 5 9
GRAP2 0.03 0.008 -10000 0 -10000 0 0
mol:IP3 0.005 0.043 -10000 0 -0.2 8 8
EntrezGene:6957 0 0.001 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.01 0.036 -10000 0 -0.2 8 8
ORAI1 -0.33 0.5 -10000 0 -1.1 155 155
CSK 0.008 0.048 0.19 5 -0.27 7 12
B7 family/CD28 0.05 0.058 0.22 4 -0.27 5 9
CHUK 0.024 0.015 -10000 0 -0.063 1 1
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.012 0.048 0.13 1 -0.28 8 9
PTPN6 0.004 0.047 0.17 9 -0.25 8 17
VAV1 0.011 0.056 0.19 16 -0.28 7 23
Monovalent TCR/CD3 0.014 0.029 -10000 0 -0.2 7 7
CBL 0.032 0.004 -10000 0 -10000 0 0
LCK 0.005 0.052 0.19 7 -0.25 7 14
PAG1 0.01 0.046 0.21 2 -0.27 7 9
RAP1A 0.032 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.011 0.048 0.13 3 -0.27 8 11
CD80 0.032 0.007 -10000 0 -0.065 1 1
CD86 0.027 0.021 -10000 0 -0.063 24 24
PDK1/CARD11/BCL10/MALT1 0.002 0.033 -10000 0 -0.12 13 13
HRAS 0.031 0.007 -10000 0 -10000 0 0
GO:0035030 -0.001 0.041 0.16 5 -0.2 8 13
CD8A 0 0.001 -10000 0 -10000 0 0
CD8B 0.032 0.007 -10000 0 -0.064 2 2
PTPRC 0.009 0.041 -10000 0 -0.063 121 121
PDK1/PKC theta -0.003 0.069 0.25 11 -0.26 8 19
CSK/PAG1 0.006 0.044 0.16 2 -0.26 7 9
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I 0.046 0.011 -10000 0 -0.05 1 1
GRAP2/SLP76 0.034 0.057 0.2 4 -0.27 7 11
STIM1 -0.065 0.12 1.1 2 -10000 0 2
RAS family/GTP -0.007 0.049 0.16 10 -0.15 21 31
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.014 0.052 -10000 0 -0.38 6 6
mol:DAG -0.021 0.026 -10000 0 -0.18 9 9
RAP1A/GDP 0 0.021 0.063 15 -0.045 11 26
PLCG1 0.03 0.009 -10000 0 -10000 0 0
CD247 0.032 0.008 -10000 0 -0.068 2 2
cytotoxic T cell degranulation -0.12 0.26 -10000 0 -0.58 126 126
RAP1A/GTP 0.003 0.007 -10000 0 -0.056 4 4
mol:PI-3-4-5-P3 0.004 0.06 0.2 10 -0.22 12 22
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.012 0.053 -10000 0 -0.25 7 7
NRAS 0.009 0.041 -10000 0 -0.063 125 125
ZAP70 0.032 0.003 -10000 0 -10000 0 0
GRB2/SOS1 0.023 0.004 -10000 0 0 15 15
LAT/GRAP2/SLP76/VAV1 0.011 0.052 0.19 8 -0.25 7 15
MALT1 0.028 0.02 -10000 0 -0.063 21 21
TRAF6 0.032 0.005 -10000 0 -10000 0 0
CD8 heterodimer 0.023 0.008 -10000 0 -0.022 13 13
CARD11 0 0 -10000 0 -10000 0 0
PRKCB -0.016 0.02 -10000 0 -0.13 9 9
PRKCE -0.011 0.039 0.18 4 -0.16 5 9
PRKCQ 0 0.068 0.23 13 -0.25 11 24
LCP2 0.026 0.022 -10000 0 -0.063 29 29
BCL10 0.031 0.009 -10000 0 -0.063 3 3
regulation of survival gene product expression 0.001 0.056 0.18 10 -0.2 11 21
IKK complex -0.006 0.036 0.2 6 -0.085 5 11
RAS family/GDP -0.006 0.01 -10000 0 -0.031 11 11
MAP3K14 -0.003 0.038 0.13 6 -0.15 12 18
PDPK1 -0.001 0.056 0.19 11 -0.2 11 22
TCR/CD3/MHC I/CD8/Fyn 0.014 0.055 0.25 1 -0.36 6 7
Regulation of Telomerase

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
Telomerase catalytic core complex 0.021 0.087 0.3 2 -0.33 14 16
RAD9A 0.032 0.006 -10000 0 -0.063 1 1
AP1 0.021 0.041 -10000 0 -0.05 117 117
IFNAR2 0.032 0.005 -10000 0 -10000 0 0
AKT1 0.016 0.016 -10000 0 -0.054 20 20
ER alpha/Oestrogen 0.023 0.006 -10000 0 -10000 0 0
NFX1/SIN3/HDAC complex -0.004 0.051 -10000 0 -0.14 46 46
EGF 0.032 0.007 -10000 0 -0.062 2 2
SMG5 0.032 0.005 -10000 0 -10000 0 0
SMG6 0.032 0.005 -10000 0 -10000 0 0
SP3/HDAC2 0.032 0.035 -10000 0 -0.052 65 65
TERT/c-Abl 0.033 0.088 0.24 1 -0.31 14 15
SAP18 0.031 0.008 -10000 0 -10000 0 0
MRN complex 0.062 0.019 -10000 0 -0.044 1 1
WT1 0.031 0.011 -10000 0 -0.064 5 5
WRN 0.031 0.009 -10000 0 -0.063 4 4
SP1 0.032 0.005 -10000 0 -10000 0 0
SP3 0.019 0.034 -10000 0 -0.063 74 74
TERF2IP 0.029 0.01 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.046 0.097 -10000 0 -0.31 14 14
Mad/Max 0.045 0.013 -10000 0 -10000 0 0
TERT 0.021 0.088 0.3 2 -0.33 14 16
CCND1 0.011 0.089 0.32 1 -0.36 11 12
MAX 0.03 0.008 -10000 0 -10000 0 0
RBBP7 0.032 0.002 -10000 0 -10000 0 0
RBBP4 0.015 0.036 -10000 0 -0.063 89 89
TERF2 -0.02 0.02 0.047 30 -10000 0 30
PTGES3 0.031 0.007 -10000 0 0 24 24
SIN3A 0 0 -10000 0 -10000 0 0
Telomerase/911 0.043 0.062 -10000 0 -0.34 6 6
CDKN1B -0.025 0.011 -10000 0 -0.057 1 1
RAD1 0.032 0.007 -10000 0 -0.063 2 2
XRCC5 0.032 0.002 -10000 0 -10000 0 0
XRCC6 0.03 0.009 -10000 0 -10000 0 0
SAP30 0.032 0.006 -10000 0 -10000 0 0
TRF2/PARP2 0.038 0.018 0.088 4 -10000 0 4
UBE3A 0.032 0.005 -10000 0 -10000 0 0
JUN 0.032 0.005 -10000 0 -10000 0 0
E6 0 0.001 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.024 0.004 -10000 0 -10000 0 0
FOS 0.008 0.04 -10000 0 -0.063 120 120
IFN-gamma/IRF1 0.037 0.035 -10000 0 -0.05 62 62
PARP2 0.031 0.008 -10000 0 -10000 0 0
BLM 0.01 0.04 -10000 0 -0.063 119 119
Telomerase 0.006 0.065 -10000 0 -0.24 31 31
IRF1 0.021 0.033 -10000 0 -0.063 66 66
ESR1 0.031 0.008 -10000 0 -10000 0 0
KU/TER 0.045 0.013 -10000 0 -10000 0 0
ATM/TRF2 0.036 0.029 -10000 0 -0.06 30 30
ubiquitin-dependent protein catabolic process -0.003 0.053 -10000 0 -0.16 34 34
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex -0.002 0.053 -10000 0 -0.16 34 34
HDAC1 0.02 0.031 -10000 0 -0.063 61 61
HDAC2 0.03 0.012 -10000 0 -0.065 4 4
ATM 0.012 0.017 0.091 6 -0.053 25 31
SMAD3 -0.023 0.008 -10000 0 -0.049 26 26
ABL1 0.031 0.008 -10000 0 -0.063 1 1
MXD1 0.033 0.002 -10000 0 -10000 0 0
MRE11A 0.032 0.005 -10000 0 -10000 0 0
HUS1 0.023 0.015 -10000 0 -10000 0 0
RPS6KB1 0.032 0.006 -10000 0 -0.063 1 1
TERT/NF kappa B1/14-3-3 0.042 0.11 0.29 1 -0.35 20 21
NR2F2 0.031 0.009 -10000 0 -0.06 4 4
MAPK3 -0.022 0.004 -10000 0 -10000 0 0
MAPK1 -0.02 0.007 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.026 0.022 -10000 0 -0.034 48 48
NFKB1 0.031 0.009 -10000 0 -0.063 4 4
HNRNPC 0.031 0.008 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.012 0.017 0.091 6 -0.053 25 31
NBN 0.032 0.004 -10000 0 -10000 0 0
EGFR 0.012 0.018 -10000 0 -0.063 6 6
mol:Oestrogen 0 0.001 -10000 0 -10000 0 0
EGF/EGFR 0.018 0.025 -10000 0 -0.05 8 8
MYC 0.009 0.04 -10000 0 -0.063 119 119
IL2 0.032 0.005 -10000 0 -10000 0 0
KU 0.045 0.013 -10000 0 -10000 0 0
RAD50 0.032 0.004 -10000 0 -10000 0 0
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
TGFB1 0.026 0.022 -10000 0 -0.034 48 48
TRF2/BLM 0.018 0.041 0.088 3 -0.053 114 117
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.042 0.097 0.26 1 -0.32 14 15
SP1/HDAC2 0.043 0.017 -10000 0 -0.053 4 4
PINX1 0 0 -10000 0 -10000 0 0
Telomerase/EST1A 0.046 0.098 -10000 0 -0.32 13 13
Smad3/Myc 0.007 0.035 -10000 0 -0.05 137 137
911 complex 0.045 0.032 -10000 0 -0.046 4 4
IFNG 0.032 0.008 -10000 0 -10000 0 0
Telomerase/PinX1 0.035 0.09 -10000 0 -0.31 13 13
Telomerase/AKT1/mTOR/p70S6K 0.009 0.094 0.18 2 -0.29 37 39
SIN3B 0.031 0.006 -10000 0 -10000 0 0
YWHAE 0.032 0.005 -10000 0 -10000 0 0
Telomerase/EST1B 0.047 0.096 -10000 0 -0.33 11 11
response to DNA damage stimulus 0.003 0.014 -10000 0 -0.1 6 6
MRN complex/TRF2/Rap1 0.075 0.039 -10000 0 -10000 0 0
TRF2/WRN 0.04 0.018 -10000 0 -0.052 4 4
Telomerase/hnRNP C1/C2 0.045 0.098 -10000 0 -0.31 14 14
E2F1 0.03 0.008 -10000 0 -10000 0 0
ZNFX1 0 0 -10000 0 -10000 0 0
PIF1 0 0 -10000 0 -10000 0 0
NCL 0.032 0.002 -10000 0 -10000 0 0
DKC1 0.031 0.011 -10000 0 -0.063 7 7
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.032 0.008 -9999 0 -0.062 2 2
SVIL 0.023 0.02 -9999 0 -0.062 14 14
ZNF318 0.031 0.003 -9999 0 -10000 0 0
JMJD2C 0.003 0 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 0.044 0.016 -9999 0 -0.039 9 9
CARM1 0.031 0.006 -9999 0 -10000 0 0
PRDX1 0.032 0.005 -9999 0 -10000 0 0
PELP1 0.032 0.005 -9999 0 -10000 0 0
CTNNB1 0.032 0.005 -9999 0 -10000 0 0
AKT1 0.03 0.008 -9999 0 -10000 0 0
PTK2B 0.032 0.005 -9999 0 -10000 0 0
MED1 0.032 0.003 -9999 0 -10000 0 0
MAK 0.03 0.012 -9999 0 -0.064 7 7
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.017 0.025 -9999 0 -0.062 30 30
GSN 0.029 0.017 -9999 0 -0.062 15 15
NCOA2 0.032 0.004 -9999 0 -10000 0 0
NCOA6 0.031 0.008 -9999 0 -10000 0 0
DNA-PK 0.053 0.034 -9999 0 -0.051 22 22
NCOA4 0.025 0.014 -9999 0 -10000 0 0
PIAS3 0.032 0.004 -9999 0 -10000 0 0
cell proliferation 0.006 0.053 -9999 0 -0.42 7 7
XRCC5 0.032 0.002 -9999 0 -10000 0 0
UBE3A 0.033 0.005 -9999 0 -10000 0 0
T-DHT/AR/SNURF 0.024 0.01 -9999 0 -0.026 14 14
FHL2 0.012 0.028 -9999 0 -0.22 4 4
RANBP9 0.033 0.004 -9999 0 -10000 0 0
JMJD1A 0.006 0.002 -9999 0 -0.023 3 3
CDK6 0.022 0.015 -9999 0 -10000 0 0
TGFB1I1 -0.047 0.035 -9999 0 -0.062 424 424
T-DHT/AR/CyclinD1 0.031 0.034 -9999 0 -0.039 92 92
XRCC6 0.03 0.009 -9999 0 -10000 0 0
T-DHT/AR 0.039 0.03 -9999 0 -0.047 9 9
CTDSP1 0.032 0.007 -9999 0 -0.063 3 3
CTDSP2 0.027 0.011 -9999 0 -10000 0 0
BRCA1 0.032 0.01 -9999 0 -0.062 5 5
TCF4 0.031 0.007 -9999 0 -10000 0 0
CDKN2A 0.003 0.026 -9999 0 -0.063 52 52
SRF 0.033 0.01 -9999 0 -0.045 3 3
NKX3-1 0.006 0.016 -9999 0 -0.054 1 1
KLK3 0.02 0.033 -9999 0 -10000 0 0
TMF1 0.031 0.01 -9999 0 -0.063 4 4
HNRNPA1 0.031 0.005 -9999 0 0 14 14
AOF2 0.001 0 -9999 0 -10000 0 0
APPL1 -0.021 0.007 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 0.043 0.019 -9999 0 -0.041 17 17
AR 0.031 0.014 -9999 0 -0.051 12 12
UBA3 0 0 -9999 0 -10000 0 0
PATZ1 0.03 0.008 -9999 0 -10000 0 0
PAWR 0.032 0.006 -9999 0 -10000 0 0
PRKDC 0.028 0.019 -9999 0 -0.063 21 21
PA2G4 0.031 0.007 -9999 0 -10000 0 0
UBE2I 0.032 0.003 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.042 0.014 -9999 0 -0.035 8 8
RPS6KA3 0.033 0.005 -9999 0 -0.062 1 1
T-DHT/AR/ARA70 0.034 0.025 -9999 0 -0.042 10 10
LATS2 0 0 -9999 0 -10000 0 0
T-DHT/AR/PRX1 0.041 0.015 -9999 0 -0.035 8 8
Cyclin D3/CDK11 p58 0.024 0.002 -9999 0 -10000 0 0
VAV3 0.026 0.025 -9999 0 -0.062 36 36
KLK2 0.004 0.019 -9999 0 -0.28 1 1
CASP8 0.031 0.013 -9999 0 -0.063 9 9
T-DHT/AR/TIF2/CARM1 0.059 0.024 -9999 0 -10000 0 0
TMPRSS2 0.004 0.026 -9999 0 -0.17 6 6
CCND1 0.015 0.036 -9999 0 -0.063 90 90
PIAS1 0.033 0.004 -9999 0 -10000 0 0
mol:T-DHT 0.001 0.001 -9999 0 -0.009 6 6
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.033 0.006 -9999 0 -10000 0 0
T-DHT/AR/CDK6 0.03 0.025 -9999 0 -0.039 5 5
CMTM2 0 0 -9999 0 -10000 0 0
SNURF 0 0 -9999 0 -10000 0 0
ZMIZ1 0.024 0.016 -9999 0 -0.029 3 3
CCND3 0.032 0.003 -9999 0 -10000 0 0
TGIF1 -0.033 0.043 -9999 0 -0.063 343 343
FKBP4 0.032 0.007 -9999 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.007 0.053 -10000 0 -0.3 14 14
KLHL20 0.028 0.068 0.18 30 -0.19 13 43
CYFIP2 0.018 0.016 -10000 0 -10000 0 0
Rac1/GDP 0.005 0.039 0.17 9 -0.16 10 19
ENAH 0.005 0.055 -10000 0 -0.3 15 15
AP1M1 0 0 -10000 0 -10000 0 0
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.032 0.004 -10000 0 -10000 0 0
CTNNB1 0.032 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.028 0.033 0.11 20 -0.12 7 27
ABI1/Sra1/Nap1 -0.01 0.022 -10000 0 -0.12 14 14
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.072 0.035 -10000 0 -0.069 1 1
RAPGEF1 -0.003 0.059 0.16 30 -0.28 11 41
CTNND1 0.03 0.014 -10000 0 -0.063 10 10
regulation of calcium-dependent cell-cell adhesion 0.02 0.056 -10000 0 -0.3 14 14
CRK 0.005 0.061 0.17 25 -0.29 13 38
E-cadherin/gamma catenin/alpha catenin 0.058 0.029 -10000 0 -0.054 20 20
alphaE/beta7 Integrin 0.046 0.012 -10000 0 -0.05 2 2
IQGAP1 0.01 0.04 -10000 0 -0.063 120 120
NCKAP1 0.032 0.002 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.036 0.018 -10000 0 -0.024 40 40
DLG1 0.006 0.055 -10000 0 -0.29 15 15
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.03 0.018 -10000 0 -0.093 12 12
MLLT4 0.03 0.008 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.036 0.018 -10000 0 -0.024 30 30
PI3K -0.036 0.022 -10000 0 -0.12 12 12
ARF6 0.031 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.043 0.021 -10000 0 -0.057 19 19
TIAM1 0.031 0.008 -10000 0 -10000 0 0
E-cadherin(dimer)/Ca2+ 0.066 0.034 -10000 0 -10000 0 0
AKT1 -0.016 0.036 0.14 9 -0.1 1 10
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
CDH1 0.03 0.013 -10000 0 -0.063 8 8
RhoA/GDP 0.012 0.061 0.18 26 -0.17 16 42
actin cytoskeleton organization 0.023 0.054 0.14 32 -0.14 12 44
CDC42/GDP 0.011 0.057 0.18 23 -0.17 16 39
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.011 0.026 -10000 0 -0.11 19 19
ITGB7 0.032 0.008 -10000 0 -0.063 2 2
RAC1 0.023 0.015 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.072 0.036 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0.052 0.022 -10000 0 -0.04 9 9
mol:GDP -0.002 0.063 0.18 26 -0.18 16 42
CDC42/GTP/IQGAP1 0.023 0.035 -10000 0 -0.04 118 118
JUP 0.029 0.017 -10000 0 -0.063 16 16
p120 catenin/RhoA/GDP 0.025 0.064 0.19 27 -0.18 15 42
RAC1/GTP/IQGAP1 0.016 0.032 -10000 0 -0.04 89 89
PIP5K1C/AP1M1 0.022 0.006 -10000 0 -10000 0 0
RHOA 0.032 0.006 -10000 0 -10000 0 0
CDC42 0.031 0.006 -10000 0 -10000 0 0
CTNNA1 0.032 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.015 0.041 0.11 29 -0.095 14 43
NME1 0 0 -10000 0 0 5 5
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.006 0.055 -10000 0 -0.3 15 15
regulation of cell-cell adhesion -0.03 0.017 0.043 1 -0.1 13 14
WASF2 -0.006 0.012 -10000 0 -0.067 14 14
Rap1/GTP -0.022 0.045 0.14 29 -0.14 4 33
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.082 0.043 -10000 0 -0.089 1 1
CCND1 0.017 0.047 0.13 28 -0.12 14 42
VAV2 0.013 0.11 -10000 0 -0.58 13 13
RAP1/GDP -0.011 0.052 0.16 31 -0.17 3 34
adherens junction assembly 0.006 0.053 -10000 0 -0.29 15 15
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.025 0.014 -10000 0 -10000 0 0
PIP5K1C 0.03 0.008 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.054 0.038 0.19 2 -0.091 1 3
E-cadherin/beta catenin 0.005 0.022 -10000 0 -0.15 6 6
mol:GTP 0 0 -10000 0 0 6 6
SRC 0.005 0.053 -10000 0 -0.3 14 14
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
Rac1/GTP -0.007 0.055 -10000 0 -0.28 14 14
E-cadherin/beta catenin/alpha catenin 0.059 0.025 -10000 0 -0.049 9 9
ITGAE 0.032 0.005 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.02 0.057 -10000 0 -0.3 14 14
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.02 0.031 -9999 0 -0.063 61 61
Ran/GTP/Exportin 1/HDAC4 -0.027 0.011 -9999 0 -0.062 39 39
MDM2/SUMO1 0.034 0.039 -9999 0 -0.098 36 36
HDAC4 0.032 0.003 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.029 0.012 -9999 0 -0.066 38 38
SUMO1 0.033 0.001 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.01 0.003 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 -0.005 0.026 -9999 0 -0.096 39 39
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.032 0.004 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.032 0.002 -9999 0 -10000 0 0
SUMO1/HDAC4 0.038 0.039 -9999 0 -0.097 39 39
SUMO1/HDAC1 0.03 0.043 -9999 0 -0.1 38 38
RANGAP1 0.03 0.008 -9999 0 0 37 37
MDM2/SUMO1/SUMO1 0.07 0.034 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.003 0.028 -9999 0 -0.095 39 39
Ran/GTP 0.021 0.033 -9999 0 -0.092 39 39
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.029 0.011 -9999 0 -0.063 1 1
UBE2I 0.032 0.003 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.015 0.032 -9999 0 -0.096 39 39
NPC 0.019 0.001 -9999 0 -10000 0 0
PIAS2 0.031 0.006 -9999 0 0 18 18
PIAS1 0.032 0.004 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
BCR signaling 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
JUN 0.011 0.08 0.26 10 -0.26 11 21
IKBKB 0.017 0.059 0.27 6 -0.24 8 14
AKT1 0.013 0.077 0.22 36 -10000 0 36
IKBKG 0.012 0.05 0.25 5 -0.21 8 13
CALM1 -0.009 0.047 0.2 2 -0.18 13 15
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
MAP3K1 0.034 0.094 0.29 17 -0.39 7 24
MAP3K7 0.031 0.008 -10000 0 -0.063 1 1
mol:Ca2+ -0.006 0.053 0.21 1 -0.18 17 18
DOK1 0.032 0.002 -10000 0 -10000 0 0
AP-1 -0.006 0.062 0.23 6 -0.19 10 16
LYN 0.021 0.031 -10000 0 -0.063 60 60
BLNK 0.013 0.031 -10000 0 -0.063 59 59
SHC1 0.024 0.026 -10000 0 -0.063 40 40
BCR complex 0.045 0.014 -10000 0 -0.063 2 2
CD22 -0.007 0.03 -10000 0 -0.24 2 2
CAMK2G 0 0.032 0.23 3 -0.2 5 8
CSNK2A1 0.03 0.008 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.048 0.02 -10000 0 -0.096 25 25
GO:0007205 -0.007 0.053 0.21 1 -0.18 17 18
SYK 0.025 0.024 -10000 0 -0.063 34 34
ELK1 -0.013 0.053 0.18 2 -0.19 11 13
NFATC1 -0.015 0.064 0.27 8 -0.24 13 21
B-cell antigen/BCR complex 0.045 0.014 -10000 0 -0.063 2 2
PAG1/CSK 0.024 0.003 -10000 0 -10000 0 0
NFKBIB 0.021 0.033 0.16 4 -0.13 14 18
HRAS -0.013 0.053 0.18 6 -0.18 16 22
NFKBIA 0.021 0.033 0.15 5 -0.12 14 19
NF-kappa-B/RelA/I kappa B beta 0.024 0.03 0.15 5 -0.096 14 19
RasGAP/Csk 0.051 0.066 -10000 0 -0.09 2 2
mol:GDP -0.005 0.054 0.19 2 -0.18 16 18
PTEN 0.023 0.016 -10000 0 -0.063 2 2
CD79B 0.032 0.005 -10000 0 -0.062 1 1
NF-kappa-B/RelA/I kappa B alpha 0.024 0.029 0.15 5 -0.093 14 19
GRB2 0.032 0.006 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.005 0.081 0.37 4 -0.32 3 7
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
mol:IP3 -0.006 0.053 0.22 1 -0.18 17 18
CSK 0.032 0.005 -10000 0 -10000 0 0
FOS -0.02 0.051 0.17 3 -0.2 9 12
CHUK -0.048 0.12 0.25 5 -0.25 122 127
IBTK 0.031 0.007 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.015 0.071 -10000 0 -0.18 12 12
PTPN6 -0.018 0.031 0.14 4 -0.23 2 6
RELA 0.032 0.004 -10000 0 -10000 0 0
BCL2A1 0.012 0.021 0.1 5 -0.069 14 19
VAV2 -0.011 0.055 0.16 3 -0.28 13 16
ubiquitin-dependent protein catabolic process 0.022 0.033 0.16 4 -0.12 14 18
BTK 0.016 0.011 -10000 0 -10000 0 0
CD19 -0.008 0.032 -10000 0 -0.24 2 2
MAP4K1 0.031 0.008 -10000 0 -0.063 1 1
CD72 0.03 0.009 -10000 0 -10000 0 0
PAG1 0 0 -10000 0 -10000 0 0
MAPK14 0.027 0.086 0.27 17 -0.34 7 24
SH3BP5 0.029 0.01 -10000 0 -10000 0 0
PIK3AP1 -0.007 0.051 -10000 0 -0.18 18 18
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.002 0.06 -10000 0 -0.27 16 16
RAF1 -0.017 0.052 0.18 7 -0.19 11 18
RasGAP/p62DOK/SHIP 0.042 0.057 -10000 0 -0.079 2 2
CD79A 0.031 0.009 -10000 0 -0.063 2 2
re-entry into mitotic cell cycle -0.006 0.061 0.23 6 -0.19 10 16
RASA1 0.032 0.006 -10000 0 -10000 0 0
MAPK3 -0.023 0.052 0.19 8 -0.19 7 15
MAPK1 -0.022 0.05 0.19 8 -0.2 5 13
CD72/SHP1 0.007 0.064 0.22 26 -0.23 2 28
NFKB1 0.031 0.009 -10000 0 -0.063 4 4
MAPK8 0.026 0.087 0.28 16 -0.34 7 23
actin cytoskeleton organization 0.031 0.088 0.2 49 -0.26 5 54
NF-kappa-B/RelA 0.047 0.057 0.27 5 -0.19 14 19
Calcineurin 0.009 0.065 0.2 1 -0.19 10 11
PI3K -0.025 0.049 -10000 0 -0.18 5 5
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.001 0.043 -10000 0 -0.22 5 5
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 0.036 0.079 -10000 0 -0.57 6 6
DAPP1 0.019 0.074 -10000 0 -0.64 5 5
cytokine secretion -0.014 0.062 0.26 8 -0.22 13 21
mol:DAG -0.006 0.053 0.22 1 -0.18 17 18
PLCG2 0.03 0.014 -10000 0 -0.063 10 10
MAP2K1 -0.021 0.05 0.18 7 -0.19 10 17
B-cell antigen/BCR complex/FcgammaRIIB 0.034 0.049 -10000 0 -0.049 121 121
mol:PI-3-4-5-P3 -0.02 0.05 0.19 12 -10000 0 12
ETS1 0.021 0.066 0.19 16 -0.23 2 18
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.027 0.073 -10000 0 -0.09 18 18
B-cell antigen/BCR complex/LYN 0.006 0.036 -10000 0 -0.24 2 2
MALT1 0.028 0.02 -10000 0 -0.063 21 21
TRAF6 0.032 0.005 -10000 0 -10000 0 0
RAC1 0.028 0.085 0.19 46 -0.27 5 51
B-cell antigen/BCR complex/LYN/SYK 0.043 0.062 0.22 16 -0.3 1 17
CARD11 -0.007 0.052 0.19 2 -0.18 17 19
FCGR2B 0.01 0.04 -10000 0 -0.063 120 120
PPP3CA 0.026 0.013 -10000 0 -10000 0 0
BCL10 0.031 0.009 -10000 0 -0.063 3 3
IKK complex 0.003 0.039 0.16 9 -0.12 10 19
PTPRC 0.009 0.04 -10000 0 -0.063 121 121
PDPK1 -0.015 0.051 0.2 16 -10000 0 16
PPP3CB 0.024 0.014 -10000 0 -10000 0 0
PPP3CC 0.032 0.005 -10000 0 -10000 0 0
POU2F2 0.016 0.021 0.12 6 -0.067 11 17
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.033 0.04 0.13 31 -10000 0 31
GNAI2 0.032 0.006 -10000 0 -10000 0 0
S1P/S1P5/G12 0.015 0.01 -10000 0 0 151 151
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.003 0.009 -10000 0 -10000 0 0
RhoA/GTP -0.033 0.041 -10000 0 -0.13 31 31
negative regulation of cAMP metabolic process 0.002 0.012 0.082 6 -0.11 2 8
GNAZ 0.027 0.013 -10000 0 -10000 0 0
GNAI3 0.021 0.03 -10000 0 -0.063 58 58
GNA12 0.023 0.015 -10000 0 -10000 0 0
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.002 0.012 0.083 6 -0.11 2 8
RhoA/GDP 0.023 0.004 -10000 0 -10000 0 0
RHOA 0.032 0.006 -10000 0 -10000 0 0
GNAI1 0.019 0.016 -10000 0 -0.063 1 1
Class I PI3K 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
ARF5/GTP -0.02 0.031 0.16 7 -10000 0 7
DAPP1 0.005 0.061 0.15 22 -0.24 10 32
Src family/SYK family/BLNK-LAT/BTK-ITK -0.004 0.07 0.32 1 -0.26 16 17
mol:DAG -0.005 0.054 0.23 11 -0.14 3 14
HRAS 0.035 0.01 0.08 3 -10000 0 3
RAP1A 0.035 0.008 -10000 0 -10000 0 0
ARF5/GDP 0.016 0.056 0.14 3 -0.23 17 20
PLCG2 0.03 0.014 -10000 0 -0.063 10 10
PLCG1 0.03 0.009 -10000 0 -10000 0 0
ARF5 0.023 0.015 -10000 0 -10000 0 0
mol:GTP -0.021 0.041 0.18 13 -10000 0 13
ARF1/GTP -0.014 0.031 0.15 11 -0.11 1 12
RHOA 0.032 0.006 -10000 0 -10000 0 0
YES1 0.017 0.034 -10000 0 -0.063 75 75
RAP1A/GTP -0.022 0.032 0.15 10 -10000 0 10
ADAP1 -0.021 0.036 0.16 12 -10000 0 12
ARAP3 -0.021 0.04 0.18 13 -10000 0 13
INPPL1 0.032 0.004 -10000 0 -10000 0 0
PREX1 0 0 -10000 0 -10000 0 0
ARHGEF6 0.03 0.012 -10000 0 -0.063 7 7
ARHGEF7 0.031 0.007 -10000 0 -10000 0 0
ARF1 0.032 0.006 -10000 0 -10000 0 0
NRAS 0.012 0.042 -10000 0 -0.059 124 124
FYN 0.029 0.011 -10000 0 -0.063 1 1
ARF6 0.031 0.008 -10000 0 -10000 0 0
FGR 0.029 0.017 -10000 0 -0.063 15 15
mol:Ca2+ -0.004 0.037 0.13 25 -10000 0 25
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.031 0.008 -10000 0 -10000 0 0
ZAP70 0.032 0.002 -10000 0 -10000 0 0
mol:IP3 -0.008 0.042 0.14 22 -10000 0 22
LYN 0.021 0.031 -10000 0 -0.063 60 60
ARF1/GDP 0.028 0.066 0.16 6 -0.22 23 29
RhoA/GDP 0.037 0.065 0.17 27 -0.12 6 33
PDK1/Src/Hsp90 0.055 0.029 -10000 0 -0.044 2 2
BLNK 0.013 0.031 -10000 0 -0.063 59 59
actin cytoskeleton reorganization 0.027 0.08 0.17 84 -0.18 6 90
SRC 0.031 0.008 -10000 0 -10000 0 0
PLEKHA2 -0.017 0.003 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
PTEN 0.023 0.019 -10000 0 -0.039 15 15
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
ARF6/GTP -0.023 0.042 0.19 12 -10000 0 12
RhoA/GTP -0.023 0.043 0.19 13 -10000 0 13
Src family/SYK family/BLNK-LAT -0.019 0.068 -10000 0 -0.2 37 37
BLK 0.032 0.005 -10000 0 -10000 0 0
PDPK1 0.032 0.004 -10000 0 -10000 0 0
CYTH1 -0.021 0.036 0.16 12 -10000 0 12
HCK 0.014 0.036 -10000 0 -0.044 120 120
CYTH3 -0.021 0.036 0.16 12 -10000 0 12
CYTH2 -0.021 0.036 0.16 12 -10000 0 12
KRAS 0.034 0.011 0.079 1 -10000 0 1
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.005 0.028 0.3 1 -0.17 7 8
SGK1 0.001 0.03 -10000 0 -0.17 11 11
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.012 0.066 0.16 10 -0.22 24 34
SOS1 0 0 -10000 0 -10000 0 0
SYK 0.025 0.024 -10000 0 -0.063 34 34
ARF6/GDP -0.018 0.043 0.2 11 -0.13 1 12
mol:PI-3-4-5-P3 -0.023 0.031 0.14 11 -10000 0 11
ARAP3/RAP1A/GTP -0.022 0.033 0.15 10 -10000 0 10
VAV1 0.032 0.007 -10000 0 -0.063 1 1
mol:PI-3-4-P2 -0.011 0.001 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.057 0.081 0.2 95 -10000 0 95
PLEKHA1 -0.011 0.009 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.058 0.17 4 -0.23 18 22
LAT 0.032 0.005 -10000 0 -0.063 1 1
Rac1/GTP 0.022 0.061 0.16 1 -0.25 17 18
ITK -0.025 0.038 0.16 11 -10000 0 11
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.011 0.059 0.26 8 -0.17 5 13
LCK 0.031 0.01 -10000 0 -0.063 4 4
BTK -0.025 0.041 0.17 13 -10000 0 13
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 0.032 0.007 -9999 0 -0.063 2 2
mol:S1P 0 0 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.018 0.026 -9999 0 -0.15 3 3
GNAO1 0.003 0.009 -9999 0 -10000 0 0
S1P/S1P3/G12/G13 0.03 0.02 -9999 0 -0.023 2 2
AKT1 -0.008 0.069 -9999 0 -0.43 13 13
AKT3 -0.008 0.046 -9999 0 -0.29 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.032 0.007 -9999 0 -0.063 2 2
GNAI2 0.032 0.006 -9999 0 -0.028 1 1
GNAI3 0.022 0.03 -9999 0 -0.062 58 58
GNAI1 0.02 0.017 -9999 0 -0.062 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.001 0 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.002 0.013 -9999 0 -0.12 1 1
MAPK3 0.001 0.013 -9999 0 -0.14 2 2
MAPK1 0.001 0.01 -9999 0 -10000 0 0
JAK2 -0.009 0.036 -9999 0 -0.16 16 16
CXCR4 0 0.009 -9999 0 -0.12 1 1
FLT1 0.031 0.009 -9999 0 -0.028 1 1
RhoA/GDP 0.023 0.004 -9999 0 -10000 0 0
Rac1/GDP 0.017 0.011 -9999 0 -10000 0 0
SRC 0.001 0.013 -9999 0 -0.14 2 2
S1P/S1P3/Gi 0.002 0.013 -9999 0 -0.12 1 1
RAC1 0.023 0.015 -9999 0 -10000 0 0
RhoA/GTP -0.031 0.041 -9999 0 -0.14 24 24
VEGFA -0.019 0.047 -9999 0 -0.062 275 275
S1P/S1P2/Gi 0.002 0.013 -9999 0 -0.11 2 2
VEGFR1 homodimer/VEGFA homodimer -0.003 0.048 -9999 0 -0.049 254 254
RHOA 0.032 0.006 -9999 0 -10000 0 0
S1P/S1P3/Gq 0.017 0.009 -9999 0 -0.1 1 1
GNAQ 0.031 0.006 -9999 0 -10000 0 0
GNAZ 0.027 0.013 -9999 0 -10000 0 0
G12/G13 0.034 0.022 -9999 0 -10000 0 0
GNA14 0.031 0.009 -9999 0 -0.063 2 2
GNA15 0.03 0.013 -9999 0 -0.063 7 7
GNA12 0.023 0.015 -9999 0 -10000 0 0
GNA13 0.032 0.007 -9999 0 -0.063 2 2
GNA11 0.031 0.006 -9999 0 -10000 0 0
Rac1/GTP -0.027 0.037 -9999 0 -0.13 17 17
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.026 0.07 0.22 31 -0.32 5 36
PDGFB-D/PDGFRB/SLAP 0.04 0.026 -10000 0 -0.051 34 34
PDGFB-D/PDGFRB/APS/CBL 0.043 0.009 -10000 0 -0.04 2 2
AKT1 -0.019 0.078 0.29 13 -10000 0 13
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.035 0.075 0.24 32 -0.36 5 37
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
FGR 0.009 0.063 0.19 15 -0.37 7 22
mol:Ca2+ 0.024 0.071 0.22 29 -0.39 5 34
MYC 0.045 0.12 0.3 42 -0.31 4 46
SHC1 0.024 0.026 -10000 0 -0.063 40 40
HRAS/GDP -0.017 0.053 0.17 36 -10000 0 36
LRP1/PDGFRB/PDGFB 0.054 0.031 -10000 0 -0.043 33 33
GRB10 0.021 0.018 -10000 0 -0.063 6 6
PTPN11 0.032 0.003 -10000 0 -10000 0 0
GO:0007205 0.024 0.072 0.22 29 -0.4 5 34
PTEN 0.023 0.016 -10000 0 -0.063 2 2
GRB2 0.032 0.006 -10000 0 0 15 15
GRB7 0.032 0.005 -10000 0 -0.063 1 1
PDGFB-D/PDGFRB/SHP2 0.047 0.01 -10000 0 -0.05 2 2
PDGFB-D/PDGFRB/GRB10 0.031 0.025 -10000 0 -0.05 8 8
cell cycle arrest 0.04 0.026 -10000 0 -0.051 34 34
HRAS 0.031 0.007 -10000 0 -10000 0 0
HIF1A -0.023 0.071 0.27 13 -10000 0 13
GAB1 0.019 0.077 0.23 25 -0.34 8 33
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.015 0.083 0.24 37 -0.28 8 45
PDGFB-D/PDGFRB 0.055 0.026 -10000 0 -0.047 11 11
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.047 0.011 -10000 0 -0.05 2 2
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.01 0.053 0.2 10 -0.26 5 15
positive regulation of MAPKKK cascade 0.047 0.01 -10000 0 -0.05 2 2
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
mol:IP3 0.024 0.072 0.22 29 -0.4 5 34
E5 -0.001 0.001 -10000 0 -10000 0 0
CSK 0.031 0.01 -10000 0 -0.032 10 10
PDGFB-D/PDGFRB/GRB7 0.047 0.011 -10000 0 -0.05 3 3
SHB 0.03 0.009 -10000 0 -10000 0 0
BLK 0.009 0.058 0.34 1 -0.36 7 8
PTPN2 0.032 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.047 0.01 -10000 0 -0.05 2 2
BCAR1 0 0 -10000 0 -10000 0 0
VAV2 0.016 0.084 0.25 25 -0.34 8 33
CBL 0.032 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.046 0.011 -10000 0 -0.05 2 2
LCK 0.013 0.057 0.2 14 -0.34 5 19
PDGFRB 0.032 0.008 -10000 0 -0.052 3 3
ACP1 0.032 0.005 -10000 0 -10000 0 0
HCK 0 0.035 -10000 0 -10000 0 0
ABL1 0.02 0.073 0.22 31 -0.27 8 39
PDGFB-D/PDGFRB/CBL 0.023 0.08 0.26 13 -0.38 8 21
PTPN1 0.03 0.009 -10000 0 -10000 0 0
SNX15 0.032 0.004 -10000 0 -10000 0 0
STAT3 0.03 0.014 -10000 0 -0.063 10 10
STAT1 0.029 0.018 -10000 0 -0.063 18 18
cell proliferation 0.045 0.11 0.29 44 -0.29 4 48
SLA 0.026 0.024 -10000 0 -0.063 33 33
actin cytoskeleton reorganization -0.016 0.067 0.2 41 -10000 0 41
SRC 0.01 0.044 0.18 1 -0.73 1 2
PI3K -0.043 0.021 -10000 0 -0.093 2 2
PDGFB-D/PDGFRB/GRB7/SHC 0.054 0.035 -10000 0 -0.048 46 46
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.035 0.076 0.24 31 -0.37 5 36
LYN 0.004 0.041 -10000 0 -0.35 1 1
LRP1 0.029 0.016 -10000 0 -0.063 13 13
SOS1 0 0 -10000 0 -10000 0 0
STAT5B 0.032 0.004 -10000 0 -10000 0 0
STAT5A 0.032 0.005 -10000 0 -0.063 1 1
NCK1-2/p130 Cas 0.066 0.038 -10000 0 -0.068 1 1
SPHK1 0.029 0.019 -10000 0 -0.063 19 19
EDG1 0 0.003 -10000 0 -10000 0 0
mol:DAG 0.024 0.072 0.22 29 -0.4 5 34
PLCG1 0.024 0.073 0.22 29 -0.41 5 34
NHERF/PDGFRB 0.063 0.018 -10000 0 -0.043 9 9
YES1 -0.006 0.095 0.24 1 -0.57 11 12
cell migration 0.062 0.018 -10000 0 -0.043 9 9
SHC/Grb2/SOS1 0.058 0.045 -10000 0 -0.073 2 2
SLC9A3R2 0.032 0.004 -10000 0 -10000 0 0
SLC9A3R1 0.032 0.007 -10000 0 -0.063 2 2
NHERF1-2/PDGFRB/PTEN 0.046 0.056 -10000 0 -0.057 2 2
FYN -0.019 0.11 -10000 0 -0.36 44 44
DOK1 -0.016 0.053 0.17 38 -10000 0 38
HRAS/GTP 0.023 0.005 -10000 0 -10000 0 0
PDGFB 0.03 0.008 -10000 0 -10000 0 0
RAC1 0.055 0.12 0.25 99 -0.42 4 103
PRKCD -0.015 0.053 0.17 37 -10000 0 37
FER -0.016 0.053 0.17 36 -10000 0 36
MAPKKK cascade -0.011 0.072 0.18 56 -10000 0 56
RASA1 -0.015 0.053 0.17 36 -10000 0 36
NCK1 0.03 0.015 -10000 0 -0.063 11 11
NCK2 0.032 0.004 -10000 0 -10000 0 0
p62DOK/Csk -0.02 0.052 0.17 37 -10000 0 37
PDGFB-D/PDGFRB/SHB 0.044 0.015 -10000 0 -0.05 2 2
chemotaxis 0.02 0.072 0.21 31 -0.27 8 39
STAT1-3-5/STAT1-3-5 0.063 0.043 -10000 0 -0.092 1 1
Bovine Papilomavirus E5/PDGFRB 0.023 0.006 0.052 2 -0.04 2 4
PTPRJ 0.032 0.006 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.03 0.009 -10000 0 -10000 0 0
VLDLR 0.029 0.012 -10000 0 -0.063 3 3
LRPAP1 0.032 0.003 -10000 0 -10000 0 0
NUDC 0.032 0.006 -10000 0 -10000 0 0
RELN/LRP8 0.02 0.031 -10000 0 -0.041 5 5
CaM/Ca2+ 0.021 0.008 -10000 0 -10000 0 0
KATNA1 0.029 0.012 -10000 0 -0.063 5 5
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.012 0.063 0.18 63 -10000 0 63
IQGAP1/CaM 0.021 0.04 -10000 0 -0.05 111 111
DAB1 0.032 0.005 -10000 0 -10000 0 0
IQGAP1 0.01 0.04 -10000 0 -0.063 120 120
PLA2G7 0.031 0.012 -10000 0 -0.063 8 8
CALM1 0.029 0.01 -10000 0 -10000 0 0
DYNLT1 0.017 0.033 -10000 0 -0.063 72 72
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.047 0.009 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.032 0.003 -10000 0 -10000 0 0
CDK5R1 0.026 0.013 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A -0.016 0.005 -10000 0 -10000 0 0
CDK5R2 0.012 0.016 -10000 0 -10000 0 0
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.019 0.032 -10000 0 -0.038 13 13
YWHAE 0.032 0.005 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.025 0.095 0.3 49 -10000 0 49
MAP1B 0.005 0.002 -10000 0 -10000 0 0
RAC1 0.002 0.016 -10000 0 -0.25 1 1
p35/CDK5 0.009 0.044 0.17 5 -10000 0 5
RELN 0.01 0.016 -10000 0 -0.063 2 2
PAFAH/LIS1 0.025 0.015 -10000 0 -0.042 16 16
LIS1/CLIP170 0.026 0.012 -10000 0 -0.035 10 10
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.006 0.039 0.15 3 -10000 0 3
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.001 0.046 0.13 4 -0.21 21 25
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.019 0.074 0.3 29 -10000 0 29
LIS1/IQGAP1 0.009 0.033 -10000 0 -0.047 124 124
RHOA 0 0.031 -10000 0 -0.26 6 6
PAFAH1B1 -0.02 0.007 0 50 -10000 0 50
PAFAH1B3 0.031 0.007 -10000 0 -10000 0 0
PAFAH1B2 0.032 0.004 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.02 0.027 0.11 1 -0.15 5 6
NDEL1/Katanin 60/Dynein heavy chain 0.027 0.095 0.3 45 -10000 0 45
LRP8 0.032 0.005 -10000 0 -10000 0 0
NDEL1/Katanin 60 0.022 0.091 0.29 44 -10000 0 44
P39/CDK5 0.003 0.03 0.17 3 -10000 0 3
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.026 0.012 -10000 0 -0.035 9 9
CDK5 0.011 0.043 0.18 10 -10000 0 10
PPP2R5D 0.032 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.023 0.01 -10000 0 -0.029 10 10
CSNK2A1 0.03 0.008 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.019 0.035 0.17 5 -10000 0 5
RELN/VLDLR 0.024 0.04 -10000 0 -10000 0 0
CDC42 -0.001 0.033 -10000 0 -0.26 7 7
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.016 0.027 -10000 0 -0.059 6 6
EPHB2 0.031 0.007 -10000 0 -0.063 1 1
Syndecan-2/TACI 0.027 0.011 -10000 0 -0.052 5 5
LAMA1 0 0 -10000 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 0.024 0.053 -10000 0 -0.071 4 4
HRAS 0.031 0.007 -10000 0 -10000 0 0
Syndecan-2/CASK -0.007 0.005 -10000 0 -0.062 1 1
ITGA5 0.019 0.033 -10000 0 -0.063 68 68
BAX -0.012 0.012 -10000 0 -0.12 3 3
EPB41 0.032 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.025 0.01 -10000 0 -0.049 3 3
LAMA3 0.029 0.017 -10000 0 -0.063 15 15
EZR 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.014 0.029 -10000 0 -0.063 49 49
Syndecan-2/MMP2 -0.003 0.034 -10000 0 -0.066 7 7
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.024 0.035 -10000 0 -0.05 64 64
dendrite morphogenesis 0.027 0.012 -10000 0 -0.052 5 5
Syndecan-2/GM-CSF 0.027 0.011 -10000 0 -0.052 5 5
determination of left/right symmetry -0.009 0.006 -10000 0 -0.077 1 1
Syndecan-2/PKC delta 0.027 0.012 -10000 0 -0.052 5 5
GNB2L1 0.032 0.004 -10000 0 -10000 0 0
MAPK3 -0.018 0.026 0.19 8 -10000 0 8
MAPK1 -0.017 0.027 0.19 8 -10000 0 8
Syndecan-2/RACK1 0.041 0.02 -10000 0 -0.065 1 1
NF1 0.032 0.003 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 -0.009 0.006 -10000 0 -0.077 1 1
ITGA2 0.015 0.036 -10000 0 -0.063 90 90
MAPK8 -0.011 0.009 -10000 0 -0.1 1 1
Syndecan-2/alpha2/beta1 Integrin 0.016 0.039 -10000 0 -0.056 5 5
Syndecan-2/Kininogen 0.027 0.011 -10000 0 -0.054 4 4
ITGB1 0.025 0.014 -10000 0 -10000 0 0
SRC -0.02 0.028 0.17 9 -10000 0 9
Syndecan-2/CASK/Protein 4.1 0.025 0.011 -10000 0 -0.05 3 3
extracellular matrix organization 0.023 0.018 -10000 0 -0.053 6 6
actin cytoskeleton reorganization 0.016 0.027 -10000 0 -0.058 6 6
Syndecan-2/Caveolin-2/Ras 0.023 0.031 -10000 0 -0.065 2 2
Syndecan-2/Laminin alpha3 0.026 0.015 -10000 0 -0.057 5 5
Syndecan-2/RasGAP 0.054 0.027 -10000 0 -0.069 1 1
alpha5/beta1 Integrin 0.025 0.034 -10000 0 -0.05 61 61
PRKCD 0.032 0.006 -10000 0 -10000 0 0
Syndecan-2 dimer 0.027 0.012 -10000 0 -0.052 5 5
GO:0007205 0.001 0.003 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.027 0.023 0.18 3 -10000 0 3
RHOA 0.032 0.006 -10000 0 -10000 0 0
SDCBP 0.032 0.004 -10000 0 -10000 0 0
TNFRSF13B 0.032 0.004 -10000 0 -10000 0 0
RASA1 0.032 0.006 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.024 0.035 -10000 0 -0.05 64 64
Syndecan-2/Synbindin 0.027 0.011 -10000 0 -0.052 5 5
TGFB1 0.026 0.022 -10000 0 -0.063 26 26
CASP3 -0.021 0.027 0.19 7 -10000 0 7
FN1 0.014 0.037 -10000 0 -0.063 96 96
Syndecan-2/IL8 0.013 0.029 -10000 0 -0.053 6 6
SDC2 -0.009 0.006 -10000 0 -0.077 1 1
KNG1 0.032 0.006 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.028 0.011 -10000 0 -0.052 5 5
TRAPPC4 0.032 0.005 -10000 0 -10000 0 0
CSF2 0.032 0.004 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.023 0.018 -10000 0 -0.053 6 6
Syndecan-2/Syntenin/PI-4-5-P2 0.025 0.01 -10000 0 -0.05 3 3
Syndecan-2/Ezrin 0.025 0.011 -10000 0 -0.046 5 5
PRKACA -0.017 0.028 0.19 9 -10000 0 9
angiogenesis 0.013 0.029 -10000 0 -0.053 6 6
MMP2 -0.013 0.047 -10000 0 -0.063 241 241
IL8 0.012 0.039 -10000 0 -0.063 110 110
calcineurin-NFAT signaling pathway 0.027 0.011 -10000 0 -0.052 5 5
Signaling events mediated by HDAC Class III

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
EP300 0.03 0.008 -10000 0 -10000 0 0
HDAC4 0.032 0.003 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.007 0.011 -10000 0 -10000 0 0
CDKN1A 0 0.04 0.065 118 -0.073 45 163
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.03 0.013 -10000 0 -0.063 6 6
FOXO3 0 0.012 0.027 76 -10000 0 76
FOXO1 0.028 0.016 -10000 0 -0.063 11 11
FOXO4 0.011 0.003 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.03 0.009 -10000 0 -10000 0 0
TAT 0.032 0.005 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.011 0.002 -10000 0 -10000 0 0
PPARGC1A 0.032 0.008 -10000 0 -0.063 3 3
FHL2 0.03 0.01 -10000 0 -0.063 3 3
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.037 0.022 -10000 0 -10000 0 0
HIST2H4A -0.007 0.011 -10000 0 -10000 0 0
SIRT1/FOXO3a 0.019 0.019 0.15 4 -10000 0 4
SIRT1 0.026 0.016 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.041 0.044 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.023 0.026 -10000 0 -0.14 8 8
apoptosis -0.037 0.047 0.048 37 -10000 0 37
SIRT1/PGC1A 0.033 0.021 -10000 0 -0.041 3 3
p53/SIRT1 0.032 0.034 0.1 37 -0.055 30 67
SIRT1/FOXO4 0.024 0.022 -10000 0 -0.12 6 6
FOXO1/FHL2/SIRT1 0.035 0.044 -10000 0 -0.036 124 124
HIST1H1E 0.011 0.004 -10000 0 -0.028 1 1
SIRT1/p300 0.037 0.022 -10000 0 -10000 0 0
muscle cell differentiation 0.01 0.016 -10000 0 -10000 0 0
TP53 0.02 0.033 -10000 0 -0.061 65 65
KU70/SIRT1/BAX 0.038 0.047 -10000 0 -0.048 37 37
CREBBP 0.032 0.004 -10000 0 -10000 0 0
MEF2D 0.032 0.005 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.037 0.022 -10000 0 -10000 0 0
ACSS2 -0.007 0.011 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.01 0.016 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.032 0.004 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.03 0.07 -10000 0 -0.24 21 21
Syndecan-3/Neurocan 0.011 0.068 -10000 0 -0.29 21 21
POMC 0.032 0.004 -10000 0 -10000 0 0
EGFR 0.012 0.018 -10000 0 -0.063 6 6
Syndecan-3/EGFR 0 0.063 -10000 0 -0.26 22 22
AGRP 0.032 0.004 -10000 0 -10000 0 0
NCSTN 0.027 0.022 -10000 0 -0.063 28 28
PSENEN 0.031 0.007 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.032 0.005 -10000 0 -10000 0 0
APH1A 0.031 0.012 -10000 0 -0.063 7 7
NCAN 0.026 0.014 -10000 0 -0.063 2 2
long-term memory 0.029 0.076 -10000 0 -0.3 22 22
Syndecan-3/IL8 0.003 0.082 -10000 0 -0.35 22 22
PSEN1 0.03 0.008 -10000 0 -10000 0 0
Src/Cortactin 0.045 0.013 -10000 0 -10000 0 0
FYN 0.029 0.011 -10000 0 -0.063 1 1
limb bud formation -0.006 0.074 -10000 0 -0.36 20 20
MC4R 0.031 0.007 -10000 0 -0.063 1 1
SRC 0.031 0.008 -10000 0 -10000 0 0
PTN 0.021 0.015 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-3 -0.006 0.074 -10000 0 -0.36 20 20
neuron projection morphogenesis 0.014 0.086 0.16 105 -0.25 9 114
Syndecan-3/AgRP 0.015 0.081 -10000 0 -0.35 22 22
Syndecan-3/AgRP/MC4R 0.031 0.084 -10000 0 -0.34 22 22
Fyn/Cortactin 0.043 0.016 -10000 0 -0.05 1 1
SDC3 -0.006 0.075 -10000 0 -0.37 20 20
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.003 0.081 -10000 0 -0.35 22 22
IL8 0.012 0.039 -10000 0 -0.063 110 110
Syndecan-3/Fyn/Cortactin 0.03 0.077 -10000 0 -0.3 22 22
Syndecan-3/CASK -0.008 0.073 -10000 0 -0.34 22 22
alpha-MSH/MC4R 0.046 0.011 -10000 0 -0.05 1 1
Gamma Secretase 0.072 0.053 -10000 0 -0.075 2 2
EPHB forward signaling

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
Ephrin A5/EPHB2 0.042 0.01 -10000 0 -0.04 1 1
cell-cell adhesion 0.029 0.024 -10000 0 -10000 0 0
Ephrin B/EPHB2/RasGAP 0.077 0.045 -10000 0 -10000 0 0
ITSN1 0.032 0.005 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
SHC1 0.024 0.026 -10000 0 -0.063 40 40
Ephrin B1/EPHB3 0.041 0.013 -10000 0 -0.04 7 7
Ephrin B1/EPHB1 0.042 0.013 -10000 0 -0.04 9 9
HRAS/GDP 0.021 0.051 -10000 0 -0.15 24 24
Ephrin B/EPHB1/GRB7 0.078 0.046 -10000 0 -0.075 1 1
Endophilin/SYNJ1 -0.023 0.038 0.18 13 -10000 0 13
KRAS 0.031 0.008 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.073 0.048 -10000 0 -0.075 1 1
endothelial cell migration 0.037 0.038 -10000 0 -0.053 1 1
GRB2 0.032 0.006 -10000 0 -10000 0 0
GRB7 0.032 0.005 -10000 0 -0.063 1 1
PAK1 -0.028 0.047 0.19 14 -10000 0 14
HRAS 0.031 0.007 -10000 0 -10000 0 0
RRAS -0.022 0.045 0.19 16 -10000 0 16
DNM1 0.006 0.012 -10000 0 -10000 0 0
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.024 0.038 0.17 13 -10000 0 13
lamellipodium assembly -0.029 0.024 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.018 0.035 -10000 0 -0.15 9 9
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
EPHB2 0.031 0.007 -10000 0 -0.063 1 1
EPHB3 0.03 0.013 -10000 0 -0.063 7 7
EPHB1 0.03 0.013 -10000 0 -0.063 9 9
EPHB4 0.023 0.015 -10000 0 -10000 0 0
mol:GDP -0.011 0.043 0.15 13 -0.16 19 32
Ephrin B/EPHB2 0.063 0.035 -10000 0 -10000 0 0
Ephrin B/EPHB3 0.062 0.036 -10000 0 -0.054 2 2
JNK cascade -0.027 0.053 0.24 17 -10000 0 17
Ephrin B/EPHB1 0.062 0.037 -10000 0 -0.057 2 2
RAP1/GDP 0.029 0.1 0.19 128 -0.18 13 141
EFNB2 0.03 0.01 -10000 0 -10000 0 0
EFNB3 0.031 0.006 -10000 0 -10000 0 0
EFNB1 0.032 0.002 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.05 0.03 -10000 0 -0.043 12 12
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.032 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.057 0.049 0.14 1 -0.11 21 22
Rap1/GTP -0.044 0.016 -10000 0 -10000 0 0
axon guidance 0.041 0.01 -10000 0 -0.039 1 1
MAPK3 -0.007 0.035 0.17 3 -0.19 4 7
MAPK1 -0.007 0.032 0.16 2 -0.19 4 6
Rac1/GDP -0.006 0.066 0.21 31 -0.18 12 43
actin cytoskeleton reorganization -0.035 0.033 0.034 1 -0.13 19 20
CDC42/GDP 0.036 0.11 0.2 134 -0.18 13 147
PI3K 0.041 0.042 -10000 0 -0.054 1 1
EFNA5 0.032 0.004 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.028 0.021 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.012 0.032 -10000 0 -0.12 23 23
CDC42 0.031 0.006 -10000 0 -10000 0 0
RAS family/GTP -0.05 0.022 -10000 0 -10000 0 0
PTK2 -0.006 0.086 0.55 12 -10000 0 12
MAP4K4 -0.027 0.053 0.24 17 -10000 0 17
SRC 0.031 0.008 -10000 0 -10000 0 0
KALRN 0.032 0.005 -10000 0 -10000 0 0
Intersectin/N-WASP 0.033 0.022 -10000 0 -10000 0 0
neuron projection morphogenesis 0.059 0.16 0.33 128 -0.17 2 130
MAP2K1 0.004 0.035 -10000 0 -0.12 20 20
WASL 0.023 0.015 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.072 0.035 -10000 0 -10000 0 0
cell migration -0.001 0.055 0.17 10 -0.22 8 18
NRAS 0.009 0.041 -10000 0 -0.063 125 125
SYNJ1 -0.023 0.039 0.18 13 -10000 0 13
PXN 0.032 0.003 -10000 0 -10000 0 0
TF -0.016 0.034 0.18 8 -10000 0 8
HRAS/GTP 0.046 0.04 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2 0.057 0.023 -10000 0 -0.036 22 22
cell adhesion mediated by integrin 0.014 0.039 -10000 0 -0.2 9 9
RAC1 0.023 0.015 -10000 0 -10000 0 0
mol:GTP 0.051 0.039 0.14 5 -10000 0 5
RAC1-CDC42/GTP -0.034 0.028 -10000 0 -10000 0 0
RASA1 0.032 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.019 0.065 0.22 24 -0.17 14 38
ruffle organization 0.066 0.16 0.32 130 -10000 0 130
NCK1 0.03 0.015 -10000 0 -0.063 11 11
receptor internalization -0.005 0.024 0.22 3 -10000 0 3
Ephrin B/EPHB2/KALRN 0.077 0.045 -10000 0 -10000 0 0
ROCK1 -0.015 0.04 0.18 21 -10000 0 21
RAS family/GDP -0.035 0.034 -10000 0 -0.13 24 24
Rac1/GTP -0.029 0.026 0.047 4 -10000 0 4
Ephrin B/EPHB1/Src/Paxillin 0.015 0.037 -10000 0 -0.12 32 32
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.046 0.01 -10000 0 -10000 0 0
Necdin/E2F1 0.028 0.024 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.068 0.032 -10000 0 -0.054 1 1
NGF (dimer)/p75(NTR)/BEX1 0.028 0.024 -10000 0 -0.04 16 16
NT-4/5 (dimer)/p75(NTR) 0.021 0.013 -10000 0 -0.039 21 21
IKBKB 0.032 0.003 -10000 0 -10000 0 0
AKT1 -0.014 0.046 0.17 22 -10000 0 22
IKBKG 0.032 0.003 -10000 0 -10000 0 0
BDNF 0.009 0.015 -10000 0 -10000 0 0
MGDIs/NGR/p75(NTR)/LINGO1 0.02 0.011 -10000 0 -0.031 21 21
FURIN 0.032 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.017 0.03 -10000 0 -0.047 9 9
LINGO1 0 0 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF -0.049 0.015 -10000 0 -10000 0 0
proBDNF (dimer) 0.009 0.015 -10000 0 -10000 0 0
NTRK1 0.032 0.006 -10000 0 -0.063 1 1
RTN4R 0 0 -10000 0 -10000 0 0
neuron apoptosis 0.023 0.079 0.23 6 -0.31 17 23
IRAK1 0.032 0.003 -10000 0 -10000 0 0
SHC1 -0.02 0.008 -10000 0 -0.04 59 59
ARHGDIA 0.032 0.003 -10000 0 -10000 0 0
RhoA/GTP 0.023 0.004 -10000 0 -10000 0 0
Gamma Secretase 0.072 0.053 -10000 0 -0.075 2 2
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.052 0.027 -10000 0 -0.04 23 23
MAGEH1 0.03 0.009 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.034 0.034 -10000 0 -0.038 23 23
Mammalian IAPs/DIABLO 0.054 0.028 -10000 0 -0.042 37 37
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.032 0.003 -10000 0 -10000 0 0
APP 0.032 0.005 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.03 0.011 -10000 0 -0.063 3 3
RhoA/GDP/RHOGDI 0.037 0.018 -10000 0 -0.039 22 22
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest -0.017 0.027 0.2 6 -10000 0 6
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.011 0.028 -10000 0 -0.11 15 15
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.039 0.018 -10000 0 -0.04 21 21
NCSTN 0.027 0.022 -10000 0 -0.063 28 28
mol:GTP 0.035 0.021 -10000 0 -0.04 20 20
PSENEN 0.031 0.007 -10000 0 -10000 0 0
mol:ceramide -0.02 0.025 0.18 7 -10000 0 7
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.011 0.023 -10000 0 -0.1 16 16
p75(NTR)/beta APP 0.043 0.021 -10000 0 -0.05 20 20
BEX1 0.023 0.015 -10000 0 -10000 0 0
mol:GDP -0.01 0.004 -10000 0 -10000 0 0
NGF (dimer) 0.039 0.043 -10000 0 -0.043 75 75
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.038 0.016 -10000 0 -0.034 22 22
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
RAC1/GTP 0.024 0.021 -10000 0 -0.031 21 21
MYD88 0.019 0.032 -10000 0 -0.063 67 67
CHUK 0.024 0.015 -10000 0 -0.063 1 1
NGF (dimer)/p75(NTR)/PKA 0.036 0.021 -10000 0 -0.04 20 20
RHOB 0.03 0.011 -10000 0 -0.063 4 4
RHOA 0.032 0.006 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.022 0.006 -10000 0 -10000 0 0
NT3 (dimer) 0.031 0.007 -10000 0 -10000 0 0
TP53 0.033 0.064 0.23 25 -10000 0 25
PRDM4 -0.021 0.024 0.18 7 -10000 0 7
BDNF (dimer) 0.014 0.038 -10000 0 -0.066 4 4
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
SORT1 0.032 0.004 -10000 0 -10000 0 0
activation of caspase activity 0.061 0.03 -10000 0 -0.053 1 1
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.055 0.027 -10000 0 -0.038 34 34
RHOC 0.003 0.044 -10000 0 -0.063 155 155
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 0.038 0.074 0.19 79 -10000 0 79
DIABLO 0.032 0.004 -10000 0 -10000 0 0
SMPD2 -0.02 0.025 0.18 7 -10000 0 7
APH1B 0.032 0.005 -10000 0 -10000 0 0
APH1A 0.031 0.012 -10000 0 -0.063 7 7
proNGF (dimer)/p75(NTR)/Sortilin 0.04 0.018 -10000 0 -0.04 20 20
PSEN1 0.03 0.008 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.046 0.012 -10000 0 -0.05 3 3
NT3 (dimer)/p75(NTR) 0.042 0.021 -10000 0 -0.05 20 20
MAPK8 0.035 0.066 0.18 69 -0.14 1 70
MAPK9 0.065 0.087 0.19 137 -10000 0 137
APAF1 0.032 0.004 -10000 0 -10000 0 0
NTF3 0.031 0.007 -10000 0 -10000 0 0
NTF4 0 0 -10000 0 -10000 0 0
NDN 0.02 0.016 -10000 0 -10000 0 0
RAC1/GDP 0.017 0.011 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.023 0.056 -10000 0 -0.062 16 16
p75 CTF/Sortilin/TRAF6/NRIF 0.071 0.036 -10000 0 -10000 0 0
RhoA-B-C/GTP 0.035 0.021 -10000 0 -0.04 20 20
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.023 0.043 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.021 0.038 -10000 0 -10000 0 0
PRKACB 0.029 0.01 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD 0.013 0.022 -10000 0 -0.05 3 3
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.026 0.023 -10000 0 -0.063 30 30
BIRC2 0.032 0.004 -10000 0 -10000 0 0
neuron projection morphogenesis -0.008 0.023 -10000 0 -0.12 2 2
BAD 0.048 0.082 0.22 61 -0.16 2 63
RIPK2 0.032 0.006 -10000 0 -0.063 1 1
NGFR 0.028 0.019 -10000 0 -0.051 26 26
CYCS -0.018 0.022 0.17 4 -10000 0 4
ADAM17 0.031 0.01 -10000 0 -0.063 5 5
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.055 0.026 -10000 0 -0.039 31 31
BCL2L11 0.048 0.083 0.22 61 -0.16 2 63
BDNF (dimer)/p75(NTR) 0.012 0.023 -10000 0 -0.05 9 9
PI3K 0.048 0.033 -10000 0 -0.041 40 40
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.037 0.017 -10000 0 -0.033 25 25
NDNL2 0 0 -10000 0 -10000 0 0
YWHAE 0.032 0.005 -10000 0 -10000 0 0
PRKCI 0.032 0.006 -10000 0 -0.063 1 1
NGF (dimer)/p75(NTR) 0.021 0.013 -10000 0 -0.039 21 21
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.056 0.024 -10000 0 -0.04 25 25
TRAF6 0.032 0.005 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
PLG 0.03 0.008 -10000 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.005 0.012 0.14 1 -10000 0 1
SQSTM1 0.032 0.006 -10000 0 -0.063 1 1
NGFRAP1 0.032 0.004 -10000 0 -10000 0 0
CASP3 0.046 0.081 0.21 59 -0.17 3 62
E2F1 0.03 0.008 -10000 0 -10000 0 0
CASP9 0.031 0.009 -10000 0 -0.063 3 3
IKK complex 0.037 0.049 -10000 0 -0.13 8 8
NGF (dimer)/TRKA 0.023 0.004 -10000 0 -0.039 1 1
MMP7 0.018 0.034 -10000 0 -0.063 75 75
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.062 0.038 -10000 0 -0.047 22 22
MMP3 0.031 0.012 -10000 0 -0.063 7 7
APAF-1/Caspase 9 -0.036 0.026 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.03 0.008 -10000 0 -10000 0 0
NFATC1 0.018 0.051 0.23 3 -0.24 10 13
NFATC2 -0.036 0.079 0.16 2 -0.17 121 123
NFATC3 0.009 0.004 -10000 0 -10000 0 0
YWHAE 0.032 0.005 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.023 0.076 0.15 3 -0.22 43 46
Exportin 1/Ran/NUP214 0.061 0.019 -10000 0 -0.036 12 12
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.009 0.089 0.15 2 -0.22 40 42
BCL2/BAX 0.043 0.017 -10000 0 -0.05 6 6
CaM/Ca2+/Calcineurin A alpha-beta B1 0.021 0.008 -10000 0 -10000 0 0
CaM/Ca2+ 0.021 0.008 -10000 0 -10000 0 0
BAX 0.03 0.013 -10000 0 -0.063 6 6
MAPK14 0.032 0.005 -10000 0 -0.063 1 1
BAD 0.032 0.004 -10000 0 -10000 0 0
CABIN1/MEF2D -0.008 0.081 0.15 2 -0.22 41 43
Calcineurin A alpha-beta B1/BCL2 0.031 0.006 -10000 0 -10000 0 0
FKBP8 0.031 0.006 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.008 0.08 0.22 41 -0.15 2 43
KPNB1 0.032 0.003 -10000 0 -10000 0 0
KPNA2 0.03 0.014 -10000 0 -0.063 11 11
XPO1 0.033 0.001 -10000 0 0 1 1
SFN 0.026 0.023 -10000 0 -0.063 31 31
MAP3K8 0.018 0.026 -10000 0 -0.063 37 37
NFAT4/CK1 alpha 0.022 0.03 -10000 0 -0.079 37 37
MEF2D/NFAT1/Cbp/p300 0.009 0.1 -10000 0 -0.17 110 110
CABIN1 -0.023 0.076 0.15 3 -0.23 41 44
CALM1 0.029 0.01 -10000 0 -10000 0 0
RAN 0.032 0.004 -10000 0 -10000 0 0
MAP3K1 0.032 0.006 -10000 0 -0.063 1 1
CAMK4 0.032 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
MAPK3 0.032 0.002 -10000 0 -10000 0 0
YWHAH 0.015 0.016 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.044 0.015 -10000 0 -10000 0 0
YWHAB 0.03 0.009 -10000 0 0 39 39
MAPK8 0.025 0.014 -10000 0 -10000 0 0
MAPK9 0.032 0.005 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
FKBP1A 0.03 0.009 -10000 0 -0.063 1 1
NFAT1-c-4/YWHAQ 0.007 0.072 0.26 1 -0.23 21 22
PRKCH 0.03 0.01 -10000 0 -0.063 2 2
CABIN1/Cbp/p300 0.044 0.014 -10000 0 -10000 0 0
CASP3 0.014 0.037 -10000 0 -0.063 94 94
PIM1 0.032 0.005 -10000 0 -0.063 1 1
Calcineurin A alpha-beta B1/FKBP12/FK506 0.02 0.006 -10000 0 -0.001 37 37
apoptosis 0.017 0.024 -10000 0 -0.097 17 17
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.001 0.036 -10000 0 -0.19 11 11
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.032 0.002 -10000 0 -10000 0 0
JNK2/NFAT4 0.022 0.03 0.099 1 -0.16 6 7
BAD/BCL-XL 0.044 0.013 -10000 0 -10000 0 0
PRKCD 0.032 0.006 -10000 0 -10000 0 0
NUP214 0.031 0.007 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
PRKCA 0.032 0.004 -10000 0 0 6 6
PRKCG 0.031 0.008 -10000 0 -10000 0 0
PRKCQ 0.024 0.014 -10000 0 -10000 0 0
FKBP38/BCL2 0.045 0.012 -10000 0 -10000 0 0
EP300 0.03 0.008 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.03 0.008 -10000 0 -10000 0 0
NFATc/JNK1 0.026 0.049 0.27 1 -0.24 10 11
CaM/Ca2+/FKBP38 0.037 0.016 -10000 0 -10000 0 0
FKBP12/FK506 0.022 0.007 -10000 0 -0.001 37 37
CSNK1A1 -0.016 0.006 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.038 0.015 -10000 0 -10000 0 0
NFATc/ERK1 0.035 0.054 0.23 2 -0.23 10 12
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.008 0.09 0.15 2 -0.22 40 42
NR4A1 -0.046 0.066 0.14 7 -0.16 108 115
GSK3B 0.032 0.006 -10000 0 -10000 0 0
positive T cell selection 0.009 0.004 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.024 0.059 0.086 4 -0.12 117 121
RCH1/ KPNB1 0.046 0.015 -10000 0 -0.05 11 11
YWHAQ 0.032 0.004 -10000 0 -10000 0 0
PRKACA 0.031 0.006 -10000 0 -10000 0 0
AKAP5 0.03 0.008 -10000 0 -10000 0 0
MEF2D 0.032 0.005 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.032 0.006 -10000 0 -10000 0 0
NFATc/p38 alpha 0.035 0.055 0.24 3 -0.24 10 13
CREBBP 0.032 0.004 -10000 0 -10000 0 0
BCL2 0.032 0.006 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.031 0.007 -10000 0 -10000 0 0
Rac1/GDP 0.025 0.018 -10000 0 -0.026 4 4
DOCK1 0.023 0.015 -10000 0 -10000 0 0
ITGA4 0.031 0.01 -10000 0 -0.063 5 5
RAC1 0.023 0.015 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.046 0.013 -10000 0 -0.06 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.032 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.042 0.043 -10000 0 -0.05 5 5
alpha4/beta7 Integrin/Paxillin 0.046 0.015 -10000 0 -0.058 5 5
lamellipodium assembly -0.011 0.081 -10000 0 -0.34 18 18
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
PI3K 0.039 0.023 -10000 0 -0.05 16 16
ARF6 0.031 0.008 -10000 0 -10000 0 0
TLN1 0.021 0.027 -10000 0 -0.063 43 43
PXN -0.022 0.005 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
ARF6/GTP 0.04 0.05 0.15 7 -10000 0 7
cell adhesion 0.031 0.053 0.16 6 -0.071 1 7
CRKL/CBL 0.045 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.037 0.023 -10000 0 -0.052 5 5
ITGB1 0.025 0.014 -10000 0 -10000 0 0
ITGB7 0.032 0.008 -10000 0 -0.063 2 2
ARF6/GDP 0.033 0.013 -10000 0 -0.026 7 7
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.021 0.054 0.17 3 -0.071 2 5
p130Cas/Crk/Dock1 0.031 0.02 -10000 0 -10000 0 0
VCAM1 -0.03 0.045 -10000 0 -0.063 333 333
alpha4/beta1 Integrin/Paxillin/Talin 0.033 0.054 0.17 6 -10000 0 6
alpha4/beta1 Integrin/Paxillin/GIT1 0.044 0.048 0.17 7 -10000 0 7
BCAR1 0 0 -10000 0 -10000 0 0
mol:GDP -0.042 0.047 -10000 0 -0.16 7 7
CBL 0.032 0.004 -10000 0 -10000 0 0
PRKACA 0.032 0.006 -10000 0 -10000 0 0
GIT1 0.032 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.033 0.054 0.17 6 -10000 0 6
Rac1/GTP -0.013 0.089 -10000 0 -0.38 18 18
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.032 0.005 -10000 0 -0.033 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.007 0.074 0.21 8 -0.25 17 25
ERC1 0.031 0.006 -10000 0 -10000 0 0
RIP2/NOD2 0.045 0.015 -10000 0 -0.05 9 9
NFKBIA -0.028 0.017 0.2 2 -10000 0 2
BIRC2 0.032 0.004 -10000 0 -10000 0 0
IKBKB 0.032 0.003 -10000 0 -10000 0 0
RIPK2 0.032 0.006 -10000 0 -0.063 1 1
IKBKG 0.018 0.051 -10000 0 -0.28 10 10
IKK complex/A20 0.035 0.068 -10000 0 -0.37 6 6
NEMO/A20/RIP2 0.032 0.006 -10000 0 -0.063 1 1
XPO1 0.033 0.001 -10000 0 0 1 1
NEMO/ATM 0.035 0.055 0.19 1 -0.38 6 7
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.032 0.004 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.043 0.006 -10000 0 -10000 0 0
IKK complex/ELKS 0.039 0.059 -10000 0 -0.36 6 6
BCL10/MALT1/TRAF6 0.054 0.033 -10000 0 -0.048 24 24
NOD2 0.031 0.013 -10000 0 -0.063 8 8
NFKB1 0.031 0.01 -10000 0 -0.058 5 5
RELA 0.032 0.005 -10000 0 -0.033 1 1
MALT1 0.028 0.02 -10000 0 -0.063 21 21
cIAP1/UbcH5C 0.047 0.009 -10000 0 -10000 0 0
ATM 0.027 0.021 -10000 0 -0.063 25 25
TNF/TNFR1A 0.014 0.045 -10000 0 -0.05 166 166
TRAF6 0.032 0.005 -10000 0 -10000 0 0
PRKCA 0.032 0.004 -10000 0 0 6 6
CHUK 0.024 0.015 -10000 0 -0.063 1 1
UBE2D3 0.032 0.005 -10000 0 -10000 0 0
TNF 0.032 0.006 -10000 0 -0.063 2 2
NF kappa B1 p50/RelA 0.065 0.025 -10000 0 -0.055 5 5
BCL10 0.031 0.009 -10000 0 -0.063 3 3
proteasomal ubiquitin-dependent protein catabolic process -0.028 0.017 0.2 2 -10000 0 2
beta TrCP1/SCF ubiquitin ligase complex 0.032 0.005 -10000 0 -0.033 1 1
TNFRSF1A 0 0.044 -10000 0 -0.063 165 165
IKK complex 0.04 0.061 -10000 0 -0.38 6 6
CYLD 0.032 0.004 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.049 0.066 -10000 0 -0.37 6 6
Thromboxane A2 receptor signaling

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
TGM2 0.03 0.011 -10000 0 -0.063 3 3
GNB1/GNG2 -0.031 0.026 -10000 0 -0.12 12 12
AKT1 -0.006 0.084 0.23 15 -0.26 28 43
EGF 0.032 0.007 -10000 0 -0.063 2 2
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR -0.022 0.062 0.28 16 -0.15 4 20
mol:Ca2+ -0.008 0.075 0.26 10 -0.27 14 24
LYN -0.024 0.065 0.28 18 -0.16 4 22
RhoA/GTP -0.006 0.036 -10000 0 -0.11 7 7
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.018 0.079 0.29 12 -0.26 12 24
GNG2 0 0 -10000 0 -10000 0 0
ARRB2 0.032 0.005 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.007 0.051 0.14 7 -0.22 15 22
G beta5/gamma2 -0.035 0.036 -10000 0 -0.16 6 6
PRKCH -0.014 0.077 0.27 9 -0.29 13 22
DNM1 0.006 0.012 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin3 0.002 0.008 -10000 0 -10000 0 0
mol:GTP 0 0.001 0.004 14 -0.002 13 27
PTGDR 0.031 0.008 -10000 0 -10000 0 0
G12 family/GTP -0.023 0.05 -10000 0 -0.25 7 7
ADRBK1 0.032 0.004 -10000 0 -10000 0 0
ADRBK2 0.031 0.008 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.042 0.01 -10000 0 -10000 0 0
mol:GDP 0.004 0.082 0.3 17 -0.27 9 26
mol:NADP 0.022 0.015 -10000 0 -10000 0 0
RAB11A 0.032 0.005 -10000 0 -10000 0 0
PRKG1 0.025 0.014 -10000 0 -10000 0 0
mol:IP3 -0.011 0.087 0.29 9 -0.33 14 23
cell morphogenesis 0.041 0.01 -10000 0 -10000 0 0
PLCB2 -0.017 0.1 0.34 6 -0.44 14 20
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.021 0.064 0.28 18 -0.15 4 22
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.029 0.045 0.24 9 -0.16 3 12
RHOA 0.032 0.006 -10000 0 -10000 0 0
PTGIR 0.031 0.007 -10000 0 -10000 0 0
PRKCB1 -0.014 0.079 0.27 8 -0.3 13 21
GNAQ 0.031 0.006 -10000 0 -10000 0 0
mol:L-citrulline 0.022 0.015 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.024 0.095 0.33 6 -0.37 13 19
LCK -0.022 0.064 0.28 17 -0.15 4 21
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.027 0.038 0.19 2 -0.1 27 29
TXA2-R family/G12 family/GDP/G beta/gamma 0.003 0.087 -10000 0 -0.42 20 20
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.026 0.039 0.19 2 -0.1 28 30
MAPK14 -0.016 0.061 0.24 12 -0.19 11 23
TGM2/GTP -0.011 0.092 0.33 5 -0.36 13 18
MAPK11 -0.015 0.06 0.24 11 -0.19 11 22
ARHGEF1 -0.018 0.032 -10000 0 -0.15 7 7
GNAI2 0.032 0.006 -10000 0 -10000 0 0
JNK cascade -0.017 0.08 0.28 10 -0.29 13 23
RAB11/GDP 0.031 0.009 -10000 0 -0.03 8 8
ICAM1 -0.014 0.062 0.22 11 -0.21 14 25
cAMP biosynthetic process -0.012 0.083 0.28 10 -0.31 14 24
Gq family/GTP/EBP50 0.013 0.041 0.22 9 -0.2 8 17
actin cytoskeleton reorganization 0.041 0.01 -10000 0 -10000 0 0
SRC -0.027 0.045 0.24 9 -0.15 4 13
GNB5 0.031 0.006 -10000 0 -10000 0 0
GNB1 0.031 0.008 -10000 0 -10000 0 0
EGF/EGFR 0.01 0.077 0.26 27 -0.16 10 37
VCAM1 -0.02 0.065 0.23 10 -0.21 14 24
TP beta/Gq family/GDP/G beta5/gamma2 0.007 0.051 0.14 7 -0.22 15 22
platelet activation -0.018 0.078 0.3 12 -0.25 12 24
PGI2/IP 0.023 0.005 -10000 0 -10000 0 0
PRKACA 0.009 0.029 -10000 0 -0.09 38 38
Gq family/GDP/G beta5/gamma2 0.01 0.045 0.14 8 -0.2 16 24
TXA2/TP beta/beta Arrestin2 -0.007 0.057 -10000 0 -0.33 14 14
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.015 0.024 -10000 0 -0.095 39 39
mol:DAG -0.014 0.088 0.3 8 -0.34 13 21
EGFR 0.012 0.018 -10000 0 -0.063 6 6
TXA2/TP alpha -0.016 0.1 0.33 9 -0.41 14 23
Gq family/GTP 0.008 0.026 0.21 6 -0.21 2 8
YES1 -0.025 0.058 0.27 14 -0.16 4 18
GNAI2/GTP 0.016 0.038 -10000 0 -0.1 36 36
PGD2/DP 0.023 0.006 -10000 0 -10000 0 0
SLC9A3R1 0.032 0.007 -10000 0 -0.063 2 2
FYN -0.018 0.064 0.28 18 -0.15 4 22
mol:NO 0.022 0.015 -10000 0 -10000 0 0
GNA15 0.03 0.013 -10000 0 -0.063 7 7
PGK/cGMP 0.026 0.022 -10000 0 -10000 0 0
RhoA/GDP 0.031 0.009 -10000 0 -0.03 7 7
TP alpha/TGM2/GDP/G beta/gamma 0.026 0.038 0.18 1 -0.1 27 28
NOS3 0.022 0.015 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
PRKCA -0.014 0.077 0.26 11 -0.28 13 24
PRKCB -0.012 0.075 0.26 9 -0.27 13 22
PRKCE -0.015 0.076 0.26 10 -0.28 13 23
PRKCD -0.017 0.078 0.26 11 -0.29 13 24
PRKCG -0.015 0.082 0.29 10 -0.31 14 24
muscle contraction -0.025 0.094 0.33 7 -0.36 14 21
PRKCZ -0.016 0.073 0.26 10 -0.26 13 23
ARR3 0.032 0.002 -10000 0 0 2 2
TXA2/TP beta 0.027 0.041 0.15 2 -0.1 34 36
PRKCQ -0.018 0.07 0.29 6 -0.28 13 19
MAPKKK cascade -0.019 0.092 0.3 8 -0.37 14 22
SELE -0.014 0.063 0.23 10 -0.21 14 24
TP beta/GNAI2/GDP/G beta/gamma 0.028 0.039 0.18 2 -0.1 25 27
ROCK1 0.032 0.005 -10000 0 -10000 0 0
GNA14 0.031 0.009 -10000 0 -0.063 2 2
chemotaxis -0.029 0.095 0.33 6 -0.38 9 15
GNA12 0.023 0.015 -10000 0 -10000 0 0
GNA13 0.032 0.007 -10000 0 -0.063 2 2
GNA11 0.031 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.017 0.011 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.02 0.031 -10000 0 -0.063 61 61
HDAC2 0.03 0.012 -10000 0 -0.063 4 4
GNB1/GNG2 0.028 0.021 -10000 0 -10000 0 0
forebrain development 0.026 0.055 0.22 14 -10000 0 14
GNAO1 0.003 0.009 -10000 0 -10000 0 0
SMO/beta Arrestin2 0.033 0.023 -10000 0 -10000 0 0
SMO 0.023 0.015 -10000 0 -10000 0 0
ARRB2 0.032 0.005 -10000 0 -10000 0 0
GLI3/SPOP 0.01 0.069 -10000 0 -0.2 21 21
mol:GTP 0 0 -10000 0 -10000 0 0
GSK3B 0.032 0.006 -10000 0 -10000 0 0
GNAI2 0.032 0.006 -10000 0 -0.026 1 1
SIN3/HDAC complex 0.053 0.028 -10000 0 -0.039 5 5
GNAI1 0.019 0.016 -10000 0 -0.063 1 1
XPO1 0.033 0.007 -10000 0 -0.027 6 6
GLI1/Su(fu) 0.005 0.025 -10000 0 -0.24 1 1
SAP30 0.032 0.006 -10000 0 -10000 0 0
mol:GDP 0.023 0.015 -10000 0 -10000 0 0
MIM/GLI2A 0.034 0.008 -10000 0 -0.04 3 3
IFT88 0.031 0.008 -10000 0 -10000 0 0
GNAI3 0.021 0.03 -10000 0 -0.063 58 58
GLI2 0.012 0.048 0.15 10 -0.22 9 19
GLI3 -0.005 0.062 -10000 0 -0.21 18 18
CSNK1D 0.032 0.007 -10000 0 -0.063 2 2
CSNK1E 0.03 0.008 -10000 0 -10000 0 0
SAP18 0.031 0.008 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.031 0.008 -10000 0 -10000 0 0
GNG2 0 0 -10000 0 -10000 0 0
Gi family/GTP 0.001 0.01 0.089 1 -0.12 2 3
SIN3B 0.031 0.006 -10000 0 -10000 0 0
SIN3A 0 0 -10000 0 -10000 0 0
GLI3/Su(fu) -0.004 0.046 0.1 1 -0.18 19 20
GLI2/Su(fu) 0.006 0.035 0.12 3 -0.2 7 10
FOXA2 0.037 0.037 -10000 0 -0.47 2 2
neural tube patterning 0.026 0.055 0.22 14 -10000 0 14
SPOP 0.032 0.004 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.044 0.034 0.093 151 -0.063 8 159
GNB1 0.031 0.008 -10000 0 -10000 0 0
CSNK1G2 0.031 0.006 -10000 0 -10000 0 0
CSNK1G3 0.032 0.004 -10000 0 -10000 0 0
MTSS1 0.034 0.008 -10000 0 -0.04 3 3
embryonic limb morphogenesis 0.026 0.055 0.22 14 -10000 0 14
SUFU -0.002 0.002 -10000 0 -10000 0 0
LGALS3 0.019 0.031 -10000 0 -0.063 60 60
catabolic process 0.026 0.077 0.19 6 -0.29 14 20
GLI3A/CBP 0.036 0.016 -10000 0 -0.083 8 8
KIF3A 0.029 0.01 -10000 0 -10000 0 0
GLI1 0.026 0.055 0.22 14 -10000 0 14
RAB23 0.031 0.01 -10000 0 -0.063 5 5
CSNK1A1 0.032 0.004 -10000 0 -10000 0 0
IFT172 0 0 -10000 0 -10000 0 0
RBBP7 0.032 0.002 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.034 0.038 0.093 126 -0.062 6 132
GNAZ 0.027 0.013 -10000 0 -10000 0 0
RBBP4 0.015 0.036 -10000 0 -0.063 89 89
CSNK1G1 0.032 0.005 -10000 0 -10000 0 0
PIAS1 0.032 0.004 -10000 0 -10000 0 0
PRKACA 0.032 0.006 -10000 0 -10000 0 0
GLI2/SPOP 0.029 0.051 0.15 10 -0.22 9 19
STK36 0.001 0.001 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0 0.014 -10000 0 -0.14 4 4
PTCH1 0.024 0.064 0.35 7 -10000 0 7
MIM/GLI1 0.043 0.058 0.23 12 -10000 0 12
CREBBP 0.036 0.016 -10000 0 -0.083 8 8
Su(fu)/SIN3/HDAC complex 0.008 0.058 0.13 4 -0.18 31 35
Presenilin action in Notch and Wnt 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
Delta 1/NOTCH/NOTCH(cleaved) 0.011 0.083 -10000 0 -0.39 19 19
HDAC1 0.022 0.031 -10000 0 -0.059 61 61
AES 0.032 0.007 -10000 0 -10000 0 0
FBXW11 0.032 0.005 -10000 0 -10000 0 0
DTX1 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.032 0.024 -10000 0 -0.05 4 4
TLE1 0.032 0.006 -10000 0 -10000 0 0
AP1 0.002 0.022 -10000 0 -0.14 4 4
NCSTN 0.027 0.022 -10000 0 -0.063 28 28
ADAM10 0.028 0.018 -10000 0 -0.063 18 18
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.021 0.058 -10000 0 -0.51 4 4
NICD/RBPSUH 0.028 0.088 -10000 0 -0.39 19 19
WIF1 0.004 0.01 -10000 0 -10000 0 0
NOTCH1 0.012 0.082 -10000 0 -0.44 15 15
PSENEN 0.031 0.007 -10000 0 -10000 0 0
KREMEN2 0.032 0.003 -10000 0 -10000 0 0
DKK1 0.006 0.037 -10000 0 -0.063 101 101
beta catenin/beta TrCP1 0.063 0.078 0.2 73 -0.23 6 79
APH1B 0.032 0.005 -10000 0 -10000 0 0
APH1A 0.031 0.012 -10000 0 -0.063 7 7
AXIN1 0.026 0.047 0.26 4 -0.25 1 5
CtBP/CBP/TCF1/TLE1/AES 0.022 0.031 -10000 0 -0.12 11 11
PSEN1 0.03 0.008 -10000 0 -10000 0 0
FOS 0.007 0.04 -10000 0 -0.063 120 120
JUN 0.032 0.005 -10000 0 -10000 0 0
MAP3K7 0.031 0.009 -10000 0 -0.063 1 1
CTNNB1 0.048 0.08 0.19 85 -0.23 6 91
MAPK3 0.032 0.002 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.059 0.025 -10000 0 -0.048 9 9
HNF1A 0.033 0.003 -10000 0 -10000 0 0
CTBP1 0.032 0.006 -10000 0 -10000 0 0
MYC -0.005 0.065 -10000 0 -0.74 1 1
NKD1 0 0.001 -10000 0 -10000 0 0
FZD1 0.022 0.017 -10000 0 -0.063 4 4
NOTCH1 precursor/Deltex homolog 1 0.005 0.081 -10000 0 -0.39 19 19
apoptosis 0.002 0.022 -10000 0 -0.14 4 4
Delta 1/NOTCHprecursor 0.005 0.081 -10000 0 -0.39 19 19
DLL1 0 0 -10000 0 -10000 0 0
PPARD 0.018 0.063 -10000 0 -0.78 3 3
Gamma Secretase 0.071 0.053 -10000 0 -0.076 2 2
APC 0.01 0.084 0.26 3 -0.33 20 23
DVL1 0.018 0.021 -10000 0 -0.21 2 2
CSNK2A1 0.03 0.008 -10000 0 -10000 0 0
MAP3K7IP1 0.001 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.017 0.053 -10000 0 -0.048 102 102
LRP6 0.031 0.007 -10000 0 -10000 0 0
CSNK1A1 0.032 0.004 -10000 0 -10000 0 0
NLK 0.014 0.006 -10000 0 -0.038 1 1
CCND1 -0.005 0.1 -10000 0 -0.8 7 7
WNT1 0.031 0.006 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.043 0.085 0.26 18 -0.4 4 22
DKK2 0.031 0.012 -10000 0 -0.063 8 8
NOTCH1 precursor/DVL1 0.034 0.091 0.25 1 -0.39 15 16
GSK3B 0.032 0.006 -10000 0 -10000 0 0
FRAT1 0.025 0.014 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.011 0.083 -10000 0 -0.39 19 19
PPP2R5D 0.015 0.03 -10000 0 -0.39 2 2
MAPK1 0.03 0.009 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.007 0.024 -10000 0 -10000 0 0
RBPJ 0.032 0.004 -10000 0 -10000 0 0
CREBBP 0.031 0.005 -10000 0 -0.022 1 1
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.05 0.051 -10000 0 -0.069 6 6
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.031 0.007 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.043 0.053 0.2 18 -10000 0 18
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.046 0.042 0.16 1 -0.047 78 79
antigen processing and presentation of peptide antigen via MHC class I -0.038 0.033 -10000 0 -0.1 38 38
CaM/Ca2+ 0.047 0.055 -10000 0 -0.077 1 1
RAP1A 0.032 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.034 0.035 0.15 16 -10000 0 16
AKT1 -0.023 0.064 0.2 22 -10000 0 22
MAP2K1 -0.032 0.045 0.16 20 -10000 0 20
MAP3K11 -0.028 0.051 0.18 22 -10000 0 22
IFNGR1 0.029 0.017 0.085 3 -0.067 11 14
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.056 0.088 -10000 0 -0.23 87 87
Rap1/GTP -0.045 0.017 -10000 0 -10000 0 0
CRKL/C3G 0.044 0.014 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.063 0.06 -10000 0 -10000 0 0
CEBPB -0.01 0.092 0.33 6 -0.3 22 28
STAT3 0.03 0.014 -10000 0 -0.063 10 10
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.058 0.087 -10000 0 -0.74 4 4
STAT1 -0.031 0.047 0.17 20 -10000 0 20
CALM1 0.029 0.01 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.03 0.01 -10000 0 -0.029 5 5
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
STAT1 (dimer)/PIAS1 -0.034 0.05 0.18 20 -10000 0 20
CEBPB/PTGES2/Cbp/p300 0.006 0.073 -10000 0 -0.22 34 34
mol:Ca2+ 0.047 0.049 -10000 0 -0.068 6 6
MAPK3 -0.002 0.059 0.51 1 -0.57 2 3
STAT1 (dimer) -0.048 0.044 0.08 3 -0.15 23 26
MAPK1 -0.051 0.19 0.46 2 -0.67 40 42
JAK2 0.03 0.012 0.085 3 -10000 0 3
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
JAK1 0.031 0.01 0.07 1 -0.029 6 7
CAMK2D 0 0 -10000 0 -10000 0 0
DAPK1 -0.004 0.071 0.28 8 -0.19 28 36
SMAD7 -0.016 0.041 0.16 13 -0.089 1 14
CBL/CRKL/C3G -0.037 0.052 0.19 20 -10000 0 20
PI3K 0.041 0.056 -10000 0 -10000 0 0
IFNG 0.03 0.01 -10000 0 -0.029 5 5
apoptosis 0.001 0.066 0.32 5 -0.38 3 8
CAMK2G 0.012 0.016 -10000 0 -10000 0 0
STAT3 (dimer) 0.03 0.014 -10000 0 -0.063 10 10
CAMK2A 0.031 0.007 -10000 0 -10000 0 0
CAMK2B 0.003 0.009 -10000 0 -10000 0 0
FRAP1 -0.023 0.058 0.18 22 -10000 0 22
PRKCD -0.025 0.067 0.21 21 -10000 0 21
RAP1B 0 0 -10000 0 -10000 0 0
negative regulation of cell growth -0.038 0.033 -10000 0 -0.1 38 38
PTPN2 0.031 0.006 -10000 0 -10000 0 0
EP300 0.03 0.008 -10000 0 -10000 0 0
IRF1 -0.042 0.052 0.3 6 -10000 0 6
STAT1 (dimer)/PIASy -0.035 0.047 0.17 19 -10000 0 19
SOCS1 0.017 0.093 -10000 0 -1 4 4
mol:GDP -0.036 0.049 0.18 20 -10000 0 20
CASP1 -0.02 0.045 0.15 15 -0.091 8 23
PTGES2 0.031 0.006 -10000 0 -10000 0 0
IRF9 -0.008 0.041 0.18 8 -0.11 18 26
mol:PI-3-4-5-P3 0.028 0.047 -10000 0 -0.077 3 3
RAP1/GDP -0.043 0.029 0.098 15 -10000 0 15
CBL -0.028 0.051 0.18 22 -10000 0 22
MAP3K1 -0.029 0.045 0.17 20 -10000 0 20
PIAS1 0.032 0.004 -10000 0 -10000 0 0
PIAS4 0.031 0.006 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.038 0.033 -10000 0 -0.1 38 38
PTPN11 -0.025 0.044 0.16 23 -10000 0 23
CREBBP 0.032 0.004 -10000 0 -10000 0 0
RAPGEF1 0.031 0.006 -10000 0 -10000 0 0
FoxO family signaling

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
G6PC -0.014 0.05 0.24 1 -0.28 1 2
PLK1 -0.052 0.081 -10000 0 -0.43 2 2
CDKN1B -0.09 0.15 0.23 2 -0.33 128 130
FOXO3 -0.049 0.082 -10000 0 -0.34 11 11
KAT2B -0.003 0.005 -10000 0 -10000 0 0
FOXO1/SIRT1 0.005 0.053 -10000 0 -0.2 20 20
CAT -0.049 0.077 -10000 0 -0.39 2 2
CTNNB1 0.032 0.005 -10000 0 -10000 0 0
AKT1 0.016 0.026 -10000 0 -10000 0 0
FOXO1 -0.012 0.057 0.29 1 -0.2 22 23
MAPK10 0.021 0.072 0.18 85 -10000 0 85
mol:GTP 0 0.001 -10000 0 -10000 0 0
FOXO4 -0.001 0.08 0.31 5 -0.24 1 6
response to oxidative stress -0.002 0.005 -10000 0 -10000 0 0
FOXO3A/SIRT1 -0.035 0.084 -10000 0 -0.33 11 11
XPO1 0.033 0.001 -10000 0 0 1 1
EP300 0.03 0.009 -10000 0 -10000 0 0
BCL2L11 0.019 0.012 -10000 0 -10000 0 0
FOXO1/SKP2 0.006 0.059 0.24 1 -0.2 21 22
mol:GDP -0.002 0.005 -10000 0 -10000 0 0
RAN 0.032 0.004 -10000 0 -10000 0 0
GADD45A -0.065 0.15 0.34 1 -0.46 22 23
YWHAQ 0.032 0.004 -10000 0 -10000 0 0
FOXO1/14-3-3 family -0.021 0.078 -10000 0 -0.27 25 25
MST1 0.015 0.028 -10000 0 -0.066 6 6
CSNK1D 0.032 0.007 -10000 0 -0.063 2 2
CSNK1E 0.03 0.008 -10000 0 -10000 0 0
FOXO4/14-3-3 family -0.047 0.09 -10000 0 -0.31 21 21
YWHAB 0.03 0.009 -10000 0 0 39 39
MAPK8 0.012 0.071 0.18 73 -10000 0 73
MAPK9 0.039 0.095 0.18 153 -10000 0 153
YWHAG 0 0 -10000 0 -10000 0 0
YWHAE 0.032 0.005 -10000 0 -10000 0 0
YWHAZ 0.032 0.006 -10000 0 -10000 0 0
SIRT1 0.023 0.015 -10000 0 -0.025 9 9
SOD2 -0.093 0.12 0.46 1 -0.46 28 29
RBL2 -0.028 0.1 -10000 0 -0.7 7 7
RAL/GDP 0.027 0.023 -10000 0 -10000 0 0
CHUK 0.009 0.025 -10000 0 -0.059 1 1
Ran/GTP 0.023 0.004 -10000 0 -10000 0 0
CSNK1G2 0.031 0.006 -10000 0 -10000 0 0
RAL/GTP 0.024 0.023 -10000 0 -10000 0 0
CSNK1G1 0.032 0.005 -10000 0 -10000 0 0
FASLG 0.016 0.032 -10000 0 -0.61 1 1
SKP2 0.032 0.007 -10000 0 -0.063 2 2
USP7 0.032 0.003 -10000 0 -10000 0 0
IKBKB 0.016 0.027 -10000 0 -10000 0 0
CCNB1 -0.073 0.09 -10000 0 -0.4 4 4
FOXO1-3a-4/beta catenin -0.027 0.081 0.21 1 -0.3 2 3
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.059 0.24 1 -0.19 21 22
CSNK1A1 0.032 0.004 -10000 0 -10000 0 0
SGK1 -0.003 0.005 -10000 0 -10000 0 0
CSNK1G3 0.032 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.043 0.006 -10000 0 -10000 0 0
ZFAND5 0.003 0.082 0.32 10 -10000 0 10
SFN 0.026 0.023 -10000 0 -0.063 31 31
CDK2 0.028 0.021 -10000 0 -0.06 24 24
FOXO3A/14-3-3 -0.048 0.076 -10000 0 -0.26 25 25
CREBBP 0.033 0.004 -10000 0 -10000 0 0
FBXO32 -0.047 0.076 -10000 0 -0.32 10 10
BCL6 -0.032 0.1 -10000 0 -0.67 7 7
RALB 0.032 0.005 -10000 0 -0.062 1 1
RALA 0.021 0.019 -10000 0 -0.063 11 11
YWHAH 0.015 0.016 -10000 0 -10000 0 0
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.059 0.13 0.4 31 -10000 0 31
CRP 0.05 0.12 0.47 11 -10000 0 11
cell cycle arrest 0.052 0.12 0.38 14 -10000 0 14
TIMP1 0.016 0.11 0.41 6 -0.53 1 7
IL6ST 0.031 0.011 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.056 0.22 10 -0.22 3 13
AP1 0.033 0.064 -10000 0 -0.35 5 5
GAB2 0.032 0.007 -10000 0 -0.026 1 1
TNFSF11 0.046 0.11 0.43 8 -10000 0 8
HSP90B1 0.043 0.051 -10000 0 -0.49 2 2
GAB1 0.032 0.009 -10000 0 -0.054 4 4
MAPK14 0.011 0.045 0.18 2 -0.21 3 5
AKT1 0.022 0.041 0.23 1 -0.45 2 3
FOXO1 0.016 0.043 0.2 4 -0.44 2 6
MAP2K6 0.008 0.039 0.11 23 -0.22 3 26
mol:GTP 0 0.001 -10000 0 -10000 0 0
MAP2K4 0.009 0.062 0.26 11 -0.26 1 12
MITF 0.007 0.039 0.11 28 -0.21 2 30
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.031 0.007 -10000 0 -10000 0 0
A2M -0.021 0.18 -10000 0 -0.94 18 18
CEBPB 0.03 0.017 -10000 0 -0.059 12 12
GRB2/SOS1/GAB family/SHP2 0.022 0.044 0.23 1 -0.27 4 5
STAT3 0.051 0.12 0.46 8 -10000 0 8
STAT1 0.017 0.023 -10000 0 -10000 0 0
CEBPD 0.048 0.11 0.41 11 -10000 0 11
PIK3CA 0.028 0.018 -10000 0 -0.061 18 18
PI3K 0.04 0.023 -10000 0 -0.049 17 17
JUN 0.032 0.005 -10000 0 -10000 0 0
PIAS3/MITF 0.055 0.076 0.19 76 -0.21 2 78
MAPK11 0.008 0.043 0.18 2 -0.21 3 5
STAT3 (dimer)/FOXO1 -0.004 0.066 0.27 1 -0.4 1 2
GRB2/SOS1/GAB family 0.058 0.058 0.17 6 -0.21 3 9
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK 0.004 0.033 -10000 0 -0.17 6 6
GRB2 0.032 0.006 -10000 0 -0.027 1 1
JAK2 0.029 0.01 -10000 0 -10000 0 0
LBP 0.061 0.12 0.37 24 -0.62 1 25
PIK3R1 0.03 0.01 -10000 0 -0.026 1 1
JAK1 0.032 0.007 -10000 0 -10000 0 0
MYC 0.042 0.12 0.42 12 -10000 0 12
FGG 0.046 0.11 0.43 8 -10000 0 8
macrophage differentiation 0.052 0.12 0.38 14 -10000 0 14
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.046 0.059 -10000 0 -10000 0 0
JUNB 0.05 0.12 0.4 21 -10000 0 21
FOS 0.007 0.04 -10000 0 -0.063 120 120
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 0.013 0.041 0.13 12 -0.23 3 15
STAT1/PIAS1 0.041 0.064 0.2 17 -0.19 1 18
GRB2/SOS1/GAB family/SHP2/PI3K 0.032 0.04 -10000 0 -0.47 2 2
STAT3 (dimer) 0.052 0.12 0.42 11 -10000 0 11
PRKCD 0.071 0.15 0.3 128 -10000 0 128
IL6R 0.032 0.006 -10000 0 -10000 0 0
SOCS3 0.049 0.084 0.39 9 -10000 0 9
gp130 (dimer)/JAK1/JAK1/LMO4 0.061 0.023 -10000 0 -10000 0 0
Rac1/GTP 0.014 0.051 0.19 3 -0.22 3 6
HCK 0.014 0.036 -10000 0 -0.063 85 85
MAPKKK cascade 0.042 0.059 0.27 2 -0.38 5 7
bone resorption 0.046 0.11 0.42 8 -10000 0 8
IRF1 0.043 0.12 0.42 9 -10000 0 9
mol:GDP 0.005 0.04 0.11 22 -0.22 3 25
SOS1 0 0.002 -10000 0 -10000 0 0
VAV1 0.005 0.04 0.11 22 -0.22 3 25
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.019 0.046 0.19 2 -0.3 5 7
PTPN11 0.018 0.044 -10000 0 -0.63 2 2
IL6/IL6RA 0.026 0.031 -10000 0 -0.059 1 1
gp130 (dimer)/TYK2/TYK2/LMO4 0.059 0.022 -10000 0 -10000 0 0
gp130 (dimer)/JAK2/JAK2/LMO4 0.054 0.03 -10000 0 -10000 0 0
IL6 0.015 0.027 -10000 0 -0.065 37 37
PIAS3 0.032 0.004 -10000 0 -10000 0 0
PTPRE 0.023 0.015 -10000 0 -10000 0 0
PIAS1 0.032 0.004 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0.016 0.036 0.11 43 -0.11 4 47
LMO4 0.03 0.011 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 0.023 0.077 -10000 0 -10000 0 0
MCL1 0.021 0.049 0.25 3 -0.41 2 5
Stabilization and expansion of the E-cadherin adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
adherens junction organization -0.022 0.03 -10000 0 -0.13 24 24
epithelial cell differentiation 0.06 0.032 -10000 0 -10000 0 0
CYFIP2 0.018 0.016 -10000 0 -10000 0 0
ENAH -0.045 0.051 0.41 4 -10000 0 4
EGFR 0.012 0.018 -10000 0 -0.063 6 6
EPHA2 0.029 0.015 -10000 0 -0.063 12 12
MYO6 -0.029 0.03 0.16 11 -10000 0 11
CTNNB1 0.032 0.005 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.024 0.039 -10000 0 -10000 0 0
AQP5 -0.014 0.045 0.16 7 -0.31 8 15
CTNND1 0.03 0.014 -10000 0 -0.063 10 10
mol:PI-4-5-P2 -0.029 0.026 0.16 8 -10000 0 8
regulation of calcium-dependent cell-cell adhesion -0.028 0.03 0.16 11 -10000 0 11
EGF 0.032 0.007 -10000 0 -0.063 2 2
NCKAP1 0.032 0.002 -10000 0 -10000 0 0
AQP3 -0.03 0.076 0.16 5 -0.32 31 36
cortical microtubule organization 0.06 0.032 -10000 0 -10000 0 0
GO:0000145 -0.028 0.024 0.15 8 -10000 0 8
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.066 0.034 -10000 0 -10000 0 0
MLLT4 0.03 0.008 -10000 0 -10000 0 0
ARF6/GDP -0.053 0.015 -10000 0 -0.098 2 2
ARF6 0.031 0.008 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.067 0.042 -10000 0 -0.072 7 7
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.017 0.022 0.16 2 -0.19 1 3
PVRL2 0.031 0.007 -10000 0 -10000 0 0
ZYX -0.025 0.026 0.16 5 -10000 0 5
ARF6/GTP 0.069 0.051 -10000 0 -0.073 7 7
CDH1 0.03 0.013 -10000 0 -0.063 8 8
EGFR/EGFR/EGF/EGF 0.019 0.035 -10000 0 -10000 0 0
RhoA/GDP 0.061 0.034 -10000 0 -10000 0 0
actin cytoskeleton organization -0.024 0.025 0.14 7 -10000 0 7
IGF-1R heterotetramer 0.032 0.004 -10000 0 -10000 0 0
GIT1 0.032 0.004 -10000 0 -10000 0 0
IGF1R 0.032 0.004 -10000 0 -10000 0 0
IGF1 0.032 0.009 -10000 0 -0.063 4 4
DIAPH1 -0.22 0.26 -10000 0 -0.49 133 133
Wnt receptor signaling pathway -0.06 0.032 -10000 0 -10000 0 0
RHOA 0.032 0.006 -10000 0 -10000 0 0
RhoA/GTP -0.053 0.015 -10000 0 -0.098 2 2
CTNNA1 0.032 0.004 -10000 0 -10000 0 0
VCL -0.024 0.026 0.14 7 -10000 0 7
EFNA1 0.028 0.019 -10000 0 -0.063 20 20
LPP -0.035 0.023 0.15 5 -10000 0 5
Ephrin A1/EPHA2 0.047 0.041 -10000 0 -0.072 7 7
SEC6/SEC8 -0.043 0.011 -10000 0 -10000 0 0
MGAT3 -0.028 0.03 0.16 11 -10000 0 11
HGF/MET 0.035 0.038 -10000 0 -0.072 1 1
HGF 0.022 0.016 -10000 0 -0.063 1 1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.022 0.03 -10000 0 -0.13 24 24
actin cable formation -0.039 0.079 0.34 12 -0.23 10 22
KIAA1543 -0.024 0.023 0.15 9 -10000 0 9
KIFC3 -0.031 0.024 0.16 7 -10000 0 7
NCK1 0.03 0.015 -10000 0 -0.063 11 11
EXOC3 0.032 0.006 -10000 0 -10000 0 0
ACTN1 -0.03 0.027 0.16 8 -10000 0 8
NCK1/GIT1 0.044 0.017 -10000 0 -0.05 11 11
mol:GDP 0.06 0.032 -10000 0 -10000 0 0
EXOC4 0 0 -10000 0 -10000 0 0
STX4 -0.031 0.027 0.16 9 -10000 0 9
PIP5K1C -0.029 0.026 0.16 8 -10000 0 8
LIMA1 -0.048 0.034 -10000 0 -0.063 425 425
ABI1 0.025 0.014 -10000 0 -10000 0 0
ROCK1 -0.041 0.069 0.41 8 -10000 0 8
adherens junction assembly -0.023 0.045 0.23 6 -0.2 9 15
IGF-1R heterotetramer/IGF1 0.053 0.035 -10000 0 -0.072 2 2
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.043 0.015 -10000 0 -10000 0 0
MET 0.022 0.016 -10000 0 -0.063 2 2
PLEKHA7 -0.028 0.005 -10000 0 -10000 0 0
mol:GTP 0.065 0.041 -10000 0 -0.071 7 7
establishment of epithelial cell apical/basal polarity -0.04 0.041 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization -0.022 0.03 -10000 0 -0.13 24 24
regulation of cell-cell adhesion -0.024 0.025 0.14 7 -10000 0 7
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.022 0.03 -10000 0 -0.13 24 24
IL2 signaling events mediated by STAT5

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GAB2 0.032 0.006 -10000 0 -10000 0 0
ELF1 0.033 0.018 -10000 0 -0.064 11 11
CCNA2 0.007 0.042 -10000 0 -0.063 135 135
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
JAK3 0.032 0.006 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
JAK1 0.032 0.006 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.009 0.057 0.16 1 -0.22 11 12
SHC1 0.024 0.026 -10000 0 -0.063 40 40
SP1 0.033 0.02 -10000 0 -0.072 14 14
IL2RA -0.014 0.012 -10000 0 -0.071 10 10
IL2RB 0.03 0.011 -10000 0 -0.063 4 4
SOS1 0 0 -10000 0 -10000 0 0
IL2RG 0.031 0.013 -10000 0 -0.063 9 9
G1/S transition of mitotic cell cycle 0.024 0.093 0.27 14 -0.32 17 31
PTPN11 0.033 0.003 -10000 0 -10000 0 0
CCND2 -0.018 0.011 -10000 0 -0.097 8 8
LCK 0.031 0.01 -10000 0 -0.063 4 4
GRB2 0.032 0.006 -10000 0 -10000 0 0
IL2 0.032 0.004 -10000 0 -10000 0 0
CDK6 0.022 0.015 -10000 0 -10000 0 0
CCND3 0.006 0.055 0.19 2 -0.26 4 6
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.031 0.007 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 0.004 0.035 -10000 0 -0.13 21 21
NT3 (dimer)/TRKC 0.044 0.013 -10000 0 -10000 0 0
NT3 (dimer)/TRKB 0.05 0.033 -10000 0 -0.044 28 28
SHC/Grb2/SOS1/GAB1/PI3K 0.013 0.024 -10000 0 -0.12 10 10
RAPGEF1 0.031 0.006 -10000 0 -10000 0 0
BDNF 0.009 0.015 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
DYNLT1 0.017 0.033 -10000 0 -0.063 72 72
NTRK1 0.032 0.006 -10000 0 -0.063 1 1
NTRK2 0.028 0.011 -10000 0 -10000 0 0
NTRK3 0.031 0.006 -10000 0 -10000 0 0
NT-4/5 (dimer)/TRKB 0.035 0.021 -10000 0 -0.04 18 18
neuron apoptosis 0.03 0.056 0.18 12 -10000 0 12
SHC 2-3/Grb2 -0.032 0.059 -10000 0 -0.19 12 12
SHC1 0.024 0.026 -10000 0 -0.063 40 40
SHC2 -0.033 0.045 -10000 0 -0.29 3 3
SHC3 -0.038 0.062 -10000 0 -0.3 16 16
STAT3 (dimer) 0.017 0.042 -10000 0 -0.068 98 98
NT3 (dimer)/TRKA 0.057 0.028 -10000 0 -0.047 25 25
RIN/GDP 0.005 0.045 0.18 8 -0.16 10 18
GIPC1 0.031 0.006 -10000 0 0 18 18
KRAS 0.031 0.008 -10000 0 -10000 0 0
DNAJA3 -0.008 0.018 0.074 15 -0.15 1 16
RIN/GTP 0.013 0.012 -10000 0 -0.039 2 2
CCND1 -0.032 0.03 -10000 0 -0.098 87 87
MAGED1 0.032 0.003 -10000 0 -10000 0 0
PTPN11 0.032 0.003 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.035 0.024 -10000 0 -0.04 40 40
GRB2 0.032 0.006 -10000 0 0 15 15
NGF (dimer)/TRKA/MATK 0.042 0.011 -10000 0 -0.04 1 1
TRKA/NEDD4-2 0.046 0.011 -10000 0 -0.05 1 1
ELMO1 0.015 0.016 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.017 0.021 -10000 0 -10000 0 0
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.031 0.007 -10000 0 -10000 0 0
DOCK1 0.023 0.015 -10000 0 -10000 0 0
GAB2 0.032 0.006 -10000 0 -10000 0 0
RIT2 0.017 0.017 -10000 0 -0.063 2 2
RIT1 0.003 0.043 -10000 0 -0.063 152 152
FRS2 0.031 0.007 -10000 0 -10000 0 0
DNM1 0.006 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.032 0.005 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.012 0.023 -10000 0 -10000 0 0
mol:GDP -0.002 0.074 0.22 16 -0.22 17 33
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.011 0.012 -10000 0 -10000 0 0
RIT1/GDP -0.002 0.053 0.14 12 -0.16 19 31
TIAM1 0.031 0.008 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
BDNF (dimer)/TRKB 0.012 0.028 -10000 0 -0.048 11 11
KIDINS220/CRKL/C3G 0.044 0.014 -10000 0 -10000 0 0
SHC/RasGAP 0.038 0.028 -10000 0 -0.05 40 40
FRS2 family/SHP2 0.062 0.017 -10000 0 -0.037 5 5
SHC/GRB2/SOS1/GAB1 0.05 0.033 -10000 0 -0.042 47 47
RIT1/GTP 0.005 0.029 -10000 0 -0.039 152 152
NT3 (dimer) 0.031 0.007 -10000 0 -10000 0 0
RAP1/GDP -0.002 0.04 -10000 0 -0.13 20 20
KIDINS220/CRKL 0.031 0.007 -10000 0 -10000 0 0
BDNF (dimer) 0.009 0.015 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.041 0.01 -10000 0 -0.039 1 1
Schwann cell development -0.002 0.006 -10000 0 -0.033 1 1
EHD4 0.026 0.023 -10000 0 -0.063 31 31
FRS2 family/GRB2/SOS1 0.058 0.018 -10000 0 -0.039 1 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.02 0.038 -10000 0 -0.13 22 22
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.032 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.009 0.027 0.15 4 -10000 0 4
ABL1 0.031 0.008 -10000 0 -0.063 1 1
SH2B family/GRB2/SOS1 0.023 0.004 -10000 0 -10000 0 0
Rap1/GTP 0.001 0.034 -10000 0 -0.19 13 13
STAT3 0.017 0.042 -10000 0 -0.068 98 98
axon guidance -0.008 0.018 0.04 2 -10000 0 2
MAPK3 -0.013 0.044 0.18 25 -10000 0 25
MAPK1 -0.014 0.04 0.18 20 -10000 0 20
CDC42/GDP 0.006 0.053 0.14 15 -0.16 17 32
NTF3 0.031 0.007 -10000 0 -10000 0 0
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.039 0.018 -10000 0 -0.04 19 19
PI3K 0.039 0.023 -10000 0 -0.05 16 16
FRS3 0.032 0.002 -10000 0 -10000 0 0
FAIM 0.028 0.018 -10000 0 -0.063 18 18
GAB1 0.032 0.008 -10000 0 -0.063 3 3
RASGRF1 -0.009 0.018 0.074 13 -0.15 1 14
SOS1 0 0 -10000 0 -10000 0 0
MCF2L -0.02 0.011 -10000 0 -10000 0 0
RGS19 0.03 0.009 -10000 0 -10000 0 0
CDC42 0.031 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.011 0.055 0.21 2 -0.26 11 13
Rac1/GDP 0.005 0.044 0.16 9 -0.16 9 18
NGF (dimer)/TRKA/GRIT 0.021 0.004 -10000 0 -0.031 1 1
neuron projection morphogenesis 0.014 0.072 -10000 0 -0.72 4 4
NGF (dimer)/TRKA/NEDD4-2 0.042 0.01 -10000 0 -0.04 1 1
MAP2K1 -0.02 0.043 0.17 23 -10000 0 23
NGFR 0.028 0.019 -10000 0 -0.051 26 26
NGF (dimer)/TRKA/GIPC/GAIP 0.002 0.014 -10000 0 -0.14 3 3
RAS family/GTP/PI3K 0.003 0.035 -10000 0 -0.12 27 27
FRS2 family/SHP2/GRB2/SOS1 0.071 0.023 -10000 0 -10000 0 0
NRAS 0.009 0.041 -10000 0 -0.063 125 125
GRB2/SOS1 0.023 0.004 -10000 0 -10000 0 0
PRKCI 0.032 0.006 -10000 0 -0.063 1 1
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade 0.023 0.048 -10000 0 -0.39 5 5
RASA1 0.032 0.006 -10000 0 -10000 0 0
TRKA/c-Abl 0.045 0.013 -10000 0 -0.05 2 2
SQSTM1 0.032 0.006 -10000 0 -0.063 1 1
BDNF (dimer)/TRKB/GIPC 0.013 0.035 -10000 0 -0.058 1 1
NGF (dimer)/TRKA/p62/Atypical PKCs 0.054 0.018 -10000 0 -0.039 3 3
MATK 0.032 0.006 -10000 0 -10000 0 0
NEDD4L 0.032 0.006 -10000 0 -10000 0 0
RAS family/GDP -0.013 0.034 -10000 0 -0.11 31 31
NGF (dimer)/TRKA 0.01 0.016 -10000 0 -0.16 1 1
Rac1/GTP -0.003 0.028 -10000 0 -0.13 8 8
FRS2 family/SHP2/CRK family 0.084 0.039 -10000 0 -10000 0 0
Signaling events mediated by PRL

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCNE1 0.03 0.011 -10000 0 -0.063 4 4
mol:Halofuginone 0.002 0.004 -10000 0 -0.037 4 4
ITGA1 0 0 -10000 0 -10000 0 0
CDKN1A 0.005 0.052 -10000 0 -0.34 10 10
PRL-3/alpha Tubulin 0.04 0.024 -10000 0 -0.05 28 28
mol:Ca2+ -0.023 0.021 0.053 27 -10000 0 27
AGT 0.029 0.01 -10000 0 -10000 0 0
CCNA2 -0.026 0.012 -10000 0 -0.071 5 5
TUBA1B 0.032 0.006 -10000 0 -10000 0 0
EGR1 0.008 0.008 -10000 0 -0.038 16 16
CDK2/Cyclin E1 0.035 0.062 -10000 0 -0.32 9 9
MAPK3 -0.023 0.008 0 19 -0.05 30 49
PRL-2 /Rab GGTase beta 0.047 0.009 -10000 0 -10000 0 0
MAPK1 -0.022 0.01 0 58 -0.05 30 88
PTP4A1 -0.017 0.007 -10000 0 -0.1 1 1
PTP4A3 0.026 0.023 -10000 0 -0.063 30 30
PTP4A2 0.032 0.006 -10000 0 -10000 0 0
ITGB1 -0.018 0.012 -10000 0 -0.05 23 23
SRC 0.031 0.008 -10000 0 -10000 0 0
RAC1 0.007 0.033 -10000 0 -0.33 4 4
Rab GGTase beta/Rab GGTase alpha 0.045 0.013 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.014 0.043 0.18 22 -10000 0 22
RABGGTA 0.031 0.008 -10000 0 -10000 0 0
BCAR1 -0.015 0.016 0.049 30 -10000 0 30
RHOC -0.007 0.046 -10000 0 -0.34 6 6
RHOA 0.006 0.052 -10000 0 -0.33 11 11
cell motility 0.012 0.052 -10000 0 -0.29 5 5
PRL-1/alpha Tubulin -0.012 0.049 0.18 29 -10000 0 29
PRL-3/alpha1 Integrin 0.02 0.015 -10000 0 -0.039 30 30
ROCK1 0.012 0.05 -10000 0 -0.3 4 4
RABGGTB 0.032 0.005 -10000 0 -10000 0 0
CDK2 0.027 0.021 -10000 0 -0.063 24 24
mitosis -0.017 0.007 -10000 0 -0.1 1 1
ATF5 0.031 0.009 -10000 0 -0.063 1 1
Regulation of p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
RIP1/MEKK3 0.042 0.013 -10000 0 -0.04 9 9
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.03 0.013 -10000 0 -0.063 9 9
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.032 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.031 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0 0.013 -10000 0 -0.11 5 5
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.017 0.034 -10000 0 -0.063 75 75
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.032 0.003 -10000 0 -10000 0 0
FYN 0.029 0.011 -10000 0 -0.063 1 1
MAP3K12 0.032 0.005 -10000 0 -10000 0 0
FGR 0.029 0.017 -10000 0 -0.063 15 15
p38 alpha/TAB1 -0.019 0.049 -10000 0 -0.22 19 19
PRKG1 0.024 0.014 -10000 0 -10000 0 0
DUSP8 0.024 0.015 -10000 0 -10000 0 0
PGK/cGMP/p38 alpha 0.001 0.065 0.14 3 -0.24 15 18
apoptosis -0.019 0.047 -10000 0 -0.21 19 19
RAL/GTP 0.029 0.023 -10000 0 -0.04 12 12
LYN 0.021 0.031 -10000 0 -0.063 60 60
DUSP1 0.029 0.017 -10000 0 -0.063 16 16
PAK1 0.032 0.004 -10000 0 -10000 0 0
SRC 0.031 0.008 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.043 0.03 -10000 0 -0.032 8 8
TRAF6 0.032 0.005 -10000 0 -10000 0 0
RAC1 0.023 0.015 -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 0 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.03 0.02 -10000 0 -10000 0 0
MAPK11 0.004 0.08 0.18 21 -0.26 14 35
BLK 0.032 0.005 -10000 0 -10000 0 0
HCK 0.014 0.036 -10000 0 -0.044 120 120
MAP2K3 0.032 0.004 -10000 0 0 8 8
DUSP16 0 0 -10000 0 -10000 0 0
DUSP10 0.03 0.012 -10000 0 -0.063 6 6
TRAF6/MEKK3 0.04 0.01 -10000 0 -0.023 9 9
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0.075 0.16 17 -0.26 15 32
positive regulation of innate immune response 0.004 0.091 0.19 22 -0.3 16 38
LCK 0.031 0.01 -10000 0 -0.063 4 4
p38alpha-beta/MKP7 0.001 0.087 0.17 25 -0.29 16 41
p38alpha-beta/MKP5 0.012 0.094 0.19 20 -0.3 13 33
PGK/cGMP 0.018 0.01 -10000 0 -10000 0 0
PAK2 0.028 0.02 -10000 0 -0.063 21 21
p38alpha-beta/MKP1 0.011 0.096 0.2 20 -0.31 14 34
CDC42 0.031 0.006 -10000 0 -10000 0 0
RALB 0.032 0.005 -10000 0 -0.063 1 1
RALA 0.021 0.019 -10000 0 -0.063 11 11
PAK3 0.005 0.012 -10000 0 -10000 0 0
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.003 0.009 -10000 0 -10000 0 0
CDC42/GTP -0.033 0.041 -10000 0 -0.13 32 32
PLCG1 0 0.013 0.073 5 -0.13 3 8
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.032 0.006 -10000 0 -10000 0 0
GNAI3 0.021 0.03 -10000 0 -0.063 58 58
G12/G13 0.034 0.022 -10000 0 -10000 0 0
cell migration -0.032 0.04 -10000 0 -0.13 32 32
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
MAPK3 0 0.013 0.073 6 -0.13 3 9
MAPK1 0.001 0.01 0.073 6 -0.096 1 7
S1P/S1P5/Gi 0.002 0.012 0.083 6 -0.11 2 8
GNAI1 0.019 0.016 -10000 0 -0.063 1 1
CDC42/GDP 0.023 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.015 0.01 -10000 0 -10000 0 0
RHOA 0.039 0.095 0.18 148 -10000 0 148
S1P/S1P4/Gi 0.002 0.012 0.083 6 -0.11 2 8
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.027 0.013 -10000 0 -10000 0 0
S1P/S1P4/G12/G13 0.029 0.019 -10000 0 -0.023 2 2
GNA12 0.023 0.015 -10000 0 -10000 0 0
GNA13 0.032 0.007 -10000 0 -0.063 2 2
CDC42 0.031 0.006 -10000 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.006 0.034 0.13 31 -0.14 3 34
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A -0.006 0.041 0.12 4 -0.13 11 15
AP2 0.023 0.005 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.03 0.022 -10000 0 -0.04 1 1
CLTB 0.032 0.005 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.008 0.031 -10000 0 -0.1 35 35
CD4 0.028 0.019 -10000 0 -0.063 18 18
CLTA 0.03 0.009 -10000 0 -10000 0 0
mol:GTP -0.003 0.001 -10000 0 -10000 0 0
ARFGAP1 -0.01 0.003 0 43 -10000 0 43
mol:PI-4-5-P2 0.004 0.007 0.074 4 -0.034 1 5
ARF1/GTP 0.018 0.009 -10000 0 -0.036 10 10
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.001 0.02 -10000 0 -0.09 24 24
mol:Choline 0.004 0.007 0.075 4 -0.034 1 5
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.032 0.006 -10000 0 -10000 0 0
DDEF1 0.002 0.007 0.074 4 -0.034 1 5
ARF1/GDP 0.004 0.012 -10000 0 -0.082 7 7
AP2M1 0.031 0.007 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.011 0.009 -10000 0 -10000 0 0
Rac/GTP 0.017 0.011 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.038 0.015 -10000 0 -0.031 1 1
ARFIP2 0.029 0.014 -10000 0 -0.04 11 11
COPA 0.032 0.005 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.004 0.039 0.1 1 -0.14 30 31
ARF1/GTP/ARHGAP10 0.02 0.004 -10000 0 -10000 0 0
GGA3 0.032 0.004 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.024 0.024 -10000 0 -0.26 3 3
AP2A1 0 0 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.005 0.028 -10000 0 -0.1 27 27
ARF1/GDP/Membrin 0.027 0.027 -10000 0 -0.29 3 3
Arfaptin 2/Rac/GDP 0.03 0.021 -10000 0 -0.038 1 1
CYTH2 -0.003 0.001 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.041 0.01 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.017 0.011 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.008 0.028 -10000 0 -0.092 29 29
PLD2 0.004 0.007 0.075 4 -0.034 1 5
ARF-GAP1/v-SNARE -0.01 0.003 0 43 -10000 0 43
PIP5K1A 0.004 0.007 0.074 4 -0.034 1 5
ARF1/GTP/Membrin/GBF1/p115 0.003 0.033 -10000 0 -0.056 116 116
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.004 0.007 0.075 4 -0.034 1 5
KDEL Receptor/Ligand/ARF-GAP1 -0.01 0.003 0 43 -10000 0 43
GOSR2 0.011 0.029 -10000 0 -0.36 3 3
USO1 0.012 0.02 -10000 0 -0.29 2 2
GBF1 -0.063 0.14 -10000 0 -0.32 115 115
ARF1/GTP/Arfaptin 2 0.042 0.011 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.037 0.02 -10000 0 -0.04 18 18
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.017 0.008 0.016 12 -10000 0 12
RAS family/GTP 0.015 0.056 -10000 0 -0.12 6 6
NFATC4 -0.026 0.039 0.24 5 -10000 0 5
ERBB2IP 0.027 0.023 -10000 0 -0.06 32 32
HSP90 (dimer) 0.03 0.008 -10000 0 -10000 0 0
mammary gland morphogenesis -0.031 0.031 0.14 5 -10000 0 5
JUN 0.001 0.046 0.18 7 -10000 0 7
HRAS 0.031 0.007 -10000 0 -10000 0 0
DOCK7 -0.032 0.025 0.12 5 -10000 0 5
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.039 0.045 0.17 3 -10000 0 3
AKT1 -0.01 0.007 0.016 16 -10000 0 16
BAD -0.017 0.006 0.015 3 -10000 0 3
MAPK10 0.003 0.049 0.19 12 -10000 0 12
mol:GTP 0 0 -10000 0 -0.004 1 1
ErbB2/ErbB3/neuregulin 1 beta -0.032 0.034 0.15 5 -10000 0 5
RAF1 -0.019 0.064 0.22 20 -10000 0 20
ErbB2/ErbB3/neuregulin 2 0.032 0.03 -10000 0 -0.065 1 1
STAT3 0.027 0.091 -10000 0 -0.96 4 4
cell migration -0.014 0.047 0.21 9 -0.13 2 11
mol:PI-3-4-5-P3 -0.001 0.001 0.004 9 -10000 0 9
cell proliferation -0.004 0.099 0.44 3 -0.45 9 12
FOS -0.007 0.076 0.32 5 -0.28 9 14
NRAS 0.009 0.041 -10000 0 -0.063 125 125
mol:Ca2+ -0.031 0.031 0.14 5 -10000 0 5
MAPK3 0.009 0.066 0.39 4 -10000 0 4
MAPK1 -0.016 0.12 0.45 3 -0.52 13 16
JAK2 -0.031 0.034 0.12 6 -10000 0 6
NF2 0.009 0.004 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.006 0.021 0.1 11 -0.057 1 12
NRG1 0.032 0.004 -10000 0 -10000 0 0
GRB2/SOS1 0.023 0.004 -10000 0 0 15 15
MAPK8 -0.017 0.057 0.17 2 -0.18 32 34
MAPK9 0.006 0.066 0.18 27 -10000 0 27
ERBB2 -0.026 0.02 0.05 32 -10000 0 32
ERBB3 0.023 0.024 -10000 0 -0.064 28 28
SHC1 0.024 0.026 -10000 0 -0.063 40 40
RAC1 0.023 0.015 -10000 0 -10000 0 0
apoptosis 0.009 0.005 -10000 0 -10000 0 0
STAT3 (dimer) 0.028 0.088 -10000 0 -0.93 4 4
RNF41 -0.022 0.009 -10000 0 -10000 0 0
FRAP1 -0.009 0.004 0.007 15 -10000 0 15
RAC1-CDC42/GTP -0.027 0.022 -10000 0 -0.086 2 2
ErbB2/ErbB2/HSP90 (dimer) -0.024 0.026 0.051 46 -10000 0 46
CHRNA1 0.006 0.069 0.36 4 -0.26 3 7
myelination -0.028 0.057 0.3 11 -10000 0 11
PPP3CB -0.026 0.029 0.12 4 -10000 0 4
KRAS 0.031 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.021 0.04 -10000 0 -0.11 4 4
NRG2 0.032 0.004 -10000 0 -10000 0 0
mol:GDP 0.006 0.021 0.1 11 -0.057 1 12
SOS1 0 0 -10000 0 -10000 0 0
MAP2K2 -0.023 0.059 0.2 19 -10000 0 19
SRC 0.031 0.008 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 0.003 3 -10000 0 3
PTPN11 -0.034 0.036 0.12 8 -10000 0 8
MAP2K1 -0.01 0.12 0.43 3 -0.53 21 24
heart morphogenesis -0.031 0.031 0.14 5 -10000 0 5
RAS family/GDP 0.018 0.061 -10000 0 -0.12 7 7
GRB2 0.032 0.006 -10000 0 0 15 15
PRKACA 0.017 0.005 -10000 0 -10000 0 0
CHRNE 0.002 0.014 0.066 6 -10000 0 6
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
activation of caspase activity 0.01 0.007 -10000 0 -0.016 16 16
nervous system development -0.031 0.031 0.14 5 -10000 0 5
CDC42 0.031 0.006 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EEF2K -0.018 0.005 0 11 -0.039 15 26
SNTA1 0.03 0.009 -10000 0 0 38 38
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.026 0.007 -10000 0 -0.048 15 15
MAPK12 -0.011 0.017 0.2 3 -10000 0 3
CCND1 -0.007 0.046 -10000 0 -0.35 7 7
p38 gamma/SNTA1 -0.016 0.024 0.19 4 -10000 0 4
MAP2K3 0.032 0.004 -10000 0 0 8 8
PKN1 0.03 0.013 -10000 0 -0.063 8 8
G2/M transition checkpoint -0.011 0.017 0.2 3 -10000 0 3
MAP2K6 -0.007 0.004 -10000 0 -0.038 8 8
MAPT -0.025 0.045 0.14 3 -0.14 16 19
MAPK13 -0.023 0.006 0 11 -0.05 15 26
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.012 0.007 -10000 0 -0.036 8 8
Signaling events mediated by HDAC Class II

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 0.056 0.023 -10000 0 -0.032 26 26
HDAC3 0.032 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.025 0.003 -10000 0 -10000 0 0
GATA1/HDAC4 0.048 0.006 -10000 0 -10000 0 0
GATA1/HDAC5 0.048 0.006 -10000 0 -10000 0 0
GATA2/HDAC5 0.047 0.009 -10000 0 -10000 0 0
HDAC5/BCL6/BCoR 0.058 0.028 -10000 0 -0.044 31 31
HDAC9 0.022 0.016 -10000 0 -0.063 2 2
Glucocorticoid receptor/Hsp90/HDAC6 0.059 0.027 -10000 0 -0.036 36 36
HDAC4/ANKRA2 0.047 0.009 -10000 0 -0.05 1 1
HDAC5/YWHAB 0.044 0.014 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.003 0.028 -10000 0 -0.095 39 39
GATA2 0.032 0.005 -10000 0 -10000 0 0
HDAC4/RFXANK 0.038 0.029 -10000 0 -0.05 45 45
BCOR 0.032 0.01 -10000 0 -0.063 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0 0 -10000 0 -10000 0 0
HDAC5 0.032 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.023 0.006 -10000 0 -10000 0 0
Histones 0.035 0.031 0.083 144 -0.095 3 147
ADRBK1 0.032 0.004 -10000 0 -10000 0 0
HDAC4 0.032 0.003 -10000 0 -10000 0 0
XPO1 0.033 0.001 -10000 0 0 1 1
HDAC5/ANKRA2 0.047 0.009 -10000 0 -0.05 1 1
HDAC4/Ubc9 0.048 0.006 -10000 0 -10000 0 0
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.047 0.008 -10000 0 -10000 0 0
TUBA1B 0.032 0.006 -10000 0 -10000 0 0
HDAC6 0.032 0.002 -10000 0 -10000 0 0
HDAC5/RFXANK 0.038 0.028 -10000 0 -0.05 43 43
CAMK4 0.032 0.004 -10000 0 -10000 0 0
Tubulin/HDAC6 0.058 0.023 -10000 0 -0.044 2 2
SUMO1 0.033 0.001 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.03 0.009 -10000 0 0 39 39
GATA1 0.032 0.002 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.032 0.005 -10000 0 -10000 0 0
NR3C1 0.032 0.004 -10000 0 -10000 0 0
SUMO1/HDAC4 0.038 0.039 -10000 0 -0.097 39 39
SRF 0.032 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.044 0.014 -10000 0 -10000 0 0
Tubulin 0.043 0.015 -10000 0 -10000 0 0
HDAC4/14-3-3 E 0.047 0.009 -10000 0 -10000 0 0
GNB1 0.031 0.008 -10000 0 -10000 0 0
RANGAP1 0.03 0.008 -10000 0 0 37 37
BCL6/BCoR 0.043 0.021 -10000 0 -0.05 19 19
HDAC4/HDAC3/SMRT (N-CoR2) 0.063 0.016 -10000 0 -10000 0 0
HDAC4/SRF 0.063 0.018 -10000 0 -10000 0 0
HDAC4/ER alpha 0.045 0.012 -10000 0 -10000 0 0
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.035 0.031 0.082 144 -0.094 3 147
cell motility 0.058 0.023 -10000 0 -0.044 2 2
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.032 0.003 -10000 0 -10000 0 0
HDAC7/HDAC3 0.024 0.003 -10000 0 -10000 0 0
BCL6 0.029 0.017 -10000 0 -0.063 15 15
HDAC4/CaMK II delta B 0.032 0.003 -10000 0 -10000 0 0
Hsp90/HDAC6 0.045 0.012 -10000 0 -10000 0 0
ESR1 0.031 0.008 -10000 0 -10000 0 0
HDAC6/HDAC11 0.047 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.037 0.039 -10000 0 -0.096 39 39
NPC 0.019 0.001 -10000 0 -10000 0 0
MEF2C 0.027 0.012 -10000 0 -10000 0 0
RAN 0.032 0.004 -10000 0 -10000 0 0
HDAC4/MEF2C 0.077 0.041 -10000 0 -10000 0 0
GNG2 0 0 -10000 0 -10000 0 0
NCOR2 0.032 0.004 -10000 0 0 6 6
TUBB2A 0.03 0.009 -10000 0 -10000 0 0
HDAC11 0.032 0.004 -10000 0 -10000 0 0
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
RANBP2 0.032 0.002 -10000 0 -10000 0 0
ANKRA2 0.032 0.006 -10000 0 -0.063 1 1
RFXANK 0.023 0.027 -10000 0 -0.063 45 45
nuclear import -0.032 0.023 0.11 10 -10000 0 10
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.002 0.056 -10000 0 -0.17 22 22
TBX21 -0.019 0.12 -10000 0 -0.41 1 1
B2M 0.032 0.006 -10000 0 -10000 0 0
TYK2 0.021 0.029 -10000 0 -10000 0 0
IL12RB1 0.021 0.029 -10000 0 -10000 0 0
GADD45B 0.003 0.095 -10000 0 -0.41 2 2
IL12RB2 0.02 0.03 -10000 0 -10000 0 0
GADD45G 0.002 0.1 0.37 1 -0.46 4 5
natural killer cell activation -0.002 0.01 -10000 0 -0.033 1 1
RELB 0.031 0.008 -10000 0 -0.002 27 27
RELA 0.032 0.004 -10000 0 -10000 0 0
IL18 0.025 0.027 -10000 0 -0.061 46 46
IL2RA 0.023 0.017 -10000 0 -0.063 6 6
IFNG 0.03 0.008 -10000 0 -10000 0 0
STAT3 (dimer) -0.005 0.11 0.27 2 -0.39 5 7
HLA-DRB5 -0.001 0.002 -10000 0 -10000 0 0
FASLG -0.017 0.12 0.39 1 -0.41 1 2
NF kappa B2 p52/RelB -0.008 0.13 -10000 0 -0.35 14 14
CD4 0.027 0.019 -10000 0 -0.063 19 19
SOCS1 0.032 0.004 -10000 0 -10000 0 0
EntrezGene:6955 -0.001 0.002 -10000 0 -10000 0 0
CD3D 0.027 0.019 -10000 0 -0.063 21 21
CD3E 0.031 0.007 -10000 0 -0.048 2 2
CD3G 0.031 0.007 -10000 0 -0.051 2 2
IL12Rbeta2/JAK2 0.031 0.04 -10000 0 -10000 0 0
CCL3 -0.018 0.12 -10000 0 -0.34 14 14
CCL4 -0.067 0.23 -10000 0 -0.61 72 72
HLA-A 0.032 0.005 -10000 0 -0.063 1 1
IL18/IL18R 0.058 0.042 -10000 0 -10000 0 0
NOS2 -0.013 0.1 -10000 0 -0.39 3 3
IL12/IL12R/TYK2/JAK2/SPHK2 0.002 0.058 -10000 0 -0.18 24 24
IL1R1 -0.02 0.12 0.39 1 -0.41 1 2
IL4 0.034 0.014 -10000 0 -0.028 8 8
JAK2 0.019 0.029 -10000 0 -10000 0 0
EntrezGene:6957 -0.001 0.002 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.008 0.035 -10000 0 -0.12 24 24
RAB7A 0.013 0.098 0.32 5 -0.41 2 7
lysosomal transport 0.013 0.096 0.32 5 -0.4 2 7
FOS -0.058 0.17 -10000 0 -0.58 40 40
STAT4 (dimer) -0.015 0.12 0.38 2 -0.48 3 5
STAT5A (dimer) 0 0.13 -10000 0 -0.34 13 13
GZMA -0.024 0.12 0.28 1 -0.4 2 3
GZMB -0.025 0.12 -10000 0 -0.4 2 2
HLX 0.031 0.009 -10000 0 -0.063 3 3
LCK -0.025 0.12 0.26 4 -0.36 15 19
TCR/CD3/MHC II/CD4 -0.009 0.031 -10000 0 -0.1 7 7
IL2/IL2R 0.049 0.056 -10000 0 -0.057 15 15
MAPK14 0.014 0.1 0.36 1 -0.47 2 3
CCR5 -0.002 0.11 -10000 0 -0.53 4 4
IL1B 0.018 0.033 -10000 0 -0.065 13 13
STAT6 0.003 0.066 -10000 0 -0.38 8 8
STAT4 0.019 0.016 -10000 0 -10000 0 0
STAT3 0.03 0.014 -10000 0 -0.063 10 10
STAT1 0.029 0.018 -10000 0 -0.063 18 18
NFKB1 0.031 0.009 -10000 0 -0.063 4 4
NFKB2 0.024 0.014 -10000 0 -10000 0 0
IL12B 0.021 0.03 -10000 0 -10000 0 0
CD8A 0 0 -10000 0 -10000 0 0
CD8B 0.032 0.006 -10000 0 -0.063 2 2
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.003 0.056 0.17 22 -10000 0 22
IL2RB 0.03 0.011 -10000 0 -0.007 36 36
proteasomal ubiquitin-dependent protein catabolic process -0.013 0.11 0.38 2 -0.45 3 5
IL2RG 0.031 0.013 -10000 0 -0.063 9 9
IL12 0.032 0.042 -10000 0 -10000 0 0
STAT5A 0.032 0.005 -10000 0 -0.063 1 1
CD247 0.031 0.008 -10000 0 -0.054 3 3
IL2 0.032 0.004 -10000 0 -10000 0 0
SPHK2 0.031 0.008 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.02 0.03 -10000 0 -10000 0 0
IL12/IL12R/TYK2/JAK2 -0.018 0.12 -10000 0 -0.37 17 17
MAP2K3 0.009 0.1 0.35 1 -0.53 2 3
RIPK2 0.032 0.006 -10000 0 -0.063 1 1
MAP2K6 0.01 0.1 0.35 1 -0.47 1 2
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.021 0.047 -10000 0 -0.064 280 280
IL18RAP 0.033 0.006 -10000 0 -0.028 3 3
IL12Rbeta1/TYK2 0.032 0.039 -10000 0 -10000 0 0
EOMES 0.004 0.019 0.069 5 -0.072 5 10
STAT1 (dimer) -0.002 0.11 -10000 0 -0.41 2 2
T cell proliferation -0.018 0.095 0.38 1 -0.39 4 5
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.033 0.006 -10000 0 -0.028 3 3
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.014 0.12 -10000 0 -0.41 3 3
ATF2 0.007 0.1 0.53 1 -0.45 2 3
Cellular roles of Anthrax toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 0.032 0.008 -10000 0 -0.063 3 3
ANTXR2 0 0 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0 -10000 0 -0.008 3 3
monocyte activation -0.017 0.045 -10000 0 -0.33 7 7
MAP2K2 0.017 0.027 -10000 0 -0.58 1 1
MAP2K1 -0.008 0.002 -10000 0 -0.017 1 1
MAP2K7 -0.008 0.002 -10000 0 -0.017 1 1
MAP2K6 -0.009 0.001 -10000 0 -0.017 1 1
CYAA -0.007 0.001 0 1 -0.022 4 5
MAP2K4 -0.008 0.002 -10000 0 -10000 0 0
IL1B -0.013 0.019 0.16 4 -10000 0 4
Channel 0.021 0.004 -10000 0 -0.024 4 4
NLRP1 -0.009 0.002 -10000 0 -10000 0 0
CALM1 0.029 0.01 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.028 0.12 -10000 0 -0.37 55 55
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0 0.008 3 -10000 0 3
MAPK3 -0.009 0.001 -10000 0 -0.017 1 1
MAPK1 -0.008 0.003 -10000 0 -0.017 1 1
PGR -0.009 0.001 -10000 0 -10000 0 0
PA/Cellular Receptors 0.022 0.004 -10000 0 -0.018 5 5
apoptosis -0.002 0 -10000 0 -0.008 3 3
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.02 0.004 -10000 0 -0.026 4 4
macrophage activation -0.014 0.004 -10000 0 -10000 0 0
TNF 0.032 0.006 -10000 0 -0.063 2 2
VCAM1 -0.017 0.045 -10000 0 -0.33 7 7
platelet activation -0.028 0.12 -10000 0 -0.37 55 55
MAPKKK cascade 0.004 0.017 0.064 1 -0.067 24 25
IL18 -0.014 0.013 0.11 2 -0.079 2 4
negative regulation of macrophage activation -0.002 0 -10000 0 -0.008 3 3
LEF -0.002 0 -10000 0 -0.008 3 3
CASP1 -0.006 0.007 -10000 0 -0.016 164 164
mol:cAMP -0.028 0.12 -10000 0 -0.37 55 55
necrosis -0.002 0 -10000 0 -0.008 3 3
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.02 0.004 -10000 0 -0.022 4 4
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 -0.007 0.03 -10000 0 -0.26 6 6
SMARCC2 0.031 0.006 -10000 0 -10000 0 0
SMARCC1 0.029 0.018 -10000 0 -0.063 17 17
TBX21 0.006 0.016 -10000 0 -10000 0 0
SUMO2 0.032 0.005 -10000 0 -0.027 1 1
STAT1 (dimer) 0.022 0.035 -10000 0 -0.063 74 74
FKBP4 0.031 0.006 -10000 0 -10000 0 0
FKBP5 0.027 0.021 -10000 0 -0.063 26 26
GR alpha/HSP90/FKBP51/HSP90 0.08 0.054 -10000 0 -0.073 5 5
PRL -0.041 0.059 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 -0.014 0.039 -10000 0 -10000 0 0
RELA 0.015 0.039 -10000 0 -0.069 39 39
FGG 0.12 0.14 0.27 25 -10000 0 25
GR beta/TIF2 0.005 0.049 -10000 0 -10000 0 0
IFNG -0.06 0.092 -10000 0 -0.23 19 19
apoptosis 0.02 0.091 -10000 0 -0.35 9 9
CREB1 0.036 0.011 -10000 0 -0.067 6 6
histone acetylation 0.009 0.014 -10000 0 -10000 0 0
BGLAP 0.01 0.017 -10000 0 -10000 0 0
GR/PKAc 0.093 0.054 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.027 0.06 -10000 0 -0.1 39 39
SMARCD1 0.032 0.005 -10000 0 -10000 0 0
MDM2 0.003 0.027 0.11 26 -10000 0 26
GATA3 0.028 0.017 -10000 0 -10000 0 0
AKT1 0.029 0.009 0.063 4 -10000 0 4
CSF2 -0.071 0.072 -10000 0 -0.24 2 2
GSK3B 0.032 0.006 -10000 0 -0.027 1 1
NR1I3 0.024 0.09 -10000 0 -0.33 7 7
CSN2 0.12 0.14 0.27 27 -10000 0 27
BRG1/BAF155/BAF170/BAF60A 0.07 0.036 -10000 0 -0.066 1 1
NFATC1 0.035 0.007 -10000 0 -10000 0 0
POU2F1 0.034 0.01 -10000 0 -0.054 3 3
CDKN1A -0.014 0.051 -10000 0 -0.36 1 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.001 -10000 0 -10000 0 0
SFN 0.026 0.023 -10000 0 -0.063 31 31
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.087 0.062 -10000 0 -0.081 6 6
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.024 0.091 -10000 0 -0.38 6 6
JUN 0.001 0.022 0.28 2 -10000 0 2
IL4 0.011 0.018 -10000 0 -10000 0 0
CDK5R1 0.026 0.013 -10000 0 -10000 0 0
PRKACA 0.032 0.006 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.027 0.038 -10000 0 -0.12 5 5
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.093 0.056 -10000 0 -0.07 10 10
cortisol/GR alpha (monomer) -0.02 0.039 -10000 0 -10000 0 0
NCOA2 0.032 0.004 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS 0.011 0.043 -10000 0 -0.08 4 4
AP-1/NFAT1-c-4 -0.015 0.042 0.24 1 -0.2 1 2
AFP -0.053 0.059 0.3 1 -0.37 1 2
SUV420H1 0.032 0.005 -10000 0 -10000 0 0
IRF1 0.001 0.044 0.17 18 -0.12 10 28
TP53 0.016 0.044 -10000 0 -10000 0 0
PPP5C 0.031 0.007 -10000 0 -10000 0 0
KRT17 -0.062 0.093 0.17 1 -0.21 18 19
KRT14 -0.042 0.069 0.17 13 -0.13 29 42
TBP 0.035 0.009 -10000 0 -10000 0 0
CREBBP 0.03 0.006 -10000 0 -10000 0 0
HDAC1 0.018 0.031 -10000 0 -0.065 61 61
HDAC2 0.029 0.011 -10000 0 -0.063 4 4
AP-1 -0.015 0.042 0.24 1 -0.2 1 2
MAPK14 0.032 0.006 -10000 0 -0.044 2 2
MAPK10 0.018 0.016 -10000 0 -10000 0 0
MAPK11 0.03 0.01 -10000 0 -0.027 1 1
KRT5 -0.06 0.092 -10000 0 -0.21 23 23
interleukin-1 receptor activity -0.001 0 -10000 0 -10000 0 0
NCOA1 0.031 0.011 -10000 0 -0.032 8 8
STAT1 0.022 0.035 -10000 0 -0.063 74 74
CGA 0.01 0.019 -10000 0 -0.11 1 1
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.053 0.08 0.15 4 -0.18 11 15
MAPK3 0.032 0.005 -10000 0 -0.026 3 3
MAPK1 0.03 0.009 -10000 0 -0.026 1 1
ICAM1 -0.017 0.07 0.13 1 -0.17 75 76
NFKB1 0.014 0.039 -10000 0 -0.069 42 42
MAPK8 0.005 0.018 -10000 0 -10000 0 0
MAPK9 0.032 0.006 -10000 0 -0.026 1 1
cortisol/GR alpha (dimer) 0.016 0.09 0.24 1 -0.35 10 11
BAX -0.012 0.057 -10000 0 -0.37 3 3
POMC -0.073 0.08 0.26 2 -0.38 1 3
EP300 0.028 0.009 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 -0.015 0.041 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.034 0.22 3 -10000 0 3
SGK1 0.018 0.05 0.19 1 -0.15 23 24
IL13 -0.044 0.068 -10000 0 -0.24 3 3
IL6 -0.017 0.067 0.13 1 -0.18 63 64
PRKACG 0.031 0.006 -10000 0 -10000 0 0
IL5 -0.051 0.07 -10000 0 -0.28 3 3
IL2 -0.06 0.092 0.17 1 -0.21 17 18
CDK5 0.021 0.016 -10000 0 -10000 0 0
PRKACB 0.029 0.01 -10000 0 -10000 0 0
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
IL8 -0.025 0.083 0.13 1 -0.2 80 81
CDK5R1/CDK5 0.025 0.024 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc 0.068 0.062 -10000 0 -0.11 3 3
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 -0.012 0.042 -10000 0 -10000 0 0
SMARCA4 0.031 0.007 -10000 0 -10000 0 0
chromatin remodeling 0.073 0.079 0.17 7 -0.19 3 10
NF kappa B1 p50/RelA/Cbp 0.04 0.075 -10000 0 -0.15 2 2
JUN (dimer) 0.001 0.022 0.28 2 -10000 0 2
YWHAH 0.015 0.016 -10000 0 -10000 0 0
VIPR1 0.008 0.034 0.34 4 -10000 0 4
NR3C1 -0.016 0.03 -10000 0 -10000 0 0
NR4A1 0.034 0.006 -10000 0 -10000 0 0
TIF2/SUV420H1 0.046 0.01 -10000 0 -10000 0 0
MAPKKK cascade 0.02 0.091 -10000 0 -0.35 9 9
cortisol/GR alpha (dimer)/Src-1 -0.013 0.038 -10000 0 -10000 0 0
PBX1 0.034 0.01 -10000 0 -10000 0 0
POU1F1 0.033 0.011 -10000 0 -0.063 1 1
SELE -0.016 0.068 0.13 1 -0.17 77 78
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.073 0.08 0.17 7 -0.19 3 10
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.012 0.042 -10000 0 -10000 0 0
mol:cortisol -0.011 0.02 -10000 0 -10000 0 0
MMP1 0.002 0.046 -10000 0 -0.35 5 5
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.011 0.002 0 18 -10000 0 18
GNB1/GNG2 0.037 0.017 -10000 0 -0.027 27 27
regulation of S phase of mitotic cell cycle 0.014 0.022 -10000 0 -0.1 12 12
GNAO1 0.003 0.009 -10000 0 -10000 0 0
HRAS 0.031 0.007 -10000 0 -10000 0 0
SHBG/T-DHT 0.021 0.004 -10000 0 0 17 17
PELP1 0.032 0.005 -10000 0 -10000 0 0
AKT1 -0.011 0.003 0 35 -10000 0 35
MAP2K1 -0.029 0.048 0.15 31 -0.14 2 33
T-DHT/AR 0.023 0.008 -10000 0 -0.039 8 8
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -0.004 6 6
GNAI2 0.032 0.006 -10000 0 -10000 0 0
GNAI3 0.021 0.03 -10000 0 -0.063 58 58
GNAI1 0.019 0.016 -10000 0 -0.063 1 1
mol:GDP -0.012 0.008 -10000 0 -10000 0 0
cell proliferation -0.023 0.067 0.21 15 -0.25 4 19
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
FOS -0.023 0.066 0.2 5 -0.28 4 9
mol:Ca2+ 0 0.002 -10000 0 -0.033 2 2
MAPK3 -0.021 0.061 0.19 21 -0.24 2 23
MAPK1 -0.025 0.098 0.16 1 -0.35 36 37
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.003 3 3
cAMP biosynthetic process -0.001 0.003 -10000 0 -10000 0 0
GNG2 0 0 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.001 -10000 0 -0.003 3 3
HRAS/GTP 0.049 0.03 -10000 0 -0.076 2 2
actin cytoskeleton reorganization 0.029 0.029 -10000 0 -0.044 11 11
SRC 0.03 0.008 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.003 3 3
PI3K 0.036 0.02 -10000 0 -0.04 16 16
apoptosis 0.015 0.065 0.23 9 -0.21 4 13
T-DHT/AR/PELP1 0.041 0.013 -10000 0 -0.041 9 9
HRAS/GDP 0.016 0.033 -10000 0 -10000 0 0
CREB1 -0.016 0.066 0.22 4 -0.23 8 12
RAC1-CDC42/GTP 0.036 0.035 -10000 0 -0.051 1 1
AR 0.031 0.012 -10000 0 -0.063 8 8
GNB1 0.031 0.008 -10000 0 -10000 0 0
RAF1 -0.022 0.051 0.16 34 -10000 0 34
RAC1-CDC42/GDP 0.027 0.03 -10000 0 -10000 0 0
T-DHT/AR/PELP1/Src 0.055 0.022 -10000 0 -0.046 7 7
MAP2K2 -0.032 0.043 0.15 23 -0.14 2 25
T-DHT/AR/PELP1/Src/PI3K 0.014 0.022 -10000 0 -0.1 12 12
GNAZ 0.027 0.013 -10000 0 -10000 0 0
SHBG 0.032 0.006 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.065 0.1 -10000 0 -0.35 38 38
mol:T-DHT 0 0 -10000 0 -0.002 4 4
RAC1 0.023 0.015 -10000 0 -10000 0 0
GNRH1 -0.011 0.002 0 11 -10000 0 11
Gi family/GTP 0 0.008 -10000 0 -0.11 2 2
CDC42 0.031 0.006 -10000 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.051 0.073 -10000 0 -10000 0 0
NCK1/PAK1/Dok-R -0.031 0.04 -10000 0 -0.24 1 1
NCK1/Dok-R -0.005 0.06 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
mol:beta2-estradiol 0.004 0.013 -10000 0 -10000 0 0
RELA 0.032 0.004 -10000 0 -10000 0 0
SHC1 0.024 0.026 -10000 0 -0.063 40 40
Rac/GDP 0.017 0.011 -10000 0 -10000 0 0
F2 0.037 0.019 -10000 0 -0.064 2 2
TNIP2 0.03 0.014 -10000 0 -0.063 11 11
NF kappa B/RelA 0.015 0.081 -10000 0 -10000 0 0
FN1 0.014 0.037 -10000 0 -0.063 96 96
PLD2 -0.013 0.04 -10000 0 -0.24 1 1
PTPN11 0.032 0.003 -10000 0 -10000 0 0
GRB14 0.029 0.018 -10000 0 -0.063 18 18
ELK1 -0.024 0.051 -10000 0 -10000 0 0
GRB7 0.032 0.005 -10000 0 -0.063 1 1
PAK1 0.032 0.004 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.011 0.079 -10000 0 -10000 0 0
CDKN1A -0.057 0.078 -10000 0 -0.4 1 1
ITGA5 0.019 0.033 -10000 0 -0.063 68 68
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.004 0.06 -10000 0 -10000 0 0
CRK 0.032 0.005 -10000 0 -10000 0 0
mol:NO -0.006 0.095 0.3 3 -10000 0 3
PLG -0.011 0.037 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.012 0.082 -10000 0 -10000 0 0
GRB2 0.032 0.006 -10000 0 -10000 0 0
PIK3R1 0.029 0.009 -10000 0 -10000 0 0
ANGPT2 -0.049 0.069 -10000 0 -0.39 2 2
BMX -0.013 0.04 -10000 0 -0.24 1 1
ANGPT1 -0.007 0.037 -10000 0 -0.2 1 1
tube development -0.061 0.074 -10000 0 -0.32 1 1
ANGPT4 0.029 0.008 -10000 0 -10000 0 0
response to hypoxia -0.003 0.005 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.006 0.063 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.025 0.034 -10000 0 -0.05 61 61
FGF2 0.034 0.007 -10000 0 -0.061 2 2
STAT5A (dimer) -0.061 0.091 -10000 0 -10000 0 0
mol:L-citrulline -0.006 0.095 0.3 3 -10000 0 3
AGTR1 0.022 0.02 -10000 0 -0.028 67 67
MAPK14 -0.02 0.072 -10000 0 -0.56 3 3
Tie2/SHP2 -0.028 0.12 -10000 0 -0.27 100 100
TEK -0.037 0.12 -10000 0 -0.29 94 94
RPS6KB1 -0.046 0.072 -10000 0 -0.37 1 1
Angiotensin II/AT1 0 0.023 -10000 0 -0.022 266 266
Tie2/Ang1/GRB2 -0.004 0.063 -10000 0 -10000 0 0
MAPK3 -0.029 0.046 0.19 1 -0.24 1 2
MAPK1 -0.026 0.044 -10000 0 -0.24 1 1
Tie2/Ang1/GRB7 -0.004 0.064 -10000 0 -10000 0 0
NFKB1 0.031 0.009 -10000 0 -0.063 4 4
MAPK8 -0.008 0.03 -10000 0 -0.24 1 1
PI3K -0.041 0.073 -10000 0 -0.39 1 1
FES -0.022 0.072 -10000 0 -0.47 2 2
Crk/Dok-R -0.005 0.061 -10000 0 -10000 0 0
Tie2/Ang1/ABIN2 -0.005 0.063 -10000 0 -10000 0 0
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.05 0.071 -10000 0 -10000 0 0
STAT5A 0.032 0.005 -10000 0 -0.063 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.044 0.076 0.3 2 -10000 0 2
Tie2/Ang2 -0.059 0.083 -10000 0 -0.35 2 2
Tie2/Ang1 -0.004 0.043 -10000 0 -0.25 1 1
FOXO1 -0.058 0.074 -10000 0 -10000 0 0
ELF1 0.035 0.018 -10000 0 -0.063 6 6
ELF2 -0.007 0.037 -10000 0 -0.21 1 1
mol:Choline -0.013 0.041 -10000 0 -0.24 1 1
cell migration -0.022 0.03 -10000 0 -10000 0 0
FYN -0.063 0.077 -10000 0 -0.34 1 1
DOK2 0 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.053 0.074 -10000 0 -0.37 1 1
ETS1 0.023 0.031 -10000 0 -10000 0 0
PXN -0.044 0.076 0.29 2 -10000 0 2
ITGB1 0.025 0.014 -10000 0 -10000 0 0
NOS3 -0.012 0.095 0.31 3 -10000 0 3
RAC1 0.023 0.015 -10000 0 -10000 0 0
TNF 0.021 0.031 -10000 0 -0.063 2 2
MAPKKK cascade -0.013 0.041 -10000 0 -0.24 1 1
RASA1 0.032 0.006 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.011 0.062 -10000 0 -10000 0 0
NCK1 0.03 0.015 -10000 0 -0.063 11 11
vasculogenesis -0.002 0.092 0.28 4 -10000 0 4
mol:Phosphatidic acid -0.013 0.041 -10000 0 -0.24 1 1
mol:Angiotensin II -0.003 0.004 -10000 0 -10000 0 0
mol:NADP -0.006 0.095 0.3 3 -10000 0 3
Rac1/GTP -0.026 0.064 -10000 0 -0.36 1 1
MMP2 -0.019 0.04 -10000 0 -0.22 2 2
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.057 0.03 -9999 0 -0.053 20 20
E-cadherin/beta catenin 0.045 0.016 -9999 0 -0.05 8 8
CTNNB1 0.032 0.005 -9999 0 -10000 0 0
JUP 0.029 0.017 -9999 0 -0.063 16 16
CDH1 0.03 0.013 -9999 0 -0.063 8 8
Nephrin/Neph1 signaling in the kidney podocyte

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
positive regulation of NF-kappaB transcription factor activity -0.049 0.018 0.054 1 -0.12 4 5
KIRREL 0.035 0.011 0.084 1 -0.038 5 6
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.049 0.019 0.12 4 -0.054 1 5
PLCG1 0.03 0.009 -10000 0 -10000 0 0
ARRB2 0.032 0.005 -10000 0 -10000 0 0
WASL 0.023 0.015 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.069 0.046 0.18 7 -10000 0 7
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.016 0.019 -10000 0 -0.12 4 4
FYN -0.009 0.045 0.17 28 -10000 0 28
mol:Ca2+ 0.074 0.036 0.17 19 -10000 0 19
mol:DAG 0.076 0.037 0.18 19 -10000 0 19
NPHS2 0.035 0.01 0.084 1 -0.03 4 5
mol:IP3 0.076 0.037 0.18 19 -10000 0 19
regulation of endocytosis 0.055 0.03 0.14 1 -10000 0 1
Nephrin/NEPH1/podocin/Cholesterol 0.062 0.029 0.16 19 -10000 0 19
establishment of cell polarity 0.049 0.018 0.12 4 -0.054 1 5
Nephrin/NEPH1/podocin/NCK1-2 0.091 0.039 0.19 10 -10000 0 10
Nephrin/NEPH1/beta Arrestin2 0.058 0.03 0.14 1 -10000 0 1
NPHS1 0.035 0.011 0.093 1 -10000 0 1
Nephrin/NEPH1/podocin 0.059 0.024 0.17 4 -0.056 4 8
TJP1 0.032 0.005 -10000 0 -10000 0 0
NCK1 0.03 0.015 -10000 0 -0.063 11 11
NCK2 0.032 0.004 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.077 0.038 0.18 19 -10000 0 19
CD2AP 0.023 0.028 -10000 0 -0.063 48 48
Nephrin/NEPH1/podocin/GRB2 0.079 0.035 0.18 16 -10000 0 16
GRB2 0.032 0.006 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.012 0.052 0.18 30 -10000 0 30
cytoskeleton organization -0.008 0.032 0.17 11 -0.15 3 14
Nephrin/NEPH1 0.041 0.016 0.097 4 -0.029 5 9
Nephrin/NEPH1/ZO-1 0.063 0.024 -10000 0 -0.049 1 1
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.028 0.033 -10000 0 -0.12 8 8
BIRC5 -0.006 0.046 -10000 0 -0.063 202 202
NFKBIA -0.006 0.015 0.17 2 -10000 0 2
CPEB1 0.024 0.014 -10000 0 -10000 0 0
AKT1 -0.006 0.015 0.14 3 -10000 0 3
NDEL1 0.031 0.008 -10000 0 -10000 0 0
Aurora A/BRCA1 0.025 0.024 0.099 2 -0.12 8 10
NDEL1/TACC3 0.033 0.039 -10000 0 -0.12 8 8
GADD45A 0.024 0.026 -10000 0 -0.063 39 39
GSK3B 0.032 0.007 0.082 2 -10000 0 2
PAK1/Aurora A 0.034 0.029 -10000 0 -0.12 8 8
MDM2 0.029 0.011 -10000 0 -0.063 1 1
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.034 0.017 -10000 0 -10000 0 0
TP53 0.009 0.034 -10000 0 -0.2 10 10
DLG7 0.006 0.009 0.096 2 -10000 0 2
AURKAIP1 0.031 0.007 -10000 0 -10000 0 0
ARHGEF7 0.031 0.007 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.035 0.042 -10000 0 -0.13 8 8
G2/M transition of mitotic cell cycle 0.024 0.024 0.098 2 -0.11 8 10
AURKA 0.014 0.013 0.13 2 -0.042 1 3
AURKB 0.007 0.025 -10000 0 -0.15 8 8
CDC25B 0.012 0.019 0.097 2 -0.21 2 4
G2/M transition checkpoint 0.007 0.017 0.076 2 -0.1 8 10
mRNA polyadenylation 0.019 0.021 0.098 1 -0.11 5 6
Aurora A/CPEB 0.019 0.021 0.099 1 -0.11 5 6
Aurora A/TACC1/TRAP/chTOG 0.065 0.037 -10000 0 -0.12 7 7
BRCA1 0.031 0.01 -10000 0 -0.063 5 5
centrosome duplication 0.034 0.029 -10000 0 -0.12 8 8
regulation of centrosome cycle 0.032 0.039 -10000 0 -0.12 8 8
spindle assembly 0.063 0.036 -10000 0 -0.12 7 7
TDRD7 0.031 0.006 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.025 0.054 -10000 0 -0.13 8 8
CENPA 0.01 0.024 -10000 0 -0.24 2 2
Aurora A/PP2A 0.035 0.027 -10000 0 -0.12 5 5
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.001 0.03 0.089 5 -0.19 8 13
negative regulation of DNA binding 0.009 0.034 -10000 0 -0.2 10 10
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.045 0.012 -10000 0 -10000 0 0
RASA1 0.032 0.006 -10000 0 -10000 0 0
Ajuba/Aurora A 0.007 0.017 0.076 2 -0.1 8 10
mitotic prometaphase -0.002 0.012 0.071 11 -10000 0 11
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.013 0.13 2 -0.041 1 3
TACC1 0.032 0.004 -10000 0 -10000 0 0
TACC3 0.015 0.037 -10000 0 -0.063 92 92
Aurora A/Antizyme1 0.049 0.031 -10000 0 -0.12 8 8
Aurora A/RasGAP 0.034 0.029 -10000 0 -0.13 7 7
OAZ1 0.031 0.006 -10000 0 -10000 0 0
RAN 0.032 0.004 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.031 0.008 0.082 2 -10000 0 2
GIT1 0.032 0.004 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.06 0.024 -10000 0 -0.044 2 2
Importin alpha/Importin beta/TPX2 -0.034 0.017 -10000 0 -10000 0 0
PPP2R5D 0.032 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 -0.025 0.02 -10000 0 -0.14 8 8
PAK1 0.032 0.004 -10000 0 -10000 0 0
CKAP5 0.032 0.006 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.045 0.012 -10000 0 -10000 0 0
FBXW11 0.032 0.005 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.028 0.011 -10000 0 -0.04 11 11
NF kappa B1 p50/RelA/I kappa B alpha 0.022 0.051 0.12 25 -0.17 11 36
NFKBIA 0.003 0.033 0.11 23 -0.097 29 52
MAPK14 0.032 0.005 -10000 0 -0.063 1 1
NF kappa B1 p105/p50 0.028 0.011 -10000 0 -0.039 10 10
ARRB2 0.013 0.003 -10000 0 -0.036 1 1
REL 0.032 0.002 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.027 0.012 -10000 0 -0.041 9 9
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.028 0.011 -10000 0 -0.04 11 11
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
NF kappa B1 p50 dimer -0.022 0.018 0.26 2 -10000 0 2
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
NFKB1 -0.022 0.004 -10000 0 -0.05 4 4
RELA 0.032 0.004 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.01 0.028 0.11 2 -0.12 13 15
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.023 0.053 0.17 3 -0.2 10 13
SRC 0.031 0.008 -10000 0 -10000 0 0
PI3K 0.039 0.023 -10000 0 -0.05 16 16
NF kappa B1 p50/RelA 0.011 0.026 0.11 2 -0.14 6 8
IKBKB 0.032 0.003 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.032 0.005 -10000 0 -10000 0 0
SYK 0.025 0.024 -10000 0 -0.063 34 34
I kappa B alpha/PIK3R1 0.02 0.047 0.18 3 -0.19 8 11
cell death 0.022 0.051 0.16 3 -0.19 10 13
NF kappa B1 p105/c-Rel 0.028 0.011 -10000 0 -0.04 11 11
LCK 0.031 0.01 -10000 0 -0.063 4 4
BCL3 0.031 0.007 -10000 0 -10000 0 0
Effects of Botulinum toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
STX1A 0 0.002 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.043 0.015 -10000 0 -10000 0 0
STXBP1 0.003 0.009 -10000 0 -10000 0 0
ACh/CHRNA1 0.034 0.027 0.081 30 -0.049 9 39
RAB3GAP2/RIMS1/UNC13B 0.053 0.032 -10000 0 -0.044 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.031 0.006 -10000 0 -10000 0 0
mol:ACh 0.018 0.035 0.067 136 -0.059 7 143
RAB3GAP2 0.032 0.006 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.001 0.01 0.14 1 -10000 0 1
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.034 0.027 0.081 30 -0.049 9 39
UNC13B 0.03 0.009 -10000 0 -10000 0 0
CHRNA1 0.032 0.008 -10000 0 -0.063 3 3
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.002 0.01 0.074 4 -10000 0 4
SNAP25 0 0.001 -10000 0 -10000 0 0
VAMP2 0.003 0.001 -10000 0 -10000 0 0
SYT1 0.002 0.007 -10000 0 -10000 0 0
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.001 0.004 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.001 0.01 0.14 1 -10000 0 1
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.017 0.007 -10000 0 -10000 0 0
NFATC2 -0.01 0.004 -10000 0 -10000 0 0
NFATC3 -0.017 0.007 -10000 0 -10000 0 0
CD40LG -0.038 0.044 0.21 8 -10000 0 8
PTGS2 -0.04 0.039 0.17 6 -10000 0 6
JUNB 0.03 0.013 -10000 0 -0.063 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 0.021 0.009 -10000 0 -0.02 4 4
CaM/Ca2+ 0.021 0.009 -10000 0 -0.02 4 4
CALM1 0.029 0.01 -10000 0 -10000 0 0
JUN 0.032 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.001 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.02 0.006 -10000 0 -0.001 37 37
FOSL1 0.03 0.015 -10000 0 -0.063 12 12
CREM 0.025 0.013 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.024 0.032 -10000 0 -10000 0 0
FOS 0.007 0.04 -10000 0 -0.064 120 120
IFNG -0.037 0.039 0.19 5 -10000 0 5
AP-1/NFAT1-c-4 0.032 0.073 0.2 4 -0.12 1 5
FASLG -0.039 0.039 0.17 6 -10000 0 6
NFAT1-c-4/ICER1 0.003 0.036 -10000 0 -10000 0 0
IL2RA -0.029 0.042 0.2 6 -10000 0 6
FKBP12/FK506 0.022 0.007 -10000 0 -0.001 37 37
CSF2 -0.039 0.041 0.19 7 -10000 0 7
JunB/Fra1/NFAT1-c-4 0.032 0.041 0.15 7 -10000 0 7
IL4 -0.038 0.041 0.19 7 -10000 0 7
IL2 0.016 0.088 -10000 0 -0.86 5 5
IL3 0.027 0.073 -10000 0 -0.59 7 7
FKBP1A 0.03 0.009 -10000 0 -0.063 1 1
BATF3 0 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.034 0.005 -10000 0 -10000 0 0
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.033 0.041 -10000 0 -0.055 3 3
TC10/GTP 0.026 0.041 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 0.078 0.033 -10000 0 -0.051 3 3
HRAS 0.031 0.007 -10000 0 -10000 0 0
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 0.029 0.018 -10000 0 -0.063 18 18
FOXO3 -0.021 0.14 -10000 0 -0.57 29 29
AKT1 -0.022 0.062 0.29 5 -10000 0 5
INSR 0.034 0.01 0.07 20 -10000 0 20
Insulin Receptor/Insulin 0.058 0.032 0.22 4 -0.052 2 6
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.021 0.018 -10000 0 -0.063 6 6
SORBS1 0.024 0.014 -10000 0 -10000 0 0
CRK 0.032 0.005 -10000 0 -10000 0 0
PTPN1 -0.019 0.022 0.14 7 -10000 0 7
CAV1 -0.025 0.029 0.18 4 -10000 0 4
CBL/APS/CAP/Crk-II/C3G 0.045 0.051 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/NCK2 0.078 0.033 -10000 0 -0.052 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.053 0.038 -10000 0 -0.059 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.028 0.037 0.18 16 -0.19 3 19
RPS6KB1 -0.027 0.057 0.27 5 -10000 0 5
PARD6A 0.032 0.004 -10000 0 -10000 0 0
CBL 0.032 0.004 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.02 0.014 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.033 0.058 0.15 23 -10000 0 23
HRAS/GTP -0.032 0.018 0.029 21 -10000 0 21
Insulin Receptor 0.034 0.01 0.07 20 -10000 0 20
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.075 0.054 -10000 0 -0.072 1 1
PRKCI 0.035 0.035 -10000 0 -0.32 4 4
Insulin Receptor/Insulin/GRB14/PDK1 0.03 0.033 -10000 0 -10000 0 0
SHC1 0.024 0.026 -10000 0 -0.063 40 40
negative regulation of MAPKKK cascade 0.033 0.044 -10000 0 -10000 0 0
PI3K 0.065 0.044 -10000 0 -10000 0 0
NCK2 0.032 0.004 -10000 0 -10000 0 0
RHOQ 0.032 0.002 -10000 0 -10000 0 0
mol:H2O2 -0.003 0.003 -10000 0 -10000 0 0
HRAS/GDP 0.023 0.005 -10000 0 -10000 0 0
AKT2 -0.026 0.059 0.29 5 -10000 0 5
PRKCZ 0.017 0.017 -10000 0 -0.29 1 1
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.019 0.037 0.16 16 -10000 0 16
F2RL2 0.032 0.004 -10000 0 -10000 0 0
TRIP10 0.031 0.012 -10000 0 -0.063 6 6
Insulin Receptor/Insulin/Shc 0.05 0.037 -10000 0 -0.04 56 56
TC10/GTP/CIP4/Exocyst 0.042 0.012 -10000 0 -0.04 6 6
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.06 0.044 -10000 0 -0.047 37 37
RAPGEF1 0.031 0.006 -10000 0 -10000 0 0
RASA1 0.032 0.006 -10000 0 -10000 0 0
NCK1 0.03 0.015 -10000 0 -0.063 11 11
CBL/APS/CAP/Crk-II 0.037 0.042 -10000 0 -0.032 135 135
TC10/GDP 0.024 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.044 0.051 -10000 0 -0.052 37 37
INPP5D -0.019 0.013 0.034 24 -10000 0 24
SOS1 0 0 -10000 0 -10000 0 0
SGK1 -0.005 0.002 -10000 0 -10000 0 0
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.032 0.003 -10000 0 -10000 0 0
IRS1 0.032 0.009 -10000 0 -0.063 4 4
p62DOK/RasGAP 0.033 0.044 -10000 0 -10000 0 0
INS 0.035 0.013 0.078 32 -10000 0 32
mol:PI-3-4-P2 -0.018 0.013 0.034 24 -10000 0 24
GRB2 0.032 0.006 -10000 0 0 15 15
EIF4EBP1 -0.041 0.046 0.35 2 -10000 0 2
PTPRA 0.031 0.01 0.07 1 -10000 0 1
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
TC10/GTP/CIP4 0.042 0.012 -10000 0 -0.04 6 6
PDPK1 0.032 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.014 0.028 -10000 0 -0.11 17 17
Insulin Receptor/Insulin/IRS1 0.06 0.025 -10000 0 -0.035 21 21
Insulin Receptor/Insulin/IRS3 0.049 0.018 0.11 20 -10000 0 20
Par3/Par6 0.07 0.026 -10000 0 -10000 0 0
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.032 0.004 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.05 0.033 -9999 0 -0.043 32 32
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.009 0.016 -9999 0 -0.33 1 1
AURKB 0.027 0.021 -9999 0 -0.063 26 26
AURKC 0.03 0.01 -9999 0 -0.063 2 2
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.054 0.16 0.45 1 -0.68 2 3
STAT6 (cleaved dimer) -0.051 0.14 -10000 0 -0.7 2 2
IGHG1 -0.022 0.084 -10000 0 -0.49 1 1
IGHG3 -0.063 0.14 -10000 0 -0.66 2 2
AKT1 -0.022 0.11 -10000 0 -0.62 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.001 0.079 0.26 1 -0.5 2 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.015 0.1 -10000 0 -0.63 1 1
THY1 -0.17 0.31 -10000 0 -0.7 92 92
MYB 0.029 0.014 -10000 0 -0.063 7 7
HMGA1 0.032 0.002 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.025 0.11 -10000 0 -0.64 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.019 0.1 -10000 0 -0.64 1 1
SP1 -0.005 0.04 -10000 0 -0.044 251 251
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.031 0.017 -10000 0 -0.034 1 1
STAT6 (dimer)/ETS1 -0.045 0.15 -10000 0 -0.72 1 1
SOCS1 -0.044 0.13 0.29 1 -0.53 1 2
SOCS3 -0.03 0.095 -10000 0 -0.55 1 1
FCER2 -0.046 0.13 -10000 0 -0.62 2 2
PARP14 0.001 0 -10000 0 -10000 0 0
CCL17 -0.069 0.15 -10000 0 -0.68 2 2
GRB2 0.032 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.018 0.086 -10000 0 -0.58 1 1
T cell proliferation -0.057 0.15 -10000 0 -0.85 1 1
IL4R/JAK1 -0.06 0.16 -10000 0 -0.66 2 2
EGR2 -0.071 0.15 -10000 0 -0.69 2 2
JAK2 0.009 0.038 -10000 0 -10000 0 0
JAK3 0.032 0.013 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
JAK1 0.019 0.026 -10000 0 -10000 0 0
COL1A2 -0.054 0.11 0.26 1 -0.72 5 6
CCL26 -0.066 0.15 -10000 0 -0.68 2 2
IL4R -0.07 0.16 -10000 0 -0.7 2 2
PTPN6 0.03 0.017 -10000 0 -0.047 17 17
IL13RA2 -0.088 0.15 -10000 0 -0.68 2 2
IL13RA1 0.001 0.05 -10000 0 -0.1 5 5
IRF4 0.012 0.065 -10000 0 -0.45 3 3
ARG1 -0.021 0.091 -10000 0 -0.39 4 4
CBL -0.03 0.1 0.29 1 -0.61 1 2
GTF3A 0.023 0.026 -10000 0 -0.043 63 63
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
IL13RA1/JAK2 0.005 0.055 -10000 0 -10000 0 0
IRF4/BCL6 0.02 0.068 -10000 0 -0.43 3 3
CD40LG 0.035 0.004 -10000 0 -0.039 1 1
MAPK14 -0.03 0.1 0.27 1 -0.61 1 2
mitosis -0.019 0.11 0.27 1 -0.58 3 4
STAT6 -0.069 0.16 -10000 0 -0.75 2 2
SPI1 0.032 0.013 -10000 0 -0.061 8 8
RPS6KB1 -0.023 0.11 -10000 0 -0.57 3 3
STAT6 (dimer) -0.068 0.17 -10000 0 -0.74 2 2
STAT6 (dimer)/PARP14 -0.069 0.15 -10000 0 -0.71 2 2
mast cell activation 0.003 0.007 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.014 0.092 -10000 0 -0.63 1 1
FRAP1 -0.02 0.12 -10000 0 -0.61 3 3
LTA -0.07 0.15 -10000 0 -0.7 2 2
FES 0.032 0.004 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.069 0.16 0.74 2 -10000 0 2
CCL11 -0.067 0.14 -10000 0 -0.66 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.011 0.097 -10000 0 -0.88 1 1
IL2RG 0.03 0.019 -10000 0 -0.06 10 10
IL10 -0.064 0.16 -10000 0 -0.68 2 2
IRS1 0.032 0.009 -10000 0 -0.063 4 4
IRS2 0.03 0.008 -10000 0 -10000 0 0
IL4 -0.01 0.085 -10000 0 -0.56 6 6
IL5 -0.069 0.15 -10000 0 -0.68 2 2
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.067 0.16 -10000 0 -0.66 3 3
COL1A1 -0.04 0.12 -10000 0 -0.6 10 10
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.062 0.16 -10000 0 -0.71 1 1
IL2R gamma/JAK3 0.048 0.018 -10000 0 -0.05 8 8
TFF3 -0.069 0.15 -10000 0 -0.68 2 2
ALOX15 -0.07 0.15 -10000 0 -0.68 2 2
MYBL1 0.017 0.034 -10000 0 -0.063 78 78
T-helper 2 cell differentiation -0.053 0.14 -10000 0 -0.78 2 2
SHC1 0.024 0.026 -10000 0 -0.063 40 40
CEBPB 0.03 0.016 -10000 0 -0.061 11 11
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.021 0.1 -10000 0 -0.68 2 2
mol:PI-3-4-5-P3 -0.02 0.12 -10000 0 -0.61 3 3
PI3K -0.021 0.12 -10000 0 -0.65 3 3
DOK2 0 0 -10000 0 -10000 0 0
ETS1 0.033 0.013 -10000 0 -0.034 6 6
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.016 0.083 -10000 0 -0.52 1 1
ITGB3 -0.069 0.15 -10000 0 -0.68 2 2
PIGR -0.064 0.16 -10000 0 -0.68 2 2
IGHE 0.014 0.04 0.14 24 -0.096 3 27
MAPKKK cascade -0.016 0.082 -10000 0 -0.52 1 1
BCL6 0.028 0.017 -10000 0 -0.063 15 15
OPRM1 -0.069 0.15 -10000 0 -0.68 2 2
RETNLB -0.066 0.15 -10000 0 -0.68 2 2
SELP -0.066 0.15 -10000 0 -0.68 2 2
AICDA -0.063 0.15 0.41 1 -0.68 2 3
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.025 0.024 -10000 0 -10000 0 0
VLDLR 0.029 0.012 -10000 0 -0.063 3 3
CRKL 0.031 0.007 -10000 0 -10000 0 0
LRPAP1 0.032 0.003 -10000 0 -10000 0 0
FYN 0.029 0.011 -10000 0 -0.063 1 1
ITGA3 0.029 0.017 -10000 0 -0.063 17 17
RELN/VLDLR/Fyn 0.017 0.031 -10000 0 -0.04 14 14
MAPK8IP1/MKK7/MAP3K11/JNK1 0.061 0.06 -10000 0 -10000 0 0
AKT1 -0.004 0.029 -10000 0 -0.13 24 24
MAP2K7 0.031 0.006 -10000 0 -10000 0 0
RAPGEF1 0.031 0.006 -10000 0 -10000 0 0
DAB1 0.032 0.005 -10000 0 -10000 0 0
RELN/LRP8/DAB1 0.02 0.03 -10000 0 -0.041 3 3
LRPAP1/LRP8 0.047 0.009 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn 0.022 0.036 -10000 0 -10000 0 0
DAB1/alpha3/beta1 Integrin 0.017 0.038 -10000 0 -10000 0 0
long-term memory 0.016 0.035 0.17 2 -10000 0 2
DAB1/LIS1 0.026 0.045 -10000 0 -10000 0 0
DAB1/CRLK/C3G 0.02 0.038 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
DAB1/NCK2 0.027 0.046 -10000 0 -10000 0 0
ARHGEF2 0.032 0.005 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.021 0.015 -10000 0 -10000 0 0
CDK5R1 0.026 0.013 -10000 0 -10000 0 0
RELN 0.01 0.016 -10000 0 -0.063 2 2
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
RELN/LRP8/Fyn 0.018 0.031 -10000 0 -0.038 9 9
GRIN2A/RELN/LRP8/DAB1/Fyn 0.021 0.041 -10000 0 -10000 0 0
MAPK8 0.025 0.014 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.018 0.03 -10000 0 -0.034 13 13
ITGB1 0.025 0.014 -10000 0 -10000 0 0
MAP1B 0.008 0.05 0.15 55 -10000 0 55
RELN/LRP8 0.02 0.031 -10000 0 -0.041 5 5
GRIN2B/RELN/LRP8/DAB1/Fyn 0.025 0.045 -10000 0 -10000 0 0
PI3K 0.039 0.023 -10000 0 -0.05 16 16
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.034 0.025 -10000 0 -0.05 15 15
RAP1A 0.052 0.092 0.31 17 -10000 0 17
PAFAH1B1 0.032 0.006 -10000 0 -10000 0 0
MAPK8IP1 0.032 0.006 -10000 0 -10000 0 0
CRLK/C3G 0.044 0.014 -10000 0 -10000 0 0
GRIN2B 0.031 0.007 -10000 0 -10000 0 0
NCK2 0.032 0.004 -10000 0 -10000 0 0
neuron differentiation -0.016 0.059 -10000 0 -0.17 41 41
neuron adhesion 0.039 0.091 0.31 18 -10000 0 18
LRP8 0.032 0.005 -10000 0 -10000 0 0
GSK3B -0.003 0.039 0.077 46 -0.14 24 70
RELN/VLDLR/DAB1/Fyn 0.02 0.036 -10000 0 -10000 0 0
MAP3K11 0.032 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K 0.004 0.018 -10000 0 -0.1 9 9
CDK5 0.021 0.016 -10000 0 -10000 0 0
MAPT 0.004 0.056 0.72 1 -10000 0 1
neuron migration -0.015 0.08 0.19 44 -0.16 14 58
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.016 0.06 -10000 0 -0.17 41 41
RELN/VLDLR 0.024 0.04 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.031 0.008 -10000 0 -10000 0 0
SPHK1 0.029 0.018 -10000 0 -0.063 19 19
GNAI2 0.032 0.006 -10000 0 -10000 0 0
mol:S1P 0.009 0.01 -10000 0 -0.031 23 23
GNAO1 0.003 0.009 -10000 0 -10000 0 0
mol:Sphinganine-1-P -0.022 0.008 -10000 0 -0.05 19 19
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.028 0.035 -10000 0 -0.11 14 14
GNAI3 0.021 0.03 -10000 0 -0.063 58 58
G12/G13 0.034 0.022 -10000 0 -10000 0 0
S1PR3 0 0 -10000 0 -10000 0 0
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.002 0.024 -10000 0 -0.11 21 21
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
GNAI1 0.019 0.016 -10000 0 -0.063 1 1
S1P/S1P5/G12 0.016 0.027 -10000 0 -0.11 14 14
S1P/S1P3/Gq 0.02 0.045 0.15 9 -0.28 8 17
S1P/S1P4/Gi -0.005 0.041 -10000 0 -0.22 16 16
GNAQ 0.031 0.006 -10000 0 -10000 0 0
GNAZ 0.027 0.013 -10000 0 -10000 0 0
GNA14 0.031 0.009 -10000 0 -0.063 2 2
GNA15 0.03 0.013 -10000 0 -0.063 7 7
GNA12 0.023 0.015 -10000 0 -10000 0 0
GNA13 0.032 0.007 -10000 0 -0.063 2 2
GNA11 0.031 0.006 -10000 0 -10000 0 0
ABCC1 0.031 0.012 -10000 0 -0.063 8 8
Insulin-mediated glucose transport

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Insulin responsive Vesicles -0.01 0.082 -10000 0 -0.23 42 42
CaM/Ca2+ 0.021 0.008 -10000 0 -10000 0 0
AKT1 0.03 0.008 -10000 0 -10000 0 0
AKT2 0.031 0.006 -10000 0 -10000 0 0
STXBP4 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.027 0.077 0.21 1 -0.24 45 46
YWHAZ 0.032 0.006 -10000 0 -10000 0 0
CALM1 0.029 0.01 -10000 0 -10000 0 0
YWHAQ 0.032 0.004 -10000 0 -10000 0 0
TBC1D4 -0.02 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.015 0.016 -10000 0 -10000 0 0
YWHAB 0.03 0.009 -10000 0 0 39 39
SNARE/Synip 0.039 0.014 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
ASIP 0.03 0.008 -10000 0 -10000 0 0
PRKCI 0.032 0.006 -10000 0 -0.063 1 1
AS160/CaM/Ca2+ 0.021 0.008 -10000 0 -10000 0 0
RHOQ 0.032 0.002 -10000 0 -10000 0 0
GYS1 -0.006 0.006 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
TRIP10 0.031 0.012 -10000 0 -0.063 6 6
TC10/GTP/CIP4/Exocyst 0.042 0.012 -10000 0 -0.04 6 6
AS160/14-3-3 -0.021 0.045 0.1 1 -0.17 17 18
VAMP2 0.029 0.011 -10000 0 -10000 0 0
SLC2A4 -0.03 0.085 0.21 1 -0.26 45 46
STX4 0.032 0.002 -10000 0 -10000 0 0
GSK3B 0.017 0.006 -10000 0 -10000 0 0
SFN 0.026 0.023 -10000 0 -0.063 31 31
LNPEP 0.032 0.006 -10000 0 -0.063 1 1
YWHAE 0.032 0.005 -10000 0 -10000 0 0
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.032 0.004 -10000 0 -10000 0 0
PTK2 0.031 0.006 -10000 0 -10000 0 0
CRKL -0.021 0.007 -10000 0 -10000 0 0
GRB2/SOS1/SHC 0.035 0.024 -10000 0 -0.04 40 40
HRAS 0.031 0.007 -10000 0 -10000 0 0
IRS1/Crk 0.024 0.013 -10000 0 -0.058 9 9
IGF-1R heterotetramer/IGF1/PTP1B 0.057 0.022 -10000 0 -0.048 9 9
AKT1 -0.022 0.044 0.17 17 -10000 0 17
BAD -0.027 0.042 0.15 17 -10000 0 17
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.022 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.032 0.015 -10000 0 -0.072 6 6
RAF1 -0.007 0.054 0.24 3 -0.43 3 6
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.053 0.019 -10000 0 -0.067 6 6
YWHAZ 0.032 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.04 0.015 -10000 0 -0.058 10 10
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
RPS6KB1 -0.024 0.045 0.17 18 -10000 0 18
GNB2L1 0.032 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.011 0.055 0.23 7 -0.35 3 10
PXN 0.032 0.003 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.023 0.004 -10000 0 -10000 0 0
HRAS/GTP 0.023 0.028 -10000 0 -0.071 6 6
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.061 0.039 -10000 0 -0.061 1 1
IGF-1R heterotetramer 0.034 0.008 0.098 1 -0.031 5 6
IGF-1R heterotetramer/IGF1/IRS/Nck 0.058 0.019 -10000 0 -0.071 6 6
Crk/p130 Cas/Paxillin 0.047 0.018 0.21 1 -0.072 6 7
IGF1R 0.034 0.008 0.098 1 -0.031 5 6
IGF1 0.033 0.012 -10000 0 -0.052 9 9
IRS2/Crk -0.025 0.009 -10000 0 -10000 0 0
PI3K 0.062 0.037 -10000 0 -0.074 4 4
apoptosis 0.027 0.051 -10000 0 -0.17 18 18
HRAS/GDP 0.023 0.005 -10000 0 -10000 0 0
PRKCD 0.002 0.018 -10000 0 -0.14 4 4
RAF1/14-3-3 E -0.006 0.058 0.27 4 -0.38 3 7
BAD/14-3-3 -0.028 0.053 0.17 18 -10000 0 18
PRKCZ -0.018 0.043 0.16 19 -10000 0 19
Crk/p130 Cas/Paxillin/FAK1 -0.037 0.04 0.12 16 -10000 0 16
PTPN1 0.03 0.009 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.01 0.022 -10000 0 -0.15 5 5
BCAR1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.044 0.047 -10000 0 -0.07 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
IRS1/NCK2 0.033 0.017 0.13 4 -0.071 6 10
GRB10 0.021 0.018 -10000 0 -0.063 6 6
PTPN11 -0.022 0.006 -10000 0 -10000 0 0
IRS1 -0.016 0.014 0.12 4 -10000 0 4
IRS2 -0.021 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 0.045 0.011 -10000 0 -0.054 4 4
GRB2 0.032 0.006 -10000 0 0 15 15
PDPK1 -0.019 0.046 0.18 19 -10000 0 19
YWHAE 0.032 0.005 -10000 0 -10000 0 0
PRKD1 -0.003 0.021 -10000 0 -0.13 8 8
SHC1 0.024 0.026 -10000 0 -0.063 40 40
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 -0.014 0.009 0 13 -0.039 61 74
SMARCC1 0.004 0.02 -10000 0 -10000 0 0
REL 0.032 0.002 -10000 0 -10000 0 0
HDAC7 -0.036 0.03 0.16 2 -0.14 3 5
JUN 0.032 0.005 -10000 0 -10000 0 0
EP300 0.03 0.008 -10000 0 -10000 0 0
KAT2B 0 0 -10000 0 -10000 0 0
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 -0.021 0.011 0.019 29 -0.051 1 30
FOXO1 0.028 0.016 -10000 0 -0.063 11 11
T-DHT/AR 0.01 0.052 0.21 2 -0.14 3 5
MAP2K6 0.032 0.004 -10000 0 -10000 0 0
BRM/BAF57 0.043 0.015 -10000 0 -10000 0 0
MAP2K4 0.031 0.008 -10000 0 -10000 0 0
SMARCA2 0.029 0.01 -10000 0 -10000 0 0
PDE9A 0.014 0.063 -10000 0 -0.5 7 7
NCOA2 0.032 0.004 -10000 0 0 9 9
CEBPA 0.028 0.017 -10000 0 -0.063 15 15
EHMT2 0.033 0.003 -10000 0 -10000 0 0
cell proliferation -0.022 0.075 0.24 9 -0.24 23 32
NR0B1 0.024 0.027 -10000 0 -0.063 46 46
EGR1 0.029 0.017 -10000 0 -0.062 15 15
RXRs/9cRA 0.058 0.021 -10000 0 -0.041 4 4
AR/RACK1/Src -0.023 0.052 0.17 11 -0.15 1 12
AR/GR 0.003 0.044 0.14 5 -0.19 7 12
GNB2L1 0.032 0.004 -10000 0 -10000 0 0
PKN1 0.03 0.013 -10000 0 -0.063 8 8
RCHY1 0.032 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 -0.016 0.012 0.019 15 -10000 0 15
T-DHT/AR/TIF2/CARM1 -0.03 0.044 0.2 7 -0.15 1 8
SRC -0.024 0.025 0.18 4 -10000 0 4
NR3C1 0.032 0.004 -10000 0 -10000 0 0
KLK3 -0.02 0.062 0.22 1 -0.34 6 7
APPBP2 0.033 0.004 -10000 0 -10000 0 0
TRIM24 0.022 0.016 -10000 0 -0.062 2 2
T-DHT/AR/TIP60 -0.029 0.021 0.042 3 -0.086 15 18
TMPRSS2 0.013 0.068 -10000 0 -0.5 8 8
RXRG 0.032 0.008 -10000 0 -0.017 11 11
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.031 0.007 -10000 0 -10000 0 0
RXRB 0.032 0.003 -10000 0 -10000 0 0
CARM1 0.032 0.006 -10000 0 -10000 0 0
NR2C2 0.032 0.004 -10000 0 -10000 0 0
KLK2 -0.016 0.045 0.16 7 -0.18 13 20
AR -0.003 0.019 0.14 5 -0.16 2 7
SENP1 0 0 -10000 0 -10000 0 0
HSP90AA1 0.03 0.008 -10000 0 -10000 0 0
MDM2 0.029 0.011 -10000 0 -0.063 1 1
SRY 0 0 -10000 0 -10000 0 0
GATA2 0.032 0.005 -10000 0 -10000 0 0
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 0.033 0.003 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src -0.024 0.053 0.18 11 -0.16 1 12
positive regulation of transcription 0.032 0.005 -10000 0 -10000 0 0
DNAJA1 0.03 0.01 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.019 -10000 0 -0.2 3 3
NCOA1 0.032 0.02 0.11 4 -10000 0 4
SPDEF 0.033 0.003 -10000 0 -10000 0 0
T-DHT/AR/TIF2 -0.035 0.082 0.15 6 -0.18 97 103
T-DHT/AR/Hsp90 -0.028 0.037 0.18 6 -0.16 1 7
GSK3B 0.032 0.006 -10000 0 -10000 0 0
NR2C1 0.032 0.004 -10000 0 -10000 0 0
mol:T-DHT -0.022 0.015 -10000 0 -10000 0 0
SIRT1 0.025 0.014 -10000 0 -10000 0 0
ZMIZ2 0.022 0.015 -10000 0 -10000 0 0
POU2F1 0.036 0.01 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.033 0.037 0.18 6 -0.15 1 7
CREBBP 0.032 0.004 -10000 0 -10000 0 0
SMARCE1 0.032 0.004 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.021 0.017 -10000 0 -0.1 8 8
TRAF2/ASK1 0.039 0.014 -10000 0 -10000 0 0
ATM 0.027 0.021 -10000 0 -0.063 25 25
MAP2K3 0.028 0.059 0.18 5 -0.24 12 17
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.025 0.056 0.18 10 -0.2 16 26
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.029 0.015 -10000 0 -0.063 12 12
TXN 0.006 0.001 -10000 0 -10000 0 0
CALM1 0.029 0.01 -10000 0 -10000 0 0
GADD45A 0.024 0.026 -10000 0 -0.063 39 39
GADD45B 0.03 0.013 -10000 0 -0.063 8 8
MAP3K1 0.032 0.006 -10000 0 -0.063 1 1
MAP3K6 0.031 0.008 -10000 0 -0.063 2 2
MAP3K7 0.031 0.008 -10000 0 -0.063 1 1
MAP3K4 0.03 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.043 0.016 -10000 0 -0.05 2 2
TAK1/TAB family 0.002 0.023 0.074 42 -0.069 7 49
RAC1/OSM/MEKK3 0.029 0.02 -10000 0 -0.023 3 3
TRAF2 0.031 0.006 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.021 0.048 -10000 0 -0.21 12 12
TRAF6 0.006 0.001 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.003 0.009 -10000 0 -10000 0 0
CCM2 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.004 0.013 -10000 0 -10000 0 0
MAPK11 0.029 0.01 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.005 0.018 -10000 0 -0.031 2 2
OSM/MEKK3 0.024 0.002 -10000 0 -10000 0 0
TAOK1 0.004 0.009 -10000 0 -0.037 25 25
TAOK2 0.01 0.011 -10000 0 -0.036 25 25
TAOK3 0.01 0.011 -10000 0 -0.036 25 25
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.032 0.005 -10000 0 -0.063 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.03 0.009 -10000 0 -10000 0 0
MAP3K10 0.031 0.006 -10000 0 -10000 0 0
MAP3K3 0.032 0.003 -10000 0 -10000 0 0
TRX/ASK1 0.025 0.016 -10000 0 -0.11 5 5
GADD45/MTK1/MTK1 0.052 0.047 -10000 0 -0.056 7 7
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.009 0.001 0 2 -10000 0 2
ADCY5 -0.009 0.001 0 2 -10000 0 2
ADCY6 -0.017 0.003 0 17 -10000 0 17
ADCY7 -0.018 0.003 -10000 0 -0.04 5 5
ADCY1 -0.013 0.008 -10000 0 -10000 0 0
ADCY2 -0.017 0.003 -10000 0 -10000 0 0
ADCY3 -0.009 0.001 0 2 -10000 0 2
ADCY8 -0.017 0.004 0 17 -0.04 5 22
PRKCE -0.011 0.001 0 2 -10000 0 2
ADCY9 -0.018 0.002 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.009 0.043 0.18 12 -0.12 1 13
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.031 0.029 -10000 0 -10000 0 0
epithelial cell differentiation 0.011 0.064 -10000 0 -10000 0 0
ITCH 0.031 0.012 -10000 0 -0.052 2 2
WWP1 0.009 0.023 0.21 6 -10000 0 6
FYN 0.029 0.011 -10000 0 -0.063 1 1
EGFR 0.012 0.018 -10000 0 -0.063 6 6
PRL 0.031 0.011 -10000 0 -0.063 6 6
neuron projection morphogenesis -0.022 0.047 0.18 18 -10000 0 18
PTPRZ1 0.018 0.021 -10000 0 -0.063 17 17
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.052 0.047 0.23 1 -10000 0 1
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.014 0.019 -10000 0 -10000 0 0
ADAM17 0.03 0.017 -10000 0 -0.055 5 5
ErbB4/ErbB4 0.014 0.014 0.12 6 -0.079 1 7
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.005 0.017 -10000 0 -10000 0 0
NCOR1 0.032 0.004 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.03 0.025 -10000 0 -10000 0 0
GRIN2B -0.012 0.021 0.18 2 -10000 0 2
ErbB4/ErbB2/betacellulin 0.032 0.025 -10000 0 -10000 0 0
STAT1 0.029 0.018 -10000 0 -0.063 18 18
HBEGF 0.032 0.007 -10000 0 -0.063 2 2
PRLR 0.032 0.005 -10000 0 -10000 0 0
E4ICDs/ETO2 0.03 0.028 -10000 0 -10000 0 0
axon guidance -0.006 0.043 0.2 1 -10000 0 1
NEDD4 0.027 0.021 -10000 0 -0.063 14 14
Prolactin receptor/Prolactin receptor/Prolactin 0.046 0.013 -10000 0 -0.05 6 6
CBFA2T3 0.031 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/HBEGF 0.032 0.025 -10000 0 -10000 0 0
MAPK3 -0.018 0.049 0.19 17 -10000 0 17
STAT1 (dimer) 0.029 0.03 -10000 0 -10000 0 0
MAPK1 -0.016 0.049 0.19 19 -10000 0 19
JAK2 0.029 0.01 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta 0.012 0.019 -10000 0 -10000 0 0
NRG1 -0.021 0.012 0.024 12 -10000 0 12
NRG3 0 0 -10000 0 -10000 0 0
NRG2 0.032 0.004 -10000 0 -10000 0 0
NRG4 0 0 -10000 0 -10000 0 0
heart development -0.006 0.043 0.2 1 -10000 0 1
neural crest cell migration 0.012 0.019 -10000 0 -10000 0 0
ERBB2 -0.021 0.011 0.024 12 -10000 0 12
WWOX/E4ICDs 0.03 0.028 -10000 0 -10000 0 0
SHC1 0.024 0.026 -10000 0 -0.063 40 40
ErbB4/EGFR/neuregulin 4 0.012 0.021 -10000 0 -10000 0 0
apoptosis -0.015 0.022 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.031 0.029 -10000 0 -10000 0 0
ErbB4/ErbB2/epiregulin 0.031 0.027 -10000 0 -10000 0 0
ErbB4/ErbB4/betacellulin/betacellulin 0.03 0.029 -10000 0 -10000 0 0
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.066 0.05 -10000 0 -10000 0 0
MDM2 0.023 0.071 0.25 43 -10000 0 43
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.029 0.018 -10000 0 -10000 0 0
STAT5A -0.014 0.045 0.21 2 -10000 0 2
ErbB4/EGFR/neuregulin 1 beta 0.013 0.022 -10000 0 -10000 0 0
DLG4 0.032 0.005 -10000 0 -10000 0 0
GRB2/SHC 0.038 0.028 -10000 0 -0.05 40 40
E4ICDs/TAB2/NCoR1 0.028 0.027 -10000 0 -10000 0 0
STAT5A (dimer) 0.019 0.073 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.003 0.057 0.23 1 -10000 0 1
LRIG1 0.028 0.02 -10000 0 -0.063 21 21
EREG 0.031 0.013 -10000 0 -0.063 9 9
BTC 0.032 0.004 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.006 0.043 0.2 1 -10000 0 1
ERBB4 0.014 0.014 0.12 6 -0.079 1 7
STAT5B 0.032 0.004 -10000 0 -10000 0 0
YAP1 0.009 0.06 -10000 0 -0.45 7 7
GRB2 0.032 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.012 0.019 -10000 0 -10000 0 0
glial cell differentiation -0.027 0.026 -10000 0 -10000 0 0
WWOX 0.032 0.006 -10000 0 -10000 0 0
cell proliferation -0.002 0.03 0.18 2 -0.22 2 4
RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 -0.011 0.06 0.32 14 -10000 0 14
VDR 0.031 0.006 -10000 0 -10000 0 0
FAM120B 0 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.023 0.039 -10000 0 -0.15 17 17
RXRs/LXRs/DNA/Oxysterols -0.03 0.046 -10000 0 -0.17 19 19
MED1 0.032 0.004 -10000 0 -10000 0 0
mol:9cRA -0.006 0.005 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.02 0.035 -10000 0 -0.16 17 17
RXRs/NUR77 0.059 0.031 -10000 0 -10000 0 0
RXRs/PPAR 0.003 0.046 -10000 0 -0.12 56 56
NCOR2 0.032 0.004 -10000 0 0 6 6
VDR/VDR/Vit D3 0.023 0.005 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.07 0.026 -10000 0 -10000 0 0
RARA 0.032 0.004 -10000 0 -10000 0 0
NCOA1 0.031 0.007 -10000 0 -10000 0 0
VDR/VDR/DNA 0.031 0.006 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.051 0.016 -10000 0 -10000 0 0
RARG 0.032 0.005 -10000 0 -10000 0 0
RPS6KB1 -0.012 0.059 0.56 5 -10000 0 5
RARs/THRs/DNA/SMRT 0.023 0.032 -10000 0 -0.17 12 12
THRA 0.032 0.004 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.023 0.005 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.011 0.053 -10000 0 -10000 0 0
NR1H4 0.032 0.004 -10000 0 -10000 0 0
RXRs/LXRs/DNA -0.016 0.073 -10000 0 -10000 0 0
NR1H2 -0.008 0.027 -10000 0 -10000 0 0
NR1H3 -0.01 0.028 -10000 0 -0.066 4 4
RXRs/VDR/DNA/Vit D3 0.053 0.031 -10000 0 -10000 0 0
NR4A1 0.032 0.006 -10000 0 -10000 0 0
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.004 0.028 -10000 0 -0.12 16 16
RXRG -0.007 0.029 -10000 0 -0.055 5 5
RXR alpha/CCPG 0.019 0.007 -10000 0 -0.018 7 7
RXRA -0.007 0.028 -10000 0 -10000 0 0
RXRB -0.008 0.029 -10000 0 -0.039 2 2
THRB 0.032 0.004 -10000 0 -10000 0 0
PPARG 0.031 0.009 -10000 0 -0.063 4 4
PPARD 0.032 0.002 -10000 0 -10000 0 0
TNF -0.032 0.041 -10000 0 -0.15 18 18
mol:Oxysterols -0.005 0.004 -10000 0 -10000 0 0
cholesterol transport -0.03 0.046 -10000 0 -0.17 19 19
PPARA 0.03 0.009 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.032 0.004 -10000 0 -10000 0 0
RXRs/NUR77/BCL2 0.011 0.032 -10000 0 -0.12 27 27
SREBF1 -0.031 0.041 -10000 0 -0.16 17 17
RXRs/RXRs/DNA/9cRA -0.011 0.053 -10000 0 -10000 0 0
ABCA1 -0.059 0.056 -10000 0 -0.19 17 17
RARs/THRs 0.091 0.027 -10000 0 -10000 0 0
RXRs/FXR 0.06 0.029 -10000 0 -10000 0 0
BCL2 0.032 0.006 -10000 0 -10000 0 0
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.03 0.01 -10000 0 -10000 0 0
EPHB2 0.031 0.007 -10000 0 -0.064 1 1
EFNB1 -0.004 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.009 0.026 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.05 0.03 -10000 0 -0.04 14 14
neuron projection morphogenesis 0.006 0.018 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/Tiam1 0.011 0.026 0.16 1 -10000 0 1
DNM1 0.006 0.012 -10000 0 -10000 0 0
cell-cell signaling -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.007 0.037 0.2 1 -0.38 4 5
YES1 0.008 0.061 -10000 0 -0.61 4 4
Ephrin B1/EPHB1-2/NCK2 0.011 0.026 0.16 1 -10000 0 1
PI3K 0.039 0.048 -10000 0 -0.32 5 5
mol:GDP 0.01 0.025 0.16 1 -10000 0 1
ITGA2B 0.032 0.003 -10000 0 -10000 0 0
endothelial cell proliferation 0.027 0.021 -10000 0 -10000 0 0
FYN 0.01 0.063 -10000 0 -0.61 4 4
MAP3K7 -0.001 0.032 -10000 0 -0.39 3 3
FGR 0.013 0.057 -10000 0 -0.6 4 4
TIAM1 0.031 0.008 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
RGS3 0.031 0.007 -10000 0 -0.063 1 1
cell adhesion 0.02 0.042 -10000 0 -0.31 5 5
LYN 0.01 0.058 -10000 0 -0.6 4 4
Ephrin B1/EPHB1-2/Src Family Kinases 0.007 0.054 -10000 0 -0.57 4 4
Ephrin B1/EPHB1-2 0.006 0.036 -10000 0 -0.42 3 3
SRC 0.013 0.058 -10000 0 -0.6 4 4
ITGB3 0.032 0.003 -10000 0 -10000 0 0
EPHB1 0.03 0.013 -10000 0 -0.061 9 9
EPHB4 0.023 0.015 -10000 0 -10000 0 0
RAC1 0.023 0.015 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.028 0.021 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.048 0.005 -10000 0 -10000 0 0
BLK 0.014 0.058 -10000 0 -0.58 4 4
HCK 0.01 0.057 -10000 0 -0.58 4 4
regulation of stress fiber formation -0.011 0.025 -10000 0 -0.16 1 1
MAPK8 -0.008 0.04 0.22 1 -0.38 4 5
Ephrin B1/EPHB1-2/RGS3 0.011 0.025 -10000 0 -10000 0 0
endothelial cell migration 0.047 0.095 0.19 136 -0.33 3 139
NCK2 0.032 0.004 -10000 0 -10000 0 0
PTPN13 0.027 0.023 -10000 0 -0.073 24 24
regulation of focal adhesion formation -0.011 0.025 -10000 0 -0.16 1 1
chemotaxis -0.01 0.025 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
Rac1/GTP 0.008 0.022 -10000 0 -10000 0 0
angiogenesis 0.005 0.041 -10000 0 -0.42 4 4
LCK 0.013 0.058 -10000 0 -0.6 4 4
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.02 0.064 -9999 0 -0.26 1 1
CLOCK 0.021 0.023 -9999 0 -0.033 2 2
TIMELESS/CRY2 0.01 0.052 -9999 0 -0.26 1 1
DEC1/BMAL1 0.045 0.011 -9999 0 -10000 0 0
ATR 0.032 0.005 -9999 0 -10000 0 0
NR1D1 -0.002 0.029 -9999 0 -0.24 1 1
ARNTL 0.022 0.024 -9999 0 -0.033 2 2
TIMELESS -0.01 0.044 -9999 0 -0.27 1 1
NPAS2 0.022 0.024 -9999 0 -0.032 18 18
CRY2 0.032 0.006 -9999 0 -10000 0 0
mol:CO 0.001 0.011 -9999 0 -10000 0 0
CHEK1 0.021 0.03 -9999 0 -0.063 58 58
mol:HEME -0.001 0.011 -9999 0 -10000 0 0
PER1 0.031 0.009 -9999 0 -0.063 3 3
BMAL/CLOCK/NPAS2 0.046 0.046 -9999 0 -10000 0 0
BMAL1/CLOCK 0.011 0.041 -9999 0 -0.34 1 1
S phase of mitotic cell cycle 0.02 0.064 -9999 0 -0.26 1 1
TIMELESS/CHEK1/ATR 0.021 0.065 -9999 0 -0.26 1 1
mol:NADPH -0.001 0.011 -9999 0 -10000 0 0
PER1/TIMELESS 0.008 0.054 -9999 0 -0.27 1 1
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 0.032 0.006 -9999 0 -10000 0 0
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.029 0.022 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.002 0.054 -10000 0 -10000 0 0
IL27/IL27R/JAK1 0.049 0.028 -10000 0 -10000 0 0
TBX21 -0.019 0.067 0.32 14 -10000 0 14
IL12B 0.032 0.004 -10000 0 -10000 0 0
IL12A -0.011 0.002 0 13 -10000 0 13
IL6ST 0.032 0.005 -10000 0 -10000 0 0
IL27RA/JAK1 0.024 0.04 -10000 0 -10000 0 0
IL27 -0.001 0.003 -10000 0 -10000 0 0
TYK2 0.031 0.007 -10000 0 -10000 0 0
T-helper cell lineage commitment 0.046 0.083 -10000 0 -0.29 1 1
T-helper 2 cell differentiation 0.002 0.054 -10000 0 -10000 0 0
T cell proliferation during immune response 0.002 0.054 -10000 0 -10000 0 0
MAPKKK cascade -0.002 0.054 -10000 0 -10000 0 0
STAT3 0.03 0.014 -10000 0 -0.063 10 10
STAT2 0.031 0.006 -10000 0 -10000 0 0
STAT1 0.029 0.018 -10000 0 -0.063 18 18
IL12RB1 0.031 0.007 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.022 0.061 0.32 12 -10000 0 12
IL27/IL27R/JAK2/TYK2 -0.002 0.055 -10000 0 -10000 0 0
positive regulation of T cell mediated cytotoxicity -0.002 0.054 -10000 0 -10000 0 0
STAT1 (dimer) 0.056 0.035 -10000 0 -10000 0 0
JAK2 0.029 0.01 -10000 0 -10000 0 0
JAK1 0.031 0.006 -10000 0 -10000 0 0
STAT2 (dimer) 0.021 0.068 0.23 8 -10000 0 8
T cell proliferation -0.003 0.034 -10000 0 -10000 0 0
IL12/IL12R/TYK2/JAK2 0.031 0.092 -10000 0 -0.67 8 8
IL17A 0.045 0.083 -10000 0 -0.29 1 1
mast cell activation 0.002 0.054 -10000 0 -10000 0 0
IFNG 0.004 0.022 0.061 9 -0.083 15 24
T cell differentiation -0.001 0.001 -10000 0 -10000 0 0
STAT3 (dimer) 0.02 0.071 0.23 9 -10000 0 9
STAT5A (dimer) 0.022 0.071 0.23 10 -10000 0 10
STAT4 (dimer) 0.014 0.049 0.23 2 -10000 0 2
STAT4 0.019 0.016 -10000 0 -10000 0 0
T cell activation -0.003 0.001 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.044 0.038 -10000 0 -10000 0 0
GATA3 0.001 0.076 0.64 7 -10000 0 7
IL18 -0.013 0.008 0 7 -0.039 43 50
positive regulation of mast cell cytokine production 0.02 0.07 0.23 9 -10000 0 9
IL27/EBI3 0.023 0.009 -10000 0 -0.039 3 3
IL27RA 0.003 0.027 0.25 5 -10000 0 5
IL6 0.017 0.027 -10000 0 -10000 0 0
STAT5A 0.032 0.005 -10000 0 -0.063 1 1
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.007 0.027 0.32 3 -10000 0 3
IL1B -0.012 0.004 -10000 0 -0.039 13 13
EBI3 0.032 0.01 -10000 0 -0.063 3 3
TNF -0.011 0.002 0 3 -0.039 2 5
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.034 0.015 -10000 0 -0.022 26 26
MAPK9 0.006 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.011 0.002 0 8 -0.039 1 9
GNB1/GNG2 0.021 0.005 -10000 0 0 32 32
GNB1 0.031 0.008 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.006 0.002 -10000 0 -0.037 1 1
Gs family/GTP 0.02 0.005 -10000 0 -0.016 8 8
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.003 0 0.005 8 0 7 15
GNAL 0.032 0.006 -10000 0 -10000 0 0
GNG2 0 0 -10000 0 -10000 0 0
CRH 0.032 0.006 -10000 0 -0.063 1 1
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.005 0.003 -10000 0 -10000 0 0
MAPK11 0.006 0.002 -10000 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.025 0.014 -9999 0 -10000 0 0
ITGB7 0.032 0.008 -9999 0 -0.063 2 2
ITGA4 0.031 0.01 -9999 0 -0.063 5 5
alpha4/beta7 Integrin 0.046 0.013 -9999 0 -0.06 5 5
alpha4/beta1 Integrin 0.036 0.022 -9999 0 -0.05 4 4
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.035 0.022 -9999 0 -0.05 3 3
FBXW11 0.032 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.032 0.005 -9999 0 -10000 0 0
CHUK 0.024 0.015 -9999 0 -0.063 1 1
NF kappa B2 p100/RelB 0.054 0.066 -9999 0 -10000 0 0
NFKB1 0.031 0.009 -9999 0 -0.063 4 4
MAP3K14 0.032 0.007 -9999 0 -0.063 2 2
NF kappa B1 p50/RelB 0.044 0.015 -9999 0 -0.05 5 5
RELB 0.031 0.008 -9999 0 -0.002 27 27
NFKB2 0.024 0.014 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0.032 0.02 -9999 0 -0.04 1 1
regulation of B cell activation 0.031 0.02 -9999 0 -0.039 1 1
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.02 0.15 -10000 0 -0.64 13 13
IL23A 0.007 0.09 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.04 0.12 -10000 0 -10000 0 0
positive regulation of T cell mediated cytotoxicity 0.005 0.12 -10000 0 -10000 0 0
ITGA3 0.003 0.1 -10000 0 -10000 0 0
IL17F -0.011 0.084 -10000 0 -10000 0 0
IL12B 0.027 0.03 -10000 0 -10000 0 0
STAT1 (dimer) 0.013 0.12 -10000 0 -10000 0 0
CD4 0.006 0.11 0.4 1 -10000 0 1
IL23 0.026 0.096 -10000 0 -10000 0 0
IL23R 0.004 0.03 -10000 0 -10000 0 0
IL1B 0.007 0.096 -10000 0 -10000 0 0
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.006 0.11 -10000 0 -10000 0 0
TYK2 0.022 0.027 -10000 0 -10000 0 0
STAT4 0.019 0.016 -10000 0 -10000 0 0
STAT3 0.03 0.014 -10000 0 -0.063 10 10
IL18RAP 0.033 0.003 -10000 0 -10000 0 0
IL12RB1 0.022 0.027 -10000 0 -10000 0 0
PIK3CA 0.028 0.018 -10000 0 -0.063 17 17
IL12Rbeta1/TYK2 0.041 0.029 -10000 0 -10000 0 0
IL23R/JAK2 0.027 0.046 -10000 0 -10000 0 0
positive regulation of chronic inflammatory response 0.005 0.12 -10000 0 -10000 0 0
natural killer cell activation 0 0.003 -10000 0 -10000 0 0
JAK2 0.024 0.03 -10000 0 -10000 0 0
PIK3R1 0.03 0.009 -10000 0 -10000 0 0
NFKB1 0.032 0.01 -10000 0 -0.066 4 4
RELA 0.033 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation 0.026 0.095 -10000 0 -10000 0 0
ALOX12B 0.001 0.11 -10000 0 -10000 0 0
CXCL1 0 0.11 -10000 0 -10000 0 0
T cell proliferation 0.005 0.12 -10000 0 -10000 0 0
NFKBIA 0.031 0.009 -10000 0 -0.067 1 1
IL17A 0.008 0.081 0.26 1 -10000 0 1
PI3K 0.023 0.12 -10000 0 -10000 0 0
IFNG 0.005 0.017 0.08 3 -0.066 18 21
STAT3 (dimer) 0.032 0.13 -10000 0 -10000 0 0
IL18R1 0.033 0.003 -10000 0 -10000 0 0
IL23/IL23R/JAK2/TYK2/SOCS3 0.009 0.09 0.29 1 -10000 0 1
IL18/IL18R 0.057 0.033 -10000 0 -0.052 1 1
macrophage activation -0.001 0.006 -10000 0 -10000 0 0
TNF 0.006 0.095 -10000 0 -10000 0 0
STAT3/STAT4 0.001 0.1 -10000 0 -10000 0 0
STAT4 (dimer) 0 0.096 -10000 0 -10000 0 0
IL18 0.024 0.026 -10000 0 -0.062 43 43
IL19 0.006 0.11 -10000 0 -10000 0 0
STAT5A (dimer) 0.015 0.12 -10000 0 -10000 0 0
STAT1 0.029 0.018 -10000 0 -0.063 18 18
SOCS3 0.032 0.004 -10000 0 -10000 0 0
CXCL9 -0.003 0.11 -10000 0 -10000 0 0
MPO 0.003 0.11 -10000 0 -10000 0 0
positive regulation of humoral immune response 0.005 0.12 -10000 0 -10000 0 0
IL23/IL23R/JAK2/TYK2 0.006 0.12 -10000 0 -10000 0 0
IL6 0.055 0.13 0.4 9 -10000 0 9
STAT5A 0.032 0.005 -10000 0 -0.063 1 1
IL2 0.033 0.006 -10000 0 -0.036 1 1
positive regulation of tyrosine phosphorylation of STAT protein 0 0.003 -10000 0 -10000 0 0
CD3E 0.002 0.11 -10000 0 -10000 0 0
keratinocyte proliferation 0.005 0.12 -10000 0 -10000 0 0
NOS2 0.005 0.11 -10000 0 -10000 0 0
Visual signal transduction: Rods

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:K + 0.032 0.005 -10000 0 -10000 0 0
GNAT1/GTP 0.023 0.004 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.042 0.01 -10000 0 -0.04 1 1
PDE6G/GNAT1/GTP 0.043 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.032 0.005 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel 0.059 0.025 -10000 0 -10000 0 0
mol:Na + 0.037 0.018 -10000 0 -0.045 1 1
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.042 0.01 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.047 0.02 -10000 0 -10000 0 0
CNGB1 0.032 0.005 -10000 0 -10000 0 0
RDH5 0.031 0.007 -10000 0 -0.063 1 1
SAG 0.032 0.006 -10000 0 -0.063 1 1
mol:Ca2+ -0.034 0.024 0.15 8 -10000 0 8
Na + (4 Units) 0.035 0.02 -10000 0 -10000 0 0
RGS9 0.032 0.004 -10000 0 -10000 0 0
GNB1/GNGT1 0.031 0.023 -10000 0 -10000 0 0
GNAT1/GDP 0.052 0.02 -10000 0 -10000 0 0
GUCY2D 0.032 0.005 -10000 0 -10000 0 0
GNGT1 0.023 0.015 -10000 0 -10000 0 0
GUCY2F 0.033 0.001 -10000 0 -10000 0 0
GNB5 0.031 0.006 -10000 0 -10000 0 0
mol:GMP (4 units) -0.028 0.006 -10000 0 -10000 0 0
mol:11-cis-retinal 0.031 0.007 -10000 0 -0.063 1 1
mol:cGMP 0.024 0.009 -10000 0 -0.029 15 15
GNB1 0.031 0.008 -10000 0 -10000 0 0
Rhodopsin 0.045 0.012 -10000 0 -0.049 1 1
SLC24A1 0.032 0.005 -10000 0 -10000 0 0
CNGA1 0.032 0.004 -10000 0 0 6 6
Metarhodopsin II 0.02 0.005 -10000 0 -0.016 6 6
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.04 0.011 -10000 0 -0.024 14 14
RGS9BP 0 0 -10000 0 -10000 0 0
Metarhodopsin II/Transducin 0.007 0.028 -10000 0 -0.11 23 23
GCAP Family/Ca ++ 0.021 0.003 -10000 0 -0.016 4 4
PDE6A/B 0.047 0.007 -10000 0 -10000 0 0
mol:Pi 0.041 0.009 -10000 0 -10000 0 0
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.039 0.032 -10000 0 -0.039 2 2
PDE6B 0.032 0.004 -10000 0 -10000 0 0
PDE6A 0.032 0.004 -10000 0 -10000 0 0
PDE6G 0.032 0.003 -10000 0 -10000 0 0
RHO 0.032 0.005 -10000 0 -10000 0 0
PDE6 0.074 0.026 -10000 0 -10000 0 0
GUCA1A 0 0 -10000 0 -10000 0 0
GC2/GCAP Family 0.041 0.007 -10000 0 -0.023 5 5
GUCA1C 0 0 -10000 0 -10000 0 0
GUCA1B 0.032 0.004 -10000 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.023 0.015 -9999 0 -9999 0 0
PLK4 0.032 0.004 -9999 0 -9999 0 0
regulation of centriole replication -0.016 0.01 -9999 0 -9999 0 0
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0.042 0.007 -10000 0 -9999 0 0
EFNA5 0.032 0.004 -10000 0 -9999 0 0
FYN -0.02 0.017 0.18 3 -9999 0 3
neuron projection morphogenesis 0.042 0.007 -10000 0 -9999 0 0
cell-cell signaling 0 0 -10000 0 -9999 0 0
Ephrin A5/EPHA5 0.043 0.007 -10000 0 -9999 0 0
EPHA5 0.032 0.004 -10000 0 -9999 0 0
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.032 0.005 -9999 0 -9999 0 0
PI3K Class IB/PDE3B 0.032 0.005 -9999 0 -9999 0 0
PDE3B 0.032 0.005 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 509 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.87.5896 TCGA.81.5910 TCGA.76.6285 TCGA.76.6282
109_MAP3K5 0.15 0.018 -0.36 0.018
47_PPARGC1A 0.033 0.033 0.033 0.033
105_BMP4 0.033 0.033 0 0.033
105_BMP6 0.033 0.033 0 0.033
105_BMP7 0.033 0.033 0 0.033
105_BMP2 0.033 0.033 -0.063 0.033
131_RELN/VLDLR 0 0 0.084 0
30_TGFB1/TGF beta receptor Type II 0 0.032 0 -0.063
84_STAT5B 0.046 0.035 -0.32 0.035
84_STAT5A 0.046 0.035 -0.32 0.035
Methods & Data
Input

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

  • mRNA Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/GBM-TP/3348661/GDAC_MergeDataFiles_3125105/GBM-TP.transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data.data.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/GBM-TP/3471856/all_data_by_genes.txt

Data Sets and Pathway Interactions

Both copy number and expression data are incorporated into PARADIGM's inference. Whenever normal tissue controls are available for analysis in the expression data, each patient's gene-value is normalized by subtracting the gene's median level observed in the normal control. Copy number data is also normalized to reflect the difference in copy number between a gene's levels detected in tumor versus control (e.g. blood normal). The collection of pathways used by PARADIGM includes those from NCI-PID on September 15, 2009 containing 131 pathways, 11,563 interactions, and 7,204 entities. All gene identifiers were translated into HUGO standard identifiers wherever possible. We refer to molecular entities as "concepts," which include gene products such as proteins and miRNAs, small molecules, protein complexes, and abstract concepts. Each concept is represented as "node" in PARADIGM's graphical model. The abstract concepts correspond to general cellular processes (such as "apoptosis" or "DNA damage response") and families of genes that share functional activity such as the RAS family of signal transducers. Various types of concept-concept interactions are included in the pathways including protein-protein interactions, transcriptional regulatory interactions, and protein modifications such as phosphorylation and ubiquitinylation interactions.

Pathway Inference Method

The PARADIGM algorithm (described in PMID: 20529912) assigns an integrated pathway level (IPL) reflecting the activity of a concept determined through a belief propagation strategy. The belief propagation is given the copy number and gene expression measurements of all of the genes and iteratively updates hidden states reflecting the activities of all of the genes in a pathway so as to maximize the likelihood of the observed data given the interactions in the pathway. In the end, the inferred level of a concept reflects both the data observed for the concept and the neighborhood of activity surrounding the concept.

Determining significantly altered levels

The significance of the IPL obtained for each concept in each patient sample is assessed using a permutation analysis. Importantly, the permutation analysis preserves data tuples so as to preserve any implicit correlations between the different data modalities. For example, genes that are deleted have concomitantly lower expression levels. Preserving the copy number and expression pairs therefore retains this data property. The simulation therefore makes "null samples" by permuting data tuples across all of the genes in the genome so that each gene in a null sample is associated with a random tuple of another gene with equal probability. This approach has the added benefit of preserving the pathway structure so that every observed IPL can be compared to a distribution of random IPLs derived from exactly the same interaction context. PARADIGM inferences are then obtained for 1000 "null" patients and serve as a background distribution to contrast the observed IPLs against. Pathway concepts are excluded from further analysis if they did not obtain a minimum IPL of 0.5 in any patient sample both observed or simulated.

An IPL I(i,j) for concept i in sample j, is considered to be deviated if its absolute level is two standard deviations from the average level observed for concept i in the 1000 null samples. The degree to which a concept has significantly altered levels across a patient cohort is summarized in the proportion of deviated samples (PDS) score. For example, a protein with a PDS of 0.10 reflects that the protein's level of activity was inferred to be significantly higher or lower in tumors compared to normal in 10% of the patient samples. An average PDS for a pathway is also reported by computing the mean PDS over all concepts in the pathway.

Download Results

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

References
[2] Charles J. Vaske, Stephen C. Benz, J. Zachary Sanborn, Dent Earl, Christopher Szeto, Jingchun Zhu, David Haussler, and Joshua M. Stuart, Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM, Bioinformatics 12(26):237-245 (2010)
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